PARADIGM pathway analysis of mRNASeq expression and copy number data
Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1TQ60KN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1TQ60KN
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 57 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
HIF-1-alpha transcription factor network 216
VEGFR1 specific signals 173
Endothelins 170
FOXA2 and FOXA3 transcription factor networks 154
Signaling events mediated by VEGFR1 and VEGFR2 151
HIF-2-alpha transcription factor network 142
Angiopoietin receptor Tie2-mediated signaling 133
Ephrin A reverse signaling 124
Syndecan-1-mediated signaling events 120
S1P1 pathway 110
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 889 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 889 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
HIF-1-alpha transcription factor network 0.2430 216 16449 76 -0.54 0.048 1000 -1000 -0.069 -1000
VEGFR1 specific signals 0.1946 173 9689 56 -0.25 0.033 1000 -1000 -0.054 -1000
Endothelins 0.1912 170 16359 96 -0.3 0.031 1000 -1000 -0.065 -1000
FOXA2 and FOXA3 transcription factor networks 0.1732 154 7103 46 -0.57 0.035 1000 -1000 -0.097 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1699 151 18984 125 -0.27 0.045 1000 -1000 -0.059 -1000
HIF-2-alpha transcription factor network 0.1597 142 6113 43 -0.4 0.25 1000 -1000 -0.046 -1000
Angiopoietin receptor Tie2-mediated signaling 0.1496 133 11705 88 -0.35 0.038 1000 -1000 -0.076 -1000
Ephrin A reverse signaling 0.1395 124 871 7 -0.061 0.007 1000 -1000 -0.007 -1000
Syndecan-1-mediated signaling events 0.1350 120 4100 34 -0.16 0.033 1000 -1000 -0.042 -1000
S1P1 pathway 0.1237 110 3987 36 -0.16 0.03 1000 -1000 -0.038 -1000
IL23-mediated signaling events 0.1226 109 6578 60 -0.45 0.031 1000 -1000 -0.1 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1204 107 3670 34 -0.13 0.033 1000 -1000 -0.038 -1000
Thromboxane A2 receptor signaling 0.1192 106 11206 105 -0.15 0.049 1000 -1000 -0.046 -1000
TCR signaling in naïve CD8+ T cells 0.1159 103 9621 93 -0.18 0.091 1000 -1000 -0.051 -1000
Syndecan-4-mediated signaling events 0.1159 103 6918 67 -0.22 0.087 1000 -1000 -0.046 -1000
IL4-mediated signaling events 0.1125 100 9174 91 -0.7 0.5 1000 -1000 -0.12 -1000
Signaling events mediated by the Hedgehog family 0.1114 99 5154 52 -0.27 0.04 1000 -1000 -0.044 -1000
p75(NTR)-mediated signaling 0.1080 96 12049 125 -0.2 0.086 1000 -1000 -0.064 -1000
Signaling mediated by p38-alpha and p38-beta 0.1080 96 4257 44 -0.13 0.031 1000 -1000 -0.03 -1000
IL12-mediated signaling events 0.0979 87 7603 87 -0.26 0.049 1000 -1000 -0.066 -1000
amb2 Integrin signaling 0.0945 84 6926 82 -0.14 0.04 1000 -1000 -0.036 -1000
EGFR-dependent Endothelin signaling events 0.0945 84 1767 21 -0.1 0.043 1000 -1000 -0.046 -1000
PDGFR-alpha signaling pathway 0.0911 81 3604 44 -0.12 0.037 1000 -1000 -0.051 -1000
BMP receptor signaling 0.0900 80 6544 81 -0.15 0.063 1000 -1000 -0.058 -1000
Wnt signaling 0.0877 78 549 7 -0.055 -0.012 1000 -1000 -0.026 -1000
Integrins in angiogenesis 0.0844 75 6382 84 -0.18 0.064 1000 -1000 -0.05 -1000
PDGFR-beta signaling pathway 0.0821 73 7146 97 -0.1 0.037 1000 -1000 -0.055 -1000
Class IB PI3K non-lipid kinase events 0.0810 72 216 3 -0.002 -1000 1000 -1000 -0.009 -1000
LPA4-mediated signaling events 0.0799 71 855 12 -0.084 0.009 1000 -1000 -0.025 -1000
Glypican 2 network 0.0799 71 287 4 -0.007 0.011 1000 -1000 0.012 -1000
Fc-epsilon receptor I signaling in mast cells 0.0776 69 6733 97 -0.064 0.033 1000 -1000 -0.053 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0776 69 4721 68 -0.26 0.085 1000 -1000 -0.08 -1000
Reelin signaling pathway 0.0742 66 3710 56 -0.13 0.08 1000 -1000 -0.039 -1000
Effects of Botulinum toxin 0.0686 61 1591 26 -0.096 0.035 1000 -1000 -0.003 -1000
Arf6 signaling events 0.0675 60 3722 62 -0.098 0.06 1000 -1000 -0.042 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0664 59 7175 120 -0.12 0.092 1000 -1000 -0.05 -1000
Glypican 1 network 0.0652 58 2794 48 -0.12 0.053 1000 -1000 -0.039 -1000
Signaling events regulated by Ret tyrosine kinase 0.0641 57 4727 82 -0.066 0.033 1000 -1000 -0.064 -1000
BCR signaling pathway 0.0641 57 5649 99 -0.11 0.064 1000 -1000 -0.058 -1000
IL6-mediated signaling events 0.0630 56 4205 75 -0.28 0.047 1000 -1000 -0.051 -1000
Noncanonical Wnt signaling pathway 0.0619 55 1437 26 -0.059 0.031 1000 -1000 -0.05 -1000
EPO signaling pathway 0.0619 55 3069 55 -0.094 0.032 1000 -1000 -0.034 -1000
Calcium signaling in the CD4+ TCR pathway 0.0607 54 1703 31 -0.15 0.031 1000 -1000 -0.049 -1000
Nongenotropic Androgen signaling 0.0596 53 2766 52 -0.047 0.048 1000 -1000 -0.042 -1000
S1P3 pathway 0.0596 53 2240 42 -0.15 0.04 1000 -1000 -0.028 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0596 53 4208 78 -0.1 0.042 1000 -1000 -0.036 -1000
Glucocorticoid receptor regulatory network 0.0585 52 5948 114 -0.35 0.11 1000 -1000 -0.06 -1000
Caspase cascade in apoptosis 0.0574 51 3820 74 -0.081 0.048 1000 -1000 -0.042 -1000
EPHB forward signaling 0.0574 51 4376 85 -0.061 0.043 1000 -1000 -0.063 -1000
Plasma membrane estrogen receptor signaling 0.0574 51 4428 86 -0.086 0.054 1000 -1000 -0.056 -1000
Ephrin B reverse signaling 0.0562 50 2408 48 -0.037 0.032 1000 -1000 -0.028 -1000
Visual signal transduction: Rods 0.0551 49 2571 52 -0.05 0.035 1000 -1000 -0.032 -1000
FOXM1 transcription factor network 0.0551 49 2545 51 -0.038 0.066 1000 -1000 -0.12 -1000
JNK signaling in the CD4+ TCR pathway 0.0540 48 820 17 -0.047 0.032 1000 -1000 -0.029 -1000
Signaling events mediated by PTP1B 0.0517 46 3562 76 -0.066 0.053 1000 -1000 -0.044 -1000
LPA receptor mediated events 0.0517 46 4714 102 -0.075 0.034 1000 -1000 -0.071 -1000
TCGA08_retinoblastoma 0.0517 46 370 8 -0.01 0.025 1000 -1000 -0.002 -1000
a4b1 and a4b7 Integrin signaling 0.0484 43 217 5 -0.013 0.026 1000 -1000 0.01 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0484 43 1601 37 -0.096 0.049 1000 -1000 -0.029 -1000
ceramide signaling pathway 0.0472 42 2080 49 -0.015 0.047 1000 -1000 -0.041 -1000
IL2 signaling events mediated by PI3K 0.0461 41 2417 58 -0.039 0.052 1000 -1000 -0.04 -1000
Canonical Wnt signaling pathway 0.0450 40 2055 51 -0.072 0.037 1000 -1000 -0.048 -1000
Cellular roles of Anthrax toxin 0.0439 39 1524 39 -0.072 0.032 1000 -1000 -0.022 -1000
Syndecan-3-mediated signaling events 0.0439 39 1375 35 -0.054 0.086 1000 -1000 -0.03 -1000
Coregulation of Androgen receptor activity 0.0427 38 2920 76 -0.19 0.063 1000 -1000 -0.029 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0427 38 2839 74 -0.059 0.066 1000 -1000 -0.067 -1000
ErbB2/ErbB3 signaling events 0.0416 37 2445 65 -0.083 0.043 1000 -1000 -0.056 -1000
Osteopontin-mediated events 0.0416 37 1440 38 -0.026 0.046 1000 -1000 -0.05 -1000
Syndecan-2-mediated signaling events 0.0416 37 2570 69 -0.082 0.055 1000 -1000 -0.031 -1000
TRAIL signaling pathway 0.0405 36 1770 48 -0.012 0.058 1000 -1000 -0.038 -1000
IL2 signaling events mediated by STAT5 0.0394 35 785 22 -0.055 0.032 1000 -1000 -0.047 -1000
Ras signaling in the CD4+ TCR pathway 0.0394 35 607 17 -0.024 0.053 1000 -1000 -0.031 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0382 34 1147 33 -0.11 0.074 1000 -1000 -0.033 -1000
E-cadherin signaling events 0.0382 34 171 5 -0.005 0.03 1000 -1000 0.007 -1000
Visual signal transduction: Cones 0.0371 33 1280 38 -0.038 0.037 1000 -1000 -0.015 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0371 33 1807 54 -0.1 0.047 1000 -1000 -0.053 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0371 33 1526 45 -0.071 0.082 1000 -1000 -0.05 -1000
IL27-mediated signaling events 0.0371 33 1689 51 -0.12 0.045 1000 -1000 -0.043 -1000
FoxO family signaling 0.0360 32 2056 64 -0.24 0.084 1000 -1000 -0.054 -1000
FAS signaling pathway (CD95) 0.0360 32 1540 47 -0.18 0.048 1000 -1000 -0.031 -1000
Regulation of p38-alpha and p38-beta 0.0360 32 1771 54 -0.066 0.068 1000 -1000 -0.051 -1000
Ceramide signaling pathway 0.0349 31 2397 76 -0.059 0.081 1000 -1000 -0.039 -1000
Class I PI3K signaling events 0.0349 31 2275 73 -0.06 0.058 1000 -1000 -0.045 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0337 30 2625 85 -0.063 0.054 1000 -1000 -0.049 -1000
Presenilin action in Notch and Wnt signaling 0.0337 30 1850 61 -0.049 0.086 1000 -1000 -0.05 -1000
IFN-gamma pathway 0.0337 30 2041 68 -0.093 0.057 1000 -1000 -0.056 -1000
Nectin adhesion pathway 0.0337 30 1919 63 -0.055 0.055 1000 -1000 -0.04 -1000
IL1-mediated signaling events 0.0337 30 1894 62 -0.07 0.069 1000 -1000 -0.045 -1000
Aurora B signaling 0.0337 30 2064 67 -0.13 0.057 1000 -1000 -0.035 -1000
ErbB4 signaling events 0.0326 29 2042 69 -0.071 0.042 1000 -1000 -0.044 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0326 29 817 28 -0.037 0.05 1000 -1000 -0.017 -1000
PLK1 signaling events 0.0326 29 2479 85 -0.007 0.054 1000 -1000 -0.025 -1000
Regulation of Androgen receptor activity 0.0326 29 2091 70 -0.21 0.046 1000 -1000 -0.064 -1000
E-cadherin signaling in keratinocytes 0.0315 28 1222 43 -0.047 0.039 1000 -1000 -0.036 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0292 26 1367 52 -0.04 0.082 1000 -1000 -0.034 -1000
Insulin-mediated glucose transport 0.0281 25 817 32 -0.099 0.056 1000 -1000 -0.029 -1000
Signaling mediated by p38-gamma and p38-delta 0.0270 24 360 15 -0.032 0.032 1000 -1000 -0.03 -1000
Paxillin-dependent events mediated by a4b1 0.0270 24 899 36 -0.042 0.054 1000 -1000 -0.034 -1000
Regulation of nuclear SMAD2/3 signaling 0.0259 23 3171 136 -0.26 0.25 1000 -1000 -0.057 -1000
S1P5 pathway 0.0259 23 391 17 -0.011 0.031 1000 -1000 -0.016 -1000
S1P4 pathway 0.0259 23 599 25 -0.011 0.042 1000 -1000 -0.026 -1000
TCGA08_rtk_signaling 0.0247 22 595 26 -0.086 0.08 1000 -1000 -0.011 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0236 21 1788 83 -0.099 0.06 1000 -1000 -0.04 -1000
IGF1 pathway 0.0236 21 1216 57 -0.022 0.062 1000 -1000 -0.051 -1000
Hedgehog signaling events mediated by Gli proteins 0.0225 20 1345 65 -0.044 0.066 1000 -1000 -0.046 -1000
E-cadherin signaling in the nascent adherens junction 0.0225 20 1591 76 -0.028 0.055 1000 -1000 -0.062 -1000
Signaling events mediated by PRL 0.0225 20 690 34 -0.049 0.046 1000 -1000 -0.048 -1000
Insulin Pathway 0.0214 19 1430 74 -0.05 0.078 1000 -1000 -0.047 -1000
BARD1 signaling events 0.0202 18 1036 57 -0.05 0.064 1000 -1000 -0.046 -1000
Regulation of Telomerase 0.0202 18 1917 102 -0.13 0.078 1000 -1000 -0.053 -1000
PLK2 and PLK4 events 0.0191 17 51 3 0.008 0.031 1000 -1000 -0.008 -1000
mTOR signaling pathway 0.0191 17 935 53 -0.034 0.052 1000 -1000 -0.038 -1000
p38 MAPK signaling pathway 0.0191 17 758 44 -0.093 0.051 1000 -1000 -0.029 -1000
TCGA08_p53 0.0180 16 113 7 -0.013 0.031 1000 -1000 -0.012 -1000
Retinoic acid receptors-mediated signaling 0.0169 15 873 58 -0.005 0.063 1000 -1000 -0.036 -1000
Atypical NF-kappaB pathway 0.0169 15 488 31 -0.015 0.04 1000 -1000 -0.024 -1000
Rapid glucocorticoid signaling 0.0157 14 284 20 -0.014 0.031 1000 -1000 -0.006 -1000
Aurora C signaling 0.0146 13 91 7 0 0.037 1000 -1000 -0.011 -1000
Class I PI3K signaling events mediated by Akt 0.0135 12 818 68 -0.099 0.063 1000 -1000 -0.035 -1000
Aurora A signaling 0.0124 11 713 60 -0.098 0.072 1000 -1000 -0.024 -1000
Arf6 trafficking events 0.0124 11 799 71 -0.043 0.054 1000 -1000 -0.028 -1000
Signaling events mediated by HDAC Class II 0.0112 10 780 75 -0.038 0.067 1000 -1000 -0.03 -1000
Signaling events mediated by HDAC Class III 0.0112 10 433 40 -0.056 0.057 1000 -1000 -0.027 -1000
Canonical NF-kappaB pathway 0.0101 9 355 39 -0.011 0.071 1000 -1000 -0.033 -1000
Arf6 downstream pathway 0.0101 9 416 43 -0.049 0.052 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class I 0.0101 9 1021 104 -0.062 0.077 1000 -1000 -0.039 -1000
Circadian rhythm pathway 0.0079 7 163 22 -0.012 0.058 1000 -1000 -0.036 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0056 5 125 23 -0.008 0.06 1000 -1000 -0.025 -1000
Arf1 pathway 0.0056 5 320 54 -0.001 0.051 1000 -1000 -0.019 -1000
Alternative NF-kappaB pathway 0.0034 3 43 13 0 0.073 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0011 1 44 27 0 0.074 1000 -1000 -0.041 -1000
Total NA 6577 396061 7203 -14 -990 131000 -131000 -5.3 -131000
HIF-1-alpha transcription factor network

Figure S1.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S1.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.43 0.64 -10000 0 -1.2 326 326
HDAC7 0.03 0.03 -10000 0 -0.55 2 2
HIF1A/ARNT/Cbp/p300/Src-1 -0.31 0.54 -10000 0 -0.94 311 311
SMAD4 0.032 0.009 -10000 0 -10000 0 0
ID2 -0.42 0.65 -10000 0 -1.2 309 309
AP1 -0.008 0.12 -10000 0 -0.31 113 113
ABCG2 -0.44 0.66 -10000 0 -1.2 320 320
HIF1A -0.04 0.11 -10000 0 -0.46 11 11
TFF3 -0.45 0.68 -10000 0 -1.2 323 323
GATA2 -0.021 0.14 -10000 0 -0.42 93 93
AKT1 -0.035 0.11 -10000 0 -0.35 4 4
response to hypoxia -0.056 0.1 -10000 0 -0.28 29 29
MCL1 -0.42 0.65 -10000 0 -1.2 311 311
NDRG1 -0.43 0.66 -10000 0 -1.2 314 314
SERPINE1 -0.45 0.67 -10000 0 -1.2 314 314
FECH -0.42 0.65 -10000 0 -1.2 313 313
FURIN -0.42 0.65 -10000 0 -1.2 311 311
NCOA2 -0.016 0.14 -10000 0 -0.55 55 55
EP300 -0.037 0.13 -10000 0 -0.32 47 47
HMOX1 -0.44 0.67 -10000 0 -1.2 321 321
BHLHE40 -0.43 0.64 -10000 0 -1.2 315 315
BHLHE41 -0.43 0.67 -10000 0 -1.2 312 312
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.005 0.16 -10000 0 -0.44 14 14
ENG -0.024 0.14 0.39 3 -0.59 12 15
JUN 0.025 0.034 -10000 0 -0.39 4 4
RORA -0.42 0.65 -10000 0 -1.2 317 317
ABCB1 -0.27 0.5 -10000 0 -1.2 167 167
TFRC -0.42 0.65 -10000 0 -1.2 312 312
CXCR4 -0.43 0.67 -10000 0 -1.2 311 311
TF -0.45 0.65 -10000 0 -1.2 318 318
CITED2 -0.42 0.65 -10000 0 -1.2 314 314
HIF1A/ARNT -0.51 0.88 -10000 0 -1.5 311 311
LDHA -0.065 0.25 -10000 0 -1 48 48
ETS1 -0.43 0.66 -10000 0 -1.2 316 316
PGK1 -0.42 0.65 -10000 0 -1.2 313 313
NOS2 -0.44 0.66 -10000 0 -1.2 314 314
ITGB2 -0.43 0.66 -10000 0 -1.2 314 314
ALDOA -0.42 0.65 -10000 0 -1.2 314 314
Cbp/p300/CITED2 -0.43 0.67 -10000 0 -1.2 316 316
FOS -0.031 0.16 -10000 0 -0.42 112 112
HK2 -0.43 0.67 -10000 0 -1.2 319 319
SP1 0.015 0.051 -10000 0 -10000 0 0
GCK -0.097 0.27 -10000 0 -0.85 37 37
HK1 -0.42 0.65 -10000 0 -1.2 313 313
NPM1 -0.42 0.65 -10000 0 -1.2 312 312
EGLN1 -0.42 0.65 -10000 0 -1.2 311 311
CREB1 0.037 0.014 -10000 0 -10000 0 0
PGM1 -0.42 0.65 -10000 0 -1.2 312 312
SMAD3 0.033 0.007 -10000 0 -10000 0 0
EDN1 -0.22 0.5 -10000 0 -1.3 137 137
IGFBP1 -0.46 0.65 -10000 0 -1.2 312 312
VEGFA -0.34 0.54 -10000 0 -0.97 333 333
HIF1A/JAB1 -0.018 0.084 -10000 0 -0.37 9 9
CP -0.54 0.7 -10000 0 -1.3 345 345
CXCL12 -0.43 0.66 -10000 0 -1.2 316 316
COPS5 0.022 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4 0.048 0.014 -10000 0 -10000 0 0
BNIP3 -0.42 0.65 -10000 0 -1.2 316 316
EGLN3 -0.47 0.71 -10000 0 -1.3 333 333
CA9 -0.49 0.72 -10000 0 -1.3 340 340
TERT -0.43 0.65 -10000 0 -1.2 315 315
ENO1 -0.42 0.65 -10000 0 -1.2 312 312
PFKL -0.42 0.65 -10000 0 -1.2 312 312
NCOA1 0.029 0.011 -10000 0 -10000 0 0
ADM -0.46 0.69 -10000 0 -1.3 324 324
ARNT -0.029 0.1 -10000 0 -0.38 7 7
HNF4A -0.06 0.21 -10000 0 -0.55 137 137
ADFP -0.43 0.64 -10000 0 -1.2 326 326
SLC2A1 -0.3 0.5 -10000 0 -0.9 310 310
LEP -0.42 0.64 -10000 0 -1.2 314 314
HIF1A/ARNT/Cbp/p300 -0.32 0.56 -10000 0 -0.97 315 315
EPO -0.31 0.45 -10000 0 -1 162 162
CREBBP -0.028 0.13 0.23 1 -0.29 41 42
HIF1A/ARNT/Cbp/p300/HDAC7 -0.33 0.6 -10000 0 -1 315 315
PFKFB3 -0.43 0.66 -10000 0 -1.2 312 312
NT5E -0.43 0.66 -10000 0 -1.2 317 317
VEGFR1 specific signals

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer -0.16 0.34 -10000 0 -0.72 224 224
VEGFR1 homodimer/NRP1 -0.18 0.32 -10000 0 -0.72 224 224
mol:DAG -0.23 0.35 -10000 0 -0.79 230 230
VEGFR1 homodimer/NRP1/VEGFR 121 -0.22 0.41 -10000 0 -0.84 254 254
CaM/Ca2+ -0.21 0.35 -10000 0 -0.76 229 229
HIF1A -0.068 0.18 -10000 0 -0.37 230 230
GAB1 0.032 0.02 -10000 0 -0.55 1 1
AKT1 -0.19 0.32 -10000 0 -0.72 223 223
PLCG1 -0.23 0.36 -10000 0 -0.8 230 230
NOS3 -0.2 0.35 0.46 1 -0.76 224 225
CBL 0.032 0.02 -10000 0 -0.55 1 1
mol:NO -0.18 0.33 0.46 1 -0.72 225 226
FLT1 -0.19 0.37 -10000 0 -0.81 224 224
PGF -0.13 0.23 -10000 0 -0.44 310 310
VEGFR1 homodimer/NRP2/VEGFR121 -0.22 0.45 -10000 0 -0.89 255 255
CALM1 0.032 0.006 -10000 0 -10000 0 0
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
eNOS/Hsp90 -0.17 0.32 0.4 3 -0.69 224 227
endothelial cell proliferation -0.22 0.33 -10000 0 -0.75 225 225
mol:Ca2+ -0.23 0.35 -10000 0 -0.78 230 230
MAPK3 -0.19 0.29 0.36 1 -0.67 215 216
MAPK1 -0.2 0.3 0.36 1 -0.69 217 218
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
PLGF homodimer -0.13 0.23 -10000 0 -0.43 310 310
PRKACA 0.033 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.016 0.15 -10000 0 -0.54 69 69
VEGFA homodimer -0.12 0.25 -10000 0 -0.54 225 225
VEGFR1 homodimer/VEGFA homodimer -0.23 0.44 -10000 0 -0.89 254 254
platelet activating factor biosynthetic process -0.19 0.28 0.35 1 -0.65 215 216
PI3K -0.2 0.37 -10000 0 -0.78 230 230
PRKCA -0.21 0.32 -10000 0 -0.72 218 218
PRKCB -0.22 0.32 -10000 0 -0.73 227 227
VEGFR1 homodimer/PLGF homodimer -0.25 0.4 -10000 0 -0.84 248 248
VEGFA -0.12 0.25 -10000 0 -0.55 225 225
VEGFB 0.033 0.004 -10000 0 -10000 0 0
mol:IP3 -0.23 0.35 -10000 0 -0.79 230 230
RASA1 -0.16 0.3 -10000 0 -0.68 222 222
NRP2 -0.009 0.15 -10000 0 -0.54 62 62
VEGFR1 homodimer -0.19 0.37 -10000 0 -0.81 224 224
VEGFB homodimer 0.033 0.004 -10000 0 -10000 0 0
NCK1 0.03 0.029 -10000 0 -0.55 2 2
eNOS/Caveolin-1 -0.18 0.33 0.45 1 -0.71 214 215
PTPN11 0.031 0.021 -10000 0 -0.55 1 1
mol:PI-3-4-5-P3 -0.2 0.36 -10000 0 -0.76 230 230
mol:L-citrulline -0.18 0.33 0.46 1 -0.72 225 226
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.18 0.41 -10000 0 -0.86 229 229
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.2 0.42 -10000 0 -0.88 229 229
CD2AP 0.031 0.008 -10000 0 -10000 0 0
PI3K/GAB1 -0.18 0.36 -10000 0 -0.75 226 226
PDPK1 -0.2 0.32 0.35 1 -0.72 222 223
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.2 0.42 -10000 0 -0.83 249 249
mol:NADP -0.18 0.33 0.46 1 -0.72 225 226
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.18 0.4 -10000 0 -0.84 229 229
VEGFR1 homodimer/NRP2 -0.18 0.37 -10000 0 -0.78 231 231
Endothelins

Figure S3.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S3.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.17 0.36 0.28 46 -0.66 238 284
PTK2B 0.031 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.27 0.49 0.53 2 -0.99 260 262
EDN1 -0.067 0.22 0.25 37 -0.52 129 166
EDN3 0 0.091 -10000 0 -0.32 64 64
EDN2 -0.071 0.2 -10000 0 -0.44 187 187
HRAS/GDP -0.16 0.34 0.28 6 -0.65 235 241
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.17 0.35 0.2 33 -0.63 262 295
ADCY4 -0.18 0.34 0.27 1 -0.72 202 203
ADCY5 -0.18 0.32 0.48 1 -0.65 221 222
ADCY6 -0.15 0.3 -10000 0 -0.64 185 185
ADCY7 -0.15 0.29 0.27 1 -0.63 187 188
ADCY1 -0.18 0.33 0.39 1 -0.66 226 227
ADCY2 -0.23 0.32 -10000 0 -0.63 260 260
ADCY3 -0.16 0.32 0.27 1 -0.66 198 199
ADCY8 -0.22 0.3 0.27 1 -0.62 250 251
ADCY9 -0.15 0.29 -10000 0 -0.62 196 196
arachidonic acid secretion -0.16 0.33 0.42 7 -0.63 242 249
ETB receptor/Endothelin-1/Gq/GTP -0.079 0.2 -10000 0 -0.41 199 199
GNAO1 -0.001 0.12 -10000 0 -0.42 63 63
HRAS 0.03 0.038 -10000 0 -0.46 5 5
ETA receptor/Endothelin-1/G12/GTP -0.11 0.35 0.38 55 -0.65 194 249
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.36 0.36 61 -0.62 229 290
mol:GTP -0.001 0.006 -10000 0 -10000 0 0
COL3A1 -0.21 0.42 0.28 3 -0.81 219 222
EDNRB -0.013 0.15 -10000 0 -0.53 61 61
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.23 0.4 -10000 0 -0.82 219 219
CYSLTR1 -0.2 0.41 -10000 0 -0.85 195 195
SLC9A1 -0.08 0.2 0.2 41 -0.38 193 234
mol:GDP -0.18 0.37 0.34 8 -0.71 242 250
SLC9A3 -0.26 0.48 -10000 0 -1 204 204
RAF1 -0.16 0.33 0.38 6 -0.66 215 221
JUN -0.19 0.39 0.43 1 -0.78 227 228
JAK2 -0.17 0.36 0.28 46 -0.66 237 283
mol:IP3 -0.16 0.34 -10000 0 -0.63 246 246
ETA receptor/Endothelin-1 -0.16 0.43 0.42 74 -0.74 240 314
PLCB1 -0.062 0.21 -10000 0 -0.55 141 141
PLCB2 0.012 0.1 -10000 0 -0.53 30 30
ETA receptor/Endothelin-3 -0.095 0.24 -10000 0 -0.5 199 199
FOS -0.14 0.31 0.45 5 -0.76 130 135
Gai/GDP -0.06 0.28 -10000 0 -0.8 93 93
CRK 0.029 0.016 -10000 0 -0.32 1 1
mol:Ca ++ -0.25 0.47 0.26 2 -0.86 269 271
BCAR1 0.029 0.035 -10000 0 -0.55 3 3
PRKCB1 -0.16 0.32 -10000 0 -0.6 253 253
GNAQ 0.027 0.017 -10000 0 -10000 0 0
GNAZ 0.026 0.056 -10000 0 -0.48 10 10
GNAL 0.019 0.077 -10000 0 -0.41 26 26
Gs family/GDP -0.16 0.32 0.3 5 -0.63 237 242
ETA receptor/Endothelin-1/Gq/GTP -0.16 0.36 0.22 38 -0.67 232 270
MAPK14 -0.1 0.24 -10000 0 -0.5 182 182
TRPC6 -0.3 0.54 0.53 2 -1.1 259 261
GNAI2 0.03 0.009 -10000 0 -10000 0 0
GNAI3 0.031 0.008 -10000 0 -10000 0 0
GNAI1 0.023 0.059 -10000 0 -0.55 9 9
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.11 0.26 -10000 0 -0.49 216 216
ETB receptor/Endothelin-2 -0.069 0.2 -10000 0 -0.36 226 226
ETB receptor/Endothelin-3 -0.013 0.13 -10000 0 -0.32 114 114
ETB receptor/Endothelin-1 -0.06 0.22 -10000 0 -0.51 129 129
MAPK3 -0.16 0.34 0.45 5 -0.77 162 167
MAPK1 -0.16 0.35 0.46 5 -0.78 163 168
Rac1/GDP -0.15 0.32 0.36 3 -0.64 217 220
cAMP biosynthetic process -0.22 0.32 0.38 8 -0.66 253 261
MAPK8 -0.25 0.51 0.46 1 -0.97 254 255
SRC 0.031 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.044 0.17 0.18 1 -0.41 115 116
p130Cas/CRK/Src/PYK2 -0.19 0.38 0.4 11 -0.72 255 266
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.15 0.32 0.36 3 -0.64 217 220
COL1A2 -0.19 0.42 -10000 0 -0.78 221 221
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.16 0.27 -10000 0 -0.51 283 283
mol:DAG -0.16 0.34 -10000 0 -0.63 246 246
MAP2K2 -0.16 0.32 0.45 6 -0.68 194 200
MAP2K1 -0.16 0.32 0.45 5 -0.68 189 194
EDNRA -0.13 0.31 0.25 39 -0.68 192 231
positive regulation of muscle contraction -0.13 0.31 0.27 49 -0.65 176 225
Gq family/GDP -0.14 0.34 0.31 2 -0.66 210 212
HRAS/GTP -0.17 0.34 0.31 4 -0.66 235 239
PRKCH -0.17 0.35 -10000 0 -0.68 234 234
RAC1 0.029 0.011 -10000 0 -10000 0 0
PRKCA -0.14 0.31 0.28 6 -0.61 226 232
PRKCB -0.16 0.34 0.29 6 -0.64 234 240
PRKCE -0.16 0.32 -10000 0 -0.62 233 233
PRKCD -0.16 0.32 0.3 2 -0.63 238 240
PRKCG -0.17 0.33 0.25 1 -0.64 244 245
regulation of vascular smooth muscle contraction -0.17 0.37 0.55 3 -0.91 133 136
PRKCQ -0.17 0.33 -10000 0 -0.65 235 235
PLA2G4A -0.19 0.37 0.42 7 -0.7 245 252
GNA14 -0.034 0.18 -10000 0 -0.55 93 93
GNA15 0.011 0.1 -10000 0 -0.5 31 31
GNA12 0.029 0.011 -10000 0 -10000 0 0
GNA11 0.014 0.089 -10000 0 -0.44 30 30
Rac1/GTP -0.11 0.35 0.38 55 -0.64 195 250
MMP1 -0.22 0.47 0.35 23 -1 188 211
FOXA2 and FOXA3 transcription factor networks

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.41 0.47 -10000 0 -1.1 239 239
PCK1 -0.45 0.6 -10000 0 -1.5 177 177
HNF4A -0.53 0.6 -10000 0 -1.3 284 284
KCNJ11 -0.44 0.53 -10000 0 -1.2 236 236
AKT1 -0.17 0.22 -10000 0 -0.49 150 150
response to starvation -0.015 0.038 -10000 0 -0.3 4 4
DLK1 -0.43 0.5 -10000 0 -1.1 238 238
NKX2-1 -0.12 0.2 0.4 14 -0.44 123 137
ACADM -0.42 0.47 -10000 0 -1.1 246 246
TAT -0.23 0.25 -10000 0 -0.74 63 63
CEBPB 0 0.055 -10000 0 -0.35 9 9
CEBPA -0.018 0.11 -10000 0 -0.47 36 36
TTR -0.26 0.32 -10000 0 -0.96 90 90
PKLR -0.49 0.57 -10000 0 -1.2 276 276
APOA1 -0.49 0.56 -10000 0 -1.3 245 245
CPT1C -0.48 0.52 -10000 0 -1.1 293 293
ALAS1 -0.17 0.22 -10000 0 -0.68 51 51
TFRC -0.28 0.34 -10000 0 -0.92 107 107
FOXF1 -0.022 0.16 -10000 0 -0.51 85 85
NF1 0.035 0.013 -10000 0 -10000 0 0
HNF1A (dimer) -0.057 0.17 -10000 0 -0.54 83 83
CPT1A -0.41 0.47 -10000 0 -1.1 244 244
HMGCS1 -0.41 0.47 -10000 0 -1.1 238 238
NR3C1 -0.005 0.078 -10000 0 -0.32 14 14
CPT1B -0.45 0.51 -10000 0 -1.1 268 268
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.031 0.013 -10000 0 -10000 0 0
GCK -0.41 0.48 -10000 0 -1.1 232 232
CREB1 -0.024 0.08 -10000 0 -0.24 38 38
IGFBP1 -0.31 0.47 -10000 0 -1.5 104 104
PDX1 -0.23 0.34 -10000 0 -1 93 93
UCP2 -0.42 0.48 -10000 0 -1.1 239 239
ALDOB -0.54 0.6 -10000 0 -1.3 287 287
AFP -0.1 0.16 -10000 0 -0.57 41 41
BDH1 -0.47 0.52 -10000 0 -1.1 279 279
HADH -0.41 0.5 -10000 0 -1.1 226 226
F2 -0.57 0.64 -10000 0 -1.4 279 279
HNF1A -0.057 0.17 -10000 0 -0.54 83 83
G6PC -0.33 0.54 -10000 0 -1.4 164 164
SLC2A2 -0.45 0.68 -10000 0 -1.6 193 193
INS 0.013 0.074 0.26 11 -0.34 2 13
FOXA1 -0.074 0.16 -10000 0 -0.34 201 201
FOXA3 -0.13 0.2 -10000 0 -0.43 218 218
FOXA2 -0.47 0.57 -10000 0 -1.2 260 260
ABCC8 -0.43 0.5 -10000 0 -1.1 240 240
ALB -0.17 0.32 -10000 0 -0.97 100 100
Signaling events mediated by VEGFR1 and VEGFR2

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.019 0.096 -10000 0 -0.32 57 57
AKT1 -0.18 0.35 -10000 0 -0.72 242 242
PTK2B -0.2 0.37 -10000 0 -0.82 224 224
VEGFR2 homodimer/Frs2 -0.15 0.33 -10000 0 -0.72 221 221
CAV1 -0.016 0.15 -10000 0 -0.54 69 69
CALM1 0.032 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.2 0.42 -10000 0 -0.88 227 227
endothelial cell proliferation -0.15 0.33 0.54 15 -0.64 239 254
mol:Ca2+ -0.2 0.37 -10000 0 -0.82 223 223
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.17 0.39 -10000 0 -0.81 227 227
RP11-342D11.1 -0.21 0.37 -10000 0 -0.82 228 228
CDH5 -0.047 0.2 -10000 0 -0.55 118 118
VEGFA homodimer -0.028 0.17 -10000 0 -0.32 207 207
SHC1 0.031 0.014 -10000 0 -0.32 1 1
SHC2 0.011 0.11 -10000 0 -0.49 37 37
HRAS/GDP -0.15 0.33 -10000 0 -0.7 222 222
SH2D2A -0.013 0.14 -10000 0 -0.43 83 83
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.14 0.35 -10000 0 -0.72 221 221
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.23 0.44 -10000 0 -0.93 232 232
VEGFR1 homodimer -0.11 0.25 -10000 0 -0.54 222 222
SHC/GRB2/SOS1 -0.15 0.38 -10000 0 -0.79 221 221
GRB10 -0.19 0.36 0.36 1 -0.78 223 224
PTPN11 0.031 0.021 -10000 0 -0.55 1 1
GRB2 0.029 0.011 -10000 0 -10000 0 0
PAK1 0.033 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.19 0.45 -10000 0 -0.94 222 222
HRAS 0.03 0.038 -10000 0 -0.46 5 5
VEGF/Rho/ROCK1/Integrin Complex -0.13 0.27 -10000 0 -0.55 232 232
HIF1A 0.027 0.048 -10000 0 -0.42 9 9
FRS2 0.031 0.007 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.17 0.38 -10000 0 -0.79 227 227
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 -0.059 0.21 -10000 0 -0.55 136 136
Nck/Pak 0.045 0.024 -10000 0 -0.4 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.21 0.43 -10000 0 -0.92 227 227
mol:GDP -0.15 0.36 -10000 0 -0.75 221 221
mol:NADP -0.13 0.3 0.63 6 -0.6 225 231
eNOS/Hsp90 -0.11 0.28 -10000 0 -0.56 221 221
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
mol:IP3 -0.2 0.38 -10000 0 -0.83 223 223
HIF1A/ARNT 0.041 0.039 -10000 0 -0.3 9 9
SHB 0.032 0.02 -10000 0 -0.55 1 1
VEGFA -0.12 0.25 -10000 0 -0.54 225 225
VEGFC 0.014 0.099 -10000 0 -0.52 29 29
FAK1/Vinculin -0.21 0.4 0.38 2 -0.84 236 238
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.03 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.19 0.41 -10000 0 -0.85 229 229
PTPN6 0.031 0.021 -10000 0 -0.55 1 1
EPAS1 -0.075 0.21 -10000 0 -0.41 222 222
mol:L-citrulline -0.13 0.3 0.63 6 -0.6 225 231
ITGAV 0.027 0.05 -10000 0 -0.52 7 7
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.17 0.4 -10000 0 -0.83 220 220
VEGFR2 homodimer/VEGFA homodimer -0.21 0.43 -10000 0 -0.91 228 228
VEGFR2/3 heterodimer -0.2 0.41 -10000 0 -0.88 229 229
VEGFB 0.033 0.004 -10000 0 -10000 0 0
MAPK11 -0.22 0.39 0.43 3 -0.84 231 234
VEGFR2 homodimer -0.19 0.37 -10000 0 -0.83 222 222
FLT1 -0.11 0.25 -10000 0 -0.55 222 222
NEDD4 0.021 0.085 -10000 0 -0.55 19 19
MAPK3 -0.18 0.32 -10000 0 -0.71 225 225
MAPK1 -0.18 0.32 0.27 1 -0.71 227 228
VEGFA145/NRP2 -0.093 0.23 -10000 0 -0.46 238 238
VEGFR1/2 heterodimer -0.23 0.45 -10000 0 -0.92 248 248
KDR -0.19 0.37 -10000 0 -0.83 222 222
VEGFA165/NRP1/VEGFR2 homodimer -0.2 0.43 -10000 0 -0.9 228 228
SRC 0.031 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.19 0.34 0.62 6 -0.73 226 232
PI3K -0.24 0.46 -10000 0 -0.96 239 239
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.2 0.42 -10000 0 -0.89 227 227
FES -0.22 0.4 0.37 1 -0.87 229 230
GAB1 -0.24 0.46 -10000 0 -0.98 240 240
VEGFR2 homodimer/VEGFA homodimer/Src -0.2 0.42 -10000 0 -0.88 227 227
CTNNB1 0.03 0.01 -10000 0 -10000 0 0
SOS1 0.031 0.007 -10000 0 -10000 0 0
ARNT 0.031 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.11 0.28 0.62 1 -0.56 223 224
VEGFR2 homodimer/VEGFA homodimer/Yes -0.2 0.42 -10000 0 -0.9 227 227
PI3K/GAB1 -0.17 0.36 -10000 0 -0.75 237 237
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.16 0.4 -10000 0 -0.82 220 220
PRKACA 0.033 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.19 0.41 -10000 0 -0.86 228 228
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
CDC42 -0.21 0.4 0.37 1 -0.86 228 229
actin cytoskeleton reorganization -0.22 0.43 -10000 0 -0.92 232 232
PTK2 -0.24 0.44 0.33 1 -0.94 230 231
EDG1 -0.21 0.37 -10000 0 -0.82 228 228
mol:DAG -0.2 0.38 -10000 0 -0.83 223 223
CaM/Ca2+ -0.18 0.36 -10000 0 -0.77 222 222
MAP2K3 -0.2 0.36 0.37 3 -0.79 222 225
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.18 0.39 -10000 0 -0.83 222 222
PLCG1 -0.21 0.39 -10000 0 -0.85 223 223
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.18 0.41 -10000 0 -0.86 221 221
IQGAP1 0.033 0.004 -10000 0 -10000 0 0
YES1 0.032 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.2 0.42 -10000 0 -0.89 227 227
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.2 0.42 -10000 0 -0.88 227 227
cell migration -0.17 0.34 0.32 1 -0.7 227 228
mol:PI-3-4-5-P3 -0.2 0.4 -10000 0 -0.84 239 239
FYN 0.025 0.056 -10000 0 -0.55 8 8
VEGFB/NRP1 -0.19 0.36 -10000 0 -0.78 228 228
mol:NO -0.13 0.3 0.63 6 -0.6 225 231
PXN 0.032 0.007 -10000 0 -10000 0 0
HRAS/GTP -0.17 0.32 -10000 0 -0.7 222 222
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.19 0.39 -10000 0 -0.83 222 222
VHL 0.028 0.04 -10000 0 -0.55 4 4
ITGB3 0.001 0.12 -10000 0 -0.45 51 51
NOS3 -0.16 0.35 0.64 6 -0.71 225 231
VEGFR2 homodimer/VEGFA homodimer/Sck -0.22 0.43 -10000 0 -0.91 232 232
RAC1 0.029 0.011 -10000 0 -10000 0 0
PRKCA -0.18 0.34 0.37 1 -0.75 218 219
PRKCB -0.2 0.34 -10000 0 -0.76 225 225
VCL 0.031 0.008 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.21 0.39 -10000 0 -0.85 228 228
VEGFR1/2 heterodimer/VEGFA homodimer -0.27 0.52 -10000 0 -1.1 244 244
VEGFA165/NRP2 -0.093 0.23 -10000 0 -0.46 238 238
MAPKKK cascade -0.14 0.31 0.36 1 -0.67 214 215
NRP2 -0.009 0.15 -10000 0 -0.54 62 62
VEGFC homodimer 0.014 0.099 -10000 0 -0.52 29 29
NCK1 0.03 0.029 -10000 0 -0.55 2 2
ROCK1 0.03 0.034 -10000 0 -0.55 3 3
FAK1/Paxillin -0.21 0.4 0.33 1 -0.83 236 237
MAP3K13 -0.21 0.39 0.37 1 -0.86 225 226
PDPK1 -0.17 0.33 -10000 0 -0.7 236 236
HIF-2-alpha transcription factor network

Figure S6.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S6.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.01 0.21 -10000 0 -1.1 27 27
oxygen homeostasis -0.005 0.016 -10000 0 -10000 0 0
TCEB2 0.027 0.044 -10000 0 -0.41 8 8
TCEB1 0.032 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.069 0.22 -10000 0 -0.42 179 179
EPO -0.25 0.36 -10000 0 -0.7 287 287
FIH (dimer) 0.014 0.032 -10000 0 -10000 0 0
APEX1 0.015 0.035 -10000 0 -10000 0 0
SERPINE1 -0.25 0.45 -10000 0 -0.85 265 265
FLT1 -0.4 0.7 -10000 0 -1.4 264 264
ADORA2A -0.23 0.4 0.4 2 -0.76 274 276
germ cell development -0.23 0.42 -10000 0 -0.77 294 294
SLC11A2 -0.22 0.42 -10000 0 -0.78 262 262
BHLHE40 -0.22 0.41 -10000 0 -0.78 268 268
HIF1AN 0.014 0.032 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.15 0.27 -10000 0 -0.52 239 239
ETS1 -0.025 0.14 -10000 0 -0.56 33 33
CITED2 -0.032 0.22 -10000 0 -0.84 54 54
KDR -0.38 0.69 -10000 0 -1.5 242 242
PGK1 -0.22 0.42 -10000 0 -0.79 269 269
SIRT1 0.029 0.021 -10000 0 -0.55 1 1
response to hypoxia -0.002 0.004 -10000 0 -10000 0 0
HIF2A/ARNT -0.27 0.54 -10000 0 -0.98 274 274
EPAS1 -0.099 0.22 -10000 0 -0.45 202 202
SP1 0.036 0.018 -10000 0 -10000 0 0
ABCG2 -0.24 0.44 -10000 0 -0.82 275 275
EFNA1 -0.22 0.42 -10000 0 -0.8 266 266
FXN -0.23 0.4 0.4 2 -0.76 273 275
POU5F1 -0.25 0.44 -10000 0 -0.82 294 294
neuron apoptosis 0.25 0.51 0.92 274 -10000 0 274
EP300 0.031 0.028 -10000 0 -0.55 2 2
EGLN3 -0.12 0.25 -10000 0 -0.56 215 215
EGLN2 0.017 0.042 -10000 0 -0.49 3 3
EGLN1 0.014 0.032 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.053 0.045 -10000 0 -0.37 6 6
VHL 0.028 0.04 -10000 0 -0.55 4 4
ARNT 0.013 0.035 -10000 0 -10000 0 0
SLC2A1 -0.25 0.42 0.4 2 -0.81 274 276
TWIST1 -0.24 0.41 0.4 2 -0.78 270 272
ELK1 0.039 0.006 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.1 0.28 -10000 0 -0.52 211 211
VEGFA -0.28 0.49 -10000 0 -0.92 296 296
CREBBP 0.031 0.008 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

Figure S7.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S7.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.24 0.51 -10000 0 -1.1 189 189
NCK1/PAK1/Dok-R -0.13 0.19 -10000 0 -0.46 187 187
NCK1/Dok-R -0.24 0.61 -10000 0 -1.4 180 180
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
mol:beta2-estradiol 0.038 0.09 0.24 140 -10000 0 140
RELA 0.033 0.004 -10000 0 -10000 0 0
SHC1 0.03 0.014 -10000 0 -0.32 1 1
Rac/GDP 0.021 0.008 -10000 0 -10000 0 0
F2 -0.059 0.24 0.28 119 -0.4 250 369
TNIP2 0.031 0.028 -10000 0 -0.55 2 2
NF kappa B/RelA -0.19 0.55 -10000 0 -1.2 179 179
FN1 -0.042 0.18 -10000 0 -0.48 127 127
PLD2 -0.26 0.62 -10000 0 -1.4 179 179
PTPN11 0.031 0.021 -10000 0 -0.55 1 1
GRB14 -0.025 0.15 -10000 0 -0.38 124 124
ELK1 -0.21 0.52 -10000 0 -1.2 179 179
GRB7 0.02 0.071 -10000 0 -0.47 17 17
PAK1 0.033 0.004 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.23 0.6 -10000 0 -1.4 181 181
CDKN1A -0.18 0.38 -10000 0 -0.71 270 270
ITGA5 0.016 0.091 -10000 0 -0.5 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.24 0.61 -10000 0 -1.4 180 180
CRK 0.029 0.016 -10000 0 -0.32 1 1
mol:NO -0.15 0.36 0.44 4 -0.76 189 193
PLG -0.34 0.61 -10000 0 -1.5 179 179
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.2 0.45 -10000 0 -1 182 182
GRB2 0.029 0.011 -10000 0 -10000 0 0
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
ANGPT2 -0.35 0.62 -10000 0 -1.3 250 250
BMX -0.3 0.63 -10000 0 -1.5 179 179
ANGPT1 -0.24 0.6 -10000 0 -1.5 147 147
tube development -0.21 0.42 -10000 0 -0.83 271 271
ANGPT4 -0.015 0.12 -10000 0 -0.4 71 71
response to hypoxia -0.017 0.029 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.29 0.67 -10000 0 -1.6 179 179
alpha5/beta1 Integrin 0.033 0.07 -10000 0 -0.36 25 25
FGF2 0.005 0.13 -10000 0 -0.54 47 47
STAT5A (dimer) -0.24 0.5 -10000 0 -0.96 269 269
mol:L-citrulline -0.15 0.36 0.44 4 -0.76 189 193
AGTR1 -0.11 0.2 -10000 0 -0.41 260 260
MAPK14 -0.29 0.64 -10000 0 -1.5 189 189
Tie2/SHP2 -0.18 0.51 -10000 0 -1.3 134 134
TEK -0.21 0.57 -10000 0 -1.5 137 137
RPS6KB1 -0.2 0.46 -10000 0 -1 182 182
Angiotensin II/AT1 -0.082 0.15 -10000 0 -0.29 260 260
Tie2/Ang1/GRB2 -0.27 0.66 -10000 0 -1.5 179 179
MAPK3 -0.22 0.53 -10000 0 -1.2 179 179
MAPK1 -0.23 0.54 -10000 0 -1.3 179 179
Tie2/Ang1/GRB7 -0.27 0.66 -10000 0 -1.5 179 179
NFKB1 0.032 0.02 -10000 0 -0.55 1 1
MAPK8 -0.27 0.63 -10000 0 -1.5 179 179
PI3K -0.28 0.6 -10000 0 -1.4 182 182
FES -0.28 0.64 -10000 0 -1.5 181 181
Crk/Dok-R -0.23 0.6 -10000 0 -1.4 180 180
Tie2/Ang1/ABIN2 -0.27 0.67 -10000 0 -1.5 179 179
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.2 0.44 -10000 0 -0.96 190 190
STAT5A 0.028 0.035 -10000 0 -0.55 3 3
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.21 0.47 -10000 0 -1.1 182 182
Tie2/Ang2 -0.35 0.63 -10000 0 -1.3 271 271
Tie2/Ang1 -0.31 0.74 -10000 0 -1.7 179 179
FOXO1 -0.23 0.47 -10000 0 -0.92 250 250
ELF1 0.016 0.064 -10000 0 -0.57 3 3
ELF2 -0.26 0.63 -10000 0 -1.5 179 179
mol:Choline -0.24 0.57 -10000 0 -1.3 179 179
cell migration -0.072 0.1 -10000 0 -0.25 186 186
FYN -0.26 0.5 -10000 0 -0.98 271 271
DOK2 -0.002 0.14 -10000 0 -0.54 52 52
negative regulation of cell cycle -0.15 0.34 -10000 0 -0.64 270 270
ETS1 -0.03 0.16 -10000 0 -0.35 137 137
PXN -0.15 0.37 0.5 3 -0.82 182 185
ITGB1 0.031 0.008 -10000 0 -10000 0 0
NOS3 -0.18 0.41 0.48 2 -0.89 188 190
RAC1 0.029 0.011 -10000 0 -10000 0 0
TNF -0.052 0.17 -10000 0 -0.36 179 179
MAPKKK cascade -0.24 0.57 -10000 0 -1.3 179 179
RASA1 0.03 0.034 -10000 0 -0.55 3 3
Tie2/Ang1/Shc -0.27 0.67 -10000 0 -1.6 179 179
NCK1 0.03 0.029 -10000 0 -0.55 2 2
vasculogenesis -0.13 0.32 0.4 6 -0.66 190 196
mol:Phosphatidic acid -0.24 0.57 -10000 0 -1.3 179 179
mol:Angiotensin II -0.006 0.014 -10000 0 -10000 0 0
mol:NADP -0.15 0.36 0.44 4 -0.76 189 193
Rac1/GTP -0.18 0.42 -10000 0 -0.94 182 182
MMP2 -0.27 0.62 -10000 0 -1.5 179 179
Ephrin A reverse signaling

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.033 0.14 -10000 0 -0.3 178 178
EFNA5 -0.061 0.2 -10000 0 -0.48 157 157
FYN -0.039 0.13 0.18 13 -0.33 128 141
neuron projection morphogenesis -0.033 0.14 -10000 0 -0.3 178 178
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.033 0.14 -10000 0 -0.3 178 178
EPHA5 0.007 0.071 -10000 0 -0.32 39 39
Syndecan-1-mediated signaling events

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.021 0.082 -10000 0 -0.53 19 19
CCL5 -0.008 0.13 -10000 0 -0.4 76 76
SDCBP 0.032 0.006 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.15 0.21 -10000 0 -0.46 192 192
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.14 0.21 0.27 1 -0.45 190 191
Syndecan-1/Syntenin -0.14 0.21 0.23 1 -0.45 189 190
MAPK3 -0.13 0.19 -10000 0 -0.5 115 115
HGF/MET -0.001 0.12 -10000 0 -0.33 99 99
TGFB1/TGF beta receptor Type II 0.021 0.082 -10000 0 -0.52 19 19
BSG 0.03 0.033 -10000 0 -0.36 6 6
keratinocyte migration -0.14 0.2 0.27 1 -0.44 191 192
Syndecan-1/RANTES -0.15 0.22 0.43 3 -0.48 173 176
Syndecan-1/CD147 -0.13 0.21 -10000 0 -0.52 126 126
Syndecan-1/Syntenin/PIP2 -0.14 0.2 -10000 0 -0.43 189 189
LAMA5 0.027 0.05 -10000 0 -0.52 7 7
positive regulation of cell-cell adhesion -0.14 0.19 -10000 0 -0.42 189 189
MMP7 -0.13 0.23 -10000 0 -0.43 302 302
HGF -0.024 0.16 -10000 0 -0.46 95 95
Syndecan-1/CASK -0.15 0.2 -10000 0 -0.44 194 194
Syndecan-1/HGF/MET -0.14 0.22 -10000 0 -0.5 163 163
regulation of cell adhesion -0.12 0.18 0.32 1 -0.48 114 115
HPSE -0.008 0.14 -10000 0 -0.51 66 66
positive regulation of cell migration -0.15 0.21 -10000 0 -0.46 192 192
SDC1 -0.16 0.21 -10000 0 -0.47 194 194
Syndecan-1/Collagen -0.15 0.21 -10000 0 -0.46 192 192
PPIB 0.033 0.003 -10000 0 -10000 0 0
MET 0.025 0.045 -10000 0 -0.55 5 5
PRKACA 0.033 0.003 -10000 0 -10000 0 0
MMP9 -0.054 0.18 -10000 0 -0.4 171 171
MAPK1 -0.13 0.19 -10000 0 -0.49 123 123
homophilic cell adhesion -0.15 0.21 -10000 0 -0.46 193 193
MMP1 -0.14 0.24 -10000 0 -0.46 309 309
S1P1 pathway

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.16 0.32 -10000 0 -0.63 268 268
PDGFRB -0.055 0.21 -10000 0 -0.55 132 132
SPHK1 -0.04 0.18 -10000 0 -0.76 45 45
mol:S1P -0.035 0.16 -10000 0 -0.65 45 45
S1P1/S1P/Gi -0.095 0.22 0.25 1 -0.53 137 138
GNAO1 -0.002 0.12 -10000 0 -0.42 63 63
PDGFB-D/PDGFRB/PLCgamma1 -0.091 0.24 0.38 8 -0.58 140 148
PLCG1 -0.088 0.21 0.24 2 -0.51 127 129
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.055 0.21 -10000 0 -0.54 132 132
GNAI2 0.03 0.013 -10000 0 -10000 0 0
GNAI3 0.03 0.011 -10000 0 -10000 0 0
GNAI1 0.022 0.06 -10000 0 -0.56 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.16 0.27 -10000 0 -0.55 267 267
S1P1/S1P -0.14 0.24 -10000 0 -0.5 258 258
negative regulation of cAMP metabolic process -0.092 0.22 0.25 1 -0.51 137 138
MAPK3 -0.1 0.24 0.36 3 -0.59 123 126
calcium-dependent phospholipase C activity -0.001 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.022 0.007 -10000 0 -10000 0 0
KDR -0.12 0.26 -10000 0 -0.54 233 233
PLCB2 -0.13 0.23 0.3 5 -0.46 260 265
RAC1 0.029 0.011 -10000 0 -10000 0 0
RhoA/GTP -0.12 0.2 -10000 0 -0.42 249 249
receptor internalization -0.13 0.22 -10000 0 -0.46 258 258
PTGS2 -0.12 0.33 0.48 11 -0.93 97 108
Rac1/GTP -0.11 0.19 -10000 0 -0.4 238 238
RHOA 0.03 0.009 -10000 0 -10000 0 0
VEGFA -0.12 0.25 -10000 0 -0.55 225 225
negative regulation of T cell proliferation -0.092 0.22 0.25 1 -0.51 137 138
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.025 0.056 -10000 0 -0.48 10 10
MAPK1 -0.11 0.26 0.24 1 -0.73 101 102
S1P1/S1P/PDGFB-D/PDGFRB -0.16 0.3 0.25 2 -0.57 260 262
ABCC1 0.03 0.022 -10000 0 -0.56 1 1
IL23-mediated signaling events

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.34 0.55 -10000 0 -1.3 157 157
IL23A -0.34 0.54 -10000 0 -1.3 170 170
NF kappa B1 p50/RelA/I kappa B alpha -0.32 0.57 -10000 0 -1.3 172 172
positive regulation of T cell mediated cytotoxicity -0.39 0.64 -10000 0 -1.5 182 182
ITGA3 -0.32 0.53 -10000 0 -1.3 163 163
IL17F -0.2 0.34 -10000 0 -0.76 165 165
IL12B -0.029 0.11 -10000 0 -0.37 63 63
STAT1 (dimer) -0.36 0.61 -10000 0 -1.4 182 182
CD4 -0.32 0.52 -10000 0 -1.3 152 152
IL23 -0.33 0.52 -10000 0 -1.2 172 172
IL23R -0.083 0.29 -10000 0 -1.2 46 46
IL1B -0.36 0.57 -10000 0 -1.4 171 171
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.32 0.51 -10000 0 -1.3 150 150
TYK2 0.001 0.048 -10000 0 -0.58 2 2
STAT4 0.001 0.13 -10000 0 -0.54 47 47
STAT3 0.03 0.01 -10000 0 -10000 0 0
IL18RAP -0.004 0.13 -10000 0 -0.49 55 55
IL12RB1 -0.03 0.14 -10000 0 -0.53 57 57
PIK3CA 0.028 0.048 -10000 0 -0.55 6 6
IL12Rbeta1/TYK2 -0.016 0.12 -10000 0 -0.4 59 59
IL23R/JAK2 -0.084 0.28 -10000 0 -1.2 46 46
positive regulation of chronic inflammatory response -0.39 0.64 -10000 0 -1.5 182 182
natural killer cell activation 0.004 0.009 0.039 2 -10000 0 2
JAK2 0 0.052 -10000 0 -0.58 1 1
PIK3R1 0.03 0.038 -10000 0 -0.46 5 5
NFKB1 0.03 0.021 -10000 0 -0.56 1 1
RELA 0.031 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.31 0.49 -10000 0 -1.1 172 172
ALOX12B -0.36 0.57 -10000 0 -1.3 199 199
CXCL1 -0.44 0.62 -10000 0 -1.3 243 243
T cell proliferation -0.39 0.64 -10000 0 -1.5 182 182
NFKBIA 0.031 0.007 -10000 0 -10000 0 0
IL17A -0.15 0.27 -10000 0 -0.59 142 142
PI3K -0.34 0.58 -10000 0 -1.3 178 178
IFNG -0.018 0.045 -10000 0 -0.13 56 56
STAT3 (dimer) -0.31 0.54 -10000 0 -1.2 172 172
IL18R1 -0.006 0.14 -10000 0 -0.54 54 54
IL23/IL23R/JAK2/TYK2/SOCS3 -0.2 0.4 -10000 0 -1 102 102
IL18/IL18R -0.008 0.15 -10000 0 -0.38 108 108
macrophage activation -0.016 0.021 -10000 0 -0.046 92 92
TNF -0.36 0.58 -10000 0 -1.4 176 176
STAT3/STAT4 -0.34 0.58 -10000 0 -1.3 180 180
STAT4 (dimer) -0.37 0.62 -10000 0 -1.4 187 187
IL18 0.013 0.088 -10000 0 -0.4 36 36
IL19 -0.32 0.51 -10000 0 -1.2 164 164
STAT5A (dimer) -0.36 0.6 -10000 0 -1.4 179 179
STAT1 0.028 0.041 -10000 0 -0.38 8 8
SOCS3 0.01 0.095 -10000 0 -0.44 36 36
CXCL9 -0.43 0.62 -10000 0 -1.4 230 230
MPO -0.33 0.53 -10000 0 -1.3 172 172
positive regulation of humoral immune response -0.39 0.64 -10000 0 -1.5 182 182
IL23/IL23R/JAK2/TYK2 -0.45 0.81 -10000 0 -1.8 182 182
IL6 -0.38 0.58 -10000 0 -1.3 197 197
STAT5A 0.027 0.035 -10000 0 -0.55 3 3
IL2 0.012 0.048 -10000 0 -0.32 12 12
positive regulation of tyrosine phosphorylation of STAT protein 0.004 0.009 0.039 2 -10000 0 2
CD3E -0.35 0.56 -10000 0 -1.4 160 160
keratinocyte proliferation -0.39 0.64 -10000 0 -1.5 182 182
NOS2 -0.36 0.56 -10000 0 -1.3 182 182
Nephrin/Neph1 signaling in the kidney podocyte

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.058 0.17 0.34 213 -10000 0 213
KIRREL -0.031 0.16 -10000 0 -0.56 69 69
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.059 0.17 -10000 0 -0.34 213 213
PLCG1 0.031 0.008 -10000 0 -10000 0 0
ARRB2 0.029 0.01 -10000 0 -10000 0 0
WASL 0.029 0.011 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.032 0.16 -10000 0 -0.32 166 166
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.03 0.11 -10000 0 -0.29 92 92
FYN -0.057 0.13 0.27 7 -0.29 173 180
mol:Ca2+ -0.032 0.15 -10000 0 -0.31 156 156
mol:DAG -0.031 0.15 -10000 0 -0.31 156 156
NPHS2 -0.036 0.12 -10000 0 -0.34 109 109
mol:IP3 -0.031 0.15 -10000 0 -0.31 156 156
regulation of endocytosis -0.027 0.13 -10000 0 -0.28 155 155
Nephrin/NEPH1/podocin/Cholesterol -0.045 0.15 -10000 0 -0.32 169 169
establishment of cell polarity -0.058 0.17 -10000 0 -0.34 213 213
Nephrin/NEPH1/podocin/NCK1-2 -0.014 0.15 -10000 0 -0.29 158 158
Nephrin/NEPH1/beta Arrestin2 -0.026 0.14 -10000 0 -0.28 154 154
NPHS1 -0.059 0.17 -10000 0 -0.4 162 162
Nephrin/NEPH1/podocin -0.038 0.14 -10000 0 -0.3 173 173
TJP1 0.033 0.004 -10000 0 -10000 0 0
NCK1 0.03 0.029 -10000 0 -0.55 2 2
NCK2 0.032 0.007 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.03 0.15 -10000 0 -0.32 156 156
CD2AP 0.031 0.008 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.027 0.15 -10000 0 -0.32 145 145
GRB2 0.029 0.011 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.13 0.18 0.28 5 -0.35 301 306
cytoskeleton organization -0.043 0.12 0.21 5 -0.35 84 89
Nephrin/NEPH1 -0.036 0.12 -10000 0 -0.26 166 166
Nephrin/NEPH1/ZO-1 -0.024 0.15 -10000 0 -0.34 112 112
Thromboxane A2 receptor signaling

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.009 0.14 -10000 0 -0.52 63 63
GNB1/GNG2 -0.066 0.09 -10000 0 -0.2 251 251
AKT1 -0.031 0.13 0.28 11 -0.26 83 94
EGF -0.059 0.19 -10000 0 -0.41 181 181
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.023 0.14 0.49 7 -0.47 54 61
mol:Ca2+ -0.065 0.18 0.29 4 -0.33 245 249
LYN -0.022 0.13 0.39 2 -0.44 49 51
RhoA/GTP -0.021 0.071 -10000 0 -0.14 80 80
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.078 0.2 0.34 6 -0.37 251 257
GNG2 0.011 0.11 -10000 0 -0.55 32 32
ARRB2 0.029 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.027 0.16 -10000 0 -0.52 63 63
G beta5/gamma2 -0.087 0.12 -10000 0 -0.28 246 246
PRKCH -0.089 0.21 0.29 3 -0.4 248 251
DNM1 -0.037 0.18 -10000 0 -0.45 127 127
TXA2/TP beta/beta Arrestin3 -0.016 0.069 -10000 0 -0.26 3 3
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.011 0.15 -10000 0 -0.52 67 67
G12 family/GTP -0.065 0.16 -10000 0 -0.32 204 204
ADRBK1 0.031 0.028 -10000 0 -0.55 2 2
ADRBK2 0.031 0.021 -10000 0 -0.55 1 1
RhoA/GTP/ROCK1 0.038 0.026 -10000 0 -0.34 3 3
mol:GDP 0.049 0.16 0.4 109 -0.3 4 113
mol:NADP 0 0.12 -10000 0 -0.54 43 43
RAB11A 0.033 0.003 -10000 0 -10000 0 0
PRKG1 -0.066 0.22 -10000 0 -0.54 148 148
mol:IP3 -0.088 0.22 0.31 4 -0.42 249 253
cell morphogenesis 0.038 0.026 -10000 0 -0.34 3 3
PLCB2 -0.13 0.3 0.37 2 -0.58 245 247
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.045 0.14 0.39 3 -0.44 63 66
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.024 0.13 0.38 2 -0.48 45 47
RHOA 0.03 0.009 -10000 0 -10000 0 0
PTGIR -0.002 0.13 -10000 0 -0.5 57 57
PRKCB1 -0.087 0.21 0.35 4 -0.41 250 254
GNAQ 0.032 0.005 -10000 0 -10000 0 0
mol:L-citrulline 0 0.12 -10000 0 -0.54 43 43
TXA2/TXA2-R family -0.13 0.29 0.42 4 -0.57 251 255
LCK -0.036 0.17 0.49 7 -0.5 70 77
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.022 0.16 -10000 0 -0.44 84 84
TXA2-R family/G12 family/GDP/G beta/gamma -0.017 0.16 -10000 0 -0.53 60 60
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.014 0.15 -10000 0 -0.54 45 45
MAPK14 -0.046 0.13 0.28 6 -0.24 233 239
TGM2/GTP -0.1 0.25 0.37 2 -0.48 245 247
MAPK11 -0.047 0.14 0.29 7 -0.25 249 256
ARHGEF1 -0.032 0.098 0.23 1 -0.19 187 188
GNAI2 0.03 0.009 -10000 0 -10000 0 0
JNK cascade -0.088 0.22 0.37 5 -0.41 251 256
RAB11/GDP 0.033 0.004 -10000 0 -10000 0 0
ICAM1 -0.061 0.17 0.3 6 -0.31 248 254
cAMP biosynthetic process -0.084 0.2 0.36 5 -0.39 246 251
Gq family/GTP/EBP50 -0.013 0.1 0.24 1 -0.33 49 50
actin cytoskeleton reorganization 0.038 0.026 -10000 0 -0.34 3 3
SRC -0.021 0.12 0.38 2 -0.44 41 43
GNB5 0.032 0.02 -10000 0 -0.55 1 1
GNB1 0.031 0.008 -10000 0 -10000 0 0
EGF/EGFR -0.035 0.15 0.4 18 -0.36 83 101
VCAM1 -0.074 0.19 0.32 5 -0.35 250 255
TP beta/Gq family/GDP/G beta5/gamma2 -0.027 0.16 -10000 0 -0.52 63 63
platelet activation -0.06 0.18 0.35 8 -0.32 247 255
PGI2/IP -0.001 0.097 -10000 0 -0.36 57 57
PRKACA -0.015 0.13 -10000 0 -0.36 85 85
Gq family/GDP/G beta5/gamma2 -0.024 0.15 -10000 0 -0.49 66 66
TXA2/TP beta/beta Arrestin2 -0.045 0.17 -10000 0 -0.55 80 80
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.048 0.18 -10000 0 -0.42 127 127
mol:DAG -0.1 0.24 0.35 2 -0.46 250 252
EGFR 0.008 0.1 -10000 0 -0.47 36 36
TXA2/TP alpha -0.12 0.28 0.46 3 -0.54 246 249
Gq family/GTP -0.018 0.094 -10000 0 -0.24 125 125
YES1 -0.021 0.13 0.36 5 -0.44 47 52
GNAI2/GTP -0.022 0.14 -10000 0 -0.44 66 66
PGD2/DP -0.008 0.11 -10000 0 -0.37 71 71
SLC9A3R1 0.024 0.056 -10000 0 -0.55 8 8
FYN -0.02 0.14 0.54 8 -0.46 51 59
mol:NO 0 0.12 -10000 0 -0.54 43 43
GNA15 0.014 0.1 -10000 0 -0.5 31 31
PGK/cGMP -0.032 0.16 -10000 0 -0.35 145 145
RhoA/GDP 0.03 0.01 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.026 0.21 -10000 0 -0.61 71 71
NOS3 0 0.12 -10000 0 -0.55 43 43
RAC1 0.029 0.011 -10000 0 -10000 0 0
PRKCA -0.073 0.2 0.32 9 -0.38 221 230
PRKCB -0.081 0.21 0.29 11 -0.4 237 248
PRKCE -0.08 0.2 0.3 5 -0.38 240 245
PRKCD -0.091 0.22 0.35 5 -0.42 246 251
PRKCG -0.094 0.22 0.33 3 -0.43 249 252
muscle contraction -0.12 0.27 0.43 4 -0.53 251 255
PRKCZ -0.077 0.19 0.35 5 -0.36 249 254
ARR3 0.022 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.016 0.17 -10000 0 -0.49 72 72
PRKCQ -0.087 0.21 0.27 5 -0.4 247 252
MAPKKK cascade -0.11 0.26 0.4 4 -0.51 249 253
SELE -0.08 0.19 0.31 5 -0.37 247 252
TP beta/GNAI2/GDP/G beta/gamma -0.011 0.19 -10000 0 -0.65 53 53
ROCK1 0.03 0.034 -10000 0 -0.55 3 3
GNA14 -0.029 0.18 -10000 0 -0.55 93 93
chemotaxis -0.15 0.32 0.43 4 -0.64 250 254
GNA12 0.029 0.011 -10000 0 -10000 0 0
GNA13 0.029 0.011 -10000 0 -10000 0 0
GNA11 0.017 0.089 -10000 0 -0.44 30 30
Rac1/GTP 0.021 0.008 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.069 0.26 0.36 7 -0.6 144 151
FYN -0.13 0.36 0.42 12 -0.81 162 174
LAT/GRAP2/SLP76 -0.094 0.29 0.26 2 -0.65 157 159
IKBKB 0.032 0.007 -10000 0 -10000 0 0
AKT1 -0.056 0.23 0.39 30 -0.47 161 191
B2M 0.03 0.029 -10000 0 -0.56 2 2
IKBKG -0.008 0.068 0.11 46 -0.16 77 123
MAP3K8 0.029 0.033 -10000 0 -0.44 4 4
mol:Ca2+ -0.018 0.035 0.096 26 -0.089 106 132
integrin-mediated signaling pathway 0.032 0.057 -10000 0 -0.33 19 19
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.34 0.42 22 -0.74 163 185
TRPV6 0.091 0.4 1.1 113 -0.62 10 123
CD28 0.003 0.12 -10000 0 -0.5 47 47
SHC1 -0.13 0.34 0.32 12 -0.78 163 175
receptor internalization -0.15 0.39 -10000 0 -0.83 180 180
PRF1 -0.16 0.44 -10000 0 -1.2 125 125
KRAS 0.031 0.008 -10000 0 -10000 0 0
GRB2 0.029 0.011 -10000 0 -10000 0 0
COT/AKT1 -0.029 0.19 0.37 29 -0.37 146 175
LAT -0.13 0.34 0.32 8 -0.76 172 180
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.046 0.19 -10000 0 -0.48 134 134
CD3E -0.036 0.18 -10000 0 -0.49 116 116
CD3G -0.067 0.21 -10000 0 -0.48 169 169
RASGRP2 -0.005 0.044 0.09 6 -0.19 37 43
RASGRP1 -0.057 0.23 0.44 28 -0.47 155 183
HLA-A -0.001 0.006 0.05 2 -10000 0 2
RASSF5 0.019 0.083 -10000 0 -0.54 19 19
RAP1A/GTP/RAPL 0.032 0.057 -10000 0 -0.33 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.11 0.28 50 -0.13 103 153
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.049 0.088 -10000 0 -0.25 115 115
PRKCA -0.033 0.12 0.19 9 -0.28 132 141
GRAP2 -0.001 0.14 -10000 0 -0.55 50 50
mol:IP3 -0.071 0.2 0.19 43 -0.46 155 198
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.16 0.44 -10000 0 -0.9 171 171
ORAI1 -0.074 0.31 0.85 3 -0.91 98 101
CSK -0.14 0.35 0.3 6 -0.78 169 175
B7 family/CD28 -0.12 0.38 0.42 2 -0.82 165 167
CHUK 0.03 0.021 -10000 0 -0.55 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.17 0.43 -10000 0 -0.92 175 175
PTPN6 -0.14 0.36 0.23 4 -0.8 166 170
VAV1 -0.14 0.36 0.34 6 -0.79 169 175
Monovalent TCR/CD3 -0.12 0.34 -10000 0 -0.7 173 173
CBL 0.032 0.02 -10000 0 -0.55 1 1
LCK -0.15 0.4 0.39 13 -0.88 167 180
PAG1 -0.14 0.36 0.25 6 -0.79 171 177
RAP1A 0.031 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.17 0.44 0.26 4 -0.95 170 174
CD80 -0.009 0.14 -10000 0 -0.46 72 72
CD86 0.011 0.11 -10000 0 -0.55 31 31
PDK1/CARD11/BCL10/MALT1 -0.037 0.12 -10000 0 -0.3 119 119
HRAS 0.03 0.038 -10000 0 -0.46 5 5
GO:0035030 -0.11 0.28 0.39 4 -0.64 166 170
CD8A -0.053 0.19 -10000 0 -0.43 164 164
CD8B -0.061 0.19 -10000 0 -0.43 177 177
PTPRC 0.006 0.12 -10000 0 -0.52 40 40
PDK1/PKC theta -0.076 0.28 0.48 33 -0.6 156 189
CSK/PAG1 -0.13 0.34 0.35 4 -0.78 162 166
SOS1 0.031 0.007 -10000 0 -10000 0 0
peptide-MHC class I 0.019 0.026 -10000 0 -0.32 3 3
GRAP2/SLP76 -0.11 0.34 0.27 1 -0.76 162 163
STIM1 -0.027 0.17 1 4 -0.83 27 31
RAS family/GTP 0.009 0.12 0.3 33 -0.19 112 145
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.17 0.46 -10000 0 -0.94 181 181
mol:DAG -0.085 0.16 0.12 1 -0.4 158 159
RAP1A/GDP 0.013 0.066 0.18 43 -0.067 1 44
PLCG1 0.031 0.008 -10000 0 -10000 0 0
CD247 -0.006 0.14 -10000 0 -0.51 61 61
cytotoxic T cell degranulation -0.14 0.41 -10000 0 -1.1 132 132
RAP1A/GTP 0 0.016 -10000 0 -0.069 35 35
mol:PI-3-4-5-P3 -0.078 0.27 0.4 23 -0.58 163 186
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.091 0.27 0.25 10 -0.62 154 164
NRAS 0.031 0.008 -10000 0 -10000 0 0
ZAP70 -0.003 0.13 -10000 0 -0.46 61 61
GRB2/SOS1 0.043 0.016 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.098 0.27 -10000 0 -0.62 158 158
MALT1 0.031 0.02 -10000 0 -0.55 1 1
TRAF6 0.033 0.004 -10000 0 -10000 0 0
CD8 heterodimer -0.078 0.24 -10000 0 -0.46 217 217
CARD11 -0.008 0.13 -10000 0 -0.42 72 72
PRKCB -0.042 0.14 0.19 8 -0.32 132 140
PRKCE -0.037 0.13 0.19 9 -0.3 133 142
PRKCQ -0.1 0.32 0.43 25 -0.69 164 189
LCP2 0.003 0.12 -10000 0 -0.54 43 43
BCL10 0.031 0.008 -10000 0 -10000 0 0
regulation of survival gene product expression -0.042 0.2 0.38 31 -0.39 157 188
IKK complex 0.019 0.12 0.27 77 -0.12 69 146
RAS family/GDP -0.003 0.015 -10000 0 -0.07 4 4
MAP3K14 -0.022 0.14 0.34 16 -0.3 123 139
PDPK1 -0.048 0.22 0.42 33 -0.44 155 188
TCR/CD3/MHC I/CD8/Fyn -0.18 0.46 -10000 0 -1 169 169
Syndecan-4-mediated signaling events

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.081 0.2 -10000 0 -0.58 97 97
Syndecan-4/Syndesmos -0.18 0.25 -10000 0 -0.62 166 166
positive regulation of JNK cascade -0.19 0.25 -10000 0 -0.58 193 193
Syndecan-4/ADAM12 -0.21 0.26 -10000 0 -0.63 192 192
CCL5 -0.008 0.13 -10000 0 -0.4 76 76
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
DNM2 0.033 0.003 -10000 0 -10000 0 0
ITGA5 0.016 0.091 -10000 0 -0.5 25 25
SDCBP 0.032 0.006 -10000 0 -10000 0 0
PLG -0.14 0.21 -10000 0 -0.39 336 336
ADAM12 -0.035 0.16 -10000 0 -0.38 140 140
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.03 0.024 -10000 0 -0.44 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.055 0.036 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.21 0.26 -10000 0 -0.62 191 191
Syndecan-4/CXCL12/CXCR4 -0.2 0.27 -10000 0 -0.62 193 193
Syndecan-4/Laminin alpha3 -0.2 0.26 -10000 0 -0.63 173 173
MDK -0.007 0.14 -10000 0 -0.45 73 73
Syndecan-4/FZD7 -0.2 0.26 -10000 0 -0.62 178 178
Syndecan-4/Midkine -0.2 0.26 -10000 0 -0.63 186 186
FZD7 0.011 0.1 -10000 0 -0.46 37 37
Syndecan-4/FGFR1/FGF -0.19 0.25 -10000 0 -0.59 181 181
THBS1 -0.01 0.15 -10000 0 -0.54 66 66
integrin-mediated signaling pathway -0.2 0.25 -10000 0 -0.61 191 191
positive regulation of MAPKKK cascade -0.19 0.25 -10000 0 -0.58 193 193
Syndecan-4/TACI -0.19 0.25 -10000 0 -0.63 163 163
CXCR4 0.006 0.12 -10000 0 -0.54 40 40
cell adhesion 0.001 0.097 0.2 11 -0.35 48 59
Syndecan-4/Dynamin -0.19 0.25 -10000 0 -0.62 168 168
Syndecan-4/TSP1 -0.21 0.27 -10000 0 -0.63 192 192
Syndecan-4/GIPC -0.19 0.25 -10000 0 -0.62 168 168
Syndecan-4/RANTES -0.2 0.26 -10000 0 -0.63 171 171
ITGB1 0.031 0.008 -10000 0 -10000 0 0
LAMA1 -0.014 0.15 -10000 0 -0.49 77 77
LAMA3 0.003 0.1 -10000 0 -0.34 68 68
RAC1 0.029 0.011 -10000 0 -10000 0 0
PRKCA 0.087 0.22 0.93 52 -10000 0 52
Syndecan-4/alpha-Actinin -0.19 0.26 -10000 0 -0.63 170 170
TFPI -0.029 0.18 -10000 0 -0.54 92 92
F2 -0.1 0.2 -10000 0 -0.4 264 264
alpha5/beta1 Integrin 0.033 0.07 -10000 0 -0.36 25 25
positive regulation of cell adhesion -0.21 0.26 -10000 0 -0.62 194 194
ACTN1 0.025 0.062 -10000 0 -0.55 10 10
TNC -0.025 0.16 -10000 0 -0.44 107 107
Syndecan-4/CXCL12 -0.2 0.26 -10000 0 -0.63 180 180
FGF6 0.018 0.012 -10000 0 -0.32 1 1
RHOA 0.03 0.009 -10000 0 -10000 0 0
CXCL12 0.002 0.12 -10000 0 -0.47 51 51
TNFRSF13B 0.003 0.088 -10000 0 -0.32 58 58
FGF2 0.002 0.13 -10000 0 -0.54 47 47
FGFR1 0.028 0.041 -10000 0 -0.5 5 5
Syndecan-4/PI-4-5-P2 -0.19 0.25 -10000 0 -0.62 169 169
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.04 0.18 -10000 0 -0.47 127 127
cell migration -0.02 0.018 -10000 0 -10000 0 0
PRKCD 0.011 0.086 -10000 0 -0.32 53 53
vasculogenesis -0.2 0.25 -10000 0 -0.6 192 192
SDC4 -0.19 0.27 -10000 0 -0.66 168 168
Syndecan-4/Tenascin C -0.21 0.27 -10000 0 -0.64 191 191
Syndecan-4/PI-4-5-P2/PKC alpha -0.044 0.029 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.19 0.25 -10000 0 -0.62 168 168
MMP9 -0.057 0.18 -10000 0 -0.4 171 171
Rac1/GTP 0 0.099 0.21 10 -0.36 48 58
cytoskeleton organization -0.18 0.24 -10000 0 -0.59 166 166
GIPC1 0.03 0.036 -10000 0 -0.49 4 4
Syndecan-4/TFPI -0.22 0.27 -10000 0 -0.63 200 200
IL4-mediated signaling events

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.43 0.55 -10000 0 -1.4 164 164
STAT6 (cleaved dimer) -0.46 0.59 -10000 0 -1.4 205 205
IGHG1 -0.13 0.18 -10000 0 -0.44 32 32
IGHG3 -0.42 0.52 -10000 0 -1.3 189 189
AKT1 -0.22 0.37 0.56 1 -1.1 102 103
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.2 0.42 -10000 0 -1.4 75 75
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.26 0.44 -10000 0 -1.3 92 92
THY1 -0.51 0.66 -10000 0 -1.6 203 203
MYB 0.008 0.095 -10000 0 -0.36 51 51
HMGA1 0.017 0.074 -10000 0 -0.36 31 31
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.31 0.49 -10000 0 -1.2 134 134
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.25 0.44 -10000 0 -1.4 89 89
SP1 0.025 0.037 -10000 0 -10000 0 0
INPP5D 0.029 0.04 -10000 0 -0.55 4 4
SOCS5 0.037 0.026 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.46 0.6 -10000 0 -1.4 201 201
SOCS1 -0.28 0.36 -10000 0 -0.83 164 164
SOCS3 -0.25 0.38 -10000 0 -1.1 97 97
FCER2 -0.35 0.46 -10000 0 -1.1 154 154
PARP14 0.031 0.01 -10000 0 -10000 0 0
CCL17 -0.48 0.6 -10000 0 -1.4 199 199
GRB2 0.029 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.38 -10000 0 -1.1 87 87
T cell proliferation -0.45 0.59 -10000 0 -1.4 187 187
IL4R/JAK1 -0.44 0.56 -10000 0 -1.4 177 177
EGR2 -0.46 0.58 -10000 0 -1.4 176 176
JAK2 -0.018 0.052 -10000 0 -0.59 1 1
JAK3 0.006 0.12 -10000 0 -0.51 46 46
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
JAK1 0.011 0.026 -10000 0 -10000 0 0
COL1A2 -0.21 0.44 -10000 0 -1.7 62 62
CCL26 -0.43 0.56 -10000 0 -1.4 171 171
IL4R -0.47 0.61 -10000 0 -1.5 172 172
PTPN6 0.039 0.026 -10000 0 -0.54 1 1
IL13RA2 -0.55 0.65 -10000 0 -1.5 237 237
IL13RA1 -0.017 0.049 -10000 0 -10000 0 0
IRF4 -0.23 0.52 -10000 0 -1.4 116 116
ARG1 -0.11 0.19 -10000 0 -0.9 16 16
CBL -0.28 0.43 -10000 0 -1.1 123 123
GTF3A 0.024 0.037 -10000 0 -10000 0 0
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
IL13RA1/JAK2 -0.018 0.071 -10000 0 -0.44 1 1
IRF4/BCL6 -0.2 0.47 -10000 0 -1.3 115 115
CD40LG -0.021 0.16 -10000 0 -0.53 80 80
MAPK14 -0.29 0.46 -10000 0 -1.2 118 118
mitosis -0.21 0.34 0.56 1 -0.96 102 103
STAT6 -0.53 0.74 -10000 0 -1.7 186 186
SPI1 0.025 0.072 -10000 0 -0.5 15 15
RPS6KB1 -0.19 0.32 0.54 1 -0.91 97 98
STAT6 (dimer) -0.53 0.75 -10000 0 -1.7 186 186
STAT6 (dimer)/PARP14 -0.47 0.62 -10000 0 -1.5 184 184
mast cell activation 0.01 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.26 0.46 -10000 0 -1.4 93 93
FRAP1 -0.22 0.37 0.56 1 -1.1 102 103
LTA -0.47 0.59 -10000 0 -1.4 183 183
FES 0.021 0.08 -10000 0 -0.55 17 17
T-helper 1 cell differentiation 0.5 0.66 1.6 186 -10000 0 186
CCL11 -0.47 0.56 -10000 0 -1.3 211 211
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.25 0.45 -10000 0 -1.4 88 88
IL2RG -0.014 0.15 -10000 0 -0.47 84 84
IL10 -0.46 0.58 -10000 0 -1.4 184 184
IRS1 0.016 0.083 -10000 0 -0.4 31 31
IRS2 0.013 0.079 -10000 0 -0.32 45 45
IL4 -0.087 0.15 -10000 0 -1.2 5 5
IL5 -0.43 0.55 -10000 0 -1.4 169 169
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.34 0.44 -10000 0 -1 170 170
COL1A1 -0.25 0.47 -10000 0 -1.6 79 79
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.45 0.59 -10000 0 -1.5 156 156
IL2R gamma/JAK3 -0.007 0.16 -10000 0 -0.43 102 102
TFF3 -0.51 0.65 -10000 0 -1.5 207 207
ALOX15 -0.43 0.55 -10000 0 -1.4 164 164
MYBL1 0.024 0.053 -10000 0 -0.32 20 20
T-helper 2 cell differentiation -0.39 0.53 -10000 0 -1.2 185 185
SHC1 0.031 0.014 -10000 0 -0.32 1 1
CEBPB 0.029 0.04 -10000 0 -0.33 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.25 0.44 -10000 0 -1.3 95 95
mol:PI-3-4-5-P3 -0.22 0.37 0.57 1 -1.1 102 103
PI3K -0.25 0.42 0.57 1 -1.2 102 103
DOK2 -0.002 0.14 -10000 0 -0.54 52 52
ETS1 0.016 0.11 -10000 0 -0.52 33 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.37 -10000 0 -1.1 88 88
ITGB3 -0.45 0.59 -10000 0 -1.4 183 183
PIGR -0.7 0.69 -10000 0 -1.5 356 356
IGHE 0.032 0.06 0.2 34 -10000 0 34
MAPKKK cascade -0.19 0.35 -10000 0 -1 89 89
BCL6 0.029 0.04 -10000 0 -0.55 4 4
OPRM1 -0.44 0.55 -10000 0 -1.4 164 164
RETNLB -0.44 0.54 -10000 0 -1.4 166 166
SELP -0.46 0.59 -10000 0 -1.5 172 172
AICDA -0.45 0.57 -10000 0 -1.4 184 184
Signaling events mediated by the Hedgehog family

Figure S17.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S17.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.17 0.26 -10000 0 -0.6 194 194
IHH -0.098 0.2 -10000 0 -0.5 161 161
SHH Np/Cholesterol/GAS1 -0.009 0.1 -10000 0 -0.32 66 66
LRPAP1 0.031 0.028 -10000 0 -0.55 2 2
dorsoventral neural tube patterning 0.009 0.1 0.32 66 -10000 0 66
SMO/beta Arrestin2 -0.088 0.18 -10000 0 -0.48 68 68
SMO -0.1 0.18 -10000 0 -0.45 124 124
AKT1 -0.032 0.13 -10000 0 -0.58 26 26
ARRB2 0.029 0.01 -10000 0 -10000 0 0
BOC 0.019 0.083 -10000 0 -0.54 19 19
ADRBK1 0.031 0.028 -10000 0 -0.55 2 2
heart looping -0.099 0.18 -10000 0 -0.44 124 124
STIL -0.085 0.16 0.26 1 -0.4 91 92
DHH N/PTCH2 0.006 0.12 -10000 0 -0.33 85 85
DHH N/PTCH1 -0.1 0.17 -10000 0 -0.43 101 101
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
DHH -0.001 0.12 -10000 0 -0.45 59 59
PTHLH -0.27 0.41 -10000 0 -0.97 195 195
determination of left/right symmetry -0.099 0.18 -10000 0 -0.44 124 124
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
skeletal system development -0.27 0.4 -10000 0 -0.96 195 195
IHH N/Hhip -0.1 0.18 -10000 0 -0.35 270 270
DHH N/Hhip -0.038 0.16 -10000 0 -0.3 208 208
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.099 0.18 -10000 0 -0.44 124 124
pancreas development -0.05 0.17 -10000 0 -0.38 173 173
HHAT 0.028 0.044 -10000 0 -0.55 5 5
PI3K 0.04 0.049 -10000 0 -0.37 11 11
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.017 0.081 -10000 0 -0.38 32 32
somite specification -0.099 0.18 -10000 0 -0.44 124 124
SHH Np/Cholesterol/PTCH1 -0.095 0.16 -10000 0 -0.4 105 105
SHH Np/Cholesterol/PTCH2 -0.012 0.1 -10000 0 -0.31 73 73
SHH Np/Cholesterol/Megalin -0.046 0.15 -10000 0 -0.36 144 144
SHH -0.021 0.11 -10000 0 -0.41 58 58
catabolic process -0.11 0.18 -10000 0 -0.36 239 239
SMO/Vitamin D3 -0.098 0.18 -10000 0 -0.45 105 105
SHH Np/Cholesterol/Hhip -0.037 0.14 -10000 0 -0.35 104 104
LRP2 -0.046 0.2 -10000 0 -0.54 118 118
receptor-mediated endocytosis -0.12 0.21 -10000 0 -0.52 132 132
SHH Np/Cholesterol/BOC -0.008 0.1 -10000 0 -0.32 73 73
SHH Np/Cholesterol/CDO -0.014 0.11 -10000 0 -0.33 80 80
mesenchymal cell differentiation 0.037 0.13 0.35 104 -10000 0 104
mol:Vitamin D3 -0.086 0.17 0.38 1 -0.41 97 98
IHH N/PTCH2 -0.058 0.15 -10000 0 -0.34 160 160
CDON 0.007 0.11 -10000 0 -0.49 43 43
IHH N/PTCH1 -0.11 0.18 -10000 0 -0.37 241 241
Megalin/LRPAP1 -0.018 0.15 -10000 0 -0.4 114 114
PTCH2 0.014 0.092 -10000 0 -0.44 32 32
SHH Np/Cholesterol -0.012 0.09 -10000 0 -0.32 58 58
PTCH1 -0.11 0.18 -10000 0 -0.36 239 239
HHIP -0.05 0.17 -10000 0 -0.38 173 173
p75(NTR)-mediated signaling

Figure S18.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S18.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.044 0.029 -10000 0 -0.4 3 3
Necdin/E2F1 0.011 0.12 -10000 0 -0.38 63 63
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.024 0.2 -10000 0 -0.4 160 160
NGF (dimer)/p75(NTR)/BEX1 -0.16 0.23 -10000 0 -0.43 311 311
NT-4/5 (dimer)/p75(NTR) -0.038 0.17 -10000 0 -0.37 162 162
IKBKB 0.032 0.007 -10000 0 -10000 0 0
AKT1 -0.062 0.18 0.36 6 -0.39 158 164
IKBKG 0.031 0.034 -10000 0 -0.55 3 3
BDNF -0.041 0.18 -10000 0 -0.46 131 131
MGDIs/NGR/p75(NTR)/LINGO1 -0.061 0.21 -10000 0 -0.44 170 170
FURIN 0.031 0.028 -10000 0 -0.55 2 2
proBDNF (dimer)/p75(NTR)/Sortilin -0.049 0.18 -10000 0 -0.37 179 179
LINGO1 -0.069 0.22 -10000 0 -0.52 160 160
Sortilin/TRAF6/NRIF 0.039 0.039 -10000 0 -0.52 1 1
proBDNF (dimer) -0.041 0.18 -10000 0 -0.46 131 131
NTRK1 0.005 0.097 -10000 0 -0.36 56 56
RTN4R 0.024 0.063 -10000 0 -0.42 16 16
neuron apoptosis -0.07 0.19 0.38 8 -0.48 106 114
IRAK1 0.032 0.02 -10000 0 -0.55 1 1
SHC1 -0.083 0.19 -10000 0 -0.46 157 157
ARHGDIA 0.028 0.03 -10000 0 -0.55 2 2
RhoA/GTP 0.022 0.007 -10000 0 -10000 0 0
Gamma Secretase 0.086 0.045 -10000 0 -0.29 7 7
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.042 0.2 -10000 0 -0.42 161 161
MAGEH1 0.03 0.041 -10000 0 -0.5 5 5
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.064 0.23 -10000 0 -0.46 191 191
Mammalian IAPs/DIABLO 0.048 0.1 -10000 0 -0.31 58 58
proNGF (dimer) -0.074 0.21 -10000 0 -0.49 175 175
MAGED1 0.033 0.012 -10000 0 -0.32 1 1
APP 0.031 0.021 -10000 0 -0.55 1 1
NT-4/5 (dimer) 0.005 0.078 -10000 0 -0.32 48 48
ZNF274 0.032 0.02 -10000 0 -0.55 1 1
RhoA/GDP/RHOGDI -0.051 0.18 -10000 0 -0.4 154 154
NGF -0.074 0.21 -10000 0 -0.5 175 175
cell cycle arrest -0.05 0.18 0.25 29 -0.38 149 178
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.057 0.17 -10000 0 -0.37 168 168
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.015 0.15 -10000 0 -0.38 110 110
NCSTN 0.03 0.021 -10000 0 -0.55 1 1
mol:GTP -0.059 0.21 -10000 0 -0.46 157 157
PSENEN 0.033 0.003 -10000 0 -10000 0 0
mol:ceramide -0.071 0.18 -10000 0 -0.42 158 158
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.044 0.15 -10000 0 -0.41 95 95
p75(NTR)/beta APP -0.024 0.15 -10000 0 -0.37 138 138
BEX1 -0.13 0.23 -10000 0 -0.42 309 309
mol:GDP -0.095 0.19 -10000 0 -0.46 157 157
NGF (dimer) -0.2 0.22 -10000 0 -0.4 379 379
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.036 0.2 -10000 0 -0.41 168 168
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
RAC1/GTP -0.041 0.17 -10000 0 -0.38 144 144
MYD88 0.022 0.068 -10000 0 -0.55 12 12
CHUK 0.03 0.021 -10000 0 -0.55 1 1
NGF (dimer)/p75(NTR)/PKA -0.059 0.21 -10000 0 -0.46 157 157
RHOB 0.024 0.065 -10000 0 -0.5 13 13
RHOA 0.03 0.009 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.044 0.028 -10000 0 -0.25 6 6
NT3 (dimer) -0.021 0.16 -10000 0 -0.48 89 89
TP53 -0.054 0.14 0.4 5 -0.31 165 170
PRDM4 -0.07 0.18 -10000 0 -0.42 153 153
BDNF (dimer) -0.19 0.21 -10000 0 -0.41 347 347
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
SORT1 0.029 0.035 -10000 0 -0.55 3 3
activation of caspase activity -0.028 0.2 -10000 0 -0.4 160 160
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.04 0.2 -10000 0 -0.42 158 158
RHOC 0.031 0.008 -10000 0 -10000 0 0
XIAP 0.033 0.002 -10000 0 -10000 0 0
MAPK10 -0.079 0.19 0.33 19 -0.45 135 154
DIABLO 0.032 0.007 -10000 0 -10000 0 0
SMPD2 -0.071 0.19 -10000 0 -0.42 158 158
APH1B 0.029 0.048 -10000 0 -0.55 6 6
APH1A 0.031 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.06 0.21 -10000 0 -0.46 158 158
PSEN1 0.032 0.006 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.043 0.022 -10000 0 -0.4 1 1
NT3 (dimer)/p75(NTR) -0.053 0.2 -10000 0 -0.41 175 175
MAPK8 -0.072 0.19 0.35 18 -0.45 127 145
MAPK9 -0.073 0.18 0.35 20 -0.44 126 146
APAF1 0.031 0.021 -10000 0 -0.55 1 1
NTF3 -0.021 0.16 -10000 0 -0.48 89 89
NTF4 0.005 0.078 -10000 0 -0.32 48 48
NDN -0.015 0.16 -10000 0 -0.54 73 73
RAC1/GDP 0.021 0.008 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.031 0.18 -10000 0 -0.38 155 155
p75 CTF/Sortilin/TRAF6/NRIF 0.074 0.045 -10000 0 -0.31 8 8
RhoA-B-C/GTP -0.059 0.21 -10000 0 -0.45 157 157
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.018 0.17 -10000 0 -0.32 179 179
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.03 0.17 -10000 0 -0.34 178 178
PRKACB 0.031 0.008 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.012 0.14 -10000 0 -0.34 132 132
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.015 0.15 -10000 0 -0.5 79 79
BIRC2 0.032 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.061 0.21 0.24 20 -0.44 168 188
BAD -0.076 0.19 0.37 20 -0.44 135 155
RIPK2 0.032 0.013 -10000 0 -0.32 1 1
NGFR -0.058 0.2 -10000 0 -0.49 146 146
CYCS -0.064 0.16 0.36 1 -0.39 148 149
ADAM17 0.029 0.04 -10000 0 -0.55 4 4
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.04 0.2 -10000 0 -0.42 155 155
BCL2L11 -0.076 0.19 0.34 22 -0.44 137 159
BDNF (dimer)/p75(NTR) -0.075 0.2 -10000 0 -0.37 246 246
PI3K -0.04 0.2 -10000 0 -0.41 162 162
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.04 0.2 -10000 0 -0.42 158 158
NDNL2 0.033 0.004 -10000 0 -10000 0 0
YWHAE 0.029 0.01 -10000 0 -10000 0 0
PRKCI 0.031 0.014 -10000 0 -0.32 1 1
NGF (dimer)/p75(NTR) -0.087 0.23 -10000 0 -0.42 241 241
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.041 0.2 -10000 0 -0.42 158 158
TRAF6 0.033 0.004 -10000 0 -10000 0 0
RAC1 0.029 0.011 -10000 0 -10000 0 0
PRKCZ 0.025 0.056 -10000 0 -0.55 8 8
PLG -0.14 0.22 -10000 0 -0.4 332 332
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.11 0.21 -10000 0 -0.42 223 223
SQSTM1 0.028 0.032 -10000 0 -0.32 7 7
NGFRAP1 0.03 0.044 -10000 0 -0.55 5 5
CASP3 -0.069 0.18 0.34 21 -0.4 137 158
E2F1 0.029 0.034 -10000 0 -0.36 6 6
CASP9 0.031 0.008 -10000 0 -10000 0 0
IKK complex -0.041 0.2 -10000 0 -0.44 126 126
NGF (dimer)/TRKA -0.055 0.18 -10000 0 -0.35 216 216
MMP7 -0.13 0.23 -10000 0 -0.43 302 302
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.027 0.2 -10000 0 -0.4 157 157
MMP3 -0.002 0.091 -10000 0 -0.32 66 66
APAF-1/Caspase 9 -0.063 0.15 -10000 0 -0.43 73 73
Signaling mediated by p38-alpha and p38-beta

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.1 0.34 -10000 0 -1.1 79 79
MKNK1 0.031 0.008 -10000 0 -10000 0 0
MAPK14 -0.02 0.14 -10000 0 -0.36 98 98
ATF2/c-Jun -0.027 0.14 -10000 0 -0.48 41 41
MAPK11 -0.028 0.16 -10000 0 -0.39 112 112
MITF -0.04 0.17 -10000 0 -0.41 122 122
MAPKAPK5 -0.035 0.16 -10000 0 -0.41 117 117
KRT8 -0.037 0.16 -10000 0 -0.42 118 118
MAPKAPK3 0.029 0.022 -10000 0 -0.55 1 1
MAPKAPK2 0.031 0.008 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.044 0.22 -10000 0 -0.56 113 113
CEBPB -0.038 0.16 -10000 0 -0.41 118 118
SLC9A1 -0.035 0.17 -10000 0 -0.42 120 120
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.036 0.18 -10000 0 -0.42 125 125
p38alpha-beta/MNK1 -0.017 0.2 -10000 0 -0.46 112 112
JUN -0.027 0.13 -10000 0 -0.47 41 41
PPARGC1A -0.069 0.2 -10000 0 -0.42 175 175
USF1 -0.035 0.16 -10000 0 -0.42 121 121
RAB5/GDP/GDI1 -0.021 0.12 -10000 0 -0.41 37 37
NOS2 -0.093 0.32 -10000 0 -1.1 75 75
DDIT3 -0.04 0.17 -10000 0 -0.42 117 117
RAB5A 0.03 0.009 -10000 0 -10000 0 0
HSPB1 -0.009 0.14 0.29 57 -0.35 84 141
p38alpha-beta/HBP1 -0.016 0.18 -10000 0 -0.45 92 92
CREB1 -0.04 0.18 -10000 0 -0.45 124 124
RAB5/GDP 0.022 0.007 -10000 0 -10000 0 0
EIF4E -0.039 0.16 0.25 1 -0.43 100 101
RPS6KA4 -0.038 0.17 -10000 0 -0.41 125 125
PLA2G4A -0.048 0.18 -10000 0 -0.44 112 112
GDI1 -0.038 0.17 -10000 0 -0.41 124 124
TP53 -0.052 0.19 -10000 0 -0.54 100 100
RPS6KA5 -0.045 0.18 -10000 0 -0.43 129 129
ESR1 -0.054 0.21 -10000 0 -0.48 136 136
HBP1 0.029 0.011 -10000 0 -10000 0 0
MEF2C -0.057 0.22 -10000 0 -0.52 129 129
MEF2A -0.039 0.17 -10000 0 -0.42 125 125
EIF4EBP1 -0.047 0.19 -10000 0 -0.46 131 131
KRT19 -0.13 0.22 -10000 0 -0.42 259 259
ELK4 -0.035 0.17 -10000 0 -0.42 122 122
ATF6 -0.035 0.16 -10000 0 -0.42 121 121
ATF1 -0.043 0.18 -10000 0 -0.45 126 126
p38alpha-beta/MAPKAPK2 -0.017 0.2 -10000 0 -0.46 112 112
p38alpha-beta/MAPKAPK3 -0.018 0.19 -10000 0 -0.46 106 106
IL12-mediated signaling events

Figure S20.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S20.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.049 0.17 -10000 0 -0.43 93 93
TBX21 -0.18 0.52 0.58 2 -1.3 130 132
B2M 0.028 0.032 -10000 0 -0.55 2 2
TYK2 0.02 0.047 -10000 0 -0.56 2 2
IL12RB1 -0.012 0.14 -10000 0 -0.53 57 57
GADD45B -0.12 0.43 -10000 0 -1.1 102 102
IL12RB2 -0.089 0.18 -10000 0 -0.36 264 264
GADD45G -0.14 0.44 -10000 0 -1.1 131 131
natural killer cell activation 0.002 0.022 0.051 11 -0.041 86 97
RELB 0.032 0.02 -10000 0 -0.55 1 1
RELA 0.033 0.004 -10000 0 -10000 0 0
IL18 0.014 0.09 -10000 0 -0.4 36 36
IL2RA -0.032 0.16 -10000 0 -0.43 119 119
IFNG -0.038 0.15 -10000 0 -0.37 146 146
STAT3 (dimer) -0.13 0.39 -10000 0 -0.88 155 155
HLA-DRB5 -0.001 0.004 -10000 0 -0.022 16 16
FASLG -0.21 0.55 -10000 0 -1.3 147 147
NF kappa B2 p52/RelB -0.16 0.5 -10000 0 -1.1 149 149
CD4 0.016 0.091 -10000 0 -0.55 22 22
SOCS1 0.001 0.11 -10000 0 -0.37 64 64
EntrezGene:6955 -0.002 0.01 -10000 0 -0.034 50 50
CD3D -0.05 0.19 -10000 0 -0.48 134 134
CD3E -0.039 0.18 -10000 0 -0.48 116 116
CD3G -0.07 0.21 -10000 0 -0.48 169 169
IL12Rbeta2/JAK2 -0.05 0.15 -10000 0 -0.29 163 163
CCL3 -0.18 0.51 0.58 2 -1.2 139 141
CCL4 -0.18 0.51 0.58 2 -1.2 142 144
HLA-A -0.002 0.009 -10000 0 -0.04 28 28
IL18/IL18R 0.013 0.17 -10000 0 -0.4 103 103
NOS2 -0.21 0.55 -10000 0 -1.3 156 156
IL12/IL12R/TYK2/JAK2/SPHK2 -0.041 0.15 -10000 0 -0.39 89 89
IL1R1 -0.17 0.49 -10000 0 -1.2 130 130
IL4 -0.002 0.039 -10000 0 -10000 0 0
JAK2 0.02 0.043 -10000 0 -0.59 1 1
EntrezGene:6957 -0.002 0.01 -10000 0 -0.036 44 44
TCR/CD3/MHC I/CD8 -0.26 0.65 -10000 0 -1.3 189 189
RAB7A -0.083 0.36 0.55 2 -0.85 112 114
lysosomal transport -0.075 0.34 0.54 2 -0.78 117 119
FOS -0.18 0.48 -10000 0 -1.2 127 127
STAT4 (dimer) -0.16 0.47 0.73 1 -1.1 157 158
STAT5A (dimer) -0.18 0.5 -10000 0 -1.1 174 174
GZMA -0.19 0.53 -10000 0 -1.3 140 140
GZMB -0.22 0.57 -10000 0 -1.3 160 160
HLX -0.005 0.14 -10000 0 -0.5 59 59
LCK -0.21 0.58 -10000 0 -1.3 158 158
TCR/CD3/MHC II/CD4 -0.12 0.31 -10000 0 -0.64 172 172
IL2/IL2R -0.022 0.2 -10000 0 -0.45 133 133
MAPK14 -0.13 0.47 0.61 1 -1.1 141 142
CCR5 -0.16 0.48 -10000 0 -1.2 127 127
IL1B -0.011 0.14 -10000 0 -0.49 60 60
STAT6 -0.011 0.12 -10000 0 -0.33 14 14
STAT4 0.001 0.13 -10000 0 -0.54 47 47
STAT3 0.029 0.01 -10000 0 -10000 0 0
STAT1 0.028 0.041 -10000 0 -0.38 8 8
NFKB1 0.032 0.02 -10000 0 -0.55 1 1
NFKB2 0.031 0.008 -10000 0 -10000 0 0
IL12B -0.006 0.11 -10000 0 -0.36 63 63
CD8A -0.056 0.19 -10000 0 -0.43 164 164
CD8B -0.063 0.19 -10000 0 -0.43 177 177
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.049 0.16 0.43 93 -10000 0 93
IL2RB -0.006 0.14 -10000 0 -0.51 62 62
proteasomal ubiquitin-dependent protein catabolic process -0.13 0.41 0.72 1 -0.91 156 157
IL2RG -0.016 0.15 -10000 0 -0.48 84 84
IL12 0.008 0.1 -10000 0 -0.29 67 67
STAT5A 0.027 0.035 -10000 0 -0.55 3 3
CD247 -0.01 0.14 -10000 0 -0.51 61 61
IL2 0.02 0.041 -10000 0 -0.32 12 12
SPHK2 0.031 0.034 -10000 0 -0.55 3 3
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.011 0.081 -10000 0 -0.47 18 18
IL12/IL12R/TYK2/JAK2 -0.26 0.74 -10000 0 -1.6 153 153
MAP2K3 -0.14 0.48 0.59 1 -1.1 144 145
RIPK2 0.032 0.013 -10000 0 -0.32 1 1
MAP2K6 -0.14 0.48 0.59 1 -1.1 136 137
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.001 0.005 -10000 0 -0.025 21 21
IL18RAP -0.002 0.13 -10000 0 -0.49 55 55
IL12Rbeta1/TYK2 0.008 0.12 -10000 0 -0.41 58 58
EOMES -0.2 0.49 -10000 0 -1.5 100 100
STAT1 (dimer) -0.14 0.4 -10000 0 -0.86 167 167
T cell proliferation -0.089 0.33 0.44 4 -0.72 145 149
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.005 0.14 -10000 0 -0.55 54 54
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.11 0.36 -10000 0 -0.78 155 155
ATF2 -0.12 0.41 0.77 1 -0.94 138 139
amb2 Integrin signaling

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.002 0.16 -10000 0 -0.47 65 65
alphaM/beta2 Integrin/GPIbA 0.007 0.14 -10000 0 -0.47 57 57
alphaM/beta2 Integrin/proMMP-9 -0.038 0.19 -10000 0 -0.39 137 137
PLAUR 0.018 0.082 -10000 0 -0.4 30 30
HMGB1 0.01 0.037 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.014 0.14 -10000 0 -0.53 43 43
AGER -0.008 0.092 -10000 0 -0.41 33 33
RAP1A 0.031 0.008 -10000 0 -10000 0 0
SELPLG 0.019 0.085 -10000 0 -0.55 19 19
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.025 0.19 -10000 0 -0.48 76 76
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.054 0.18 -10000 0 -0.4 171 171
CYR61 0.001 0.12 -10000 0 -0.46 53 53
TLN1 0.032 0.02 -10000 0 -0.55 1 1
Rap1/GTP -0.088 0.22 -10000 0 -0.56 105 105
RHOA 0.03 0.009 -10000 0 -10000 0 0
P-selectin oligomer -0.001 0.13 -10000 0 -0.49 54 54
MYH2 -0.13 0.22 -10000 0 -0.56 131 131
MST1R -0.027 0.14 -10000 0 -0.37 123 123
leukocyte activation during inflammatory response -0.085 0.18 -10000 0 -0.37 165 165
APOB -0.13 0.23 -10000 0 -0.42 311 311
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.009 0.097 -10000 0 -0.39 46 46
JAM3 -0.019 0.16 -10000 0 -0.55 78 78
GP1BA 0.018 0.077 -10000 0 -0.5 18 18
alphaM/beta2 Integrin/CTGF 0.005 0.15 -10000 0 -0.48 58 58
alphaM/beta2 Integrin -0.12 0.26 -10000 0 -0.57 139 139
JAM3 homodimer -0.019 0.16 -10000 0 -0.55 78 78
ICAM2 0.026 0.042 -10000 0 -0.5 5 5
ICAM1 0.004 0.13 -10000 0 -0.55 44 44
phagocytosis triggered by activation of immune response cell surface activating receptor -0.12 0.26 -10000 0 -0.56 138 138
cell adhesion 0.006 0.14 -10000 0 -0.46 57 57
NFKB1 -0.082 0.23 0.45 3 -0.52 136 139
THY1 -0.049 0.2 -10000 0 -0.54 126 126
RhoA/GDP 0.022 0.007 -10000 0 -10000 0 0
Lipoprotein(a) -0.083 0.15 -10000 0 -0.26 348 348
alphaM/beta2 Integrin/LRP/tPA 0.02 0.15 -10000 0 -0.52 49 49
IL6 -0.13 0.28 -10000 0 -0.73 122 122
ITGB2 -0.01 0.11 -10000 0 -0.56 29 29
elevation of cytosolic calcium ion concentration 0.011 0.16 -10000 0 -0.56 49 49
alphaM/beta2 Integrin/JAM2/JAM3 -0.006 0.18 -10000 0 -0.42 113 113
JAM2 0.013 0.099 -10000 0 -0.52 28 28
alphaM/beta2 Integrin/ICAM1 -0.015 0.2 -10000 0 -0.48 103 103
alphaM/beta2 Integrin/uPA/Plg -0.088 0.19 -10000 0 -0.4 157 157
RhoA/GTP -0.14 0.25 -10000 0 -0.56 155 155
positive regulation of phagocytosis -0.076 0.21 -10000 0 -0.61 81 81
Ron/MSP -0.016 0.14 -10000 0 -0.29 156 156
alphaM/beta2 Integrin/uPAR/uPA 0.013 0.17 -10000 0 -0.56 49 49
alphaM/beta2 Integrin/uPAR 0.006 0.16 -10000 0 -0.51 55 55
PLAU 0.015 0.081 -10000 0 -0.36 36 36
PLAT 0.02 0.078 -10000 0 -0.46 21 21
actin filament polymerization -0.12 0.21 0.22 1 -0.52 131 132
MST1 0.007 0.11 -10000 0 -0.46 42 42
alphaM/beta2 Integrin/lipoprotein(a) -0.083 0.18 -10000 0 -0.37 165 165
TNF -0.1 0.26 0.44 3 -0.71 97 100
RAP1B 0.031 0.007 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.004 0.15 -10000 0 -0.48 58 58
fibrinolysis -0.088 0.19 -10000 0 -0.4 157 157
HCK 0.021 0.075 -10000 0 -0.52 16 16
dendritic cell antigen processing and presentation -0.12 0.26 -10000 0 -0.56 138 138
VTN -0.034 0.15 -10000 0 -0.36 144 144
alphaM/beta2 Integrin/CYR61 -0.005 0.17 -10000 0 -0.47 76 76
LPA 0.002 0.082 -10000 0 -0.32 53 53
LRP1 0.025 0.062 -10000 0 -0.55 10 10
cell migration -0.047 0.19 -10000 0 -0.46 102 102
FN1 -0.042 0.18 -10000 0 -0.48 127 127
alphaM/beta2 Integrin/Thy1 -0.031 0.19 -10000 0 -0.42 139 139
MPO -0.003 0.11 -10000 0 -0.38 68 68
KNG1 -0.082 0.19 -10000 0 -0.39 230 230
RAP1/GDP 0.04 0.014 -10000 0 -10000 0 0
ROCK1 -0.13 0.23 -10000 0 -0.54 142 142
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.14 0.22 -10000 0 -0.4 332 332
CTGF 0.017 0.078 -10000 0 -0.39 29 29
alphaM/beta2 Integrin/Hck 0.011 0.16 -10000 0 -0.62 42 42
ITGAM -0.014 0.12 -10000 0 -0.55 39 39
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.006 0.18 -10000 0 -0.53 69 69
HP -0.11 0.21 -10000 0 -0.39 280 280
leukocyte adhesion -0.093 0.25 -10000 0 -0.58 131 131
SELP -0.001 0.13 -10000 0 -0.49 54 54
EGFR-dependent Endothelin signaling events

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.03 0.038 -9999 0 -0.46 5 5
EGFR 0.008 0.1 -9999 0 -0.47 36 36
EGF/EGFR -0.098 0.2 -9999 0 -0.37 255 255
EGF/EGFR dimer/SHC/GRB2/SOS1 0.012 0.14 -9999 0 -0.32 85 85
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.092 0.24 -9999 0 -0.54 191 191
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.059 0.19 -9999 0 -0.41 181 181
EGF/EGFR dimer/SHC -0.017 0.14 -9999 0 -0.37 88 88
mol:GDP 0.007 0.13 -9999 0 -0.32 85 85
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.04 0.18 -9999 0 -0.5 118 118
GRB2/SOS1 0.043 0.016 -9999 0 -10000 0 0
HRAS/GTP -0.006 0.12 -9999 0 -0.29 88 88
SHC1 0.031 0.014 -9999 0 -0.32 1 1
HRAS/GDP 0.007 0.13 -9999 0 -0.3 88 88
FRAP1 -0.048 0.095 -9999 0 -0.3 85 85
EGF/EGFR dimer -0.04 0.16 -9999 0 -0.32 192 192
SOS1 0.031 0.007 -9999 0 -10000 0 0
GRB2 0.029 0.011 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.1 0.23 -9999 0 -0.42 269 269
PDGFR-alpha signaling pathway

Figure S23.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S23.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.091 0.21 -10000 0 -0.44 220 220
PDGF/PDGFRA/CRKL -0.042 0.16 -10000 0 -0.31 215 215
positive regulation of JUN kinase activity -0.001 0.13 -10000 0 -0.3 92 92
CRKL 0.032 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.054 0.16 -10000 0 -0.33 188 188
AP1 -0.11 0.25 -10000 0 -0.92 59 59
mol:IP3 -0.064 0.15 -10000 0 -0.39 117 117
PLCG1 -0.065 0.15 -10000 0 -0.39 117 117
PDGF/PDGFRA/alphaV Integrin -0.046 0.16 -10000 0 -0.38 129 129
RAPGEF1 0.032 0.005 -10000 0 -10000 0 0
CRK 0.029 0.016 -10000 0 -0.32 1 1
mol:Ca2+ -0.064 0.15 -10000 0 -0.39 117 117
CAV3 0.016 0.037 -10000 0 -0.32 10 10
CAV1 -0.016 0.15 -10000 0 -0.54 69 69
SHC/Grb2/SOS1 0 0.13 -10000 0 -0.3 92 92
PDGF/PDGFRA/Shf -0.045 0.16 -10000 0 -0.4 118 118
FOS -0.12 0.24 0.32 1 -0.9 59 60
JUN -0.027 0.026 -10000 0 -0.26 4 4
oligodendrocyte development -0.046 0.16 -10000 0 -0.38 129 129
GRB2 0.029 0.011 -10000 0 -10000 0 0
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
mol:DAG -0.064 0.15 -10000 0 -0.39 117 117
PDGF/PDGFRA -0.091 0.21 -10000 0 -0.44 220 220
actin cytoskeleton reorganization -0.043 0.16 -10000 0 -0.38 128 128
SRF 0.02 0.01 -10000 0 -10000 0 0
SHC1 0.031 0.014 -10000 0 -0.32 1 1
PI3K -0.021 0.14 -10000 0 -0.34 111 111
PDGF/PDGFRA/Crk/C3G -0.018 0.14 -10000 0 -0.33 100 100
JAK1 -0.06 0.14 -10000 0 -0.38 117 117
ELK1/SRF -0.042 0.11 -10000 0 -0.32 102 102
SHB 0.032 0.02 -10000 0 -0.55 1 1
SHF 0.029 0.043 -10000 0 -0.47 6 6
CSNK2A1 0.037 0.017 -10000 0 -10000 0 0
GO:0007205 -0.071 0.15 -10000 0 -0.43 109 109
SOS1 0.031 0.007 -10000 0 -10000 0 0
Ras protein signal transduction -0.001 0.13 -10000 0 -0.3 92 92
PDGF/PDGFRA/SHB -0.043 0.16 -10000 0 -0.38 128 128
PDGF/PDGFRA/Caveolin-1 -0.072 0.18 -10000 0 -0.41 159 159
ITGAV 0.027 0.05 -10000 0 -0.52 7 7
ELK1 -0.067 0.13 -10000 0 -0.38 109 109
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
PDGF/PDGFRA/Crk -0.042 0.15 -10000 0 -0.38 114 114
JAK-STAT cascade -0.06 0.14 -10000 0 -0.37 117 117
cell proliferation -0.045 0.16 -10000 0 -0.4 118 118
BMP receptor signaling

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.14 0.21 -10000 0 -0.38 313 313
SMAD6-7/SMURF1 0.054 0.039 -10000 0 -0.34 5 5
NOG -0.069 0.19 -10000 0 -0.4 197 197
SMAD9 -0.076 0.25 -10000 0 -0.64 125 125
SMAD4 0.032 0.006 -10000 0 -10000 0 0
SMAD5 -0.055 0.14 -10000 0 -0.41 63 63
BMP7/USAG1 -0.15 0.21 -10000 0 -0.35 424 424
SMAD5/SKI -0.037 0.15 0.28 7 -0.42 56 63
SMAD1 0.011 0.066 -10000 0 -0.54 6 6
BMP2 0.013 0.1 -10000 0 -0.55 27 27
SMAD1/SMAD1/SMAD4 0.028 0.068 -10000 0 -0.47 6 6
BMPR1A 0.031 0.021 -10000 0 -0.55 1 1
BMPR1B -0.12 0.22 -10000 0 -0.41 302 302
BMPR1A-1B/BAMBI -0.066 0.17 -10000 0 -0.36 171 171
AHSG 0.006 0.075 -10000 0 -0.32 44 44
CER1 0.02 0.029 -10000 0 -0.32 6 6
BMP2-4/CER1 0.023 0.12 -10000 0 -0.39 54 54
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.037 0.14 -10000 0 -0.44 55 55
BMP2-4 (homodimer) 0.011 0.12 -10000 0 -0.4 65 65
RGMB 0.031 0.021 -10000 0 -0.32 3 3
BMP6/BMPR2/BMPR1A-1B -0.031 0.16 -10000 0 -0.32 141 141
RGMA -0.005 0.14 -10000 0 -0.5 63 63
SMURF1 0.029 0.011 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.055 0.15 -10000 0 -0.42 81 81
BMP2-4/USAG1 -0.074 0.19 -10000 0 -0.39 184 184
SMAD6/SMURF1/SMAD5 -0.04 0.14 0.28 3 -0.43 51 54
SOSTDC1 -0.12 0.23 -10000 0 -0.44 281 281
BMP7/BMPR2/BMPR1A-1B -0.1 0.19 -10000 0 -0.36 243 243
SKI 0.031 0.008 -10000 0 -10000 0 0
BMP6 (homodimer) 0.017 0.082 -10000 0 -0.43 27 27
HFE2 0.013 0.07 -10000 0 -0.32 37 37
ZFYVE16 0.032 0.006 -10000 0 -10000 0 0
MAP3K7 0.031 0.008 -10000 0 -10000 0 0
BMP2-4/CHRD -0.014 0.17 -10000 0 -0.4 123 123
SMAD5/SMAD5/SMAD4 -0.039 0.15 0.28 5 -0.42 54 59
MAPK1 0.031 0.02 -10000 0 -0.55 1 1
TAK1/TAB family -0.034 0.14 -10000 0 -0.42 49 49
BMP7 (homodimer) -0.11 0.2 -10000 0 -0.39 281 281
NUP214 0.032 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.015 0.084 -10000 0 -0.26 70 70
SMAD1/SKI 0.031 0.084 0.38 11 -0.49 7 18
SMAD6 0.03 0.039 -10000 0 -0.55 4 4
CTDSP2 0.032 0.007 -10000 0 -10000 0 0
BMP2-4/FETUA 0.014 0.12 -10000 0 -0.39 50 50
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.13 0.23 -10000 0 -0.43 312 312
BMPR2 (homodimer) 0.031 0.021 -10000 0 -0.55 1 1
GADD34/PP1CA 0.063 0.031 -10000 0 -0.49 2 2
BMPR1A-1B (homodimer) -0.07 0.17 -10000 0 -0.29 303 303
CHRDL1 -0.15 0.24 -10000 0 -0.43 353 353
ENDOFIN/SMAD1 0.027 0.086 0.37 10 -0.5 7 17
SMAD6-7/SMURF1/SMAD1 0.041 0.081 -10000 0 -0.53 6 6
SMAD6/SMURF1 0.029 0.011 -10000 0 -10000 0 0
BAMBI -0.005 0.14 -10000 0 -0.48 62 62
SMURF2 0.028 0.025 -10000 0 -0.44 2 2
BMP2-4/CHRDL1 -0.089 0.19 -10000 0 -0.39 196 196
BMP2-4/GREM1 -0.075 0.19 -10000 0 -0.4 165 165
SMAD7 0.031 0.02 -10000 0 -0.55 1 1
SMAD8A/SMAD8A/SMAD4 -0.062 0.24 -10000 0 -0.61 128 128
SMAD1/SMAD6 0.017 0.074 0.52 1 -0.51 7 8
TAK1/SMAD6 0.04 0.02 -10000 0 -10000 0 0
BMP7 -0.11 0.2 -10000 0 -0.39 281 281
BMP6 0.017 0.083 -10000 0 -0.43 27 27
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.039 0.14 -10000 0 -0.42 68 68
PPM1A 0.032 0.006 -10000 0 -10000 0 0
SMAD1/SMURF2 0.024 0.081 0.42 6 -0.55 6 12
SMAD7/SMURF1 0.041 0.023 -10000 0 -0.4 1 1
CTDSPL 0.03 0.015 -10000 0 -0.32 1 1
PPP1CA 0.031 0.028 -10000 0 -0.55 2 2
XIAP 0.033 0.002 -10000 0 -10000 0 0
CTDSP1 0.031 0.021 -10000 0 -0.55 1 1
PPP1R15A 0.032 0.02 -10000 0 -0.55 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.097 0.2 -10000 0 -0.5 119 119
CHRD -0.038 0.18 -10000 0 -0.52 111 111
BMPR2 0.031 0.021 -10000 0 -0.55 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.062 0.16 -10000 0 -0.42 90 90
BMP4 0.005 0.12 -10000 0 -0.5 45 45
FST -0.065 0.19 -10000 0 -0.42 188 188
BMP2-4/NOG -0.038 0.16 -10000 0 -0.38 116 116
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.081 0.18 -10000 0 -0.34 228 228
Wnt signaling

Figure S25.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S25.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.055 0.14 -9999 0 -0.4 67 67
FZD6 0.031 0.024 -9999 0 -0.44 2 2
WNT6 -0.034 0.16 -9999 0 -0.41 127 127
WNT4 -0.029 0.15 -9999 0 -0.4 124 124
FZD3 0.031 0.008 -9999 0 -10000 0 0
WNT5A -0.012 0.12 -9999 0 -0.35 96 96
WNT11 -0.029 0.15 -9999 0 -0.37 133 133
Integrins in angiogenesis

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.16 0.32 -10000 0 -0.62 268 268
alphaV beta3 Integrin 0.016 0.13 -10000 0 -0.37 71 71
PTK2 -0.18 0.28 0.31 1 -0.57 258 259
IGF1R 0.031 0.034 -10000 0 -0.55 3 3
PI4KB 0.031 0.008 -10000 0 -10000 0 0
MFGE8 0.005 0.12 -10000 0 -0.54 43 43
SRC 0.031 0.008 -10000 0 -10000 0 0
CDKN1B -0.022 0.12 -10000 0 -0.41 54 54
VEGFA -0.12 0.25 -10000 0 -0.55 225 225
ILK -0.025 0.13 -10000 0 -0.46 50 50
ROCK1 0.03 0.034 -10000 0 -0.55 3 3
AKT1 -0.026 0.12 -10000 0 -0.44 47 47
PTK2B -0.13 0.24 -10000 0 -0.49 256 256
alphaV/beta3 Integrin/JAM-A -0.007 0.14 -10000 0 -0.36 79 79
CBL 0.032 0.02 -10000 0 -0.55 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.064 0.16 -10000 0 -0.38 117 117
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.04 0.11 -10000 0 -0.33 45 45
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.11 0.21 -10000 0 -0.43 231 231
alphaV/beta3 Integrin/Syndecan-1 0.029 0.1 -10000 0 -0.37 42 42
PI4KA 0.031 0.02 -10000 0 -0.55 1 1
IGF-1R heterotetramer/IGF1/IRS1 -0.027 0.18 -10000 0 -0.51 56 56
PI4 Kinase 0.044 0.021 -10000 0 -0.4 1 1
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
alphaV/beta3 Integrin/Osteopontin 0.017 0.13 -10000 0 -0.4 59 59
RPS6KB1 -0.049 0.16 0.5 7 -0.5 49 56
TLN1 0.032 0.02 -10000 0 -0.55 1 1
MAPK3 -0.052 0.19 -10000 0 -0.6 80 80
GPR124 -0.05 0.2 -10000 0 -0.55 123 123
MAPK1 -0.053 0.19 -10000 0 -0.62 78 78
PXN 0.032 0.007 -10000 0 -10000 0 0
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
alphaV/beta3 Integrin/Tumstatin 0.012 0.13 -10000 0 -0.37 76 76
cell adhesion -0.057 0.16 -10000 0 -0.36 130 130
ANGPTL3 -0.12 0.22 -10000 0 -0.4 312 312
VEGFR2 homodimer/VEGFA homodimer/Src -0.12 0.28 -10000 0 -0.56 243 243
IGF-1R heterotetramer 0.031 0.034 -10000 0 -0.55 3 3
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
TGFBR2 0.028 0.04 -10000 0 -0.55 4 4
ITGB3 0.001 0.12 -10000 0 -0.45 51 51
IGF1 -0.008 0.13 -10000 0 -0.4 80 80
RAC1 0.029 0.011 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.013 0.15 -10000 0 -0.37 120 120
apoptosis 0.027 0.05 -10000 0 -0.52 7 7
CD47 0.031 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.036 0.087 -10000 0 -0.35 29 29
VCL 0.031 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.027 0.17 -10000 0 -0.38 136 136
CSF1 0.022 0.072 -10000 0 -0.52 15 15
PIK3C2A -0.026 0.13 -10000 0 -0.47 51 51
PI4 Kinase/Pyk2 -0.13 0.24 -10000 0 -0.52 196 196
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.28 -10000 0 -0.51 264 264
FAK1/Vinculin -0.13 0.23 0.5 6 -0.44 254 260
alphaV beta3/Integrin/ppsTEM5 -0.012 0.16 -10000 0 -0.37 120 120
RHOA 0.03 0.009 -10000 0 -10000 0 0
VTN -0.034 0.15 -10000 0 -0.36 144 144
BCAR1 0.029 0.035 -10000 0 -0.55 3 3
FGF2 0.002 0.13 -10000 0 -0.54 47 47
F11R -0.002 0.091 -10000 0 -0.39 46 46
alphaV/beta3 Integrin/Lactadherin 0.02 0.12 -10000 0 -0.39 58 58
alphaV/beta3 Integrin/TGFBR2 0.032 0.09 -10000 0 -0.36 31 31
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.064 0.068 -10000 0 -0.36 16 16
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.035 0.083 -10000 0 -0.33 32 32
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.042 0.18 -10000 0 -0.48 127 127
alphaV/beta3 Integrin/Pyk2 -0.11 0.26 -10000 0 -0.49 258 258
SDC1 0.019 0.076 -10000 0 -0.41 25 25
VAV3 0.021 0.082 0.38 9 -0.32 28 37
PTPN11 0.031 0.021 -10000 0 -0.55 1 1
IRS1 0.016 0.083 -10000 0 -0.4 31 31
FAK1/Paxillin -0.13 0.22 0.28 2 -0.44 246 248
cell migration -0.12 0.2 0.27 2 -0.41 220 222
ITGAV 0.027 0.05 -10000 0 -0.52 7 7
PI3K 0.006 0.14 -10000 0 -0.46 27 27
SPP1 0 0.12 -10000 0 -0.43 63 63
KDR -0.12 0.25 -10000 0 -0.54 233 233
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.05 -10000 0 -0.52 7 7
COL4A3 -0.006 0.14 -10000 0 -0.52 59 59
angiogenesis -0.051 0.2 0.29 2 -0.62 78 80
Rac1/GTP 0.026 0.064 -10000 0 -0.3 26 26
EDIL3 -0.071 0.22 -10000 0 -0.51 166 166
cell proliferation 0.032 0.09 -10000 0 -0.36 31 31
PDGFR-beta signaling pathway

Figure S27.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S27.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.052 0.19 -10000 0 -0.48 131 131
PDGFB-D/PDGFRB/SLAP -0.036 0.18 -10000 0 -0.4 157 157
PDGFB-D/PDGFRB/APS/CBL 0.002 0.13 -10000 0 -0.35 92 92
AKT1 0.017 0.15 0.46 47 -0.45 6 53
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.049 0.21 0.32 5 -0.52 131 136
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
FGR -0.068 0.22 0.32 2 -0.47 161 163
mol:Ca2+ -0.055 0.22 0.29 13 -0.55 132 145
MYC -0.029 0.23 0.44 18 -0.66 63 81
SHC1 0.031 0.014 -10000 0 -0.32 1 1
HRAS/GDP -0.001 0.12 -10000 0 -0.29 114 114
LRP1/PDGFRB/PDGFB -0.001 0.15 -10000 0 -0.35 120 120
GRB10 0.028 0.022 -10000 0 -0.55 1 1
PTPN11 0.031 0.021 -10000 0 -0.55 1 1
GO:0007205 -0.057 0.22 0.29 13 -0.56 132 145
PTEN 0.031 0.008 -10000 0 -10000 0 0
GRB2 0.029 0.011 -10000 0 -10000 0 0
GRB7 0.02 0.071 -10000 0 -0.47 17 17
PDGFB-D/PDGFRB/SHP2 -0.018 0.15 -10000 0 -0.39 117 117
PDGFB-D/PDGFRB/GRB10 -0.012 0.14 -10000 0 -0.39 88 88
cell cycle arrest -0.036 0.18 -10000 0 -0.4 157 157
HRAS 0.03 0.038 -10000 0 -0.46 5 5
HIF1A 0.011 0.14 0.42 51 -0.41 9 60
GAB1 -0.054 0.22 0.32 14 -0.53 131 145
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.048 0.2 0.33 18 -0.49 126 144
PDGFB-D/PDGFRB 0.001 0.14 -10000 0 -0.35 110 110
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.021 0.16 -10000 0 -0.39 128 128
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.049 0.18 -10000 0 -0.47 122 122
positive regulation of MAPKKK cascade -0.018 0.15 -10000 0 -0.39 117 117
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
mol:IP3 -0.057 0.23 0.3 13 -0.56 132 145
E5 -0.001 0.002 -10000 0 -10000 0 0
CSK 0.031 0.028 -10000 0 -0.55 2 2
PDGFB-D/PDGFRB/GRB7 -0.023 0.15 -10000 0 -0.38 123 123
SHB 0.032 0.02 -10000 0 -0.55 1 1
BLK -0.077 0.21 0.29 1 -0.46 165 166
PTPN2 0.032 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.021 0.16 -10000 0 -0.39 132 132
BCAR1 0.029 0.035 -10000 0 -0.55 3 3
VAV2 -0.055 0.23 0.34 14 -0.53 139 153
CBL 0.032 0.02 -10000 0 -0.55 1 1
PDGFB-D/PDGFRB/DEP1 -0.022 0.16 -10000 0 -0.39 134 134
LCK -0.1 0.28 0.32 2 -0.57 183 185
PDGFRB -0.056 0.21 -10000 0 -0.55 132 132
ACP1 0.031 0.007 -10000 0 -10000 0 0
HCK -0.038 0.17 -10000 0 -0.42 116 116
ABL1 -0.049 0.2 0.31 14 -0.47 141 155
PDGFB-D/PDGFRB/CBL -0.069 0.25 -10000 0 -0.6 137 137
PTPN1 0.03 0.022 -10000 0 -0.56 1 1
SNX15 0.033 0.004 -10000 0 -10000 0 0
STAT3 0.029 0.01 -10000 0 -10000 0 0
STAT1 0.028 0.041 -10000 0 -0.38 8 8
cell proliferation -0.023 0.21 0.44 18 -0.58 64 82
SLA 0.01 0.11 -10000 0 -0.51 35 35
actin cytoskeleton reorganization 0.006 0.12 0.4 10 -0.34 5 15
SRC -0.026 0.13 -10000 0 -0.37 53 53
PI3K -0.02 0.094 -10000 0 -0.45 6 6
PDGFB-D/PDGFRB/GRB7/SHC -0.002 0.14 -10000 0 -0.34 110 110
SH2B2 0.019 0.074 -10000 0 -0.53 15 15
PLCgamma1/SPHK1 -0.051 0.22 0.33 5 -0.54 131 136
LYN -0.034 0.15 0.31 1 -0.38 121 122
LRP1 0.025 0.062 -10000 0 -0.55 10 10
SOS1 0.031 0.007 -10000 0 -10000 0 0
STAT5B 0.029 0.01 -10000 0 -10000 0 0
STAT5A 0.027 0.035 -10000 0 -0.55 3 3
NCK1-2/p130 Cas 0.037 0.12 -10000 0 -0.29 94 94
SPHK1 0.002 0.1 -10000 0 -0.36 61 61
EDG1 -0.001 0.004 -10000 0 -10000 0 0
mol:DAG -0.057 0.23 0.3 13 -0.56 132 145
PLCG1 -0.059 0.23 0.3 12 -0.58 132 144
NHERF/PDGFRB 0.003 0.13 -10000 0 -0.34 97 97
YES1 -0.034 0.16 0.32 3 -0.4 112 115
cell migration 0.003 0.13 -10000 0 -0.34 97 97
SHC/Grb2/SOS1 0.036 0.12 -10000 0 -0.29 90 90
SLC9A3R2 0.028 0.04 -10000 0 -0.44 6 6
SLC9A3R1 0.024 0.056 -10000 0 -0.55 8 8
NHERF1-2/PDGFRB/PTEN 0.018 0.13 -10000 0 -0.31 97 97
FYN -0.062 0.21 0.31 1 -0.45 156 157
DOK1 -0.015 0.12 -10000 0 -0.32 115 115
HRAS/GTP 0.022 0.028 -10000 0 -0.33 5 5
PDGFB 0.029 0.044 -10000 0 -0.55 5 5
RAC1 -0.032 0.22 0.38 25 -0.51 117 142
PRKCD -0.025 0.13 -10000 0 -0.32 105 105
FER -0.018 0.12 -10000 0 -0.32 112 112
MAPKKK cascade -0.016 0.12 0.35 28 -0.28 38 66
RASA1 -0.017 0.12 -10000 0 -0.32 111 111
NCK1 0.03 0.029 -10000 0 -0.55 2 2
NCK2 0.032 0.007 -10000 0 -10000 0 0
p62DOK/Csk 0.001 0.12 -10000 0 -0.3 116 116
PDGFB-D/PDGFRB/SHB -0.021 0.16 -10000 0 -0.39 133 133
chemotaxis -0.047 0.2 0.3 14 -0.45 141 155
STAT1-3-5/STAT1-3-5 0.025 0.12 -10000 0 -0.28 91 91
Bovine Papilomavirus E5/PDGFRB -0.041 0.15 -10000 0 -0.39 133 133
PTPRJ 0.032 0.023 -10000 0 -0.44 2 2
Class IB PI3K non-lipid kinase events

Figure S28.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S28.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.002 0.12 0.39 72 -10000 0 72
PI3K Class IB/PDE3B -0.002 0.12 -10000 0 -0.39 72 72
PDE3B -0.002 0.12 -10000 0 -0.39 72 72
LPA4-mediated signaling events

Figure S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S29.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.027 0.1 -10000 0 -0.34 80 80
ADCY5 -0.029 0.11 -10000 0 -0.35 85 85
ADCY6 0.005 0.028 -10000 0 -0.44 3 3
ADCY7 0.005 0.025 -10000 0 -0.49 2 2
ADCY1 -0.043 0.11 -10000 0 -0.35 89 89
ADCY2 -0.082 0.14 -10000 0 -0.34 166 166
ADCY3 -0.004 0.059 -10000 0 -0.34 26 26
ADCY8 -0.08 0.12 -10000 0 -0.23 302 302
PRKCE 0.009 0.024 -10000 0 -0.4 3 3
ADCY9 0.005 0.02 -10000 0 -0.34 3 3
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.084 0.13 0.33 20 -0.34 76 96
Glypican 2 network

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.007 0.14 -9999 0 -0.45 73 73
GPC2 0.011 0.098 -9999 0 -0.5 30 30
GPC2/Midkine 0.001 0.12 -9999 0 -0.34 92 92
neuron projection morphogenesis 0.001 0.12 -9999 0 -0.34 92 92
Fc-epsilon receptor I signaling in mast cells

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.028 0.048 -10000 0 -0.55 6 6
LAT2 -0.048 0.18 -10000 0 -0.45 115 115
AP1 -0.036 0.25 0.28 5 -0.61 106 111
mol:PIP3 -0.019 0.24 0.45 52 -0.61 74 126
IKBKB 0.005 0.16 0.35 63 -0.33 66 129
AKT1 -0.031 0.14 0.34 16 -0.47 38 54
IKBKG 0.004 0.15 0.34 62 -0.33 70 132
MS4A2 -0.045 0.19 -10000 0 -0.49 128 128
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.027 0.049 -10000 0 -0.55 6 6
MAP3K1 -0.021 0.19 0.31 39 -0.52 71 110
mol:Ca2+ -0.004 0.19 0.4 55 -0.43 73 128
LYN 0.029 0.031 -10000 0 -0.58 2 2
CBLB -0.044 0.16 0.18 1 -0.41 116 117
SHC1 0.031 0.014 -10000 0 -0.32 1 1
RasGAP/p62DOK 0.015 0.12 -10000 0 -0.32 92 92
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.029 0.04 -10000 0 -0.55 4 4
PLD2 -0.042 0.14 0.3 12 -0.35 116 128
PTPN13 -0.033 0.22 0.42 3 -0.67 63 66
PTPN11 0.025 0.029 -10000 0 -0.57 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.005 0.16 0.43 40 -0.38 48 88
SYK 0.022 0.075 -10000 0 -0.5 17 17
GRB2 0.029 0.011 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.057 0.2 -10000 0 -0.62 77 77
LAT -0.05 0.18 -10000 0 -0.44 114 114
PAK2 -0.031 0.21 0.32 31 -0.58 77 108
NFATC2 -0.063 0.19 -10000 0 -0.62 82 82
HRAS -0.045 0.23 0.27 13 -0.63 83 96
GAB2 0.03 0.035 -10000 0 -0.41 5 5
PLA2G1B -0.019 0.21 -10000 0 -0.86 52 52
Fc epsilon R1 -0.031 0.18 -10000 0 -0.4 144 144
Antigen/IgE/Fc epsilon R1 -0.025 0.17 -10000 0 -0.36 140 140
mol:GDP -0.053 0.24 0.23 3 -0.67 88 91
JUN 0.029 0.029 -10000 0 -0.38 4 4
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
FOS -0.026 0.16 -10000 0 -0.42 112 112
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.043 0.18 -10000 0 -0.43 120 120
CHUK 0.005 0.15 0.36 58 -0.34 63 121
KLRG1 -0.041 0.16 -10000 0 -0.38 114 114
VAV1 -0.056 0.2 0.19 1 -0.47 123 124
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.045 0.17 -10000 0 -0.42 116 116
negative regulation of mast cell degranulation -0.024 0.16 0.23 1 -0.46 73 74
BTK -0.053 0.24 -10000 0 -0.7 81 81
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.064 0.22 -10000 0 -0.52 127 127
GAB2/PI3K/SHP2 -0.046 0.14 -10000 0 -0.47 48 48
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.035 0.16 -10000 0 -0.48 74 74
RAF1 -0.025 0.23 -10000 0 -0.94 52 52
Fc epsilon R1/FcgammaRIIB/SHIP -0.022 0.21 -10000 0 -0.41 153 153
FCER1G 0.023 0.076 -10000 0 -0.48 18 18
FCER1A -0.023 0.16 -10000 0 -0.47 94 94
Antigen/IgE/Fc epsilon R1/Fyn -0.013 0.17 -10000 0 -0.35 138 138
MAPK3 -0.02 0.22 -10000 0 -0.86 52 52
MAPK1 -0.022 0.22 -10000 0 -0.87 52 52
NFKB1 0.032 0.02 -10000 0 -0.55 1 1
MAPK8 -0.029 0.28 -10000 0 -0.94 68 68
DUSP1 -0.032 0.18 -10000 0 -0.54 97 97
NF-kappa-B/RelA 0.004 0.08 0.16 21 -0.22 40 61
actin cytoskeleton reorganization -0.03 0.21 -10000 0 -0.66 60 60
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.029 0.21 -10000 0 -0.6 78 78
FER -0.045 0.17 -10000 0 -0.42 116 116
RELA 0.033 0.004 -10000 0 -10000 0 0
ITK -0.047 0.16 -10000 0 -0.51 85 85
SOS1 0.031 0.007 -10000 0 -10000 0 0
PLCG1 -0.04 0.24 0.32 27 -0.66 84 111
cytokine secretion -0.004 0.052 -10000 0 -10000 0 0
SPHK1 -0.052 0.17 -10000 0 -0.42 123 123
PTK2 -0.034 0.22 -10000 0 -0.71 60 60
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.052 0.21 0.23 1 -0.54 112 113
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.018 0.23 0.4 54 -0.57 77 131
MAP2K2 -0.026 0.22 -10000 0 -0.89 52 52
MAP2K1 -0.025 0.22 -10000 0 -0.88 52 52
MAP2K7 0.032 0.028 -10000 0 -0.55 2 2
KLRG1/SHP2 -0.028 0.15 0.23 1 -0.44 71 72
MAP2K4 -0.012 0.23 -10000 0 -0.96 48 48
Fc epsilon R1/FcgammaRIIB -0.036 0.21 -10000 0 -0.42 160 160
mol:Choline -0.041 0.14 0.3 12 -0.34 116 128
SHC/Grb2/SOS1 0.001 0.17 -10000 0 -0.48 65 65
FYN 0.025 0.056 -10000 0 -0.55 8 8
DOK1 0.028 0.044 -10000 0 -0.55 5 5
PXN -0.022 0.21 0.39 17 -0.65 58 75
HCLS1 -0.052 0.19 -10000 0 -0.45 121 121
PRKCB -0.008 0.2 0.39 59 -0.48 72 131
FCGR2B -0.011 0.14 -10000 0 -0.46 75 75
IGHE -0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.024 0.16 0.23 1 -0.47 73 74
LCP2 0.003 0.12 -10000 0 -0.55 43 43
PLA2G4A -0.05 0.18 -10000 0 -0.42 128 128
RASA1 0.03 0.034 -10000 0 -0.55 3 3
mol:Phosphatidic acid -0.041 0.14 0.3 12 -0.34 116 128
IKK complex 0.013 0.13 0.34 59 -0.25 51 110
WIPF1 0.031 0.007 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.032 0.15 -10000 0 -0.38 123 123
NFATC2 -0.064 0.27 -10000 0 -0.69 92 92
NFATC3 -0.005 0.09 -10000 0 -0.31 23 23
CD40LG -0.2 0.42 0.57 1 -1.1 122 123
ITCH 0.015 0.082 -10000 0 -0.38 1 1
CBLB 0.015 0.082 -10000 0 -0.38 1 1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.24 0.47 -10000 0 -1.1 156 156
JUNB 0.023 0.071 -10000 0 -0.47 17 17
CaM/Ca2+/Calcineurin A alpha-beta B1 0.018 0.1 -10000 0 -0.29 79 79
T cell anergy -0.015 0.16 -10000 0 -0.48 79 79
TLE4 -0.041 0.2 -10000 0 -0.59 63 63
Jun/NFAT1-c-4/p21SNFT -0.11 0.39 -10000 0 -1.1 82 82
AP-1/NFAT1-c-4 -0.19 0.5 -10000 0 -1.3 112 112
IKZF1 -0.048 0.24 -10000 0 -0.79 61 61
T-helper 2 cell differentiation -0.13 0.32 -10000 0 -0.92 90 90
AP-1/NFAT1 -0.059 0.23 -10000 0 -0.56 93 93
CALM1 0.025 0.063 -10000 0 -10000 0 0
EGR2 -0.14 0.43 -10000 0 -1.4 71 71
EGR3 -0.15 0.44 -10000 0 -1.5 68 68
NFAT1/FOXP3 -0.074 0.26 -10000 0 -0.6 111 111
EGR1 -0.023 0.15 -10000 0 -0.43 98 98
JUN 0.015 0.045 -10000 0 -0.41 4 4
EGR4 0.004 0.08 -10000 0 -0.32 47 47
mol:Ca2+ -0.006 0.057 -10000 0 -0.25 6 6
GBP3 -0.074 0.26 -10000 0 -0.7 104 104
FOSL1 -0.008 0.13 -10000 0 -0.41 81 81
NFAT1-c-4/MAF/IRF4 -0.11 0.38 -10000 0 -1 85 85
DGKA -0.051 0.24 -10000 0 -0.74 63 63
CREM 0.03 0.014 -10000 0 -0.32 1 1
NFAT1-c-4/PPARG -0.1 0.35 -10000 0 -1.1 73 73
CTLA4 -0.1 0.27 -10000 0 -0.64 141 141
NFAT1-c-4 (dimer)/EGR1 -0.13 0.39 -10000 0 -1.1 82 82
NFAT1-c-4 (dimer)/EGR4 -0.11 0.36 -10000 0 -1.1 76 76
FOS -0.042 0.16 -10000 0 -0.43 112 112
IFNG -0.17 0.4 -10000 0 -1 115 115
T cell activation -0.074 0.22 0.48 1 -0.73 44 45
MAF 0.016 0.093 -10000 0 -0.55 23 23
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.085 0.28 0.94 55 -10000 0 55
TNF -0.15 0.36 -10000 0 -0.98 100 100
FASLG -0.26 0.62 -10000 0 -1.7 130 130
TBX21 -0.004 0.11 -10000 0 -0.52 34 34
BATF3 0.013 0.098 -10000 0 -0.48 32 32
PRKCQ -0.003 0.11 -10000 0 -0.46 44 44
PTPN1 -0.042 0.2 -10000 0 -0.62 55 55
NFAT1-c-4/ICER1 -0.1 0.35 -10000 0 -1 75 75
GATA3 -0.041 0.17 -10000 0 -0.4 148 148
T-helper 1 cell differentiation -0.16 0.38 -10000 0 -1 115 115
IL2RA -0.2 0.43 -10000 0 -1 144 144
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.04 0.19 -10000 0 -0.62 53 53
E2F1 0.034 0.034 -10000 0 -0.35 6 6
PPARG 0.027 0.043 -10000 0 -0.47 6 6
SLC3A2 -0.043 0.2 -10000 0 -0.63 55 55
IRF4 -0.02 0.15 -10000 0 -0.41 100 100
PTGS2 -0.21 0.42 0.57 1 -1 132 133
CSF2 -0.19 0.38 -10000 0 -1 112 112
JunB/Fra1/NFAT1-c-4 -0.1 0.37 -10000 0 -1 84 84
IL4 -0.14 0.34 -10000 0 -0.99 87 87
IL5 -0.19 0.38 -10000 0 -1 111 111
IL2 -0.076 0.23 -10000 0 -0.75 40 40
IL3 -0.049 0.22 -10000 0 -0.94 41 41
RNF128 -0.023 0.2 -10000 0 -0.62 86 86
NFATC1 -0.086 0.28 -10000 0 -0.96 54 54
CDK4 0.065 0.18 0.68 25 -10000 0 25
PTPRK -0.04 0.2 -10000 0 -0.59 63 63
IL8 -0.21 0.41 -10000 0 -1 130 130
POU2F1 0.03 0.029 -10000 0 -0.55 2 2
Reelin signaling pathway

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.039 0.026 -10000 0 -0.31 2 2
VLDLR 0.029 0.042 -10000 0 -0.42 7 7
CRKL 0.032 0.006 -10000 0 -10000 0 0
LRPAP1 0.031 0.028 -10000 0 -0.55 2 2
FYN 0.025 0.056 -10000 0 -0.55 8 8
ITGA3 0.018 0.075 -10000 0 -0.44 21 21
RELN/VLDLR/Fyn -0.041 0.15 -10000 0 -0.35 123 123
MAPK8IP1/MKK7/MAP3K11/JNK1 0.08 0.073 -10000 0 -0.36 16 16
AKT1 -0.04 0.099 -10000 0 -0.26 124 124
MAP2K7 0.032 0.028 -10000 0 -0.55 2 2
RAPGEF1 0.032 0.005 -10000 0 -10000 0 0
DAB1 0.002 0.087 -10000 0 -0.32 59 59
RELN/LRP8/DAB1 -0.052 0.14 -10000 0 -0.32 129 129
LRPAP1/LRP8 0.036 0.051 -10000 0 -0.23 25 25
RELN/LRP8/DAB1/Fyn -0.042 0.14 -10000 0 -0.31 133 133
DAB1/alpha3/beta1 Integrin -0.039 0.14 -10000 0 -0.43 13 13
long-term memory -0.12 0.19 -10000 0 -0.35 280 280
DAB1/LIS1 -0.029 0.14 -10000 0 -0.3 117 117
DAB1/CRLK/C3G -0.036 0.13 -10000 0 -0.3 62 62
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
DAB1/NCK2 -0.029 0.14 -10000 0 -0.3 122 122
ARHGEF2 0.03 0.021 -10000 0 -0.55 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.13 0.23 -10000 0 -0.43 308 308
CDK5R1 0.029 0.02 -10000 0 -0.32 2 2
RELN -0.1 0.21 -10000 0 -0.42 252 252
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
RELN/LRP8/Fyn -0.045 0.15 -10000 0 -0.35 121 121
GRIN2A/RELN/LRP8/DAB1/Fyn -0.12 0.19 -10000 0 -0.36 273 273
MAPK8 0.025 0.062 -10000 0 -0.55 10 10
RELN/VLDLR/DAB1 -0.049 0.14 -10000 0 -0.32 129 129
ITGB1 0.031 0.008 -10000 0 -10000 0 0
MAP1B -0.054 0.14 -10000 0 -0.32 145 145
RELN/LRP8 -0.043 0.15 -10000 0 -0.35 117 117
GRIN2B/RELN/LRP8/DAB1/Fyn -0.045 0.15 -10000 0 -0.31 147 147
PI3K 0.04 0.049 -10000 0 -0.37 11 11
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.034 0.059 -10000 0 -0.32 20 20
RAP1A -0.036 0.14 0.4 9 -0.39 10 19
PAFAH1B1 0.029 0.01 -10000 0 -10000 0 0
MAPK8IP1 0.028 0.048 -10000 0 -0.46 8 8
CRLK/C3G 0.047 0.011 -10000 0 -10000 0 0
GRIN2B 0.005 0.082 -10000 0 -0.32 52 52
NCK2 0.032 0.007 -10000 0 -10000 0 0
neuron differentiation -0.029 0.14 -10000 0 -0.49 52 52
neuron adhesion -0.027 0.15 0.34 54 -0.4 12 66
LRP8 0.02 0.063 -10000 0 -0.33 27 27
GSK3B -0.035 0.099 -10000 0 -0.32 21 21
RELN/VLDLR/DAB1/Fyn -0.04 0.14 -10000 0 -0.3 134 134
MAP3K11 0.031 0.028 -10000 0 -0.55 2 2
RELN/VLDLR/DAB1/P13K -0.04 0.11 -10000 0 -0.27 125 125
CDK5 0.028 0.023 -10000 0 -0.55 1 1
MAPT -0.01 0.22 0.68 45 -0.5 81 126
neuron migration -0.041 0.14 0.3 6 -0.34 108 114
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.029 0.14 -10000 0 -0.5 51 51
RELN/VLDLR -0.028 0.15 -10000 0 -0.32 120 120
Effects of Botulinum toxin

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.005 0.037 -10000 0 -0.3 12 12
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.015 0.085 -10000 0 -0.22 97 97
STXBP1 0.031 0.023 -10000 0 -0.44 2 2
ACh/CHRNA1 -0.06 0.14 -10000 0 -0.26 225 225
RAB3GAP2/RIMS1/UNC13B 0.035 0.076 -10000 0 -0.19 61 61
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.011 0.11 -10000 0 -0.32 98 98
mol:ACh 0.002 0.068 0.12 110 -0.14 109 219
RAB3GAP2 0.031 0.008 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.004 0.1 -10000 0 -0.31 41 41
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.06 0.14 -10000 0 -0.26 225 225
UNC13B 0.032 0.013 -10000 0 -0.32 1 1
CHRNA1 -0.096 0.21 -10000 0 -0.41 252 252
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.012 0.1 -10000 0 -0.24 107 107
SNAP25 -0.03 0.1 -10000 0 -0.3 108 108
VAMP2 0.006 0.002 -10000 0 -10000 0 0
SYT1 -0.012 0.14 -10000 0 -0.4 88 88
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.023 0.038 -10000 0 -0.25 14 14
STX1A/SNAP25 fragment 1/VAMP2 0.004 0.1 -10000 0 -0.31 41 41
Arf6 signaling events

Figure S35.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S35.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.019 0.071 -10000 0 -0.23 56 56
ARNO/beta Arrestin1-2 0.021 0.092 -10000 0 -0.81 5 5
EGFR 0.008 0.1 -10000 0 -0.47 36 36
EPHA2 0.027 0.049 -10000 0 -0.55 6 6
USP6 0.024 0.046 -10000 0 -0.34 13 13
IQSEC1 0.03 0.009 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.04 0.16 -10000 0 -0.32 192 192
ARRB2 0.002 0.039 -10000 0 -0.34 1 1
mol:GTP 0.021 0.066 0.19 57 -0.26 13 70
ARRB1 0.025 0.066 -10000 0 -0.53 12 12
FBXO8 0.032 0.005 -10000 0 -10000 0 0
TSHR -0.054 0.19 -10000 0 -0.48 145 145
EGF -0.059 0.19 -10000 0 -0.41 181 181
somatostatin receptor activity 0 0 0.001 63 -0.001 87 150
ARAP2 0.029 0.044 -10000 0 -0.55 5 5
mol:GDP -0.032 0.13 0.21 37 -0.3 100 137
mol:PI-3-4-5-P3 0 0 0.001 48 -0.001 43 91
ITGA2B -0.008 0.13 -10000 0 -0.42 72 72
ARF6 0.032 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.074 -10000 0 -0.34 22 22
ADAP1 0.019 0.066 -10000 0 -0.38 21 21
KIF13B 0.012 0.081 -10000 0 -0.32 49 49
HGF/MET -0.001 0.12 -10000 0 -0.33 99 99
PXN 0.032 0.007 -10000 0 -10000 0 0
ARF6/GTP -0.023 0.14 0.3 57 -0.29 92 149
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.019 0.14 -10000 0 -0.37 88 88
ADRB2 0.01 0.093 -10000 0 -0.37 47 47
receptor agonist activity 0 0 0.001 56 0 86 142
actin filament binding 0 0 0.001 66 -0.001 87 153
SRC 0.031 0.008 -10000 0 -10000 0 0
ITGB3 0.001 0.12 -10000 0 -0.45 51 51
GNAQ 0.032 0.005 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.002 76 -0.001 56 132
ARF6/GDP -0.007 0.14 0.28 9 -0.43 62 71
ARF6/GDP/GULP/ACAP1 -0.024 0.15 0.24 5 -0.37 85 90
alphaIIb/beta3 Integrin/paxillin/GIT1 0.03 0.12 -10000 0 -0.34 57 57
ACAP1 0.005 0.11 -10000 0 -0.46 44 44
ACAP2 0.031 0.021 -10000 0 -0.55 1 1
LHCGR/beta Arrestin2 0.004 0.057 -10000 0 -0.48 1 1
EFNA1 0.021 0.076 -10000 0 -0.55 15 15
HGF -0.025 0.16 -10000 0 -0.46 95 95
CYTH3 0.009 0.004 -10000 0 -10000 0 0
CYTH2 0.017 0.08 -10000 0 -1.2 4 4
NCK1 0.03 0.029 -10000 0 -0.55 2 2
fibronectin binding 0 0 0.001 63 0 84 147
endosomal lumen acidification 0 0 0.001 53 0 95 148
microtubule-based process 0 0 -10000 0 0 8 8
GULP1 0.004 0.12 -10000 0 -0.49 47 47
GNAQ/ARNO 0.037 0.075 -10000 0 -1.1 4 4
mol:Phosphatidic acid 0 0 0 30 -10000 0 30
PIP3-E 0 0 0 53 0 23 76
MET 0.025 0.045 -10000 0 -0.55 5 5
GNA14 -0.029 0.18 -10000 0 -0.55 93 93
GNA15 0.014 0.1 -10000 0 -0.5 31 31
GIT1 0.028 0.029 -10000 0 -0.55 2 2
mol:PI-4-5-P2 0 0.001 0.001 74 -0.001 67 141
GNA11 0.017 0.089 -10000 0 -0.44 30 30
LHCGR -0.015 0.097 -10000 0 -0.32 76 76
AGTR1 -0.098 0.21 -10000 0 -0.4 260 260
desensitization of G-protein coupled receptor protein signaling pathway 0.004 0.057 -10000 0 -0.32 2 2
IPCEF1/ARNO -0.01 0.13 -10000 0 -0.9 5 5
alphaIIb/beta3 Integrin -0.006 0.14 -10000 0 -0.33 112 112
Neurotrophic factor-mediated Trk receptor signaling

Figure S36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.032 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.007 0.089 -10000 0 -0.29 41 41
NT3 (dimer)/TRKC -0.041 0.18 -10000 0 -0.38 174 174
NT3 (dimer)/TRKB -0.088 0.22 -10000 0 -0.45 191 191
SHC/Grb2/SOS1/GAB1/PI3K 0.033 0.036 -10000 0 -0.31 6 6
RAPGEF1 0.032 0.005 -10000 0 -10000 0 0
BDNF -0.041 0.18 -10000 0 -0.46 131 131
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
DYNLT1 0.031 0.009 -10000 0 -10000 0 0
NTRK1 0.005 0.097 -10000 0 -0.36 56 56
NTRK2 -0.071 0.2 -10000 0 -0.45 190 190
NTRK3 -0.037 0.17 -10000 0 -0.44 129 129
NT-4/5 (dimer)/TRKB -0.077 0.2 -10000 0 -0.42 177 177
neuron apoptosis 0.092 0.2 0.46 159 -10000 0 159
SHC 2-3/Grb2 -0.1 0.23 -10000 0 -0.5 159 159
SHC1 0.031 0.014 -10000 0 -0.32 1 1
SHC2 -0.11 0.24 -10000 0 -0.54 162 162
SHC3 -0.1 0.21 -10000 0 -0.47 166 166
STAT3 (dimer) 0.023 0.072 -10000 0 -0.35 29 29
NT3 (dimer)/TRKA -0.043 0.18 -10000 0 -0.42 138 138
RIN/GDP 0.006 0.12 0.29 32 -0.3 55 87
GIPC1 0.03 0.036 -10000 0 -0.49 4 4
KRAS 0.031 0.008 -10000 0 -10000 0 0
DNAJA3 -0.078 0.17 -10000 0 -0.4 172 172
RIN/GTP 0.015 0.014 -10000 0 -0.22 3 3
CCND1 -0.004 0.15 -10000 0 -0.82 29 29
MAGED1 0.033 0.012 -10000 0 -0.32 1 1
PTPN11 0.031 0.021 -10000 0 -0.55 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.005 0.078 -10000 0 -0.32 48 48
SHC/GRB2/SOS1 0.058 0.025 -10000 0 -10000 0 0
GRB2 0.029 0.011 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.05 0.19 -10000 0 -0.4 159 159
TRKA/NEDD4-2 0.013 0.094 -10000 0 -0.42 12 12
ELMO1 0.009 0.11 -10000 0 -0.55 30 30
RhoG/GTP/ELMO1/DOCK1 0.023 0.074 -10000 0 -0.35 31 31
NGF -0.074 0.21 -10000 0 -0.5 175 175
HRAS 0.03 0.038 -10000 0 -0.46 5 5
DOCK1 0.03 0.029 -10000 0 -0.55 2 2
GAB2 0.03 0.035 -10000 0 -0.41 5 5
RIT2 0.02 0.021 -10000 0 -0.32 3 3
RIT1 0.031 0.008 -10000 0 -10000 0 0
FRS2 0.031 0.007 -10000 0 -10000 0 0
DNM1 -0.037 0.18 -10000 0 -0.45 127 127
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.016 -10000 0 -0.32 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.072 0.19 -10000 0 -0.45 138 138
mol:GDP -0.005 0.18 0.37 36 -0.47 60 96
NGF (dimer) -0.074 0.21 -10000 0 -0.49 175 175
RhoG/GDP 0.007 0.077 -10000 0 -0.4 30 30
RIT1/GDP 0.012 0.13 0.32 35 -0.3 55 90
TIAM1 0.026 0.053 -10000 0 -0.52 8 8
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
BDNF (dimer)/TRKB -0.055 0.19 -10000 0 -0.39 173 173
KIDINS220/CRKL/C3G 0.047 0.011 -10000 0 -10000 0 0
SHC/RasGAP 0.043 0.031 -10000 0 -0.36 4 4
FRS2 family/SHP2 0.058 0.032 -10000 0 -0.34 3 3
SHC/GRB2/SOS1/GAB1 0.071 0.034 -10000 0 -0.25 1 1
RIT1/GTP 0.023 0.008 -10000 0 -10000 0 0
NT3 (dimer) -0.021 0.16 -10000 0 -0.48 89 89
RAP1/GDP 0 0.091 0.15 1 -0.25 53 54
KIDINS220/CRKL 0.032 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.041 0.18 -10000 0 -0.46 131 131
ubiquitin-dependent protein catabolic process -0.04 0.16 -10000 0 -0.36 142 142
Schwann cell development -0.028 0.034 -10000 0 -10000 0 0
EHD4 0.033 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.07 0.037 -10000 0 -0.31 2 2
FRS2 family/SHP2/CRK family/C3G/GAB2 0.036 0.044 -10000 0 -0.28 11 11
RAP1B 0.031 0.007 -10000 0 -10000 0 0
RAP1A 0.031 0.008 -10000 0 -10000 0 0
CDC42/GTP -0.092 0.2 -10000 0 -0.51 103 103
ABL1 0.032 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.043 0.016 -10000 0 -10000 0 0
Rap1/GTP -0.011 0.12 -10000 0 -0.45 30 30
STAT3 0.023 0.071 -10000 0 -0.35 29 29
axon guidance -0.096 0.19 -10000 0 -0.46 114 114
MAPK3 -0.062 0.15 -10000 0 -0.36 141 141
MAPK1 -0.067 0.16 -10000 0 -0.37 159 159
CDC42/GDP 0.015 0.13 0.31 38 -0.3 55 93
NTF3 -0.021 0.16 -10000 0 -0.48 89 89
NTF4 0.005 0.078 -10000 0 -0.32 48 48
NGF (dimer)/TRKA/FAIM -0.026 0.16 -10000 0 -0.36 121 121
PI3K 0.04 0.049 -10000 0 -0.37 11 11
FRS3 0.03 0.029 -10000 0 -0.55 2 2
FAIM 0.032 0.007 -10000 0 -10000 0 0
GAB1 0.032 0.02 -10000 0 -0.55 1 1
RASGRF1 -0.095 0.18 -10000 0 -0.4 199 199
SOS1 0.031 0.007 -10000 0 -10000 0 0
MCF2L -0.05 0.15 -10000 0 -0.38 130 130
RGS19 0.03 0.029 -10000 0 -0.55 2 2
CDC42 0.031 0.008 -10000 0 -10000 0 0
RAS family/GTP 0 0.14 0.31 3 -0.53 43 46
Rac1/GDP 0.004 0.11 0.27 10 -0.3 54 64
NGF (dimer)/TRKA/GRIT -0.044 0.15 -10000 0 -0.3 215 215
neuron projection morphogenesis -0.094 0.26 0.39 1 -0.73 98 99
NGF (dimer)/TRKA/NEDD4-2 -0.039 0.17 -10000 0 -0.36 142 142
MAP2K1 0.038 0.06 0.38 12 -10000 0 12
NGFR -0.058 0.2 -10000 0 -0.49 146 146
NGF (dimer)/TRKA/GIPC/GAIP -0.058 0.16 -10000 0 -0.32 202 202
RAS family/GTP/PI3K 0.026 0.042 -10000 0 -0.31 12 12
FRS2 family/SHP2/GRB2/SOS1 0.08 0.044 -10000 0 -0.3 3 3
NRAS 0.031 0.008 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.016 -10000 0 -10000 0 0
PRKCI 0.031 0.014 -10000 0 -0.32 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.029 0.011 -10000 0 -10000 0 0
PRKCZ 0.025 0.056 -10000 0 -0.55 8 8
MAPKKK cascade -0.12 0.3 -10000 0 -0.68 183 183
RASA1 0.03 0.034 -10000 0 -0.55 3 3
TRKA/c-Abl 0.026 0.074 -10000 0 -0.25 52 52
SQSTM1 0.028 0.032 -10000 0 -0.32 7 7
BDNF (dimer)/TRKB/GIPC -0.039 0.18 -10000 0 -0.36 176 176
NGF (dimer)/TRKA/p62/Atypical PKCs -0.002 0.15 -10000 0 -0.32 125 125
MATK -0.003 0.13 -10000 0 -0.48 60 60
NEDD4L 0.012 0.083 -10000 0 -0.33 48 48
RAS family/GDP -0.03 0.063 -10000 0 -0.23 38 38
NGF (dimer)/TRKA -0.084 0.19 -10000 0 -0.41 184 184
Rac1/GTP -0.058 0.12 -10000 0 -0.33 112 112
FRS2 family/SHP2/CRK family 0.079 0.046 -10000 0 -0.34 3 3
Glypican 1 network

Figure S37.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S37.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.035 0.1 -10000 0 -0.37 50 50
fibroblast growth factor receptor signaling pathway 0.034 0.1 -10000 0 -0.37 50 50
LAMA1 -0.014 0.15 -10000 0 -0.49 77 77
PRNP 0.029 0.037 -10000 0 -0.49 4 4
GPC1/SLIT2 -0.025 0.15 -10000 0 -0.32 154 154
SMAD2 0.021 0.043 -10000 0 -0.31 9 9
GPC1/PrPc/Cu2+ 0.036 0.041 -10000 0 -0.3 11 11
GPC1/Laminin alpha1 0.008 0.12 -10000 0 -0.41 60 60
TDGF1 -0.025 0.13 -10000 0 -0.33 129 129
CRIPTO/GPC1 -0.002 0.1 -10000 0 -0.23 123 123
APP/GPC1 0.041 0.042 -10000 0 -0.34 9 9
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.012 0.077 -10000 0 -0.34 9 9
FLT1 -0.11 0.25 -10000 0 -0.55 222 222
GPC1/TGFB/TGFBR1/TGFBR2 0.053 0.048 -10000 0 -0.34 9 9
SERPINC1 0.006 0.089 -10000 0 -0.33 57 57
FYN -0.014 0.081 -10000 0 -0.34 16 16
FGR -0.017 0.089 -10000 0 -0.35 24 24
positive regulation of MAPKKK cascade -0.046 0.16 0.38 9 -0.52 50 59
SLIT2 -0.057 0.19 -10000 0 -0.42 173 173
GPC1/NRG 0.007 0.12 -10000 0 -0.36 79 79
NRG1 -0.013 0.15 -10000 0 -0.48 75 75
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.12 0.29 -10000 0 -0.57 245 245
LYN -0.013 0.079 -10000 0 -0.34 12 12
mol:Spermine 0.007 0.034 -10000 0 -0.33 8 8
cell growth 0.034 0.1 -10000 0 -0.37 50 50
BMP signaling pathway -0.027 0.049 0.46 8 -10000 0 8
SRC -0.012 0.076 -10000 0 -0.34 9 9
TGFBR1 0.032 0.005 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.023 0.12 -10000 0 -0.32 120 120
GPC1 0.027 0.049 -10000 0 -0.46 8 8
TGFBR1 (dimer) 0.032 0.005 -10000 0 -10000 0 0
VEGFA -0.12 0.25 -10000 0 -0.55 225 225
BLK -0.043 0.12 -10000 0 -0.37 55 55
HCK -0.018 0.088 -10000 0 -0.36 23 23
FGF2 0.002 0.13 -10000 0 -0.54 47 47
FGFR1 0.028 0.041 -10000 0 -0.5 5 5
VEGFR1 homodimer -0.11 0.25 -10000 0 -0.54 222 222
TGFBR2 0.028 0.04 -10000 0 -0.55 4 4
cell death 0.04 0.042 -10000 0 -0.34 9 9
ATIII/GPC1 0.023 0.077 -10000 0 -0.24 65 65
PLA2G2A/GPC1 0.001 0.098 -10000 0 -0.23 126 126
LCK -0.036 0.12 -10000 0 -0.36 66 66
neuron differentiation 0.007 0.12 -10000 0 -0.36 79 79
PrPc/Cu2+ 0.021 0.027 -10000 0 -0.36 4 4
APP 0.031 0.021 -10000 0 -0.55 1 1
TGFBR2 (dimer) 0.027 0.04 -10000 0 -0.55 4 4
Signaling events regulated by Ret tyrosine kinase

Figure S38.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S38.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.013 0.1 -10000 0 -0.46 23 23
Crk/p130 Cas/Paxillin -0.046 0.11 -10000 0 -0.32 79 79
JUN -0.029 0.11 -10000 0 -0.42 30 30
HRAS 0.03 0.038 -10000 0 -0.46 5 5
RET51/GFRalpha1/GDNF/GRB10 -0.02 0.14 -10000 0 -0.34 96 96
RAP1A 0.031 0.008 -10000 0 -10000 0 0
FRS2 0.031 0.007 -10000 0 -10000 0 0
RAP1A/GDP 0.023 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.023 0.16 -10000 0 -0.35 114 114
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.031 0.021 -10000 0 -0.55 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.016 -10000 0 -0.32 1 1
RET9/GFRalpha1/GDNF/Enigma -0.014 0.13 -10000 0 -0.32 85 85
RHOA 0.03 0.009 -10000 0 -10000 0 0
RAP1A/GTP -0.021 0.15 -10000 0 -0.32 118 118
GRB7 0.02 0.071 -10000 0 -0.47 17 17
RET51/GFRalpha1/GDNF -0.021 0.15 -10000 0 -0.34 110 110
MAPKKK cascade -0.029 0.13 -10000 0 -0.34 84 84
BCAR1 0.029 0.035 -10000 0 -0.55 3 3
RET9/GFRalpha1/GDNF/IRS1 -0.022 0.13 -10000 0 -0.33 96 96
lamellipodium assembly -0.032 0.11 -10000 0 -0.3 84 84
RET51/GFRalpha1/GDNF/SHC -0.021 0.15 -10000 0 -0.34 111 111
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
RET9/GFRalpha1/GDNF/SHC -0.013 0.12 -10000 0 -0.32 85 85
RET9/GFRalpha1/GDNF/Shank3 -0.017 0.13 -10000 0 -0.32 91 91
MAPK3 -0.049 0.12 0.42 2 -0.32 107 109
DOK1 0.028 0.044 -10000 0 -0.55 5 5
DOK6 -0.041 0.19 -10000 0 -0.53 113 113
PXN 0.032 0.007 -10000 0 -10000 0 0
neurite development -0.06 0.13 -10000 0 -0.4 57 57
DOK5 -0.02 0.15 -10000 0 -0.45 93 93
GFRA1 -0.066 0.19 -10000 0 -0.43 185 185
MAPK8 -0.03 0.12 -10000 0 -0.42 36 36
HRAS/GTP -0.022 0.15 -10000 0 -0.36 103 103
tube development -0.004 0.12 -10000 0 -0.3 77 77
MAPK1 -0.042 0.13 0.4 8 -0.32 102 110
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.018 0.093 -10000 0 -0.26 93 93
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
SRC 0.031 0.008 -10000 0 -10000 0 0
PDLIM7 0.029 0.037 -10000 0 -0.49 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.048 0.19 -10000 0 -0.36 176 176
SHC1 0.031 0.014 -10000 0 -0.32 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.027 0.16 -10000 0 -0.36 120 120
RET51/GFRalpha1/GDNF/Dok5 -0.048 0.18 -10000 0 -0.38 147 147
PRKCA 0.029 0.016 -10000 0 -0.32 1 1
HRAS/GDP 0.022 0.028 -10000 0 -0.33 5 5
CREB1 -0.017 0.11 -10000 0 -0.32 79 79
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.022 0.1 -10000 0 -0.28 96 96
RET51/GFRalpha1/GDNF/Grb7 -0.025 0.16 -10000 0 -0.36 104 104
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.006 0.12 -10000 0 -0.39 78 78
DOK4 0.016 0.091 -10000 0 -0.55 22 22
JNK cascade -0.028 0.11 -10000 0 -0.41 30 30
RET9/GFRalpha1/GDNF/FRS2 -0.013 0.12 -10000 0 -0.32 81 81
SHANK3 0.027 0.052 -10000 0 -0.47 9 9
RASA1 0.03 0.034 -10000 0 -0.55 3 3
NCK1 0.03 0.029 -10000 0 -0.55 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.022 0.1 -10000 0 -0.28 97 97
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.026 0.11 -10000 0 -0.29 93 93
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.033 0.13 -10000 0 -0.36 63 63
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.024 0.11 -10000 0 -0.3 96 96
PI3K -0.048 0.16 -10000 0 -0.44 90 90
SOS1 0.031 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.002 0.12 -10000 0 -0.3 77 77
GRB10 0.028 0.022 -10000 0 -0.55 1 1
activation of MAPKK activity -0.024 0.1 -10000 0 -0.32 36 36
RET51/GFRalpha1/GDNF/FRS2 -0.02 0.15 -10000 0 -0.34 105 105
GAB1 0.032 0.02 -10000 0 -0.55 1 1
IRS1 0.016 0.083 -10000 0 -0.4 31 31
IRS2 0.013 0.079 -10000 0 -0.32 45 45
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.032 0.12 -10000 0 -0.3 118 118
RET51/GFRalpha1/GDNF/PKC alpha -0.02 0.15 -10000 0 -0.34 97 97
GRB2 0.029 0.011 -10000 0 -10000 0 0
PRKACA 0.033 0.003 -10000 0 -10000 0 0
GDNF 0.017 0.044 -10000 0 -0.32 14 14
RAC1 0.029 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.03 0.16 -10000 0 -0.35 124 124
Rac1/GTP -0.035 0.13 -10000 0 -0.36 82 82
RET9/GFRalpha1/GDNF -0.033 0.13 -10000 0 -0.26 187 187
GFRalpha1/GDNF -0.042 0.15 -10000 0 -0.31 187 187
BCR signaling pathway

Figure S39.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S39.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.036 0.19 0.33 12 -0.5 99 111
IKBKB 0.01 0.11 0.29 37 -0.31 24 61
AKT1 -0.016 0.12 0.34 40 -0.26 38 78
IKBKG 0.018 0.1 0.28 34 -0.3 19 53
CALM1 -0.025 0.15 0.28 9 -0.51 49 58
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
MAP3K1 -0.043 0.23 0.36 19 -0.6 95 114
MAP3K7 0.031 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.026 0.16 0.28 5 -0.5 61 66
DOK1 0.028 0.044 -10000 0 -0.55 5 5
AP-1 -0.017 0.12 0.24 26 -0.28 85 111
LYN 0.03 0.028 -10000 0 -0.55 2 2
BLNK 0.015 0.087 -10000 0 -0.42 31 31
SHC1 0.031 0.014 -10000 0 -0.32 1 1
BCR complex -0.037 0.16 -10000 0 -0.31 193 193
CD22 -0.082 0.22 -10000 0 -0.61 102 102
CAMK2G -0.02 0.14 0.28 7 -0.5 42 49
CSNK2A1 0.031 0.008 -10000 0 -10000 0 0
INPP5D 0.029 0.04 -10000 0 -0.55 4 4
SHC/GRB2/SOS1 -0.023 0.13 -10000 0 -0.51 30 30
GO:0007205 -0.028 0.16 0.28 5 -0.52 61 66
SYK 0.022 0.072 -10000 0 -0.48 17 17
ELK1 -0.027 0.15 0.26 6 -0.51 53 59
NFATC1 -0.047 0.16 0.33 9 -0.49 65 74
B-cell antigen/BCR complex -0.037 0.16 -10000 0 -0.31 193 193
PAG1/CSK 0.035 0.074 -10000 0 -0.39 24 24
NFKBIB 0.026 0.049 0.15 40 -0.13 15 55
HRAS -0.019 0.13 0.29 6 -0.47 44 50
NFKBIA 0.026 0.048 0.15 40 -0.12 14 54
NF-kappa-B/RelA/I kappa B beta 0.031 0.044 0.15 37 -0.17 1 38
RasGAP/Csk -0.014 0.17 -10000 0 -0.38 109 109
mol:GDP -0.026 0.16 0.27 5 -0.51 56 61
PTEN 0.031 0.008 -10000 0 -10000 0 0
CD79B -0.001 0.12 -10000 0 -0.5 51 51
NF-kappa-B/RelA/I kappa B alpha 0.031 0.044 0.15 38 -0.17 1 39
GRB2 0.029 0.011 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.049 0.21 0.36 9 -0.54 96 105
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
mol:IP3 -0.029 0.16 0.28 5 -0.52 62 67
CSK 0.031 0.028 -10000 0 -0.55 2 2
FOS -0.047 0.17 0.29 8 -0.53 61 69
CHUK 0.006 0.12 0.28 31 -0.34 49 80
IBTK 0.031 0.008 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.007 0.16 0.33 22 -0.51 43 65
PTPN6 -0.078 0.2 -10000 0 -0.58 95 95
RELA 0.033 0.004 -10000 0 -10000 0 0
BCL2A1 0.019 0.041 0.13 18 -0.11 8 26
VAV2 -0.076 0.21 0.29 1 -0.61 83 84
ubiquitin-dependent protein catabolic process 0.03 0.048 0.15 40 -0.13 15 55
BTK -0.028 0.24 -10000 0 -1.2 38 38
CD19 -0.083 0.21 -10000 0 -0.58 93 93
MAP4K1 -0.009 0.14 -10000 0 -0.5 69 69
CD72 0.014 0.093 -10000 0 -0.42 36 36
PAG1 0.017 0.093 -10000 0 -0.55 23 23
MAPK14 -0.031 0.19 0.32 24 -0.5 91 115
SH3BP5 -0.005 0.14 -10000 0 -0.54 54 54
PIK3AP1 -0.034 0.18 0.3 5 -0.53 76 81
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.045 0.22 -10000 0 -0.6 83 83
RAF1 -0.014 0.12 0.28 12 -0.47 34 46
RasGAP/p62DOK/SHIP -0.012 0.17 -10000 0 -0.38 107 107
CD79A -0.053 0.18 -10000 0 -0.4 175 175
re-entry into mitotic cell cycle -0.017 0.12 0.24 27 -0.28 85 112
RASA1 0.03 0.034 -10000 0 -0.55 3 3
MAPK3 0.002 0.12 0.34 34 -0.41 28 62
MAPK1 -0.006 0.11 0.34 13 -0.4 32 45
CD72/SHP1 -0.062 0.21 0.31 2 -0.57 99 101
NFKB1 0.032 0.02 -10000 0 -0.55 1 1
MAPK8 -0.033 0.19 0.34 24 -0.5 94 118
actin cytoskeleton organization -0.046 0.18 0.39 7 -0.55 61 68
NF-kappa-B/RelA 0.064 0.082 0.28 37 -0.24 1 38
Calcineurin 0.006 0.13 0.29 1 -0.48 35 36
PI3K -0.064 0.16 -10000 0 -0.48 73 73
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.033 0.18 0.31 6 -0.56 66 72
SOS1 0.031 0.007 -10000 0 -10000 0 0
Bam32/HPK1 -0.09 0.33 -10000 0 -0.9 110 110
DAPP1 -0.11 0.36 -10000 0 -1 106 106
cytokine secretion -0.043 0.15 0.33 9 -0.45 65 74
mol:DAG -0.029 0.16 0.28 5 -0.52 62 67
PLCG2 -0.002 0.11 -10000 0 -0.34 76 76
MAP2K1 -0.01 0.12 0.28 15 -0.44 33 48
B-cell antigen/BCR complex/FcgammaRIIB -0.043 0.18 -10000 0 -0.42 111 111
mol:PI-3-4-5-P3 -0.05 0.11 -10000 0 -0.34 61 61
ETS1 -0.028 0.14 0.4 6 -0.48 49 55
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.001 0.16 -10000 0 -0.4 81 81
B-cell antigen/BCR complex/LYN -0.068 0.22 -10000 0 -0.62 96 96
MALT1 0.031 0.02 -10000 0 -0.55 1 1
TRAF6 0.033 0.004 -10000 0 -10000 0 0
RAC1 -0.053 0.19 0.35 5 -0.59 61 66
B-cell antigen/BCR complex/LYN/SYK -0.048 0.22 0.3 1 -0.58 87 88
CARD11 -0.022 0.19 0.33 34 -0.58 54 88
FCGR2B -0.011 0.14 -10000 0 -0.46 75 75
PPP3CA 0.032 0.005 -10000 0 -10000 0 0
BCL10 0.031 0.008 -10000 0 -10000 0 0
IKK complex 0.016 0.062 0.18 57 -0.13 5 62
PTPRC 0.006 0.12 -10000 0 -0.52 40 40
PDPK1 -0.03 0.085 0.33 9 -0.25 42 51
PPP3CB 0.031 0.008 -10000 0 -10000 0 0
PPP3CC 0.031 0.008 -10000 0 -10000 0 0
POU2F2 0.024 0.037 0.14 20 -0.11 6 26
IL6-mediated signaling events

Figure S40.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S40.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.13 0.25 0.6 2 -0.73 51 53
CRP -0.16 0.27 0.52 3 -0.76 62 65
cell cycle arrest -0.16 0.28 -10000 0 -0.74 99 99
TIMP1 -0.13 0.29 -10000 0 -0.9 70 70
IL6ST -0.038 0.18 -10000 0 -0.55 95 95
Rac1/GDP -0.075 0.18 -10000 0 -0.5 82 82
AP1 -0.003 0.17 -10000 0 -0.64 36 36
GAB2 0.031 0.035 -10000 0 -0.41 5 5
TNFSF11 -0.16 0.28 0.64 1 -0.84 69 70
HSP90B1 0.016 0.06 -10000 0 -0.86 1 1
GAB1 0.033 0.02 -10000 0 -0.55 1 1
MAPK14 -0.05 0.17 -10000 0 -0.62 46 46
AKT1 0.037 0.062 -10000 0 -0.66 3 3
FOXO1 0.041 0.057 -10000 0 -0.71 2 2
MAP2K6 -0.059 0.16 -10000 0 -0.48 70 70
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.088 0.18 0.29 2 -0.53 75 77
MITF -0.07 0.15 -10000 0 -0.43 86 86
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.032 0.028 -10000 0 -0.55 2 2
A2M -0.054 0.35 -10000 0 -1.5 48 48
CEBPB 0.032 0.037 -10000 0 -0.32 9 9
GRB2/SOS1/GAB family/SHP2 -0.007 0.15 0.3 1 -0.65 35 36
STAT3 -0.17 0.3 -10000 0 -0.79 99 99
STAT1 -0.019 0.16 -10000 0 -0.8 34 34
CEBPD -0.14 0.25 0.56 1 -0.75 52 53
PIK3CA 0.029 0.049 -10000 0 -0.55 6 6
PI3K 0.042 0.049 -10000 0 -0.37 11 11
JUN 0.029 0.029 -10000 0 -0.38 4 4
PIAS3/MITF -0.057 0.16 0.25 1 -0.44 69 70
MAPK11 -0.056 0.18 -10000 0 -0.62 53 53
STAT3 (dimer)/FOXO1 -0.12 0.24 -10000 0 -0.64 75 75
GRB2/SOS1/GAB family -0.011 0.16 0.29 1 -0.49 43 44
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.06 0.16 -10000 0 -0.42 104 104
GRB2 0.03 0.011 -10000 0 -10000 0 0
JAK2 0.031 0.02 -10000 0 -0.55 1 1
LBP -0.2 0.34 0.53 2 -0.89 125 127
PIK3R1 0.03 0.038 -10000 0 -0.46 5 5
JAK1 0.028 0.016 -10000 0 -10000 0 0
MYC -0.16 0.3 0.56 1 -0.93 69 70
FGG -0.28 0.42 -10000 0 -1 173 173
macrophage differentiation -0.16 0.28 -10000 0 -0.74 99 99
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.037 0.17 -10000 0 -0.36 133 133
JUNB -0.14 0.26 -10000 0 -0.77 59 59
FOS -0.026 0.16 -10000 0 -0.42 112 112
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.073 0.16 -10000 0 -0.42 104 104
STAT1/PIAS1 -0.069 0.16 -10000 0 -0.44 74 74
GRB2/SOS1/GAB family/SHP2/PI3K 0.039 0.054 -10000 0 -1.1 1 1
STAT3 (dimer) -0.17 0.3 -10000 0 -0.78 98 98
PRKCD -0.11 0.22 0.35 14 -0.6 83 97
IL6R 0.016 0.085 -10000 0 -0.54 19 19
SOCS3 -0.064 0.26 -10000 0 -1 45 45
gp130 (dimer)/JAK1/JAK1/LMO4 0.005 0.13 -10000 0 -0.34 96 96
Rac1/GTP -0.084 0.18 -10000 0 -0.51 84 84
HCK 0.021 0.075 -10000 0 -0.52 16 16
MAPKKK cascade 0.007 0.16 -10000 0 -0.67 37 37
bone resorption -0.16 0.27 0.64 1 -0.77 71 72
IRF1 -0.13 0.25 0.55 4 -0.72 55 59
mol:GDP -0.086 0.18 -10000 0 -0.46 109 109
SOS1 0.032 0.009 -10000 0 -10000 0 0
VAV1 -0.087 0.18 -10000 0 -0.46 113 113
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.069 0.24 -10000 0 -0.83 59 59
PTPN11 0.012 0.045 -10000 0 -1.2 1 1
IL6/IL6RA -0.051 0.15 -10000 0 -0.3 220 220
gp130 (dimer)/TYK2/TYK2/LMO4 0.011 0.13 -10000 0 -0.34 97 97
gp130 (dimer)/JAK2/JAK2/LMO4 0.01 0.13 -10000 0 -0.35 95 95
IL6 -0.081 0.19 -10000 0 -0.4 213 213
PIAS3 0.031 0.008 -10000 0 -10000 0 0
PTPRE 0.032 0.038 -10000 0 -0.55 3 3
PIAS1 0.033 0.003 -10000 0 -10000 0 0
RAC1 0.028 0.011 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.058 0.14 -10000 0 -0.35 112 112
LMO4 0.024 0.025 -10000 0 -0.32 1 1
STAT3 (dimer)/PIAS3 -0.16 0.28 -10000 0 -0.75 91 91
MCL1 0.047 0.06 -10000 0 -0.86 1 1
Noncanonical Wnt signaling pathway

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.022 0.16 -10000 0 -0.52 84 84
GNB1/GNG2 -0.046 0.15 -10000 0 -0.39 77 77
mol:DAG -0.053 0.13 -10000 0 -0.39 55 55
PLCG1 -0.054 0.13 -10000 0 -0.4 55 55
YES1 -0.055 0.13 -10000 0 -0.38 65 65
FZD3 0.031 0.008 -10000 0 -10000 0 0
FZD6 0.031 0.024 -10000 0 -0.44 2 2
G protein -0.039 0.15 0.27 5 -0.41 54 59
MAP3K7 -0.055 0.11 -10000 0 -0.36 44 44
mol:Ca2+ -0.051 0.12 -10000 0 -0.38 55 55
mol:IP3 -0.053 0.13 -10000 0 -0.39 55 55
NLK -0.024 0.18 -10000 0 -0.87 37 37
GNB1 0.031 0.008 -10000 0 -10000 0 0
CAMK2A -0.059 0.12 -10000 0 -0.37 54 54
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.055 0.14 -10000 0 -0.4 67 67
CSNK1A1 0.031 0.008 -10000 0 -10000 0 0
GNAS -0.054 0.12 -10000 0 -0.38 65 65
GO:0007205 -0.056 0.12 -10000 0 -0.39 55 55
WNT6 -0.034 0.16 -10000 0 -0.41 127 127
WNT4 -0.029 0.15 -10000 0 -0.4 124 124
NFAT1/CK1 alpha -0.059 0.15 -10000 0 -0.44 42 42
GNG2 0.011 0.11 -10000 0 -0.55 32 32
WNT5A -0.012 0.12 -10000 0 -0.35 96 96
WNT11 -0.029 0.15 -10000 0 -0.37 133 133
CDC42 -0.049 0.12 -10000 0 -0.37 54 54
EPO signaling pathway

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.012 0.11 -10000 0 -0.52 2 2
CRKL -0.003 0.13 0.38 29 -0.26 62 91
mol:DAG -0.013 0.11 0.25 5 -0.33 58 63
HRAS 0.01 0.13 0.35 64 -0.54 2 66
MAPK8 -0.024 0.12 0.2 17 -0.3 65 82
RAP1A -0.001 0.13 0.39 33 -0.27 50 83
GAB1 -0.003 0.13 0.38 29 -0.26 62 91
MAPK14 -0.02 0.12 0.2 19 -0.29 61 80
EPO -0.094 0.19 -10000 0 -0.37 266 266
PLCG1 -0.014 0.11 0.25 5 -0.34 58 63
EPOR/TRPC2/IP3 Receptors 0.029 0.037 -10000 0 -0.39 4 4
RAPGEF1 0.032 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.04 0.14 -10000 0 -0.33 95 95
GAB1/SHC/GRB2/SOS1 0.007 0.11 0.28 8 -0.56 1 9
EPO/EPOR (dimer) -0.05 0.15 -10000 0 -0.26 266 266
IRS2 -0.01 0.13 0.39 30 -0.27 61 91
STAT1 -0.01 0.11 0.26 7 -0.34 63 70
STAT5B -0.012 0.11 0.26 6 -0.34 57 63
cell proliferation -0.016 0.12 0.26 30 -0.28 55 85
GAB1/SHIP/PIK3R1/SHP2/SHC -0.001 0.1 -10000 0 -0.46 4 4
TEC -0.002 0.13 0.38 29 -0.26 61 90
SOCS3 0.01 0.095 -10000 0 -0.44 36 36
STAT1 (dimer) -0.009 0.11 0.26 7 -0.33 63 70
JAK2 0.03 0.031 -10000 0 -0.6 1 1
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
EPO/EPOR (dimer)/JAK2 0.005 0.12 -10000 0 -0.28 62 62
EPO/EPOR -0.05 0.15 -10000 0 -0.26 266 266
LYN 0.031 0.029 -10000 0 -0.55 2 2
TEC/VAV2 0 0.11 0.29 8 -0.62 1 9
elevation of cytosolic calcium ion concentration 0.029 0.037 -10000 0 -0.39 4 4
SHC1 0.031 0.014 -10000 0 -0.32 1 1
EPO/EPOR (dimer)/LYN -0.022 0.13 -10000 0 -0.33 62 62
mol:IP3 -0.013 0.11 0.25 5 -0.33 58 63
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.01 0.14 0.38 27 -0.42 8 35
SH2B3 0.027 0.028 -10000 0 -0.55 1 1
NFKB1 -0.021 0.12 0.2 22 -0.3 62 84
EPO/EPOR (dimer)/JAK2/SOCS3 -0.039 0.095 -10000 0 -0.3 74 74
PTPN6 -0.015 0.11 0.3 2 -0.27 62 64
TEC/VAV2/GRB2 0.003 0.11 0.29 7 -0.6 1 8
EPOR 0.03 0.037 -10000 0 -0.39 4 4
INPP5D 0.029 0.04 -10000 0 -0.55 4 4
mol:GDP 0.006 0.11 0.28 8 -0.58 1 9
SOS1 0.031 0.007 -10000 0 -10000 0 0
PLCG2 -0.002 0.11 -10000 0 -0.34 76 76
CRKL/CBL/C3G 0.008 0.12 0.29 8 -0.83 1 9
VAV2 -0.001 0.13 0.39 31 -0.26 56 87
CBL -0.003 0.13 0.39 30 -0.27 62 92
SHC/Grb2/SOS1 -0.011 0.095 -10000 0 -0.6 1 1
STAT5A -0.013 0.11 0.26 6 -0.34 60 66
GRB2 0.029 0.011 -10000 0 -10000 0 0
STAT5 (dimer) 0.004 0.11 -10000 0 -0.4 6 6
LYN/PLCgamma2 0.02 0.085 -10000 0 -0.24 70 70
PTPN11 0.031 0.021 -10000 0 -0.55 1 1
BTK -0.01 0.14 0.39 32 -0.29 83 115
BCL2 0.003 0.16 0.41 2 -0.8 16 18
Calcium signaling in the CD4+ TCR pathway

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.006 0.056 -10000 0 -0.37 11 11
NFATC2 -0.033 0.11 -10000 0 -0.35 82 82
NFATC3 0 0.038 -10000 0 -0.36 1 1
CD40LG -0.14 0.28 0.49 7 -0.66 138 145
PTGS2 -0.14 0.28 0.51 7 -0.63 155 162
JUNB 0.023 0.071 -10000 0 -0.47 17 17
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.03 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.03 -10000 0 -10000 0 0
CALM1 0.023 0.022 -10000 0 -10000 0 0
JUN 0.021 0.037 -10000 0 -0.4 4 4
mol:Ca2+ -0.007 0.013 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.011 -10000 0 -10000 0 0
FOSL1 -0.008 0.13 -10000 0 -0.41 81 81
CREM 0.031 0.014 -10000 0 -0.32 1 1
Jun/NFAT1-c-4/p21SNFT -0.049 0.18 -10000 0 -0.46 61 61
FOS -0.035 0.16 -10000 0 -0.44 112 112
IFNG -0.14 0.27 0.38 3 -0.6 154 157
AP-1/NFAT1-c-4 -0.12 0.31 -10000 0 -0.66 143 143
FASLG -0.15 0.29 0.5 6 -0.66 149 155
NFAT1-c-4/ICER1 -0.031 0.13 -10000 0 -0.39 42 42
IL2RA -0.14 0.29 0.49 7 -0.65 149 156
FKBP12/FK506 0.023 0.006 -10000 0 -10000 0 0
CSF2 -0.13 0.24 0.37 3 -0.6 113 116
JunB/Fra1/NFAT1-c-4 -0.042 0.16 -10000 0 -0.44 60 60
IL4 -0.13 0.24 0.37 3 -0.6 108 111
IL2 0.007 0.11 -10000 0 -0.96 9 9
IL3 -0.028 0.2 -10000 0 -0.85 43 43
FKBP1A 0.031 0.008 -10000 0 -10000 0 0
BATF3 0.012 0.098 -10000 0 -0.48 32 32
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.03 0.029 -10000 0 -0.55 2 2
Nongenotropic Androgen signaling

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.01 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.001 0.14 -10000 0 -0.32 132 132
regulation of S phase of mitotic cell cycle -0.007 0.11 -10000 0 -0.28 97 97
GNAO1 -0.001 0.12 -10000 0 -0.42 63 63
HRAS 0.029 0.038 -10000 0 -0.46 5 5
SHBG/T-DHT 0 0.071 -10000 0 -0.23 69 69
PELP1 0.029 0.011 -10000 0 -10000 0 0
AKT1 0.01 0.014 -10000 0 -0.4 1 1
MAP2K1 -0.015 0.1 0.34 7 -0.36 14 21
T-DHT/AR -0.031 0.14 -10000 0 -0.38 120 120
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 114 114
GNAI2 0.03 0.009 -10000 0 -10000 0 0
GNAI3 0.031 0.008 -10000 0 -10000 0 0
GNAI1 0.023 0.059 -10000 0 -0.55 9 9
mol:GDP -0.046 0.15 -10000 0 -0.46 101 101
cell proliferation -0.019 0.16 0.41 28 -0.46 46 74
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
FOS -0.047 0.23 0.43 14 -0.82 57 71
mol:Ca2+ -0.005 0.023 -10000 0 -0.07 60 60
MAPK3 -0.011 0.14 0.39 34 -0.44 22 56
MAPK1 -0.007 0.11 0.28 16 -0.5 20 36
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
mol:IP3 0 0.002 -10000 0 -0.004 114 114
cAMP biosynthetic process -0.011 0.073 0.24 14 -0.23 64 78
GNG2 0.011 0.11 -10000 0 -0.55 32 32
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 114 114
HRAS/GTP 0.012 0.11 -10000 0 -0.28 96 96
actin cytoskeleton reorganization 0.038 0.037 -10000 0 -0.27 7 7
SRC 0.031 0.008 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 114 114
PI3K 0.037 0.042 -10000 0 -0.31 11 11
apoptosis 0.017 0.15 0.48 51 -0.34 25 76
T-DHT/AR/PELP1 -0.008 0.12 -10000 0 -0.33 111 111
HRAS/GDP -0.028 0.15 -10000 0 -0.44 102 102
CREB1 -0.02 0.16 0.36 24 -0.52 51 75
RAC1-CDC42/GTP 0.048 0.041 -10000 0 -0.28 7 7
AR -0.043 0.19 -10000 0 -0.52 120 120
GNB1 0.031 0.008 -10000 0 -10000 0 0
RAF1 -0.009 0.11 0.35 9 -0.28 80 89
RAC1-CDC42/GDP -0.009 0.15 -10000 0 -0.42 97 97
T-DHT/AR/PELP1/Src 0.012 0.12 -10000 0 -0.31 93 93
MAP2K2 -0.017 0.11 0.35 8 -0.39 16 24
T-DHT/AR/PELP1/Src/PI3K -0.007 0.11 -10000 0 -0.29 97 97
GNAZ 0.026 0.056 -10000 0 -0.48 10 10
SHBG -0.003 0.12 -10000 0 -0.4 66 66
Gi family/GNB1/GNG2/GDP -0.023 0.15 -10000 0 -0.49 55 55
mol:T-DHT 0 0.002 -10000 0 -0.007 46 46
RAC1 0.029 0.011 -10000 0 -10000 0 0
GNRH1 -0.006 0.075 -10000 0 -0.35 39 39
Gi family/GTP -0.017 0.084 -10000 0 -0.27 53 53
CDC42 0.031 0.008 -10000 0 -10000 0 0
S1P3 pathway

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.055 0.2 -9999 0 -0.54 132 132
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.008 0.068 -9999 0 -0.26 36 36
GNAO1 0 0.12 -9999 0 -0.42 63 63
S1P/S1P3/G12/G13 0.025 0.092 -9999 0 -0.31 45 45
AKT1 -0.067 0.25 -9999 0 -0.61 138 138
AKT3 -0.1 0.25 -9999 0 -0.62 107 107
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.055 0.2 -9999 0 -0.54 132 132
GNAI2 0.031 0.011 -9999 0 -10000 0 0
GNAI3 0.032 0.01 -9999 0 -10000 0 0
GNAI1 0.024 0.06 -9999 0 -0.55 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.031 0.18 -9999 0 -0.51 104 104
S1PR2 0.03 0.035 -9999 0 -0.41 5 5
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.005 0.12 -9999 0 -0.35 70 70
MAPK3 -0.008 0.12 -9999 0 -0.44 34 34
MAPK1 -0.007 0.11 -9999 0 -0.45 32 32
JAK2 -0.008 0.13 -9999 0 -0.47 41 41
CXCR4 -0.017 0.14 -9999 0 -0.46 53 53
FLT1 -0.11 0.25 -9999 0 -0.54 222 222
RhoA/GDP 0.022 0.007 -9999 0 -10000 0 0
Rac1/GDP 0.021 0.008 -9999 0 -10000 0 0
SRC -0.007 0.11 -9999 0 -0.44 33 33
S1P/S1P3/Gi -0.005 0.12 -9999 0 -0.35 70 70
RAC1 0.029 0.011 -9999 0 -10000 0 0
RhoA/GTP 0.003 0.12 -9999 0 -0.42 37 37
VEGFA -0.12 0.25 -9999 0 -0.54 225 225
S1P/S1P2/Gi 0.017 0.077 -9999 0 -0.29 29 29
VEGFR1 homodimer/VEGFA homodimer -0.15 0.32 -9999 0 -0.62 260 260
RHOA 0.03 0.009 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.043 0.18 -9999 0 -0.37 164 164
GNAQ 0.032 0.005 -9999 0 -10000 0 0
GNAZ 0.027 0.056 -9999 0 -0.48 10 10
G12/G13 0.04 0.019 -9999 0 -10000 0 0
GNA14 -0.029 0.18 -9999 0 -0.55 93 93
GNA15 0.014 0.1 -9999 0 -0.5 31 31
GNA12 0.029 0.011 -9999 0 -10000 0 0
GNA13 0.029 0.011 -9999 0 -10000 0 0
GNA11 0.017 0.089 -9999 0 -0.44 30 30
Rac1/GTP 0.002 0.11 -9999 0 -0.41 35 35
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.043 0.15 -10000 0 -0.44 91 91
CRKL -0.027 0.14 -10000 0 -0.5 52 52
HRAS -0.024 0.17 -10000 0 -0.48 85 85
mol:PIP3 -0.02 0.14 0.26 1 -0.45 57 58
SPRED1 0.031 0.034 -10000 0 -0.55 3 3
SPRED2 0.03 0.029 -10000 0 -0.55 2 2
GAB1 -0.028 0.15 -10000 0 -0.52 54 54
FOXO3 -0.002 0.15 0.29 6 -0.44 60 66
AKT1 -0.006 0.16 0.3 6 -0.47 65 71
BAD -0.005 0.15 0.29 6 -0.45 60 66
megakaryocyte differentiation -0.044 0.16 -10000 0 -0.44 104 104
GSK3B 0.002 0.16 0.38 21 -0.44 60 81
RAF1 -0.017 0.14 0.28 7 -0.41 61 68
SHC1 0.031 0.014 -10000 0 -0.32 1 1
STAT3 -0.026 0.14 -10000 0 -0.5 55 55
STAT1 -0.07 0.3 -10000 0 -1 66 66
HRAS/SPRED1 -0.001 0.15 0.27 9 -0.4 78 87
cell proliferation -0.027 0.15 -10000 0 -0.51 56 56
PIK3CA 0.028 0.048 -10000 0 -0.55 6 6
TEC 0.032 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.022 0.17 0.25 1 -0.43 88 89
HRAS/SPRED2 -0.001 0.15 0.28 7 -0.38 79 86
LYN/TEC/p62DOK 0.012 0.16 -10000 0 -0.5 54 54
MAPK3 0.003 0.12 0.32 28 -0.3 54 82
STAP1 -0.056 0.18 -10000 0 -0.46 92 92
GRAP2 -0.001 0.14 -10000 0 -0.55 50 50
JAK2 -0.061 0.26 -10000 0 -0.9 65 65
STAT1 (dimer) -0.066 0.29 -10000 0 -1 66 66
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.007 0.17 -10000 0 -0.46 79 79
actin filament polymerization -0.034 0.14 -10000 0 -0.48 62 62
LYN 0.03 0.028 -10000 0 -0.55 2 2
STAP1/STAT5A (dimer) -0.066 0.22 -10000 0 -0.59 100 100
PIK3R1 0.03 0.038 -10000 0 -0.46 5 5
CBL/CRKL/GRB2 0.003 0.13 -10000 0 -0.45 47 47
PI3K 0.002 0.16 -10000 0 -0.49 55 55
PTEN 0.031 0.008 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.1 0.35 -10000 0 -1.4 52 52
MAPK8 -0.028 0.15 -10000 0 -0.52 56 56
STAT3 (dimer) -0.025 0.14 -10000 0 -0.48 55 55
positive regulation of transcription 0.008 0.1 0.3 32 -0.25 50 82
mol:GDP -0.02 0.18 -10000 0 -0.48 86 86
PIK3C2B -0.025 0.15 -10000 0 -0.51 55 55
CBL/CRKL -0.011 0.14 -10000 0 -0.46 53 53
FER -0.029 0.15 -10000 0 -0.52 53 53
SH2B3 -0.028 0.14 -10000 0 -0.51 54 54
PDPK1 -0.01 0.13 0.32 14 -0.42 47 61
SNAI2 -0.056 0.18 -10000 0 -0.56 68 68
positive regulation of cell proliferation -0.045 0.23 -10000 0 -0.76 66 66
KITLG 0.004 0.11 -10000 0 -0.42 48 48
cell motility -0.045 0.23 -10000 0 -0.76 66 66
PTPN6 0.031 0.022 -10000 0 -0.54 1 1
EPOR 0.016 0.12 -10000 0 -0.94 5 5
STAT5A (dimer) -0.04 0.2 -10000 0 -0.64 67 67
SOCS1 0.001 0.11 -10000 0 -0.37 64 64
cell migration 0.042 0.16 0.5 73 -10000 0 73
SOS1 0.031 0.007 -10000 0 -10000 0 0
EPO -0.1 0.19 -10000 0 -0.37 266 266
VAV1 0.006 0.12 -10000 0 -0.53 42 42
GRB10 -0.031 0.14 -10000 0 -0.53 49 49
PTPN11 0.031 0.021 -10000 0 -0.54 1 1
SCF/KIT -0.029 0.16 -10000 0 -0.51 63 63
GO:0007205 0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.004 0.12 0.34 24 -0.33 53 77
CBL 0.032 0.02 -10000 0 -0.55 1 1
KIT -0.068 0.36 -10000 0 -1.4 55 55
MAP2K2 -0.005 0.13 0.33 26 -0.33 56 82
SHC/Grb2/SOS1 0.014 0.15 -10000 0 -0.5 46 46
STAT5A -0.042 0.21 -10000 0 -0.66 67 67
GRB2 0.029 0.011 -10000 0 -10000 0 0
response to radiation -0.055 0.18 -10000 0 -0.55 68 68
SHC/GRAP2 0.02 0.1 -10000 0 -0.38 51 51
PTPRO -0.045 0.17 -10000 0 -0.45 104 104
SH2B2 -0.035 0.15 -10000 0 -0.49 62 62
DOK1 0.028 0.044 -10000 0 -0.55 5 5
MATK -0.043 0.17 -10000 0 -0.52 73 73
CREBBP 0.034 0.045 -10000 0 -0.18 2 2
BCL2 -0.008 0.23 -10000 0 -1.3 23 23
Glucocorticoid receptor regulatory network

Figure S47.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S47.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.034 0.098 0.33 8 -1.1 2 10
SMARCC2 0.03 0.021 -10000 0 -10000 0 0
SMARCC1 0.029 0.02 -10000 0 -10000 0 0
TBX21 -0.048 0.2 0.44 3 -0.82 41 44
SUMO2 0.028 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0.035 0.042 -10000 0 -0.38 8 8
FKBP4 0.031 0.008 -10000 0 -10000 0 0
FKBP5 -0.012 0.14 -10000 0 -0.41 85 85
GR alpha/HSP90/FKBP51/HSP90 0.041 0.13 0.34 22 -0.31 30 52
PRL -0.02 0.1 -10000 0 -0.58 4 4
cortisol/GR alpha (dimer)/TIF2 0.078 0.24 0.55 86 -0.4 14 100
RELA -0.047 0.11 -10000 0 -0.26 93 93
FGG -0.043 0.3 0.47 64 -0.55 121 185
GR beta/TIF2 0.032 0.15 0.33 43 -0.36 53 96
IFNG -0.2 0.33 -10000 0 -0.85 114 114
apoptosis -0.012 0.15 0.58 13 -0.56 17 30
CREB1 0.028 0.027 -10000 0 -10000 0 0
histone acetylation -0.014 0.15 0.42 7 -0.44 53 60
BGLAP -0.018 0.12 -10000 0 -0.6 11 11
GR/PKAc 0.077 0.1 0.34 27 -0.32 1 28
NF kappa B1 p50/RelA -0.081 0.2 -10000 0 -0.39 181 181
SMARCD1 0.03 0.022 -10000 0 -10000 0 0
MDM2 0.039 0.089 0.27 56 -10000 0 56
GATA3 -0.038 0.17 -10000 0 -0.4 148 148
AKT1 0.026 0.023 -10000 0 -0.56 1 1
CSF2 -0.028 0.12 -10000 0 -0.6 11 11
GSK3B 0.03 0.012 -10000 0 -10000 0 0
NR1I3 0.009 0.16 0.55 16 -0.62 9 25
CSN2 0.046 0.17 0.39 77 -0.32 7 84
BRG1/BAF155/BAF170/BAF60A 0.072 0.064 -10000 0 -0.32 13 13
NFATC1 0.026 0.065 -10000 0 -0.55 11 11
POU2F1 0.03 0.031 -10000 0 -0.55 2 2
CDKN1A 0.013 0.15 -10000 0 -1.7 6 6
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.001 0.007 -10000 0 -10000 0 0
SFN -0.099 0.2 -10000 0 -0.39 274 274
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.02 0.17 0.35 12 -0.37 79 91
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.023 0.24 0.53 19 -0.84 48 67
JUN -0.13 0.17 0.3 1 -0.47 83 84
IL4 -0.036 0.13 -10000 0 -0.63 13 13
CDK5R1 0.028 0.02 -10000 0 -0.33 2 2
PRKACA 0.033 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.2 0.22 87 -0.43 169 256
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.056 0.13 0.35 20 -0.31 17 37
cortisol/GR alpha (monomer) 0.11 0.28 0.63 103 -0.41 9 112
NCOA2 -0.005 0.14 -10000 0 -0.55 55 55
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.098 0.16 -10000 0 -0.47 113 113
AP-1/NFAT1-c-4 -0.25 0.28 -10000 0 -0.66 190 190
AFP -0.11 0.18 -10000 0 -1.1 7 7
SUV420H1 0.033 0.004 -10000 0 -10000 0 0
IRF1 0.067 0.14 0.5 28 -0.41 3 31
TP53 0.043 0.053 -10000 0 -0.48 8 8
PPP5C 0.033 0.003 -10000 0 -10000 0 0
KRT17 -0.27 0.43 -10000 0 -1.1 160 160
KRT14 -0.072 0.18 -10000 0 -1.1 14 14
TBP 0.038 0.018 -10000 0 -0.33 1 1
CREBBP 0.038 0.065 0.34 7 -0.27 21 28
HDAC1 0.029 0.009 -10000 0 -10000 0 0
HDAC2 0.03 0.009 -10000 0 -10000 0 0
AP-1 -0.26 0.28 -10000 0 -0.67 192 192
MAPK14 0.03 0.011 -10000 0 -10000 0 0
MAPK10 0.017 0.089 -10000 0 -0.55 21 21
MAPK11 0.021 0.071 -10000 0 -0.53 14 14
KRT5 -0.21 0.34 -10000 0 -0.98 95 95
interleukin-1 receptor activity 0 0.003 -10000 0 -10000 0 0
NCOA1 0.033 0.013 -10000 0 -10000 0 0
STAT1 0.035 0.042 -10000 0 -0.38 8 8
CGA -0.047 0.14 -10000 0 -0.52 40 40
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.028 0.12 0.44 16 -0.41 12 28
MAPK3 0.029 0.023 -10000 0 -0.55 1 1
MAPK1 0.03 0.022 -10000 0 -0.55 1 1
ICAM1 -0.14 0.34 0.43 1 -0.81 128 129
NFKB1 -0.046 0.11 -10000 0 -0.26 87 87
MAPK8 -0.091 0.16 -10000 0 -0.43 77 77
MAPK9 0.03 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.014 0.16 0.59 13 -0.58 17 30
BAX 0.023 0.091 -10000 0 -1.6 2 2
POMC -0.091 0.27 -10000 0 -1 35 35
EP300 0.038 0.07 0.34 7 -0.29 23 30
cortisol/GR alpha (dimer)/p53 0.087 0.21 0.55 55 -0.46 2 57
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.079 0.29 32 -10000 0 32
SGK1 0.02 0.27 1 1 -1.6 22 23
IL13 -0.16 0.26 -10000 0 -0.86 69 69
IL6 -0.19 0.4 0.63 2 -0.99 141 143
PRKACG 0.021 0.018 -10000 0 -0.32 2 2
IL5 -0.13 0.21 -10000 0 -0.76 54 54
IL2 -0.15 0.23 -10000 0 -0.69 65 65
CDK5 0.028 0.022 -10000 0 -0.54 1 1
PRKACB 0.031 0.008 -10000 0 -10000 0 0
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
IL8 -0.17 0.37 0.63 2 -0.84 149 151
CDK5R1/CDK5 0.038 0.026 -10000 0 -0.3 2 2
NF kappa B1 p50/RelA/PKAc -0.033 0.17 -10000 0 -0.38 77 77
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.11 0.22 0.52 92 -0.38 1 93
SMARCA4 0.031 0.028 -10000 0 -0.55 1 1
chromatin remodeling 0.062 0.15 0.4 56 -0.38 7 63
NF kappa B1 p50/RelA/Cbp -0.026 0.2 0.42 4 -0.45 82 86
JUN (dimer) -0.13 0.17 0.3 1 -0.46 83 84
YWHAH 0.032 0.006 -10000 0 -10000 0 0
VIPR1 -0.066 0.19 0.49 1 -0.6 64 65
NR3C1 0.066 0.17 0.47 67 -0.44 3 70
NR4A1 -0.043 0.18 -10000 0 -0.42 150 150
TIF2/SUV420H1 0.019 0.11 -10000 0 -0.4 55 55
MAPKKK cascade -0.012 0.15 0.58 13 -0.56 17 30
cortisol/GR alpha (dimer)/Src-1 0.1 0.23 0.54 89 -0.41 1 90
PBX1 0.023 0.072 -10000 0 -0.55 13 13
POU1F1 0.023 0.016 -10000 0 -10000 0 0
SELE -0.24 0.47 0.43 1 -1 194 195
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.062 0.15 0.4 56 -0.39 7 63
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.11 0.22 0.52 92 -0.38 1 93
mol:cortisol 0.047 0.17 0.37 104 -0.22 30 134
MMP1 -0.35 0.55 -10000 0 -1.4 196 196
Caspase cascade in apoptosis

Figure S48.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S48.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 -0.02 0.15 -10000 0 -0.43 82 82
ACTA1 -0.056 0.19 0.23 4 -0.52 101 105
NUMA1 -0.019 0.16 -10000 0 -0.51 56 56
SPTAN1 -0.053 0.19 0.23 1 -0.52 99 100
LIMK1 -0.032 0.18 0.29 13 -0.52 82 95
BIRC3 -0.015 0.15 -10000 0 -0.5 79 79
BIRC2 0.032 0.005 -10000 0 -10000 0 0
BAX 0.031 0.028 -10000 0 -0.55 2 2
CASP10 -0.051 0.16 -10000 0 -0.45 103 103
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.033 0.002 -10000 0 -10000 0 0
PTK2 -0.021 0.16 0.24 1 -0.51 60 61
DIABLO 0.032 0.007 -10000 0 -10000 0 0
apoptotic nuclear changes -0.052 0.18 0.23 1 -0.51 99 100
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.032 0.007 -10000 0 -10000 0 0
GSN -0.054 0.19 0.23 3 -0.52 101 104
MADD 0.033 0.004 -10000 0 -10000 0 0
TFAP2A -0.081 0.29 -10000 0 -0.79 113 113
BID -0.022 0.094 -10000 0 -0.27 91 91
MAP3K1 -0.003 0.074 -10000 0 -0.44 7 7
TRADD 0.03 0.021 -10000 0 -0.55 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.043 0.022 -10000 0 -0.4 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.05 0.2 0.3 9 -0.58 88 97
CASP9 0.031 0.008 -10000 0 -10000 0 0
DNA repair 0.01 0.081 0.32 30 -0.19 18 48
neuron apoptosis -0.005 0.16 -10000 0 -0.68 42 42
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.037 0.19 0.32 1 -0.49 100 101
APAF1 0.031 0.021 -10000 0 -0.55 1 1
CASP6 0.005 0.14 -10000 0 -0.77 17 17
TRAF2 0.031 0.028 -10000 0 -0.55 2 2
ICAD/CAD -0.05 0.18 0.35 1 -0.51 96 97
CASP7 0.012 0.081 0.3 37 -0.3 13 50
KRT18 0.02 0.044 -10000 0 -0.61 2 2
apoptosis -0.042 0.17 0.43 5 -0.56 59 64
DFFA -0.053 0.19 0.23 1 -0.52 99 100
DFFB -0.053 0.19 0.26 4 -0.52 99 103
PARP1 -0.01 0.082 0.19 18 -0.32 30 48
actin filament polymerization 0.027 0.17 0.49 76 -0.36 12 88
TNF -0.011 0.14 -10000 0 -0.43 80 80
CYCS -0.01 0.073 0.21 10 -0.23 45 55
SATB1 0.007 0.14 0.43 5 -0.78 15 20
SLK -0.053 0.19 0.28 6 -0.51 103 109
p15 BID/BAX -0.009 0.1 0.19 3 -0.34 47 50
CASP2 0.005 0.12 0.22 56 -0.4 35 91
JNK cascade 0.003 0.073 0.43 7 -10000 0 7
CASP3 -0.056 0.2 0.24 4 -0.53 104 108
LMNB2 0.031 0.13 0.3 35 -0.48 18 53
RIPK1 0.031 0.008 -10000 0 -10000 0 0
CASP4 0.03 0.034 -10000 0 -0.55 3 3
Mammalian IAPs/DIABLO 0.048 0.1 -10000 0 -0.31 58 58
negative regulation of DNA binding -0.08 0.29 -10000 0 -0.78 113 113
stress fiber formation -0.051 0.18 0.28 6 -0.5 103 109
GZMB -0.054 0.18 -10000 0 -0.44 138 138
CASP1 0.008 0.076 -10000 0 -0.4 26 26
LMNB1 0.027 0.13 0.3 33 -0.43 30 63
APP -0.006 0.16 -10000 0 -0.69 42 42
TNFRSF1A 0.031 0.008 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.009 0.014 -10000 0 -0.4 1 1
VIM -0.039 0.16 0.33 5 -0.53 62 67
LMNA 0.017 0.17 0.31 33 -0.54 50 83
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.004 0.11 -10000 0 -0.38 48 48
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.044 0.18 0.26 5 -0.52 86 91
APAF-1/Caspase 9 -0.018 0.16 -10000 0 -0.64 53 53
nuclear fragmentation during apoptosis -0.018 0.15 -10000 0 -0.5 56 56
CFL2 -0.029 0.18 0.36 12 -0.51 76 88
GAS2 -0.071 0.19 0.31 6 -0.54 98 104
positive regulation of apoptosis 0.029 0.14 0.31 35 -0.43 47 82
PRF1 -0.006 0.14 -10000 0 -0.5 62 62
EPHB forward signaling

Figure S49.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S49.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.033 0.14 -10000 0 -0.29 189 189
cell-cell adhesion 0.033 0.1 0.4 30 -10000 0 30
Ephrin B/EPHB2/RasGAP 0.031 0.13 -10000 0 -0.33 74 74
ITSN1 0.031 0.008 -10000 0 -10000 0 0
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
SHC1 0.031 0.014 -10000 0 -0.32 1 1
Ephrin B1/EPHB3 0.011 0.1 -10000 0 -0.3 80 80
Ephrin B1/EPHB1 0.016 0.082 -10000 0 -0.22 86 86
HRAS/GDP -0.008 0.13 -10000 0 -0.36 67 67
Ephrin B/EPHB1/GRB7 0.017 0.14 -10000 0 -0.34 82 82
Endophilin/SYNJ1 -0.01 0.11 0.35 4 -0.3 75 79
KRAS 0.031 0.008 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.021 0.14 -10000 0 -0.35 75 75
endothelial cell migration 0.038 0.084 -10000 0 -0.3 43 43
GRB2 0.029 0.011 -10000 0 -10000 0 0
GRB7 0.02 0.071 -10000 0 -0.47 17 17
PAK1 -0.004 0.13 0.39 19 -0.32 70 89
HRAS 0.03 0.038 -10000 0 -0.46 5 5
RRAS -0.008 0.11 0.35 5 -0.31 73 78
DNM1 -0.037 0.18 -10000 0 -0.45 127 127
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.025 0.11 -10000 0 -0.33 73 73
lamellipodium assembly -0.033 0.1 -10000 0 -0.4 30 30
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.003 0.1 -10000 0 -0.38 37 37
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
EPHB2 0.012 0.087 -10000 0 -0.36 42 42
EPHB3 -0.017 0.15 -10000 0 -0.49 81 81
EPHB1 -0.009 0.12 -10000 0 -0.38 86 86
EPHB4 0.025 0.049 -10000 0 -0.55 6 6
mol:GDP -0.02 0.12 0.3 14 -0.39 61 75
Ephrin B/EPHB2 0.018 0.12 -10000 0 -0.32 73 73
Ephrin B/EPHB3 0.004 0.15 -10000 0 -0.36 99 99
JNK cascade 0 0.098 0.36 21 -0.31 35 56
Ephrin B/EPHB1 0.008 0.13 -10000 0 -0.35 75 75
RAP1/GDP 0.013 0.14 0.31 21 -0.39 41 62
EFNB2 0.008 0.11 -10000 0 -0.55 35 35
EFNB3 -0.011 0.13 -10000 0 -0.41 79 79
EFNB1 0.032 0.02 -10000 0 -0.55 1 1
Ephrin B2/EPHB1-2 0.007 0.12 -10000 0 -0.34 64 64
RAP1B 0.031 0.007 -10000 0 -10000 0 0
RAP1A 0.031 0.008 -10000 0 -10000 0 0
CDC42/GTP -0.001 0.13 -10000 0 -0.37 65 65
Rap1/GTP -0.017 0.11 -10000 0 -0.42 27 27
axon guidance -0.033 0.14 -10000 0 -0.29 189 189
MAPK3 -0.006 0.088 0.2 1 -0.35 23 24
MAPK1 -0.009 0.094 0.2 1 -0.37 29 30
Rac1/GDP -0.014 0.12 0.29 5 -0.37 60 65
actin cytoskeleton reorganization -0.026 0.091 -10000 0 -0.34 36 36
CDC42/GDP 0.004 0.14 0.32 23 -0.36 62 85
PI3K 0.043 0.086 -10000 0 -0.3 43 43
EFNA5 -0.061 0.2 -10000 0 -0.48 157 157
Ephrin B2/EPHB4 0.019 0.08 -10000 0 -0.34 38 38
Ephrin B/EPHB2/Intersectin/N-WASP -0.002 0.098 -10000 0 -0.29 76 76
CDC42 0.031 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.022 0.11 -10000 0 -0.4 31 31
PTK2 0.013 0.074 0.53 17 -10000 0 17
MAP4K4 0 0.098 0.36 21 -0.31 35 56
SRC 0.031 0.008 -10000 0 -10000 0 0
KALRN 0.025 0.061 -10000 0 -0.51 11 11
Intersectin/N-WASP 0.041 0.019 -10000 0 -10000 0 0
neuron projection morphogenesis 0.009 0.15 0.38 59 -0.38 31 90
MAP2K1 -0.007 0.098 -10000 0 -0.36 36 36
WASL 0.029 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.036 0.1 -10000 0 -0.32 35 35
cell migration 0.007 0.15 0.39 41 -0.38 32 73
NRAS 0.031 0.008 -10000 0 -10000 0 0
SYNJ1 -0.011 0.11 0.35 4 -0.31 75 79
PXN 0.032 0.007 -10000 0 -10000 0 0
TF -0.057 0.12 -10000 0 -0.32 105 105
HRAS/GTP -0.002 0.13 -10000 0 -0.33 81 81
Ephrin B1/EPHB1-2 0.02 0.097 -10000 0 -0.32 33 33
cell adhesion mediated by integrin 0.032 0.11 0.33 71 -0.2 27 98
RAC1 0.029 0.011 -10000 0 -10000 0 0
mol:GTP 0 0.13 -10000 0 -0.33 84 84
RAC1-CDC42/GTP -0.044 0.13 -10000 0 -0.44 43 43
RASA1 0.03 0.034 -10000 0 -0.55 3 3
RAC1-CDC42/GDP -0.002 0.12 0.29 5 -0.38 42 47
ruffle organization -0.005 0.14 0.36 49 -0.42 29 78
NCK1 0.03 0.029 -10000 0 -0.55 2 2
receptor internalization -0.044 0.13 0.34 4 -0.32 126 130
Ephrin B/EPHB2/KALRN 0.029 0.13 -10000 0 -0.33 76 76
ROCK1 -0.001 0.096 0.18 24 -0.32 62 86
RAS family/GDP -0.032 0.091 -10000 0 -0.35 36 36
Rac1/GTP -0.027 0.11 -10000 0 -0.43 30 30
Ephrin B/EPHB1/Src/Paxillin -0.006 0.11 -10000 0 -0.31 74 74
Plasma membrane estrogen receptor signaling

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.032 0.12 -10000 0 -0.34 62 62
ER alpha/Gai/GDP/Gbeta gamma -0.044 0.22 -10000 0 -0.6 96 96
AKT1 -0.059 0.29 -10000 0 -0.86 99 99
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.057 0.3 -10000 0 -0.88 98 98
mol:Ca2+ -0.079 0.2 -10000 0 -0.5 132 132
IGF1R 0.031 0.034 -10000 0 -0.55 3 3
E2/ER alpha (dimer)/Striatin 0.009 0.11 -10000 0 -0.34 71 71
SHC1 0.031 0.014 -10000 0 -0.32 1 1
apoptosis 0.054 0.28 0.8 100 -10000 0 100
RhoA/GTP 0.016 0.051 -10000 0 -0.26 20 20
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.006 0.18 -10000 0 -0.5 85 85
regulation of stress fiber formation -0.013 0.087 0.36 4 -0.34 24 28
E2/ERA-ERB (dimer) 0.013 0.092 -10000 0 -0.27 73 73
KRAS 0.031 0.008 -10000 0 -10000 0 0
G13/GTP 0.022 0.064 -10000 0 -0.27 32 32
pseudopodium formation 0.013 0.087 0.34 24 -0.36 4 28
E2/ER alpha (dimer)/PELP1 0.023 0.071 -10000 0 -0.3 32 32
GRB2 0.029 0.011 -10000 0 -10000 0 0
GNG2 0.011 0.11 -10000 0 -0.55 32 32
GNAO1 -0.001 0.12 -10000 0 -0.42 63 63
HRAS 0.03 0.038 -10000 0 -0.46 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.035 0.24 0.33 16 -0.6 108 124
E2/ER beta (dimer) 0.013 0.054 -10000 0 -0.24 34 34
mol:GDP 0 0.091 -10000 0 -0.33 50 50
mol:NADP -0.035 0.24 0.33 16 -0.6 108 124
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
mol:IP3 -0.086 0.21 -10000 0 -0.52 132 132
IGF-1R heterotetramer 0.031 0.034 -10000 0 -0.55 3 3
PLCB1 -0.076 0.2 -10000 0 -0.5 125 125
PLCB2 -0.046 0.18 -10000 0 -0.48 116 116
IGF1 -0.008 0.13 -10000 0 -0.4 80 80
mol:L-citrulline -0.035 0.24 0.33 16 -0.6 108 124
RHOA 0.03 0.009 -10000 0 -10000 0 0
Gai/GDP -0.032 0.22 -10000 0 -0.65 87 87
JNK cascade 0.013 0.054 -10000 0 -0.24 34 34
BCAR1 0.029 0.035 -10000 0 -0.55 3 3
ESR2 0.017 0.076 -10000 0 -0.35 34 34
GNAQ 0.032 0.005 -10000 0 -10000 0 0
ESR1 0.005 0.12 -10000 0 -0.5 42 42
Gq family/GDP/Gbeta gamma -0.037 0.22 -10000 0 -0.67 71 71
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.019 0.26 -10000 0 -1.1 44 44
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.005 0.18 -10000 0 -0.49 85 85
GNAZ 0.026 0.056 -10000 0 -0.48 10 10
E2/ER alpha (dimer) 0.002 0.086 -10000 0 -0.36 42 42
STRN 0.01 0.11 -10000 0 -0.55 33 33
GNAL 0.019 0.077 -10000 0 -0.41 26 26
PELP1 0.029 0.01 -10000 0 -10000 0 0
MAPK11 0.005 0.063 -10000 0 -0.25 45 45
GNAI2 0.03 0.009 -10000 0 -10000 0 0
GNAI3 0.031 0.008 -10000 0 -10000 0 0
GNAI1 0.023 0.059 -10000 0 -0.55 9 9
HBEGF -0.038 0.22 0.38 29 -0.57 90 119
cAMP biosynthetic process 0.006 0.085 -10000 0 -0.29 48 48
SRC -0.04 0.21 0.23 8 -0.56 95 103
PI3K 0.04 0.049 -10000 0 -0.37 11 11
GNB1 0.031 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.021 0.11 -10000 0 -0.41 34 34
SOS1 0.031 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.036 0.15 -10000 0 -0.44 82 82
Gs family/GTP 0.013 0.089 -10000 0 -0.3 48 48
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.054 0.032 -10000 0 -0.31 3 3
vasodilation -0.03 0.22 0.32 16 -0.56 109 125
mol:DAG -0.086 0.21 -10000 0 -0.52 132 132
Gs family/GDP/Gbeta gamma -0.004 0.11 -10000 0 -0.41 35 35
MSN 0.013 0.09 0.35 24 -0.39 4 28
Gq family/GTP -0.034 0.18 -10000 0 -0.48 106 106
mol:PI-3-4-5-P3 -0.052 0.29 -10000 0 -0.84 98 98
NRAS 0.031 0.008 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.03 0.22 0.56 109 -0.32 16 125
GRB2/SOS1 0.043 0.016 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.097 -10000 0 -0.35 35 35
NOS3 -0.04 0.25 0.33 16 -0.65 108 124
GNA11 0.017 0.089 -10000 0 -0.44 30 30
MAPKKK cascade -0.024 0.24 0.4 16 -0.65 100 116
E2/ER alpha (dimer)/PELP1/Src -0.013 0.19 0.28 2 -0.51 89 91
ruffle organization 0.013 0.087 0.34 24 -0.36 4 28
ROCK2 0.02 0.094 0.37 23 -0.45 3 26
GNA14 -0.029 0.18 -10000 0 -0.55 93 93
GNA15 0.014 0.1 -10000 0 -0.5 31 31
GNA13 0.029 0.011 -10000 0 -10000 0 0
MMP9 -0.062 0.22 0.37 9 -0.58 97 106
MMP2 -0.034 0.2 0.27 13 -0.55 90 103
Ephrin B reverse signaling

Figure S51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.008 0.11 -10000 0 -0.55 35 35
EPHB2 0.011 0.087 -10000 0 -0.36 42 42
EFNB1 -0.03 0.13 -10000 0 -0.33 124 124
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.13 -10000 0 -0.32 81 81
Ephrin B2/EPHB1-2 0.006 0.12 -10000 0 -0.34 64 64
neuron projection morphogenesis -0.012 0.12 -10000 0 -0.3 87 87
Ephrin B1/EPHB1-2/Tiam1 -0.011 0.14 -10000 0 -0.33 109 109
DNM1 -0.037 0.18 -10000 0 -0.45 127 127
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.002 0.13 0.24 5 -0.6 31 36
YES1 -0.009 0.17 -10000 0 -0.88 30 30
Ephrin B1/EPHB1-2/NCK2 -0.007 0.14 -10000 0 -0.32 102 102
PI3K 0.023 0.13 -10000 0 -0.57 37 37
mol:GDP -0.012 0.14 -10000 0 -0.32 109 109
ITGA2B -0.008 0.13 -10000 0 -0.42 72 72
endothelial cell proliferation 0.019 0.08 -10000 0 -0.34 38 38
FYN -0.017 0.17 -10000 0 -0.88 31 31
MAP3K7 -0.014 0.12 -10000 0 -0.67 29 29
FGR -0.015 0.17 -10000 0 -0.9 30 30
TIAM1 0.026 0.053 -10000 0 -0.52 8 8
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
RGS3 0.032 0.017 -10000 0 -0.32 2 2
cell adhesion -0.017 0.15 -10000 0 -0.57 40 40
LYN -0.009 0.17 -10000 0 -0.88 30 30
Ephrin B1/EPHB1-2/Src Family Kinases -0.015 0.16 -10000 0 -0.81 31 31
Ephrin B1/EPHB1-2 -0.015 0.13 -10000 0 -0.74 28 28
SRC -0.007 0.16 -10000 0 -0.86 30 30
ITGB3 0.001 0.12 -10000 0 -0.45 51 51
EPHB1 -0.009 0.12 -10000 0 -0.38 86 86
EPHB4 0.025 0.049 -10000 0 -0.55 6 6
RAC1 0.029 0.011 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.019 0.08 -10000 0 -0.34 38 38
alphaIIb/beta3 Integrin -0.006 0.14 -10000 0 -0.33 112 112
BLK -0.019 0.17 -10000 0 -0.89 29 29
HCK -0.01 0.16 -10000 0 -0.88 29 29
regulation of stress fiber formation 0.008 0.14 0.32 103 -10000 0 103
MAPK8 -0.004 0.12 0.35 3 -0.57 31 34
Ephrin B1/EPHB1-2/RGS3 -0.008 0.14 -10000 0 -0.32 106 106
endothelial cell migration -0.004 0.14 0.3 13 -0.42 63 76
NCK2 0.032 0.007 -10000 0 -10000 0 0
PTPN13 0.018 0.11 -10000 0 -0.66 22 22
regulation of focal adhesion formation 0.008 0.14 0.32 103 -10000 0 103
chemotaxis 0.009 0.14 0.32 106 -10000 0 106
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
Rac1/GTP -0.004 0.13 -10000 0 -0.31 84 84
angiogenesis -0.015 0.13 -10000 0 -0.72 29 29
LCK -0.024 0.18 -10000 0 -0.89 31 31
Visual signal transduction: Rods

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.033 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.026 -10000 0 -0.22 10 10
Metarhodopsin II/Arrestin 0.024 0.033 -10000 0 -0.18 19 19
PDE6G/GNAT1/GTP 0.01 0.073 -10000 0 -0.22 73 73
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.018 0.037 -10000 0 -0.32 10 10
GRK1 0.016 0.039 -10000 0 -0.32 11 11
CNG Channel -0.036 0.15 -10000 0 -0.36 111 111
mol:Na + -0.021 0.13 -10000 0 -0.31 90 90
mol:ADP 0.016 0.039 -10000 0 -0.32 11 11
RGS9-1/Gbeta5/R9AP -0.011 0.14 -10000 0 -0.36 89 89
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.013 0.14 -10000 0 -0.32 87 87
CNGB1 -0.005 0.1 -10000 0 -0.32 78 78
RDH5 -0.035 0.18 -10000 0 -0.53 105 105
SAG 0.018 0.017 -10000 0 -0.32 2 2
mol:Ca2+ -0.043 0.14 0.41 27 -0.42 16 43
Na + (4 Units) -0.023 0.12 -10000 0 -0.4 18 18
RGS9 -0.038 0.17 -10000 0 -0.44 127 127
GNB1/GNGT1 -0.02 0.14 -10000 0 -0.38 117 117
GNAT1/GDP -0.004 0.13 -10000 0 -0.31 90 90
GUCY2D 0.01 0.076 -10000 0 -0.33 40 40
GNGT1 -0.05 0.19 -10000 0 -0.51 123 123
GUCY2F 0.02 0.005 -10000 0 -10000 0 0
GNB5 0.032 0.02 -10000 0 -0.55 1 1
mol:GMP (4 units) -0.014 0.11 -10000 0 -0.34 61 61
mol:11-cis-retinal -0.035 0.18 -10000 0 -0.52 105 105
mol:cGMP 0.02 0.085 -10000 0 -0.32 24 24
GNB1 0.031 0.008 -10000 0 -10000 0 0
Rhodopsin -0.014 0.14 -10000 0 -0.36 120 120
SLC24A1 0.033 0.003 -10000 0 -10000 0 0
CNGA1 -0.032 0.17 -10000 0 -0.43 121 121
Metarhodopsin II 0.022 0.037 -10000 0 -0.17 27 27
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.029 0.091 -10000 0 -0.33 24 24
RGS9BP -0.001 0.12 -10000 0 -0.41 66 66
Metarhodopsin II/Transducin -0.024 0.098 -10000 0 -0.28 102 102
GCAP Family/Ca ++ 0.025 0.075 -10000 0 -0.33 21 21
PDE6A/B 0.01 0.11 -10000 0 -0.36 73 73
mol:Pi -0.012 0.14 -10000 0 -0.36 89 89
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin -0.007 0.12 -10000 0 -0.31 101 101
PDE6B -0.003 0.14 -10000 0 -0.55 54 54
PDE6A 0.02 0.055 -10000 0 -0.32 22 22
PDE6G 0 0.11 -10000 0 -0.37 64 64
RHO 0.018 0.05 -10000 0 -0.32 18 18
PDE6 -0.021 0.18 -10000 0 -0.37 129 129
GUCA1A 0.015 0.051 -10000 0 -0.32 19 19
GC2/GCAP Family 0.035 0.081 -10000 0 -0.33 21 21
GUCA1C 0.01 0.063 -10000 0 -0.32 30 30
GUCA1B 0.016 0.089 -10000 0 -0.5 25 25
FOXM1 transcription factor network

Figure S53.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S53.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.051 0.41 0.87 5 -1.1 52 57
PLK1 0.032 0.16 -10000 0 -1.4 8 8
BIRC5 -0.038 0.34 -10000 0 -1.3 54 54
HSPA1B 0.04 0.42 0.78 2 -1.1 56 58
MAP2K1 0.045 0.05 -10000 0 -10000 0 0
BRCA2 0.021 0.46 0.74 3 -1.2 75 78
FOXM1 0.019 0.51 0.79 4 -1.4 67 71
XRCC1 0.043 0.42 0.89 3 -1.1 48 51
FOXM1B/p19 0.011 0.44 0.75 1 -1.1 77 78
Cyclin D1/CDK4 0.013 0.43 -10000 0 -1 77 77
CDC2 0.039 0.44 0.75 4 -1.1 66 70
TGFA -0.006 0.45 0.75 2 -1 85 87
SKP2 0.045 0.42 0.82 4 -1.1 47 51
CCNE1 0.028 0.059 -10000 0 -0.34 21 21
CKS1B 0.041 0.42 0.7 4 -1 69 73
RB1 0.052 0.26 -10000 0 -0.88 27 27
FOXM1C/SP1 0.024 0.46 -10000 0 -1.2 67 67
AURKB -0.033 0.34 -10000 0 -1.2 52 52
CENPF 0.033 0.44 0.78 2 -1.2 61 63
CDK4 0.033 0.026 -10000 0 -10000 0 0
MYC 0.031 0.4 -10000 0 -0.96 76 76
CHEK2 0.042 0.069 -10000 0 -0.55 6 6
ONECUT1 0.019 0.44 0.7 2 -1 76 78
CDKN2A -0.004 0.13 -10000 0 -0.5 54 54
LAMA4 -0.027 0.54 0.78 2 -1.2 120 122
FOXM1B/HNF6 -0.004 0.51 0.76 1 -1.3 79 80
FOS -0.004 0.5 0.98 3 -1.2 87 90
SP1 0.032 0.01 -10000 0 -10000 0 0
CDC25B 0.049 0.42 0.9 4 -1.1 54 58
response to radiation 0.017 0.031 -10000 0 -10000 0 0
CENPB 0.049 0.42 0.98 3 -1.1 46 49
CENPA 0.036 0.43 0.82 3 -1.1 57 60
NEK2 0.029 0.45 0.78 2 -1.2 69 71
HIST1H2BA 0.037 0.42 0.77 2 -1.1 56 58
CCNA2 0.031 0.051 -10000 0 -0.37 13 13
EP300 0.031 0.028 -10000 0 -0.55 2 2
CCNB1/CDK1 0.024 0.47 0.77 3 -1.3 56 59
CCNB2 0.034 0.43 0.9 3 -1.1 59 62
CCNB1 0.04 0.44 0.78 4 -1.2 56 60
ETV5 0.047 0.41 0.74 4 -1.1 52 56
ESR1 0.007 0.49 0.78 2 -1.2 88 90
CCND1 0.01 0.44 0.65 1 -1.1 80 81
GSK3A 0.043 0.044 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.066 0.078 -10000 0 -0.37 8 8
CDK2 0.036 0.011 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.02 0.036 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.043 0.44 -10000 0 -1.2 60 60
GAS1 0.032 0.44 0.78 2 -1.1 61 63
MMP2 0.034 0.44 0.87 5 -1.2 63 68
RB1/FOXM1C 0.011 0.44 -10000 0 -1.1 78 78
CREBBP 0.031 0.008 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.006 0.2 -10000 0 -0.53 85 85
MAP4K1 -0.009 0.14 -10000 0 -0.5 69 69
MAP3K8 0.029 0.033 -10000 0 -0.44 4 4
PRKCB 0.002 0.12 -10000 0 -0.52 46 46
DBNL 0.029 0.011 -10000 0 -10000 0 0
CRKL 0.032 0.006 -10000 0 -10000 0 0
MAP3K1 -0.017 0.18 -10000 0 -0.65 52 52
JUN -0.04 0.29 0.32 1 -0.86 81 82
MAP3K7 -0.016 0.18 -10000 0 -0.64 53 53
GRAP2 -0.001 0.14 -10000 0 -0.55 50 50
CRK 0.029 0.016 -10000 0 -0.32 1 1
MAP2K4 -0.006 0.2 0.26 22 -0.72 49 71
LAT 0.01 0.096 -10000 0 -0.41 41 41
LCP2 0.003 0.12 -10000 0 -0.54 43 43
MAPK8 -0.047 0.31 0.34 1 -0.93 81 82
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.015 0.19 -10000 0 -0.61 64 64
LAT/GRAP2/SLP76/HPK1/HIP-55 0.016 0.19 -10000 0 -0.52 77 77
Signaling events mediated by PTP1B

Figure S55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.055 0.2 -10000 0 -0.54 132 132
Jak2/Leptin Receptor -0.006 0.14 0.25 5 -0.45 50 55
PTP1B/AKT1 0.016 0.11 0.24 26 -0.37 31 57
FYN 0.025 0.056 -10000 0 -0.55 8 8
p210 bcr-abl/PTP1B 0.003 0.12 0.24 46 -0.36 42 88
EGFR 0.004 0.1 -10000 0 -0.48 36 36
EGF/EGFR -0.032 0.16 0.22 1 -0.37 114 115
CSF1 0.022 0.072 -10000 0 -0.52 15 15
AKT1 0.032 0.021 -10000 0 -0.56 1 1
INSR 0.032 0.028 -10000 0 -0.55 2 2
PTP1B/N-cadherin -0.019 0.17 0.24 24 -0.41 110 134
Insulin Receptor/Insulin 0.033 0.1 0.26 11 -0.4 14 25
HCK 0.021 0.075 -10000 0 -0.52 16 16
CRK 0.029 0.016 -10000 0 -0.32 1 1
TYK2 0.002 0.12 0.27 31 -0.39 34 65
EGF -0.059 0.19 -10000 0 -0.41 181 181
YES1 0.032 0.006 -10000 0 -10000 0 0
CAV1 0 0.16 0.31 59 -0.43 44 103
TXN 0.03 0.032 -10000 0 -0.32 7 7
PTP1B/IRS1/GRB2 0.011 0.12 0.28 5 -0.43 29 34
cell migration -0.003 0.12 0.36 42 -0.24 46 88
STAT3 0.03 0.01 -10000 0 -10000 0 0
PRLR -0.05 0.18 -10000 0 -0.4 166 166
ITGA2B -0.009 0.13 -10000 0 -0.42 72 72
CSF1R 0.017 0.089 -10000 0 -0.52 23 23
Prolactin Receptor/Prolactin -0.024 0.13 -10000 0 -0.32 108 108
FGR 0.019 0.081 -10000 0 -0.51 19 19
PTP1B/p130 Cas 0.006 0.11 0.23 6 -0.37 39 45
Crk/p130 Cas 0.015 0.11 0.24 2 -0.4 29 31
DOK1 -0.023 0.14 0.28 27 -0.37 60 87
JAK2 -0.014 0.15 0.24 16 -0.42 71 87
Jak2/Leptin Receptor/Leptin -0.003 0.13 -10000 0 -0.43 39 39
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
PTPN1 0.003 0.12 0.24 46 -0.37 42 88
LYN 0.03 0.028 -10000 0 -0.55 2 2
CDH2 -0.036 0.19 -10000 0 -0.55 102 102
SRC 0.03 0.081 -10000 0 -0.62 9 9
ITGB3 0.001 0.12 -10000 0 -0.45 51 51
CAT1/PTP1B -0.013 0.2 0.32 46 -0.52 74 120
CAPN1 0.032 0.029 -10000 0 -0.56 2 2
CSK 0.031 0.028 -10000 0 -0.55 2 2
PI3K 0.038 0.1 -10000 0 -0.42 13 13
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.001 0.13 -10000 0 -0.42 42 42
negative regulation of transcription -0.013 0.15 0.24 16 -0.42 71 87
FCGR2A 0.02 0.079 -10000 0 -0.54 17 17
FER 0.03 0.035 -10000 0 -0.56 3 3
alphaIIb/beta3 Integrin -0.006 0.14 -10000 0 -0.34 112 112
BLK -0.025 0.15 -10000 0 -0.4 112 112
Insulin Receptor/Insulin/Shc 0.053 0.03 -10000 0 -0.35 2 2
RHOA 0.03 0.01 -10000 0 -10000 0 0
LEPR 0.025 0.054 -10000 0 -0.49 9 9
BCAR1 0.029 0.035 -10000 0 -0.55 3 3
p210 bcr-abl/Grb2 0.029 0.011 -10000 0 -10000 0 0
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.034 0.21 0.27 16 -0.59 82 98
PRL -0.001 0.04 -10000 0 -0.32 9 9
SOCS3 -0.066 0.35 -10000 0 -1.4 57 57
SPRY2 0.031 0.029 -10000 0 -0.56 2 2
Insulin Receptor/Insulin/IRS1 0.043 0.065 -10000 0 -0.36 13 13
CSF1/CSF1R 0.015 0.14 0.26 19 -0.42 42 61
Ras protein signal transduction 0.028 0.11 0.41 65 -10000 0 65
IRS1 0.016 0.083 -10000 0 -0.4 31 31
INS 0.012 0.025 -10000 0 -0.32 3 3
LEP -0.013 0.1 -10000 0 -0.32 85 85
STAT5B -0.002 0.14 0.24 24 -0.38 68 92
STAT5A -0.002 0.14 0.24 24 -0.37 71 95
GRB2 0.029 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.029 0.14 0.25 16 -0.33 108 124
CSN2 -0.02 0.063 -10000 0 -0.57 2 2
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
LAT -0.01 0.17 0.27 1 -0.57 66 67
YBX1 0.039 0.018 -10000 0 -0.37 1 1
LCK -0.015 0.15 -10000 0 -0.48 78 78
SHC1 0.031 0.014 -10000 0 -0.32 1 1
NOX4 0 0.13 -10000 0 -0.52 51 51
LPA receptor mediated events

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.013 0.14 -10000 0 -0.37 85 85
NF kappa B1 p50/RelA/I kappa B alpha 0.014 0.11 0.31 10 -0.4 19 29
AP1 -0.022 0.14 -10000 0 -0.34 103 103
mol:PIP3 -0.021 0.094 -10000 0 -0.39 17 17
AKT1 0.013 0.12 0.34 24 -0.39 18 42
PTK2B -0.01 0.1 0.32 3 -0.37 35 38
RHOA 0 0.089 0.25 7 -0.38 16 23
PIK3CB 0.032 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.09 0.28 10 -0.43 15 25
MAGI3 0.025 0.049 -10000 0 -0.32 17 17
RELA 0.033 0.004 -10000 0 -10000 0 0
apoptosis -0.011 0.098 -10000 0 -0.31 71 71
HRAS/GDP 0.022 0.028 -10000 0 -0.33 5 5
positive regulation of microtubule depolymerization -0.016 0.14 0.32 32 -0.37 46 78
NF kappa B1 p50/RelA -0.013 0.12 0.25 4 -0.44 28 32
endothelial cell migration -0.018 0.14 -10000 0 -0.38 92 92
ADCY4 -0.032 0.15 -10000 0 -0.45 82 82
ADCY5 -0.035 0.14 -10000 0 -0.42 81 81
ADCY6 -0.016 0.13 -10000 0 -0.42 63 63
ADCY7 -0.015 0.12 -10000 0 -0.42 60 60
ADCY1 -0.048 0.15 -10000 0 -0.45 83 83
ADCY2 -0.064 0.17 -10000 0 -0.48 90 90
ADCY3 -0.021 0.14 -10000 0 -0.45 67 67
ADCY8 -0.05 0.14 -10000 0 -0.43 77 77
ADCY9 -0.015 0.12 -10000 0 -0.42 60 60
GSK3B -0.003 0.1 0.26 21 -0.39 23 44
arachidonic acid secretion -0.024 0.13 -10000 0 -0.4 76 76
GNG2 0.011 0.11 -10000 0 -0.55 32 32
TRIP6 0.018 0.059 -10000 0 -0.48 10 10
GNAO1 -0.026 0.12 -10000 0 -0.35 89 89
HRAS 0.03 0.038 -10000 0 -0.46 5 5
NFKBIA -0.009 0.12 0.36 17 -0.41 28 45
GAB1 0.032 0.02 -10000 0 -0.55 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.02 0.26 -10000 0 -0.92 62 62
JUN 0.029 0.029 -10000 0 -0.38 4 4
LPA/LPA2/NHERF2 0.034 0.051 -10000 0 -0.38 8 8
TIAM1 -0.044 0.31 -10000 0 -1.1 66 66
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
mol:IP3 -0.005 0.09 0.28 9 -0.44 15 24
PLCB3 0.024 0.064 0.19 38 -0.41 9 47
FOS -0.026 0.16 -10000 0 -0.42 112 112
positive regulation of mitosis -0.024 0.13 -10000 0 -0.4 76 76
LPA/LPA1-2-3 0.016 0.12 -10000 0 -0.33 77 77
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0.029 0.035 -10000 0 -0.55 3 3
stress fiber formation -0.002 0.1 0.35 3 -0.37 31 34
GNAZ -0.013 0.11 -10000 0 -0.35 75 75
EGFR/PI3K-beta/Gab1 -0.011 0.1 -10000 0 -0.41 17 17
positive regulation of dendritic cell cytokine production 0.014 0.12 -10000 0 -0.32 77 77
LPA/LPA2/MAGI-3 0.031 0.054 -10000 0 -0.35 7 7
ARHGEF1 0.027 0.12 0.37 37 -0.3 51 88
GNAI2 -0.01 0.1 -10000 0 -0.33 71 71
GNAI3 -0.011 0.11 -10000 0 -0.34 73 73
GNAI1 -0.013 0.11 -10000 0 -0.34 74 74
LPA/LPA3 0.009 0.046 -10000 0 -0.2 28 28
LPA/LPA2 0.017 0.046 -10000 0 -0.34 8 8
LPA/LPA1 -0.012 0.13 -10000 0 -0.39 81 81
HB-EGF/EGFR -0.032 0.13 -10000 0 -0.38 76 76
HBEGF -0.044 0.13 -10000 0 -0.3 171 171
mol:DAG -0.005 0.09 0.28 9 -0.44 15 24
cAMP biosynthetic process -0.029 0.16 0.37 30 -0.41 81 111
NFKB1 0.032 0.02 -10000 0 -0.55 1 1
SRC 0.031 0.008 -10000 0 -10000 0 0
GNB1 0.031 0.009 -10000 0 -10000 0 0
LYN -0.01 0.12 0.35 14 -0.45 29 43
GNAQ 0.01 0.045 -10000 0 -0.29 10 10
LPAR2 0.029 0.049 -10000 0 -0.52 7 7
LPAR3 0.013 0.054 -10000 0 -0.32 21 21
LPAR1 -0.012 0.15 -10000 0 -0.5 68 68
IL8 -0.075 0.18 0.31 3 -0.47 99 102
PTK2 -0.012 0.1 -10000 0 -0.32 63 63
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
CASP3 -0.011 0.099 -10000 0 -0.31 71 71
EGFR 0.008 0.1 -10000 0 -0.47 36 36
PLCG1 -0.009 0.081 -10000 0 -0.32 32 32
PLD2 -0.013 0.1 -10000 0 -0.32 60 60
G12/G13 0.024 0.1 -10000 0 -0.31 58 58
PI3K-beta -0.013 0.1 -10000 0 -0.42 21 21
cell migration 0.009 0.086 -10000 0 -0.27 54 54
SLC9A3R2 0.028 0.04 -10000 0 -0.44 6 6
PXN -0.002 0.1 0.35 3 -0.38 31 34
HRAS/GTP -0.025 0.14 -10000 0 -0.42 76 76
RAC1 0.029 0.011 -10000 0 -10000 0 0
MMP9 -0.054 0.18 -10000 0 -0.4 171 171
PRKCE 0.029 0.035 -10000 0 -0.55 3 3
PRKCD -0.009 0.11 0.35 18 -0.41 22 40
Gi(beta/gamma) -0.021 0.14 -10000 0 -0.42 77 77
mol:LPA -0.005 0.036 -10000 0 -0.2 19 19
TRIP6/p130 Cas/FAK1/Paxillin 0.019 0.12 -10000 0 -0.49 16 16
MAPKKK cascade -0.024 0.13 -10000 0 -0.4 76 76
contractile ring contraction involved in cytokinesis 0.002 0.094 0.25 14 -0.36 19 33
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.023 0.11 -10000 0 -0.32 97 97
GNA15 0.001 0.081 -10000 0 -0.37 32 32
GNA12 0.029 0.011 -10000 0 -10000 0 0
GNA13 0.029 0.011 -10000 0 -10000 0 0
MAPT -0.017 0.14 0.32 32 -0.38 47 79
GNA11 0.002 0.069 -10000 0 -0.29 33 33
Rac1/GTP -0.023 0.28 -10000 0 -0.99 62 62
MMP2 -0.018 0.14 -10000 0 -0.38 92 92
TCGA08_retinoblastoma

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.02 0.072 -10000 0 -0.48 16 16
CDKN2C 0.025 0.075 -10000 0 -0.52 16 16
CDKN2A 0.003 0.12 -10000 0 -0.48 54 54
CCND2 0.005 0.064 0.23 50 -0.13 14 64
RB1 -0.01 0.072 0.14 1 -0.26 53 54
CDK4 0.008 0.072 0.25 56 -10000 0 56
CDK6 0.008 0.074 0.27 51 -0.24 1 52
G1/S progression 0.011 0.076 0.27 57 -0.14 1 58
a4b1 and a4b7 Integrin signaling

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.031 0.008 -9999 0 -10000 0 0
ITGB7 0.026 0.056 -9999 0 -0.55 8 8
ITGA4 -0.013 0.15 -9999 0 -0.54 68 68
alpha4/beta7 Integrin 0.007 0.12 -9999 0 -0.38 74 74
alpha4/beta1 Integrin 0.01 0.12 -9999 0 -0.39 67 67
Paxillin-independent events mediated by a4b1 and a4b7

Figure S59.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S59.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.003 0.11 -10000 0 -0.39 62 62
CRKL 0.032 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
DOCK1 0.03 0.029 -10000 0 -0.55 2 2
ITGA4 -0.013 0.15 -10000 0 -0.54 68 68
alpha4/beta7 Integrin/MAdCAM1 0.029 0.12 -10000 0 -0.33 61 61
EPO -0.096 0.19 -10000 0 -0.37 266 266
alpha4/beta7 Integrin 0.007 0.12 -10000 0 -0.38 74 74
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.016 -10000 0 -0.32 1 1
alpha4/beta1 Integrin 0.01 0.12 -10000 0 -0.39 67 67
EPO/EPOR (dimer) -0.054 0.14 -10000 0 -0.26 268 268
lamellipodium assembly 0.02 0.068 -10000 0 -0.45 7 7
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
PI3K 0.04 0.049 -10000 0 -0.37 11 11
ARF6 0.032 0.006 -10000 0 -10000 0 0
JAK2 -0.043 0.12 -10000 0 -0.31 98 98
PXN 0.032 0.007 -10000 0 -10000 0 0
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
MADCAM1 0.01 0.083 -10000 0 -0.32 51 51
cell adhesion 0.027 0.11 -10000 0 -0.32 61 61
CRKL/CBL 0.047 0.018 -10000 0 -0.4 1 1
ITGB1 0.031 0.008 -10000 0 -10000 0 0
SRC -0.03 0.13 -10000 0 -0.34 108 108
ITGB7 0.026 0.056 -10000 0 -0.55 8 8
RAC1 0.029 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.008 0.16 -10000 0 -0.37 126 126
p130Cas/Crk/Dock1 0.002 0.12 0.36 1 -0.46 17 18
VCAM1 -0.019 0.16 -10000 0 -0.55 76 76
RHOA 0.03 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.049 0.093 -10000 0 -0.32 42 42
BCAR1 -0.033 0.11 0.38 1 -0.32 99 100
EPOR 0.031 0.029 -10000 0 -0.38 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.032 0.02 -10000 0 -0.55 1 1
GIT1 0.028 0.029 -10000 0 -0.55 2 2
Rac1/GTP 0.02 0.07 -10000 0 -0.46 7 7
ceramide signaling pathway

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.008 0.15 0.28 1 -0.54 47 48
BAG4 0.028 0.044 -10000 0 -0.55 5 5
BAD 0.011 0.068 0.24 25 -0.23 12 37
NFKBIA 0.032 0.006 -10000 0 -10000 0 0
BIRC3 -0.015 0.15 -10000 0 -0.5 79 79
BAX 0.011 0.067 0.22 29 -0.18 32 61
EnzymeConsortium:3.1.4.12 0.007 0.042 0.12 38 -0.11 45 83
IKBKB -0.002 0.14 0.29 7 -0.51 47 54
MAP2K2 0.021 0.095 0.29 61 -0.27 11 72
MAP2K1 0.022 0.093 0.29 61 -0.24 9 70
SMPD1 0.01 0.046 0.15 29 -0.13 33 62
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.002 0.16 0.32 1 -0.56 48 49
MAP2K4 0.024 0.085 0.27 65 -0.21 5 70
protein ubiquitination 0.002 0.16 0.36 18 -0.52 48 66
EnzymeConsortium:2.7.1.37 0.025 0.11 0.35 58 -0.27 10 68
response to UV 0 0.002 0.005 67 -0.003 6 73
RAF1 0.021 0.094 0.29 61 -0.24 14 75
CRADD 0.032 0.007 -10000 0 -10000 0 0
mol:ceramide 0.011 0.062 0.17 39 -0.16 44 83
I-kappa-B-alpha/RELA/p50/ubiquitin 0.043 0.009 -10000 0 -10000 0 0
MADD 0.033 0.004 -10000 0 -10000 0 0
MAP3K1 0.014 0.067 0.21 43 -0.18 19 62
TRADD 0.03 0.021 -10000 0 -0.55 1 1
RELA/p50 0.033 0.004 -10000 0 -10000 0 0
MAPK3 0.024 0.093 0.28 59 -0.33 5 64
MAPK1 0.023 0.095 0.29 61 -0.28 5 66
p50/RELA/I-kappa-B-alpha 0.047 0.009 -10000 0 -10000 0 0
FADD -0.009 0.15 0.32 1 -0.55 46 47
KSR1 0.018 0.085 0.25 60 -0.23 21 81
MAPK8 0.025 0.081 0.28 60 -0.22 8 68
TRAF2 0.031 0.028 -10000 0 -0.55 2 2
response to radiation 0 0.001 0.004 36 -0.002 1 37
CHUK 0 0.14 0.3 7 -0.51 45 52
TNF R/SODD 0.042 0.034 -10000 0 -0.4 4 4
TNF -0.011 0.14 -10000 0 -0.43 80 80
CYCS 0.018 0.079 0.22 50 -0.22 17 67
IKBKG -0.003 0.15 0.29 8 -0.52 48 56
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.012 0.16 -10000 0 -0.58 46 46
RELA 0.033 0.004 -10000 0 -10000 0 0
RIPK1 0.031 0.008 -10000 0 -10000 0 0
AIFM1 0.012 0.068 0.21 34 -0.21 14 48
TNF/TNF R/SODD 0.027 0.098 -10000 0 -0.34 38 38
TNFRSF1A 0.031 0.008 -10000 0 -10000 0 0
response to heat 0 0.001 0.004 36 -0.002 1 37
CASP8 0.001 0.18 -10000 0 -0.84 38 38
NSMAF -0.008 0.15 -10000 0 -0.54 45 45
response to hydrogen peroxide 0 0.002 0.005 67 -0.003 6 73
BCL2 0.023 0.07 -10000 0 -0.55 13 13
IL2 signaling events mediated by PI3K

Figure S61.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S61.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.018 0.2 -10000 0 -0.69 57 57
UGCG -0.009 0.16 -10000 0 -0.78 34 34
AKT1/mTOR/p70S6K/Hsp90/TERT -0.008 0.22 0.34 6 -0.58 88 94
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.008 0.16 -10000 0 -0.76 34 34
mol:DAG -0.039 0.22 -10000 0 -0.94 47 47
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.22 0.29 1 -0.56 94 95
FRAP1 -0.021 0.26 0.37 4 -0.66 99 103
FOXO3 -0.022 0.25 0.35 5 -0.67 94 99
AKT1 -0.03 0.28 0.31 2 -0.73 100 102
GAB2 0.031 0.035 -10000 0 -0.42 5 5
SMPD1 0.013 0.1 -10000 0 -0.94 8 8
SGMS1 -0.027 0.22 -10000 0 -0.94 47 47
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.008 0.038 -10000 0 -0.34 9 9
CALM1 0.032 0.006 -10000 0 -10000 0 0
cell proliferation -0.026 0.24 0.32 5 -0.76 63 68
EIF3A 0.031 0.008 -10000 0 -10000 0 0
PI3K 0.044 0.05 -10000 0 -0.37 11 11
RPS6KB1 -0.021 0.22 -10000 0 -1.1 35 35
mol:sphingomyelin -0.039 0.22 -10000 0 -0.94 47 47
natural killer cell activation 0 0.003 -10000 0 -0.017 10 10
JAK3 0.006 0.13 -10000 0 -0.52 46 46
PIK3R1 0.032 0.039 -10000 0 -0.46 5 5
JAK1 0.033 0.009 -10000 0 -10000 0 0
NFKB1 0.032 0.02 -10000 0 -0.55 1 1
MYC -0.025 0.28 0.49 5 -0.82 75 80
MYB -0.017 0.22 -10000 0 -1.4 20 20
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.038 0.27 -10000 0 -0.71 101 101
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.013 0.21 -10000 0 -0.96 35 35
mol:PI-3-4-5-P3 -0.034 0.26 -10000 0 -0.68 100 100
Rac1/GDP 0.025 0.036 -10000 0 -0.31 7 7
T cell proliferation -0.026 0.24 0.26 4 -0.64 94 98
SHC1 0.031 0.015 -10000 0 -0.32 1 1
RAC1 0.029 0.011 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.002 0.012 -10000 0 -0.04 61 61
PRKCZ -0.031 0.25 -10000 0 -0.68 93 93
NF kappa B1 p50/RelA 0.012 0.23 0.31 1 -0.59 84 85
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.029 0.22 -10000 0 -0.68 81 81
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
RELA 0.033 0.004 -10000 0 -10000 0 0
IL2RA -0.032 0.16 -10000 0 -0.43 119 119
IL2RB -0.004 0.14 -10000 0 -0.51 62 62
TERT -0.006 0.098 -10000 0 -0.32 78 78
E2F1 0.008 0.1 -10000 0 -0.51 23 23
SOS1 0.032 0.008 -10000 0 -10000 0 0
RPS6 0.032 0.017 -10000 0 -0.32 2 2
mol:cAMP -0.001 0.005 0.018 54 -10000 0 54
PTPN11 0.031 0.021 -10000 0 -0.56 1 1
IL2RG -0.014 0.16 -10000 0 -0.48 84 84
actin cytoskeleton organization -0.026 0.24 0.26 4 -0.64 94 98
GRB2 0.03 0.011 -10000 0 -10000 0 0
IL2 0.021 0.042 -10000 0 -0.32 12 12
PIK3CA 0.03 0.049 -10000 0 -0.55 6 6
Rac1/GTP 0.052 0.045 -10000 0 -0.3 7 7
LCK -0.012 0.15 -10000 0 -0.48 78 78
BCL2 -0.009 0.22 0.48 2 -0.63 72 74
Canonical Wnt signaling pathway

Figure S62.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S62.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.033 0.026 0.26 2 -10000 0 2
AES 0.034 0.029 -10000 0 -0.55 1 1
FBXW11 0.031 0.008 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0.008 0.12 -10000 0 -0.4 66 66
SMAD4 0.032 0.006 -10000 0 -10000 0 0
DKK2 -0.043 0.18 -10000 0 -0.43 142 142
TLE1 0.033 0.034 0.24 1 -0.55 2 3
MACF1 0.032 0.009 -10000 0 -10000 0 0
CTNNB1 0.024 0.14 0.4 45 -0.41 13 58
WIF1 0 0.068 -10000 0 -0.32 34 34
beta catenin/RanBP3 0.014 0.13 0.41 48 -0.42 7 55
KREMEN2 0.006 0.093 -10000 0 -0.34 55 55
DKK1 -0.033 0.16 -10000 0 -0.43 119 119
beta catenin/beta TrCP1 0.032 0.13 0.4 34 -0.42 8 42
FZD1 -0.014 0.15 -10000 0 -0.55 65 65
AXIN2 0.029 0.21 0.7 35 -1.5 7 42
AXIN1 0.03 0.029 -10000 0 -0.55 2 2
RAN 0.032 0.007 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.026 0.082 -10000 0 -0.58 13 13
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.026 0.18 0.3 2 -0.47 94 96
Axin1/APC/GSK3 0.029 0.082 0.29 13 -0.4 7 20
Axin1/APC/GSK3/beta catenin/Macf1 0.024 0.13 0.38 20 -0.54 9 29
HNF1A -0.014 0.16 -10000 0 -0.55 71 71
CTBP1 0.034 0.02 0.25 1 -10000 0 1
MYC -0.048 0.33 0.64 11 -1.6 36 47
RANBP3 0.032 0.02 -10000 0 -0.55 1 1
DKK2/LRP6/Kremen 2 -0.004 0.13 -10000 0 -0.35 73 73
NKD1 -0.003 0.11 -10000 0 -0.37 71 71
TCF4 -0.024 0.17 -10000 0 -0.52 90 90
TCF3 0.035 0.02 0.25 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.037 0.11 -10000 0 -0.32 67 67
Ran/GTP 0.024 0.006 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.032 0.18 0.46 37 -0.46 63 100
LEF1 -0.072 0.21 -10000 0 -0.45 192 192
DVL1 0.014 0.078 -10000 0 -0.32 31 31
CSNK2A1 0.032 0.008 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.034 0.21 0.3 4 -0.52 95 99
DKK1/LRP6/Kremen 2 0.002 0.12 -10000 0 -0.36 54 54
LRP6 0.031 0.021 -10000 0 -0.55 1 1
CSNK1A1 0.035 0.028 0.28 2 -10000 0 2
NLK 0.029 0.012 -10000 0 -10000 0 0
CCND1 -0.064 0.35 0.82 2 -1.6 42 44
WNT1 0.022 0.049 -10000 0 -0.33 15 15
GSK3A 0.033 0.004 -10000 0 -10000 0 0
GSK3B 0.032 0.007 -10000 0 -10000 0 0
FRAT1 0.03 0.014 -10000 0 -0.32 1 1
PPP2R5D 0.009 0.13 0.28 17 -0.43 54 71
APC 0.037 0.16 0.5 51 -0.3 67 118
WNT1/LRP6/FZD1 0.011 0.083 0.22 3 -0.26 58 61
CREBBP 0.032 0.018 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.023 0.071 -10000 0 -0.55 13 13
ANTXR2 0.01 0.11 -10000 0 -0.54 35 35
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.017 -10000 0 -0.075 44 44
monocyte activation -0.072 0.2 -10000 0 -0.47 169 169
MAP2K2 0.013 0.066 -10000 0 -0.66 8 8
MAP2K1 -0.004 0.015 -10000 0 -0.1 3 3
MAP2K7 -0.005 0.021 -10000 0 -0.3 2 2
MAP2K6 -0.004 0.03 0.12 5 -0.25 9 14
CYAA -0.014 0.069 -10000 0 -0.31 43 43
MAP2K4 -0.002 0.015 0.12 4 -0.1 2 6
IL1B -0.016 0.083 0.24 1 -0.26 67 68
Channel 0.022 0.083 -10000 0 -0.33 43 43
NLRP1 -0.009 0.044 0.12 1 -0.24 25 26
CALM1 0.032 0.006 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.002 0.071 -10000 0 -0.41 23 23
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.017 0.075 44 -10000 0 44
MAPK3 -0.003 0.02 0.12 6 -0.15 4 10
MAPK1 -0.004 0.018 -10000 0 -0.3 1 1
PGR -0.054 0.11 -10000 0 -0.25 180 180
PA/Cellular Receptors 0.022 0.09 -10000 0 -0.36 43 43
apoptosis -0.003 0.017 -10000 0 -0.075 44 44
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.022 0.078 -10000 0 -0.31 43 43
macrophage activation -0.004 0.021 0.11 4 -0.28 2 6
TNF -0.011 0.14 -10000 0 -0.43 80 80
VCAM1 -0.072 0.2 -10000 0 -0.47 168 168
platelet activation 0.002 0.071 -10000 0 -0.41 23 23
MAPKKK cascade -0.007 0.038 0.14 7 -0.13 55 62
IL18 -0.009 0.065 0.11 36 -0.23 50 86
negative regulation of macrophage activation -0.003 0.017 -10000 0 -0.075 44 44
LEF -0.003 0.017 -10000 0 -0.075 44 44
CASP1 -0.005 0.041 0.051 1 -0.16 38 39
mol:cAMP 0.002 0.071 -10000 0 -0.41 23 23
necrosis -0.003 0.017 -10000 0 -0.075 44 44
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.022 0.078 -10000 0 -0.31 43 43
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.033 0.004 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.005 0.15 -9999 0 -0.42 55 55
Syndecan-3/Neurocan 0.006 0.1 -9999 0 -0.37 56 56
POMC 0.014 0.087 -9999 0 -0.4 35 35
EGFR 0.008 0.1 -9999 0 -0.47 36 36
Syndecan-3/EGFR -0.001 0.12 -9999 0 -0.38 69 69
AGRP 0.016 0.059 -9999 0 -0.32 26 26
NCSTN 0.03 0.021 -9999 0 -0.55 1 1
PSENEN 0.033 0.003 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.029 0.048 -9999 0 -0.55 6 6
APH1A 0.031 0.008 -9999 0 -10000 0 0
NCAN 0.018 0.06 -9999 0 -0.32 27 27
long-term memory 0.029 0.1 -9999 0 -0.33 56 56
Syndecan-3/IL8 -0.024 0.14 -9999 0 -0.36 99 99
PSEN1 0.032 0.006 -9999 0 -10000 0 0
Src/Cortactin 0.046 0.013 -9999 0 -10000 0 0
FYN 0.025 0.056 -9999 0 -0.55 8 8
limb bud formation -0.005 0.096 -9999 0 -0.38 52 52
MC4R 0.016 0.045 -9999 0 -0.32 15 15
SRC 0.031 0.008 -9999 0 -10000 0 0
PTN -0.054 0.19 -9999 0 -0.46 147 147
FGFR/FGF/Syndecan-3 -0.005 0.097 -9999 0 -0.38 52 52
neuron projection morphogenesis -0.019 0.15 -9999 0 -0.42 52 52
Syndecan-3/AgRP 0.005 0.1 -9999 0 -0.38 52 52
Syndecan-3/AgRP/MC4R 0.013 0.11 -9999 0 -0.37 52 52
Fyn/Cortactin 0.041 0.045 -9999 0 -0.4 8 8
SDC3 -0.005 0.098 -9999 0 -0.39 52 52
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.023 0.14 -9999 0 -0.35 99 99
IL8 -0.043 0.17 -9999 0 -0.4 152 152
Syndecan-3/Fyn/Cortactin 0.03 0.1 -9999 0 -0.34 56 56
Syndecan-3/CASK -0.007 0.095 -9999 0 -0.36 56 56
alpha-MSH/MC4R 0.021 0.075 -9999 0 -0.27 49 49
Gamma Secretase 0.086 0.045 -9999 0 -0.29 7 7
Coregulation of Androgen receptor activity

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.024 0.04 -9999 0 -0.5 4 4
SVIL 0.027 0.025 -9999 0 -0.55 1 1
ZNF318 0.034 0.015 -9999 0 -10000 0 0
JMJD2C -0.002 0.016 -9999 0 -0.055 63 63
T-DHT/AR/Ubc9 -0.037 0.14 -9999 0 -0.38 109 109
CARM1 0.032 0.02 -9999 0 -0.55 1 1
PRDX1 0.031 0.014 -9999 0 -0.32 1 1
PELP1 0.03 0.011 -9999 0 -10000 0 0
CTNNB1 0.028 0.013 -9999 0 -10000 0 0
AKT1 0.033 0.021 -9999 0 -0.55 1 1
PTK2B 0.031 0.008 -9999 0 -10000 0 0
MED1 0.03 0.011 -9999 0 -10000 0 0
MAK 0.017 0.084 -9999 0 -0.38 34 34
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.017 0.069 -9999 0 -0.56 12 12
GSN 0.025 0.027 -9999 0 -0.55 1 1
NCOA2 -0.005 0.14 -9999 0 -0.55 55 55
NCOA6 0.026 0.017 -9999 0 -10000 0 0
DNA-PK 0.063 0.025 -9999 0 -10000 0 0
NCOA4 0.03 0.021 -9999 0 -0.55 1 1
PIAS3 0.029 0.011 -9999 0 -10000 0 0
cell proliferation -0.04 0.17 -9999 0 -0.6 65 65
XRCC5 0.032 0.008 -9999 0 -10000 0 0
UBE3A 0.025 0.022 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.056 0.17 -9999 0 -0.4 140 140
FHL2 -0.061 0.26 -9999 0 -0.89 70 70
RANBP9 0.027 0.016 -9999 0 -10000 0 0
JMJD1A -0.024 0.052 -9999 0 -0.11 211 211
CDK6 0.026 0.039 -9999 0 -0.46 5 5
TGFB1I1 -0.01 0.14 -9999 0 -0.54 56 56
T-DHT/AR/CyclinD1 -0.055 0.16 -9999 0 -0.38 149 149
XRCC6 0.033 0.007 -9999 0 -10000 0 0
T-DHT/AR -0.056 0.18 -9999 0 -0.39 143 143
CTDSP1 0.03 0.021 -9999 0 -0.55 1 1
CTDSP2 0.035 0.013 -9999 0 -10000 0 0
BRCA1 0.022 0.049 -9999 0 -0.52 6 6
TCF4 -0.023 0.17 -9999 0 -0.53 90 90
CDKN2A 0 0.13 -9999 0 -0.5 54 54
SRF 0.031 0.035 -9999 0 -10000 0 0
NKX3-1 -0.063 0.11 -9999 0 -0.21 267 267
KLK3 -0.011 0.087 -9999 0 -10000 0 0
TMF1 0.028 0.04 -9999 0 -0.55 4 4
HNRNPA1 0.033 0.009 -9999 0 -10000 0 0
AOF2 -0.002 0.006 -9999 0 -10000 0 0
APPL1 0.02 0.018 -9999 0 -0.4 1 1
T-DHT/AR/Caspase 8 -0.036 0.14 -9999 0 -0.38 112 112
AR -0.07 0.2 -9999 0 -0.55 120 120
UBA3 0.03 0.022 -9999 0 -0.56 1 1
PATZ1 0.033 0.008 -9999 0 -10000 0 0
PAWR 0.03 0.029 -9999 0 -0.55 2 2
PRKDC 0.033 0.008 -9999 0 -10000 0 0
PA2G4 0.033 0.009 -9999 0 -10000 0 0
UBE2I 0.031 0.008 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.032 0.13 -9999 0 -0.34 112 112
RPS6KA3 0.026 0.027 -9999 0 -0.56 1 1
T-DHT/AR/ARA70 -0.038 0.15 -9999 0 -0.38 114 114
LATS2 0.033 0.009 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.031 0.13 -9999 0 -0.34 113 113
Cyclin D3/CDK11 p58 0.023 0.006 -9999 0 -10000 0 0
VAV3 0.02 0.073 -9999 0 -0.55 14 14
KLK2 -0.044 0.11 -9999 0 -0.4 47 47
CASP8 0.031 0.021 -9999 0 -0.54 1 1
T-DHT/AR/TIF2/CARM1 -0.043 0.17 -9999 0 -0.4 136 136
TMPRSS2 -0.19 0.36 -9999 0 -0.83 184 184
CCND1 0.006 0.12 -9999 0 -0.54 41 41
PIAS1 0.025 0.022 -9999 0 -10000 0 0
mol:T-DHT -0.016 0.032 -9999 0 -0.071 188 188
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.022 0.039 -9999 0 -0.55 2 2
T-DHT/AR/CDK6 -0.04 0.14 -9999 0 -0.38 105 105
CMTM2 0.011 0.089 -9999 0 -0.38 41 41
SNURF 0.005 0.12 -9999 0 -0.55 40 40
ZMIZ1 0.009 0.047 -9999 0 -0.55 1 1
CCND3 0.031 0.009 -9999 0 -10000 0 0
TGIF1 0.033 0.007 -9999 0 -10000 0 0
FKBP4 0.026 0.017 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.012 0.063 -10000 0 -0.25 39 39
epithelial cell differentiation 0.037 0.081 -10000 0 -0.29 35 35
CYFIP2 0.026 0.05 -10000 0 -0.45 9 9
ENAH 0.028 0.14 0.5 46 -0.34 15 61
EGFR 0.008 0.1 -10000 0 -0.47 36 36
EPHA2 0.027 0.049 -10000 0 -0.55 6 6
MYO6 0.027 0.1 0.36 31 -0.3 36 67
CTNNB1 0.03 0.01 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.056 0.04 -10000 0 -0.34 5 5
AQP5 0.003 0.076 0.31 2 -0.58 2 4
CTNND1 0.033 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.026 0.1 0.36 29 -0.28 37 66
regulation of calcium-dependent cell-cell adhesion -0.034 0.14 0.36 10 -0.32 123 133
EGF -0.059 0.19 -10000 0 -0.41 181 181
NCKAP1 0.031 0.007 -10000 0 -10000 0 0
AQP3 -0.02 0.15 0.35 1 -0.53 59 60
cortical microtubule organization 0.037 0.081 -10000 0 -0.29 35 35
GO:0000145 0.013 0.097 0.31 38 -0.26 37 75
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.043 0.084 -10000 0 -0.3 35 35
MLLT4 0.031 0.009 -10000 0 -10000 0 0
ARF6/GDP -0.013 0.074 -10000 0 -0.45 13 13
ARF6 0.032 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.074 -10000 0 -0.34 22 22
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.006 0.077 0.35 4 -0.34 6 10
PVRL2 0.032 0.02 -10000 0 -0.55 1 1
ZYX 0.01 0.081 0.35 6 -0.28 36 42
ARF6/GTP 0.066 0.073 -10000 0 -0.32 21 21
CDH1 -0.005 0.13 -10000 0 -0.44 66 66
EGFR/EGFR/EGF/EGF -0.025 0.14 -10000 0 -0.31 125 125
RhoA/GDP 0.04 0.079 -10000 0 -0.28 35 35
actin cytoskeleton organization 0.019 0.098 0.35 28 -0.29 35 63
IGF-1R heterotetramer 0.031 0.034 -10000 0 -0.55 3 3
GIT1 0.028 0.029 -10000 0 -0.55 2 2
IGF1R 0.031 0.034 -10000 0 -0.55 3 3
IGF1 -0.008 0.13 -10000 0 -0.4 80 80
DIAPH1 0.029 0.14 -10000 0 -0.64 15 15
Wnt receptor signaling pathway -0.037 0.081 0.29 35 -10000 0 35
RHOA 0.03 0.009 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.075 -10000 0 -0.46 13 13
CTNNA1 0.031 0.008 -10000 0 -10000 0 0
VCL 0.019 0.099 0.36 28 -0.3 35 63
EFNA1 0.021 0.076 -10000 0 -0.55 15 15
LPP 0.005 0.086 0.25 15 -0.29 40 55
Ephrin A1/EPHA2 0.025 0.097 -10000 0 -0.33 47 47
SEC6/SEC8 -0.001 0.058 -10000 0 -10000 0 0
MGAT3 -0.034 0.14 0.36 10 -0.32 123 133
HGF/MET 0.002 0.12 -10000 0 -0.32 76 76
HGF -0.024 0.16 -10000 0 -0.46 95 95
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.012 0.063 -10000 0 -0.25 39 39
actin cable formation 0.057 0.17 0.51 69 -0.32 13 82
KIAA1543 0.011 0.11 0.32 37 -0.3 41 78
KIFC3 0.003 0.094 0.35 2 -0.3 58 60
NCK1 0.03 0.029 -10000 0 -0.55 2 2
EXOC3 0.031 0.021 -10000 0 -0.55 1 1
ACTN1 0.022 0.1 0.36 26 -0.29 42 68
NCK1/GIT1 0.041 0.032 -10000 0 -0.4 3 3
mol:GDP 0.037 0.081 -10000 0 -0.29 35 35
EXOC4 0.029 0.011 -10000 0 -10000 0 0
STX4 0.011 0.079 0.35 3 -0.28 36 39
PIP5K1C 0.026 0.1 0.36 29 -0.28 37 66
LIMA1 0.025 0.05 -10000 0 -0.33 16 16
ABI1 0.031 0.008 -10000 0 -10000 0 0
ROCK1 0.037 0.15 0.51 50 -0.4 15 65
adherens junction assembly 0.019 0.15 0.4 51 -0.49 29 80
IGF-1R heterotetramer/IGF1 0.012 0.11 -10000 0 -0.3 62 62
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.044 0.02 -10000 0 -0.4 1 1
MET 0.025 0.045 -10000 0 -0.55 5 5
PLEKHA7 0.024 0.11 0.37 28 -0.31 41 69
mol:GTP 0.058 0.073 -10000 0 -0.34 22 22
establishment of epithelial cell apical/basal polarity 0.029 0.1 0.39 24 -0.49 1 25
cortical actin cytoskeleton stabilization 0.012 0.063 -10000 0 -0.25 39 39
regulation of cell-cell adhesion 0.019 0.098 0.35 28 -0.29 35 63
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.012 0.063 -10000 0 -0.25 39 39
ErbB2/ErbB3 signaling events

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.004 0.019 -10000 0 -0.35 2 2
RAS family/GTP 0.001 0.15 0.26 1 -0.49 41 42
NFATC4 -0.02 0.11 0.32 26 -0.35 20 46
ERBB2IP 0.031 0.021 -10000 0 -0.54 1 1
HSP90 (dimer) 0.032 0.006 -10000 0 -10000 0 0
mammary gland morphogenesis -0.012 0.11 -10000 0 -0.33 68 68
JUN 0.01 0.11 0.34 22 -0.41 26 48
HRAS 0.029 0.038 -10000 0 -0.46 5 5
DOCK7 -0.024 0.1 0.28 1 -0.43 17 18
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.007 0.12 -10000 0 -0.35 82 82
AKT1 0.008 0.016 -10000 0 -0.4 1 1
BAD 0.004 0.029 -10000 0 -0.38 4 4
MAPK10 -0.003 0.081 0.2 40 -0.27 17 57
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.012 0.12 -10000 0 -0.35 68 68
RAF1 -0.021 0.14 0.36 22 -0.5 36 58
ErbB2/ErbB3/neuregulin 2 -0.003 0.12 0.24 1 -0.39 56 57
STAT3 -0.001 0.19 -10000 0 -0.91 37 37
cell migration 0.017 0.12 0.32 66 -0.25 22 88
mol:PI-3-4-5-P3 -0.001 0.003 -10000 0 -10000 0 0
cell proliferation -0.08 0.26 0.46 14 -0.63 115 129
FOS -0.053 0.2 0.43 16 -0.46 88 104
NRAS 0.031 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.11 -10000 0 -0.33 68 68
MAPK3 -0.056 0.22 0.43 16 -0.51 100 116
MAPK1 -0.063 0.23 0.44 18 -0.54 108 126
JAK2 -0.023 0.1 0.28 1 -0.41 20 21
NF2 0.013 0.036 -10000 0 -0.7 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.021 0.15 0.23 2 -0.4 93 95
NRG1 -0.013 0.15 -10000 0 -0.49 75 75
GRB2/SOS1 0.043 0.016 -10000 0 -10000 0 0
MAPK8 -0.013 0.11 0.24 1 -0.32 78 79
MAPK9 0.001 0.074 0.21 39 -0.23 11 50
ERBB2 -0.02 0.03 0.37 1 -0.38 4 5
ERBB3 0.004 0.12 -10000 0 -0.55 41 41
SHC1 0.03 0.014 -10000 0 -0.32 1 1
RAC1 0.029 0.011 -10000 0 -10000 0 0
apoptosis 0.001 0.032 0.46 3 -0.15 2 5
STAT3 (dimer) 0 0.19 -10000 0 -0.89 37 37
RNF41 -0.002 0.017 -10000 0 -0.32 2 2
FRAP1 0.002 0.013 -10000 0 -0.34 1 1
RAC1-CDC42/GTP -0.013 0.073 -10000 0 -0.32 14 14
ErbB2/ErbB2/HSP90 (dimer) 0.015 0.029 0.27 1 -0.36 3 4
CHRNA1 -0.083 0.26 0.4 17 -0.65 115 132
myelination -0.017 0.13 0.42 35 -0.36 16 51
PPP3CB -0.021 0.095 0.27 1 -0.4 16 17
KRAS 0.031 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.005 0.14 0.27 1 -0.46 46 47
NRG2 -0.009 0.12 -10000 0 -0.38 85 85
mol:GDP -0.021 0.15 0.23 2 -0.4 93 95
SOS1 0.031 0.007 -10000 0 -10000 0 0
MAP2K2 -0.032 0.14 0.33 20 -0.48 38 58
SRC 0.031 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.023 0.1 0.28 1 -0.44 17 18
MAP2K1 -0.058 0.2 0.43 9 -0.6 39 48
heart morphogenesis -0.012 0.11 -10000 0 -0.33 68 68
RAS family/GDP 0.013 0.15 0.28 1 -0.49 41 42
GRB2 0.029 0.011 -10000 0 -10000 0 0
PRKACA 0.015 0.038 -10000 0 -0.74 2 2
CHRNE 0.01 0.049 0.15 27 -0.19 29 56
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
activation of caspase activity -0.008 0.016 0.4 1 -10000 0 1
nervous system development -0.012 0.11 -10000 0 -0.33 68 68
CDC42 0.031 0.008 -10000 0 -10000 0 0
Osteopontin-mediated events

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.011 0.12 -10000 0 -0.34 64 64
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.15 0.38 48 -0.5 25 73
alphaV/beta3 Integrin/Osteopontin/Src 0.024 0.1 -10000 0 -0.37 41 41
AP1 0.01 0.17 0.36 3 -0.5 45 48
ILK 0.008 0.11 -10000 0 -0.35 56 56
bone resorption 0.009 0.14 0.33 13 -0.49 28 41
PTK2B 0.031 0.008 -10000 0 -10000 0 0
PYK2/p130Cas 0.046 0.13 -10000 0 -0.41 27 27
ITGAV 0.03 0.05 -10000 0 -0.51 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.018 0.1 -10000 0 -0.35 62 62
alphaV/beta3 Integrin/Osteopontin 0.027 0.13 -10000 0 -0.38 60 60
MAP3K1 0.007 0.11 -10000 0 -0.35 58 58
JUN 0.029 0.03 -10000 0 -0.38 4 4
MAPK3 -0.01 0.11 -10000 0 -0.45 29 29
MAPK1 -0.01 0.11 -10000 0 -0.44 31 31
Rac1/GDP 0.021 0.008 -10000 0 -10000 0 0
NFKB1 0.032 0.02 -10000 0 -0.55 1 1
MAPK8 0.003 0.12 0.37 9 -0.35 58 67
ITGB3 0.004 0.12 -10000 0 -0.45 51 51
NFKBIA -0.013 0.12 -10000 0 -0.5 30 30
FOS -0.026 0.16 -10000 0 -0.42 112 112
CD44 0.014 0.095 -10000 0 -0.44 35 35
CHUK 0.03 0.021 -10000 0 -0.55 1 1
PLAU -0.002 0.21 0.53 15 -0.99 20 35
NF kappa B1 p50/RelA 0.033 0.13 -10000 0 -0.5 20 20
BCAR1 0.029 0.035 -10000 0 -0.55 3 3
RELA 0.033 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.025 0.096 -10000 0 -0.32 55 55
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.003 0.12 -10000 0 -0.36 70 70
VAV3 -0.002 0.13 0.37 9 -0.34 78 87
MAP3K14 -0.004 0.12 -10000 0 -0.36 67 67
ROCK2 0.013 0.1 -10000 0 -0.55 27 27
SPP1 0.003 0.12 -10000 0 -0.42 63 63
RAC1 0.029 0.011 -10000 0 -10000 0 0
Rac1/GTP 0 0.11 0.35 3 -0.31 70 73
MMP2 -0.022 0.15 0.39 3 -0.51 39 42
Syndecan-2-mediated signaling events

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.016 0.12 -10000 0 -0.3 131 131
EPHB2 0.012 0.087 -10000 0 -0.36 42 42
Syndecan-2/TACI 0.011 0.069 -10000 0 -0.33 14 14
LAMA1 -0.014 0.15 -10000 0 -0.49 77 77
Syndecan-2/alpha2 ITGB1 0.036 0.095 -10000 0 -0.33 33 33
HRAS 0.03 0.038 -10000 0 -0.46 5 5
Syndecan-2/CASK 0.007 0.042 -10000 0 -0.29 16 16
ITGA5 0.016 0.091 -10000 0 -0.5 25 25
BAX 0.004 0.078 -10000 0 -0.99 3 3
EPB41 0.029 0.027 -10000 0 -0.4 3 3
positive regulation of cell-cell adhesion 0.028 0.041 -10000 0 -0.26 16 16
LAMA3 0.003 0.1 -10000 0 -0.34 68 68
EZR 0.03 0.021 -10000 0 -0.55 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.02 0.072 -10000 0 -0.53 14 14
Syndecan-2/MMP2 0.016 0.077 -10000 0 -0.26 57 57
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.034 0.071 -10000 0 -0.38 24 24
dendrite morphogenesis 0.018 0.069 -10000 0 -0.23 54 54
Syndecan-2/GM-CSF 0.019 0.053 -10000 0 -0.3 15 15
determination of left/right symmetry 0.011 0.049 -10000 0 -0.34 16 16
Syndecan-2/PKC delta 0.016 0.067 -10000 0 -0.21 61 61
GNB2L1 0.031 0.008 -10000 0 -10000 0 0
MAPK3 0.011 0.052 0.19 10 -0.34 10 20
MAPK1 0.012 0.052 0.19 12 -0.31 12 24
Syndecan-2/RACK1 0.042 0.052 -10000 0 -0.32 13 13
NF1 0.03 0.01 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.011 0.049 -10000 0 -0.34 16 16
ITGA2 0.017 0.091 -10000 0 -0.52 24 24
MAPK8 0.009 0.059 -10000 0 -0.35 21 21
Syndecan-2/alpha2/beta1 Integrin 0.028 0.12 -10000 0 -0.32 75 75
Syndecan-2/Kininogen -0.038 0.13 -10000 0 -0.34 83 83
ITGB1 0.031 0.008 -10000 0 -10000 0 0
SRC 0.027 0.057 0.35 1 -0.31 13 14
Syndecan-2/CASK/Protein 4.1 0.025 0.044 -10000 0 -0.3 13 13
extracellular matrix organization 0.023 0.072 -10000 0 -0.34 30 30
actin cytoskeleton reorganization -0.016 0.12 -10000 0 -0.3 131 131
Syndecan-2/Caveolin-2/Ras 0.035 0.073 -10000 0 -0.34 25 25
Syndecan-2/Laminin alpha3 0.013 0.076 -10000 0 -0.22 76 76
Syndecan-2/RasGAP 0.055 0.058 -10000 0 -0.32 16 16
alpha5/beta1 Integrin 0.033 0.07 -10000 0 -0.36 25 25
PRKCD 0.009 0.084 -10000 0 -0.32 53 53
Syndecan-2 dimer 0.018 0.069 -10000 0 -0.23 54 54
GO:0007205 0.003 0.006 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.043 0.058 -10000 0 -0.3 16 16
RHOA 0.03 0.009 -10000 0 -10000 0 0
SDCBP 0.032 0.006 -10000 0 -10000 0 0
TNFRSF13B 0.003 0.088 -10000 0 -0.32 58 58
RASA1 0.03 0.034 -10000 0 -0.55 3 3
alpha2/beta1 Integrin 0.034 0.071 -10000 0 -0.38 24 24
Syndecan-2/Synbindin 0.03 0.045 -10000 0 -0.33 12 12
TGFB1 0.021 0.082 -10000 0 -0.53 19 19
CASP3 0.009 0.061 0.2 12 -0.31 14 26
FN1 -0.042 0.18 -10000 0 -0.48 127 127
Syndecan-2/IL8 -0.016 0.12 -10000 0 -0.24 163 163
SDC2 0.011 0.05 -10000 0 -0.34 16 16
KNG1 -0.082 0.19 -10000 0 -0.39 230 230
Syndecan-2/Neurofibromin 0.027 0.045 -10000 0 -0.29 14 14
TRAPPC4 0.032 0.005 -10000 0 -10000 0 0
CSF2 0.017 0.048 -10000 0 -0.32 17 17
Syndecan-2/TGFB1 0.023 0.072 -10000 0 -0.34 30 30
Syndecan-2/Syntenin/PI-4-5-P2 0.028 0.041 -10000 0 -0.26 16 16
Syndecan-2/Ezrin 0.042 0.049 -10000 0 -0.31 12 12
PRKACA 0.019 0.045 0.2 14 -0.31 10 24
angiogenesis -0.016 0.12 -10000 0 -0.24 163 163
MMP2 0.009 0.097 -10000 0 -0.39 46 46
IL8 -0.043 0.17 -10000 0 -0.4 152 152
calcineurin-NFAT signaling pathway 0.011 0.068 -10000 0 -0.33 14 14
TRAIL signaling pathway

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.008 0.15 -10000 0 -0.55 59 59
positive regulation of NF-kappaB transcription factor activity 0.01 0.12 -10000 0 -0.42 64 64
MAP2K4 0.01 0.11 0.22 21 -0.46 36 57
IKBKB 0.032 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.031 0.021 -10000 0 -0.55 1 1
TNFRSF10A 0.009 0.11 -10000 0 -0.55 34 34
SMPD1 0.002 0.066 -10000 0 -0.23 59 59
IKBKG 0.031 0.034 -10000 0 -0.55 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.025 0.06 -10000 0 -0.53 10 10
TRAIL/TRAILR2 0.014 0.11 -10000 0 -0.4 60 60
TRAIL/TRAILR3 0.006 0.13 -10000 0 -0.41 73 73
TRAIL/TRAILR1 -0.002 0.15 -10000 0 -0.46 79 79
TRAIL/TRAILR4 0.01 0.12 -10000 0 -0.42 64 64
TRAIL/TRAILR1/DAP3/GTP 0.018 0.12 -10000 0 -0.36 78 78
IKK complex 0.008 0.1 -10000 0 -0.45 32 32
RIPK1 0.031 0.008 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.023 0.006 -10000 0 -10000 0 0
MAPK3 -0.009 0.1 -10000 0 -0.4 58 58
MAP3K1 0.007 0.12 -10000 0 -0.49 39 39
TRAILR4 (trimer) 0.025 0.06 -10000 0 -0.53 10 10
TRADD 0.03 0.021 -10000 0 -0.55 1 1
TRAILR1 (trimer) 0.009 0.11 -10000 0 -0.55 34 34
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0 0.13 -10000 0 -0.38 78 78
CFLAR 0.031 0.007 -10000 0 -10000 0 0
MAPK1 -0.009 0.1 -10000 0 -0.4 57 57
TRAIL/TRAILR1/FADD/TRADD/RIP 0.046 0.13 -10000 0 -0.34 76 76
mol:ceramide 0.002 0.066 -10000 0 -0.23 59 59
FADD 0.033 0.004 -10000 0 -10000 0 0
MAPK8 0.018 0.098 0.29 6 -0.44 23 29
TRAF2 0.031 0.028 -10000 0 -0.55 2 2
TRAILR3 (trimer) 0.019 0.079 -10000 0 -0.45 23 23
CHUK 0.03 0.021 -10000 0 -0.55 1 1
TRAIL/TRAILR1/FADD 0.019 0.14 -10000 0 -0.4 78 78
DAP3 0.031 0.008 -10000 0 -10000 0 0
CASP10 -0.012 0.13 0.34 4 -0.44 55 59
JNK cascade 0.01 0.12 -10000 0 -0.42 64 64
TRAIL (trimer) -0.008 0.14 -10000 0 -0.55 59 59
TNFRSF10C 0.019 0.079 -10000 0 -0.45 23 23
TRAIL/TRAILR1/DAP3/GTP/FADD 0.033 0.12 -10000 0 -0.34 77 77
TRAIL/TRAILR2/FADD 0.033 0.1 -10000 0 -0.34 58 58
cell death 0.002 0.066 -10000 0 -0.23 59 59
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.011 0.098 -10000 0 -0.33 60 60
TRAILR2 (trimer) 0.031 0.021 -10000 0 -0.55 1 1
CASP8 -0.006 0.14 -10000 0 -0.7 33 33
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.058 0.099 -10000 0 -0.28 59 59
IL2 signaling events mediated by STAT5

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.031 0.035 -10000 0 -0.41 5 5
ELF1 -0.004 0.11 -10000 0 -0.36 65 65
CCNA2 0.027 0.048 -10000 0 -0.36 13 13
PIK3CA 0.028 0.049 -10000 0 -0.55 6 6
JAK3 0.004 0.12 -10000 0 -0.52 46 46
PIK3R1 0.03 0.038 -10000 0 -0.46 5 5
JAK1 0.032 0.008 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.037 0.26 -10000 0 -0.71 95 95
SHC1 0.031 0.014 -10000 0 -0.32 1 1
SP1 0.017 0.092 -10000 0 -0.36 48 48
IL2RA -0.055 0.22 -10000 0 -0.76 67 67
IL2RB -0.006 0.14 -10000 0 -0.51 62 62
SOS1 0.032 0.007 -10000 0 -10000 0 0
IL2RG -0.015 0.15 -10000 0 -0.48 84 84
G1/S transition of mitotic cell cycle 0.003 0.22 0.37 26 -0.82 51 77
PTPN11 0.032 0.021 -10000 0 -0.55 1 1
CCND2 -0.019 0.19 -10000 0 -0.81 47 47
LCK -0.014 0.15 -10000 0 -0.48 78 78
GRB2 0.03 0.011 -10000 0 -10000 0 0
IL2 0.021 0.041 -10000 0 -0.32 12 12
CDK6 0.026 0.039 -10000 0 -0.46 5 5
CCND3 -0.019 0.21 0.36 1 -0.65 67 68
Ras signaling in the CD4+ TCR pathway

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.009 0.25 0.32 4 -0.75 66 70
MAP3K8 0.028 0.034 -10000 0 -0.43 4 4
FOS -0.013 0.23 0.31 10 -0.73 64 74
PRKCA 0.027 0.018 -10000 0 -0.32 1 1
PTPN7 0.003 0.1 -10000 0 -0.42 45 45
HRAS 0.029 0.038 -10000 0 -0.46 5 5
PRKCB 0 0.12 -10000 0 -0.53 46 46
NRAS 0.031 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.053 0.033 -10000 0 -0.31 3 3
MAPK3 -0.018 0.22 -10000 0 -0.77 58 58
MAP2K1 -0.001 0.16 -10000 0 -0.62 44 44
ELK1 0.03 0.015 -10000 0 -10000 0 0
BRAF -0.003 0.13 -10000 0 -0.58 39 39
mol:GTP -0.001 0.002 -10000 0 -0.005 111 111
MAPK1 -0.024 0.23 -10000 0 -0.74 66 66
RAF1 -0.004 0.13 -10000 0 -0.57 41 41
KRAS 0.031 0.008 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.034 0.17 -10000 0 -0.44 124 124
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.027 0.044 -10000 0 -0.41 8 8
TCEB1 0.032 0.006 -10000 0 -10000 0 0
HIF1A/p53 -0.008 0.11 0.3 5 -0.42 41 46
HIF1A -0.025 0.11 -10000 0 -0.42 49 49
COPS5 0.032 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.074 0.057 -10000 0 -0.33 8 8
FIH (dimer) 0.031 0.008 -10000 0 -10000 0 0
CDKN2A -0.001 0.13 -10000 0 -0.5 54 54
ARNT/IPAS -0.004 0.13 -10000 0 -0.31 122 122
HIF1AN 0.031 0.008 -10000 0 -10000 0 0
GNB2L1 0.031 0.008 -10000 0 -10000 0 0
HIF1A/ARNT -0.008 0.11 0.3 5 -0.43 40 45
CUL2 0.031 0.021 -10000 0 -0.55 1 1
OS9 0.032 0.007 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.055 0.036 -10000 0 -0.34 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.009 0.11 -10000 0 -0.44 40 40
PHD1-3/OS9 -0.017 0.16 -10000 0 -0.31 201 201
HIF1A/RACK1/Elongin B/Elongin C 0.009 0.12 -10000 0 -0.42 41 41
VHL 0.028 0.04 -10000 0 -0.55 4 4
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
HIF1A/JAB1 -0.01 0.11 -10000 0 -0.44 40 40
EGLN3 -0.11 0.25 -10000 0 -0.55 215 215
EGLN2 0.031 0.03 -10000 0 -0.47 3 3
EGLN1 0.031 0.008 -10000 0 -10000 0 0
TP53 0.029 0.022 -10000 0 -0.55 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.001 0.16 -10000 0 -0.55 67 67
ARNT 0.031 0.008 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.032 0.013 -10000 0 -0.32 1 1
HIF1A/p19ARF -0.023 0.13 0.29 4 -0.41 71 75
E-cadherin signaling events

Figure S74.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S74.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.028 0.097 -9999 0 -0.37 35 35
E-cadherin/beta catenin 0.015 0.099 -9999 0 -0.32 63 63
CTNNB1 0.03 0.01 -9999 0 -10000 0 0
JUP 0.025 0.053 -9999 0 -0.55 7 7
CDH1 -0.005 0.13 -9999 0 -0.44 66 66
Visual signal transduction: Cones

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin 0.013 0.096 -10000 0 -0.3 57 57
RGS9BP -0.001 0.12 -10000 0 -0.41 66 66
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.016 0.039 -10000 0 -0.32 11 11
mol:Na + 0.013 0.057 -10000 0 -0.18 47 47
mol:ADP -0.013 0.03 -10000 0 -0.22 14 14
GNAT2 0.029 0.009 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.011 0.14 -10000 0 -0.36 89 89
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.032 0.016 -10000 0 -0.18 1 1
GRK7 0.025 0.022 -10000 0 -0.32 3 3
CNGB3 0.002 0.083 -10000 0 -0.32 54 54
Cone Metarhodopsin II/X-Arrestin 0.017 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.032 0.068 0.26 1 -0.31 30 31
Cone PDE6 0.007 0.13 -10000 0 -0.32 88 88
Cone Metarhodopsin II 0.026 0.027 -10000 0 -0.17 14 14
Na + (4 Units) 0.013 0.082 -10000 0 -0.31 30 30
GNAT2/GDP 0.004 0.13 -10000 0 -0.31 88 88
GNB5 0.032 0.02 -10000 0 -0.55 1 1
mol:GMP (4 units) 0.003 0.03 0.18 4 -10000 0 4
Cone Transducin 0.015 0.1 -10000 0 -0.31 57 57
SLC24A2 -0.001 0.084 -10000 0 -0.32 57 57
GNB3/GNGT2 -0.004 0.12 -10000 0 -0.32 107 107
GNB3 -0.02 0.15 -10000 0 -0.42 98 98
GNAT2/GTP 0.021 0.007 -10000 0 -10000 0 0
CNGA3 0.014 0.052 -10000 0 -0.32 20 20
ARR3 0.022 0.006 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.013 0.058 -10000 0 -0.19 47 47
mol:Pi -0.012 0.14 -10000 0 -0.36 89 89
Cone CNG Channel 0.037 0.059 -10000 0 -0.29 1 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.001 0.084 -10000 0 -0.32 57 57
RGS9 -0.038 0.17 -10000 0 -0.44 127 127
PDE6C 0.022 0.022 -10000 0 -0.32 3 3
GNGT2 0.019 0.077 -10000 0 -0.52 17 17
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.021 0.018 -10000 0 -0.32 2 2
Lissencephaly gene (LIS1) in neuronal migration and development

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.032 0.006 -10000 0 -10000 0 0
VLDLR 0.029 0.042 -10000 0 -0.42 7 7
LRPAP1 0.031 0.028 -10000 0 -0.55 2 2
NUDC 0.031 0.008 -10000 0 -10000 0 0
RELN/LRP8 -0.043 0.15 -10000 0 -0.35 117 117
CaM/Ca2+ 0.024 0.005 -10000 0 -10000 0 0
KATNA1 0.031 0.009 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.035 0.14 -10000 0 -0.31 117 117
IQGAP1/CaM 0.047 0.01 -10000 0 -10000 0 0
DAB1 0.002 0.087 -10000 0 -0.32 59 59
IQGAP1 0.033 0.004 -10000 0 -10000 0 0
PLA2G7 -0.015 0.14 -10000 0 -0.45 84 84
CALM1 0.032 0.006 -10000 0 -10000 0 0
DYNLT1 0.031 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.036 0.051 -10000 0 -0.23 25 25
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.032 0.007 -10000 0 -10000 0 0
CDK5R1 0.029 0.02 -10000 0 -0.32 2 2
LIS1/Poliovirus Protein 3A 0.013 0.005 -10000 0 -10000 0 0
CDK5R2 -0.007 0.1 -10000 0 -0.32 86 86
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.055 0.15 -10000 0 -0.35 129 129
YWHAE 0.029 0.01 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.016 0.14 0.32 58 -0.35 11 69
MAP1B 0 0.049 -10000 0 -0.3 22 22
RAC1 0.017 0.009 -10000 0 -10000 0 0
p35/CDK5 -0.04 0.12 0.37 2 -0.28 103 105
RELN -0.1 0.21 -10000 0 -0.42 252 252
PAFAH/LIS1 0.007 0.088 -10000 0 -0.34 39 39
LIS1/CLIP170 0.034 0.014 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.024 0.097 -10000 0 -0.42 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.035 0.11 -10000 0 -0.37 30 30
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.033 0.13 0.31 43 -0.36 14 57
LIS1/IQGAP1 0.034 0.014 -10000 0 -10000 0 0
RHOA 0.017 0.009 -10000 0 -10000 0 0
PAFAH1B1 0.018 0.007 -10000 0 -10000 0 0
PAFAH1B3 0.029 0.043 -10000 0 -0.41 8 8
PAFAH1B2 0.023 0.076 -10000 0 -0.55 15 15
MAP1B/LIS1/Dynein heavy chain 0.028 0.039 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.01 0.14 0.32 52 -0.4 3 55
LRP8 0.02 0.063 -10000 0 -0.33 27 27
NDEL1/Katanin 60 -0.016 0.14 0.32 61 -0.35 11 72
P39/CDK5 -0.055 0.12 0.35 1 -0.31 65 66
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.033 0.015 -10000 0 -10000 0 0
CDK5 -0.056 0.11 0.38 1 -0.3 115 116
PPP2R5D 0.031 0.008 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.029 0.012 -10000 0 -10000 0 0
CSNK2A1 0.031 0.008 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.035 0.14 -10000 0 -0.3 125 125
RELN/VLDLR -0.028 0.15 -10000 0 -0.32 120 120
CDC42 0.018 0.008 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure S77.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S77.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.028 0.044 -10000 0 -0.55 5 5
Caspase 8 (4 units) 0.01 0.11 -10000 0 -0.35 25 25
NEF -0.016 0.048 -10000 0 -0.19 34 34
NFKBIA 0.022 0.04 -10000 0 -10000 0 0
BIRC3 -0.018 0.17 -10000 0 -0.51 83 83
CYCS -0.014 0.1 -10000 0 -0.45 23 23
RIPK1 0.031 0.008 -10000 0 -10000 0 0
CD247 -0.028 0.17 -10000 0 -0.62 61 61
MAP2K7 -0.017 0.21 0.34 1 -0.8 50 51
protein ubiquitination 0.03 0.14 0.34 52 -0.41 39 91
CRADD 0.032 0.007 -10000 0 -10000 0 0
DAXX 0.031 0.008 -10000 0 -10000 0 0
FAS 0.025 0.059 -10000 0 -0.55 9 9
BID -0.009 0.099 -10000 0 -0.46 14 14
NF-kappa-B/RelA/I kappa B alpha 0.041 0.1 -10000 0 -0.29 62 62
TRADD 0.03 0.021 -10000 0 -0.55 1 1
MAP3K5 0.029 0.029 -10000 0 -0.55 2 2
CFLAR 0.031 0.007 -10000 0 -10000 0 0
FADD 0.033 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.041 0.1 -10000 0 -0.3 62 62
MAPK8 -0.015 0.2 0.34 3 -0.72 51 54
APAF1 0.031 0.021 -10000 0 -0.55 1 1
TRAF1 0.028 0.051 -10000 0 -0.49 8 8
TRAF2 0.031 0.028 -10000 0 -0.55 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.006 0.11 -10000 0 -0.3 74 74
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.003 0.14 -10000 0 -0.5 43 43
CHUK 0.019 0.14 0.3 26 -0.44 41 67
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.082 0.054 -10000 0 -0.29 10 10
TCRz/NEF -0.039 0.17 -10000 0 -0.47 99 99
TNF -0.011 0.14 -10000 0 -0.43 80 80
FASLG -0.071 0.24 -10000 0 -0.53 156 156
NFKB1 0.021 0.045 -10000 0 -0.38 2 2
TNFR1A/BAG4/TNF-alpha 0.026 0.098 -10000 0 -0.34 38 38
CASP6 0.007 0.18 -10000 0 -0.66 47 47
CASP7 -0.02 0.2 0.31 4 -0.6 77 81
RELA 0.023 0.04 -10000 0 -0.21 1 1
CASP2 0.029 0.011 -10000 0 -10000 0 0
CASP3 -0.017 0.19 0.33 2 -0.61 67 69
TNFRSF1A 0.031 0.008 -10000 0 -10000 0 0
TNFR1A/BAG4 0.042 0.034 -10000 0 -0.4 4 4
CASP8 0.031 0.021 -10000 0 -0.55 1 1
CASP9 0.031 0.008 -10000 0 -10000 0 0
MAP3K14 0.004 0.14 -10000 0 -0.48 47 47
APAF-1/Caspase 9 -0.01 0.16 -10000 0 -0.48 63 63
BCL2 -0.015 0.18 0.37 5 -0.64 51 56
IL27-mediated signaling events

Figure S78.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S78.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.022 0.082 -10000 0 -0.52 19 19
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.045 0.18 0.88 23 -0.5 1 24
IL27/IL27R/JAK1 -0.049 0.24 0.95 1 -1.2 20 21
TBX21 -0.083 0.19 0.66 3 -0.65 49 52
IL12B -0.002 0.1 -10000 0 -0.35 63 63
IL12A 0 0.051 -10000 0 -0.33 18 18
IL6ST -0.037 0.18 -10000 0 -0.56 95 95
IL27RA/JAK1 -0.015 0.2 -10000 0 -1.4 17 17
IL27 0.009 0.064 -10000 0 -0.33 27 27
TYK2 0.022 0.036 -10000 0 -0.57 2 2
T-helper cell lineage commitment -0.029 0.14 -10000 0 -0.92 5 5
T-helper 2 cell differentiation 0.045 0.18 0.88 23 -0.5 1 24
T cell proliferation during immune response 0.045 0.18 0.88 23 -0.5 1 24
MAPKKK cascade -0.045 0.18 0.5 1 -0.88 23 24
STAT3 0.029 0.01 -10000 0 -10000 0 0
STAT2 0.032 0.007 -10000 0 -10000 0 0
STAT1 0.027 0.041 -10000 0 -0.38 8 8
IL12RB1 -0.002 0.13 -10000 0 -0.5 57 57
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.12 0.22 0.66 3 -0.55 106 109
IL27/IL27R/JAK2/TYK2 -0.046 0.19 0.5 1 -0.91 23 24
positive regulation of T cell mediated cytotoxicity -0.045 0.18 0.5 1 -0.88 23 24
STAT1 (dimer) -0.075 0.28 0.63 8 -0.96 39 47
JAK2 0.027 0.026 -10000 0 -0.56 1 1
JAK1 0.03 0.01 -10000 0 -10000 0 0
STAT2 (dimer) -0.028 0.18 -10000 0 -0.84 23 23
T cell proliferation -0.082 0.2 0.66 1 -0.71 43 44
IL12/IL12R/TYK2/JAK2 -0.018 0.17 -10000 0 -0.75 28 28
IL17A -0.03 0.14 -10000 0 -0.92 5 5
mast cell activation 0.045 0.18 0.88 23 -0.5 1 24
IFNG -0.009 0.04 0.11 1 -0.12 54 55
T cell differentiation -0.005 0.008 -10000 0 -0.024 56 56
STAT3 (dimer) -0.026 0.18 0.44 1 -0.88 21 22
STAT5A (dimer) -0.026 0.18 0.44 1 -0.88 22 23
STAT4 (dimer) -0.046 0.21 0.44 1 -0.77 38 39
STAT4 0.001 0.13 -10000 0 -0.54 47 47
T cell activation -0.006 0.018 0.12 16 -10000 0 16
IL27R/JAK2/TYK2 -0.028 0.22 -10000 0 -1.3 18 18
GATA3 -0.11 0.38 0.69 4 -1.5 57 61
IL18 -0.002 0.06 -10000 0 -0.28 36 36
positive regulation of mast cell cytokine production -0.024 0.17 0.44 1 -0.84 21 22
IL27/EBI3 0.011 0.098 0.26 1 -0.34 57 58
IL27RA -0.028 0.21 -10000 0 -1.5 17 17
IL6 -0.074 0.19 -10000 0 -0.4 213 213
STAT5A 0.027 0.035 -10000 0 -0.55 3 3
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 -0.003 0.089 0.54 17 -10000 0 17
IL1B -0.015 0.091 -10000 0 -0.34 60 60
EBI3 0.006 0.11 -10000 0 -0.49 37 37
TNF -0.019 0.094 -10000 0 -0.3 80 80
FoxO family signaling

Figure S79.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S79.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.24 0.55 0.58 14 -1.4 145 159
PLK1 0.019 0.22 0.54 3 -0.96 20 23
CDKN1B 0.053 0.17 0.48 31 -0.35 48 79
FOXO3 0.028 0.18 -10000 0 -0.72 27 27
KAT2B 0.031 0.033 -10000 0 -0.6 1 1
FOXO1/SIRT1 -0.061 0.22 0.35 9 -0.48 142 151
CAT 0.014 0.19 -10000 0 -0.97 14 14
CTNNB1 0.03 0.01 -10000 0 -10000 0 0
AKT1 0.016 0.049 -10000 0 -0.3 4 4
FOXO1 -0.078 0.24 0.4 18 -0.52 142 160
MAPK10 0.04 0.077 0.21 64 -0.29 20 84
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.084 0.1 0.41 34 -0.38 3 37
response to oxidative stress -0.006 0.032 -10000 0 -0.19 4 4
FOXO3A/SIRT1 0.054 0.16 -10000 0 -0.67 19 19
XPO1 0.032 0.007 -10000 0 -10000 0 0
EP300 0.005 0.051 -10000 0 -0.35 5 5
BCL2L11 0.003 0.18 -10000 0 -0.89 32 32
FOXO1/SKP2 -0.065 0.22 0.32 13 -0.49 136 149
mol:GDP -0.006 0.032 -10000 0 -0.19 4 4
RAN 0.033 0.007 -10000 0 -10000 0 0
GADD45A 0.062 0.21 0.45 4 -0.71 49 53
YWHAQ 0.031 0.007 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.003 0.15 0.24 1 -0.56 43 44
MST1 0.009 0.11 -10000 0 -0.46 42 42
CSNK1D 0.029 0.011 -10000 0 -10000 0 0
CSNK1E 0.032 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.022 0.16 -10000 0 -0.57 47 47
YWHAB 0.031 0.008 -10000 0 -10000 0 0
MAPK8 0.046 0.063 0.22 65 -0.28 3 68
MAPK9 0.045 0.058 0.21 72 -10000 0 72
YWHAG 0.029 0.011 -10000 0 -10000 0 0
YWHAE 0.029 0.01 -10000 0 -10000 0 0
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
SIRT1 0.034 0.029 -10000 0 -0.55 1 1
SOD2 0.027 0.21 0.5 17 -0.59 51 68
RBL2 0.049 0.16 -10000 0 -0.83 13 13
RAL/GDP 0.038 0.029 -10000 0 -10000 0 0
CHUK 0.032 0.032 -10000 0 -0.54 1 1
Ran/GTP 0.027 0.007 -10000 0 -10000 0 0
CSNK1G2 0.031 0.034 -10000 0 -0.55 3 3
RAL/GTP 0.043 0.028 -10000 0 -10000 0 0
CSNK1G1 0.033 0.003 -10000 0 -10000 0 0
FASLG -0.16 0.5 -10000 0 -1.4 112 112
SKP2 0.03 0.036 -10000 0 -0.49 4 4
USP7 0.032 0.009 -10000 0 -10000 0 0
IKBKB 0.034 0.025 -10000 0 -10000 0 0
CCNB1 0.017 0.18 -10000 0 -0.88 13 13
FOXO1-3a-4/beta catenin 0.051 0.16 0.4 13 -0.41 15 28
proteasomal ubiquitin-dependent protein catabolic process -0.064 0.22 0.32 13 -0.48 136 149
CSNK1A1 0.031 0.008 -10000 0 -10000 0 0
SGK1 0.027 0.065 -10000 0 -0.53 10 10
CSNK1G3 0.031 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.046 0.015 -10000 0 -10000 0 0
ZFAND5 0.08 0.098 0.47 19 -10000 0 19
SFN -0.099 0.2 -10000 0 -0.39 274 274
CDK2 -0.002 0.055 -10000 0 -0.33 2 2
FOXO3A/14-3-3 -0.017 0.17 -10000 0 -0.56 53 53
CREBBP -0.001 0.051 -10000 0 -10000 0 0
FBXO32 0.018 0.18 0.55 2 -0.86 12 14
BCL6 0.047 0.18 -10000 0 -0.92 14 14
RALB 0.033 0.007 -10000 0 -10000 0 0
RALA 0.03 0.011 -10000 0 -10000 0 0
YWHAH 0.032 0.006 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

Figure S80.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S80.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.003 0.045 0.25 16 -0.23 1 17
RFC1 0.003 0.042 0.25 14 -0.23 1 15
PRKDC 0.005 0.05 0.26 21 -0.23 1 22
RIPK1 0.032 0.009 -10000 0 -10000 0 0
CASP7 -0.001 0.11 -10000 0 -0.67 17 17
FASLG/FAS/FADD/FAF1 -0.019 0.087 0.21 8 -0.3 56 64
MAP2K4 -0.067 0.24 0.32 5 -0.66 87 92
mol:ceramide -0.032 0.14 -10000 0 -0.38 90 90
GSN 0.003 0.045 0.25 16 -0.23 1 17
FASLG/FAS/FADD/FAF1/Caspase 8 -0.025 0.11 -10000 0 -0.37 55 55
FAS 0.02 0.061 -10000 0 -0.56 9 9
BID -0.01 0.05 0.31 18 -0.36 1 19
MAP3K1 -0.035 0.18 0.28 9 -0.61 55 64
MAP3K7 0.03 0.009 -10000 0 -10000 0 0
RB1 0.003 0.051 0.26 17 -0.3 4 21
CFLAR 0.033 0.008 -10000 0 -10000 0 0
HGF/MET 0.009 0.13 -10000 0 -0.37 73 73
ARHGDIB 0.005 0.068 0.23 43 -0.33 10 53
FADD 0.027 0.015 -10000 0 -10000 0 0
actin filament polymerization -0.002 0.047 0.22 2 -0.25 16 18
NFKB1 -0.016 0.1 -10000 0 -0.63 11 11
MAPK8 -0.09 0.25 0.33 6 -0.59 140 146
DFFA 0.003 0.042 0.25 14 -10000 0 14
DNA fragmentation during apoptosis 0.002 0.045 0.27 14 -0.22 1 15
FAS/FADD/MET 0.043 0.056 -10000 0 -0.35 11 11
CFLAR/RIP1 0.048 0.015 -10000 0 -10000 0 0
FAIM3 0.016 0.091 -10000 0 -0.5 26 26
FAF1 0.025 0.018 -10000 0 -10000 0 0
PARP1 0.003 0.042 0.25 14 -10000 0 14
DFFB 0.003 0.044 0.27 14 -0.23 1 15
CHUK -0.016 0.094 -10000 0 -0.62 9 9
FASLG -0.049 0.18 -10000 0 -0.44 139 139
FAS/FADD 0.032 0.053 -10000 0 -0.38 8 8
HGF -0.024 0.16 -10000 0 -0.46 95 95
LMNA 0.001 0.043 0.22 13 -0.3 2 15
CASP6 0.003 0.043 0.25 15 -0.23 1 16
CASP10 0.023 0.046 -10000 0 -0.55 5 5
CASP3 0.005 0.052 0.26 30 -0.25 1 31
PTPN13 0.018 0.09 -10000 0 -0.54 22 22
CASP8 -0.011 0.065 0.39 20 -0.42 1 21
IL6 -0.18 0.45 -10000 0 -1.4 104 104
MET 0.025 0.045 -10000 0 -0.55 5 5
ICAD/CAD 0.002 0.04 0.26 10 -10000 0 10
FASLG/FAS/FADD/FAF1/Caspase 10 -0.033 0.14 -10000 0 -0.39 90 90
activation of caspase activity by cytochrome c -0.01 0.05 0.31 18 -0.36 1 19
PAK2 0.01 0.066 0.27 39 -0.23 1 40
BCL2 0.024 0.07 -10000 0 -0.55 13 13
Regulation of p38-alpha and p38-beta

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.039 0.016 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.031 0.008 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.048 -10000 0 -0.48 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.029 0.01 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.003 0.068 -10000 0 -0.24 55 55
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.032 0.006 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.029 0.011 -10000 0 -10000 0 0
FYN 0.025 0.056 -10000 0 -0.55 8 8
MAP3K12 0.029 0.04 -10000 0 -0.55 4 4
FGR 0.019 0.081 -10000 0 -0.51 19 19
p38 alpha/TAB1 -0.052 0.16 -10000 0 -0.57 62 62
PRKG1 -0.066 0.22 -10000 0 -0.54 148 148
DUSP8 0.017 0.079 -10000 0 -0.36 35 35
PGK/cGMP/p38 alpha -0.037 0.19 -10000 0 -0.53 84 84
apoptosis -0.049 0.15 -10000 0 -0.53 63 63
RAL/GTP 0.037 0.017 -10000 0 -10000 0 0
LYN 0.03 0.028 -10000 0 -0.55 2 2
DUSP1 -0.032 0.18 -10000 0 -0.54 97 97
PAK1 0.033 0.004 -10000 0 -10000 0 0
SRC 0.031 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.068 0.037 -10000 0 -0.31 1 1
TRAF6 0.033 0.004 -10000 0 -10000 0 0
RAC1 0.029 0.011 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.028 0.022 -10000 0 -0.55 1 1
RAC1-CDC42/GTP 0.036 0.018 -10000 0 -10000 0 0
MAPK11 0.015 0.2 0.36 61 -0.53 64 125
BLK -0.025 0.15 -10000 0 -0.4 112 112
HCK 0.021 0.075 -10000 0 -0.52 16 16
MAP2K3 0.029 0.022 -10000 0 -0.55 1 1
DUSP16 0.031 0.008 -10000 0 -10000 0 0
DUSP10 0.027 0.042 -10000 0 -0.42 7 7
TRAF6/MEKK3 0.037 0.014 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.21 0.31 61 -0.65 59 120
positive regulation of innate immune response 0.018 0.23 0.4 61 -0.64 62 123
LCK -0.015 0.15 -10000 0 -0.48 78 78
p38alpha-beta/MKP7 0.017 0.21 0.38 33 -0.61 60 93
p38alpha-beta/MKP5 0.031 0.22 0.41 60 -0.61 62 122
PGK/cGMP -0.049 0.16 -10000 0 -0.39 148 148
PAK2 0.032 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.003 0.22 0.4 31 -0.6 74 105
CDC42 0.031 0.008 -10000 0 -10000 0 0
RALB 0.032 0.007 -10000 0 -10000 0 0
RALA 0.029 0.011 -10000 0 -10000 0 0
PAK3 -0.042 0.18 -10000 0 -0.44 135 135
Ceramide signaling pathway

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.011 0.054 -10000 0 -0.39 15 15
MAP4K4 -0.004 0.11 0.22 1 -0.43 41 42
BAG4 0.028 0.044 -10000 0 -0.55 5 5
PKC zeta/ceramide -0.021 0.085 -10000 0 -0.21 117 117
NFKBIA 0.032 0.006 -10000 0 -10000 0 0
BIRC3 -0.015 0.15 -10000 0 -0.5 79 79
BAX -0.003 0.042 -10000 0 -0.3 8 8
RIPK1 0.031 0.008 -10000 0 -10000 0 0
AKT1 0.01 0.085 0.81 9 -0.48 1 10
BAD -0.034 0.072 -10000 0 -0.2 97 97
SMPD1 0.006 0.074 0.22 18 -0.21 47 65
RB1 -0.033 0.076 0.18 2 -0.21 93 95
FADD/Caspase 8 -0.004 0.14 -10000 0 -0.52 42 42
MAP2K4 -0.018 0.066 0.18 13 -0.32 10 23
NSMAF 0.032 0.006 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.019 0.073 0.2 5 -0.34 14 19
EGF -0.059 0.19 -10000 0 -0.41 181 181
mol:ceramide -0.036 0.079 0.16 3 -0.21 110 113
MADD 0.033 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.051 -10000 0 -0.32 19 19
ASAH1 0.028 0.032 -10000 0 -0.32 7 7
negative regulation of cell cycle -0.032 0.075 0.18 2 -0.21 93 95
cell proliferation -0.016 0.095 -10000 0 -0.31 27 27
BID -0.002 0.15 -10000 0 -0.7 26 26
MAP3K1 -0.031 0.073 0.18 6 -0.2 98 104
EIF2A -0.02 0.071 0.33 7 -0.33 8 15
TRADD 0.03 0.021 -10000 0 -0.55 1 1
CRADD 0.032 0.007 -10000 0 -10000 0 0
MAPK3 -0.013 0.068 0.21 1 -0.36 8 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.014 0.071 0.23 1 -0.36 10 11
Cathepsin D/ceramide -0.018 0.082 -10000 0 -0.2 105 105
FADD -0.004 0.11 -10000 0 -0.44 38 38
KSR1 -0.024 0.076 0.19 13 -0.23 67 80
MAPK8 -0.027 0.086 0.2 1 -0.27 56 57
PRKRA -0.031 0.075 0.19 2 -0.21 91 93
PDGFA 0.021 0.066 -10000 0 -0.53 12 12
TRAF2 0.031 0.028 -10000 0 -0.55 2 2
IGF1 -0.008 0.13 -10000 0 -0.4 80 80
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.036 0.079 0.15 3 -0.21 110 113
CTSD 0.03 0.035 -10000 0 -0.41 5 5
regulation of nitric oxide biosynthetic process 0.047 0.017 -10000 0 -0.4 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.016 0.1 -10000 0 -0.34 26 26
PRKCD 0.009 0.084 -10000 0 -0.32 53 53
PRKCZ 0.025 0.056 -10000 0 -0.55 8 8
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.051 -10000 0 -0.32 19 19
RelA/NF kappa B1 0.047 0.017 -10000 0 -0.4 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.03 0.029 -10000 0 -0.55 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.004 0.12 -10000 0 -0.46 40 40
TNFR1A/BAG4/TNF-alpha 0.026 0.098 -10000 0 -0.34 38 38
mol:Sphingosine-1-phosphate 0.011 0.054 -10000 0 -0.39 15 15
MAP2K1 -0.017 0.071 0.23 1 -0.33 12 13
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.033 0.004 -10000 0 -10000 0 0
CYCS -0.005 0.043 0.17 5 -0.25 10 15
TNFRSF1A 0.031 0.008 -10000 0 -10000 0 0
NFKB1 0.032 0.02 -10000 0 -0.55 1 1
TNFR1A/BAG4 0.042 0.034 -10000 0 -0.4 4 4
EIF2AK2 -0.029 0.073 0.24 4 -0.32 14 18
TNF-alpha/TNFR1A/FAN 0.029 0.094 -10000 0 -0.34 34 34
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.14 -10000 0 -0.56 42 42
MAP2K2 -0.018 0.069 0.23 1 -0.35 9 10
SMPD3 0 0.075 -10000 0 -0.29 28 28
TNF -0.011 0.14 -10000 0 -0.43 80 80
PKC zeta/PAR4 0.038 0.052 -10000 0 -0.44 9 9
mol:PHOSPHOCHOLINE 0.014 0.088 0.23 78 -0.22 15 93
NF kappa B1/RelA/I kappa B alpha 0.081 0.055 -10000 0 -0.37 7 7
AIFM1 -0.013 0.055 0.17 5 -0.25 12 17
BCL2 0.023 0.07 -10000 0 -0.55 13 13
Class I PI3K signaling events

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.004 0.072 0.29 2 -0.52 1 3
DAPP1 -0.039 0.21 0.34 12 -0.61 81 93
Src family/SYK family/BLNK-LAT/BTK-ITK -0.06 0.27 0.32 4 -0.67 115 119
mol:DAG -0.009 0.13 0.29 47 -0.28 78 125
HRAS 0.026 0.042 -10000 0 -0.46 5 5
RAP1A 0.027 0.02 -10000 0 -10000 0 0
ARF5/GDP 0.016 0.11 0.24 3 -0.36 49 52
PLCG2 -0.002 0.11 -10000 0 -0.34 76 76
PLCG1 0.031 0.008 -10000 0 -10000 0 0
ARF5 0.028 0.023 -10000 0 -0.55 1 1
mol:GTP -0.03 0.085 0.3 4 -0.26 85 89
ARF1/GTP -0.013 0.075 0.37 1 -0.37 3 4
RHOA 0.03 0.009 -10000 0 -10000 0 0
YES1 0.032 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.007 0.091 0.3 3 -0.26 88 91
ADAP1 -0.024 0.079 0.28 3 -0.4 4 7
ARAP3 -0.03 0.085 0.3 4 -0.26 88 92
INPPL1 0.031 0.028 -10000 0 -0.55 2 2
PREX1 0.025 0.062 -10000 0 -0.55 10 10
ARHGEF6 0.024 0.07 -10000 0 -0.55 13 13
ARHGEF7 0.031 0.007 -10000 0 -10000 0 0
ARF1 0.031 0.008 -10000 0 -10000 0 0
NRAS 0.027 0.02 -10000 0 -10000 0 0
FYN 0.025 0.056 -10000 0 -0.55 8 8
ARF6 0.032 0.006 -10000 0 -10000 0 0
FGR 0.019 0.081 -10000 0 -0.51 19 19
mol:Ca2+ 0.003 0.071 0.26 24 -10000 0 24
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.026 0.053 -10000 0 -0.52 8 8
ZAP70 -0.003 0.13 -10000 0 -0.46 61 61
mol:IP3 -0.002 0.087 0.21 45 -0.2 46 91
LYN 0.03 0.028 -10000 0 -0.55 2 2
ARF1/GDP 0.021 0.11 0.26 7 -0.38 43 50
RhoA/GDP 0.017 0.099 0.3 12 -0.36 11 23
PDK1/Src/Hsp90 0.058 0.029 -10000 0 -0.34 2 2
BLNK 0.015 0.087 -10000 0 -0.42 31 31
actin cytoskeleton reorganization 0.004 0.13 0.34 24 -0.47 23 47
SRC 0.031 0.008 -10000 0 -10000 0 0
PLEKHA2 0.007 0.029 -10000 0 -0.34 6 6
RAC1 0.029 0.011 -10000 0 -10000 0 0
PTEN 0.03 0.018 -10000 0 -10000 0 0
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.006 0.089 0.3 1 -0.52 2 3
RhoA/GTP -0.006 0.085 0.3 4 -0.27 2 6
Src family/SYK family/BLNK-LAT -0.047 0.23 -10000 0 -0.63 89 89
BLK -0.025 0.15 -10000 0 -0.4 112 112
PDPK1 0.03 0.029 -10000 0 -0.55 2 2
CYTH1 -0.02 0.082 0.28 7 -0.27 3 10
HCK 0.021 0.075 -10000 0 -0.52 16 16
CYTH3 -0.02 0.073 0.28 3 -0.27 3 6
CYTH2 -0.025 0.093 0.28 8 -0.53 2 10
KRAS 0.027 0.02 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.009 0.08 -10000 0 -0.52 11 11
SGK1 0.009 0.093 -10000 0 -0.51 15 15
INPP5D 0.029 0.04 -10000 0 -0.55 4 4
mol:GDP 0.006 0.12 0.24 12 -0.37 56 68
SOS1 0.031 0.007 -10000 0 -10000 0 0
SYK 0.022 0.072 -10000 0 -0.48 17 17
ARF6/GDP 0.005 0.094 0.26 12 -0.36 12 24
mol:PI-3-4-5-P3 -0.032 0.084 -10000 0 -0.26 85 85
ARAP3/RAP1A/GTP -0.007 0.092 0.3 3 -0.26 88 91
VAV1 0.006 0.12 -10000 0 -0.53 42 42
mol:PI-3-4-P2 0.016 0.035 -10000 0 -0.4 6 6
RAS family/GTP/PI3K Class I 0.02 0.1 -10000 0 -0.26 88 88
PLEKHA1 0.007 0.029 -10000 0 -0.34 6 6
Rac1/GDP 0.016 0.11 0.26 2 -0.38 44 46
LAT 0.01 0.096 -10000 0 -0.41 41 41
Rac1/GTP 0.015 0.11 -10000 0 -0.49 31 31
ITK -0.052 0.12 0.28 4 -0.4 56 60
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.026 0.16 0.3 37 -0.39 85 122
LCK -0.015 0.15 -10000 0 -0.48 78 78
BTK -0.029 0.1 0.28 12 -0.34 20 32
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 0.037 0.038 -10000 0 -0.4 5 5
CRKL 0.026 0.11 0.31 11 -0.5 13 24
mol:PIP3 -0.007 0.051 -10000 0 -0.67 5 5
AKT1 0.003 0.065 0.37 2 -0.51 5 7
PTK2B 0.031 0.008 -10000 0 -10000 0 0
RAPGEF1 0.029 0.11 0.34 18 -0.5 11 29
RANBP10 0.031 0.009 -10000 0 -10000 0 0
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
HGF/MET/SHIP2 0.017 0.11 -10000 0 -0.34 63 63
MAP3K5 0.027 0.14 0.34 37 -0.47 35 72
HGF/MET/CIN85/CBL/ENDOPHILINS 0.032 0.12 -10000 0 -0.34 60 60
AP1 0.009 0.11 -10000 0 -0.25 109 109
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.031 0.014 -10000 0 -0.32 1 1
apoptosis -0.063 0.3 -10000 0 -0.88 98 98
STAT3 (dimer) 0.005 0.086 -10000 0 -0.4 16 16
GAB1/CRKL/SHP2/PI3K 0.053 0.11 0.34 2 -0.53 11 13
INPP5D 0.029 0.04 -10000 0 -0.55 4 4
CBL/CRK 0.054 0.13 0.36 46 -0.52 12 58
PTPN11 0.031 0.021 -10000 0 -0.55 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.031 0.008 -10000 0 -10000 0 0
PTEN 0.031 0.008 -10000 0 -10000 0 0
ELK1 0.041 0.15 0.37 127 -0.21 4 131
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.008 0.059 -10000 0 -0.26 20 20
PAK1 0.005 0.073 0.52 6 -0.49 5 11
HGF/MET/RANBP10 0.018 0.11 -10000 0 -0.34 57 57
HRAS -0.016 0.14 -10000 0 -0.5 49 49
DOCK1 0.029 0.11 0.35 20 -0.49 13 33
GAB1 0.018 0.1 -10000 0 -0.53 13 13
CRK 0.034 0.12 0.35 41 -0.53 12 53
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.019 0.16 -10000 0 -0.52 66 66
JUN 0.029 0.029 -10000 0 -0.38 4 4
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.005 0.061 -10000 0 -0.21 66 66
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
cell morphogenesis 0.027 0.13 0.38 37 -0.48 14 51
GRB2/SHC 0.034 0.071 -10000 0 -0.24 8 8
FOS -0.026 0.16 -10000 0 -0.42 112 112
GLMN 0.004 0.013 -10000 0 -0.26 2 2
cell motility 0.041 0.15 0.37 127 -0.21 4 131
HGF/MET/MUC20 0.002 0.1 -10000 0 -0.28 99 99
cell migration 0.033 0.07 -10000 0 -0.24 8 8
GRB2 0.029 0.011 -10000 0 -10000 0 0
CBL 0.032 0.02 -10000 0 -0.55 1 1
MET/RANBP10 0.039 0.038 -10000 0 -0.4 5 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.008 0.084 -10000 0 -0.28 58 58
MET/MUC20 0.019 0.033 -10000 0 -0.4 5 5
RAP1B 0.038 0.12 0.41 40 -0.49 9 49
RAP1A 0.029 0.1 0.36 20 -0.47 10 30
HGF/MET/RANBP9 0.016 0.11 -10000 0 -0.34 60 60
RAF1 -0.009 0.14 -10000 0 -0.48 46 46
STAT3 0.005 0.086 -10000 0 -0.41 16 16
cell proliferation 0.007 0.11 0.31 4 -0.37 52 56
RPS6KB1 0.004 0.056 -10000 0 -0.37 15 15
MAPK3 0.025 0.14 0.51 38 -10000 0 38
MAPK1 0.036 0.17 0.59 51 -10000 0 51
RANBP9 0.031 0.008 -10000 0 -10000 0 0
MAPK8 0.037 0.18 0.42 58 -0.5 44 102
SRC 0.002 0.077 -10000 0 -0.39 11 11
PI3K 0.033 0.082 -10000 0 -0.3 15 15
MET/Glomulin 0.014 0.043 -10000 0 -0.3 8 8
SOS1 0.031 0.007 -10000 0 -10000 0 0
MAP2K1 0.009 0.15 0.37 10 -0.51 29 39
MET 0.025 0.045 -10000 0 -0.55 5 5
MAP4K1 0.027 0.15 0.32 44 -0.5 35 79
PTK2 0.032 0.006 -10000 0 -10000 0 0
MAP2K2 0.007 0.15 0.35 8 -0.5 33 41
BAD 0.004 0.077 0.52 6 -0.49 7 13
MAP2K4 0.039 0.15 0.4 62 -0.43 35 97
SHP2/GRB2/SOS1/GAB1 0.031 0.092 -10000 0 -0.46 14 14
INPPL1 0.031 0.028 -10000 0 -0.55 2 2
PXN 0.032 0.007 -10000 0 -10000 0 0
SH3KBP1 0.03 0.044 -10000 0 -0.55 5 5
HGS -0.005 0.054 -10000 0 -0.2 48 48
PLCgamma1/PKC 0.023 0.006 -10000 0 -10000 0 0
HGF -0.024 0.16 -10000 0 -0.46 95 95
RASA1 0.03 0.034 -10000 0 -0.55 3 3
NCK1 0.03 0.029 -10000 0 -0.55 2 2
PTPRJ 0.032 0.023 -10000 0 -0.44 2 2
NCK/PLCgamma1 0.027 0.074 -10000 0 -0.22 57 57
PDPK1 0.001 0.064 -10000 0 -0.48 7 7
HGF/MET/SHIP 0.015 0.12 -10000 0 -0.35 60 60
Presenilin action in Notch and Wnt signaling

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.001 0.14 -10000 0 -0.63 18 18
HDAC1 0.03 0.014 -10000 0 -10000 0 0
AES 0.032 0.02 -10000 0 -0.55 1 1
FBXW11 0.031 0.008 -10000 0 -10000 0 0
DTX1 0.004 0.12 -10000 0 -0.46 49 49
LRP6/FZD1 0.008 0.12 -10000 0 -0.4 66 66
TLE1 0.031 0.028 -10000 0 -0.55 2 2
AP1 -0.013 0.096 0.2 1 -0.32 54 55
NCSTN 0.03 0.021 -10000 0 -0.55 1 1
ADAM10 0.026 0.06 -10000 0 -0.53 10 10
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.005 0.12 -10000 0 -0.56 15 15
NICD/RBPSUH 0.043 0.094 -10000 0 -0.53 18 18
WIF1 0.011 0.067 -10000 0 -0.32 34 34
NOTCH1 0.025 0.091 -10000 0 -0.55 18 18
PSENEN 0.033 0.003 -10000 0 -10000 0 0
KREMEN2 0.006 0.093 -10000 0 -0.34 55 55
DKK1 -0.033 0.16 -10000 0 -0.43 119 119
beta catenin/beta TrCP1 0.016 0.11 0.28 4 -0.39 22 26
APH1B 0.029 0.048 -10000 0 -0.55 6 6
APH1A 0.031 0.008 -10000 0 -10000 0 0
AXIN1 0.016 0.053 0.27 5 -0.4 3 8
CtBP/CBP/TCF1/TLE1/AES 0.007 0.096 -10000 0 -0.31 61 61
PSEN1 0.032 0.006 -10000 0 -10000 0 0
FOS -0.026 0.16 -10000 0 -0.42 112 112
JUN 0.029 0.029 -10000 0 -0.38 4 4
MAP3K7 0.031 0.01 -10000 0 -10000 0 0
CTNNB1 0.003 0.11 0.28 10 -0.35 41 51
MAPK3 0.03 0.021 -10000 0 -0.55 1 1
DKK2/LRP6/Kremen 2 -0.004 0.13 -10000 0 -0.35 73 73
HNF1A -0.016 0.16 -10000 0 -0.55 71 71
CTBP1 0.032 0.006 -10000 0 -10000 0 0
MYC -0.038 0.33 -10000 0 -1.5 41 41
NKD1 -0.003 0.11 -10000 0 -0.37 71 71
FZD1 -0.014 0.15 -10000 0 -0.55 65 65
NOTCH1 precursor/Deltex homolog 1 0.027 0.11 -10000 0 -0.54 19 19
apoptosis -0.013 0.095 0.2 1 -0.32 54 55
Delta 1/NOTCHprecursor -0.002 0.14 -10000 0 -0.62 18 18
DLL1 -0.049 0.2 -10000 0 -0.51 130 130
PPARD -0.033 0.25 -10000 0 -0.92 59 59
Gamma Secretase 0.086 0.045 -10000 0 -0.3 7 7
APC 0.014 0.068 0.28 3 -0.52 6 9
DVL1 0.005 0.083 -10000 0 -0.34 38 38
CSNK2A1 0.031 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.002 0.12 -10000 0 -0.36 54 54
LRP6 0.031 0.021 -10000 0 -0.55 1 1
CSNK1A1 0.031 0.008 -10000 0 -10000 0 0
NLK 0.017 0.013 -10000 0 -10000 0 0
CCND1 -0.041 0.34 -10000 0 -1.5 44 44
WNT1 0.023 0.049 -10000 0 -0.34 15 15
Axin1/APC/beta catenin 0.037 0.11 0.36 24 -0.52 8 32
DKK2 -0.043 0.18 -10000 0 -0.43 142 142
NOTCH1 precursor/DVL1 0.026 0.12 -10000 0 -0.57 21 21
GSK3B 0.031 0.007 -10000 0 -10000 0 0
FRAT1 0.031 0.014 -10000 0 -0.32 1 1
NOTCH/Deltex homolog 1 0.029 0.11 -10000 0 -0.61 14 14
PPP2R5D 0.002 0.14 0.28 15 -0.48 57 72
MAPK1 0.031 0.02 -10000 0 -0.55 1 1
WNT1/LRP6/FZD1 0.027 0.12 -10000 0 -0.33 67 67
RBPJ 0.032 0.005 -10000 0 -10000 0 0
CREBBP 0.031 0.013 -10000 0 -10000 0 0
IFN-gamma pathway

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.034 0.097 -10000 0 -0.28 33 33
positive regulation of NF-kappaB transcription factor activity 0 0.002 -10000 0 -10000 0 0
CRKL 0.032 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.036 0.098 0.32 18 -0.56 2 20
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.057 0.041 -10000 0 -0.42 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.017 0.087 -10000 0 -0.31 33 33
CaM/Ca2+ 0.036 0.094 -10000 0 -0.27 26 26
RAP1A 0.031 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.01 0.085 0.23 1 -0.28 31 32
AKT1 0.013 0.11 0.35 33 -0.4 4 37
MAP2K1 0.002 0.089 0.29 30 -0.35 3 33
MAP3K11 0.005 0.092 0.3 26 -0.28 28 54
IFNGR1 0.03 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.024 0.13 -10000 0 -0.41 24 24
Rap1/GTP 0.001 0.063 -10000 0 -0.58 1 1
CRKL/C3G 0.047 0.011 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.04 0.11 -10000 0 -0.28 33 33
CEBPB 0.025 0.15 0.39 33 -0.44 42 75
STAT3 0.029 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.012 0.21 -10000 0 -1.2 18 18
STAT1 0.005 0.093 0.3 26 -0.28 31 57
CALM1 0.032 0.006 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.037 0.15 -10000 0 -0.37 146 146
PIK3CA 0.028 0.048 -10000 0 -0.55 6 6
STAT1 (dimer)/PIAS1 0.021 0.096 0.3 29 -0.35 4 33
CEBPB/PTGES2/Cbp/p300 0.028 0.094 -10000 0 -0.37 13 13
mol:Ca2+ 0.031 0.094 -10000 0 -0.27 33 33
MAPK3 0.013 0.098 0.43 1 -0.77 4 5
STAT1 (dimer) -0.013 0.12 -10000 0 -0.44 33 33
MAPK1 0.006 0.14 0.41 2 -0.71 22 24
JAK2 0.031 0.027 -10000 0 -0.59 1 1
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
JAK1 0.03 0.018 -10000 0 -10000 0 0
CAMK2D 0.032 0.005 -10000 0 -10000 0 0
DAPK1 0.012 0.17 0.34 36 -0.61 46 82
SMAD7 0.017 0.09 0.28 51 -0.19 13 64
CBL/CRKL/C3G 0.034 0.098 0.3 30 -0.71 1 31
PI3K 0.03 0.098 -10000 0 -0.33 9 9
IFNG -0.037 0.15 -10000 0 -0.37 146 146
apoptosis -0.011 0.15 0.33 19 -0.43 78 97
CAMK2G 0.031 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.029 0.01 -10000 0 -10000 0 0
CAMK2A 0.011 0.079 -10000 0 -0.34 42 42
CAMK2B -0.093 0.2 -10000 0 -0.4 249 249
FRAP1 0.003 0.1 0.34 33 -0.37 4 37
PRKCD -0.002 0.1 0.3 26 -0.43 5 31
RAP1B 0.031 0.007 -10000 0 -10000 0 0
negative regulation of cell growth -0.017 0.087 -10000 0 -0.31 33 33
PTPN2 0.032 0.006 -10000 0 -10000 0 0
EP300 0.031 0.028 -10000 0 -0.55 2 2
IRF1 0.009 0.11 0.38 34 -0.45 9 43
STAT1 (dimer)/PIASy 0.021 0.1 0.29 32 -0.35 6 38
SOCS1 -0.013 0.22 -10000 0 -1.5 18 18
mol:GDP 0.031 0.093 0.28 30 -0.67 1 31
CASP1 0.011 0.1 0.26 52 -0.3 30 82
PTGES2 0.029 0.04 -10000 0 -0.38 8 8
IRF9 0.034 0.065 0.23 39 -0.18 1 40
mol:PI-3-4-5-P3 0.016 0.087 -10000 0 -0.32 9 9
RAP1/GDP 0.021 0.074 -10000 0 -0.58 1 1
CBL 0.004 0.093 0.29 27 -0.28 26 53
MAP3K1 0.006 0.092 0.3 27 -0.27 26 53
PIAS1 0.033 0.003 -10000 0 -10000 0 0
PIAS4 0.031 0.028 -10000 0 -0.55 2 2
antigen processing and presentation of peptide antigen via MHC class II -0.017 0.087 -10000 0 -0.31 33 33
PTPN11 -0.004 0.077 0.21 1 -0.28 30 31
CREBBP 0.031 0.008 -10000 0 -10000 0 0
RAPGEF1 0.032 0.005 -10000 0 -10000 0 0
Nectin adhesion pathway

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.055 0.2 -10000 0 -0.54 132 132
alphaV beta3 Integrin 0.019 0.096 -10000 0 -0.32 57 57
PTK2 0.009 0.12 -10000 0 -0.47 30 30
positive regulation of JNK cascade 0.012 0.11 -10000 0 -0.34 59 59
CDC42/GDP 0.042 0.16 0.38 8 -0.44 61 69
Rac1/GDP 0.025 0.15 0.51 1 -0.44 59 60
RAP1B 0.031 0.007 -10000 0 -10000 0 0
RAP1A 0.031 0.008 -10000 0 -10000 0 0
CTNNB1 0.03 0.01 -10000 0 -10000 0 0
CDC42/GTP 0.023 0.14 -10000 0 -0.43 59 59
nectin-3/I-afadin 0.032 0.07 -10000 0 -0.4 21 21
RAPGEF1 0.018 0.14 0.3 3 -0.46 32 35
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.007 0.14 -10000 0 -0.5 35 35
PDGFB-D/PDGFRB -0.055 0.2 -10000 0 -0.54 132 132
TLN1 0.001 0.052 -10000 0 -0.41 9 9
Rap1/GTP 0.014 0.096 -10000 0 -0.33 28 28
IQGAP1 0.033 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.055 0.022 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.032 0.07 -10000 0 -0.4 21 21
PVR 0.032 0.012 -10000 0 -0.32 1 1
Necl-5(dimer) 0.032 0.012 -10000 0 -0.32 1 1
mol:GDP 0.024 0.18 0.4 8 -0.55 61 69
MLLT4 0.031 0.009 -10000 0 -10000 0 0
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
PI3K 0.021 0.15 -10000 0 -0.32 125 125
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.042 0.035 -10000 0 -0.28 8 8
positive regulation of lamellipodium assembly 0.015 0.11 -10000 0 -0.33 59 59
PVRL1 0.029 0.043 -10000 0 -0.41 8 8
PVRL3 0.017 0.089 -10000 0 -0.55 21 21
PVRL2 0.032 0.02 -10000 0 -0.55 1 1
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
CDH1 -0.005 0.13 -10000 0 -0.44 66 66
CLDN1 -0.029 0.16 -10000 0 -0.45 110 110
JAM-A/CLDN1 0.027 0.12 -10000 0 -0.31 76 76
SRC 0.005 0.16 -10000 0 -0.52 49 49
ITGB3 0.001 0.12 -10000 0 -0.45 51 51
nectin-1(dimer)/I-afadin/I-afadin 0.042 0.035 -10000 0 -0.28 8 8
FARP2 0.009 0.2 -10000 0 -0.63 58 58
RAC1 0.029 0.011 -10000 0 -10000 0 0
CTNNA1 0.031 0.008 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.049 0.065 -10000 0 -0.34 20 20
nectin-1/I-afadin 0.042 0.035 -10000 0 -0.28 8 8
nectin-2/I-afadin 0.044 0.02 -10000 0 -0.4 1 1
RAC1/GTP/IQGAP1/filamentous actin 0.039 0.015 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.046 0.072 -10000 0 -0.33 27 27
CDC42/GTP/IQGAP1/filamentous actin 0.042 0.012 -10000 0 -10000 0 0
F11R 0.031 0.008 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.012 0.11 -10000 0 -0.34 59 59
alphaV/beta3 Integrin/Talin 0.019 0.093 0.33 2 -0.32 37 39
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.044 0.02 -10000 0 -0.4 1 1
nectin-2(dimer)/I-afadin/I-afadin 0.044 0.02 -10000 0 -0.4 1 1
PIP5K1C 0.004 0.055 -10000 0 -0.41 10 10
VAV2 0.019 0.18 0.39 2 -0.57 44 46
RAP1/GDP 0.038 0.14 0.26 1 -0.39 60 61
ITGAV 0.027 0.05 -10000 0 -0.52 7 7
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.049 0.066 -10000 0 -0.34 21 21
nectin-3(dimer)/I-afadin/I-afadin 0.032 0.07 -10000 0 -0.4 21 21
Rac1/GTP 0.019 0.13 -10000 0 -0.4 59 59
PTPRM 0.008 0.059 -10000 0 -0.28 28 28
E-cadherin/beta catenin/alpha catenin 0.053 0.094 -10000 0 -0.29 41 41
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.031 0.008 -10000 0 -10000 0 0
IL1-mediated signaling events

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.023 0.005 -10000 0 -10000 0 0
PRKCZ 0.025 0.056 -10000 0 -0.55 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.031 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.01 0.13 -10000 0 -0.52 33 33
IRAK/TOLLIP 0.038 0.015 -10000 0 -0.31 1 1
IKBKB 0.032 0.007 -10000 0 -10000 0 0
IKBKG 0.031 0.034 -10000 0 -0.55 3 3
IL1 alpha/IL1R2 -0.043 0.15 -10000 0 -0.28 235 235
IL1A 0.016 0.068 -10000 0 -0.32 34 34
IL1B -0.017 0.12 -10000 0 -0.4 77 77
IRAK/TRAF6/p62/Atypical PKCs 0.069 0.056 -10000 0 -0.32 6 6
IL1R2 -0.07 0.19 -10000 0 -0.39 210 210
IL1R1 0.025 0.06 -10000 0 -0.53 10 10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.002 0.12 0.26 2 -0.56 26 28
TOLLIP 0.033 0.004 -10000 0 -10000 0 0
TICAM2 0.027 0.052 -10000 0 -0.55 7 7
MAP3K3 0.029 0.011 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.021 0.006 -10000 0 -10000 0 0
IKK complex/ELKS 0.04 0.071 -10000 0 -0.52 3 3
JUN 0.007 0.041 0.29 4 -0.25 8 12
MAP3K7 0.031 0.008 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.035 0.14 -10000 0 -0.38 72 72
IL1 alpha/IL1R1/IL1RAP/MYD88 0.045 0.1 -10000 0 -0.38 32 32
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.054 0.1 -10000 0 -0.37 31 31
IL1 beta fragment/IL1R1/IL1RAP 0.008 0.13 -10000 0 -0.38 76 76
NFKB1 0.032 0.02 -10000 0 -0.55 1 1
MAPK8 0.013 0.042 0.3 4 -0.27 8 12
IRAK1 0.019 0.013 -10000 0 -0.34 1 1
IL1RN/IL1R1 0.015 0.1 -10000 0 -0.4 31 31
IRAK4 0.032 0.007 -10000 0 -10000 0 0
PRKCI 0.031 0.014 -10000 0 -0.32 1 1
TRAF6 0.033 0.004 -10000 0 -10000 0 0
PI3K 0.04 0.049 -10000 0 -0.37 11 11
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.01 0.14 -10000 0 -0.58 33 33
CHUK 0.03 0.021 -10000 0 -0.55 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.008 0.13 -10000 0 -0.38 76 76
IL1 beta/IL1R2 -0.055 0.17 -10000 0 -0.41 119 119
IRAK/TRAF6/TAK1/TAB1/TAB2 0.044 0.02 -10000 0 -0.27 1 1
NF kappa B1 p50/RelA 0.022 0.13 -10000 0 -0.49 27 27
IRAK3 0.011 0.1 -10000 0 -0.54 31 31
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.033 0.13 -10000 0 -0.36 69 69
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.013 0.097 -10000 0 -0.42 32 32
IL1 alpha/IL1R1/IL1RAP 0.036 0.09 -10000 0 -0.37 25 25
RELA 0.033 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.028 0.032 -10000 0 -0.32 7 7
MYD88 0.022 0.068 -10000 0 -0.55 12 12
IRAK/TRAF6/MEKK3 0.055 0.031 -10000 0 -0.3 1 1
IL1RAP 0.017 0.089 -10000 0 -0.5 25 25
UBE2N 0.032 0.007 -10000 0 -10000 0 0
IRAK/TRAF6 0.007 0.11 -10000 0 -0.44 22 22
CASP1 0.015 0.099 -10000 0 -0.55 26 26
IL1RN/IL1R2 -0.056 0.17 -10000 0 -0.3 259 259
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.019 0.14 -10000 0 -0.39 76 76
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0 0.13 -10000 0 -0.56 27 27
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
IL1RN -0.002 0.12 -10000 0 -0.39 70 70
TRAF6/TAK1/TAB1/TAB2 0.043 0.016 -10000 0 -10000 0 0
MAP2K6 0.022 0.041 0.31 4 -0.28 5 9
Aurora B signaling

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.011 0.086 -10000 0 -0.32 35 35
STMN1 0.005 0.064 -10000 0 -0.26 43 43
Aurora B/RasGAP/Survivin 0.028 0.11 -10000 0 -0.37 53 53
Chromosomal passenger complex/Cul3 protein complex -0.001 0.096 -10000 0 -0.31 59 59
BIRC5 0.002 0.11 -10000 0 -0.4 56 56
DES -0.13 0.29 -10000 0 -0.66 188 188
Aurora C/Aurora B/INCENP 0.039 0.073 -10000 0 -0.32 14 14
Aurora B/TACC1 0.024 0.066 -10000 0 -0.22 49 49
Aurora B/PP2A 0.028 0.07 -10000 0 -0.25 44 44
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.009 0.021 -10000 0 -0.16 9 9
mitotic metaphase/anaphase transition 0 0.006 0.12 1 -10000 0 1
NDC80 -0.012 0.11 -10000 0 -0.34 73 73
Cul3 protein complex 0.048 0.071 -10000 0 -0.28 33 33
KIF2C -0.012 0.13 -10000 0 -0.43 59 59
PEBP1 0.032 0.008 -10000 0 -10000 0 0
KIF20A 0.003 0.12 -10000 0 -0.42 56 56
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.026 0.077 -10000 0 -0.27 47 47
SEPT1 0.023 0.06 -10000 0 -0.39 17 17
SMC2 0.032 0.02 -10000 0 -0.55 1 1
SMC4 0.028 0.044 -10000 0 -0.55 5 5
NSUN2/NPM1/Nucleolin -0.016 0.19 0.29 1 -0.72 52 53
PSMA3 0.032 0.006 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.003 -10000 0 -10000 0 0
H3F3B 0.01 0.045 -10000 0 -0.34 9 9
AURKB 0.011 0.093 -10000 0 -0.37 46 46
AURKC 0.024 0.061 -10000 0 -0.38 18 18
CDCA8 0.025 0.053 -10000 0 -0.33 18 18
cytokinesis -0.015 0.12 0.36 1 -0.4 63 64
Aurora B/Septin1 0.014 0.14 -10000 0 -0.41 53 53
AURKA 0.028 0.037 -10000 0 -0.32 9 9
INCENP 0.032 0.03 -10000 0 -0.55 2 2
KLHL13 0.013 0.099 -10000 0 -0.44 37 37
BUB1 0.011 0.09 -10000 0 -0.36 46 46
hSgo1/Aurora B/Survivin 0.018 0.12 -10000 0 -0.36 63 63
EVI5 0.032 0.009 -10000 0 -10000 0 0
RhoA/GTP 0.025 0.13 -10000 0 -0.34 70 70
SGOL1 0.013 0.084 -10000 0 -0.38 36 36
CENPA 0.001 0.1 0.17 1 -0.36 51 52
NCAPG 0.011 0.1 -10000 0 -0.45 38 38
Aurora B/HC8 Proteasome 0.028 0.07 -10000 0 -0.25 43 43
NCAPD2 0.031 0.014 -10000 0 -0.32 1 1
Aurora B/PP1-gamma 0.028 0.072 -10000 0 -0.25 46 46
RHOA 0.03 0.009 -10000 0 -10000 0 0
NCAPH 0.017 0.081 -10000 0 -0.41 29 29
NPM1 -0.008 0.11 -10000 0 -0.55 22 22
RASA1 0.03 0.034 -10000 0 -0.55 3 3
KLHL9 0.032 0.006 -10000 0 -10000 0 0
mitotic prometaphase 0 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.07 -10000 0 -0.25 43 43
PPP1CC 0.032 0.007 -10000 0 -10000 0 0
Centraspindlin 0.02 0.13 -10000 0 -0.37 72 72
RhoA/GDP 0.022 0.007 -10000 0 -10000 0 0
NSUN2 -0.007 0.11 -10000 0 -0.54 23 23
MYLK -0.01 0.095 -10000 0 -0.35 55 55
KIF23 0.023 0.068 -10000 0 -0.37 24 24
VIM -0.01 0.11 -10000 0 -0.35 67 67
RACGAP1 0.031 0.019 -10000 0 -0.33 2 2
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.027 0.19 -10000 0 -0.76 49 49
Chromosomal passenger complex -0.009 0.12 -10000 0 -0.36 73 73
Chromosomal passenger complex/EVI5 0.057 0.12 -10000 0 -0.36 52 52
TACC1 0.029 0.04 -10000 0 -0.55 4 4
PPP2R5D 0.031 0.008 -10000 0 -10000 0 0
CUL3 0.031 0.008 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
ErbB4 signaling events

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.001 0.091 -10000 0 -0.42 10 10
epithelial cell differentiation -0.012 0.11 -10000 0 -0.43 11 11
ITCH 0.04 0.02 -10000 0 -10000 0 0
WWP1 0.001 0.063 -10000 0 -0.68 1 1
FYN 0.025 0.056 -10000 0 -0.55 8 8
EGFR 0.008 0.1 -10000 0 -0.47 36 36
PRL 0.018 0.035 -10000 0 -0.32 9 9
neuron projection morphogenesis -0.005 0.11 0.35 23 -0.43 10 33
PTPRZ1 -0.001 0.091 -10000 0 -0.32 63 63
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.019 0.12 -10000 0 -0.39 23 23
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.018 0.11 -10000 0 -0.4 36 36
ADAM17 0.036 0.042 -10000 0 -0.54 4 4
ErbB4/ErbB4 -0.002 0.075 -10000 0 -0.52 4 4
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.015 0.12 -10000 0 -0.35 61 61
NCOR1 0.029 0.01 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.006 0.12 -10000 0 -0.4 36 36
GRIN2B -0.029 0.11 0.26 2 -0.42 25 27
ErbB4/ErbB2/betacellulin 0 0.1 -10000 0 -0.41 16 16
STAT1 0.028 0.041 -10000 0 -0.38 8 8
HBEGF 0.025 0.055 -10000 0 -0.41 13 13
PRLR -0.05 0.18 -10000 0 -0.4 166 166
E4ICDs/ETO2 0 0.094 -10000 0 -0.4 15 15
axon guidance -0.004 0.073 -10000 0 -0.47 6 6
NEDD4 0.028 0.086 -10000 0 -0.54 19 19
Prolactin receptor/Prolactin receptor/Prolactin -0.024 0.13 -10000 0 -0.28 175 175
CBFA2T3 0.02 0.076 -10000 0 -0.51 17 17
ErbB4/ErbB2/HBEGF 0.015 0.075 -10000 0 -0.4 5 5
MAPK3 -0.009 0.1 0.34 2 -0.38 21 23
STAT1 (dimer) 0.007 0.086 -10000 0 -0.41 9 9
MAPK1 -0.009 0.1 0.34 2 -0.38 21 23
JAK2 0.031 0.02 -10000 0 -0.55 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.013 0.1 -10000 0 -0.43 20 20
NRG1 -0.008 0.1 -10000 0 -0.4 49 49
NRG3 -0.012 0.15 -10000 0 -0.5 70 70
NRG2 -0.009 0.12 -10000 0 -0.38 85 85
NRG4 -0.014 0.12 -10000 0 -0.34 109 109
heart development -0.004 0.073 -10000 0 -0.47 6 6
neural crest cell migration -0.013 0.1 -10000 0 -0.43 20 20
ERBB2 0.019 0.035 -10000 0 -0.4 5 5
WWOX/E4ICDs 0.005 0.082 -10000 0 -0.45 4 4
SHC1 0.031 0.014 -10000 0 -0.32 1 1
ErbB4/EGFR/neuregulin 4 -0.011 0.13 -10000 0 -0.4 53 53
apoptosis 0.038 0.16 0.47 90 -10000 0 90
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.015 0.12 -10000 0 -0.37 56 56
ErbB4/ErbB2/epiregulin -0.025 0.12 -10000 0 -0.39 24 24
ErbB4/ErbB4/betacellulin/betacellulin -0.015 0.12 -10000 0 -0.35 55 55
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.006 0.14 -10000 0 -0.44 21 21
MDM2 0.002 0.074 0.26 16 -0.54 3 19
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.002 0.1 -10000 0 -0.37 33 33
STAT5A 0.001 0.071 0.29 4 -0.42 6 10
ErbB4/EGFR/neuregulin 1 beta -0.017 0.13 -10000 0 -0.41 47 47
DLG4 0.022 0.063 -10000 0 -0.53 11 11
GRB2/SHC 0.042 0.019 -10000 0 -0.22 1 1
E4ICDs/TAB2/NCoR1 0.006 0.074 -10000 0 -0.4 5 5
STAT5A (dimer) -0.005 0.12 -10000 0 -0.51 7 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.012 0.075 0.34 1 -0.44 5 6
LRIG1 0.028 0.037 -10000 0 -0.49 4 4
EREG -0.071 0.18 -10000 0 -0.37 221 221
BTC -0.006 0.14 -10000 0 -0.47 66 66
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.004 0.073 -10000 0 -0.47 6 6
ERBB4 -0.002 0.075 -10000 0 -0.52 4 4
STAT5B 0.029 0.01 -10000 0 -10000 0 0
YAP1 0.01 0.065 -10000 0 -0.57 9 9
GRB2 0.029 0.011 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.003 0.1 -10000 0 -0.4 9 9
glial cell differentiation -0.006 0.073 0.4 5 -10000 0 5
WWOX 0.03 0.015 -10000 0 -0.32 1 1
cell proliferation -0.033 0.17 0.41 5 -0.57 47 52
Sphingosine 1-phosphate (S1P) pathway

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.031 0.034 -10000 0 -0.55 3 3
SPHK1 0.002 0.1 -10000 0 -0.36 61 61
GNAI2 0.03 0.009 -10000 0 -10000 0 0
mol:S1P 0.007 0.059 -10000 0 -0.32 17 17
GNAO1 -0.001 0.12 -10000 0 -0.42 63 63
mol:Sphinganine-1-P -0.002 0.078 -10000 0 -0.26 60 60
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.05 0.067 -10000 0 -0.5 5 5
GNAI3 0.031 0.008 -10000 0 -10000 0 0
G12/G13 0.04 0.019 -10000 0 -10000 0 0
S1PR3 -0.032 0.18 -10000 0 -0.51 104 104
S1PR2 0.03 0.035 -10000 0 -0.41 5 5
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0 0.054 -10000 0 -0.27 19 19
S1PR5 -0.011 0.15 -10000 0 -0.5 72 72
S1PR4 0.012 0.11 -10000 0 -0.52 33 33
GNAI1 0.023 0.059 -10000 0 -0.55 9 9
S1P/S1P5/G12 0.022 0.091 -10000 0 -0.31 41 41
S1P/S1P3/Gq -0.037 0.18 -10000 0 -0.44 115 115
S1P/S1P4/Gi 0.005 0.11 0.19 1 -0.38 44 45
GNAQ 0.032 0.005 -10000 0 -10000 0 0
GNAZ 0.026 0.056 -10000 0 -0.48 10 10
GNA14 -0.029 0.18 -10000 0 -0.55 93 93
GNA15 0.014 0.1 -10000 0 -0.5 31 31
GNA12 0.029 0.011 -10000 0 -10000 0 0
GNA13 0.029 0.011 -10000 0 -10000 0 0
GNA11 0.017 0.089 -10000 0 -0.44 30 30
ABCC1 0.03 0.021 -10000 0 -0.55 1 1
PLK1 signaling events

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.002 0.05 0.14 73 -0.12 23 96
BUB1B 0.014 0.054 0.18 20 -0.23 20 40
PLK1 0.013 0.036 0.13 34 -0.15 8 42
PLK1S1 0.017 0.029 0.13 31 -0.18 3 34
KIF2A 0.012 0.055 0.24 27 -0.19 14 41
regulation of mitotic centrosome separation 0.013 0.036 0.13 34 -0.15 8 42
GOLGA2 0.032 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.021 0.1 0.19 2 -0.3 65 67
WEE1 0.024 0.052 0.23 4 -0.35 9 13
cytokinesis 0.001 0.12 0.24 16 -0.46 33 49
PP2A-alpha B56 0.038 0.14 -10000 0 -0.56 44 44
AURKA 0.015 0.026 0.14 10 -0.2 2 12
PICH/PLK1 0.016 0.055 -10000 0 -0.31 17 17
CENPE 0.002 0.071 0.26 14 -0.23 45 59
RhoA/GTP 0.022 0.007 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.012 0.055 0.24 27 -0.19 14 41
PPP2CA 0.031 0.008 -10000 0 -10000 0 0
FZR1 0.031 0.028 -10000 0 -0.55 2 2
TPX2 0.012 0.046 0.15 16 -0.27 13 29
PAK1 0.033 0.004 -10000 0 -10000 0 0
SPC24 0.01 0.1 -10000 0 -0.42 43 43
FBXW11 0.031 0.008 -10000 0 -10000 0 0
CLSPN -0.007 0.085 0.14 4 -0.27 78 82
GORASP1 0.03 0.01 -10000 0 -10000 0 0
metaphase 0.001 0.005 0.019 59 -0.018 6 65
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.02 0.065 47 -0.066 11 58
G2 phase of mitotic cell cycle -0.001 0.002 0.014 14 -10000 0 14
STAG2 0.031 0.034 -10000 0 -0.55 3 3
GRASP65/GM130/RAB1/GTP -0.003 0.12 -10000 0 -0.48 55 55
spindle elongation 0.013 0.036 0.13 34 -0.15 8 42
ODF2 0.032 0.02 -10000 0 -0.56 1 1
BUB1 0.005 0.14 -10000 0 -0.61 43 43
TPT1 0.007 0.051 0.13 10 -0.21 40 50
CDC25C 0.003 0.079 0.16 1 -0.38 31 32
CDC25B 0.029 0.033 -10000 0 -0.32 7 7
SGOL1 -0.002 0.05 0.12 23 -0.14 73 96
RHOA 0.03 0.009 -10000 0 -10000 0 0
CCNB1/CDK1 0.042 0.043 -10000 0 -0.31 5 5
CDC14B 0.01 0.002 -10000 0 -10000 0 0
CDC20 0.017 0.073 -10000 0 -0.34 34 34
PLK1/PBIP1 0.011 0.034 0.11 10 -0.22 8 18
mitosis -0.002 0.002 0.019 2 -10000 0 2
FBXO5 0.009 0.041 0.15 19 -0.19 6 25
CDC2 0.001 0.002 -10000 0 -0.013 6 6
NDC80 0.004 0.12 -10000 0 -0.51 45 45
metaphase plate congression 0.002 0.072 0.15 4 -0.26 57 61
ERCC6L 0.021 0.055 -10000 0 -0.3 18 18
NLP/gamma Tubulin 0.009 0.037 0.1 41 -0.12 37 78
microtubule cytoskeleton organization 0.007 0.051 0.13 10 -0.21 40 50
G2/M transition DNA damage checkpoint -0.001 0.002 0.014 6 -10000 0 6
PPP1R12A 0.032 0.007 -10000 0 -10000 0 0
interphase -0.001 0.002 0.014 6 -10000 0 6
PLK1/PRC1-2 0.028 0.085 0.22 1 -0.29 42 43
GRASP65/GM130/RAB1/GTP/PLK1 0.054 0.036 0.19 2 -0.2 1 3
RAB1A 0.032 0.007 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.01 0.03 0.1 49 -0.12 5 54
mitotic prometaphase 0 0.005 0.018 52 -0.013 1 53
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.041 -10000 0 -0.44 4 4
microtubule-based process 0.014 0.073 0.17 7 -0.24 51 58
Golgi organization 0.013 0.036 0.13 34 -0.15 8 42
Cohesin/SA2 0.028 0.036 0.15 10 -0.25 5 15
PPP1CB/MYPT1 0.045 0.014 -10000 0 -10000 0 0
KIF20A 0.002 0.12 -10000 0 -0.42 56 56
APC/C/CDC20 0.026 0.053 0.16 10 -0.2 33 43
PPP2R1A 0.032 0.02 -10000 0 -0.55 1 1
chromosome segregation 0.011 0.033 0.11 10 -0.22 8 18
PRC1 0.028 0.05 -10000 0 -0.45 9 9
ECT2 0.02 0.064 0.26 44 -0.22 6 50
C13orf34 0.01 0.03 0.11 35 -0.12 8 43
NUDC 0.002 0.072 0.15 4 -0.26 57 61
regulation of attachment of spindle microtubules to kinetochore 0.014 0.053 0.18 20 -0.23 20 40
spindle assembly 0.014 0.041 0.13 56 -0.15 8 64
spindle stabilization 0.017 0.029 0.13 31 -0.18 3 34
APC/C/HCDH1 0.03 0.019 -10000 0 -0.35 2 2
MKLP2/PLK1 0.014 0.073 0.17 7 -0.25 51 58
CCNB1 0.027 0.049 -10000 0 -0.34 15 15
PPP1CB 0.032 0.007 -10000 0 -10000 0 0
BTRC 0.031 0.008 -10000 0 -10000 0 0
ROCK2 -0.005 0.11 0.25 6 -0.37 63 69
TUBG1 0.007 0.057 0.12 23 -0.24 37 60
G2/M transition of mitotic cell cycle 0.01 0.035 -10000 0 -0.3 5 5
MLF1IP 0.008 0.028 -10000 0 -0.41 4 4
INCENP 0.031 0.028 -10000 0 -0.55 2 2
Regulation of Androgen receptor activity

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.018 0.006 -10000 0 -10000 0 0
SMARCC1 0.016 0.052 -10000 0 -0.8 3 3
REL 0.015 0.098 -10000 0 -0.53 27 27
HDAC7 -0.031 0.11 -10000 0 -0.41 23 23
JUN 0.029 0.029 -10000 0 -0.38 4 4
EP300 0.031 0.028 -10000 0 -0.55 2 2
KAT2B 0.029 0.022 -10000 0 -0.55 1 1
KAT5 0.033 0.004 -10000 0 -10000 0 0
MAPK14 0.005 0.04 -10000 0 -0.36 7 7
FOXO1 0.029 0.028 -10000 0 -0.32 5 5
T-DHT/AR -0.014 0.13 -10000 0 -0.42 23 23
MAP2K6 0.019 0.051 -10000 0 -0.49 7 7
BRM/BAF57 0.042 0.017 -10000 0 -10000 0 0
MAP2K4 0.023 0.02 -10000 0 -10000 0 0
SMARCA2 0.032 0.006 -10000 0 -10000 0 0
PDE9A -0.057 0.23 -10000 0 -0.9 51 51
NCOA2 -0.005 0.14 -10000 0 -0.55 55 55
CEBPA 0.013 0.099 -10000 0 -0.45 36 36
EHMT2 0.029 0.029 -10000 0 -0.55 2 2
cell proliferation -0.007 0.22 0.52 61 -0.5 60 121
NR0B1 -0.01 0.1 -10000 0 -0.32 87 87
EGR1 -0.021 0.15 -10000 0 -0.43 98 98
RXRs/9cRA 0.046 0.047 -10000 0 -0.21 12 12
AR/RACK1/Src -0.007 0.11 0.31 24 -0.43 18 42
AR/GR -0.011 0.15 0.26 38 -0.37 90 128
GNB2L1 0.031 0.008 -10000 0 -10000 0 0
PKN1 0.031 0.028 -10000 0 -0.55 2 2
RCHY1 0.032 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -10000 0 -0.021 2 2
MAPK8 0.005 0.041 -10000 0 -0.41 6 6
T-DHT/AR/TIF2/CARM1 -0.005 0.15 0.36 34 -0.43 45 79
SRC -0.009 0.045 0.21 7 -0.31 8 15
NR3C1 0.029 0.037 -10000 0 -0.49 4 4
KLK3 -0.062 0.18 -10000 0 -0.67 41 41
APPBP2 0.022 0.028 -10000 0 -0.56 1 1
TRIM24 0.028 0.011 -10000 0 -10000 0 0
T-DHT/AR/TIP60 0 0.12 0.34 36 -0.4 24 60
TMPRSS2 -0.21 0.44 -10000 0 -1.1 162 162
RXRG 0.014 0.061 -10000 0 -0.32 27 27
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.031 0.028 -10000 0 -0.55 2 2
RXRB 0.03 0.021 -10000 0 -0.55 1 1
CARM1 0.032 0.02 -10000 0 -0.55 1 1
NR2C2 0.025 0.056 -10000 0 -0.55 8 8
KLK2 -0.019 0.16 0.38 35 -0.48 48 83
AR -0.022 0.1 -10000 0 -0.32 87 87
SENP1 0.031 0.007 -10000 0 -10000 0 0
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
MDM2 0.033 0.009 -10000 0 -10000 0 0
SRY 0.001 0.005 0.014 67 -10000 0 67
GATA2 -0.015 0.14 -10000 0 -0.41 93 93
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 -0.049 0.15 -10000 0 -0.35 168 168
T-DHT/AR/RACK1/Src 0.002 0.12 0.37 36 -0.42 18 54
positive regulation of transcription -0.015 0.14 -10000 0 -0.41 93 93
DNAJA1 0.027 0.019 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.009 -10000 0 -10000 0 0
NCOA1 0.038 0.021 -10000 0 -10000 0 0
SPDEF -0.011 0.11 -10000 0 -0.33 97 97
T-DHT/AR/TIF2 -0.007 0.13 0.28 22 -0.44 43 65
T-DHT/AR/Hsp90 -0.001 0.12 0.33 34 -0.4 23 57
GSK3B 0.031 0.008 -10000 0 -10000 0 0
NR2C1 0.032 0.007 -10000 0 -10000 0 0
mol:T-DHT -0.011 0.047 0.15 1 -0.33 10 11
SIRT1 0.03 0.021 -10000 0 -0.55 1 1
ZMIZ2 0.029 0.03 -10000 0 -0.55 2 2
POU2F1 0.012 0.061 -10000 0 -0.56 2 2
T-DHT/AR/DAX-1 -0.022 0.13 0.33 32 -0.39 34 66
CREBBP 0.031 0.008 -10000 0 -10000 0 0
SMARCE1 0.029 0.01 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.02 0.066 0.22 10 -0.32 12 22
adherens junction organization 0 0.094 0.22 11 -0.3 46 57
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.083 0.24 8 -0.34 18 26
FMN1 -0.017 0.1 -10000 0 -0.3 79 79
mol:IP3 0.015 0.058 -10000 0 -0.28 11 11
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.004 0.086 -10000 0 -0.3 44 44
CTNNB1 0.03 0.01 -10000 0 -10000 0 0
AKT1 0.021 0.071 0.25 5 -0.29 14 19
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.002 0.12 -10000 0 -0.44 39 39
CTNND1 0.035 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.005 0.076 -10000 0 -0.28 37 37
VASP 0.001 0.082 -10000 0 -0.29 41 41
ZYX -0.002 0.084 -10000 0 -0.3 42 42
JUB 0.001 0.081 -10000 0 -0.28 44 44
EGFR(dimer) 0.006 0.1 0.21 1 -0.32 58 59
E-cadherin/beta catenin-gamma catenin 0.028 0.093 -10000 0 -0.35 35 35
mol:PI-3-4-5-P3 0.037 0.08 0.24 15 -0.31 13 28
PIK3CA 0.029 0.049 -10000 0 -0.55 6 6
PI3K 0.039 0.082 0.24 15 -0.32 13 28
FYN -0.045 0.13 0.26 8 -0.39 53 61
mol:Ca2+ 0.015 0.057 -10000 0 -0.28 11 11
JUP 0.025 0.052 -10000 0 -0.55 7 7
PIK3R1 0.032 0.039 -10000 0 -0.46 5 5
mol:DAG 0.015 0.058 -10000 0 -0.28 11 11
CDH1 -0.005 0.13 -10000 0 -0.44 66 66
RhoA/GDP 0.027 0.089 0.24 10 -0.34 17 27
establishment of polarity of embryonic epithelium 0.001 0.08 -10000 0 -0.28 41 41
SRC 0.031 0.008 -10000 0 -10000 0 0
RAC1 0.029 0.011 -10000 0 -10000 0 0
RHOA 0.03 0.009 -10000 0 -10000 0 0
EGFR 0.008 0.1 -10000 0 -0.47 36 36
CASR -0.047 0.12 0.25 7 -0.28 129 136
RhoA/GTP 0.029 0.058 -10000 0 -0.35 3 3
AKT2 0.022 0.074 0.25 7 -0.33 10 17
actin cable formation -0.016 0.1 0.2 4 -0.36 30 34
apoptosis -0.034 0.1 0.31 15 -0.34 42 57
CTNNA1 0.033 0.011 -10000 0 -10000 0 0
mol:GDP 0.001 0.077 -10000 0 -0.34 23 23
PIP5K1A 0.005 0.077 -10000 0 -0.29 37 37
PLCG1 0.015 0.059 -10000 0 -0.29 11 11
Rac1/GTP 0.018 0.1 -10000 0 -0.39 22 22
homophilic cell adhesion 0.002 0.007 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.008 0.19 0.35 1 -1.2 17 18
VDR 0.008 0.09 -10000 0 -0.33 56 56
FAM120B 0.031 0.009 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.029 0.093 -10000 0 -0.38 20 20
RXRs/LXRs/DNA/Oxysterols 0.025 0.12 -10000 0 -0.44 46 46
MED1 0.029 0.01 -10000 0 -10000 0 0
mol:9cRA 0.002 0.013 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.014 0.08 -10000 0 -0.28 52 52
RXRs/NUR77 0.021 0.13 -10000 0 -0.31 65 65
RXRs/PPAR 0.029 0.056 -10000 0 -0.34 12 12
NCOR2 0.03 0.029 -10000 0 -0.55 2 2
VDR/VDR/Vit D3 0.007 0.062 -10000 0 -0.23 56 56
RARs/VDR/DNA/Vit D3 0.047 0.071 -10000 0 -0.3 13 13
RARA 0.028 0.029 -10000 0 -0.55 2 2
NCOA1 0.031 0.007 -10000 0 -10000 0 0
VDR/VDR/DNA 0.008 0.09 -10000 0 -0.33 56 56
RARs/RARs/DNA/9cRA 0.044 0.044 -10000 0 -0.3 9 9
RARG 0.03 0.031 -10000 0 -0.47 3 3
RPS6KB1 0.043 0.14 0.52 62 -0.4 11 73
RARs/THRs/DNA/SMRT 0.013 0.084 -10000 0 -0.28 54 54
THRA 0.028 0.029 -10000 0 -0.55 2 2
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.007 0.062 -10000 0 -0.23 56 56
RXRs/PPAR/9cRA/PGJ2/DNA 0.053 0.073 0.35 5 -0.34 6 11
NR1H4 -0.016 0.16 -10000 0 -0.55 72 72
RXRs/LXRs/DNA 0.082 0.096 -10000 0 -0.44 7 7
NR1H2 0.03 0.037 -10000 0 -0.58 2 2
NR1H3 0.031 0.025 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.05 0.082 -10000 0 -0.3 18 18
NR4A1 -0.04 0.17 -10000 0 -0.41 142 142
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.01 0.14 -10000 0 -0.39 81 81
RXRG 0.015 0.064 -10000 0 -0.32 27 27
RXR alpha/CCPG 0.044 0.03 -10000 0 -0.41 2 2
RXRA 0.03 0.036 -10000 0 -0.56 2 2
RXRB 0.029 0.031 -10000 0 -0.57 1 1
THRB -0.001 0.12 -10000 0 -0.4 62 62
PPARG 0.027 0.043 -10000 0 -0.47 6 6
PPARD 0.03 0.021 -10000 0 -0.55 1 1
TNF -0.02 0.26 -10000 0 -1 49 49
mol:Oxysterols 0.002 0.012 -10000 0 -10000 0 0
cholesterol transport 0.025 0.12 -10000 0 -0.43 46 46
PPARA 0.032 0.006 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.026 0.049 -10000 0 -0.55 6 6
RXRs/NUR77/BCL2 -0.014 0.11 -10000 0 -0.3 87 87
SREBF1 0.019 0.13 -10000 0 -1.1 4 4
RXRs/RXRs/DNA/9cRA 0.053 0.073 0.34 5 -0.34 6 11
ABCA1 0.02 0.13 -10000 0 -0.59 18 18
RARs/THRs 0.057 0.091 -10000 0 -0.31 31 31
RXRs/FXR 0.04 0.12 -10000 0 -0.32 73 73
BCL2 0.023 0.07 -10000 0 -0.55 13 13
Insulin-mediated glucose transport

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles 0.019 0.17 0.26 29 -0.52 57 86
CaM/Ca2+ 0.024 0.005 -10000 0 -10000 0 0
AKT1 0.031 0.021 -10000 0 -0.55 1 1
AKT2 0.032 0.02 -10000 0 -0.55 1 1
STXBP4 0.029 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.016 0.19 0.3 70 -0.54 64 134
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
CALM1 0.032 0.006 -10000 0 -10000 0 0
YWHAQ 0.031 0.007 -10000 0 -10000 0 0
TBC1D4 0.017 0.023 -10000 0 -0.25 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.032 0.006 -10000 0 -10000 0 0
YWHAB 0.031 0.008 -10000 0 -10000 0 0
SNARE/Synip 0.056 0.028 -10000 0 -0.34 1 1
YWHAG 0.029 0.011 -10000 0 -10000 0 0
ASIP -0.023 0.14 -10000 0 -0.4 104 104
PRKCI 0.031 0.014 -10000 0 -0.32 1 1
AS160/CaM/Ca2+ 0.024 0.005 -10000 0 -10000 0 0
RHOQ 0.031 0.007 -10000 0 -10000 0 0
GYS1 0.018 0.026 -10000 0 -0.74 1 1
PRKCZ 0.025 0.056 -10000 0 -0.55 8 8
TRIP10 0.027 0.059 -10000 0 -0.55 9 9
TC10/GTP/CIP4/Exocyst 0.039 0.039 -10000 0 -0.33 9 9
AS160/14-3-3 -0.012 0.094 -10000 0 -0.35 30 30
VAMP2 0.029 0.01 -10000 0 -10000 0 0
SLC2A4 0.01 0.21 0.31 66 -0.62 64 130
STX4 0.03 0.021 -10000 0 -0.55 1 1
GSK3B 0.027 0.03 -10000 0 -0.82 1 1
SFN -0.099 0.2 -10000 0 -0.39 274 274
LNPEP 0.019 0.087 -10000 0 -0.55 20 20
YWHAE 0.029 0.01 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.002 0.048 -10000 0 -0.34 16 16
SNTA1 0.024 0.058 -10000 0 -0.4 15 15
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0 0.054 -10000 0 -0.34 20 20
MAPK12 -0.01 0.058 -10000 0 -0.34 17 17
CCND1 -0.005 0.099 -10000 0 -0.42 41 41
p38 gamma/SNTA1 0.014 0.077 -10000 0 -0.33 19 19
MAP2K3 0.029 0.022 -10000 0 -0.55 1 1
PKN1 0.032 0.028 -10000 0 -0.55 2 2
G2/M transition checkpoint -0.009 0.058 0.18 1 -0.34 17 18
MAP2K6 0.003 0.03 -10000 0 -0.29 9 9
MAPT -0.032 0.16 0.3 47 -0.37 133 180
MAPK13 0.008 0.063 -10000 0 -0.4 20 20
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.009 0.017 -10000 0 -0.35 2 2
Paxillin-dependent events mediated by a4b1

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.032 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.028 0.015 -10000 0 -10000 0 0
DOCK1 0.03 0.029 -10000 0 -0.55 2 2
ITGA4 -0.013 0.15 -10000 0 -0.54 68 68
RAC1 0.029 0.011 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.007 0.12 -10000 0 -0.38 74 74
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.016 -10000 0 -0.32 1 1
alpha4/beta1 Integrin 0.031 0.11 -10000 0 -0.34 63 63
alpha4/beta7 Integrin/Paxillin 0.023 0.1 -10000 0 -0.32 65 65
lamellipodium assembly 0.031 0.076 0.27 1 -0.44 16 17
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
PI3K 0.04 0.049 -10000 0 -0.37 11 11
ARF6 0.032 0.006 -10000 0 -10000 0 0
TLN1 0.032 0.02 -10000 0 -0.55 1 1
PXN 0.019 0.004 -10000 0 -10000 0 0
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
ARF6/GTP 0.042 0.081 -10000 0 -0.28 37 37
cell adhesion 0.039 0.095 -10000 0 -0.3 59 59
CRKL/CBL 0.047 0.018 -10000 0 -0.4 1 1
alpha4/beta1 Integrin/Paxillin 0.025 0.094 -10000 0 -0.31 58 58
ITGB1 0.031 0.008 -10000 0 -10000 0 0
ITGB7 0.026 0.056 -10000 0 -0.55 8 8
ARF6/GDP 0.031 0.014 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.008 0.14 -10000 0 -0.32 117 117
p130Cas/Crk/Dock1 0.054 0.041 -10000 0 -0.38 5 5
VCAM1 -0.019 0.16 -10000 0 -0.55 76 76
alpha4/beta1 Integrin/Paxillin/Talin 0.041 0.097 -10000 0 -0.3 59 59
alpha4/beta1 Integrin/Paxillin/GIT1 0.044 0.087 -10000 0 -0.3 42 42
BCAR1 0.029 0.035 -10000 0 -0.55 3 3
mol:GDP -0.042 0.086 0.3 42 -10000 0 42
CBL 0.032 0.02 -10000 0 -0.55 1 1
PRKACA 0.033 0.003 -10000 0 -10000 0 0
GIT1 0.028 0.029 -10000 0 -0.55 2 2
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.041 0.097 -10000 0 -0.3 59 59
Rac1/GTP 0.032 0.085 0.28 1 -0.5 16 17
Regulation of nuclear SMAD2/3 signaling

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.016 0.041 -10000 0 -0.55 2 2
HSPA8 0.033 0.028 -10000 0 -0.53 2 2
SMAD3/SMAD4/ER alpha 0.055 0.11 0.29 9 -0.35 31 40
AKT1 0.032 0.027 -10000 0 -0.55 1 1
GSC -0.01 0.22 -10000 0 -1.5 16 16
NKX2-5 -0.001 0.016 -10000 0 -10000 0 0
muscle cell differentiation -0.043 0.1 0.46 11 -10000 0 11
SMAD2-3/SMAD4/SP1 0.083 0.11 -10000 0 -0.41 16 16
SMAD4 0.029 0.056 -10000 0 -0.28 5 5
CBFB 0.03 0.021 -10000 0 -0.55 1 1
SAP18 0.032 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.037 0.065 -10000 0 -0.23 28 28
SMAD3/SMAD4/VDR 0.071 0.086 -10000 0 -0.34 1 1
MYC 0.01 0.1 -10000 0 -0.52 32 32
CDKN2B 0.002 0.25 -10000 0 -1.4 22 22
AP1 0.029 0.11 -10000 0 -0.38 21 21
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.027 0.13 -10000 0 -0.48 44 44
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.025 0.074 -10000 0 -0.4 19 19
SP3 0.032 0.029 -10000 0 -0.55 2 2
CREB1 0.031 0.007 -10000 0 -10000 0 0
FOXH1 0.011 0.086 -10000 0 -0.37 35 35
SMAD3/SMAD4/GR 0.077 0.074 -10000 0 -0.34 2 2
GATA3 -0.048 0.18 -10000 0 -0.42 148 148
SKI/SIN3/HDAC complex/NCoR1 0.029 0.13 -10000 0 -0.7 23 23
MEF2C/TIF2 -0.001 0.16 0.32 1 -0.52 53 54
endothelial cell migration 0.25 0.56 1.5 147 -10000 0 147
MAX 0.041 0.022 -10000 0 -10000 0 0
RBBP7 0.034 0.003 -10000 0 -10000 0 0
RBBP4 0.031 0.021 -10000 0 -0.55 1 1
RUNX2 0.021 0.073 -10000 0 -0.48 17 17
RUNX3 0.01 0.1 -10000 0 -0.52 33 33
RUNX1 0.016 0.092 -10000 0 -0.54 23 23
CTBP1 0.032 0.005 -10000 0 -10000 0 0
NR3C1 0.038 0.039 -10000 0 -0.43 4 4
VDR 0.008 0.09 -10000 0 -0.33 56 56
CDKN1A 0.016 0.16 -10000 0 -1.3 7 7
KAT2B 0.024 0.026 -10000 0 -0.55 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.052 0.099 -10000 0 -0.33 26 26
DCP1A 0.03 0.009 -10000 0 -10000 0 0
SKI 0.031 0.009 -10000 0 -10000 0 0
SERPINE1 -0.26 0.57 -10000 0 -1.5 147 147
SMAD3/SMAD4/ATF2 0.056 0.085 -10000 0 -0.38 15 15
SMAD3/SMAD4/ATF3 0.036 0.11 -10000 0 -0.41 21 21
SAP30 0.013 0.11 -10000 0 -0.55 30 30
Cbp/p300/PIAS3 0.034 0.054 -10000 0 -0.35 2 2
JUN 0.017 0.1 0.33 4 -0.38 19 23
SMAD3/SMAD4/IRF7 0.061 0.083 -10000 0 -0.39 11 11
TFE3 0.018 0.039 -10000 0 -10000 0 0
COL1A2 -0.04 0.24 0.42 4 -0.88 58 62
mesenchymal cell differentiation -0.052 0.087 0.37 15 -10000 0 15
DLX1 -0.038 0.18 -10000 0 -0.48 116 116
TCF3 0.033 0.003 -10000 0 -10000 0 0
FOS -0.021 0.16 -10000 0 -0.42 112 112
SMAD3/SMAD4/Max 0.082 0.071 -10000 0 -0.34 2 2
Cbp/p300/SNIP1 0.047 0.039 -10000 0 -0.35 2 2
ZBTB17 0.028 0.036 -10000 0 -0.55 3 3
LAMC1 0.024 0.059 -10000 0 -0.42 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.065 0.064 -10000 0 -0.41 2 2
IRF7 0.026 0.063 -10000 0 -0.48 13 13
ESR1 0.01 0.11 0.19 3 -0.48 42 45
HNF4A -0.06 0.21 -10000 0 -0.55 137 137
MEF2C 0.004 0.14 0.43 5 -0.54 42 47
SMAD2-3/SMAD4 0.068 0.08 -10000 0 -0.36 6 6
Cbp/p300/Src-1 0.044 0.043 -10000 0 -0.35 2 2
IGHV3OR16-13 0.008 0.063 -10000 0 -0.42 16 16
TGIF2/HDAC complex 0.031 0.008 -10000 0 -10000 0 0
CREBBP 0.022 0.023 -10000 0 -10000 0 0
SKIL 0.026 0.056 -10000 0 -0.55 8 8
HDAC1 0.032 0.008 -10000 0 -10000 0 0
HDAC2 0.032 0.009 -10000 0 -10000 0 0
SNIP1 0.032 0.009 -10000 0 -10000 0 0
GCN5L2 -0.006 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.057 0.082 -10000 0 -0.4 4 4
MSG1/HSC70 0.041 0.056 -10000 0 -0.24 30 30
SMAD2 0.029 0.035 -10000 0 -0.22 1 1
SMAD3 0.031 0.052 -10000 0 -0.32 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 0.038 0.05 -10000 0 -0.36 3 3
SMAD2/SMAD2/SMAD4 -0.001 0.057 0.33 2 -0.39 4 6
NCOR1 0.03 0.011 -10000 0 -10000 0 0
NCOA2 -0.005 0.14 -10000 0 -0.55 55 55
NCOA1 0.031 0.007 -10000 0 -10000 0 0
MYOD/E2A 0.035 0.038 -10000 0 -0.22 19 19
SMAD2-3/SMAD4/SP1/MIZ-1 0.09 0.12 -10000 0 -0.43 12 12
IFNB1 0.02 0.066 -10000 0 -0.38 8 8
SMAD3/SMAD4/MEF2C 0.04 0.15 -10000 0 -0.54 41 41
CITED1 0.02 0.07 -10000 0 -0.34 30 30
SMAD2-3/SMAD4/ARC105 0.084 0.079 -10000 0 -0.34 6 6
RBL1 0.025 0.059 -10000 0 -0.55 9 9
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.032 0.1 -10000 0 -0.61 18 18
RUNX1-3/PEBPB2 0.034 0.096 -10000 0 -0.36 38 38
SMAD7 0.037 0.12 -10000 0 -0.57 15 15
MYC/MIZ-1 0.025 0.085 -10000 0 -0.38 33 33
SMAD3/SMAD4 -0.059 0.19 0.3 7 -0.47 130 137
IL10 -0.03 0.18 -10000 0 -0.61 50 50
PIASy/HDAC complex 0.037 0.032 -10000 0 -0.55 2 2
PIAS3 0.024 0.019 -10000 0 -10000 0 0
CDK2 0.022 0.022 -10000 0 -10000 0 0
IL5 -0.02 0.13 -10000 0 -0.47 30 30
CDK4 0.022 0.023 -10000 0 -10000 0 0
PIAS4 0.037 0.032 -10000 0 -0.55 2 2
ATF3 -0.005 0.12 -10000 0 -0.37 79 79
SMAD3/SMAD4/SP1 0.059 0.11 -10000 0 -0.4 19 19
FOXG1 -0.004 0.063 -10000 0 -0.32 28 28
FOXO3 0.019 0.025 -10000 0 -0.4 1 1
FOXO1 0.018 0.029 -10000 0 -0.24 6 6
FOXO4 0.02 0.024 -10000 0 -0.4 1 1
heart looping 0.004 0.14 0.43 5 -0.53 43 48
CEBPB 0.028 0.038 -10000 0 -0.32 9 9
SMAD3/SMAD4/DLX1 0.014 0.14 -10000 0 -0.36 84 84
MYOD1 0.015 0.05 -10000 0 -0.32 19 19
SMAD3/SMAD4/HNF4 0.001 0.16 -10000 0 -0.36 136 136
SMAD3/SMAD4/GATA3 0.009 0.16 -10000 0 -0.45 55 55
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.056 -10000 0 -0.55 8 8
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.069 0.11 -10000 0 -0.4 22 22
SMAD3/SMAD4/SP1-3 0.079 0.1 -10000 0 -0.41 11 11
MED15 0.031 0.028 -10000 0 -0.55 2 2
SP1 0.02 0.056 -10000 0 -0.22 12 12
SIN3B 0.032 0.028 -10000 0 -0.55 2 2
SIN3A 0.034 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.05 0.11 -10000 0 -0.31 47 47
ITGB5 0.034 0.084 0.4 4 -0.47 5 9
TGIF/SIN3/HDAC complex/CtBP 0.029 0.098 -10000 0 -0.53 23 23
SMAD3/SMAD4/AR 0.013 0.15 -10000 0 -0.36 106 106
AR -0.042 0.19 -10000 0 -0.52 120 120
negative regulation of cell growth 0.033 0.062 -10000 0 -0.4 2 2
SMAD3/SMAD4/MYOD 0.052 0.077 -10000 0 -0.32 6 6
E2F5 0.029 0.041 -10000 0 -0.5 5 5
E2F4 0.031 0.009 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.067 0.097 -10000 0 -0.34 14 14
SMAD2-3/SMAD4/FOXO1-3a-4 0.034 0.078 -10000 0 -0.43 19 19
TFDP1 0.031 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.053 0.12 -10000 0 -0.39 19 19
SMAD3/SMAD4/RUNX2 0.053 0.087 -10000 0 -0.37 15 15
TGIF2 0.031 0.008 -10000 0 -10000 0 0
TGIF1 0.032 0.006 -10000 0 -10000 0 0
ATF2 0.023 0.071 -10000 0 -0.55 13 13
S1P5 pathway

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.008 0.11 0.39 34 -10000 0 34
GNAI2 0.03 0.009 -10000 0 -10000 0 0
S1P/S1P5/G12 0.017 0.082 -10000 0 -0.29 47 47
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.001 0.12 -10000 0 -0.42 63 63
RhoA/GTP 0.008 0.11 -10000 0 -0.4 34 34
negative regulation of cAMP metabolic process -0.002 0.11 -10000 0 -0.34 61 61
GNAZ 0.026 0.056 -10000 0 -0.48 10 10
GNAI3 0.031 0.008 -10000 0 -10000 0 0
GNA12 0.029 0.011 -10000 0 -10000 0 0
S1PR5 -0.011 0.15 -10000 0 -0.5 72 72
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.002 0.11 -10000 0 -0.35 61 61
RhoA/GDP 0.022 0.007 -10000 0 -10000 0 0
RHOA 0.03 0.009 -10000 0 -10000 0 0
GNAI1 0.023 0.059 -10000 0 -0.55 9 9
S1P4 pathway

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.001 0.12 -10000 0 -0.42 63 63
CDC42/GTP 0.015 0.099 -10000 0 -0.32 41 41
PLCG1 0.001 0.094 -10000 0 -0.35 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.03 0.009 -10000 0 -10000 0 0
GNAI3 0.031 0.008 -10000 0 -10000 0 0
G12/G13 0.04 0.019 -10000 0 -10000 0 0
cell migration 0.014 0.097 -10000 0 -0.32 41 41
S1PR5 -0.011 0.15 -10000 0 -0.5 72 72
S1PR4 0.012 0.11 -10000 0 -0.52 33 33
MAPK3 0 0.096 -10000 0 -0.36 38 38
MAPK1 0.002 0.095 -10000 0 -0.35 39 39
S1P/S1P5/Gi -0.002 0.11 -10000 0 -0.35 61 61
GNAI1 0.023 0.059 -10000 0 -0.55 9 9
CDC42/GDP 0.023 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.017 0.082 -10000 0 -0.29 47 47
RHOA 0.036 0.086 0.36 25 -0.28 16 41
S1P/S1P4/Gi 0.005 0.1 -10000 0 -0.33 49 49
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.026 0.056 -10000 0 -0.48 10 10
S1P/S1P4/G12/G13 0.042 0.06 -10000 0 -0.31 18 18
GNA12 0.029 0.011 -10000 0 -10000 0 0
GNA13 0.029 0.011 -10000 0 -10000 0 0
CDC42 0.031 0.008 -10000 0 -10000 0 0
TCGA08_rtk_signaling

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.086 0.21 -10000 0 -0.44 220 220
HRAS 0.03 0.038 -10000 0 -0.46 5 5
EGFR 0.008 0.1 -10000 0 -0.47 36 36
AKT 0.046 0.1 0.28 68 -0.34 8 76
FOXO3 0.031 0.008 -10000 0 -10000 0 0
AKT1 0.031 0.021 -10000 0 -0.55 1 1
FOXO1 0.029 0.027 -10000 0 -0.32 5 5
AKT3 0.026 0.056 -10000 0 -0.55 8 8
FOXO4 0.033 0.001 -10000 0 -10000 0 0
MET 0.025 0.045 -10000 0 -0.55 5 5
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
PIK3CB 0.032 0.007 -10000 0 -10000 0 0
NRAS 0.031 0.008 -10000 0 -10000 0 0
PIK3CG -0.004 0.13 -10000 0 -0.52 51 51
PIK3R3 0.021 0.075 -10000 0 -0.52 16 16
PIK3R2 0.032 0.02 -10000 0 -0.55 1 1
NF1 0.03 0.01 -10000 0 -10000 0 0
RAS -0.004 0.061 -10000 0 -0.29 10 10
ERBB2 0.027 0.037 -10000 0 -0.49 4 4
proliferation/survival/translation -0.046 0.054 0.27 7 -0.24 5 12
PI3K 0.013 0.087 0.31 33 -0.23 23 56
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
KRAS 0.031 0.008 -10000 0 -10000 0 0
FOXO 0.08 0.078 0.27 76 -0.14 1 77
AKT2 0.032 0.02 -10000 0 -0.55 1 1
PTEN 0.031 0.008 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.031 0.008 -10000 0 -10000 0 0
NFATC1 0.036 0.12 0.34 29 -0.5 14 43
NFATC2 -0.005 0.1 0.23 10 -0.32 60 70
NFATC3 0.02 0.044 -10000 0 -0.4 9 9
YWHAE 0.029 0.01 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.02 0.14 0.26 14 -0.43 63 77
Exportin 1/Ran/NUP214 0.06 0.021 -10000 0 -10000 0 0
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.008 0.16 0.27 1 -0.49 58 59
BCL2/BAX 0.039 0.059 -10000 0 -0.4 15 15
CaM/Ca2+/Calcineurin A alpha-beta B1 0.018 0.017 -10000 0 -10000 0 0
CaM/Ca2+ 0.018 0.017 -10000 0 -10000 0 0
BAX 0.031 0.028 -10000 0 -0.55 2 2
MAPK14 0.03 0.009 -10000 0 -10000 0 0
BAD 0.03 0.036 -10000 0 -0.49 4 4
CABIN1/MEF2D -0.005 0.14 0.25 10 -0.42 56 66
Calcineurin A alpha-beta B1/BCL2 0.023 0.07 -10000 0 -0.55 13 13
FKBP8 0.032 0.028 -10000 0 -0.55 2 2
activation-induced cell death of T cells 0.005 0.14 0.42 56 -0.25 10 66
KPNB1 0.029 0.011 -10000 0 -10000 0 0
KPNA2 0.028 0.026 -10000 0 -0.32 4 4
XPO1 0.031 0.007 -10000 0 -10000 0 0
SFN -0.099 0.2 -10000 0 -0.39 274 274
MAP3K8 0.028 0.033 -10000 0 -0.43 4 4
NFAT4/CK1 alpha 0.03 0.037 -10000 0 -0.26 7 7
MEF2D/NFAT1/Cbp/p300 0.01 0.15 -10000 0 -0.35 70 70
CABIN1 -0.021 0.14 0.25 11 -0.44 63 74
CALM1 0.031 0.009 -10000 0 -10000 0 0
RAN 0.031 0.007 -10000 0 -10000 0 0
MAP3K1 0.032 0.013 -10000 0 -0.32 1 1
CAMK4 -0.01 0.15 -10000 0 -0.54 64 64
mol:Ca2+ -0.002 0.006 -10000 0 -10000 0 0
MAPK3 0.03 0.021 -10000 0 -0.55 1 1
YWHAH 0.032 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.025 0.086 -10000 0 -0.29 57 57
YWHAB 0.031 0.008 -10000 0 -10000 0 0
MAPK8 0.023 0.062 -10000 0 -0.55 10 10
MAPK9 0.031 0.008 -10000 0 -10000 0 0
YWHAG 0.029 0.011 -10000 0 -10000 0 0
FKBP1A 0.031 0.008 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.044 0.12 0.31 15 -0.43 23 38
PRKCH -0.004 0.14 -10000 0 -0.55 54 54
CABIN1/Cbp/p300 0.04 0.03 -10000 0 -0.4 2 2
CASP3 0.032 0.006 -10000 0 -10000 0 0
PIM1 0.028 0.034 -10000 0 -0.36 6 6
Calcineurin A alpha-beta B1/FKBP12/FK506 0.02 0.007 -10000 0 -10000 0 0
apoptosis 0.023 0.038 -10000 0 -0.55 3 3
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.006 0.083 -10000 0 -0.33 26 26
PRKCB 0.002 0.12 -10000 0 -0.52 46 46
PRKCE 0.029 0.035 -10000 0 -0.55 3 3
JNK2/NFAT4 0.027 0.058 -10000 0 -0.36 9 9
BAD/BCL-XL 0.044 0.03 -10000 0 -0.36 4 4
PRKCD 0.009 0.084 -10000 0 -0.32 53 53
NUP214 0.032 0.005 -10000 0 -10000 0 0
PRKCZ 0.024 0.056 -10000 0 -0.55 8 8
PRKCA 0.029 0.016 -10000 0 -0.32 1 1
PRKCG 0 0.092 -10000 0 -0.32 67 67
PRKCQ 0.007 0.11 -10000 0 -0.46 44 44
FKBP38/BCL2 0.04 0.059 -10000 0 -0.4 15 15
EP300 0.027 0.031 -10000 0 -0.55 2 2
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.031 0.008 -10000 0 -10000 0 0
NFATc/JNK1 0.048 0.12 0.35 23 -0.47 14 37
CaM/Ca2+/FKBP38 0.039 0.024 -10000 0 -0.35 2 2
FKBP12/FK506 0.023 0.006 -10000 0 -10000 0 0
CSNK1A1 0.013 0.016 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.011 0.098 -10000 0 -0.34 60 60
NFATc/ERK1 0.04 0.11 0.29 9 -0.48 15 24
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.007 0.16 0.27 1 -0.48 58 59
NR4A1 -0.035 0.18 0.28 3 -0.5 78 81
GSK3B 0.031 0.008 -10000 0 -10000 0 0
positive T cell selection 0.02 0.044 -10000 0 -0.4 9 9
NFAT1/CK1 alpha -0.003 0.072 0.19 1 -0.26 25 26
RCH1/ KPNB1 0.042 0.024 -10000 0 -0.22 4 4
YWHAQ 0.031 0.007 -10000 0 -10000 0 0
PRKACA 0.032 0.004 -10000 0 -10000 0 0
AKAP5 0.004 0.11 -10000 0 -0.4 57 57
MEF2D 0.028 0.016 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
NFATc/p38 alpha 0.053 0.12 0.34 30 -0.47 13 43
CREBBP 0.029 0.013 -10000 0 -10000 0 0
BCL2 0.023 0.07 -10000 0 -0.55 13 13
IGF1 pathway

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.032 0.007 -10000 0 -10000 0 0
PTK2 0.032 0.006 -10000 0 -10000 0 0
CRKL 0 0.074 -10000 0 -0.28 39 39
GRB2/SOS1/SHC 0.058 0.025 -10000 0 -10000 0 0
HRAS 0.03 0.038 -10000 0 -0.46 5 5
IRS1/Crk 0.009 0.074 -10000 0 -0.28 36 36
IGF-1R heterotetramer/IGF1/PTP1B 0.032 0.089 -10000 0 -0.34 27 27
AKT1 -0.002 0.08 0.28 4 -0.42 10 14
BAD -0.007 0.079 0.27 4 -0.43 11 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.001 0.069 -10000 0 -0.31 26 26
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.014 0.081 -10000 0 -0.31 32 32
RAF1 -0.012 0.13 0.34 1 -0.44 45 46
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.044 0.083 -10000 0 -0.3 23 23
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.013 0.085 -10000 0 -0.3 44 44
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
RPS6KB1 -0.001 0.074 0.3 4 -0.41 9 13
GNB2L1 0.031 0.008 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.009 0.11 0.29 4 -0.36 41 45
PXN 0.032 0.007 -10000 0 -10000 0 0
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.043 0.016 -10000 0 -10000 0 0
HRAS/GTP 0.016 0.069 -10000 0 -0.37 7 7
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.062 0.079 -10000 0 -0.28 19 19
IGF-1R heterotetramer 0.025 0.048 -10000 0 -0.6 3 3
IGF-1R heterotetramer/IGF1/IRS/Nck 0.031 0.085 -10000 0 -0.28 40 40
Crk/p130 Cas/Paxillin 0.047 0.085 -10000 0 -0.3 23 23
IGF1R 0.025 0.048 -10000 0 -0.6 3 3
IGF1 -0.008 0.13 -10000 0 -0.4 80 80
IRS2/Crk 0.003 0.082 -10000 0 -0.29 38 38
PI3K 0.04 0.095 -10000 0 -0.3 38 38
apoptosis -0.022 0.097 0.39 10 -0.34 30 40
HRAS/GDP 0.022 0.028 -10000 0 -0.33 5 5
PRKCD -0.006 0.11 -10000 0 -0.38 54 54
RAF1/14-3-3 E 0.007 0.12 0.43 2 -0.38 44 46
BAD/14-3-3 0.023 0.1 0.35 30 -0.41 10 40
PRKCZ -0.003 0.084 0.3 5 -0.36 19 24
Crk/p130 Cas/Paxillin/FAK1 0.026 0.074 -10000 0 -0.38 10 10
PTPN1 0.031 0.021 -10000 0 -0.55 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.004 0.089 -10000 0 -0.36 41 41
BCAR1 0.029 0.035 -10000 0 -0.55 3 3
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.044 0.082 -10000 0 -0.31 23 23
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.031 0.007 -10000 0 -10000 0 0
IRS1/NCK2 0.02 0.081 0.22 2 -0.28 40 42
GRB10 0.028 0.022 -10000 0 -0.55 1 1
PTPN11 0 0.075 -10000 0 -0.31 32 32
IRS1 0.001 0.082 -10000 0 -0.3 44 44
IRS2 -0.008 0.084 -10000 0 -0.3 43 43
IGF-1R heterotetramer/IGF1 0.012 0.11 -10000 0 -0.31 69 69
GRB2 0.029 0.011 -10000 0 -10000 0 0
PDPK1 0.006 0.085 0.3 5 -0.32 31 36
YWHAE 0.029 0.01 -10000 0 -10000 0 0
PRKD1 0.004 0.095 -10000 0 -0.4 34 34
SHC1 0.031 0.014 -10000 0 -0.32 1 1
Hedgehog signaling events mediated by Gli proteins

Figure S105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.031 0.008 -10000 0 -10000 0 0
HDAC2 0.031 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.08 -10000 0 -0.34 31 31
forebrain development -0.006 0.24 0.5 26 -0.78 51 77
GNAO1 -0.002 0.12 -10000 0 -0.42 63 63
SMO/beta Arrestin2 0.032 0.058 -10000 0 -0.4 14 14
SMO 0.019 0.073 -10000 0 -0.55 14 14
ARRB2 0.029 0.011 -10000 0 -10000 0 0
GLI3/SPOP 0.012 0.18 -10000 0 -0.68 44 44
mol:GTP 0 0.003 -10000 0 -10000 0 0
GSK3B 0.031 0.007 -10000 0 -10000 0 0
GNAI2 0.03 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.066 0.075 -10000 0 -0.31 32 32
GNAI1 0.023 0.059 -10000 0 -0.55 9 9
XPO1 0.031 0.012 -10000 0 -10000 0 0
GLI1/Su(fu) -0.016 0.2 -10000 0 -0.86 36 36
SAP30 0.012 0.11 -10000 0 -0.55 30 30
mol:GDP 0.019 0.073 -10000 0 -0.55 14 14
MIM/GLI2A 0.014 0.067 -10000 0 -0.43 12 12
IFT88 0.029 0.04 -10000 0 -0.55 4 4
GNAI3 0.031 0.009 -10000 0 -10000 0 0
GLI2 0.019 0.09 0.3 11 -0.32 8 19
GLI3 0.001 0.2 0.32 5 -0.73 46 51
CSNK1D 0.029 0.011 -10000 0 -10000 0 0
CSNK1E 0.032 0.006 -10000 0 -10000 0 0
SAP18 0.032 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.029 0.04 -10000 0 -0.55 4 4
GNG2 0.011 0.11 -10000 0 -0.55 32 32
Gi family/GTP 0.004 0.082 -10000 0 -0.31 43 43
SIN3B 0.032 0.028 -10000 0 -0.55 2 2
SIN3A 0.033 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.005 0.19 -10000 0 -0.73 45 45
GLI2/Su(fu) 0.029 0.08 -10000 0 -0.41 12 12
FOXA2 -0.044 0.24 -10000 0 -1 41 41
neural tube patterning -0.006 0.24 0.5 26 -0.78 51 77
SPOP 0.029 0.011 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.041 0.058 -10000 0 -0.39 6 6
GNB1 0.031 0.008 -10000 0 -10000 0 0
CSNK1G2 0.031 0.034 -10000 0 -0.55 3 3
CSNK1G3 0.031 0.007 -10000 0 -10000 0 0
MTSS1 0.014 0.067 -10000 0 -0.43 12 12
embryonic limb morphogenesis -0.006 0.24 0.5 26 -0.78 51 77
SUFU 0.022 0.039 -10000 0 -0.46 3 3
LGALS3 0.012 0.087 -10000 0 -0.35 46 46
catabolic process 0.025 0.18 0.29 6 -0.66 41 47
GLI3A/CBP 0.006 0.1 -10000 0 -0.36 54 54
KIF3A 0.031 0.008 -10000 0 -10000 0 0
GLI1 -0.008 0.25 0.5 25 -0.82 50 75
RAB23 0.031 0.014 -10000 0 -0.32 1 1
CSNK1A1 0.031 0.008 -10000 0 -10000 0 0
IFT172 0.031 0.007 -10000 0 -10000 0 0
RBBP7 0.033 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.028 0.085 -10000 0 -0.33 29 29
GNAZ 0.026 0.056 -10000 0 -0.48 10 10
RBBP4 0.03 0.021 -10000 0 -0.55 1 1
CSNK1G1 0.033 0.003 -10000 0 -10000 0 0
PIAS1 0.033 0.003 -10000 0 -10000 0 0
PRKACA 0.033 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.03 0.081 0.29 5 -0.31 4 9
STK36 0.03 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.006 0.098 -10000 0 -0.42 34 34
PTCH1 -0.002 0.22 0.56 13 -0.86 32 45
MIM/GLI1 -0.015 0.26 0.51 15 -0.73 63 78
CREBBP 0.007 0.1 -10000 0 -0.36 54 54
Su(fu)/SIN3/HDAC complex 0.007 0.19 0.27 4 -0.7 51 55
E-cadherin signaling in the nascent adherens junction

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.005 0.12 -10000 0 -0.48 38 38
KLHL20 0.023 0.073 0.19 18 -0.25 11 29
CYFIP2 0.026 0.05 -10000 0 -0.45 9 9
Rac1/GDP 0.022 0.088 0.31 15 -0.33 6 21
ENAH -0.005 0.12 -10000 0 -0.47 39 39
AP1M1 0.032 0.02 -10000 0 -0.55 1 1
RAP1B 0.031 0.007 -10000 0 -10000 0 0
RAP1A 0.031 0.008 -10000 0 -10000 0 0
CTNNB1 0.03 0.01 -10000 0 -10000 0 0
CDC42/GTP 0.022 0.057 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.013 0.036 -10000 0 -0.18 13 13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.041 0.098 -10000 0 -0.33 40 40
RAPGEF1 0.003 0.11 0.27 13 -0.42 31 44
CTNND1 0.033 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.001 0.13 -10000 0 -0.49 38 38
CRK -0.006 0.11 -10000 0 -0.45 32 32
E-cadherin/gamma catenin/alpha catenin 0.029 0.096 -10000 0 -0.36 35 35
alphaE/beta7 Integrin 0.038 0.046 -10000 0 -0.38 9 9
IQGAP1 0.033 0.004 -10000 0 -10000 0 0
NCKAP1 0.031 0.007 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.055 0.022 -10000 0 -10000 0 0
DLG1 -0.005 0.12 -10000 0 -0.47 38 38
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.038 -10000 0 -0.2 2 2
MLLT4 0.031 0.009 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.05 0.04 -10000 0 -0.3 6 6
PI3K 0.003 0.05 -10000 0 -0.26 2 2
ARF6 0.032 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.014 0.1 -10000 0 -0.36 54 54
TIAM1 0.026 0.053 -10000 0 -0.52 8 8
E-cadherin(dimer)/Ca2+ 0.043 0.084 -10000 0 -0.3 35 35
AKT1 0.01 0.037 0.14 4 -0.19 1 5
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
CDH1 -0.005 0.13 -10000 0 -0.44 66 66
RhoA/GDP 0.039 0.099 0.32 37 -0.32 6 43
actin cytoskeleton organization 0.025 0.064 0.19 40 -0.21 6 46
CDC42/GDP 0.046 0.12 0.38 57 -0.3 28 85
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.006 0.068 -10000 0 -0.28 36 36
ITGB7 0.026 0.056 -10000 0 -0.55 8 8
RAC1 0.029 0.011 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.046 0.09 -10000 0 -0.31 35 35
E-cadherin/Ca2+/beta catenin/alpha catenin 0.028 0.078 -10000 0 -0.29 35 35
mol:GDP 0.031 0.13 0.38 59 -0.34 31 90
CDC42/GTP/IQGAP1 0.042 0.012 -10000 0 -10000 0 0
JUP 0.025 0.053 -10000 0 -0.55 7 7
p120 catenin/RhoA/GDP 0.035 0.096 0.31 21 -0.32 6 27
RAC1/GTP/IQGAP1 0.039 0.015 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.047 0.031 -10000 0 -0.56 2 2
RHOA 0.03 0.009 -10000 0 -10000 0 0
CDC42 0.031 0.008 -10000 0 -10000 0 0
CTNNA1 0.031 0.008 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.027 0.081 0.23 58 -0.2 34 92
NME1 0.029 0.016 -10000 0 -0.32 1 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.006 0.12 -10000 0 -0.48 38 38
regulation of cell-cell adhesion 0.012 0.047 -10000 0 -10000 0 0
WASF2 0.013 0.031 0.095 12 -10000 0 12
Rap1/GTP 0.029 0.07 0.27 7 -10000 0 7
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.1 -10000 0 -0.34 41 41
CCND1 0.027 0.089 0.25 48 -0.25 34 82
VAV2 0.008 0.15 0.38 4 -0.49 45 49
RAP1/GDP 0.041 0.093 0.34 27 -0.34 2 29
adherens junction assembly -0.006 0.12 -10000 0 -0.46 38 38
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.031 0.008 -10000 0 -10000 0 0
PIP5K1C 0.031 0.028 -10000 0 -0.55 2 2
regulation of heterotypic cell-cell adhesion 0.041 0.099 -10000 0 -0.32 40 40
E-cadherin/beta catenin -0.005 0.084 -10000 0 -0.37 39 39
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.006 0.12 -10000 0 -0.48 37 37
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
Rac1/GTP -0.028 0.079 -10000 0 -0.37 21 21
E-cadherin/beta catenin/alpha catenin 0.031 0.091 -10000 0 -0.34 35 35
ITGAE 0.029 0.022 -10000 0 -0.55 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.002 0.13 -10000 0 -0.5 38 38
Signaling events mediated by PRL

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.024 0.056 -10000 0 -0.33 21 21
mol:Halofuginone 0.005 0.001 -10000 0 -10000 0 0
ITGA1 -0.032 0.18 -10000 0 -0.55 97 97
CDKN1A 0.011 0.065 -10000 0 -0.51 4 4
PRL-3/alpha Tubulin 0.042 0.038 -10000 0 -0.35 7 7
mol:Ca2+ -0.049 0.11 0.38 3 -0.39 71 74
AGT -0.022 0.16 -10000 0 -0.51 86 86
CCNA2 -0.015 0.072 -10000 0 -0.42 2 2
TUBA1B 0.032 0.007 -10000 0 -10000 0 0
EGR1 -0.014 0.1 -10000 0 -0.29 98 98
CDK2/Cyclin E1 0.023 0.12 -10000 0 -0.39 39 39
MAPK3 0.016 0.034 -10000 0 -0.35 7 7
PRL-2 /Rab GGTase beta 0.046 0.012 -10000 0 -10000 0 0
MAPK1 0.016 0.037 -10000 0 -0.36 8 8
PTP4A1 -0.01 0.069 -10000 0 -10000 0 0
PTP4A3 0.028 0.047 -10000 0 -0.48 7 7
PTP4A2 0.031 0.008 -10000 0 -10000 0 0
ITGB1 0.016 0.034 -10000 0 -0.35 7 7
SRC 0.031 0.008 -10000 0 -10000 0 0
RAC1 0.014 0.053 -10000 0 -0.46 6 6
Rab GGTase beta/Rab GGTase alpha 0.044 0.025 -10000 0 -0.4 2 2
PRL-1/ATF-5 0.017 0.092 -10000 0 -0.41 2 2
RABGGTA 0.031 0.028 -10000 0 -0.55 2 2
BCAR1 -0.018 0.036 0.49 3 -0.42 1 4
RHOC 0.011 0.067 -10000 0 -0.48 8 8
RHOA 0 0.092 -10000 0 -0.36 47 47
cell motility 0.018 0.093 0.3 8 -0.37 23 31
PRL-1/alpha Tubulin 0.017 0.085 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.005 0.14 -10000 0 -0.4 101 101
ROCK1 0.018 0.084 0.28 4 -0.4 15 19
RABGGTB 0.031 0.008 -10000 0 -10000 0 0
CDK2 0.032 0.007 -10000 0 -10000 0 0
mitosis -0.01 0.069 -10000 0 -10000 0 0
ATF5 0.028 0.039 -10000 0 -0.32 11 11
Insulin Pathway

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.028 0.093 -10000 0 -0.31 44 44
TC10/GTP 0.034 0.075 -10000 0 -0.29 31 31
Insulin Receptor/Insulin/IRS1/Shp2 0.06 0.068 -10000 0 -0.34 14 14
HRAS 0.03 0.038 -10000 0 -0.46 5 5
APS homodimer 0.019 0.074 -10000 0 -0.53 15 15
GRB14 -0.025 0.15 -10000 0 -0.38 124 124
FOXO3 -0.028 0.2 -10000 0 -0.71 69 69
AKT1 0.003 0.13 0.43 29 -0.48 8 37
INSR 0.035 0.029 -10000 0 -0.55 2 2
Insulin Receptor/Insulin 0.064 0.035 -10000 0 -0.38 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.028 0.022 -10000 0 -0.55 1 1
SORBS1 0.011 0.11 -10000 0 -0.55 30 30
CRK 0.029 0.016 -10000 0 -0.32 1 1
PTPN1 0.012 0.027 -10000 0 -0.58 1 1
CAV1 -0.016 0.1 0.5 1 -0.32 74 75
CBL/APS/CAP/Crk-II/C3G 0.058 0.091 -10000 0 -0.3 41 41
Insulin Receptor/Insulin/IRS1/NCK2 0.064 0.066 -10000 0 -0.33 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.045 0.068 -10000 0 -0.31 21 21
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.029 0.063 -10000 0 -0.46 6 6
RPS6KB1 -0.021 0.086 0.35 8 -0.42 8 16
PARD6A 0.026 0.048 -10000 0 -0.42 9 9
CBL 0.032 0.02 -10000 0 -0.55 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 -0.003 0.12 -10000 0 -0.56 40 40
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.016 0.092 -10000 0 -0.45 6 6
HRAS/GTP 0.012 0.048 -10000 0 -0.36 1 1
Insulin Receptor 0.035 0.029 -10000 0 -0.55 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.068 0.068 -10000 0 -0.31 12 12
PRKCI 0.015 0.11 -10000 0 -0.46 34 34
Insulin Receptor/Insulin/GRB14/PDK1 0 0.1 -10000 0 -0.52 8 8
SHC1 0.031 0.014 -10000 0 -0.32 1 1
negative regulation of MAPKKK cascade 0.03 0.12 -10000 0 -0.48 40 40
PI3K 0.057 0.073 -10000 0 -0.31 21 21
NCK2 0.032 0.007 -10000 0 -10000 0 0
RHOQ 0.031 0.007 -10000 0 -10000 0 0
mol:H2O2 0 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.022 0.028 -10000 0 -0.33 5 5
AKT2 0.003 0.13 0.43 29 -0.48 8 37
PRKCZ 0.003 0.14 -10000 0 -0.53 48 48
SH2B2 0.019 0.074 -10000 0 -0.53 15 15
SHC/SHIP 0.028 0.058 0.3 1 -0.3 17 18
F2RL2 -0.05 0.19 -10000 0 -0.46 147 147
TRIP10 0.027 0.059 -10000 0 -0.55 9 9
Insulin Receptor/Insulin/Shc 0.054 0.029 -10000 0 -0.3 2 2
TC10/GTP/CIP4/Exocyst 0.039 0.039 -10000 0 -0.33 9 9
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.078 0.041 -10000 0 -0.28 2 2
RAPGEF1 0.032 0.005 -10000 0 -10000 0 0
RASA1 0.03 0.034 -10000 0 -0.55 3 3
NCK1 0.03 0.029 -10000 0 -0.55 2 2
CBL/APS/CAP/Crk-II 0.048 0.09 -10000 0 -0.32 43 43
TC10/GDP 0.023 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.063 0.039 -10000 0 -0.29 2 2
INPP5D 0.011 0.055 0.31 1 -0.31 17 18
SOS1 0.031 0.007 -10000 0 -10000 0 0
SGK1 -0.048 0.22 -10000 0 -0.79 71 71
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.031 0.021 -10000 0 -0.55 1 1
IRS1 0.016 0.083 -10000 0 -0.4 31 31
p62DOK/RasGAP 0.031 0.12 -10000 0 -0.48 40 40
INS 0.022 0.021 -10000 0 -0.29 3 3
mol:PI-3-4-P2 0.011 0.055 0.31 1 -0.31 17 18
GRB2 0.029 0.011 -10000 0 -10000 0 0
EIF4EBP1 -0.018 0.12 0.41 27 -0.43 21 48
PTPRA 0.033 0.009 -10000 0 -10000 0 0
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
TC10/GTP/CIP4 0.039 0.039 -10000 0 -0.33 9 9
PDPK1 0.03 0.029 -10000 0 -0.55 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.026 0.048 -10000 0 -0.28 15 15
Insulin Receptor/Insulin/IRS1 0.044 0.061 -10000 0 -0.33 13 13
Insulin Receptor/Insulin/IRS3 0.042 0.029 -10000 0 -0.31 4 4
Par3/Par6 0.017 0.12 -10000 0 -0.32 80 80
BARD1 signaling events

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.023 0.093 -10000 0 -0.37 43 43
ATM 0.031 0.028 -10000 0 -0.55 2 2
UBE2D3 0.032 0.005 -10000 0 -10000 0 0
PRKDC 0.032 0.007 -10000 0 -10000 0 0
ATR 0.031 0.021 -10000 0 -0.55 1 1
UBE2L3 0.032 0.006 -10000 0 -10000 0 0
FANCD2 0.024 0.037 -10000 0 -0.44 4 4
protein ubiquitination 0.052 0.094 -10000 0 -0.32 38 38
XRCC5 0.031 0.008 -10000 0 -10000 0 0
XRCC6 0.032 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.058 0.035 -10000 0 -0.34 4 4
MRE11A 0.032 0.02 -10000 0 -0.55 1 1
DNA-PK 0.06 0.021 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.023 0.096 -10000 0 -0.52 15 15
FANCF 0.033 0.004 -10000 0 -10000 0 0
BRCA1 0.026 0.046 -10000 0 -0.51 6 6
CCNE1 0.024 0.056 -10000 0 -0.33 21 21
CDK2/Cyclin E1 0.04 0.044 -10000 0 -0.4 1 1
FANCG 0.032 0.02 -10000 0 -0.55 1 1
BRCA1/BACH1/BARD1 0.019 0.1 -10000 0 -0.38 48 48
FANCE 0.03 0.024 -10000 0 -0.44 2 2
FANCC 0.031 0.023 -10000 0 -0.44 2 2
NBN 0.031 0.013 -10000 0 -0.32 1 1
FANCA 0.028 0.039 -10000 0 -0.46 5 5
DNA repair 0.036 0.12 0.38 43 -0.44 11 54
BRCA1/BARD1/ubiquitin 0.019 0.1 -10000 0 -0.38 48 48
BARD1/DNA-PK 0.056 0.088 -10000 0 -0.31 42 42
FANCL 0.032 0.007 -10000 0 -10000 0 0
mRNA polyadenylation -0.023 0.093 0.37 43 -10000 0 43
BRCA1/BARD1/CTIP/M/R/N Complex 0.015 0.084 -10000 0 -0.45 9 9
BRCA1/BACH1/BARD1/TopBP1 0.036 0.092 -10000 0 -0.35 40 40
BRCA1/BARD1/P53 0.053 0.09 -10000 0 -0.33 39 39
BARD1/CSTF1/BRCA1 0.037 0.09 -10000 0 -0.36 37 37
BRCA1/BACH1 0.026 0.046 -10000 0 -0.51 6 6
BARD1 0.003 0.13 -10000 0 -0.55 43 43
PCNA 0.031 0.008 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.037 0.092 -10000 0 -0.36 39 39
BRCA1/BARD1/UbcH7 0.036 0.092 -10000 0 -0.35 40 40
BRCA1/BARD1/RAD51/PCNA 0.05 0.095 -10000 0 -0.34 38 38
BARD1/DNA-PK/P53 0.064 0.085 -10000 0 -0.3 36 36
BRCA1/BARD1/Ubiquitin 0.019 0.1 -10000 0 -0.38 48 48
BRCA1/BARD1/CTIP 0.028 0.09 -10000 0 -0.34 42 42
FA complex 0.034 0.044 -10000 0 -0.34 7 7
BARD1/EWS 0.022 0.098 -10000 0 -0.4 43 43
RBBP8 0.017 0.039 -10000 0 -0.52 4 4
TP53 0.029 0.022 -10000 0 -0.55 1 1
TOPBP1 0.031 0.021 -10000 0 -0.55 1 1
G1/S transition of mitotic cell cycle -0.05 0.089 0.32 39 -10000 0 39
BRCA1/BARD1 0.058 0.098 -10000 0 -0.32 38 38
CSTF1 0.031 0.008 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.001 0.093 -10000 0 -0.4 43 43
CDK2 0.032 0.007 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.028 0.044 -10000 0 -0.37 10 10
RAD50 0.029 0.035 -10000 0 -0.55 3 3
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.019 0.1 -10000 0 -0.38 48 48
EWSR1 0.032 0.006 -10000 0 -10000 0 0
Regulation of Telomerase

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.046 0.17 0.53 4 -0.63 18 22
RAD9A 0.031 0.026 -10000 0 -0.4 3 3
AP1 -0.002 0.12 -10000 0 -0.31 113 113
IFNAR2 0.029 0.023 -10000 0 -0.55 1 1
AKT1 0.007 0.058 -10000 0 -0.24 33 33
ER alpha/Oestrogen 0.001 0.086 -10000 0 -0.36 42 42
NFX1/SIN3/HDAC complex 0.014 0.12 -10000 0 -0.46 41 41
EGF -0.059 0.19 -10000 0 -0.41 181 181
SMG5 0.031 0.008 -10000 0 -10000 0 0
SMG6 0.029 0.01 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.03 -10000 0 -0.4 2 2
TERT/c-Abl -0.035 0.17 0.51 4 -0.6 16 20
SAP18 0.031 0.007 -10000 0 -10000 0 0
MRN complex 0.058 0.035 -10000 0 -0.34 4 4
WT1 -0.13 0.22 -10000 0 -0.42 307 307
WRN 0.031 0.021 -10000 0 -0.55 1 1
SP1 0.028 0.017 -10000 0 -10000 0 0
SP3 0.03 0.029 -10000 0 -0.55 2 2
TERF2IP 0.031 0.009 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.016 0.16 -10000 0 -0.57 12 12
Mad/Max 0.043 0.02 -10000 0 -0.22 2 2
TERT -0.048 0.18 0.55 3 -0.67 13 16
CCND1 -0.076 0.28 0.66 5 -1.2 44 49
MAX 0.031 0.008 -10000 0 -10000 0 0
RBBP7 0.033 0.003 -10000 0 -10000 0 0
RBBP4 0.03 0.021 -10000 0 -0.55 1 1
TERF2 0.027 0.01 -10000 0 -10000 0 0
PTGES3 0.032 0.007 -10000 0 -10000 0 0
SIN3A 0.033 0.004 -10000 0 -10000 0 0
Telomerase/911 0.043 0.042 -10000 0 -10000 0 0
CDKN1B -0.01 0.092 -10000 0 -0.33 34 34
RAD1 0.032 0.006 -10000 0 -10000 0 0
XRCC5 0.031 0.008 -10000 0 -10000 0 0
XRCC6 0.032 0.006 -10000 0 -10000 0 0
SAP30 0.012 0.11 -10000 0 -0.55 30 30
TRF2/PARP2 0.043 0.015 -10000 0 -10000 0 0
UBE3A 0.032 0.005 -10000 0 -10000 0 0
JUN 0.029 0.029 -10000 0 -0.38 4 4
E6 0 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.01 -10000 0 -10000 0 0
FOS -0.026 0.16 -10000 0 -0.42 112 112
IFN-gamma/IRF1 0 0.12 -10000 0 -0.33 51 51
PARP2 0.032 0.006 -10000 0 -10000 0 0
BLM 0.026 0.053 -10000 0 -0.39 13 13
Telomerase 0.012 0.093 -10000 0 -0.5 16 16
IRF1 0.034 0.019 -10000 0 -0.31 2 2
ESR1 0.005 0.12 -10000 0 -0.5 42 42
KU/TER 0.045 0.014 -10000 0 -10000 0 0
ATM/TRF2 0.045 0.024 -10000 0 -0.37 2 2
ubiquitin-dependent protein catabolic process 0.029 0.092 -10000 0 -0.43 26 26
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.029 0.094 -10000 0 -0.44 26 26
HDAC1 0.031 0.008 -10000 0 -10000 0 0
HDAC2 0.027 0.017 -10000 0 -10000 0 0
ATM 0.011 0.022 -10000 0 -0.42 2 2
SMAD3 0.012 0.058 -10000 0 -0.38 18 18
ABL1 0.032 0.005 -10000 0 -10000 0 0
MXD1 0.03 0.018 -10000 0 -0.32 2 2
MRE11A 0.032 0.02 -10000 0 -0.55 1 1
HUS1 0.029 0.011 -10000 0 -10000 0 0
RPS6KB1 0.029 0.011 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.016 0.16 -10000 0 -0.62 10 10
NR2F2 0.032 0.029 -10000 0 -0.55 2 2
MAPK3 0.002 0.034 -10000 0 -0.23 13 13
MAPK1 0.002 0.034 -10000 0 -0.23 13 13
TGFB1/TGF beta receptor Type II 0.021 0.082 -10000 0 -0.52 19 19
NFKB1 0.032 0.02 -10000 0 -0.55 1 1
HNRNPC 0.032 0.006 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.021 -10000 0 -0.42 2 2
NBN 0.031 0.013 -10000 0 -0.32 1 1
EGFR 0.008 0.1 -10000 0 -0.47 36 36
mol:Oestrogen 0 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.04 0.16 -10000 0 -0.32 193 193
MYC 0.011 0.11 -10000 0 -0.54 32 32
IL2 0.015 0.045 -10000 0 -0.32 12 12
KU 0.045 0.014 -10000 0 -10000 0 0
RAD50 0.029 0.035 -10000 0 -0.55 3 3
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
TGFB1 0.021 0.082 -10000 0 -0.52 19 19
TRF2/BLM 0.04 0.035 -10000 0 -0.24 11 11
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.024 0.17 -10000 0 -0.62 12 12
SP1/HDAC2 0.038 0.029 -10000 0 -10000 0 0
PINX1 0.03 0.029 -10000 0 -0.55 2 2
Telomerase/EST1A -0.016 0.16 -10000 0 -0.57 11 11
Smad3/Myc 0.018 0.09 -10000 0 -0.37 42 42
911 complex 0.056 0.03 -10000 0 -0.34 1 1
IFNG -0.034 0.15 -10000 0 -0.36 146 146
Telomerase/PinX1 -0.018 0.16 -10000 0 -0.57 13 13
Telomerase/AKT1/mTOR/p70S6K 0.014 0.077 -10000 0 -0.47 8 8
SIN3B 0.031 0.028 -10000 0 -0.55 2 2
YWHAE 0.029 0.01 -10000 0 -10000 0 0
Telomerase/EST1B -0.015 0.16 -10000 0 -0.56 11 11
response to DNA damage stimulus 0.005 0.015 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.078 0.043 -10000 0 -0.29 4 4
TRF2/WRN 0.041 0.021 -10000 0 -0.38 1 1
Telomerase/hnRNP C1/C2 -0.016 0.16 -10000 0 -0.58 11 11
E2F1 0.027 0.035 -10000 0 -0.36 6 6
ZNFX1 0.031 0.008 -10000 0 -10000 0 0
PIF1 0.011 0.095 -10000 0 -0.38 47 47
NCL 0.031 0.007 -10000 0 -10000 0 0
DKC1 0.033 0.002 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
PLK2 and PLK4 events

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.017 0.092 -9999 0 -0.54 23 23
PLK4 0.031 0.021 -9999 0 -0.32 3 3
regulation of centriole replication 0.008 0.066 -9999 0 -0.37 25 25
mTOR signaling pathway

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.031 0.008 -10000 0 -10000 0 0
mol:PIP3 0.003 0.056 -10000 0 -0.32 20 20
FRAP1 0.027 0.061 0.37 14 -0.31 1 15
AKT1 0.005 0.058 0.2 2 -0.3 18 20
INSR 0.032 0.028 -10000 0 -0.55 2 2
Insulin Receptor/Insulin 0.033 0.023 -10000 0 -0.25 5 5
mol:GTP 0.033 0.063 0.25 2 -0.34 8 10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.013 0.033 -10000 0 -0.23 3 3
TSC2 0.029 0.035 -10000 0 -0.55 3 3
RHEB/GDP 0.018 0.049 -10000 0 -0.31 8 8
TSC1 0.033 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.016 0.068 -10000 0 -0.23 53 53
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.028 0.045 -10000 0 -0.27 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.031 0.008 -10000 0 -10000 0 0
RPS6KB1 0.03 0.094 0.37 27 -0.29 12 39
MAP3K5 -0.005 0.052 -10000 0 -0.19 65 65
PIK3R1 0.03 0.038 -10000 0 -0.46 5 5
apoptosis -0.005 0.052 -10000 0 -0.19 65 65
mol:LY294002 0 0 0.001 1 -0.001 50 51
EIF4B 0.037 0.11 0.36 49 -0.4 3 52
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.052 0.083 0.36 23 -0.4 3 26
eIF4E/eIF4G1/eIF4A1 0.023 0.021 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.03 0.075 -10000 0 -0.32 23 23
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.044 0.24 13 -0.19 3 16
FKBP1A 0.031 0.008 -10000 0 -10000 0 0
RHEB/GTP 0.033 0.056 0.22 1 -0.32 7 8
mol:Amino Acids 0 0 0.001 1 -0.001 50 51
FKBP12/Rapamycin 0.023 0.006 -10000 0 -10000 0 0
PDPK1 -0.001 0.058 0.18 3 -0.32 19 22
EIF4E 0.032 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.006 0.16 -10000 0 -0.56 65 65
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.02 0.029 -10000 0 -0.27 1 1
TSC1/TSC2 0.039 0.071 0.28 3 -0.37 8 11
tumor necrosis factor receptor activity 0 0 0.001 50 -0.001 1 51
RPS6 0.032 0.017 -10000 0 -0.32 2 2
PPP5C 0.033 0.003 -10000 0 -10000 0 0
EIF4G1 0.032 0.007 -10000 0 -10000 0 0
IRS1 -0.004 0.065 -10000 0 -0.24 52 52
INS 0.018 0.02 -10000 0 -0.32 3 3
PTEN 0.03 0.01 -10000 0 -10000 0 0
PDK2 0.001 0.053 0.2 6 -0.3 17 23
EIF4EBP1 -0.034 0.26 -10000 0 -1.1 47 47
PIK3CA 0.028 0.048 -10000 0 -0.55 6 6
PPP2R5D 0.027 0.06 0.35 15 -0.26 1 16
peptide biosynthetic process 0.014 0.027 -10000 0 -0.32 4 4
RHEB 0.029 0.011 -10000 0 -10000 0 0
EIF4A1 0.029 0.01 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.002 0.007 36 -0.003 2 38
EEF2 0.014 0.027 -10000 0 -0.32 4 4
eIF4E/4E-BP1 -0.014 0.25 -10000 0 -1 47 47
p38 MAPK signaling pathway

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.024 0.018 -10000 0 -0.29 2 2
TRAF2/ASK1 0.039 0.029 -10000 0 -0.34 4 4
ATM 0.031 0.028 -10000 0 -0.55 2 2
MAP2K3 0.026 0.09 0.27 31 -0.45 8 39
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.015 0.11 0.24 16 -0.37 42 58
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.004 0.11 -10000 0 -0.34 87 87
TXN 0.009 0.012 -10000 0 -0.13 7 7
CALM1 0.032 0.006 -10000 0 -10000 0 0
GADD45A 0.031 0.014 -10000 0 -0.32 1 1
GADD45B 0.022 0.07 -10000 0 -0.4 22 22
MAP3K1 0.032 0.013 -10000 0 -0.32 1 1
MAP3K6 0.03 0.029 -10000 0 -0.55 2 2
MAP3K7 0.031 0.008 -10000 0 -10000 0 0
MAP3K4 0.031 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.043 0.033 -10000 0 -0.4 4 4
TAK1/TAB family -0.001 0.024 0.18 10 -10000 0 10
RAC1/OSM/MEKK3 0.051 0.028 -10000 0 -0.31 1 1
TRAF2 0.031 0.028 -10000 0 -0.55 2 2
RAC1/OSM/MEKK3/MKK3 0.027 0.064 -10000 0 -0.36 8 8
TRAF6 0.01 0.001 -10000 0 -10000 0 0
RAC1 0.029 0.011 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.093 0.2 -10000 0 -0.4 249 249
CCM2 0.028 0.022 -10000 0 -0.55 1 1
CaM/Ca2+/CAMKIIB -0.04 0.13 -10000 0 -0.34 83 83
MAPK11 0.023 0.071 -10000 0 -0.53 14 14
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.024 0.13 -10000 0 -0.31 85 85
OSM/MEKK3 0.039 0.024 -10000 0 -0.4 1 1
TAOK1 0 0.083 -10000 0 -0.34 44 44
TAOK2 0.018 0.018 -10000 0 -0.34 2 2
TAOK3 0.018 0.022 -10000 0 -0.34 3 3
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.031 0.008 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.029 0.029 -10000 0 -0.55 2 2
MAP3K10 0.031 0.034 -10000 0 -0.55 3 3
MAP3K3 0.029 0.011 -10000 0 -10000 0 0
TRX/ASK1 0.027 0.026 -10000 0 -0.38 2 2
GADD45/MTK1/MTK1 0.047 0.085 -10000 0 -0.32 19 19
TCGA08_p53

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.013 0.092 -10000 0 -0.36 54 54
TP53 -0.002 0.038 -10000 0 -0.36 5 5
Senescence -0.002 0.038 -10000 0 -0.36 5 5
Apoptosis -0.002 0.038 -10000 0 -0.36 5 5
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.01 0.073 0.29 44 -10000 0 44
MDM4 0.031 0.008 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.031 0.008 -10000 0 -10000 0 0
HDAC3 0.031 0.008 -10000 0 -10000 0 0
VDR 0.008 0.09 -10000 0 -0.33 56 56
Cbp/p300/PCAF 0.056 0.036 -10000 0 -0.49 2 2
EP300 0.031 0.028 -10000 0 -0.55 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.019 0.078 -10000 0 -0.29 38 38
KAT2B 0.03 0.022 -10000 0 -0.55 1 1
MAPK14 0.031 0.008 -10000 0 -10000 0 0
AKT1 0.013 0.066 0.25 11 -0.3 6 17
RAR alpha/9cRA/Cyclin H 0.05 0.084 0.26 6 -0.31 3 9
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.028 0.067 0.21 5 -0.38 6 11
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.019 0.091 -10000 0 -0.33 45 45
NCOR2 0.03 0.029 -10000 0 -0.55 2 2
VDR/VDR/Vit D3 0.007 0.062 -10000 0 -0.23 56 56
RXRs/RARs/NRIP1/9cRA 0.019 0.1 0.31 1 -0.47 12 13
NCOA2 -0.005 0.14 -10000 0 -0.55 55 55
NCOA3 0.031 0.008 -10000 0 -10000 0 0
NCOA1 0.031 0.007 -10000 0 -10000 0 0
VDR/VDR/DNA 0.008 0.09 -10000 0 -0.33 56 56
RARG 0.031 0.031 -10000 0 -0.47 3 3
RAR gamma1/9cRA 0.042 0.022 -10000 0 -0.29 3 3
MAPK3 0.031 0.022 -10000 0 -0.55 1 1
MAPK1 0.031 0.02 -10000 0 -0.55 1 1
MAPK8 0.026 0.062 -10000 0 -0.55 10 10
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.021 0.099 -10000 0 -0.38 32 32
RARA 0.016 0.037 -10000 0 -0.25 9 9
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.015 0.087 0.21 4 -0.34 22 26
PRKCA 0.031 0.017 -10000 0 -0.32 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 0.02 0.12 0.33 2 -0.44 33 35
RXRG 0.012 0.043 -10000 0 -0.27 5 5
RXRA 0.022 0.041 -10000 0 -0.24 9 9
RXRB 0.017 0.038 -10000 0 -0.29 3 3
VDR/Vit D3/DNA 0.007 0.062 -10000 0 -0.23 56 56
RBP1 0.022 0.066 -10000 0 -0.4 19 19
CRBP1/9-cic-RA 0.016 0.047 -10000 0 -0.29 19 19
RARB 0.028 0.049 -10000 0 -0.55 6 6
PRKCG 0.002 0.092 -10000 0 -0.32 67 67
MNAT1 0.032 0.006 -10000 0 -10000 0 0
RAR alpha/RXRs 0.015 0.09 -10000 0 -0.4 7 7
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.025 0.092 0.27 2 -0.4 10 12
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.12 0.3 47 -0.37 38 85
RXRs/RARs/NRIP1/9cRA/HDAC3 0.024 0.11 0.36 3 -0.5 13 16
positive regulation of DNA binding 0.032 0.071 -10000 0 -0.3 3 3
NRIP1 0.015 0.13 -10000 0 -0.9 7 7
RXRs/RARs 0.009 0.11 -10000 0 -0.4 36 36
RXRs/RXRs/DNA/9cRA 0.015 0.073 -10000 0 -0.37 8 8
PRKACA 0.033 0.003 -10000 0 -10000 0 0
CDK7 0.032 0.005 -10000 0 -10000 0 0
TFIIH 0.063 0.016 -10000 0 -10000 0 0
RAR alpha/9cRA 0.055 0.081 -10000 0 -0.27 29 29
CCNH 0.032 0.006 -10000 0 -10000 0 0
CREBBP 0.031 0.008 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.056 0.03 -10000 0 -0.28 2 2
Atypical NF-kappaB pathway

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.044 0.043 -10000 0 -0.35 10 10
FBXW11 0.031 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.024 0.066 -10000 0 -0.34 26 26
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.093 -10000 0 -0.37 18 18
NFKBIA 0.004 0.078 -10000 0 -0.28 48 48
MAPK14 0.031 0.008 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.035 0.018 -10000 0 -0.34 1 1
ARRB2 0.018 0.007 -10000 0 -10000 0 0
REL 0.014 0.098 -10000 0 -0.53 27 27
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.033 0.039 -10000 0 -0.34 8 8
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.037 0.016 -10000 0 -0.34 1 1
PIK3CA 0.027 0.048 -10000 0 -0.55 6 6
NF kappa B1 p50 dimer 0.027 0.022 0.25 4 -0.4 1 5
PIK3R1 0.029 0.038 -10000 0 -0.46 5 5
NFKB1 0.019 0.015 -10000 0 -0.4 1 1
RELA 0.033 0.004 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.002 0.089 -10000 0 -0.26 66 66
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.02 0.095 -10000 0 -0.37 16 16
SRC 0.031 0.008 -10000 0 -10000 0 0
PI3K 0.04 0.049 -10000 0 -0.37 11 11
NF kappa B1 p50/RelA -0.002 0.089 -10000 0 -0.27 66 66
IKBKB 0.032 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.031 0.008 -10000 0 -10000 0 0
SYK 0.022 0.072 -10000 0 -0.48 17 17
I kappa B alpha/PIK3R1 0.007 0.098 -10000 0 -0.37 26 26
cell death 0.02 0.091 -10000 0 -0.36 16 16
NF kappa B1 p105/c-Rel 0.024 0.066 -10000 0 -0.34 26 26
LCK -0.015 0.15 -10000 0 -0.48 78 78
BCL3 0.027 0.056 -10000 0 -0.48 10 10
Rapid glucocorticoid signaling

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.033 0.078 -10000 0 -0.29 40 40
MAPK9 0.01 0.003 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.014 0.045 -10000 0 -0.22 39 39
GNB1/GNG2 0.027 0.073 -10000 0 -0.34 32 32
GNB1 0.031 0.008 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.01 0.003 -10000 0 -10000 0 0
Gs family/GTP 0.014 0.043 -10000 0 -0.22 26 26
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.002 0.011 0.06 26 -10000 0 26
GNAL 0.019 0.077 -10000 0 -0.41 26 26
GNG2 0.011 0.11 -10000 0 -0.55 32 32
CRH 0.007 0.071 -10000 0 -0.32 39 39
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.038 -10000 0 -0.35 10 10
MAPK11 0.004 0.044 -10000 0 -0.33 14 14
Aurora C signaling

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.031 0.028 -9999 0 -0.55 2 2
Aurora C/Aurora B/INCENP 0.037 0.071 -9999 0 -0.32 14 14
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.008 0.049 -9999 0 -0.39 11 11
AURKB 0.009 0.091 -9999 0 -0.36 46 46
AURKC 0.024 0.061 -9999 0 -0.38 18 18
Class I PI3K signaling events mediated by Akt

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.019 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.052 0.028 -10000 0 -0.31 3 3
CDKN1B 0.021 0.076 -10000 0 -0.51 8 8
CDKN1A 0.022 0.065 -10000 0 -0.56 4 4
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.032 0.007 -10000 0 -10000 0 0
FOXO3 0.022 0.063 -10000 0 -0.51 5 5
AKT1 0.013 0.073 -10000 0 -0.4 18 18
BAD 0.03 0.036 -10000 0 -0.49 4 4
AKT3 0.014 0.037 -10000 0 -0.34 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.02 0.076 -10000 0 -0.37 20 20
AKT1/ASK1 0.037 0.08 -10000 0 -0.52 7 7
BAD/YWHAZ 0.063 0.029 -10000 0 -0.34 3 3
RICTOR 0.031 0.021 -10000 0 -0.55 1 1
RAF1 0.03 0.009 -10000 0 -10000 0 0
JNK cascade -0.035 0.077 0.5 7 -10000 0 7
TSC1 0.021 0.068 -10000 0 -0.56 4 4
YWHAZ 0.032 0.006 -10000 0 -10000 0 0
AKT1/RAF1 0.038 0.081 0.31 2 -0.58 6 8
EP300 0.031 0.028 -10000 0 -0.55 2 2
mol:GDP 0.018 0.076 -10000 0 -0.38 20 20
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.013 0.076 -10000 0 -0.54 8 8
YWHAQ 0.031 0.007 -10000 0 -10000 0 0
TBC1D4 0.01 0.023 -10000 0 -0.29 3 3
MAP3K5 0.029 0.029 -10000 0 -0.55 2 2
MAPKAP1 0.032 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.014 0.1 0.35 28 -0.27 23 51
YWHAH 0.032 0.006 -10000 0 -10000 0 0
AKT1S1 0.02 0.078 -10000 0 -0.62 6 6
CASP9 0.024 0.057 -10000 0 -0.48 4 4
YWHAB 0.031 0.008 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.043 0.085 0.3 16 -0.55 6 22
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.058 0.029 -10000 0 -0.34 2 2
YWHAE 0.029 0.01 -10000 0 -10000 0 0
SRC 0.031 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.019 0.068 -10000 0 -0.54 6 6
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.016 0.022 -10000 0 -10000 0 0
CHUK 0.021 0.07 -10000 0 -0.58 6 6
BAD/BCL-XL 0.044 0.08 -10000 0 -0.59 6 6
mTORC2 0.04 0.015 -10000 0 -0.31 1 1
AKT2 0.018 0.022 -10000 0 -0.34 3 3
FOXO1-3a-4/14-3-3 family 0.016 0.13 0.35 22 -0.5 20 42
PDPK1 0.03 0.029 -10000 0 -0.55 2 2
MDM2 0.021 0.076 -10000 0 -0.58 6 6
MAPKKK cascade -0.037 0.08 0.57 6 -0.3 2 8
MDM2/Cbp/p300 0.053 0.083 0.32 2 -0.49 8 10
TSC1/TSC2 0.027 0.093 0.29 42 -0.6 6 48
proteasomal ubiquitin-dependent protein catabolic process 0.05 0.08 0.28 9 -0.46 8 17
glucose import -0.003 0.075 0.21 28 -0.3 32 60
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.021 0.046 0.21 2 -0.34 6 8
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.01 0.065 -10000 0 -0.3 32 32
GSK3A 0.02 0.075 -10000 0 -0.58 6 6
FOXO1 0.021 0.062 -10000 0 -0.47 5 5
GSK3B 0.019 0.072 -10000 0 -0.54 7 7
SFN -0.099 0.2 -10000 0 -0.39 274 274
G1/S transition of mitotic cell cycle 0.027 0.086 0.3 25 -0.56 6 31
p27Kip1/14-3-3 family 0.01 0.098 -10000 0 -0.41 19 19
PRKACA 0.033 0.003 -10000 0 -10000 0 0
KPNA1 0.031 0.007 -10000 0 -10000 0 0
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
YWHAG 0.029 0.011 -10000 0 -10000 0 0
RHEB 0.029 0.011 -10000 0 -10000 0 0
CREBBP 0.031 0.008 -10000 0 -10000 0 0
Aurora A signaling

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.035 0.026 -10000 0 -10000 0 0
BIRC5 0.002 0.11 -10000 0 -0.39 56 56
NFKBIA 0.018 0.025 0.25 2 -10000 0 2
CPEB1 -0.098 0.21 -10000 0 -0.42 248 248
AKT1 0.017 0.026 0.25 1 -0.33 1 2
NDEL1 0.029 0.01 -10000 0 -10000 0 0
Aurora A/BRCA1 0.028 0.034 -10000 0 -0.31 5 5
NDEL1/TACC3 0.049 0.033 -10000 0 -10000 0 0
GADD45A 0.031 0.014 -10000 0 -0.32 1 1
GSK3B 0.032 0.013 -10000 0 -10000 0 0
PAK1/Aurora A 0.04 0.028 -10000 0 -10000 0 0
MDM2 0.031 0.007 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.008 0.057 -10000 0 -0.28 30 30
TP53 0.027 0.023 -10000 0 -0.32 2 2
DLG7 0.017 0.023 -10000 0 -0.22 1 1
AURKAIP1 0.029 0.033 -10000 0 -0.44 4 4
ARHGEF7 0.031 0.007 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.052 0.035 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.028 0.034 -10000 0 -0.3 5 5
AURKA 0.027 0.03 -10000 0 -0.26 1 1
AURKB 0.01 0.042 -10000 0 -0.28 12 12
CDC25B 0.026 0.023 -10000 0 -10000 0 0
G2/M transition checkpoint 0.015 0.02 -10000 0 -0.19 1 1
mRNA polyadenylation -0.036 0.12 -10000 0 -0.3 117 117
Aurora A/CPEB -0.037 0.12 -10000 0 -0.3 117 117
Aurora A/TACC1/TRAP/chTOG 0.072 0.043 -10000 0 -0.28 4 4
BRCA1 0.026 0.046 -10000 0 -0.51 6 6
centrosome duplication 0.04 0.028 -10000 0 -10000 0 0
regulation of centrosome cycle 0.047 0.032 -10000 0 -10000 0 0
spindle assembly 0.069 0.042 -10000 0 -0.28 4 4
TDRD7 0.032 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.044 0.077 -10000 0 -0.31 19 19
CENPA 0.015 0.04 -10000 0 -0.31 8 8
Aurora A/PP2A 0.036 0.023 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.02 0.022 -10000 0 -10000 0 0
negative regulation of DNA binding 0.027 0.023 -10000 0 -0.32 2 2
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.042 0.027 -10000 0 -0.4 2 2
RASA1 0.03 0.034 -10000 0 -0.55 3 3
Ajuba/Aurora A 0.015 0.02 -10000 0 -0.2 1 1
mitotic prometaphase 0.002 0.018 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.03 -10000 0 -0.26 1 1
TACC1 0.029 0.04 -10000 0 -0.55 4 4
TACC3 0.03 0.029 -10000 0 -0.32 6 6
Aurora A/Antizyme1 0.055 0.035 -10000 0 -0.3 2 2
Aurora A/RasGAP 0.038 0.035 -10000 0 -0.33 3 3
OAZ1 0.032 0.012 -10000 0 -0.32 1 1
RAN 0.032 0.007 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.033 0.011 -10000 0 -10000 0 0
GIT1 0.028 0.029 -10000 0 -0.55 2 2
GIT1/beta-PIX/PAK1 0.057 0.03 -10000 0 -0.34 2 2
Importin alpha/Importin beta/TPX2 0.008 0.057 -10000 0 -0.28 30 30
PPP2R5D 0.031 0.008 -10000 0 -10000 0 0
Aurora A/TPX2 0.023 0.051 -10000 0 -0.3 8 8
PAK1 0.033 0.004 -10000 0 -10000 0 0
CKAP5 0.032 0.02 -10000 0 -0.55 1 1
Arf6 trafficking events

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.014 0.13 -10000 0 -0.39 92 92
CLTC 0.024 0.064 -10000 0 -0.37 18 18
calcium ion-dependent exocytosis 0.022 0.031 -10000 0 -0.26 2 2
Dynamin 2/GTP 0.031 0.014 -10000 0 -10000 0 0
EXOC4 0.029 0.011 -10000 0 -10000 0 0
CD59 0.018 0.049 -10000 0 -0.3 17 17
CPE -0.023 0.11 -10000 0 -0.29 123 123
CTNNB1 0.03 0.01 -10000 0 -10000 0 0
membrane fusion 0.023 0.025 -10000 0 -10000 0 0
CTNND1 0.032 0.044 -10000 0 -10000 0 0
DNM2 0.033 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.021 0.043 0.25 1 -0.32 6 7
TSHR -0.033 0.12 -10000 0 -0.29 145 145
INS 0.015 0.055 -10000 0 -0.51 8 8
BIN1 0.013 0.084 -10000 0 -0.35 42 42
mol:Choline 0.023 0.025 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.01 -10000 0 -0.18 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.032 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.03 0.014 -10000 0 -10000 0 0
JUP 0.016 0.053 -10000 0 -0.3 19 19
ASAP2/amphiphysin II 0.045 0.061 -10000 0 -0.31 10 10
ARF6/GTP 0.024 0.004 -10000 0 -10000 0 0
CDH1 0.007 0.068 -10000 0 -0.33 18 18
clathrin-independent pinocytosis 0.024 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.066 -10000 0 -0.48 14 14
positive regulation of endocytosis 0.024 0.004 -10000 0 -10000 0 0
EXOC2 0.031 0.008 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.029 0.046 -10000 0 -0.35 9 9
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.029 0.011 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.037 0.072 0.4 5 -10000 0 5
positive regulation of phagocytosis 0.019 0.006 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.045 -10000 0 -0.3 13 13
ACAP1 0.023 0.035 -10000 0 -0.25 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.011 0.048 -10000 0 -0.31 18 18
clathrin heavy chain/ACAP1 0.026 0.058 0.26 3 -0.39 5 8
JIP4/KLC1 0.054 0.023 -10000 0 -10000 0 0
EXOC1 0.032 0.005 -10000 0 -10000 0 0
exocyst 0.029 0.046 -10000 0 -0.36 9 9
RALA/GTP 0.021 0.008 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.038 0.016 -10000 0 -10000 0 0
receptor recycling 0.024 0.004 -10000 0 -10000 0 0
CTNNA1 0.03 0.044 -10000 0 -10000 0 0
NME1 0.017 0.01 -10000 0 -0.18 1 1
clathrin coat assembly 0.03 0.083 0.25 25 -0.37 18 43
IL2RA 0.001 0.078 -10000 0 -0.37 19 19
VAMP3 0.019 0.006 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.016 0.09 -10000 0 -0.42 6 6
EXOC6 0.031 0.008 -10000 0 -10000 0 0
PLD1 0.019 0.008 -10000 0 -10000 0 0
PLD2 0.016 0.023 -10000 0 -0.22 7 7
EXOC5 0.032 0.006 -10000 0 -10000 0 0
PIP5K1C 0.02 0.042 -10000 0 -0.32 6 6
SDC1 0.015 0.056 -10000 0 -0.3 19 19
ARF6/GDP 0.027 0.013 -10000 0 -0.18 1 1
EXOC7 0.029 0.022 -10000 0 -0.55 1 1
E-cadherin/beta catenin 0.039 0.074 -10000 0 -0.41 5 5
mol:Phosphatidic acid 0.023 0.025 -10000 0 -10000 0 0
endocytosis -0.043 0.06 0.31 10 -10000 0 10
SCAMP2 0.033 0.003 -10000 0 -10000 0 0
ADRB2 0.034 0.11 0.3 31 -0.38 19 50
EXOC3 0.031 0.021 -10000 0 -0.55 1 1
ASAP2 0.029 0.04 -10000 0 -0.55 4 4
Dynamin 2/GDP 0.034 0.016 -10000 0 -10000 0 0
KLC1 0.032 0.006 -10000 0 -10000 0 0
AVPR2 0.006 0.12 0.29 16 -0.43 20 36
RALA 0.029 0.011 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.041 0.076 0.29 4 -0.38 5 9
Signaling events mediated by HDAC Class II

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.06 0.073 -10000 0 -0.34 20 20
HDAC3 0.031 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.008 0.004 -10000 0 -10000 0 0
GATA1/HDAC4 0.035 0.05 -10000 0 -0.22 30 30
GATA1/HDAC5 0.032 0.054 -10000 0 -0.24 30 30
GATA2/HDAC5 0.01 0.1 -10000 0 -0.28 89 89
HDAC5/BCL6/BCoR 0.054 0.046 -10000 0 -0.38 7 7
HDAC9 0.014 0.091 -10000 0 -0.55 22 22
Glucocorticoid receptor/Hsp90/HDAC6 0.059 0.032 -10000 0 -0.34 3 3
HDAC4/ANKRA2 0.045 0.015 -10000 0 -10000 0 0
HDAC5/YWHAB 0.041 0.031 -10000 0 -0.4 3 3
NPC/RanGAP1/SUMO1/Ubc9 0.019 0.014 -10000 0 -0.22 2 2
GATA2 -0.015 0.14 -10000 0 -0.41 93 93
HDAC4/RFXANK 0.045 0.027 -10000 0 -0.34 3 3
BCOR 0.032 0.02 -10000 0 -0.55 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.03 0.034 -10000 0 -0.55 3 3
HDAC5 0.027 0.035 -10000 0 -0.55 3 3
GNB1/GNG2 0.028 0.085 -10000 0 -0.4 32 32
Histones 0.024 0.082 -10000 0 -0.5 13 13
ADRBK1 0.031 0.028 -10000 0 -0.55 2 2
HDAC4 0.031 0.008 -10000 0 -10000 0 0
XPO1 0.032 0.007 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.041 0.031 -10000 0 -0.4 3 3
HDAC4/Ubc9 0.043 0.017 -10000 0 -10000 0 0
HDAC7 0.03 0.029 -10000 0 -0.55 2 2
HDAC5/14-3-3 E 0.042 0.031 -10000 0 -0.4 3 3
TUBA1B 0.032 0.007 -10000 0 -10000 0 0
HDAC6 0.033 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.041 0.044 -10000 0 -0.52 4 4
CAMK4 -0.01 0.15 -10000 0 -0.54 64 64
Tubulin/HDAC6 0.055 0.041 -10000 0 -0.34 2 2
SUMO1 0.031 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.031 0.008 -10000 0 -10000 0 0
GATA1 0.018 0.065 -10000 0 -0.32 31 31
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.029 0.01 -10000 0 -10000 0 0
NR3C1 0.029 0.037 -10000 0 -0.49 4 4
SUMO1/HDAC4 0.048 0.045 -10000 0 -10000 0 0
SRF 0.031 0.008 -10000 0 -10000 0 0
HDAC4/YWHAB 0.044 0.016 -10000 0 -10000 0 0
Tubulin 0.039 0.041 -10000 0 -0.24 15 15
HDAC4/14-3-3 E 0.043 0.017 -10000 0 -10000 0 0
GNB1 0.031 0.008 -10000 0 -10000 0 0
RANGAP1 0.03 0.031 -10000 0 -0.47 3 3
BCL6/BCoR 0.044 0.039 -10000 0 -0.48 4 4
HDAC4/HDAC3/SMRT (N-CoR2) 0.057 0.031 -10000 0 -0.34 2 2
HDAC4/SRF 0.031 0.1 -10000 0 -0.34 57 57
HDAC4/ER alpha 0.023 0.091 -10000 0 -0.36 41 41
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.024 0.081 -10000 0 -0.5 13 13
cell motility 0.054 0.041 -10000 0 -0.34 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.031 0.008 -10000 0 -10000 0 0
HDAC7/HDAC3 0.043 0.026 -10000 0 -0.4 2 2
BCL6 0.029 0.04 -10000 0 -0.55 4 4
HDAC4/CaMK II delta B 0.031 0.008 -10000 0 -10000 0 0
Hsp90/HDAC6 0.047 0.01 -10000 0 -10000 0 0
ESR1 0.005 0.12 -10000 0 -0.5 42 42
HDAC6/HDAC11 0.044 0.024 -10000 0 -0.31 2 2
Ran/GTP/Exportin 1 0.047 0.045 -10000 0 -10000 0 0
NPC 0.019 0.004 -10000 0 -10000 0 0
MEF2C 0.006 0.12 -10000 0 -0.54 39 39
RAN 0.032 0.007 -10000 0 -10000 0 0
HDAC4/MEF2C 0.067 0.078 -10000 0 -0.3 27 27
GNG2 0.011 0.11 -10000 0 -0.55 32 32
NCOR2 0.03 0.029 -10000 0 -0.55 2 2
TUBB2A 0.024 0.051 -10000 0 -0.35 15 15
HDAC11 0.029 0.031 -10000 0 -0.47 3 3
HSP90AA1 0.032 0.006 -10000 0 -10000 0 0
RANBP2 0.032 0.007 -10000 0 -10000 0 0
ANKRA2 0.032 0.006 -10000 0 -10000 0 0
RFXANK 0.031 0.03 -10000 0 -0.47 3 3
nuclear import -0.038 0.028 0.32 3 -10000 0 3
Signaling events mediated by HDAC Class III

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.031 0.028 -10000 0 -0.55 2 2
HDAC4 0.031 0.008 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.015 0.022 0.27 4 -10000 0 4
CDKN1A -0.009 0.05 -10000 0 -0.74 4 4
KAT2B 0.03 0.022 -10000 0 -0.55 1 1
BAX 0.031 0.028 -10000 0 -0.55 2 2
FOXO3 -0.006 0.023 0.48 2 -10000 0 2
FOXO1 0.029 0.027 -10000 0 -0.32 5 5
FOXO4 0.02 0.016 -10000 0 -0.29 2 2
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.032 0.006 -10000 0 -10000 0 0
TAT 0.012 0.074 -10000 0 -0.32 41 41
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.037 -10000 0 -0.23 20 20
PPARGC1A -0.019 0.15 -10000 0 -0.44 95 95
FHL2 0.005 0.12 -10000 0 -0.52 43 43
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.042 0.021 -10000 0 -0.4 1 1
HIST2H4A 0.015 0.022 -10000 0 -0.27 4 4
SIRT1/FOXO3a 0.016 0.027 0.3 1 -10000 0 1
SIRT1 0.027 0.024 0.22 3 -0.55 1 4
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.057 0.026 -10000 0 -0.34 1 1
SIRT1/Histone H1b 0.028 0.046 0.3 1 -0.26 7 8
apoptosis -0.056 0.031 0.34 3 -10000 0 3
SIRT1/PGC1A 0.007 0.098 -10000 0 -0.29 73 73
p53/SIRT1 0.032 0.033 0.42 3 -0.4 2 5
SIRT1/FOXO4 0.035 0.034 0.3 1 -0.4 2 3
FOXO1/FHL2/SIRT1 0.036 0.083 -10000 0 -0.32 39 39
HIST1H1E 0.015 0.027 -10000 0 -0.26 3 3
SIRT1/p300 0.041 0.033 -10000 0 -0.57 2 2
muscle cell differentiation -0.029 0.042 0.35 2 -0.35 1 3
TP53 0.025 0.024 0.22 3 -0.55 1 4
KU70/SIRT1/BAX 0.057 0.031 -10000 0 -0.34 3 3
CREBBP 0.031 0.008 -10000 0 -10000 0 0
MEF2D 0.031 0.008 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.026 0.058 -10000 0 -0.22 41 41
ACSS2 0.013 0.031 0.34 1 -0.24 10 11
SIRT1/PCAF/MYOD 0.029 0.042 0.35 1 -0.35 2 3
Canonical NF-kappaB pathway

Figure S124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.034 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.069 0.082 0.3 31 -0.33 3 34
ERC1 0.031 0.008 -10000 0 -10000 0 0
RIP2/NOD2 0.021 0.095 -10000 0 -0.34 53 53
NFKBIA 0.022 0.016 -10000 0 -0.3 1 1
BIRC2 0.032 0.005 -10000 0 -10000 0 0
IKBKB 0.032 0.007 -10000 0 -10000 0 0
RIPK2 0.032 0.013 -10000 0 -0.32 1 1
IKBKG 0.027 0.066 -10000 0 -0.39 9 9
IKK complex/A20 0.048 0.11 -10000 0 -0.44 11 11
NEMO/A20/RIP2 0.032 0.013 -10000 0 -0.32 1 1
XPO1 0.032 0.007 -10000 0 -10000 0 0
NEMO/ATM 0.048 0.076 -10000 0 -0.34 12 12
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.032 0.007 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.041 0.013 -10000 0 -10000 0 0
IKK complex/ELKS 0.054 0.073 -10000 0 -0.36 5 5
BCL10/MALT1/TRAF6 0.061 0.024 -10000 0 -0.34 1 1
NOD2 0.001 0.12 -10000 0 -0.47 53 53
NFKB1 0.035 0.02 -10000 0 -0.55 1 1
RELA 0.036 0.004 -10000 0 -10000 0 0
MALT1 0.031 0.02 -10000 0 -0.55 1 1
cIAP1/UbcH5C 0.047 0.009 -10000 0 -10000 0 0
ATM 0.031 0.028 -10000 0 -0.55 2 2
TNF/TNFR1A 0.011 0.1 -10000 0 -0.3 74 74
TRAF6 0.033 0.004 -10000 0 -10000 0 0
PRKCA 0.029 0.016 -10000 0 -0.32 1 1
CHUK 0.03 0.021 -10000 0 -0.55 1 1
UBE2D3 0.032 0.005 -10000 0 -10000 0 0
TNF -0.011 0.14 -10000 0 -0.43 80 80
NF kappa B1 p50/RelA 0.071 0.025 -10000 0 -0.33 1 1
BCL10 0.031 0.008 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.016 -10000 0 -0.3 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.034 0.009 -10000 0 -10000 0 0
TNFRSF1A 0.031 0.008 -10000 0 -10000 0 0
IKK complex 0.063 0.079 -10000 0 -0.37 7 7
CYLD 0.031 0.008 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.068 0.077 -10000 0 -0.38 5 5
Arf6 downstream pathway

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.014 0.14 -10000 0 -1.1 11 11
regulation of axonogenesis -0.013 0.038 0.23 14 -10000 0 14
myoblast fusion -0.022 0.067 0.48 11 -10000 0 11
mol:GTP 0.018 0.039 -10000 0 -0.25 13 13
regulation of calcium-dependent cell-cell adhesion -0.049 0.058 0.3 10 -10000 0 10
ARF1/GTP 0.033 0.04 -10000 0 -0.23 4 4
mol:GM1 0.006 0.032 -10000 0 -0.2 11 11
mol:Choline 0.011 0.03 -10000 0 -0.29 3 3
lamellipodium assembly 0.006 0.086 -10000 0 -0.42 28 28
MAPK3 0.023 0.051 -10000 0 -0.35 11 11
ARF6/GTP/NME1/Tiam1 0.05 0.059 -10000 0 -0.3 10 10
ARF1 0.031 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.022 0.067 -10000 0 -0.48 11 11
ARF1/GDP 0.026 0.073 0.26 1 -0.43 12 13
ARF6 0.034 0.027 -10000 0 -0.21 1 1
RAB11A 0.033 0.003 -10000 0 -10000 0 0
TIAM1 0.027 0.054 -10000 0 -0.52 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.023 0.057 -10000 0 -0.39 12 12
actin filament bundle formation -0.029 0.072 0.45 10 -10000 0 10
KALRN 0.01 0.059 -10000 0 -0.34 19 19
RAB11FIP3/RAB11A 0.045 0.02 -10000 0 -0.4 1 1
RhoA/GDP 0.03 0.072 -10000 0 -0.45 10 10
NME1 0.03 0.017 -10000 0 -0.32 1 1
Rac1/GDP 0.027 0.072 -10000 0 -0.44 11 11
substrate adhesion-dependent cell spreading 0.018 0.039 -10000 0 -0.25 13 13
cortical actin cytoskeleton organization 0.006 0.086 -10000 0 -0.42 28 28
RAC1 0.029 0.011 -10000 0 -10000 0 0
liver development 0.018 0.039 -10000 0 -0.25 13 13
ARF6/GTP 0.018 0.039 -10000 0 -0.25 13 13
RhoA/GTP 0.033 0.039 -10000 0 -0.23 4 4
mol:GDP 0.009 0.065 -10000 0 -0.49 10 10
ARF6/GTP/RAB11FIP3/RAB11A 0.052 0.043 -10000 0 -0.28 3 3
RHOA 0.03 0.009 -10000 0 -10000 0 0
PLD1 0.019 0.033 -10000 0 -0.24 3 3
RAB11FIP3 0.03 0.021 -10000 0 -0.55 1 1
tube morphogenesis 0.006 0.086 -10000 0 -0.42 28 28
ruffle organization 0.013 0.038 -10000 0 -0.23 14 14
regulation of epithelial cell migration 0.018 0.039 -10000 0 -0.25 13 13
PLD2 0.018 0.037 -10000 0 -0.28 5 5
PIP5K1A 0.013 0.038 -10000 0 -0.23 14 14
mol:Phosphatidic acid 0.011 0.03 -10000 0 -0.29 3 3
Rac1/GTP 0.006 0.087 -10000 0 -0.42 28 28
Signaling events mediated by HDAC Class I

Figure S126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA 0.042 0.097 -10000 0 -0.34 29 29
Ran/GTP/Exportin 1/HDAC1 0.008 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.027 0.093 -10000 0 -0.32 29 29
SUMO1 0.031 0.007 -10000 0 -10000 0 0
ZFPM1 0.024 0.057 -10000 0 -0.43 13 13
NPC/RanGAP1/SUMO1/Ubc9 0.019 0.014 -10000 0 -0.22 2 2
FKBP3 0.032 0.006 -10000 0 -10000 0 0
Histones 0.062 0.062 -10000 0 -10000 0 0
YY1/LSF 0.031 0.052 -10000 0 -0.38 3 3
SMG5 0.031 0.008 -10000 0 -10000 0 0
RAN 0.032 0.007 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.015 0.063 -10000 0 -0.27 28 28
I kappa B alpha/HDAC1 0.03 0.057 -10000 0 -0.43 1 1
SAP18 0.032 0.007 -10000 0 -10000 0 0
RELA 0.016 0.064 -10000 0 -0.24 30 30
HDAC1/Smad7 0.053 0.03 -10000 0 -0.34 1 1
RANGAP1 0.03 0.031 -10000 0 -0.47 3 3
HDAC3/TR2 0.028 0.053 -10000 0 -0.26 1 1
NuRD/MBD3 Complex 0.04 0.057 -10000 0 -0.42 9 9
NF kappa B1 p50/RelA 0.036 0.083 0.27 5 -0.33 10 15
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.015 0.14 -10000 0 -0.41 93 93
GATA1 0.018 0.065 -10000 0 -0.32 31 31
Mad/Max 0.045 0.018 -10000 0 -0.22 2 2
NuRD/MBD3 Complex/GATA1/Fog1 0.027 0.098 -10000 0 -0.36 43 43
RBBP7 0.033 0.003 -10000 0 -10000 0 0
NPC 0.019 0.004 -10000 0 -10000 0 0
RBBP4 0.03 0.021 -10000 0 -0.55 1 1
MAX 0.032 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.031 0.008 -10000 0 -10000 0 0
NFKBIA 0.014 0.049 -10000 0 -0.47 1 1
KAT2B 0.03 0.022 -10000 0 -0.55 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.023 0.091 -10000 0 -0.55 19 19
SIN3 complex 0.066 0.075 -10000 0 -0.31 32 32
SMURF1 0.029 0.011 -10000 0 -10000 0 0
CHD3 0.028 0.03 -10000 0 -0.55 2 2
SAP30 0.012 0.11 -10000 0 -0.55 30 30
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.029 0.01 -10000 0 -10000 0 0
YY1/HDAC3 0.021 0.059 -10000 0 -0.43 2 2
YY1/HDAC2 0.033 0.049 -10000 0 -0.42 2 2
YY1/HDAC1 0.033 0.05 -10000 0 -0.42 2 2
NuRD/MBD2 Complex (MeCP1) 0.041 0.055 -10000 0 -0.44 8 8
PPARG 0.006 0.088 -10000 0 -0.35 41 41
HDAC8/hEST1B 0.063 0.017 -10000 0 -10000 0 0
UBE2I 0.031 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.031 0.008 -10000 0 -10000 0 0
TNFRSF1A 0.031 0.008 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.028 0.056 -10000 0 -0.34 3 3
MBD3L2 0.019 0.002 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.052 0.03 -10000 0 -0.34 1 1
CREBBP 0.031 0.008 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.03 0.094 -10000 0 -0.36 33 33
HDAC1 0.031 0.008 -10000 0 -10000 0 0
HDAC3 0.015 0.048 -10000 0 -0.29 1 1
HDAC2 0.031 0.008 -10000 0 -10000 0 0
YY1 0.024 0.028 -10000 0 -0.48 2 2
HDAC8 0.033 0.001 -10000 0 -10000 0 0
SMAD7 0.031 0.02 -10000 0 -0.55 1 1
NCOR2 0.03 0.029 -10000 0 -0.55 2 2
MXD1 0.031 0.018 -10000 0 -0.32 2 2
STAT3 0.025 0.016 -10000 0 -0.33 1 1
NFKB1 0.032 0.02 -10000 0 -0.55 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.032 0.007 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.047 0.054 -10000 0 -0.43 2 2
YY1/SAP30/HDAC1 0.041 0.078 -10000 0 -0.29 29 29
EP300 0.031 0.028 -10000 0 -0.55 2 2
STAT3 (dimer non-phopshorylated) 0.025 0.016 -10000 0 -0.33 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.049 -10000 0 -0.46 1 1
histone deacetylation 0.026 0.1 -10000 0 -0.44 37 37
STAT3 (dimer non-phopshorylated)/HDAC3 0.026 0.045 -10000 0 -10000 0 0
nuclear export -0.062 0.017 -10000 0 -10000 0 0
PRKACA 0.033 0.003 -10000 0 -10000 0 0
GATAD2B 0.031 0.008 -10000 0 -10000 0 0
GATAD2A 0.033 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.006 0.1 -10000 0 -0.32 42 42
GATA1/HDAC1 0.035 0.05 -10000 0 -0.22 31 31
GATA1/HDAC3 0.024 0.063 -10000 0 -0.28 2 2
CHD4 0.031 0.008 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.011 0.1 -10000 0 -0.3 74 74
SIN3/HDAC complex/Mad/Max 0.024 0.11 -10000 0 -0.61 23 23
NuRD Complex 0.034 0.093 -10000 0 -0.36 32 32
positive regulation of chromatin silencing 0.059 0.061 -10000 0 -10000 0 0
SIN3B 0.032 0.028 -10000 0 -0.55 2 2
MTA2 0.033 0.004 -10000 0 -10000 0 0
SIN3A 0.033 0.003 -10000 0 -10000 0 0
XPO1 0.032 0.007 -10000 0 -10000 0 0
SUMO1/HDAC1 0.048 0.044 -10000 0 -10000 0 0
HDAC complex 0.077 0.028 -10000 0 -0.31 1 1
GATA1/Fog1 0.03 0.064 -10000 0 -0.25 40 40
FKBP25/HDAC1/HDAC2 0.06 0.021 -10000 0 -10000 0 0
TNF -0.011 0.14 -10000 0 -0.43 80 80
negative regulation of cell growth 0.018 0.12 -10000 0 -0.55 35 35
NuRD/MBD2/PRMT5 Complex 0.041 0.055 -10000 0 -0.44 8 8
Ran/GTP/Exportin 1 0.047 0.045 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.011 0.083 -10000 0 -0.33 32 32
SIN3/HDAC complex/NCoR1 0.024 0.11 -10000 0 -0.64 20 20
TFCP2 0.031 0.021 -10000 0 -0.55 1 1
NR2C1 0.032 0.007 -10000 0 -10000 0 0
MBD3 0.03 0.041 -10000 0 -0.5 5 5
MBD2 0.032 0.006 -10000 0 -10000 0 0
Circadian rhythm pathway

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.057 0.041 -10000 0 -10000 0 0
CLOCK 0.013 0.11 -10000 0 -0.55 33 33
TIMELESS/CRY2 0.045 0.037 -10000 0 -10000 0 0
DEC1/BMAL1 0.039 0.027 -10000 0 -0.31 4 4
ATR 0.031 0.021 -10000 0 -0.55 1 1
NR1D1 0.021 0.076 -10000 0 -1.4 2 2
ARNTL 0.034 0.029 -10000 0 -0.55 2 2
TIMELESS 0.025 0.033 -10000 0 -10000 0 0
NPAS2 0.009 0.12 -10000 0 -0.54 39 39
CRY2 0.033 0.004 -10000 0 -10000 0 0
mol:CO -0.012 0.008 0.14 2 -10000 0 2
CHEK1 0.033 0.004 -10000 0 -10000 0 0
mol:HEME 0.012 0.008 -10000 0 -0.14 2 2
PER1 0.028 0.032 -10000 0 -0.47 3 3
BMAL/CLOCK/NPAS2 0.04 0.12 -10000 0 -0.34 65 65
BMAL1/CLOCK 0.024 0.11 -10000 0 -0.8 5 5
S phase of mitotic cell cycle 0.057 0.041 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.058 0.042 -10000 0 -10000 0 0
mol:NADPH 0.012 0.008 -10000 0 -0.14 2 2
PER1/TIMELESS 0.041 0.043 -10000 0 -0.63 1 1
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.02 0.017 -10000 0 -0.32 2 2
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.032 0.006 -10000 0 -10000 0 0
SMAD2 -0.008 0.051 -10000 0 -0.26 12 12
SMAD3 0.031 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4 0.018 0.13 0.32 3 -0.49 49 52
SMAD4/Ubc9/PIASy 0.06 0.028 -10000 0 -0.34 2 2
SMAD2/SMAD2/SMAD4 0.05 0.063 -10000 0 -10000 0 0
PPM1A 0.032 0.006 -10000 0 -10000 0 0
CALM1 0.032 0.006 -10000 0 -10000 0 0
SMAD2/SMAD4 0.01 0.055 -10000 0 -0.29 2 2
MAP3K1 0.032 0.013 -10000 0 -0.32 1 1
TRAP-1/SMAD4 0.034 0.072 -10000 0 -0.4 22 22
MAPK3 0.03 0.021 -10000 0 -0.55 1 1
MAPK1 0.031 0.02 -10000 0 -0.55 1 1
NUP214 0.032 0.005 -10000 0 -10000 0 0
CTDSP1 0.031 0.021 -10000 0 -0.55 1 1
CTDSP2 0.032 0.007 -10000 0 -10000 0 0
CTDSPL 0.03 0.015 -10000 0 -0.32 1 1
KPNB1 0.029 0.011 -10000 0 -10000 0 0
TGFBRAP1 0.016 0.093 -10000 0 -0.55 23 23
UBE2I 0.031 0.008 -10000 0 -10000 0 0
NUP153 0.03 0.021 -10000 0 -0.55 1 1
KPNA2 0.028 0.026 -10000 0 -0.32 4 4
PIAS4 0.031 0.028 -10000 0 -0.55 2 2
Arf1 pathway

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.021 0.048 0.19 37 -0.43 2 39
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.002 0.082 0.14 1 -0.35 39 40
AP2 0.046 0.019 -10000 0 -0.4 1 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.038 0.023 -10000 0 -0.37 1 1
CLTB 0.03 0.029 -10000 0 -0.55 2 2
coatomer protein complex/ARF1/GTP/ER cargo protein 0.025 0.018 -10000 0 -0.28 2 2
CD4 0.017 0.091 -10000 0 -0.55 22 22
CLTA 0.033 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.014 -10000 0 -0.4 1 1
mol:PI-4-5-P2 0.008 0.017 -10000 0 -0.23 3 3
ARF1/GTP 0.038 0.021 -10000 0 -0.29 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.016 0.019 -10000 0 -0.48 1 1
mol:Choline 0.008 0.017 -10000 0 -0.23 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.032 0.009 -10000 0 -10000 0 0
DDEF1 0.007 0.017 -10000 0 -0.24 3 3
ARF1/GDP 0.005 0.02 -10000 0 -0.37 1 1
AP2M1 0.032 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.015 0.008 -10000 0 -10000 0 0
Rac/GTP 0.022 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.041 0.023 -10000 0 -0.33 1 1
ARFIP2 0.027 0.024 -10000 0 -0.54 1 1
COPA 0.031 0.008 -10000 0 -10000 0 0
RAC1 0.029 0.011 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.065 -10000 0 -0.28 37 37
ARF1/GTP/ARHGAP10 0.022 0.007 -10000 0 -10000 0 0
GGA3 0.029 0.011 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.025 0.055 -10000 0 -0.24 33 33
AP2A1 0.032 0.02 -10000 0 -0.55 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.034 -10000 0 -0.33 6 6
ARF1/GDP/Membrin 0.021 0.07 -10000 0 -0.32 34 34
Arfaptin 2/Rac/GDP 0.038 0.021 -10000 0 -0.36 1 1
CYTH2 0.033 0.028 -10000 0 -0.55 2 2
ARF1/GTP/GGA3 0.039 0.016 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.021 0.008 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.015 0.063 -10000 0 -0.29 24 24
PLD2 0.008 0.017 -10000 0 -0.23 3 3
ARF-GAP1/v-SNARE 0.009 0.014 -10000 0 -0.4 1 1
PIP5K1A 0.008 0.017 -10000 0 -0.23 3 3
ARF1/GTP/Membrin/GBF1/p115 0.028 0.035 0.14 3 -0.31 1 4
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.008 0.016 -10000 0 -0.23 3 3
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.014 -10000 0 -0.4 1 1
GOSR2 0.015 0.017 -10000 0 -0.41 1 1
USO1 0.013 0.036 -10000 0 -0.38 6 6
GBF1 0.01 0.048 -10000 0 -0.35 14 14
ARF1/GTP/Arfaptin 2 0.044 0.02 -10000 0 -0.4 1 1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.051 0.066 -10000 0 -0.34 22 22
Alternative NF-kappaB pathway

Figure S130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S130.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.034 0.059 -9999 0 -0.38 14 14
FBXW11 0.031 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.031 0.008 -9999 0 -10000 0 0
CHUK 0.03 0.021 -9999 0 -0.55 1 1
NF kappa B2 p100/RelB 0.073 0.063 -9999 0 -0.33 9 9
NFKB1 0.032 0.02 -9999 0 -0.55 1 1
MAP3K14 0.021 0.069 -9999 0 -0.53 13 13
NF kappa B1 p50/RelB 0.047 0.023 -9999 0 -0.4 2 2
RELB 0.032 0.02 -9999 0 -0.55 1 1
NFKB2 0.031 0.008 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.041 0.017 -9999 0 -0.34 1 1
regulation of B cell activation 0.041 0.017 -9999 0 -0.34 1 1
Sumoylation by RanBP2 regulates transcriptional repression

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.031 0.008 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.008 0.009 -9999 0 -10000 0 0
MDM2/SUMO1 0.044 0.047 -9999 0 -10000 0 0
HDAC4 0.031 0.008 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.008 0.008 -9999 0 -10000 0 0
SUMO1 0.031 0.007 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.01 0.039 -9999 0 -0.18 33 33
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.016 0.015 -9999 0 -0.21 2 2
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.032 0.007 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.032 0.007 -9999 0 -10000 0 0
SUMO1/HDAC4 0.048 0.045 -9999 0 -10000 0 0
SUMO1/HDAC1 0.048 0.044 -9999 0 -10000 0 0
RANGAP1 0.03 0.031 -9999 0 -0.47 3 3
MDM2/SUMO1/SUMO1 0.074 0.031 -9999 0 -0.31 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.019 0.014 -9999 0 -0.22 2 2
Ran/GTP 0.03 0.044 -9999 0 -0.24 2 2
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.031 0.007 -9999 0 -10000 0 0
UBE2I 0.031 0.008 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.04 -9999 0 -10000 0 0
NPC 0.019 0.004 -9999 0 -10000 0 0
PIAS2 0.031 0.02 -9999 0 -0.55 1 1
PIAS1 0.033 0.003 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 879 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.Y8.A8S1 TCGA.Y8.A8S0 TCGA.Y8.A8RZ TCGA.Y8.A8RY
109_MAP3K5 0.047 0.16 -0.15 0.16
47_PPARGC1A 0.033 0.033 0.033 0.033
105_BMP4 0.033 0.033 0.033 0.033
105_BMP6 0.033 0.033 0.033 0.033
105_BMP7 -0.32 -0.32 0.033 0.033
105_BMP2 0.033 0.033 0.033 0.033
131_RELN/VLDLR 0.085 0 0.085 0
30_TGFB1/TGF beta receptor Type II 0.033 0.033 0.033 0.033
84_STAT5B 0.05 -0.0056 -0.19 0.091
84_STAT5A 0.05 -0.0056 -0.19 0.091
Methods & Data
Input

  • Expression Data Normalization = Tumor samples were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/KIPAN-TP/14527269/KIPAN-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/KIPAN-TP/15081086/GDAC_Gistic2Report_15084507/all_data_by_genes.txt

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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