PARADIGM pathway analysis of mRNASeq expression and copy number data
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1ZK5DRB
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1ZK5DRB
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 40 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
Signaling events mediated by the Hedgehog family 58
Signaling mediated by p38-alpha and p38-beta 47
IL4-mediated signaling events 42
Syndecan-1-mediated signaling events 41
EPHB forward signaling 39
Ephrin A reverse signaling 37
IL23-mediated signaling events 37
Endothelins 34
TCR signaling in naïve CD8+ T cells 34
Noncanonical Wnt signaling pathway 33
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 370 . 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 ( 370 ).

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
Signaling events mediated by the Hedgehog family 0.1568 58 3036 52 -0.13 0.048 1000 -1000 -0.03 -1000
Signaling mediated by p38-alpha and p38-beta 0.1270 47 2075 44 -0.12 0.025 1000 -1000 -0.024 -1000
IL4-mediated signaling events 0.1135 42 3880 91 -0.55 0.43 1000 -1000 -0.11 -1000
Syndecan-1-mediated signaling events 0.1108 41 1406 34 -0.086 0.024 1000 -1000 -0.025 -1000
EPHB forward signaling 0.1054 39 3349 85 -0.068 0.068 1000 -1000 -0.046 -1000
Ephrin A reverse signaling 0.1000 37 261 7 -0.039 0.017 1000 -1000 -0.006 -1000
IL23-mediated signaling events 0.1000 37 2225 60 -0.34 0.025 1000 -1000 -0.1 -1000
Endothelins 0.0919 34 3298 96 -0.11 0.053 1000 -1000 -0.046 -1000
TCR signaling in naïve CD8+ T cells 0.0919 34 3235 93 -0.098 0.035 1000 -1000 -0.039 -1000
Noncanonical Wnt signaling pathway 0.0892 33 875 26 -0.064 0.025 1000 -1000 -0.027 -1000
TCGA08_retinoblastoma 0.0865 32 258 8 -0.021 0.02 1000 -1000 -0.004 -1000
Ephrin B reverse signaling 0.0838 31 1522 48 -0.076 0.025 1000 -1000 -0.023 -1000
Wnt signaling 0.0811 30 210 7 -0.062 0.008 1000 -1000 -0.008 -1000
LPA receptor mediated events 0.0811 30 3061 102 -0.079 0.028 1000 -1000 -0.048 -1000
HIF-1-alpha transcription factor network 0.0784 29 2224 76 -0.15 0.036 1000 -1000 -0.072 -1000
FOXA2 and FOXA3 transcription factor networks 0.0757 28 1325 46 -0.27 0.027 1000 -1000 -0.087 -1000
IGF1 pathway 0.0703 26 1494 57 -0.041 0.039 1000 -1000 -0.027 -1000
Signaling events regulated by Ret tyrosine kinase 0.0676 25 2090 82 -0.041 0.026 1000 -1000 -0.036 -1000
p75(NTR)-mediated signaling 0.0649 24 3034 125 -0.086 0.058 1000 -1000 -0.051 -1000
Glucocorticoid receptor regulatory network 0.0649 24 2758 114 -0.31 0.16 1000 -1000 -0.055 -1000
Reelin signaling pathway 0.0649 24 1360 56 -0.053 0.049 1000 -1000 -0.026 -1000
Thromboxane A2 receptor signaling 0.0622 23 2515 105 -0.078 0.035 1000 -1000 -0.032 -1000
Fc-epsilon receptor I signaling in mast cells 0.0622 23 2269 97 -0.072 0.046 1000 -1000 -0.06 -1000
TCGA08_p53 0.0622 23 167 7 -0.025 0.021 1000 -1000 -0.004 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0622 23 1630 68 -0.17 0.065 1000 -1000 -0.059 -1000
Plasma membrane estrogen receptor signaling 0.0622 23 2063 86 -0.079 0.074 1000 -1000 -0.037 -1000
Glypican 1 network 0.0595 22 1072 48 -0.071 0.046 1000 -1000 -0.022 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0595 22 1184 52 -0.068 0.046 1000 -1000 -0.023 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0595 22 1741 78 -0.078 0.037 1000 -1000 -0.049 -1000
BMP receptor signaling 0.0568 21 1773 81 -0.086 0.048 1000 -1000 -0.033 -1000
Nectin adhesion pathway 0.0568 21 1326 63 -0.039 0.058 1000 -1000 -0.039 -1000
BCR signaling pathway 0.0568 21 2124 99 -0.09 0.035 1000 -1000 -0.044 -1000
IL12-mediated signaling events 0.0541 20 1795 87 -0.16 0.025 1000 -1000 -0.082 -1000
Osteopontin-mediated events 0.0541 20 764 38 -0.037 0.026 1000 -1000 -0.028 -1000
Glypican 2 network 0.0541 20 83 4 -0.003 0.007 1000 -1000 0.011 -1000
Syndecan-4-mediated signaling events 0.0541 20 1351 67 -0.079 0.035 1000 -1000 -0.025 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0541 20 1836 88 -0.083 0.035 1000 -1000 -0.063 -1000
Caspase cascade in apoptosis 0.0514 19 1414 74 -0.076 0.042 1000 -1000 -0.027 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0514 19 2305 120 -0.078 0.068 1000 -1000 -0.037 -1000
FOXM1 transcription factor network 0.0514 19 992 51 -0.12 0.032 1000 -1000 -0.089 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0486 18 616 34 -0.009 0.037 1000 -1000 -0.021 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0486 18 1551 85 -0.037 0.025 1000 -1000 -0.028 -1000
Retinoic acid receptors-mediated signaling 0.0486 18 1061 58 -0.065 0.049 1000 -1000 -0.023 -1000
PDGFR-alpha signaling pathway 0.0432 16 706 44 -0.033 0.037 1000 -1000 -0.032 -1000
amb2 Integrin signaling 0.0432 16 1323 82 -0.096 0.034 1000 -1000 -0.031 -1000
FAS signaling pathway (CD95) 0.0432 16 755 47 -0.029 0.037 1000 -1000 -0.035 -1000
Canonical Wnt signaling pathway 0.0432 16 818 51 -0.11 0.061 1000 -1000 -0.036 -1000
Arf6 signaling events 0.0405 15 935 62 -0.019 0.04 1000 -1000 -0.037 -1000
Signaling events mediated by PTP1B 0.0405 15 1160 76 -0.053 0.034 1000 -1000 -0.033 -1000
S1P1 pathway 0.0405 15 549 36 -0.13 0.025 1000 -1000 -0.031 -1000
Integrins in angiogenesis 0.0405 15 1300 84 -0.07 0.047 1000 -1000 -0.031 -1000
Nongenotropic Androgen signaling 0.0405 15 814 52 -0.038 0.037 1000 -1000 -0.022 -1000
IL6-mediated signaling events 0.0405 15 1163 75 -0.12 0.057 1000 -1000 -0.043 -1000
Visual signal transduction: Rods 0.0405 15 782 52 -0.042 0.041 1000 -1000 -0.018 -1000
Syndecan-2-mediated signaling events 0.0378 14 1012 69 -0.071 0.037 1000 -1000 -0.034 -1000
Presenilin action in Notch and Wnt signaling 0.0378 14 874 61 -0.11 0.051 1000 -1000 -0.036 -1000
IL1-mediated signaling events 0.0378 14 884 62 -0.02 0.048 1000 -1000 -0.028 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0378 14 645 45 -0.028 0.06 1000 -1000 -0.042 -1000
Calcium signaling in the CD4+ TCR pathway 0.0378 14 442 31 -0.081 0.025 1000 -1000 -0.035 -1000
EGFR-dependent Endothelin signaling events 0.0378 14 295 21 -0.025 0.035 1000 -1000 -0.03 -1000
Class IB PI3K non-lipid kinase events 0.0378 14 42 3 -0.002 0.002 1000 -1000 -0.012 -1000
Coregulation of Androgen receptor activity 0.0351 13 1028 76 -0.076 0.044 1000 -1000 -0.019 -1000
Cellular roles of Anthrax toxin 0.0351 13 518 39 -0.047 0.025 1000 -1000 -0.017 -1000
Effects of Botulinum toxin 0.0351 13 347 26 -0.038 0.039 1000 -1000 -0.004 -1000
ErbB2/ErbB3 signaling events 0.0324 12 837 65 -0.027 0.043 1000 -1000 -0.044 -1000
Regulation of nuclear SMAD2/3 signaling 0.0324 12 1724 136 -0.24 0.073 1000 -1000 -0.038 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0324 12 652 54 -0.053 0.036 1000 -1000 -0.029 -1000
ceramide signaling pathway 0.0324 12 604 49 -0.018 0.037 1000 -1000 -0.037 -1000
HIF-2-alpha transcription factor network 0.0324 12 518 43 -0.043 0.053 1000 -1000 -0.044 -1000
IL2 signaling events mediated by PI3K 0.0324 12 717 58 -0.042 0.035 1000 -1000 -0.035 -1000
LPA4-mediated signaling events 0.0297 11 137 12 -0.035 0.006 1000 -1000 -0.017 -1000
IFN-gamma pathway 0.0297 11 748 68 -0.042 0.052 1000 -1000 -0.041 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0297 11 852 74 -0.051 0.048 1000 -1000 -0.047 -1000
E-cadherin signaling in keratinocytes 0.0297 11 482 43 -0.014 0.038 1000 -1000 -0.031 -1000
Regulation of Androgen receptor activity 0.0297 11 798 70 -0.1 0.029 1000 -1000 -0.036 -1000
Ras signaling in the CD4+ TCR pathway 0.0297 11 192 17 -0.015 0.042 1000 -1000 -0.018 -1000
JNK signaling in the CD4+ TCR pathway 0.0270 10 179 17 -0.024 0.043 1000 -1000 -0.036 -1000
Hedgehog signaling events mediated by Gli proteins 0.0270 10 660 65 -0.18 0.058 1000 -1000 -0.044 -1000
Ceramide signaling pathway 0.0270 10 825 76 -0.032 0.068 1000 -1000 -0.03 -1000
Aurora B signaling 0.0270 10 697 67 -0.15 0.062 1000 -1000 -0.026 -1000
EPO signaling pathway 0.0243 9 543 55 -0.001 0.052 1000 -1000 -0.029 -1000
S1P5 pathway 0.0243 9 155 17 -0.001 0.025 1000 -1000 -0.008 -1000
IL27-mediated signaling events 0.0243 9 501 51 -0.041 0.026 1000 -1000 -0.044 -1000
Regulation of Telomerase 0.0243 9 925 102 -0.14 0.057 1000 -1000 -0.044 -1000
BARD1 signaling events 0.0216 8 474 57 -0.036 0.046 1000 -1000 -0.029 -1000
a4b1 and a4b7 Integrin signaling 0.0216 8 41 5 0.011 0.025 1000 -1000 0.009 -1000
mTOR signaling pathway 0.0216 8 452 53 -0.02 0.028 1000 -1000 -0.027 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0216 8 332 37 -0.022 0.052 1000 -1000 -0.021 -1000
TRAIL signaling pathway 0.0216 8 411 48 -0.005 0.05 1000 -1000 -0.022 -1000
Class I PI3K signaling events 0.0216 8 623 73 -0.038 0.047 1000 -1000 -0.029 -1000
S1P4 pathway 0.0216 8 216 25 -0.007 0.038 1000 -1000 -0.02 -1000
PLK1 signaling events 0.0189 7 649 85 -0.006 0.039 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class III 0.0189 7 295 40 -0.052 0.046 1000 -1000 -0.021 -1000
TCGA08_rtk_signaling 0.0189 7 197 26 -0.036 0.05 1000 -1000 -0.009 -1000
E-cadherin signaling in the nascent adherens junction 0.0189 7 591 76 -0.037 0.055 1000 -1000 -0.044 -1000
IL2 signaling events mediated by STAT5 0.0189 7 172 22 -0.012 0.026 1000 -1000 -0.031 -1000
Insulin Pathway 0.0189 7 560 74 -0.044 0.059 1000 -1000 -0.032 -1000
PDGFR-beta signaling pathway 0.0189 7 723 97 -0.045 0.062 1000 -1000 -0.041 -1000
PLK2 and PLK4 events 0.0162 6 20 3 0.002 0.019 1000 -1000 -0.008 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0162 6 561 83 -0.049 0.047 1000 -1000 -0.027 -1000
Signaling mediated by p38-gamma and p38-delta 0.0162 6 101 15 -0.015 0.024 1000 -1000 -0.026 -1000
Paxillin-dependent events mediated by a4b1 0.0162 6 242 36 -0.041 0.043 1000 -1000 -0.028 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0162 6 219 33 -0.051 0.061 1000 -1000 -0.041 -1000
Signaling events mediated by PRL 0.0162 6 209 34 -0.042 0.037 1000 -1000 -0.028 -1000
Canonical NF-kappaB pathway 0.0135 5 216 39 -0.017 0.055 1000 -1000 -0.024 -1000
ErbB4 signaling events 0.0135 5 379 69 -0.025 0.03 1000 -1000 -0.031 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0135 5 143 28 0 0.045 1000 -1000 -0.016 -1000
Visual signal transduction: Cones 0.0135 5 221 38 -0.01 0.04 1000 -1000 -0.009 -1000
Class I PI3K signaling events mediated by Akt 0.0135 5 348 68 -0.032 0.047 1000 -1000 -0.025 -1000
Signaling events mediated by HDAC Class I 0.0135 5 540 104 -0.038 0.063 1000 -1000 -0.026 -1000
Syndecan-3-mediated signaling events 0.0135 5 207 35 -0.034 0.052 1000 -1000 -0.016 -1000
Regulation of p38-alpha and p38-beta 0.0135 5 300 54 -0.034 0.058 1000 -1000 -0.04 -1000
FoxO family signaling 0.0108 4 289 64 -0.064 0.056 1000 -1000 -0.059 -1000
Atypical NF-kappaB pathway 0.0108 4 144 31 0 0.025 1000 -1000 -0.009 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0108 4 512 125 -0.008 0.062 1000 -1000 -0.034 -1000
S1P3 pathway 0.0108 4 183 42 -0.002 0.043 1000 -1000 -0.032 -1000
E-cadherin signaling events 0.0108 4 20 5 0.017 0.038 1000 -1000 0.01 -1000
p38 MAPK signaling pathway 0.0108 4 200 44 -0.042 0.05 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class II 0.0081 3 269 75 -0.03 0.067 1000 -1000 -0.027 -1000
Arf6 downstream pathway 0.0081 3 157 43 -0.04 0.044 1000 -1000 -0.022 -1000
Aurora C signaling 0.0081 3 23 7 0 0.038 1000 -1000 -0.006 -1000
Insulin-mediated glucose transport 0.0081 3 116 32 -0.012 0.045 1000 -1000 -0.021 -1000
VEGFR1 specific signals 0.0081 3 178 56 -0.017 0.049 1000 -1000 -0.034 -1000
Aurora A signaling 0.0054 2 139 60 0 0.049 1000 -1000 -0.015 -1000
Arf6 trafficking events 0.0054 2 162 71 -0.041 0.045 1000 -1000 -0.023 -1000
Arf1 pathway 0.0054 2 155 54 -0.001 0.038 1000 -1000 -0.012 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0027 1 38 23 0.004 0.048 1000 -1000 -0.024 -1000
Circadian rhythm pathway 0.0027 1 37 22 -0.007 0.043 1000 -1000 -0.036 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0027 1 47 27 0 0.057 1000 -1000 -0.029 -1000
Rapid glucocorticoid signaling 0.0027 1 33 20 -0.007 0.029 1000 -1000 -0.002 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.066 1000 -1000 0 -1000
Total NA 1910 115890 7203 -7.9 6 131000 -131000 -4.1 -131000
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.09 0.19 -10000 0 -0.56 34 34
IHH -0.13 0.2 -10000 0 -0.44 105 105
SHH Np/Cholesterol/GAS1 -0.038 0.1 -10000 0 -0.24 65 65
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.037 0.1 0.24 65 -10000 0 65
SMO/beta Arrestin2 -0.092 0.19 -10000 0 -0.36 101 101
SMO -0.11 0.19 -10000 0 -0.38 103 103
AKT1 -0.052 0.16 -10000 0 -0.51 27 27
ARRB2 0.024 0.006 -10000 0 -10000 0 0
BOC 0.015 0.05 -10000 0 -0.4 4 4
ADRBK1 0.025 0.004 -10000 0 -10000 0 0
heart looping -0.11 0.19 -10000 0 -0.37 103 103
STIL -0.071 0.16 0.18 25 -0.34 58 83
DHH N/PTCH2 0.009 0.092 -10000 0 -0.32 25 25
DHH N/PTCH1 -0.075 0.15 -10000 0 -0.26 130 130
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
DHH 0.001 0.094 -10000 0 -0.4 18 18
PTHLH -0.12 0.23 -10000 0 -0.62 41 41
determination of left/right symmetry -0.11 0.19 -10000 0 -0.37 103 103
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
skeletal system development -0.12 0.23 -10000 0 -0.61 41 41
IHH N/Hhip -0.098 0.18 -10000 0 -0.33 125 125
DHH N/Hhip -0.03 0.13 -10000 0 -0.3 63 63
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.11 0.19 -10000 0 -0.37 103 103
pancreas development -0.042 0.15 -10000 0 -0.4 50 50
HHAT 0.011 0.067 -10000 0 -0.4 9 9
PI3K 0.025 0.052 -10000 0 -0.28 9 9
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.024 0.12 -10000 0 -0.4 31 31
somite specification -0.11 0.19 -10000 0 -0.37 103 103
SHH Np/Cholesterol/PTCH1 -0.087 0.15 -10000 0 -0.29 104 104
SHH Np/Cholesterol/PTCH2 -0.021 0.092 -10000 0 -0.24 47 47
SHH Np/Cholesterol/Megalin -0.058 0.11 -10000 0 -0.25 83 83
SHH -0.035 0.1 -10000 0 -0.3 44 44
catabolic process -0.076 0.15 -10000 0 -0.29 110 110
SMO/Vitamin D3 -0.083 0.2 -10000 0 -0.34 106 106
SHH Np/Cholesterol/Hhip -0.048 0.12 -10000 0 -0.26 77 77
LRP2 -0.071 0.15 -10000 0 -0.4 60 60
receptor-mediated endocytosis -0.12 0.2 -10000 0 -0.42 73 73
SHH Np/Cholesterol/BOC -0.02 0.088 -10000 0 -0.24 46 46
SHH Np/Cholesterol/CDO -0.019 0.092 -10000 0 -0.25 45 45
mesenchymal cell differentiation 0.048 0.11 0.25 77 -10000 0 77
mol:Vitamin D3 -0.065 0.18 0.2 34 -0.34 66 100
IHH N/PTCH2 -0.059 0.14 -10000 0 -0.27 106 106
CDON 0.017 0.052 -10000 0 -0.4 5 5
IHH N/PTCH1 -0.074 0.16 -10000 0 -0.28 121 121
Megalin/LRPAP1 -0.038 0.12 -10000 0 -0.28 60 60
PTCH2 0.011 0.072 -10000 0 -0.4 10 10
SHH Np/Cholesterol -0.022 0.08 -10000 0 -0.23 44 44
PTCH1 -0.076 0.15 -10000 0 -0.29 110 110
HHIP -0.042 0.15 -10000 0 -0.4 50 50
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.12 0.32 -10000 0 -0.91 47 47
MKNK1 0.025 0.003 -10000 0 -10000 0 0
MAPK14 -0.032 0.12 -10000 0 -0.31 58 58
ATF2/c-Jun -0.03 0.11 -10000 0 -0.34 16 16
MAPK11 -0.033 0.12 -10000 0 -0.32 55 55
MITF -0.043 0.15 -10000 0 -0.37 59 59
MAPKAPK5 -0.039 0.14 -10000 0 -0.36 57 57
KRT8 -0.041 0.15 -10000 0 -0.36 58 58
MAPKAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPKAPK2 0.022 0.009 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.052 0.18 -10000 0 -0.45 59 59
CEBPB -0.038 0.14 -10000 0 -0.36 56 56
SLC9A1 -0.039 0.14 -10000 0 -0.36 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.038 0.14 -10000 0 -0.35 57 57
p38alpha-beta/MNK1 -0.018 0.16 -10000 0 -0.37 55 55
JUN -0.03 0.11 -10000 0 -0.34 16 16
PPARGC1A -0.088 0.2 -10000 0 -0.37 98 98
USF1 -0.037 0.14 -10000 0 -0.35 54 54
RAB5/GDP/GDI1 -0.024 0.11 -10000 0 -0.26 56 56
NOS2 -0.067 0.24 -10000 0 -0.78 27 27
DDIT3 -0.04 0.14 -10000 0 -0.36 58 58
RAB5A 0.025 0.005 -10000 0 -10000 0 0
HSPB1 -0.037 0.12 0.27 5 -0.3 59 64
p38alpha-beta/HBP1 -0.02 0.16 -10000 0 -0.37 58 58
CREB1 -0.043 0.16 -10000 0 -0.39 57 57
RAB5/GDP 0.018 0.004 -10000 0 -10000 0 0
EIF4E -0.042 0.13 0.19 1 -0.34 52 53
RPS6KA4 -0.041 0.14 -10000 0 -0.36 59 59
PLA2G4A -0.059 0.15 0.19 1 -0.36 64 65
GDI1 -0.04 0.14 -10000 0 -0.36 58 58
TP53 -0.064 0.17 -10000 0 -0.46 55 55
RPS6KA5 -0.042 0.15 -10000 0 -0.37 58 58
ESR1 -0.08 0.2 -10000 0 -0.41 85 85
HBP1 0.025 0.005 -10000 0 -10000 0 0
MEF2C -0.04 0.14 -10000 0 -0.36 58 58
MEF2A -0.038 0.14 -10000 0 -0.36 56 56
EIF4EBP1 -0.043 0.16 -10000 0 -0.39 57 57
KRT19 -0.053 0.16 -10000 0 -0.36 69 69
ELK4 -0.039 0.14 -10000 0 -0.35 56 56
ATF6 -0.037 0.14 -10000 0 -0.35 54 54
ATF1 -0.042 0.15 -10000 0 -0.38 57 57
p38alpha-beta/MAPKAPK2 -0.022 0.15 -10000 0 -0.35 57 57
p38alpha-beta/MAPKAPK3 -0.019 0.16 -10000 0 -0.36 56 56
IL4-mediated signaling events

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
BCL2L1 -0.38 0.5 -10000 0 -1.2 71 71
STAT6 (cleaved dimer) -0.4 0.53 -10000 0 -1.2 88 88
IGHG1 -0.12 0.18 -10000 0 -0.48 17 17
IGHG3 -0.37 0.49 -10000 0 -1.1 85 85
AKT1 -0.2 0.3 -10000 0 -0.79 45 45
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.29 -10000 0 -0.84 33 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.3 -10000 0 -0.83 37 37
THY1 -0.38 0.51 -10000 0 -1.2 76 76
MYB 0.009 0.083 -10000 0 -0.4 14 14
HMGA1 0.023 0.023 -10000 0 -0.4 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.24 0.36 -10000 0 -0.81 66 66
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.19 0.31 -10000 0 -0.88 35 35
SP1 0.025 0.022 -10000 0 -0.13 2 2
INPP5D 0.014 0.067 -10000 0 -0.4 9 9
SOCS5 0.033 0.022 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.38 0.54 -10000 0 -1.2 81 81
SOCS1 -0.25 0.33 -10000 0 -0.74 78 78
SOCS3 -0.22 0.33 -10000 0 -0.94 38 38
FCER2 -0.32 0.44 -10000 0 -1 77 77
PARP14 0.02 0.045 -10000 0 -0.4 4 4
CCL17 -0.42 0.55 -10000 0 -1.3 86 86
GRB2 0.024 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.25 -10000 0 -0.72 28 28
T cell proliferation -0.39 0.53 -10000 0 -1.2 81 81
IL4R/JAK1 -0.38 0.52 -10000 0 -1.2 78 78
EGR2 -0.38 0.52 -10000 0 -1.2 75 75
JAK2 -0.025 0.08 -10000 0 -0.44 9 9
JAK3 0.017 0.047 -10000 0 -0.39 4 4
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
JAK1 -0.003 0.053 -10000 0 -0.4 5 5
COL1A2 -0.13 0.26 -10000 0 -1.2 12 12
CCL26 -0.38 0.51 -10000 0 -1.2 75 75
IL4R -0.41 0.55 -10000 0 -1.3 76 76
PTPN6 0.029 0.04 -10000 0 -0.39 3 3
IL13RA2 -0.43 0.56 -10000 0 -1.3 87 87
IL13RA1 -0.015 0.047 -10000 0 -10000 0 0
IRF4 -0.19 0.42 -10000 0 -1.2 49 49
ARG1 -0.093 0.17 -10000 0 -0.73 8 8
CBL -0.23 0.33 -10000 0 -0.76 66 66
GTF3A 0.026 0.017 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.021 0.079 -10000 0 -0.32 9 9
IRF4/BCL6 -0.17 0.4 -10000 0 -1.1 49 49
CD40LG -0.014 0.11 -10000 0 -0.41 22 22
MAPK14 -0.23 0.34 -10000 0 -0.8 61 61
mitosis -0.18 0.29 -10000 0 -0.74 45 45
STAT6 -0.45 0.66 -10000 0 -1.4 82 82
SPI1 0.019 0.052 -10000 0 -0.4 5 5
RPS6KB1 -0.18 0.27 -10000 0 -0.72 42 42
STAT6 (dimer) -0.45 0.65 -10000 0 -1.4 82 82
STAT6 (dimer)/PARP14 -0.41 0.57 -10000 0 -1.3 83 83
mast cell activation 0.009 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.33 -10000 0 -0.88 43 43
FRAP1 -0.2 0.3 -10000 0 -0.79 45 45
LTA -0.4 0.54 -10000 0 -1.3 80 80
FES 0.022 0.032 -10000 0 -0.4 2 2
T-helper 1 cell differentiation 0.43 0.6 1.3 82 -10000 0 82
CCL11 -0.41 0.53 -10000 0 -1.2 89 89
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.19 0.32 -10000 0 -0.86 39 39
IL2RG 0.006 0.079 -10000 0 -0.4 12 12
IL10 -0.38 0.55 -10000 0 -1.2 80 80
IRS1 0.008 0.083 -10000 0 -0.4 14 14
IRS2 0.007 0.068 -10000 0 -0.4 8 8
IL4 -0.088 0.18 -10000 0 -1.2 6 6
IL5 -0.39 0.51 -10000 0 -1.2 75 75
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.31 0.41 -10000 0 -0.94 73 73
COL1A1 -0.16 0.31 -10000 0 -1.1 22 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.54 -10000 0 -1.3 76 76
IL2R gamma/JAK3 0.015 0.074 -10000 0 -0.32 14 14
TFF3 -0.55 0.68 -10000 0 -1.4 127 127
ALOX15 -0.45 0.58 -10000 0 -1.3 89 89
MYBL1 0.02 0.039 -10000 0 -0.4 3 3
T-helper 2 cell differentiation -0.34 0.46 -10000 0 -1 85 85
SHC1 0.021 0.01 -10000 0 -10000 0 0
CEBPB 0.026 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.19 0.3 -10000 0 -0.81 37 37
mol:PI-3-4-5-P3 -0.2 0.3 -10000 0 -0.8 44 44
PI3K -0.21 0.33 -10000 0 -0.87 44 44
DOK2 0.018 0.041 -10000 0 -0.4 3 3
ETS1 0.032 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.13 0.23 -10000 0 -0.67 27 27
ITGB3 -0.42 0.55 -10000 0 -1.2 86 86
PIGR -0.53 0.7 -10000 0 -1.4 126 126
IGHE 0.028 0.055 0.18 20 -10000 0 20
MAPKKK cascade -0.13 0.22 -10000 0 -0.65 27 27
BCL6 0.022 0.023 -10000 0 -0.4 1 1
OPRM1 -0.39 0.51 -10000 0 -1.2 76 76
RETNLB -0.38 0.51 -10000 0 -1.2 73 73
SELP -0.4 0.59 -10000 0 -1.3 82 82
AICDA -0.37 0.49 -10000 0 -1.2 74 74
Syndecan-1-mediated signaling events

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
TGFB1 0.024 0.009 -10000 0 -10000 0 0
CCL5 0.003 0.082 -10000 0 -0.4 13 13
SDCBP 0.024 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.076 0.14 0.27 2 -0.27 83 85
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 -0.067 0.14 0.21 6 -0.28 72 78
Syndecan-1/Syntenin -0.065 0.14 0.23 6 -0.35 37 43
MAPK3 -0.066 0.13 0.23 3 -0.35 34 37
HGF/MET -0.008 0.11 -10000 0 -0.3 42 42
TGFB1/TGF beta receptor Type II 0.024 0.009 -10000 0 -10000 0 0
BSG 0.024 0.006 -10000 0 -10000 0 0
keratinocyte migration -0.066 0.14 0.21 6 -0.27 72 78
Syndecan-1/RANTES -0.075 0.15 0.23 6 -0.34 49 55
Syndecan-1/CD147 -0.058 0.15 0.23 4 -0.37 34 38
Syndecan-1/Syntenin/PIP2 -0.063 0.14 0.22 6 -0.34 37 43
LAMA5 0.023 0.023 -10000 0 -0.4 1 1
positive regulation of cell-cell adhesion -0.063 0.13 0.2 5 -0.33 37 42
MMP7 -0.086 0.18 -10000 0 -0.4 85 85
HGF -0.004 0.099 -10000 0 -0.4 20 20
Syndecan-1/CASK -0.082 0.13 -10000 0 -0.26 89 89
Syndecan-1/HGF/MET -0.082 0.17 0.22 6 -0.37 60 66
regulation of cell adhesion -0.07 0.12 0.21 2 -0.36 30 32
HPSE 0.013 0.065 -10000 0 -0.4 8 8
positive regulation of cell migration -0.076 0.14 0.27 2 -0.27 83 85
SDC1 -0.075 0.14 -10000 0 -0.24 129 129
Syndecan-1/Collagen -0.076 0.14 0.27 2 -0.27 83 85
PPIB 0.024 0.005 -10000 0 -10000 0 0
MET -0.006 0.11 -10000 0 -0.4 24 24
PRKACA 0.024 0.006 -10000 0 -10000 0 0
MMP9 -0.022 0.12 -10000 0 -0.26 60 60
MAPK1 -0.068 0.13 0.18 3 -0.36 33 36
homophilic cell adhesion -0.075 0.14 0.22 7 -0.27 85 92
MMP1 -0.035 0.13 -10000 0 -0.4 40 40
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.032 0.12 -10000 0 -0.24 80 80
cell-cell adhesion 0.068 0.1 0.23 84 -10000 0 84
Ephrin B/EPHB2/RasGAP -0.002 0.14 -10000 0 -0.25 72 72
ITSN1 0.025 0.006 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
SHC1 0.021 0.01 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.002 0.081 -10000 0 -0.25 30 30
Ephrin B1/EPHB1 0.003 0.076 -10000 0 -0.24 29 29
HRAS/GDP -0.038 0.13 -10000 0 -0.27 56 56
Ephrin B/EPHB1/GRB7 -0.004 0.13 -10000 0 -0.24 73 73
Endophilin/SYNJ1 -0.054 0.1 0.17 7 -0.24 72 79
KRAS 0.025 0.004 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.003 0.13 -10000 0 -0.25 71 71
endothelial cell migration 0.032 0.06 -10000 0 -0.2 19 19
GRB2 0.024 0.006 -10000 0 -10000 0 0
GRB7 0.019 0.04 -10000 0 -0.4 3 3
PAK1 -0.054 0.12 0.21 11 -0.25 73 84
HRAS 0.024 0.005 -10000 0 -10000 0 0
RRAS -0.054 0.11 0.18 5 -0.24 72 77
DNM1 0.013 0.058 -10000 0 -0.4 6 6
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.048 0.1 0.21 10 -0.23 69 79
lamellipodium assembly -0.068 0.1 -10000 0 -0.23 84 84
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.023 0.1 -10000 0 -0.27 35 35
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
EPHB2 -0.014 0.12 -10000 0 -0.4 30 30
EPHB3 -0.019 0.12 -10000 0 -0.4 29 29
EPHB1 -0.018 0.11 -10000 0 -0.4 26 26
EPHB4 0.023 0.023 -10000 0 -0.4 1 1
mol:GDP -0.048 0.12 0.16 1 -0.29 56 57
Ephrin B/EPHB2 -0.011 0.13 -10000 0 -0.25 72 72
Ephrin B/EPHB3 -0.012 0.13 -10000 0 -0.24 73 73
JNK cascade -0.036 0.1 0.34 11 -0.23 51 62
Ephrin B/EPHB1 -0.01 0.12 -10000 0 -0.24 71 71
RAP1/GDP -0.036 0.12 0.22 1 -0.27 50 51
EFNB2 0.011 0.071 -10000 0 -0.4 10 10
EFNB3 -0.038 0.14 -10000 0 -0.4 48 48
EFNB1 0.022 0.039 -10000 0 -0.4 3 3
Ephrin B2/EPHB1-2 -0.005 0.11 -10000 0 -0.25 56 56
RAP1B 0.025 0.002 -10000 0 -10000 0 0
RAP1A 0.025 0.001 -10000 0 -10000 0 0
CDC42/GTP -0.038 0.15 -10000 0 -0.3 71 71
Rap1/GTP -0.046 0.12 -10000 0 -0.27 55 55
axon guidance -0.033 0.12 -10000 0 -0.24 80 80
MAPK3 -0.028 0.092 0.19 1 -0.33 16 17
MAPK1 -0.028 0.092 -10000 0 -0.34 15 15
Rac1/GDP -0.046 0.12 -10000 0 -0.28 50 50
actin cytoskeleton reorganization -0.056 0.1 -10000 0 -0.25 49 49
CDC42/GDP -0.043 0.12 0.2 2 -0.28 50 52
PI3K 0.036 0.062 -10000 0 -0.21 19 19
EFNA5 -0.039 0.15 -10000 0 -0.4 52 52
Ephrin B2/EPHB4 0.022 0.048 -10000 0 -0.24 11 11
Ephrin B/EPHB2/Intersectin/N-WASP -0.036 0.13 -10000 0 -0.26 73 73
CDC42 0.025 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.05 0.12 -10000 0 -0.33 30 30
PTK2 0.04 0.14 0.56 25 -10000 0 25
MAP4K4 -0.036 0.11 0.34 11 -0.23 51 62
SRC 0.022 0.032 -10000 0 -0.4 2 2
KALRN 0.016 0.059 -10000 0 -0.4 7 7
Intersectin/N-WASP 0.036 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis -0.046 0.13 0.33 10 -0.36 25 35
MAP2K1 -0.026 0.097 -10000 0 -0.26 33 33
WASL 0.025 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.014 0.11 -10000 0 -0.25 52 52
cell migration -0.022 0.13 0.24 11 -0.37 20 31
NRAS 0.02 0.05 -10000 0 -0.4 5 5
SYNJ1 -0.055 0.11 0.17 7 -0.24 72 79
PXN 0.025 0.003 -10000 0 -10000 0 0
TF -0.062 0.11 0.17 3 -0.24 78 81
HRAS/GTP -0.03 0.13 -10000 0 -0.24 85 85
Ephrin B1/EPHB1-2 0.002 0.11 -10000 0 -0.24 52 52
cell adhesion mediated by integrin 0.042 0.095 0.24 50 -0.24 3 53
RAC1 0.025 0.005 -10000 0 -10000 0 0
mol:GTP -0.03 0.14 -10000 0 -0.25 85 85
RAC1-CDC42/GTP -0.068 0.12 -10000 0 -0.29 57 57
RASA1 0.025 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.036 0.12 -10000 0 -0.31 30 30
ruffle organization -0.057 0.12 0.34 7 -0.39 22 29
NCK1 0.025 0.005 -10000 0 -10000 0 0
receptor internalization -0.058 0.11 0.17 4 -0.24 71 75
Ephrin B/EPHB2/KALRN -0.006 0.14 -10000 0 -0.26 74 74
ROCK1 0 0.083 0.18 22 -0.23 30 52
RAS family/GDP -0.068 0.095 -10000 0 -0.26 49 49
Rac1/GTP -0.051 0.12 -10000 0 -0.24 84 84
Ephrin B/EPHB1/Src/Paxillin -0.035 0.12 -10000 0 -0.25 71 71
Ephrin A reverse signaling

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
MAPKKK cascade -0.013 0.095 -10000 0 -0.24 52 52
EFNA5 -0.039 0.15 -10000 0 -0.4 52 52
FYN -0.033 0.078 0.18 1 -0.22 52 53
neuron projection morphogenesis -0.013 0.095 -10000 0 -0.24 52 52
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.013 0.095 -10000 0 -0.24 52 52
EPHA5 0.017 0.017 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.27 0.45 -10000 0 -1.1 54 54
IL23A -0.28 0.46 -10000 0 -1.2 54 54
NF kappa B1 p50/RelA/I kappa B alpha -0.25 0.46 -10000 0 -1.1 64 64
positive regulation of T cell mediated cytotoxicity -0.3 0.5 -10000 0 -1.2 64 64
ITGA3 -0.27 0.44 -10000 0 -1.1 54 54
IL17F -0.18 0.29 -10000 0 -0.7 55 55
IL12B -0.008 0.044 -10000 0 -10000 0 0
STAT1 (dimer) -0.28 0.48 -10000 0 -1.1 63 63
CD4 -0.27 0.44 -10000 0 -1.1 56 56
IL23 -0.27 0.45 -10000 0 -1.1 52 52
IL23R -0.026 0.097 -10000 0 -1.2 1 1
IL1B -0.28 0.47 -10000 0 -1.2 57 57
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.24 0.43 -10000 0 -1.1 49 49
TYK2 -0.001 0.034 -10000 0 -10000 0 0
STAT4 0.014 0.064 -10000 0 -0.4 8 8
STAT3 0.024 0.006 -10000 0 -10000 0 0
IL18RAP -0.004 0.099 -10000 0 -0.4 20 20
IL12RB1 -0.017 0.086 -10000 0 -0.44 12 12
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.008 0.069 -10000 0 -0.32 10 10
IL23R/JAK2 -0.033 0.12 -10000 0 -1.1 1 1
positive regulation of chronic inflammatory response -0.3 0.5 -10000 0 -1.2 64 64
natural killer cell activation 0.004 0.007 -10000 0 -10000 0 0
JAK2 -0.012 0.078 -10000 0 -0.43 9 9
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
NFKB1 0.024 0.005 -10000 0 -10000 0 0
RELA 0.024 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.25 0.42 -10000 0 -1.1 52 52
ALOX12B -0.28 0.45 -10000 0 -1.1 60 60
CXCL1 -0.34 0.53 -10000 0 -1.2 85 85
T cell proliferation -0.3 0.5 -10000 0 -1.2 64 64
NFKBIA 0.024 0.005 -10000 0 -10000 0 0
IL17A -0.14 0.24 -10000 0 -0.54 54 54
PI3K -0.27 0.46 -10000 0 -1.1 60 60
IFNG -0.013 0.036 0.12 1 -0.12 18 19
STAT3 (dimer) -0.25 0.44 -10000 0 -1.1 59 59
IL18R1 0.003 0.089 -10000 0 -0.4 16 16
IL23/IL23R/JAK2/TYK2/SOCS3 -0.16 0.28 -10000 0 -0.75 37 37
IL18/IL18R 0.009 0.11 -10000 0 -0.28 41 41
macrophage activation -0.014 0.019 -10000 0 -0.044 46 46
TNF -0.3 0.5 -10000 0 -1.2 62 62
STAT3/STAT4 -0.26 0.47 -10000 0 -1.1 63 63
STAT4 (dimer) -0.28 0.49 -10000 0 -1.2 63 63
IL18 0.007 0.08 -10000 0 -0.4 13 13
IL19 -0.31 0.52 -10000 0 -1.2 80 80
STAT5A (dimer) -0.28 0.48 -10000 0 -1.1 63 63
STAT1 0.025 0.009 -10000 0 -10000 0 0
SOCS3 0.012 0.071 -10000 0 -0.4 10 10
CXCL9 -0.33 0.52 -10000 0 -1.2 77 77
MPO -0.29 0.47 -10000 0 -1.1 63 63
positive regulation of humoral immune response -0.3 0.5 -10000 0 -1.2 64 64
IL23/IL23R/JAK2/TYK2 -0.31 0.55 -10000 0 -1.3 60 60
IL6 -0.28 0.45 -10000 0 -1.1 60 60
STAT5A 0.024 0.006 -10000 0 -10000 0 0
IL2 0.011 0.028 -10000 0 -0.14 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.004 0.007 -10000 0 -10000 0 0
CD3E -0.29 0.48 -10000 0 -1.2 62 62
keratinocyte proliferation -0.3 0.5 -10000 0 -1.2 64 64
NOS2 -0.29 0.46 -10000 0 -1.1 63 63
Endothelins

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
AKT1 0.01 0.13 0.25 34 -0.29 35 69
PTK2B 0.022 0.024 -10000 0 -0.41 1 1
mol:Ca2+ -0.044 0.24 -10000 0 -0.72 30 30
EDN1 0.019 0.11 0.21 34 -0.34 17 51
EDN3 -0.11 0.18 -10000 0 -0.4 97 97
EDN2 -0.012 0.11 -10000 0 -0.4 25 25
HRAS/GDP -0.039 0.17 0.23 3 -0.41 47 50
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.012 0.15 0.16 22 -0.39 33 55
ADCY4 0.003 0.11 0.21 7 -0.31 20 27
ADCY5 -0.022 0.12 0.22 5 -0.25 58 63
ADCY6 0.004 0.11 0.21 7 -0.31 21 28
ADCY7 0.002 0.1 0.21 6 -0.34 17 23
ADCY1 -0.014 0.12 0.21 6 -0.3 31 37
ADCY2 -0.012 0.12 0.19 5 -0.3 34 39
ADCY3 0.004 0.1 0.21 6 -0.32 17 23
ADCY8 -0.003 0.097 0.19 3 -0.32 15 18
ADCY9 -0.003 0.12 0.22 5 -0.33 24 29
arachidonic acid secretion -0.05 0.18 0.25 2 -0.44 45 47
ETB receptor/Endothelin-1/Gq/GTP -0.008 0.12 -10000 0 -0.37 24 24
GNAO1 0.014 0.053 -10000 0 -0.4 5 5
HRAS 0.024 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.052 0.14 0.34 33 -0.26 35 68
ETA receptor/Endothelin-1/Gs/GTP 0.044 0.14 0.32 31 -0.26 36 67
mol:GTP 0 0.003 -10000 0 -10000 0 0
COL3A1 -0.004 0.17 0.25 33 -0.51 25 58
EDNRB 0.008 0.075 -10000 0 -0.41 10 10
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 0.007 0.13 0.25 32 -0.41 14 46
CYSLTR1 0 0.16 0.25 34 -0.44 26 60
SLC9A1 0.013 0.086 0.18 34 -0.23 20 54
mol:GDP -0.053 0.18 0.22 4 -0.42 54 58
SLC9A3 -0.044 0.24 -10000 0 -0.66 38 38
RAF1 -0.049 0.17 0.24 3 -0.43 42 45
JUN -0.034 0.21 -10000 0 -0.71 20 20
JAK2 0.003 0.13 0.25 31 -0.3 41 72
mol:IP3 -0.017 0.15 -10000 0 -0.41 33 33
ETA receptor/Endothelin-1 0.043 0.17 0.4 34 -0.34 36 70
PLCB1 0.007 0.086 -10000 0 -0.4 15 15
PLCB2 0.018 0.047 -10000 0 -0.4 4 4
ETA receptor/Endothelin-3 -0.064 0.15 0.17 11 -0.28 105 116
FOS -0.04 0.17 0.27 1 -0.51 26 27
Gai/GDP -0.069 0.26 -10000 0 -0.7 48 48
CRK 0.024 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.015 0.16 0.21 24 -0.45 33 57
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
PRKCB1 -0.02 0.15 -10000 0 -0.41 34 34
GNAQ 0.022 0.025 -10000 0 -0.4 1 1
GNAZ 0.013 0.067 -10000 0 -0.4 9 9
GNAL 0.016 0.052 -10000 0 -0.4 5 5
Gs family/GDP -0.043 0.17 0.22 3 -0.4 50 53
ETA receptor/Endothelin-1/Gq/GTP -0.003 0.15 0.18 26 -0.43 27 53
MAPK14 -0.017 0.12 0.21 2 -0.34 28 30
TRPC6 -0.048 0.25 -10000 0 -0.77 30 30
GNAI2 0.024 0.006 -10000 0 -10000 0 0
GNAI3 0.025 0.002 -10000 0 -10000 0 0
GNAI1 0.012 0.071 -10000 0 -0.4 10 10
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.017 0.12 -10000 0 -0.35 32 32
ETB receptor/Endothelin-2 -0.004 0.097 -10000 0 -0.29 34 34
ETB receptor/Endothelin-3 -0.079 0.14 -10000 0 -0.3 100 100
ETB receptor/Endothelin-1 0.023 0.1 -10000 0 -0.29 24 24
MAPK3 -0.046 0.17 0.28 1 -0.5 32 33
MAPK1 -0.047 0.17 0.28 1 -0.5 32 33
Rac1/GDP -0.041 0.18 0.23 3 -0.41 47 50
cAMP biosynthetic process -0.027 0.14 0.26 7 -0.36 32 39
MAPK8 -0.044 0.25 -10000 0 -0.64 43 43
SRC 0.022 0.032 -10000 0 -0.4 2 2
ETB receptor/Endothelin-1/Gi/GTP -0.004 0.087 0.16 1 -0.28 17 18
p130Cas/CRK/Src/PYK2 -0.066 0.2 0.26 3 -0.51 45 48
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.04 0.17 0.23 3 -0.42 45 48
COL1A2 0.001 0.17 0.25 1 -0.56 19 20
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.009 0.11 0.17 26 -0.28 34 60
mol:DAG -0.017 0.15 -10000 0 -0.41 33 33
MAP2K2 -0.047 0.16 0.25 2 -0.45 36 38
MAP2K1 -0.046 0.16 0.25 2 -0.45 35 37
EDNRA 0.026 0.098 0.21 34 -0.34 10 44
positive regulation of muscle contraction 0.012 0.11 0.21 39 -0.33 14 53
Gq family/GDP -0.032 0.17 0.24 1 -0.41 43 44
HRAS/GTP -0.053 0.18 0.21 3 -0.42 49 52
PRKCH -0.023 0.15 -10000 0 -0.42 33 33
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCA -0.023 0.15 0.21 2 -0.41 37 39
PRKCB -0.03 0.16 -10000 0 -0.41 40 40
PRKCE -0.023 0.15 0.21 2 -0.4 35 37
PRKCD -0.022 0.15 0.22 1 -0.4 34 35
PRKCG -0.047 0.16 0.22 3 -0.41 40 43
regulation of vascular smooth muscle contraction -0.05 0.19 -10000 0 -0.6 25 25
PRKCQ -0.044 0.17 0.25 6 -0.42 45 51
PLA2G4A -0.056 0.19 0.25 2 -0.48 45 47
GNA14 0.014 0.064 -10000 0 -0.4 8 8
GNA15 0.015 0.057 -10000 0 -0.41 6 6
GNA12 0.024 0.005 -10000 0 -10000 0 0
GNA11 0.015 0.056 -10000 0 -0.4 6 6
Rac1/GTP 0.053 0.14 0.34 33 -0.27 34 67
MMP1 -0.089 0.24 0.24 3 -0.76 40 43
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.007 0.21 0.28 41 -0.45 45 86
FYN -0.053 0.25 0.31 8 -0.6 46 54
LAT/GRAP2/SLP76 -0.039 0.21 0.23 5 -0.5 48 53
IKBKB 0.023 0.007 -10000 0 -10000 0 0
AKT1 -0.036 0.17 0.25 9 -0.4 52 61
B2M 0.019 0.042 -10000 0 -0.41 3 3
IKBKG -0.009 0.052 0.14 3 -0.13 34 37
MAP3K8 0.02 0.045 -10000 0 -0.4 4 4
mol:Ca2+ -0.022 0.024 0.089 3 -0.057 78 81
integrin-mediated signaling pathway 0.027 0.024 -10000 0 -0.24 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.063 0.24 0.29 8 -0.57 54 62
TRPV6 -0.071 0.23 1.2 6 -0.4 74 80
CD28 -0.002 0.1 -10000 0 -0.41 21 21
SHC1 -0.038 0.26 0.29 41 -0.57 48 89
receptor internalization -0.066 0.26 0.22 1 -0.62 49 50
PRF1 -0.079 0.31 0.36 1 -0.91 37 38
KRAS 0.025 0.004 -10000 0 -10000 0 0
GRB2 0.024 0.006 -10000 0 -10000 0 0
COT/AKT1 -0.018 0.14 0.24 8 -0.31 50 58
LAT -0.062 0.24 0.23 5 -0.59 48 53
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.013 0.12 -10000 0 -0.41 27 27
CD3E -0.012 0.11 -10000 0 -0.41 26 26
CD3G -0.003 0.096 -10000 0 -0.41 18 18
RASGRP2 0 0.034 0.081 1 -0.18 10 11
RASGRP1 -0.042 0.18 0.26 8 -0.4 52 60
HLA-A 0.013 0.065 -10000 0 -0.41 8 8
RASSF5 0.019 0.033 -10000 0 -0.4 2 2
RAP1A/GTP/RAPL 0.027 0.024 -10000 0 -0.24 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.072 0.14 49 -0.12 35 84
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.03 0.078 -10000 0 -0.2 50 50
PRKCA -0.023 0.1 0.15 9 -0.25 43 52
GRAP2 0.002 0.089 -10000 0 -0.4 16 16
mol:IP3 -0.017 0.17 0.19 59 -0.37 46 105
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.064 0.24 -10000 0 -0.66 37 37
ORAI1 0.033 0.16 0.4 5 -0.98 6 11
CSK -0.062 0.25 0.24 4 -0.59 49 53
B7 family/CD28 -0.046 0.26 0.22 1 -0.56 54 55
CHUK 0.024 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.077 0.29 0.23 1 -0.67 51 52
PTPN6 -0.064 0.25 0.22 5 -0.58 50 55
VAV1 -0.066 0.25 0.23 4 -0.6 49 53
Monovalent TCR/CD3 -0.04 0.17 -10000 0 -0.44 43 43
CBL 0.025 0.004 -10000 0 -10000 0 0
LCK -0.059 0.26 0.32 7 -0.64 46 53
PAG1 -0.061 0.25 0.2 12 -0.58 50 62
RAP1A 0.025 0.001 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.073 0.28 0.27 2 -0.66 50 52
CD80 0.006 0.084 -10000 0 -0.41 14 14
CD86 0.01 0.075 -10000 0 -0.41 11 11
PDK1/CARD11/BCL10/MALT1 -0.029 0.097 -10000 0 -0.24 50 50
HRAS 0.024 0.005 -10000 0 -10000 0 0
GO:0035030 -0.057 0.2 0.16 3 -0.46 54 57
CD8A -0.012 0.11 -10000 0 -0.41 25 25
CD8B -0.015 0.11 -10000 0 -0.41 23 23
PTPRC 0.001 0.087 -10000 0 -0.41 15 15
PDK1/PKC theta -0.055 0.21 0.3 7 -0.48 53 60
CSK/PAG1 -0.058 0.24 0.22 14 -0.58 47 61
SOS1 0.025 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.023 0.06 -10000 0 -0.3 11 11
GRAP2/SLP76 -0.048 0.25 0.25 3 -0.58 50 53
STIM1 0.016 0.049 -10000 0 -10000 0 0
RAS family/GTP 0.012 0.087 0.16 39 -0.17 33 72
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.073 0.28 0.22 1 -0.68 49 50
mol:DAG -0.04 0.13 0.11 8 -0.32 50 58
RAP1A/GDP 0.011 0.034 0.072 40 -0.059 21 61
PLCG1 0.025 0.005 -10000 0 -10000 0 0
CD247 0.003 0.082 -10000 0 -0.41 13 13
cytotoxic T cell degranulation -0.073 0.29 0.35 2 -0.86 37 39
RAP1A/GTP 0 0.013 -10000 0 -0.064 11 11
mol:PI-3-4-5-P3 -0.047 0.2 0.27 9 -0.46 54 63
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.022 0.21 0.21 53 -0.48 46 99
NRAS 0.02 0.05 -10000 0 -0.4 5 5
ZAP70 -0.004 0.1 -10000 0 -0.4 20 20
GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.048 0.2 -10000 0 -0.48 49 49
MALT1 0.023 0.011 -10000 0 -10000 0 0
TRAF6 0.025 0.005 -10000 0 -10000 0 0
CD8 heterodimer -0.018 0.13 -10000 0 -0.39 34 34
CARD11 -0.002 0.091 -10000 0 -0.4 16 16
PRKCB -0.024 0.11 0.14 9 -0.27 41 50
PRKCE -0.019 0.097 0.14 10 -0.24 41 51
PRKCQ -0.066 0.24 0.3 8 -0.54 56 64
LCP2 0.018 0.051 -10000 0 -0.4 5 5
BCL10 0.025 0.002 -10000 0 -10000 0 0
regulation of survival gene product expression -0.028 0.15 0.24 9 -0.34 51 60
IKK complex 0.005 0.057 0.16 16 -0.11 25 41
RAS family/GDP -0.003 0.013 -10000 0 -0.046 9 9
MAP3K14 -0.014 0.11 0.2 8 -0.24 47 55
PDPK1 -0.033 0.16 0.25 9 -0.38 51 60
TCR/CD3/MHC I/CD8/Fyn -0.098 0.31 -10000 0 -0.74 51 51
Noncanonical Wnt signaling 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
NFATC2 0.003 0.093 -10000 0 -0.4 18 18
GNB1/GNG2 -0.043 0.16 -10000 0 -0.28 86 86
mol:DAG -0.053 0.14 0.2 8 -0.41 32 40
PLCG1 -0.055 0.15 0.21 8 -0.42 32 40
YES1 -0.064 0.15 -10000 0 -0.29 84 84
FZD3 0.023 0.008 -10000 0 -10000 0 0
FZD6 0.02 0.039 -10000 0 -0.4 3 3
G protein -0.037 0.16 0.24 2 -0.43 31 33
MAP3K7 -0.055 0.12 0.18 9 -0.36 30 39
mol:Ca2+ -0.052 0.14 0.2 8 -0.39 32 40
mol:IP3 -0.053 0.14 0.2 8 -0.41 32 40
NLK -0.017 0.15 -10000 0 -0.77 13 13
GNB1 0.025 0.005 -10000 0 -10000 0 0
CAMK2A -0.055 0.13 0.19 9 -0.39 30 39
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.062 0.16 -10000 0 -0.3 85 85
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
GNAS -0.063 0.15 -10000 0 -0.29 84 84
GO:0007205 -0.056 0.14 0.2 8 -0.4 31 39
WNT6 -0.027 0.11 -10000 0 -0.4 26 26
WNT4 -0.014 0.12 -10000 0 -0.4 28 28
NFAT1/CK1 alpha -0.05 0.16 -10000 0 -0.44 33 33
GNG2 0.018 0.047 -10000 0 -0.4 4 4
WNT5A 0.008 0.08 -10000 0 -0.4 13 13
WNT11 -0.054 0.15 -10000 0 -0.4 55 55
CDC42 -0.063 0.14 0.16 1 -0.43 32 33
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.071 -10000 0 -0.38 11 11
CDKN2C 0.014 0.068 -10000 0 -0.36 10 10
CDKN2A -0.021 0.11 -10000 0 -0.37 28 28
CCND2 0.015 0.06 0.17 39 -0.12 1 40
RB1 -0.019 0.07 0.36 1 -0.2 40 41
CDK4 0.02 0.067 0.2 40 -10000 0 40
CDK6 0.017 0.071 0.2 38 -0.14 8 46
G1/S progression 0.019 0.07 0.2 41 -0.36 1 42
Ephrin B reverse signaling

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
EFNB2 0.011 0.071 -10000 0 -0.4 10 10
EPHB2 -0.014 0.12 -10000 0 -0.4 30 30
EFNB1 0 0.05 -10000 0 -0.31 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.008 0.11 -10000 0 -0.24 58 58
Ephrin B2/EPHB1-2 -0.004 0.11 -10000 0 -0.25 56 56
neuron projection morphogenesis -0.007 0.1 -10000 0 -0.22 58 58
Ephrin B1/EPHB1-2/Tiam1 -0.001 0.12 -10000 0 -0.25 60 60
DNM1 0.014 0.057 -10000 0 -0.4 6 6
cell-cell signaling 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.055 0.17 0.24 1 -0.54 38 39
YES1 -0.068 0.24 -10000 0 -0.74 40 40
Ephrin B1/EPHB1-2/NCK2 0.004 0.11 -10000 0 -0.24 56 56
PI3K -0.031 0.18 -10000 0 -0.53 39 39
mol:GDP -0.002 0.12 -10000 0 -0.24 60 60
ITGA2B -0.004 0.1 -10000 0 -0.4 21 21
endothelial cell proliferation 0.022 0.048 -10000 0 -0.24 11 11
FYN -0.067 0.24 -10000 0 -0.74 40 40
MAP3K7 -0.057 0.18 0.22 1 -0.56 39 40
FGR -0.065 0.24 -10000 0 -0.76 37 37
TIAM1 0.016 0.063 -10000 0 -0.4 8 8
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
RGS3 0.024 0.007 -10000 0 -10000 0 0
cell adhesion -0.062 0.18 -10000 0 -0.53 41 41
LYN -0.067 0.24 -10000 0 -0.75 39 39
Ephrin B1/EPHB1-2/Src Family Kinases -0.067 0.22 -10000 0 -0.69 40 40
Ephrin B1/EPHB1-2 -0.056 0.19 -10000 0 -0.63 35 35
SRC -0.066 0.24 -10000 0 -0.74 39 39
ITGB3 -0.008 0.096 -10000 0 -0.4 18 18
EPHB1 -0.018 0.11 -10000 0 -0.4 26 26
EPHB4 0.023 0.023 -10000 0 -0.4 1 1
RAC1 0.025 0.005 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.022 0.048 -10000 0 -0.24 11 11
alphaIIb/beta3 Integrin -0.011 0.1 -10000 0 -0.29 38 38
BLK -0.076 0.24 -10000 0 -0.75 39 39
HCK -0.067 0.24 -10000 0 -0.76 37 37
regulation of stress fiber formation -0.003 0.11 0.24 56 -10000 0 56
MAPK8 -0.049 0.16 0.22 1 -0.52 36 37
Ephrin B1/EPHB1-2/RGS3 0.004 0.11 -10000 0 -0.24 56 56
endothelial cell migration -0.049 0.16 0.24 4 -0.5 35 39
NCK2 0.025 0.003 -10000 0 -10000 0 0
PTPN13 -0.022 0.15 -10000 0 -0.52 31 31
regulation of focal adhesion formation -0.003 0.11 0.24 56 -10000 0 56
chemotaxis -0.003 0.11 0.23 56 -10000 0 56
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.002 0.11 -10000 0 -0.23 58 58
angiogenesis -0.057 0.19 -10000 0 -0.61 37 37
LCK -0.067 0.24 -10000 0 -0.75 38 38
Wnt 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
Noncanonical Wnts/FZD -0.062 0.16 -9999 0 -0.3 85 85
FZD6 0.02 0.039 -9999 0 -0.4 3 3
WNT6 -0.027 0.11 -9999 0 -0.4 26 26
WNT4 -0.014 0.12 -9999 0 -0.4 28 28
FZD3 0.023 0.008 -9999 0 -10000 0 0
WNT5A 0.008 0.08 -9999 0 -0.4 13 13
WNT11 -0.054 0.15 -9999 0 -0.4 55 55
LPA receptor mediated events

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
GNB1/GNG2 0.024 0.081 -10000 0 -0.23 29 29
NF kappa B1 p50/RelA/I kappa B alpha -0.035 0.13 0.38 2 -0.31 17 19
AP1 -0.03 0.11 -10000 0 -0.21 91 91
mol:PIP3 -0.053 0.1 -10000 0 -0.21 95 95
AKT1 -0.004 0.079 0.26 1 -0.33 8 9
PTK2B -0.035 0.11 -10000 0 -0.31 33 33
RHOA -0.002 0.059 0.22 3 -0.3 8 11
PIK3CB 0.025 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.04 0.095 0.21 4 -0.25 22 26
MAGI3 0.024 0.023 -10000 0 -0.4 1 1
RELA 0.025 0.003 -10000 0 -10000 0 0
apoptosis -0.053 0.12 -10000 0 -0.24 90 90
HRAS/GDP 0.018 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.034 0.1 0.19 5 -0.31 30 35
NF kappa B1 p50/RelA -0.045 0.13 -10000 0 -0.25 83 83
endothelial cell migration -0.019 0.12 -10000 0 -0.42 26 26
ADCY4 -0.024 0.1 -10000 0 -0.32 29 29
ADCY5 -0.047 0.12 -10000 0 -0.36 32 32
ADCY6 -0.025 0.1 -10000 0 -0.32 28 28
ADCY7 -0.022 0.1 -10000 0 -0.32 27 27
ADCY1 -0.04 0.12 -10000 0 -0.36 36 36
ADCY2 -0.037 0.12 -10000 0 -0.37 31 31
ADCY3 -0.024 0.1 -10000 0 -0.32 28 28
ADCY8 -0.026 0.1 -10000 0 -0.32 26 26
ADCY9 -0.029 0.11 -10000 0 -0.33 32 32
GSK3B -0.033 0.11 0.2 5 -0.32 30 35
arachidonic acid secretion -0.031 0.11 -10000 0 -0.31 38 38
GNG2 0.018 0.047 -10000 0 -0.4 4 4
TRIP6 0.009 0.052 -10000 0 -0.33 8 8
GNAO1 -0.011 0.081 -10000 0 -0.26 29 29
HRAS 0.024 0.005 -10000 0 -10000 0 0
NFKBIA -0.058 0.12 0.4 1 -0.31 29 30
GAB1 0.024 0.023 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.01 0.17 -10000 0 -0.84 14 14
JUN 0.024 0.023 -10000 0 -0.4 1 1
LPA/LPA2/NHERF2 0.027 0.032 -10000 0 -0.26 2 2
TIAM1 -0.004 0.19 -10000 0 -0.97 14 14
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:IP3 -0.04 0.096 0.21 4 -0.25 24 28
PLCB3 0.013 0.037 0.18 9 -0.23 2 11
FOS 0.014 0.055 -10000 0 -0.4 5 5
positive regulation of mitosis -0.031 0.11 -10000 0 -0.31 38 38
LPA/LPA1-2-3 -0.024 0.12 -10000 0 -0.23 88 88
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
stress fiber formation -0.033 0.097 -10000 0 -0.32 19 19
GNAZ -0.012 0.082 -10000 0 -0.25 35 35
EGFR/PI3K-beta/Gab1 -0.048 0.11 -10000 0 -0.22 95 95
positive regulation of dendritic cell cytokine production -0.024 0.12 -10000 0 -0.23 88 88
LPA/LPA2/MAGI-3 0.028 0.029 -10000 0 -0.24 1 1
ARHGEF1 -0.001 0.068 0.18 9 -0.22 24 33
GNAI2 -0.006 0.072 -10000 0 -0.24 28 28
GNAI3 -0.007 0.074 -10000 0 -0.24 30 30
GNAI1 -0.014 0.083 -10000 0 -0.25 36 36
LPA/LPA3 -0.05 0.12 -10000 0 -0.26 82 82
LPA/LPA2 0.013 0.025 -10000 0 -0.1 12 12
LPA/LPA1 -0.006 0.088 -10000 0 -0.28 31 31
HB-EGF/EGFR -0.01 0.084 -10000 0 -0.24 40 40
HBEGF -0.021 0.085 -10000 0 -0.29 32 32
mol:DAG -0.04 0.096 0.21 4 -0.25 24 28
cAMP biosynthetic process -0.04 0.11 0.18 3 -0.3 39 42
NFKB1 0.025 0.004 -10000 0 -10000 0 0
SRC 0.022 0.032 -10000 0 -0.4 2 2
GNB1 0.025 0.005 -10000 0 -10000 0 0
LYN -0.052 0.12 0.25 3 -0.26 71 74
GNAQ -0.039 0.094 -10000 0 -0.22 70 70
LPAR2 0.024 0.005 -10000 0 -10000 0 0
LPAR3 -0.065 0.17 -10000 0 -0.4 70 70
LPAR1 -0.001 0.094 -10000 0 -0.31 26 26
IL8 -0.079 0.16 0.25 1 -0.42 48 49
PTK2 -0.045 0.1 0.18 2 -0.22 83 85
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
CASP3 -0.053 0.12 -10000 0 -0.24 90 90
EGFR 0.013 0.07 -10000 0 -0.4 10 10
PLCG1 -0.043 0.11 0.16 3 -0.24 76 79
PLD2 -0.048 0.1 0.18 3 -0.22 89 92
G12/G13 0.027 0.076 -10000 0 -0.23 25 25
PI3K-beta -0.01 0.082 -10000 0 -0.34 12 12
cell migration -0.012 0.071 -10000 0 -0.26 14 14
SLC9A3R2 0.022 0.032 -10000 0 -0.4 2 2
PXN -0.033 0.098 -10000 0 -0.33 19 19
HRAS/GTP -0.032 0.11 -10000 0 -0.32 38 38
RAC1 0.025 0.005 -10000 0 -10000 0 0
MMP9 -0.022 0.12 -10000 0 -0.26 60 60
PRKCE 0.024 0.023 -10000 0 -0.4 1 1
PRKCD -0.043 0.098 0.24 5 -0.3 13 18
Gi(beta/gamma) -0.02 0.099 -10000 0 -0.3 31 31
mol:LPA -0.006 0.032 -10000 0 -0.14 16 16
TRIP6/p130 Cas/FAK1/Paxillin -0.033 0.12 -10000 0 -0.35 17 17
MAPKKK cascade -0.031 0.11 -10000 0 -0.31 38 38
contractile ring contraction involved in cytokinesis -0.002 0.063 0.2 4 -0.28 10 14
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.043 0.099 -10000 0 -0.23 76 76
GNA15 -0.042 0.1 -10000 0 -0.24 71 71
GNA12 0.024 0.005 -10000 0 -10000 0 0
GNA13 0.024 0.006 -10000 0 -10000 0 0
MAPT -0.034 0.1 0.19 5 -0.32 30 35
GNA11 -0.041 0.099 -10000 0 -0.23 74 74
Rac1/GTP 0.01 0.18 -10000 0 -0.88 14 14
MMP2 -0.019 0.12 -10000 0 -0.42 26 26
HIF-1-alpha transcription factor network

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
PKM2 -0.099 0.31 0.52 1 -0.74 38 39
HDAC7 0.025 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.07 0.26 -10000 0 -0.67 24 24
SMAD4 0.025 0.005 -10000 0 -10000 0 0
ID2 -0.097 0.31 0.52 1 -0.73 41 42
AP1 0.025 0.049 -10000 0 -0.27 7 7
ABCG2 -0.11 0.32 0.52 1 -0.76 41 42
HIF1A -0.02 0.077 -10000 0 -0.21 11 11
TFF3 -0.15 0.36 0.52 1 -0.76 60 61
GATA2 -0.026 0.14 -10000 0 -0.4 41 41
AKT1 -0.022 0.083 -10000 0 -0.22 13 13
response to hypoxia -0.034 0.07 -10000 0 -0.18 28 28
MCL1 -0.11 0.29 -10000 0 -0.72 37 37
NDRG1 -0.096 0.31 0.52 1 -0.76 34 35
SERPINE1 -0.1 0.32 -10000 0 -0.72 45 45
FECH -0.099 0.31 0.52 1 -0.73 40 41
FURIN -0.1 0.31 0.52 1 -0.74 40 41
NCOA2 0.011 0.074 -10000 0 -0.4 11 11
EP300 -0.02 0.096 -10000 0 -0.27 24 24
HMOX1 -0.1 0.31 0.52 1 -0.75 38 39
BHLHE40 -0.1 0.31 -10000 0 -0.74 39 39
BHLHE41 -0.12 0.34 0.52 1 -0.78 45 46
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.023 0.095 -10000 0 -10000 0 0
ENG 0.024 0.097 0.24 14 -10000 0 14
JUN 0.022 0.026 -10000 0 -0.4 1 1
RORA -0.11 0.32 0.52 1 -0.75 40 41
ABCB1 -0.071 0.26 -10000 0 -1 21 21
TFRC -0.09 0.31 0.52 1 -0.74 34 35
CXCR4 -0.098 0.32 0.52 1 -0.74 40 41
TF -0.1 0.32 0.52 1 -0.72 44 45
CITED2 -0.098 0.32 0.52 1 -0.74 40 41
HIF1A/ARNT -0.1 0.37 -10000 0 -0.86 35 35
LDHA -0.012 0.13 -10000 0 -0.63 11 11
ETS1 -0.097 0.31 0.52 1 -0.74 38 39
PGK1 -0.099 0.32 0.52 1 -0.75 38 39
NOS2 -0.11 0.32 0.52 1 -0.74 46 47
ITGB2 -0.099 0.32 0.52 1 -0.76 38 39
ALDOA -0.096 0.31 0.52 1 -0.73 39 40
Cbp/p300/CITED2 -0.098 0.33 -10000 0 -0.81 33 33
FOS 0.012 0.056 -10000 0 -0.41 5 5
HK2 -0.097 0.31 0.52 1 -0.73 40 41
SP1 0.022 0.03 -10000 0 -0.14 3 3
GCK -0.075 0.23 -10000 0 -1.1 10 10
HK1 -0.098 0.31 0.52 1 -0.74 38 39
NPM1 -0.098 0.31 0.52 1 -0.74 39 40
EGLN1 -0.11 0.29 0.52 1 -0.71 40 41
CREB1 0.029 0.004 -10000 0 -10000 0 0
PGM1 -0.097 0.31 0.52 1 -0.73 40 41
SMAD3 0.025 0.006 -10000 0 -10000 0 0
EDN1 -0.075 0.25 -10000 0 -0.96 20 20
IGFBP1 -0.1 0.31 0.52 1 -0.72 42 43
VEGFA -0.05 0.23 -10000 0 -0.6 21 21
HIF1A/JAB1 0.005 0.059 -10000 0 -0.16 1 1
CP -0.13 0.34 0.52 1 -0.75 51 52
CXCL12 -0.11 0.32 0.52 1 -0.75 41 42
COPS5 0.024 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4 0.036 0.01 -10000 0 -10000 0 0
BNIP3 -0.1 0.31 0.52 1 -0.74 39 40
EGLN3 -0.11 0.32 -10000 0 -0.77 41 41
CA9 -0.13 0.34 0.52 1 -0.75 52 53
TERT -0.12 0.32 0.52 1 -0.76 43 44
ENO1 -0.096 0.31 0.52 1 -0.74 39 40
PFKL -0.095 0.31 0.52 1 -0.74 38 39
NCOA1 0.025 0.005 -10000 0 -10000 0 0
ADM -0.1 0.32 0.52 1 -0.74 41 42
ARNT -0.011 0.061 -10000 0 -10000 0 0
HNF4A -0.066 0.16 -10000 0 -0.39 65 65
ADFP -0.12 0.3 0.35 3 -0.7 46 49
SLC2A1 -0.053 0.24 -10000 0 -0.61 21 21
LEP -0.099 0.31 -10000 0 -0.74 37 37
HIF1A/ARNT/Cbp/p300 -0.079 0.27 -10000 0 -0.68 26 26
EPO -0.045 0.22 -10000 0 -0.68 11 11
CREBBP -0.019 0.093 -10000 0 -0.27 20 20
HIF1A/ARNT/Cbp/p300/HDAC7 -0.065 0.27 -10000 0 -0.69 21 21
PFKFB3 -0.1 0.32 0.52 1 -0.75 40 41
NT5E -0.12 0.34 0.52 1 -0.79 46 47
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.13 0.22 -10000 0 -0.69 16 16
PCK1 -0.27 0.43 -10000 0 -1.1 68 68
HNF4A -0.24 0.37 -10000 0 -0.85 81 81
KCNJ11 -0.14 0.25 -10000 0 -0.76 24 24
AKT1 -0.049 0.13 -10000 0 -0.39 6 6
response to starvation -0.005 0.02 -10000 0 -10000 0 0
DLK1 -0.14 0.23 -10000 0 -0.64 26 26
NKX2-1 -0.011 0.15 0.42 1 -10000 0 1
ACADM -0.14 0.24 -10000 0 -0.75 23 23
TAT -0.13 0.18 -10000 0 -0.59 21 21
CEBPB 0.025 0.006 -10000 0 -10000 0 0
CEBPA 0.001 0.098 -10000 0 -0.4 20 20
TTR -0.24 0.29 -10000 0 -0.78 57 57
PKLR -0.1 0.24 -10000 0 -0.77 13 13
APOA1 -0.24 0.39 -10000 0 -1 48 48
CPT1C -0.14 0.24 -10000 0 -0.8 21 21
ALAS1 -0.064 0.14 -10000 0 -0.57 3 3
TFRC -0.15 0.24 -10000 0 -0.83 16 16
FOXF1 0.017 0.037 -10000 0 -0.4 2 2
NF1 0.027 0.008 -10000 0 -10000 0 0
HNF1A (dimer) -0.074 0.17 -10000 0 -0.36 92 92
CPT1A -0.13 0.23 -10000 0 -0.76 15 15
HMGCS1 -0.13 0.22 -10000 0 -0.69 14 14
NR3C1 0.017 0.061 -10000 0 -0.4 7 7
CPT1B -0.14 0.24 -10000 0 -0.79 19 19
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.008 0.055 -10000 0 -0.19 22 22
GCK -0.14 0.24 -10000 0 -0.84 17 17
CREB1 -0.01 0.074 -10000 0 -0.18 52 52
IGFBP1 -0.064 0.13 -10000 0 -0.63 2 2
PDX1 -0.21 0.37 -10000 0 -1 50 50
UCP2 -0.14 0.24 -10000 0 -0.82 16 16
ALDOB -0.13 0.23 -10000 0 -0.8 10 10
AFP -0.12 0.15 -10000 0 -0.37 56 56
BDH1 -0.12 0.23 -10000 0 -0.77 15 15
HADH -0.13 0.23 -10000 0 -0.68 19 19
F2 -0.2 0.31 -10000 0 -0.85 30 30
HNF1A -0.074 0.17 -10000 0 -0.36 92 92
G6PC -0.1 0.16 -10000 0 -0.55 19 19
SLC2A2 -0.15 0.24 -10000 0 -0.67 40 40
INS -0.014 0.016 -10000 0 -10000 0 0
FOXA1 -0.11 0.18 -10000 0 -0.38 108 108
FOXA3 -0.093 0.18 -10000 0 -0.36 91 91
FOXA2 -0.15 0.27 -10000 0 -0.71 29 29
ABCC8 -0.14 0.24 -10000 0 -0.81 16 16
ALB -0.16 0.24 -10000 0 -0.66 48 48
IGF1 pathway

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
NCK2 0.025 0.003 -10000 0 -10000 0 0
PTK2 0.023 0.007 -10000 0 -10000 0 0
CRKL -0.028 0.097 0.16 1 -0.25 51 52
GRB2/SOS1/SHC 0.039 0.022 -10000 0 -10000 0 0
HRAS 0.024 0.005 -10000 0 -10000 0 0
IRS1/Crk -0.02 0.1 -10000 0 -0.25 50 50
IGF-1R heterotetramer/IGF1/PTP1B 0.004 0.11 -10000 0 -0.27 48 48
AKT1 -0.035 0.094 0.17 12 -0.32 19 31
BAD -0.035 0.088 0.16 12 -0.32 17 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.026 0.096 0.16 1 -0.26 48 49
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.013 0.1 -10000 0 -0.25 52 52
RAF1 -0.024 0.1 -10000 0 -0.38 15 15
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.012 0.11 -10000 0 -0.24 48 48
YWHAZ 0.023 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.014 0.11 -10000 0 -0.26 58 58
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
RPS6KB1 -0.037 0.092 0.17 10 -0.31 21 31
GNB2L1 0.025 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.015 0.092 0.25 2 -0.3 11 13
PXN 0.025 0.003 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
HRAS/GTP -0.007 0.084 -10000 0 -0.22 42 42
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.024 0.093 -10000 0 -0.22 40 40
IGF-1R heterotetramer -0.014 0.12 -10000 0 -0.44 25 25
IGF-1R heterotetramer/IGF1/IRS/Nck 0 0.11 -10000 0 -0.24 57 57
Crk/p130 Cas/Paxillin 0.007 0.1 0.21 1 -0.23 50 51
IGF1R -0.014 0.12 -10000 0 -0.44 25 25
IGF1 -0.029 0.13 -10000 0 -0.43 33 33
IRS2/Crk -0.026 0.1 -10000 0 -0.25 55 55
PI3K 0.006 0.12 -10000 0 -0.26 50 50
apoptosis 0.03 0.081 0.29 16 -0.23 3 19
HRAS/GDP 0.018 0.004 -10000 0 -10000 0 0
PRKCD -0.032 0.12 -10000 0 -0.32 47 47
RAF1/14-3-3 E -0.004 0.099 -10000 0 -0.35 12 12
BAD/14-3-3 -0.031 0.086 0.24 4 -0.31 16 20
PRKCZ -0.036 0.095 0.17 12 -0.32 20 32
Crk/p130 Cas/Paxillin/FAK1 -0.008 0.089 -10000 0 -0.31 15 15
PTPN1 0.024 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.031 0.13 -10000 0 -0.33 49 49
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.01 0.11 -10000 0 -0.25 45 45
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.025 0.004 -10000 0 -10000 0 0
IRS1/NCK2 -0.016 0.1 -10000 0 -0.25 51 51
GRB10 0.015 0.063 -10000 0 -0.4 8 8
PTPN11 -0.029 0.098 0.16 1 -0.25 52 53
IRS1 -0.029 0.1 0.12 5 -0.27 52 57
IRS2 -0.036 0.1 -10000 0 -0.26 56 56
IGF-1R heterotetramer/IGF1 -0.025 0.14 -10000 0 -0.34 51 51
GRB2 0.024 0.006 -10000 0 -10000 0 0
PDPK1 -0.022 0.1 0.18 11 -0.25 46 57
YWHAE 0.024 0.006 -10000 0 -10000 0 0
PRKD1 -0.041 0.13 -10000 0 -0.33 50 50
SHC1 0.021 0.01 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.001 0.058 -10000 0 -0.33 8 8
Crk/p130 Cas/Paxillin -0.041 0.097 -10000 0 -0.25 47 47
JUN -0.026 0.084 -10000 0 -0.3 12 12
HRAS 0.024 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0 0.12 -10000 0 -0.26 58 58
RAP1A 0.025 0.001 -10000 0 -10000 0 0
FRS2 0.025 0.002 -10000 0 -10000 0 0
RAP1A/GDP 0.019 0.001 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.004 0.11 -10000 0 -0.24 55 55
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.014 0.074 -10000 0 -0.22 29 29
RHOA 0.024 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.004 0.1 -10000 0 -0.22 54 54
GRB7 0.019 0.04 -10000 0 -0.4 3 3
RET51/GFRalpha1/GDNF 0.004 0.11 -10000 0 -0.24 55 55
MAPKKK cascade -0.016 0.098 -10000 0 -0.24 51 51
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
RET9/GFRalpha1/GDNF/IRS1 0.005 0.09 -10000 0 -0.24 40 40
lamellipodium assembly -0.027 0.098 -10000 0 -0.25 42 42
RET51/GFRalpha1/GDNF/SHC 0.001 0.1 -10000 0 -0.25 47 47
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.01 0.07 -10000 0 -0.22 26 26
RET9/GFRalpha1/GDNF/Shank3 0.013 0.074 -10000 0 -0.22 30 30
MAPK3 -0.034 0.1 0.28 17 -0.21 52 69
DOK1 0.025 0.004 -10000 0 -10000 0 0
DOK6 -0.003 0.093 -10000 0 -0.4 17 17
PXN 0.025 0.003 -10000 0 -10000 0 0
neurite development -0.031 0.1 0.27 15 -0.28 20 35
DOK5 -0.013 0.1 -10000 0 -0.4 22 22
GFRA1 -0.021 0.12 -10000 0 -0.4 30 30
MAPK8 -0.025 0.084 -10000 0 -0.22 52 52
HRAS/GTP 0.001 0.11 -10000 0 -0.26 52 52
tube development 0.014 0.071 0.2 3 -0.21 29 32
MAPK1 -0.033 0.1 0.27 18 -0.21 52 70
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.001 0.064 -10000 0 -0.21 30 30
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
SRC 0.022 0.032 -10000 0 -0.4 2 2
PDLIM7 0.024 0.009 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.002 0.12 -10000 0 -0.25 63 63
SHC1 0.021 0.01 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.002 0.11 -10000 0 -0.24 55 55
RET51/GFRalpha1/GDNF/Dok5 -0.011 0.13 -10000 0 -0.26 69 69
PRKCA 0.008 0.08 -10000 0 -0.4 13 13
HRAS/GDP 0.018 0.004 -10000 0 -10000 0 0
CREB1 -0.016 0.089 -10000 0 -0.29 27 27
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.003 0.06 -10000 0 -0.21 26 26
RET51/GFRalpha1/GDNF/Grb7 0.002 0.11 -10000 0 -0.25 55 55
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.03 0.12 -10000 0 -0.19 93 93
DOK4 0.023 0.008 -10000 0 -10000 0 0
JNK cascade -0.026 0.084 -10000 0 -0.29 13 13
RET9/GFRalpha1/GDNF/FRS2 0.014 0.075 -10000 0 -0.22 30 30
SHANK3 0.023 0.007 -10000 0 -10000 0 0
RASA1 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.003 0.061 -10000 0 -0.21 27 27
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.019 0.092 -10000 0 -0.23 53 53
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.02 0.092 -10000 0 -0.23 53 53
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.022 0.095 -10000 0 -0.24 47 47
PI3K -0.032 0.14 -10000 0 -0.35 44 44
SOS1 0.025 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.026 0.073 -10000 0 -0.21 29 29
GRB10 0.015 0.063 -10000 0 -0.4 8 8
activation of MAPKK activity -0.013 0.078 -10000 0 -0.22 31 31
RET51/GFRalpha1/GDNF/FRS2 0.005 0.11 -10000 0 -0.24 55 55
GAB1 0.024 0.023 -10000 0 -0.4 1 1
IRS1 0.008 0.083 -10000 0 -0.4 14 14
IRS2 0.007 0.068 -10000 0 -0.4 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.023 0.096 -10000 0 -0.24 48 48
RET51/GFRalpha1/GDNF/PKC alpha -0.004 0.12 -10000 0 -0.26 61 61
GRB2 0.024 0.006 -10000 0 -10000 0 0
PRKACA 0.024 0.006 -10000 0 -10000 0 0
GDNF 0.016 0.02 -10000 0 -0.085 13 13
RAC1 0.025 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.005 0.12 -10000 0 -0.25 65 65
Rac1/GTP -0.025 0.12 -10000 0 -0.3 39 39
RET9/GFRalpha1/GDNF -0.003 0.077 -10000 0 -0.23 32 32
GFRalpha1/GDNF -0.005 0.091 -10000 0 -0.28 32 32
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.036 0.008 -10000 0 -10000 0 0
Necdin/E2F1 0.022 0.059 -10000 0 -0.28 12 12
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.027 0.1 -10000 0 -0.22 49 49
NGF (dimer)/p75(NTR)/BEX1 -0.034 0.14 -10000 0 -0.28 81 81
NT-4/5 (dimer)/p75(NTR) -0.025 0.11 -10000 0 -0.3 47 47
IKBKB 0.023 0.007 -10000 0 -10000 0 0
AKT1 -0.034 0.089 0.18 17 -0.22 47 64
IKBKG 0.025 0.003 -10000 0 -10000 0 0
BDNF -0.018 0.11 -10000 0 -0.4 25 25
MGDIs/NGR/p75(NTR)/LINGO1 0.014 0.1 -10000 0 -0.28 32 32
FURIN 0.023 0.023 -10000 0 -0.4 1 1
proBDNF (dimer)/p75(NTR)/Sortilin 0.006 0.11 -10000 0 -0.27 44 44
LINGO1 0.007 0.068 -10000 0 -0.4 8 8
Sortilin/TRAF6/NRIF 0.022 0.028 -10000 0 -0.19 3 3
proBDNF (dimer) -0.018 0.11 -10000 0 -0.4 25 25
NTRK1 -0.005 0.092 -10000 0 -0.4 17 17
RTN4R 0.016 0.056 -10000 0 -0.4 6 6
neuron apoptosis -0.047 0.13 -10000 0 -0.4 23 23
IRAK1 0.025 0.004 -10000 0 -10000 0 0
SHC1 -0.023 0.084 -10000 0 -0.26 37 37
ARHGDIA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.051 0.044 -10000 0 -0.2 4 4
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.018 0.11 -10000 0 -0.24 47 47
MAGEH1 0.016 0.057 -10000 0 -0.4 6 6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.013 0.11 -10000 0 -0.24 54 54
Mammalian IAPs/DIABLO 0.042 0.077 -10000 0 -0.23 26 26
proNGF (dimer) -0.009 0.11 -10000 0 -0.4 25 25
MAGED1 0.017 0.059 -10000 0 -0.4 7 7
APP 0.025 0.003 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.016 0.11 -10000 0 -0.4 25 25
ZNF274 0.025 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.005 0.084 -10000 0 -0.22 43 43
NGF -0.009 0.11 -10000 0 -0.4 25 25
cell cycle arrest -0.027 0.077 0.2 3 -0.19 43 46
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.008 0.084 -10000 0 -0.22 44 44
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.002 0.1 -10000 0 -0.25 47 47
NCSTN 0.021 0.01 -10000 0 -10000 0 0
mol:GTP 0.004 0.11 -10000 0 -0.26 50 50
PSENEN 0.023 0.023 -10000 0 -0.4 1 1
mol:ceramide -0.024 0.083 0.18 3 -0.23 44 47
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.008 0.076 -10000 0 -0.38 5 5
p75(NTR)/beta APP 0.005 0.082 -10000 0 -0.28 24 24
BEX1 -0.049 0.14 -10000 0 -0.4 49 49
mol:GDP -0.041 0.082 -10000 0 -0.25 44 44
NGF (dimer) -0.04 0.15 -10000 0 -0.24 115 115
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.026 0.097 -10000 0 -0.26 32 32
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
RAC1/GTP 0.008 0.086 -10000 0 -0.22 43 43
MYD88 0.025 0.005 -10000 0 -10000 0 0
CHUK 0.024 0.006 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.004 0.11 -10000 0 -0.26 50 50
RHOB 0.023 0.023 -10000 0 -0.4 1 1
RHOA 0.024 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.032 0.027 -10000 0 -0.28 2 2
NT3 (dimer) -0.009 0.1 -10000 0 -0.4 20 20
TP53 -0.044 0.082 0.18 7 -0.31 9 16
PRDM4 -0.024 0.084 0.18 3 -0.23 44 47
BDNF (dimer) -0.077 0.17 -10000 0 -0.29 130 130
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
SORT1 0.025 0.002 -10000 0 -10000 0 0
activation of caspase activity 0.022 0.1 -10000 0 -0.22 49 49
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.022 0.1 -10000 0 -0.23 44 44
RHOC 0.025 0.001 -10000 0 -10000 0 0
XIAP 0.025 0.001 -10000 0 -10000 0 0
MAPK10 -0.051 0.12 0.24 1 -0.35 36 37
DIABLO 0.025 0.003 -10000 0 -10000 0 0
SMPD2 -0.024 0.084 0.18 3 -0.23 44 47
APH1B 0.021 0.039 -10000 0 -0.4 3 3
APH1A 0.021 0.01 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.009 0.1 -10000 0 -0.26 44 44
PSEN1 0.025 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.036 0.008 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.018 0.11 -10000 0 -0.31 40 40
MAPK8 -0.035 0.1 0.24 1 -0.3 27 28
MAPK9 -0.035 0.1 0.24 1 -0.3 28 29
APAF1 0.025 0.003 -10000 0 -10000 0 0
NTF3 -0.009 0.1 -10000 0 -0.4 20 20
NTF4 -0.016 0.11 -10000 0 -0.4 25 25
NDN 0.009 0.075 -10000 0 -0.4 11 11
RAC1/GDP 0.018 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.021 0.096 -10000 0 -0.21 50 50
p75 CTF/Sortilin/TRAF6/NRIF 0.058 0.028 -10000 0 -0.22 2 2
RhoA-B-C/GTP 0.003 0.11 -10000 0 -0.25 50 50
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.029 0.1 -10000 0 -0.23 43 43
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.019 0.1 -10000 0 -0.24 44 44
PRKACB 0.018 0.055 -10000 0 -0.4 6 6
proBDNF (dimer)/p75 ECD 0.002 0.086 -10000 0 -0.3 24 24
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.11 -10000 0 -0.4 26 26
BIRC2 0.023 0.032 -10000 0 -0.4 2 2
neuron projection morphogenesis -0.028 0.098 -10000 0 -0.25 38 38
BAD -0.042 0.11 0.22 2 -0.32 31 33
RIPK2 0.023 0.009 -10000 0 -10000 0 0
NGFR -0.015 0.11 -10000 0 -0.4 24 24
CYCS -0.04 0.08 0.18 7 -0.22 50 57
ADAM17 0.022 0.032 -10000 0 -0.4 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.019 0.099 -10000 0 -0.23 44 44
BCL2L11 -0.042 0.11 0.24 1 -0.32 31 32
BDNF (dimer)/p75(NTR) -0.025 0.12 -10000 0 -0.32 44 44
PI3K 0.011 0.11 -10000 0 -0.24 51 51
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.022 0.099 -10000 0 -0.23 44 44
NDNL2 0.024 0.008 -10000 0 -10000 0 0
YWHAE 0.024 0.006 -10000 0 -10000 0 0
PRKCI 0.022 0.023 -10000 0 -0.4 1 1
NGF (dimer)/p75(NTR) -0.017 0.11 -10000 0 -0.3 44 44
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.017 0.1 -10000 0 -0.23 50 50
TRAF6 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.032 -10000 0 -0.4 2 2
PLG -0.012 0.097 -10000 0 -0.4 18 18
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.039 0.11 0.15 1 -0.26 60 61
SQSTM1 0.024 0.007 -10000 0 -10000 0 0
NGFRAP1 0.019 0.05 -10000 0 -0.4 5 5
CASP3 -0.039 0.11 0.2 4 -0.3 33 37
E2F1 0.021 0.033 -10000 0 -0.4 2 2
CASP9 0.025 0.005 -10000 0 -10000 0 0
IKK complex 0.003 0.11 -10000 0 -0.31 24 24
NGF (dimer)/TRKA -0.011 0.1 -10000 0 -0.29 39 39
MMP7 -0.086 0.18 -10000 0 -0.4 85 85
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.031 0.099 -10000 0 -0.22 44 44
MMP3 -0.042 0.14 -10000 0 -0.4 43 43
APAF-1/Caspase 9 -0.057 0.074 -10000 0 -0.25 20 20
Glucocorticoid receptor regulatory network

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
PCK2 0.054 0.077 0.31 3 -0.32 1 4
SMARCC2 0.025 0.011 -10000 0 -10000 0 0
SMARCC1 0.025 0.009 -10000 0 -10000 0 0
TBX21 -0.076 0.18 0.36 1 -0.61 26 27
SUMO2 0.024 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0.029 0.01 -10000 0 -10000 0 0
FKBP4 0.025 0.004 -10000 0 -10000 0 0
FKBP5 0.01 0.072 -10000 0 -0.4 10 10
GR alpha/HSP90/FKBP51/HSP90 0.086 0.099 0.27 35 -0.22 10 45
PRL -0.034 0.087 -10000 0 -0.55 1 1
cortisol/GR alpha (dimer)/TIF2 0.12 0.2 0.5 51 -10000 0 51
RELA 0 0.071 -10000 0 -0.22 11 11
FGG 0.11 0.17 0.44 44 -10000 0 44
GR beta/TIF2 0.064 0.11 0.28 32 -0.29 12 44
IFNG -0.17 0.27 -10000 0 -0.74 46 46
apoptosis 0.016 0.19 0.5 20 -0.48 19 39
CREB1 0.023 0.015 -10000 0 -10000 0 0
histone acetylation -0.016 0.11 0.28 12 -0.3 16 28
BGLAP -0.04 0.11 -10000 0 -0.63 4 4
GR/PKAc 0.09 0.091 0.28 27 -0.24 5 32
NF kappa B1 p50/RelA 0.001 0.12 -10000 0 -0.29 43 43
SMARCD1 0.026 0.008 -10000 0 -10000 0 0
MDM2 0.056 0.08 0.22 43 -0.25 2 45
GATA3 0.008 0.077 -10000 0 -0.4 11 11
AKT1 0.021 0.003 -10000 0 -10000 0 0
CSF2 -0.041 0.092 -10000 0 -0.46 1 1
GSK3B 0.025 0.014 -10000 0 -10000 0 0
NR1I3 0.022 0.26 0.52 18 -0.8 20 38
CSN2 0.087 0.14 0.36 45 -0.25 2 47
BRG1/BAF155/BAF170/BAF60A 0.058 0.037 -10000 0 -0.2 4 4
NFATC1 0.016 0.063 -10000 0 -0.4 8 8
POU2F1 0.019 0.021 -10000 0 -10000 0 0
CDKN1A -0.052 0.28 -10000 0 -1.4 15 15
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.002 0.009 -10000 0 -10000 0 0
SFN -0.012 0.11 -10000 0 -0.4 26 26
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.075 0.11 0.27 29 -0.21 23 52
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.014 0.19 0.46 20 -0.61 14 34
JUN -0.12 0.16 0.29 3 -0.4 56 59
IL4 -0.061 0.12 -10000 0 -0.51 7 7
CDK5R1 0.021 0.034 -10000 0 -0.4 2 2
PRKACA 0.024 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.069 0.13 0.2 25 -0.33 39 64
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.096 0.096 0.28 30 -0.2 9 39
cortisol/GR alpha (monomer) 0.16 0.24 0.59 57 -10000 0 57
NCOA2 0.01 0.074 -10000 0 -0.4 11 11
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.042 0.088 -10000 0 -0.22 32 32
AP-1/NFAT1-c-4 -0.19 0.27 -10000 0 -0.53 122 122
AFP -0.089 0.13 -10000 0 -0.47 3 3
SUV420H1 0.025 0.004 -10000 0 -10000 0 0
IRF1 0.096 0.12 0.41 20 -10000 0 20
TP53 0.003 0.14 -10000 0 -0.49 22 22
PPP5C 0.025 0.004 -10000 0 -10000 0 0
KRT17 -0.26 0.41 -10000 0 -1 70 70
KRT14 -0.21 0.41 -10000 0 -1.2 49 49
TBP 0.029 0.018 -10000 0 -0.3 1 1
CREBBP 0.06 0.096 0.29 48 -0.25 3 51
HDAC1 0.025 0.003 -10000 0 -10000 0 0
HDAC2 0.025 0.003 -10000 0 -10000 0 0
AP-1 -0.19 0.27 -10000 0 -0.53 122 122
MAPK14 0.025 0.013 -10000 0 -10000 0 0
MAPK10 -0.012 0.12 -10000 0 -0.4 29 29
MAPK11 0.021 0.028 -10000 0 -0.4 1 1
KRT5 -0.31 0.46 -10000 0 -1.1 88 88
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.029 0.01 -10000 0 -10000 0 0
CGA -0.06 0.11 -10000 0 -0.45 5 5
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.082 0.13 0.36 37 -0.36 4 41
MAPK3 0.024 0.014 -10000 0 -10000 0 0
MAPK1 0.024 0.013 -10000 0 -10000 0 0
ICAM1 -0.077 0.17 -10000 0 -0.61 19 19
NFKB1 0 0.072 -10000 0 -0.18 32 32
MAPK8 -0.092 0.14 0.34 2 -0.35 49 51
MAPK9 0.025 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.016 0.19 0.51 20 -0.5 19 39
BAX -0.011 0.1 -10000 0 -0.61 2 2
POMC -0.13 0.33 0.62 1 -1.3 22 23
EP300 0.058 0.092 0.28 47 -0.26 2 49
cortisol/GR alpha (dimer)/p53 0.12 0.22 0.52 47 -0.54 3 50
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.077 0.22 29 -0.22 2 31
SGK1 0.056 0.19 -10000 0 -1.4 4 4
IL13 -0.13 0.19 -10000 0 -0.64 17 17
IL6 -0.1 0.23 -10000 0 -0.72 30 30
PRKACG 0.016 0.01 -10000 0 -10000 0 0
IL5 -0.11 0.16 -10000 0 -0.56 13 13
IL2 -0.16 0.22 -10000 0 -0.6 42 42
CDK5 0.025 0.007 -10000 0 -10000 0 0
PRKACB 0.018 0.055 -10000 0 -0.4 6 6
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
IL8 -0.12 0.28 -10000 0 -0.83 39 39
CDK5R1/CDK5 0.032 0.029 -10000 0 -0.28 2 2
NF kappa B1 p50/RelA/PKAc 0.031 0.1 -10000 0 -0.25 23 23
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.19 0.47 64 -10000 0 64
SMARCA4 0.021 0.034 -10000 0 -0.4 2 2
chromatin remodeling 0.092 0.13 0.35 40 -0.41 2 42
NF kappa B1 p50/RelA/Cbp 0.06 0.14 0.33 36 -0.33 11 47
JUN (dimer) -0.12 0.16 0.29 3 -0.4 56 59
YWHAH 0.024 0.006 -10000 0 -10000 0 0
VIPR1 -0.086 0.2 0.33 1 -0.68 30 31
NR3C1 0.095 0.15 0.39 48 -0.43 2 50
NR4A1 -0.013 0.13 -10000 0 -0.48 23 23
TIF2/SUV420H1 0.024 0.056 -10000 0 -0.28 11 11
MAPKKK cascade 0.016 0.19 0.5 20 -0.48 19 39
cortisol/GR alpha (dimer)/Src-1 0.15 0.2 0.49 62 -10000 0 62
PBX1 0.016 0.047 -10000 0 -0.4 4 4
POU1F1 0.016 0.015 -10000 0 -10000 0 0
SELE -0.11 0.26 -10000 0 -0.76 39 39
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.092 0.13 0.35 40 -0.41 2 42
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.19 0.47 64 -10000 0 64
mol:cortisol 0.086 0.14 0.35 54 -10000 0 54
MMP1 -0.17 0.36 -10000 0 -1.1 48 48
Reelin signaling pathway

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
CDK5R1/CDK5 0.032 0.027 -10000 0 -0.28 2 2
VLDLR 0.013 0.07 -10000 0 -0.4 10 10
CRKL 0.025 0.005 -10000 0 -10000 0 0
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
FYN 0.025 0.007 -10000 0 -10000 0 0
ITGA3 0.017 0.051 -10000 0 -0.4 5 5
RELN/VLDLR/Fyn 0 0.11 -10000 0 -0.24 58 58
MAPK8IP1/MKK7/MAP3K11/JNK1 0.049 0.047 -10000 0 -0.21 5 5
AKT1 -0.035 0.091 -10000 0 -0.22 62 62
MAP2K7 0.024 0.007 -10000 0 -10000 0 0
RAPGEF1 0.024 0.007 -10000 0 -10000 0 0
DAB1 0.013 0.029 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.001 0.094 -10000 0 -0.22 52 52
LRPAP1/LRP8 0.034 0.026 -10000 0 -0.28 2 2
RELN/LRP8/DAB1/Fyn 0.012 0.094 -10000 0 -0.21 52 52
DAB1/alpha3/beta1 Integrin 0.002 0.098 -10000 0 -0.2 61 61
long-term memory -0.007 0.11 -10000 0 -0.22 67 67
DAB1/LIS1 0.015 0.1 -10000 0 -0.2 60 60
DAB1/CRLK/C3G 0.005 0.095 -10000 0 -0.2 60 60
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
DAB1/NCK2 0.02 0.1 -10000 0 -0.2 60 60
ARHGEF2 0.02 0.011 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.013 0.1 -10000 0 -0.4 22 22
CDK5R1 0.021 0.034 -10000 0 -0.4 2 2
RELN -0.053 0.15 -10000 0 -0.4 50 50
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
RELN/LRP8/Fyn 0.005 0.1 -10000 0 -0.24 52 52
GRIN2A/RELN/LRP8/DAB1/Fyn 0.003 0.12 -10000 0 -0.23 68 68
MAPK8 0.023 0.023 -10000 0 -0.4 1 1
RELN/VLDLR/DAB1 -0.007 0.098 -10000 0 -0.22 58 58
ITGB1 0.024 0.005 -10000 0 -10000 0 0
MAP1B -0.046 0.099 0.16 4 -0.23 76 80
RELN/LRP8 0.005 0.1 -10000 0 -0.24 52 52
GRIN2B/RELN/LRP8/DAB1/Fyn 0.018 0.1 -10000 0 -0.21 51 51
PI3K 0.025 0.052 -10000 0 -0.28 9 9
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.029 0.04 -10000 0 -0.28 5 5
RAP1A -0.041 0.082 0.28 3 -0.22 5 8
PAFAH1B1 0.024 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.017 0.055 -10000 0 -0.4 6 6
CRLK/C3G 0.035 0.01 -10000 0 -10000 0 0
GRIN2B 0.016 0.022 -10000 0 -10000 0 0
NCK2 0.025 0.003 -10000 0 -10000 0 0
neuron differentiation 0.002 0.077 -10000 0 -0.3 5 5
neuron adhesion -0.036 0.095 0.34 5 -0.37 1 6
LRP8 0.022 0.033 -10000 0 -0.4 2 2
GSK3B -0.033 0.085 0.16 1 -0.21 60 61
RELN/VLDLR/DAB1/Fyn 0.007 0.098 -10000 0 -0.21 58 58
MAP3K11 0.025 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.029 0.098 -10000 0 -0.23 63 63
CDK5 0.024 0.005 -10000 0 -10000 0 0
MAPT -0.002 0.067 0.71 2 -0.37 4 6
neuron migration -0.04 0.11 0.25 3 -0.27 54 57
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.002 0.077 -10000 0 -0.3 5 5
RELN/VLDLR 0.011 0.1 -10000 0 -0.22 60 60
Thromboxane A2 receptor signaling

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
TGM2 0.014 0.058 -10000 0 -0.4 6 6
GNB1/GNG2 -0.038 0.065 -10000 0 -0.19 48 48
AKT1 -0.015 0.094 0.25 5 -0.24 22 27
EGF -0.011 0.1 -10000 0 -0.4 21 21
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.004 0.067 0.22 8 -0.28 4 12
mol:Ca2+ -0.035 0.13 0.27 5 -0.29 61 66
LYN 0.004 0.054 0.21 5 -0.19 1 6
RhoA/GTP -0.013 0.053 -10000 0 -0.13 43 43
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.044 0.14 0.27 5 -0.34 49 54
GNG2 0.018 0.047 -10000 0 -0.4 4 4
ARRB2 0.024 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.043 0.19 -10000 0 -0.51 41 41
G beta5/gamma2 -0.041 0.088 -10000 0 -0.25 47 47
PRKCH -0.042 0.14 0.28 4 -0.35 51 55
DNM1 0.013 0.058 -10000 0 -0.4 6 6
TXA2/TP beta/beta Arrestin3 0.01 0.028 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.002 0.1 -10000 0 -0.4 21 21
G12 family/GTP -0.041 0.12 -10000 0 -0.3 54 54
ADRBK1 0.025 0.004 -10000 0 -10000 0 0
ADRBK2 0.017 0.055 -10000 0 -0.4 6 6
RhoA/GTP/ROCK1 0.032 0.008 -10000 0 -10000 0 0
mol:GDP 0.025 0.12 0.39 21 -0.2 2 23
mol:NADP 0.02 0.035 -10000 0 -0.4 2 2
RAB11A 0.024 0.005 -10000 0 -10000 0 0
PRKG1 0.002 0.089 -10000 0 -0.4 16 16
mol:IP3 -0.047 0.16 0.29 5 -0.37 61 66
cell morphogenesis 0.032 0.008 -10000 0 -10000 0 0
PLCB2 -0.069 0.21 0.34 2 -0.5 61 63
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.011 0.074 0.22 4 -0.27 11 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0 0.068 0.24 6 -0.26 7 13
RHOA 0.024 0.005 -10000 0 -10000 0 0
PTGIR 0.022 0.033 -10000 0 -0.4 2 2
PRKCB1 -0.045 0.15 0.27 5 -0.36 56 61
GNAQ 0.023 0.023 -10000 0 -0.4 1 1
mol:L-citrulline 0.02 0.035 -10000 0 -0.4 2 2
TXA2/TXA2-R family -0.069 0.2 0.34 2 -0.52 51 53
LCK 0.001 0.065 0.22 6 -0.28 3 9
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.018 0.049 -10000 0 -0.18 14 14
TXA2-R family/G12 family/GDP/G beta/gamma 0.004 0.098 -10000 0 -0.45 14 14
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.021 0.05 -10000 0 -0.18 14 14
MAPK14 -0.025 0.098 0.22 5 -0.23 47 52
TGM2/GTP -0.054 0.18 0.34 4 -0.42 58 62
MAPK11 -0.026 0.094 0.22 5 -0.23 48 53
ARHGEF1 -0.022 0.072 0.16 1 -0.18 48 49
GNAI2 0.024 0.006 -10000 0 -10000 0 0
JNK cascade -0.047 0.16 0.29 5 -0.38 52 57
RAB11/GDP 0.024 0.006 -10000 0 -10000 0 0
ICAM1 -0.031 0.12 0.24 5 -0.28 48 53
cAMP biosynthetic process -0.047 0.15 0.28 5 -0.34 61 66
Gq family/GTP/EBP50 -0.006 0.077 -10000 0 -0.24 31 31
actin cytoskeleton reorganization 0.032 0.008 -10000 0 -10000 0 0
SRC 0.005 0.058 0.22 6 -10000 0 6
GNB5 0.021 0.039 -10000 0 -0.4 3 3
GNB1 0.025 0.005 -10000 0 -10000 0 0
EGF/EGFR -0.005 0.084 0.23 12 -0.24 15 27
VCAM1 -0.039 0.13 0.25 5 -0.34 48 53
TP beta/Gq family/GDP/G beta5/gamma2 -0.043 0.19 -10000 0 -0.51 41 41
platelet activation -0.035 0.13 0.27 5 -0.3 51 56
PGI2/IP 0.016 0.023 -10000 0 -0.28 2 2
PRKACA 0.003 0.051 -10000 0 -0.21 19 19
Gq family/GDP/G beta5/gamma2 -0.035 0.16 -10000 0 -0.46 39 39
TXA2/TP beta/beta Arrestin2 -0.002 0.079 0.16 1 -0.39 13 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.001 0.042 -10000 0 -0.2 15 15
mol:DAG -0.052 0.17 0.29 5 -0.42 54 59
EGFR 0.013 0.07 -10000 0 -0.4 10 10
TXA2/TP alpha -0.066 0.2 0.34 3 -0.47 60 63
Gq family/GTP -0.012 0.076 -10000 0 -0.24 33 33
YES1 0.008 0.059 0.23 7 -10000 0 7
GNAI2/GTP 0.008 0.05 -10000 0 -0.17 18 18
PGD2/DP -0.001 0.071 -10000 0 -0.28 21 21
SLC9A3R1 0.02 0.04 -10000 0 -0.4 3 3
FYN 0.006 0.059 0.25 5 -10000 0 5
mol:NO 0.02 0.035 -10000 0 -0.4 2 2
GNA15 0.015 0.056 -10000 0 -0.4 6 6
PGK/cGMP 0.016 0.059 -10000 0 -0.24 17 17
RhoA/GDP 0.024 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.031 0.066 -10000 0 -0.19 21 21
NOS3 0.02 0.035 -10000 0 -0.4 2 2
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCA -0.043 0.15 0.27 4 -0.36 51 55
PRKCB -0.045 0.15 0.23 4 -0.36 51 55
PRKCE -0.038 0.14 0.29 5 -0.35 50 55
PRKCD -0.044 0.15 0.29 4 -0.38 51 55
PRKCG -0.054 0.16 0.28 5 -0.39 53 58
muscle contraction -0.066 0.19 0.34 3 -0.48 54 57
PRKCZ -0.043 0.14 0.27 5 -0.34 52 57
ARR3 0.019 0.009 -10000 0 -10000 0 0
TXA2/TP beta 0.02 0.058 -10000 0 -0.18 20 20
PRKCQ -0.053 0.16 0.29 6 -0.38 53 59
MAPKKK cascade -0.061 0.18 0.3 3 -0.44 58 61
SELE -0.04 0.13 0.25 5 -0.34 48 53
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.059 -10000 0 -0.18 16 16
ROCK1 0.025 0.004 -10000 0 -10000 0 0
GNA14 0.015 0.063 -10000 0 -0.4 8 8
chemotaxis -0.078 0.23 0.36 2 -0.6 48 50
GNA12 0.024 0.005 -10000 0 -10000 0 0
GNA13 0.024 0.006 -10000 0 -10000 0 0
GNA11 0.016 0.055 -10000 0 -0.4 6 6
Rac1/GTP 0.018 0.004 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.023 0.023 -10000 0 -0.4 1 1
LAT2 -0.015 0.077 -10000 0 -0.27 18 18
AP1 0.016 0.14 -10000 0 -0.42 22 22
mol:PIP3 0.017 0.14 0.23 53 -0.36 17 70
IKBKB 0.026 0.11 0.19 70 -0.25 11 81
AKT1 0.026 0.15 0.31 63 -0.28 4 67
IKBKG 0.016 0.099 0.19 51 -0.24 12 63
MS4A2 0.013 0.036 -10000 0 -0.4 1 1
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
MAP3K1 0.022 0.12 0.25 27 -0.37 12 39
mol:Ca2+ 0.02 0.12 0.21 56 -0.29 15 71
LYN 0.021 0.041 -10000 0 -0.41 3 3
CBLB -0.015 0.076 -10000 0 -0.29 15 15
SHC1 0.021 0.01 -10000 0 -10000 0 0
RasGAP/p62DOK 0.046 0.013 -10000 0 -10000 0 0
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.014 0.067 -10000 0 -0.4 9 9
PLD2 0.026 0.15 0.33 62 -0.22 32 94
PTPN13 -0.005 0.13 -10000 0 -0.59 8 8
PTPN11 0.022 0.018 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.023 0.12 0.3 14 -0.32 7 21
SYK 0.017 0.062 -10000 0 -0.41 7 7
GRB2 0.024 0.006 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.011 0.1 0.18 1 -0.3 32 33
LAT -0.016 0.078 -10000 0 -0.29 16 16
PAK2 0.022 0.13 0.22 54 -0.38 13 67
NFATC2 -0.023 0.099 -10000 0 -0.42 19 19
HRAS 0.012 0.12 0.2 45 -0.38 16 61
GAB2 0.025 0.006 -10000 0 -10000 0 0
PLA2G1B -0.014 0.14 -10000 0 -0.86 9 9
Fc epsilon R1 0.01 0.094 -10000 0 -0.27 34 34
Antigen/IgE/Fc epsilon R1 0.011 0.085 -10000 0 -0.24 34 34
mol:GDP -0.015 0.11 0.19 1 -0.4 20 21
JUN 0.024 0.023 -10000 0 -0.4 1 1
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
FOS 0.014 0.055 -10000 0 -0.4 5 5
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.011 0.081 -10000 0 -0.22 34 34
CHUK 0.019 0.1 0.19 58 -0.24 12 70
KLRG1 -0.017 0.078 -10000 0 -0.21 41 41
VAV1 -0.014 0.078 -10000 0 -0.26 21 21
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.014 0.076 -10000 0 -0.28 15 15
negative regulation of mast cell degranulation -0.008 0.088 -10000 0 -0.28 19 19
BTK -0.019 0.13 -10000 0 -0.5 18 18
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.015 0.099 -10000 0 -0.26 40 40
GAB2/PI3K/SHP2 -0.037 0.064 -10000 0 -0.22 37 37
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.01 0.075 -10000 0 -0.22 35 35
RAF1 -0.017 0.16 -10000 0 -0.95 9 9
Fc epsilon R1/FcgammaRIIB/SHIP 0.019 0.11 -10000 0 -0.26 43 43
FCER1G 0.012 0.057 -10000 0 -0.4 6 6
FCER1A -0.021 0.12 -10000 0 -0.41 29 29
Antigen/IgE/Fc epsilon R1/Fyn 0.021 0.084 -10000 0 -0.22 34 34
MAPK3 -0.015 0.14 -10000 0 -0.87 9 9
MAPK1 -0.016 0.15 -10000 0 -0.88 9 9
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.024 0.19 -10000 0 -0.57 31 31
DUSP1 0.022 0.018 -10000 0 -10000 0 0
NF-kappa-B/RelA 0.014 0.055 0.11 39 -0.16 10 49
actin cytoskeleton reorganization 0.011 0.12 -10000 0 -0.59 8 8
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.004 0.1 0.2 1 -0.35 15 16
FER -0.015 0.077 -10000 0 -0.28 17 17
RELA 0.025 0.003 -10000 0 -10000 0 0
ITK -0.017 0.084 -10000 0 -0.34 21 21
SOS1 0.025 0.004 -10000 0 -10000 0 0
PLCG1 0.007 0.13 0.23 11 -0.4 19 30
cytokine secretion -0.001 0.03 -10000 0 -0.13 5 5
SPHK1 -0.015 0.076 -10000 0 -0.27 17 17
PTK2 0.011 0.13 -10000 0 -0.63 8 8
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.006 0.11 0.24 1 -0.3 31 32
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.017 0.14 0.24 50 -0.35 18 68
MAP2K2 -0.019 0.14 -10000 0 -0.88 9 9
MAP2K1 -0.018 0.14 -10000 0 -0.88 9 9
MAP2K7 0.024 0.007 -10000 0 -10000 0 0
KLRG1/SHP2 -0.008 0.079 -10000 0 -0.2 39 39
MAP2K4 -0.072 0.31 -10000 0 -0.89 43 43
Fc epsilon R1/FcgammaRIIB 0.016 0.1 -10000 0 -0.25 40 40
mol:Choline 0.026 0.15 0.33 62 -0.22 32 94
SHC/Grb2/SOS1 0.019 0.085 0.23 1 -0.31 10 11
FYN 0.025 0.007 -10000 0 -10000 0 0
DOK1 0.025 0.004 -10000 0 -10000 0 0
PXN 0.011 0.12 0.32 1 -0.57 8 9
HCLS1 -0.017 0.082 -10000 0 -0.3 17 17
PRKCB 0.014 0.12 0.2 51 -0.3 17 68
FCGR2B 0.009 0.067 -10000 0 -0.4 9 9
IGHE 0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.008 0.09 -10000 0 -0.29 19 19
LCP2 0.018 0.051 -10000 0 -0.4 5 5
PLA2G4A -0.03 0.097 -10000 0 -0.26 39 39
RASA1 0.025 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.026 0.15 0.33 62 -0.22 32 94
IKK complex 0.031 0.1 0.18 76 -0.2 8 84
WIPF1 0.022 0.032 -10000 0 -0.4 2 2
TCGA08_p53

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
CDKN2A -0.025 0.076 -10000 0 -0.28 27 27
TP53 -0.021 0.076 0.14 2 -0.19 49 51
Senescence -0.021 0.076 0.14 2 -0.25 27 29
Apoptosis -0.021 0.076 0.14 2 -0.25 27 29
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.012 0.06 0.2 29 -0.27 2 31
MDM4 0.021 0.01 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0 0.066 -10000 0 -0.19 29 29
NFATC2 -0.025 0.19 -10000 0 -0.49 34 34
NFATC3 0 0.067 -10000 0 -0.24 10 10
CD40LG -0.14 0.3 -10000 0 -0.82 42 42
ITCH 0.006 0.055 -10000 0 -0.23 15 15
CBLB 0.006 0.051 -10000 0 -0.21 16 16
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.14 0.35 -10000 0 -0.88 55 55
JUNB 0.019 0.045 -10000 0 -0.4 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.064 -10000 0 -0.25 17 17
T cell anergy -0.008 0.084 0.26 3 -0.33 17 20
TLE4 -0.023 0.14 -10000 0 -0.43 23 23
Jun/NFAT1-c-4/p21SNFT -0.071 0.28 -10000 0 -0.81 32 32
AP-1/NFAT1-c-4 -0.1 0.35 -10000 0 -0.89 43 43
IKZF1 -0.031 0.17 -10000 0 -0.53 26 26
T-helper 2 cell differentiation -0.054 0.21 -10000 0 -0.7 22 22
AP-1/NFAT1 -0.009 0.15 -10000 0 -0.36 28 28
CALM1 0.013 0.043 -10000 0 -10000 0 0
EGR2 -0.083 0.29 -10000 0 -0.92 28 28
EGR3 -0.099 0.32 -10000 0 -1.1 30 30
NFAT1/FOXP3 -0.018 0.17 -10000 0 -0.4 41 41
EGR1 0.01 0.06 -10000 0 -0.36 7 7
JUN 0.007 0.039 -10000 0 -0.44 1 1
EGR4 0.012 0.029 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.033 -10000 0 -0.15 17 17
GBP3 -0.044 0.2 -10000 0 -0.58 34 34
FOSL1 0.01 0.07 -10000 0 -0.4 9 9
NFAT1-c-4/MAF/IRF4 -0.068 0.29 -10000 0 -0.8 38 38
DGKA -0.019 0.13 -10000 0 -0.38 26 26
CREM 0.024 0.006 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.093 0.29 -10000 0 -0.81 37 37
CTLA4 -0.062 0.2 -10000 0 -0.55 43 43
NFAT1-c-4 (dimer)/EGR1 -0.068 0.28 -10000 0 -0.82 33 33
NFAT1-c-4 (dimer)/EGR4 -0.065 0.28 -10000 0 -0.79 35 35
FOS -0.002 0.061 -10000 0 -0.41 5 5
IFNG -0.089 0.27 -10000 0 -0.85 31 31
T cell activation -0.059 0.16 -10000 0 -0.64 10 10
MAF 0.019 0.035 -10000 0 -0.4 2 2
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.065 0.24 0.77 28 -10000 0 28
TNF -0.11 0.27 -10000 0 -0.68 52 52
FASLG -0.17 0.48 -10000 0 -1.3 46 46
TBX21 -0.004 0.093 -10000 0 -0.32 23 23
BATF3 0.014 0.052 -10000 0 -0.4 5 5
PRKCQ -0.041 0.15 -10000 0 -0.41 51 51
PTPN1 -0.018 0.13 -10000 0 -0.43 16 16
NFAT1-c-4/ICER1 -0.061 0.27 -10000 0 -0.8 33 33
GATA3 0.007 0.076 -10000 0 -0.4 11 11
T-helper 1 cell differentiation -0.087 0.26 -10000 0 -0.83 31 31
IL2RA -0.1 0.29 -10000 0 -0.77 43 43
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.017 0.12 -10000 0 -0.4 20 20
E2F1 0.025 0.034 -10000 0 -0.4 2 2
PPARG -0.041 0.15 -10000 0 -0.4 50 50
SLC3A2 -0.019 0.13 -10000 0 -0.4 20 20
IRF4 -0.023 0.12 -10000 0 -0.4 32 32
PTGS2 -0.14 0.3 -10000 0 -0.78 47 47
CSF2 -0.13 0.28 -10000 0 -0.79 42 42
JunB/Fra1/NFAT1-c-4 -0.057 0.28 -10000 0 -0.79 32 32
IL4 -0.056 0.22 -10000 0 -0.76 20 20
IL5 -0.13 0.28 -10000 0 -0.78 43 43
IL2 -0.06 0.16 -10000 0 -0.67 9 9
IL3 -0.022 0.12 -10000 0 -0.78 6 6
RNF128 -0.015 0.11 -10000 0 -0.48 17 17
NFATC1 -0.065 0.24 -10000 0 -0.77 28 28
CDK4 0.051 0.15 0.61 12 -10000 0 12
PTPRK -0.019 0.13 -10000 0 -0.41 22 22
IL8 -0.14 0.3 -10000 0 -0.82 46 46
POU2F1 0.019 0.017 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.025 0.089 -10000 0 -0.21 45 45
ER alpha/Gai/GDP/Gbeta gamma -0.057 0.18 -10000 0 -0.42 52 52
AKT1 -0.079 0.27 -10000 0 -0.74 49 49
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.077 0.27 -10000 0 -0.75 49 49
mol:Ca2+ -0.029 0.11 0.16 1 -0.32 33 34
IGF1R -0.005 0.11 -10000 0 -0.4 25 25
E2/ER alpha (dimer)/Striatin -0.001 0.09 -10000 0 -0.24 45 45
SHC1 0.021 0.01 -10000 0 -10000 0 0
apoptosis 0.074 0.26 0.7 49 -10000 0 49
RhoA/GTP -0.003 0.072 -10000 0 -0.2 39 39
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.033 0.16 -10000 0 -0.39 47 47
regulation of stress fiber formation 0.022 0.065 0.29 3 -0.23 4 7
E2/ERA-ERB (dimer) 0.001 0.088 -10000 0 -0.24 43 43
KRAS 0.025 0.004 -10000 0 -10000 0 0
G13/GTP 0.002 0.078 -10000 0 -0.21 42 42
pseudopodium formation -0.022 0.065 0.23 4 -0.29 3 7
E2/ER alpha (dimer)/PELP1 0 0.088 -10000 0 -0.24 43 43
GRB2 0.024 0.006 -10000 0 -10000 0 0
GNG2 0.018 0.047 -10000 0 -0.4 4 4
GNAO1 0.014 0.053 -10000 0 -0.4 5 5
HRAS 0.024 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.058 0.19 -10000 0 -0.47 52 52
E2/ER beta (dimer) 0.018 0.006 -10000 0 -10000 0 0
mol:GDP -0.024 0.12 -10000 0 -0.34 40 40
mol:NADP -0.058 0.19 -10000 0 -0.47 52 52
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:IP3 -0.03 0.11 -10000 0 -0.34 33 33
IGF-1R heterotetramer -0.005 0.11 -10000 0 -0.4 25 25
PLCB1 -0.028 0.12 -10000 0 -0.35 33 33
PLCB2 -0.02 0.1 -10000 0 -0.38 22 22
IGF1 -0.021 0.12 -10000 0 -0.4 33 33
mol:L-citrulline -0.058 0.19 -10000 0 -0.47 52 52
RHOA 0.024 0.005 -10000 0 -10000 0 0
Gai/GDP -0.053 0.21 -10000 0 -0.58 46 46
JNK cascade 0.018 0.006 -10000 0 -10000 0 0
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
ESR2 0.024 0.009 -10000 0 -10000 0 0
GNAQ 0.023 0.023 -10000 0 -0.4 1 1
ESR1 -0.027 0.14 -10000 0 -0.4 44 44
Gq family/GDP/Gbeta gamma -0.051 0.23 -10000 0 -0.65 41 41
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.011 0.13 -10000 0 -0.6 9 9
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.036 0.15 -10000 0 -0.41 36 36
GNAZ 0.013 0.067 -10000 0 -0.4 9 9
E2/ER alpha (dimer) -0.018 0.098 -10000 0 -0.28 44 44
STRN 0.02 0.045 -10000 0 -0.4 4 4
GNAL 0.016 0.052 -10000 0 -0.4 5 5
PELP1 0.024 0.006 -10000 0 -10000 0 0
MAPK11 0.011 0.015 -10000 0 -0.24 1 1
GNAI2 0.024 0.006 -10000 0 -10000 0 0
GNAI3 0.025 0.002 -10000 0 -10000 0 0
GNAI1 0.012 0.071 -10000 0 -0.4 10 10
HBEGF -0.059 0.17 0.26 2 -0.4 50 52
cAMP biosynthetic process -0.002 0.074 -10000 0 -0.19 46 46
SRC -0.051 0.17 0.21 4 -0.4 48 52
PI3K 0.025 0.052 -10000 0 -0.28 9 9
GNB1 0.025 0.005 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.005 0.12 -10000 0 -0.31 39 39
SOS1 0.025 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.06 0.14 -10000 0 -0.39 43 43
Gs family/GTP 0.004 0.077 -10000 0 -0.19 46 46
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.033 -10000 0 -0.22 5 5
vasodilation -0.054 0.18 -10000 0 -0.44 52 52
mol:DAG -0.03 0.11 -10000 0 -0.34 33 33
Gs family/GDP/Gbeta gamma -0.014 0.11 -10000 0 -0.3 38 38
MSN -0.023 0.068 0.24 4 -0.31 3 7
Gq family/GTP -0.009 0.11 -10000 0 -0.43 17 17
mol:PI-3-4-5-P3 -0.073 0.26 -10000 0 -0.72 49 49
NRAS 0.02 0.05 -10000 0 -0.4 5 5
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.054 0.18 0.44 52 -10000 0 52
GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
RhoA/GDP -0.009 0.12 -10000 0 -0.33 39 39
NOS3 -0.062 0.2 -10000 0 -0.49 52 52
GNA11 0.016 0.055 -10000 0 -0.4 6 6
MAPKKK cascade -0.047 0.2 -10000 0 -0.52 47 47
E2/ER alpha (dimer)/PELP1/Src -0.04 0.17 -10000 0 -0.41 47 47
ruffle organization -0.022 0.065 0.23 4 -0.29 3 7
ROCK2 -0.022 0.075 0.26 5 -0.34 3 8
GNA14 0.015 0.063 -10000 0 -0.4 8 8
GNA15 0.015 0.056 -10000 0 -0.4 6 6
GNA13 0.024 0.006 -10000 0 -10000 0 0
MMP9 -0.063 0.17 0.37 1 -0.39 50 51
MMP2 -0.052 0.16 0.21 1 -0.39 51 52
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.068 -10000 0 -0.24 20 20
fibroblast growth factor receptor signaling pathway 0.029 0.068 -10000 0 -0.24 20 20
LAMA1 -0.071 0.17 -10000 0 -0.4 76 76
PRNP 0.011 0.074 -10000 0 -0.35 13 13
GPC1/SLIT2 -0.01 0.11 -10000 0 -0.29 44 44
SMAD2 0.013 0.033 0.18 6 -0.21 4 10
GPC1/PrPc/Cu2+ 0.022 0.052 -10000 0 -0.24 13 13
GPC1/Laminin alpha1 -0.039 0.13 -10000 0 -0.29 78 78
TDGF1 -0.049 0.15 -10000 0 -0.4 52 52
CRIPTO/GPC1 -0.023 0.12 -10000 0 -0.29 53 53
APP/GPC1 0.033 0.031 -10000 0 -0.28 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.032 0.093 -10000 0 -0.25 53 53
FLT1 0.023 0.024 -10000 0 -0.4 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.043 0.036 -10000 0 -0.23 5 5
SERPINC1 0.018 0.015 -10000 0 -10000 0 0
FYN -0.03 0.091 -10000 0 -0.25 50 50
FGR -0.037 0.1 -10000 0 -0.26 58 58
positive regulation of MAPKKK cascade -0.047 0.14 0.27 6 -0.35 50 56
SLIT2 -0.033 0.14 -10000 0 -0.4 42 42
GPC1/NRG 0.012 0.071 -10000 0 -0.29 17 17
NRG1 0 0.085 -10000 0 -0.4 14 14
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.046 0.03 -10000 0 -0.24 3 3
LYN -0.028 0.093 -10000 0 -0.26 46 46
mol:Spermine 0.004 0.027 -10000 0 -0.28 3 3
cell growth 0.029 0.068 -10000 0 -0.24 20 20
BMP signaling pathway -0.021 0.04 0.4 3 -10000 0 3
SRC -0.032 0.093 -10000 0 -0.25 53 53
TGFBR1 0.024 0.007 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A 0.001 0.072 -10000 0 -0.4 9 9
GPC1 0.021 0.04 -10000 0 -0.4 3 3
TGFBR1 (dimer) 0.024 0.007 -10000 0 -10000 0 0
VEGFA 0.024 0.011 -10000 0 -0.085 3 3
BLK -0.05 0.11 0.17 2 -0.26 66 68
HCK -0.036 0.1 -10000 0 -0.26 55 55
FGF2 0.003 0.087 -10000 0 -0.4 15 15
FGFR1 0.017 0.051 -10000 0 -0.4 5 5
VEGFR1 homodimer 0.023 0.024 -10000 0 -0.4 1 1
TGFBR2 0.022 0.032 -10000 0 -0.4 2 2
cell death 0.033 0.031 -10000 0 -0.28 3 3
ATIII/GPC1 0.025 0.035 -10000 0 -0.3 3 3
PLA2G2A/GPC1 0.014 0.062 -10000 0 -0.29 12 12
LCK -0.039 0.11 -10000 0 -0.27 57 57
neuron differentiation 0.012 0.07 -10000 0 -0.28 17 17
PrPc/Cu2+ 0.009 0.052 -10000 0 -0.28 11 11
APP 0.025 0.003 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.022 0.032 -10000 0 -0.4 2 2
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.012 0.073 0.4 9 -10000 0 9
VDR 0.021 0.039 -10000 0 -0.4 3 3
FAM120B 0.025 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.028 0.12 -10000 0 -0.25 65 65
RXRs/LXRs/DNA/Oxysterols -0.023 0.15 -10000 0 -0.41 38 38
MED1 0.024 0.006 -10000 0 -10000 0 0
mol:9cRA -0.002 0.015 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.022 0.1 -10000 0 -0.22 68 68
RXRs/NUR77 0.008 0.1 -10000 0 -0.23 46 46
RXRs/PPAR -0.047 0.12 -10000 0 -0.24 87 87
NCOR2 0.025 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.027 -10000 0 -0.28 3 3
RARs/VDR/DNA/Vit D3 0.046 0.048 -10000 0 -0.2 11 11
RARA 0.024 0.006 -10000 0 -10000 0 0
NCOA1 0.025 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.039 -10000 0 -0.4 3 3
RARs/RARs/DNA/9cRA 0.031 0.044 -10000 0 -0.2 9 9
RARG 0.022 0.032 -10000 0 -0.4 2 2
RPS6KB1 0.021 0.079 0.59 6 -0.39 1 7
RARs/THRs/DNA/SMRT -0.022 0.1 -10000 0 -0.22 69 69
THRA 0.023 0.023 -10000 0 -0.4 1 1
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.027 -10000 0 -0.28 3 3
RXRs/PPAR/9cRA/PGJ2/DNA -0.003 0.1 -10000 0 -0.2 64 64
NR1H4 0.013 0.021 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.011 0.12 -10000 0 -0.22 63 63
NR1H2 0.02 0.023 -10000 0 -10000 0 0
NR1H3 0.02 0.025 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.008 0.095 -10000 0 -0.22 40 40
NR4A1 0.017 0.04 -10000 0 -0.4 2 2
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.022 0.081 -10000 0 -0.2 51 51
RXRG -0.044 0.14 -10000 0 -0.38 47 47
RXR alpha/CCPG 0.029 0.028 -10000 0 -0.29 1 1
RXRA 0.018 0.032 -10000 0 -0.4 1 1
RXRB 0.02 0.025 -10000 0 -10000 0 0
THRB -0.055 0.16 -10000 0 -0.4 65 65
PPARG -0.041 0.15 -10000 0 -0.4 50 50
PPARD 0.025 0.004 -10000 0 -10000 0 0
TNF -0.068 0.28 -10000 0 -0.83 36 36
mol:Oxysterols -0.001 0.014 -10000 0 -10000 0 0
cholesterol transport -0.022 0.15 -10000 0 -0.41 38 38
PPARA 0.023 0.007 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.014 0.06 -10000 0 -0.4 7 7
RXRs/NUR77/BCL2 -0.023 0.1 -10000 0 -0.27 44 44
SREBF1 -0.023 0.15 -10000 0 -0.42 32 32
RXRs/RXRs/DNA/9cRA -0.003 0.1 -10000 0 -0.2 64 64
ABCA1 -0.036 0.2 -10000 0 -0.56 33 33
RARs/THRs 0.012 0.12 -10000 0 -0.22 67 67
RXRs/FXR 0.005 0.1 -10000 0 -0.24 41 41
BCL2 0.007 0.083 -10000 0 -0.4 14 14
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.033 0.13 0.21 1 -0.42 27 28
CRKL -0.034 0.13 -10000 0 -0.44 28 28
HRAS -0.025 0.12 -10000 0 -0.4 26 26
mol:PIP3 -0.007 0.15 0.27 6 -0.41 28 34
SPRED1 0.024 0.006 -10000 0 -10000 0 0
SPRED2 0.025 0.005 -10000 0 -10000 0 0
GAB1 -0.033 0.14 -10000 0 -0.44 30 30
FOXO3 -0.018 0.14 0.31 2 -0.43 26 28
AKT1 -0.019 0.15 0.28 1 -0.46 28 29
BAD -0.017 0.14 0.27 1 -0.43 26 27
megakaryocyte differentiation -0.038 0.14 -10000 0 -0.43 32 32
GSK3B -0.015 0.14 0.29 3 -0.44 24 27
RAF1 -0.005 0.11 0.25 5 -0.32 25 30
SHC1 0.021 0.01 -10000 0 -10000 0 0
STAT3 -0.033 0.14 -10000 0 -0.46 28 28
STAT1 -0.078 0.3 -10000 0 -0.87 39 39
HRAS/SPRED1 0.002 0.12 -10000 0 -0.33 25 25
cell proliferation -0.032 0.14 -10000 0 -0.44 29 29
PIK3CA 0.023 0.007 -10000 0 -10000 0 0
TEC 0.018 0.055 -10000 0 -0.4 6 6
RPS6KB1 -0.029 0.16 -10000 0 -0.47 34 34
HRAS/SPRED2 0.002 0.12 -10000 0 -0.33 25 25
LYN/TEC/p62DOK 0.001 0.15 -10000 0 -0.47 24 24
MAPK3 0.003 0.097 0.24 11 -0.25 21 32
STAP1 -0.035 0.14 -10000 0 -0.45 29 29
GRAP2 0.002 0.089 -10000 0 -0.4 16 16
JAK2 -0.065 0.26 -10000 0 -0.75 39 39
STAT1 (dimer) -0.077 0.29 -10000 0 -0.85 39 39
mol:Gleevec 0.001 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.005 0.15 -10000 0 -0.45 28 28
actin filament polymerization -0.034 0.14 -10000 0 -0.44 29 29
LYN 0.02 0.039 -10000 0 -0.4 3 3
STAP1/STAT5A (dimer) -0.059 0.21 -10000 0 -0.62 36 36
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
CBL/CRKL/GRB2 -0.008 0.13 -10000 0 -0.42 25 25
PI3K -0.012 0.16 0.26 1 -0.47 32 33
PTEN 0.024 0.007 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.069 0.35 -10000 0 -1.2 29 29
MAPK8 -0.032 0.14 -10000 0 -0.45 29 29
STAT3 (dimer) -0.031 0.14 0.3 1 -0.44 28 29
positive regulation of transcription 0.005 0.085 0.22 11 -0.22 16 27
mol:GDP -0.019 0.13 -10000 0 -0.42 26 26
PIK3C2B -0.034 0.14 0.35 1 -0.44 28 29
CBL/CRKL -0.02 0.13 -10000 0 -0.42 27 27
FER -0.034 0.14 -10000 0 -0.45 30 30
SH2B3 -0.032 0.14 -10000 0 -0.45 28 28
PDPK1 -0.006 0.14 0.31 6 -0.38 26 32
SNAI2 -0.033 0.14 0.33 1 -0.44 28 29
positive regulation of cell proliferation -0.063 0.24 -10000 0 -0.69 40 40
KITLG -0.004 0.1 -10000 0 -0.42 18 18
cell motility -0.063 0.24 -10000 0 -0.69 40 40
PTPN6 0.023 0.039 -10000 0 -0.4 3 3
EPOR -0.026 0.21 -10000 0 -0.95 13 13
STAT5A (dimer) -0.054 0.21 -10000 0 -0.63 36 36
SOCS1 0.02 0.045 -10000 0 -0.4 4 4
cell migration 0.037 0.14 0.45 29 -10000 0 29
SOS1 0.025 0.004 -10000 0 -10000 0 0
EPO 0.012 0.029 -10000 0 -10000 0 0
VAV1 0.009 0.077 -10000 0 -0.34 15 15
GRB10 -0.038 0.14 -10000 0 -0.45 30 30
PTPN11 0.026 0.006 -10000 0 -10000 0 0
SCF/KIT -0.032 0.15 -10000 0 -0.46 31 31
GO:0007205 0.002 0.007 -10000 0 -10000 0 0
MAP2K1 0.001 0.098 0.26 9 -0.26 24 33
CBL 0.025 0.004 -10000 0 -10000 0 0
KIT -0.067 0.32 -10000 0 -1.1 26 26
MAP2K2 0.003 0.098 0.26 9 -0.26 23 32
SHC/Grb2/SOS1 -0.003 0.14 -10000 0 -0.44 26 26
STAT5A -0.055 0.22 -10000 0 -0.65 36 36
GRB2 0.024 0.006 -10000 0 -10000 0 0
response to radiation -0.032 0.14 0.33 1 -0.43 28 29
SHC/GRAP2 0.017 0.055 -10000 0 -0.28 10 10
PTPRO -0.039 0.14 -10000 0 -0.44 32 32
SH2B2 -0.035 0.14 -10000 0 -0.45 29 29
DOK1 0.025 0.004 -10000 0 -10000 0 0
MATK -0.038 0.14 -10000 0 -0.46 29 29
CREBBP 0.021 0.045 -10000 0 -0.17 3 3
BCL2 -0.063 0.3 -10000 0 -1 27 27
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.029 0.14 -10000 0 -0.24 105 105
SMAD6-7/SMURF1 0.046 0.022 -10000 0 -0.24 1 1
NOG -0.029 0.13 -10000 0 -0.4 39 39
SMAD9 -0.046 0.18 -10000 0 -0.53 40 40
SMAD4 0.025 0.005 -10000 0 -10000 0 0
SMAD5 -0.027 0.11 -10000 0 -0.38 19 19
BMP7/USAG1 -0.086 0.16 -10000 0 -0.32 101 101
SMAD5/SKI -0.019 0.12 0.29 1 -0.39 22 23
SMAD1 0.012 0.054 0.25 1 -0.38 3 4
BMP2 -0.015 0.11 -10000 0 -0.4 24 24
SMAD1/SMAD1/SMAD4 0.02 0.056 -10000 0 -0.3 2 2
BMPR1A 0.023 0.023 -10000 0 -0.4 1 1
BMPR1B -0.022 0.13 -10000 0 -0.4 38 38
BMPR1A-1B/BAMBI -0.01 0.12 -10000 0 -0.26 67 67
AHSG 0.017 0.019 -10000 0 -10000 0 0
CER1 0.017 0.014 -10000 0 -10000 0 0
BMP2-4/CER1 0.004 0.09 -10000 0 -0.27 28 28
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.03 0.12 -10000 0 -0.39 21 21
BMP2-4 (homodimer) -0.016 0.1 -10000 0 -0.32 31 31
RGMB 0.025 0.004 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.021 0.097 -10000 0 -0.23 45 45
RGMA -0.015 0.12 -10000 0 -0.4 32 32
SMURF1 0.025 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.033 0.12 -10000 0 -0.39 21 21
BMP2-4/USAG1 -0.033 0.14 -10000 0 -0.28 83 83
SMAD6/SMURF1/SMAD5 -0.02 0.12 -10000 0 -0.4 21 21
SOSTDC1 -0.063 0.16 -10000 0 -0.4 63 63
BMP7/BMPR2/BMPR1A-1B -0.012 0.13 -10000 0 -0.24 82 82
SKI 0.025 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.009 0.072 -10000 0 -0.4 10 10
HFE2 0.017 0.014 -10000 0 -10000 0 0
ZFYVE16 0.024 0.005 -10000 0 -10000 0 0
MAP3K7 0.025 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD 0.007 0.1 -10000 0 -0.27 42 42
SMAD5/SMAD5/SMAD4 -0.019 0.12 0.29 1 -0.39 21 22
MAPK1 0.025 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.016 0.11 -10000 0 -0.35 21 21
BMP7 (homodimer) -0.06 0.15 -10000 0 -0.4 54 54
NUP214 0.024 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.018 0.057 -10000 0 -0.29 10 10
SMAD1/SKI 0.02 0.066 0.25 1 -0.36 3 4
SMAD6 0.023 0.024 -10000 0 -0.4 1 1
CTDSP2 0.025 0.001 -10000 0 -10000 0 0
BMP2-4/FETUA 0.011 0.085 -10000 0 -0.26 26 26
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.023 0.12 -10000 0 -0.4 33 33
BMPR2 (homodimer) 0.025 0.004 -10000 0 -10000 0 0
GADD34/PP1CA 0.048 0.015 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0 0.097 -10000 0 -0.28 37 37
CHRDL1 -0.05 0.15 -10000 0 -0.4 50 50
ENDOFIN/SMAD1 0.02 0.066 0.25 1 -0.35 3 4
SMAD6-7/SMURF1/SMAD1 0.036 0.07 -10000 0 -0.35 2 2
SMAD6/SMURF1 0.025 0.004 -10000 0 -10000 0 0
BAMBI -0.024 0.12 -10000 0 -0.4 34 34
SMURF2 0.024 0.006 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.026 0.13 -10000 0 -0.27 76 76
BMP2-4/GREM1 -0.01 0.12 -10000 0 -0.27 60 60
SMAD7 0.024 0.006 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.04 0.18 -10000 0 -0.5 44 44
SMAD1/SMAD6 0.017 0.067 0.25 1 -0.36 3 4
TAK1/SMAD6 0.037 0.007 -10000 0 -10000 0 0
BMP7 -0.06 0.15 -10000 0 -0.4 54 54
BMP6 0.009 0.073 -10000 0 -0.4 10 10
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.027 0.11 -10000 0 -0.38 21 21
PPM1A 0.025 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.021 0.065 0.25 1 -0.35 3 4
SMAD7/SMURF1 0.035 0.01 -10000 0 -10000 0 0
CTDSPL 0.023 0.023 -10000 0 -0.4 1 1
PPP1CA 0.025 0.004 -10000 0 -10000 0 0
XIAP 0.025 0.001 -10000 0 -10000 0 0
CTDSP1 0.025 0.005 -10000 0 -10000 0 0
PPP1R15A 0.024 0.009 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.055 0.14 -10000 0 -0.43 29 29
CHRD -0.003 0.099 -10000 0 -0.4 20 20
BMPR2 0.025 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.038 0.12 -10000 0 -0.39 23 23
BMP4 -0.005 0.081 -10000 0 -0.4 11 11
FST -0.03 0.12 -10000 0 -0.4 32 32
BMP2-4/NOG -0.015 0.13 -10000 0 -0.28 62 62
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.003 0.12 -10000 0 -0.22 81 81
Nectin adhesion pathway

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
PDGFRB 0.021 0.034 -10000 0 -0.4 2 2
alphaV beta3 Integrin 0.006 0.08 -10000 0 -0.28 23 23
PTK2 -0.028 0.14 -10000 0 -0.4 35 35
positive regulation of JNK cascade -0.009 0.11 -10000 0 -0.3 38 38
CDC42/GDP -0.007 0.16 -10000 0 -0.4 41 41
Rac1/GDP -0.009 0.15 -10000 0 -0.4 42 42
RAP1B 0.025 0.002 -10000 0 -10000 0 0
RAP1A 0.025 0.001 -10000 0 -10000 0 0
CTNNB1 0.023 0.023 -10000 0 -0.4 1 1
CDC42/GTP -0.007 0.14 -10000 0 -0.36 38 38
nectin-3/I-afadin 0.003 0.096 -10000 0 -0.28 35 35
RAPGEF1 -0.019 0.14 -10000 0 -0.42 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.028 0.16 -10000 0 -0.46 41 41
PDGFB-D/PDGFRB 0.021 0.034 -10000 0 -0.4 2 2
TLN1 -0.036 0.095 -10000 0 -0.23 58 58
Rap1/GTP -0.014 0.11 -10000 0 -0.3 41 41
IQGAP1 0.025 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.01 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.003 0.096 -10000 0 -0.28 35 35
PVR 0.025 0.004 -10000 0 -10000 0 0
Necl-5(dimer) 0.025 0.004 -10000 0 -10000 0 0
mol:GDP -0.027 0.18 -10000 0 -0.49 42 42
MLLT4 0.025 0.004 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.033 0.097 -10000 0 -0.23 40 40
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.035 0.02 -10000 0 -0.28 1 1
positive regulation of lamellipodium assembly -0.017 0.13 -10000 0 -0.33 42 42
PVRL1 0.023 0.024 -10000 0 -0.4 1 1
PVRL3 -0.019 0.13 -10000 0 -0.4 35 35
PVRL2 0.025 0.005 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
CDH1 0.017 0.05 -10000 0 -0.4 5 5
CLDN1 -0.012 0.11 -10000 0 -0.4 27 27
JAM-A/CLDN1 0.009 0.1 -10000 0 -0.24 45 45
SRC -0.035 0.18 -10000 0 -0.5 44 44
ITGB3 -0.008 0.096 -10000 0 -0.4 18 18
nectin-1(dimer)/I-afadin/I-afadin 0.035 0.02 -10000 0 -0.28 1 1
FARP2 -0.021 0.18 -10000 0 -0.48 39 39
RAC1 0.025 0.005 -10000 0 -10000 0 0
CTNNA1 0.025 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.02 0.086 -10000 0 -0.24 35 35
nectin-1/I-afadin 0.035 0.02 -10000 0 -0.28 1 1
nectin-2/I-afadin 0.036 0.009 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.032 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.019 0.088 -10000 0 -0.24 36 36
CDC42/GTP/IQGAP1/filamentous actin 0.033 0.008 -10000 0 -10000 0 0
F11R 0.018 0.04 -10000 0 -0.4 3 3
positive regulation of filopodium formation -0.009 0.11 -10000 0 -0.3 38 38
alphaV/beta3 Integrin/Talin -0.025 0.12 0.24 3 -0.28 54 57
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.009 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.036 0.009 -10000 0 -10000 0 0
PIP5K1C -0.035 0.1 -10000 0 -0.24 60 60
VAV2 -0.039 0.21 -10000 0 -0.53 43 43
RAP1/GDP -0.002 0.14 -10000 0 -0.37 43 43
ITGAV 0.02 0.045 -10000 0 -0.4 4 4
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.019 0.086 -10000 0 -0.24 35 35
nectin-3(dimer)/I-afadin/I-afadin 0.003 0.096 -10000 0 -0.28 35 35
Rac1/GTP -0.018 0.16 -10000 0 -0.4 42 42
PTPRM -0.036 0.12 -10000 0 -0.26 63 63
E-cadherin/beta catenin/alpha catenin 0.058 0.048 -10000 0 -0.23 6 6
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.025 0.005 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN -0.017 0.14 0.28 7 -0.37 29 36
IKBKB -0.006 0.087 0.26 6 -0.28 14 20
AKT1 -0.021 0.098 0.26 12 -0.24 18 30
IKBKG -0.007 0.082 0.22 6 -0.29 12 18
CALM1 -0.028 0.12 0.21 4 -0.4 23 27
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
MAP3K1 -0.04 0.2 0.3 6 -0.51 40 46
MAP3K7 0.025 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.031 0.13 0.22 4 -0.43 23 27
DOK1 0.025 0.004 -10000 0 -10000 0 0
AP-1 -0.007 0.087 0.25 7 -0.24 19 26
LYN 0.02 0.039 -10000 0 -0.4 3 3
BLNK 0.013 0.067 -10000 0 -0.4 9 9
SHC1 0.021 0.01 -10000 0 -10000 0 0
BCR complex -0.021 0.11 -10000 0 -0.3 43 43
CD22 -0.055 0.15 -10000 0 -0.41 40 40
CAMK2G -0.021 0.12 0.24 10 -0.38 20 30
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
INPP5D 0.014 0.067 -10000 0 -0.4 9 9
SHC/GRB2/SOS1 -0.014 0.076 -10000 0 -0.22 34 34
GO:0007205 -0.032 0.13 0.22 4 -0.44 24 28
SYK 0.015 0.059 -10000 0 -0.4 7 7
ELK1 -0.032 0.13 0.24 6 -0.41 25 31
NFATC1 -0.038 0.16 0.24 8 -0.43 35 43
B-cell antigen/BCR complex -0.021 0.11 -10000 0 -0.3 43 43
PAG1/CSK 0.029 0.04 -10000 0 -0.28 5 5
NFKBIB 0.012 0.042 0.13 7 -0.13 14 21
HRAS -0.022 0.12 0.25 6 -0.37 23 29
NFKBIA 0.012 0.041 0.13 7 -0.12 14 21
NF-kappa-B/RelA/I kappa B beta 0.017 0.036 0.13 7 -10000 0 7
RasGAP/Csk 0.018 0.097 -10000 0 -0.23 37 37
mol:GDP -0.032 0.13 0.22 4 -0.42 25 29
PTEN 0.024 0.007 -10000 0 -10000 0 0
CD79B 0.003 0.082 -10000 0 -0.4 13 13
NF-kappa-B/RelA/I kappa B alpha 0.017 0.036 0.13 7 -10000 0 7
GRB2 0.024 0.006 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.057 0.19 0.27 2 -0.5 41 43
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:IP3 -0.03 0.13 0.22 3 -0.45 23 26
CSK 0.024 0.005 -10000 0 -10000 0 0
FOS -0.033 0.12 0.29 4 -0.4 25 29
CHUK -0.012 0.096 0.22 5 -0.33 18 23
IBTK 0.024 0.023 -10000 0 -0.4 1 1
CARD11/BCL10/MALT1/TAK1 -0.014 0.12 0.22 1 -0.36 25 26
PTPN6 -0.053 0.15 -10000 0 -0.46 29 29
RELA 0.025 0.003 -10000 0 -10000 0 0
BCL2A1 0.011 0.028 0.11 2 -0.11 1 3
VAV2 -0.044 0.18 -10000 0 -0.52 32 32
ubiquitin-dependent protein catabolic process 0.015 0.041 0.13 7 -0.12 14 21
BTK -0.017 0.2 -10000 0 -0.98 15 15
CD19 -0.048 0.14 -10000 0 -0.47 28 28
MAP4K1 0.016 0.052 -10000 0 -0.4 5 5
CD72 0.021 0.035 -10000 0 -0.4 2 2
PAG1 0.017 0.051 -10000 0 -0.4 5 5
MAPK14 -0.029 0.17 0.28 7 -0.44 37 44
SH3BP5 0.01 0.077 -10000 0 -0.4 12 12
PIK3AP1 -0.028 0.13 0.21 5 -0.43 25 30
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.039 0.17 0.21 1 -0.4 48 49
RAF1 -0.019 0.12 0.23 8 -0.36 22 30
RasGAP/p62DOK/SHIP 0.019 0.11 -10000 0 -0.24 41 41
CD79A -0.032 0.13 -10000 0 -0.4 34 34
re-entry into mitotic cell cycle -0.008 0.087 0.25 7 -0.24 19 26
RASA1 0.025 0.005 -10000 0 -10000 0 0
MAPK3 -0.015 0.1 0.26 6 -0.32 18 24
MAPK1 -0.016 0.097 0.26 3 -0.31 19 22
CD72/SHP1 -0.03 0.16 0.27 5 -0.45 27 32
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.028 0.17 0.28 11 -0.44 38 49
actin cytoskeleton organization -0.034 0.16 0.32 5 -0.45 32 37
NF-kappa-B/RelA 0.035 0.07 0.24 7 -0.19 4 11
Calcineurin -0.007 0.12 -10000 0 -0.35 21 21
PI3K -0.063 0.14 -10000 0 -0.37 41 41
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.022 0.14 0.2 4 -0.44 25 29
SOS1 0.025 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.067 0.29 -10000 0 -0.78 44 44
DAPP1 -0.09 0.32 -10000 0 -0.88 44 44
cytokine secretion -0.034 0.15 0.24 8 -0.4 35 43
mol:DAG -0.03 0.13 0.22 3 -0.45 23 26
PLCG2 0.019 0.035 -10000 0 -0.4 2 2
MAP2K1 -0.017 0.11 0.23 6 -0.33 21 27
B-cell antigen/BCR complex/FcgammaRIIB 0.001 0.1 -10000 0 -0.27 38 38
mol:PI-3-4-5-P3 -0.046 0.1 -10000 0 -0.28 33 33
ETS1 -0.019 0.11 0.23 9 -0.35 21 30
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.014 0.11 -10000 0 -0.23 49 49
B-cell antigen/BCR complex/LYN -0.03 0.14 -10000 0 -0.37 38 38
MALT1 0.023 0.011 -10000 0 -10000 0 0
TRAF6 0.025 0.005 -10000 0 -10000 0 0
RAC1 -0.04 0.17 0.31 2 -0.48 32 34
B-cell antigen/BCR complex/LYN/SYK -0.033 0.16 -10000 0 -0.41 34 34
CARD11 -0.04 0.14 0.26 5 -0.43 27 32
FCGR2B 0.009 0.067 -10000 0 -0.4 9 9
PPP3CA 0.02 0.045 -10000 0 -0.4 4 4
BCL10 0.025 0.002 -10000 0 -10000 0 0
IKK complex 0.009 0.05 0.16 13 -0.12 9 22
PTPRC 0.001 0.086 -10000 0 -0.4 15 15
PDPK1 -0.024 0.088 0.23 12 -0.21 22 34
PPP3CB 0.024 0.006 -10000 0 -10000 0 0
PPP3CC 0.015 0.055 -10000 0 -0.4 6 6
POU2F2 0.012 0.03 0.15 4 -10000 0 4
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.016 0.12 -10000 0 -0.36 21 21
TBX21 -0.12 0.4 -10000 0 -1.1 40 40
B2M 0.018 0.042 -10000 0 -0.4 3 3
TYK2 0.014 0.032 -10000 0 -10000 0 0
IL12RB1 -0.003 0.087 -10000 0 -0.43 12 12
GADD45B -0.097 0.34 -10000 0 -0.98 34 34
IL12RB2 -0.002 0.08 -10000 0 -0.36 12 12
GADD45G -0.096 0.34 -10000 0 -1.1 26 26
natural killer cell activation -0.002 0.019 -10000 0 -10000 0 0
RELB 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.003 -10000 0 -10000 0 0
IL18 0.007 0.082 -10000 0 -0.41 13 13
IL2RA 0.004 0.086 -10000 0 -0.4 15 15
IFNG 0.002 0.08 -10000 0 -0.4 12 12
STAT3 (dimer) -0.094 0.31 -10000 0 -0.78 44 44
HLA-DRB5 -0.02 0.12 -10000 0 -0.4 33 33
FASLG -0.11 0.43 0.5 1 -1.1 44 45
NF kappa B2 p52/RelB -0.099 0.36 -10000 0 -0.92 44 44
CD4 0.013 0.071 -10000 0 -0.4 10 10
SOCS1 0.02 0.045 -10000 0 -0.4 4 4
EntrezGene:6955 -0.001 0.009 -10000 0 -10000 0 0
CD3D -0.014 0.12 -10000 0 -0.41 27 27
CD3E -0.013 0.11 -10000 0 -0.41 26 26
CD3G -0.004 0.096 -10000 0 -0.41 18 18
IL12Rbeta2/JAK2 0.006 0.087 -10000 0 -0.3 19 19
CCL3 -0.12 0.38 -10000 0 -1.1 40 40
CCL4 -0.12 0.39 -10000 0 -1.1 39 39
HLA-A 0.013 0.065 -10000 0 -0.4 8 8
IL18/IL18R 0.017 0.12 -10000 0 -0.3 41 41
NOS2 -0.14 0.42 -10000 0 -1.1 48 48
IL12/IL12R/TYK2/JAK2/SPHK2 -0.015 0.11 -10000 0 -0.32 21 21
IL1R1 -0.12 0.38 -10000 0 -1 44 44
IL4 0.005 0.032 -10000 0 -10000 0 0
JAK2 0.004 0.075 -10000 0 -0.42 9 9
EntrezGene:6957 -0.001 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.088 0.28 -10000 0 -0.78 42 42
RAB7A -0.07 0.28 0.45 1 -0.83 27 28
lysosomal transport -0.064 0.27 0.44 1 -0.77 28 29
FOS -0.074 0.31 -10000 0 -0.84 38 38
STAT4 (dimer) -0.076 0.34 -10000 0 -0.88 39 39
STAT5A (dimer) -0.11 0.37 -10000 0 -0.91 47 47
GZMA -0.14 0.44 -10000 0 -1.2 44 44
GZMB -0.16 0.45 -10000 0 -1.2 51 51
HLX 0.021 0.011 -10000 0 -10000 0 0
LCK -0.13 0.41 -10000 0 -1 47 47
TCR/CD3/MHC II/CD4 -0.057 0.24 -10000 0 -0.59 42 42
IL2/IL2R 0.021 0.1 -10000 0 -0.29 30 30
MAPK14 -0.099 0.35 -10000 0 -0.97 36 36
CCR5 -0.11 0.38 -10000 0 -1.2 29 29
IL1B -0.004 0.091 -10000 0 -0.4 15 15
STAT6 -0.011 0.11 -10000 0 -0.3 13 13
STAT4 0.014 0.064 -10000 0 -0.4 8 8
STAT3 0.024 0.006 -10000 0 -10000 0 0
STAT1 0.025 0.009 -10000 0 -10000 0 0
NFKB1 0.025 0.004 -10000 0 -10000 0 0
NFKB2 0.024 0.006 -10000 0 -10000 0 0
IL12B 0.011 0.035 -10000 0 -10000 0 0
CD8A -0.013 0.11 -10000 0 -0.4 25 25
CD8B -0.016 0.11 -10000 0 -0.39 24 24
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.016 0.12 0.35 22 -10000 0 22
IL2RB 0.006 0.081 -10000 0 -0.4 13 13
proteasomal ubiquitin-dependent protein catabolic process -0.064 0.3 0.37 1 -0.79 39 40
IL2RG 0.008 0.078 -10000 0 -0.4 12 12
IL12 0.002 0.085 -10000 0 -0.29 19 19
STAT5A 0.024 0.006 -10000 0 -10000 0 0
CD247 0.001 0.081 -10000 0 -0.4 13 13
IL2 0.015 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.016 0.1 -10000 0 -0.41 19 19
IL12/IL12R/TYK2/JAK2 -0.14 0.47 -10000 0 -1.1 46 46
MAP2K3 -0.1 0.36 -10000 0 -1 35 35
RIPK2 0.023 0.009 -10000 0 -10000 0 0
MAP2K6 -0.1 0.36 -10000 0 -1 35 35
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0 0.099 -10000 0 -0.4 20 20
IL18RAP -0.005 0.1 -10000 0 -0.41 20 20
IL12Rbeta1/TYK2 0.012 0.071 -10000 0 -0.32 10 10
EOMES -0.049 0.25 -10000 0 -1 21 21
STAT1 (dimer) -0.088 0.3 -10000 0 -0.74 46 46
T cell proliferation -0.05 0.25 0.33 2 -0.65 35 37
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.003 0.091 -10000 0 -0.41 16 16
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.068 0.27 -10000 0 -0.68 41 41
ATF2 -0.088 0.32 -10000 0 -0.88 35 35
Osteopontin-mediated events

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
IKK alpha homodimer 0.001 0.079 0.19 3 -0.22 33 36
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.098 0.32 4 -0.32 9 13
alphaV/beta3 Integrin/Osteopontin/Src 0.016 0.077 -10000 0 -0.28 21 21
AP1 0.006 0.12 -10000 0 -0.32 21 21
ILK -0.013 0.08 0.19 4 -0.23 35 39
bone resorption -0.01 0.09 0.28 1 -0.28 13 14
PTK2B 0.021 0.024 -10000 0 -0.4 1 1
PYK2/p130Cas 0.019 0.093 -10000 0 -0.21 43 43
ITGAV 0.021 0.046 -10000 0 -0.4 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.026 0.056 -10000 0 -0.28 11 11
alphaV/beta3 Integrin/Osteopontin 0.018 0.097 -10000 0 -0.25 38 38
MAP3K1 -0.013 0.082 0.18 5 -0.23 38 43
JUN 0.023 0.024 -10000 0 -0.4 1 1
MAPK3 -0.018 0.077 0.19 4 -0.22 38 42
MAPK1 -0.017 0.077 0.19 5 -0.22 39 44
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.021 0.074 0.18 4 -0.22 36 40
ITGB3 -0.007 0.096 -10000 0 -0.4 18 18
NFKBIA -0.015 0.08 0.22 3 -0.33 10 13
FOS 0.013 0.055 -10000 0 -0.4 5 5
CD44 0.01 0.077 -10000 0 -0.4 12 12
CHUK 0.024 0.006 -10000 0 -10000 0 0
PLAU -0.025 0.16 0.43 2 -0.92 8 10
NF kappa B1 p50/RelA 0.022 0.091 0.3 1 -0.39 6 7
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
RELA 0.025 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.009 0.081 -10000 0 -0.28 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.017 0.086 0.18 5 -0.23 44 49
VAV3 -0.037 0.098 0.21 6 -0.23 64 70
MAP3K14 -0.012 0.082 0.19 4 -0.22 39 43
ROCK2 0.025 0.005 -10000 0 -10000 0 0
SPP1 0.001 0.092 -10000 0 -0.38 18 18
RAC1 0.025 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.023 0.094 0.21 4 -0.22 58 62
MMP2 -0.031 0.12 0.31 2 -0.42 21 23
Glypican 2 network

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
MDK 0.014 0.067 -9999 0 -0.4 9 9
GPC2 -0.003 0.099 -9999 0 -0.4 20 20
GPC2/Midkine 0.007 0.091 -9999 0 -0.3 27 27
neuron projection morphogenesis 0.007 0.091 -9999 0 -0.3 27 27
Syndecan-4-mediated signaling events

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
PTK2 0.002 0.094 -10000 0 -0.48 10 10
Syndecan-4/Syndesmos -0.027 0.16 0.29 3 -0.44 35 38
positive regulation of JNK cascade -0.026 0.16 0.29 2 -0.42 35 37
Syndecan-4/ADAM12 -0.028 0.16 0.28 2 -0.44 34 36
CCL5 0.003 0.082 -10000 0 -0.4 13 13
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
DNM2 0.024 0.006 -10000 0 -10000 0 0
ITGA5 0.024 0.023 -10000 0 -0.4 1 1
SDCBP 0.024 0.007 -10000 0 -10000 0 0
PLG -0.013 0.094 -10000 0 -0.38 18 18
ADAM12 0.014 0.057 -10000 0 -0.4 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.025 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.015 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.067 0.18 0.29 3 -0.44 44 47
Syndecan-4/CXCL12/CXCR4 -0.026 0.17 0.3 2 -0.44 35 37
Syndecan-4/Laminin alpha3 -0.038 0.17 0.29 3 -0.45 39 42
MDK 0.014 0.067 -10000 0 -0.4 9 9
Syndecan-4/FZD7 -0.045 0.16 0.28 2 -0.44 36 38
Syndecan-4/Midkine -0.032 0.16 0.3 2 -0.44 34 36
FZD7 -0.018 0.12 -10000 0 -0.4 31 31
Syndecan-4/FGFR1/FGF -0.024 0.16 -10000 0 -0.43 33 33
THBS1 0.012 0.065 -10000 0 -0.4 8 8
integrin-mediated signaling pathway -0.037 0.16 0.28 1 -0.44 36 37
positive regulation of MAPKKK cascade -0.026 0.16 0.29 2 -0.42 35 37
Syndecan-4/TACI -0.031 0.16 0.3 2 -0.44 36 38
CXCR4 0.022 0.039 -10000 0 -0.4 3 3
cell adhesion 0.007 0.05 0.18 6 -0.22 8 14
Syndecan-4/Dynamin -0.028 0.16 0.3 2 -0.44 34 36
Syndecan-4/TSP1 -0.033 0.16 0.3 2 -0.45 37 39
Syndecan-4/GIPC -0.027 0.16 0.3 2 -0.43 35 37
Syndecan-4/RANTES -0.035 0.17 0.28 2 -0.44 38 40
ITGB1 0.024 0.005 -10000 0 -10000 0 0
LAMA1 -0.071 0.17 -10000 0 -0.4 76 76
LAMA3 -0.001 0.1 -10000 0 -0.4 21 21
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCA 0 0.12 0.75 6 -0.36 13 19
Syndecan-4/alpha-Actinin -0.027 0.16 0.3 2 -0.43 36 38
TFPI 0.007 0.074 -10000 0 -0.4 10 10
F2 0.008 0.034 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.035 0.02 -10000 0 -0.28 1 1
positive regulation of cell adhesion -0.079 0.17 0.27 2 -0.44 48 50
ACTN1 0.025 0.004 -10000 0 -10000 0 0
TNC -0.001 0.096 -10000 0 -0.4 19 19
Syndecan-4/CXCL12 -0.035 0.16 0.29 3 -0.46 33 36
FGF6 0.015 0.008 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CXCL12 -0.002 0.099 -10000 0 -0.4 20 20
TNFRSF13B 0.01 0.043 -10000 0 -0.4 2 2
FGF2 0.003 0.087 -10000 0 -0.4 15 15
FGFR1 0.017 0.051 -10000 0 -0.4 5 5
Syndecan-4/PI-4-5-P2 -0.045 0.15 -10000 0 -0.43 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.01 0.059 -10000 0 -0.35 7 7
cell migration -0.014 0.012 -10000 0 -10000 0 0
PRKCD 0.021 0.034 -10000 0 -0.29 3 3
vasculogenesis -0.032 0.16 0.3 2 -0.43 37 39
SDC4 -0.04 0.16 -10000 0 -0.45 35 35
Syndecan-4/Tenascin C -0.039 0.17 0.28 1 -0.46 36 37
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.012 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.027 0.15 0.3 2 -0.43 34 36
MMP9 -0.022 0.12 -10000 0 -0.39 33 33
Rac1/GTP 0.007 0.051 0.18 6 -0.24 7 13
cytoskeleton organization -0.025 0.15 0.29 3 -0.42 35 38
GIPC1 0.024 0.006 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.033 0.17 0.28 2 -0.44 38 40
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.051 0.26 -10000 0 -0.78 35 35
NCK1/PAK1/Dok-R -0.051 0.12 -10000 0 -0.38 34 34
NCK1/Dok-R -0.045 0.27 -10000 0 -0.87 33 33
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
mol:beta2-estradiol 0.012 0.059 0.23 24 -10000 0 24
RELA 0.025 0.003 -10000 0 -10000 0 0
SHC1 0.021 0.01 -10000 0 -10000 0 0
Rac/GDP 0.018 0.004 -10000 0 -10000 0 0
F2 0.015 0.072 0.26 23 -10000 0 23
TNIP2 0.025 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.028 0.26 -10000 0 -0.84 33 33
FN1 0.012 0.059 -10000 0 -0.4 6 6
PLD2 -0.067 0.27 -10000 0 -0.91 33 33
PTPN11 0.025 0.003 -10000 0 -10000 0 0
GRB14 -0.044 0.15 -10000 0 -0.4 50 50
ELK1 -0.059 0.25 -10000 0 -0.85 33 33
GRB7 0.019 0.04 -10000 0 -0.4 3 3
PAK1 0.025 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.035 0.27 -10000 0 -0.87 33 33
CDKN1A -0.042 0.23 -10000 0 -0.73 25 25
ITGA5 0.024 0.023 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.045 0.27 -10000 0 -0.88 33 33
CRK 0.024 0.006 -10000 0 -10000 0 0
mol:NO -0.033 0.2 -10000 0 -0.59 35 35
PLG -0.08 0.27 -10000 0 -0.92 33 33
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.053 0.24 -10000 0 -0.75 34 34
GRB2 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
ANGPT2 -0.034 0.19 -10000 0 -0.89 9 9
BMX -0.079 0.28 -10000 0 -0.93 33 33
ANGPT1 -0.073 0.28 -10000 0 -1.1 24 24
tube development -0.038 0.21 -10000 0 -0.61 34 34
ANGPT4 0.014 0.023 -10000 0 -10000 0 0
response to hypoxia -0.007 0.019 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.083 0.29 -10000 0 -0.95 33 33
alpha5/beta1 Integrin 0.035 0.02 -10000 0 -0.28 1 1
FGF2 0.003 0.087 -10000 0 -0.4 15 15
STAT5A (dimer) -0.041 0.25 -10000 0 -0.71 36 36
mol:L-citrulline -0.033 0.2 -10000 0 -0.59 35 35
AGTR1 0.019 0.017 -10000 0 -10000 0 0
MAPK14 -0.059 0.28 -10000 0 -0.92 34 34
Tie2/SHP2 -0.013 0.18 -10000 0 -0.92 11 11
TEK -0.018 0.19 -10000 0 -1 11 11
RPS6KB1 -0.044 0.24 -10000 0 -0.75 34 34
Angiotensin II/AT1 0.015 0.014 -10000 0 -10000 0 0
Tie2/Ang1/GRB2 -0.055 0.28 -10000 0 -0.92 33 33
MAPK3 -0.062 0.26 -10000 0 -0.86 33 33
MAPK1 -0.064 0.26 -10000 0 -0.86 33 33
Tie2/Ang1/GRB7 -0.056 0.28 -10000 0 -0.92 33 33
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.068 0.27 -10000 0 -0.91 33 33
PI3K -0.06 0.28 -10000 0 -0.88 34 34
FES -0.068 0.29 -10000 0 -0.92 34 34
Crk/Dok-R -0.045 0.27 -10000 0 -0.87 33 33
Tie2/Ang1/ABIN2 -0.055 0.28 -10000 0 -0.93 33 33
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.044 0.23 -10000 0 -0.7 35 35
STAT5A 0.024 0.006 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.038 0.25 -10000 0 -0.75 33 33
Tie2/Ang2 -0.058 0.27 -10000 0 -0.84 30 30
Tie2/Ang1 -0.067 0.29 -10000 0 -0.96 33 33
FOXO1 -0.044 0.24 -10000 0 -0.7 38 38
ELF1 0.022 0.026 -10000 0 -10000 0 0
ELF2 -0.064 0.27 -10000 0 -0.9 33 33
mol:Choline -0.064 0.26 -10000 0 -0.88 33 33
cell migration -0.022 0.07 -10000 0 -0.22 35 35
FYN -0.047 0.24 -10000 0 -0.7 31 31
DOK2 0.018 0.041 -10000 0 -0.4 3 3
negative regulation of cell cycle -0.035 0.21 -10000 0 -0.65 25 25
ETS1 0.01 0.066 -10000 0 -0.24 23 23
PXN -0.028 0.21 0.4 2 -0.63 33 35
ITGB1 0.024 0.005 -10000 0 -10000 0 0
NOS3 -0.04 0.22 -10000 0 -0.66 35 35
RAC1 0.025 0.005 -10000 0 -10000 0 0
TNF -0.032 0.13 -10000 0 -0.33 51 51
MAPKKK cascade -0.064 0.26 -10000 0 -0.88 33 33
RASA1 0.025 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.059 0.28 -10000 0 -0.91 33 33
NCK1 0.025 0.005 -10000 0 -10000 0 0
vasculogenesis -0.027 0.18 -10000 0 -0.53 35 35
mol:Phosphatidic acid -0.064 0.26 -10000 0 -0.88 33 33
mol:Angiotensin II 0 0.004 -10000 0 -10000 0 0
mol:NADP -0.033 0.2 -10000 0 -0.59 35 35
Rac1/GTP -0.038 0.23 -10000 0 -0.71 34 34
MMP2 -0.077 0.28 -10000 0 -0.93 33 33
Caspase cascade in apoptosis

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
TOP1 -0.013 0.11 0.26 1 -0.38 21 22
ACTA1 -0.016 0.12 0.21 9 -0.3 34 43
NUMA1 -0.013 0.11 0.26 1 -0.36 22 23
SPTAN1 -0.025 0.12 0.19 4 -0.33 31 35
LIMK1 -0.023 0.12 0.3 4 -0.32 31 35
BIRC3 -0.01 0.11 -10000 0 -0.4 26 26
BIRC2 0.023 0.032 -10000 0 -0.4 2 2
BAX 0.025 0.004 -10000 0 -10000 0 0
CASP10 -0.043 0.091 -10000 0 -0.28 40 40
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.025 0.001 -10000 0 -10000 0 0
PTK2 -0.017 0.12 0.26 1 -0.39 22 23
DIABLO 0.025 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.025 0.11 0.19 5 -0.32 31 36
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.025 0.003 -10000 0 -10000 0 0
GSN -0.026 0.12 0.19 4 -0.34 31 35
MADD 0.025 0.005 -10000 0 -10000 0 0
TFAP2A -0.076 0.23 -10000 0 -0.55 63 63
BID -0.018 0.067 -10000 0 -0.2 37 37
MAP3K1 -0.011 0.094 -10000 0 -0.41 14 14
TRADD 0.023 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.008 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.024 0.12 0.24 4 -0.32 31 35
CASP9 0.025 0.005 -10000 0 -10000 0 0
DNA repair -0.014 0.054 0.29 2 -0.17 12 14
neuron apoptosis 0.011 0.086 -10000 0 -1.1 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.019 0.12 0.25 1 -0.32 36 37
APAF1 0.025 0.003 -10000 0 -10000 0 0
CASP6 -0.022 0.17 -10000 0 -0.82 12 12
TRAF2 0.024 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.025 0.11 0.23 1 -0.34 27 28
CASP7 0.019 0.079 0.26 22 -0.25 9 31
KRT18 0.008 0.06 -10000 0 -0.67 2 2
apoptosis -0.015 0.14 0.44 11 -0.4 20 31
DFFA -0.023 0.12 0.19 4 -0.33 30 34
DFFB -0.025 0.12 0.19 4 -0.33 31 35
PARP1 0.014 0.054 0.18 12 -0.3 2 14
actin filament polymerization 0.021 0.11 0.32 28 -0.28 7 35
TNF -0.017 0.11 -10000 0 -0.4 27 27
CYCS -0.009 0.064 0.21 3 -0.21 17 20
SATB1 -0.032 0.17 -10000 0 -0.8 12 12
SLK -0.02 0.13 0.31 12 -0.33 32 44
p15 BID/BAX -0.003 0.073 0.21 1 -0.25 16 17
CASP2 -0.009 0.085 0.2 4 -0.32 15 19
JNK cascade 0.011 0.093 0.41 14 -10000 0 14
CASP3 -0.025 0.12 0.2 5 -0.33 34 39
LMNB2 -0.029 0.16 0.22 2 -0.45 32 34
RIPK1 0.025 0.004 -10000 0 -10000 0 0
CASP4 0.019 0.05 -10000 0 -0.4 5 5
Mammalian IAPs/DIABLO 0.042 0.077 -10000 0 -0.23 26 26
negative regulation of DNA binding -0.074 0.23 -10000 0 -0.54 63 63
stress fiber formation -0.019 0.12 0.3 12 -0.32 31 43
GZMB -0.031 0.11 -10000 0 -0.34 36 36
CASP1 0.002 0.06 -10000 0 -0.31 12 12
LMNB1 -0.014 0.13 0.22 2 -0.5 16 18
APP 0.011 0.088 -10000 0 -1.1 2 2
TNFRSF1A 0.024 0.023 -10000 0 -0.4 1 1
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.006 0.015 -10000 0 -0.28 1 1
VIM -0.019 0.13 0.33 8 -0.39 22 30
LMNA -0.011 0.095 0.21 1 -0.38 13 14
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.087 -10000 0 -0.35 14 14
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.023 0.12 0.19 7 -0.32 31 38
APAF-1/Caspase 9 0.007 0.11 0.37 1 -0.65 9 10
nuclear fragmentation during apoptosis -0.013 0.11 0.26 1 -0.35 22 23
CFL2 -0.021 0.11 0.28 7 -0.32 28 35
GAS2 -0.041 0.13 -10000 0 -0.34 39 39
positive regulation of apoptosis -0.018 0.13 0.21 2 -0.48 18 20
PRF1 0.003 0.085 -10000 0 -0.4 14 14
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.025 0.005 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.009 0.07 -10000 0 -0.23 17 17
NT3 (dimer)/TRKC -0.023 0.12 -10000 0 -0.32 46 46
NT3 (dimer)/TRKB -0.013 0.13 -10000 0 -0.28 60 60
SHC/Grb2/SOS1/GAB1/PI3K 0.015 0.035 -10000 0 -0.2 6 6
RAPGEF1 0.024 0.007 -10000 0 -10000 0 0
BDNF -0.018 0.11 -10000 0 -0.4 25 25
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
DYNLT1 0.025 0.004 -10000 0 -10000 0 0
NTRK1 -0.005 0.092 -10000 0 -0.4 17 17
NTRK2 -0.016 0.11 -10000 0 -0.4 25 25
NTRK3 -0.022 0.12 -10000 0 -0.4 32 32
NT-4/5 (dimer)/TRKB -0.022 0.12 -10000 0 -0.27 68 68
neuron apoptosis 0.057 0.18 0.41 51 -0.23 1 52
SHC 2-3/Grb2 -0.063 0.19 0.24 1 -0.45 51 52
SHC1 0.021 0.01 -10000 0 -10000 0 0
SHC2 -0.062 0.18 0.23 1 -0.48 43 44
SHC3 -0.078 0.21 0.23 1 -0.51 53 54
STAT3 (dimer) 0.017 0.062 -10000 0 -0.31 12 12
NT3 (dimer)/TRKA -0.006 0.11 -10000 0 -0.28 46 46
RIN/GDP 0.009 0.096 0.21 11 -0.23 20 31
GIPC1 0.024 0.006 -10000 0 -10000 0 0
KRAS 0.025 0.004 -10000 0 -10000 0 0
DNAJA3 -0.034 0.11 0.2 5 -0.27 49 54
RIN/GTP 0.012 0.004 -10000 0 -10000 0 0
CCND1 -0.007 0.12 -10000 0 -0.62 13 13
MAGED1 0.017 0.059 -10000 0 -0.4 7 7
PTPN11 0.025 0.003 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.016 0.11 -10000 0 -0.4 25 25
SHC/GRB2/SOS1 0.039 0.022 -10000 0 -10000 0 0
GRB2 0.024 0.006 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.001 0.099 -10000 0 -0.25 44 44
TRKA/NEDD4-2 0.011 0.068 -10000 0 -0.28 16 16
ELMO1 0.022 0.033 -10000 0 -0.4 2 2
RhoG/GTP/ELMO1/DOCK1 0.03 0.023 -10000 0 -0.24 2 2
NGF -0.009 0.11 -10000 0 -0.4 25 25
HRAS 0.024 0.005 -10000 0 -10000 0 0
DOCK1 0.024 0.006 -10000 0 -10000 0 0
GAB2 0.025 0.006 -10000 0 -10000 0 0
RIT2 0.017 0.005 -10000 0 -10000 0 0
RIT1 0.019 0.025 -10000 0 -0.4 1 1
FRS2 0.025 0.002 -10000 0 -10000 0 0
DNM1 0.013 0.058 -10000 0 -0.4 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.024 0.12 0.2 4 -0.27 50 54
mol:GDP 0 0.13 0.25 11 -0.32 26 37
NGF (dimer) -0.009 0.11 -10000 0 -0.4 25 25
RhoG/GDP 0.016 0.023 -10000 0 -0.28 2 2
RIT1/GDP -0.008 0.079 0.26 3 -0.23 18 21
TIAM1 0.016 0.063 -10000 0 -0.4 8 8
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
BDNF (dimer)/TRKB 0.006 0.11 -10000 0 -0.28 43 43
KIDINS220/CRKL/C3G 0.035 0.01 -10000 0 -10000 0 0
SHC/RasGAP 0.03 0.016 -10000 0 -10000 0 0
FRS2 family/SHP2 0.049 0.018 -10000 0 -0.24 1 1
SHC/GRB2/SOS1/GAB1 0.048 0.032 -10000 0 -0.22 1 1
RIT1/GTP 0.014 0.017 -10000 0 -0.28 1 1
NT3 (dimer) -0.009 0.1 -10000 0 -0.4 20 20
RAP1/GDP 0.003 0.077 -10000 0 -0.2 20 20
KIDINS220/CRKL 0.025 0.005 -10000 0 -10000 0 0
BDNF (dimer) -0.018 0.11 -10000 0 -0.4 25 25
ubiquitin-dependent protein catabolic process 0.008 0.091 -10000 0 -0.25 38 38
Schwann cell development -0.021 0.026 -10000 0 -10000 0 0
EHD4 0.024 0.006 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.059 0.024 -10000 0 -0.22 1 1
FRS2 family/SHP2/CRK family/C3G/GAB2 0.018 0.043 -10000 0 -0.26 2 2
RAP1B 0.025 0.002 -10000 0 -10000 0 0
RAP1A 0.025 0.001 -10000 0 -10000 0 0
CDC42/GTP -0.038 0.13 -10000 0 -0.25 83 83
ABL1 0.024 0.007 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
Rap1/GTP 0.003 0.076 -10000 0 -0.28 7 7
STAT3 0.017 0.062 -10000 0 -0.31 12 12
axon guidance -0.052 0.12 -10000 0 -0.24 83 83
MAPK3 0.001 0.11 0.18 51 -0.23 43 94
MAPK1 0.001 0.11 0.18 51 -0.23 43 94
CDC42/GDP 0.013 0.096 0.21 11 -0.23 19 30
NTF3 -0.009 0.1 -10000 0 -0.4 20 20
NTF4 -0.016 0.11 -10000 0 -0.4 25 25
NGF (dimer)/TRKA/FAIM 0.007 0.093 -10000 0 -0.25 40 40
PI3K 0.025 0.052 -10000 0 -0.28 9 9
FRS3 0.024 0.023 -10000 0 -0.4 1 1
FAIM 0.023 0.023 -10000 0 -0.4 1 1
GAB1 0.024 0.023 -10000 0 -0.4 1 1
RASGRF1 -0.051 0.13 0.2 5 -0.28 65 70
SOS1 0.025 0.004 -10000 0 -10000 0 0
MCF2L -0.038 0.11 -10000 0 -0.28 54 54
RGS19 0.022 0.032 -10000 0 -0.4 2 2
CDC42 0.025 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.019 0.094 0.26 2 -0.39 9 11
Rac1/GDP 0.009 0.096 0.21 9 -0.23 20 29
NGF (dimer)/TRKA/GRIT -0.007 0.087 -10000 0 -0.25 39 39
neuron projection morphogenesis -0.055 0.23 -10000 0 -0.76 27 27
NGF (dimer)/TRKA/NEDD4-2 0.008 0.091 -10000 0 -0.25 38 38
MAP2K1 0.033 0.09 0.2 77 -0.21 1 78
NGFR -0.015 0.11 -10000 0 -0.4 24 24
NGF (dimer)/TRKA/GIPC/GAIP -0.011 0.084 -10000 0 -0.23 41 41
RAS family/GTP/PI3K 0.011 0.056 -10000 0 -0.26 13 13
FRS2 family/SHP2/GRB2/SOS1 0.068 0.027 -10000 0 -0.21 1 1
NRAS 0.02 0.05 -10000 0 -0.4 5 5
GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
PRKCI 0.022 0.023 -10000 0 -0.4 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCZ 0.022 0.032 -10000 0 -0.4 2 2
MAPKKK cascade -0.059 0.2 -10000 0 -0.57 41 41
RASA1 0.025 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.01 0.069 -10000 0 -0.28 17 17
SQSTM1 0.024 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.019 0.1 -10000 0 -0.26 41 41
NGF (dimer)/TRKA/p62/Atypical PKCs 0.023 0.09 -10000 0 -0.22 37 37
MATK 0.007 0.075 -10000 0 -0.4 11 11
NEDD4L 0.023 0.023 -10000 0 -0.4 1 1
RAS family/GDP -0.026 0.052 -10000 0 -0.18 21 21
NGF (dimer)/TRKA -0.037 0.12 0.21 4 -0.28 56 60
Rac1/GTP -0.048 0.088 -10000 0 -0.24 42 42
FRS2 family/SHP2/CRK family 0.068 0.028 -10000 0 -0.21 1 1
FOXM1 transcription factor network

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
NFATC3 -0.04 0.33 -9999 0 -1 21 21
PLK1 0.003 0.18 -9999 0 -0.94 11 11
BIRC5 -0.033 0.28 -9999 0 -1.1 21 21
HSPA1B -0.042 0.34 -9999 0 -1 22 22
MAP2K1 0.019 0.04 -9999 0 -10000 0 0
BRCA2 -0.059 0.37 -9999 0 -1.1 29 29
FOXM1 -0.062 0.42 -9999 0 -1.3 23 23
XRCC1 -0.04 0.33 -9999 0 -1 21 21
FOXM1B/p19 -0.064 0.35 -9999 0 -1 25 25
Cyclin D1/CDK4 -0.05 0.34 -9999 0 -0.93 27 27
CDC2 -0.045 0.34 -9999 0 -1 23 23
TGFA -0.07 0.34 -9999 0 -0.92 32 32
SKP2 -0.034 0.33 -9999 0 -1 21 21
CCNE1 0.01 0.072 -9999 0 -0.41 10 10
CKS1B -0.01 0.34 -9999 0 -1 19 19
RB1 -0.03 0.25 -9999 0 -0.74 25 25
FOXM1C/SP1 -0.048 0.37 -9999 0 -1.2 23 23
AURKB -0.041 0.26 -9999 0 -0.87 30 30
CENPF -0.025 0.37 -9999 0 -1.2 20 20
CDK4 0.021 0.022 -9999 0 -10000 0 0
MYC -0.037 0.3 -9999 0 -0.88 25 25
CHEK2 0.018 0.047 -9999 0 -0.45 1 1
ONECUT1 -0.054 0.34 -9999 0 -0.99 23 23
CDKN2A -0.026 0.12 -9999 0 -0.4 27 27
LAMA4 -0.041 0.33 -9999 0 -1 21 21
FOXM1B/HNF6 -0.07 0.38 -9999 0 -1.2 23 23
FOS -0.049 0.34 -9999 0 -1 25 25
SP1 0.025 0.008 -9999 0 -10000 0 0
CDC25B -0.036 0.33 -9999 0 -1 22 22
response to radiation 0.004 0.022 -9999 0 -10000 0 0
CENPB -0.036 0.33 -9999 0 -1 21 21
CENPA -0.045 0.35 -9999 0 -1.1 22 22
NEK2 -0.018 0.35 -9999 0 -1.1 20 20
HIST1H2BA -0.043 0.33 -9999 0 -1 22 22
CCNA2 0.018 0.053 -9999 0 -0.42 5 5
EP300 0.024 0.006 -9999 0 -10000 0 0
CCNB1/CDK1 -0.055 0.37 -9999 0 -1.2 23 23
CCNB2 -0.041 0.33 -9999 0 -1 21 21
CCNB1 -0.045 0.35 -9999 0 -1 23 23
ETV5 -0.058 0.39 -9999 0 -1.1 34 34
ESR1 -0.12 0.46 -9999 0 -1.1 58 58
CCND1 -0.062 0.34 -9999 0 -0.96 27 27
GSK3A 0.018 0.037 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.032 0.073 -9999 0 -0.26 15 15
CDK2 0.023 0.014 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.004 0.027 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.041 0.35 -9999 0 -1.1 23 23
GAS1 -0.1 0.43 -9999 0 -1.1 46 46
MMP2 -0.078 0.4 -9999 0 -1.1 36 36
RB1/FOXM1C -0.062 0.35 -9999 0 -1 26 26
CREBBP 0.025 0.004 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.003 0.08 0.3 22 -10000 0 22
KIRREL -0.009 0.11 -10000 0 -0.41 23 23
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.004 0.08 -10000 0 -0.3 22 22
PLCG1 0.025 0.005 -10000 0 -10000 0 0
ARRB2 0.024 0.006 -10000 0 -10000 0 0
WASL 0.025 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.019 0.083 -10000 0 -0.23 33 33
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.002 0.057 -10000 0 -0.21 22 22
FYN 0.033 0.11 0.25 62 -0.21 22 84
mol:Ca2+ 0.026 0.067 -10000 0 -0.22 22 22
mol:DAG 0.026 0.067 -10000 0 -0.22 22 22
NPHS2 0.01 0.021 -10000 0 -10000 0 0
mol:IP3 0.026 0.067 -10000 0 -0.22 22 22
regulation of endocytosis 0.022 0.061 -10000 0 -0.2 22 22
Nephrin/NEPH1/podocin/Cholesterol 0.016 0.063 -10000 0 -0.22 22 22
establishment of cell polarity 0.003 0.08 -10000 0 -0.3 22 22
Nephrin/NEPH1/podocin/NCK1-2 0.037 0.068 -10000 0 -0.2 22 22
Nephrin/NEPH1/beta Arrestin2 0.024 0.062 -10000 0 -0.2 22 22
NPHS1 0.022 0.031 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin 0.018 0.062 0.17 1 -0.21 22 23
TJP1 0.024 0.006 -10000 0 -10000 0 0
NCK1 0.025 0.005 -10000 0 -10000 0 0
NCK2 0.025 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.027 0.068 -10000 0 -0.22 22 22
CD2AP 0.012 0.074 -10000 0 -0.4 11 11
Nephrin/NEPH1/podocin/GRB2 0.026 0.068 -10000 0 -0.22 22 22
GRB2 0.024 0.006 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.018 0.12 0.25 59 -0.21 25 84
cytoskeleton organization -0.005 0.065 0.2 6 -0.24 22 28
Nephrin/NEPH1 0.007 0.056 -10000 0 -0.2 22 22
Nephrin/NEPH1/ZO-1 0.02 0.069 -10000 0 -0.23 22 22
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.013 0.081 -10000 0 -0.28 24 24
CRKL -0.013 0.11 0.28 2 -0.38 17 19
mol:PIP3 -0.026 0.15 -10000 0 -0.8 13 13
AKT1 -0.022 0.14 0.38 1 -0.7 13 14
PTK2B 0.021 0.024 -10000 0 -0.4 1 1
RAPGEF1 -0.013 0.1 0.34 1 -0.38 15 16
RANBP10 0.023 0.008 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.015 0.097 -10000 0 -0.25 41 41
MAP3K5 -0.013 0.12 0.34 1 -0.38 19 20
HGF/MET/CIN85/CBL/ENDOPHILINS 0.025 0.097 -10000 0 -0.23 44 44
AP1 0.015 0.059 0.17 2 -0.3 6 8
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.021 0.01 -10000 0 -10000 0 0
apoptosis 0.001 0.15 -10000 0 -0.79 12 12
STAT3 (dimer) -0.009 0.084 -10000 0 -0.24 34 34
GAB1/CRKL/SHP2/PI3K 0.011 0.12 -10000 0 -0.38 18 18
INPP5D 0.014 0.067 -10000 0 -0.4 9 9
CBL/CRK 0 0.12 0.3 2 -0.39 16 18
PTPN11 0.025 0.003 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.025 0.005 -10000 0 -10000 0 0
PTEN 0.024 0.007 -10000 0 -10000 0 0
ELK1 -0.004 0.095 0.31 21 -10000 0 21
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.004 0.066 -10000 0 -0.23 14 14
PAK1 -0.022 0.13 0.37 2 -0.67 13 15
HGF/MET/RANBP10 0.01 0.097 -10000 0 -0.25 42 42
HRAS -0.035 0.17 -10000 0 -0.53 33 33
DOCK1 -0.009 0.12 0.29 8 -0.37 17 25
GAB1 -0.013 0.11 -10000 0 -0.32 32 32
CRK -0.012 0.11 0.3 2 -0.38 16 18
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.037 0.17 -10000 0 -0.46 49 49
JUN 0.024 0.023 -10000 0 -0.4 1 1
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.016 0.072 -10000 0 -0.21 42 42
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
cell morphogenesis -0.009 0.12 0.35 6 -0.39 14 20
GRB2/SHC 0.009 0.07 -10000 0 -0.19 32 32
FOS 0.014 0.055 -10000 0 -0.4 5 5
GLMN -0.005 0.043 -10000 0 -0.22 14 14
cell motility -0.005 0.095 0.31 21 -10000 0 21
HGF/MET/MUC20 -0.005 0.092 -10000 0 -0.25 42 42
cell migration 0.008 0.069 -10000 0 -0.19 32 32
GRB2 0.024 0.006 -10000 0 -10000 0 0
CBL 0.025 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.01 0.08 -10000 0 -0.28 24 24
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0 0.076 -10000 0 -0.23 33 33
MET/MUC20 -0.003 0.075 -10000 0 -0.28 24 24
RAP1B -0.015 0.1 0.33 2 -0.38 14 16
RAP1A -0.016 0.1 0.33 1 -0.38 14 15
HGF/MET/RANBP9 0.015 0.096 -10000 0 -0.25 40 40
RAF1 -0.029 0.16 0.31 1 -0.49 34 35
STAT3 -0.008 0.084 -10000 0 -0.24 34 34
cell proliferation 0.008 0.14 0.28 8 -0.35 32 40
RPS6KB1 -0.014 0.075 -10000 0 -0.3 17 17
MAPK3 -0.008 0.12 0.56 13 -10000 0 13
MAPK1 -0.002 0.14 0.65 13 -10000 0 13
RANBP9 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.007 0.12 0.3 2 -0.4 17 19
SRC -0.008 0.073 -10000 0 -0.22 34 34
PI3K 0.004 0.089 -10000 0 -0.21 45 45
MET/Glomulin -0.007 0.078 -10000 0 -0.23 36 36
SOS1 0.025 0.004 -10000 0 -10000 0 0
MAP2K1 -0.027 0.15 0.32 2 -0.45 34 36
MET -0.006 0.11 -10000 0 -0.4 24 24
MAP4K1 -0.012 0.12 0.35 1 -0.38 21 22
PTK2 0.023 0.007 -10000 0 -10000 0 0
MAP2K2 -0.028 0.15 0.3 1 -0.45 34 35
BAD -0.021 0.13 0.4 2 -0.66 13 15
MAP2K4 -0.013 0.11 0.32 1 -0.34 19 20
SHP2/GRB2/SOS1/GAB1 0.003 0.12 -10000 0 -0.32 33 33
INPPL1 0.025 0.003 -10000 0 -10000 0 0
PXN 0.025 0.003 -10000 0 -10000 0 0
SH3KBP1 0.023 0.032 -10000 0 -0.4 2 2
HGS -0.017 0.065 -10000 0 -0.19 40 40
PLCgamma1/PKC 0.018 0.004 -10000 0 -10000 0 0
HGF -0.004 0.099 -10000 0 -0.4 20 20
RASA1 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.005 -10000 0 -10000 0 0
PTPRJ 0.024 0.012 -10000 0 -10000 0 0
NCK/PLCgamma1 0.012 0.078 -10000 0 -0.2 38 38
PDPK1 -0.024 0.14 -10000 0 -0.74 13 13
HGF/MET/SHIP 0.007 0.11 -10000 0 -0.26 49 49
Retinoic acid receptors-mediated signaling

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
HDAC1 0.025 0.003 -10000 0 -10000 0 0
HDAC3 0.025 0.004 -10000 0 -10000 0 0
VDR 0.021 0.039 -10000 0 -0.4 3 3
Cbp/p300/PCAF 0.042 0.039 -10000 0 -0.23 6 6
EP300 0.024 0.006 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.002 0.079 -10000 0 -0.29 16 16
KAT2B 0.016 0.059 -10000 0 -0.4 7 7
MAPK14 0.025 0.004 -10000 0 -10000 0 0
AKT1 0.009 0.089 0.18 38 -0.24 14 52
RAR alpha/9cRA/Cyclin H -0.003 0.12 -10000 0 -0.33 20 20
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.009 0.091 -10000 0 -0.33 17 17
CDC2 0 0.002 -10000 0 -10000 0 0
response to UV 0 0.003 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.012 0.093 -10000 0 -0.28 22 22
NCOR2 0.025 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.027 -10000 0 -0.28 3 3
RXRs/RARs/NRIP1/9cRA -0.05 0.19 0.24 1 -0.47 50 51
NCOA2 0.01 0.074 -10000 0 -0.4 11 11
NCOA3 0.024 0.005 -10000 0 -10000 0 0
NCOA1 0.025 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.039 -10000 0 -0.4 3 3
RARG 0.022 0.033 -10000 0 -0.4 2 2
RAR gamma1/9cRA 0.031 0.022 -10000 0 -0.24 2 2
MAPK3 0.024 0.009 -10000 0 -10000 0 0
MAPK1 0.025 0.005 -10000 0 -10000 0 0
MAPK8 0.023 0.025 -10000 0 -0.42 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.039 0.17 -10000 0 -0.41 49 49
RARA -0.018 0.089 -10000 0 -0.24 44 44
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.014 0.093 -10000 0 -0.33 17 17
PRKCA 0.008 0.081 -10000 0 -0.41 13 13
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.057 0.2 -10000 0 -0.49 50 50
RXRG -0.059 0.14 -10000 0 -0.33 70 70
RXRA -0.017 0.082 -10000 0 -0.21 48 48
RXRB -0.027 0.11 -10000 0 -0.31 44 44
VDR/Vit D3/DNA 0.016 0.027 -10000 0 -0.28 3 3
RBP1 -0.036 0.14 -10000 0 -0.4 48 48
CRBP1/9-cic-RA -0.024 0.1 -10000 0 -0.28 48 48
RARB 0.015 0.061 -10000 0 -0.4 7 7
PRKCG -0.04 0.13 -10000 0 -0.38 39 39
MNAT1 0.025 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.047 0.18 -10000 0 -0.44 47 47
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.035 0.16 0.22 3 -0.37 52 55
proteasomal ubiquitin-dependent protein catabolic process -0.018 0.12 0.21 4 -0.34 29 33
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.057 0.2 -10000 0 -0.49 50 50
positive regulation of DNA binding -0.009 0.1 -10000 0 -0.31 20 20
NRIP1 -0.065 0.24 -10000 0 -0.77 26 26
RXRs/RARs -0.054 0.2 -10000 0 -0.43 62 62
RXRs/RXRs/DNA/9cRA -0.06 0.16 -10000 0 -0.39 59 59
PRKACA 0.024 0.006 -10000 0 -10000 0 0
CDK7 0.024 0.005 -10000 0 -10000 0 0
TFIIH 0.049 0.013 -10000 0 -10000 0 0
RAR alpha/9cRA 0.017 0.092 -10000 0 -0.31 11 11
CCNH 0.025 0.005 -10000 0 -10000 0 0
CREBBP 0.025 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.043 0.025 -10000 0 -0.2 2 2
PDGFR-alpha signaling pathway

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
PDGFRA -0.009 0.11 -10000 0 -0.4 27 27
PDGF/PDGFRA/CRKL 0.011 0.083 -10000 0 -0.28 27 27
positive regulation of JUN kinase activity 0.036 0.058 -10000 0 -0.21 15 15
CRKL 0.025 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 0.006 0.08 -10000 0 -0.28 26 26
AP1 -0.031 0.12 0.3 2 -0.88 5 7
mol:IP3 -0.012 0.077 -10000 0 -0.29 25 25
PLCG1 -0.012 0.077 -10000 0 -0.29 25 25
PDGF/PDGFRA/alphaV Integrin 0.009 0.091 -10000 0 -0.3 28 28
RAPGEF1 0.024 0.007 -10000 0 -10000 0 0
CRK 0.024 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.077 -10000 0 -0.29 25 25
CAV3 0.016 0.009 -10000 0 -10000 0 0
CAV1 0.022 0.026 -10000 0 -0.4 1 1
SHC/Grb2/SOS1 0.037 0.059 -10000 0 -0.21 15 15
PDGF/PDGFRA/Shf 0.007 0.089 -10000 0 -0.29 29 29
FOS -0.033 0.11 -10000 0 -0.86 5 5
JUN -0.021 0.02 -10000 0 -0.3 1 1
oligodendrocyte development 0.008 0.091 -10000 0 -0.3 28 28
GRB2 0.024 0.006 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:DAG -0.012 0.077 -10000 0 -0.29 25 25
PDGF/PDGFRA -0.009 0.11 -10000 0 -0.4 27 27
actin cytoskeleton reorganization 0.01 0.084 -10000 0 -0.28 28 28
SRF 0.012 0.006 -10000 0 -10000 0 0
SHC1 0.021 0.01 -10000 0 -10000 0 0
PI3K 0.022 0.084 -10000 0 -0.26 28 28
PDGF/PDGFRA/Crk/C3G 0.027 0.072 -10000 0 -0.22 26 26
JAK1 -0.016 0.083 -10000 0 -0.28 32 32
ELK1/SRF -0.021 0.055 0.16 6 -0.23 19 25
SHB 0.024 0.023 -10000 0 -0.4 1 1
SHF 0.02 0.04 -10000 0 -0.4 3 3
CSNK2A1 0.026 0.011 -10000 0 -10000 0 0
GO:0007205 -0.019 0.081 -10000 0 -0.31 25 25
SOS1 0.025 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.036 0.058 -10000 0 -0.21 15 15
PDGF/PDGFRA/SHB 0.01 0.084 -10000 0 -0.28 28 28
PDGF/PDGFRA/Caveolin-1 0.01 0.082 -10000 0 -0.28 26 26
ITGAV 0.02 0.045 -10000 0 -0.4 4 4
ELK1 -0.025 0.068 -10000 0 -0.27 25 25
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.011 0.081 -10000 0 -0.27 26 26
JAK-STAT cascade -0.016 0.083 -10000 0 -0.28 32 32
cell proliferation 0.007 0.089 -10000 0 -0.29 29 29
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.01 0.092 -10000 0 -0.28 27 27
alphaM/beta2 Integrin/GPIbA 0.021 0.072 -10000 0 -0.25 16 16
alphaM/beta2 Integrin/proMMP-9 0 0.11 -10000 0 -0.27 40 40
PLAUR 0.022 0.033 -10000 0 -0.4 2 2
HMGB1 0.014 0.04 -10000 0 -0.4 2 2
alphaM/beta2 Integrin/Talin 0.026 0.067 -10000 0 -0.27 12 12
AGER 0.011 0.052 -10000 0 -0.35 5 5
RAP1A 0.025 0.001 -10000 0 -10000 0 0
SELPLG 0.021 0.04 -10000 0 -0.4 3 3
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.021 0.1 -10000 0 -0.22 51 51
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.022 0.12 -10000 0 -0.4 32 32
CYR61 0.021 0.035 -10000 0 -0.4 2 2
TLN1 0.025 0.004 -10000 0 -10000 0 0
Rap1/GTP -0.037 0.12 -10000 0 -0.34 27 27
RHOA 0.024 0.005 -10000 0 -10000 0 0
P-selectin oligomer -0.015 0.11 -10000 0 -0.4 28 28
MYH2 -0.063 0.13 0.18 3 -0.38 26 29
MST1R -0.011 0.12 -10000 0 -0.4 29 29
leukocyte activation during inflammatory response 0.012 0.079 -10000 0 -0.22 26 26
APOB 0.017 0.02 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.002 0.092 -10000 0 -0.4 17 17
JAM3 0.022 0.025 -10000 0 -0.4 1 1
GP1BA 0.018 0.041 -10000 0 -0.4 3 3
alphaM/beta2 Integrin/CTGF 0.023 0.073 -10000 0 -0.28 14 14
alphaM/beta2 Integrin -0.051 0.12 -10000 0 -0.37 24 24
JAM3 homodimer 0.022 0.025 -10000 0 -0.4 1 1
ICAM2 0.02 0.04 -10000 0 -0.4 3 3
ICAM1 0.02 0.034 -10000 0 -0.4 2 2
phagocytosis triggered by activation of immune response cell surface activating receptor -0.05 0.12 -10000 0 -0.37 24 24
cell adhesion 0.02 0.071 -10000 0 -0.25 16 16
NFKB1 -0.029 0.12 0.35 1 -0.34 39 40
THY1 0.022 0.026 -10000 0 -0.4 1 1
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
Lipoprotein(a) 0.003 0.061 -10000 0 -0.24 17 17
alphaM/beta2 Integrin/LRP/tPA 0.029 0.08 -10000 0 -0.25 20 20
IL6 -0.043 0.15 0.34 1 -0.43 36 37
ITGB2 0.008 0.06 -10000 0 -0.4 6 6
elevation of cytosolic calcium ion concentration 0.029 0.078 -10000 0 -0.28 14 14
alphaM/beta2 Integrin/JAM2/JAM3 0.028 0.087 -10000 0 -0.26 22 22
JAM2 0.008 0.078 -10000 0 -0.4 12 12
alphaM/beta2 Integrin/ICAM1 0.021 0.1 -10000 0 -0.24 39 39
alphaM/beta2 Integrin/uPA/Plg 0.02 0.092 -10000 0 -0.25 28 28
RhoA/GTP -0.068 0.14 -10000 0 -0.4 29 29
positive regulation of phagocytosis -0.034 0.12 -10000 0 -0.36 25 25
Ron/MSP 0.002 0.094 -10000 0 -0.28 34 34
alphaM/beta2 Integrin/uPAR/uPA 0.031 0.079 -10000 0 -0.29 14 14
alphaM/beta2 Integrin/uPAR 0.024 0.073 -10000 0 -0.28 13 13
PLAU 0.017 0.047 -10000 0 -0.4 4 4
PLAT 0.01 0.065 -10000 0 -0.4 8 8
actin filament polymerization -0.061 0.12 -10000 0 -0.37 26 26
MST1 0.016 0.053 -10000 0 -0.4 5 5
alphaM/beta2 Integrin/lipoprotein(a) 0.016 0.082 -10000 0 -0.23 26 26
TNF -0.062 0.19 0.32 1 -0.56 38 39
RAP1B 0.025 0.002 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.021 0.074 -10000 0 -0.28 14 14
fibrinolysis 0.019 0.09 -10000 0 -0.25 28 28
HCK 0.009 0.075 -10000 0 -0.4 11 11
dendritic cell antigen processing and presentation -0.05 0.12 -10000 0 -0.37 24 24
VTN 0.018 0.031 -10000 0 -0.4 1 1
alphaM/beta2 Integrin/CYR61 0.024 0.071 -10000 0 -0.26 14 14
LPA -0.012 0.094 -10000 0 -0.4 17 17
LRP1 0.023 0.025 -10000 0 -0.4 1 1
cell migration -0.021 0.11 -10000 0 -0.26 51 51
FN1 0.012 0.059 -10000 0 -0.4 6 6
alphaM/beta2 Integrin/Thy1 0.025 0.069 -10000 0 -0.26 13 13
MPO -0.004 0.095 -10000 0 -0.4 18 18
KNG1 0.015 0.022 -10000 0 -10000 0 0
RAP1/GDP 0.034 0.003 -10000 0 -10000 0 0
ROCK1 -0.066 0.13 0.18 1 -0.38 29 30
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.012 0.097 -10000 0 -0.4 18 18
CTGF 0.02 0.041 -10000 0 -0.4 3 3
alphaM/beta2 Integrin/Hck 0.017 0.088 -10000 0 -0.32 17 17
ITGAM 0.006 0.066 -10000 0 -0.41 7 7
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.012 0.096 -10000 0 -0.25 32 32
HP -0.096 0.17 -10000 0 -0.4 79 79
leukocyte adhesion 0.005 0.1 -10000 0 -0.31 16 16
SELP -0.015 0.11 -10000 0 -0.4 28 28
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.033 0.17 12 -0.17 1 13
RFC1 0.002 0.037 0.18 14 -0.17 2 16
PRKDC 0.012 0.067 0.22 30 -0.2 4 34
RIPK1 0.025 0.004 -10000 0 -10000 0 0
CASP7 -0.004 0.11 0.24 1 -0.62 10 11
FASLG/FAS/FADD/FAF1 0.004 0.064 0.18 14 -0.23 15 29
MAP2K4 0.003 0.12 0.43 3 -0.33 22 25
mol:ceramide -0.005 0.086 -10000 0 -0.29 23 23
GSN 0.001 0.033 0.18 11 -0.17 2 13
FASLG/FAS/FADD/FAF1/Caspase 8 0.003 0.082 0.22 3 -0.28 17 20
FAS 0.016 0.051 -10000 0 -0.4 5 5
BID -0.012 0.031 0.25 4 -0.25 1 5
MAP3K1 0.005 0.1 0.31 5 -0.38 12 17
MAP3K7 0.025 0.003 -10000 0 -10000 0 0
RB1 -0.003 0.051 0.18 14 -0.21 11 25
CFLAR 0.025 0.004 -10000 0 -10000 0 0
HGF/MET -0.01 0.13 -10000 0 -0.26 67 67
ARHGDIB 0.002 0.04 0.18 14 -10000 0 14
FADD 0.023 0.01 -10000 0 -10000 0 0
actin filament polymerization 0.002 0.04 0.18 6 -0.18 11 17
NFKB1 -0.011 0.13 -10000 0 -0.67 11 11
MAPK8 0.001 0.14 0.34 11 -0.44 18 29
DFFA 0.003 0.042 0.2 14 -10000 0 14
DNA fragmentation during apoptosis -0.001 0.042 0.18 13 -0.18 7 20
FAS/FADD/MET 0.02 0.079 -10000 0 -0.24 28 28
CFLAR/RIP1 0.037 0.008 -10000 0 -10000 0 0
FAIM3 0.014 0.056 -10000 0 -0.4 6 6
FAF1 0.024 0.01 -10000 0 -10000 0 0
PARP1 0.003 0.042 0.18 16 -10000 0 16
DFFB 0.002 0.035 0.18 13 -0.17 1 14
CHUK -0.012 0.12 -10000 0 -0.62 11 11
FASLG -0.01 0.1 -10000 0 -0.4 22 22
FAS/FADD 0.028 0.041 -10000 0 -0.28 5 5
HGF -0.004 0.099 -10000 0 -0.4 20 20
LMNA 0.007 0.062 0.21 22 -10000 0 22
CASP6 0.002 0.041 0.2 13 -0.17 2 15
CASP10 0.018 0.046 -10000 0 -0.4 4 4
CASP3 0.004 0.044 0.22 13 -0.19 3 16
PTPN13 -0.014 0.12 -10000 0 -0.4 31 31
CASP8 -0.011 0.047 0.32 6 -0.3 1 7
IL6 -0.029 0.25 -10000 0 -1 20 20
MET -0.006 0.11 -10000 0 -0.4 24 24
ICAD/CAD 0.001 0.037 0.18 10 -10000 0 10
FASLG/FAS/FADD/FAF1/Caspase 10 -0.005 0.087 -10000 0 -0.29 23 23
activation of caspase activity by cytochrome c -0.012 0.031 0.25 4 -0.25 1 5
PAK2 0.014 0.069 0.22 31 -0.17 3 34
BCL2 0.007 0.083 -10000 0 -0.4 14 14
Canonical Wnt signaling pathway

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
HDAC1 0.03 0.029 0.25 3 -10000 0 3
AES 0.027 0.034 0.27 2 -0.4 1 3
FBXW11 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0.003 -10000 0 -10000 0 0
LRP6/FZD1 0.036 0.019 -10000 0 -0.28 1 1
SMAD4 0.025 0.005 -10000 0 -10000 0 0
DKK2 -0.029 0.13 -10000 0 -0.4 37 37
TLE1 0.028 0.026 0.25 3 -10000 0 3
MACF1 0.025 0.004 -10000 0 -10000 0 0
CTNNB1 0.039 0.092 0.3 13 -0.29 3 16
WIF1 -0.11 0.17 -10000 0 -0.4 86 86
beta catenin/RanBP3 0.04 0.14 0.45 31 -0.28 1 32
KREMEN2 -0.003 0.091 -10000 0 -0.4 16 16
DKK1 -0.053 0.13 -10000 0 -0.4 41 41
beta catenin/beta TrCP1 0.048 0.083 0.27 10 -0.27 2 12
FZD1 0.023 0.024 -10000 0 -0.4 1 1
AXIN2 -0.028 0.25 0.7 5 -1.2 13 18
AXIN1 0.025 0.005 -10000 0 -10000 0 0
RAN 0.025 0.004 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.03 0.075 -10000 0 -0.52 4 4
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 -0.043 0.2 0.29 1 -0.54 36 37
Axin1/APC/GSK3 0.035 0.049 0.2 8 -0.23 1 9
Axin1/APC/GSK3/beta catenin/Macf1 0.033 0.064 0.36 4 -0.26 2 6
HNF1A -0.055 0.17 0.23 2 -0.4 70 72
CTBP1 0.028 0.023 0.23 2 -10000 0 2
MYC 0.047 0.28 0.65 39 -1.1 10 49
RANBP3 0.024 0.007 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.006 0.11 -10000 0 -0.25 49 49
NKD1 -0.008 0.079 -10000 0 -0.4 10 10
TCF4 0.024 0.051 0.28 2 -0.39 4 6
TCF3 0.028 0.025 0.27 2 -10000 0 2
WNT1/LRP6/FZD1/Axin1 0.061 0.023 -10000 0 -0.25 1 1
Ran/GTP 0.019 0.006 0.12 1 -10000 0 1
CtBP/CBP/TCF/TLE1/AES -0.036 0.18 0.45 14 -0.49 23 37
LEF1 -0.024 0.14 0.22 1 -0.39 43 44
DVL1 0.033 0.06 0.23 5 -0.35 4 9
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.057 0.21 -10000 0 -0.57 35 35
DKK1/LRP6/Kremen 2 -0.001 0.11 -10000 0 -0.25 55 55
LRP6 0.026 0.004 -10000 0 -10000 0 0
CSNK1A1 0.029 0.023 0.24 1 -10000 0 1
NLK 0.022 0.011 -10000 0 -10000 0 0
CCND1 -0.03 0.28 0.64 7 -1.3 15 22
WNT1 0.021 0.019 -10000 0 -10000 0 0
GSK3A 0.025 0.004 -10000 0 -10000 0 0
GSK3B 0.025 0.005 -10000 0 -10000 0 0
FRAT1 0.022 0.023 -10000 0 -0.4 1 1
PPP2R5D 0.042 0.054 0.28 10 -0.23 1 11
APC 0.005 0.04 0.19 12 -0.23 1 13
WNT1/LRP6/FZD1 0.059 0.074 0.2 71 -10000 0 71
CREBBP 0.029 0.023 0.23 2 -10000 0 2
Arf6 signaling events

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
CENTA1/KIF3B 0.024 0.039 -10000 0 -0.24 7 7
ARNO/beta Arrestin1-2 0.016 0.1 -10000 0 -0.75 5 5
EGFR 0.013 0.07 -10000 0 -0.4 10 10
EPHA2 0.017 0.056 -10000 0 -0.4 6 6
USP6 0.023 0.009 -10000 0 -10000 0 0
IQSEC1 0.023 0.023 -10000 0 -0.4 1 1
EGFR/EGFR/EGF/EGF 0 0.093 -10000 0 -0.3 30 30
ARRB2 0.008 0.003 -10000 0 -10000 0 0
mol:GTP 0.004 0.058 0.13 16 -0.17 18 34
ARRB1 0.022 0.033 -10000 0 -0.4 2 2
FBXO8 0.024 0.009 -10000 0 -10000 0 0
TSHR 0.012 0.033 -10000 0 -10000 0 0
EGF -0.011 0.1 -10000 0 -0.4 21 21
somatostatin receptor activity 0 0 0.001 4 -0.001 36 40
ARAP2 0.01 0.08 -10000 0 -0.4 13 13
mol:GDP -0.018 0.097 0.18 6 -0.28 30 36
mol:PI-3-4-5-P3 0 0 0.001 4 -0.001 19 23
ITGA2B -0.004 0.1 -10000 0 -0.4 21 21
ARF6 0.025 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.04 0.054 -10000 0 -0.22 11 11
ADAP1 0.015 0.063 -10000 0 -0.4 8 8
KIF13B 0.023 0.008 -10000 0 -10000 0 0
HGF/MET -0.008 0.11 -10000 0 -0.3 42 42
PXN 0.025 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.019 0.099 0.23 7 -0.26 34 41
EGFR/EGFR/EGF/EGF/ARFGEP100 0.022 0.084 -10000 0 -0.25 30 30
ADRB2 -0.01 0.1 -10000 0 -0.4 21 21
receptor agonist activity 0 0 0 6 0 32 38
actin filament binding 0 0 0.001 4 0 36 40
SRC 0.022 0.032 -10000 0 -0.4 2 2
ITGB3 -0.008 0.096 -10000 0 -0.4 18 18
GNAQ 0.023 0.023 -10000 0 -0.4 1 1
EFA6/PI-4-5-P2 0 0 0.002 8 -0.001 25 33
ARF6/GDP 0.002 0.14 0.24 12 -0.46 22 34
ARF6/GDP/GULP/ACAP1 -0.004 0.13 0.2 4 -0.32 33 37
alphaIIb/beta3 Integrin/paxillin/GIT1 0.03 0.089 -10000 0 -0.23 37 37
ACAP1 0.02 0.035 -10000 0 -0.4 2 2
ACAP2 0.022 0.023 -10000 0 -0.4 1 1
LHCGR/beta Arrestin2 0.012 0.015 -10000 0 -10000 0 0
EFNA1 0.014 0.055 -10000 0 -0.4 6 6
HGF -0.004 0.099 -10000 0 -0.26 36 36
CYTH3 0.006 0.003 -10000 0 -10000 0 0
CYTH2 0.004 0.12 -10000 0 -0.98 5 5
NCK1 0.025 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 0 8 0 31 39
endosomal lumen acidification 0 0 0.001 10 0 25 35
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 -0.009 0.12 -10000 0 -0.4 29 29
GNAQ/ARNO 0.018 0.11 -10000 0 -0.9 5 5
mol:Phosphatidic acid 0 0 0 1 -10000 0 1
PIP3-E 0 0 0 5 0 5 10
MET -0.006 0.11 -10000 0 -0.4 24 24
GNA14 0.015 0.063 -10000 0 -0.4 8 8
GNA15 0.015 0.056 -10000 0 -0.4 6 6
GIT1 0.024 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 9 -0.001 27 36
GNA11 0.016 0.055 -10000 0 -0.4 6 6
LHCGR 0.013 0.011 -10000 0 -10000 0 0
AGTR1 0.019 0.015 -10000 0 -10000 0 0
desensitization of G-protein coupled receptor protein signaling pathway 0.012 0.015 -10000 0 -10000 0 0
IPCEF1/ARNO 0.011 0.12 -10000 0 -0.83 5 5
alphaIIb/beta3 Integrin -0.011 0.1 -10000 0 -0.29 38 38
Signaling events mediated by PTP1B

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
PDGFRB 0.021 0.034 -10000 0 -0.4 2 2
Jak2/Leptin Receptor -0.023 0.14 -10000 0 -0.43 26 26
PTP1B/AKT1 -0.007 0.095 0.26 1 -0.28 26 27
FYN 0.025 0.007 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.02 0.097 0.29 1 -0.3 26 27
EGFR 0.01 0.072 -10000 0 -0.41 10 10
EGF/EGFR -0.013 0.12 0.25 1 -0.28 42 43
CSF1 0.018 0.055 -10000 0 -0.4 6 6
AKT1 0.025 0.005 -10000 0 -10000 0 0
INSR 0.024 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.038 0.12 -10000 0 -0.32 36 36
Insulin Receptor/Insulin 0.008 0.089 0.24 1 -0.29 14 15
HCK 0.009 0.075 -10000 0 -0.4 11 11
CRK 0.024 0.006 -10000 0 -10000 0 0
TYK2 -0.01 0.1 0.22 14 -0.3 21 35
EGF -0.012 0.1 -10000 0 -0.41 21 21
YES1 0.025 0.005 -10000 0 -10000 0 0
CAV1 -0.02 0.1 0.22 5 -0.34 20 25
TXN 0.023 0.009 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.006 0.11 -10000 0 -0.29 29 29
cell migration 0.02 0.097 0.3 26 -0.29 1 27
STAT3 0.024 0.006 -10000 0 -10000 0 0
PRLR -0.025 0.13 -10000 0 -0.4 39 39
ITGA2B -0.005 0.1 -10000 0 -0.4 21 21
CSF1R 0.012 0.071 -10000 0 -0.4 10 10
Prolactin Receptor/Prolactin -0.009 0.1 -10000 0 -0.29 39 39
FGR 0.015 0.06 -10000 0 -0.4 7 7
PTP1B/p130 Cas -0.008 0.095 0.27 1 -0.28 26 27
Crk/p130 Cas 0.001 0.097 0.27 1 -0.29 20 21
DOK1 -0.015 0.099 0.34 1 -0.4 13 14
JAK2 -0.034 0.14 0.26 1 -0.43 29 30
Jak2/Leptin Receptor/Leptin -0.015 0.13 -10000 0 -0.36 28 28
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
PTPN1 -0.02 0.098 0.29 1 -0.3 26 27
LYN 0.02 0.039 -10000 0 -0.4 3 3
CDH2 -0.053 0.15 -10000 0 -0.4 53 53
SRC -0.004 0.12 -10000 0 -0.52 16 16
ITGB3 -0.009 0.097 -10000 0 -0.4 18 18
CAT1/PTP1B -0.053 0.15 0.27 5 -0.37 39 44
CAPN1 0.025 0.003 -10000 0 -10000 0 0
CSK 0.024 0.005 -10000 0 -10000 0 0
PI3K 0.013 0.09 -10000 0 -0.29 15 15
mol:H2O2 -0.001 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.013 0.12 -10000 0 -0.34 28 28
negative regulation of transcription -0.033 0.14 0.26 1 -0.43 29 30
FCGR2A 0.016 0.046 -10000 0 -0.4 4 4
FER 0.022 0.033 -10000 0 -0.41 2 2
alphaIIb/beta3 Integrin -0.012 0.1 -10000 0 -0.3 38 38
BLK -0.014 0.1 -10000 0 -0.4 22 22
Insulin Receptor/Insulin/Shc 0.034 0.02 -10000 0 -10000 0 0
RHOA 0.024 0.006 -10000 0 -10000 0 0
LEPR 0.021 0.041 -10000 0 -0.4 3 3
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
p210 bcr-abl/Grb2 0.024 0.006 -10000 0 -10000 0 0
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.05 0.15 0.26 3 -0.44 28 31
PRL 0.013 0.029 -10000 0 -10000 0 0
SOCS3 -0.034 0.27 -10000 0 -1.2 18 18
SPRY2 0.008 0.076 -10000 0 -0.41 11 11
Insulin Receptor/Insulin/IRS1 0.03 0.058 -10000 0 -0.25 14 14
CSF1/CSF1R -0.006 0.11 -10000 0 -0.31 29 29
Ras protein signal transduction 0.018 0.1 0.55 12 -10000 0 12
IRS1 0.008 0.083 -10000 0 -0.4 14 14
INS 0.01 0.014 -10000 0 -10000 0 0
LEP 0.014 0.021 -10000 0 -10000 0 0
STAT5B -0.029 0.13 0.28 1 -0.36 33 34
STAT5A -0.029 0.13 0.28 1 -0.35 34 35
GRB2 0.024 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.01 0.099 -10000 0 -0.3 25 25
CSN2 -0.006 0.067 -10000 0 -0.48 2 2
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
LAT -0.002 0.099 -10000 0 -0.45 14 14
YBX1 0.029 0.023 -10000 0 -0.4 1 1
LCK 0.008 0.078 -10000 0 -0.4 12 12
SHC1 0.021 0.01 -10000 0 -10000 0 0
NOX4 0.01 0.075 -10000 0 -0.41 11 11
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.029 0.027 -10000 0 -0.28 1 1
PDGFRB 0.021 0.034 -10000 0 -0.41 2 2
SPHK1 -0.017 0.13 -10000 0 -0.73 11 11
mol:S1P -0.02 0.12 -10000 0 -0.64 11 11
S1P1/S1P/Gi -0.055 0.17 0.2 2 -0.4 53 55
GNAO1 0.008 0.055 -10000 0 -0.36 6 6
PDGFB-D/PDGFRB/PLCgamma1 -0.043 0.15 0.31 1 -0.38 47 48
PLCG1 -0.053 0.15 0.22 3 -0.38 51 54
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.034 -10000 0 -0.41 2 2
GNAI2 0.019 0.016 -10000 0 -10000 0 0
GNAI3 0.02 0.015 -10000 0 -10000 0 0
GNAI1 0.008 0.072 -10000 0 -0.41 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.003 0.018 -10000 0 -0.23 1 1
S1P1/S1P -0.02 0.091 0.17 1 -0.43 11 12
negative regulation of cAMP metabolic process -0.053 0.16 0.19 2 -0.39 53 55
MAPK3 -0.078 0.21 -10000 0 -0.56 49 49
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
KDR 0.02 0.026 -10000 0 -0.4 1 1
PLCB2 -0.013 0.091 0.2 5 -0.37 12 17
RAC1 0.025 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.012 0.079 -10000 0 -0.37 11 11
receptor internalization -0.019 0.085 -10000 0 -0.4 11 11
PTGS2 -0.13 0.33 -10000 0 -0.95 48 48
Rac1/GTP -0.013 0.08 -10000 0 -0.37 11 11
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFA 0.021 0.016 -10000 0 -0.09 3 3
negative regulation of T cell proliferation -0.053 0.16 0.19 2 -0.39 53 55
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.008 0.069 -10000 0 -0.41 9 9
MAPK1 -0.077 0.21 -10000 0 -0.57 49 49
S1P1/S1P/PDGFB-D/PDGFRB -0.01 0.098 0.24 4 -0.35 13 17
ABCC1 0.024 0.005 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.034 0.021 -10000 0 -0.28 1 1
alphaV beta3 Integrin 0.016 0.089 -10000 0 -0.24 37 37
PTK2 0.006 0.12 0.33 10 -0.35 18 28
IGF1R -0.005 0.11 -10000 0 -0.4 25 25
PI4KB 0.02 0.01 -10000 0 -10000 0 0
MFGE8 0.019 0.045 -10000 0 -0.4 4 4
SRC 0.022 0.032 -10000 0 -0.4 2 2
CDKN1B -0.016 0.11 -10000 0 -0.44 20 20
VEGFA 0.024 0.011 -10000 0 -10000 0 0
ILK 0.005 0.048 -10000 0 -0.35 3 3
ROCK1 0.025 0.004 -10000 0 -10000 0 0
AKT1 0 0.037 -10000 0 -0.3 2 2
PTK2B -0.02 0.065 0.22 9 -0.22 21 30
alphaV/beta3 Integrin/JAM-A 0.019 0.077 -10000 0 -0.22 27 27
CBL 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.023 0.072 -10000 0 -0.24 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.009 0.12 -10000 0 -0.26 58 58
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.008 0.057 -10000 0 -0.28 6 6
alphaV/beta3 Integrin/Syndecan-1 0.024 0.079 -10000 0 -0.24 29 29
PI4KA 0.025 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.023 0.14 -10000 0 -0.25 86 86
PI4 Kinase 0.029 0.016 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.013 0.095 -10000 0 -0.25 38 38
RPS6KB1 -0.07 0.11 -10000 0 -0.37 23 23
TLN1 0.025 0.004 -10000 0 -10000 0 0
MAPK3 -0.042 0.14 -10000 0 -0.42 33 33
GPR124 0.017 0.046 -10000 0 -0.4 4 4
MAPK1 -0.044 0.14 -10000 0 -0.42 34 34
PXN 0.025 0.003 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
alphaV/beta3 Integrin/Tumstatin 0.01 0.098 -10000 0 -0.25 41 41
cell adhesion 0.019 0.08 -10000 0 -0.27 23 23
ANGPTL3 0.019 0.011 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.03 -10000 0 -0.24 3 3
IGF-1R heterotetramer -0.005 0.11 -10000 0 -0.4 25 25
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
TGFBR2 0.022 0.032 -10000 0 -0.4 2 2
ITGB3 -0.008 0.096 -10000 0 -0.4 18 18
IGF1 -0.021 0.12 -10000 0 -0.4 33 33
RAC1 0.025 0.005 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.024 0.078 -10000 0 -0.26 23 23
apoptosis 0.02 0.045 -10000 0 -0.4 4 4
CD47 0.023 0.023 -10000 0 -0.4 1 1
alphaV/beta3 Integrin/CD47 0.028 0.072 -10000 0 -0.24 23 23
VCL 0.024 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.006 0.11 -10000 0 -0.27 46 46
CSF1 0.018 0.055 -10000 0 -0.4 6 6
PIK3C2A 0.006 0.043 -10000 0 -0.32 2 2
PI4 Kinase/Pyk2 0 0.061 -10000 0 -0.24 5 5
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.041 0.07 -10000 0 -0.22 22 22
FAK1/Vinculin 0.012 0.1 0.28 7 -0.29 14 21
alphaV beta3/Integrin/ppsTEM5 0.024 0.079 -10000 0 -0.26 23 23
RHOA 0.024 0.005 -10000 0 -10000 0 0
VTN 0.018 0.031 -10000 0 -0.4 1 1
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
FGF2 0.003 0.087 -10000 0 -0.4 15 15
F11R -0.003 0.056 -10000 0 -0.29 13 13
alphaV/beta3 Integrin/Lactadherin 0.027 0.08 -10000 0 -0.27 22 22
alphaV/beta3 Integrin/TGFBR2 0.028 0.075 -10000 0 -0.25 23 23
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.047 0.052 -10000 0 -0.22 11 11
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.029 0.064 -10000 0 -0.22 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.012 0.059 -10000 0 -0.4 6 6
alphaV/beta3 Integrin/Pyk2 0.023 0.066 0.18 4 -0.22 21 25
SDC1 0.012 0.071 -10000 0 -0.4 10 10
VAV3 -0.025 0.069 0.18 9 -0.22 33 42
PTPN11 0.025 0.003 -10000 0 -10000 0 0
IRS1 0.008 0.083 -10000 0 -0.4 14 14
FAK1/Paxillin 0.015 0.11 0.32 9 -0.3 15 24
cell migration 0.009 0.093 0.28 7 -0.27 14 21
ITGAV 0.02 0.045 -10000 0 -0.4 4 4
PI3K 0.021 0.084 -10000 0 -0.22 31 31
SPP1 0 0.092 -10000 0 -0.4 17 17
KDR 0.024 0.023 -10000 0 -0.4 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.02 0.045 -10000 0 -0.4 4 4
COL4A3 -0.009 0.1 -10000 0 -0.4 21 21
angiogenesis -0.026 0.16 -10000 0 -0.44 31 31
Rac1/GTP 0.007 0.07 0.17 7 -0.2 30 37
EDIL3 -0.014 0.12 -10000 0 -0.4 30 30
cell proliferation 0.028 0.074 -10000 0 -0.25 23 23
Nongenotropic Androgen signaling

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
PTK2 0.006 0.002 -10000 0 -10000 0 0
GNB1/GNG2 0.013 0.089 -10000 0 -0.22 45 45
regulation of S phase of mitotic cell cycle -0.008 0.083 -10000 0 -0.24 38 38
GNAO1 0.014 0.053 -10000 0 -0.4 5 5
HRAS 0.024 0.005 -10000 0 -10000 0 0
SHBG/T-DHT 0.005 0.051 -10000 0 -0.24 15 15
PELP1 0.024 0.006 -10000 0 -10000 0 0
AKT1 0.006 0.001 -10000 0 -10000 0 0
MAP2K1 -0.022 0.065 0.19 10 -0.23 3 13
T-DHT/AR -0.018 0.096 -10000 0 -0.28 42 42
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.006 5 5
GNAI2 0.024 0.006 -10000 0 -10000 0 0
GNAI3 0.025 0.002 -10000 0 -10000 0 0
GNAI1 0.012 0.071 -10000 0 -0.4 10 10
mol:GDP -0.038 0.12 -10000 0 -0.35 40 40
cell proliferation -0.02 0.093 0.24 4 -0.4 10 14
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
FOS -0.012 0.11 0.25 1 -0.6 8 9
mol:Ca2+ -0.004 0.018 -10000 0 -0.057 24 24
MAPK3 -0.019 0.084 0.26 4 -0.33 8 12
MAPK1 -0.011 0.081 0.21 1 -0.37 12 13
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:IP3 0 0.001 -10000 0 -0.004 5 5
cAMP biosynthetic process -0.009 0.046 -10000 0 -0.22 15 15
GNG2 0.018 0.047 -10000 0 -0.4 4 4
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 5 5
HRAS/GTP 0.018 0.076 -10000 0 -0.2 38 38
actin cytoskeleton reorganization 0.029 0.036 -10000 0 -0.19 8 8
SRC 0.022 0.032 -10000 0 -0.41 2 2
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 5 5
PI3K 0.023 0.044 -10000 0 -0.24 9 9
apoptosis 0.009 0.085 0.36 12 -0.22 3 15
T-DHT/AR/PELP1 -0.001 0.087 -10000 0 -0.24 42 42
HRAS/GDP -0.024 0.12 -10000 0 -0.33 40 40
CREB1 -0.01 0.089 0.24 2 -0.38 12 14
RAC1-CDC42/GTP 0.037 0.039 -10000 0 -0.19 8 8
AR -0.028 0.14 -10000 0 -0.4 42 42
GNB1 0.025 0.005 -10000 0 -10000 0 0
RAF1 -0.005 0.073 0.2 13 -0.19 33 46
RAC1-CDC42/GDP -0.005 0.12 -10000 0 -0.32 39 39
T-DHT/AR/PELP1/Src 0.017 0.081 -10000 0 -0.22 38 38
MAP2K2 -0.023 0.063 0.2 8 -0.23 3 11
T-DHT/AR/PELP1/Src/PI3K -0.008 0.084 -10000 0 -0.24 38 38
GNAZ 0.013 0.067 -10000 0 -0.4 9 9
SHBG 0.005 0.086 -10000 0 -0.4 15 15
Gi family/GNB1/GNG2/GDP -0.029 0.13 -10000 0 -0.41 25 25
mol:T-DHT 0 0 -10000 0 -0.002 3 3
RAC1 0.025 0.005 -10000 0 -10000 0 0
GNRH1 -0.003 0.05 -10000 0 -0.28 11 11
Gi family/GTP -0.015 0.069 -10000 0 -0.22 25 25
CDC42 0.025 0.005 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.037 0.2 -10000 0 -0.74 8 8
CRP -0.022 0.22 0.43 2 -0.65 11 13
cell cycle arrest -0.054 0.23 -10000 0 -0.61 30 30
TIMP1 -0.03 0.2 -10000 0 -0.76 11 11
IL6ST -0.012 0.11 -10000 0 -0.4 25 25
Rac1/GDP -0.021 0.13 0.22 1 -0.37 26 27
AP1 0.036 0.1 -10000 0 -0.53 3 3
GAB2 0.025 0.007 -10000 0 -10000 0 0
TNFSF11 -0.12 0.34 -10000 0 -0.96 46 46
HSP90B1 0.018 0.09 -10000 0 -0.74 3 3
GAB1 0.024 0.023 -10000 0 -0.4 1 1
MAPK14 -0.025 0.15 -10000 0 -0.55 20 20
AKT1 0.025 0.061 0.26 2 -0.4 4 6
FOXO1 0.024 0.059 0.24 2 -0.38 4 6
MAP2K6 -0.035 0.13 -10000 0 -0.43 24 24
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.03 0.14 -10000 0 -0.38 26 26
MITF -0.033 0.12 -10000 0 -0.39 24 24
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.024 0.007 -10000 0 -10000 0 0
A2M 0.007 0.14 -10000 0 -1.2 5 5
CEBPB 0.025 0.014 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.016 0.081 -10000 0 -0.48 4 4
STAT3 -0.059 0.25 -10000 0 -0.66 30 30
STAT1 0.015 0.062 -10000 0 -0.76 2 2
CEBPD -0.04 0.22 -10000 0 -0.74 15 15
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.026 0.052 -10000 0 -0.28 9 9
JUN 0.024 0.023 -10000 0 -0.4 1 1
PIAS3/MITF -0.018 0.12 -10000 0 -0.38 23 23
MAPK11 -0.026 0.15 -10000 0 -0.54 20 20
STAT3 (dimer)/FOXO1 -0.025 0.19 0.35 2 -0.49 26 28
GRB2/SOS1/GAB family 0.019 0.12 -10000 0 -0.34 15 15
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.021 0.11 -10000 0 -0.32 29 29
GRB2 0.024 0.006 -10000 0 -10000 0 0
JAK2 0.014 0.067 -10000 0 -0.4 9 9
LBP -0.099 0.32 0.42 1 -0.85 47 48
PIK3R1 0.004 0.091 -10000 0 -0.4 17 17
JAK1 0.015 0.053 -10000 0 -0.41 5 5
MYC -0.038 0.24 0.45 1 -0.94 12 13
FGG -0.048 0.2 -10000 0 -0.72 9 9
macrophage differentiation -0.054 0.23 -10000 0 -0.61 30 30
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.011 0.11 -10000 0 -0.26 43 43
JUNB -0.04 0.21 -10000 0 -0.66 18 18
FOS 0.013 0.055 -10000 0 -0.4 5 5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.027 0.12 -10000 0 -0.41 21 21
STAT1/PIAS1 -0.007 0.12 -10000 0 -0.37 17 17
GRB2/SOS1/GAB family/SHP2/PI3K 0.026 0.06 -10000 0 -0.45 3 3
STAT3 (dimer) -0.057 0.24 -10000 0 -0.65 30 30
PRKCD -0.037 0.16 0.33 3 -0.45 25 28
IL6R 0 0.085 -10000 0 -0.4 15 15
SOCS3 -0.034 0.22 -10000 0 -0.99 14 14
gp130 (dimer)/JAK1/JAK1/LMO4 0.013 0.092 -10000 0 -0.25 33 33
Rac1/GTP -0.024 0.14 0.22 1 -0.38 26 27
HCK 0.009 0.074 -10000 0 -0.4 11 11
MAPKKK cascade 0.024 0.083 -10000 0 -0.53 4 4
bone resorption -0.1 0.32 -10000 0 -0.89 46 46
IRF1 -0.045 0.2 -10000 0 -0.69 10 10
mol:GDP -0.033 0.12 -10000 0 -0.37 26 26
SOS1 0.025 0.005 -10000 0 -10000 0 0
VAV1 -0.034 0.12 -10000 0 -0.38 26 26
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.024 0.18 -10000 0 -0.56 27 27
PTPN11 0.014 0.064 -10000 0 -0.65 3 3
IL6/IL6RA -0.004 0.087 -10000 0 -0.3 25 25
gp130 (dimer)/TYK2/TYK2/LMO4 0.019 0.079 -10000 0 -0.24 26 26
gp130 (dimer)/JAK2/JAK2/LMO4 0.013 0.093 -10000 0 -0.25 35 35
IL6 -0.003 0.079 -10000 0 -0.41 11 11
PIAS3 0.024 0.005 -10000 0 -10000 0 0
PTPRE 0.023 0.02 -10000 0 -10000 0 0
PIAS1 0.024 0.006 -10000 0 -10000 0 0
RAC1 0.024 0.005 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.02 0.1 -10000 0 -0.27 39 39
LMO4 0.016 0.045 -10000 0 -0.42 3 3
STAT3 (dimer)/PIAS3 -0.047 0.23 -10000 0 -0.6 29 29
MCL1 0.057 0.096 0.41 1 -0.45 2 3
Visual signal transduction: Rods

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
mol:K + 0.024 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.011 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.024 0.013 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.007 0.064 -10000 0 -0.24 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.018 0.017 -10000 0 -10000 0 0
GRK1 0.015 0.014 -10000 0 -10000 0 0
CNG Channel -0.029 0.12 -10000 0 -0.23 82 82
mol:Na + -0.007 0.091 -10000 0 -0.21 50 50
mol:ADP 0.015 0.014 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.025 0.072 -10000 0 -0.25 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.003 0.097 -10000 0 -0.22 50 50
CNGB1 -0.009 0.099 -10000 0 -0.4 20 20
RDH5 0.016 0.049 -10000 0 -0.4 4 4
SAG 0.019 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.042 0.085 0.36 4 -0.26 12 16
Na + (4 Units) -0.013 0.086 -10000 0 -0.2 50 50
RGS9 -0.006 0.098 -10000 0 -0.4 19 19
GNB1/GNGT1 0.009 0.088 -10000 0 -0.28 30 30
GNAT1/GDP 0.031 0.065 -10000 0 -0.21 21 21
GUCY2D 0.017 0.022 -10000 0 -10000 0 0
GNGT1 -0.011 0.12 -10000 0 -0.4 30 30
GUCY2F 0.019 0.009 -10000 0 -10000 0 0
GNB5 0.021 0.039 -10000 0 -0.4 3 3
mol:GMP (4 units) -0.02 0.087 0.14 2 -0.22 48 50
mol:11-cis-retinal 0.016 0.049 -10000 0 -0.4 4 4
mol:cGMP 0.027 0.05 -10000 0 -0.22 10 10
GNB1 0.025 0.005 -10000 0 -10000 0 0
Rhodopsin 0.024 0.039 -10000 0 -0.29 4 4
SLC24A1 0.024 0.005 -10000 0 -10000 0 0
CNGA1 -0.008 0.11 -10000 0 -0.4 24 24
Metarhodopsin II 0.02 0.013 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.039 0.054 -10000 0 -0.22 12 12
RGS9BP 0.018 0.024 -10000 0 -10000 0 0
Metarhodopsin II/Transducin -0.006 0.063 -10000 0 -0.22 29 29
GCAP Family/Ca ++ 0.028 0.049 -10000 0 -0.21 12 12
PDE6A/B -0.004 0.093 -10000 0 -0.28 32 32
mol:Pi 0.025 0.072 -10000 0 -0.25 22 22
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.02 0.073 -10000 0 -0.22 30 30
PDE6B -0.027 0.12 -10000 0 -0.4 32 32
PDE6A 0.024 0.009 -10000 0 -10000 0 0
PDE6G -0.008 0.1 -10000 0 -0.4 20 20
RHO 0.017 0.014 -10000 0 -10000 0 0
PDE6 0.007 0.12 -10000 0 -0.24 63 63
GUCA1A 0.018 0.021 -10000 0 -10000 0 0
GC2/GCAP Family 0.041 0.05 -10000 0 -0.22 10 10
GUCA1C 0.015 0.012 -10000 0 -10000 0 0
GUCA1B 0.01 0.075 -10000 0 -0.4 11 11
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.01 0.054 -10000 0 -0.23 16 16
EPHB2 -0.014 0.12 -10000 0 -0.4 30 30
Syndecan-2/TACI 0.008 0.049 -10000 0 -0.24 12 12
LAMA1 -0.071 0.17 -10000 0 -0.4 76 76
Syndecan-2/alpha2 ITGB1 0.015 0.09 -10000 0 -0.22 42 42
HRAS 0.024 0.005 -10000 0 -10000 0 0
Syndecan-2/CASK 0 0.041 -10000 0 -0.23 11 11
ITGA5 0.024 0.023 -10000 0 -0.4 1 1
BAX -0.002 0.036 -10000 0 -10000 0 0
EPB41 0.025 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.015 0.04 -10000 0 -0.21 11 11
LAMA3 -0.001 0.1 -10000 0 -0.4 21 21
EZR 0.025 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.039 -10000 0 -0.4 3 3
Syndecan-2/MMP2 0.002 0.069 -10000 0 -0.24 25 25
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.016 0.074 -10000 0 -0.28 20 20
dendrite morphogenesis -0.005 0.082 -10000 0 -0.24 38 38
Syndecan-2/GM-CSF 0.012 0.046 -10000 0 -0.24 11 11
determination of left/right symmetry 0.001 0.049 -10000 0 -0.28 11 11
Syndecan-2/PKC delta 0.016 0.047 -10000 0 -0.23 12 12
GNB2L1 0.025 0.004 -10000 0 -10000 0 0
MAPK3 0.013 0.058 0.19 20 -0.22 11 31
MAPK1 0.013 0.058 0.19 20 -0.22 11 31
Syndecan-2/RACK1 0.027 0.043 -10000 0 -0.2 11 11
NF1 0.024 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.001 0.049 -10000 0 -0.28 11 11
ITGA2 -0.002 0.1 -10000 0 -0.4 21 21
MAPK8 0.001 0.041 -10000 0 -0.23 11 11
Syndecan-2/alpha2/beta1 Integrin -0.02 0.12 -10000 0 -0.22 89 89
Syndecan-2/Kininogen 0.011 0.044 -10000 0 -0.24 10 10
ITGB1 0.024 0.005 -10000 0 -10000 0 0
SRC 0.018 0.062 0.18 26 -0.2 12 38
Syndecan-2/CASK/Protein 4.1 0.015 0.041 -10000 0 -0.21 11 11
extracellular matrix organization 0.016 0.045 -10000 0 -0.23 11 11
actin cytoskeleton reorganization 0.01 0.054 -10000 0 -0.23 16 16
Syndecan-2/Caveolin-2/Ras 0.027 0.049 -10000 0 -0.21 13 13
Syndecan-2/Laminin alpha3 0.002 0.073 -10000 0 -0.24 29 29
Syndecan-2/RasGAP 0.037 0.045 -10000 0 -0.19 11 11
alpha5/beta1 Integrin 0.035 0.02 -10000 0 -0.28 1 1
PRKCD 0.022 0.032 -10000 0 -0.4 2 2
Syndecan-2 dimer -0.005 0.082 -10000 0 -0.24 38 38
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.047 0.18 3 -0.2 12 15
RHOA 0.024 0.005 -10000 0 -10000 0 0
SDCBP 0.024 0.007 -10000 0 -10000 0 0
TNFRSF13B 0.01 0.043 -10000 0 -0.4 2 2
RASA1 0.025 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.016 0.074 -10000 0 -0.28 20 20
Syndecan-2/Synbindin 0.016 0.045 -10000 0 -0.23 11 11
TGFB1 0.024 0.009 -10000 0 -10000 0 0
CASP3 0.015 0.059 0.19 20 -0.21 12 32
FN1 0.012 0.059 -10000 0 -0.4 6 6
Syndecan-2/IL8 -0.005 0.082 -10000 0 -0.26 32 32
SDC2 0.001 0.05 -10000 0 -0.28 11 11
KNG1 0.015 0.022 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.016 0.045 -10000 0 -0.23 11 11
TRAPPC4 0.025 0.005 -10000 0 -10000 0 0
CSF2 0.018 0.017 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.016 0.045 -10000 0 -0.23 11 11
Syndecan-2/Syntenin/PI-4-5-P2 0.015 0.041 -10000 0 -0.21 11 11
Syndecan-2/Ezrin 0.029 0.045 -10000 0 -0.21 11 11
PRKACA 0.014 0.053 0.19 16 -0.21 10 26
angiogenesis -0.005 0.082 -10000 0 -0.26 32 32
MMP2 -0.002 0.092 -10000 0 -0.4 17 17
IL8 -0.015 0.11 -10000 0 -0.4 27 27
calcineurin-NFAT signaling pathway 0.008 0.049 -10000 0 -0.24 12 12
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.003 0.12 -10000 0 -0.4 27 27
HDAC1 0.025 0.009 -10000 0 -10000 0 0
AES 0.022 0.024 -10000 0 -0.4 1 1
FBXW11 0.025 0.004 -10000 0 -10000 0 0
DTX1 0.011 0.074 -10000 0 -0.4 11 11
LRP6/FZD1 0.035 0.02 -10000 0 -0.28 1 1
TLE1 0.024 0.007 -10000 0 -10000 0 0
AP1 -0.001 0.053 -10000 0 -0.22 17 17
NCSTN 0.021 0.01 -10000 0 -10000 0 0
ADAM10 0.019 0.045 -10000 0 -0.4 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.026 0.15 -10000 0 -0.6 14 14
NICD/RBPSUH -0.001 0.12 -10000 0 -0.4 27 27
WIF1 -0.11 0.17 -10000 0 -0.4 86 86
NOTCH1 -0.004 0.1 -10000 0 -0.42 20 20
PSENEN 0.023 0.023 -10000 0 -0.4 1 1
KREMEN2 -0.003 0.091 -10000 0 -0.4 16 16
DKK1 -0.053 0.13 -10000 0 -0.4 41 41
beta catenin/beta TrCP1 0.029 0.071 0.22 1 -0.3 4 5
APH1B 0.021 0.039 -10000 0 -0.4 3 3
APH1A 0.021 0.01 -10000 0 -10000 0 0
AXIN1 -0.014 0.11 -10000 0 -0.46 14 14
CtBP/CBP/TCF1/TLE1/AES -0.022 0.1 0.17 1 -0.23 61 62
PSEN1 0.025 0.004 -10000 0 -10000 0 0
FOS 0.014 0.055 -10000 0 -0.4 5 5
JUN 0.024 0.023 -10000 0 -0.4 1 1
MAP3K7 0.025 0.005 -10000 0 -10000 0 0
CTNNB1 0.018 0.071 0.21 2 -0.3 5 7
MAPK3 0.024 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.006 0.11 -10000 0 -0.26 49 49
HNF1A -0.058 0.17 -10000 0 -0.4 70 70
CTBP1 0.024 0.006 -10000 0 -10000 0 0
MYC -0.013 0.2 -10000 0 -1.2 10 10
NKD1 -0.008 0.078 -10000 0 -0.4 10 10
FZD1 0.023 0.024 -10000 0 -0.4 1 1
NOTCH1 precursor/Deltex homolog 1 -0.007 0.13 -10000 0 -0.41 26 26
apoptosis -0.001 0.053 -10000 0 -0.22 17 17
Delta 1/NOTCHprecursor -0.004 0.12 -10000 0 -0.4 27 27
DLL1 0.018 0.051 -10000 0 -0.4 5 5
PPARD 0.02 0.058 -10000 0 -0.99 1 1
Gamma Secretase 0.051 0.044 -10000 0 -0.2 4 4
APC -0.017 0.12 -10000 0 -0.49 16 16
DVL1 -0.003 0.066 -10000 0 -0.36 9 9
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
MAP3K7IP1 0 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.001 0.11 -10000 0 -0.25 55 55
LRP6 0.025 0.003 -10000 0 -10000 0 0
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
NLK 0.013 0.009 -10000 0 -10000 0 0
CCND1 -0.028 0.26 -10000 0 -1.2 15 15
WNT1 0.02 0.018 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.011 0.13 0.25 3 -0.44 17 20
DKK2 -0.029 0.13 -10000 0 -0.4 37 37
NOTCH1 precursor/DVL1 -0.017 0.14 -10000 0 -0.51 19 19
GSK3B 0.025 0.004 -10000 0 -10000 0 0
FRAT1 0.023 0.023 -10000 0 -0.4 1 1
NOTCH/Deltex homolog 1 -0.006 0.13 -10000 0 -0.41 26 26
PPP2R5D 0.023 0.044 0.23 9 -0.29 1 10
MAPK1 0.025 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.007 0.12 -10000 0 -0.22 83 83
RBPJ 0.025 0.007 -10000 0 -10000 0 0
CREBBP 0.025 0.008 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.012 0.068 -10000 0 -0.28 16 16
PRKCZ 0.022 0.032 -10000 0 -0.4 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.025 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.006 0.061 -10000 0 -0.23 16 16
IRAK/TOLLIP 0.011 0.053 -10000 0 -0.22 16 16
IKBKB 0.023 0.007 -10000 0 -10000 0 0
IKBKG 0.025 0.003 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.013 0.1 -10000 0 -0.29 42 42
IL1A 0 0.076 -10000 0 -0.4 10 10
IL1B -0.008 0.078 -10000 0 -0.34 17 17
IRAK/TRAF6/p62/Atypical PKCs 0.043 0.059 -10000 0 -0.2 16 16
IL1R2 -0.017 0.12 -10000 0 -0.4 33 33
IL1R1 0.015 0.063 -10000 0 -0.4 8 8
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.001 0.068 0.16 2 -0.27 12 14
TOLLIP 0.024 0.005 -10000 0 -10000 0 0
TICAM2 0.01 0.077 -10000 0 -0.4 12 12
MAP3K3 0.024 0.006 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.017 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.022 0.056 0.26 3 -0.3 2 5
JUN -0.02 0.061 0.18 12 -0.27 4 16
MAP3K7 0.025 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.029 0.09 -10000 0 -0.22 36 36
IL1 alpha/IL1R1/IL1RAP/MYD88 0.039 0.07 -10000 0 -0.22 22 22
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.048 0.071 -10000 0 -0.21 22 22
IL1 beta fragment/IL1R1/IL1RAP 0.012 0.082 -10000 0 -0.25 28 28
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MAPK8 -0.018 0.063 0.2 12 -0.2 22 34
IRAK1 -0.015 0.051 -10000 0 -0.24 16 16
IL1RN/IL1R1 0.008 0.089 -10000 0 -0.3 25 25
IRAK4 0.025 0.003 -10000 0 -10000 0 0
PRKCI 0.022 0.023 -10000 0 -0.4 1 1
TRAF6 0.025 0.005 -10000 0 -10000 0 0
PI3K 0.025 0.052 -10000 0 -0.28 9 9
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.003 0.073 -10000 0 -0.26 19 19
CHUK 0.024 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.012 0.082 -10000 0 -0.25 28 28
IL1 beta/IL1R2 -0.011 0.11 0.22 3 -0.28 45 48
IRAK/TRAF6/TAK1/TAB1/TAB2 0.019 0.048 -10000 0 -0.19 15 15
NF kappa B1 p50/RelA 0.019 0.081 -10000 0 -0.22 32 32
IRAK3 0.01 0.067 -10000 0 -0.4 8 8
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.028 0.096 -10000 0 -0.24 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.009 0.058 -10000 0 -0.21 22 22
IL1 alpha/IL1R1/IL1RAP 0.028 0.071 -10000 0 -0.24 22 22
RELA 0.025 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.024 0.007 -10000 0 -10000 0 0
MYD88 0.025 0.005 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.026 0.059 0.18 7 -0.21 16 23
IL1RAP 0.016 0.056 -10000 0 -0.4 6 6
UBE2N 0.025 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.009 0.087 -10000 0 -0.3 12 12
CASP1 0.013 0.065 -10000 0 -0.4 8 8
IL1RN/IL1R2 -0.014 0.12 -10000 0 -0.32 45 45
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.023 0.083 -10000 0 -0.24 28 28
TMEM189-UBE2V1 -0.007 0.089 -10000 0 -0.4 16 16
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.002 0.073 -10000 0 -0.29 12 12
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
IL1RN -0.004 0.099 -10000 0 -0.4 20 20
TRAF6/TAK1/TAB1/TAB2 0.034 0.05 -10000 0 -0.2 15 15
MAP2K6 -0.017 0.065 0.2 14 -0.2 23 37
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.022 0.024 -10000 0 -0.4 1 1
Caspase 8 (4 units) 0.018 0.072 -10000 0 -0.28 6 6
NEF -0.009 0.041 -10000 0 -0.17 19 19
NFKBIA 0.015 0.033 -10000 0 -10000 0 0
BIRC3 -0.018 0.12 -10000 0 -0.45 26 26
CYCS 0.012 0.085 0.17 41 -0.24 18 59
RIPK1 0.025 0.004 -10000 0 -10000 0 0
CD247 -0.007 0.099 -10000 0 -0.3 29 29
MAP2K7 -0.011 0.2 -10000 0 -0.67 24 24
protein ubiquitination -0.003 0.091 0.29 5 -0.3 10 15
CRADD 0.025 0.003 -10000 0 -10000 0 0
DAXX 0.025 0.003 -10000 0 -10000 0 0
FAS 0.017 0.051 -10000 0 -0.4 5 5
BID 0.018 0.089 0.18 47 -0.25 18 65
NF-kappa-B/RelA/I kappa B alpha 0.029 0.08 -10000 0 -0.24 26 26
TRADD 0.023 0.008 -10000 0 -10000 0 0
MAP3K5 0.023 0.025 -10000 0 -0.4 1 1
CFLAR 0.025 0.003 -10000 0 -10000 0 0
FADD 0.025 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.029 0.08 -10000 0 -0.24 26 26
MAPK8 -0.005 0.19 0.39 4 -0.62 24 28
APAF1 0.025 0.003 -10000 0 -10000 0 0
TRAF1 0.022 0.024 -10000 0 -0.4 1 1
TRAF2 0.024 0.006 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.002 0.073 0.16 4 -0.25 23 27
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.014 0.1 -10000 0 -0.33 20 20
CHUK -0.006 0.091 0.25 3 -0.31 11 14
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.06 0.046 -10000 0 -0.21 7 7
TCRz/NEF -0.011 0.097 -10000 0 -0.32 29 29
TNF -0.017 0.11 -10000 0 -0.4 27 27
FASLG -0.028 0.14 -10000 0 -0.48 28 28
NFKB1 0.016 0.032 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.028 0.072 -10000 0 -0.25 21 21
CASP6 0.032 0.12 -10000 0 -0.5 11 11
CASP7 -0.007 0.15 -10000 0 -0.47 28 28
RELA 0.016 0.033 -10000 0 -10000 0 0
CASP2 0.024 0.005 -10000 0 -10000 0 0
CASP3 -0.001 0.16 0.36 5 -0.46 27 32
TNFRSF1A 0.024 0.023 -10000 0 -0.4 1 1
TNFR1A/BAG4 0.032 0.026 -10000 0 -0.28 2 2
CASP8 0.024 0.023 -10000 0 -0.4 1 1
CASP9 0.025 0.005 -10000 0 -10000 0 0
MAP3K14 -0.007 0.092 -10000 0 -0.32 13 13
APAF-1/Caspase 9 0.003 0.11 0.16 1 -0.34 21 22
BCL2 -0.01 0.18 0.33 4 -0.54 27 31
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.008 0.047 -10000 0 -0.26 8 8
NFATC2 -0.015 0.06 -10000 0 -0.25 18 18
NFATC3 -0.002 0.027 -10000 0 -10000 0 0
CD40LG -0.077 0.17 0.33 1 -0.45 37 38
PTGS2 -0.081 0.17 0.33 1 -0.43 52 53
JUNB 0.019 0.045 -10000 0 -0.4 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.023 -10000 0 -10000 0 0
CaM/Ca2+ 0.006 0.023 -10000 0 -10000 0 0
CALM1 0.013 0.022 -10000 0 -10000 0 0
JUN 0.012 0.032 -10000 0 -0.42 1 1
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.013 0.01 -10000 0 -10000 0 0
FOSL1 0.01 0.07 -10000 0 -0.4 9 9
CREM 0.024 0.006 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.022 0.11 -10000 0 -0.31 21 21
FOS 0.002 0.058 -10000 0 -0.41 5 5
IFNG -0.074 0.16 0.33 1 -0.41 40 41
AP-1/NFAT1-c-4 -0.048 0.18 -10000 0 -0.43 34 34
FASLG -0.069 0.16 0.33 1 -0.43 41 42
NFAT1-c-4/ICER1 -0.018 0.084 -10000 0 -0.24 25 25
IL2RA -0.072 0.16 0.33 1 -0.44 35 36
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSF2 -0.068 0.14 0.33 1 -0.4 28 29
JunB/Fra1/NFAT1-c-4 -0.016 0.094 -10000 0 -0.24 25 25
IL4 -0.068 0.14 0.33 1 -0.4 28 29
IL2 -0.014 0.16 -10000 0 -0.91 11 11
IL3 -0.002 0.096 -10000 0 -0.61 8 8
FKBP1A 0.025 0.004 -10000 0 -10000 0 0
BATF3 0.014 0.052 -10000 0 -0.4 5 5
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.017 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.024 0.005 -9999 0 -10000 0 0
EGFR 0.013 0.07 -9999 0 -0.4 10 10
EGF/EGFR 0.016 0.085 -9999 0 -0.21 42 42
EGF/EGFR dimer/SHC/GRB2/SOS1 0.033 0.079 -9999 0 -0.22 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.019 0.041 -9999 0 -0.4 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.011 0.1 -9999 0 -0.4 21 21
EGF/EGFR dimer/SHC 0.018 0.08 -9999 0 -0.25 27 27
mol:GDP 0.029 0.076 -9999 0 -0.21 27 27
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.01 0.077 -9999 0 -0.4 12 12
GRB2/SOS1 0.035 0.01 -9999 0 -10000 0 0
HRAS/GTP 0.016 0.066 -9999 0 -0.2 27 27
SHC1 0.021 0.01 -9999 0 -10000 0 0
HRAS/GDP 0.028 0.073 -9999 0 -0.2 27 27
FRAP1 -0.025 0.053 -9999 0 -0.2 27 27
EGF/EGFR dimer 0.001 0.093 -9999 0 -0.3 30 30
SOS1 0.025 0.004 -9999 0 -10000 0 0
GRB2 0.024 0.006 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.02 0.066 -9999 0 -0.28 15 15
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.002 0.085 0.4 14 -10000 0 14
PI3K Class IB/PDE3B 0.002 0.085 -10000 0 -0.4 14 14
PDE3B 0.002 0.085 -10000 0 -0.4 14 14
Coregulation of Androgen receptor activity

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
NRIP1 0.015 0.064 -10000 0 -0.4 8 8
SVIL 0.013 0.067 -10000 0 -0.4 9 9
ZNF318 0.026 0.018 0.19 4 -10000 0 4
JMJD2C 0.001 0.01 -10000 0 -0.1 2 2
T-DHT/AR/Ubc9 -0.01 0.1 -10000 0 -0.24 52 52
CARM1 0.023 0.008 -10000 0 -10000 0 0
PRDX1 0.025 0.003 -10000 0 -10000 0 0
PELP1 0.024 0.007 -10000 0 -10000 0 0
CTNNB1 0.023 0.025 -10000 0 -0.4 1 1
AKT1 0.025 0.006 -10000 0 -10000 0 0
PTK2B 0.021 0.025 -10000 0 -0.4 1 1
MED1 0.024 0.008 -10000 0 -10000 0 0
MAK 0.001 0.091 0.19 3 -0.4 16 19
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.022 0.034 -10000 0 -0.4 2 2
GSN 0.022 0.026 -10000 0 -0.4 1 1
NCOA2 0.01 0.074 -10000 0 -0.4 11 11
NCOA6 0.024 0.011 -10000 0 -10000 0 0
DNA-PK 0.044 0.032 0.21 3 -0.24 2 5
NCOA4 0.024 0.008 -10000 0 -10000 0 0
PIAS3 0.024 0.01 -10000 0 -10000 0 0
cell proliferation -0.022 0.14 -10000 0 -0.66 16 16
XRCC5 0.025 0.006 -10000 0 -10000 0 0
UBE3A 0.023 0.016 -10000 0 -0.12 4 4
T-DHT/AR/SNURF -0.04 0.12 -10000 0 -0.25 82 82
FHL2 -0.018 0.17 -10000 0 -0.86 12 12
RANBP9 0.024 0.011 -10000 0 -10000 0 0
JMJD1A -0.01 0.049 -10000 0 -0.14 44 44
CDK6 0.009 0.078 -10000 0 -0.4 12 12
TGFB1I1 0.021 0.029 -10000 0 -0.4 1 1
T-DHT/AR/CyclinD1 -0.019 0.11 -10000 0 -0.24 63 63
XRCC6 0.024 0.008 -10000 0 -10000 0 0
T-DHT/AR -0.011 0.13 -10000 0 -0.24 74 74
CTDSP1 0.024 0.007 -10000 0 -10000 0 0
CTDSP2 0.026 0.012 0.16 1 -10000 0 1
BRCA1 0.021 0.034 -10000 0 -0.4 2 2
TCF4 0.019 0.051 -10000 0 -0.4 5 5
CDKN2A -0.024 0.12 -10000 0 -0.4 27 27
SRF 0.025 0.028 -10000 0 -0.14 5 5
NKX3-1 -0.067 0.23 -10000 0 -0.68 36 36
KLK3 -0.013 0.14 -10000 0 -1.3 4 4
TMF1 0.024 0.007 -10000 0 -10000 0 0
HNRNPA1 0.026 0.006 -10000 0 -10000 0 0
AOF2 -0.001 0.007 -10000 0 -0.069 4 4
APPL1 0.013 0.011 0.13 1 -10000 0 1
T-DHT/AR/Caspase 8 -0.009 0.1 -10000 0 -0.26 45 45
AR -0.038 0.14 -10000 0 -0.4 46 46
UBA3 0.024 0.008 -10000 0 -10000 0 0
PATZ1 0.025 0.008 -10000 0 -10000 0 0
PAWR 0.025 0.005 -10000 0 -10000 0 0
PRKDC 0.021 0.033 -10000 0 -0.4 2 2
PA2G4 0.025 0.009 -10000 0 -10000 0 0
UBE2I 0.025 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.005 0.092 -10000 0 -0.22 49 49
RPS6KA3 0.024 0.012 -10000 0 -0.1 1 1
T-DHT/AR/ARA70 -0.008 0.1 -10000 0 -0.24 48 48
LATS2 0.025 0.008 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.006 0.094 0.14 2 -0.22 51 53
Cyclin D3/CDK11 p58 0.019 0.003 -10000 0 -10000 0 0
VAV3 -0.005 0.11 -10000 0 -0.4 25 25
KLK2 -0.017 0.086 -10000 0 -0.74 3 3
CASP8 0.024 0.023 -10000 0 -0.4 1 1
T-DHT/AR/TIF2/CARM1 0 0.1 -10000 0 -0.24 45 45
TMPRSS2 -0.076 0.26 -10000 0 -0.83 34 34
CCND1 0.008 0.08 -10000 0 -0.4 13 13
PIAS1 0.023 0.016 -10000 0 -0.12 4 4
mol:T-DHT -0.007 0.025 -10000 0 -0.068 44 44
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.022 0.022 -10000 0 -0.17 4 4
T-DHT/AR/CDK6 -0.016 0.11 -10000 0 -0.25 59 59
CMTM2 0.011 0.067 -10000 0 -0.4 9 9
SNURF -0.026 0.12 -10000 0 -0.4 33 33
ZMIZ1 0.013 0.034 -10000 0 -0.13 2 2
CCND3 0.025 0.003 -10000 0 -10000 0 0
TGIF1 0.025 0.007 -10000 0 -10000 0 0
FKBP4 0.024 0.011 -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 0.017 0.059 -10000 0 -0.4 7 7
ANTXR2 0.012 0.071 -10000 0 -0.4 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.012 -10000 0 -0.063 13 13
monocyte activation -0.038 0.15 -10000 0 -0.42 46 46
MAP2K2 -0.028 0.15 -10000 0 -0.58 26 26
MAP2K1 -0.004 0.012 0.11 1 -0.085 2 3
MAP2K7 -0.004 0.012 0.14 1 -0.085 2 3
MAP2K6 -0.01 0.036 -10000 0 -0.2 11 11
CYAA -0.013 0.047 -10000 0 -0.24 13 13
MAP2K4 -0.006 0.018 -10000 0 -0.14 4 4
IL1B -0.01 0.052 0.21 5 -0.19 19 24
Channel 0.02 0.057 -10000 0 -0.26 13 13
NLRP1 -0.008 0.027 -10000 0 -0.15 10 10
CALM1 0.025 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.002 0.052 -10000 0 -0.38 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.012 0.063 13 -10000 0 13
MAPK3 -0.004 0.013 0.14 1 -0.079 3 4
MAPK1 -0.005 0.011 -10000 0 -0.085 3 3
PGR -0.047 0.083 0.14 1 -0.2 79 80
PA/Cellular Receptors 0.02 0.063 -10000 0 -0.29 13 13
apoptosis -0.003 0.012 -10000 0 -0.063 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.019 0.055 -10000 0 -0.25 13 13
macrophage activation -0.005 0.018 0.16 3 -10000 0 3
TNF -0.017 0.11 -10000 0 -0.4 27 27
VCAM1 -0.038 0.15 -10000 0 -0.42 46 46
platelet activation 0.002 0.052 -10000 0 -0.38 6 6
MAPKKK cascade 0.002 0.024 0.11 7 -0.097 8 15
IL18 -0.013 0.044 -10000 0 -0.22 13 13
negative regulation of macrophage activation -0.003 0.012 -10000 0 -0.063 13 13
LEF -0.003 0.012 -10000 0 -0.063 13 13
CASP1 -0.004 0.019 -10000 0 -0.076 22 22
mol:cAMP 0.002 0.052 -10000 0 -0.38 6 6
necrosis -0.003 0.012 -10000 0 -0.063 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.02 0.054 -10000 0 -0.24 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.006 0.015 -10000 0 -0.28 1 1
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.03 0.019 -10000 0 -10000 0 0
STXBP1 0.011 0.071 -10000 0 -0.4 10 10
ACh/CHRNA1 -0.019 0.083 0.11 1 -0.23 40 41
RAB3GAP2/RIMS1/UNC13B 0.039 0.02 -10000 0 -10000 0 0
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 0.017 0.022 -10000 0 -10000 0 0
mol:ACh -0.008 0.037 0.086 12 -0.11 28 40
RAB3GAP2 0.021 0.009 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.011 0.062 -10000 0 -0.16 29 29
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.019 0.083 0.11 1 -0.23 40 41
UNC13B 0.025 0.004 -10000 0 -10000 0 0
CHRNA1 -0.024 0.12 -10000 0 -0.4 31 31
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.028 0.09 -10000 0 -0.25 44 44
SNAP25 -0.018 0.067 -10000 0 -0.25 28 28
VAMP2 0.004 0.001 -10000 0 -10000 0 0
SYT1 -0.038 0.14 -10000 0 -0.4 42 42
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.013 0.045 -10000 0 -0.24 11 11
STX1A/SNAP25 fragment 1/VAMP2 0.011 0.062 -10000 0 -0.16 29 29
ErbB2/ErbB3 signaling events

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
USP8 -0.004 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.077 0.2 1 -0.23 7 8
NFATC4 -0.004 0.083 0.36 11 -0.23 3 14
ERBB2IP 0.021 0.033 -10000 0 -0.4 2 2
HSP90 (dimer) 0.025 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis 0.005 0.056 0.17 2 -0.22 17 19
JUN 0.012 0.081 0.2 9 -0.32 10 19
HRAS 0.024 0.005 -10000 0 -10000 0 0
DOCK7 -0.018 0.058 0.25 3 -0.21 16 19
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.018 0.058 0.23 1 -0.22 15 16
AKT1 0.006 0.007 -10000 0 -10000 0 0
BAD -0.004 0.007 -10000 0 -10000 0 0
MAPK10 -0.008 0.077 0.26 14 -0.17 15 29
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.008 0.062 0.18 2 -0.23 17 19
RAF1 0.025 0.088 0.27 11 -0.3 3 14
ErbB2/ErbB3/neuregulin 2 0.006 0.07 0.23 1 -0.23 26 27
STAT3 -0.011 0.19 -10000 0 -0.82 18 18
cell migration 0.006 0.087 0.27 22 -0.19 5 27
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.026 0.22 0.37 1 -0.55 48 49
FOS -0.004 0.15 0.27 5 -0.34 46 51
NRAS 0.019 0.05 -10000 0 -0.4 5 5
mol:Ca2+ 0.005 0.056 0.17 2 -0.22 17 19
MAPK3 -0.016 0.19 0.33 3 -0.49 39 42
MAPK1 -0.019 0.2 0.31 5 -0.49 41 46
JAK2 -0.021 0.06 0.25 3 -0.21 17 20
NF2 0.01 0.011 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.003 0.053 0.18 3 -0.22 15 18
NRG1 0 0.085 -10000 0 -0.4 14 14
GRB2/SOS1 0.035 0.01 -10000 0 -10000 0 0
MAPK8 -0.002 0.067 0.2 1 -0.25 15 16
MAPK9 0.001 0.069 0.27 14 -10000 0 14
ERBB2 -0.015 0.04 0.46 2 -0.3 1 3
ERBB3 0.02 0.045 -10000 0 -0.4 4 4
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
apoptosis 0.003 0.013 -10000 0 -0.21 1 1
STAT3 (dimer) -0.01 0.18 -10000 0 -0.8 18 18
RNF41 -0.007 0.008 -10000 0 -10000 0 0
FRAP1 -0.002 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.009 0.04 -10000 0 -0.16 16 16
ErbB2/ErbB2/HSP90 (dimer) 0.009 0.024 0.24 1 -0.25 1 2
CHRNA1 -0.027 0.21 0.29 5 -0.56 41 46
myelination 0.013 0.11 0.36 23 -0.28 1 24
PPP3CB -0.017 0.054 0.24 3 -0.2 15 18
KRAS 0.025 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.039 0.065 0.21 2 -0.2 14 16
NRG2 -0.009 0.11 -10000 0 -0.4 24 24
mol:GDP 0.003 0.052 0.18 3 -0.22 15 18
SOS1 0.025 0.004 -10000 0 -10000 0 0
MAP2K2 0.012 0.091 0.27 10 -0.32 3 13
SRC 0.022 0.032 -10000 0 -0.4 2 2
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.018 0.059 0.25 3 -0.21 16 19
MAP2K1 -0.011 0.18 0.34 1 -0.54 18 19
heart morphogenesis 0.005 0.056 0.17 2 -0.22 17 19
RAS family/GDP 0.043 0.078 0.25 2 -0.21 14 16
GRB2 0.024 0.006 -10000 0 -10000 0 0
PRKACA 0.012 0.008 -10000 0 -10000 0 0
CHRNE 0.005 0.034 0.077 5 -0.17 10 15
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
activation of caspase activity -0.006 0.007 -10000 0 -10000 0 0
nervous system development 0.005 0.056 0.17 2 -0.22 17 19
CDC42 0.025 0.005 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.029 0.02 -10000 0 -10000 0 0
HSPA8 0.014 0.046 -10000 0 -0.4 4 4
SMAD3/SMAD4/ER alpha 0.006 0.12 0.21 3 -0.27 45 48
AKT1 0.022 0.02 -10000 0 -10000 0 0
GSC -0.24 0.5 -10000 0 -1.2 73 73
NKX2-5 0.008 0.037 -10000 0 -0.16 2 2
muscle cell differentiation 0.007 0.098 0.33 11 -10000 0 11
SMAD2-3/SMAD4/SP1 0.028 0.1 -10000 0 -0.28 10 10
SMAD4 -0.001 0.059 -10000 0 -0.22 6 6
CBFB 0.023 0.008 -10000 0 -10000 0 0
SAP18 0.024 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.046 0.065 -10000 0 -0.24 13 13
SMAD3/SMAD4/VDR 0.073 0.064 -10000 0 -0.23 2 2
MYC 0.014 0.061 -10000 0 -0.41 7 7
CDKN2B -0.052 0.24 -10000 0 -1.1 14 14
AP1 0.026 0.055 -10000 0 -0.28 4 4
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.009 0.078 -10000 0 -0.4 7 7
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.048 0.11 -10000 0 -0.35 22 22
SP3 0.026 0.005 -10000 0 -10000 0 0
CREB1 0.025 0.004 -10000 0 -10000 0 0
FOXH1 -0.025 0.11 -10000 0 -0.2 71 71
SMAD3/SMAD4/GR 0.035 0.072 -10000 0 -0.25 9 9
GATA3 -0.002 0.084 -10000 0 -0.32 17 17
SKI/SIN3/HDAC complex/NCoR1 0.015 0.061 -10000 0 -0.46 4 4
MEF2C/TIF2 -0.036 0.11 -10000 0 -0.26 30 30
endothelial cell migration 0.005 0.21 0.97 15 -10000 0 15
MAX 0.025 0.009 -10000 0 -10000 0 0
RBBP7 0.025 0.003 -10000 0 -10000 0 0
RBBP4 0.024 0.004 -10000 0 -10000 0 0
RUNX2 0.001 0.079 -10000 0 -0.4 11 11
RUNX3 -0.001 0.097 -10000 0 -0.4 19 19
RUNX1 0.018 0.055 -10000 0 -0.4 6 6
CTBP1 0.024 0.005 -10000 0 -10000 0 0
NR3C1 0.016 0.059 -10000 0 -0.39 7 7
VDR 0.021 0.039 -10000 0 -0.4 3 3
CDKN1A -0.017 0.24 -10000 0 -1.1 15 15
KAT2B 0.018 0.06 -10000 0 -0.4 7 7
SMAD2/SMAD2/SMAD4/FOXH1 -0.02 0.14 -10000 0 -0.26 80 80
DCP1A 0.024 0.005 -10000 0 -10000 0 0
SKI 0.024 0.005 -10000 0 -10000 0 0
SERPINE1 -0.006 0.22 -10000 0 -1 14 14
SMAD3/SMAD4/ATF2 0.04 0.056 -10000 0 -0.19 2 2
SMAD3/SMAD4/ATF3 0.029 0.063 -10000 0 -0.25 6 6
SAP30 0.023 0.023 -10000 0 -0.4 1 1
Cbp/p300/PIAS3 0.06 0.046 0.2 1 -10000 0 1
JUN 0.009 0.05 -10000 0 -0.28 4 4
SMAD3/SMAD4/IRF7 0.033 0.074 -10000 0 -0.28 9 9
TFE3 0.025 0.018 -10000 0 -10000 0 0
COL1A2 0.011 0.13 -10000 0 -0.79 9 9
mesenchymal cell differentiation -0.024 0.079 0.26 12 -10000 0 12
DLX1 0.011 0.032 -10000 0 -10000 0 0
TCF3 0.024 0.007 -10000 0 -10000 0 0
FOS 0.012 0.057 -10000 0 -0.41 5 5
SMAD3/SMAD4/Max 0.041 0.059 -10000 0 -0.19 2 2
Cbp/p300/SNIP1 0.051 0.024 -10000 0 -10000 0 0
ZBTB17 0.026 0.013 -10000 0 -10000 0 0
LAMC1 0.006 0.049 0.21 3 -0.5 1 4
TGIF2/HDAC complex/SMAD3/SMAD4 0.038 0.06 -10000 0 -0.22 4 4
IRF7 0.014 0.067 -10000 0 -0.4 9 9
ESR1 -0.027 0.14 -10000 0 -0.4 44 44
HNF4A -0.064 0.16 -10000 0 -0.4 62 62
MEF2C -0.035 0.12 0.24 9 -0.23 68 77
SMAD2-3/SMAD4 0.014 0.087 -10000 0 -0.25 8 8
Cbp/p300/Src-1 0.054 0.032 -10000 0 -10000 0 0
IGHV3OR16-13 0.003 0.041 -10000 0 -0.34 4 4
TGIF2/HDAC complex 0.022 0.032 -10000 0 -0.4 2 2
CREBBP 0.028 0.015 -10000 0 -10000 0 0
SKIL 0.021 0.032 -10000 0 -0.4 2 2
HDAC1 0.025 0.003 -10000 0 -10000 0 0
HDAC2 0.025 0.003 -10000 0 -10000 0 0
SNIP1 0.024 0.005 -10000 0 -10000 0 0
GCN5L2 0.005 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.044 0.062 -10000 0 -0.25 2 2
MSG1/HSC70 0.011 0.071 -10000 0 -0.29 17 17
SMAD2 -0.002 0.059 -10000 0 -0.12 48 48
SMAD3 0.021 0.042 -10000 0 -0.15 2 2
SMAD3/E2F4-5/DP1/p107/SMAD4 0.018 0.038 -10000 0 -0.24 2 2
SMAD2/SMAD2/SMAD4 -0.01 0.062 0.2 2 -0.24 16 18
NCOR1 0.023 0.007 -10000 0 -10000 0 0
NCOA2 0.01 0.074 -10000 0 -0.4 11 11
NCOA1 0.025 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.025 0.022 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.038 0.1 -10000 0 -0.29 7 7
IFNB1 -0.007 0.055 0.2 1 -0.25 9 10
SMAD3/SMAD4/MEF2C -0.01 0.12 -10000 0 -0.3 18 18
CITED1 0.001 0.083 -10000 0 -0.4 13 13
SMAD2-3/SMAD4/ARC105 0.027 0.085 -10000 0 -0.24 6 6
RBL1 0.023 0.032 -10000 0 -0.4 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.001 0.092 -10000 0 -0.42 13 13
RUNX1-3/PEBPB2 0.028 0.074 -10000 0 -0.25 23 23
SMAD7 0.019 0.078 -10000 0 -0.46 2 2
MYC/MIZ-1 0.027 0.05 0.18 6 -0.29 7 13
SMAD3/SMAD4 0.046 0.12 0.26 56 -0.38 8 64
IL10 -0.015 0.1 0.2 3 -0.41 16 19
PIASy/HDAC complex 0.012 0.024 -10000 0 -10000 0 0
PIAS3 0.026 0.01 -10000 0 -10000 0 0
CDK2 0.028 0.015 -10000 0 -10000 0 0
IL5 -0.01 0.08 0.2 6 -0.27 21 27
CDK4 0.03 0.015 -10000 0 -10000 0 0
PIAS4 0.012 0.024 -10000 0 -10000 0 0
ATF3 0.014 0.044 -10000 0 -0.4 3 3
SMAD3/SMAD4/SP1 0.041 0.079 -10000 0 -0.23 14 14
FOXG1 -0.1 0.18 -10000 0 -0.4 96 96
FOXO3 0.009 0.021 -10000 0 -10000 0 0
FOXO1 0.009 0.021 -10000 0 -10000 0 0
FOXO4 0.009 0.021 -10000 0 -10000 0 0
heart looping -0.034 0.12 0.24 9 -0.23 68 77
CEBPB 0.023 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.035 0.059 -10000 0 -0.18 4 4
MYOD1 0.011 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.015 0.12 -10000 0 -0.26 65 65
SMAD3/SMAD4/GATA3 0.025 0.097 -10000 0 -0.3 21 21
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.032 -10000 0 -0.4 2 2
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.043 0.09 -10000 0 -0.24 21 21
SMAD3/SMAD4/SP1-3 0.057 0.077 -10000 0 -0.23 6 6
MED15 0.025 0.005 -10000 0 -10000 0 0
SP1 0.019 0.037 -10000 0 -0.16 6 6
SIN3B 0.024 0.006 -10000 0 -10000 0 0
SIN3A 0.024 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.008 0.13 -10000 0 -0.24 80 80
ITGB5 0.008 0.058 0.2 6 -0.25 3 9
TGIF/SIN3/HDAC complex/CtBP 0.021 0.052 -10000 0 -0.46 3 3
SMAD3/SMAD4/AR 0.005 0.11 -10000 0 -0.26 46 46
AR -0.028 0.14 -10000 0 -0.4 42 42
negative regulation of cell growth 0.022 0.06 -10000 0 -0.32 1 1
SMAD3/SMAD4/MYOD 0.034 0.057 -10000 0 -0.18 5 5
E2F5 0.024 0.007 -10000 0 -10000 0 0
E2F4 0.023 0.008 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.009 0.11 -10000 0 -0.19 76 76
SMAD2-3/SMAD4/FOXO1-3a-4 -0.001 0.076 -10000 0 -0.32 14 14
TFDP1 0.024 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.047 0.064 -10000 0 -0.28 4 4
SMAD3/SMAD4/RUNX2 0.025 0.079 -10000 0 -0.26 12 12
TGIF2 0.022 0.032 -10000 0 -0.4 2 2
TGIF1 0.025 0.005 -10000 0 -10000 0 0
ATF2 0.025 0.004 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.004 -10000 0 -10000 0 0
VLDLR 0.013 0.07 -10000 0 -0.4 10 10
LRPAP1 0.025 0.005 -10000 0 -10000 0 0
NUDC 0.025 0.004 -10000 0 -10000 0 0
RELN/LRP8 0.005 0.1 -10000 0 -0.24 52 52
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
KATNA1 0.025 0.003 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.028 0.084 0.18 6 -0.22 52 58
IQGAP1/CaM 0.036 0.009 -10000 0 -10000 0 0
DAB1 0.013 0.029 -10000 0 -10000 0 0
IQGAP1 0.025 0.005 -10000 0 -10000 0 0
PLA2G7 0.01 0.072 -10000 0 -0.4 10 10
CALM1 0.025 0.004 -10000 0 -10000 0 0
DYNLT1 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.034 0.026 -10000 0 -0.28 2 2
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.025 0.003 -10000 0 -10000 0 0
CDK5R1 0.021 0.034 -10000 0 -0.4 2 2
LIS1/Poliovirus Protein 3A 0.009 0.003 -10000 0 -10000 0 0
CDK5R2 0.012 0.031 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.009 0.11 -10000 0 -0.24 58 58
YWHAE 0.024 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.018 0.078 0.31 3 -0.24 2 5
MAP1B -0.009 0.058 -10000 0 -0.25 20 20
RAC1 0.012 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.023 0.077 0.18 2 -0.2 51 53
RELN -0.053 0.15 -10000 0 -0.4 50 50
PAFAH/LIS1 0.016 0.046 -10000 0 -0.24 10 10
LIS1/CLIP170 0.026 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.012 0.069 -10000 0 -0.23 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.02 0.09 -10000 0 -0.21 61 61
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.027 0.07 0.24 2 -0.23 4 6
LIS1/IQGAP1 0.025 0.009 -10000 0 -10000 0 0
RHOA 0.012 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.011 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.025 0.007 -10000 0 -10000 0 0
PAFAH1B2 0.024 0.023 -10000 0 -0.4 1 1
MAP1B/LIS1/Dynein heavy chain 0.011 0.047 -10000 0 -0.16 18 18
NDEL1/Katanin 60/Dynein heavy chain -0.012 0.083 0.3 3 -0.25 2 5
LRP8 0.022 0.033 -10000 0 -0.4 2 2
NDEL1/Katanin 60 -0.021 0.079 0.31 3 -0.24 3 6
P39/CDK5 -0.031 0.074 0.18 3 -0.2 46 49
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.008 -10000 0 -10000 0 0
CDK5 -0.041 0.071 0.17 4 -0.21 52 56
PPP2R5D 0.025 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.022 0.007 -10000 0 -10000 0 0
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.003 0.096 -10000 0 -0.21 57 57
RELN/VLDLR 0.011 0.1 -10000 0 -0.22 60 60
CDC42 0.012 0.004 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 -0.018 0.11 -10000 0 -0.4 19 19
BAG4 0.022 0.024 -10000 0 -0.4 1 1
BAD -0.003 0.045 0.14 7 -0.15 10 17
NFKBIA 0.025 0.004 -10000 0 -10000 0 0
BIRC3 -0.011 0.11 -10000 0 -0.4 26 26
BAX -0.005 0.044 0.15 5 -0.15 10 15
EnzymeConsortium:3.1.4.12 -0.004 0.03 0.065 6 -0.094 18 24
IKBKB -0.002 0.11 0.28 8 -0.39 13 21
MAP2K2 -0.004 0.054 0.2 9 -0.21 6 15
MAP2K1 -0.005 0.054 0.2 9 -0.22 6 15
SMPD1 -0.004 0.035 -10000 0 -0.13 10 10
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.009 0.12 0.24 2 -0.39 18 20
MAP2K4 -0.004 0.044 0.15 4 -0.2 6 10
protein ubiquitination -0.011 0.11 0.27 5 -0.38 17 22
EnzymeConsortium:2.7.1.37 -0.007 0.06 0.21 9 -0.23 6 15
response to UV 0 0.001 0.002 10 -0.002 4 14
RAF1 -0.005 0.057 0.2 9 -0.22 6 15
CRADD 0.025 0.003 -10000 0 -10000 0 0
mol:ceramide -0.004 0.044 0.11 4 -0.13 19 23
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.006 -10000 0 -10000 0 0
MADD 0.025 0.005 -10000 0 -10000 0 0
MAP3K1 -0.005 0.045 0.14 5 -0.16 10 15
TRADD 0.023 0.008 -10000 0 -10000 0 0
RELA/p50 0.025 0.003 -10000 0 -10000 0 0
MAPK3 -0.004 0.058 0.2 9 -0.2 8 17
MAPK1 -0.005 0.061 0.2 9 -0.22 9 18
p50/RELA/I-kappa-B-alpha 0.037 0.007 -10000 0 -10000 0 0
FADD -0.015 0.11 0.21 3 -0.4 18 21
KSR1 -0.005 0.052 0.17 6 -0.19 10 16
MAPK8 -0.003 0.053 0.18 12 -0.19 6 18
TRAF2 0.024 0.006 -10000 0 -10000 0 0
response to radiation 0 0 0.002 4 -0.002 2 6
CHUK -0.01 0.12 0.29 5 -0.39 18 23
TNF R/SODD 0.032 0.026 -10000 0 -0.28 2 2
TNF -0.017 0.11 -10000 0 -0.4 27 27
CYCS 0.001 0.047 0.12 14 -0.15 8 22
IKBKG -0.014 0.11 0.32 1 -0.39 18 19
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.014 0.12 -10000 0 -0.44 17 17
RELA 0.025 0.003 -10000 0 -10000 0 0
RIPK1 0.025 0.004 -10000 0 -10000 0 0
AIFM1 0.001 0.044 0.12 8 -0.16 4 12
TNF/TNF R/SODD 0.028 0.072 -10000 0 -0.25 21 21
TNFRSF1A 0.024 0.023 -10000 0 -0.4 1 1
response to heat 0 0 0.002 4 -0.002 2 6
CASP8 0.012 0.089 -10000 0 -0.58 7 7
NSMAF -0.009 0.11 0.21 11 -0.4 15 26
response to hydrogen peroxide 0 0.001 0.002 10 -0.002 4 14
BCL2 0.007 0.083 -10000 0 -0.4 14 14
HIF-2-alpha transcription factor network

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
MMP14 0.016 0.12 -10000 0 -0.8 6 6
oxygen homeostasis 0.001 0.011 -10000 0 -10000 0 0
TCEB2 0.025 0.005 -10000 0 -10000 0 0
TCEB1 0.024 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.053 0.094 0.3 4 -0.29 4 8
EPO 0.027 0.14 -10000 0 -0.51 6 6
FIH (dimer) 0.018 0.024 -10000 0 -10000 0 0
APEX1 0.019 0.027 -10000 0 -10000 0 0
SERPINE1 0.012 0.16 -10000 0 -0.51 17 17
FLT1 -0.003 0.15 -10000 0 -0.63 15 15
ADORA2A 0.047 0.17 0.33 39 -0.46 13 52
germ cell development 0.001 0.18 0.47 1 -0.48 32 33
SLC11A2 0.019 0.15 0.48 1 -0.47 13 14
BHLHE40 0.018 0.15 0.48 1 -0.48 13 14
HIF1AN 0.018 0.024 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.029 0.1 -10000 0 -0.36 6 6
ETS1 0.032 0.012 -10000 0 -0.16 1 1
CITED2 0.005 0.15 -10000 0 -0.8 10 10
KDR 0.006 0.14 -10000 0 -0.67 10 10
PGK1 0.017 0.15 0.48 1 -0.49 13 14
SIRT1 0.024 0.006 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.044 0.18 -10000 0 -0.53 13 13
EPAS1 0.005 0.072 -10000 0 -0.29 7 7
SP1 0.028 0.011 -10000 0 -10000 0 0
ABCG2 0.008 0.17 0.48 1 -0.5 20 21
EFNA1 0.016 0.15 -10000 0 -0.5 16 16
FXN 0.047 0.17 0.33 40 -0.46 13 53
POU5F1 0 0.19 0.48 1 -0.5 32 33
neuron apoptosis -0.043 0.17 0.52 13 -10000 0 13
EP300 0.024 0.006 -10000 0 -10000 0 0
EGLN3 0.003 0.085 -10000 0 -0.4 14 14
EGLN2 0.019 0.024 -10000 0 -10000 0 0
EGLN1 0.017 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.045 0.023 -10000 0 -0.24 1 1
VHL 0.023 0.023 -10000 0 -0.4 1 1
ARNT 0.016 0.024 -10000 0 -10000 0 0
SLC2A1 0.048 0.17 0.33 40 -0.45 14 54
TWIST1 0.029 0.2 0.32 35 -0.49 27 62
ELK1 0.027 0.014 -10000 0 -0.097 4 4
HIF2A/ARNT/Cbp/p300 0.037 0.11 -10000 0 -0.36 6 6
VEGFA 0.02 0.15 0.48 1 -0.47 13 14
CREBBP 0.025 0.004 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.001 0.11 -10000 0 -0.61 5 5
UGCG -0.042 0.2 -10000 0 -0.67 33 33
AKT1/mTOR/p70S6K/Hsp90/TERT -0.015 0.17 0.31 1 -0.45 33 34
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.041 0.2 -10000 0 -0.66 33 33
mol:DAG 0 0.1 -10000 0 -0.86 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.16 0.31 1 -0.44 29 30
FRAP1 -0.004 0.19 0.34 1 -0.5 33 34
FOXO3 0.003 0.17 0.33 1 -0.49 25 26
AKT1 0 0.19 0.29 2 -0.54 25 27
GAB2 0.025 0.008 -10000 0 -10000 0 0
SMPD1 -0.002 0.12 -10000 0 -0.66 11 11
SGMS1 0.009 0.081 -10000 0 -0.63 5 5
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 -0.002 0.038 -10000 0 -0.24 9 9
CALM1 0.025 0.004 -10000 0 -10000 0 0
cell proliferation -0.008 0.17 0.33 1 -0.52 24 25
EIF3A 0.024 0.006 -10000 0 -10000 0 0
PI3K 0.026 0.053 -10000 0 -0.28 9 9
RPS6KB1 -0.018 0.18 -10000 0 -0.83 15 15
mol:sphingomyelin 0 0.1 -10000 0 -0.86 5 5
natural killer cell activation 0 0.002 -10000 0 -0.011 7 7
JAK3 0.019 0.046 -10000 0 -0.4 4 4
PIK3R1 0.004 0.091 -10000 0 -0.4 17 17
JAK1 0.021 0.05 -10000 0 -0.4 5 5
NFKB1 0.025 0.004 -10000 0 -10000 0 0
MYC 0.015 0.2 0.35 7 -0.71 16 23
MYB -0.034 0.24 -10000 0 -1.1 16 16
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.006 0.14 -10000 0 -0.46 20 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.01 0.17 -10000 0 -0.77 14 14
mol:PI-3-4-5-P3 0.007 0.14 -10000 0 -0.44 21 21
Rac1/GDP 0.012 0.039 -10000 0 -0.21 9 9
T cell proliferation 0.005 0.13 0.22 2 -0.45 18 20
SHC1 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0 0.014 -10000 0 -0.065 15 15
PRKCZ 0.004 0.14 0.22 1 -0.47 18 19
NF kappa B1 p50/RelA 0.019 0.17 0.33 1 -0.46 28 29
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.006 0.12 -10000 0 -0.48 15 15
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
RELA 0.025 0.003 -10000 0 -10000 0 0
IL2RA 0.004 0.086 -10000 0 -0.4 15 15
IL2RB 0.007 0.081 -10000 0 -0.4 13 13
TERT -0.028 0.13 -10000 0 -0.4 38 38
E2F1 -0.005 0.13 -10000 0 -0.51 18 18
SOS1 0.024 0.007 -10000 0 -10000 0 0
RPS6 0.024 0.023 -10000 0 -0.4 1 1
mol:cAMP 0 0.006 0.032 13 -10000 0 13
PTPN11 0.024 0.007 -10000 0 -10000 0 0
IL2RG 0.008 0.079 -10000 0 -0.4 12 12
actin cytoskeleton organization 0.005 0.13 0.22 2 -0.45 18 20
GRB2 0.024 0.008 -10000 0 -10000 0 0
IL2 0.014 0.022 -10000 0 -10000 0 0
PIK3CA 0.024 0.009 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.045 -10000 0 -0.2 9 9
LCK 0.009 0.078 -10000 0 -0.4 12 12
BCL2 -0.013 0.21 0.32 1 -0.68 25 26
LPA4-mediated signaling events

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
ADCY4 -0.008 0.022 -10000 0 -0.24 3 3
ADCY5 -0.035 0.075 -10000 0 -0.24 43 43
ADCY6 -0.007 0.017 -10000 0 -0.24 2 2
ADCY7 -0.007 0.018 -10000 0 -0.24 2 2
ADCY1 -0.027 0.06 -10000 0 -0.24 26 26
ADCY2 -0.025 0.061 -10000 0 -0.24 27 27
ADCY3 -0.006 0.012 -10000 0 -0.24 1 1
ADCY8 -0.01 0.014 -10000 0 -0.24 1 1
PRKCE 0.006 0.015 -10000 0 -0.28 1 1
ADCY9 -0.012 0.035 -10000 0 -0.24 8 8
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.007 0.072 0.22 15 -0.2 8 23
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.069 0.2 1 -0.19 26 27
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.025 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.029 0.062 0.3 1 -10000 0 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.036 0.061 -10000 0 -0.24 14 14
antigen processing and presentation of peptide antigen via MHC class I -0.01 0.065 -10000 0 -0.21 15 15
CaM/Ca2+ 0.044 0.066 -10000 0 -0.19 23 23
RAP1A 0.025 0.001 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.012 0.061 -10000 0 -0.19 26 26
AKT1 -0.004 0.079 0.29 6 -0.25 3 9
MAP2K1 -0.02 0.054 0.17 6 -0.19 1 7
MAP3K11 -0.001 0.06 0.23 2 -0.19 24 26
IFNGR1 0.022 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.021 0.12 -10000 0 -0.37 13 13
Rap1/GTP 0.003 0.048 -10000 0 -10000 0 0
CRKL/C3G 0.035 0.01 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.052 0.074 -10000 0 -0.2 26 26
CEBPB -0.008 0.13 0.35 2 -0.49 17 19
STAT3 0.024 0.006 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.027 0.17 -10000 0 -0.8 12 12
STAT1 -0.002 0.059 0.23 2 -0.19 24 26
CALM1 0.025 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0 0.081 -10000 0 -0.41 12 12
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.01 0.061 0.23 2 -0.18 4 6
CEBPB/PTGES2/Cbp/p300 0.012 0.089 -10000 0 -0.33 14 14
mol:Ca2+ 0.039 0.067 0.19 1 -0.19 26 27
MAPK3 -0.016 0.13 -10000 0 -0.64 12 12
STAT1 (dimer) -0.006 0.09 -10000 0 -0.28 14 14
MAPK1 -0.023 0.16 -10000 0 -0.66 17 17
JAK2 0.012 0.068 -10000 0 -0.41 9 9
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
JAK1 0.017 0.052 -10000 0 -0.41 5 5
CAMK2D 0.015 0.063 -10000 0 -0.4 8 8
DAPK1 -0.001 0.1 0.3 2 -0.44 12 14
SMAD7 0.003 0.051 0.18 10 -0.17 1 11
CBL/CRKL/C3G 0.021 0.064 0.29 1 -10000 0 1
PI3K 0.031 0.078 -10000 0 -0.2 33 33
IFNG 0 0.081 -10000 0 -0.41 12 12
apoptosis 0 0.085 0.23 1 -0.36 11 12
CAMK2G 0.024 0.006 -10000 0 -10000 0 0
STAT3 (dimer) 0.024 0.006 -10000 0 -10000 0 0
CAMK2A 0.02 0.02 -10000 0 -10000 0 0
CAMK2B -0.042 0.14 -10000 0 -0.4 46 46
FRAP1 -0.012 0.073 0.26 7 -0.24 3 10
PRKCD -0.015 0.08 0.21 18 -0.23 6 24
RAP1B 0.025 0.002 -10000 0 -10000 0 0
negative regulation of cell growth -0.01 0.065 -10000 0 -0.21 15 15
PTPN2 0.025 0.004 -10000 0 -10000 0 0
EP300 0.024 0.006 -10000 0 -10000 0 0
IRF1 -0.008 0.057 0.26 2 -0.3 4 6
STAT1 (dimer)/PIASy 0.009 0.062 0.29 1 -10000 0 1
SOCS1 -0.012 0.2 -10000 0 -1.1 12 12
mol:GDP 0.018 0.061 0.27 1 -10000 0 1
CASP1 0 0.061 0.18 10 -0.21 10 20
PTGES2 0.024 0.006 -10000 0 -10000 0 0
IRF9 0.01 0.046 0.16 3 -0.17 9 12
mol:PI-3-4-5-P3 0.018 0.071 -10000 0 -0.19 33 33
RAP1/GDP 0.019 0.056 -10000 0 -10000 0 0
CBL -0.004 0.059 0.23 2 -0.19 23 25
MAP3K1 -0.003 0.059 0.23 2 -0.19 24 26
PIAS1 0.024 0.006 -10000 0 -10000 0 0
PIAS4 0.024 0.007 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.01 0.065 -10000 0 -0.21 15 15
PTPN11 -0.002 0.059 0.15 8 -0.19 26 34
CREBBP 0.025 0.004 -10000 0 -10000 0 0
RAPGEF1 0.024 0.007 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.016 0.038 -10000 0 -0.23 7 7
epithelial cell differentiation 0.043 0.037 -10000 0 -0.2 6 6
CYFIP2 0.014 0.067 -10000 0 -0.4 9 9
ENAH -0.007 0.062 0.27 7 -0.29 3 10
EGFR 0.013 0.07 -10000 0 -0.4 10 10
EPHA2 0.017 0.056 -10000 0 -0.4 6 6
MYO6 -0.011 0.043 0.18 4 -0.25 7 11
CTNNB1 0.023 0.023 -10000 0 -0.4 1 1
ABI1/Sra1/Nap1 0.041 0.044 -10000 0 -0.24 8 8
AQP5 -0.051 0.16 -10000 0 -0.42 52 52
CTNND1 0.025 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.01 0.028 0.18 2 -0.2 5 7
regulation of calcium-dependent cell-cell adhesion -0.023 0.061 0.18 4 -0.21 28 32
EGF -0.011 0.1 -10000 0 -0.4 21 21
NCKAP1 0.025 0.003 -10000 0 -10000 0 0
AQP3 -0.013 0.11 -10000 0 -0.44 21 21
cortical microtubule organization 0.043 0.037 -10000 0 -0.2 6 6
GO:0000145 -0.01 0.027 0.16 2 -0.19 5 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.048 0.039 -10000 0 -0.2 6 6
MLLT4 0.025 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.02 0.04 -10000 0 -0.22 10 10
ARF6 0.025 0.004 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.04 0.054 -10000 0 -0.22 11 11
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.004 0.028 0.17 3 -10000 0 3
PVRL2 0.025 0.005 -10000 0 -10000 0 0
ZYX -0.008 0.032 0.18 4 -0.2 5 9
ARF6/GTP 0.045 0.054 -10000 0 -0.2 11 11
CDH1 0.017 0.05 -10000 0 -0.4 5 5
EGFR/EGFR/EGF/EGF 0.017 0.076 -10000 0 -0.2 34 34
RhoA/GDP 0.044 0.035 -10000 0 -0.2 5 5
actin cytoskeleton organization -0.012 0.039 0.16 3 -0.26 5 8
IGF-1R heterotetramer -0.005 0.11 -10000 0 -0.4 25 25
GIT1 0.024 0.005 -10000 0 -10000 0 0
IGF1R -0.005 0.11 -10000 0 -0.4 25 25
IGF1 -0.021 0.12 -10000 0 -0.4 33 33
DIAPH1 0.011 0.13 -10000 0 -0.54 12 12
Wnt receptor signaling pathway -0.043 0.037 0.2 6 -10000 0 6
RHOA 0.024 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.019 0.04 -10000 0 -0.34 2 2
CTNNA1 0.025 0.004 -10000 0 -10000 0 0
VCL -0.012 0.04 0.17 3 -0.27 5 8
EFNA1 0.014 0.055 -10000 0 -0.4 6 6
LPP -0.01 0.03 0.17 3 -0.19 5 8
Ephrin A1/EPHA2 0.023 0.056 -10000 0 -0.22 15 15
SEC6/SEC8 -0.016 0.023 -10000 0 -0.18 6 6
MGAT3 -0.023 0.061 0.18 4 -0.21 28 32
HGF/MET 0.012 0.088 -10000 0 -0.22 40 40
HGF -0.004 0.099 -10000 0 -0.4 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.016 0.038 -10000 0 -0.24 7 7
actin cable formation 0.046 0.11 0.24 67 -0.23 3 70
KIAA1543 -0.009 0.037 0.16 5 -0.21 7 12
KIFC3 -0.012 0.036 0.18 4 -0.2 8 12
NCK1 0.025 0.005 -10000 0 -10000 0 0
EXOC3 0.024 0.006 -10000 0 -10000 0 0
ACTN1 -0.009 0.032 0.18 4 -0.2 5 9
NCK1/GIT1 0.035 0.01 -10000 0 -10000 0 0
mol:GDP 0.043 0.037 -10000 0 -0.2 6 6
EXOC4 0.024 0.005 -10000 0 -10000 0 0
STX4 -0.008 0.034 0.18 5 -0.2 5 10
PIP5K1C -0.01 0.029 0.18 2 -0.2 5 7
LIMA1 0.024 0.023 -10000 0 -0.4 1 1
ABI1 0.024 0.006 -10000 0 -10000 0 0
ROCK1 0.022 0.095 0.34 12 -0.31 1 13
adherens junction assembly -0.039 0.14 0.21 1 -0.52 23 24
IGF-1R heterotetramer/IGF1 0.003 0.1 -10000 0 -0.23 51 51
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.036 0.009 -10000 0 -10000 0 0
MET -0.006 0.11 -10000 0 -0.4 24 24
PLEKHA7 -0.009 0.039 0.18 5 -0.22 7 12
mol:GTP 0.039 0.053 -10000 0 -0.22 11 11
establishment of epithelial cell apical/basal polarity 0.002 0.071 0.35 7 -10000 0 7
cortical actin cytoskeleton stabilization 0.016 0.038 -10000 0 -0.23 7 7
regulation of cell-cell adhesion -0.012 0.039 0.16 3 -0.26 5 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.016 0.038 -10000 0 -0.24 7 7
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.002 0.073 0.2 2 -0.29 13 15
adherens junction organization -0.012 0.11 0.22 2 -0.39 22 24
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.009 0.073 0.22 1 -0.3 7 8
FMN1 -0.008 0.092 -10000 0 -0.38 16 16
mol:IP3 0 0.059 -10000 0 -0.28 9 9
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.008 0.1 -10000 0 -0.37 21 21
CTNNB1 0.024 0.023 -10000 0 -0.41 1 1
AKT1 0.001 0.068 -10000 0 -0.29 11 11
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.01 0.14 -10000 0 -0.57 15 15
CTNND1 0.026 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.013 0.086 -10000 0 -0.33 20 20
VASP -0.01 0.094 -10000 0 -0.35 20 20
ZYX -0.009 0.093 -10000 0 -0.36 19 19
JUB -0.01 0.096 -10000 0 -0.35 21 21
EGFR(dimer) -0.002 0.11 -10000 0 -0.36 22 22
E-cadherin/beta catenin-gamma catenin 0.038 0.048 -10000 0 -0.29 6 6
mol:PI-3-4-5-P3 0.014 0.08 -10000 0 -0.3 13 13
PIK3CA 0.024 0.008 -10000 0 -10000 0 0
PI3K 0.015 0.081 -10000 0 -0.31 13 13
FYN 0.003 0.062 0.21 1 -0.29 8 9
mol:Ca2+ 0.001 0.058 -10000 0 -0.28 9 9
JUP 0.022 0.032 -10000 0 -0.4 2 2
PIK3R1 0.004 0.09 -10000 0 -0.4 17 17
mol:DAG 0 0.059 -10000 0 -0.28 9 9
CDH1 0.017 0.05 -10000 0 -0.4 5 5
RhoA/GDP 0.013 0.072 0.22 1 -0.3 7 8
establishment of polarity of embryonic epithelium -0.009 0.093 -10000 0 -0.35 20 20
SRC 0.022 0.032 -10000 0 -0.4 2 2
RAC1 0.025 0.005 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
EGFR 0.013 0.07 -10000 0 -0.4 10 10
CASR -0.004 0.061 0.15 5 -0.29 7 12
RhoA/GTP 0.016 0.062 -10000 0 -0.28 7 7
AKT2 -0.001 0.07 -10000 0 -0.29 13 13
actin cable formation -0.014 0.095 0.25 1 -0.35 20 21
apoptosis -0.004 0.08 0.3 12 -0.25 4 16
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
mol:GDP -0.003 0.068 0.16 10 -0.3 8 18
PIP5K1A -0.013 0.088 -10000 0 -0.33 20 20
PLCG1 0 0.06 -10000 0 -0.29 9 9
Rac1/GTP 0.006 0.1 -10000 0 -0.34 21 21
homophilic cell adhesion 0 0.003 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.012 0.004 -10000 0 -10000 0 0
SMARCC1 0.013 0.01 -10000 0 -10000 0 0
REL 0.024 0.023 -10000 0 -0.4 1 1
HDAC7 -0.014 0.1 0.22 2 -0.33 20 22
JUN 0.024 0.023 -10000 0 -0.4 1 1
EP300 0.024 0.006 -10000 0 -10000 0 0
KAT2B 0.016 0.059 -10000 0 -0.4 7 7
KAT5 0.025 0.003 -10000 0 -10000 0 0
MAPK14 0 0.05 -10000 0 -0.3 9 9
FOXO1 0.024 0.008 -10000 0 -10000 0 0
T-DHT/AR 0.005 0.11 0.24 2 -0.34 21 23
MAP2K6 0.009 0.069 -10000 0 -0.38 10 10
BRM/BAF57 0.029 0.042 -10000 0 -0.28 6 6
MAP2K4 0.016 0.035 -10000 0 -0.4 2 2
SMARCA2 0.016 0.06 -10000 0 -0.4 7 7
PDE9A -0.042 0.2 -10000 0 -0.94 14 14
NCOA2 0.01 0.074 -10000 0 -0.4 11 11
CEBPA 0 0.098 -10000 0 -0.4 20 20
EHMT2 0.025 0.005 -10000 0 -10000 0 0
cell proliferation -0.016 0.15 0.3 12 -0.41 23 35
NR0B1 0.012 0.026 -10000 0 -10000 0 0
EGR1 0.014 0.058 -10000 0 -0.36 7 7
RXRs/9cRA 0.006 0.085 -10000 0 -0.22 41 41
AR/RACK1/Src -0.001 0.082 0.2 5 -0.34 9 14
AR/GR -0.013 0.098 0.2 2 -0.25 41 43
GNB2L1 0.025 0.004 -10000 0 -10000 0 0
PKN1 0.024 0.006 -10000 0 -10000 0 0
RCHY1 0.025 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 0.005 0.027 -10000 0 -0.29 2 2
T-DHT/AR/TIF2/CARM1 0.006 0.083 0.25 1 -0.31 11 12
SRC -0.018 0.049 0.19 3 -0.26 9 12
NR3C1 0.015 0.06 -10000 0 -0.4 7 7
KLK3 -0.1 0.18 -10000 0 -0.65 17 17
APPBP2 0.019 0.017 -10000 0 -10000 0 0
TRIM24 0.024 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.001 0.081 0.19 9 -0.35 9 18
TMPRSS2 -0.086 0.3 -10000 0 -0.97 34 34
RXRG -0.041 0.14 -10000 0 -0.4 43 43
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.022 0.023 -10000 0 -0.4 1 1
RXRB 0.025 0.003 -10000 0 -10000 0 0
CARM1 0.024 0.007 -10000 0 -10000 0 0
NR2C2 0.025 0.005 -10000 0 -10000 0 0
KLK2 -0.005 0.083 0.23 1 -0.37 8 9
AR -0.02 0.088 0.12 1 -0.28 33 34
SENP1 0.025 0.003 -10000 0 -10000 0 0
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
MDM2 0.023 0.032 -10000 0 -0.4 2 2
SRY 0 0.003 0.03 4 -10000 0 4
GATA2 -0.025 0.14 -10000 0 -0.4 41 41
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.073 0.18 -10000 0 -0.4 79 79
T-DHT/AR/RACK1/Src -0.001 0.083 0.22 6 -0.33 10 16
positive regulation of transcription -0.025 0.14 -10000 0 -0.4 41 41
DNAJA1 0.02 0.017 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.023 -10000 0 -0.29 2 2
NCOA1 0.029 0.015 -10000 0 -10000 0 0
SPDEF -0.074 0.18 -10000 0 -0.4 83 83
T-DHT/AR/TIF2 0.001 0.09 0.23 9 -0.28 17 26
T-DHT/AR/Hsp90 -0.001 0.081 0.19 9 -0.35 9 18
GSK3B 0.024 0.006 -10000 0 -10000 0 0
NR2C1 0.025 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.018 0.047 -10000 0 -0.28 8 8
SIRT1 0.024 0.006 -10000 0 -10000 0 0
ZMIZ2 0.025 0.006 -10000 0 -10000 0 0
POU2F1 0.014 0.044 -10000 0 -0.2 4 4
T-DHT/AR/DAX-1 -0.009 0.08 0.2 3 -0.36 9 12
CREBBP 0.025 0.004 -10000 0 -10000 0 0
SMARCE1 0.023 0.008 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.01 0.14 -10000 0 -0.47 22 22
MAP3K8 0.02 0.045 -10000 0 -0.41 4 4
FOS -0.002 0.14 0.22 1 -0.54 17 18
PRKCA 0.008 0.08 -10000 0 -0.4 13 13
PTPN7 0.014 0.048 -10000 0 -0.4 4 4
HRAS 0.024 0.005 -10000 0 -10000 0 0
PRKCB 0.005 0.082 -10000 0 -0.4 13 13
NRAS 0.02 0.05 -10000 0 -0.4 5 5
RAS family/GTP 0.042 0.034 -10000 0 -0.22 5 5
MAPK3 -0.006 0.13 -10000 0 -0.63 13 13
MAP2K1 -0.015 0.13 -10000 0 -0.4 29 29
ELK1 0.025 0.008 -10000 0 -10000 0 0
BRAF -0.008 0.1 -10000 0 -0.37 24 24
mol:GTP 0 0.001 -10000 0 -0.005 5 5
MAPK1 -0.007 0.12 -10000 0 -0.54 15 15
RAF1 -0.007 0.1 -10000 0 -0.38 22 22
KRAS 0.025 0.004 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.034 0.086 -10000 0 -0.25 25 25
MAP4K1 0.016 0.052 -10000 0 -0.4 5 5
MAP3K8 0.02 0.045 -10000 0 -0.4 4 4
PRKCB 0.005 0.082 -10000 0 -0.4 13 13
DBNL 0.025 0.004 -10000 0 -10000 0 0
CRKL 0.025 0.005 -10000 0 -10000 0 0
MAP3K1 -0.001 0.081 -10000 0 -0.42 7 7
JUN -0.024 0.18 -10000 0 -0.61 27 27
MAP3K7 -0.002 0.079 -10000 0 -0.4 7 7
GRAP2 0.002 0.089 -10000 0 -0.4 16 16
CRK 0.024 0.006 -10000 0 -10000 0 0
MAP2K4 -0.003 0.092 0.17 2 -0.43 9 11
LAT 0.019 0.046 -10000 0 -0.4 4 4
LCP2 0.018 0.051 -10000 0 -0.4 5 5
MAPK8 -0.023 0.18 -10000 0 -0.65 27 27
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.007 0.081 -10000 0 -0.42 7 7
LAT/GRAP2/SLP76/HPK1/HIP-55 0.043 0.084 -10000 0 -0.25 21 21
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.025 0.003 -10000 0 -10000 0 0
HDAC2 0.025 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.038 0.052 -10000 0 -0.24 11 11
forebrain development -0.073 0.21 -10000 0 -0.59 39 39
GNAO1 0.013 0.053 -10000 0 -0.4 5 5
SMO/beta Arrestin2 0.02 0.051 -10000 0 -0.28 8 8
SMO 0.01 0.064 -10000 0 -0.4 8 8
ARRB2 0.022 0.009 -10000 0 -10000 0 0
GLI3/SPOP 0.027 0.081 -10000 0 -0.31 3 3
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.025 0.004 -10000 0 -10000 0 0
GNAI2 0.024 0.006 -10000 0 -10000 0 0
SIN3/HDAC complex 0.058 0.023 -10000 0 -10000 0 0
GNAI1 0.012 0.071 -10000 0 -0.4 10 10
XPO1 0.019 0.017 -10000 0 -10000 0 0
GLI1/Su(fu) -0.06 0.19 -10000 0 -0.56 31 31
SAP30 0.024 0.023 -10000 0 -0.4 1 1
mol:GDP 0.01 0.064 -10000 0 -0.4 8 8
MIM/GLI2A -0.001 0.072 -10000 0 -0.35 8 8
IFT88 0.024 0.005 -10000 0 -10000 0 0
GNAI3 0.025 0.004 -10000 0 -10000 0 0
GLI2 0.008 0.076 0.28 1 -0.34 10 11
GLI3 0.018 0.083 0.22 1 -0.3 5 6
CSNK1D 0.024 0.006 -10000 0 -10000 0 0
CSNK1E 0.024 0.006 -10000 0 -10000 0 0
SAP18 0.025 0.005 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.024 0.005 -10000 0 -10000 0 0
GNG2 0.018 0.047 -10000 0 -0.4 4 4
Gi family/GTP -0.005 0.074 -10000 0 -0.22 32 32
SIN3B 0.024 0.006 -10000 0 -10000 0 0
SIN3A 0.025 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) 0.021 0.077 -10000 0 -0.35 7 7
GLI2/Su(fu) 0.013 0.087 0.25 1 -0.36 12 13
FOXA2 -0.18 0.42 -10000 0 -0.98 78 78
neural tube patterning -0.073 0.21 -10000 0 -0.59 39 39
SPOP 0.024 0.006 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.022 0.044 -10000 0 -0.33 1 1
GNB1 0.025 0.005 -10000 0 -10000 0 0
CSNK1G2 0.024 0.007 -10000 0 -10000 0 0
CSNK1G3 0.025 0.004 -10000 0 -10000 0 0
MTSS1 -0.001 0.072 -10000 0 -0.35 8 8
embryonic limb morphogenesis -0.073 0.21 -10000 0 -0.59 39 39
SUFU 0.012 0.033 -10000 0 -0.36 1 1
LGALS3 0.02 0.045 -10000 0 -0.4 4 4
catabolic process 0.028 0.1 0.27 2 -0.35 15 17
GLI3A/CBP -0.012 0.11 -10000 0 -0.32 40 40
KIF3A 0.024 0.023 -10000 0 -0.4 1 1
GLI1 -0.076 0.22 -10000 0 -0.62 37 37
RAB23 0.024 0.023 -10000 0 -0.4 1 1
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
IFT172 0.025 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.003 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.018 0.052 -10000 0 -0.23 5 5
GNAZ 0.012 0.067 -10000 0 -0.4 9 9
RBBP4 0.025 0.004 -10000 0 -10000 0 0
CSNK1G1 0.024 0.006 -10000 0 -10000 0 0
PIAS1 0.024 0.006 -10000 0 -10000 0 0
PRKACA 0.024 0.006 -10000 0 -10000 0 0
GLI2/SPOP 0.02 0.08 0.25 1 -0.33 12 13
STK36 0.018 0.028 -10000 0 -0.4 1 1
Gi family/GNB1/GNG2/GDP -0.002 0.07 -10000 0 -0.32 6 6
PTCH1 -0.067 0.2 -10000 0 -0.61 29 29
MIM/GLI1 -0.091 0.26 -10000 0 -0.56 75 75
CREBBP -0.012 0.11 -10000 0 -0.32 40 40
Su(fu)/SIN3/HDAC complex 0.019 0.076 0.18 3 -0.39 8 11
Ceramide signaling pathway

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
SPHK2 0.003 0.045 -10000 0 -0.28 8 8
MAP4K4 -0.015 0.089 0.19 1 -0.37 13 14
BAG4 0.022 0.024 -10000 0 -0.4 1 1
PKC zeta/ceramide 0.011 0.045 0.15 1 -0.19 12 13
NFKBIA 0.025 0.004 -10000 0 -10000 0 0
BIRC3 -0.01 0.11 -10000 0 -0.4 26 26
BAX 0.006 0.045 -10000 0 -0.34 5 5
RIPK1 0.025 0.004 -10000 0 -10000 0 0
AKT1 -0.001 0.062 0.67 3 -10000 0 3
BAD -0.001 0.044 0.18 6 -0.18 10 16
SMPD1 -0.004 0.066 0.16 7 -0.22 14 21
RB1 -0.008 0.047 0.16 3 -0.19 17 20
FADD/Caspase 8 -0.011 0.096 0.2 2 -0.39 13 15
MAP2K4 -0.006 0.04 0.19 2 -0.18 12 14
NSMAF 0.024 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.003 0.052 0.2 10 -0.18 12 22
EGF -0.011 0.1 -10000 0 -0.4 21 21
mol:ceramide -0.002 0.041 0.12 7 -0.19 10 17
MADD 0.025 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.003 0.042 -10000 0 -0.28 7 7
ASAH1 0.023 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.008 0.047 0.16 3 -0.19 17 20
cell proliferation 0.001 0.071 0.18 3 -0.19 27 30
BID -0.017 0.15 -10000 0 -0.63 16 16
MAP3K1 -0.004 0.041 0.18 3 -0.18 10 13
EIF2A 0.006 0.061 0.19 25 -0.18 7 32
TRADD 0.023 0.008 -10000 0 -10000 0 0
CRADD 0.025 0.003 -10000 0 -10000 0 0
MAPK3 -0.001 0.053 0.2 10 -0.19 10 20
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.003 0.054 0.2 10 -0.18 7 17
Cathepsin D/ceramide 0.013 0.042 0.15 1 -0.18 10 11
FADD -0.015 0.09 0.2 2 -0.37 13 15
KSR1 -0.004 0.046 0.18 6 -0.19 12 18
MAPK8 -0.002 0.054 -10000 0 -0.26 5 5
PRKRA -0.002 0.041 0.18 4 -0.18 9 13
PDGFA 0.012 0.065 -10000 0 -0.4 8 8
TRAF2 0.024 0.006 -10000 0 -10000 0 0
IGF1 -0.021 0.12 -10000 0 -0.4 33 33
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.002 0.041 0.12 7 -0.19 10 17
CTSD 0.024 0.01 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.036 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.002 0.076 0.19 3 -0.2 27 30
PRKCD 0.022 0.032 -10000 0 -0.4 2 2
PRKCZ 0.022 0.032 -10000 0 -0.4 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.003 0.042 -10000 0 -0.28 7 7
RelA/NF kappa B1 0.036 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.025 0.002 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.008 0.092 -10000 0 -0.4 13 13
TNFR1A/BAG4/TNF-alpha 0.028 0.072 -10000 0 -0.25 21 21
mol:Sphingosine-1-phosphate 0.003 0.045 -10000 0 -0.28 8 8
MAP2K1 -0.004 0.051 0.19 10 -0.18 9 19
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.025 0.003 -10000 0 -10000 0 0
CYCS 0.01 0.043 0.15 13 -0.16 4 17
TNFRSF1A 0.024 0.023 -10000 0 -0.4 1 1
NFKB1 0.025 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.032 0.026 -10000 0 -0.28 2 2
EIF2AK2 -0.001 0.049 0.2 9 -0.18 10 19
TNF-alpha/TNFR1A/FAN 0.028 0.073 -10000 0 -0.25 22 22
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.004 0.084 -10000 0 -0.38 10 10
MAP2K2 -0.004 0.05 0.2 9 -0.18 10 19
SMPD3 -0.032 0.12 0.15 2 -0.29 51 53
TNF -0.017 0.11 -10000 0 -0.4 27 27
PKC zeta/PAR4 0.035 0.025 -10000 0 -0.28 2 2
mol:PHOSPHOCHOLINE 0.007 0.059 0.19 23 -0.15 5 28
NF kappa B1/RelA/I kappa B alpha 0.068 0.029 -10000 0 -0.21 2 2
AIFM1 0.01 0.044 0.15 13 -0.17 3 16
BCL2 0.007 0.083 -10000 0 -0.4 14 14
Aurora B signaling

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
Condensin I complex 0 0.083 -10000 0 -0.26 23 23
STMN1 0.003 0.052 -10000 0 -0.29 11 11
Aurora B/RasGAP/Survivin 0.035 0.074 -10000 0 -0.31 14 14
Chromosomal passenger complex/Cul3 protein complex -0.017 0.094 -10000 0 -0.22 46 46
BIRC5 0.009 0.083 -10000 0 -0.42 13 13
DES -0.15 0.29 -10000 0 -0.59 106 106
Aurora C/Aurora B/INCENP 0.04 0.046 -10000 0 -0.22 9 9
Aurora B/TACC1 0.026 0.037 -10000 0 -0.24 6 6
Aurora B/PP2A 0.032 0.04 -10000 0 -0.29 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.007 0.018 -10000 0 -0.14 5 5
mitotic metaphase/anaphase transition 0 0.004 -10000 0 -10000 0 0
NDC80 0.001 0.066 -10000 0 -0.36 11 11
Cul3 protein complex 0.015 0.096 -10000 0 -0.25 42 42
KIF2C 0.003 0.083 -10000 0 -0.45 7 7
PEBP1 0.025 0.006 -10000 0 -10000 0 0
KIF20A 0.023 0.032 -10000 0 -0.4 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.032 0.04 -10000 0 -0.29 5 5
SEPT1 0.019 0.042 -10000 0 -0.4 3 3
SMC2 0.024 0.007 -10000 0 -10000 0 0
SMC4 0.018 0.05 -10000 0 -0.4 5 5
NSUN2/NPM1/Nucleolin -0.024 0.16 0.26 2 -0.53 30 32
PSMA3 0.025 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.003 -10000 0 -10000 0 0
H3F3B 0.009 0.035 -10000 0 -0.28 5 5
AURKB 0.02 0.053 -10000 0 -0.42 5 5
AURKC 0.019 0.046 -10000 0 -0.24 8 8
CDCA8 0.023 0.034 -10000 0 -0.43 2 2
cytokinesis -0.005 0.11 -10000 0 -0.42 16 16
Aurora B/Septin1 0.013 0.12 -10000 0 -0.41 16 16
AURKA 0.021 0.039 -10000 0 -0.4 3 3
INCENP 0.025 0.008 -10000 0 -10000 0 0
KLHL13 -0.025 0.14 -10000 0 -0.4 42 42
BUB1 0.017 0.06 -10000 0 -0.41 7 7
hSgo1/Aurora B/Survivin 0.026 0.088 -10000 0 -0.29 22 22
EVI5 0.026 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.03 0.096 -10000 0 -0.39 12 12
SGOL1 0.01 0.077 -10000 0 -0.4 12 12
CENPA -0.002 0.1 -10000 0 -0.34 21 21
NCAPG 0.019 0.05 -10000 0 -0.4 5 5
Aurora B/HC8 Proteasome 0.032 0.04 -10000 0 -0.29 5 5
NCAPD2 0.025 0.004 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.032 0.04 -10000 0 -0.29 5 5
RHOA 0.024 0.005 -10000 0 -10000 0 0
NCAPH 0.019 0.05 -10000 0 -0.4 5 5
NPM1 -0.014 0.12 -10000 0 -0.37 28 28
RASA1 0.025 0.005 -10000 0 -10000 0 0
KLHL9 0.024 0.023 -10000 0 -0.4 1 1
mitotic prometaphase 0 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.032 0.04 -10000 0 -0.29 5 5
PPP1CC 0.025 0.003 -10000 0 -10000 0 0
Centraspindlin 0.023 0.1 -10000 0 -0.42 12 12
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
NSUN2 -0.005 0.085 -10000 0 -0.32 23 23
MYLK 0.007 0.041 -10000 0 -0.28 7 7
KIF23 0.022 0.033 -10000 0 -0.42 2 2
VIM -0.003 0.064 -10000 0 -0.29 17 17
RACGAP1 0.024 0.024 -10000 0 -0.41 1 1
mitosis 0 0 -10000 0 -10000 0 0
NCL -0.011 0.11 -10000 0 -0.36 27 27
Chromosomal passenger complex -0.003 0.094 -10000 0 -0.3 23 23
Chromosomal passenger complex/EVI5 0.062 0.086 -10000 0 -0.3 14 14
TACC1 0.021 0.026 -10000 0 -0.4 1 1
PPP2R5D 0.025 0.004 -10000 0 -10000 0 0
CUL3 0.025 0.004 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 0.025 0.085 0.37 1 -0.4 1 2
CRKL 0.014 0.058 0.26 4 -0.2 8 12
mol:DAG 0.015 0.057 -10000 0 -0.29 7 7
HRAS 0.02 0.081 0.29 9 -0.24 1 10
MAPK8 0.019 0.06 0.17 31 -0.22 7 38
RAP1A 0.014 0.06 0.26 4 -0.2 8 12
GAB1 0.013 0.06 0.26 4 -0.2 9 13
MAPK14 0.021 0.063 0.18 35 -0.22 7 42
EPO 0.016 0.028 -10000 0 -10000 0 0
PLCG1 0.015 0.059 -10000 0 -0.3 7 7
EPOR/TRPC2/IP3 Receptors 0.017 0.048 -10000 0 -0.4 4 4
RAPGEF1 0.024 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.032 0.061 -10000 0 -0.25 14 14
GAB1/SHC/GRB2/SOS1 0.033 0.052 0.27 2 -0.25 1 3
EPO/EPOR (dimer) 0.024 0.044 -10000 0 -0.28 4 4
IRS2 0.006 0.065 0.26 4 -0.2 15 19
STAT1 0.017 0.067 -10000 0 -0.3 9 9
STAT5B 0.016 0.061 -10000 0 -0.31 7 7
cell proliferation 0.005 0.074 0.2 37 -0.21 6 43
GAB1/SHIP/PIK3R1/SHP2/SHC 0.015 0.066 -10000 0 -0.29 4 4
TEC 0.009 0.066 0.26 4 -0.24 6 10
SOCS3 0.012 0.071 -10000 0 -0.4 10 10
STAT1 (dimer) 0.017 0.067 -10000 0 -0.29 9 9
JAK2 0.014 0.066 -10000 0 -0.39 9 9
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
EPO/EPOR (dimer)/JAK2 0.052 0.059 0.21 1 -0.19 11 12
EPO/EPOR 0.024 0.044 -10000 0 -0.28 4 4
LYN 0.019 0.04 -10000 0 -0.4 3 3
TEC/VAV2 0.02 0.065 0.28 3 -0.44 1 4
elevation of cytosolic calcium ion concentration 0.017 0.048 -10000 0 -0.4 4 4
SHC1 0.021 0.01 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.038 0.049 -10000 0 -0.24 7 7
mol:IP3 0.015 0.057 -10000 0 -0.29 7 7
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.014 0.085 0.29 2 -0.27 10 12
SH2B3 0.025 0.014 -10000 0 -10000 0 0
NFKB1 0.022 0.063 0.18 37 -0.22 7 44
EPO/EPOR (dimer)/JAK2/SOCS3 -0.001 0.051 -10000 0 -0.19 21 21
PTPN6 0.013 0.057 0.16 11 -0.2 8 19
TEC/VAV2/GRB2 0.029 0.064 0.28 2 -0.43 1 3
EPOR 0.017 0.048 -10000 0 -0.4 4 4
INPP5D 0.014 0.067 -10000 0 -0.4 9 9
mol:GDP 0.031 0.053 0.27 2 -0.26 1 3
SOS1 0.025 0.004 -10000 0 -10000 0 0
PLCG2 0.019 0.035 -10000 0 -0.4 2 2
CRKL/CBL/C3G 0.035 0.059 0.28 3 -0.26 1 4
VAV2 0.012 0.057 0.29 3 -0.23 2 5
CBL 0.014 0.059 0.29 3 -0.21 4 7
SHC/Grb2/SOS1 0.025 0.043 -10000 0 -0.19 7 7
STAT5A 0.016 0.061 -10000 0 -0.31 7 7
GRB2 0.024 0.006 -10000 0 -10000 0 0
STAT5 (dimer) 0.029 0.077 -10000 0 -0.33 9 9
LYN/PLCgamma2 0.026 0.04 -10000 0 -0.28 5 5
PTPN11 0.025 0.003 -10000 0 -10000 0 0
BTK 0.007 0.071 0.25 3 -0.22 16 19
BCL2 0.005 0.17 0.37 1 -0.71 16 17
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.001 0.077 0.23 20 -10000 0 20
GNAI2 0.024 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.018 0.052 -10000 0 -0.24 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.014 0.053 -10000 0 -0.4 5 5
RhoA/GTP 0.002 0.079 -10000 0 -0.23 20 20
negative regulation of cAMP metabolic process -0.001 0.072 -10000 0 -0.21 32 32
GNAZ 0.013 0.067 -10000 0 -0.4 9 9
GNAI3 0.025 0.002 -10000 0 -10000 0 0
GNA12 0.024 0.005 -10000 0 -10000 0 0
S1PR5 0.003 0.084 -10000 0 -0.4 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.001 0.072 -10000 0 -0.22 32 32
RhoA/GDP 0.018 0.004 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
GNAI1 0.012 0.071 -10000 0 -0.4 10 10
IL27-mediated 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
TGFB1 0.025 0.011 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.026 0.14 0.6 12 -10000 0 12
IL27/IL27R/JAK1 0.007 0.16 -10000 0 -0.74 9 9
TBX21 -0.041 0.14 -10000 0 -0.5 18 18
IL12B 0.018 0.016 -10000 0 -10000 0 0
IL12A -0.015 0.065 -10000 0 -0.28 19 19
IL6ST -0.01 0.11 -10000 0 -0.41 25 25
IL27RA/JAK1 0.005 0.14 -10000 0 -1.1 5 5
IL27 0.016 0.023 -10000 0 -10000 0 0
TYK2 0.021 0.014 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.005 0.066 0.41 1 -0.4 1 2
T-helper 2 cell differentiation 0.026 0.14 0.6 12 -10000 0 12
T cell proliferation during immune response 0.026 0.14 0.6 12 -10000 0 12
MAPKKK cascade -0.026 0.14 -10000 0 -0.6 12 12
STAT3 0.024 0.006 -10000 0 -10000 0 0
STAT2 0.025 0.004 -10000 0 -10000 0 0
STAT1 0.024 0.01 -10000 0 -10000 0 0
IL12RB1 0.006 0.079 -10000 0 -0.4 12 12
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.037 0.14 0.39 1 -0.47 19 20
IL27/IL27R/JAK2/TYK2 -0.027 0.14 -10000 0 -0.61 12 12
positive regulation of T cell mediated cytotoxicity -0.026 0.14 -10000 0 -0.6 12 12
STAT1 (dimer) -0.008 0.18 0.5 4 -0.64 15 19
JAK2 0.013 0.068 -10000 0 -0.4 9 9
JAK1 0.019 0.05 -10000 0 -0.4 5 5
STAT2 (dimer) -0.013 0.14 -10000 0 -0.57 12 12
T cell proliferation -0.036 0.14 -10000 0 -0.57 13 13
IL12/IL12R/TYK2/JAK2 -0.023 0.17 -10000 0 -0.69 17 17
IL17A 0.004 0.064 0.41 1 -0.4 1 2
mast cell activation 0.026 0.14 0.6 12 -10000 0 12
IFNG -0.003 0.034 -10000 0 -0.11 22 22
T cell differentiation -0.002 0.006 -10000 0 -0.021 22 22
STAT3 (dimer) -0.012 0.14 -10000 0 -0.57 12 12
STAT5A (dimer) -0.012 0.14 -10000 0 -0.57 12 12
STAT4 (dimer) -0.018 0.15 -10000 0 -0.56 14 14
STAT4 0.014 0.064 -10000 0 -0.4 8 8
T cell activation -0.004 0.013 0.12 4 -10000 0 4
IL27R/JAK2/TYK2 0.002 0.15 -10000 0 -0.93 6 6
GATA3 -0.013 0.24 0.63 14 -1.2 11 25
IL18 -0.005 0.054 -10000 0 -0.28 13 13
positive regulation of mast cell cytokine production -0.012 0.14 -10000 0 -0.56 12 12
IL27/EBI3 0.018 0.056 -10000 0 -0.28 9 9
IL27RA -0.007 0.15 -10000 0 -1.2 5 5
IL6 0.002 0.078 -10000 0 -0.4 11 11
STAT5A 0.024 0.006 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.005 0.057 0.46 5 -10000 0 5
IL1B -0.006 0.056 -10000 0 -0.28 14 14
EBI3 0.008 0.069 -10000 0 -0.4 9 9
TNF -0.021 0.076 -10000 0 -0.28 27 27
Regulation of Telomerase

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
Telomerase catalytic core complex -0.13 0.36 -10000 0 -1 45 45
RAD9A 0.025 0.004 -10000 0 -10000 0 0
AP1 0.019 0.05 -10000 0 -0.29 6 6
IFNAR2 0.017 0.029 -10000 0 -0.4 1 1
AKT1 -0.013 0.068 -10000 0 -0.25 11 11
ER alpha/Oestrogen -0.022 0.098 -10000 0 -0.28 44 44
NFX1/SIN3/HDAC complex 0.014 0.053 -10000 0 -0.32 6 6
EGF -0.015 0.1 -10000 0 -0.4 21 21
SMG5 0.02 0.01 -10000 0 -10000 0 0
SMG6 0.024 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.027 0.028 -10000 0 -10000 0 0
TERT/c-Abl -0.11 0.34 -10000 0 -0.98 44 44
SAP18 0.024 0.005 -10000 0 -10000 0 0
MRN complex 0.045 0.023 -10000 0 -0.24 1 1
WT1 -0.055 0.15 -10000 0 -0.37 58 58
WRN 0.023 0.008 -10000 0 -10000 0 0
SP1 0.017 0.024 -10000 0 -10000 0 0
SP3 0.02 0.016 -10000 0 -10000 0 0
TERF2IP 0.023 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.085 0.31 -10000 0 -0.86 45 45
Mad/Max 0.027 0.025 -10000 0 -10000 0 0
TERT -0.14 0.38 -10000 0 -1.1 44 44
CCND1 -0.13 0.35 -10000 0 -0.96 54 54
MAX 0.02 0.016 -10000 0 -10000 0 0
RBBP7 0.025 0.003 -10000 0 -10000 0 0
RBBP4 0.024 0.004 -10000 0 -10000 0 0
TERF2 0.02 0.01 -10000 0 -10000 0 0
PTGES3 0.025 0.003 -10000 0 -10000 0 0
SIN3A 0.024 0.005 -10000 0 -10000 0 0
Telomerase/911 0.022 0.047 0.2 1 -0.26 1 2
CDKN1B -0.023 0.12 -10000 0 -0.4 29 29
RAD1 0.025 0.005 -10000 0 -10000 0 0
XRCC5 0.025 0.004 -10000 0 -10000 0 0
XRCC6 0.024 0.006 -10000 0 -10000 0 0
SAP30 0.023 0.023 -10000 0 -0.4 1 1
TRF2/PARP2 0.032 0.013 -10000 0 -10000 0 0
UBE3A 0.02 0.015 -10000 0 -10000 0 0
JUN 0.019 0.028 -10000 0 -0.4 1 1
E6 -0.001 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.013 0.015 -10000 0 -10000 0 0
FOS 0.009 0.056 -10000 0 -0.32 7 7
IFN-gamma/IRF1 0.002 0.088 -10000 0 -0.28 29 29
PARP2 0.025 0.004 -10000 0 -10000 0 0
BLM 0.021 0.039 -10000 0 -0.4 3 3
Telomerase -0.001 0.1 -10000 0 -0.39 13 13
IRF1 0.014 0.042 -10000 0 -0.16 17 17
ESR1 -0.028 0.14 -10000 0 -0.4 44 44
KU/TER 0.035 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.033 0.013 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.019 0.053 -10000 0 -0.29 6 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.019 0.054 -10000 0 -0.3 6 6
HDAC1 0.025 0.004 -10000 0 -10000 0 0
HDAC2 0.017 0.023 -10000 0 -10000 0 0
ATM 0.016 0.019 -10000 0 -10000 0 0
SMAD3 0.013 0.008 -10000 0 -10000 0 0
ABL1 0.024 0.007 -10000 0 -10000 0 0
MXD1 0.019 0.017 -10000 0 -10000 0 0
MRE11A 0.025 0.004 -10000 0 -10000 0 0
HUS1 0.025 0.004 -10000 0 -10000 0 0
RPS6KB1 0.023 0.023 -10000 0 -0.4 1 1
TERT/NF kappa B1/14-3-3 -0.1 0.34 -10000 0 -0.96 45 45
NR2F2 0.021 0.051 -10000 0 -0.4 5 5
MAPK3 -0.007 0.018 -10000 0 -10000 0 0
MAPK1 -0.007 0.018 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.025 0.009 -10000 0 -10000 0 0
NFKB1 0.025 0.004 -10000 0 -10000 0 0
HNRNPC 0.025 0.004 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.016 0.019 -10000 0 -10000 0 0
NBN 0.022 0.024 -10000 0 -0.4 1 1
EGFR 0.008 0.071 -10000 0 -0.4 10 10
mol:Oestrogen -0.001 0.003 -10000 0 -10000 0 0
EGF/EGFR -0.007 0.093 -10000 0 -0.3 30 30
MYC 0.009 0.06 -10000 0 -0.4 7 7
IL2 0.006 0.03 -10000 0 -0.12 2 2
KU 0.035 0.01 -10000 0 -10000 0 0
RAD50 0.025 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
TGFB1 0.025 0.009 -10000 0 -10000 0 0
TRF2/BLM 0.03 0.03 -10000 0 -0.27 3 3
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.1 0.34 -10000 0 -0.97 45 45
SP1/HDAC2 0.026 0.034 -10000 0 -10000 0 0
PINX1 0.023 0.008 -10000 0 -10000 0 0
Telomerase/EST1A -0.085 0.31 -10000 0 -0.86 45 45
Smad3/Myc 0.019 0.039 -10000 0 -0.24 7 7
911 complex 0.048 0.014 -10000 0 -10000 0 0
IFNG -0.008 0.087 -10000 0 -0.26 29 29
Telomerase/PinX1 -0.089 0.31 -10000 0 -0.86 45 45
Telomerase/AKT1/mTOR/p70S6K -0.013 0.099 -10000 0 -0.48 7 7
SIN3B 0.024 0.006 -10000 0 -10000 0 0
YWHAE 0.024 0.006 -10000 0 -10000 0 0
Telomerase/EST1B -0.085 0.3 -10000 0 -0.85 44 44
response to DNA damage stimulus 0.005 0.018 -10000 0 -0.1 7 7
MRN complex/TRF2/Rap1 0.057 0.033 -10000 0 -0.21 1 1
TRF2/WRN 0.03 0.015 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.085 0.31 -10000 0 -0.86 45 45
E2F1 0.015 0.038 -10000 0 -0.4 2 2
ZNFX1 0.024 0.004 -10000 0 -10000 0 0
PIF1 0.017 0.055 -10000 0 -0.4 6 6
NCL 0.025 0.004 -10000 0 -10000 0 0
DKC1 0.025 0.003 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 0.023 0.063 -10000 0 -0.28 14 14
ATM 0.025 0.004 -10000 0 -10000 0 0
UBE2D3 0.025 0.004 -10000 0 -10000 0 0
PRKDC 0.021 0.032 -10000 0 -0.4 2 2
ATR 0.024 0.005 -10000 0 -10000 0 0
UBE2L3 0.025 0.005 -10000 0 -10000 0 0
FANCD2 0.019 0.006 -10000 0 -10000 0 0
protein ubiquitination 0.04 0.071 -10000 0 -0.2 25 25
XRCC5 0.025 0.004 -10000 0 -10000 0 0
XRCC6 0.024 0.006 -10000 0 -10000 0 0
M/R/N Complex 0.045 0.023 -10000 0 -0.24 1 1
MRE11A 0.025 0.004 -10000 0 -10000 0 0
DNA-PK 0.043 0.028 -10000 0 -0.24 2 2
FA complex/FANCD2/Ubiquitin 0.003 0.097 -10000 0 -0.37 17 17
FANCF 0.018 0.055 -10000 0 -0.4 6 6
BRCA1 0.022 0.032 -10000 0 -0.4 2 2
CCNE1 0.011 0.07 -10000 0 -0.4 10 10
CDK2/Cyclin E1 0.025 0.054 -10000 0 -0.28 10 10
FANCG 0.025 0.004 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.02 0.067 -10000 0 -0.28 16 16
FANCE 0.025 0.004 -10000 0 -10000 0 0
FANCC 0.023 0.023 -10000 0 -0.4 1 1
NBN 0.022 0.024 -10000 0 -0.4 1 1
FANCA 0.023 0.008 -10000 0 -10000 0 0
DNA repair -0.001 0.079 0.26 4 -0.33 7 11
BRCA1/BARD1/ubiquitin 0.02 0.067 -10000 0 -0.28 16 16
BARD1/DNA-PK 0.046 0.058 -10000 0 -0.24 12 12
FANCL 0.024 0.023 -10000 0 -0.4 1 1
mRNA polyadenylation -0.023 0.063 0.28 14 -10000 0 14
BRCA1/BARD1/CTIP/M/R/N Complex 0.012 0.055 -10000 0 -0.2 17 17
BRCA1/BACH1/BARD1/TopBP1 0.034 0.061 -10000 0 -0.24 16 16
BRCA1/BARD1/P53 0.037 0.074 -10000 0 -0.22 25 25
BARD1/CSTF1/BRCA1 0.034 0.061 -10000 0 -0.24 16 16
BRCA1/BACH1 0.022 0.032 -10000 0 -0.4 2 2
BARD1 0.008 0.083 -10000 0 -0.4 14 14
PCNA 0.025 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.035 0.061 -10000 0 -0.24 16 16
BRCA1/BARD1/UbcH7 0.035 0.061 -10000 0 -0.24 16 16
BRCA1/BARD1/RAD51/PCNA 0.043 0.065 -10000 0 -0.22 19 19
BARD1/DNA-PK/P53 0.045 0.074 -10000 0 -0.22 23 23
BRCA1/BARD1/Ubiquitin 0.02 0.067 -10000 0 -0.28 16 16
BRCA1/BARD1/CTIP 0.025 0.057 -10000 0 -0.22 17 17
FA complex 0.018 0.052 -10000 0 -0.28 6 6
BARD1/EWS 0.022 0.063 -10000 0 -0.28 14 14
RBBP8 0.011 0.016 -10000 0 -0.29 1 1
TP53 0.01 0.077 -10000 0 -0.4 12 12
TOPBP1 0.025 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.036 0.073 0.22 25 -10000 0 25
BRCA1/BARD1 0.045 0.074 -10000 0 -0.21 25 25
CSTF1 0.025 0.004 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.006 0.058 -10000 0 -0.28 14 14
CDK2 0.025 0.004 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.021 0.039 -10000 0 -0.4 3 3
RAD50 0.025 0.004 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.02 0.067 -10000 0 -0.28 16 16
EWSR1 0.024 0.006 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.024 0.005 -9999 0 -10000 0 0
ITGB7 0.017 0.055 -9999 0 -0.4 6 6
ITGA4 0.011 0.072 -9999 0 -0.4 10 10
alpha4/beta7 Integrin 0.021 0.066 -9999 0 -0.29 15 15
alpha4/beta1 Integrin 0.025 0.055 -9999 0 -0.28 10 10
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.025 0.003 -10000 0 -10000 0 0
mol:PIP3 -0.01 0.064 -10000 0 -0.24 25 25
FRAP1 0.011 0.042 0.27 2 -0.42 1 3
AKT1 -0.009 0.065 0.16 15 -0.22 21 36
INSR 0.024 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.025 0.009 -10000 0 -10000 0 0
mol:GTP 0.015 0.065 0.21 2 -0.2 15 17
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.003 0.037 -10000 0 -0.18 7 7
TSC2 0.025 0.004 -10000 0 -10000 0 0
RHEB/GDP 0.005 0.05 -10000 0 -0.18 15 15
TSC1 0.022 0.023 -10000 0 -0.4 1 1
Insulin Receptor/IRS1 0.007 0.068 -10000 0 -0.27 20 20
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.012 0.046 -10000 0 -0.2 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.024 0.006 -10000 0 -10000 0 0
RPS6KB1 0.005 0.077 0.28 4 -0.33 8 12
MAP3K5 0.003 0.031 0.18 2 -0.23 5 7
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
apoptosis 0.003 0.031 0.18 2 -0.23 5 7
mol:LY294002 0 0 -10000 0 -0.001 20 20
EIF4B 0.006 0.073 0.27 6 -0.29 7 13
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.023 0.068 0.28 3 -0.27 7 10
eIF4E/eIF4G1/eIF4A1 0.014 0.024 -10000 0 -0.26 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.015 0.075 -10000 0 -0.25 25 25
mTOR/RHEB/GTP/Raptor/GBL 0.003 0.048 0.24 5 -0.16 4 9
FKBP1A 0.025 0.004 -10000 0 -10000 0 0
RHEB/GTP 0.018 0.058 0.17 1 -0.22 3 4
mol:Amino Acids 0 0 -10000 0 -0.001 20 20
FKBP12/Rapamycin 0.019 0.004 -10000 0 -10000 0 0
PDPK1 -0.02 0.058 0.15 4 -0.23 21 25
EIF4E 0.024 0.023 -10000 0 -0.4 1 1
ASK1/PP5C 0.028 0.082 -10000 0 -0.56 6 6
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.001 0.08 -10000 0 -0.66 3 3
TSC1/TSC2 0.017 0.07 0.21 3 -0.21 15 18
tumor necrosis factor receptor activity 0 0 0.001 20 -10000 0 20
RPS6 0.024 0.023 -10000 0 -0.4 1 1
PPP5C 0.025 0.004 -10000 0 -10000 0 0
EIF4G1 0.024 0.007 -10000 0 -10000 0 0
IRS1 -0.008 0.069 -10000 0 -0.28 20 20
INS 0.015 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.007 -10000 0 -10000 0 0
PDK2 -0.019 0.058 0.15 4 -0.23 21 25
EIF4EBP1 -0.015 0.2 -10000 0 -1.1 12 12
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PPP2R5D 0.012 0.048 0.32 3 -0.38 1 4
peptide biosynthetic process -0.008 0.015 0.18 2 -10000 0 2
RHEB 0.024 0.008 -10000 0 -10000 0 0
EIF4A1 0.024 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.003 24 -0.002 1 25
EEF2 -0.008 0.015 0.18 2 -10000 0 2
eIF4E/4E-BP1 -0.002 0.18 -10000 0 -0.99 12 12
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.009 0.053 -10000 0 -0.27 12 12
CRKL 0.025 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.018 0.004 -10000 0 -10000 0 0
DOCK1 0.024 0.006 -10000 0 -10000 0 0
ITGA4 0.011 0.072 -10000 0 -0.4 10 10
alpha4/beta7 Integrin/MAdCAM1 0.034 0.081 -10000 0 -0.22 31 31
EPO 0.016 0.025 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.021 0.066 -10000 0 -0.29 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.025 0.055 -10000 0 -0.28 10 10
EPO/EPOR (dimer) 0.023 0.041 -10000 0 -0.29 4 4
lamellipodium assembly 0.01 0.076 -10000 0 -0.4 6 6
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.025 0.052 -10000 0 -0.28 9 9
ARF6 0.025 0.004 -10000 0 -10000 0 0
JAK2 0.009 0.06 -10000 0 -0.27 14 14
PXN 0.025 0.003 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
MADCAM1 -0.004 0.09 -10000 0 -0.4 16 16
cell adhesion 0.032 0.08 -10000 0 -0.22 31 31
CRKL/CBL 0.036 0.009 -10000 0 -10000 0 0
ITGB1 0.024 0.005 -10000 0 -10000 0 0
SRC -0.004 0.079 0.18 12 -0.25 27 39
ITGB7 0.017 0.055 -10000 0 -0.4 6 6
RAC1 0.025 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.024 0.09 -10000 0 -0.28 27 27
p130Cas/Crk/Dock1 0.009 0.067 -10000 0 -0.36 3 3
VCAM1 -0.008 0.11 -10000 0 -0.4 24 24
RHOA 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.052 0.05 -10000 0 -0.22 10 10
BCAR1 -0.022 0.072 0.2 11 -0.23 27 38
EPOR 0.018 0.047 -10000 0 -0.4 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.025 0.004 -10000 0 -10000 0 0
GIT1 0.024 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.01 0.078 -10000 0 -0.41 6 6
TRAIL signaling pathway

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
TNFSF10 0.01 0.074 -10000 0 -0.4 11 11
positive regulation of NF-kappaB transcription factor activity 0.013 0.075 -10000 0 -0.3 18 18
MAP2K4 0.007 0.051 -10000 0 -0.34 1 1
IKBKB 0.023 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.023 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.017 0.05 -10000 0 -0.4 5 5
SMPD1 0.006 0.029 -10000 0 -0.16 10 10
IKBKG 0.025 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.009 0.071 -10000 0 -0.4 10 10
TRAIL/TRAILR2 0.022 0.054 -10000 0 -0.28 10 10
TRAIL/TRAILR3 0.003 0.095 -10000 0 -0.32 26 26
TRAIL/TRAILR1 0.018 0.067 -10000 0 -0.3 14 14
TRAIL/TRAILR4 0.013 0.075 -10000 0 -0.3 18 18
TRAIL/TRAILR1/DAP3/GTP 0.023 0.054 -10000 0 -0.23 12 12
IKK complex 0.017 0.03 -10000 0 -10000 0 0
RIPK1 0.025 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.015 0.008 -10000 0 -10000 0 0
MAPK3 0.002 0.051 -10000 0 -0.28 11 11
MAP3K1 0.008 0.06 -10000 0 -0.23 16 16
TRAILR4 (trimer) 0.009 0.071 -10000 0 -0.4 10 10
TRADD 0.023 0.008 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.017 0.05 -10000 0 -0.4 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.012 0.051 -10000 0 -0.22 15 15
CFLAR 0.025 0.003 -10000 0 -10000 0 0
MAPK1 0.003 0.049 -10000 0 -0.28 10 10
TRAIL/TRAILR1/FADD/TRADD/RIP 0.046 0.061 -10000 0 -0.21 14 14
mol:ceramide 0.006 0.029 -10000 0 -0.16 10 10
FADD 0.025 0.004 -10000 0 -10000 0 0
MAPK8 0.012 0.06 0.2 6 -0.33 2 8
TRAF2 0.024 0.006 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.005 0.1 -10000 0 -0.4 21 21
CHUK 0.024 0.006 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.03 0.062 -10000 0 -0.26 14 14
DAP3 0.02 0.01 -10000 0 -10000 0 0
CASP10 0.01 0.075 0.17 29 -0.29 11 40
JNK cascade 0.013 0.075 -10000 0 -0.3 18 18
TRAIL (trimer) 0.01 0.074 -10000 0 -0.4 11 11
TNFRSF10C -0.005 0.1 -10000 0 -0.4 21 21
TRAIL/TRAILR1/DAP3/GTP/FADD 0.03 0.056 -10000 0 -0.22 12 12
TRAIL/TRAILR2/FADD 0.034 0.051 -10000 0 -0.24 10 10
cell death 0.006 0.029 -10000 0 -0.16 10 10
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.016 0.038 -10000 0 -0.2 9 9
TRAILR2 (trimer) 0.023 0.008 -10000 0 -10000 0 0
CASP8 0.014 0.056 -10000 0 -0.67 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.05 0.053 -10000 0 -0.21 9 9
Class I PI3K 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
ARF5/GTP -0.022 0.039 0.15 5 -0.36 1 6
DAPP1 -0.014 0.12 0.26 4 -0.41 19 23
Src family/SYK family/BLNK-LAT/BTK-ITK -0.038 0.17 0.32 1 -0.52 29 30
mol:DAG -0.012 0.076 0.2 8 -0.24 16 24
HRAS 0.023 0.011 -10000 0 -10000 0 0
RAP1A 0.025 0.01 -10000 0 -10000 0 0
ARF5/GDP 0.011 0.078 0.2 1 -0.3 11 12
PLCG2 0.019 0.035 -10000 0 -0.4 2 2
PLCG1 0.025 0.005 -10000 0 -10000 0 0
ARF5 0.025 0.005 -10000 0 -10000 0 0
mol:GTP -0.02 0.039 0.14 4 -0.2 12 16
ARF1/GTP -0.012 0.04 -10000 0 -0.37 1 1
RHOA 0.024 0.005 -10000 0 -10000 0 0
YES1 0.025 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.02 0.039 0.16 4 -0.2 12 16
ADAP1 -0.023 0.047 0.15 3 -0.21 11 14
ARAP3 -0.02 0.039 0.14 4 -0.2 12 16
INPPL1 0.025 0.003 -10000 0 -10000 0 0
PREX1 0.018 0.051 -10000 0 -0.4 5 5
ARHGEF6 0.02 0.045 -10000 0 -0.4 4 4
ARHGEF7 0.024 0.006 -10000 0 -10000 0 0
ARF1 0.021 0.01 -10000 0 -10000 0 0
NRAS 0.019 0.051 -10000 0 -0.41 5 5
FYN 0.025 0.007 -10000 0 -10000 0 0
ARF6 0.025 0.004 -10000 0 -10000 0 0
FGR 0.015 0.06 -10000 0 -0.4 7 7
mol:Ca2+ 0 0.056 0.2 15 -0.12 11 26
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.016 0.063 -10000 0 -0.4 8 8
ZAP70 -0.004 0.1 -10000 0 -0.4 20 20
mol:IP3 -0.004 0.07 0.24 14 -0.17 15 29
LYN 0.02 0.039 -10000 0 -0.4 3 3
ARF1/GDP 0.009 0.073 -10000 0 -0.28 11 11
RhoA/GDP 0.016 0.059 0.19 2 -0.34 1 3
PDK1/Src/Hsp90 0.047 0.025 -10000 0 -0.24 2 2
BLNK 0.013 0.067 -10000 0 -0.4 9 9
actin cytoskeleton reorganization -0.002 0.077 0.24 5 -0.29 8 13
SRC 0.022 0.032 -10000 0 -0.4 2 2
PLEKHA2 -0.013 0.034 -10000 0 -0.24 8 8
RAC1 0.025 0.005 -10000 0 -10000 0 0
PTEN 0.024 0.01 -10000 0 -10000 0 0
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.021 0.04 0.15 6 -0.36 1 7
RhoA/GTP -0.021 0.038 0.15 4 -0.23 5 9
Src family/SYK family/BLNK-LAT -0.021 0.13 -10000 0 -0.44 20 20
BLK -0.014 0.1 -10000 0 -0.4 22 22
PDPK1 0.025 0.004 -10000 0 -10000 0 0
CYTH1 -0.02 0.04 0.16 2 -0.23 5 7
HCK 0.009 0.075 -10000 0 -0.4 11 11
CYTH3 -0.02 0.041 0.15 3 -0.23 5 8
CYTH2 -0.02 0.041 0.15 3 -0.23 5 8
KRAS 0.024 0.011 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.008 0.051 -10000 0 -0.42 3 3
SGK1 0.012 0.054 -10000 0 -0.45 3 3
INPP5D 0.014 0.067 -10000 0 -0.4 9 9
mol:GDP -0.001 0.079 0.2 1 -0.27 18 19
SOS1 0.025 0.004 -10000 0 -10000 0 0
SYK 0.015 0.059 -10000 0 -0.4 7 7
ARF6/GDP 0.003 0.053 0.18 1 -0.33 1 2
mol:PI-3-4-5-P3 -0.02 0.04 0.15 1 -0.2 12 13
ARAP3/RAP1A/GTP -0.02 0.04 0.16 4 -0.2 12 16
VAV1 0.009 0.077 -10000 0 -0.4 12 12
mol:PI-3-4-P2 0.004 0.046 -10000 0 -0.28 9 9
RAS family/GTP/PI3K Class I 0.031 0.051 0.2 7 -0.2 12 19
PLEKHA1 -0.012 0.03 -10000 0 -0.24 6 6
Rac1/GDP 0.012 0.077 0.2 1 -0.31 10 11
LAT 0.019 0.046 -10000 0 -0.4 4 4
Rac1/GTP 0.005 0.08 -10000 0 -0.34 14 14
ITK -0.03 0.05 -10000 0 -0.21 19 19
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.023 0.095 0.19 4 -0.33 17 21
LCK 0.008 0.078 -10000 0 -0.4 12 12
BTK -0.026 0.054 0.15 3 -0.24 14 17
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.014 0.053 -10000 0 -0.4 5 5
CDC42/GTP 0.001 0.081 -10000 0 -0.26 15 15
PLCG1 -0.007 0.069 -10000 0 -0.26 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.006 -10000 0 -10000 0 0
GNAI3 0.025 0.002 -10000 0 -10000 0 0
G12/G13 0.035 0.011 -10000 0 -10000 0 0
cell migration 0.001 0.079 -10000 0 -0.26 15 15
S1PR5 0.003 0.084 -10000 0 -0.4 14 14
S1PR4 0.009 0.069 -10000 0 -0.4 9 9
MAPK3 -0.006 0.069 -10000 0 -0.26 15 15
MAPK1 -0.004 0.068 -10000 0 -0.26 15 15
S1P/S1P5/Gi -0.001 0.072 -10000 0 -0.22 32 32
GNAI1 0.012 0.071 -10000 0 -0.4 10 10
CDC42/GDP 0.018 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.018 0.052 -10000 0 -0.24 13 13
RHOA 0.008 0.038 0.18 6 -0.2 7 13
S1P/S1P4/Gi 0.001 0.073 -10000 0 -0.23 28 28
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.013 0.067 -10000 0 -0.4 9 9
S1P/S1P4/G12/G13 0.038 0.041 -10000 0 -0.21 8 8
GNA12 0.024 0.005 -10000 0 -10000 0 0
GNA13 0.024 0.006 -10000 0 -10000 0 0
CDC42 0.025 0.005 -10000 0 -10000 0 0
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 0.006 0.048 0.18 23 -0.097 3 26
BUB1B 0 0.051 0.11 1 -0.21 14 15
PLK1 0.005 0.025 0.078 10 -0.11 7 17
PLK1S1 0.007 0.026 0.12 1 -0.22 3 4
KIF2A 0.003 0.025 0.27 1 -0.15 1 2
regulation of mitotic centrosome separation 0.005 0.025 0.078 10 -0.11 7 17
GOLGA2 0.024 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.015 0.074 -10000 0 -0.24 23 23
WEE1 0.007 0.059 -10000 0 -0.3 11 11
cytokinesis 0.01 0.049 0.16 2 -0.28 5 7
PP2A-alpha B56 0.034 0.12 -10000 0 -0.57 14 14
AURKA 0.006 0.031 -10000 0 -0.25 4 4
PICH/PLK1 0.011 0.034 -10000 0 -0.25 4 4
CENPE -0.004 0.044 -10000 0 -0.22 12 12
RhoA/GTP 0.018 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.003 0.026 0.27 1 -0.15 1 2
PPP2CA 0.025 0.004 -10000 0 -10000 0 0
FZR1 0.024 0.007 -10000 0 -10000 0 0
TPX2 0.007 0.041 0.11 3 -0.28 6 9
PAK1 0.025 0.003 -10000 0 -10000 0 0
SPC24 0.004 0.091 -10000 0 -0.4 17 17
FBXW11 0.025 0.004 -10000 0 -10000 0 0
CLSPN -0.001 0.06 -10000 0 -0.28 15 15
GORASP1 0.025 0.005 -10000 0 -10000 0 0
metaphase 0 0.003 0.014 10 -0.017 3 13
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.002 0.013 0.044 11 -0.055 6 17
G2 phase of mitotic cell cycle 0 0.004 0.013 20 -0.01 3 23
STAG2 0.023 0.032 -10000 0 -0.4 2 2
GRASP65/GM130/RAB1/GTP 0.007 0.088 -10000 0 -0.51 10 10
spindle elongation 0.005 0.025 0.078 10 -0.11 7 17
ODF2 0.024 0.007 -10000 0 -10000 0 0
BUB1 0.006 0.13 -10000 0 -0.62 14 14
TPT1 0.002 0.042 -10000 0 -0.2 13 13
CDC25C 0.003 0.06 -10000 0 -0.34 10 10
CDC25B 0.023 0.013 -10000 0 -10000 0 0
SGOL1 -0.006 0.048 0.097 3 -0.18 23 26
RHOA 0.024 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.032 0.036 -10000 0 -0.21 3 3
CDC14B 0.003 0.027 -10000 0 -0.29 3 3
CDC20 0.023 0.032 -10000 0 -0.4 2 2
PLK1/PBIP1 0.005 0.024 0.076 2 -0.14 5 7
mitosis -0.001 0.004 0.032 4 -10000 0 4
FBXO5 0.002 0.036 0.12 5 -0.19 8 13
CDC2 0.001 0.002 -10000 0 -0.012 4 4
NDC80 0.014 0.067 -10000 0 -0.4 9 9
metaphase plate congression 0.005 0.041 -10000 0 -0.23 9 9
ERCC6L 0.013 0.038 -10000 0 -0.23 5 5
NLP/gamma Tubulin 0.001 0.023 0.067 3 -0.098 12 15
microtubule cytoskeleton organization 0.002 0.042 -10000 0 -0.2 13 13
G2/M transition DNA damage checkpoint 0 0.002 0.011 3 -10000 0 3
PPP1R12A 0.026 0.003 -10000 0 -10000 0 0
interphase 0 0.002 0.011 3 -10000 0 3
PLK1/PRC1-2 0.032 0.034 -10000 0 -0.21 3 3
GRASP65/GM130/RAB1/GTP/PLK1 0.039 0.029 -10000 0 -10000 0 0
RAB1A 0.025 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.004 0.022 0.081 10 -0.098 6 16
mitotic prometaphase -0.001 0.003 0.018 8 -0.01 2 10
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.042 -10000 0 -0.46 2 2
microtubule-based process 0.019 0.031 0.1 2 -0.16 6 8
Golgi organization 0.005 0.025 0.078 10 -0.11 7 17
Cohesin/SA2 0.017 0.029 -10000 0 -0.15 5 5
PPP1CB/MYPT1 0.035 0.026 -10000 0 -0.29 2 2
KIF20A 0.023 0.032 -10000 0 -0.4 2 2
APC/C/CDC20 0.018 0.034 0.1 2 -0.2 4 6
PPP2R1A 0.025 0.004 -10000 0 -10000 0 0
chromosome segregation 0.005 0.024 0.075 2 -0.14 5 7
PRC1 0.025 0.005 -10000 0 -10000 0 0
ECT2 0.016 0.075 0.22 31 -0.23 8 39
C13orf34 0.004 0.021 0.072 10 -0.09 7 17
NUDC 0.005 0.042 -10000 0 -0.24 9 9
regulation of attachment of spindle microtubules to kinetochore 0 0.05 0.11 1 -0.21 14 15
spindle assembly 0.003 0.021 0.084 5 -0.097 6 11
spindle stabilization 0.007 0.026 0.12 1 -0.22 3 4
APC/C/HCDH1 0.019 0.025 -10000 0 -0.24 3 3
MKLP2/PLK1 0.019 0.032 0.1 2 -0.16 6 8
CCNB1 0.024 0.024 -10000 0 -0.42 1 1
PPP1CB 0.023 0.032 -10000 0 -0.41 2 2
BTRC 0.024 0.006 -10000 0 -10000 0 0
ROCK2 0.013 0.041 -10000 0 -0.28 3 3
TUBG1 -0.002 0.047 -10000 0 -0.19 19 19
G2/M transition of mitotic cell cycle 0.004 0.029 -10000 0 -0.25 2 2
MLF1IP 0.005 0.016 -10000 0 -0.29 1 1
INCENP 0.025 0.003 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.024 0.006 -10000 0 -10000 0 0
HDAC4 0.025 0.007 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.011 0.032 0.25 2 -0.16 7 9
CDKN1A -0.023 0.11 0.39 1 -0.58 12 13
KAT2B 0.016 0.059 -10000 0 -0.4 7 7
BAX 0.025 0.004 -10000 0 -10000 0 0
FOXO3 -0.005 0.005 -10000 0 -10000 0 0
FOXO1 0.024 0.008 -10000 0 -10000 0 0
FOXO4 0.014 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.024 0.006 -10000 0 -10000 0 0
TAT 0.018 0.015 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.014 0.043 -10000 0 -0.29 7 7
PPARGC1A -0.052 0.15 -10000 0 -0.4 52 52
FHL2 0.013 0.07 -10000 0 -0.4 10 10
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.035 0.021 0.16 7 -10000 0 7
HIST2H4A 0.011 0.032 0.16 7 -0.25 2 9
SIRT1/FOXO3a 0.02 0.034 0.16 10 -0.19 2 12
SIRT1 0.026 0.028 0.2 8 -10000 0 8
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.04 0.026 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.014 0.057 -10000 0 -0.21 15 15
apoptosis -0.046 0.022 -10000 0 -10000 0 0
SIRT1/PGC1A -0.014 0.095 0.14 6 -0.24 49 55
p53/SIRT1 0.027 0.072 0.38 8 -0.29 9 17
SIRT1/FOXO4 0.023 0.036 -10000 0 -0.2 2 2
FOXO1/FHL2/SIRT1 0.038 0.048 -10000 0 -0.22 10 10
HIST1H1E 0.003 0.05 -10000 0 -0.25 13 13
SIRT1/p300 0.035 0.021 0.16 7 -10000 0 7
muscle cell differentiation -0.021 0.045 0.23 7 -10000 0 7
TP53 0.015 0.072 0.2 8 -0.4 9 17
KU70/SIRT1/BAX 0.046 0.022 -10000 0 -10000 0 0
CREBBP 0.025 0.004 -10000 0 -10000 0 0
MEF2D 0.021 0.01 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.029 0.022 0.16 3 -10000 0 3
ACSS2 0.013 0.02 0.13 8 -10000 0 8
SIRT1/PCAF/MYOD 0.021 0.045 -10000 0 -0.24 7 7
TCGA08_rtk_signaling

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
PDGFRA -0.009 0.11 -10000 0 -0.4 27 27
HRAS 0.024 0.005 -10000 0 -10000 0 0
EGFR 0.013 0.07 -10000 0 -0.4 10 10
AKT 0.02 0.069 0.24 4 -0.22 6 10
FOXO3 0.025 0.003 -10000 0 -10000 0 0
AKT1 0.025 0.004 -10000 0 -10000 0 0
FOXO1 0.024 0.008 -10000 0 -10000 0 0
AKT3 0.015 0.042 -10000 0 -0.4 3 3
FOXO4 0.025 0.002 -10000 0 -10000 0 0
MET -0.006 0.11 -10000 0 -0.4 24 24
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PIK3CB 0.025 0.005 -10000 0 -10000 0 0
NRAS 0.02 0.05 -10000 0 -0.4 5 5
PIK3CG 0.001 0.094 -10000 0 -0.4 18 18
PIK3R3 0.018 0.055 -10000 0 -0.4 6 6
PIK3R2 0.024 0.006 -10000 0 -10000 0 0
NF1 0.024 0.007 -10000 0 -10000 0 0
RAS 0 0.061 -10000 0 -0.15 41 41
ERBB2 0.022 0.024 -10000 0 -0.4 1 1
proliferation/survival/translation -0.036 0.052 0.2 1 -0.24 4 5
PI3K 0.008 0.068 0.19 10 -0.25 10 20
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
KRAS 0.025 0.004 -10000 0 -10000 0 0
FOXO 0.05 0.047 0.2 10 -10000 0 10
AKT2 0.025 0.005 -10000 0 -10000 0 0
PTEN 0.024 0.007 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.012 0.1 -10000 0 -0.35 13 13
KLHL20 -0.008 0.074 0.17 1 -0.23 22 23
CYFIP2 0.014 0.067 -10000 0 -0.4 9 9
Rac1/GDP 0.002 0.075 -10000 0 -0.27 10 10
ENAH -0.018 0.1 -10000 0 -0.35 14 14
AP1M1 0.024 0.006 -10000 0 -10000 0 0
RAP1B 0.025 0.002 -10000 0 -10000 0 0
RAP1A 0.025 0.001 -10000 0 -10000 0 0
CTNNB1 0.023 0.023 -10000 0 -0.4 1 1
CDC42/GTP 0.018 0.035 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.021 0.045 -10000 0 -0.16 23 23
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.046 0.054 -10000 0 -0.22 12 12
RAPGEF1 -0.007 0.08 -10000 0 -0.34 8 8
CTNND1 0.025 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.009 0.11 -10000 0 -0.29 42 42
CRK -0.008 0.083 -10000 0 -0.36 8 8
E-cadherin/gamma catenin/alpha catenin 0.039 0.048 -10000 0 -0.32 5 5
alphaE/beta7 Integrin 0.029 0.043 -10000 0 -0.28 6 6
IQGAP1 0.025 0.005 -10000 0 -10000 0 0
NCKAP1 0.025 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.01 -10000 0 -10000 0 0
DLG1 -0.01 0.097 -10000 0 -0.36 13 13
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.03 -10000 0 -0.2 3 3
MLLT4 0.025 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.039 0.041 -10000 0 -0.22 8 8
PI3K 0.002 0.039 -10000 0 -0.26 3 3
ARF6 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.027 0.051 -10000 0 -0.38 5 5
TIAM1 0.016 0.063 -10000 0 -0.4 8 8
E-cadherin(dimer)/Ca2+ 0.048 0.039 -10000 0 -0.2 6 6
AKT1 -0.009 0.025 0.099 1 -0.16 2 3
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
CDH1 0.017 0.05 -10000 0 -0.4 5 5
RhoA/GDP 0.004 0.073 -10000 0 -0.27 9 9
actin cytoskeleton organization -0.004 0.056 0.17 2 -0.17 20 22
CDC42/GDP 0.005 0.074 -10000 0 -0.27 11 11
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.039 -10000 0 -0.29 5 5
ITGB7 0.017 0.055 -10000 0 -0.4 6 6
RAC1 0.025 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.052 0.042 -10000 0 -0.22 6 6
E-cadherin/Ca2+/beta catenin/alpha catenin 0.035 0.035 -10000 0 -0.2 6 6
mol:GDP -0.011 0.08 -10000 0 -0.31 11 11
CDC42/GTP/IQGAP1 0.033 0.008 -10000 0 -10000 0 0
JUP 0.022 0.032 -10000 0 -0.4 2 2
p120 catenin/RhoA/GDP 0.011 0.076 -10000 0 -0.27 9 9
RAC1/GTP/IQGAP1 0.032 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.034 0.012 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
CDC42 0.025 0.005 -10000 0 -10000 0 0
CTNNA1 0.025 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.001 0.051 0.14 3 -0.17 18 21
NME1 0.024 0.006 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.007 0.093 -10000 0 -0.29 33 33
regulation of cell-cell adhesion 0.011 0.03 -10000 0 -10000 0 0
WASF2 -0.001 0.031 -10000 0 -0.11 3 3
Rap1/GTP 0.022 0.044 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.055 0.061 -10000 0 -0.24 11 11
CCND1 -0.002 0.062 0.16 3 -0.21 18 21
VAV2 -0.037 0.18 -10000 0 -0.61 26 26
RAP1/GDP 0.019 0.065 0.21 1 -0.29 3 4
adherens junction assembly -0.006 0.091 -10000 0 -0.28 33 33
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.024 0.006 -10000 0 -10000 0 0
PIP5K1C 0.024 0.007 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.039 0.056 -10000 0 -0.23 12 12
E-cadherin/beta catenin 0.007 0.039 -10000 0 -0.29 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.014 0.1 -10000 0 -0.35 15 15
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.027 0.11 -10000 0 -0.36 26 26
E-cadherin/beta catenin/alpha catenin 0.04 0.04 -10000 0 -0.24 6 6
ITGAE 0.024 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.01 0.11 -10000 0 -0.3 42 42
IL2 signaling events mediated by STAT5

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
GAB2 0.025 0.006 -10000 0 -10000 0 0
ELF1 0.016 0.066 -10000 0 -0.32 13 13
CCNA2 0.019 0.05 -10000 0 -0.4 5 5
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
JAK3 0.019 0.046 -10000 0 -0.4 4 4
PIK3R1 0.004 0.091 -10000 0 -0.4 17 17
JAK1 0.02 0.05 -10000 0 -0.4 5 5
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.015 0.12 0.23 2 -0.45 16 18
SHC1 0.021 0.01 -10000 0 -10000 0 0
SP1 0.022 0.047 -10000 0 -0.32 6 6
IL2RA -0.012 0.13 -10000 0 -0.63 15 15
IL2RB 0.006 0.081 -10000 0 -0.4 13 13
SOS1 0.025 0.004 -10000 0 -10000 0 0
IL2RG 0.008 0.078 -10000 0 -0.4 12 12
G1/S transition of mitotic cell cycle -0.011 0.14 0.32 2 -0.47 22 24
PTPN11 0.026 0.003 -10000 0 -10000 0 0
CCND2 0.003 0.088 -10000 0 -0.66 6 6
LCK 0.009 0.078 -10000 0 -0.4 12 12
GRB2 0.025 0.006 -10000 0 -10000 0 0
IL2 0.015 0.02 -10000 0 -10000 0 0
CDK6 0.009 0.078 -10000 0 -0.4 12 12
CCND3 0.018 0.11 0.32 1 -0.46 9 10
Insulin Pathway

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
CBL/APS/CAP 0.03 0.057 -10000 0 -0.2 19 19
TC10/GTP 0.037 0.035 -10000 0 -0.19 6 6
Insulin Receptor/Insulin/IRS1/Shp2 0.045 0.058 -10000 0 -0.23 14 14
HRAS 0.024 0.005 -10000 0 -10000 0 0
APS homodimer 0.019 0.05 -10000 0 -0.4 5 5
GRB14 -0.044 0.15 -10000 0 -0.4 50 50
FOXO3 0.01 0.081 -10000 0 -0.58 6 6
AKT1 -0.034 0.095 0.25 8 -0.4 3 11
INSR 0.026 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.048 0.022 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.015 0.063 -10000 0 -0.4 8 8
SORBS1 0.019 0.03 -10000 0 -0.4 1 1
CRK 0.024 0.006 -10000 0 -10000 0 0
PTPN1 0 0.022 -10000 0 -10000 0 0
CAV1 -0.016 0.043 0.15 2 -0.21 15 17
CBL/APS/CAP/Crk-II/C3G 0.059 0.045 -10000 0 -0.21 6 6
Insulin Receptor/Insulin/IRS1/NCK2 0.044 0.058 -10000 0 -0.23 14 14
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.027 0.063 -10000 0 -0.2 22 22
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.003 0.082 -10000 0 -0.32 15 15
RPS6KB1 -0.036 0.086 0.21 8 -0.36 4 12
PARD6A 0.019 0.039 -10000 0 -0.4 3 3
CBL 0.025 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.016 0.033 -10000 0 -0.56 1 1
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.009 0.088 -10000 0 -0.26 8 8
HRAS/GTP 0.006 0.036 -10000 0 -0.18 11 11
Insulin Receptor 0.026 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.046 0.05 -10000 0 -0.21 7 7
PRKCI -0.002 0.083 -10000 0 -0.38 6 6
Insulin Receptor/Insulin/GRB14/PDK1 -0.02 0.091 -10000 0 -0.21 62 62
SHC1 0.021 0.01 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.04 0.036 -10000 0 -0.37 2 2
PI3K 0.035 0.067 -10000 0 -0.21 22 22
NCK2 0.025 0.003 -10000 0 -10000 0 0
RHOQ 0.025 0.004 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.018 0.004 -10000 0 -10000 0 0
AKT2 -0.033 0.093 0.26 6 -0.35 4 10
PRKCZ -0.005 0.093 -10000 0 -0.38 12 12
SH2B2 0.019 0.05 -10000 0 -0.4 5 5
SHC/SHIP 0.014 0.044 -10000 0 -0.2 13 13
F2RL2 -0.018 0.12 -10000 0 -0.4 31 31
TRIP10 0.024 0.007 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.034 0.021 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.031 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.053 0.034 -10000 0 -10000 0 0
RAPGEF1 0.024 0.007 -10000 0 -10000 0 0
RASA1 0.025 0.005 -10000 0 -10000 0 0
NCK1 0.025 0.005 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.051 0.042 -10000 0 -0.22 6 6
TC10/GDP 0.018 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.04 0.048 -10000 0 -0.22 8 8
INPP5D -0.019 0.049 0.15 1 -0.21 21 22
SOS1 0.025 0.004 -10000 0 -10000 0 0
SGK1 -0.003 0.1 -10000 0 -0.73 7 7
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.003 -10000 0 -10000 0 0
IRS1 0.008 0.083 -10000 0 -0.4 14 14
p62DOK/RasGAP 0.041 0.037 -10000 0 -0.37 2 2
INS 0.018 0.007 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.019 0.048 0.15 1 -0.21 21 22
GRB2 0.024 0.006 -10000 0 -10000 0 0
EIF4EBP1 -0.035 0.086 0.25 6 -0.38 3 9
PTPRA 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.031 0.01 -10000 0 -10000 0 0
PDPK1 0.025 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.013 0.037 -10000 0 -0.19 10 10
Insulin Receptor/Insulin/IRS1 0.03 0.054 -10000 0 -0.22 14 14
Insulin Receptor/Insulin/IRS3 0.031 0.012 -10000 0 -10000 0 0
Par3/Par6 0.028 0.075 -10000 0 -0.21 30 30
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.02 0.081 0.25 6 -0.4 6 12
PDGFB-D/PDGFRB/SLAP 0.027 0.042 -10000 0 -0.29 5 5
PDGFB-D/PDGFRB/APS/CBL 0.042 0.043 -10000 0 -0.24 7 7
AKT1 0.006 0.087 0.36 10 -0.33 1 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.022 0.087 0.24 7 -0.43 6 13
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
FGR -0.006 0.11 0.36 1 -0.51 13 14
mol:Ca2+ 0.014 0.09 0.24 7 -0.42 8 15
MYC 0.025 0.16 0.33 13 -0.73 10 23
SHC1 0.021 0.01 -10000 0 -10000 0 0
HRAS/GDP 0.028 0.032 0.17 10 -0.2 2 12
LRP1/PDGFRB/PDGFB 0.045 0.031 -10000 0 -0.24 3 3
GRB10 0.015 0.063 -10000 0 -0.4 8 8
PTPN11 0.025 0.003 -10000 0 -10000 0 0
GO:0007205 0.013 0.091 0.24 7 -0.42 8 15
PTEN 0.024 0.007 -10000 0 -10000 0 0
GRB2 0.024 0.006 -10000 0 -10000 0 0
GRB7 0.019 0.04 -10000 0 -0.4 3 3
PDGFB-D/PDGFRB/SHP2 0.035 0.021 -10000 0 -0.28 1 1
PDGFB-D/PDGFRB/GRB10 0.027 0.054 -10000 0 -0.29 10 10
cell cycle arrest 0.027 0.041 -10000 0 -0.29 5 5
HRAS 0.024 0.005 -10000 0 -10000 0 0
HIF1A 0.004 0.081 0.34 10 -0.3 1 11
GAB1 0.013 0.096 0.25 5 -0.43 8 13
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.016 0.094 0.27 12 -0.41 7 19
PDGFB-D/PDGFRB 0.046 0.029 -10000 0 -0.25 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.033 0.027 -10000 0 -0.29 2 2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.02 0.077 0.22 8 -0.36 8 16
positive regulation of MAPKKK cascade 0.035 0.021 -10000 0 -0.28 1 1
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:IP3 0.013 0.092 0.24 7 -0.43 8 15
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.024 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.028 0.041 -10000 0 -0.29 5 5
SHB 0.024 0.023 -10000 0 -0.4 1 1
BLK -0.045 0.17 -10000 0 -0.48 43 43
PTPN2 0.025 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.034 0.027 -10000 0 -0.29 2 2
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
VAV2 0.013 0.11 0.27 6 -0.48 9 15
CBL 0.025 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.033 0.028 -10000 0 -0.29 2 2
LCK -0.007 0.099 -10000 0 -0.44 14 14
PDGFRB 0.022 0.035 -10000 0 -0.41 2 2
ACP1 0.024 0.005 -10000 0 -10000 0 0
HCK -0.005 0.11 0.35 1 -0.54 12 13
ABL1 0.009 0.094 0.24 7 -0.38 9 16
PDGFB-D/PDGFRB/CBL 0.011 0.11 0.25 3 -0.44 11 14
PTPN1 0.025 0.007 -10000 0 -10000 0 0
SNX15 0.025 0.003 -10000 0 -10000 0 0
STAT3 0.024 0.006 -10000 0 -10000 0 0
STAT1 0.025 0.009 -10000 0 -10000 0 0
cell proliferation 0.026 0.14 0.3 18 -0.64 10 28
SLA 0.018 0.041 -10000 0 -0.4 3 3
actin cytoskeleton reorganization 0.032 0.055 0.28 7 -10000 0 7
SRC 0.005 0.083 0.35 1 -0.63 4 5
PI3K -0.001 0.042 -10000 0 -0.21 10 10
PDGFB-D/PDGFRB/GRB7/SHC 0.034 0.04 -10000 0 -0.24 5 5
SH2B2 0.019 0.05 -10000 0 -0.4 5 5
PLCgamma1/SPHK1 0.022 0.089 0.24 7 -0.44 6 13
LYN 0.003 0.067 0.35 1 -0.4 6 7
LRP1 0.023 0.025 -10000 0 -0.16 4 4
SOS1 0.025 0.004 -10000 0 -10000 0 0
STAT5B 0.024 0.006 -10000 0 -10000 0 0
STAT5A 0.024 0.006 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.062 0.04 -10000 0 -0.2 3 3
SPHK1 0.019 0.042 -10000 0 -0.4 3 3
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.013 0.092 0.24 7 -0.43 8 15
PLCG1 0.013 0.094 0.24 6 -0.44 8 14
NHERF/PDGFRB 0.043 0.045 -10000 0 -0.28 6 6
YES1 0 0.095 0.36 1 -0.56 8 9
cell migration 0.042 0.045 -10000 0 -0.28 6 6
SHC/Grb2/SOS1 0.054 0.042 -10000 0 -0.2 2 2
SLC9A3R2 0.022 0.032 -10000 0 -0.4 2 2
SLC9A3R1 0.02 0.04 -10000 0 -0.4 3 3
NHERF1-2/PDGFRB/PTEN 0.052 0.048 -10000 0 -0.26 6 6
FYN 0.007 0.064 -10000 0 -0.62 2 2
DOK1 0.016 0.035 0.17 11 -0.22 2 13
HRAS/GTP 0.018 0.004 -10000 0 -10000 0 0
PDGFB 0.024 0.008 -10000 0 -10000 0 0
RAC1 0.01 0.14 0.31 5 -0.6 12 17
PRKCD 0.016 0.04 0.18 13 -0.23 3 16
FER 0.016 0.042 0.18 14 -0.22 4 18
MAPKKK cascade 0.03 0.088 0.19 66 -0.2 2 68
RASA1 0.018 0.039 0.18 14 -0.22 2 16
NCK1 0.025 0.005 -10000 0 -10000 0 0
NCK2 0.025 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.03 0.033 0.17 11 -0.21 2 13
PDGFB-D/PDGFRB/SHB 0.033 0.032 -10000 0 -0.29 3 3
chemotaxis 0.009 0.091 0.24 7 -0.37 9 16
STAT1-3-5/STAT1-3-5 0.055 0.03 -10000 0 -0.2 2 2
Bovine Papilomavirus E5/PDGFRB 0.016 0.025 -10000 0 -0.29 2 2
PTPRJ 0.024 0.012 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.017 0.052 -9999 0 -0.4 5 5
PLK4 0.019 0.05 -9999 0 -0.4 5 5
regulation of centriole replication 0.002 0.049 -9999 0 -0.28 10 10
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.024 0.006 -10000 0 -10000 0 0
NFATC1 0.019 0.071 0.28 2 -0.31 2 4
NFATC2 0.013 0.058 0.14 14 -0.22 8 22
NFATC3 0.016 0.027 -10000 0 -0.33 2 2
YWHAE 0.024 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.049 0.13 0.17 4 -0.37 34 38
Exportin 1/Ran/NUP214 0.047 0.015 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.021 0.13 -10000 0 -0.35 31 31
BCL2/BAX 0.022 0.063 -10000 0 -0.28 14 14
CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.004 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.004 -10000 0 -10000 0 0
BAX 0.025 0.004 -10000 0 -10000 0 0
MAPK14 0.025 0.004 -10000 0 -10000 0 0
BAD 0.025 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D -0.029 0.12 -10000 0 -0.35 30 30
Calcineurin A alpha-beta B1/BCL2 0.007 0.083 -10000 0 -0.4 14 14
FKBP8 0.024 0.006 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.029 0.12 0.34 30 -10000 0 30
KPNB1 0.024 0.006 -10000 0 -10000 0 0
KPNA2 0.024 0.006 -10000 0 -10000 0 0
XPO1 0.025 0.004 -10000 0 -10000 0 0
SFN -0.012 0.11 -10000 0 -0.4 26 26
MAP3K8 0.02 0.045 -10000 0 -0.4 4 4
NFAT4/CK1 alpha 0.025 0.025 -10000 0 -0.19 3 3
MEF2D/NFAT1/Cbp/p300 0.04 0.066 -10000 0 -0.27 5 5
CABIN1 -0.049 0.13 0.17 4 -0.38 34 38
CALM1 0.025 0.004 -10000 0 -10000 0 0
RAN 0.025 0.004 -10000 0 -10000 0 0
MAP3K1 0.023 0.023 -10000 0 -0.4 1 1
CAMK4 0.006 0.079 -10000 0 -0.4 12 12
mol:Ca2+ 0 0.001 -10000 0 -10000 0 0
MAPK3 0.024 0.005 -10000 0 -10000 0 0
YWHAH 0.024 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.03 0.036 -10000 0 -0.28 4 4
YWHAB 0.024 0.005 -10000 0 -10000 0 0
MAPK8 0.023 0.023 -10000 0 -0.4 1 1
MAPK9 0.025 0.004 -10000 0 -10000 0 0
YWHAG 0.025 0.004 -10000 0 -10000 0 0
FKBP1A 0.025 0.004 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.029 0.08 0.25 3 -0.3 6 9
PRKCH 0.022 0.032 -10000 0 -0.4 2 2
CABIN1/Cbp/p300 0.035 0.01 -10000 0 -10000 0 0
CASP3 0.025 0.005 -10000 0 -10000 0 0
PIM1 0.025 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.003 -10000 0 -10000 0 0
apoptosis 0.013 0.03 -10000 0 -0.27 2 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.052 -10000 0 -0.36 3 3
PRKCB 0.005 0.082 -10000 0 -0.4 13 13
PRKCE 0.024 0.023 -10000 0 -0.4 1 1
JNK2/NFAT4 0.016 0.056 -10000 0 -0.3 2 2
BAD/BCL-XL 0.035 0.01 -10000 0 -10000 0 0
PRKCD 0.022 0.032 -10000 0 -0.4 2 2
NUP214 0.024 0.006 -10000 0 -10000 0 0
PRKCZ 0.022 0.032 -10000 0 -0.4 2 2
PRKCA 0.008 0.08 -10000 0 -0.4 13 13
PRKCG -0.04 0.13 -10000 0 -0.4 36 36
PRKCQ -0.038 0.15 -10000 0 -0.4 50 50
FKBP38/BCL2 0.021 0.063 -10000 0 -0.28 14 14
EP300 0.024 0.006 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.025 0.004 -10000 0 -10000 0 0
NFATc/JNK1 0.03 0.072 0.28 2 -0.3 2 4
CaM/Ca2+/FKBP38 0.032 0.01 -10000 0 -10000 0 0
FKBP12/FK506 0.018 0.003 -10000 0 -10000 0 0
CSNK1A1 0.012 0.007 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.021 0.051 -10000 0 -0.24 12 12
NFATc/ERK1 0.031 0.071 0.28 2 -0.29 2 4
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.025 0.14 -10000 0 -0.35 35 35
NR4A1 0.042 0.085 0.19 50 -0.52 2 52
GSK3B 0.025 0.004 -10000 0 -10000 0 0
positive T cell selection 0.016 0.026 -10000 0 -0.33 2 2
NFAT1/CK1 alpha 0.015 0.041 0.12 1 -0.22 2 3
RCH1/ KPNB1 0.035 0.01 -10000 0 -10000 0 0
YWHAQ 0.025 0.005 -10000 0 -10000 0 0
PRKACA 0.024 0.006 -10000 0 -10000 0 0
AKAP5 0.018 0.047 -10000 0 -0.4 4 4
MEF2D 0.021 0.01 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.023 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha 0.031 0.07 0.32 1 -0.3 2 3
CREBBP 0.025 0.004 -10000 0 -10000 0 0
BCL2 0.007 0.083 -10000 0 -0.4 14 14
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.011 0.027 -10000 0 -0.24 5 5
SNTA1 0.024 0.023 -10000 0 -0.4 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.015 0.04 -10000 0 -0.24 11 11
MAPK12 -0.006 0.037 -10000 0 -0.21 11 11
CCND1 -0.008 0.079 -10000 0 -0.4 13 13
p38 gamma/SNTA1 0.014 0.05 0.25 3 -0.2 12 15
MAP2K3 0.024 0.006 -10000 0 -10000 0 0
PKN1 0.024 0.006 -10000 0 -10000 0 0
G2/M transition checkpoint -0.005 0.04 0.21 2 -0.21 11 13
MAP2K6 0 0.036 -10000 0 -0.23 9 9
MAPT 0 0.057 0.19 5 -0.24 12 17
MAPK13 0.007 0.035 -10000 0 -0.29 5 5
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.012 0.016 -10000 0 -0.28 1 1
Paxillin-dependent events mediated by a4b1

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
CRKL 0.025 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.012 -10000 0 -10000 0 0
DOCK1 0.024 0.006 -10000 0 -10000 0 0
ITGA4 0.011 0.072 -10000 0 -0.4 10 10
RAC1 0.025 0.005 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.021 0.066 -10000 0 -0.29 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.024 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.038 0.05 -10000 0 -0.24 10 10
alpha4/beta7 Integrin/Paxillin 0.027 0.053 -10000 0 -0.22 14 14
lamellipodium assembly -0.004 0.1 -10000 0 -0.38 22 22
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
PI3K 0.025 0.052 -10000 0 -0.28 9 9
ARF6 0.025 0.004 -10000 0 -10000 0 0
TLN1 0.025 0.004 -10000 0 -10000 0 0
PXN 0.012 0.003 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
ARF6/GTP 0.041 0.044 -10000 0 -0.19 10 10
cell adhesion 0.042 0.044 -10000 0 -0.21 9 9
CRKL/CBL 0.036 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.029 0.046 -10000 0 -0.22 10 10
ITGB1 0.024 0.005 -10000 0 -10000 0 0
ITGB7 0.017 0.055 -10000 0 -0.4 6 6
ARF6/GDP 0.023 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.03 0.079 -10000 0 -0.25 24 24
p130Cas/Crk/Dock1 0.042 0.025 -10000 0 -0.24 1 1
VCAM1 -0.008 0.11 -10000 0 -0.4 24 24
alpha4/beta1 Integrin/Paxillin/Talin 0.043 0.045 -10000 0 -0.21 9 9
alpha4/beta1 Integrin/Paxillin/GIT1 0.042 0.047 -10000 0 -0.21 10 10
BCAR1 0.022 0.024 -10000 0 -0.4 1 1
mol:GDP -0.041 0.046 0.21 10 -10000 0 10
CBL 0.025 0.004 -10000 0 -10000 0 0
PRKACA 0.024 0.006 -10000 0 -10000 0 0
GIT1 0.024 0.005 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.043 0.045 -10000 0 -0.21 9 9
Rac1/GTP -0.007 0.12 -10000 0 -0.42 22 22
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.051 0.14 -9999 0 -0.4 46 46
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.025 0.005 -9999 0 -10000 0 0
TCEB1 0.024 0.007 -9999 0 -10000 0 0
HIF1A/p53 0.02 0.075 -9999 0 -0.32 10 10
HIF1A 0.009 0.053 -9999 0 -0.26 10 10
COPS5 0.024 0.007 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.061 0.033 -9999 0 -0.21 1 1
FIH (dimer) 0.024 0.006 -9999 0 -10000 0 0
CDKN2A -0.025 0.12 -9999 0 -0.4 27 27
ARNT/IPAS -0.014 0.092 -9999 0 -0.28 33 33
HIF1AN 0.024 0.006 -9999 0 -10000 0 0
GNB2L1 0.025 0.004 -9999 0 -10000 0 0
HIF1A/ARNT 0.012 0.05 -9999 0 -0.25 9 9
CUL2 0.024 0.006 -9999 0 -10000 0 0
OS9 0.025 0.001 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.046 0.016 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.027 0.058 -9999 0 -0.25 10 10
PHD1-3/OS9 0.045 0.051 -9999 0 -0.22 9 9
HIF1A/RACK1/Elongin B/Elongin C 0.044 0.057 -9999 0 -0.24 8 8
VHL 0.023 0.023 -9999 0 -0.4 1 1
HSP90AA1 0.025 0.004 -9999 0 -10000 0 0
HIF1A/JAB1 0.026 0.054 -9999 0 -0.25 7 7
EGLN3 0.008 0.083 -9999 0 -0.4 14 14
EGLN2 0.025 0.004 -9999 0 -10000 0 0
EGLN1 0.021 0.009 -9999 0 -10000 0 0
TP53 0.01 0.077 -9999 0 -0.4 12 12
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.019 0.1 -9999 0 -0.53 12 12
ARNT 0.02 0.01 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.024 0.006 -9999 0 -10000 0 0
HIF1A/p19ARF 0.011 0.079 -9999 0 -0.28 10 10
Signaling events mediated by PRL

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
CCNE1 0.011 0.07 -10000 0 -0.4 10 10
mol:Halofuginone 0.003 0.01 -10000 0 -0.19 1 1
ITGA1 0.017 0.048 -10000 0 -0.4 4 4
CDKN1A 0.003 0.085 -10000 0 -0.41 13 13
PRL-3/alpha Tubulin 0.032 0.031 -10000 0 -0.28 3 3
mol:Ca2+ -0.042 0.086 0.32 2 -0.3 33 35
AGT -0.037 0.13 -10000 0 -0.4 40 40
CCNA2 -0.012 0.048 -10000 0 -0.47 2 2
TUBA1B 0.025 0.002 -10000 0 -10000 0 0
EGR1 0.006 0.042 -10000 0 -0.28 7 7
CDK2/Cyclin E1 0.025 0.089 -10000 0 -0.36 11 11
MAPK3 0.009 0.027 -10000 0 -0.28 3 3
PRL-2 /Rab GGTase beta 0.037 0.005 -10000 0 -10000 0 0
MAPK1 0.009 0.027 -10000 0 -0.28 3 3
PTP4A1 -0.004 0.045 -10000 0 -0.5 2 2
PTP4A3 0.02 0.039 -10000 0 -0.4 3 3
PTP4A2 0.025 0.003 -10000 0 -10000 0 0
ITGB1 0.009 0.027 -10000 0 -0.28 3 3
SRC 0.022 0.032 -10000 0 -0.4 2 2
RAC1 0.005 0.077 -10000 0 -0.41 10 10
Rab GGTase beta/Rab GGTase alpha 0.037 0.006 -10000 0 -10000 0 0
PRL-1/ATF-5 0.018 0.058 -10000 0 -0.47 2 2
RABGGTA 0.025 0.004 -10000 0 -10000 0 0
BCAR1 -0.014 0.035 0.32 3 -0.3 1 4
RHOC 0.008 0.064 -10000 0 -0.38 8 8
RHOA 0.003 0.073 -10000 0 -0.35 13 13
cell motility 0.018 0.08 0.28 1 -0.38 9 10
PRL-1/alpha Tubulin 0.019 0.059 -10000 0 -0.47 2 2
PRL-3/alpha1 Integrin 0.026 0.044 -10000 0 -0.28 6 6
ROCK1 0.015 0.079 0.28 1 -0.38 9 10
RABGGTB 0.025 0.002 -10000 0 -10000 0 0
CDK2 0.025 0.004 -10000 0 -10000 0 0
mitosis -0.004 0.045 -10000 0 -0.49 2 2
ATF5 0.023 0.013 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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
FBXW11 0.026 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.028 0.092 0.24 6 -0.32 8 14
ERC1 0.025 0.004 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.043 -10000 0 -0.28 6 6
NFKBIA 0.011 0.011 0.21 1 -10000 0 1
BIRC2 0.023 0.032 -10000 0 -0.4 2 2
IKBKB 0.023 0.007 -10000 0 -10000 0 0
RIPK2 0.023 0.009 -10000 0 -10000 0 0
IKBKG 0.018 0.04 -10000 0 -0.32 2 2
IKK complex/A20 0.016 0.11 -10000 0 -0.31 24 24
NEMO/A20/RIP2 0.023 0.009 -10000 0 -10000 0 0
XPO1 0.025 0.004 -10000 0 -10000 0 0
NEMO/ATM 0.014 0.11 -10000 0 -0.32 26 26
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.025 0.004 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.033 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.019 0.094 -10000 0 -0.3 21 21
BCL10/MALT1/TRAF6 0.048 0.014 -10000 0 -10000 0 0
NOD2 0.014 0.063 -10000 0 -0.4 8 8
NFKB1 0.026 0.005 -10000 0 -10000 0 0
RELA 0.027 0.003 -10000 0 -10000 0 0
MALT1 0.023 0.011 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.034 0.025 -10000 0 -0.28 2 2
ATM 0.025 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.004 0.088 -10000 0 -0.29 26 26
TRAF6 0.025 0.005 -10000 0 -10000 0 0
PRKCA 0.008 0.08 -10000 0 -0.4 13 13
CHUK 0.024 0.006 -10000 0 -10000 0 0
UBE2D3 0.025 0.004 -10000 0 -10000 0 0
TNF -0.017 0.11 -10000 0 -0.4 27 27
NF kappa B1 p50/RelA 0.055 0.014 -10000 0 -10000 0 0
BCL10 0.025 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.011 0.21 1 -10000 0 1
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.024 0.023 -10000 0 -0.4 1 1
IKK complex 0.02 0.1 0.26 1 -0.32 21 22
CYLD 0.023 0.007 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.021 0.11 0.26 1 -0.32 19 20
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.013 0.067 -10000 0 -0.31 2 2
epithelial cell differentiation -0.004 0.098 -10000 0 -0.38 7 7
ITCH 0.03 0.027 -10000 0 -0.4 1 1
WWP1 0.005 0.064 -10000 0 -10000 0 0
FYN 0.025 0.007 -10000 0 -10000 0 0
EGFR 0.013 0.07 -10000 0 -0.4 10 10
PRL 0.015 0.028 -10000 0 -10000 0 0
neuron projection morphogenesis 0.029 0.1 0.34 8 -10000 0 8
PTPRZ1 0.011 0.03 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.017 0.067 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.009 0.063 -10000 0 -0.29 3 3
ADAM17 0.029 0.035 -10000 0 -0.4 2 2
ErbB4/ErbB4 -0.004 0.061 -10000 0 -0.34 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.006 0.067 -10000 0 -0.31 2 2
NCOR1 0.024 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.002 0.066 -10000 0 -0.28 1 1
GRIN2B -0.002 0.073 0.25 6 -10000 0 6
ErbB4/ErbB2/betacellulin 0.002 0.075 -10000 0 -0.28 4 4
STAT1 0.025 0.009 -10000 0 -10000 0 0
HBEGF 0.025 0.007 -10000 0 -10000 0 0
PRLR -0.025 0.13 -10000 0 -0.4 39 39
E4ICDs/ETO2 0.006 0.074 -10000 0 -0.33 4 4
axon guidance 0.001 0.066 -10000 0 -10000 0 0
NEDD4 0.023 0.051 -10000 0 -0.39 5 5
Prolactin receptor/Prolactin receptor/Prolactin -0.009 0.1 -10000 0 -0.29 39 39
CBFA2T3 0.008 0.069 -10000 0 -0.4 9 9
ErbB4/ErbB2/HBEGF 0.015 0.055 -10000 0 -0.28 1 1
MAPK3 0.027 0.091 0.31 5 -10000 0 5
STAT1 (dimer) 0.011 0.068 -10000 0 -0.3 2 2
MAPK1 0.027 0.092 0.31 5 -10000 0 5
JAK2 0.014 0.067 -10000 0 -0.4 9 9
ErbB4/ErbB2/neuregulin 1 beta -0.007 0.061 -10000 0 -0.28 2 2
NRG1 -0.004 0.064 -10000 0 -0.29 16 16
NRG3 0.012 0.027 -10000 0 -10000 0 0
NRG2 -0.009 0.11 -10000 0 -0.4 24 24
NRG4 -0.005 0.1 -10000 0 -0.4 22 22
heart development 0.001 0.066 -10000 0 -10000 0 0
neural crest cell migration -0.007 0.061 -10000 0 -0.28 2 2
ERBB2 0.012 0.028 -10000 0 -0.28 3 3
WWOX/E4ICDs 0.012 0.064 -10000 0 -0.31 1 1
SHC1 0.021 0.01 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.003 0.095 -10000 0 -0.32 6 6
apoptosis -0.004 0.062 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.003 0.09 -10000 0 -0.36 7 7
ErbB4/ErbB2/epiregulin 0.004 0.075 -10000 0 -0.28 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.002 0.088 -10000 0 -0.32 5 5
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.01 0.12 -10000 0 -0.33 20 20
MDM2 -0.004 0.063 -10000 0 -0.32 4 4
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.002 0.059 -10000 0 -0.26 1 1
STAT5A 0.001 0.064 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.004 0.076 -10000 0 -0.33 4 4
DLG4 0.023 0.023 -10000 0 -0.4 1 1
GRB2/SHC 0.029 0.016 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.01 0.06 -10000 0 -0.28 1 1
STAT5A (dimer) 0.006 0.11 -10000 0 -0.41 7 7
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.014 0.073 -10000 0 -10000 0 0
LRIG1 0.003 0.093 -10000 0 -0.4 18 18
EREG -0.02 0.1 -10000 0 -0.4 20 20
BTC -0.001 0.1 -10000 0 -0.4 22 22
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.002 0.06 -10000 0 -10000 0 0
ERBB4 -0.004 0.061 -10000 0 -0.35 2 2
STAT5B 0.024 0.006 -10000 0 -10000 0 0
YAP1 0.006 0.074 -10000 0 -0.49 7 7
GRB2 0.024 0.006 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.003 0.078 -10000 0 -0.32 5 5
glial cell differentiation -0.009 0.059 0.28 1 -10000 0 1
WWOX 0.023 0.008 -10000 0 -10000 0 0
cell proliferation -0.012 0.11 0.3 2 -0.43 7 9
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.025 0.004 -9999 0 -10000 0 0
SPHK1 0.018 0.042 -9999 0 -0.4 3 3
GNAI2 0.024 0.006 -9999 0 -10000 0 0
mol:S1P 0.011 0.029 -9999 0 -0.29 3 3
GNAO1 0.014 0.053 -9999 0 -0.4 5 5
mol:Sphinganine-1-P 0.009 0.024 -9999 0 -0.28 2 2
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.045 0.045 -9999 0 -0.25 4 4
GNAI3 0.025 0.002 -9999 0 -10000 0 0
G12/G13 0.035 0.011 -9999 0 -10000 0 0
S1PR3 0.02 0.04 -9999 0 -0.4 3 3
S1PR2 0.023 0.023 -9999 0 -0.4 1 1
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.002 0.035 -9999 0 -0.23 6 6
S1PR5 0.003 0.084 -9999 0 -0.4 14 14
S1PR4 0.009 0.069 -9999 0 -0.4 9 9
GNAI1 0.012 0.071 -9999 0 -0.4 10 10
S1P/S1P5/G12 0.025 0.061 -9999 0 -0.22 17 17
S1P/S1P3/Gq 0.003 0.096 -9999 0 -0.34 20 20
S1P/S1P4/Gi 0.004 0.075 -9999 0 -0.26 16 16
GNAQ 0.023 0.023 -9999 0 -0.4 1 1
GNAZ 0.013 0.067 -9999 0 -0.4 9 9
GNA14 0.015 0.063 -9999 0 -0.4 8 8
GNA15 0.015 0.056 -9999 0 -0.4 6 6
GNA12 0.024 0.005 -9999 0 -10000 0 0
GNA13 0.024 0.006 -9999 0 -10000 0 0
GNA11 0.016 0.055 -9999 0 -0.4 6 6
ABCC1 0.025 0.004 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.023 0.066 -10000 0 -0.21 24 24
RGS9BP 0.018 0.024 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.015 0.014 -10000 0 -10000 0 0
mol:Na + 0.023 0.016 -10000 0 -10000 0 0
mol:ADP -0.01 0.012 -10000 0 -10000 0 0
GNAT2 0.023 0.011 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.025 0.072 -10000 0 -0.25 22 22
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.026 0.01 -10000 0 -10000 0 0
GRK7 0.02 0.013 -10000 0 -10000 0 0
CNGB3 0.016 0.018 -10000 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.014 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.036 0.18 12 -10000 0 12
Cone PDE6 0.036 0.07 -10000 0 -0.22 21 21
Cone Metarhodopsin II 0.022 0.013 -10000 0 -10000 0 0
Na + (4 Units) 0.033 0.018 -10000 0 -10000 0 0
GNAT2/GDP 0.034 0.067 -10000 0 -0.21 22 22
GNB5 0.021 0.039 -10000 0 -0.4 3 3
mol:GMP (4 units) -0.01 0.017 0.18 2 -10000 0 2
Cone Transducin 0.025 0.07 -10000 0 -0.23 24 24
SLC24A2 0.017 0.014 -10000 0 -10000 0 0
GNB3/GNGT2 0.008 0.084 -10000 0 -0.29 24 24
GNB3 -0.004 0.1 -10000 0 -0.4 21 21
GNAT2/GTP 0.017 0.007 -10000 0 -10000 0 0
CNGA3 0.019 0.015 -10000 0 -10000 0 0
ARR3 0.019 0.009 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.023 0.016 -10000 0 -10000 0 0
mol:Pi 0.025 0.072 -10000 0 -0.25 22 22
Cone CNG Channel 0.04 0.023 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.017 0.014 -10000 0 -10000 0 0
RGS9 -0.006 0.098 -10000 0 -0.4 19 19
PDE6C 0.018 0.01 -10000 0 -10000 0 0
GNGT2 0.016 0.052 -10000 0 -0.4 5 5
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.017 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.011 0.004 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.036 0.016 -10000 0 -10000 0 0
CDKN1B 0.002 0.06 -10000 0 -0.29 8 8
CDKN1A 0.006 0.062 0.2 3 -0.35 7 10
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.021 0.032 -10000 0 -0.4 2 2
FOXO3 0.012 0.043 0.2 1 -0.31 5 6
AKT1 0.011 0.041 -10000 0 -0.32 5 5
BAD 0.025 0.004 -10000 0 -10000 0 0
AKT3 0.008 0.027 -10000 0 -0.28 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.01 0.047 -10000 0 -0.3 7 7
AKT1/ASK1 0.029 0.054 -10000 0 -0.29 7 7
BAD/YWHAZ 0.044 0.018 -10000 0 -10000 0 0
RICTOR 0.022 0.032 -10000 0 -0.4 2 2
RAF1 0.024 0.005 -10000 0 -10000 0 0
JNK cascade -0.028 0.052 0.28 7 -10000 0 7
TSC1 0.012 0.036 -10000 0 -0.33 3 3
YWHAZ 0.023 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.032 0.054 0.24 1 -0.3 6 7
EP300 0.024 0.006 -10000 0 -10000 0 0
mol:GDP 0.011 0.048 -10000 0 -0.31 7 7
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.011 0.044 -10000 0 -0.3 6 6
YWHAQ 0.025 0.005 -10000 0 -10000 0 0
TBC1D4 0.001 0.034 -10000 0 -0.22 8 8
MAP3K5 0.023 0.025 -10000 0 -0.4 1 1
MAPKAP1 0.024 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.014 0.077 0.38 7 -0.2 3 10
YWHAH 0.024 0.006 -10000 0 -10000 0 0
AKT1S1 0.011 0.049 0.2 2 -0.3 7 9
CASP9 0.012 0.042 0.2 1 -0.31 5 6
YWHAB 0.024 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.022 0.074 0.28 5 -0.29 7 12
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.047 0.025 -10000 0 -0.24 2 2
YWHAE 0.024 0.006 -10000 0 -10000 0 0
SRC 0.022 0.032 -10000 0 -0.4 2 2
AKT2/p21CIP1 0.01 0.06 0.21 5 -0.33 6 11
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.05 -10000 0 -0.27 10 10
CHUK 0.015 0.049 0.2 8 -0.31 5 13
BAD/BCL-XL 0.035 0.047 -10000 0 -0.3 4 4
mTORC2 0.028 0.021 -10000 0 -0.22 2 2
AKT2 0.013 0.003 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.02 0.088 0.22 6 -0.41 7 13
PDPK1 0.025 0.004 -10000 0 -10000 0 0
MDM2 0.01 0.05 0.2 1 -0.29 8 9
MAPKKK cascade -0.032 0.053 0.3 6 -0.24 1 7
MDM2/Cbp/p300 0.041 0.059 0.24 2 -0.28 6 8
TSC1/TSC2 0.011 0.039 0.25 2 -0.32 3 5
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.057 0.23 2 -0.27 6 8
glucose import -0.011 0.054 0.21 3 -0.21 23 26
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.04 0.17 1 -0.19 6 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.012 0.052 0.2 1 -0.21 23 24
GSK3A 0.011 0.049 0.2 2 -0.3 7 9
FOXO1 0.011 0.042 -10000 0 -0.31 5 5
GSK3B 0.011 0.05 0.2 3 -0.3 7 10
SFN -0.012 0.11 -10000 0 -0.4 26 26
G1/S transition of mitotic cell cycle 0.013 0.058 0.22 11 -0.29 7 18
p27Kip1/14-3-3 family 0.016 0.083 -10000 0 -0.71 3 3
PRKACA 0.024 0.006 -10000 0 -10000 0 0
KPNA1 0.025 0.004 -10000 0 -10000 0 0
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
YWHAG 0.025 0.004 -10000 0 -10000 0 0
RHEB 0.024 0.008 -10000 0 -10000 0 0
CREBBP 0.025 0.004 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.032 0.093 -10000 0 -0.27 28 28
Ran/GTP/Exportin 1/HDAC1 -0.008 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.012 0.09 -10000 0 -0.27 28 28
SUMO1 0.024 0.023 -10000 0 -0.4 1 1
ZFPM1 0.017 0.046 -10000 0 -0.4 4 4
NPC/RanGAP1/SUMO1/Ubc9 0.012 0.011 -10000 0 -0.18 1 1
FKBP3 0.022 0.039 -10000 0 -0.4 3 3
Histones 0.046 0.06 -10000 0 -0.26 2 2
YY1/LSF 0.011 0.072 -10000 0 -0.24 21 21
SMG5 0.02 0.01 -10000 0 -10000 0 0
RAN 0.025 0.004 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.006 0.063 -10000 0 -0.22 26 26
I kappa B alpha/HDAC1 0.02 0.055 -10000 0 -0.2 2 2
SAP18 0.025 0.005 -10000 0 -10000 0 0
RELA 0.007 0.066 -10000 0 -0.21 26 26
HDAC1/Smad7 0.047 0.015 -10000 0 -10000 0 0
RANGAP1 0.024 0.007 -10000 0 -10000 0 0
HDAC3/TR2 0.02 0.058 -10000 0 -0.23 4 4
NuRD/MBD3 Complex 0.036 0.036 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.012 0.081 0.19 1 -0.29 11 12
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.025 0.14 -10000 0 -0.4 41 41
GATA1 0.019 0.014 -10000 0 -10000 0 0
Mad/Max 0.036 0.01 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.028 0.068 -10000 0 -0.32 5 5
RBBP7 0.025 0.003 -10000 0 -10000 0 0
NPC 0.015 0.002 -10000 0 -10000 0 0
RBBP4 0.025 0.004 -10000 0 -10000 0 0
MAX 0.025 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.025 0.004 -10000 0 -10000 0 0
NFKBIA 0.007 0.047 -10000 0 -0.25 1 1
KAT2B 0.016 0.059 -10000 0 -0.4 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.024 0.012 -10000 0 -10000 0 0
SIN3 complex 0.058 0.022 -10000 0 -10000 0 0
SMURF1 0.025 0.004 -10000 0 -10000 0 0
CHD3 0.024 0.006 -10000 0 -10000 0 0
SAP30 0.024 0.023 -10000 0 -0.4 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.024 0.007 -10000 0 -10000 0 0
YY1/HDAC3 0.008 0.064 -10000 0 -0.31 6 6
YY1/HDAC2 0.015 0.064 -10000 0 -0.24 16 16
YY1/HDAC1 0.017 0.061 -10000 0 -0.24 14 14
NuRD/MBD2 Complex (MeCP1) 0.037 0.036 -10000 0 -10000 0 0
PPARG -0.038 0.13 -10000 0 -0.29 70 70
HDAC8/hEST1B 0.039 0.023 -10000 0 -10000 0 0
UBE2I 0.025 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.024 0.023 -10000 0 -0.4 1 1
HDAC3/SMRT (N-CoR2) 0.021 0.056 -10000 0 -0.25 3 3
MBD3L2 0.014 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.047 0.015 -10000 0 -10000 0 0
CREBBP 0.025 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.031 0.064 -10000 0 -0.29 7 7
HDAC1 0.025 0.003 -10000 0 -10000 0 0
HDAC3 0.006 0.051 -10000 0 -0.31 2 2
HDAC2 0.025 0.003 -10000 0 -10000 0 0
YY1 0.015 0.027 -10000 0 -0.23 4 4
HDAC8 0.025 0.002 -10000 0 -10000 0 0
SMAD7 0.024 0.006 -10000 0 -10000 0 0
NCOR2 0.025 0.004 -10000 0 -10000 0 0
MXD1 0.024 0.007 -10000 0 -10000 0 0
STAT3 0.018 0.006 -10000 0 -10000 0 0
NFKB1 0.025 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.025 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.026 0.069 -10000 0 -0.23 18 18
YY1/SAP30/HDAC1 0.031 0.061 -10000 0 -0.22 14 14
EP300 0.024 0.006 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.006 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.047 -10000 0 -0.25 1 1
histone deacetylation 0.037 0.036 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.013 0.05 -10000 0 -0.29 3 3
nuclear export -0.038 0.022 -10000 0 -10000 0 0
PRKACA 0.024 0.006 -10000 0 -10000 0 0
GATAD2B 0.021 0.01 -10000 0 -10000 0 0
GATAD2A 0.024 0.006 -10000 0 -10000 0 0
GATA2/HDAC3 -0.007 0.093 -10000 0 -0.22 43 43
GATA1/HDAC1 0.032 0.012 -10000 0 -10000 0 0
GATA1/HDAC3 0.017 0.057 -10000 0 -0.23 4 4
CHD4 0.025 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.004 0.088 -10000 0 -0.29 26 26
SIN3/HDAC complex/Mad/Max 0.027 0.041 -10000 0 -0.57 1 1
NuRD Complex 0.034 0.06 -10000 0 -0.28 6 6
positive regulation of chromatin silencing 0.043 0.059 -10000 0 -0.26 2 2
SIN3B 0.024 0.006 -10000 0 -10000 0 0
MTA2 0.025 0.004 -10000 0 -10000 0 0
SIN3A 0.024 0.005 -10000 0 -10000 0 0
XPO1 0.025 0.004 -10000 0 -10000 0 0
SUMO1/HDAC1 0.031 0.042 -10000 0 -0.19 7 7
HDAC complex 0.063 0.014 -10000 0 -10000 0 0
GATA1/Fog1 0.025 0.034 -10000 0 -0.29 3 3
FKBP25/HDAC1/HDAC2 0.047 0.029 -10000 0 -0.24 3 3
TNF -0.017 0.11 -10000 0 -0.4 27 27
negative regulation of cell growth 0.026 0.046 -10000 0 -0.35 3 3
NuRD/MBD2/PRMT5 Complex 0.037 0.036 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.041 -10000 0 -0.23 1 1
NF kappa B/RelA/I kappa B alpha -0.003 0.086 -10000 0 -0.28 30 30
SIN3/HDAC complex/NCoR1 0.021 0.046 -10000 0 -0.31 4 4
TFCP2 0.017 0.059 -10000 0 -0.4 7 7
NR2C1 0.025 0.003 -10000 0 -10000 0 0
MBD3 0.023 0.023 -10000 0 -0.4 1 1
MBD2 0.024 0.005 -10000 0 -10000 0 0
Syndecan-3-mediated signaling 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
CTTN 0.025 0.004 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.032 0.093 -9999 0 -0.36 5 5
Syndecan-3/Neurocan 0.018 0.046 -9999 0 -0.37 4 4
POMC -0.009 0.1 -9999 0 -0.4 20 20
EGFR 0.013 0.07 -9999 0 -0.4 10 10
Syndecan-3/EGFR 0.013 0.063 -9999 0 -0.37 6 6
AGRP 0.019 0.01 -9999 0 -10000 0 0
NCSTN 0.021 0.01 -9999 0 -10000 0 0
PSENEN 0.023 0.023 -9999 0 -0.4 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.021 0.039 -9999 0 -0.4 3 3
APH1A 0.021 0.01 -9999 0 -10000 0 0
NCAN 0.016 0.021 -9999 0 -10000 0 0
long-term memory 0.05 0.06 -9999 0 -0.34 5 5
Syndecan-3/IL8 0.008 0.078 -9999 0 -0.4 7 7
PSEN1 0.025 0.004 -9999 0 -10000 0 0
Src/Cortactin 0.034 0.026 -9999 0 -0.28 2 2
FYN 0.025 0.007 -9999 0 -10000 0 0
limb bud formation 0.004 0.051 -9999 0 -0.42 5 5
MC4R 0.013 0.026 -9999 0 -10000 0 0
SRC 0.022 0.032 -9999 0 -0.4 2 2
PTN -0.034 0.14 -9999 0 -0.4 43 43
FGFR/FGF/Syndecan-3 0.004 0.052 -9999 0 -0.42 5 5
neuron projection morphogenesis -0.005 0.074 -9999 0 -0.35 3 3
Syndecan-3/AgRP 0.014 0.053 -9999 0 -0.37 6 6
Syndecan-3/AgRP/MC4R 0.042 0.066 -9999 0 -0.36 6 6
Fyn/Cortactin 0.036 0.009 -9999 0 -10000 0 0
SDC3 0.004 0.052 -9999 0 -0.43 5 5
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.008 0.077 -9999 0 -0.4 7 7
IL8 -0.015 0.11 -9999 0 -0.4 27 27
Syndecan-3/Fyn/Cortactin 0.052 0.061 -9999 0 -0.35 5 5
Syndecan-3/CASK 0.002 0.051 -9999 0 -0.37 6 6
alpha-MSH/MC4R 0.001 0.077 -9999 0 -0.29 20 20
Gamma Secretase 0.051 0.044 -9999 0 -0.2 4 4
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.032 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.025 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.013 0.067 -10000 0 -0.4 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.021 0.032 -10000 0 -0.4 2 2
RAC1-CDC42/GTP/PAK family 0.013 0.01 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.025 0.005 -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 0.024 0.006 -10000 0 -10000 0 0
FYN 0.025 0.007 -10000 0 -10000 0 0
MAP3K12 0.023 0.032 -10000 0 -0.4 2 2
FGR 0.015 0.06 -10000 0 -0.4 7 7
p38 alpha/TAB1 -0.034 0.083 -10000 0 -0.3 21 21
PRKG1 0.002 0.089 -10000 0 -0.4 16 16
DUSP8 0.017 0.055 -10000 0 -0.4 6 6
PGK/cGMP/p38 alpha -0.007 0.1 -10000 0 -0.35 18 18
apoptosis -0.032 0.079 -10000 0 -0.28 21 21
RAL/GTP 0.033 0.006 -10000 0 -10000 0 0
LYN 0.02 0.039 -10000 0 -0.4 3 3
DUSP1 0.022 0.018 -10000 0 -10000 0 0
PAK1 0.025 0.003 -10000 0 -10000 0 0
SRC 0.022 0.032 -10000 0 -0.4 2 2
RAC1/OSM/MEKK3/MKK3 0.058 0.021 -10000 0 -10000 0 0
TRAF6 0.025 0.005 -10000 0 -10000 0 0
RAC1 0.025 0.005 -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 0.025 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.032 0.008 -10000 0 -10000 0 0
MAPK11 -0.005 0.11 0.27 3 -0.34 19 22
BLK -0.014 0.1 -10000 0 -0.4 22 22
HCK 0.009 0.075 -10000 0 -0.4 11 11
MAP2K3 0.024 0.006 -10000 0 -10000 0 0
DUSP16 0.025 0.003 -10000 0 -10000 0 0
DUSP10 0.018 0.04 -10000 0 -0.4 3 3
TRAF6/MEKK3 0.03 0.009 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.002 0.11 0.2 7 -0.36 16 23
positive regulation of innate immune response -0.004 0.12 0.28 4 -0.39 19 23
LCK 0.008 0.078 -10000 0 -0.4 12 12
p38alpha-beta/MKP7 0.006 0.12 0.3 3 -0.39 17 20
p38alpha-beta/MKP5 0.002 0.12 0.28 4 -0.4 17 21
PGK/cGMP 0.003 0.062 -10000 0 -0.28 16 16
PAK2 0.024 0.007 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.006 0.12 0.3 3 -0.39 17 20
CDC42 0.025 0.005 -10000 0 -10000 0 0
RALB 0.025 0.003 -10000 0 -10000 0 0
RALA 0.025 0.004 -10000 0 -10000 0 0
PAK3 0.017 0.024 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.008 0.038 -10000 0 -10000 0 0
PLK1 0.025 0.17 -10000 0 -0.93 7 7
CDKN1B 0.038 0.14 0.4 1 -0.42 26 27
FOXO3 0.034 0.14 -10000 0 -0.7 6 6
KAT2B 0.018 0.062 -10000 0 -0.4 7 7
FOXO1/SIRT1 0.025 0.04 -10000 0 -10000 0 0
CAT 0.032 0.14 -10000 0 -0.78 4 4
CTNNB1 0.023 0.023 -10000 0 -0.4 1 1
AKT1 0.027 0.02 -10000 0 -10000 0 0
FOXO1 0.012 0.042 0.22 1 -10000 0 1
MAPK10 0.005 0.067 0.22 7 -0.2 28 35
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
FOXO4 0.031 0.07 0.35 4 -0.38 1 5
response to oxidative stress 0.006 0.011 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.048 0.12 -10000 0 -0.6 6 6
XPO1 0.025 0.004 -10000 0 -10000 0 0
EP300 0.025 0.007 -10000 0 -10000 0 0
BCL2L11 0.018 0.093 -10000 0 -0.72 5 5
FOXO1/SKP2 0.024 0.04 -10000 0 -10000 0 0
mol:GDP 0.006 0.011 -10000 0 -10000 0 0
RAN 0.026 0.004 -10000 0 -10000 0 0
GADD45A 0.054 0.11 0.36 1 -0.97 2 3
YWHAQ 0.025 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.007 0.14 0.24 1 -0.53 19 20
MST1 0.017 0.056 -10000 0 -0.4 5 5
CSNK1D 0.024 0.006 -10000 0 -10000 0 0
CSNK1E 0.024 0.006 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.001 0.13 -10000 0 -0.5 14 14
YWHAB 0.024 0.005 -10000 0 -10000 0 0
MAPK8 0.02 0.026 0.19 5 -0.2 1 6
MAPK9 0.023 0.032 0.21 8 -10000 0 8
YWHAG 0.025 0.004 -10000 0 -10000 0 0
YWHAE 0.024 0.006 -10000 0 -10000 0 0
YWHAZ 0.023 0.007 -10000 0 -10000 0 0
SIRT1 0.025 0.016 -10000 0 -10000 0 0
SOD2 0.056 0.1 0.37 4 -0.6 2 6
RBL2 -0.007 0.23 -10000 0 -0.69 32 32
RAL/GDP 0.039 0.015 -10000 0 -10000 0 0
CHUK 0.025 0.02 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CSNK1G2 0.024 0.007 -10000 0 -10000 0 0
RAL/GTP 0.041 0.015 -10000 0 -10000 0 0
CSNK1G1 0.024 0.006 -10000 0 -10000 0 0
FASLG -0.064 0.33 -10000 0 -1.3 25 25
SKP2 0.024 0.005 -10000 0 -10000 0 0
USP7 0.025 0.005 -10000 0 -10000 0 0
IKBKB 0.024 0.02 -10000 0 -10000 0 0
CCNB1 0.03 0.15 0.5 1 -0.85 5 6
FOXO1-3a-4/beta catenin 0.054 0.1 0.33 3 -0.4 4 7
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.04 -10000 0 -10000 0 0
CSNK1A1 0.025 0.004 -10000 0 -10000 0 0
SGK1 0.021 0.046 -10000 0 -0.4 3 3
CSNK1G3 0.025 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.036 0.009 -10000 0 -10000 0 0
ZFAND5 0.03 0.063 0.4 2 -10000 0 2
SFN -0.012 0.11 -10000 0 -0.4 26 26
CDK2 0.025 0.004 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.009 0.12 0.2 1 -0.54 11 12
CREBBP 0.025 0.004 -10000 0 -10000 0 0
FBXO32 0.044 0.16 0.53 1 -0.9 4 5
BCL6 0.039 0.13 -10000 0 -0.69 5 5
RALB 0.026 0.003 -10000 0 -10000 0 0
RALA 0.025 0.004 -10000 0 -10000 0 0
YWHAH 0.024 0.006 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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
BCL3/RelA 0.035 0.019 -10000 0 -0.28 1 1
FBXW11 0.025 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.024 0.017 -10000 0 -0.24 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.058 0.19 1 -0.28 4 5
NFKBIA 0.005 0.056 -10000 0 -0.22 17 17
MAPK14 0.025 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.025 0.01 -10000 0 -10000 0 0
ARRB2 0.013 0.004 -10000 0 -10000 0 0
REL 0.024 0.023 -10000 0 -0.4 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.023 0.017 -10000 0 -0.24 1 1
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.025 0.009 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.018 0.007 -10000 0 -10000 0 0
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
NFKB1 0.011 0.004 -10000 0 -10000 0 0
RELA 0.025 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.011 0.056 -10000 0 -0.21 18 18
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.019 0.054 -10000 0 -0.27 2 2
SRC 0.022 0.032 -10000 0 -0.4 2 2
PI3K 0.025 0.052 -10000 0 -0.28 9 9
NF kappa B1 p50/RelA 0.011 0.056 -10000 0 -0.21 18 18
IKBKB 0.023 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -10000 0 -10000 0 0
SYK 0.015 0.059 -10000 0 -0.4 7 7
I kappa B alpha/PIK3R1 0.009 0.072 0.19 1 -0.21 28 29
cell death 0.018 0.052 -10000 0 -0.26 2 2
NF kappa B1 p105/c-Rel 0.024 0.017 -10000 0 -0.24 1 1
LCK 0.008 0.078 -10000 0 -0.4 12 12
BCL3 0.023 0.024 -10000 0 -0.4 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.006 0.08 -10000 0 -0.28 23 23
AKT1 0.018 0.097 0.29 3 -0.48 6 9
PTK2B -0.003 0.073 0.34 1 -0.81 1 2
VEGFR2 homodimer/Frs2 0.027 0.042 -10000 0 -0.66 1 1
CAV1 0.022 0.026 -10000 0 -0.4 1 1
CALM1 0.025 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.04 0.049 -10000 0 -0.67 1 1
endothelial cell proliferation 0.016 0.11 0.37 6 -0.43 7 13
mol:Ca2+ 0.011 0.064 -10000 0 -0.31 7 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.051 0.051 -10000 0 -0.64 1 1
RP11-342D11.1 0.002 0.062 -10000 0 -0.3 7 7
CDH5 0.021 0.025 -10000 0 -0.4 1 1
VEGFA homodimer 0.048 0.032 -10000 0 -0.22 1 1
SHC1 0.021 0.01 -10000 0 -10000 0 0
SHC2 0.005 0.071 -10000 0 -0.4 9 9
HRAS/GDP 0.025 0.055 -10000 0 -0.49 1 1
SH2D2A 0.015 0.043 -10000 0 -0.4 3 3
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.036 0.092 -10000 0 -0.5 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.03 0.056 -10000 0 -0.33 4 4
VEGFR1 homodimer 0.023 0.024 -10000 0 -0.4 1 1
SHC/GRB2/SOS1 0.044 0.066 -10000 0 -0.27 7 7
GRB10 0.006 0.09 -10000 0 -0.52 8 8
PTPN11 0.025 0.003 -10000 0 -10000 0 0
GRB2 0.024 0.006 -10000 0 -10000 0 0
PAK1 0.025 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.056 0.061 -10000 0 -0.8 1 1
HRAS 0.024 0.005 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.009 0.064 -10000 0 -0.3 8 8
HIF1A 0.025 0.004 -10000 0 -10000 0 0
FRS2 0.025 0.002 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.049 0.05 -10000 0 -0.64 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.023 0.024 -10000 0 -0.4 1 1
Nck/Pak 0.036 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.04 0.049 -10000 0 -0.67 1 1
mol:GDP 0.034 0.06 -10000 0 -0.27 7 7
mol:NADP 0.022 0.09 0.32 5 -0.47 4 9
eNOS/Hsp90 0.032 0.088 0.32 5 -0.44 4 9
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
mol:IP3 0.011 0.064 -10000 0 -0.31 7 7
HIF1A/ARNT 0.029 0.016 -10000 0 -10000 0 0
SHB 0.024 0.023 -10000 0 -0.4 1 1
VEGFA 0.023 0.017 -10000 0 -10000 0 0
VEGFC 0.019 0.05 -10000 0 -0.4 5 5
FAK1/Vinculin 0.019 0.085 0.3 2 -0.5 3 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.036 0.077 -10000 0 -0.45 2 2
PTPN6 0.021 0.039 -10000 0 -0.4 3 3
EPAS1 0.027 0.033 -10000 0 -0.37 2 2
mol:L-citrulline 0.022 0.09 0.32 5 -0.47 4 9
ITGAV 0.02 0.045 -10000 0 -0.4 4 4
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.052 0.044 -10000 0 -0.48 1 1
VEGFR2 homodimer/VEGFA homodimer 0.036 0.069 -10000 0 -0.32 8 8
VEGFR2/3 heterodimer 0.026 0.051 -10000 0 -0.85 1 1
VEGFB 0.025 0.004 -10000 0 -10000 0 0
MAPK11 -0.003 0.075 0.46 1 -0.37 7 8
VEGFR2 homodimer 0.015 0.043 -10000 0 -0.75 1 1
FLT1 0.023 0.024 -10000 0 -0.4 1 1
NEDD4 0.018 0.051 -10000 0 -0.4 5 5
MAPK3 -0.003 0.083 0.32 9 -0.39 3 12
MAPK1 -0.004 0.082 0.33 7 -0.39 3 10
VEGFA145/NRP2 0.024 0.058 -10000 0 -0.29 11 11
VEGFR1/2 heterodimer 0.026 0.051 -10000 0 -0.85 1 1
KDR 0.015 0.044 -10000 0 -0.75 1 1
VEGFA165/NRP1/VEGFR2 homodimer 0.029 0.076 -10000 0 -0.29 8 8
SRC 0.022 0.032 -10000 0 -0.4 2 2
platelet activating factor biosynthetic process -0.002 0.087 0.34 7 -0.38 4 11
PI3K 0.021 0.082 -10000 0 -0.58 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.039 0.043 -10000 0 -0.5 1 1
FES 0.01 0.068 -10000 0 -0.31 7 7
GAB1 0.015 0.063 -10000 0 -0.46 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.038 0.053 -10000 0 -0.37 3 3
CTNNB1 0.023 0.023 -10000 0 -0.4 1 1
SOS1 0.025 0.004 -10000 0 -10000 0 0
ARNT 0.02 0.01 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.03 0.087 0.32 4 -0.46 4 8
VEGFR2 homodimer/VEGFA homodimer/Yes 0.039 0.049 -10000 0 -0.67 1 1
PI3K/GAB1 0.033 0.09 -10000 0 -0.52 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.062 0.047 -10000 0 -0.46 1 1
PRKACA 0.024 0.006 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.035 0.059 -10000 0 -0.3 7 7
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
CDC42 0.012 0.065 -10000 0 -0.32 6 6
actin cytoskeleton reorganization 0.029 0.055 -10000 0 -0.32 4 4
PTK2 0.006 0.076 0.32 3 -0.52 3 6
EDG1 0.002 0.062 -10000 0 -0.3 7 7
mol:DAG 0.011 0.064 -10000 0 -0.31 7 7
CaM/Ca2+ 0.023 0.061 -10000 0 -0.66 1 1
MAP2K3 -0.001 0.062 -10000 0 -0.48 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.032 0.095 -10000 0 -0.52 8 8
PLCG1 0.011 0.065 -10000 0 -0.31 7 7
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.049 0.055 -10000 0 -0.48 2 2
IQGAP1 0.025 0.005 -10000 0 -10000 0 0
YES1 0.025 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.04 0.049 -10000 0 -0.67 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.038 0.054 -10000 0 -0.33 4 4
cell migration 0.021 0.078 0.26 2 -0.55 2 4
mol:PI-3-4-5-P3 0.021 0.077 -10000 0 -0.53 3 3
FYN 0.025 0.007 -10000 0 -10000 0 0
VEGFB/NRP1 0.017 0.06 -10000 0 -0.29 7 7
mol:NO 0.022 0.09 0.32 5 -0.47 4 9
PXN 0.025 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.012 0.049 -10000 0 -0.49 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.023 0.092 -10000 0 -0.52 8 8
VHL 0.023 0.023 -10000 0 -0.4 1 1
ITGB3 -0.008 0.096 -10000 0 -0.4 18 18
NOS3 0.021 0.099 0.33 5 -0.55 4 9
VEGFR2 homodimer/VEGFA homodimer/Sck 0.032 0.063 -10000 0 -0.26 9 9
RAC1 0.025 0.005 -10000 0 -10000 0 0
PRKCA -0.003 0.07 0.34 1 -0.42 3 4
PRKCB -0.004 0.075 0.33 1 -0.45 3 4
VCL 0.024 0.007 -10000 0 -10000 0 0
VEGFA165/NRP1 0.02 0.065 -10000 0 -0.3 7 7
VEGFR1/2 heterodimer/VEGFA homodimer 0.039 0.057 -10000 0 -0.85 1 1
VEGFA165/NRP2 0.024 0.058 -10000 0 -0.29 11 11
MAPKKK cascade 0.042 0.099 0.34 1 -0.43 8 9
NRP2 0.01 0.077 -10000 0 -0.4 12 12
VEGFC homodimer 0.019 0.05 -10000 0 -0.4 5 5
NCK1 0.025 0.005 -10000 0 -10000 0 0
ROCK1 0.025 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.021 0.092 0.32 4 -0.47 4 8
MAP3K13 0.006 0.069 -10000 0 -0.32 7 7
PDPK1 0.009 0.068 0.26 1 -0.47 3 4
S1P3 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
PDGFRB 0.021 0.034 -9999 0 -0.4 2 2
mol:S1P 0.001 0.002 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.002 0.072 -9999 0 -0.22 29 29
GNAO1 0.014 0.054 -9999 0 -0.4 5 5
S1P/S1P3/G12/G13 0.043 0.029 -9999 0 -0.22 3 3
AKT1 0.015 0.076 -9999 0 -0.52 6 6
AKT3 0.003 0.11 -9999 0 -0.99 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.021 0.034 -9999 0 -0.4 2 2
GNAI2 0.025 0.008 -9999 0 -10000 0 0
GNAI3 0.026 0.005 -9999 0 -10000 0 0
GNAI1 0.013 0.071 -9999 0 -0.4 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.02 0.041 -9999 0 -0.41 3 3
S1PR2 0.023 0.023 -9999 0 -0.4 1 1
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.009 0.068 -9999 0 -0.29 10 10
MAPK3 0.001 0.066 -9999 0 -0.38 5 5
MAPK1 0.003 0.065 -9999 0 -0.38 5 5
JAK2 0 0.073 -9999 0 -0.39 6 6
CXCR4 0 0.068 -9999 0 -0.38 5 5
FLT1 0.023 0.025 -9999 0 -0.4 1 1
RhoA/GDP 0.018 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.018 0.004 -9999 0 -10000 0 0
SRC -0.001 0.069 -9999 0 -0.37 6 6
S1P/S1P3/Gi 0.009 0.069 -9999 0 -0.3 10 10
RAC1 0.025 0.005 -9999 0 -10000 0 0
RhoA/GTP 0.009 0.077 -9999 0 -0.36 5 5
VEGFA 0.025 0.012 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.009 0.061 -9999 0 -0.26 9 9
VEGFR1 homodimer/VEGFA homodimer 0.037 0.024 -9999 0 -0.28 1 1
RHOA 0.024 0.005 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.006 0.072 -9999 0 -0.27 21 21
GNAQ 0.023 0.023 -9999 0 -0.4 1 1
GNAZ 0.013 0.067 -9999 0 -0.4 9 9
G12/G13 0.035 0.011 -9999 0 -10000 0 0
GNA14 0.015 0.063 -9999 0 -0.4 8 8
GNA15 0.015 0.056 -9999 0 -0.4 6 6
GNA12 0.024 0.005 -9999 0 -10000 0 0
GNA13 0.024 0.006 -9999 0 -10000 0 0
GNA11 0.016 0.055 -9999 0 -0.4 6 6
Rac1/GTP 0.006 0.077 -9999 0 -0.36 5 5
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.038 0.05 -9999 0 -0.31 6 6
E-cadherin/beta catenin 0.028 0.042 -9999 0 -0.28 6 6
CTNNB1 0.023 0.023 -9999 0 -0.4 1 1
JUP 0.022 0.032 -9999 0 -0.4 2 2
CDH1 0.017 0.05 -9999 0 -0.4 5 5
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.016 0.021 -10000 0 -0.2 1 1
TRAF2/ASK1 0.03 0.019 -10000 0 -0.24 1 1
ATM 0.025 0.004 -10000 0 -10000 0 0
MAP2K3 -0.002 0.089 0.25 1 -0.34 15 16
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.005 0.088 0.18 2 -0.35 13 15
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.019 0.036 -10000 0 -0.4 2 2
TXN 0.006 0.002 -10000 0 -10000 0 0
CALM1 0.025 0.004 -10000 0 -10000 0 0
GADD45A 0.024 0.023 -10000 0 -0.4 1 1
GADD45B 0.019 0.035 -10000 0 -0.4 2 2
MAP3K1 0.023 0.023 -10000 0 -0.4 1 1
MAP3K6 0.025 0.004 -10000 0 -10000 0 0
MAP3K7 0.025 0.003 -10000 0 -10000 0 0
MAP3K4 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.035 0.02 -10000 0 -0.28 1 1
TAK1/TAB family 0 0.019 0.15 1 -0.13 1 2
RAC1/OSM/MEKK3 0.045 0.014 -10000 0 -10000 0 0
TRAF2 0.024 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.015 0.076 -10000 0 -0.3 11 11
TRAF6 0.007 0.001 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.042 0.14 -10000 0 -0.4 46 46
CCM2 0.025 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.01 0.091 -10000 0 -0.24 46 46
MAPK11 0.021 0.025 -10000 0 -0.4 1 1
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.012 0.09 -10000 0 -0.22 46 46
OSM/MEKK3 0.035 0.01 -10000 0 -10000 0 0
TAOK1 0.013 0.004 -10000 0 -10000 0 0
TAOK2 0.013 0.003 -10000 0 -10000 0 0
TAOK3 0.013 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.025 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.023 0.025 -10000 0 -0.4 1 1
MAP3K10 0.023 0.023 -10000 0 -0.4 1 1
MAP3K3 0.024 0.006 -10000 0 -10000 0 0
TRX/ASK1 0.015 0.032 -10000 0 -0.23 1 1
GADD45/MTK1/MTK1 0.05 0.037 -10000 0 -0.21 5 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.058 0.028 -9999 0 -0.21 2 2
HDAC3 0.025 0.004 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.008 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.031 0.014 -9999 0 -10000 0 0
GATA1/HDAC5 0.031 0.013 -9999 0 -10000 0 0
GATA2/HDAC5 -0.002 0.1 -9999 0 -0.28 41 41
HDAC5/BCL6/BCoR 0.045 0.023 -9999 0 -0.24 1 1
HDAC9 0.006 0.088 -9999 0 -0.4 16 16
Glucocorticoid receptor/Hsp90/HDAC6 0.043 0.044 -9999 0 -0.24 8 8
HDAC4/ANKRA2 0.035 0.01 -9999 0 -10000 0 0
HDAC5/YWHAB 0.035 0.011 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.012 0.011 -9999 0 -0.18 1 1
GATA2 -0.025 0.14 -9999 0 -0.4 41 41
HDAC4/RFXANK 0.035 0.012 -9999 0 -10000 0 0
BCOR 0.025 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.023 0.007 -9999 0 -10000 0 0
HDAC5 0.024 0.006 -9999 0 -10000 0 0
GNB1/GNG2 0.031 0.036 -9999 0 -0.28 4 4
Histones 0.012 0.055 -9999 0 -0.27 5 5
ADRBK1 0.025 0.004 -9999 0 -10000 0 0
HDAC4 0.025 0.007 -9999 0 -10000 0 0
XPO1 0.025 0.004 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.035 0.01 -9999 0 -10000 0 0
HDAC4/Ubc9 0.036 0.009 -9999 0 -10000 0 0
HDAC7 0.025 0.005 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.035 0.011 -9999 0 -10000 0 0
TUBA1B 0.025 0.002 -9999 0 -10000 0 0
HDAC6 0.024 0.023 -9999 0 -0.4 1 1
HDAC5/RFXANK 0.035 0.011 -9999 0 -10000 0 0
CAMK4 0.006 0.079 -9999 0 -0.4 12 12
Tubulin/HDAC6 0.049 0.019 -9999 0 -0.24 1 1
SUMO1 0.024 0.023 -9999 0 -0.4 1 1
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.024 0.005 -9999 0 -10000 0 0
GATA1 0.019 0.014 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.024 0.006 -9999 0 -10000 0 0
NR3C1 0.015 0.06 -9999 0 -0.4 7 7
SUMO1/HDAC4 0.03 0.044 -9999 0 -0.19 7 7
SRF 0.025 0.004 -9999 0 -10000 0 0
HDAC4/YWHAB 0.035 0.011 -9999 0 -10000 0 0
Tubulin 0.036 0.011 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.035 0.012 -9999 0 -10000 0 0
GNB1 0.025 0.005 -9999 0 -10000 0 0
RANGAP1 0.024 0.007 -9999 0 -10000 0 0
BCL6/BCoR 0.034 0.02 -9999 0 -0.28 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.049 0.012 -9999 0 -10000 0 0
HDAC4/SRF 0.039 0.052 -9999 0 -0.24 11 11
HDAC4/ER alpha -0.002 0.1 -9999 0 -0.28 43 43
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.012 0.055 -9999 0 -0.27 5 5
cell motility 0.048 0.019 -9999 0 -0.24 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.025 0.004 -9999 0 -10000 0 0
HDAC7/HDAC3 0.036 0.008 -9999 0 -10000 0 0
BCL6 0.022 0.023 -9999 0 -0.4 1 1
HDAC4/CaMK II delta B 0.025 0.007 -9999 0 -10000 0 0
Hsp90/HDAC6 0.035 0.019 -9999 0 -0.28 1 1
ESR1 -0.027 0.14 -9999 0 -0.4 44 44
HDAC6/HDAC11 0.033 0.027 -9999 0 -0.28 2 2
Ran/GTP/Exportin 1 0.031 0.041 -9999 0 -0.23 1 1
NPC 0.015 0.002 -9999 0 -10000 0 0
MEF2C 0.021 0.039 -9999 0 -0.4 3 3
RAN 0.025 0.004 -9999 0 -10000 0 0
HDAC4/MEF2C 0.067 0.033 -9999 0 -0.21 3 3
GNG2 0.018 0.047 -9999 0 -0.4 4 4
NCOR2 0.025 0.004 -9999 0 -10000 0 0
TUBB2A 0.024 0.012 -9999 0 -10000 0 0
HDAC11 0.022 0.025 -9999 0 -0.4 1 1
HSP90AA1 0.025 0.004 -9999 0 -10000 0 0
RANBP2 0.025 0.003 -9999 0 -10000 0 0
ANKRA2 0.024 0.005 -9999 0 -10000 0 0
RFXANK 0.024 0.006 -9999 0 -10000 0 0
nuclear import -0.03 0.011 -9999 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.015 0.076 -10000 0 -0.98 2 2
regulation of axonogenesis -0.006 0.025 0.23 3 -10000 0 3
myoblast fusion -0.02 0.04 0.39 2 -10000 0 2
mol:GTP 0.016 0.028 -10000 0 -0.17 7 7
regulation of calcium-dependent cell-cell adhesion -0.04 0.05 0.22 10 -10000 0 10
ARF1/GTP 0.027 0.022 -10000 0 -10000 0 0
mol:GM1 0.007 0.02 -10000 0 -0.16 2 2
mol:Choline 0.006 0.02 -10000 0 -0.17 3 3
lamellipodium assembly 0.007 0.06 -10000 0 -0.38 7 7
MAPK3 0.019 0.03 -10000 0 -0.33 2 2
ARF6/GTP/NME1/Tiam1 0.041 0.05 -10000 0 -0.22 10 10
ARF1 0.021 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.02 0.041 -10000 0 -0.39 2 2
ARF1/GDP 0.02 0.042 -10000 0 -0.23 4 4
ARF6 0.03 0.015 -10000 0 -10000 0 0
RAB11A 0.024 0.005 -10000 0 -10000 0 0
TIAM1 0.016 0.063 -10000 0 -0.4 8 8
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.018 0.031 -10000 0 -0.33 2 2
actin filament bundle formation -0.026 0.046 0.28 5 -10000 0 5
KALRN 0.008 0.04 -10000 0 -0.23 9 9
RAB11FIP3/RAB11A 0.035 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.027 0.047 -10000 0 -0.29 5 5
NME1 0.024 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.027 0.048 -10000 0 -0.29 5 5
substrate adhesion-dependent cell spreading 0.016 0.028 -10000 0 -0.17 7 7
cortical actin cytoskeleton organization 0.007 0.06 -10000 0 -0.38 7 7
RAC1 0.025 0.005 -10000 0 -10000 0 0
liver development 0.016 0.028 -10000 0 -0.17 7 7
ARF6/GTP 0.016 0.028 -10000 0 -0.17 7 7
RhoA/GTP 0.031 0.024 -10000 0 -0.17 2 2
mol:GDP 0.01 0.037 -10000 0 -0.3 4 4
ARF6/GTP/RAB11FIP3/RAB11A 0.044 0.024 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
PLD1 0.014 0.022 -10000 0 -0.17 2 2
RAB11FIP3 0.025 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.007 0.06 -10000 0 -0.38 7 7
ruffle organization 0.006 0.025 -10000 0 -0.23 3 3
regulation of epithelial cell migration 0.016 0.028 -10000 0 -0.17 7 7
PLD2 0.015 0.025 -10000 0 -0.19 3 3
PIP5K1A 0.006 0.025 -10000 0 -0.24 3 3
mol:Phosphatidic acid 0.006 0.02 -10000 0 -0.17 3 3
Rac1/GTP 0.007 0.061 -10000 0 -0.38 7 7
Aurora C signaling

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
INCENP 0.025 0.003 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.038 0.043 -9999 0 -0.22 9 9
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.009 0.021 -9999 0 -0.29 1 1
AURKB 0.018 0.05 -9999 0 -0.4 5 5
AURKC 0.019 0.046 -9999 0 -0.24 8 8
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.015 0.12 0.22 1 -0.39 21 22
CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
AKT1 0.025 0.004 -10000 0 -10000 0 0
AKT2 0.025 0.005 -10000 0 -10000 0 0
STXBP4 0.023 0.023 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.006 0.13 0.2 2 -0.41 23 25
YWHAZ 0.023 0.007 -10000 0 -10000 0 0
CALM1 0.025 0.004 -10000 0 -10000 0 0
YWHAQ 0.025 0.005 -10000 0 -10000 0 0
TBC1D4 0.003 0.049 -10000 0 -0.29 10 10
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.024 0.006 -10000 0 -10000 0 0
YWHAB 0.024 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.045 0.022 -10000 0 -0.22 1 1
YWHAG 0.025 0.004 -10000 0 -10000 0 0
ASIP 0.019 0.015 -10000 0 -10000 0 0
PRKCI 0.022 0.023 -10000 0 -0.4 1 1
AS160/CaM/Ca2+ 0.018 0.003 -10000 0 -10000 0 0
RHOQ 0.025 0.004 -10000 0 -10000 0 0
GYS1 0.01 0.003 -10000 0 -10000 0 0
PRKCZ 0.022 0.032 -10000 0 -0.4 2 2
TRIP10 0.024 0.007 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.031 0.01 -10000 0 -10000 0 0
AS160/14-3-3 0.008 0.056 -10000 0 -0.3 3 3
VAMP2 0.024 0.006 -10000 0 -10000 0 0
SLC2A4 -0.009 0.14 0.23 1 -0.45 24 25
STX4 0.024 0.005 -10000 0 -10000 0 0
GSK3B 0.019 0.006 -10000 0 -10000 0 0
SFN -0.012 0.11 -10000 0 -0.4 26 26
LNPEP 0.025 0.005 -10000 0 -10000 0 0
YWHAE 0.024 0.006 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.027 0.034 -10000 0 -0.58 1 1
VEGFR1 homodimer/NRP1 0.01 0.032 -10000 0 -0.58 1 1
mol:DAG 0.009 0.037 0.19 1 -0.54 1 2
VEGFR1 homodimer/NRP1/VEGFR 121 0.025 0.032 -10000 0 -0.54 1 1
CaM/Ca2+ 0.022 0.037 -10000 0 -0.51 1 1
HIF1A 0.029 0.02 -10000 0 -0.32 1 1
GAB1 0.024 0.023 -10000 0 -0.4 1 1
AKT1 0.007 0.058 -10000 0 -0.52 1 1
PLCG1 0.009 0.038 0.19 1 -0.54 1 2
NOS3 0.012 0.061 0.31 1 -0.54 2 3
CBL 0.025 0.004 -10000 0 -10000 0 0
mol:NO 0.017 0.065 0.3 2 -0.52 2 4
FLT1 0.014 0.037 -10000 0 -0.66 1 1
PGF 0.02 0.036 -10000 0 -0.4 2 2
VEGFR1 homodimer/NRP2/VEGFR121 0.032 0.056 -10000 0 -0.25 12 12
CALM1 0.025 0.004 -10000 0 -10000 0 0
PIK3CA 0.024 0.007 -10000 0 -10000 0 0
eNOS/Hsp90 0.03 0.067 0.31 1 -0.49 2 3
endothelial cell proliferation -0.004 0.07 0.32 1 -0.42 4 5
mol:Ca2+ 0.009 0.037 0.19 1 -0.53 1 2
MAPK3 -0.015 0.046 0.26 2 -0.34 2 4
MAPK1 -0.015 0.048 0.23 3 -0.34 2 5
PIK3R1 0.003 0.091 -10000 0 -0.4 17 17
PLGF homodimer 0.02 0.036 -10000 0 -0.4 2 2
PRKACA 0.024 0.006 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.022 0.026 -10000 0 -0.4 1 1
VEGFA homodimer 0.024 0.011 -10000 0 -0.085 3 3
VEGFR1 homodimer/VEGFA homodimer 0.027 0.035 -10000 0 -0.58 1 1
platelet activating factor biosynthetic process -0.016 0.044 0.33 1 -0.34 2 3
PI3K 0.042 0.056 -10000 0 -0.53 1 1
PRKCA -0.015 0.046 0.18 2 -0.3 4 6
PRKCB -0.017 0.053 0.18 2 -0.68 1 3
VEGFR1 homodimer/PLGF homodimer 0.024 0.041 -10000 0 -0.35 3 3
VEGFA 0.024 0.011 -10000 0 -0.085 3 3
VEGFB 0.025 0.004 -10000 0 -10000 0 0
mol:IP3 0.009 0.037 0.19 1 -0.54 1 2
RASA1 0.012 0.034 0.19 3 -0.54 1 4
NRP2 0.01 0.077 -10000 0 -0.34 15 15
VEGFR1 homodimer 0.014 0.036 -10000 0 -0.66 1 1
VEGFB homodimer 0.025 0.004 -10000 0 -10000 0 0
NCK1 0.025 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.028 0.071 0.3 2 -0.57 2 4
PTPN11 0.025 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.04 0.055 -10000 0 -0.52 1 1
mol:L-citrulline 0.017 0.065 0.3 2 -0.52 2 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.045 0.056 -10000 0 -0.24 10 10
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.04 0.027 -10000 0 -0.37 1 1
CD2AP 0.012 0.074 -10000 0 -0.4 11 11
PI3K/GAB1 0.049 0.06 -10000 0 -0.51 1 1
PDPK1 0.011 0.056 -10000 0 -0.5 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.041 0.034 -10000 0 -0.54 1 1
mol:NADP 0.017 0.065 0.3 2 -0.52 2 4
HSP90AA1 0.025 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.043 0.055 -10000 0 -0.23 10 10
VEGFR1 homodimer/NRP2 0.019 0.058 -10000 0 -0.26 13 13
Aurora A signaling

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
Aurora A/GADD45A 0.026 0.026 -10000 0 -0.23 1 1
BIRC5 0.009 0.08 -10000 0 -0.4 13 13
NFKBIA 0.008 0.026 0.25 2 -10000 0 2
CPEB1 0.007 0.07 -10000 0 -0.4 9 9
AKT1 0.007 0.023 0.25 1 -0.16 1 2
NDEL1 0.024 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.023 0.024 -10000 0 -0.21 1 1
NDEL1/TACC3 0.04 0.026 -10000 0 -10000 0 0
GADD45A 0.024 0.023 -10000 0 -0.4 1 1
GSK3B 0.025 0.01 -10000 0 -10000 0 0
PAK1/Aurora A 0.027 0.023 -10000 0 -0.16 1 1
MDM2 0.023 0.032 -10000 0 -0.4 2 2
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.008 0.035 -10000 0 -0.29 5 5
TP53 0.012 0.05 -10000 0 -0.27 10 10
DLG7 0.008 0.019 -10000 0 -0.14 3 3
AURKAIP1 0.025 0.005 -10000 0 -10000 0 0
ARHGEF7 0.024 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.042 0.027 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.022 0.024 -10000 0 -0.21 1 1
AURKA 0.015 0.024 -10000 0 -0.17 3 3
AURKB 0.005 0.053 -10000 0 -0.26 11 11
CDC25B 0.015 0.019 -10000 0 -10000 0 0
G2/M transition checkpoint 0.009 0.017 -10000 0 -0.13 3 3
mRNA polyadenylation 0.017 0.042 -10000 0 -0.2 9 9
Aurora A/CPEB 0.017 0.042 -10000 0 -0.2 9 9
Aurora A/TACC1/TRAP/chTOG 0.049 0.036 -10000 0 -0.24 1 1
BRCA1 0.022 0.032 -10000 0 -0.4 2 2
centrosome duplication 0.027 0.023 -10000 0 -0.16 1 1
regulation of centrosome cycle 0.039 0.025 -10000 0 -10000 0 0
spindle assembly 0.048 0.035 -10000 0 -0.23 1 1
TDRD7 0.021 0.032 -10000 0 -0.4 2 2
Aurora A/RasGAP/Survivin 0.042 0.055 -10000 0 -0.21 11 11
CENPA 0.006 0.063 -10000 0 -0.36 9 9
Aurora A/PP2A 0.027 0.022 -10000 0 -0.16 1 1
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.01 0.027 -10000 0 -10000 0 0
negative regulation of DNA binding 0.011 0.05 -10000 0 -0.27 10 10
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.035 0.011 -10000 0 -10000 0 0
RASA1 0.025 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.009 0.017 -10000 0 -0.13 3 3
mitotic prometaphase 0.003 0.02 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.024 -10000 0 -0.17 3 3
TACC1 0.021 0.026 -10000 0 -0.4 1 1
TACC3 0.024 0.006 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.042 0.027 -10000 0 -10000 0 0
Aurora A/RasGAP 0.026 0.023 -10000 0 -0.16 1 1
OAZ1 0.024 0.006 -10000 0 -10000 0 0
RAN 0.025 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.024 0.01 -10000 0 -10000 0 0
GIT1 0.024 0.005 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.047 0.015 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.008 0.035 -10000 0 -0.28 5 5
PPP2R5D 0.025 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.015 0.033 -10000 0 -0.34 2 2
PAK1 0.025 0.003 -10000 0 -10000 0 0
CKAP5 0.024 0.005 -10000 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 0.002 0.087 -10000 0 -0.4 15 15
CLTC 0.016 0.059 -10000 0 -0.45 5 5
calcium ion-dependent exocytosis 0.01 0.034 -10000 0 -0.24 5 5
Dynamin 2/GTP 0.023 0.008 -10000 0 -10000 0 0
EXOC4 0.024 0.005 -10000 0 -10000 0 0
CD59 0.011 0.037 -10000 0 -0.32 4 4
CPE 0.004 0.042 -10000 0 -0.24 10 10
CTNNB1 0.023 0.023 -10000 0 -0.4 1 1
membrane fusion 0.012 0.013 -10000 0 -10000 0 0
CTNND1 0.013 0.024 0.18 7 -10000 0 7
DNM2 0.024 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.01 0.04 0.17 1 -0.4 2 3
TSHR 0.002 0.018 -10000 0 -10000 0 0
INS -0.004 0.088 -10000 0 -0.45 13 13
BIN1 0.021 0.045 -10000 0 -0.4 4 4
mol:Choline 0.012 0.013 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.004 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.025 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.008 -10000 0 -10000 0 0
JUP 0.012 0.028 -10000 0 -0.28 2 2
ASAP2/amphiphysin II 0.043 0.033 -10000 0 -0.22 5 5
ARF6/GTP 0.019 0.003 -10000 0 -10000 0 0
CDH1 0.009 0.039 -10000 0 -0.34 3 3
clathrin-independent pinocytosis 0.019 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.022 0.032 -10000 0 -0.4 2 2
positive regulation of endocytosis 0.019 0.003 -10000 0 -10000 0 0
EXOC2 0.025 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.018 0.035 -10000 0 -0.24 2 2
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.024 0.006 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.033 0.05 0.34 3 -10000 0 3
positive regulation of phagocytosis 0.013 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.031 0.022 -10000 0 -0.24 2 2
ACAP1 0.014 0.027 -10000 0 -0.24 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.008 0.037 -10000 0 -0.32 4 4
clathrin heavy chain/ACAP1 0.013 0.052 0.18 1 -0.35 5 6
JIP4/KLC1 0.045 0.014 -10000 0 -10000 0 0
EXOC1 0.025 0.004 -10000 0 -10000 0 0
exocyst 0.018 0.035 -10000 0 -0.24 2 2
RALA/GTP 0.018 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.032 0.009 -10000 0 -10000 0 0
receptor recycling 0.019 0.003 -10000 0 -10000 0 0
CTNNA1 0.012 0.022 0.18 6 -10000 0 6
NME1 0.012 0.004 -10000 0 -10000 0 0
clathrin coat assembly 0.016 0.062 0.26 1 -0.44 5 6
IL2RA 0.006 0.058 -10000 0 -0.38 4 4
VAMP3 0.013 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.019 0.067 -10000 0 -0.33 5 5
EXOC6 0.024 0.007 -10000 0 -10000 0 0
PLD1 0.012 0.007 -10000 0 -10000 0 0
PLD2 0.011 0.022 -10000 0 -0.39 1 1
EXOC5 0.021 0.039 -10000 0 -0.4 3 3
PIP5K1C 0.012 0.032 -10000 0 -0.49 1 1
SDC1 0.006 0.066 -10000 0 -0.45 6 6
ARF6/GDP 0.022 0.006 -10000 0 -10000 0 0
EXOC7 0.024 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.035 0.052 -10000 0 -0.35 3 3
mol:Phosphatidic acid 0.012 0.013 -10000 0 -10000 0 0
endocytosis -0.041 0.032 0.22 5 -10000 0 5
SCAMP2 0.024 0.005 -10000 0 -10000 0 0
ADRB2 0 0.076 0.3 1 -0.4 6 7
EXOC3 0.024 0.006 -10000 0 -10000 0 0
ASAP2 0.023 0.023 -10000 0 -0.4 1 1
Dynamin 2/GDP 0.026 0.01 -10000 0 -10000 0 0
KLC1 0.025 0.004 -10000 0 -10000 0 0
AVPR2 0.002 0.079 0.23 5 -0.44 4 9
RALA 0.025 0.004 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.029 0.05 0.33 1 -0.33 3 4
Arf1 pathway

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
coatomer protein complex 0.008 0.032 0.15 12 -0.32 1 13
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.029 0.053 0.13 52 -0.19 5 57
AP2 0.034 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.031 0.011 -10000 0 -10000 0 0
CLTB 0.025 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.016 0.009 -10000 0 -10000 0 0
CD4 0.013 0.07 -10000 0 -0.4 10 10
CLTA 0.025 0.004 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.005 0.015 -10000 0 -0.28 1 1
mol:PI-4-5-P2 0.005 0.011 -10000 0 -0.15 1 1
ARF1/GTP 0.024 0.017 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.008 0.015 -10000 0 -0.26 1 1
mol:Choline 0.004 0.011 -10000 0 -0.16 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.023 0.011 -10000 0 -10000 0 0
DDEF1 0.003 0.011 -10000 0 -0.16 1 1
ARF1/GDP 0.002 0.02 -10000 0 -0.17 2 2
AP2M1 0.024 0.007 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.011 0.007 -10000 0 -10000 0 0
Rac/GTP 0.021 0.007 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.027 0.021 -10000 0 -0.21 1 1
ARFIP2 0.015 0.017 -10000 0 -10000 0 0
COPA 0.021 0.01 -10000 0 -10000 0 0
RAC1 0.025 0.005 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.011 0.021 -10000 0 -0.23 1 1
ARF1/GTP/ARHGAP10 0.014 0.008 -10000 0 -10000 0 0
GGA3 0.024 0.006 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.01 0.045 -10000 0 -0.18 17 17
AP2A1 0.025 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.01 0.023 -10000 0 -0.19 3 3
ARF1/GDP/Membrin 0.01 0.055 -10000 0 -0.22 17 17
Arfaptin 2/Rac/GDP 0.029 0.011 -10000 0 -10000 0 0
CYTH2 0.03 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.028 0.015 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.018 0.004 -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 0.013 0.029 -10000 0 -0.17 4 4
PLD2 0.004 0.011 -10000 0 -0.16 1 1
ARF-GAP1/v-SNARE 0.005 0.015 -10000 0 -0.28 1 1
PIP5K1A 0.005 0.011 -10000 0 -0.15 1 1
ARF1/GTP/Membrin/GBF1/p115 0.015 0.022 -10000 0 -0.12 2 2
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.011 -10000 0 -0.16 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.005 0.015 -10000 0 -0.28 1 1
GOSR2 0.007 0.031 -10000 0 -0.32 3 3
USO1 0.008 0.025 -10000 0 -0.31 2 2
GBF1 0.006 0.034 -10000 0 -0.35 3 3
ARF1/GTP/Arfaptin 2 0.029 0.016 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.038 0.05 -10000 0 -0.24 10 10
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.025 0.005 -10000 0 -10000 0 0
SMAD2 0.004 0.04 0.22 2 -0.25 4 6
SMAD3 0.021 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4 0.023 0.088 -10000 0 -0.5 9 9
SMAD4/Ubc9/PIASy 0.046 0.017 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.048 0.046 0.23 1 -0.27 1 2
PPM1A 0.025 0.004 -10000 0 -10000 0 0
CALM1 0.025 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.017 0.043 0.23 1 -0.22 6 7
MAP3K1 0.023 0.023 -10000 0 -0.4 1 1
TRAP-1/SMAD4 0.031 0.042 -10000 0 -0.28 6 6
MAPK3 0.024 0.005 -10000 0 -10000 0 0
MAPK1 0.025 0.005 -10000 0 -10000 0 0
NUP214 0.024 0.006 -10000 0 -10000 0 0
CTDSP1 0.025 0.005 -10000 0 -10000 0 0
CTDSP2 0.025 0.001 -10000 0 -10000 0 0
CTDSPL 0.023 0.023 -10000 0 -0.4 1 1
KPNB1 0.024 0.006 -10000 0 -10000 0 0
TGFBRAP1 0.018 0.055 -10000 0 -0.4 6 6
UBE2I 0.025 0.004 -10000 0 -10000 0 0
NUP153 0.025 0.004 -10000 0 -10000 0 0
KPNA2 0.024 0.006 -10000 0 -10000 0 0
PIAS4 0.024 0.007 -10000 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.042 0.024 -9999 0 -10000 0 0
CLOCK 0.026 0.023 -9999 0 -0.4 1 1
TIMELESS/CRY2 0.032 0.021 -9999 0 -10000 0 0
DEC1/BMAL1 0.029 0.019 -9999 0 -0.28 1 1
ATR 0.024 0.005 -9999 0 -10000 0 0
NR1D1 0.015 0.02 -9999 0 -10000 0 0
ARNTL 0.025 0.023 -9999 0 -0.4 1 1
TIMELESS 0.016 0.015 -9999 0 -10000 0 0
NPAS2 0.007 0.088 -9999 0 -0.4 16 16
CRY2 0.025 0.005 -9999 0 -10000 0 0
mol:CO -0.007 0.001 -9999 0 -10000 0 0
CHEK1 0.025 0.005 -9999 0 -10000 0 0
mol:HEME 0.007 0.001 -9999 0 -10000 0 0
PER1 0.023 0.009 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.043 0.065 -9999 0 -0.24 18 18
BMAL1/CLOCK 0.017 0.058 -9999 0 -10000 0 0
S phase of mitotic cell cycle 0.042 0.024 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.043 0.024 -9999 0 -10000 0 0
mol:NADPH 0.007 0.001 -9999 0 -10000 0 0
PER1/TIMELESS 0.031 0.021 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0.016 0.006 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.025 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.004 0.011 -10000 0 -10000 0 0
MDM2/SUMO1 0.028 0.046 -10000 0 -0.19 8 8
HDAC4 0.025 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.005 0.011 -10000 0 -10000 0 0
SUMO1 0.024 0.023 -10000 0 -0.4 1 1
NPC/RanGAP1/SUMO1 0.009 0.022 -10000 0 -0.21 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.008 0.01 -10000 0 -0.17 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.025 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.025 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.03 0.044 -10000 0 -0.19 7 7
SUMO1/HDAC1 0.031 0.042 -10000 0 -0.19 7 7
RANGAP1 0.024 0.007 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.057 0.032 -10000 0 -0.22 3 3
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.012 0.011 -10000 0 -0.18 1 1
Ran/GTP 0.02 0.038 -10000 0 -0.17 8 8
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.023 0.032 -10000 0 -0.4 2 2
UBE2I 0.025 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.02 0.042 0.2 5 -0.23 1 6
NPC 0.015 0.002 -10000 0 -10000 0 0
PIAS2 0.024 0.005 -10000 0 -10000 0 0
PIAS1 0.024 0.006 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.036 0.042 -10000 0 -0.22 8 8
MAPK9 0.007 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.007 0.008 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.031 -10000 0 -0.23 4 4
GNB1 0.025 0.005 -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 0.007 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.011 0.028 -10000 0 -0.21 5 5
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 0.007 0.059 5 -10000 0 5
GNAL 0.016 0.052 -10000 0 -0.4 5 5
GNG2 0.018 0.047 -10000 0 -0.4 4 4
CRH 0.013 0.015 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.015 -10000 0 -0.28 1 1
MAPK11 0.005 0.015 -10000 0 -0.28 1 1
Alternative NF-kappaB pathway

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
IKK alpha homodimer 0.034 0.011 -9999 0 -9999 0 0
FBXW11 0.025 0.004 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.025 0.004 -9999 0 -9999 0 0
CHUK 0.024 0.006 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.066 0.026 -9999 0 -9999 0 0
NFKB1 0.025 0.004 -9999 0 -9999 0 0
MAP3K14 0.024 0.006 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.036 0.009 -9999 0 -9999 0 0
RELB 0.025 0.004 -9999 0 -9999 0 0
NFKB2 0.024 0.006 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.031 0.01 -9999 0 -9999 0 0
regulation of B cell activation 0.031 0.01 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 362 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.FI.A2F9 TCGA.FI.A2F8 TCGA.FI.A2F4 TCGA.FI.A2EX
109_MAP3K5 -0.017 0.028 -0.19 0.067
47_PPARGC1A -0.085 0.026 -0.4 0.026
105_BMP4 0.026 0.026 0.026 0.026
105_BMP6 0 0.026 0.026 0.026
105_BMP7 0 -0.085 -0.4 -0.085
105_BMP2 0.026 0.026 0.026 0.026
131_RELN/VLDLR 0.064 0.066 0.066 0.064
30_TGFB1/TGF beta receptor Type II 0.025 0.025 0.025 0
84_STAT5B 0.027 0.032 -0.11 0.054
84_STAT5A 0.027 0.032 -0.11 0.054
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/UCEC-TP/3353328/UCEC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/UCEC-TP/3472019/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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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