PARADIGM pathway analysis of mRNA expression data
Glioblastoma Multiforme (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C18W3BXW
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNA expression data. Broad Institute of MIT and Harvard. doi:10.7908/C18W3BXW
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 47 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
Glypican 2 network 224
HIF-1-alpha transcription factor network 216
FOXM1 transcription factor network 201
TCGA08_retinoblastoma 152
Endothelins 141
Osteopontin-mediated events 132
Syndecan-1-mediated signaling events 130
EGFR-dependent Endothelin signaling events 118
LPA receptor mediated events 113
amb2 Integrin signaling 107
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 528 . 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 ( 528 ).

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
Glypican 2 network 0.4242 224 897 4 -0.23 0 1000 -1000 0 -1000
HIF-1-alpha transcription factor network 0.4091 216 16479 76 -0.55 0.023 1000 -1000 -0.011 -1000
FOXM1 transcription factor network 0.3807 201 10257 51 -0.75 0.017 1000 -1000 -0.058 -1000
TCGA08_retinoblastoma 0.2879 152 1218 8 -0.23 0.073 1000 -1000 -0.001 -1000
Endothelins 0.2670 141 13577 96 -0.47 0.084 1000 -1000 -0.007 -1000
Osteopontin-mediated events 0.2500 132 5037 38 -0.32 0.017 1000 -1000 0 -1000
Syndecan-1-mediated signaling events 0.2462 130 4450 34 -0.29 0.018 1000 -1000 0 -1000
EGFR-dependent Endothelin signaling events 0.2235 118 2483 21 -0.14 0.017 1000 -1000 -0.002 -1000
LPA receptor mediated events 0.2140 113 11553 102 -0.18 0.017 1000 -1000 -0.036 -1000
amb2 Integrin signaling 0.2027 107 8852 82 -0.25 0.022 1000 -1000 0 -1000
PLK1 signaling events 0.1705 90 7688 85 -0.25 0.022 1000 -1000 -0.006 -1000
BARD1 signaling events 0.1591 84 4842 57 -0.26 0.049 1000 -1000 -0.014 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1515 80 10058 125 -0.25 0.026 1000 -1000 -0.034 -1000
Syndecan-4-mediated signaling events 0.1477 78 5269 67 -0.39 0.021 1000 -1000 -0.01 -1000
HIF-2-alpha transcription factor network 0.1420 75 3251 43 -0.21 0.11 1000 -1000 -0.035 -1000
Wnt signaling 0.1326 70 495 7 -0.12 0.017 1000 -1000 0.002 -1000
Fc-epsilon receptor I signaling in mast cells 0.1307 69 6715 97 -0.19 0.032 1000 -1000 -0.03 -1000
Regulation of nuclear SMAD2/3 signaling 0.1250 66 8997 136 -0.28 0.16 1000 -1000 -0.015 -1000
Aurora B signaling 0.1250 66 4477 67 -0.31 0.023 1000 -1000 -0.013 -1000
VEGFR1 specific signals 0.1193 63 3546 56 -0.25 0.039 1000 -1000 -0.007 -1000
PDGFR-alpha signaling pathway 0.1042 55 2457 44 -0.25 0.023 1000 -1000 -0.002 -1000
S1P1 pathway 0.1004 53 1928 36 -0.21 0.022 1000 -1000 -0.027 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.1004 53 3950 74 -0.35 0.033 1000 -1000 -0.033 -1000
Noncanonical Wnt signaling pathway 0.0966 51 1331 26 -0.12 0.017 1000 -1000 -0.018 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0966 51 1905 37 -0.27 0.042 1000 -1000 -0.006 -1000
FAS signaling pathway (CD95) 0.0966 51 2398 47 -0.045 0.031 1000 -1000 -0.008 -1000
TCGA08_p53 0.0947 50 353 7 -0.025 0.009 1000 -1000 -0.003 -1000
Circadian rhythm pathway 0.0909 48 1065 22 -0.046 0.026 1000 -1000 -0.007 -1000
Class I PI3K signaling events 0.0909 48 3519 73 -0.093 0.035 1000 -1000 -0.005 -1000
Aurora A signaling 0.0871 46 2775 60 -0.16 0.042 1000 -1000 -0.001 -1000
Ras signaling in the CD4+ TCR pathway 0.0833 44 762 17 -0.094 0.016 1000 -1000 -0.006 -1000
E-cadherin signaling in keratinocytes 0.0814 43 1866 43 -0.14 0.028 1000 -1000 -0.004 -1000
BCR signaling pathway 0.0795 42 4213 99 -0.087 0.048 1000 -1000 -0.03 -1000
IL1-mediated signaling events 0.0777 41 2593 62 -0.12 0.049 1000 -1000 -0.014 -1000
Integrins in angiogenesis 0.0777 41 3451 84 -0.22 0.04 1000 -1000 -0.018 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0701 37 2927 78 -0.047 0.033 1000 -1000 -0.017 -1000
Syndecan-2-mediated signaling events 0.0663 35 2436 69 -0.19 0.034 1000 -1000 -0.003 -1000
Signaling events mediated by HDAC Class I 0.0644 34 3614 104 -0.13 0.034 1000 -1000 -0.016 -1000
Syndecan-3-mediated signaling events 0.0644 34 1219 35 -0.14 0.032 1000 -1000 -0.007 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0625 33 2968 88 -0.2 0.037 1000 -1000 -0.046 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0606 32 739 23 -0.085 0.018 1000 -1000 -0.002 -1000
Glypican 1 network 0.0606 32 1562 48 -0.22 0.028 1000 -1000 -0.006 -1000
Plasma membrane estrogen receptor signaling 0.0606 32 2755 86 -0.42 0.13 1000 -1000 -0.029 -1000
Visual signal transduction: Cones 0.0549 29 1104 38 -0.13 0.04 1000 -1000 -0.001 -1000
Signaling mediated by p38-alpha and p38-beta 0.0530 28 1272 44 -0.043 0.033 1000 -1000 0 -1000
S1P3 pathway 0.0530 28 1212 42 -0.22 0.022 1000 -1000 0 -1000
Paxillin-dependent events mediated by a4b1 0.0511 27 994 36 -0.27 0.042 1000 -1000 -0.012 -1000
Arf6 downstream pathway 0.0492 26 1139 43 -0.016 0.025 1000 -1000 -0.011 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0492 26 1176 45 -0.13 0.026 1000 -1000 -0.006 -1000
Nongenotropic Androgen signaling 0.0492 26 1352 52 -0.059 0.027 1000 -1000 -0.017 -1000
EPO signaling pathway 0.0473 25 1424 55 -0.033 0.053 1000 -1000 -0.007 -1000
TRAIL signaling pathway 0.0473 25 1200 48 -0.02 0.022 1000 -1000 0 -1000
Signaling events mediated by PRL 0.0473 25 868 34 -0.038 0.025 1000 -1000 -0.005 -1000
ErbB2/ErbB3 signaling events 0.0455 24 1567 65 -0.094 0.022 1000 -1000 -0.025 -1000
Signaling events mediated by PTP1B 0.0455 24 1844 76 -0.2 0.033 1000 -1000 -0.01 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0455 24 1257 52 -0.24 0.051 1000 -1000 0 -1000
Canonical Wnt signaling pathway 0.0455 24 1272 51 -0.11 0.1 1000 -1000 -0.011 -1000
IL6-mediated signaling events 0.0455 24 1834 75 -0.2 0.034 1000 -1000 -0.016 -1000
Caspase cascade in apoptosis 0.0436 23 1713 74 -0.13 0.024 1000 -1000 -0.016 -1000
FoxO family signaling 0.0436 23 1473 64 -0.2 0.022 1000 -1000 -0.015 -1000
Presenilin action in Notch and Wnt signaling 0.0417 22 1358 61 -0.092 0.035 1000 -1000 -0.008 -1000
TCGA08_rtk_signaling 0.0417 22 583 26 -0.14 0.021 1000 -1000 0.002 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0417 22 1537 68 -0.19 0.084 1000 -1000 -0.04 -1000
Regulation of Telomerase 0.0417 22 2299 102 -0.14 0.044 1000 -1000 -0.032 -1000
Cellular roles of Anthrax toxin 0.0398 21 831 39 -0.084 0.016 1000 -1000 -0.005 -1000
Glucocorticoid receptor regulatory network 0.0398 21 2447 114 -0.099 0.075 1000 -1000 -0.023 -1000
Ceramide signaling pathway 0.0398 21 1650 76 -0.13 0.039 1000 -1000 -0.005 -1000
E-cadherin signaling in the nascent adherens junction 0.0379 20 1524 76 -0.086 0.039 1000 -1000 -0.035 -1000
Coregulation of Androgen receptor activity 0.0360 19 1481 76 -0.34 0.047 1000 -1000 0 -1000
BMP receptor signaling 0.0360 19 1578 81 -0.085 0.047 1000 -1000 -0.027 -1000
IL2 signaling events mediated by PI3K 0.0360 19 1111 58 -0.043 0.037 1000 -1000 -0.02 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0360 19 2316 120 -0.12 0.05 1000 -1000 -0.025 -1000
IFN-gamma pathway 0.0341 18 1251 68 -0.064 0.043 1000 -1000 -0.029 -1000
ceramide signaling pathway 0.0341 18 913 49 -0.13 0.025 1000 -1000 -0.009 -1000
Regulation of p38-alpha and p38-beta 0.0341 18 972 54 -0.053 0.033 1000 -1000 0 -1000
Retinoic acid receptors-mediated signaling 0.0322 17 1031 58 -0.18 0.069 1000 -1000 -0.007 -1000
IL23-mediated signaling events 0.0322 17 1038 60 -0.026 0.046 1000 -1000 -0.029 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0303 16 892 54 -0.086 0.026 1000 -1000 -0.008 -1000
TCR signaling in naïve CD8+ T cells 0.0303 16 1490 93 -0.094 0.033 1000 -1000 -0.027 -1000
PDGFR-beta signaling pathway 0.0303 16 1573 97 -0.067 0.04 1000 -1000 -0.029 -1000
p75(NTR)-mediated signaling 0.0284 15 1905 125 -0.12 0.082 1000 -1000 -0.031 -1000
IL2 signaling events mediated by STAT5 0.0284 15 336 22 -0.096 0.042 1000 -1000 -0.003 -1000
Canonical NF-kappaB pathway 0.0265 14 547 39 -0.13 0.061 1000 -1000 0 -1000
ErbB4 signaling events 0.0265 14 1001 69 -0.14 0.051 1000 -1000 -0.012 -1000
IL4-mediated signaling events 0.0265 14 1274 91 -0.15 0.051 1000 -1000 -0.1 -1000
IL12-mediated signaling events 0.0246 13 1145 87 -0.22 0.048 1000 -1000 -0.059 -1000
Signaling mediated by p38-gamma and p38-delta 0.0246 13 209 15 -0.013 0.025 1000 -1000 -0.003 -1000
Insulin Pathway 0.0246 13 1010 74 -0.11 0.048 1000 -1000 -0.027 -1000
Arf6 signaling events 0.0227 12 757 62 -0.14 0.044 1000 -1000 0 -1000
S1P5 pathway 0.0227 12 206 17 -0.036 0.017 1000 -1000 -0.008 -1000
IGF1 pathway 0.0227 12 728 57 -0.032 0.034 1000 -1000 -0.012 -1000
Thromboxane A2 receptor signaling 0.0208 11 1158 105 -0.14 0.035 1000 -1000 -0.034 -1000
Signaling events mediated by the Hedgehog family 0.0189 10 559 52 -0.03 0.045 1000 -1000 -0.007 -1000
JNK signaling in the CD4+ TCR pathway 0.0189 10 186 17 -0.017 0.027 1000 -1000 -0.005 -1000
Class I PI3K signaling events mediated by Akt 0.0189 10 711 68 -0.026 0.036 1000 -1000 -0.005 -1000
Nectin adhesion pathway 0.0189 10 688 63 -0.086 0.054 1000 -1000 -0.033 -1000
Calcium signaling in the CD4+ TCR pathway 0.0189 10 312 31 -0.082 0.055 1000 -1000 -0.018 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0189 10 356 33 -0.039 0.041 1000 -1000 -0.001 -1000
E-cadherin signaling events 0.0189 10 51 5 0.004 0.023 1000 -1000 0.003 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0170 9 256 27 -0.036 0.036 1000 -1000 -0.018 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0152 8 233 28 -0.036 0.024 1000 -1000 0 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0152 8 760 85 -0.085 0.049 1000 -1000 -0.023 -1000
Hedgehog signaling events mediated by Gli proteins 0.0152 8 543 65 -0.064 0.042 1000 -1000 -0.004 -1000
Aurora C signaling 0.0152 8 58 7 -0.005 0.02 1000 -1000 0 -1000
Atypical NF-kappaB pathway 0.0152 8 263 31 -0.012 0.033 1000 -1000 0 -1000
EPHB forward signaling 0.0152 8 689 85 -0.094 0.048 1000 -1000 -0.032 -1000
Arf6 trafficking events 0.0152 8 589 71 -0.026 0.028 1000 -1000 -0.01 -1000
Signaling events mediated by HDAC Class III 0.0133 7 294 40 -0.034 0.038 1000 -1000 -0.01 -1000
Ephrin B reverse signaling 0.0133 7 379 48 -0.016 0.026 1000 -1000 -0.011 -1000
mTOR signaling pathway 0.0114 6 354 53 -0.1 0.034 1000 -1000 -0.022 -1000
Signaling events regulated by Ret tyrosine kinase 0.0114 6 549 82 -0.02 0.043 1000 -1000 -0.026 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0095 5 173 34 -0.027 0.047 1000 -1000 -0.006 -1000
FOXA2 and FOXA3 transcription factor networks 0.0095 5 270 46 -0.018 0.19 1000 -1000 -0.002 -1000
p38 MAPK signaling pathway 0.0095 5 250 44 -0.02 0.048 1000 -1000 -0.007 -1000
Regulation of Androgen receptor activity 0.0095 5 382 70 -0.027 0.068 1000 -1000 -0.005 -1000
Insulin-mediated glucose transport 0.0076 4 132 32 -0.01 0.021 1000 -1000 -0.001 -1000
Reelin signaling pathway 0.0076 4 279 56 -0.003 0.08 1000 -1000 -0.001 -1000
IL27-mediated signaling events 0.0076 4 204 51 -0.025 0.044 1000 -1000 -0.019 -1000
S1P4 pathway 0.0076 4 124 25 -0.036 0.022 1000 -1000 0 -1000
Signaling events mediated by HDAC Class II 0.0057 3 237 75 -0.029 0.043 1000 -1000 -0.015 -1000
a4b1 and a4b7 Integrin signaling 0.0057 3 17 5 0.013 0.023 1000 -1000 0.006 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0057 3 270 83 -0.062 0.047 1000 -1000 -0.005 -1000
LPA4-mediated signaling events 0.0019 1 12 12 0 0.014 1000 -1000 -0.003 -1000
Effects of Botulinum toxin 0.0019 1 41 26 0 0.035 1000 -1000 0 -1000
Arf1 pathway 0.0019 1 70 54 0 0.027 1000 -1000 -0.003 -1000
Alternative NF-kappaB pathway 0.0019 1 22 13 0 0.049 1000 -1000 0 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.012 0.017 1000 -1000 0.002 -1000
Ephrin A reverse signaling 0.0000 0 2 7 0 0.023 1000 -1000 0 -1000
Rapid glucocorticoid signaling 0.0000 0 4 20 0 0.017 1000 -1000 0 -1000
Visual signal transduction: Rods 0.0000 0 5 52 0 0.042 1000 -1000 -0.008 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.017 0.017 1000 -1000 -0.005 -1000
Total NA 4443 254103 7203 -16 5.2 131000 -131000 -1.7 -131000
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.23 0.21 -9999 0 -0.41 299 299
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.16 0.15 -9999 0 -0.29 299 299
neuron projection morphogenesis -0.16 0.15 -9999 0 -0.29 299 299
HIF-1-alpha transcription factor network

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
PKM2 -0.45 0.47 -10000 0 -0.8 300 300
HDAC7 -0.006 0.012 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.34 0.37 0.36 28 -0.65 269 297
SMAD4 -0.085 0.18 -10000 0 -0.41 126 126
ID2 -0.45 0.47 -10000 0 -0.8 299 299
AP1 -0.047 0.13 -10000 0 -0.29 125 125
ABCG2 -0.45 0.47 -10000 0 -0.79 301 301
HIF1A -0.062 0.08 -10000 0 -0.14 150 150
TFF3 -0.45 0.47 -10000 0 -0.8 302 302
GATA2 0.017 0.019 -10000 0 -0.41 1 1
AKT1 -0.055 0.082 0.26 2 -0.15 65 67
response to hypoxia -0.068 0.069 0.31 1 -0.13 227 228
MCL1 -0.45 0.47 -10000 0 -0.8 300 300
NDRG1 -0.45 0.47 -10000 0 -0.8 300 300
SERPINE1 -0.52 0.53 -10000 0 -0.88 312 312
FECH -0.45 0.47 -10000 0 -0.8 300 300
FURIN -0.45 0.47 -10000 0 -0.8 300 300
NCOA2 0.019 0.001 -10000 0 -10000 0 0
EP300 -0.026 0.12 0.45 5 -0.19 6 11
HMOX1 -0.55 0.53 -10000 0 -0.9 328 328
BHLHE40 -0.45 0.47 -10000 0 -0.8 300 300
BHLHE41 -0.45 0.47 -10000 0 -0.8 300 300
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.1 0.13 -10000 0 -0.24 160 160
ENG -0.07 0.15 0.34 5 -0.29 91 96
JUN 0.017 0.019 -10000 0 -0.41 1 1
RORA -0.45 0.47 -10000 0 -0.8 299 299
ABCB1 -0.093 0.087 -10000 0 -0.18 213 213
TFRC -0.45 0.47 -10000 0 -0.79 302 302
CXCR4 -0.54 0.53 -10000 0 -0.89 323 323
TF -0.42 0.47 -10000 0 -0.81 270 270
CITED2 -0.45 0.48 -10000 0 -0.8 300 300
HIF1A/ARNT -0.49 0.57 0.48 28 -0.93 284 312
LDHA -0.052 0.054 -10000 0 -0.12 17 17
ETS1 -0.45 0.47 -10000 0 -0.8 300 300
PGK1 -0.45 0.47 -10000 0 -0.8 300 300
NOS2 -0.45 0.47 -10000 0 -0.8 300 300
ITGB2 -0.52 0.53 -10000 0 -0.89 309 309
ALDOA -0.45 0.47 -10000 0 -0.8 300 300
Cbp/p300/CITED2 -0.45 0.48 -10000 0 -0.8 300 300
FOS -0.084 0.18 -10000 0 -0.41 125 125
HK2 -0.45 0.47 -10000 0 -0.8 300 300
SP1 0.023 0.008 -10000 0 -10000 0 0
GCK -0.037 0.17 0.58 5 -0.26 7 12
HK1 -0.45 0.47 -10000 0 -0.8 298 298
NPM1 -0.45 0.47 -10000 0 -0.8 301 301
EGLN1 -0.45 0.47 -10000 0 -0.8 300 300
CREB1 0.023 0.002 -10000 0 -10000 0 0
PGM1 -0.45 0.47 -10000 0 -0.8 300 300
SMAD3 0.017 0.003 -10000 0 -10000 0 0
EDN1 -0.036 0.15 0.51 1 -0.29 43 44
IGFBP1 -0.45 0.48 -10000 0 -0.8 301 301
VEGFA -0.41 0.42 -10000 0 -0.71 318 318
HIF1A/JAB1 -0.033 0.054 -10000 0 -0.4 2 2
CP -0.5 0.51 -10000 0 -0.86 307 307
CXCL12 -0.45 0.48 -10000 0 -0.8 300 300
COPS5 0.018 0.001 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.048 0.13 -10000 0 -0.28 126 126
BNIP3 -0.45 0.47 -10000 0 -0.8 300 300
EGLN3 -0.45 0.47 -10000 0 -0.8 300 300
CA9 -0.46 0.48 -10000 0 -0.81 301 301
TERT -0.45 0.47 -10000 0 -0.8 300 300
ENO1 -0.45 0.47 -10000 0 -0.8 300 300
PFKL -0.45 0.47 -10000 0 -0.8 300 300
NCOA1 0.017 0.003 -10000 0 -10000 0 0
ADM -0.55 0.52 -10000 0 -0.88 333 333
ARNT -0.063 0.07 -10000 0 -0.13 204 204
HNF4A 0.021 0 -10000 0 -10000 0 0
ADFP -0.52 0.53 -10000 0 -0.88 315 315
SLC2A1 -0.32 0.36 -10000 0 -0.64 268 268
LEP -0.45 0.47 -10000 0 -0.8 300 300
HIF1A/ARNT/Cbp/p300 -0.35 0.38 0.36 28 -0.68 269 297
EPO -0.18 0.28 0.52 6 -0.44 230 236
CREBBP -0.026 0.12 0.44 6 -0.19 6 12
HIF1A/ARNT/Cbp/p300/HDAC7 -0.39 0.4 0.36 28 -0.7 297 325
PFKFB3 -0.45 0.47 -10000 0 -0.8 300 300
NT5E -0.47 0.48 -10000 0 -0.82 305 305
FOXM1 transcription factor network

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
NFATC3 -0.55 0.55 -9999 0 -1 269 269
PLK1 -0.031 0.098 -9999 0 -0.46 22 22
BIRC5 -0.18 0.23 -9999 0 -0.46 211 211
HSPA1B -0.56 0.55 -9999 0 -1 274 274
MAP2K1 -0.013 0.036 -9999 0 -10000 0 0
BRCA2 -0.55 0.55 -9999 0 -1 269 269
FOXM1 -0.75 0.8 -9999 0 -1.3 293 293
XRCC1 -0.55 0.55 -9999 0 -1 269 269
FOXM1B/p19 -0.64 0.6 -9999 0 -1.1 274 274
Cyclin D1/CDK4 -0.6 0.55 -9999 0 -1.1 285 285
CDC2 -0.63 0.63 -9999 0 -1.2 272 272
TGFA -0.49 0.48 -9999 0 -0.92 267 267
SKP2 -0.55 0.55 -9999 0 -1 268 268
CCNE1 0.005 0.05 -9999 0 -0.42 7 7
CKS1B -0.59 0.58 -9999 0 -1.1 273 273
RB1 -0.26 0.23 -9999 0 -0.5 197 197
FOXM1C/SP1 -0.68 0.68 -9999 0 -1.2 274 274
AURKB -0.034 0.11 -9999 0 -0.46 27 27
CENPF -0.6 0.59 -9999 0 -1.1 272 272
CDK4 -0.27 0.21 -9999 0 -0.43 342 342
MYC -0.53 0.5 -9999 0 -0.94 281 281
CHEK2 -0.026 0.086 -9999 0 -0.46 16 16
ONECUT1 -0.55 0.54 -9999 0 -1 270 270
CDKN2A -0.032 0.14 -9999 0 -0.41 59 59
LAMA4 -0.55 0.55 -9999 0 -1 270 270
FOXM1B/HNF6 -0.68 0.68 -9999 0 -1.3 270 270
FOS -0.59 0.56 -9999 0 -1 281 281
SP1 0.016 0.006 -9999 0 -10000 0 0
CDC25B -0.56 0.56 -9999 0 -1 271 271
response to radiation -0.02 0.026 -9999 0 -10000 0 0
CENPB -0.56 0.55 -9999 0 -1 269 269
CENPA -0.57 0.58 -9999 0 -1.1 269 269
NEK2 -0.56 0.56 -9999 0 -1 269 269
HIST1H2BA -0.56 0.55 -9999 0 -1 274 274
CCNA2 -0.1 0.19 -9999 0 -0.43 139 139
EP300 0.017 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.71 0.71 -9999 0 -1.3 283 283
CCNB2 -0.65 0.6 -9999 0 -1.1 296 296
CCNB1 -0.64 0.63 -9999 0 -1.2 281 281
ETV5 -0.55 0.55 -9999 0 -1 269 269
ESR1 -0.55 0.55 -9999 0 -1 269 269
CCND1 -0.56 0.53 -9999 0 -1 271 271
GSK3A -0.009 0.029 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.075 0.16 -9999 0 -0.31 146 146
CDK2 -0.011 0.097 -9999 0 -0.43 27 27
G2/M transition of mitotic cell cycle -0.024 0.033 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.61 0.62 -9999 0 -1.1 272 272
GAS1 -0.57 0.56 -9999 0 -1.1 273 273
MMP2 -0.63 0.57 -9999 0 -1.1 293 293
RB1/FOXM1C -0.59 0.55 -9999 0 -1.1 274 274
CREBBP 0.017 0 -9999 0 -10000 0 0
TCGA08_retinoblastoma

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
CDKN2B 0 0.018 -10000 0 -10000 0 0
CDKN2C -0.23 0.21 -10000 0 -0.41 310 310
CDKN2A -0.014 0.13 -10000 0 -0.38 59 59
CCND2 0.044 0.062 0.13 113 -10000 0 113
RB1 -0.048 0.068 -10000 0 -0.14 113 113
CDK4 0.031 0.071 0.14 113 -0.081 86 199
CDK6 0.073 0.074 0.13 311 -10000 0 311
G1/S progression 0.048 0.068 0.14 113 -10000 0 113
Endothelins

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
AKT1 -0.26 0.22 -10000 0 -0.35 396 396
PTK2B 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ -0.039 0.099 -10000 0 -0.48 5 5
EDN1 -0.11 0.11 -10000 0 -0.24 143 143
EDN3 0.014 0.037 -10000 0 -0.41 4 4
EDN2 0.016 0.019 -10000 0 -0.41 1 1
HRAS/GDP -0.023 0.11 -10000 0 -0.22 53 53
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.087 0.1 -10000 0 -0.2 196 196
ADCY4 -0.22 0.18 -10000 0 -0.29 396 396
ADCY5 -0.22 0.18 -10000 0 -0.29 396 396
ADCY6 -0.21 0.18 -10000 0 -0.34 291 291
ADCY7 -0.21 0.18 -10000 0 -0.35 291 291
ADCY1 -0.21 0.18 -10000 0 -0.34 291 291
ADCY2 -0.21 0.18 -10000 0 -0.34 291 291
ADCY3 -0.22 0.18 -10000 0 -0.29 396 396
ADCY8 -0.21 0.18 -10000 0 -0.35 293 293
ADCY9 -0.21 0.18 -10000 0 -0.34 291 291
arachidonic acid secretion -0.067 0.14 -10000 0 -0.3 104 104
ETB receptor/Endothelin-1/Gq/GTP -0.032 0.062 -10000 0 -0.16 54 54
GNAO1 0.002 0.005 -10000 0 -10000 0 0
HRAS 0.016 0.019 -10000 0 -0.41 1 1
ETA receptor/Endothelin-1/G12/GTP -0.23 0.21 0.25 1 -0.37 315 316
ETA receptor/Endothelin-1/Gs/GTP -0.22 0.2 0.24 1 -0.34 321 322
mol:GTP 0 0.003 -10000 0 -10000 0 0
COL3A1 -0.41 0.28 -10000 0 -0.55 400 400
EDNRB -0.047 0.12 -10000 0 -0.42 41 41
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.26 0.21 -10000 0 -0.41 291 291
CYSLTR1 -0.26 0.21 -10000 0 -0.35 397 397
SLC9A1 -0.13 0.11 -10000 0 -0.21 291 291
mol:GDP -0.03 0.11 0.18 1 -0.2 92 93
SLC9A3 -0.084 0.12 -10000 0 -0.35 37 37
RAF1 -0.05 0.12 -10000 0 -0.26 95 95
JUN -0.041 0.098 -10000 0 -0.35 10 10
JAK2 -0.26 0.22 -10000 0 -0.35 396 396
mol:IP3 -0.077 0.09 -10000 0 -0.18 172 172
ETA receptor/Endothelin-1 -0.3 0.25 0.28 1 -0.41 397 398
PLCB1 0.017 0.002 -10000 0 -10000 0 0
PLCB2 0.016 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.17 0.18 -10000 0 -0.3 266 266
FOS -0.075 0.18 -10000 0 -0.38 125 125
Gai/GDP -0.47 0.17 -10000 0 -0.52 481 481
CRK 0.017 0 -10000 0 -10000 0 0
mol:Ca ++ -0.23 0.21 -10000 0 -0.38 298 298
BCAR1 0 0 -10000 0 -10000 0 0
PRKCB1 -0.015 0.046 -10000 0 -0.19 19 19
GNAQ 0.018 0.004 -10000 0 -10000 0 0
GNAZ 0.015 0.006 -10000 0 -10000 0 0
GNAL 0.017 0 -10000 0 -10000 0 0
Gs family/GDP -0.023 0.1 -10000 0 -0.22 53 53
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.12 -10000 0 -0.21 270 270
MAPK14 -0.018 0.052 -10000 0 -0.16 27 27
TRPC6 -0.041 0.1 -10000 0 -0.38 10 10
GNAI2 0.017 0.001 -10000 0 -10000 0 0
GNAI3 -0.036 0.14 -10000 0 -0.41 65 65
GNAI1 0.014 0.02 -10000 0 -0.41 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.022 0.055 -10000 0 -0.15 40 40
ETB receptor/Endothelin-2 -0.022 0.083 -10000 0 -0.29 42 42
ETB receptor/Endothelin-3 -0.024 0.086 -10000 0 -0.29 45 45
ETB receptor/Endothelin-1 -0.11 0.12 -10000 0 -0.25 168 168
MAPK3 -0.069 0.17 -10000 0 -0.36 117 117
MAPK1 -0.073 0.17 -10000 0 -0.36 117 117
Rac1/GDP -0.023 0.1 0.18 1 -0.22 53 54
cAMP biosynthetic process -0.17 0.16 -10000 0 -0.3 271 271
MAPK8 -0.054 0.11 -10000 0 -0.36 13 13
SRC 0.017 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.033 0.078 -10000 0 -0.2 88 88
p130Cas/CRK/Src/PYK2 0.005 0.098 -10000 0 -0.28 13 13
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.024 0.1 0.18 1 -0.22 55 56
COL1A2 -0.35 0.29 -10000 0 -0.57 305 305
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.16 0.18 -10000 0 -0.29 275 275
mol:DAG -0.077 0.09 -10000 0 -0.18 172 172
MAP2K2 -0.061 0.14 -10000 0 -0.3 116 116
MAP2K1 -0.059 0.15 -10000 0 -0.3 116 116
EDNRA -0.24 0.23 -10000 0 -0.33 393 393
positive regulation of muscle contraction -0.22 0.19 -10000 0 -0.36 293 293
Gq family/GDP 0.033 0.098 -10000 0 -0.19 45 45
HRAS/GTP -0.04 0.1 -10000 0 -0.2 92 92
PRKCH -0.072 0.09 -10000 0 -0.18 164 164
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.071 0.088 -10000 0 -0.18 158 158
PRKCB -0.076 0.088 -10000 0 -0.18 167 167
PRKCE -0.072 0.088 -10000 0 -0.18 165 165
PRKCD -0.072 0.089 -10000 0 -0.18 154 154
PRKCG -0.072 0.089 -10000 0 -0.18 165 165
regulation of vascular smooth muscle contraction -0.081 0.19 -10000 0 -0.41 117 117
PRKCQ -0.072 0.088 -10000 0 -0.18 164 164
PLA2G4A -0.071 0.15 -10000 0 -0.31 104 104
GNA14 0.016 0.027 -10000 0 -0.41 2 2
GNA15 0.012 0.049 -10000 0 -0.41 7 7
GNA12 0.014 0.037 -10000 0 -0.41 4 4
GNA11 0.017 0.003 -10000 0 -10000 0 0
Rac1/GTP -0.23 0.21 0.25 1 -0.36 321 322
MMP1 0.084 0.15 0.19 243 -0.34 43 286
Osteopontin-mediated events

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
IKK alpha homodimer -0.066 0.13 -9999 0 -0.23 186 186
NF kappa B1 p50/RelA/I kappa B alpha -0.056 0.14 -9999 0 -0.3 83 83
alphaV/beta3 Integrin/Osteopontin/Src -0.098 0.16 -9999 0 -0.32 185 185
AP1 -0.2 0.22 -9999 0 -0.43 203 203
ILK -0.08 0.13 -9999 0 -0.24 185 185
bone resorption -0.21 0.16 -9999 0 -0.27 429 429
PTK2B 0.017 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.066 0.14 -9999 0 -0.23 199 199
ITGAV 0 0.075 -9999 0 -0.42 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.22 0.13 -9999 0 -0.28 415 415
alphaV/beta3 Integrin/Osteopontin -0.076 0.15 -9999 0 -0.27 185 185
MAP3K1 -0.082 0.13 -9999 0 -0.25 186 186
JUN 0.014 0.019 -9999 0 -0.41 1 1
MAPK3 -0.08 0.14 -9999 0 -0.25 185 185
MAPK1 -0.081 0.14 -9999 0 -0.25 185 185
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
NFKB1 0.014 0.037 -9999 0 -0.41 4 4
MAPK8 -0.084 0.12 -9999 0 -0.24 186 186
ITGB3 0.013 0.011 -9999 0 -10000 0 0
NFKBIA -0.076 0.14 -9999 0 -0.27 129 129
FOS -0.088 0.18 -9999 0 -0.42 125 125
CD44 -0.32 0.18 -9999 0 -0.41 415 415
CHUK 0.016 0.019 -9999 0 -0.41 1 1
PLAU -0.13 0.22 -9999 0 -0.48 131 131
NF kappa B1 p50/RelA -0.06 0.15 -9999 0 -0.33 83 83
BCAR1 0 0 -9999 0 -10000 0 0
RELA 0.017 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.009 0.057 -9999 0 -0.29 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.087 0.15 -9999 0 -0.26 199 199
VAV3 -0.094 0.15 -9999 0 -0.25 221 221
MAP3K14 -0.079 0.14 -9999 0 -0.25 185 185
ROCK2 0.017 0 -9999 0 -10000 0 0
SPP1 -0.14 0.21 -9999 0 -0.42 181 181
RAC1 0.017 0 -9999 0 -10000 0 0
Rac1/GTP -0.08 0.14 -9999 0 -0.22 221 221
MMP2 -0.24 0.24 -9999 0 -0.44 297 297
Syndecan-1-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
TGFB1 -0.005 0.095 -9999 0 -0.41 27 27
CCL5 -0.006 0.096 -9999 0 -0.41 28 28
SDCBP 0.017 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.077 0.14 -9999 0 -0.21 218 218
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.072 0.14 -9999 0 -0.31 109 109
Syndecan-1/Syntenin -0.067 0.14 -9999 0 -0.3 100 100
MAPK3 -0.19 0.16 -9999 0 -0.25 394 394
HGF/MET 0.018 0.046 -9999 0 -0.28 12 12
TGFB1/TGF beta receptor Type II -0.005 0.095 -9999 0 -0.41 27 27
BSG 0.017 0 -9999 0 -10000 0 0
keratinocyte migration -0.071 0.14 -9999 0 -0.3 109 109
Syndecan-1/RANTES -0.077 0.16 -9999 0 -0.33 107 107
Syndecan-1/CD147 -0.2 0.17 -9999 0 -0.27 394 394
Syndecan-1/Syntenin/PIP2 -0.065 0.13 -9999 0 -0.29 100 100
LAMA5 0.006 0.069 -9999 0 -0.41 14 14
positive regulation of cell-cell adhesion -0.064 0.13 -9999 0 -0.28 100 100
MMP7 -0.046 0.15 -9999 0 -0.41 78 78
HGF 0.015 0.026 -9999 0 -0.41 2 2
Syndecan-1/CASK -0.075 0.13 -9999 0 -0.2 218 218
Syndecan-1/HGF/MET -0.062 0.14 -9999 0 -0.29 108 108
regulation of cell adhesion -0.18 0.15 -9999 0 -0.24 392 392
HPSE -0.019 0.12 -9999 0 -0.41 44 44
positive regulation of cell migration -0.077 0.14 -9999 0 -0.21 218 218
SDC1 -0.078 0.14 -9999 0 -0.21 218 218
Syndecan-1/Collagen -0.077 0.14 -9999 0 -0.21 218 218
PPIB -0.29 0.2 -9999 0 -0.41 373 373
MET 0.009 0.059 -9999 0 -0.41 10 10
PRKACA 0.017 0 -9999 0 -10000 0 0
MMP9 -0.13 0.2 -9999 0 -0.41 179 179
MAPK1 -0.19 0.16 -9999 0 -0.25 392 392
homophilic cell adhesion -0.077 0.14 -9999 0 -0.21 218 218
MMP1 -0.018 0.12 -9999 0 -0.41 43 43
EGFR-dependent Endothelin signaling events

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
HRAS 0.016 0.019 -9999 0 -0.41 1 1
EGFR -0.14 0.21 -9999 0 -0.41 194 194
EGF/EGFR -0.11 0.14 -9999 0 -0.22 304 304
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.067 0.12 -9999 0 -0.2 236 236
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.11 0.2 -9999 0 -0.41 154 154
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF 0.015 0.026 -9999 0 -0.41 2 2
EGF/EGFR dimer/SHC -0.088 0.14 -9999 0 -0.24 237 237
mol:GDP -0.068 0.12 -9999 0 -0.2 236 236
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.01 0.056 -9999 0 -0.41 9 9
GRB2/SOS1 0.013 0.001 -9999 0 -10000 0 0
HRAS/GTP -0.066 0.1 -9999 0 -0.18 237 237
SHC1 -0.02 0.12 -9999 0 -0.41 46 46
HRAS/GDP -0.062 0.11 -9999 0 -0.18 237 237
FRAP1 -0.07 0.11 -9999 0 -0.19 236 236
EGF/EGFR dimer -0.09 0.15 -9999 0 -0.28 196 196
SOS1 0 0 -9999 0 -10000 0 0
GRB2 0.017 0.002 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.07 0.15 -9999 0 -0.29 158 158
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.069 0.091 -10000 0 -0.17 250 250
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.053 -10000 0 -0.21 5 5
AP1 -0.1 0.12 -10000 0 -0.2 302 302
mol:PIP3 -0.12 0.11 -10000 0 -0.24 194 194
AKT1 -0.032 0.073 0.17 3 -0.21 9 12
PTK2B -0.041 0.059 -10000 0 -0.1 250 250
RHOA -0.035 0.049 -10000 0 -0.15 6 6
PIK3CB 0.017 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.029 -10000 0 -10000 0 0
MAGI3 0 0.001 -10000 0 -0.003 13 13
RELA 0.017 0 -10000 0 -10000 0 0
apoptosis -0.098 0.12 -10000 0 -0.19 285 285
HRAS/GDP 0.012 0.013 -10000 0 -0.29 1 1
positive regulation of microtubule depolymerization -0.006 0.07 0.13 62 -0.1 1 63
NF kappa B1 p50/RelA -0.055 0.06 -10000 0 -0.17 19 19
endothelial cell migration -0.18 0.21 -10000 0 -0.41 250 250
ADCY4 -0.015 0.054 -10000 0 -0.19 45 45
ADCY5 -0.015 0.054 -10000 0 -0.19 45 45
ADCY6 -0.015 0.053 -10000 0 -0.18 45 45
ADCY7 -0.016 0.056 -10000 0 -0.19 48 48
ADCY1 -0.015 0.053 -10000 0 -0.18 45 45
ADCY2 -0.015 0.053 -10000 0 -0.18 45 45
ADCY3 -0.015 0.054 -10000 0 -0.19 45 45
ADCY8 -0.015 0.054 -10000 0 -0.18 46 46
ADCY9 -0.015 0.053 -10000 0 -0.18 45 45
GSK3B -0.035 0.056 -10000 0 -0.097 65 65
arachidonic acid secretion -0.048 0.069 -10000 0 -0.13 197 197
GNG2 0 0.001 -10000 0 -0.004 23 23
TRIP6 -0.11 0.11 -10000 0 -0.21 284 284
GNAO1 -0.005 0.032 -10000 0 -0.18 16 16
HRAS 0.016 0.019 -10000 0 -0.41 1 1
NFKBIA -0.02 0.047 -10000 0 -0.14 5 5
GAB1 0.014 0.037 -10000 0 -0.41 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.14 -10000 0 -0.7 21 21
JUN 0.016 0.019 -10000 0 -0.41 1 1
LPA/LPA2/NHERF2 -0.024 0.04 -10000 0 -10000 0 0
TIAM1 -0.008 0.16 -10000 0 -0.8 21 21
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
mol:IP3 -0.009 0.03 -10000 0 -0.1 6 6
PLCB3 -0.017 0.035 -10000 0 -10000 0 0
FOS -0.085 0.18 -10000 0 -0.41 125 125
positive regulation of mitosis -0.048 0.069 -10000 0 -0.13 197 197
LPA/LPA1-2-3 -0.077 0.088 -10000 0 -0.17 250 250
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation -0.041 0.065 -10000 0 -0.11 250 250
GNAZ -0.068 0.097 -10000 0 -0.18 215 215
EGFR/PI3K-beta/Gab1 -0.12 0.12 -10000 0 -0.25 194 194
positive regulation of dendritic cell cytokine production -0.076 0.087 -10000 0 -0.17 250 250
LPA/LPA2/MAGI-3 -0.032 0.036 -10000 0 -0.07 250 250
ARHGEF1 -0.06 0.089 -10000 0 -0.15 251 251
GNAI2 -0.079 0.1 -10000 0 -0.18 250 250
GNAI3 -0.11 0.13 -10000 0 -0.22 281 281
GNAI1 -0.071 0.098 -10000 0 -0.19 222 222
LPA/LPA3 -0.04 0.045 -10000 0 -0.087 250 250
LPA/LPA2 -0.04 0.045 -10000 0 -0.087 250 250
LPA/LPA1 -0.1 0.12 -10000 0 -0.23 250 250
HB-EGF/EGFR -0.16 0.16 -10000 0 -0.27 320 320
HBEGF -0.086 0.15 -10000 0 -0.29 179 179
mol:DAG -0.009 0.03 -10000 0 -0.1 6 6
cAMP biosynthetic process 0.001 0.09 0.15 9 -0.16 50 59
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
SRC 0.017 0 -10000 0 -10000 0 0
GNB1 0.017 0.002 -10000 0 -10000 0 0
LYN -0.039 0.073 -10000 0 -0.19 65 65
GNAQ -0.023 0.035 -10000 0 -0.06 250 250
LPAR2 0 0.001 -10000 0 -0.003 15 15
LPAR3 0 0 -10000 0 -10000 0 0
LPAR1 -0.063 0.07 -10000 0 -0.14 250 250
IL8 -0.16 0.15 -10000 0 -0.28 296 296
PTK2 -0.065 0.084 -10000 0 -0.15 250 250
Rac1/GDP 0.013 0 -10000 0 -10000 0 0
CASP3 -0.099 0.12 -10000 0 -0.19 285 285
EGFR -0.14 0.21 -10000 0 -0.41 194 194
PLCG1 -0.016 0.033 -10000 0 -0.05 252 252
PLD2 -0.065 0.084 -10000 0 -0.15 250 250
G12/G13 -0.064 0.1 -10000 0 -0.17 251 251
PI3K-beta -0.054 0.06 -10000 0 -0.2 5 5
cell migration -0.046 0.059 -10000 0 -0.21 21 21
SLC9A3R2 0.017 0 -10000 0 -10000 0 0
PXN -0.041 0.066 -10000 0 -0.11 250 250
HRAS/GTP -0.049 0.07 -10000 0 -0.14 195 195
RAC1 0.017 0 -10000 0 -10000 0 0
MMP9 -0.13 0.2 -10000 0 -0.41 179 179
PRKCE 0.017 0.001 -10000 0 -10000 0 0
PRKCD -0.005 0.028 -10000 0 -10000 0 0
Gi(beta/gamma) -0.017 0.057 -10000 0 -0.19 50 50
mol:LPA -0.063 0.07 -10000 0 -0.14 250 250
TRIP6/p130 Cas/FAK1/Paxillin -0.11 0.1 -10000 0 -0.19 255 255
MAPKKK cascade -0.048 0.069 -10000 0 -0.13 197 197
contractile ring contraction involved in cytokinesis -0.035 0.049 -10000 0 -0.16 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.024 0.036 -10000 0 -0.061 252 252
GNA15 -0.026 0.043 -10000 0 -0.065 250 250
GNA12 0.014 0.037 -10000 0 -0.41 4 4
GNA13 0.016 0.026 -10000 0 -0.41 2 2
MAPT -0.022 0.048 -10000 0 -0.11 1 1
GNA11 -0.023 0.035 -10000 0 -0.06 250 250
Rac1/GTP 0.002 0.15 -10000 0 -0.73 21 21
MMP2 -0.18 0.21 -10000 0 -0.41 250 250
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.2 0.18 -9999 0 -0.31 356 356
alphaM/beta2 Integrin/GPIbA -0.079 0.14 -9999 0 -0.24 220 220
alphaM/beta2 Integrin/proMMP-9 -0.16 0.19 -9999 0 -0.31 298 298
PLAUR -0.021 0.12 -9999 0 -0.41 47 47
HMGB1 0.015 0.011 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.1 0.16 -9999 0 -0.26 241 241
AGER 0.012 0.04 -9999 0 -0.43 4 4
RAP1A 0.017 0 -9999 0 -10000 0 0
SELPLG 0.017 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.065 0.14 -9999 0 -0.22 222 222
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.13 0.2 -9999 0 -0.41 179 179
CYR61 -0.12 0.2 -9999 0 -0.41 163 163
TLN1 -0.02 0.12 -9999 0 -0.41 46 46
Rap1/GTP -0.037 0.09 -9999 0 -0.19 109 109
RHOA 0.017 0.001 -9999 0 -10000 0 0
P-selectin oligomer 0.016 0.019 -9999 0 -0.41 1 1
MYH2 -0.024 0.096 -9999 0 -0.2 83 83
MST1R 0.015 0.026 -9999 0 -0.41 2 2
leukocyte activation during inflammatory response -0.062 0.12 -9999 0 -0.2 223 223
APOB 0.015 0.032 -9999 0 -0.41 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.19 0.22 -9999 0 -0.41 250 250
JAM3 0.016 0.019 -9999 0 -0.41 1 1
GP1BA 0.017 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.096 0.15 -9999 0 -0.26 236 236
alphaM/beta2 Integrin -0.046 0.11 -9999 0 -0.22 110 110
JAM3 homodimer 0.016 0.019 -9999 0 -0.41 1 1
ICAM2 0.015 0.032 -9999 0 -0.41 3 3
ICAM1 0.003 0.076 -9999 0 -0.41 17 17
phagocytosis triggered by activation of immune response cell surface activating receptor -0.046 0.1 -9999 0 -0.22 110 110
cell adhesion -0.079 0.14 -9999 0 -0.24 220 220
NFKB1 -0.07 0.15 -9999 0 -0.37 56 56
THY1 0.013 0.008 -9999 0 -10000 0 0
RhoA/GDP 0.013 0.001 -9999 0 -10000 0 0
Lipoprotein(a) 0.022 0.02 -9999 0 -0.24 3 3
alphaM/beta2 Integrin/LRP/tPA -0.18 0.18 -9999 0 -0.28 353 353
IL6 -0.08 0.18 -9999 0 -0.5 56 56
ITGB2 -0.16 0.21 -9999 0 -0.42 220 220
elevation of cytosolic calcium ion concentration -0.13 0.21 -9999 0 -0.32 255 255
alphaM/beta2 Integrin/JAM2/JAM3 -0.097 0.14 -9999 0 -0.23 266 266
JAM2 -0.044 0.15 -9999 0 -0.41 75 75
alphaM/beta2 Integrin/ICAM1 -0.061 0.13 -9999 0 -0.21 230 230
alphaM/beta2 Integrin/uPA/Plg -0.11 0.18 -9999 0 -0.28 254 254
RhoA/GTP -0.029 0.1 -9999 0 -0.2 109 109
positive regulation of phagocytosis -0.089 0.16 -9999 0 -0.25 223 223
Ron/MSP 0.021 0.038 -9999 0 -0.28 8 8
alphaM/beta2 Integrin/uPAR/uPA -0.13 0.21 -9999 0 -0.32 255 255
alphaM/beta2 Integrin/uPAR -0.099 0.17 -9999 0 -0.28 226 226
PLAU -0.083 0.18 -9999 0 -0.41 123 123
PLAT -0.18 0.21 -9999 0 -0.41 244 244
actin filament polymerization -0.023 0.093 -9999 0 -0.2 83 83
MST1 0.012 0.046 -9999 0 -0.41 6 6
alphaM/beta2 Integrin/lipoprotein(a) -0.06 0.12 -9999 0 -0.2 223 223
TNF -0.062 0.14 -9999 0 -0.39 42 42
RAP1B 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.13 0.19 -9999 0 -0.32 254 254
fibrinolysis -0.11 0.18 -9999 0 -0.28 254 254
HCK -0.053 0.16 -9999 0 -0.41 86 86
dendritic cell antigen processing and presentation -0.046 0.1 -9999 0 -0.22 110 110
VTN 0.015 0.026 -9999 0 -0.41 2 2
alphaM/beta2 Integrin/CYR61 -0.15 0.19 -9999 0 -0.31 285 285
LPA 0.017 0 -9999 0 -10000 0 0
LRP1 0.002 0.078 -9999 0 -0.41 18 18
cell migration -0.25 0.22 -9999 0 -0.35 388 388
FN1 -0.065 0.17 -9999 0 -0.41 101 101
alphaM/beta2 Integrin/Thy1 -0.077 0.12 -9999 0 -0.24 188 188
MPO 0.017 0 -9999 0 -10000 0 0
KNG1 0.016 0.019 -9999 0 -0.41 1 1
RAP1/GDP 0.012 0 -9999 0 -10000 0 0
ROCK1 -0.024 0.096 -9999 0 -0.2 83 83
ELA2 0.017 0 -9999 0 -10000 0 0
PLG 0.017 0 -9999 0 -10000 0 0
CTGF -0.014 0.11 -9999 0 -0.41 38 38
alphaM/beta2 Integrin/Hck -0.12 0.19 -9999 0 -0.32 223 223
ITGAM 0.015 0.011 -9999 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.063 0.13 -9999 0 -0.21 220 220
HP -0.051 0.16 -9999 0 -0.41 84 84
leukocyte adhesion -0.074 0.12 -9999 0 -0.31 61 61
SELP 0.016 0.019 -9999 0 -0.41 1 1
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.006 0.012 0.041 37 -10000 0 37
BUB1B -0.099 0.12 -10000 0 -0.21 241 241
PLK1 -0.012 0.035 -10000 0 -0.12 37 37
PLK1S1 -0.008 0.02 -10000 0 -0.066 37 37
KIF2A -0.006 0.033 0.14 2 -0.13 22 24
regulation of mitotic centrosome separation -0.012 0.035 -10000 0 -0.12 37 37
GOLGA2 0.017 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.073 0.12 -10000 0 -0.23 184 184
WEE1 -0.1 0.11 -10000 0 -0.22 218 218
cytokinesis -0.1 0.14 -10000 0 -0.28 188 188
PP2A-alpha B56 0.004 0.038 -10000 0 -0.22 2 2
AURKA -0.008 0.036 -10000 0 -0.14 30 30
PICH/PLK1 -0.2 0.2 -10000 0 -0.33 307 307
CENPE -0.034 0.094 -10000 0 -0.26 70 70
RhoA/GTP 0.013 0.001 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.006 0.033 0.14 2 -0.13 22 24
PPP2CA 0.017 0.001 -10000 0 -10000 0 0
FZR1 0.017 0 -10000 0 -10000 0 0
TPX2 -0.065 0.067 -10000 0 -0.12 296 296
PAK1 0.015 0.001 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
CLSPN -0.001 0.019 -10000 0 -0.089 13 13
GORASP1 0.017 0 -10000 0 -10000 0 0
metaphase -0.001 0.002 -10000 0 -0.01 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.008 0.02 -10000 0 -0.066 37 37
G2 phase of mitotic cell cycle -0.002 0.002 -10000 0 -0.011 19 19
STAG2 -0.005 0.095 -10000 0 -0.41 27 27
GRASP65/GM130/RAB1/GTP -0.011 0.028 -10000 0 -10000 0 0
spindle elongation -0.012 0.035 -10000 0 -0.12 37 37
ODF2 0.015 0.002 -10000 0 -10000 0 0
BUB1 -0.013 0.036 -10000 0 -0.24 4 4
TPT1 -0.003 0.02 -10000 0 -0.095 13 13
CDC25C 0.001 0.019 -10000 0 -0.1 6 6
CDC25B -0.006 0.072 -10000 0 -0.42 15 15
SGOL1 -0.006 0.012 -10000 0 -0.041 37 37
RHOA 0.017 0.001 -10000 0 -10000 0 0
CCNB1/CDK1 -0.2 0.2 -10000 0 -0.31 367 367
CDC14B 0.008 0.002 -10000 0 -10000 0 0
CDC20 -0.23 0.21 -10000 0 -0.41 303 303
PLK1/PBIP1 -0.18 0.083 -10000 0 -0.21 449 449
mitosis -0.003 0.005 0.016 9 -0.021 21 30
FBXO5 -0.085 0.11 -10000 0 -0.22 195 195
CDC2 -0.15 0.21 -10000 0 -0.42 193 193
NDC80 -0.13 0.2 -10000 0 -0.41 183 183
metaphase plate congression -0.002 0.021 -10000 0 -0.11 8 8
ERCC6L -0.2 0.19 -10000 0 -0.33 307 307
NLP/gamma Tubulin -0.008 0.025 -10000 0 -0.089 31 31
microtubule cytoskeleton organization -0.003 0.02 -10000 0 -0.094 13 13
G2/M transition DNA damage checkpoint -0.002 0.002 -10000 0 -0.009 16 16
PPP1R12A 0.016 0.019 -10000 0 -0.41 1 1
interphase -0.002 0.002 -10000 0 -0.009 16 16
PLK1/PRC1-2 -0.15 0.2 -10000 0 -0.35 249 249
GRASP65/GM130/RAB1/GTP/PLK1 0.019 0.032 -10000 0 -0.13 13 13
RAB1A 0.017 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.014 0.055 -10000 0 -0.22 30 30
mitotic prometaphase -0.001 0.001 -10000 0 -0.008 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.028 0.048 -10000 0 -0.11 19 19
microtubule-based process -0.078 0.12 -10000 0 -0.24 186 186
Golgi organization -0.012 0.035 -10000 0 -0.12 37 37
Cohesin/SA2 -0.014 0.059 -10000 0 -0.17 53 53
PPP1CB/MYPT1 0.022 0.023 -10000 0 -0.29 3 3
KIF20A -0.13 0.2 -10000 0 -0.41 186 186
APC/C/CDC20 -0.13 0.13 -10000 0 -0.24 303 303
PPP2R1A 0.017 0.003 -10000 0 -10000 0 0
chromosome segregation -0.17 0.082 -10000 0 -0.21 449 449
PRC1 -0.16 0.21 -10000 0 -0.41 224 224
ECT2 -0.082 0.12 -10000 0 -0.24 183 183
C13orf34 -0.014 0.055 -10000 0 -0.23 27 27
NUDC -0.002 0.021 -10000 0 -0.11 8 8
regulation of attachment of spindle microtubules to kinetochore -0.098 0.12 -10000 0 -0.21 241 241
spindle assembly -0.01 0.032 -10000 0 -0.11 36 36
spindle stabilization -0.008 0.02 -10000 0 -0.066 37 37
APC/C/HCDH1 0.018 0.001 -10000 0 -10000 0 0
MKLP2/PLK1 -0.079 0.12 -10000 0 -0.24 186 186
CCNB1 -0.23 0.22 -10000 0 -0.42 296 296
PPP1CB 0.015 0.026 -10000 0 -0.41 2 2
BTRC 0.017 0 -10000 0 -10000 0 0
ROCK2 0.003 0.024 -10000 0 -0.11 13 13
TUBG1 -0.003 0.024 -10000 0 -0.12 15 15
G2/M transition of mitotic cell cycle -0.21 0.19 -10000 0 -0.31 367 367
MLF1IP -0.25 0.11 -10000 0 -0.3 449 449
INCENP 0.016 0.001 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 -0.048 0.13 -10000 0 -0.28 125 125
ATM -0.003 0.091 -10000 0 -0.41 25 25
UBE2D3 0.017 0.001 -10000 0 -10000 0 0
PRKDC -0.002 0.088 -10000 0 -0.41 23 23
ATR 0.017 0 -10000 0 -10000 0 0
UBE2L3 0.017 0 -10000 0 -10000 0 0
FANCD2 0.005 0.042 -10000 0 -0.18 25 25
protein ubiquitination -0.035 0.14 -10000 0 -0.24 148 148
XRCC5 0.017 0 -10000 0 -10000 0 0
XRCC6 0.017 0 -10000 0 -10000 0 0
M/R/N Complex 0.035 0 -10000 0 -10000 0 0
MRE11A 0.017 0 -10000 0 -10000 0 0
DNA-PK 0.023 0.055 -10000 0 -0.24 23 23
FA complex/FANCD2/Ubiquitin 0 0.071 -10000 0 -0.17 68 68
FANCF 0.015 0.026 -10000 0 -0.41 2 2
BRCA1 0.013 0.042 -10000 0 -0.41 5 5
CCNE1 0.011 0.049 -10000 0 -0.41 7 7
CDK2/Cyclin E1 0.006 0.082 -10000 0 -0.32 30 30
FANCG -0.037 0.14 -10000 0 -0.41 66 66
BRCA1/BACH1/BARD1 -0.051 0.14 -10000 0 -0.29 126 126
FANCE 0.016 0.019 -10000 0 -0.41 1 1
FANCC 0.017 0 -10000 0 -10000 0 0
NBN 0.017 0 -10000 0 -10000 0 0
FANCA 0.017 0 -10000 0 -10000 0 0
DNA repair -0.14 0.16 -10000 0 -0.34 153 153
BRCA1/BARD1/ubiquitin -0.051 0.14 -10000 0 -0.29 126 126
BARD1/DNA-PK -0.026 0.12 -10000 0 -0.22 138 138
FANCL 0 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.048 0.13 0.28 125 -10000 0 125
BRCA1/BARD1/CTIP/M/R/N Complex -0.1 0.1 -10000 0 -0.24 140 140
BRCA1/BACH1/BARD1/TopBP1 -0.032 0.12 -10000 0 -0.24 126 126
BRCA1/BARD1/P53 -0.048 0.15 -10000 0 -0.25 166 166
BARD1/CSTF1/BRCA1 -0.031 0.12 -10000 0 -0.24 126 126
BRCA1/BACH1 0.013 0.042 -10000 0 -0.41 5 5
BARD1 -0.085 0.18 -10000 0 -0.41 125 125
PCNA -0.26 0.2 -10000 0 -0.41 342 342
BRCA1/BARD1/UbcH5C -0.031 0.12 -10000 0 -0.24 126 126
BRCA1/BARD1/UbcH7 -0.031 0.12 -10000 0 -0.24 126 126
BRCA1/BARD1/RAD51/PCNA -0.17 0.17 -10000 0 -0.27 359 359
BARD1/DNA-PK/P53 -0.045 0.15 -10000 0 -0.24 171 171
BRCA1/BARD1/Ubiquitin -0.051 0.14 -10000 0 -0.29 126 126
BRCA1/BARD1/CTIP -0.22 0.16 -10000 0 -0.28 423 423
FA complex 0.01 0.051 -10000 0 -0.12 67 67
BARD1/EWS -0.048 0.13 -10000 0 -0.28 125 125
RBBP8 -0.23 0.14 -10000 0 -0.3 411 411
TP53 -0.039 0.14 -10000 0 -0.41 69 69
TOPBP1 0.016 0.019 -10000 0 -0.41 1 1
G1/S transition of mitotic cell cycle 0.049 0.14 0.25 166 -10000 0 166
BRCA1/BARD1 -0.032 0.15 -10000 0 -0.25 148 148
CSTF1 0.017 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.059 0.13 -10000 0 -0.29 125 125
CDK2 -0.005 0.095 -10000 0 -0.41 27 27
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.017 0 -10000 0 -10000 0 0
RAD50 0.017 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.051 0.14 -10000 0 -0.29 126 126
EWSR1 0.017 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.016 0.053 -10000 0 -0.28 16 16
AKT1 -0.049 0.11 -10000 0 -0.28 48 48
PTK2B -0.089 0.13 -10000 0 -0.36 40 40
VEGFR2 homodimer/Frs2 0.021 0.072 -10000 0 -0.33 20 20
CAV1 -0.25 0.21 -10000 0 -0.41 324 324
CALM1 0.016 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.098 0.14 -10000 0 -0.22 290 290
endothelial cell proliferation -0.04 0.1 -10000 0 -0.26 49 49
mol:Ca2+ -0.091 0.14 -10000 0 -0.4 39 39
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.13 0.18 -10000 0 -0.25 326 326
RP11-342D11.1 -0.097 0.13 -10000 0 -0.4 39 39
CDH5 -0.006 0.098 -10000 0 -0.41 29 29
VEGFA homodimer -0.099 0.12 -10000 0 -0.21 289 289
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
SHC2 0.017 0 -10000 0 -10000 0 0
HRAS/GDP -0.093 0.13 -10000 0 -0.37 55 55
SH2D2A 0.017 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.047 0.11 -10000 0 -0.31 37 37
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.096 0.14 -10000 0 -0.22 290 290
VEGFR1 homodimer 0.017 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.093 0.15 -10000 0 -0.41 55 55
GRB10 -0.096 0.15 -10000 0 -0.48 39 39
PTPN11 0.017 0 -10000 0 -10000 0 0
GRB2 0.017 0.002 -10000 0 -10000 0 0
PAK1 0.017 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.13 0.19 -10000 0 -0.4 122 122
HRAS 0.016 0.019 -10000 0 -0.41 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.034 0.077 -10000 0 -0.2 40 40
HIF1A 0.015 0.026 -10000 0 -0.41 2 2
FRS2 0.015 0.032 -10000 0 -0.41 3 3
oxygen and reactive oxygen species metabolic process -0.13 0.18 -10000 0 -0.25 326 326
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.017 0 -10000 0 -10000 0 0
Nck/Pak 0.019 0.044 -10000 0 -0.28 11 11
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.098 0.14 -10000 0 -0.22 289 289
mol:GDP -0.095 0.14 -10000 0 -0.4 55 55
mol:NADP -0.041 0.098 -10000 0 -0.27 35 35
eNOS/Hsp90 -0.034 0.096 -10000 0 -0.26 35 35
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
mol:IP3 -0.092 0.14 -10000 0 -0.4 39 39
HIF1A/ARNT 0.024 0.019 -10000 0 -0.28 2 2
SHB 0.017 0 -10000 0 -10000 0 0
VEGFA -0.21 0.22 -10000 0 -0.41 287 287
VEGFC 0.007 0.067 -10000 0 -0.41 13 13
FAK1/Vinculin -0.059 0.12 -10000 0 -0.3 40 40
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.017 0.001 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.09 0.14 -10000 0 -0.2 296 296
PTPN6 0.008 0.061 -10000 0 -0.41 11 11
EPAS1 0.018 0.051 -10000 0 -0.24 17 17
mol:L-citrulline -0.041 0.098 -10000 0 -0.27 35 35
ITGAV 0.004 0.074 -10000 0 -0.41 16 16
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.085 0.14 -10000 0 -0.2 290 290
VEGFR2 homodimer/VEGFA homodimer -0.096 0.16 -10000 0 -0.22 293 293
VEGFR2/3 heterodimer 0.022 0.07 -10000 0 -0.35 17 17
VEGFB 0.017 0 -10000 0 -10000 0 0
MAPK11 -0.089 0.13 -10000 0 -0.39 39 39
VEGFR2 homodimer 0.016 0.08 -10000 0 -0.41 17 17
FLT1 0.017 0 -10000 0 -10000 0 0
NEDD4 0.007 0.067 -10000 0 -0.39 14 14
MAPK3 -0.087 0.12 -10000 0 -0.37 39 39
MAPK1 -0.087 0.12 -10000 0 -0.37 39 39
VEGFA145/NRP2 -0.14 0.16 -10000 0 -0.28 288 288
VEGFR1/2 heterodimer 0.022 0.07 -10000 0 -0.35 17 17
KDR 0.016 0.08 -10000 0 -0.42 17 17
VEGFA165/NRP1/VEGFR2 homodimer -0.082 0.14 -10000 0 -0.4 39 39
SRC 0.017 0 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.084 0.13 -10000 0 -0.37 39 39
PI3K -0.066 0.13 -10000 0 -0.33 51 51
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.1 0.14 -10000 0 -0.22 299 299
FES -0.093 0.14 -10000 0 -0.41 39 39
GAB1 -0.077 0.13 -10000 0 -0.32 58 58
VEGFR2 homodimer/VEGFA homodimer/Src -0.096 0.14 -10000 0 -0.22 290 290
CTNNB1 0.017 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0.017 0 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.14 0.14 -10000 0 -0.27 223 223
VEGFR2 homodimer/VEGFA homodimer/Yes -0.13 0.16 -10000 0 -0.24 325 325
PI3K/GAB1 -0.053 0.12 -10000 0 -0.3 51 51
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.08 0.14 -10000 0 -0.19 299 299
PRKACA 0.017 0 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.026 0.078 -10000 0 -0.28 28 28
HSP90AA1 0.017 0 -10000 0 -10000 0 0
CDC42 -0.093 0.14 -10000 0 -0.41 39 39
actin cytoskeleton reorganization -0.096 0.14 -10000 0 -0.22 290 290
PTK2 -0.069 0.12 -10000 0 -0.32 40 40
EDG1 -0.09 0.14 -10000 0 -0.4 39 39
mol:DAG -0.092 0.14 -10000 0 -0.4 39 39
CaM/Ca2+ -0.08 0.13 -10000 0 -0.37 39 39
MAP2K3 -0.086 0.13 -10000 0 -0.39 39 39
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.09 0.16 -10000 0 -0.49 39 39
PLCG1 -0.093 0.14 -10000 0 -0.41 39 39
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.083 0.14 -10000 0 -0.2 290 290
IQGAP1 -0.086 0.18 -10000 0 -0.41 127 127
YES1 -0.047 0.15 -10000 0 -0.41 79 79
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.096 0.14 -10000 0 -0.22 290 290
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.1 0.15 -10000 0 -0.22 298 298
cell migration -0.077 0.14 -10000 0 -0.27 126 126
mol:PI-3-4-5-P3 -0.063 0.12 -10000 0 -0.32 51 51
FYN 0.015 0.027 -10000 0 -0.41 2 2
VEGFB/NRP1 -0.085 0.13 -10000 0 -0.38 39 39
mol:NO -0.041 0.098 -10000 0 -0.27 35 35
PXN 0.017 0 -10000 0 -10000 0 0
HRAS/GTP -0.11 0.12 -10000 0 -0.37 55 55
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.092 0.16 -10000 0 -0.49 39 39
VHL 0 0 -10000 0 -10000 0 0
ITGB3 0.017 0 -10000 0 -10000 0 0
NOS3 -0.046 0.11 -10000 0 -0.3 35 35
VEGFR2 homodimer/VEGFA homodimer/Sck -0.096 0.14 -10000 0 -0.22 290 290
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.084 0.13 -10000 0 -0.38 39 39
PRKCB -0.089 0.13 -10000 0 -0.38 39 39
VCL 0.017 0 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.095 0.14 -10000 0 -0.21 290 290
VEGFR1/2 heterodimer/VEGFA homodimer -0.096 0.14 -10000 0 -0.22 290 290
VEGFA165/NRP2 -0.14 0.16 -10000 0 -0.28 288 288
MAPKKK cascade -0.084 0.15 0.25 1 -0.41 55 56
NRP2 0.016 0.019 -10000 0 -0.41 1 1
VEGFC homodimer 0.007 0.067 -10000 0 -0.41 13 13
NCK1 0.008 0.061 -10000 0 -0.41 11 11
ROCK1 0.017 0 -10000 0 -10000 0 0
FAK1/Paxillin -0.059 0.12 -10000 0 -0.3 40 40
MAP3K13 -0.093 0.14 -10000 0 -0.41 39 39
PDPK1 -0.057 0.11 -10000 0 -0.28 51 51
Syndecan-4-mediated signaling 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
PTK2 -0.031 0.1 -9999 0 -0.23 104 104
Syndecan-4/Syndesmos -0.066 0.12 -9999 0 -0.3 80 80
positive regulation of JNK cascade -0.15 0.17 -9999 0 -0.35 176 176
Syndecan-4/ADAM12 -0.059 0.13 -9999 0 -0.3 80 80
CCL5 -0.006 0.096 -9999 0 -0.41 28 28
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
DNM2 0.017 0 -9999 0 -10000 0 0
ITGA5 -0.043 0.15 -9999 0 -0.41 74 74
SDCBP 0.017 0 -9999 0 -10000 0 0
PLG 0.019 0.005 -9999 0 -10000 0 0
ADAM12 0.016 0.019 -9999 0 -0.41 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.025 0.04 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.066 0.12 -9999 0 -0.3 80 80
Syndecan-4/CXCL12/CXCR4 -0.15 0.18 -9999 0 -0.37 176 176
Syndecan-4/Laminin alpha3 -0.064 0.14 -9999 0 -0.3 89 89
MDK -0.23 0.21 -9999 0 -0.41 299 299
Syndecan-4/FZD7 -0.15 0.16 -9999 0 -0.36 148 148
Syndecan-4/Midkine -0.17 0.16 -9999 0 -0.36 173 173
FZD7 -0.18 0.21 -9999 0 -0.41 244 244
Syndecan-4/FGFR1/FGF -0.046 0.13 -9999 0 -0.27 83 83
THBS1 -0.018 0.12 -9999 0 -0.41 43 43
integrin-mediated signaling pathway -0.24 0.12 -9999 0 -0.36 229 229
positive regulation of MAPKKK cascade -0.15 0.17 -9999 0 -0.35 176 176
Syndecan-4/TACI -0.058 0.13 -9999 0 -0.29 80 80
CXCR4 -0.21 0.22 -9999 0 -0.41 275 275
cell adhesion -0.026 0.091 -9999 0 -0.2 102 102
Syndecan-4/Dynamin -0.058 0.13 -9999 0 -0.29 80 80
Syndecan-4/TSP1 -0.073 0.15 -9999 0 -0.33 96 96
Syndecan-4/GIPC -0.058 0.13 -9999 0 -0.29 80 80
Syndecan-4/RANTES -0.068 0.14 -9999 0 -0.32 90 90
ITGB1 0.017 0 -9999 0 -10000 0 0
LAMA1 0 0 -9999 0 -10000 0 0
LAMA3 0.005 0.071 -9999 0 -0.41 15 15
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCA 0.021 0.03 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.074 0.14 -9999 0 -0.31 95 95
TFPI -0.078 0.18 -9999 0 -0.41 117 117
F2 0.01 0.028 -9999 0 -0.42 2 2
alpha5/beta1 Integrin -0.018 0.11 -9999 0 -0.28 74 74
positive regulation of cell adhesion -0.064 0.13 -9999 0 -0.29 89 89
ACTN1 -0.017 0.12 -9999 0 -0.41 42 42
TNC -0.39 0.09 -9999 0 -0.41 504 504
Syndecan-4/CXCL12 -0.064 0.14 -9999 0 -0.31 83 83
FGF6 0.017 0 -9999 0 -10000 0 0
RHOA 0.017 0.001 -9999 0 -10000 0 0
CXCL12 0.005 0.071 -9999 0 -0.41 15 15
TNFRSF13B 0.017 0 -9999 0 -10000 0 0
FGF2 0.015 0.026 -9999 0 -0.41 2 2
FGFR1 0.015 0.026 -9999 0 -0.41 2 2
Syndecan-4/PI-4-5-P2 -0.066 0.12 -9999 0 -0.3 80 80
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.065 0.17 -9999 0 -0.41 101 101
cell migration -0.012 0.012 -9999 0 -10000 0 0
PRKCD 0.019 0.005 -9999 0 -10000 0 0
vasculogenesis -0.071 0.14 -9999 0 -0.32 96 96
SDC4 -0.064 0.13 -9999 0 -0.31 80 80
Syndecan-4/Tenascin C -0.24 0.13 -9999 0 -0.37 229 229
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.029 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.058 0.13 -9999 0 -0.29 80 80
MMP9 -0.13 0.2 -9999 0 -0.41 179 179
Rac1/GTP -0.026 0.093 -9999 0 -0.2 101 101
cytoskeleton organization -0.064 0.12 -9999 0 -0.29 80 80
GIPC1 0.017 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.1 0.15 -9999 0 -0.34 117 117
HIF-2-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
MMP14 -0.008 0.033 -10000 0 -0.41 2 2
oxygen homeostasis -0.008 0.013 -10000 0 -10000 0 0
TCEB2 0.017 0 -10000 0 -10000 0 0
TCEB1 0.017 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.017 0.075 -10000 0 -0.19 13 13
EPO -0.078 0.18 -10000 0 -0.29 182 182
FIH (dimer) 0.006 0.016 -10000 0 -10000 0 0
APEX1 0.005 0.021 -10000 0 -10000 0 0
SERPINE1 -0.18 0.28 -10000 0 -0.47 228 228
FLT1 -0.006 0.028 -10000 0 -10000 0 0
ADORA2A -0.11 0.2 -10000 0 -0.34 182 182
germ cell development -0.11 0.2 -10000 0 -0.34 182 182
SLC11A2 -0.11 0.21 -10000 0 -0.35 182 182
BHLHE40 -0.12 0.21 -10000 0 -0.35 182 182
HIF1AN 0.006 0.016 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.046 0.13 -10000 0 -0.26 45 45
ETS1 0.027 0.012 -10000 0 -10000 0 0
CITED2 -0.017 0.066 -10000 0 -0.4 14 14
KDR -0.016 0.077 -10000 0 -0.42 17 17
PGK1 -0.11 0.21 -10000 0 -0.35 182 182
SIRT1 0.017 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.12 0.25 -10000 0 -0.4 182 182
EPAS1 -0.029 0.084 0.29 1 -0.22 13 14
SP1 0.023 0.004 -10000 0 -10000 0 0
ABCG2 -0.11 0.21 -10000 0 -0.35 183 183
EFNA1 -0.12 0.22 -10000 0 -0.36 191 191
FXN -0.11 0.2 -10000 0 -0.34 182 182
POU5F1 -0.12 0.21 -10000 0 -0.35 182 182
neuron apoptosis 0.11 0.24 0.39 182 -10000 0 182
EP300 0.017 0 -10000 0 -10000 0 0
EGLN3 0.003 0.042 -10000 0 -0.44 4 4
EGLN2 0.006 0.016 -10000 0 -10000 0 0
EGLN1 0.006 0.025 -10000 0 -0.42 1 1
VHL/Elongin B/Elongin C 0.023 0 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.005 0.021 -10000 0 -10000 0 0
SLC2A1 -0.11 0.2 -10000 0 -0.34 183 183
TWIST1 -0.12 0.22 -10000 0 -0.37 192 192
ELK1 0.021 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.045 0.13 -10000 0 -0.26 45 45
VEGFA -0.21 0.28 -10000 0 -0.42 299 299
CREBBP 0.017 0 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.047 0.1 -9999 0 -0.16 220 220
FZD6 -0.064 0.17 -9999 0 -0.41 100 100
WNT6 0.017 0 -9999 0 -10000 0 0
WNT4 0.015 0.026 -9999 0 -0.41 2 2
FZD3 0.014 0.032 -9999 0 -0.41 3 3
WNT5A -0.12 0.2 -9999 0 -0.41 168 168
WNT11 0.015 0.026 -9999 0 -0.41 2 2
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.016 0.019 -10000 0 -0.41 1 1
LAT2 -0.058 0.1 -10000 0 -0.24 76 76
AP1 -0.063 0.12 -10000 0 -0.27 102 102
mol:PIP3 -0.054 0.12 -10000 0 -0.27 65 65
IKBKB -0.026 0.07 -10000 0 -0.19 41 41
AKT1 -0.056 0.11 0.22 16 -0.24 35 51
IKBKG -0.026 0.07 -10000 0 -0.19 41 41
MS4A2 0.021 0.005 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA -0.004 0.091 -10000 0 -0.41 25 25
MAP3K1 -0.041 0.096 -10000 0 -0.22 81 81
mol:Ca2+ -0.041 0.092 -10000 0 -0.21 65 65
LYN -0.038 0.14 -10000 0 -0.42 64 64
CBLB -0.057 0.1 -10000 0 -0.26 66 66
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
RasGAP/p62DOK 0.024 0.044 -10000 0 -0.21 18 18
positive regulation of cell migration 0.009 0.001 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.078 0.1 -10000 0 -0.18 259 259
PTPN13 -0.049 0.1 -10000 0 -0.31 38 38
PTPN11 0.013 0.01 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.027 0.09 0.21 9 -0.2 40 49
SYK -0.015 0.11 -10000 0 -0.42 36 36
GRB2 0.017 0.002 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.078 0.1 -10000 0 -0.26 75 75
LAT -0.058 0.1 -10000 0 -0.23 80 80
PAK2 -0.048 0.1 -10000 0 -0.23 87 87
NFATC2 -0.039 0.04 -10000 0 -0.079 259 259
HRAS -0.046 0.099 -10000 0 -0.24 71 71
GAB2 0.016 0.019 -10000 0 -0.41 1 1
PLA2G1B 0.031 0.021 -10000 0 -10000 0 0
Fc epsilon R1 -0.1 0.14 -10000 0 -0.24 259 259
Antigen/IgE/Fc epsilon R1 -0.09 0.13 -10000 0 -0.22 259 259
mol:GDP -0.045 0.096 -10000 0 -0.22 77 77
JUN 0.016 0.019 -10000 0 -0.41 1 1
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.015 0.004 -10000 0 -10000 0 0
FOS -0.085 0.18 -10000 0 -0.41 125 125
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.063 0.11 -10000 0 -0.16 259 259
CHUK -0.026 0.07 -10000 0 -0.18 42 42
KLRG1 -0.06 0.1 -10000 0 -0.24 78 78
VAV1 -0.059 0.1 -10000 0 -0.24 76 76
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.057 0.1 -10000 0 -0.23 79 79
negative regulation of mast cell degranulation -0.057 0.095 -10000 0 -0.23 76 76
BTK -0.047 0.094 -10000 0 -0.22 77 77
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.07 0.11 -10000 0 -0.2 155 155
GAB2/PI3K/SHP2 -0.086 0.09 -10000 0 -0.22 73 73
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.077 0.13 -10000 0 -0.18 272 272
RAF1 0.025 0.019 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.13 0.17 -10000 0 -0.27 282 282
FCER1G -0.19 0.22 -10000 0 -0.42 255 255
FCER1A 0.005 0.059 -10000 0 -0.42 10 10
Antigen/IgE/Fc epsilon R1/Fyn -0.078 0.12 -10000 0 -0.2 259 259
MAPK3 0.032 0.02 -10000 0 -10000 0 0
MAPK1 0.028 0.027 -10000 0 -10000 0 0
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
MAPK8 -0.004 0.076 -10000 0 -0.34 21 21
DUSP1 0.002 0.078 -10000 0 -0.41 18 18
NF-kappa-B/RelA -0.014 0.047 -10000 0 -0.12 40 40
actin cytoskeleton reorganization -0.043 0.099 -10000 0 -0.32 28 28
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.044 0.1 -10000 0 -0.24 76 76
FER -0.057 0.1 -10000 0 -0.24 76 76
RELA 0.017 0 -10000 0 -10000 0 0
ITK -0.011 0.032 -10000 0 -0.092 32 32
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.044 0.099 -10000 0 -0.24 67 67
cytokine secretion -0.02 0.026 -10000 0 -0.092 37 37
SPHK1 -0.064 0.11 -10000 0 -0.25 90 90
PTK2 -0.045 0.1 -10000 0 -0.33 28 28
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.081 0.1 -10000 0 -0.3 65 65
EDG1 0.009 0.001 -10000 0 -10000 0 0
mol:DAG -0.05 0.11 -10000 0 -0.26 66 66
MAP2K2 0.026 0.016 -10000 0 -10000 0 0
MAP2K1 0.029 0.025 -10000 0 -10000 0 0
MAP2K7 0.017 0 -10000 0 -10000 0 0
KLRG1/SHP2 -0.055 0.1 -10000 0 -0.25 66 66
MAP2K4 -0.008 0.14 -10000 0 -0.72 21 21
Fc epsilon R1/FcgammaRIIB -0.14 0.18 -10000 0 -0.29 282 282
mol:Choline -0.077 0.1 -10000 0 -0.18 259 259
SHC/Grb2/SOS1 -0.063 0.12 -10000 0 -0.27 95 95
FYN 0.015 0.027 -10000 0 -0.41 2 2
DOK1 0.017 0 -10000 0 -10000 0 0
PXN -0.039 0.097 -10000 0 -0.31 28 28
HCLS1 -0.094 0.16 -10000 0 -0.36 117 117
PRKCB -0.04 0.09 -10000 0 -0.21 66 66
FCGR2B -0.087 0.18 -10000 0 -0.41 128 128
IGHE -0.004 0.006 -10000 0 -10000 0 0
KLRG1/SHIP -0.057 0.096 -10000 0 -0.23 76 76
LCP2 -0.008 0.1 -10000 0 -0.41 30 30
PLA2G4A -0.11 0.14 -10000 0 -0.28 177 177
RASA1 0.017 0.002 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.077 0.1 -10000 0 -0.18 259 259
IKK complex -0.014 0.057 -10000 0 -0.14 39 39
WIPF1 0.008 0.061 -10000 0 -0.41 11 11
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.008 0.012 -10000 0 -10000 0 0
HSPA8 0.019 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.017 0.16 0.18 19 -0.26 121 140
AKT1 0.016 0.037 -10000 0 -0.41 4 4
GSC 0.017 0.037 0.1 25 -10000 0 25
NKX2-5 0.016 0.007 -10000 0 -10000 0 0
muscle cell differentiation 0.025 0.098 0.22 71 -10000 0 71
SMAD2-3/SMAD4/SP1 -0.083 0.15 -10000 0 -0.26 152 152
SMAD4 -0.11 0.2 -10000 0 -0.35 176 176
CBFB 0.014 0.037 -10000 0 -0.41 4 4
SAP18 0.018 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.007 0.059 -10000 0 -0.24 25 25
SMAD3/SMAD4/VDR -0.034 0.11 -10000 0 -0.2 122 122
MYC -0.097 0.19 -10000 0 -0.42 137 137
CDKN2B 0.044 0.053 -10000 0 -10000 0 0
AP1 -0.074 0.14 -10000 0 -0.27 137 137
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.013 0.094 -10000 0 -0.19 87 87
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.001 0.065 -10000 0 -0.18 21 21
SP3 -0.045 0.15 -10000 0 -0.41 77 77
CREB1 0.017 0 -10000 0 -10000 0 0
FOXH1 0.016 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.036 0.14 -10000 0 -0.26 127 127
GATA3 0.018 0.042 -10000 0 -0.41 5 5
SKI/SIN3/HDAC complex/NCoR1 0.006 0.058 -10000 0 -0.17 20 20
MEF2C/TIF2 -0.016 0.083 -10000 0 -0.2 53 53
endothelial cell migration 0.16 0.2 0.4 215 -10000 0 215
MAX 0.025 0.012 -10000 0 -10000 0 0
RBBP7 0.018 0.001 -10000 0 -10000 0 0
RBBP4 -0.064 0.17 -10000 0 -0.41 100 100
RUNX2 0.017 0 -10000 0 -10000 0 0
RUNX3 0.015 0.032 -10000 0 -0.41 3 3
RUNX1 0.017 0 -10000 0 -10000 0 0
CTBP1 0.017 0.002 -10000 0 -10000 0 0
NR3C1 0.025 0.012 -10000 0 -10000 0 0
VDR 0.017 0 -10000 0 -10000 0 0
CDKN1A -0.098 0.17 -10000 0 -0.38 111 111
KAT2B -0.003 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.033 0.11 -10000 0 -0.23 112 112
DCP1A 0.017 0 -10000 0 -10000 0 0
SKI 0.018 0.001 -10000 0 -10000 0 0
SERPINE1 -0.16 0.2 -10000 0 -0.4 215 215
SMAD3/SMAD4/ATF2 -0.057 0.14 -10000 0 -0.26 138 138
SMAD3/SMAD4/ATF3 -0.11 0.18 -10000 0 -0.31 210 210
SAP30 0.018 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.016 0.029 -10000 0 -0.24 2 2
JUN -0.077 0.14 -10000 0 -0.27 137 137
SMAD3/SMAD4/IRF7 -0.058 0.15 -10000 0 -0.26 144 144
TFE3 -0.032 0.06 -10000 0 -0.13 87 87
COL1A2 -0.2 0.21 -10000 0 -0.41 261 261
mesenchymal cell differentiation 0.058 0.14 0.26 140 -10000 0 140
DLX1 0 0 -10000 0 -10000 0 0
TCF3 0.017 0 -10000 0 -10000 0 0
FOS -0.094 0.18 -10000 0 -0.42 125 125
SMAD3/SMAD4/Max -0.036 0.14 -10000 0 -0.26 129 129
Cbp/p300/SNIP1 0.029 0.008 -10000 0 -10000 0 0
ZBTB17 0.015 0 -10000 0 -10000 0 0
LAMC1 -0.18 0.24 -10000 0 -0.45 216 216
TGIF2/HDAC complex/SMAD3/SMAD4 -0.061 0.15 -10000 0 -0.27 142 142
IRF7 0.01 0.064 -10000 0 -0.41 12 12
ESR1 0.03 0.017 -10000 0 -10000 0 0
HNF4A 0.017 0 -10000 0 -10000 0 0
MEF2C -0.024 0.085 -10000 0 -0.22 56 56
SMAD2-3/SMAD4 -0.057 0.14 -10000 0 -0.26 134 134
Cbp/p300/Src-1 0.022 0.017 -10000 0 -10000 0 0
IGHV3OR16-13 -0.012 0.026 -10000 0 -0.1 1 1
TGIF2/HDAC complex 0.011 0.052 -10000 0 -0.41 8 8
CREBBP 0.011 0.008 -10000 0 -10000 0 0
SKIL 0.017 0 -10000 0 -10000 0 0
HDAC1 -0.035 0.14 -10000 0 -0.41 65 65
HDAC2 0.014 0.042 -10000 0 -0.41 5 5
SNIP1 0.018 0.002 -10000 0 -10000 0 0
GCN5L2 0.01 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.11 0.18 -10000 0 -0.28 253 253
MSG1/HSC70 0.013 0.066 -10000 0 -0.28 25 25
SMAD2 0.018 0.008 -10000 0 -10000 0 0
SMAD3 -0.022 0.062 -10000 0 -0.15 15 15
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.026 0.085 -10000 0 -0.16 121 121
SMAD2/SMAD2/SMAD4 -0.028 0.076 0.11 5 -0.15 120 125
NCOR1 0.018 0.001 -10000 0 -10000 0 0
NCOA2 0.017 0 -10000 0 -10000 0 0
NCOA1 0.017 0.003 -10000 0 -10000 0 0
MYOD/E2A 0.025 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 -0.068 0.14 -10000 0 -0.28 109 109
IFNB1 -0.054 0.12 -10000 0 -0.24 126 126
SMAD3/SMAD4/MEF2C -0.024 0.11 -10000 0 -0.26 56 56
CITED1 -0.003 0.091 -10000 0 -0.41 25 25
SMAD2-3/SMAD4/ARC105 -0.04 0.12 -10000 0 -0.23 119 119
RBL1 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.005 0.07 -10000 0 -0.21 13 13
RUNX1-3/PEBPB2 0.031 0.031 -10000 0 -0.24 7 7
SMAD7 -0.083 0.15 -10000 0 -0.3 135 135
MYC/MIZ-1 -0.06 0.14 -10000 0 -0.29 137 137
SMAD3/SMAD4 -0.17 0.14 -10000 0 -0.27 289 289
IL10 -0.047 0.12 -10000 0 -0.28 77 77
PIASy/HDAC complex 0.022 0.006 -10000 0 -10000 0 0
PIAS3 0.013 0.027 -10000 0 -0.42 2 2
CDK2 -0.01 0.094 -10000 0 -0.42 27 27
IL5 -0.047 0.12 -10000 0 -0.28 78 78
CDK4 -0.27 0.2 -10000 0 -0.42 342 342
PIAS4 0.022 0.006 -10000 0 -10000 0 0
ATF3 -0.071 0.17 -10000 0 -0.41 108 108
SMAD3/SMAD4/SP1 -0.11 0.16 -10000 0 -0.27 222 222
FOXG1 0.016 0.006 -10000 0 -10000 0 0
FOXO3 0.018 0.026 -10000 0 -0.28 4 4
FOXO1 0.012 0.053 -10000 0 -0.3 14 14
FOXO4 0.018 0.026 -10000 0 -0.28 4 4
heart looping -0.024 0.085 -10000 0 -0.21 56 56
CEBPB 0.009 0.061 -10000 0 -0.41 11 11
SMAD3/SMAD4/DLX1 -0.065 0.14 -10000 0 -0.22 189 189
MYOD1 0.017 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.057 0.14 -10000 0 -0.26 136 136
SMAD3/SMAD4/GATA3 -0.049 0.15 -10000 0 -0.27 121 121
SnoN/SIN3/HDAC complex/NCoR1 0.017 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.03 0.13 -10000 0 -0.25 88 88
SMAD3/SMAD4/SP1-3 -0.12 0.2 -10000 0 -0.33 184 184
MED15 0.017 0 -10000 0 -10000 0 0
SP1 -0.029 0.053 -10000 0 -0.15 4 4
SIN3B 0.018 0.001 -10000 0 -10000 0 0
SIN3A 0.001 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.014 0.1 -10000 0 -0.2 110 110
ITGB5 -0.12 0.18 -10000 0 -0.35 144 144
TGIF/SIN3/HDAC complex/CtBP -0.073 0.086 -10000 0 -0.19 138 138
SMAD3/SMAD4/AR -0.061 0.14 -10000 0 -0.27 140 140
AR 0.011 0.052 -10000 0 -0.41 8 8
negative regulation of cell growth -0.043 0.1 -10000 0 -0.19 141 141
SMAD3/SMAD4/MYOD -0.057 0.14 -10000 0 -0.26 136 136
E2F5 0.017 0 -10000 0 -10000 0 0
E2F4 0.017 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.016 0.096 -10000 0 -0.19 110 110
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.074 -10000 0 -0.2 26 26
TFDP1 0.005 0.071 -10000 0 -0.41 15 15
SMAD3/SMAD4/AP1 -0.066 0.15 -10000 0 -0.28 137 137
SMAD3/SMAD4/RUNX2 -0.057 0.14 -10000 0 -0.26 140 140
TGIF2 0.011 0.052 -10000 0 -0.41 8 8
TGIF1 -0.28 0.2 -10000 0 -0.41 371 371
ATF2 0.017 0 -10000 0 -10000 0 0
Aurora B 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
Condensin I complex -0.16 0.18 -9999 0 -0.22 405 405
STMN1 0.001 0.067 -9999 0 -0.29 27 27
Aurora B/RasGAP/Survivin -0.083 0.15 -9999 0 -0.26 207 207
Chromosomal passenger complex/Cul3 protein complex -0.038 0.085 -9999 0 -0.13 211 211
BIRC5 -0.16 0.21 -9999 0 -0.42 211 211
DES -0.004 0.058 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.017 0.057 -9999 0 -0.22 29 29
Aurora B/TACC1 0.009 0.057 -9999 0 -0.23 27 27
Aurora B/PP2A 0.009 0.069 -9999 0 -0.29 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.007 0.021 -9999 0 -0.082 27 27
mitotic metaphase/anaphase transition 0 0.003 -9999 0 -10000 0 0
NDC80 -0.1 0.17 -9999 0 -0.33 184 184
Cul3 protein complex 0.023 0.003 -9999 0 -10000 0 0
KIF2C -0.046 0.1 -9999 0 -0.19 135 135
PEBP1 0.014 0.005 -9999 0 -10000 0 0
KIF20A -0.14 0.21 -9999 0 -0.42 186 186
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.008 0.069 -9999 0 -0.29 27 27
SEPT1 0 0 -9999 0 -10000 0 0
SMC2 -0.033 0.14 -9999 0 -0.41 61 61
SMC4 -0.31 0.18 -9999 0 -0.41 401 401
NSUN2/NPM1/Nucleolin -0.023 0.078 -9999 0 -0.29 29 29
PSMA3 0.017 0.001 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -9999 0 -10000 0 0
H3F3B 0.004 0.044 -9999 0 -0.19 27 27
AURKB -0.006 0.097 -9999 0 -0.42 27 27
AURKC 0.015 0.026 -9999 0 -0.41 2 2
CDCA8 0 0.079 -9999 0 -0.43 17 17
cytokinesis -0.11 0.2 -9999 0 -0.34 187 187
Aurora B/Septin1 -0.1 0.19 -9999 0 -0.33 187 187
AURKA 0.001 0.08 -9999 0 -0.42 19 19
INCENP 0.013 0.008 -9999 0 -10000 0 0
KLHL13 0 0 -9999 0 -10000 0 0
BUB1 0.014 0.038 -9999 0 -0.42 4 4
hSgo1/Aurora B/Survivin -0.084 0.14 -9999 0 -0.24 211 211
EVI5 0.016 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.12 0.22 -9999 0 -0.38 180 180
SGOL1 0 0 -9999 0 -10000 0 0
CENPA -0.039 0.11 -9999 0 -0.26 86 86
NCAPG -0.077 0.18 -9999 0 -0.41 116 116
Aurora B/HC8 Proteasome 0.009 0.069 -9999 0 -0.29 27 27
NCAPD2 -0.068 0.17 -9999 0 -0.41 105 105
Aurora B/PP1-gamma 0.009 0.069 -9999 0 -0.29 27 27
RHOA 0.017 0.001 -9999 0 -10000 0 0
NCAPH 0.004 0.074 -9999 0 -0.41 16 16
NPM1 -0.009 0.064 -9999 0 -0.25 32 32
RASA1 0.017 0.002 -9999 0 -10000 0 0
KLHL9 0.017 0.003 -9999 0 -10000 0 0
mitotic prometaphase -0.003 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.069 -9999 0 -0.29 27 27
PPP1CC 0.017 0.001 -9999 0 -10000 0 0
Centraspindlin -0.13 0.23 -9999 0 -0.38 204 204
RhoA/GDP 0.013 0.001 -9999 0 -10000 0 0
NSUN2 -0.013 0.055 -9999 0 -0.24 27 27
MYLK -0.003 0.059 -9999 0 -0.2 42 42
KIF23 -0.05 0.16 -9999 0 -0.42 79 79
VIM -0.01 0.085 -9999 0 -0.29 45 45
RACGAP1 -0.12 0.2 -9999 0 -0.42 166 166
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.006 0.055 -9999 0 -0.23 27 27
Chromosomal passenger complex -0.066 0.13 -9999 0 -0.21 185 185
Chromosomal passenger complex/EVI5 -0.069 0.16 -9999 0 -0.24 211 211
TACC1 0.017 0.001 -9999 0 -10000 0 0
PPP2R5D 0.017 0 -9999 0 -10000 0 0
CUL3 0.017 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.031 0.016 -9999 0 -0.22 2 2
VEGFR1 homodimer/NRP1 0.019 0.015 -9999 0 -0.23 2 2
mol:DAG 0.019 0.047 -9999 0 -0.2 23 23
VEGFR1 homodimer/NRP1/VEGFR 121 -0.1 0.12 -9999 0 -0.21 289 289
CaM/Ca2+ 0.026 0.045 -9999 0 -0.18 22 22
HIF1A 0.024 0.026 -9999 0 -0.4 2 2
GAB1 0.014 0.037 -9999 0 -0.41 4 4
AKT1 0.016 0.059 -9999 0 -0.31 3 3
PLCG1 0.019 0.047 -9999 0 -0.2 23 23
NOS3 0.03 0.043 -9999 0 -0.19 3 3
CBL 0.017 0 -9999 0 -10000 0 0
mol:NO 0.03 0.042 -9999 0 -0.19 3 3
FLT1 0.025 0.019 -9999 0 -0.28 2 2
PGF 0 0.084 -9999 0 -0.41 21 21
VEGFR1 homodimer/NRP2/VEGFR121 -0.093 0.12 -9999 0 -0.2 290 290
CALM1 0.016 0.004 -9999 0 -10000 0 0
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
eNOS/Hsp90 0.039 0.042 -9999 0 -0.2 2 2
endothelial cell proliferation 0.021 0.04 -9999 0 -0.17 23 23
mol:Ca2+ 0.018 0.047 -9999 0 -0.2 23 23
MAPK3 0.019 0.04 -9999 0 -0.17 23 23
MAPK1 0.018 0.04 -9999 0 -0.17 23 23
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
PLGF homodimer 0 0.084 -9999 0 -0.41 21 21
PRKACA 0.017 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.25 0.21 -9999 0 -0.41 324 324
VEGFA homodimer -0.22 0.21 -9999 0 -0.41 287 287
VEGFR1 homodimer/VEGFA homodimer -0.11 0.13 -9999 0 -0.23 289 289
platelet activating factor biosynthetic process 0.02 0.039 -9999 0 -10000 0 0
PI3K 0.026 0.069 -9999 0 -0.2 43 43
PRKCA 0.018 0.043 -9999 0 -0.18 23 23
PRKCB 0.013 0.042 -9999 0 -0.19 23 23
VEGFR1 homodimer/PLGF homodimer 0.021 0.053 -9999 0 -0.23 23 23
VEGFA -0.22 0.21 -9999 0 -0.41 287 287
VEGFB 0.017 0 -9999 0 -10000 0 0
mol:IP3 0.019 0.047 -9999 0 -0.2 23 23
RASA1 0.027 0.014 -9999 0 -0.2 2 2
NRP2 0.016 0.019 -9999 0 -0.41 1 1
VEGFR1 homodimer 0.025 0.018 -9999 0 -0.27 2 2
VEGFB homodimer 0.017 0 -9999 0 -10000 0 0
NCK1 0.008 0.061 -9999 0 -0.41 11 11
eNOS/Caveolin-1 -0.079 0.1 -9999 0 -0.25 34 34
PTPN11 0.017 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.025 0.068 -9999 0 -0.19 43 43
mol:L-citrulline 0.03 0.042 -9999 0 -0.19 3 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.1 0.13 -9999 0 -0.2 314 314
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.097 0.12 -9999 0 -0.2 298 298
CD2AP -0.023 0.12 -9999 0 -0.41 49 49
PI3K/GAB1 0.031 0.071 -9999 0 -0.2 27 27
PDPK1 0.014 0.06 -9999 0 -0.36 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.092 0.12 -9999 0 -0.2 289 289
mol:NADP 0.03 0.042 -9999 0 -0.19 3 3
HSP90AA1 0.017 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.099 0.13 -9999 0 -0.2 314 314
VEGFR1 homodimer/NRP2 0.031 0.019 -9999 0 -0.23 3 3
PDGFR-alpha 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
PDGFRA -0.032 0.13 -9999 0 -0.42 51 51
PDGF/PDGFRA/CRKL -0.007 0.089 -9999 0 -0.28 51 51
positive regulation of JUN kinase activity -0.014 0.092 -9999 0 -0.21 92 92
CRKL 0.017 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.007 0.089 -9999 0 -0.28 51 51
AP1 -0.09 0.19 -9999 0 -0.41 125 125
mol:IP3 -0.021 0.091 -9999 0 -0.29 51 51
PLCG1 -0.021 0.091 -9999 0 -0.29 51 51
PDGF/PDGFRA/alphaV Integrin -0.016 0.1 -9999 0 -0.28 67 67
RAPGEF1 0.017 0 -9999 0 -10000 0 0
CRK 0.017 0 -9999 0 -10000 0 0
mol:Ca2+ -0.021 0.091 -9999 0 -0.29 51 51
CAV3 0.017 0 -9999 0 -10000 0 0
CAV1 -0.25 0.21 -9999 0 -0.41 324 324
SHC/Grb2/SOS1 -0.013 0.092 -9999 0 -0.21 92 92
PDGF/PDGFRA/Shf -0.021 0.087 -9999 0 -0.28 51 51
FOS -0.092 0.18 -9999 0 -0.41 125 125
JUN -0.011 0.027 -9999 0 -0.34 1 1
oligodendrocyte development -0.016 0.1 -9999 0 -0.28 67 67
GRB2 0.017 0.002 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
mol:DAG -0.021 0.091 -9999 0 -0.29 51 51
PDGF/PDGFRA -0.032 0.13 -9999 0 -0.42 51 51
actin cytoskeleton reorganization -0.007 0.089 -9999 0 -0.28 51 51
SRF 0.021 0.007 -9999 0 -10000 0 0
SHC1 -0.02 0.12 -9999 0 -0.41 46 46
PI3K -0.006 0.093 -9999 0 -0.24 69 69
PDGF/PDGFRA/Crk/C3G 0.007 0.077 -9999 0 -0.23 51 51
JAK1 -0.016 0.087 -9999 0 -0.28 51 51
ELK1/SRF -0.004 0.062 -9999 0 -0.18 51 51
SHB 0.017 0 -9999 0 -10000 0 0
SHF 0 0 -9999 0 -10000 0 0
CSNK2A1 0.023 0.014 -9999 0 -10000 0 0
GO:0007205 -0.022 0.086 -9999 0 -0.28 51 51
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.014 0.092 -9999 0 -0.21 92 92
PDGF/PDGFRA/SHB -0.007 0.089 -9999 0 -0.28 51 51
PDGF/PDGFRA/Caveolin-1 -0.2 0.17 -9999 0 -0.31 347 347
ITGAV 0.004 0.074 -9999 0 -0.41 16 16
ELK1 -0.021 0.077 -9999 0 -0.24 51 51
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
PDGF/PDGFRA/Crk -0.007 0.089 -9999 0 -0.28 51 51
JAK-STAT cascade -0.016 0.087 -9999 0 -0.28 51 51
cell proliferation -0.021 0.086 -9999 0 -0.28 51 51
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.14 0.16 -9999 0 -0.29 290 290
PDGFRB 0.014 0.032 -9999 0 -0.42 3 3
SPHK1 -0.005 0.04 -9999 0 -0.2 19 19
mol:S1P -0.005 0.05 -9999 0 -0.21 25 25
S1P1/S1P/Gi -0.08 0.1 -9999 0 -0.27 84 84
GNAO1 0.002 0.005 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.064 0.088 -9999 0 -0.23 79 79
PLCG1 -0.068 0.093 -9999 0 -0.24 85 85
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.014 0.032 -9999 0 -0.41 3 3
GNAI2 0.022 0.004 -9999 0 -10000 0 0
GNAI3 -0.036 0.14 -9999 0 -0.41 65 65
GNAI1 0.013 0.02 -9999 0 -0.41 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.11 0.14 -9999 0 -0.23 290 290
S1P1/S1P -0.074 0.11 -9999 0 -0.28 42 42
negative regulation of cAMP metabolic process -0.079 0.099 -9999 0 -0.26 84 84
MAPK3 -0.076 0.11 -9999 0 -0.29 76 76
calcium-dependent phospholipase C activity 0 0.002 -9999 0 -10000 0 0
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.013 0.001 -9999 0 -10000 0 0
KDR 0.007 0.076 -9999 0 -0.41 17 17
PLCB2 -0.067 0.1 -9999 0 -0.26 41 41
RAC1 0.017 0 -9999 0 -10000 0 0
RhoA/GTP -0.069 0.092 -9999 0 -0.25 41 41
receptor internalization -0.071 0.1 -9999 0 -0.27 42 42
PTGS2 -0.084 0.12 -9999 0 -0.32 72 72
Rac1/GTP -0.069 0.092 -9999 0 -0.25 40 40
RHOA 0.017 0.001 -9999 0 -10000 0 0
VEGFA -0.21 0.21 -9999 0 -0.4 287 287
negative regulation of T cell proliferation -0.079 0.099 -9999 0 -0.26 84 84
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.015 0.006 -9999 0 -10000 0 0
MAPK1 -0.075 0.11 -9999 0 -0.29 74 74
S1P1/S1P/PDGFB-D/PDGFRB -0.07 0.12 -9999 0 -0.25 75 75
ABCC1 0.01 0.056 -9999 0 -0.41 9 9
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.11 0.059 -10000 0 -0.13 455 455
epithelial cell differentiation 0.029 0.042 -10000 0 -0.19 18 18
CYFIP2 0.01 0.008 -10000 0 -10000 0 0
ENAH 0.008 0.071 -10000 0 -0.26 20 20
EGFR -0.14 0.21 -10000 0 -0.41 194 194
EPHA2 0.007 0.067 -10000 0 -0.41 13 13
MYO6 0.018 0.037 -10000 0 -0.18 18 18
CTNNB1 0.017 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.02 0.017 -10000 0 -10000 0 0
AQP5 0.027 0.033 -10000 0 -10000 0 0
CTNND1 0.009 0.059 -10000 0 -0.41 10 10
mol:PI-4-5-P2 0.017 0.036 -10000 0 -0.18 17 17
regulation of calcium-dependent cell-cell adhesion 0.018 0.037 -10000 0 -0.18 18 18
EGF 0.015 0.026 -10000 0 -0.41 2 2
NCKAP1 0.017 0 -10000 0 -10000 0 0
AQP3 0.024 0.045 -10000 0 -0.32 3 3
cortical microtubule organization 0.029 0.042 -10000 0 -0.19 18 18
GO:0000145 0.012 0.034 -10000 0 -0.17 17 17
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.043 -10000 0 -0.19 18 18
MLLT4 0.017 0 -10000 0 -10000 0 0
ARF6/GDP -0.019 0.068 -10000 0 -0.35 15 15
ARF6 0.017 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.022 0.085 -10000 0 -0.26 38 38
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.015 0.078 -10000 0 -0.22 39 39
PVRL2 0.017 0 -10000 0 -10000 0 0
ZYX -0.033 0.099 -10000 0 -0.19 140 140
ARF6/GTP 0.028 0.08 -10000 0 -0.24 38 38
CDH1 0.011 0.052 -10000 0 -0.41 8 8
EGFR/EGFR/EGF/EGF -0.05 0.11 -10000 0 -0.18 207 207
RhoA/GDP 0.03 0.039 -10000 0 -0.18 18 18
actin cytoskeleton organization 0.019 0.035 -10000 0 -0.17 18 18
IGF-1R heterotetramer 0.017 0 -10000 0 -10000 0 0
GIT1 0.017 0 -10000 0 -10000 0 0
IGF1R 0.017 0 -10000 0 -10000 0 0
IGF1 0.014 0.037 -10000 0 -0.41 4 4
DIAPH1 -0.13 0.2 -10000 0 -0.36 224 224
Wnt receptor signaling pathway -0.029 0.042 0.19 18 -10000 0 18
RHOA 0.017 0.001 -10000 0 -10000 0 0
RhoA/GTP -0.019 0.068 -10000 0 -0.35 15 15
CTNNA1 0.017 0 -10000 0 -10000 0 0
VCL 0.019 0.036 -10000 0 -0.17 18 18
EFNA1 -0.002 0.09 -10000 0 -0.41 24 24
LPP 0.003 0.069 -10000 0 -0.19 55 55
Ephrin A1/EPHA2 0.012 0.071 -10000 0 -0.2 47 47
SEC6/SEC8 -0.005 0.029 -10000 0 -0.16 18 18
MGAT3 0.018 0.037 -10000 0 -0.18 18 18
HGF/MET 0.022 0.052 -10000 0 -0.19 27 27
HGF 0.015 0.026 -10000 0 -0.41 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.11 0.059 -10000 0 -0.13 455 455
actin cable formation -0.006 0.07 -10000 0 -0.23 25 25
KIAA1543 0.007 0.034 -10000 0 -0.18 18 18
KIFC3 0.018 0.037 -10000 0 -0.18 18 18
NCK1 0.008 0.061 -10000 0 -0.41 11 11
EXOC3 0.017 0 -10000 0 -10000 0 0
ACTN1 0.002 0.072 -10000 0 -0.2 54 54
NCK1/GIT1 0.019 0.044 -10000 0 -0.28 11 11
mol:GDP 0.029 0.042 -10000 0 -0.19 18 18
EXOC4 0 0 -10000 0 -10000 0 0
STX4 0.018 0.037 -10000 0 -0.18 18 18
PIP5K1C 0.018 0.037 -10000 0 -0.18 17 17
LIMA1 -0.35 0.15 -10000 0 -0.41 453 453
ABI1 0.017 0 -10000 0 -10000 0 0
ROCK1 0.015 0.069 -10000 0 -0.31 15 15
adherens junction assembly 0.015 0.037 -10000 0 -0.17 11 11
IGF-1R heterotetramer/IGF1 0.025 0.044 -10000 0 -0.19 20 20
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.025 0 -10000 0 -10000 0 0
MET 0.009 0.059 -10000 0 -0.41 10 10
PLEKHA7 0.007 0.036 -10000 0 -0.18 18 18
mol:GTP 0.021 0.084 -10000 0 -0.26 38 38
establishment of epithelial cell apical/basal polarity 0.026 0.034 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.11 0.059 -10000 0 -0.13 455 455
regulation of cell-cell adhesion 0.019 0.035 -10000 0 -0.17 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.11 0.059 -10000 0 -0.13 455 455
Noncanonical Wnt signaling pathway

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
NFATC2 0 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.035 0.096 -9999 0 -0.25 51 51
mol:DAG -0.031 0.088 -9999 0 -0.23 51 51
PLCG1 -0.032 0.09 -9999 0 -0.24 51 51
YES1 -0.072 0.13 -9999 0 -0.28 110 110
FZD3 0.014 0.032 -9999 0 -0.41 3 3
FZD6 -0.064 0.17 -9999 0 -0.41 100 100
G protein -0.031 0.092 -9999 0 -0.24 51 51
MAP3K7 -0.02 0.074 -9999 0 -0.19 48 48
mol:Ca2+ -0.031 0.086 -9999 0 -0.22 51 51
mol:IP3 -0.031 0.088 -9999 0 -0.23 51 51
NLK 0.017 0.056 -9999 0 -0.71 3 3
GNB1 0.017 0.002 -9999 0 -10000 0 0
CAMK2A -0.024 0.079 -9999 0 -0.21 47 47
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.047 0.1 -9999 0 -0.16 220 220
CSNK1A1 0.017 0 -9999 0 -10000 0 0
GNAS -0.041 0.096 -9999 0 -0.26 51 51
GO:0007205 -0.032 0.085 -9999 0 -0.22 51 51
WNT6 0.017 0 -9999 0 -10000 0 0
WNT4 0.015 0.026 -9999 0 -0.41 2 2
NFAT1/CK1 alpha -0.055 0.12 -9999 0 -0.25 110 110
GNG2 0 0 -9999 0 -10000 0 0
WNT5A -0.12 0.2 -9999 0 -0.41 168 168
WNT11 0.015 0.026 -9999 0 -0.41 2 2
CDC42 -0.065 0.13 -9999 0 -0.27 110 110
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.023 0.031 -9999 0 -0.28 5 5
CRKL 0.017 0 -9999 0 -10000 0 0
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
DOCK1 0.017 0 -9999 0 -10000 0 0
ITGA4 0.013 0.042 -9999 0 -0.41 5 5
alpha4/beta7 Integrin/MAdCAM1 0.041 0.034 -9999 0 -0.29 5 5
EPO 0.017 0 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.022 0.041 -9999 0 -0.38 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.017 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.023 0.03 -9999 0 -0.28 5 5
EPO/EPOR (dimer) 0.025 0 -9999 0 -10000 0 0
lamellipodium assembly 0.01 0.037 -9999 0 -0.15 25 25
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
PI3K 0.009 0.065 -9999 0 -0.28 25 25
ARF6 0.017 0 -9999 0 -10000 0 0
JAK2 0.028 0.016 -9999 0 -0.14 5 5
PXN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
MADCAM1 0.017 0 -9999 0 -10000 0 0
cell adhesion 0.039 0.034 -9999 0 -0.29 5 5
CRKL/CBL 0.025 0 -9999 0 -10000 0 0
ITGB1 0.017 0 -9999 0 -10000 0 0
SRC -0.13 0.11 -9999 0 -0.21 353 353
ITGB7 0.015 0.026 -9999 0 -0.41 2 2
RAC1 0.017 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.15 0.13 -9999 0 -0.24 353 353
p130Cas/Crk/Dock1 -0.1 0.099 -9999 0 -0.17 353 353
VCAM1 -0.27 0.2 -9999 0 -0.41 351 351
RHOA 0.017 0.001 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.042 0.024 -9999 0 -0.21 5 5
BCAR1 -0.12 0.1 -9999 0 -0.19 353 353
EPOR 0.017 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.017 0 -9999 0 -10000 0 0
GIT1 0.017 0 -9999 0 -10000 0 0
Rac1/GTP 0.01 0.038 -9999 0 -0.16 25 25
FAS signaling pathway (CD95)

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
SPTAN1 -0.025 0.057 -10000 0 -0.14 103 103
RFC1 -0.025 0.058 -10000 0 -0.14 105 105
PRKDC -0.035 0.077 -10000 0 -0.17 119 119
RIPK1 0.01 0.056 -10000 0 -0.41 9 9
CASP7 -0.009 0.072 -10000 0 -0.23 31 31
FASLG/FAS/FADD/FAF1 -0.002 0.062 0.14 25 -0.15 65 90
MAP2K4 0.001 0.078 -10000 0 -0.21 37 37
mol:ceramide 0.01 0.069 -10000 0 -0.22 23 23
GSN -0.031 0.069 -10000 0 -0.16 117 117
FASLG/FAS/FADD/FAF1/Caspase 8 0.006 0.064 0.13 24 -0.19 25 49
FAS -0.039 0.14 -10000 0 -0.42 68 68
BID -0.004 0.045 0.14 1 -0.25 17 18
MAP3K1 -0.014 0.079 -10000 0 -0.22 40 40
MAP3K7 0.016 0.019 -10000 0 -0.41 1 1
RB1 -0.025 0.058 -10000 0 -0.14 105 105
CFLAR 0.013 0.041 -10000 0 -0.41 5 5
HGF/MET 0.014 0.074 -10000 0 -0.24 41 41
ARHGDIB -0.045 0.089 -10000 0 -0.18 140 140
FADD 0.015 0.027 -10000 0 -0.41 2 2
actin filament polymerization 0.031 0.069 0.15 117 -10000 0 117
NFKB1 0.007 0.045 -10000 0 -0.24 2 2
MAPK8 0 0.094 -10000 0 -0.24 53 53
DFFA -0.025 0.058 -10000 0 -0.14 105 105
DNA fragmentation during apoptosis -0.025 0.058 -10000 0 -0.14 105 105
FAS/FADD/MET -0.007 0.099 -10000 0 -0.24 79 79
CFLAR/RIP1 0.018 0.05 -10000 0 -0.28 14 14
FAIM3 0.016 0.019 -10000 0 -0.41 1 1
FAF1 0.016 0.007 -10000 0 -10000 0 0
PARP1 -0.025 0.058 -10000 0 -0.14 105 105
DFFB -0.025 0.058 -10000 0 -0.14 105 105
CHUK 0.009 0.042 -10000 0 -0.21 3 3
FASLG 0.016 0.007 -10000 0 -10000 0 0
FAS/FADD -0.017 0.11 -10000 0 -0.29 70 70
HGF 0.015 0.026 -10000 0 -0.41 2 2
LMNA -0.033 0.081 -10000 0 -0.27 34 34
CASP6 -0.037 0.08 -10000 0 -0.17 121 121
CASP10 0.017 0.004 -10000 0 -10000 0 0
CASP3 -0.033 0.066 -10000 0 -0.16 105 105
PTPN13 -0.007 0.099 -10000 0 -0.41 30 30
CASP8 -0.01 0.041 0.22 1 -0.3 10 11
IL6 -0.011 0.13 -10000 0 -0.39 52 52
MET 0.009 0.059 -10000 0 -0.41 10 10
ICAD/CAD -0.019 0.054 -10000 0 -0.14 12 12
FASLG/FAS/FADD/FAF1/Caspase 10 0.01 0.069 -10000 0 -0.22 23 23
activation of caspase activity by cytochrome c -0.004 0.044 0.14 1 -0.25 17 18
PAK2 -0.035 0.08 -10000 0 -0.17 118 118
BCL2 0.017 0 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.025 0.094 -10000 0 -0.29 59 59
TP53 -0.02 0.067 0.17 13 -0.17 57 70
Senescence -0.02 0.067 0.17 13 -0.17 57 70
Apoptosis -0.02 0.067 0.17 13 -0.17 57 70
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.009 0.071 0.16 53 -0.26 18 71
MDM4 0.007 0.067 -10000 0 -0.41 13 13
Circadian rhythm pathway

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
chromatin modification -0.046 0.19 -10000 0 -0.42 99 99
CLOCK 0.009 0.038 -10000 0 -0.44 3 3
TIMELESS/CRY2 -0.035 0.15 -10000 0 -0.35 99 99
DEC1/BMAL1 0.024 0.007 -10000 0 -10000 0 0
ATR 0.017 0 -10000 0 -10000 0 0
NR1D1 -0.006 0.08 -10000 0 -0.17 98 98
ARNTL 0.012 0.016 -10000 0 -10000 0 0
TIMELESS -0.046 0.16 -10000 0 -0.38 99 99
NPAS2 0.011 0.024 -10000 0 -0.41 1 1
CRY2 0.017 0 -10000 0 -10000 0 0
mol:CO 0.005 0.034 0.077 99 -10000 0 99
CHEK1 -0.033 0.14 -10000 0 -0.41 61 61
mol:HEME -0.005 0.034 -10000 0 -0.077 99 99
PER1 0.015 0.032 -10000 0 -0.41 3 3
BMAL/CLOCK/NPAS2 0.026 0.05 -10000 0 -0.29 4 4
BMAL1/CLOCK -0.003 0.1 -10000 0 -0.34 4 4
S phase of mitotic cell cycle -0.046 0.19 -10000 0 -0.42 99 99
TIMELESS/CHEK1/ATR -0.046 0.19 -10000 0 -0.43 99 99
mol:NADPH -0.005 0.034 -10000 0 -0.077 99 99
PER1/TIMELESS -0.036 0.15 -10000 0 -0.35 99 99
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.017 0 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.028 0.078 -9999 0 -0.16 131 131
DAPP1 -0.015 0.088 -9999 0 -0.2 75 75
Src family/SYK family/BLNK-LAT/BTK-ITK -0.035 0.14 -9999 0 -0.3 90 90
mol:DAG -0.019 0.078 -9999 0 -0.16 92 92
HRAS 0.01 0.022 -9999 0 -0.41 1 1
RAP1A 0.015 0.004 -9999 0 -10000 0 0
ARF5/GDP 0.003 0.053 -9999 0 -0.19 25 25
PLCG2 0.009 0.059 -9999 0 -0.41 10 10
PLCG1 0.017 0 -9999 0 -10000 0 0
ARF5 0.017 0 -9999 0 -10000 0 0
mol:GTP -0.039 0.078 -9999 0 -0.17 131 131
ARF1/GTP -0.033 0.073 -9999 0 -0.16 131 131
RHOA 0.017 0.001 -9999 0 -10000 0 0
YES1 -0.047 0.15 -9999 0 -0.41 79 79
RAP1A/GTP -0.032 0.082 -9999 0 -0.17 131 131
ADAP1 -0.037 0.075 -9999 0 -0.17 131 131
ARAP3 -0.038 0.077 -9999 0 -0.17 131 131
INPPL1 0.017 0 -9999 0 -10000 0 0
PREX1 0 0 -9999 0 -10000 0 0
ARHGEF6 0.01 0.053 -9999 0 -0.41 8 8
ARHGEF7 0.016 0.019 -9999 0 -0.41 1 1
ARF1 0.017 0.001 -9999 0 -10000 0 0
NRAS -0.093 0.19 -9999 0 -0.41 136 136
FYN 0.015 0.027 -9999 0 -0.41 2 2
ARF6 0.017 0 -9999 0 -10000 0 0
FGR 0.003 0.076 -9999 0 -0.41 17 17
mol:Ca2+ -0.006 0.042 -9999 0 -0.12 18 18
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.016 0.003 -9999 0 -10000 0 0
ZAP70 0.017 0 -9999 0 -10000 0 0
mol:IP3 -0.01 0.057 -9999 0 -0.12 62 62
LYN -0.035 0.14 -9999 0 -0.41 64 64
ARF1/GDP 0.003 0.053 -9999 0 -0.19 25 25
RhoA/GDP -0.018 0.08 -9999 0 -0.15 131 131
PDK1/Src/Hsp90 0.035 0 -9999 0 -10000 0 0
BLNK -0.038 0.14 -9999 0 -0.41 68 68
actin cytoskeleton reorganization -0.012 0.069 -9999 0 -0.18 11 11
SRC 0.017 0 -9999 0 -10000 0 0
PLEKHA2 0.011 0.011 -9999 0 -0.24 1 1
RAC1 0.017 0 -9999 0 -10000 0 0
PTEN 0.019 0.027 -9999 0 -0.41 2 2
HSP90AA1 0.017 0 -9999 0 -10000 0 0
ARF6/GTP -0.028 0.078 -9999 0 -0.16 131 131
RhoA/GTP -0.027 0.079 -9999 0 -0.16 131 131
Src family/SYK family/BLNK-LAT -0.032 0.13 -9999 0 -0.29 90 90
BLK 0.017 0 -9999 0 -10000 0 0
PDPK1 0.017 0 -9999 0 -10000 0 0
CYTH1 -0.037 0.075 -9999 0 -0.17 131 131
HCK -0.053 0.16 -9999 0 -0.41 86 86
CYTH3 -0.037 0.075 -9999 0 -0.17 131 131
CYTH2 -0.037 0.075 -9999 0 -0.17 131 131
KRAS 0.011 0.011 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.004 0.044 -9999 0 -10000 0 0
SGK1 -0.008 0.047 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.006 0.053 -9999 0 -0.21 25 25
SOS1 0 0 -9999 0 -10000 0 0
SYK -0.012 0.11 -9999 0 -0.41 36 36
ARF6/GDP -0.021 0.076 -9999 0 -0.15 131 131
mol:PI-3-4-5-P3 -0.038 0.079 -9999 0 -0.17 131 131
ARAP3/RAP1A/GTP -0.032 0.083 -9999 0 -0.17 131 131
VAV1 0.016 0.019 -9999 0 -0.41 1 1
mol:PI-3-4-P2 0.009 0 -9999 0 -10000 0 0
RAS family/GTP/PI3K Class I -0.024 0.089 -9999 0 -0.18 131 131
PLEKHA1 0.01 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.003 0.053 -9999 0 -0.19 25 25
LAT 0.016 0.019 -9999 0 -0.41 1 1
Rac1/GTP 0.011 0.041 -9999 0 -0.21 11 11
ITK -0.034 0.08 -9999 0 -0.17 133 133
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.03 0.1 -9999 0 -0.21 92 92
LCK 0.014 0.037 -9999 0 -0.41 4 4
BTK -0.032 0.077 -9999 0 -0.16 132 132
Aurora A 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
Aurora A/GADD45A 0.002 0.077 -9999 0 -0.23 47 47
BIRC5 -0.16 0.21 -9999 0 -0.41 211 211
NFKBIA 0.017 0.031 -9999 0 -0.13 17 17
CPEB1 0.013 0.007 -9999 0 -10000 0 0
AKT1 0.016 0.036 -9999 0 -0.14 23 23
NDEL1 0.016 0.004 -9999 0 -10000 0 0
Aurora A/BRCA1 0.02 0.036 -9999 0 -0.14 22 22
NDEL1/TACC3 -0.009 0.093 -9999 0 -0.2 92 92
GADD45A -0.02 0.12 -9999 0 -0.41 46 46
GSK3B 0.019 0.007 -9999 0 -10000 0 0
PAK1/Aurora A 0.024 0.03 -9999 0 -0.12 19 19
MDM2 0.002 0.078 -9999 0 -0.41 18 18
JUB 0 0 -9999 0 -10000 0 0
TPX2 -0.15 0.15 -9999 0 -0.29 295 295
TP53 -0.001 0.065 -9999 0 -0.14 81 81
DLG7 -0.092 0.13 -9999 0 -0.24 230 230
AURKAIP1 0.017 0 -9999 0 -10000 0 0
ARHGEF7 0.016 0.019 -9999 0 -0.41 1 1
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.01 0.099 -9999 0 -0.22 92 92
G2/M transition of mitotic cell cycle 0.02 0.036 -9999 0 -0.14 22 22
AURKA 0.018 0.036 -9999 0 -0.15 19 19
AURKB -0.002 0.047 -9999 0 -0.18 30 30
CDC25B 0.015 0.039 -9999 0 -0.13 30 30
G2/M transition checkpoint 0.01 0.025 -9999 0 -0.11 19 19
mRNA polyadenylation 0.017 0.022 -9999 0 -0.11 8 8
Aurora A/CPEB 0.017 0.022 -9999 0 -0.11 8 8
Aurora A/TACC1/TRAP/chTOG 0.042 0.027 -9999 0 -10000 0 0
BRCA1 0.013 0.042 -9999 0 -0.41 5 5
centrosome duplication 0.024 0.03 -9999 0 -0.12 19 19
regulation of centrosome cycle -0.009 0.092 -9999 0 -0.2 92 92
spindle assembly 0.041 0.027 -9999 0 -10000 0 0
TDRD7 0.017 0.001 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.05 0.12 -9999 0 -0.19 207 207
CENPA -0.003 0.054 -9999 0 -0.12 85 85
Aurora A/PP2A 0.024 0.03 -9999 0 -0.12 19 19
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process -0.051 0.091 -9999 0 -0.16 194 194
negative regulation of DNA binding -0.001 0.065 -9999 0 -0.14 81 81
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.025 0.014 -9999 0 -0.28 1 1
RASA1 0.017 0.002 -9999 0 -10000 0 0
Ajuba/Aurora A 0.011 0.025 -9999 0 -0.11 19 19
mitotic prometaphase 0 0.009 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.036 -9999 0 -0.15 19 19
TACC1 0.017 0.001 -9999 0 -10000 0 0
TACC3 -0.061 0.17 -9999 0 -0.41 96 96
Aurora A/Antizyme1 0.033 0.028 -9999 0 -10000 0 0
Aurora A/RasGAP 0.024 0.03 -9999 0 -0.12 16 16
OAZ1 0.017 0 -9999 0 -10000 0 0
RAN 0.017 0.001 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.019 0.007 -9999 0 -10000 0 0
GIT1 0.017 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.034 0.012 -9999 0 -0.24 1 1
Importin alpha/Importin beta/TPX2 -0.15 0.15 -9999 0 -0.28 295 295
PPP2R5D 0.017 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.1 0.12 -9999 0 -0.21 296 296
PAK1 0.017 0 -9999 0 -10000 0 0
CKAP5 0.017 0 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.021 0.11 -10000 0 -0.21 127 127
MAP3K8 -0.018 0.12 -10000 0 -0.42 42 42
FOS -0.012 0.069 -10000 0 -0.18 20 20
PRKCA 0.013 0.009 -10000 0 -10000 0 0
PTPN7 0.011 0.022 -10000 0 -0.41 1 1
HRAS 0.016 0.019 -10000 0 -0.41 1 1
PRKCB -0.002 0.006 0.01 2 -0.012 125 127
NRAS -0.094 0.19 -10000 0 -0.41 136 136
RAS family/GTP -0.034 0.1 -10000 0 -0.21 133 133
MAPK3 0.004 0.038 -10000 0 -0.19 1 1
MAP2K1 -0.009 0.048 -10000 0 -0.14 29 29
ELK1 0.011 0.013 -10000 0 -10000 0 0
BRAF -0.003 0.028 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 0.002 1 -0.004 125 126
MAPK1 -0.005 0.062 -10000 0 -0.27 18 18
RAF1 -0.003 0.029 -10000 0 -0.17 1 1
KRAS 0.016 0.002 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.02 0.048 -10000 0 -0.16 31 31
adherens junction organization 0.02 0.038 -10000 0 -0.18 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.042 0.1 -10000 0 -0.16 196 196
FMN1 0.019 0.038 -10000 0 -0.19 10 10
mol:IP3 0.017 0.048 -10000 0 -0.17 26 26
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.02 0.04 -10000 0 -0.2 10 10
CTNNB1 0.017 0.002 -10000 0 -10000 0 0
AKT1 0.02 0.051 -10000 0 -0.16 30 30
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.028 0.041 -10000 0 -0.25 6 6
CTNND1 0.009 0.059 -10000 0 -0.41 10 10
mol:PI-4-5-P2 0.022 0.04 -10000 0 -0.19 11 11
VASP 0.022 0.04 -10000 0 -0.19 11 11
ZYX -0.026 0.094 -10000 0 -0.18 137 137
JUB 0.019 0.038 -10000 0 -0.19 10 10
EGFR(dimer) -0.046 0.11 -10000 0 -0.18 202 202
E-cadherin/beta catenin-gamma catenin 0.022 0.063 -10000 0 -0.29 19 19
mol:PI-3-4-5-P3 0.024 0.052 -10000 0 -0.17 26 26
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
PI3K 0.024 0.053 -10000 0 -0.18 26 26
FYN 0.023 0.044 -10000 0 -0.14 27 27
mol:Ca2+ 0.017 0.047 -10000 0 -0.16 26 26
JUP 0.004 0.073 -10000 0 -0.41 16 16
PIK3R1 0.016 0.005 -10000 0 -10000 0 0
mol:DAG 0.017 0.048 -10000 0 -0.17 26 26
CDH1 0.011 0.052 -10000 0 -0.41 8 8
RhoA/GDP -0.042 0.1 -10000 0 -0.16 196 196
establishment of polarity of embryonic epithelium 0.022 0.039 -10000 0 -0.19 11 11
SRC 0.017 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
RHOA 0.017 0.001 -10000 0 -10000 0 0
EGFR -0.14 0.21 -10000 0 -0.41 194 194
CASR 0.018 0.045 -10000 0 -0.15 26 26
RhoA/GTP 0.023 0.045 -10000 0 -0.15 26 26
AKT2 0.022 0.048 -10000 0 -0.16 26 26
actin cable formation 0.021 0.039 -10000 0 -0.18 11 11
apoptosis -0.019 0.048 0.16 31 -10000 0 31
CTNNA1 0.018 0.002 -10000 0 -10000 0 0
mol:GDP -0.051 0.1 -10000 0 -0.17 207 207
PIP5K1A 0.022 0.04 -10000 0 -0.19 11 11
PLCG1 0.017 0.048 -10000 0 -0.17 26 26
Rac1/GTP -0.038 0.1 -10000 0 -0.16 201 201
homophilic cell adhesion 0 0.002 -10000 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0 0.078 -10000 0 -0.19 53 53
IKBKB 0.007 0.051 -10000 0 -0.17 17 17
AKT1 -0.013 0.069 0.18 1 -0.17 58 59
IKBKG 0.007 0.053 -10000 0 -0.16 24 24
CALM1 -0.011 0.079 -10000 0 -0.25 38 38
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
MAP3K1 -0.01 0.095 -10000 0 -0.23 58 58
MAP3K7 0.016 0.019 -10000 0 -0.41 1 1
mol:Ca2+ -0.016 0.087 -10000 0 -0.22 62 62
DOK1 0.017 0 -10000 0 -10000 0 0
AP-1 -0.011 0.071 -10000 0 -0.17 49 49
LYN -0.035 0.14 -10000 0 -0.41 64 64
BLNK -0.038 0.14 -10000 0 -0.41 68 68
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
BCR complex 0.024 0.028 -10000 0 -0.41 2 2
CD22 -0.038 0.11 -10000 0 -0.24 93 93
CAMK2G -0.006 0.058 0.14 1 -0.23 25 26
CSNK2A1 0.017 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.07 0.14 -10000 0 -0.27 135 135
GO:0007205 -0.016 0.087 -10000 0 -0.22 62 62
SYK -0.012 0.11 -10000 0 -0.41 36 36
ELK1 -0.012 0.083 -10000 0 -0.26 40 40
NFATC1 -0.019 0.093 0.14 1 -0.23 65 66
B-cell antigen/BCR complex 0.024 0.028 -10000 0 -0.41 2 2
PAG1/CSK 0.013 0 -10000 0 -10000 0 0
NFKBIB 0.013 0.021 -10000 0 -0.097 1 1
HRAS -0.016 0.094 -10000 0 -0.25 56 56
NFKBIA 0.013 0.021 -10000 0 -0.098 1 1
NF-kappa-B/RelA/I kappa B beta 0.017 0.02 -10000 0 -0.091 4 4
RasGAP/Csk -0.009 0.11 -10000 0 -0.2 125 125
mol:GDP -0.013 0.084 -10000 0 -0.23 50 50
PTEN 0.015 0.026 -10000 0 -0.41 2 2
CD79B 0.016 0.019 -10000 0 -0.41 1 1
NF-kappa-B/RelA/I kappa B alpha 0.017 0.02 -10000 0 -0.092 4 4
GRB2 0.017 0.002 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.024 0.11 -10000 0 -0.29 60 60
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
mol:IP3 -0.016 0.088 -10000 0 -0.22 62 62
CSK 0.017 0 -10000 0 -10000 0 0
FOS -0.051 0.12 -10000 0 -0.22 147 147
CHUK 0.007 0.053 -10000 0 -0.16 25 25
IBTK 0.017 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.006 0.093 -10000 0 -0.22 62 62
PTPN6 -0.037 0.11 -10000 0 -0.25 93 93
RELA 0.017 0 -10000 0 -10000 0 0
BCL2A1 -0.001 0.037 -10000 0 -0.064 129 129
VAV2 -0.034 0.12 -10000 0 -0.29 67 67
ubiquitin-dependent protein catabolic process 0.016 0.021 -10000 0 -0.091 1 1
BTK 0.011 0.009 -10000 0 -10000 0 0
CD19 -0.039 0.11 -10000 0 -0.25 93 93
MAP4K1 0.016 0.019 -10000 0 -0.41 1 1
CD72 0.017 0 -10000 0 -10000 0 0
PAG1 0 0 -10000 0 -10000 0 0
MAPK14 -0.005 0.086 -10000 0 -0.21 59 59
SH3BP5 0.016 0.005 -10000 0 -10000 0 0
PIK3AP1 -0.018 0.09 -10000 0 -0.23 63 63
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.009 0.11 -10000 0 -0.24 74 74
RAF1 -0.012 0.089 -10000 0 -0.26 47 47
RasGAP/p62DOK/SHIP -0.013 0.099 -10000 0 -0.19 125 125
CD79A 0.015 0.026 -10000 0 -0.41 2 2
re-entry into mitotic cell cycle -0.011 0.071 -10000 0 -0.17 49 49
RASA1 0.017 0.002 -10000 0 -10000 0 0
MAPK3 -0.001 0.079 0.16 2 -0.23 40 42
MAPK1 -0.002 0.079 0.26 1 -0.23 40 41
CD72/SHP1 -0.027 0.11 -10000 0 -0.24 93 93
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
MAPK8 -0.004 0.085 -10000 0 -0.21 57 57
actin cytoskeleton organization -0.027 0.1 -10000 0 -0.26 64 64
NF-kappa-B/RelA 0.037 0.036 -10000 0 -0.15 2 2
Calcineurin 0.005 0.069 -10000 0 -0.21 35 35
PI3K -0.061 0.11 -10000 0 -0.3 79 79
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.019 0.095 -10000 0 -0.23 66 66
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.012 0.094 -10000 0 -0.26 23 23
DAPP1 -0.022 0.095 -10000 0 -0.27 38 38
cytokine secretion -0.017 0.088 0.14 1 -0.22 65 66
mol:DAG -0.016 0.088 -10000 0 -0.22 62 62
PLCG2 0.009 0.059 -10000 0 -0.41 10 10
MAP2K1 -0.008 0.083 0.17 1 -0.24 43 44
B-cell antigen/BCR complex/FcgammaRIIB -0.032 0.12 -10000 0 -0.24 128 128
mol:PI-3-4-5-P3 -0.046 0.084 0.27 1 -0.23 73 74
ETS1 0.048 0.091 0.22 18 -0.2 30 48
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.023 0.16 -10000 0 -0.3 111 111
B-cell antigen/BCR complex/LYN -0.043 0.11 -10000 0 -0.22 135 135
MALT1 -0.002 0.09 -10000 0 -0.41 24 24
TRAF6 0.017 0 -10000 0 -10000 0 0
RAC1 -0.029 0.11 -10000 0 -0.28 64 64
B-cell antigen/BCR complex/LYN/SYK -0.042 0.16 -10000 0 -0.37 75 75
CARD11 -0.015 0.083 -10000 0 -0.21 62 62
FCGR2B -0.087 0.18 -10000 0 -0.41 128 128
PPP3CA 0.014 0.007 -10000 0 -10000 0 0
BCL10 0.014 0.037 -10000 0 -0.41 4 4
IKK complex 0.011 0.025 -10000 0 -0.071 9 9
PTPRC -0.086 0.18 -10000 0 -0.41 127 127
PDPK1 -0.016 0.069 0.17 1 -0.16 66 67
PPP3CB 0.017 0.002 -10000 0 -10000 0 0
PPP3CC 0.017 0 -10000 0 -10000 0 0
POU2F2 0.016 0.013 -10000 0 -0.052 2 2
IL1-mediated signaling 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
UBC13/UEV1A 0.013 0.001 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0.017 0 -9999 0 -10000 0 0
ERC1 0.016 0.019 -9999 0 -0.41 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.047 0.1 -9999 0 -0.23 94 94
IRAK/TOLLIP 0.025 0.002 -9999 0 -10000 0 0
IKBKB 0.017 0 -9999 0 -10000 0 0
IKBKG 0.017 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 0 0.085 -9999 0 -0.28 43 43
IL1A 0.015 0.032 -9999 0 -0.41 3 3
IL1B -0.089 0.15 -9999 0 -0.3 179 179
IRAK/TRAF6/p62/Atypical PKCs 0.038 0.013 -9999 0 -0.18 2 2
IL1R2 -0.015 0.11 -9999 0 -0.41 40 40
IL1R1 0.015 0.032 -9999 0 -0.41 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.035 0.09 -9999 0 -0.22 71 71
TOLLIP 0.017 0 -9999 0 -10000 0 0
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.034 0.012 -9999 0 -0.24 1 1
IKK complex/ELKS 0.049 0.015 -9999 0 -0.25 1 1
JUN 0.027 0.012 -9999 0 -10000 0 0
MAP3K7 0.016 0.019 -9999 0 -0.41 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.057 0.14 -9999 0 -0.22 197 197
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.013 0.12 -9999 0 -0.23 111 111
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.004 0.11 -9999 0 -0.21 112 112
IL1 beta fragment/IL1R1/IL1RAP -0.07 0.15 -9999 0 -0.24 199 199
NFKB1 0.014 0.037 -9999 0 -0.41 4 4
MAPK8 0.027 0.009 -9999 0 -10000 0 0
IRAK1 0.016 0.001 -9999 0 -10000 0 0
IL1RN/IL1R1 0.024 0.023 -9999 0 -0.28 3 3
IRAK4 0.016 0.019 -9999 0 -0.41 1 1
PRKCI 0.016 0.019 -9999 0 -0.41 1 1
TRAF6 0.017 0 -9999 0 -10000 0 0
PI3K 0.009 0.065 -9999 0 -0.28 25 25
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.043 0.1 -9999 0 -0.26 72 72
CHUK 0.016 0.019 -9999 0 -0.41 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.07 0.15 -9999 0 -0.24 199 199
IL1 beta/IL1R2 -0.083 0.15 -9999 0 -0.26 202 202
IRAK/TRAF6/TAK1/TAB1/TAB2 0.048 0.01 -9999 0 -0.17 1 1
NF kappa B1 p50/RelA -0.056 0.13 -9999 0 -0.37 41 41
IRAK3 0.015 0.026 -9999 0 -0.41 2 2
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.057 0.14 -9999 0 -0.22 199 199
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.003 0.071 -9999 0 -0.13 112 112
IL1 alpha/IL1R1/IL1RAP 0.009 0.081 -9999 0 -0.24 50 50
RELA 0.017 0 -9999 0 -10000 0 0
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
SQSTM1 0.016 0.019 -9999 0 -0.41 1 1
MYD88 -0.041 0.15 -9999 0 -0.41 71 71
IRAK/TRAF6/MEKK3 0.035 0.002 -9999 0 -10000 0 0
IL1RAP -0.02 0.12 -9999 0 -0.41 45 45
UBE2N 0.017 0.001 -9999 0 -10000 0 0
IRAK/TRAF6 -0.053 0.11 -9999 0 -0.34 33 33
CASP1 -0.12 0.2 -9999 0 -0.41 173 173
IL1RN/IL1R2 0.002 0.082 -9999 0 -0.28 40 40
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.086 0.17 -9999 0 -0.27 221 221
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.004 0.063 -9999 0 -0.23 11 11
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
IL1RN 0.017 0 -9999 0 -10000 0 0
TRAF6/TAK1/TAB1/TAB2 0.042 0.01 -9999 0 -0.18 1 1
MAP2K6 0.027 0.01 -9999 0 -0.17 1 1
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.15 0.16 -9999 0 -0.3 292 292
alphaV beta3 Integrin 0.026 0.049 -9999 0 -0.24 18 18
PTK2 -0.059 0.096 -9999 0 -0.28 29 29
IGF1R 0.017 0 -9999 0 -10000 0 0
PI4KB 0.016 0.019 -9999 0 -0.41 1 1
MFGE8 0.015 0.032 -9999 0 -0.41 3 3
SRC 0.017 0 -9999 0 -10000 0 0
CDKN1B 0.022 0.023 -9999 0 -0.19 2 2
VEGFA -0.22 0.21 -9999 0 -0.41 287 287
ILK 0.022 0.023 -9999 0 -0.19 2 2
ROCK1 0.017 0 -9999 0 -10000 0 0
AKT1 0.021 0.028 -9999 0 -0.18 6 6
PTK2B -0.1 0.12 -9999 0 -0.2 298 298
alphaV/beta3 Integrin/JAM-A 0.021 0.071 -9999 0 -0.19 54 54
CBL 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.027 0.046 -9999 0 -0.24 16 16
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.04 0.033 -9999 0 -0.21 9 9
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.041 0.07 -9999 0 -0.21 21 21
alphaV/beta3 Integrin/Syndecan-1 0.003 0.092 -9999 0 -0.25 59 59
PI4KA 0.006 0.008 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.011 0.1 -9999 0 -0.19 114 114
PI4 Kinase 0.009 0.014 -9999 0 -0.14 1 1
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
alphaV/beta3 Integrin/Osteopontin -0.065 0.14 -9999 0 -0.25 185 185
RPS6KB1 -0.013 0.095 -9999 0 -0.36 13 13
TLN1 -0.02 0.12 -9999 0 -0.41 46 46
MAPK3 0.002 0.07 -9999 0 -0.18 50 50
GPR124 0.014 0.037 -9999 0 -0.41 4 4
MAPK1 0.003 0.069 -9999 0 -0.19 46 46
PXN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.027 0.046 -9999 0 -0.24 16 16
cell adhesion 0.029 0.045 -9999 0 -0.2 20 20
ANGPTL3 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.12 0.14 -9999 0 -0.24 292 292
IGF-1R heterotetramer 0.017 0 -9999 0 -10000 0 0
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.052 -9999 0 -0.41 8 8
ITGB3 0.017 0 -9999 0 -10000 0 0
IGF1 0.014 0.037 -9999 0 -0.41 4 4
RAC1 0.017 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0.024 0.051 -9999 0 -0.23 20 20
apoptosis 0.004 0.073 -9999 0 -0.41 16 16
CD47 0.015 0.026 -9999 0 -0.41 2 2
alphaV/beta3 Integrin/CD47 0.026 0.049 -9999 0 -0.24 18 18
VCL 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.027 0.046 -9999 0 -0.24 16 16
CSF1 0.017 0 -9999 0 -10000 0 0
PIK3C2A 0.012 0.023 -9999 0 -0.2 2 2
PI4 Kinase/Pyk2 -0.055 0.079 -9999 0 -0.28 23 23
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.11 0.14 -9999 0 -0.22 298 298
FAK1/Vinculin -0.045 0.085 -9999 0 -0.23 29 29
alphaV beta3/Integrin/ppsTEM5 0.025 0.051 -9999 0 -0.24 20 20
RHOA 0.017 0.001 -9999 0 -10000 0 0
VTN 0.015 0.026 -9999 0 -0.41 2 2
BCAR1 0 0 -9999 0 -10000 0 0
FGF2 0.015 0.026 -9999 0 -0.41 2 2
F11R -0.003 0.077 -9999 0 -0.29 36 36
alphaV/beta3 Integrin/Lactadherin 0.025 0.05 -9999 0 -0.24 19 19
alphaV/beta3 Integrin/TGFBR2 0.023 0.056 -9999 0 -0.24 24 24
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.026 0.042 -9999 0 -0.21 16 16
HSP90AA1 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.005 0.084 -9999 0 -0.23 57 57
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.065 0.17 -9999 0 -0.41 101 101
alphaV/beta3 Integrin/Pyk2 -0.098 0.13 -9999 0 -0.2 298 298
SDC1 -0.021 0.12 -9999 0 -0.41 47 47
VAV3 0.001 0.069 -9999 0 -0.21 48 48
PTPN11 0.017 0 -9999 0 -10000 0 0
IRS1 0.013 0.042 -9999 0 -0.41 5 5
FAK1/Paxillin -0.045 0.085 -9999 0 -0.23 29 29
cell migration -0.039 0.079 -9999 0 -0.21 29 29
ITGAV 0.004 0.074 -9999 0 -0.41 16 16
PI3K 0.021 0.073 -9999 0 -0.18 52 52
SPP1 -0.13 0.2 -9999 0 -0.41 181 181
KDR 0.003 0.076 -9999 0 -0.41 17 17
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.004 0.074 -9999 0 -0.41 16 16
COL4A3 0.017 0 -9999 0 -10000 0 0
angiogenesis 0.008 0.065 -9999 0 -0.22 19 19
Rac1/GTP 0.011 0.066 -9999 0 -0.19 48 48
EDIL3 0.017 0 -9999 0 -10000 0 0
cell proliferation 0.022 0.056 -9999 0 -0.23 24 24
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.004 0.084 -10000 0 -0.23 52 52
CRKL 0.001 0.088 -10000 0 -0.24 52 52
HRAS 0.008 0.096 -10000 0 -0.23 52 52
mol:PIP3 -0.007 0.086 0.18 3 -0.24 51 54
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0.017 0 -10000 0 -10000 0 0
GAB1 -0.002 0.092 -10000 0 -0.25 61 61
FOXO3 0.005 0.089 -10000 0 -0.24 51 51
AKT1 0.001 0.094 -10000 0 -0.26 51 51
BAD 0.005 0.089 -10000 0 -0.24 51 51
megakaryocyte differentiation 0.001 0.087 0.16 1 -0.24 57 58
GSK3B 0.006 0.089 -10000 0 -0.24 51 51
RAF1 0.011 0.082 -10000 0 -0.19 52 52
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
STAT3 -0.004 0.094 -10000 0 -0.25 63 63
STAT1 -0.003 0.16 -10000 0 -0.44 52 52
HRAS/SPRED1 0.007 0.081 -10000 0 -0.19 52 52
cell proliferation 0 0.09 -10000 0 -0.24 61 61
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
TEC 0.017 0 -10000 0 -10000 0 0
RPS6KB1 0.003 0.094 -10000 0 -0.26 52 52
HRAS/SPRED2 0.015 0.084 -10000 0 -0.19 47 47
LYN/TEC/p62DOK -0.003 0.11 -10000 0 -0.24 56 56
MAPK3 0.018 0.063 -10000 0 -0.2 11 11
STAP1 -0.001 0.093 -10000 0 -0.25 61 61
GRAP2 0.017 0 -10000 0 -10000 0 0
JAK2 0 0.14 -10000 0 -0.4 52 52
STAT1 (dimer) -0.002 0.15 -10000 0 -0.43 52 52
mol:Gleevec -0.001 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.021 0.092 -10000 0 -0.24 52 52
actin filament polymerization -0.004 0.09 -10000 0 -0.25 61 61
LYN -0.035 0.14 -10000 0 -0.41 64 64
STAP1/STAT5A (dimer) 0.005 0.12 -10000 0 -0.33 52 52
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.018 0.086 -10000 0 -0.22 52 52
PI3K 0.008 0.097 -10000 0 -0.25 46 46
PTEN 0.015 0.026 -10000 0 -0.41 2 2
SCF/KIT/EPO/EPOR 0.009 0.17 -10000 0 -0.47 52 52
MAPK8 0 0.091 -10000 0 -0.25 61 61
STAT3 (dimer) -0.004 0.093 -10000 0 -0.24 63 63
positive regulation of transcription 0.018 0.055 -10000 0 -0.17 11 11
mol:GDP 0.007 0.1 -10000 0 -0.24 53 53
PIK3C2B -0.003 0.094 -10000 0 -0.25 64 64
CBL/CRKL 0.011 0.086 -10000 0 -0.23 52 52
FER 0 0.091 -10000 0 -0.25 61 61
SH2B3 -0.004 0.096 -10000 0 -0.26 61 61
PDPK1 -0.004 0.081 0.18 3 -0.22 51 54
SNAI2 -0.047 0.12 -10000 0 -0.29 66 66
positive regulation of cell proliferation -0.001 0.14 -10000 0 -0.38 52 52
KITLG 0.018 0.011 -10000 0 -10000 0 0
cell motility -0.001 0.14 -10000 0 -0.38 52 52
PTPN6 0.008 0.062 -10000 0 -0.42 11 11
EPOR 0.024 0.065 -10000 0 -10000 0 0
STAT5A (dimer) 0.004 0.12 -10000 0 -0.33 52 52
SOCS1 0.017 0 -10000 0 -10000 0 0
cell migration 0 0.09 0.24 61 -10000 0 61
SOS1 0 0 -10000 0 -10000 0 0
EPO 0.018 0.005 -10000 0 -10000 0 0
VAV1 0.016 0.019 -10000 0 -0.41 1 1
GRB10 -0.006 0.1 -10000 0 -0.27 61 61
PTPN11 0.017 0.004 -10000 0 -10000 0 0
SCF/KIT -0.003 0.096 -10000 0 -0.26 61 61
GO:0007205 0 0.006 -10000 0 -10000 0 0
MAP2K1 0.013 0.068 -10000 0 -0.22 13 13
CBL 0.017 0 -10000 0 -10000 0 0
KIT 0.033 0.067 -10000 0 -0.4 11 11
MAP2K2 0.014 0.068 -10000 0 -0.22 13 13
SHC/Grb2/SOS1 -0.005 0.11 -10000 0 -0.28 53 53
STAT5A 0.004 0.12 -10000 0 -0.34 52 52
GRB2 0.017 0.002 -10000 0 -10000 0 0
response to radiation -0.046 0.12 -10000 0 -0.28 66 66
SHC/GRAP2 -0.002 0.088 -10000 0 -0.28 46 46
PTPRO 0.001 0.089 0.16 1 -0.25 57 58
SH2B2 -0.004 0.091 -10000 0 -0.25 61 61
DOK1 0.017 0 -10000 0 -10000 0 0
MATK 0 0.091 -10000 0 -0.25 61 61
CREBBP 0.026 0.03 -10000 0 -10000 0 0
BCL2 0.025 0.064 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.03 0.11 -9999 0 -0.24 105 105
EPHB2 0.015 0.026 -9999 0 -0.41 2 2
Syndecan-2/TACI 0.019 0.036 -9999 0 -0.25 8 8
LAMA1 0 0 -9999 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.009 0.1 -9999 0 -0.21 106 106
HRAS 0.016 0.019 -9999 0 -0.41 1 1
Syndecan-2/CASK 0.007 0.034 -9999 0 -0.25 8 8
ITGA5 -0.043 0.15 -9999 0 -0.41 74 74
BAX 0.018 0.056 -9999 0 -0.3 14 14
EPB41 0.017 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.032 -9999 0 -0.22 8 8
LAMA3 0.005 0.071 -9999 0 -0.41 15 15
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.041 0.15 -9999 0 -0.41 72 72
Syndecan-2/MMP2 -0.1 0.13 -9999 0 -0.24 253 253
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.029 0.12 -9999 0 -0.28 93 93
dendrite morphogenesis 0.018 0.039 -9999 0 -0.24 10 10
Syndecan-2/GM-CSF 0.019 0.036 -9999 0 -0.25 8 8
determination of left/right symmetry 0.01 0.041 -9999 0 -0.24 13 13
Syndecan-2/PKC delta 0.019 0.036 -9999 0 -0.25 8 8
GNB2L1 0.017 0 -9999 0 -10000 0 0
MAPK3 0.019 0.032 -9999 0 -0.22 8 8
MAPK1 0.018 0.032 -9999 0 -0.22 8 8
Syndecan-2/RACK1 0.027 0.033 -9999 0 -0.2 9 9
NF1 0.017 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.041 -9999 0 -0.24 13 13
ITGA2 -0.059 0.16 -9999 0 -0.41 93 93
MAPK8 0.017 0.042 -9999 0 -0.24 13 13
Syndecan-2/alpha2/beta1 Integrin -0.012 0.091 -9999 0 -0.2 99 99
Syndecan-2/Kininogen 0.019 0.037 -9999 0 -0.25 9 9
ITGB1 0.017 0 -9999 0 -10000 0 0
SRC 0.021 0.03 -9999 0 -0.19 9 9
Syndecan-2/CASK/Protein 4.1 0.017 0.032 -9999 0 -0.22 8 8
extracellular matrix organization 0.006 0.067 -9999 0 -0.24 34 34
actin cytoskeleton reorganization -0.03 0.11 -9999 0 -0.24 105 105
Syndecan-2/Caveolin-2/Ras -0.004 0.091 -9999 0 -0.22 76 76
Syndecan-2/Laminin alpha3 0.012 0.056 -9999 0 -0.24 23 23
Syndecan-2/RasGAP 0.034 0.033 -9999 0 -0.19 9 9
alpha5/beta1 Integrin -0.018 0.11 -9999 0 -0.28 74 74
PRKCD 0.017 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.018 0.039 -9999 0 -0.24 10 10
GO:0007205 0.002 0.01 -9999 0 -0.11 1 1
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.033 0.031 -9999 0 -0.18 9 9
RHOA 0.017 0.001 -9999 0 -10000 0 0
SDCBP 0.017 0 -9999 0 -10000 0 0
TNFRSF13B 0.017 0 -9999 0 -10000 0 0
RASA1 0.017 0.002 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.029 0.12 -9999 0 -0.28 93 93
Syndecan-2/Synbindin 0.019 0.036 -9999 0 -0.25 8 8
TGFB1 -0.005 0.095 -9999 0 -0.41 27 27
CASP3 -0.024 0.094 -9999 0 -0.21 104 104
FN1 -0.065 0.17 -9999 0 -0.41 101 101
Syndecan-2/IL8 -0.037 0.11 -9999 0 -0.24 121 121
SDC2 0.01 0.041 -9999 0 -0.24 13 13
KNG1 0.016 0.019 -9999 0 -0.41 1 1
Syndecan-2/Neurofibromin 0.019 0.036 -9999 0 -0.25 8 8
TRAPPC4 0.017 0.001 -9999 0 -10000 0 0
CSF2 0.017 0 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.006 0.067 -9999 0 -0.24 34 34
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.032 -9999 0 -0.22 8 8
Syndecan-2/Ezrin 0.017 0.032 -9999 0 -0.22 8 8
PRKACA 0.019 0.032 -9999 0 -0.22 8 8
angiogenesis -0.037 0.11 -9999 0 -0.24 121 121
MMP2 -0.19 0.22 -9999 0 -0.41 250 250
IL8 -0.076 0.18 -9999 0 -0.41 115 115
calcineurin-NFAT signaling pathway 0.019 0.036 -9999 0 -0.25 8 8
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.032 0.11 -9999 0 -0.18 187 187
Ran/GTP/Exportin 1/HDAC1 -0.021 0.058 -9999 0 -0.17 65 65
NF kappa B1 p50/RelA/I kappa B alpha -0.02 0.086 -9999 0 -0.14 187 187
SUMO1 0.017 0 -9999 0 -10000 0 0
ZFPM1 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.005 -9999 0 -0.11 1 1
FKBP3 0.017 0.001 -9999 0 -10000 0 0
Histones -0.032 0.092 -9999 0 -0.22 68 68
YY1/LSF 0.026 0 -9999 0 -10000 0 0
SMG5 0.017 0 -9999 0 -10000 0 0
RAN 0.017 0.001 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.03 0.081 -9999 0 -0.14 186 186
I kappa B alpha/HDAC1 -0.042 0.096 -9999 0 -0.24 66 66
SAP18 0.017 0 -9999 0 -10000 0 0
RELA -0.02 0.07 -9999 0 -0.12 185 185
HDAC1/Smad7 0.001 0.09 -9999 0 -0.24 65 65
RANGAP1 0.017 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.014 0.064 -9999 0 -10000 0 0
NuRD/MBD3 Complex -0.009 0.068 -9999 0 -0.18 40 40
NF kappa B1 p50/RelA -0.013 0.07 -9999 0 -0.25 4 4
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.016 0.019 -9999 0 -0.41 1 1
GATA1 0.017 0 -9999 0 -10000 0 0
Mad/Max 0.025 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.007 0.072 -9999 0 -0.19 40 40
RBBP7 0.017 0 -9999 0 -10000 0 0
NPC 0.01 0.009 -9999 0 -0.2 1 1
RBBP4 -0.064 0.17 -9999 0 -0.41 100 100
MAX 0.017 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.017 0 -9999 0 -10000 0 0
NFKBIA -0.025 0.068 -9999 0 -0.12 186 186
KAT2B 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex -0.009 0.069 -9999 0 -0.23 20 20
SIN3 complex 0.033 0 -9999 0 -10000 0 0
SMURF1 0.017 0 -9999 0 -10000 0 0
CHD3 0.017 0 -9999 0 -10000 0 0
SAP30 0.017 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.017 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.008 0.056 -9999 0 -10000 0 0
YY1/HDAC2 0.024 0.024 -9999 0 -0.22 5 5
YY1/HDAC1 -0.004 0.081 -9999 0 -0.22 65 65
NuRD/MBD2 Complex (MeCP1) -0.009 0.068 -9999 0 -0.18 40 40
PPARG -0.034 0.088 -9999 0 -0.15 189 189
HDAC8/hEST1B 0.023 0 -9999 0 -10000 0 0
UBE2I 0.017 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
TNFRSF1A -0.13 0.2 -9999 0 -0.41 183 183
HDAC3/SMRT (N-CoR2) -0.014 0.064 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.001 0.09 -9999 0 -0.24 65 65
CREBBP 0.017 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.011 0.076 -9999 0 -0.2 40 40
HDAC1 -0.036 0.14 -9999 0 -0.41 65 65
HDAC3 -0.025 0.068 -9999 0 -0.12 185 185
HDAC2 0.013 0.042 -9999 0 -0.41 5 5
YY1 0.018 0 -9999 0 -10000 0 0
HDAC8 0 0 -9999 0 -10000 0 0
SMAD7 0.016 0.019 -9999 0 -0.41 1 1
NCOR2 0.017 0 -9999 0 -10000 0 0
MXD1 0.017 0 -9999 0 -10000 0 0
STAT3 0.019 0.027 -9999 0 -0.18 10 10
NFKB1 0.014 0.037 -9999 0 -0.41 4 4
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0.019 -9999 0 -0.41 1 1
YY1/LSF/HDAC1 0.006 0.077 -9999 0 -0.2 65 65
YY1/SAP30/HDAC1 0.006 0.077 -9999 0 -0.2 65 65
EP300 0.017 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.019 0.027 -9999 0 -0.18 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.025 0.068 -9999 0 -0.12 186 186
histone deacetylation -0.008 0.067 -9999 0 -0.18 40 40
STAT3 (dimer non-phopshorylated)/HDAC3 -0.009 0.063 -9999 0 -0.22 10 10
nuclear export -0.023 0 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
GATAD2B 0 0 -9999 0 -10000 0 0
GATAD2A -0.023 0.12 -9999 0 -0.41 49 49
GATA2/HDAC3 -0.015 0.064 -9999 0 -0.2 1 1
GATA1/HDAC1 -0.013 0.1 -9999 0 -0.28 65 65
GATA1/HDAC3 -0.014 0.064 -9999 0 -10000 0 0
CHD4 0.017 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.083 0.15 -9999 0 -0.28 185 185
SIN3/HDAC complex/Mad/Max 0.001 0.058 -9999 0 -0.18 20 20
NuRD Complex -0.007 0.076 -9999 0 -0.2 40 40
positive regulation of chromatin silencing -0.033 0.09 -9999 0 -0.21 68 68
SIN3B 0.017 0 -9999 0 -10000 0 0
MTA2 0.017 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
XPO1 0.017 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.006 0.071 -9999 0 -0.18 65 65
HDAC complex -0.035 0.13 -9999 0 -0.24 149 149
GATA1/Fog1 0.013 0 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 -0.001 0.093 -9999 0 -0.24 68 68
TNF 0.015 0.026 -9999 0 -0.41 2 2
negative regulation of cell growth 0.001 0.058 -9999 0 -0.18 20 20
NuRD/MBD2/PRMT5 Complex -0.009 0.068 -9999 0 -0.18 40 40
Ran/GTP/Exportin 1 0.034 0.006 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.027 0.084 -9999 0 -0.14 186 186
SIN3/HDAC complex/NCoR1 -0.005 0.064 -9999 0 -0.2 20 20
TFCP2 0.017 0 -9999 0 -10000 0 0
NR2C1 0.017 0 -9999 0 -10000 0 0
MBD3 0.017 0 -9999 0 -10000 0 0
MBD2 0.017 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.017 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.023 0.063 -9999 0 -0.22 25 25
Syndecan-3/Neurocan 0.003 0.062 -9999 0 -0.2 37 37
POMC 0.017 0 -9999 0 -10000 0 0
EGFR -0.14 0.21 -9999 0 -0.41 194 194
Syndecan-3/EGFR -0.073 0.12 -9999 0 -0.21 219 219
AGRP 0.017 0 -9999 0 -10000 0 0
NCSTN -0.007 0.099 -9999 0 -0.41 30 30
PSENEN 0.017 0.001 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.017 0 -9999 0 -10000 0 0
APH1A 0.009 0.059 -9999 0 -0.41 10 10
NCAN 0.013 0.027 -9999 0 -0.41 2 2
long-term memory 0.014 0.065 -9999 0 -0.21 37 37
Syndecan-3/IL8 -0.042 0.11 -9999 0 -0.21 145 145
PSEN1 0.016 0.019 -9999 0 -0.41 1 1
Src/Cortactin 0.025 0 -9999 0 -10000 0 0
FYN 0.015 0.027 -9999 0 -0.41 2 2
limb bud formation 0.001 0.058 -9999 0 -0.26 21 21
MC4R 0.016 0.019 -9999 0 -0.41 1 1
SRC 0.017 0 -9999 0 -10000 0 0
PTN 0.016 0.004 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-3 0.001 0.059 -9999 0 -0.26 21 21
neuron projection morphogenesis 0.016 0.05 -9999 0 -0.23 12 12
Syndecan-3/AgRP 0.004 0.073 -9999 0 -0.25 36 36
Syndecan-3/AgRP/MC4R 0.013 0.073 -9999 0 -0.24 37 37
Fyn/Cortactin 0.023 0.02 -9999 0 -0.28 2 2
SDC3 0.001 0.059 -9999 0 -0.26 21 21
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.042 0.11 -9999 0 -0.21 145 145
IL8 -0.076 0.18 -9999 0 -0.41 115 115
Syndecan-3/Fyn/Cortactin 0.014 0.066 -9999 0 -0.23 30 30
Syndecan-3/CASK -0.007 0.071 -9999 0 -0.25 36 36
alpha-MSH/MC4R 0.025 0.014 -9999 0 -0.28 1 1
Gamma Secretase 0.032 0.067 -9999 0 -0.2 39 39
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.13 0.17 -10000 0 -0.44 52 52
NCK1/PAK1/Dok-R -0.083 0.075 -10000 0 -0.24 47 47
NCK1/Dok-R -0.011 0.11 -10000 0 -0.31 8 8
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
mol:beta2-estradiol 0.013 0.044 0.12 78 -10000 0 78
RELA 0.017 0 -10000 0 -10000 0 0
SHC1 -0.022 0.12 -10000 0 -0.41 46 46
Rac/GDP 0.013 0 -10000 0 -10000 0 0
F2 0.037 0.054 0.16 38 -0.42 2 40
TNIP2 0.008 0.061 -10000 0 -0.41 11 11
NF kappa B/RelA 0.005 0.11 -10000 0 -0.35 6 6
FN1 -0.065 0.17 -10000 0 -0.41 101 101
PLD2 -0.013 0.1 -10000 0 -0.27 41 41
PTPN11 0.017 0 -10000 0 -10000 0 0
GRB14 0.002 0.078 -10000 0 -0.41 18 18
ELK1 -0.003 0.098 -10000 0 -0.28 2 2
GRB7 0.016 0.019 -10000 0 -0.41 1 1
PAK1 0.017 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.055 0.17 -10000 0 -0.4 59 59
CDKN1A -0.16 0.2 -10000 0 -0.47 93 93
ITGA5 -0.043 0.15 -10000 0 -0.41 74 74
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.007 0.1 -10000 0 -0.28 6 6
CRK 0.017 0 -10000 0 -10000 0 0
mol:NO -0.1 0.14 -10000 0 -0.36 52 52
PLG -0.013 0.1 -10000 0 -0.27 46 46
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.1 0.15 -10000 0 -0.4 50 50
GRB2 0.017 0.002 -10000 0 -10000 0 0
PIK3R1 0.015 0.004 -10000 0 -10000 0 0
ANGPT2 -0.2 0.21 -10000 0 -0.39 280 280
BMX -0.013 0.1 -10000 0 -0.27 46 46
ANGPT1 -0.038 0.13 -10000 0 -0.34 78 78
tube development -0.16 0.19 0.28 1 -0.44 86 87
ANGPT4 0.012 0.005 -10000 0 -10000 0 0
response to hypoxia -0.006 0.012 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.014 0.11 -10000 0 -0.32 12 12
alpha5/beta1 Integrin -0.018 0.11 -10000 0 -0.28 74 74
FGF2 0.02 0.027 -10000 0 -0.41 2 2
STAT5A (dimer) -0.17 0.22 -10000 0 -0.51 87 87
mol:L-citrulline -0.1 0.14 -10000 0 -0.36 52 52
AGTR1 0.002 0.029 -10000 0 -0.41 2 2
MAPK14 -0.048 0.12 -10000 0 -0.33 39 39
Tie2/SHP2 0.016 0.046 -10000 0 -0.21 1 1
TEK 0.009 0.05 -10000 0 -0.24 1 1
RPS6KB1 -0.1 0.15 -10000 0 -0.4 43 43
Angiotensin II/AT1 -0.006 0.026 -10000 0 -0.29 2 2
Tie2/Ang1/GRB2 -0.006 0.11 -10000 0 -0.29 6 6
MAPK3 -0.009 0.099 -10000 0 -0.26 15 15
MAPK1 -0.01 0.097 -10000 0 -0.27 10 10
Tie2/Ang1/GRB7 -0.007 0.11 -10000 0 -0.29 6 6
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
MAPK8 -0.013 0.1 -10000 0 -0.27 46 46
PI3K -0.12 0.16 -10000 0 -0.42 57 57
FES -0.049 0.12 -10000 0 -0.33 39 39
Crk/Dok-R -0.007 0.1 -10000 0 -0.28 6 6
Tie2/Ang1/ABIN2 -0.011 0.11 -10000 0 -0.31 13 13
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.12 0.16 -10000 0 -0.41 52 52
STAT5A 0.016 0.019 -10000 0 -0.41 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.1 0.15 -10000 0 -0.4 42 42
Tie2/Ang2 -0.19 0.23 -10000 0 -0.51 100 100
Tie2/Ang1 -0.017 0.11 -10000 0 -0.29 46 46
FOXO1 -0.14 0.18 -10000 0 -0.43 80 80
ELF1 0.016 0.05 -10000 0 -0.41 7 7
ELF2 -0.015 0.11 -10000 0 -0.28 46 46
mol:Choline -0.013 0.1 -10000 0 -0.27 41 41
cell migration -0.064 0.058 -10000 0 -0.16 101 101
FYN -0.17 0.2 -10000 0 -0.48 86 86
DOK2 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.14 0.19 -10000 0 -0.44 88 88
ETS1 0.008 0.047 -10000 0 -10000 0 0
PXN -0.09 0.14 -10000 0 -0.36 41 41
ITGB1 0.017 0 -10000 0 -10000 0 0
NOS3 -0.11 0.16 -10000 0 -0.4 52 52
RAC1 0.017 0 -10000 0 -10000 0 0
TNF 0.002 0.053 -10000 0 -0.41 2 2
MAPKKK cascade -0.013 0.1 -10000 0 -0.27 41 41
RASA1 0.017 0.002 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.031 0.12 -10000 0 -0.37 19 19
NCK1 0.008 0.061 -10000 0 -0.41 11 11
vasculogenesis -0.097 0.14 -10000 0 -0.34 52 52
mol:Phosphatidic acid -0.013 0.1 -10000 0 -0.27 41 41
mol:Angiotensin II -0.009 0.01 -10000 0 -10000 0 0
mol:NADP -0.1 0.14 -10000 0 -0.36 52 52
Rac1/GTP -0.099 0.14 -10000 0 -0.39 42 42
MMP2 -0.11 0.14 -10000 0 -0.37 61 61
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 -0.085 0.18 -9999 0 -0.41 126 126
SMAD2 0.013 0.02 -9999 0 -0.12 2 2
SMAD3 0.018 0.04 -9999 0 -0.12 37 37
SMAD3/SMAD4 0.001 0.069 -9999 0 -0.2 18 18
SMAD4/Ubc9/PIASy -0.029 0.12 -9999 0 -0.24 126 126
SMAD2/SMAD2/SMAD4 -0.01 0.1 -9999 0 -0.19 122 122
PPM1A 0.017 0 -9999 0 -10000 0 0
CALM1 0.016 0.004 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.032 0.097 -9999 0 -0.2 126 126
MAP3K1 0.016 0.019 -9999 0 -0.41 1 1
TRAP-1/SMAD4 -0.049 0.13 -9999 0 -0.28 126 126
MAPK3 0.017 0 -9999 0 -10000 0 0
MAPK1 0.017 0.003 -9999 0 -10000 0 0
NUP214 0.017 0 -9999 0 -10000 0 0
CTDSP1 0.015 0.032 -9999 0 -0.41 3 3
CTDSP2 -0.013 0.11 -9999 0 -0.41 37 37
CTDSPL 0.017 0 -9999 0 -10000 0 0
KPNB1 0.017 0 -9999 0 -10000 0 0
TGFBRAP1 0.017 0 -9999 0 -10000 0 0
UBE2I 0.017 0 -9999 0 -10000 0 0
NUP153 0.015 0.032 -9999 0 -0.41 3 3
KPNA2 0.007 0.064 -9999 0 -0.41 12 12
PIAS4 0.017 0 -9999 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.04 -10000 0 -0.24 12 12
fibroblast growth factor receptor signaling pathway 0.028 0.04 -10000 0 -0.23 12 12
LAMA1 0 0 -10000 0 -10000 0 0
PRNP 0.016 0.004 -10000 0 -10000 0 0
GPC1/SLIT2 0.012 0.037 -10000 0 -0.22 11 11
SMAD2 0.017 0.04 -10000 0 -0.21 16 16
GPC1/PrPc/Cu2+ 0.018 0.032 -10000 0 -0.24 8 8
GPC1/Laminin alpha1 0.008 0.037 -10000 0 -0.29 8 8
TDGF1 0.015 0.026 -10000 0 -0.41 2 2
CRIPTO/GPC1 0.02 0.042 -10000 0 -0.28 10 10
APP/GPC1 0.021 0.038 -10000 0 -0.28 8 8
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.021 0.1 -10000 0 -0.25 85 85
FLT1 0.017 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.027 0.046 -10000 0 -0.24 16 16
SERPINC1 0.016 0.019 -10000 0 -0.41 1 1
FYN 0.015 0.038 -10000 0 -0.23 12 12
FGR 0.009 0.056 -10000 0 -0.24 27 27
positive regulation of MAPKKK cascade -0.022 0.096 -10000 0 -0.22 77 77
SLIT2 0.009 0.033 -10000 0 -0.41 3 3
GPC1/NRG 0.021 0.038 -10000 0 -0.28 8 8
NRG1 0.017 0 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.12 0.14 -10000 0 -0.24 290 290
LYN -0.014 0.09 -10000 0 -0.24 73 73
mol:Spermine 0.004 0.036 -10000 0 -0.29 8 8
cell growth 0.028 0.04 -10000 0 -0.23 12 12
BMP signaling pathway -0.011 0.052 0.41 8 -10000 0 8
SRC 0.017 0.035 -10000 0 -0.23 10 10
TGFBR1 0.017 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.14 0.21 -10000 0 -0.41 191 191
GPC1 0.011 0.052 -10000 0 -0.41 8 8
TGFBR1 (dimer) 0.017 0 -10000 0 -10000 0 0
VEGFA -0.22 0.21 -10000 0 -0.41 287 287
BLK 0.017 0.035 -10000 0 -0.23 10 10
HCK -0.025 0.1 -10000 0 -0.24 95 95
FGF2 0.015 0.026 -10000 0 -0.41 2 2
FGFR1 0.015 0.026 -10000 0 -0.41 2 2
VEGFR1 homodimer 0.017 0 -10000 0 -10000 0 0
TGFBR2 0.011 0.052 -10000 0 -0.41 8 8
cell death 0.021 0.038 -10000 0 -0.28 8 8
ATIII/GPC1 0.02 0.04 -10000 0 -0.28 9 9
PLA2G2A/GPC1 -0.091 0.15 -10000 0 -0.29 196 196
LCK 0.015 0.043 -10000 0 -0.25 13 13
neuron differentiation 0.021 0.038 -10000 0 -0.28 8 8
PrPc/Cu2+ 0.012 0.003 -10000 0 -10000 0 0
APP 0.017 0.001 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.011 0.052 -10000 0 -0.41 8 8
Plasma membrane estrogen receptor 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
GNB1/GNG2 0.03 0.003 -10000 0 -10000 0 0
ER alpha/Gai/GDP/Gbeta gamma -0.063 0.064 -10000 0 -0.2 63 63
AKT1 0.007 0.03 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.005 0.031 -10000 0 -10000 0 0
mol:Ca2+ 0.03 0.018 -10000 0 -0.14 2 2
IGF1R 0.017 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.023 0 -10000 0 -10000 0 0
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
apoptosis -0.007 0.03 -10000 0 -10000 0 0
RhoA/GTP -0.044 0.074 -10000 0 -0.17 134 134
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.047 0.046 -10000 0 -0.15 49 49
regulation of stress fiber formation 0.13 0.11 0.3 95 -0.21 1 96
E2/ERA-ERB (dimer) 0.023 0 -10000 0 -10000 0 0
KRAS 0.017 0.002 -10000 0 -10000 0 0
G13/GTP 0.021 0.015 -10000 0 -0.22 2 2
pseudopodium formation -0.13 0.11 0.21 1 -0.3 95 96
E2/ER alpha (dimer)/PELP1 0.023 0 -10000 0 -10000 0 0
GRB2 0.017 0.002 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
GNAO1 0.002 0.005 -10000 0 -10000 0 0
HRAS 0.016 0.019 -10000 0 -0.41 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.03 0.037 -10000 0 -0.15 13 13
E2/ER beta (dimer) 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.006 0.052 -10000 0 -0.2 2 2
mol:NADP -0.03 0.037 -10000 0 -0.15 13 13
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
mol:IP3 0.03 0.018 -10000 0 -0.14 2 2
IGF-1R heterotetramer 0.017 0 -10000 0 -10000 0 0
PLCB1 0.028 0.019 -10000 0 -0.15 2 2
PLCB2 0.028 0.019 -10000 0 -0.15 2 2
IGF1 0.014 0.037 -10000 0 -0.41 4 4
mol:L-citrulline -0.03 0.037 -10000 0 -0.15 13 13
RHOA 0.017 0.001 -10000 0 -10000 0 0
Gai/GDP -0.42 0.15 -10000 0 -0.46 480 480
JNK cascade 0.013 0 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.017 0 -10000 0 -10000 0 0
GNAQ 0.017 0 -10000 0 -10000 0 0
ESR1 0.017 0 -10000 0 -10000 0 0
Gq family/GDP/Gbeta gamma 0.026 0.026 -10000 0 -0.14 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.008 0.066 -10000 0 -0.48 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.058 0.074 -10000 0 -0.24 54 54
GNAZ 0.015 0.006 -10000 0 -10000 0 0
E2/ER alpha (dimer) 0.013 0 -10000 0 -10000 0 0
STRN 0.017 0 -10000 0 -10000 0 0
GNAL 0.017 0 -10000 0 -10000 0 0
PELP1 0.017 0 -10000 0 -10000 0 0
MAPK11 0.016 0 -10000 0 -10000 0 0
GNAI2 0.017 0.001 -10000 0 -10000 0 0
GNAI3 -0.036 0.14 -10000 0 -0.41 65 65
GNAI1 0.014 0.02 -10000 0 -0.41 1 1
HBEGF -0.16 0.1 -10000 0 -0.22 326 326
cAMP biosynthetic process 0.02 0 -10000 0 -10000 0 0
SRC -0.059 0.062 -10000 0 -0.19 66 66
PI3K 0.009 0.065 -10000 0 -0.28 25 25
GNB1 0.017 0.002 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.002 0.05 -10000 0 -0.21 2 2
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.05 0.06 -10000 0 -0.2 54 54
Gs family/GTP 0.025 0 -10000 0 -10000 0 0
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.03 0.11 -10000 0 -0.21 133 133
vasodilation -0.03 0.036 -10000 0 -0.14 13 13
mol:DAG 0.03 0.018 -10000 0 -0.14 2 2
Gs family/GDP/Gbeta gamma -0.02 0.034 -10000 0 -0.22 1 1
MSN -0.14 0.11 0.21 1 -0.32 95 96
Gq family/GTP 0.028 0.02 -10000 0 -0.12 9 9
mol:PI-3-4-5-P3 0.005 0.03 -10000 0 -10000 0 0
NRAS -0.094 0.19 -10000 0 -0.41 136 136
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.03 0.036 0.14 13 -10000 0 13
GRB2/SOS1 0.013 0.001 -10000 0 -10000 0 0
RhoA/GDP 0.002 0.053 -10000 0 -0.18 2 2
NOS3 -0.031 0.038 -10000 0 -0.15 13 13
GNA11 0.017 0 -10000 0 -10000 0 0
MAPKKK cascade -0.015 0.047 -10000 0 -0.19 14 14
E2/ER alpha (dimer)/PELP1/Src -0.048 0.048 -10000 0 -0.16 49 49
ruffle organization -0.13 0.11 0.21 1 -0.3 95 96
ROCK2 -0.018 0.083 0.22 1 -0.33 1 2
GNA14 0.015 0.026 -10000 0 -0.41 2 2
GNA15 0.011 0.049 -10000 0 -0.41 7 7
GNA13 0.015 0.026 -10000 0 -0.41 2 2
MMP9 -0.13 0.11 -10000 0 -0.24 229 229
MMP2 -0.15 0.12 -10000 0 -0.25 285 285
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.02 0 -9999 0 -10000 0 0
RGS9BP 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + -0.068 0.12 -9999 0 -0.24 184 184
mol:ADP 0 0 -9999 0 -10000 0 0
GNAT2 0.017 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.023 0.003 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.023 0 -9999 0 -10000 0 0
GRK7 0 0 -9999 0 -10000 0 0
CNGB3 0.017 0 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.061 0.11 -9999 0 -0.21 184 184
Cone PDE6 0.04 0.005 -9999 0 -10000 0 0
Cone Metarhodopsin II 0 0 -9999 0 -10000 0 0
Na + (4 Units) -0.052 0.12 -9999 0 -0.21 184 184
GNAT2/GDP 0.03 0.003 -9999 0 -10000 0 0
GNB5 0.017 0.002 -9999 0 -10000 0 0
mol:GMP (4 units) 0.02 0 -9999 0 -10000 0 0
Cone Transducin 0.022 0 -9999 0 -10000 0 0
SLC24A2 0.017 0 -9999 0 -10000 0 0
GNB3/GNGT2 0.013 0 -9999 0 -10000 0 0
GNB3 0.017 0 -9999 0 -10000 0 0
GNAT2/GTP 0.013 0 -9999 0 -10000 0 0
CNGA3 -0.13 0.2 -9999 0 -0.41 184 184
ARR3 0.017 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.068 0.12 -9999 0 -0.24 184 184
mol:Pi 0.023 0.003 -9999 0 -10000 0 0
Cone CNG Channel -0.036 0.11 -9999 0 -0.18 184 184
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.017 0 -9999 0 -10000 0 0
RGS9 0.017 0 -9999 0 -10000 0 0
PDE6C 0.017 0 -9999 0 -10000 0 0
GNGT2 0 0 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.017 0 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.011 0.096 -9999 0 -0.37 31 31
MKNK1 0.017 0 -9999 0 -10000 0 0
MAPK14 0.015 0.049 -9999 0 -0.17 31 31
ATF2/c-Jun 0.027 0.034 -9999 0 -0.39 1 1
MAPK11 0.017 0.042 -9999 0 -0.16 29 29
MITF 0.021 0.046 -9999 0 -0.16 33 33
MAPKAPK5 0.022 0.044 -9999 0 -0.15 31 31
KRT8 0.011 0.069 -9999 0 -0.19 53 53
MAPKAPK3 0.015 0.026 -9999 0 -0.41 2 2
MAPKAPK2 0.017 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 0.022 0.059 -9999 0 -0.21 31 31
CEBPB 0.018 0.06 -9999 0 -0.19 36 36
SLC9A1 0.022 0.044 -9999 0 -0.15 31 31
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.025 0.045 -9999 0 -0.15 31 31
p38alpha-beta/MNK1 0.033 0.048 -9999 0 -0.16 31 31
JUN 0.025 0.034 -9999 0 -0.39 1 1
PPARGC1A 0.021 0.048 -9999 0 -0.16 33 33
USF1 0.015 0.044 -9999 0 -0.16 31 31
RAB5/GDP/GDI1 0.021 0.033 -9999 0 -0.13 9 9
NOS2 0.015 0.044 -9999 0 -0.16 31 31
DDIT3 0.006 0.074 -9999 0 -0.18 67 67
RAB5A 0.017 0 -9999 0 -10000 0 0
HSPB1 0.016 0.05 -9999 0 -0.24 10 10
p38alpha-beta/HBP1 0.033 0.048 -9999 0 -0.16 31 31
CREB1 0.026 0.043 -9999 0 -0.14 31 31
RAB5/GDP 0.013 0 -9999 0 -10000 0 0
EIF4E 0.019 0.045 -9999 0 -0.2 7 7
RPS6KA4 0.022 0.044 -9999 0 -0.15 31 31
PLA2G4A -0.043 0.12 -9999 0 -0.23 143 143
GDI1 0.023 0.039 -9999 0 -0.16 23 23
TP53 -0.005 0.079 -9999 0 -0.17 95 95
RPS6KA5 0.022 0.044 -9999 0 -0.15 31 31
ESR1 0.022 0.044 -9999 0 -0.15 31 31
HBP1 0.017 0 -9999 0 -10000 0 0
MEF2C 0.02 0.039 -9999 0 -0.16 22 22
MEF2A 0.022 0.044 -9999 0 -0.15 31 31
EIF4EBP1 -0.009 0.058 -9999 0 -0.19 31 31
KRT19 0.011 0.068 -9999 0 -0.18 55 55
ELK4 0.022 0.044 -9999 0 -0.15 31 31
ATF6 0.022 0.044 -9999 0 -0.15 31 31
ATF1 0.022 0.047 -9999 0 -0.16 31 31
p38alpha-beta/MAPKAPK2 0.033 0.048 -9999 0 -0.16 31 31
p38alpha-beta/MAPKAPK3 0.032 0.051 -9999 0 -0.16 33 33
S1P3 pathway

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
PDGFRB 0.015 0.032 -9999 0 -0.41 3 3
mol:S1P 0.001 0.001 -9999 0 -0.015 1 1
S1P1/S1P/Gi -0.015 0.052 -9999 0 -0.15 62 62
GNAO1 0.002 0.005 -9999 0 -10000 0 0
S1P/S1P3/G12/G13 0.021 0.025 -9999 0 -0.21 6 6
AKT1 0 0.02 -9999 0 -0.16 7 7
AKT3 -0.059 0.065 -9999 0 -0.18 38 38
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.032 -9999 0 -0.41 3 3
GNAI2 0.018 0.002 -9999 0 -10000 0 0
GNAI3 -0.035 0.14 -9999 0 -0.41 65 65
GNAI1 0.015 0.02 -9999 0 -0.41 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0.001 -9999 0 -0.022 1 1
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.017 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.002 0.016 -9999 0 -0.25 1 1
MAPK3 0.002 0.015 -9999 0 -0.23 1 1
MAPK1 0.002 0.015 -9999 0 -0.23 1 1
JAK2 -0.074 0.081 -9999 0 -0.19 114 114
CXCR4 -0.11 0.11 -9999 0 -0.21 272 272
FLT1 0.019 0.002 -9999 0 -10000 0 0
RhoA/GDP 0.013 0.001 -9999 0 -10000 0 0
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
SRC 0.002 0.015 -9999 0 -0.23 1 1
S1P/S1P3/Gi 0.002 0.016 -9999 0 -0.25 1 1
RAC1 0.017 0 -9999 0 -10000 0 0
RhoA/GTP -0.011 0.039 -9999 0 -0.16 13 13
VEGFA -0.22 0.21 -9999 0 -0.41 287 287
S1P/S1P2/Gi 0.001 0.014 -9999 0 -0.12 4 4
VEGFR1 homodimer/VEGFA homodimer -0.14 0.16 -9999 0 -0.28 287 287
RHOA 0.017 0.001 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.02 0.02 -9999 0 -0.13 9 9
GNAQ 0.017 0 -9999 0 -10000 0 0
GNAZ 0.016 0.006 -9999 0 -10000 0 0
G12/G13 0.022 0.033 -9999 0 -0.28 6 6
GNA14 0.015 0.026 -9999 0 -0.41 2 2
GNA15 0.011 0.049 -9999 0 -0.41 7 7
GNA12 0.014 0.037 -9999 0 -0.41 4 4
GNA13 0.015 0.026 -9999 0 -0.41 2 2
GNA11 0.017 0 -9999 0 -10000 0 0
Rac1/GTP -0.011 0.039 -9999 0 -0.16 13 13
Paxillin-dependent events mediated by a4b1

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
CRKL 0.017 0 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.003 -10000 0 -10000 0 0
DOCK1 0.017 0 -10000 0 -10000 0 0
ITGA4 0.013 0.042 -10000 0 -0.41 5 5
RAC1 0.017 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.022 0.041 -10000 0 -0.38 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.017 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.032 0.026 -10000 0 -0.24 5 5
alpha4/beta7 Integrin/Paxillin 0.032 0.033 -10000 0 -0.29 5 5
lamellipodium assembly 0.018 0.05 -10000 0 -0.26 1 1
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
PI3K 0.009 0.065 -10000 0 -0.28 25 25
ARF6 0.017 0 -10000 0 -10000 0 0
TLN1 -0.02 0.12 -10000 0 -0.41 46 46
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
ARF6/GTP 0.04 0.021 -10000 0 -0.17 5 5
cell adhesion 0.021 0.07 -10000 0 -0.19 50 50
CRKL/CBL 0.025 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.033 0.024 -10000 0 -0.21 5 5
ITGB1 0.017 0 -10000 0 -10000 0 0
ITGB7 0.015 0.026 -10000 0 -0.41 2 2
ARF6/GDP 0.013 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.11 0.11 -10000 0 -0.19 353 353
p130Cas/Crk/Dock1 0.023 0 -10000 0 -10000 0 0
VCAM1 -0.27 0.2 -10000 0 -0.41 351 351
alpha4/beta1 Integrin/Paxillin/Talin 0.022 0.071 -10000 0 -0.2 50 50
alpha4/beta1 Integrin/Paxillin/GIT1 0.042 0.023 -10000 0 -0.19 5 5
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP -0.041 0.023 0.19 5 -10000 0 5
CBL 0.017 0 -10000 0 -10000 0 0
PRKACA 0.017 0 -10000 0 -10000 0 0
GIT1 0.017 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.022 0.071 -10000 0 -0.2 50 50
Rac1/GTP 0.018 0.053 -10000 0 -0.28 1 1
Arf6 downstream pathway

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
PLAUR -0.006 0.12 -10000 0 -0.38 47 47
regulation of axonogenesis -0.013 0.029 0.13 3 -10000 0 3
myoblast fusion -0.002 0.062 0.2 47 -10000 0 47
mol:GTP 0.001 0.041 -10000 0 -0.13 47 47
regulation of calcium-dependent cell-cell adhesion -0.016 0.041 0.12 45 -10000 0 45
ARF1/GTP 0.014 0.033 -10000 0 -10000 0 0
mol:GM1 0 0.03 -10000 0 -0.095 47 47
mol:Choline 0.011 0.03 -10000 0 -0.22 2 2
lamellipodium assembly 0.001 0.063 -10000 0 -0.2 47 47
MAPK3 0.007 0.059 -10000 0 -0.18 47 47
ARF6/GTP/NME1/Tiam1 0.016 0.042 -10000 0 -0.12 45 45
ARF1 0.017 0.001 -10000 0 -10000 0 0
ARF6/GDP 0.002 0.063 -10000 0 -0.2 47 47
ARF1/GDP 0.01 0.058 -10000 0 -0.18 47 47
ARF6 0.011 0.027 -10000 0 -10000 0 0
RAB11A 0.017 0.001 -10000 0 -10000 0 0
TIAM1 0.015 0.008 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.007 0.059 -10000 0 -0.18 47 47
actin filament bundle formation -0.012 0.059 0.18 47 -10000 0 47
KALRN 0.003 0.049 -10000 0 -0.16 47 47
RAB11FIP3/RAB11A 0.025 0.001 -10000 0 -10000 0 0
RhoA/GDP 0.013 0.06 -10000 0 -0.18 47 47
NME1 -0.001 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.013 0.06 -10000 0 -0.18 47 47
substrate adhesion-dependent cell spreading 0.001 0.041 -10000 0 -0.13 47 47
cortical actin cytoskeleton organization 0.001 0.064 -10000 0 -0.2 47 47
RAC1 0.017 0 -10000 0 -10000 0 0
liver development 0.001 0.041 -10000 0 -0.13 47 47
ARF6/GTP 0.001 0.041 -10000 0 -0.13 47 47
RhoA/GTP 0.014 0.033 -10000 0 -0.091 47 47
mol:GDP -0.001 0.062 -10000 0 -0.2 47 47
ARF6/GTP/RAB11FIP3/RAB11A 0.025 0.031 -10000 0 -10000 0 0
RHOA 0.017 0.001 -10000 0 -10000 0 0
PLD1 0.009 0.035 -10000 0 -0.26 2 2
RAB11FIP3 0.017 0 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.063 -10000 0 -0.2 47 47
ruffle organization 0.013 0.029 -10000 0 -0.13 3 3
regulation of epithelial cell migration 0.001 0.041 -10000 0 -0.13 47 47
PLD2 0.01 0.031 -10000 0 -10000 0 0
PIP5K1A 0.013 0.029 -10000 0 -0.13 3 3
mol:Phosphatidic acid 0.011 0.03 -10000 0 -0.22 2 2
Rac1/GTP 0.001 0.064 -10000 0 -0.2 47 47
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.017 0 -9999 0 -10000 0 0
Caspase 8 (4 units) 0.018 0.068 -9999 0 -0.27 13 13
NEF 0.004 0 -9999 0 -10000 0 0
NFKBIA 0.012 0.032 -9999 0 -0.5 1 1
BIRC3 0.002 0.11 -9999 0 -0.39 36 36
CYCS 0.012 0.054 -9999 0 -0.2 13 13
RIPK1 0.01 0.056 -9999 0 -0.41 9 9
CD247 0.019 0.026 -9999 0 -0.41 2 2
MAP2K7 0.02 0.044 -9999 0 -0.22 1 1
protein ubiquitination 0.009 0.056 -9999 0 -0.18 8 8
CRADD 0.017 0 -9999 0 -10000 0 0
DAXX 0.016 0.019 -9999 0 -0.41 1 1
FAS -0.038 0.14 -9999 0 -0.41 68 68
BID 0.01 0.057 -9999 0 -0.21 13 13
NF-kappa-B/RelA/I kappa B alpha 0.026 0.07 -9999 0 -0.23 36 36
TRADD 0.017 0 -9999 0 -10000 0 0
MAP3K5 0.017 0.001 -9999 0 -10000 0 0
CFLAR 0.013 0.042 -9999 0 -0.41 5 5
FADD 0.015 0.026 -9999 0 -0.41 2 2
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.026 0.071 -9999 0 -0.23 36 36
MAPK8 0.023 0.042 -9999 0 -0.21 1 1
APAF1 0.017 0 -9999 0 -10000 0 0
TRAF1 0.016 0.019 -9999 0 -0.41 1 1
TRAF2 0.017 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.011 0.055 -9999 0 -0.12 69 69
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.004 0.064 -9999 0 -0.17 24 24
CHUK 0.009 0.058 -9999 0 -0.19 8 8
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.014 0.092 -9999 0 -0.21 75 75
TCRz/NEF 0.021 0.019 -9999 0 -0.28 2 2
TNF 0.015 0.026 -9999 0 -0.41 2 2
FASLG 0.022 0.015 -9999 0 -0.23 2 2
NFKB1 0.01 0.045 -9999 0 -0.43 4 4
TNFR1A/BAG4/TNF-alpha -0.06 0.13 -9999 0 -0.24 185 185
CASP6 0.022 0.069 -9999 0 -0.27 14 14
CASP7 0.007 0.11 -9999 0 -0.28 51 51
RELA 0.013 0.023 -9999 0 -10000 0 0
CASP2 0.016 0.019 -9999 0 -0.41 1 1
CASP3 -0.003 0.11 -9999 0 -0.28 49 49
TNFRSF1A -0.13 0.2 -9999 0 -0.41 183 183
TNFR1A/BAG4 -0.082 0.15 -9999 0 -0.28 183 183
CASP8 0.009 0.059 -9999 0 -0.41 10 10
CASP9 0.014 0.037 -9999 0 -0.41 4 4
MAP3K14 0.006 0.062 -9999 0 -0.16 26 26
APAF-1/Caspase 9 0.012 0.089 -9999 0 -0.28 37 37
BCL2 0.025 0.04 -9999 0 -0.19 1 1
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.009 0.001 -10000 0 -10000 0 0
GNB1/GNG2 0.018 0.029 -10000 0 -0.22 8 8
regulation of S phase of mitotic cell cycle 0.014 0.038 -10000 0 -0.13 32 32
GNAO1 0.002 0.005 -10000 0 -10000 0 0
HRAS 0.016 0.019 -10000 0 -0.41 1 1
SHBG/T-DHT 0.012 0 -10000 0 -10000 0 0
PELP1 0.017 0.001 -10000 0 -10000 0 0
AKT1 0.007 0.026 -10000 0 -0.29 4 4
MAP2K1 0.005 0.044 -10000 0 -0.18 10 10
T-DHT/AR 0.008 0.037 -10000 0 -0.29 8 8
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.005 127 127
GNAI2 0.017 0.001 -10000 0 -10000 0 0
GNAI3 -0.036 0.14 -10000 0 -0.41 65 65
GNAI1 0.014 0.02 -10000 0 -0.41 1 1
mol:GDP -0.007 0.036 -10000 0 -0.14 31 31
cell proliferation -0.011 0.096 -10000 0 -0.28 6 6
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
FOS -0.046 0.15 -10000 0 -0.32 125 125
mol:Ca2+ 0 0.006 -10000 0 -0.047 8 8
MAPK3 -0.003 0.073 -10000 0 -0.26 4 4
MAPK1 -0.011 0.07 -10000 0 -0.23 21 21
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
mol:IP3 -0.001 0.001 -10000 0 -0.003 127 127
cAMP biosynthetic process 0.001 0.005 -10000 0 -10000 0 0
GNG2 0 0 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.001 -10000 0 -0.003 127 127
HRAS/GTP 0.018 0.037 -10000 0 -0.2 9 9
actin cytoskeleton reorganization 0.015 0.044 -10000 0 -0.18 24 24
SRC 0.017 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.001 -10000 0 -0.003 127 127
PI3K 0.01 0.055 -10000 0 -0.23 25 25
apoptosis 0.018 0.098 0.19 127 -10000 0 127
T-DHT/AR/PELP1 0.018 0.032 -10000 0 -0.24 8 8
HRAS/GDP 0.012 0.04 -10000 0 -0.2 9 9
CREB1 -0.019 0.1 -10000 0 -0.2 125 125
RAC1-CDC42/GTP 0.021 0.046 -10000 0 -0.19 24 24
AR 0.01 0.053 -10000 0 -0.41 8 8
GNB1 0.017 0.002 -10000 0 -10000 0 0
RAF1 0.009 0.04 -10000 0 -0.19 10 10
RAC1-CDC42/GDP 0.023 0.039 -10000 0 -0.19 8 8
T-DHT/AR/PELP1/Src 0.027 0.031 -10000 0 -0.22 8 8
MAP2K2 0.006 0.045 -10000 0 -0.2 5 5
T-DHT/AR/PELP1/Src/PI3K 0.014 0.038 -10000 0 -0.13 32 32
GNAZ 0.015 0.006 -10000 0 -10000 0 0
SHBG 0.017 0 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.059 0.063 -10000 0 -0.2 65 65
mol:T-DHT 0 0.001 -10000 0 -0.002 1 1
RAC1 0.017 0 -10000 0 -10000 0 0
GNRH1 0.009 0 -10000 0 -10000 0 0
Gi family/GTP -0.001 0.021 -10000 0 -0.16 7 7
CDC42 0.017 0 -10000 0 -10000 0 0
EPO signaling pathway

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
BCL2L1 0.033 0.072 -10000 0 -0.24 18 18
CRKL 0.027 0.04 -10000 0 -0.17 19 19
mol:DAG 0.017 0.076 -10000 0 -0.17 64 64
HRAS 0.016 0.068 -10000 0 -0.3 8 8
MAPK8 -0.001 0.08 -10000 0 -0.22 64 64
RAP1A 0.027 0.04 -10000 0 -0.17 19 19
GAB1 0.026 0.043 -10000 0 -0.17 23 23
MAPK14 -0.002 0.081 -10000 0 -0.22 66 66
EPO 0.019 0.007 -10000 0 -10000 0 0
PLCG1 0.017 0.077 -10000 0 -0.18 64 64
EPOR/TRPC2/IP3 Receptors 0.019 0.007 -10000 0 -10000 0 0
RAPGEF1 0.017 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.038 0.006 -10000 0 -10000 0 0
GAB1/SHC/GRB2/SOS1 0.018 0.073 -10000 0 -0.18 47 47
EPO/EPOR (dimer) 0.028 0.011 -10000 0 -10000 0 0
IRS2 0.027 0.039 -10000 0 -0.17 18 18
STAT1 0.019 0.088 -10000 0 -0.18 76 76
STAT5B 0.021 0.077 -10000 0 -0.18 64 64
cell proliferation -0.001 0.074 -10000 0 -0.2 66 66
GAB1/SHIP/PIK3R1/SHP2/SHC 0.012 0.064 -10000 0 -0.3 8 8
TEC 0.027 0.04 -10000 0 -0.17 19 19
SOCS3 0.017 0 -10000 0 -10000 0 0
STAT1 (dimer) 0.019 0.087 -10000 0 -0.18 76 76
JAK2 0.018 0.007 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.053 0.047 -10000 0 -0.18 19 19
EPO/EPOR 0.028 0.011 -10000 0 -10000 0 0
LYN -0.033 0.14 -10000 0 -0.41 64 64
TEC/VAV2 0.038 0.04 -10000 0 -0.16 19 19
elevation of cytosolic calcium ion concentration 0.019 0.007 -10000 0 -10000 0 0
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
EPO/EPOR (dimer)/LYN 0.009 0.096 -10000 0 -0.25 64 64
mol:IP3 0.017 0.076 -10000 0 -0.17 64 64
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.032 0.036 -10000 0 -0.16 15 15
SH2B3 0.01 0.059 -10000 0 -0.42 10 10
NFKB1 -0.003 0.084 -10000 0 -0.22 66 66
EPO/EPOR (dimer)/JAK2/SOCS3 0.017 0.02 0.16 10 -10000 0 10
PTPN6 0.024 0.041 -10000 0 -0.18 19 19
TEC/VAV2/GRB2 0.045 0.04 -10000 0 -0.31 2 2
EPOR 0.019 0.007 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.073 -10000 0 -0.22 23 23
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 0.009 0.059 -10000 0 -0.41 10 10
CRKL/CBL/C3G 0.046 0.04 -10000 0 -0.31 2 2
VAV2 0.027 0.04 -10000 0 -0.17 19 19
CBL 0.027 0.04 -10000 0 -0.17 19 19
SHC/Grb2/SOS1 0.009 0.071 -10000 0 -0.18 54 54
STAT5A 0.021 0.078 -10000 0 -0.17 65 65
GRB2 0.017 0.002 -10000 0 -10000 0 0
STAT5 (dimer) 0.038 0.083 -10000 0 -0.3 13 13
LYN/PLCgamma2 -0.016 0.12 -10000 0 -0.32 65 65
PTPN11 0.017 0 -10000 0 -10000 0 0
BTK 0.027 0.042 -10000 0 -0.18 19 19
BCL2 0.033 0.072 -10000 0 -0.24 18 18
TRAIL signaling pathway

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
TNFSF10 -0.02 0.12 -9999 0 -0.41 46 46
positive regulation of NF-kappaB transcription factor activity -0.002 0.087 -9999 0 -0.28 46 46
MAP2K4 0.018 0.043 -9999 0 -0.19 5 5
IKBKB 0.017 0 -9999 0 -10000 0 0
TNFRSF10B 0.011 0.052 -9999 0 -0.41 8 8
TNFRSF10A 0 0 -9999 0 -10000 0 0
SMPD1 0.002 0.044 -9999 0 -0.13 52 52
IKBKG 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.017 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.006 0.097 -9999 0 -0.3 52 52
TRAIL/TRAILR3 -0.002 0.088 -9999 0 -0.28 46 46
TRAIL/TRAILR1 -0.014 0.085 -9999 0 -0.29 46 46
TRAIL/TRAILR4 -0.002 0.088 -9999 0 -0.28 46 46
TRAIL/TRAILR1/DAP3/GTP 0.001 0.067 -9999 0 -0.22 46 46
IKK complex 0.021 0.037 -9999 0 -0.15 6 6
RIPK1 0.01 0.056 -9999 0 -0.41 9 9
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.009 0.085 -9999 0 -0.28 46 46
MAP3K1 0.016 0.048 -9999 0 -0.12 54 54
TRAILR4 (trimer) 0.017 0 -9999 0 -10000 0 0
TRADD 0.017 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.011 0.049 -9999 0 -0.13 54 54
CFLAR 0.013 0.042 -9999 0 -0.41 5 5
MAPK1 -0.006 0.081 -9999 0 -0.28 41 41
TRAIL/TRAILR1/FADD/TRADD/RIP 0.016 0.076 -9999 0 -0.21 54 54
mol:ceramide 0.002 0.044 -9999 0 -0.13 52 52
FADD 0.015 0.026 -9999 0 -0.41 2 2
MAPK8 0.02 0.041 -9999 0 -0.19 4 4
TRAF2 0.017 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.017 0 -9999 0 -10000 0 0
CHUK 0.016 0.019 -9999 0 -0.41 1 1
TRAIL/TRAILR1/FADD 0 0.077 -9999 0 -0.24 47 47
DAP3 0.017 0 -9999 0 -10000 0 0
CASP10 -0.006 0.064 -9999 0 -0.19 53 53
JNK cascade -0.002 0.087 -9999 0 -0.28 46 46
TRAIL (trimer) -0.02 0.12 -9999 0 -0.41 46 46
TNFRSF10C 0.017 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.01 0.067 -9999 0 -0.2 47 47
TRAIL/TRAILR2/FADD 0.007 0.086 -9999 0 -0.25 53 53
cell death 0.002 0.044 -9999 0 -0.13 52 52
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.014 0.054 -9999 0 -0.13 60 60
TRAILR2 (trimer) 0.011 0.052 -9999 0 -0.41 8 8
CASP8 0.01 0.036 -9999 0 -0.22 7 7
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.022 0.084 -9999 0 -0.21 60 60
Signaling events mediated by PRL

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
CCNE1 0.011 0.049 -10000 0 -0.41 7 7
mol:Halofuginone 0.004 0.015 -10000 0 -0.17 4 4
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A 0.009 0.052 -10000 0 -0.14 54 54
PRL-3/alpha Tubulin 0.007 0.073 -10000 0 -0.28 31 31
mol:Ca2+ 0.009 0.052 0.22 31 -10000 0 31
AGT 0.016 0.005 -10000 0 -10000 0 0
CCNA2 -0.038 0.1 -10000 0 -0.2 148 148
TUBA1B 0.017 0 -10000 0 -10000 0 0
EGR1 0.011 0.051 -10000 0 -0.28 16 16
CDK2/Cyclin E1 0.012 0.076 -10000 0 -0.28 13 13
MAPK3 0 0.071 -10000 0 -0.28 31 31
PRL-2 /Rab GGTase beta 0.025 0.001 -10000 0 -10000 0 0
MAPK1 -0.001 0.071 -10000 0 -0.28 31 31
PTP4A1 0.015 0.044 -10000 0 -0.21 19 19
PTP4A3 -0.008 0.1 -10000 0 -0.41 31 31
PTP4A2 0.017 0.001 -10000 0 -10000 0 0
ITGB1 0 0.071 -10000 0 -0.28 31 31
SRC 0.017 0 -10000 0 -10000 0 0
RAC1 0.015 0.043 -10000 0 -0.14 32 32
Rab GGTase beta/Rab GGTase alpha 0.025 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.024 0.043 -10000 0 -0.19 20 20
RABGGTA 0.017 0 -10000 0 -10000 0 0
BCAR1 0.002 0.051 0.21 31 -10000 0 31
RHOC -0.032 0.081 -10000 0 -0.14 184 184
RHOA 0.015 0.043 -10000 0 -0.14 32 32
cell motility -0.004 0.055 -10000 0 -0.21 12 12
PRL-1/alpha Tubulin 0.024 0.043 -10000 0 -0.19 19 19
PRL-3/alpha1 Integrin -0.005 0.071 -10000 0 -0.29 31 31
ROCK1 -0.004 0.055 -10000 0 -0.21 13 13
RABGGTB 0.017 0 -10000 0 -10000 0 0
CDK2 -0.005 0.095 -10000 0 -0.41 27 27
mitosis 0.015 0.044 -10000 0 -0.21 19 19
ATF5 0.016 0.019 -10000 0 -0.41 1 1
ErbB2/ErbB3 signaling events

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
USP8 0.01 0.022 -10000 0 -0.24 4 4
RAS family/GTP -0.034 0.1 -10000 0 -0.19 133 133
NFATC4 0.015 0.04 -10000 0 -10000 0 0
ERBB2IP -0.008 0.1 -10000 0 -0.41 31 31
HSP90 (dimer) 0.017 0 -10000 0 -10000 0 0
mammary gland morphogenesis 0.019 0.054 0.15 18 -0.15 34 52
JUN 0.015 0.047 -10000 0 -10000 0 0
HRAS 0.016 0.019 -10000 0 -0.41 1 1
DOCK7 0.009 0.046 -10000 0 -0.14 34 34
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.005 0.085 0.16 26 -0.2 66 92
AKT1 0.007 0.026 -10000 0 -0.29 4 4
BAD 0.01 0.022 -10000 0 -0.24 4 4
MAPK10 0.01 0.026 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.003 1 1
ErbB2/ErbB3/neuregulin 1 beta 0.021 0.058 0.16 18 -0.16 34 52
RAF1 -0.032 0.099 -10000 0 -0.21 65 65
ErbB2/ErbB3/neuregulin 2 0.015 0.066 0.16 30 -0.21 32 62
STAT3 0.019 0.027 -10000 0 -10000 0 0
cell migration 0.011 0.029 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.001 -10000 0 -0.003 34 34
cell proliferation -0.026 0.12 -10000 0 -0.36 13 13
FOS -0.039 0.13 -10000 0 -0.24 121 121
NRAS -0.094 0.19 -10000 0 -0.41 136 136
mol:Ca2+ 0.019 0.054 0.15 18 -0.15 34 52
MAPK3 -0.017 0.098 -10000 0 -0.33 8 8
MAPK1 -0.027 0.11 -10000 0 -0.39 15 15
JAK2 0.016 0.047 -10000 0 -0.16 4 4
NF2 0.012 0.007 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.004 0.061 -10000 0 -0.15 75 75
NRG1 0.017 0.001 -10000 0 -10000 0 0
GRB2/SOS1 0.013 0.001 -10000 0 -10000 0 0
MAPK8 0.022 0.042 -10000 0 -0.13 5 5
MAPK9 0.019 0.029 -10000 0 -10000 0 0
ERBB2 0.009 0.052 0.22 31 -10000 0 31
ERBB3 -0.01 0.1 -10000 0 -0.41 32 32
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
RAC1 0.017 0 -10000 0 -10000 0 0
apoptosis -0.007 0.022 0.23 4 -10000 0 4
STAT3 (dimer) 0.019 0.027 -10000 0 -10000 0 0
RNF41 0.012 0.02 -10000 0 -0.21 4 4
FRAP1 0.01 0.024 -10000 0 -0.24 5 5
RAC1-CDC42/GTP -0.006 0.027 -10000 0 -0.12 4 4
ErbB2/ErbB2/HSP90 (dimer) 0.022 0.035 0.16 31 -10000 0 31
CHRNA1 -0.011 0.085 -10000 0 -0.25 13 13
myelination 0.021 0.042 -10000 0 -10000 0 0
PPP3CB 0.015 0.045 -10000 0 -0.15 4 4
KRAS 0.017 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.014 0.058 -10000 0 -0.18 9 9
NRG2 0.017 0 -10000 0 -10000 0 0
mol:GDP -0.003 0.061 -10000 0 -0.15 75 75
SOS1 0 0 -10000 0 -10000 0 0
MAP2K2 -0.026 0.095 -10000 0 -0.23 46 46
SRC 0.017 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.016 0.047 -10000 0 -0.16 4 4
MAP2K1 -0.028 0.12 -10000 0 -0.41 20 20
heart morphogenesis 0.019 0.054 0.15 18 -0.15 34 52
RAS family/GDP -0.032 0.11 -10000 0 -0.2 133 133
GRB2 0.017 0.002 -10000 0 -10000 0 0
PRKACA 0.01 0.006 -10000 0 -10000 0 0
CHRNE 0.01 0.013 -10000 0 -10000 0 0
HSP90AA1 0.017 0 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.026 0.29 4 -10000 0 4
nervous system development 0.019 0.054 0.15 18 -0.15 34 52
CDC42 0.017 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.015 0.032 -10000 0 -0.41 3 3
Jak2/Leptin Receptor 0.017 0.034 -10000 0 -0.16 3 3
PTP1B/AKT1 -0.002 0.048 -10000 0 -0.22 6 6
FYN 0.015 0.027 -10000 0 -0.41 2 2
p210 bcr-abl/PTP1B -0.01 0.046 -10000 0 -0.15 11 11
EGFR -0.14 0.21 -10000 0 -0.41 194 194
EGF/EGFR -0.055 0.1 -10000 0 -0.18 197 197
CSF1 0.017 0 -10000 0 -10000 0 0
AKT1 0.014 0.037 -10000 0 -0.41 4 4
INSR 0.017 0 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.004 0.049 -10000 0 -0.18 9 9
Insulin Receptor/Insulin 0.018 0.041 -10000 0 -0.21 4 4
HCK -0.053 0.16 -10000 0 -0.41 86 86
CRK 0.017 0 -10000 0 -10000 0 0
TYK2 -0.007 0.044 -10000 0 -0.18 5 5
EGF 0.013 0.027 -10000 0 -0.41 2 2
YES1 -0.047 0.15 -10000 0 -0.41 79 79
CAV1 -0.069 0.068 -10000 0 -0.17 120 120
TXN 0.015 0.002 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.003 0.051 -10000 0 -0.18 7 7
cell migration 0.01 0.046 0.15 11 -10000 0 11
STAT3 0.009 0.059 -10000 0 -0.41 10 10
PRLR 0.02 0 -10000 0 -10000 0 0
ITGA2B 0.016 0 -10000 0 -10000 0 0
CSF1R -0.016 0.12 -10000 0 -0.41 41 41
Prolactin Receptor/Prolactin 0.029 0.033 -10000 0 -0.28 6 6
FGR 0.003 0.076 -10000 0 -0.41 17 17
PTP1B/p130 Cas -0.01 0.043 -10000 0 -0.12 41 41
Crk/p130 Cas -0.003 0.044 -10000 0 -0.14 7 7
DOK1 0.003 0.04 -10000 0 -0.16 4 4
JAK2 0.011 0.03 -10000 0 -10000 0 0
Jak2/Leptin Receptor/Leptin 0.022 0.051 -10000 0 -0.21 8 8
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
PTPN1 -0.01 0.046 -10000 0 -0.13 42 42
LYN -0.035 0.14 -10000 0 -0.41 64 64
CDH2 0.014 0.032 -10000 0 -0.41 3 3
SRC 0.014 0.019 -10000 0 -10000 0 0
ITGB3 0.016 0 -10000 0 -10000 0 0
CAT1/PTP1B -0.027 0.094 -10000 0 -0.22 76 76
CAPN1 0.016 0.001 -10000 0 -10000 0 0
CSK 0.017 0 -10000 0 -10000 0 0
PI3K 0.015 0.057 -10000 0 -0.19 18 18
mol:H2O2 -0.002 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.022 0.049 -10000 0 -0.21 8 8
negative regulation of transcription 0.011 0.03 -10000 0 -10000 0 0
FCGR2A -0.2 0.22 -10000 0 -0.41 265 265
FER 0.015 0.002 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.023 0.001 -10000 0 -10000 0 0
BLK 0.017 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.011 0.077 -10000 0 -0.24 46 46
RHOA 0.016 0.001 -10000 0 -10000 0 0
LEPR 0.014 0.032 -10000 0 -0.41 3 3
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.017 0.002 -10000 0 -10000 0 0
mol:NADPH -0.002 0.002 -10000 0 -10000 0 0
TRPV6 -0.021 0.1 -10000 0 -0.23 75 75
PRL 0.015 0.045 -10000 0 -0.41 6 6
SOCS3 0.009 0.009 -10000 0 -10000 0 0
SPRY2 0.009 0.053 -10000 0 -0.42 8 8
Insulin Receptor/Insulin/IRS1 0.033 0.026 -10000 0 -0.24 5 5
CSF1/CSF1R -0.011 0.068 -10000 0 -0.18 43 43
Ras protein signal transduction 0.013 0.031 0.29 5 -10000 0 5
IRS1 0.013 0.042 -10000 0 -0.41 5 5
INS 0.017 0 -10000 0 -10000 0 0
LEP 0.017 0 -10000 0 -10000 0 0
STAT5B 0.003 0.039 -10000 0 -0.16 2 2
STAT5A 0.003 0.039 -10000 0 -0.16 2 2
GRB2 0.017 0.002 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.004 0.048 -10000 0 -0.16 10 10
CSN2 0.023 0.015 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
LAT -0.065 0.081 -10000 0 -0.16 124 124
YBX1 0.015 0.064 -10000 0 -0.4 12 12
LCK 0.014 0.037 -10000 0 -0.41 4 4
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
NOX4 -0.042 0.15 -10000 0 -0.42 70 70
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.005 0.093 -9999 0 -0.39 28 28
VDR 0.017 0 -9999 0 -10000 0 0
FAM120B 0 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.074 0.079 -9999 0 -0.26 5 5
RXRs/LXRs/DNA/Oxysterols -0.12 0.11 -9999 0 -0.18 381 381
MED1 0.017 0 -9999 0 -10000 0 0
mol:9cRA -0.021 0.016 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.031 0.005 -9999 0 -10000 0 0
RXRs/NUR77 -0.008 0.044 -9999 0 -0.26 3 3
RXRs/PPAR 0.002 0.028 -9999 0 -0.16 5 5
NCOR2 0.017 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.013 0 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.041 0 -9999 0 -10000 0 0
RARA 0.017 0 -9999 0 -10000 0 0
NCOA1 0.017 0.003 -9999 0 -10000 0 0
VDR/VDR/DNA 0.017 0 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.02 0.009 -9999 0 -10000 0 0
RARG 0.017 0 -9999 0 -10000 0 0
RPS6KB1 0.017 0.057 -9999 0 -0.22 28 28
RARs/THRs/DNA/SMRT 0.032 0 -9999 0 -10000 0 0
THRA 0.017 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.013 0 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.035 0.056 -9999 0 -0.29 3 3
NR1H4 0.017 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA -0.041 0.075 -9999 0 -0.29 5 5
NR1H2 -0.006 0.017 -9999 0 -10000 0 0
NR1H3 -0.012 0.041 -9999 0 -0.42 4 4
RXRs/VDR/DNA/Vit D3 -0.008 0.041 -9999 0 -0.24 3 3
NR4A1 0.017 0 -9999 0 -10000 0 0
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.015 0.032 -9999 0 -0.15 3 3
RXRG -0.009 0.037 -9999 0 -0.44 3 3
RXR alpha/CCPG -0.003 0.012 -9999 0 -10000 0 0
RXRA -0.006 0.017 -9999 0 -10000 0 0
RXRB -0.009 0.02 -9999 0 -10000 0 0
THRB 0.017 0 -9999 0 -10000 0 0
PPARG 0.013 0.042 -9999 0 -0.41 5 5
PPARD 0.017 0 -9999 0 -10000 0 0
TNF -0.1 0.1 -9999 0 -0.3 7 7
mol:Oxysterols -0.017 0.014 -9999 0 -10000 0 0
cholesterol transport -0.11 0.11 -9999 0 -0.18 381 381
PPARA 0.017 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.017 0 -9999 0 -10000 0 0
RXRs/NUR77/BCL2 0.013 0.016 -9999 0 -0.15 3 3
SREBF1 -0.1 0.099 -9999 0 -0.28 5 5
RXRs/RXRs/DNA/9cRA -0.035 0.056 -9999 0 -0.29 3 3
ABCA1 -0.24 0.18 -9999 0 -0.35 379 379
RARs/THRs 0.051 0 -9999 0 -10000 0 0
RXRs/FXR -0.008 0.044 -9999 0 -0.26 3 3
BCL2 0.017 0 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 -0.022 0.14 -10000 0 -0.39 65 65
AES 0.028 0.021 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.019 0.044 -10000 0 -0.28 11 11
SMAD4 -0.085 0.18 -10000 0 -0.41 126 126
DKK2 0.009 0.059 -10000 0 -0.41 10 10
TLE1 0.028 0.02 -10000 0 -10000 0 0
MACF1 0.018 0.001 -10000 0 -10000 0 0
CTNNB1 0.065 0.034 0.22 1 -0.14 1 2
WIF1 0.002 0.006 -10000 0 -10000 0 0
beta catenin/RanBP3 0.092 0.13 0.26 187 -10000 0 187
KREMEN2 0.017 0 -10000 0 -10000 0 0
DKK1 -0.077 0.18 -10000 0 -0.41 116 116
beta catenin/beta TrCP1 0.072 0.033 0.22 1 -10000 0 1
FZD1 0.009 0.059 -10000 0 -0.41 10 10
AXIN2 -0.043 0.066 -10000 0 -0.13 169 169
AXIN1 0.018 0 -10000 0 -10000 0 0
RAN 0.017 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.046 0.036 -10000 0 -0.31 4 4
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.042 0.065 -10000 0 -0.16 3 3
Axin1/APC/GSK3 0.059 0.02 0.19 1 -10000 0 1
Axin1/APC/GSK3/beta catenin/Macf1 0.056 0.036 -10000 0 -10000 0 0
HNF1A 0.029 0.021 -10000 0 -10000 0 0
CTBP1 0.029 0.022 -10000 0 -10000 0 0
MYC -0.11 0.19 -10000 0 -0.43 137 137
RANBP3 0.018 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.03 0.039 -10000 0 -0.24 11 11
NKD1 0 0 -10000 0 -10000 0 0
TCF4 0.028 0.022 -10000 0 -10000 0 0
TCF3 0.029 0.021 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.038 0.036 -10000 0 -0.21 11 11
Ran/GTP 0.014 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.1 0.14 0.28 169 -0.18 1 170
LEF1 0.027 0.039 -10000 0 -0.39 3 3
DVL1 0.004 0.012 -10000 0 -10000 0 0
CSNK2A1 0.017 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.039 0.053 -10000 0 -0.17 4 4
DKK1/LRP6/Kremen 2 -0.024 0.11 -10000 0 -0.23 117 117
LRP6 0.016 0.019 -10000 0 -0.41 1 1
CSNK1A1 0.031 0.024 -10000 0 -10000 0 0
NLK 0.015 0.005 -10000 0 -10000 0 0
CCND1 -0.088 0.18 -10000 0 -0.44 99 99
WNT1 0.017 0.001 -10000 0 -10000 0 0
GSK3A 0.017 0.001 -10000 0 -10000 0 0
GSK3B 0.017 0.002 -10000 0 -10000 0 0
FRAT1 0.016 0.019 -10000 0 -0.41 1 1
PPP2R5D 0.007 0.016 -10000 0 -10000 0 0
APC 0.021 0.031 -10000 0 -0.19 11 11
WNT1/LRP6/FZD1 0.003 0.012 -10000 0 -0.12 2 2
CREBBP 0.029 0.021 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.038 0.16 -10000 0 -0.43 36 36
CRP -0.038 0.16 -10000 0 -0.43 37 37
cell cycle arrest -0.059 0.17 -10000 0 -0.44 56 56
TIMP1 -0.2 0.22 -10000 0 -0.46 146 146
IL6ST 0.016 0.008 -10000 0 -10000 0 0
Rac1/GDP 0.007 0.076 -10000 0 -0.23 16 16
AP1 -0.035 0.1 -10000 0 -0.24 52 52
GAB2 0.017 0.019 -10000 0 -0.41 1 1
TNFSF11 -0.038 0.16 -10000 0 -0.43 37 37
HSP90B1 0.014 0.055 -10000 0 -0.39 2 2
GAB1 0.014 0.037 -10000 0 -0.41 4 4
MAPK14 0.019 0.048 -10000 0 -0.18 1 1
AKT1 0.028 0.04 -10000 0 -0.2 7 7
FOXO1 0.025 0.05 -10000 0 -0.25 6 6
MAP2K6 0.012 0.056 -10000 0 -0.17 14 14
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.001 0.097 -10000 0 -0.3 14 14
MITF 0.004 0.067 -10000 0 -0.2 29 29
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.016 0.019 -10000 0 -0.41 1 1
A2M -0.01 0.11 -10000 0 -0.44 30 30
CEBPB 0.015 0.062 -10000 0 -0.41 11 11
GRB2/SOS1/GAB family/SHP2 0.009 0.052 0.14 1 -0.28 4 5
STAT3 -0.061 0.18 -10000 0 -0.45 56 56
STAT1 0.003 0.046 -10000 0 -0.25 4 4
CEBPD -0.038 0.16 -10000 0 -0.42 40 40
PIK3CA -0.002 0.091 -10000 0 -0.41 25 25
PI3K 0.011 0.065 -10000 0 -0.28 25 25
JUN 0.016 0.019 -10000 0 -0.41 1 1
PIAS3/MITF 0.011 0.068 -10000 0 -0.21 18 18
MAPK11 0.02 0.047 -10000 0 -10000 0 0
STAT3 (dimer)/FOXO1 -0.037 0.16 -10000 0 -0.45 28 28
GRB2/SOS1/GAB family 0.007 0.077 -10000 0 -0.22 22 22
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.008 0.085 -10000 0 -0.18 68 68
GRB2 0.017 0.003 -10000 0 -10000 0 0
JAK2 0.017 0 -10000 0 -10000 0 0
LBP -0.027 0.15 -10000 0 -0.4 35 35
PIK3R1 0.017 0.005 -10000 0 -10000 0 0
JAK1 0.017 0.003 -10000 0 -10000 0 0
MYC -0.084 0.22 -10000 0 -0.46 95 95
FGG -0.042 0.17 -10000 0 -0.46 41 41
macrophage differentiation -0.059 0.17 -10000 0 -0.44 56 56
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.025 0.079 -10000 0 -0.21 52 52
JUNB -0.04 0.16 -10000 0 -0.45 37 37
FOS -0.085 0.18 -10000 0 -0.41 125 125
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 0.002 0.07 -10000 0 -0.2 32 32
STAT1/PIAS1 -0.005 0.086 -10000 0 -0.23 29 29
GRB2/SOS1/GAB family/SHP2/PI3K 0.024 0.033 -10000 0 -0.23 2 2
STAT3 (dimer) -0.061 0.18 -10000 0 -0.45 56 56
PRKCD -0.008 0.12 -10000 0 -0.36 14 14
IL6R 0.018 0.003 -10000 0 -10000 0 0
SOCS3 0.027 0.04 -10000 0 -10000 0 0
gp130 (dimer)/JAK1/JAK1/LMO4 0.033 0.018 -10000 0 -10000 0 0
Rac1/GTP 0.003 0.084 -10000 0 -0.26 16 16
HCK -0.053 0.16 -10000 0 -0.41 86 86
MAPKKK cascade 0.014 0.052 -10000 0 -0.35 4 4
bone resorption -0.036 0.16 -10000 0 -0.42 36 36
IRF1 -0.061 0.2 -10000 0 -0.48 72 72
mol:GDP 0.003 0.07 -10000 0 -0.21 26 26
SOS1 0.001 0.003 -10000 0 -10000 0 0
VAV1 0.003 0.071 -10000 0 -0.21 27 27
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.025 0.047 -10000 0 -0.25 2 2
PTPN11 0.011 0.017 -10000 0 -10000 0 0
IL6/IL6RA -0.006 0.096 -10000 0 -0.29 52 52
gp130 (dimer)/TYK2/TYK2/LMO4 0.033 0.016 -10000 0 -0.23 1 1
gp130 (dimer)/JAK2/JAK2/LMO4 0.034 0.012 -10000 0 -10000 0 0
IL6 -0.026 0.13 -10000 0 -0.42 52 52
PIAS3 0.015 0.026 -10000 0 -0.41 2 2
PTPRE 0.017 0.01 -10000 0 -10000 0 0
PIAS1 0.017 0 -10000 0 -10000 0 0
RAC1 0.017 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 0.004 0.055 -10000 0 -0.15 51 51
LMO4 0.016 0.008 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.044 0.17 -10000 0 -0.48 37 37
MCL1 0.03 0.049 -10000 0 -0.38 4 4
Caspase cascade in apoptosis

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
TOP1 0.01 0.055 -10000 0 -0.21 9 9
ACTA1 0.004 0.062 0.14 20 -0.19 19 39
NUMA1 0.01 0.055 -10000 0 -0.21 9 9
SPTAN1 0.012 0.064 0.16 30 -0.19 12 42
LIMK1 0.006 0.06 0.15 15 -0.18 17 32
BIRC3 -0.01 0.1 -10000 0 -0.41 33 33
BIRC2 0.017 0 -10000 0 -10000 0 0
BAX 0.011 0.049 -10000 0 -0.41 7 7
CASP10 0.006 0.056 -10000 0 -0.26 22 22
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.009 0.057 -10000 0 -0.2 11 11
DIABLO 0.017 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.014 0.065 0.16 31 -0.19 11 42
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.017 0 -10000 0 -10000 0 0
GSN 0 0.068 0.15 16 -0.19 29 45
MADD 0.017 0.001 -10000 0 -10000 0 0
TFAP2A 0.019 0.026 -10000 0 -0.28 1 1
BID 0.006 0.041 -10000 0 -0.14 36 36
MAP3K1 0.011 0.029 -10000 0 -0.15 2 2
TRADD 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.023 0.027 -10000 0 -0.28 4 4
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.011 0.087 0.16 13 -0.22 52 65
CASP9 0.014 0.037 -10000 0 -0.41 4 4
DNA repair -0.006 0.039 0.099 17 -0.13 23 40
neuron apoptosis 0.014 0.037 -10000 0 -0.56 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.011 0.059 0.16 6 -0.22 9 15
APAF1 0.017 0 -10000 0 -10000 0 0
CASP6 0.004 0.056 -10000 0 -10000 0 0
TRAF2 0.017 0 -10000 0 -10000 0 0
ICAD/CAD 0.009 0.058 0.15 8 -0.21 9 17
CASP7 -0.008 0.07 0.19 26 -0.18 54 80
KRT18 0.001 0.049 -10000 0 -0.19 22 22
apoptosis 0.005 0.071 0.18 6 -0.22 18 24
DFFA 0.006 0.06 0.15 15 -0.18 17 32
DFFB 0.006 0.06 0.15 15 -0.18 17 32
PARP1 0.006 0.039 0.13 23 -0.1 17 40
actin filament polymerization -0.006 0.057 0.17 17 -0.14 15 32
TNF 0.015 0.026 -10000 0 -0.41 2 2
CYCS 0.011 0.029 -10000 0 -0.11 19 19
SATB1 0.024 0.059 -10000 0 -10000 0 0
SLK 0.006 0.06 0.15 15 -0.18 17 32
p15 BID/BAX 0.012 0.047 -10000 0 -0.19 17 17
CASP2 -0.005 0.058 -10000 0 -0.16 25 25
JNK cascade -0.011 0.029 0.15 2 -10000 0 2
CASP3 0.003 0.064 0.15 22 -0.19 19 41
LMNB2 0.002 0.051 -10000 0 -0.23 5 5
RIPK1 0.01 0.056 -10000 0 -0.41 9 9
CASP4 -0.07 0.17 -10000 0 -0.41 107 107
Mammalian IAPs/DIABLO 0.018 0.059 -10000 0 -0.21 33 33
negative regulation of DNA binding 0.019 0.026 -10000 0 -0.28 1 1
stress fiber formation 0.006 0.06 0.15 15 -0.18 17 32
GZMB 0.004 0.067 -10000 0 -0.31 22 22
CASP1 -0.088 0.14 -10000 0 -0.26 195 195
LMNB1 -0.014 0.06 -10000 0 -0.21 12 12
APP 0.014 0.037 -10000 0 -0.56 1 1
TNFRSF1A -0.13 0.2 -10000 0 -0.41 183 183
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.003 0.041 -10000 0 -0.29 10 10
VIM 0.002 0.073 0.17 12 -0.22 21 33
LMNA 0.005 0.048 -10000 0 -0.19 5 5
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.009 0.061 -10000 0 -0.18 24 24
LRDD 0.017 0 -10000 0 -10000 0 0
SREBF1 0.006 0.06 0.15 15 -0.18 17 32
APAF-1/Caspase 9 0.01 0.026 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.01 0.055 0.14 2 -0.2 9 11
CFL2 0.006 0.057 0.14 15 -0.18 17 32
GAS2 -0.009 0.083 0.15 14 -0.2 55 69
positive regulation of apoptosis -0.003 0.055 -10000 0 -0.21 9 9
PRF1 0.007 0.064 -10000 0 -0.41 12 12
FoxO family signaling

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
G6PC 0.016 0.041 -9999 0 -0.24 2 2
PLK1 -0.078 0.15 -9999 0 -0.53 23 23
CDKN1B -0.071 0.1 -9999 0 -0.24 38 38
FOXO3 -0.083 0.14 -9999 0 -0.31 51 51
KAT2B -0.012 0.016 -9999 0 -0.042 23 23
FOXO1/SIRT1 0.014 0.045 -9999 0 -0.17 7 7
CAT -0.071 0.13 -9999 0 -0.36 26 26
CTNNB1 0.017 0 -9999 0 -10000 0 0
AKT1 -0.001 0.042 -9999 0 -0.43 4 4
FOXO1 0.011 0.046 -9999 0 -0.15 37 37
MAPK10 -0.002 0.045 -9999 0 -0.21 22 22
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
FOXO4 -0.013 0.082 -9999 0 -0.23 33 33
response to oxidative stress -0.01 0.016 -9999 0 -0.039 26 26
FOXO3A/SIRT1 -0.095 0.12 -9999 0 -0.34 34 34
XPO1 0.017 0.001 -9999 0 -10000 0 0
EP300 0.018 0.001 -9999 0 -10000 0 0
BCL2L11 0.006 0.022 -9999 0 -10000 0 0
FOXO1/SKP2 0.018 0.048 -9999 0 -0.29 4 4
mol:GDP -0.01 0.016 -9999 0 -0.039 26 26
RAN 0.017 0.002 -9999 0 -10000 0 0
GADD45A -0.063 0.14 -9999 0 -0.43 47 47
YWHAQ 0.017 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.012 0.044 -9999 0 -0.16 5 5
MST1 -0.004 0.05 -9999 0 -0.43 6 6
CSNK1D 0.015 0.026 -9999 0 -0.41 2 2
CSNK1E 0.017 0.001 -9999 0 -10000 0 0
FOXO4/14-3-3 family -0.035 0.079 -9999 0 -0.25 28 28
YWHAB 0.017 0.001 -9999 0 -10000 0 0
MAPK8 -0.008 0.064 -9999 0 -0.21 46 46
MAPK9 -0.007 0.064 -9999 0 -0.21 46 46
YWHAG 0 0 -9999 0 -10000 0 0
YWHAE 0.017 0.001 -9999 0 -10000 0 0
YWHAZ 0.017 0.002 -9999 0 -10000 0 0
SIRT1 0.013 0.006 -9999 0 -10000 0 0
SOD2 -0.2 0.2 -9999 0 -0.36 291 291
RBL2 -0.051 0.1 -9999 0 -0.28 10 10
RAL/GDP -0.01 0.075 -9999 0 -0.25 46 46
CHUK 0 0.026 -9999 0 -0.4 1 1
Ran/GTP 0.012 0.005 -9999 0 -10000 0 0
CSNK1G2 0.017 0 -9999 0 -10000 0 0
RAL/GTP -0.008 0.07 -9999 0 -0.23 46 46
CSNK1G1 0.017 0 -9999 0 -10000 0 0
FASLG 0.006 0.022 -9999 0 -10000 0 0
SKP2 0.015 0.026 -9999 0 -0.41 2 2
USP7 0.017 0.002 -9999 0 -10000 0 0
IKBKB 0.001 0.02 -9999 0 -10000 0 0
CCNB1 -0.18 0.21 -9999 0 -0.36 296 296
FOXO1-3a-4/beta catenin -0.08 0.13 -9999 0 -0.32 19 19
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.047 -9999 0 -0.29 4 4
CSNK1A1 0.017 0 -9999 0 -10000 0 0
SGK1 -0.012 0.016 -9999 0 -0.042 23 23
CSNK1G3 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.007 -9999 0 -10000 0 0
ZFAND5 -0.005 0.073 -9999 0 -0.24 12 12
SFN -0.01 0.1 -9999 0 -0.41 33 33
CDK2 -0.003 0.094 -9999 0 -0.41 27 27
FOXO3A/14-3-3 -0.041 0.072 -9999 0 -0.22 36 36
CREBBP 0.019 0.002 -9999 0 -10000 0 0
FBXO32 -0.077 0.12 -9999 0 -0.34 29 29
BCL6 -0.06 0.12 -9999 0 -0.45 16 16
RALB 0.016 0.019 -9999 0 -0.41 1 1
RALA -0.02 0.12 -9999 0 -0.41 45 45
YWHAH 0.008 0.009 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.007 0.057 -10000 0 -0.2 34 34
HDAC1 -0.029 0.14 -10000 0 -0.4 65 65
AES 0.019 0.005 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
DTX1 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.019 0.045 -10000 0 -0.29 11 11
TLE1 0.019 0.004 -10000 0 -10000 0 0
AP1 -0.02 0.068 -10000 0 -0.14 125 125
NCSTN -0.007 0.1 -10000 0 -0.41 30 30
ADAM10 0.003 0.078 -10000 0 -0.41 18 18
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.016 0.081 -10000 0 -0.22 11 11
NICD/RBPSUH 0.018 0.059 -10000 0 -0.26 10 10
WIF1 0.002 0.006 -10000 0 -10000 0 0
NOTCH1 0.009 0.061 -10000 0 -0.21 34 34
PSENEN 0.017 0.001 -10000 0 -10000 0 0
KREMEN2 0.017 0 -10000 0 -10000 0 0
DKK1 -0.077 0.18 -10000 0 -0.41 116 116
beta catenin/beta TrCP1 0.023 0.03 -10000 0 -10000 0 0
APH1B 0.017 0 -10000 0 -10000 0 0
APH1A 0.009 0.059 -10000 0 -0.41 10 10
AXIN1 0.003 0.028 0.18 5 -10000 0 5
CtBP/CBP/TCF1/TLE1/AES 0.035 0.065 0.17 32 -0.13 31 63
PSEN1 0.016 0.019 -10000 0 -0.41 1 1
FOS -0.085 0.18 -10000 0 -0.41 125 125
JUN 0.016 0.019 -10000 0 -0.41 1 1
MAP3K7 0.019 0.02 -10000 0 -0.41 1 1
CTNNB1 0.016 0.029 -10000 0 -10000 0 0
MAPK3 0.017 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.029 0.039 -10000 0 -0.24 11 11
HNF1A 0.019 0.004 -10000 0 -10000 0 0
CTBP1 0.019 0.005 -10000 0 -10000 0 0
MYC -0.092 0.18 -10000 0 -0.4 137 137
NKD1 0.001 0.002 -10000 0 -10000 0 0
FZD1 0.009 0.059 -10000 0 -0.41 10 10
NOTCH1 precursor/Deltex homolog 1 0.007 0.057 -10000 0 -0.2 34 34
apoptosis -0.02 0.068 -10000 0 -0.14 125 125
Delta 1/NOTCHprecursor 0.007 0.057 -10000 0 -0.2 34 34
DLL1 0 0 -10000 0 -10000 0 0
PPARD 0.003 0.031 -10000 0 -10000 0 0
Gamma Secretase 0.031 0.067 -10000 0 -0.2 39 39
APC -0.01 0.063 0.18 2 -0.29 21 23
DVL1 0.003 0.009 -10000 0 -10000 0 0
CSNK2A1 0.016 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0.02 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.025 0.11 -10000 0 -0.24 117 117
LRP6 0.016 0.019 -10000 0 -0.41 1 1
CSNK1A1 0.016 0.002 -10000 0 -10000 0 0
NLK 0.028 0.017 -10000 0 -0.18 1 1
CCND1 -0.066 0.17 -10000 0 -0.41 99 99
WNT1 0.017 0 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.024 0.052 0.19 2 -0.2 6 8
DKK2 0.009 0.059 -10000 0 -0.41 10 10
NOTCH1 precursor/DVL1 0.01 0.051 -10000 0 -0.2 12 12
GSK3B 0.017 0.002 -10000 0 -10000 0 0
FRAT1 0.017 0.019 -10000 0 -0.41 1 1
NOTCH/Deltex homolog 1 0.007 0.057 -10000 0 -0.2 34 34
PPP2R5D 0.002 0.007 -10000 0 -10000 0 0
MAPK1 0.017 0.003 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.003 0.023 -10000 0 -0.21 2 2
RBPJ 0.017 0 -10000 0 -10000 0 0
CREBBP 0.013 0.01 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
PDGFRA -0.025 0.13 -9999 0 -0.41 51 51
HRAS 0.016 0.019 -9999 0 -0.41 1 1
EGFR -0.14 0.21 -9999 0 -0.41 194 194
AKT 0.015 0.035 -9999 0 -0.27 5 5
FOXO3 0.017 0 -9999 0 -10000 0 0
AKT1 0.014 0.037 -9999 0 -0.41 4 4
FOXO1 0.008 0.061 -9999 0 -0.41 11 11
AKT3 0.016 0.019 -9999 0 -0.41 1 1
FOXO4 0.017 0 -9999 0 -10000 0 0
MET 0.009 0.059 -9999 0 -0.41 10 10
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
PIK3CB 0.017 0 -9999 0 -10000 0 0
NRAS -0.094 0.19 -9999 0 -0.41 136 136
PIK3CG 0.017 0 -9999 0 -10000 0 0
PIK3R3 0.016 0.019 -9999 0 -0.41 1 1
PIK3R2 0.017 0 -9999 0 -10000 0 0
NF1 0.017 0 -9999 0 -10000 0 0
RAS -0.047 0.064 -9999 0 -0.17 61 61
ERBB2 0.017 0 -9999 0 -10000 0 0
proliferation/survival/translation -0.041 0.026 -9999 0 -10000 0 0
PI3K -0.028 0.056 -9999 0 -0.12 71 71
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
KRAS 0.017 0.002 -9999 0 -10000 0 0
FOXO 0.021 0.034 -9999 0 -0.12 10 10
AKT2 0.017 0 -9999 0 -10000 0 0
PTEN 0.015 0.026 -9999 0 -0.41 2 2
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.022 0.005 -10000 0 -10000 0 0
NFATC2 0.041 0.11 -10000 0 -0.28 17 17
NFATC3 0.031 0.086 0.2 2 -0.22 1 3
CD40LG -0.038 0.18 -10000 0 -0.42 46 46
ITCH 0.026 0.037 -10000 0 -0.17 17 17
CBLB 0.026 0.035 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment 0.004 0.12 -10000 0 -0.35 15 15
JUNB 0.011 0.053 -10000 0 -0.41 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.043 -10000 0 -0.21 16 16
T cell anergy 0.012 0.053 -10000 0 -0.22 18 18
TLE4 0.031 0.073 -10000 0 -0.18 13 13
Jun/NFAT1-c-4/p21SNFT 0.028 0.16 -10000 0 -0.33 18 18
AP-1/NFAT1-c-4 -0.022 0.22 -10000 0 -0.46 46 46
IKZF1 0.031 0.073 -10000 0 -0.18 13 13
T-helper 2 cell differentiation 0.02 0.091 -10000 0 -10000 0 0
AP-1/NFAT1 -0.029 0.14 -10000 0 -0.25 103 103
CALM1 0.022 0.026 -10000 0 -10000 0 0
EGR2 0.076 0.14 -10000 0 -0.36 13 13
EGR3 0.084 0.12 -10000 0 -0.38 3 3
NFAT1/FOXP3 0.042 0.082 -10000 0 -0.22 5 5
EGR1 0.006 0.071 -10000 0 -0.41 15 15
JUN 0.013 0.028 -10000 0 -0.41 1 1
EGR4 0.018 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.005 0.029 -10000 0 -0.14 20 20
GBP3 0.024 0.07 -10000 0 -0.18 15 15
FOSL1 0.007 0.067 -10000 0 -0.41 13 13
NFAT1-c-4/MAF/IRF4 0.034 0.15 -10000 0 -0.28 21 21
DGKA 0.031 0.073 -10000 0 -0.22 5 5
CREM 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG 0.023 0.16 -10000 0 -0.31 25 25
CTLA4 0.037 0.056 -10000 0 -0.19 2 2
NFAT1-c-4 (dimer)/EGR1 0.023 0.16 -10000 0 -0.32 26 26
NFAT1-c-4 (dimer)/EGR4 0.029 0.16 -10000 0 -0.3 21 21
FOS -0.088 0.19 -10000 0 -0.42 125 125
IFNG 0.019 0.08 -10000 0 -0.45 1 1
T cell activation -0.002 0.11 -10000 0 -0.38 2 2
MAF 0.018 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.083 0.13 0.32 6 -0.3 74 80
TNF 0.017 0.14 -10000 0 -0.34 9 9
FASLG -0.012 0.21 -10000 0 -0.38 80 80
TBX21 0.023 0.004 -10000 0 -10000 0 0
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ 0.02 0.001 -10000 0 -10000 0 0
PTPN1 0.031 0.073 -10000 0 -0.22 5 5
NFAT1-c-4/ICER1 0.023 0.16 -10000 0 -0.3 23 23
GATA3 0.016 0.042 -10000 0 -0.41 5 5
T-helper 1 cell differentiation 0.019 0.08 -10000 0 -0.44 1 1
IL2RA 0.003 0.13 -10000 0 -0.37 15 15
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.025 0.16 -10000 0 -0.34 99 99
E2F1 -0.059 0.062 -10000 0 -10000 0 0
PPARG 0.013 0.042 -10000 0 -0.41 5 5
SLC3A2 0.025 0.093 -10000 0 -0.31 19 19
IRF4 0.017 0.019 -10000 0 -0.41 1 1
PTGS2 -0.048 0.2 -10000 0 -0.49 51 51
CSF2 -0.038 0.18 -10000 0 -0.42 46 46
JunB/Fra1/NFAT1-c-4 0.023 0.16 -10000 0 -0.3 24 24
IL4 0.02 0.092 -10000 0 -10000 0 0
IL5 -0.038 0.18 -10000 0 -0.42 46 46
IL2 -0.003 0.11 -10000 0 -0.38 2 2
IL3 -0.001 0.03 -10000 0 -10000 0 0
RNF128 0.016 0.076 -10000 0 -0.37 19 19
NFATC1 0.083 0.13 0.3 74 -0.32 6 80
CDK4 -0.19 0.18 0.29 4 -0.44 155 159
PTPRK 0.031 0.073 -10000 0 -0.18 13 13
IL8 -0.08 0.23 -10000 0 -0.46 109 109
POU2F1 0.023 0 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.029 0.11 -9999 0 -0.28 35 35
RAD9A 0.016 0.019 -9999 0 -0.41 1 1
AP1 -0.049 0.13 -9999 0 -0.29 125 125
IFNAR2 0.017 0.005 -9999 0 -10000 0 0
AKT1 0.018 0.021 -9999 0 -0.2 4 4
ER alpha/Oestrogen 0.012 0.003 -9999 0 -10000 0 0
NFX1/SIN3/HDAC complex -0.006 0.06 -9999 0 -0.18 23 23
EGF 0.015 0.026 -9999 0 -0.41 2 2
SMG5 0.017 0 -9999 0 -10000 0 0
SMG6 0.017 0 -9999 0 -10000 0 0
SP3/HDAC2 -0.023 0.12 -9999 0 -0.3 78 78
TERT/c-Abl -0.024 0.1 -9999 0 -0.31 17 17
SAP18 0.017 0.001 -9999 0 -10000 0 0
MRN complex 0.035 0 -9999 0 -10000 0 0
WT1 0.013 0.042 -9999 0 -0.42 5 5
WRN 0.013 0.042 -9999 0 -0.41 5 5
SP1 0.016 0.008 -9999 0 -10000 0 0
SP3 -0.046 0.15 -9999 0 -0.41 77 77
TERF2IP 0.016 0.005 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.01 0.1 -9999 0 -0.31 11 11
Mad/Max 0.025 0.006 -9999 0 -10000 0 0
TERT -0.03 0.11 -9999 0 -0.29 37 37
CCND1 -0.054 0.17 -9999 0 -0.39 99 99
MAX 0.017 0.002 -9999 0 -10000 0 0
RBBP7 0.017 0.001 -9999 0 -10000 0 0
RBBP4 -0.064 0.17 -9999 0 -0.41 100 100
TERF2 0.016 0.01 -9999 0 -10000 0 0
PTGES3 0.017 0.001 -9999 0 -10000 0 0
SIN3A 0 0.001 -9999 0 -10000 0 0
Telomerase/911 0.026 0.034 -9999 0 -0.2 7 7
CDKN1B -0.005 0.087 -9999 0 -0.22 71 71
RAD1 0.015 0.026 -9999 0 -0.41 2 2
XRCC5 0.017 0 -9999 0 -10000 0 0
XRCC6 0.017 0 -9999 0 -10000 0 0
SAP30 0.017 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0.024 0.01 -9999 0 -10000 0 0
UBE3A 0.017 0.002 -9999 0 -10000 0 0
JUN 0.016 0.019 -9999 0 -0.41 1 1
E6 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.012 0.006 -9999 0 -10000 0 0
FOS -0.085 0.18 -9999 0 -0.41 125 125
IFN-gamma/IRF1 -0.008 0.11 -9999 0 -0.28 71 71
PARP2 0.017 0.001 -9999 0 -10000 0 0
BLM -0.084 0.18 -9999 0 -0.41 124 124
Telomerase 0.013 0.035 -9999 0 -0.17 7 7
IRF1 -0.036 0.14 -9999 0 -0.41 70 70
ESR1 0.017 0.001 -9999 0 -10000 0 0
KU/TER 0.025 0 -9999 0 -10000 0 0
ATM/TRF2 0.011 0.056 -9999 0 -0.24 25 25
ubiquitin-dependent protein catabolic process -0.003 0.063 -9999 0 -0.19 22 22
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.003 0.064 -9999 0 -0.19 22 22
HDAC1 -0.036 0.14 -9999 0 -0.41 65 65
HDAC2 0.012 0.043 -9999 0 -0.42 5 5
ATM -0.007 0.056 -9999 0 -0.26 25 25
SMAD3 0.002 0.067 -9999 0 -0.28 27 27
ABL1 0.016 0.019 -9999 0 -0.41 1 1
MXD1 0.017 0.002 -9999 0 -10000 0 0
MRE11A 0.017 0 -9999 0 -10000 0 0
HUS1 0.017 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0.019 -9999 0 -0.41 1 1
TERT/NF kappa B1/14-3-3 -0.004 0.1 -9999 0 -0.31 8 8
NR2F2 0.014 0.037 -9999 0 -0.41 4 4
MAPK3 0.017 0.004 -9999 0 -10000 0 0
MAPK1 0.017 0.005 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II -0.005 0.094 -9999 0 -0.41 27 27
NFKB1 0.014 0.037 -9999 0 -0.41 4 4
HNRNPC 0.017 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.007 0.056 -9999 0 -0.26 25 25
NBN 0.017 0 -9999 0 -10000 0 0
EGFR -0.14 0.21 -9999 0 -0.41 194 194
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.09 0.15 -9999 0 -0.28 196 196
MYC -0.095 0.19 -9999 0 -0.41 137 137
IL2 0.016 0.009 -9999 0 -10000 0 0
KU 0.025 0 -9999 0 -10000 0 0
RAD50 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0 -9999 0 -10000 0 0
TGFB1 -0.005 0.095 -9999 0 -0.41 27 27
TRF2/BLM -0.045 0.12 -9999 0 -0.26 124 124
FRAP1 0.016 0.019 -9999 0 -0.41 1 1
KU/TERT -0.014 0.11 -9999 0 -0.31 12 12
SP1/HDAC2 0.021 0.034 -9999 0 -0.3 5 5
PINX1 0 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.01 0.1 -9999 0 -0.31 11 11
Smad3/Myc -0.054 0.13 -9999 0 -0.25 153 153
911 complex 0.033 0.02 -9999 0 -0.24 3 3
IFNG 0.02 0.019 -9999 0 -0.41 1 1
Telomerase/PinX1 -0.033 0.091 -9999 0 -0.3 15 15
Telomerase/AKT1/mTOR/p70S6K 0.023 0.041 -9999 0 -0.21 3 3
SIN3B 0.017 0.001 -9999 0 -10000 0 0
YWHAE 0.017 0.001 -9999 0 -10000 0 0
Telomerase/EST1B -0.01 0.1 -9999 0 -0.31 11 11
response to DNA damage stimulus 0 0.014 -9999 0 -0.062 25 25
MRN complex/TRF2/Rap1 0.044 0.017 -9999 0 -10000 0 0
TRF2/WRN 0.021 0.03 -9999 0 -0.26 5 5
Telomerase/hnRNP C1/C2 -0.01 0.1 -9999 0 -0.31 11 11
E2F1 0.017 0.005 -9999 0 -10000 0 0
ZNFX1 0 0.001 -9999 0 -10000 0 0
PIF1 0 0 -9999 0 -10000 0 0
NCL 0.017 0 -9999 0 -10000 0 0
DKC1 0.011 0.049 -9999 0 -0.41 7 7
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.037 -10000 0 -0.41 4 4
ANTXR2 0 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0.004 -10000 0 -0.051 4 4
monocyte activation -0.084 0.071 -10000 0 -0.13 353 353
MAP2K2 0.012 0.002 -10000 0 -10000 0 0
MAP2K1 0.004 0.004 -10000 0 -10000 0 0
MAP2K7 0.005 0.004 -10000 0 -10000 0 0
MAP2K6 0.005 0.004 -10000 0 -10000 0 0
CYAA 0.002 0.018 -10000 0 -0.2 4 4
MAP2K4 0.004 0.004 -10000 0 -10000 0 0
IL1B -0.006 0.036 -10000 0 -0.21 14 14
Channel 0.009 0.02 -10000 0 -0.22 4 4
NLRP1 0.005 0.004 -10000 0 -10000 0 0
CALM1 0.016 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.01 0.006 -10000 0 -0.055 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0.004 0.051 4 -10000 0 4
MAPK3 0.005 0.004 -10000 0 -10000 0 0
MAPK1 0.004 0.004 -10000 0 -10000 0 0
PGR 0.005 0.004 -10000 0 -10000 0 0
PA/Cellular Receptors 0.01 0.022 -10000 0 -0.24 4 4
apoptosis 0 0.004 -10000 0 -0.051 4 4
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.009 0.018 -10000 0 -0.2 4 4
macrophage activation 0.008 0.004 -10000 0 -10000 0 0
TNF 0.015 0.026 -10000 0 -0.41 2 2
VCAM1 -0.084 0.071 -10000 0 -0.14 353 353
platelet activation 0.01 0.006 -10000 0 -0.055 4 4
MAPKKK cascade -0.009 0.009 -10000 0 -10000 0 0
IL18 -0.018 0.062 -10000 0 -0.22 45 45
negative regulation of macrophage activation 0 0.004 -10000 0 -0.051 4 4
LEF 0 0.004 -10000 0 -0.052 4 4
CASP1 -0.005 0.015 -10000 0 -0.063 4 4
mol:cAMP 0.01 0.006 -10000 0 -0.055 4 4
necrosis 0 0.004 -10000 0 -0.051 4 4
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.009 0.019 -10000 0 -0.2 4 4
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.01 0.052 0.2 5 -0.33 10 15
SMARCC2 0.016 0.019 -10000 0 -0.41 1 1
SMARCC1 0.002 0.078 -10000 0 -0.41 18 18
TBX21 0.016 0.033 0.17 1 -0.19 1 2
SUMO2 0.018 0.004 -10000 0 -10000 0 0
STAT1 (dimer) -0.012 0.11 -10000 0 -0.27 60 60
FKBP4 0.017 0 -10000 0 -10000 0 0
FKBP5 -0.004 0.093 -10000 0 -0.41 26 26
GR alpha/HSP90/FKBP51/HSP90 -0.009 0.048 0.2 1 -0.27 11 12
PRL 0.014 0.056 -10000 0 -0.42 6 6
cortisol/GR alpha (dimer)/TIF2 -0.015 0.059 0.32 6 -0.33 2 8
RELA -0.01 0.073 -10000 0 -0.2 40 40
FGG -0.021 0.061 0.29 2 -0.41 5 7
GR beta/TIF2 -0.005 0.026 0.2 1 -10000 0 1
IFNG -0.038 0.13 -10000 0 -0.28 92 92
apoptosis 0.022 0.078 0.32 25 -0.27 2 27
CREB1 0.023 0.024 -10000 0 -0.19 7 7
histone acetylation 0.013 0.025 0.15 1 -10000 0 1
BGLAP 0.017 0.034 -10000 0 -10000 0 0
GR/PKAc 0.006 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.014 0.14 -10000 0 -0.24 110 110
SMARCD1 0.017 0 -10000 0 -10000 0 0
MDM2 -0.009 0.029 0.16 1 -0.13 14 15
GATA3 0.026 0.042 -10000 0 -0.4 5 5
AKT1 0.01 0.041 0.14 4 -0.42 4 8
CSF2 0.004 0.04 -10000 0 -10000 0 0
GSK3B 0.018 0.004 -10000 0 -10000 0 0
NR1I3 0.075 0.1 0.36 16 -0.25 2 18
CSN2 0 0.086 0.32 28 -0.29 2 30
BRG1/BAF155/BAF170/BAF60A 0.035 0.047 -10000 0 -0.21 19 19
NFATC1 0.026 0 -10000 0 -10000 0 0
POU2F1 0.022 0.015 -10000 0 -10000 0 0
CDKN1A -0.058 0.15 -10000 0 -0.32 102 102
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.005 -10000 0 -10000 0 0
SFN -0.01 0.1 -10000 0 -0.41 33 33
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.012 0.063 -10000 0 -0.24 28 28
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.069 0.11 0.35 15 -0.33 6 21
JUN 0.018 0.058 -10000 0 -0.3 9 9
IL4 0.018 0.033 -10000 0 -0.18 1 1
CDK5R1 0.014 0.007 -10000 0 -10000 0 0
PRKACA 0.017 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.021 0.081 0.12 7 -0.25 44 51
GR alpha/HSP90/FKBP51/HSP90/PP5C 0 0.045 0.2 1 -0.24 11 12
cortisol/GR alpha (monomer) -0.022 0.07 0.35 6 -0.39 2 8
NCOA2 0.017 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.071 0.18 -10000 0 -0.4 125 125
AP-1/NFAT1-c-4 -0.027 0.13 -10000 0 -0.42 22 22
AFP 0.017 0.062 -10000 0 -0.51 2 2
SUV420H1 0.016 0.019 -10000 0 -0.41 1 1
IRF1 -0.043 0.11 0.22 2 -0.31 65 67
TP53 -0.046 0.17 -10000 0 -0.43 71 71
PPP5C 0.017 0 -10000 0 -10000 0 0
KRT17 -0.043 0.14 -10000 0 -0.31 90 90
KRT14 0.003 0.063 -10000 0 -0.48 8 8
TBP 0.025 0.019 -10000 0 -0.4 1 1
CREBBP 0.01 0.018 0.16 8 -10000 0 8
HDAC1 -0.041 0.14 -10000 0 -0.42 65 65
HDAC2 0.011 0.042 -10000 0 -0.42 5 5
AP-1 -0.027 0.13 -10000 0 -0.42 22 22
MAPK14 0.017 0.027 -10000 0 -0.41 2 2
MAPK10 0.01 0.01 -10000 0 -10000 0 0
MAPK11 0.018 0.004 -10000 0 -10000 0 0
KRT5 -0.043 0.14 -10000 0 -0.31 92 92
interleukin-1 receptor activity -0.002 0 -10000 0 -10000 0 0
NCOA1 0.017 0.01 -10000 0 -10000 0 0
STAT1 -0.012 0.11 -10000 0 -0.27 60 60
CGA 0.012 0.059 -10000 0 -0.4 7 7
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.007 0.034 0.18 5 -0.21 3 8
MAPK3 0.018 0.005 -10000 0 -10000 0 0
MAPK1 0.018 0.005 -10000 0 -10000 0 0
ICAM1 -0.052 0.16 -10000 0 -0.33 110 110
NFKB1 -0.013 0.084 -10000 0 -0.23 43 43
MAPK8 0.019 0.048 0.19 1 -0.23 7 8
MAPK9 0.018 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.022 0.078 0.33 24 -0.28 2 26
BAX -0.035 0.1 -10000 0 -0.25 56 56
POMC -0.045 0.083 0.21 1 -10000 0 1
EP300 0.01 0.018 0.16 7 -10000 0 7
cortisol/GR alpha (dimer)/p53 -0.029 0.088 0.34 5 -0.33 22 27
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.018 0.12 1 -0.19 1 2
SGK1 0.024 0.029 0.18 8 -10000 0 8
IL13 -0.015 0.092 -10000 0 -0.26 20 20
IL6 -0.069 0.2 -10000 0 -0.4 114 114
PRKACG 0.017 0 -10000 0 -10000 0 0
IL5 -0.004 0.088 0.24 6 -0.22 14 20
IL2 -0.037 0.13 -10000 0 -0.28 91 91
CDK5 0.017 0.005 -10000 0 -10000 0 0
PRKACB 0.016 0.005 -10000 0 -10000 0 0
HSP90AA1 0.017 0 -10000 0 -10000 0 0
IL8 -0.099 0.23 0.18 1 -0.47 134 135
CDK5R1/CDK5 0.021 0.012 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.021 0.1 -10000 0 -0.26 36 36
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 -0.011 0.055 0.31 6 -0.29 2 8
SMARCA4 0.017 0.001 -10000 0 -10000 0 0
chromatin remodeling -0.007 0.034 0.2 4 -0.17 6 10
NF kappa B1 p50/RelA/Cbp 0.004 0.11 0.22 2 -0.28 41 43
JUN (dimer) 0.018 0.058 -10000 0 -0.3 9 9
YWHAH 0.008 0.009 -10000 0 -10000 0 0
VIPR1 0.016 0.033 0.17 1 -0.19 1 2
NR3C1 -0.013 0.039 0.21 3 -0.21 2 5
NR4A1 0.024 0.001 -10000 0 -10000 0 0
TIF2/SUV420H1 0.025 0.014 -10000 0 -0.28 1 1
MAPKKK cascade 0.022 0.078 0.32 25 -0.27 2 27
cortisol/GR alpha (dimer)/Src-1 -0.015 0.055 0.36 3 -0.28 2 5
PBX1 0.022 0.015 -10000 0 -10000 0 0
POU1F1 0.022 0.015 -10000 0 -10000 0 0
SELE -0.045 0.14 -10000 0 -0.3 109 109
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.007 0.034 0.2 4 -0.18 6 10
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 -0.011 0.055 0.31 6 -0.29 2 8
mol:cortisol -0.017 0.041 0.17 5 -0.16 9 14
MMP1 -0.025 0.13 -10000 0 -0.44 43 43
Ceramide signaling pathway

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
SPHK2 0.011 0.043 -10000 0 -0.28 11 11
MAP4K4 -0.015 0.068 -10000 0 -0.2 24 24
BAG4 0.017 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.004 0.02 0.1 11 -0.1 8 19
NFKBIA 0.016 0.019 -10000 0 -0.41 1 1
BIRC3 -0.01 0.1 -10000 0 -0.41 33 33
BAX 0.004 0.021 -10000 0 -0.16 7 7
RIPK1 0.01 0.056 -10000 0 -0.41 9 9
AKT1 0.007 0.034 -10000 0 -0.38 4 4
BAD -0.001 0.021 0.11 11 -0.097 8 19
SMPD1 -0.021 0.057 -10000 0 -0.097 185 185
RB1 -0.001 0.021 0.11 11 -10000 0 11
FADD/Caspase 8 -0.007 0.069 -10000 0 -0.19 33 33
MAP2K4 0.003 0.021 0.11 11 -0.19 1 12
NSMAF 0.015 0.026 -10000 0 -0.41 2 2
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.002 0.021 0.11 11 -0.19 1 12
EGF 0.015 0.026 -10000 0 -0.41 2 2
mol:ceramide -0.005 0.022 0.12 11 -0.11 8 19
MADD 0.017 0.001 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.011 0.043 -10000 0 -0.28 11 11
ASAH1 0.017 0.001 -10000 0 -10000 0 0
negative regulation of cell cycle -0.001 0.02 0.11 11 -10000 0 11
cell proliferation 0.026 0.026 -10000 0 -0.16 5 5
BID -0.002 0.053 -10000 0 -0.21 4 4
MAP3K1 -0.001 0.022 0.11 11 -0.11 9 20
EIF2A 0.003 0.02 -10000 0 -10000 0 0
TRADD 0.017 0 -10000 0 -10000 0 0
CRADD 0.017 0 -10000 0 -10000 0 0
MAPK3 0.011 0.022 -10000 0 -0.18 1 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.008 0.028 -10000 0 -0.18 2 2
Cathepsin D/ceramide 0.001 0.042 0.11 11 -0.19 19 30
FADD -0.015 0.068 -10000 0 -0.2 26 26
KSR1 -0.001 0.021 0.11 11 -0.1 3 14
MAPK8 0.008 0.024 0.11 11 -0.12 1 12
PRKRA -0.001 0.021 0.11 11 -0.097 8 19
PDGFA 0.008 0.061 -10000 0 -0.41 11 11
TRAF2 0.017 0 -10000 0 -10000 0 0
IGF1 0.014 0.037 -10000 0 -0.41 4 4
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.004 0.022 0.12 11 -0.11 8 19
CTSD 0.004 0.074 -10000 0 -0.41 16 16
regulation of nitric oxide biosynthetic process 0.023 0.027 -10000 0 -0.28 4 4
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.029 0.028 -10000 0 -0.16 5 5
PRKCD 0.017 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.011 0.043 -10000 0 -0.28 11 11
RelA/NF kappa B1 0.023 0.027 -10000 0 -0.28 4 4
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.017 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.018 0.072 -10000 0 -0.21 24 24
TNFR1A/BAG4/TNF-alpha -0.06 0.13 -10000 0 -0.24 185 185
mol:Sphingosine-1-phosphate 0.011 0.043 -10000 0 -0.28 11 11
MAP2K1 0.006 0.02 -10000 0 -0.18 1 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
CYCS 0.002 0.018 -10000 0 -0.16 1 1
TNFRSF1A -0.13 0.2 -10000 0 -0.41 183 183
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
TNFR1A/BAG4 -0.082 0.15 -10000 0 -0.28 183 183
EIF2AK2 0.003 0.021 0.11 13 -10000 0 13
TNF-alpha/TNFR1A/FAN -0.061 0.13 -10000 0 -0.24 187 187
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.004 0.052 -10000 0 -0.2 12 12
MAP2K2 0.006 0.02 -10000 0 -0.18 1 1
SMPD3 -0.018 0.058 -10000 0 -0.096 185 185
TNF 0.015 0.026 -10000 0 -0.41 2 2
PKC zeta/PAR4 0.013 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE -0.013 0.023 0.1 9 -0.088 1 10
NF kappa B1/RelA/I kappa B alpha 0.039 0.023 -10000 0 -0.2 5 5
AIFM1 -0.001 0.028 -10000 0 -0.15 11 11
BCL2 0.017 0 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.025 0.029 -9999 0 -0.15 8 8
KLHL20 0.004 0.065 -9999 0 -0.13 87 87
CYFIP2 0.01 0.008 -9999 0 -10000 0 0
Rac1/GDP 0.033 0.027 -9999 0 -10000 0 0
ENAH 0.016 0.053 -9999 0 -0.18 33 33
AP1M1 0 0 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 0 4 4
RAP1A 0.017 0 -9999 0 -10000 0 0
CTNNB1 0.017 0 -9999 0 -10000 0 0
CDC42/GTP 0 0.02 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.032 -9999 0 -0.099 13 13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.039 0.037 -9999 0 -0.23 9 9
RAPGEF1 0.027 0.026 -9999 0 -10000 0 0
CTNND1 0.009 0.059 -9999 0 -0.41 10 10
regulation of calcium-dependent cell-cell adhesion 0.024 0.03 -9999 0 -0.16 8 8
CRK 0.026 0.028 -9999 0 -0.15 4 4
E-cadherin/gamma catenin/alpha catenin 0.023 0.064 -9999 0 -0.29 19 19
alphaE/beta7 Integrin 0.024 0.019 -9999 0 -0.28 2 2
IQGAP1 -0.086 0.18 -9999 0 -0.41 127 127
NCKAP1 0.017 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.022 0.001 -9999 0 -10000 0 0
DLG1 0.025 0.03 -9999 0 -0.16 9 9
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.006 0.025 -9999 0 -0.17 4 4
MLLT4 0.017 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.021 0.004 -9999 0 -10000 0 0
PI3K -0.008 0.031 -9999 0 -0.21 4 4
ARF6 0.017 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -0.001 97 97
E-cadherin/gamma catenin 0.012 0.073 -9999 0 -0.35 19 19
TIAM1 0.016 0.003 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.032 0.043 -9999 0 -0.2 18 18
AKT1 0.016 0.028 -9999 0 -0.12 8 8
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
CDH1 0.01 0.053 -9999 0 -0.41 8 8
RhoA/GDP 0.034 0.025 -9999 0 -10000 0 0
actin cytoskeleton organization 0.004 0.049 -9999 0 -0.099 87 87
CDC42/GDP 0.035 0.025 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.012 0.043 -9999 0 -0.16 28 28
ITGB7 0.015 0.026 -9999 0 -0.41 2 2
RAC1 0.017 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.035 0.046 -9999 0 -0.21 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin 0.027 0.028 -9999 0 -0.2 8 8
mol:GDP 0.027 0.027 -9999 0 -0.16 1 1
CDC42/GTP/IQGAP1 -0.04 0.11 -9999 0 -0.24 127 127
JUP 0.004 0.074 -9999 0 -0.41 16 16
p120 catenin/RhoA/GDP 0.036 0.032 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 -0.04 0.11 -9999 0 -0.24 127 127
PIP5K1C/AP1M1 0.012 0.002 -9999 0 -10000 0 0
RHOA 0.017 0.001 -9999 0 -10000 0 0
CDC42 0.017 0 -9999 0 -10000 0 0
CTNNA1 0.017 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.013 0.074 -9999 0 -0.17 99 99
NME1 0 0 -9999 0 -0.001 99 99
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.025 0.029 -9999 0 -0.15 8 8
regulation of cell-cell adhesion -0.003 0.016 -9999 0 -10000 0 0
WASF2 -0.008 0.018 -9999 0 -0.055 13 13
Rap1/GTP 0.025 0.026 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.039 0.062 -9999 0 -0.25 20 20
CCND1 -0.017 0.091 -9999 0 -0.21 99 99
VAV2 0.031 0.03 -9999 0 -10000 0 0
RAP1/GDP 0.028 0.026 -9999 0 -0.15 2 2
adherens junction assembly 0.025 0.028 -9999 0 -0.15 8 8
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.017 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0.003 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.037 0.058 -9999 0 -0.24 20 20
E-cadherin/beta catenin 0.019 0.032 -9999 0 -0.16 8 8
mol:GTP 0 0 -9999 0 -0.001 99 99
SRC 0.025 0.029 -9999 0 -0.16 8 8
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
Rac1/GTP -0.038 0.078 -9999 0 -0.2 95 95
E-cadherin/beta catenin/alpha catenin 0.03 0.033 -9999 0 -0.24 8 8
ITGAE 0.017 0.001 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.024 0.03 -9999 0 -0.16 8 8
Coregulation of Androgen receptor activity

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
NRIP1 0.016 0.032 -9999 0 -0.41 3 3
SVIL 0.004 0.078 -9999 0 -0.41 18 18
ZNF318 0.014 0 -9999 0 -10000 0 0
JMJD2C 0.023 0 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 0.03 0.034 -9999 0 -0.23 8 8
CARM1 0.017 0 -9999 0 -10000 0 0
PRDX1 0.017 0.001 -9999 0 -10000 0 0
PELP1 0.017 0 -9999 0 -10000 0 0
CTNNB1 0.018 0 -9999 0 -10000 0 0
AKT1 0.013 0.037 -9999 0 -0.41 4 4
PTK2B 0.018 0 -9999 0 -10000 0 0
MED1 0.016 0 -9999 0 -10000 0 0
MAK 0.008 0.052 -9999 0 -0.42 8 8
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 -0.026 0.13 -9999 0 -0.41 54 54
GSN 0.006 0.071 -9999 0 -0.41 15 15
NCOA2 0.017 0 -9999 0 -10000 0 0
NCOA6 0.018 0.001 -9999 0 -10000 0 0
DNA-PK 0.02 0.055 -9999 0 -0.24 23 23
NCOA4 0.017 0.001 -9999 0 -10000 0 0
PIAS3 0.016 0.026 -9999 0 -0.41 2 2
cell proliferation 0.012 0.033 -9999 0 -0.24 8 8
XRCC5 0.017 0 -9999 0 -10000 0 0
UBE3A 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.019 0.033 -9999 0 -0.23 8 8
FHL2 0.028 0.039 -9999 0 -0.37 4 4
RANBP9 0.018 0.001 -9999 0 -10000 0 0
JMJD1A 0.021 0.065 -9999 0 -0.4 12 12
CDK6 0.017 0 -9999 0 -10000 0 0
TGFB1I1 -0.34 0.16 -9999 0 -0.41 441 441
T-DHT/AR/CyclinD1 -0.018 0.11 -9999 0 -0.24 104 104
XRCC6 0.017 0 -9999 0 -10000 0 0
T-DHT/AR 0.047 0.04 -9999 0 -0.22 8 8
CTDSP1 0.015 0.032 -9999 0 -0.41 3 3
CTDSP2 -0.015 0.11 -9999 0 -0.42 37 37
BRCA1 0.014 0.042 -9999 0 -0.41 5 5
TCF4 0.016 0.002 -9999 0 -10000 0 0
CDKN2A -0.032 0.14 -9999 0 -0.41 59 59
SRF 0.021 0.011 -9999 0 -10000 0 0
NKX3-1 0.032 0.038 -9999 0 -0.18 11 11
KLK3 0.017 0.029 -9999 0 -10000 0 0
TMF1 0.014 0.037 -9999 0 -0.41 4 4
HNRNPA1 0.016 0 -9999 0 -10000 0 0
AOF2 0.013 0.049 -9999 0 -0.41 7 7
APPL1 0.014 0.026 -9999 0 -0.29 4 4
T-DHT/AR/Caspase 8 0.024 0.05 -9999 0 -0.24 18 18
AR 0.015 0.053 -9999 0 -0.4 8 8
UBA3 0 0 -9999 0 -10000 0 0
PATZ1 0.016 0 -9999 0 -10000 0 0
PAWR 0.017 0 -9999 0 -10000 0 0
PRKDC -0.002 0.088 -9999 0 -0.41 23 23
PA2G4 0.015 0.019 -9999 0 -0.41 1 1
UBE2I 0.017 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.028 0.032 -9999 0 -0.2 9 9
RPS6KA3 0.018 0.019 -9999 0 -0.41 1 1
T-DHT/AR/ARA70 0.03 0.034 -9999 0 -0.23 8 8
LATS2 -0.001 0 -9999 0 -10000 0 0
T-DHT/AR/PRX1 0.027 0.031 -9999 0 -0.2 8 8
Cyclin D3/CDK11 p58 0.012 0.013 -9999 0 -0.29 1 1
VAV3 -0.011 0.11 -9999 0 -0.41 36 36
KLK2 0.033 0.017 -9999 0 -10000 0 0
CASP8 0.009 0.059 -9999 0 -0.41 10 10
T-DHT/AR/TIF2/CARM1 0.04 0.033 -9999 0 -0.2 8 8
TMPRSS2 0.031 0.047 -9999 0 -0.22 14 14
CCND1 -0.063 0.17 -9999 0 -0.41 99 99
PIAS1 0.019 0 -9999 0 -10000 0 0
mol:T-DHT 0.005 0.006 -9999 0 -0.045 7 7
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.02 0 -9999 0 -10000 0 0
T-DHT/AR/CDK6 0.029 0.034 -9999 0 -0.23 8 8
CMTM2 0 0 -9999 0 -10000 0 0
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.021 0.009 -9999 0 -10000 0 0
CCND3 0.016 0.019 -9999 0 -0.41 1 1
TGIF1 -0.29 0.2 -9999 0 -0.41 371 371
FKBP4 0.018 0 -9999 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.04 0.051 -9999 0 -0.19 25 25
SMAD6-7/SMURF1 0.034 0.012 -9999 0 -0.24 1 1
NOG 0 0 -9999 0 -10000 0 0
SMAD9 0.02 0.019 -9999 0 -10000 0 0
SMAD4 -0.085 0.18 -9999 0 -0.41 126 126
SMAD5 0.02 0.034 -9999 0 -0.17 8 8
BMP7/USAG1 0.02 0.04 -9999 0 -0.28 9 9
SMAD5/SKI 0.029 0.035 -9999 0 -0.19 5 5
SMAD1 -0.004 0.074 -9999 0 -0.14 114 114
BMP2 -0.027 0.13 -9999 0 -0.41 54 54
SMAD1/SMAD1/SMAD4 -0.058 0.084 -9999 0 -0.26 49 49
BMPR1A 0.012 0.046 -9999 0 -0.41 6 6
BMPR1B 0.016 0.019 -9999 0 -0.41 1 1
BMPR1A-1B/BAMBI 0.014 0.075 -9999 0 -0.25 39 39
AHSG 0.015 0.026 -9999 0 -0.41 2 2
CER1 0.017 0 -9999 0 -10000 0 0
BMP2-4/CER1 0.003 0.087 -9999 0 -0.24 62 62
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA 0.016 0.046 -9999 0 -0.2 9 9
BMP2-4 (homodimer) -0.011 0.1 -9999 0 -0.28 62 62
RGMB 0 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.04 0.033 -9999 0 -0.21 9 9
RGMA 0 0 -9999 0 -10000 0 0
SMURF1 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP 0.007 0.04 -9999 0 -0.15 11 11
BMP2-4/USAG1 0 0.094 -9999 0 -0.24 66 66
SMAD6/SMURF1/SMAD5 0.029 0.035 -9999 0 -0.19 5 5
SOSTDC1 0.011 0.049 -9999 0 -0.41 7 7
BMP7/BMPR2/BMPR1A-1B 0.04 0.033 -9999 0 -0.21 9 9
SKI 0.017 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.015 0.026 -9999 0 -0.41 2 2
HFE2 0 0 -9999 0 -10000 0 0
ZFYVE16 0.013 0.042 -9999 0 -0.41 5 5
MAP3K7 0.016 0.019 -9999 0 -0.41 1 1
BMP2-4/CHRD 0.003 0.087 -9999 0 -0.24 62 62
SMAD5/SMAD5/SMAD4 -0.019 0.098 -9999 0 -0.18 127 127
MAPK1 0.017 0.003 -9999 0 -10000 0 0
TAK1/TAB family 0.035 0.041 -9999 0 -0.16 6 6
BMP7 (homodimer) 0.015 0.026 -9999 0 -0.41 2 2
NUP214 0.017 0 -9999 0 -10000 0 0
BMP6/FETUA 0.023 0.027 -9999 0 -0.28 4 4
SMAD1/SKI 0.002 0.075 -9999 0 -0.25 8 8
SMAD6 0.017 0 -9999 0 -10000 0 0
CTDSP2 -0.013 0.11 -9999 0 -0.41 37 37
BMP2-4/FETUA 0.002 0.089 -9999 0 -0.24 63 63
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
GREM1 -0.002 0.088 -9999 0 -0.41 23 23
BMPR2 (homodimer) 0.017 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.032 0.029 -9999 0 -0.24 6 6
BMPR1A-1B (homodimer) 0.021 0.036 -9999 0 -0.28 7 7
CHRDL1 0 0 -9999 0 -10000 0 0
ENDOFIN/SMAD1 0.001 0.077 -9999 0 -0.23 13 13
SMAD6-7/SMURF1/SMAD1 0.016 0.075 -9999 0 -0.23 8 8
SMAD6/SMURF1 0.017 0 -9999 0 -10000 0 0
BAMBI -0.011 0.1 -9999 0 -0.41 34 34
SMURF2 0.015 0.026 -9999 0 -0.41 2 2
BMP2-4/CHRDL1 -0.007 0.084 -9999 0 -0.24 62 62
BMP2-4/GREM1 -0.008 0.1 -9999 0 -0.24 82 82
SMAD7 0.016 0.019 -9999 0 -0.41 1 1
SMAD8A/SMAD8A/SMAD4 -0.023 0.096 -9999 0 -0.19 126 126
SMAD1/SMAD6 0.002 0.075 -9999 0 -0.25 8 8
TAK1/SMAD6 0.025 0.014 -9999 0 -0.28 1 1
BMP7 0.015 0.026 -9999 0 -0.41 2 2
BMP6 0.015 0.026 -9999 0 -0.41 2 2
MAP3K7IP2 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 0.013 0.038 -9999 0 -0.19 5 5
PPM1A 0.017 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.002 0.075 -9999 0 -0.23 10 10
SMAD7/SMURF1 0.025 0.014 -9999 0 -0.28 1 1
CTDSPL 0.017 0 -9999 0 -10000 0 0
PPP1CA 0.017 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.015 0.032 -9999 0 -0.41 3 3
PPP1R15A 0.016 0.019 -9999 0 -0.41 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS 0.007 0.047 -9999 0 -0.14 26 26
CHRD 0.017 0 -9999 0 -10000 0 0
BMPR2 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM 0.006 0.045 -9999 0 -0.11 64 64
BMP4 0.011 0.052 -9999 0 -0.41 8 8
FST 0.004 0.074 -9999 0 -0.41 16 16
BMP2-4/NOG -0.007 0.084 -9999 0 -0.24 62 62
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.047 0.031 -9999 0 -0.19 9 9
IL2 signaling events mediated by PI3K

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
BCL2L1 0.034 0.044 -10000 0 -0.26 5 5
UGCG 0.012 0.026 -10000 0 -0.22 1 1
AKT1/mTOR/p70S6K/Hsp90/TERT 0.017 0.092 -10000 0 -0.24 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.012 0.026 -10000 0 -0.22 1 1
mol:DAG 0.006 0.01 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.01 0.1 -10000 0 -0.24 35 35
FRAP1 0.002 0.12 -10000 0 -0.26 51 51
FOXO3 -0.003 0.12 -10000 0 -0.27 44 44
AKT1 -0.008 0.13 -10000 0 -0.28 50 50
GAB2 0.015 0.019 -10000 0 -0.41 1 1
SMPD1 0.013 0.024 -10000 0 -10000 0 0
SGMS1 0.012 0.027 -10000 0 -0.26 1 1
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 -0.001 0.053 -10000 0 -0.24 25 25
CALM1 0.016 0.004 -10000 0 -10000 0 0
cell proliferation -0.001 0.077 -10000 0 -0.26 4 4
EIF3A 0.017 0 -10000 0 -10000 0 0
PI3K 0.011 0.066 -10000 0 -0.28 25 25
RPS6KB1 0.017 0.027 -10000 0 -0.34 1 1
mol:sphingomyelin 0.006 0.01 -10000 0 -10000 0 0
natural killer cell activation -0.001 0.003 -10000 0 -0.006 134 134
JAK3 0.018 0.003 -10000 0 -10000 0 0
PIK3R1 0.017 0.006 -10000 0 -10000 0 0
JAK1 0.018 0.004 -10000 0 -10000 0 0
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
MYC -0.043 0.18 -10000 0 -0.35 137 137
MYB 0.023 0.05 -10000 0 -0.38 8 8
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.008 0.092 -10000 0 -0.23 37 37
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.037 0.026 -10000 0 -0.31 1 1
mol:PI-3-4-5-P3 0.009 0.091 -10000 0 -0.22 37 37
Rac1/GDP 0.01 0.049 -10000 0 -0.21 24 24
T cell proliferation 0.008 0.086 -10000 0 -0.21 38 38
SHC1 -0.021 0.12 -10000 0 -0.42 46 46
RAC1 0.017 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.005 -10000 0 -0.039 8 8
PRKCZ 0.007 0.088 -10000 0 -0.21 38 38
NF kappa B1 p50/RelA 0.014 0.12 -10000 0 -0.27 30 30
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.03 0.047 -10000 0 -0.28 5 5
HSP90AA1 0.017 0 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
IL2RA 0.011 0.046 -10000 0 -0.41 6 6
IL2RB 0.015 0.038 -10000 0 -0.42 4 4
TERT 0.017 0 -10000 0 -10000 0 0
E2F1 0.023 0.032 -10000 0 -0.23 8 8
SOS1 -0.001 0.003 -10000 0 -0.006 134 134
RPS6 0.017 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.002 0.018 8 -10000 0 8
PTPN11 0.016 0.003 -10000 0 -10000 0 0
IL2RG 0.01 0.056 -10000 0 -0.42 9 9
actin cytoskeleton organization 0.008 0.086 -10000 0 -0.21 38 38
GRB2 0.016 0.003 -10000 0 -10000 0 0
IL2 0.018 0.004 -10000 0 -10000 0 0
PIK3CA -0.003 0.092 -10000 0 -0.41 25 25
Rac1/GTP 0.019 0.052 -10000 0 -0.2 24 24
LCK 0.014 0.038 -10000 0 -0.42 4 4
BCL2 0.012 0.1 -10000 0 -0.22 43 43
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.017 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.01 0.065 -10000 0 -0.12 131 131
NT3 (dimer)/TRKC 0.025 0.004 -10000 0 -10000 0 0
NT3 (dimer)/TRKB 0.021 0.052 -10000 0 -0.24 20 20
SHC/Grb2/SOS1/GAB1/PI3K 0.004 0.057 -10000 0 -0.14 70 70
RAPGEF1 0.017 0 -10000 0 -10000 0 0
BDNF 0.005 0.008 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
DYNLT1 -0.044 0.15 -10000 0 -0.41 75 75
NTRK1 0.015 0.026 -10000 0 -0.41 2 2
NTRK2 0.015 0.005 -10000 0 -10000 0 0
NTRK3 0.017 0.003 -10000 0 -10000 0 0
NT-4/5 (dimer)/TRKB 0.011 0.051 -10000 0 -0.23 22 22
neuron apoptosis 0.01 0.048 0.19 17 -10000 0 17
SHC 2-3/Grb2 -0.011 0.051 -10000 0 -0.2 17 17
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
SHC2 -0.012 0.05 -10000 0 -0.17 37 37
SHC3 -0.014 0.06 -10000 0 -0.19 40 40
STAT3 (dimer) -0.028 0.11 -10000 0 -0.24 105 105
NT3 (dimer)/TRKA 0.023 0.058 -10000 0 -0.24 23 23
RIN/GDP 0.015 0.028 -10000 0 -0.12 6 6
GIPC1 0.017 0 -10000 0 -10000 0 0
KRAS 0.017 0.002 -10000 0 -10000 0 0
DNAJA3 0.002 0.043 -10000 0 -0.17 23 23
RIN/GTP 0.005 0.023 -10000 0 -0.29 3 3
CCND1 -0.059 0.17 -10000 0 -0.4 105 105
MAGED1 0.017 0.001 -10000 0 -10000 0 0
PTPN11 0.017 0 -10000 0 -10000 0 0
RICS 0.013 0.008 -10000 0 -10000 0 0
NT-4/5 (dimer) 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0 0.074 -10000 0 -0.24 46 46
GRB2 0.017 0.002 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.022 0.016 -10000 0 -0.24 2 2
TRKA/NEDD4-2 0.024 0.019 -10000 0 -0.28 2 2
ELMO1 0.011 0.008 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.015 0.011 -10000 0 -10000 0 0
NGF 0 0 -10000 0 -10000 0 0
HRAS 0.016 0.019 -10000 0 -0.41 1 1
DOCK1 0.017 0 -10000 0 -10000 0 0
GAB2 0.016 0.019 -10000 0 -0.41 1 1
RIT2 0.007 0.033 -10000 0 -0.41 3 3
RIT1 -0.12 0.2 -10000 0 -0.41 163 163
FRS2 0.015 0.032 -10000 0 -0.41 3 3
DNM1 0.003 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.017 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.004 0.04 -10000 0 -0.17 19 19
mol:GDP 0.017 0.047 -10000 0 -0.14 11 11
NGF (dimer) 0 0 -10000 0 -10000 0 0
RhoG/GDP 0.008 0.006 -10000 0 -10000 0 0
RIT1/GDP -0.023 0.08 -10000 0 -0.13 159 159
TIAM1 0.016 0.003 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.001 0.044 -10000 0 -0.24 12 12
KIDINS220/CRKL/C3G 0.025 0 -10000 0 -10000 0 0
SHC/RasGAP -0.002 0.088 -10000 0 -0.28 46 46
FRS2 family/SHP2 0.033 0.02 -10000 0 -0.24 3 3
SHC/GRB2/SOS1/GAB1 0.01 0.072 -10000 0 -0.21 50 50
RIT1/GTP -0.081 0.14 -10000 0 -0.29 163 163
NT3 (dimer) 0.017 0 -10000 0 -10000 0 0
RAP1/GDP -0.005 0.021 -10000 0 -10000 0 0
KIDINS220/CRKL 0.017 0 -10000 0 -10000 0 0
BDNF (dimer) 0.005 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.022 0.016 -10000 0 -0.24 2 2
Schwann cell development -0.002 0.007 -10000 0 -10000 0 0
EHD4 -0.011 0.1 -10000 0 -0.41 34 34
FRS2 family/GRB2/SOS1 0.031 0.019 -10000 0 -0.21 3 3
FRS2 family/SHP2/CRK family/C3G/GAB2 0.033 0.011 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.017 0 -10000 0 -10000 0 0
CDC42/GTP 0.002 0.03 -10000 0 -0.16 9 9
ABL1 0.016 0.019 -10000 0 -0.41 1 1
SH2B family/GRB2/SOS1 0.013 0.001 -10000 0 -10000 0 0
Rap1/GTP 0.005 0.021 -10000 0 -10000 0 0
STAT3 -0.028 0.11 -10000 0 -0.24 105 105
axon guidance 0 0.027 -10000 0 -0.16 9 9
MAPK3 0.019 0.014 -10000 0 -0.21 2 2
MAPK1 0.018 0.015 -10000 0 -0.21 2 2
CDC42/GDP 0.02 0.037 -10000 0 -0.1 6 6
NTF3 0.017 0 -10000 0 -10000 0 0
NTF4 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM 0.013 0.051 -10000 0 -0.24 21 21
PI3K 0.009 0.065 -10000 0 -0.28 25 25
FRS3 0.017 0 -10000 0 -10000 0 0
FAIM 0.002 0.08 -10000 0 -0.41 19 19
GAB1 0.014 0.037 -10000 0 -0.41 4 4
RASGRF1 0.001 0.045 -10000 0 -0.17 24 24
SOS1 0 0 -10000 0 -10000 0 0
MCF2L 0.018 0.008 -10000 0 -10000 0 0
RGS19 0.017 0 -10000 0 -10000 0 0
CDC42 0.017 0 -10000 0 -10000 0 0
RAS family/GTP 0.001 0.061 -10000 0 -0.18 28 28
Rac1/GDP 0.02 0.037 -10000 0 -0.1 6 6
NGF (dimer)/TRKA/GRIT 0.016 0.019 -10000 0 -0.24 2 2
neuron projection morphogenesis 0 0.064 -10000 0 -0.3 7 7
NGF (dimer)/TRKA/NEDD4-2 0.022 0.016 -10000 0 -0.24 2 2
MAP2K1 0.002 0.063 -10000 0 -0.19 50 50
NGFR -0.001 0.086 -10000 0 -0.41 22 22
NGF (dimer)/TRKA/GIPC/GAIP -0.015 0.052 -10000 0 -0.14 76 76
RAS family/GTP/PI3K -0.022 0.076 -10000 0 -0.14 156 156
FRS2 family/SHP2/GRB2/SOS1 0.039 0.018 -10000 0 -0.19 3 3
NRAS -0.094 0.19 -10000 0 -0.41 136 136
GRB2/SOS1 0.013 0.001 -10000 0 -10000 0 0
PRKCI 0.016 0.019 -10000 0 -0.41 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.003 0.031 -10000 0 -0.17 1 1
RASA1 0.017 0.002 -10000 0 -10000 0 0
TRKA/c-Abl 0.024 0.023 -10000 0 -0.28 3 3
SQSTM1 0.016 0.019 -10000 0 -0.41 1 1
BDNF (dimer)/TRKB/GIPC -0.005 0.049 -10000 0 -0.21 15 15
NGF (dimer)/TRKA/p62/Atypical PKCs 0.029 0.02 -10000 0 -0.2 4 4
MATK 0.017 0 -10000 0 -10000 0 0
NEDD4L 0.017 0 -10000 0 -10000 0 0
RAS family/GDP -0.025 0.041 -10000 0 -0.15 24 24
NGF (dimer)/TRKA -0.001 0.046 -10000 0 -0.14 44 44
Rac1/GTP -0.015 0.033 -10000 0 -0.15 15 15
FRS2 family/SHP2/CRK family 0.05 0.018 -10000 0 -0.19 3 3
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.028 0.046 -10000 0 -0.18 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.017 0 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.01 0.11 -10000 0 -0.25 70 70
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.027 0.043 -10000 0 -0.24 13 13
antigen processing and presentation of peptide antigen via MHC class I -0.051 0.077 -10000 0 -0.18 113 113
CaM/Ca2+ 0.028 0.042 -10000 0 -0.17 12 12
RAP1A 0.017 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.009 0.068 -10000 0 -0.22 32 32
AKT1 0.008 0.054 -10000 0 -0.2 10 10
MAP2K1 0.017 0.036 -10000 0 -0.16 14 14
MAP3K11 0.016 0.038 -10000 0 -0.17 14 14
IFNGR1 0.007 0.067 -10000 0 -0.41 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.003 0.033 -10000 0 -0.19 10 10
Rap1/GTP -0.006 0.022 -10000 0 -0.17 3 3
CRKL/C3G 0.025 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.042 0.041 -10000 0 -0.19 15 15
CEBPB 0.037 0.056 -10000 0 -0.26 5 5
STAT3 0.009 0.059 -10000 0 -0.41 10 10
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.043 0.036 -10000 0 -10000 0 0
STAT1 0.003 0.066 -10000 0 -0.22 32 32
CALM1 0.016 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.016 0.019 -10000 0 -0.41 1 1
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
STAT1 (dimer)/PIAS1 0.012 0.065 -10000 0 -0.23 22 22
CEBPB/PTGES2/Cbp/p300 -0.002 0.041 -10000 0 -0.23 4 4
mol:Ca2+ 0.026 0.045 -10000 0 -0.18 14 14
MAPK3 0.03 0.035 -10000 0 -10000 0 0
STAT1 (dimer) -0.064 0.11 -10000 0 -0.24 113 113
MAPK1 0.013 0.11 -10000 0 -0.58 15 15
JAK2 0.017 0.006 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
JAK1 0.017 0.006 -10000 0 -10000 0 0
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.038 0.042 -10000 0 -0.19 3 3
SMAD7 -0.002 0.06 -10000 0 -0.13 29 29
CBL/CRKL/C3G 0.031 0.039 -10000 0 -0.2 3 3
PI3K 0.016 0.059 -10000 0 -0.18 32 32
IFNG 0.016 0.019 -10000 0 -0.41 1 1
apoptosis 0.026 0.043 0.22 4 -0.21 1 5
CAMK2G 0.008 0.009 -10000 0 -10000 0 0
STAT3 (dimer) 0.009 0.058 -10000 0 -0.41 10 10
CAMK2A 0.016 0.004 -10000 0 -10000 0 0
CAMK2B 0.002 0.006 -10000 0 -10000 0 0
FRAP1 0.016 0.058 0.19 2 -0.23 6 8
PRKCD 0.015 0.059 0.2 2 -0.2 10 12
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.051 0.077 -10000 0 -0.18 113 113
PTPN2 0.016 0.019 -10000 0 -0.41 1 1
EP300 0.017 0.002 -10000 0 -10000 0 0
IRF1 -0.016 0.14 -10000 0 -0.36 70 70
STAT1 (dimer)/PIASy 0.009 0.065 -10000 0 -0.23 22 22
SOCS1 0.017 0.003 -10000 0 -10000 0 0
mol:GDP 0.028 0.037 -10000 0 -0.19 3 3
CASP1 -0.045 0.12 -10000 0 -0.21 173 173
PTGES2 0.017 0 -10000 0 -10000 0 0
IRF9 0.029 0.028 -10000 0 -0.12 1 1
mol:PI-3-4-5-P3 0.008 0.054 -10000 0 -0.18 32 32
RAP1/GDP 0.02 0.031 -10000 0 -0.17 3 3
CBL 0.015 0.038 -10000 0 -0.17 14 14
MAP3K1 0.016 0.039 -10000 0 -0.17 15 15
PIAS1 0.017 0 -10000 0 -10000 0 0
PIAS4 0.017 0 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.051 0.077 -10000 0 -0.18 113 113
PTPN11 0.011 0.039 -10000 0 -0.18 14 14
CREBBP 0.017 0.002 -10000 0 -10000 0 0
RAPGEF1 0.017 0 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 -0.013 0.074 -10000 0 -0.21 24 24
BAG4 0.017 0 -10000 0 -10000 0 0
BAD 0.003 0.027 -10000 0 -10000 0 0
NFKBIA 0.016 0.019 -10000 0 -0.41 1 1
BIRC3 -0.009 0.1 -10000 0 -0.41 33 33
BAX 0.001 0.037 -10000 0 -0.21 7 7
EnzymeConsortium:3.1.4.12 -0.002 0.021 -10000 0 -0.055 24 24
IKBKB -0.009 0.071 -10000 0 -0.2 24 24
MAP2K2 0.01 0.026 -10000 0 -0.15 1 1
MAP2K1 0.009 0.025 -10000 0 -0.15 1 1
SMPD1 0.002 0.021 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.009 0.074 -10000 0 -0.19 31 31
MAP2K4 0.006 0.026 -10000 0 -0.16 1 1
protein ubiquitination -0.009 0.072 0.15 1 -0.2 24 25
EnzymeConsortium:2.7.1.37 0.015 0.03 -10000 0 -0.15 1 1
response to UV 0 0 -10000 0 -0.001 1 1
RAF1 0.008 0.027 -10000 0 -0.16 1 1
CRADD 0.017 0 -10000 0 -10000 0 0
mol:ceramide 0 0.028 -10000 0 -0.074 24 24
I-kappa-B-alpha/RELA/p50/ubiquitin 0.023 0.011 -10000 0 -0.24 1 1
MADD 0.017 0.002 -10000 0 -10000 0 0
MAP3K1 0.003 0.028 -10000 0 -0.17 1 1
TRADD 0.017 0 -10000 0 -10000 0 0
RELA/p50 0.017 0 -10000 0 -10000 0 0
MAPK3 0.014 0.028 -10000 0 -0.14 1 1
MAPK1 0.012 0.029 -10000 0 -0.14 1 1
p50/RELA/I-kappa-B-alpha 0.025 0.014 -10000 0 -0.28 1 1
FADD -0.014 0.074 -10000 0 -0.21 26 26
KSR1 0.004 0.027 -10000 0 -10000 0 0
MAPK8 0.013 0.033 0.13 5 -0.14 1 6
TRAF2 0.017 0.001 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK -0.01 0.071 -10000 0 -0.2 25 25
TNF R/SODD -0.082 0.15 -10000 0 -0.28 183 183
TNF 0.016 0.026 -10000 0 -0.41 2 2
CYCS 0.002 0.03 -10000 0 -0.14 5 5
IKBKG -0.009 0.071 -10000 0 -0.2 24 24
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.017 0.077 -10000 0 -0.22 24 24
RELA 0.017 0 -10000 0 -10000 0 0
RIPK1 0.01 0.056 -10000 0 -0.41 9 9
AIFM1 0 0.033 -10000 0 -0.14 9 9
TNF/TNF R/SODD -0.059 0.13 -10000 0 -0.24 185 185
TNFRSF1A -0.13 0.2 -10000 0 -0.41 183 183
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.013 0.033 -10000 0 -0.21 1 1
NSMAF -0.013 0.073 -10000 0 -0.2 26 26
response to hydrogen peroxide 0 0 -10000 0 -0.001 1 1
BCL2 0.017 0 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.019 0.034 -9999 0 -0.24 9 9
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.01 0.056 -9999 0 -0.41 9 9
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.003 0.028 -9999 0 -0.13 24 24
response to UV 0 0 -9999 0 -10000 0 0
YES1 -0.047 0.15 -9999 0 -0.41 79 79
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0 -9999 0 -10000 0 0
FYN 0.015 0.027 -9999 0 -0.41 2 2
MAP3K12 0.017 0 -9999 0 -10000 0 0
FGR 0.003 0.076 -9999 0 -0.41 17 17
p38 alpha/TAB1 -0.003 0.067 -9999 0 -0.16 47 47
PRKG1 0.017 0 -9999 0 -10000 0 0
DUSP8 0.013 0.007 -9999 0 -10000 0 0
PGK/cGMP/p38 alpha -0.005 0.064 -9999 0 -0.16 48 48
apoptosis -0.003 0.065 -9999 0 -0.16 47 47
RAL/GTP 0 0.074 -9999 0 -0.24 46 46
LYN -0.035 0.14 -9999 0 -0.41 64 64
DUSP1 0.002 0.078 -9999 0 -0.41 18 18
PAK1 0.017 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.033 0 -9999 0 -10000 0 0
TRAF6 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.023 0 -9999 0 -10000 0 0
MAPK11 -0.014 0.076 -9999 0 -0.18 55 55
BLK 0.017 0 -9999 0 -10000 0 0
HCK -0.053 0.16 -9999 0 -0.41 86 86
MAP2K3 0.017 0 -9999 0 -10000 0 0
DUSP16 0 0 -9999 0 -10000 0 0
DUSP10 0.011 0.049 -9999 0 -0.41 7 7
TRAF6/MEKK3 0.022 0 -9999 0 -10000 0 0
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
MAPK14 -0.01 0.07 -9999 0 -0.15 72 72
positive regulation of innate immune response -0.015 0.087 -9999 0 -0.18 78 78
LCK 0.014 0.037 -9999 0 -0.41 4 4
p38alpha-beta/MKP7 -0.016 0.083 -9999 0 -0.18 78 78
p38alpha-beta/MKP5 -0.01 0.09 -9999 0 -0.21 52 52
PGK/cGMP 0.013 0 -9999 0 -10000 0 0
PAK2 -0.002 0.09 -9999 0 -0.41 24 24
p38alpha-beta/MKP1 -0.013 0.097 -9999 0 -0.22 60 60
CDC42 0.017 0 -9999 0 -10000 0 0
RALB 0.016 0.019 -9999 0 -0.41 1 1
RALA -0.02 0.12 -9999 0 -0.41 45 45
PAK3 0.003 0.006 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 -0.036 0.14 -10000 0 -0.41 65 65
HDAC3 0.017 0 -10000 0 -10000 0 0
VDR 0.017 0 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.023 0 -10000 0 -10000 0 0
EP300 0.017 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.034 0.011 -10000 0 -0.082 2 2
KAT2B 0 0 -10000 0 -10000 0 0
MAPK14 0.015 0.026 -10000 0 -0.41 2 2
AKT1 0.069 0.053 0.13 234 -0.12 3 237
RAR alpha/9cRA/Cyclin H 0.012 0.053 -10000 0 -0.2 6 6
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.031 0.006 -10000 0 -10000 0 0
CDC2 -0.14 0.21 -10000 0 -0.41 193 193
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.025 0.004 -10000 0 -10000 0 0
NCOR2 0.017 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.013 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA 0.043 0.034 -10000 0 -0.24 3 3
NCOA2 0.017 0 -10000 0 -10000 0 0
NCOA3 0.015 0.032 -10000 0 -0.41 3 3
NCOA1 0.017 0.003 -10000 0 -10000 0 0
VDR/VDR/DNA 0.017 0 -10000 0 -10000 0 0
RARG 0.018 0.001 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.024 0.001 -10000 0 -10000 0 0
MAPK3 0.018 0.001 -10000 0 -10000 0 0
MAPK1 0.017 0.003 -10000 0 -10000 0 0
MAPK8 0.018 0.002 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.012 0.052 -10000 0 -0.23 3 3
RARA 0.025 0.004 -10000 0 -10000 0 0
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.032 0.003 -10000 0 -10000 0 0
PRKCA 0.02 0.003 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.023 0.042 -10000 0 -0.32 3 3
RXRG 0.025 0.016 -10000 0 -0.17 3 3
RXRA -0.013 0.061 -10000 0 -0.2 3 3
RXRB 0.026 0.004 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.013 0 -10000 0 -10000 0 0
RBP1 -0.18 0.21 -10000 0 -0.41 237 237
CRBP1/9-cic-RA -0.12 0.15 -10000 0 -0.29 237 237
RARB 0.019 0.001 -10000 0 -10000 0 0
PRKCG 0.02 0.003 -10000 0 -10000 0 0
MNAT1 0.016 0.019 -10000 0 -0.41 1 1
RAR alpha/RXRs 0.057 0.059 -10000 0 -0.23 1 1
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.049 0.027 -10000 0 -0.14 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.01 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 0.029 0.036 -10000 0 -0.3 3 3
positive regulation of DNA binding 0.007 0.047 -10000 0 -0.19 6 6
NRIP1 0.032 0.038 -10000 0 -0.4 3 3
RXRs/RARs 0.029 0.03 -10000 0 -0.23 3 3
RXRs/RXRs/DNA/9cRA 0.004 0.05 -10000 0 -0.24 3 3
PRKACA 0.017 0 -10000 0 -10000 0 0
CDK7 0.015 0.026 -10000 0 -0.41 2 2
TFIIH 0.033 0.02 -10000 0 -0.24 3 3
RAR alpha/9cRA 0.045 0.016 -10000 0 -0.16 3 3
CCNH 0.017 0.001 -10000 0 -10000 0 0
CREBBP 0.017 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.032 0.02 -10000 0 -0.17 5 5
IL23-mediated signaling events

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
CCL2 -0.026 0.29 -9999 0 -0.7 39 39
IL23A 0.027 0.23 -9999 0 -0.71 18 18
NF kappa B1 p50/RelA/I kappa B alpha 0.033 0.23 -9999 0 -0.67 20 20
positive regulation of T cell mediated cytotoxicity 0.027 0.24 -9999 0 -0.6 41 41
ITGA3 0.025 0.24 -9999 0 -0.68 22 22
IL17F 0.025 0.18 -9999 0 -0.48 21 21
IL12B 0.025 0.029 -9999 0 -10000 0 0
STAT1 (dimer) 0.017 0.23 -9999 0 -0.68 21 21
CD4 0.025 0.24 -9999 0 -0.69 24 24
IL23 0.025 0.23 -9999 0 -0.7 18 18
IL23R 0.019 0.063 -9999 0 -0.13 16 16
IL1B 0.026 0.24 -9999 0 -0.73 19 19
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 0.032 0.22 -9999 0 -0.66 19 19
TYK2 0.02 0.027 -9999 0 -0.39 1 1
STAT4 0.01 0.008 -9999 0 -10000 0 0
STAT3 0.009 0.059 -9999 0 -0.41 10 10
IL18RAP 0.018 0.002 -9999 0 -10000 0 0
IL12RB1 0.021 0.021 -9999 0 -10000 0 0
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
IL12Rbeta1/TYK2 0.028 0.029 -9999 0 -0.26 1 1
IL23R/JAK2 0.034 0.086 -9999 0 -0.18 5 5
positive regulation of chronic inflammatory response 0.027 0.24 -9999 0 -0.6 41 41
natural killer cell activation -0.001 0.006 -9999 0 -10000 0 0
JAK2 0.025 0.029 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
NFKB1 0.015 0.038 -9999 0 -0.42 4 4
RELA 0.018 0.003 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.026 0.22 -9999 0 -0.67 18 18
ALOX12B 0.032 0.22 -9999 0 -0.65 20 20
CXCL1 0.022 0.25 -9999 0 -0.69 31 31
T cell proliferation 0.027 0.24 -9999 0 -0.6 41 41
NFKBIA 0.017 0.019 -9999 0 -0.42 1 1
IL17A 0.046 0.16 -9999 0 -0.42 15 15
PI3K 0.024 0.22 -9999 0 -0.66 18 18
IFNG 0.012 0.017 -9999 0 -0.044 17 17
STAT3 (dimer) 0.027 0.22 -9999 0 -0.64 21 21
IL18R1 0.018 0.002 -9999 0 -10000 0 0
IL23/IL23R/JAK2/TYK2/SOCS3 0.039 0.16 -9999 0 -0.42 12 12
IL18/IL18R 0.016 0.075 -9999 0 -0.23 45 45
macrophage activation 0.001 0.014 -9999 0 -0.039 12 12
TNF 0.028 0.23 -9999 0 -0.68 20 20
STAT3/STAT4 -0.017 0.2 -9999 0 -0.68 19 19
STAT4 (dimer) -0.019 0.2 -9999 0 -0.68 18 18
IL18 -0.019 0.12 -9999 0 -0.41 45 45
IL19 0.032 0.22 -9999 0 -0.65 19 19
STAT5A (dimer) 0.023 0.23 -9999 0 -0.69 19 19
STAT1 0.002 0.078 -9999 0 -0.41 18 18
SOCS3 0.017 0 -9999 0 -10000 0 0
CXCL9 0.009 0.25 -9999 0 -0.68 30 30
MPO 0.032 0.22 -9999 0 -0.66 18 18
positive regulation of humoral immune response 0.027 0.24 -9999 0 -0.6 41 41
IL23/IL23R/JAK2/TYK2 0.026 0.24 -9999 0 -0.6 41 41
IL6 0.014 0.26 -9999 0 -0.73 33 33
STAT5A 0.016 0.019 -9999 0 -0.41 1 1
IL2 0.019 0.004 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.006 -9999 0 -10000 0 0
CD3E 0.032 0.22 -9999 0 -0.65 19 19
keratinocyte proliferation 0.027 0.24 -9999 0 -0.6 41 41
NOS2 0.026 0.22 -9999 0 -0.55 40 40
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.017 0.002 -9999 0 -10000 0 0
VLDLR 0.015 0.032 -9999 0 -0.41 3 3
LRPAP1 0.017 0 -9999 0 -10000 0 0
NUDC 0.017 0 -9999 0 -10000 0 0
RELN/LRP8 0.015 0.026 -9999 0 -0.24 3 3
CaM/Ca2+ 0.012 0.003 -9999 0 -10000 0 0
KATNA1 0.012 0.046 -9999 0 -0.41 6 6
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 0.01 0.019 -9999 0 -0.21 2 2
IQGAP1/CaM -0.048 0.13 -9999 0 -0.28 127 127
DAB1 0.017 0 -9999 0 -10000 0 0
IQGAP1 -0.086 0.18 -9999 0 -0.41 127 127
PLA2G7 0.011 0.052 -9999 0 -0.41 8 8
CALM1 0.016 0.004 -9999 0 -10000 0 0
DYNLT1 -0.044 0.15 -9999 0 -0.41 75 75
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.025 0 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.017 0 -9999 0 -10000 0 0
CDK5R1 0.014 0.007 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.013 0.001 -9999 0 -10000 0 0
CDK5R2 0.007 0.008 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 0.014 0.029 -9999 0 -0.24 4 4
YWHAE 0.017 0.001 -9999 0 -10000 0 0
NDEL1/14-3-3 E 0.025 0.045 -9999 0 -10000 0 0
MAP1B 0.006 0.002 -9999 0 -10000 0 0
RAC1 -0.01 0.049 -9999 0 -0.096 127 127
p35/CDK5 0.013 0.019 -9999 0 -0.18 1 1
RELN 0.006 0.033 -9999 0 -0.41 3 3
PAFAH/LIS1 0.022 0.032 -9999 0 -0.24 8 8
LIS1/CLIP170 0.026 0.003 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.004 0.039 -9999 0 -0.27 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 0.015 0.02 -9999 0 -0.11 3 3
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 0.023 0.043 -9999 0 -0.16 1 1
LIS1/IQGAP1 -0.037 0.11 -9999 0 -0.24 127 127
RHOA -0.01 0.049 -9999 0 -0.096 127 127
PAFAH1B1 0.018 0.002 -9999 0 -10000 0 0
PAFAH1B3 0.016 0.019 -9999 0 -0.41 1 1
PAFAH1B2 0.017 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.023 0.008 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.025 0.048 -9999 0 -10000 0 0
LRP8 0.017 0 -9999 0 -10000 0 0
NDEL1/Katanin 60 0.024 0.047 -9999 0 -10000 0 0
P39/CDK5 0.006 0.016 -9999 0 -0.18 1 1
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.003 -9999 0 -10000 0 0
CDK5 0.009 0.017 -9999 0 -0.19 2 2
PPP2R5D 0.017 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.022 0.002 -9999 0 -10000 0 0
CSNK2A1 0.017 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.019 0.029 -9999 0 -0.19 4 4
RELN/VLDLR 0.019 0.03 -9999 0 -0.21 4 4
CDC42 -0.01 0.049 -9999 0 -0.096 127 127
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.016 0.071 -9999 0 -0.2 33 33
FYN 0.011 0.079 -9999 0 -0.25 25 25
LAT/GRAP2/SLP76 0.026 0.074 -9999 0 -0.23 33 33
IKBKB 0.017 0 -9999 0 -10000 0 0
AKT1 0.029 0.054 -9999 0 -0.21 13 13
B2M 0.018 0.004 -9999 0 -10000 0 0
IKBKG 0.016 0.026 -9999 0 -0.089 12 12
MAP3K8 -0.017 0.12 -9999 0 -0.41 42 42
mol:Ca2+ -0.001 0.006 -9999 0 -10000 0 0
integrin-mediated signaling pathway 0.011 0 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.029 0.068 -9999 0 -0.26 15 15
TRPV6 0.002 0.003 -9999 0 -10000 0 0
CD28 0.017 0.001 -9999 0 -10000 0 0
SHC1 0.012 0.081 -9999 0 -0.23 33 33
receptor internalization 0.029 0.046 -9999 0 -0.26 7 7
PRF1 0.027 0.073 -9999 0 -0.42 12 12
KRAS 0.017 0.002 -9999 0 -10000 0 0
GRB2 0.017 0.002 -9999 0 -10000 0 0
COT/AKT1 0.022 0.076 -9999 0 -0.2 43 43
LAT 0.027 0.055 -9999 0 -0.28 8 8
EntrezGene:6955 0.001 0.002 -9999 0 -10000 0 0
CD3D 0.002 0.083 -9999 0 -0.42 20 20
CD3E 0.017 0.019 -9999 0 -0.42 1 1
CD3G 0.017 0.02 -9999 0 -0.42 1 1
RASGRP2 0.01 0.008 -9999 0 -10000 0 0
RASGRP1 -0.006 0.076 -9999 0 -0.23 29 29
HLA-A 0.017 0.019 -9999 0 -0.41 1 1
RASSF5 0 0 -9999 0 -10000 0 0
RAP1A/GTP/RAPL 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:GDP 0.004 0.032 -9999 0 -0.081 27 27
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.01 0.03 -9999 0 -0.13 21 21
PRKCA 0.021 0.042 -9999 0 -0.16 13 13
GRAP2 0.017 0 -9999 0 -10000 0 0
mol:IP3 -0.014 0.048 -9999 0 -0.2 24 24
EntrezGene:6957 0.001 0.003 -9999 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.025 0.039 -9999 0 -0.26 6 6
ORAI1 0 0 -9999 0 -10000 0 0
CSK 0.026 0.055 -9999 0 -0.27 9 9
B7 family/CD28 0.033 0.082 -9999 0 -0.24 34 34
CHUK 0.016 0.019 -9999 0 -0.41 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.025 0.059 -9999 0 -0.24 14 14
PTPN6 0.02 0.07 -9999 0 -0.3 17 17
VAV1 0.027 0.056 -9999 0 -0.28 9 9
Monovalent TCR/CD3 0.017 0.041 -9999 0 -0.17 20 20
CBL 0.017 0 -9999 0 -10000 0 0
LCK 0.01 0.079 -9999 0 -0.25 26 26
PAG1 0.024 0.055 -9999 0 -0.23 14 14
RAP1A 0.017 0 -9999 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.023 0.062 -9999 0 -0.26 14 14
CD80 0.017 0.019 -9999 0 -0.41 1 1
CD86 -0.003 0.092 -9999 0 -0.41 25 25
PDK1/CARD11/BCL10/MALT1 -0.011 0.037 -9999 0 -0.15 22 22
HRAS 0.016 0.019 -9999 0 -0.41 1 1
GO:0035030 0.019 0.07 -9999 0 -0.21 34 34
CD8A 0.001 0.003 -9999 0 -10000 0 0
CD8B 0.016 0.027 -9999 0 -0.42 2 2
PTPRC -0.086 0.18 -9999 0 -0.41 127 127
PDK1/PKC theta 0.033 0.063 -9999 0 -0.25 13 13
CSK/PAG1 0.026 0.053 -9999 0 -0.24 11 11
SOS1 0 0 -9999 0 -10000 0 0
peptide-MHC class I 0.026 0.015 -9999 0 -0.28 1 1
GRAP2/SLP76 0.027 0.081 -9999 0 -0.24 35 35
STIM1 0.002 0.003 -9999 0 -10000 0 0
RAS family/GTP -0.005 0.052 -9999 0 -0.12 45 45
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.029 0.047 -9999 0 -0.27 7 7
mol:DAG -0.013 0.044 -9999 0 -0.19 24 24
RAP1A/GDP 0.004 0.015 -9999 0 -0.041 12 12
PLCG1 0.017 0 -9999 0 -10000 0 0
CD247 0.016 0.027 -9999 0 -0.42 2 2
cytotoxic T cell degranulation 0.027 0.072 -9999 0 -0.41 12 12
RAP1A/GTP 0 0.002 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.029 0.061 -9999 0 -0.23 15 15
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.015 0.058 -9999 0 -0.24 24 24
NRAS -0.094 0.19 -9999 0 -0.41 136 136
ZAP70 0.017 0 -9999 0 -10000 0 0
GRB2/SOS1 0.013 0.001 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.023 0.071 -9999 0 -0.24 24 24
MALT1 -0.002 0.09 -9999 0 -0.41 24 24
TRAF6 0.017 0 -9999 0 -10000 0 0
CD8 heterodimer 0.013 0.019 -9999 0 -0.29 2 2
CARD11 0 0 -9999 0 -10000 0 0
PRKCB -0.01 0.032 -9999 0 -0.14 24 24
PRKCE 0.021 0.042 -9999 0 -0.14 24 24
PRKCQ 0.031 0.067 -9999 0 -0.27 14 14
LCP2 -0.007 0.099 -9999 0 -0.41 30 30
BCL10 0.014 0.037 -9999 0 -0.41 4 4
regulation of survival gene product expression 0.028 0.049 -9999 0 -0.19 13 13
IKK complex 0.025 0.022 -9999 0 -0.068 7 7
RAS family/GDP -0.013 0.02 -9999 0 -0.046 135 135
MAP3K14 0.021 0.061 -9999 0 -0.16 44 44
PDPK1 0.03 0.053 -9999 0 -0.21 12 12
TCR/CD3/MHC I/CD8/Fyn 0.028 0.051 -9999 0 -0.3 7 7
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.011 0.06 -9999 0 -0.2 21 21
PDGFB-D/PDGFRB/SLAP 0.002 0.083 -9999 0 -0.3 37 37
PDGFB-D/PDGFRB/APS/CBL 0.021 0.02 -9999 0 -0.24 3 3
AKT1 0.026 0.052 -9999 0 -0.24 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.007 0.058 -9999 0 -0.21 21 21
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
FGR 0.004 0.044 -9999 0 -0.19 20 20
mol:Ca2+ 0.008 0.038 -9999 0 -0.22 4 4
MYC -0.067 0.17 -9999 0 -0.34 138 138
SHC1 -0.02 0.12 -9999 0 -0.41 46 46
HRAS/GDP 0.027 0.022 -9999 0 -0.19 5 5
LRP1/PDGFRB/PDGFB 0.023 0.053 -9999 0 -0.24 21 21
GRB10 0.004 0.074 -9999 0 -0.41 16 16
PTPN11 0.017 0 -9999 0 -10000 0 0
GO:0007205 0.008 0.039 -9999 0 -0.22 4 4
PTEN 0.015 0.026 -9999 0 -0.41 2 2
GRB2 0.017 0.002 -9999 0 -10000 0 0
GRB7 0.016 0.019 -9999 0 -0.41 1 1
PDGFB-D/PDGFRB/SHP2 0.023 0.023 -9999 0 -0.28 3 3
PDGFB-D/PDGFRB/GRB10 0.013 0.058 -9999 0 -0.29 19 19
cell cycle arrest 0.002 0.082 -9999 0 -0.3 37 37
HRAS 0.016 0.019 -9999 0 -0.41 1 1
HIF1A 0.025 0.049 -9999 0 -0.21 1 1
GAB1 -0.008 0.065 -9999 0 -0.2 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.008 0.065 -9999 0 -0.19 23 23
PDGFB-D/PDGFRB 0.027 0.029 -9999 0 -0.24 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.023 0.024 -9999 0 -0.28 3 3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.003 0.079 -9999 0 -0.22 30 30
positive regulation of MAPKKK cascade 0.023 0.023 -9999 0 -0.28 3 3
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
mol:IP3 0.008 0.039 -9999 0 -0.22 4 4
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.017 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.022 0.027 -9999 0 -0.29 4 4
SHB 0.017 0 -9999 0 -10000 0 0
BLK -0.002 0.022 -9999 0 -0.21 4 4
PTPN2 0.015 0.019 -9999 0 -0.42 1 1
PDGFB-D/PDGFRB/SNX15 0.023 0.023 -9999 0 -0.28 3 3
BCAR1 0 0 -9999 0 -10000 0 0
VAV2 -0.024 0.093 -9999 0 -0.23 50 50
CBL 0.017 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.023 0.023 -9999 0 -0.28 3 3
LCK -0.005 0.028 -9999 0 -0.2 8 8
PDGFRB 0.014 0.033 -9999 0 -0.42 3 3
ACP1 0.017 0.001 -9999 0 -10000 0 0
HCK -0.031 0.065 -9999 0 -0.18 71 71
ABL1 -0.003 0.055 -9999 0 -0.18 18 18
PDGFB-D/PDGFRB/CBL -0.006 0.065 -9999 0 -0.21 19 19
PTPN1 0.016 0.003 -9999 0 -10000 0 0
SNX15 0.017 0 -9999 0 -10000 0 0
STAT3 0.009 0.059 -9999 0 -0.41 10 10
STAT1 0.002 0.078 -9999 0 -0.41 18 18
cell proliferation -0.061 0.16 -9999 0 -0.32 138 138
SLA -0.011 0.11 -9999 0 -0.41 35 35
actin cytoskeleton reorganization 0.026 0.036 -9999 0 -0.18 15 15
SRC -0.003 0.022 -9999 0 -0.21 4 4
PI3K -0.01 0.039 -9999 0 -0.18 13 13
PDGFB-D/PDGFRB/GRB7/SHC 0.009 0.081 -9999 0 -0.24 49 49
SH2B2 0 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 0.007 0.059 -9999 0 -0.22 21 21
LYN -0.025 0.06 -9999 0 -0.18 67 67
LRP1 0.002 0.078 -9999 0 -0.41 18 18
SOS1 0 0 -9999 0 -10000 0 0
STAT5B 0.017 0 -9999 0 -10000 0 0
STAT5A 0.016 0.019 -9999 0 -0.41 1 1
NCK1-2/p130 Cas 0.032 0.04 -9999 0 -0.19 15 15
SPHK1 0.001 0.08 -9999 0 -0.41 19 19
EDG1 0.017 0.002 -9999 0 -10000 0 0
mol:DAG 0.008 0.039 -9999 0 -0.22 4 4
PLCG1 0.008 0.039 -9999 0 -0.23 4 4
NHERF/PDGFRB 0.032 0.026 -9999 0 -0.24 5 5
YES1 -0.028 0.063 -9999 0 -0.17 81 81
cell migration 0.031 0.026 -9999 0 -0.24 5 5
SHC/Grb2/SOS1 0.017 0.07 -9999 0 -0.2 48 48
SLC9A3R2 0.017 0 -9999 0 -10000 0 0
SLC9A3R1 0.015 0.026 -9999 0 -0.41 2 2
NHERF1-2/PDGFRB/PTEN 0.04 0.029 -9999 0 -0.21 7 7
FYN -0.014 0.064 -9999 0 -0.31 22 22
DOK1 0.021 0.021 -9999 0 -0.21 4 4
HRAS/GTP 0.012 0.013 -9999 0 -0.29 1 1
PDGFB 0.017 0 -9999 0 -10000 0 0
RAC1 -0.041 0.12 -9999 0 -0.23 139 139
PRKCD 0.02 0.022 -9999 0 -0.22 4 4
FER 0.02 0.022 -9999 0 -0.22 4 4
MAPKKK cascade -0.018 0.057 -9999 0 -0.19 48 48
RASA1 0.02 0.022 -9999 0 -0.22 4 4
NCK1 0.008 0.061 -9999 0 -0.41 11 11
NCK2 0.017 0.001 -9999 0 -10000 0 0
p62DOK/Csk 0.033 0.019 -9999 0 -0.19 4 4
PDGFB-D/PDGFRB/SHB 0.023 0.023 -9999 0 -0.28 3 3
chemotaxis -0.003 0.054 -9999 0 -0.18 18 18
STAT1-3-5/STAT1-3-5 0.025 0.055 -9999 0 -0.19 31 31
Bovine Papilomavirus E5/PDGFRB 0.009 0.023 -9999 0 -0.29 3 3
PTPRJ 0.017 0 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.025 0 -9999 0 -10000 0 0
Necdin/E2F1 0.016 0.012 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.03 0.047 -9999 0 -0.19 22 22
NGF (dimer)/p75(NTR)/BEX1 0.007 0.048 -9999 0 -0.21 22 22
NT-4/5 (dimer)/p75(NTR) 0 0.06 -9999 0 -0.29 22 22
IKBKB 0.017 0 -9999 0 -10000 0 0
AKT1 0.001 0.067 -9999 0 -0.21 47 47
IKBKG 0.017 0 -9999 0 -10000 0 0
BDNF 0.005 0.008 -9999 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.001 0.051 -9999 0 -0.24 22 22
FURIN 0.017 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.002 0.04 -9999 0 -0.24 10 10
LINGO1 0 0 -9999 0 -10000 0 0
Sortilin/TRAF6/NRIF -0.014 0.049 -9999 0 -0.21 8 8
proBDNF (dimer) 0.005 0.008 -9999 0 -10000 0 0
NTRK1 0.015 0.026 -9999 0 -0.41 2 2
RTN4R 0 0 -9999 0 -10000 0 0
neuron apoptosis 0.051 0.072 -9999 0 -0.21 12 12
IRAK1 0.017 0.001 -9999 0 -10000 0 0
SHC1 -0.017 0.087 -9999 0 -0.25 66 66
ARHGDIA 0.017 0 -9999 0 -10000 0 0
RhoA/GTP 0.013 0.001 -9999 0 -10000 0 0
Gamma Secretase 0.032 0.067 -9999 0 -0.2 39 39
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.021 0.048 -9999 0 -0.21 20 20
MAGEH1 0.016 0.005 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.012 0.043 -9999 0 -0.21 15 15
Mammalian IAPs/DIABLO 0.018 0.059 -9999 0 -0.21 33 33
proNGF (dimer) 0 0 -9999 0 -10000 0 0
MAGED1 0.017 0.001 -9999 0 -10000 0 0
APP 0.017 0.001 -9999 0 -10000 0 0
NT-4/5 (dimer) 0 0 -9999 0 -10000 0 0
ZNF274 0.012 0.046 -9999 0 -0.41 6 6
RhoA/GDP/RHOGDI 0.018 0.045 -9999 0 -0.2 22 22
NGF 0 0 -9999 0 -10000 0 0
cell cycle arrest 0 0.042 -9999 0 -0.2 22 22
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0 0.059 -9999 0 -0.13 92 92
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.012 0.052 -9999 0 -0.24 22 22
NCSTN -0.007 0.099 -9999 0 -0.41 30 30
mol:GTP 0.01 0.051 -9999 0 -0.23 22 22
PSENEN 0.017 0.001 -9999 0 -10000 0 0
mol:ceramide 0.01 0.046 -9999 0 -0.21 22 22
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.026 -9999 0 -0.098 25 25
p75(NTR)/beta APP 0.012 0.062 -9999 0 -0.28 22 22
BEX1 0.012 0.008 -9999 0 -10000 0 0
mol:GDP -0.004 0.05 -9999 0 -0.24 22 22
NGF (dimer) -0.003 0.087 -9999 0 -0.21 78 78
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.012 0.047 -9999 0 -0.22 22 22
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
RAC1/GTP 0.011 0.044 -9999 0 -0.2 22 22
MYD88 -0.041 0.15 -9999 0 -0.41 71 71
CHUK 0.016 0.019 -9999 0 -0.41 1 1
NGF (dimer)/p75(NTR)/PKA 0.011 0.051 -9999 0 -0.23 22 22
RHOB 0.013 0.037 -9999 0 -0.41 4 4
RHOA 0.017 0.001 -9999 0 -10000 0 0
MAGE-G1/E2F1 0.013 0 -9999 0 -10000 0 0
NT3 (dimer) 0.017 0 -9999 0 -10000 0 0
TP53 -0.016 0.062 -9999 0 -0.21 39 39
PRDM4 0.01 0.046 -9999 0 -0.21 22 22
BDNF (dimer) -0.012 0.068 -9999 0 -0.23 32 32
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
SORT1 0.017 0 -9999 0 -10000 0 0
activation of caspase activity 0.027 0.046 -9999 0 -0.19 22 22
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.023 0.049 -9999 0 -0.21 22 22
RHOC -0.12 0.2 -9999 0 -0.41 163 163
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 0.044 0.061 -9999 0 -10000 0 0
DIABLO 0.017 0 -9999 0 -10000 0 0
SMPD2 0.01 0.046 -9999 0 -0.21 22 22
APH1B 0.017 0 -9999 0 -10000 0 0
APH1A 0.009 0.059 -9999 0 -0.41 10 10
proNGF (dimer)/p75(NTR)/Sortilin 0.012 0.052 -9999 0 -0.24 22 22
PSEN1 0.016 0.019 -9999 0 -0.41 1 1
APAF-1/Pro-Caspase 9 0.023 0.027 -9999 0 -0.28 4 4
NT3 (dimer)/p75(NTR) 0.013 0.062 -9999 0 -0.28 22 22
MAPK8 0.081 0.054 -9999 0 -10000 0 0
MAPK9 0.08 0.054 -9999 0 -10000 0 0
APAF1 0.017 0 -9999 0 -10000 0 0
NTF3 0.017 0 -9999 0 -10000 0 0
NTF4 0 0 -9999 0 -10000 0 0
NDN 0.011 0.008 -9999 0 -10000 0 0
RAC1/GDP 0.013 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.04 0.11 -9999 0 -0.19 170 170
p75 CTF/Sortilin/TRAF6/NRIF 0.039 0.036 -9999 0 -0.21 11 11
RhoA-B-C/GTP 0.01 0.051 -9999 0 -0.23 22 22
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.006 0.042 -9999 0 -0.19 13 13
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.006 0.039 -9999 0 -0.21 10 10
PRKACB 0.016 0.005 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.005 0.026 -9999 0 -0.23 5 5
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.01 0.1 -9999 0 -0.41 33 33
BIRC2 0.017 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.007 0.035 -9999 0 -0.18 20 20
BAD 0.082 0.053 -9999 0 -10000 0 0
RIPK2 0.016 0.019 -9999 0 -0.41 1 1
NGFR -0.001 0.086 -9999 0 -0.41 22 22
CYCS 0.014 0.043 -9999 0 -0.19 22 22
ADAM17 0.013 0.042 -9999 0 -0.41 5 5
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.022 0.05 -9999 0 -0.21 23 23
BCL2L11 0.082 0.053 -9999 0 -10000 0 0
BDNF (dimer)/p75(NTR) -0.002 0.046 -9999 0 -0.2 22 22
PI3K 0.01 0.072 -9999 0 -0.23 43 43
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.012 0.047 -9999 0 -0.22 22 22
NDNL2 0 0 -9999 0 -10000 0 0
YWHAE 0.017 0.001 -9999 0 -10000 0 0
PRKCI 0.016 0.019 -9999 0 -0.41 1 1
NGF (dimer)/p75(NTR) 0 0.06 -9999 0 -0.29 22 22
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.023 0.049 -9999 0 -0.21 22 22
TRAF6 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG 0.017 0 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.007 0.049 -9999 0 -0.2 19 19
SQSTM1 0.016 0.019 -9999 0 -0.41 1 1
NGFRAP1 0.017 0.002 -9999 0 -10000 0 0
CASP3 0.077 0.052 -9999 0 -10000 0 0
E2F1 0.017 0 -9999 0 -10000 0 0
CASP9 0.014 0.037 -9999 0 -0.41 4 4
IKK complex 0.037 0.029 -9999 0 -0.19 3 3
NGF (dimer)/TRKA 0.012 0.019 -9999 0 -0.29 2 2
MMP7 -0.046 0.15 -9999 0 -0.41 78 78
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.028 0.053 -9999 0 -0.19 28 28
MMP3 0.011 0.049 -9999 0 -0.41 7 7
APAF-1/Caspase 9 -0.016 0.046 -9999 0 -0.31 1 1
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0.019 -9999 0 -0.41 1 1
ELF1 0.018 0.055 -9999 0 -0.32 13 13
CCNA2 -0.096 0.19 -9999 0 -0.41 139 139
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
JAK3 0.018 0 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
JAK1 0.018 0.002 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.039 0.054 -9999 0 -0.2 11 11
SHC1 -0.02 0.12 -9999 0 -0.41 46 46
SP1 0.019 0.039 -9999 0 -0.22 14 14
IL2RA 0.018 0.056 -9999 0 -0.33 13 13
IL2RB 0.014 0.037 -9999 0 -0.41 4 4
SOS1 0.001 0 -9999 0 -10000 0 0
IL2RG 0.01 0.056 -9999 0 -0.41 9 9
G1/S transition of mitotic cell cycle -0.027 0.1 -9999 0 -0.27 38 38
PTPN11 0.018 0 -9999 0 -10000 0 0
CCND2 0.014 0.068 -9999 0 -0.4 14 14
LCK 0.014 0.037 -9999 0 -0.41 4 4
GRB2 0.017 0.002 -9999 0 -10000 0 0
IL2 0.018 0 -9999 0 -10000 0 0
CDK6 0.017 0 -9999 0 -10000 0 0
CCND3 0.042 0.052 -9999 0 -0.26 5 5
Canonical NF-kappaB pathway

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
FBXW11 0.019 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.061 0.024 -9999 0 -0.16 2 2
ERC1 0.016 0.019 -9999 0 -0.41 1 1
RIP2/NOD2 0.02 0.04 -9999 0 -0.28 9 9
NFKBIA 0.025 0.027 -9999 0 -0.24 5 5
BIRC2 0.017 0 -9999 0 -10000 0 0
IKBKB 0.017 0 -9999 0 -10000 0 0
RIPK2 0.016 0.019 -9999 0 -0.41 1 1
IKBKG 0.031 0.025 -9999 0 -0.17 1 1
IKK complex/A20 -0.017 0.1 -9999 0 -0.23 25 25
NEMO/A20/RIP2 0.016 0.019 -9999 0 -0.41 1 1
XPO1 0.017 0 -9999 0 -10000 0 0
NEMO/ATM 0.03 0.051 -9999 0 -0.17 26 26
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.017 0.001 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.023 0.002 -9999 0 -10000 0 0
IKK complex/ELKS 0.043 0.028 -9999 0 -0.32 1 1
BCL10/MALT1/TRAF6 0.021 0.062 -9999 0 -0.24 27 27
NOD2 0.011 0.052 -9999 0 -0.41 8 8
NFKB1 0.016 0.037 -9999 0 -0.41 4 4
RELA 0.019 0.004 -9999 0 -10000 0 0
MALT1 -0.002 0.09 -9999 0 -0.41 24 24
cIAP1/UbcH5C 0.025 0.001 -9999 0 -10000 0 0
ATM -0.003 0.091 -9999 0 -0.41 25 25
TNF/TNFR1A -0.083 0.15 -9999 0 -0.28 185 185
TRAF6 0.017 0 -9999 0 -10000 0 0
PRKCA 0.017 0 -9999 0 -10000 0 0
CHUK 0.016 0.019 -9999 0 -0.41 1 1
UBE2D3 0.017 0.001 -9999 0 -10000 0 0
TNF 0.015 0.026 -9999 0 -0.41 2 2
NF kappa B1 p50/RelA 0.042 0.026 -9999 0 -0.22 5 5
BCL10 0.014 0.037 -9999 0 -0.41 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.027 -9999 0 -0.24 5 5
beta TrCP1/SCF ubiquitin ligase complex 0.019 0.004 -9999 0 -10000 0 0
TNFRSF1A -0.13 0.2 -9999 0 -0.41 183 183
IKK complex 0.048 0.028 -9999 0 -0.15 2 2
CYLD 0.017 0 -9999 0 -10000 0 0
IKK complex/PKC alpha 0.053 0.028 -9999 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.029 0.029 -10000 0 -0.22 3 3
epithelial cell differentiation 0.032 0.031 -10000 0 -0.21 1 1
ITCH 0.018 0.02 -10000 0 -0.41 1 1
WWP1 0.025 0.025 -10000 0 -0.26 2 2
FYN 0.015 0.027 -10000 0 -0.41 2 2
EGFR -0.14 0.21 -10000 0 -0.41 194 194
PRL 0.012 0.046 -10000 0 -0.41 6 6
neuron projection morphogenesis 0.022 0.058 -10000 0 -0.2 6 6
PTPRZ1 -0.003 0.088 -10000 0 -0.41 23 23
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.032 0.068 -10000 0 -0.21 8 8
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.026 0.028 -10000 0 -0.21 6 6
ADAM17 0.014 0.041 -10000 0 -0.4 5 5
ErbB4/ErbB4 0.026 0.025 -10000 0 -0.24 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.017 0.023 -10000 0 -0.26 1 1
NCOR1 0.017 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.034 0.026 -10000 0 -0.2 5 5
GRIN2B 0.033 0.024 -10000 0 -0.21 2 2
ErbB4/ErbB2/betacellulin 0.035 0.027 -10000 0 -0.19 6 6
STAT1 0.002 0.078 -10000 0 -0.41 18 18
HBEGF 0.015 0.026 -10000 0 -0.41 2 2
PRLR 0.017 0 -10000 0 -10000 0 0
E4ICDs/ETO2 0.03 0.025 -10000 0 -0.26 1 1
axon guidance 0.023 0.031 -10000 0 -0.27 1 1
NEDD4 0.007 0.069 -10000 0 -0.41 14 14
Prolactin receptor/Prolactin receptor/Prolactin 0.022 0.033 -10000 0 -0.28 6 6
CBFA2T3 0.017 0 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF 0.034 0.03 -10000 0 -0.2 6 6
MAPK3 0.022 0.061 -10000 0 -0.2 8 8
STAT1 (dimer) 0.021 0.051 -10000 0 -0.22 19 19
MAPK1 0.021 0.061 -10000 0 -0.2 8 8
JAK2 0.017 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta 0.03 0.027 -10000 0 -0.19 6 6
NRG1 0.016 0.028 -10000 0 -0.27 5 5
NRG3 0 0 -10000 0 -10000 0 0
NRG2 0.017 0 -10000 0 -10000 0 0
NRG4 0 0 -10000 0 -10000 0 0
heart development 0.023 0.031 -10000 0 -0.27 1 1
neural crest cell migration 0.029 0.026 -10000 0 -0.19 6 6
ERBB2 0.016 0.028 -10000 0 -0.27 5 5
WWOX/E4ICDs 0.03 0.025 -10000 0 -0.26 1 1
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
ErbB4/EGFR/neuregulin 4 -0.055 0.11 -10000 0 -0.2 194 194
apoptosis -0.022 0.026 0.2 2 -10000 0 2
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.03 0.025 -10000 0 -0.26 1 1
ErbB4/ErbB2/epiregulin 0.031 0.043 -10000 0 -0.21 14 14
ErbB4/ErbB4/betacellulin/betacellulin 0.03 0.025 -10000 0 -0.26 1 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.051 0.035 -10000 0 -0.21 1 1
MDM2 0.018 0.047 -10000 0 -0.21 20 20
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta 0.03 0.027 -10000 0 -0.19 7 7
STAT5A 0.027 0.032 -10000 0 -0.25 1 1
ErbB4/EGFR/neuregulin 1 beta -0.046 0.11 -10000 0 -0.19 195 195
DLG4 0.017 0 -10000 0 -10000 0 0
GRB2/SHC -0.002 0.088 -10000 0 -0.28 46 46
E4ICDs/TAB2/NCoR1 0.038 0.023 -10000 0 -0.24 1 1
STAT5A (dimer) 0.047 0.036 -10000 0 -0.23 1 1
MAP3K7IP2 0.017 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.034 0.031 -10000 0 -0.25 1 1
LRIG1 -0.002 0.088 -10000 0 -0.41 23 23
EREG 0.009 0.059 -10000 0 -0.41 10 10
BTC 0.017 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.023 0.031 -10000 0 -0.27 1 1
ERBB4 0.026 0.025 -10000 0 -0.24 2 2
STAT5B 0.017 0 -10000 0 -10000 0 0
YAP1 -0.001 0.062 -10000 0 -0.2 46 46
GRB2 0.017 0.002 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.023 0.026 -10000 0 -0.2 6 6
glial cell differentiation -0.038 0.023 0.24 1 -10000 0 1
WWOX 0.017 0 -10000 0 -10000 0 0
cell proliferation 0.033 0.025 -10000 0 -0.2 1 1
IL4-mediated 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
BCL2L1 -0.053 0.22 -10000 0 -0.71 11 11
STAT6 (cleaved dimer) -0.11 0.16 -10000 0 -0.71 12 12
IGHG1 -0.015 0.12 -10000 0 -0.39 13 13
IGHG3 -0.059 0.21 -10000 0 -0.69 11 11
AKT1 -0.004 0.15 -10000 0 -0.5 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 0.015 0.12 -10000 0 -0.4 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.008 0.14 -10000 0 -0.53 5 5
THY1 -0.076 0.28 -10000 0 -0.7 46 46
MYB 0.011 0.052 -10000 0 -0.41 8 8
HMGA1 0.016 0.019 -10000 0 -0.41 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.013 0.16 -10000 0 -0.5 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.011 0.14 -10000 0 -0.52 5 5
SP1 -0.021 0.045 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.015 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.041 0.21 -10000 0 -0.76 9 9
SOCS1 -0.012 0.18 -10000 0 -0.54 9 9
SOCS3 -0.006 0.14 -10000 0 -0.52 5 5
FCER2 -0.034 0.19 -10000 0 -0.69 6 6
PARP14 0.001 0.001 -10000 0 -10000 0 0
CCL17 -0.053 0.22 -10000 0 -0.71 11 11
GRB2 0.017 0.002 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.015 0.14 -10000 0 -0.43 14 14
T cell proliferation -0.042 0.22 -10000 0 -0.78 9 9
IL4R/JAK1 -0.056 0.22 -10000 0 -0.76 10 10
EGR2 -0.057 0.24 -10000 0 -0.72 16 16
JAK2 0.013 0.03 -10000 0 -10000 0 0
JAK3 0.021 0.003 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
JAK1 0.017 0.013 -10000 0 -10000 0 0
COL1A2 -0.15 0.23 -10000 0 -0.46 120 120
CCL26 -0.06 0.22 -10000 0 -0.72 11 11
IL4R -0.06 0.24 -10000 0 -0.73 14 14
PTPN6 0.01 0.061 -10000 0 -0.4 11 11
IL13RA2 -0.13 0.28 -10000 0 -0.67 42 42
IL13RA1 -0.055 0.16 -10000 0 -0.43 80 80
IRF4 0.017 0.075 -10000 0 -0.62 1 1
ARG1 0.002 0.11 -10000 0 -0.38 13 13
CBL -0.016 0.15 -10000 0 -0.53 7 7
GTF3A 0.014 0.027 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
IL13RA1/JAK2 -0.029 0.12 -10000 0 -0.3 80 80
IRF4/BCL6 0.013 0.078 -10000 0 -0.56 1 1
CD40LG 0.024 0.003 -10000 0 -10000 0 0
MAPK14 -0.012 0.15 -10000 0 -0.52 8 8
mitosis -0.002 0.15 -10000 0 -0.48 8 8
STAT6 -0.038 0.24 -10000 0 -0.67 20 20
SPI1 0.016 0.053 -10000 0 -0.41 8 8
RPS6KB1 0 0.14 -10000 0 -0.46 9 9
STAT6 (dimer) -0.038 0.24 -10000 0 -0.57 40 40
STAT6 (dimer)/PARP14 -0.068 0.22 -10000 0 -0.78 9 9
mast cell activation 0 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.001 0.13 -10000 0 -0.44 9 9
FRAP1 -0.004 0.15 -10000 0 -0.5 8 8
LTA -0.054 0.22 -10000 0 -0.73 11 11
FES 0.017 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.051 0.24 0.69 17 -10000 0 17
CCL11 -0.055 0.22 -10000 0 -0.7 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES 0.002 0.14 -10000 0 -0.44 8 8
IL2RG 0.013 0.056 -10000 0 -0.41 9 9
IL10 -0.053 0.22 -10000 0 -0.71 11 11
IRS1 0.013 0.042 -10000 0 -0.41 5 5
IRS2 0.017 0.002 -10000 0 -10000 0 0
IL4 0.005 0.087 -10000 0 -10000 0 0
IL5 -0.053 0.22 -10000 0 -0.71 11 11
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.053 0.22 -10000 0 -0.59 18 18
COL1A1 -0.044 0.19 -10000 0 -0.47 66 66
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.056 0.22 -10000 0 -0.78 9 9
IL2R gamma/JAK3 0.026 0.041 -10000 0 -0.29 9 9
TFF3 -0.058 0.23 -10000 0 -0.7 19 19
ALOX15 -0.053 0.22 -10000 0 -0.71 11 11
MYBL1 -0.048 0.15 -10000 0 -0.41 80 80
T-helper 2 cell differentiation -0.041 0.2 -10000 0 -0.71 7 7
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
CEBPB 0.013 0.062 -10000 0 -0.41 11 11
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.006 0.14 -10000 0 -0.48 6 6
mol:PI-3-4-5-P3 -0.003 0.15 -10000 0 -0.5 8 8
PI3K -0.005 0.15 -10000 0 -0.52 8 8
DOK2 0 0 -10000 0 -10000 0 0
ETS1 0.016 0.015 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.012 0.14 -10000 0 -0.41 14 14
ITGB3 -0.053 0.22 -10000 0 -0.71 11 11
PIGR -0.054 0.23 -10000 0 -0.71 12 12
IGHE 0.021 0.05 0.14 29 -0.13 1 30
MAPKKK cascade -0.012 0.13 -10000 0 -0.41 13 13
BCL6 0.003 0.074 -10000 0 -0.41 16 16
OPRM1 -0.053 0.22 -10000 0 -0.71 11 11
RETNLB -0.06 0.22 -10000 0 -0.72 11 11
SELP -0.054 0.22 -10000 0 -0.72 11 11
AICDA -0.053 0.21 -10000 0 -0.74 9 9
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.037 0.043 -10000 0 -0.17 1 1
TBX21 0.045 0.12 -10000 0 -0.44 12 12
B2M 0.017 0 -10000 0 -10000 0 0
TYK2 0.017 0.026 -10000 0 -0.44 1 1
IL12RB1 0.017 0.016 -10000 0 -10000 0 0
GADD45B 0.046 0.12 -10000 0 -0.44 14 14
IL12RB2 0.018 0.017 -10000 0 -10000 0 0
GADD45G 0.044 0.12 -10000 0 -0.39 13 13
natural killer cell activation 0.002 0.014 -10000 0 -10000 0 0
RELB 0.016 0.019 -10000 0 -0.41 1 1
RELA 0.017 0 -10000 0 -10000 0 0
IL18 -0.017 0.12 -10000 0 -0.41 45 45
IL2RA 0.012 0.046 -10000 0 -0.41 6 6
IFNG 0.016 0.019 -10000 0 -0.41 1 1
STAT3 (dimer) 0.042 0.14 -10000 0 -0.42 11 11
HLA-DRB5 -0.002 0.005 -10000 0 -10000 0 0
FASLG 0.045 0.12 -10000 0 -0.39 18 18
NF kappa B2 p52/RelB 0.028 0.14 -10000 0 -0.44 12 12
CD4 -0.002 0.083 -10000 0 -0.42 20 20
SOCS1 0.017 0 -10000 0 -10000 0 0
EntrezGene:6955 -0.003 0.006 -10000 0 -10000 0 0
CD3D -0.003 0.082 -10000 0 -0.42 20 20
CD3E 0.014 0.02 -10000 0 -0.41 1 1
CD3G 0.012 0.021 -10000 0 -0.41 1 1
IL12Rbeta2/JAK2 0.028 0.027 -10000 0 -10000 0 0
CCL3 0.038 0.12 -10000 0 -0.38 23 23
CCL4 0.045 0.14 -10000 0 -0.49 19 19
HLA-A 0.016 0.019 -10000 0 -0.41 1 1
IL18/IL18R 0.033 0.083 -10000 0 -0.23 45 45
NOS2 0.039 0.12 -10000 0 -0.35 22 22
IL12/IL12R/TYK2/JAK2/SPHK2 0.037 0.043 -10000 0 -0.17 1 1
IL1R1 0.043 0.13 -10000 0 -0.4 20 20
IL4 0.015 0.014 -10000 0 -10000 0 0
JAK2 0.017 0.016 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.016 0.032 -10000 0 -0.16 9 9
RAB7A 0.048 0.12 -10000 0 -0.41 5 5
lysosomal transport 0.048 0.12 -10000 0 -0.4 5 5
FOS -0.081 0.2 -10000 0 -0.4 130 130
STAT4 (dimer) 0.038 0.13 -10000 0 -0.44 8 8
STAT5A (dimer) 0.027 0.14 -10000 0 -0.42 13 13
GZMA 0.034 0.15 -10000 0 -0.53 19 19
GZMB 0.038 0.14 -10000 0 -0.52 17 17
HLX 0.013 0.042 -10000 0 -0.41 5 5
LCK 0.041 0.13 -10000 0 -0.39 25 25
TCR/CD3/MHC II/CD4 -0.075 0.1 -10000 0 -0.23 110 110
IL2/IL2R 0.035 0.053 -10000 0 -0.26 15 15
MAPK14 0.043 0.13 -10000 0 -0.44 8 8
CCR5 0.043 0.13 -10000 0 -0.45 16 16
IL1B 0.006 0.071 -10000 0 -0.41 14 14
STAT6 0.033 0.048 -10000 0 -0.16 5 5
STAT4 0.01 0.008 -10000 0 -10000 0 0
STAT3 0.009 0.059 -10000 0 -0.41 10 10
STAT1 0.002 0.078 -10000 0 -0.41 18 18
NFKB1 0.014 0.037 -10000 0 -0.41 4 4
NFKB2 0.017 0 -10000 0 -10000 0 0
IL12B 0.018 0.017 -10000 0 -10000 0 0
CD8A 0 0 -10000 0 -10000 0 0
CD8B 0.015 0.026 -10000 0 -0.41 2 2
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.037 0.043 0.17 1 -10000 0 1
IL2RB 0.014 0.037 -10000 0 -0.41 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.13 -10000 0 -0.41 8 8
IL2RG 0.01 0.056 -10000 0 -0.41 9 9
IL12 0.028 0.027 -10000 0 -10000 0 0
STAT5A 0.016 0.019 -10000 0 -0.41 1 1
CD247 0.013 0.027 -10000 0 -0.42 2 2
IL2 0.017 0 -10000 0 -10000 0 0
SPHK2 0.017 0 -10000 0 -10000 0 0
FRAP1 0.016 0.019 -10000 0 -0.41 1 1
IL12A 0.017 0.016 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 0.047 0.13 -10000 0 -0.42 21 21
MAP2K3 0.039 0.13 -10000 0 -0.42 11 11
RIPK2 0.016 0.019 -10000 0 -0.41 1 1
MAP2K6 0.039 0.13 -10000 0 -0.42 11 11
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.22 0.21 -10000 0 -0.42 292 292
IL18RAP 0.02 0.006 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.025 0.028 -10000 0 -0.32 1 1
EOMES -0.002 0.019 -10000 0 -10000 0 0
STAT1 (dimer) 0.039 0.13 -10000 0 -0.47 7 7
T cell proliferation 0.024 0.12 -10000 0 -0.36 8 8
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.02 0.006 -10000 0 -10000 0 0
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.028 0.088 -10000 0 -0.36 16 16
ATF2 0.045 0.13 -10000 0 -0.45 5 5
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.005 0.042 -9999 0 -0.24 15 15
SNTA1 0.017 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.01 0.042 -9999 0 -0.24 15 15
MAPK12 0.015 0.02 -9999 0 -0.13 10 10
CCND1 -0.013 0.062 -9999 0 -0.14 99 99
p38 gamma/SNTA1 0.025 0.02 -9999 0 -10000 0 0
MAP2K3 0.017 0 -9999 0 -10000 0 0
PKN1 0.009 0.059 -9999 0 -0.41 10 10
G2/M transition checkpoint 0.015 0.02 -9999 0 -0.13 10 10
MAP2K6 0.013 0.023 -9999 0 -0.15 10 10
MAPT 0.009 0.035 -9999 0 -0.18 15 15
MAPK13 0.009 0.05 -9999 0 -0.29 15 15
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.011 0.027 -9999 0 -0.18 10 10
Insulin Pathway

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
CBL/APS/CAP 0.029 0.02 -9999 0 -0.18 5 5
TC10/GTP 0.027 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.044 0.025 -9999 0 -0.21 5 5
HRAS 0.016 0.019 -9999 0 -0.41 1 1
APS homodimer 0 0 -9999 0 -10000 0 0
GRB14 0.002 0.078 -9999 0 -0.41 18 18
FOXO3 0.012 0.013 -9999 0 -10000 0 0
AKT1 0.021 0.062 -9999 0 -0.33 1 1
INSR 0.019 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.048 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.004 0.074 -9999 0 -0.41 16 16
SORBS1 0.017 0 -9999 0 -10000 0 0
CRK 0.017 0 -9999 0 -10000 0 0
PTPN1 0.024 0.009 -9999 0 -10000 0 0
CAV1 -0.11 0.11 -9999 0 -0.2 324 324
CBL/APS/CAP/Crk-II/C3G 0.041 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0.044 0.025 -9999 0 -0.21 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.023 0.049 -9999 0 -0.18 27 27
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.023 0.044 -9999 0 -0.23 3 3
RPS6KB1 0.022 0.058 -9999 0 -0.3 1 1
PARD6A 0.017 0 -9999 0 -10000 0 0
CBL 0.017 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.016 0.011 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.022 0.054 -9999 0 -0.29 1 1
HRAS/GTP -0.016 0.051 -9999 0 -0.17 49 49
Insulin Receptor 0.019 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.029 0.076 -9999 0 -0.21 48 48
PRKCI 0.025 0.028 -9999 0 -0.15 6 6
Insulin Receptor/Insulin/GRB14/PDK1 -0.014 0.047 -9999 0 -0.17 43 43
SHC1 -0.02 0.12 -9999 0 -0.41 46 46
negative regulation of MAPKKK cascade 0.029 0.033 -9999 0 -0.19 11 11
PI3K 0.03 0.052 -9999 0 -0.18 27 27
NCK2 0.017 0.001 -9999 0 -10000 0 0
RHOQ 0.017 0 -9999 0 -10000 0 0
mol:H2O2 0 0.001 -9999 0 -10000 0 0
HRAS/GDP 0.012 0.013 -9999 0 -0.29 1 1
AKT2 0.023 0.059 -9999 0 -0.33 1 1
PRKCZ 0.015 0.026 -9999 0 -0.16 6 6
SH2B2 0 0 -9999 0 -10000 0 0
SHC/SHIP 0.003 0.066 -9999 0 -0.2 48 48
F2RL2 0.017 0 -9999 0 -10000 0 0
TRIP10 0.012 0.046 -9999 0 -0.41 6 6
Insulin Receptor/Insulin/Shc 0.013 0.071 -9999 0 -0.22 46 46
TC10/GTP/CIP4/Exocyst 0.02 0.028 -9999 0 -0.24 6 6
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.022 0.068 -9999 0 -0.2 46 46
RAPGEF1 0.017 0 -9999 0 -10000 0 0
RASA1 0.017 0.002 -9999 0 -10000 0 0
NCK1 0.008 0.061 -9999 0 -0.41 11 11
CBL/APS/CAP/Crk-II 0.033 0 -9999 0 -10000 0 0
TC10/GDP 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.016 0.086 -9999 0 -0.22 59 59
INPP5D 0.011 0.021 -9999 0 -0.2 5 5
SOS1 0 0 -9999 0 -10000 0 0
SGK1 -0.002 0.005 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.017 0 -9999 0 -10000 0 0
IRS1 0.013 0.042 -9999 0 -0.41 5 5
p62DOK/RasGAP 0.03 0.034 -9999 0 -0.19 11 11
INS 0.019 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.011 0.021 -9999 0 -0.2 5 5
GRB2 0.017 0.002 -9999 0 -10000 0 0
EIF4EBP1 -0.071 0.11 -9999 0 -0.31 27 27
PTPRA 0.019 0.002 -9999 0 -10000 0 0
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
TC10/GTP/CIP4 0.02 0.028 -9999 0 -0.24 6 6
PDPK1 0.017 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.013 0.047 -9999 0 -0.13 48 48
Insulin Receptor/Insulin/IRS1 0.033 0.024 -9999 0 -0.22 5 5
Insulin Receptor/Insulin/IRS3 0.028 0 -9999 0 -10000 0 0
Par3/Par6 0.038 0.025 -9999 0 -0.19 6 6
Arf6 signaling events

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
CENTA1/KIF3B 0.011 0.016 -9999 0 -0.24 2 2
ARNO/beta Arrestin1-2 0.025 0.009 -9999 0 -0.17 1 1
EGFR -0.14 0.21 -9999 0 -0.41 194 194
EPHA2 0.007 0.067 -9999 0 -0.41 13 13
USP6 0.017 0 -9999 0 -10000 0 0
IQSEC1 0.017 0.002 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.09 0.15 -9999 0 -0.28 196 196
ARRB2 0.015 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.005 -9999 0 -10000 0 0
ARRB1 0.017 0 -9999 0 -10000 0 0
FBXO8 0 0 -9999 0 -10000 0 0
TSHR 0.014 0.037 -9999 0 -0.41 4 4
EGF 0.015 0.026 -9999 0 -0.41 2 2
somatostatin receptor activity 0 0 -9999 0 0 1 1
ARAP2 0 0 -9999 0 0 1 1
mol:GDP 0.019 0.019 -9999 0 -0.089 1 1
mol:PI-3-4-5-P3 0 0 -9999 0 0 1 1
ITGA2B 0.017 0 -9999 0 -10000 0 0
ARF6 0.017 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.022 0.085 -9999 0 -0.26 38 38
ADAP1 0 0 -9999 0 -10000 0 0
KIF13B 0.015 0.026 -9999 0 -0.41 2 2
HGF/MET 0.018 0.046 -9999 0 -0.28 12 12
PXN 0.017 0 -9999 0 -10000 0 0
ARF6/GTP 0.028 0.033 -9999 0 -0.095 1 1
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.065 0.13 -9999 0 -0.24 194 194
ADRB2 0.016 0.019 -9999 0 -0.41 1 1
receptor agonist activity 0 0 0 4 0 1 5
actin filament binding 0 0 -9999 0 0 1 1
SRC 0.017 0 -9999 0 -10000 0 0
ITGB3 0.017 0 -9999 0 -10000 0 0
GNAQ 0.017 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 0 1 1
ARF6/GDP 0.021 0.025 -9999 0 -0.11 6 6
ARF6/GDP/GULP/ACAP1 0.033 0.024 -9999 0 -0.17 4 4
alphaIIb/beta3 Integrin/paxillin/GIT1 0.044 0 -9999 0 -10000 0 0
ACAP1 0 0 -9999 0 -10000 0 0
ACAP2 0 0 -9999 0 0 1 1
LHCGR/beta Arrestin2 0.018 0 -9999 0 -10000 0 0
EFNA1 -0.002 0.09 -9999 0 -0.41 24 24
HGF 0.015 0.026 -9999 0 -0.41 2 2
CYTH3 0 0 -9999 0 0 1 1
CYTH2 0 0 -9999 0 -0.002 2 2
NCK1 0.008 0.061 -9999 0 -0.41 11 11
fibronectin binding 0 0 -9999 0 0 1 1
endosomal lumen acidification 0 0 -9999 0 0 1 1
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.014 0.037 -9999 0 -0.41 4 4
GNAQ/ARNO 0.013 0.001 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 0 1 1
PIP3-E 0.001 0.004 -9999 0 -10000 0 0
MET 0.009 0.059 -9999 0 -0.41 10 10
GNA14 0.016 0.026 -9999 0 -0.41 2 2
GNA15 0.011 0.049 -9999 0 -0.41 7 7
GIT1 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 0 1 1
GNA11 0.017 0 -9999 0 -10000 0 0
LHCGR 0.017 0 -9999 0 -10000 0 0
AGTR1 0.016 0.026 -9999 0 -0.41 2 2
desensitization of G-protein coupled receptor protein signaling pathway 0.018 0 -9999 0 -10000 0 0
IPCEF1/ARNO -0.029 0.042 -9999 0 -0.18 6 6
alphaIIb/beta3 Integrin 0.025 0 -9999 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.015 0.038 0.11 63 -10000 0 63
GNAI2 0.017 0.001 -10000 0 -10000 0 0
S1P/S1P5/G12 0.01 0.022 -10000 0 -0.24 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.002 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.039 -10000 0 -0.11 63 63
negative regulation of cAMP metabolic process 0.001 0.01 -10000 0 -0.1 3 3
GNAZ 0.015 0.006 -10000 0 -10000 0 0
GNAI3 -0.036 0.14 -10000 0 -0.41 65 65
GNA12 0.014 0.037 -10000 0 -0.41 4 4
S1PR5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.001 0.01 -10000 0 -0.1 3 3
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
RHOA 0.017 0.001 -10000 0 -10000 0 0
GNAI1 0.014 0.02 -10000 0 -0.41 1 1
IGF1 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
NCK2 0.017 0.001 -10000 0 -10000 0 0
PTK2 0.017 0.001 -10000 0 -10000 0 0
CRKL 0.018 0.023 -10000 0 -0.16 9 9
GRB2/SOS1/SHC 0 0.074 -10000 0 -0.24 46 46
HRAS 0.016 0.019 -10000 0 -0.41 1 1
IRS1/Crk 0.022 0.024 -10000 0 -0.16 9 9
IGF-1R heterotetramer/IGF1/PTP1B 0.031 0.022 -10000 0 -0.21 4 4
AKT1 0.012 0.046 -10000 0 -0.17 28 28
BAD 0.021 0.05 -10000 0 -0.16 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.018 0.023 -10000 0 -0.16 9 9
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.024 0.024 -10000 0 -0.16 9 9
RAF1 0.027 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.029 0.024 -10000 0 -0.15 9 9
YWHAZ 0.017 0.002 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.021 0.026 -10000 0 -0.18 9 9
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
RPS6KB1 0.013 0.044 -10000 0 -0.17 25 25
GNB2L1 0.017 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.02 0.047 0.28 2 -10000 0 2
PXN 0.017 0 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.013 0.001 -10000 0 -10000 0 0
HRAS/GTP -0.001 0.059 -10000 0 -0.18 47 47
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.017 0.072 -10000 0 -0.21 49 49
IGF-1R heterotetramer 0.017 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.031 0.025 -10000 0 -0.16 9 9
Crk/p130 Cas/Paxillin 0.031 0.022 -10000 0 -0.14 9 9
IGF1R 0.017 0.008 -10000 0 -10000 0 0
IGF1 0.014 0.038 -10000 0 -0.41 4 4
IRS2/Crk 0.025 0.023 -10000 0 -0.14 9 9
PI3K 0.027 0.053 -10000 0 -0.18 30 30
apoptosis -0.028 0.047 -10000 0 -10000 0 0
HRAS/GDP 0.012 0.013 -10000 0 -0.29 1 1
PRKCD 0.016 0.035 -10000 0 -0.16 7 7
RAF1/14-3-3 E 0.034 0.045 -10000 0 -10000 0 0
BAD/14-3-3 0.029 0.049 -10000 0 -10000 0 0
PRKCZ 0.009 0.042 -10000 0 -0.17 24 24
Crk/p130 Cas/Paxillin/FAK1 0.021 0.04 -10000 0 -10000 0 0
PTPN1 0.017 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.013 0.037 -10000 0 -0.17 7 7
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.01 0.091 -10000 0 -0.24 62 62
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 0.024 0.024 -10000 0 -0.16 9 9
GRB10 0.004 0.074 -10000 0 -0.41 16 16
PTPN11 0.018 0.023 -10000 0 -0.16 9 9
IRS1 0.014 0.025 -10000 0 -0.18 9 9
IRS2 0.018 0.023 -10000 0 -0.16 9 9
IGF-1R heterotetramer/IGF1 0.021 0.028 -10000 0 -0.28 4 4
GRB2 0.017 0.002 -10000 0 -10000 0 0
PDPK1 0.014 0.046 -10000 0 -0.18 24 24
YWHAE 0.017 0.001 -10000 0 -10000 0 0
PRKD1 -0.032 0.09 -10000 0 -0.18 131 131
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
Thromboxane A2 receptor signaling

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
TGM2 0.013 0.037 -10000 0 -0.41 4 4
GNB1/GNG2 -0.046 0.035 -10000 0 -0.14 15 15
AKT1 -0.016 0.082 -10000 0 -0.17 6 6
EGF 0.015 0.026 -10000 0 -0.41 2 2
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR 0.023 0.033 -10000 0 -0.16 17 17
mol:Ca2+ -0.029 0.11 -10000 0 -0.23 15 15
LYN 0.007 0.06 -10000 0 -0.15 64 64
RhoA/GTP -0.031 0.027 -10000 0 -0.099 15 15
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.047 0.12 -10000 0 -0.27 36 36
GNG2 0 0 -10000 0 -10000 0 0
ARRB2 0.017 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.027 0.019 -10000 0 -0.13 7 7
G beta5/gamma2 -0.058 0.045 -10000 0 -0.19 15 15
PRKCH -0.041 0.12 -10000 0 -0.28 16 16
DNM1 0.003 0.007 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.002 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.002 15 15
PTGDR 0.017 0 -10000 0 -10000 0 0
G12 family/GTP -0.071 0.055 -10000 0 -0.22 19 19
ADRBK1 0.017 0 -10000 0 -10000 0 0
ADRBK2 0.017 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.023 0.002 -10000 0 -10000 0 0
mol:GDP 0.003 0.065 0.17 1 -10000 0 1
mol:NADP 0.017 0 -10000 0 -10000 0 0
RAB11A 0.017 0.001 -10000 0 -10000 0 0
PRKG1 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.039 0.12 -10000 0 -0.28 15 15
cell morphogenesis 0.023 0.002 -10000 0 -10000 0 0
PLCB2 -0.054 0.14 -10000 0 -0.36 15 15
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK 0.029 0.006 -10000 0 -10000 0 0
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0 0.068 -10000 0 -0.15 86 86
RHOA 0.017 0.001 -10000 0 -10000 0 0
PTGIR 0.017 0 -10000 0 -10000 0 0
PRKCB1 -0.009 0.049 -10000 0 -0.24 15 15
GNAQ 0.017 0 -10000 0 -10000 0 0
mol:L-citrulline 0.017 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.062 0.15 -10000 0 -0.38 15 15
LCK 0.028 0.017 -10000 0 -0.15 4 4
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.033 0.002 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.039 -10000 0 -0.31 6 6
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.033 0.002 -10000 0 -10000 0 0
MAPK14 -0.028 0.093 -10000 0 -0.18 38 38
TGM2/GTP -0.035 0.13 -10000 0 -0.3 15 15
MAPK11 -0.028 0.093 -10000 0 -0.18 36 36
ARHGEF1 -0.018 0.07 -10000 0 -0.14 15 15
GNAI2 0.017 0.001 -10000 0 -10000 0 0
JNK cascade -0.045 0.13 -10000 0 -0.29 15 15
RAB11/GDP 0.017 0.001 -10000 0 -10000 0 0
ICAM1 -0.034 0.11 -10000 0 -0.28 17 17
cAMP biosynthetic process -0.032 0.11 -10000 0 -0.25 15 15
Gq family/GTP/EBP50 0.02 0.021 -10000 0 -0.12 10 10
actin cytoskeleton reorganization 0.023 0.002 -10000 0 -10000 0 0
SRC 0.029 0.006 -10000 0 -10000 0 0
GNB5 0.017 0.002 -10000 0 -10000 0 0
GNB1 0.017 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.013 0.061 -10000 0 -0.17 33 33
VCAM1 -0.078 0.13 -10000 0 -0.25 30 30
TP beta/Gq family/GDP/G beta5/gamma2 0.027 0.019 -10000 0 -0.13 7 7
platelet activation -0.03 0.12 -10000 0 -0.24 17 17
PGI2/IP 0.013 0.001 -10000 0 -10000 0 0
PRKACA 0.019 0.001 -10000 0 -10000 0 0
Gq family/GDP/G beta5/gamma2 0.026 0.019 -10000 0 -0.12 7 7
TXA2/TP beta/beta Arrestin2 0.002 0.006 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.019 0.002 -10000 0 -10000 0 0
mol:DAG -0.049 0.13 -10000 0 -0.32 15 15
EGFR -0.14 0.21 -10000 0 -0.41 194 194
TXA2/TP alpha -0.041 0.14 -10000 0 -0.33 15 15
Gq family/GTP 0.016 0.017 -10000 0 -0.11 9 9
YES1 0.002 0.065 -10000 0 -0.15 79 79
GNAI2/GTP 0.023 0.005 -10000 0 -10000 0 0
PGD2/DP 0.013 0.001 -10000 0 -10000 0 0
SLC9A3R1 0.015 0.026 -10000 0 -0.41 2 2
FYN 0.027 0.013 -10000 0 -0.15 2 2
mol:NO 0.017 0 -10000 0 -10000 0 0
GNA15 0.011 0.049 -10000 0 -0.41 7 7
PGK/cGMP 0.023 0.001 -10000 0 -10000 0 0
RhoA/GDP 0.017 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.034 0.018 -10000 0 -0.17 4 4
NOS3 0.017 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.041 0.12 -10000 0 -0.27 15 15
PRKCB -0.046 0.12 -10000 0 -0.27 15 15
PRKCE -0.044 0.12 -10000 0 -0.28 15 15
PRKCD -0.051 0.12 -10000 0 -0.29 15 15
PRKCG -0.047 0.12 -10000 0 -0.29 15 15
muscle contraction -0.055 0.14 -10000 0 -0.36 15 15
PRKCZ -0.041 0.12 -10000 0 -0.26 15 15
ARR3 0.017 0 -10000 0 -10000 0 0
TXA2/TP beta 0.034 0.005 -10000 0 -10000 0 0
PRKCQ -0.044 0.12 -10000 0 -0.27 15 15
MAPKKK cascade -0.051 0.13 -10000 0 -0.33 15 15
SELE -0.038 0.11 -10000 0 -0.24 15 15
TP beta/GNAI2/GDP/G beta/gamma 0.035 0.004 -10000 0 -10000 0 0
ROCK1 0.017 0 -10000 0 -10000 0 0
GNA14 0.015 0.026 -10000 0 -0.41 2 2
chemotaxis -0.077 0.16 -10000 0 -0.44 15 15
GNA12 0.014 0.037 -10000 0 -0.41 4 4
GNA13 0.015 0.026 -10000 0 -0.41 2 2
GNA11 0.017 0 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.001 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 0.033 0.074 -10000 0 -0.32 22 22
IHH 0.024 0.023 -10000 0 -10000 0 0
SHH Np/Cholesterol/GAS1 -0.002 0.074 -10000 0 -0.21 58 58
LRPAP1 0.017 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.002 0.073 0.21 58 -10000 0 58
SMO/beta Arrestin2 0.045 0.047 -10000 0 -0.27 7 7
SMO 0.038 0.048 -10000 0 -0.28 7 7
AKT1 0.029 0.055 -10000 0 -0.21 19 19
ARRB2 0.017 0 -10000 0 -10000 0 0
BOC 0 0 -10000 0 -10000 0 0
ADRBK1 0.017 0 -10000 0 -10000 0 0
heart looping 0.038 0.048 -10000 0 -0.28 7 7
STIL 0.004 0.084 -10000 0 -0.18 75 75
DHH N/PTCH2 0.013 0 -10000 0 -10000 0 0
DHH N/PTCH1 0.025 0.053 -10000 0 -0.22 22 22
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
DHH 0 0 -10000 0 -10000 0 0
PTHLH 0.033 0.076 -10000 0 -0.33 22 22
determination of left/right symmetry 0.038 0.048 -10000 0 -0.28 7 7
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
skeletal system development 0.033 0.075 -10000 0 -0.33 22 22
IHH N/Hhip 0.016 0.012 -10000 0 -10000 0 0
DHH N/Hhip 0 0 -10000 0 -10000 0 0
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.038 0.048 -10000 0 -0.28 7 7
pancreas development 0 0 -10000 0 -10000 0 0
HHAT 0.017 0 -10000 0 -10000 0 0
PI3K 0.009 0.065 -10000 0 -0.28 25 25
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.03 0.13 -10000 0 -0.41 58 58
somite specification 0.038 0.048 -10000 0 -0.28 7 7
SHH Np/Cholesterol/PTCH1 0.035 0.048 -10000 0 -0.22 14 14
SHH Np/Cholesterol/PTCH2 0.024 0 -10000 0 -10000 0 0
SHH Np/Cholesterol/Megalin 0.023 0.01 -10000 0 -0.21 1 1
SHH 0.018 0 -10000 0 -10000 0 0
catabolic process 0.03 0.061 -10000 0 -0.25 22 22
SMO/Vitamin D3 0.042 0.047 -10000 0 -0.28 7 7
SHH Np/Cholesterol/Hhip 0.012 0 -10000 0 -10000 0 0
LRP2 0.016 0.019 -10000 0 -0.41 1 1
receptor-mediated endocytosis 0.042 0.044 -10000 0 -0.25 7 7
SHH Np/Cholesterol/BOC 0.012 0 -10000 0 -10000 0 0
SHH Np/Cholesterol/CDO 0.024 0 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.012 0 -10000 0 -10000 0 0
mol:Vitamin D3 0.037 0.049 -10000 0 -0.22 14 14
IHH N/PTCH2 0.029 0.014 -10000 0 -10000 0 0
CDON 0.017 0 -10000 0 -10000 0 0
IHH N/PTCH1 0.038 0.063 -10000 0 -0.25 22 22
Megalin/LRPAP1 0.025 0.014 -10000 0 -0.28 1 1
PTCH2 0.017 0 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.015 0 -10000 0 -10000 0 0
PTCH1 0.03 0.061 -10000 0 -0.25 22 22
HHIP 0 0 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.029 0.06 -9999 0 -0.21 32 32
MAP4K1 0.016 0.019 -9999 0 -0.41 1 1
MAP3K8 -0.017 0.12 -9999 0 -0.41 42 42
PRKCB 0 0 -9999 0 -10000 0 0
DBNL 0 0 -9999 0 -10000 0 0
CRKL 0.017 0 -9999 0 -10000 0 0
MAP3K1 0.021 0.034 -9999 0 -0.18 1 1
JUN 0.019 0.015 -9999 0 -0.18 1 1
MAP3K7 0.021 0.034 -9999 0 -0.18 1 1
GRAP2 0.017 0 -9999 0 -10000 0 0
CRK 0.017 0 -9999 0 -10000 0 0
MAP2K4 0.018 0.045 -9999 0 -0.18 15 15
LAT 0.016 0.019 -9999 0 -0.41 1 1
LCP2 -0.007 0.099 -9999 0 -0.41 30 30
MAPK8 0.016 0.014 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.035 -9999 0 -0.12 30 30
LAT/GRAP2/SLP76/HPK1/HIP-55 0.027 0.056 -9999 0 -0.19 32 32
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.018 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.035 0.004 -10000 0 -10000 0 0
CDKN1B 0.02 0.037 -10000 0 -0.14 27 27
CDKN1A -0.001 0.069 -10000 0 -0.16 80 80
FRAP1 0.016 0.019 -10000 0 -0.41 1 1
PRKDC -0.002 0.088 -10000 0 -0.41 23 23
FOXO3 0.02 0.037 -10000 0 -0.14 27 27
AKT1 0.017 0.039 -10000 0 -0.15 27 27
BAD 0.017 0 -10000 0 -10000 0 0
AKT3 0.015 0.009 -10000 0 -0.18 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.02 0.037 -10000 0 -0.14 27 27
AKT1/ASK1 0.025 0.037 -10000 0 -0.18 1 1
BAD/YWHAZ 0.035 0.004 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0.016 0.019 -10000 0 -0.41 1 1
JNK cascade -0.024 0.036 0.18 1 -10000 0 1
TSC1 0.019 0.037 -10000 0 -0.14 27 27
YWHAZ 0.017 0.002 -10000 0 -10000 0 0
AKT1/RAF1 0.026 0.039 -10000 0 -0.14 28 28
EP300 0.017 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.038 -10000 0 -0.15 27 27
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.02 0.037 -10000 0 -0.14 27 27
YWHAQ 0.017 0 -10000 0 -10000 0 0
TBC1D4 0.016 0 -10000 0 -10000 0 0
MAP3K5 0.017 0.001 -10000 0 -10000 0 0
MAPKAP1 0.017 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.002 0.036 0.15 10 -10000 0 10
YWHAH 0.008 0.009 -10000 0 -10000 0 0
AKT1S1 0.016 0.037 -10000 0 -0.14 27 27
CASP9 0.018 0.045 -10000 0 -0.16 28 28
YWHAB 0.017 0.001 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.029 0.037 -10000 0 -0.18 1 1
GBL 0.017 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.035 0 -10000 0 -10000 0 0
YWHAE 0.017 0.001 -10000 0 -10000 0 0
SRC 0.017 0 -10000 0 -10000 0 0
AKT2/p21CIP1 0.004 0.066 -10000 0 -0.16 55 55
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.026 0.015 -10000 0 -0.17 1 1
CHUK 0.019 0.038 -10000 0 -0.14 28 28
BAD/BCL-XL 0.036 0.037 -10000 0 -0.17 1 1
mTORC2 0.033 0.011 -10000 0 -0.21 1 1
AKT2 0.015 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.005 0.048 -10000 0 -0.2 10 10
PDPK1 0.017 0 -10000 0 -10000 0 0
MDM2 0.013 0.051 -10000 0 -0.16 44 44
MAPKKK cascade -0.026 0.039 0.14 28 -10000 0 28
MDM2/Cbp/p300 0.031 0.052 -10000 0 -0.24 2 2
TSC1/TSC2 0.022 0.036 -10000 0 -0.17 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.05 -10000 0 -0.16 19 19
glucose import 0.018 0 -10000 0 -10000 0 0
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.027 0.027 -10000 0 -0.22 1 1
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.018 0 -10000 0 -10000 0 0
GSK3A 0.02 0.037 -10000 0 -0.14 27 27
FOXO1 0.016 0.047 -10000 0 -0.15 37 37
GSK3B 0.02 0.036 -10000 0 -0.14 26 26
SFN -0.01 0.1 -10000 0 -0.41 33 33
G1/S transition of mitotic cell cycle 0.022 0.035 -10000 0 -0.18 1 1
p27Kip1/14-3-3 family 0.012 0.026 -10000 0 -0.15 4 4
PRKACA 0.017 0 -10000 0 -10000 0 0
KPNA1 0.017 0 -10000 0 -10000 0 0
HSP90AA1 0.017 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0.017 0 -10000 0 -10000 0 0
CREBBP 0.017 0 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.015 0.032 -9999 0 -0.41 3 3
alphaV beta3 Integrin 0.016 0.053 -9999 0 -0.28 16 16
PTK2 0.026 0.04 -9999 0 -0.24 2 2
positive regulation of JNK cascade 0 0.007 -9999 0 -10000 0 0
CDC42/GDP 0.053 0.02 -9999 0 -10000 0 0
Rac1/GDP 0.054 0.02 -9999 0 -10000 0 0
RAP1B 0 0 -9999 0 -10000 0 0
RAP1A 0.017 0 -9999 0 -10000 0 0
CTNNB1 0.017 0 -9999 0 -10000 0 0
CDC42/GTP 0.04 0.018 -9999 0 -10000 0 0
nectin-3/I-afadin 0.024 0.019 -9999 0 -0.28 2 2
RAPGEF1 0.041 0.022 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.04 0.023 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.032 -9999 0 -0.41 3 3
TLN1 0 0.059 -9999 0 -0.19 46 46
Rap1/GTP 0 0.008 -9999 0 -10000 0 0
IQGAP1 -0.086 0.18 -9999 0 -0.41 127 127
Rap1/GTP/I-afadin 0.022 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.024 0.019 -9999 0 -0.28 2 2
PVR 0.017 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.017 0 -9999 0 -10000 0 0
mol:GDP 0.049 0.022 -9999 0 -10000 0 0
MLLT4 0.017 0 -9999 0 -10000 0 0
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
PI3K 0.034 0.056 -9999 0 -0.19 29 29
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.025 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly 0 0.008 -9999 0 -10000 0 0
PVRL1 0.017 0 -9999 0 -10000 0 0
PVRL3 0.015 0.026 -9999 0 -0.41 2 2
PVRL2 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
CDH1 0.011 0.052 -9999 0 -0.41 8 8
CLDN1 0.01 0.056 -9999 0 -0.41 9 9
JAM-A/CLDN1 0.023 0.08 -9999 0 -0.26 36 36
SRC 0.035 0.025 -9999 0 -10000 0 0
ITGB3 0.017 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0.025 0 -9999 0 -10000 0 0
FARP2 0.046 0.021 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
CTNNA1 0.017 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.034 0.017 -9999 0 -0.24 2 2
nectin-1/I-afadin 0.025 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0.025 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin -0.04 0.11 -9999 0 -0.24 127 127
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.034 0.017 -9999 0 -0.24 2 2
CDC42/GTP/IQGAP1/filamentous actin -0.04 0.11 -9999 0 -0.24 127 127
F11R -0.011 0.1 -9999 0 -0.41 34 34
positive regulation of filopodium formation 0 0.007 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.012 0.073 -9999 0 -0.19 56 56
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.025 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.025 0 -9999 0 -10000 0 0
PIP5K1C 0.017 0.009 -9999 0 -10000 0 0
VAV2 0.047 0.022 -9999 0 -10000 0 0
RAP1/GDP 0.041 0.019 -9999 0 -10000 0 0
ITGAV 0.004 0.074 -9999 0 -0.41 16 16
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.034 0.017 -9999 0 -0.24 2 2
nectin-3(dimer)/I-afadin/I-afadin 0.024 0.019 -9999 0 -0.28 2 2
Rac1/GTP 0.045 0.018 -9999 0 -10000 0 0
PTPRM 0.016 0.009 -9999 0 -0.12 2 2
E-cadherin/beta catenin/alpha catenin 0.047 0.028 -9999 0 -0.18 8 8
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.017 0 -9999 0 -10000 0 0
Calcium signaling in the CD4+ TCR 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
NFATC1 0.021 0.012 -9999 0 -10000 0 0
NFATC2 0.012 0.01 -9999 0 -10000 0 0
NFATC3 0.021 0.012 -9999 0 -10000 0 0
CD40LG 0.019 0.1 -9999 0 -0.33 15 15
PTGS2 0.009 0.13 -9999 0 -0.39 31 31
JUNB 0.011 0.052 -9999 0 -0.41 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.008 -9999 0 -10000 0 0
CaM/Ca2+ 0.015 0.008 -9999 0 -10000 0 0
CALM1 0.018 0.005 -9999 0 -10000 0 0
JUN 0.019 0.019 -9999 0 -0.41 1 1
mol:Ca2+ 0.002 0.004 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.011 -9999 0 -0.24 1 1
FOSL1 0.007 0.067 -9999 0 -0.41 13 13
CREM 0.017 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.055 0.041 -9999 0 -0.19 3 3
FOS -0.082 0.18 -9999 0 -0.41 125 125
IFNG 0.019 0.1 -9999 0 -0.33 16 16
AP-1/NFAT1-c-4 0.05 0.13 -9999 0 -0.37 15 15
FASLG 0.019 0.1 -9999 0 -0.33 15 15
NFAT1-c-4/ICER1 0.039 0.026 -9999 0 -10000 0 0
IL2RA 0.017 0.11 -9999 0 -0.37 17 17
FKBP12/FK506 0.012 0.013 -9999 0 -0.29 1 1
CSF2 0.019 0.1 -9999 0 -0.33 15 15
JunB/Fra1/NFAT1-c-4 0.042 0.051 -9999 0 -0.18 20 20
IL4 0.019 0.1 -9999 0 -0.33 15 15
IL2 0.001 0.004 -9999 0 -10000 0 0
IL3 0.004 0.008 -9999 0 -10000 0 0
FKBP1A 0.016 0.019 -9999 0 -0.41 1 1
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.023 0 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.017 0 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.017 0 -9999 0 -10000 0 0
TCEB1 0.017 0 -9999 0 -10000 0 0
HIF1A/p53 -0.001 0.073 -9999 0 -0.18 69 69
HIF1A 0.015 0.021 -9999 0 -0.11 3 3
COPS5 0.017 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.041 0 -9999 0 -10000 0 0
FIH (dimer) 0.017 0 -9999 0 -10000 0 0
CDKN2A -0.031 0.14 -9999 0 -0.41 59 59
ARNT/IPAS 0.025 0 -9999 0 -10000 0 0
HIF1AN 0.017 0 -9999 0 -10000 0 0
GNB2L1 0.017 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.024 0.023 -9999 0 -10000 0 0
CUL2 0.017 0 -9999 0 -10000 0 0
OS9 -0.018 0.12 -9999 0 -0.41 43 43
RACK1/Elongin B/Elongin C 0.035 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.024 0.023 -9999 0 -10000 0 0
PHD1-3/OS9 0.021 0.072 -9999 0 -0.21 48 48
HIF1A/RACK1/Elongin B/Elongin C 0.038 0.024 -9999 0 -10000 0 0
VHL 0 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.024 0.023 -9999 0 -10000 0 0
EGLN3 0.014 0.037 -9999 0 -0.41 4 4
EGLN2 0.017 0 -9999 0 -10000 0 0
EGLN1 0.016 0.019 -9999 0 -0.41 1 1
TP53 -0.039 0.14 -9999 0 -0.41 69 69
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.028 0.005 -9999 0 -10000 0 0
ARNT 0.017 0 -9999 0 -10000 0 0
ARD1A 0.016 0.019 -9999 0 -0.41 1 1
RBX1 0.017 0 -9999 0 -10000 0 0
HIF1A/p19ARF 0.003 0.071 -9999 0 -0.19 59 59
E-cadherin signaling 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
E-cadherin/beta catenin-gamma catenin 0.023 0.064 -9999 0 -0.29 19 19
E-cadherin/beta catenin 0.021 0.038 -9999 0 -0.28 8 8
CTNNB1 0.017 0 -9999 0 -10000 0 0
JUP 0.004 0.074 -9999 0 -0.41 16 16
CDH1 0.011 0.052 -9999 0 -0.41 8 8
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 -0.036 0.14 -9999 0 -0.41 65 65
Ran/GTP/Exportin 1/HDAC4 0 0.007 -9999 0 -0.16 1 1
MDM2/SUMO1 0.026 0.039 -9999 0 -0.18 18 18
HDAC4 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.02 0.053 -9999 0 -0.16 65 65
SUMO1 0.017 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.014 0.005 -9999 0 -0.11 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.02 0.005 -9999 0 -0.097 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.017 0.001 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0.019 -9999 0 -0.41 1 1
SUMO1/HDAC4 0.033 0.005 -9999 0 -10000 0 0
SUMO1/HDAC1 0.006 0.071 -9999 0 -0.18 65 65
RANGAP1 0.017 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.036 0.046 -9999 0 -0.21 18 18
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.018 0.005 -9999 0 -0.11 1 1
Ran/GTP 0.026 0.006 -9999 0 -0.093 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.002 0.078 -9999 0 -0.41 18 18
UBE2I 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.028 0.005 -9999 0 -10000 0 0
NPC 0.01 0.009 -9999 0 -0.2 1 1
PIAS2 0.017 0 -9999 0 -10000 0 0
PIAS1 0.017 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.017 0 -9999 0 -10000 0 0
SPHK1 0.002 0.08 -9999 0 -0.41 19 19
GNAI2 0.017 0.001 -9999 0 -10000 0 0
mol:S1P 0.01 0.04 -9999 0 -0.16 26 26
GNAO1 0.002 0.005 -9999 0 -10000 0 0
mol:Sphinganine-1-P 0.007 0.056 -9999 0 -0.28 19 19
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.024 0.04 -9999 0 -0.21 8 8
GNAI3 -0.036 0.14 -9999 0 -0.41 65 65
G12/G13 0.022 0.033 -9999 0 -0.28 6 6
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 0.017 0.001 -9999 0 -10000 0 0
S1P1/S1P 0.018 0.035 -9999 0 -0.13 25 25
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 0.014 0.02 -9999 0 -0.41 1 1
S1P/S1P5/G12 0.015 0.037 -9999 0 -0.13 30 30
S1P/S1P3/Gq 0.023 0.029 -9999 0 -0.17 7 7
S1P/S1P4/Gi 0 0.027 -9999 0 -0.32 3 3
GNAQ 0.017 0 -9999 0 -10000 0 0
GNAZ 0.015 0.006 -9999 0 -10000 0 0
GNA14 0.015 0.026 -9999 0 -0.41 2 2
GNA15 0.011 0.049 -9999 0 -0.41 7 7
GNA12 0.014 0.037 -9999 0 -0.41 4 4
GNA13 0.015 0.026 -9999 0 -0.41 2 2
GNA11 0.017 0 -9999 0 -10000 0 0
ABCC1 0.01 0.056 -9999 0 -0.41 9 9
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.02 0.042 -10000 0 -0.28 10 10
CRKL 0.027 0.022 -10000 0 -10000 0 0
mol:PIP3 -0.011 0.023 0.35 2 -10000 0 2
AKT1 -0.003 0.025 0.26 2 -0.21 4 6
PTK2B 0.017 0 -10000 0 -10000 0 0
RAPGEF1 0.03 0.021 -10000 0 -10000 0 0
RANBP10 0.017 0 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
HGF/MET/SHIP2 0.029 0.04 -10000 0 -0.24 12 12
MAP3K5 0.038 0.022 -10000 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS 0.028 0.036 -10000 0 -0.21 12 12
AP1 -0.042 0.12 -10000 0 -0.25 125 125
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
apoptosis -0.015 0.082 -10000 0 -0.66 2 2
STAT3 (dimer) 0.029 0.021 -10000 0 -10000 0 0
GAB1/CRKL/SHP2/PI3K 0.038 0.047 -10000 0 -0.26 1 1
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK 0.037 0.022 -10000 0 -10000 0 0
PTPN11 0.017 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.017 0 -10000 0 -10000 0 0
PTEN 0.015 0.026 -10000 0 -0.41 2 2
ELK1 -0.001 0.044 0.21 17 -0.16 10 27
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.021 0.015 -10000 0 -10000 0 0
PAK1 0.001 0.023 0.24 2 -0.2 4 6
HGF/MET/RANBP10 0.029 0.04 -10000 0 -0.24 12 12
HRAS 0.028 0.029 -10000 0 -10000 0 0
DOCK1 0.03 0.021 -10000 0 -10000 0 0
GAB1 0.025 0.023 -10000 0 -10000 0 0
CRK 0.027 0.022 -10000 0 -10000 0 0
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.027 0.028 -10000 0 -0.16 10 10
JUN 0.016 0.019 -10000 0 -0.41 1 1
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.01 0.022 -10000 0 -0.14 12 12
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
cell morphogenesis 0.041 0.047 -10000 0 -0.19 1 1
GRB2/SHC 0.011 0.067 -10000 0 -0.18 54 54
FOS -0.085 0.18 -10000 0 -0.41 125 125
GLMN 0.003 0 -10000 0 -10000 0 0
cell motility -0.001 0.044 0.21 17 -0.16 10 27
HGF/MET/MUC20 0.017 0.039 -10000 0 -0.24 12 12
cell migration 0.011 0.066 -10000 0 -0.18 54 54
GRB2 0.017 0.002 -10000 0 -10000 0 0
CBL 0.017 0 -10000 0 -10000 0 0
MET/RANBP10 0.02 0.042 -10000 0 -0.28 10 10
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.028 0.023 -10000 0 -10000 0 0
MET/MUC20 0.007 0.041 -10000 0 -0.29 10 10
RAP1B 0.029 0.02 -10000 0 -10000 0 0
RAP1A 0.032 0.02 -10000 0 -10000 0 0
HGF/MET/RANBP9 0.029 0.04 -10000 0 -0.24 12 12
RAF1 0.03 0.029 -10000 0 -10000 0 0
STAT3 0.029 0.022 -10000 0 -10000 0 0
cell proliferation 0.019 0.06 -10000 0 -0.23 9 9
RPS6KB1 0.012 0.01 -10000 0 -0.087 1 1
MAPK3 -0.013 0.02 -10000 0 -10000 0 0
MAPK1 0.006 0.11 0.59 17 -10000 0 17
RANBP9 0.017 0.001 -10000 0 -10000 0 0
MAPK8 0.049 0.027 -10000 0 -10000 0 0
SRC 0.028 0.021 -10000 0 -10000 0 0
PI3K 0.019 0.049 -10000 0 -0.17 31 31
MET/Glomulin 0.01 0.036 -10000 0 -0.25 10 10
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 0.032 0.028 -10000 0 -10000 0 0
MET 0.009 0.059 -10000 0 -0.41 10 10
MAP4K1 0.035 0.022 -10000 0 -10000 0 0
PTK2 0.017 0.001 -10000 0 -10000 0 0
MAP2K2 0.032 0.029 -10000 0 -10000 0 0
BAD 0.001 0.023 0.24 2 -0.2 4 6
MAP2K4 0.038 0.022 -10000 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 0.028 0.027 -10000 0 -10000 0 0
INPPL1 0.017 0 -10000 0 -10000 0 0
PXN 0.017 0 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS 0.013 0.021 -10000 0 -0.12 12 12
PLCgamma1/PKC 0.013 0 -10000 0 -10000 0 0
HGF 0.015 0.026 -10000 0 -0.41 2 2
RASA1 0.017 0.002 -10000 0 -10000 0 0
NCK1 0.008 0.061 -10000 0 -0.41 11 11
PTPRJ 0.017 0 -10000 0 -10000 0 0
NCK/PLCgamma1 0.027 0.037 -10000 0 -0.15 21 21
PDPK1 -0.006 0.019 0.29 2 -10000 0 2
HGF/MET/SHIP 0.017 0.039 -10000 0 -0.24 12 12
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 -0.036 0.14 -9999 0 -0.41 65 65
HDAC2 0.013 0.042 -9999 0 -0.41 5 5
GNB1/GNG2 0.023 0.012 -9999 0 -0.24 1 1
forebrain development 0.02 0.049 -9999 0 -0.31 8 8
GNAO1 0.002 0.005 -9999 0 -10000 0 0
SMO/beta Arrestin2 0.027 0.014 -9999 0 -0.28 1 1
SMO 0.017 0.019 -9999 0 -0.41 1 1
ARRB2 0.018 0.001 -9999 0 -10000 0 0
GLI3/SPOP 0.02 0.04 -9999 0 -0.21 3 3
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
GSK3B 0.017 0.001 -9999 0 -10000 0 0
GNAI2 0.018 0.001 -9999 0 -10000 0 0
SIN3/HDAC complex 0.032 0.001 -9999 0 -10000 0 0
GNAI1 0.014 0.02 -9999 0 -0.41 1 1
XPO1 0.019 0.003 -9999 0 -10000 0 0
GLI1/Su(fu) -0.001 0.038 -9999 0 -0.28 7 7
SAP30 0.017 0 -9999 0 -10000 0 0
mol:GDP 0.017 0.019 -9999 0 -0.41 1 1
MIM/GLI2A 0.023 0.007 -9999 0 -10000 0 0
IFT88 0.017 0 -9999 0 -10000 0 0
GNAI3 -0.035 0.14 -9999 0 -0.41 65 65
GLI2 0.035 0.008 -9999 0 -10000 0 0
GLI3 0.011 0.04 -9999 0 -0.15 10 10
CSNK1D 0.015 0.026 -9999 0 -0.41 2 2
CSNK1E 0.017 0.001 -9999 0 -10000 0 0
SAP18 0.017 0 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.017 0 -9999 0 -10000 0 0
GNG2 0 0 -9999 0 -10000 0 0
Gi family/GTP 0.001 0.017 -9999 0 -0.2 2 2
SIN3B 0.017 0 -9999 0 -10000 0 0
SIN3A 0 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.017 0.031 -9999 0 -0.17 3 3
GLI2/Su(fu) 0.037 0.01 -9999 0 -10000 0 0
FOXA2 0.03 0.037 -9999 0 -0.38 4 4
neural tube patterning 0.02 0.049 -9999 0 -0.31 8 8
SPOP 0.017 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.02 0.006 -9999 0 -0.11 1 1
GNB1 0.017 0.002 -9999 0 -10000 0 0
CSNK1G2 0.017 0 -9999 0 -10000 0 0
CSNK1G3 0.017 0 -9999 0 -10000 0 0
MTSS1 0.023 0.007 -9999 0 -10000 0 0
embryonic limb morphogenesis 0.02 0.049 -9999 0 -0.31 8 8
SUFU 0.009 0.007 -9999 0 -0.13 1 1
LGALS3 -0.034 0.14 -9999 0 -0.41 62 62
catabolic process 0.041 0.039 -9999 0 -0.18 3 3
GLI3A/CBP 0.023 0.03 -9999 0 -0.22 8 8
KIF3A 0.016 0.005 -9999 0 -10000 0 0
GLI1 0.021 0.05 -9999 0 -0.31 8 8
RAB23 0.013 0.042 -9999 0 -0.41 5 5
CSNK1A1 0.017 0 -9999 0 -10000 0 0
IFT172 0 0 -9999 0 -10000 0 0
RBBP7 0.017 0 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.007 0.075 -9999 0 -0.21 62 62
GNAZ 0.015 0.006 -9999 0 -10000 0 0
RBBP4 -0.064 0.17 -9999 0 -0.41 100 100
CSNK1G1 0.017 0 -9999 0 -10000 0 0
PIAS1 0.017 0 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
GLI2/SPOP 0.042 0.008 -9999 0 -10000 0 0
STK36 0.002 0.002 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.01 0.039 -9999 0 -0.12 53 53
PTCH1 0.023 0.064 -9999 0 -0.47 7 7
MIM/GLI1 0.038 0.055 -9999 0 -0.3 10 10
CREBBP 0.023 0.03 -9999 0 -0.22 8 8
Su(fu)/SIN3/HDAC complex -0.005 0.061 -9999 0 -0.2 20 20
Aurora C signaling

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
INCENP 0.017 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.02 0.056 -9999 0 -0.21 29 29
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.01 0.017 -9999 0 -10000 0 0
AURKB -0.005 0.095 -9999 0 -0.41 27 27
AURKC 0.015 0.026 -9999 0 -0.41 2 2
Atypical 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
BCL3/RelA 0.025 0 -9999 0 -10000 0 0
FBXW11 0.017 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.024 0.023 -9999 0 -0.24 4 4
NF kappa B1 p50/RelA/I kappa B alpha 0.03 0.043 -9999 0 -0.25 6 6
NFKBIA 0.012 0.037 -9999 0 -0.11 40 40
MAPK14 0.015 0.026 -9999 0 -0.41 2 2
NF kappa B1 p105/p50 0.024 0.023 -9999 0 -0.24 4 4
ARRB2 0.014 0.012 -9999 0 -0.18 2 2
REL 0.017 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.024 0.023 -9999 0 -0.24 4 4
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.024 0.023 -9999 0 -0.24 4 4
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
NF kappa B1 p50 dimer 0.016 0.026 -9999 0 -0.28 4 4
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
NFKB1 0.015 0.026 -9999 0 -0.29 4 4
RELA 0.017 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.017 0.038 -9999 0 -0.11 40 40
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.033 0.043 -9999 0 -0.24 6 6
SRC 0.017 0 -9999 0 -10000 0 0
PI3K 0.009 0.065 -9999 0 -0.28 25 25
NF kappa B1 p50/RelA 0.017 0.038 -9999 0 -0.11 40 40
IKBKB 0.017 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
SYK -0.012 0.11 -9999 0 -0.41 36 36
I kappa B alpha/PIK3R1 0.021 0.033 -9999 0 -0.18 3 3
cell death 0.032 0.041 -9999 0 -0.24 6 6
NF kappa B1 p105/c-Rel 0.024 0.023 -9999 0 -0.24 4 4
LCK 0.014 0.037 -9999 0 -0.41 4 4
BCL3 0.017 0 -9999 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 0.022 0.016 -10000 0 -0.24 2 2
cell-cell adhesion 0.004 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.047 0.019 -10000 0 -0.19 2 2
ITSN1 0.017 0 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
SHC1 -0.02 0.12 -10000 0 -0.41 46 46
Ephrin B1/EPHB3 0.017 0.041 -10000 0 -0.24 13 13
Ephrin B1/EPHB1 0.017 0.039 -10000 0 -0.24 12 12
HRAS/GDP 0.024 0.029 -10000 0 -0.15 1 1
Ephrin B/EPHB1/GRB7 0.043 0.038 -10000 0 -0.19 12 12
Endophilin/SYNJ1 0.022 0.014 -10000 0 -0.18 2 2
KRAS 0.017 0.002 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.043 0.036 -10000 0 -0.19 11 11
endothelial cell migration 0.023 0.048 -10000 0 -0.19 23 23
GRB2 0.017 0.002 -10000 0 -10000 0 0
GRB7 0.016 0.019 -10000 0 -0.41 1 1
PAK1 0.027 0.014 -10000 0 -0.18 2 2
HRAS 0.016 0.019 -10000 0 -0.41 1 1
RRAS 0.016 0.039 -10000 0 -0.18 19 19
DNM1 0.003 0.007 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.02 0.03 -10000 0 -0.18 11 11
lamellipodium assembly -0.004 0.024 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.05 -10000 0 -0.12 57 57
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
EPHB2 0.015 0.026 -10000 0 -0.41 2 2
EPHB3 0.007 0.067 -10000 0 -0.41 13 13
EPHB1 0.007 0.064 -10000 0 -0.41 12 12
EPHB4 0.017 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.029 -10000 0 -0.16 1 1
Ephrin B/EPHB2 0.038 0.017 -10000 0 -0.19 2 2
Ephrin B/EPHB3 0.033 0.037 -10000 0 -0.19 13 13
JNK cascade 0.016 0.047 -10000 0 -0.19 26 26
Ephrin B/EPHB1 0.034 0.035 -10000 0 -0.19 11 11
RAP1/GDP 0.03 0.028 -10000 0 -10000 0 0
EFNB2 0.016 0.003 -10000 0 -10000 0 0
EFNB3 0.017 0.001 -10000 0 -10000 0 0
EFNB1 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.026 0.039 -10000 0 -0.21 13 13
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0.017 0 -10000 0 -10000 0 0
CDC42/GTP 0.037 0.032 -10000 0 -10000 0 0
Rap1/GTP -0.004 0.024 -10000 0 -10000 0 0
axon guidance 0.022 0.016 -10000 0 -0.24 2 2
MAPK3 0.018 0.044 -10000 0 -0.18 5 5
MAPK1 0.017 0.044 -10000 0 -0.18 5 5
Rac1/GDP 0.033 0.029 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.031 0.053 -10000 0 -0.26 4 4
CDC42/GDP 0.033 0.029 -10000 0 -10000 0 0
PI3K 0.026 0.049 -10000 0 -0.2 23 23
EFNA5 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.022 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.03 0.012 -10000 0 -0.12 2 2
CDC42 0.017 0 -10000 0 -10000 0 0
RAS family/GTP -0.04 0.069 -10000 0 -0.32 4 4
PTK2 0.008 0.007 -10000 0 -10000 0 0
MAP4K4 0.016 0.047 -10000 0 -0.19 26 26
SRC 0.017 0 -10000 0 -10000 0 0
KALRN 0.017 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0.025 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.04 0.028 -10000 0 -10000 0 0
MAP2K1 0.016 0.046 -10000 0 -0.17 7 7
WASL 0.017 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.032 0.054 -10000 0 -0.21 25 25
cell migration 0.024 0.048 0.17 3 -0.18 7 10
NRAS -0.094 0.19 -10000 0 -0.41 136 136
SYNJ1 0.022 0.015 -10000 0 -0.18 2 2
PXN 0.017 0 -10000 0 -10000 0 0
TF 0.016 0.02 -10000 0 -10000 0 0
HRAS/GTP 0.034 0.034 -10000 0 -0.16 14 14
Ephrin B1/EPHB1-2 0.027 0.039 -10000 0 -0.21 14 14
cell adhesion mediated by integrin -0.015 0.031 -10000 0 -0.13 22 22
RAC1 0.017 0 -10000 0 -10000 0 0
mol:GTP 0.038 0.036 -10000 0 -0.17 13 13
RAC1-CDC42/GTP -0.007 0.033 -10000 0 -10000 0 0
RASA1 0.017 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.041 0.028 -10000 0 -10000 0 0
ruffle organization 0.03 0.032 -10000 0 -10000 0 0
NCK1 0.008 0.061 -10000 0 -0.41 11 11
receptor internalization 0.005 0.012 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN 0.048 0.018 -10000 0 -0.19 2 2
ROCK1 0.014 0.036 -10000 0 -0.21 13 13
RAS family/GDP -0.032 0.055 -10000 0 -0.25 4 4
Rac1/GTP -0.004 0.025 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0.027 0.024 -10000 0 -0.13 12 12
Arf6 trafficking events

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
SLC2A4 0.017 0 -9999 0 -10000 0 0
CLTC 0.018 0.013 -9999 0 -10000 0 0
calcium ion-dependent exocytosis 0.01 0.033 -9999 0 -0.097 45 45
Dynamin 2/GTP 0.018 0 -9999 0 -10000 0 0
EXOC4 0 0 -9999 0 -10000 0 0
CD59 0.014 0.017 -9999 0 -10000 0 0
CPE 0.014 0.004 -9999 0 -10000 0 0
CTNNB1 0.017 0 -9999 0 -10000 0 0
membrane fusion 0.009 0.036 -9999 0 -0.11 45 45
CTNND1 0.014 0.03 -9999 0 -0.2 10 10
DNM2 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.015 0.023 -9999 0 -0.11 1 1
TSHR 0.014 0.022 -9999 0 -0.24 4 4
INS 0.015 0.008 -9999 0 -10000 0 0
BIN1 0.016 0.005 -9999 0 -10000 0 0
mol:Choline 0.009 0.036 -9999 0 -0.11 45 45
growth hormone secretagogue receptor activity 0 0 -9999 0 -10000 0 0
mol:GDP 0.006 0 -9999 0 -10000 0 0
membrane depolarization 0 0 -9999 0 -10000 0 0
ARF6 0.017 0 -9999 0 -10000 0 0
mol:Ca2+ 0.017 0 -9999 0 -10000 0 0
JUP 0.01 0.029 -9999 0 -0.12 16 16
ASAP2/amphiphysin II 0.02 0.006 -9999 0 -10000 0 0
ARF6/GTP 0.013 0 -9999 0 -10000 0 0
CDH1 0.012 0.023 -9999 0 -0.11 8 8
clathrin-independent pinocytosis 0.013 0 -9999 0 -10000 0 0
MAPK8IP3 0.017 0 -9999 0 -10000 0 0
positive regulation of endocytosis 0.013 0 -9999 0 -10000 0 0
EXOC2 0.017 0 -9999 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.019 0.024 -9999 0 -0.092 24 24
insulin receptor binding 0 0 -9999 0 -10000 0 0
SPAG9 0.016 0.019 -9999 0 -0.41 1 1
regulation of calcium-dependent cell-cell adhesion -0.026 0.02 -9999 0 -10000 0 0
positive regulation of phagocytosis 0.015 0.011 -9999 0 -0.24 1 1
ARF6/GTP/JIP3 0.023 0 -9999 0 -10000 0 0
ACAP1 0.009 0.031 -9999 0 -0.092 45 45
mol:GTP 0 0 -9999 0 -10000 0 0
CHRM2 0.014 0.017 -9999 0 -10000 0 0
clathrin heavy chain/ACAP1 0.016 0.027 -9999 0 -0.14 1 1
JIP4/KLC1 0.024 0.018 -9999 0 -0.21 1 1
EXOC1 0.011 0.049 -9999 0 -0.41 7 7
exocyst 0.019 0.025 -9999 0 -0.093 24 24
RALA/GTP -0.013 0.084 -9999 0 -0.29 45 45
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.023 0.011 -9999 0 -0.24 1 1
receptor recycling 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.018 0 -9999 0 -10000 0 0
NME1 0.006 0 -9999 0 -10000 0 0
clathrin coat assembly 0.018 0.013 -9999 0 -10000 0 0
IL2RA 0.013 0.021 -9999 0 -0.11 6 6
VAMP3 0.015 0.011 -9999 0 -0.24 1 1
GLUT4/clathrin heavy chain/ACAP1 0.023 0.027 -9999 0 -0.13 1 1
EXOC6 0 0 -9999 0 -10000 0 0
PLD1 0.008 0.032 -9999 0 -0.094 46 46
PLD2 0.009 0.03 -9999 0 -0.09 45 45
EXOC5 0.003 0.076 -9999 0 -0.41 17 17
PIP5K1C 0.015 0.022 -9999 0 -0.11 1 1
SDC1 0.003 0.041 -9999 0 -0.12 47 47
ARF6/GDP 0.013 0 -9999 0 -10000 0 0
EXOC7 0.017 0 -9999 0 -10000 0 0
E-cadherin/beta catenin 0.028 0.021 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.009 0.036 -9999 0 -0.11 45 45
endocytosis -0.02 0.006 -9999 0 -10000 0 0
SCAMP2 0.017 0 -9999 0 -10000 0 0
ADRB2 0.02 0.015 -9999 0 -0.17 1 1
EXOC3 0.017 0 -9999 0 -10000 0 0
ASAP2 0 0 -9999 0 -10000 0 0
Dynamin 2/GDP 0.017 0 -9999 0 -10000 0 0
KLC1 0.013 0.008 -9999 0 -10000 0 0
AVPR2 0.02 0.013 -9999 0 -10000 0 0
RALA -0.02 0.12 -9999 0 -0.41 45 45
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.028 0.032 -9999 0 -0.15 10 10
Signaling events mediated by HDAC Class III

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
EP300 0.017 0 -10000 0 -10000 0 0
HDAC4 0.017 0 -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 0.014 -10000 0 -10000 0 0
CDKN1A -0.019 0.098 -10000 0 -0.3 54 54
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.011 0.049 -10000 0 -0.41 7 7
FOXO3 -0.006 0.003 -10000 0 -10000 0 0
FOXO1 0.008 0.061 -10000 0 -0.41 11 11
FOXO4 0.018 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.017 0 -10000 0 -10000 0 0
TAT 0.017 0 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.009 0 -10000 0 -10000 0 0
PPARGC1A 0.015 0.032 -10000 0 -0.41 3 3
FHL2 0.013 0.037 -10000 0 -0.41 4 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.029 0.019 -10000 0 -10000 0 0
HIST2H4A 0.011 0.014 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.012 0.02 -10000 0 -10000 0 0
SIRT1 0.022 0.027 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.038 0.018 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.029 0.021 -10000 0 -0.12 1 1
apoptosis -0.034 0.035 0.23 7 -10000 0 7
SIRT1/PGC1A 0.025 0.027 -10000 0 -0.24 3 3
p53/SIRT1 -0.004 0.12 0.25 43 -0.28 69 112
SIRT1/FOXO4 0.03 0.02 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 0.028 0.044 -10000 0 -0.21 15 15
HIST1H1E 0.018 0.007 -10000 0 -0.15 1 1
SIRT1/p300 0.029 0.019 -10000 0 -10000 0 0
muscle cell differentiation -0.019 0.018 -10000 0 -10000 0 0
TP53 -0.034 0.15 -10000 0 -0.41 69 69
KU70/SIRT1/BAX 0.034 0.035 -10000 0 -0.23 7 7
CREBBP 0.017 0 -10000 0 -10000 0 0
MEF2D 0.017 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.029 0.019 -10000 0 -10000 0 0
ACSS2 0.011 0.014 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.019 0.018 -10000 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0.016 0.003 -10000 0 -10000 0 0
EPHB2 0.016 0.026 -10000 0 -0.41 2 2
EFNB1 0.003 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.006 0.024 -10000 0 -0.18 1 1
Ephrin B2/EPHB1-2 0.026 0.039 -10000 0 -0.21 13 13
neuron projection morphogenesis 0.004 0.019 -10000 0 -0.17 1 1
Ephrin B1/EPHB1-2/Tiam1 0.005 0.024 -10000 0 -0.2 1 1
DNM1 0.003 0.006 -10000 0 -10000 0 0
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.007 0.038 -10000 0 -0.16 8 8
YES1 -0.015 0.053 -10000 0 -0.25 14 14
Ephrin B1/EPHB1-2/NCK2 0.005 0.024 -10000 0 -0.2 1 1
PI3K 0.01 0.063 -10000 0 -0.2 32 32
mol:GDP 0.005 0.023 -10000 0 -0.19 1 1
ITGA2B 0.017 0 -10000 0 -10000 0 0
endothelial cell proliferation 0.022 0.005 -10000 0 -10000 0 0
FYN -0.006 0.048 -10000 0 -0.22 9 9
MAP3K7 -0.007 0.038 -10000 0 -0.16 31 31
FGR -0.01 0.046 -10000 0 -0.21 8 8
TIAM1 0.016 0.003 -10000 0 -10000 0 0
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
RGS3 0.016 0.019 -10000 0 -0.41 1 1
cell adhesion 0.015 0.058 -10000 0 -0.19 24 24
LYN -0.013 0.05 -10000 0 -0.23 8 8
Ephrin B1/EPHB1-2/Src Family Kinases -0.008 0.041 -10000 0 -0.18 14 14
Ephrin B1/EPHB1-2 -0.009 0.042 -10000 0 -0.18 30 30
SRC -0.008 0.045 -10000 0 -0.2 8 8
ITGB3 0.017 0 -10000 0 -10000 0 0
EPHB1 0.007 0.064 -10000 0 -0.41 12 12
EPHB4 0.017 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.022 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.025 0 -10000 0 -10000 0 0
BLK -0.006 0.045 -10000 0 -0.19 20 20
HCK -0.016 0.051 -10000 0 -0.23 12 12
regulation of stress fiber formation -0.005 0.023 0.19 1 -10000 0 1
MAPK8 0.015 0.043 -10000 0 -0.17 1 1
Ephrin B1/EPHB1-2/RGS3 0.005 0.024 -10000 0 -0.2 1 1
endothelial cell migration -0.001 0.04 0.13 12 -0.15 17 29
NCK2 0.017 0.001 -10000 0 -10000 0 0
PTPN13 -0.009 0.099 -10000 0 -0.41 30 30
regulation of focal adhesion formation -0.005 0.023 0.19 1 -10000 0 1
chemotaxis -0.005 0.023 0.19 1 -10000 0 1
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
Rac1/GTP 0.005 0.022 -10000 0 -0.18 1 1
angiogenesis -0.009 0.042 -10000 0 -0.18 30 30
LCK -0.008 0.045 -10000 0 -0.2 8 8
mTOR signaling pathway

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
GBL 0.017 0 -10000 0 -10000 0 0
MKNK1 0.017 0 -10000 0 -10000 0 0
mol:PIP3 0.002 0.044 0.22 2 -0.18 27 29
FRAP1 0.018 0.026 -10000 0 -0.37 1 1
AKT1 0.007 0.041 0.16 2 -0.16 24 26
INSR 0.017 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.023 0 -10000 0 -10000 0 0
mol:GTP 0.027 0.042 0.19 1 -0.14 25 26
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.006 0.025 -10000 0 -0.15 9 9
TSC2 0.017 0 -10000 0 -10000 0 0
RHEB/GDP 0.016 0.035 -10000 0 -0.17 2 2
TSC1 0.016 0.019 -10000 0 -0.41 1 1
Insulin Receptor/IRS1 0.018 0.015 -10000 0 -0.14 5 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.018 0.036 -10000 0 -0.15 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.017 0 -10000 0 -10000 0 0
RPS6KB1 0.022 0.034 0.17 1 -0.26 1 2
MAP3K5 0.007 0.008 -10000 0 -0.086 4 4
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
apoptosis 0.007 0.008 -10000 0 -0.086 4 4
mol:LY294002 0 0 0.001 1 -0.001 5 6
EIF4B 0.024 0.031 0.16 1 -0.22 1 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.031 0.16 1 -0.21 1 2
eIF4E/eIF4G1/eIF4A1 -0.005 0.026 -10000 0 -0.18 6 6
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.017 0.047 -10000 0 -0.18 27 27
mTOR/RHEB/GTP/Raptor/GBL 0.027 0.029 0.16 1 -0.2 1 2
FKBP1A 0.016 0.019 -10000 0 -0.42 1 1
RHEB/GTP 0.024 0.037 -10000 0 -0.16 2 2
mol:Amino Acids 0 0 0.001 1 -0.001 5 6
FKBP12/Rapamycin 0.012 0.013 -10000 0 -0.29 1 1
PDPK1 0.005 0.042 0.17 2 -0.17 24 26
EIF4E 0.013 0.042 -10000 0 -0.41 5 5
ASK1/PP5C 0.028 0.05 -10000 0 -0.45 5 5
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.021 0.018 -10000 0 -0.16 5 5
TSC1/TSC2 0.03 0.045 0.2 1 -0.15 25 26
tumor necrosis factor receptor activity 0 0 0.001 5 -0.001 1 6
RPS6 0.017 0 -10000 0 -10000 0 0
PPP5C 0.017 0 -10000 0 -10000 0 0
EIF4G1 0.014 0.037 -10000 0 -0.41 4 4
IRS1 0.007 0.015 -10000 0 -0.15 5 5
INS 0.017 0 -10000 0 -10000 0 0
PTEN 0.015 0.026 -10000 0 -0.41 2 2
PDK2 0.005 0.042 0.17 2 -0.17 24 26
EIF4EBP1 -0.1 0.12 -10000 0 -10000 0 0
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
PPP2R5D 0.02 0.024 -10000 0 -0.33 1 1
peptide biosynthetic process 0.02 0 -10000 0 -10000 0 0
RHEB 0.017 0 -10000 0 -10000 0 0
EIF4A1 0.009 0.059 -10000 0 -0.41 10 10
mol:Rapamycin 0 0.001 0.003 1 -0.002 24 25
EEF2 0.02 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 -0.088 0.11 -10000 0 -0.41 2 2
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.026 0.006 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.007 0.024 -9999 0 -0.18 5 5
JUN 0.028 0.023 -9999 0 -0.17 1 1
HRAS 0.016 0.019 -9999 0 -0.41 1 1
RET51/GFRalpha1/GDNF/GRB10 0.035 0.047 -9999 0 -0.21 19 19
RAP1A 0.017 0 -9999 0 -10000 0 0
FRS2 0.015 0.032 -9999 0 -0.41 3 3
RAP1A/GDP 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.043 0.019 -9999 0 -0.21 3 3
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.017 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.032 0.015 -9999 0 -0.21 2 2
RHOA 0.017 0.001 -9999 0 -10000 0 0
RAP1A/GTP 0.04 0.017 -9999 0 -0.18 3 3
GRB7 0.016 0.019 -9999 0 -0.41 1 1
RET51/GFRalpha1/GDNF 0.043 0.019 -9999 0 -0.21 3 3
MAPKKK cascade 0.029 0.023 -9999 0 -0.15 4 4
BCAR1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.03 0.028 -9999 0 -0.21 7 7
lamellipodium assembly 0.02 0.036 -9999 0 -0.18 5 5
RET51/GFRalpha1/GDNF/SHC 0.021 0.075 -9999 0 -0.22 47 47
PIK3CA -0.003 0.091 -9999 0 -0.41 25 25
RET9/GFRalpha1/GDNF/SHC 0.011 0.073 -9999 0 -0.22 46 46
RET9/GFRalpha1/GDNF/Shank3 0.021 0.015 -9999 0 -0.22 2 2
MAPK3 0.026 0.015 -9999 0 -0.17 3 3
DOK1 0.017 0 -9999 0 -10000 0 0
DOK6 0 0 -9999 0 -10000 0 0
PXN 0.017 0 -9999 0 -10000 0 0
neurite development 0.03 0.015 -9999 0 -10000 0 0
DOK5 0.015 0.019 -9999 0 -0.41 1 1
GFRA1 0.015 0.026 -9999 0 -0.41 2 2
MAPK8 0.028 0.023 -9999 0 -10000 0 0
HRAS/GTP 0.037 0.027 -9999 0 -0.17 4 4
tube development 0.023 0.014 -9999 0 -0.2 2 2
MAPK1 0.026 0.016 -9999 0 -0.17 3 3
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.025 0.015 -9999 0 -0.12 5 5
Rac1/GDP 0.013 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
PDLIM7 0.017 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 0.039 0.018 -9999 0 -0.19 3 3
SHC1 -0.02 0.12 -9999 0 -0.41 46 46
RET51/GFRalpha1/GDNF/Dok4 0.043 0.019 -9999 0 -0.21 3 3
RET51/GFRalpha1/GDNF/Dok5 0.039 0.024 -9999 0 -0.21 4 4
PRKCA 0.017 0 -9999 0 -10000 0 0
HRAS/GDP 0.012 0.013 -9999 0 -0.29 1 1
CREB1 0.014 0.044 -9999 0 -0.13 46 46
PIK3R1 0.016 0.004 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.012 0.047 -9999 0 -0.13 50 50
RET51/GFRalpha1/GDNF/Grb7 0.042 0.022 -9999 0 -0.21 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
RET 0.016 0.019 -9999 0 -0.41 1 1
DOK4 0.017 0 -9999 0 -10000 0 0
JNK cascade 0.028 0.023 -9999 0 -0.16 1 1
RET9/GFRalpha1/GDNF/FRS2 0.031 0.024 -9999 0 -0.21 5 5
SHANK3 0 0 -9999 0 -10000 0 0
RASA1 0.017 0.002 -9999 0 -10000 0 0
NCK1 0.008 0.061 -9999 0 -0.41 11 11
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.008 0.045 -9999 0 -0.14 46 46
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.03 0.016 -9999 0 -0.12 6 6
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK 0.028 0.025 -9999 0 -0.12 14 14
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.013 0.045 -9999 0 -0.13 47 47
PI3K 0.027 0.047 -9999 0 -0.2 9 9
SOS1 0 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.029 0.014 -9999 0 -0.2 2 2
GRB10 0.004 0.074 -9999 0 -0.41 16 16
activation of MAPKK activity 0.029 0.015 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2 0.041 0.027 -9999 0 -0.21 6 6
GAB1 0.014 0.037 -9999 0 -0.41 4 4
IRS1 0.013 0.042 -9999 0 -0.41 5 5
IRS2 0.017 0.002 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.017 0.047 -9999 0 -0.26 2 2
RET51/GFRalpha1/GDNF/PKC alpha 0.043 0.019 -9999 0 -0.21 3 3
GRB2 0.017 0.002 -9999 0 -10000 0 0
PRKACA 0.017 0 -9999 0 -10000 0 0
GDNF 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.04 0.031 -9999 0 -0.21 8 8
Rac1/GTP 0.025 0.042 -9999 0 -0.2 5 5
RET9/GFRalpha1/GDNF 0.022 0.016 -9999 0 -0.24 2 2
GFRalpha1/GDNF 0.024 0.019 -9999 0 -0.28 2 2
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.027 0.022 0.28 2 -10000 0 2
KIRREL 0.018 0.02 -10000 0 -0.41 1 1
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.027 0.022 -10000 0 -0.28 2 2
PLCG1 0.017 0 -10000 0 -10000 0 0
ARRB2 0.017 0 -10000 0 -10000 0 0
WASL 0.017 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.019 0.078 -10000 0 -0.22 51 51
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.029 0.021 -10000 0 -10000 0 0
FYN 0.019 0.017 -10000 0 -0.17 4 4
mol:Ca2+ 0.043 0.023 -10000 0 -0.19 2 2
mol:DAG 0.044 0.024 -10000 0 -0.19 2 2
NPHS2 0.019 0.006 -10000 0 -10000 0 0
mol:IP3 0.044 0.024 -10000 0 -0.19 2 2
regulation of endocytosis 0.037 0.019 -10000 0 -0.16 4 4
Nephrin/NEPH1/podocin/Cholesterol 0.034 0.024 -10000 0 -0.2 2 2
establishment of cell polarity 0.027 0.022 -10000 0 -0.28 2 2
Nephrin/NEPH1/podocin/NCK1-2 0.047 0.037 -10000 0 -0.17 13 13
Nephrin/NEPH1/beta Arrestin2 0.039 0.019 -10000 0 -0.16 4 4
NPHS1 0.018 0.02 -10000 0 -0.41 1 1
Nephrin/NEPH1/podocin 0.032 0.019 -10000 0 -0.17 4 4
TJP1 0.017 0 -10000 0 -10000 0 0
NCK1 0.008 0.061 -10000 0 -0.41 11 11
NCK2 0.017 0.001 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.045 0.024 -10000 0 -0.19 2 2
CD2AP -0.023 0.12 -10000 0 -0.41 49 49
Nephrin/NEPH1/podocin/GRB2 0.044 0.023 -10000 0 -0.19 2 2
GRB2 0.017 0.002 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.022 0.023 -10000 0 -0.19 5 5
cytoskeleton organization 0.031 0.023 0.19 2 -0.15 2 4
Nephrin/NEPH1 0.023 0.016 -10000 0 -0.19 2 2
Nephrin/NEPH1/ZO-1 0.036 0.018 -10000 0 -0.22 2 2
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.12 0.1 -10000 0 -0.44 6 6
PCK1 0.11 0.074 -10000 0 -0.34 7 7
HNF4A 0.14 0.11 -10000 0 -0.58 5 5
KCNJ11 0.14 0.11 -10000 0 -0.46 5 5
AKT1 0.096 0.069 -10000 0 -0.26 7 7
response to starvation 0.005 0.004 -10000 0 -10000 0 0
DLK1 0.12 0.16 -10000 0 -0.47 13 13
NKX2-1 0.1 0.076 0.27 17 -0.31 4 21
ACADM 0.12 0.1 -10000 0 -0.43 7 7
TAT 0.11 0.065 -10000 0 -0.4 2 2
CEBPB 0.013 0.061 -10000 0 -0.41 11 11
CEBPA 0.01 0.074 -10000 0 -0.41 16 16
TTR 0.095 0.083 -10000 0 -0.66 3 3
PKLR 0.12 0.1 -10000 0 -0.46 5 5
APOA1 0.15 0.12 -10000 0 -0.6 5 5
CPT1C 0.12 0.099 -10000 0 -0.47 5 5
ALAS1 0.11 0.068 -10000 0 -0.33 2 2
TFRC 0.13 0.093 -10000 0 -0.3 11 11
FOXF1 -0.018 0.11 -10000 0 -0.41 36 36
NF1 0.023 0.006 -10000 0 -10000 0 0
HNF1A (dimer) 0.033 0.004 -10000 0 -10000 0 0
CPT1A 0.12 0.1 -10000 0 -0.46 5 5
HMGCS1 0.12 0.1 -10000 0 -0.46 5 5
NR3C1 0.026 0.019 -10000 0 -10000 0 0
CPT1B 0.12 0.1 -10000 0 -0.46 5 5
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.023 0 -10000 0 -10000 0 0
GCK 0.12 0.1 -10000 0 -0.46 5 5
CREB1 0.025 0.011 -10000 0 -10000 0 0
IGFBP1 0.09 0.085 -10000 0 -0.31 13 13
PDX1 0.12 0.066 -10000 0 -0.29 2 2
UCP2 0.096 0.16 -10000 0 -0.42 20 20
ALDOB 0.14 0.11 -10000 0 -0.45 5 5
AFP 0.026 0.031 -10000 0 -0.43 2 2
BDH1 0.12 0.1 -10000 0 -0.46 5 5
HADH 0.14 0.11 -10000 0 -0.44 6 6
F2 0.15 0.12 -10000 0 -0.66 4 4
HNF1A 0.033 0.004 -10000 0 -10000 0 0
G6PC 0.048 0.037 -10000 0 -0.23 1 1
SLC2A2 0.13 0.082 -10000 0 -0.41 3 3
INS 0.008 0.019 -10000 0 -10000 0 0
FOXA1 0.012 0.019 0.13 3 -0.19 3 6
FOXA3 0.036 0.025 -10000 0 -0.16 3 3
FOXA2 0.19 0.13 -10000 0 -0.53 5 5
ABCC8 0.14 0.11 -10000 0 -0.45 5 5
ALB 0.026 0.031 -10000 0 -0.33 3 3
p38 MAPK signaling 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
TRAF6/ASK1 0.02 0.002 -10000 0 -10000 0 0
TRAF2/ASK1 0.023 0.002 -10000 0 -10000 0 0
ATM -0.003 0.091 -10000 0 -0.41 25 25
MAP2K3 0.048 0.035 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.046 0.035 -10000 0 -0.13 3 3
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.007 0.067 -10000 0 -0.41 13 13
TXN 0.007 0 -10000 0 -10000 0 0
CALM1 0.016 0.004 -10000 0 -10000 0 0
GADD45A -0.02 0.12 -10000 0 -0.41 46 46
GADD45B 0.01 0.056 -10000 0 -0.41 9 9
MAP3K1 0.016 0.019 -10000 0 -0.41 1 1
MAP3K6 0.015 0.032 -10000 0 -0.41 3 3
MAP3K7 0.016 0.019 -10000 0 -0.41 1 1
MAP3K4 0.017 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.024 0.023 -10000 0 -0.28 3 3
TAK1/TAB family 0.012 0.009 0.12 2 -0.12 1 3
RAC1/OSM/MEKK3 0.022 0 -10000 0 -10000 0 0
TRAF2 0.017 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.001 0.022 -10000 0 -10000 0 0
TRAF6 0.015 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.002 0.006 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.003 0.008 -10000 0 -10000 0 0
MAPK11 0.017 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.005 0.012 -10000 0 -10000 0 0
OSM/MEKK3 0.013 0 -10000 0 -10000 0 0
TAOK1 -0.002 0.042 -10000 0 -0.19 25 25
TAOK2 0.005 0.042 -10000 0 -0.18 25 25
TAOK3 0.005 0.042 -10000 0 -0.18 25 25
MAP3K7IP1 0.017 0 -10000 0 -10000 0 0
MAPK14 0.015 0.026 -10000 0 -0.41 2 2
MAP3K7IP2 0.017 0 -10000 0 -10000 0 0
MAP3K5 0.017 0.001 -10000 0 -10000 0 0
MAP3K10 0.017 0 -10000 0 -10000 0 0
MAP3K3 0.017 0 -10000 0 -10000 0 0
TRX/ASK1 0.018 0.002 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.011 0.081 -10000 0 -0.2 66 66
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 -0.027 0.098 -9999 0 -0.29 65 65
SMARCC1 0.012 0.075 -9999 0 -0.39 18 18
REL 0.016 0 -9999 0 -10000 0 0
HDAC7 0.038 0.029 -9999 0 -10000 0 0
JUN 0.017 0.019 -9999 0 -0.41 1 1
EP300 0.017 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 0.02 0.019 -9999 0 -0.28 2 2
FOXO1 0.008 0.061 -9999 0 -0.41 11 11
T-DHT/AR 0.059 0.034 -9999 0 -10000 0 0
MAP2K6 0.019 0.002 -9999 0 -10000 0 0
BRM/BAF57 0.027 0 -9999 0 -10000 0 0
MAP2K4 0.018 0.004 -9999 0 -10000 0 0
SMARCA2 0.018 0 -9999 0 -10000 0 0
PDE9A 0.035 0.041 -9999 0 -0.4 4 4
NCOA2 0.018 0 -9999 0 -10000 0 0
CEBPA 0.004 0.074 -9999 0 -0.41 16 16
EHMT2 0.018 0 -9999 0 -10000 0 0
cell proliferation 0.068 0.03 -9999 0 -0.18 1 1
NR0B1 -0.023 0.12 -9999 0 -0.41 49 49
EGR1 0.005 0.071 -9999 0 -0.41 15 15
RXRs/9cRA 0.033 0.018 -9999 0 -0.21 3 3
AR/RACK1/Src 0.043 0.02 -9999 0 -10000 0 0
AR/GR 0.034 0.02 -9999 0 -0.12 1 1
GNB2L1 0.017 0 -9999 0 -10000 0 0
PKN1 0.009 0.059 -9999 0 -0.41 10 10
RCHY1 0.017 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
MAPK8 0.02 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 0.052 0.023 -9999 0 -0.16 2 2
SRC 0.024 0.016 -9999 0 -0.18 2 2
NR3C1 0.017 0 -9999 0 -10000 0 0
KLK3 0.025 0.024 -9999 0 -10000 0 0
APPBP2 0.018 0.002 -9999 0 -10000 0 0
TRIM24 0.011 0.056 -9999 0 -0.41 9 9
T-DHT/AR/TIP60 0.023 0.018 -9999 0 -0.17 2 2
TMPRSS2 0.035 0.035 -9999 0 -0.33 4 4
RXRG 0.015 0.032 -9999 0 -0.41 3 3
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.017 0 -9999 0 -10000 0 0
RXRB 0.017 0 -9999 0 -10000 0 0
CARM1 0.018 0 -9999 0 -10000 0 0
NR2C2 0.017 0 -9999 0 -10000 0 0
KLK2 0.055 0.02 -9999 0 -10000 0 0
AR 0.026 0.022 -9999 0 -0.12 10 10
SENP1 0 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0 -9999 0 -10000 0 0
MDM2 0.001 0.078 -9999 0 -0.41 18 18
SRY 0.015 0.019 -9999 0 -0.41 1 1
GATA2 0.016 0.019 -9999 0 -0.41 1 1
MYST2 0.017 0 -9999 0 -10000 0 0
HOXB13 0.018 0 -9999 0 -10000 0 0
T-DHT/AR/RACK1/Src 0.04 0.02 -9999 0 -10000 0 0
positive regulation of transcription 0.016 0.019 -9999 0 -0.41 1 1
DNAJA1 0.018 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.062 -9999 0 -0.15 80 80
NCOA1 0.017 0.02 -9999 0 -10000 0 0
SPDEF 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/TIF2 0.035 0.022 -9999 0 -0.12 1 1
T-DHT/AR/Hsp90 0.035 0.021 -9999 0 -0.17 2 2
GSK3B 0.018 0.002 -9999 0 -10000 0 0
NR2C1 0.017 0 -9999 0 -10000 0 0
mol:T-DHT 0.023 0.017 -9999 0 -0.2 2 2
SIRT1 0.017 0 -9999 0 -10000 0 0
ZMIZ2 0.016 0 -9999 0 -10000 0 0
POU2F1 0.028 0.009 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 0.015 0.064 -9999 0 -0.18 48 48
CREBBP 0.017 0 -9999 0 -10000 0 0
SMARCE1 0.018 0 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.01 0.028 -9999 0 -0.2 1 1
CaM/Ca2+ 0.012 0.003 -9999 0 -10000 0 0
AKT1 0.014 0.037 -9999 0 -0.41 4 4
AKT2 0.017 0 -9999 0 -10000 0 0
STXBP4 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose -0.002 0.03 -9999 0 -0.13 4 4
YWHAZ 0.017 0.002 -9999 0 -10000 0 0
CALM1 0.016 0.004 -9999 0 -10000 0 0
YWHAQ 0.017 0 -9999 0 -10000 0 0
TBC1D4 0.015 0.026 -9999 0 -0.28 4 4
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.008 0.009 -9999 0 -10000 0 0
YWHAB 0.017 0.001 -9999 0 -10000 0 0
SNARE/Synip 0.021 0.007 -9999 0 -10000 0 0
YWHAG 0 0 -9999 0 -10000 0 0
ASIP 0.017 0 -9999 0 -10000 0 0
PRKCI 0.016 0.019 -9999 0 -0.41 1 1
AS160/CaM/Ca2+ 0.012 0.003 -9999 0 -10000 0 0
RHOQ 0.017 0 -9999 0 -10000 0 0
GYS1 0.004 0.063 -9999 0 -0.22 40 40
PRKCZ 0 0 -9999 0 -10000 0 0
TRIP10 0.012 0.046 -9999 0 -0.41 6 6
TC10/GTP/CIP4/Exocyst 0.02 0.028 -9999 0 -0.24 6 6
AS160/14-3-3 0.006 0.037 -9999 0 -0.13 24 24
VAMP2 0.016 0.005 -9999 0 -10000 0 0
SLC2A4 -0.003 0.031 -9999 0 -0.14 4 4
STX4 0.017 0 -9999 0 -10000 0 0
GSK3B 0.021 0.017 -9999 0 -0.18 4 4
SFN -0.01 0.1 -9999 0 -0.41 33 33
LNPEP 0.016 0.019 -9999 0 -0.41 1 1
YWHAE 0.017 0.001 -9999 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.02 0.011 -10000 0 -10000 0 0
VLDLR 0.015 0.032 -10000 0 -0.41 3 3
CRKL 0.017 0 -10000 0 -10000 0 0
LRPAP1 0.017 0 -10000 0 -10000 0 0
FYN 0.015 0.027 -10000 0 -0.41 2 2
ITGA3 0.002 0.08 -10000 0 -0.41 19 19
RELN/VLDLR/Fyn 0.013 0.03 -10000 0 -0.24 4 4
MAPK8IP1/MKK7/MAP3K11/JNK1 0.051 0 -10000 0 -10000 0 0
AKT1 0.001 0.044 -10000 0 -0.15 33 33
MAP2K7 0.017 0 -10000 0 -10000 0 0
RAPGEF1 0.017 0 -10000 0 -10000 0 0
DAB1 0.017 0 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0.014 0.024 -10000 0 -0.21 3 3
LRPAP1/LRP8 0.025 0 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.017 0.027 -10000 0 -0.19 3 3
DAB1/alpha3/beta1 Integrin 0.014 0.035 -10000 0 -0.2 6 6
long-term memory 0.016 0.028 -10000 0 -0.18 2 2
DAB1/LIS1 0.021 0.031 -10000 0 -0.18 4 4
DAB1/CRLK/C3G 0.017 0.026 -10000 0 -0.17 4 4
PIK3CA -0.003 0.091 -10000 0 -0.41 25 25
DAB1/NCK2 0.022 0.031 -10000 0 -0.18 4 4
ARHGEF2 0.017 0 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.011 0.008 -10000 0 -10000 0 0
CDK5R1 0.014 0.007 -10000 0 -10000 0 0
RELN 0.006 0.033 -10000 0 -0.41 3 3
PIK3R1 0.016 0.004 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.014 0.027 -10000 0 -0.24 3 3
GRIN2A/RELN/LRP8/DAB1/Fyn 0.016 0.028 -10000 0 -0.19 2 2
MAPK8 0.017 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.013 0.027 -10000 0 -0.21 4 4
ITGB1 0.017 0 -10000 0 -10000 0 0
MAP1B 0.011 0.018 -10000 0 -0.18 2 2
RELN/LRP8 0.015 0.026 -10000 0 -0.24 3 3
GRIN2B/RELN/LRP8/DAB1/Fyn 0.021 0.031 -10000 0 -0.19 3 3
PI3K 0.009 0.065 -10000 0 -0.28 25 25
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.014 0.058 -10000 0 -0.28 19 19
RAP1A 0.08 0.052 -10000 0 -10000 0 0
PAFAH1B1 0.017 0.002 -10000 0 -10000 0 0
MAPK8IP1 0.017 0 -10000 0 -10000 0 0
CRLK/C3G 0.025 0 -10000 0 -10000 0 0
GRIN2B 0.017 0 -10000 0 -10000 0 0
NCK2 0.017 0.001 -10000 0 -10000 0 0
neuron differentiation 0.016 0.021 -10000 0 -0.12 2 2
neuron adhesion 0.077 0.058 -10000 0 -0.32 1 1
LRP8 0.017 0 -10000 0 -10000 0 0
GSK3B 0.003 0.041 -10000 0 -0.18 17 17
RELN/VLDLR/DAB1/Fyn 0.016 0.029 -10000 0 -0.19 4 4
MAP3K11 0.017 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K 0.002 0.043 -10000 0 -0.16 30 30
CDK5 0.016 0.004 -10000 0 -10000 0 0
MAPT 0.023 0.08 0.34 32 -10000 0 32
neuron migration 0.01 0.035 -10000 0 -0.16 11 11
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.016 0.021 -10000 0 -0.12 2 2
RELN/VLDLR 0.019 0.03 -10000 0 -0.21 4 4
IL27-mediated signaling events

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
TGFB1 0.002 0.094 -10000 0 -0.4 27 27
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response -0.025 0.011 -10000 0 -10000 0 0
IL27/IL27R/JAK1 0.037 0.019 -10000 0 -10000 0 0
TBX21 0.024 0.033 -10000 0 -10000 0 0
IL12B 0.018 0.001 -10000 0 -10000 0 0
IL12A 0.009 0 -10000 0 -10000 0 0
IL6ST 0.018 0.001 -10000 0 -10000 0 0
IL27RA/JAK1 0.022 0.003 -10000 0 -10000 0 0
IL27 0.001 0.001 -10000 0 -10000 0 0
TYK2 0.018 0.019 -10000 0 -0.41 1 1
T-helper cell lineage commitment 0.002 0.071 -10000 0 -0.29 7 7
T-helper 2 cell differentiation -0.025 0.011 -10000 0 -10000 0 0
T cell proliferation during immune response -0.025 0.011 -10000 0 -10000 0 0
MAPKKK cascade 0.025 0.011 -10000 0 -10000 0 0
STAT3 0.009 0.059 -10000 0 -0.41 10 10
STAT2 0.017 0 -10000 0 -10000 0 0
STAT1 0.003 0.078 -10000 0 -0.41 18 18
IL12RB1 0.018 0 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.025 0.033 -10000 0 -10000 0 0
IL27/IL27R/JAK2/TYK2 0.025 0.012 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.025 0.011 -10000 0 -10000 0 0
STAT1 (dimer) 0.037 0.046 0.28 4 -0.34 1 5
JAK2 0.017 0.001 -10000 0 -10000 0 0
JAK1 0.017 0.002 -10000 0 -10000 0 0
STAT2 (dimer) 0.034 0.012 -10000 0 -10000 0 0
T cell proliferation 0.009 0.062 -10000 0 -0.27 2 2
IL12/IL12R/TYK2/JAK2 0.044 0.011 -10000 0 -10000 0 0
IL17A 0.002 0.071 -10000 0 -0.29 7 7
mast cell activation -0.025 0.011 -10000 0 -10000 0 0
IFNG 0.011 0.004 -10000 0 -0.072 1 1
T cell differentiation 0.001 0.001 -10000 0 -0.013 1 1
STAT3 (dimer) 0.03 0.031 -10000 0 -10000 0 0
STAT5A (dimer) 0.034 0.015 -10000 0 -10000 0 0
STAT4 (dimer) 0.019 0.02 -10000 0 -10000 0 0
STAT4 0.01 0.008 -10000 0 -10000 0 0
T cell activation -0.006 0 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.041 0.011 -10000 0 -10000 0 0
GATA3 0.003 0.035 -10000 0 -0.35 5 5
IL18 -0.016 0.084 -10000 0 -0.29 45 45
positive regulation of mast cell cytokine production 0.03 0.03 -10000 0 -10000 0 0
IL27/EBI3 0.011 0.023 -10000 0 -0.29 3 3
IL27RA 0.012 0.002 -10000 0 -10000 0 0
IL6 -0.018 0.13 -10000 0 -0.4 52 52
STAT5A 0.016 0.019 -10000 0 -0.41 1 1
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.005 0.002 -10000 0 -10000 0 0
IL1B 0.001 0.048 -10000 0 -0.29 14 14
EBI3 0.014 0.032 -10000 0 -0.41 3 3
TNF 0.008 0.018 -10000 0 -0.29 2 2
S1P4 pathway

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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.002 0.005 -9999 0 -10000 0 0
CDC42/GTP -0.015 0.039 -9999 0 -0.16 12 12
PLCG1 0.002 0.01 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.017 0.001 -9999 0 -10000 0 0
GNAI3 -0.036 0.14 -9999 0 -0.41 65 65
G12/G13 0.022 0.033 -9999 0 -0.28 6 6
cell migration -0.015 0.038 -9999 0 -0.16 12 12
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
MAPK3 0.002 0.01 -9999 0 -10000 0 0
MAPK1 0.002 0.01 -9999 0 -10000 0 0
S1P/S1P5/Gi 0.001 0.01 -9999 0 -0.1 3 3
GNAI1 0.014 0.02 -9999 0 -0.41 1 1
CDC42/GDP 0.013 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.01 0.022 -9999 0 -0.24 4 4
RHOA 0.016 0.023 -9999 0 -0.2 6 6
S1P/S1P4/Gi 0.001 0.01 -9999 0 -0.1 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.015 0.006 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 0.019 0.025 -9999 0 -0.22 6 6
GNA12 0.014 0.037 -9999 0 -0.41 4 4
GNA13 0.015 0.026 -9999 0 -0.41 2 2
CDC42 0.017 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.033 0.004 -9999 0 -10000 0 0
HDAC3 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.007 -9999 0 -0.17 1 1
GATA1/HDAC4 0.025 0 -9999 0 -10000 0 0
GATA1/HDAC5 0.025 0 -9999 0 -10000 0 0
GATA2/HDAC5 0.025 0.014 -9999 0 -0.28 1 1
HDAC5/BCL6/BCoR 0.024 0.053 -9999 0 -0.24 21 21
HDAC9 0.015 0.026 -9999 0 -0.41 2 2
Glucocorticoid receptor/Hsp90/HDAC6 0.035 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.025 0.014 -9999 0 -0.28 1 1
HDAC5/YWHAB 0.025 0.002 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.018 0.005 -9999 0 -0.11 1 1
GATA2 0.016 0.019 -9999 0 -0.41 1 1
HDAC4/RFXANK -0.006 0.093 -9999 0 -0.28 53 53
BCOR 0.013 0.042 -9999 0 -0.41 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0 0 -9999 0 -10000 0 0
HDAC5 0.017 0 -9999 0 -10000 0 0
GNB1/GNG2 0.013 0.001 -9999 0 -10000 0 0
Histones 0.024 0.008 -9999 0 -0.1 2 2
ADRBK1 0.017 0 -9999 0 -10000 0 0
HDAC4 0.017 0 -9999 0 -10000 0 0
XPO1 0.017 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.025 0.014 -9999 0 -0.28 1 1
HDAC4/Ubc9 0.025 0 -9999 0 -10000 0 0
HDAC7 0 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.025 0.002 -9999 0 -10000 0 0
TUBA1B 0.017 0 -9999 0 -10000 0 0
HDAC6 0.017 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.006 0.093 -9999 0 -0.28 53 53
CAMK4 0.017 0 -9999 0 -10000 0 0
Tubulin/HDAC6 0.033 0.009 -9999 0 -10000 0 0
SUMO1 0.017 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.017 0.001 -9999 0 -10000 0 0
GATA1 0.017 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.017 0.001 -9999 0 -10000 0 0
NR3C1 0.017 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.033 0.005 -9999 0 -10000 0 0
SRF 0.017 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0.025 0.002 -9999 0 -10000 0 0
Tubulin 0.024 0.006 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.025 0.002 -9999 0 -10000 0 0
GNB1 0.017 0.002 -9999 0 -10000 0 0
RANGAP1 0.017 0 -9999 0 -10000 0 0
BCL6/BCoR 0.013 0.061 -9999 0 -0.28 21 21
HDAC4/HDAC3/SMRT (N-CoR2) 0.035 0 -9999 0 -10000 0 0
HDAC4/SRF 0.035 0 -9999 0 -10000 0 0
HDAC4/ER alpha 0.025 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.024 0.008 -9999 0 -0.1 2 2
cell motility 0.032 0.008 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.017 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0.013 0 -9999 0 -10000 0 0
BCL6 0.004 0.074 -9999 0 -0.41 16 16
HDAC4/CaMK II delta B 0.017 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0.025 0 -9999 0 -10000 0 0
ESR1 0.017 0 -9999 0 -10000 0 0
HDAC6/HDAC11 0.025 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.006 -9999 0 -10000 0 0
NPC 0.01 0.009 -9999 0 -0.2 1 1
MEF2C 0.014 0.006 -9999 0 -10000 0 0
RAN 0.017 0.001 -9999 0 -10000 0 0
HDAC4/MEF2C 0.043 0.019 -9999 0 -10000 0 0
GNG2 0 0 -9999 0 -10000 0 0
NCOR2 0.017 0 -9999 0 -10000 0 0
TUBB2A 0.016 0.004 -9999 0 -10000 0 0
HDAC11 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.017 0 -9999 0 -10000 0 0
RANBP2 0.016 0.019 -9999 0 -0.41 1 1
ANKRA2 0.016 0.019 -9999 0 -0.41 1 1
RFXANK -0.026 0.13 -9999 0 -0.41 53 53
nuclear import -0.029 0.002 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin 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
ITGB1 0.017 0 -9999 0 -10000 0 0
ITGB7 0.015 0.026 -9999 0 -0.41 2 2
ITGA4 0.013 0.042 -9999 0 -0.41 5 5
alpha4/beta7 Integrin 0.022 0.041 -9999 0 -0.38 5 5
alpha4/beta1 Integrin 0.023 0.03 -9999 0 -0.28 5 5
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.017 0 -10000 0 -10000 0 0
NFATC1 0.038 0.016 -10000 0 -10000 0 0
NFATC2 0.009 0.032 -10000 0 -0.11 7 7
NFATC3 0.012 0.003 -10000 0 -10000 0 0
YWHAE 0.017 0.001 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.001 0.011 -10000 0 -0.14 2 2
Exportin 1/Ran/NUP214 0.035 0.003 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.029 0.012 -10000 0 -10000 0 0
BCL2/BAX 0.021 0.036 -10000 0 -0.28 7 7
CaM/Ca2+/Calcineurin A alpha-beta B1 0.013 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.013 0.003 -10000 0 -10000 0 0
BAX 0.011 0.049 -10000 0 -0.41 7 7
MAPK14 0.016 0.026 -10000 0 -0.41 2 2
BAD 0.017 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.016 0.011 -10000 0 -0.13 2 2
Calcineurin A alpha-beta B1/BCL2 0.017 0 -10000 0 -10000 0 0
FKBP8 0.017 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.015 0.011 0.13 2 -10000 0 2
KPNB1 0.017 0 -10000 0 -10000 0 0
KPNA2 0.007 0.064 -10000 0 -0.41 12 12
XPO1 0.017 0 -10000 0 -10000 0 0
SFN -0.01 0.1 -10000 0 -0.41 33 33
MAP3K8 -0.017 0.12 -10000 0 -0.41 42 42
NFAT4/CK1 alpha 0.027 0.011 -10000 0 -0.19 1 1
MEF2D/NFAT1/Cbp/p300 0.047 0.031 -10000 0 -10000 0 0
CABIN1 0.001 0.011 -10000 0 -0.14 2 2
CALM1 0.016 0.004 -10000 0 -10000 0 0
RAN 0.017 0.001 -10000 0 -10000 0 0
MAP3K1 0.016 0.019 -10000 0 -0.41 1 1
CAMK4 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0 -10000 0 -10000 0 0
MAPK3 0.017 0 -10000 0 -10000 0 0
YWHAH 0.008 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.026 0 -10000 0 -10000 0 0
YWHAB 0.017 0.001 -10000 0 -10000 0 0
MAPK8 0.017 0 -10000 0 -10000 0 0
MAPK9 0.017 0.001 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0.016 0.019 -10000 0 -0.41 1 1
NFAT1-c-4/YWHAQ 0.043 0.024 -10000 0 -10000 0 0
PRKCH 0.015 0.026 -10000 0 -0.41 2 2
CABIN1/Cbp/p300 0.026 0 -10000 0 -10000 0 0
CASP3 -0.062 0.17 -10000 0 -0.41 97 97
PIM1 0.015 0.026 -10000 0 -0.41 2 2
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.011 -10000 0 -0.24 1 1
apoptosis 0.015 0.019 -10000 0 -0.15 7 7
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.038 -10000 0 -0.14 25 25
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.017 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.022 0.005 -10000 0 -10000 0 0
BAD/BCL-XL 0.025 0 -10000 0 -10000 0 0
PRKCD 0.017 0 -10000 0 -10000 0 0
NUP214 0.017 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
PRKCA 0.017 0 -10000 0 -10000 0 0
PRKCG 0.017 0 -10000 0 -10000 0 0
PRKCQ 0.017 0 -10000 0 -10000 0 0
FKBP38/BCL2 0.025 0 -10000 0 -10000 0 0
EP300 0.018 0 -10000 0 -10000 0 0
PRKCB1 0.001 0.004 -10000 0 -10000 0 0
CSNK2A1 0.017 0 -10000 0 -10000 0 0
NFATc/JNK1 0.047 0.017 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.023 0.005 -10000 0 -10000 0 0
FKBP12/FK506 0.012 0.013 -10000 0 -0.29 1 1
CSNK1A1 0.016 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.023 0.005 -10000 0 -10000 0 0
NFATc/ERK1 0.046 0.017 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.029 0.012 -10000 0 -10000 0 0
NR4A1 0.032 0.028 -10000 0 -10000 0 0
GSK3B 0.017 0.002 -10000 0 -10000 0 0
positive T cell selection 0.012 0.003 -10000 0 -10000 0 0
NFAT1/CK1 alpha 0.013 0.023 -10000 0 -10000 0 0
RCH1/ KPNB1 0.018 0.046 -10000 0 -0.28 12 12
YWHAQ 0.017 0 -10000 0 -10000 0 0
PRKACA 0.017 0 -10000 0 -10000 0 0
AKAP5 0.017 0 -10000 0 -10000 0 0
MEF2D 0.018 0 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.017 0.002 -10000 0 -10000 0 0
NFATc/p38 alpha 0.046 0.022 -10000 0 -0.21 2 2
CREBBP 0.018 0 -10000 0 -10000 0 0
BCL2 0.017 0 -10000 0 -10000 0 0
LPA4-mediated signaling events

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
ADCY4 0.006 0 -9999 0 -10000 0 0
ADCY5 0.006 0 -9999 0 -10000 0 0
ADCY6 0.012 0 -9999 0 -10000 0 0
ADCY7 0.009 0.024 -9999 0 -0.24 5 5
ADCY1 0.012 0 -9999 0 -10000 0 0
ADCY2 0.012 0 -9999 0 -10000 0 0
ADCY3 0.006 0 -9999 0 -10000 0 0
ADCY8 0.008 0.029 -9999 0 -0.24 7 7
PRKCE 0.009 0 -9999 0 -10000 0 0
ADCY9 0.012 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0.014 0.013 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.025 0.001 -10000 0 -10000 0 0
STXBP1 0.002 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 0.029 0.021 -10000 0 -0.24 3 3
RAB3GAP2/RIMS1/UNC13B 0.035 0.002 -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 -10000 0 -10000 0 0
mol:ACh 0.03 0.012 0.051 32 -10000 0 32
RAB3GAP2 0.017 0 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.001 0.006 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.029 0.021 -10000 0 -0.24 3 3
UNC13B 0.017 0.001 -10000 0 -10000 0 0
CHRNA1 0.015 0.032 -10000 0 -0.41 3 3
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.002 0.008 -10000 0 -10000 0 0
SNAP25 0.001 0.002 -10000 0 -10000 0 0
VAMP2 0.005 0.002 -10000 0 -10000 0 0
SYT1 0.001 0.004 -10000 0 -10000 0 0
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.001 0.003 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.001 0.006 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.015 0.006 0.11 2 -10000 0 2
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.007 -10000 0 -10000 0 0
AP2 0.012 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.024 0.001 -10000 0 -10000 0 0
CLTB 0.017 0.001 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.002 -10000 0 -10000 0 0
CD4 0.001 0.082 -10000 0 -0.41 20 20
CLTA 0.017 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
ARFGAP1 0.009 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.007 -10000 0 -0.15 1 1
ARF1/GTP 0.01 0.006 -10000 0 -0.12 1 1
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.019 0.002 -10000 0 -10000 0 0
mol:Choline 0.007 0.007 -10000 0 -0.14 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.017 0.001 -10000 0 -10000 0 0
DDEF1 0.007 0.007 -10000 0 -0.14 1 1
ARF1/GDP 0.007 0.002 -10000 0 -10000 0 0
AP2M1 0.017 0.002 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.001 -10000 0 -10000 0 0
Rac/GTP 0.013 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.027 0.002 -10000 0 -10000 0 0
ARFIP2 0.016 0.001 -10000 0 -10000 0 0
COPA 0.017 0 -10000 0 -10000 0 0
RAC1 0.017 0 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.019 0.003 -10000 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.011 0.001 -10000 0 -10000 0 0
GGA3 0.017 0 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.016 0.004 -10000 0 -10000 0 0
AP2A1 0 0 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.021 0.002 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.018 0.003 -10000 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.023 0.001 -10000 0 -10000 0 0
CYTH2 0 0.001 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.022 0.001 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.013 0 -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 0.019 0.024 -10000 0 -0.1 20 20
PLD2 0.007 0.007 -10000 0 -0.15 1 1
ARF-GAP1/v-SNARE 0.009 0 -10000 0 -10000 0 0
PIP5K1A 0.008 0.007 -10000 0 -0.15 1 1
ARF1/GTP/Membrin/GBF1/p115 0.016 0.005 -10000 0 -0.099 1 1
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.007 -10000 0 -0.14 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.009 0 -10000 0 -10000 0 0
GOSR2 0.012 0.003 -10000 0 -10000 0 0
USO1 0.012 0.003 -10000 0 -10000 0 0
GBF1 0.012 0.003 -10000 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.023 0.002 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.013 0.05 -10000 0 -0.24 20 20
Alternative NF-kappaB 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
IKK alpha homodimer 0.024 0.023 -9999 0 -0.28 3 3
FBXW11 0.017 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
CHUK 0.016 0.019 -9999 0 -0.41 1 1
NF kappa B2 p100/RelB 0.049 0.021 -9999 0 -0.19 4 4
NFKB1 0.014 0.037 -9999 0 -0.41 4 4
MAP3K14 0.015 0.026 -9999 0 -0.41 2 2
NF kappa B1 p50/RelB 0.023 0.03 -9999 0 -0.28 5 5
RELB 0.016 0.019 -9999 0 -0.41 1 1
NFKB2 0.017 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.023 0.011 -9999 0 -0.24 1 1
regulation of B cell activation 0.022 0.011 -9999 0 -0.24 1 1
PLK2 and PLK4 events

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
PLK2 0.012 0.008 -9999 0 -9999 0 0
PLK4 0.017 0 -9999 0 -9999 0 0
regulation of centriole replication 0.013 0.008 -9999 0 -9999 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.023 0 -9999 0 -10000 0 0
EFNA5 0.017 0 -9999 0 -10000 0 0
FYN 0.018 0.015 -9999 0 -0.21 2 2
neuron projection morphogenesis 0.023 0 -9999 0 -10000 0 0
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 0.023 0 -9999 0 -10000 0 0
EPHA5 0.017 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.02 0.002 -9999 0 -10000 0 0
MAPK9 0.007 0.001 -9999 0 -10000 0 0
adrenocorticotropin secretion 0.008 0.013 -9999 0 -0.29 1 1
GNB1/GNG2 0.011 0.001 -9999 0 -10000 0 0
GNB1 0.017 0.002 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.007 0.012 -9999 0 -0.19 2 2
Gs family/GTP 0.011 0 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0 0 -9999 0 -10000 0 0
GNAL 0.017 0 -9999 0 -10000 0 0
GNG2 0 0 -9999 0 -10000 0 0
CRH 0.016 0.019 -9999 0 -0.41 1 1
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.007 0 -9999 0 -10000 0 0
MAPK11 0.007 0 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.017 0 -9999 0 -10000 0 0
GNAT1/GTP 0.013 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin 0.023 0.011 -9999 0 -0.24 1 1
PDE6G/GNAT1/GTP 0.023 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.017 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel 0.034 0 -9999 0 -10000 0 0
mol:Na + 0.027 0 -9999 0 -10000 0 0
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.023 0.003 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel 0.034 0 -9999 0 -10000 0 0
CNGB1 0.017 0 -9999 0 -10000 0 0
RDH5 0.016 0.019 -9999 0 -0.41 1 1
SAG 0.016 0.019 -9999 0 -0.41 1 1
mol:Ca2+ 0.027 0 -9999 0 -10000 0 0
Na + (4 Units) 0.024 0 -9999 0 -10000 0 0
RGS9 0.017 0 -9999 0 -10000 0 0
GNB1/GNGT1 0.025 0.003 -9999 0 -10000 0 0
GNAT1/GDP 0.03 0.003 -9999 0 -10000 0 0
GUCY2D 0.017 0 -9999 0 -10000 0 0
GNGT1 0.017 0 -9999 0 -10000 0 0
GUCY2F 0.017 0 -9999 0 -10000 0 0
GNB5 0.017 0.002 -9999 0 -10000 0 0
mol:GMP (4 units) 0.028 0 -9999 0 -10000 0 0
mol:11-cis-retinal 0.016 0.019 -9999 0 -0.41 1 1
mol:cGMP 0.022 0 -9999 0 -10000 0 0
GNB1 0.017 0.002 -9999 0 -10000 0 0
Rhodopsin 0.025 0.013 -9999 0 -0.28 1 1
SLC24A1 0.017 0 -9999 0 -10000 0 0
CNGA1 0.017 0 -9999 0 -10000 0 0
Metarhodopsin II 0.011 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.022 0 -9999 0 -10000 0 0
RGS9BP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Transducin 0.021 0.002 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0.011 0 -9999 0 -10000 0 0
PDE6A/B 0.025 0 -9999 0 -10000 0 0
mol:Pi 0.023 0.003 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.033 0.004 -9999 0 -10000 0 0
PDE6B 0.017 0 -9999 0 -10000 0 0
PDE6A 0.017 0 -9999 0 -10000 0 0
PDE6G 0.017 0 -9999 0 -10000 0 0
RHO 0.017 0 -9999 0 -10000 0 0
PDE6 0.042 0.005 -9999 0 -10000 0 0
GUCA1A 0 0 -9999 0 -10000 0 0
GC2/GCAP Family 0.022 0 -9999 0 -10000 0 0
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.017 0 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.017 0 -9999 0 -9999 0 0
PI3K Class IB/PDE3B 0.017 0 -9999 0 -9999 0 0
PDE3B 0.017 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 528 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.87.5896 TCGA.81.5910 TCGA.76.6285 TCGA.76.6282
109_MAP3K5 -0.074 0.041 0.041 0.041
47_PPARGC1A 0.017 0.017 0.017 0.017
105_BMP4 0.017 0.017 0.017 0.017
105_BMP6 0.017 0.017 0.017 0.017
105_BMP7 0.017 0.017 0.017 0.017
105_BMP2 0.017 0.017 -0.41 0.017
131_RELN/VLDLR 0.044 -0.093 0.044 0
30_TGFB1/TGF beta receptor Type II -0.41 0.017 0.019 -0.41
84_STAT5B -0.16 -0.098 0.034 -0.098
84_STAT5A -0.16 -0.098 0.034 -0.098
Methods & Data
Input

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

  • mRNA Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/GBM-TP/8016781/GDAC_MergeDataFiles_4396203/GBM-TP.transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.data.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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