PARADIGM pathway analysis of mRNASeq expression data
Bladder Urothelial Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C10Z72F1
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C10Z72F1
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 71 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
FOXM1 transcription factor network 177
Aurora B signaling 123
Signaling events regulated by Ret tyrosine kinase 121
Glypican 2 network 116
TCGA08_retinoblastoma 99
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 98
IGF1 pathway 94
Endothelins 87
Nongenotropic Androgen signaling 84
Signaling mediated by p38-alpha and p38-beta 82
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 408 . 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 ( 408 ).

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
FOXM1 transcription factor network 0.4338 177 9036 51 -0.04 0.74 1000 -1000 -0.069 -1000
Aurora B signaling 0.3015 123 8295 67 -0.15 0.26 1000 -1000 -0.009 -1000
Signaling events regulated by Ret tyrosine kinase 0.2966 121 9956 82 -0.16 0.014 1000 -1000 -0.025 -1000
Glypican 2 network 0.2843 116 465 4 0.025 0.099 1000 -1000 0.006 -1000
TCGA08_retinoblastoma 0.2426 99 794 8 -0.058 0.14 1000 -1000 -0.002 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2402 98 6678 68 -0.61 0.32 1000 -1000 -0.034 -1000
IGF1 pathway 0.2304 94 5372 57 -0.12 0.038 1000 -1000 -0.012 -1000
Endothelins 0.2132 87 8415 96 -0.36 0.19 1000 -1000 -0.005 -1000
Nongenotropic Androgen signaling 0.2059 84 4376 52 -0.24 0.14 1000 -1000 -0.006 -1000
Signaling mediated by p38-alpha and p38-beta 0.2010 82 3650 44 -0.19 0.01 1000 -1000 -0.005 -1000
Fc-epsilon receptor I signaling in mast cells 0.1936 79 7745 97 -0.12 0.022 1000 -1000 -0.024 -1000
Signaling events mediated by the Hedgehog family 0.1863 76 4000 52 -0.081 0.081 1000 -1000 -0.01 -1000
Syndecan-1-mediated signaling events 0.1838 75 2561 34 -0.049 0.16 1000 -1000 -0.003 -1000
Reelin signaling pathway 0.1789 73 4103 56 -0.093 0.058 1000 -1000 -0.002 -1000
PLK1 signaling events 0.1765 72 6150 85 -0.052 0.2 1000 -1000 -0.01 -1000
IL4-mediated signaling events 0.1691 69 6312 91 -0.6 0.4 1000 -1000 -0.11 -1000
IL23-mediated signaling events 0.1691 69 4163 60 -0.31 0.08 1000 -1000 -0.066 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1667 68 5310 78 -0.24 0.081 1000 -1000 -0.026 -1000
Thromboxane A2 receptor signaling 0.1569 64 6748 105 -0.22 0.055 1000 -1000 -0.026 -1000
p75(NTR)-mediated signaling 0.1544 63 7902 125 -0.076 0.071 1000 -1000 -0.019 -1000
Plasma membrane estrogen receptor signaling 0.1471 60 5180 86 -0.23 0.13 1000 -1000 -0.024 -1000
TCGA08_p53 0.1397 57 405 7 -0.044 0.024 1000 -1000 -0.001 -1000
Aurora C signaling 0.1373 56 392 7 0 0.13 1000 -1000 -0.003 -1000
S1P4 pathway 0.1373 56 1423 25 -0.084 0.019 1000 -1000 0 -1000
S1P5 pathway 0.1299 53 901 17 -0.084 0.064 1000 -1000 -0.006 -1000
HIF-1-alpha transcription factor network 0.1250 51 3918 76 -0.09 0.29 1000 -1000 -0.025 -1000
TCR signaling in naïve CD8+ T cells 0.1225 50 4676 93 -0.091 0.044 1000 -1000 -0.022 -1000
Ephrin A reverse signaling 0.1201 49 344 7 -0.033 0 1000 -1000 0 -1000
amb2 Integrin signaling 0.1201 49 4021 82 -0.22 0.069 1000 -1000 -0.01 -1000
Integrins in angiogenesis 0.1201 49 4187 84 -0.18 0.12 1000 -1000 -0.002 -1000
Ras signaling in the CD4+ TCR pathway 0.1201 49 839 17 -0.12 0.011 1000 -1000 -0.003 -1000
LPA receptor mediated events 0.1176 48 4913 102 -0.17 0.069 1000 -1000 -0.026 -1000
BMP receptor signaling 0.1152 47 3815 81 -0.16 0.043 1000 -1000 -0.021 -1000
S1P1 pathway 0.1152 47 1705 36 -0.28 0.01 1000 -1000 -0.01 -1000
Rapid glucocorticoid signaling 0.1152 47 957 20 -0.12 0.07 1000 -1000 -0.001 -1000
Osteopontin-mediated events 0.1127 46 1773 38 -0.084 0.12 1000 -1000 -0.009 -1000
Glucocorticoid receptor regulatory network 0.1078 44 5127 114 -0.43 0.16 1000 -1000 -0.026 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.1078 44 5327 120 -0.15 0.13 1000 -1000 -0.021 -1000
JNK signaling in the CD4+ TCR pathway 0.1054 43 731 17 -0.15 0.011 1000 -1000 -0.011 -1000
Calcium signaling in the CD4+ TCR pathway 0.1054 43 1363 31 -0.077 0.014 1000 -1000 -0.017 -1000
Glypican 1 network 0.1029 42 2051 48 -0.13 0.041 1000 -1000 -0.005 -1000
FOXA2 and FOXA3 transcription factor networks 0.1005 41 1900 46 -0.11 0.31 1000 -1000 -0.015 -1000
IL6-mediated signaling events 0.0956 39 2995 75 -0.19 0.044 1000 -1000 -0.019 -1000
ErbB2/ErbB3 signaling events 0.0931 38 2526 65 -0.12 0.015 1000 -1000 -0.021 -1000
IL12-mediated signaling events 0.0907 37 3227 87 -0.36 0.059 1000 -1000 -0.071 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0907 37 1999 54 -0.093 0.058 1000 -1000 -0.003 -1000
PDGFR-alpha signaling pathway 0.0907 37 1657 44 -0.23 0.023 1000 -1000 0.003 -1000
BCR signaling pathway 0.0907 37 3719 99 -0.083 0.017 1000 -1000 -0.022 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0858 35 1821 52 -0.16 0.018 1000 -1000 -0.013 -1000
Aurora A signaling 0.0833 34 2056 60 -0.13 0.2 1000 -1000 0 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0809 33 2909 88 -0.12 0.045 1000 -1000 -0.033 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0784 32 1094 34 -0.01 0.013 1000 -1000 -0.007 -1000
Visual signal transduction: Cones 0.0784 32 1222 38 -0.054 0.078 1000 -1000 0 -1000
Arf6 signaling events 0.0784 32 1998 62 -0.12 0.029 1000 -1000 -0.006 -1000
FAS signaling pathway (CD95) 0.0784 32 1517 47 -0.5 0.022 1000 -1000 -0.003 -1000
S1P3 pathway 0.0784 32 1374 42 -0.085 0.016 1000 -1000 -0.009 -1000
Coregulation of Androgen receptor activity 0.0760 31 2376 76 -0.13 0.14 1000 -1000 -0.008 -1000
Syndecan-2-mediated signaling events 0.0760 31 2192 69 -0.033 0.056 1000 -1000 0 -1000
Wnt signaling 0.0760 31 223 7 -0.007 0.025 1000 -1000 0.002 -1000
Syndecan-4-mediated signaling events 0.0735 30 2018 67 -0.089 0.073 1000 -1000 -0.006 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0686 28 2393 85 -0.23 0.016 1000 -1000 -0.005 -1000
Noncanonical Wnt signaling pathway 0.0637 26 689 26 -0.042 0.025 1000 -1000 -0.006 -1000
Class IB PI3K non-lipid kinase events 0.0637 26 78 3 -0.009 -1000 1000 -1000 -0.009 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0613 25 725 28 -0.084 0.045 1000 -1000 0 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0613 25 833 33 -0.14 0.14 1000 -1000 -0.007 -1000
Visual signal transduction: Rods 0.0613 25 1342 52 -0.054 0.12 1000 -1000 0 -1000
Presenilin action in Notch and Wnt signaling 0.0564 23 1442 61 -0.084 0.12 1000 -1000 -0.017 -1000
Canonical Wnt signaling pathway 0.0564 23 1204 51 -0.08 0.12 1000 -1000 -0.017 -1000
Regulation of Androgen receptor activity 0.0564 23 1662 70 -0.15 0.024 1000 -1000 -0.018 -1000
EGFR-dependent Endothelin signaling events 0.0539 22 473 21 -0.033 0.037 1000 -1000 0 -1000
Effects of Botulinum toxin 0.0515 21 563 26 -0.01 0.054 1000 -1000 -0.001 -1000
Hedgehog signaling events mediated by Gli proteins 0.0490 20 1357 65 -0.083 0.042 1000 -1000 -0.014 -1000
Ephrin B reverse signaling 0.0490 20 994 48 -0.024 0.029 1000 -1000 -0.017 -1000
IL27-mediated signaling events 0.0490 20 1045 51 -0.12 0.074 1000 -1000 -0.014 -1000
FoxO family signaling 0.0466 19 1273 64 0.001 0.23 1000 -1000 -0.013 -1000
Cellular roles of Anthrax toxin 0.0441 18 710 39 -0.008 0.023 1000 -1000 -0.006 -1000
Insulin Pathway 0.0441 18 1336 74 -0.13 0.045 1000 -1000 -0.017 -1000
Nectin adhesion pathway 0.0417 17 1074 63 -0.024 0.024 1000 -1000 -0.024 -1000
EPHB forward signaling 0.0417 17 1446 85 -0.01 0.038 1000 -1000 -0.022 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0417 17 1267 74 -0.12 0.029 1000 -1000 -0.019 -1000
Caspase cascade in apoptosis 0.0392 16 1211 74 -0.01 0.029 1000 -1000 -0.015 -1000
IL2 signaling events mediated by PI3K 0.0368 15 905 58 -0.022 0.12 1000 -1000 -0.012 -1000
IL2 signaling events mediated by STAT5 0.0368 15 336 22 -0.03 0.077 1000 -1000 -0.009 -1000
BARD1 signaling events 0.0343 14 814 57 -0.021 0.1 1000 -1000 -0.02 -1000
IL1-mediated signaling events 0.0343 14 928 62 0 0.033 1000 -1000 -0.007 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0343 14 1171 83 -0.18 0.037 1000 -1000 -0.005 -1000
Regulation of nuclear SMAD2/3 signaling 0.0319 13 1892 136 -0.099 0.087 1000 -1000 -0.027 -1000
ErbB4 signaling events 0.0319 13 899 69 -0.12 0.031 1000 -1000 -0.007 -1000
Signaling events mediated by PTP1B 0.0294 12 951 76 -0.12 0.039 1000 -1000 -0.023 -1000
IFN-gamma pathway 0.0294 12 825 68 -0.085 0.059 1000 -1000 -0.022 -1000
Regulation of Telomerase 0.0294 12 1250 102 -0.044 0.17 1000 -1000 -0.02 -1000
PDGFR-beta signaling pathway 0.0294 12 1169 97 -0.035 0.045 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class III 0.0270 11 471 40 -0.11 0.02 1000 -1000 -0.019 -1000
Regulation of p38-alpha and p38-beta 0.0270 11 619 54 -0.077 0.026 1000 -1000 -0.025 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0245 10 456 45 -0.007 0.029 1000 -1000 -0.012 -1000
LPA4-mediated signaling events 0.0221 9 113 12 -0.041 0.008 1000 -1000 0 -1000
a4b1 and a4b7 Integrin signaling 0.0221 9 49 5 0.002 0.009 1000 -1000 0.006 -1000
Ceramide signaling pathway 0.0221 9 754 76 -0.12 0.028 1000 -1000 -0.008 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0221 9 346 37 -0.001 0.03 1000 -1000 0 -1000
TCGA08_rtk_signaling 0.0221 9 234 26 -0.031 0.028 1000 -1000 -0.009 -1000
E-cadherin signaling events 0.0221 9 45 5 0 0.013 1000 -1000 0.006 -1000
EPO signaling pathway 0.0196 8 443 55 -0.022 0.042 1000 -1000 -0.003 -1000
TRAIL signaling pathway 0.0196 8 405 48 0 0.038 1000 -1000 -0.011 -1000
HIF-2-alpha transcription factor network 0.0196 8 357 43 -0.12 0.12 1000 -1000 -0.078 -1000
Signaling mediated by p38-gamma and p38-delta 0.0196 8 129 15 -0.009 0.019 1000 -1000 -0.002 -1000
Retinoic acid receptors-mediated signaling 0.0196 8 484 58 -0.05 0.025 1000 -1000 -0.009 -1000
Syndecan-3-mediated signaling events 0.0196 8 284 35 -0.038 0.03 1000 -1000 -0.003 -1000
E-cadherin signaling in the nascent adherens junction 0.0196 8 643 76 -0.006 0.022 1000 -1000 -0.025 -1000
Signaling events mediated by PRL 0.0196 8 280 34 -0.039 0.03 1000 -1000 -0.003 -1000
PLK2 and PLK4 events 0.0172 7 22 3 0.011 0.016 1000 -1000 0.008 -1000
Arf6 trafficking events 0.0172 7 500 71 -0.2 0.019 1000 -1000 -0.014 -1000
ceramide signaling pathway 0.0147 6 296 49 -0.004 0.028 1000 -1000 -0.008 -1000
E-cadherin signaling in keratinocytes 0.0147 6 285 43 -0.013 0.017 1000 -1000 -0.003 -1000
Class I PI3K signaling events mediated by Akt 0.0123 5 350 68 -0.094 0.028 1000 -1000 -0.011 -1000
Paxillin-dependent events mediated by a4b1 0.0123 5 214 36 -0.02 0.022 1000 -1000 -0.021 -1000
Class I PI3K signaling events 0.0123 5 395 73 -0.011 0.02 1000 -1000 -0.003 -1000
Signaling events mediated by HDAC Class II 0.0098 4 339 75 -0.043 0.024 1000 -1000 -0.011 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0098 4 527 125 -0.024 0.033 1000 -1000 -0.022 -1000
p38 MAPK signaling pathway 0.0098 4 177 44 -0.001 0.037 1000 -1000 -0.011 -1000
Canonical NF-kappaB pathway 0.0049 2 110 39 0 0.044 1000 -1000 -0.008 -1000
Circadian rhythm pathway 0.0049 2 54 22 -0.007 0.027 1000 -1000 -0.01 -1000
Insulin-mediated glucose transport 0.0049 2 76 32 -0.11 0.027 1000 -1000 -0.004 -1000
mTOR signaling pathway 0.0049 2 150 53 -0.003 0.022 1000 -1000 -0.017 -1000
Atypical NF-kappaB pathway 0.0049 2 62 31 0 0.021 1000 -1000 -0.001 -1000
Signaling events mediated by HDAC Class I 0.0025 1 126 104 -0.02 0.035 1000 -1000 -0.014 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0025 1 39 27 0 0.03 1000 -1000 -0.015 -1000
VEGFR1 specific signals 0.0025 1 82 56 -0.02 0.036 1000 -1000 -0.002 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 14 23 0.005 0.027 1000 -1000 -0.001 -1000
Arf6 downstream pathway 0.0000 0 16 43 -0.022 0.022 1000 -1000 -0.017 -1000
Arf1 pathway 0.0000 0 6 54 0 0.019 1000 -1000 -0.002 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.03 1000 -1000 0 -1000
Total NA 4281 249111 7203 -13 -990 131000 -131000 -1.7 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.6 0.56 1.1 193 -0.92 5 198
PLK1 0.33 0.29 0.63 173 -10000 0 173
BIRC5 0.42 0.3 0.63 236 -1.3 1 237
HSPA1B 0.6 0.56 1.1 204 -0.88 6 210
MAP2K1 0.18 0.15 0.32 208 -10000 0 208
BRCA2 0.61 0.58 1.1 205 -0.88 6 211
FOXM1 0.74 0.73 1.3 213 -0.81 21 234
XRCC1 0.6 0.56 1.1 199 -0.88 6 205
FOXM1B/p19 0.14 0.42 0.88 68 -0.77 18 86
Cyclin D1/CDK4 0.5 0.49 0.91 196 -0.8 7 203
CDC2 0.67 0.64 1.2 213 -0.74 20 233
TGFA 0.52 0.5 0.94 199 -0.78 6 205
SKP2 0.6 0.56 1.1 204 -0.88 6 210
CCNE1 0.082 0.1 0.31 64 -10000 0 64
CKS1B 0.6 0.57 1.1 204 -0.88 6 210
RB1 0.026 0.21 0.7 28 -0.62 2 30
FOXM1C/SP1 0.51 0.52 0.94 197 -0.77 21 218
AURKB 0.35 0.29 0.62 195 -10000 0 195
CENPF 0.7 0.63 1.2 217 -0.87 6 223
CDK4 0.073 0.059 0.15 98 -10000 0 98
MYC 0.5 0.5 0.91 202 -0.8 9 211
CHEK2 0.18 0.15 0.31 213 -10000 0 213
ONECUT1 0.54 0.52 0.98 199 -0.85 6 205
CDKN2A 0.005 0.16 0.21 112 -0.2 99 211
LAMA4 0.59 0.59 1.1 201 -1.1 8 209
FOXM1B/HNF6 0.54 0.54 1 191 -0.96 6 197
FOS 0.32 0.7 1.1 147 -0.99 33 180
SP1 0.009 0.016 -10000 0 -10000 0 0
CDC25B 0.6 0.57 1.1 204 -0.88 6 210
response to radiation 0.13 0.11 0.23 208 -10000 0 208
CENPB 0.6 0.56 1.1 193 -0.92 5 198
CENPA 0.7 0.63 1.2 220 -0.87 6 226
NEK2 0.7 0.63 1.2 212 -0.95 4 216
HIST1H2BA 0.59 0.56 1.1 194 -0.88 6 200
CCNA2 0.11 0.13 0.32 106 -10000 0 106
EP300 0.01 0 -10000 0 -10000 0 0
CCNB1/CDK1 0.65 0.63 1.2 200 -1 6 206
CCNB2 0.7 0.63 1.2 219 -0.87 6 225
CCNB1 0.7 0.67 1.2 211 -0.93 6 217
ETV5 0.6 0.57 1.1 204 -0.91 7 211
ESR1 0.45 0.69 1.1 183 -1.1 26 209
CCND1 0.54 0.53 0.99 201 -0.84 6 207
GSK3A 0.14 0.11 0.24 194 -10000 0 194
Cyclin A-E1/CDK1-2 0.2 0.16 0.34 212 -10000 0 212
CDK2 0.044 0.033 0.12 3 -10000 0 3
G2/M transition of mitotic cell cycle 0.17 0.15 0.29 229 -10000 0 229
FOXM1B/Cbp/p300 -0.04 0.2 -10000 0 -0.73 22 22
GAS1 0.43 0.77 1.1 186 -1 53 239
MMP2 0.53 0.64 1.1 201 -0.97 16 217
RB1/FOXM1C 0.5 0.49 0.91 197 -0.85 7 204
CREBBP 0.01 0 -10000 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.14 0.095 0.22 210 -10000 0 210
STMN1 0.095 0.095 0.18 195 -10000 0 195
Aurora B/RasGAP/Survivin 0.21 0.13 0.27 296 -0.16 1 297
Chromosomal passenger complex/Cul3 protein complex 0.079 0.1 0.19 143 -0.16 23 166
BIRC5 0.2 0.12 0.28 292 -0.3 1 293
DES -0.15 0.25 0.26 1 -0.4 185 186
Aurora C/Aurora B/INCENP 0.1 0.078 0.18 194 -10000 0 194
Aurora B/TACC1 0.084 0.078 0.17 182 -0.15 1 183
Aurora B/PP2A 0.095 0.086 0.19 184 -10000 0 184
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.033 0.029 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.004 0.004 -10000 0 -10000 0 0
NDC80 0.13 0.13 0.24 212 -10000 0 212
Cul3 protein complex -0.024 0.08 -10000 0 -0.16 98 98
KIF2C 0.17 0.11 0.24 256 -10000 0 256
PEBP1 0.014 0.003 -10000 0 -10000 0 0
KIF20A 0.2 0.11 0.27 300 -10000 0 300
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.095 0.086 0.19 184 -10000 0 184
SEPT1 0.011 0.027 0.27 3 -0.29 1 4
SMC2 0.011 0.013 0.27 1 -10000 0 1
SMC4 0.01 0 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.11 0.11 0.22 182 -10000 0 182
PSMA3 0.01 0 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.006 0.005 -10000 0 -10000 0 0
H3F3B 0.067 0.062 0.14 184 -10000 0 184
AURKB 0.13 0.13 0.27 184 -10000 0 184
AURKC 0.018 0.045 0.27 13 -10000 0 13
CDCA8 0.088 0.12 0.28 109 -10000 0 109
cytokinesis 0.14 0.15 0.3 182 -0.18 1 183
Aurora B/Septin1 0.19 0.16 0.32 218 -0.16 1 219
AURKA 0.083 0.12 0.26 124 -10000 0 124
INCENP 0.02 0.014 0.28 1 -10000 0 1
KLHL13 -0.054 0.12 -10000 0 -0.29 88 88
BUB1 0.056 0.1 0.26 80 -10000 0 80
hSgo1/Aurora B/Survivin 0.26 0.17 0.33 316 -0.14 1 317
EVI5 0.016 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.18 0.16 0.34 202 -10000 0 202
SGOL1 0.12 0.13 0.27 172 -10000 0 172
CENPA 0.2 0.13 0.26 282 -10000 0 282
NCAPG 0.12 0.13 0.27 181 -10000 0 181
Aurora B/HC8 Proteasome 0.095 0.086 0.19 184 -10000 0 184
NCAPD2 0.011 0.013 0.27 1 -10000 0 1
Aurora B/PP1-gamma 0.095 0.086 0.19 184 -10000 0 184
RHOA 0.01 0 -10000 0 -10000 0 0
NCAPH 0.17 0.13 0.27 253 -10000 0 253
NPM1 0.08 0.087 0.18 184 -10000 0 184
RASA1 0.01 0 -10000 0 -10000 0 0
KLHL9 -0.001 0.056 -10000 0 -0.29 15 15
mitotic prometaphase 0.004 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.095 0.085 0.19 184 -10000 0 184
PPP1CC 0.01 0 -10000 0 -10000 0 0
Centraspindlin 0.22 0.17 0.35 236 -10000 0 236
RhoA/GDP 0.007 0 -10000 0 -10000 0 0
NSUN2 0.08 0.087 0.18 182 -10000 0 182
MYLK -0.015 0.13 0.13 119 -0.17 138 257
KIF23 0.14 0.13 0.28 202 -10000 0 202
VIM 0.076 0.079 0.16 181 -0.19 4 185
RACGAP1 0.023 0.027 0.29 4 -10000 0 4
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.08 0.087 0.18 182 -10000 0 182
Chromosomal passenger complex 0.2 0.12 0.26 287 -0.12 1 288
Chromosomal passenger complex/EVI5 0.25 0.15 0.34 266 -0.13 1 267
TACC1 0.008 0.025 -10000 0 -0.29 3 3
PPP2R5D 0.01 0 -10000 0 -10000 0 0
CUL3 0.01 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.019 0.03 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.11 0.096 -10000 0 -0.19 225 225
JUN -0.08 0.091 -10000 0 -0.16 225 225
HRAS 0.01 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.07 0.092 0.17 6 -0.15 227 233
RAP1A 0.01 0 -10000 0 -10000 0 0
FRS2 0.014 0.034 0.27 7 -10000 0 7
RAP1A/GDP 0.007 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.068 0.09 0.17 7 -0.14 225 232
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.071 0.077 -10000 0 -0.14 225 225
RHOA 0.01 0 -10000 0 -10000 0 0
RAP1A/GTP -0.059 0.079 0.14 4 -0.13 225 229
GRB7 0.014 0.062 0.27 14 -0.29 7 21
RET51/GFRalpha1/GDNF -0.068 0.09 0.17 6 -0.14 225 231
MAPKKK cascade -0.074 0.088 -10000 0 -0.15 225 225
BCAR1 0.01 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.074 0.082 -10000 0 -0.14 227 227
lamellipodium assembly -0.1 0.1 -10000 0 -0.19 229 229
RET51/GFRalpha1/GDNF/SHC -0.068 0.09 0.17 6 -0.14 224 230
PIK3CA 0.01 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.071 0.077 -10000 0 -0.14 224 224
RET9/GFRalpha1/GDNF/Shank3 -0.071 0.077 -10000 0 -0.14 225 225
MAPK3 -0.06 0.07 -10000 0 -0.12 225 225
DOK1 0.011 0.013 0.27 1 -10000 0 1
DOK6 -0.098 0.14 -10000 0 -0.29 148 148
PXN 0.01 0 -10000 0 -10000 0 0
neurite development -0.079 0.081 -10000 0 -0.18 109 109
DOK5 -0.015 0.089 0.27 3 -0.29 37 40
GFRA1 -0.16 0.15 -10000 0 -0.29 228 228
MAPK8 -0.082 0.092 -10000 0 -0.16 225 225
HRAS/GTP -0.081 0.1 -10000 0 -0.17 225 225
tube development -0.064 0.072 -10000 0 -0.13 225 225
MAPK1 -0.06 0.07 -10000 0 -0.12 225 225
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.086 0.091 -10000 0 -0.17 222 222
Rac1/GDP 0.007 0 -10000 0 -10000 0 0
SRC 0.01 0 -10000 0 -10000 0 0
PDLIM7 0.01 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.11 0.12 0.17 5 -0.18 267 272
SHC1 0.011 0.013 0.27 1 -10000 0 1
RET51/GFRalpha1/GDNF/Dok4 -0.068 0.09 0.17 6 -0.14 225 231
RET51/GFRalpha1/GDNF/Dok5 -0.081 0.1 0.18 8 -0.16 234 242
PRKCA 0.006 0.033 -10000 0 -0.29 5 5
HRAS/GDP 0.007 0 -10000 0 -10000 0 0
CREB1 -0.11 0.12 -10000 0 -0.21 223 223
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.087 0.09 -10000 0 -0.17 224 224
RET51/GFRalpha1/GDNF/Grb7 -0.068 0.093 0.17 9 -0.15 217 226
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.006 0.059 0.27 7 -0.29 11 18
DOK4 0.01 0 -10000 0 -10000 0 0
JNK cascade -0.079 0.09 -10000 0 -0.16 225 225
RET9/GFRalpha1/GDNF/FRS2 -0.069 0.08 0.17 4 -0.14 222 226
SHANK3 0.01 0 -10000 0 -10000 0 0
RASA1 0.01 0 -10000 0 -10000 0 0
NCK1 0.01 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.088 0.09 -10000 0 -0.17 224 224
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.087 0.1 0.2 1 -0.17 222 223
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.088 0.099 -10000 0 -0.17 225 225
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.089 0.1 -10000 0 -0.18 224 224
PI3K -0.14 0.15 -10000 0 -0.26 229 229
SOS1 0.01 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.063 0.074 -10000 0 -0.13 225 225
GRB10 0.006 0.033 -10000 0 -0.29 5 5
activation of MAPKK activity -0.08 0.092 0.16 1 -0.16 221 222
RET51/GFRalpha1/GDNF/FRS2 -0.066 0.093 0.19 9 -0.14 222 231
GAB1 0.01 0 -10000 0 -10000 0 0
IRS1 0.003 0.046 -10000 0 -0.29 10 10
IRS2 -0.002 0.058 -10000 0 -0.29 16 16
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.089 0.1 -10000 0 -0.18 224 224
RET51/GFRalpha1/GDNF/PKC alpha -0.07 0.092 0.17 6 -0.15 225 231
GRB2 0.01 0 -10000 0 -10000 0 0
PRKACA 0.01 0 -10000 0 -10000 0 0
GDNF 0.007 0.023 0.27 3 -10000 0 3
RAC1 0.01 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.072 0.094 0.17 6 -0.15 227 233
Rac1/GTP -0.12 0.12 -10000 0 -0.22 226 226
RET9/GFRalpha1/GDNF -0.084 0.084 -10000 0 -0.16 225 225
GFRalpha1/GDNF -0.1 0.1 -10000 0 -0.19 225 225
Glypican 2 network

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
MDK 0.025 0.06 0.27 23 -9999 0 23
GPC2 0.099 0.12 0.27 140 -9999 0 140
GPC2/Midkine 0.086 0.098 0.21 151 -9999 0 151
neuron projection morphogenesis 0.086 0.098 0.21 151 -9999 0 151
TCGA08_retinoblastoma

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
CDKN2B 0.016 0.078 0.27 22 -0.28 11 33
CDKN2C -0.003 0.025 0.27 2 -10000 0 2
CDKN2A 0.14 0.14 0.27 201 -0.26 4 205
CCND2 -0.051 0.065 0.17 7 -0.1 198 205
RB1 0.055 0.071 0.11 200 -0.19 8 208
CDK4 -0.056 0.069 0.18 7 -0.19 34 41
CDK6 -0.058 0.072 0.19 7 -0.2 42 49
G1/S progression -0.055 0.072 0.17 12 -0.19 39 51
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.024 0.064 0.35 13 -10000 0 13
NFATC2 -0.093 0.22 0.37 4 -0.46 70 74
NFATC3 -0.094 0.13 -10000 0 -0.25 142 142
CD40LG -0.39 0.48 0.46 2 -0.82 204 206
ITCH 0 0.062 0.32 1 -0.17 43 44
CBLB 0 0.061 -10000 0 -0.17 43 43
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.26 0.44 0.53 17 -0.75 129 146
JUNB 0.006 0.033 -10000 0 -0.29 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.075 0.19 4 -0.21 43 47
T cell anergy -0.035 0.1 0.22 1 -0.31 43 44
TLE4 -0.066 0.17 -10000 0 -0.38 64 64
Jun/NFAT1-c-4/p21SNFT -0.35 0.5 0.48 4 -0.81 202 206
AP-1/NFAT1-c-4 -0.42 0.57 0.62 6 -0.94 196 202
IKZF1 -0.062 0.17 0.38 2 -0.36 65 67
T-helper 2 cell differentiation -0.2 0.32 -10000 0 -0.78 74 74
AP-1/NFAT1 -0.091 0.19 0.33 8 -0.3 137 145
CALM1 0.002 0.045 -10000 0 -10000 0 0
EGR2 -0.44 0.61 -10000 0 -1 178 178
EGR3 -0.6 0.7 -10000 0 -1.3 202 202
NFAT1/FOXP3 -0.044 0.19 0.42 19 -0.33 66 85
EGR1 -0.061 0.13 -10000 0 -0.29 99 99
JUN 0.001 0.06 -10000 0 -0.29 15 15
EGR4 0.007 0.062 0.27 7 -0.29 12 19
mol:Ca2+ -0.007 0.043 -10000 0 -0.13 43 43
GBP3 -0.06 0.16 -10000 0 -0.36 53 53
FOSL1 -0.011 0.075 -10000 0 -0.29 28 28
NFAT1-c-4/MAF/IRF4 -0.36 0.48 0.46 1 -0.81 202 203
DGKA -0.057 0.15 -10000 0 -0.34 53 53
CREM 0.01 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.37 0.48 -10000 0 -0.83 202 202
CTLA4 -0.041 0.16 0.44 14 -0.32 51 65
NFAT1-c-4 (dimer)/EGR1 -0.39 0.52 0.49 3 -0.88 201 204
NFAT1-c-4 (dimer)/EGR4 -0.36 0.5 0.49 3 -0.83 202 205
FOS -0.066 0.13 -10000 0 -0.29 103 103
IFNG -0.12 0.31 0.4 19 -0.65 65 84
T cell activation -0.19 0.27 -10000 0 -0.52 120 120
MAF 0.002 0.048 -10000 0 -0.29 11 11
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.32 0.43 0.71 199 -10000 0 199
TNF -0.35 0.47 0.46 11 -0.79 201 212
FASLG -0.61 0.75 -10000 0 -1.3 207 207
TBX21 0.017 0.088 0.16 10 -0.29 23 33
BATF3 0.009 0.042 0.27 4 -0.29 5 9
PRKCQ -0.013 0.089 0.27 4 -0.29 35 39
PTPN1 -0.057 0.15 -10000 0 -0.32 64 64
NFAT1-c-4/ICER1 -0.36 0.49 0.43 1 -0.82 201 202
GATA3 -0.008 0.077 0.27 2 -0.29 27 29
T-helper 1 cell differentiation -0.12 0.3 0.4 19 -0.64 66 85
IL2RA -0.26 0.42 0.51 17 -0.7 147 164
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.057 0.15 -10000 0 -0.32 65 65
E2F1 0.074 0.11 0.27 97 -10000 0 97
PPARG -0.008 0.075 0.27 2 -0.29 26 28
SLC3A2 -0.057 0.15 -10000 0 -0.32 65 65
IRF4 -0.009 0.08 0.27 3 -0.29 29 32
PTGS2 -0.4 0.49 0.46 2 -0.84 205 207
CSF2 -0.35 0.5 0.52 16 -0.81 198 214
JunB/Fra1/NFAT1-c-4 -0.36 0.48 -10000 0 -0.8 201 201
IL4 -0.21 0.34 -10000 0 -0.83 73 73
IL5 -0.38 0.47 0.5 4 -0.8 203 207
IL2 -0.2 0.28 -10000 0 -0.54 117 117
IL3 -0.071 0.064 -10000 0 -10000 0 0
RNF128 -0.022 0.13 0.32 3 -0.39 43 46
NFATC1 -0.32 0.44 -10000 0 -0.72 199 199
CDK4 0.22 0.28 0.55 123 -10000 0 123
PTPRK -0.058 0.15 -10000 0 -0.33 61 61
IL8 -0.39 0.48 0.46 2 -0.82 204 206
POU2F1 0.01 0.001 -10000 0 -10000 0 0
IGF1 pathway

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
NCK2 0.01 0 -10000 0 -10000 0 0
PTK2 0.01 0 -10000 0 -10000 0 0
CRKL -0.061 0.082 0.15 2 -0.15 183 185
GRB2/SOS1/SHC 0.021 0.008 0.18 1 -10000 0 1
HRAS 0.01 0 -10000 0 -10000 0 0
IRS1/Crk -0.06 0.083 -10000 0 -0.15 183 183
IGF-1R heterotetramer/IGF1/PTP1B -0.059 0.087 -10000 0 -0.15 183 183
AKT1 -0.049 0.07 -10000 0 -0.12 183 183
BAD -0.046 0.066 -10000 0 -0.12 183 183
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.062 0.081 -10000 0 -0.15 183 183
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.06 0.084 -10000 0 -0.15 183 183
RAF1 -0.04 0.066 -10000 0 -0.2 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.05 0.083 -10000 0 -0.14 183 183
YWHAZ 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.067 0.091 -10000 0 -0.17 183 183
PIK3CA 0.01 0 -10000 0 -10000 0 0
RPS6KB1 -0.049 0.07 -10000 0 -0.12 183 183
GNB2L1 0.01 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.038 0.059 -10000 0 -0.17 10 10
PXN 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.015 0 -10000 0 -10000 0 0
HRAS/GTP -0.049 0.069 -10000 0 -0.12 182 182
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.035 0.073 -10000 0 -0.12 182 182
IGF-1R heterotetramer -0.016 0.035 -10000 0 -0.13 9 9
IGF-1R heterotetramer/IGF1/IRS/Nck -0.057 0.086 -10000 0 -0.15 183 183
Crk/p130 Cas/Paxillin -0.046 0.08 -10000 0 -0.13 183 183
IGF1R -0.016 0.035 -10000 0 -0.13 9 9
IGF1 -0.002 0.05 -10000 0 -0.34 9 9
IRS2/Crk -0.06 0.087 -10000 0 -0.15 184 184
PI3K -0.05 0.083 -10000 0 -0.14 183 183
apoptosis 0.038 0.062 0.1 183 -10000 0 183
HRAS/GDP 0.007 0 -10000 0 -10000 0 0
PRKCD -0.11 0.14 -10000 0 -0.26 183 183
RAF1/14-3-3 E -0.033 0.062 -10000 0 -0.19 4 4
BAD/14-3-3 -0.04 0.065 -10000 0 -0.11 183 183
PRKCZ -0.05 0.071 -10000 0 -0.13 183 183
Crk/p130 Cas/Paxillin/FAK1 -0.037 0.066 -10000 0 -0.19 10 10
PTPN1 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.15 -10000 0 -0.28 183 183
BCAR1 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.046 0.08 -10000 0 -0.13 184 184
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.01 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.059 0.083 -10000 0 -0.15 183 183
GRB10 0.006 0.033 -10000 0 -0.29 5 5
PTPN11 -0.062 0.081 -10000 0 -0.15 183 183
IRS1 -0.069 0.089 -10000 0 -0.17 183 183
IRS2 -0.066 0.09 -10000 0 -0.16 183 183
IGF-1R heterotetramer/IGF1 -0.088 0.11 -10000 0 -0.21 183 183
GRB2 0.01 0 -10000 0 -10000 0 0
PDPK1 -0.052 0.074 -10000 0 -0.13 183 183
YWHAE 0.009 0.015 -10000 0 -0.29 1 1
PRKD1 -0.11 0.15 -10000 0 -0.27 183 183
SHC1 0.011 0.013 0.27 1 -10000 0 1
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.076 0.12 0.26 2 -0.3 58 60
PTK2B 0.009 0.015 -10000 0 -0.29 1 1
mol:Ca2+ -0.093 0.17 -10000 0 -0.53 36 36
EDN1 -0.036 0.066 0.21 7 -0.2 22 29
EDN3 0.008 0.035 0.27 7 -10000 0 7
EDN2 0.011 0.099 0.27 29 -0.29 23 52
HRAS/GDP -0.13 0.17 -10000 0 -0.31 151 151
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.088 0.13 -10000 0 -0.26 108 108
ADCY4 -0.12 0.12 0.18 2 -0.25 143 145
ADCY5 -0.17 0.16 0.18 2 -0.29 229 231
ADCY6 -0.12 0.12 0.18 2 -0.25 142 144
ADCY7 -0.12 0.12 0.18 2 -0.25 142 144
ADCY1 -0.11 0.12 0.18 2 -0.25 141 143
ADCY2 -0.16 0.15 0.18 2 -0.28 209 211
ADCY3 -0.12 0.12 0.18 2 -0.25 142 144
ADCY8 -0.12 0.12 0.17 4 -0.25 141 145
ADCY9 -0.12 0.13 0.18 2 -0.25 144 146
arachidonic acid secretion -0.19 0.24 -10000 0 -0.45 157 157
ETB receptor/Endothelin-1/Gq/GTP -0.06 0.12 -10000 0 -0.25 88 88
GNAO1 -0.084 0.14 -10000 0 -0.29 129 129
HRAS 0.009 0.002 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.066 0.11 0.31 2 -0.28 55 57
ETA receptor/Endothelin-1/Gs/GTP -0.12 0.13 0.29 2 -0.26 138 140
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
COL3A1 -0.079 0.14 0.43 2 -0.36 52 54
EDNRB -0.029 0.097 -10000 0 -0.29 47 47
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.071 0.12 0.29 5 -0.32 52 57
CYSLTR1 -0.083 0.14 0.28 3 -0.37 56 59
SLC9A1 -0.051 0.073 0.18 2 -0.2 53 55
mol:GDP -0.14 0.18 -10000 0 -0.33 153 153
SLC9A3 -0.096 0.2 -10000 0 -0.53 57 57
RAF1 -0.17 0.21 -10000 0 -0.39 171 171
JUN -0.11 0.23 -10000 0 -0.76 35 35
JAK2 -0.076 0.12 0.26 2 -0.31 58 60
mol:IP3 -0.094 0.14 -10000 0 -0.31 95 95
ETA receptor/Endothelin-1 -0.092 0.14 0.37 2 -0.36 58 60
PLCB1 -0.002 0.051 -10000 0 -0.29 12 12
PLCB2 0.004 0.022 -10000 0 -0.29 2 2
ETA receptor/Endothelin-3 -0.049 0.094 0.2 2 -0.24 62 64
FOS -0.3 0.4 -10000 0 -0.84 141 141
Gai/GDP -0.25 0.36 -10000 0 -0.78 129 129
CRK 0.01 0 -10000 0 -10000 0 0
mol:Ca ++ -0.13 0.17 0.26 2 -0.35 117 119
BCAR1 0.01 0 -10000 0 -10000 0 0
PRKCB1 -0.094 0.14 -10000 0 -0.3 99 99
GNAQ 0.005 0.009 -10000 0 -10000 0 0
GNAZ -0.055 0.12 -10000 0 -0.29 89 89
GNAL -0.12 0.15 -10000 0 -0.29 178 178
Gs family/GDP -0.18 0.18 -10000 0 -0.34 185 185
ETA receptor/Endothelin-1/Gq/GTP -0.089 0.13 -10000 0 -0.28 104 104
MAPK14 -0.059 0.11 -10000 0 -0.24 86 86
TRPC6 -0.096 0.18 -10000 0 -0.56 35 35
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.025 -10000 0 -0.29 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.064 0.12 -10000 0 -0.25 90 90
ETB receptor/Endothelin-2 -0.012 0.096 0.19 24 -0.21 61 85
ETB receptor/Endothelin-3 -0.013 0.072 0.19 7 -0.2 47 54
ETB receptor/Endothelin-1 -0.043 0.088 0.26 2 -0.22 64 66
MAPK3 -0.28 0.36 -10000 0 -0.72 152 152
MAPK1 -0.28 0.36 -10000 0 -0.72 152 152
Rac1/GDP -0.13 0.16 -10000 0 -0.31 151 151
cAMP biosynthetic process -0.19 0.16 -10000 0 -0.3 233 233
MAPK8 -0.11 0.19 -10000 0 -0.54 48 48
SRC 0.01 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.11 0.15 -10000 0 -0.25 180 180
p130Cas/CRK/Src/PYK2 -0.12 0.18 -10000 0 -0.4 85 85
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.13 0.16 -10000 0 -0.31 150 150
COL1A2 -0.11 0.2 0.45 2 -0.46 70 72
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.049 0.11 0.2 6 -0.23 88 94
mol:DAG -0.094 0.14 -10000 0 -0.31 95 95
MAP2K2 -0.22 0.28 -10000 0 -0.54 156 156
MAP2K1 -0.22 0.28 -10000 0 -0.54 156 156
EDNRA -0.081 0.13 0.18 2 -0.32 74 76
positive regulation of muscle contraction -0.063 0.1 0.22 2 -0.26 58 60
Gq family/GDP -0.12 0.17 -10000 0 -0.35 109 109
HRAS/GTP -0.14 0.17 -10000 0 -0.31 156 156
PRKCH -0.093 0.14 -10000 0 -0.3 98 98
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA -0.094 0.14 -10000 0 -0.3 102 102
PRKCB -0.13 0.16 -10000 0 -0.32 135 135
PRKCE -0.092 0.14 -10000 0 -0.3 97 97
PRKCD -0.094 0.14 -10000 0 -0.3 99 99
PRKCG -0.093 0.14 -10000 0 -0.3 98 98
regulation of vascular smooth muscle contraction -0.36 0.48 -10000 0 -0.99 141 141
PRKCQ -0.1 0.15 -10000 0 -0.3 111 111
PLA2G4A -0.2 0.26 -10000 0 -0.49 157 157
GNA14 -0.037 0.1 -10000 0 -0.29 58 58
GNA15 0.005 0.026 -10000 0 -0.29 3 3
GNA12 0.01 0 -10000 0 -10000 0 0
GNA11 0.007 0.016 -10000 0 -0.29 1 1
Rac1/GTP -0.066 0.11 0.31 2 -0.29 54 56
MMP1 0.19 0.15 0.31 221 -0.55 1 222
Nongenotropic Androgen signaling

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
PTK2 0.005 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.042 0.078 -10000 0 -0.14 152 152
regulation of S phase of mitotic cell cycle -0.055 0.087 -10000 0 -0.17 149 149
GNAO1 -0.085 0.14 -10000 0 -0.29 129 129
HRAS 0.009 0.002 -10000 0 -10000 0 0
SHBG/T-DHT 0.006 0.001 -10000 0 -10000 0 0
PELP1 0.009 0.002 -10000 0 -10000 0 0
AKT1 0.005 0 -10000 0 -10000 0 0
MAP2K1 -0.067 0.083 -10000 0 -0.14 222 222
T-DHT/AR -0.069 0.096 -10000 0 -0.2 148 148
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.002 0.003 -10000 0 -0.006 129 129
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.025 -10000 0 -0.29 3 3
mol:GDP -0.1 0.14 -10000 0 -0.29 149 149
cell proliferation -0.15 0.19 -10000 0 -0.42 129 129
PIK3CA 0.01 0 -10000 0 -10000 0 0
FOS -0.24 0.34 -10000 0 -0.74 129 129
mol:Ca2+ -0.032 0.035 -10000 0 -0.07 166 166
MAPK3 -0.12 0.14 -10000 0 -0.3 129 129
MAPK1 -0.073 0.097 -10000 0 -0.21 129 129
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
mol:IP3 -0.001 0.002 -10000 0 -0.004 129 129
cAMP biosynthetic process 0.022 0.026 0.061 105 -10000 0 105
GNG2 0.006 0.036 -10000 0 -0.29 6 6
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 129 129
HRAS/GTP -0.051 0.074 -10000 0 -0.14 148 148
actin cytoskeleton reorganization 0.014 0.007 -10000 0 -0.12 1 1
SRC 0.009 0.002 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 129 129
PI3K 0.013 0.009 -10000 0 -0.16 1 1
apoptosis 0.14 0.19 0.42 129 -10000 0 129
T-DHT/AR/PELP1 -0.055 0.082 -10000 0 -0.16 148 148
HRAS/GDP -0.098 0.14 -10000 0 -0.28 149 149
CREB1 -0.15 0.21 -10000 0 -0.45 129 129
RAC1-CDC42/GTP 0.018 0.007 -10000 0 -0.13 1 1
AR -0.1 0.14 -10000 0 -0.29 148 148
GNB1 0.01 0 -10000 0 -10000 0 0
RAF1 -0.06 0.075 -10000 0 -0.14 147 147
RAC1-CDC42/GDP -0.086 0.14 -10000 0 -0.27 148 148
T-DHT/AR/PELP1/Src -0.048 0.076 -10000 0 -0.15 148 148
MAP2K2 -0.067 0.083 -10000 0 -0.14 222 222
T-DHT/AR/PELP1/Src/PI3K -0.055 0.088 -10000 0 -0.17 149 149
GNAZ -0.055 0.12 -10000 0 -0.29 89 89
SHBG 0.009 0.002 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.13 0.17 -10000 0 -0.34 147 147
mol:T-DHT 0 0.001 -10000 0 -0.002 46 46
RAC1 0.01 0 -10000 0 -10000 0 0
GNRH1 0.005 0 -10000 0 -10000 0 0
Gi family/GTP -0.11 0.13 -10000 0 -0.24 164 164
CDC42 0.01 0 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.19 0.39 -10000 0 -0.87 100 100
MKNK1 0.01 0 -10000 0 -10000 0 0
MAPK14 -0.046 0.14 -10000 0 -0.27 105 105
ATF2/c-Jun -0.048 0.14 -10000 0 -0.51 20 20
MAPK11 -0.046 0.14 -10000 0 -0.27 105 105
MITF -0.074 0.18 -10000 0 -0.35 101 101
MAPKAPK5 -0.056 0.16 -10000 0 -0.32 98 98
KRT8 -0.061 0.17 -10000 0 -0.34 99 99
MAPKAPK3 0.01 0 -10000 0 -10000 0 0
MAPKAPK2 0.01 0 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.067 0.19 -10000 0 -0.38 105 105
CEBPB -0.057 0.16 -10000 0 -0.33 98 98
SLC9A1 -0.056 0.16 -10000 0 -0.32 98 98
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.055 0.16 -10000 0 -0.32 98 98
p38alpha-beta/MNK1 -0.045 0.16 -10000 0 -0.31 98 98
JUN -0.048 0.14 -10000 0 -0.54 18 18
PPARGC1A -0.16 0.21 -10000 0 -0.32 217 217
USF1 -0.056 0.16 -10000 0 -0.32 98 98
RAB5/GDP/GDI1 -0.04 0.11 -10000 0 -0.23 98 98
NOS2 -0.048 0.21 0.33 28 -0.62 16 44
DDIT3 -0.056 0.16 -10000 0 -0.32 98 98
RAB5A 0.01 0 -10000 0 -10000 0 0
HSPB1 -0.046 0.13 -10000 0 -0.26 105 105
p38alpha-beta/HBP1 -0.045 0.16 -10000 0 -0.31 98 98
CREB1 -0.065 0.18 -10000 0 -0.35 105 105
RAB5/GDP 0.007 0 -10000 0 -10000 0 0
EIF4E -0.047 0.13 -10000 0 -0.27 98 98
RPS6KA4 -0.056 0.16 -10000 0 -0.32 98 98
PLA2G4A -0.054 0.14 -10000 0 -0.29 100 100
GDI1 -0.056 0.16 -10000 0 -0.32 98 98
TP53 -0.074 0.19 -10000 0 -0.38 105 105
RPS6KA5 -0.062 0.17 -10000 0 -0.34 102 102
ESR1 -0.1 0.2 -10000 0 -0.34 144 144
HBP1 0.01 0 -10000 0 -10000 0 0
MEF2C -0.064 0.17 -10000 0 -0.34 100 100
MEF2A -0.056 0.16 -10000 0 -0.32 98 98
EIF4EBP1 -0.062 0.18 0.23 1 -0.35 105 106
KRT19 -0.067 0.17 -10000 0 -0.35 98 98
ELK4 -0.056 0.16 -10000 0 -0.32 98 98
ATF6 -0.056 0.16 -10000 0 -0.32 98 98
ATF1 -0.065 0.18 -10000 0 -0.35 105 105
p38alpha-beta/MAPKAPK2 -0.045 0.16 -10000 0 -0.31 98 98
p38alpha-beta/MAPKAPK3 -0.045 0.16 -10000 0 -0.31 98 98
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.008 0.021 -10000 0 -0.29 2 2
LAT2 -0.077 0.13 0.18 1 -0.22 162 163
AP1 -0.12 0.18 -10000 0 -0.37 104 104
mol:PIP3 -0.092 0.15 0.19 3 -0.29 124 127
IKBKB -0.07 0.1 0.14 3 -0.2 142 145
AKT1 -0.041 0.079 -10000 0 -0.16 102 102
IKBKG -0.07 0.1 0.14 3 -0.2 142 145
MS4A2 -0.072 0.13 -10000 0 -0.29 111 111
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.009 0.001 -10000 0 -10000 0 0
MAP3K1 -0.075 0.14 -10000 0 -0.25 123 123
mol:Ca2+ -0.071 0.12 0.17 3 -0.22 124 127
LYN 0.009 0.003 -10000 0 -10000 0 0
CBLB -0.077 0.13 -10000 0 -0.21 162 162
SHC1 0.011 0.013 0.27 1 -10000 0 1
RasGAP/p62DOK -0.027 0.072 -10000 0 -0.14 118 118
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.005 0.039 -10000 0 -0.29 7 7
PLD2 -0.053 0.088 -10000 0 -0.15 166 166
PTPN13 -0.085 0.14 -10000 0 -0.36 58 58
PTPN11 0.005 0.01 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.051 0.097 -10000 0 -0.23 59 59
SYK 0.006 0.031 -10000 0 -0.3 4 4
GRB2 0.01 0.001 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.14 -10000 0 -0.29 124 124
LAT -0.076 0.13 0.18 1 -0.21 162 163
PAK2 -0.084 0.15 -10000 0 -0.28 123 123
NFATC2 -0.097 0.17 -10000 0 -0.46 72 72
HRAS -0.091 0.16 -10000 0 -0.3 125 125
GAB2 0.009 0.015 -10000 0 -0.29 1 1
PLA2G1B 0.022 0.017 -10000 0 -10000 0 0
Fc epsilon R1 -0.067 0.12 0.18 7 -0.2 165 172
Antigen/IgE/Fc epsilon R1 -0.057 0.11 0.17 7 -0.17 165 172
mol:GDP -0.1 0.18 0.18 2 -0.32 125 127
JUN -0.002 0.058 -10000 0 -0.29 16 16
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
FOS -0.084 0.14 -10000 0 -0.29 129 129
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.082 0.13 0.14 1 -0.23 163 164
CHUK -0.07 0.1 0.14 3 -0.2 142 145
KLRG1 -0.064 0.11 0.16 1 -0.18 161 162
VAV1 -0.08 0.13 -10000 0 -0.22 162 162
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.077 0.13 -10000 0 -0.21 162 162
negative regulation of mast cell degranulation -0.06 0.11 0.15 1 -0.18 159 160
BTK -0.11 0.19 -10000 0 -0.35 122 122
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.09 0.15 -10000 0 -0.24 172 172
GAB2/PI3K/SHP2 -0.055 0.076 -10000 0 -0.17 103 103
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.079 0.14 -10000 0 -0.25 120 120
RAF1 0.02 0.02 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.056 0.12 0.17 8 -0.21 120 128
FCER1G 0.02 0.057 0.27 14 -0.29 4 18
FCER1A -0.069 0.14 0.27 1 -0.3 104 105
Antigen/IgE/Fc epsilon R1/Fyn -0.05 0.1 0.16 7 -0.16 166 173
MAPK3 0.021 0.017 -10000 0 -10000 0 0
MAPK1 0.021 0.017 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 -0.018 0.068 -10000 0 -0.55 3 3
DUSP1 -0.077 0.14 -10000 0 -0.29 119 119
NF-kappa-B/RelA -0.043 0.064 -10000 0 -0.14 108 108
actin cytoskeleton reorganization -0.086 0.15 -10000 0 -0.38 54 54
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.077 0.14 -10000 0 -0.26 123 123
FER -0.077 0.13 -10000 0 -0.22 162 162
RELA 0.01 0 -10000 0 -10000 0 0
ITK -0.05 0.12 -10000 0 -0.25 82 82
SOS1 0.01 0 -10000 0 -10000 0 0
PLCG1 -0.098 0.17 0.18 2 -0.32 125 127
cytokine secretion -0.032 0.047 -10000 0 -0.1 87 87
SPHK1 -0.067 0.13 0.18 6 -0.22 150 156
PTK2 -0.089 0.15 -10000 0 -0.39 54 54
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.15 -10000 0 -0.3 123 123
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.09 0.15 0.17 3 -0.29 123 126
MAP2K2 0.02 0.018 -10000 0 -10000 0 0
MAP2K1 0.02 0.018 -10000 0 -10000 0 0
MAP2K7 0.01 0 -10000 0 -10000 0 0
KLRG1/SHP2 -0.054 0.099 -10000 0 -0.19 104 104
MAP2K4 0.009 0.009 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.062 0.12 0.17 8 -0.18 174 182
mol:Choline -0.052 0.088 -10000 0 -0.15 166 166
SHC/Grb2/SOS1 -0.062 0.12 -10000 0 -0.23 115 115
FYN 0.008 0.025 -10000 0 -0.29 3 3
DOK1 0.011 0.013 0.27 1 -10000 0 1
PXN -0.083 0.14 -10000 0 -0.36 54 54
HCLS1 -0.077 0.13 -10000 0 -0.22 162 162
PRKCB -0.099 0.14 0.16 3 -0.27 142 145
FCGR2B -0.008 0.078 0.27 3 -0.29 27 30
IGHE -0.002 0.003 -10000 0 -10000 0 0
KLRG1/SHIP -0.061 0.11 0.15 1 -0.18 159 160
LCP2 0.007 0.026 -10000 0 -0.29 3 3
PLA2G4A -0.083 0.14 -10000 0 -0.23 162 162
RASA1 0.01 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.052 0.088 -10000 0 -0.15 166 166
IKK complex -0.05 0.08 0.13 3 -0.16 108 111
WIPF1 0.001 0.05 -10000 0 -0.29 12 12
Signaling events mediated by the Hedgehog family

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
TGFB2 0.001 0.19 0.29 43 -0.46 48 91
IHH 0.038 0.083 0.22 47 -0.1 31 78
SHH Np/Cholesterol/GAS1 -0.078 0.089 -10000 0 -0.16 219 219
LRPAP1 0.011 0.013 0.27 1 -10000 0 1
dorsoventral neural tube patterning 0.078 0.088 0.15 219 -10000 0 219
SMO/beta Arrestin2 -0.017 0.13 0.25 1 -0.32 45 46
SMO -0.02 0.14 0.27 1 -0.34 45 46
AKT1 0.003 0.075 -10000 0 -0.26 8 8
ARRB2 0.01 0 -10000 0 -10000 0 0
BOC -0.016 0.087 0.27 1 -0.29 37 38
ADRBK1 0.01 0 -10000 0 -10000 0 0
heart looping -0.02 0.14 0.27 1 -0.33 45 46
STIL -0.02 0.11 0.24 9 -0.23 45 54
DHH N/PTCH2 -0.005 0.062 -10000 0 -0.2 38 38
DHH N/PTCH1 0.007 0.11 0.25 1 -0.25 48 49
PIK3CA 0.01 0 -10000 0 -10000 0 0
DHH -0.005 0.063 -10000 0 -0.29 19 19
PTHLH -0.027 0.28 0.34 40 -0.74 48 88
determination of left/right symmetry -0.02 0.14 0.27 1 -0.33 45 46
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
skeletal system development -0.026 0.28 0.34 40 -0.73 48 88
IHH N/Hhip -0.032 0.12 0.17 26 -0.21 107 133
DHH N/Hhip -0.048 0.1 0.19 2 -0.2 119 121
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.02 0.14 0.27 1 -0.33 45 46
pancreas development -0.067 0.13 0.27 2 -0.29 105 107
HHAT 0.01 0 -10000 0 -10000 0 0
PI3K 0.014 0.01 -10000 0 -0.19 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.059 0.13 0.27 2 -0.29 96 98
somite specification -0.02 0.14 0.27 1 -0.33 45 46
SHH Np/Cholesterol/PTCH1 -0.038 0.11 0.23 1 -0.25 51 52
SHH Np/Cholesterol/PTCH2 -0.051 0.079 -10000 0 -0.14 163 163
SHH Np/Cholesterol/Megalin -0.019 0.094 0.17 48 -0.14 114 162
SHH -0.066 0.096 -10000 0 -0.19 150 150
catabolic process 0.013 0.12 0.22 29 -0.27 48 77
SMO/Vitamin D3 -0.039 0.13 0.29 1 -0.31 45 46
SHH Np/Cholesterol/Hhip -0.081 0.099 0.17 1 -0.17 210 211
LRP2 0.062 0.1 0.27 84 -10000 0 84
receptor-mediated endocytosis -0.035 0.13 0.23 5 -0.31 37 42
SHH Np/Cholesterol/BOC -0.057 0.083 0.17 1 -0.15 175 176
SHH Np/Cholesterol/CDO -0.064 0.084 -10000 0 -0.15 194 194
mesenchymal cell differentiation 0.081 0.098 0.17 210 -0.17 1 211
mol:Vitamin D3 -0.031 0.12 0.2 23 -0.27 41 64
IHH N/PTCH2 0.018 0.074 0.16 32 -0.2 25 57
CDON -0.032 0.1 -10000 0 -0.29 57 57
IHH N/PTCH1 0.024 0.13 0.25 40 -0.27 48 88
Megalin/LRPAP1 0.051 0.072 0.19 85 -10000 0 85
PTCH2 -0.005 0.064 -10000 0 -0.29 20 20
SHH Np/Cholesterol -0.047 0.072 -10000 0 -0.14 150 150
PTCH1 0.013 0.12 0.22 29 -0.27 48 77
HHIP -0.067 0.13 0.27 2 -0.29 105 107
Syndecan-1-mediated signaling events

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
TGFB1 0.01 0 -10000 0 -10000 0 0
CCL5 0.004 0.08 0.27 13 -0.29 20 33
SDCBP 0.01 0 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.084 0.1 0.2 123 -0.18 23 146
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.078 0.091 0.18 123 -0.2 11 134
Syndecan-1/Syntenin 0.078 0.091 0.18 123 -0.21 10 133
MAPK3 0.077 0.085 0.17 123 -0.19 10 133
HGF/MET -0.026 0.09 0.19 9 -0.19 87 96
TGFB1/TGF beta receptor Type II 0.01 0 -10000 0 -10000 0 0
BSG 0.01 0 -10000 0 -10000 0 0
keratinocyte migration 0.077 0.09 0.17 123 -0.2 11 134
Syndecan-1/RANTES 0.079 0.11 0.19 126 -0.24 16 142
Syndecan-1/CD147 0.077 0.086 0.21 39 -0.2 10 49
Syndecan-1/Syntenin/PIP2 0.023 0.061 -10000 0 -0.2 10 10
LAMA5 0.01 0 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.023 0.059 -10000 0 -0.2 10 10
MMP7 0.044 0.13 0.27 78 -0.29 21 99
HGF -0.049 0.13 0.27 7 -0.29 87 94
Syndecan-1/CASK 0.071 0.09 0.17 123 -0.17 23 146
Syndecan-1/HGF/MET 0.055 0.11 0.23 40 -0.25 20 60
regulation of cell adhesion 0.076 0.084 0.17 123 -0.23 5 128
HPSE 0.031 0.079 0.27 37 -0.29 3 40
positive regulation of cell migration 0.084 0.1 0.2 123 -0.18 23 146
SDC1 0.084 0.1 0.2 123 -0.18 23 146
Syndecan-1/Collagen 0.084 0.1 0.2 123 -0.18 23 146
PPIB 0.01 0 -10000 0 -10000 0 0
MET 0.011 0.018 0.27 2 -10000 0 2
PRKACA 0.01 0 -10000 0 -10000 0 0
MMP9 0.069 0.12 0.27 102 -0.29 8 110
MAPK1 0.077 0.085 0.21 42 -0.24 5 47
homophilic cell adhesion 0.084 0.1 0.2 123 -0.18 23 146
MMP1 0.16 0.13 0.27 230 -0.29 1 231
Reelin signaling pathway

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
CDK5R1/CDK5 0.024 0.04 0.19 22 -10000 0 22
VLDLR 0.003 0.046 -10000 0 -0.29 10 10
CRKL 0.011 0.018 0.27 2 -10000 0 2
LRPAP1 0.011 0.013 0.27 1 -10000 0 1
FYN 0.008 0.025 -10000 0 -0.29 3 3
ITGA3 0.014 0.034 0.27 7 -10000 0 7
RELN/VLDLR/Fyn -0.046 0.09 0.18 4 -0.16 153 157
MAPK8IP1/MKK7/MAP3K11/JNK1 0.028 0.02 0.17 1 -0.13 6 7
AKT1 -0.059 0.1 -10000 0 -0.17 161 161
MAP2K7 0.01 0 -10000 0 -10000 0 0
RAPGEF1 0.01 0 -10000 0 -10000 0 0
DAB1 -0.002 0.11 0.27 25 -0.29 34 59
RELN/LRP8/DAB1 -0.021 0.11 0.18 54 -0.15 123 177
LRPAP1/LRP8 0.048 0.069 0.19 77 -10000 0 77
RELN/LRP8/DAB1/Fyn -0.017 0.1 0.17 53 -0.14 125 178
DAB1/alpha3/beta1 Integrin -0.02 0.087 0.2 8 -0.13 125 133
long-term memory -0.042 0.12 0.17 39 -0.16 157 196
DAB1/LIS1 -0.016 0.097 0.16 33 -0.13 125 158
DAB1/CRLK/C3G -0.021 0.085 0.2 5 -0.13 125 130
PIK3CA 0.01 0 -10000 0 -10000 0 0
DAB1/NCK2 -0.015 0.098 0.17 29 -0.13 125 154
ARHGEF2 0.01 0 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.055 0.12 0.27 3 -0.29 89 92
CDK5R1 0.024 0.058 0.27 22 -10000 0 22
RELN -0.093 0.14 0.27 4 -0.29 143 147
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
RELN/LRP8/Fyn -0.019 0.11 0.19 45 -0.16 114 159
GRIN2A/RELN/LRP8/DAB1/Fyn -0.047 0.12 0.17 40 -0.17 162 202
MAPK8 0.008 0.025 -10000 0 -0.29 3 3
RELN/VLDLR/DAB1 -0.046 0.098 0.17 19 -0.16 160 179
ITGB1 0.01 0 -10000 0 -10000 0 0
MAP1B -0.047 0.1 0.16 4 -0.17 131 135
RELN/LRP8 -0.017 0.11 0.19 46 -0.16 111 157
GRIN2B/RELN/LRP8/DAB1/Fyn -0.012 0.11 0.17 57 -0.14 122 179
PI3K 0.014 0.01 -10000 0 -0.19 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.018 0.023 0.19 7 -10000 0 7
RAP1A -0.025 0.074 0.14 5 -0.12 125 130
PAFAH1B1 0.01 0 -10000 0 -10000 0 0
MAPK8IP1 0.008 0.029 0.27 1 -0.29 3 4
CRLK/C3G 0.016 0.012 0.19 2 -10000 0 2
GRIN2B 0.012 0.047 0.27 13 -10000 0 13
NCK2 0.01 0 -10000 0 -10000 0 0
neuron differentiation -0.03 0.09 0.16 5 -0.2 33 38
neuron adhesion -0.02 0.073 0.14 9 -0.19 17 26
LRP8 0.058 0.1 0.27 76 -10000 0 76
GSK3B -0.055 0.095 -10000 0 -0.16 161 161
RELN/VLDLR/DAB1/Fyn -0.04 0.093 0.16 18 -0.14 162 180
MAP3K11 0.01 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.064 0.11 -10000 0 -0.19 161 161
CDK5 0.01 0 -10000 0 -10000 0 0
MAPT -0.009 0.075 0.18 2 -0.25 34 36
neuron migration -0.057 0.12 0.18 8 -0.2 156 164
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.031 0.091 0.16 5 -0.2 33 38
RELN/VLDLR -0.013 0.1 0.18 43 -0.14 115 158
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.052 0.052 -10000 0 -0.11 172 172
BUB1B 0.073 0.066 0.14 169 -10000 0 169
PLK1 0.034 0.031 0.081 105 -10000 0 105
PLK1S1 0.019 0.014 -10000 0 -10000 0 0
KIF2A 0.032 0.028 0.078 80 -10000 0 80
regulation of mitotic centrosome separation 0.034 0.031 0.081 105 -10000 0 105
GOLGA2 0.01 0 -10000 0 -10000 0 0
Hec1/SPC24 0.15 0.14 0.29 195 -10000 0 195
WEE1 0.042 0.035 0.13 6 -10000 0 6
cytokinesis 0.12 0.078 0.18 212 -0.14 5 217
PP2A-alpha B56 0.058 0.057 0.3 1 -10000 0 1
AURKA 0.045 0.05 0.12 124 -10000 0 124
PICH/PLK1 0.084 0.088 0.18 167 -10000 0 167
CENPE 0.048 0.051 0.12 126 -10000 0 126
RhoA/GTP 0.007 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.032 0.028 0.078 80 -10000 0 80
PPP2CA 0.01 0 -10000 0 -10000 0 0
FZR1 0.01 0 -10000 0 -10000 0 0
TPX2 0.069 0.057 0.12 219 -10000 0 219
PAK1 0.009 0.015 -10000 0 -0.3 1 1
SPC24 0.11 0.12 0.27 153 -10000 0 153
FBXW11 0.01 0 -10000 0 -10000 0 0
CLSPN 0.061 0.061 0.14 152 -10000 0 152
GORASP1 0.01 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.016 0.014 0.037 95 -10000 0 95
G2 phase of mitotic cell cycle 0.001 0.002 -10000 0 -10000 0 0
STAG2 0.008 0.021 -10000 0 -0.29 2 2
GRASP65/GM130/RAB1/GTP 0.011 0.01 -10000 0 -10000 0 0
spindle elongation 0.034 0.031 0.081 105 -10000 0 105
ODF2 0.011 0.002 -10000 0 -10000 0 0
BUB1 0.045 0.073 0.36 1 -10000 0 1
TPT1 0.019 0.014 -10000 0 -10000 0 0
CDC25C 0.097 0.068 0.15 252 -10000 0 252
CDC25B 0.018 0.032 0.28 6 -10000 0 6
SGOL1 0.052 0.052 0.11 172 -10000 0 172
RHOA 0.01 0 -10000 0 -10000 0 0
CCNB1/CDK1 0.073 0.084 0.18 145 -10000 0 145
CDC14B 0.005 0.01 -10000 0 -0.2 1 1
CDC20 0.16 0.13 0.27 231 -10000 0 231
PLK1/PBIP1 0.012 0.027 0.14 15 -10000 0 15
mitosis 0 0.002 -10000 0 -10000 0 0
FBXO5 0.029 0.025 0.077 43 -10000 0 43
CDC2 0.004 0.005 0.01 145 -10000 0 145
NDC80 0.096 0.12 0.27 135 -10000 0 135
metaphase plate congression 0.025 0.021 -10000 0 -10000 0 0
ERCC6L 0.083 0.087 0.18 167 -10000 0 167
NLP/gamma Tubulin 0.018 0.014 0.045 39 -10000 0 39
microtubule cytoskeleton organization 0.019 0.014 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 0.009 1 -10000 0 1
PPP1R12A 0.01 0.001 -10000 0 -10000 0 0
interphase 0 0.001 0.009 1 -10000 0 1
PLK1/PRC1-2 0.18 0.12 0.24 302 -10000 0 302
GRASP65/GM130/RAB1/GTP/PLK1 0.039 0.02 -10000 0 -10000 0 0
RAB1A 0.01 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.03 0.029 0.077 98 -10000 0 98
mitotic prometaphase 0.001 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.059 0.038 -10000 0 -10000 0 0
microtubule-based process 0.16 0.09 0.21 300 -10000 0 300
Golgi organization 0.034 0.031 0.081 105 -10000 0 105
Cohesin/SA2 0.032 0.027 0.078 39 -0.13 2 41
PPP1CB/MYPT1 0.016 0.002 -10000 0 -10000 0 0
KIF20A 0.2 0.11 0.27 300 -10000 0 300
APC/C/CDC20 0.13 0.1 0.22 232 -10000 0 232
PPP2R1A 0.01 0 -10000 0 -10000 0 0
chromosome segregation 0.011 0.027 0.14 15 -10000 0 15
PRC1 0.06 0.1 0.27 79 -10000 0 79
ECT2 0.04 0.044 0.11 95 -10000 0 95
C13orf34 0.029 0.027 0.074 81 -10000 0 81
NUDC 0.025 0.021 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.072 0.066 0.14 169 -10000 0 169
spindle assembly 0.026 0.022 0.061 91 -10000 0 91
spindle stabilization 0.019 0.014 -10000 0 -10000 0 0
APC/C/HCDH1 0.011 0.008 -10000 0 -0.16 1 1
MKLP2/PLK1 0.16 0.09 0.21 300 -10000 0 300
CCNB1 0.1 0.12 0.27 145 -10000 0 145
PPP1CB 0.01 0.001 -10000 0 -10000 0 0
BTRC 0.01 0 -10000 0 -10000 0 0
ROCK2 0.023 0.052 -10000 0 -0.34 7 7
TUBG1 0.019 0.014 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.05 0.059 0.13 145 -10000 0 145
MLF1IP 0.011 0.029 0.16 15 -10000 0 15
INCENP 0.011 0.013 0.27 1 -10000 0 1
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.36 0.58 0.78 2 -1.1 113 115
STAT6 (cleaved dimer) -0.47 0.52 -10000 0 -1 157 157
IGHG1 -0.091 0.24 0.48 12 -0.39 35 47
IGHG3 -0.35 0.55 0.66 2 -1 137 139
AKT1 -0.17 0.34 0.56 4 -0.67 69 73
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.13 0.3 0.51 5 -0.69 43 48
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.17 0.34 0.58 4 -0.66 68 72
THY1 -0.36 0.58 0.78 2 -1.1 114 116
MYB 0.045 0.091 0.27 56 -0.29 1 57
HMGA1 0.015 0.036 0.27 8 -10000 0 8
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.22 0.42 0.62 10 -0.76 100 110
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.17 0.34 0.58 4 -0.65 71 75
SP1 0.008 0.025 -10000 0 -10000 0 0
INPP5D 0.005 0.039 -10000 0 -0.29 7 7
SOCS5 0.017 0.028 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.39 0.59 0.62 2 -1.1 136 138
SOCS1 -0.23 0.39 0.57 5 -0.71 115 120
SOCS3 -0.25 0.46 0.6 2 -1.2 57 59
FCER2 -0.58 0.73 0.8 5 -1.3 185 190
PARP14 0.002 0.023 -10000 0 -0.14 2 2
CCL17 -0.34 0.6 0.84 8 -1.1 110 118
GRB2 0.01 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.13 0.27 0.54 4 -0.52 55 59
T cell proliferation -0.38 0.59 0.67 2 -1.1 123 125
IL4R/JAK1 -0.37 0.57 0.64 2 -1.1 134 136
EGR2 -0.52 0.73 0.83 2 -1.3 157 159
JAK2 -0.006 0.059 0.17 8 -0.32 1 9
JAK3 0.009 0.024 0.32 2 -10000 0 2
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
JAK1 0.012 0.022 -10000 0 -10000 0 0
COL1A2 -0.16 0.39 0.5 2 -1.4 27 29
CCL26 -0.36 0.59 0.77 2 -1.1 118 120
IL4R -0.38 0.63 0.8 7 -1.2 123 130
PTPN6 0.015 0.022 0.22 1 -10000 0 1
IL13RA2 -0.37 0.6 0.85 3 -1.1 114 117
IL13RA1 -0.006 0.059 0.17 7 -0.33 1 8
IRF4 -0.2 0.44 0.66 3 -1.1 60 63
ARG1 -0.05 0.21 0.52 7 -0.65 5 12
CBL -0.21 0.39 0.58 6 -0.7 105 111
GTF3A 0.012 0.021 0.15 5 -10000 0 5
PIK3CA 0.01 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.001 0.085 0.24 10 -0.23 2 12
IRF4/BCL6 -0.17 0.4 0.47 1 -1 58 59
CD40LG -0.028 0.097 0.25 3 -0.29 44 47
MAPK14 -0.23 0.42 0.62 4 -0.8 96 100
mitosis -0.16 0.32 0.56 4 -0.63 69 73
STAT6 -0.41 0.7 0.87 9 -1.2 134 143
SPI1 0.018 0.048 0.27 5 -0.29 4 9
RPS6KB1 -0.16 0.31 0.54 4 -0.61 67 71
STAT6 (dimer) -0.41 0.7 0.87 9 -1.2 134 143
STAT6 (dimer)/PARP14 -0.43 0.63 0.72 1 -1.1 152 153
mast cell activation 0.006 0.02 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.35 0.58 4 -0.69 67 71
FRAP1 -0.17 0.34 0.56 4 -0.67 69 73
LTA -0.37 0.6 0.83 3 -1.1 116 119
FES 0.009 0.015 -10000 0 -0.29 1 1
T-helper 1 cell differentiation 0.4 0.68 1.2 134 -0.87 9 143
CCL11 -0.39 0.61 -10000 0 -1.2 120 120
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.17 0.34 0.58 4 -0.67 67 71
IL2RG 0.006 0.062 0.28 9 -0.28 10 19
IL10 -0.38 0.61 0.78 2 -1.2 117 119
IRS1 0.003 0.046 -10000 0 -0.29 10 10
IRS2 -0.002 0.058 -10000 0 -0.29 16 16
IL4 -0.055 0.19 0.63 2 -10000 0 2
IL5 -0.36 0.58 0.87 2 -1.1 113 115
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.26 0.48 0.76 9 -0.84 114 123
COL1A1 -0.12 0.33 0.6 3 -1.5 12 15
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.38 0.59 -10000 0 -1.1 114 114
IL2R gamma/JAK3 0.01 0.053 0.25 9 -0.19 10 19
TFF3 -0.48 0.71 0.84 4 -1.3 149 153
ALOX15 -0.33 0.6 0.8 8 -1.1 109 117
MYBL1 0.012 0.026 0.27 4 -10000 0 4
T-helper 2 cell differentiation -0.3 0.5 0.67 4 -0.9 123 127
SHC1 0.011 0.013 0.27 1 -10000 0 1
CEBPB 0.017 0.029 -10000 0 -0.29 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.16 0.33 0.56 4 -0.6 81 85
mol:PI-3-4-5-P3 -0.17 0.34 0.57 4 -0.67 69 73
PI3K -0.18 0.36 0.57 4 -0.72 69 73
DOK2 0.002 0.056 0.27 2 -0.29 13 15
ETS1 0.011 0.028 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.12 0.26 0.46 10 -0.48 56 66
ITGB3 -0.42 0.65 0.78 2 -1.2 127 129
PIGR -0.6 0.72 0.8 6 -1.2 198 204
IGHE 0.023 0.066 0.12 1 -0.2 9 10
MAPKKK cascade -0.11 0.26 0.45 10 -0.48 55 65
BCL6 0.014 0.012 -10000 0 -10000 0 0
OPRM1 -0.36 0.58 0.77 2 -1.1 113 115
RETNLB -0.36 0.58 0.77 2 -1.1 114 116
SELP -0.47 0.7 0.78 2 -1.3 141 143
AICDA -0.35 0.56 0.72 3 -1.1 114 117
IL23-mediated signaling events

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
CCL2 -0.067 0.64 0.83 40 -1.2 69 109
IL23A -0.018 0.58 0.92 33 -1.1 50 83
NF kappa B1 p50/RelA/I kappa B alpha -0.21 0.4 -10000 0 -0.99 70 70
positive regulation of T cell mediated cytotoxicity -0.021 0.64 0.93 51 -1.1 70 121
ITGA3 -0.02 0.56 0.83 35 -1.1 50 85
IL17F 0.007 0.4 0.61 50 -0.65 69 119
IL12B 0.053 0.11 0.28 57 -10000 0 57
STAT1 (dimer) -0.051 0.58 0.74 42 -1.1 70 112
CD4 -0.017 0.56 0.83 41 -0.97 69 110
IL23 -0.027 0.55 0.83 29 -1.1 49 78
IL23R 0.072 0.21 0.56 35 -10000 0 35
IL1B -0.031 0.62 0.91 36 -1.2 51 87
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.001 0.58 0.92 44 -1 57 101
TYK2 0.03 0.063 0.18 34 -10000 0 34
STAT4 -0.005 0.064 -10000 0 -0.29 20 20
STAT3 0.01 0.002 -10000 0 -10000 0 0
IL18RAP -0.001 0.067 -10000 0 -0.29 21 21
IL12RB1 0.036 0.11 0.25 51 -0.32 10 61
PIK3CA 0.01 0.002 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.04 0.1 0.22 59 -0.23 10 69
IL23R/JAK2 0.08 0.22 0.54 42 -10000 0 42
positive regulation of chronic inflammatory response -0.021 0.64 0.93 51 -1.1 70 121
natural killer cell activation -0.007 0.019 -10000 0 -0.058 25 25
JAK2 0.046 0.096 0.25 48 -0.32 1 49
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
NFKB1 0.012 0.01 -10000 0 -10000 0 0
RELA 0.012 0.01 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.019 0.53 0.83 29 -1 50 79
ALOX12B -0.005 0.56 0.87 42 -1 54 96
CXCL1 -0.046 0.64 0.9 44 -1.1 76 120
T cell proliferation -0.021 0.64 0.93 51 -1.1 70 121
NFKBIA 0.012 0.01 -10000 0 -10000 0 0
IL17A 0.035 0.35 0.58 51 -0.52 57 108
PI3K -0.21 0.41 -10000 0 -1 70 70
IFNG 0.038 0.079 0.17 87 -0.084 2 89
STAT3 (dimer) -0.21 0.39 -10000 0 -0.97 70 70
IL18R1 0.012 0.027 -10000 0 -0.28 3 3
IL23/IL23R/JAK2/TYK2/SOCS3 0.025 0.43 0.68 56 -0.69 57 113
IL18/IL18R 0.029 0.072 0.15 1 -0.17 27 28
macrophage activation 0.002 0.037 0.07 66 -0.044 42 108
TNF -0.016 0.59 0.92 36 -1.1 50 86
STAT3/STAT4 -0.22 0.42 -10000 0 -1 71 71
STAT4 (dimer) -0.059 0.58 0.74 40 -1.1 70 110
IL18 0.01 0.037 -10000 0 -0.29 6 6
IL19 -0.007 0.56 0.85 41 -1 53 94
STAT5A (dimer) -0.053 0.57 0.74 40 -1.1 70 110
STAT1 0.012 0.026 0.27 4 -10000 0 4
SOCS3 -0.022 0.092 -10000 0 -0.29 43 43
CXCL9 0.003 0.61 0.89 51 -1.1 53 104
MPO -0.015 0.56 0.83 40 -1 54 94
positive regulation of humoral immune response -0.021 0.64 0.93 51 -1.1 70 121
IL23/IL23R/JAK2/TYK2 -0.035 0.67 0.93 51 -1.2 70 121
IL6 -0.31 0.77 0.82 38 -1.1 181 219
STAT5A 0.009 0.015 -10000 0 -0.29 1 1
IL2 0.015 0.03 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.007 0.019 -10000 0 -0.058 25 25
CD3E -0.062 0.63 0.83 41 -1.1 77 118
keratinocyte proliferation -0.021 0.64 0.93 51 -1.1 70 121
NOS2 -0.014 0.57 0.86 42 -1 58 100
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.072 0.17 0.19 2 -0.36 97 99
CRKL -0.075 0.18 0.2 2 -0.38 97 99
HRAS -0.071 0.17 -10000 0 -0.35 99 99
mol:PIP3 -0.073 0.16 -10000 0 -0.36 96 96
SPRED1 0.01 0 -10000 0 -10000 0 0
SPRED2 0.01 0 -10000 0 -10000 0 0
GAB1 -0.08 0.18 0.21 2 -0.4 97 99
FOXO3 -0.065 0.16 -10000 0 -0.36 90 90
AKT1 -0.072 0.17 -10000 0 -0.39 90 90
BAD -0.065 0.16 -10000 0 -0.36 90 90
megakaryocyte differentiation -0.079 0.18 0.21 2 -0.4 96 98
GSK3B -0.065 0.16 -10000 0 -0.36 90 90
RAF1 -0.057 0.14 -10000 0 -0.29 99 99
SHC1 0.011 0.013 0.27 1 -10000 0 1
STAT3 -0.08 0.18 0.21 2 -0.4 97 99
STAT1 -0.19 0.41 -10000 0 -0.91 97 97
HRAS/SPRED1 -0.054 0.14 -10000 0 -0.29 99 99
cell proliferation -0.079 0.18 0.21 2 -0.4 97 99
PIK3CA 0.01 0 -10000 0 -10000 0 0
TEC 0.01 0 -10000 0 -10000 0 0
RPS6KB1 -0.077 0.18 -10000 0 -0.4 96 96
HRAS/SPRED2 -0.054 0.14 -10000 0 -0.29 99 99
LYN/TEC/p62DOK -0.065 0.18 -10000 0 -0.39 90 90
MAPK3 -0.037 0.1 -10000 0 -0.21 99 99
STAP1 -0.081 0.19 0.21 2 -0.41 97 99
GRAP2 -0.023 0.093 -10000 0 -0.29 45 45
JAK2 -0.16 0.35 -10000 0 -0.77 97 97
STAT1 (dimer) -0.18 0.4 -10000 0 -0.89 97 97
mol:Gleevec 0.003 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.069 0.18 -10000 0 -0.39 97 97
actin filament polymerization -0.078 0.18 0.22 3 -0.39 97 100
LYN 0.01 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.11 0.26 -10000 0 -0.56 97 97
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
CBL/CRKL/GRB2 -0.06 0.16 -10000 0 -0.36 90 90
PI3K -0.067 0.18 -10000 0 -0.4 90 90
PTEN 0.01 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.21 0.48 -10000 0 -1.1 90 90
MAPK8 -0.081 0.18 0.21 2 -0.4 97 99
STAT3 (dimer) -0.078 0.18 0.21 2 -0.39 97 99
positive regulation of transcription -0.029 0.086 0.14 1 -0.17 98 99
mol:GDP -0.072 0.17 -10000 0 -0.36 99 99
PIK3C2B -0.08 0.18 0.21 2 -0.4 97 99
CBL/CRKL -0.066 0.17 -10000 0 -0.36 97 97
FER -0.081 0.18 0.21 2 -0.4 97 99
SH2B3 -0.08 0.18 0.21 2 -0.4 97 99
PDPK1 -0.067 0.15 -10000 0 -0.35 90 90
SNAI2 -0.081 0.19 0.21 2 -0.41 97 99
positive regulation of cell proliferation -0.14 0.31 -10000 0 -0.68 97 97
KITLG 0 0.039 -10000 0 -0.31 5 5
cell motility -0.14 0.31 -10000 0 -0.68 97 97
PTPN6 0.014 0.016 0.27 1 -10000 0 1
EPOR -0.039 0.14 -10000 0 -10000 0 0
STAT5A (dimer) -0.11 0.26 -10000 0 -0.56 97 97
SOCS1 0.011 0.013 0.27 1 -10000 0 1
cell migration 0.081 0.19 0.41 98 -0.21 2 100
SOS1 0.01 0 -10000 0 -10000 0 0
EPO 0.024 0.069 0.26 31 -10000 0 31
VAV1 -0.001 0.061 0.27 2 -0.29 16 18
GRB10 -0.081 0.18 0.21 2 -0.4 97 99
PTPN11 0.012 0.008 -10000 0 -10000 0 0
SCF/KIT -0.085 0.19 0.22 2 -0.42 97 99
GO:0007205 0.004 0.01 -10000 0 -10000 0 0
MAP2K1 -0.043 0.11 -10000 0 -0.23 99 99
CBL 0.01 0 -10000 0 -10000 0 0
KIT -0.24 0.5 -10000 0 -1.2 90 90
MAP2K2 -0.043 0.11 -10000 0 -0.23 99 99
SHC/Grb2/SOS1 -0.065 0.18 -10000 0 -0.38 96 96
STAT5A -0.12 0.26 -10000 0 -0.58 97 97
GRB2 0.01 0 -10000 0 -10000 0 0
response to radiation -0.079 0.18 0.21 2 -0.4 97 99
SHC/GRAP2 -0.008 0.066 0.19 1 -0.19 45 46
PTPRO -0.081 0.18 0.21 2 -0.41 96 98
SH2B2 -0.079 0.18 0.22 3 -0.4 97 100
DOK1 0.011 0.013 0.27 1 -10000 0 1
MATK -0.083 0.19 0.21 2 -0.41 98 100
CREBBP -0.004 0.056 0.16 6 -0.16 8 14
BCL2 -0.077 0.26 -10000 0 -1.2 16 16
Thromboxane A2 receptor 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
TGM2 0.004 0.063 0.27 7 -0.29 13 20
GNB1/GNG2 -0.077 0.088 -10000 0 -0.18 167 167
AKT1 -0.062 0.12 0.31 5 -0.19 166 171
EGF 0.025 0.062 0.27 25 -10000 0 25
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.004 0.03 -10000 0 -0.12 17 17
mol:Ca2+ -0.1 0.16 0.37 5 -0.29 166 171
LYN 0.004 0.03 -10000 0 -0.12 19 19
RhoA/GTP -0.045 0.067 -10000 0 -0.12 166 166
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.12 0.18 0.38 5 -0.33 166 171
GNG2 0.005 0.036 -10000 0 -0.29 6 6
ARRB2 0.01 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.004 0.05 -10000 0 -0.28 5 5
G beta5/gamma2 -0.099 0.12 -10000 0 -0.24 167 167
PRKCH -0.12 0.19 0.38 5 -0.34 166 171
DNM1 0.002 0.048 -10000 0 -0.29 11 11
TXA2/TP beta/beta Arrestin3 0 0.027 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
PTGDR -0.005 0.063 -10000 0 -0.29 19 19
G12 family/GTP -0.12 0.14 -10000 0 -0.3 166 166
ADRBK1 0.01 0 -10000 0 -10000 0 0
ADRBK2 0.01 0.02 0.27 1 -0.29 1 2
RhoA/GTP/ROCK1 0.013 0.001 -10000 0 -10000 0 0
mol:GDP 0.055 0.1 0.19 80 -0.25 5 85
mol:NADP 0.01 0.013 0.27 1 -10000 0 1
RAB11A 0.01 0 -10000 0 -10000 0 0
PRKG1 -0.059 0.13 -10000 0 -0.29 94 94
mol:IP3 -0.13 0.2 0.4 5 -0.36 166 171
cell morphogenesis 0.013 0.001 -10000 0 -10000 0 0
PLCB2 -0.18 0.27 0.5 3 -0.49 166 169
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK 0.008 0.044 0.15 16 -0.13 19 35
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.005 0.04 0.16 5 -0.14 19 24
RHOA 0.01 0 -10000 0 -10000 0 0
PTGIR 0.009 0.015 -10000 0 -0.29 1 1
PRKCB1 -0.13 0.2 0.39 5 -0.36 166 171
GNAQ 0.01 0 -10000 0 -10000 0 0
mol:L-citrulline 0.01 0.013 0.27 1 -10000 0 1
TXA2/TXA2-R family -0.19 0.27 0.51 3 -0.51 166 169
LCK 0.005 0.033 0.15 2 -0.13 19 21
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.007 0.032 -10000 0 -0.13 19 19
TXA2-R family/G12 family/GDP/G beta/gamma 0.013 0.02 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.012 0.033 -10000 0 -0.13 19 19
MAPK14 -0.075 0.13 0.32 5 -0.22 166 171
TGM2/GTP -0.15 0.23 0.42 5 -0.41 166 171
MAPK11 -0.075 0.13 0.32 5 -0.22 166 171
ARHGEF1 -0.058 0.1 0.25 5 -0.17 166 171
GNAI2 0.01 0 -10000 0 -10000 0 0
JNK cascade -0.13 0.21 0.4 5 -0.38 166 171
RAB11/GDP 0.01 0.002 -10000 0 -10000 0 0
ICAM1 -0.095 0.16 0.38 5 -0.28 163 168
cAMP biosynthetic process -0.12 0.19 0.36 5 -0.34 166 171
Gq family/GTP/EBP50 -0.006 0.056 -10000 0 -0.14 52 52
actin cytoskeleton reorganization 0.013 0.001 -10000 0 -10000 0 0
SRC 0.004 0.03 -10000 0 -0.12 19 19
GNB5 0.01 0 -10000 0 -10000 0 0
GNB1 0.01 0 -10000 0 -10000 0 0
EGF/EGFR 0.006 0.048 -10000 0 -0.17 11 11
VCAM1 -0.1 0.16 0.36 5 -0.3 164 169
TP beta/Gq family/GDP/G beta5/gamma2 -0.004 0.05 -10000 0 -0.28 5 5
platelet activation -0.099 0.17 0.38 5 -0.29 166 171
PGI2/IP 0.006 0.01 -10000 0 -0.2 1 1
PRKACA 0.001 0.038 -10000 0 -0.16 20 20
Gq family/GDP/G beta5/gamma2 -0.005 0.049 -10000 0 -0.26 5 5
TXA2/TP beta/beta Arrestin2 -0.002 0.068 -10000 0 -0.4 11 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.001 0.036 -10000 0 -0.15 20 20
mol:DAG -0.14 0.22 0.41 5 -0.4 166 171
EGFR 0.008 0.057 0.27 8 -0.29 9 17
TXA2/TP alpha -0.17 0.25 0.49 3 -0.46 166 169
Gq family/GTP -0.017 0.065 -10000 0 -0.17 61 61
YES1 0.004 0.03 -10000 0 -0.13 13 13
GNAI2/GTP 0 0.033 -10000 0 -0.14 19 19
PGD2/DP -0.003 0.042 -10000 0 -0.2 19 19
SLC9A3R1 0.023 0.057 0.27 21 -10000 0 21
FYN 0.004 0.032 -10000 0 -0.13 19 19
mol:NO 0.01 0.013 0.27 1 -10000 0 1
GNA15 0.008 0.025 -10000 0 -0.29 3 3
PGK/cGMP -0.027 0.073 0.17 1 -0.16 94 95
RhoA/GDP 0.01 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.015 0.053 0.16 7 -0.16 23 30
NOS3 0.01 0.013 0.27 1 -10000 0 1
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA -0.12 0.19 0.38 5 -0.34 166 171
PRKCB -0.14 0.2 0.36 5 -0.38 166 171
PRKCE -0.12 0.19 0.39 5 -0.34 166 171
PRKCD -0.13 0.2 0.39 5 -0.37 166 171
PRKCG -0.13 0.21 0.39 5 -0.37 166 171
muscle contraction -0.17 0.26 0.42 5 -0.47 166 171
PRKCZ -0.12 0.19 0.38 5 -0.33 166 171
ARR3 0.002 0.004 -10000 0 -10000 0 0
TXA2/TP beta 0.009 0.037 0.16 1 -0.15 19 20
PRKCQ -0.12 0.2 0.38 5 -0.35 166 171
MAPKKK cascade -0.16 0.24 0.4 5 -0.44 166 171
SELE -0.13 0.2 0.36 5 -0.36 166 171
TP beta/GNAI2/GDP/G beta/gamma 0.016 0.038 -10000 0 -0.14 19 19
ROCK1 0.01 0 -10000 0 -10000 0 0
GNA14 -0.032 0.1 -10000 0 -0.29 58 58
chemotaxis -0.22 0.31 0.54 3 -0.59 166 169
GNA12 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0 -10000 0 -10000 0 0
GNA11 0.009 0.015 -10000 0 -0.29 1 1
Rac1/GTP 0.007 0.002 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.015 0 -10000 0 -10000 0 0
Necdin/E2F1 0.029 0.1 0.19 81 -0.19 33 114
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.024 0.092 0.17 5 -0.16 121 126
NGF (dimer)/p75(NTR)/BEX1 -0.05 0.12 0.2 10 -0.2 137 147
NT-4/5 (dimer)/p75(NTR) -0.042 0.1 0.19 4 -0.2 108 112
IKBKB 0.01 0 -10000 0 -10000 0 0
AKT1 -0.035 0.081 -10000 0 -0.15 122 122
IKBKG 0.01 0 -10000 0 -10000 0 0
BDNF -0.047 0.12 -10000 0 -0.29 78 78
MGDIs/NGR/p75(NTR)/LINGO1 0.013 0.11 0.2 66 -0.16 78 144
FURIN 0.011 0.013 0.27 1 -10000 0 1
proBDNF (dimer)/p75(NTR)/Sortilin -0.049 0.1 0.18 5 -0.18 145 150
LINGO1 0.022 0.055 0.27 19 -10000 0 19
Sortilin/TRAF6/NRIF 0.013 0 -10000 0 -10000 0 0
proBDNF (dimer) -0.047 0.12 -10000 0 -0.29 78 78
NTRK1 0.013 0.034 0.27 7 -10000 0 7
RTN4R 0.049 0.093 0.27 62 -10000 0 62
neuron apoptosis -0.037 0.12 -10000 0 -0.28 40 40
IRAK1 0.01 0 -10000 0 -10000 0 0
SHC1 -0.045 0.096 0.12 5 -0.18 120 125
ARHGDIA 0.01 0 -10000 0 -10000 0 0
RhoA/GTP 0.007 0 -10000 0 -10000 0 0
Gamma Secretase 0.03 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.03 0.096 0.18 5 -0.17 121 126
MAGEH1 0.008 0.021 -10000 0 -0.29 2 2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.047 0.11 0.18 4 -0.18 143 147
Mammalian IAPs/DIABLO 0.019 0.045 0.21 5 -0.14 22 27
proNGF (dimer) -0.03 0.1 -10000 0 -0.29 54 54
MAGED1 0.01 0 -10000 0 -10000 0 0
APP 0.008 0.021 -10000 0 -0.29 2 2
NT-4/5 (dimer) -0.01 0.074 -10000 0 -0.29 27 27
ZNF274 0.01 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.032 0.084 -10000 0 -0.15 121 121
NGF -0.03 0.1 -10000 0 -0.29 54 54
cell cycle arrest -0.026 0.07 0.099 17 -0.12 121 138
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.045 0.1 -10000 0 -0.2 121 121
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.028 0.088 0.18 4 -0.17 107 111
NCSTN 0.01 0 -10000 0 -10000 0 0
mol:GTP -0.04 0.1 0.18 5 -0.18 123 128
PSENEN 0.01 0 -10000 0 -10000 0 0
mol:ceramide -0.038 0.086 -10000 0 -0.16 121 121
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.039 0.096 -10000 0 -0.3 24 24
p75(NTR)/beta APP -0.03 0.091 0.19 5 -0.19 91 96
BEX1 -0.011 0.088 0.27 7 -0.29 32 39
mol:GDP -0.05 0.095 0.11 5 -0.19 121 126
NGF (dimer) 0.021 0.094 0.17 76 -0.15 63 139
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.019 0.1 0.2 66 -0.14 78 144
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
RAC1/GTP -0.032 0.086 0.16 5 -0.15 121 126
MYD88 0.01 0 -10000 0 -10000 0 0
CHUK 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.04 0.1 0.18 5 -0.18 123 128
RHOB 0.01 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.057 0.075 0.19 97 -10000 0 97
NT3 (dimer) -0.045 0.12 0.27 1 -0.29 76 77
TP53 -0.039 0.079 -10000 0 -0.14 145 145
PRDM4 -0.039 0.087 -10000 0 -0.16 121 121
BDNF (dimer) 0.003 0.13 0.18 90 -0.17 107 197
PIK3CA 0.01 0 -10000 0 -10000 0 0
SORT1 0.01 0 -10000 0 -10000 0 0
activation of caspase activity -0.025 0.09 0.16 5 -0.15 121 126
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.029 0.094 0.18 5 -0.16 121 126
RHOC 0.01 0 -10000 0 -10000 0 0
XIAP 0.01 0.02 0.27 1 -0.29 1 2
MAPK10 -0.076 0.12 -10000 0 -0.26 105 105
DIABLO 0.01 0 -10000 0 -10000 0 0
SMPD2 -0.039 0.087 -10000 0 -0.16 121 121
APH1B 0.01 0 -10000 0 -10000 0 0
APH1A 0.01 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.039 0.1 0.18 5 -0.18 121 126
PSEN1 0.01 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.015 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.065 0.12 0.19 5 -0.22 143 148
MAPK8 -0.063 0.12 -10000 0 -0.24 102 102
MAPK9 -0.062 0.12 -10000 0 -0.24 102 102
APAF1 0.01 0 -10000 0 -10000 0 0
NTF3 -0.045 0.12 0.27 1 -0.29 76 77
NTF4 -0.01 0.074 -10000 0 -0.29 27 27
NDN -0.026 0.097 -10000 0 -0.29 49 49
RAC1/GDP 0.007 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.022 0.081 -10000 0 -0.14 123 123
p75 CTF/Sortilin/TRAF6/NRIF 0.026 0.007 0.18 1 -10000 0 1
RhoA-B-C/GTP -0.04 0.1 0.18 5 -0.18 123 128
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.032 0.092 0.17 5 -0.15 145 150
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.038 0.096 0.18 5 -0.16 145 150
PRKACB 0.008 0.021 -10000 0 -0.29 2 2
proBDNF (dimer)/p75 ECD -0.025 0.081 -10000 0 -0.19 78 78
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.004 0.071 0.27 3 -0.29 22 25
BIRC2 0.011 0.018 0.27 2 -10000 0 2
neuron projection morphogenesis -0.053 0.1 0.11 15 -0.2 114 129
BAD -0.069 0.12 -10000 0 -0.25 105 105
RIPK2 0.01 0 -10000 0 -10000 0 0
NGFR -0.053 0.13 0.27 5 -0.29 90 95
CYCS -0.034 0.081 -10000 0 -0.15 121 121
ADAM17 0.011 0.013 0.27 1 -10000 0 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.029 0.094 0.18 5 -0.16 121 126
BCL2L11 -0.069 0.12 -10000 0 -0.25 105 105
BDNF (dimer)/p75(NTR) -0.066 0.12 0.19 5 -0.22 145 150
PI3K -0.029 0.094 0.18 5 -0.16 122 127
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.029 0.094 0.18 5 -0.16 121 126
NDNL2 0.01 0 -10000 0 -10000 0 0
YWHAE 0.009 0.015 -10000 0 -0.29 1 1
PRKCI 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.054 0.12 0.19 5 -0.22 121 126
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.029 0.094 0.18 5 -0.16 121 126
TRAF6 0.01 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCZ 0.008 0.025 -10000 0 -0.29 3 3
PLG 0.005 0.03 0.27 5 -10000 0 5
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.071 0.12 -10000 0 -0.2 164 164
SQSTM1 0.01 0 -10000 0 -10000 0 0
NGFRAP1 0.008 0.021 -10000 0 -0.29 2 2
CASP3 -0.065 0.12 -10000 0 -0.24 102 102
E2F1 0.071 0.11 0.27 97 -10000 0 97
CASP9 0.01 0 -10000 0 -10000 0 0
IKK complex -0.03 0.1 0.19 2 -0.25 54 56
NGF (dimer)/TRKA -0.011 0.075 0.19 7 -0.19 54 61
MMP7 0.044 0.13 0.27 78 -0.29 21 99
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.023 0.09 0.17 5 -0.15 121 126
MMP3 -0.007 0.13 0.27 33 -0.29 51 84
APAF-1/Caspase 9 -0.04 0.063 -10000 0 -0.21 31 31
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.005 0.063 0.16 2 -0.13 77 79
ER alpha/Gai/GDP/Gbeta gamma -0.16 0.24 -10000 0 -0.41 155 155
AKT1 -0.14 0.31 -10000 0 -0.79 73 73
PIK3CA 0.01 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.14 0.32 -10000 0 -0.81 73 73
mol:Ca2+ -0.04 0.11 -10000 0 -0.29 63 63
IGF1R 0.008 0.025 -10000 0 -0.29 3 3
E2/ER alpha (dimer)/Striatin -0.017 0.066 -10000 0 -0.16 73 73
SHC1 0.011 0.013 0.27 1 -10000 0 1
apoptosis 0.13 0.29 0.75 73 -10000 0 73
RhoA/GTP -0.012 0.046 -10000 0 -0.11 72 72
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.12 0.2 -10000 0 -0.41 111 111
regulation of stress fiber formation 0.006 0.042 0.096 72 -10000 0 72
E2/ERA-ERB (dimer) -0.016 0.067 0.17 2 -0.16 73 75
KRAS 0.011 0.013 0.27 1 -10000 0 1
G13/GTP -0.015 0.059 -10000 0 -0.14 73 73
pseudopodium formation -0.006 0.042 -10000 0 -0.096 72 72
E2/ER alpha (dimer)/PELP1 -0.017 0.066 -10000 0 -0.16 73 73
GRB2 0.01 0 -10000 0 -10000 0 0
GNG2 0.006 0.036 -10000 0 -0.29 6 6
GNAO1 -0.084 0.14 -10000 0 -0.29 129 129
HRAS 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.12 0.23 -10000 0 -0.44 111 111
E2/ER beta (dimer) 0.008 0.012 0.18 2 -10000 0 2
mol:GDP -0.035 0.11 -10000 0 -0.26 73 73
mol:NADP -0.12 0.23 -10000 0 -0.44 111 111
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
mol:IP3 -0.042 0.12 -10000 0 -0.3 63 63
IGF-1R heterotetramer 0.008 0.025 -10000 0 -0.29 3 3
PLCB1 -0.043 0.12 -10000 0 -0.31 63 63
PLCB2 -0.042 0.12 -10000 0 -0.31 60 60
IGF1 -0.12 0.15 -10000 0 -0.29 182 182
mol:L-citrulline -0.12 0.23 -10000 0 -0.44 111 111
RHOA 0.01 0 -10000 0 -10000 0 0
Gai/GDP -0.23 0.34 -10000 0 -0.71 129 129
JNK cascade 0.008 0.012 0.18 2 -10000 0 2
BCAR1 0.01 0 -10000 0 -10000 0 0
ESR2 0.011 0.018 0.27 2 -10000 0 2
GNAQ 0.01 0 -10000 0 -10000 0 0
ESR1 -0.043 0.11 -10000 0 -0.29 73 73
Gq family/GDP/Gbeta gamma -0.015 0.074 -10000 0 -0.38 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.035 0.09 -10000 0 -0.23 47 47
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.12 0.2 -10000 0 -0.41 111 111
GNAZ -0.055 0.12 -10000 0 -0.29 89 89
E2/ER alpha (dimer) -0.029 0.077 -10000 0 -0.19 73 73
STRN 0.01 0 -10000 0 -10000 0 0
GNAL -0.12 0.15 -10000 0 -0.29 178 178
PELP1 0.01 0 -10000 0 -10000 0 0
MAPK11 0.009 0.007 0.11 2 -10000 0 2
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.025 -10000 0 -0.29 3 3
HBEGF -0.13 0.23 -10000 0 -0.38 154 154
cAMP biosynthetic process -0.069 0.088 0.11 1 -0.15 207 208
SRC -0.15 0.23 -10000 0 -0.39 155 155
PI3K 0.014 0.01 -10000 0 -0.19 1 1
GNB1 0.01 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.023 0.097 -10000 0 -0.23 73 73
SOS1 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.15 0.18 -10000 0 -0.34 161 161
Gs family/GTP -0.069 0.09 0.13 1 -0.15 207 208
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.02 0.007 0.17 1 -10000 0 1
vasodilation -0.12 0.22 -10000 0 -0.42 111 111
mol:DAG -0.042 0.12 -10000 0 -0.3 63 63
Gs family/GDP/Gbeta gamma -0.077 0.11 -10000 0 -0.28 75 75
MSN -0.007 0.045 -10000 0 -0.1 72 72
Gq family/GTP -0.044 0.12 -10000 0 -0.32 60 60
mol:PI-3-4-5-P3 -0.14 0.3 -10000 0 -0.78 73 73
NRAS 0.01 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.12 0.22 0.42 111 -10000 0 111
GRB2/SOS1 0.015 0 -10000 0 -10000 0 0
RhoA/GDP -0.028 0.1 -10000 0 -0.25 73 73
NOS3 -0.13 0.24 -10000 0 -0.47 111 111
GNA11 0.009 0.015 -10000 0 -0.29 1 1
MAPKKK cascade -0.12 0.24 -10000 0 -0.6 74 74
E2/ER alpha (dimer)/PELP1/Src -0.13 0.21 -10000 0 -0.43 111 111
ruffle organization -0.006 0.042 -10000 0 -0.096 72 72
ROCK2 -0.008 0.047 -10000 0 -0.11 72 72
GNA14 -0.032 0.1 -10000 0 -0.29 58 58
GNA15 0.008 0.025 -10000 0 -0.29 3 3
GNA13 0.01 0 -10000 0 -10000 0 0
MMP9 -0.12 0.23 -10000 0 -0.37 151 151
MMP2 -0.15 0.22 -10000 0 -0.38 157 157
TCGA08_p53

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
CDKN2A 0.078 0.08 0.16 201 -0.19 4 205
TP53 0.024 0.028 -10000 0 -10000 0 0
Senescence 0.024 0.028 -10000 0 -10000 0 0
Apoptosis 0.024 0.028 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.044 0.054 0.13 6 -0.098 194 200
MDM4 0.01 0 -10000 0 -10000 0 0
Aurora C signaling

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
INCENP 0.011 0.013 0.27 1 -9999 0 1
Aurora C/Aurora B/INCENP 0.092 0.078 0.17 194 -9999 0 194
metaphase 0 0 -10000 0 -9999 0 0
mitosis 0 0 -10000 0 -9999 0 0
H3F3B 0.004 0.004 -10000 0 -9999 0 0
AURKB 0.13 0.13 0.27 184 -9999 0 184
AURKC 0.018 0.045 0.27 13 -9999 0 13
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.084 0.14 -10000 0 -0.29 129 129
CDC42/GTP -0.067 0.12 -10000 0 -0.2 165 165
PLCG1 -0.073 0.12 -10000 0 -0.2 165 165
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
G12/G13 0.015 0 -10000 0 -10000 0 0
cell migration -0.066 0.12 -10000 0 -0.19 165 165
S1PR5 0.017 0.052 0.27 14 -0.29 2 16
S1PR4 0.009 0.037 0.27 3 -0.29 4 7
MAPK3 -0.073 0.12 -10000 0 -0.2 165 165
MAPK1 -0.073 0.12 -10000 0 -0.2 165 165
S1P/S1P5/Gi -0.075 0.13 -10000 0 -0.22 162 162
GNAI1 0.008 0.025 -10000 0 -0.29 3 3
CDC42/GDP 0.007 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.018 0.031 0.17 14 -0.16 2 16
RHOA 0.011 0.015 -10000 0 -0.13 4 4
S1P/S1P4/Gi -0.078 0.13 -10000 0 -0.22 165 165
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.055 0.12 -10000 0 -0.29 89 89
S1P/S1P4/G12/G13 0.019 0.02 0.17 3 -0.14 4 7
GNA12 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0 -10000 0 -10000 0 0
CDC42 0.01 0 -10000 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.064 0.12 0.19 162 -10000 0 162
GNAI2 0.01 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.018 0.031 0.17 14 -0.16 2 16
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.084 0.14 -10000 0 -0.29 129 129
RhoA/GTP -0.064 0.12 -10000 0 -0.2 162 162
negative regulation of cAMP metabolic process -0.074 0.13 -10000 0 -0.22 162 162
GNAZ -0.055 0.12 -10000 0 -0.29 89 89
GNAI3 0.01 0 -10000 0 -10000 0 0
GNA12 0.01 0 -10000 0 -10000 0 0
S1PR5 0.017 0.052 0.27 14 -0.29 2 16
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.075 0.13 -10000 0 -0.22 162 162
RhoA/GDP 0.007 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
GNAI1 0.008 0.025 -10000 0 -0.29 3 3
HIF-1-alpha transcription factor network

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
PKM2 0.15 0.27 0.57 40 -0.48 19 59
HDAC7 0.011 0.003 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.16 0.31 0.65 46 -0.5 23 69
SMAD4 0.01 0 -10000 0 -10000 0 0
ID2 0.15 0.27 0.57 40 -0.49 19 59
AP1 -0.056 0.11 -10000 0 -0.21 130 130
ABCG2 0.15 0.27 0.58 41 -0.48 19 60
HIF1A 0.058 0.076 0.2 41 -10000 0 41
TFF3 0.14 0.3 0.6 47 -0.5 30 77
GATA2 0.014 0.06 0.27 13 -0.29 7 20
AKT1 0.053 0.086 0.24 15 -0.14 15 30
response to hypoxia 0.041 0.085 0.19 48 -0.13 24 72
MCL1 0.15 0.27 0.57 40 -0.48 19 59
NDRG1 0.16 0.27 0.58 41 -0.47 19 60
SERPINE1 0.16 0.27 0.58 41 -0.5 19 60
FECH 0.15 0.27 0.57 40 -0.48 19 59
FURIN 0.15 0.27 0.57 41 -0.48 19 60
NCOA2 -0.003 0.072 -10000 0 -0.29 24 24
EP300 0.075 0.13 0.29 41 -0.26 26 67
HMOX1 0.16 0.27 0.59 44 -0.48 19 63
BHLHE40 0.15 0.27 0.57 40 -0.48 19 59
BHLHE41 0.15 0.27 0.57 40 -0.5 20 60
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.087 0.11 0.35 13 -10000 0 13
ENG 0.071 0.087 0.26 12 -10000 0 12
JUN -0.001 0.058 -10000 0 -0.29 16 16
RORA 0.15 0.27 0.57 40 -0.49 20 60
ABCB1 -0.09 0.23 -10000 0 -0.7 47 47
TFRC 0.15 0.27 0.58 40 -0.48 19 59
CXCR4 0.15 0.27 0.57 40 -0.5 19 59
TF 0.17 0.29 0.61 56 -0.48 19 75
CITED2 0.15 0.27 0.57 40 -0.48 19 59
HIF1A/ARNT 0.2 0.38 0.86 44 -0.61 10 54
LDHA -0.012 0.028 -10000 0 -10000 0 0
ETS1 0.15 0.27 0.57 40 -0.48 19 59
PGK1 0.15 0.27 0.57 40 -0.48 19 59
NOS2 0.17 0.28 0.62 50 -0.48 21 71
ITGB2 0.15 0.27 0.59 43 -0.5 19 62
ALDOA 0.15 0.27 0.57 40 -0.48 19 59
Cbp/p300/CITED2 0.14 0.31 0.6 42 -0.54 25 67
FOS -0.083 0.14 -10000 0 -0.29 128 128
HK2 0.15 0.27 0.58 40 -0.48 19 59
SP1 -0.004 0.047 -10000 0 -0.16 15 15
GCK 0.062 0.34 0.54 7 -1.1 27 34
HK1 0.15 0.27 0.57 40 -0.48 19 59
NPM1 0.15 0.27 0.57 40 -0.48 19 59
EGLN1 0.15 0.27 0.57 40 -0.48 19 59
CREB1 0.013 0 -10000 0 -10000 0 0
PGM1 0.15 0.27 0.57 40 -0.48 19 59
SMAD3 0.01 0 -10000 0 -10000 0 0
EDN1 0.031 0.19 0.47 2 -0.58 14 16
IGFBP1 0.17 0.28 0.6 50 -0.48 19 69
VEGFA 0.14 0.25 0.57 16 -0.45 22 38
HIF1A/JAB1 0.052 0.059 0.19 25 -10000 0 25
CP 0.15 0.31 0.62 56 -0.49 31 87
CXCL12 0.11 0.3 0.56 39 -0.5 32 71
COPS5 0.013 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4 0.016 0 -10000 0 -10000 0 0
BNIP3 0.15 0.27 0.57 41 -0.48 19 60
EGLN3 0.15 0.27 0.57 40 -0.48 20 60
CA9 0.29 0.3 0.63 105 -0.47 14 119
TERT 0.24 0.3 0.62 92 -0.49 15 107
ENO1 0.15 0.27 0.57 40 -0.48 19 59
PFKL 0.15 0.27 0.57 40 -0.48 19 59
NCOA1 0.011 0.004 -10000 0 -10000 0 0
ADM 0.15 0.27 0.57 40 -0.48 19 59
ARNT 0.055 0.075 0.24 15 -10000 0 15
HNF4A 0.028 0.085 0.26 41 -0.12 11 52
ADFP 0.14 0.27 0.55 46 -0.48 19 65
SLC2A1 0.15 0.25 0.59 16 -0.45 22 38
LEP 0.15 0.29 0.59 43 -0.48 25 68
HIF1A/ARNT/Cbp/p300 0.16 0.32 0.68 44 -0.52 23 67
EPO 0.15 0.24 0.61 26 -0.47 6 32
CREBBP 0.075 0.13 0.29 40 -0.26 25 65
HIF1A/ARNT/Cbp/p300/HDAC7 0.16 0.31 0.65 45 -0.5 22 67
PFKFB3 0.15 0.27 0.57 40 -0.47 20 60
NT5E 0.14 0.28 0.57 42 -0.49 27 69
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.049 0.19 -10000 0 -0.42 72 72
FYN -0.071 0.25 0.24 10 -0.55 73 83
LAT/GRAP2/SLP76 -0.061 0.2 -10000 0 -0.45 71 71
IKBKB 0.01 0 -10000 0 -10000 0 0
AKT1 -0.04 0.17 0.23 11 -0.38 70 81
B2M 0.01 0.006 -10000 0 -10000 0 0
IKBKG -0.008 0.047 -10000 0 -0.11 62 62
MAP3K8 0.008 0.025 -10000 0 -0.29 3 3
mol:Ca2+ -0.004 0.017 0.031 35 -0.039 52 87
integrin-mediated signaling pathway 0.012 0.017 -10000 0 -0.16 4 4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.067 0.24 0.26 11 -0.55 70 81
TRPV6 -0.014 0.12 0.23 34 -0.29 47 81
CD28 -0.001 0.062 0.27 2 -0.29 16 18
SHC1 -0.065 0.24 0.24 10 -0.52 73 83
receptor internalization -0.07 0.24 0.26 5 -0.51 74 79
PRF1 -0.07 0.29 0.38 11 -0.8 42 53
KRAS 0.011 0.013 0.27 1 -10000 0 1
GRB2 0.01 0 -10000 0 -10000 0 0
COT/AKT1 -0.026 0.14 0.21 11 -0.3 70 81
LAT -0.065 0.24 0.24 10 -0.51 73 83
EntrezGene:6955 0 0.005 0.03 5 -10000 0 5
CD3D -0.014 0.091 0.28 3 -0.3 36 39
CD3E -0.021 0.094 -10000 0 -0.3 42 42
CD3G -0.024 0.096 -10000 0 -0.29 46 46
RASGRP2 -0.039 0.074 -10000 0 -0.16 106 106
RASGRP1 -0.036 0.17 0.23 12 -0.38 66 78
HLA-A 0.009 0.017 -10000 0 -0.3 1 1
RASSF5 0.007 0.029 -10000 0 -0.29 4 4
RAP1A/GTP/RAPL 0.012 0.017 -10000 0 -0.16 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.007 0.059 0.14 12 -0.12 60 72
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.035 0.071 -10000 0 -0.18 71 71
PRKCA -0.025 0.098 0.13 5 -0.23 65 70
GRAP2 -0.023 0.093 -10000 0 -0.29 45 45
mol:IP3 -0.049 0.16 0.16 43 -0.34 75 118
EntrezGene:6957 0 0.006 0.029 3 -10000 0 3
TCR/CD3/MHC I/CD8 -0.064 0.22 0.21 11 -0.54 59 70
ORAI1 0.008 0.074 0.17 48 -0.16 34 82
CSK -0.066 0.24 0.24 10 -0.52 72 82
B7 family/CD28 -0.033 0.24 0.37 16 -0.52 63 79
CHUK 0.01 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.079 0.27 0.25 10 -0.59 73 83
PTPN6 -0.065 0.24 0.25 10 -0.51 73 83
VAV1 -0.068 0.24 0.24 11 -0.53 73 84
Monovalent TCR/CD3 -0.046 0.16 0.19 2 -0.34 73 75
CBL 0.01 0 -10000 0 -10000 0 0
LCK -0.071 0.25 0.23 11 -0.54 73 84
PAG1 -0.066 0.24 0.24 10 -0.52 72 82
RAP1A 0.01 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.076 0.27 0.26 10 -0.57 73 83
CD80 0.044 0.088 0.27 54 -10000 0 54
CD86 0.008 0.033 0.27 1 -0.29 4 5
PDK1/CARD11/BCL10/MALT1 -0.042 0.085 0.083 1 -0.22 71 72
HRAS 0.01 0 -10000 0 -10000 0 0
GO:0035030 -0.038 0.19 0.28 14 -0.43 64 78
CD8A -0.018 0.092 0.3 1 -0.3 39 40
CD8B -0.013 0.096 0.28 7 -0.3 37 44
PTPRC -0.024 0.1 0.27 2 -0.29 48 50
PDK1/PKC theta -0.053 0.21 0.25 11 -0.45 72 83
CSK/PAG1 -0.061 0.23 0.24 10 -0.52 69 79
SOS1 0.01 0 -10000 0 -10000 0 0
peptide-MHC class I 0.014 0.016 -10000 0 -0.21 1 1
GRAP2/SLP76 -0.069 0.24 0.21 7 -0.5 77 84
STIM1 0.004 0.03 -10000 0 -10000 0 0
RAS family/GTP 0.001 0.071 0.16 11 -0.15 56 67
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.076 0.26 0.26 5 -0.55 74 79
mol:DAG -0.054 0.13 -10000 0 -0.3 78 78
RAP1A/GDP -0.003 0.027 0.064 11 -0.055 50 61
PLCG1 0.01 0 -10000 0 -10000 0 0
CD247 0.006 0.042 0.27 1 -0.3 7 8
cytotoxic T cell degranulation -0.065 0.27 0.38 11 -0.75 42 53
RAP1A/GTP -0.017 0.026 -10000 0 -0.06 106 106
mol:PI-3-4-5-P3 -0.051 0.2 0.25 11 -0.45 70 81
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.065 0.2 0.17 44 -0.47 65 109
NRAS 0.01 0 -10000 0 -10000 0 0
ZAP70 -0.001 0.058 0.27 1 -0.29 15 16
GRB2/SOS1 0.015 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.066 0.19 -10000 0 -0.45 70 70
MALT1 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
CD8 heterodimer -0.018 0.11 0.24 7 -0.27 55 62
CARD11 0.007 0.049 0.27 4 -0.29 8 12
PRKCB -0.038 0.12 0.13 5 -0.25 83 88
PRKCE -0.024 0.097 0.13 5 -0.23 65 70
PRKCQ -0.065 0.24 0.26 11 -0.52 72 83
LCP2 0.008 0.025 -10000 0 -0.29 3 3
BCL10 0.01 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.031 0.15 0.22 11 -0.32 70 81
IKK complex -0.007 0.052 0.12 11 -0.099 66 77
RAS family/GDP -0.007 0.011 -10000 0 -0.035 32 32
MAP3K14 -0.017 0.11 0.18 11 -0.23 70 81
PDPK1 -0.036 0.16 0.23 11 -0.36 70 81
TCR/CD3/MHC I/CD8/Fyn -0.091 0.3 0.28 5 -0.67 69 74
Ephrin A reverse signaling

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
MAPKKK cascade -0.017 0.066 0.17 3 -0.16 66 69
EFNA5 0 0.056 0.27 1 -0.29 14 15
FYN -0.015 0.058 -10000 0 -0.14 66 66
neuron projection morphogenesis -0.017 0.066 0.17 3 -0.16 66 69
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.017 0.066 0.17 3 -0.16 66 69
EPHA5 -0.033 0.1 0.27 2 -0.29 54 56
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.028 0.092 0.2 8 -0.23 49 57
alphaM/beta2 Integrin/GPIbA -0.012 0.078 0.21 13 -0.23 22 35
alphaM/beta2 Integrin/proMMP-9 0.024 0.12 0.2 85 -0.28 22 107
PLAUR 0.01 0 -10000 0 -10000 0 0
HMGB1 -0.01 0.027 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.014 0.072 0.2 7 -0.23 21 28
AGER -0.006 0.041 0.26 6 -10000 0 6
RAP1A 0.01 0 -10000 0 -10000 0 0
SELPLG 0.006 0.043 0.27 2 -0.29 7 9
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.053 0.12 0.34 1 -0.18 180 181
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.069 0.12 0.27 102 -0.29 8 110
CYR61 -0.075 0.13 -10000 0 -0.29 116 116
TLN1 0.01 0 -10000 0 -10000 0 0
Rap1/GTP -0.025 0.097 -10000 0 -0.36 22 22
RHOA 0.01 0 -10000 0 -10000 0 0
P-selectin oligomer -0.052 0.12 -10000 0 -0.29 84 84
MYH2 -0.011 0.11 0.17 6 -0.26 38 44
MST1R 0.002 0.072 0.27 8 -0.29 18 26
leukocyte activation during inflammatory response -0.038 0.086 0.18 8 -0.17 92 100
APOB -0.031 0.11 0.27 7 -0.29 59 66
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.016 0.085 -10000 0 -0.29 36 36
JAM3 -0.011 0.075 -10000 0 -0.29 28 28
GP1BA 0.013 0.039 0.27 8 -0.29 1 9
alphaM/beta2 Integrin/CTGF -0.047 0.11 0.19 9 -0.23 91 100
alphaM/beta2 Integrin -0.019 0.12 0.17 3 -0.3 39 42
JAM3 homodimer -0.011 0.075 -10000 0 -0.29 28 28
ICAM2 0.009 0.015 -10000 0 -0.29 1 1
ICAM1 0.015 0.041 0.27 9 -0.29 1 10
phagocytosis triggered by activation of immune response cell surface activating receptor -0.018 0.12 0.17 3 -0.3 39 42
cell adhesion -0.012 0.077 0.21 13 -0.23 22 35
NFKB1 -0.11 0.18 0.25 20 -0.29 187 207
THY1 0.012 0.022 0.27 3 -10000 0 3
RhoA/GDP 0.007 0 -10000 0 -10000 0 0
Lipoprotein(a) -0.023 0.081 0.17 11 -0.17 83 94
alphaM/beta2 Integrin/LRP/tPA -0.015 0.082 0.22 8 -0.22 34 42
IL6 -0.22 0.29 -10000 0 -0.54 188 188
ITGB2 -0.011 0.062 0.26 8 -0.31 8 16
elevation of cytosolic calcium ion concentration 0.013 0.089 0.19 45 -0.21 21 66
alphaM/beta2 Integrin/JAM2/JAM3 -0.056 0.12 0.2 7 -0.21 120 127
JAM2 -0.07 0.13 -10000 0 -0.29 109 109
alphaM/beta2 Integrin/ICAM1 0.003 0.082 0.19 23 -0.17 36 59
alphaM/beta2 Integrin/uPA/Plg 0.012 0.09 0.19 45 -0.21 21 66
RhoA/GTP -0.009 0.11 0.18 7 -0.27 38 45
positive regulation of phagocytosis -0.028 0.11 0.26 5 -0.36 28 33
Ron/MSP 0.018 0.068 0.2 28 -0.19 19 47
alphaM/beta2 Integrin/uPAR/uPA 0.014 0.091 0.19 45 -0.21 21 66
alphaM/beta2 Integrin/uPAR -0.014 0.072 0.18 10 -0.23 21 31
PLAU 0.044 0.088 0.27 54 -10000 0 54
PLAT -0.002 0.064 0.27 2 -0.29 18 20
actin filament polymerization -0.011 0.1 0.17 7 -0.28 29 36
MST1 0.023 0.06 0.27 22 -0.29 1 23
alphaM/beta2 Integrin/lipoprotein(a) -0.037 0.088 0.19 8 -0.17 92 100
TNF -0.092 0.17 0.33 20 -0.27 176 196
RAP1B 0.01 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.008 0.097 0.19 48 -0.23 21 69
fibrinolysis 0.011 0.088 0.18 45 -0.21 21 66
HCK 0.004 0.058 0.27 5 -0.29 12 17
dendritic cell antigen processing and presentation -0.018 0.12 0.17 3 -0.3 39 42
VTN -0.034 0.12 0.27 7 -0.29 66 73
alphaM/beta2 Integrin/CYR61 -0.059 0.12 0.2 7 -0.23 116 123
LPA -0.013 0.086 0.27 6 -0.29 32 38
LRP1 0.007 0.029 -10000 0 -0.29 4 4
cell migration -0.001 0.11 0.2 20 -0.23 48 68
FN1 0.018 0.083 0.27 26 -0.29 12 38
alphaM/beta2 Integrin/Thy1 -0.013 0.073 0.18 12 -0.23 21 33
MPO 0.01 0.019 0.27 2 -10000 0 2
KNG1 0 0 -10000 0 -10000 0 0
RAP1/GDP 0.014 0 -10000 0 -10000 0 0
ROCK1 -0.007 0.1 0.17 5 -0.33 21 26
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.005 0.03 0.27 5 -10000 0 5
CTGF -0.051 0.12 -10000 0 -0.29 84 84
alphaM/beta2 Integrin/Hck -0.016 0.091 0.25 9 -0.27 25 34
ITGAM -0.022 0.073 0.26 3 -0.31 19 22
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.04 0.1 0.22 8 -0.19 90 98
HP 0.036 0.086 0.27 46 -0.29 2 48
leukocyte adhesion -0.086 0.14 0.2 7 -0.3 90 97
SELP -0.052 0.12 -10000 0 -0.29 84 84
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.014 0.014 -10000 0 -0.19 2 2
alphaV beta3 Integrin -0.056 0.11 -10000 0 -0.19 146 146
PTK2 -0.08 0.14 -10000 0 -0.35 69 69
IGF1R 0.008 0.025 -10000 0 -0.29 3 3
PI4KB 0.01 0 -10000 0 -10000 0 0
MFGE8 0.008 0.021 -10000 0 -0.29 2 2
SRC 0.01 0 -10000 0 -10000 0 0
CDKN1B -0.083 0.17 -10000 0 -0.45 66 66
VEGFA 0.01 0 -10000 0 -10000 0 0
ILK -0.083 0.17 -10000 0 -0.45 66 66
ROCK1 0.01 0 -10000 0 -10000 0 0
AKT1 -0.077 0.16 -10000 0 -0.42 66 66
PTK2B -0.003 0.047 -10000 0 -0.13 47 47
alphaV/beta3 Integrin/JAM-A -0.061 0.12 0.18 6 -0.19 168 174
CBL 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0 0.059 0.18 4 -0.16 45 49
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.052 0.087 -10000 0 -0.14 186 186
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.026 0.089 -10000 0 -0.31 17 17
alphaV/beta3 Integrin/Syndecan-1 -0.003 0.061 -10000 0 -0.16 53 53
PI4KA 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.096 0.14 -10000 0 -0.22 206 206
PI4 Kinase 0.015 0 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.063 0.11 0.18 160 -0.16 41 201
RPS6KB1 -0.094 0.13 -10000 0 -0.26 127 127
TLN1 0.01 0 -10000 0 -10000 0 0
MAPK3 -0.18 0.25 -10000 0 -0.49 148 148
GPR124 -0.024 0.094 -10000 0 -0.29 46 46
MAPK1 -0.18 0.25 -10000 0 -0.49 148 148
PXN 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
alphaV/beta3 Integrin/Tumstatin -0.046 0.1 0.18 4 -0.18 140 144
cell adhesion -0.001 0.062 -10000 0 -0.17 45 45
ANGPTL3 0.01 0.029 0.27 5 -10000 0 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.019 0.012 -10000 0 -0.16 2 2
IGF-1R heterotetramer 0.008 0.025 -10000 0 -0.29 3 3
Rac1/GDP 0.007 0 -10000 0 -10000 0 0
TGFBR2 0.008 0.025 -10000 0 -0.29 3 3
ITGB3 -0.024 0.094 -10000 0 -0.29 46 46
IGF1 -0.12 0.15 -10000 0 -0.29 182 182
RAC1 0.01 0 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.018 0.09 -10000 0 -0.21 69 69
apoptosis 0.009 0.015 -10000 0 -0.29 1 1
CD47 0.01 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0 0.057 -10000 0 -0.16 46 46
VCL 0.009 0.015 -10000 0 -0.29 1 1
alphaV/beta3 Integrin/Del1 -0.023 0.093 -10000 0 -0.2 80 80
CSF1 -0.001 0.056 -10000 0 -0.29 15 15
PIK3C2A -0.083 0.17 -10000 0 -0.45 66 66
PI4 Kinase/Pyk2 -0.056 0.1 -10000 0 -0.24 68 68
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.006 0.055 -10000 0 -0.14 47 47
FAK1/Vinculin -0.063 0.12 -10000 0 -0.28 69 69
alphaV beta3/Integrin/ppsTEM5 -0.018 0.09 -10000 0 -0.21 69 69
RHOA 0.01 0 -10000 0 -10000 0 0
VTN -0.034 0.12 0.27 7 -0.29 66 73
BCAR1 0.01 0 -10000 0 -10000 0 0
FGF2 -0.089 0.14 -10000 0 -0.29 136 136
F11R -0.057 0.095 -10000 0 -0.19 135 135
alphaV/beta3 Integrin/Lactadherin -0.001 0.059 -10000 0 -0.16 47 47
alphaV/beta3 Integrin/TGFBR2 -0.001 0.06 -10000 0 -0.16 48 48
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.019 0.032 -10000 0 -0.14 16 16
HSP90AA1 0.01 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.001 0.052 -10000 0 -0.14 46 46
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.018 0.083 0.27 26 -0.29 12 38
alphaV/beta3 Integrin/Pyk2 0.004 0.051 -10000 0 -0.13 48 48
SDC1 0.005 0.039 -10000 0 -0.29 7 7
VAV3 0.01 0.032 0.17 5 -0.13 16 21
PTPN11 0.01 0 -10000 0 -10000 0 0
IRS1 0.003 0.046 -10000 0 -0.29 10 10
FAK1/Paxillin -0.063 0.12 -10000 0 -0.28 69 69
cell migration -0.057 0.11 -10000 0 -0.26 69 69
ITGAV 0.009 0.015 -10000 0 -0.29 1 1
PI3K -0.052 0.11 -10000 0 -0.26 68 68
SPP1 0.12 0.13 0.27 165 -10000 0 165
KDR 0.008 0.021 -10000 0 -0.29 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.009 0.015 -10000 0 -0.29 1 1
COL4A3 -0.07 0.14 0.27 4 -0.29 112 116
angiogenesis -0.18 0.25 -10000 0 -0.48 158 158
Rac1/GTP 0.014 0.032 0.16 5 -0.11 19 24
EDIL3 -0.032 0.1 -10000 0 -0.29 57 57
cell proliferation -0.001 0.059 -10000 0 -0.16 48 48
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 -0.12 0.18 -10000 0 -0.34 132 132
MAP3K8 0.004 0.026 -10000 0 -0.29 3 3
FOS -0.093 0.14 -10000 0 -0.37 54 54
PRKCA 0.001 0.034 -10000 0 -0.29 5 5
PTPN7 0.001 0.049 0.25 5 -0.29 7 12
HRAS 0.009 0.001 -10000 0 -10000 0 0
PRKCB -0.081 0.13 -10000 0 -0.29 118 118
NRAS 0.009 0.001 -10000 0 -10000 0 0
RAS family/GTP 0.011 0.015 0.14 1 -10000 0 1
MAPK3 -0.053 0.1 -10000 0 -0.43 12 12
MAP2K1 -0.1 0.17 -10000 0 -0.35 120 120
ELK1 0.002 0.013 -10000 0 -10000 0 0
BRAF -0.094 0.15 -10000 0 -0.32 120 120
mol:GTP -0.001 0.002 -10000 0 -0.004 129 129
MAPK1 -0.053 0.1 -10000 0 -0.43 12 12
RAF1 -0.094 0.16 -10000 0 -0.32 120 120
KRAS 0.01 0.013 0.27 1 -10000 0 1
LPA receptor mediated events

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
GNB1/GNG2 -0.007 0.073 -10000 0 -0.17 63 63
NF kappa B1 p50/RelA/I kappa B alpha -0.013 0.073 -10000 0 -0.19 36 36
AP1 -0.062 0.11 -10000 0 -0.17 172 172
mol:PIP3 -0.03 0.063 -10000 0 -0.14 84 84
AKT1 -0.001 0.053 -10000 0 -0.21 10 10
PTK2B -0.019 0.071 -10000 0 -0.18 58 58
RHOA -0.001 0.03 -10000 0 -10000 0 0
PIK3CB 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.056 -10000 0 -0.15 44 44
MAGI3 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
apoptosis -0.03 0.089 -10000 0 -0.19 84 84
HRAS/GDP 0.007 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.024 0.071 -10000 0 -0.19 36 36
NF kappa B1 p50/RelA -0.026 0.08 -10000 0 -0.19 61 61
endothelial cell migration -0.035 0.12 -10000 0 -0.3 60 60
ADCY4 -0.087 0.14 -10000 0 -0.3 101 101
ADCY5 -0.17 0.19 -10000 0 -0.37 161 161
ADCY6 -0.087 0.14 -10000 0 -0.3 101 101
ADCY7 -0.087 0.14 -10000 0 -0.3 101 101
ADCY1 -0.086 0.14 -10000 0 -0.3 100 100
ADCY2 -0.15 0.18 -10000 0 -0.35 147 147
ADCY3 -0.087 0.14 -10000 0 -0.3 101 101
ADCY8 -0.088 0.14 -10000 0 -0.3 101 101
ADCY9 -0.09 0.15 -10000 0 -0.31 102 102
GSK3B -0.017 0.067 -10000 0 -0.17 58 58
arachidonic acid secretion -0.092 0.15 -10000 0 -0.31 103 103
GNG2 0.006 0.036 -10000 0 -0.29 6 6
TRIP6 0.009 0.013 -10000 0 -10000 0 0
GNAO1 -0.033 0.11 -10000 0 -0.27 60 60
HRAS 0.01 0 -10000 0 -10000 0 0
NFKBIA -0.022 0.076 -10000 0 -0.2 45 45
GAB1 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.012 0.075 -10000 0 -0.86 3 3
JUN -0.002 0.058 -10000 0 -0.29 16 16
LPA/LPA2/NHERF2 0.009 0.024 0.17 2 -10000 0 2
TIAM1 0.007 0.087 -10000 0 -1 3 3
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
mol:IP3 -0.015 0.056 -10000 0 -0.15 44 44
PLCB3 0.006 0.019 -10000 0 -10000 0 0
FOS -0.084 0.14 -10000 0 -0.29 129 129
positive regulation of mitosis -0.092 0.15 -10000 0 -0.31 103 103
LPA/LPA1-2-3 -0.015 0.085 0.17 6 -0.17 83 89
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.01 0 -10000 0 -10000 0 0
stress fiber formation -0.017 0.072 -10000 0 -0.2 37 37
GNAZ -0.027 0.091 -10000 0 -0.23 60 60
EGFR/PI3K-beta/Gab1 -0.023 0.069 -10000 0 -0.15 84 84
positive regulation of dendritic cell cytokine production -0.016 0.084 0.17 6 -0.17 83 89
LPA/LPA2/MAGI-3 0.009 0.024 0.17 2 -10000 0 2
ARHGEF1 -0.01 0.061 -10000 0 -0.15 60 60
GNAI2 -0.018 0.072 -10000 0 -0.19 60 60
GNAI3 -0.018 0.072 -10000 0 -0.19 60 60
GNAI1 -0.018 0.072 -10000 0 -0.19 60 60
LPA/LPA3 -0.013 0.063 0.18 4 -0.15 59 63
LPA/LPA2 0.002 0.028 0.15 3 -0.083 28 31
LPA/LPA1 -0.023 0.087 -10000 0 -0.23 60 60
HB-EGF/EGFR 0.032 0.079 0.14 94 -0.19 22 116
HBEGF 0.041 0.078 0.16 102 -0.19 13 115
mol:DAG -0.015 0.056 -10000 0 -0.15 44 44
cAMP biosynthetic process -0.11 0.16 -10000 0 -0.28 149 149
NFKB1 0.01 0 -10000 0 -10000 0 0
SRC 0.01 0 -10000 0 -10000 0 0
GNB1 0.01 0 -10000 0 -10000 0 0
LYN -0.022 0.076 -10000 0 -0.19 52 52
GNAQ -0.008 0.053 0.099 5 -0.17 33 38
LPAR2 0.012 0.022 0.27 3 -10000 0 3
LPAR3 -0.011 0.087 0.27 5 -0.29 33 38
LPAR1 -0.023 0.091 -10000 0 -0.22 60 60
IL8 -0.075 0.19 0.3 1 -0.45 72 73
PTK2 -0.021 0.074 -10000 0 -0.16 83 83
Rac1/GDP 0.007 0 -10000 0 -10000 0 0
CASP3 -0.03 0.089 -10000 0 -0.2 84 84
EGFR 0.008 0.057 0.27 8 -0.29 9 17
PLCG1 -0.013 0.064 0.1 4 -0.19 44 48
PLD2 -0.021 0.074 -10000 0 -0.16 83 83
G12/G13 -0.004 0.069 -10000 0 -0.16 60 60
PI3K-beta -0.02 0.051 -10000 0 -0.23 10 10
cell migration 0.001 0.045 -10000 0 -0.23 4 4
SLC9A3R2 0.01 0 -10000 0 -10000 0 0
PXN -0.018 0.073 -10000 0 -0.2 37 37
HRAS/GTP -0.094 0.15 -10000 0 -0.32 103 103
RAC1 0.01 0 -10000 0 -10000 0 0
MMP9 0.069 0.12 0.27 102 -0.29 8 110
PRKCE 0.01 0 -10000 0 -10000 0 0
PRKCD -0.013 0.054 -10000 0 -0.15 44 44
Gi(beta/gamma) -0.085 0.14 -10000 0 -0.29 103 103
mol:LPA -0.009 0.036 -10000 0 -0.12 36 36
TRIP6/p130 Cas/FAK1/Paxillin -0.011 0.083 -10000 0 -0.23 27 27
MAPKKK cascade -0.092 0.15 -10000 0 -0.31 103 103
contractile ring contraction involved in cytokinesis -0.001 0.029 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.016 0.066 0.099 4 -0.19 45 49
GNA15 -0.008 0.054 -10000 0 -0.17 34 34
GNA12 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0 -10000 0 -10000 0 0
MAPT -0.024 0.073 -10000 0 -0.2 37 37
GNA11 -0.008 0.055 0.098 6 -0.18 33 39
Rac1/GTP 0.012 0.079 -10000 0 -0.91 3 3
MMP2 -0.035 0.12 -10000 0 -0.31 60 60
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.022 0.093 0.18 28 -0.14 136 164
SMAD6-7/SMURF1 0.021 0.018 0.18 3 -0.16 2 5
NOG 0.028 0.069 0.27 31 -10000 0 31
SMAD9 -0.12 0.21 -10000 0 -0.46 106 106
SMAD4 0.01 0 -10000 0 -10000 0 0
SMAD5 -0.015 0.068 -10000 0 -0.2 15 15
BMP7/USAG1 -0.12 0.13 0.19 3 -0.23 227 230
SMAD5/SKI -0.011 0.066 -10000 0 -0.2 15 15
SMAD1 0.021 0.009 -10000 0 -10000 0 0
BMP2 -0.022 0.092 -10000 0 -0.29 43 43
SMAD1/SMAD1/SMAD4 0 0.01 -10000 0 -10000 0 0
BMPR1A 0.01 0 -10000 0 -10000 0 0
BMPR1B 0.039 0.097 0.27 54 -0.29 6 60
BMPR1A-1B/BAMBI 0.025 0.074 0.18 50 -0.16 28 78
AHSG 0.033 0.084 0.27 46 -10000 0 46
CER1 0.002 0.004 -10000 0 -10000 0 0
BMP2-4/CER1 -0.008 0.065 0.17 5 -0.16 59 64
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.036 0.096 -10000 0 -0.28 18 18
BMP2-4 (homodimer) -0.013 0.078 0.19 5 -0.2 59 64
RGMB 0.01 0 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.043 0.057 0.18 56 -0.14 7 63
RGMA -0.077 0.14 -10000 0 -0.29 119 119
SMURF1 0.01 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.039 0.096 -10000 0 -0.25 27 27
BMP2-4/USAG1 -0.058 0.11 0.18 10 -0.18 166 176
SMAD6/SMURF1/SMAD5 -0.011 0.066 -10000 0 -0.2 15 15
SOSTDC1 -0.083 0.14 0.27 7 -0.29 130 137
BMP7/BMPR2/BMPR1A-1B -0.021 0.092 0.18 29 -0.14 127 156
SKI 0.01 0 -10000 0 -10000 0 0
BMP6 (homodimer) 0.01 0.023 0.27 2 -0.29 1 3
HFE2 0.007 0.027 0.27 4 -10000 0 4
ZFYVE16 0.01 0 -10000 0 -10000 0 0
MAP3K7 0.01 0 -10000 0 -10000 0 0
BMP2-4/CHRD -0.019 0.087 0.18 6 -0.18 88 94
SMAD5/SMAD5/SMAD4 -0.011 0.066 -10000 0 -0.2 15 15
MAPK1 0.01 0 -10000 0 -10000 0 0
TAK1/TAB family -0.037 0.076 -10000 0 -0.26 19 19
BMP7 (homodimer) -0.097 0.14 -10000 0 -0.29 147 147
NUP214 0.01 0 -10000 0 -10000 0 0
BMP6/FETUA 0.031 0.06 0.19 48 -0.19 1 49
SMAD1/SKI 0.026 0.008 -10000 0 -10000 0 0
SMAD6 0.011 0.027 0.27 3 -0.29 1 4
CTDSP2 0.01 0 -10000 0 -10000 0 0
BMP2-4/FETUA 0.009 0.082 0.18 42 -0.16 50 92
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.006 0.15 0.27 62 -0.29 59 121
BMPR2 (homodimer) 0.01 0 -10000 0 -10000 0 0
GADD34/PP1CA 0.02 0 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.035 0.066 0.19 54 -0.19 6 60
CHRDL1 -0.16 0.15 -10000 0 -0.29 235 235
ENDOFIN/SMAD1 0.026 0.008 -10000 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.034 0.016 -10000 0 -10000 0 0
SMAD6/SMURF1 0.01 0 -10000 0 -10000 0 0
BAMBI -0.01 0.089 0.27 7 -0.29 33 40
SMURF2 0.01 0 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.1 0.1 -10000 0 -0.18 254 254
BMP2-4/GREM1 -0.005 0.11 0.18 64 -0.16 112 176
SMAD7 0.009 0.015 -10000 0 -0.29 1 1
SMAD8A/SMAD8A/SMAD4 -0.11 0.2 -10000 0 -0.43 106 106
SMAD1/SMAD6 0.026 0.008 -10000 0 -10000 0 0
TAK1/SMAD6 0.015 0 -10000 0 -10000 0 0
BMP7 -0.098 0.14 -10000 0 -0.29 147 147
BMP6 0.01 0.023 0.27 2 -0.29 1 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.038 0.094 -10000 0 -0.29 19 19
PPM1A 0.01 0 -10000 0 -10000 0 0
SMAD1/SMURF2 0.026 0.008 -10000 0 -10000 0 0
SMAD7/SMURF1 0.014 0.01 -10000 0 -0.19 1 1
CTDSPL 0.01 0 -10000 0 -10000 0 0
PPP1CA 0.01 0 -10000 0 -10000 0 0
XIAP 0.01 0.02 0.27 1 -0.29 1 2
CTDSP1 0.01 0 -10000 0 -10000 0 0
PPP1R15A 0.01 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.051 0.12 0.16 2 -0.19 123 125
CHRD -0.018 0.089 0.27 1 -0.29 39 40
BMPR2 0.01 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.046 0.1 -10000 0 -0.17 145 145
BMP4 0.001 0.067 0.27 5 -0.29 17 22
FST 0 0.08 0.27 10 -0.29 22 32
BMP2-4/NOG 0.006 0.076 0.19 23 -0.16 48 71
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.015 0.087 0.17 29 -0.13 127 156
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.009 0.018 -10000 0 -0.19 2 2
PDGFRB -0.001 0.047 -10000 0 -0.3 10 10
SPHK1 0.001 0.081 -10000 0 -0.87 1 1
mol:S1P -0.008 0.08 -10000 0 -0.79 1 1
S1P1/S1P/Gi -0.15 0.22 -10000 0 -0.36 187 187
GNAO1 -0.089 0.14 -10000 0 -0.29 129 129
PDGFB-D/PDGFRB/PLCgamma1 -0.14 0.19 -10000 0 -0.37 146 146
PLCG1 -0.15 0.2 -10000 0 -0.39 145 145
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.001 0.047 -10000 0 -0.3 10 10
GNAI2 0.005 0.009 -10000 0 -10000 0 0
GNAI3 0.005 0.009 -10000 0 -10000 0 0
GNAI1 0.003 0.027 -10000 0 -0.3 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0 0.016 -10000 0 -0.16 2 2
S1P1/S1P -0.031 0.067 -10000 0 -0.18 16 16
negative regulation of cAMP metabolic process -0.15 0.21 -10000 0 -0.35 187 187
MAPK3 -0.2 0.27 -10000 0 -0.52 145 145
calcium-dependent phospholipase C activity -0.003 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.007 0 -10000 0 -10000 0 0
RhoA/GDP 0.007 0 -10000 0 -10000 0 0
KDR 0.006 0.022 -10000 0 -0.29 2 2
PLCB2 -0.016 0.077 -10000 0 -0.16 18 18
RAC1 0.01 0 -10000 0 -10000 0 0
RhoA/GTP -0.033 0.054 -10000 0 -0.16 16 16
receptor internalization -0.03 0.064 -10000 0 -0.14 46 46
PTGS2 -0.28 0.41 -10000 0 -0.95 103 103
Rac1/GTP -0.033 0.054 -10000 0 -0.16 16 16
RHOA 0.01 0 -10000 0 -10000 0 0
VEGFA 0.007 0.007 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.15 0.21 -10000 0 -0.35 187 187
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.06 0.12 -10000 0 -0.29 89 89
MAPK1 -0.2 0.27 -10000 0 -0.52 145 145
S1P1/S1P/PDGFB-D/PDGFRB -0.04 0.083 -10000 0 -0.17 97 97
ABCC1 0.007 0.02 0.27 2 -10000 0 2
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.049 0.076 -10000 0 -0.13 180 180
MAPK9 0.004 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.04 0.074 0.16 107 -0.19 7 114
GNB1/GNG2 0.011 0.021 -10000 0 -0.16 6 6
GNB1 0.01 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.004 0 -10000 0 -10000 0 0
Gs family/GTP -0.059 0.074 -10000 0 -0.14 178 178
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.018 0.021 0.042 178 -10000 0 178
GNAL -0.12 0.15 -10000 0 -0.29 178 178
GNG2 0.006 0.036 -10000 0 -0.29 6 6
CRH 0.07 0.12 0.27 107 -0.29 7 114
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.002 0.02 -10000 0 -0.23 3 3
MAPK11 0.004 0 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.051 0.083 0.21 35 -0.14 9 44
NF kappa B1 p50/RelA/I kappa B alpha 0.06 0.087 0.25 35 -10000 0 35
alphaV/beta3 Integrin/Osteopontin/Src 0.093 0.091 0.2 165 -0.16 1 166
AP1 0 0.14 0.26 20 -0.28 47 67
ILK 0.041 0.08 -10000 0 -0.17 6 6
bone resorption 0.037 0.079 0.23 1 -0.22 10 11
PTK2B 0.009 0.015 -10000 0 -0.29 1 1
PYK2/p130Cas 0.078 0.1 0.23 35 -0.19 1 36
ITGAV 0.014 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.005 0.047 0.19 1 -0.19 21 22
alphaV/beta3 Integrin/Osteopontin 0.078 0.12 0.2 159 -0.16 41 200
MAP3K1 0.04 0.08 0.17 35 -0.14 41 76
JUN -0.002 0.058 -10000 0 -0.29 16 16
MAPK3 0.054 0.095 0.24 53 -0.14 8 61
MAPK1 0.054 0.095 0.24 53 -0.14 8 61
Rac1/GDP 0.007 0 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 0.036 0.076 0.16 35 -0.13 41 76
ITGB3 -0.019 0.095 -10000 0 -0.29 45 45
NFKBIA 0.056 0.096 0.25 53 -10000 0 53
FOS -0.084 0.14 -10000 0 -0.29 129 129
CD44 0 0.056 0.27 1 -0.29 14 15
CHUK 0.01 0 -10000 0 -10000 0 0
PLAU 0.069 0.13 0.38 46 -10000 0 46
NF kappa B1 p50/RelA 0.067 0.093 0.26 53 -10000 0 53
BCAR1 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
alphaV beta3 Integrin 0 0.071 -10000 0 -0.2 46 46
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.04 0.078 0.16 35 -0.14 41 76
VAV3 0.037 0.072 0.15 37 -0.13 41 78
MAP3K14 0.05 0.09 0.2 52 -0.14 41 93
ROCK2 0.005 0.039 -10000 0 -0.29 7 7
SPP1 0.12 0.13 0.27 165 -10000 0 165
RAC1 0.01 0 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.067 0.18 3 -0.13 9 12
MMP2 -0.019 0.14 0.19 20 -0.3 57 77
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 -0.024 0.047 0.25 1 -10000 0 1
SMARCC2 0.008 0.014 -10000 0 -10000 0 0
SMARCC1 0.008 0.015 -10000 0 -10000 0 0
TBX21 0.001 0.16 0.48 1 -0.52 26 27
SUMO2 0.006 0.009 -10000 0 -10000 0 0
STAT1 (dimer) 0.016 0.025 0.27 4 -10000 0 4
FKBP4 0.01 0 -10000 0 -10000 0 0
FKBP5 -0.003 0.06 -10000 0 -0.29 17 17
GR alpha/HSP90/FKBP51/HSP90 0.026 0.093 0.22 18 -0.17 6 24
PRL -0.018 0.1 0.45 2 -10000 0 2
cortisol/GR alpha (dimer)/TIF2 0.031 0.23 0.42 51 -0.42 25 76
RELA -0.11 0.11 -10000 0 -0.21 215 215
FGG 0.08 0.24 0.41 77 -0.41 22 99
GR beta/TIF2 0.016 0.11 0.23 27 -0.23 14 41
IFNG -0.021 0.3 0.52 46 -0.49 47 93
apoptosis -0.045 0.18 0.48 3 -0.45 17 20
CREB1 0.018 0.028 -10000 0 -10000 0 0
histone acetylation -0.092 0.13 -10000 0 -0.33 51 51
BGLAP 0.005 0.11 0.35 1 -0.37 1 2
GR/PKAc 0.034 0.087 0.22 19 -10000 0 19
NF kappa B1 p50/RelA -0.2 0.2 0.28 2 -0.36 238 240
SMARCD1 0.008 0.015 -10000 0 -10000 0 0
MDM2 0.038 0.091 0.18 67 -0.14 7 74
GATA3 -0.005 0.078 0.26 3 -0.29 27 30
AKT1 0.007 0.007 -10000 0 -0.14 1 1
CSF2 -0.041 0.12 -10000 0 -0.44 5 5
GSK3B 0.006 0.009 -10000 0 -10000 0 0
NR1I3 -0.031 0.16 0.5 2 -0.45 7 9
CSN2 0.051 0.2 0.33 60 -0.37 24 84
BRG1/BAF155/BAF170/BAF60A 0.02 0.048 -10000 0 -0.22 15 15
NFATC1 -0.003 0.063 -10000 0 -0.29 19 19
POU2F1 0.013 0.014 -10000 0 -10000 0 0
CDKN1A 0.011 0.087 -10000 0 -1.2 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.007 -10000 0 -10000 0 0
SFN 0.027 0.076 0.27 32 -0.29 4 36
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.043 0.087 0.22 19 -0.17 1 20
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.14 0.32 0.48 2 -0.69 100 102
JUN 0.039 0.21 0.4 61 -0.32 36 97
IL4 -0.011 0.12 -10000 0 -0.43 13 13
CDK5R1 0.022 0.059 0.27 22 -10000 0 22
PRKACA 0.01 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.037 0.068 -10000 0 -0.22 32 32
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.033 0.088 0.22 16 -0.17 1 17
cortisol/GR alpha (monomer) 0.044 0.26 0.48 57 -0.48 23 80
NCOA2 -0.008 0.07 -10000 0 -0.29 24 24
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.019 0.17 0.24 53 -0.3 77 130
AP-1/NFAT1-c-4 -0.008 0.32 0.52 60 -0.46 78 138
AFP 0.005 0.18 0.46 10 -10000 0 10
SUV420H1 0.01 0 -10000 0 -10000 0 0
IRF1 0.045 0.14 0.35 13 -10000 0 13
TP53 0.017 0.035 -10000 0 -0.49 2 2
PPP5C 0.01 0 -10000 0 -10000 0 0
KRT17 -0.063 0.37 0.57 36 -0.77 49 85
KRT14 0.1 0.25 0.44 41 -1.1 4 45
TBP 0.015 0.009 -10000 0 -10000 0 0
CREBBP -0.059 0.083 0.25 4 -0.29 16 20
HDAC1 0.008 0.011 -10000 0 -10000 0 0
HDAC2 0.004 0.011 -10000 0 -10000 0 0
AP-1 -0.008 0.32 0.52 60 -0.46 78 138
MAPK14 0.006 0.008 -10000 0 -10000 0 0
MAPK10 -0.021 0.085 -10000 0 -0.29 37 37
MAPK11 0.006 0.009 -10000 0 -10000 0 0
KRT5 -0.2 0.52 0.55 42 -0.93 120 162
interleukin-1 receptor activity -0.005 0.009 -10000 0 -10000 0 0
NCOA1 0.011 0.001 -10000 0 -10000 0 0
STAT1 0.016 0.026 0.27 4 -10000 0 4
CGA 0.009 0.12 0.35 9 -0.3 9 18
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.11 0.18 0.31 1 -0.4 81 82
MAPK3 0.006 0.009 -10000 0 -10000 0 0
MAPK1 0.006 0.008 -10000 0 -10000 0 0
ICAM1 -0.16 0.23 0.38 4 -0.44 124 128
NFKB1 -0.11 0.11 -10000 0 -0.2 224 224
MAPK8 0.032 0.17 0.36 46 -0.26 39 85
MAPK9 0.006 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.057 0.18 0.48 3 -0.47 17 20
BAX 0.016 0.027 -10000 0 -10000 0 0
POMC -0.16 0.26 0.45 1 -0.84 19 20
EP300 -0.059 0.083 0.25 4 -0.29 16 20
cortisol/GR alpha (dimer)/p53 0.046 0.23 0.43 54 -0.42 20 74
proteasomal ubiquitin-dependent protein catabolic process 0.025 0.073 0.16 20 -10000 0 20
SGK1 -0.076 0.26 -10000 0 -1.2 16 16
IL13 -0.055 0.23 0.5 7 -0.59 16 23
IL6 -0.43 0.48 -10000 0 -0.89 201 201
PRKACG 0.001 0.003 -10000 0 -10000 0 0
IL5 -0.055 0.2 0.46 7 -0.52 13 20
IL2 -0.06 0.26 0.46 27 -0.47 61 88
CDK5 0.008 0.006 -10000 0 -10000 0 0
PRKACB 0.008 0.021 -10000 0 -0.29 2 2
HSP90AA1 0.01 0 -10000 0 -10000 0 0
IL8 -0.24 0.36 0.47 1 -0.72 109 110
CDK5R1/CDK5 0.02 0.041 0.19 22 -10000 0 22
NF kappa B1 p50/RelA/PKAc -0.14 0.16 0.23 2 -0.27 212 214
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.049 0.21 0.4 55 -0.38 23 78
SMARCA4 0.008 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.039 0.16 0.32 27 -0.34 12 39
NF kappa B1 p50/RelA/Cbp -0.22 0.18 0.3 1 -0.38 191 192
JUN (dimer) 0.039 0.21 0.4 61 -0.32 36 97
YWHAH 0.01 0 -10000 0 -10000 0 0
VIPR1 0.004 0.15 0.28 2 -0.48 25 27
NR3C1 0.036 0.15 0.3 46 -0.26 20 66
NR4A1 -0.16 0.16 -10000 0 -0.29 226 226
TIF2/SUV420H1 0.003 0.049 -10000 0 -0.19 24 24
MAPKKK cascade -0.045 0.18 0.48 3 -0.45 17 20
cortisol/GR alpha (dimer)/Src-1 0.044 0.23 0.42 56 -0.41 23 79
PBX1 0 0.061 -10000 0 -0.29 17 17
POU1F1 0.008 0.027 0.27 3 -10000 0 3
SELE -0.4 0.46 0.31 2 -0.86 193 195
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.038 0.16 0.32 27 -0.35 12 39
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.049 0.21 0.4 55 -0.38 23 78
mol:cortisol 0.03 0.15 0.27 62 -0.26 24 86
MMP1 0.16 0.21 0.44 76 -0.87 1 77
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.011 0.018 0.27 2 -10000 0 2
RAS family/GTP/Tiam1 -0.056 0.068 -10000 0 -0.17 49 49
NT3 (dimer)/TRKC -0.12 0.13 0.19 1 -0.23 225 226
NT3 (dimer)/TRKB -0.11 0.14 0.2 8 -0.22 218 226
SHC/Grb2/SOS1/GAB1/PI3K 0.017 0.01 -10000 0 -0.16 1 1
RAPGEF1 0.01 0 -10000 0 -10000 0 0
BDNF -0.047 0.12 -10000 0 -0.29 78 78
PIK3CA 0.01 0 -10000 0 -10000 0 0
DYNLT1 0.01 0 -10000 0 -10000 0 0
NTRK1 0.013 0.034 0.27 7 -10000 0 7
NTRK2 -0.1 0.15 0.27 7 -0.29 157 164
NTRK3 -0.14 0.15 -10000 0 -0.29 196 196
NT-4/5 (dimer)/TRKB -0.09 0.13 0.2 8 -0.21 203 211
neuron apoptosis 0.13 0.18 0.35 132 -10000 0 132
SHC 2-3/Grb2 -0.14 0.19 -10000 0 -0.38 132 132
SHC1 0.011 0.013 0.27 1 -10000 0 1
SHC2 -0.15 0.21 -10000 0 -0.46 101 101
SHC3 -0.14 0.19 -10000 0 -0.42 109 109
STAT3 (dimer) 0.015 0.047 0.16 14 -0.28 7 21
NT3 (dimer)/TRKA -0.046 0.11 0.2 10 -0.18 143 153
RIN/GDP -0.05 0.068 0.15 1 -0.16 58 59
GIPC1 0.01 0 -10000 0 -10000 0 0
KRAS 0.011 0.013 0.27 1 -10000 0 1
DNAJA3 -0.058 0.12 0.18 2 -0.23 121 123
RIN/GTP 0.001 0.009 0.18 1 -10000 0 1
CCND1 0.015 0.091 0.31 14 -0.54 7 21
MAGED1 0.01 0 -10000 0 -10000 0 0
PTPN11 0.01 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.01 0.074 -10000 0 -0.29 27 27
SHC/GRB2/SOS1 0.021 0.008 0.18 1 -10000 0 1
GRB2 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.008 0.081 0.18 12 -0.17 68 80
TRKA/NEDD4-2 0.017 0.023 0.19 7 -10000 0 7
ELMO1 0.008 0.025 -10000 0 -0.29 3 3
RhoG/GTP/ELMO1/DOCK1 0.011 0.022 -10000 0 -0.2 4 4
NGF -0.03 0.1 -10000 0 -0.29 54 54
HRAS 0.01 0 -10000 0 -10000 0 0
DOCK1 0.008 0.021 -10000 0 -0.29 2 2
GAB2 0.009 0.015 -10000 0 -0.29 1 1
RIT2 0.001 0.014 0.27 1 -10000 0 1
RIT1 0.01 0 -10000 0 -10000 0 0
FRS2 0.014 0.034 0.27 7 -10000 0 7
DNM1 0.002 0.048 -10000 0 -0.29 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.054 0.12 0.18 2 -0.22 121 123
mol:GDP -0.072 0.094 -10000 0 -0.22 69 69
NGF (dimer) -0.03 0.1 -10000 0 -0.29 54 54
RhoG/GDP 0.006 0.017 -10000 0 -0.19 3 3
RIT1/GDP -0.049 0.068 -10000 0 -0.16 55 55
TIAM1 0.008 0.025 -10000 0 -0.29 3 3
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
BDNF (dimer)/TRKB -0.076 0.12 0.18 7 -0.19 194 201
KIDINS220/CRKL/C3G 0.016 0.012 0.19 2 -10000 0 2
SHC/RasGAP 0.015 0.009 0.19 1 -10000 0 1
FRS2 family/SHP2 0.023 0.021 0.18 7 -10000 0 7
SHC/GRB2/SOS1/GAB1 0.026 0.007 0.18 1 -10000 0 1
RIT1/GTP 0.007 0 -10000 0 -10000 0 0
NT3 (dimer) -0.045 0.12 0.27 1 -0.29 76 77
RAP1/GDP -0.046 0.054 -10000 0 -0.14 55 55
KIDINS220/CRKL 0.011 0.018 0.27 2 -10000 0 2
BDNF (dimer) -0.047 0.12 -10000 0 -0.29 78 78
ubiquitin-dependent protein catabolic process -0.001 0.064 0.18 7 -0.16 54 61
Schwann cell development -0.034 0.027 -10000 0 -0.093 4 4
EHD4 0.01 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.028 0.02 0.18 7 -10000 0 7
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.014 -10000 0 -0.15 1 1
RAP1B 0.01 0 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.13 -10000 0 -0.21 285 285
ABL1 0.01 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.015 0 -10000 0 -10000 0 0
Rap1/GTP -0.022 0.056 -10000 0 -10000 0 0
STAT3 0.015 0.047 0.16 14 -0.28 7 21
axon guidance -0.14 0.13 -10000 0 -0.2 285 285
MAPK3 -0.013 0.067 -10000 0 -0.15 68 68
MAPK1 -0.013 0.067 -10000 0 -0.15 68 68
CDC42/GDP -0.049 0.068 -10000 0 -0.16 55 55
NTF3 -0.045 0.12 0.27 1 -0.29 76 77
NTF4 -0.01 0.074 -10000 0 -0.29 27 27
NGF (dimer)/TRKA/FAIM -0.001 0.064 0.18 7 -0.16 54 61
PI3K 0.014 0.01 -10000 0 -0.19 1 1
FRS3 0.01 0 -10000 0 -10000 0 0
FAIM 0.01 0 -10000 0 -10000 0 0
GAB1 0.01 0 -10000 0 -10000 0 0
RASGRF1 -0.047 0.13 0.23 3 -0.23 119 122
SOS1 0.01 0 -10000 0 -10000 0 0
MCF2L -0.1 0.12 0.12 1 -0.2 225 226
RGS19 0.011 0.013 0.27 1 -10000 0 1
CDC42 0.01 0 -10000 0 -10000 0 0
RAS family/GTP 0.005 0.055 -10000 0 -10000 0 0
Rac1/GDP -0.049 0.068 -10000 0 -0.16 55 55
NGF (dimer)/TRKA/GRIT -0.007 0.063 0.17 7 -0.16 54 61
neuron projection morphogenesis -0.054 0.13 -10000 0 -0.39 25 25
NGF (dimer)/TRKA/NEDD4-2 -0.001 0.064 0.18 7 -0.16 54 61
MAP2K1 0.014 0.004 -10000 0 -10000 0 0
NGFR -0.053 0.13 0.27 5 -0.29 90 95
NGF (dimer)/TRKA/GIPC/GAIP -0.01 0.075 -10000 0 -0.18 59 59
RAS family/GTP/PI3K 0.014 0.01 -10000 0 -0.17 1 1
FRS2 family/SHP2/GRB2/SOS1 0.032 0.018 0.17 7 -10000 0 7
NRAS 0.01 0 -10000 0 -10000 0 0
GRB2/SOS1 0.015 0 -10000 0 -10000 0 0
PRKCI 0.01 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCZ 0.008 0.025 -10000 0 -0.29 3 3
MAPKKK cascade -0.094 0.21 -10000 0 -0.61 54 54
RASA1 0.01 0 -10000 0 -10000 0 0
TRKA/c-Abl 0.017 0.023 0.19 7 -10000 0 7
SQSTM1 0.01 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.063 0.11 0.18 7 -0.17 194 201
NGF (dimer)/TRKA/p62/Atypical PKCs 0.009 0.058 0.17 6 -0.13 55 61
MATK -0.003 0.076 0.27 6 -0.29 23 29
NEDD4L 0.01 0 -10000 0 -10000 0 0
RAS family/GDP -0.048 0.046 -10000 0 -0.13 45 45
NGF (dimer)/TRKA -0.062 0.12 0.2 2 -0.24 121 123
Rac1/GTP -0.065 0.079 -10000 0 -0.18 117 117
FRS2 family/SHP2/CRK family 0.033 0.021 0.17 9 -10000 0 9
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.004 0.067 0.18 4 -0.16 50 54
MAP4K1 0.005 0.051 0.27 3 -0.29 10 13
MAP3K8 0.008 0.025 -10000 0 -0.29 3 3
PRKCB -0.076 0.14 -10000 0 -0.29 118 118
DBNL 0.01 0 -10000 0 -10000 0 0
CRKL 0.011 0.018 0.27 2 -10000 0 2
MAP3K1 -0.005 0.07 -10000 0 -0.18 50 50
JUN -0.15 0.25 -10000 0 -0.53 121 121
MAP3K7 -0.005 0.07 -10000 0 -0.18 50 50
GRAP2 -0.023 0.093 -10000 0 -0.29 45 45
CRK 0.01 0 -10000 0 -10000 0 0
MAP2K4 -0.004 0.073 -10000 0 -0.18 46 46
LAT 0.011 0.013 0.27 1 -10000 0 1
LCP2 0.008 0.025 -10000 0 -0.29 3 3
MAPK8 -0.15 0.26 -10000 0 -0.55 121 121
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.006 0.074 -10000 0 -0.19 50 50
LAT/GRAP2/SLP76/HPK1/HIP-55 0.009 0.064 0.17 4 -0.15 50 54
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.007 0.051 0.11 20 -0.19 15 35
NFATC2 -0.002 0.064 0.13 7 -0.19 33 40
NFATC3 0.014 0.034 0.11 20 -10000 0 20
CD40LG -0.063 0.21 0.38 16 -0.36 95 111
PTGS2 -0.077 0.22 0.38 15 -0.38 115 130
JUNB 0.006 0.033 -10000 0 -0.29 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.02 0.098 2 -10000 0 2
CaM/Ca2+ 0.007 0.02 0.098 2 -10000 0 2
CALM1 0.01 0.012 -10000 0 -10000 0 0
JUN -0.001 0.059 -10000 0 -0.29 15 15
mol:Ca2+ 0 0.011 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.007 0.007 -10000 0 -10000 0 0
FOSL1 -0.011 0.075 -10000 0 -0.29 28 28
CREM 0.01 0 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.007 0.14 0.33 16 -0.26 56 72
FOS -0.058 0.13 -10000 0 -0.29 90 90
IFNG -0.015 0.24 0.41 54 -0.34 83 137
AP-1/NFAT1-c-4 -0.042 0.24 0.54 15 -0.38 83 98
FASLG -0.053 0.21 0.4 19 -0.35 89 108
NFAT1-c-4/ICER1 -0.006 0.1 0.22 14 -0.22 42 56
IL2RA -0.044 0.22 0.43 24 -0.36 84 108
FKBP12/FK506 0.007 0 -10000 0 -10000 0 0
CSF2 -0.018 0.23 0.4 50 -0.34 83 133
JunB/Fra1/NFAT1-c-4 -0.013 0.11 0.21 14 -0.22 51 65
IL4 -0.053 0.19 0.37 16 -0.34 83 99
IL2 -0.005 0.009 -10000 0 -10000 0 0
IL3 -0.012 0.016 -10000 0 -10000 0 0
FKBP1A 0.01 0 -10000 0 -10000 0 0
BATF3 0.009 0.042 0.27 4 -0.29 5 9
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.01 0.001 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.073 0.13 0.18 1 -0.23 156 157
fibroblast growth factor receptor signaling pathway -0.073 0.13 0.18 1 -0.22 156 157
LAMA1 0.041 0.12 0.27 66 -0.29 15 81
PRNP 0.003 0.046 -10000 0 -0.29 10 10
GPC1/SLIT2 -0.079 0.1 -10000 0 -0.19 184 184
SMAD2 0.012 0.013 -10000 0 -0.14 3 3
GPC1/PrPc/Cu2+ 0.01 0.028 0.17 1 -0.16 10 11
GPC1/Laminin alpha1 0.036 0.08 0.2 66 -0.19 15 81
TDGF1 0.007 0.023 0.27 3 -10000 0 3
CRIPTO/GPC1 0.013 0.018 0.19 4 -10000 0 4
APP/GPC1 0.014 0.017 0.19 1 -0.19 2 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.011 0.01 0.12 3 -10000 0 3
FLT1 0.01 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.019 0.017 0.18 1 -0.16 3 4
SERPINC1 0.027 0.068 0.27 30 -10000 0 30
FYN 0.011 0.01 0.11 4 -10000 0 4
FGR 0.011 0.01 0.11 4 -10000 0 4
positive regulation of MAPKKK cascade 0.004 0.047 -10000 0 -0.26 3 3
SLIT2 -0.13 0.15 -10000 0 -0.29 185 185
GPC1/NRG -0.014 0.091 0.19 19 -0.19 73 92
NRG1 -0.032 0.13 0.27 18 -0.29 73 91
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.021 0.008 0.18 1 -10000 0 1
LYN 0.011 0.01 0.12 3 -10000 0 3
mol:Spermine 0.005 0.008 0.16 1 -10000 0 1
cell growth -0.073 0.13 0.18 1 -0.22 156 157
BMP signaling pathway -0.011 0.013 -10000 0 -0.27 1 1
SRC 0.011 0.01 0.11 4 -10000 0 4
TGFBR1 0.01 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.12 0.15 0.27 3 -0.29 182 185
GPC1 0.011 0.013 0.27 1 -10000 0 1
TGFBR1 (dimer) 0.01 0 -10000 0 -10000 0 0
VEGFA 0.01 0 -10000 0 -10000 0 0
BLK 0.015 0.032 0.16 16 -10000 0 16
HCK 0.013 0.02 0.14 9 -10000 0 9
FGF2 -0.089 0.14 -10000 0 -0.29 136 136
FGFR1 -0.058 0.12 -10000 0 -0.29 93 93
VEGFR1 homodimer 0.01 0 -10000 0 -10000 0 0
TGFBR2 0.008 0.025 -10000 0 -0.29 3 3
cell death 0.014 0.017 0.19 1 -0.19 2 3
ATIII/GPC1 0.027 0.047 0.19 31 -10000 0 31
PLA2G2A/GPC1 -0.076 0.1 0.19 3 -0.19 181 184
LCK 0.012 0.015 0.13 6 -10000 0 6
neuron differentiation -0.014 0.091 0.19 19 -0.19 73 92
PrPc/Cu2+ 0.002 0.031 -10000 0 -0.19 10 10
APP 0.008 0.021 -10000 0 -0.29 2 2
TGFBR2 (dimer) 0.008 0.025 -10000 0 -0.29 3 3
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.19 0.19 0.59 31 -10000 0 31
PCK1 0.19 0.19 0.6 45 -10000 0 45
HNF4A 0.23 0.24 0.71 52 -10000 0 52
KCNJ11 0.19 0.27 0.61 35 -0.7 18 53
AKT1 0.13 0.14 0.38 49 -0.38 1 50
response to starvation 0.016 0.032 0.15 12 -10000 0 12
DLK1 0.18 0.27 0.61 39 -0.62 19 58
NKX2-1 0.24 0.2 0.67 41 -10000 0 41
ACADM 0.19 0.2 0.57 36 -0.53 2 38
TAT 0.19 0.19 0.59 44 -10000 0 44
CEBPB 0.023 0.029 0.15 10 -10000 0 10
CEBPA 0.033 0.062 0.25 20 -0.29 2 22
TTR 0.18 0.25 0.6 70 -0.44 3 73
PKLR 0.2 0.21 0.58 49 -10000 0 49
APOA1 0.26 0.28 0.82 48 -10000 0 48
CPT1C 0.19 0.2 0.57 40 -0.68 1 41
ALAS1 0.16 0.14 0.5 17 -10000 0 17
TFRC 0.24 0.22 0.65 58 -10000 0 58
FOXF1 -0.11 0.15 -10000 0 -0.3 148 148
NF1 0.013 0 -10000 0 -10000 0 0
HNF1A (dimer) 0.071 0.071 0.25 24 -10000 0 24
CPT1A 0.19 0.19 0.57 37 -0.7 1 38
HMGCS1 0.19 0.19 0.57 35 -10000 0 35
NR3C1 0.022 0.064 0.21 8 -0.29 10 18
CPT1B 0.19 0.19 0.58 35 -0.7 1 36
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.057 0.054 -10000 0 -10000 0 0
GCK 0.16 0.27 0.57 35 -0.63 25 60
CREB1 0.025 0.036 0.18 6 -10000 0 6
IGFBP1 0.16 0.17 0.57 30 -10000 0 30
PDX1 0.26 0.23 0.57 99 -10000 0 99
UCP2 0.19 0.19 0.56 40 -10000 0 40
ALDOB 0.23 0.25 0.72 48 -10000 0 48
AFP 0.05 0.11 0.34 18 -10000 0 18
BDH1 0.19 0.19 0.57 38 -10000 0 38
HADH 0.21 0.21 0.6 35 -10000 0 35
F2 0.25 0.27 0.82 43 -10000 0 43
HNF1A 0.071 0.071 0.25 24 -10000 0 24
G6PC 0.1 0.12 0.5 25 -10000 0 25
SLC2A2 0.21 0.21 0.61 49 -10000 0 49
INS -0.017 0.033 -10000 0 -10000 0 0
FOXA1 0.007 0.12 0.25 22 -0.29 40 62
FOXA3 0.13 0.14 0.33 116 -10000 0 116
FOXA2 0.31 0.32 0.83 69 -10000 0 69
ABCC8 0.21 0.21 0.61 36 -10000 0 36
ALB 0.064 0.13 0.31 61 -10000 0 61
IL6-mediated signaling events

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
BCL2L1 0.012 0.22 0.56 12 -0.62 11 23
CRP 0.014 0.23 0.61 14 -0.6 13 27
cell cycle arrest 0.002 0.24 0.59 12 -0.65 17 29
TIMP1 0.014 0.21 0.53 13 -0.51 15 28
IL6ST -0.022 0.1 -10000 0 -0.29 51 51
Rac1/GDP -0.068 0.19 0.3 10 -0.38 80 90
AP1 0.004 0.12 0.31 8 -0.31 9 17
GAB2 0.012 0.016 -10000 0 -0.28 1 1
TNFSF11 0.011 0.24 0.58 13 -0.7 15 28
HSP90B1 0.027 0.072 -10000 0 -0.57 1 1
GAB1 0.012 0.004 -10000 0 -10000 0 0
MAPK14 -0.12 0.23 -10000 0 -0.55 77 77
AKT1 0.03 0.022 -10000 0 -10000 0 0
FOXO1 0.029 0.021 -10000 0 -10000 0 0
MAP2K6 -0.1 0.21 0.25 3 -0.45 82 85
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.038 0.21 0.36 23 -0.41 60 83
MITF -0.086 0.2 0.27 10 -0.39 88 98
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.01 0 -10000 0 -10000 0 0
A2M -0.1 0.35 -10000 0 -1.2 37 37
CEBPB 0.016 0.017 -10000 0 -0.29 1 1
GRB2/SOS1/GAB family/SHP2 -0.005 0.088 0.26 4 -0.35 3 7
STAT3 -0.006 0.25 0.59 12 -0.69 17 29
STAT1 0.014 0.04 0.27 4 -10000 0 4
CEBPD 0.01 0.22 0.56 11 -0.78 7 18
PIK3CA 0.011 0.001 -10000 0 -10000 0 0
PI3K 0.015 0.01 -10000 0 -0.19 1 1
JUN -0.001 0.058 -10000 0 -0.29 16 16
PIAS3/MITF -0.082 0.19 0.25 10 -0.37 87 97
MAPK11 -0.12 0.23 -10000 0 -0.55 77 77
STAT3 (dimer)/FOXO1 -0.011 0.22 0.47 19 -0.51 24 43
GRB2/SOS1/GAB family -0.068 0.16 0.24 2 -0.32 78 80
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.095 0.18 0.21 5 -0.38 82 87
GRB2 0.012 0.004 -10000 0 -10000 0 0
JAK2 0.009 0.015 -10000 0 -0.29 1 1
LBP 0.044 0.23 0.56 24 -0.55 6 30
PIK3R1 0.01 0.015 -10000 0 -0.29 1 1
JAK1 0.011 0.011 -10000 0 -10000 0 0
MYC -0.012 0.28 0.56 12 -0.86 23 35
FGG 0.022 0.24 0.59 22 -0.61 12 34
macrophage differentiation 0.002 0.24 0.59 12 -0.65 17 29
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.064 0.13 -10000 0 -0.27 75 75
JUNB 0.006 0.23 0.54 12 -0.69 15 27
FOS -0.084 0.14 -10000 0 -0.29 129 129
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.082 0.2 0.3 10 -0.41 77 87
STAT1/PIAS1 -0.046 0.18 0.3 21 -0.37 54 75
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.024 -10000 0 -0.23 1 1
STAT3 (dimer) -0.004 0.24 0.59 12 -0.68 17 29
PRKCD -0.015 0.22 0.42 23 -0.47 40 63
IL6R -0.013 0.084 -10000 0 -0.29 34 34
SOCS3 -0.19 0.34 -10000 0 -0.99 55 55
gp130 (dimer)/JAK1/JAK1/LMO4 0.009 0.08 0.22 3 -0.16 54 57
Rac1/GTP -0.061 0.2 0.3 19 -0.38 77 96
HCK 0.005 0.058 0.27 5 -0.29 12 17
MAPKKK cascade 0.022 0.079 0.27 2 -0.64 1 3
bone resorption 0.013 0.23 0.58 13 -0.66 15 28
IRF1 0.011 0.22 0.56 11 -0.68 8 19
mol:GDP -0.077 0.2 0.3 10 -0.39 81 91
SOS1 0.013 0.006 -10000 0 -10000 0 0
VAV1 -0.078 0.2 0.3 10 -0.4 81 91
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.27 -10000 0 -0.6 80 80
PTPN11 0.013 0.032 -10000 0 -10000 0 0
IL6/IL6RA -0.086 0.13 -10000 0 -0.21 193 193
gp130 (dimer)/TYK2/TYK2/LMO4 0.004 0.072 0.22 1 -0.16 59 60
gp130 (dimer)/JAK2/JAK2/LMO4 0.004 0.074 0.22 1 -0.16 59 60
IL6 -0.1 0.15 -10000 0 -0.29 155 155
PIAS3 0.01 0 -10000 0 -10000 0 0
PTPRE 0 0.032 0.27 2 -0.2 2 4
PIAS1 0.01 0 -10000 0 -10000 0 0
RAC1 0.011 0.002 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.097 0.17 0.2 3 -0.25 170 173
LMO4 0.015 0.024 -10000 0 -0.3 1 1
STAT3 (dimer)/PIAS3 -0.018 0.23 0.53 10 -0.66 17 27
MCL1 0.031 0.021 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 0.004 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.004 0.085 0.2 2 -0.16 67 69
NFATC4 -0.014 0.058 -10000 0 -0.12 75 75
ERBB2IP 0.01 0.002 -10000 0 -10000 0 0
HSP90 (dimer) 0.01 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.012 0.075 0.16 12 -0.15 75 87
JUN -0.01 0.082 0.23 6 -0.3 1 7
HRAS 0.01 0.001 -10000 0 -10000 0 0
DOCK7 -0.016 0.066 -10000 0 -0.14 75 75
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.003 0.074 0.17 17 -0.14 75 92
AKT1 0.003 0.003 -10000 0 -10000 0 0
BAD 0.005 0.002 -10000 0 -10000 0 0
MAPK10 -0.009 0.043 -10000 0 -0.11 29 29
mol:GTP 0 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.012 0.08 0.17 12 -0.16 75 87
RAF1 -0.004 0.092 0.18 34 -0.21 21 55
ErbB2/ErbB3/neuregulin 2 -0.056 0.081 0.17 2 -0.15 170 172
STAT3 0.013 0.004 -10000 0 -10000 0 0
cell migration -0.014 0.051 -10000 0 -0.13 22 22
mol:PI-3-4-5-P3 -0.001 0.001 -10000 0 -10000 0 0
cell proliferation -0.059 0.22 0.37 5 -0.55 32 37
FOS -0.1 0.25 0.3 34 -0.44 130 164
NRAS 0.01 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.075 0.16 12 -0.15 75 87
MAPK3 -0.029 0.17 0.34 5 -0.41 32 37
MAPK1 -0.029 0.17 0.34 5 -0.41 32 37
JAK2 -0.016 0.066 -10000 0 -0.14 75 75
NF2 0.004 0.007 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.017 0.082 -10000 0 -0.19 70 70
NRG1 -0.033 0.13 0.27 18 -0.29 73 91
GRB2/SOS1 0.015 0.001 -10000 0 -10000 0 0
MAPK8 -0.027 0.092 -10000 0 -0.2 84 84
MAPK9 -0.007 0.039 -10000 0 -0.091 24 24
ERBB2 0.001 0.028 0.15 13 -10000 0 13
ERBB3 0.003 0.05 0.27 2 -0.29 10 12
SHC1 0.011 0.013 0.27 1 -10000 0 1
RAC1 0.01 0 -10000 0 -10000 0 0
apoptosis 0.004 0.01 -10000 0 -10000 0 0
STAT3 (dimer) 0.013 0.004 -10000 0 -10000 0 0
RNF41 0.004 0.005 -10000 0 -10000 0 0
FRAP1 0.002 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.019 0.045 -10000 0 -0.11 70 70
ErbB2/ErbB2/HSP90 (dimer) 0.009 0.02 0.12 10 -10000 0 10
CHRNA1 -0.004 0.16 0.34 34 -0.38 15 49
myelination -0.016 0.056 -10000 0 -0.12 77 77
PPP3CB -0.015 0.063 -10000 0 -0.14 75 75
KRAS 0.011 0.013 0.27 1 -10000 0 1
RAC1-CDC42/GDP -0.008 0.076 -10000 0 -0.16 75 75
NRG2 -0.12 0.15 -10000 0 -0.29 172 172
mol:GDP -0.019 0.083 -10000 0 -0.18 75 75
SOS1 0.01 0.001 -10000 0 -10000 0 0
MAP2K2 -0.005 0.1 0.21 34 -0.2 31 65
SRC 0.01 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 -0.016 0.066 -10000 0 -0.14 75 75
MAP2K1 -0.045 0.17 0.34 2 -0.41 31 33
heart morphogenesis -0.012 0.075 0.16 12 -0.15 75 87
RAS family/GDP -0.004 0.079 -10000 0 -0.16 70 70
GRB2 0.01 0.001 -10000 0 -10000 0 0
PRKACA 0.003 0.007 -10000 0 -10000 0 0
CHRNE 0.003 0.026 0.19 2 -0.16 1 3
HSP90AA1 0.01 0 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.003 -10000 0 -10000 0 0
nervous system development -0.012 0.075 0.16 12 -0.15 75 87
CDC42 0.01 0 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.023 0.12 0.3 27 -0.27 16 43
TBX21 -0.11 0.47 0.74 8 -1.1 59 67
B2M 0.009 0.01 -10000 0 -10000 0 0
TYK2 0.007 0.033 0.17 3 -10000 0 3
IL12RB1 0.013 0.091 0.32 20 -0.33 10 30
GADD45B -0.069 0.37 0.64 7 -0.9 48 55
IL12RB2 0.043 0.11 0.28 64 -0.31 5 69
GADD45G -0.063 0.35 0.64 7 -0.86 46 53
natural killer cell activation -0.001 0.03 0.14 5 -10000 0 5
RELB 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
IL18 0.007 0.039 -10000 0 -0.29 6 6
IL2RA 0.009 0.084 0.27 19 -0.29 18 37
IFNG 0.059 0.1 0.27 81 -10000 0 81
STAT3 (dimer) -0.063 0.34 0.59 8 -0.74 64 72
HLA-DRB5 -0.001 0.072 0.26 12 -0.29 15 27
FASLG -0.12 0.47 0.83 7 -1.1 62 69
NF kappa B2 p52/RelB -0.16 0.38 -10000 0 -0.96 62 62
CD4 0.001 0.024 -10000 0 -0.29 2 2
SOCS1 0.011 0.013 0.27 1 -10000 0 1
EntrezGene:6955 -0.008 0.015 -10000 0 -10000 0 0
CD3D -0.024 0.089 0.26 3 -0.3 36 39
CD3E -0.029 0.091 -10000 0 -0.29 42 42
CD3G -0.033 0.095 -10000 0 -0.3 46 46
IL12Rbeta2/JAK2 0.037 0.092 0.22 60 -0.22 7 67
CCL3 -0.11 0.47 0.76 9 -1.1 59 68
CCL4 -0.13 0.51 0.74 8 -1.2 64 72
HLA-A 0.008 0.018 -10000 0 -0.29 1 1
IL18/IL18R 0.027 0.076 0.24 2 -0.19 26 28
NOS2 -0.076 0.4 0.72 7 -0.91 56 63
IL12/IL12R/TYK2/JAK2/SPHK2 0.023 0.12 0.29 27 -0.27 16 43
IL1R1 -0.093 0.43 0.71 8 -1 56 64
IL4 0.002 0.03 -10000 0 -0.16 3 3
JAK2 0.007 0.036 0.19 2 -0.3 1 3
EntrezGene:6957 -0.007 0.013 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.11 0.29 0.26 2 -0.66 67 69
RAB7A -0.041 0.3 0.62 5 -0.71 46 51
lysosomal transport -0.036 0.29 0.6 6 -0.67 46 52
FOS -0.36 0.57 0.56 4 -1 159 163
STAT4 (dimer) -0.07 0.37 0.61 8 -0.83 63 71
STAT5A (dimer) -0.1 0.43 0.47 36 -0.97 62 98
GZMA -0.13 0.5 0.79 7 -1.2 59 66
GZMB -0.11 0.48 0.76 9 -1.1 58 67
HLX 0.011 0.013 0.27 1 -10000 0 1
LCK -0.11 0.47 0.68 9 -1.1 62 71
TCR/CD3/MHC II/CD4 -0.11 0.2 0.16 1 -0.3 169 170
IL2/IL2R 0.019 0.07 0.2 25 -0.18 25 50
MAPK14 -0.065 0.36 0.63 7 -0.83 55 62
CCR5 -0.079 0.39 0.66 7 -1 46 53
IL1B 0.002 0.092 0.27 16 -0.31 20 36
STAT6 -0.002 0.15 0.42 10 -0.28 41 51
STAT4 -0.005 0.064 -10000 0 -0.29 20 20
STAT3 0.01 0 -10000 0 -10000 0 0
STAT1 0.012 0.026 0.27 4 -10000 0 4
NFKB1 0.01 0 -10000 0 -10000 0 0
NFKB2 0.01 0 -10000 0 -10000 0 0
IL12B 0.014 0.062 0.29 15 -10000 0 15
CD8A -0.019 0.09 0.3 1 -0.29 39 40
CD8B -0.014 0.095 0.28 7 -0.29 37 44
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.023 0.12 0.26 16 -0.3 27 43
IL2RB 0.008 0.038 0.27 2 -0.29 5 7
proteasomal ubiquitin-dependent protein catabolic process -0.058 0.34 0.61 8 -0.75 63 71
IL2RG 0.008 0.06 0.27 9 -0.29 10 19
IL12 0.021 0.069 0.22 25 -10000 0 25
STAT5A 0.009 0.015 -10000 0 -0.29 1 1
CD247 -0.003 0.043 0.27 1 -0.29 7 8
IL2 0.003 0.004 -10000 0 -10000 0 0
SPHK2 0.011 0.013 0.27 1 -10000 0 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.012 0.049 0.25 11 -10000 0 11
IL12/IL12R/TYK2/JAK2 -0.12 0.53 0.79 10 -1.2 62 72
MAP2K3 -0.065 0.36 0.63 7 -0.8 60 67
RIPK2 0.01 0 -10000 0 -10000 0 0
MAP2K6 -0.068 0.36 0.63 7 -0.81 60 67
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.008 0.055 0.27 1 -0.29 13 14
IL18RAP -0.003 0.067 -10000 0 -0.29 20 20
IL12Rbeta1/TYK2 0.015 0.077 0.25 20 -0.25 10 30
EOMES -0.064 0.25 -10000 0 -1.1 20 20
STAT1 (dimer) -0.03 0.36 0.58 21 -0.74 61 82
T cell proliferation -0.049 0.28 0.53 6 -0.6 60 66
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.009 0.029 -10000 0 -0.3 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.13 0.23 -10000 0 -0.63 63 63
ATF2 -0.056 0.33 0.59 7 -0.76 55 62
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.01 0 -10000 0 -10000 0 0
VLDLR 0.003 0.046 -10000 0 -0.29 10 10
LRPAP1 0.011 0.013 0.27 1 -10000 0 1
NUDC 0.01 0 -10000 0 -10000 0 0
RELN/LRP8 -0.017 0.11 0.19 46 -0.16 111 157
CaM/Ca2+ 0.007 0 -10000 0 -10000 0 0
KATNA1 0.01 0 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.024 0.078 0.18 3 -0.14 111 114
IQGAP1/CaM 0.015 0 -10000 0 -10000 0 0
DAB1 -0.002 0.11 0.27 25 -0.29 34 59
IQGAP1 0.01 0 -10000 0 -10000 0 0
PLA2G7 0.043 0.086 0.27 52 -10000 0 52
CALM1 0.01 0 -10000 0 -10000 0 0
DYNLT1 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.048 0.069 0.19 77 -10000 0 77
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.01 0 -10000 0 -10000 0 0
CDK5R1 0.024 0.058 0.27 22 -10000 0 22
LIS1/Poliovirus Protein 3A 0.007 0 -10000 0 -10000 0 0
CDK5R2 0.024 0.065 0.27 27 -10000 0 27
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.052 0.11 0.18 19 -0.17 160 179
YWHAE 0.009 0.015 -10000 0 -0.29 1 1
NDEL1/14-3-3 E -0.002 0.073 0.18 16 -10000 0 16
MAP1B -0.02 0.068 -10000 0 -0.21 45 45
RAC1 0.009 0 -10000 0 -10000 0 0
p35/CDK5 -0.009 0.081 0.22 16 -0.12 107 123
RELN -0.093 0.14 0.27 4 -0.29 143 147
PAFAH/LIS1 0.037 0.059 0.19 52 -10000 0 52
LIS1/CLIP170 0.014 0 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.013 0.045 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.053 0.11 0.2 2 -0.18 152 154
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.007 0.075 0.18 17 -10000 0 17
LIS1/IQGAP1 0.014 0 -10000 0 -10000 0 0
RHOA 0.009 0 -10000 0 -10000 0 0
PAFAH1B1 0.009 0 -10000 0 -10000 0 0
PAFAH1B3 0.025 0.06 0.27 23 -10000 0 23
PAFAH1B2 0.01 0 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain -0.002 0.045 -10000 0 -0.13 45 45
NDEL1/Katanin 60/Dynein heavy chain 0.001 0.072 0.24 4 -10000 0 4
LRP8 0.058 0.1 0.27 76 -10000 0 76
NDEL1/Katanin 60 -0.002 0.073 0.18 17 -10000 0 17
P39/CDK5 -0.008 0.085 0.22 22 -0.12 108 130
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.014 0 -10000 0 -10000 0 0
CDK5 -0.022 0.071 0.16 3 -0.13 111 114
PPP2R5D 0.01 0 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.012 0 -10000 0 -10000 0 0
CSNK2A1 0.01 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.037 0.094 0.17 19 -0.14 160 179
RELN/VLDLR -0.013 0.1 0.18 43 -0.14 115 158
CDC42 0.009 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.022 0.079 -10000 0 -0.33 24 24
PDGF/PDGFRA/CRKL -0.022 0.072 0.17 1 -0.2 55 56
positive regulation of JUN kinase activity -0.001 0.056 0.17 1 -0.14 56 57
CRKL 0.011 0.018 0.27 2 -10000 0 2
PDGF/PDGFRA/Caveolin-3 -0.025 0.072 0.19 2 -0.2 55 57
AP1 -0.23 0.34 -10000 0 -0.74 129 129
mol:IP3 -0.037 0.078 -10000 0 -0.22 56 56
PLCG1 -0.037 0.078 -10000 0 -0.22 56 56
PDGF/PDGFRA/alphaV Integrin -0.023 0.073 -10000 0 -0.2 56 56
RAPGEF1 0.01 0 -10000 0 -10000 0 0
CRK 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ -0.037 0.078 -10000 0 -0.22 56 56
CAV3 0.005 0.023 0.27 3 -10000 0 3
CAV1 -0.004 0.063 -10000 0 -0.29 19 19
SHC/Grb2/SOS1 -0.001 0.057 0.18 1 -0.14 56 57
PDGF/PDGFRA/Shf -0.026 0.078 -10000 0 -0.21 60 60
FOS -0.23 0.34 -10000 0 -0.73 129 129
JUN -0.028 0.053 -10000 0 -0.25 16 16
oligodendrocyte development -0.023 0.073 -10000 0 -0.2 56 56
GRB2 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
mol:DAG -0.037 0.078 -10000 0 -0.22 56 56
PDGF/PDGFRA -0.022 0.079 -10000 0 -0.33 24 24
actin cytoskeleton reorganization -0.023 0.071 -10000 0 -0.2 56 56
SRF 0.017 0.011 -10000 0 -10000 0 0
SHC1 0.011 0.013 0.27 1 -10000 0 1
PI3K -0.013 0.061 -10000 0 -0.16 57 57
PDGF/PDGFRA/Crk/C3G -0.013 0.06 -10000 0 -0.16 56 56
JAK1 -0.011 0.052 -10000 0 -0.21 24 24
ELK1/SRF -0.023 0.063 -10000 0 -0.17 56 56
SHB 0.01 0 -10000 0 -10000 0 0
SHF 0.005 0.039 -10000 0 -0.29 7 7
CSNK2A1 0.023 0.019 -10000 0 -10000 0 0
GO:0007205 -0.045 0.09 -10000 0 -0.26 56 56
SOS1 0.01 0 -10000 0 -10000 0 0
Ras protein signal transduction -0.001 0.056 0.17 1 -0.14 56 57
PDGF/PDGFRA/SHB -0.023 0.072 -10000 0 -0.2 56 56
PDGF/PDGFRA/Caveolin-1 -0.031 0.09 -10000 0 -0.23 64 64
ITGAV 0.009 0.015 -10000 0 -0.29 1 1
ELK1 -0.048 0.085 -10000 0 -0.23 56 56
PIK3CA 0.01 0 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.023 0.072 -10000 0 -0.2 56 56
JAK-STAT cascade -0.011 0.052 -10000 0 -0.21 24 24
cell proliferation -0.026 0.078 -10000 0 -0.21 60 60
BCR signaling 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
JUN -0.044 0.13 0.24 6 -0.28 71 77
IKBKB -0.008 0.059 0.23 2 -0.22 8 10
AKT1 -0.032 0.087 0.27 7 -0.18 75 82
IKBKG -0.009 0.061 0.22 2 -0.21 11 13
CALM1 -0.031 0.11 0.25 2 -0.34 30 32
PIK3CA 0.01 0 -10000 0 -10000 0 0
MAP3K1 -0.058 0.17 0.29 7 -0.38 67 74
MAP3K7 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ -0.034 0.11 0.26 2 -0.34 33 35
DOK1 0.011 0.013 0.27 1 -10000 0 1
AP-1 -0.038 0.082 0.18 6 -0.19 64 70
LYN 0.01 0 -10000 0 -10000 0 0
BLNK 0 0.052 -10000 0 -0.29 13 13
SHC1 0.011 0.013 0.27 1 -10000 0 1
BCR complex -0.02 0.11 0.29 14 -0.22 78 92
CD22 -0.067 0.19 0.33 7 -0.37 90 97
CAMK2G -0.027 0.1 0.24 2 -0.31 30 32
CSNK2A1 0.01 0 -10000 0 -10000 0 0
INPP5D 0.005 0.039 -10000 0 -0.29 7 7
SHC/GRB2/SOS1 -0.019 0.064 -10000 0 -0.13 87 87
GO:0007205 -0.035 0.11 0.26 2 -0.34 33 35
SYK 0.007 0.029 -10000 0 -0.29 4 4
ELK1 -0.032 0.11 0.25 2 -0.34 30 32
NFATC1 -0.06 0.16 0.25 7 -0.35 69 76
B-cell antigen/BCR complex -0.02 0.11 0.29 14 -0.22 78 92
PAG1/CSK 0.015 0 -10000 0 -10000 0 0
NFKBIB 0.004 0.022 0.12 2 -10000 0 2
HRAS -0.026 0.095 0.23 2 -0.28 33 35
NFKBIA 0.004 0.022 0.12 2 -10000 0 2
NF-kappa-B/RelA/I kappa B beta 0.007 0.02 0.12 2 -10000 0 2
RasGAP/Csk -0.005 0.1 0.24 15 -0.17 83 98
mol:GDP -0.033 0.11 0.26 2 -0.35 30 32
PTEN 0.01 0 -10000 0 -10000 0 0
CD79B 0.003 0.068 0.27 7 -0.29 16 23
NF-kappa-B/RelA/I kappa B alpha 0.007 0.019 0.12 2 -10000 0 2
GRB2 0.01 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.071 0.18 0.38 7 -0.39 80 87
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
mol:IP3 -0.035 0.12 0.26 2 -0.35 33 35
CSK 0.01 0 -10000 0 -10000 0 0
FOS -0.065 0.12 -10000 0 -0.3 55 55
CHUK -0.009 0.061 0.22 2 -0.21 12 14
IBTK 0.01 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.022 0.098 -10000 0 -0.29 34 34
PTPN6 -0.062 0.18 0.31 7 -0.35 90 97
RELA 0.01 0 -10000 0 -10000 0 0
BCL2A1 0.006 0.021 0.14 2 -10000 0 2
VAV2 -0.071 0.18 0.3 7 -0.42 65 72
ubiquitin-dependent protein catabolic process 0.006 0.022 0.12 2 -10000 0 2
BTK -0.047 0.23 -10000 0 -1 21 21
CD19 -0.06 0.18 0.28 11 -0.34 90 101
MAP4K1 0.005 0.051 0.27 3 -0.29 10 13
CD72 0.017 0.048 0.27 13 -0.29 1 14
PAG1 0.01 0 -10000 0 -10000 0 0
MAPK14 -0.048 0.14 0.26 8 -0.33 64 72
SH3BP5 0.009 0.015 -10000 0 -0.29 1 1
PIK3AP1 -0.033 0.12 0.22 7 -0.37 34 41
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.045 0.16 0.26 8 -0.34 77 85
RAF1 -0.023 0.091 0.23 2 -0.27 33 35
RasGAP/p62DOK/SHIP -0.006 0.1 0.28 7 -0.17 84 91
CD79A -0.035 0.13 0.27 14 -0.29 73 87
re-entry into mitotic cell cycle -0.038 0.082 0.18 6 -0.19 64 70
RASA1 0.01 0 -10000 0 -10000 0 0
MAPK3 -0.017 0.078 0.21 2 -0.25 26 28
MAPK1 -0.017 0.078 0.21 2 -0.25 26 28
CD72/SHP1 -0.058 0.18 0.32 13 -0.33 89 102
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 -0.048 0.14 0.26 8 -0.33 66 74
actin cytoskeleton organization -0.063 0.16 0.29 7 -0.37 64 71
NF-kappa-B/RelA 0.016 0.037 0.22 2 -10000 0 2
Calcineurin -0.019 0.093 -10000 0 -0.29 30 30
PI3K -0.082 0.13 -10000 0 -0.29 95 95
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.034 0.12 0.2 7 -0.35 35 42
SOS1 0.01 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.071 0.22 0.35 4 -0.61 48 52
DAPP1 -0.083 0.24 0.31 2 -0.68 46 48
cytokine secretion -0.056 0.15 0.24 7 -0.32 69 76
mol:DAG -0.035 0.12 0.26 2 -0.35 33 35
PLCG2 0.01 0.03 0.27 3 -0.29 2 5
MAP2K1 -0.02 0.085 0.22 2 -0.26 29 31
B-cell antigen/BCR complex/FcgammaRIIB -0.019 0.12 0.26 15 -0.21 83 98
mol:PI-3-4-5-P3 -0.056 0.098 -10000 0 -0.22 87 87
ETS1 -0.024 0.092 0.23 2 -0.29 30 32
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.002 0.093 0.24 14 -0.16 87 101
B-cell antigen/BCR complex/LYN -0.055 0.17 0.28 7 -0.31 94 101
MALT1 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
RAC1 -0.067 0.17 0.29 7 -0.39 64 71
B-cell antigen/BCR complex/LYN/SYK -0.053 0.17 0.38 7 -0.32 87 94
CARD11 -0.033 0.11 0.25 2 -0.34 34 36
FCGR2B -0.008 0.078 0.27 3 -0.29 27 30
PPP3CA 0.01 0 -10000 0 -10000 0 0
BCL10 0.01 0 -10000 0 -10000 0 0
IKK complex 0 0.03 0.13 7 -0.083 7 14
PTPRC -0.024 0.098 0.27 2 -0.29 48 50
PDPK1 -0.032 0.078 0.23 7 -0.15 87 94
PPP3CB 0.01 0 -10000 0 -10000 0 0
PPP3CC 0.01 0 -10000 0 -10000 0 0
POU2F2 0.006 0.018 0.14 2 -0.073 2 4
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.015 0.008 -10000 0 -10000 0 0
VDR 0.009 0.024 0.27 1 -0.29 2 3
FAM120B 0.01 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.011 0.092 -10000 0 -0.38 1 1
RXRs/LXRs/DNA/Oxysterols -0.001 0.091 -10000 0 -0.35 1 1
MED1 0.01 0 -10000 0 -10000 0 0
mol:9cRA 0.005 0.01 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.008 0.071 -10000 0 -0.19 51 51
RXRs/NUR77 -0.098 0.11 0.18 1 -0.17 259 260
RXRs/PPAR -0.037 0.09 -10000 0 -0.17 118 118
NCOR2 0.01 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.007 0.017 0.18 1 -0.19 2 3
RARs/VDR/DNA/Vit D3 0.011 0.045 0.16 1 -0.13 35 36
RARA 0.01 0 -10000 0 -10000 0 0
NCOA1 0.01 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.009 0.024 0.27 1 -0.29 2 3
RARs/RARs/DNA/9cRA 0.008 0.041 -10000 0 -0.13 34 34
RARG 0.01 0 -10000 0 -10000 0 0
RPS6KB1 0.017 0.016 -10000 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.008 0.071 -10000 0 -0.19 51 51
THRA 0.01 0 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.007 0.017 0.18 1 -0.19 2 3
RXRs/PPAR/9cRA/PGJ2/DNA -0.008 0.081 -10000 0 -0.27 1 1
NR1H4 -0.037 0.13 0.27 16 -0.29 73 89
RXRs/LXRs/DNA 0.007 0.081 -10000 0 -0.25 1 1
NR1H2 0.015 0.009 -10000 0 -10000 0 0
NR1H3 0.015 0.01 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.008 0.074 0.22 2 -0.13 101 103
NR4A1 -0.16 0.15 -10000 0 -0.29 230 230
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.05 0.11 0.18 2 -0.18 143 145
RXRG -0.063 0.13 0.27 1 -0.29 100 101
RXR alpha/CCPG 0.018 0.012 -10000 0 -0.19 1 1
RXRA 0.014 0.018 -10000 0 -0.29 1 1
RXRB 0.015 0.01 -10000 0 -10000 0 0
THRB -0.008 0.07 -10000 0 -0.29 24 24
PPARG -0.008 0.075 0.27 2 -0.29 26 28
PPARD 0.01 0 -10000 0 -10000 0 0
TNF 0.007 0.098 -10000 0 -10000 0 0
mol:Oxysterols 0.005 0.009 -10000 0 -10000 0 0
cholesterol transport -0.001 0.091 -10000 0 -0.35 1 1
PPARA 0.008 0.021 -10000 0 -0.29 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.015 0.082 -10000 0 -0.29 34 34
RXRs/NUR77/BCL2 -0.14 0.13 -10000 0 -0.21 275 275
SREBF1 0.003 0.085 0.34 1 -10000 0 1
RXRs/RXRs/DNA/9cRA -0.008 0.081 -10000 0 -0.27 1 1
ABCA1 0.002 0.083 -10000 0 -10000 0 0
RARs/THRs 0.008 0.06 -10000 0 -0.14 51 51
RXRs/FXR -0.033 0.1 0.21 9 -0.16 143 152
BCL2 -0.002 0.058 -10000 0 -0.29 16 16
Aurora A 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
Aurora A/GADD45A 0.012 0.04 -10000 0 -10000 0 0
BIRC5 0.2 0.12 0.27 292 -0.29 1 293
NFKBIA 0.011 0.04 -10000 0 -10000 0 0
CPEB1 -0.13 0.15 -10000 0 -0.29 192 192
AKT1 0.011 0.04 -10000 0 -10000 0 0
NDEL1 0.01 0 -10000 0 -10000 0 0
Aurora A/BRCA1 0.011 0.037 0.22 1 -10000 0 1
NDEL1/TACC3 0.027 0.056 0.2 19 -10000 0 19
GADD45A 0.01 0 -10000 0 -10000 0 0
GSK3B -0.01 0.013 -10000 0 -10000 0 0
PAK1/Aurora A 0.012 0.04 -10000 0 -10000 0 0
MDM2 0.018 0.045 0.27 13 -10000 0 13
JUB 0.012 0.022 0.27 3 -10000 0 3
TPX2 0.091 0.076 0.16 219 -10000 0 219
TP53 0.018 0.038 0.17 6 -10000 0 6
DLG7 0.009 0.04 -10000 0 -10000 0 0
AURKAIP1 0.011 0.013 0.27 1 -10000 0 1
ARHGEF7 0.01 0 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.028 0.059 0.21 19 -10000 0 19
G2/M transition of mitotic cell cycle 0.011 0.037 0.22 1 -10000 0 1
AURKA 0.013 0.053 -10000 0 -10000 0 0
AURKB 0.099 0.07 0.16 207 -10000 0 207
CDC25B 0.015 0.043 0.18 6 -10000 0 6
G2/M transition checkpoint 0.012 0.038 0.19 3 -10000 0 3
mRNA polyadenylation -0.06 0.074 -10000 0 -0.15 116 116
Aurora A/CPEB -0.06 0.074 -10000 0 -0.16 116 116
Aurora A/TACC1/TRAP/chTOG 0.019 0.039 -10000 0 -0.16 1 1
BRCA1 0.011 0.013 0.27 1 -10000 0 1
centrosome duplication 0.012 0.04 -10000 0 -10000 0 0
regulation of centrosome cycle 0.026 0.054 0.2 19 -10000 0 19
spindle assembly 0.018 0.038 -10000 0 -0.16 1 1
TDRD7 0.01 0 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.13 0.077 0.2 154 -10000 0 154
CENPA 0.12 0.074 0.16 281 -10000 0 281
Aurora A/PP2A 0.012 0.04 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.015 0.038 -10000 0 -10000 0 0
negative regulation of DNA binding 0.018 0.038 0.17 6 -10000 0 6
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.015 0 -10000 0 -10000 0 0
RASA1 0.01 0 -10000 0 -10000 0 0
Ajuba/Aurora A 0.012 0.039 0.19 3 -10000 0 3
mitotic prometaphase -0.013 0.013 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.053 -10000 0 -10000 0 0
TACC1 0.008 0.025 -10000 0 -0.29 3 3
TACC3 0.03 0.069 0.27 31 -10000 0 31
Aurora A/Antizyme1 0.016 0.038 -10000 0 -10000 0 0
Aurora A/RasGAP 0.012 0.04 -10000 0 -10000 0 0
OAZ1 0.01 0 -10000 0 -10000 0 0
RAN 0.01 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.01 0.013 -10000 0 -10000 0 0
GIT1 0.01 0 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.02 0.009 -10000 0 -0.16 1 1
Importin alpha/Importin beta/TPX2 0.091 0.076 0.16 219 -10000 0 219
PPP2R5D 0.01 0 -10000 0 -10000 0 0
Aurora A/TPX2 0.075 0.077 0.18 120 -10000 0 120
PAK1 0.009 0.015 -10000 0 -0.29 1 1
CKAP5 0.01 0 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.046 0.25 -10000 0 -0.76 42 42
NCK1/PAK1/Dok-R -0.044 0.12 -10000 0 -0.39 42 42
NCK1/Dok-R -0.058 0.28 -10000 0 -0.88 42 42
PIK3CA 0.01 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.014 0.064 0.22 34 -0.1 2 36
RELA 0.01 0 -10000 0 -10000 0 0
SHC1 0.011 0.013 0.27 1 -10000 0 1
Rac/GDP 0.007 0 -10000 0 -10000 0 0
F2 0.037 0.098 0.27 60 -10000 0 60
TNIP2 0.01 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.048 0.27 -10000 0 -0.83 42 42
FN1 0.018 0.083 0.27 26 -0.29 12 38
PLD2 -0.065 0.28 -10000 0 -0.9 42 42
PTPN11 0.01 0 -10000 0 -10000 0 0
GRB14 0.045 0.089 0.27 56 -10000 0 56
ELK1 -0.057 0.26 -10000 0 -0.83 42 42
GRB7 0.014 0.062 0.27 14 -0.29 7 21
PAK1 0.009 0.015 -10000 0 -0.29 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.049 0.29 -10000 0 -0.89 42 42
CDKN1A -0.04 0.18 -10000 0 -0.52 44 44
ITGA5 -0.002 0.058 -10000 0 -0.29 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.058 0.28 -10000 0 -0.88 42 42
CRK 0.01 0 -10000 0 -10000 0 0
mol:NO -0.029 0.19 -10000 0 -0.58 42 42
PLG -0.066 0.28 -10000 0 -0.9 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.046 0.24 -10000 0 -0.74 42 42
GRB2 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
ANGPT2 -0.073 0.16 0.33 1 -0.51 30 31
BMX -0.079 0.29 -10000 0 -0.94 42 42
ANGPT1 -0.077 0.31 -10000 0 -1.1 34 34
tube development -0.047 0.19 -10000 0 -0.57 43 43
ANGPT4 0.012 0.037 0.27 8 -10000 0 8
response to hypoxia -0.005 0.02 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.043 0.3 -10000 0 -0.91 42 42
alpha5/beta1 Integrin 0.007 0.04 -10000 0 -0.19 16 16
FGF2 -0.089 0.14 -10000 0 -0.29 136 136
STAT5A (dimer) -0.049 0.21 -10000 0 -0.63 44 44
mol:L-citrulline -0.029 0.19 -10000 0 -0.58 42 42
AGTR1 -0.12 0.15 -10000 0 -0.29 175 175
MAPK14 -0.067 0.29 -10000 0 -0.91 42 42
Tie2/SHP2 -0.015 0.15 -10000 0 -0.93 9 9
TEK -0.02 0.17 -10000 0 -1 9 9
RPS6KB1 -0.047 0.24 -10000 0 -0.74 42 42
Angiotensin II/AT1 -0.078 0.1 -10000 0 -0.19 175 175
Tie2/Ang1/GRB2 -0.064 0.29 -10000 0 -0.92 42 42
MAPK3 -0.06 0.27 -10000 0 -0.84 42 42
MAPK1 -0.06 0.27 -10000 0 -0.84 42 42
Tie2/Ang1/GRB7 -0.059 0.3 -10000 0 -0.92 42 42
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 -0.065 0.28 -10000 0 -0.9 42 42
PI3K -0.059 0.27 -10000 0 -0.85 42 42
FES -0.068 0.29 -10000 0 -0.9 42 42
Crk/Dok-R -0.058 0.28 -10000 0 -0.88 42 42
Tie2/Ang1/ABIN2 -0.064 0.29 -10000 0 -0.92 42 42
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.039 0.22 -10000 0 -0.69 42 42
STAT5A 0.009 0.015 -10000 0 -0.29 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.047 0.24 -10000 0 -0.74 42 42
Tie2/Ang2 -0.064 0.24 -10000 0 -0.72 43 43
Tie2/Ang1 -0.07 0.3 -10000 0 -0.95 42 42
FOXO1 -0.036 0.22 -10000 0 -0.69 42 42
ELF1 0.009 0.019 -10000 0 -10000 0 0
ELF2 -0.064 0.28 -10000 0 -0.89 42 42
mol:Choline -0.062 0.28 -10000 0 -0.87 42 42
cell migration -0.025 0.069 -10000 0 -0.22 42 42
FYN -0.054 0.21 -10000 0 -0.63 43 43
DOK2 0.002 0.056 0.27 2 -0.29 13 15
negative regulation of cell cycle -0.035 0.16 -10000 0 -0.48 44 44
ETS1 -0.005 0.065 -10000 0 -0.22 34 34
PXN -0.036 0.2 -10000 0 -0.62 42 42
ITGB1 0.01 0 -10000 0 -10000 0 0
NOS3 -0.035 0.21 -10000 0 -0.65 42 42
RAC1 0.01 0 -10000 0 -10000 0 0
TNF 0.008 0.088 0.27 20 -0.22 33 53
MAPKKK cascade -0.062 0.28 -10000 0 -0.87 42 42
RASA1 0.01 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.063 0.29 -10000 0 -0.92 42 42
NCK1 0.01 0 -10000 0 -10000 0 0
vasculogenesis -0.023 0.17 -10000 0 -0.52 42 42
mol:Phosphatidic acid -0.062 0.28 -10000 0 -0.87 42 42
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP -0.029 0.19 -10000 0 -0.58 42 42
Rac1/GTP -0.045 0.22 -10000 0 -0.69 42 42
MMP2 -0.071 0.29 -10000 0 -0.92 42 42
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.01 0.071 0.2 46 -0.18 6 52
KIRREL 0.008 0.023 -10000 0 -0.32 2 2
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.01 0.071 0.18 6 -0.2 46 52
PLCG1 0.01 0 -10000 0 -10000 0 0
ARRB2 0.01 0 -10000 0 -10000 0 0
WASL 0.01 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.007 0.059 0.16 20 -0.14 41 61
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.002 0.061 -10000 0 -0.17 41 41
FYN -0.004 0.051 -10000 0 -0.14 41 41
mol:Ca2+ 0.006 0.058 0.16 20 -0.14 41 61
mol:DAG 0.007 0.059 0.16 20 -0.14 41 61
NPHS2 0.013 0.055 0.26 19 -10000 0 19
mol:IP3 0.007 0.059 0.16 20 -0.14 41 61
regulation of endocytosis 0.006 0.053 0.15 6 -0.13 41 47
Nephrin/NEPH1/podocin/Cholesterol 0.001 0.058 0.16 20 -0.14 41 61
establishment of cell polarity -0.01 0.071 0.18 6 -0.2 46 52
Nephrin/NEPH1/podocin/NCK1-2 0.013 0.056 0.16 20 -0.12 41 61
Nephrin/NEPH1/beta Arrestin2 0.007 0.054 0.16 6 -0.13 41 47
NPHS1 0.005 0.034 0.26 6 -10000 0 6
Nephrin/NEPH1/podocin 0.002 0.06 0.16 20 -0.14 41 61
TJP1 0.01 0 -10000 0 -10000 0 0
NCK1 0.01 0 -10000 0 -10000 0 0
NCK2 0.01 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.007 0.059 0.16 20 -0.14 41 61
CD2AP 0.01 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.007 0.059 0.16 20 -0.14 41 61
GRB2 0.01 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.002 0.047 -10000 0 -0.13 41 41
cytoskeleton organization -0.002 0.06 -10000 0 -0.17 41 41
Nephrin/NEPH1 -0.005 0.049 0.15 6 -0.13 46 52
Nephrin/NEPH1/ZO-1 0 0.057 0.17 6 -0.15 46 52
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.016 0.025 0.16 5 -0.13 7 12
RGS9BP 0.001 0.059 0.27 3 -0.29 14 17
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.001 0.014 0.27 1 -10000 0 1
mol:Na + 0.034 0.086 0.17 96 -0.16 28 124
mol:ADP 0.005 0.011 0.16 2 -10000 0 2
GNAT2 0.01 0.026 0.27 4 -10000 0 4
RGS9-1/Gbeta5/R9AP -0.022 0.081 0.18 3 -0.16 97 100
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.009 0.02 0.17 6 -10000 0 6
GRK7 0.009 0.013 0.27 1 -10000 0 1
CNGB3 0.078 0.12 0.27 108 -10000 0 108
Cone Metarhodopsin II/X-Arrestin 0.001 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0.023 0.07 0.2 21 -0.14 27 48
Cone PDE6 -0.016 0.069 0.16 4 -0.13 96 100
Cone Metarhodopsin II 0.006 0.011 0.16 2 -10000 0 2
Na + (4 Units) 0.044 0.092 0.18 107 -0.14 27 134
GNAT2/GDP -0.013 0.071 0.16 7 -0.13 97 104
GNB5 0.01 0 -10000 0 -10000 0 0
mol:GMP (4 units) 0.005 0.01 -10000 0 -10000 0 0
Cone Transducin 0.017 0.027 0.17 5 -0.14 7 12
SLC24A2 0.021 0.059 0.27 22 -10000 0 22
GNB3/GNGT2 0.012 0.028 0.19 1 -0.19 7 8
GNB3 0.008 0.029 0.27 1 -0.29 3 4
GNAT2/GTP 0.008 0.018 0.18 4 -10000 0 4
CNGA3 -0.022 0.088 -10000 0 -0.29 40 40
ARR3 0.002 0.004 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.034 0.087 0.17 96 -0.16 28 124
mol:Pi -0.022 0.08 0.18 3 -0.16 97 100
Cone CNG Channel 0.032 0.068 0.14 2 -0.12 28 30
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.021 0.059 0.27 22 -10000 0 22
RGS9 -0.054 0.12 -10000 0 -0.29 87 87
PDE6C 0.002 0.004 -10000 0 -10000 0 0
GNGT2 0.007 0.029 -10000 0 -0.29 4 4
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.003 0.019 0.27 2 -10000 0 2
Arf6 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
CENTA1/KIF3B 0.012 0.017 -10000 0 -0.16 4 4
ARNO/beta Arrestin1-2 -0.001 0.043 -10000 0 -10000 0 0
EGFR 0.008 0.057 0.27 8 -0.29 9 17
EPHA2 0.006 0.033 -10000 0 -0.29 5 5
USP6 0.01 0 -10000 0 -10000 0 0
IQSEC1 0.01 0.013 0.27 1 -10000 0 1
EGFR/EGFR/EGF/EGF 0.024 0.058 0.19 33 -0.19 9 42
ARRB2 0.006 0.009 0.14 2 -10000 0 2
mol:GTP 0.004 0.024 -10000 0 -0.15 5 5
ARRB1 0.007 0.029 -10000 0 -0.29 4 4
FBXO8 0.01 0 -10000 0 -10000 0 0
TSHR 0.012 0.034 0.27 7 -10000 0 7
EGF 0.025 0.062 0.27 25 -10000 0 25
somatostatin receptor activity 0 0 -10000 0 0 101 101
ARAP2 0.008 0.021 -10000 0 -0.29 2 2
mol:GDP -0.06 0.086 -10000 0 -0.18 102 102
mol:PI-3-4-5-P3 0 0 -10000 0 0 66 66
ITGA2B 0.029 0.069 0.27 31 -10000 0 31
ARF6 0.01 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.027 0.029 0.18 9 -0.14 5 14
ADAP1 0.007 0.029 -10000 0 -0.29 4 4
KIF13B 0.01 0 -10000 0 -10000 0 0
HGF/MET -0.026 0.091 0.19 9 -0.19 87 96
PXN 0.01 0 -10000 0 -10000 0 0
ARF6/GTP -0.054 0.085 -10000 0 -0.18 93 93
EGFR/EGFR/EGF/EGF/ARFGEP100 0.029 0.052 0.18 34 -0.16 9 43
ADRB2 -0.028 0.099 -10000 0 -0.29 52 52
receptor agonist activity 0 0 -10000 0 0 105 105
actin filament binding 0 0 -10000 0 0 101 101
SRC 0.01 0 -10000 0 -10000 0 0
ITGB3 -0.024 0.094 -10000 0 -0.29 46 46
GNAQ 0.01 0 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 73 73
ARF6/GDP -0.013 0.071 -10000 0 -0.28 19 19
ARF6/GDP/GULP/ACAP1 -0.067 0.11 0.18 3 -0.22 106 109
alphaIIb/beta3 Integrin/paxillin/GIT1 0.018 0.065 0.18 26 -0.14 41 67
ACAP1 0 0.065 0.27 4 -0.29 17 21
ACAP2 0.01 0 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.005 0.016 0.22 2 -10000 0 2
EFNA1 0.016 0.038 0.27 9 -10000 0 9
HGF -0.05 0.13 0.27 7 -0.29 87 94
CYTH3 0.005 0 -10000 0 -10000 0 0
CYTH2 0.006 0.002 -10000 0 -10000 0 0
NCK1 0.01 0 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 73 73
endosomal lumen acidification 0 0 -10000 0 0 92 92
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.036 0.11 -10000 0 -0.29 63 63
GNAQ/ARNO 0.011 0.003 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 0 1 1
PIP3-E 0 0 -10000 0 0 10 10
MET 0.011 0.018 0.27 2 -10000 0 2
GNA14 -0.033 0.1 -10000 0 -0.29 58 58
GNA15 0.008 0.025 -10000 0 -0.29 3 3
GIT1 0.01 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 0 87 87
GNA11 0.009 0.015 -10000 0 -0.29 1 1
LHCGR 0.004 0.019 0.27 2 -10000 0 2
AGTR1 -0.12 0.15 -10000 0 -0.29 175 175
desensitization of G-protein coupled receptor protein signaling pathway 0.005 0.016 0.22 2 -10000 0 2
IPCEF1/ARNO 0.024 0.044 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.004 0.08 0.19 26 -0.19 41 67
FAS signaling pathway (CD95)

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
SPTAN1 0.005 0.035 0.16 20 -10000 0 20
RFC1 0.005 0.035 0.16 20 -10000 0 20
PRKDC 0.005 0.035 0.16 20 -10000 0 20
RIPK1 0.014 0.005 -10000 0 -10000 0 0
CASP7 -0.025 0.047 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 -0.025 0.059 0.15 5 -0.2 23 28
MAP2K4 -0.11 0.15 -10000 0 -0.27 191 191
mol:ceramide -0.066 0.11 -10000 0 -0.3 24 24
GSN 0.002 0.038 0.16 18 -0.15 5 23
FASLG/FAS/FADD/FAF1/Caspase 8 -0.038 0.077 -10000 0 -0.26 22 22
FAS -0.006 0.038 -10000 0 -0.3 6 6
BID -0.001 0.03 0.25 4 -0.14 4 8
MAP3K1 -0.058 0.09 -10000 0 -0.23 17 17
MAP3K7 0.004 0.007 -10000 0 -10000 0 0
RB1 0.005 0.036 0.16 20 -0.16 1 21
CFLAR 0.014 0.005 -10000 0 -10000 0 0
HGF/MET -0.017 0.081 0.18 9 -0.16 93 102
ARHGDIB 0.005 0.035 0.16 20 -10000 0 20
FADD 0.002 0.034 0.26 6 -10000 0 6
actin filament polymerization -0.002 0.038 0.15 5 -0.16 18 23
NFKB1 -0.082 0.1 -10000 0 -0.2 179 179
MAPK8 -0.18 0.23 -10000 0 -0.43 184 184
DFFA 0.005 0.035 0.16 20 -10000 0 20
DNA fragmentation during apoptosis 0.005 0.035 0.16 20 -10000 0 20
FAS/FADD/MET 0.005 0.036 0.17 8 -0.17 6 14
CFLAR/RIP1 0.022 0.008 -10000 0 -10000 0 0
FAIM3 0.012 0.039 0.27 4 -0.29 4 8
FAF1 -0.004 0.016 -10000 0 -10000 0 0
PARP1 0.005 0.035 0.16 20 -10000 0 20
DFFB 0.005 0.035 0.16 20 -10000 0 20
CHUK -0.073 0.096 -10000 0 -0.22 17 17
FASLG -0.015 0.076 0.26 7 -0.3 21 28
FAS/FADD -0.002 0.038 0.18 6 -0.21 6 12
HGF -0.049 0.13 0.27 7 -0.29 87 94
LMNA 0.006 0.032 0.14 20 -10000 0 20
CASP6 0.005 0.035 0.16 20 -10000 0 20
CASP10 -0.001 0.013 -10000 0 -10000 0 0
CASP3 0.004 0.042 0.18 20 -10000 0 20
PTPN13 0.004 0.041 -10000 0 -0.29 8 8
CASP8 -0.006 0.034 0.28 4 -0.18 4 8
IL6 -0.5 0.57 -10000 0 -1.1 184 184
MET 0.011 0.018 0.27 2 -10000 0 2
ICAD/CAD 0.006 0.032 0.14 20 -10000 0 20
FASLG/FAS/FADD/FAF1/Caspase 10 -0.067 0.11 -10000 0 -0.31 24 24
activation of caspase activity by cytochrome c -0.001 0.03 0.25 4 -0.14 4 8
PAK2 0.003 0.036 0.15 20 -10000 0 20
BCL2 -0.001 0.058 -10000 0 -0.29 16 16
S1P3 pathway

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
PDGFRB 0.003 0.046 -10000 0 -0.29 10 10
mol:S1P 0 0.004 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.079 0.13 -10000 0 -0.22 164 164
GNAO1 -0.085 0.14 -10000 0 -0.29 129 129
S1P/S1P3/G12/G13 0.016 0.025 0.17 1 -0.14 8 9
AKT1 -0.028 0.12 -10000 0 -0.52 15 15
AKT3 -0.069 0.21 -10000 0 -1.1 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.003 0.046 -10000 0 -0.29 10 10
GNAI2 0.009 0.006 -10000 0 -10000 0 0
GNAI3 0.01 0.005 -10000 0 -10000 0 0
GNAI1 0.007 0.026 -10000 0 -0.29 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.004 0.044 0.27 1 -0.29 8 9
S1PR2 0.01 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.084 0.14 -10000 0 -0.35 70 70
MAPK3 -0.079 0.14 -10000 0 -0.33 70 70
MAPK1 -0.079 0.14 -10000 0 -0.33 70 70
JAK2 -0.083 0.14 -10000 0 -0.35 70 70
CXCR4 -0.081 0.14 -10000 0 -0.34 70 70
FLT1 0.01 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.007 0 -10000 0 -10000 0 0
Rac1/GDP 0.007 0 -10000 0 -10000 0 0
SRC -0.079 0.14 -10000 0 -0.33 70 70
S1P/S1P3/Gi -0.085 0.14 -10000 0 -0.35 70 70
RAC1 0.01 0 -10000 0 -10000 0 0
RhoA/GTP -0.073 0.13 -10000 0 -0.32 70 70
VEGFA 0.01 0.008 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.079 0.13 -10000 0 -0.22 164 164
VEGFR1 homodimer/VEGFA homodimer 0.016 0.013 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.016 0.074 -10000 0 -0.18 66 66
GNAQ 0.01 0 -10000 0 -10000 0 0
GNAZ -0.055 0.12 -10000 0 -0.29 89 89
G12/G13 0.015 0 -10000 0 -10000 0 0
GNA14 -0.032 0.1 -10000 0 -0.29 58 58
GNA15 0.008 0.025 -10000 0 -0.29 3 3
GNA12 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0 -10000 0 -10000 0 0
GNA11 0.009 0.015 -10000 0 -0.29 1 1
Rac1/GTP -0.073 0.13 -10000 0 -0.32 70 70
Coregulation of Androgen receptor activity

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
NRIP1 0.009 0.021 0.27 1 -10000 0 1
SVIL 0.006 0.029 -10000 0 -0.29 3 3
ZNF318 0.014 0.033 0.17 16 -10000 0 16
JMJD2C 0.017 0.041 0.14 41 -10000 0 41
T-DHT/AR/Ubc9 -0.049 0.098 0.19 3 -0.18 135 138
CARM1 0.009 0.004 -10000 0 -10000 0 0
PRDX1 0.01 0.002 -10000 0 -10000 0 0
PELP1 0.01 0.005 -10000 0 -10000 0 0
CTNNB1 0.008 0.012 -10000 0 -10000 0 0
AKT1 0.01 0.01 -10000 0 -10000 0 0
PTK2B 0.008 0.018 -10000 0 -0.29 1 1
MED1 0.011 0.01 -10000 0 -10000 0 0
MAK 0.019 0.049 0.2 25 -10000 0 25
response to oxidative stress 0 0.002 -10000 0 -10000 0 0
HIP1 0.007 0.026 -10000 0 -0.29 2 2
GSN 0.004 0.039 -10000 0 -0.29 6 6
NCOA2 -0.008 0.07 -10000 0 -0.29 24 24
NCOA6 0.009 0.019 0.27 1 -10000 0 1
DNA-PK 0.023 0.031 0.17 16 -10000 0 16
NCOA4 0.01 0.002 -10000 0 -10000 0 0
PIAS3 0.008 0.012 -10000 0 -10000 0 0
cell proliferation 0 0.049 0.22 9 -10000 0 9
XRCC5 0.01 0.008 -10000 0 -10000 0 0
UBE3A 0.007 0.022 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.061 0.11 0.19 3 -0.19 151 154
FHL2 -0.021 0.086 -10000 0 -0.79 3 3
RANBP9 0.008 0.015 -10000 0 -10000 0 0
JMJD1A -0.012 0.058 0.16 12 -0.12 73 85
CDK6 0.002 0.048 -10000 0 -0.29 11 11
TGFB1I1 -0.001 0.055 -10000 0 -0.29 13 13
T-DHT/AR/CyclinD1 -0.05 0.1 0.19 7 -0.18 133 140
XRCC6 0.01 0.008 -10000 0 -10000 0 0
T-DHT/AR -0.044 0.13 0.22 19 -0.18 162 181
CTDSP1 0.009 0.006 -10000 0 -10000 0 0
CTDSP2 0.012 0.021 -10000 0 -10000 0 0
BRCA1 0.009 0.021 0.29 1 -10000 0 1
TCF4 0.007 0.039 -10000 0 -0.29 6 6
CDKN2A 0.14 0.14 0.27 201 -0.29 4 205
SRF 0.013 0.015 -10000 0 -0.13 1 1
NKX3-1 -0.049 0.13 0.42 2 -0.32 44 46
KLK3 -0.041 0.26 -10000 0 -1.3 16 16
TMF1 0.009 0.004 -10000 0 -10000 0 0
HNRNPA1 0.011 0.011 -10000 0 -10000 0 0
AOF2 -0.001 0.014 -10000 0 -0.065 16 16
APPL1 0.011 0.019 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.048 0.098 0.17 3 -0.17 141 144
AR -0.094 0.15 0.14 1 -0.3 135 136
UBA3 0.009 0.006 -10000 0 -10000 0 0
PATZ1 0.011 0.011 -10000 0 -10000 0 0
PAWR 0.009 0.015 -10000 0 -0.29 1 1
PRKDC 0.01 0.008 -10000 0 -10000 0 0
PA2G4 0.011 0.015 -10000 0 -10000 0 0
UBE2I 0.01 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.042 0.089 0.16 3 -0.16 135 138
RPS6KA3 0.008 0.016 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.05 0.098 0.2 3 -0.18 135 138
LATS2 0.01 0.019 -10000 0 -0.29 1 1
T-DHT/AR/PRX1 -0.042 0.09 0.2 1 -0.16 131 132
Cyclin D3/CDK11 p58 0.008 0.002 -10000 0 -10000 0 0
VAV3 0.009 0.039 0.26 5 -0.28 3 8
KLK2 0.002 0.11 0.3 36 -10000 0 36
CASP8 0.01 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.048 0.1 0.2 3 -0.17 147 150
TMPRSS2 -0.13 0.3 0.36 8 -0.78 69 77
CCND1 0.013 0.061 0.27 14 -0.29 6 20
PIAS1 0.007 0.022 -10000 0 -10000 0 0
mol:T-DHT -0.002 0.023 0.096 3 -0.056 29 32
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.006 0.034 -10000 0 -0.16 16 16
T-DHT/AR/CDK6 -0.053 0.1 0.18 3 -0.18 147 150
CMTM2 0.013 0.029 0.27 5 -10000 0 5
SNURF -0.013 0.078 -10000 0 -0.29 30 30
ZMIZ1 0.007 0.025 0.14 1 -10000 0 1
CCND3 0.01 0.001 -10000 0 -10000 0 0
TGIF1 0.011 0.011 -10000 0 -10000 0 0
FKBP4 0.008 0.015 -10000 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin 0.008 0.07 0.19 25 -0.16 38 63
EPHB2 0.028 0.065 0.27 28 -10000 0 28
Syndecan-2/TACI -0.01 0.068 0.19 7 -0.16 59 66
LAMA1 0.041 0.12 0.27 66 -0.29 15 81
Syndecan-2/alpha2 ITGB1 0.015 0.081 0.18 37 -0.14 59 96
HRAS 0.01 0 -10000 0 -10000 0 0
Syndecan-2/CASK -0.005 0.042 -10000 0 -0.16 29 29
ITGA5 -0.002 0.058 -10000 0 -0.29 16 16
BAX 0.013 0.004 -10000 0 -10000 0 0
EPB41 0.01 0 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.002 0.038 -10000 0 -0.14 29 29
LAMA3 0.005 0.12 0.27 35 -0.29 37 72
EZR 0.01 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.007 0.029 -10000 0 -0.29 4 4
Syndecan-2/MMP2 -0.013 0.072 -10000 0 -0.19 52 52
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.016 0.022 0.19 5 -0.19 1 6
dendrite morphogenesis 0.014 0.063 0.19 27 -0.15 28 55
Syndecan-2/GM-CSF 0.033 0.083 0.19 71 -0.16 25 96
determination of left/right symmetry -0.006 0.051 -10000 0 -0.19 29 29
Syndecan-2/PKC delta 0.002 0.043 -10000 0 -0.16 29 29
GNB2L1 0.01 0 -10000 0 -10000 0 0
MAPK3 0.02 0.057 0.12 71 -0.14 25 96
MAPK1 0.02 0.057 -10000 0 -0.14 25 25
Syndecan-2/RACK1 0.008 0.037 -10000 0 -0.13 29 29
NF1 0.01 0 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.006 0.051 -10000 0 -0.19 29 29
ITGA2 0.012 0.032 0.27 5 -0.29 1 6
MAPK8 0.011 0.003 -10000 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin 0.033 0.079 0.18 64 -0.13 38 102
Syndecan-2/Kininogen -0.005 0.042 -10000 0 -0.16 29 29
ITGB1 0.01 0 -10000 0 -10000 0 0
SRC 0.004 0.034 -10000 0 -0.12 29 29
Syndecan-2/CASK/Protein 4.1 0.002 0.039 -10000 0 -0.14 29 29
extracellular matrix organization 0.002 0.043 -10000 0 -0.15 29 29
actin cytoskeleton reorganization 0.008 0.07 0.19 25 -0.16 38 63
Syndecan-2/Caveolin-2/Ras 0.007 0.044 -10000 0 -0.14 32 32
Syndecan-2/Laminin alpha3 0.002 0.088 0.19 34 -0.17 59 93
Syndecan-2/RasGAP 0.013 0.037 -10000 0 -0.12 29 29
alpha5/beta1 Integrin 0.007 0.04 -10000 0 -0.19 16 16
PRKCD 0.01 0 -10000 0 -10000 0 0
Syndecan-2 dimer 0.014 0.064 0.19 27 -0.16 28 55
GO:0007205 0.002 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.011 0.035 -10000 0 -0.11 29 29
RHOA 0.01 0 -10000 0 -10000 0 0
SDCBP 0.01 0 -10000 0 -10000 0 0
TNFRSF13B -0.012 0.089 0.27 7 -0.29 33 40
RASA1 0.01 0 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.016 0.022 0.19 5 -0.19 1 6
Syndecan-2/Synbindin 0.002 0.043 -10000 0 -0.16 29 29
TGFB1 0.01 0 -10000 0 -10000 0 0
CASP3 0.002 0.038 -10000 0 -0.14 29 29
FN1 0.018 0.083 0.27 26 -0.29 12 38
Syndecan-2/IL8 -0.022 0.074 0.19 1 -0.16 83 84
SDC2 -0.006 0.051 -10000 0 -0.19 29 29
KNG1 0 0 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.002 0.043 -10000 0 -0.16 29 29
TRAPPC4 0.01 0 -10000 0 -10000 0 0
CSF2 0.056 0.1 0.27 75 -10000 0 75
Syndecan-2/TGFB1 0.002 0.043 -10000 0 -0.16 29 29
Syndecan-2/Syntenin/PI-4-5-P2 0.002 0.039 -10000 0 -0.14 29 29
Syndecan-2/Ezrin 0.008 0.04 -10000 0 -0.14 29 29
PRKACA 0.002 0.038 -10000 0 -0.14 29 29
angiogenesis -0.022 0.074 0.19 1 -0.16 83 84
MMP2 -0.016 0.085 -10000 0 -0.29 36 36
IL8 -0.033 0.11 0.27 1 -0.29 59 60
calcineurin-NFAT signaling pathway -0.01 0.068 0.19 7 -0.16 59 66
Wnt signaling

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
Noncanonical Wnts/FZD 0.004 0.093 0.2 9 -0.19 57 66
FZD6 0.01 0 -10000 0 -10000 0 0
WNT6 0.025 0.095 0.27 39 -0.29 13 52
WNT4 -0.007 0.077 0.27 3 -0.29 26 29
FZD3 0.008 0.025 -10000 0 -0.29 3 3
WNT5A 0.011 0.056 0.27 10 -0.29 7 17
WNT11 0.015 0.1 0.27 34 -0.29 22 56
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.022 0.081 0.22 1 -0.38 12 13
Syndecan-4/Syndesmos 0.052 0.1 0.23 26 -0.41 9 35
positive regulation of JNK cascade 0.011 0.12 -10000 0 -0.36 18 18
Syndecan-4/ADAM12 0.067 0.12 0.28 42 -0.41 9 51
CCL5 0.004 0.08 0.27 13 -0.29 20 33
Rac1/GDP 0.007 0 -10000 0 -10000 0 0
DNM2 0.01 0 -10000 0 -10000 0 0
ITGA5 -0.002 0.058 -10000 0 -0.29 16 16
SDCBP 0.01 0 -10000 0 -10000 0 0
PLG 0.004 0.03 0.27 5 -10000 0 5
ADAM12 0.035 0.077 0.27 40 -10000 0 40
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.01 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha 0.004 0.011 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.073 0.13 0.28 50 -0.41 11 61
Syndecan-4/CXCL12/CXCR4 0.016 0.13 0.25 7 -0.38 18 25
Syndecan-4/Laminin alpha3 0.058 0.12 0.28 43 -0.41 10 53
MDK 0.025 0.06 0.27 23 -10000 0 23
Syndecan-4/FZD7 0.049 0.1 0.23 26 -0.41 9 35
Syndecan-4/Midkine 0.06 0.1 0.24 31 -0.4 9 40
FZD7 -0.004 0.063 -10000 0 -0.29 19 19
Syndecan-4/FGFR1/FGF -0.052 0.12 -10000 0 -0.27 67 67
THBS1 0 0.052 -10000 0 -0.29 13 13
integrin-mediated signaling pathway 0.048 0.11 0.25 30 -0.38 15 45
positive regulation of MAPKKK cascade 0.011 0.12 -10000 0 -0.36 18 18
Syndecan-4/TACI 0.049 0.1 0.24 25 -0.42 9 34
CXCR4 0.004 0.041 -10000 0 -0.29 8 8
cell adhesion 0.007 0.063 0.12 14 -0.28 12 26
Syndecan-4/Dynamin 0.052 0.1 0.23 20 -0.41 9 29
Syndecan-4/TSP1 0.05 0.1 0.23 20 -0.41 10 30
Syndecan-4/GIPC 0.052 0.1 0.23 26 -0.41 9 35
Syndecan-4/RANTES 0.054 0.11 0.25 33 -0.43 11 44
ITGB1 0.01 0 -10000 0 -10000 0 0
LAMA1 0.041 0.12 0.27 66 -0.29 15 81
LAMA3 0.005 0.12 0.27 35 -0.29 37 72
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA -0.015 0.035 -10000 0 -0.23 6 6
Syndecan-4/alpha-Actinin 0.052 0.1 0.23 26 -0.41 9 35
TFPI 0.003 0.044 -10000 0 -0.29 9 9
F2 0.029 0.07 0.28 30 -10000 0 30
alpha5/beta1 Integrin 0.007 0.04 -10000 0 -0.19 16 16
positive regulation of cell adhesion 0.064 0.12 0.26 58 -0.39 12 70
ACTN1 0.01 0 -10000 0 -10000 0 0
TNC -0.008 0.091 0.27 9 -0.29 33 42
Syndecan-4/CXCL12 0.036 0.11 0.23 17 -0.4 16 33
FGF6 0 0.001 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
CXCL12 -0.073 0.13 -10000 0 -0.29 114 114
TNFRSF13B -0.012 0.089 0.27 7 -0.29 33 40
FGF2 -0.089 0.14 -10000 0 -0.29 136 136
FGFR1 -0.058 0.12 -10000 0 -0.29 93 93
Syndecan-4/PI-4-5-P2 0.045 0.099 0.22 26 -0.41 9 35
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.017 0.081 0.27 26 -0.27 12 38
cell migration -0.006 0.006 -10000 0 -10000 0 0
PRKCD 0.008 0.005 -10000 0 -10000 0 0
vasculogenesis 0.049 0.099 0.22 25 -0.4 10 35
SDC4 0.049 0.1 0.24 26 -0.43 9 35
Syndecan-4/Tenascin C 0.049 0.12 0.25 30 -0.39 15 45
Syndecan-4/PI-4-5-P2/PKC alpha -0.003 0.005 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.052 0.1 0.23 26 -0.41 9 35
MMP9 0.071 0.12 0.27 102 -0.28 8 110
Rac1/GTP 0.007 0.064 0.12 14 -0.29 12 26
cytoskeleton organization 0.051 0.097 0.22 26 -0.4 9 35
GIPC1 0.01 0 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.05 0.1 0.23 20 -0.42 11 31
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.016 0.012 0.19 2 -10000 0 2
CRKL -0.016 0.068 -10000 0 -0.23 2 2
mol:PIP3 -0.003 0.005 -10000 0 -10000 0 0
AKT1 0.001 0.004 -10000 0 -10000 0 0
PTK2B 0.009 0.015 -10000 0 -0.29 1 1
RAPGEF1 -0.014 0.065 -10000 0 -0.22 2 2
RANBP10 0.01 0 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.014 0.078 0.18 9 -0.16 87 96
MAP3K5 -0.013 0.073 -10000 0 -0.23 13 13
HGF/MET/CIN85/CBL/ENDOPHILINS -0.006 0.072 0.18 9 -0.14 87 96
AP1 -0.05 0.094 -10000 0 -0.18 130 130
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.011 0.013 0.27 1 -10000 0 1
apoptosis -0.23 0.35 -10000 0 -0.73 130 130
STAT3 (dimer) -0.021 0.08 -10000 0 -0.17 87 87
GAB1/CRKL/SHP2/PI3K -0.003 0.068 -10000 0 -0.22 3 3
INPP5D 0.005 0.039 -10000 0 -0.29 7 7
CBL/CRK -0.01 0.067 -10000 0 -0.22 2 2
PTPN11 0.01 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.01 0 -10000 0 -10000 0 0
PTEN 0.01 0 -10000 0 -10000 0 0
ELK1 -0.005 0.006 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.011 0.05 -10000 0 -0.11 87 87
PAK1 0.002 0.007 -10000 0 -0.12 1 1
HGF/MET/RANBP10 -0.014 0.078 0.18 9 -0.16 87 96
HRAS -0.023 0.087 -10000 0 -0.24 1 1
DOCK1 -0.014 0.066 -10000 0 -0.23 3 3
GAB1 -0.019 0.072 -10000 0 -0.25 2 2
CRK -0.016 0.069 -10000 0 -0.23 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.065 0.17 -10000 0 -0.38 87 87
JUN -0.002 0.058 -10000 0 -0.29 16 16
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.022 0.062 0.1 2 -0.14 87 89
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
cell morphogenesis -0.018 0.087 -10000 0 -0.18 86 86
GRB2/SHC -0.009 0.059 0.17 1 -0.12 87 88
FOS -0.084 0.14 -10000 0 -0.29 129 129
GLMN 0.002 0 -10000 0 -10000 0 0
cell motility -0.005 0.006 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.02 0.076 0.17 9 -0.16 87 96
cell migration -0.009 0.058 0.17 1 -0.12 87 88
GRB2 0.01 0 -10000 0 -10000 0 0
CBL 0.01 0 -10000 0 -10000 0 0
MET/RANBP10 0.016 0.012 0.19 2 -10000 0 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.02 0.078 -10000 0 -0.17 87 87
MET/MUC20 0.008 0.012 0.18 2 -10000 0 2
RAP1B -0.011 0.063 -10000 0 -0.21 2 2
RAP1A -0.011 0.063 -10000 0 -0.21 2 2
HGF/MET/RANBP9 -0.014 0.078 0.18 9 -0.16 87 96
RAF1 -0.02 0.083 -10000 0 -0.23 1 1
STAT3 -0.021 0.08 -10000 0 -0.17 87 87
cell proliferation -0.036 0.11 -10000 0 -0.25 87 87
RPS6KB1 -0.004 0.024 -10000 0 -0.12 1 1
MAPK3 -0.007 0.005 -10000 0 -10000 0 0
MAPK1 -0.007 0.005 -10000 0 -10000 0 0
RANBP9 0.01 0 -10000 0 -10000 0 0
MAPK8 -0.006 0.069 -10000 0 -0.29 7 7
SRC -0.018 0.072 -10000 0 -0.16 87 87
PI3K -0.009 0.059 -10000 0 -0.12 87 87
MET/Glomulin 0.01 0.013 0.2 2 -10000 0 2
SOS1 0.01 0 -10000 0 -10000 0 0
MAP2K1 -0.018 0.079 -10000 0 -0.22 1 1
MET 0.011 0.018 0.27 2 -10000 0 2
MAP4K1 -0.015 0.076 -10000 0 -0.25 12 12
PTK2 0.01 0 -10000 0 -10000 0 0
MAP2K2 -0.018 0.079 -10000 0 -0.22 1 1
BAD 0.002 0.004 -10000 0 -10000 0 0
MAP2K4 -0.011 0.069 -10000 0 -0.22 13 13
SHP2/GRB2/SOS1/GAB1 -0.01 0.064 -10000 0 -0.2 2 2
INPPL1 0.01 0 -10000 0 -10000 0 0
PXN 0.01 0 -10000 0 -10000 0 0
SH3KBP1 0.01 0 -10000 0 -10000 0 0
HGS -0.019 0.057 -10000 0 -0.13 87 87
PLCgamma1/PKC 0.007 0 -10000 0 -10000 0 0
HGF -0.049 0.13 0.27 7 -0.29 87 94
RASA1 0.01 0 -10000 0 -10000 0 0
NCK1 0.01 0 -10000 0 -10000 0 0
PTPRJ 0.009 0.015 -10000 0 -0.29 1 1
NCK/PLCgamma1 -0.012 0.065 -10000 0 -0.13 87 87
PDPK1 -0.001 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP -0.017 0.082 0.18 9 -0.16 90 99
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.042 0.11 -10000 0 -0.29 71 71
GNB1/GNG2 0.011 0.088 0.18 8 -0.36 7 15
mol:DAG 0.006 0.079 0.15 9 -0.33 7 16
PLCG1 0.006 0.081 0.16 8 -0.34 7 15
YES1 0.003 0.086 0.17 9 -0.18 57 66
FZD3 0.008 0.025 -10000 0 -0.29 3 3
FZD6 0.01 0 -10000 0 -10000 0 0
G protein 0.011 0.083 -10000 0 -0.34 7 7
MAP3K7 -0.01 0.083 0.14 7 -0.25 30 37
mol:Ca2+ 0.006 0.077 0.15 9 -0.32 7 16
mol:IP3 0.006 0.079 0.15 9 -0.33 7 16
NLK 0.003 0.007 -10000 0 -10000 0 0
GNB1 0.01 0 -10000 0 -10000 0 0
CAMK2A -0.011 0.088 0.14 7 -0.27 30 37
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.004 0.093 0.2 9 -0.19 57 66
CSNK1A1 0.01 0 -10000 0 -10000 0 0
GNAS 0.003 0.086 0.17 9 -0.18 57 66
GO:0007205 0.004 0.078 0.15 8 -0.33 7 15
WNT6 0.025 0.095 0.27 39 -0.29 13 52
WNT4 -0.007 0.077 0.27 3 -0.29 26 29
NFAT1/CK1 alpha -0.006 0.096 -10000 0 -0.29 17 17
GNG2 0.006 0.036 -10000 0 -0.29 6 6
WNT5A 0.011 0.056 0.27 10 -0.29 7 17
WNT11 0.015 0.1 0.27 34 -0.29 22 56
CDC42 0.004 0.081 0.16 9 -0.17 57 66
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.009 0.073 0.29 26 -10000 0 26
PI3K Class IB/PDE3B -0.009 0.073 -10000 0 -0.29 26 26
PDE3B -0.009 0.073 -10000 0 -0.29 26 26
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.011 0.013 0.27 1 -10000 0 1
SPHK1 0.045 0.091 0.27 56 -0.29 1 57
GNAI2 0.01 0 -10000 0 -10000 0 0
mol:S1P 0.025 0.039 0.12 59 -0.2 1 60
GNAO1 -0.084 0.14 -10000 0 -0.29 129 129
mol:Sphinganine-1-P 0.03 0.054 0.16 57 -0.19 1 58
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.034 0.023 -10000 0 -0.14 1 1
GNAI3 0.01 0 -10000 0 -10000 0 0
G12/G13 0.015 0 -10000 0 -10000 0 0
S1PR3 0.005 0.043 0.27 1 -0.29 8 9
S1PR2 0.01 0 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.017 0.027 -10000 0 -0.17 1 1
S1PR5 0.017 0.052 0.27 14 -0.29 2 16
S1PR4 0.009 0.037 0.27 3 -0.29 4 7
GNAI1 0.008 0.025 -10000 0 -0.29 3 3
S1P/S1P5/G12 0.034 0.041 0.19 14 -0.14 3 17
S1P/S1P3/Gq -0.011 0.088 -10000 0 -0.21 56 56
S1P/S1P4/Gi -0.069 0.13 -10000 0 -0.22 157 157
GNAQ 0.01 0 -10000 0 -10000 0 0
GNAZ -0.055 0.12 -10000 0 -0.29 89 89
GNA14 -0.032 0.1 -10000 0 -0.29 58 58
GNA15 0.008 0.025 -10000 0 -0.29 3 3
GNA12 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0 -10000 0 -10000 0 0
GNA11 0.009 0.015 -10000 0 -0.29 1 1
ABCC1 0.011 0.018 0.27 2 -10000 0 2
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.14 0.15 -10000 0 -0.29 206 206
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.011 0.013 0.27 1 -10000 0 1
TCEB1 0.01 0 -10000 0 -10000 0 0
HIF1A/p53 0.014 0.008 -10000 0 -10000 0 0
HIF1A 0.008 0.008 -10000 0 -10000 0 0
COPS5 0.01 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.03 0.007 0.17 1 -10000 0 1
FIH (dimer) 0.01 0 -10000 0 -10000 0 0
CDKN2A 0.14 0.14 0.27 201 -0.29 4 205
ARNT/IPAS -0.09 0.1 -10000 0 -0.19 206 206
HIF1AN 0.01 0 -10000 0 -10000 0 0
GNB2L1 0.01 0 -10000 0 -10000 0 0
HIF1A/ARNT 0.014 0.008 -10000 0 -10000 0 0
CUL2 0.01 0 -10000 0 -10000 0 0
OS9 0.01 0 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.021 0.008 0.18 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.014 0.008 -10000 0 -10000 0 0
PHD1-3/OS9 0.022 0.023 -10000 0 -0.14 8 8
HIF1A/RACK1/Elongin B/Elongin C 0.023 0.011 -10000 0 -10000 0 0
VHL 0.01 0 -10000 0 -10000 0 0
HSP90AA1 0.01 0 -10000 0 -10000 0 0
HIF1A/JAB1 0.014 0.008 -10000 0 -10000 0 0
EGLN3 0.004 0.041 -10000 0 -0.29 8 8
EGLN2 0.01 0 -10000 0 -10000 0 0
EGLN1 0.01 0 -10000 0 -10000 0 0
TP53 0.01 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.021 0.004 -10000 0 -10000 0 0
ARNT 0.01 0 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.01 0 -10000 0 -10000 0 0
HIF1A/p19ARF 0.091 0.078 0.17 197 -10000 0 197
Visual signal transduction: Rods

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
mol:K + 0.01 0 -10000 0 -10000 0 0
GNAT1/GTP 0.006 0.018 0.18 4 -10000 0 4
Metarhodopsin II/Arrestin 0.002 0.003 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.018 0.034 0.17 19 -10000 0 19
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.009 0.026 0.27 4 -10000 0 4
GRK1 0.001 0.014 0.27 1 -10000 0 1
CNG Channel 0.05 0.072 0.2 28 -0.12 25 53
mol:Na + 0.068 0.076 0.22 36 -0.12 15 51
mol:ADP 0.001 0.014 0.27 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.022 0.081 0.18 3 -0.16 97 100
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.084 0.088 0.26 36 -0.12 3 39
CNGB1 0.12 0.13 0.27 174 -10000 0 174
RDH5 0.009 0.015 -10000 0 -0.29 1 1
SAG 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.047 0.054 0.15 36 -0.11 15 51
Na + (4 Units) 0.04 0.055 0.17 24 -10000 0 24
RGS9 -0.054 0.12 -10000 0 -0.29 87 87
GNB1/GNGT1 0.023 0.039 0.19 20 -10000 0 20
GNAT1/GDP -0.014 0.071 0.16 7 -0.13 97 104
GUCY2D 0.037 0.082 0.27 45 -10000 0 45
GNGT1 0.021 0.056 0.27 20 -10000 0 20
GUCY2F 0.001 0.003 -10000 0 -10000 0 0
GNB5 0.01 0 -10000 0 -10000 0 0
mol:GMP (4 units) 0.015 0.039 0.16 6 -0.13 16 22
mol:11-cis-retinal 0.009 0.015 -10000 0 -0.29 1 1
mol:cGMP 0.033 0.048 0.18 23 -0.13 1 24
GNB1 0.01 0 -10000 0 -10000 0 0
Rhodopsin 0.009 0.01 -10000 0 -0.19 1 1
SLC24A1 0.01 0 -10000 0 -10000 0 0
CNGA1 0.008 0.098 0.27 25 -0.29 25 50
Metarhodopsin II 0.002 0.008 0.16 1 -10000 0 1
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.042 0.061 0.18 66 -0.14 1 67
RGS9BP 0.001 0.059 0.27 3 -0.29 14 17
Metarhodopsin II/Transducin 0.013 0.021 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.02 0.038 0.17 23 -0.14 1 24
PDE6A/B 0.008 0.046 0.19 6 -0.19 16 22
mol:Pi -0.022 0.08 0.18 3 -0.16 97 100
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.025 0.036 0.17 24 -10000 0 24
PDE6B -0.002 0.061 0.27 1 -0.29 17 18
PDE6A 0.013 0.031 0.27 6 -10000 0 6
PDE6G 0.019 0.049 0.27 15 -10000 0 15
RHO 0.002 0.004 -10000 0 -10000 0 0
PDE6 -0.007 0.082 0.28 1 -0.14 102 103
GUCA1A 0.021 0.058 0.27 21 -10000 0 21
GC2/GCAP Family 0.021 0.038 0.17 23 -0.14 1 24
GUCA1C 0.001 0.014 0.27 1 -10000 0 1
GUCA1B 0.01 0.023 0.27 2 -0.29 1 3
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.019 0.018 -10000 0 -10000 0 0
HDAC1 0.009 0.011 -10000 0 -10000 0 0
AES 0.01 0.004 -10000 0 -10000 0 0
FBXW11 0.01 0 -10000 0 -10000 0 0
DTX1 0.004 0.062 0.27 6 -0.29 13 19
LRP6/FZD1 0.015 0.014 0.19 1 -0.19 1 2
TLE1 0.008 0.026 -10000 0 -0.29 3 3
AP1 -0.066 0.12 -10000 0 -0.21 141 141
NCSTN 0.01 0 -10000 0 -10000 0 0
ADAM10 0.01 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.013 0.066 -10000 0 -0.3 3 3
NICD/RBPSUH 0.02 0.001 -10000 0 -10000 0 0
WIF1 -0.048 0.13 0.27 9 -0.29 81 90
NOTCH1 0.015 0.001 -10000 0 -10000 0 0
PSENEN 0.01 0 -10000 0 -10000 0 0
KREMEN2 0.11 0.13 0.27 158 -10000 0 158
DKK1 -0.022 0.12 0.27 15 -0.29 57 72
beta catenin/beta TrCP1 0.014 0.035 -10000 0 -10000 0 0
APH1B 0.01 0 -10000 0 -10000 0 0
APH1A 0.01 0 -10000 0 -10000 0 0
AXIN1 0.003 0.008 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.015 0.043 0.26 3 -0.17 3 6
PSEN1 0.01 0 -10000 0 -10000 0 0
FOS -0.084 0.14 -10000 0 -0.29 129 129
JUN -0.002 0.058 -10000 0 -0.29 16 16
MAP3K7 0.01 0.005 -10000 0 -10000 0 0
CTNNB1 0.009 0.036 -10000 0 -10000 0 0
MAPK3 0.01 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.12 0.11 0.21 207 -0.16 1 208
HNF1A 0.013 0.029 0.27 5 -10000 0 5
CTBP1 0.011 0.013 0.26 1 -10000 0 1
MYC -0.043 0.25 -10000 0 -1.2 18 18
NKD1 -0.005 0.079 0.27 6 -0.29 25 31
FZD1 0.01 0.02 0.27 1 -0.29 1 2
NOTCH1 precursor/Deltex homolog 1 0.022 0.02 -10000 0 -10000 0 0
apoptosis -0.066 0.12 -10000 0 -0.21 141 141
Delta 1/NOTCHprecursor 0.021 0.012 -10000 0 -10000 0 0
DLL1 0.008 0.035 0.27 2 -0.29 4 6
PPARD 0.008 0.024 -10000 0 -10000 0 0
Gamma Secretase 0.03 0.002 -10000 0 -10000 0 0
APC 0.003 0.008 -10000 0 -10000 0 0
DVL1 0.006 0.017 -10000 0 -10000 0 0
CSNK2A1 0.01 0.001 -10000 0 -10000 0 0
MAP3K7IP1 0 0.005 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.058 0.11 0.19 142 -0.16 32 174
LRP6 0.01 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0.001 -10000 0 -10000 0 0
NLK 0.008 0.011 -10000 0 -10000 0 0
CCND1 -0.003 0.17 -10000 0 -1.2 7 7
WNT1 0.009 0.023 0.27 3 -10000 0 3
Axin1/APC/beta catenin 0.016 0.026 -10000 0 -10000 0 0
DKK2 0.068 0.11 0.27 93 -0.29 1 94
NOTCH1 precursor/DVL1 0.018 0.015 -10000 0 -10000 0 0
GSK3B 0.01 0.001 -10000 0 -10000 0 0
FRAT1 0.01 0.002 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.018 0.031 -10000 0 -10000 0 0
PPP2R5D 0.014 0.044 0.18 21 -10000 0 21
MAPK1 0.01 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.007 0.071 0.18 12 -0.14 80 92
RBPJ 0.01 0 -10000 0 -10000 0 0
CREBBP 0.011 0.004 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0.028 0.18 3 -10000 0 3
AES 0.015 0.023 0.15 3 -10000 0 3
FBXW11 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.015 0.014 0.19 1 -0.19 1 2
SMAD4 0.01 0 -10000 0 -10000 0 0
DKK2 0.068 0.11 0.27 93 -0.29 1 94
TLE1 0.012 0.035 0.16 3 -0.29 3 6
MACF1 0.01 0 -10000 0 -10000 0 0
CTNNB1 0.065 0.058 0.19 26 -10000 0 26
WIF1 -0.048 0.12 0.27 9 -0.29 81 90
beta catenin/RanBP3 0.039 0.12 0.38 46 -10000 0 46
KREMEN2 0.11 0.13 0.27 158 -10000 0 158
DKK1 -0.022 0.12 0.27 15 -0.29 57 72
beta catenin/beta TrCP1 0.067 0.055 0.19 20 -10000 0 20
FZD1 0.01 0.02 0.27 1 -0.29 1 2
AXIN2 -0.08 0.31 -10000 0 -1.2 29 29
AXIN1 0.01 0.001 -10000 0 -10000 0 0
RAN 0.01 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.034 0.021 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.05 0.044 0.21 2 -0.23 2 4
Axin1/APC/GSK3 0.032 0.035 0.15 5 -10000 0 5
Axin1/APC/GSK3/beta catenin/Macf1 0.038 0.024 -10000 0 -10000 0 0
HNF1A 0.018 0.037 0.22 8 -10000 0 8
CTBP1 0.016 0.027 0.19 4 -10000 0 4
MYC -0.061 0.27 -10000 0 -1.3 18 18
RANBP3 0.01 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.12 0.11 0.21 207 -0.16 1 208
NKD1 -0.005 0.079 0.27 6 -0.29 25 31
TCF4 0.012 0.036 0.16 3 -0.29 3 6
TCF3 0.015 0.024 0.16 3 -10000 0 3
WNT1/LRP6/FZD1/Axin1 0.026 0.017 0.18 4 -0.14 1 5
Ran/GTP 0.008 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.045 0.15 0.43 46 -10000 0 46
LEF1 0.019 0.04 0.23 10 -10000 0 10
DVL1 0.016 0.021 -10000 0 -10000 0 0
CSNK2A1 0.01 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.031 0.075 0.21 1 -0.26 8 9
DKK1/LRP6/Kremen 2 0.058 0.11 0.19 142 -0.16 32 174
LRP6 0.01 0 -10000 0 -10000 0 0
CSNK1A1 0.016 0.028 0.18 3 -10000 0 3
NLK 0.008 0.006 -10000 0 -10000 0 0
CCND1 -0.024 0.19 -10000 0 -1.3 7 7
WNT1 0.01 0.023 0.27 3 -10000 0 3
GSK3A 0.01 0.001 -10000 0 -10000 0 0
GSK3B 0.01 0.001 -10000 0 -10000 0 0
FRAT1 0.01 0 -10000 0 -10000 0 0
PPP2R5D 0.027 0.049 0.19 25 -10000 0 25
APC 0.015 0.01 -10000 0 -0.12 1 1
WNT1/LRP6/FZD1 0.043 0.062 0.16 80 -10000 0 80
CREBBP 0.015 0.024 0.16 3 -10000 0 3
Regulation 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
HDAC1 0.009 0.004 -10000 0 -10000 0 0
SMARCC1 0.008 0.01 -10000 0 -10000 0 0
REL 0.008 0.032 0.28 2 -0.29 3 5
HDAC7 -0.036 0.1 0.19 3 -0.23 63 66
JUN -0.002 0.058 -10000 0 -0.29 16 16
EP300 0.01 0.001 -10000 0 -10000 0 0
KAT2B 0.009 0.015 -10000 0 -0.29 1 1
KAT5 0.01 0.001 -10000 0 -10000 0 0
MAPK14 0.003 0.029 0.16 1 -0.2 5 6
FOXO1 0.009 0.015 -10000 0 -0.29 1 1
T-DHT/AR -0.032 0.11 0.23 9 -0.25 61 70
MAP2K6 0.003 0.037 0.27 1 -0.29 5 6
BRM/BAF57 0.015 0.011 -10000 0 -10000 0 0
MAP2K4 0.006 0.011 -10000 0 -10000 0 0
SMARCA2 0.01 0.006 -10000 0 -10000 0 0
PDE9A -0.12 0.33 -10000 0 -1 49 49
NCOA2 -0.006 0.07 -10000 0 -0.29 24 24
CEBPA 0.015 0.045 0.27 10 -0.29 2 12
EHMT2 0.01 0.003 -10000 0 -10000 0 0
cell proliferation -0.024 0.13 0.26 7 -0.26 64 71
NR0B1 0.024 0.072 0.27 32 -10000 0 32
EGR1 -0.06 0.13 -10000 0 -0.29 96 96
RXRs/9cRA -0.024 0.071 0.17 1 -0.14 106 107
AR/RACK1/Src -0.001 0.084 0.21 30 -0.17 14 44
AR/GR -0.061 0.1 -10000 0 -0.19 146 146
GNB2L1 0.011 0.002 -10000 0 -10000 0 0
PKN1 0.009 0.015 -10000 0 -0.29 1 1
RCHY1 0.01 0 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0.003 -10000 0 -10000 0 0
MAPK8 0.004 0.022 -10000 0 -0.19 2 2
T-DHT/AR/TIF2/CARM1 -0.01 0.089 0.21 22 -0.18 34 56
SRC 0.002 0.037 0.12 3 -0.094 14 17
NR3C1 0.001 0.05 -10000 0 -0.29 12 12
KLK3 -0.071 0.24 0.34 13 -0.93 21 34
APPBP2 0.005 0.011 -10000 0 -10000 0 0
TRIM24 0.012 0.022 0.26 3 -10000 0 3
T-DHT/AR/TIP60 -0.02 0.062 -10000 0 -0.17 25 25
TMPRSS2 -0.15 0.38 0.39 1 -0.97 69 70
RXRG -0.071 0.13 0.27 1 -0.29 106 107
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.009 0.015 -10000 0 -0.29 1 1
RXRB 0.01 0.001 -10000 0 -10000 0 0
CARM1 0.011 0.003 -10000 0 -10000 0 0
NR2C2 0.01 0.02 0.27 1 -0.29 1 2
KLK2 0.01 0.11 0.32 35 -0.26 5 40
AR -0.069 0.11 -10000 0 -0.21 147 147
SENP1 0.01 0.001 -10000 0 -10000 0 0
HSP90AA1 0.01 0 -10000 0 -10000 0 0
MDM2 0.018 0.047 0.27 13 -10000 0 13
SRY 0.007 0.033 0.27 6 -10000 0 6
GATA2 0.013 0.06 0.27 13 -0.29 7 20
MYST2 0.01 0.001 -10000 0 -10000 0 0
HOXB13 -0.026 0.11 0.28 9 -0.29 56 65
T-DHT/AR/RACK1/Src -0.011 0.067 0.18 3 -0.16 24 27
positive regulation of transcription 0.013 0.06 0.27 13 -0.29 7 20
DNAJA1 0.005 0.011 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.021 0.13 12 -10000 0 12
NCOA1 0.014 0.007 -10000 0 -10000 0 0
SPDEF -0.002 0.13 0.27 34 -0.29 47 81
T-DHT/AR/TIF2 -0.017 0.063 -10000 0 -0.21 18 18
T-DHT/AR/Hsp90 -0.02 0.063 -10000 0 -0.17 25 25
GSK3B 0.009 0.005 -10000 0 -10000 0 0
NR2C1 0.009 0.004 -10000 0 -10000 0 0
mol:T-DHT 0.001 0.035 0.12 3 -0.078 26 29
SIRT1 0.01 0.001 -10000 0 -10000 0 0
ZMIZ2 0.009 0.01 -10000 0 -10000 0 0
POU2F1 -0.007 0.059 0.15 9 -0.15 27 36
T-DHT/AR/DAX-1 -0.01 0.076 0.19 17 -0.17 24 41
CREBBP 0.01 0.001 -10000 0 -10000 0 0
SMARCE1 0.01 0.006 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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
HRAS 0.01 0 -10000 0 -10000 0 0
EGFR 0.008 0.057 0.27 8 -0.29 9 17
EGF/EGFR 0.005 0.067 0.14 34 -0.13 65 99
EGF/EGFR dimer/SHC/GRB2/SOS1 0.037 0.047 0.18 33 -0.13 9 42
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA -0.033 0.1 -10000 0 -0.29 59 59
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.025 0.062 0.27 25 -10000 0 25
EGF/EGFR dimer/SHC 0.029 0.053 0.18 33 -0.16 9 42
mol:GDP 0.034 0.044 0.16 33 -0.13 9 42
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 0.011 0.038 0.27 5 -0.29 3 8
GRB2/SOS1 0.015 0 -10000 0 -10000 0 0
HRAS/GTP 0.022 0.031 0.19 1 -0.12 9 10
SHC1 0.011 0.013 0.27 1 -10000 0 1
HRAS/GDP 0.031 0.037 0.25 1 -0.12 9 10
FRAP1 0.011 0.028 0.14 1 -0.12 9 10
EGF/EGFR dimer 0.024 0.058 0.19 33 -0.19 9 42
SOS1 0.01 0 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.014 0.079 0.19 5 -0.2 61 66
Effects of Botulinum toxin

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
STX1A 0.006 0.015 0.16 4 -10000 0 4
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.005 0.038 0.19 1 -0.19 14 15
STXBP1 -0.002 0.058 -10000 0 -0.29 16 16
ACh/CHRNA1 0.039 0.079 0.21 71 -0.067 26 97
RAB3GAP2/RIMS1/UNC13B 0.012 0.033 0.18 1 -0.16 14 15
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 -0.003 0.055 0.27 1 -0.29 14 15
mol:ACh -0.001 0.026 0.062 12 -0.091 27 39
RAB3GAP2 0.01 0 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.002 0.049 0.23 1 -0.14 28 29
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.039 0.079 0.21 71 -0.066 26 97
UNC13B 0.01 0 -10000 0 -10000 0 0
CHRNA1 0.054 0.098 0.27 71 -10000 0 71
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.006 0.048 0.22 8 -0.12 27 35
SNAP25 -0.008 0.057 0.11 12 -0.21 27 39
VAMP2 0.003 0 -10000 0 -10000 0 0
SYT1 -0.01 0.091 0.27 8 -0.29 34 42
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.005 0.035 0.12 4 -0.16 16 20
STX1A/SNAP25 fragment 1/VAMP2 0.002 0.049 0.23 1 -0.14 28 29
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.01 0.001 -10000 0 -10000 0 0
HDAC2 0.01 0.001 -10000 0 -10000 0 0
GNB1/GNG2 0.01 0.045 -10000 0 -0.16 26 26
forebrain development -0.058 0.19 -10000 0 -0.46 60 60
GNAO1 -0.083 0.14 -10000 0 -0.29 129 129
SMO/beta Arrestin2 0.008 0.047 -10000 0 -0.19 21 21
SMO -0.003 0.066 -10000 0 -0.29 21 21
ARRB2 0.011 0.003 -10000 0 -10000 0 0
GLI3/SPOP 0.021 0.044 -10000 0 -0.19 12 12
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.01 0 -10000 0 -10000 0 0
GNAI2 0.011 0.002 -10000 0 -10000 0 0
SIN3/HDAC complex 0.024 0.002 -10000 0 -10000 0 0
GNAI1 0.009 0.026 -10000 0 -0.29 3 3
XPO1 0.014 0.007 -10000 0 -10000 0 0
GLI1/Su(fu) -0.034 0.16 -10000 0 -0.49 29 29
SAP30 0.01 0.001 -10000 0 -10000 0 0
mol:GDP -0.003 0.066 -10000 0 -0.29 21 21
MIM/GLI2A 0.033 0.052 0.16 62 -10000 0 62
IFT88 0.01 0 -10000 0 -10000 0 0
GNAI3 0.011 0.002 -10000 0 -10000 0 0
GLI2 -0.004 0.053 -10000 0 -10000 0 0
GLI3 0.016 0.046 -10000 0 -0.2 12 12
CSNK1D 0.01 0 -10000 0 -10000 0 0
CSNK1E 0.01 0 -10000 0 -10000 0 0
SAP18 0.01 0.001 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.01 0 -10000 0 -10000 0 0
GNG2 0.006 0.036 -10000 0 -0.29 6 6
Gi family/GTP -0.081 0.14 -10000 0 -0.24 157 157
SIN3B 0.01 0.001 -10000 0 -10000 0 0
SIN3A 0.01 0.001 -10000 0 -10000 0 0
GLI3/Su(fu) 0.022 0.03 -10000 0 -10000 0 0
GLI2/Su(fu) 0.004 0.059 -10000 0 -0.2 15 15
FOXA2 0.042 0.12 0.33 52 -10000 0 52
neural tube patterning -0.058 0.19 -10000 0 -0.46 60 60
SPOP 0.01 0 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.014 0.029 -10000 0 -10000 0 0
GNB1 0.01 0 -10000 0 -10000 0 0
CSNK1G2 0.01 0 -10000 0 -10000 0 0
CSNK1G3 0.01 0 -10000 0 -10000 0 0
MTSS1 0.033 0.052 0.16 62 -10000 0 62
embryonic limb morphogenesis -0.058 0.19 -10000 0 -0.46 60 60
SUFU 0.009 0.031 -10000 0 -10000 0 0
LGALS3 0.009 0.015 -10000 0 -0.29 1 1
catabolic process 0.015 0.056 -10000 0 -0.26 6 6
GLI3A/CBP -0.027 0.1 -10000 0 -0.28 61 61
KIF3A 0.01 0 -10000 0 -10000 0 0
GLI1 -0.059 0.2 -10000 0 -0.48 60 60
RAB23 0.009 0.015 -10000 0 -0.29 1 1
CSNK1A1 0.01 0 -10000 0 -10000 0 0
IFT172 0.01 0 -10000 0 -10000 0 0
RBBP7 0.01 0.001 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.014 0.029 -10000 0 -10000 0 0
GNAZ -0.054 0.12 -10000 0 -0.29 89 89
RBBP4 0.01 0.001 -10000 0 -10000 0 0
CSNK1G1 0.01 0 -10000 0 -10000 0 0
PIAS1 0.01 0 -10000 0 -10000 0 0
PRKACA 0.01 0 -10000 0 -10000 0 0
GLI2/SPOP 0.002 0.051 -10000 0 -10000 0 0
STK36 0.014 0.007 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.077 0.14 -10000 0 -0.23 154 154
PTCH1 -0.05 0.18 -10000 0 -0.57 26 26
MIM/GLI1 -0.03 0.21 0.3 34 -0.46 56 90
CREBBP -0.027 0.1 -10000 0 -0.28 61 61
Su(fu)/SIN3/HDAC complex 0.018 0.01 -10000 0 -10000 0 0
Ephrin B reverse signaling

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
EFNB2 0.011 0.018 0.27 2 -10000 0 2
EPHB2 0.028 0.065 0.27 28 -10000 0 28
EFNB1 0.004 0.033 -10000 0 -0.19 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.061 0.16 31 -0.2 6 37
Ephrin B2/EPHB1-2 0.021 0.06 0.17 32 -0.14 27 59
neuron projection morphogenesis 0.013 0.052 -10000 0 -0.12 37 37
Ephrin B1/EPHB1-2/Tiam1 0.022 0.066 0.18 31 -0.14 37 68
DNM1 0.002 0.048 -10000 0 -0.29 11 11
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.002 0.069 -10000 0 -0.49 8 8
YES1 -0.007 0.1 -10000 0 -0.72 8 8
Ephrin B1/EPHB1-2/NCK2 0.023 0.065 0.18 32 -0.14 36 68
PI3K 0.007 0.071 -10000 0 -0.49 8 8
mol:GDP 0.02 0.065 0.17 31 -0.14 37 68
ITGA2B 0.029 0.069 0.27 31 -10000 0 31
endothelial cell proliferation 0.014 0.011 0.17 2 -10000 0 2
FYN -0.008 0.1 -10000 0 -0.74 8 8
MAP3K7 -0.004 0.073 -10000 0 -0.52 8 8
FGR -0.006 0.1 -10000 0 -0.72 8 8
TIAM1 0.008 0.025 -10000 0 -0.29 3 3
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
RGS3 0.01 0 -10000 0 -10000 0 0
cell adhesion 0.001 0.082 -10000 0 -0.46 8 8
LYN -0.007 0.1 -10000 0 -0.72 8 8
Ephrin B1/EPHB1-2/Src Family Kinases -0.009 0.093 -10000 0 -0.66 8 8
Ephrin B1/EPHB1-2 -0.006 0.079 -10000 0 -0.56 8 8
SRC -0.005 0.1 -10000 0 -0.71 8 8
ITGB3 -0.024 0.094 -10000 0 -0.29 46 46
EPHB1 -0.008 0.08 0.27 4 -0.29 28 32
EPHB4 0.01 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.014 0.011 0.17 2 -10000 0 2
alphaIIb/beta3 Integrin 0.004 0.08 0.19 26 -0.19 41 67
BLK -0.018 0.11 -10000 0 -0.72 8 8
HCK -0.01 0.1 -10000 0 -0.72 8 8
regulation of stress fiber formation -0.022 0.064 0.14 36 -0.17 32 68
MAPK8 -0.001 0.071 -10000 0 -0.5 8 8
Ephrin B1/EPHB1-2/RGS3 0.023 0.065 0.18 32 -0.14 36 68
endothelial cell migration -0.001 0.06 -10000 0 -0.42 8 8
NCK2 0.01 0 -10000 0 -10000 0 0
PTPN13 0.009 0.021 -10000 0 -0.42 1 1
regulation of focal adhesion formation -0.022 0.064 0.14 36 -0.17 32 68
chemotaxis -0.022 0.064 0.14 36 -0.17 32 68
PIK3CA 0.01 0 -10000 0 -10000 0 0
Rac1/GTP 0.019 0.057 -10000 0 -0.16 12 12
angiogenesis -0.006 0.079 -10000 0 -0.56 8 8
LCK -0.007 0.1 -10000 0 -0.71 8 8
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.011 0.002 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response -0.041 0.12 0.36 1 -0.31 19 20
IL27/IL27R/JAK1 0.065 0.14 0.48 19 -10000 0 19
TBX21 0.05 0.16 0.36 49 -0.4 8 57
IL12B 0.021 0.052 0.29 14 -10000 0 14
IL12A 0.011 0.022 0.16 8 -10000 0 8
IL6ST -0.017 0.099 -10000 0 -0.3 45 45
IL27RA/JAK1 0.03 0.045 -10000 0 -10000 0 0
IL27 0.03 0.066 0.29 23 -10000 0 23
TYK2 0.021 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.087 0.1 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.041 0.12 0.36 1 -0.31 19 20
T cell proliferation during immune response -0.041 0.12 0.36 1 -0.31 19 20
MAPKKK cascade 0.041 0.12 0.31 19 -0.36 1 20
STAT3 0.01 0 -10000 0 -10000 0 0
STAT2 0.01 0 -10000 0 -10000 0 0
STAT1 0.014 0.027 0.28 4 -10000 0 4
IL12RB1 0.018 0.075 0.28 20 -0.29 10 30
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.074 0.18 0.39 70 -0.35 8 78
IL27/IL27R/JAK2/TYK2 0.041 0.12 0.31 18 -0.37 1 19
positive regulation of T cell mediated cytotoxicity 0.041 0.12 0.31 19 -0.36 1 20
STAT1 (dimer) 0.067 0.2 0.51 47 -0.41 3 50
JAK2 0.017 0.021 -10000 0 -0.29 1 1
JAK1 0.012 0.006 -10000 0 -10000 0 0
STAT2 (dimer) 0.039 0.11 0.31 11 -0.35 1 12
T cell proliferation 0.02 0.11 0.3 14 -0.31 15 29
IL12/IL12R/TYK2/JAK2 0.07 0.11 0.41 15 -10000 0 15
IL17A -0.086 0.1 -10000 0 -10000 0 0
mast cell activation -0.041 0.12 0.36 1 -0.31 19 20
IFNG 0.029 0.056 0.14 77 -0.065 1 78
T cell differentiation 0 0.005 0.012 37 -0.014 7 44
STAT3 (dimer) 0.039 0.11 0.31 11 -0.35 1 12
STAT5A (dimer) 0.039 0.11 0.31 11 -0.35 1 12
STAT4 (dimer) 0.036 0.11 0.31 11 -0.31 6 17
STAT4 -0.005 0.064 -10000 0 -0.29 20 20
T cell activation -0.006 0.011 -10000 0 -0.12 4 4
IL27R/JAK2/TYK2 0.034 0.098 0.33 1 -10000 0 1
GATA3 -0.081 0.29 -10000 0 -1.2 27 27
IL18 0.003 0.024 -10000 0 -0.19 6 6
positive regulation of mast cell cytokine production 0.039 0.11 0.3 11 -0.34 1 12
IL27/EBI3 0.038 0.067 0.24 30 -0.2 4 34
IL27RA 0.025 0.046 0.34 1 -10000 0 1
IL6 -0.12 0.15 -10000 0 -0.29 184 184
STAT5A 0.009 0.015 -10000 0 -0.29 1 1
monocyte differentiation 0.001 0.003 -10000 0 -10000 0 0
IL2 -0.017 0.035 -10000 0 -0.31 1 1
IL1B 0.002 0.053 0.16 15 -0.19 20 35
EBI3 0.019 0.048 0.28 7 -0.29 4 11
TNF 0.014 0.034 0.16 21 -10000 0 21
FoxO family signaling

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
G6PC 0.043 0.077 0.34 23 -10000 0 23
PLK1 0.23 0.24 0.59 92 -10000 0 92
CDKN1B 0.18 0.13 0.37 93 -10000 0 93
FOXO3 0.21 0.21 0.53 93 -0.39 1 94
KAT2B 0.044 0.042 0.13 1 -0.28 1 2
FOXO1/SIRT1 0.018 0.04 0.2 14 -10000 0 14
CAT 0.19 0.19 0.48 92 -10000 0 92
CTNNB1 0.01 0 -10000 0 -10000 0 0
AKT1 0.048 0.04 0.14 9 -10000 0 9
FOXO1 0.04 0.059 0.26 24 -10000 0 24
MAPK10 0.026 0.017 0.13 1 -10000 0 1
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.054 0.044 -10000 0 -10000 0 0
response to oxidative stress 0.039 0.04 0.1 95 -10000 0 95
FOXO3A/SIRT1 0.17 0.16 0.43 87 -10000 0 87
XPO1 0.01 0 -10000 0 -10000 0 0
EP300 0.014 0.01 -10000 0 -10000 0 0
BCL2L11 0.058 0.059 -10000 0 -10000 0 0
FOXO1/SKP2 0.042 0.051 0.21 31 -10000 0 31
mol:GDP 0.039 0.04 0.1 95 -10000 0 95
RAN 0.011 0 -10000 0 -10000 0 0
GADD45A 0.14 0.11 -10000 0 -10000 0 0
YWHAQ 0.01 0 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.043 0.027 -10000 0 -10000 0 0
MST1 0.058 0.067 0.29 22 -10000 0 22
CSNK1D 0.01 0 -10000 0 -10000 0 0
CSNK1E 0.01 0 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.033 0.034 -10000 0 -10000 0 0
YWHAB 0.01 0 -10000 0 -10000 0 0
MAPK8 0.03 0.016 0.13 1 -10000 0 1
MAPK9 0.03 0.016 0.13 1 -10000 0 1
YWHAG 0.01 0 -10000 0 -10000 0 0
YWHAE 0.009 0.015 -10000 0 -0.29 1 1
YWHAZ 0.01 0 -10000 0 -10000 0 0
SIRT1 0.006 0.02 0.13 3 -10000 0 3
SOD2 0.18 0.13 0.5 5 -10000 0 5
RBL2 0.17 0.16 0.46 7 -10000 0 7
RAL/GDP 0.042 0.028 0.24 1 -10000 0 1
CHUK 0.044 0.039 -10000 0 -10000 0 0
Ran/GTP 0.009 0 -10000 0 -10000 0 0
CSNK1G2 0.01 0 -10000 0 -10000 0 0
RAL/GTP 0.043 0.027 0.23 1 -10000 0 1
CSNK1G1 0.01 0 -10000 0 -10000 0 0
FASLG 0.003 0.29 0.46 5 -1.2 21 26
SKP2 0.016 0.038 0.27 9 -10000 0 9
USP7 0.011 0 -10000 0 -10000 0 0
IKBKB 0.044 0.039 -10000 0 -10000 0 0
CCNB1 0.23 0.24 0.59 93 -10000 0 93
FOXO1-3a-4/beta catenin 0.16 0.12 0.35 80 -10000 0 80
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.051 0.21 31 -10000 0 31
CSNK1A1 0.01 0 -10000 0 -10000 0 0
SGK1 0.036 0.064 0.13 5 -0.29 10 15
CSNK1G3 0.01 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.016 0 -10000 0 -10000 0 0
ZFAND5 0.054 0.04 -10000 0 -10000 0 0
SFN 0.027 0.076 0.27 32 -0.29 4 36
CDK2 0.013 0.016 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.082 0.067 0.24 17 -10000 0 17
CREBBP 0.013 0.016 -10000 0 -10000 0 0
FBXO32 0.19 0.2 0.48 92 -0.74 1 93
BCL6 0.17 0.16 0.4 78 -10000 0 78
RALB 0.01 0 -10000 0 -10000 0 0
RALA 0.011 0.013 0.27 1 -10000 0 1
YWHAH 0.01 0 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.007 0.029 -10000 0 -0.29 4 4
ANTXR2 -0.008 0.071 -10000 0 -0.29 25 25
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.01 -10000 0 -0.041 28 28
monocyte activation 0 0.081 -10000 0 -0.36 17 17
MAP2K2 0.006 0.006 -10000 0 -10000 0 0
MAP2K1 0 0.01 -10000 0 -0.036 28 28
MAP2K7 0 0.01 -10000 0 -0.036 28 28
MAP2K6 0 0.013 0.078 1 -0.041 28 29
CYAA -0.006 0.036 -10000 0 -0.14 28 28
MAP2K4 0 0.01 -10000 0 -0.036 28 28
IL1B -0.005 0.039 0.075 14 -0.12 32 46
Channel 0.002 0.041 -10000 0 -0.15 28 28
NLRP1 0 0.013 -10000 0 -0.041 28 28
CALM1 0.01 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.003 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.01 0.041 28 -10000 0 28
MAPK3 0 0.01 -10000 0 -0.036 28 28
MAPK1 0 0.01 -10000 0 -0.036 28 28
PGR -0.007 0.037 -10000 0 -0.13 28 28
PA/Cellular Receptors 0.001 0.045 -10000 0 -0.16 28 28
apoptosis -0.003 0.01 -10000 0 -0.041 28 28
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.002 0.04 -10000 0 -0.14 28 28
macrophage activation 0.002 0.009 -10000 0 -10000 0 0
TNF 0.023 0.057 0.27 21 -10000 0 21
VCAM1 0 0.081 -10000 0 -0.36 17 17
platelet activation 0.003 0.012 -10000 0 -10000 0 0
MAPKKK cascade -0.001 0.012 0.07 2 -10000 0 2
IL18 -0.003 0.029 -10000 0 -0.12 17 17
negative regulation of macrophage activation -0.003 0.01 -10000 0 -0.041 28 28
LEF -0.003 0.011 -10000 0 -0.041 28 28
CASP1 -0.001 0.017 -10000 0 -0.051 28 28
mol:cAMP 0.003 0.012 -10000 0 -10000 0 0
necrosis -0.003 0.01 -10000 0 -0.041 28 28
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.002 0.038 -10000 0 -0.14 28 28
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.047 0.073 -10000 0 -0.12 193 193
TC10/GTP -0.042 0.068 -10000 0 -0.12 189 189
Insulin Receptor/Insulin/IRS1/Shp2 0.016 0.025 -10000 0 -0.14 10 10
HRAS 0.01 0 -10000 0 -10000 0 0
APS homodimer 0.013 0.028 0.27 5 -10000 0 5
GRB14 0.045 0.089 0.27 56 -10000 0 56
FOXO3 -0.009 0.1 -10000 0 -0.51 16 16
AKT1 0.02 0.028 -10000 0 -0.1 9 9
INSR 0.011 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.021 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.006 0.033 -10000 0 -0.29 5 5
SORBS1 -0.13 0.15 -10000 0 -0.29 189 189
CRK 0.01 0 -10000 0 -10000 0 0
PTPN1 0.01 0 -10000 0 -10000 0 0
CAV1 0.006 0.032 -10000 0 -0.18 10 10
CBL/APS/CAP/Crk-II/C3G -0.041 0.081 0.17 5 -0.13 189 194
Insulin Receptor/Insulin/IRS1/NCK2 0.016 0.025 -10000 0 -0.14 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.013 0.023 -10000 0 -0.12 11 11
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.013 0.023 -10000 0 -10000 0 0
RPS6KB1 0.019 0.027 -10000 0 -0.097 9 9
PARD6A 0.009 0.015 -10000 0 -0.29 1 1
CBL 0.01 0 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.009 0.012 0.24 1 -10000 0 1
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.013 0.019 -10000 0 -10000 0 0
HRAS/GTP -0.004 0.021 -10000 0 -0.1 17 17
Insulin Receptor 0.011 0 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.022 0.025 0.17 1 -0.13 10 11
PRKCI 0.014 0.021 -10000 0 -0.38 1 1
Insulin Receptor/Insulin/GRB14/PDK1 0.007 0.019 -10000 0 -0.11 9 9
SHC1 0.011 0.013 0.27 1 -10000 0 1
negative regulation of MAPKKK cascade 0.02 0.008 -10000 0 -10000 0 0
PI3K 0.017 0.023 -10000 0 -0.12 11 11
NCK2 0.01 0 -10000 0 -10000 0 0
RHOQ 0.01 0 -10000 0 -10000 0 0
mol:H2O2 0 0 -10000 0 -10000 0 0
HRAS/GDP 0.007 0 -10000 0 -10000 0 0
AKT2 0.02 0.028 -10000 0 -0.1 9 9
PRKCZ 0.011 0.041 -10000 0 -0.39 4 4
SH2B2 0.013 0.028 0.27 5 -10000 0 5
SHC/SHIP 0.011 0.029 0.17 1 -0.12 17 18
F2RL2 0.007 0.073 0.27 13 -0.29 15 28
TRIP10 0.009 0.015 -10000 0 -0.29 1 1
Insulin Receptor/Insulin/Shc 0.014 0.008 0.17 1 -10000 0 1
TC10/GTP/CIP4/Exocyst 0.013 0.008 -10000 0 -0.16 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.025 0.007 0.17 1 -10000 0 1
RAPGEF1 0.01 0 -10000 0 -10000 0 0
RASA1 0.01 0 -10000 0 -10000 0 0
NCK1 0.01 0 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.048 0.085 0.18 5 -0.14 189 194
TC10/GDP 0.007 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.019 0.02 0.17 1 -0.14 5 6
INPP5D 0.007 0.022 -10000 0 -0.13 10 10
SOS1 0.01 0 -10000 0 -10000 0 0
SGK1 -0.023 0.15 -10000 0 -0.75 16 16
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.01 0 -10000 0 -10000 0 0
IRS1 0.003 0.046 -10000 0 -0.29 10 10
p62DOK/RasGAP 0.02 0.008 -10000 0 -10000 0 0
INS 0.001 0 -10000 0 -10000 0 0
mol:PI-3-4-P2 0.007 0.022 -10000 0 -0.13 10 10
GRB2 0.01 0 -10000 0 -10000 0 0
EIF4EBP1 0.023 0.033 0.17 3 -0.097 9 12
PTPRA 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.013 0.008 -10000 0 -0.16 1 1
PDPK1 0.01 0 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.011 0.028 -10000 0 -0.16 10 10
Insulin Receptor/Insulin/IRS1 0.01 0.025 -10000 0 -0.14 10 10
Insulin Receptor/Insulin/IRS3 0.009 0 -10000 0 -10000 0 0
Par3/Par6 0.022 0.04 0.16 13 -0.13 17 30
Nectin adhesion pathway

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
PDGFRB 0.003 0.046 -10000 0 -0.29 10 10
alphaV beta3 Integrin -0.009 0.067 -10000 0 -0.2 46 46
PTK2 -0.013 0.094 -10000 0 -0.32 30 30
positive regulation of JNK cascade -0.021 0.07 -10000 0 -0.27 29 29
CDC42/GDP -0.001 0.1 -10000 0 -0.36 29 29
Rac1/GDP -0.001 0.1 -10000 0 -0.36 29 29
RAP1B 0.01 0 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
CTNNB1 0.01 0 -10000 0 -10000 0 0
CDC42/GTP -0.004 0.092 -10000 0 -0.33 29 29
nectin-3/I-afadin 0.001 0.055 0.19 2 -0.19 29 31
RAPGEF1 -0.01 0.11 -10000 0 -0.39 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.014 0.12 -10000 0 -0.44 29 29
PDGFB-D/PDGFRB 0.003 0.046 -10000 0 -0.29 10 10
TLN1 -0.001 0.04 -10000 0 -0.12 35 35
Rap1/GTP -0.022 0.074 -10000 0 -0.29 29 29
IQGAP1 0.01 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.019 0 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.001 0.055 0.19 2 -0.19 29 31
PVR 0.01 0 -10000 0 -10000 0 0
Necl-5(dimer) 0.01 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.12 -10000 0 -0.43 29 29
MLLT4 0.01 0 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
PI3K 0.015 0.049 0.17 2 -0.13 39 41
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.014 0.01 -10000 0 -0.19 1 1
positive regulation of lamellipodium assembly -0.023 0.075 -10000 0 -0.28 31 31
PVRL1 0.009 0.015 -10000 0 -0.29 1 1
PVRL3 -0.01 0.079 0.27 2 -0.29 29 31
PVRL2 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
CDH1 0 0.054 -10000 0 -0.29 14 14
CLDN1 0.003 0.07 0.27 8 -0.29 17 25
JAM-A/CLDN1 0.01 0.057 0.18 8 -0.14 44 52
SRC -0.017 0.13 -10000 0 -0.48 29 29
ITGB3 -0.024 0.094 -10000 0 -0.29 46 46
nectin-1(dimer)/I-afadin/I-afadin 0.014 0.01 -10000 0 -0.19 1 1
FARP2 -0.009 0.12 -10000 0 -0.42 29 29
RAC1 0.01 0 -10000 0 -10000 0 0
CTNNA1 0.01 0 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.009 0.047 0.18 2 -0.16 29 31
nectin-1/I-afadin 0.014 0.01 -10000 0 -0.19 1 1
nectin-2/I-afadin 0.015 0 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.014 0 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.008 0.048 0.18 2 -0.16 30 32
CDC42/GTP/IQGAP1/filamentous actin 0.014 0 -10000 0 -10000 0 0
F11R 0.009 0.015 -10000 0 -0.29 1 1
positive regulation of filopodium formation -0.021 0.07 -10000 0 -0.27 29 29
alphaV/beta3 Integrin/Talin -0.005 0.063 -10000 0 -0.23 15 15
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.015 0 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.015 0 -10000 0 -10000 0 0
PIP5K1C -0.003 0.043 -10000 0 -0.13 35 35
VAV2 -0.011 0.12 -10000 0 -0.43 31 31
RAP1/GDP -0.001 0.095 -10000 0 -0.34 29 29
ITGAV 0.009 0.015 -10000 0 -0.29 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.009 0.047 0.18 2 -0.16 29 31
nectin-3(dimer)/I-afadin/I-afadin 0.001 0.055 0.19 2 -0.19 29 31
Rac1/GTP -0.005 0.097 -10000 0 -0.34 31 31
PTPRM -0.005 0.048 -10000 0 -0.15 35 35
E-cadherin/beta catenin/alpha catenin 0.024 0.029 -10000 0 -0.13 14 14
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.01 0 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.019 0.053 0.17 29 -0.16 14 43
cell-cell adhesion 0.01 0.031 0.18 2 -10000 0 2
Ephrin B/EPHB2/RasGAP 0.037 0.051 0.17 35 -0.13 12 47
ITSN1 0.01 0 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
SHC1 0.011 0.013 0.27 1 -10000 0 1
Ephrin B1/EPHB3 0.019 0.033 0.17 16 -0.16 2 18
Ephrin B1/EPHB1 0.003 0.046 0.17 4 -0.16 28 32
HRAS/GDP 0.004 0.043 0.19 1 -0.15 13 14
Ephrin B/EPHB1/GRB7 0.02 0.064 0.18 23 -0.13 44 67
Endophilin/SYNJ1 0.014 0.031 0.15 1 -0.12 12 13
KRAS 0.011 0.013 0.27 1 -10000 0 1
Ephrin B/EPHB1/Src 0.018 0.055 0.18 10 -0.13 38 48
endothelial cell migration 0.022 0.012 0.15 2 -0.13 1 3
GRB2 0.01 0 -10000 0 -10000 0 0
GRB7 0.014 0.062 0.27 14 -0.29 7 21
PAK1 0.016 0.033 0.15 1 -0.12 14 15
HRAS 0.01 0 -10000 0 -10000 0 0
RRAS 0.014 0.033 0.15 1 -0.13 12 13
DNM1 0.002 0.048 -10000 0 -0.29 11 11
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.002 0.043 0.15 1 -0.12 38 39
lamellipodium assembly -0.01 0.031 -10000 0 -0.18 2 2
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.003 0.056 0.18 1 -0.16 38 39
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
EPHB2 0.028 0.065 0.27 28 -10000 0 28
EPHB3 0.019 0.055 0.27 16 -0.29 2 18
EPHB1 -0.008 0.08 0.27 4 -0.29 28 32
EPHB4 0.01 0 -10000 0 -10000 0 0
mol:GDP 0.005 0.043 0.14 2 -0.17 12 14
Ephrin B/EPHB2 0.031 0.05 0.17 35 -0.13 12 47
Ephrin B/EPHB3 0.026 0.044 0.16 23 -0.13 13 36
JNK cascade 0.009 0.043 -10000 0 -0.13 28 28
Ephrin B/EPHB1 0.012 0.054 0.18 10 -0.13 38 48
RAP1/GDP 0.014 0.042 -10000 0 -0.15 11 11
EFNB2 0.011 0.018 0.27 2 -10000 0 2
EFNB3 0.005 0.066 0.27 8 -0.29 14 22
EFNB1 0.01 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.021 0.06 0.18 32 -0.14 27 59
RAP1B 0.01 0 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
CDC42/GTP 0.02 0.054 0.22 2 -0.16 11 13
Rap1/GTP 0.001 0.035 -10000 0 -0.18 2 2
axon guidance 0.019 0.052 0.17 29 -0.16 14 43
MAPK3 0.004 0.05 0.15 1 -0.15 28 29
MAPK1 0.004 0.05 0.15 1 -0.15 28 29
Rac1/GDP 0.01 0.042 0.14 1 -0.16 12 13
actin cytoskeleton reorganization -0.009 0.027 -10000 0 -0.12 11 11
CDC42/GDP 0.01 0.042 0.14 1 -0.16 12 13
PI3K 0.024 0.012 0.16 2 -0.13 1 3
EFNA5 0 0.056 0.27 1 -0.29 14 15
Ephrin B2/EPHB4 0.014 0.011 0.17 2 -10000 0 2
Ephrin B/EPHB2/Intersectin/N-WASP 0.019 0.042 0.19 1 -0.16 12 13
CDC42 0.01 0 -10000 0 -10000 0 0
RAS family/GTP -0.01 0.031 -10000 0 -0.18 2 2
PTK2 0.006 0.009 -10000 0 -10000 0 0
MAP4K4 0.009 0.043 -10000 0 -0.13 28 28
SRC 0.01 0 -10000 0 -10000 0 0
KALRN 0.011 0.033 0.27 4 -0.29 2 6
Intersectin/N-WASP 0.015 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.017 0.046 0.16 2 -0.19 3 5
MAP2K1 0.004 0.053 0.16 1 -0.16 28 29
WASL 0.01 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.026 0.06 0.18 32 -0.14 28 60
cell migration 0.001 0.062 0.18 1 -0.18 38 39
NRAS 0.01 0 -10000 0 -10000 0 0
SYNJ1 0.015 0.031 0.15 1 -0.12 12 13
PXN 0.01 0 -10000 0 -10000 0 0
TF 0.023 0.041 0.12 41 -0.11 10 51
HRAS/GTP 0.018 0.049 0.2 2 -0.2 2 4
Ephrin B1/EPHB1-2 0.02 0.059 0.17 32 -0.14 28 60
cell adhesion mediated by integrin -0.003 0.027 0.13 13 -10000 0 13
RAC1 0.01 0 -10000 0 -10000 0 0
mol:GTP 0.022 0.056 0.18 9 -0.12 37 46
RAC1-CDC42/GTP -0.01 0.031 -10000 0 -0.18 2 2
RASA1 0.01 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.014 0.042 -10000 0 -0.18 3 3
ruffle organization 0.011 0.042 0.14 2 -0.19 2 4
NCK1 0.01 0 -10000 0 -10000 0 0
receptor internalization 0.013 0.031 0.14 1 -0.12 12 13
Ephrin B/EPHB2/KALRN 0.038 0.053 0.17 39 -0.13 14 53
ROCK1 0.013 0.019 -10000 0 -0.14 2 2
RAS family/GDP -0.008 0.026 -10000 0 -0.13 11 11
Rac1/GTP -0.01 0.033 -10000 0 -0.19 2 2
Ephrin B/EPHB1/Src/Paxillin 0.002 0.059 0.2 1 -0.17 38 39
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.008 0.033 -10000 0 -0.17 14 14
epithelial cell differentiation 0.016 0.027 -10000 0 -0.13 14 14
CYFIP2 0.002 0.048 -10000 0 -0.29 11 11
ENAH 0.013 0.023 -10000 0 -0.16 1 1
EGFR 0.008 0.057 0.27 8 -0.29 9 17
EPHA2 0.006 0.033 -10000 0 -0.29 5 5
MYO6 0.008 0.024 -10000 0 -0.12 14 14
CTNNB1 0.01 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.016 0.029 -10000 0 -0.16 11 11
AQP5 0.021 0.04 -10000 0 -10000 0 0
CTNND1 0.01 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.024 -10000 0 -0.12 14 14
regulation of calcium-dependent cell-cell adhesion 0.016 0.04 0.17 19 -0.12 12 31
EGF 0.025 0.062 0.27 25 -10000 0 25
NCKAP1 0.01 0 -10000 0 -10000 0 0
AQP3 -0.06 0.16 -10000 0 -0.37 80 80
cortical microtubule organization 0.016 0.027 -10000 0 -0.13 14 14
GO:0000145 0.005 0.022 -10000 0 -0.11 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.018 0.028 -10000 0 -0.13 14 14
MLLT4 0.01 0 -10000 0 -10000 0 0
ARF6/GDP -0.005 0.023 -10000 0 -0.21 1 1
ARF6 0.01 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.027 0.029 0.18 9 -0.14 5 14
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.01 0.025 -10000 0 -0.18 1 1
PVRL2 0.01 0 -10000 0 -10000 0 0
ZYX 0.008 0.024 -10000 0 -0.12 14 14
ARF6/GTP 0.029 0.026 0.16 9 -0.12 5 14
CDH1 0 0.054 -10000 0 -0.29 14 14
EGFR/EGFR/EGF/EGF 0.018 0.04 -10000 0 -0.12 20 20
RhoA/GDP 0.017 0.026 -10000 0 -0.12 14 14
actin cytoskeleton organization 0.008 0.024 -10000 0 -0.12 14 14
IGF-1R heterotetramer 0.008 0.025 -10000 0 -0.29 3 3
GIT1 0.01 0 -10000 0 -10000 0 0
IGF1R 0.008 0.025 -10000 0 -0.29 3 3
IGF1 -0.12 0.15 -10000 0 -0.29 182 182
DIAPH1 0.009 0.088 -10000 0 -0.52 11 11
Wnt receptor signaling pathway -0.016 0.027 0.13 14 -10000 0 14
RHOA 0.01 0 -10000 0 -10000 0 0
RhoA/GTP -0.005 0.023 -10000 0 -0.21 1 1
CTNNA1 0.01 0 -10000 0 -10000 0 0
VCL 0.008 0.025 -10000 0 -0.12 14 14
EFNA1 0.016 0.038 0.27 9 -10000 0 9
LPP 0.008 0.023 -10000 0 -0.11 14 14
Ephrin A1/EPHA2 0.015 0.032 -10000 0 -0.12 18 18
SEC6/SEC8 -0.004 0.019 -10000 0 -0.11 14 14
MGAT3 0.016 0.041 0.17 19 -0.12 12 31
HGF/MET -0.013 0.06 -10000 0 -0.12 99 99
HGF -0.049 0.13 0.27 7 -0.29 87 94
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.008 0.033 -10000 0 -0.17 14 14
actin cable formation 0.019 0.025 -10000 0 -0.13 1 1
KIAA1543 0.005 0.039 -10000 0 -0.19 14 14
KIFC3 0.008 0.024 -10000 0 -0.12 14 14
NCK1 0.01 0 -10000 0 -10000 0 0
EXOC3 0.01 0 -10000 0 -10000 0 0
ACTN1 0.008 0.024 -10000 0 -0.12 14 14
NCK1/GIT1 0.015 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.027 -10000 0 -0.13 14 14
EXOC4 0.01 0 -10000 0 -10000 0 0
STX4 0.008 0.024 -10000 0 -0.12 14 14
PIP5K1C 0.008 0.024 -10000 0 -0.12 14 14
LIMA1 0.01 0 -10000 0 -10000 0 0
ABI1 0.01 0 -10000 0 -10000 0 0
ROCK1 0.013 0.025 -10000 0 -0.19 1 1
adherens junction assembly 0.008 0.048 -10000 0 -0.27 9 9
IGF-1R heterotetramer/IGF1 -0.046 0.07 -10000 0 -0.12 194 194
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.015 0 -10000 0 -10000 0 0
MET 0.011 0.018 0.27 2 -10000 0 2
PLEKHA7 0.008 0.027 -10000 0 -0.13 14 14
mol:GTP 0.026 0.028 0.17 9 -0.14 5 14
establishment of epithelial cell apical/basal polarity 0.013 0.022 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.008 0.033 -10000 0 -0.17 14 14
regulation of cell-cell adhesion 0.008 0.024 -10000 0 -0.12 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.008 0.033 -10000 0 -0.17 14 14
Caspase cascade in apoptosis

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
TOP1 0.008 0.081 0.17 9 -0.27 22 31
ACTA1 -0.001 0.1 0.15 20 -0.32 26 46
NUMA1 0.008 0.081 0.17 9 -0.27 22 31
SPTAN1 -0.001 0.097 0.18 9 -0.32 24 33
LIMK1 -0.001 0.097 0.18 9 -0.32 24 33
BIRC3 -0.004 0.071 0.27 3 -0.29 22 25
BIRC2 0.011 0.018 0.27 2 -10000 0 2
BAX 0.01 0 -10000 0 -10000 0 0
CASP10 0.012 0.054 0.14 34 -0.16 18 52
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.01 0.02 0.27 1 -0.29 1 2
PTK2 0.008 0.081 0.17 9 -0.27 22 31
DIABLO 0.01 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0 0.096 0.18 9 -0.32 24 33
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.01 0 -10000 0 -10000 0 0
GSN -0.003 0.1 0.18 9 -0.33 26 35
MADD 0.01 0 -10000 0 -10000 0 0
TFAP2A 0.029 0.062 0.32 3 -0.46 2 5
BID 0.003 0.057 0.14 11 -0.16 31 42
MAP3K1 0.006 0.038 -10000 0 -0.18 7 7
TRADD 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.015 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.001 0.097 0.18 9 -0.32 24 33
CASP9 0.01 0 -10000 0 -10000 0 0
DNA repair -0.008 0.034 0.12 4 -0.13 12 16
neuron apoptosis 0.011 0.051 -10000 0 -0.7 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.005 0.094 0.18 9 -0.31 24 33
APAF1 0.01 0 -10000 0 -10000 0 0
CASP6 0.015 0.053 -10000 0 -10000 0 0
TRAF2 0.01 0 -10000 0 -10000 0 0
ICAD/CAD 0.001 0.094 0.18 9 -0.31 24 33
CASP7 0.008 0.057 0.23 22 -0.15 4 26
KRT18 0.015 0.04 -10000 0 -0.47 1 1
apoptosis 0.007 0.085 0.17 10 -0.29 22 32
DFFA -0.001 0.097 0.18 9 -0.32 24 33
DFFB -0.001 0.097 0.18 9 -0.32 24 33
PARP1 0.008 0.034 0.13 12 -0.12 4 16
actin filament polymerization 0 0.092 0.3 24 -0.18 9 33
TNF 0.023 0.057 0.27 21 -10000 0 21
CYCS 0.005 0.037 0.11 9 -0.15 10 19
SATB1 0.011 0.055 -10000 0 -10000 0 0
SLK -0.001 0.097 0.18 9 -0.32 24 33
p15 BID/BAX 0.008 0.05 0.12 9 -0.14 31 40
CASP2 0.016 0.036 0.15 1 -10000 0 1
JNK cascade -0.006 0.038 0.17 7 -10000 0 7
CASP3 -0.002 0.1 0.16 20 -0.34 24 44
LMNB2 0.021 0.033 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
CASP4 0.011 0.013 0.27 1 -10000 0 1
Mammalian IAPs/DIABLO 0.019 0.045 0.21 5 -0.14 22 27
negative regulation of DNA binding 0.029 0.062 0.32 3 -0.46 2 5
stress fiber formation 0 0.096 0.15 20 -0.32 24 44
GZMB 0.015 0.075 0.2 34 -0.19 21 55
CASP1 0.003 0.036 0.14 1 -0.23 9 10
LMNB1 0.024 0.036 -10000 0 -10000 0 0
APP 0.011 0.052 -10000 0 -0.7 2 2
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.005 0 -10000 0 -10000 0 0
VIM 0.006 0.084 0.17 10 -0.28 22 32
LMNA 0.02 0.033 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.016 0.039 0.16 1 -10000 0 1
LRDD 0.01 0 -10000 0 -10000 0 0
SREBF1 0 0.097 0.15 20 -0.32 24 44
APAF-1/Caspase 9 0.007 0.03 0.24 1 -10000 0 1
nuclear fragmentation during apoptosis 0.008 0.08 0.17 9 -0.27 22 31
CFL2 0 0.094 0.18 9 -0.31 24 33
GAS2 -0.01 0.11 0.18 9 -0.33 25 34
positive regulation of apoptosis 0.025 0.033 -10000 0 -10000 0 0
PRF1 0.005 0.073 0.27 11 -0.29 16 27
IL2 signaling events mediated by PI3K

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
BCL2L1 0.02 0.054 0.34 1 -0.46 1 2
UGCG -0.022 0.15 -10000 0 -0.61 23 23
AKT1/mTOR/p70S6K/Hsp90/TERT 0.058 0.1 0.26 2 -0.26 22 24
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.022 0.14 -10000 0 -0.6 23 23
mol:DAG 0.005 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.12 -10000 0 -0.38 34 34
FRAP1 0.011 0.15 0.26 1 -0.44 34 35
FOXO3 0.013 0.12 0.26 1 -0.4 26 27
AKT1 0.011 0.13 0.27 1 -0.42 27 28
GAB2 0.009 0.015 -10000 0 -0.29 1 1
SMPD1 0.012 0.023 -10000 0 -10000 0 0
SGMS1 0.012 0.023 -10000 0 -10000 0 0
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 0.007 0.01 -10000 0 -0.16 1 1
CALM1 0.01 0 -10000 0 -10000 0 0
cell proliferation -0.007 0.12 -10000 0 -0.31 39 39
EIF3A 0.01 0 -10000 0 -10000 0 0
PI3K 0.016 0.013 -10000 0 -0.19 1 1
RPS6KB1 0.031 0.05 -10000 0 -10000 0 0
mol:sphingomyelin 0.005 0.004 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -10000 0 0
JAK3 0.012 0.019 0.27 2 -10000 0 2
PIK3R1 0.01 0.015 -10000 0 -0.29 1 1
JAK1 0.011 0.004 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
MYC -0.006 0.2 -10000 0 -0.72 26 26
MYB 0.081 0.13 0.42 30 -1 1 31
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.017 0.096 0.25 2 -0.3 23 25
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.038 0.044 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.018 0.094 0.25 2 -0.29 23 25
Rac1/GDP 0.013 0.01 -10000 0 -0.14 1 1
T cell proliferation 0.018 0.088 0.24 2 -0.28 23 25
SHC1 0.01 0.013 0.27 1 -10000 0 1
RAC1 0.01 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.017 0.038 0.11 56 -0.082 1 57
PRKCZ 0.017 0.091 0.24 2 -0.28 23 25
NF kappa B1 p50/RelA 0.018 0.13 -10000 0 -0.38 34 34
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.019 0.057 0.25 2 -0.35 7 9
HSP90AA1 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
IL2RA 0.009 0.084 0.27 19 -0.29 18 37
IL2RB 0.008 0.038 0.27 2 -0.29 5 7
TERT 0.12 0.13 0.27 176 -10000 0 176
E2F1 0.079 0.11 0.32 56 -0.28 1 57
SOS1 0.01 0.003 -10000 0 -10000 0 0
RPS6 0.01 0 -10000 0 -10000 0 0
mol:cAMP -0.008 0.018 0.034 1 -0.054 56 57
PTPN11 0.01 0.004 -10000 0 -10000 0 0
IL2RG 0.009 0.061 0.27 9 -0.29 10 19
actin cytoskeleton organization 0.018 0.088 0.24 2 -0.28 23 25
GRB2 0.01 0.003 -10000 0 -10000 0 0
IL2 0.004 0.006 -10000 0 -10000 0 0
PIK3CA 0.011 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.023 0.015 -10000 0 -0.13 1 1
LCK 0.009 0.035 0.27 2 -0.29 4 6
BCL2 0.001 0.18 -10000 0 -0.73 20 20
IL2 signaling events mediated by STAT5

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
GAB2 0.009 0.015 -10000 0 -0.29 1 1
ELF1 0.009 0.069 0.16 19 -0.28 18 37
CCNA2 0.077 0.11 0.27 106 -10000 0 106
PIK3CA 0.01 0 -10000 0 -10000 0 0
JAK3 0.011 0.018 0.27 2 -10000 0 2
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
JAK1 0.01 0 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.024 0.073 0.3 1 -0.46 4 5
SHC1 0.011 0.013 0.27 1 -10000 0 1
SP1 -0.008 0.079 -10000 0 -0.28 32 32
IL2RA 0.004 0.13 0.31 19 -0.54 18 37
IL2RB 0.008 0.038 0.27 2 -0.29 5 7
SOS1 0.01 0 -10000 0 -10000 0 0
IL2RG 0.009 0.06 0.27 9 -0.29 10 19
G1/S transition of mitotic cell cycle -0.008 0.2 -10000 0 -0.58 37 37
PTPN11 0.01 0 -10000 0 -10000 0 0
CCND2 -0.03 0.15 -10000 0 -0.54 32 32
LCK 0.009 0.035 0.27 2 -0.29 4 6
GRB2 0.01 0 -10000 0 -10000 0 0
IL2 0.003 0.004 -10000 0 -10000 0 0
CDK6 0.002 0.048 -10000 0 -0.29 11 11
CCND3 0.026 0.065 -10000 0 -0.47 2 2
BARD1 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
BARD1/CSTF1 0.01 0.032 -10000 0 -0.19 10 10
ATM 0.01 0 -10000 0 -10000 0 0
UBE2D3 0.01 0 -10000 0 -10000 0 0
PRKDC 0.01 0 -10000 0 -10000 0 0
ATR 0.01 0 -10000 0 -10000 0 0
UBE2L3 0.01 0 -10000 0 -10000 0 0
FANCD2 0.013 0.013 0.14 4 -10000 0 4
protein ubiquitination 0.043 0.054 0.16 64 -0.13 9 73
XRCC5 0.01 0 -10000 0 -10000 0 0
XRCC6 0.01 0 -10000 0 -10000 0 0
M/R/N Complex 0.02 0 -10000 0 -10000 0 0
MRE11A 0.01 0 -10000 0 -10000 0 0
DNA-PK 0.02 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.025 0.025 -10000 0 -10000 0 0
FANCF 0.01 0.02 0.27 1 -0.29 1 2
BRCA1 0.011 0.013 0.27 1 -10000 0 1
CCNE1 0.051 0.094 0.27 64 -10000 0 64
CDK2/Cyclin E1 0.043 0.064 0.19 64 -10000 0 64
FANCG 0.01 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.01 0.033 0.19 1 -0.19 10 11
FANCE 0.011 0.013 0.27 1 -10000 0 1
FANCC 0.011 0.013 0.27 1 -10000 0 1
NBN 0.01 0 -10000 0 -10000 0 0
FANCA 0.027 0.064 0.27 27 -10000 0 27
DNA repair 0.053 0.044 0.22 2 -10000 0 2
BRCA1/BARD1/ubiquitin 0.01 0.033 0.19 1 -0.19 10 11
BARD1/DNA-PK 0.022 0.025 -10000 0 -0.14 10 10
FANCL 0.011 0.013 0.27 1 -10000 0 1
mRNA polyadenylation -0.01 0.032 0.19 10 -10000 0 10
BRCA1/BARD1/CTIP/M/R/N Complex 0.013 0.028 -10000 0 -0.16 10 10
BRCA1/BACH1/BARD1/TopBP1 0.016 0.028 0.18 1 -0.16 10 11
BRCA1/BARD1/P53 0.022 0.026 0.18 1 -0.14 10 11
BARD1/CSTF1/BRCA1 0.016 0.028 0.18 1 -0.16 10 11
BRCA1/BACH1 0.011 0.013 0.27 1 -10000 0 1
BARD1 0.002 0.046 -10000 0 -0.29 10 10
PCNA 0.011 0.013 0.27 1 -10000 0 1
BRCA1/BARD1/UbcH5C 0.016 0.028 0.18 1 -0.16 10 11
BRCA1/BARD1/UbcH7 0.016 0.028 0.18 1 -0.16 10 11
BRCA1/BARD1/RAD51/PCNA 0.075 0.078 0.18 144 -0.14 7 151
BARD1/DNA-PK/P53 0.026 0.024 -10000 0 -0.13 10 10
BRCA1/BARD1/Ubiquitin 0.01 0.033 0.19 1 -0.19 10 11
BRCA1/BARD1/CTIP 0.016 0.026 0.18 1 -0.14 10 11
FA complex 0.024 0.026 0.18 2 -10000 0 2
BARD1/EWS 0.01 0.032 -10000 0 -0.19 10 10
RBBP8 0.009 0 -10000 0 -10000 0 0
TP53 0.01 0 -10000 0 -10000 0 0
TOPBP1 0.01 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.021 0.026 0.14 10 -0.17 1 11
BRCA1/BARD1 0.048 0.058 0.17 64 -0.13 9 73
CSTF1 0.01 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.002 0.031 -10000 0 -0.19 10 10
CDK2 0.01 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.1 0.12 0.27 145 -10000 0 145
RAD50 0.01 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.01 0.033 0.19 1 -0.19 10 11
EWSR1 0.01 0 -10000 0 -10000 0 0
IL1-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
UBC13/UEV1A 0.011 0.004 -10000 0 -10000 0 0
PRKCZ 0.008 0.025 -10000 0 -0.29 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.01 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.035 -10000 0 -0.18 2 2
IRAK/TOLLIP 0.016 0.001 -10000 0 -10000 0 0
IKBKB 0.01 0 -10000 0 -10000 0 0
IKBKG 0.01 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.026 0.11 0.21 71 -0.19 43 114
IL1A 0.008 0.12 0.27 40 -0.29 37 77
IL1B 0.002 0.059 0.16 15 -0.19 27 42
IRAK/TRAF6/p62/Atypical PKCs 0.028 0.012 -10000 0 -10000 0 0
IL1R2 0.029 0.086 0.27 38 -0.29 7 45
IL1R1 0.009 0.015 -10000 0 -0.29 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.016 0.039 -10000 0 -0.23 2 2
TOLLIP 0.01 0 -10000 0 -10000 0 0
TICAM2 0.009 0.015 -10000 0 -0.29 1 1
MAP3K3 0.01 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.007 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.026 0.005 -10000 0 -10000 0 0
JUN 0.011 0.005 -10000 0 -10000 0 0
MAP3K7 0.01 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.025 0.052 0.19 11 -0.24 2 13
IL1 alpha/IL1R1/IL1RAP/MYD88 0.029 0.075 0.18 49 -0.14 37 86
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.033 0.071 0.18 49 -0.13 37 86
IL1 beta fragment/IL1R1/IL1RAP 0.016 0.056 0.2 11 -0.15 28 39
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 0.011 0.005 0.1 1 -10000 0 1
IRAK1 0.01 0.001 -10000 0 -10000 0 0
IL1RN/IL1R1 0.017 0.039 0.19 11 -0.24 4 15
IRAK4 0.01 0 -10000 0 -10000 0 0
PRKCI 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
PI3K 0.014 0.01 -10000 0 -0.19 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.014 0.04 0.16 2 -0.25 2 4
CHUK 0.01 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.016 0.056 0.2 11 -0.15 28 39
IL1 beta/IL1R2 0.018 0.076 0.19 36 -0.17 31 67
IRAK/TRAF6/TAK1/TAB1/TAB2 0.018 0.001 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.014 0.04 0.16 2 -0.22 2 4
IRAK3 0.001 0.05 -10000 0 -0.29 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.025 0.052 0.19 11 -0.24 2 13
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.065 0.19 2 -0.17 37 39
IL1 alpha/IL1R1/IL1RAP 0.024 0.08 0.19 49 -0.16 37 86
RELA 0.01 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.01 0 -10000 0 -10000 0 0
MYD88 0.01 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.021 0.001 -10000 0 -10000 0 0
IL1RAP 0.017 0.042 0.27 11 -10000 0 11
UBE2N 0.01 0 -10000 0 -10000 0 0
IRAK/TRAF6 0.008 0.034 -10000 0 -0.21 2 2
CASP1 0.003 0.044 -10000 0 -0.29 9 9
IL1RN/IL1R2 0.031 0.072 0.2 47 -0.21 10 57
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.022 0.054 0.19 11 -0.14 28 39
TMEM189-UBE2V1 0.005 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.014 0.056 -10000 0 -0.4 1 1
PIK3CA 0.01 0 -10000 0 -10000 0 0
IL1RN 0.014 0.052 0.27 11 -0.29 4 15
TRAF6/TAK1/TAB1/TAB2 0.017 0.002 -10000 0 -10000 0 0
MAP2K6 0.012 0.008 0.16 1 -10000 0 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.011 0.013 0.27 1 -10000 0 1
NFATC1 0.003 0.057 -10000 0 -0.24 19 19
NFATC2 -0.033 0.052 -10000 0 -0.15 46 46
NFATC3 0.002 0.025 -10000 0 -0.28 3 3
YWHAE 0.009 0.015 -10000 0 -0.29 1 1
Calcineurin A alpha-beta B1/CABIN1 -0.041 0.1 -10000 0 -0.32 29 29
Exportin 1/Ran/NUP214 0.017 0.003 -10000 0 -10000 0 0
mol:DAG -0.002 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.043 0.091 -10000 0 -0.28 35 35
BCL2/BAX 0.007 0.04 -10000 0 -0.19 16 16
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.009 -10000 0 -10000 0 0
CaM/Ca2+ -0.003 0.009 -10000 0 -10000 0 0
BAX 0.01 0 -10000 0 -10000 0 0
MAPK14 0.007 0.003 -10000 0 -10000 0 0
BAD 0.01 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.038 0.097 -10000 0 -0.3 29 29
Calcineurin A alpha-beta B1/BCL2 -0.002 0.058 -10000 0 -0.29 16 16
FKBP8 0.01 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.037 0.095 0.3 29 -10000 0 29
KPNB1 0.01 0 -10000 0 -10000 0 0
KPNA2 0.012 0.026 0.27 4 -10000 0 4
XPO1 0.009 0.001 -10000 0 -10000 0 0
SFN 0.027 0.076 0.27 32 -0.29 4 36
MAP3K8 0.005 0.026 -10000 0 -0.29 3 3
NFAT4/CK1 alpha 0.002 0.017 -10000 0 -0.13 3 3
MEF2D/NFAT1/Cbp/p300 -0.1 0.12 -10000 0 -0.2 230 230
CABIN1 -0.041 0.1 -10000 0 -0.32 29 29
CALM1 0.007 0.003 -10000 0 -10000 0 0
RAN 0.009 0.001 -10000 0 -10000 0 0
MAP3K1 0.01 0 -10000 0 -10000 0 0
CAMK4 0.003 0.048 0.27 1 -0.29 10 11
mol:Ca2+ -0.006 0.006 -10000 0 -10000 0 0
MAPK3 0.01 0 -10000 0 -10000 0 0
YWHAH 0.01 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.014 0.017 0.19 4 -10000 0 4
YWHAB 0.01 0 -10000 0 -10000 0 0
MAPK8 0.004 0.025 -10000 0 -0.29 3 3
MAPK9 0.01 0 -10000 0 -10000 0 0
YWHAG 0.01 0 -10000 0 -10000 0 0
FKBP1A 0.01 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.01 0.059 -10000 0 -0.24 19 19
PRKCH 0.01 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.016 -10000 0 -10000 0 0
CASP3 0.007 0.003 -10000 0 -10000 0 0
PIM1 0.01 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.005 -10000 0 -10000 0 0
apoptosis 0.01 0.006 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.019 0.023 -10000 0 -10000 0 0
PRKCB -0.076 0.14 -10000 0 -0.29 118 118
PRKCE 0.01 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.009 0.023 -10000 0 -0.25 3 3
BAD/BCL-XL 0.015 0.009 0.19 1 -10000 0 1
PRKCD 0.01 0 -10000 0 -10000 0 0
NUP214 0.009 0.001 -10000 0 -10000 0 0
PRKCZ 0.004 0.026 -10000 0 -0.29 3 3
PRKCA 0.006 0.033 -10000 0 -0.29 5 5
PRKCG 0.014 0.048 0.27 14 -10000 0 14
PRKCQ -0.013 0.088 0.27 4 -0.29 35 39
FKBP38/BCL2 0.007 0.04 -10000 0 -0.19 16 16
EP300 -0.001 0.01 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.01 0 -10000 0 -10000 0 0
NFATc/JNK1 0.004 0.056 -10000 0 -0.23 19 19
CaM/Ca2+/FKBP38 0.002 0.01 -10000 0 -10000 0 0
FKBP12/FK506 0.007 0 -10000 0 -10000 0 0
CSNK1A1 -0.003 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.002 0.029 0.15 1 -0.16 10 11
NFATc/ERK1 0.009 0.055 -10000 0 -0.23 19 19
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.037 0.091 -10000 0 -0.27 35 35
NR4A1 -0.18 0.17 -10000 0 -0.32 230 230
GSK3B 0.006 0.003 -10000 0 -10000 0 0
positive T cell selection 0.002 0.025 -10000 0 -0.27 3 3
NFAT1/CK1 alpha -0.028 0.043 -10000 0 -0.12 46 46
RCH1/ KPNB1 0.017 0.017 0.19 4 -10000 0 4
YWHAQ 0.01 0 -10000 0 -10000 0 0
PRKACA 0.007 0.003 -10000 0 -10000 0 0
AKAP5 0.012 0.026 0.27 4 -10000 0 4
MEF2D -0.001 0.01 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.01 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.005 0.055 -10000 0 -0.23 19 19
CREBBP -0.001 0.01 -10000 0 -10000 0 0
BCL2 -0.002 0.058 -10000 0 -0.29 16 16
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.008 0.009 -10000 0 -10000 0 0
HSPA8 0.01 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.014 0.087 0.24 1 -0.19 68 69
AKT1 0.011 0.017 -10000 0 -10000 0 0
GSC 0.033 0.071 0.37 3 -10000 0 3
NKX2-5 0.044 0.098 0.27 65 -10000 0 65
muscle cell differentiation -0.001 0.052 0.25 11 -10000 0 11
SMAD2-3/SMAD4/SP1 0.025 0.076 -10000 0 -0.24 15 15
SMAD4 0.001 0.037 -10000 0 -0.13 15 15
CBFB 0.01 0 -10000 0 -10000 0 0
SAP18 0.01 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.021 0.026 0.18 8 -10000 0 8
SMAD3/SMAD4/VDR 0.02 0.038 -10000 0 -0.2 2 2
MYC -0.007 0.065 -10000 0 -0.29 18 18
CDKN2B 0 0.22 -10000 0 -1.2 11 11
AP1 -0.034 0.11 -10000 0 -0.33 26 26
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.027 0.017 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.024 0.07 0.2 3 -0.31 11 14
SP3 0.011 0 -10000 0 -10000 0 0
CREB1 0.01 0 -10000 0 -10000 0 0
FOXH1 0.07 0.11 0.27 92 -10000 0 92
SMAD3/SMAD4/GR 0.003 0.056 -10000 0 -0.2 15 15
GATA3 -0.011 0.079 0.27 2 -0.29 26 28
SKI/SIN3/HDAC complex/NCoR1 0.022 0.005 -10000 0 -10000 0 0
MEF2C/TIF2 0.034 0.079 0.26 1 -0.3 13 14
endothelial cell migration 0 0.14 1.2 5 -0.33 5 10
MAX 0.008 0.01 -10000 0 -10000 0 0
RBBP7 0.01 0.001 -10000 0 -10000 0 0
RBBP4 0.01 0.001 -10000 0 -10000 0 0
RUNX2 0.012 0.032 0.27 5 -0.29 1 6
RUNX3 0 0.054 -10000 0 -0.29 14 14
RUNX1 0.01 0 -10000 0 -10000 0 0
CTBP1 0.011 0.013 0.27 1 -10000 0 1
NR3C1 0 0.051 -10000 0 -0.29 12 12
VDR 0.009 0.024 0.27 1 -0.29 2 3
CDKN1A -0.002 0.094 -10000 0 -1.1 2 2
KAT2B 0.008 0.015 -10000 0 -0.29 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.062 0.08 0.2 74 -0.17 2 76
DCP1A 0.01 0 -10000 0 -10000 0 0
SKI 0.01 0.001 -10000 0 -10000 0 0
SERPINE1 0 0.14 0.33 5 -1.2 5 10
SMAD3/SMAD4/ATF2 0.011 0.043 -10000 0 -0.15 5 5
SMAD3/SMAD4/ATF3 -0.02 0.089 -10000 0 -0.19 77 77
SAP30 0.01 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.018 0.018 0.15 1 -10000 0 1
JUN -0.039 0.1 -10000 0 -0.33 26 26
SMAD3/SMAD4/IRF7 0.019 0.061 0.22 11 -0.18 6 17
TFE3 0.012 0.012 -10000 0 -0.16 1 1
COL1A2 -0.027 0.19 0.32 2 -0.72 27 29
mesenchymal cell differentiation -0.013 0.046 0.14 8 -0.2 2 10
DLX1 0.035 0.079 0.27 42 -10000 0 42
TCF3 0.01 0 -10000 0 -10000 0 0
FOS -0.008 0.073 -10000 0 -0.34 19 19
SMAD3/SMAD4/Max 0.008 0.043 -10000 0 -0.15 5 5
Cbp/p300/SNIP1 0.019 0.008 -10000 0 -10000 0 0
ZBTB17 0.007 0.017 -10000 0 -10000 0 0
LAMC1 0.009 0.038 -10000 0 -0.24 2 2
TGIF2/HDAC complex/SMAD3/SMAD4 0.011 0.043 -10000 0 -0.15 5 5
IRF7 0.018 0.052 0.27 13 -0.29 2 15
ESR1 -0.035 0.11 -10000 0 -0.29 62 62
HNF4A 0.034 0.079 0.27 41 -10000 0 41
MEF2C 0.037 0.079 0.24 2 -0.3 14 16
SMAD2-3/SMAD4 0.016 0.054 -10000 0 -0.17 10 10
Cbp/p300/Src-1 0.018 0.012 -10000 0 -10000 0 0
IGHV3OR16-13 0.004 0.012 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.01 0 -10000 0 -10000 0 0
CREBBP 0.008 0.007 -10000 0 -10000 0 0
SKIL 0.011 0.013 0.27 1 -10000 0 1
HDAC1 0.01 0.001 -10000 0 -10000 0 0
HDAC2 0.01 0.001 -10000 0 -10000 0 0
SNIP1 0.01 0.002 -10000 0 -10000 0 0
GCN5L2 -0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.018 0.048 -10000 0 -0.16 6 6
MSG1/HSC70 0.019 0.025 0.19 8 -10000 0 8
SMAD2 0.013 0.021 -10000 0 -10000 0 0
SMAD3 0 0.034 -10000 0 -0.12 10 10
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.028 -10000 0 -0.17 1 1
SMAD2/SMAD2/SMAD4 0 0.021 -10000 0 -0.25 1 1
NCOR1 0.01 0.001 -10000 0 -10000 0 0
NCOA2 -0.008 0.07 -10000 0 -0.29 24 24
NCOA1 0.01 0 -10000 0 -10000 0 0
MYOD/E2A 0.007 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.032 0.076 -10000 0 -0.23 14 14
IFNB1 0.011 0.059 0.31 9 -0.18 3 12
SMAD3/SMAD4/MEF2C 0.042 0.088 0.3 2 -0.32 14 16
CITED1 0.015 0.036 0.27 8 -10000 0 8
SMAD2-3/SMAD4/ARC105 0.021 0.051 -10000 0 -0.19 4 4
RBL1 0.011 0.018 0.27 2 -10000 0 2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.016 0.098 0.23 1 -0.5 11 12
RUNX1-3/PEBPB2 0.014 0.032 -10000 0 -0.16 14 14
SMAD7 -0.033 0.12 -10000 0 -0.37 23 23
MYC/MIZ-1 0.001 0.054 0.15 11 -0.2 18 29
SMAD3/SMAD4 -0.007 0.07 0.32 1 -0.39 6 7
IL10 -0.013 0.092 0.32 1 -0.35 21 22
PIASy/HDAC complex 0.011 0.006 -10000 0 -10000 0 0
PIAS3 0.009 0.003 -10000 0 -10000 0 0
CDK2 0.009 0.006 -10000 0 -10000 0 0
IL5 -0.008 0.065 0.31 2 -0.19 22 24
CDK4 0.009 0.015 0.27 1 -10000 0 1
PIAS4 0.011 0.006 -10000 0 -10000 0 0
ATF3 -0.043 0.11 -10000 0 -0.29 72 72
SMAD3/SMAD4/SP1 0.011 0.069 -10000 0 -0.22 20 20
FOXG1 0.038 0.091 0.27 55 -10000 0 55
FOXO3 0.012 0.021 -10000 0 -0.094 1 1
FOXO1 0.011 0.024 -10000 0 -0.2 1 1
FOXO4 0.012 0.023 0.16 1 -0.093 2 3
heart looping 0.037 0.078 0.24 2 -0.3 14 16
CEBPB 0.01 0.018 -10000 0 -0.29 1 1
SMAD3/SMAD4/DLX1 0.028 0.067 0.2 26 -0.14 8 34
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.026 0.066 0.2 26 -0.14 7 33
SMAD3/SMAD4/GATA3 -0.001 0.078 0.21 2 -0.2 42 44
SnoN/SIN3/HDAC complex/NCoR1 0.011 0.013 0.27 1 -10000 0 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.016 0.051 -10000 0 -0.17 15 15
SMAD3/SMAD4/SP1-3 0.022 0.063 -10000 0 -0.2 14 14
MED15 0.01 0 -10000 0 -10000 0 0
SP1 0.005 0.032 -10000 0 -10000 0 0
SIN3B 0.01 0.001 -10000 0 -10000 0 0
SIN3A 0.01 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.087 0.1 0.29 32 -0.19 11 43
ITGB5 0.007 0.049 -10000 0 -0.2 10 10
TGIF/SIN3/HDAC complex/CtBP 0.021 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.056 0.096 -10000 0 -0.18 144 144
AR -0.099 0.14 -10000 0 -0.29 148 148
negative regulation of cell growth -0.007 0.066 -10000 0 -0.23 8 8
SMAD3/SMAD4/MYOD 0.006 0.041 -10000 0 -0.15 6 6
E2F5 0.01 0.023 0.27 2 -0.29 1 3
E2F4 0.01 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.066 0.07 0.25 8 -10000 0 8
SMAD2-3/SMAD4/FOXO1-3a-4 0.017 0.073 0.2 1 -0.34 12 13
TFDP1 0.01 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.027 0.11 -10000 0 -0.34 26 26
SMAD3/SMAD4/RUNX2 0.013 0.047 0.2 2 -0.14 8 10
TGIF2 0.01 0 -10000 0 -10000 0 0
TGIF1 0.01 0 -10000 0 -10000 0 0
ATF2 0.01 0 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.02 0.023 -10000 0 -10000 0 0
epithelial cell differentiation -0.003 0.059 -10000 0 -0.24 2 2
ITCH 0.01 0.014 0.27 1 -10000 0 1
WWP1 0.02 0.015 -10000 0 -10000 0 0
FYN 0.008 0.025 -10000 0 -0.29 3 3
EGFR 0.008 0.057 0.27 8 -0.29 9 17
PRL 0.008 0.035 0.27 7 -10000 0 7
neuron projection morphogenesis 0.004 0.05 -10000 0 -0.19 2 2
PTPRZ1 -0.032 0.16 0.27 42 -0.29 91 133
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.011 0.06 -10000 0 -0.21 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.019 0.029 -10000 0 -0.22 1 1
ADAM17 0.01 0.014 0.27 1 -10000 0 1
ErbB4/ErbB4 0.019 0.028 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.023 0.041 0.25 1 -10000 0 1
NCOR1 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn 0.001 0.061 -10000 0 -0.23 2 2
GRIN2B 0.001 0.057 -10000 0 -0.22 2 2
ErbB4/ErbB2/betacellulin 0.008 0.053 -10000 0 -0.2 2 2
STAT1 0.012 0.026 0.27 4 -10000 0 4
HBEGF 0 0.052 -10000 0 -0.29 13 13
PRLR 0.014 0.093 0.27 28 -0.29 19 47
E4ICDs/ETO2 0.02 0.023 -10000 0 -10000 0 0
axon guidance 0.009 0.074 -10000 0 -0.26 1 1
NEDD4 0.008 0.016 -10000 0 -0.29 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.016 0.068 0.19 35 -0.19 19 54
CBFA2T3 0 0.052 -10000 0 -0.29 13 13
ErbB4/ErbB2/HBEGF 0.022 0.032 -10000 0 -10000 0 0
MAPK3 0.004 0.052 -10000 0 -0.2 2 2
STAT1 (dimer) 0.022 0.029 -10000 0 -10000 0 0
MAPK1 0.004 0.052 -10000 0 -0.2 2 2
JAK2 0.009 0.015 -10000 0 -0.29 1 1
ErbB4/ErbB2/neuregulin 1 beta 0.001 0.06 -10000 0 -0.2 1 1
NRG1 -0.021 0.089 0.17 19 -0.2 73 92
NRG3 0.014 0.048 0.27 14 -10000 0 14
NRG2 -0.12 0.15 -10000 0 -0.29 172 172
NRG4 -0.019 0.088 -10000 0 -0.29 39 39
heart development 0.009 0.074 -10000 0 -0.26 1 1
neural crest cell migration 0.001 0.059 -10000 0 -0.2 1 1
ERBB2 0.014 0.029 0.16 14 -10000 0 14
WWOX/E4ICDs 0.021 0.023 -10000 0 -10000 0 0
SHC1 0.011 0.013 0.27 1 -10000 0 1
ErbB4/EGFR/neuregulin 4 0.011 0.06 -10000 0 -0.25 4 4
apoptosis -0.026 0.036 -10000 0 -0.22 1 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.01 0.033 -10000 0 -0.25 4 4
ErbB4/ErbB2/epiregulin 0.029 0.079 0.2 1 -0.2 2 3
ErbB4/ErbB4/betacellulin/betacellulin 0.017 0.029 -10000 0 -0.25 2 2
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.031 0.06 -10000 0 -0.21 1 1
MDM2 0.02 0.029 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.003 0.061 0.18 1 -0.18 1 2
STAT5A 0.009 0.069 -10000 0 -0.25 1 1
ErbB4/EGFR/neuregulin 1 beta 0.002 0.069 -10000 0 -0.24 4 4
DLG4 0.009 0.015 -10000 0 -0.29 1 1
GRB2/SHC 0.015 0.009 0.19 1 -10000 0 1
E4ICDs/TAB2/NCoR1 0.019 0.02 -10000 0 -10000 0 0
STAT5A (dimer) 0.004 0.067 -10000 0 -0.26 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.013 0.069 -10000 0 -0.25 1 1
LRIG1 -0.018 0.087 -10000 0 -0.29 38 38
EREG 0.002 0.15 0.27 54 -0.29 57 111
BTC -0.027 0.098 -10000 0 -0.29 50 50
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.008 0.074 -10000 0 -0.27 1 1
ERBB4 0.022 0.019 -10000 0 -10000 0 0
STAT5B 0.01 0 -10000 0 -10000 0 0
YAP1 0.012 0.033 0.22 1 -0.6 1 2
GRB2 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.013 0.044 -10000 0 -0.2 1 1
glial cell differentiation -0.018 0.02 -10000 0 -10000 0 0
WWOX 0.009 0.015 -10000 0 -0.29 1 1
cell proliferation -0.03 0.098 -10000 0 -0.29 19 19
Signaling events mediated by PTP1B

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
PDGFRB 0.003 0.046 -10000 0 -0.29 10 10
Jak2/Leptin Receptor 0.028 0.074 0.24 6 -0.25 6 12
PTP1B/AKT1 0.022 0.035 -10000 0 -0.18 1 1
FYN 0.008 0.025 -10000 0 -0.29 3 3
p210 bcr-abl/PTP1B 0.019 0.038 -10000 0 -0.2 1 1
EGFR 0.01 0.058 0.27 8 -0.29 9 17
EGF/EGFR 0.027 0.057 0.19 28 -0.18 2 30
CSF1 -0.001 0.056 -10000 0 -0.29 15 15
AKT1 0.01 0 -10000 0 -10000 0 0
INSR 0.01 0 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.039 0.066 0.21 38 -0.18 2 40
Insulin Receptor/Insulin 0.015 0.025 -10000 0 -10000 0 0
HCK 0.004 0.058 0.27 5 -0.29 12 17
CRK 0.01 0 -10000 0 -10000 0 0
TYK2 0.02 0.036 -10000 0 -0.19 1 1
EGF 0.025 0.062 0.27 25 -10000 0 25
YES1 0.01 0 -10000 0 -10000 0 0
CAV1 0.019 0.047 -10000 0 -0.18 4 4
TXN 0.012 0.018 0.27 2 -10000 0 2
PTP1B/IRS1/GRB2 0.025 0.042 -10000 0 -0.2 4 4
cell migration -0.019 0.038 0.2 1 -10000 0 1
STAT3 0.01 0.001 -10000 0 -10000 0 0
PRLR 0.015 0.094 0.27 28 -0.29 19 47
ITGA2B 0.029 0.069 0.27 31 -10000 0 31
CSF1R -0.003 0.067 0.27 2 -0.29 20 22
Prolactin Receptor/Prolactin 0.02 0.071 0.2 35 -0.19 19 54
FGR 0.008 0.021 -10000 0 -0.29 2 2
PTP1B/p130 Cas 0.023 0.036 -10000 0 -0.19 1 1
Crk/p130 Cas 0.028 0.036 -10000 0 -0.19 1 1
DOK1 0.019 0.044 -10000 0 -0.19 7 7
JAK2 0.019 0.067 0.21 4 -0.21 19 23
Jak2/Leptin Receptor/Leptin -0.011 0.08 0.18 4 -0.2 33 37
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
PTPN1 0.019 0.038 -10000 0 -0.21 1 1
LYN 0.01 0 -10000 0 -10000 0 0
CDH2 0.033 0.084 0.27 41 -0.29 4 45
SRC 0.019 0.017 -10000 0 -10000 0 0
ITGB3 -0.023 0.095 -10000 0 -0.29 46 46
CAT1/PTP1B 0.007 0.076 -10000 0 -0.26 8 8
CAPN1 0.011 0.002 -10000 0 -10000 0 0
CSK 0.01 0 -10000 0 -10000 0 0
PI3K 0.013 0.023 -10000 0 -10000 0 0
mol:H2O2 0.001 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.014 0.085 0.17 3 -0.22 35 38
negative regulation of transcription 0.022 0.067 0.21 4 -0.21 19 23
FCGR2A 0.017 0.046 0.27 12 -0.29 1 13
FER 0.008 0.026 -10000 0 -0.29 3 3
alphaIIb/beta3 Integrin 0.004 0.08 0.19 26 -0.19 41 67
BLK -0.009 0.1 0.27 16 -0.29 37 53
Insulin Receptor/Insulin/Shc 0.015 0.008 0.17 1 -10000 0 1
RHOA 0.011 0.002 -10000 0 -10000 0 0
LEPR 0.001 0.052 -10000 0 -0.28 13 13
BCAR1 0.01 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.01 0 -10000 0 -10000 0 0
mol:NADPH 0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.011 0.094 0.17 3 -0.23 29 32
PRL 0.01 0.035 0.27 7 -10000 0 7
SOCS3 -0.12 0.36 -10000 0 -1.2 43 43
SPRY2 0.004 0.042 -10000 0 -0.29 8 8
Insulin Receptor/Insulin/IRS1 0.01 0.027 -10000 0 -0.16 10 10
CSF1/CSF1R 0.017 0.058 0.23 1 -0.21 11 12
Ras protein signal transduction -0.004 0.013 -10000 0 -10000 0 0
IRS1 0.003 0.046 -10000 0 -0.29 10 10
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.009 0.1 0.27 16 -0.29 36 52
STAT5B 0.024 0.044 0.16 3 -0.17 3 6
STAT5A 0.024 0.044 0.16 2 -0.17 3 5
GRB2 0.01 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.021 0.042 -10000 0 -0.17 7 7
CSN2 -0.002 0.031 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
LAT 0.022 0.035 -10000 0 -0.36 1 1
YBX1 0.016 0.013 0.27 1 -10000 0 1
LCK 0.008 0.035 0.27 2 -0.29 4 6
SHC1 0.011 0.013 0.27 1 -10000 0 1
NOX4 0.03 0.067 0.27 30 -10000 0 30
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.053 0.057 0.17 80 -0.13 1 81
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.011 0.018 0.27 2 -10000 0 2
STAT1 (dimer)/Cbp/p300 0.044 0.03 0.22 4 -10000 0 4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.025 0.013 -10000 0 -0.16 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.007 0.04 -10000 0 -0.19 9 9
CaM/Ca2+ 0.048 0.047 -10000 0 -0.12 1 1
RAP1A 0.01 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.034 0.034 0.22 4 -0.12 1 5
AKT1 0.027 0.024 -10000 0 -0.11 1 1
MAP2K1 0.026 0.026 -10000 0 -0.11 1 1
MAP3K11 0.027 0.027 -10000 0 -0.12 1 1
IFNGR1 0.012 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.056 0.14 -10000 0 -0.27 127 127
Rap1/GTP 0 0.005 -10000 0 -10000 0 0
CRKL/C3G 0.016 0.012 0.19 2 -10000 0 2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.057 0.057 0.17 80 -0.13 1 81
CEBPB 0.037 0.052 0.26 2 -0.39 4 6
STAT3 0.01 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.056 0.057 0.35 1 -10000 0 1
STAT1 0.029 0.033 0.23 4 -0.12 1 5
CALM1 0.01 0 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.059 0.1 0.26 81 -10000 0 81
PIK3CA 0.01 0 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.033 0.031 0.22 4 -10000 0 4
CEBPB/PTGES2/Cbp/p300 0.019 0.032 -10000 0 -0.26 4 4
mol:Ca2+ 0.05 0.054 0.16 80 -0.12 1 81
MAPK3 0.032 0.031 -10000 0 -10000 0 0
STAT1 (dimer) -0.004 0.056 -10000 0 -0.25 9 9
MAPK1 0.032 0.031 -10000 0 -10000 0 0
JAK2 0.012 0.003 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
JAK1 0.012 0.003 -10000 0 -10000 0 0
CAMK2D 0.008 0.021 -10000 0 -0.29 2 2
DAPK1 0.032 0.065 0.32 2 -0.55 4 6
SMAD7 0.009 0.033 -10000 0 -0.14 4 4
CBL/CRKL/C3G 0.036 0.027 0.2 2 -10000 0 2
PI3K 0.043 0.04 -10000 0 -0.12 1 1
IFNG 0.059 0.1 0.26 81 -10000 0 81
apoptosis 0.025 0.052 0.27 2 -0.42 4 6
CAMK2G 0.01 0 -10000 0 -10000 0 0
STAT3 (dimer) 0.01 0 -10000 0 -10000 0 0
CAMK2A -0.085 0.14 -10000 0 -0.29 129 129
CAMK2B 0.037 0.08 0.27 43 -10000 0 43
FRAP1 0.023 0.023 -10000 0 -0.1 1 1
PRKCD 0.027 0.024 -10000 0 -0.11 1 1
RAP1B 0.01 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.007 0.04 -10000 0 -0.19 9 9
PTPN2 0.01 0 -10000 0 -10000 0 0
EP300 0.01 0 -10000 0 -10000 0 0
IRF1 0.031 0.024 0.2 1 -10000 0 1
STAT1 (dimer)/PIASy 0.032 0.031 0.22 4 -10000 0 4
SOCS1 0.008 0.016 0.32 1 -10000 0 1
mol:GDP 0.033 0.025 0.18 2 -10000 0 2
CASP1 0.007 0.041 -10000 0 -0.19 10 10
PTGES2 0.01 0 -10000 0 -10000 0 0
IRF9 0.025 0.019 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.032 0.031 -10000 0 -0.11 1 1
RAP1/GDP 0.016 0.012 0.14 1 -10000 0 1
CBL 0.027 0.027 -10000 0 -0.12 1 1
MAP3K1 0.028 0.028 -10000 0 -0.12 1 1
PIAS1 0.01 0 -10000 0 -10000 0 0
PIAS4 0.01 0.001 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.007 0.04 -10000 0 -0.19 9 9
PTPN11 0.025 0.027 -10000 0 -0.12 1 1
CREBBP 0.01 0 -10000 0 -10000 0 0
RAPGEF1 0.01 0 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex 0.17 0.18 0.38 117 -0.39 3 120
RAD9A 0.014 0.031 0.27 6 -10000 0 6
AP1 -0.044 0.11 -10000 0 -0.2 130 130
IFNAR2 0.024 0.015 -10000 0 -10000 0 0
AKT1 0.01 0.059 0.12 3 -0.13 35 38
ER alpha/Oestrogen -0.021 0.078 -10000 0 -0.19 73 73
NFX1/SIN3/HDAC complex 0.042 0.025 -10000 0 -10000 0 0
EGF 0.03 0.063 0.28 25 -10000 0 25
SMG5 0.01 0 -10000 0 -10000 0 0
SMG6 0.01 0 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.026 -10000 0 -10000 0 0
TERT/c-Abl 0.015 0.052 -10000 0 -0.36 3 3
SAP18 0.012 0.003 -10000 0 -10000 0 0
MRN complex 0.02 0 -10000 0 -10000 0 0
WT1 0.054 0.089 0.28 52 -10000 0 52
WRN 0.01 0 -10000 0 -10000 0 0
SP1 0.029 0.022 -10000 0 -10000 0 0
SP3 0.016 0.008 -10000 0 -10000 0 0
TERF2IP 0.01 0 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.004 0.04 -10000 0 -0.34 3 3
Mad/Max 0.032 0.021 0.22 1 -10000 0 1
TERT 0.17 0.18 0.41 71 -0.39 3 74
CCND1 0.16 0.21 0.48 15 -0.91 7 22
MAX 0.017 0.008 -10000 0 -10000 0 0
RBBP7 0.013 0.003 -10000 0 -10000 0 0
RBBP4 0.012 0.003 -10000 0 -10000 0 0
TERF2 0.009 0 -10000 0 -10000 0 0
PTGES3 0.01 0 -10000 0 -10000 0 0
SIN3A 0.012 0.003 -10000 0 -10000 0 0
Telomerase/911 0.065 0.048 0.21 6 -10000 0 6
CDKN1B 0.045 0.044 -10000 0 -10000 0 0
RAD1 0.01 0 -10000 0 -10000 0 0
XRCC5 0.01 0 -10000 0 -10000 0 0
XRCC6 0.01 0 -10000 0 -10000 0 0
SAP30 0.013 0.003 -10000 0 -10000 0 0
TRF2/PARP2 0.014 0 -10000 0 -10000 0 0
UBE3A 0.016 0.007 -10000 0 -10000 0 0
JUN 0.003 0.058 -10000 0 -0.28 16 16
E6 0.006 0.006 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.022 0.016 -10000 0 -10000 0 0
FOS -0.04 0.12 -10000 0 -0.29 72 72
IFN-gamma/IRF1 0.07 0.076 0.22 81 -10000 0 81
PARP2 0.01 0 -10000 0 -10000 0 0
BLM 0.018 0.044 0.27 12 -10000 0 12
Telomerase 0.043 0.058 0.2 15 -0.3 1 16
IRF1 0.019 0.008 -10000 0 -10000 0 0
ESR1 -0.039 0.11 -10000 0 -0.28 72 72
KU/TER 0.015 0 -10000 0 -10000 0 0
ATM/TRF2 0.015 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.044 0.024 -10000 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.044 0.024 -10000 0 -10000 0 0
HDAC1 0.012 0.003 -10000 0 -10000 0 0
HDAC2 0.026 0.019 -10000 0 -10000 0 0
ATM 0.003 0 -10000 0 -10000 0 0
SMAD3 0 0.011 -10000 0 -10000 0 0
ABL1 0.01 0 -10000 0 -10000 0 0
MXD1 0.017 0.015 0.28 1 -10000 0 1
MRE11A 0.01 0 -10000 0 -10000 0 0
HUS1 0.01 0 -10000 0 -10000 0 0
RPS6KB1 0.01 0 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.02 0.068 -10000 0 -0.37 3 3
NR2F2 -0.006 0.022 -10000 0 -0.29 1 1
MAPK3 0.018 0.014 -10000 0 -10000 0 0
MAPK1 0.018 0.014 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.003 0.008 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
HNRNPC 0.01 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.003 0 -10000 0 -10000 0 0
NBN 0.01 0 -10000 0 -10000 0 0
EGFR 0.018 0.042 0.27 8 -0.29 2 10
mol:Oestrogen 0.003 0.004 -10000 0 -10000 0 0
EGF/EGFR 0.036 0.06 0.2 33 -0.18 9 42
MYC 0.005 0.061 -10000 0 -0.28 17 17
IL2 0.022 0.022 -10000 0 -10000 0 0
KU 0.015 0 -10000 0 -10000 0 0
RAD50 0.01 0 -10000 0 -10000 0 0
HSP90AA1 0.01 0 -10000 0 -10000 0 0
TGFB1 0.003 0.008 -10000 0 -10000 0 0
TRF2/BLM 0.019 0.029 0.18 12 -10000 0 12
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.14 0.14 0.34 48 -0.36 3 51
SP1/HDAC2 0.052 0.041 0.17 5 -10000 0 5
PINX1 0.01 0 -10000 0 -10000 0 0
Telomerase/EST1A 0.004 0.04 -10000 0 -0.34 3 3
Smad3/Myc -0.003 0.035 -10000 0 -0.16 18 18
911 complex 0.023 0.019 0.18 6 -10000 0 6
IFNG 0.068 0.1 0.28 81 -10000 0 81
Telomerase/PinX1 0.004 0.04 -10000 0 -0.34 3 3
Telomerase/AKT1/mTOR/p70S6K 0.079 0.077 0.2 36 -10000 0 36
SIN3B 0.013 0.003 -10000 0 -10000 0 0
YWHAE 0.009 0.015 -10000 0 -0.29 1 1
Telomerase/EST1B 0.004 0.04 -10000 0 -0.34 3 3
response to DNA damage stimulus 0.002 0 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.028 0 -10000 0 -10000 0 0
TRF2/WRN 0.014 0 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.004 0.04 -10000 0 -0.34 3 3
E2F1 0.085 0.11 0.28 97 -10000 0 97
ZNFX1 0.012 0.003 -10000 0 -10000 0 0
PIF1 0.031 0.073 0.27 34 -0.29 1 35
NCL 0.01 0 -10000 0 -10000 0 0
DKC1 0.01 0 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.022 0.089 0.17 50 -0.4 10 60
PDGFB-D/PDGFRB/SLAP 0.004 0.056 0.2 1 -0.24 18 19
PDGFB-D/PDGFRB/APS/CBL 0.018 0.033 0.18 5 -0.16 10 15
AKT1 0.016 0.024 -10000 0 -0.11 3 3
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.025 0.095 0.18 50 -0.43 10 60
PIK3CA 0.01 0 -10000 0 -10000 0 0
FGR -0.001 0.049 -10000 0 -0.26 12 12
mol:Ca2+ 0.003 0.079 -10000 0 -0.46 10 10
MYC -0.013 0.16 -10000 0 -0.59 27 27
SHC1 0.011 0.013 0.27 1 -10000 0 1
HRAS/GDP 0.014 0.023 -10000 0 -0.13 10 10
LRP1/PDGFRB/PDGFB 0.015 0.033 0.18 1 -0.16 14 15
GRB10 0.006 0.033 -10000 0 -0.29 5 5
PTPN11 0.01 0 -10000 0 -10000 0 0
GO:0007205 0.003 0.08 -10000 0 -0.47 10 10
PTEN 0.01 0 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
GRB7 0.014 0.062 0.27 14 -0.29 7 21
PDGFB-D/PDGFRB/SHP2 0.01 0.032 -10000 0 -0.19 10 10
PDGFB-D/PDGFRB/GRB10 0.007 0.039 -10000 0 -0.19 15 15
cell cycle arrest 0.004 0.056 0.2 1 -0.24 18 19
HRAS 0.01 0 -10000 0 -10000 0 0
HIF1A 0.016 0.022 -10000 0 -0.1 3 3
GAB1 0.005 0.081 -10000 0 -0.43 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.007 0.075 -10000 0 -0.39 10 10
PDGFB-D/PDGFRB 0.016 0.03 -10000 0 -0.17 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.01 0.032 -10000 0 -0.19 10 10
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.023 0.088 0.17 56 -0.32 12 68
positive regulation of MAPKKK cascade 0.01 0.032 -10000 0 -0.19 10 10
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
mol:IP3 0.003 0.08 -10000 0 -0.47 10 10
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.01 0.001 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.012 0.054 0.19 14 -0.19 17 31
SHB 0.01 0 -10000 0 -10000 0 0
BLK -0.035 0.15 -10000 0 -0.43 43 43
PTPN2 0.01 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.01 0.032 -10000 0 -0.19 10 10
BCAR1 0.01 0 -10000 0 -10000 0 0
VAV2 0.001 0.095 -10000 0 -0.32 27 27
CBL 0.01 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.01 0.036 -10000 0 -0.21 10 10
LCK -0.003 0.069 -10000 0 -0.32 13 13
PDGFRB 0.003 0.047 -10000 0 -0.3 10 10
ACP1 0.01 0 -10000 0 -10000 0 0
HCK -0.011 0.12 -10000 0 -0.48 18 18
ABL1 0.003 0.071 -10000 0 -0.37 10 10
PDGFB-D/PDGFRB/CBL 0.002 0.092 -10000 0 -0.51 10 10
PTPN1 0.01 0.004 -10000 0 -10000 0 0
SNX15 0.01 0 -10000 0 -10000 0 0
STAT3 0.01 0 -10000 0 -10000 0 0
STAT1 0.012 0.026 0.27 4 -10000 0 4
cell proliferation -0.01 0.15 -10000 0 -0.53 27 27
SLA 0.001 0.054 0.27 1 -0.29 13 14
actin cytoskeleton reorganization 0.017 0.023 -10000 0 -0.12 7 7
SRC 0.002 0.037 -10000 0 -0.22 10 10
PI3K -0.003 0.018 -10000 0 -0.12 10 10
PDGFB-D/PDGFRB/GRB7/SHC 0.019 0.047 0.18 15 -0.16 17 32
SH2B2 0.013 0.028 0.27 5 -10000 0 5
PLCgamma1/SPHK1 0.025 0.097 0.18 50 -0.45 10 60
LYN 0.002 0.037 -10000 0 -0.22 10 10
LRP1 0.007 0.029 -10000 0 -0.29 4 4
SOS1 0.01 0 -10000 0 -10000 0 0
STAT5B 0.01 0 -10000 0 -10000 0 0
STAT5A 0.009 0.015 -10000 0 -0.29 1 1
NCK1-2/p130 Cas 0.026 0.025 -10000 0 -0.13 3 3
SPHK1 0.045 0.091 0.27 56 -0.3 1 57
EDG1 0 0.002 -10000 0 -10000 0 0
mol:DAG 0.003 0.08 -10000 0 -0.47 10 10
PLCG1 0.003 0.082 -10000 0 -0.49 10 10
NHERF/PDGFRB 0.024 0.046 0.18 21 -0.16 10 31
YES1 0.002 0.037 -10000 0 -0.22 10 10
cell migration 0.024 0.045 0.18 21 -0.16 10 31
SHC/Grb2/SOS1 0.026 0.026 -10000 0 -0.13 10 10
SLC9A3R2 0.01 0 -10000 0 -10000 0 0
SLC9A3R1 0.023 0.057 0.27 21 -10000 0 21
NHERF1-2/PDGFRB/PTEN 0.03 0.043 0.18 21 -0.14 10 31
FYN -0.001 0.054 -10000 0 -0.27 13 13
DOK1 0.009 0.026 0.17 1 -0.14 10 11
HRAS/GTP 0.007 0 -10000 0 -10000 0 0
PDGFB 0.011 0.013 0.27 1 -10000 0 1
RAC1 -0.003 0.12 -10000 0 -0.42 27 27
PRKCD 0.009 0.025 -10000 0 -0.15 10 10
FER 0.009 0.025 -10000 0 -0.15 10 10
MAPKKK cascade -0.003 0.019 -10000 0 -0.12 10 10
RASA1 0.009 0.025 -10000 0 -0.15 10 10
NCK1 0.01 0 -10000 0 -10000 0 0
NCK2 0.01 0 -10000 0 -10000 0 0
p62DOK/Csk 0.015 0.024 0.16 1 -0.13 10 11
PDGFB-D/PDGFRB/SHB 0.01 0.032 -10000 0 -0.19 10 10
chemotaxis 0.003 0.07 -10000 0 -0.36 10 10
STAT1-3-5/STAT1-3-5 0.021 0.026 -10000 0 -0.12 11 11
Bovine Papilomavirus E5/PDGFRB 0.003 0.032 -10000 0 -0.2 10 10
PTPRJ 0.009 0.015 -10000 0 -0.29 1 1
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.01 0 -10000 0 -10000 0 0
HDAC4 0.01 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.02 0.042 -10000 0 -0.16 32 32
CDKN1A 0.001 0.036 -10000 0 -0.52 2 2
KAT2B 0.009 0.015 -10000 0 -0.29 1 1
BAX 0.01 0 -10000 0 -10000 0 0
FOXO3 -0.003 0 -10000 0 -10000 0 0
FOXO1 0.009 0.015 -10000 0 -0.29 1 1
FOXO4 0.01 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.01 0 -10000 0 -10000 0 0
TAT 0.018 0.054 0.27 18 -10000 0 18
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.004 0.01 -10000 0 -0.19 1 1
PPARGC1A -0.11 0.15 0.27 1 -0.29 169 170
FHL2 0.008 0.025 -10000 0 -0.29 3 3
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.014 0.008 0.13 2 -10000 0 2
HIST2H4A 0.02 0.042 0.16 32 -10000 0 32
SIRT1/FOXO3a 0.004 0.008 -10000 0 -10000 0 0
SIRT1 0.009 0.011 0.17 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.019 0.007 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.02 0.023 0.13 2 -10000 0 2
apoptosis -0.019 0.007 -10000 0 -10000 0 0
SIRT1/PGC1A -0.059 0.085 0.17 1 -0.16 168 169
p53/SIRT1 0.011 0.022 0.33 2 -10000 0 2
SIRT1/FOXO4 0.014 0.009 0.13 2 -10000 0 2
FOXO1/FHL2/SIRT1 0.017 0.015 -10000 0 -0.14 3 3
HIST1H1E 0.02 0.032 -10000 0 -10000 0 0
SIRT1/p300 0.014 0.008 0.13 2 -10000 0 2
muscle cell differentiation -0.013 0.011 0.16 1 -10000 0 1
TP53 0.009 0.011 0.17 2 -10000 0 2
KU70/SIRT1/BAX 0.019 0.007 -10000 0 -10000 0 0
CREBBP 0.01 0 -10000 0 -10000 0 0
MEF2D 0.01 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.019 0.038 0.18 20 -10000 0 20
ACSS2 0.009 0.011 0.14 3 -10000 0 3
SIRT1/PCAF/MYOD 0.013 0.011 -10000 0 -0.16 1 1
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.014 0 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.007 0.035 0.27 1 -0.29 5 6
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.01 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.013 0.015 -10000 0 -0.15 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.01 0 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.01 0 -10000 0 -10000 0 0
FYN 0.008 0.025 -10000 0 -0.29 3 3
MAP3K12 0.009 0.015 -10000 0 -0.29 1 1
FGR 0.008 0.021 -10000 0 -0.29 2 2
p38 alpha/TAB1 -0.019 0.048 -10000 0 -0.22 13 13
PRKG1 -0.059 0.12 -10000 0 -0.29 94 94
DUSP8 -0.013 0.079 -10000 0 -0.29 31 31
PGK/cGMP/p38 alpha -0.025 0.08 -10000 0 -0.23 33 33
apoptosis -0.019 0.046 -10000 0 -0.21 13 13
RAL/GTP 0.014 0.008 0.17 1 -10000 0 1
LYN 0.01 0 -10000 0 -10000 0 0
DUSP1 -0.077 0.14 -10000 0 -0.29 119 119
PAK1 0.009 0.015 -10000 0 -0.29 1 1
SRC 0.01 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.026 0.007 0.18 1 -10000 0 1
TRAF6 0.01 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.011 0.013 0.27 1 -10000 0 1
RAC1-CDC42/GTP 0.014 0 -10000 0 -10000 0 0
MAPK11 0 0.072 -10000 0 -0.26 13 13
BLK -0.009 0.1 0.27 16 -0.29 37 53
HCK 0.004 0.058 0.27 5 -0.29 12 17
MAP2K3 0.01 0 -10000 0 -10000 0 0
DUSP16 0.01 0 -10000 0 -10000 0 0
DUSP10 0.013 0.028 0.27 5 -10000 0 5
TRAF6/MEKK3 0.013 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.003 0.062 -10000 0 -0.23 13 13
positive regulation of innate immune response 0.002 0.08 -10000 0 -0.29 13 13
LCK 0.008 0.035 0.27 2 -0.29 4 6
p38alpha-beta/MKP7 0.006 0.079 -10000 0 -0.28 13 13
p38alpha-beta/MKP5 0.008 0.08 -10000 0 -0.28 13 13
PGK/cGMP -0.039 0.085 -10000 0 -0.19 94 94
PAK2 0.01 0 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.012 0.1 -10000 0 -0.26 46 46
CDC42 0.01 0 -10000 0 -10000 0 0
RALB 0.01 0 -10000 0 -10000 0 0
RALA 0.011 0.013 0.27 1 -10000 0 1
PAK3 0.013 0.045 0.27 12 -10000 0 12
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.01 0 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.011 0.05 -10000 0 -0.18 22 22
NEF -0.004 0.033 -10000 0 -0.14 21 21
NFKBIA 0.007 0.019 -10000 0 -10000 0 0
BIRC3 -0.001 0.084 0.32 3 -0.33 22 25
CYCS 0.006 0.058 -10000 0 -0.2 25 25
RIPK1 0.01 0 -10000 0 -10000 0 0
CD247 0.001 0.053 0.27 1 -0.17 28 29
MAP2K7 0.015 0.055 -10000 0 -0.39 2 2
protein ubiquitination 0.024 0.034 -10000 0 -0.24 1 1
CRADD 0.01 0 -10000 0 -10000 0 0
DAXX 0.01 0 -10000 0 -10000 0 0
FAS 0.006 0.036 -10000 0 -0.29 6 6
BID 0.005 0.061 -10000 0 -0.21 25 25
NF-kappa-B/RelA/I kappa B alpha 0.015 0.051 0.21 3 -0.19 22 25
TRADD 0.01 0 -10000 0 -10000 0 0
MAP3K5 0.009 0.015 -10000 0 -0.29 1 1
CFLAR 0.01 0 -10000 0 -10000 0 0
FADD 0.014 0.031 0.27 6 -10000 0 6
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.016 0.052 0.21 3 -0.19 22 25
MAPK8 0.015 0.053 -10000 0 -0.37 2 2
APAF1 0.01 0 -10000 0 -10000 0 0
TRAF1 0.009 0.024 0.27 1 -0.29 2 3
TRAF2 0.01 0 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.005 0.063 0.15 7 -0.22 25 32
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.024 0.04 -10000 0 -0.31 1 1
CHUK 0.024 0.035 -10000 0 -0.26 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.029 0.028 0.17 6 -0.15 6 12
TCRz/NEF 0 0.063 0.18 8 -0.21 28 36
TNF 0.023 0.057 0.27 21 -10000 0 21
FASLG -0.007 0.1 0.31 7 -0.4 21 28
NFKB1 0.007 0.019 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.028 0.035 0.18 21 -10000 0 21
CASP6 0.019 0.043 -10000 0 -0.38 1 1
CASP7 0.003 0.11 0.24 3 -0.4 24 27
RELA 0.007 0.019 -10000 0 -10000 0 0
CASP2 0.01 0 -10000 0 -10000 0 0
CASP3 0.003 0.11 0.24 3 -0.4 24 27
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.015 0 -10000 0 -10000 0 0
CASP8 0.01 0 -10000 0 -10000 0 0
CASP9 0.01 0 -10000 0 -10000 0 0
MAP3K14 0.024 0.038 -10000 0 -0.29 1 1
APAF-1/Caspase 9 0.002 0.073 0.19 3 -0.25 24 27
BCL2 0.012 0.055 -10000 0 -0.31 3 3
LPA4-mediated signaling events

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
ADCY4 0.006 0 -10000 0 -10000 0 0
ADCY5 0.003 0.003 -10000 0 -10000 0 0
ADCY6 0.006 0 -10000 0 -10000 0 0
ADCY7 0.006 0 -10000 0 -10000 0 0
ADCY1 0.008 0.017 0.11 10 -10000 0 10
ADCY2 0.003 0.003 -10000 0 -10000 0 0
ADCY3 0.006 0 -10000 0 -10000 0 0
ADCY8 0.005 0.011 0.11 4 -10000 0 4
PRKCE 0.005 0 -10000 0 -10000 0 0
ADCY9 0.006 0.001 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.041 0.047 -10000 0 -0.11 99 99
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.01 0 -10000 0 -10000 0 0
ITGB7 0.006 0.033 -10000 0 -0.29 5 5
ITGA4 0.002 0.052 0.27 1 -0.29 12 13
alpha4/beta7 Integrin 0.007 0.042 0.19 1 -0.19 17 18
alpha4/beta1 Integrin 0.009 0.036 0.19 1 -0.19 12 13
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.01 0.011 0.16 2 -10000 0 2
MAP4K4 0.014 0.039 0.15 1 -10000 0 1
BAG4 0.01 0 -10000 0 -10000 0 0
PKC zeta/ceramide 0.006 0.007 -10000 0 -10000 0 0
NFKBIA 0.01 0 -10000 0 -10000 0 0
BIRC3 -0.004 0.071 0.27 3 -0.29 22 25
BAX 0.005 0.004 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
AKT1 0.003 0.001 -10000 0 -10000 0 0
BAD 0.001 0.008 -10000 0 -10000 0 0
SMPD1 0.012 0.018 -10000 0 -10000 0 0
RB1 0.001 0.01 -10000 0 -0.13 1 1
FADD/Caspase 8 0.02 0.04 -10000 0 -10000 0 0
MAP2K4 0.002 0.007 -10000 0 -10000 0 0
NSMAF 0.01 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.003 0.008 0.094 1 -10000 0 1
EGF 0.025 0.062 0.27 25 -10000 0 25
mol:ceramide -0.001 0.008 -10000 0 -0.065 2 2
MADD 0.01 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.008 0.16 1 -10000 0 1
ASAH1 0.01 0 -10000 0 -10000 0 0
negative regulation of cell cycle 0.001 0.01 -10000 0 -0.13 1 1
cell proliferation -0.037 0.059 -10000 0 -0.1 174 174
BID 0.018 0.031 -10000 0 -10000 0 0
MAP3K1 0.001 0.008 -10000 0 -10000 0 0
EIF2A 0.004 0.007 -10000 0 -10000 0 0
TRADD 0.01 0 -10000 0 -10000 0 0
CRADD 0.01 0 -10000 0 -10000 0 0
MAPK3 0.006 0.008 0.092 1 -10000 0 1
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.008 0.092 1 -10000 0 1
Cathepsin D/ceramide 0.006 0.008 -10000 0 -10000 0 0
FADD 0.016 0.041 0.16 3 -10000 0 3
KSR1 0.001 0.008 -10000 0 -10000 0 0
MAPK8 0.004 0.024 -10000 0 -0.19 6 6
PRKRA 0.001 0.008 -10000 0 -10000 0 0
PDGFA 0.011 0.013 0.27 1 -10000 0 1
TRAF2 0.01 0 -10000 0 -10000 0 0
IGF1 -0.12 0.15 -10000 0 -0.29 182 182
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.001 0.008 -10000 0 -0.064 2 2
CTSD 0.01 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.015 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.038 0.063 -10000 0 -0.11 174 174
PRKCD 0.01 0 -10000 0 -10000 0 0
PRKCZ 0.008 0.025 -10000 0 -0.29 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.008 0.16 1 -10000 0 1
RelA/NF kappa B1 0.015 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.009 0.015 -10000 0 -0.29 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.042 0.16 1 -10000 0 1
TNFR1A/BAG4/TNF-alpha 0.028 0.035 0.18 21 -10000 0 21
mol:Sphingosine-1-phosphate 0.01 0.011 0.16 2 -10000 0 2
MAP2K1 0.004 0.008 0.092 1 -10000 0 1
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
CYCS 0.008 0.024 0.13 15 -10000 0 15
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.015 0 -10000 0 -10000 0 0
EIF2AK2 0.002 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN 0.028 0.035 0.18 21 -10000 0 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.019 0.026 -10000 0 -10000 0 0
MAP2K2 0.004 0.008 0.092 1 -10000 0 1
SMPD3 0.015 0.024 -10000 0 -10000 0 0
TNF 0.023 0.057 0.27 21 -10000 0 21
PKC zeta/PAR4 0.013 0.02 -10000 0 -0.19 4 4
mol:PHOSPHOCHOLINE -0.008 0.025 -10000 0 -0.1 24 24
NF kappa B1/RelA/I kappa B alpha 0.028 0.015 -10000 0 -0.13 4 4
AIFM1 0.008 0.024 0.13 15 -10000 0 15
BCL2 -0.002 0.058 -10000 0 -0.29 16 16
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.005 0.045 0.14 1 -0.2 17 18
CRKL 0.011 0.018 0.27 2 -10000 0 2
Rac1/GDP 0.007 0 -10000 0 -10000 0 0
DOCK1 0.008 0.021 -10000 0 -0.29 2 2
ITGA4 0.002 0.052 0.27 1 -0.29 12 13
alpha4/beta7 Integrin/MAdCAM1 0.023 0.042 0.18 13 -0.14 15 28
EPO 0.028 0.069 0.27 31 -10000 0 31
alpha4/beta7 Integrin 0.007 0.042 0.19 1 -0.19 17 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.009 0.036 0.19 1 -0.19 12 13
EPO/EPOR (dimer) 0.03 0.053 0.19 39 -10000 0 39
lamellipodium assembly 0.016 0.01 -10000 0 -0.18 1 1
PIK3CA 0.01 0 -10000 0 -10000 0 0
PI3K 0.014 0.01 -10000 0 -0.19 1 1
ARF6 0.01 0 -10000 0 -10000 0 0
JAK2 0.018 0.041 -10000 0 -0.17 11 11
PXN 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
MADCAM1 0.017 0.048 0.27 14 -10000 0 14
cell adhesion 0.022 0.041 0.17 13 -0.14 15 28
CRKL/CBL 0.016 0.012 0.19 2 -10000 0 2
ITGB1 0.01 0 -10000 0 -10000 0 0
SRC 0.003 0.046 -10000 0 -0.17 23 23
ITGB7 0.006 0.033 -10000 0 -0.29 5 5
RAC1 0.01 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.009 0.054 0.18 3 -0.2 23 26
p130Cas/Crk/Dock1 0.013 0.042 -10000 0 -0.23 6 6
VCAM1 -0.001 0.063 0.27 2 -0.29 17 19
RHOA 0.01 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.021 0.029 0.18 1 -0.14 12 13
BCAR1 0.003 0.042 -10000 0 -0.16 23 23
EPOR 0.015 0.036 0.27 8 -10000 0 8
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.01 0 -10000 0 -10000 0 0
GIT1 0.01 0 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.011 -10000 0 -0.18 1 1
TCGA08_rtk_signaling

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
PDGFRA -0.031 0.1 -10000 0 -0.29 56 56
HRAS 0.01 0 -10000 0 -10000 0 0
EGFR 0.008 0.057 0.27 8 -0.29 9 17
AKT 0.022 0.017 -10000 0 -10000 0 0
FOXO3 0.01 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
FOXO1 0.009 0.015 -10000 0 -0.29 1 1
AKT3 0 0.054 -10000 0 -0.29 14 14
FOXO4 0.011 0.013 0.27 1 -10000 0 1
MET 0.011 0.018 0.27 2 -10000 0 2
PIK3CA 0.01 0 -10000 0 -10000 0 0
PIK3CB 0.01 0 -10000 0 -10000 0 0
NRAS 0.01 0 -10000 0 -10000 0 0
PIK3CG 0.002 0.056 0.27 2 -0.29 13 15
PIK3R3 0.01 0 -10000 0 -10000 0 0
PIK3R2 0.01 0 -10000 0 -10000 0 0
NF1 0.01 0 -10000 0 -10000 0 0
RAS -0.003 0.049 -10000 0 -0.11 59 59
ERBB2 0.018 0.045 0.27 13 -10000 0 13
proliferation/survival/translation -0.015 0.029 0.2 2 -10000 0 2
PI3K 0.005 0.042 -10000 0 -0.098 51 51
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
KRAS 0.011 0.013 0.27 1 -10000 0 1
FOXO 0.028 0.019 0.13 1 -10000 0 1
AKT2 0.01 0 -10000 0 -10000 0 0
PTEN 0.01 0 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.013 0.036 -9999 0 -0.17 15 15
E-cadherin/beta catenin 0.008 0.038 -9999 0 -0.19 14 14
CTNNB1 0.01 0 -9999 0 -10000 0 0
JUP 0.008 0.021 -9999 0 -0.29 2 2
CDH1 0 0.054 -9999 0 -0.29 14 14
EPO signaling pathway

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
BCL2L1 0.029 0.07 0.34 1 -10000 0 1
CRKL 0.021 0.029 0.17 2 -0.11 1 3
mol:DAG 0.027 0.039 -10000 0 -10000 0 0
HRAS 0.023 0.024 -10000 0 -10000 0 0
MAPK8 0.02 0.023 -10000 0 -10000 0 0
RAP1A 0.02 0.027 -10000 0 -0.11 1 1
GAB1 0.02 0.027 -10000 0 -0.11 1 1
MAPK14 0.02 0.023 -10000 0 -10000 0 0
EPO 0.028 0.068 0.26 31 -10000 0 31
PLCG1 0.027 0.04 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.016 0.035 0.26 8 -10000 0 8
RAPGEF1 0.01 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.014 0.072 0.17 32 -0.17 37 69
GAB1/SHC/GRB2/SOS1 0.029 0.025 0.15 1 -10000 0 1
EPO/EPOR (dimer) 0.031 0.051 0.18 39 -10000 0 39
IRS2 0.019 0.031 -10000 0 -0.17 3 3
STAT1 0.03 0.055 0.22 1 -0.2 13 14
STAT5B 0.028 0.047 -10000 0 -0.16 13 13
cell proliferation 0.018 0.02 -10000 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC 0.015 0.024 -10000 0 -0.13 1 1
TEC 0.02 0.027 -10000 0 -0.11 1 1
SOCS3 -0.022 0.092 -10000 0 -0.29 43 43
STAT1 (dimer) 0.03 0.055 0.22 1 -0.2 13 14
JAK2 0.011 0.004 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
EPO/EPOR (dimer)/JAK2 0.042 0.048 0.22 1 -10000 0 1
EPO/EPOR 0.031 0.051 0.18 39 -10000 0 39
LYN 0.01 0.005 -10000 0 -10000 0 0
TEC/VAV2 0.026 0.03 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.016 0.035 0.26 8 -10000 0 8
SHC1 0.011 0.013 0.27 1 -10000 0 1
EPO/EPOR (dimer)/LYN 0.036 0.045 0.18 36 -10000 0 36
mol:IP3 0.027 0.039 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.021 0.042 -10000 0 -0.18 4 4
SH2B3 0.011 0.004 -10000 0 -10000 0 0
NFKB1 0.02 0.023 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 -0.003 0.059 -10000 0 -0.16 37 37
PTPN6 0.019 0.028 0.16 1 -0.12 1 2
TEC/VAV2/GRB2 0.03 0.03 -10000 0 -10000 0 0
EPOR 0.016 0.035 0.26 8 -10000 0 8
INPP5D 0.005 0.039 -10000 0 -0.29 7 7
mol:GDP 0.029 0.025 0.15 1 -10000 0 1
SOS1 0.01 0 -10000 0 -10000 0 0
PLCG2 0.01 0.03 0.27 3 -0.29 2 5
CRKL/CBL/C3G 0.032 0.029 -10000 0 -10000 0 0
VAV2 0.02 0.027 -10000 0 -0.11 1 1
CBL 0.02 0.027 -10000 0 -0.11 1 1
SHC/Grb2/SOS1 0.022 0.026 -10000 0 -10000 0 0
STAT5A 0.027 0.048 -10000 0 -0.17 4 4
GRB2 0.01 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.034 0.068 0.28 1 -0.25 16 17
LYN/PLCgamma2 0.015 0.021 0.19 3 -0.19 2 5
PTPN11 0.01 0 -10000 0 -10000 0 0
BTK 0.019 0.034 0.19 2 -0.18 4 6
BCL2 0.011 0.15 -10000 0 -0.72 16 16
TRAIL signaling pathway

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
TNFSF10 0.022 0.055 0.27 19 -10000 0 19
positive regulation of NF-kappaB transcription factor activity 0.02 0.044 0.19 19 -0.19 5 24
MAP2K4 0.024 0.02 -10000 0 -10000 0 0
IKBKB 0.01 0 -10000 0 -10000 0 0
TNFRSF10B 0.01 0 -10000 0 -10000 0 0
TNFRSF10A 0.009 0.015 -10000 0 -0.29 1 1
SMPD1 0.012 0.015 -10000 0 -10000 0 0
IKBKG 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.006 0.033 -10000 0 -0.29 5 5
TRAIL/TRAILR2 0.023 0.037 0.19 19 -10000 0 19
TRAIL/TRAILR3 0.023 0.047 0.19 24 -0.19 4 28
TRAIL/TRAILR1 0.023 0.039 0.19 19 -0.19 1 20
TRAIL/TRAILR4 0.02 0.044 0.19 19 -0.19 5 24
TRAIL/TRAILR1/DAP3/GTP 0.026 0.033 0.17 19 -0.14 1 20
IKK complex 0.018 0.005 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.007 0 -10000 0 -10000 0 0
MAPK3 0.016 0.032 0.16 19 -10000 0 19
MAP3K1 0.024 0.021 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.006 0.033 -10000 0 -0.29 5 5
TRADD 0.01 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.009 0.015 -10000 0 -0.29 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.023 0.023 -10000 0 -0.16 1 1
CFLAR 0.01 0 -10000 0 -10000 0 0
MAPK1 0.016 0.032 0.16 19 -10000 0 19
TRAIL/TRAILR1/FADD/TRADD/RIP 0.038 0.035 0.17 25 -0.13 1 26
mol:ceramide 0.012 0.015 -10000 0 -10000 0 0
FADD 0.014 0.031 0.27 6 -10000 0 6
MAPK8 0.023 0.022 -10000 0 -10000 0 0
TRAF2 0.01 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.01 0.041 0.27 5 -0.29 4 9
CHUK 0.01 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.03 0.039 0.18 25 -0.16 1 26
DAP3 0.01 0 -10000 0 -10000 0 0
CASP10 0.016 0.029 0.18 5 -10000 0 5
JNK cascade 0.02 0.044 0.19 19 -0.19 5 24
TRAIL (trimer) 0.022 0.054 0.27 19 -10000 0 19
TNFRSF10C 0.01 0.041 0.27 5 -0.29 4 9
TRAIL/TRAILR1/DAP3/GTP/FADD 0.032 0.035 0.16 25 -0.13 1 26
TRAIL/TRAILR2/FADD 0.03 0.038 0.18 25 -10000 0 25
cell death 0.012 0.015 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.023 0.021 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.01 0 -10000 0 -10000 0 0
CASP8 0.004 0.009 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.038 0.034 0.17 25 -10000 0 25
HIF-2-alpha transcription factor network

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
MMP14 0.015 0.027 0.35 1 -10000 0 1
oxygen homeostasis 0.006 0.012 -10000 0 -10000 0 0
TCEB2 0.011 0.013 0.27 1 -10000 0 1
TCEB1 0.01 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.044 0.059 0.27 1 -0.2 3 4
EPO 0.096 0.16 0.5 15 -0.35 3 18
FIH (dimer) 0.015 0.013 -10000 0 -10000 0 0
APEX1 0.016 0.017 -10000 0 -10000 0 0
SERPINE1 0.081 0.15 0.47 8 -0.42 5 13
FLT1 0.015 0.025 -10000 0 -10000 0 0
ADORA2A 0.075 0.14 0.4 15 -0.36 3 18
germ cell development 0.1 0.17 0.54 14 -0.34 5 19
SLC11A2 0.08 0.14 0.44 8 -0.37 3 11
BHLHE40 0.079 0.14 0.44 8 -0.36 4 12
HIF1AN 0.015 0.013 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.077 0.12 0.38 15 -0.24 4 19
ETS1 0.016 0.007 -10000 0 -10000 0 0
CITED2 0.014 0.02 -10000 0 -10000 0 0
KDR 0.011 0.075 -10000 0 -1 2 2
PGK1 0.08 0.14 0.44 8 -0.37 3 11
SIRT1 0.011 0.002 -10000 0 -10000 0 0
response to hypoxia 0.001 0.002 -10000 0 -10000 0 0
HIF2A/ARNT 0.12 0.18 0.55 15 -0.42 3 18
EPAS1 0.043 0.073 0.26 8 -0.24 3 11
SP1 0.014 0.007 -10000 0 -10000 0 0
ABCG2 0.077 0.15 0.49 9 -0.35 13 22
EFNA1 0.083 0.14 0.49 8 -0.37 3 11
FXN 0.074 0.13 0.4 15 -0.36 3 18
POU5F1 0.1 0.17 0.55 14 -0.36 5 19
neuron apoptosis -0.12 0.17 0.41 3 -0.54 15 18
EP300 0.01 0 -10000 0 -10000 0 0
EGLN3 0.01 0.042 -10000 0 -0.29 7 7
EGLN2 0.015 0.013 -10000 0 -10000 0 0
EGLN1 0.015 0.013 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.021 0.008 0.18 1 -10000 0 1
VHL 0.01 0 -10000 0 -10000 0 0
ARNT 0.017 0.017 -10000 0 -10000 0 0
SLC2A1 0.076 0.14 0.4 15 -0.36 3 18
TWIST1 0.052 0.18 0.4 15 -0.34 47 62
ELK1 0.013 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.069 0.1 0.34 8 -0.24 4 12
VEGFA 0.08 0.14 0.44 8 -0.37 3 11
CREBBP 0.01 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.009 0.005 0.12 1 -10000 0 1
SNTA1 0.01 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.019 0.032 0.12 41 -10000 0 41
MAPK12 0.007 0.022 -10000 0 -0.14 7 7
CCND1 0.007 0.055 0.14 14 -0.36 7 21
p38 gamma/SNTA1 0.013 0.021 -10000 0 -0.13 7 7
MAP2K3 0.01 0 -10000 0 -10000 0 0
PKN1 0.009 0.015 -10000 0 -0.29 1 1
G2/M transition checkpoint 0.007 0.022 -10000 0 -0.14 7 7
MAP2K6 0.006 0.023 -10000 0 -0.16 7 7
MAPT -0.009 0.066 -10000 0 -0.22 34 34
MAPK13 0.01 0.008 0.16 1 -10000 0 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.017 -10000 0 -0.23 2 2
Retinoic acid receptors-mediated 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
HDAC1 0.01 0 -10000 0 -10000 0 0
HDAC3 0.01 0 -10000 0 -10000 0 0
VDR 0.009 0.024 0.27 1 -0.29 2 3
Cbp/p300/PCAF 0.02 0.009 -10000 0 -0.16 1 1
EP300 0.01 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.008 0.044 -10000 0 -0.19 3 3
KAT2B 0.009 0.015 -10000 0 -0.29 1 1
MAPK14 0.01 0 -10000 0 -10000 0 0
AKT1 0.005 0.058 0.16 17 -0.17 27 44
RAR alpha/9cRA/Cyclin H 0.021 0.028 -10000 0 -0.19 4 4
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.005 0.048 -10000 0 -0.15 35 35
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.009 0.029 -10000 0 -0.21 6 6
NCOR2 0.01 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.007 0.017 0.18 1 -0.19 2 3
RXRs/RARs/NRIP1/9cRA -0.006 0.069 -10000 0 -0.33 5 5
NCOA2 -0.008 0.07 -10000 0 -0.29 24 24
NCOA3 0.01 0 -10000 0 -10000 0 0
NCOA1 0.01 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.009 0.024 0.27 1 -0.29 2 3
RARG 0.01 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.014 0 -10000 0 -10000 0 0
MAPK3 0.01 0 -10000 0 -10000 0 0
MAPK1 0.01 0 -10000 0 -10000 0 0
MAPK8 0.008 0.025 -10000 0 -0.29 3 3
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.005 0.05 -10000 0 -0.3 4 4
RARA 0.012 0.031 -10000 0 -0.18 7 7
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.005 0.066 -10000 0 -0.16 55 55
PRKCA 0.008 0.029 -10000 0 -0.29 4 4
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.013 0.076 -10000 0 -0.36 5 5
RXRG -0.05 0.11 0.14 9 -0.23 106 115
RXRA 0.013 0.027 -10000 0 -0.16 7 7
RXRB 0.013 0.033 -10000 0 -0.22 4 4
VDR/Vit D3/DNA 0.007 0.017 0.18 1 -0.19 2 3
RBP1 -0.006 0.074 0.27 3 -0.29 24 27
CRBP1/9-cic-RA -0.003 0.05 0.18 3 -0.19 24 27
RARB -0.014 0.083 -10000 0 -0.29 34 34
PRKCG 0.015 0.048 0.27 14 -10000 0 14
MNAT1 0.01 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.002 0.067 -10000 0 -0.32 6 6
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.002 0.064 -10000 0 -0.26 9 9
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.048 -10000 0 -0.25 3 3
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.013 0.076 -10000 0 -0.36 5 5
positive regulation of DNA binding 0.016 0.026 -10000 0 -0.17 6 6
NRIP1 -0.013 0.076 -10000 0 -0.54 1 1
RXRs/RARs -0.018 0.083 -10000 0 -0.34 9 9
RXRs/RXRs/DNA/9cRA 0.001 0.048 -10000 0 -0.31 4 4
PRKACA 0.01 0 -10000 0 -10000 0 0
CDK7 0.01 0 -10000 0 -10000 0 0
TFIIH 0.02 0 -10000 0 -10000 0 0
RAR alpha/9cRA 0.025 0.02 -10000 0 -10000 0 0
CCNH 0.01 0 -10000 0 -10000 0 0
CREBBP 0.01 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.019 0 -10000 0 -10000 0 0
Syndecan-3-mediated signaling 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
CTTN 0.011 0.013 0.27 1 -10000 0 1
Syndecan-3/Src/Cortactin 0.003 0.072 -10000 0 -0.56 1 1
Syndecan-3/Neurocan 0.014 0.036 0.18 11 -0.48 1 12
POMC 0.012 0.054 0.27 10 -0.29 6 16
EGFR 0.008 0.057 0.27 8 -0.29 9 17
Syndecan-3/EGFR 0.016 0.033 0.18 8 -0.48 1 9
AGRP 0.007 0.023 0.27 3 -10000 0 3
NCSTN 0.01 0 -10000 0 -10000 0 0
PSENEN 0.01 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.01 0 -10000 0 -10000 0 0
APH1A 0.01 0 -10000 0 -10000 0 0
NCAN 0.012 0.043 0.27 11 -10000 0 11
long-term memory 0.018 0.031 -10000 0 -0.56 1 1
Syndecan-3/IL8 0.011 0.032 0.18 1 -0.6 1 2
PSEN1 0.01 0 -10000 0 -10000 0 0
Src/Cortactin 0.015 0.009 0.19 1 -10000 0 1
FYN 0.008 0.025 -10000 0 -0.29 3 3
limb bud formation 0.007 0.025 -10000 0 -0.49 1 1
MC4R 0.007 0.03 0.27 5 -10000 0 5
SRC 0.01 0 -10000 0 -10000 0 0
PTN -0.038 0.14 0.27 20 -0.29 83 103
FGFR/FGF/Syndecan-3 0.007 0.025 -10000 0 -0.5 1 1
neuron projection morphogenesis -0.003 0.065 0.22 1 -0.54 1 2
Syndecan-3/AgRP 0.011 0.028 0.18 3 -0.48 1 4
Syndecan-3/AgRP/MC4R 0.015 0.032 -10000 0 -0.46 1 1
Fyn/Cortactin 0.014 0.02 0.19 1 -0.19 3 4
SDC3 0.007 0.025 -10000 0 -0.5 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.011 0.031 0.17 1 -0.59 1 2
IL8 -0.033 0.11 0.27 1 -0.29 59 60
Syndecan-3/Fyn/Cortactin 0.018 0.032 -10000 0 -0.58 1 1
Syndecan-3/CASK 0.006 0.024 -10000 0 -0.48 1 1
alpha-MSH/MC4R 0.013 0.042 0.19 15 -0.19 6 21
Gamma Secretase 0.03 0 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.005 0.067 -10000 0 -0.35 14 14
KLHL20 0.017 0.044 0.16 14 -0.14 10 24
CYFIP2 0.002 0.048 -10000 0 -0.29 11 11
Rac1/GDP 0.016 0.04 -10000 0 -0.19 14 14
ENAH 0.005 0.067 -10000 0 -0.35 14 14
AP1M1 0.01 0 -10000 0 -10000 0 0
RAP1B 0.01 0 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
CTNNB1 0.01 0 -10000 0 -10000 0 0
CDC42/GTP 0.013 0.024 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.006 0.022 -10000 0 -0.1 10 10
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.018 0.036 -10000 0 -0.14 18 18
RAPGEF1 0.007 0.059 -10000 0 -0.31 14 14
CTNND1 0.01 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.005 0.069 -10000 0 -0.36 14 14
CRK 0.006 0.063 -10000 0 -0.33 14 14
E-cadherin/gamma catenin/alpha catenin 0.013 0.036 -10000 0 -0.17 15 15
alphaE/beta7 Integrin 0.012 0.023 -10000 0 -0.19 5 5
IQGAP1 0.01 0 -10000 0 -10000 0 0
NCKAP1 0.01 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.019 0 -10000 0 -10000 0 0
DLG1 0.005 0.067 -10000 0 -0.35 14 14
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.016 -10000 0 -0.087 14 14
MLLT4 0.01 0 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.019 0.016 0.17 1 -0.14 3 4
PI3K -0.004 0.02 -10000 0 -0.11 14 14
ARF6 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.007 0.042 -10000 0 -0.2 15 15
TIAM1 0.008 0.025 -10000 0 -0.29 3 3
E-cadherin(dimer)/Ca2+ 0.019 0.028 -10000 0 -0.13 14 14
AKT1 0.011 0.015 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
CDH1 0 0.054 -10000 0 -0.29 14 14
RhoA/GDP 0.015 0.04 -10000 0 -0.19 14 14
actin cytoskeleton organization 0.014 0.035 0.14 14 -0.11 10 24
CDC42/GDP 0.015 0.04 -10000 0 -0.19 14 14
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.005 0.037 -10000 0 -0.18 15 15
ITGB7 0.006 0.033 -10000 0 -0.29 5 5
RAC1 0.01 0 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.02 0.03 -10000 0 -0.14 14 14
E-cadherin/Ca2+/beta catenin/alpha catenin 0.013 0.027 -10000 0 -0.13 14 14
mol:GDP 0.011 0.045 -10000 0 -0.22 14 14
CDC42/GTP/IQGAP1 0.014 0 -10000 0 -10000 0 0
JUP 0.008 0.021 -10000 0 -0.29 2 2
p120 catenin/RhoA/GDP 0.017 0.041 -10000 0 -0.2 14 14
RAC1/GTP/IQGAP1 0.014 0 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.015 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
CDC42 0.01 0 -10000 0 -10000 0 0
CTNNA1 0.01 0 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.014 0.046 0.22 14 -0.13 9 23
NME1 0.011 0.013 0.27 1 -10000 0 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.005 0.067 -10000 0 -0.35 14 14
regulation of cell-cell adhesion -0.003 0.019 -10000 0 -0.1 14 14
WASF2 0.006 0.015 -10000 0 -0.075 3 3
Rap1/GTP 0.017 0.027 -10000 0 -0.13 14 14
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.022 0.037 -10000 0 -0.14 19 19
CCND1 0.016 0.054 0.25 14 -0.16 9 23
VAV2 0.008 0.078 -10000 0 -0.37 16 16
RAP1/GDP 0.018 0.032 -10000 0 -0.15 13 13
adherens junction assembly 0.005 0.065 -10000 0 -0.34 14 14
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.01 0 -10000 0 -10000 0 0
PIP5K1C 0.01 0 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.02 0.035 -10000 0 -0.13 19 19
E-cadherin/beta catenin -0.001 0.048 -10000 0 -0.25 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.005 0.067 -10000 0 -0.35 14 14
PIK3CA 0.01 0 -10000 0 -10000 0 0
Rac1/GTP -0.003 0.066 0.25 14 -0.22 10 24
E-cadherin/beta catenin/alpha catenin 0.014 0.032 -10000 0 -0.16 14 14
ITGAE 0.01 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.005 0.07 -10000 0 -0.37 14 14
Signaling events mediated by PRL

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
CCNE1 0.051 0.094 0.27 64 -10000 0 64
mol:Halofuginone 0.003 0 -10000 0 -10000 0 0
ITGA1 0.01 0 -10000 0 -10000 0 0
CDKN1A 0.009 0.035 -10000 0 -0.48 2 2
PRL-3/alpha Tubulin 0.015 0 -10000 0 -10000 0 0
mol:Ca2+ -0.027 0.066 0.15 3 -0.2 51 54
AGT -0.025 0.1 0.27 3 -0.29 51 54
CCNA2 0.025 0.032 -10000 0 -10000 0 0
TUBA1B 0.01 0 -10000 0 -10000 0 0
EGR1 -0.039 0.086 -10000 0 -0.19 100 100
CDK2/Cyclin E1 0.03 0.071 -10000 0 -0.37 2 2
MAPK3 0.009 0 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.015 0 -10000 0 -10000 0 0
MAPK1 0.009 0 -10000 0 -10000 0 0
PTP4A1 0.009 0.005 -10000 0 -10000 0 0
PTP4A3 0.01 0 -10000 0 -10000 0 0
PTP4A2 0.01 0 -10000 0 -10000 0 0
ITGB1 0.009 0 -10000 0 -10000 0 0
SRC 0.01 0 -10000 0 -10000 0 0
RAC1 0.011 0.006 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.015 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.016 0.061 -10000 0 -10000 0 0
RABGGTA 0.01 0 -10000 0 -10000 0 0
BCAR1 -0.003 0 -10000 0 -10000 0 0
RHOC 0.011 0.006 -10000 0 -10000 0 0
RHOA 0.011 0.006 -10000 0 -10000 0 0
cell motility -0.002 0.034 -10000 0 -10000 0 0
PRL-1/alpha Tubulin -0.017 0.06 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.015 0 -10000 0 -10000 0 0
ROCK1 -0.002 0.034 -10000 0 -10000 0 0
RABGGTB 0.01 0 -10000 0 -10000 0 0
CDK2 0.01 0 -10000 0 -10000 0 0
mitosis 0.009 0.005 -10000 0 -10000 0 0
ATF5 0.012 0.026 0.27 4 -10000 0 4
PLK2 and PLK4 events

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
PLK2 0.011 0.013 0.27 1 -9999 0 1
PLK4 0.016 0.04 0.27 10 -9999 0 10
regulation of centriole replication 0.013 0.025 0.16 11 -9999 0 11
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.2 0.13 -10000 0 -0.29 294 294
CLTC 0.014 0.004 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.011 0.007 -10000 0 -10000 0 0
Dynamin 2/GTP 0.013 0.005 -10000 0 -10000 0 0
EXOC4 0.01 0 -10000 0 -10000 0 0
CD59 0.012 0.003 -10000 0 -10000 0 0
CPE 0.009 0.008 0.16 1 -10000 0 1
CTNNB1 0.01 0 -10000 0 -10000 0 0
membrane fusion 0.011 0.003 -10000 0 -10000 0 0
CTNND1 0.011 0.004 -10000 0 -10000 0 0
DNM2 0.01 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.013 0.004 -10000 0 -10000 0 0
TSHR 0.01 0.02 0.16 7 -10000 0 7
INS 0.005 0.001 -10000 0 -10000 0 0
BIN1 -0.03 0.1 -10000 0 -0.29 54 54
mol:Choline 0.011 0.003 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.009 0.007 0.16 1 -10000 0 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0.013 0.005 -10000 0 -10000 0 0
JUP 0.011 0.01 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.002 0.054 -10000 0 -0.14 54 54
ARF6/GTP 0.007 0 -10000 0 -10000 0 0
CDH1 0.007 0.026 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.007 0 -10000 0 -10000 0 0
MAPK8IP3 0.012 0.03 0.27 4 -0.29 1 5
positive regulation of endocytosis 0.007 0 -10000 0 -10000 0 0
EXOC2 0.01 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.019 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.01 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.017 0.019 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.008 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.015 0.018 0.17 4 -0.16 1 5
ACAP1 0.007 0.027 -10000 0 -0.12 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.042 0.069 -10000 0 -0.18 1 1
clathrin heavy chain/ACAP1 0.014 0.008 -10000 0 -10000 0 0
JIP4/KLC1 0.019 0 -10000 0 -10000 0 0
EXOC1 0.01 0 -10000 0 -10000 0 0
exocyst 0.019 0 -10000 0 -10000 0 0
RALA/GTP 0.008 0.009 0.18 1 -10000 0 1
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.014 0 -10000 0 -10000 0 0
receptor recycling 0.007 0 -10000 0 -10000 0 0
CTNNA1 0.011 0.004 -10000 0 -10000 0 0
NME1 0.009 0.008 0.16 1 -10000 0 1
clathrin coat assembly 0.014 0.004 -10000 0 -10000 0 0
IL2RA 0.009 0.033 -10000 0 -10000 0 0
VAMP3 0.009 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.07 0.055 -10000 0 -0.17 1 1
EXOC6 0.01 0 -10000 0 -10000 0 0
PLD1 0.009 0.011 -10000 0 -0.21 1 1
PLD2 0.01 0.003 -10000 0 -10000 0 0
EXOC5 0.01 0 -10000 0 -10000 0 0
PIP5K1C 0.013 0.003 -10000 0 -10000 0 0
SDC1 0.01 0.019 -10000 0 -10000 0 0
ARF6/GDP 0.011 0.005 0.12 1 -10000 0 1
EXOC7 0.01 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.018 0.02 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.011 0.003 -10000 0 -10000 0 0
endocytosis 0.002 0.053 0.14 54 -10000 0 54
SCAMP2 0.01 0 -10000 0 -10000 0 0
ADRB2 -0.001 0.042 -10000 0 -10000 0 0
EXOC3 0.01 0 -10000 0 -10000 0 0
ASAP2 0.01 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.015 0.006 0.14 1 -10000 0 1
KLC1 0.01 0 -10000 0 -10000 0 0
AVPR2 0.003 0.038 -10000 0 -10000 0 0
RALA 0.011 0.013 0.27 1 -10000 0 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.019 0.019 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.014 0.055 -10000 0 -0.21 22 22
BAG4 0.01 0 -10000 0 -10000 0 0
BAD 0.01 0.019 -10000 0 -10000 0 0
NFKBIA 0.01 0 -10000 0 -10000 0 0
BIRC3 -0.004 0.071 0.27 3 -0.29 22 25
BAX 0.01 0.019 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.005 0.014 0.059 1 -10000 0 1
IKBKB 0.014 0.053 -10000 0 -0.2 22 22
MAP2K2 0.013 0.016 -10000 0 -10000 0 0
MAP2K1 0.013 0.016 -10000 0 -10000 0 0
SMPD1 0.007 0.014 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.018 0.055 -10000 0 -0.2 2 2
MAP2K4 0.011 0.018 -10000 0 -10000 0 0
protein ubiquitination 0.014 0.054 -10000 0 -0.2 22 22
EnzymeConsortium:2.7.1.37 0.015 0.016 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.012 0.017 -10000 0 -10000 0 0
CRADD 0.01 0 -10000 0 -10000 0 0
mol:ceramide 0.008 0.02 0.081 1 -10000 0 1
I-kappa-B-alpha/RELA/p50/ubiquitin 0.014 0 -10000 0 -10000 0 0
MADD 0.01 0 -10000 0 -10000 0 0
MAP3K1 0.01 0.019 -10000 0 -10000 0 0
TRADD 0.01 0 -10000 0 -10000 0 0
RELA/p50 0.01 0 -10000 0 -10000 0 0
MAPK3 0.014 0.016 -10000 0 -10000 0 0
MAPK1 0.014 0.016 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0.015 0 -10000 0 -10000 0 0
FADD 0.015 0.056 -10000 0 -0.21 22 22
KSR1 0.01 0.018 -10000 0 -10000 0 0
MAPK8 0.011 0.019 -10000 0 -0.1 3 3
TRAF2 0.01 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.014 0.053 -10000 0 -0.2 22 22
TNF R/SODD 0.015 0 -10000 0 -10000 0 0
TNF 0.023 0.057 0.27 21 -10000 0 21
CYCS 0.013 0.025 0.1 15 -10000 0 15
IKBKG 0.014 0.053 -10000 0 -0.2 22 22
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.013 0.058 -10000 0 -0.22 22 22
RELA 0.01 0 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
AIFM1 0.013 0.025 0.1 15 -10000 0 15
TNF/TNF R/SODD 0.028 0.035 0.18 21 -10000 0 21
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.016 0.016 -10000 0 -10000 0 0
NSMAF 0.014 0.054 -10000 0 -0.2 22 22
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 -0.002 0.058 -10000 0 -0.29 16 16
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.014 0.025 -10000 0 -0.2 2 2
adherens junction organization 0.01 0.043 -10000 0 -0.2 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.033 -10000 0 -0.21 2 2
FMN1 0.011 0.044 -10000 0 -0.2 14 14
mol:IP3 0.012 0.024 -10000 0 -0.18 2 2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.008 0.044 -10000 0 -0.21 15 15
CTNNB1 0.01 0.002 -10000 0 -10000 0 0
AKT1 0.014 0.029 -10000 0 -0.28 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.009 0.059 -10000 0 -0.3 14 14
CTNND1 0.01 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.009 0.041 -10000 0 -0.19 15 15
VASP 0.009 0.042 -10000 0 -0.2 15 15
ZYX 0.009 0.042 -10000 0 -0.2 15 15
JUB 0.009 0.042 -10000 0 -0.2 14 14
EGFR(dimer) 0.016 0.05 0.18 8 -0.2 15 23
E-cadherin/beta catenin-gamma catenin 0.013 0.032 -10000 0 -0.15 15 15
mol:PI-3-4-5-P3 0.017 0.031 -10000 0 -0.3 1 1
PIK3CA 0.01 0.001 -10000 0 -10000 0 0
PI3K 0.017 0.031 -10000 0 -0.3 1 1
FYN 0.015 0.032 -10000 0 -0.22 4 4
mol:Ca2+ 0.012 0.024 -10000 0 -0.18 2 2
JUP 0.009 0.021 -10000 0 -0.28 2 2
PIK3R1 0.01 0.015 -10000 0 -0.29 1 1
mol:DAG 0.012 0.024 -10000 0 -0.18 2 2
CDH1 0 0.054 -10000 0 -0.29 14 14
RhoA/GDP 0.017 0.033 -10000 0 -0.21 2 2
establishment of polarity of embryonic epithelium 0.009 0.041 -10000 0 -0.19 15 15
SRC 0.01 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
EGFR 0.008 0.057 0.27 8 -0.29 9 17
CASR 0.014 0.027 -10000 0 -0.17 2 2
RhoA/GTP 0.016 0.023 -10000 0 -0.22 1 1
AKT2 0.014 0.029 -10000 0 -0.28 1 1
actin cable formation 0.012 0.043 -10000 0 -0.19 14 14
apoptosis -0.013 0.028 0.21 2 -10000 0 2
CTNNA1 0.01 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.033 -10000 0 -0.23 2 2
PIP5K1A 0.009 0.042 -10000 0 -0.2 15 15
PLCG1 0.012 0.025 -10000 0 -0.18 2 2
Rac1/GTP 0.017 0.049 0.16 8 -0.19 15 23
homophilic cell adhesion 0 0.001 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.01 0.008 0.16 1 -10000 0 1
BAD/BCL-XL/YWHAZ 0.02 0.005 -10000 0 -10000 0 0
CDKN1B 0.014 0 -10000 0 -10000 0 0
CDKN1A 0.014 0.009 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.01 0 -10000 0 -10000 0 0
FOXO3 0.014 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
BAD 0.01 0 -10000 0 -10000 0 0
AKT3 0 0.043 -10000 0 -0.23 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.014 0.003 -10000 0 -10000 0 0
AKT1/ASK1 0.018 0.006 -10000 0 -10000 0 0
BAD/YWHAZ 0.02 0 -10000 0 -10000 0 0
RICTOR 0.01 0 -10000 0 -10000 0 0
RAF1 0.011 0.013 0.27 1 -10000 0 1
JNK cascade -0.017 0.006 -10000 0 -10000 0 0
TSC1 0.014 0 -10000 0 -10000 0 0
YWHAZ 0.01 0 -10000 0 -10000 0 0
AKT1/RAF1 0.019 0.008 0.18 1 -10000 0 1
EP300 0.01 0 -10000 0 -10000 0 0
mol:GDP 0.013 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.014 0 -10000 0 -10000 0 0
YWHAQ 0.01 0 -10000 0 -10000 0 0
TBC1D4 0.008 0 -10000 0 -10000 0 0
MAP3K5 0.009 0.015 -10000 0 -0.29 1 1
MAPKAP1 0.01 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.022 0.018 -10000 0 -10000 0 0
YWHAH 0.01 0 -10000 0 -10000 0 0
AKT1S1 0.014 0 -10000 0 -10000 0 0
CASP9 0.014 0 -10000 0 -10000 0 0
YWHAB 0.01 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.02 0 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.02 0 -10000 0 -10000 0 0
YWHAE 0.009 0.015 -10000 0 -0.29 1 1
SRC 0.01 0 -10000 0 -10000 0 0
AKT2/p21CIP1 0.015 0.009 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.009 0 -10000 0 -10000 0 0
CHUK 0.014 0 -10000 0 -10000 0 0
BAD/BCL-XL 0.024 0.005 -10000 0 -10000 0 0
mTORC2 0.013 0 -10000 0 -10000 0 0
AKT2 0.008 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.028 0.02 -10000 0 -10000 0 0
PDPK1 0.01 0 -10000 0 -10000 0 0
MDM2 0.016 0.012 -10000 0 -10000 0 0
MAPKKK cascade -0.019 0.008 -10000 0 -0.18 1 1
MDM2/Cbp/p300 0.027 0.011 -10000 0 -10000 0 0
TSC1/TSC2 0.015 0 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.01 -10000 0 -10000 0 0
glucose import -0.094 0.064 -10000 0 -0.13 294 294
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.002 0.004 -10000 0 -10000 0 0
GSK3A 0.014 0 -10000 0 -10000 0 0
FOXO1 0.014 0.006 -10000 0 -10000 0 0
GSK3B 0.014 0 -10000 0 -10000 0 0
SFN 0.027 0.076 0.27 32 -0.29 4 36
G1/S transition of mitotic cell cycle 0.015 0 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.025 0.023 -10000 0 -10000 0 0
PRKACA 0.01 0 -10000 0 -10000 0 0
KPNA1 0.01 0 -10000 0 -10000 0 0
HSP90AA1 0.01 0 -10000 0 -10000 0 0
YWHAG 0.01 0 -10000 0 -10000 0 0
RHEB 0.01 0 -10000 0 -10000 0 0
CREBBP 0.01 0 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.011 0.018 0.27 2 -10000 0 2
Rac1/GDP 0.008 0.004 -10000 0 -10000 0 0
DOCK1 0.008 0.021 -10000 0 -0.29 2 2
ITGA4 0.002 0.052 0.27 1 -0.29 12 13
RAC1 0.01 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.007 0.042 0.19 1 -0.19 17 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.015 0.031 0.18 1 -0.16 12 13
alpha4/beta7 Integrin/Paxillin 0.014 0.033 0.18 1 -0.14 17 18
lamellipodium assembly 0.021 0.02 -10000 0 -0.29 1 1
PIK3CA 0.01 0 -10000 0 -10000 0 0
PI3K 0.014 0.01 -10000 0 -0.19 1 1
ARF6 0.01 0 -10000 0 -10000 0 0
TLN1 0.01 0 -10000 0 -10000 0 0
PXN 0.009 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
ARF6/GTP 0.02 0.024 -10000 0 -0.12 12 12
cell adhesion 0.02 0.026 0.17 1 -0.13 12 13
CRKL/CBL 0.016 0.012 0.19 2 -10000 0 2
alpha4/beta1 Integrin/Paxillin 0.016 0.028 0.18 1 -0.14 12 13
ITGB1 0.01 0 -10000 0 -10000 0 0
ITGB7 0.006 0.033 -10000 0 -0.29 5 5
ARF6/GDP 0.008 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.016 0.047 0.18 3 -0.16 23 26
p130Cas/Crk/Dock1 0.019 0.012 -10000 0 -0.16 2 2
VCAM1 -0.001 0.063 0.27 2 -0.29 17 19
alpha4/beta1 Integrin/Paxillin/Talin 0.021 0.027 0.18 1 -0.13 12 13
alpha4/beta1 Integrin/Paxillin/GIT1 0.021 0.027 0.18 1 -0.13 12 13
BCAR1 0.01 0 -10000 0 -10000 0 0
mol:GDP -0.02 0.026 0.13 12 -0.17 1 13
CBL 0.01 0 -10000 0 -10000 0 0
PRKACA 0.01 0 -10000 0 -10000 0 0
GIT1 0.01 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.021 0.027 0.18 1 -0.13 12 13
Rac1/GTP 0.022 0.022 -10000 0 -0.32 1 1
Class I PI3K signaling events

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
ARF5/GTP 0.014 0.003 -10000 0 -10000 0 0
DAPP1 -0.001 0.068 0.15 2 -0.3 7 9
Src family/SYK family/BLNK-LAT/BTK-ITK -0.011 0.11 0.21 2 -0.35 24 26
mol:DAG 0.001 0.055 0.2 2 -0.16 22 24
HRAS 0.01 0 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
ARF5/GDP 0.013 0.036 -10000 0 -0.18 3 3
PLCG2 0.01 0.03 0.27 3 -0.29 2 5
PLCG1 0.01 0 -10000 0 -10000 0 0
ARF5 0.01 0 -10000 0 -10000 0 0
mol:GTP 0.006 0.003 -10000 0 -10000 0 0
ARF1/GTP 0.01 0.003 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
YES1 0.01 0 -10000 0 -10000 0 0
RAP1A/GTP 0.011 0.003 -10000 0 -10000 0 0
ADAP1 0.007 0.003 -10000 0 -10000 0 0
ARAP3 0.006 0.003 -10000 0 -10000 0 0
INPPL1 0.01 0 -10000 0 -10000 0 0
PREX1 0.01 0 -10000 0 -10000 0 0
ARHGEF6 0.008 0.025 -10000 0 -0.29 3 3
ARHGEF7 0.01 0 -10000 0 -10000 0 0
ARF1 0.01 0 -10000 0 -10000 0 0
NRAS 0.01 0 -10000 0 -10000 0 0
FYN 0.008 0.025 -10000 0 -0.29 3 3
ARF6 0.01 0 -10000 0 -10000 0 0
FGR 0.008 0.021 -10000 0 -0.29 2 2
mol:Ca2+ 0.003 0.032 0.13 2 -0.096 16 18
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.008 0.025 -10000 0 -0.29 3 3
ZAP70 0 0.058 0.27 1 -0.29 15 16
mol:IP3 0.001 0.043 0.16 2 -0.11 36 38
LYN 0.01 0 -10000 0 -10000 0 0
ARF1/GDP 0.013 0.036 -10000 0 -0.18 3 3
RhoA/GDP 0.019 0.017 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.02 0 -10000 0 -10000 0 0
BLNK 0 0.052 -10000 0 -0.29 13 13
actin cytoskeleton reorganization 0.016 0.027 -10000 0 -10000 0 0
SRC 0.01 0 -10000 0 -10000 0 0
PLEKHA2 0.006 0.021 -10000 0 -0.16 7 7
RAC1 0.01 0 -10000 0 -10000 0 0
PTEN 0.009 0 -10000 0 -10000 0 0
HSP90AA1 0.01 0 -10000 0 -10000 0 0
ARF6/GTP 0.014 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.012 0.003 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.004 0.082 -10000 0 -0.33 13 13
BLK -0.009 0.1 0.27 16 -0.29 37 53
PDPK1 0.01 0 -10000 0 -10000 0 0
CYTH1 0.007 0.003 -10000 0 -10000 0 0
HCK 0.004 0.058 0.27 5 -0.29 12 17
CYTH3 0.007 0.003 -10000 0 -10000 0 0
CYTH2 0.007 0.003 -10000 0 -10000 0 0
KRAS 0.011 0.013 0.27 1 -10000 0 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.002 0.075 -10000 0 -0.37 16 16
SGK1 0 0.08 -10000 0 -0.4 16 16
INPP5D 0.005 0.039 -10000 0 -0.29 7 7
mol:GDP 0.008 0.037 -10000 0 -0.14 22 22
SOS1 0.01 0 -10000 0 -10000 0 0
SYK 0.007 0.029 -10000 0 -0.29 4 4
ARF6/GDP 0.015 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.006 0.003 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.011 0.003 -10000 0 -10000 0 0
VAV1 -0.001 0.061 0.27 2 -0.29 16 18
mol:PI-3-4-P2 0.006 0.026 -10000 0 -0.19 7 7
RAS family/GTP/PI3K Class I 0.018 0.007 0.16 1 -10000 0 1
PLEKHA1 0.006 0.021 -10000 0 -0.16 7 7
Rac1/GDP 0.013 0.036 -10000 0 -0.18 3 3
LAT 0.011 0.013 0.27 1 -10000 0 1
Rac1/GTP 0.009 0.041 -10000 0 -0.22 6 6
ITK 0.007 0.004 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.002 0.072 0.22 2 -0.22 22 24
LCK 0.008 0.035 0.27 2 -0.29 4 6
BTK 0.008 0.008 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.023 0.02 -10000 0 -0.14 6 6
HDAC3 0.01 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -10000 0 0
GATA1/HDAC4 0.012 0.003 -10000 0 -10000 0 0
GATA1/HDAC5 0.012 0.003 -10000 0 -10000 0 0
GATA2/HDAC5 0.017 0.042 0.19 13 -0.19 7 20
HDAC5/BCL6/BCoR 0.02 0 -10000 0 -10000 0 0
HDAC9 -0.011 0.075 -10000 0 -0.29 28 28
Glucocorticoid receptor/Hsp90/HDAC6 0.015 0.03 -10000 0 -0.16 12 12
HDAC4/ANKRA2 0.015 0 -10000 0 -10000 0 0
HDAC5/YWHAB 0.015 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.009 0 -10000 0 -10000 0 0
GATA2 0.013 0.06 0.27 13 -0.29 7 20
HDAC4/RFXANK 0.015 0.009 0.19 1 -10000 0 1
BCOR 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.01 0 -10000 0 -10000 0 0
HDAC5 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 0.012 0.025 -10000 0 -0.19 6 6
Histones 0.005 0.045 -10000 0 -0.16 4 4
ADRBK1 0.01 0 -10000 0 -10000 0 0
HDAC4 0.01 0 -10000 0 -10000 0 0
XPO1 0.01 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.015 0 -10000 0 -10000 0 0
HDAC4/Ubc9 0.015 0 -10000 0 -10000 0 0
HDAC7 0.01 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.014 0.01 -10000 0 -0.19 1 1
TUBA1B 0.01 0 -10000 0 -10000 0 0
HDAC6 0.01 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.015 0.009 0.19 1 -10000 0 1
CAMK4 0.003 0.048 0.27 1 -0.29 10 11
Tubulin/HDAC6 0.019 0.012 -10000 0 -0.16 2 2
SUMO1 0.01 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.01 0 -10000 0 -10000 0 0
GATA1 0.007 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.009 0.015 -10000 0 -0.29 1 1
NR3C1 0.001 0.05 -10000 0 -0.29 12 12
SUMO1/HDAC4 0.019 0 -10000 0 -10000 0 0
SRF 0.01 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0.015 0 -10000 0 -10000 0 0
Tubulin 0.014 0.014 -10000 0 -0.19 2 2
HDAC4/14-3-3 E 0.014 0.01 -10000 0 -0.19 1 1
GNB1 0.01 0 -10000 0 -10000 0 0
RANGAP1 0.01 0 -10000 0 -10000 0 0
BCL6/BCoR 0.015 0 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.02 0 -10000 0 -10000 0 0
HDAC4/SRF 0.016 0.028 0.18 1 -0.16 10 11
HDAC4/ER alpha -0.022 0.079 -10000 0 -0.19 73 73
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.005 0.045 -10000 0 -0.16 4 4
cell motility 0.019 0.012 -10000 0 -0.16 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.01 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.015 0 -10000 0 -10000 0 0
BCL6 0.01 0 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.01 0 -10000 0 -10000 0 0
Hsp90/HDAC6 0.015 0 -10000 0 -10000 0 0
ESR1 -0.043 0.11 -10000 0 -0.29 73 73
HDAC6/HDAC11 0.013 0.022 0.19 1 -0.19 4 5
Ran/GTP/Exportin 1 0.02 0 -10000 0 -10000 0 0
NPC 0.006 0 -10000 0 -10000 0 0
MEF2C 0 0.054 -10000 0 -0.29 14 14
RAN 0.01 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0.024 0.028 -10000 0 -0.13 14 14
GNG2 0.006 0.036 -10000 0 -0.29 6 6
NCOR2 0.01 0 -10000 0 -10000 0 0
TUBB2A 0.008 0.021 -10000 0 -0.29 2 2
HDAC11 0.008 0.032 0.27 1 -0.29 4 5
HSP90AA1 0.01 0 -10000 0 -10000 0 0
RANBP2 0.01 0 -10000 0 -10000 0 0
ANKRA2 0.01 0 -10000 0 -10000 0 0
RFXANK 0.011 0.013 0.27 1 -10000 0 1
nuclear import -0.016 0.01 0.19 1 -10000 0 1
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.009 0.067 -10000 0 -0.2 46 46
AKT1 0.026 0.045 -10000 0 -0.52 2 2
PTK2B 0.001 0.057 -10000 0 -0.33 5 5
VEGFR2 homodimer/Frs2 0.019 0.044 0.2 7 -0.5 2 9
CAV1 -0.004 0.063 -10000 0 -0.29 19 19
CALM1 0.01 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.025 0.043 -10000 0 -0.48 2 2
endothelial cell proliferation 0 0.065 -10000 0 -0.36 5 5
mol:Ca2+ 0.015 0.041 -10000 0 -0.28 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.027 0.036 -10000 0 -0.46 2 2
RP11-342D11.1 0.01 0.04 -10000 0 -0.28 6 6
CDH5 0.008 0.021 -10000 0 -0.29 2 2
VEGFA homodimer 0.026 0.009 0.18 1 -10000 0 1
SHC1 0.011 0.013 0.27 1 -10000 0 1
SHC2 -0.008 0.073 0.27 1 -0.29 25 26
HRAS/GDP 0.018 0.036 -10000 0 -0.24 6 6
SH2D2A 0.012 0.026 0.27 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.033 0.039 -10000 0 -0.42 2 2
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.023 0.041 -10000 0 -0.48 2 2
VEGFR1 homodimer 0.01 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.031 0.041 -10000 0 -0.26 6 6
GRB10 0.014 0.055 -10000 0 -0.42 6 6
PTPN11 0.01 0 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
PAK1 0.009 0.015 -10000 0 -0.29 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.03 0.043 -10000 0 -0.56 2 2
HRAS 0.01 0 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.001 0.06 -10000 0 -0.3 5 5
HIF1A 0.011 0.013 0.27 1 -10000 0 1
FRS2 0.014 0.034 0.27 7 -10000 0 7
oxygen and reactive oxygen species metabolic process 0.026 0.036 -10000 0 -0.45 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.009 0.015 -10000 0 -0.29 1 1
Nck/Pak 0.014 0.01 -10000 0 -0.19 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.021 0.04 -10000 0 -0.48 2 2
mol:GDP 0.024 0.039 -10000 0 -0.26 6 6
mol:NADP 0.024 0.033 -10000 0 -0.37 2 2
eNOS/Hsp90 0.028 0.032 -10000 0 -0.35 2 2
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
mol:IP3 0.015 0.041 -10000 0 -0.28 6 6
HIF1A/ARNT 0.015 0.009 0.19 1 -10000 0 1
SHB 0.01 0 -10000 0 -10000 0 0
VEGFA 0.01 0.006 -10000 0 -10000 0 0
VEGFC 0.008 0.029 0.27 1 -0.29 3 4
FAK1/Vinculin 0.009 0.065 -10000 0 -0.37 5 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.01 0.064 -10000 0 -0.35 5 5
PTPN6 0.011 0.013 0.27 1 -10000 0 1
EPAS1 0.013 0.022 -10000 0 -0.29 2 2
mol:L-citrulline 0.024 0.033 -10000 0 -0.37 2 2
ITGAV 0.009 0.015 -10000 0 -0.29 1 1
PIK3CA 0.01 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.03 0.041 -10000 0 -0.46 2 2
VEGFR2 homodimer/VEGFA homodimer 0.024 0.045 -10000 0 -0.31 6 6
VEGFR2/3 heterodimer 0.015 0.042 -10000 0 -0.57 2 2
VEGFB 0.01 0 -10000 0 -10000 0 0
MAPK11 0.012 0.043 -10000 0 -0.3 6 6
VEGFR2 homodimer 0.012 0.042 -10000 0 -0.58 2 2
FLT1 0.01 0 -10000 0 -10000 0 0
NEDD4 0.009 0.016 -10000 0 -0.29 1 1
MAPK3 -0.01 0.053 -10000 0 -0.28 7 7
MAPK1 -0.01 0.053 -10000 0 -0.28 7 7
VEGFA145/NRP2 0.005 0.044 -10000 0 -0.19 19 19
VEGFR1/2 heterodimer 0.016 0.037 -10000 0 -0.5 2 2
KDR 0.012 0.042 -10000 0 -0.58 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.018 0.052 -10000 0 -0.3 6 6
SRC 0.01 0 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.008 0.052 -10000 0 -0.29 7 7
PI3K 0.026 0.049 -10000 0 -0.57 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.022 0.038 -10000 0 -0.48 2 2
FES 0.015 0.042 -10000 0 -0.28 6 6
GAB1 0.022 0.042 -10000 0 -0.53 2 2
VEGFR2 homodimer/VEGFA homodimer/Src 0.022 0.038 -10000 0 -0.48 2 2
CTNNB1 0.01 0 -10000 0 -10000 0 0
SOS1 0.01 0 -10000 0 -10000 0 0
ARNT 0.01 0 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.027 0.033 -10000 0 -0.35 2 2
VEGFR2 homodimer/VEGFA homodimer/Yes 0.022 0.038 -10000 0 -0.48 2 2
PI3K/GAB1 0.031 0.047 -10000 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.033 0.041 -10000 0 -0.44 2 2
PRKACA 0.01 0 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.02 0.042 -10000 0 -0.52 2 2
HSP90AA1 0.01 0 -10000 0 -10000 0 0
CDC42 0.015 0.042 -10000 0 -0.28 6 6
actin cytoskeleton reorganization 0.023 0.041 -10000 0 -0.48 2 2
PTK2 0.003 0.067 -10000 0 -0.39 5 5
EDG1 0.01 0.04 -10000 0 -0.28 6 6
mol:DAG 0.015 0.041 -10000 0 -0.28 6 6
CaM/Ca2+ 0.019 0.038 -10000 0 -0.26 6 6
MAP2K3 0.015 0.041 -10000 0 -0.27 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.024 0.057 -10000 0 -0.42 6 6
PLCG1 0.015 0.042 -10000 0 -0.28 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.027 0.036 -10000 0 -0.46 2 2
IQGAP1 0.01 0 -10000 0 -10000 0 0
YES1 0.01 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.022 0.038 -10000 0 -0.48 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.022 0.039 -10000 0 -0.48 2 2
cell migration 0.016 0.06 -10000 0 -0.55 2 2
mol:PI-3-4-5-P3 0.026 0.045 -10000 0 -0.52 2 2
FYN 0.008 0.025 -10000 0 -0.29 3 3
VEGFB/NRP1 0.016 0.039 -10000 0 -0.26 6 6
mol:NO 0.024 0.033 -10000 0 -0.37 2 2
PXN 0.01 0 -10000 0 -10000 0 0
HRAS/GTP -0.004 0.033 -10000 0 -0.24 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.022 0.057 -10000 0 -0.42 6 6
VHL 0.01 0 -10000 0 -10000 0 0
ITGB3 -0.024 0.094 -10000 0 -0.29 46 46
NOS3 0.025 0.037 -10000 0 -0.41 2 2
VEGFR2 homodimer/VEGFA homodimer/Sck 0.013 0.057 -10000 0 -0.44 3 3
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA 0.013 0.04 -10000 0 -0.26 7 7
PRKCB 0.007 0.049 -10000 0 -0.35 6 6
VCL 0.009 0.015 -10000 0 -0.29 1 1
VEGFA165/NRP1 0.016 0.041 -10000 0 -0.28 6 6
VEGFR1/2 heterodimer/VEGFA homodimer 0.022 0.038 -10000 0 -0.48 2 2
VEGFA165/NRP2 0.005 0.044 -10000 0 -0.19 19 19
MAPKKK cascade 0.025 0.049 -10000 0 -0.36 6 6
NRP2 -0.004 0.063 -10000 0 -0.29 19 19
VEGFC homodimer 0.008 0.029 0.27 1 -0.29 3 4
NCK1 0.01 0 -10000 0 -10000 0 0
ROCK1 0.01 0 -10000 0 -10000 0 0
FAK1/Paxillin 0.009 0.065 -10000 0 -0.37 5 5
MAP3K13 0.016 0.044 -10000 0 -0.28 6 6
PDPK1 0.022 0.041 -10000 0 -0.47 2 2
p38 MAPK signaling 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
TRAF6/ASK1 0.009 0.007 -10000 0 -0.13 1 1
TRAF2/ASK1 0.013 0.008 -10000 0 -0.16 1 1
ATM 0.01 0 -10000 0 -10000 0 0
MAP2K3 0.02 0.011 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.019 0.023 -10000 0 -0.18 2 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.006 0.036 -10000 0 -0.29 6 6
TXN 0.005 0.009 0.13 2 -10000 0 2
CALM1 0.01 0 -10000 0 -10000 0 0
GADD45A 0.01 0 -10000 0 -10000 0 0
GADD45B 0.002 0.048 -10000 0 -0.29 11 11
MAP3K1 0.01 0 -10000 0 -10000 0 0
MAP3K6 0.01 0 -10000 0 -10000 0 0
MAP3K7 0.01 0 -10000 0 -10000 0 0
MAP3K4 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.014 0.01 -10000 0 -0.19 1 1
TAK1/TAB family -0.001 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3 0.02 0.007 0.17 1 -10000 0 1
TRAF2 0.01 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.02 0.011 -10000 0 -10000 0 0
TRAF6 0.004 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.037 0.08 0.27 43 -10000 0 43
CCM2 0.011 0.013 0.27 1 -10000 0 1
CaM/Ca2+/CAMKIIB 0.03 0.049 0.17 43 -10000 0 43
MAPK11 0.01 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.035 0.047 0.17 43 -0.14 1 44
OSM/MEKK3 0.015 0.009 0.19 1 -10000 0 1
TAOK1 0.008 0.012 -10000 0 -0.23 1 1
TAOK2 0.008 0 -10000 0 -10000 0 0
TAOK3 0.008 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.01 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.009 0.015 -10000 0 -0.29 1 1
MAP3K10 0.011 0.013 0.27 1 -10000 0 1
MAP3K3 0.01 0 -10000 0 -10000 0 0
TRX/ASK1 0.01 0.01 -10000 0 -0.15 1 1
GADD45/MTK1/MTK1 0.017 0.032 -10000 0 -0.14 16 16
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.037 0.018 -10000 0 -10000 0 0
ERC1 0.01 0 -10000 0 -10000 0 0
RIP2/NOD2 0.025 0.045 0.19 25 -0.19 2 27
NFKBIA 0.014 0 -10000 0 -10000 0 0
BIRC2 0.011 0.018 0.27 2 -10000 0 2
IKBKB 0.01 0 -10000 0 -10000 0 0
RIPK2 0.01 0 -10000 0 -10000 0 0
IKBKG 0.024 0.021 -10000 0 -10000 0 0
IKK complex/A20 0.044 0.038 0.23 5 -10000 0 5
NEMO/A20/RIP2 0.01 0 -10000 0 -10000 0 0
XPO1 0.01 0 -10000 0 -10000 0 0
NEMO/ATM 0.029 0.02 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.01 0 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.014 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.025 0.012 -10000 0 -10000 0 0
BCL10/MALT1/TRAF6 0.02 0 -10000 0 -10000 0 0
NOD2 0.024 0.066 0.27 25 -0.29 2 27
NFKB1 0.011 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
MALT1 0.01 0 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.016 0.012 0.19 2 -10000 0 2
ATM 0.01 0 -10000 0 -10000 0 0
TNF/TNFR1A 0.024 0.039 0.19 21 -10000 0 21
TRAF6 0.01 0 -10000 0 -10000 0 0
PRKCA 0.006 0.033 -10000 0 -0.29 5 5
CHUK 0.01 0 -10000 0 -10000 0 0
UBE2D3 0.01 0 -10000 0 -10000 0 0
TNF 0.023 0.057 0.27 21 -10000 0 21
NF kappa B1 p50/RelA 0.026 0 -10000 0 -10000 0 0
BCL10 0.01 0 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.014 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -10000 0 -10000 0 0
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
IKK complex 0.034 0.019 -10000 0 -10000 0 0
CYLD 0.01 0 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.035 0.023 -10000 0 -10000 0 0
Circadian rhythm pathway

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
chromatin modification 0.027 0.018 -10000 0 -10000 0 0
CLOCK 0.011 0.002 -10000 0 -10000 0 0
TIMELESS/CRY2 0.022 0.02 -10000 0 -10000 0 0
DEC1/BMAL1 0.014 0.028 0.19 10 -10000 0 10
ATR 0.01 0 -10000 0 -10000 0 0
NR1D1 0.018 0.016 -10000 0 -10000 0 0
ARNTL 0.011 0.002 -10000 0 -10000 0 0
TIMELESS 0.019 0.027 -10000 0 -10000 0 0
NPAS2 0.01 0.021 -10000 0 -0.29 2 2
CRY2 0.01 0 -10000 0 -10000 0 0
mol:CO -0.007 0.009 -10000 0 -0.11 3 3
CHEK1 0.013 0.028 0.27 5 -10000 0 5
mol:HEME 0.007 0.009 0.11 3 -10000 0 3
PER1 -0.002 0.058 -10000 0 -0.29 16 16
BMAL/CLOCK/NPAS2 0.027 0.016 -10000 0 -0.15 2 2
BMAL1/CLOCK 0.022 0.026 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.027 0.018 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.027 0.018 -10000 0 -10000 0 0
mol:NADPH 0.007 0.009 0.11 3 -10000 0 3
PER1/TIMELESS 0.021 0.023 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.008 0.042 0.27 10 -10000 0 10
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.093 0.078 -10000 0 -0.25 10 10
CaM/Ca2+ 0.007 0 -10000 0 -10000 0 0
AKT1 0.01 0 -10000 0 -10000 0 0
AKT2 0.01 0 -10000 0 -10000 0 0
STXBP4 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.1 0.08 -10000 0 -0.27 10 10
YWHAZ 0.01 0 -10000 0 -10000 0 0
CALM1 0.01 0 -10000 0 -10000 0 0
YWHAQ 0.01 0 -10000 0 -10000 0 0
TBC1D4 0.009 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.01 0 -10000 0 -10000 0 0
YWHAB 0.01 0 -10000 0 -10000 0 0
SNARE/Synip 0.02 0 -10000 0 -10000 0 0
YWHAG 0.01 0 -10000 0 -10000 0 0
ASIP 0.009 0.026 0.27 4 -10000 0 4
PRKCI 0.01 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.007 0 -10000 0 -10000 0 0
RHOQ 0.01 0 -10000 0 -10000 0 0
GYS1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.008 0.025 -10000 0 -0.29 3 3
TRIP10 0.009 0.015 -10000 0 -0.29 1 1
TC10/GTP/CIP4/Exocyst 0.013 0.008 -10000 0 -0.16 1 1
AS160/14-3-3 0.023 0.026 -10000 0 -10000 0 0
VAMP2 0.01 0 -10000 0 -10000 0 0
SLC2A4 -0.11 0.087 -10000 0 -0.3 10 10
STX4 0.01 0 -10000 0 -10000 0 0
GSK3B 0.012 0 -10000 0 -10000 0 0
SFN 0.027 0.076 0.27 32 -0.29 4 36
LNPEP 0.01 0 -10000 0 -10000 0 0
YWHAE 0.009 0.015 -10000 0 -0.29 1 1
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.01 0 -10000 0 -10000 0 0
mol:PIP3 0 0.036 -10000 0 -0.22 11 11
FRAP1 0.005 0.006 -10000 0 -10000 0 0
AKT1 0.003 0.031 -10000 0 -0.18 11 11
INSR 0.01 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.007 0 -10000 0 -10000 0 0
mol:GTP 0.013 0.026 -10000 0 -0.15 10 10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.008 -10000 0 -10000 0 0
TSC2 0.01 0 -10000 0 -10000 0 0
RHEB/GDP 0.01 0.022 -10000 0 -0.12 11 11
TSC1 0.01 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.004 0.043 -10000 0 -0.27 10 10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.013 0.012 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.01 0 -10000 0 -10000 0 0
RPS6KB1 0.008 0.016 -10000 0 -10000 0 0
MAP3K5 0.004 0.014 -10000 0 -0.28 1 1
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
apoptosis 0.004 0.014 -10000 0 -0.28 1 1
mol:LY294002 0 0 -10000 0 -0.001 10 10
EIF4B 0.009 0.015 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.016 0.015 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0.009 0.004 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.01 0.041 -10000 0 -0.23 11 11
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.01 -10000 0 -10000 0 0
FKBP1A 0.01 0 -10000 0 -10000 0 0
RHEB/GTP 0.014 0.023 -10000 0 -0.13 10 10
mol:Amino Acids 0 0 -10000 0 -0.001 10 10
FKBP12/Rapamycin 0.007 0 -10000 0 -10000 0 0
PDPK1 0.001 0.034 -10000 0 -0.2 11 11
EIF4E 0.01 0 -10000 0 -10000 0 0
ASK1/PP5C 0.013 0.03 -10000 0 -0.58 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.008 0 -10000 0 -10000 0 0
TSC1/TSC2 0.014 0.028 -10000 0 -0.16 10 10
tumor necrosis factor receptor activity 0 0 0.001 10 -10000 0 10
RPS6 0.01 0 -10000 0 -10000 0 0
PPP5C 0.01 0 -10000 0 -10000 0 0
EIF4G1 0.01 0 -10000 0 -10000 0 0
IRS1 -0.003 0.045 -10000 0 -0.29 10 10
INS 0 0 -10000 0 -10000 0 0
PTEN 0.01 0 -10000 0 -10000 0 0
PDK2 0.001 0.034 -10000 0 -0.2 11 11
EIF4EBP1 0.02 0.05 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
PPP2R5D 0.006 0.006 -10000 0 -10000 0 0
peptide biosynthetic process 0.008 0 -10000 0 -10000 0 0
RHEB 0.01 0 -10000 0 -10000 0 0
EIF4A1 0.01 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.008 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.022 0.034 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.014 0.01 -10000 0 -0.19 1 1
FBXW11 0.01 0 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.014 0.019 0.19 2 -0.16 3 5
NF kappa B1 p50/RelA/I kappa B alpha 0.019 0.021 -10000 0 -10000 0 0
NFKBIA 0.009 0.023 -10000 0 -0.15 8 8
MAPK14 0.01 0 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.014 0 -10000 0 -10000 0 0
ARRB2 0.008 0 -10000 0 -10000 0 0
REL 0.009 0.031 0.27 2 -0.29 3 5
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.014 0.008 -10000 0 -0.16 1 1
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
NFKB1 0.009 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.012 0.024 -10000 0 -0.15 8 8
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.021 0.021 -10000 0 -10000 0 0
SRC 0.01 0 -10000 0 -10000 0 0
PI3K 0.014 0.01 -10000 0 -0.19 1 1
NF kappa B1 p50/RelA 0.012 0.024 -10000 0 -0.15 8 8
IKBKB 0.01 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.01 0 -10000 0 -10000 0 0
SYK 0.007 0.029 -10000 0 -0.29 4 4
I kappa B alpha/PIK3R1 0.014 0.025 -10000 0 -0.16 8 8
cell death 0.02 0.02 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.014 0.019 0.19 2 -0.16 3 5
LCK 0.008 0.035 0.27 2 -0.29 4 6
BCL3 0.009 0.015 -10000 0 -0.29 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.035 0.033 0.18 21 -10000 0 21
Ran/GTP/Exportin 1/HDAC1 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.029 0.02 -10000 0 -10000 0 0
SUMO1 0.01 0 -10000 0 -10000 0 0
ZFPM1 0.01 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.009 0 -10000 0 -10000 0 0
FKBP3 0.01 0 -10000 0 -10000 0 0
Histones 0.031 0.011 -10000 0 -10000 0 0
YY1/LSF 0.016 0.009 -10000 0 -0.17 1 1
SMG5 0.01 0 -10000 0 -10000 0 0
RAN 0.01 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.02 0.019 -10000 0 -10000 0 0
I kappa B alpha/HDAC1 0.021 0.012 -10000 0 -10000 0 0
SAP18 0.01 0 -10000 0 -10000 0 0
RELA 0.021 0.018 -10000 0 -10000 0 0
HDAC1/Smad7 0.02 0.009 -10000 0 -0.16 1 1
RANGAP1 0.01 0 -10000 0 -10000 0 0
HDAC3/TR2 0.021 0.012 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.021 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.024 0.015 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.013 0.06 0.27 13 -0.29 7 20
GATA1 0.007 0.005 -10000 0 -10000 0 0
Mad/Max 0.015 0.009 0.19 1 -10000 0 1
NuRD/MBD3 Complex/GATA1/Fog1 0.025 0.001 -10000 0 -10000 0 0
RBBP7 0.01 0 -10000 0 -10000 0 0
NPC 0.006 0 -10000 0 -10000 0 0
RBBP4 0.01 0 -10000 0 -10000 0 0
MAX 0.01 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.01 0 -10000 0 -10000 0 0
NFKBIA 0.017 0.015 -10000 0 -10000 0 0
KAT2B 0.009 0.015 -10000 0 -0.29 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.019 0 -10000 0 -10000 0 0
SIN3 complex 0.026 0 -10000 0 -10000 0 0
SMURF1 0.01 0 -10000 0 -10000 0 0
CHD3 0.01 0 -10000 0 -10000 0 0
SAP30 0.01 0 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.01 0 -10000 0 -10000 0 0
YY1/HDAC3 0.023 0.015 -10000 0 -10000 0 0
YY1/HDAC2 0.016 0.009 -10000 0 -0.17 1 1
YY1/HDAC1 0.016 0.009 -10000 0 -0.17 1 1
NuRD/MBD2 Complex (MeCP1) 0.021 0 -10000 0 -10000 0 0
PPARG 0.01 0.053 -10000 0 -0.22 18 18
HDAC8/hEST1B 0.02 0 -10000 0 -10000 0 0
UBE2I 0.01 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.01 0 -10000 0 -10000 0 0
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.021 0.012 -10000 0 -10000 0 0
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.02 0.009 -10000 0 -0.16 1 1
CREBBP 0.01 0 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.023 0 -10000 0 -10000 0 0
HDAC1 0.01 0 -10000 0 -10000 0 0
HDAC3 0.017 0.015 -10000 0 -10000 0 0
HDAC2 0.01 0 -10000 0 -10000 0 0
YY1 0.013 0.011 -10000 0 -0.2 1 1
HDAC8 0.01 0 -10000 0 -10000 0 0
SMAD7 0.009 0.015 -10000 0 -0.29 1 1
NCOR2 0.01 0 -10000 0 -10000 0 0
MXD1 0.011 0.013 0.27 1 -10000 0 1
STAT3 0.012 0 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.01 0 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.022 0.009 -10000 0 -0.15 1 1
YY1/SAP30/HDAC1 0.022 0.009 -10000 0 -0.15 1 1
EP300 0.01 0 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.012 0 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.015 -10000 0 -10000 0 0
histone deacetylation 0.021 0 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.022 0.012 -10000 0 -10000 0 0
nuclear export -0.02 0 -10000 0 -10000 0 0
PRKACA 0.01 0 -10000 0 -10000 0 0
GATAD2B 0.01 0 -10000 0 -10000 0 0
GATAD2A 0.01 0 -10000 0 -10000 0 0
GATA2/HDAC3 0.024 0.038 0.19 13 -10000 0 13
GATA1/HDAC1 0.012 0.003 -10000 0 -10000 0 0
GATA1/HDAC3 0.019 0.013 -10000 0 -10000 0 0
CHD4 0.01 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.024 0.039 0.19 21 -10000 0 21
SIN3/HDAC complex/Mad/Max 0.021 0.003 -10000 0 -10000 0 0
NuRD Complex 0.025 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.03 0.01 -10000 0 -10000 0 0
SIN3B 0.01 0 -10000 0 -10000 0 0
MTA2 0.01 0 -10000 0 -10000 0 0
SIN3A 0.01 0 -10000 0 -10000 0 0
XPO1 0.01 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0.019 0 -10000 0 -10000 0 0
HDAC complex 0.026 0 -10000 0 -10000 0 0
GATA1/Fog1 0.012 0.003 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.02 0 -10000 0 -10000 0 0
TNF 0.023 0.057 0.27 21 -10000 0 21
negative regulation of cell growth 0.021 0.003 -10000 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.021 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.02 0 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.024 0.022 -10000 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.02 0 -10000 0 -10000 0 0
TFCP2 0.01 0 -10000 0 -10000 0 0
NR2C1 0.01 0 -10000 0 -10000 0 0
MBD3 0.01 0 -10000 0 -10000 0 0
MBD2 0.01 0 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.01 0 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -9999 0 0
MDM2/SUMO1 0.024 0.027 0.18 13 -9999 0 13
HDAC4 0.01 0 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -10000 0 -9999 0 0
SUMO1 0.01 0 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.008 0 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
XPO1 0.01 0 -10000 0 -9999 0 0
EntrezGene:23636 0 0 -10000 0 -9999 0 0
RAN 0.01 0 -10000 0 -9999 0 0
EntrezGene:8021 0 0 -10000 0 -9999 0 0
RANBP2 0.01 0 -10000 0 -9999 0 0
SUMO1/HDAC4 0.019 0 -10000 0 -9999 0 0
SUMO1/HDAC1 0.019 0 -10000 0 -9999 0 0
RANGAP1 0.01 0 -10000 0 -9999 0 0
MDM2/SUMO1/SUMO1 0.03 0.026 0.18 13 -9999 0 13
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.009 0 -10000 0 -9999 0 0
Ran/GTP 0.014 0 -10000 0 -9999 0 0
EntrezGene:23225 0 0 -10000 0 -9999 0 0
MDM2 0.018 0.045 0.27 13 -9999 0 13
UBE2I 0.01 0 -10000 0 -9999 0 0
Ran/GTP/Exportin 1 0.016 0 -10000 0 -9999 0 0
NPC 0.006 0 -10000 0 -9999 0 0
PIAS2 0.01 0 -10000 0 -9999 0 0
PIAS1 0.01 0 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 0 -9999 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.018 0.005 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.011 0.005 -10000 0 -10000 0 0
mol:DAG 0.018 0.019 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.017 0.005 -10000 0 -10000 0 0
CaM/Ca2+ 0.023 0.017 -10000 0 -10000 0 0
HIF1A 0.015 0.013 0.27 1 -10000 0 1
GAB1 0.01 0 -10000 0 -10000 0 0
AKT1 0.021 0.016 -10000 0 -10000 0 0
PLCG1 0.018 0.019 -10000 0 -10000 0 0
NOS3 0.025 0.015 -10000 0 -10000 0 0
CBL 0.01 0 -10000 0 -10000 0 0
mol:NO 0.025 0.015 -10000 0 -10000 0 0
FLT1 0.015 0.007 -10000 0 -10000 0 0
PGF 0.018 0.045 0.27 13 -10000 0 13
VEGFR1 homodimer/NRP2/VEGFR121 0.016 0.034 -10000 0 -10000 0 0
CALM1 0.01 0 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
eNOS/Hsp90 0.03 0.014 -10000 0 -10000 0 0
endothelial cell proliferation -0.02 0.065 -10000 0 -0.23 3 3
mol:Ca2+ 0.018 0.019 -10000 0 -10000 0 0
MAPK3 0.016 0.013 -10000 0 -10000 0 0
MAPK1 0.016 0.013 -10000 0 -10000 0 0
PIK3R1 0.009 0.015 -10000 0 -0.29 1 1
PLGF homodimer 0.018 0.045 0.27 13 -10000 0 13
PRKACA 0.01 0 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.004 0.063 -10000 0 -0.29 19 19
VEGFA homodimer 0.01 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.018 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.016 0.012 -10000 0 -10000 0 0
PI3K 0.033 0.028 -10000 0 -10000 0 0
PRKCA 0.016 0.015 -10000 0 -10000 0 0
PRKCB 0.012 0.014 -10000 0 -10000 0 0
VEGFR1 homodimer/PLGF homodimer 0.024 0.032 0.2 13 -10000 0 13
VEGFA 0.01 0 -10000 0 -10000 0 0
VEGFB 0.01 0 -10000 0 -10000 0 0
mol:IP3 0.018 0.019 -10000 0 -10000 0 0
RASA1 0.015 0.004 -10000 0 -10000 0 0
NRP2 -0.004 0.063 -10000 0 -0.29 19 19
VEGFR1 homodimer 0.015 0.007 -10000 0 -10000 0 0
VEGFB homodimer 0.01 0 -10000 0 -10000 0 0
NCK1 0.01 0 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.028 0.015 -10000 0 -10000 0 0
PTPN11 0.01 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.032 0.027 -10000 0 -10000 0 0
mol:L-citrulline 0.025 0.015 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.029 0.005 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.023 0.005 -10000 0 -10000 0 0
CD2AP 0.01 0 -10000 0 -10000 0 0
PI3K/GAB1 0.036 0.026 -10000 0 -10000 0 0
PDPK1 0.019 0.015 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.023 0.005 -10000 0 -10000 0 0
mol:NADP 0.025 0.015 -10000 0 -10000 0 0
HSP90AA1 0.01 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.028 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.01 0.037 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.01 0 -10000 0 -10000 0 0
SMAD2 0.005 0 -10000 0 -10000 0 0
SMAD3 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4 0.024 0.011 -10000 0 -10000 0 0
SMAD4/Ubc9/PIASy 0.02 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.027 0.013 -10000 0 -10000 0 0
PPM1A 0.01 0 -10000 0 -10000 0 0
CALM1 0.01 0 -10000 0 -10000 0 0
SMAD2/SMAD4 0.011 0 -10000 0 -10000 0 0
MAP3K1 0.01 0 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.012 0.023 -10000 0 -0.19 5 5
MAPK3 0.01 0 -10000 0 -10000 0 0
MAPK1 0.01 0 -10000 0 -10000 0 0
NUP214 0.01 0 -10000 0 -10000 0 0
CTDSP1 0.01 0 -10000 0 -10000 0 0
CTDSP2 0.01 0 -10000 0 -10000 0 0
CTDSPL 0.01 0 -10000 0 -10000 0 0
KPNB1 0.01 0 -10000 0 -10000 0 0
TGFBRAP1 0.006 0.033 -10000 0 -0.29 5 5
UBE2I 0.01 0 -10000 0 -10000 0 0
NUP153 0.01 0 -10000 0 -10000 0 0
KPNA2 0.012 0.026 0.27 4 -10000 0 4
PIAS4 0.01 0 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.017 0.003 -10000 0 -10000 0 0
regulation of axonogenesis -0.012 0.001 -10000 0 -10000 0 0
myoblast fusion -0.011 0.006 -10000 0 -10000 0 0
mol:GTP 0.008 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.016 0.15 3 -0.18 1 4
ARF1/GTP 0.014 0.002 -10000 0 -10000 0 0
mol:GM1 0.006 0.002 -10000 0 -10000 0 0
mol:Choline 0.011 0.002 -10000 0 -10000 0 0
lamellipodium assembly 0.012 0.005 -10000 0 -10000 0 0
MAPK3 0.014 0.002 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.022 0.017 0.18 1 -0.15 3 4
ARF1 0.01 0 -10000 0 -10000 0 0
ARF6/GDP 0.011 0.006 -10000 0 -10000 0 0
ARF1/GDP 0.015 0.007 -10000 0 -10000 0 0
ARF6 0.011 0.002 -10000 0 -10000 0 0
RAB11A 0.01 0 -10000 0 -10000 0 0
TIAM1 0.008 0.026 -10000 0 -0.29 3 3
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.014 0.002 -10000 0 -10000 0 0
actin filament bundle formation -0.015 0.005 -10000 0 -10000 0 0
KALRN 0.011 0.009 0.099 4 -10000 0 4
RAB11FIP3/RAB11A 0.015 0 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.006 -10000 0 -10000 0 0
NME1 0.011 0.013 0.27 1 -10000 0 1
Rac1/GDP 0.015 0.006 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.008 0.003 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.012 0.005 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
liver development 0.008 0.003 -10000 0 -10000 0 0
ARF6/GTP 0.008 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.014 0.002 -10000 0 -10000 0 0
mol:GDP 0.011 0.005 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.02 0.001 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
PLD1 0.011 0.002 -10000 0 -10000 0 0
RAB11FIP3 0.01 0 -10000 0 -10000 0 0
tube morphogenesis 0.012 0.005 -10000 0 -10000 0 0
ruffle organization 0.012 0.001 -10000 0 -10000 0 0
regulation of epithelial cell migration 0.008 0.003 -10000 0 -10000 0 0
PLD2 0.011 0.002 -10000 0 -10000 0 0
PIP5K1A 0.012 0.001 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.011 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.005 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.008 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.009 0 -9999 0 -10000 0 0
AP2 0.015 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.014 0 -9999 0 -10000 0 0
CLTB 0.01 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.012 0 -9999 0 -10000 0 0
CD4 0.008 0.021 -9999 0 -0.29 2 2
CLTA 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
ARFGAP1 0.005 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.005 0 -9999 0 -10000 0 0
ARF1/GTP 0.012 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.01 0 -9999 0 -10000 0 0
mol:Choline 0.005 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.01 0 -9999 0 -10000 0 0
DDEF1 0.005 0 -9999 0 -10000 0 0
ARF1/GDP 0.004 0 -9999 0 -10000 0 0
AP2M1 0.01 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.008 0 -9999 0 -10000 0 0
Rac/GTP 0.008 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.016 0 -9999 0 -10000 0 0
ARFIP2 0.009 0 -9999 0 -10000 0 0
COPA 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.007 0 -9999 0 -10000 0 0
GGA3 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.011 0 -9999 0 -10000 0 0
AP2A1 0.01 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.011 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0.013 0 -9999 0 -10000 0 0
CYTH2 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.014 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.007 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.015 0.012 -9999 0 -0.15 2 2
PLD2 0.005 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.005 0 -9999 0 -10000 0 0
PIP5K1A 0.005 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.012 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.005 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.005 0 -9999 0 -10000 0 0
GOSR2 0.007 0 -9999 0 -10000 0 0
USO1 0.007 0 -9999 0 -10000 0 0
GBF1 0.007 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0.015 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.019 0.012 -9999 0 -0.16 2 2
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.015 0 -9999 0 -9999 0 0
FBXW11 0.01 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.01 0 -9999 0 -9999 0 0
CHUK 0.01 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.03 0 -9999 0 -9999 0 0
NFKB1 0.01 0 -9999 0 -9999 0 0
MAP3K14 0.01 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.015 0 -9999 0 -9999 0 0
RELB 0.01 0 -9999 0 -9999 0 0
NFKB2 0.01 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.014 0 -9999 0 -9999 0 0
regulation of B cell activation 0.013 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 408 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.ZF.AA5P TCGA.ZF.AA5N TCGA.ZF.AA5H TCGA.ZF.AA58
109_MAP3K5 0.022 -0.12 0.096 0.022
47_PPARGC1A 0.0099 0 -0.29 -0.29
105_BMP4 0.0099 0.0099 0.0099 0.0099
105_BMP6 0.0099 0.0099 0.0099 0.0099
105_BMP7 0.0099 0.0099 -0.29 -0.29
105_BMP2 0.0099 0.0099 0.0099 0.0099
131_RELN/VLDLR 0.026 0.019 0.026 -0.14
30_TGFB1/TGF beta receptor Type II -0.007 -0.0065 -0.0073 0.0096
84_STAT5B 0.011 -0.11 0.02 0.0092
84_STAT5A 0.011 -0.11 0.02 0.0092
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BLCA-TP/19437945/BLCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.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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