PARADIGM pathway analysis of mRNASeq expression and copy number data
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1NS0S9F
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1NS0S9F
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 36 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
IL4-mediated signaling events 110
HIF-1-alpha transcription factor network 101
Syndecan-1-mediated signaling events 70
TCGA08_retinoblastoma 63
Glypican 2 network 50
amb2 Integrin signaling 48
Endothelins 47
Syndecan-2-mediated signaling events 45
Syndecan-4-mediated signaling events 45
Osteopontin-mediated events 39
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 424 . 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 ( 424 ).

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
IL4-mediated signaling events 0.2594 110 10017 91 -1.3 1 1000 -1000 -0.13 -1000
HIF-1-alpha transcription factor network 0.2382 101 7697 76 -0.69 0.039 1000 -1000 -0.14 -1000
Syndecan-1-mediated signaling events 0.1651 70 2391 34 -0.32 0.028 1000 -1000 -0.043 -1000
TCGA08_retinoblastoma 0.1486 63 505 8 -0.14 0.086 1000 -1000 -0.005 -1000
Glypican 2 network 0.1179 50 203 4 -0.035 -0.015 1000 -1000 0.001 -1000
amb2 Integrin signaling 0.1132 48 3941 82 -0.27 0.035 1000 -1000 -0.041 -1000
Endothelins 0.1108 47 4517 96 -0.24 0.027 1000 -1000 -0.08 -1000
Syndecan-2-mediated signaling events 0.1061 45 3113 69 -0.2 0.038 1000 -1000 -0.047 -1000
Syndecan-4-mediated signaling events 0.1061 45 3051 67 -0.3 0.046 1000 -1000 -0.056 -1000
Osteopontin-mediated events 0.0920 39 1487 38 -0.2 0.033 1000 -1000 -0.047 -1000
Signaling events regulated by Ret tyrosine kinase 0.0920 39 3225 82 -0.084 0.028 1000 -1000 -0.067 -1000
IL23-mediated signaling events 0.0873 37 2242 60 -0.54 0.028 1000 -1000 -0.14 -1000
TCGA08_p53 0.0849 36 258 7 -0.1 0.061 1000 -1000 -0.008 -1000
Nongenotropic Androgen signaling 0.0778 33 1746 52 -0.11 0.071 1000 -1000 -0.043 -1000
p75(NTR)-mediated signaling 0.0755 32 4040 125 -0.25 0.073 1000 -1000 -0.07 -1000
Calcium signaling in the CD4+ TCR pathway 0.0755 32 997 31 -0.3 0.028 1000 -1000 -0.051 -1000
Visual signal transduction: Rods 0.0755 32 1667 52 -0.22 0.039 1000 -1000 -0.047 -1000
BMP receptor signaling 0.0731 31 2547 81 -0.2 0.049 1000 -1000 -0.06 -1000
Effects of Botulinum toxin 0.0731 31 821 26 -0.12 0.028 1000 -1000 -0.018 -1000
Coregulation of Androgen receptor activity 0.0708 30 2299 76 -0.46 0.067 1000 -1000 -0.026 -1000
TCR signaling in naïve CD8+ T cells 0.0708 30 2802 93 -0.21 0.11 1000 -1000 -0.064 -1000
FOXA2 and FOXA3 transcription factor networks 0.0684 29 1342 46 -0.46 0.033 1000 -1000 -0.13 -1000
Glypican 1 network 0.0660 28 1355 48 -0.28 0.048 1000 -1000 -0.038 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0660 28 2231 78 -0.12 0.035 1000 -1000 -0.062 -1000
Canonical Wnt signaling pathway 0.0637 27 1383 51 -0.2 0.15 1000 -1000 -0.057 -1000
Reelin signaling pathway 0.0590 25 1425 56 -0.18 0.069 1000 -1000 -0.059 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0590 25 3104 120 -0.17 0.075 1000 -1000 -0.057 -1000
LPA4-mediated signaling events 0.0566 24 296 12 -0.087 0.008 1000 -1000 -0.025 -1000
Thromboxane A2 receptor signaling 0.0566 24 2594 105 -0.08 0.033 1000 -1000 -0.053 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0566 24 1669 68 -0.32 0.037 1000 -1000 -0.1 -1000
IGF1 pathway 0.0566 24 1401 57 -0.044 0.055 1000 -1000 -0.05 -1000
Presenilin action in Notch and Wnt signaling 0.0542 23 1427 61 -0.2 0.074 1000 -1000 -0.054 -1000
PDGFR-beta signaling pathway 0.0542 23 2313 97 -0.069 0.054 1000 -1000 -0.06 -1000
Visual signal transduction: Cones 0.0519 22 847 38 -0.065 0.051 1000 -1000 -0.019 -1000
Fc-epsilon receptor I signaling in mast cells 0.0519 22 2208 97 -0.14 0.033 1000 -1000 -0.071 -1000
EGFR-dependent Endothelin signaling events 0.0519 22 470 21 -0.062 0.041 1000 -1000 -0.049 -1000
LPA receptor mediated events 0.0472 20 2085 102 -0.27 0.028 1000 -1000 -0.066 -1000
IL12-mediated signaling events 0.0448 19 1732 87 -0.18 0.039 1000 -1000 -0.097 -1000
Signaling events mediated by the Hedgehog family 0.0448 19 1023 52 -0.22 0.029 1000 -1000 -0.05 -1000
Arf6 signaling events 0.0448 19 1234 62 -0.12 0.055 1000 -1000 -0.047 -1000
Signaling events mediated by PTP1B 0.0448 19 1458 76 -0.096 0.046 1000 -1000 -0.057 -1000
Glucocorticoid receptor regulatory network 0.0448 19 2166 114 -0.34 0.17 1000 -1000 -0.061 -1000
Signaling mediated by p38-gamma and p38-delta 0.0448 19 290 15 -0.13 0.027 1000 -1000 -0.039 -1000
Integrins in angiogenesis 0.0448 19 1622 84 -0.18 0.057 1000 -1000 -0.052 -1000
Regulation of Androgen receptor activity 0.0448 19 1334 70 -0.5 0.036 1000 -1000 -0.06 -1000
ErbB2/ErbB3 signaling events 0.0425 18 1171 65 -0.25 0.04 1000 -1000 -0.054 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0425 18 1013 54 -0.14 0.038 1000 -1000 -0.054 -1000
IL1-mediated signaling events 0.0425 18 1126 62 -0.13 0.05 1000 -1000 -0.053 -1000
EPHB forward signaling 0.0425 18 1548 85 -0.17 0.094 1000 -1000 -0.068 -1000
Caspase cascade in apoptosis 0.0401 17 1261 74 -0.088 0.056 1000 -1000 -0.043 -1000
ErbB4 signaling events 0.0401 17 1238 69 -0.25 0.04 1000 -1000 -0.051 -1000
Ephrin B reverse signaling 0.0401 17 818 48 -0.056 0.033 1000 -1000 -0.036 -1000
BCR signaling pathway 0.0401 17 1758 99 -0.061 0.05 1000 -1000 -0.07 -1000
Plasma membrane estrogen receptor signaling 0.0401 17 1546 86 -0.12 0.047 1000 -1000 -0.067 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0401 17 1526 88 -0.18 0.045 1000 -1000 -0.081 -1000
Ephrin A reverse signaling 0.0377 16 115 7 -0.01 0.016 1000 -1000 -0.017 -1000
Signaling mediated by p38-alpha and p38-beta 0.0354 15 669 44 -0.13 0.028 1000 -1000 -0.039 -1000
IL27-mediated signaling events 0.0354 15 785 51 -0.097 0.046 1000 -1000 -0.053 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0354 15 518 33 -0.14 0.063 1000 -1000 -0.037 -1000
Signaling events mediated by HDAC Class III 0.0330 14 576 40 -0.13 0.051 1000 -1000 -0.021 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0330 14 737 52 -0.14 0.046 1000 -1000 -0.049 -1000
Wnt signaling 0.0330 14 103 7 -0.019 0.024 1000 -1000 -0.027 -1000
Regulation of nuclear SMAD2/3 signaling 0.0307 13 1829 136 -0.35 0.17 1000 -1000 -0.055 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0307 13 475 34 -0.024 0.037 1000 -1000 -0.038 -1000
PDGFR-alpha signaling pathway 0.0307 13 581 44 -0.12 0.06 1000 -1000 -0.041 -1000
Syndecan-3-mediated signaling events 0.0307 13 475 35 -0.15 0.073 1000 -1000 -0.029 -1000
mTOR signaling pathway 0.0283 12 642 53 -0.025 0.062 1000 -1000 -0.044 -1000
Ceramide signaling pathway 0.0283 12 966 76 -0.062 0.072 1000 -1000 -0.045 -1000
S1P1 pathway 0.0259 11 410 36 -0.062 0.026 1000 -1000 -0.057 -1000
Noncanonical Wnt signaling pathway 0.0236 10 265 26 -0.046 0.027 1000 -1000 -0.056 -1000
Cellular roles of Anthrax toxin 0.0236 10 414 39 -0.026 0.028 1000 -1000 -0.024 -1000
S1P3 pathway 0.0236 10 453 42 -0.062 0.046 1000 -1000 -0.044 -1000
Signaling events mediated by PRL 0.0236 10 362 34 -0.06 0.043 1000 -1000 -0.05 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0212 9 791 85 -0.099 0.069 1000 -1000 -0.06 -1000
EPO signaling pathway 0.0212 9 513 55 -0.011 0.052 1000 -1000 -0.051 -1000
IFN-gamma pathway 0.0212 9 663 68 -0.12 0.039 1000 -1000 -0.07 -1000
FAS signaling pathway (CD95) 0.0212 9 459 47 -0.07 0.043 1000 -1000 -0.039 -1000
Retinoic acid receptors-mediated signaling 0.0212 9 525 58 -0.048 0.051 1000 -1000 -0.052 -1000
IL6-mediated signaling events 0.0212 9 681 75 -0.096 0.052 1000 -1000 -0.07 -1000
Rapid glucocorticoid signaling 0.0212 9 183 20 -0.027 0.035 1000 -1000 -0.009 -1000
Class IB PI3K non-lipid kinase events 0.0212 9 27 3 -0.018 0.018 1000 -1000 -0.003 -1000
BARD1 signaling events 0.0189 8 491 57 -0.035 0.052 1000 -1000 -0.05 -1000
PLK1 signaling events 0.0189 8 693 85 -0.047 0.066 1000 -1000 -0.04 -1000
Class I PI3K signaling events mediated by Akt 0.0189 8 569 68 -0.096 0.062 1000 -1000 -0.045 -1000
Nectin adhesion pathway 0.0189 8 515 63 -0.062 0.063 1000 -1000 -0.07 -1000
IL2 signaling events mediated by PI3K 0.0189 8 505 58 -0.098 0.082 1000 -1000 -0.054 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0189 8 390 45 -0.024 0.053 1000 -1000 -0.057 -1000
Regulation of p38-alpha and p38-beta 0.0189 8 470 54 -0.039 0.06 1000 -1000 -0.056 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0189 8 659 74 -0.29 0.059 1000 -1000 -0.072 -1000
p38 MAPK signaling pathway 0.0189 8 385 44 -0.094 0.056 1000 -1000 -0.038 -1000
Circadian rhythm pathway 0.0165 7 158 22 -0.057 0.059 1000 -1000 -0.047 -1000
JNK signaling in the CD4+ TCR pathway 0.0165 7 134 17 0.007 0.052 1000 -1000 -0.04 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0165 7 271 37 -0.023 0.062 1000 -1000 -0.039 -1000
ceramide signaling pathway 0.0165 7 381 49 0 0.067 1000 -1000 -0.045 -1000
Regulation of Telomerase 0.0165 7 719 102 -0.075 0.06 1000 -1000 -0.066 -1000
Insulin Pathway 0.0165 7 571 74 -0.11 0.074 1000 -1000 -0.055 -1000
FOXM1 transcription factor network 0.0165 7 374 51 -0.14 0.14 1000 -1000 -0.16 -1000
Ras signaling in the CD4+ TCR pathway 0.0165 7 132 17 -0.001 0.044 1000 -1000 -0.034 -1000
TCGA08_rtk_signaling 0.0142 6 164 26 -0.062 0.087 1000 -1000 -0.023 -1000
VEGFR1 specific signals 0.0142 6 363 56 -0.044 0.052 1000 -1000 -0.057 -1000
Aurora B signaling 0.0142 6 457 67 -0.3 0.088 1000 -1000 -0.039 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0118 5 154 28 -0.048 0.05 1000 -1000 -0.031 -1000
a4b1 and a4b7 Integrin signaling 0.0118 5 28 5 0.02 0.034 1000 -1000 0.001 -1000
Hedgehog signaling events mediated by Gli proteins 0.0118 5 358 65 -0.026 0.066 1000 -1000 -0.056 -1000
IL2 signaling events mediated by STAT5 0.0118 5 119 22 -0.018 0.044 1000 -1000 -0.065 -1000
Arf6 trafficking events 0.0118 5 360 71 -0.18 0.049 1000 -1000 -0.036 -1000
S1P4 pathway 0.0118 5 137 25 0 0.037 1000 -1000 -0.037 -1000
HIF-2-alpha transcription factor network 0.0094 4 202 43 -0.099 0.044 1000 -1000 -0.083 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0094 4 543 125 -0.03 0.072 1000 -1000 -0.072 -1000
Class I PI3K signaling events 0.0094 4 323 73 -0.039 0.049 1000 -1000 -0.057 -1000
E-cadherin signaling in keratinocytes 0.0094 4 200 43 -0.039 0.061 1000 -1000 -0.044 -1000
Aurora A signaling 0.0071 3 211 60 -0.039 0.057 1000 -1000 -0.027 -1000
TRAIL signaling pathway 0.0071 3 184 48 0 0.069 1000 -1000 -0.04 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0071 3 316 83 -0.029 0.054 1000 -1000 -0.045 -1000
Signaling events mediated by HDAC Class I 0.0071 3 329 104 -0.079 0.066 1000 -1000 -0.045 -1000
FoxO family signaling 0.0071 3 233 64 -0.013 0.084 1000 -1000 -0.067 -1000
E-cadherin signaling in the nascent adherens junction 0.0071 3 244 76 -0.021 0.07 1000 -1000 -0.07 -1000
E-cadherin signaling events 0.0071 3 15 5 0.022 0.044 1000 -1000 -0.002 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0047 2 46 23 0.004 0.05 1000 -1000 -0.035 -1000
Canonical NF-kappaB pathway 0.0047 2 99 39 0 0.062 1000 -1000 -0.048 -1000
Aurora C signaling 0.0047 2 18 7 0 0.044 1000 -1000 -0.014 -1000
Insulin-mediated glucose transport 0.0047 2 94 32 -0.068 0.054 1000 -1000 -0.036 -1000
S1P5 pathway 0.0047 2 44 17 -0.023 0.033 1000 -1000 -0.025 -1000
Paxillin-dependent events mediated by a4b1 0.0047 2 99 36 -0.052 0.054 1000 -1000 -0.053 -1000
Signaling events mediated by HDAC Class II 0.0024 1 140 75 -0.034 0.07 1000 -1000 -0.033 -1000
Arf6 downstream pathway 0.0024 1 77 43 -0.04 0.043 1000 -1000 -0.043 -1000
Atypical NF-kappaB pathway 0.0024 1 60 31 0 0.036 1000 -1000 -0.029 -1000
PLK2 and PLK4 events 0.0000 0 2 3 0.013 0.027 1000 -1000 -0.024 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 15 27 0 0.061 1000 -1000 -0.041 -1000
Arf1 pathway 0.0000 0 39 54 -0.001 0.038 1000 -1000 -0.023 -1000
Alternative NF-kappaB pathway 0.0000 0 8 13 0 0.075 1000 -1000 0 -1000
Total NA 2227 136895 7203 -17 7.9 131000 -131000 -6.5 -131000
IL4-mediated signaling events

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
BCL2L1 -0.9 0.46 -10000 0 -1.2 246 246
STAT6 (cleaved dimer) -0.91 0.48 -10000 0 -1.2 273 273
IGHG1 -0.31 0.16 -10000 0 -0.52 65 65
IGHG3 -0.87 0.44 -10000 0 -1.1 271 271
AKT1 -0.38 0.2 -10000 0 -0.79 37 37
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.16 -10000 0 -0.71 22 22
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.38 0.21 -10000 0 -0.8 39 39
THY1 -0.94 0.47 -10000 0 -1.3 252 252
MYB -0.024 0.15 -10000 0 -0.46 44 44
HMGA1 0.027 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.46 0.21 -10000 0 -0.64 151 151
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.38 0.21 -10000 0 -0.81 38 38
SP1 -0.002 0.041 -10000 0 -10000 0 0
INPP5D 0.026 0.025 -10000 0 -0.47 1 1
SOCS5 0.049 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.9 0.47 -10000 0 -1.2 255 255
SOCS1 -0.58 0.26 -10000 0 -0.77 219 219
SOCS3 -0.39 0.18 -10000 0 -0.8 16 16
FCER2 -0.71 0.36 -10000 0 -0.99 214 214
PARP14 0.024 0.023 -10000 0 -0.39 1 1
CCL17 -0.93 0.48 -10000 0 -1.3 246 246
GRB2 0.028 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.32 0.18 -10000 0 -0.68 37 37
T cell proliferation -0.9 0.48 -10000 0 -1.2 250 250
IL4R/JAK1 -0.9 0.46 -10000 0 -1.2 254 254
EGR2 -0.92 0.46 -10000 0 -1.2 251 251
JAK2 -0.049 0.03 -10000 0 -10000 0 0
JAK3 0.023 0.069 -10000 0 -0.39 11 11
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
JAK1 -0.012 0.016 -10000 0 -10000 0 0
COL1A2 -0.36 0.21 -10000 0 -0.61 135 135
CCL26 -0.92 0.46 -10000 0 -1.2 253 253
IL4R -0.96 0.49 -10000 0 -1.3 250 250
PTPN6 0.046 0.014 -10000 0 -10000 0 0
IL13RA2 -0.93 0.48 -10000 0 -1.3 239 239
IL13RA1 -0.053 0.027 -10000 0 -10000 0 0
IRF4 -0.25 0.32 -10000 0 -0.91 63 63
ARG1 -0.47 0.51 -10000 0 -1.3 100 100
CBL -0.43 0.2 -10000 0 -0.61 132 132
GTF3A -0.02 0.04 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.061 0.04 -10000 0 -10000 0 0
IRF4/BCL6 -0.2 0.29 -10000 0 -0.82 60 60
CD40LG -0.035 0.16 -10000 0 -0.47 52 52
MAPK14 -0.43 0.2 -10000 0 -0.67 75 75
mitosis -0.36 0.19 -10000 0 -0.75 36 36
STAT6 -1.1 0.59 -10000 0 -1.4 266 266
SPI1 -0.009 0.07 -10000 0 -0.46 2 2
RPS6KB1 -0.35 0.18 -10000 0 -0.72 35 35
STAT6 (dimer) -1.1 0.59 -10000 0 -1.4 266 266
STAT6 (dimer)/PARP14 -0.96 0.53 -10000 0 -1.3 258 258
mast cell activation 0.02 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.37 0.22 -10000 0 -0.8 40 40
FRAP1 -0.38 0.2 -10000 0 -0.79 37 37
LTA -0.92 0.46 -10000 0 -1.3 237 237
FES 0.028 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 1 0.54 1.4 266 -10000 0 266
CCL11 -0.95 0.44 -10000 0 -1.2 266 266
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.35 0.19 -10000 0 -0.73 36 36
IL2RG 0.02 0.079 -10000 0 -0.4 14 14
IL10 -0.91 0.46 -10000 0 -1.2 234 234
IRS1 0.025 0.034 -10000 0 -0.47 2 2
IRS2 0.025 0.034 -10000 0 -0.47 2 2
IL4 -0.24 0.25 -10000 0 -1.2 26 26
IL5 -0.91 0.46 -10000 0 -1.3 232 232
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.71 0.35 -10000 0 -0.93 253 253
COL1A1 -0.48 0.26 -10000 0 -0.69 176 176
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.93 0.49 -10000 0 -1.3 245 245
IL2R gamma/JAK3 0.023 0.082 -10000 0 -0.3 23 23
TFF3 -1.1 0.6 -10000 0 -1.5 273 273
ALOX15 -0.98 0.51 -10000 0 -1.3 243 243
MYBL1 0.021 0.042 -10000 0 -0.39 4 4
T-helper 2 cell differentiation -0.8 0.4 -10000 0 -1 266 266
SHC1 0.028 0.004 -10000 0 -10000 0 0
CEBPB -0.005 0.061 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.36 0.2 -10000 0 -0.75 36 36
mol:PI-3-4-5-P3 -0.38 0.2 -10000 0 -0.79 37 37
PI3K -0.39 0.22 -10000 0 -0.86 37 37
DOK2 0.023 0.038 -10000 0 -0.42 3 3
ETS1 0.041 0.039 -10000 0 -0.38 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.3 0.16 -10000 0 -0.62 31 31
ITGB3 -0.92 0.47 -10000 0 -1.2 247 247
PIGR -1.3 0.62 -10000 0 -1.6 299 299
IGHE 0.049 0.054 0.2 13 -10000 0 13
MAPKKK cascade -0.29 0.15 -10000 0 -0.61 31 31
BCL6 0.02 0.013 -10000 0 -10000 0 0
OPRM1 -0.91 0.45 -10000 0 -1.3 231 231
RETNLB -0.9 0.47 -10000 0 -1.2 251 251
SELP -0.99 0.53 -10000 0 -1.3 257 257
AICDA -0.88 0.44 -10000 0 -1.2 248 248
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.57 0.39 -10000 0 -0.98 152 152
HDAC7 0.028 0.005 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.42 0.29 -10000 0 -0.78 85 85
SMAD4 0.026 0.009 -10000 0 -10000 0 0
ID2 -0.57 0.39 -10000 0 -0.98 153 153
AP1 -0.008 0.12 -10000 0 -0.34 53 53
ABCG2 -0.57 0.4 -10000 0 -0.98 153 153
HIF1A -0.088 0.064 -10000 0 -0.24 4 4
TFF3 -0.66 0.45 -10000 0 -1 200 200
GATA2 0.023 0.039 -10000 0 -0.42 3 3
AKT1 -0.091 0.071 -10000 0 -0.41 2 2
response to hypoxia -0.11 0.08 -10000 0 -0.31 24 24
MCL1 -0.57 0.39 -10000 0 -0.96 160 160
NDRG1 -0.54 0.39 -10000 0 -0.97 142 142
SERPINE1 -0.65 0.42 -10000 0 -1 183 183
FECH -0.57 0.39 -10000 0 -0.98 153 153
FURIN -0.57 0.39 -10000 0 -0.98 151 151
NCOA2 -0.001 0.11 -10000 0 -0.47 21 21
EP300 -0.092 0.088 -10000 0 -0.32 24 24
HMOX1 -0.57 0.4 -10000 0 -0.98 150 150
BHLHE40 -0.57 0.39 -10000 0 -0.97 158 158
BHLHE41 -0.57 0.4 -10000 0 -0.98 156 156
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.079 0.094 -10000 0 -0.34 2 2
ENG -0.074 0.088 0.33 5 -10000 0 5
JUN 0.028 0.007 -10000 0 -10000 0 0
RORA -0.57 0.4 -10000 0 -0.98 161 161
ABCB1 -0.17 0.3 -10000 0 -1.2 31 31
TFRC -0.54 0.39 -10000 0 -0.96 142 142
CXCR4 -0.57 0.4 -10000 0 -0.98 155 155
TF -0.68 0.45 -10000 0 -1 227 227
CITED2 -0.57 0.4 -10000 0 -0.98 152 152
HIF1A/ARNT -0.63 0.47 -10000 0 -1.1 162 162
LDHA -0.08 0.16 -10000 0 -0.8 18 18
ETS1 -0.57 0.39 -10000 0 -0.98 153 153
PGK1 -0.57 0.39 -10000 0 -0.98 151 151
NOS2 -0.6 0.41 -10000 0 -1 163 163
ITGB2 -0.57 0.4 -10000 0 -0.97 158 158
ALDOA -0.57 0.39 -10000 0 -0.97 154 154
Cbp/p300/CITED2 -0.56 0.4 -10000 0 -1 130 130
FOS -0.036 0.16 -10000 0 -0.47 53 53
HK2 -0.57 0.39 -10000 0 -0.98 151 151
SP1 0.027 0.029 -10000 0 -10000 0 0
GCK -0.15 0.15 -10000 0 -0.61 19 19
HK1 -0.57 0.39 -10000 0 -0.98 151 151
NPM1 -0.57 0.39 -10000 0 -0.95 166 166
EGLN1 -0.57 0.39 -10000 0 -0.98 150 150
CREB1 0.033 0.006 -10000 0 -10000 0 0
PGM1 -0.57 0.4 -10000 0 -0.98 152 152
SMAD3 0.028 0.005 -10000 0 -10000 0 0
EDN1 -0.089 0.15 -10000 0 -1.1 4 4
IGFBP1 -0.57 0.4 -10000 0 -0.97 160 160
VEGFA -0.36 0.25 -10000 0 -0.7 65 65
HIF1A/JAB1 -0.048 0.05 -10000 0 -10000 0 0
CP -0.62 0.44 -10000 0 -1 184 184
CXCL12 -0.59 0.42 -10000 0 -1 156 156
COPS5 0.024 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.014 -10000 0 -10000 0 0
BNIP3 -0.57 0.4 -10000 0 -0.98 153 153
EGLN3 -0.57 0.4 -10000 0 -0.99 155 155
CA9 -0.69 0.41 -10000 0 -1 207 207
TERT -0.58 0.4 -10000 0 -0.98 161 161
ENO1 -0.57 0.39 -10000 0 -0.97 157 157
PFKL -0.57 0.39 -10000 0 -0.96 165 165
NCOA1 0.028 0.005 -10000 0 -10000 0 0
ADM -0.57 0.4 -10000 0 -0.97 161 161
ARNT -0.098 0.07 -10000 0 -0.34 9 9
HNF4A -0.017 0.12 -10000 0 -0.39 38 38
ADFP -0.57 0.39 -10000 0 -0.95 172 172
SLC2A1 -0.37 0.25 -10000 0 -0.71 68 68
LEP -0.6 0.42 -10000 0 -0.99 173 173
HIF1A/ARNT/Cbp/p300 -0.43 0.3 -10000 0 -0.78 101 101
EPO -0.32 0.25 -10000 0 -0.79 48 48
CREBBP -0.09 0.085 -10000 0 -0.32 18 18
HIF1A/ARNT/Cbp/p300/HDAC7 -0.41 0.3 -10000 0 -0.8 78 78
PFKFB3 -0.57 0.39 -10000 0 -0.97 158 158
NT5E -0.6 0.41 -10000 0 -1 173 173
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.021 -10000 0 -0.39 1 1
CCL5 -0.032 0.15 -10000 0 -0.4 60 60
SDCBP 0.025 0.009 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.18 0.14 0.29 9 -0.35 92 101
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 -0.18 0.13 0.31 1 -0.34 93 94
Syndecan-1/Syntenin -0.16 0.13 0.32 3 -0.33 86 89
MAPK3 -0.16 0.12 0.25 9 -0.33 72 81
HGF/MET 0.023 0.075 -10000 0 -0.31 20 20
TGFB1/TGF beta receptor Type II 0.026 0.021 -10000 0 -0.39 1 1
BSG 0.027 0.005 -10000 0 -10000 0 0
keratinocyte migration -0.18 0.12 0.31 1 -0.34 93 94
Syndecan-1/RANTES -0.2 0.15 0.31 5 -0.36 137 142
Syndecan-1/CD147 -0.16 0.13 0.31 5 -0.33 85 90
Syndecan-1/Syntenin/PIP2 -0.16 0.13 0.29 3 -0.32 86 89
LAMA5 0.027 0.006 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.15 0.12 0.29 3 -0.32 86 89
MMP7 -0.048 0.16 -10000 0 -0.41 69 69
HGF 0.008 0.091 -10000 0 -0.44 16 16
Syndecan-1/CASK -0.18 0.12 -10000 0 -0.34 95 95
Syndecan-1/HGF/MET -0.17 0.14 0.31 4 -0.35 88 92
regulation of cell adhesion -0.16 0.12 0.28 5 -0.37 36 41
HPSE 0.022 0.048 -10000 0 -0.47 4 4
positive regulation of cell migration -0.18 0.14 0.29 9 -0.35 92 101
SDC1 -0.18 0.12 -10000 0 -0.35 89 89
Syndecan-1/Collagen -0.18 0.14 0.29 9 -0.35 92 101
PPIB 0.028 0.005 -10000 0 -10000 0 0
MET 0.023 0.043 -10000 0 -0.41 4 4
PRKACA 0.028 0.003 -10000 0 -10000 0 0
MMP9 -0.27 0.19 -10000 0 -0.39 293 293
MAPK1 -0.16 0.12 0.25 9 -0.32 75 84
homophilic cell adhesion -0.18 0.14 0.29 9 -0.35 94 103
MMP1 -0.32 0.16 -10000 0 -0.39 348 348
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B 0.011 0.072 -10000 0 -0.44 10 10
CDKN2C 0.021 0.071 -10000 0 -0.36 12 12
CDKN2A -0.14 0.2 -10000 0 -0.4 159 159
CCND2 0.041 0.064 0.18 44 -10000 0 44
RB1 -0.081 0.097 -10000 0 -0.24 93 93
CDK4 0.049 0.075 0.2 48 -10000 0 48
CDK6 0.046 0.072 0.21 40 -10000 0 40
G1/S progression 0.086 0.099 0.24 99 -10000 0 99
Glypican 2 network

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
MDK 0.017 0.066 -9999 0 -0.4 10 10
GPC2 -0.035 0.15 -9999 0 -0.39 61 61
GPC2/Midkine -0.015 0.12 -9999 0 -0.29 66 66
neuron projection morphogenesis -0.015 0.12 -9999 0 -0.29 66 66
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.027 0.14 -10000 0 -0.28 88 88
alphaM/beta2 Integrin/GPIbA 0.002 0.12 -10000 0 -0.3 44 44
alphaM/beta2 Integrin/proMMP-9 -0.18 0.16 -10000 0 -0.26 295 295
PLAUR 0.005 0.096 -10000 0 -0.39 23 23
HMGB1 0.019 0.027 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.01 0.1 -10000 0 -0.3 32 32
AGER 0.016 0.044 -10000 0 -0.4 3 3
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.028 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.014 0.13 -10000 0 -0.39 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.27 0.19 -10000 0 -0.39 293 293
CYR61 0.022 0.049 -10000 0 -0.42 5 5
TLN1 0.024 0.01 -10000 0 -10000 0 0
Rap1/GTP -0.081 0.12 -10000 0 -0.32 30 30
RHOA 0.024 0.01 -10000 0 -10000 0 0
P-selectin oligomer -0.06 0.19 -10000 0 -0.47 74 74
MYH2 -0.23 0.18 -10000 0 -0.4 188 188
MST1R 0.02 0.049 -10000 0 -0.47 4 4
leukocyte activation during inflammatory response 0.003 0.11 -10000 0 -0.33 20 20
APOB 0.002 0.082 -10000 0 -0.4 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.036 0.15 -10000 0 -0.39 63 63
JAM3 0.025 0.022 -10000 0 -0.39 1 1
GP1BA 0.006 0.086 -10000 0 -0.42 16 16
alphaM/beta2 Integrin/CTGF 0.009 0.11 -10000 0 -0.3 40 40
alphaM/beta2 Integrin -0.1 0.12 -10000 0 -0.28 88 88
JAM3 homodimer 0.025 0.022 -10000 0 -0.39 1 1
ICAM2 0.025 0.04 -10000 0 -0.44 3 3
ICAM1 0.007 0.092 -10000 0 -0.39 21 21
phagocytosis triggered by activation of immune response cell surface activating receptor -0.1 0.12 -10000 0 -0.28 85 85
cell adhesion 0.001 0.12 -10000 0 -0.3 44 44
NFKB1 -0.03 0.15 0.6 1 -0.39 43 44
THY1 -0.094 0.19 -10000 0 -0.39 120 120
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
Lipoprotein(a) 0.016 0.065 -10000 0 -0.23 26 26
alphaM/beta2 Integrin/LRP/tPA 0.022 0.11 -10000 0 -0.36 16 16
IL6 -0.065 0.22 -10000 0 -0.68 38 38
ITGB2 0.006 0.078 -10000 0 -0.4 13 13
elevation of cytosolic calcium ion concentration -0.099 0.17 -10000 0 -0.38 54 54
alphaM/beta2 Integrin/JAM2/JAM3 0.021 0.11 -10000 0 -0.29 36 36
JAM2 0.017 0.072 -10000 0 -0.47 9 9
alphaM/beta2 Integrin/ICAM1 0.018 0.12 -10000 0 -0.38 20 20
alphaM/beta2 Integrin/uPA/Plg -0.094 0.16 -10000 0 -0.34 44 44
RhoA/GTP -0.14 0.15 -10000 0 -0.35 101 101
positive regulation of phagocytosis -0.069 0.11 -10000 0 -0.35 23 23
Ron/MSP 0.03 0.05 -10000 0 -0.31 8 8
alphaM/beta2 Integrin/uPAR/uPA -0.099 0.17 -10000 0 -0.38 54 54
alphaM/beta2 Integrin/uPAR -0.001 0.13 -10000 0 -0.31 49 49
PLAU -0.16 0.21 -10000 0 -0.39 184 184
PLAT 0.016 0.064 -10000 0 -0.39 10 10
actin filament polymerization -0.23 0.17 0.23 1 -0.38 188 189
MST1 0.02 0.044 -10000 0 -0.42 4 4
alphaM/beta2 Integrin/lipoprotein(a) 0.007 0.11 -10000 0 -0.33 20 20
TNF -0.044 0.15 -10000 0 -0.62 12 12
RAP1B 0.027 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.1 0.16 -10000 0 -0.26 196 196
fibrinolysis -0.094 0.16 -10000 0 -0.34 45 45
HCK 0.023 0.04 -10000 0 -0.44 3 3
dendritic cell antigen processing and presentation -0.1 0.12 -10000 0 -0.28 85 85
VTN -0.002 0.11 -10000 0 -0.39 29 29
alphaM/beta2 Integrin/CYR61 0.01 0.11 -10000 0 -0.3 37 37
LPA -0.001 0.065 -10000 0 -0.39 10 10
LRP1 0.027 0.024 -10000 0 -0.47 1 1
cell migration -0.19 0.17 -10000 0 -0.4 105 105
FN1 -0.18 0.21 -10000 0 -0.39 203 203
alphaM/beta2 Integrin/Thy1 -0.063 0.16 -10000 0 -0.28 124 124
MPO 0.012 0.08 -10000 0 -0.45 12 12
KNG1 -0.012 0.065 -10000 0 -0.39 11 11
RAP1/GDP 0.035 0.01 -10000 0 -10000 0 0
ROCK1 -0.13 0.15 -10000 0 -0.35 82 82
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.015 0.041 -10000 0 -0.39 4 4
CTGF 0.02 0.062 -10000 0 -0.46 7 7
alphaM/beta2 Integrin/Hck 0.012 0.11 -10000 0 -0.31 31 31
ITGAM -0.011 0.11 -10000 0 -0.4 30 30
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.022 0.15 -10000 0 -0.29 85 85
HP -0.17 0.24 -10000 0 -0.46 164 164
leukocyte adhesion -0.052 0.15 -10000 0 -0.39 35 35
SELP -0.06 0.19 -10000 0 -0.47 74 74
Endothelins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.13 0.19 0.25 3 -0.43 57 60
PTK2B 0.026 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.052 0.17 -10000 0 -0.64 8 8
EDN1 -0.079 0.14 -10000 0 -0.29 49 49
EDN3 -0.18 0.23 -10000 0 -0.47 165 165
EDN2 -0.04 0.16 -10000 0 -0.44 61 61
HRAS/GDP -0.07 0.15 0.28 3 -0.44 23 26
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.062 0.13 -10000 0 -0.38 27 27
ADCY4 -0.13 0.16 0.27 5 -0.39 71 76
ADCY5 -0.18 0.18 0.25 1 -0.41 108 109
ADCY6 -0.13 0.17 0.26 6 -0.39 76 82
ADCY7 -0.13 0.17 0.26 6 -0.39 72 78
ADCY1 -0.13 0.17 0.28 4 -0.39 78 82
ADCY2 -0.19 0.18 0.26 2 -0.42 116 118
ADCY3 -0.13 0.17 0.25 7 -0.39 71 78
ADCY8 -0.12 0.16 0.29 3 -0.39 70 73
ADCY9 -0.13 0.17 0.24 5 -0.39 72 77
arachidonic acid secretion -0.098 0.19 0.25 3 -0.5 52 55
ETB receptor/Endothelin-1/Gq/GTP -0.06 0.12 -10000 0 -0.33 39 39
GNAO1 0.023 0.043 -10000 0 -0.41 4 4
HRAS 0.026 0.022 -10000 0 -0.4 1 1
ETA receptor/Endothelin-1/G12/GTP -0.059 0.23 0.32 7 -0.4 54 61
ETA receptor/Endothelin-1/Gs/GTP -0.091 0.22 0.32 4 -0.4 75 79
mol:GTP 0 0.004 -10000 0 -10000 0 0
COL3A1 -0.24 0.27 -10000 0 -0.49 187 187
EDNRB -0.015 0.062 -10000 0 -0.46 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.16 0.22 -10000 0 -0.53 68 68
CYSLTR1 -0.17 0.24 -10000 0 -0.54 80 80
SLC9A1 -0.057 0.12 -10000 0 -0.32 25 25
mol:GDP -0.079 0.16 0.28 3 -0.45 26 29
SLC9A3 -0.16 0.29 -10000 0 -0.66 86 86
RAF1 -0.1 0.17 0.25 3 -0.46 45 48
JUN -0.056 0.16 -10000 0 -0.68 9 9
JAK2 -0.13 0.19 0.25 3 -0.42 64 67
mol:IP3 -0.076 0.14 -10000 0 -0.41 36 36
ETA receptor/Endothelin-1 -0.1 0.28 0.4 5 -0.47 75 80
PLCB1 0.024 0.025 -10000 0 -0.47 1 1
PLCB2 0.024 0.033 -10000 0 -0.44 2 2
ETA receptor/Endothelin-3 -0.18 0.19 -10000 0 -0.39 168 168
FOS -0.15 0.32 -10000 0 -0.91 58 58
Gai/GDP -0.083 0.27 -10000 0 -0.71 63 63
CRK 0.027 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.14 0.18 -10000 0 -0.47 52 52
BCAR1 0.027 0.006 -10000 0 -10000 0 0
PRKCB1 -0.074 0.14 0.25 1 -0.39 35 36
GNAQ 0.027 0.009 -10000 0 -10000 0 0
GNAZ 0.011 0.083 -10000 0 -0.42 15 15
GNAL -0.027 0.15 -10000 0 -0.47 45 45
Gs family/GDP -0.09 0.16 0.25 1 -0.46 28 29
ETA receptor/Endothelin-1/Gq/GTP -0.077 0.14 -10000 0 -0.38 44 44
MAPK14 -0.043 0.099 -10000 0 -0.4 11 11
TRPC6 -0.054 0.18 -10000 0 -0.67 8 8
GNAI2 0.024 0.01 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.025 -10000 0 -0.47 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.046 0.11 -10000 0 -0.37 19 19
ETB receptor/Endothelin-2 -0.045 0.12 -10000 0 -0.32 64 64
ETB receptor/Endothelin-3 -0.13 0.17 -10000 0 -0.35 162 162
ETB receptor/Endothelin-1 -0.062 0.14 -10000 0 -0.26 57 57
MAPK3 -0.14 0.28 -10000 0 -0.75 61 61
MAPK1 -0.14 0.28 -10000 0 -0.75 62 62
Rac1/GDP -0.068 0.15 0.28 2 -0.44 18 20
cAMP biosynthetic process -0.15 0.17 0.28 6 -0.43 60 66
MAPK8 -0.067 0.19 -10000 0 -0.68 17 17
SRC 0.026 0.007 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.026 0.089 -10000 0 -0.32 19 19
p130Cas/CRK/Src/PYK2 -0.076 0.16 0.26 2 -0.5 16 18
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.069 0.15 0.28 2 -0.44 19 21
COL1A2 -0.18 0.25 -10000 0 -0.46 156 156
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.09 0.16 -10000 0 -0.37 64 64
mol:DAG -0.077 0.14 -10000 0 -0.41 36 36
MAP2K2 -0.12 0.21 0.27 3 -0.56 62 65
MAP2K1 -0.12 0.21 0.26 2 -0.56 62 64
EDNRA -0.079 0.15 -10000 0 -0.34 26 26
positive regulation of muscle contraction -0.098 0.17 0.27 9 -0.39 48 57
Gq family/GDP -0.057 0.17 -10000 0 -0.45 27 27
HRAS/GTP -0.09 0.15 0.25 3 -0.43 35 38
PRKCH -0.067 0.14 0.24 4 -0.4 31 35
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA -0.074 0.14 0.25 2 -0.4 30 32
PRKCB -0.078 0.14 0.25 1 -0.4 36 37
PRKCE -0.072 0.13 0.25 1 -0.39 32 33
PRKCD -0.07 0.13 -10000 0 -0.4 28 28
PRKCG -0.095 0.15 0.25 1 -0.41 41 42
regulation of vascular smooth muscle contraction -0.18 0.37 -10000 0 -1.1 58 58
PRKCQ -0.078 0.14 0.28 2 -0.44 26 28
PLA2G4A -0.11 0.21 0.26 2 -0.54 52 54
GNA14 -0.049 0.18 -10000 0 -0.47 64 64
GNA15 0.024 0.035 -10000 0 -0.47 2 2
GNA12 0.025 0.022 -10000 0 -0.39 1 1
GNA11 0.024 0.035 -10000 0 -0.47 2 2
Rac1/GTP -0.059 0.23 0.34 5 -0.4 53 58
MMP1 -0.23 0.2 0.46 18 -0.33 247 265
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.089 0.14 -10000 0 -0.24 180 180
EPHB2 -0.057 0.17 -10000 0 -0.39 84 84
Syndecan-2/TACI -0.009 0.088 -10000 0 -0.23 56 56
LAMA1 -0.12 0.2 -10000 0 -0.4 149 149
Syndecan-2/alpha2 ITGB1 -0.014 0.12 -10000 0 -0.4 4 4
HRAS 0.026 0.022 -10000 0 -0.4 1 1
Syndecan-2/CASK 0.001 0.043 -10000 0 -0.22 15 15
ITGA5 -0.11 0.2 -10000 0 -0.39 134 134
BAX 0 0.048 -10000 0 -0.43 1 1
EPB41 0.028 0.004 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.017 0.042 -10000 0 -0.2 14 14
LAMA3 -0.09 0.19 -10000 0 -0.39 116 116
EZR 0.028 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.025 0.035 -10000 0 -0.47 2 2
Syndecan-2/MMP2 -0.018 0.1 -10000 0 -0.26 64 64
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.038 0.021 -10000 0 -0.34 1 1
dendrite morphogenesis -0.024 0.1 -10000 0 -0.23 81 81
Syndecan-2/GM-CSF -0.1 0.13 -10000 0 -0.24 205 205
determination of left/right symmetry 0.002 0.052 -10000 0 -0.27 15 15
Syndecan-2/PKC delta 0.015 0.047 -10000 0 -0.22 15 15
GNB2L1 0.026 0.007 -10000 0 -10000 0 0
MAPK3 -0.087 0.13 0.19 22 -0.3 19 41
MAPK1 -0.085 0.13 0.19 21 -0.21 197 218
Syndecan-2/RACK1 0.027 0.047 -10000 0 -0.19 16 16
NF1 0.028 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.002 0.052 -10000 0 -0.27 15 15
ITGA2 0.026 0.025 -10000 0 -0.47 1 1
MAPK8 0.001 0.052 -10000 0 -0.34 3 3
Syndecan-2/alpha2/beta1 Integrin -0.036 0.12 -10000 0 -0.37 8 8
Syndecan-2/Kininogen 0.006 0.055 -10000 0 -0.25 16 16
ITGB1 0.028 0.005 -10000 0 -10000 0 0
SRC 0.027 0.065 0.18 38 -10000 0 38
Syndecan-2/CASK/Protein 4.1 0.016 0.043 -10000 0 -0.2 15 15
extracellular matrix organization 0.017 0.051 -10000 0 -0.24 15 15
actin cytoskeleton reorganization -0.088 0.14 -10000 0 -0.24 180 180
Syndecan-2/Caveolin-2/Ras 0.028 0.054 -10000 0 -0.22 15 15
Syndecan-2/Laminin alpha3 -0.041 0.12 -10000 0 -0.23 109 109
Syndecan-2/RasGAP 0.038 0.054 -10000 0 -0.41 1 1
alpha5/beta1 Integrin -0.06 0.15 -10000 0 -0.28 133 133
PRKCD 0.024 0.01 -10000 0 -10000 0 0
Syndecan-2 dimer -0.024 0.1 -10000 0 -0.23 81 81
GO:0007205 0.003 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.027 0.049 -10000 0 -0.4 1 1
RHOA 0.024 0.01 -10000 0 -10000 0 0
SDCBP 0.025 0.009 -10000 0 -10000 0 0
TNFRSF13B -0.023 0.13 -10000 0 -0.4 45 45
RASA1 0.026 0.025 -10000 0 -0.47 1 1
alpha2/beta1 Integrin 0.038 0.021 -10000 0 -0.34 1 1
Syndecan-2/Synbindin 0.016 0.048 -10000 0 -0.22 15 15
TGFB1 0.027 0.021 -10000 0 -0.39 1 1
CASP3 0.025 0.068 0.19 41 -0.2 12 53
FN1 -0.18 0.21 -10000 0 -0.39 203 203
Syndecan-2/IL8 -0.031 0.11 -10000 0 -0.24 91 91
SDC2 0.002 0.052 -10000 0 -0.27 15 15
KNG1 -0.012 0.065 -10000 0 -0.39 11 11
Syndecan-2/Neurofibromin 0.018 0.048 -10000 0 -0.22 15 15
TRAPPC4 0.026 0.008 -10000 0 -10000 0 0
CSF2 -0.2 0.21 -10000 0 -0.39 228 228
Syndecan-2/TGFB1 0.017 0.051 -10000 0 -0.24 15 15
Syndecan-2/Syntenin/PI-4-5-P2 0.017 0.042 -10000 0 -0.2 14 14
Syndecan-2/Ezrin 0.028 0.047 -10000 0 -0.2 13 13
PRKACA 0.03 0.072 0.19 50 -10000 0 50
angiogenesis -0.031 0.11 -10000 0 -0.24 91 91
MMP2 -0.036 0.15 -10000 0 -0.39 63 63
IL8 -0.062 0.17 -10000 0 -0.4 89 89
calcineurin-NFAT signaling pathway -0.009 0.088 -10000 0 -0.23 56 56
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.11 0.17 -10000 0 -0.52 34 34
Syndecan-4/Syndesmos -0.17 0.16 -10000 0 -0.66 16 16
positive regulation of JNK cascade -0.18 0.16 -10000 0 -0.53 30 30
Syndecan-4/ADAM12 -0.3 0.19 -10000 0 -0.45 191 191
CCL5 -0.032 0.15 -10000 0 -0.4 60 60
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
DNM2 0.028 0.004 -10000 0 -10000 0 0
ITGA5 -0.11 0.2 -10000 0 -0.39 134 134
SDCBP 0.025 0.009 -10000 0 -10000 0 0
PLG 0.015 0.045 -10000 0 -0.38 4 4
ADAM12 -0.29 0.18 -10000 0 -0.39 313 313
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.028 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.08 0.044 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.22 0.19 -10000 0 -0.47 95 95
Syndecan-4/CXCL12/CXCR4 -0.19 0.17 -10000 0 -0.58 28 28
Syndecan-4/Laminin alpha3 -0.21 0.18 -10000 0 -0.46 85 85
MDK 0.017 0.066 -10000 0 -0.4 10 10
Syndecan-4/FZD7 -0.17 0.16 -10000 0 -0.65 17 17
Syndecan-4/Midkine -0.17 0.16 -10000 0 -0.57 23 23
FZD7 0.021 0.052 -10000 0 -0.4 6 6
Syndecan-4/FGFR1/FGF -0.15 0.16 -10000 0 -0.61 17 17
THBS1 0.013 0.079 -10000 0 -0.41 14 14
integrin-mediated signaling pathway -0.19 0.17 -10000 0 -0.46 68 68
positive regulation of MAPKKK cascade -0.18 0.16 -10000 0 -0.53 30 30
Syndecan-4/TACI -0.19 0.17 -10000 0 -0.53 33 33
CXCR4 0.014 0.076 -10000 0 -0.39 14 14
cell adhesion -0.077 0.1 0.2 4 -0.22 99 103
Syndecan-4/Dynamin -0.17 0.16 -10000 0 -0.64 17 17
Syndecan-4/TSP1 -0.17 0.17 -10000 0 -0.56 27 27
Syndecan-4/GIPC -0.17 0.16 -10000 0 -0.65 17 17
Syndecan-4/RANTES -0.19 0.17 -10000 0 -0.5 46 46
ITGB1 0.028 0.005 -10000 0 -10000 0 0
LAMA1 -0.12 0.2 -10000 0 -0.4 149 149
LAMA3 -0.09 0.19 -10000 0 -0.39 116 116
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.046 0.11 0.9 6 -0.37 1 7
Syndecan-4/alpha-Actinin -0.16 0.16 -10000 0 -0.64 17 17
TFPI 0.024 0.038 -10000 0 -0.42 3 3
F2 -0.035 0.12 -10000 0 -0.39 41 41
alpha5/beta1 Integrin -0.06 0.15 -10000 0 -0.28 133 133
positive regulation of cell adhesion -0.26 0.2 -10000 0 -0.49 127 127
ACTN1 0.027 0.007 -10000 0 -10000 0 0
TNC -0.05 0.16 -10000 0 -0.39 77 77
Syndecan-4/CXCL12 -0.19 0.17 -10000 0 -0.61 25 25
FGF6 -0.009 0.018 -10000 0 -10000 0 0
RHOA 0.024 0.01 -10000 0 -10000 0 0
CXCL12 -0.022 0.15 -10000 0 -0.47 42 42
TNFRSF13B -0.023 0.13 -10000 0 -0.4 45 45
FGF2 0.01 0.089 -10000 0 -0.45 15 15
FGFR1 0.02 0.046 -10000 0 -0.39 5 5
Syndecan-4/PI-4-5-P2 -0.17 0.15 -10000 0 -0.5 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.17 0.21 -10000 0 -0.39 203 203
cell migration -0.032 0.017 -10000 0 -10000 0 0
PRKCD 0.029 0.016 -10000 0 -10000 0 0
vasculogenesis -0.17 0.16 -10000 0 -0.53 27 27
SDC4 -0.18 0.16 -10000 0 -0.51 37 37
Syndecan-4/Tenascin C -0.2 0.18 -10000 0 -0.48 68 68
Syndecan-4/PI-4-5-P2/PKC alpha -0.064 0.035 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.16 0.16 -10000 0 -0.63 17 17
MMP9 -0.26 0.19 -10000 0 -0.39 293 293
Rac1/GTP -0.079 0.1 0.21 4 -0.22 98 102
cytoskeleton organization -0.16 0.16 -10000 0 -0.62 16 16
GIPC1 0.028 0.003 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.17 0.16 -10000 0 -0.62 18 18
Osteopontin-mediated events

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
IKK alpha homodimer -0.12 0.13 -10000 0 -0.3 43 43
NF kappa B1 p50/RelA/I kappa B alpha -0.11 0.13 0.32 1 -0.4 7 8
alphaV/beta3 Integrin/Osteopontin/Src -0.13 0.16 -10000 0 -0.29 201 201
AP1 -0.16 0.18 -10000 0 -0.44 76 76
ILK -0.12 0.13 -10000 0 -0.37 14 14
bone resorption -0.089 0.12 -10000 0 -0.38 12 12
PTK2B 0.026 0.008 -10000 0 -10000 0 0
PYK2/p130Cas -0.077 0.14 -10000 0 -0.39 10 10
ITGAV 0.023 0.025 -10000 0 -0.41 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.033 0.049 -10000 0 -0.33 7 7
alphaV/beta3 Integrin/Osteopontin -0.12 0.15 -10000 0 -0.28 131 131
MAP3K1 -0.12 0.13 -10000 0 -0.3 46 46
JUN 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.14 0.13 -10000 0 -0.31 98 98
MAPK1 -0.13 0.13 -10000 0 -0.3 105 105
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.12 0.12 -10000 0 -0.32 44 44
ITGB3 0.003 0.097 -10000 0 -0.43 20 20
NFKBIA -0.13 0.13 -10000 0 -0.33 43 43
FOS -0.037 0.16 -10000 0 -0.47 53 53
CD44 0.026 0.025 -10000 0 -0.47 1 1
CHUK 0.028 0.004 -10000 0 -10000 0 0
PLAU -0.2 0.19 -10000 0 -0.5 51 51
NF kappa B1 p50/RelA -0.12 0.15 -10000 0 -0.44 6 6
BCAR1 0.027 0.006 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.007 0.08 -10000 0 -0.31 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.11 0.13 -10000 0 -0.3 41 41
VAV3 -0.12 0.13 -10000 0 -0.39 28 28
MAP3K14 -0.13 0.13 -10000 0 -0.29 108 108
ROCK2 0.02 0.064 -10000 0 -0.47 7 7
SPP1 -0.19 0.21 -10000 0 -0.4 209 209
RAC1 0.026 0.007 -10000 0 -10000 0 0
Rac1/GTP -0.1 0.12 -10000 0 -0.38 24 24
MMP2 -0.16 0.18 -10000 0 -0.46 79 79
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.036 0.13 -10000 0 -0.51 21 21
Crk/p130 Cas/Paxillin -0.065 0.12 -10000 0 -0.35 21 21
JUN -0.041 0.12 -10000 0 -0.36 21 21
HRAS 0.026 0.022 -10000 0 -0.4 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.048 0.16 -10000 0 -0.32 83 83
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.051 0.16 -10000 0 -0.31 91 91
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.038 0.14 -10000 0 -0.27 106 106
RHOA 0.024 0.01 -10000 0 -10000 0 0
RAP1A/GTP -0.045 0.15 -10000 0 -0.28 88 88
GRB7 0.027 0.024 -10000 0 -0.47 1 1
RET51/GFRalpha1/GDNF -0.052 0.16 -10000 0 -0.31 93 93
MAPKKK cascade -0.049 0.13 -10000 0 -0.37 23 23
BCAR1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.039 0.14 -10000 0 -0.27 106 106
lamellipodium assembly -0.043 0.11 -10000 0 -0.28 52 52
RET51/GFRalpha1/GDNF/SHC -0.052 0.16 -10000 0 -0.31 91 91
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.036 0.14 -10000 0 -0.27 104 104
RET9/GFRalpha1/GDNF/Shank3 -0.036 0.14 -10000 0 -0.27 104 104
MAPK3 -0.057 0.14 0.34 4 -0.39 22 26
DOK1 0.028 0.003 -10000 0 -10000 0 0
DOK6 0.014 0.07 -10000 0 -0.43 10 10
PXN 0.028 0.003 -10000 0 -10000 0 0
neurite development -0.052 0.13 0.33 4 -0.35 20 24
DOK5 0.005 0.1 -10000 0 -0.45 19 19
GFRA1 -0.084 0.21 -10000 0 -0.47 95 95
MAPK8 -0.052 0.11 -10000 0 -0.34 28 28
HRAS/GTP -0.047 0.15 -10000 0 -0.31 71 71
tube development -0.033 0.13 -10000 0 -0.27 80 80
MAPK1 -0.056 0.14 0.32 5 -0.39 19 24
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.039 0.11 -10000 0 -0.24 78 78
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
SRC 0.027 0.007 -10000 0 -10000 0 0
PDLIM7 0.022 0.046 -10000 0 -0.39 5 5
RET51/GFRalpha1/GDNF/Dok6 -0.045 0.16 -10000 0 -0.3 82 82
SHC1 0.028 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.051 0.16 -10000 0 -0.31 91 91
RET51/GFRalpha1/GDNF/Dok5 -0.062 0.17 -10000 0 -0.33 94 94
PRKCA 0.027 0.021 -10000 0 -0.39 1 1
HRAS/GDP 0.019 0.015 -10000 0 -0.28 1 1
CREB1 -0.051 0.13 -10000 0 -0.29 79 79
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.039 0.11 -10000 0 -0.24 80 80
RET51/GFRalpha1/GDNF/Grb7 -0.051 0.16 -10000 0 -0.28 131 131
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.022 0.14 -10000 0 -0.4 49 49
DOK4 0.027 0.006 -10000 0 -10000 0 0
JNK cascade -0.04 0.12 -10000 0 -0.35 21 21
RET9/GFRalpha1/GDNF/FRS2 -0.037 0.14 -10000 0 -0.27 103 103
SHANK3 0.027 0.005 -10000 0 -10000 0 0
RASA1 0.026 0.025 -10000 0 -0.47 1 1
NCK1 0.024 0.01 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.038 0.11 -10000 0 -0.24 77 77
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.048 0.12 -10000 0 -0.34 21 21
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.048 0.12 -10000 0 -0.34 26 26
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.048 0.12 -10000 0 -0.3 43 43
PI3K -0.06 0.17 -10000 0 -0.4 58 58
SOS1 0.028 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.024 0.14 -10000 0 -0.27 80 80
GRB10 0.025 0.022 -10000 0 -0.39 1 1
activation of MAPKK activity -0.038 0.12 -10000 0 -0.33 20 20
RET51/GFRalpha1/GDNF/FRS2 -0.052 0.16 -10000 0 -0.31 90 90
GAB1 0.027 0.006 -10000 0 -10000 0 0
IRS1 0.025 0.034 -10000 0 -0.47 2 2
IRS2 0.025 0.034 -10000 0 -0.47 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.051 0.12 -10000 0 -0.26 89 89
RET51/GFRalpha1/GDNF/PKC alpha -0.051 0.16 -10000 0 -0.31 88 88
GRB2 0.028 0.004 -10000 0 -10000 0 0
PRKACA 0.028 0.003 -10000 0 -10000 0 0
GDNF -0.015 0.11 -10000 0 -0.39 32 32
RAC1 0.026 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.054 0.17 -10000 0 -0.28 133 133
Rac1/GTP -0.045 0.14 -10000 0 -0.33 51 51
RET9/GFRalpha1/GDNF -0.053 0.14 -10000 0 -0.3 105 105
GFRalpha1/GDNF -0.062 0.17 -10000 0 -0.35 105 105
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.43 0.41 -10000 0 -1.2 63 63
IL23A -0.41 0.37 -10000 0 -1.1 53 53
NF kappa B1 p50/RelA/I kappa B alpha -0.4 0.38 -10000 0 -1.1 58 58
positive regulation of T cell mediated cytotoxicity -0.45 0.42 -10000 0 -1.2 65 65
ITGA3 -0.41 0.36 -10000 0 -1.1 51 51
IL17F -0.27 0.26 -10000 0 -0.72 50 50
IL12B -0.064 0.12 -10000 0 -0.42 39 39
STAT1 (dimer) -0.44 0.41 -10000 0 -1.2 67 67
CD4 -0.4 0.36 -10000 0 -1.1 52 52
IL23 -0.4 0.36 -10000 0 -1.1 54 54
IL23R -0.073 0.14 -10000 0 -0.89 9 9
IL1B -0.42 0.38 -10000 0 -1.2 58 58
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.49 0.36 -10000 0 -1.1 66 66
TYK2 -0.02 0.034 -10000 0 -0.43 1 1
STAT4 0.02 0.056 -10000 0 -0.4 7 7
STAT3 0.028 0.004 -10000 0 -10000 0 0
IL18RAP 0.008 0.079 -10000 0 -0.44 12 12
IL12RB1 -0.055 0.12 -10000 0 -0.43 37 37
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.045 0.094 -10000 0 -0.32 38 38
IL23R/JAK2 -0.083 0.13 -10000 0 -0.83 8 8
positive regulation of chronic inflammatory response -0.45 0.42 -10000 0 -1.2 65 65
natural killer cell activation 0.007 0.006 0.042 4 -10000 0 4
JAK2 -0.023 0.03 -10000 0 -10000 0 0
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
NFKB1 0.025 0.005 -10000 0 -10000 0 0
RELA 0.024 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.39 0.34 -10000 0 -1 54 54
ALOX12B -0.48 0.43 -10000 0 -1.2 74 74
CXCL1 -0.43 0.4 -10000 0 -1.2 65 65
T cell proliferation -0.45 0.42 -10000 0 -1.2 65 65
NFKBIA 0.024 0.007 -10000 0 -10000 0 0
IL17A -0.21 0.2 -10000 0 -0.57 35 35
PI3K -0.39 0.38 -10000 0 -1.1 57 57
IFNG -0.024 0.035 0.095 3 -0.11 11 14
STAT3 (dimer) -0.37 0.36 -10000 0 -1.1 56 56
IL18R1 0.019 0.042 -10000 0 -0.42 3 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.26 0.22 -10000 0 -0.8 23 23
IL18/IL18R 0.023 0.085 -10000 0 -0.3 20 20
macrophage activation -0.023 0.015 -10000 0 -0.045 16 16
TNF -0.42 0.38 -10000 0 -1.2 55 55
STAT3/STAT4 -0.42 0.39 -10000 0 -1.1 64 64
STAT4 (dimer) -0.43 0.41 -10000 0 -1.2 64 64
IL18 0.01 0.069 -10000 0 -0.46 8 8
IL19 -0.54 0.51 -10000 0 -1.3 113 113
STAT5A (dimer) -0.43 0.41 -10000 0 -1.2 61 61
STAT1 0.007 0.09 -10000 0 -0.39 20 20
SOCS3 0.027 0.024 -10000 0 -0.47 1 1
CXCL9 -0.47 0.38 -10000 0 -1.1 70 70
MPO -0.42 0.38 -10000 0 -1.1 62 62
positive regulation of humoral immune response -0.45 0.42 -10000 0 -1.2 65 65
IL23/IL23R/JAK2/TYK2 -0.47 0.46 -10000 0 -1.3 61 61
IL6 -0.43 0.43 -10000 0 -1.2 68 68
STAT5A 0.028 0.003 -10000 0 -10000 0 0
IL2 0.014 0.03 -10000 0 -0.38 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.007 0.006 0.042 4 -10000 0 4
CD3E -0.41 0.36 -10000 0 -1.1 55 55
keratinocyte proliferation -0.45 0.42 -10000 0 -1.2 65 65
NOS2 -0.44 0.39 -10000 0 -1.2 63 63
TCGA08_p53

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
CDKN2A -0.1 0.14 -10000 0 -0.28 159 159
TP53 -0.033 0.068 -10000 0 -0.3 19 19
Senescence -0.038 0.076 -10000 0 -0.3 26 26
Apoptosis -0.038 0.076 -10000 0 -0.3 26 26
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.061 0.094 0.28 28 -10000 0 28
MDM4 0.028 0.005 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.006 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.027 0.13 -10000 0 -0.26 102 102
regulation of S phase of mitotic cell cycle -0.025 0.093 -10000 0 -0.23 67 67
GNAO1 0.023 0.043 -10000 0 -0.41 4 4
HRAS 0.026 0.022 -10000 0 -0.4 1 1
SHBG/T-DHT 0.018 0.004 -10000 0 -10000 0 0
PELP1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.051 0.11 0.25 2 -0.32 15 17
T-DHT/AR -0.071 0.15 -10000 0 -0.33 107 107
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 56 56
GNAI2 0.024 0.01 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.025 -10000 0 -0.47 1 1
mol:GDP -0.082 0.15 -10000 0 -0.35 98 98
cell proliferation -0.09 0.18 0.28 3 -0.45 60 63
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
FOS -0.11 0.28 0.29 4 -0.79 57 61
mol:Ca2+ -0.009 0.023 -10000 0 -0.071 25 25
MAPK3 -0.077 0.14 0.3 2 -0.41 30 32
MAPK1 -0.036 0.1 0.2 1 -0.32 21 22
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
mol:IP3 0 0.002 -10000 0 -0.004 56 56
cAMP biosynthetic process 0.004 0.018 -10000 0 -10000 0 0
GNG2 0.027 0.007 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 56 56
HRAS/GTP -0.029 0.12 -10000 0 -0.24 95 95
actin cytoskeleton reorganization 0.027 0.028 -10000 0 -0.23 2 2
SRC 0.026 0.007 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 56 56
PI3K 0.024 0.028 -10000 0 -0.28 2 2
apoptosis 0.071 0.17 0.42 65 -0.25 2 67
T-DHT/AR/PELP1 -0.047 0.14 -10000 0 -0.28 107 107
HRAS/GDP -0.07 0.15 -10000 0 -0.34 94 94
CREB1 -0.077 0.18 0.26 2 -0.45 65 67
RAC1-CDC42/GTP 0.034 0.033 -10000 0 -0.23 2 2
AR -0.1 0.21 -10000 0 -0.47 107 107
GNB1 0.027 0.006 -10000 0 -10000 0 0
RAF1 -0.045 0.11 0.33 1 -0.29 16 17
RAC1-CDC42/GDP -0.035 0.16 -10000 0 -0.37 62 62
T-DHT/AR/PELP1/Src -0.028 0.13 -10000 0 -0.26 99 99
MAP2K2 -0.051 0.11 0.32 1 -0.31 16 17
T-DHT/AR/PELP1/Src/PI3K -0.026 0.094 -10000 0 -0.24 67 67
GNAZ 0.011 0.083 -10000 0 -0.42 15 15
SHBG 0.025 0.012 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.031 0.14 -10000 0 -0.47 26 26
mol:T-DHT 0 0.001 0.002 4 -0.002 33 37
RAC1 0.026 0.007 -10000 0 -10000 0 0
GNRH1 -0.001 0.048 -10000 0 -0.28 12 12
Gi family/GTP -0.03 0.085 -10000 0 -0.28 24 24
CDC42 0.027 0.005 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.027 0.066 -10000 0 -0.34 13 13
Necdin/E2F1 0.021 0.075 -10000 0 -0.31 20 20
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.001 0.13 -10000 0 -0.26 29 29
NGF (dimer)/p75(NTR)/BEX1 -0.031 0.14 -10000 0 -0.25 115 115
NT-4/5 (dimer)/p75(NTR) 0.022 0.082 -10000 0 -0.33 21 21
IKBKB 0.026 0.008 -10000 0 -10000 0 0
AKT1 0.004 0.12 -10000 0 -0.38 1 1
IKBKG 0.027 0.005 -10000 0 -10000 0 0
BDNF -0.006 0.12 -10000 0 -0.43 31 31
MGDIs/NGR/p75(NTR)/LINGO1 0.01 0.12 -10000 0 -0.27 56 56
FURIN 0.028 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.005 0.12 -10000 0 -0.27 62 62
LINGO1 -0.006 0.11 -10000 0 -0.39 33 33
Sortilin/TRAF6/NRIF 0.025 0.047 -10000 0 -10000 0 0
proBDNF (dimer) -0.006 0.12 -10000 0 -0.43 31 31
NTRK1 -0.005 0.11 -10000 0 -0.39 32 32
RTN4R 0.015 0.073 -10000 0 -0.39 13 13
neuron apoptosis -0.042 0.13 0.46 1 -0.45 17 18
IRAK1 0.027 0.006 -10000 0 -10000 0 0
SHC1 -0.04 0.11 -10000 0 -0.24 92 92
ARHGDIA 0.028 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.007 -10000 0 -10000 0 0
Gamma Secretase 0.073 0.029 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.01 0.13 -10000 0 -0.23 105 105
MAGEH1 0.027 0.021 -10000 0 -0.39 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.013 0.14 -10000 0 -0.24 107 107
Mammalian IAPs/DIABLO 0.056 0.047 -10000 0 -0.21 4 4
proNGF (dimer) -0.052 0.16 -10000 0 -0.4 77 77
MAGED1 0.023 0.045 -10000 0 -0.43 4 4
APP 0.026 0.021 -10000 0 -0.39 1 1
NT-4/5 (dimer) 0.025 0.032 -10000 0 -0.43 2 2
ZNF274 0.027 0.006 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.018 0.1 -10000 0 -0.21 81 81
NGF -0.052 0.16 -10000 0 -0.4 77 77
cell cycle arrest -0.064 0.1 -10000 0 -0.3 15 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.004 0.065 -10000 0 -0.23 14 14
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.037 0.074 -10000 0 -0.28 20 20
NCSTN 0.028 0.005 -10000 0 -10000 0 0
mol:GTP -0.015 0.12 -10000 0 -0.24 96 96
PSENEN 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide -0.046 0.11 -10000 0 -0.28 29 29
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0 0.048 -10000 0 -0.28 2 2
p75(NTR)/beta APP 0.022 0.077 -10000 0 -0.3 22 22
BEX1 -0.01 0.1 -10000 0 -0.39 27 27
mol:GDP -0.051 0.1 -10000 0 -0.24 96 96
NGF (dimer) -0.041 0.14 -10000 0 -0.24 128 128
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.026 0.11 -10000 0 -0.25 51 51
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
RAC1/GTP -0.008 0.1 -10000 0 -0.2 86 86
MYD88 0.024 0.01 -10000 0 -10000 0 0
CHUK 0.028 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.014 0.13 -10000 0 -0.24 96 96
RHOB 0.028 0.003 -10000 0 -10000 0 0
RHOA 0.024 0.01 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.027 0.058 -10000 0 -0.28 14 14
NT3 (dimer) -0.12 0.22 -10000 0 -0.47 126 126
TP53 -0.018 0.098 0.53 1 -0.45 4 5
PRDM4 -0.047 0.11 -10000 0 -0.28 30 30
BDNF (dimer) -0.18 0.16 -10000 0 -0.27 286 286
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
SORT1 0.011 0.089 -10000 0 -0.47 14 14
activation of caspase activity -0.004 0.13 -10000 0 -0.26 29 29
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.008 0.13 -10000 0 -0.23 101 101
RHOC 0.027 0.006 -10000 0 -10000 0 0
XIAP 0.028 0.004 -10000 0 -10000 0 0
MAPK10 -0.044 0.12 0.31 3 -0.38 16 19
DIABLO 0.028 0.003 -10000 0 -10000 0 0
SMPD2 -0.047 0.11 -10000 0 -0.28 29 29
APH1B 0.028 0.005 -10000 0 -10000 0 0
APH1A 0.027 0.005 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.025 0.14 -10000 0 -0.25 108 108
PSEN1 0.026 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.02 -10000 0 -0.34 1 1
NT3 (dimer)/p75(NTR) -0.088 0.18 -10000 0 -0.34 138 138
MAPK8 -0.037 0.11 0.35 2 -0.35 11 13
MAPK9 -0.036 0.11 0.34 3 -0.35 10 13
APAF1 0.027 0.024 -10000 0 -0.47 1 1
NTF3 -0.12 0.23 -10000 0 -0.47 126 126
NTF4 0.025 0.032 -10000 0 -0.43 2 2
NDN 0.02 0.062 -10000 0 -0.46 7 7
RAC1/GDP 0.019 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.006 0.11 -10000 0 -0.24 13 13
p75 CTF/Sortilin/TRAF6/NRIF 0.053 0.064 -10000 0 -0.26 14 14
RhoA-B-C/GTP -0.015 0.12 -10000 0 -0.24 96 96
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.03 0.11 -10000 0 -0.27 31 31
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.021 0.12 -10000 0 -0.25 59 59
PRKACB 0.028 0.005 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.014 0.093 -10000 0 -0.31 32 32
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.014 0.065 -10000 0 -0.4 10 10
BIRC2 0.024 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.049 0.1 0.21 1 -0.28 32 33
BAD -0.04 0.11 0.38 2 -0.38 9 11
RIPK2 0.025 0.009 -10000 0 -10000 0 0
NGFR 0.006 0.099 -10000 0 -0.42 21 21
CYCS -0.041 0.1 -10000 0 -0.37 5 5
ADAM17 0.026 0.034 -10000 0 -0.47 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.006 0.11 -10000 0 -0.27 12 12
BCL2L11 -0.041 0.11 0.38 2 -0.38 9 11
BDNF (dimer)/p75(NTR) -0.002 0.11 -10000 0 -0.3 52 52
PI3K -0.007 0.11 -10000 0 -0.27 13 13
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.009 0.13 -10000 0 -0.23 105 105
NDNL2 0.028 0.004 -10000 0 -10000 0 0
YWHAE 0.027 0.006 -10000 0 -10000 0 0
PRKCI 0.02 0.013 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.035 0.14 -10000 0 -0.29 96 96
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.012 0.14 -10000 0 -0.24 106 106
TRAF6 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCZ 0.026 0.025 -10000 0 -0.47 1 1
PLG -0.015 0.041 -10000 0 -0.39 4 4
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.05 0.12 -10000 0 -0.34 34 34
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
NGFRAP1 0.026 0.029 -10000 0 -0.39 2 2
CASP3 -0.038 0.11 0.37 2 -0.35 11 13
E2F1 0.012 0.076 -10000 0 -0.39 14 14
CASP9 0.027 0.006 -10000 0 -10000 0 0
IKK complex 0.014 0.11 -10000 0 -0.3 2 2
NGF (dimer)/TRKA -0.042 0.14 -10000 0 -0.29 104 104
MMP7 -0.048 0.16 -10000 0 -0.41 69 69
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.002 0.13 -10000 0 -0.26 27 27
MMP3 -0.25 0.2 -10000 0 -0.4 272 272
APAF-1/Caspase 9 -0.031 0.086 -10000 0 -0.34 3 3
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.021 0.033 -10000 0 -10000 0 0
NFATC2 -0.051 0.093 -10000 0 -0.32 41 41
NFATC3 -0.024 0.033 -10000 0 -10000 0 0
CD40LG -0.23 0.26 0.35 6 -0.63 89 95
PTGS2 -0.23 0.25 0.35 5 -0.6 90 95
JUNB 0.028 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.013 0.026 -10000 0 -10000 0 0
CaM/Ca2+ -0.012 0.026 -10000 0 -10000 0 0
CALM1 0.007 0.026 -10000 0 -10000 0 0
JUN 0.007 0.027 -10000 0 -10000 0 0
mol:Ca2+ -0.012 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.008 0.015 -10000 0 -10000 0 0
FOSL1 0.018 0.062 -10000 0 -0.4 9 9
CREM 0.027 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.11 0.14 -10000 0 -0.39 37 37
FOS -0.056 0.16 -10000 0 -0.48 53 53
IFNG -0.24 0.26 0.35 4 -0.61 96 100
AP-1/NFAT1-c-4 -0.24 0.27 -10000 0 -0.63 88 88
FASLG -0.22 0.25 0.34 4 -0.63 75 79
NFAT1-c-4/ICER1 -0.075 0.1 -10000 0 -0.33 31 31
IL2RA -0.22 0.25 0.35 6 -0.62 78 84
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSF2 -0.3 0.27 0.35 5 -0.6 143 148
JunB/Fra1/NFAT1-c-4 -0.072 0.11 -10000 0 -0.34 26 26
IL4 -0.21 0.23 0.34 6 -0.59 67 73
IL2 -0.015 0.16 -10000 0 -0.94 12 12
IL3 -0.037 0.17 -10000 0 -0.71 24 24
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
BATF3 0.026 0.029 -10000 0 -0.39 2 2
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.028 0.005 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.028 0.005 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.025 -10000 0 -0.27 3 3
Metarhodopsin II/Arrestin 0.021 0.024 -10000 0 -0.24 3 3
PDE6G/GNAT1/GTP 0.02 0.05 -10000 0 -0.23 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.002 0.04 -10000 0 -0.39 3 3
GRK1 -0.01 0.026 -10000 0 -0.39 1 1
CNG Channel -0.22 0.18 -10000 0 -0.42 138 138
mol:Na + -0.12 0.14 -10000 0 -0.38 42 42
mol:ADP -0.01 0.026 -10000 0 -0.39 1 1
RGS9-1/Gbeta5/R9AP 0.039 0.067 -10000 0 -0.27 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.12 0.15 -10000 0 -0.39 42 42
CNGB1 -0.2 0.21 -10000 0 -0.4 224 224
RDH5 0.027 0.024 -10000 0 -0.47 1 1
SAG -0.013 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.12 0.15 0.36 7 -0.38 42 49
Na + (4 Units) -0.12 0.13 -10000 0 -0.37 42 42
RGS9 0.021 0.056 -10000 0 -0.4 7 7
GNB1/GNGT1 0.004 0.095 -10000 0 -0.27 43 43
GNAT1/GDP 0.039 0.067 -10000 0 -0.26 14 14
GUCY2D 0.006 0.09 -10000 0 -0.39 20 20
GNGT1 -0.023 0.13 -10000 0 -0.39 43 43
GUCY2F -0.009 0.019 -10000 0 -10000 0 0
GNB5 0.028 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.12 0.15 -10000 0 -0.26 187 187
mol:11-cis-retinal 0.027 0.024 -10000 0 -0.47 1 1
mol:cGMP 0.005 0.094 -10000 0 -0.34 5 5
GNB1 0.027 0.006 -10000 0 -10000 0 0
Rhodopsin 0.029 0.034 -10000 0 -0.29 4 4
SLC24A1 0.028 0.005 -10000 0 -10000 0 0
CNGA1 -0.004 0.12 -10000 0 -0.47 26 26
Metarhodopsin II 0.021 0.022 -10000 0 -0.21 3 3
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.013 0.1 -10000 0 -0.23 55 55
RGS9BP 0.013 0.079 -10000 0 -0.47 11 11
Metarhodopsin II/Transducin -0.005 0.054 -10000 0 -0.27 9 9
GCAP Family/Ca ++ 0.011 0.084 -10000 0 -0.22 46 46
PDE6A/B -0.15 0.2 -10000 0 -0.35 201 201
mol:Pi 0.039 0.067 -10000 0 -0.27 17 17
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.012 0.079 -10000 0 -0.21 42 42
PDE6B -0.007 0.12 -10000 0 -0.44 30 30
PDE6A -0.19 0.24 -10000 0 -0.47 185 185
PDE6G 0.016 0.07 -10000 0 -0.39 12 12
RHO -0.007 0.038 -10000 0 -0.39 3 3
PDE6 -0.1 0.17 -10000 0 -0.42 28 28
GUCA1A -0.021 0.13 -10000 0 -0.39 46 46
GC2/GCAP Family 0.019 0.09 -10000 0 -0.23 44 44
GUCA1C -0.017 0.006 -10000 0 -10000 0 0
GUCA1B 0.022 0.048 -10000 0 -0.47 4 4
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.067 0.17 -10000 0 -0.36 51 51
SMAD6-7/SMURF1 0.048 0.022 -10000 0 -10000 0 0
NOG -0.017 0.13 -10000 0 -0.42 38 38
SMAD9 -0.065 0.19 -10000 0 -0.54 49 49
SMAD4 0.025 0.009 -10000 0 -10000 0 0
SMAD5 -0.05 0.13 -10000 0 -0.44 26 26
BMP7/USAG1 -0.071 0.18 -10000 0 -0.36 112 112
SMAD5/SKI -0.045 0.14 0.24 2 -0.43 27 29
SMAD1 0.023 0.041 -10000 0 -10000 0 0
BMP2 0.012 0.077 -10000 0 -0.4 14 14
SMAD1/SMAD1/SMAD4 0.026 0.052 -10000 0 -10000 0 0
BMPR1A 0.028 0.004 -10000 0 -10000 0 0
BMPR1B -0.019 0.14 -10000 0 -0.41 45 45
BMPR1A-1B/BAMBI 0.009 0.11 -10000 0 -0.26 60 60
AHSG -0.006 0.079 -10000 0 -0.39 16 16
CER1 -0.01 0.042 -10000 0 -0.39 4 4
BMP2-4/CER1 0.021 0.076 -10000 0 -0.26 26 26
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.082 0.17 -10000 0 -0.45 44 44
BMP2-4 (homodimer) 0.019 0.08 -10000 0 -0.31 22 22
RGMB 0.027 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.032 0.094 -10000 0 -0.22 43 43
RGMA -0.031 0.16 -10000 0 -0.47 50 50
SMURF1 0.026 0.008 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.076 0.15 -10000 0 -0.42 42 42
BMP2-4/USAG1 -0.045 0.15 -10000 0 -0.29 110 110
SMAD6/SMURF1/SMAD5 -0.045 0.14 0.24 2 -0.43 26 28
SOSTDC1 -0.096 0.21 -10000 0 -0.46 104 104
BMP7/BMPR2/BMPR1A-1B 0.012 0.12 -10000 0 -0.27 36 36
SKI 0.027 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.021 0.048 -10000 0 -0.41 5 5
HFE2 -0.13 0.21 -10000 0 -0.47 121 121
ZFYVE16 0.027 0.007 -10000 0 -10000 0 0
MAP3K7 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.015 0.082 -10000 0 -0.26 29 29
SMAD5/SMAD5/SMAD4 -0.042 0.14 0.24 2 -0.43 26 28
MAPK1 0.027 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.057 0.14 -10000 0 -0.4 33 33
BMP7 (homodimer) -0.006 0.12 -10000 0 -0.46 28 28
NUP214 0.027 0.005 -10000 0 -10000 0 0
BMP6/FETUA 0.013 0.066 -10000 0 -0.28 19 19
SMAD1/SKI 0.024 0.07 -10000 0 -0.36 1 1
SMAD6 0.028 0.005 -10000 0 -10000 0 0
CTDSP2 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/FETUA 0.014 0.079 -10000 0 -0.25 29 29
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.16 0.21 -10000 0 -0.39 192 192
BMPR2 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.049 0.021 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) 0.005 0.1 -10000 0 -0.29 45 45
CHRDL1 -0.2 0.24 -10000 0 -0.47 195 195
ENDOFIN/SMAD1 0.026 0.069 -10000 0 -0.34 1 1
SMAD6-7/SMURF1/SMAD1 0.043 0.067 -10000 0 -10000 0 0
SMAD6/SMURF1 0.026 0.008 -10000 0 -10000 0 0
BAMBI 0.006 0.098 -10000 0 -0.44 19 19
SMURF2 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.11 0.18 -10000 0 -0.3 183 183
BMP2-4/GREM1 -0.081 0.15 -10000 0 -0.25 175 175
SMAD7 0.026 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.059 0.19 -10000 0 -0.51 52 52
SMAD1/SMAD6 0.022 0.069 -10000 0 -0.34 1 1
TAK1/SMAD6 0.037 0.013 -10000 0 -10000 0 0
BMP7 -0.006 0.12 -10000 0 -0.46 28 28
BMP6 0.021 0.048 -10000 0 -0.41 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.064 0.15 -10000 0 -0.42 39 39
PPM1A 0.026 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 0.025 0.071 -10000 0 -0.36 1 1
SMAD7/SMURF1 0.035 0.016 -10000 0 -10000 0 0
CTDSPL 0.024 0.01 -10000 0 -10000 0 0
PPP1CA 0.026 0.009 -10000 0 -10000 0 0
XIAP 0.028 0.004 -10000 0 -10000 0 0
CTDSP1 0.027 0.006 -10000 0 -10000 0 0
PPP1R15A 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.12 0.17 -10000 0 -0.44 60 60
CHRD 0.006 0.076 -10000 0 -0.4 14 14
BMPR2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.085 0.16 -10000 0 -0.43 46 46
BMP4 0.016 0.071 -10000 0 -0.46 9 9
FST -0.13 0.2 -10000 0 -0.39 157 157
BMP2-4/NOG 0.009 0.11 -10000 0 -0.26 52 52
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.021 0.11 -10000 0 -0.26 31 31
Effects of Botulinum toxin

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
STX1A -0.003 0.054 -10000 0 -0.28 16 16
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.005 0.098 -10000 0 -0.33 32 32
STXBP1 0.028 0.005 -10000 0 -10000 0 0
ACh/CHRNA1 -0.075 0.14 -10000 0 -0.27 135 135
RAB3GAP2/RIMS1/UNC13B 0.02 0.089 -10000 0 -0.28 31 31
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 -0.024 0.13 -10000 0 -0.46 32 32
mol:ACh 0.002 0.034 0.081 33 -0.11 9 42
RAB3GAP2 0.028 0.005 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.008 0.082 -10000 0 -0.27 5 5
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.075 0.14 -10000 0 -0.27 135 135
UNC13B 0.022 0.035 -10000 0 -0.47 2 2
CHRNA1 -0.12 0.21 -10000 0 -0.43 135 135
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.047 0.12 -10000 0 -0.24 106 106
SNAP25 -0.002 0.032 -10000 0 -0.13 23 23
VAMP2 0.005 0.001 -10000 0 -10000 0 0
SYT1 -0.08 0.18 -10000 0 -0.4 106 106
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.015 0.049 -10000 0 -0.23 16 16
STX1A/SNAP25 fragment 1/VAMP2 0.008 0.082 -10000 0 -0.27 5 5
Coregulation of Androgen receptor activity

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
NRIP1 0.009 0.042 -10000 0 -10000 0 0
SVIL 0.01 0.039 -10000 0 -10000 0 0
ZNF318 0.053 0.061 0.21 18 -10000 0 18
JMJD2C 0.006 0.019 0.05 1 -0.076 13 14
T-DHT/AR/Ubc9 -0.094 0.15 -10000 0 -0.32 107 107
CARM1 0.023 0.014 -10000 0 -10000 0 0
PRDX1 0.03 0.006 -10000 0 -10000 0 0
PELP1 0.031 0.012 -10000 0 -10000 0 0
CTNNB1 0.011 0.032 -10000 0 -10000 0 0
AKT1 0.033 0.02 -10000 0 -10000 0 0
PTK2B 0.012 0.031 -10000 0 -10000 0 0
MED1 0.037 0.019 -10000 0 -10000 0 0
MAK 0.039 0.095 0.19 49 -0.43 10 59
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 0.009 0.045 -10000 0 -0.47 1 1
GSN 0.008 0.043 -10000 0 -10000 0 0
NCOA2 -0.003 0.11 -10000 0 -0.47 21 21
NCOA6 0.01 0.038 -10000 0 -10000 0 0
DNA-PK 0.067 0.058 0.25 1 -10000 0 1
NCOA4 0.027 0.005 -10000 0 -10000 0 0
PIAS3 0.013 0.034 -10000 0 -10000 0 0
cell proliferation -0.014 0.13 -10000 0 -0.6 15 15
XRCC5 0.033 0.015 -10000 0 -10000 0 0
UBE3A 0.004 0.052 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.11 0.16 -10000 0 -0.34 120 120
FHL2 -0.014 0.091 -10000 0 -0.48 4 4
RANBP9 0.011 0.038 -10000 0 -10000 0 0
JMJD1A -0.06 0.07 -10000 0 -0.13 208 208
CDK6 0.025 0.033 -10000 0 -0.43 2 2
TGFB1I1 -0.003 0.081 -10000 0 -0.4 13 13
T-DHT/AR/CyclinD1 -0.084 0.14 -10000 0 -0.33 84 84
XRCC6 0.034 0.015 -10000 0 -10000 0 0
T-DHT/AR -0.12 0.17 -10000 0 -0.36 108 108
CTDSP1 0.018 0.022 -10000 0 -10000 0 0
CTDSP2 0.046 0.04 0.17 1 -10000 0 1
BRCA1 0.01 0.039 -10000 0 -10000 0 0
TCF4 0.037 0.031 -10000 0 -10000 0 0
CDKN2A -0.13 0.2 -10000 0 -0.38 159 159
SRF 0.041 0.021 -10000 0 -10000 0 0
NKX3-1 -0.14 0.16 -10000 0 -0.51 29 29
KLK3 -0.22 0.52 -10000 0 -1.4 72 72
TMF1 0.018 0.017 -10000 0 -10000 0 0
HNRNPA1 0.038 0.023 -10000 0 -10000 0 0
AOF2 -0.012 0.027 -10000 0 -0.07 71 71
APPL1 0.025 0.034 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.087 0.15 -10000 0 -0.32 104 104
AR -0.14 0.21 -10000 0 -0.5 107 107
UBA3 0.016 0.022 -10000 0 -10000 0 0
PATZ1 0.037 0.023 -10000 0 -10000 0 0
PAWR 0.021 0.017 -10000 0 -10000 0 0
PRKDC 0.03 0.017 -10000 0 -10000 0 0
PA2G4 0.04 0.027 -10000 0 -10000 0 0
UBE2I 0.028 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.078 0.14 -10000 0 -0.29 102 102
RPS6KA3 0.006 0.054 -10000 0 -0.47 2 2
T-DHT/AR/ARA70 -0.097 0.15 -10000 0 -0.32 106 106
LATS2 0.036 0.024 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.071 0.14 -10000 0 -0.29 105 105
Cyclin D3/CDK11 p58 0.022 0.006 -10000 0 -10000 0 0
VAV3 -0.014 0.12 -10000 0 -0.47 23 23
KLK2 -0.06 0.11 -10000 0 -0.46 17 17
CASP8 0.03 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.092 0.15 -10000 0 -0.32 101 101
TMPRSS2 -0.46 0.46 -10000 0 -0.92 210 210
CCND1 0.011 0.04 -10000 0 -0.47 2 2
PIAS1 0.004 0.052 -10000 0 -10000 0 0
mol:T-DHT -0.025 0.03 0.042 1 -0.061 152 153
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.006 0.074 -10000 0 -0.18 26 26
T-DHT/AR/CDK6 -0.089 0.14 -10000 0 -0.32 101 101
CMTM2 0.015 0.071 -10000 0 -0.39 12 12
SNURF -0.003 0.11 -10000 0 -0.47 21 21
ZMIZ1 -0.013 0.046 -10000 0 -10000 0 0
CCND3 0.028 0.007 -10000 0 -10000 0 0
TGIF1 0.034 0.024 -10000 0 -10000 0 0
FKBP4 0.01 0.037 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.007 0.16 0.32 11 -0.43 30 41
FYN -0.023 0.19 0.3 16 -0.52 30 46
LAT/GRAP2/SLP76 -0.014 0.17 0.27 6 -0.46 34 40
IKBKB 0.026 0.008 -10000 0 -10000 0 0
AKT1 -0.02 0.15 0.25 15 -0.37 37 52
B2M 0.026 0.012 -10000 0 -10000 0 0
IKBKG -0.002 0.05 0.096 20 -0.14 8 28
MAP3K8 0.025 0.034 -10000 0 -0.47 2 2
mol:Ca2+ -0.037 0.032 -10000 0 -0.091 42 42
integrin-mediated signaling pathway 0.034 0.024 -10000 0 -0.28 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.033 0.19 0.28 14 -0.52 36 50
TRPV6 -0.21 0.26 1.1 4 -0.47 195 199
CD28 0.01 0.086 -10000 0 -0.4 17 17
SHC1 -0.029 0.19 0.31 12 -0.49 39 51
receptor internalization -0.036 0.19 0.24 1 -0.48 50 51
PRF1 -0.04 0.21 -10000 0 -0.69 24 24
KRAS 0.027 0.007 -10000 0 -10000 0 0
GRB2 0.028 0.004 -10000 0 -10000 0 0
COT/AKT1 -0.005 0.13 0.22 14 -0.33 26 40
LAT -0.034 0.19 0.3 5 -0.51 40 45
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D 0.014 0.068 -10000 0 -0.44 9 9
CD3E 0.014 0.067 -10000 0 -0.43 9 9
CD3G 0 0.1 -10000 0 -0.44 22 22
RASGRP2 0.006 0.02 -10000 0 -0.16 1 1
RASGRP1 -0.021 0.16 0.26 16 -0.41 32 48
HLA-A 0.02 0.049 -10000 0 -0.41 5 5
RASSF5 0.025 0.034 -10000 0 -0.47 2 2
RAP1A/GTP/RAPL 0.035 0.024 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.063 0.15 34 -0.13 6 40
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.024 0.065 -10000 0 -0.22 21 21
PRKCA -0.005 0.09 0.16 16 -0.26 18 34
GRAP2 0.018 0.066 -10000 0 -0.43 9 9
mol:IP3 0.041 0.17 0.21 149 -0.37 25 174
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.024 0.16 -10000 0 -0.47 35 35
ORAI1 0.11 0.16 0.6 2 -0.92 4 6
CSK -0.03 0.18 0.27 6 -0.49 39 45
B7 family/CD28 -0.053 0.19 -10000 0 -0.53 33 33
CHUK 0.028 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.046 0.2 0.27 3 -0.53 42 45
PTPN6 -0.034 0.18 0.26 6 -0.5 35 41
VAV1 -0.034 0.19 0.27 5 -0.5 40 45
Monovalent TCR/CD3 -0.006 0.11 -10000 0 -0.38 25 25
CBL 0.026 0.008 -10000 0 -10000 0 0
LCK -0.026 0.19 0.28 15 -0.51 34 49
PAG1 -0.024 0.18 0.28 11 -0.49 38 49
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.047 0.19 0.25 7 -0.52 41 48
CD80 -0.08 0.18 -10000 0 -0.39 105 105
CD86 0.024 0.022 -10000 0 -0.39 1 1
PDK1/CARD11/BCL10/MALT1 -0.021 0.082 -10000 0 -0.26 23 23
HRAS 0.026 0.022 -10000 0 -0.4 1 1
GO:0035030 -0.061 0.15 0.2 4 -0.44 34 38
CD8A -0.01 0.13 -10000 0 -0.43 35 35
CD8B -0.02 0.14 -10000 0 -0.42 43 43
PTPRC 0.015 0.075 -10000 0 -0.44 11 11
PDK1/PKC theta -0.027 0.17 0.29 14 -0.46 33 47
CSK/PAG1 -0.02 0.18 0.3 14 -0.5 33 47
SOS1 0.028 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.033 0.04 -10000 0 -0.29 5 5
GRAP2/SLP76 -0.017 0.19 0.27 4 -0.5 37 41
STIM1 0.057 0.1 1.2 2 -10000 0 2
RAS family/GTP 0.016 0.077 0.15 37 -0.18 11 48
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.04 0.2 0.24 1 -0.5 50 51
mol:DAG -0.012 0.12 0.12 10 -0.32 31 41
RAP1A/GDP 0.013 0.031 0.084 22 -10000 0 22
PLCG1 0.027 0.007 -10000 0 -10000 0 0
CD247 0.009 0.088 -10000 0 -0.42 17 17
cytotoxic T cell degranulation -0.038 0.2 -10000 0 -0.66 24 24
RAP1A/GTP 0.002 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.024 0.17 0.26 16 -0.43 35 51
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.038 0.2 0.23 130 -0.48 27 157
NRAS 0.027 0.006 -10000 0 -10000 0 0
ZAP70 0.008 0.092 -10000 0 -0.41 19 19
GRB2/SOS1 0.041 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.021 0.17 0.36 2 -0.47 32 34
MALT1 0.025 0.009 -10000 0 -10000 0 0
TRAF6 0.027 0.006 -10000 0 -10000 0 0
CD8 heterodimer -0.018 0.16 -10000 0 -0.4 57 57
CARD11 0.004 0.094 -10000 0 -0.4 21 21
PRKCB -0.006 0.096 0.16 16 -0.29 20 36
PRKCE -0.005 0.09 0.16 15 -0.26 19 34
PRKCQ -0.032 0.19 0.29 14 -0.52 33 47
LCP2 0.024 0.036 -10000 0 -0.39 3 3
BCL10 0.028 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.014 0.13 0.23 17 -0.32 35 52
IKK complex 0.017 0.065 0.15 39 -0.12 7 46
RAS family/GDP -0.002 0.01 -10000 0 -10000 0 0
MAP3K14 -0.006 0.099 0.18 16 -0.27 19 35
PDPK1 -0.016 0.14 0.25 16 -0.37 28 44
TCR/CD3/MHC I/CD8/Fyn -0.05 0.21 -10000 0 -0.6 37 37
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.18 0.27 -10000 0 -0.87 25 25
PCK1 -0.46 0.58 -10000 0 -1.2 145 145
HNF4A -0.21 0.3 -10000 0 -1 25 25
KCNJ11 -0.27 0.4 -10000 0 -0.99 71 71
AKT1 -0.095 0.15 -10000 0 -0.49 11 11
response to starvation -0.003 0.015 -10000 0 -10000 0 0
DLK1 -0.34 0.46 -10000 0 -1 119 119
NKX2-1 -0.034 0.22 0.46 3 -0.59 12 15
ACADM -0.19 0.28 -10000 0 -0.88 27 27
TAT -0.13 0.19 -10000 0 -0.7 14 14
CEBPB 0.027 0.009 -10000 0 -10000 0 0
CEBPA 0.024 0.042 -10000 0 -0.47 3 3
TTR -0.27 0.3 -10000 0 -0.79 69 69
PKLR -0.2 0.29 -10000 0 -0.85 36 36
APOA1 -0.22 0.32 -10000 0 -1 23 23
CPT1C -0.18 0.28 -10000 0 -0.89 24 24
ALAS1 -0.089 0.16 -10000 0 -0.66 6 6
TFRC -0.16 0.22 -10000 0 -0.79 9 9
FOXF1 0.03 0.054 -10000 0 -0.37 5 5
NF1 0.033 0.005 -10000 0 -10000 0 0
HNF1A (dimer) 0.019 0.059 -10000 0 -0.39 7 7
CPT1A -0.16 0.28 -10000 0 -0.86 24 24
HMGCS1 -0.17 0.27 -10000 0 -0.82 29 29
NR3C1 0.028 0.025 -10000 0 -10000 0 0
CPT1B -0.19 0.29 -10000 0 -0.98 23 23
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.026 0.024 -10000 0 -10000 0 0
GCK -0.19 0.28 -10000 0 -0.83 33 33
CREB1 -0.041 0.1 -10000 0 -0.23 47 47
IGFBP1 -0.085 0.15 -10000 0 -0.61 9 9
PDX1 -0.098 0.17 -10000 0 -0.68 7 7
UCP2 -0.17 0.27 -10000 0 -0.89 22 22
ALDOB -0.2 0.3 -10000 0 -0.89 32 32
AFP -0.15 0.16 -10000 0 -0.43 57 57
BDH1 -0.15 0.28 0.52 1 -0.92 18 19
HADH -0.19 0.29 -10000 0 -0.89 27 27
F2 -0.22 0.32 -10000 0 -1 24 24
HNF1A 0.019 0.059 -10000 0 -0.39 7 7
G6PC -0.054 0.1 -10000 0 -10000 0 0
SLC2A2 -0.1 0.17 -10000 0 -1.2 1 1
INS -0.023 0.036 -10000 0 -0.4 2 2
FOXA1 -0.17 0.25 -10000 0 -0.48 163 163
FOXA3 -0.085 0.16 -10000 0 -0.39 52 52
FOXA2 -0.23 0.33 -10000 0 -0.93 38 38
ABCC8 -0.2 0.29 -10000 0 -0.88 29 29
ALB -0.16 0.19 -10000 0 -0.49 63 63
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.035 0.065 -10000 0 -0.26 17 17
fibroblast growth factor receptor signaling pathway 0.034 0.065 -10000 0 -0.26 17 17
LAMA1 -0.12 0.2 -10000 0 -0.4 149 149
PRNP 0.027 0.007 -10000 0 -10000 0 0
GPC1/SLIT2 0 0.11 -10000 0 -0.33 43 43
SMAD2 0.017 0.03 -10000 0 -0.26 1 1
GPC1/PrPc/Cu2+ 0.034 0.018 -10000 0 -0.23 1 1
GPC1/Laminin alpha1 -0.076 0.15 -10000 0 -0.28 149 149
TDGF1 0.005 0.045 -10000 0 -0.4 4 4
CRIPTO/GPC1 0.03 0.036 -10000 0 -0.27 5 5
APP/GPC1 0.038 0.024 -10000 0 -0.28 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.003 0.026 -10000 0 -0.22 4 4
FLT1 0.026 0.022 -10000 0 -0.39 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.046 0.031 -10000 0 -0.25 2 2
SERPINC1 0.013 0.062 -10000 0 -0.39 9 9
FYN 0.002 0.031 -10000 0 -0.22 6 6
FGR 0.002 0.03 -10000 0 -0.23 5 5
positive regulation of MAPKKK cascade 0.001 0.097 0.25 14 -0.36 7 21
SLIT2 -0.023 0.15 -10000 0 -0.47 42 42
GPC1/NRG -0.015 0.12 -10000 0 -0.28 69 69
NRG1 -0.043 0.16 -10000 0 -0.4 68 68
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.048 0.037 -10000 0 -0.3 3 3
LYN 0.002 0.029 -10000 0 -0.23 5 5
mol:Spermine 0.007 0.014 -10000 0 -0.27 1 1
cell growth 0.034 0.065 -10000 0 -0.26 17 17
BMP signaling pathway -0.026 0.021 0.39 1 -10000 0 1
SRC 0.002 0.029 -10000 0 -0.23 5 5
TGFBR1 0.028 0.005 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.28 0.24 -10000 0 -0.47 258 258
GPC1 0.026 0.021 -10000 0 -0.39 1 1
TGFBR1 (dimer) 0.028 0.005 -10000 0 -10000 0 0
VEGFA 0.024 0.036 -10000 0 -0.39 3 3
BLK -0.032 0.088 -10000 0 -0.24 62 62
HCK 0 0.039 -10000 0 -0.27 7 7
FGF2 0.01 0.089 -10000 0 -0.45 15 15
FGFR1 0.02 0.046 -10000 0 -0.39 5 5
VEGFR1 homodimer 0.026 0.022 -10000 0 -0.39 1 1
TGFBR2 0.023 0.026 -10000 0 -0.47 1 1
cell death 0.038 0.024 -10000 0 -0.28 2 2
ATIII/GPC1 0.031 0.049 -10000 0 -0.28 10 10
PLA2G2A/GPC1 -0.19 0.18 -10000 0 -0.33 258 258
LCK -0.003 0.045 -10000 0 -0.23 14 14
neuron differentiation -0.015 0.12 -10000 0 -0.28 69 69
PrPc/Cu2+ 0.02 0.005 -10000 0 -10000 0 0
APP 0.026 0.021 -10000 0 -0.39 1 1
TGFBR2 (dimer) 0.023 0.026 -10000 0 -0.47 1 1
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.03 0.14 0.31 3 -0.38 44 47
CRKL -0.032 0.14 -10000 0 -0.4 44 44
HRAS -0.017 0.13 -10000 0 -0.4 12 12
mol:PIP3 -0.015 0.14 0.31 1 -0.37 47 48
SPRED1 0.028 0.004 -10000 0 -10000 0 0
SPRED2 0.027 0.024 -10000 0 -0.47 1 1
GAB1 -0.031 0.14 -10000 0 -0.42 46 46
FOXO3 -0.021 0.15 0.36 1 -0.38 44 45
AKT1 -0.024 0.16 -10000 0 -0.4 50 50
BAD -0.019 0.15 0.31 1 -0.38 43 44
megakaryocyte differentiation -0.036 0.14 -10000 0 -0.41 48 48
GSK3B -0.004 0.15 0.32 4 -0.38 32 36
RAF1 -0.013 0.11 -10000 0 -0.34 8 8
SHC1 0.028 0.004 -10000 0 -10000 0 0
STAT3 -0.032 0.14 -10000 0 -0.42 46 46
STAT1 -0.1 0.34 -10000 0 -1 48 48
HRAS/SPRED1 -0.003 0.12 -10000 0 -0.35 7 7
cell proliferation -0.035 0.15 -10000 0 -0.42 48 48
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
TEC 0.003 0.11 -10000 0 -0.47 21 21
RPS6KB1 -0.024 0.15 -10000 0 -0.4 49 49
HRAS/SPRED2 -0.003 0.12 -10000 0 -0.36 8 8
LYN/TEC/p62DOK -0.01 0.16 -10000 0 -0.43 36 36
MAPK3 -0.006 0.087 -10000 0 -0.3 4 4
STAP1 -0.044 0.15 0.25 1 -0.42 49 50
GRAP2 0.018 0.066 -10000 0 -0.43 9 9
JAK2 -0.085 0.3 -10000 0 -0.88 48 48
STAT1 (dimer) -0.098 0.33 -10000 0 -0.99 48 48
mol:Gleevec 0 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.01 0.16 -10000 0 -0.4 44 44
actin filament polymerization -0.034 0.14 -10000 0 -0.41 45 45
LYN 0.025 0.009 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.062 0.21 -10000 0 -0.6 49 49
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
CBL/CRKL/GRB2 -0.005 0.13 0.28 1 -0.37 38 39
PI3K -0.01 0.14 -10000 0 -0.4 34 34
PTEN 0.028 0.005 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.11 0.4 -10000 0 -1.2 47 47
MAPK8 -0.036 0.15 -10000 0 -0.43 48 48
STAT3 (dimer) -0.032 0.14 -10000 0 -0.41 46 46
positive regulation of transcription -0.003 0.074 -10000 0 -0.25 3 3
mol:GDP -0.016 0.14 -10000 0 -0.37 35 35
PIK3C2B -0.033 0.15 -10000 0 -0.42 47 47
CBL/CRKL -0.017 0.14 0.28 1 -0.38 43 44
FER -0.032 0.14 -10000 0 -0.42 48 48
SH2B3 -0.032 0.14 -10000 0 -0.42 47 47
PDPK1 -0.011 0.13 0.3 1 -0.36 39 40
SNAI2 -0.031 0.14 -10000 0 -0.41 39 39
positive regulation of cell proliferation -0.069 0.26 -10000 0 -0.74 48 48
KITLG 0.018 0.049 -10000 0 -0.49 3 3
cell motility -0.069 0.26 -10000 0 -0.74 48 48
PTPN6 0.027 0.011 -10000 0 -10000 0 0
EPOR -0.01 0.17 -10000 0 -0.84 9 9
STAT5A (dimer) -0.051 0.21 -10000 0 -0.6 49 49
SOCS1 0.005 0.096 -10000 0 -0.39 23 23
cell migration 0.035 0.14 0.42 48 -10000 0 48
SOS1 0.028 0.004 -10000 0 -10000 0 0
EPO -0.018 0.12 -10000 0 -0.39 38 38
VAV1 0.022 0.054 -10000 0 -0.47 5 5
GRB10 -0.03 0.14 -10000 0 -0.42 41 41
PTPN11 0.029 0.007 -10000 0 -10000 0 0
SCF/KIT -0.031 0.15 -10000 0 -0.44 47 47
GO:0007205 0.001 0.008 -10000 0 -10000 0 0
MAP2K1 -0.008 0.088 0.19 1 -0.3 3 4
CBL 0.026 0.008 -10000 0 -10000 0 0
KIT -0.12 0.42 -10000 0 -1.2 51 51
MAP2K2 -0.008 0.086 0.19 1 -0.3 2 3
SHC/Grb2/SOS1 0.004 0.15 -10000 0 -0.39 42 42
STAT5A -0.049 0.22 -10000 0 -0.62 49 49
GRB2 0.028 0.004 -10000 0 -10000 0 0
response to radiation -0.029 0.14 0.24 2 -0.4 39 41
SHC/GRAP2 0.033 0.051 -10000 0 -0.3 9 9
PTPRO -0.037 0.15 -10000 0 -0.42 48 48
SH2B2 -0.034 0.14 -10000 0 -0.42 45 45
DOK1 0.028 0.003 -10000 0 -10000 0 0
MATK -0.036 0.15 -10000 0 -0.42 48 48
CREBBP 0.027 0.049 -10000 0 -10000 0 0
BCL2 -0.067 0.29 -10000 0 -1.1 23 23
Canonical Wnt signaling 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
HDAC1 0.026 0.017 0.22 2 -10000 0 2
AES 0.026 0.015 0.21 1 -10000 0 1
FBXW11 0.027 0.007 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.036 0.028 -10000 0 -0.3 2 2
SMAD4 0.025 0.009 -10000 0 -10000 0 0
DKK2 0.009 0.089 -10000 0 -0.42 17 17
TLE1 0.026 0.015 0.21 1 -10000 0 1
MACF1 0.028 0.005 -10000 0 -10000 0 0
CTNNB1 0.034 0.12 0.3 10 -0.39 10 20
WIF1 -0.2 0.23 -10000 0 -0.46 178 178
beta catenin/RanBP3 -0.01 0.1 0.39 10 -0.39 4 14
KREMEN2 -0.12 0.2 -10000 0 -0.39 147 147
DKK1 -0.11 0.2 -10000 0 -0.4 135 135
beta catenin/beta TrCP1 0.046 0.12 0.3 10 -0.4 5 15
FZD1 0.026 0.022 -10000 0 -0.39 1 1
AXIN2 -0.005 0.16 0.6 4 -1.3 5 9
AXIN1 0.028 0.005 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.026 0.093 -10000 0 -0.58 7 7
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.043 0.12 0.34 2 -0.5 9 11
Axin1/APC/GSK3 0.043 0.071 0.25 5 -0.43 2 7
Axin1/APC/GSK3/beta catenin/Macf1 0.038 0.1 0.31 7 -0.44 4 11
HNF1A 0.019 0.056 0.2 2 -0.4 7 9
CTBP1 0.025 0.017 0.23 1 -10000 0 1
MYC 0.12 0.24 0.58 87 -0.51 2 89
RANBP3 0.027 0.005 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.054 0.14 -10000 0 -0.24 150 150
NKD1 0.009 0.084 -10000 0 -0.4 17 17
TCF4 0.024 0.017 0.22 1 -10000 0 1
TCF3 0.026 0.015 0.22 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.057 0.044 -10000 0 -0.27 1 1
Ran/GTP 0.021 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.005 0.11 0.44 12 -0.4 5 17
LEF1 0.021 0.05 0.2 2 -0.41 5 7
DVL1 0.049 0.064 0.23 1 -0.49 2 3
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.064 0.092 0.27 3 -0.47 3 6
DKK1/LRP6/Kremen 2 -0.12 0.18 -10000 0 -0.28 219 219
LRP6 0.026 0.025 -10000 0 -0.47 1 1
CSNK1A1 0.026 0.018 0.22 2 -10000 0 2
NLK 0.028 0.007 -10000 0 -10000 0 0
CCND1 0.15 0.28 0.58 106 -1.5 2 108
WNT1 0.016 0.052 -10000 0 -0.39 6 6
GSK3A 0.028 0.005 -10000 0 -10000 0 0
GSK3B 0.025 0.009 -10000 0 -10000 0 0
FRAT1 0.028 0.004 -10000 0 -10000 0 0
PPP2R5D 0.039 0.08 0.23 12 -0.41 6 18
APC 0.026 0.067 0.32 5 -0.25 2 7
WNT1/LRP6/FZD1 0.082 0.097 0.21 140 -10000 0 140
CREBBP 0.026 0.015 0.2 2 -10000 0 2
Reelin signaling pathway

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
CDK5R1/CDK5 0.038 0.019 -10000 0 -0.28 1 1
VLDLR 0.021 0.043 -10000 0 -0.47 3 3
CRKL 0.027 0.021 -10000 0 -0.39 1 1
LRPAP1 0.026 0.008 -10000 0 -10000 0 0
FYN 0.027 0.021 -10000 0 -0.39 1 1
ITGA3 0.011 0.084 -10000 0 -0.4 17 17
RELN/VLDLR/Fyn -0.012 0.13 -10000 0 -0.28 73 73
MAPK8IP1/MKK7/MAP3K11/JNK1 0.069 0.046 -10000 0 -0.24 4 4
AKT1 -0.019 0.076 -10000 0 -0.32 6 6
MAP2K7 0.028 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
DAB1 -0.002 0.078 -10000 0 -0.39 15 15
RELN/LRP8/DAB1 -0.02 0.13 -10000 0 -0.26 90 90
LRPAP1/LRP8 0.032 0.047 -10000 0 -0.27 9 9
RELN/LRP8/DAB1/Fyn -0.009 0.13 -10000 0 -0.26 70 70
DAB1/alpha3/beta1 Integrin -0.019 0.12 -10000 0 -0.38 5 5
long-term memory -0.05 0.16 -10000 0 -0.45 17 17
DAB1/LIS1 -0.003 0.12 -10000 0 -0.38 4 4
DAB1/CRLK/C3G -0.011 0.12 -10000 0 -0.38 5 5
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
DAB1/NCK2 -0.002 0.13 -10000 0 -0.38 4 4
ARHGEF2 0.028 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.061 0.18 -10000 0 -0.44 78 78
CDK5R1 0.027 0.021 -10000 0 -0.39 1 1
RELN -0.061 0.19 -10000 0 -0.47 73 73
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
RELN/LRP8/Fyn -0.014 0.13 -10000 0 -0.29 80 80
GRIN2A/RELN/LRP8/DAB1/Fyn -0.048 0.16 -10000 0 -0.29 99 99
MAPK8 0.021 0.059 -10000 0 -0.47 6 6
RELN/VLDLR/DAB1 -0.019 0.12 -10000 0 -0.25 84 84
ITGB1 0.028 0.005 -10000 0 -10000 0 0
MAP1B -0.033 0.13 0.2 1 -0.28 64 65
RELN/LRP8 -0.015 0.13 -10000 0 -0.29 78 78
GRIN2B/RELN/LRP8/DAB1/Fyn -0.003 0.13 -10000 0 -0.27 55 55
PI3K 0.027 0.032 -10000 0 -0.34 2 2
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.064 -10000 0 -0.28 17 17
RAP1A -0.026 0.12 0.34 10 -0.38 4 14
PAFAH1B1 0.027 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.024 0.038 -10000 0 -0.42 3 3
CRLK/C3G 0.039 0.018 -10000 0 -0.28 1 1
GRIN2B -0.009 0.043 -10000 0 -0.39 4 4
NCK2 0.028 0.003 -10000 0 -10000 0 0
neuron differentiation -0.01 0.089 -10000 0 -0.31 11 11
neuron adhesion -0.033 0.12 0.33 10 -0.37 5 15
LRP8 0.019 0.061 -10000 0 -0.39 9 9
GSK3B -0.01 0.085 -10000 0 -0.3 7 7
RELN/VLDLR/DAB1/Fyn -0.009 0.12 -10000 0 -0.25 70 70
MAP3K11 0.027 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.018 0.086 -10000 0 -0.24 47 47
CDK5 0.027 0.007 -10000 0 -10000 0 0
MAPT -0.18 0.22 0.8 1 -0.43 175 176
neuron migration -0.018 0.13 0.31 7 -0.34 7 14
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.011 0.089 -10000 0 -0.31 11 11
RELN/VLDLR -0.004 0.13 -10000 0 -0.26 77 77
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.027 0.021 -10000 0 -0.39 1 1
RAS family/GTP/Tiam1 -0.063 0.1 -10000 0 -0.24 54 54
NT3 (dimer)/TRKC -0.15 0.22 -10000 0 -0.4 183 183
NT3 (dimer)/TRKB -0.14 0.22 -10000 0 -0.36 191 191
SHC/Grb2/SOS1/GAB1/PI3K 0.021 0.024 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
BDNF -0.006 0.12 -10000 0 -0.43 31 31
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
DYNLT1 0.028 0.004 -10000 0 -10000 0 0
NTRK1 -0.005 0.11 -10000 0 -0.39 32 32
NTRK2 -0.1 0.21 -10000 0 -0.45 114 114
NTRK3 -0.099 0.21 -10000 0 -0.47 103 103
NT-4/5 (dimer)/TRKB -0.05 0.16 -10000 0 -0.29 126 126
neuron apoptosis 0.043 0.12 0.38 16 -10000 0 16
SHC 2-3/Grb2 -0.046 0.13 -10000 0 -0.41 16 16
SHC1 0.028 0.004 -10000 0 -10000 0 0
SHC2 -0.046 0.12 -10000 0 -0.38 22 22
SHC3 -0.043 0.12 -10000 0 -0.45 14 14
STAT3 (dimer) 0.025 0.06 -10000 0 -0.34 11 11
NT3 (dimer)/TRKA -0.08 0.17 -10000 0 -0.3 157 157
RIN/GDP -0.03 0.098 0.23 8 -0.25 4 12
GIPC1 0.028 0.003 -10000 0 -10000 0 0
KRAS 0.027 0.007 -10000 0 -10000 0 0
DNAJA3 -0.011 0.085 0.24 3 -0.28 8 11
RIN/GTP 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.011 0.052 -10000 0 -0.73 2 2
MAGED1 0.023 0.045 -10000 0 -0.43 4 4
PTPN11 0.028 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.025 0.032 -10000 0 -0.43 2 2
SHC/GRB2/SOS1 0.055 0.013 -10000 0 -10000 0 0
GRB2 0.028 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.029 0.13 -10000 0 -0.24 113 113
TRKA/NEDD4-2 0.014 0.081 -10000 0 -0.28 30 30
ELMO1 0.025 0.025 -10000 0 -0.47 1 1
RhoG/GTP/ELMO1/DOCK1 0.034 0.025 -10000 0 -0.28 2 2
NGF -0.052 0.16 -10000 0 -0.4 77 77
HRAS 0.026 0.022 -10000 0 -0.4 1 1
DOCK1 0.027 0.024 -10000 0 -0.47 1 1
GAB2 0.023 0.035 -10000 0 -0.47 2 2
RIT2 -0.015 0.011 -10000 0 -10000 0 0
RIT1 0.028 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
DNM1 -0.002 0.11 -10000 0 -0.39 29 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.002 0.087 0.22 1 -0.28 9 10
mol:GDP -0.047 0.13 0.29 7 -0.35 7 14
NGF (dimer) -0.052 0.16 -10000 0 -0.4 77 77
RhoG/GDP 0.019 0.018 -10000 0 -0.33 1 1
RIT1/GDP -0.03 0.095 0.19 6 -0.24 4 10
TIAM1 0.021 0.054 -10000 0 -0.47 5 5
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
BDNF (dimer)/TRKB -0.057 0.16 -10000 0 -0.28 136 136
KIDINS220/CRKL/C3G 0.039 0.018 -10000 0 -0.28 1 1
SHC/RasGAP 0.039 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2 0.053 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.067 0.021 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.004 -10000 0 -10000 0 0
NT3 (dimer) -0.12 0.22 -10000 0 -0.47 126 126
RAP1/GDP -0.029 0.078 0.13 2 -0.21 2 4
KIDINS220/CRKL 0.027 0.021 -10000 0 -0.39 1 1
BDNF (dimer) -0.006 0.12 -10000 0 -0.43 31 31
ubiquitin-dependent protein catabolic process -0.022 0.12 -10000 0 -0.24 102 102
Schwann cell development -0.037 0.032 -10000 0 -10000 0 0
EHD4 0.028 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.065 0.024 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.03 0.043 -10000 0 -10000 0 0
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.17 0.22 -10000 0 -0.48 116 116
ABL1 0.028 0.005 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.041 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.01 0.082 -10000 0 -0.38 5 5
STAT3 0.025 0.06 -10000 0 -0.34 11 11
axon guidance -0.17 0.21 -10000 0 -0.46 116 116
MAPK3 -0.044 0.11 -10000 0 -0.32 10 10
MAPK1 -0.043 0.11 -10000 0 -0.32 10 10
CDC42/GDP -0.027 0.099 0.23 9 -0.24 4 13
NTF3 -0.12 0.23 -10000 0 -0.47 126 126
NTF4 0.025 0.032 -10000 0 -0.43 2 2
NGF (dimer)/TRKA/FAIM -0.023 0.12 -10000 0 -0.24 95 95
PI3K 0.027 0.032 -10000 0 -0.34 2 2
FRS3 0.027 0.006 -10000 0 -10000 0 0
FAIM 0.024 0.011 -10000 0 -10000 0 0
GAB1 0.027 0.006 -10000 0 -10000 0 0
RASGRF1 -0.047 0.12 0.21 2 -0.3 38 40
SOS1 0.028 0.004 -10000 0 -10000 0 0
MCF2L -0.15 0.2 -10000 0 -0.36 185 185
RGS19 0.027 0.006 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.031 0.07 0.26 2 -0.43 1 3
Rac1/GDP -0.026 0.093 0.2 6 -0.24 4 10
NGF (dimer)/TRKA/GRIT -0.033 0.12 -10000 0 -0.24 104 104
neuron projection morphogenesis 0.006 0.11 0.33 1 -0.69 5 6
NGF (dimer)/TRKA/NEDD4-2 -0.022 0.13 -10000 0 -0.24 102 102
MAP2K1 0.023 0.038 0.36 1 -10000 0 1
NGFR 0.006 0.099 -10000 0 -0.42 21 21
NGF (dimer)/TRKA/GIPC/GAIP -0.012 0.071 -10000 0 -0.32 1 1
RAS family/GTP/PI3K 0.017 0.022 -10000 0 -0.22 2 2
FRS2 family/SHP2/GRB2/SOS1 0.075 0.027 -10000 0 -10000 0 0
NRAS 0.027 0.006 -10000 0 -10000 0 0
GRB2/SOS1 0.041 0.008 -10000 0 -10000 0 0
PRKCI 0.02 0.013 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCZ 0.026 0.025 -10000 0 -0.47 1 1
MAPKKK cascade -0.028 0.11 -10000 0 -0.45 19 19
RASA1 0.026 0.025 -10000 0 -0.47 1 1
TRKA/c-Abl 0.016 0.084 -10000 0 -0.28 32 32
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.038 0.16 -10000 0 -0.26 130 130
NGF (dimer)/TRKA/p62/Atypical PKCs -0.007 0.11 -10000 0 -0.3 7 7
MATK 0.017 0.064 -10000 0 -0.39 10 10
NEDD4L 0.025 0.009 -10000 0 -10000 0 0
RAS family/GDP -0.047 0.058 -10000 0 -0.2 5 5
NGF (dimer)/TRKA -0.025 0.073 0.21 3 -0.26 16 19
Rac1/GTP -0.068 0.081 -10000 0 -0.26 20 20
FRS2 family/SHP2/CRK family 0.072 0.033 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.004 0.001 -10000 0 -10000 0 0
ADCY5 -0.067 0.12 -10000 0 -0.28 95 95
ADCY6 -0.012 0.045 -10000 0 -0.28 11 11
ADCY7 -0.004 0.001 -10000 0 -10000 0 0
ADCY1 -0.015 0.047 -10000 0 -0.23 19 19
ADCY2 -0.087 0.13 -10000 0 -0.28 125 125
ADCY3 -0.005 0.001 -10000 0 -10000 0 0
ADCY8 -0.013 0.034 -10000 0 -0.23 10 10
PRKCE 0.008 0.001 -10000 0 -10000 0 0
ADCY9 -0.006 0.019 -10000 0 -0.28 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.007 0.11 0.22 30 -0.3 4 34
Thromboxane A2 receptor 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
TGM2 -0.002 0.1 -10000 0 -0.39 28 28
GNB1/GNG2 -0.043 0.066 -10000 0 -0.18 52 52
AKT1 -0.017 0.11 0.2 10 -0.27 22 32
EGF -0.062 0.19 -10000 0 -0.47 75 75
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.02 0.077 0.27 7 -0.31 1 8
mol:Ca2+ -0.03 0.14 0.25 2 -0.3 56 58
LYN 0.016 0.071 0.28 5 -0.31 1 6
RhoA/GTP -0.014 0.057 0.11 1 -0.14 3 4
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.036 0.15 0.26 6 -0.34 57 63
GNG2 0.027 0.007 -10000 0 -10000 0 0
ARRB2 0.027 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.011 0.12 0.27 1 -0.52 14 15
G beta5/gamma2 -0.054 0.087 -10000 0 -0.24 47 47
PRKCH -0.036 0.16 0.28 10 -0.35 56 66
DNM1 -0.002 0.11 -10000 0 -0.39 29 29
TXA2/TP beta/beta Arrestin3 0.005 0.042 -10000 0 -0.47 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.019 0.057 -10000 0 -0.42 7 7
G12 family/GTP -0.044 0.12 -10000 0 -0.3 52 52
ADRBK1 0.026 0.008 -10000 0 -10000 0 0
ADRBK2 0.027 0.021 -10000 0 -0.39 1 1
RhoA/GTP/ROCK1 0.033 0.014 -10000 0 -10000 0 0
mol:GDP 0.009 0.095 0.33 7 -0.22 1 8
mol:NADP 0.021 0.046 -10000 0 -0.39 5 5
RAB11A 0.028 0.005 -10000 0 -10000 0 0
PRKG1 0.007 0.093 -10000 0 -0.42 19 19
mol:IP3 -0.042 0.17 0.3 1 -0.37 57 58
cell morphogenesis 0.032 0.014 -10000 0 -10000 0 0
PLCB2 -0.065 0.22 0.33 1 -0.51 57 58
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.007 0.1 0.27 7 -0.34 3 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.017 0.076 0.27 7 -0.31 1 8
RHOA 0.024 0.01 -10000 0 -10000 0 0
PTGIR 0.013 0.078 -10000 0 -0.39 15 15
PRKCB1 -0.043 0.16 0.28 1 -0.37 61 62
GNAQ 0.028 0.005 -10000 0 -10000 0 0
mol:L-citrulline 0.021 0.046 -10000 0 -0.39 5 5
TXA2/TXA2-R family -0.066 0.22 0.33 1 -0.51 62 63
LCK 0.016 0.083 0.27 7 -0.31 1 8
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.017 0.071 -10000 0 -0.31 8 8
TXA2-R family/G12 family/GDP/G beta/gamma 0.018 0.08 -10000 0 -0.44 10 10
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.022 0.07 -10000 0 -0.3 8 8
MAPK14 -0.018 0.11 0.21 13 -0.23 51 64
TGM2/GTP -0.059 0.18 -10000 0 -0.42 49 49
MAPK11 -0.018 0.11 0.23 11 -0.23 42 53
ARHGEF1 -0.018 0.082 0.18 4 -0.18 40 44
GNAI2 0.024 0.01 -10000 0 -10000 0 0
JNK cascade -0.043 0.17 0.26 4 -0.38 62 66
RAB11/GDP 0.027 0.005 -10000 0 -10000 0 0
ICAM1 -0.03 0.13 0.23 3 -0.28 69 72
cAMP biosynthetic process -0.041 0.15 0.3 1 -0.35 51 52
Gq family/GTP/EBP50 -0.011 0.093 0.23 6 -0.38 8 14
actin cytoskeleton reorganization 0.032 0.014 -10000 0 -10000 0 0
SRC 0.018 0.074 0.27 7 -0.31 1 8
GNB5 0.028 0.005 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
EGF/EGFR 0.01 0.1 0.23 29 -0.27 2 31
VCAM1 -0.036 0.14 0.22 3 -0.3 74 77
TP beta/Gq family/GDP/G beta5/gamma2 -0.011 0.12 0.27 1 -0.52 14 15
platelet activation -0.023 0.14 0.29 10 -0.3 51 61
PGI2/IP 0.01 0.055 -10000 0 -0.28 15 15
PRKACA 0.012 0.037 -10000 0 -0.25 4 4
Gq family/GDP/G beta5/gamma2 -0.006 0.1 0.28 1 -0.43 14 15
TXA2/TP beta/beta Arrestin2 0.001 0.049 -10000 0 -0.29 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.006 0.064 -10000 0 -0.32 10 10
mol:DAG -0.049 0.18 0.31 1 -0.42 60 61
EGFR 0.022 0.035 -10000 0 -0.47 2 2
TXA2/TP alpha -0.059 0.2 0.35 1 -0.47 53 54
Gq family/GTP -0.026 0.095 0.26 3 -0.23 64 67
YES1 0.016 0.07 0.27 5 -0.31 1 6
GNAI2/GTP 0.007 0.058 -10000 0 -0.27 7 7
PGD2/DP 0.014 0.04 -10000 0 -0.29 7 7
SLC9A3R1 0.023 0.048 -10000 0 -0.47 4 4
FYN 0.019 0.077 0.27 6 -0.3 2 8
mol:NO 0.021 0.046 -10000 0 -0.39 5 5
GNA15 0.025 0.034 -10000 0 -0.47 2 2
PGK/cGMP 0.019 0.066 -10000 0 -0.24 24 24
RhoA/GDP 0.024 0.01 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.019 0.092 -10000 0 -0.35 11 11
NOS3 0.021 0.046 -10000 0 -0.39 5 5
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA -0.038 0.15 0.27 2 -0.35 58 60
PRKCB -0.041 0.16 0.29 3 -0.35 63 66
PRKCE -0.037 0.16 0.28 2 -0.35 59 61
PRKCD -0.046 0.16 0.27 1 -0.37 63 64
PRKCG -0.052 0.17 0.28 1 -0.39 67 68
muscle contraction -0.06 0.2 0.31 1 -0.47 62 63
PRKCZ -0.039 0.15 0.24 4 -0.34 61 65
ARR3 -0.013 0.015 -10000 0 -10000 0 0
TXA2/TP beta 0.021 0.07 -10000 0 -0.3 7 7
PRKCQ -0.042 0.16 0.28 1 -0.35 63 64
MAPKKK cascade -0.055 0.19 0.32 1 -0.44 59 60
SELE -0.044 0.16 0.22 3 -0.37 64 67
TP beta/GNAI2/GDP/G beta/gamma 0.03 0.073 -10000 0 -0.31 8 8
ROCK1 0.028 0.003 -10000 0 -10000 0 0
GNA14 -0.048 0.18 -10000 0 -0.47 64 64
chemotaxis -0.08 0.25 0.32 1 -0.58 68 69
GNA12 0.025 0.022 -10000 0 -0.39 1 1
GNA13 0.028 0.004 -10000 0 -10000 0 0
GNA11 0.025 0.034 -10000 0 -0.47 2 2
Rac1/GTP 0.019 0.006 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.054 0.18 -10000 0 -0.46 65 65
NFATC2 -0.025 0.19 -10000 0 -0.6 26 26
NFATC3 -0.003 0.067 -10000 0 -0.29 3 3
CD40LG -0.25 0.31 -10000 0 -0.82 55 55
ITCH 0.005 0.077 -10000 0 -10000 0 0
CBLB 0.002 0.079 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.2 0.31 -10000 0 -0.86 55 55
JUNB 0.028 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.098 -10000 0 -0.26 44 44
T cell anergy -0.009 0.14 0.3 6 -0.37 43 49
TLE4 -0.015 0.14 -10000 0 -0.53 12 12
Jun/NFAT1-c-4/p21SNFT -0.09 0.23 -10000 0 -0.87 15 15
AP-1/NFAT1-c-4 -0.24 0.31 -10000 0 -0.9 40 40
IKZF1 -0.019 0.16 -10000 0 -0.63 15 15
T-helper 2 cell differentiation -0.059 0.2 -10000 0 -0.72 21 21
AP-1/NFAT1 -0.088 0.18 -10000 0 -0.47 39 39
CALM1 0.015 0.062 -10000 0 -10000 0 0
EGR2 -0.061 0.27 -10000 0 -1.3 14 14
EGR3 -0.049 0.22 -10000 0 -1.1 10 10
NFAT1/FOXP3 -0.063 0.22 -10000 0 -0.52 54 54
EGR1 0.008 0.093 -10000 0 -0.47 15 15
JUN -0.021 0.043 -10000 0 -0.2 1 1
EGR4 -0.023 0.14 -10000 0 -0.4 48 48
mol:Ca2+ -0.011 0.056 -10000 0 -0.24 2 2
GBP3 -0.032 0.18 -10000 0 -0.64 24 24
FOSL1 0.018 0.062 -10000 0 -0.4 9 9
NFAT1-c-4/MAF/IRF4 -0.049 0.22 -10000 0 -0.89 14 14
DGKA -0.015 0.14 -10000 0 -0.51 12 12
CREM 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.14 0.24 -10000 0 -0.83 22 22
CTLA4 -0.089 0.22 -10000 0 -0.57 58 58
NFAT1-c-4 (dimer)/EGR1 -0.056 0.23 -10000 0 -0.92 15 15
NFAT1-c-4 (dimer)/EGR4 -0.071 0.22 -10000 0 -0.85 17 17
FOS -0.082 0.16 -10000 0 -0.49 53 53
IFNG -0.12 0.23 -10000 0 -0.67 36 36
T cell activation -0.088 0.16 -10000 0 -0.65 10 10
MAF 0.022 0.048 -10000 0 -0.47 4 4
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.037 0.14 0.66 13 -10000 0 13
TNF -0.09 0.22 -10000 0 -0.83 20 20
FASLG -0.11 0.33 -10000 0 -1.4 20 20
TBX21 -0.011 0.11 -10000 0 -0.45 22 22
BATF3 0.026 0.029 -10000 0 -0.39 2 2
PRKCQ 0.016 0.065 -10000 0 -0.45 7 7
PTPN1 -0.015 0.14 -10000 0 -0.48 15 15
NFAT1-c-4/ICER1 -0.048 0.21 -10000 0 -0.89 13 13
GATA3 0.013 0.078 -10000 0 -0.4 14 14
T-helper 1 cell differentiation -0.11 0.23 -10000 0 -0.65 37 37
IL2RA -0.18 0.28 -10000 0 -0.75 59 59
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.015 0.13 -10000 0 -0.47 17 17
E2F1 0.016 0.076 -10000 0 -0.39 14 14
PPARG -0.14 0.23 -10000 0 -0.47 140 140
SLC3A2 -0.014 0.13 -10000 0 -0.5 13 13
IRF4 -0.004 0.11 -10000 0 -0.41 29 29
PTGS2 -0.25 0.3 -10000 0 -0.8 57 57
CSF2 -0.32 0.32 -10000 0 -0.79 78 78
JunB/Fra1/NFAT1-c-4 -0.035 0.21 -10000 0 -0.87 13 13
IL4 -0.061 0.21 -10000 0 -0.76 20 20
IL5 -0.23 0.28 -10000 0 -0.81 38 38
IL2 -0.089 0.16 -10000 0 -0.66 10 10
IL3 -0.056 0.15 -10000 0 -0.66 19 19
RNF128 -0.038 0.19 -10000 0 -0.54 51 51
NFATC1 -0.036 0.14 -10000 0 -0.67 13 13
CDK4 0.035 0.12 0.63 3 -10000 0 3
PTPRK -0.015 0.13 -10000 0 -0.47 17 17
IL8 -0.26 0.31 -10000 0 -0.79 58 58
POU2F1 0.028 0.005 -10000 0 -10000 0 0
IGF1 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
NCK2 0.028 0.003 -10000 0 -10000 0 0
PTK2 0.023 0.011 -10000 0 -10000 0 0
CRKL -0.019 0.091 -10000 0 -0.24 55 55
GRB2/SOS1/SHC 0.055 0.013 -10000 0 -10000 0 0
HRAS 0.026 0.022 -10000 0 -0.4 1 1
IRS1/Crk -0.011 0.094 -10000 0 -0.24 55 55
IGF-1R heterotetramer/IGF1/PTP1B 0.009 0.11 -10000 0 -0.27 56 56
AKT1 0.011 0.1 0.18 83 -0.4 2 85
BAD 0.007 0.097 0.22 11 -0.38 2 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.019 0.09 -10000 0 -0.24 55 55
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.006 0.097 0.21 1 -0.25 55 56
RAF1 -0.011 0.16 0.28 9 -0.44 35 44
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.025 0.1 -10000 0 -0.24 50 50
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.007 0.1 -10000 0 -0.26 60 60
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
RPS6KB1 0.015 0.11 0.18 93 -0.4 2 95
GNB2L1 0.026 0.007 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.008 0.14 0.26 12 -0.36 26 38
PXN 0.028 0.003 -10000 0 -10000 0 0
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.041 0.008 -10000 0 -10000 0 0
HRAS/GTP -0.001 0.085 -10000 0 -0.39 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.039 0.1 -10000 0 -0.27 1 1
IGF-1R heterotetramer 0.015 0.038 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.01 0.1 -10000 0 -0.25 53 53
Crk/p130 Cas/Paxillin 0.021 0.099 -10000 0 -0.37 1 1
IGF1R 0.015 0.038 -10000 0 -10000 0 0
IGF1 -0.044 0.18 -10000 0 -0.47 62 62
IRS2/Crk -0.01 0.091 -10000 0 -0.23 55 55
PI3K 0.015 0.09 -10000 0 -0.24 33 33
apoptosis -0.028 0.091 0.32 1 -0.26 12 13
HRAS/GDP 0.019 0.015 -10000 0 -0.28 1 1
PRKCD -0.027 0.12 -10000 0 -0.34 49 49
RAF1/14-3-3 E 0 0.16 0.29 11 -0.38 33 44
BAD/14-3-3 0.029 0.095 0.27 12 -0.34 1 13
PRKCZ 0.009 0.11 0.23 11 -0.4 2 13
Crk/p130 Cas/Paxillin/FAK1 0.024 0.078 -10000 0 -0.32 1 1
PTPN1 0.027 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.03 0.13 -10000 0 -0.36 55 55
BCAR1 0.027 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.022 0.11 -10000 0 -0.36 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.028 0.004 -10000 0 -10000 0 0
IRS1/NCK2 -0.003 0.096 -10000 0 -0.24 53 53
GRB10 0.025 0.022 -10000 0 -0.39 1 1
PTPN11 -0.018 0.091 -10000 0 -0.25 55 55
IRS1 -0.021 0.099 -10000 0 -0.26 56 56
IRS2 -0.02 0.092 -10000 0 -0.25 56 56
IGF-1R heterotetramer/IGF1 -0.014 0.14 -10000 0 -0.35 59 59
GRB2 0.028 0.004 -10000 0 -10000 0 0
PDPK1 0.023 0.11 0.25 8 -0.42 2 10
YWHAE 0.027 0.006 -10000 0 -10000 0 0
PRKD1 -0.034 0.13 -10000 0 -0.36 47 47
SHC1 0.028 0.004 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.03 0.09 -10000 0 -0.4 11 11
HDAC1 0.025 0.006 -10000 0 -10000 0 0
AES 0.027 0.005 -10000 0 -10000 0 0
FBXW11 0.027 0.007 -10000 0 -10000 0 0
DTX1 0.026 0.034 -10000 0 -0.47 2 2
LRP6/FZD1 0.035 0.028 -10000 0 -0.31 2 2
TLE1 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.021 0.094 -10000 0 -0.25 54 54
NCSTN 0.028 0.005 -10000 0 -10000 0 0
ADAM10 0.026 0.025 -10000 0 -0.47 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.018 0.12 -10000 0 -0.71 9 9
NICD/RBPSUH 0.03 0.086 -10000 0 -0.4 9 9
WIF1 -0.2 0.23 -10000 0 -0.46 178 178
NOTCH1 0.013 0.083 -10000 0 -0.4 16 16
PSENEN 0.027 0.005 -10000 0 -10000 0 0
KREMEN2 -0.12 0.2 -10000 0 -0.39 147 147
DKK1 -0.11 0.2 -10000 0 -0.4 135 135
beta catenin/beta TrCP1 -0.008 0.11 -10000 0 -0.4 16 16
APH1B 0.028 0.005 -10000 0 -10000 0 0
APH1A 0.027 0.005 -10000 0 -10000 0 0
AXIN1 0.004 0.069 -10000 0 -0.41 7 7
CtBP/CBP/TCF1/TLE1/AES 0.017 0.03 -10000 0 -0.26 1 1
PSEN1 0.026 0.007 -10000 0 -10000 0 0
FOS -0.036 0.16 -10000 0 -0.47 53 53
JUN 0.028 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 -0.02 0.11 0.25 1 -0.4 20 21
MAPK3 0.028 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.054 0.14 -10000 0 -0.24 150 150
HNF1A 0.02 0.054 -10000 0 -0.39 7 7
CTBP1 0.025 0.008 -10000 0 -10000 0 0
MYC 0.021 0.044 -10000 0 -0.77 1 1
NKD1 0.009 0.084 -10000 0 -0.4 17 17
FZD1 0.025 0.022 -10000 0 -0.39 1 1
NOTCH1 precursor/Deltex homolog 1 0.032 0.091 -10000 0 -0.41 12 12
apoptosis -0.021 0.094 -10000 0 -0.25 54 54
Delta 1/NOTCHprecursor 0.029 0.09 -10000 0 -0.4 11 11
DLL1 0.021 0.059 -10000 0 -0.47 6 6
PPARD 0.007 0.14 -10000 0 -0.83 11 11
Gamma Secretase 0.074 0.029 -10000 0 -10000 0 0
APC -0.01 0.1 -10000 0 -0.4 22 22
DVL1 -0.013 0.074 -10000 0 -0.4 8 8
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.12 0.18 -10000 0 -0.28 219 219
LRP6 0.026 0.025 -10000 0 -0.47 1 1
CSNK1A1 0.027 0.007 -10000 0 -10000 0 0
NLK 0.013 0.005 -10000 0 -10000 0 0
CCND1 -0.001 0.14 -10000 0 -0.95 7 7
WNT1 0.01 0.053 -10000 0 -0.39 6 6
Axin1/APC/beta catenin -0.004 0.13 0.29 3 -0.48 18 21
DKK2 0.009 0.089 -10000 0 -0.42 17 17
NOTCH1 precursor/DVL1 -0.003 0.11 -10000 0 -0.55 10 10
GSK3B 0.025 0.009 -10000 0 -10000 0 0
FRAT1 0.027 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.033 0.091 -10000 0 -0.41 12 12
PPP2R5D 0.006 0.082 0.21 7 -0.38 12 19
MAPK1 0.027 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.075 0.15 -10000 0 -0.26 153 153
RBPJ 0.026 0.008 -10000 0 -10000 0 0
CREBBP 0.03 0.006 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.007 0.1 0.21 1 -0.37 12 13
PDGFB-D/PDGFRB/SLAP -0.028 0.12 -10000 0 -0.27 82 82
PDGFB-D/PDGFRB/APS/CBL -0.008 0.11 -10000 0 -0.23 83 83
AKT1 0.018 0.12 0.38 11 -0.33 2 13
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.002 0.12 0.28 12 -0.39 16 28
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
FGR -0.024 0.12 0.34 1 -0.55 11 12
mol:Ca2+ -0.007 0.13 0.28 12 -0.4 21 33
MYC 0.054 0.14 0.38 31 -0.37 1 32
SHC1 0.028 0.004 -10000 0 -10000 0 0
HRAS/GDP -0.003 0.097 -10000 0 -0.23 1 1
LRP1/PDGFRB/PDGFB -0.009 0.12 -10000 0 -0.24 91 91
GRB10 0.025 0.022 -10000 0 -0.39 1 1
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GO:0007205 -0.007 0.13 0.28 12 -0.41 21 33
PTEN 0.028 0.005 -10000 0 -10000 0 0
GRB2 0.028 0.004 -10000 0 -10000 0 0
GRB7 0.027 0.024 -10000 0 -0.47 1 1
PDGFB-D/PDGFRB/SHP2 -0.026 0.13 -10000 0 -0.27 89 89
PDGFB-D/PDGFRB/GRB10 -0.024 0.12 -10000 0 -0.27 84 84
cell cycle arrest -0.028 0.12 -10000 0 -0.27 82 82
HRAS 0.026 0.022 -10000 0 -0.4 1 1
HIF1A 0.014 0.11 0.36 11 -0.31 1 12
GAB1 -0.002 0.12 0.3 6 -0.4 14 20
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.001 0.11 0.27 12 -0.37 10 22
PDGFB-D/PDGFRB -0.007 0.11 -10000 0 -0.23 83 83
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.026 0.13 -10000 0 -0.27 89 89
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.008 0.087 -10000 0 -0.39 4 4
positive regulation of MAPKKK cascade -0.026 0.13 -10000 0 -0.27 89 89
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
mol:IP3 -0.007 0.13 0.28 12 -0.41 21 33
E5 0 0.002 -10000 0 -10000 0 0
CSK 0.027 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.026 0.13 -10000 0 -0.28 88 88
SHB 0.024 0.026 -10000 0 -0.47 1 1
BLK -0.069 0.17 -10000 0 -0.53 35 35
PTPN2 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.026 0.13 -10000 0 -0.27 88 88
BCAR1 0.027 0.006 -10000 0 -10000 0 0
VAV2 0.004 0.12 0.3 12 -0.4 14 26
CBL 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.025 0.13 -10000 0 -0.27 87 87
LCK -0.025 0.12 0.34 1 -0.54 11 12
PDGFRB -0.061 0.17 -10000 0 -0.39 89 89
ACP1 0.028 0.003 -10000 0 -10000 0 0
HCK -0.017 0.1 -10000 0 -0.69 4 4
ABL1 -0.005 0.12 0.28 12 -0.4 13 25
PDGFB-D/PDGFRB/CBL -0.005 0.13 0.36 3 -0.43 20 23
PTPN1 0.027 0.007 -10000 0 -10000 0 0
SNX15 0.027 0.006 -10000 0 -10000 0 0
STAT3 0.028 0.003 -10000 0 -10000 0 0
STAT1 0.007 0.09 -10000 0 -0.39 20 20
cell proliferation 0.054 0.13 0.36 34 -0.34 1 35
SLA 0.021 0.031 -10000 0 -0.39 2 2
actin cytoskeleton reorganization 0.021 0.12 0.34 9 -10000 0 9
SRC -0.02 0.11 -10000 0 -0.64 6 6
PI3K -0.022 0.072 -10000 0 -0.36 2 2
PDGFB-D/PDGFRB/GRB7/SHC -0.005 0.12 -10000 0 -0.23 86 86
SH2B2 0.025 0.022 -10000 0 -0.39 1 1
PLCgamma1/SPHK1 0.001 0.13 0.28 12 -0.4 16 28
LYN -0.014 0.078 -10000 0 -10000 0 0
LRP1 0.027 0.024 -10000 0 -0.47 1 1
SOS1 0.028 0.004 -10000 0 -10000 0 0
STAT5B 0.028 0.003 -10000 0 -10000 0 0
STAT5A 0.028 0.003 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.013 0.1 -10000 0 -10000 0 0
SPHK1 0.02 0.057 -10000 0 -0.39 8 8
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG -0.007 0.13 0.28 12 -0.41 21 33
PLCG1 -0.008 0.13 0.28 12 -0.42 21 33
NHERF/PDGFRB -0.009 0.12 -10000 0 -0.24 90 90
YES1 -0.027 0.099 0.35 1 -0.64 5 6
cell migration -0.009 0.12 -10000 0 -0.24 90 90
SHC/Grb2/SOS1 0.02 0.1 -10000 0 -10000 0 0
SLC9A3R2 0.027 0.021 -10000 0 -0.39 1 1
SLC9A3R1 0.023 0.048 -10000 0 -0.47 4 4
NHERF1-2/PDGFRB/PTEN 0.006 0.12 -10000 0 -0.22 78 78
FYN -0.018 0.091 -10000 0 -0.38 4 4
DOK1 -0.016 0.1 -10000 0 -0.23 1 1
HRAS/GTP 0.019 0.015 -10000 0 -0.28 1 1
PDGFB 0.022 0.05 -10000 0 -0.39 6 6
RAC1 0.018 0.12 0.35 14 -0.4 10 24
PRKCD -0.017 0.099 0.19 7 -10000 0 7
FER -0.015 0.1 -10000 0 -10000 0 0
MAPKKK cascade -0.022 0.1 0.36 6 -10000 0 6
RASA1 -0.015 0.1 0.19 8 -0.24 2 10
NCK1 0.024 0.01 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
p62DOK/Csk -0.004 0.1 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB -0.027 0.13 -10000 0 -0.27 88 88
chemotaxis -0.005 0.12 0.28 12 -0.38 13 25
STAT1-3-5/STAT1-3-5 -0.001 0.11 -10000 0 -0.35 7 7
Bovine Papilomavirus E5/PDGFRB -0.041 0.12 -10000 0 -0.27 89 89
PTPRJ 0.028 0.005 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.037 0.047 -10000 0 -0.21 13 13
RGS9BP 0.013 0.079 -10000 0 -0.47 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.01 0.026 -10000 0 -0.39 1 1
mol:Na + -0.01 0.094 -10000 0 -0.23 62 62
mol:ADP -0.023 0.063 -10000 0 -0.28 23 23
GNAT2 0.02 0.017 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.039 0.067 -10000 0 -0.27 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.009 -10000 0 -10000 0 0
GRK7 -0.004 0.097 -10000 0 -0.39 24 24
CNGB3 -0.044 0.15 -10000 0 -0.39 63 63
Cone Metarhodopsin II/X-Arrestin 0.014 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.051 0.13 0.18 38 -0.23 118 156
Cone PDE6 0.051 0.064 -10000 0 -0.26 9 9
Cone Metarhodopsin II 0.011 0.055 -10000 0 -0.21 23 23
Na + (4 Units) -0.044 0.13 -10000 0 -0.23 122 122
GNAT2/GDP 0.047 0.062 -10000 0 -0.24 12 12
GNB5 0.028 0.005 -10000 0 -10000 0 0
mol:GMP (4 units) -0.007 0.039 0.18 15 -10000 0 15
Cone Transducin 0.04 0.05 -10000 0 -0.23 13 13
SLC24A2 -0.065 0.17 -10000 0 -0.39 85 85
GNB3/GNGT2 0.029 0.059 -10000 0 -0.3 13 13
GNB3 0.015 0.067 -10000 0 -0.41 10 10
GNAT2/GTP 0.019 0.005 -10000 0 -10000 0 0
CNGA3 0.009 0.03 -10000 0 -0.39 1 1
ARR3 -0.013 0.015 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel -0.01 0.094 -10000 0 -0.23 62 62
mol:Pi 0.039 0.067 -10000 0 -0.27 17 17
Cone CNG Channel 0.01 0.088 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + -0.065 0.17 -10000 0 -0.39 85 85
RGS9 0.021 0.056 -10000 0 -0.4 7 7
PDE6C -0.012 0.017 -10000 0 -10000 0 0
GNGT2 0.025 0.04 -10000 0 -0.44 3 3
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.012 0.016 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.027 0.006 -10000 0 -10000 0 0
LAT2 -0.041 0.1 -10000 0 -0.32 14 14
AP1 -0.018 0.14 0.3 1 -0.41 8 9
mol:PIP3 -0.054 0.15 0.35 10 -0.42 13 23
IKBKB -0.022 0.1 0.24 19 -0.26 7 26
AKT1 -0.023 0.16 0.4 18 -0.37 7 25
IKBKG -0.023 0.11 0.26 15 -0.26 7 22
MS4A2 0.013 0.077 -10000 0 -0.45 11 11
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
MAP3K1 0.024 0.13 0.26 60 -0.35 4 64
mol:Ca2+ -0.04 0.12 0.3 12 -0.32 13 25
LYN 0.025 0.012 -10000 0 -10000 0 0
CBLB -0.038 0.099 -10000 0 -0.33 11 11
SHC1 0.028 0.004 -10000 0 -10000 0 0
RasGAP/p62DOK 0.033 0.07 -10000 0 -0.26 22 22
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.026 0.025 -10000 0 -0.47 1 1
PLD2 -0.07 0.14 0.36 9 -0.42 10 19
PTPN13 -0.029 0.12 0.36 1 -0.66 2 3
PTPN11 0.015 0.026 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.001 0.14 0.32 27 -0.34 4 31
SYK 0.025 0.036 -10000 0 -0.48 2 2
GRB2 0.028 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.063 0.13 -10000 0 -0.42 13 13
LAT -0.044 0.11 -10000 0 -0.34 16 16
PAK2 0.02 0.14 0.27 60 -0.39 4 64
NFATC2 -0.079 0.18 -10000 0 -0.56 44 44
HRAS -0.02 0.11 0.26 7 -0.38 9 16
GAB2 0.023 0.035 -10000 0 -0.47 2 2
PLA2G1B -0.077 0.29 -10000 0 -0.81 55 55
Fc epsilon R1 -0.076 0.18 -10000 0 -0.31 151 151
Antigen/IgE/Fc epsilon R1 -0.067 0.16 -10000 0 -0.28 150 150
mol:GDP -0.021 0.11 0.25 2 -0.4 7 9
JUN 0.028 0.005 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
FOS -0.036 0.16 -10000 0 -0.47 53 53
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.04 0.11 -10000 0 -0.32 18 18
CHUK -0.028 0.099 0.26 12 -0.26 7 19
KLRG1 -0.046 0.11 -10000 0 -0.33 16 16
VAV1 -0.043 0.11 -10000 0 -0.34 16 16
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.04 0.1 -10000 0 -0.32 13 13
negative regulation of mast cell degranulation -0.029 0.11 0.24 2 -0.32 13 15
BTK -0.023 0.1 -10000 0 -0.41 5 5
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.075 0.15 -10000 0 -0.41 30 30
GAB2/PI3K/SHP2 -0.059 0.11 -10000 0 -0.4 7 7
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.052 0.11 -10000 0 -0.4 9 9
RAF1 -0.088 0.32 -10000 0 -0.9 55 55
Fc epsilon R1/FcgammaRIIB/SHIP -0.048 0.17 -10000 0 -0.28 115 115
FCER1G 0.018 0.059 -10000 0 -0.4 8 8
FCER1A -0.14 0.24 -10000 0 -0.48 142 142
Antigen/IgE/Fc epsilon R1/Fyn -0.053 0.16 -10000 0 -0.26 137 137
MAPK3 -0.08 0.29 -10000 0 -0.82 55 55
MAPK1 -0.08 0.29 -10000 0 -0.82 55 55
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 0.009 0.14 0.33 1 -0.56 16 17
DUSP1 0.002 0.11 -10000 0 -0.47 21 21
NF-kappa-B/RelA -0.012 0.061 0.14 1 -10000 0 1
actin cytoskeleton reorganization -0.025 0.12 0.37 1 -0.69 2 3
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.017 0.1 -10000 0 -0.41 4 4
FER -0.039 0.1 -10000 0 -0.32 15 15
RELA 0.027 0.006 -10000 0 -10000 0 0
ITK -0.02 0.072 -10000 0 -0.28 21 21
SOS1 0.028 0.004 -10000 0 -10000 0 0
PLCG1 -0.02 0.12 0.31 7 -0.4 8 15
cytokine secretion -0.012 0.041 -10000 0 -10000 0 0
SPHK1 -0.043 0.11 -10000 0 -0.32 20 20
PTK2 -0.026 0.12 0.38 1 -0.74 2 3
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.057 0.14 -10000 0 -0.42 12 12
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.051 0.15 0.35 9 -0.4 13 22
MAP2K2 -0.085 0.29 -10000 0 -0.84 55 55
MAP2K1 -0.085 0.29 -10000 0 -0.84 55 55
MAP2K7 0.028 0.004 -10000 0 -10000 0 0
KLRG1/SHP2 -0.034 0.12 0.22 10 -0.32 15 25
MAP2K4 0.004 0.18 -10000 0 -0.81 19 19
Fc epsilon R1/FcgammaRIIB -0.06 0.17 -10000 0 -0.29 145 145
mol:Choline -0.069 0.14 0.35 9 -0.41 10 19
SHC/Grb2/SOS1 -0.007 0.12 0.25 1 -0.39 5 6
FYN 0.027 0.021 -10000 0 -0.39 1 1
DOK1 0.028 0.003 -10000 0 -10000 0 0
PXN -0.025 0.12 0.36 1 -0.66 2 3
HCLS1 -0.038 0.099 -10000 0 -0.33 12 12
PRKCB -0.04 0.12 0.3 11 -0.34 10 21
FCGR2B 0.021 0.059 -10000 0 -0.47 6 6
IGHE -0.001 0.008 -10000 0 -10000 0 0
KLRG1/SHIP -0.029 0.12 0.24 2 -0.33 13 15
LCP2 0.024 0.036 -10000 0 -0.39 3 3
PLA2G4A -0.051 0.12 -10000 0 -0.34 25 25
RASA1 0.026 0.025 -10000 0 -0.47 1 1
mol:Phosphatidic acid -0.069 0.14 0.35 9 -0.41 10 19
IKK complex -0.011 0.092 0.23 21 -0.22 2 23
WIPF1 0.025 0.03 -10000 0 -0.39 2 2
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.022 -9999 0 -0.4 1 1
EGFR 0.022 0.035 -9999 0 -0.47 2 2
EGF/EGFR -0.005 0.11 -9999 0 -0.24 65 65
EGF/EGFR dimer/SHC/GRB2/SOS1 0.015 0.12 -9999 0 -0.25 62 62
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.025 0.03 -9999 0 -0.39 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.062 0.19 -9999 0 -0.47 75 75
EGF/EGFR dimer/SHC -0.008 0.12 -9999 0 -0.28 66 66
mol:GDP 0.011 0.11 -9999 0 -0.24 62 62
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.024 0.035 -9999 0 -0.47 2 2
GRB2/SOS1 0.041 0.008 -9999 0 -10000 0 0
HRAS/GTP -0.002 0.1 -9999 0 -10000 0 0
SHC1 0.028 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.01 0.11 -9999 0 -10000 0 0
FRAP1 -0.044 0.081 -9999 0 -0.23 62 62
EGF/EGFR dimer -0.025 0.14 -9999 0 -0.33 67 67
SOS1 0.028 0.004 -9999 0 -10000 0 0
GRB2 0.028 0.004 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.035 0.036 -9999 0 -0.31 4 4
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.016 0.086 -10000 0 -0.27 10 10
NF kappa B1 p50/RelA/I kappa B alpha 0.006 0.077 0.28 2 -0.34 2 4
AP1 -0.034 0.11 -10000 0 -0.3 20 20
mol:PIP3 -0.017 0.07 -10000 0 -0.39 4 4
AKT1 0.004 0.1 0.27 5 -0.32 3 8
PTK2B -0.015 0.072 0.19 1 -0.28 7 8
RHOA -0.03 0.1 0.19 1 -0.32 37 38
PIK3CB 0.024 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.06 0.22 1 -0.33 3 4
MAGI3 0.025 0.035 -10000 0 -0.47 2 2
RELA 0.027 0.006 -10000 0 -10000 0 0
apoptosis -0.014 0.081 -10000 0 -0.28 21 21
HRAS/GDP 0.019 0.015 -10000 0 -0.28 1 1
positive regulation of microtubule depolymerization -0.089 0.13 0.22 6 -0.32 36 42
NF kappa B1 p50/RelA -0.018 0.086 -10000 0 -0.36 5 5
endothelial cell migration -0.044 0.14 -10000 0 -0.36 69 69
ADCY4 -0.009 0.082 0.24 1 -0.35 11 12
ADCY5 -0.045 0.1 -10000 0 -0.39 16 16
ADCY6 -0.013 0.094 0.24 1 -0.41 12 13
ADCY7 -0.008 0.082 0.24 1 -0.37 10 11
ADCY1 -0.012 0.083 0.23 2 -0.36 10 12
ADCY2 -0.06 0.11 -10000 0 -0.39 15 15
ADCY3 -0.008 0.081 0.24 1 -0.36 10 11
ADCY8 -0.015 0.079 0.24 1 -0.35 10 11
ADCY9 -0.009 0.084 0.24 1 -0.37 10 11
GSK3B 0.004 0.09 0.21 33 -0.25 5 38
arachidonic acid secretion -0.008 0.082 -10000 0 -0.37 10 10
GNG2 0.027 0.007 -10000 0 -10000 0 0
TRIP6 0.014 0.019 -10000 0 -10000 0 0
GNAO1 -0.017 0.082 -10000 0 -0.29 13 13
HRAS 0.026 0.022 -10000 0 -0.4 1 1
NFKBIA -0.008 0.076 0.28 3 -0.36 3 6
GAB1 0.027 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.008 0.18 -10000 0 -0.8 20 20
JUN 0.028 0.005 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.021 0.044 -10000 0 -0.25 2 2
TIAM1 -0.014 0.21 -10000 0 -0.96 20 20
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
mol:IP3 -0.015 0.059 0.22 1 -0.33 3 4
PLCB3 0.006 0.038 0.19 3 -0.26 1 4
FOS -0.036 0.16 -10000 0 -0.47 53 53
positive regulation of mitosis -0.008 0.082 -10000 0 -0.37 10 10
LPA/LPA1-2-3 0.01 0.099 -10000 0 -0.28 20 20
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.027 0.006 -10000 0 -10000 0 0
stress fiber formation 0.002 0.072 0.2 3 -0.34 2 5
GNAZ -0.024 0.096 -10000 0 -0.29 27 27
EGFR/PI3K-beta/Gab1 -0.01 0.076 -10000 0 -0.4 4 4
positive regulation of dendritic cell cytokine production 0.009 0.098 -10000 0 -0.28 20 20
LPA/LPA2/MAGI-3 0.019 0.046 -10000 0 -0.26 3 3
ARHGEF1 0.004 0.092 0.36 2 -0.28 7 9
GNAI2 -0.018 0.081 -10000 0 -0.29 13 13
GNAI3 -0.016 0.083 -10000 0 -0.3 13 13
GNAI1 -0.017 0.084 -10000 0 -0.3 14 14
LPA/LPA3 -0.002 0.063 -10000 0 -0.25 15 15
LPA/LPA2 0.006 0.041 -10000 0 -0.25 1 1
LPA/LPA1 -0.018 0.1 -10000 0 -0.23 73 73
HB-EGF/EGFR -0.14 0.12 -10000 0 -0.23 260 260
HBEGF -0.19 0.13 -10000 0 -0.28 292 292
mol:DAG -0.015 0.059 0.22 1 -0.33 3 4
cAMP biosynthetic process -0.018 0.085 -10000 0 -0.35 11 11
NFKB1 0.028 0.005 -10000 0 -10000 0 0
SRC 0.027 0.007 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
LYN 0 0.081 0.27 4 -0.36 3 7
GNAQ 0.002 0.046 -10000 0 -0.26 8 8
LPAR2 0.028 0.003 -10000 0 -10000 0 0
LPAR3 0.018 0.068 -10000 0 -0.47 8 8
LPAR1 -0.005 0.09 -10000 0 -0.39 13 13
IL8 -0.12 0.13 0.33 3 -0.39 28 31
PTK2 -0.014 0.08 -10000 0 -0.3 9 9
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
CASP3 -0.014 0.081 -10000 0 -0.28 21 21
EGFR 0.022 0.035 -10000 0 -0.47 2 2
PLCG1 -0.015 0.065 0.16 1 -0.28 12 13
PLD2 -0.013 0.086 -10000 0 -0.27 19 19
G12/G13 0.014 0.088 -10000 0 -0.27 12 12
PI3K-beta -0.022 0.082 -10000 0 -0.32 7 7
cell migration 0.01 0.067 0.17 1 -0.25 13 14
SLC9A3R2 0.027 0.021 -10000 0 -0.39 1 1
PXN 0.001 0.073 0.2 3 -0.35 2 5
HRAS/GTP -0.009 0.083 -10000 0 -0.36 11 11
RAC1 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.27 0.19 -10000 0 -0.39 293 293
PRKCE 0.028 0.003 -10000 0 -10000 0 0
PRKCD -0.013 0.055 0.2 1 -0.34 2 3
Gi(beta/gamma) -0.005 0.079 -10000 0 -0.35 8 8
mol:LPA -0.019 0.051 -10000 0 -0.22 7 7
TRIP6/p130 Cas/FAK1/Paxillin 0.013 0.078 -10000 0 -0.44 1 1
MAPKKK cascade -0.008 0.082 -10000 0 -0.37 10 10
contractile ring contraction involved in cytokinesis -0.035 0.11 0.19 1 -0.32 41 42
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.04 0.11 -10000 0 -0.26 71 71
GNA15 0 0.054 -10000 0 -0.28 10 10
GNA12 0.025 0.022 -10000 0 -0.39 1 1
GNA13 0.028 0.004 -10000 0 -10000 0 0
MAPT -0.091 0.14 0.22 6 -0.33 36 42
GNA11 0 0.05 -10000 0 -0.25 11 11
Rac1/GTP 0.008 0.19 -10000 0 -0.85 20 20
MMP2 -0.044 0.14 -10000 0 -0.36 69 69
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.024 0.12 -10000 0 -0.32 30 30
TBX21 -0.09 0.33 -10000 0 -1 34 34
B2M 0.021 0.02 -10000 0 -10000 0 0
TYK2 0.018 0.038 -10000 0 -0.41 1 1
IL12RB1 -0.016 0.13 -10000 0 -0.42 37 37
GADD45B -0.04 0.23 -10000 0 -0.76 14 14
IL12RB2 -0.056 0.16 -10000 0 -0.4 76 76
GADD45G -0.044 0.25 -10000 0 -0.82 16 16
natural killer cell activation 0.002 0.019 -10000 0 -10000 0 0
RELB 0.026 0.029 -10000 0 -0.39 2 2
RELA 0.027 0.006 -10000 0 -10000 0 0
IL18 0.015 0.069 -10000 0 -0.46 8 8
IL2RA -0.014 0.12 -10000 0 -0.39 41 41
IFNG -0.058 0.16 -10000 0 -0.39 82 82
STAT3 (dimer) -0.048 0.24 -10000 0 -0.7 27 27
HLA-DRB5 0.012 0.07 -10000 0 -0.45 9 9
FASLG -0.09 0.34 0.57 1 -1 33 34
NF kappa B2 p52/RelB -0.061 0.29 -10000 0 -0.83 30 30
CD4 0.019 0.036 -10000 0 -0.44 2 2
SOCS1 0.005 0.096 -10000 0 -0.39 23 23
EntrezGene:6955 -0.004 0.012 -10000 0 -10000 0 0
CD3D 0.005 0.07 -10000 0 -0.44 9 9
CD3E 0.005 0.069 -10000 0 -0.43 9 9
CD3G -0.009 0.1 -10000 0 -0.44 22 22
IL12Rbeta2/JAK2 -0.026 0.12 -10000 0 -0.28 68 68
CCL3 -0.078 0.3 -10000 0 -0.94 26 26
CCL4 -0.075 0.3 -10000 0 -0.93 26 26
HLA-A 0.015 0.05 -10000 0 -0.41 5 5
IL18/IL18R 0.039 0.094 -10000 0 -0.3 20 20
NOS2 -0.089 0.32 -10000 0 -1 30 30
IL12/IL12R/TYK2/JAK2/SPHK2 -0.016 0.12 0.21 1 -0.33 24 25
IL1R1 -0.07 0.29 0.57 1 -0.88 26 27
IL4 -0.004 0.035 -10000 0 -10000 0 0
JAK2 0.016 0.031 -10000 0 -10000 0 0
EntrezGene:6957 -0.004 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.064 0.22 -10000 0 -0.57 45 45
RAB7A -0.009 0.22 0.46 1 -0.69 10 11
lysosomal transport -0.007 0.22 0.46 1 -0.65 10 11
FOS -0.18 0.47 -10000 0 -1.2 67 67
STAT4 (dimer) -0.037 0.26 0.42 1 -0.74 25 26
STAT5A (dimer) -0.094 0.31 -10000 0 -0.82 43 43
GZMA -0.095 0.34 -10000 0 -1 36 36
GZMB -0.086 0.32 -10000 0 -0.96 28 28
HLX 0.027 0.021 -10000 0 -0.39 1 1
LCK -0.084 0.3 -10000 0 -0.92 30 30
TCR/CD3/MHC II/CD4 -0.028 0.15 -10000 0 -0.46 28 28
IL2/IL2R 0.022 0.11 -10000 0 -0.41 11 11
MAPK14 -0.038 0.25 -10000 0 -0.76 18 18
CCR5 -0.075 0.28 -10000 0 -0.91 21 21
IL1B -0.026 0.14 -10000 0 -0.4 46 46
STAT6 -0.005 0.11 -10000 0 -0.9 2 2
STAT4 0.02 0.056 -10000 0 -0.4 7 7
STAT3 0.028 0.003 -10000 0 -10000 0 0
STAT1 0.007 0.09 -10000 0 -0.39 20 20
NFKB1 0.028 0.005 -10000 0 -10000 0 0
NFKB2 0.028 0.004 -10000 0 -10000 0 0
IL12B -0.02 0.13 -10000 0 -0.4 39 39
CD8A -0.015 0.13 -10000 0 -0.43 35 35
CD8B -0.024 0.14 -10000 0 -0.43 43 43
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.024 0.12 0.32 30 -10000 0 30
IL2RB 0.02 0.059 -10000 0 -0.4 8 8
proteasomal ubiquitin-dependent protein catabolic process -0.03 0.24 0.39 2 -0.68 25 27
IL2RG 0.014 0.077 -10000 0 -0.4 14 14
IL12 -0.013 0.11 -10000 0 -0.3 45 45
STAT5A 0.028 0.003 -10000 0 -10000 0 0
CD247 -0.001 0.089 -10000 0 -0.42 17 17
IL2 -0.003 0.029 -10000 0 -0.39 1 1
SPHK2 0.028 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0 0.083 -10000 0 -0.47 11 11
IL12/IL12R/TYK2/JAK2 -0.081 0.32 -10000 0 -0.96 30 30
MAP2K3 -0.04 0.24 -10000 0 -0.73 19 19
RIPK2 0.025 0.009 -10000 0 -10000 0 0
MAP2K6 -0.044 0.26 -10000 0 -0.78 20 20
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.017 0.05 -10000 0 -0.45 4 4
IL18RAP 0.013 0.08 -10000 0 -0.44 12 12
IL12Rbeta1/TYK2 0.004 0.11 -10000 0 -0.31 38 38
EOMES -0.12 0.28 -10000 0 -0.68 60 60
STAT1 (dimer) -0.067 0.26 -10000 0 -0.7 34 34
T cell proliferation -0.01 0.21 -10000 0 -0.56 20 20
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.024 0.041 -10000 0 -0.43 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.049 0.21 -10000 0 -0.64 19 19
ATF2 -0.029 0.24 0.45 1 -0.71 18 19
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.16 0.14 -10000 0 -0.55 15 15
IHH -0.041 0.058 -10000 0 -0.37 2 2
SHH Np/Cholesterol/GAS1 0.002 0.069 -10000 0 -0.22 37 37
LRPAP1 0.026 0.008 -10000 0 -10000 0 0
dorsoventral neural tube patterning -0.002 0.069 0.21 37 -10000 0 37
SMO/beta Arrestin2 -0.088 0.12 -10000 0 -0.46 21 21
SMO -0.093 0.12 -10000 0 -0.48 22 22
AKT1 -0.044 0.12 -10000 0 -0.51 16 16
ARRB2 0.027 0.006 -10000 0 -10000 0 0
BOC -0.015 0.13 -10000 0 -0.46 34 34
ADRBK1 0.026 0.008 -10000 0 -10000 0 0
heart looping -0.091 0.12 -10000 0 -0.48 22 22
STIL -0.09 0.1 -10000 0 -0.4 14 14
DHH N/PTCH2 0.029 0.061 -10000 0 -0.3 13 13
DHH N/PTCH1 -0.089 0.1 -10000 0 -0.5 8 8
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
DHH 0.022 0.032 -10000 0 -0.39 2 2
PTHLH -0.22 0.18 -10000 0 -0.6 24 24
determination of left/right symmetry -0.091 0.12 -10000 0 -0.48 22 22
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
skeletal system development -0.22 0.18 -10000 0 -0.59 24 24
IHH N/Hhip -0.033 0.084 -10000 0 -0.32 26 26
DHH N/Hhip 0.018 0.077 -10000 0 -0.28 26 26
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.091 0.12 -10000 0 -0.48 22 22
pancreas development -0.006 0.098 -10000 0 -0.4 24 24
HHAT 0.025 0.034 -10000 0 -0.47 2 2
PI3K 0.027 0.032 -10000 0 -0.34 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.022 0.049 -10000 0 -0.42 5 5
somite specification -0.091 0.12 -10000 0 -0.48 22 22
SHH Np/Cholesterol/PTCH1 -0.096 0.1 -10000 0 -0.35 30 30
SHH Np/Cholesterol/PTCH2 -0.001 0.079 -10000 0 -0.23 41 41
SHH Np/Cholesterol/Megalin -0.01 0.084 -10000 0 -0.23 49 49
SHH -0.02 0.078 -10000 0 -0.28 33 33
catabolic process -0.1 0.11 -10000 0 -0.44 14 14
SMO/Vitamin D3 -0.089 0.12 -10000 0 -0.47 13 13
SHH Np/Cholesterol/Hhip -0.012 0.089 -10000 0 -0.24 49 49
LRP2 -0.005 0.097 -10000 0 -0.39 24 24
receptor-mediated endocytosis -0.093 0.12 -10000 0 -0.51 14 14
SHH Np/Cholesterol/BOC -0.016 0.093 -10000 0 -0.24 59 59
SHH Np/Cholesterol/CDO -0.002 0.076 -10000 0 -0.23 41 41
mesenchymal cell differentiation 0.012 0.088 0.24 49 -10000 0 49
mol:Vitamin D3 -0.091 0.11 0.37 1 -0.39 19 20
IHH N/PTCH2 -0.022 0.07 -10000 0 -0.34 13 13
CDON 0.015 0.072 -10000 0 -0.47 9 9
IHH N/PTCH1 -0.1 0.11 -10000 0 -0.44 14 14
Megalin/LRPAP1 0.019 0.073 -10000 0 -0.27 24 24
PTCH2 0.015 0.074 -10000 0 -0.44 11 11
SHH Np/Cholesterol -0.002 0.062 -10000 0 -0.21 33 33
PTCH1 -0.1 0.11 -10000 0 -0.44 14 14
HHIP -0.006 0.098 -10000 0 -0.4 24 24
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.028 0.038 -10000 0 -0.28 5 5
ARNO/beta Arrestin1-2 0.012 0.12 -10000 0 -0.74 8 8
EGFR 0.022 0.035 -10000 0 -0.47 2 2
EPHA2 0.021 0.054 -10000 0 -0.47 5 5
USP6 0.027 0.006 -10000 0 -10000 0 0
IQSEC1 0.025 0.01 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.025 0.14 -10000 0 -0.33 67 67
ARRB2 0.01 0.003 -10000 0 -10000 0 0
mol:GTP 0.035 0.05 0.13 53 -0.16 2 55
ARRB1 0.023 0.035 -10000 0 -0.47 2 2
FBXO8 0.027 0.006 -10000 0 -10000 0 0
TSHR 0 0.088 -10000 0 -0.39 19 19
EGF -0.062 0.19 -10000 0 -0.47 75 75
somatostatin receptor activity 0 0 0.001 25 -0.001 19 44
ARAP2 0.023 0.042 -10000 0 -0.47 3 3
mol:GDP -0.005 0.092 0.19 10 -0.28 19 29
mol:PI-3-4-5-P3 0 0 0.001 12 -0.001 5 17
ITGA2B -0.006 0.12 -10000 0 -0.39 34 34
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.055 0.043 -10000 0 -0.26 4 4
ADAP1 0.025 0.025 -10000 0 -0.47 1 1
KIF13B 0.02 0.054 -10000 0 -0.47 5 5
HGF/MET 0.023 0.075 -10000 0 -0.31 20 20
PXN 0.028 0.003 -10000 0 -10000 0 0
ARF6/GTP -0.008 0.11 0.22 20 -0.28 18 38
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.012 0.12 -10000 0 -0.28 67 67
ADRB2 -0.003 0.12 -10000 0 -0.47 25 25
receptor agonist activity 0 0 0 18 0 9 27
actin filament binding 0 0 0 24 -0.001 18 42
SRC 0.027 0.007 -10000 0 -10000 0 0
ITGB3 0.007 0.096 -10000 0 -0.42 20 20
GNAQ 0.028 0.005 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 38 -0.001 11 49
ARF6/GDP 0.036 0.13 0.23 29 -0.46 12 41
ARF6/GDP/GULP/ACAP1 -0.051 0.16 0.23 2 -0.35 48 50
alphaIIb/beta3 Integrin/paxillin/GIT1 0.035 0.099 -10000 0 -0.29 9 9
ACAP1 0.018 0.061 -10000 0 -0.39 9 9
ACAP2 0.021 0.013 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.016 0.015 -10000 0 -10000 0 0
EFNA1 0.028 0.005 -10000 0 -10000 0 0
HGF 0.008 0.091 -10000 0 -0.44 16 16
CYTH3 0.007 0.002 -10000 0 -10000 0 0
CYTH2 0.001 0.14 -10000 0 -0.98 8 8
NCK1 0.024 0.01 -10000 0 -10000 0 0
fibronectin binding 0 0 0 16 0 11 27
endosomal lumen acidification 0 0 0 37 0 14 51
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.12 0.23 -10000 0 -0.47 128 128
GNAQ/ARNO 0.018 0.13 -10000 0 -0.9 8 8
mol:Phosphatidic acid 0 0 0 2 -10000 0 2
PIP3-E 0 0 0 10 -10000 0 10
MET 0.023 0.043 -10000 0 -0.41 4 4
GNA14 -0.048 0.18 -10000 0 -0.47 64 64
GNA15 0.025 0.034 -10000 0 -0.47 2 2
GIT1 0.028 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 32 -0.001 14 46
GNA11 0.025 0.034 -10000 0 -0.47 2 2
LHCGR -0.012 0.016 -10000 0 -10000 0 0
AGTR1 -0.022 0.13 -10000 0 -0.46 34 34
desensitization of G-protein coupled receptor protein signaling pathway 0.016 0.014 -10000 0 -10000 0 0
IPCEF1/ARNO -0.013 0.14 -10000 0 -0.79 8 8
alphaIIb/beta3 Integrin 0 0.11 -10000 0 -0.29 52 52
Signaling events mediated by PTP1B

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
PDGFRB -0.062 0.17 -10000 0 -0.39 89 89
Jak2/Leptin Receptor -0.059 0.17 -10000 0 -0.47 42 42
PTP1B/AKT1 -0.023 0.1 -10000 0 -0.34 16 16
FYN 0.027 0.021 -10000 0 -0.39 1 1
p210 bcr-abl/PTP1B -0.032 0.1 0.22 3 -0.32 26 29
EGFR 0.015 0.039 -10000 0 -0.47 2 2
EGF/EGFR -0.051 0.13 -10000 0 -0.35 34 34
CSF1 0.021 0.054 -10000 0 -0.47 5 5
AKT1 0.026 0.008 -10000 0 -10000 0 0
INSR 0.028 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.045 0.12 0.26 1 -0.34 26 27
Insulin Receptor/Insulin -0.011 0.1 -10000 0 -0.41 6 6
HCK 0.023 0.04 -10000 0 -0.44 3 3
CRK 0.027 0.006 -10000 0 -10000 0 0
TYK2 -0.031 0.1 0.26 1 -0.35 16 17
EGF -0.061 0.19 -10000 0 -0.47 75 75
YES1 0.025 0.009 -10000 0 -10000 0 0
CAV1 -0.039 0.12 0.22 9 -0.36 24 33
TXN 0.027 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.013 0.11 0.27 1 -0.36 13 14
cell migration 0.032 0.1 0.32 26 -0.22 3 29
STAT3 0.028 0.003 -10000 0 -10000 0 0
PRLR -0.062 0.19 -10000 0 -0.46 74 74
ITGA2B -0.006 0.12 -10000 0 -0.39 34 34
CSF1R 0.024 0.035 -10000 0 -0.47 2 2
Prolactin Receptor/Prolactin -0.035 0.14 -10000 0 -0.34 74 74
FGR 0.027 0.021 -10000 0 -0.39 1 1
PTP1B/p130 Cas -0.021 0.1 0.26 1 -0.35 15 16
Crk/p130 Cas -0.01 0.11 0.27 1 -0.37 11 12
DOK1 -0.046 0.12 0.24 3 -0.39 19 22
JAK2 -0.071 0.18 0.21 1 -0.44 55 56
Jak2/Leptin Receptor/Leptin -0.05 0.14 0.23 1 -0.45 16 17
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
PTPN1 -0.032 0.11 0.22 3 -0.32 26 29
LYN 0.025 0.009 -10000 0 -10000 0 0
CDH2 -0.031 0.14 -10000 0 -0.4 55 55
SRC -0.002 0.12 -10000 0 -0.55 16 16
ITGB3 0.006 0.096 -10000 0 -0.42 20 20
CAT1/PTP1B -0.096 0.15 0.21 5 -0.44 31 36
CAPN1 0.026 0.006 -10000 0 -10000 0 0
CSK 0.028 0.005 -10000 0 -10000 0 0
PI3K 0.009 0.085 -10000 0 -0.39 3 3
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.041 0.13 0.21 1 -0.39 17 18
negative regulation of transcription -0.069 0.17 0.21 1 -0.44 55 56
FCGR2A 0.004 0.098 -10000 0 -0.39 24 24
FER 0.025 0.025 -10000 0 -0.47 1 1
alphaIIb/beta3 Integrin -0.001 0.11 -10000 0 -0.29 52 52
BLK -0.039 0.15 -10000 0 -0.41 61 61
Insulin Receptor/Insulin/Shc 0.046 0.024 -10000 0 -0.24 2 2
RHOA 0.024 0.01 -10000 0 -10000 0 0
LEPR 0.028 0.005 -10000 0 -10000 0 0
BCAR1 0.027 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.028 0.004 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.087 0.15 0.24 3 -0.44 33 36
PRL -0.003 0.045 -10000 0 -0.39 4 4
SOCS3 0.026 0.099 -10000 0 -1.1 3 3
SPRY2 0.02 0.06 -10000 0 -0.47 6 6
Insulin Receptor/Insulin/IRS1 0.044 0.034 -10000 0 -0.26 4 4
CSF1/CSF1R -0.015 0.11 0.27 1 -0.36 13 14
Ras protein signal transduction 0.012 0.072 0.55 6 -10000 0 6
IRS1 0.025 0.034 -10000 0 -0.47 2 2
INS -0.003 0.034 -10000 0 -0.4 2 2
LEP -0.051 0.16 -10000 0 -0.44 63 63
STAT5B -0.04 0.12 0.23 2 -0.37 33 35
STAT5A -0.04 0.12 0.23 2 -0.38 30 32
GRB2 0.028 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.06 0.14 0.26 1 -0.35 32 33
CSN2 -0.012 0.093 0.35 1 -0.49 5 6
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
LAT 0.002 0.079 -10000 0 -0.53 5 5
YBX1 0.033 0.006 -10000 0 -10000 0 0
LCK 0.018 0.064 -10000 0 -0.39 10 10
SHC1 0.028 0.004 -10000 0 -10000 0 0
NOX4 -0.066 0.17 -10000 0 -0.39 91 91
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.05 0.066 -10000 0 -10000 0 0
SMARCC2 0.029 0.009 -10000 0 -10000 0 0
SMARCC1 0.025 0.013 -10000 0 -10000 0 0
TBX21 -0.085 0.16 -10000 0 -0.55 32 32
SUMO2 0.027 0.01 -10000 0 -10000 0 0
STAT1 (dimer) 0.013 0.089 -10000 0 -0.39 20 20
FKBP4 0.026 0.008 -10000 0 -10000 0 0
FKBP5 0.025 0.035 -10000 0 -0.47 2 2
GR alpha/HSP90/FKBP51/HSP90 0.088 0.079 0.3 19 -10000 0 19
PRL -0.078 0.14 -10000 0 -0.47 19 19
cortisol/GR alpha (dimer)/TIF2 0.12 0.18 0.53 36 -10000 0 36
RELA -0.01 0.09 -10000 0 -0.25 13 13
FGG 0.083 0.16 0.43 27 -0.37 12 39
GR beta/TIF2 0.06 0.11 0.32 17 -0.3 11 28
IFNG -0.2 0.2 -10000 0 -0.56 65 65
apoptosis 0.022 0.14 0.5 7 -0.56 7 14
CREB1 0.029 0.016 -10000 0 -10000 0 0
histone acetylation -0.009 0.11 0.28 13 -0.36 13 26
BGLAP -0.044 0.098 -10000 0 -0.5 5 5
GR/PKAc 0.1 0.076 0.32 13 -10000 0 13
NF kappa B1 p50/RelA -0.02 0.16 -10000 0 -0.4 27 27
SMARCD1 0.029 0.009 -10000 0 -10000 0 0
MDM2 0.054 0.067 0.23 28 -10000 0 28
GATA3 0.015 0.079 -10000 0 -0.4 14 14
AKT1 0.021 0.006 -10000 0 -10000 0 0
CSF2 -0.15 0.14 -10000 0 -0.51 16 16
GSK3B 0.025 0.012 -10000 0 -10000 0 0
NR1I3 0.027 0.14 0.47 7 -0.66 3 10
CSN2 0.077 0.12 0.35 29 -10000 0 29
BRG1/BAF155/BAF170/BAF60A 0.065 0.039 -10000 0 -0.4 1 1
NFATC1 0.025 0.01 -10000 0 -10000 0 0
POU2F1 0.028 0.014 -10000 0 -10000 0 0
CDKN1A 0.017 0.061 0.72 1 -10000 0 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.006 -10000 0 -10000 0 0
SFN 0.023 0.045 -10000 0 -0.43 4 4
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.096 0.082 0.31 16 -10000 0 16
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.007 0.19 0.46 6 -0.8 17 23
JUN -0.15 0.13 -10000 0 -0.47 34 34
IL4 -0.052 0.09 -10000 0 -0.47 4 4
CDK5R1 0.027 0.021 -10000 0 -0.39 1 1
PRKACA 0.028 0.003 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.096 0.2 0.17 5 -0.4 85 90
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.098 0.08 0.31 17 -10000 0 17
cortisol/GR alpha (monomer) 0.17 0.22 0.62 43 -10000 0 43
NCOA2 0 0.11 -10000 0 -0.47 21 21
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.12 0.16 -10000 0 -0.51 53 53
AP-1/NFAT1-c-4 -0.25 0.19 -10000 0 -0.56 75 75
AFP -0.11 0.13 -10000 0 -0.6 9 9
SUV420H1 0.026 0.008 -10000 0 -10000 0 0
IRF1 0.083 0.11 0.42 12 -10000 0 12
TP53 0.038 0.049 -10000 0 -0.46 4 4
PPP5C 0.028 0.005 -10000 0 -10000 0 0
KRT17 -0.22 0.24 -10000 0 -0.62 71 71
KRT14 -0.16 0.31 0.38 1 -0.89 47 48
TBP 0.033 0.018 -10000 0 -10000 0 0
CREBBP 0.067 0.075 0.32 24 -0.34 1 25
HDAC1 0.027 0.008 -10000 0 -10000 0 0
HDAC2 0.043 0.017 -10000 0 -10000 0 0
AP-1 -0.25 0.19 -10000 0 -0.57 75 75
MAPK14 0.027 0.01 -10000 0 -10000 0 0
MAPK10 0.002 0.11 -10000 0 -0.46 21 21
MAPK11 0.027 0.011 -10000 0 -10000 0 0
KRT5 -0.17 0.2 -10000 0 -0.76 22 22
interleukin-1 receptor activity 0.015 0.016 -10000 0 -10000 0 0
NCOA1 0.03 0.004 -10000 0 -10000 0 0
STAT1 0.013 0.09 -10000 0 -0.39 20 20
CGA -0.05 0.095 -10000 0 -0.49 6 6
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.15 0.14 0.37 61 -0.33 1 62
MAPK3 0.027 0.01 -10000 0 -10000 0 0
MAPK1 0.027 0.01 -10000 0 -10000 0 0
ICAM1 -0.091 0.18 -10000 0 -0.52 27 27
NFKB1 -0.013 0.094 -10000 0 -0.26 16 16
MAPK8 -0.12 0.13 -10000 0 -0.42 37 37
MAPK9 0.026 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.022 0.14 0.5 7 -0.57 8 15
BAX 0.013 0.05 -10000 0 -10000 0 0
POMC -0.11 0.25 -10000 0 -1.3 13 13
EP300 0.064 0.08 0.31 23 -0.38 3 26
cortisol/GR alpha (dimer)/p53 0.16 0.18 0.54 41 -0.4 1 42
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.055 0.23 10 -10000 0 10
SGK1 0.07 0.13 0.46 1 -1.1 2 3
IL13 -0.15 0.15 -10000 0 -0.6 19 19
IL6 -0.14 0.3 -10000 0 -0.87 50 50
PRKACG -0.01 0.026 -10000 0 -0.39 1 1
IL5 -0.13 0.13 -10000 0 -0.65 4 4
IL2 -0.17 0.16 -10000 0 -0.59 26 26
CDK5 0.027 0.008 -10000 0 -10000 0 0
PRKACB 0.028 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.008 -10000 0 -10000 0 0
IL8 -0.13 0.21 -10000 0 -0.6 36 36
CDK5R1/CDK5 0.039 0.02 -10000 0 -0.28 1 1
NF kappa B1 p50/RelA/PKAc 0.01 0.13 -10000 0 -0.36 9 9
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.14 0.17 0.52 39 -10000 0 39
SMARCA4 0.029 0.01 -10000 0 -10000 0 0
chromatin remodeling 0.089 0.1 0.35 26 -0.48 1 27
NF kappa B1 p50/RelA/Cbp 0.058 0.16 0.35 18 -0.37 13 31
JUN (dimer) -0.15 0.13 -10000 0 -0.47 34 34
YWHAH 0.028 0.004 -10000 0 -10000 0 0
VIPR1 -0.077 0.16 -10000 0 -0.73 18 18
NR3C1 0.1 0.13 0.42 31 -10000 0 31
NR4A1 -0.005 0.11 -10000 0 -0.47 18 18
TIF2/SUV420H1 0.019 0.075 -10000 0 -0.34 17 17
MAPKKK cascade 0.022 0.14 0.5 7 -0.56 7 14
cortisol/GR alpha (dimer)/Src-1 0.16 0.18 0.54 43 -10000 0 43
PBX1 -0.059 0.19 -10000 0 -0.47 74 74
POU1F1 -0.001 0.023 -10000 0 -10000 0 0
SELE -0.17 0.35 -10000 0 -0.9 69 69
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.089 0.11 0.35 25 -0.49 1 26
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.14 0.17 0.52 39 -10000 0 39
mol:cortisol 0.085 0.12 0.36 43 -10000 0 43
MMP1 -0.34 0.18 -10000 0 -0.55 95 95
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.009 0.027 -10000 0 -0.28 4 4
SNTA1 0.026 0.008 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.01 0.031 -10000 0 -0.28 5 5
MAPK12 -0.012 0.069 0.2 4 -0.26 19 23
CCND1 -0.001 0.064 -10000 0 -0.46 6 6
p38 gamma/SNTA1 0.01 0.077 0.32 2 -0.25 18 20
MAP2K3 0.027 0.006 -10000 0 -10000 0 0
PKN1 0.027 0.021 -10000 0 -0.39 1 1
G2/M transition checkpoint -0.01 0.072 0.21 8 -0.26 19 27
MAP2K6 -0.004 0.057 -10000 0 -0.27 18 18
MAPT -0.13 0.16 0.21 3 -0.3 178 181
MAPK13 0.011 0.034 -10000 0 -0.34 4 4
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.015 0.01 -10000 0 -0.16 1 1
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.035 0.037 -10000 0 -0.29 5 5
alphaV beta3 Integrin 0.028 0.093 -10000 0 -0.28 32 32
PTK2 0.004 0.11 0.32 6 -0.5 4 10
IGF1R 0.027 0.005 -10000 0 -10000 0 0
PI4KB 0.027 0.005 -10000 0 -10000 0 0
MFGE8 0.028 0.005 -10000 0 -10000 0 0
SRC 0.027 0.007 -10000 0 -10000 0 0
CDKN1B 0.004 0.055 -10000 0 -0.26 1 1
VEGFA 0.024 0.036 -10000 0 -0.39 3 3
ILK 0.004 0.059 -10000 0 -0.35 2 2
ROCK1 0.028 0.003 -10000 0 -10000 0 0
AKT1 -0.001 0.052 -10000 0 -0.41 1 1
PTK2B 0.01 0.068 -10000 0 -0.38 2 2
alphaV/beta3 Integrin/JAM-A 0.018 0.11 -10000 0 -0.31 19 19
CBL 0.026 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.033 0.071 -10000 0 -0.26 23 23
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.02 0.12 -10000 0 -0.26 60 60
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.01 0.051 -10000 0 -0.35 2 2
alphaV/beta3 Integrin/Syndecan-1 0.039 0.069 -10000 0 -0.25 21 21
PI4KA 0.028 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.11 0.16 -10000 0 -0.43 39 39
PI4 Kinase 0.04 0.01 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.098 0.15 -10000 0 -0.24 213 213
RPS6KB1 -0.13 0.13 0.22 1 -0.41 39 40
TLN1 0.024 0.01 -10000 0 -10000 0 0
MAPK3 -0.061 0.14 -10000 0 -0.51 24 24
GPR124 0.021 0.042 -10000 0 -0.39 4 4
MAPK1 -0.06 0.14 -10000 0 -0.49 26 26
PXN 0.028 0.003 -10000 0 -10000 0 0
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
alphaV/beta3 Integrin/Tumstatin 0.002 0.12 -10000 0 -0.26 68 68
cell adhesion 0.027 0.064 -10000 0 -0.3 7 7
ANGPTL3 -0.005 0.04 -10000 0 -0.39 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.038 -10000 0 -0.24 5 5
IGF-1R heterotetramer 0.027 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
TGFBR2 0.023 0.026 -10000 0 -0.47 1 1
ITGB3 0.007 0.096 -10000 0 -0.42 20 20
IGF1 -0.044 0.17 -10000 0 -0.46 62 62
RAC1 0.026 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.032 0.073 -10000 0 -0.26 22 22
apoptosis 0.026 0.021 -10000 0 -0.39 1 1
CD47 0.025 0.009 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.034 0.069 -10000 0 -0.25 21 21
VCL 0.028 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.001 0.13 -10000 0 -0.27 68 68
CSF1 0.021 0.054 -10000 0 -0.47 5 5
PIK3C2A 0.004 0.059 -10000 0 -0.35 2 2
PI4 Kinase/Pyk2 0.004 0.09 -10000 0 -0.42 5 5
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.074 -10000 0 -0.24 22 22
FAK1/Vinculin 0.014 0.1 0.3 7 -0.39 4 11
alphaV beta3/Integrin/ppsTEM5 0.033 0.073 -10000 0 -0.26 22 22
RHOA 0.024 0.01 -10000 0 -10000 0 0
VTN -0.002 0.11 -10000 0 -0.39 29 29
BCAR1 0.027 0.006 -10000 0 -10000 0 0
FGF2 0.01 0.089 -10000 0 -0.45 15 15
F11R 0.002 0.062 -10000 0 -0.32 15 15
alphaV/beta3 Integrin/Lactadherin 0.039 0.069 -10000 0 -0.25 21 21
alphaV/beta3 Integrin/TGFBR2 0.032 0.071 -10000 0 -0.25 22 22
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.057 0.044 -10000 0 -0.26 4 4
HSP90AA1 0.026 0.008 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.032 0.063 -10000 0 -0.23 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.18 0.21 -10000 0 -0.39 203 203
alphaV/beta3 Integrin/Pyk2 0.035 0.071 -10000 0 -0.28 7 7
SDC1 0.028 0.004 -10000 0 -10000 0 0
VAV3 0.003 0.073 -10000 0 -0.47 2 2
PTPN11 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.025 0.034 -10000 0 -0.47 2 2
FAK1/Paxillin 0.013 0.1 0.3 7 -0.39 4 11
cell migration 0.01 0.093 0.25 13 -0.36 4 17
ITGAV 0.026 0.021 -10000 0 -0.39 1 1
PI3K 0.016 0.1 -10000 0 -0.4 7 7
SPP1 -0.18 0.21 -10000 0 -0.39 209 209
KDR 0.025 0.032 -10000 0 -0.43 2 2
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.026 0.021 -10000 0 -0.39 1 1
COL4A3 -0.028 0.14 -10000 0 -0.41 51 51
angiogenesis -0.052 0.14 -10000 0 -0.5 26 26
Rac1/GTP 0.017 0.07 -10000 0 -0.44 2 2
EDIL3 -0.034 0.15 -10000 0 -0.42 57 57
cell proliferation 0.031 0.07 -10000 0 -0.25 22 22
Regulation of Androgen receptor activity

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
HDAC1 0.01 0.012 -10000 0 -10000 0 0
SMARCC1 0.003 0.038 -10000 0 -0.6 1 1
REL 0.024 0.059 -10000 0 -0.46 6 6
HDAC7 -0.098 0.14 0.23 2 -0.46 21 23
JUN 0.026 0.006 -10000 0 -10000 0 0
EP300 0.025 0.034 -10000 0 -0.47 2 2
KAT2B 0.01 0.083 -10000 0 -0.47 12 12
KAT5 0.027 0.006 -10000 0 -10000 0 0
MAPK14 -0.024 0.077 -10000 0 -0.36 19 19
FOXO1 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.093 0.16 -10000 0 -0.47 23 23
MAP2K6 -0.017 0.1 -10000 0 -0.48 19 19
BRM/BAF57 0.023 0.035 -10000 0 -0.34 1 1
MAP2K4 0.004 0.026 -10000 0 -10000 0 0
SMARCA2 0.015 0.031 -10000 0 -0.47 1 1
PDE9A -0.085 0.22 -10000 0 -0.99 18 18
NCOA2 0 0.11 -10000 0 -0.47 21 21
CEBPA 0.024 0.042 -10000 0 -0.47 3 3
EHMT2 0.025 0.007 -10000 0 -10000 0 0
cell proliferation -0.082 0.16 0.28 9 -0.45 25 34
NR0B1 -0.019 0.084 -10000 0 -0.39 19 19
EGR1 0.002 0.092 -10000 0 -0.47 15 15
RXRs/9cRA 0.008 0.094 -10000 0 -0.26 42 42
AR/RACK1/Src -0.045 0.11 0.24 2 -0.38 19 21
AR/GR -0.061 0.13 -10000 0 -0.32 55 55
GNB2L1 0.027 0.007 -10000 0 -10000 0 0
PKN1 0.027 0.021 -10000 0 -0.39 1 1
RCHY1 0.027 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -0.014 1 1
MAPK8 -0.011 0.043 -10000 0 -0.36 4 4
T-DHT/AR/TIF2/CARM1 -0.048 0.12 -10000 0 -0.39 26 26
SRC -0.04 0.075 0.2 7 -0.3 20 27
NR3C1 0.027 0.006 -10000 0 -10000 0 0
KLK3 -0.26 0.43 -10000 0 -1.2 73 73
APPBP2 0.005 0.027 -10000 0 -10000 0 0
TRIM24 0.017 0.031 -10000 0 -0.47 1 1
T-DHT/AR/TIP60 -0.048 0.11 0.23 1 -0.38 18 19
TMPRSS2 -0.5 0.54 -10000 0 -1 209 209
RXRG -0.03 0.15 -10000 0 -0.46 45 45
mol:9cRA -0.001 0.003 -10000 0 -0.012 1 1
RXRA 0.027 0.005 -10000 0 -10000 0 0
RXRB 0.026 0.006 -10000 0 -10000 0 0
CARM1 0.028 0.004 -10000 0 -10000 0 0
NR2C2 0.021 0.043 -10000 0 -0.47 3 3
KLK2 -0.044 0.12 -10000 0 -0.43 15 15
AR -0.075 0.13 -10000 0 -0.31 88 88
SENP1 0.027 0.003 -10000 0 -10000 0 0
HSP90AA1 0.026 0.008 -10000 0 -10000 0 0
MDM2 0.032 0.013 -10000 0 -10000 0 0
SRY 0.005 0.011 0.029 75 -10000 0 75
GATA2 0.022 0.039 -10000 0 -0.42 3 3
MYST2 0.001 0.001 -10000 0 -10000 0 0
HOXB13 -0.14 0.19 -10000 0 -0.4 146 146
T-DHT/AR/RACK1/Src -0.041 0.11 0.24 3 -0.38 20 23
positive regulation of transcription 0.022 0.038 -10000 0 -0.42 3 3
DNAJA1 0.003 0.025 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.008 -10000 0 -10000 0 0
NCOA1 0.036 0.029 -10000 0 -10000 0 0
SPDEF -0.14 0.22 -10000 0 -0.46 134 134
T-DHT/AR/TIF2 -0.047 0.13 -10000 0 -0.39 33 33
T-DHT/AR/Hsp90 -0.051 0.11 0.22 1 -0.39 20 21
GSK3B 0.023 0.009 -10000 0 -10000 0 0
NR2C1 0.029 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.046 0.076 0.24 1 -0.31 23 24
SIRT1 0.026 0.024 -10000 0 -0.47 1 1
ZMIZ2 0.032 0.014 -10000 0 -10000 0 0
POU2F1 -0.028 0.071 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.065 0.11 -10000 0 -0.39 23 23
CREBBP 0.027 0.004 -10000 0 -10000 0 0
SMARCE1 0.019 0.02 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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
USP8 -0.005 0.006 -10000 0 -10000 0 0
RAS family/GTP -0.004 0.083 -10000 0 -0.38 1 1
NFATC4 -0.025 0.071 0.27 4 -0.34 2 6
ERBB2IP 0.028 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.026 0.008 -10000 0 -10000 0 0
mammary gland morphogenesis -0.016 0.078 -10000 0 -0.26 3 3
JUN -0.003 0.072 0.2 6 -0.32 3 9
HRAS 0.025 0.022 -10000 0 -0.4 1 1
DOCK7 -0.03 0.074 0.29 1 -10000 0 1
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.002 0.098 -10000 0 -0.28 7 7
AKT1 0.005 0.006 -10000 0 -10000 0 0
BAD -0.004 0.004 -10000 0 -10000 0 0
MAPK10 -0.016 0.068 0.2 11 -0.25 3 14
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.016 0.084 -10000 0 -0.28 3 3
RAF1 -0.019 0.09 0.28 7 -0.38 1 8
ErbB2/ErbB3/neuregulin 2 -0.14 0.15 -10000 0 -0.28 223 223
STAT3 0.014 0.12 -10000 0 -0.81 9 9
cell migration -0.009 0.066 0.22 11 -0.21 3 14
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.14 0.26 0.33 2 -0.58 83 85
FOS -0.11 0.21 0.32 7 -0.41 114 121
NRAS 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.016 0.078 -10000 0 -0.26 3 3
MAPK3 -0.11 0.21 0.31 3 -0.48 71 74
MAPK1 -0.11 0.22 0.31 3 -0.49 72 75
JAK2 -0.028 0.069 -10000 0 -10000 0 0
NF2 0.009 0.032 -10000 0 -0.62 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.006 0.063 -10000 0 -0.27 7 7
NRG1 -0.044 0.16 -10000 0 -0.4 68 68
GRB2/SOS1 0.04 0.008 -10000 0 -10000 0 0
MAPK8 -0.008 0.078 0.2 6 -0.28 10 16
MAPK9 -0.012 0.057 0.2 9 -10000 0 9
ERBB2 -0.02 0.007 -10000 0 -10000 0 0
ERBB3 0.02 0.059 -10000 0 -0.47 6 6
SHC1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
apoptosis 0.009 0.035 -10000 0 -0.17 13 13
STAT3 (dimer) 0.014 0.12 -10000 0 -0.8 9 9
RNF41 -0.007 0.007 -10000 0 -10000 0 0
FRAP1 -0.002 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.021 0.051 -10000 0 -10000 0 0
ErbB2/ErbB2/HSP90 (dimer) 0 0.02 -10000 0 -10000 0 0
CHRNA1 -0.13 0.25 0.29 3 -0.59 74 77
myelination -0.016 0.084 0.3 10 -0.32 2 12
PPP3CB -0.028 0.071 0.28 1 -10000 0 1
KRAS 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.02 0.069 -10000 0 -10000 0 0
NRG2 -0.25 0.24 -10000 0 -0.47 231 231
mol:GDP -0.006 0.063 -10000 0 -0.26 7 7
SOS1 0.027 0.004 -10000 0 -10000 0 0
MAP2K2 -0.032 0.1 0.27 7 -0.38 1 8
SRC 0.027 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.029 0.075 0.29 1 -10000 0 1
MAP2K1 -0.11 0.21 0.32 1 -0.57 33 34
heart morphogenesis -0.016 0.078 -10000 0 -0.26 3 3
RAS family/GDP 0.014 0.081 -10000 0 -0.38 1 1
GRB2 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.012 0.033 -10000 0 -0.65 1 1
CHRNE 0.004 0.023 0.09 1 -0.14 5 6
HSP90AA1 0.026 0.008 -10000 0 -10000 0 0
activation of caspase activity -0.005 0.006 -10000 0 -10000 0 0
nervous system development -0.016 0.078 -10000 0 -0.26 3 3
CDC42 0.027 0.005 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.008 -10000 0 -10000 0 0
VLDLR 0.021 0.043 -10000 0 -0.47 3 3
LRPAP1 0.026 0.008 -10000 0 -10000 0 0
NUDC 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.015 0.13 -10000 0 -0.29 78 78
CaM/Ca2+ 0.019 0.006 -10000 0 -10000 0 0
KATNA1 0.028 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.027 0.12 0.18 24 -0.27 68 92
IQGAP1/CaM 0.038 0.012 -10000 0 -10000 0 0
DAB1 -0.002 0.078 -10000 0 -0.39 15 15
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
PLA2G7 -0.14 0.2 -10000 0 -0.39 167 167
CALM1 0.026 0.008 -10000 0 -10000 0 0
DYNLT1 0.028 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.032 0.047 -10000 0 -0.27 9 9
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.024 -10000 0 -0.47 1 1
CDK5R1 0.027 0.021 -10000 0 -0.39 1 1
LIS1/Poliovirus Protein 3A 0.01 0.003 -10000 0 -10000 0 0
CDK5R2 -0.045 0.14 -10000 0 -0.39 60 60
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.023 0.13 -10000 0 -0.28 84 84
YWHAE 0.027 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.024 0.12 0.31 6 -0.36 8 14
MAP1B 0.002 0.03 -10000 0 -0.33 2 2
RAC1 0.014 0.006 -10000 0 -10000 0 0
p35/CDK5 -0.019 0.11 -10000 0 -0.4 3 3
RELN -0.061 0.19 -10000 0 -0.47 73 73
PAFAH/LIS1 -0.072 0.13 -10000 0 -0.23 160 160
LIS1/CLIP170 0.029 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.017 0.096 -10000 0 -0.36 3 3
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.029 0.12 -10000 0 -0.35 20 20
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.036 0.12 0.3 5 -0.32 16 21
LIS1/IQGAP1 0.029 0.01 -10000 0 -10000 0 0
RHOA 0.013 0.007 -10000 0 -10000 0 0
PAFAH1B1 0.014 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.028 0.005 -10000 0 -10000 0 0
PAFAH1B2 0.024 0.026 -10000 0 -0.47 1 1
MAP1B/LIS1/Dynein heavy chain 0.019 0.036 -10000 0 -0.26 1 1
NDEL1/Katanin 60/Dynein heavy chain -0.014 0.12 0.3 5 -0.35 7 12
LRP8 0.019 0.061 -10000 0 -0.39 9 9
NDEL1/Katanin 60 -0.024 0.12 0.31 6 -0.36 8 14
P39/CDK5 -0.046 0.13 0.2 1 -0.42 12 13
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0.011 -10000 0 -10000 0 0
CDK5 -0.042 0.1 0.18 19 -0.42 3 22
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.025 0.01 -10000 0 -10000 0 0
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.012 0.12 -10000 0 -0.25 58 58
RELN/VLDLR -0.004 0.13 -10000 0 -0.26 77 77
CDC42 0.014 0.005 -10000 0 -10000 0 0
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.038 0.01 -10000 0 -10000 0 0
PRKCZ 0.026 0.025 -10000 0 -0.47 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.026 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.07 -10000 0 -0.44 3 3
IRAK/TOLLIP 0.03 0.012 -10000 0 -10000 0 0
IKBKB 0.026 0.008 -10000 0 -10000 0 0
IKBKG 0.027 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.11 0.18 -10000 0 -0.32 172 172
IL1A -0.076 0.18 -10000 0 -0.4 103 103
IL1B -0.019 0.092 -10000 0 -0.28 46 46
IRAK/TRAF6/p62/Atypical PKCs 0.049 0.041 -10000 0 -10000 0 0
IL1R2 -0.067 0.19 -10000 0 -0.46 81 81
IL1R1 0.027 0.024 -10000 0 -0.47 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.016 0.059 0.25 1 -0.63 1 2
TOLLIP 0.027 0.006 -10000 0 -10000 0 0
TICAM2 0.026 0.008 -10000 0 -10000 0 0
MAP3K3 0.028 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.019 0.003 -10000 0 -10000 0 0
IKK complex/ELKS 0.046 0.057 0.33 2 -10000 0 2
JUN -0.01 0.064 0.32 2 -10000 0 2
MAP3K7 0.028 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.025 0.085 -10000 0 -0.67 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.009 0.11 -10000 0 -0.72 1 1
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.002 0.11 -10000 0 -0.69 1 1
IL1 beta fragment/IL1R1/IL1RAP 0.007 0.08 -10000 0 -0.23 36 36
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.009 0.068 0.34 2 -10000 0 2
IRAK1 0.01 0.013 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.065 0.17 -10000 0 -0.34 117 117
IRAK4 0.027 0.024 -10000 0 -0.47 1 1
PRKCI 0.02 0.013 -10000 0 -10000 0 0
TRAF6 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.027 0.032 -10000 0 -0.34 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.015 0.068 -10000 0 -0.44 3 3
CHUK 0.028 0.004 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.007 0.08 -10000 0 -0.23 36 36
IL1 beta/IL1R2 -0.053 0.14 0.22 1 -0.28 118 119
IRAK/TRAF6/TAK1/TAB1/TAB2 0.037 0.015 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.014 0.074 -10000 0 -0.62 1 1
IRAK3 0.021 0.053 -10000 0 -0.42 6 6
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.026 0.085 -10000 0 -0.67 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.009 0.071 -10000 0 -0.3 9 9
IL1 alpha/IL1R1/IL1RAP -0.018 0.12 -10000 0 -0.24 82 82
RELA 0.027 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.026 0.007 -10000 0 -10000 0 0
MYD88 0.024 0.01 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.05 0.029 -10000 0 -10000 0 0
IL1RAP 0.018 0.034 -10000 0 -0.43 2 2
UBE2N 0.028 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 0.006 0.065 -10000 0 -0.58 1 1
CASP1 0.024 0.026 -10000 0 -0.47 1 1
IL1RN/IL1R2 -0.13 0.23 -10000 0 -0.4 158 158
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.015 0.081 -10000 0 -0.69 1 1
TMEM189-UBE2V1 0.017 0.02 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.003 0.091 -10000 0 -0.33 9 9
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
IL1RN -0.11 0.22 -10000 0 -0.47 117 117
TRAF6/TAK1/TAB1/TAB2 0.049 0.018 -10000 0 -10000 0 0
MAP2K6 0.009 0.071 0.34 3 -10000 0 3
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.03 0.12 -10000 0 -0.25 97 97
cell-cell adhesion 0.033 0.082 0.38 4 -10000 0 4
Ephrin B/EPHB2/RasGAP 0.002 0.13 -10000 0 -0.26 21 21
ITSN1 0.027 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.022 0.044 -10000 0 -0.28 7 7
Ephrin B1/EPHB1 0.02 0.06 -10000 0 -0.25 18 18
HRAS/GDP -0.011 0.098 -10000 0 -0.33 10 10
Ephrin B/EPHB1/GRB7 0.042 0.091 -10000 0 -0.27 21 21
Endophilin/SYNJ1 -0.035 0.099 0.2 3 -0.4 2 5
KRAS 0.027 0.007 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.041 0.089 -10000 0 -0.27 19 19
endothelial cell migration 0.037 0.038 -10000 0 -0.24 3 3
GRB2 0.028 0.004 -10000 0 -10000 0 0
GRB7 0.027 0.024 -10000 0 -0.47 1 1
PAK1 -0.03 0.12 0.32 4 -0.43 7 11
HRAS 0.026 0.022 -10000 0 -0.4 1 1
RRAS -0.035 0.1 0.2 3 -0.41 2 5
DNM1 -0.002 0.11 -10000 0 -0.39 29 29
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.016 0.093 0.32 5 -0.26 19 24
lamellipodium assembly -0.033 0.082 -10000 0 -0.38 4 4
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.01 0.067 -10000 0 -0.41 2 2
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
EPHB2 -0.057 0.17 -10000 0 -0.39 84 84
EPHB3 0.011 0.068 -10000 0 -0.47 8 8
EPHB1 0.004 0.094 -10000 0 -0.42 19 19
EPHB4 0.026 0.008 -10000 0 -10000 0 0
mol:GDP -0.033 0.09 0.29 1 -0.34 11 12
Ephrin B/EPHB2 -0.007 0.12 -10000 0 -0.21 101 101
Ephrin B/EPHB3 0.029 0.072 -10000 0 -0.24 21 21
JNK cascade 0.009 0.14 0.36 35 -0.42 1 36
Ephrin B/EPHB1 0.031 0.084 -10000 0 -0.27 20 20
RAP1/GDP -0.013 0.1 0.26 5 -0.34 6 11
EFNB2 0.026 0.025 -10000 0 -0.47 1 1
EFNB3 0.001 0.11 -10000 0 -0.47 22 22
EFNB1 0.028 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.011 0.11 -10000 0 -0.22 84 84
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.005 0.11 -10000 0 -0.42 4 4
Rap1/GTP -0.025 0.092 -10000 0 -0.39 4 4
axon guidance -0.03 0.12 -10000 0 -0.25 97 97
MAPK3 0.004 0.061 0.19 3 -0.38 2 5
MAPK1 0.006 0.065 0.2 9 -0.38 2 11
Rac1/GDP -0.024 0.095 0.27 2 -0.33 8 10
actin cytoskeleton reorganization -0.039 0.077 -10000 0 -0.31 5 5
CDC42/GDP -0.021 0.099 0.26 5 -0.33 8 13
PI3K 0.04 0.041 -10000 0 -0.24 3 3
EFNA5 0.005 0.1 -10000 0 -0.47 18 18
Ephrin B2/EPHB4 0.033 0.02 -10000 0 -0.28 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.014 0.081 -10000 0 -0.3 9 9
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.026 0.088 -10000 0 -0.38 4 4
PTK2 0.094 0.21 0.57 66 -10000 0 66
MAP4K4 0.009 0.14 0.36 35 -0.42 1 36
SRC 0.027 0.007 -10000 0 -10000 0 0
KALRN -0.006 0.12 -10000 0 -0.47 26 26
Intersectin/N-WASP 0.038 0.012 -10000 0 -10000 0 0
neuron projection morphogenesis -0.002 0.12 0.31 24 -0.36 8 32
MAP2K1 0.005 0.062 -10000 0 -0.39 2 2
WASL 0.027 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.002 0.11 -10000 0 -0.22 81 81
cell migration 0.01 0.092 0.23 8 -0.4 3 11
NRAS 0.027 0.006 -10000 0 -10000 0 0
SYNJ1 -0.035 0.1 0.2 3 -0.41 2 5
PXN 0.028 0.003 -10000 0 -10000 0 0
TF -0.17 0.15 0.2 2 -0.41 65 67
HRAS/GTP -0.01 0.1 -10000 0 -0.4 4 4
Ephrin B1/EPHB1-2 -0.009 0.11 -10000 0 -0.22 83 83
cell adhesion mediated by integrin 0 0.066 0.24 14 -0.25 5 19
RAC1 0.026 0.007 -10000 0 -10000 0 0
mol:GTP -0.008 0.11 -10000 0 -0.42 4 4
RAC1-CDC42/GTP -0.033 0.087 -10000 0 -0.38 4 4
RASA1 0.026 0.025 -10000 0 -0.47 1 1
RAC1-CDC42/GDP -0.015 0.098 0.27 2 -0.34 6 8
ruffle organization -0.013 0.12 0.38 12 -0.39 4 16
NCK1 0.024 0.01 -10000 0 -10000 0 0
receptor internalization -0.058 0.1 0.2 3 -0.36 15 18
Ephrin B/EPHB2/KALRN -0.009 0.13 -10000 0 -0.29 34 34
ROCK1 0.055 0.082 0.18 106 -0.26 6 112
RAS family/GDP -0.044 0.076 -10000 0 -0.31 5 5
Rac1/GTP -0.029 0.089 -10000 0 -0.4 4 4
Ephrin B/EPHB1/Src/Paxillin 0.008 0.07 -10000 0 -0.25 22 22
Caspase cascade in apoptosis

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
TOP1 -0.019 0.13 0.25 4 -0.44 14 18
ACTA1 -0.088 0.12 0.22 3 -0.33 57 60
NUMA1 -0.026 0.13 0.25 3 -0.46 15 18
SPTAN1 -0.029 0.12 0.27 5 -0.32 30 35
LIMK1 -0.029 0.12 0.26 6 -0.31 33 39
BIRC3 0.014 0.065 -10000 0 -0.4 10 10
BIRC2 0.024 0.01 -10000 0 -10000 0 0
BAX 0.028 0.004 -10000 0 -10000 0 0
CASP10 -0.058 0.12 -10000 0 -0.31 72 72
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0.004 -10000 0 -10000 0 0
PTK2 -0.015 0.1 0.24 3 -0.37 8 11
DIABLO 0.028 0.003 -10000 0 -10000 0 0
apoptotic nuclear changes -0.029 0.12 0.27 5 -0.32 30 35
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.028 0.002 -10000 0 -10000 0 0
GSN -0.029 0.12 0.26 5 -0.32 32 37
MADD 0.028 0.005 -10000 0 -10000 0 0
TFAP2A -0.008 0.19 -10000 0 -0.79 20 20
BID -0.019 0.062 -10000 0 -0.21 26 26
MAP3K1 -0.02 0.11 0.19 1 -0.43 21 22
TRADD 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.039 0.02 -10000 0 -0.34 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.025 0.12 0.36 4 -0.32 31 35
CASP9 0.027 0.006 -10000 0 -10000 0 0
DNA repair 0.002 0.052 0.2 2 -0.22 2 4
neuron apoptosis 0 0.14 -10000 0 -0.67 15 15
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.034 0.13 0.28 4 -0.36 29 33
APAF1 0.027 0.024 -10000 0 -0.47 1 1
CASP6 -0.007 0.15 -10000 0 -0.9 10 10
TRAF2 0.024 0.036 -10000 0 -0.39 3 3
ICAD/CAD -0.032 0.11 0.28 6 -0.31 30 36
CASP7 -0.008 0.086 0.28 4 -0.35 4 8
KRT18 0.007 0.077 -10000 0 -0.49 8 8
apoptosis -0.03 0.12 0.26 4 -0.43 9 13
DFFA -0.033 0.11 0.25 5 -0.32 33 38
DFFB -0.032 0.11 0.26 6 -0.32 33 39
PARP1 -0.002 0.052 0.22 2 -0.21 2 4
actin filament polymerization 0.02 0.12 0.3 29 -0.34 15 44
TNF 0.007 0.09 -10000 0 -0.4 19 19
CYCS -0.003 0.067 0.19 4 -0.27 4 8
SATB1 -0.014 0.14 -10000 0 -0.83 10 10
SLK -0.034 0.11 0.26 4 -0.32 32 36
p15 BID/BAX 0.002 0.073 0.2 2 -0.26 2 4
CASP2 0.016 0.054 0.21 3 -0.44 1 4
JNK cascade 0.02 0.11 0.43 21 -0.19 1 22
CASP3 -0.034 0.12 0.27 5 -0.33 34 39
LMNB2 0.014 0.12 0.24 3 -0.48 13 16
RIPK1 0.027 0.006 -10000 0 -10000 0 0
CASP4 0.024 0.026 -10000 0 -0.47 1 1
Mammalian IAPs/DIABLO 0.056 0.047 -10000 0 -0.21 3 3
negative regulation of DNA binding -0.007 0.19 -10000 0 -0.78 20 20
stress fiber formation -0.033 0.11 0.26 4 -0.31 32 36
GZMB -0.05 0.15 -10000 0 -0.36 72 72
CASP1 0.013 0.035 -10000 0 -0.7 1 1
LMNB1 0.004 0.14 0.24 3 -0.51 18 21
APP 0 0.14 -10000 0 -0.68 15 15
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.002 -10000 0 -10000 0 0
VIM -0.027 0.12 0.26 4 -0.42 11 15
LMNA 0.021 0.09 0.26 1 -0.47 8 9
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.021 0.055 -10000 0 -0.29 5 5
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.033 0.11 0.24 5 -0.32 33 38
APAF-1/Caspase 9 -0.003 0.1 -10000 0 -0.62 11 11
nuclear fragmentation during apoptosis -0.026 0.13 0.25 3 -0.44 15 18
CFL2 -0.021 0.12 0.34 15 -0.31 29 44
GAS2 -0.062 0.14 0.25 5 -0.34 49 54
positive regulation of apoptosis 0.016 0.12 0.23 4 -0.56 11 15
PRF1 -0.003 0.11 -10000 0 -0.4 30 30
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.002 0.081 -10000 0 -10000 0 0
epithelial cell differentiation -0.029 0.11 -10000 0 -0.37 5 5
ITCH 0.038 0.02 -10000 0 -10000 0 0
WWP1 -0.002 0.079 -10000 0 -10000 0 0
FYN 0.027 0.021 -10000 0 -0.39 1 1
EGFR 0.022 0.035 -10000 0 -0.47 2 2
PRL -0.007 0.044 -10000 0 -0.4 4 4
neuron projection morphogenesis -0.023 0.098 0.25 4 -0.42 1 5
PTPRZ1 0.015 0.076 -10000 0 -0.47 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.005 0.11 -10000 0 -0.37 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.038 0.1 -10000 0 -0.32 21 21
ADAM17 0.038 0.04 -10000 0 -0.46 2 2
ErbB4/ErbB4 -0.014 0.084 -10000 0 -0.27 3 3
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.012 0.09 -10000 0 -0.34 3 3
NCOR1 0.027 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.026 0.11 -10000 0 -0.39 4 4
GRIN2B -0.032 0.1 0.26 2 -0.38 4 6
ErbB4/ErbB2/betacellulin -0.07 0.13 -10000 0 -0.32 37 37
STAT1 0.007 0.09 -10000 0 -0.39 20 20
HBEGF 0.027 0.006 -10000 0 -10000 0 0
PRLR -0.062 0.19 -10000 0 -0.46 74 74
E4ICDs/ETO2 -0.004 0.082 -10000 0 -10000 0 0
axon guidance -0.009 0.076 0.38 1 -0.32 3 4
NEDD4 0.04 0.019 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.034 0.14 -10000 0 -0.34 74 74
CBFA2T3 0.026 0.025 -10000 0 -0.47 1 1
ErbB4/ErbB2/HBEGF 0.011 0.066 -10000 0 -0.3 1 1
MAPK3 -0.019 0.1 0.26 3 -0.43 1 4
STAT1 (dimer) -0.013 0.097 -10000 0 -0.34 8 8
MAPK1 -0.018 0.1 0.28 4 -0.38 2 6
JAK2 0.024 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.032 0.1 -10000 0 -0.3 20 20
NRG1 -0.029 0.11 -10000 0 -0.28 68 68
NRG3 -0.002 0.067 -10000 0 -0.45 8 8
NRG2 -0.25 0.24 -10000 0 -0.47 231 231
NRG4 -0.011 0.13 -10000 0 -0.46 31 31
heart development -0.009 0.076 0.38 1 -0.32 3 4
neural crest cell migration -0.032 0.1 -10000 0 -0.3 20 20
ERBB2 0.022 0.031 0.23 2 -0.32 2 4
WWOX/E4ICDs -0.003 0.082 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.011 0.11 -10000 0 -0.36 14 14
apoptosis 0.028 0.097 0.41 6 -10000 0 6
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.16 0.16 -10000 0 -0.36 84 84
ErbB4/ErbB2/epiregulin -0.047 0.12 -10000 0 -0.31 32 32
ErbB4/ErbB4/betacellulin/betacellulin -0.089 0.15 -10000 0 -0.37 44 44
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.024 0.13 -10000 0 -0.35 14 14
MDM2 -0.008 0.079 0.27 8 -10000 0 8
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.022 0.093 -10000 0 -0.37 3 3
STAT5A -0.008 0.074 0.34 1 -0.35 1 2
ErbB4/EGFR/neuregulin 1 beta -0.025 0.1 -10000 0 -0.3 17 17
DLG4 0.026 0.025 -10000 0 -0.47 1 1
GRB2/SHC 0.04 0.009 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.003 0.075 -10000 0 -10000 0 0
STAT5A (dimer) -0.026 0.12 -10000 0 -0.4 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.003 0.084 0.33 1 -0.35 1 2
LRIG1 0.016 0.064 -10000 0 -0.47 7 7
EREG -0.09 0.21 -10000 0 -0.46 100 100
BTC -0.13 0.23 -10000 0 -0.47 131 131
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.009 0.074 0.38 1 -0.32 3 4
ERBB4 -0.02 0.073 -10000 0 -10000 0 0
STAT5B 0.028 0.003 -10000 0 -10000 0 0
YAP1 -0.014 0.1 -10000 0 -0.43 22 22
GRB2 0.028 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.007 0.097 -10000 0 -0.33 15 15
glial cell differentiation 0.004 0.074 -10000 0 -10000 0 0
WWOX 0.027 0.006 -10000 0 -10000 0 0
cell proliferation -0.1 0.16 0.29 2 -0.43 41 43
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.026 0.025 -10000 0 -0.47 1 1
EPHB2 -0.056 0.17 -10000 0 -0.39 84 84
EFNB1 -0.005 0.072 -10000 0 -0.27 28 28
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.008 0.12 -10000 0 -0.37 9 9
Ephrin B2/EPHB1-2 -0.01 0.11 -10000 0 -0.22 82 82
neuron projection morphogenesis -0.02 0.1 -10000 0 -0.35 9 9
Ephrin B1/EPHB1-2/Tiam1 -0.017 0.12 -10000 0 -0.32 18 18
DNM1 -0.001 0.11 -10000 0 -0.39 29 29
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.014 0.098 -10000 0 -0.46 18 18
YES1 -0.017 0.15 -10000 0 -0.69 19 19
Ephrin B1/EPHB1-2/NCK2 -0.014 0.12 -10000 0 -0.34 14 14
PI3K 0.011 0.1 -10000 0 -0.45 16 16
mol:GDP -0.018 0.12 -10000 0 -0.32 18 18
ITGA2B -0.006 0.12 -10000 0 -0.39 34 34
endothelial cell proliferation 0.033 0.02 -10000 0 -0.28 1 1
FYN -0.016 0.15 -10000 0 -0.69 19 19
MAP3K7 -0.016 0.1 0.24 1 -0.5 18 19
FGR -0.013 0.15 -10000 0 -0.68 19 19
TIAM1 0.021 0.054 -10000 0 -0.47 5 5
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
RGS3 0.028 0.005 -10000 0 -10000 0 0
cell adhesion -0.014 0.12 -10000 0 -0.47 16 16
LYN -0.016 0.15 -10000 0 -0.69 19 19
Ephrin B1/EPHB1-2/Src Family Kinases -0.022 0.14 -10000 0 -0.62 21 21
Ephrin B1/EPHB1-2 -0.015 0.11 -10000 0 -0.55 16 16
SRC -0.013 0.15 -10000 0 -0.68 19 19
ITGB3 0.007 0.096 -10000 0 -0.42 20 20
EPHB1 0.004 0.093 -10000 0 -0.42 19 19
EPHB4 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.02 -10000 0 -0.28 1 1
alphaIIb/beta3 Integrin 0 0.11 -10000 0 -0.29 52 52
BLK -0.024 0.15 -10000 0 -0.68 20 20
HCK -0.013 0.15 -10000 0 -0.68 19 19
regulation of stress fiber formation 0.014 0.12 0.33 14 -10000 0 14
MAPK8 -0.016 0.1 -10000 0 -0.46 18 18
Ephrin B1/EPHB1-2/RGS3 -0.014 0.12 -10000 0 -0.34 14 14
endothelial cell migration 0.002 0.097 0.24 10 -0.42 14 24
NCK2 0.028 0.003 -10000 0 -10000 0 0
PTPN13 0.017 0.078 -10000 0 -0.58 7 7
regulation of focal adhesion formation 0.014 0.12 0.33 14 -10000 0 14
chemotaxis 0.014 0.12 0.33 14 -10000 0 14
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
Rac1/GTP -0.015 0.11 -10000 0 -0.36 9 9
angiogenesis -0.017 0.11 -10000 0 -0.53 18 18
LCK -0.014 0.15 -10000 0 -0.68 19 19
BCR signaling pathway

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
JUN -0.018 0.12 0.23 5 -0.4 14 19
IKBKB 0.008 0.1 0.29 9 -0.33 9 18
AKT1 0.006 0.11 0.27 29 -0.25 8 37
IKBKG 0.019 0.081 0.26 8 -0.3 3 11
CALM1 -0.003 0.099 0.27 7 -0.37 9 16
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
MAP3K1 -0.024 0.14 0.28 5 -0.51 15 20
MAP3K7 0.028 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.098 0.26 3 -0.39 10 13
DOK1 0.028 0.003 -10000 0 -10000 0 0
AP-1 -0.012 0.093 0.22 13 -0.24 13 26
LYN 0.025 0.009 -10000 0 -10000 0 0
BLNK -0.019 0.14 -10000 0 -0.47 40 40
SHC1 0.028 0.004 -10000 0 -10000 0 0
BCR complex -0.034 0.15 -10000 0 -0.33 84 84
CD22 -0.046 0.14 -10000 0 -0.42 36 36
CAMK2G -0.002 0.094 0.26 7 -0.38 6 13
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
INPP5D 0.026 0.025 -10000 0 -0.47 1 1
SHC/GRB2/SOS1 -0.037 0.12 -10000 0 -0.4 21 21
GO:0007205 -0.009 0.099 0.28 2 -0.4 10 12
SYK 0.025 0.034 -10000 0 -0.47 2 2
ELK1 -0.008 0.096 0.26 3 -0.38 10 13
NFATC1 -0.041 0.12 0.25 6 -0.38 23 29
B-cell antigen/BCR complex -0.034 0.15 -10000 0 -0.33 84 84
PAG1/CSK 0.035 0.021 -10000 0 -0.28 1 1
NFKBIB 0.019 0.046 0.13 12 -0.13 13 25
HRAS -0.012 0.1 0.25 4 -0.38 10 14
NFKBIA 0.02 0.046 0.13 12 -0.13 11 23
NF-kappa-B/RelA/I kappa B beta 0.023 0.041 0.14 12 -10000 0 12
RasGAP/Csk 0.008 0.14 -10000 0 -0.42 16 16
mol:GDP -0.006 0.095 0.26 2 -0.38 10 12
PTEN 0.028 0.005 -10000 0 -10000 0 0
CD79B 0.013 0.08 -10000 0 -0.41 14 14
NF-kappa-B/RelA/I kappa B alpha 0.024 0.041 0.14 12 -10000 0 12
GRB2 0.028 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.043 0.16 0.29 2 -0.5 17 19
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
mol:IP3 -0.01 0.098 0.25 2 -0.39 11 13
CSK 0.028 0.005 -10000 0 -10000 0 0
FOS -0.029 0.12 0.26 9 -0.36 22 31
CHUK 0.011 0.092 0.25 8 -0.34 8 16
IBTK 0.028 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.009 0.11 0.24 5 -0.35 13 18
PTPN6 -0.046 0.13 -10000 0 -0.51 19 19
RELA 0.027 0.006 -10000 0 -10000 0 0
BCL2A1 0.015 0.033 0.12 5 -0.11 1 6
VAV2 -0.055 0.15 -10000 0 -0.49 22 22
ubiquitin-dependent protein catabolic process 0.022 0.046 0.13 14 -0.13 13 27
BTK 0.018 0.053 -10000 0 -1 1 1
CD19 -0.06 0.16 -10000 0 -0.38 58 58
MAP4K1 0.016 0.071 -10000 0 -0.41 11 11
CD72 -0.012 0.12 -10000 0 -0.4 36 36
PAG1 0.024 0.022 -10000 0 -0.39 1 1
MAPK14 -0.017 0.13 0.3 5 -0.44 14 19
SH3BP5 0.022 0.035 -10000 0 -0.47 2 2
PIK3AP1 -0.015 0.1 -10000 0 -0.38 15 15
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.035 0.14 -10000 0 -0.45 22 22
RAF1 -0.013 0.096 0.25 3 -0.37 9 12
RasGAP/p62DOK/SHIP 0.007 0.14 -10000 0 -0.41 17 17
CD79A -0.061 0.18 -10000 0 -0.42 84 84
re-entry into mitotic cell cycle -0.012 0.092 0.22 13 -0.24 13 26
RASA1 0.026 0.025 -10000 0 -0.47 1 1
MAPK3 -0.008 0.088 0.24 4 -0.32 8 12
MAPK1 -0.005 0.092 0.25 8 -0.32 9 17
CD72/SHP1 -0.038 0.16 0.3 4 -0.53 25 29
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.022 0.13 0.28 5 -0.43 16 21
actin cytoskeleton organization -0.041 0.14 0.33 2 -0.44 20 22
NF-kappa-B/RelA 0.05 0.078 0.24 14 -0.21 3 17
Calcineurin 0.019 0.095 0.26 4 -0.35 6 10
PI3K -0.049 0.13 -10000 0 -0.41 31 31
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.007 0.098 0.22 2 -0.4 13 15
SOS1 0.028 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.028 0.2 -10000 0 -0.7 25 25
DAPP1 -0.04 0.2 -10000 0 -0.76 25 25
cytokine secretion -0.038 0.12 0.24 6 -0.36 23 29
mol:DAG -0.01 0.098 0.25 2 -0.39 11 13
PLCG2 0.026 0.025 -10000 0 -0.47 1 1
MAP2K1 -0.009 0.093 0.24 4 -0.35 9 13
B-cell antigen/BCR complex/FcgammaRIIB -0.018 0.15 -10000 0 -0.29 85 85
mol:PI-3-4-5-P3 -0.032 0.1 0.22 1 -0.3 27 28
ETS1 -0.004 0.088 0.25 7 -0.35 6 13
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.018 0.15 -10000 0 -0.32 59 59
B-cell antigen/BCR complex/LYN -0.028 0.13 -10000 0 -0.46 19 19
MALT1 0.025 0.009 -10000 0 -10000 0 0
TRAF6 0.027 0.006 -10000 0 -10000 0 0
RAC1 -0.046 0.14 0.33 1 -0.47 20 21
B-cell antigen/BCR complex/LYN/SYK -0.016 0.16 0.37 1 -0.44 33 34
CARD11 -0.006 0.12 0.27 12 -0.38 16 28
FCGR2B 0.021 0.059 -10000 0 -0.47 6 6
PPP3CA 0.028 0.005 -10000 0 -10000 0 0
BCL10 0.028 0.004 -10000 0 -10000 0 0
IKK complex 0.017 0.053 0.17 21 -0.12 5 26
PTPRC 0.015 0.074 -10000 0 -0.43 11 11
PDPK1 -0.004 0.1 0.24 28 -0.23 12 40
PPP3CB 0.028 0.004 -10000 0 -10000 0 0
PPP3CC 0.026 0.008 -10000 0 -10000 0 0
POU2F2 0.016 0.033 0.12 5 -10000 0 5
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.042 0.072 -10000 0 -0.22 26 26
ER alpha/Gai/GDP/Gbeta gamma -0.022 0.16 -10000 0 -0.51 28 28
AKT1 0.005 0.14 -10000 0 -0.74 12 12
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.01 0.14 -10000 0 -0.76 12 12
mol:Ca2+ -0.036 0.14 -10000 0 -0.36 57 57
IGF1R 0.027 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.011 0.085 -10000 0 -0.26 37 37
SHC1 0.028 0.004 -10000 0 -10000 0 0
apoptosis -0.005 0.13 0.7 12 -10000 0 12
RhoA/GTP 0.012 0.047 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.016 0.13 -10000 0 -0.48 16 16
regulation of stress fiber formation 0.006 0.06 0.31 1 -0.18 6 7
E2/ERA-ERB (dimer) 0.016 0.073 -10000 0 -0.25 28 28
KRAS 0.027 0.007 -10000 0 -10000 0 0
G13/GTP 0.022 0.057 -10000 0 -0.22 22 22
pseudopodium formation -0.006 0.06 0.18 6 -0.31 1 7
E2/ER alpha (dimer)/PELP1 0.022 0.062 -10000 0 -0.24 22 22
GRB2 0.028 0.004 -10000 0 -10000 0 0
GNG2 0.027 0.007 -10000 0 -10000 0 0
GNAO1 0.023 0.043 -10000 0 -0.41 4 4
HRAS 0.026 0.022 -10000 0 -0.4 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.003 0.15 0.25 8 -0.52 22 30
E2/ER beta (dimer) 0.014 0.042 -10000 0 -0.28 8 8
mol:GDP 0.005 0.064 -10000 0 -0.35 7 7
mol:NADP -0.003 0.15 0.25 8 -0.52 22 30
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
mol:IP3 -0.043 0.14 -10000 0 -0.37 57 57
IGF-1R heterotetramer 0.027 0.005 -10000 0 -10000 0 0
PLCB1 -0.04 0.14 -10000 0 -0.38 57 57
PLCB2 -0.041 0.14 -10000 0 -0.38 61 61
IGF1 -0.044 0.17 -10000 0 -0.46 62 62
mol:L-citrulline -0.003 0.15 0.25 8 -0.52 22 30
RHOA 0.024 0.01 -10000 0 -10000 0 0
Gai/GDP -0.056 0.24 -10000 0 -0.61 58 58
JNK cascade 0.014 0.042 -10000 0 -0.28 8 8
BCAR1 0.027 0.006 -10000 0 -10000 0 0
ESR2 0.018 0.059 -10000 0 -0.4 8 8
GNAQ 0.028 0.005 -10000 0 -10000 0 0
ESR1 0.005 0.098 -10000 0 -0.41 22 22
Gq family/GDP/Gbeta gamma -0.025 0.16 -10000 0 -0.69 16 16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.032 0.079 -10000 0 -0.82 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.016 0.13 -10000 0 -0.47 17 17
GNAZ 0.011 0.083 -10000 0 -0.42 15 15
E2/ER alpha (dimer) 0.005 0.069 -10000 0 -0.29 22 22
STRN 0.009 0.095 -10000 0 -0.47 16 16
GNAL -0.027 0.15 -10000 0 -0.47 45 45
PELP1 0.027 0.006 -10000 0 -10000 0 0
MAPK11 0.01 0.036 0.17 1 -0.24 8 9
GNAI2 0.024 0.01 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.026 0.025 -10000 0 -0.47 1 1
HBEGF -0.086 0.17 0.32 12 -0.54 30 42
cAMP biosynthetic process -0.014 0.096 -10000 0 -0.23 67 67
SRC -0.016 0.15 0.21 15 -0.51 24 39
PI3K 0.027 0.032 -10000 0 -0.34 2 2
GNB1 0.027 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.034 0.069 -10000 0 -0.35 5 5
SOS1 0.028 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.035 0.12 -10000 0 -0.42 19 19
Gs family/GTP -0.008 0.1 -10000 0 -0.23 67 67
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.047 0.023 -10000 0 -0.22 1 1
vasodilation -0.002 0.14 0.25 8 -0.49 22 30
mol:DAG -0.043 0.14 -10000 0 -0.37 57 57
Gs family/GDP/Gbeta gamma -0.009 0.088 -10000 0 -0.35 8 8
MSN -0.006 0.063 0.19 3 -0.34 1 4
Gq family/GTP -0.039 0.15 -10000 0 -0.39 61 61
mol:PI-3-4-5-P3 0.01 0.14 -10000 0 -0.72 12 12
NRAS 0.027 0.006 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.002 0.14 0.49 22 -0.25 8 30
GRB2/SOS1 0.041 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.065 -10000 0 -0.34 6 6
NOS3 -0.005 0.16 0.26 8 -0.55 22 30
GNA11 0.025 0.034 -10000 0 -0.47 2 2
MAPKKK cascade 0.011 0.14 -10000 0 -0.54 14 14
E2/ER alpha (dimer)/PELP1/Src 0.016 0.14 0.28 4 -0.47 20 24
ruffle organization -0.006 0.06 0.18 6 -0.31 1 7
ROCK2 -0.005 0.068 0.2 3 -0.36 1 4
GNA14 -0.048 0.18 -10000 0 -0.47 64 64
GNA15 0.025 0.034 -10000 0 -0.47 2 2
GNA13 0.028 0.004 -10000 0 -10000 0 0
MMP9 -0.12 0.18 0.37 14 -0.54 31 45
MMP2 -0.03 0.15 0.27 8 -0.5 21 29
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.015 0.2 -10000 0 -0.87 16 16
NCK1/PAK1/Dok-R -0.024 0.08 -10000 0 -0.4 14 14
NCK1/Dok-R 0.011 0.22 -10000 0 -1 16 16
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
mol:beta2-estradiol -0.001 0.041 0.25 11 -10000 0 11
RELA 0.027 0.006 -10000 0 -10000 0 0
SHC1 0.028 0.005 -10000 0 -10000 0 0
Rac/GDP 0.019 0.006 -10000 0 -10000 0 0
F2 -0.041 0.13 0.27 11 -0.4 41 52
TNIP2 0.026 0.008 -10000 0 -10000 0 0
NF kappa B/RelA 0.032 0.21 -10000 0 -0.93 17 17
FN1 -0.18 0.21 -10000 0 -0.39 203 203
PLD2 -0.006 0.23 -10000 0 -1.1 17 17
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GRB14 -0.02 0.14 -10000 0 -0.46 40 40
ELK1 0.002 0.21 -10000 0 -0.95 17 17
GRB7 0.027 0.024 -10000 0 -0.47 1 1
PAK1 0.026 0.009 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.13 0.26 -10000 0 -1.1 17 17
CDKN1A 0.029 0.16 0.44 1 -0.62 12 13
ITGA5 -0.11 0.2 -10000 0 -0.39 134 134
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0.017 0.23 -10000 0 -1.1 16 16
CRK 0.027 0.006 -10000 0 -10000 0 0
mol:NO 0.024 0.16 0.44 2 -0.64 16 18
PLG -0.01 0.23 -10000 0 -1.1 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.017 0.19 -10000 0 -0.81 17 17
GRB2 0.028 0.004 -10000 0 -10000 0 0
PIK3R1 0.024 0.042 -10000 0 -0.47 3 3
ANGPT2 0.009 0.16 -10000 0 -0.57 6 6
BMX -0.026 0.24 -10000 0 -1.1 17 17
ANGPT1 -0.005 0.2 -10000 0 -1.2 11 11
tube development 0.018 0.18 0.38 1 -0.66 15 16
ANGPT4 0.018 0.017 -10000 0 -10000 0 0
response to hypoxia -0.002 0.014 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.015 0.25 -10000 0 -1.1 17 17
alpha5/beta1 Integrin -0.06 0.15 -10000 0 -0.28 133 133
FGF2 0.01 0.088 -10000 0 -0.45 15 15
STAT5A (dimer) 0.027 0.2 -10000 0 -0.8 12 12
mol:L-citrulline 0.024 0.16 0.44 2 -0.64 16 18
AGTR1 -0.021 0.13 -10000 0 -0.46 34 34
MAPK14 -0.002 0.25 -10000 0 -1.1 18 18
Tie2/SHP2 -0.006 0.2 -10000 0 -1.1 11 11
TEK -0.001 0.21 -10000 0 -1.2 11 11
RPS6KB1 0.016 0.2 -10000 0 -0.82 17 17
Angiotensin II/AT1 -0.013 0.095 -10000 0 -0.33 34 34
Tie2/Ang1/GRB2 0.008 0.24 -10000 0 -1.1 17 17
MAPK3 -0.005 0.21 -10000 0 -0.97 17 17
MAPK1 -0.004 0.21 -10000 0 -0.97 17 17
Tie2/Ang1/GRB7 0.007 0.24 -10000 0 -1.1 16 16
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MAPK8 -0.006 0.23 -10000 0 -1.1 16 16
PI3K -0.006 0.22 -10000 0 -0.99 17 17
FES 0.003 0.24 -10000 0 -1.1 18 18
Crk/Dok-R 0.017 0.23 -10000 0 -1.1 16 16
Tie2/Ang1/ABIN2 0.007 0.24 -10000 0 -1.1 17 17
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.02 0.19 -10000 0 -0.77 16 16
STAT5A 0.028 0.003 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.041 0.21 0.44 3 -0.8 16 19
Tie2/Ang2 0.008 0.22 -10000 0 -0.94 13 13
Tie2/Ang1 -0.004 0.25 -10000 0 -1.1 17 17
FOXO1 0.022 0.19 -10000 0 -0.77 16 16
ELF1 0.029 0.042 -10000 0 -0.48 2 2
ELF2 -0.001 0.23 -10000 0 -1.1 16 16
mol:Choline -0.004 0.22 -10000 0 -1 17 17
cell migration -0.047 0.061 -10000 0 -0.23 18 18
FYN 0.012 0.19 -10000 0 -0.76 14 14
DOK2 0.023 0.038 -10000 0 -0.42 3 3
negative regulation of cell cycle 0.03 0.16 0.43 1 -0.57 12 13
ETS1 0.022 0.059 -10000 0 -0.29 13 13
PXN 0.045 0.18 0.41 4 -0.66 16 20
ITGB1 0.028 0.005 -10000 0 -10000 0 0
NOS3 0.021 0.18 0.5 1 -0.73 16 17
RAC1 0.026 0.007 -10000 0 -10000 0 0
TNF 0.007 0.1 -10000 0 -0.35 29 29
MAPKKK cascade -0.004 0.22 -10000 0 -1 17 17
RASA1 0.026 0.025 -10000 0 -0.47 1 1
Tie2/Ang1/Shc 0.008 0.24 -10000 0 -1.1 17 17
NCK1 0.024 0.01 -10000 0 -10000 0 0
vasculogenesis 0.026 0.15 0.39 3 -0.57 16 19
mol:Phosphatidic acid -0.004 0.22 -10000 0 -1 17 17
mol:Angiotensin II 0 0.005 -10000 0 -10000 0 0
mol:NADP 0.024 0.16 0.44 2 -0.64 16 18
Rac1/GTP 0.019 0.18 -10000 0 -0.76 17 17
MMP2 -0.031 0.23 -10000 0 -1 17 17
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade 0.016 0.071 -10000 0 -0.27 23 23
EFNA5 0.005 0.1 -10000 0 -0.47 18 18
FYN -0.01 0.061 0.18 1 -0.26 22 23
neuron projection morphogenesis 0.016 0.071 -10000 0 -0.27 23 23
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.016 0.071 -10000 0 -0.27 23 23
EPHA5 0.002 0.049 -10000 0 -0.4 5 5
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.047 0.16 -10000 0 -0.59 14 14
MKNK1 0.028 0.003 -10000 0 -10000 0 0
MAPK14 -0.016 0.098 -10000 0 -0.3 20 20
ATF2/c-Jun -0.009 0.071 -10000 0 -0.36 3 3
MAPK11 -0.015 0.098 -10000 0 -0.3 19 19
MITF -0.029 0.11 -10000 0 -0.37 20 20
MAPKAPK5 -0.02 0.1 -10000 0 -0.36 15 15
KRT8 -0.068 0.16 -10000 0 -0.42 36 36
MAPKAPK3 0.024 0.01 -10000 0 -10000 0 0
MAPKAPK2 0.028 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.023 0.14 -10000 0 -0.43 19 19
CEBPB -0.021 0.1 -10000 0 -0.37 16 16
SLC9A1 -0.021 0.1 -10000 0 -0.36 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.016 0.1 -10000 0 -0.35 14 14
p38alpha-beta/MNK1 -0.001 0.12 -10000 0 -0.35 18 18
JUN -0.006 0.073 -10000 0 -0.36 3 3
PPARGC1A -0.12 0.19 -10000 0 -0.47 56 56
USF1 -0.018 0.1 -10000 0 -0.36 15 15
RAB5/GDP/GDI1 -0.004 0.074 -10000 0 -0.33 4 4
NOS2 -0.065 0.22 -10000 0 -0.8 22 22
DDIT3 -0.022 0.1 -10000 0 -0.37 17 17
RAB5A 0.025 0.01 -10000 0 -10000 0 0
HSPB1 -0.013 0.094 0.29 11 -0.3 15 26
p38alpha-beta/HBP1 -0.001 0.12 -10000 0 -0.37 13 13
CREB1 -0.018 0.1 -10000 0 -0.37 16 16
RAB5/GDP 0.018 0.007 -10000 0 -10000 0 0
EIF4E -0.017 0.094 0.24 1 -0.33 13 14
RPS6KA4 -0.02 0.1 -10000 0 -0.36 15 15
PLA2G4A -0.03 0.11 -10000 0 -0.33 16 16
GDI1 -0.016 0.098 -10000 0 -0.37 14 14
TP53 -0.035 0.12 -10000 0 -0.42 21 21
RPS6KA5 -0.023 0.1 -10000 0 -0.35 15 15
ESR1 -0.031 0.12 -10000 0 -0.34 26 26
HBP1 0.027 0.007 -10000 0 -10000 0 0
MEF2C -0.025 0.11 -10000 0 -0.37 16 16
MEF2A -0.019 0.1 -10000 0 -0.36 15 15
EIF4EBP1 -0.019 0.1 -10000 0 -0.4 15 15
KRT19 -0.13 0.18 -10000 0 -0.47 45 45
ELK4 -0.018 0.1 -10000 0 -0.36 15 15
ATF6 -0.018 0.1 -10000 0 -0.36 15 15
ATF1 -0.019 0.1 -10000 0 -0.39 15 15
p38alpha-beta/MAPKAPK2 0.001 0.12 -10000 0 -0.35 18 18
p38alpha-beta/MAPKAPK3 -0.004 0.12 -10000 0 -0.37 13 13
IL27-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
TGFB1 0.028 0.031 -10000 0 -0.39 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.046 0.12 0.44 17 -10000 0 17
IL27/IL27R/JAK1 -0.025 0.14 -10000 0 -0.51 7 7
TBX21 -0.076 0.16 -10000 0 -0.46 36 36
IL12B -0.017 0.12 -10000 0 -0.4 39 39
IL12A -0.006 0.054 -10000 0 -0.34 11 11
IL6ST -0.025 0.14 -10000 0 -0.48 37 37
IL27RA/JAK1 -0.001 0.064 -10000 0 -10000 0 0
IL27 -0.003 0.087 -10000 0 -0.4 18 18
TYK2 0.017 0.03 -10000 0 -0.41 1 1
T-helper cell lineage commitment 0.004 0.11 0.43 2 -10000 0 2
T-helper 2 cell differentiation 0.046 0.12 0.44 17 -10000 0 17
T cell proliferation during immune response 0.046 0.12 0.44 17 -10000 0 17
MAPKKK cascade -0.046 0.12 -10000 0 -0.44 17 17
STAT3 0.028 0.003 -10000 0 -10000 0 0
STAT2 0.028 0.003 -10000 0 -10000 0 0
STAT1 0.006 0.091 -10000 0 -0.4 20 20
IL12RB1 -0.01 0.12 -10000 0 -0.4 37 37
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.097 0.19 -10000 0 -0.48 49 49
IL27/IL27R/JAK2/TYK2 -0.046 0.13 -10000 0 -0.44 17 17
positive regulation of T cell mediated cytotoxicity -0.046 0.12 -10000 0 -0.44 17 17
STAT1 (dimer) -0.063 0.2 0.52 1 -0.54 27 28
JAK2 0.017 0.02 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
STAT2 (dimer) -0.036 0.13 -10000 0 -0.43 15 15
T cell proliferation -0.061 0.14 0.34 1 -0.44 27 28
IL12/IL12R/TYK2/JAK2 -0.053 0.19 -10000 0 -0.73 23 23
IL17A 0.004 0.11 0.43 2 -10000 0 2
mast cell activation 0.046 0.12 0.44 17 -10000 0 17
IFNG -0.01 0.038 -10000 0 -0.091 18 18
T cell differentiation -0.005 0.007 -10000 0 -0.018 54 54
STAT3 (dimer) -0.035 0.13 -10000 0 -0.43 16 16
STAT5A (dimer) -0.035 0.13 -10000 0 -0.44 15 15
STAT4 (dimer) -0.037 0.13 -10000 0 -0.43 18 18
STAT4 0.02 0.056 -10000 0 -0.4 7 7
T cell activation -0.005 0.011 0.05 15 -10000 0 15
IL27R/JAK2/TYK2 -0.011 0.12 -10000 0 -0.66 1 1
GATA3 -0.004 0.11 0.54 3 -1.3 2 5
IL18 0 0.047 -10000 0 -0.33 8 8
positive regulation of mast cell cytokine production -0.034 0.13 -10000 0 -0.42 16 16
IL27/EBI3 0.007 0.083 -10000 0 -0.3 26 26
IL27RA -0.009 0.065 -10000 0 -10000 0 0
IL6 -0.017 0.14 -10000 0 -0.45 40 40
STAT5A 0.028 0.003 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 -0.003 0.045 -10000 0 -10000 0 0
IL1B -0.025 0.089 -10000 0 -0.28 46 46
EBI3 0.012 0.064 -10000 0 -0.43 8 8
TNF -0.007 0.061 -10000 0 -0.28 19 19
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.1 0.21 -10000 0 -0.46 109 109
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.027 0.021 -10000 0 -0.39 1 1
TCEB1 0.025 0.009 -10000 0 -10000 0 0
HIF1A/p53 0.025 0.065 0.25 2 -0.3 8 10
HIF1A 0.006 0.042 -10000 0 -0.28 7 7
COPS5 0.025 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.063 0.037 -10000 0 -10000 0 0
FIH (dimer) 0.028 0.004 -10000 0 -10000 0 0
CDKN2A -0.14 0.2 -10000 0 -0.4 159 159
ARNT/IPAS -0.054 0.16 -10000 0 -0.33 105 105
HIF1AN 0.028 0.004 -10000 0 -10000 0 0
GNB2L1 0.026 0.007 -10000 0 -10000 0 0
HIF1A/ARNT 0.025 0.058 0.25 1 -0.28 8 9
CUL2 0.027 0.005 -10000 0 -10000 0 0
OS9 0.028 0.004 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.046 0.023 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.023 0.053 -10000 0 -0.28 8 8
PHD1-3/OS9 0.051 0.064 -10000 0 -0.26 4 4
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.056 -10000 0 -0.31 3 3
VHL 0.025 0.01 -10000 0 -10000 0 0
HSP90AA1 0.026 0.008 -10000 0 -10000 0 0
HIF1A/JAB1 0.022 0.055 -10000 0 -0.28 7 7
EGLN3 0.006 0.093 -10000 0 -0.41 20 20
EGLN2 0.027 0.005 -10000 0 -10000 0 0
EGLN1 0.028 0.005 -10000 0 -10000 0 0
TP53 0.022 0.048 -10000 0 -0.47 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.02 0.18 -10000 0 -0.5 48 48
ARNT 0.027 0.005 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.028 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF -0.054 0.1 -10000 0 -0.28 24 24
Signaling events mediated by HDAC Class III

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
EP300 0.025 0.034 -10000 0 -0.47 2 2
HDAC4 0.027 0.006 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.002 0.064 0.28 21 -10000 0 21
CDKN1A -0.006 0.012 -10000 0 -10000 0 0
KAT2B 0.01 0.083 -10000 0 -0.47 12 12
BAX 0.028 0.004 -10000 0 -10000 0 0
FOXO3 -0.004 0.027 0.38 2 -10000 0 2
FOXO1 0.026 0.007 -10000 0 -10000 0 0
FOXO4 0.014 0.032 -10000 0 -0.3 4 4
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.028 0.004 -10000 0 -10000 0 0
TAT 0.002 0.049 -10000 0 -0.39 5 5
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.052 0.13 -10000 0 -0.35 64 64
PPARGC1A -0.13 0.23 -10000 0 -0.47 129 129
FHL2 0.027 0.024 -10000 0 -0.47 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.037 0.02 -10000 0 -0.34 1 1
HIST2H4A -0.002 0.064 -10000 0 -0.28 21 21
SIRT1/FOXO3a 0.014 0.028 0.27 1 -0.21 4 5
SIRT1 0.023 0.024 -10000 0 -0.47 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.05 0.022 -10000 0 -0.29 1 1
SIRT1/Histone H1b 0.018 0.05 -10000 0 -0.24 7 7
apoptosis -0.051 0.021 0.28 1 -10000 0 1
SIRT1/PGC1A -0.068 0.15 -10000 0 -0.29 128 128
p53/SIRT1 0.026 0.04 -10000 0 -0.33 5 5
SIRT1/FOXO4 0.025 0.04 -10000 0 -0.26 5 5
FOXO1/FHL2/SIRT1 0.046 0.026 -10000 0 -0.26 2 2
HIST1H1E 0.008 0.04 -10000 0 -0.29 4 4
SIRT1/p300 0.035 0.032 -10000 0 -0.33 3 3
muscle cell differentiation 0.025 0.12 0.29 70 -10000 0 70
TP53 0.019 0.048 -10000 0 -0.47 4 4
KU70/SIRT1/BAX 0.051 0.021 -10000 0 -0.29 1 1
CREBBP 0.028 0.004 -10000 0 -10000 0 0
MEF2D 0.028 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.029 0.04 -10000 0 -0.29 6 6
ACSS2 0.011 0.017 -10000 0 -0.34 1 1
SIRT1/PCAF/MYOD -0.025 0.12 -10000 0 -0.29 70 70
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.01 0.056 0.89 1 -10000 0 1
VDR 0.027 0.024 -10000 0 -0.47 1 1
FAM120B 0.028 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.008 0.089 -10000 0 -0.35 5 5
RXRs/LXRs/DNA/Oxysterols 0.016 0.095 -10000 0 -0.37 10 10
MED1 0.028 0.003 -10000 0 -10000 0 0
mol:9cRA 0.003 0.009 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.008 0.091 -10000 0 -0.32 4 4
RXRs/NUR77 0.027 0.11 -10000 0 -0.26 45 45
RXRs/PPAR -0.081 0.14 -10000 0 -0.35 29 29
NCOR2 0.028 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.017 -10000 0 -0.33 1 1
RARs/VDR/DNA/Vit D3 0.033 0.082 -10000 0 -0.24 31 31
RARA 0.028 0.004 -10000 0 -10000 0 0
NCOA1 0.028 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.027 0.024 -10000 0 -0.47 1 1
RARs/RARs/DNA/9cRA 0.022 0.076 -10000 0 -0.24 30 30
RARG 0.027 0.024 -10000 0 -0.47 1 1
RPS6KB1 0.017 0.05 0.56 3 -10000 0 3
RARs/THRs/DNA/SMRT -0.009 0.092 -10000 0 -0.23 51 51
THRA 0.028 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.017 -10000 0 -0.33 1 1
RXRs/PPAR/9cRA/PGJ2/DNA 0.024 0.098 -10000 0 -0.25 38 38
NR1H4 -0.004 0.029 -10000 0 -0.39 1 1
RXRs/LXRs/DNA 0.046 0.11 -10000 0 -0.32 1 1
NR1H2 0.029 0.016 -10000 0 -10000 0 0
NR1H3 0.026 0.039 -10000 0 -0.39 3 3
RXRs/VDR/DNA/Vit D3 0.031 0.096 -10000 0 -0.24 38 38
NR4A1 0.016 0.076 -10000 0 -0.47 10 10
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.006 0.07 -10000 0 -0.26 4 4
RXRG -0.025 0.15 -10000 0 -0.46 45 45
RXR alpha/CCPG 0.041 0.014 -10000 0 -10000 0 0
RXRA 0.028 0.016 -10000 0 -10000 0 0
RXRB 0.028 0.017 -10000 0 -10000 0 0
THRB 0 0.11 -10000 0 -0.47 21 21
PPARG -0.14 0.23 -10000 0 -0.47 140 140
PPARD 0.027 0.006 -10000 0 -10000 0 0
TNF 0.002 0.13 -10000 0 -0.85 5 5
mol:Oxysterols 0.003 0.008 -10000 0 -10000 0 0
cholesterol transport 0.016 0.095 -10000 0 -0.37 10 10
PPARA 0.027 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.01 0.12 -10000 0 -0.46 29 29
RXRs/NUR77/BCL2 -0.01 0.09 -10000 0 -0.24 48 48
SREBF1 0.012 0.087 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.024 0.098 -10000 0 -0.25 38 38
ABCA1 0.007 0.11 -10000 0 -1 2 2
RARs/THRs 0.03 0.11 -10000 0 -0.25 48 48
RXRs/FXR 0.03 0.1 -10000 0 -0.26 38 38
BCL2 0.021 0.043 -10000 0 -0.41 4 4
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.013 0.088 -9999 0 -0.37 9 9
FZD6 0.024 0.01 -9999 0 -10000 0 0
WNT6 -0.004 0.11 -9999 0 -0.41 30 30
WNT4 0.014 0.079 -9999 0 -0.44 12 12
FZD3 0.02 0.054 -9999 0 -0.47 5 5
WNT5A 0.02 0.045 -9999 0 -0.43 4 4
WNT11 -0.019 0.13 -9999 0 -0.41 43 43
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.004 0.041 -10000 0 -0.46 2 2
HSPA8 0.027 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.06 0.1 -10000 0 -0.28 8 8
AKT1 0.006 0.046 -10000 0 -10000 0 0
GSC 0.007 0.12 -10000 0 -0.68 1 1
NKX2-5 -0.076 0.18 -10000 0 -0.41 97 97
muscle cell differentiation 0.062 0.16 0.43 44 -10000 0 44
SMAD2-3/SMAD4/SP1 -0.012 0.12 -10000 0 -0.32 1 1
SMAD4 0.008 0.049 -10000 0 -10000 0 0
CBFB 0.027 0.006 -10000 0 -10000 0 0
SAP18 0.027 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.015 0.057 -10000 0 -0.24 10 10
SMAD3/SMAD4/VDR 0.057 0.061 -10000 0 -10000 0 0
MYC 0.028 0.023 -10000 0 -10000 0 0
CDKN2B -0.35 0.64 -10000 0 -1.5 97 97
AP1 0.003 0.097 -10000 0 -0.29 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.033 0.086 -10000 0 -0.43 7 7
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.066 0.16 -10000 0 -0.36 81 81
SP3 0.029 0.007 -10000 0 -10000 0 0
CREB1 0.028 0.005 -10000 0 -10000 0 0
FOXH1 -0.019 0.12 -10000 0 -0.39 38 38
SMAD3/SMAD4/GR 0.064 0.066 -10000 0 -10000 0 0
GATA3 0.013 0.08 -10000 0 -0.4 14 14
SKI/SIN3/HDAC complex/NCoR1 0.03 0.059 -10000 0 -0.52 3 3
MEF2C/TIF2 -0.046 0.14 0.35 2 -0.46 18 20
endothelial cell migration 0.17 0.17 0.61 4 -10000 0 4
MAX 0.039 0.016 -10000 0 -10000 0 0
RBBP7 0.028 0.005 -10000 0 -10000 0 0
RBBP4 0.026 0.035 -10000 0 -0.47 2 2
RUNX2 0.026 0.025 -10000 0 -0.47 1 1
RUNX3 0.022 0.046 -10000 0 -0.39 5 5
RUNX1 0.027 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.008 -10000 0 -10000 0 0
NR3C1 0.039 0.015 -10000 0 -10000 0 0
VDR 0.027 0.024 -10000 0 -0.47 1 1
CDKN1A -0.015 0.099 -10000 0 -0.61 5 5
KAT2B 0.008 0.082 -10000 0 -0.47 12 12
SMAD2/SMAD2/SMAD4/FOXH1 0.001 0.098 -10000 0 -0.3 10 10
DCP1A 0.024 0.01 -10000 0 -10000 0 0
SKI 0.028 0.006 -10000 0 -10000 0 0
SERPINE1 -0.17 0.17 -10000 0 -0.66 3 3
SMAD3/SMAD4/ATF2 0.035 0.062 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.03 0.077 -10000 0 -0.32 6 6
SAP30 0.028 0.007 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.015 0.049 -10000 0 -0.27 2 2
JUN -0.003 0.095 0.29 1 -0.28 1 2
SMAD3/SMAD4/IRF7 0.027 0.086 -10000 0 -0.36 5 5
TFE3 -0.002 0.03 -10000 0 -10000 0 0
COL1A2 -0.12 0.17 -10000 0 -0.32 157 157
mesenchymal cell differentiation -0.035 0.064 0.33 1 -10000 0 1
DLX1 -0.16 0.21 -10000 0 -0.39 186 186
TCF3 0.027 0.005 -10000 0 -10000 0 0
FOS -0.034 0.17 -10000 0 -0.47 53 53
SMAD3/SMAD4/Max 0.062 0.066 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.046 0.026 -10000 0 -0.27 2 2
ZBTB17 0.03 0.013 -10000 0 -10000 0 0
LAMC1 -0.001 0.045 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.035 0.062 -10000 0 -10000 0 0
IRF7 0.013 0.078 -10000 0 -0.41 13 13
ESR1 0.014 0.1 -10000 0 -0.41 22 22
HNF4A -0.022 0.12 -10000 0 -0.39 38 38
MEF2C -0.036 0.14 0.35 3 -0.45 11 14
SMAD2-3/SMAD4 0.029 0.08 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.039 0.032 -10000 0 -0.27 2 2
IGHV3OR16-13 0.006 0.046 -10000 0 -0.34 7 7
TGIF2/HDAC complex 0.026 0.007 -10000 0 -10000 0 0
CREBBP 0.01 0.023 -10000 0 -10000 0 0
SKIL 0.02 0.013 -10000 0 -10000 0 0
HDAC1 0.028 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
SNIP1 0.029 0.005 -10000 0 -10000 0 0
GCN5L2 -0.005 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.017 0.061 -10000 0 -10000 0 0
MSG1/HSC70 0.034 0.046 -10000 0 -0.28 8 8
SMAD2 0.007 0.043 -10000 0 -10000 0 0
SMAD3 0.012 0.047 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.017 0.045 -10000 0 -0.32 2 2
SMAD2/SMAD2/SMAD4 -0.056 0.13 0.2 2 -0.41 41 43
NCOR1 0.028 0.006 -10000 0 -10000 0 0
NCOA2 0 0.11 -10000 0 -0.47 21 21
NCOA1 0.028 0.004 -10000 0 -10000 0 0
MYOD/E2A -0.018 0.13 -10000 0 -0.33 62 62
SMAD2-3/SMAD4/SP1/MIZ-1 0.005 0.12 -10000 0 -0.34 1 1
IFNB1 -0.004 0.077 -10000 0 -0.41 7 7
SMAD3/SMAD4/MEF2C -0.025 0.15 0.41 1 -0.46 9 10
CITED1 0.019 0.058 -10000 0 -0.39 8 8
SMAD2-3/SMAD4/ARC105 0.041 0.081 -10000 0 -10000 0 0
RBL1 0.025 0.025 -10000 0 -0.47 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.084 0.23 -10000 0 -0.53 84 84
RUNX1-3/PEBPB2 0.048 0.035 -10000 0 -0.23 4 4
SMAD7 -0.019 0.11 -10000 0 -0.42 1 1
MYC/MIZ-1 0.04 0.037 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.07 0.11 0.26 3 -0.42 7 10
IL10 0 0.082 -10000 0 -0.38 8 8
PIASy/HDAC complex 0.032 0.013 -10000 0 -10000 0 0
PIAS3 0.025 0.006 -10000 0 -10000 0 0
CDK2 0.017 0.018 -10000 0 -10000 0 0
IL5 -0.004 0.07 -10000 0 -0.38 3 3
CDK4 0.01 0.023 -10000 0 -10000 0 0
PIAS4 0.032 0.013 -10000 0 -10000 0 0
ATF3 0.019 0.065 -10000 0 -0.45 8 8
SMAD3/SMAD4/SP1 -0.019 0.1 -10000 0 -0.3 2 2
FOXG1 -0.056 0.15 -10000 0 -0.43 57 57
FOXO3 -0.006 0.048 -10000 0 -10000 0 0
FOXO1 -0.006 0.047 -10000 0 -10000 0 0
FOXO4 -0.007 0.051 -10000 0 -0.33 1 1
heart looping -0.036 0.14 0.34 3 -0.44 11 14
CEBPB 0.013 0.032 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.089 0.15 -10000 0 -0.29 57 57
MYOD1 -0.064 0.17 -10000 0 -0.46 62 62
SMAD3/SMAD4/HNF4 0.007 0.099 -10000 0 -0.27 13 13
SMAD3/SMAD4/GATA3 0.03 0.086 -10000 0 -0.35 1 1
SnoN/SIN3/HDAC complex/NCoR1 0.02 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.058 0.07 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 -0.001 0.098 -10000 0 -10000 0 0
MED15 0.027 0.021 -10000 0 -0.39 1 1
SP1 -0.024 0.063 -10000 0 -10000 0 0
SIN3B 0.029 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.038 0.14 -10000 0 -0.39 13 13
ITGB5 -0.017 0.075 0.3 2 -10000 0 2
TGIF/SIN3/HDAC complex/CtBP 0.035 0.041 -10000 0 -0.32 1 1
SMAD3/SMAD4/AR -0.048 0.15 -10000 0 -0.3 99 99
AR -0.1 0.21 -10000 0 -0.47 107 107
negative regulation of cell growth 0.011 0.069 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.017 0.13 -10000 0 -0.3 56 56
E2F5 0.021 0.043 -10000 0 -0.47 3 3
E2F4 0.027 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.012 0.092 -10000 0 -0.37 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 -0.043 0.16 -10000 0 -0.37 78 78
TFDP1 0.027 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.021 0.11 -10000 0 -0.29 1 1
SMAD3/SMAD4/RUNX2 0.035 0.064 -10000 0 -0.33 1 1
TGIF2 0.026 0.007 -10000 0 -10000 0 0
TGIF1 0.025 0.009 -10000 0 -10000 0 0
ATF2 0.027 0.006 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.006 0.097 0.3 36 -10000 0 36
KIRREL 0.01 0.081 -10000 0 -0.45 12 12
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.006 0.098 -10000 0 -0.3 36 36
PLCG1 0.027 0.007 -10000 0 -10000 0 0
ARRB2 0.027 0.006 -10000 0 -10000 0 0
WASL 0.027 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.027 0.092 -10000 0 -0.32 13 13
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.005 0.053 -10000 0 -0.25 10 10
FYN -0.012 0.083 0.27 10 -0.3 13 23
mol:Ca2+ 0.027 0.089 -10000 0 -0.31 12 12
mol:DAG 0.027 0.089 -10000 0 -0.31 12 12
NPHS2 -0.012 0.067 -10000 0 -0.41 10 10
mol:IP3 0.027 0.089 -10000 0 -0.31 12 12
regulation of endocytosis 0.025 0.078 -10000 0 -0.28 13 13
Nephrin/NEPH1/podocin/Cholesterol 0.015 0.086 -10000 0 -0.24 40 40
establishment of cell polarity 0.006 0.097 -10000 0 -0.3 36 36
Nephrin/NEPH1/podocin/NCK1-2 0.037 0.085 -10000 0 -0.31 9 9
Nephrin/NEPH1/beta Arrestin2 0.027 0.08 -10000 0 -0.28 13 13
NPHS1 -0.02 0.1 -10000 0 -0.4 25 25
Nephrin/NEPH1/podocin 0.019 0.08 -10000 0 -0.29 14 14
TJP1 0.028 0.004 -10000 0 -10000 0 0
NCK1 0.024 0.01 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.028 0.09 -10000 0 -0.31 12 12
CD2AP 0.027 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.029 0.092 -10000 0 -0.32 13 13
GRB2 0.028 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.024 0.094 0.28 8 -0.26 34 42
cytoskeleton organization -0.007 0.064 0.21 3 -0.3 9 12
Nephrin/NEPH1 0.01 0.069 -10000 0 -0.21 35 35
Nephrin/NEPH1/ZO-1 0.024 0.084 -10000 0 -0.24 35 35
PDGFR-alpha signaling pathway

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
PDGFRA 0.01 0.071 -10000 0 -0.46 8 8
PDGF/PDGFRA/CRKL 0.024 0.057 -10000 0 -0.32 9 9
positive regulation of JUN kinase activity 0.058 0.045 -10000 0 -0.26 5 5
CRKL 0.027 0.021 -10000 0 -0.39 1 1
PDGF/PDGFRA/Caveolin-3 -0.054 0.16 -10000 0 -0.34 89 89
AP1 -0.1 0.31 0.31 2 -0.88 55 57
mol:IP3 -0.001 0.055 -10000 0 -0.34 8 8
PLCG1 -0.001 0.055 -10000 0 -0.34 8 8
PDGF/PDGFRA/alphaV Integrin 0.024 0.055 -10000 0 -0.32 8 8
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
CRK 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.055 -10000 0 -0.34 8 8
CAV3 -0.09 0.19 -10000 0 -0.46 85 85
CAV1 -0.013 0.12 -10000 0 -0.39 40 40
SHC/Grb2/SOS1 0.06 0.045 -10000 0 -0.26 5 5
PDGF/PDGFRA/Shf 0.019 0.077 -10000 0 -0.37 13 13
FOS -0.12 0.3 0.33 1 -0.87 55 56
JUN -0.023 0.026 -10000 0 -10000 0 0
oligodendrocyte development 0.024 0.054 -10000 0 -0.32 8 8
GRB2 0.028 0.004 -10000 0 -10000 0 0
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
mol:DAG -0.001 0.055 -10000 0 -0.34 8 8
PDGF/PDGFRA 0.01 0.071 -10000 0 -0.46 8 8
actin cytoskeleton reorganization 0.021 0.057 -10000 0 -0.32 9 9
SRF 0.014 0.012 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.032 0.047 -10000 0 -0.28 6 6
PDGF/PDGFRA/Crk/C3G 0.045 0.047 -10000 0 -0.26 8 8
JAK1 0.003 0.048 -10000 0 -0.32 8 8
ELK1/SRF 0.004 0.048 0.17 2 -0.28 5 7
SHB 0.024 0.026 -10000 0 -0.47 1 1
SHF 0.02 0.064 -10000 0 -0.47 7 7
CSNK2A1 0.029 0.021 -10000 0 -10000 0 0
GO:0007205 -0.007 0.055 -10000 0 -0.35 8 8
SOS1 0.028 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.058 0.045 -10000 0 -0.26 5 5
PDGF/PDGFRA/SHB 0.021 0.057 -10000 0 -0.32 9 9
PDGF/PDGFRA/Caveolin-1 -0.005 0.11 -10000 0 -0.29 48 48
ITGAV 0.026 0.021 -10000 0 -0.39 1 1
ELK1 -0.016 0.054 -10000 0 -0.31 8 8
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.025 0.054 -10000 0 -0.32 8 8
JAK-STAT cascade 0.003 0.048 -10000 0 -0.32 8 8
cell proliferation 0.019 0.076 -10000 0 -0.37 13 13
Syndecan-3-mediated signaling events

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
CTTN 0.02 0.013 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.035 0.12 -9999 0 -0.34 5 5
Syndecan-3/Neurocan 0.016 0.069 -9999 0 -0.36 10 10
POMC -0.021 0.14 -9999 0 -0.41 47 47
EGFR 0.022 0.035 -9999 0 -0.47 2 2
Syndecan-3/EGFR 0.019 0.061 -9999 0 -0.36 9 9
AGRP -0.003 0.029 -9999 0 -0.39 1 1
NCSTN 0.028 0.005 -9999 0 -10000 0 0
PSENEN 0.027 0.005 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.028 0.005 -9999 0 -10000 0 0
APH1A 0.027 0.005 -9999 0 -10000 0 0
NCAN 0.002 0.074 -9999 0 -0.39 13 13
long-term memory 0.028 0.055 -9999 0 -0.34 6 6
Syndecan-3/IL8 -0.019 0.1 -9999 0 -0.4 10 10
PSEN1 0.026 0.007 -9999 0 -10000 0 0
Src/Cortactin 0.028 0.02 -9999 0 -10000 0 0
FYN 0.027 0.021 -9999 0 -0.39 1 1
limb bud formation 0.005 0.059 -9999 0 -0.37 10 10
MC4R 0.001 0.035 -9999 0 -0.39 2 2
SRC 0.027 0.007 -9999 0 -10000 0 0
PTN -0.15 0.24 -9999 0 -0.47 150 150
FGFR/FGF/Syndecan-3 0.005 0.059 -9999 0 -0.37 10 10
neuron projection morphogenesis -0.03 0.13 -9999 0 -0.34 6 6
Syndecan-3/AgRP 0.018 0.061 -9999 0 -0.36 10 10
Syndecan-3/AgRP/MC4R 0.028 0.064 -9999 0 -0.34 10 10
Fyn/Cortactin 0.029 0.02 -9999 0 -10000 0 0
SDC3 0.005 0.06 -9999 0 -0.37 10 10
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.019 0.1 -9999 0 -0.4 10 10
IL8 -0.062 0.17 -9999 0 -0.4 89 89
Syndecan-3/Fyn/Cortactin 0.029 0.057 -9999 0 -0.35 6 6
Syndecan-3/CASK 0.004 0.056 -9999 0 -0.35 10 10
alpha-MSH/MC4R -0.004 0.1 -9999 0 -0.29 48 48
Gamma Secretase 0.073 0.029 -9999 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.028 0.003 -10000 0 -10000 0 0
mol:PIP3 0.001 0.03 -10000 0 -0.22 2 2
FRAP1 0.028 0.067 -10000 0 -0.42 6 6
AKT1 0.033 0.073 0.16 90 -0.23 2 92
INSR 0.028 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.029 0.019 -10000 0 -0.23 2 2
mol:GTP 0.056 0.068 0.28 1 -10000 0 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.01 0.022 -10000 0 -10000 0 0
TSC2 0.028 0.004 -10000 0 -10000 0 0
RHEB/GDP 0.014 0.03 -10000 0 -10000 0 0
TSC1 0.028 0.005 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.019 0.046 -10000 0 -0.2 17 17
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.02 0.031 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.028 0.004 -10000 0 -10000 0 0
RPS6KB1 0.046 0.07 0.22 12 -0.25 3 15
MAP3K5 0.006 0.029 0.19 5 -0.18 5 10
PIK3R1 0.024 0.042 -10000 0 -0.47 3 3
apoptosis 0.006 0.029 0.19 5 -0.18 5 10
mol:LY294002 0 0 -10000 0 -0.001 16 16
EIF4B 0.043 0.068 0.23 11 -0.24 1 12
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.057 0.06 0.21 8 -10000 0 8
eIF4E/eIF4G1/eIF4A1 0.012 0.035 -10000 0 -0.26 5 5
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.042 -10000 0 -0.22 5 5
mTOR/RHEB/GTP/Raptor/GBL 0.033 0.057 0.18 19 -0.19 1 20
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
RHEB/GTP 0.052 0.058 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 16 16
FKBP12/Rapamycin 0.021 0.006 -10000 0 -10000 0 0
PDPK1 0.023 0.071 0.16 85 -0.22 2 87
EIF4E 0.028 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.042 0.087 -10000 0 -0.48 9 9
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.006 0.11 -10000 0 -0.83 5 5
TSC1/TSC2 0.062 0.074 0.28 2 -10000 0 2
tumor necrosis factor receptor activity 0 0 0.001 16 -10000 0 16
RPS6 0.025 0.009 -10000 0 -10000 0 0
PPP5C 0.028 0.005 -10000 0 -10000 0 0
EIF4G1 0.02 0.013 -10000 0 -10000 0 0
IRS1 0.002 0.046 -10000 0 -0.22 17 17
INS -0.018 0.028 -10000 0 -0.39 2 2
PTEN 0.027 0.005 -10000 0 -10000 0 0
PDK2 0.024 0.073 0.16 88 -0.22 2 90
EIF4EBP1 -0.025 0.22 -10000 0 -1 19 19
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PPP2R5D 0.03 0.07 0.25 7 -0.38 6 13
peptide biosynthetic process -0.01 0.02 0.18 2 -0.21 2 4
RHEB 0.027 0.007 -10000 0 -10000 0 0
EIF4A1 0.027 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.001 0.003 115 -10000 0 115
EEF2 -0.01 0.02 0.18 2 -0.21 2 4
eIF4E/4E-BP1 -0.009 0.2 -10000 0 -0.94 19 19
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0.021 -10000 0 -0.28 2 2
MAP4K4 0.019 0.058 0.21 1 -0.32 4 5
BAG4 0.024 0.026 -10000 0 -0.47 1 1
PKC zeta/ceramide -0.009 0.071 -10000 0 -0.22 31 31
NFKBIA 0.027 0.007 -10000 0 -10000 0 0
BIRC3 0.014 0.065 -10000 0 -0.4 10 10
BAX -0.005 0.056 -10000 0 -0.33 9 9
RIPK1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.024 0.13 0.69 16 -10000 0 16
BAD -0.02 0.07 0.2 8 -0.22 27 35
SMPD1 0.021 0.067 0.23 12 -0.24 5 17
RB1 -0.024 0.064 -10000 0 -0.21 31 31
FADD/Caspase 8 0.059 0.099 0.24 55 -0.29 3 58
MAP2K4 -0.023 0.061 0.18 2 -0.28 9 11
NSMAF 0.025 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.023 0.063 0.18 4 -0.27 10 14
EGF -0.062 0.19 -10000 0 -0.47 75 75
mol:ceramide -0.024 0.068 -10000 0 -0.22 31 31
MADD 0.028 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.011 0.021 -10000 0 -0.28 2 2
ASAH1 0.026 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.024 0.063 -10000 0 -0.21 31 31
cell proliferation -0.027 0.097 -10000 0 -0.28 18 18
BID 0.017 0.11 -10000 0 -0.68 6 6
MAP3K1 -0.024 0.065 0.19 2 -0.22 29 31
EIF2A 0.021 0.11 0.28 18 -0.27 8 26
TRADD 0.027 0.006 -10000 0 -10000 0 0
CRADD 0.028 0.002 -10000 0 -10000 0 0
MAPK3 -0.017 0.063 -10000 0 -0.28 6 6
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.016 0.064 -10000 0 -0.29 7 7
Cathepsin D/ceramide -0.009 0.071 -10000 0 -0.21 31 31
FADD 0.044 0.08 0.21 34 -0.28 3 37
KSR1 -0.024 0.066 0.19 3 -0.22 28 31
MAPK8 -0.02 0.075 -10000 0 -0.27 17 17
PRKRA -0.018 0.071 0.19 11 -0.22 25 36
PDGFA 0.024 0.03 -10000 0 -0.39 2 2
TRAF2 0.024 0.036 -10000 0 -0.39 3 3
IGF1 -0.044 0.17 -10000 0 -0.46 62 62
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.024 0.068 -10000 0 -0.22 31 31
CTSD 0.027 0.006 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.039 0.011 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.028 0.1 -10000 0 -0.3 18 18
PRKCD 0.024 0.01 -10000 0 -10000 0 0
PRKCZ 0.026 0.025 -10000 0 -0.47 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.011 0.021 -10000 0 -0.28 2 2
RelA/NF kappa B1 0.039 0.011 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.028 0.003 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.016 0.048 -10000 0 -0.33 4 4
TNFR1A/BAG4/TNF-alpha 0.033 0.064 -10000 0 -0.24 18 18
mol:Sphingosine-1-phosphate 0.012 0.02 -10000 0 -0.28 2 2
MAP2K1 -0.021 0.062 0.21 1 -0.29 6 7
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
CYCS 0.003 0.048 0.18 2 -0.2 4 6
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
NFKB1 0.028 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.024 -10000 0 -0.34 1 1
EIF2AK2 -0.018 0.069 0.2 11 -0.27 10 21
TNF-alpha/TNFR1A/FAN 0.034 0.062 -10000 0 -0.24 17 17
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.026 0.073 -10000 0 -0.4 8 8
MAP2K2 -0.021 0.062 -10000 0 -0.28 7 7
SMPD3 0.003 0.09 0.21 5 -0.28 28 33
TNF 0.007 0.09 -10000 0 -0.4 19 19
PKC zeta/PAR4 0.039 0.02 -10000 0 -0.34 1 1
mol:PHOSPHOCHOLINE 0.029 0.086 0.21 63 -0.18 4 67
NF kappa B1/RelA/I kappa B alpha 0.072 0.033 -10000 0 -0.25 1 1
AIFM1 0 0.055 0.18 3 -0.23 3 6
BCL2 0.021 0.043 -10000 0 -0.41 4 4
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.034 0.038 -10000 0 -0.29 5 5
PDGFRB -0.062 0.17 -10000 0 -0.39 89 89
SPHK1 0.001 0.052 -10000 0 -0.65 2 2
mol:S1P -0.003 0.052 -10000 0 -0.55 2 2
S1P1/S1P/Gi -0.034 0.13 0.31 1 -0.42 25 26
GNAO1 0.021 0.044 -10000 0 -0.42 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.042 0.13 0.27 1 -0.4 20 21
PLCG1 -0.037 0.11 0.41 1 -0.4 21 22
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.062 0.17 -10000 0 -0.39 89 89
GNAI2 0.023 0.011 -10000 0 -10000 0 0
GNAI3 0.026 0.007 -10000 0 -10000 0 0
GNAI1 0.025 0.026 -10000 0 -0.48 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0 0.028 -10000 0 -0.24 5 5
S1P1/S1P -0.007 0.052 -10000 0 -0.4 1 1
negative regulation of cAMP metabolic process -0.033 0.12 0.31 1 -0.41 25 26
MAPK3 -0.042 0.14 0.3 1 -0.46 20 21
calcium-dependent phospholipase C activity -0.001 0.002 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
KDR 0.025 0.032 -10000 0 -0.43 2 2
PLCB2 0 0.064 0.31 3 -0.32 2 5
RAC1 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.005 0.045 -10000 0 -0.33 1 1
receptor internalization -0.007 0.049 -10000 0 -0.38 1 1
PTGS2 -0.043 0.16 -10000 0 -0.6 13 13
Rac1/GTP -0.005 0.045 -10000 0 -0.35 1 1
RHOA 0.024 0.01 -10000 0 -10000 0 0
VEGFA 0.024 0.036 -10000 0 -0.4 3 3
negative regulation of T cell proliferation -0.033 0.12 0.31 1 -0.41 25 26
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.01 0.083 -10000 0 -0.42 15 15
MAPK1 -0.041 0.13 0.3 1 -0.46 20 21
S1P1/S1P/PDGFB-D/PDGFRB -0.02 0.09 0.25 1 -0.32 4 5
ABCC1 0.024 0.036 -10000 0 -0.39 3 3
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.025 0.15 -10000 0 -0.47 43 43
GNB1/GNG2 0.004 0.1 -10000 0 -0.36 7 7
mol:DAG -0.011 0.088 -10000 0 -0.35 5 5
PLCG1 -0.012 0.09 -10000 0 -0.36 5 5
YES1 -0.017 0.079 -10000 0 -0.38 6 6
FZD3 0.02 0.054 -10000 0 -0.47 5 5
FZD6 0.024 0.01 -10000 0 -10000 0 0
G protein 0.007 0.1 0.27 3 -0.41 3 6
MAP3K7 -0.046 0.12 0.29 6 -0.37 13 19
mol:Ca2+ -0.011 0.086 0.19 2 -0.34 5 7
mol:IP3 -0.011 0.088 -10000 0 -0.35 5 5
NLK 0.006 0.068 -10000 0 -0.79 3 3
GNB1 0.027 0.006 -10000 0 -10000 0 0
CAMK2A -0.046 0.12 0.29 6 -0.38 15 21
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.013 0.088 -10000 0 -0.37 9 9
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
GNAS -0.016 0.078 -10000 0 -0.4 5 5
GO:0007205 -0.013 0.091 0.29 5 -0.36 6 11
WNT6 -0.004 0.11 -10000 0 -0.41 30 30
WNT4 0.014 0.079 -10000 0 -0.44 12 12
NFAT1/CK1 alpha -0.01 0.13 0.28 4 -0.39 10 14
GNG2 0.027 0.007 -10000 0 -10000 0 0
WNT5A 0.02 0.045 -10000 0 -0.43 4 4
WNT11 -0.019 0.13 -10000 0 -0.41 43 43
CDC42 -0.005 0.09 -10000 0 -0.37 5 5
Cellular roles of Anthrax 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
ANTXR1 0.023 0.046 -10000 0 -0.39 5 5
ANTXR2 0.017 0.064 -10000 0 -0.39 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.009 -10000 0 -0.051 13 13
monocyte activation -0.015 0.099 -10000 0 -0.36 28 28
MAP2K2 0.003 0.088 -10000 0 -0.56 10 10
MAP2K1 -0.004 0.008 -10000 0 -10000 0 0
MAP2K7 -0.004 0.008 -10000 0 -10000 0 0
MAP2K6 -0.014 0.05 -10000 0 -0.24 19 19
CYAA -0.01 0.036 -10000 0 -0.21 13 13
MAP2K4 -0.004 0.008 -10000 0 -10000 0 0
IL1B -0.021 0.063 0.19 3 -0.19 46 49
Channel 0.027 0.046 -10000 0 -0.22 13 13
NLRP1 -0.004 0.012 -10000 0 -0.19 1 1
CALM1 0.026 0.008 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.075 -10000 0 -0.38 16 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.009 0.051 13 -10000 0 13
MAPK3 -0.004 0.008 -10000 0 -10000 0 0
MAPK1 -0.003 0.013 0.15 2 -10000 0 2
PGR -0.026 0.068 -10000 0 -0.23 41 41
PA/Cellular Receptors 0.028 0.051 -10000 0 -0.25 13 13
apoptosis -0.002 0.009 -10000 0 -0.051 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.027 0.041 -10000 0 -0.2 13 13
macrophage activation -0.004 0.012 0.14 2 -10000 0 2
TNF 0.007 0.09 -10000 0 -0.4 19 19
VCAM1 -0.013 0.095 -10000 0 -0.36 25 25
platelet activation -0.003 0.075 -10000 0 -0.38 16 16
MAPKKK cascade 0.003 0.021 -10000 0 -0.12 1 1
IL18 -0.005 0.036 0.19 1 -0.26 7 8
negative regulation of macrophage activation -0.002 0.009 -10000 0 -0.051 13 13
LEF -0.002 0.009 -10000 0 -0.051 13 13
CASP1 0 0.01 -10000 0 -0.083 3 3
mol:cAMP -0.004 0.076 -10000 0 -0.38 16 16
necrosis -0.002 0.009 -10000 0 -0.051 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.044 -10000 0 -0.21 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.062 0.17 -10000 0 -0.39 89 89
mol:S1P 0.001 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.005 0.063 -10000 0 -0.27 11 11
GNAO1 0.023 0.044 -10000 0 -0.42 4 4
S1P/S1P3/G12/G13 0.046 0.037 -10000 0 -0.24 5 5
AKT1 -0.018 0.13 -10000 0 -0.51 21 21
AKT3 0.018 0.093 -10000 0 -0.66 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.062 0.17 -10000 0 -0.39 89 89
GNAI2 0.025 0.012 -10000 0 -10000 0 0
GNAI3 0.028 0.007 -10000 0 -10000 0 0
GNAI1 0.026 0.026 -10000 0 -0.47 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.024 0.048 -10000 0 -0.45 4 4
S1PR2 0.028 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.021 0.069 -10000 0 -0.34 9 9
MAPK3 0.016 0.062 -10000 0 -0.42 4 4
MAPK1 0.013 0.063 -10000 0 -0.33 8 8
JAK2 0.015 0.087 0.21 2 -0.49 6 8
CXCR4 0.008 0.081 -10000 0 -0.38 9 9
FLT1 0.027 0.023 -10000 0 -0.39 1 1
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
SRC 0.014 0.062 -10000 0 -0.33 8 8
S1P/S1P3/Gi 0.021 0.069 -10000 0 -0.34 9 9
RAC1 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.024 0.074 -10000 0 -0.39 4 4
VEGFA 0.025 0.037 -10000 0 -0.39 3 3
S1P/S1P2/Gi 0.023 0.052 -10000 0 -0.3 4 4
VEGFR1 homodimer/VEGFA homodimer 0.039 0.038 -10000 0 -0.35 3 3
RHOA 0.024 0.01 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.016 0.1 -10000 0 -0.24 67 67
GNAQ 0.028 0.005 -10000 0 -10000 0 0
GNAZ 0.012 0.083 -10000 0 -0.42 15 15
G12/G13 0.037 0.02 -10000 0 -0.28 1 1
GNA14 -0.048 0.18 -10000 0 -0.47 64 64
GNA15 0.025 0.034 -10000 0 -0.47 2 2
GNA12 0.025 0.022 -10000 0 -0.39 1 1
GNA13 0.028 0.004 -10000 0 -10000 0 0
GNA11 0.025 0.034 -10000 0 -0.47 2 2
Rac1/GTP 0.019 0.076 -10000 0 -0.38 5 5
Signaling events mediated by PRL

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
CCNE1 0.025 0.029 -10000 0 -0.39 2 2
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 -0.041 0.16 -10000 0 -0.39 68 68
CDKN1A 0.013 0.046 -10000 0 -0.3 7 7
PRL-3/alpha Tubulin 0.031 0.035 -10000 0 -0.28 4 4
mol:Ca2+ -0.057 0.11 0.18 3 -0.34 55 58
AGT -0.06 0.19 -10000 0 -0.46 75 75
CCNA2 -0.005 0.043 -10000 0 -0.42 1 1
TUBA1B 0.028 0.003 -10000 0 -10000 0 0
EGR1 0.004 0.063 -10000 0 -0.32 15 15
CDK2/Cyclin E1 0.043 0.077 0.28 1 -0.37 4 5
MAPK3 0.009 0.029 -10000 0 -0.28 4 4
PRL-2 /Rab GGTase beta 0.041 0.008 -10000 0 -10000 0 0
MAPK1 0.009 0.029 -10000 0 -0.28 4 4
PTP4A1 -0.002 0.044 -10000 0 -10000 0 0
PTP4A3 0.019 0.042 -10000 0 -0.39 4 4
PTP4A2 0.028 0.004 -10000 0 -10000 0 0
ITGB1 0.009 0.029 -10000 0 -0.28 4 4
SRC 0.027 0.007 -10000 0 -10000 0 0
RAC1 0.013 0.027 -10000 0 -0.3 1 1
Rab GGTase beta/Rab GGTase alpha 0.038 0.012 -10000 0 -10000 0 0
PRL-1/ATF-5 0.022 0.068 -10000 0 -10000 0 0
RABGGTA 0.027 0.007 -10000 0 -10000 0 0
BCAR1 -0.013 0.02 0.18 4 -10000 0 4
RHOC 0.011 0.041 -10000 0 -0.3 5 5
RHOA -0.003 0.075 -10000 0 -0.3 23 23
cell motility 0.023 0.074 0.33 3 -0.32 1 4
PRL-1/alpha Tubulin 0.025 0.063 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.016 0.11 -10000 0 -0.28 64 64
ROCK1 0.025 0.069 0.33 3 -10000 0 3
RABGGTB 0.028 0.005 -10000 0 -10000 0 0
CDK2 0.028 0.003 -10000 0 -10000 0 0
mitosis -0.002 0.044 -10000 0 -10000 0 0
ATF5 0.021 0.054 -10000 0 -0.39 7 7
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.036 0.031 -10000 0 -0.3 3 3
CRKL 0.013 0.12 0.3 4 -0.45 18 22
mol:PIP3 0.001 0.011 -10000 0 -10000 0 0
AKT1 0.006 0.041 -10000 0 -10000 0 0
PTK2B 0.026 0.008 -10000 0 -10000 0 0
RAPGEF1 0.017 0.12 0.27 10 -0.44 15 25
RANBP10 0.027 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.034 0.065 -10000 0 -0.26 16 16
MAP3K5 0.011 0.12 0.28 4 -0.46 16 20
HGF/MET/CIN85/CBL/ENDOPHILINS 0.046 0.069 -10000 0 -0.26 12 12
AP1 -0.012 0.11 -10000 0 -0.3 53 53
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.028 0.004 -10000 0 -10000 0 0
apoptosis -0.099 0.3 -10000 0 -0.74 72 72
STAT3 (dimer) 0.02 0.064 -10000 0 -0.35 2 2
GAB1/CRKL/SHP2/PI3K 0.031 0.1 0.32 1 -0.44 8 9
INPP5D 0.026 0.025 -10000 0 -0.47 1 1
CBL/CRK 0.023 0.11 0.31 1 -0.41 18 19
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.007 -10000 0 -10000 0 0
PTEN 0.028 0.005 -10000 0 -10000 0 0
ELK1 -0.004 0.072 0.31 13 -10000 0 13
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.012 0.051 0.15 1 -0.26 6 7
PAK1 0.015 0.063 0.4 4 -10000 0 4
HGF/MET/RANBP10 0.036 0.069 -10000 0 -0.26 19 19
HRAS 0.004 0.12 -10000 0 -0.5 13 13
DOCK1 0.012 0.11 0.3 3 -0.44 17 20
GAB1 0.01 0.12 0.25 1 -0.48 17 18
CRK 0.011 0.11 0.28 2 -0.44 18 20
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP 0.004 0.12 -10000 0 -0.46 18 18
JUN 0.028 0.005 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.003 0.042 -10000 0 -0.21 13 13
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
cell morphogenesis 0.069 0.13 0.31 38 -0.41 3 41
GRB2/SHC 0.035 0.056 -10000 0 -0.24 4 4
FOS -0.036 0.16 -10000 0 -0.47 53 53
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility -0.004 0.071 0.31 13 -10000 0 13
HGF/MET/MUC20 0.022 0.064 -10000 0 -0.26 20 20
cell migration 0.034 0.055 -10000 0 -0.24 4 4
GRB2 0.028 0.004 -10000 0 -10000 0 0
CBL 0.026 0.008 -10000 0 -10000 0 0
MET/RANBP10 0.035 0.034 -10000 0 -0.29 4 4
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.016 0.046 -10000 0 -0.33 2 2
MET/MUC20 0.017 0.03 -10000 0 -0.29 4 4
RAP1B 0.021 0.11 0.26 10 -0.42 13 23
RAP1A 0.015 0.11 0.27 7 -0.41 15 22
HGF/MET/RANBP9 0.037 0.066 -10000 0 -0.27 17 17
RAF1 0.009 0.11 -10000 0 -0.49 10 10
STAT3 0.02 0.065 -10000 0 -0.36 2 2
cell proliferation 0.023 0.095 0.31 7 -0.39 6 13
RPS6KB1 0.012 0.019 -10000 0 -10000 0 0
MAPK3 -0.008 0.096 0.72 5 -10000 0 5
MAPK1 -0.009 0.09 0.73 4 -10000 0 4
RANBP9 0.027 0.007 -10000 0 -10000 0 0
MAPK8 0.023 0.13 0.29 4 -0.45 17 21
SRC 0.008 0.044 -10000 0 -0.32 2 2
PI3K 0.024 0.051 -10000 0 -0.28 4 4
MET/Glomulin 0.016 0.034 -10000 0 -0.23 5 5
SOS1 0.028 0.004 -10000 0 -10000 0 0
MAP2K1 0.009 0.1 0.3 1 -0.48 8 9
MET 0.023 0.043 -10000 0 -0.41 4 4
MAP4K1 0.01 0.13 0.29 4 -0.51 16 20
PTK2 0.023 0.011 -10000 0 -10000 0 0
MAP2K2 0.011 0.099 -10000 0 -0.46 7 7
BAD 0.01 0.051 0.38 2 -10000 0 2
MAP2K4 0.012 0.11 0.27 4 -0.43 15 19
SHP2/GRB2/SOS1/GAB1 0.033 0.1 -10000 0 -0.43 12 12
INPPL1 0.024 0.01 -10000 0 -10000 0 0
PXN 0.028 0.003 -10000 0 -10000 0 0
SH3KBP1 0.028 0.005 -10000 0 -10000 0 0
HGS 0.001 0.041 -10000 0 -0.25 4 4
PLCgamma1/PKC 0.02 0.005 -10000 0 -10000 0 0
HGF 0.008 0.091 -10000 0 -0.44 16 16
RASA1 0.026 0.025 -10000 0 -0.47 1 1
NCK1 0.024 0.01 -10000 0 -10000 0 0
PTPRJ 0.028 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.031 0.049 -10000 0 -0.24 2 2
PDPK1 0 0.019 0.3 1 -10000 0 1
HGF/MET/SHIP 0.036 0.073 -10000 0 -0.28 19 19
EPO signaling pathway

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
BCL2L1 0.048 0.081 0.34 1 -0.42 1 2
CRKL 0.025 0.083 0.32 5 -10000 0 5
mol:DAG 0.022 0.062 -10000 0 -0.3 1 1
HRAS 0.029 0.085 0.3 13 -10000 0 13
MAPK8 0.023 0.097 0.2 35 -0.29 5 40
RAP1A 0.025 0.084 0.31 6 -10000 0 6
GAB1 0.025 0.083 0.31 6 -10000 0 6
MAPK14 0.027 0.09 0.2 34 -10000 0 34
EPO -0.011 0.12 -10000 0 -0.39 38 38
PLCG1 0.022 0.062 -10000 0 -0.3 1 1
EPOR/TRPC2/IP3 Receptors 0.021 0.056 -10000 0 -0.38 7 7
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.026 0.085 -10000 0 -0.22 35 35
GAB1/SHC/GRB2/SOS1 0.052 0.079 0.27 5 -10000 0 5
EPO/EPOR (dimer) 0.01 0.096 -10000 0 -0.27 43 43
IRS2 0.025 0.084 0.31 6 -10000 0 6
STAT1 0.021 0.069 -10000 0 -0.35 1 1
STAT5B 0.025 0.065 -10000 0 -0.35 1 1
cell proliferation 0.017 0.095 0.2 42 -0.29 3 45
GAB1/SHIP/PIK3R1/SHP2/SHC 0.032 0.073 -10000 0 -0.35 2 2
TEC 0.014 0.1 0.31 6 -0.39 6 12
SOCS3 0.027 0.024 -10000 0 -0.47 1 1
STAT1 (dimer) 0.021 0.069 -10000 0 -0.34 1 1
JAK2 0.023 0.02 -10000 0 -10000 0 0
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
EPO/EPOR (dimer)/JAK2 0.047 0.083 -10000 0 -10000 0 0
EPO/EPOR 0.01 0.096 -10000 0 -0.27 43 43
LYN 0.026 0.01 -10000 0 -10000 0 0
TEC/VAV2 0.018 0.1 0.28 2 -0.43 7 9
elevation of cytosolic calcium ion concentration 0.021 0.056 -10000 0 -0.38 7 7
SHC1 0.028 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.027 0.083 -10000 0 -0.22 36 36
mol:IP3 0.022 0.062 -10000 0 -0.3 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.046 0.091 0.31 6 -0.37 2 8
SH2B3 0.026 0.028 -10000 0 -0.39 1 1
NFKB1 0.028 0.093 0.2 37 -10000 0 37
EPO/EPOR (dimer)/JAK2/SOCS3 -0.001 0.051 -10000 0 -0.24 8 8
PTPN6 0.022 0.08 0.3 3 -10000 0 3
TEC/VAV2/GRB2 0.028 0.11 0.29 2 -0.42 7 9
EPOR 0.021 0.056 -10000 0 -0.38 7 7
INPP5D 0.026 0.025 -10000 0 -0.47 1 1
mol:GDP 0.052 0.079 0.27 5 -10000 0 5
SOS1 0.028 0.004 -10000 0 -10000 0 0
PLCG2 0.026 0.025 -10000 0 -0.47 1 1
CRKL/CBL/C3G 0.039 0.078 0.29 2 -10000 0 2
VAV2 0.021 0.089 0.31 6 -0.34 2 8
CBL 0.023 0.082 0.31 6 -10000 0 6
SHC/Grb2/SOS1 0.022 0.061 -10000 0 -10000 0 0
STAT5A 0.025 0.065 -10000 0 -0.35 1 1
GRB2 0.028 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.04 0.076 -10000 0 -0.39 1 1
LYN/PLCgamma2 0.036 0.024 -10000 0 -0.34 1 1
PTPN11 0.028 0.002 -10000 0 -10000 0 0
BTK 0.025 0.083 0.32 5 -10000 0 5
BCL2 0.041 0.12 0.34 1 -0.73 4 5
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.019 0.09 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.027 0.021 -10000 0 -0.39 1 1
STAT1 (dimer)/Cbp/p300 0.022 0.1 -10000 0 -0.31 10 10
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.032 0.044 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.029 0.07 -10000 0 -0.3 2 2
CaM/Ca2+ 0.019 0.086 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.002 0.097 -10000 0 -0.34 10 10
AKT1 0.039 0.1 0.3 13 -10000 0 13
MAP2K1 -0.007 0.078 0.22 2 -10000 0 2
MAP3K11 -0.004 0.08 0.27 1 -10000 0 1
IFNGR1 0.02 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.12 0.21 -10000 0 -0.44 89 89
Rap1/GTP -0.007 0.059 -10000 0 -10000 0 0
CRKL/C3G 0.039 0.018 -10000 0 -0.28 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.02 0.1 -10000 0 -10000 0 0
CEBPB 0.018 0.11 0.29 2 -0.5 7 9
STAT3 0.028 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.004 0.14 -10000 0 -0.67 7 7
STAT1 -0.01 0.092 -10000 0 -0.34 10 10
CALM1 0.026 0.008 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.053 0.16 -10000 0 -0.39 82 82
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.005 0.095 -10000 0 -0.32 10 10
CEBPB/PTGES2/Cbp/p300 0.014 0.073 -10000 0 -0.34 5 5
mol:Ca2+ 0.016 0.087 -10000 0 -10000 0 0
MAPK3 0.002 0.12 -10000 0 -0.62 9 9
STAT1 (dimer) -0.033 0.097 -10000 0 -0.43 2 2
MAPK1 0.003 0.11 -10000 0 -0.58 8 8
JAK2 0.016 0.023 -10000 0 -10000 0 0
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
JAK1 0.02 0.023 -10000 0 -10000 0 0
CAMK2D 0.028 0.005 -10000 0 -10000 0 0
DAPK1 0.02 0.1 0.28 5 -0.48 7 12
SMAD7 0.006 0.062 0.17 16 -10000 0 16
CBL/CRKL/C3G 0.018 0.085 0.27 1 -10000 0 1
PI3K 0.01 0.077 -10000 0 -10000 0 0
IFNG -0.053 0.16 -10000 0 -0.39 82 82
apoptosis 0.018 0.088 0.26 3 -0.44 5 8
CAMK2G 0.028 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.003 -10000 0 -10000 0 0
CAMK2A -0.072 0.2 -10000 0 -0.47 84 84
CAMK2B -0.093 0.21 -10000 0 -0.46 102 102
FRAP1 0.027 0.1 0.29 13 -10000 0 13
PRKCD 0.031 0.1 0.3 9 -10000 0 9
RAP1B 0.027 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.029 0.07 -10000 0 -0.3 2 2
PTPN2 0.026 0.008 -10000 0 -10000 0 0
EP300 0.026 0.034 -10000 0 -0.47 2 2
IRF1 -0.008 0.089 0.28 4 -0.38 1 5
STAT1 (dimer)/PIASy 0.005 0.095 0.23 3 -0.32 10 13
SOCS1 -0.006 0.15 -10000 0 -1 7 7
mol:GDP 0.015 0.081 0.25 1 -10000 0 1
CASP1 0.005 0.064 0.18 16 -0.3 1 17
PTGES2 0.028 0.005 -10000 0 -10000 0 0
IRF9 0.024 0.047 0.16 10 -10000 0 10
mol:PI-3-4-5-P3 0.002 0.069 -10000 0 -10000 0 0
RAP1/GDP 0.01 0.071 -10000 0 -10000 0 0
CBL -0.002 0.079 0.27 1 -10000 0 1
MAP3K1 -0.002 0.081 0.27 1 -10000 0 1
PIAS1 0.028 0.005 -10000 0 -10000 0 0
PIAS4 0.028 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.029 0.07 -10000 0 -0.3 2 2
PTPN11 0 0.086 0.28 1 -10000 0 1
CREBBP 0.028 0.004 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.002 0.04 0.21 10 -10000 0 10
RFC1 -0.001 0.027 0.21 3 -10000 0 3
PRKDC 0.018 0.071 0.22 39 -10000 0 39
RIPK1 0.028 0.007 -10000 0 -10000 0 0
CASP7 0.014 0.076 -10000 0 -0.5 7 7
FASLG/FAS/FADD/FAF1 0 0.057 0.22 6 -0.25 9 15
MAP2K4 0.029 0.12 0.34 6 -0.42 7 13
mol:ceramide 0.011 0.083 -10000 0 -0.32 10 10
GSN 0.003 0.041 0.21 11 -10000 0 11
FASLG/FAS/FADD/FAF1/Caspase 8 0.017 0.079 0.25 1 -0.33 6 7
FAS 0.024 0.016 -10000 0 -10000 0 0
BID -0.015 0.023 0.26 1 -0.24 1 2
MAP3K1 0.043 0.096 0.34 5 -0.36 5 10
MAP3K7 0.027 0.006 -10000 0 -10000 0 0
RB1 -0.003 0.025 0.18 2 -0.19 3 5
CFLAR 0.028 0.006 -10000 0 -10000 0 0
HGF/MET 0.031 0.08 -10000 0 -0.27 25 25
ARHGDIB 0.003 0.041 0.21 11 -10000 0 11
FADD 0.017 0.017 -10000 0 -10000 0 0
actin filament polymerization 0.001 0.048 -10000 0 -0.21 11 11
NFKB1 0.001 0.11 -10000 0 -0.52 11 11
MAPK8 0.011 0.16 0.32 5 -0.44 31 36
DFFA -0.003 0.026 0.2 1 -10000 0 1
DNA fragmentation during apoptosis -0.005 0.036 0.21 2 -0.26 1 3
FAS/FADD/MET 0.032 0.039 -10000 0 -0.25 3 3
CFLAR/RIP1 0.039 0.013 -10000 0 -10000 0 0
FAIM3 0.021 0.056 -10000 0 -0.4 7 7
FAF1 0.023 0.018 -10000 0 -10000 0 0
PARP1 -0.003 0.028 0.21 2 -10000 0 2
DFFB -0.003 0.031 0.21 2 -0.26 1 3
CHUK -0.001 0.096 -10000 0 -0.5 9 9
FASLG -0.013 0.12 -10000 0 -0.42 34 34
FAS/FADD 0.024 0.025 -10000 0 -10000 0 0
HGF 0.008 0.091 -10000 0 -0.44 16 16
LMNA -0.005 0.031 0.19 1 -10000 0 1
CASP6 -0.003 0.024 0.2 1 -10000 0 1
CASP10 0.024 0.015 -10000 0 -10000 0 0
CASP3 0 0.025 0.23 2 -0.18 1 3
PTPN13 0.019 0.064 -10000 0 -0.47 7 7
CASP8 -0.016 0.03 0.2 7 -10000 0 7
IL6 -0.07 0.35 -10000 0 -1.1 38 38
MET 0.023 0.043 -10000 0 -0.41 4 4
ICAD/CAD -0.003 0.025 -10000 0 -0.25 1 1
FASLG/FAS/FADD/FAF1/Caspase 10 0.01 0.084 -10000 0 -0.33 10 10
activation of caspase activity by cytochrome c -0.015 0.023 0.26 1 -0.24 1 2
PAK2 0.037 0.092 0.22 77 -10000 0 77
BCL2 0.021 0.044 -10000 0 -0.41 4 4
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.028 0.005 -10000 0 -10000 0 0
HDAC3 0.027 0.006 -10000 0 -10000 0 0
VDR 0.027 0.024 -10000 0 -0.47 1 1
Cbp/p300/PCAF 0.037 0.066 -10000 0 -0.3 13 13
EP300 0.025 0.034 -10000 0 -0.47 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.005 0.083 -10000 0 -0.37 11 11
KAT2B 0.01 0.083 -10000 0 -0.47 12 12
MAPK14 0.027 0.006 -10000 0 -10000 0 0
AKT1 -0.014 0.093 0.19 2 -0.27 21 23
RAR alpha/9cRA/Cyclin H 0.036 0.059 0.22 1 -10000 0 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.016 0.11 -10000 0 -0.35 27 27
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.013 0.062 -10000 0 -0.38 6 6
NCOR2 0.028 0.003 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.017 -10000 0 -0.33 1 1
RXRs/RARs/NRIP1/9cRA -0.016 0.12 0.28 1 -0.57 5 6
NCOA2 0 0.11 -10000 0 -0.47 21 21
NCOA3 0.027 0.007 -10000 0 -10000 0 0
NCOA1 0.028 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.027 0.024 -10000 0 -0.47 1 1
RARG 0.027 0.024 -10000 0 -0.47 1 1
RAR gamma1/9cRA 0.037 0.017 -10000 0 -0.28 1 1
MAPK3 0.028 0.005 -10000 0 -10000 0 0
MAPK1 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.021 0.059 -10000 0 -0.47 6 6
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.015 0.078 -10000 0 -0.39 3 3
RARA 0.006 0.043 -10000 0 -0.22 5 5
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.026 0.14 -10000 0 -0.47 26 26
PRKCA 0.029 0.021 -10000 0 -0.39 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.026 0.13 -10000 0 -0.49 11 11
RXRG -0.028 0.11 -10000 0 -0.33 40 40
RXRA 0.009 0.044 -10000 0 -10000 0 0
RXRB 0.004 0.058 -10000 0 -0.33 3 3
VDR/Vit D3/DNA 0.02 0.017 -10000 0 -0.33 1 1
RBP1 -0.048 0.16 -10000 0 -0.39 71 71
CRBP1/9-cic-RA -0.033 0.11 -10000 0 -0.28 71 71
RARB -0.008 0.12 -10000 0 -0.46 29 29
PRKCG -0.017 0.13 -10000 0 -0.39 44 44
MNAT1 0.026 0.007 -10000 0 -10000 0 0
RAR alpha/RXRs -0.012 0.11 0.31 1 -0.46 6 7
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.007 0.1 -10000 0 -0.44 6 6
proteasomal ubiquitin-dependent protein catabolic process -0.027 0.13 0.3 1 -0.35 37 38
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.026 0.13 -10000 0 -0.48 12 12
positive regulation of DNA binding 0.027 0.052 -10000 0 -10000 0 0
NRIP1 -0.029 0.14 -10000 0 -0.79 4 4
RXRs/RARs -0.033 0.14 -10000 0 -0.48 17 17
RXRs/RXRs/DNA/9cRA -0.001 0.071 -10000 0 -0.4 3 3
PRKACA 0.028 0.003 -10000 0 -10000 0 0
CDK7 0.027 0.006 -10000 0 -10000 0 0
TFIIH 0.051 0.019 -10000 0 -10000 0 0
RAR alpha/9cRA 0.043 0.053 -10000 0 -10000 0 0
CCNH 0.027 0.007 -10000 0 -10000 0 0
CREBBP 0.028 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.047 0.025 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.006 0.16 -10000 0 -10000 0 0
CRP -0.025 0.17 0.49 2 -0.67 1 3
cell cycle arrest -0.025 0.16 -10000 0 -0.58 3 3
TIMP1 -0.008 0.16 -10000 0 -0.61 2 2
IL6ST -0.016 0.14 -10000 0 -0.46 37 37
Rac1/GDP -0.018 0.12 -10000 0 -0.5 11 11
AP1 0.011 0.14 -10000 0 -0.5 4 4
GAB2 0.023 0.035 -10000 0 -0.47 2 2
TNFSF11 -0.048 0.18 -10000 0 -0.63 1 1
HSP90B1 0.024 0.1 -10000 0 -0.69 5 5
GAB1 0.028 0.006 -10000 0 -10000 0 0
MAPK14 -0.022 0.12 -10000 0 -0.49 12 12
AKT1 0.049 0.066 0.3 8 -0.48 2 10
FOXO1 0.046 0.059 0.34 3 -0.55 1 4
MAP2K6 -0.029 0.12 -10000 0 -0.49 14 14
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.019 0.12 -10000 0 -0.48 11 11
MITF -0.026 0.12 -10000 0 -0.47 15 15
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.021 -10000 0 -0.39 1 1
A2M 0.022 0.082 -10000 0 -1.1 2 2
CEBPB 0.029 0.014 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.012 0.1 -10000 0 -0.47 9 9
STAT3 -0.031 0.16 -10000 0 -0.61 3 3
STAT1 0.003 0.091 -10000 0 -0.76 5 5
CEBPD -0.002 0.16 -10000 0 -10000 0 0
PIK3CA 0.021 0.013 -10000 0 -10000 0 0
PI3K 0.028 0.033 -10000 0 -0.34 2 2
JUN 0.028 0.005 -10000 0 -10000 0 0
PIAS3/MITF -0.013 0.12 -10000 0 -0.44 16 16
MAPK11 -0.021 0.12 -10000 0 -0.5 12 12
STAT3 (dimer)/FOXO1 0.018 0.15 0.39 2 -10000 0 2
GRB2/SOS1/GAB family 0.027 0.12 -10000 0 -0.46 7 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.017 0.12 -10000 0 -0.46 13 13
GRB2 0.028 0.004 -10000 0 -10000 0 0
JAK2 0.024 0.01 -10000 0 -10000 0 0
LBP -0.096 0.33 -10000 0 -0.89 54 54
PIK3R1 0.024 0.042 -10000 0 -0.47 3 3
JAK1 0.029 0.007 -10000 0 -10000 0 0
MYC 0.015 0.17 0.49 2 -10000 0 2
FGG -0.033 0.16 -10000 0 -0.59 4 4
macrophage differentiation -0.025 0.16 -10000 0 -0.58 3 3
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.014 0.13 -10000 0 -0.34 24 24
JUNB -0.018 0.14 -10000 0 -0.52 1 1
FOS -0.036 0.16 -10000 0 -0.47 53 53
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.02 0.12 -10000 0 -0.46 15 15
STAT1/PIAS1 -0.009 0.12 -10000 0 -0.44 11 11
GRB2/SOS1/GAB family/SHP2/PI3K 0.045 0.059 -10000 0 -0.52 2 2
STAT3 (dimer) -0.028 0.16 -10000 0 -0.6 3 3
PRKCD -0.008 0.14 0.34 10 -0.52 5 15
IL6R 0.023 0.055 -10000 0 -0.47 5 5
SOCS3 -0.018 0.13 -10000 0 -0.9 2 2
gp130 (dimer)/JAK1/JAK1/LMO4 0.027 0.098 -10000 0 -0.28 36 36
Rac1/GTP -0.018 0.13 -10000 0 -0.5 11 11
HCK 0.023 0.04 -10000 0 -0.44 3 3
MAPKKK cascade 0.027 0.1 -10000 0 -0.49 6 6
bone resorption -0.045 0.18 -10000 0 -0.6 1 1
IRF1 -0.02 0.15 -10000 0 -10000 0 0
mol:GDP -0.024 0.12 -10000 0 -0.49 13 13
SOS1 0.028 0.004 -10000 0 -10000 0 0
VAV1 -0.026 0.12 -10000 0 -0.49 13 13
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.017 0.13 -10000 0 -0.54 13 13
PTPN11 0.017 0.052 -10000 0 -0.68 2 2
IL6/IL6RA 0.003 0.11 -10000 0 -0.32 43 43
gp130 (dimer)/TYK2/TYK2/LMO4 0.024 0.1 -10000 0 -0.29 37 37
gp130 (dimer)/JAK2/JAK2/LMO4 0.021 0.095 -10000 0 -0.28 35 35
IL6 -0.018 0.14 -10000 0 -0.45 40 40
PIAS3 0.028 0.004 -10000 0 -10000 0 0
PTPRE 0.024 0.012 -10000 0 -10000 0 0
PIAS1 0.028 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.008 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.023 0.12 -10000 0 -0.41 18 18
LMO4 0.029 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.02 0.17 -10000 0 -0.59 4 4
MCL1 0.052 0.075 0.54 2 -0.51 1 3
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.013 0.088 -10000 0 -0.24 42 42
MAPK9 0.007 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.009 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.035 0.011 -10000 0 -10000 0 0
GNB1 0.027 0.006 -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 0.008 0.002 -10000 0 -10000 0 0
Gs family/GTP -0.012 0.084 -10000 0 -0.26 45 45
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 0.008 0.021 0.069 45 -10000 0 45
GNAL -0.027 0.15 -10000 0 -0.47 45 45
GNG2 0.027 0.007 -10000 0 -10000 0 0
CRH -0.014 0.012 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.038 -10000 0 -0.31 6 6
MAPK11 0.008 0.002 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.018 0.065 0.42 9 -10000 0 9
PI3K Class IB/PDE3B 0.018 0.065 -10000 0 -0.42 9 9
PDE3B 0.018 0.065 -10000 0 -0.42 9 9
BARD1 signaling events

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
BARD1/CSTF1 0.018 0.086 -10000 0 -0.34 23 23
ATM 0.025 0.009 -10000 0 -10000 0 0
UBE2D3 0.028 0.005 -10000 0 -10000 0 0
PRKDC 0.025 0.009 -10000 0 -10000 0 0
ATR 0.023 0.011 -10000 0 -10000 0 0
UBE2L3 0.028 0.005 -10000 0 -10000 0 0
FANCD2 0.016 0.011 -10000 0 -10000 0 0
protein ubiquitination 0.046 0.075 -10000 0 -0.24 20 20
XRCC5 0.027 0.006 -10000 0 -10000 0 0
XRCC6 0.028 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.044 0.025 -10000 0 -10000 0 0
MRE11A 0.026 0.009 -10000 0 -10000 0 0
DNA-PK 0.048 0.021 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.011 0.094 -10000 0 -0.5 8 8
FANCF 0.024 0.042 -10000 0 -0.47 3 3
BRCA1 0.028 0.003 -10000 0 -10000 0 0
CCNE1 0.025 0.029 -10000 0 -0.39 2 2
CDK2/Cyclin E1 0.039 0.024 -10000 0 -0.28 2 2
FANCG 0.024 0.01 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.019 0.086 -10000 0 -0.34 23 23
FANCE 0.027 0.006 -10000 0 -10000 0 0
FANCC 0.027 0.005 -10000 0 -10000 0 0
NBN 0.025 0.009 -10000 0 -10000 0 0
FANCA 0.025 0.03 -10000 0 -0.39 2 2
DNA repair 0.01 0.085 0.24 3 -0.38 4 7
BRCA1/BARD1/ubiquitin 0.019 0.086 -10000 0 -0.34 23 23
BARD1/DNA-PK 0.047 0.068 -10000 0 -0.26 16 16
FANCL 0.026 0.029 -10000 0 -0.39 2 2
mRNA polyadenylation -0.018 0.086 0.34 23 -10000 0 23
BRCA1/BARD1/CTIP/M/R/N Complex 0.011 0.072 -10000 0 -0.3 2 2
BRCA1/BACH1/BARD1/TopBP1 0.03 0.076 -10000 0 -0.28 21 21
BRCA1/BARD1/P53 0.037 0.077 -10000 0 -0.26 22 22
BARD1/CSTF1/BRCA1 0.033 0.079 -10000 0 -0.29 23 23
BRCA1/BACH1 0.028 0.003 -10000 0 -10000 0 0
BARD1 0 0.11 -10000 0 -0.47 23 23
PCNA 0.027 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.035 0.079 -10000 0 -0.29 23 23
BRCA1/BARD1/UbcH7 0.035 0.077 -10000 0 -0.29 22 22
BRCA1/BARD1/RAD51/PCNA 0.045 0.079 -10000 0 -0.26 23 23
BARD1/DNA-PK/P53 0.052 0.074 -10000 0 -0.25 18 18
BRCA1/BARD1/Ubiquitin 0.019 0.086 -10000 0 -0.34 23 23
BRCA1/BARD1/CTIP 0.023 0.069 -10000 0 -0.26 22 22
FA complex 0.035 0.037 -10000 0 -10000 0 0
BARD1/EWS 0.02 0.084 -10000 0 -0.34 22 22
RBBP8 0.013 0.006 -10000 0 -10000 0 0
TP53 0.022 0.048 -10000 0 -0.47 4 4
TOPBP1 0.024 0.01 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.035 0.076 0.26 22 -10000 0 22
BRCA1/BARD1 0.052 0.078 -10000 0 -0.25 20 20
CSTF1 0.027 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.001 0.081 -10000 0 -0.33 23 23
CDK2 0.028 0.003 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.027 0.021 -10000 0 -0.39 1 1
RAD50 0.027 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.019 0.086 -10000 0 -0.34 23 23
EWSR1 0.028 0.005 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.01 0.046 0.13 49 -0.12 1 50
BUB1B 0.01 0.032 0.13 2 -0.15 3 5
PLK1 0.011 0.026 0.094 11 -10000 0 11
PLK1S1 0.014 0.024 0.12 4 -0.18 2 6
KIF2A 0.008 0.021 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.011 0.026 0.094 11 -10000 0 11
GOLGA2 0.028 0.005 -10000 0 -10000 0 0
Hec1/SPC24 0.033 0.042 -10000 0 -0.21 7 7
WEE1 0.01 0.063 -10000 0 -0.3 14 14
cytokinesis 0.008 0.054 -10000 0 -0.24 5 5
PP2A-alpha B56 0.058 0.06 -10000 0 -0.52 4 4
AURKA 0.011 0.03 0.12 1 -0.17 7 8
PICH/PLK1 0.014 0.041 0.16 2 -10000 0 2
CENPE 0.008 0.021 -10000 0 -10000 0 0
RhoA/GTP 0.018 0.007 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.022 -10000 0 -10000 0 0
PPP2CA 0.027 0.006 -10000 0 -10000 0 0
FZR1 0.027 0.005 -10000 0 -10000 0 0
TPX2 0.016 0.025 0.12 7 -0.17 1 8
PAK1 0.025 0.009 -10000 0 -10000 0 0
SPC24 0.021 0.054 -10000 0 -0.39 7 7
FBXW11 0.027 0.007 -10000 0 -10000 0 0
CLSPN 0.01 0.035 -10000 0 -0.23 6 6
GORASP1 0.024 0.01 -10000 0 -10000 0 0
metaphase 0 0.002 0.015 7 -0.011 3 10
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.005 0.014 0.051 15 -10000 0 15
G2 phase of mitotic cell cycle -0.001 0.002 0.014 1 -10000 0 1
STAG2 0.028 0.004 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.047 0.18 -10000 0 -0.49 59 59
spindle elongation 0.011 0.026 0.094 11 -10000 0 11
ODF2 0.028 0.005 -10000 0 -10000 0 0
BUB1 0.027 0.06 -10000 0 -0.57 4 4
TPT1 0.001 0.048 -10000 0 -0.18 26 26
CDC25C 0.002 0.064 -10000 0 -0.27 20 20
CDC25B 0.012 0.078 -10000 0 -0.39 15 15
SGOL1 -0.01 0.046 0.12 1 -0.13 49 50
RHOA 0.024 0.01 -10000 0 -10000 0 0
CCNB1/CDK1 0.03 0.046 -10000 0 -0.23 1 1
CDC14B 0.005 0.024 -10000 0 -0.34 2 2
CDC20 0.023 0.046 -10000 0 -0.39 5 5
PLK1/PBIP1 0.009 0.023 0.091 2 -0.18 2 4
mitosis -0.001 0.005 0.025 10 -10000 0 10
FBXO5 0.009 0.026 0.15 3 -10000 0 3
CDC2 0.001 0.002 -10000 0 -0.014 1 1
NDC80 0.024 0.022 -10000 0 -0.39 1 1
metaphase plate congression 0.007 0.049 -10000 0 -0.23 15 15
ERCC6L 0.014 0.043 -10000 0 -0.22 1 1
NLP/gamma Tubulin 0.008 0.018 0.067 5 -0.11 2 7
microtubule cytoskeleton organization 0.001 0.048 -10000 0 -0.18 26 26
G2/M transition DNA damage checkpoint 0 0.003 0.013 7 -10000 0 7
PPP1R12A 0.028 0.003 -10000 0 -10000 0 0
interphase 0 0.003 0.013 7 -10000 0 7
PLK1/PRC1-2 0.041 0.028 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.044 0.031 -10000 0 -10000 0 0
RAB1A 0.028 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.009 0.023 0.084 18 -10000 0 18
mitotic prometaphase 0 0.003 0.017 15 -10000 0 15
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.06 -10000 0 -0.43 5 5
microtubule-based process 0.026 0.025 -10000 0 -10000 0 0
Golgi organization 0.011 0.026 0.094 11 -10000 0 11
Cohesin/SA2 0.024 0.022 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.041 0.006 -10000 0 -10000 0 0
KIF20A 0.027 0.006 -10000 0 -10000 0 0
APC/C/CDC20 0.024 0.035 -10000 0 -0.21 5 5
PPP2R1A 0.028 0.005 -10000 0 -10000 0 0
chromosome segregation 0.009 0.023 0.09 2 -0.18 2 4
PRC1 0.028 0.004 -10000 0 -10000 0 0
ECT2 0.066 0.098 0.22 118 -10000 0 118
C13orf34 0.009 0.022 0.078 17 -10000 0 17
NUDC 0.007 0.049 -10000 0 -0.24 15 15
regulation of attachment of spindle microtubules to kinetochore 0.01 0.032 0.13 2 -0.15 3 5
spindle assembly 0.009 0.022 0.08 10 -10000 0 10
spindle stabilization 0.014 0.024 0.12 4 -0.18 2 6
APC/C/HCDH1 0.023 0.022 -10000 0 -0.27 2 2
MKLP2/PLK1 0.026 0.025 -10000 0 -10000 0 0
CCNB1 0.028 0.008 -10000 0 -10000 0 0
PPP1CB 0.028 0.003 -10000 0 -10000 0 0
BTRC 0.028 0.004 -10000 0 -10000 0 0
ROCK2 -0.003 0.075 -10000 0 -0.35 11 11
TUBG1 0.012 0.023 -10000 0 -0.21 3 3
G2/M transition of mitotic cell cycle 0.004 0.035 -10000 0 -0.23 1 1
MLF1IP 0.005 0.02 -10000 0 -0.28 2 2
INCENP 0.028 0.005 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.014 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.038 0.021 -10000 0 -10000 0 0
CDKN1B 0.016 0.063 -10000 0 -0.28 11 11
CDKN1A 0.016 0.054 -10000 0 -0.28 7 7
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.025 0.009 -10000 0 -10000 0 0
FOXO3 0.013 0.058 -10000 0 -0.28 9 9
AKT1 0.009 0.049 -10000 0 -0.29 8 8
BAD 0.027 0.005 -10000 0 -10000 0 0
AKT3 0.014 0.017 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.013 0.06 -10000 0 -0.29 1 1
AKT1/ASK1 0.04 0.071 -10000 0 -0.27 9 9
BAD/YWHAZ 0.047 0.022 -10000 0 -10000 0 0
RICTOR 0.025 0.009 -10000 0 -10000 0 0
RAF1 0.025 0.01 -10000 0 -10000 0 0
JNK cascade -0.036 0.067 0.26 9 -10000 0 9
TSC1 0.012 0.057 -10000 0 -0.28 9 9
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
AKT1/RAF1 0.041 0.077 0.29 2 -0.29 1 3
EP300 0.025 0.034 -10000 0 -0.47 2 2
mol:GDP 0.015 0.06 -10000 0 -0.29 12 12
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.013 0.057 -10000 0 -0.29 1 1
YWHAQ 0.028 0.003 -10000 0 -10000 0 0
TBC1D4 0.008 0.003 -10000 0 -10000 0 0
MAP3K5 0.028 0.004 -10000 0 -10000 0 0
MAPKAP1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.04 0.073 0.28 9 -0.2 14 23
YWHAH 0.028 0.004 -10000 0 -10000 0 0
AKT1S1 0.014 0.054 -10000 0 -0.28 7 7
CASP9 0.015 0.049 -10000 0 -10000 0 0
YWHAB 0.027 0.007 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.047 0.077 0.3 9 -10000 0 9
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.049 0.021 -10000 0 -10000 0 0
YWHAE 0.027 0.006 -10000 0 -10000 0 0
SRC 0.027 0.007 -10000 0 -10000 0 0
AKT2/p21CIP1 0.019 0.059 -10000 0 -0.3 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0 0.086 -10000 0 -0.34 22 22
CHUK 0.013 0.057 -10000 0 -0.28 8 8
BAD/BCL-XL 0.043 0.067 -10000 0 -10000 0 0
mTORC2 0.031 0.013 -10000 0 -10000 0 0
AKT2 0.015 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.047 0.094 0.24 12 -0.38 8 20
PDPK1 0.028 0.004 -10000 0 -10000 0 0
MDM2 0.017 0.063 -10000 0 -0.29 1 1
MAPKKK cascade -0.041 0.076 0.28 5 -0.29 2 7
MDM2/Cbp/p300 0.062 0.082 0.27 7 -10000 0 7
TSC1/TSC2 0.014 0.061 0.28 5 -10000 0 5
proteasomal ubiquitin-dependent protein catabolic process 0.059 0.079 0.26 7 -10000 0 7
glucose import -0.095 0.12 0.21 2 -0.25 168 170
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.009 0.065 0.24 1 -0.34 7 8
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.096 0.12 0.21 2 -0.25 168 170
GSK3A 0.014 0.054 -10000 0 -0.28 7 7
FOXO1 0.014 0.051 -10000 0 -10000 0 0
GSK3B 0.027 0.068 -10000 0 -0.29 1 1
SFN 0.023 0.045 -10000 0 -0.43 4 4
G1/S transition of mitotic cell cycle 0.038 0.069 0.25 6 -10000 0 6
p27Kip1/14-3-3 family 0.03 0.066 -10000 0 -0.37 5 5
PRKACA 0.028 0.003 -10000 0 -10000 0 0
KPNA1 0.025 0.009 -10000 0 -10000 0 0
HSP90AA1 0.026 0.008 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
RHEB 0.027 0.007 -10000 0 -10000 0 0
CREBBP 0.028 0.004 -10000 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB -0.062 0.17 -10000 0 -0.39 89 89
alphaV beta3 Integrin 0.023 0.075 -10000 0 -0.3 21 21
PTK2 0.012 0.086 -10000 0 -0.46 6 6
positive regulation of JNK cascade 0.014 0.087 -10000 0 -0.35 7 7
CDC42/GDP 0.048 0.12 0.31 3 -0.44 7 10
Rac1/GDP 0.043 0.11 0.3 1 -0.44 5 6
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.024 0.01 -10000 0 -10000 0 0
CDC42/GTP 0.032 0.11 -10000 0 -0.43 7 7
nectin-3/I-afadin 0.024 0.065 -10000 0 -0.32 14 14
RAPGEF1 0.031 0.11 0.32 6 -0.47 6 12
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0.1 -10000 0 -0.52 7 7
PDGFB-D/PDGFRB -0.062 0.17 -10000 0 -0.39 89 89
TLN1 0.001 0.031 0.17 2 -0.31 1 3
Rap1/GTP 0.015 0.073 -10000 0 -0.34 6 6
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.017 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.024 0.065 -10000 0 -0.32 14 14
PVR 0.028 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.027 0.005 -10000 0 -10000 0 0
mol:GDP 0.036 0.13 0.34 3 -0.51 11 14
MLLT4 0.028 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PI3K -0.001 0.11 -10000 0 -0.43 2 2
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.029 -10000 0 -0.34 2 2
positive regulation of lamellipodium assembly 0.022 0.079 -10000 0 -0.35 4 4
PVRL1 0.023 0.035 -10000 0 -0.47 2 2
PVRL3 0.009 0.084 -10000 0 -0.44 14 14
PVRL2 0.028 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
CDH1 0.022 0.048 -10000 0 -0.47 4 4
CLDN1 0.003 0.09 -10000 0 -0.44 16 16
JAM-A/CLDN1 0.03 0.079 -10000 0 -0.26 19 19
SRC 0.008 0.11 -10000 0 -0.58 7 7
ITGB3 0.007 0.096 -10000 0 -0.42 20 20
nectin-1(dimer)/I-afadin/I-afadin 0.036 0.029 -10000 0 -0.34 2 2
FARP2 0.026 0.15 -10000 0 -0.6 9 9
RAC1 0.026 0.007 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.038 0.061 -10000 0 -0.29 9 9
nectin-1/I-afadin 0.036 0.029 -10000 0 -0.34 2 2
nectin-2/I-afadin 0.04 0.009 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.034 0.065 -10000 0 -0.27 16 16
CDC42/GTP/IQGAP1/filamentous actin 0.037 0.008 -10000 0 -10000 0 0
F11R 0.028 0.005 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.014 0.087 -10000 0 -0.35 7 7
alphaV/beta3 Integrin/Talin 0.046 0.092 0.26 12 -0.33 6 18
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.009 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.04 0.009 -10000 0 -10000 0 0
PIP5K1C 0.002 0.036 -10000 0 -0.35 2 2
VAV2 0.039 0.12 -10000 0 -0.56 5 5
RAP1/GDP 0.048 0.11 0.32 3 -0.41 5 8
ITGAV 0.026 0.021 -10000 0 -0.39 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.038 0.061 -10000 0 -0.29 9 9
nectin-3(dimer)/I-afadin/I-afadin 0.024 0.065 -10000 0 -0.32 14 14
Rac1/GTP 0.034 0.098 -10000 0 -0.43 4 4
PTPRM 0.006 0.041 -10000 0 -0.22 10 10
E-cadherin/beta catenin/alpha catenin 0.063 0.05 -10000 0 -0.42 1 1
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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 0.045 0.071 -10000 0 -10000 0 0
UGCG 0.009 0.1 -10000 0 -0.56 12 12
AKT1/mTOR/p70S6K/Hsp90/TERT 0.036 0.12 0.26 8 -0.38 15 23
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.011 0.1 -10000 0 -0.55 12 12
mol:DAG 0.005 0.086 -10000 0 -0.74 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 0.048 0.099 -10000 0 -0.44 4 4
FRAP1 0.045 0.11 0.29 1 -0.47 6 7
FOXO3 0.048 0.098 0.3 4 -0.38 4 8
AKT1 0.05 0.095 0.25 3 -0.38 4 7
GAB2 0.023 0.035 -10000 0 -0.47 2 2
SMPD1 0.008 0.11 -10000 0 -0.57 13 13
SGMS1 0.021 0.064 -10000 0 -0.58 4 4
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 0.004 0.021 -10000 0 -0.29 2 2
CALM1 0.026 0.008 -10000 0 -10000 0 0
cell proliferation 0.051 0.081 0.27 2 -0.38 4 6
EIF3A 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.03 0.033 -10000 0 -0.34 2 2
RPS6KB1 0.009 0.08 -10000 0 -0.86 1 1
mol:sphingomyelin 0.005 0.086 -10000 0 -0.74 5 5
natural killer cell activation 0 0.001 -10000 0 -0.011 2 2
JAK3 0.019 0.067 -10000 0 -0.39 11 11
PIK3R1 0.025 0.042 -10000 0 -0.47 3 3
JAK1 0.03 0.005 -10000 0 -10000 0 0
NFKB1 0.028 0.005 -10000 0 -10000 0 0
MYC 0.082 0.12 0.35 14 -10000 0 14
MYB -0.098 0.37 -10000 0 -1.2 44 44
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.043 0.081 -10000 0 -0.33 3 3
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.082 -10000 0 -0.79 1 1
mol:PI-3-4-5-P3 0.043 0.08 -10000 0 -0.32 3 3
Rac1/GDP 0.016 0.024 -10000 0 -0.26 2 2
T cell proliferation 0.044 0.08 0.26 7 -0.32 1 8
SHC1 0.028 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.003 0.021 -10000 0 -0.064 46 46
PRKCZ 0.042 0.078 0.24 4 -0.33 1 5
NF kappa B1 p50/RelA 0.061 0.11 0.26 1 -0.47 3 4
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.016 0.053 -10000 0 -0.38 2 2
HSP90AA1 0.026 0.008 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
IL2RA -0.013 0.12 -10000 0 -0.39 41 41
IL2RB 0.022 0.059 -10000 0 -0.4 8 8
TERT -0.041 0.15 -10000 0 -0.39 64 64
E2F1 -0.018 0.14 -10000 0 -0.42 45 45
SOS1 0.028 0.004 -10000 0 -10000 0 0
RPS6 0.025 0.009 -10000 0 -10000 0 0
mol:cAMP 0.001 0.01 0.031 46 -10000 0 46
PTPN11 0.029 0.004 -10000 0 -10000 0 0
IL2RG 0.016 0.077 -10000 0 -0.4 14 14
actin cytoskeleton organization 0.044 0.08 0.26 7 -0.32 1 8
GRB2 0.028 0.004 -10000 0 -10000 0 0
IL2 0.018 0.024 -10000 0 -0.39 1 1
PIK3CA 0.022 0.014 -10000 0 -10000 0 0
Rac1/GTP 0.035 0.035 -10000 0 -0.25 2 2
LCK 0.02 0.064 -10000 0 -0.39 10 10
BCL2 0.041 0.12 -10000 0 -0.76 5 5
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.024 0.026 -10000 0 -0.47 1 1
Caspase 8 (4 units) 0.046 0.075 -10000 0 -0.4 1 1
NEF -0.006 0.035 -10000 0 -10000 0 0
NFKBIA 0.025 0.023 -10000 0 -10000 0 0
BIRC3 0.019 0.077 -10000 0 -0.38 10 10
CYCS 0.021 0.076 0.2 17 -0.45 1 18
RIPK1 0.027 0.006 -10000 0 -10000 0 0
CD247 0.001 0.11 -10000 0 -0.47 17 17
MAP2K7 0.039 0.13 0.37 2 -0.67 9 11
protein ubiquitination 0.045 0.093 0.25 17 -0.35 7 24
CRADD 0.028 0.002 -10000 0 -10000 0 0
DAXX 0.027 0.006 -10000 0 -10000 0 0
FAS 0.028 0.005 -10000 0 -10000 0 0
BID 0.02 0.072 0.19 4 -0.28 7 11
NF-kappa-B/RelA/I kappa B alpha 0.047 0.063 -10000 0 -0.33 6 6
TRADD 0.027 0.006 -10000 0 -10000 0 0
MAP3K5 0.028 0.004 -10000 0 -10000 0 0
CFLAR 0.027 0.005 -10000 0 -10000 0 0
FADD 0.02 0.013 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.047 0.064 -10000 0 -0.34 6 6
MAPK8 0.034 0.12 0.27 2 -0.62 9 11
APAF1 0.027 0.024 -10000 0 -0.47 1 1
TRAF1 0.017 0.064 -10000 0 -0.39 10 10
TRAF2 0.024 0.036 -10000 0 -0.39 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.026 0.076 0.2 4 -0.27 9 13
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.033 0.089 -10000 0 -0.42 8 8
CHUK 0.045 0.097 0.26 16 -0.38 7 23
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.053 0.041 -10000 0 -10000 0 0
TCRz/NEF -0.005 0.1 -10000 0 -0.29 42 42
TNF 0.007 0.09 -10000 0 -0.4 19 19
FASLG -0.024 0.14 -10000 0 -0.48 35 35
NFKB1 0.026 0.026 -10000 0 -0.21 1 1
TNFR1A/BAG4/TNF-alpha 0.033 0.064 -10000 0 -0.24 18 18
CASP6 0.046 0.11 -10000 0 -0.52 10 10
CASP7 0.046 0.12 0.31 24 -0.41 7 31
RELA 0.024 0.027 -10000 0 -0.21 1 1
CASP2 0.027 0.007 -10000 0 -10000 0 0
CASP3 0.042 0.12 0.3 22 -0.42 8 30
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
TNFR1A/BAG4 0.034 0.024 -10000 0 -0.34 1 1
CASP8 0.027 0.006 -10000 0 -10000 0 0
CASP9 0.027 0.006 -10000 0 -10000 0 0
MAP3K14 0.042 0.095 0.24 8 -0.4 8 16
APAF-1/Caspase 9 0.018 0.075 -10000 0 -0.34 2 2
BCL2 0.03 0.12 0.26 2 -0.62 8 10
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.036 0.009 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.005 0.1 -10000 0 -0.47 19 19
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.027 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.008 0.026 -10000 0 -0.19 2 2
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.025 0.009 -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 0.028 0.003 -10000 0 -10000 0 0
FYN 0.027 0.021 -10000 0 -0.39 1 1
MAP3K12 0.026 0.032 -10000 0 -0.43 2 2
FGR 0.027 0.021 -10000 0 -0.39 1 1
p38 alpha/TAB1 -0.024 0.071 -10000 0 -0.31 18 18
PRKG1 0.007 0.093 -10000 0 -0.42 19 19
DUSP8 0.027 0.006 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha 0.02 0.1 0.17 5 -0.34 13 18
apoptosis -0.023 0.068 -10000 0 -0.3 18 18
RAL/GTP 0.035 0.01 -10000 0 -10000 0 0
LYN 0.025 0.009 -10000 0 -10000 0 0
DUSP1 0.002 0.11 -10000 0 -0.47 21 21
PAK1 0.026 0.009 -10000 0 -10000 0 0
SRC 0.027 0.007 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.06 0.039 -10000 0 -10000 0 0
TRAF6 0.027 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.007 -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 0.021 0.05 -10000 0 -0.39 6 6
RAC1-CDC42/GTP 0.034 0.012 -10000 0 -10000 0 0
MAPK11 0.029 0.11 0.24 24 -0.34 14 38
BLK -0.039 0.15 -10000 0 -0.41 61 61
HCK 0.023 0.04 -10000 0 -0.44 3 3
MAP2K3 0.027 0.006 -10000 0 -10000 0 0
DUSP16 0.027 0.007 -10000 0 -10000 0 0
DUSP10 0.026 0.029 -10000 0 -0.39 2 2
TRAF6/MEKK3 0.034 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.028 0.11 0.22 20 -0.35 15 35
positive regulation of innate immune response 0.033 0.13 0.26 28 -0.39 16 44
LCK 0.018 0.064 -10000 0 -0.39 10 10
p38alpha-beta/MKP7 0.04 0.13 0.27 24 -0.39 14 38
p38alpha-beta/MKP5 0.04 0.12 0.26 23 -0.38 15 38
PGK/cGMP 0.006 0.066 -10000 0 -0.29 19 19
PAK2 0.021 0.013 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.032 0.13 0.26 24 -0.39 16 40
CDC42 0.027 0.005 -10000 0 -10000 0 0
RALB 0.028 0.004 -10000 0 -10000 0 0
RALA 0.027 0.007 -10000 0 -10000 0 0
PAK3 0.001 0.084 -10000 0 -0.4 17 17
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.02 0.033 -10000 0 -0.28 4 4
epithelial cell differentiation 0.048 0.034 -10000 0 -0.24 2 2
CYFIP2 0.025 0.032 -10000 0 -0.43 2 2
ENAH 0.019 0.069 0.23 11 -10000 0 11
EGFR 0.022 0.035 -10000 0 -0.47 2 2
EPHA2 0.021 0.054 -10000 0 -0.47 5 5
MYO6 0.018 0.037 0.21 1 -10000 0 1
CTNNB1 0.024 0.01 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.05 0.028 -10000 0 -0.26 2 2
AQP5 -0.29 0.22 -10000 0 -0.46 242 242
CTNND1 0.028 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.018 0.036 0.21 1 -10000 0 1
regulation of calcium-dependent cell-cell adhesion 0.002 0.064 -10000 0 -10000 0 0
EGF -0.062 0.19 -10000 0 -0.47 75 75
NCKAP1 0.028 0.005 -10000 0 -10000 0 0
AQP3 -0.09 0.19 -10000 0 -0.46 69 69
cortical microtubule organization 0.048 0.034 -10000 0 -0.24 2 2
GO:0000145 0 0.037 0.19 3 -10000 0 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.053 0.036 -10000 0 -0.24 2 2
MLLT4 0.028 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.013 0.025 -10000 0 -10000 0 0
ARF6 0.027 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.055 0.043 -10000 0 -0.26 4 4
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.008 0.028 0.21 1 -10000 0 1
PVRL2 0.028 0.005 -10000 0 -10000 0 0
ZYX 0.018 0.035 0.21 1 -10000 0 1
ARF6/GTP 0.059 0.045 -10000 0 -0.24 4 4
CDH1 0.022 0.048 -10000 0 -0.47 4 4
EGFR/EGFR/EGF/EGF -0.007 0.1 -10000 0 -0.33 2 2
RhoA/GDP 0.05 0.033 -10000 0 -0.23 2 2
actin cytoskeleton organization -0.002 0.037 0.2 1 -10000 0 1
IGF-1R heterotetramer 0.027 0.005 -10000 0 -10000 0 0
GIT1 0.028 0.003 -10000 0 -10000 0 0
IGF1R 0.027 0.005 -10000 0 -10000 0 0
IGF1 -0.044 0.17 -10000 0 -0.46 62 62
DIAPH1 0.019 0.12 -10000 0 -0.56 1 1
Wnt receptor signaling pathway -0.048 0.034 0.24 2 -10000 0 2
RHOA 0.024 0.01 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.025 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
VCL -0.002 0.037 0.2 1 -10000 0 1
EFNA1 0.028 0.005 -10000 0 -10000 0 0
LPP -0.003 0.03 0.2 3 -10000 0 3
Ephrin A1/EPHA2 0.04 0.042 -10000 0 -10000 0 0
SEC6/SEC8 0.01 0.02 -10000 0 -10000 0 0
MGAT3 0.002 0.065 -10000 0 -10000 0 0
HGF/MET 0.03 0.062 -10000 0 -0.34 1 1
HGF 0.008 0.091 -10000 0 -0.44 16 16
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.021 0.034 -10000 0 -0.28 4 4
actin cable formation 0.055 0.094 0.23 63 -10000 0 63
KIAA1543 -0.013 0.064 0.19 3 -0.36 3 6
KIFC3 0.015 0.03 -10000 0 -10000 0 0
NCK1 0.024 0.01 -10000 0 -10000 0 0
EXOC3 0.024 0.01 -10000 0 -10000 0 0
ACTN1 0.017 0.035 0.21 1 -10000 0 1
NCK1/GIT1 0.035 0.016 -10000 0 -10000 0 0
mol:GDP 0.048 0.034 -10000 0 -0.24 2 2
EXOC4 0.027 0.007 -10000 0 -10000 0 0
STX4 0.019 0.036 0.21 1 -10000 0 1
PIP5K1C 0.018 0.037 0.21 1 -10000 0 1
LIMA1 0.028 0.003 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
ROCK1 0.026 0.08 0.27 11 -10000 0 11
adherens junction assembly -0.008 0.092 0.28 6 -0.48 5 11
IGF-1R heterotetramer/IGF1 0.008 0.095 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.009 -10000 0 -10000 0 0
MET 0.023 0.043 -10000 0 -0.41 4 4
PLEKHA7 0.004 0.069 0.21 1 -0.38 3 4
mol:GTP 0.053 0.042 -10000 0 -0.26 4 4
establishment of epithelial cell apical/basal polarity 0.024 0.081 0.33 10 -10000 0 10
cortical actin cytoskeleton stabilization 0.02 0.033 -10000 0 -0.28 4 4
regulation of cell-cell adhesion -0.002 0.037 0.2 1 -10000 0 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.021 0.034 -10000 0 -0.28 4 4
p38 MAPK signaling 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
TRAF6/ASK1 0.02 0.015 -10000 0 -10000 0 0
TRAF2/ASK1 0.034 0.024 -10000 0 -0.23 3 3
ATM 0.025 0.009 -10000 0 -10000 0 0
MAP2K3 -0.017 0.11 0.41 2 -0.36 16 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.014 0.1 0.36 2 -0.36 14 16
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.021 0.056 -10000 0 -0.44 6 6
TXN 0.008 0.001 -10000 0 -10000 0 0
CALM1 0.026 0.008 -10000 0 -10000 0 0
GADD45A 0.027 0.021 -10000 0 -0.39 1 1
GADD45B 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.027 0.007 -10000 0 -10000 0 0
MAP3K6 0.026 0.025 -10000 0 -0.47 1 1
MAP3K7 0.028 0.004 -10000 0 -10000 0 0
MAP3K4 0.028 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.039 0.021 -10000 0 -0.34 1 1
TAK1/TAB family -0.004 0.017 -10000 0 -0.13 5 5
RAC1/OSM/MEKK3 0.046 0.033 -10000 0 -0.21 5 5
TRAF2 0.024 0.036 -10000 0 -0.39 3 3
RAC1/OSM/MEKK3/MKK3 -0.003 0.09 -10000 0 -0.33 6 6
TRAF6 0.008 0.002 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.094 0.21 -10000 0 -0.46 102 102
CCM2 0.021 0.05 -10000 0 -0.39 6 6
CaM/Ca2+/CAMKIIB -0.041 0.13 -10000 0 -0.28 98 98
MAPK11 0.027 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.025 0.13 -10000 0 -0.26 97 97
OSM/MEKK3 0.035 0.036 -10000 0 -0.28 5 5
TAOK1 0.008 0.047 -10000 0 -0.32 8 8
TAOK2 0.014 0.005 -10000 0 -10000 0 0
TAOK3 0.014 0.005 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.028 0.004 -10000 0 -10000 0 0
MAP3K10 0.027 0.006 -10000 0 -10000 0 0
MAP3K3 0.028 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.025 0.008 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.056 0.042 -10000 0 -0.24 4 4
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.042 0.03 -9999 0 -10000 0 0
CLOCK 0.025 0.048 -9999 0 -0.46 4 4
TIMELESS/CRY2 0.041 0.021 -9999 0 -10000 0 0
DEC1/BMAL1 -0.014 0.12 -9999 0 -0.27 70 70
ATR 0.023 0.011 -9999 0 -10000 0 0
NR1D1 0.024 0.013 -9999 0 -10000 0 0
ARNTL 0.03 0.006 -9999 0 -10000 0 0
TIMELESS 0.025 0.013 -9999 0 -10000 0 0
NPAS2 0.025 0.054 -9999 0 -0.46 5 5
CRY2 0.027 0.006 -9999 0 -10000 0 0
mol:CO -0.01 0 -9999 0 -10000 0 0
CHEK1 0.026 0.008 -9999 0 -10000 0 0
mol:HEME 0.01 0 -9999 0 -10000 0 0
PER1 0.027 0.006 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.059 0.053 -9999 0 -0.31 7 7
BMAL1/CLOCK 0.012 0.071 -9999 0 -0.42 1 1
S phase of mitotic cell cycle 0.042 0.03 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.043 0.03 -9999 0 -10000 0 0
mol:NADPH 0.01 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.041 0.021 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.057 0.15 -9999 0 -0.39 71 71
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.045 0.098 -10000 0 -0.36 19 19
MAP4K1 0.016 0.071 -10000 0 -0.41 11 11
MAP3K8 0.025 0.034 -10000 0 -0.47 2 2
PRKCB 0.019 0.06 -10000 0 -0.41 8 8
DBNL 0.027 0.007 -10000 0 -10000 0 0
CRKL 0.027 0.021 -10000 0 -0.39 1 1
MAP3K1 0.013 0.061 0.18 1 -0.36 5 6
JUN 0.007 0.13 -10000 0 -0.59 16 16
MAP3K7 0.011 0.063 -10000 0 -0.36 5 5
GRAP2 0.018 0.066 -10000 0 -0.43 9 9
CRK 0.027 0.006 -10000 0 -10000 0 0
MAP2K4 0.014 0.072 0.25 6 -0.4 4 10
LAT 0.019 0.061 -10000 0 -0.39 9 9
LCP2 0.024 0.036 -10000 0 -0.39 3 3
MAPK8 0.008 0.13 -10000 0 -0.62 16 16
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.066 -10000 0 -0.36 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55 0.052 0.098 -10000 0 -0.4 13 13
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.016 0.034 -10000 0 -0.25 2 2
CRKL 0.027 0.021 -10000 0 -0.39 1 1
Rac1/GDP 0.019 0.006 -10000 0 -10000 0 0
DOCK1 0.027 0.024 -10000 0 -0.47 1 1
ITGA4 0.02 0.058 -10000 0 -0.39 8 8
alpha4/beta7 Integrin/MAdCAM1 0.043 0.068 -10000 0 -0.26 2 2
EPO -0.018 0.12 -10000 0 -0.39 38 38
alpha4/beta7 Integrin 0.033 0.051 -10000 0 -0.29 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.027 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.034 0.044 -10000 0 -0.28 8 8
EPO/EPOR (dimer) 0.004 0.096 -10000 0 -0.28 43 43
lamellipodium assembly 0.037 0.086 -10000 0 -0.49 4 4
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PI3K 0.027 0.032 -10000 0 -0.34 2 2
ARF6 0.027 0.007 -10000 0 -10000 0 0
JAK2 0.004 0.059 -10000 0 -0.28 8 8
PXN 0.028 0.003 -10000 0 -10000 0 0
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
MADCAM1 0 0.076 -10000 0 -0.39 14 14
cell adhesion 0.041 0.067 -10000 0 -0.26 2 2
CRKL/CBL 0.036 0.021 -10000 0 -0.28 1 1
ITGB1 0.028 0.005 -10000 0 -10000 0 0
SRC -0.006 0.083 -10000 0 -0.29 9 9
ITGB7 0.026 0.034 -10000 0 -0.47 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.019 0.098 -10000 0 -0.25 47 47
p130Cas/Crk/Dock1 0.022 0.084 -10000 0 -0.35 2 2
VCAM1 -0.015 0.13 -10000 0 -0.41 41 41
RHOA 0.024 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.062 0.043 -10000 0 -10000 0 0
BCAR1 -0.023 0.073 0.18 10 -0.38 2 12
EPOR 0.021 0.054 -10000 0 -0.39 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.026 0.008 -10000 0 -10000 0 0
GIT1 0.028 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.037 0.087 -10000 0 -0.51 4 4
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.017 0.086 0.24 3 -0.52 3 6
BAG4 0.024 0.026 -10000 0 -0.47 1 1
BAD 0.018 0.047 0.18 14 -0.21 1 15
NFKBIA 0.027 0.007 -10000 0 -10000 0 0
BIRC3 0.014 0.065 -10000 0 -0.4 10 10
BAX 0.014 0.04 0.19 5 -0.21 1 6
EnzymeConsortium:3.1.4.12 0.008 0.026 0.073 14 -0.091 5 19
IKBKB 0.027 0.087 0.33 7 -0.57 2 9
MAP2K2 0.015 0.04 0.18 9 -10000 0 9
MAP2K1 0.014 0.04 0.18 8 -10000 0 8
SMPD1 0.009 0.034 0.14 3 -0.15 4 7
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.067 0.12 0.28 39 -0.45 3 42
MAP2K4 0.014 0.04 0.21 5 -10000 0 5
protein ubiquitination 0.025 0.092 0.3 8 -0.58 2 10
EnzymeConsortium:2.7.1.37 0.016 0.045 0.19 7 -10000 0 7
response to UV 0 0 0.002 7 -10000 0 7
RAF1 0.015 0.037 0.18 7 -10000 0 7
CRADD 0.028 0.002 -10000 0 -10000 0 0
mol:ceramide 0.015 0.041 0.15 7 -0.18 2 9
I-kappa-B-alpha/RELA/p50/ubiquitin 0.034 0.012 -10000 0 -10000 0 0
MADD 0.028 0.005 -10000 0 -10000 0 0
MAP3K1 0.015 0.039 0.17 6 -0.21 1 7
TRADD 0.027 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.006 -10000 0 -10000 0 0
MAPK3 0.018 0.044 0.18 7 -10000 0 7
MAPK1 0.018 0.042 0.18 7 -10000 0 7
p50/RELA/I-kappa-B-alpha 0.038 0.013 -10000 0 -10000 0 0
FADD 0.058 0.11 0.26 28 -0.47 3 31
KSR1 0.014 0.042 0.17 7 -0.21 1 8
MAPK8 0.01 0.043 0.17 6 -0.24 1 7
TRAF2 0.024 0.036 -10000 0 -0.39 3 3
response to radiation 0 0 0.002 2 -10000 0 2
CHUK 0.019 0.087 0.3 5 -0.49 3 8
TNF R/SODD 0.034 0.024 -10000 0 -0.34 1 1
TNF 0.007 0.09 -10000 0 -0.4 19 19
CYCS 0.025 0.052 0.17 19 -10000 0 19
IKBKG 0.025 0.095 0.32 9 -0.49 3 12
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.019 0.086 -10000 0 -0.48 4 4
RELA 0.027 0.006 -10000 0 -10000 0 0
RIPK1 0.027 0.006 -10000 0 -10000 0 0
AIFM1 0.022 0.048 0.16 16 -10000 0 16
TNF/TNF R/SODD 0.033 0.063 -10000 0 -0.24 18 18
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.023 0.087 -10000 0 -0.57 8 8
NSMAF 0.031 0.097 0.28 11 -0.5 3 14
response to hydrogen peroxide 0 0 0.002 7 -10000 0 7
BCL2 0.021 0.043 -10000 0 -0.41 4 4
Regulation of Telomerase

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
Telomerase catalytic core complex -0.039 0.18 -10000 0 -0.7 7 7
RAD9A 0.026 0.009 -10000 0 -10000 0 0
AP1 -0.011 0.12 -10000 0 -0.34 53 53
IFNAR2 0.021 0.018 -10000 0 -10000 0 0
AKT1 0.002 0.054 -10000 0 -0.35 6 6
ER alpha/Oestrogen 0.003 0.07 -10000 0 -0.29 22 22
NFX1/SIN3/HDAC complex 0.022 0.049 -10000 0 -0.3 4 4
EGF -0.062 0.19 -10000 0 -0.47 75 75
SMG5 0.028 0.005 -10000 0 -10000 0 0
SMG6 0.027 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.03 0.027 -10000 0 -10000 0 0
TERT/c-Abl -0.033 0.17 -10000 0 -0.64 8 8
SAP18 0.026 0.007 -10000 0 -10000 0 0
MRN complex 0.044 0.025 -10000 0 -10000 0 0
WT1 -0.075 0.17 -10000 0 -0.4 93 93
WRN 0.026 0.008 -10000 0 -10000 0 0
SP1 0.02 0.022 -10000 0 -10000 0 0
SP3 0.026 0.007 -10000 0 -10000 0 0
TERF2IP 0.027 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.018 0.16 -10000 0 -0.61 6 6
Mad/Max 0.035 0.035 -10000 0 -0.34 3 3
TERT -0.04 0.18 -10000 0 -0.72 7 7
CCND1 0.007 0.19 0.49 1 -0.91 4 5
MAX 0.026 0.008 -10000 0 -10000 0 0
RBBP7 0.027 0.005 -10000 0 -10000 0 0
RBBP4 0.025 0.034 -10000 0 -0.47 2 2
TERF2 0.026 0.014 -10000 0 -10000 0 0
PTGES3 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.027 0.005 -10000 0 -10000 0 0
Telomerase/911 0.037 0.048 -10000 0 -10000 0 0
CDKN1B -0.025 0.098 -10000 0 -10000 0 0
RAD1 0.025 0.009 -10000 0 -10000 0 0
XRCC5 0.027 0.006 -10000 0 -10000 0 0
XRCC6 0.028 0.004 -10000 0 -10000 0 0
SAP30 0.027 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.038 0.016 -10000 0 -10000 0 0
UBE3A 0.027 0.005 -10000 0 -10000 0 0
JUN 0.027 0.006 -10000 0 -10000 0 0
E6 -0.001 0.003 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.015 0.015 -10000 0 -10000 0 0
FOS -0.037 0.16 -10000 0 -0.47 53 53
IFN-gamma/IRF1 -0.019 0.12 -10000 0 -0.27 82 82
PARP2 0.027 0.007 -10000 0 -10000 0 0
BLM 0.027 0.021 -10000 0 -0.39 1 1
Telomerase 0.008 0.1 0.23 1 -0.46 10 11
IRF1 0.029 0.008 -10000 0 -10000 0 0
ESR1 0.005 0.098 -10000 0 -0.41 22 22
KU/TER 0.04 0.01 -10000 0 -10000 0 0
ATM/TRF2 0.037 0.016 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.024 0.064 -10000 0 -0.4 5 5
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.025 0.065 -10000 0 -0.41 5 5
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.02 0.021 -10000 0 -10000 0 0
ATM 0.01 0.008 -10000 0 -10000 0 0
SMAD3 0.015 0.015 -10000 0 -0.28 1 1
ABL1 0.028 0.005 -10000 0 -10000 0 0
MXD1 0.023 0.049 -10000 0 -0.47 4 4
MRE11A 0.026 0.009 -10000 0 -10000 0 0
HUS1 0.026 0.007 -10000 0 -10000 0 0
RPS6KB1 0.028 0.003 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.011 0.18 -10000 0 -0.66 9 9
NR2F2 0.028 0.021 -10000 0 -0.38 1 1
MAPK3 -0.007 0.019 -10000 0 -0.28 1 1
MAPK1 -0.007 0.019 -10000 0 -0.28 1 1
TGFB1/TGF beta receptor Type II 0.027 0.021 -10000 0 -0.39 1 1
NFKB1 0.028 0.005 -10000 0 -10000 0 0
HNRNPC 0.027 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.008 -10000 0 -10000 0 0
NBN 0.025 0.009 -10000 0 -10000 0 0
EGFR 0.022 0.036 -10000 0 -0.47 2 2
mol:Oestrogen -0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR -0.026 0.14 -10000 0 -0.34 67 67
MYC 0.022 0.012 -10000 0 -10000 0 0
IL2 0.012 0.03 -10000 0 -0.39 1 1
KU 0.04 0.01 -10000 0 -10000 0 0
RAD50 0.027 0.007 -10000 0 -10000 0 0
HSP90AA1 0.026 0.008 -10000 0 -10000 0 0
TGFB1 0.027 0.021 -10000 0 -0.39 1 1
TRF2/BLM 0.039 0.021 -10000 0 -0.26 1 1
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.02 0.18 -10000 0 -0.65 7 7
SP1/HDAC2 0.03 0.032 -10000 0 -10000 0 0
PINX1 0.026 0.008 -10000 0 -10000 0 0
Telomerase/EST1A -0.017 0.16 -10000 0 -0.65 5 5
Smad3/Myc 0.024 0.019 -10000 0 -0.23 1 1
911 complex 0.043 0.025 -10000 0 -10000 0 0
IFNG -0.053 0.16 -10000 0 -0.39 82 82
Telomerase/PinX1 -0.017 0.16 -10000 0 -0.62 6 6
Telomerase/AKT1/mTOR/p70S6K 0 0.1 0.26 1 -0.42 12 13
SIN3B 0.028 0.003 -10000 0 -10000 0 0
YWHAE 0.027 0.006 -10000 0 -10000 0 0
Telomerase/EST1B -0.016 0.16 -10000 0 -0.62 6 6
response to DNA damage stimulus -0.003 0.029 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.06 0.036 -10000 0 -10000 0 0
TRF2/WRN 0.037 0.017 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.016 0.16 -10000 0 -0.69 4 4
E2F1 0.007 0.077 -10000 0 -0.4 14 14
ZNFX1 0.027 0.007 -10000 0 -10000 0 0
PIF1 0.007 0.092 -10000 0 -0.39 21 21
NCL 0.027 0.005 -10000 0 -10000 0 0
DKC1 0.027 0.005 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.006 0.1 -10000 0 -0.42 2 2
TC10/GTP 0.007 0.092 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0.062 0.036 -10000 0 -0.27 2 2
HRAS 0.026 0.022 -10000 0 -0.4 1 1
APS homodimer 0.025 0.022 -10000 0 -0.39 1 1
GRB14 -0.02 0.14 -10000 0 -0.46 40 40
FOXO3 0.023 0.085 -10000 0 -0.59 7 7
AKT1 0.016 0.11 0.27 5 -0.41 1 6
INSR 0.03 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.054 0.029 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.025 0.022 -10000 0 -0.39 1 1
SORBS1 -0.041 0.17 -10000 0 -0.47 58 58
CRK 0.027 0.006 -10000 0 -10000 0 0
PTPN1 0.009 0.023 -10000 0 -10000 0 0
CAV1 -0.009 0.068 0.18 2 -0.24 2 4
CBL/APS/CAP/Crk-II/C3G 0.025 0.11 -10000 0 -0.25 47 47
Insulin Receptor/Insulin/IRS1/NCK2 0.062 0.036 -10000 0 -0.27 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.035 0.04 -10000 0 -0.24 3 3
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.028 0.061 -10000 0 -0.37 3 3
RPS6KB1 0.013 0.1 0.22 10 -0.38 1 11
PARD6A 0.025 0.032 -10000 0 -0.43 2 2
CBL 0.026 0.008 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.02 0.03 -10000 0 -0.57 1 1
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.035 0.087 -10000 0 -0.39 1 1
HRAS/GTP 0.017 0.024 -10000 0 -10000 0 0
Insulin Receptor 0.03 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.07 0.04 -10000 0 -0.25 2 2
PRKCI 0.019 0.038 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 0.001 0.074 -10000 0 -0.44 1 1
SHC1 0.028 0.004 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.04 0.036 -10000 0 -0.49 1 1
PI3K 0.043 0.045 -10000 0 -0.24 3 3
NCK2 0.028 0.003 -10000 0 -10000 0 0
RHOQ 0.028 0.004 -10000 0 -10000 0 0
mol:H2O2 0 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.015 -10000 0 -0.28 1 1
AKT2 0.019 0.11 0.29 7 -0.41 1 8
PRKCZ 0.016 0.052 -10000 0 -0.41 3 3
SH2B2 0.025 0.022 -10000 0 -0.39 1 1
SHC/SHIP 0.028 0.03 -10000 0 -0.24 2 2
F2RL2 -0.11 0.2 -10000 0 -0.4 134 134
TRIP10 0.028 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.047 0.023 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.037 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.074 0.031 -10000 0 -10000 0 0
RAPGEF1 0.027 0.005 -10000 0 -10000 0 0
RASA1 0.026 0.025 -10000 0 -0.47 1 1
NCK1 0.024 0.01 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.015 0.11 -10000 0 -0.26 59 59
TC10/GDP 0.021 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.059 0.033 -10000 0 -10000 0 0
INPP5D 0.012 0.029 0.18 2 -0.24 3 5
SOS1 0.028 0.004 -10000 0 -10000 0 0
SGK1 0 0.088 -10000 0 -0.66 7 7
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.028 0.002 -10000 0 -10000 0 0
IRS1 0.025 0.034 -10000 0 -0.47 2 2
p62DOK/RasGAP 0.04 0.037 -10000 0 -0.49 1 1
INS 0.019 0.029 -10000 0 -0.39 2 2
mol:PI-3-4-P2 0.012 0.029 0.18 2 -0.24 3 5
GRB2 0.028 0.004 -10000 0 -10000 0 0
EIF4EBP1 0.008 0.096 0.24 7 -0.38 1 8
PTPRA 0.028 0.009 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.037 0.008 -10000 0 -10000 0 0
PDPK1 0.028 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.026 0.026 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.045 0.032 -10000 0 -0.23 4 4
Insulin Receptor/Insulin/IRS3 0.036 0.025 -10000 0 -0.27 2 2
Par3/Par6 -0.022 0.12 -10000 0 -0.2 124 124
FOXM1 transcription factor network

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
NFATC3 0.089 0.24 -10000 0 -1.1 3 3
PLK1 0.053 0.1 -10000 0 -0.68 6 6
BIRC5 0.048 0.095 -10000 0 -0.88 1 1
HSPA1B 0.09 0.24 -10000 0 -1.1 3 3
MAP2K1 0.036 0.038 -10000 0 -10000 0 0
BRCA2 0.081 0.26 -10000 0 -1.2 6 6
FOXM1 0.084 0.28 -10000 0 -1.6 3 3
XRCC1 0.087 0.24 -10000 0 -1.1 3 3
FOXM1B/p19 -0.014 0.25 -10000 0 -1.2 5 5
Cyclin D1/CDK4 0.063 0.26 -10000 0 -1.2 3 3
CDC2 0.089 0.25 -10000 0 -1.2 3 3
TGFA 0.073 0.26 0.57 1 -1.1 4 5
SKP2 0.11 0.25 0.74 1 -1.1 3 4
CCNE1 0.029 0.03 -10000 0 -0.38 2 2
CKS1B 0.087 0.25 0.65 1 -1.1 4 5
RB1 0.038 0.17 -10000 0 -0.8 5 5
FOXM1C/SP1 0.093 0.26 -10000 0 -1.3 3 3
AURKB 0.035 0.15 -10000 0 -0.77 11 11
CENPF 0.09 0.25 0.65 1 -1.1 3 4
CDK4 0.033 0.019 -10000 0 -10000 0 0
MYC 0.058 0.21 0.5 1 -0.96 3 4
CHEK2 0.036 0.038 -10000 0 -10000 0 0
ONECUT1 0.073 0.27 -10000 0 -1.1 5 5
CDKN2A -0.14 0.2 -10000 0 -0.4 159 159
LAMA4 0.077 0.26 -10000 0 -1.2 3 3
FOXM1B/HNF6 0.07 0.29 -10000 0 -1.4 5 5
FOS -0.011 0.45 -10000 0 -1.1 56 56
SP1 0.029 0.003 -10000 0 -10000 0 0
CDC25B 0.089 0.25 -10000 0 -1.1 3 3
response to radiation 0.015 0.024 -10000 0 -10000 0 0
CENPB 0.094 0.25 -10000 0 -1.1 3 3
CENPA 0.086 0.25 0.59 1 -1.2 3 4
NEK2 0.089 0.25 0.65 1 -1.2 3 4
HIST1H2BA 0.083 0.24 -10000 0 -1.1 3 3
CCNA2 0.03 0.024 -10000 0 -0.41 1 1
EP300 0.025 0.034 -10000 0 -0.47 2 2
CCNB1/CDK1 0.084 0.26 -10000 0 -1.4 3 3
CCNB2 0.086 0.25 0.74 1 -1.2 3 4
CCNB1 0.089 0.25 -10000 0 -1.2 3 3
ETV5 0.14 0.26 0.66 3 -1.1 3 6
ESR1 0.069 0.28 -10000 0 -1.1 9 9
CCND1 0.025 0.23 -10000 0 -1.2 3 3
GSK3A 0.037 0.034 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.063 0.047 -10000 0 -0.25 2 2
CDK2 0.031 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.016 0.026 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.093 0.26 -10000 0 -1.2 4 4
GAS1 0.084 0.26 -10000 0 -1.2 6 6
MMP2 0.067 0.26 -10000 0 -1.1 3 3
RB1/FOXM1C 0.085 0.26 0.61 1 -1.2 3 4
CREBBP 0.028 0.004 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 -0.001 0.15 -9999 0 -0.46 17 17
MAP3K8 0.024 0.035 -9999 0 -0.47 2 2
FOS 0.001 0.11 -9999 0 -0.48 9 9
PRKCA 0.021 0.026 -9999 0 -0.39 1 1
PTPN7 0.006 0.081 -9999 0 -0.4 15 15
HRAS 0.026 0.022 -9999 0 -0.4 1 1
PRKCB 0.014 0.063 -9999 0 -0.42 8 8
NRAS 0.027 0.006 -9999 0 -10000 0 0
RAS family/GTP 0.044 0.025 -9999 0 -0.22 1 1
MAPK3 0.011 0.089 -9999 0 -0.58 6 6
MAP2K1 0.012 0.071 -9999 0 -0.45 5 5
ELK1 0.021 0.021 -9999 0 -10000 0 0
BRAF 0.012 0.043 -9999 0 -0.4 2 2
mol:GTP -0.001 0.002 -9999 0 -0.005 56 56
MAPK1 0.013 0.084 -9999 0 -0.57 5 5
RAF1 0.009 0.057 -9999 0 -0.4 4 4
KRAS 0.026 0.007 -9999 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.018 0.065 -10000 0 -0.45 8 8
HRAS 0.026 0.022 -10000 0 -0.4 1 1
EGFR 0.022 0.035 -10000 0 -0.47 2 2
AKT 0.069 0.074 0.27 18 -0.27 1 19
FOXO3 0.028 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.008 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
AKT3 0.023 0.041 -10000 0 -0.39 4 4
FOXO4 0.026 0.034 -10000 0 -0.47 2 2
MET 0.023 0.043 -10000 0 -0.41 4 4
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
PIK3CB 0.024 0.011 -10000 0 -10000 0 0
NRAS 0.027 0.006 -10000 0 -10000 0 0
PIK3CG 0.005 0.095 -10000 0 -0.42 20 20
PIK3R3 0.027 0.024 -10000 0 -0.47 1 1
PIK3R2 0.028 0.003 -10000 0 -10000 0 0
NF1 0.028 0.004 -10000 0 -10000 0 0
RAS 0.026 0.038 -10000 0 -0.26 2 2
ERBB2 0.028 0.004 -10000 0 -10000 0 0
proliferation/survival/translation -0.062 0.076 0.25 6 -0.21 37 43
PI3K 0.055 0.072 0.23 27 -0.24 2 29
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
KRAS 0.027 0.007 -10000 0 -10000 0 0
FOXO 0.087 0.064 0.24 26 -10000 0 26
AKT2 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.028 0.005 -10000 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.031 0.021 -10000 0 -0.3 1 1
VEGFR1 homodimer/NRP1 0.013 0.016 -10000 0 -0.3 1 1
mol:DAG -0.019 0.084 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.026 0.031 -10000 0 -0.46 1 1
CaM/Ca2+ -0.006 0.085 -10000 0 -10000 0 0
HIF1A 0.032 0.014 -10000 0 -10000 0 0
GAB1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.02 0.096 0.35 5 -0.42 1 6
PLCG1 -0.019 0.084 -10000 0 -10000 0 0
NOS3 0.015 0.1 0.4 10 -10000 0 10
CBL 0.026 0.008 -10000 0 -10000 0 0
mol:NO 0.024 0.13 0.47 17 -0.39 2 19
FLT1 0.018 0.019 -10000 0 -0.35 1 1
PGF -0.044 0.16 -10000 0 -0.39 70 70
VEGFR1 homodimer/NRP2/VEGFR121 0.04 0.039 -10000 0 -0.46 1 1
CALM1 0.026 0.008 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
eNOS/Hsp90 0.02 0.1 0.44 4 -0.36 2 6
endothelial cell proliferation 0 0.096 0.39 10 -10000 0 10
mol:Ca2+ -0.019 0.083 -10000 0 -10000 0 0
MAPK3 -0.022 0.091 0.34 11 -10000 0 11
MAPK1 -0.022 0.09 0.34 11 -10000 0 11
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
PLGF homodimer -0.044 0.16 -10000 0 -0.39 70 70
PRKACA 0.028 0.003 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.013 0.12 -10000 0 -0.39 40 40
VEGFA homodimer 0.024 0.036 -10000 0 -0.39 3 3
VEGFR1 homodimer/VEGFA homodimer 0.028 0.034 -10000 0 -0.5 1 1
platelet activating factor biosynthetic process -0.023 0.085 0.33 10 -10000 0 10
PI3K 0.011 0.085 -10000 0 -0.42 1 1
PRKCA -0.02 0.083 0.35 4 -10000 0 4
PRKCB -0.023 0.091 0.39 5 -10000 0 5
VEGFR1 homodimer/PLGF homodimer -0.012 0.098 -10000 0 -0.3 1 1
VEGFA 0.024 0.036 -10000 0 -0.39 3 3
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.019 0.084 -10000 0 -10000 0 0
RASA1 0.022 0.039 -10000 0 -10000 0 0
NRP2 0.026 0.029 -10000 0 -0.39 2 2
VEGFR1 homodimer 0.018 0.019 -10000 0 -0.35 1 1
VEGFB homodimer 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.024 0.01 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.015 0.14 0.48 14 -0.38 3 17
PTPN11 0.028 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.01 0.084 -10000 0 -0.42 1 1
mol:L-citrulline 0.024 0.13 0.47 17 -0.39 2 19
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.052 0.036 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.036 0.038 -10000 0 -0.46 1 1
CD2AP 0.027 0.006 -10000 0 -10000 0 0
PI3K/GAB1 0.02 0.087 -10000 0 -0.41 1 1
PDPK1 0.027 0.11 0.37 10 -0.4 1 11
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.042 0.036 -10000 0 -0.46 1 1
mol:NADP 0.024 0.13 0.47 17 -0.39 2 19
HSP90AA1 0.026 0.008 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.05 0.035 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.03 0.026 -10000 0 -0.3 1 1
Aurora B signaling

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
Condensin I complex 0.018 0.028 -10000 0 -10000 0 0
STMN1 0.012 0.042 -10000 0 -0.3 7 7
Aurora B/RasGAP/Survivin 0.044 0.074 -10000 0 -0.26 19 19
Chromosomal passenger complex/Cul3 protein complex 0.011 0.05 -10000 0 -0.25 2 2
BIRC5 0.011 0.088 -10000 0 -0.39 19 19
DES -0.3 0.3 -10000 0 -0.56 228 228
Aurora C/Aurora B/INCENP 0.05 0.047 -10000 0 -0.24 8 8
Aurora B/TACC1 0.033 0.036 -10000 0 -0.23 6 6
Aurora B/PP2A 0.04 0.037 -10000 0 -0.27 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 0.008 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition 0 0.003 -10000 0 -10000 0 0
NDC80 0.011 0.035 -10000 0 -0.27 6 6
Cul3 protein complex 0.044 0.034 -10000 0 -0.29 2 2
KIF2C 0.016 0.029 -10000 0 -0.2 2 2
PEBP1 0.029 0.003 -10000 0 -10000 0 0
KIF20A 0.027 0.006 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.039 0.038 -10000 0 -0.27 5 5
SEPT1 0.022 0.05 -10000 0 -0.39 6 6
SMC2 0.028 0.005 -10000 0 -10000 0 0
SMC4 0.022 0.012 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.008 0.12 -10000 0 -0.57 15 15
PSMA3 0.027 0.007 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -10000 0 -10000 0 0
H3F3B 0.016 0.018 -10000 0 -0.15 3 3
AURKB 0.029 0.047 -10000 0 -0.39 5 5
AURKC 0.022 0.049 -10000 0 -0.42 5 5
CDCA8 0.028 0.022 -10000 0 -0.4 1 1
cytokinesis -0.008 0.06 -10000 0 -0.35 6 6
Aurora B/Septin1 0.032 0.082 -10000 0 -0.34 6 6
AURKA 0.022 0.046 -10000 0 -0.39 5 5
INCENP 0.029 0.006 -10000 0 -10000 0 0
KLHL13 0.025 0.034 -10000 0 -0.47 2 2
BUB1 0.028 0.004 -10000 0 -10000 0 0
hSgo1/Aurora B/Survivin 0.04 0.067 -10000 0 -0.25 15 15
EVI5 0.029 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.05 0.054 -10000 0 -10000 0 0
SGOL1 0.025 0.01 -10000 0 -10000 0 0
CENPA 0.018 0.051 -10000 0 -0.28 4 4
NCAPG 0.026 0.007 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.04 0.034 -10000 0 -0.27 4 4
NCAPD2 0.027 0.007 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.041 0.036 -10000 0 -0.27 5 5
RHOA 0.024 0.01 -10000 0 -10000 0 0
NCAPH 0.028 0.005 -10000 0 -10000 0 0
NPM1 -0.01 0.12 -10000 0 -0.46 16 16
RASA1 0.026 0.025 -10000 0 -0.47 1 1
KLHL9 0.024 0.01 -10000 0 -10000 0 0
mitotic prometaphase 0 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.034 -10000 0 -0.27 4 4
PPP1CC 0.028 0.003 -10000 0 -10000 0 0
Centraspindlin 0.047 0.056 -10000 0 -0.26 1 1
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
NSUN2 0.011 0.057 -10000 0 -0.28 8 8
MYLK 0.012 0.032 -10000 0 -0.32 2 2
KIF23 0.029 0.005 -10000 0 -10000 0 0
VIM 0.011 0.04 -10000 0 -0.28 8 8
RACGAP1 0.029 0.004 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.003 0.081 -10000 0 -0.35 16 16
Chromosomal passenger complex 0.017 0.045 0.17 1 -0.24 3 4
Chromosomal passenger complex/EVI5 0.088 0.085 -10000 0 -0.37 5 5
TACC1 0.024 0.026 -10000 0 -0.47 1 1
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
CUL3 0.027 0.006 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.028 0.004 -9999 0 -10000 0 0
SPHK1 0.02 0.058 -9999 0 -0.39 8 8
GNAI2 0.024 0.01 -9999 0 -10000 0 0
mol:S1P 0.013 0.022 -9999 0 -10000 0 0
GNAO1 0.023 0.043 -9999 0 -0.41 4 4
mol:Sphinganine-1-P 0.009 0.04 -9999 0 -0.28 8 8
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.05 0.041 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
G12/G13 0.037 0.02 -9999 0 -0.28 1 1
S1PR3 0.023 0.047 -9999 0 -0.45 4 4
S1PR2 0.028 0.004 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.006 0.027 -9999 0 -0.28 1 1
S1PR5 0.027 0.024 -9999 0 -0.47 1 1
S1PR4 0.007 0.091 -9999 0 -0.4 20 20
GNAI1 0.026 0.025 -9999 0 -0.47 1 1
S1P/S1P5/G12 0.037 0.04 -9999 0 -0.25 2 2
S1P/S1P3/Gq -0.016 0.11 -9999 0 -0.4 10 10
S1P/S1P4/Gi 0.015 0.074 -9999 0 -0.38 7 7
GNAQ 0.028 0.005 -9999 0 -10000 0 0
GNAZ 0.011 0.083 -9999 0 -0.42 15 15
GNA14 -0.048 0.18 -9999 0 -0.47 64 64
GNA15 0.025 0.034 -9999 0 -0.47 2 2
GNA12 0.025 0.022 -9999 0 -0.39 1 1
GNA13 0.028 0.004 -9999 0 -10000 0 0
GNA11 0.025 0.034 -9999 0 -0.47 2 2
ABCC1 0.025 0.036 -9999 0 -0.39 3 3
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.028 0.005 -9999 0 -10000 0 0
ITGB7 0.026 0.034 -9999 0 -0.47 2 2
ITGA4 0.02 0.058 -9999 0 -0.39 8 8
alpha4/beta7 Integrin 0.033 0.051 -9999 0 -0.29 10 10
alpha4/beta1 Integrin 0.034 0.044 -9999 0 -0.28 8 8
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.028 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.039 0.062 -10000 0 -0.29 13 13
forebrain development -0.024 0.14 -10000 0 -0.49 16 16
GNAO1 0.022 0.043 -10000 0 -0.41 4 4
SMO/beta Arrestin2 0.024 0.069 -10000 0 -0.34 14 14
SMO 0.008 0.091 -10000 0 -0.46 15 15
ARRB2 0.026 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.049 0.081 0.26 4 -0.35 4 8
mol:GTP 0 0.002 -10000 0 -10000 0 0
GSK3B 0.025 0.009 -10000 0 -10000 0 0
GNAI2 0.024 0.01 -10000 0 -10000 0 0
SIN3/HDAC complex 0.066 0.023 -10000 0 -10000 0 0
GNAI1 0.026 0.025 -10000 0 -0.47 1 1
XPO1 0.024 0.016 -10000 0 -10000 0 0
GLI1/Su(fu) -0.021 0.15 -10000 0 -0.52 15 15
SAP30 0.027 0.006 -10000 0 -10000 0 0
mol:GDP 0.008 0.091 -10000 0 -0.46 15 15
MIM/GLI2A 0.018 0.029 -10000 0 -10000 0 0
IFT88 0.027 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GLI2 0.019 0.068 0.21 1 -0.33 1 2
GLI3 0.036 0.082 0.25 5 -0.35 5 10
CSNK1D 0.028 0.004 -10000 0 -10000 0 0
CSNK1E 0.028 0.005 -10000 0 -10000 0 0
SAP18 0.027 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.027 0.007 -10000 0 -10000 0 0
GNG2 0.027 0.007 -10000 0 -10000 0 0
Gi family/GTP 0.008 0.075 -10000 0 -0.34 10 10
SIN3B 0.028 0.003 -10000 0 -10000 0 0
SIN3A 0.028 0.005 -10000 0 -10000 0 0
GLI3/Su(fu) 0.038 0.082 -10000 0 -0.42 5 5
GLI2/Su(fu) 0.024 0.073 -10000 0 -0.36 3 3
FOXA2 -0.017 0.14 -10000 0 -0.88 3 3
neural tube patterning -0.024 0.14 -10000 0 -0.49 16 16
SPOP 0.028 0.002 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.023 0.055 -10000 0 -10000 0 0
GNB1 0.027 0.006 -10000 0 -10000 0 0
CSNK1G2 0.027 0.005 -10000 0 -10000 0 0
CSNK1G3 0.027 0.007 -10000 0 -10000 0 0
MTSS1 0.018 0.029 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.024 0.14 -10000 0 -0.49 16 16
SUFU 0.016 0.039 -10000 0 -0.23 1 1
LGALS3 0.024 0.035 -10000 0 -0.47 2 2
catabolic process 0.051 0.098 0.27 3 -0.47 3 6
GLI3A/CBP 0.003 0.08 -10000 0 -0.2 53 53
KIF3A 0.027 0.007 -10000 0 -10000 0 0
GLI1 -0.025 0.14 -10000 0 -0.5 16 16
RAB23 0.025 0.03 -10000 0 -0.39 2 2
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
IFT172 0.028 0.003 -10000 0 -10000 0 0
RBBP7 0.028 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.021 0.058 -10000 0 -0.34 2 2
GNAZ 0.011 0.083 -10000 0 -0.42 15 15
RBBP4 0.025 0.034 -10000 0 -0.47 2 2
CSNK1G1 0.028 0.005 -10000 0 -10000 0 0
PIAS1 0.028 0.005 -10000 0 -10000 0 0
PRKACA 0.028 0.003 -10000 0 -10000 0 0
GLI2/SPOP 0.03 0.07 -10000 0 -0.32 1 1
STK36 0.024 0.016 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.005 0.077 -10000 0 -0.41 9 9
PTCH1 -0.026 0.17 -10000 0 -0.83 10 10
MIM/GLI1 -0.017 0.14 -10000 0 -0.54 9 9
CREBBP 0.003 0.079 -10000 0 -0.2 53 53
Su(fu)/SIN3/HDAC complex 0.012 0.096 -10000 0 -0.46 11 11
IL2 signaling events mediated by STAT5

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
GAB2 0.024 0.035 -10000 0 -0.47 2 2
ELF1 0.008 0.076 -10000 0 -0.46 2 2
CCNA2 0.026 0.021 -10000 0 -0.39 1 1
PIK3CA 0.021 0.013 -10000 0 -10000 0 0
JAK3 0.018 0.067 -10000 0 -0.39 11 11
PIK3R1 0.024 0.042 -10000 0 -0.47 3 3
JAK1 0.028 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.041 0.083 0.23 3 -0.37 2 5
SHC1 0.028 0.004 -10000 0 -10000 0 0
SP1 0.031 0.033 -10000 0 -0.34 3 3
IL2RA -0.018 0.11 -10000 0 -0.35 43 43
IL2RB 0.02 0.059 -10000 0 -0.4 8 8
SOS1 0.028 0.004 -10000 0 -10000 0 0
IL2RG 0.015 0.077 -10000 0 -0.4 14 14
G1/S transition of mitotic cell cycle 0.035 0.093 0.3 5 -0.55 5 10
PTPN11 0.029 0.002 -10000 0 -10000 0 0
CCND2 0.015 0.055 -10000 0 -0.6 3 3
LCK 0.018 0.064 -10000 0 -0.39 10 10
GRB2 0.028 0.004 -10000 0 -10000 0 0
IL2 0.005 0.029 -10000 0 -0.39 1 1
CDK6 0.024 0.033 -10000 0 -0.43 2 2
CCND3 0.044 0.083 0.35 1 -10000 0 1
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.18 0.24 -10000 0 -0.47 177 177
CLTC 0.026 0.063 -10000 0 -0.37 8 8
calcium ion-dependent exocytosis 0.014 0.03 -10000 0 -10000 0 0
Dynamin 2/GTP 0.026 0.014 -10000 0 -0.21 1 1
EXOC4 0.027 0.007 -10000 0 -10000 0 0
CD59 0.015 0.033 -10000 0 -0.32 2 2
CPE 0.01 0.032 -10000 0 -0.23 7 7
CTNNB1 0.024 0.01 -10000 0 -10000 0 0
membrane fusion 0.016 0.025 -10000 0 -10000 0 0
CTNND1 0.019 0.036 0.18 18 -10000 0 18
DNM2 0.028 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.03 0.053 0.26 3 -0.4 2 5
TSHR 0 0.049 -10000 0 -0.23 17 17
INS 0.004 0.094 -10000 0 -0.46 15 15
BIN1 0.021 0.055 -10000 0 -0.4 7 7
mol:Choline 0.016 0.025 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.013 -10000 0 -0.23 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.026 0.014 -10000 0 -0.21 1 1
JUP 0.014 0.034 -10000 0 -0.29 3 3
ASAP2/amphiphysin II 0.046 0.038 -10000 0 -0.22 7 7
ARF6/GTP 0.02 0.005 -10000 0 -10000 0 0
CDH1 0.015 0.029 -10000 0 -0.32 1 1
clathrin-independent pinocytosis 0.02 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.028 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.02 0.005 -10000 0 -10000 0 0
EXOC2 0.027 0.007 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.022 0.031 -10000 0 -0.28 2 2
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.028 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.035 0.052 0.35 3 -10000 0 3
positive regulation of phagocytosis 0.014 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.011 -10000 0 -10000 0 0
ACAP1 0.019 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.013 0.025 -10000 0 -0.32 1 1
clathrin heavy chain/ACAP1 0.03 0.058 -10000 0 -0.4 4 4
JIP4/KLC1 0.049 0.016 -10000 0 -10000 0 0
EXOC1 0.027 0.005 -10000 0 -10000 0 0
exocyst 0.022 0.031 -10000 0 -0.28 2 2
RALA/GTP 0.02 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.036 0.01 -10000 0 -10000 0 0
receptor recycling 0.02 0.005 -10000 0 -10000 0 0
CTNNA1 0.02 0.038 0.18 20 -10000 0 20
NME1 0.014 0.013 -10000 0 -0.23 1 1
clathrin coat assembly 0.028 0.064 -10000 0 -0.36 8 8
IL2RA 0.005 0.04 -10000 0 -0.32 2 2
VAMP3 0.014 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.057 0.12 -10000 0 -0.37 6 6
EXOC6 0.028 0.004 -10000 0 -10000 0 0
PLD1 0.01 0.015 -10000 0 -0.26 1 1
PLD2 0.015 0.006 -10000 0 -10000 0 0
EXOC5 0.026 0.007 -10000 0 -10000 0 0
PIP5K1C 0.016 0.028 -10000 0 -10000 0 0
SDC1 0.014 0.031 -10000 0 -0.32 2 2
ARF6/GDP 0.024 0.014 -10000 0 -0.23 1 1
EXOC7 0.028 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.037 0.054 -10000 0 -0.36 3 3
mol:Phosphatidic acid 0.016 0.025 -10000 0 -10000 0 0
endocytosis -0.044 0.037 0.22 7 -10000 0 7
SCAMP2 0.028 0.005 -10000 0 -10000 0 0
ADRB2 0.012 0.079 0.27 1 -0.4 5 6
EXOC3 0.024 0.01 -10000 0 -10000 0 0
ASAP2 0.028 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.03 0.015 -10000 0 -0.21 1 1
KLC1 0.026 0.008 -10000 0 -10000 0 0
AVPR2 0.022 0.089 0.24 11 -0.37 7 18
RALA 0.027 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.034 0.052 -10000 0 -0.37 2 2
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.023 0.043 -10000 0 -0.41 4 4
CDC42/GTP 0.013 0.076 -10000 0 -0.32 7 7
PLCG1 0.005 0.065 -10000 0 -0.33 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.024 0.01 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.037 0.02 -10000 0 -0.28 1 1
cell migration 0.012 0.074 -10000 0 -0.32 7 7
S1PR5 0.027 0.024 -10000 0 -0.47 1 1
S1PR4 0.007 0.091 -10000 0 -0.4 20 20
MAPK3 0.005 0.064 -10000 0 -0.35 6 6
MAPK1 0.004 0.061 -10000 0 -0.32 6 6
S1P/S1P5/Gi 0.02 0.051 -10000 0 -0.29 5 5
GNAI1 0.026 0.025 -10000 0 -0.47 1 1
CDC42/GDP 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.023 -10000 0 -0.26 2 2
RHOA 0.015 0.064 0.18 26 -0.24 1 27
S1P/S1P4/Gi 0.014 0.064 -10000 0 -0.34 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.011 0.083 -10000 0 -0.42 15 15
S1P/S1P4/G12/G13 0.035 0.058 -10000 0 -0.21 20 20
GNA12 0.025 0.022 -10000 0 -0.39 1 1
GNA13 0.028 0.004 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.011 0.14 -10000 0 -0.63 13 13
oxygen homeostasis -0.002 0.011 -10000 0 -10000 0 0
TCEB2 0.027 0.021 -10000 0 -0.39 1 1
TCEB1 0.025 0.009 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.032 0.083 0.24 1 -0.44 1 2
EPO -0.019 0.16 -10000 0 -0.57 6 6
FIH (dimer) 0.022 0.02 -10000 0 -10000 0 0
APEX1 0.022 0.023 -10000 0 -10000 0 0
SERPINE1 -0.099 0.2 -10000 0 -0.65 8 8
FLT1 -0.016 0.19 -10000 0 -0.64 27 27
ADORA2A -0.019 0.16 0.37 5 -0.61 5 10
germ cell development -0.024 0.16 -10000 0 -0.71 3 3
SLC11A2 -0.019 0.15 -10000 0 -0.62 5 5
BHLHE40 -0.022 0.15 -10000 0 -0.62 5 5
HIF1AN 0.023 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.016 0.12 -10000 0 -0.4 2 2
ETS1 0.033 0.038 -10000 0 -0.39 3 3
CITED2 0.015 0.13 -10000 0 -0.71 10 10
KDR -0.01 0.18 -10000 0 -0.65 23 23
PGK1 -0.019 0.16 -10000 0 -0.65 4 4
SIRT1 0.026 0.025 -10000 0 -0.47 1 1
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT -0.011 0.18 -10000 0 -0.72 5 5
EPAS1 -0.002 0.077 0.22 1 -0.33 4 5
SP1 0.032 0.012 -10000 0 -10000 0 0
ABCG2 -0.022 0.16 -10000 0 -0.65 5 5
EFNA1 -0.018 0.15 -10000 0 -0.74 2 2
FXN -0.017 0.16 0.37 4 -0.78 2 6
POU5F1 -0.025 0.16 -10000 0 -0.68 4 4
neuron apoptosis 0.011 0.18 0.7 5 -10000 0 5
EP300 0.025 0.034 -10000 0 -0.47 2 2
EGLN3 0.001 0.096 -10000 0 -0.42 20 20
EGLN2 0.022 0.021 -10000 0 -10000 0 0
EGLN1 0.023 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.044 0.025 -10000 0 -10000 0 0
VHL 0.025 0.01 -10000 0 -10000 0 0
ARNT 0.022 0.023 -10000 0 -10000 0 0
SLC2A1 -0.022 0.16 0.37 5 -0.6 7 12
TWIST1 -0.018 0.16 0.37 5 -0.63 6 11
ELK1 0.032 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.035 0.12 -10000 0 -10000 0 0
VEGFA -0.021 0.15 -10000 0 -0.74 2 2
CREBBP 0.028 0.004 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.023 0.075 -10000 0 -0.3 21 21
AKT1 0.058 0.093 0.35 8 -0.47 2 10
PTK2B 0.018 0.075 -10000 0 -0.75 1 1
VEGFR2 homodimer/Frs2 0.033 0.039 -10000 0 -0.47 2 2
CAV1 -0.013 0.12 -10000 0 -0.39 40 40
CALM1 0.026 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.046 0.047 -10000 0 -0.6 1 1
endothelial cell proliferation 0.057 0.11 0.34 18 -0.43 2 20
mol:Ca2+ 0.024 0.049 -10000 0 -0.44 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.057 0.049 -10000 0 -0.57 1 1
RP11-342D11.1 0.013 0.047 -10000 0 -0.44 2 2
CDH5 0.025 0.032 -10000 0 -0.43 2 2
VEGFA homodimer 0.055 0.038 -10000 0 -0.21 2 2
SHC1 0.028 0.004 -10000 0 -10000 0 0
SHC2 0.021 0.053 -10000 0 -0.42 6 6
HRAS/GDP 0.043 0.046 -10000 0 -0.42 2 2
SH2D2A -0.024 0.14 -10000 0 -0.39 51 51
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.049 0.11 0.33 3 -0.44 5 8
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.016 0.097 -10000 0 -0.49 3 3
VEGFR1 homodimer 0.026 0.022 -10000 0 -0.39 1 1
SHC/GRB2/SOS1 0.072 0.056 -10000 0 -0.53 1 1
GRB10 0.023 0.048 -10000 0 -0.55 1 1
PTPN11 0.028 0.002 -10000 0 -10000 0 0
GRB2 0.028 0.004 -10000 0 -10000 0 0
PAK1 0.026 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.064 0.059 -10000 0 -0.55 1 1
HRAS 0.026 0.022 -10000 0 -0.4 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.018 0.052 -10000 0 -0.36 3 3
HIF1A 0.026 0.008 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.055 0.048 -10000 0 -0.56 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.02 0.05 -10000 0 -0.39 6 6
Nck/Pak 0.033 0.018 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.046 0.048 -10000 0 -0.6 1 1
mol:GDP 0.056 0.049 -10000 0 -0.51 1 1
mol:NADP 0.037 0.11 0.34 6 -0.39 10 16
eNOS/Hsp90 0.043 0.1 0.33 4 -0.39 6 10
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
mol:IP3 0.024 0.05 -10000 0 -0.45 2 2
HIF1A/ARNT 0.038 0.013 -10000 0 -10000 0 0
SHB 0.024 0.026 -10000 0 -0.47 1 1
VEGFA 0.025 0.036 -10000 0 -0.39 3 3
VEGFC -0.03 0.14 -10000 0 -0.39 57 57
FAK1/Vinculin 0.044 0.09 0.3 3 -0.72 1 4
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.024 0.01 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.047 0.078 -10000 0 -0.78 1 1
PTPN6 0.027 0.007 -10000 0 -10000 0 0
EPAS1 0.034 0.023 -10000 0 -0.33 1 1
mol:L-citrulline 0.037 0.11 0.34 6 -0.39 10 16
ITGAV 0.026 0.021 -10000 0 -0.39 1 1
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.058 0.05 -10000 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer 0.05 0.051 -10000 0 -0.48 2 2
VEGFR2/3 heterodimer 0.029 0.052 -10000 0 -0.57 2 2
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.014 0.061 0.3 4 -0.57 1 5
VEGFR2 homodimer 0.021 0.042 -10000 0 -0.54 2 2
FLT1 0.026 0.022 -10000 0 -0.39 1 1
NEDD4 0.029 0.009 -10000 0 -10000 0 0
MAPK3 0.012 0.066 0.37 3 -0.5 1 4
MAPK1 0.014 0.067 0.33 5 -0.5 1 6
VEGFA145/NRP2 0.036 0.036 -10000 0 -0.27 5 5
VEGFR1/2 heterodimer 0.032 0.041 -10000 0 -0.47 2 2
KDR 0.021 0.042 -10000 0 -0.54 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.05 0.051 -10000 0 -0.44 2 2
SRC 0.027 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.021 0.073 0.34 6 -0.52 1 7
PI3K 0.033 0.055 -10000 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.041 0.047 -10000 0 -0.6 1 1
FES 0.026 0.052 0.35 1 -0.45 2 3
GAB1 0.034 0.058 -10000 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/Src 0.045 0.048 -10000 0 -0.6 1 1
CTNNB1 0.024 0.01 -10000 0 -10000 0 0
SOS1 0.028 0.004 -10000 0 -10000 0 0
ARNT 0.027 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.032 0.11 0.35 4 -0.39 6 10
VEGFR2 homodimer/VEGFA homodimer/Yes 0.043 0.048 -10000 0 -0.6 1 1
PI3K/GAB1 0.058 0.083 0.28 5 -0.54 1 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.059 0.056 -10000 0 -0.55 1 1
PRKACA 0.028 0.003 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.008 0.1 -10000 0 -0.62 2 2
HSP90AA1 0.026 0.008 -10000 0 -10000 0 0
CDC42 0.025 0.052 0.35 1 -0.45 2 3
actin cytoskeleton reorganization 0.015 0.096 -10000 0 -0.48 3 3
PTK2 0.02 0.065 -10000 0 -0.78 1 1
EDG1 0.013 0.047 -10000 0 -0.44 2 2
mol:DAG 0.024 0.05 -10000 0 -0.45 2 2
CaM/Ca2+ 0.037 0.052 -10000 0 -0.42 2 2
MAP2K3 0.007 0.052 -10000 0 -0.54 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.058 0.063 -10000 0 -0.57 1 1
PLCG1 0.024 0.05 -10000 0 -0.45 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.051 0.054 -10000 0 -0.57 1 1
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
YES1 0.025 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.048 0.047 -10000 0 -0.6 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.045 0.048 -10000 0 -0.6 1 1
cell migration 0.052 0.089 0.3 9 -0.61 1 10
mol:PI-3-4-5-P3 0.032 0.053 -10000 0 -0.54 1 1
FYN 0.027 0.021 -10000 0 -0.39 1 1
VEGFB/NRP1 0.028 0.047 -10000 0 -0.42 2 2
mol:NO 0.037 0.11 0.34 6 -0.39 10 16
PXN 0.028 0.003 -10000 0 -10000 0 0
HRAS/GTP 0.024 0.04 -10000 0 -0.41 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.04 0.047 -10000 0 -0.57 1 1
VHL 0.025 0.01 -10000 0 -10000 0 0
ITGB3 0.007 0.096 -10000 0 -0.42 20 20
NOS3 0.037 0.12 0.34 6 -0.44 10 16
VEGFR2 homodimer/VEGFA homodimer/Sck 0.045 0.055 -10000 0 -0.43 3 3
RAC1 0.026 0.007 -10000 0 -10000 0 0
PRKCA 0.017 0.053 -10000 0 -0.52 1 1
PRKCB 0.013 0.059 -10000 0 -0.52 1 1
VCL 0.028 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 0.032 0.049 -10000 0 -0.44 2 2
VEGFR1/2 heterodimer/VEGFA homodimer 0.045 0.051 -10000 0 -0.49 2 2
VEGFA165/NRP2 0.036 0.036 -10000 0 -0.27 5 5
MAPKKK cascade 0.036 0.053 -10000 0 -0.48 2 2
NRP2 0.026 0.029 -10000 0 -0.39 2 2
VEGFC homodimer -0.03 0.14 -10000 0 -0.39 57 57
NCK1 0.024 0.01 -10000 0 -10000 0 0
ROCK1 0.028 0.003 -10000 0 -10000 0 0
FAK1/Paxillin 0.043 0.091 0.32 2 -0.72 1 3
MAP3K13 0.012 0.051 -10000 0 -0.56 1 1
PDPK1 0.022 0.047 -10000 0 -0.48 1 1
Class I PI3K signaling 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
ARF5/GTP 0 0.05 -10000 0 -10000 0 0
DAPP1 0.021 0.11 0.26 13 -0.39 12 25
Src family/SYK family/BLNK-LAT/BTK-ITK 0.006 0.14 0.28 4 -0.49 11 15
mol:DAG 0.013 0.077 0.21 17 -0.22 5 22
HRAS 0.027 0.021 -10000 0 -0.38 1 1
RAP1A 0.028 0.006 -10000 0 -10000 0 0
ARF5/GDP 0.028 0.064 -10000 0 -0.32 4 4
PLCG2 0.026 0.025 -10000 0 -0.47 1 1
PLCG1 0.027 0.007 -10000 0 -10000 0 0
ARF5 0.027 0.007 -10000 0 -10000 0 0
mol:GTP -0.005 0.04 0.17 2 -10000 0 2
ARF1/GTP 0.007 0.04 0.24 1 -10000 0 1
RHOA 0.024 0.01 -10000 0 -10000 0 0
YES1 0.025 0.009 -10000 0 -10000 0 0
RAP1A/GTP -0.004 0.041 0.17 2 -10000 0 2
ADAP1 -0.006 0.038 -10000 0 -10000 0 0
ARAP3 -0.005 0.039 0.17 2 -10000 0 2
INPPL1 0.024 0.01 -10000 0 -10000 0 0
PREX1 0.027 0.007 -10000 0 -10000 0 0
ARHGEF6 0.022 0.054 -10000 0 -0.47 5 5
ARHGEF7 0.027 0.005 -10000 0 -10000 0 0
ARF1 0.028 0.005 -10000 0 -10000 0 0
NRAS 0.028 0.007 -10000 0 -10000 0 0
FYN 0.027 0.021 -10000 0 -0.39 1 1
ARF6 0.027 0.007 -10000 0 -10000 0 0
FGR 0.027 0.021 -10000 0 -0.39 1 1
mol:Ca2+ 0.008 0.044 0.18 3 -10000 0 3
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.021 0.054 -10000 0 -0.47 5 5
ZAP70 0.008 0.092 -10000 0 -0.41 19 19
mol:IP3 0.007 0.057 0.18 9 -10000 0 9
LYN 0.025 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.029 0.065 -10000 0 -0.32 4 4
RhoA/GDP 0.04 0.045 0.24 3 -10000 0 3
PDK1/Src/Hsp90 0.049 0.021 -10000 0 -10000 0 0
BLNK -0.019 0.14 -10000 0 -0.47 40 40
actin cytoskeleton reorganization 0.022 0.071 0.23 10 -0.4 1 11
SRC 0.027 0.007 -10000 0 -10000 0 0
PLEKHA2 -0.006 0.014 -10000 0 -0.28 1 1
RAC1 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.025 0.012 -10000 0 -10000 0 0
HSP90AA1 0.026 0.008 -10000 0 -10000 0 0
ARF6/GTP -0.008 0.036 -10000 0 -10000 0 0
RhoA/GTP -0.005 0.038 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.005 0.11 -10000 0 -0.38 15 15
BLK -0.039 0.15 -10000 0 -0.41 61 61
PDPK1 0.028 0.004 -10000 0 -10000 0 0
CYTH1 -0.005 0.039 -10000 0 -10000 0 0
HCK 0.023 0.04 -10000 0 -0.44 3 3
CYTH3 -0.005 0.037 -10000 0 -10000 0 0
CYTH2 -0.006 0.037 -10000 0 -10000 0 0
KRAS 0.027 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.016 0.048 -10000 0 -0.45 1 1
SGK1 0.018 0.057 -10000 0 -0.48 1 1
INPP5D 0.026 0.025 -10000 0 -0.47 1 1
mol:GDP 0.015 0.063 -10000 0 -0.32 5 5
SOS1 0.028 0.004 -10000 0 -10000 0 0
SYK 0.025 0.034 -10000 0 -0.47 2 2
ARF6/GDP 0.026 0.043 0.23 3 -10000 0 3
mol:PI-3-4-5-P3 -0.007 0.033 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP -0.004 0.041 0.17 2 -10000 0 2
VAV1 0.022 0.054 -10000 0 -0.47 5 5
mol:PI-3-4-P2 0.012 0.018 -10000 0 -0.34 1 1
RAS family/GTP/PI3K Class I 0.04 0.026 -10000 0 -10000 0 0
PLEKHA1 -0.006 0.014 -10000 0 -0.28 1 1
Rac1/GDP 0.027 0.063 -10000 0 -0.32 4 4
LAT 0.019 0.061 -10000 0 -0.39 9 9
Rac1/GTP 0.022 0.06 -10000 0 -0.45 1 1
ITK -0.012 0.046 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.011 0.095 0.23 16 -0.31 5 21
LCK 0.018 0.064 -10000 0 -0.39 10 10
BTK -0.006 0.039 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.034 0.074 0.22 4 -0.48 1 5
adherens junction organization 0.011 0.095 0.22 1 -0.35 15 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.055 0.082 0.25 3 -0.38 2 5
FMN1 0.007 0.096 -10000 0 -0.35 11 11
mol:IP3 0.012 0.045 -10000 0 -0.44 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.021 0.086 -10000 0 -0.34 10 10
CTNNB1 0.025 0.01 -10000 0 -10000 0 0
AKT1 0.011 0.05 0.19 1 -0.49 1 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.002 0.16 -10000 0 -0.69 15 15
CTNND1 0.03 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.016 0.079 -10000 0 -0.33 9 9
VASP 0.018 0.078 -10000 0 -0.33 9 9
ZYX 0.02 0.074 -10000 0 -0.33 8 8
JUB 0.018 0.081 -10000 0 -0.33 10 10
EGFR(dimer) 0.024 0.09 -10000 0 -0.33 12 12
E-cadherin/beta catenin-gamma catenin 0.042 0.043 -10000 0 -0.32 4 4
mol:PI-3-4-5-P3 0.022 0.062 0.21 1 -0.51 1 2
PIK3CA 0.021 0.013 -10000 0 -10000 0 0
PI3K 0.023 0.064 0.22 1 -0.52 1 2
FYN 0.025 0.074 0.23 7 -0.53 1 8
mol:Ca2+ 0.012 0.045 -10000 0 -0.43 1 1
JUP 0.027 0.034 -10000 0 -0.46 2 2
PIK3R1 0.026 0.042 -10000 0 -0.46 3 3
mol:DAG 0.012 0.045 -10000 0 -0.44 1 1
CDH1 0.023 0.048 -10000 0 -0.46 4 4
RhoA/GDP 0.061 0.078 0.24 4 -0.37 2 6
establishment of polarity of embryonic epithelium 0.018 0.077 -10000 0 -0.33 9 9
SRC 0.027 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.01 -10000 0 -10000 0 0
EGFR 0.022 0.035 -10000 0 -0.47 2 2
CASR 0.025 0.064 0.22 5 -0.41 1 6
RhoA/GTP 0.046 0.065 -10000 0 -0.38 1 1
AKT2 0.011 0.052 0.19 1 -0.49 1 2
actin cable formation 0.004 0.094 0.25 1 -0.39 7 8
apoptosis -0.039 0.08 0.35 3 -0.24 7 10
CTNNA1 0.03 0.008 -10000 0 -10000 0 0
mol:GDP 0.035 0.076 -10000 0 -0.4 2 2
PIP5K1A 0.016 0.08 -10000 0 -0.33 9 9
PLCG1 0.012 0.046 -10000 0 -0.46 1 1
Rac1/GTP 0.032 0.085 -10000 0 -0.41 4 4
homophilic cell adhesion 0.002 0.004 -10000 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.026 0.028 -10000 0 -0.22 1 1
BIRC5 0.009 0.088 -10000 0 -0.39 19 19
NFKBIA 0.013 0.042 0.25 11 -10000 0 11
CPEB1 -0.039 0.16 -10000 0 -0.45 56 56
AKT1 0.013 0.042 0.25 11 -10000 0 11
NDEL1 0.027 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 0.024 0.023 -10000 0 -10000 0 0
NDEL1/TACC3 0.046 0.034 -10000 0 -10000 0 0
GADD45A 0.027 0.021 -10000 0 -0.39 1 1
GSK3B 0.024 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.026 0.025 -10000 0 -10000 0 0
MDM2 0.027 0.006 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.014 0.004 -10000 0 -10000 0 0
TP53 0.018 0.026 -10000 0 -0.29 2 2
DLG7 0.008 0.015 -10000 0 -10000 0 0
AURKAIP1 0.026 0.021 -10000 0 -0.39 1 1
ARHGEF7 0.027 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.049 0.035 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.024 0.023 -10000 0 -10000 0 0
AURKA 0.015 0.02 -10000 0 -10000 0 0
AURKB 0.012 0.016 -10000 0 -0.15 2 2
CDC25B 0.01 0.03 -10000 0 -0.24 1 1
G2/M transition checkpoint 0.008 0.017 -10000 0 -10000 0 0
mRNA polyadenylation -0.009 0.089 -10000 0 -0.25 47 47
Aurora A/CPEB -0.009 0.09 -10000 0 -0.25 47 47
Aurora A/TACC1/TRAP/chTOG 0.057 0.041 -10000 0 -10000 0 0
BRCA1 0.028 0.003 -10000 0 -10000 0 0
centrosome duplication 0.026 0.025 -10000 0 -10000 0 0
regulation of centrosome cycle 0.045 0.033 -10000 0 -10000 0 0
spindle assembly 0.055 0.041 -10000 0 -10000 0 0
TDRD7 0.028 0.005 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.05 0.062 -10000 0 -0.28 3 3
CENPA 0.015 0.022 -10000 0 -0.19 3 3
Aurora A/PP2A 0.026 0.025 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.013 0.024 -10000 0 -10000 0 0
negative regulation of DNA binding 0.017 0.029 -10000 0 -0.29 2 2
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.04 0.009 -10000 0 -10000 0 0
RASA1 0.026 0.025 -10000 0 -0.47 1 1
Ajuba/Aurora A 0.008 0.017 -10000 0 -10000 0 0
mitotic prometaphase 0 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.02 -10000 0 -10000 0 0
TACC1 0.024 0.026 -10000 0 -0.47 1 1
TACC3 0.025 0.022 -10000 0 -0.39 1 1
Aurora A/Antizyme1 0.051 0.033 -10000 0 -10000 0 0
Aurora A/RasGAP 0.025 0.029 -10000 0 -0.27 1 1
OAZ1 0.027 0.005 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.026 0.004 -10000 0 -10000 0 0
GIT1 0.028 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.02 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.014 0.004 -10000 0 -10000 0 0
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
Aurora A/TPX2 0.018 0.018 -10000 0 -10000 0 0
PAK1 0.026 0.009 -10000 0 -10000 0 0
CKAP5 0.027 0.005 -10000 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.016 0.044 -10000 0 -0.41 4 4
positive regulation of NF-kappaB transcription factor activity 0.019 0.055 -10000 0 -0.28 12 12
MAP2K4 0.044 0.05 0.2 2 -10000 0 2
IKBKB 0.026 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.026 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.025 0.025 -10000 0 -0.47 1 1
SMPD1 0.009 0.016 -10000 0 -0.18 1 1
IKBKG 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.012 0.078 -10000 0 -0.4 14 14
TRAIL/TRAILR2 0.025 0.037 -10000 0 -0.29 4 4
TRAIL/TRAILR3 0.02 0.051 -10000 0 -0.28 10 10
TRAIL/TRAILR1 0.025 0.037 -10000 0 -0.29 4 4
TRAIL/TRAILR4 0.019 0.055 -10000 0 -0.28 12 12
TRAIL/TRAILR1/DAP3/GTP 0.033 0.036 -10000 0 -0.22 4 4
IKK complex 0.022 0.034 -10000 0 -10000 0 0
RIPK1 0.027 0.006 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.02 0.003 -10000 0 -10000 0 0
MAPK3 0.008 0.03 -10000 0 -0.29 4 4
MAP3K1 0.032 0.048 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.012 0.078 -10000 0 -0.4 14 14
TRADD 0.027 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.025 0.025 -10000 0 -0.47 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.022 0.037 -10000 0 -0.22 1 1
CFLAR 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.008 0.03 -10000 0 -0.29 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP 0.037 0.049 -10000 0 -0.25 1 1
mol:ceramide 0.009 0.016 -10000 0 -0.18 1 1
FADD 0.02 0.013 -10000 0 -10000 0 0
MAPK8 0.053 0.062 0.23 3 -10000 0 3
TRAF2 0.024 0.036 -10000 0 -0.39 3 3
TRAILR3 (trimer) 0.014 0.071 -10000 0 -0.4 12 12
CHUK 0.028 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.026 0.039 -10000 0 -0.25 4 4
DAP3 0.028 0.005 -10000 0 -10000 0 0
CASP10 0.069 0.098 0.34 22 -0.3 1 23
JNK cascade 0.019 0.055 -10000 0 -0.28 12 12
TRAIL (trimer) 0.016 0.044 -10000 0 -0.41 4 4
TNFRSF10C 0.014 0.071 -10000 0 -0.4 12 12
TRAIL/TRAILR1/DAP3/GTP/FADD 0.031 0.041 -10000 0 -0.21 4 4
TRAIL/TRAILR2/FADD 0.026 0.039 -10000 0 -0.25 4 4
cell death 0.009 0.016 -10000 0 -0.18 1 1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.022 0.037 -10000 0 -0.22 1 1
TRAILR2 (trimer) 0.026 0.008 -10000 0 -10000 0 0
CASP8 0.005 0.069 -10000 0 -0.5 6 6
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.037 0.049 -10000 0 -0.25 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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 0.026 0.008 -10000 0 -10000 0 0
NFATC1 0.028 0.092 0.24 4 -0.36 6 10
NFATC2 0.009 0.083 0.2 4 -0.3 15 19
NFATC3 0.02 0.02 -10000 0 -0.35 1 1
YWHAE 0.027 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.001 0.076 0.21 4 -0.3 7 11
Exportin 1/Ran/NUP214 0.054 0.014 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.014 0.088 -10000 0 -0.3 6 6
BCL2/BAX 0.034 0.035 -10000 0 -0.29 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.02 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.02 0.008 -10000 0 -10000 0 0
BAX 0.028 0.004 -10000 0 -10000 0 0
MAPK14 0.027 0.006 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.011 0.078 0.23 2 -0.29 6 8
Calcineurin A alpha-beta B1/BCL2 0.021 0.043 -10000 0 -0.41 4 4
FKBP8 0.028 0.003 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.011 0.077 0.29 6 -0.23 2 8
KPNB1 0.028 0.002 -10000 0 -10000 0 0
KPNA2 0.028 0.004 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
SFN 0.023 0.045 -10000 0 -0.43 4 4
MAP3K8 0.025 0.034 -10000 0 -0.47 2 2
NFAT4/CK1 alpha 0.03 0.022 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 0.046 0.1 0.26 1 -0.39 7 8
CABIN1 0 0.076 0.21 4 -0.3 7 11
CALM1 0.026 0.008 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
MAP3K1 0.027 0.007 -10000 0 -10000 0 0
CAMK4 0.003 0.098 -10000 0 -0.4 23 23
mol:Ca2+ 0 0.002 -10000 0 -10000 0 0
MAPK3 0.028 0.004 -10000 0 -10000 0 0
YWHAH 0.028 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.024 0.066 -10000 0 -0.28 19 19
YWHAB 0.027 0.007 -10000 0 -10000 0 0
MAPK8 0.021 0.059 -10000 0 -0.47 6 6
MAPK9 0.026 0.007 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
FKBP1A 0.027 0.007 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.037 0.099 0.26 2 -0.38 5 7
PRKCH 0.026 0.008 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.038 0.028 -10000 0 -0.32 2 2
CASP3 0.027 0.007 -10000 0 -10000 0 0
PIM1 0.027 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.006 -10000 0 -10000 0 0
apoptosis 0.018 0.013 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.028 0.042 -10000 0 -0.28 2 2
PRKCB 0.019 0.06 -10000 0 -0.41 8 8
PRKCE 0.028 0.003 -10000 0 -10000 0 0
JNK2/NFAT4 0.03 0.04 -10000 0 -0.32 1 1
BAD/BCL-XL 0.037 0.013 -10000 0 -10000 0 0
PRKCD 0.024 0.01 -10000 0 -10000 0 0
NUP214 0.028 0.005 -10000 0 -10000 0 0
PRKCZ 0.026 0.025 -10000 0 -0.47 1 1
PRKCA 0.027 0.021 -10000 0 -0.39 1 1
PRKCG -0.029 0.13 -10000 0 -0.39 44 44
PRKCQ 0.02 0.061 -10000 0 -0.45 7 7
FKBP38/BCL2 0.034 0.034 -10000 0 -0.28 4 4
EP300 0.025 0.035 -10000 0 -0.47 2 2
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.007 -10000 0 -10000 0 0
NFATc/JNK1 0.038 0.095 0.25 2 -0.34 6 8
CaM/Ca2+/FKBP38 0.035 0.013 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.014 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.019 0.062 -10000 0 -0.23 22 22
NFATc/ERK1 0.039 0.093 0.25 2 -0.36 3 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.014 0.088 -10000 0 -0.3 6 6
NR4A1 0.018 0.11 0.26 3 -0.48 12 15
GSK3B 0.025 0.009 -10000 0 -10000 0 0
positive T cell selection 0.02 0.02 -10000 0 -0.35 1 1
NFAT1/CK1 alpha 0.01 0.058 -10000 0 -0.27 8 8
RCH1/ KPNB1 0.041 0.006 -10000 0 -10000 0 0
YWHAQ 0.028 0.003 -10000 0 -10000 0 0
PRKACA 0.028 0.004 -10000 0 -10000 0 0
AKAP5 0.007 0.088 -10000 0 -0.39 19 19
MEF2D 0.027 0.008 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
NFATc/p38 alpha 0.039 0.091 0.25 2 -0.36 3 5
CREBBP 0.027 0.008 -10000 0 -10000 0 0
BCL2 0.021 0.043 -10000 0 -0.41 4 4
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.048 0.067 -10000 0 -0.3 3 3
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.032 0.068 -10000 0 -0.28 3 3
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.027 0.006 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.016 0.005 -10000 0 -10000 0 0
FKBP3 0.027 0.007 -10000 0 -10000 0 0
Histones 0.054 0.06 -10000 0 -10000 0 0
YY1/LSF 0.007 0.081 -10000 0 -0.26 18 18
SMG5 0.028 0.005 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.017 0.038 -10000 0 -0.23 3 3
I kappa B alpha/HDAC1 0.026 0.053 -10000 0 -10000 0 0
SAP18 0.027 0.007 -10000 0 -10000 0 0
RELA 0.023 0.049 0.28 1 -0.28 3 4
HDAC1/Smad7 0.048 0.022 -10000 0 -10000 0 0
RANGAP1 0.028 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.029 0.052 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.036 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.033 0.066 0.25 2 -0.3 3 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.022 0.039 -10000 0 -0.42 3 3
GATA1 0.018 0.027 -10000 0 -0.39 1 1
Mad/Max 0.036 0.034 -10000 0 -0.34 3 3
NuRD/MBD3 Complex/GATA1/Fog1 0.033 0.049 -10000 0 -0.3 1 1
RBBP7 0.028 0.005 -10000 0 -10000 0 0
NPC 0.017 0.002 -10000 0 -10000 0 0
RBBP4 0.025 0.034 -10000 0 -0.47 2 2
MAX 0.026 0.007 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.027 0.007 -10000 0 -10000 0 0
NFKBIA 0.015 0.031 -10000 0 -10000 0 0
KAT2B 0.01 0.083 -10000 0 -0.47 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.027 0.017 -10000 0 -10000 0 0
SIN3 complex 0.065 0.023 -10000 0 -10000 0 0
SMURF1 0.026 0.008 -10000 0 -10000 0 0
CHD3 0.027 0.006 -10000 0 -10000 0 0
SAP30 0.027 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.027 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.006 0.075 -10000 0 -0.36 6 6
YY1/HDAC2 0.008 0.081 -10000 0 -0.26 18 18
YY1/HDAC1 0.008 0.081 -10000 0 -0.26 18 18
NuRD/MBD2 Complex (MeCP1) 0.033 0.029 -10000 0 -10000 0 0
PPARG -0.079 0.15 -10000 0 -0.28 132 132
HDAC8/hEST1B 0.055 0.013 -10000 0 -10000 0 0
UBE2I 0.028 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.029 0.051 -10000 0 -10000 0 0
MBD3L2 -0.018 0.028 -10000 0 -0.39 2 2
ubiquitin-dependent protein catabolic process 0.047 0.022 -10000 0 -10000 0 0
CREBBP 0.028 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.031 0.046 -10000 0 -0.29 2 2
HDAC1 0.028 0.005 -10000 0 -10000 0 0
HDAC3 0.016 0.031 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
YY1 0.011 0.049 -10000 0 -0.28 11 11
HDAC8 0.028 0.003 -10000 0 -10000 0 0
SMAD7 0.026 0.008 -10000 0 -10000 0 0
NCOR2 0.028 0.003 -10000 0 -10000 0 0
MXD1 0.023 0.048 -10000 0 -0.47 4 4
STAT3 0.021 0.028 -10000 0 -0.37 2 2
NFKB1 0.028 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.028 0.003 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.022 0.081 -10000 0 -0.31 7 7
YY1/SAP30/HDAC1 0.023 0.079 -10000 0 -0.3 7 7
EP300 0.025 0.034 -10000 0 -0.47 2 2
STAT3 (dimer non-phopshorylated) 0.021 0.028 -10000 0 -0.37 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.031 -10000 0 -10000 0 0
histone deacetylation 0.029 0.036 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.024 0.04 -10000 0 -0.33 1 1
nuclear export -0.054 0.012 -10000 0 -10000 0 0
PRKACA 0.028 0.003 -10000 0 -10000 0 0
GATAD2B 0.028 0.004 -10000 0 -10000 0 0
GATAD2A 0.028 0.003 -10000 0 -10000 0 0
GATA2/HDAC3 0.024 0.053 -10000 0 -0.27 2 2
GATA1/HDAC1 0.038 0.018 -10000 0 -0.28 1 1
GATA1/HDAC3 0.028 0.051 -10000 0 -10000 0 0
CHD4 0.027 0.007 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.023 0.069 -10000 0 -0.29 19 19
SIN3/HDAC complex/Mad/Max 0.031 0.039 -10000 0 -0.3 2 2
NuRD Complex 0.03 0.052 -10000 0 -0.31 3 3
positive regulation of chromatin silencing 0.051 0.059 -10000 0 -10000 0 0
SIN3B 0.028 0.003 -10000 0 -10000 0 0
MTA2 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.028 0.005 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
SUMO1/HDAC1 0.041 0.031 -10000 0 -0.22 1 1
HDAC complex 0.066 0.026 -10000 0 -0.26 1 1
GATA1/Fog1 0.037 0.019 -10000 0 -0.28 1 1
FKBP25/HDAC1/HDAC2 0.052 0.017 -10000 0 -10000 0 0
TNF 0.007 0.09 -10000 0 -0.4 19 19
negative regulation of cell growth 0.028 0.043 -10000 0 -0.3 2 2
NuRD/MBD2/PRMT5 Complex 0.033 0.029 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.043 0.032 -10000 0 -0.23 1 1
NF kappa B/RelA/I kappa B alpha 0.018 0.051 -10000 0 -0.28 4 4
SIN3/HDAC complex/NCoR1 0.025 0.043 -10000 0 -0.45 1 1
TFCP2 0.028 0.003 -10000 0 -10000 0 0
NR2C1 0.028 0.003 -10000 0 -10000 0 0
MBD3 0.027 0.005 -10000 0 -10000 0 0
MBD2 0.026 0.008 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.006 0.046 -10000 0 -10000 0 0
PLK1 0.04 0.12 -10000 0 -0.83 2 2
CDKN1B 0.078 0.099 0.3 5 -0.37 4 9
FOXO3 0.057 0.11 -10000 0 -0.67 4 4
KAT2B 0.017 0.085 -10000 0 -0.47 12 12
FOXO1/SIRT1 0.027 0.044 -10000 0 -10000 0 0
CAT 0.045 0.13 -10000 0 -0.92 3 3
CTNNB1 0.024 0.01 -10000 0 -10000 0 0
AKT1 0.034 0.017 -10000 0 -10000 0 0
FOXO1 0.014 0.047 0.24 1 -10000 0 1
MAPK10 0.026 0.072 0.2 26 -0.23 19 45
mol:GTP 0.002 0 -10000 0 -10000 0 0
FOXO4 0.054 0.07 0.3 5 -0.4 1 6
response to oxidative stress 0.01 0.009 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.054 0.12 -10000 0 -0.78 3 3
XPO1 0.028 0.004 -10000 0 -10000 0 0
EP300 0.026 0.035 -10000 0 -0.47 2 2
BCL2L11 0.034 0.042 -10000 0 -0.66 1 1
FOXO1/SKP2 0.024 0.043 -10000 0 -10000 0 0
mol:GDP 0.01 0.009 -10000 0 -10000 0 0
RAN 0.029 0.003 -10000 0 -10000 0 0
GADD45A 0.063 0.12 -10000 0 -0.57 9 9
YWHAQ 0.028 0.003 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.037 0.1 -10000 0 -0.42 12 12
MST1 0.026 0.046 -10000 0 -0.41 4 4
CSNK1D 0.028 0.004 -10000 0 -10000 0 0
CSNK1E 0.028 0.005 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.032 0.082 0.23 1 -0.37 8 9
YWHAB 0.027 0.007 -10000 0 -10000 0 0
MAPK8 0.035 0.053 0.2 26 -0.23 5 31
MAPK9 0.036 0.044 0.2 25 -10000 0 25
YWHAG 0.027 0.006 -10000 0 -10000 0 0
YWHAE 0.027 0.006 -10000 0 -10000 0 0
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
SIRT1 0.026 0.026 -10000 0 -0.46 1 1
SOD2 0.069 0.094 -10000 0 -0.54 1 1
RBL2 0.04 0.17 -10000 0 -0.69 15 15
RAL/GDP 0.045 0.015 -10000 0 -10000 0 0
CHUK 0.034 0.015 -10000 0 -10000 0 0
Ran/GTP 0.024 0.003 -10000 0 -10000 0 0
CSNK1G2 0.027 0.005 -10000 0 -10000 0 0
RAL/GTP 0.049 0.015 -10000 0 -10000 0 0
CSNK1G1 0.028 0.005 -10000 0 -10000 0 0
FASLG -0.013 0.22 -10000 0 -1.3 10 10
SKP2 0.025 0.009 -10000 0 -10000 0 0
USP7 0.029 0.004 -10000 0 -10000 0 0
IKBKB 0.032 0.016 -10000 0 -10000 0 0
CCNB1 0.043 0.11 -10000 0 -0.76 2 2
FOXO1-3a-4/beta catenin 0.084 0.094 0.31 5 -10000 0 5
proteasomal ubiquitin-dependent protein catabolic process 0.024 0.042 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
SGK1 0.033 0.028 -10000 0 -0.46 1 1
CSNK1G3 0.027 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.042 0.008 -10000 0 -10000 0 0
ZFAND5 0.052 0.069 0.39 2 -10000 0 2
SFN 0.023 0.045 -10000 0 -0.43 4 4
CDK2 0.028 0.006 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.035 0.086 -10000 0 -0.35 9 9
CREBBP 0.028 0.007 -10000 0 -10000 0 0
FBXO32 0.068 0.17 0.45 2 -1.2 3 5
BCL6 0.054 0.095 -10000 0 -10000 0 0
RALB 0.029 0.004 -10000 0 -10000 0 0
RALA 0.028 0.007 -10000 0 -10000 0 0
YWHAH 0.028 0.004 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.006 0.086 -10000 0 -0.39 5 5
KLHL20 0.025 0.07 0.18 7 -0.32 2 9
CYFIP2 0.025 0.032 -10000 0 -0.43 2 2
Rac1/GDP 0.023 0.078 0.32 5 -0.35 1 6
ENAH -0.008 0.1 -10000 0 -0.4 7 7
AP1M1 0.028 0.003 -10000 0 -10000 0 0
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.024 0.01 -10000 0 -10000 0 0
CDC42/GTP 0.021 0.036 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.011 0.031 -10000 0 -0.19 3 3
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.057 0.042 -10000 0 -0.26 4 4
RAPGEF1 -0.001 0.099 0.27 3 -0.42 3 6
CTNND1 0.028 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.003 0.11 -10000 0 -0.36 15 15
CRK 0.003 0.096 -10000 0 -0.42 4 4
E-cadherin/gamma catenin/alpha catenin 0.048 0.046 -10000 0 -0.33 5 5
alphaE/beta7 Integrin 0.038 0.028 -10000 0 -0.34 2 2
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
NCKAP1 0.028 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.049 0.017 -10000 0 -10000 0 0
DLG1 0.001 0.08 -10000 0 -0.39 5 5
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.002 0.018 -10000 0 -10000 0 0
MLLT4 0.028 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.045 0.037 -10000 0 -0.25 5 5
PI3K 0.006 0.024 -10000 0 -10000 0 0
ARF6 0.027 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.034 0.049 -10000 0 -0.39 5 5
TIAM1 0.022 0.054 -10000 0 -0.47 5 5
E-cadherin(dimer)/Ca2+ 0.053 0.036 -10000 0 -0.24 2 2
AKT1 0.012 0.029 0.14 1 -10000 0 1
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
CDH1 0.022 0.048 -10000 0 -0.47 4 4
RhoA/GDP 0.032 0.074 0.31 7 -0.32 1 8
actin cytoskeleton organization 0.021 0.055 0.14 14 -0.22 2 16
CDC42/GDP 0.027 0.081 0.31 7 -0.32 1 8
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.017 0.036 -10000 0 -0.31 4 4
ITGB7 0.026 0.034 -10000 0 -0.47 2 2
RAC1 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.058 0.039 -10000 0 -0.26 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.04 0.033 -10000 0 -0.23 4 4
mol:GDP 0.012 0.087 0.32 7 -0.4 1 8
CDC42/GTP/IQGAP1 0.037 0.008 -10000 0 -10000 0 0
JUP 0.026 0.034 -10000 0 -0.47 2 2
p120 catenin/RhoA/GDP 0.033 0.077 0.31 5 -0.31 1 6
RAC1/GTP/IQGAP1 0.035 0.011 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.041 0.008 -10000 0 -10000 0 0
RHOA 0.024 0.01 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.011 0.04 0.18 4 -0.18 4 8
NME1 0.027 0.021 -10000 0 -0.39 1 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.006 0.1 -10000 0 -0.41 6 6
regulation of cell-cell adhesion 0.013 0.029 -10000 0 -10000 0 0
WASF2 0.013 0.028 -10000 0 -10000 0 0
Rap1/GTP 0.032 0.055 0.29 4 -0.3 1 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.07 0.052 -10000 0 -0.35 4 4
CCND1 0.012 0.046 0.25 2 -0.23 4 6
VAV2 0.015 0.12 -10000 0 -0.55 4 4
RAP1/GDP 0.036 0.067 0.31 5 -0.31 1 6
adherens junction assembly -0.005 0.098 -10000 0 -0.4 6 6
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.028 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.051 0.048 -10000 0 -0.44 2 2
E-cadherin/beta catenin 0.009 0.035 -10000 0 -0.34 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.008 0.1 -10000 0 -0.4 7 7
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
Rac1/GTP -0.021 0.074 -10000 0 -0.39 8 8
E-cadherin/beta catenin/alpha catenin 0.045 0.038 -10000 0 -0.27 4 4
ITGAE 0.027 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.11 -10000 0 -0.37 15 15
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.044 0.047 -9999 0 -0.33 5 5
E-cadherin/beta catenin 0.032 0.038 -9999 0 -0.32 4 4
CTNNB1 0.024 0.01 -9999 0 -10000 0 0
JUP 0.026 0.034 -9999 0 -0.47 2 2
CDH1 0.022 0.048 -9999 0 -0.47 4 4
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.025 0.009 -10000 0 -10000 0 0
SMAD2 0.004 0.051 0.25 2 -0.26 3 5
SMAD3 0.026 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4 0.028 0.083 -10000 0 -0.45 11 11
SMAD4/Ubc9/PIASy 0.05 0.021 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.046 0.06 -10000 0 -10000 0 0
PPM1A 0.026 0.007 -10000 0 -10000 0 0
CALM1 0.026 0.008 -10000 0 -10000 0 0
SMAD2/SMAD4 0.015 0.05 0.24 1 -0.24 3 4
MAP3K1 0.027 0.007 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.026 0.066 -10000 0 -0.34 13 13
MAPK3 0.028 0.004 -10000 0 -10000 0 0
MAPK1 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.027 0.005 -10000 0 -10000 0 0
CTDSP1 0.027 0.006 -10000 0 -10000 0 0
CTDSP2 0.028 0.004 -10000 0 -10000 0 0
CTDSPL 0.024 0.01 -10000 0 -10000 0 0
KPNB1 0.028 0.002 -10000 0 -10000 0 0
TGFBRAP1 0.013 0.086 -10000 0 -0.47 13 13
UBE2I 0.028 0.004 -10000 0 -10000 0 0
NUP153 0.027 0.006 -10000 0 -10000 0 0
KPNA2 0.028 0.004 -10000 0 -10000 0 0
PIAS4 0.028 0.005 -10000 0 -10000 0 0
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 0.029 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.059 0.082 0.26 12 -0.36 2 14
ERC1 0.026 0.007 -10000 0 -10000 0 0
RIP2/NOD2 0.033 0.032 -10000 0 -0.3 3 3
NFKBIA 0.021 0.035 -10000 0 -10000 0 0
BIRC2 0.024 0.01 -10000 0 -10000 0 0
IKBKB 0.026 0.008 -10000 0 -10000 0 0
RIPK2 0.025 0.009 -10000 0 -10000 0 0
IKBKG 0.035 0.036 -10000 0 -10000 0 0
IKK complex/A20 0.049 0.095 -10000 0 -0.41 7 7
NEMO/A20/RIP2 0.025 0.009 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
NEMO/ATM 0.041 0.087 0.26 1 -0.4 8 9
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.037 0.007 -10000 0 -10000 0 0
IKK complex/ELKS 0.046 0.079 -10000 0 -0.39 7 7
BCL10/MALT1/TRAF6 0.049 0.02 -10000 0 -10000 0 0
NOD2 0.024 0.038 -10000 0 -0.42 3 3
NFKB1 0.03 0.005 -10000 0 -10000 0 0
RELA 0.029 0.006 -10000 0 -10000 0 0
MALT1 0.025 0.009 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.035 0.016 -10000 0 -10000 0 0
ATM 0.025 0.009 -10000 0 -10000 0 0
TNF/TNFR1A 0.023 0.069 -10000 0 -0.29 19 19
TRAF6 0.027 0.006 -10000 0 -10000 0 0
PRKCA 0.027 0.021 -10000 0 -0.39 1 1
CHUK 0.028 0.004 -10000 0 -10000 0 0
UBE2D3 0.028 0.005 -10000 0 -10000 0 0
TNF 0.007 0.09 -10000 0 -0.4 19 19
NF kappa B1 p50/RelA 0.059 0.021 -10000 0 -10000 0 0
BCL10 0.028 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.035 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.007 -10000 0 -10000 0 0
IKK complex 0.054 0.092 0.27 1 -0.41 8 9
CYLD 0.027 0.007 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.062 0.092 0.27 1 -0.4 7 8
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.028 0.005 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.044 0.045 -9999 0 -0.24 8 8
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.012 0.012 -9999 0 -10000 0 0
AURKB 0.022 0.046 -9999 0 -0.39 5 5
AURKC 0.022 0.049 -9999 0 -0.42 5 5
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 -0.049 0.14 0.27 4 -0.37 17 21
CaM/Ca2+ 0.019 0.006 -10000 0 -10000 0 0
AKT1 0.026 0.008 -10000 0 -10000 0 0
AKT2 0.027 0.005 -10000 0 -10000 0 0
STXBP4 0.028 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.061 0.14 0.31 5 -0.38 22 27
YWHAZ 0.024 0.01 -10000 0 -10000 0 0
CALM1 0.026 0.008 -10000 0 -10000 0 0
YWHAQ 0.028 0.003 -10000 0 -10000 0 0
TBC1D4 0.013 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.028 0.004 -10000 0 -10000 0 0
YWHAB 0.027 0.007 -10000 0 -10000 0 0
SNARE/Synip 0.054 0.014 -10000 0 -10000 0 0
YWHAG 0.027 0.006 -10000 0 -10000 0 0
ASIP 0 0.068 -10000 0 -0.39 11 11
PRKCI 0.02 0.013 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.019 0.006 -10000 0 -10000 0 0
RHOQ 0.028 0.004 -10000 0 -10000 0 0
GYS1 0.012 0.013 0.25 1 -10000 0 1
PRKCZ 0.026 0.025 -10000 0 -0.47 1 1
TRIP10 0.028 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.037 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.03 0.042 -10000 0 -0.31 1 1
VAMP2 0.027 0.006 -10000 0 -10000 0 0
SLC2A4 -0.068 0.16 0.32 5 -0.42 22 27
STX4 0.028 0.004 -10000 0 -10000 0 0
GSK3B 0.019 0.009 -10000 0 -10000 0 0
SFN 0.023 0.045 -10000 0 -0.43 4 4
LNPEP 0.026 0.025 -10000 0 -0.47 1 1
YWHAE 0.027 0.006 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.023 0.061 0.26 5 -10000 0 5
GNAI2 0.024 0.01 -10000 0 -10000 0 0
S1P/S1P5/G12 0.033 0.023 -10000 0 -0.26 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.023 0.043 -10000 0 -0.41 4 4
RhoA/GTP 0.023 0.063 -10000 0 -0.27 5 5
negative regulation of cAMP metabolic process 0.02 0.051 -10000 0 -0.29 5 5
GNAZ 0.011 0.083 -10000 0 -0.42 15 15
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.025 0.022 -10000 0 -0.39 1 1
S1PR5 0.027 0.024 -10000 0 -0.47 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.02 0.051 -10000 0 -0.29 5 5
RhoA/GDP 0.018 0.007 -10000 0 -10000 0 0
RHOA 0.024 0.01 -10000 0 -10000 0 0
GNAI1 0.026 0.025 -10000 0 -0.47 1 1
Paxillin-dependent events mediated by a4b1

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
CRKL 0.027 0.021 -9999 0 -0.39 1 1
Rac1/GDP 0.025 0.011 -9999 0 -10000 0 0
DOCK1 0.027 0.024 -9999 0 -0.47 1 1
ITGA4 0.02 0.058 -9999 0 -0.39 8 8
RAC1 0.026 0.007 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.033 0.051 -9999 0 -0.29 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.027 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.042 -9999 0 -0.23 8 8
alpha4/beta7 Integrin/Paxillin 0.039 0.043 -9999 0 -0.26 2 2
lamellipodium assembly 0.012 0.065 -9999 0 -0.38 5 5
PIK3CA 0.02 0.013 -9999 0 -10000 0 0
PI3K 0.027 0.032 -9999 0 -0.34 2 2
ARF6 0.027 0.007 -9999 0 -10000 0 0
TLN1 0.024 0.01 -9999 0 -10000 0 0
PXN 0.015 0.002 -9999 0 -10000 0 0
PIK3R1 0.023 0.042 -9999 0 -0.47 3 3
ARF6/GTP 0.049 0.039 -9999 0 -10000 0 0
cell adhesion 0.046 0.039 -9999 0 -10000 0 0
CRKL/CBL 0.036 0.021 -9999 0 -0.28 1 1
alpha4/beta1 Integrin/Paxillin 0.04 0.038 -9999 0 -10000 0 0
ITGB1 0.028 0.005 -9999 0 -10000 0 0
ITGB7 0.026 0.034 -9999 0 -0.47 2 2
ARF6/GDP 0.025 0.011 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.028 0.088 -9999 0 -0.28 9 9
p130Cas/Crk/Dock1 0.052 0.023 -9999 0 -0.29 1 1
VCAM1 -0.015 0.13 -9999 0 -0.41 41 41
alpha4/beta1 Integrin/Paxillin/Talin 0.048 0.04 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.054 0.04 -9999 0 -10000 0 0
BCAR1 0.027 0.006 -9999 0 -10000 0 0
mol:GDP -0.052 0.039 -9999 0 -10000 0 0
CBL 0.026 0.008 -9999 0 -10000 0 0
PRKACA 0.028 0.003 -9999 0 -10000 0 0
GIT1 0.028 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.048 0.04 -9999 0 -10000 0 0
Rac1/GTP 0.011 0.07 -9999 0 -0.42 5 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.06 0.028 -9999 0 -10000 0 0
HDAC3 0.027 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.038 0.018 -9999 0 -0.28 1 1
GATA1/HDAC5 0.039 0.017 -9999 0 -0.28 1 1
GATA2/HDAC5 0.034 0.031 -9999 0 -0.3 3 3
HDAC5/BCL6/BCoR 0.041 0.026 -9999 0 -10000 0 0
HDAC9 0 0.1 -9999 0 -0.39 26 26
Glucocorticoid receptor/Hsp90/HDAC6 0.05 0.02 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.038 0.012 -9999 0 -10000 0 0
HDAC5/YWHAB 0.039 0.011 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.016 0.005 -9999 0 -10000 0 0
GATA2 0.022 0.039 -9999 0 -0.42 3 3
HDAC4/RFXANK 0.039 0.018 -9999 0 -0.28 1 1
BCOR 0.028 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.027 0.005 -9999 0 -10000 0 0
HDAC5 0.028 0.003 -9999 0 -10000 0 0
GNB1/GNG2 0.039 0.012 -9999 0 -10000 0 0
Histones 0.024 0.042 -9999 0 -10000 0 0
ADRBK1 0.026 0.008 -9999 0 -10000 0 0
HDAC4 0.027 0.006 -9999 0 -10000 0 0
XPO1 0.028 0.004 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.039 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.04 0.01 -9999 0 -10000 0 0
HDAC7 0.028 0.003 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.04 0.009 -9999 0 -10000 0 0
TUBA1B 0.028 0.003 -9999 0 -10000 0 0
HDAC6 0.028 0.004 -9999 0 -10000 0 0
HDAC5/RFXANK 0.041 0.017 -9999 0 -0.28 1 1
CAMK4 0.003 0.098 -9999 0 -0.4 23 23
Tubulin/HDAC6 0.053 0.016 -9999 0 -10000 0 0
SUMO1 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.027 0.007 -9999 0 -10000 0 0
GATA1 0.018 0.027 -9999 0 -0.39 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.027 0.006 -9999 0 -10000 0 0
NR3C1 0.027 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.042 0.029 -9999 0 -0.2 1 1
SRF 0.027 0.006 -9999 0 -10000 0 0
HDAC4/YWHAB 0.038 0.012 -9999 0 -10000 0 0
Tubulin 0.039 0.011 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0.039 0.011 -9999 0 -10000 0 0
GNB1 0.027 0.006 -9999 0 -10000 0 0
RANGAP1 0.028 0.004 -9999 0 -10000 0 0
BCL6/BCoR 0.03 0.019 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.052 0.017 -9999 0 -10000 0 0
HDAC4/SRF 0.035 0.067 -9999 0 -0.24 22 22
HDAC4/ER alpha 0.023 0.074 -9999 0 -0.29 22 22
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.024 0.042 -9999 0 -10000 0 0
cell motility 0.052 0.016 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.028 0.004 -9999 0 -10000 0 0
HDAC7/HDAC3 0.04 0.01 -9999 0 -10000 0 0
BCL6 0.02 0.013 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.027 0.006 -9999 0 -10000 0 0
Hsp90/HDAC6 0.038 0.013 -9999 0 -10000 0 0
ESR1 0.005 0.098 -9999 0 -0.41 22 22
HDAC6/HDAC11 0.035 0.024 -9999 0 -0.34 1 1
Ran/GTP/Exportin 1 0.043 0.032 -9999 0 -0.23 1 1
NPC 0.017 0.002 -9999 0 -10000 0 0
MEF2C 0.019 0.057 -9999 0 -0.41 7 7
RAN 0.028 0.003 -9999 0 -10000 0 0
HDAC4/MEF2C 0.07 0.046 -9999 0 -0.25 2 2
GNG2 0.027 0.007 -9999 0 -10000 0 0
NCOR2 0.028 0.003 -9999 0 -10000 0 0
TUBB2A 0.027 0.006 -9999 0 -10000 0 0
HDAC11 0.023 0.026 -9999 0 -0.47 1 1
HSP90AA1 0.026 0.008 -9999 0 -10000 0 0
RANBP2 0.028 0.003 -9999 0 -10000 0 0
ANKRA2 0.027 0.007 -9999 0 -10000 0 0
RFXANK 0.027 0.021 -9999 0 -0.39 1 1
nuclear import -0.034 0.013 -9999 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.01 0.078 -10000 0 -10000 0 0
regulation of axonogenesis -0.006 0.024 0.23 1 -10000 0 1
myoblast fusion -0.018 0.059 0.3 2 -10000 0 2
mol:GTP 0.013 0.038 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.04 0.058 0.26 5 -10000 0 5
ARF1/GTP 0.029 0.036 -10000 0 -10000 0 0
mol:GM1 0.005 0.028 -10000 0 -10000 0 0
mol:Choline 0.004 0.024 -10000 0 -0.29 1 1
lamellipodium assembly 0.001 0.062 -10000 0 -0.36 5 5
MAPK3 0.014 0.045 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.041 0.058 -10000 0 -0.26 5 5
ARF1 0.028 0.005 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.059 -10000 0 -0.3 2 2
ARF1/GDP 0.021 0.064 -10000 0 -0.28 2 2
ARF6 0.026 0.031 -10000 0 -10000 0 0
RAB11A 0.028 0.005 -10000 0 -10000 0 0
TIAM1 0.021 0.055 -10000 0 -0.46 5 5
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.014 0.044 -10000 0 -10000 0 0
actin filament bundle formation -0.018 0.061 0.28 2 -10000 0 2
KALRN -0.006 0.069 -10000 0 -0.26 21 21
RAB11FIP3/RAB11A 0.04 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.018 0.061 -10000 0 -0.28 2 2
NME1 0.026 0.023 -10000 0 -0.39 1 1
Rac1/GDP 0.02 0.062 -10000 0 -0.28 2 2
substrate adhesion-dependent cell spreading 0.013 0.038 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.001 0.062 -10000 0 -0.36 5 5
RAC1 0.026 0.007 -10000 0 -10000 0 0
liver development 0.013 0.038 -10000 0 -10000 0 0
ARF6/GTP 0.013 0.038 -10000 0 -10000 0 0
RhoA/GTP 0.025 0.035 -10000 0 -10000 0 0
mol:GDP 0.001 0.051 -10000 0 -0.3 2 2
ARF6/GTP/RAB11FIP3/RAB11A 0.043 0.039 -10000 0 -10000 0 0
RHOA 0.024 0.01 -10000 0 -10000 0 0
PLD1 0.008 0.032 -10000 0 -0.33 1 1
RAB11FIP3 0.028 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.001 0.062 -10000 0 -0.36 5 5
ruffle organization 0.006 0.024 -10000 0 -0.23 1 1
regulation of epithelial cell migration 0.013 0.038 -10000 0 -10000 0 0
PLD2 0.014 0.03 -10000 0 -10000 0 0
PIP5K1A 0.006 0.024 -10000 0 -0.23 1 1
mol:Phosphatidic acid 0.004 0.024 -10000 0 -0.29 1 1
Rac1/GTP 0.001 0.062 -10000 0 -0.36 5 5
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.038 0.021 -10000 0 -0.34 1 1
FBXW11 0.027 0.007 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.024 0.038 -10000 0 -0.28 6 6
NF kappa B1 p50/RelA/I kappa B alpha 0.035 0.049 0.26 2 -0.29 1 3
NFKBIA 0.016 0.033 -10000 0 -0.32 1 1
MAPK14 0.027 0.006 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.028 0.011 -10000 0 -10000 0 0
ARRB2 0.015 0.004 -10000 0 -10000 0 0
REL 0.021 0.059 -10000 0 -0.47 6 6
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.028 0.019 -10000 0 -0.29 1 1
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0.011 -10000 0 -10000 0 0
PIK3CA 0.02 0.013 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.021 0.007 -10000 0 -10000 0 0
PIK3R1 0.023 0.042 -10000 0 -0.47 3 3
NFKB1 0.014 0.005 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.019 0.031 -10000 0 -0.28 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.036 0.051 0.24 2 -0.27 2 4
SRC 0.027 0.007 -10000 0 -10000 0 0
PI3K 0.027 0.032 -10000 0 -0.34 2 2
NF kappa B1 p50/RelA 0.019 0.031 -10000 0 -0.28 1 1
IKBKB 0.026 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.007 -10000 0 -10000 0 0
SYK 0.025 0.034 -10000 0 -0.47 2 2
I kappa B alpha/PIK3R1 0.033 0.054 0.23 6 -0.26 3 9
cell death 0.034 0.048 0.26 1 -0.26 2 3
NF kappa B1 p105/c-Rel 0.024 0.038 -10000 0 -0.28 6 6
LCK 0.018 0.064 -10000 0 -0.39 10 10
BCL3 0.026 0.025 -10000 0 -0.47 1 1
PLK2 and PLK4 events

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
PLK2 0.026 0.025 -9999 0 -0.47 1 1
PLK4 0.027 0.005 -9999 0 -10000 0 0
regulation of centriole replication 0.013 0.018 -9999 0 -0.34 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.028 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.006 -10000 0 -10000 0 0
MDM2/SUMO1 0.039 0.033 -10000 0 -0.22 1 1
HDAC4 0.027 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.007 0.007 -10000 0 -10000 0 0
SUMO1 0.027 0.005 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.012 0.017 -10000 0 -0.25 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.011 0.009 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.028 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.028 0.003 -10000 0 -10000 0 0
SUMO1/HDAC4 0.042 0.029 -10000 0 -0.2 1 1
SUMO1/HDAC1 0.041 0.031 -10000 0 -0.22 1 1
RANGAP1 0.028 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.061 0.027 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.016 0.005 -10000 0 -10000 0 0
Ran/GTP 0.029 0.029 -10000 0 -0.23 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.027 0.006 -10000 0 -10000 0 0
UBE2I 0.028 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.039 0.21 9 -0.23 1 10
NPC 0.017 0.002 -10000 0 -10000 0 0
PIAS2 0.026 0.008 -10000 0 -10000 0 0
PIAS1 0.028 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -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 0.012 0.03 0.24 2 -10000 0 2
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.018 0.024 0.14 5 -10000 0 5
AP2 0.03 0.019 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.035 0.013 -10000 0 -10000 0 0
CLTB 0.027 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.018 0.009 -10000 0 -10000 0 0
CD4 0.024 0.032 -10000 0 -0.43 2 2
CLTA 0.025 0.01 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.008 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.009 -10000 0 -10000 0 0
ARF1/GTP 0.033 0.012 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.011 0.006 -10000 0 -10000 0 0
mol:Choline 0.007 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.028 0.006 -10000 0 -10000 0 0
DDEF1 0.006 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.006 0.012 -10000 0 -10000 0 0
AP2M1 0.02 0.013 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.013 0.006 -10000 0 -10000 0 0
Rac/GTP 0.02 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.038 0.014 -10000 0 -10000 0 0
ARFIP2 0.024 0.012 -10000 0 -10000 0 0
COPA 0.028 0.005 -10000 0 -10000 0 0
RAC1 0.026 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.013 0.044 -10000 0 -0.2 5 5
ARF1/GTP/ARHGAP10 0.019 0.006 -10000 0 -10000 0 0
GGA3 0.028 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.026 0.02 -10000 0 -0.22 2 2
AP2A1 0.028 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.007 0.043 -10000 0 -0.2 11 11
ARF1/GDP/Membrin 0.026 0.022 -10000 0 -0.25 2 2
Arfaptin 2/Rac/GDP 0.034 0.013 -10000 0 -10000 0 0
CYTH2 0.029 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.037 0.011 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.006 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.017 0.03 -10000 0 -0.24 1 1
PLD2 0.007 0.009 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE 0.007 0.002 -10000 0 -10000 0 0
PIP5K1A 0.008 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.022 0.018 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.007 0.009 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.002 -10000 0 -10000 0 0
GOSR2 0.012 0.023 -10000 0 -0.31 2 2
USO1 0.012 0.028 -10000 0 -0.31 3 3
GBF1 0.012 0.024 -10000 0 -0.32 2 2
ARF1/GTP/Arfaptin 2 0.038 0.012 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.037 0.034 -10000 0 -0.26 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 0.041 0.007 -9999 0 -10000 0 0
FBXW11 0.027 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.007 -9999 0 -10000 0 0
CHUK 0.028 0.004 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.075 0.031 -9999 0 -10000 0 0
NFKB1 0.028 0.005 -9999 0 -10000 0 0
MAP3K14 0.028 0.003 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.038 0.024 -9999 0 -0.28 2 2
RELB 0.026 0.029 -9999 0 -0.39 2 2
NFKB2 0.028 0.004 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0.035 0.02 -9999 0 -0.23 2 2
regulation of B cell activation 0.035 0.02 -9999 0 -0.23 2 2
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 420 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.QK.A6IJ TCGA.QK.A6II TCGA.QK.A6IH TCGA.QK.A652
109_MAP3K5 0.034 -0.11 -0.079 0.034
47_PPARGC1A -0.47 -0.47 -0.47 0.028
105_BMP4 0.028 -0.47 0.028 0.028
105_BMP6 0.028 0.028 0.028 0.028
105_BMP7 0.028 0.028 0.028 0.028
105_BMP2 0.028 -0.39 0.028 0.028
131_RELN/VLDLR 0.073 0.073 0 0.073
30_TGFB1/TGF beta receptor Type II 0.032 0.028 0.032 0.028
84_STAT5B -0.14 -0.29 -0.41 0.058
84_STAT5A -0.14 -0.29 -0.41 0.058
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/HNSC-TP/6044628/HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/HNSC-TP/6154472/Gistic2_Analysis_6154807/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle