PARADIGM pathway analysis of mRNASeq expression data
Colorectal Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C15D8QJN
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C15D8QJN
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 48 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 97
IL23-mediated signaling events 94
Ephrin A reverse signaling 85
Signaling mediated by p38-alpha and p38-beta 81
Wnt signaling 76
amb2 Integrin signaling 67
Syndecan-4-mediated signaling events 66
Glypican 1 network 64
Noncanonical Wnt signaling pathway 62
TCR signaling in naïve CD8+ T cells 58
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 595 . 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 ( 595 ).

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 0.1630 97 8838 91 -0.68 0.61 1000 -1000 -0.16 -1000
IL23-mediated signaling events 0.1580 94 5671 60 -0.54 0.011 1000 -1000 -0.18 -1000
Ephrin A reverse signaling 0.1429 85 601 7 -0.097 0 1000 -1000 -0.024 -1000
Signaling mediated by p38-alpha and p38-beta 0.1361 81 3571 44 -0.18 0.011 1000 -1000 -0.044 -1000
Wnt signaling 0.1277 76 537 7 -0.14 0.004 1000 -1000 -0.03 -1000
amb2 Integrin signaling 0.1126 67 5510 82 -0.16 0.015 1000 -1000 -0.066 -1000
Syndecan-4-mediated signaling events 0.1109 66 4448 67 -0.18 0.038 1000 -1000 -0.067 -1000
Glypican 1 network 0.1076 64 3105 48 -0.2 0.014 1000 -1000 -0.032 -1000
Noncanonical Wnt signaling pathway 0.1042 62 1627 26 -0.14 0.011 1000 -1000 -0.051 -1000
TCR signaling in naïve CD8+ T cells 0.0975 58 5447 93 -0.12 0.055 1000 -1000 -0.076 -1000
IL12-mediated signaling events 0.0958 57 5034 87 -0.29 0.066 1000 -1000 -0.13 -1000
Syndecan-1-mediated signaling events 0.0941 56 1937 34 -0.14 0.011 1000 -1000 -0.046 -1000
FOXA2 and FOXA3 transcription factor networks 0.0908 54 2509 46 -0.43 0.016 1000 -1000 -0.12 -1000
Ephrin B reverse signaling 0.0908 54 2598 48 -0.15 0.044 1000 -1000 -0.056 -1000
BCR signaling pathway 0.0891 53 5291 99 -0.17 0.014 1000 -1000 -0.085 -1000
Endothelins 0.0874 52 5067 96 -0.16 0.011 1000 -1000 -0.079 -1000
Signaling events mediated by the Hedgehog family 0.0857 51 2701 52 -0.13 0.08 1000 -1000 -0.053 -1000
TCGA08_retinoblastoma 0.0824 49 395 8 -0.07 0.027 1000 -1000 -0.017 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0807 48 1644 34 -0.059 0.011 1000 -1000 -0.036 -1000
HIF-1-alpha transcription factor network 0.0807 48 3702 76 -0.31 0.016 1000 -1000 -0.19 -1000
p75(NTR)-mediated signaling 0.0807 48 6008 125 -0.18 0.031 1000 -1000 -0.09 -1000
Fc-epsilon receptor I signaling in mast cells 0.0807 48 4682 97 -0.14 0.029 1000 -1000 -0.075 -1000
Reelin signaling pathway 0.0807 48 2723 56 -0.12 0.021 1000 -1000 -0.078 -1000
Calcium signaling in the CD4+ TCR pathway 0.0773 46 1436 31 -0.2 0.011 1000 -1000 -0.061 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0773 46 3186 68 -0.31 0.11 1000 -1000 -0.12 -1000
BMP receptor signaling 0.0723 43 3488 81 -0.17 0.026 1000 -1000 -0.085 -1000
TCGA08_p53 0.0723 43 307 7 -0.05 0.03 1000 -1000 -0.016 -1000
Thromboxane A2 receptor signaling 0.0655 39 4151 105 -0.18 0.044 1000 -1000 -0.06 -1000
EGFR-dependent Endothelin signaling events 0.0655 39 825 21 -0.18 0.016 1000 -1000 -0.063 -1000
Syndecan-2-mediated signaling events 0.0639 38 2679 69 -0.11 0.023 1000 -1000 -0.038 -1000
Osteopontin-mediated events 0.0622 37 1442 38 -0.16 0.011 1000 -1000 -0.087 -1000
Glucocorticoid receptor regulatory network 0.0622 37 4307 114 -0.34 0.21 1000 -1000 -0.067 -1000
Effects of Botulinum toxin 0.0622 37 979 26 -0.12 0.01 1000 -1000 -0.051 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0605 36 4334 120 -0.18 0.14 1000 -1000 -0.067 -1000
IL1-mediated signaling events 0.0571 34 2133 62 -0.1 0.02 1000 -1000 -0.081 -1000
Caspase cascade in apoptosis 0.0555 33 2446 74 -0.085 0.042 1000 -1000 -0.039 -1000
JNK signaling in the CD4+ TCR pathway 0.0555 33 571 17 -0.047 0.011 1000 -1000 -0.044 -1000
Signaling events regulated by Ret tyrosine kinase 0.0555 33 2743 82 -0.11 0.011 1000 -1000 -0.082 -1000
Canonical Wnt signaling pathway 0.0555 33 1709 51 -0.18 0.088 1000 -1000 -0.057 -1000
LPA receptor mediated events 0.0538 32 3304 102 -0.11 0.012 1000 -1000 -0.08 -1000
Glypican 2 network 0.0521 31 127 4 -0.011 -0.008 1000 -1000 -0.018 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0521 31 2755 88 -0.12 0.044 1000 -1000 -0.098 -1000
Visual signal transduction: Rods 0.0521 31 1638 52 -0.12 0.011 1000 -1000 -0.069 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0521 31 2441 78 -0.084 0.055 1000 -1000 -0.072 -1000
Visual signal transduction: Cones 0.0504 30 1168 38 -0.053 0.007 1000 -1000 -0.051 -1000
Cellular roles of Anthrax toxin 0.0504 30 1198 39 -0.045 0.011 1000 -1000 -0.023 -1000
Presenilin action in Notch and Wnt signaling 0.0504 30 1856 61 -0.18 0.059 1000 -1000 -0.073 -1000
Integrins in angiogenesis 0.0504 30 2526 84 -0.16 0.018 1000 -1000 -0.078 -1000
a4b1 and a4b7 Integrin signaling 0.0471 28 140 5 -0.022 -0.004 1000 -1000 -0.021 -1000
FAS signaling pathway (CD95) 0.0471 28 1331 47 -0.16 0.014 1000 -1000 -0.044 -1000
Retinoic acid receptors-mediated signaling 0.0471 28 1667 58 -0.15 0.019 1000 -1000 -0.064 -1000
EPHB forward signaling 0.0454 27 2346 85 -0.1 0.06 1000 -1000 -0.079 -1000
IL27-mediated signaling events 0.0454 27 1414 51 -0.19 0.024 1000 -1000 -0.067 -1000
Arf6 signaling events 0.0437 26 1660 62 -0.18 0.024 1000 -1000 -0.051 -1000
Signaling events mediated by PTP1B 0.0437 26 2049 76 -0.18 0.029 1000 -1000 -0.077 -1000
LPA4-mediated signaling events 0.0420 25 304 12 -0.058 0.015 1000 -1000 -0.023 -1000
Ras signaling in the CD4+ TCR pathway 0.0420 25 429 17 -0.048 0.011 1000 -1000 -0.042 -1000
IL6-mediated signaling events 0.0403 24 1870 75 -0.11 0.042 1000 -1000 -0.068 -1000
Plasma membrane estrogen receptor signaling 0.0403 24 2080 86 -0.073 0.017 1000 -1000 -0.079 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0387 23 1278 54 -0.13 0.022 1000 -1000 -0.089 -1000
Nongenotropic Androgen signaling 0.0387 23 1198 52 -0.051 0.012 1000 -1000 -0.053 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0370 22 820 37 -0.12 0.026 1000 -1000 -0.048 -1000
IGF1 pathway 0.0370 22 1309 57 -0.074 0.023 1000 -1000 -0.083 -1000
Coregulation of Androgen receptor activity 0.0353 21 1617 76 -0.16 0.04 1000 -1000 -0.038 -1000
S1P1 pathway 0.0353 21 784 36 -0.1 0.011 1000 -1000 -0.052 -1000
PDGFR-alpha signaling pathway 0.0336 20 888 44 -0.063 0.017 1000 -1000 -0.054 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0303 18 940 52 -0.12 0.034 1000 -1000 -0.043 -1000
IL2 signaling events mediated by STAT5 0.0303 18 404 22 -0.049 0.016 1000 -1000 -0.055 -1000
Class I PI3K signaling events 0.0303 18 1364 73 -0.12 0.024 1000 -1000 -0.063 -1000
Regulation of Telomerase 0.0286 17 1763 102 -0.18 0.036 1000 -1000 -0.093 -1000
FOXM1 transcription factor network 0.0286 17 867 51 -0.12 0.075 1000 -1000 -0.19 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0269 16 536 33 -0.077 0.029 1000 -1000 -0.042 -1000
Signaling events mediated by PRL 0.0269 16 546 34 -0.024 0.027 1000 -1000 -0.025 -1000
ErbB4 signaling events 0.0252 15 1070 69 -0.16 0.036 1000 -1000 -0.084 -1000
IFN-gamma pathway 0.0252 15 1064 68 -0.066 0.02 1000 -1000 -0.084 -1000
Nectin adhesion pathway 0.0252 15 965 63 -0.032 0.02 1000 -1000 -0.067 -1000
S1P4 pathway 0.0252 15 394 25 -0.046 0.015 1000 -1000 -0.033 -1000
ErbB2/ErbB3 signaling events 0.0235 14 928 65 -0.067 0.016 1000 -1000 -0.063 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0235 14 413 28 -0.046 0.018 1000 -1000 -0.038 -1000
Signaling events mediated by HDAC Class III 0.0235 14 587 40 -0.047 0.017 1000 -1000 -0.027 -1000
Regulation of p38-alpha and p38-beta 0.0235 14 772 54 -0.12 0.027 1000 -1000 -0.054 -1000
Regulation of nuclear SMAD2/3 signaling 0.0218 13 1844 136 -0.08 0.038 1000 -1000 -0.066 -1000
PLK2 and PLK4 events 0.0218 13 39 3 -0.003 0.009 1000 -1000 -0.018 -1000
Syndecan-3-mediated signaling events 0.0218 13 483 35 -0.11 0.031 1000 -1000 -0.05 -1000
PDGFR-beta signaling pathway 0.0218 13 1336 97 -0.098 0.032 1000 -1000 -0.074 -1000
Regulation of Androgen receptor activity 0.0218 13 943 70 -0.2 0.027 1000 -1000 -0.058 -1000
Ceramide signaling pathway 0.0202 12 914 76 -0.18 0.058 1000 -1000 -0.048 -1000
S1P5 pathway 0.0202 12 206 17 -0.046 0.011 1000 -1000 -0.033 -1000
Paxillin-dependent events mediated by a4b1 0.0202 12 447 36 -0.022 0.02 1000 -1000 -0.068 -1000
IL2 signaling events mediated by PI3K 0.0202 12 723 58 -0.047 0.027 1000 -1000 -0.076 -1000
Class IB PI3K non-lipid kinase events 0.0202 12 36 3 -0.001 -1000 1000 -1000 -0.012 -1000
Signaling mediated by p38-gamma and p38-delta 0.0185 11 177 15 -0.024 0.017 1000 -1000 -0.028 -1000
S1P3 pathway 0.0185 11 498 42 -0.046 0.018 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class II 0.0168 10 768 75 -0.038 0.026 1000 -1000 -0.042 -1000
Hedgehog signaling events mediated by Gli proteins 0.0168 10 675 65 -0.046 0.035 1000 -1000 -0.055 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0168 10 877 83 -0.15 0.048 1000 -1000 -0.07 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0168 10 488 45 -0.063 0.039 1000 -1000 -0.085 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0168 10 272 27 -0.017 0.016 1000 -1000 -0.052 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0151 9 848 85 -0.037 0.028 1000 -1000 -0.068 -1000
TCGA08_rtk_signaling 0.0151 9 235 26 -0.044 0.035 1000 -1000 -0.019 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0151 9 689 74 -0.18 0.051 1000 -1000 -0.075 -1000
Insulin Pathway 0.0151 9 712 74 -0.12 0.027 1000 -1000 -0.081 -1000
Rapid glucocorticoid signaling 0.0151 9 188 20 -0.02 0.011 1000 -1000 -0.015 -1000
BARD1 signaling events 0.0134 8 497 57 -0.044 0.048 1000 -1000 -0.056 -1000
EPO signaling pathway 0.0134 8 485 55 -0.025 0.04 1000 -1000 -0.08 -1000
VEGFR1 specific signals 0.0134 8 473 56 -0.017 0.031 1000 -1000 -0.058 -1000
p38 MAPK signaling pathway 0.0134 8 352 44 -0.054 0.02 1000 -1000 -0.065 -1000
Aurora B signaling 0.0134 8 562 67 -0.12 0.028 1000 -1000 -0.063 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0118 7 895 125 -0.041 0.055 1000 -1000 -0.081 -1000
Arf6 downstream pathway 0.0101 6 268 43 -0.042 0.025 1000 -1000 -0.031 -1000
Aurora C signaling 0.0101 6 42 7 -0.009 0.011 1000 -1000 -0.022 -1000
Signaling events mediated by HDAC Class I 0.0101 6 661 104 -0.022 0.041 1000 -1000 -0.052 -1000
Canonical NF-kappaB pathway 0.0084 5 232 39 -0.017 0.054 1000 -1000 -0.078 -1000
Aurora A signaling 0.0084 5 343 60 -0.052 0.029 1000 -1000 -0.033 -1000
HIF-2-alpha transcription factor network 0.0084 5 257 43 -0.08 0.082 1000 -1000 -0.077 -1000
E-cadherin signaling in the nascent adherens junction 0.0084 5 439 76 -0.044 0.044 1000 -1000 -0.076 -1000
mTOR signaling pathway 0.0067 4 243 53 -0.006 0.025 1000 -1000 -0.054 -1000
TRAIL signaling pathway 0.0067 4 223 48 -0.014 0.037 1000 -1000 -0.066 -1000
ceramide signaling pathway 0.0067 4 231 49 -0.016 0.029 1000 -1000 -0.05 -1000
FoxO family signaling 0.0067 4 280 64 -0.082 0.098 1000 -1000 -0.076 -1000
Circadian rhythm pathway 0.0050 3 70 22 -0.011 0.036 1000 -1000 -0.035 -1000
PLK1 signaling events 0.0050 3 286 85 -0.007 0.029 1000 -1000 -0.04 -1000
Class I PI3K signaling events mediated by Akt 0.0050 3 255 68 -0.032 0.042 1000 -1000 -0.046 -1000
Atypical NF-kappaB pathway 0.0050 3 118 31 -0.031 0.028 1000 -1000 -0.04 -1000
Arf6 trafficking events 0.0050 3 280 71 -0.038 0.027 1000 -1000 -0.07 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0034 2 46 23 0.004 0.034 1000 -1000 -0.052 -1000
Insulin-mediated glucose transport 0.0034 2 76 32 0 0.033 1000 -1000 -0.052 -1000
E-cadherin signaling in keratinocytes 0.0034 2 100 43 -0.032 0.037 1000 -1000 -0.055 -1000
Arf1 pathway 0.0034 2 112 54 -0.014 0.02 1000 -1000 -0.031 -1000
Alternative NF-kappaB pathway 0.0034 2 32 13 0 0.029 1000 -1000 -0.025 -1000
E-cadherin signaling events 0.0017 1 5 5 0.01 0.022 1000 -1000 -0.022 -1000
Total NA 3344 194453 7203 -14 -1000 131000 -131000 -8 -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 -0.53 0.57 -10000 0 -1.3 177 177
STAT6 (cleaved dimer) -0.58 0.56 -10000 0 -1.2 229 229
IGHG1 -0.16 0.18 -10000 0 -0.5 6 6
IGHG3 -0.51 0.54 -10000 0 -1.1 222 222
AKT1 -0.24 0.29 -10000 0 -0.73 82 82
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.19 0.26 -10000 0 -0.69 64 64
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.28 -10000 0 -0.67 90 90
THY1 -0.53 0.57 -10000 0 -1.3 176 176
MYB 0.002 0.072 -10000 0 -0.58 9 9
HMGA1 0.006 0.055 -10000 0 -0.54 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.32 0.35 -10000 0 -0.75 163 163
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.25 0.29 -10000 0 -0.68 95 95
SP1 0.015 0.025 -10000 0 -0.58 1 1
INPP5D -0.017 0.12 -10000 0 -0.58 28 28
SOCS5 0.026 0.016 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.54 0.59 -10000 0 -1.2 213 213
SOCS1 -0.35 0.36 -10000 0 -0.78 176 176
SOCS3 -0.26 0.31 -10000 0 -0.82 78 78
FCER2 -0.52 0.56 -10000 0 -1.2 176 176
PARP14 0.008 0.021 -10000 0 -0.46 1 1
CCL17 -0.57 0.61 -10000 0 -1.3 199 199
GRB2 0.011 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.23 -10000 0 -0.62 57 57
T cell proliferation -0.54 0.59 -10000 0 -1.3 194 194
IL4R/JAK1 -0.54 0.57 -10000 0 -1.2 204 204
EGR2 -0.57 0.61 -10000 0 -1.3 186 186
JAK2 -0.033 0.11 -10000 0 -0.58 21 21
JAK3 0.002 0.077 -10000 0 -0.53 12 12
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
JAK1 0.003 0.043 -10000 0 -0.58 3 3
COL1A2 -0.2 0.34 -10000 0 -1.1 46 46
CCL26 -0.58 0.62 -10000 0 -1.3 203 203
IL4R -0.57 0.61 -10000 0 -1.3 203 203
PTPN6 0.023 0.012 -10000 0 -10000 0 0
IL13RA2 -0.59 0.63 -10000 0 -1.4 196 196
IL13RA1 -0.017 0.057 -10000 0 -0.59 4 4
IRF4 -0.27 0.49 -10000 0 -1.4 85 85
ARG1 -0.14 0.18 -10000 0 -0.73 22 22
CBL -0.3 0.33 -10000 0 -0.72 151 151
GTF3A 0.011 0.04 -10000 0 -0.51 3 3
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
IL13RA1/JAK2 -0.032 0.097 -10000 0 -0.45 23 23
IRF4/BCL6 -0.24 0.45 -10000 0 -1.3 80 80
CD40LG -0.036 0.16 -10000 0 -0.58 47 47
MAPK14 -0.3 0.34 -10000 0 -0.75 137 137
mitosis -0.23 0.28 -10000 0 -0.68 82 82
STAT6 -0.64 0.75 -10000 0 -1.4 215 215
SPI1 -0.013 0.12 -10000 0 -0.52 28 28
RPS6KB1 -0.22 0.27 -10000 0 -0.68 76 76
STAT6 (dimer) -0.65 0.77 -10000 0 -1.5 215 215
STAT6 (dimer)/PARP14 -0.59 0.64 -10000 0 -1.3 214 214
mast cell activation 0.012 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.25 0.3 -10000 0 -0.74 86 86
FRAP1 -0.24 0.29 -10000 0 -0.73 82 82
LTA -0.56 0.6 -10000 0 -1.3 181 181
FES 0.001 0.077 -10000 0 -0.56 11 11
T-helper 1 cell differentiation 0.61 0.67 1.4 217 -10000 0 217
CCL11 -0.57 0.62 -10000 0 -1.4 190 190
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.24 0.3 -10000 0 -0.72 87 87
IL2RG 0 0.083 -10000 0 -0.55 13 13
IL10 -0.57 0.62 -10000 0 -1.3 191 191
IRS1 0.002 0.072 -10000 0 -0.58 9 9
IRS2 0.003 0.068 -10000 0 -0.54 9 9
IL4 -0.11 0.12 -10000 0 -10000 0 0
IL5 -0.53 0.57 -10000 0 -1.3 181 181
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.41 0.42 -10000 0 -0.91 193 193
COL1A1 -0.25 0.4 -10000 0 -1.2 67 67
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.55 0.59 -10000 0 -1.3 177 177
IL2R gamma/JAK3 -0.002 0.083 -10000 0 -0.39 25 25
TFF3 -0.57 0.61 -10000 0 -1.3 190 190
ALOX15 -0.62 0.64 -10000 0 -1.4 217 217
MYBL1 0 0.079 -10000 0 -0.55 12 12
T-helper 2 cell differentiation -0.43 0.45 -10000 0 -0.96 196 196
SHC1 0.011 0 -10000 0 -10000 0 0
CEBPB 0.009 0.043 -10000 0 -0.49 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.24 0.28 -10000 0 -0.68 79 79
mol:PI-3-4-5-P3 -0.24 0.29 -10000 0 -0.73 82 82
PI3K -0.26 0.31 -10000 0 -0.78 82 82
DOK2 -0.01 0.11 -10000 0 -0.55 23 23
ETS1 0.016 0.059 -10000 0 -0.45 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.22 -10000 0 -0.62 43 43
ITGB3 -0.53 0.58 -10000 0 -1.3 179 179
PIGR -0.68 0.7 -10000 0 -1.5 235 235
IGHE 0.04 0.052 0.26 11 -0.31 1 12
MAPKKK cascade -0.18 0.22 -10000 0 -0.61 43 43
BCL6 0.01 0.038 -10000 0 -0.45 4 4
OPRM1 -0.53 0.57 -10000 0 -1.3 181 181
RETNLB -0.68 0.67 -10000 0 -1.4 244 244
SELP -0.6 0.66 -10000 0 -1.4 194 194
AICDA -0.52 0.55 -10000 0 -1.2 187 187
IL23-mediated signaling events

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
CCL2 -0.43 0.54 -10000 0 -1.2 143 143
IL23A -0.44 0.55 -10000 0 -1.3 136 136
NF kappa B1 p50/RelA/I kappa B alpha -0.48 0.5 -10000 0 -1.2 161 161
positive regulation of T cell mediated cytotoxicity -0.48 0.62 -10000 0 -1.3 158 158
ITGA3 -0.41 0.52 -10000 0 -1.2 144 144
IL17F -0.29 0.34 -10000 0 -0.75 136 136
IL12B -0.017 0.078 -10000 0 -0.48 14 14
STAT1 (dimer) -0.46 0.59 -10000 0 -1.3 158 158
CD4 -0.42 0.52 -10000 0 -1.2 135 135
IL23 -0.43 0.52 -10000 0 -1.2 136 136
IL23R -0.1 0.3 -10000 0 -1.5 25 25
IL1B -0.46 0.57 -10000 0 -1.3 152 152
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.54 0.61 -10000 0 -1.3 205 205
TYK2 -0.002 0.033 -10000 0 -0.62 1 1
STAT4 -0.027 0.14 -10000 0 -0.56 40 40
STAT3 0.011 0.002 -10000 0 -10000 0 0
IL18RAP -0.035 0.15 -10000 0 -0.55 48 48
IL12RB1 -0.046 0.16 -10000 0 -0.57 48 48
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
IL12Rbeta1/TYK2 -0.035 0.12 -10000 0 -0.43 49 49
IL23R/JAK2 -0.12 0.3 -10000 0 -1.4 25 25
positive regulation of chronic inflammatory response -0.48 0.62 -10000 0 -1.3 158 158
natural killer cell activation 0.008 0.017 0.069 32 -10000 0 32
JAK2 -0.02 0.11 -10000 0 -0.57 21 21
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
NFKB1 0.008 0.025 -10000 0 -0.59 1 1
RELA 0.009 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.4 0.49 -10000 0 -1.1 137 137
ALOX12B -0.47 0.56 -10000 0 -1.2 169 169
CXCL1 -0.43 0.54 -10000 0 -1.2 149 149
T cell proliferation -0.48 0.62 -10000 0 -1.3 158 158
NFKBIA 0.009 0.004 -10000 0 -10000 0 0
IL17A -0.25 0.3 -10000 0 -0.62 138 138
PI3K -0.48 0.51 -10000 0 -1.2 163 163
IFNG -0.019 0.05 0.14 18 -0.12 51 69
STAT3 (dimer) -0.47 0.48 -10000 0 -1.1 169 169
IL18R1 -0.013 0.11 -10000 0 -0.56 25 25
IL23/IL23R/JAK2/TYK2/SOCS3 -0.24 0.32 -10000 0 -0.73 108 108
IL18/IL18R -0.025 0.14 -10000 0 -0.37 69 69
macrophage activation -0.023 0.018 -10000 0 -0.045 122 122
TNF -0.45 0.56 -10000 0 -1.3 146 146
STAT3/STAT4 -0.49 0.52 -10000 0 -1.2 164 164
STAT4 (dimer) -0.47 0.6 -10000 0 -1.3 160 160
IL18 0.002 0.067 -10000 0 -0.54 9 9
IL19 -0.41 0.51 -10000 0 -1.2 130 130
STAT5A (dimer) -0.46 0.59 -10000 0 -1.3 157 157
STAT1 0.006 0.051 -10000 0 -0.5 6 6
SOCS3 -0.002 0.082 -10000 0 -0.5 16 16
CXCL9 -0.47 0.58 -10000 0 -1.3 154 154
MPO -0.44 0.54 -10000 0 -1.2 154 154
positive regulation of humoral immune response -0.48 0.62 -10000 0 -1.3 158 158
IL23/IL23R/JAK2/TYK2 -0.54 0.75 -10000 0 -1.5 157 157
IL6 -0.48 0.57 -10000 0 -1.3 151 151
STAT5A 0.011 0 -10000 0 -10000 0 0
IL2 0.004 0.029 -10000 0 -0.46 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.017 0.069 32 -10000 0 32
CD3E -0.42 0.53 -10000 0 -1.2 141 141
keratinocyte proliferation -0.48 0.62 -10000 0 -1.3 158 158
NOS2 -0.48 0.57 -10000 0 -1.3 169 169
Ephrin A reverse signaling

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
MAPKKK cascade -0.061 0.14 -9999 0 -0.32 133 133
EFNA5 -0.097 0.22 -9999 0 -0.52 122 122
FYN -0.052 0.13 -9999 0 -0.35 67 67
neuron projection morphogenesis -0.061 0.14 -9999 0 -0.32 133 133
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.061 0.14 -9999 0 -0.32 133 133
EPHA5 -0.004 0.068 -9999 0 -0.46 13 13
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.16 0.35 -9999 0 -0.94 80 80
MKNK1 0.011 0 -9999 0 -10000 0 0
MAPK14 -0.063 0.14 -9999 0 -0.41 23 23
ATF2/c-Jun -0.045 0.15 -9999 0 -0.55 19 19
MAPK11 -0.078 0.17 -9999 0 -0.36 117 117
MITF -0.094 0.2 -9999 0 -0.41 132 132
MAPKAPK5 -0.074 0.18 -9999 0 -0.39 112 112
KRT8 -0.075 0.18 -9999 0 -0.4 113 113
MAPKAPK3 0.011 0 -9999 0 -10000 0 0
MAPKAPK2 0.011 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.11 0.23 -9999 0 -0.5 124 124
CEBPB -0.075 0.18 -9999 0 -0.39 114 114
SLC9A1 -0.075 0.18 -9999 0 -0.4 114 114
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.071 0.18 -9999 0 -0.54 35 35
p38alpha-beta/MNK1 -0.075 0.19 -9999 0 -0.41 111 111
JUN -0.044 0.14 -9999 0 -0.54 19 19
PPARGC1A -0.11 0.22 -9999 0 -0.43 150 150
USF1 -0.074 0.18 -9999 0 -0.39 112 112
RAB5/GDP/GDI1 -0.073 0.12 -9999 0 -0.42 35 35
NOS2 -0.18 0.4 -9999 0 -1.1 86 86
DDIT3 -0.075 0.18 -9999 0 -0.38 125 125
RAB5A 0.006 0.054 -9999 0 -0.58 5 5
HSPB1 -0.06 0.16 -9999 0 -0.46 39 39
p38alpha-beta/HBP1 -0.075 0.19 -9999 0 -0.4 112 112
CREB1 -0.074 0.18 -9999 0 -0.41 113 113
RAB5/GDP 0.005 0.04 -9999 0 -0.43 5 5
EIF4E -0.064 0.17 -9999 0 -0.56 32 32
RPS6KA4 -0.074 0.18 -9999 0 -0.39 113 113
PLA2G4A -0.15 0.22 -9999 0 -0.53 96 96
GDI1 -0.074 0.18 -9999 0 -0.39 112 112
TP53 -0.12 0.24 -9999 0 -0.51 126 126
RPS6KA5 -0.076 0.18 -9999 0 -0.39 114 114
ESR1 -0.099 0.2 -9999 0 -0.42 135 135
HBP1 0.011 0 -9999 0 -10000 0 0
MEF2C -0.08 0.18 -9999 0 -0.4 119 119
MEF2A -0.075 0.18 -9999 0 -0.4 112 112
EIF4EBP1 -0.074 0.18 -9999 0 -0.41 112 112
KRT19 -0.076 0.18 -9999 0 -0.4 114 114
ELK4 -0.076 0.18 -9999 0 -0.41 112 112
ATF6 -0.074 0.18 -9999 0 -0.38 124 124
ATF1 -0.074 0.18 -9999 0 -0.41 112 112
p38alpha-beta/MAPKAPK2 -0.075 0.19 -9999 0 -0.41 111 111
p38alpha-beta/MAPKAPK3 -0.075 0.19 -9999 0 -0.6 32 32
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.45 120 120
FZD6 0.004 0.064 -9999 0 -0.58 7 7
WNT6 -0.1 0.21 -9999 0 -0.5 130 130
WNT4 -0.053 0.18 -9999 0 -0.54 70 70
FZD3 -0.009 0.11 -9999 0 -0.58 20 20
WNT5A -0.008 0.1 -9999 0 -0.55 21 21
WNT11 -0.14 0.24 -9999 0 -0.52 169 169
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 -0.083 0.22 -9999 0 -0.47 118 118
alphaM/beta2 Integrin/GPIbA -0.073 0.19 -9999 0 -0.48 92 92
alphaM/beta2 Integrin/proMMP-9 -0.098 0.24 -9999 0 -0.49 131 131
PLAUR 0.01 0.031 -9999 0 -0.52 2 2
HMGB1 -0.012 0.097 -9999 0 -0.59 16 16
alphaM/beta2 Integrin/Talin -0.058 0.18 -9999 0 -0.43 94 94
AGER -0.011 0.094 -9999 0 -0.58 15 15
RAP1A 0.01 0.024 -9999 0 -0.58 1 1
SELPLG -0.007 0.099 -9999 0 -0.55 19 19
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.088 0.21 -9999 0 -0.47 103 103
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.059 0.18 -9999 0 -0.52 79 79
CYR61 -0.023 0.13 -9999 0 -0.48 42 42
TLN1 0.01 0.024 -9999 0 -0.58 1 1
Rap1/GTP -0.12 0.17 -9999 0 -0.46 86 86
RHOA 0.01 0.024 -9999 0 -0.58 1 1
P-selectin oligomer -0.082 0.21 -9999 0 -0.55 99 99
MYH2 -0.13 0.2 -9999 0 -0.48 105 105
MST1R 0.006 0.054 -9999 0 -0.58 5 5
leukocyte activation during inflammatory response -0.14 0.19 -9999 0 -0.4 154 154
APOB -0.12 0.22 -9999 0 -0.5 145 145
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.034 0.15 -9999 0 -0.53 50 50
JAM3 0.007 0.047 -9999 0 -0.46 6 6
GP1BA -0.015 0.11 -9999 0 -0.52 28 28
alphaM/beta2 Integrin/CTGF -0.067 0.19 -9999 0 -0.44 105 105
alphaM/beta2 Integrin -0.14 0.21 -9999 0 -0.46 125 125
JAM3 homodimer 0.007 0.047 -9999 0 -0.46 6 6
ICAM2 0.002 0.07 -9999 0 -0.5 11 11
ICAM1 0.006 0.053 -9999 0 -0.52 6 6
phagocytosis triggered by activation of immune response cell surface activating receptor -0.13 0.2 -9999 0 -0.45 125 125
cell adhesion -0.073 0.19 -9999 0 -0.47 93 93
NFKB1 -0.11 0.24 -9999 0 -0.62 68 68
THY1 0.001 0.076 -9999 0 -0.55 11 11
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
Lipoprotein(a) -0.086 0.15 -9999 0 -0.31 178 178
alphaM/beta2 Integrin/LRP/tPA -0.054 0.18 -9999 0 -0.47 75 75
IL6 -0.16 0.32 -9999 0 -0.78 101 101
ITGB2 -0.037 0.14 -9999 0 -0.53 45 45
elevation of cytosolic calcium ion concentration -0.052 0.18 -9999 0 -0.45 79 79
alphaM/beta2 Integrin/JAM2/JAM3 -0.081 0.22 -9999 0 -0.49 107 107
JAM2 -0.05 0.18 -9999 0 -0.54 66 66
alphaM/beta2 Integrin/ICAM1 -0.064 0.19 -9999 0 -0.44 93 93
alphaM/beta2 Integrin/uPA/Plg -0.078 0.2 -9999 0 -0.45 108 108
RhoA/GTP -0.14 0.21 -9999 0 -0.49 109 109
positive regulation of phagocytosis -0.13 0.21 -9999 0 -0.54 94 94
Ron/MSP -0.019 0.12 -9999 0 -0.37 55 55
alphaM/beta2 Integrin/uPAR/uPA -0.052 0.18 -9999 0 -0.45 79 79
alphaM/beta2 Integrin/uPAR -0.058 0.18 -9999 0 -0.43 95 95
PLAU -0.001 0.078 -9999 0 -0.5 14 14
PLAT 0 0.078 -9999 0 -0.54 12 12
actin filament polymerization -0.13 0.19 -9999 0 -0.45 106 106
MST1 -0.033 0.15 -9999 0 -0.51 51 51
alphaM/beta2 Integrin/lipoprotein(a) -0.13 0.2 -9999 0 -0.4 155 155
TNF -0.11 0.26 -9999 0 -0.73 58 58
RAP1B 0.011 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.064 0.19 -9999 0 -0.44 101 101
fibrinolysis -0.078 0.2 -9999 0 -0.45 108 108
HCK -0.018 0.12 -9999 0 -0.55 31 31
dendritic cell antigen processing and presentation -0.13 0.2 -9999 0 -0.45 125 125
VTN -0.051 0.17 -9999 0 -0.5 71 71
alphaM/beta2 Integrin/CYR61 -0.077 0.2 -9999 0 -0.46 106 106
LPA -0.026 0.12 -9999 0 -0.46 41 41
LRP1 0.006 0.057 -9999 0 -0.56 6 6
cell migration -0.11 0.26 -9999 0 -0.55 119 119
FN1 -0.086 0.21 -9999 0 -0.52 109 109
alphaM/beta2 Integrin/Thy1 -0.063 0.19 -9999 0 -0.45 97 97
MPO -0.039 0.16 -9999 0 -0.53 55 55
KNG1 -0.11 0.22 -9999 0 -0.52 136 136
RAP1/GDP 0.015 0.015 -9999 0 -0.36 1 1
ROCK1 -0.13 0.2 -9999 0 -0.47 107 107
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.036 0.15 -9999 0 -0.58 42 42
CTGF -0.005 0.087 -9999 0 -0.46 21 21
alphaM/beta2 Integrin/Hck -0.073 0.22 -9999 0 -0.49 102 102
ITGAM -0.071 0.19 -9999 0 -0.52 84 84
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.11 0.24 -9999 0 -0.48 138 138
HP -0.08 0.2 -9999 0 -0.5 103 103
leukocyte adhesion -0.13 0.22 -9999 0 -0.59 85 85
SELP -0.082 0.21 -9999 0 -0.55 99 99
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.067 0.18 -9999 0 -0.55 57 57
Syndecan-4/Syndesmos -0.14 0.23 -9999 0 -0.55 115 115
positive regulation of JNK cascade -0.14 0.22 -9999 0 -0.52 122 122
Syndecan-4/ADAM12 -0.18 0.27 -9999 0 -0.58 146 146
CCL5 -0.037 0.15 -9999 0 -0.51 55 55
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
DNM2 0.01 0.024 -9999 0 -0.58 1 1
ITGA5 -0.005 0.09 -9999 0 -0.49 20 20
SDCBP 0 0.08 -9999 0 -0.58 11 11
PLG -0.032 0.14 -9999 0 -0.56 42 42
ADAM12 -0.078 0.2 -9999 0 -0.51 101 101
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.01 0.027 -9999 0 -0.46 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.03 0.04 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.16 0.26 -9999 0 -0.58 131 131
Syndecan-4/CXCL12/CXCR4 -0.15 0.24 -9999 0 -0.56 122 122
Syndecan-4/Laminin alpha3 -0.15 0.24 -9999 0 -0.55 123 123
MDK -0.009 0.1 -9999 0 -0.5 23 23
Syndecan-4/FZD7 -0.14 0.24 -9999 0 -0.55 117 117
Syndecan-4/Midkine -0.14 0.24 -9999 0 -0.56 119 119
FZD7 -0.001 0.078 -9999 0 -0.5 14 14
Syndecan-4/FGFR1/FGF -0.17 0.23 -9999 0 -0.54 137 137
THBS1 -0.004 0.088 -9999 0 -0.52 17 17
integrin-mediated signaling pathway -0.16 0.25 -9999 0 -0.56 132 132
positive regulation of MAPKKK cascade -0.14 0.22 -9999 0 -0.52 122 122
Syndecan-4/TACI -0.17 0.25 -9999 0 -0.56 137 137
CXCR4 -0.016 0.11 -9999 0 -0.49 32 32
cell adhesion -0.026 0.11 -9999 0 -0.31 62 62
Syndecan-4/Dynamin -0.13 0.23 -9999 0 -0.55 113 113
Syndecan-4/TSP1 -0.14 0.24 -9999 0 -0.56 119 119
Syndecan-4/GIPC -0.14 0.23 -9999 0 -0.55 114 114
Syndecan-4/RANTES -0.16 0.24 -9999 0 -0.56 125 125
ITGB1 0.011 0 -9999 0 -10000 0 0
LAMA1 -0.055 0.18 -9999 0 -0.54 72 72
LAMA3 -0.016 0.12 -9999 0 -0.51 32 32
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA 0.038 0.055 -9999 0 -0.46 2 2
Syndecan-4/alpha-Actinin -0.13 0.23 -9999 0 -0.55 113 113
TFPI -0.008 0.1 -9999 0 -0.53 21 21
F2 -0.12 0.22 -9999 0 -0.5 146 146
alpha5/beta1 Integrin 0.005 0.065 -9999 0 -0.34 20 20
positive regulation of cell adhesion -0.17 0.25 -9999 0 -0.57 135 135
ACTN1 0.011 0 -9999 0 -10000 0 0
TNC -0.06 0.18 -9999 0 -0.52 80 80
Syndecan-4/CXCL12 -0.14 0.24 -9999 0 -0.56 122 122
FGF6 -0.001 0.019 -9999 0 -0.46 1 1
RHOA 0.01 0.024 -9999 0 -0.58 1 1
CXCL12 -0.013 0.11 -9999 0 -0.49 29 29
TNFRSF13B -0.062 0.18 -9999 0 -0.52 80 80
FGF2 -0.039 0.16 -9999 0 -0.52 56 56
FGFR1 -0.009 0.1 -9999 0 -0.52 23 23
Syndecan-4/PI-4-5-P2 -0.14 0.23 -9999 0 -0.55 113 113
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.082 0.2 -9999 0 -0.51 109 109
cell migration -0.006 0.017 -9999 0 -10000 0 0
PRKCD 0.016 0.009 -9999 0 -10000 0 0
vasculogenesis -0.14 0.23 -9999 0 -0.53 119 119
SDC4 -0.15 0.24 -9999 0 -0.58 113 113
Syndecan-4/Tenascin C -0.17 0.26 -9999 0 -0.59 132 132
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.032 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.14 0.23 -9999 0 -0.54 119 119
MMP9 -0.06 0.18 -9999 0 -0.52 79 79
Rac1/GTP -0.027 0.12 -9999 0 -0.32 62 62
cytoskeleton organization -0.13 0.22 -9999 0 -0.52 115 115
GIPC1 0.007 0.048 -9999 0 -0.58 4 4
Syndecan-4/TFPI -0.14 0.24 -9999 0 -0.56 119 119
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.028 0.14 -10000 0 -0.35 81 81
fibroblast growth factor receptor signaling pathway -0.028 0.14 -10000 0 -0.35 81 81
LAMA1 -0.055 0.18 -10000 0 -0.54 72 72
PRNP -0.002 0.089 -10000 0 -0.57 14 14
GPC1/SLIT2 -0.093 0.18 -10000 0 -0.39 161 161
SMAD2 0.014 0.065 -10000 0 -0.33 17 17
GPC1/PrPc/Cu2+ -0.001 0.076 -10000 0 -0.34 28 28
GPC1/Laminin alpha1 -0.041 0.15 -10000 0 -0.4 82 82
TDGF1 -0.072 0.2 -10000 0 -0.58 84 84
CRIPTO/GPC1 -0.054 0.16 -10000 0 -0.42 98 98
APP/GPC1 0.007 0.065 -10000 0 -0.39 15 15
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.043 0.14 -10000 0 -0.35 104 104
FLT1 0.007 0.052 -10000 0 -0.56 5 5
GPC1/TGFB/TGFBR1/TGFBR2 0.012 0.062 -10000 0 -0.33 19 19
SERPINC1 -0.012 0.091 -10000 0 -0.46 24 24
FYN -0.042 0.14 -10000 0 -0.35 103 103
FGR -0.061 0.16 -10000 0 -0.36 128 128
positive regulation of MAPKKK cascade -0.096 0.21 -10000 0 -0.46 127 127
SLIT2 -0.13 0.24 -10000 0 -0.53 152 152
GPC1/NRG -0.05 0.15 -10000 0 -0.38 99 99
NRG1 -0.068 0.19 -10000 0 -0.53 87 87
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.012 0.066 -10000 0 -0.34 19 19
LYN -0.038 0.14 -10000 0 -0.35 98 98
mol:Spermine 0 0.062 -10000 0 -0.4 14 14
cell growth -0.028 0.14 -10000 0 -0.35 81 81
BMP signaling pathway 0.002 0.085 0.54 14 -10000 0 14
SRC -0.039 0.14 -10000 0 -0.35 98 98
TGFBR1 0.007 0.048 -10000 0 -0.58 4 4
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.2 0.27 -10000 0 -0.53 233 233
GPC1 -0.002 0.085 -10000 0 -0.55 14 14
TGFBR1 (dimer) 0.007 0.048 -10000 0 -0.58 4 4
VEGFA 0.011 0.019 -10000 0 -0.46 1 1
BLK -0.12 0.2 -10000 0 -0.38 204 204
HCK -0.056 0.16 -10000 0 -0.36 121 121
FGF2 -0.039 0.16 -10000 0 -0.52 56 56
FGFR1 -0.009 0.1 -10000 0 -0.52 23 23
VEGFR1 homodimer 0.007 0.052 -10000 0 -0.56 5 5
TGFBR2 0.011 0.019 -10000 0 -0.46 1 1
cell death 0.007 0.065 -10000 0 -0.39 15 15
ATIII/GPC1 -0.009 0.089 -10000 0 -0.34 38 38
PLA2G2A/GPC1 -0.15 0.21 -10000 0 -0.39 238 238
LCK -0.063 0.17 -10000 0 -0.38 128 128
neuron differentiation -0.05 0.15 -10000 0 -0.38 99 99
PrPc/Cu2+ -0.002 0.065 -10000 0 -0.42 14 14
APP 0.01 0.024 -10000 0 -0.58 1 1
TGFBR2 (dimer) 0.011 0.019 -10000 0 -0.46 1 1
Noncanonical Wnt signaling pathway

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
NFATC2 -0.037 0.16 -9999 0 -0.57 50 50
GNB1/GNG2 -0.11 0.19 -9999 0 -0.49 81 81
mol:DAG -0.094 0.18 -9999 0 -0.45 80 80
PLCG1 -0.097 0.18 -9999 0 -0.46 80 80
YES1 -0.12 0.2 -9999 0 -0.51 83 83
FZD3 -0.009 0.11 -9999 0 -0.58 20 20
FZD6 0.004 0.064 -9999 0 -0.58 7 7
G protein -0.098 0.18 -9999 0 -0.46 80 80
MAP3K7 -0.083 0.16 -9999 0 -0.42 67 67
mol:Ca2+ -0.091 0.17 -9999 0 -0.43 80 80
mol:IP3 -0.094 0.18 -9999 0 -0.45 80 80
NLK -0.005 0.009 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CAMK2A -0.095 0.17 -9999 0 -0.45 73 73
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.13 0.21 -9999 0 -0.45 120 120
CSNK1A1 0.009 0.034 -9999 0 -0.58 2 2
GNAS -0.12 0.2 -9999 0 -0.51 79 79
GO:0007205 -0.092 0.17 -9999 0 -0.44 80 80
WNT6 -0.1 0.21 -9999 0 -0.5 130 130
WNT4 -0.053 0.18 -9999 0 -0.54 70 70
NFAT1/CK1 alpha -0.12 0.22 -9999 0 -0.55 85 85
GNG2 0.004 0.063 -9999 0 -0.53 8 8
WNT5A -0.008 0.1 -9999 0 -0.55 21 21
WNT11 -0.14 0.24 -9999 0 -0.52 169 169
CDC42 -0.11 0.2 -9999 0 -0.5 82 82
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.094 0.19 -10000 0 -0.54 79 79
FYN -0.089 0.29 -10000 0 -0.69 88 88
LAT/GRAP2/SLP76 -0.11 0.23 -10000 0 -0.58 94 94
IKBKB 0.011 0.019 -10000 0 -0.46 1 1
AKT1 -0.051 0.19 -10000 0 -0.45 89 89
B2M 0.007 0.044 -10000 0 -0.52 4 4
IKBKG -0.036 0.054 -10000 0 -0.16 60 60
MAP3K8 0.01 0.031 -10000 0 -0.52 2 2
mol:Ca2+ -0.024 0.04 -10000 0 -0.1 109 109
integrin-mediated signaling pathway 0.007 0.052 -10000 0 -0.32 14 14
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.09 0.28 -10000 0 -0.68 90 90
TRPV6 -0.094 0.19 -10000 0 -0.48 118 118
CD28 -0.034 0.15 -10000 0 -0.56 47 47
SHC1 -0.086 0.27 -10000 0 -0.67 86 86
receptor internalization -0.095 0.3 -10000 0 -0.74 84 84
PRF1 -0.1 0.33 -10000 0 -1 56 56
KRAS 0.006 0.057 -10000 0 -0.56 6 6
GRB2 0.011 0 -10000 0 -10000 0 0
COT/AKT1 -0.033 0.15 -10000 0 -0.36 83 83
LAT -0.094 0.28 -10000 0 -0.68 89 89
EntrezGene:6955 -0.001 0.004 -10000 0 -10000 0 0
CD3D -0.03 0.15 -10000 0 -0.56 43 43
CD3E -0.025 0.14 -10000 0 -0.56 38 38
CD3G -0.054 0.18 -10000 0 -0.57 67 67
RASGRP2 -0.01 0.044 -10000 0 -0.17 33 33
RASGRP1 -0.055 0.2 -10000 0 -0.47 94 94
HLA-A 0.002 0.069 -10000 0 -0.52 10 10
RASSF5 -0.001 0.08 -10000 0 -0.53 13 13
RAP1A/GTP/RAPL 0.007 0.052 -10000 0 -0.33 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.059 -10000 0 -0.12 77 77
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.065 0.096 -10000 0 -0.27 86 86
PRKCA -0.049 0.1 -10000 0 -0.28 74 74
GRAP2 -0.024 0.14 -10000 0 -0.55 37 37
mol:IP3 -0.058 0.19 0.2 73 -0.46 79 152
EntrezGene:6957 -0.001 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.088 0.29 -10000 0 -0.75 74 74
ORAI1 0.055 0.11 0.27 115 -0.33 1 116
CSK -0.089 0.28 -10000 0 -0.7 84 84
B7 family/CD28 -0.12 0.32 -10000 0 -0.72 108 108
CHUK 0.007 0.048 -10000 0 -0.58 4 4
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.11 0.33 -10000 0 -0.79 89 89
PTPN6 -0.09 0.28 -10000 0 -0.69 85 85
VAV1 -0.099 0.29 -10000 0 -0.7 92 92
Monovalent TCR/CD3 -0.067 0.26 -10000 0 -0.6 83 83
CBL 0.011 0 -10000 0 -10000 0 0
LCK -0.099 0.3 -10000 0 -0.72 90 90
PAG1 -0.091 0.28 -10000 0 -0.68 89 89
RAP1A 0.01 0.024 -10000 0 -0.58 1 1
TCR/CD3/MHC I/CD8/LCK -0.11 0.33 -10000 0 -0.8 87 87
CD80 -0.039 0.16 -10000 0 -0.56 52 52
CD86 -0.036 0.16 -10000 0 -0.54 51 51
PDK1/CARD11/BCL10/MALT1 -0.079 0.12 -10000 0 -0.32 92 92
HRAS 0.008 0.041 -10000 0 -0.49 4 4
GO:0035030 -0.09 0.25 -10000 0 -0.57 108 108
CD8A -0.06 0.19 -10000 0 -0.54 78 78
CD8B -0.045 0.17 -10000 0 -0.56 59 59
PTPRC -0.043 0.17 -10000 0 -0.55 58 58
PDK1/PKC theta -0.069 0.23 -10000 0 -0.56 90 90
CSK/PAG1 -0.084 0.27 -10000 0 -0.69 82 82
SOS1 0.01 0.024 -10000 0 -0.58 1 1
peptide-MHC class I 0.006 0.06 -10000 0 -0.38 14 14
GRAP2/SLP76 -0.12 0.27 -10000 0 -0.68 93 93
STIM1 0.03 0.053 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.083 -10000 0 -0.19 58 58
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.11 0.33 -10000 0 -0.82 84 84
mol:DAG -0.068 0.15 0.13 1 -0.39 88 89
RAP1A/GDP 0.001 0.027 -10000 0 -0.15 1 1
PLCG1 0.01 0.024 -10000 0 -0.58 1 1
CD247 -0.02 0.13 -10000 0 -0.55 33 33
cytotoxic T cell degranulation -0.096 0.31 -10000 0 -0.85 67 67
RAP1A/GTP -0.006 0.015 -10000 0 -0.069 27 27
mol:PI-3-4-5-P3 -0.068 0.22 -10000 0 -0.54 90 90
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.083 0.24 0.22 65 -0.59 85 150
NRAS 0.001 0.076 -10000 0 -0.58 10 10
ZAP70 -0.036 0.15 -10000 0 -0.53 52 52
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
LAT/GRAP2/SLP76/VAV1 -0.11 0.22 -10000 0 -0.57 95 95
MALT1 0.006 0.054 -10000 0 -0.58 5 5
TRAF6 0.01 0.024 -10000 0 -0.58 1 1
CD8 heterodimer -0.074 0.2 -10000 0 -0.46 115 115
CARD11 -0.12 0.22 -10000 0 -0.49 153 153
PRKCB -0.062 0.13 -10000 0 -0.34 84 84
PRKCE -0.048 0.1 -10000 0 -0.28 75 75
PRKCQ -0.088 0.27 -10000 0 -0.64 93 93
LCP2 -0.014 0.12 -10000 0 -0.54 27 27
BCL10 0.007 0.048 -10000 0 -0.58 4 4
regulation of survival gene product expression -0.04 0.16 -10000 0 -0.38 89 89
IKK complex 0.005 0.056 -10000 0 -0.12 58 58
RAS family/GDP -0.007 0.016 -10000 0 -0.091 11 11
MAP3K14 -0.018 0.12 -10000 0 -0.28 72 72
PDPK1 -0.046 0.18 -10000 0 -0.42 89 89
TCR/CD3/MHC I/CD8/Fyn -0.11 0.34 -10000 0 -0.79 92 92
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.067 0.19 -10000 0 -0.44 84 84
TBX21 -0.24 0.51 -10000 0 -1.1 116 116
B2M 0.004 0.045 -10000 0 -0.52 4 4
TYK2 0.007 0.034 -10000 0 -0.61 1 1
IL12RB1 -0.037 0.16 -10000 0 -0.57 48 48
GADD45B -0.15 0.37 -10000 0 -0.85 87 87
IL12RB2 -0.038 0.16 -10000 0 -0.53 53 53
GADD45G -0.15 0.38 -10000 0 -0.84 97 97
natural killer cell activation -0.003 0.023 -10000 0 -10000 0 0
RELB 0.009 0.036 -10000 0 -0.5 3 3
RELA 0.011 0 -10000 0 -10000 0 0
IL18 0.003 0.069 -10000 0 -0.55 9 9
IL2RA -0.045 0.17 -10000 0 -0.55 60 60
IFNG -0.066 0.18 -10000 0 -0.51 86 86
STAT3 (dimer) -0.15 0.36 -10000 0 -0.78 114 114
HLA-DRB5 -0.081 0.2 -10000 0 -0.52 103 103
FASLG -0.24 0.51 -10000 0 -1.1 122 122
NF kappa B2 p52/RelB -0.26 0.4 -10000 0 -0.93 129 129
CD4 -0.014 0.12 -10000 0 -0.55 27 27
SOCS1 -0.028 0.14 -10000 0 -0.49 47 47
EntrezGene:6955 -0.004 0.015 -10000 0 -10000 0 0
CD3D -0.033 0.15 -10000 0 -0.56 43 43
CD3E -0.028 0.14 -10000 0 -0.56 38 38
CD3G -0.057 0.18 -10000 0 -0.57 67 67
IL12Rbeta2/JAK2 -0.034 0.14 -10000 0 -0.4 72 72
CCL3 -0.24 0.5 -10000 0 -1.1 117 117
CCL4 -0.22 0.49 -10000 0 -1.1 111 111
HLA-A -0.001 0.069 -10000 0 -0.52 10 10
IL18/IL18R -0.012 0.15 -10000 0 -0.38 72 72
NOS2 -0.27 0.55 -10000 0 -1.2 123 123
IL12/IL12R/TYK2/JAK2/SPHK2 -0.052 0.16 -10000 0 -0.41 69 69
IL1R1 -0.21 0.46 -10000 0 -1 108 108
IL4 0.004 0.024 -10000 0 -10000 0 0
JAK2 -0.012 0.11 -10000 0 -0.57 21 21
EntrezGene:6957 -0.004 0.015 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.18 0.45 -10000 0 -1.1 99 99
RAB7A -0.11 0.32 -10000 0 -0.73 73 73
lysosomal transport -0.1 0.3 -10000 0 -0.69 73 73
FOS -0.17 0.41 -10000 0 -1.1 82 82
STAT4 (dimer) -0.17 0.41 -10000 0 -0.88 115 115
STAT5A (dimer) -0.29 0.42 -10000 0 -0.94 146 146
GZMA -0.23 0.5 -10000 0 -1.1 115 115
GZMB -0.24 0.51 -10000 0 -1.1 125 125
HLX 0.006 0.055 -10000 0 -0.54 6 6
LCK -0.24 0.51 -10000 0 -1.1 124 124
TCR/CD3/MHC II/CD4 -0.12 0.34 -10000 0 -0.74 95 95
IL2/IL2R -0.032 0.15 -10000 0 -0.41 65 65
MAPK14 -0.15 0.38 -10000 0 -0.84 99 99
CCR5 -0.17 0.42 -10000 0 -1 82 82
IL1B -0.064 0.19 -10000 0 -0.53 80 80
STAT6 -0.036 0.12 -10000 0 -10000 0 0
STAT4 -0.027 0.14 -10000 0 -0.56 40 40
STAT3 0.011 0 -10000 0 -10000 0 0
STAT1 0.006 0.051 -10000 0 -0.5 6 6
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
NFKB2 0.01 0.031 -10000 0 -0.52 2 2
IL12B -0.006 0.075 -10000 0 -0.47 14 14
CD8A -0.063 0.19 -10000 0 -0.54 78 78
CD8B -0.048 0.17 -10000 0 -0.56 59 59
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.066 0.19 0.43 84 -10000 0 84
IL2RB -0.017 0.12 -10000 0 -0.55 30 30
proteasomal ubiquitin-dependent protein catabolic process -0.15 0.37 -10000 0 -0.79 112 112
IL2RG -0.001 0.084 -10000 0 -0.56 13 13
IL12 -0.029 0.13 -10000 0 -0.4 60 60
STAT5A 0.011 0 -10000 0 -10000 0 0
CD247 -0.023 0.13 -10000 0 -0.55 33 33
IL2 0.001 0.027 -10000 0 -0.46 2 2
SPHK2 0.009 0.036 -10000 0 -0.5 3 3
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.038 0.16 -10000 0 -0.57 47 47
IL12/IL12R/TYK2/JAK2 -0.26 0.58 -10000 0 -1.2 128 128
MAP2K3 -0.15 0.38 -10000 0 -0.84 101 101
RIPK2 0.011 0 -10000 0 -10000 0 0
MAP2K6 -0.16 0.39 -10000 0 -0.84 106 106
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.042 0.16 -10000 0 -0.52 60 60
IL18RAP -0.034 0.16 -10000 0 -0.55 48 48
IL12Rbeta1/TYK2 -0.022 0.13 -10000 0 -0.43 49 49
EOMES -0.14 0.41 -10000 0 -1.3 60 60
STAT1 (dimer) -0.18 0.38 -10000 0 -0.79 133 133
T cell proliferation -0.11 0.3 0.4 1 -0.64 107 108
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.012 0.12 -10000 0 -0.56 25 25
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.19 0.28 -10000 0 -0.68 116 116
ATF2 -0.13 0.35 -10000 0 -0.78 96 96
Syndecan-1-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
TGFB1 -0.003 0.088 -9999 0 -0.55 15 15
CCL5 -0.037 0.15 -9999 0 -0.51 55 55
SDCBP 0 0.08 -9999 0 -0.58 11 11
FGFR/FGF2/Syndecan-1 -0.12 0.19 -9999 0 -0.52 68 68
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.12 0.2 -9999 0 -0.48 98 98
Syndecan-1/Syntenin -0.11 0.19 -9999 0 -0.49 77 77
MAPK3 -0.085 0.17 -9999 0 -0.46 61 61
HGF/MET -0.02 0.12 -9999 0 -0.39 54 54
TGFB1/TGF beta receptor Type II -0.003 0.088 -9999 0 -0.55 15 15
BSG 0.01 0.024 -9999 0 -0.58 1 1
keratinocyte migration -0.12 0.2 -9999 0 -0.47 98 98
Syndecan-1/RANTES -0.13 0.2 -9999 0 -0.49 100 100
Syndecan-1/CD147 -0.094 0.18 -9999 0 -0.47 68 68
Syndecan-1/Syntenin/PIP2 -0.11 0.18 -9999 0 -0.47 77 77
LAMA5 -0.031 0.15 -9999 0 -0.57 43 43
positive regulation of cell-cell adhesion -0.1 0.18 -9999 0 -0.46 77 77
MMP7 -0.14 0.24 -9999 0 -0.52 167 167
HGF -0.037 0.16 -9999 0 -0.54 52 52
Syndecan-1/CASK -0.11 0.18 -9999 0 -0.5 68 68
Syndecan-1/HGF/MET -0.12 0.21 -9999 0 -0.5 92 92
regulation of cell adhesion -0.077 0.16 -9999 0 -0.48 49 49
HPSE -0.005 0.092 -9999 0 -0.51 19 19
positive regulation of cell migration -0.12 0.19 -9999 0 -0.52 68 68
SDC1 -0.12 0.19 -9999 0 -0.52 68 68
Syndecan-1/Collagen -0.12 0.19 -9999 0 -0.52 68 68
PPIB 0.011 0 -9999 0 -10000 0 0
MET 0.01 0.031 -9999 0 -0.52 2 2
PRKACA 0.011 0 -9999 0 -10000 0 0
MMP9 -0.059 0.18 -9999 0 -0.52 79 79
MAPK1 -0.085 0.17 -9999 0 -0.44 68 68
homophilic cell adhesion -0.11 0.19 -9999 0 -0.51 68 68
MMP1 -0.12 0.24 -9999 0 -0.53 151 151
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.28 0.36 -10000 0 -0.93 85 85
PCK1 -0.27 0.45 -10000 0 -1.3 78 78
HNF4A -0.36 0.44 -10000 0 -1.1 117 117
KCNJ11 -0.27 0.37 -10000 0 -1 68 68
AKT1 -0.14 0.16 -10000 0 -0.46 18 18
response to starvation -0.019 0.035 -10000 0 -10000 0 0
DLK1 -0.28 0.37 -10000 0 -0.97 78 78
NKX2-1 -0.18 0.34 -10000 0 -1.1 43 43
ACADM -0.29 0.38 -10000 0 -1 73 73
TAT -0.18 0.22 -10000 0 -0.74 30 30
CEBPB 0.004 0.042 -10000 0 -0.49 4 4
CEBPA -0.008 0.098 -10000 0 -0.58 17 17
TTR -0.29 0.41 -10000 0 -1 104 104
PKLR -0.43 0.48 -10000 0 -1 183 183
APOA1 -0.38 0.48 -10000 0 -1.2 106 106
CPT1C -0.3 0.39 -10000 0 -1 94 94
ALAS1 -0.12 0.18 -10000 0 -0.91 2 2
TFRC -0.18 0.28 -10000 0 -1 22 22
FOXF1 0.013 0.11 0.28 7 -0.56 16 23
NF1 0.014 0.042 -10000 0 -0.58 3 3
HNF1A (dimer) 0.002 0.072 -10000 0 -0.53 7 7
CPT1A -0.28 0.36 -10000 0 -0.96 74 74
HMGCS1 -0.28 0.37 -10000 0 -0.97 81 81
NR3C1 -0.037 0.13 -10000 0 -0.55 28 28
CPT1B -0.3 0.38 -10000 0 -0.97 98 98
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.007 0.044 -10000 0 -0.58 1 1
GCK -0.3 0.39 -10000 0 -0.99 93 93
CREB1 -0.008 0.062 -10000 0 -0.6 2 2
IGFBP1 -0.27 0.4 -10000 0 -1.2 70 70
PDX1 -0.18 0.35 -10000 0 -1.4 37 37
UCP2 -0.29 0.37 -10000 0 -0.96 89 89
ALDOB -0.38 0.48 -10000 0 -1.1 134 134
AFP -0.069 0.17 -10000 0 -0.52 43 43
BDH1 -0.28 0.37 -10000 0 -0.99 73 73
HADH -0.26 0.36 -10000 0 -1 64 64
F2 -0.41 0.52 -10000 0 -1.3 120 120
HNF1A 0.002 0.072 -10000 0 -0.53 7 7
G6PC -0.032 0.14 -10000 0 -0.87 5 5
SLC2A2 -0.17 0.24 -10000 0 -0.75 34 34
INS 0.016 0.065 -10000 0 -0.46 3 3
FOXA1 -0.07 0.21 0.27 2 -0.56 79 81
FOXA3 -0.033 0.13 -10000 0 -0.51 21 21
FOXA2 -0.31 0.41 -10000 0 -1.1 85 85
ABCC8 -0.29 0.39 -10000 0 -1.1 74 74
ALB -0.076 0.18 -10000 0 -0.54 37 37
Ephrin B reverse 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
EFNB2 0.01 0.031 -10000 0 -0.52 2 2
EPHB2 0 0.08 -10000 0 -0.55 12 12
EFNB1 0.005 0.07 -10000 0 -0.36 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.063 0.15 -10000 0 -0.48 34 34
Ephrin B2/EPHB1-2 -0.05 0.13 -10000 0 -0.27 149 149
neuron projection morphogenesis -0.083 0.13 -10000 0 -0.46 34 34
Ephrin B1/EPHB1-2/Tiam1 -0.072 0.16 -10000 0 -0.38 89 89
DNM1 -0.006 0.093 -10000 0 -0.5 20 20
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.081 0.23 -10000 0 -0.66 80 80
YES1 -0.12 0.3 -10000 0 -0.89 79 79
Ephrin B1/EPHB1-2/NCK2 -0.043 0.13 -10000 0 -0.33 56 56
PI3K -0.081 0.24 -10000 0 -0.65 83 83
mol:GDP -0.072 0.16 -10000 0 -0.37 89 89
ITGA2B -0.044 0.16 -10000 0 -0.5 63 63
endothelial cell proliferation 0.014 0.019 -10000 0 -0.31 2 2
FYN -0.12 0.3 -10000 0 -0.89 79 79
MAP3K7 -0.09 0.24 -10000 0 -0.7 79 79
FGR -0.13 0.3 -10000 0 -0.88 81 81
TIAM1 -0.044 0.16 -10000 0 -0.52 62 62
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
RGS3 0.011 0 -10000 0 -10000 0 0
cell adhesion -0.099 0.24 -10000 0 -0.63 85 85
LYN -0.12 0.3 -10000 0 -0.89 79 79
Ephrin B1/EPHB1-2/Src Family Kinases -0.12 0.28 -10000 0 -0.83 79 79
Ephrin B1/EPHB1-2 -0.11 0.26 -10000 0 -0.76 79 79
SRC -0.12 0.3 -10000 0 -0.88 79 79
ITGB3 -0.006 0.098 -10000 0 -0.54 19 19
EPHB1 -0.11 0.21 -10000 0 -0.49 138 138
EPHB4 0.011 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.014 0.019 -10000 0 -0.32 2 2
alphaIIb/beta3 Integrin -0.036 0.13 -10000 0 -0.37 81 81
BLK -0.15 0.31 -10000 0 -0.9 82 82
HCK -0.13 0.3 -10000 0 -0.88 81 81
regulation of stress fiber formation 0.044 0.13 0.33 56 -10000 0 56
MAPK8 -0.072 0.22 -10000 0 -0.62 81 81
Ephrin B1/EPHB1-2/RGS3 -0.043 0.13 -10000 0 -0.33 55 55
endothelial cell migration -0.074 0.21 -10000 0 -0.6 80 80
NCK2 0.01 0.024 -10000 0 -0.58 1 1
PTPN13 -0.095 0.25 -10000 0 -0.65 98 98
regulation of focal adhesion formation 0.044 0.13 0.33 56 -10000 0 56
chemotaxis 0.043 0.13 0.32 55 -10000 0 55
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
Rac1/GTP -0.085 0.14 -10000 0 -0.47 34 34
angiogenesis -0.11 0.26 -10000 0 -0.75 79 79
LCK -0.13 0.31 -10000 0 -0.9 80 80
BCR signaling pathway

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
JUN -0.062 0.16 -10000 0 -0.41 77 77
IKBKB -0.029 0.09 -10000 0 -0.26 29 29
AKT1 -0.051 0.11 0.21 1 -0.25 91 92
IKBKG -0.03 0.097 -10000 0 -0.28 29 29
CALM1 -0.041 0.16 0.25 22 -0.46 49 71
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
MAP3K1 -0.11 0.24 -10000 0 -0.57 99 99
MAP3K7 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.17 0.25 22 -0.48 52 74
DOK1 0.011 0 -10000 0 -10000 0 0
AP-1 -0.023 0.099 0.2 18 -0.25 49 67
LYN 0.011 0 -10000 0 -10000 0 0
BLNK -0.01 0.11 -10000 0 -0.58 21 21
SHC1 0.011 0 -10000 0 -10000 0 0
BCR complex -0.097 0.22 -10000 0 -0.47 140 140
CD22 -0.16 0.28 -10000 0 -0.69 100 100
CAMK2G -0.032 0.15 0.24 21 -0.44 46 67
CSNK2A1 0.011 0 -10000 0 -10000 0 0
INPP5D -0.017 0.13 -10000 0 -0.58 28 28
SHC/GRB2/SOS1 -0.076 0.14 -10000 0 -0.46 42 42
GO:0007205 -0.05 0.17 0.25 22 -0.49 52 74
SYK 0.011 0.019 -10000 0 -0.46 1 1
ELK1 -0.042 0.16 0.24 21 -0.47 49 70
NFATC1 -0.1 0.21 -10000 0 -0.51 91 91
B-cell antigen/BCR complex -0.097 0.22 -10000 0 -0.47 140 140
PAG1/CSK 0.011 0.048 -10000 0 -0.4 8 8
NFKBIB -0.002 0.033 0.084 13 -0.12 2 15
HRAS -0.039 0.15 0.23 21 -0.42 54 75
NFKBIA -0.001 0.032 0.084 13 -0.12 2 15
NF-kappa-B/RelA/I kappa B beta 0.005 0.028 0.085 13 -0.17 1 14
RasGAP/Csk -0.1 0.22 -10000 0 -0.6 66 66
mol:GDP -0.045 0.16 0.26 22 -0.46 52 74
PTEN 0.005 0.059 -10000 0 -0.58 6 6
CD79B -0.028 0.14 -10000 0 -0.52 44 44
NF-kappa-B/RelA/I kappa B alpha 0.005 0.028 0.085 13 -0.17 1 14
GRB2 0.011 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.11 0.22 -10000 0 -0.54 95 95
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
mol:IP3 -0.051 0.17 0.25 22 -0.5 52 74
CSK 0.01 0.024 -10000 0 -0.58 1 1
FOS -0.051 0.16 0.24 18 -0.42 69 87
CHUK -0.031 0.099 -10000 0 -0.28 35 35
IBTK 0.001 0.076 -10000 0 -0.58 10 10
CARD11/BCL10/MALT1/TAK1 -0.1 0.16 -10000 0 -0.46 77 77
PTPN6 -0.13 0.27 -10000 0 -0.67 92 92
RELA 0.011 0 -10000 0 -10000 0 0
BCL2A1 -0.002 0.036 -10000 0 -0.1 40 40
VAV2 -0.15 0.29 -10000 0 -0.66 110 110
ubiquitin-dependent protein catabolic process 0.002 0.032 0.086 13 -0.11 2 15
BTK -0.055 0.27 0.36 25 -1.1 35 60
CD19 -0.17 0.28 -10000 0 -0.64 114 114
MAP4K1 -0.044 0.17 -10000 0 -0.55 59 59
CD72 -0.005 0.09 -10000 0 -0.5 19 19
PAG1 0.005 0.06 -10000 0 -0.55 7 7
MAPK14 -0.088 0.2 -10000 0 -0.48 92 92
SH3BP5 0.002 0.072 -10000 0 -0.58 9 9
PIK3AP1 -0.053 0.17 0.3 2 -0.5 57 59
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.075 0.23 -10000 0 -0.52 93 93
RAF1 -0.031 0.14 0.22 21 -0.41 48 69
RasGAP/p62DOK/SHIP -0.13 0.2 -10000 0 -0.59 69 69
CD79A -0.11 0.23 -10000 0 -0.54 134 134
re-entry into mitotic cell cycle -0.023 0.099 0.2 18 -0.25 49 67
RASA1 0.009 0.034 -10000 0 -0.58 2 2
MAPK3 -0.015 0.12 0.22 20 -0.41 27 47
MAPK1 -0.015 0.12 0.22 19 -0.41 27 46
CD72/SHP1 -0.12 0.26 -10000 0 -0.65 88 88
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 -0.089 0.2 -10000 0 -0.48 96 96
actin cytoskeleton organization -0.12 0.24 -10000 0 -0.57 100 100
NF-kappa-B/RelA 0.014 0.053 0.17 13 -0.22 2 15
Calcineurin -0.053 0.12 -10000 0 -0.46 32 32
PI3K -0.15 0.21 -10000 0 -0.53 111 111
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.055 0.17 0.31 2 -0.5 53 55
SOS1 0.01 0.024 -10000 0 -0.58 1 1
Bam32/HPK1 -0.15 0.33 -10000 0 -0.85 95 95
DAPP1 -0.17 0.36 -10000 0 -1.1 73 73
cytokine secretion -0.092 0.2 -10000 0 -0.47 91 91
mol:DAG -0.051 0.17 0.25 22 -0.5 52 74
PLCG2 -0.011 0.11 -10000 0 -0.54 24 24
MAP2K1 -0.023 0.13 0.22 20 -0.43 34 54
B-cell antigen/BCR complex/FcgammaRIIB -0.13 0.25 -10000 0 -0.51 136 136
mol:PI-3-4-5-P3 -0.1 0.14 0.28 1 -0.36 108 109
ETS1 -0.027 0.14 0.24 21 -0.46 36 57
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.064 0.18 -10000 0 -0.37 124 124
B-cell antigen/BCR complex/LYN -0.12 0.25 -10000 0 -0.53 114 114
MALT1 0.006 0.054 -10000 0 -0.58 5 5
TRAF6 0.01 0.024 -10000 0 -0.58 1 1
RAC1 -0.13 0.26 -10000 0 -0.62 100 100
B-cell antigen/BCR complex/LYN/SYK -0.14 0.25 -10000 0 -0.67 90 90
CARD11 -0.1 0.21 0.25 17 -0.5 95 112
FCGR2B -0.084 0.21 -10000 0 -0.53 104 104
PPP3CA 0.011 0 -10000 0 -10000 0 0
BCL10 0.007 0.048 -10000 0 -0.58 4 4
IKK complex -0.006 0.041 0.091 13 -0.12 6 19
PTPRC -0.043 0.17 -10000 0 -0.54 58 58
PDPK1 -0.053 0.11 0.19 1 -0.25 89 90
PPP3CB 0.011 0 -10000 0 -10000 0 0
PPP3CC 0.005 0.059 -10000 0 -0.58 6 6
POU2F2 0.004 0.028 -10000 0 -0.095 22 22
Endothelins

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
AKT1 -0.034 0.23 0.27 34 -0.6 53 87
PTK2B 0.01 0.034 -10000 0 -0.58 2 2
mol:Ca2+ -0.024 0.25 -10000 0 -0.88 36 36
EDN1 -0.022 0.17 -10000 0 -0.44 55 55
EDN3 -0.095 0.22 -10000 0 -0.55 112 112
EDN2 -0.065 0.19 -10000 0 -0.52 85 85
HRAS/GDP -0.043 0.19 -10000 0 -0.48 60 60
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.021 0.17 -10000 0 -0.45 48 48
ADCY4 -0.048 0.2 -10000 0 -0.53 59 59
ADCY5 -0.1 0.23 -10000 0 -0.53 93 93
ADCY6 -0.044 0.2 -10000 0 -0.52 57 57
ADCY7 -0.046 0.2 -10000 0 -0.53 57 57
ADCY1 -0.071 0.21 -10000 0 -0.54 69 69
ADCY2 -0.07 0.23 -10000 0 -0.56 76 76
ADCY3 -0.045 0.2 -10000 0 -0.51 60 60
ADCY8 -0.056 0.2 -10000 0 -0.52 59 59
ADCY9 -0.046 0.2 -10000 0 -0.52 57 57
arachidonic acid secretion -0.065 0.2 -10000 0 -0.5 67 67
ETB receptor/Endothelin-1/Gq/GTP -0.011 0.14 -10000 0 -0.47 30 30
GNAO1 -0.046 0.16 -10000 0 -0.49 68 68
HRAS 0.008 0.041 -10000 0 -0.49 4 4
ETA receptor/Endothelin-1/G12/GTP -0.03 0.23 0.3 99 -0.57 50 149
ETA receptor/Endothelin-1/Gs/GTP -0.045 0.23 0.29 85 -0.54 60 145
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.055 0.28 -10000 0 -0.74 64 64
EDNRB -0.01 0.11 -10000 0 -0.57 20 20
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.069 0.29 -10000 0 -0.66 85 85
CYSLTR1 -0.062 0.29 -10000 0 -0.71 74 74
SLC9A1 -0.025 0.12 0.19 49 -0.31 47 96
mol:GDP -0.051 0.2 -10000 0 -0.51 63 63
SLC9A3 -0.16 0.32 -10000 0 -0.62 155 155
RAF1 -0.047 0.18 -10000 0 -0.49 50 50
JUN -0.007 0.2 -10000 0 -0.73 27 27
JAK2 -0.046 0.24 0.27 28 -0.58 66 94
mol:IP3 -0.023 0.17 -10000 0 -0.46 45 45
ETA receptor/Endothelin-1 -0.045 0.28 0.42 55 -0.65 61 116
PLCB1 -0.032 0.15 -10000 0 -0.56 45 45
PLCB2 0.004 0.062 -10000 0 -0.52 8 8
ETA receptor/Endothelin-3 -0.096 0.21 -10000 0 -0.44 133 133
FOS -0.051 0.23 -10000 0 -0.81 36 36
Gai/GDP -0.026 0.17 -10000 0 -0.84 19 19
CRK 0.011 0.019 -10000 0 -0.46 1 1
mol:Ca ++ -0.052 0.26 -10000 0 -0.64 67 67
BCAR1 0.008 0.044 -10000 0 -0.52 4 4
PRKCB1 -0.022 0.16 -10000 0 -0.45 44 44
GNAQ 0.006 0.059 -10000 0 -0.58 6 6
GNAZ -0.012 0.11 -10000 0 -0.55 25 25
GNAL -0.02 0.12 -10000 0 -0.5 36 36
Gs family/GDP -0.09 0.16 -10000 0 -0.47 71 71
ETA receptor/Endothelin-1/Gq/GTP -0.014 0.18 -10000 0 -0.5 42 42
MAPK14 -0.012 0.13 -10000 0 -0.46 28 28
TRPC6 -0.029 0.27 -10000 0 -0.98 35 35
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 -0.003 0.089 -10000 0 -0.56 15 15
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.019 0.14 -10000 0 -0.43 38 38
ETB receptor/Endothelin-2 -0.054 0.16 -10000 0 -0.38 104 104
ETB receptor/Endothelin-3 -0.075 0.18 -10000 0 -0.41 129 129
ETB receptor/Endothelin-1 -0.02 0.16 -10000 0 -0.42 55 55
MAPK3 -0.05 0.22 -10000 0 -0.69 41 41
MAPK1 -0.05 0.22 -10000 0 -0.69 41 41
Rac1/GDP -0.041 0.18 -10000 0 -0.48 56 56
cAMP biosynthetic process -0.073 0.21 -10000 0 -0.5 78 78
MAPK8 -0.018 0.22 -10000 0 -0.7 39 39
SRC 0.01 0.024 -10000 0 -0.58 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.02 0.12 -10000 0 -0.42 31 31
p130Cas/CRK/Src/PYK2 -0.052 0.21 -10000 0 -0.61 49 49
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.041 0.18 -10000 0 -0.48 57 57
COL1A2 -0.06 0.32 -10000 0 -0.81 65 65
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.074 0.18 -10000 0 -0.41 112 112
mol:DAG -0.023 0.17 -10000 0 -0.46 45 45
MAP2K2 -0.045 0.19 -10000 0 -0.54 46 46
MAP2K1 -0.045 0.19 -10000 0 -0.54 47 47
EDNRA -0.022 0.19 -10000 0 -0.51 52 52
positive regulation of muscle contraction -0.023 0.2 -10000 0 -0.56 47 47
Gq family/GDP -0.08 0.17 -10000 0 -0.56 46 46
HRAS/GTP -0.051 0.18 -10000 0 -0.46 64 64
PRKCH -0.02 0.16 -10000 0 -0.47 44 44
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.018 0.16 -10000 0 -0.47 37 37
PRKCB -0.042 0.2 -10000 0 -0.5 67 67
PRKCE -0.016 0.16 -10000 0 -0.48 34 34
PRKCD -0.017 0.16 -10000 0 -0.45 41 41
PRKCG -0.095 0.2 -10000 0 -0.47 77 77
regulation of vascular smooth muscle contraction -0.061 0.26 -10000 0 -0.94 36 36
PRKCQ -0.045 0.19 -10000 0 -0.5 53 53
PLA2G4A -0.072 0.22 -10000 0 -0.55 67 67
GNA14 -0.006 0.1 -10000 0 -0.56 19 19
GNA15 -0.008 0.1 -10000 0 -0.54 21 21
GNA12 0.011 0 -10000 0 -10000 0 0
GNA11 0.007 0.05 -10000 0 -0.54 5 5
Rac1/GTP -0.03 0.23 0.3 97 -0.58 49 146
MMP1 -0.15 0.36 -10000 0 -0.75 138 138
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.05 0.22 -10000 0 -0.64 51 51
IHH -0.039 0.17 -10000 0 -0.62 43 43
SHH Np/Cholesterol/GAS1 -0.08 0.16 -10000 0 -0.3 185 185
LRPAP1 0.01 0.024 -10000 0 -0.58 1 1
dorsoventral neural tube patterning 0.08 0.16 0.3 185 -10000 0 185
SMO/beta Arrestin2 -0.036 0.19 -10000 0 -0.64 34 34
SMO -0.044 0.2 -10000 0 -0.67 36 36
AKT1 -0.005 0.11 -10000 0 -0.5 11 11
ARRB2 0.011 0 -10000 0 -10000 0 0
BOC -0.034 0.14 -10000 0 -0.48 55 55
ADRBK1 0.01 0.031 -10000 0 -0.52 2 2
heart looping -0.043 0.2 -10000 0 -0.65 36 36
STIL -0.026 0.16 -10000 0 -0.59 29 29
DHH N/PTCH2 -0.041 0.15 -10000 0 -0.43 77 77
DHH N/PTCH1 -0.047 0.17 -10000 0 -0.57 26 26
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
DHH -0.03 0.14 -10000 0 -0.54 44 44
PTHLH -0.075 0.29 -10000 0 -0.92 51 51
determination of left/right symmetry -0.043 0.2 -10000 0 -0.65 36 36
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
skeletal system development -0.074 0.29 -10000 0 -0.91 51 51
IHH N/Hhip -0.084 0.2 -10000 0 -0.46 126 126
DHH N/Hhip -0.079 0.19 -10000 0 -0.42 131 131
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.043 0.2 -10000 0 -0.65 36 36
pancreas development -0.08 0.21 -10000 0 -0.54 98 98
HHAT 0.004 0.064 -10000 0 -0.58 7 7
PI3K 0.013 0.04 -10000 0 -0.42 5 5
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.13 0.24 -10000 0 -0.52 160 160
somite specification -0.043 0.2 -10000 0 -0.65 36 36
SHH Np/Cholesterol/PTCH1 -0.032 0.17 -10000 0 -0.6 31 31
SHH Np/Cholesterol/PTCH2 -0.023 0.12 -10000 0 -0.32 77 77
SHH Np/Cholesterol/Megalin -0.023 0.11 -10000 0 -0.29 76 76
SHH -0.009 0.11 -10000 0 -0.41 38 38
catabolic process -0.032 0.16 -10000 0 -0.57 24 24
SMO/Vitamin D3 -0.039 0.19 -10000 0 -0.63 39 39
SHH Np/Cholesterol/Hhip -0.053 0.15 -10000 0 -0.33 124 124
LRP2 -0.028 0.12 -10000 0 -0.46 43 43
receptor-mediated endocytosis -0.043 0.19 -10000 0 -0.6 41 41
SHH Np/Cholesterol/BOC -0.026 0.12 -10000 0 -0.3 87 87
SHH Np/Cholesterol/CDO -0.008 0.1 -10000 0 -0.34 47 47
mesenchymal cell differentiation 0.053 0.15 0.33 124 -10000 0 124
mol:Vitamin D3 -0.03 0.17 -10000 0 -0.61 31 31
IHH N/PTCH2 -0.043 0.16 -10000 0 -0.44 78 78
CDON -0.001 0.081 -10000 0 -0.52 14 14
IHH N/PTCH1 -0.031 0.16 -10000 0 -0.57 24 24
Megalin/LRPAP1 -0.012 0.087 -10000 0 -0.32 44 44
PTCH2 -0.028 0.14 -10000 0 -0.54 42 42
SHH Np/Cholesterol -0.008 0.082 -10000 0 -0.32 38 38
PTCH1 -0.032 0.16 -10000 0 -0.57 24 24
HHIP -0.08 0.21 -10000 0 -0.54 98 98
TCGA08_retinoblastoma

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
CDKN2B -0.013 0.1 -10000 0 -0.51 25 25
CDKN2C 0.018 0.017 -10000 0 -10000 0 0
CDKN2A -0.07 0.19 -10000 0 -0.5 94 94
CCND2 0.019 0.072 0.21 48 -0.13 26 74
RB1 -0.016 0.077 -10000 0 -0.22 53 53
CDK4 0.027 0.075 0.23 48 -10000 0 48
CDK6 0.026 0.076 0.23 48 -10000 0 48
G1/S progression 0.016 0.077 0.22 53 -10000 0 53
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.059 0.16 0.4 104 -10000 0 104
KIRREL -0.032 0.14 -10000 0 -0.58 38 38
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.059 0.16 -10000 0 -0.4 104 104
PLCG1 0.01 0.024 -10000 0 -0.58 1 1
ARRB2 0.011 0 -10000 0 -10000 0 0
WASL 0.011 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.057 0.16 -10000 0 -0.38 89 89
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.023 0.11 -10000 0 -0.31 62 62
FYN -0.042 0.13 -10000 0 -0.34 65 65
mol:Ca2+ -0.041 0.13 -10000 0 -0.36 61 61
mol:DAG -0.041 0.14 -10000 0 -0.37 61 61
NPHS2 -0.021 0.092 -10000 0 -0.47 23 23
mol:IP3 -0.041 0.14 -10000 0 -0.37 61 61
regulation of endocytosis -0.032 0.12 -10000 0 -0.32 61 61
Nephrin/NEPH1/podocin/Cholesterol -0.047 0.13 -10000 0 -0.32 95 95
establishment of cell polarity -0.059 0.16 -10000 0 -0.4 104 104
Nephrin/NEPH1/podocin/NCK1-2 -0.031 0.13 -10000 0 -0.33 62 62
Nephrin/NEPH1/beta Arrestin2 -0.032 0.12 -10000 0 -0.33 61 61
NPHS1 -0.057 0.17 -10000 0 -0.51 73 73
Nephrin/NEPH1/podocin -0.041 0.13 -10000 0 -0.34 65 65
TJP1 0.01 0.024 -10000 0 -0.58 1 1
NCK1 0.009 0.034 -10000 0 -0.58 2 2
NCK2 0.01 0.024 -10000 0 -0.58 1 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.04 0.14 -10000 0 -0.37 61 61
CD2AP -0.017 0.13 -10000 0 -0.58 29 29
Nephrin/NEPH1/podocin/GRB2 -0.04 0.13 -10000 0 -0.36 61 61
GRB2 0.011 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.051 0.15 -10000 0 -0.39 74 74
cytoskeleton organization -0.027 0.13 -10000 0 -0.37 60 60
Nephrin/NEPH1 -0.04 0.12 -10000 0 -0.28 104 104
Nephrin/NEPH1/ZO-1 -0.039 0.14 -10000 0 -0.37 61 61
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.23 0.46 -9999 0 -1.1 65 65
HDAC7 0.011 0.025 -9999 0 -0.58 1 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.19 0.33 -9999 0 -0.91 50 50
SMAD4 0.005 0.064 -9999 0 -0.58 7 7
ID2 -0.23 0.46 -9999 0 -1.1 66 66
AP1 -0.014 0.11 -9999 0 -0.39 45 45
ABCG2 -0.26 0.48 -9999 0 -1.2 79 79
HIF1A -0.029 0.11 -9999 0 -0.68 9 9
TFF3 -0.25 0.48 -9999 0 -1.2 80 80
GATA2 -0.018 0.13 -9999 0 -0.56 31 31
AKT1 -0.024 0.087 -9999 0 -0.72 1 1
response to hypoxia -0.038 0.086 -9999 0 -0.25 6 6
MCL1 -0.23 0.46 -9999 0 -1.1 63 63
NDRG1 -0.23 0.46 -9999 0 -1.1 65 65
SERPINE1 -0.25 0.48 -9999 0 -1.2 75 75
FECH -0.23 0.46 -9999 0 -1.1 64 64
FURIN -0.23 0.46 -9999 0 -1.1 64 64
NCOA2 0.004 0.067 -9999 0 -0.56 8 8
EP300 -0.015 0.12 -9999 0 -0.37 19 19
HMOX1 -0.23 0.46 -9999 0 -1.2 64 64
BHLHE40 -0.23 0.46 -9999 0 -1.1 64 64
BHLHE41 -0.24 0.48 -9999 0 -1.2 70 70
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.036 0.11 -9999 0 -0.5 14 14
ENG -0.004 0.12 -9999 0 -0.57 8 8
JUN 0.006 0.052 -9999 0 -0.56 5 5
RORA -0.24 0.48 -9999 0 -1.2 71 71
ABCB1 -0.22 0.39 -9999 0 -1.1 91 91
TFRC -0.23 0.46 -9999 0 -1.2 64 64
CXCR4 -0.24 0.48 -9999 0 -1.2 72 72
TF -0.28 0.5 -9999 0 -1.1 89 89
CITED2 -0.23 0.46 -9999 0 -1.1 64 64
HIF1A/ARNT -0.3 0.5 -9999 0 -1.3 77 77
LDHA -0.036 0.078 -9999 0 -1.1 2 2
ETS1 -0.23 0.46 -9999 0 -1.2 64 64
PGK1 -0.23 0.46 -9999 0 -1.1 64 64
NOS2 -0.28 0.5 -9999 0 -1.2 88 88
ITGB2 -0.24 0.48 -9999 0 -1.2 74 74
ALDOA -0.23 0.46 -9999 0 -1.1 66 66
Cbp/p300/CITED2 -0.22 0.47 -9999 0 -1.1 69 69
FOS -0.026 0.14 -9999 0 -0.53 41 41
HK2 -0.23 0.46 -9999 0 -1.1 65 65
SP1 0.005 0.043 -9999 0 -0.58 1 1
GCK -0.054 0.29 -9999 0 -1.2 24 24
HK1 -0.23 0.46 -9999 0 -1.1 67 67
NPM1 -0.23 0.46 -9999 0 -1.2 65 65
EGLN1 -0.23 0.46 -9999 0 -1.1 63 63
CREB1 0.016 0.035 -9999 0 -0.58 2 2
PGM1 -0.23 0.46 -9999 0 -1.1 65 65
SMAD3 0.006 0.062 -9999 0 -0.56 7 7
EDN1 -0.061 0.27 -9999 0 -1.1 25 25
IGFBP1 -0.28 0.5 -9999 0 -1.1 93 93
VEGFA -0.12 0.34 -9999 0 -0.85 30 30
HIF1A/JAB1 -0.024 0.07 -9999 0 -0.49 10 10
CP -0.29 0.51 -9999 0 -1.2 96 96
CXCL12 -0.24 0.47 -9999 0 -1.2 72 72
COPS5 0.011 0.019 -9999 0 -0.46 1 1
SMAD3/SMAD4 0.009 0.065 -9999 0 -0.41 14 14
BNIP3 -0.26 0.49 -9999 0 -1.2 81 81
EGLN3 -0.23 0.47 -9999 0 -1.2 68 68
CA9 -0.31 0.51 -9999 0 -1.1 116 116
TERT -0.25 0.48 -9999 0 -1.1 81 81
ENO1 -0.23 0.46 -9999 0 -1.1 64 64
PFKL -0.23 0.46 -9999 0 -1.2 64 64
NCOA1 0.011 0.024 -9999 0 -0.58 1 1
ADM -0.23 0.46 -9999 0 -1.1 70 70
ARNT -0.021 0.078 -9999 0 -0.64 1 1
HNF4A 0.004 0.066 -9999 0 -0.58 7 7
ADFP -0.23 0.46 -9999 0 -1.1 73 73
SLC2A1 -0.12 0.34 -9999 0 -0.88 32 32
LEP -0.24 0.47 -9999 0 -1.2 68 68
HIF1A/ARNT/Cbp/p300 -0.2 0.34 -9999 0 -0.95 48 48
EPO -0.095 0.29 -9999 0 -0.98 13 13
CREBBP -0.013 0.12 -9999 0 -0.35 19 19
HIF1A/ARNT/Cbp/p300/HDAC7 -0.19 0.33 -9999 0 -0.94 45 45
PFKFB3 -0.23 0.46 -9999 0 -1.1 64 64
NT5E -0.24 0.48 -9999 0 -1.2 68 68
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.015 0.025 -10000 0 -0.42 2 2
Necdin/E2F1 0.008 0.059 -10000 0 -0.37 14 14
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.055 0.16 -10000 0 -0.36 105 105
NGF (dimer)/p75(NTR)/BEX1 -0.1 0.2 -10000 0 -0.38 179 179
NT-4/5 (dimer)/p75(NTR) -0.066 0.16 -10000 0 -0.37 122 122
IKBKB 0.011 0.019 -10000 0 -0.46 1 1
AKT1 -0.041 0.14 -10000 0 -0.33 86 86
IKBKG 0.01 0.024 -10000 0 -0.58 1 1
BDNF -0.021 0.13 -10000 0 -0.52 36 36
MGDIs/NGR/p75(NTR)/LINGO1 -0.062 0.16 -10000 0 -0.33 145 145
FURIN 0.01 0.031 -10000 0 -0.52 2 2
proBDNF (dimer)/p75(NTR)/Sortilin -0.053 0.15 -10000 0 -0.33 129 129
LINGO1 -0.023 0.12 -10000 0 -0.47 43 43
Sortilin/TRAF6/NRIF -0.008 0.05 -10000 0 -0.79 1 1
proBDNF (dimer) -0.021 0.13 -10000 0 -0.52 36 36
NTRK1 -0.038 0.16 -10000 0 -0.53 53 53
RTN4R -0.004 0.085 -10000 0 -0.48 18 18
neuron apoptosis -0.06 0.17 -10000 0 -0.58 27 27
IRAK1 0.01 0.031 -10000 0 -0.52 2 2
SHC1 -0.059 0.16 -10000 0 -0.35 129 129
ARHGDIA 0.008 0.042 -10000 0 -0.58 3 3
RhoA/GTP 0.008 0.018 -10000 0 -0.43 1 1
Gamma Secretase 0.031 0.033 -10000 0 -0.29 6 6
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.051 0.16 -10000 0 -0.37 86 86
MAGEH1 0.003 0.071 -10000 0 -0.57 9 9
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.051 0.16 -10000 0 -0.38 85 85
Mammalian IAPs/DIABLO 0.006 0.1 -10000 0 -0.45 21 21
proNGF (dimer) -0.032 0.14 -10000 0 -0.52 47 47
MAGED1 0.011 0 -10000 0 -10000 0 0
APP 0.01 0.024 -10000 0 -0.58 1 1
NT-4/5 (dimer) -0.014 0.09 -10000 0 -0.46 23 23
ZNF274 0.001 0.076 -10000 0 -0.58 10 10
RhoA/GDP/RHOGDI -0.045 0.14 -10000 0 -0.34 84 84
NGF -0.032 0.14 -10000 0 -0.52 47 47
cell cycle arrest -0.05 0.14 -10000 0 -0.34 80 80
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.024 0.11 -10000 0 -0.27 82 82
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.049 0.14 -10000 0 -0.31 123 123
NCSTN 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.078 0.18 -10000 0 -0.37 152 152
PSENEN 0.01 0.024 -10000 0 -0.58 1 1
mol:ceramide -0.047 0.15 -10000 0 -0.37 80 80
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.012 0.098 -10000 0 -0.44 8 8
p75(NTR)/beta APP -0.05 0.14 -10000 0 -0.36 105 105
BEX1 -0.059 0.18 -10000 0 -0.5 79 79
mol:GDP -0.067 0.16 -10000 0 -0.36 129 129
NGF (dimer) -0.11 0.18 -10000 0 -0.38 137 137
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.05 0.15 -10000 0 -0.39 62 62
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
RAC1/GTP -0.05 0.14 -10000 0 -0.3 129 129
MYD88 0.011 0 -10000 0 -10000 0 0
CHUK 0.007 0.048 -10000 0 -0.58 4 4
NGF (dimer)/p75(NTR)/PKA -0.079 0.18 -10000 0 -0.37 152 152
RHOB 0.009 0.039 -10000 0 -0.54 3 3
RHOA 0.01 0.024 -10000 0 -0.58 1 1
MAGE-G1/E2F1 0.015 0.026 -10000 0 -0.35 3 3
NT3 (dimer) -0.02 0.13 -10000 0 -0.53 34 34
TP53 -0.061 0.16 -10000 0 -0.55 20 20
PRDM4 -0.048 0.15 -10000 0 -0.37 80 80
BDNF (dimer) -0.18 0.22 -10000 0 -0.42 203 203
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
SORT1 0.01 0.024 -10000 0 -0.58 1 1
activation of caspase activity -0.057 0.16 -10000 0 -0.35 105 105
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.047 0.15 -10000 0 -0.37 81 81
RHOC 0.011 0 -10000 0 -10000 0 0
XIAP 0.01 0.024 -10000 0 -0.58 1 1
MAPK10 -0.042 0.16 -10000 0 -0.51 30 30
DIABLO 0.011 0 -10000 0 -10000 0 0
SMPD2 -0.048 0.15 -10000 0 -0.37 80 80
APH1B 0.006 0.054 -10000 0 -0.58 5 5
APH1A 0.011 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.059 0.16 -10000 0 -0.35 129 129
PSEN1 0.011 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.014 0.036 -10000 0 -0.42 4 4
NT3 (dimer)/p75(NTR) -0.07 0.17 -10000 0 -0.39 127 127
MAPK8 -0.026 0.14 -10000 0 -0.52 17 17
MAPK9 -0.026 0.14 -10000 0 -0.52 17 17
APAF1 0.008 0.042 -10000 0 -0.58 3 3
NTF3 -0.02 0.13 -10000 0 -0.53 34 34
NTF4 -0.014 0.09 -10000 0 -0.46 23 23
NDN 0.001 0.073 -10000 0 -0.52 11 11
RAC1/GDP 0.008 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.074 0.14 -10000 0 -0.47 33 33
p75 CTF/Sortilin/TRAF6/NRIF 0.021 0.061 -10000 0 -0.37 12 12
RhoA-B-C/GTP -0.078 0.18 -10000 0 -0.37 152 152
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.038 0.14 -10000 0 -0.36 66 66
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.041 0.14 -10000 0 -0.37 60 60
PRKACB -0.022 0.14 -10000 0 -0.57 34 34
proBDNF (dimer)/p75 ECD -0.008 0.097 -10000 0 -0.38 38 38
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.12 -10000 0 -0.52 30 30
BIRC2 -0.002 0.087 -10000 0 -0.58 13 13
neuron projection morphogenesis -0.063 0.16 0.19 19 -0.38 80 99
BAD -0.027 0.14 -10000 0 -0.49 22 22
RIPK2 0.011 0 -10000 0 -10000 0 0
NGFR -0.079 0.2 -10000 0 -0.51 104 104
CYCS -0.047 0.15 -10000 0 -0.35 94 94
ADAM17 0.009 0.034 -10000 0 -0.58 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.046 0.15 -10000 0 -0.37 81 81
BCL2L11 -0.026 0.14 -10000 0 -0.46 26 26
BDNF (dimer)/p75(NTR) -0.071 0.18 -10000 0 -0.39 129 129
PI3K -0.048 0.15 -10000 0 -0.36 85 85
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.046 0.15 -10000 0 -0.37 80 80
NDNL2 0.011 0 -10000 0 -10000 0 0
YWHAE 0.011 0 -10000 0 -10000 0 0
PRKCI 0.008 0.042 -10000 0 -0.58 3 3
NGF (dimer)/p75(NTR) -0.078 0.19 -10000 0 -0.42 129 129
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.046 0.15 -10000 0 -0.37 80 80
TRAF6 0.01 0.024 -10000 0 -0.58 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
PLG -0.036 0.15 -10000 0 -0.58 42 42
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.056 0.16 -10000 0 -0.37 95 95
SQSTM1 0.011 0 -10000 0 -10000 0 0
NGFRAP1 -0.021 0.14 -10000 0 -0.58 33 33
CASP3 -0.023 0.14 -10000 0 -0.45 22 22
E2F1 0.009 0.036 -10000 0 -0.5 3 3
CASP9 0.01 0.024 -10000 0 -0.58 1 1
IKK complex -0.06 0.12 -10000 0 -0.52 20 20
NGF (dimer)/TRKA -0.049 0.16 -10000 0 -0.41 90 90
MMP7 -0.14 0.24 -10000 0 -0.52 167 167
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.043 0.15 -10000 0 -0.35 87 87
MMP3 -0.13 0.24 -10000 0 -0.53 154 154
APAF-1/Caspase 9 -0.067 0.14 -10000 0 -0.57 25 25
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.01 0.031 -10000 0 -0.52 2 2
LAT2 -0.064 0.17 -10000 0 -0.41 84 84
AP1 -0.11 0.2 -10000 0 -0.58 72 72
mol:PIP3 -0.082 0.22 -10000 0 -0.57 70 70
IKBKB -0.034 0.13 0.15 13 -0.31 72 85
AKT1 -0.051 0.16 -10000 0 -0.45 47 47
IKBKG -0.034 0.13 0.15 13 -0.32 69 82
MS4A2 -0.083 0.21 -10000 0 -0.54 101 101
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
MAP3K1 -0.054 0.18 -10000 0 -0.5 64 64
mol:Ca2+ -0.057 0.16 -10000 0 -0.41 70 70
LYN 0.009 0.006 -10000 0 -10000 0 0
CBLB -0.061 0.17 -10000 0 -0.41 82 82
SHC1 0.011 0 -10000 0 -10000 0 0
RasGAP/p62DOK 0.011 0.055 -10000 0 -0.32 5 5
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D -0.017 0.12 -10000 0 -0.58 28 28
PLD2 -0.076 0.17 -10000 0 -0.39 97 97
PTPN13 -0.097 0.2 -10000 0 -0.58 56 56
PTPN11 0.003 0.056 -10000 0 -0.6 5 5
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.027 0.13 -10000 0 -0.36 42 42
SYK 0.008 0.02 -10000 0 -0.45 1 1
GRB2 0.011 0.001 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.12 0.2 -10000 0 -0.59 73 73
LAT -0.07 0.18 -10000 0 -0.45 72 72
PAK2 -0.065 0.2 -10000 0 -0.55 67 67
NFATC2 -0.081 0.18 -10000 0 -0.62 49 49
HRAS -0.077 0.22 -10000 0 -0.6 69 69
GAB2 0.009 0.034 -10000 0 -0.58 2 2
PLA2G1B 0.029 0.026 -10000 0 -10000 0 0
Fc epsilon R1 -0.12 0.2 -10000 0 -0.39 182 182
Antigen/IgE/Fc epsilon R1 -0.11 0.18 -10000 0 -0.36 182 182
mol:GDP -0.089 0.24 -10000 0 -0.66 70 70
JUN 0.007 0.052 -10000 0 -0.56 5 5
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
FOS -0.026 0.14 -10000 0 -0.53 41 41
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.069 0.17 -10000 0 -0.41 87 87
CHUK -0.035 0.13 0.15 13 -0.32 72 85
KLRG1 -0.065 0.16 -10000 0 -0.42 69 69
VAV1 -0.078 0.2 -10000 0 -0.5 74 74
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.059 0.16 -10000 0 -0.4 80 80
negative regulation of mast cell degranulation -0.069 0.17 -10000 0 -0.42 73 73
BTK -0.092 0.26 -10000 0 -0.68 71 71
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.12 0.24 -10000 0 -0.68 70 70
GAB2/PI3K/SHP2 -0.09 0.15 -10000 0 -0.5 47 47
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.06 0.16 -10000 0 -0.44 56 56
RAF1 0.023 0.025 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.14 0.25 -10000 0 -0.48 162 162
FCER1G -0.019 0.13 -10000 0 -0.54 34 34
FCER1A -0.077 0.2 -10000 0 -0.56 90 90
Antigen/IgE/Fc epsilon R1/Fyn -0.086 0.18 -10000 0 -0.38 135 135
MAPK3 0.029 0.025 -10000 0 -10000 0 0
MAPK1 0.029 0.026 -10000 0 -10000 0 0
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 -0.006 0.073 -10000 0 -0.5 5 5
DUSP1 -0.007 0.092 -10000 0 -0.47 22 22
NF-kappa-B/RelA -0.038 0.063 -10000 0 -0.22 25 25
actin cytoskeleton reorganization -0.061 0.18 -10000 0 -0.53 48 48
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.098 0.19 -10000 0 -0.56 65 65
FER -0.064 0.17 -10000 0 -0.45 66 66
RELA 0.011 0 -10000 0 -10000 0 0
ITK -0.049 0.12 -10000 0 -0.45 44 44
SOS1 0.01 0.024 -10000 0 -0.58 1 1
PLCG1 -0.086 0.24 -10000 0 -0.64 72 72
cytokine secretion -0.028 0.045 -10000 0 -10000 0 0
SPHK1 -0.08 0.19 -10000 0 -0.42 101 101
PTK2 -0.064 0.18 -10000 0 -0.6 42 42
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.12 0.21 -10000 0 -0.6 71 71
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.074 0.21 -10000 0 -0.55 69 69
MAP2K2 0.027 0.026 -10000 0 -10000 0 0
MAP2K1 0.026 0.03 -10000 0 -0.34 1 1
MAP2K7 0.01 0.024 -10000 0 -0.58 1 1
KLRG1/SHP2 -0.061 0.15 -10000 0 -0.45 51 51
MAP2K4 0.007 0.079 -10000 0 -0.94 4 4
Fc epsilon R1/FcgammaRIIB -0.14 0.25 -10000 0 -0.49 161 161
mol:Choline -0.075 0.17 -10000 0 -0.39 97 97
SHC/Grb2/SOS1 -0.047 0.16 -10000 0 -0.48 43 43
FYN 0.005 0.06 -10000 0 -0.55 7 7
DOK1 0.011 0 -10000 0 -10000 0 0
PXN -0.053 0.17 -10000 0 -0.57 38 38
HCLS1 -0.066 0.18 -10000 0 -0.41 89 89
PRKCB -0.06 0.18 0.17 12 -0.44 78 90
FCGR2B -0.084 0.21 -10000 0 -0.53 104 104
IGHE -0.003 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.07 0.17 -10000 0 -0.43 73 73
LCP2 -0.014 0.12 -10000 0 -0.55 27 27
PLA2G4A -0.14 0.22 -10000 0 -0.44 147 147
RASA1 0.009 0.034 -10000 0 -0.58 2 2
mol:Phosphatidic acid -0.075 0.17 -10000 0 -0.39 97 97
IKK complex -0.015 0.1 0.15 13 -0.25 49 62
WIPF1 -0.001 0.081 -10000 0 -0.54 13 13
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.015 0.024 -9999 0 -0.32 3 3
VLDLR -0.041 0.16 -9999 0 -0.54 56 56
CRKL 0.011 0 -9999 0 -10000 0 0
LRPAP1 0.01 0.024 -9999 0 -0.58 1 1
FYN 0.005 0.06 -9999 0 -0.55 7 7
ITGA3 0.008 0.044 -9999 0 -0.52 4 4
RELN/VLDLR/Fyn -0.078 0.17 -9999 0 -0.34 167 167
MAPK8IP1/MKK7/MAP3K11/JNK1 0.021 0.068 -9999 0 -0.33 14 14
AKT1 -0.07 0.14 -9999 0 -0.47 33 33
MAP2K7 0.01 0.024 -9999 0 -0.58 1 1
RAPGEF1 0.01 0.024 -9999 0 -0.58 1 1
DAB1 -0.079 0.2 -9999 0 -0.51 101 101
RELN/LRP8/DAB1 -0.09 0.17 -9999 0 -0.32 195 195
LRPAP1/LRP8 0.014 0.036 -9999 0 -0.42 4 4
RELN/LRP8/DAB1/Fyn -0.082 0.16 -9999 0 -0.36 113 113
DAB1/alpha3/beta1 Integrin -0.11 0.16 -9999 0 -0.5 48 48
long-term memory -0.11 0.19 -9999 0 -0.53 58 58
DAB1/LIS1 -0.11 0.16 -9999 0 -0.51 46 46
DAB1/CRLK/C3G -0.11 0.16 -9999 0 -0.5 47 47
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
DAB1/NCK2 -0.11 0.16 -9999 0 -0.52 47 47
ARHGEF2 0.011 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.019 0.11 -9999 0 -0.48 33 33
CDK5R1 0.009 0.033 -9999 0 -0.46 3 3
RELN -0.094 0.21 -9999 0 -0.52 118 118
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
RELN/LRP8/Fyn -0.049 0.14 -9999 0 -0.31 127 127
GRIN2A/RELN/LRP8/DAB1/Fyn -0.091 0.18 -9999 0 -0.37 129 129
MAPK8 0.01 0.024 -9999 0 -0.58 1 1
RELN/VLDLR/DAB1 -0.12 0.19 -9999 0 -0.34 229 229
ITGB1 0.011 0 -9999 0 -10000 0 0
MAP1B -0.11 0.19 -9999 0 -0.4 138 138
RELN/LRP8 -0.045 0.14 -9999 0 -0.35 63 63
GRIN2B/RELN/LRP8/DAB1/Fyn -0.1 0.19 -9999 0 -0.37 147 147
PI3K 0.013 0.04 -9999 0 -0.42 5 5
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.014 0.032 -9999 0 -0.37 4 4
RAP1A -0.075 0.16 -9999 0 -0.46 47 47
PAFAH1B1 0.011 0 -9999 0 -10000 0 0
MAPK8IP1 -0.01 0.11 -9999 0 -0.52 24 24
CRLK/C3G 0.016 0.018 -9999 0 -0.42 1 1
GRIN2B -0.038 0.16 -9999 0 -0.56 51 51
NCK2 0.01 0.024 -9999 0 -0.58 1 1
neuron differentiation -0.036 0.12 -9999 0 -0.38 27 27
neuron adhesion -0.063 0.16 -9999 0 -0.47 36 36
LRP8 0.008 0.042 -9999 0 -0.58 3 3
GSK3B -0.062 0.14 -9999 0 -0.45 34 34
RELN/VLDLR/DAB1/Fyn -0.11 0.18 -9999 0 -0.38 144 144
MAP3K11 0.01 0.024 -9999 0 -0.58 1 1
RELN/VLDLR/DAB1/P13K -0.08 0.15 -9999 0 -0.31 143 143
CDK5 0.011 0 -9999 0 -10000 0 0
MAPT -0.064 0.18 -9999 0 -0.46 102 102
neuron migration -0.064 0.16 -9999 0 -0.46 38 38
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.036 0.12 -9999 0 -0.38 27 27
RELN/VLDLR -0.063 0.16 -9999 0 -0.35 96 96
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.021 0.086 -9999 0 -0.34 33 33
NFATC2 -0.034 0.11 -9999 0 -0.38 50 50
NFATC3 -0.002 0.033 -9999 0 -10000 0 0
CD40LG -0.18 0.32 -9999 0 -0.73 107 107
PTGS2 -0.2 0.33 -9999 0 -0.68 142 142
JUNB 0.007 0.05 -9999 0 -0.53 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.01 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.009 0.015 -9999 0 -10000 0 0
CALM1 0.006 0.011 -9999 0 -10000 0 0
JUN 0.001 0.053 -9999 0 -0.56 5 5
mol:Ca2+ -0.009 0.013 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.004 0.007 -9999 0 -10000 0 0
FOSL1 -0.025 0.13 -9999 0 -0.51 41 41
CREM 0.01 0.019 -9999 0 -0.46 1 1
Jun/NFAT1-c-4/p21SNFT -0.1 0.2 -9999 0 -0.51 73 73
FOS -0.032 0.14 -9999 0 -0.54 41 41
IFNG -0.19 0.32 -9999 0 -0.68 144 144
AP-1/NFAT1-c-4 -0.2 0.35 -9999 0 -0.75 125 125
FASLG -0.18 0.32 -9999 0 -0.7 126 126
NFAT1-c-4/ICER1 -0.062 0.14 -9999 0 -0.4 56 56
IL2RA -0.18 0.32 -9999 0 -0.73 113 113
FKBP12/FK506 0.008 0 -9999 0 -10000 0 0
CSF2 -0.2 0.34 -9999 0 -0.68 156 156
JunB/Fra1/NFAT1-c-4 -0.076 0.15 -9999 0 -0.4 72 72
IL4 -0.16 0.28 -9999 0 -0.64 109 109
IL2 -0.007 0.024 -9999 0 -10000 0 0
IL3 -0.03 0.093 -9999 0 -0.84 7 7
FKBP1A 0.011 0 -9999 0 -10000 0 0
BATF3 -0.006 0.094 -9999 0 -0.51 20 20
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.002 0.072 -9999 0 -0.54 10 10
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.039 0.17 -10000 0 -0.6 48 48
NFATC2 -0.092 0.26 -10000 0 -0.68 64 64
NFATC3 -0.019 0.076 -10000 0 -0.26 12 12
CD40LG -0.28 0.42 -10000 0 -1 104 104
ITCH 0.028 0.084 -10000 0 -0.8 5 5
CBLB 0.028 0.08 -10000 0 -0.84 4 4
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.28 0.45 -10000 0 -1.2 95 95
JUNB 0.007 0.05 -10000 0 -0.53 5 5
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.008 0.059 -10000 0 -0.37 14 14
T cell anergy 0.004 0.1 -10000 0 -0.55 14 14
TLE4 -0.057 0.21 -10000 0 -0.7 36 36
Jun/NFAT1-c-4/p21SNFT -0.18 0.37 -10000 0 -1 60 60
AP-1/NFAT1-c-4 -0.3 0.48 -10000 0 -1.2 98 98
IKZF1 -0.075 0.26 -10000 0 -0.77 54 54
T-helper 2 cell differentiation -0.13 0.26 -10000 0 -0.78 57 57
AP-1/NFAT1 -0.093 0.21 -10000 0 -0.55 65 65
CALM1 0.018 0.033 -10000 0 -0.3 3 3
EGR2 -0.14 0.36 -10000 0 -1.2 43 43
EGR3 -0.15 0.38 -10000 0 -1.2 46 46
NFAT1/FOXP3 -0.093 0.27 -10000 0 -0.74 68 68
EGR1 -0.009 0.1 -10000 0 -0.5 24 24
JUN -0.009 0.059 -10000 0 -0.58 5 5
EGR4 -0.055 0.17 -10000 0 -0.51 74 74
mol:Ca2+ 0.007 0.035 -10000 0 -0.32 3 3
GBP3 -0.11 0.31 -10000 0 -0.8 86 86
FOSL1 -0.025 0.13 -10000 0 -0.51 41 41
NFAT1-c-4/MAF/IRF4 -0.18 0.38 -10000 0 -1.1 66 66
DGKA -0.052 0.2 -10000 0 -0.66 34 34
CREM 0.01 0.019 -10000 0 -0.46 1 1
NFAT1-c-4/PPARG -0.15 0.35 -10000 0 -1.1 49 49
CTLA4 -0.096 0.29 -10000 0 -0.78 70 70
NFAT1-c-4 (dimer)/EGR1 -0.16 0.36 -10000 0 -1.1 53 53
NFAT1-c-4 (dimer)/EGR4 -0.18 0.37 -10000 0 -1.1 60 60
FOS -0.042 0.14 -10000 0 -0.55 41 41
IFNG -0.23 0.4 -10000 0 -0.92 121 121
T cell activation -0.11 0.2 -10000 0 -0.79 15 15
MAF 0.001 0.074 -10000 0 -0.54 11 11
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.11 0.3 1.1 34 -10000 0 34
TNF -0.18 0.35 -10000 0 -0.96 68 68
FASLG -0.24 0.51 -10000 0 -1.4 76 76
TBX21 -0.061 0.19 -10000 0 -0.56 71 71
BATF3 -0.006 0.094 -10000 0 -0.51 20 20
PRKCQ -0.048 0.18 -10000 0 -0.58 57 57
PTPN1 -0.049 0.19 -10000 0 -0.64 31 31
NFAT1-c-4/ICER1 -0.15 0.35 -10000 0 -1.1 49 49
GATA3 -0.016 0.12 -10000 0 -0.52 31 31
T-helper 1 cell differentiation -0.21 0.4 -10000 0 -0.89 122 122
IL2RA -0.27 0.42 -10000 0 -1.1 97 97
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.05 0.19 -10000 0 -0.63 34 34
E2F1 0.014 0.036 -10000 0 -0.49 3 3
PPARG 0.004 0.064 -10000 0 -0.58 7 7
SLC3A2 -0.048 0.19 -10000 0 -0.63 31 31
IRF4 -0.076 0.2 -10000 0 -0.54 95 95
PTGS2 -0.3 0.44 -10000 0 -0.99 126 126
CSF2 -0.3 0.44 -10000 0 -0.99 126 126
JunB/Fra1/NFAT1-c-4 -0.16 0.34 -10000 0 -1 54 54
IL4 -0.13 0.27 -10000 0 -0.85 52 52
IL5 -0.26 0.4 -10000 0 -0.99 93 93
IL2 -0.11 0.2 -10000 0 -0.8 15 15
IL3 -0.064 0.1 -10000 0 -0.78 7 7
RNF128 0.025 0.091 -10000 0 -0.62 11 11
NFATC1 -0.12 0.3 -10000 0 -1.1 34 34
CDK4 0.081 0.18 0.58 29 -10000 0 29
PTPRK -0.049 0.19 -10000 0 -0.64 31 31
IL8 -0.31 0.44 -10000 0 -1 123 123
POU2F1 0.002 0.072 -10000 0 -0.54 10 10
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.13 0.2 -9999 0 -0.55 62 62
SMAD6-7/SMURF1 0.019 0.042 -9999 0 -0.38 6 6
NOG -0.027 0.13 -9999 0 -0.48 43 43
SMAD9 -0.063 0.16 -9999 0 -0.53 54 54
SMAD4 0.004 0.064 -9999 0 -0.58 7 7
SMAD5 -0.044 0.14 -9999 0 -0.46 26 26
BMP7/USAG1 -0.17 0.24 -9999 0 -0.44 239 239
SMAD5/SKI -0.036 0.13 -9999 0 -0.44 25 25
SMAD1 0.021 0.045 -9999 0 -0.47 3 3
BMP2 -0.003 0.087 -9999 0 -0.54 15 15
SMAD1/SMAD1/SMAD4 -0.007 0.046 -9999 0 -0.48 3 3
BMPR1A 0.01 0.024 -9999 0 -0.58 1 1
BMPR1B -0.092 0.21 -9999 0 -0.51 117 117
BMPR1A-1B/BAMBI -0.078 0.16 -9999 0 -0.38 90 90
AHSG -0.043 0.15 -9999 0 -0.46 64 64
CER1 -0.005 0.062 -9999 0 -0.46 11 11
BMP2-4/CER1 -0.01 0.095 -9999 0 -0.4 19 19
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.049 0.14 -9999 0 -0.41 46 46
BMP2-4 (homodimer) -0.01 0.1 -9999 0 -0.38 40 40
RGMB -0.013 0.11 -9999 0 -0.46 31 31
BMP6/BMPR2/BMPR1A-1B -0.044 0.14 -9999 0 -0.34 68 68
RGMA -0.071 0.2 -9999 0 -0.54 89 89
SMURF1 0.011 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.049 0.13 -9999 0 -0.38 43 43
BMP2-4/USAG1 -0.071 0.17 -9999 0 -0.38 111 111
SMAD6/SMURF1/SMAD5 -0.036 0.13 -9999 0 -0.44 24 24
SOSTDC1 -0.1 0.23 -9999 0 -0.55 120 120
BMP7/BMPR2/BMPR1A-1B -0.11 0.19 -9999 0 -0.38 149 149
SKI 0.011 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.009 0.1 -9999 0 -0.52 23 23
HFE2 0 0.038 -9999 0 -0.46 4 4
ZFYVE16 -0.005 0.096 -9999 0 -0.58 16 16
MAP3K7 0.011 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.018 0.12 -9999 0 -0.34 68 68
SMAD5/SMAD5/SMAD4 -0.039 0.13 -9999 0 -0.44 26 26
MAPK1 0.01 0.024 -9999 0 -0.58 1 1
TAK1/TAB family -0.056 0.096 -9999 0 -0.37 27 27
BMP7 (homodimer) -0.13 0.24 -9999 0 -0.54 153 153
NUP214 0.011 0 -9999 0 -10000 0 0
BMP6/FETUA -0.037 0.12 -9999 0 -0.34 86 86
SMAD1/SKI 0.026 0.043 -9999 0 -0.44 3 3
SMAD6 0.007 0.05 -9999 0 -0.53 5 5
CTDSP2 0.011 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.033 0.12 -9999 0 -0.3 99 99
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.083 0.21 -9999 0 -0.54 102 102
BMPR2 (homodimer) 0.006 0.054 -9999 0 -0.58 5 5
GADD34/PP1CA 0.013 0.062 -9999 0 -0.35 17 17
BMPR1A-1B (homodimer) -0.059 0.15 -9999 0 -0.36 118 118
CHRDL1 -0.16 0.25 -9999 0 -0.52 192 192
ENDOFIN/SMAD1 0.019 0.071 -9999 0 -0.5 5 5
SMAD6-7/SMURF1/SMAD1 -0.001 0.049 -9999 0 -0.54 3 3
SMAD6/SMURF1 0.011 0 -9999 0 -10000 0 0
BAMBI -0.049 0.17 -9999 0 -0.52 67 67
SMURF2 0.007 0.05 -9999 0 -0.53 5 5
BMP2-4/CHRDL1 -0.1 0.18 -9999 0 -0.32 219 219
BMP2-4/GREM1 -0.058 0.16 -9999 0 -0.38 83 83
SMAD7 0.009 0.034 -9999 0 -0.58 2 2
SMAD8A/SMAD8A/SMAD4 -0.057 0.16 -9999 0 -0.48 60 60
SMAD1/SMAD6 0.026 0.043 -9999 0 -0.44 3 3
TAK1/SMAD6 0.017 0 -9999 0 -10000 0 0
BMP7 -0.13 0.24 -9999 0 -0.54 153 153
BMP6 -0.009 0.1 -9999 0 -0.52 23 23
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.039 0.12 -9999 0 -0.35 44 44
PPM1A 0.011 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.024 0.054 -9999 0 -0.48 4 4
SMAD7/SMURF1 0.015 0.025 -9999 0 -0.42 2 2
CTDSPL 0.011 0 -9999 0 -10000 0 0
PPP1CA 0.011 0 -9999 0 -10000 0 0
XIAP 0.01 0.024 -9999 0 -0.58 1 1
CTDSP1 0.01 0.024 -9999 0 -0.58 1 1
PPP1R15A 0.011 0.019 -9999 0 -0.46 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.08 0.18 -9999 0 -0.49 69 69
CHRD -0.019 0.13 -9999 0 -0.55 32 32
BMPR2 0.006 0.054 -9999 0 -0.58 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.056 0.14 -9999 0 -0.42 43 43
BMP4 -0.012 0.11 -9999 0 -0.5 27 27
FST -0.051 0.17 -9999 0 -0.53 69 69
BMP2-4/NOG -0.023 0.12 -9999 0 -0.31 79 79
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.1 0.18 -9999 0 -0.54 37 37
TCGA08_p53

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2A -0.05 0.14 -10000 0 -0.37 94 94
TP53 -0.048 0.11 0.25 1 -0.36 55 56
Senescence -0.047 0.11 0.25 1 -0.35 55 56
Apoptosis -0.047 0.11 0.25 1 -0.35 55 56
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.03 0.084 0.26 39 -0.34 4 43
MDM4 0.01 0.031 -10000 0 -0.52 2 2
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.004 0.09 -10000 0 -0.54 16 16
GNB1/GNG2 -0.053 0.069 -10000 0 -0.2 81 81
AKT1 -0.022 0.092 -10000 0 -0.21 55 55
EGF -0.18 0.25 -10000 0 -0.51 216 216
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.033 0.12 -10000 0 -0.41 26 26
mol:Ca2+ -0.046 0.13 -10000 0 -0.31 81 81
LYN -0.017 0.094 -10000 0 -0.42 10 10
RhoA/GTP -0.03 0.046 -10000 0 -0.14 22 22
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.051 0.14 -10000 0 -0.35 79 79
GNG2 0.004 0.063 -10000 0 -0.53 8 8
ARRB2 0.011 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.006 0.11 -10000 0 -0.48 22 22
G beta5/gamma2 -0.067 0.092 -10000 0 -0.26 81 81
PRKCH -0.052 0.15 -10000 0 -0.36 78 78
DNM1 -0.006 0.093 -10000 0 -0.5 20 20
TXA2/TP beta/beta Arrestin3 -0.015 0.036 -10000 0 -0.3 2 2
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.12 0.23 -10000 0 -0.5 149 149
G12 family/GTP -0.073 0.11 -10000 0 -0.31 79 79
ADRBK1 0.01 0.031 -10000 0 -0.52 2 2
ADRBK2 -0.001 0.085 -10000 0 -0.57 13 13
RhoA/GTP/ROCK1 0.006 0.056 -10000 0 -0.39 11 11
mol:GDP 0.044 0.11 0.32 43 -10000 0 43
mol:NADP -0.007 0.098 -10000 0 -0.53 20 20
RAB11A 0.011 0 -10000 0 -10000 0 0
PRKG1 -0.024 0.14 -10000 0 -0.56 37 37
mol:IP3 -0.061 0.16 -10000 0 -0.38 81 81
cell morphogenesis 0.006 0.056 -10000 0 -0.39 11 11
PLCB2 -0.086 0.21 -10000 0 -0.53 80 80
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.073 0.14 -10000 0 -0.4 51 51
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.029 0.12 -10000 0 -0.44 21 21
RHOA 0.01 0.024 -10000 0 -0.58 1 1
PTGIR -0.007 0.096 -10000 0 -0.5 21 21
PRKCB1 -0.058 0.15 -10000 0 -0.37 82 82
GNAQ 0.005 0.059 -10000 0 -0.58 6 6
mol:L-citrulline -0.007 0.098 -10000 0 -0.53 20 20
TXA2/TXA2-R family -0.089 0.21 -10000 0 -0.54 82 82
LCK -0.035 0.12 -10000 0 -0.43 22 22
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.049 0.096 -10000 0 -0.5 9 9
TXA2-R family/G12 family/GDP/G beta/gamma 0.006 0.04 -10000 0 -0.3 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.046 0.094 -10000 0 -0.49 9 9
MAPK14 -0.028 0.1 -10000 0 -0.23 69 69
TGM2/GTP -0.074 0.18 -10000 0 -0.45 81 81
MAPK11 -0.032 0.11 -10000 0 -0.24 76 76
ARHGEF1 -0.023 0.08 -10000 0 -0.19 46 46
GNAI2 0.011 0 -10000 0 -10000 0 0
JNK cascade -0.062 0.16 -10000 0 -0.39 83 83
RAB11/GDP 0.012 0.001 -10000 0 -10000 0 0
ICAM1 -0.04 0.12 -10000 0 -0.29 73 73
cAMP biosynthetic process -0.064 0.15 -10000 0 -0.37 82 82
Gq family/GTP/EBP50 0.004 0.079 -10000 0 -0.34 19 19
actin cytoskeleton reorganization 0.006 0.056 -10000 0 -0.39 11 11
SRC -0.017 0.095 -10000 0 -0.42 11 11
GNB5 0.007 0.048 -10000 0 -0.58 4 4
GNB1 0.011 0 -10000 0 -10000 0 0
EGF/EGFR -0.062 0.12 -10000 0 -0.33 56 56
VCAM1 -0.049 0.14 -10000 0 -0.33 82 82
TP beta/Gq family/GDP/G beta5/gamma2 -0.006 0.11 -10000 0 -0.48 22 22
platelet activation -0.04 0.14 -10000 0 -0.31 75 75
PGI2/IP -0.005 0.069 -10000 0 -0.36 21 21
PRKACA -0.047 0.12 -10000 0 -0.31 65 65
Gq family/GDP/G beta5/gamma2 -0.01 0.1 -10000 0 -0.45 24 24
TXA2/TP beta/beta Arrestin2 -0.016 0.065 -10000 0 -0.52 8 8
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.04 0.12 -10000 0 -0.3 68 68
mol:DAG -0.065 0.17 -10000 0 -0.42 82 82
EGFR 0.004 0.063 -10000 0 -0.53 8 8
TXA2/TP alpha -0.088 0.2 -10000 0 -0.51 82 82
Gq family/GTP -0.011 0.079 -10000 0 -0.28 34 34
YES1 -0.02 0.1 -10000 0 -0.44 12 12
GNAI2/GTP -0.049 0.092 -10000 0 -0.46 12 12
PGD2/DP -0.085 0.16 -10000 0 -0.36 149 149
SLC9A3R1 0.011 0 -10000 0 -10000 0 0
FYN -0.02 0.097 -10000 0 -0.42 11 11
mol:NO -0.007 0.098 -10000 0 -0.53 20 20
GNA15 -0.008 0.1 -10000 0 -0.54 21 21
PGK/cGMP -0.018 0.11 -10000 0 -0.34 56 56
RhoA/GDP 0.011 0.024 -10000 0 -0.57 1 1
TP alpha/TGM2/GDP/G beta/gamma -0.029 0.12 -10000 0 -0.49 15 15
NOS3 -0.007 0.098 -10000 0 -0.53 20 20
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCA -0.051 0.14 -10000 0 -0.35 75 75
PRKCB -0.064 0.17 -10000 0 -0.39 91 91
PRKCE -0.048 0.14 -10000 0 -0.35 76 76
PRKCD -0.054 0.15 -10000 0 -0.37 80 80
PRKCG -0.088 0.18 -10000 0 -0.41 104 104
muscle contraction -0.082 0.2 -10000 0 -0.5 81 81
PRKCZ -0.051 0.14 -10000 0 -0.35 80 80
ARR3 -0.001 0.042 -10000 0 -0.46 5 5
TXA2/TP beta -0.036 0.12 -10000 0 -0.47 15 15
PRKCQ -0.066 0.16 -10000 0 -0.38 87 87
MAPKKK cascade -0.077 0.19 -10000 0 -0.47 82 82
SELE -0.062 0.16 -10000 0 -0.37 98 98
TP beta/GNAI2/GDP/G beta/gamma -0.022 0.11 -10000 0 -0.5 11 11
ROCK1 0 0.08 -10000 0 -0.58 11 11
GNA14 -0.007 0.1 -10000 0 -0.56 19 19
chemotaxis -0.098 0.23 -10000 0 -0.6 82 82
GNA12 0.011 0 -10000 0 -10000 0 0
GNA13 0.009 0.034 -10000 0 -0.58 2 2
GNA11 0.007 0.05 -10000 0 -0.53 5 5
Rac1/GTP 0.007 0.003 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.008 0.041 -9999 0 -0.49 4 4
EGFR 0.004 0.063 -9999 0 -0.53 8 8
EGF/EGFR -0.12 0.15 -9999 0 -0.34 129 129
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.071 0.14 -9999 0 -0.52 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.019 0.12 -9999 0 -0.52 34 34
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.18 0.25 -9999 0 -0.51 216 216
EGF/EGFR dimer/SHC -0.099 0.16 -9999 0 -0.36 93 93
mol:GDP -0.072 0.14 -9999 0 -0.51 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.022 0.13 -9999 0 -0.52 38 38
GRB2/SOS1 0.016 0.018 -9999 0 -0.42 1 1
HRAS/GTP -0.084 0.11 -9999 0 -0.45 3 3
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP -0.086 0.11 -9999 0 -0.46 3 3
FRAP1 -0.07 0.13 -9999 0 -0.49 1 1
EGF/EGFR dimer -0.13 0.19 -9999 0 -0.36 223 223
SOS1 0.01 0.024 -9999 0 -0.58 1 1
GRB2 0.011 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.029 0.13 -9999 0 -0.38 69 69
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.051 0.15 -9999 0 -0.34 117 117
EPHB2 0 0.079 -9999 0 -0.55 12 12
Syndecan-2/TACI -0.037 0.13 -9999 0 -0.32 97 97
LAMA1 -0.055 0.18 -9999 0 -0.54 72 72
Syndecan-2/alpha2 ITGB1 0.004 0.091 -9999 0 -0.6 2 2
HRAS 0.008 0.041 -9999 0 -0.49 4 4
Syndecan-2/CASK 0 0.063 -9999 0 -0.34 19 19
ITGA5 -0.005 0.09 -9999 0 -0.49 20 20
BAX 0.019 0.075 -9999 0 -1.1 1 1
EPB41 0.007 0.048 -9999 0 -0.58 4 4
positive regulation of cell-cell adhesion 0.002 0.075 -9999 0 -0.32 29 29
LAMA3 -0.016 0.12 -9999 0 -0.51 32 32
EZR 0.011 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.003 0.087 -9999 0 -0.51 17 17
Syndecan-2/MMP2 -0.018 0.13 -9999 0 -0.39 56 56
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.013 0.044 -9999 0 -0.42 6 6
dendrite morphogenesis 0.002 0.081 -9999 0 -0.34 31 31
Syndecan-2/GM-CSF -0.058 0.14 -9999 0 -0.32 138 138
determination of left/right symmetry 0.002 0.075 -9999 0 -0.4 20 20
Syndecan-2/PKC delta 0.009 0.064 -9999 0 -0.34 19 19
GNB2L1 0.011 0.019 -9999 0 -0.46 1 1
MAPK3 -0.046 0.13 -9999 0 -0.32 78 78
MAPK1 -0.046 0.13 -9999 0 -0.32 78 78
Syndecan-2/RACK1 0.013 0.062 -9999 0 -0.31 18 18
NF1 0.008 0.042 -9999 0 -0.58 3 3
FGFR/FGF/Syndecan-2 0.002 0.075 -9999 0 -0.4 20 20
ITGA2 0.005 0.059 -9999 0 -0.58 6 6
MAPK8 0.015 0.068 -9999 0 -0.35 18 18
Syndecan-2/alpha2/beta1 Integrin -0.017 0.12 -9999 0 -0.31 52 52
Syndecan-2/Kininogen -0.067 0.15 -9999 0 -0.32 152 152
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC 0.017 0.064 -9999 0 -0.31 18 18
Syndecan-2/CASK/Protein 4.1 0.006 0.064 -9999 0 -0.31 23 23
extracellular matrix organization 0 0.092 -9999 0 -0.38 30 30
actin cytoskeleton reorganization -0.05 0.15 -9999 0 -0.34 117 117
Syndecan-2/Caveolin-2/Ras 0.006 0.085 -9999 0 -0.37 21 21
Syndecan-2/Laminin alpha3 -0.008 0.095 -9999 0 -0.31 51 51
Syndecan-2/RasGAP 0.017 0.064 -9999 0 -0.3 20 20
alpha5/beta1 Integrin 0.005 0.065 -9999 0 -0.34 20 20
PRKCD 0.011 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.002 0.081 -9999 0 -0.34 31 31
GO:0007205 0.003 0.006 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.023 0.066 -9999 0 -0.52 3 3
RHOA 0.01 0.024 -9999 0 -0.58 1 1
SDCBP 0 0.08 -9999 0 -0.58 11 11
TNFRSF13B -0.062 0.18 -9999 0 -0.52 80 80
RASA1 0.009 0.034 -9999 0 -0.58 2 2
alpha2/beta1 Integrin 0.013 0.044 -9999 0 -0.42 6 6
Syndecan-2/Synbindin 0.009 0.064 -9999 0 -0.34 19 19
TGFB1 -0.003 0.088 -9999 0 -0.55 15 15
CASP3 0.014 0.061 -9999 0 -0.31 18 18
FN1 -0.086 0.21 -9999 0 -0.52 109 109
Syndecan-2/IL8 -0.064 0.16 -9999 0 -0.33 144 144
SDC2 0.002 0.075 -9999 0 -0.4 20 20
KNG1 -0.11 0.22 -9999 0 -0.52 136 136
Syndecan-2/Neurofibromin 0.007 0.069 -9999 0 -0.34 22 22
TRAPPC4 0.011 0 -9999 0 -10000 0 0
CSF2 -0.097 0.22 -9999 0 -0.52 121 121
Syndecan-2/TGFB1 0 0.092 -9999 0 -0.38 30 30
Syndecan-2/Syntenin/PI-4-5-P2 0.002 0.075 -9999 0 -0.32 29 29
Syndecan-2/Ezrin 0.015 0.06 -9999 0 -0.32 17 17
PRKACA 0.014 0.063 -9999 0 -0.31 19 19
angiogenesis -0.063 0.16 -9999 0 -0.33 144 144
MMP2 -0.034 0.15 -9999 0 -0.53 50 50
IL8 -0.11 0.22 -9999 0 -0.52 133 133
calcineurin-NFAT signaling pathway -0.036 0.13 -9999 0 -0.32 97 97
Osteopontin-mediated events

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
IKK alpha homodimer -0.065 0.16 -9999 0 -0.53 19 19
NF kappa B1 p50/RelA/I kappa B alpha -0.039 0.15 -9999 0 -0.51 17 17
alphaV/beta3 Integrin/Osteopontin/Src -0.11 0.19 -9999 0 -0.36 204 204
AP1 -0.074 0.2 -9999 0 -0.6 42 42
ILK -0.074 0.16 -9999 0 -0.45 28 28
bone resorption -0.051 0.16 -9999 0 -0.54 20 20
PTK2B 0.009 0.034 -9999 0 -0.58 2 2
PYK2/p130Cas -0.059 0.15 -9999 0 -0.5 20 20
ITGAV 0.003 0.079 -9999 0 -0.57 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.006 0.072 -9999 0 -0.45 14 14
alphaV/beta3 Integrin/Osteopontin -0.09 0.18 -9999 0 -0.37 118 118
MAP3K1 -0.079 0.17 -9999 0 -0.35 117 117
JUN 0.007 0.052 -9999 0 -0.56 5 5
MAPK3 -0.062 0.16 -9999 0 -0.49 22 22
MAPK1 -0.062 0.16 -9999 0 -0.5 22 22
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
NFKB1 0.01 0.024 -9999 0 -0.58 1 1
MAPK8 -0.068 0.17 -9999 0 -0.47 34 34
ITGB3 -0.004 0.099 -9999 0 -0.55 19 19
NFKBIA -0.053 0.16 -9999 0 -0.52 21 21
FOS -0.026 0.14 -9999 0 -0.53 41 41
CD44 0.007 0.048 -9999 0 -0.58 4 4
CHUK 0.007 0.048 -9999 0 -0.58 4 4
PLAU -0.05 0.19 -9999 0 -0.71 21 21
NF kappa B1 p50/RelA -0.077 0.12 -9999 0 -0.52 19 19
BCAR1 0.008 0.044 -9999 0 -0.52 4 4
RELA 0.011 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.001 0.095 -9999 0 -0.41 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.076 0.16 -9999 0 -0.34 112 112
VAV3 -0.1 0.19 -9999 0 -0.52 50 50
MAP3K14 -0.074 0.16 -9999 0 -0.34 117 117
ROCK2 0 0.08 -9999 0 -0.58 11 11
SPP1 -0.16 0.25 -9999 0 -0.51 194 194
RAC1 0.011 0 -9999 0 -10000 0 0
Rac1/GTP -0.092 0.18 -9999 0 -0.5 45 45
MMP2 -0.075 0.21 -9999 0 -0.6 55 55
Glucocorticoid receptor regulatory network

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
PCK2 0.021 0.074 0.31 14 -10000 0 14
SMARCC2 0.012 0.006 -10000 0 -10000 0 0
SMARCC1 0.012 0.006 -10000 0 -10000 0 0
TBX21 -0.11 0.27 -10000 0 -0.73 78 78
SUMO2 0.01 0.025 -10000 0 -0.58 1 1
STAT1 (dimer) 0.013 0.052 -10000 0 -0.49 6 6
FKBP4 0.009 0.033 -10000 0 -0.46 3 3
FKBP5 0.009 0.039 -10000 0 -0.54 3 3
GR alpha/HSP90/FKBP51/HSP90 0.075 0.11 0.3 40 -0.44 6 46
PRL -0.064 0.14 -10000 0 -0.57 15 15
cortisol/GR alpha (dimer)/TIF2 0.18 0.23 0.55 104 -0.5 5 109
RELA -0.036 0.093 -10000 0 -0.32 13 13
FGG 0.12 0.2 0.5 56 -0.44 14 70
GR beta/TIF2 0.074 0.13 0.33 45 -0.46 12 57
IFNG -0.27 0.37 -10000 0 -0.89 111 111
apoptosis 0.007 0.16 0.48 21 -0.57 7 28
CREB1 0.009 0.041 -10000 0 -0.58 2 2
histone acetylation -0.031 0.12 0.33 1 -0.36 37 38
BGLAP -0.051 0.14 -10000 0 -0.52 21 21
GR/PKAc 0.055 0.13 0.31 25 -0.41 11 36
NF kappa B1 p50/RelA -0.068 0.18 -10000 0 -0.5 43 43
SMARCD1 0.011 0.025 -10000 0 -0.58 1 1
MDM2 0.072 0.087 0.26 57 -0.28 3 60
GATA3 -0.016 0.12 -10000 0 -0.52 31 31
AKT1 0.003 0.024 -10000 0 -0.59 1 1
CSF2 -0.18 0.38 -10000 0 -1.1 80 80
GSK3B 0.009 0.035 -10000 0 -0.58 2 2
NR1I3 0.021 0.18 0.47 17 -0.82 13 30
CSN2 0.11 0.15 0.41 46 -0.37 3 49
BRG1/BAF155/BAF170/BAF60A 0.032 0.029 -10000 0 -0.31 2 2
NFATC1 -0.016 0.12 -10000 0 -0.5 33 33
POU2F1 0.001 0.075 -10000 0 -0.55 10 10
CDKN1A -0.018 0.16 -10000 0 -1.5 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.007 -10000 0 -10000 0 0
SFN 0.005 0.056 -10000 0 -0.47 8 8
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.076 0.11 0.31 30 -0.47 5 35
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.019 0.17 0.45 18 -0.79 11 29
JUN -0.16 0.19 -10000 0 -0.5 79 79
IL4 -0.076 0.14 -10000 0 -0.49 23 23
CDK5R1 0.009 0.033 -10000 0 -0.46 3 3
PRKACA 0.011 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.2 0.22 31 -0.47 89 120
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.079 0.11 0.31 32 -0.42 5 37
cortisol/GR alpha (monomer) 0.21 0.28 0.65 110 -0.46 4 114
NCOA2 0.004 0.067 -10000 0 -0.56 8 8
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.078 0.15 -10000 0 -0.58 41 41
AP-1/NFAT1-c-4 -0.27 0.3 -10000 0 -0.71 132 132
AFP -0.12 0.17 -10000 0 -0.67 19 19
SUV420H1 0.01 0.024 -10000 0 -0.58 1 1
IRF1 0.12 0.14 0.47 25 -0.58 1 26
TP53 -0.031 0.18 -10000 0 -0.57 59 59
PPP5C 0.011 0 -10000 0 -10000 0 0
KRT17 -0.34 0.44 -10000 0 -0.95 164 164
KRT14 -0.11 0.2 -10000 0 -0.66 34 34
TBP 0.017 0.026 -10000 0 -0.37 2 2
CREBBP 0.034 0.054 0.27 3 -0.24 3 6
HDAC1 0.011 0.009 -10000 0 -10000 0 0
HDAC2 0.022 0.027 -10000 0 -10000 0 0
AP-1 -0.27 0.31 -10000 0 -0.71 133 133
MAPK14 0.011 0.006 -10000 0 -10000 0 0
MAPK10 -0.032 0.15 -10000 0 -0.55 46 46
MAPK11 -0.003 0.082 -10000 0 -0.48 17 17
KRT5 -0.31 0.41 -10000 0 -0.92 140 140
interleukin-1 receptor activity 0.011 0.027 -10000 0 -10000 0 0
NCOA1 0.013 0.024 -10000 0 -0.58 1 1
STAT1 0.013 0.052 -10000 0 -0.49 6 6
CGA -0.063 0.13 -10000 0 -0.48 22 22
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.12 0.2 0.48 96 -0.52 5 101
MAPK3 0.01 0.025 -10000 0 -0.58 1 1
MAPK1 0.01 0.025 -10000 0 -0.58 1 1
ICAM1 -0.14 0.23 -10000 0 -0.66 56 56
NFKB1 -0.037 0.098 -10000 0 -0.32 21 21
MAPK8 -0.12 0.16 -10000 0 -0.43 77 77
MAPK9 0.011 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0 0.16 0.48 21 -0.6 7 28
BAX -0.013 0.13 -10000 0 -1.4 1 1
POMC -0.14 0.32 -10000 0 -1.2 33 33
EP300 0.031 0.073 0.28 3 -0.54 4 7
cortisol/GR alpha (dimer)/p53 0.15 0.26 0.56 95 -0.43 11 106
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.068 0.23 23 -0.24 3 26
SGK1 0.064 0.13 -10000 0 -1.4 3 3
IL13 -0.18 0.22 -10000 0 -0.74 38 38
IL6 -0.24 0.4 -10000 0 -0.98 109 109
PRKACG 0.001 0.033 -10000 0 -0.46 3 3
IL5 -0.15 0.18 -10000 0 -0.64 31 31
IL2 -0.2 0.23 -10000 0 -0.69 54 54
CDK5 0.011 0.003 -10000 0 -10000 0 0
PRKACB -0.022 0.14 -10000 0 -0.57 34 34
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
IL8 -0.24 0.41 -10000 0 -0.94 123 123
CDK5R1/CDK5 0.015 0.025 -10000 0 -0.32 3 3
NF kappa B1 p50/RelA/PKAc -0.05 0.16 -10000 0 -0.53 30 30
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.52 106 -0.38 2 108
SMARCA4 0.011 0.025 -10000 0 -0.58 1 1
chromatin remodeling 0.12 0.14 0.39 61 -0.41 4 65
NF kappa B1 p50/RelA/Cbp -0.016 0.16 0.31 1 -0.59 18 19
JUN (dimer) -0.16 0.19 -10000 0 -0.49 79 79
YWHAH 0.011 0 -10000 0 -10000 0 0
VIPR1 -0.078 0.21 -10000 0 -0.73 42 42
NR3C1 0.12 0.18 0.46 67 -0.48 10 77
NR4A1 -0.033 0.15 -10000 0 -0.48 55 55
TIF2/SUV420H1 0.01 0.052 -10000 0 -0.41 9 9
MAPKKK cascade 0.007 0.16 0.48 21 -0.57 7 28
cortisol/GR alpha (dimer)/Src-1 0.19 0.23 0.56 104 -0.44 3 107
PBX1 -0.005 0.092 -10000 0 -0.56 15 15
POU1F1 -0.001 0.037 -10000 0 -0.51 2 2
SELE -0.23 0.39 -10000 0 -0.92 112 112
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.12 0.14 0.39 60 -0.41 4 64
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.18 0.21 0.52 106 -0.38 2 108
mol:cortisol 0.12 0.16 0.38 116 -10000 0 116
MMP1 -0.27 0.45 -10000 0 -1.1 112 112
Effects of Botulinum toxin

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
STX1A 0.002 0.051 -9999 0 -0.34 13 13
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.03 0.12 -9999 0 -0.36 69 69
STXBP1 -0.007 0.1 -9999 0 -0.56 19 19
ACh/CHRNA1 -0.025 0.1 -9999 0 -0.35 47 47
RAB3GAP2/RIMS1/UNC13B -0.019 0.11 -9999 0 -0.3 72 72
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.052 0.16 -9999 0 -0.51 68 68
mol:ACh -0.007 0.035 -9999 0 -0.094 64 64
RAB3GAP2 0.008 0.042 -9999 0 -0.58 3 3
STX1A/SNAP25/VAMP2 -0.049 0.1 -9999 0 -0.29 70 70
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.025 0.1 -9999 0 -0.35 47 47
UNC13B 0.01 0.031 -9999 0 -0.52 2 2
CHRNA1 -0.031 0.15 -9999 0 -0.53 47 47
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.086 0.16 -9999 0 -0.38 137 137
SNAP25 -0.022 0.074 -9999 0 -0.2 82 82
VAMP2 0.005 0 -9999 0 -10000 0 0
SYT1 -0.12 0.24 -9999 0 -0.57 137 137
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.002 0.076 -9999 0 -0.32 32 32
STX1A/SNAP25 fragment 1/VAMP2 -0.049 0.1 -9999 0 -0.29 70 70
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.011 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.028 0.12 -10000 0 -0.43 22 22
NT3 (dimer)/TRKC -0.045 0.15 -10000 0 -0.39 89 89
NT3 (dimer)/TRKB -0.17 0.21 -10000 0 -0.35 299 299
SHC/Grb2/SOS1/GAB1/PI3K 0.028 0.032 -10000 0 -0.52 1 1
RAPGEF1 0.01 0.024 -10000 0 -0.58 1 1
BDNF -0.021 0.13 -10000 0 -0.52 36 36
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
DYNLT1 0.011 0 -10000 0 -10000 0 0
NTRK1 -0.038 0.16 -10000 0 -0.53 53 53
NTRK2 -0.18 0.25 -10000 0 -0.5 220 220
NTRK3 -0.043 0.16 -10000 0 -0.51 60 60
NT-4/5 (dimer)/TRKB -0.16 0.2 -10000 0 -0.34 297 297
neuron apoptosis 0.14 0.19 0.45 118 -10000 0 118
SHC 2-3/Grb2 -0.15 0.21 -10000 0 -0.5 118 118
SHC1 0.011 0 -10000 0 -10000 0 0
SHC2 -0.13 0.2 -10000 0 -0.54 85 85
SHC3 -0.14 0.21 -10000 0 -0.57 88 88
STAT3 (dimer) 0.018 0.015 -10000 0 -0.35 1 1
NT3 (dimer)/TRKA -0.081 0.18 -10000 0 -0.36 160 160
RIN/GDP -0.004 0.07 -10000 0 -0.29 7 7
GIPC1 0.007 0.048 -10000 0 -0.58 4 4
KRAS 0.006 0.057 -10000 0 -0.56 6 6
DNAJA3 -0.058 0.14 -10000 0 -0.36 68 68
RIN/GTP -0.001 0.019 -10000 0 -0.32 2 2
CCND1 0.024 0.034 -10000 0 -0.81 1 1
MAGED1 0.011 0 -10000 0 -10000 0 0
PTPN11 0.006 0.054 -10000 0 -0.58 5 5
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.014 0.09 -10000 0 -0.46 23 23
SHC/GRB2/SOS1 0.023 0.015 -10000 0 -0.35 1 1
GRB2 0.011 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.079 0.19 -10000 0 -0.42 111 111
TRKA/NEDD4-2 -0.02 0.11 -10000 0 -0.38 54 54
ELMO1 0.004 0.063 -10000 0 -0.5 9 9
RhoG/GTP/ELMO1/DOCK1 0.01 0.041 -10000 0 -0.3 10 10
NGF -0.032 0.14 -10000 0 -0.52 47 47
HRAS 0.008 0.041 -10000 0 -0.49 4 4
DOCK1 0.01 0.024 -10000 0 -0.58 1 1
GAB2 0.009 0.034 -10000 0 -0.58 2 2
RIT2 -0.001 0.027 -10000 0 -0.46 2 2
RIT1 0.011 0 -10000 0 -10000 0 0
FRS2 0.009 0.034 -10000 0 -0.58 2 2
DNM1 -0.006 0.093 -10000 0 -0.5 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0.019 -10000 0 -0.46 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.07 0.14 -10000 0 -0.36 72 72
mol:GDP -0.007 0.099 -10000 0 -0.39 12 12
NGF (dimer) -0.032 0.14 -10000 0 -0.52 47 47
RhoG/GDP 0.003 0.045 -10000 0 -0.36 9 9
RIT1/GDP 0.002 0.07 -10000 0 -0.28 7 7
TIAM1 -0.044 0.16 -10000 0 -0.52 62 62
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
BDNF (dimer)/TRKB -0.11 0.18 -10000 0 -0.32 239 239
KIDINS220/CRKL/C3G 0.016 0.018 -10000 0 -0.42 1 1
SHC/RasGAP 0.015 0.025 -10000 0 -0.42 2 2
FRS2 family/SHP2 0.018 0.052 -10000 0 -0.44 7 7
SHC/GRB2/SOS1/GAB1 0.029 0.014 -10000 0 -0.32 1 1
RIT1/GTP 0.008 0 -10000 0 -10000 0 0
NT3 (dimer) -0.02 0.13 -10000 0 -0.53 34 34
RAP1/GDP -0.021 0.046 -10000 0 -0.28 4 4
KIDINS220/CRKL 0.011 0 -10000 0 -10000 0 0
BDNF (dimer) -0.021 0.13 -10000 0 -0.52 36 36
ubiquitin-dependent protein catabolic process -0.035 0.14 -10000 0 -0.34 91 91
Schwann cell development -0.032 0.032 -10000 0 -10000 0 0
EHD4 0.011 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.027 0.03 -10000 0 -0.32 4 4
FRS2 family/SHP2/CRK family/C3G/GAB2 0.028 0.049 -10000 0 -0.5 4 4
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.01 0.024 -10000 0 -0.58 1 1
CDC42/GTP -0.13 0.16 -10000 0 -0.47 66 66
ABL1 0.01 0.024 -10000 0 -0.58 1 1
SH2B family/GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
Rap1/GTP -0.018 0.081 -10000 0 -0.43 2 2
STAT3 0.018 0.015 -10000 0 -0.35 1 1
axon guidance -0.13 0.15 -10000 0 -0.45 66 66
MAPK3 -0.067 0.17 -10000 0 -0.39 106 106
MAPK1 -0.067 0.17 -10000 0 -0.39 106 106
CDC42/GDP 0 0.074 -10000 0 -0.35 6 6
NTF3 -0.02 0.13 -10000 0 -0.53 34 34
NTF4 -0.014 0.09 -10000 0 -0.46 23 23
NGF (dimer)/TRKA/FAIM -0.037 0.14 -10000 0 -0.35 95 95
PI3K 0.013 0.04 -10000 0 -0.42 5 5
FRS3 0.01 0.031 -10000 0 -0.52 2 2
FAIM 0.006 0.057 -10000 0 -0.56 6 6
GAB1 0.011 0 -10000 0 -10000 0 0
RASGRF1 -0.092 0.17 -10000 0 -0.38 105 105
SOS1 0.01 0.024 -10000 0 -0.58 1 1
MCF2L -0.033 0.13 -10000 0 -0.32 94 94
RGS19 -0.002 0.085 -10000 0 -0.55 14 14
CDC42 0.006 0.054 -10000 0 -0.58 5 5
RAS family/GTP -0.003 0.095 -10000 0 -0.6 7 7
Rac1/GDP 0.002 0.07 -10000 0 -0.29 6 6
NGF (dimer)/TRKA/GRIT -0.041 0.14 -10000 0 -0.35 90 90
neuron projection morphogenesis -0.041 0.13 -10000 0 -0.61 9 9
NGF (dimer)/TRKA/NEDD4-2 -0.034 0.14 -10000 0 -0.35 91 91
MAP2K1 0.03 0.023 -10000 0 -0.29 3 3
NGFR -0.079 0.2 -10000 0 -0.51 104 104
NGF (dimer)/TRKA/GIPC/GAIP -0.022 0.12 -10000 0 -0.35 28 28
RAS family/GTP/PI3K 0.014 0.08 -10000 0 -0.42 15 15
FRS2 family/SHP2/GRB2/SOS1 0.029 0.047 -10000 0 -0.36 8 8
NRAS 0.001 0.076 -10000 0 -0.58 10 10
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
PRKCI 0.008 0.042 -10000 0 -0.58 3 3
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
MAPKKK cascade -0.09 0.19 -10000 0 -0.63 58 58
RASA1 0.009 0.034 -10000 0 -0.58 2 2
TRKA/c-Abl -0.02 0.12 -10000 0 -0.38 54 54
SQSTM1 0.011 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.098 0.16 -10000 0 -0.36 105 105
NGF (dimer)/TRKA/p62/Atypical PKCs -0.018 0.12 -10000 0 -0.33 64 64
MATK -0.064 0.19 -10000 0 -0.52 84 84
NEDD4L 0.01 0.024 -10000 0 -0.58 1 1
RAS family/GDP -0.021 0.049 -10000 0 -0.28 7 7
NGF (dimer)/TRKA -0.076 0.14 -10000 0 -0.33 112 112
Rac1/GTP -0.079 0.11 -10000 0 -0.34 58 58
FRS2 family/SHP2/CRK family 0.029 0.049 -10000 0 -0.4 7 7
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A -0.036 0.12 -10000 0 -0.33 85 85
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.009 0.033 -10000 0 -0.46 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.013 0.081 -10000 0 -0.28 21 21
IRAK/TOLLIP -0.015 0.096 -10000 0 -0.41 7 7
IKBKB 0.011 0.019 -10000 0 -0.46 1 1
IKBKG 0.01 0.024 -10000 0 -0.58 1 1
IL1 alpha/IL1R2 -0.1 0.2 -10000 0 -0.4 169 169
IL1A -0.09 0.21 -10000 0 -0.51 115 115
IL1B -0.056 0.17 -10000 0 -0.4 107 107
IRAK/TRAF6/p62/Atypical PKCs 0.002 0.096 -10000 0 -0.58 5 5
IL1R2 -0.055 0.18 -10000 0 -0.52 74 74
IL1R1 -0.005 0.092 -10000 0 -0.51 19 19
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.008 0.09 0.2 10 -0.31 19 29
TOLLIP 0.01 0.024 -10000 0 -0.58 1 1
TICAM2 -0.011 0.11 -10000 0 -0.58 21 21
MAP3K3 0.009 0.034 -10000 0 -0.58 2 2
TAK1/TAB1/TAB2 0.008 0 -10000 0 -10000 0 0
IKK complex/ELKS 0.02 0.087 -10000 0 -0.61 4 4
JUN -0.002 0.089 -10000 0 -0.55 4 4
MAP3K7 0.011 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.031 0.14 -10000 0 -0.54 17 17
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.043 0.14 -10000 0 -0.34 69 69
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.034 0.13 -10000 0 -0.32 69 69
IL1 beta fragment/IL1R1/IL1RAP -0.045 0.15 -10000 0 -0.37 73 73
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 -0.006 0.089 -10000 0 -0.53 4 4
IRAK1 -0.024 0.1 -10000 0 -0.27 86 86
IL1RN/IL1R1 -0.04 0.14 -10000 0 -0.39 84 84
IRAK4 0.011 0 -10000 0 -10000 0 0
PRKCI 0.008 0.042 -10000 0 -0.58 3 3
TRAF6 0.01 0.024 -10000 0 -0.58 1 1
PI3K 0.013 0.04 -10000 0 -0.42 5 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.013 0.096 -10000 0 -0.31 29 29
CHUK 0.007 0.048 -10000 0 -0.58 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.045 0.15 -10000 0 -0.37 73 73
IL1 beta/IL1R2 -0.081 0.19 -10000 0 -0.37 155 155
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.018 0.082 -10000 0 -0.36 7 7
NF kappa B1 p50/RelA -0.055 0.11 -10000 0 -0.49 18 18
IRAK3 -0.026 0.14 -10000 0 -0.54 41 41
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.04 0.15 -10000 0 -0.54 19 19
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.022 0.11 -10000 0 -0.27 70 70
IL1 alpha/IL1R1/IL1RAP -0.056 0.15 -10000 0 -0.32 137 137
RELA 0.011 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.011 0 -10000 0 -10000 0 0
MYD88 0.011 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.008 0.094 -10000 0 -0.36 9 9
IL1RAP 0.001 0.076 -10000 0 -0.58 10 10
UBE2N 0.01 0.024 -10000 0 -0.58 1 1
IRAK/TRAF6 -0.081 0.14 -10000 0 -0.45 47 47
CASP1 -0.021 0.13 -10000 0 -0.54 35 35
IL1RN/IL1R2 -0.074 0.19 -10000 0 -0.43 122 122
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.035 0.14 -10000 0 -0.34 73 73
TMEM189-UBE2V1 -0.062 0.16 -10000 0 -0.46 85 85
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.025 0.11 -10000 0 -0.4 21 21
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
IL1RN -0.051 0.17 -10000 0 -0.52 70 70
TRAF6/TAK1/TAB1/TAB2 -0.031 0.079 -10000 0 -0.38 5 5
MAP2K6 -0.011 0.091 -10000 0 -0.33 15 15
Caspase cascade in apoptosis

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
TOP1 -0.028 0.12 0.19 2 -0.33 63 65
ACTA1 -0.049 0.16 0.22 3 -0.42 66 69
NUMA1 -0.027 0.12 0.19 2 -0.33 62 64
SPTAN1 -0.041 0.15 0.23 2 -0.41 62 64
LIMK1 -0.041 0.15 0.23 2 -0.41 61 63
BIRC3 -0.016 0.12 -10000 0 -0.52 30 30
BIRC2 -0.002 0.087 -10000 0 -0.58 13 13
BAX 0.01 0.024 -10000 0 -0.58 1 1
CASP10 -0.055 0.16 -10000 0 -0.34 129 129
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.01 0.024 -10000 0 -0.58 1 1
PTK2 -0.027 0.12 0.19 2 -0.33 61 63
DIABLO 0.011 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.04 0.15 0.23 2 -0.4 62 64
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.01 0.024 -10000 0 -0.58 1 1
GSN -0.046 0.16 0.23 2 -0.41 66 68
MADD 0.011 0 -10000 0 -10000 0 0
TFAP2A -0.085 0.2 -10000 0 -0.56 83 83
BID -0.022 0.086 -10000 0 -0.23 64 64
MAP3K1 -0.014 0.07 -10000 0 -0.31 14 14
TRADD 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.014 0.036 -10000 0 -0.42 4 4
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.042 0.16 0.23 2 -0.42 62 64
CASP9 0.011 0.024 -10000 0 -0.58 1 1
DNA repair 0.004 0.049 0.15 8 -0.18 11 19
neuron apoptosis 0.012 0.036 -10000 0 -0.49 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.033 0.15 0.22 2 -0.4 59 61
APAF1 0.008 0.042 -10000 0 -0.58 3 3
CASP6 -0.005 0.085 -10000 0 -0.36 14 14
TRAF2 0.01 0.024 -10000 0 -0.58 1 1
ICAD/CAD -0.034 0.15 0.22 2 -0.4 59 61
CASP7 0.009 0.058 0.27 20 -10000 0 20
KRT18 0.006 0.033 -10000 0 -0.55 1 1
apoptosis -0.038 0.14 0.25 2 -0.37 68 70
DFFA -0.04 0.15 0.23 2 -0.41 61 63
DFFB -0.04 0.15 0.23 2 -0.41 61 63
PARP1 -0.004 0.049 0.18 11 -0.15 8 19
actin filament polymerization 0.042 0.15 0.39 60 -0.22 2 62
TNF -0.017 0.12 -10000 0 -0.54 30 30
CYCS -0.022 0.086 -10000 0 -0.26 42 42
SATB1 -0.019 0.11 -10000 0 -0.41 20 20
SLK -0.052 0.16 0.23 2 -0.41 76 78
p15 BID/BAX -0.014 0.078 -10000 0 -0.3 13 13
CASP2 0.022 0.06 -10000 0 -0.4 2 2
JNK cascade 0.014 0.07 0.31 14 -10000 0 14
CASP3 -0.049 0.16 0.23 3 -0.44 63 66
LMNB2 0.016 0.061 -10000 0 -0.36 6 6
RIPK1 0.011 0 -10000 0 -10000 0 0
CASP4 0.009 0.039 -10000 0 -0.54 3 3
Mammalian IAPs/DIABLO 0.006 0.1 -10000 0 -0.45 21 21
negative regulation of DNA binding -0.084 0.2 -10000 0 -0.56 83 83
stress fiber formation -0.051 0.16 0.23 2 -0.41 76 78
GZMB -0.073 0.18 -10000 0 -0.4 128 128
CASP1 -0.006 0.079 -10000 0 -0.3 38 38
LMNB1 0.017 0.054 -10000 0 -0.27 5 5
APP 0.012 0.037 -10000 0 -0.5 2 2
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.008 0.018 -10000 0 -0.43 1 1
VIM -0.031 0.13 0.22 6 -0.35 61 67
LMNA 0.017 0.059 -10000 0 -0.35 5 5
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.017 0.064 -10000 0 -0.43 2 2
LRDD 0.008 0.042 -10000 0 -0.58 3 3
SREBF1 -0.042 0.15 0.23 2 -0.41 62 64
APAF-1/Caspase 9 -0.003 0.065 0.4 7 -0.75 1 8
nuclear fragmentation during apoptosis -0.026 0.12 0.19 2 -0.33 62 64
CFL2 -0.044 0.15 -10000 0 -0.4 60 60
GAS2 -0.071 0.17 0.23 1 -0.41 94 95
positive regulation of apoptosis 0.02 0.059 -10000 0 -0.32 6 6
PRF1 -0.039 0.15 -10000 0 -0.5 58 58
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.047 0.19 -9999 0 -0.49 74 74
MAP4K1 -0.044 0.17 -9999 0 -0.55 59 59
MAP3K8 0.01 0.031 -9999 0 -0.52 2 2
PRKCB -0.041 0.16 -9999 0 -0.54 56 56
DBNL 0.01 0.024 -9999 0 -0.58 1 1
CRKL 0.011 0 -9999 0 -10000 0 0
MAP3K1 -0.021 0.15 -9999 0 -0.54 36 36
JUN -0.031 0.2 -9999 0 -0.72 40 40
MAP3K7 -0.018 0.15 -9999 0 -0.55 33 33
GRAP2 -0.024 0.14 -9999 0 -0.55 37 37
CRK 0.011 0.019 -9999 0 -0.46 1 1
MAP2K4 -0.014 0.15 -9999 0 -0.53 35 35
LAT -0.01 0.1 -9999 0 -0.51 24 24
LCP2 -0.014 0.12 -9999 0 -0.54 27 27
MAPK8 -0.037 0.2 -9999 0 -0.76 39 39
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.025 0.16 -9999 0 -0.58 33 33
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.039 0.18 -9999 0 -0.46 74 74
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.026 0.051 -9999 0 -0.56 2 2
Crk/p130 Cas/Paxillin -0.06 0.11 -9999 0 -0.4 27 27
JUN -0.03 0.12 -9999 0 -0.44 24 24
HRAS 0.008 0.041 -9999 0 -0.49 4 4
RET51/GFRalpha1/GDNF/GRB10 -0.074 0.17 -9999 0 -0.41 87 87
RAP1A 0.01 0.024 -9999 0 -0.58 1 1
FRS2 0.009 0.034 -9999 0 -0.58 2 2
RAP1A/GDP 0.008 0.018 -9999 0 -0.43 1 1
RET51/GFRalpha1/GDNF/DOK1 -0.072 0.17 -9999 0 -0.4 86 86
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.006 0.054 -9999 0 -0.58 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0.019 -9999 0 -0.46 1 1
RET9/GFRalpha1/GDNF/Enigma -0.03 0.12 -9999 0 -0.34 53 53
RHOA 0.01 0.024 -9999 0 -0.58 1 1
RAP1A/GTP -0.082 0.14 -9999 0 -0.52 28 28
GRB7 0.002 0.066 -9999 0 -0.46 12 12
RET51/GFRalpha1/GDNF -0.072 0.17 -9999 0 -0.4 86 86
MAPKKK cascade -0.074 0.13 -9999 0 -0.47 33 33
BCAR1 0.008 0.044 -9999 0 -0.52 4 4
RET9/GFRalpha1/GDNF/IRS1 -0.032 0.12 -9999 0 -0.34 60 60
lamellipodium assembly -0.055 0.098 -9999 0 -0.36 28 28
RET51/GFRalpha1/GDNF/SHC -0.072 0.17 -9999 0 -0.4 86 86
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
RET9/GFRalpha1/GDNF/SHC -0.027 0.11 -9999 0 -0.33 54 54
RET9/GFRalpha1/GDNF/Shank3 -0.03 0.12 -9999 0 -0.34 57 57
MAPK3 -0.054 0.15 -9999 0 -0.49 28 28
DOK1 0.011 0 -9999 0 -10000 0 0
DOK6 -0.03 0.15 -9999 0 -0.55 44 44
PXN 0.011 0 -9999 0 -10000 0 0
neurite development -0.049 0.15 -9999 0 -0.47 35 35
DOK5 -0.049 0.17 -9999 0 -0.54 65 65
GFRA1 -0.069 0.19 -9999 0 -0.53 89 89
MAPK8 -0.035 0.12 -9999 0 -0.45 21 21
HRAS/GTP -0.082 0.14 -9999 0 -0.41 59 59
tube development -0.023 0.11 -9999 0 -0.32 56 56
MAPK1 -0.054 0.15 -9999 0 -0.49 28 28
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.014 0.093 -9999 0 -0.27 59 59
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
SRC 0.01 0.024 -9999 0 -0.58 1 1
PDLIM7 0.006 0.052 -9999 0 -0.47 7 7
RET51/GFRalpha1/GDNF/Dok6 -0.084 0.19 -9999 0 -0.41 112 112
SHC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.073 0.17 -9999 0 -0.4 86 86
RET51/GFRalpha1/GDNF/Dok5 -0.11 0.2 -9999 0 -0.43 123 123
PRKCA 0.01 0.031 -9999 0 -0.52 2 2
HRAS/GDP 0.006 0.03 -9999 0 -0.35 4 4
CREB1 -0.028 0.12 -9999 0 -0.35 54 54
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.01 0.086 -9999 0 -0.26 53 53
RET51/GFRalpha1/GDNF/Grb7 -0.077 0.17 -9999 0 -0.4 87 87
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.084 0.2 -9999 0 -0.5 111 111
DOK4 0.01 0.024 -9999 0 -0.58 1 1
JNK cascade -0.029 0.12 -9999 0 -0.43 24 24
RET9/GFRalpha1/GDNF/FRS2 -0.028 0.11 -9999 0 -0.29 93 93
SHANK3 0.006 0.055 -9999 0 -0.54 6 6
RASA1 0.009 0.034 -9999 0 -0.58 2 2
NCK1 0.009 0.034 -9999 0 -0.58 2 2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.011 0.087 -9999 0 -0.26 54 54
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.045 0.13 -9999 0 -0.47 23 23
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.043 0.13 -9999 0 -0.48 20 20
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.045 0.14 -9999 0 -0.58 20 20
PI3K -0.046 0.17 -9999 0 -0.55 29 29
SOS1 0.01 0.024 -9999 0 -0.58 1 1
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.022 0.11 -9999 0 -0.32 56 56
GRB10 0.007 0.048 -9999 0 -0.58 4 4
activation of MAPKK activity -0.035 0.12 -9999 0 -0.42 22 22
RET51/GFRalpha1/GDNF/FRS2 -0.073 0.17 -9999 0 -0.4 88 88
GAB1 0.011 0 -9999 0 -10000 0 0
IRS1 0.002 0.072 -9999 0 -0.58 9 9
IRS2 0.003 0.068 -9999 0 -0.54 9 9
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.045 0.14 -9999 0 -0.58 20 20
RET51/GFRalpha1/GDNF/PKC alpha -0.073 0.17 -9999 0 -0.4 86 86
GRB2 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GDNF 0.006 0.036 -9999 0 -0.5 3 3
RAC1 0.011 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.077 0.18 -9999 0 -0.41 90 90
Rac1/GTP -0.064 0.12 -9999 0 -0.43 28 28
RET9/GFRalpha1/GDNF -0.038 0.12 -9999 0 -0.32 91 91
GFRalpha1/GDNF -0.046 0.14 -9999 0 -0.38 91 91
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.015 0.025 -10000 0 -10000 0 0
AES 0.013 0.032 -10000 0 -0.58 1 1
FBXW11 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.014 0.039 -10000 0 -0.4 5 5
SMAD4 0.004 0.064 -10000 0 -0.58 7 7
DKK2 -0.087 0.21 -10000 0 -0.54 106 106
TLE1 0.01 0.053 -10000 0 -0.58 4 4
MACF1 0.012 0 -10000 0 -10000 0 0
CTNNB1 0.05 0.099 0.26 9 -0.95 2 11
WIF1 -0.18 0.25 -10000 0 -0.5 222 222
beta catenin/RanBP3 0.025 0.13 0.39 55 -0.7 2 57
KREMEN2 -0.038 0.15 -10000 0 -0.48 60 60
DKK1 -0.15 0.24 -10000 0 -0.51 185 185
beta catenin/beta TrCP1 0.054 0.091 0.25 9 -0.8 2 11
FZD1 0.009 0.039 -10000 0 -0.54 3 3
AXIN2 -0.11 0.42 -10000 0 -1.4 54 54
AXIN1 0.011 0.024 -10000 0 -0.58 1 1
RAN 0.012 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.014 0.082 -10000 0 -1.2 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.049 0.1 0.23 1 -0.62 7 8
Axin1/APC/GSK3 0.046 0.079 0.24 5 -0.78 2 7
Axin1/APC/GSK3/beta catenin/Macf1 0.036 0.094 -10000 0 -0.71 4 4
HNF1A 0.008 0.058 -10000 0 -0.53 6 6
CTBP1 0.013 0.033 -10000 0 -0.58 1 1
MYC -0.013 0.15 -10000 0 -1.5 5 5
RANBP3 0.011 0.024 -10000 0 -0.58 1 1
DKK2/LRP6/Kremen 2 -0.069 0.16 -10000 0 -0.32 159 159
NKD1 -0.13 0.24 -10000 0 -0.52 158 158
TCF4 0.001 0.085 -10000 0 -0.52 14 14
TCF3 0.013 0.033 -10000 0 -0.58 1 1
WNT1/LRP6/FZD1/Axin1 0.016 0.061 -10000 0 -0.36 6 6
Ran/GTP 0.009 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.028 0.16 0.46 51 -0.62 6 57
LEF1 -0.009 0.11 -10000 0 -0.52 26 26
DVL1 0.045 0.061 -10000 0 -0.5 4 4
CSNK2A1 0.012 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.042 0.11 -10000 0 -0.52 11 11
DKK1/LRP6/Kremen 2 -0.11 0.18 -10000 0 -0.32 225 225
LRP6 0.01 0.035 -10000 0 -0.58 2 2
CSNK1A1 0.013 0.043 -10000 0 -0.59 2 2
NLK 0.011 0.004 -10000 0 -10000 0 0
CCND1 -0.005 0.093 -10000 0 -1.4 1 1
WNT1 -0.009 0.087 -10000 0 -0.46 21 21
GSK3A 0.012 0.001 -10000 0 -10000 0 0
GSK3B 0.009 0.034 -10000 0 -0.58 2 2
FRAT1 0.01 0.024 -10000 0 -0.58 1 1
PPP2R5D 0.088 0.11 0.27 153 -10000 0 153
APC 0.01 0.083 -10000 0 -0.33 24 24
WNT1/LRP6/FZD1 0.071 0.1 0.23 78 -0.69 3 81
CREBBP 0.014 0.022 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 -0.015 0.12 -9999 0 -0.39 37 37
NF kappa B1 p50/RelA/I kappa B alpha -0.014 0.11 -9999 0 -0.46 7 7
AP1 -0.085 0.14 -9999 0 -0.52 32 32
mol:PIP3 -0.065 0.12 -9999 0 -0.49 24 24
AKT1 0.01 0.091 -9999 0 -0.42 12 12
PTK2B -0.014 0.094 -9999 0 -0.35 20 20
RHOA 0.01 0.051 -9999 0 -0.35 3 3
PIK3CB 0.008 0.046 -9999 0 -0.55 4 4
mol:Ca2+ -0.018 0.11 -9999 0 -0.44 13 13
MAGI3 0.008 0.042 -9999 0 -0.58 3 3
RELA 0.011 0 -9999 0 -10000 0 0
apoptosis -0.052 0.14 -9999 0 -0.36 72 72
HRAS/GDP 0.006 0.03 -9999 0 -0.35 4 4
positive regulation of microtubule depolymerization -0.044 0.13 -9999 0 -0.43 24 24
NF kappa B1 p50/RelA -0.064 0.12 -9999 0 -0.48 27 27
endothelial cell migration -0.046 0.19 -9999 0 -0.51 77 77
ADCY4 -0.039 0.16 -9999 0 -0.5 46 46
ADCY5 -0.072 0.19 -9999 0 -0.56 60 60
ADCY6 -0.037 0.16 -9999 0 -0.51 43 43
ADCY7 -0.038 0.16 -9999 0 -0.52 43 43
ADCY1 -0.049 0.16 -9999 0 -0.51 49 49
ADCY2 -0.054 0.18 -9999 0 -0.52 63 63
ADCY3 -0.037 0.16 -9999 0 -0.51 44 44
ADCY8 -0.042 0.16 -9999 0 -0.52 43 43
ADCY9 -0.038 0.16 -9999 0 -0.51 44 44
GSK3B -0.009 0.092 -9999 0 -0.38 14 14
arachidonic acid secretion -0.033 0.15 -9999 0 -0.48 44 44
GNG2 0.004 0.063 -9999 0 -0.53 8 8
TRIP6 -0.014 0.12 -9999 0 -0.42 40 40
GNAO1 -0.054 0.16 -9999 0 -0.34 117 117
HRAS 0.008 0.041 -9999 0 -0.49 4 4
NFKBIA -0.02 0.12 -9999 0 -0.44 15 15
GAB1 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.032 0.2 -9999 0 -0.91 30 30
JUN 0.006 0.052 -9999 0 -0.56 5 5
LPA/LPA2/NHERF2 0.007 0.046 -9999 0 -0.32 7 7
TIAM1 -0.059 0.24 -9999 0 -1.1 30 30
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
mol:IP3 -0.019 0.11 -9999 0 -0.45 13 13
PLCB3 0.012 0.055 -9999 0 -0.57 3 3
FOS -0.026 0.14 -9999 0 -0.53 41 41
positive regulation of mitosis -0.033 0.15 -9999 0 -0.48 44 44
LPA/LPA1-2-3 -0.063 0.15 -9999 0 -0.38 72 72
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.008 0.044 -9999 0 -0.52 4 4
stress fiber formation -0.023 0.11 -9999 0 -0.43 15 15
GNAZ -0.034 0.14 -9999 0 -0.36 78 78
EGFR/PI3K-beta/Gab1 -0.067 0.13 -9999 0 -0.52 24 24
positive regulation of dendritic cell cytokine production -0.063 0.15 -9999 0 -0.38 72 72
LPA/LPA2/MAGI-3 0.006 0.05 -9999 0 -0.33 9 9
ARHGEF1 -0.007 0.11 -9999 0 -0.36 30 30
GNAI2 -0.02 0.12 -9999 0 -0.35 57 57
GNAI3 -0.02 0.12 -9999 0 -0.35 57 57
GNAI1 -0.028 0.14 -9999 0 -0.38 65 65
LPA/LPA3 -0.056 0.14 -9999 0 -0.37 91 91
LPA/LPA2 -0.002 0.047 -9999 0 -0.34 7 7
LPA/LPA1 -0.034 0.14 -9999 0 -0.37 77 77
HB-EGF/EGFR -0.035 0.12 -9999 0 -0.31 96 96
HBEGF -0.041 0.14 -9999 0 -0.37 90 90
mol:DAG -0.019 0.11 -9999 0 -0.45 13 13
cAMP biosynthetic process -0.051 0.17 -9999 0 -0.48 60 60
NFKB1 0.01 0.024 -9999 0 -0.58 1 1
SRC 0.01 0.024 -9999 0 -0.58 1 1
GNB1 0.011 0.001 -9999 0 -10000 0 0
LYN -0.02 0.12 -9999 0 -0.43 17 17
GNAQ -0.031 0.1 -9999 0 -0.32 46 46
LPAR2 0.006 0.053 -9999 0 -0.47 7 7
LPAR3 -0.07 0.19 -9999 0 -0.51 91 91
LPAR1 -0.033 0.15 -9999 0 -0.61 35 35
IL8 -0.11 0.21 -9999 0 -0.49 99 99
PTK2 -0.051 0.15 -9999 0 -0.45 31 31
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
CASP3 -0.053 0.14 -9999 0 -0.36 72 72
EGFR 0.004 0.063 -9999 0 -0.53 8 8
PLCG1 -0.032 0.12 -9999 0 -0.35 47 47
PLD2 -0.05 0.14 -9999 0 -0.37 57 57
G12/G13 -0.011 0.11 -9999 0 -0.37 36 36
PI3K-beta -0.03 0.087 -9999 0 -0.43 16 16
cell migration -0.018 0.088 -9999 0 -0.26 40 40
SLC9A3R2 0.01 0.024 -9999 0 -0.58 1 1
PXN -0.023 0.11 -9999 0 -0.45 14 14
HRAS/GTP -0.034 0.16 -9999 0 -0.5 44 44
RAC1 0.011 0 -9999 0 -10000 0 0
MMP9 -0.059 0.18 -9999 0 -0.52 79 79
PRKCE 0.011 0 -9999 0 -10000 0 0
PRKCD -0.012 0.11 -9999 0 -0.47 9 9
Gi(beta/gamma) -0.033 0.15 -9999 0 -0.49 44 44
mol:LPA -0.01 0.045 -9999 0 -0.19 22 22
TRIP6/p130 Cas/FAK1/Paxillin -0.074 0.14 -9999 0 -0.53 24 24
MAPKKK cascade -0.033 0.15 -9999 0 -0.48 44 44
contractile ring contraction involved in cytokinesis 0.01 0.051 -9999 0 -0.34 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.038 0.12 -9999 0 -0.34 57 57
GNA15 -0.038 0.11 -9999 0 -0.33 53 53
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.034 -9999 0 -0.58 2 2
MAPT -0.045 0.13 -9999 0 -0.44 24 24
GNA11 -0.03 0.1 -9999 0 -0.32 44 44
Rac1/GTP -0.034 0.22 -9999 0 -0.96 30 30
MMP2 -0.046 0.19 -9999 0 -0.52 77 77
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.009 0.1 -9999 0 -0.5 23 23
GPC2 -0.008 0.1 -9999 0 -0.55 20 20
GPC2/Midkine -0.011 0.1 -9999 0 -0.38 42 42
neuron projection morphogenesis -0.011 0.1 -9999 0 -0.38 42 42
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.025 0.26 -10000 0 -0.87 38 38
NCK1/PAK1/Dok-R -0.038 0.11 -10000 0 -0.41 41 41
NCK1/Dok-R -0.026 0.3 -10000 0 -1.1 38 38
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
mol:beta2-estradiol 0.006 0.057 0.24 30 -10000 0 30
RELA 0.011 0 -10000 0 -10000 0 0
SHC1 0.012 0.001 -10000 0 -10000 0 0
Rac/GDP 0.008 0 -10000 0 -10000 0 0
F2 -0.11 0.23 0.24 25 -0.5 143 168
TNIP2 0.01 0.024 -10000 0 -0.58 1 1
NF kappa B/RelA -0.04 0.26 -10000 0 -0.98 38 38
FN1 -0.086 0.21 -10000 0 -0.52 109 109
PLD2 -0.007 0.3 -10000 0 -1.1 38 38
PTPN11 0.006 0.054 -10000 0 -0.58 5 5
GRB14 -0.12 0.24 -10000 0 -0.54 142 142
ELK1 0.005 0.27 -10000 0 -0.98 38 38
GRB7 0.002 0.066 -10000 0 -0.46 12 12
PAK1 0.011 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.085 0.3 -10000 0 -1.1 41 41
CDKN1A 0.041 0.2 -10000 0 -0.67 24 24
ITGA5 -0.005 0.09 -10000 0 -0.49 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.026 0.3 -10000 0 -1.1 38 38
CRK 0.011 0.019 -10000 0 -0.46 1 1
mol:NO 0.033 0.21 -10000 0 -0.64 41 41
PLG -0.032 0.31 -10000 0 -1.1 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.02 0.24 -10000 0 -0.84 38 38
GRB2 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.042 -10000 0 -0.58 3 3
ANGPT2 0.018 0.2 -10000 0 -0.74 15 15
BMX -0.052 0.32 -10000 0 -1.1 40 40
ANGPT1 -0.018 0.31 -10000 0 -1.2 34 34
tube development 0.035 0.22 -10000 0 -0.68 34 34
ANGPT4 0.001 0.042 -10000 0 -0.45 5 5
response to hypoxia -0.001 0.019 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.077 0.33 -10000 0 -1.2 39 39
alpha5/beta1 Integrin 0.005 0.065 -10000 0 -0.34 20 20
FGF2 -0.039 0.16 -10000 0 -0.52 56 56
STAT5A (dimer) 0.036 0.24 -10000 0 -0.75 35 35
mol:L-citrulline 0.033 0.21 -10000 0 -0.64 41 41
AGTR1 -0.093 0.21 -10000 0 -0.51 118 118
MAPK14 0.001 0.3 -10000 0 -1.1 37 37
Tie2/SHP2 -0.038 0.19 -10000 0 -1 17 17
TEK -0.016 0.21 -10000 0 -1.3 13 13
RPS6KB1 0.024 0.25 -10000 0 -0.85 38 38
Angiotensin II/AT1 -0.066 0.15 -10000 0 -0.37 118 118
Tie2/Ang1/GRB2 -0.011 0.31 -10000 0 -1.1 38 38
MAPK3 0.001 0.28 -10000 0 -1 38 38
MAPK1 0.001 0.28 -10000 0 -1 38 38
Tie2/Ang1/GRB7 -0.015 0.31 -10000 0 -1.1 38 38
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 -0.007 0.3 -10000 0 -1.1 38 38
PI3K 0.013 0.29 -10000 0 -1 38 38
FES -0.005 0.31 -10000 0 -1.1 38 38
Crk/Dok-R -0.026 0.29 -10000 0 -1.1 38 38
Tie2/Ang1/ABIN2 -0.011 0.31 -10000 0 -1.1 38 38
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.03 0.23 -10000 0 -0.77 38 38
STAT5A 0.012 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.026 0.25 -10000 0 -0.83 38 38
Tie2/Ang2 0.021 0.27 -10000 0 -0.91 34 34
Tie2/Ang1 -0.015 0.33 -10000 0 -1.2 38 38
FOXO1 0.032 0.24 -10000 0 -0.77 41 41
ELF1 0.013 0.046 -10000 0 -0.59 3 3
ELF2 -0.008 0.3 -10000 0 -1.1 38 38
mol:Choline -0.003 0.29 -10000 0 -1 38 38
cell migration -0.03 0.067 -10000 0 -0.23 42 42
FYN 0.03 0.24 -10000 0 -0.78 34 34
DOK2 -0.01 0.11 -10000 0 -0.55 23 23
negative regulation of cell cycle 0.044 0.19 -10000 0 -0.55 37 37
ETS1 -0.003 0.083 -10000 0 -0.43 13 13
PXN 0.037 0.21 -10000 0 -0.68 38 38
ITGB1 0.011 0 -10000 0 -10000 0 0
NOS3 0.028 0.23 -10000 0 -0.73 41 41
RAC1 0.011 0 -10000 0 -10000 0 0
TNF -0.022 0.14 -10000 0 -0.53 34 34
MAPKKK cascade -0.003 0.29 -10000 0 -1 38 38
RASA1 0.009 0.034 -10000 0 -0.58 2 2
Tie2/Ang1/Shc -0.01 0.31 -10000 0 -1.1 38 38
NCK1 0.009 0.034 -10000 0 -0.58 2 2
vasculogenesis 0.036 0.19 -10000 0 -0.57 41 41
mol:Phosphatidic acid -0.003 0.29 -10000 0 -1 38 38
mol:Angiotensin II 0.001 0.004 -10000 0 -10000 0 0
mol:NADP 0.033 0.21 -10000 0 -0.64 41 41
Rac1/GTP -0.06 0.2 -10000 0 -0.78 38 38
MMP2 -0.028 0.32 -10000 0 -1.2 39 39
Visual signal transduction: Rods

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
mol:K + 0.009 0.034 -9999 0 -0.58 2 2
GNAT1/GTP 0.001 0.019 -9999 0 -0.32 2 2
Metarhodopsin II/Arrestin 0 0.023 -9999 0 -0.27 4 4
PDE6G/GNAT1/GTP -0.015 0.088 -9999 0 -0.33 42 42
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.001 0.027 -9999 0 -0.46 2 2
GRK1 -0.003 0.046 -9999 0 -0.46 6 6
CNG Channel -0.12 0.18 -9999 0 -0.57 48 48
mol:Na + -0.067 0.13 -9999 0 -0.5 24 24
mol:ADP -0.003 0.046 -9999 0 -0.46 6 6
RGS9-1/Gbeta5/R9AP -0.022 0.12 -9999 0 -0.32 75 75
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.069 0.14 -9999 0 -0.51 24 24
CNGB1 -0.005 0.068 -9999 0 -0.46 13 13
RDH5 0 0.079 -9999 0 -0.52 13 13
SAG 0.002 0.019 -9999 0 -0.46 1 1
mol:Ca2+ -0.044 0.14 -9999 0 -0.48 24 24
Na + (4 Units) -0.064 0.12 -9999 0 -0.46 24 24
RGS9 -0.036 0.15 -9999 0 -0.52 52 52
GNB1/GNGT1 -0.023 0.12 -9999 0 -0.37 58 58
GNAT1/GDP -0.018 0.1 -9999 0 -0.31 49 49
GUCY2D -0.015 0.1 -9999 0 -0.46 29 29
GNGT1 -0.043 0.16 -9999 0 -0.52 58 58
GUCY2F 0 0.019 -9999 0 -0.46 1 1
GNB5 0.007 0.048 -9999 0 -0.58 4 4
mol:GMP (4 units) -0.083 0.17 -9999 0 -0.36 123 123
mol:11-cis-retinal 0 0.079 -9999 0 -0.52 13 13
mol:cGMP -0.025 0.11 -9999 0 -0.34 36 36
GNB1 0.011 0 -9999 0 -10000 0 0
Rhodopsin -0.001 0.062 -9999 0 -0.37 16 16
SLC24A1 0.009 0.034 -9999 0 -0.58 2 2
CNGA1 -0.052 0.17 -9999 0 -0.52 70 70
Metarhodopsin II -0.002 0.033 -9999 0 -0.28 8 8
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.027 0.11 -9999 0 -0.35 36 36
RGS9BP -0.009 0.1 -9999 0 -0.54 21 21
Metarhodopsin II/Transducin -0.012 0.071 -9999 0 -0.28 33 33
GCAP Family/Ca ++ -0.02 0.094 -9999 0 -0.28 65 65
PDE6A/B -0.096 0.2 -9999 0 -0.41 157 157
mol:Pi -0.022 0.12 -9999 0 -0.32 75 75
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.016 0.092 -9999 0 -0.29 59 59
PDE6B -0.03 0.14 -9999 0 -0.52 46 46
PDE6A -0.1 0.22 -9999 0 -0.54 125 125
PDE6G -0.026 0.14 -9999 0 -0.54 40 40
RHO -0.001 0.032 -9999 0 -0.46 3 3
PDE6 -0.12 0.18 -9999 0 -0.55 51 51
GUCA1A -0.022 0.12 -9999 0 -0.49 36 36
GC2/GCAP Family -0.02 0.096 -9999 0 -0.34 32 32
GUCA1C -0.001 0.026 -9999 0 -0.46 2 2
GUCA1B -0.015 0.12 -9999 0 -0.54 28 28
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.032 0.14 -10000 0 -0.41 45 45
CRKL -0.012 0.12 -10000 0 -0.42 38 38
HRAS -0.025 0.15 -10000 0 -0.48 34 34
mol:PIP3 -0.021 0.12 -10000 0 -0.4 39 39
SPRED1 0.005 0.059 -10000 0 -0.58 6 6
SPRED2 0.008 0.042 -10000 0 -0.58 3 3
GAB1 -0.019 0.13 -10000 0 -0.44 39 39
FOXO3 -0.007 0.12 -10000 0 -0.38 40 40
AKT1 -0.014 0.13 -10000 0 -0.42 40 40
BAD -0.008 0.12 -10000 0 -0.39 40 40
megakaryocyte differentiation -0.082 0.18 -10000 0 -0.5 52 52
GSK3B -0.008 0.12 -10000 0 -0.39 41 41
RAF1 -0.013 0.13 -10000 0 -0.39 31 31
SHC1 0.011 0 -10000 0 -10000 0 0
STAT3 -0.019 0.13 -10000 0 -0.44 39 39
STAT1 -0.064 0.32 -10000 0 -1 50 50
HRAS/SPRED1 -0.016 0.13 -10000 0 -0.41 33 33
cell proliferation -0.018 0.13 -10000 0 -0.43 39 39
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
TEC 0.011 0.019 -10000 0 -0.46 1 1
RPS6KB1 -0.02 0.14 -10000 0 -0.46 40 40
HRAS/SPRED2 -0.015 0.13 -10000 0 -0.39 34 34
LYN/TEC/p62DOK -0.007 0.12 -10000 0 -0.41 38 38
MAPK3 0.001 0.096 -10000 0 -0.28 29 29
STAP1 -0.051 0.17 -10000 0 -0.42 78 78
GRAP2 -0.024 0.14 -10000 0 -0.55 37 37
JAK2 -0.056 0.29 -10000 0 -0.97 42 42
STAT1 (dimer) -0.061 0.31 -10000 0 -0.98 50 50
mol:Gleevec 0 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.043 0.16 -10000 0 -0.48 52 52
actin filament polymerization -0.03 0.14 -10000 0 -0.46 41 41
LYN 0.011 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.058 0.22 -10000 0 -0.64 56 56
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
CBL/CRKL/GRB2 0.001 0.12 -10000 0 -0.39 33 33
PI3K -0.011 0.14 -10000 0 -0.45 40 40
PTEN 0.005 0.059 -10000 0 -0.58 6 6
SCF/KIT/EPO/EPOR -0.066 0.35 -10000 0 -1.3 38 38
MAPK8 -0.019 0.13 -10000 0 -0.44 39 39
STAT3 (dimer) -0.018 0.13 -10000 0 -0.43 39 39
positive regulation of transcription 0.005 0.081 -10000 0 -0.24 19 19
mol:GDP -0.035 0.16 -10000 0 -0.45 58 58
PIK3C2B -0.018 0.13 -10000 0 -0.44 39 39
CBL/CRKL -0.004 0.12 -10000 0 -0.39 37 37
FER -0.023 0.14 -10000 0 -0.47 41 41
SH2B3 -0.019 0.13 -10000 0 -0.44 39 39
PDPK1 -0.014 0.11 -10000 0 -0.38 38 38
SNAI2 -0.027 0.14 -10000 0 -0.43 49 49
positive regulation of cell proliferation -0.04 0.23 -10000 0 -0.75 45 45
KITLG -0.005 0.1 -10000 0 -0.6 17 17
cell motility -0.04 0.23 -10000 0 -0.75 45 45
PTPN6 0.011 0.007 -10000 0 -10000 0 0
EPOR -0.001 0.14 -10000 0 -1 5 5
STAT5A (dimer) -0.031 0.19 -10000 0 -0.62 46 46
SOCS1 -0.028 0.14 -10000 0 -0.49 47 47
cell migration 0.055 0.16 0.47 50 -10000 0 50
SOS1 0.01 0.024 -10000 0 -0.58 1 1
EPO 0 0.054 -10000 0 -0.46 8 8
VAV1 -0.026 0.14 -10000 0 -0.57 38 38
GRB10 -0.021 0.14 -10000 0 -0.45 41 41
PTPN11 0.006 0.054 -10000 0 -0.57 5 5
SCF/KIT -0.026 0.14 -10000 0 -0.44 45 45
GO:0007205 0 0.007 -10000 0 -10000 0 0
MAP2K1 -0.003 0.1 -10000 0 -0.31 30 30
CBL 0.011 0 -10000 0 -10000 0 0
KIT -0.067 0.33 -10000 0 -1.4 33 33
MAP2K2 -0.002 0.1 -10000 0 -0.31 29 29
SHC/Grb2/SOS1 -0.007 0.13 -10000 0 -0.42 38 38
STAT5A -0.033 0.2 -10000 0 -0.64 46 46
GRB2 0.011 0 -10000 0 -10000 0 0
response to radiation -0.026 0.14 -10000 0 -0.42 49 49
SHC/GRAP2 -0.009 0.1 -10000 0 -0.4 37 37
PTPRO -0.084 0.18 -10000 0 -0.51 52 52
SH2B2 -0.031 0.15 -10000 0 -0.47 41 41
DOK1 0.011 0 -10000 0 -10000 0 0
MATK -0.056 0.16 -10000 0 -0.48 50 50
CREBBP 0.022 0.031 -10000 0 -10000 0 0
BCL2 -0.021 0.24 -10000 0 -1.3 16 16
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.016 0.1 -9999 0 -0.32 46 46
RGS9BP -0.009 0.1 -9999 0 -0.54 21 21
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.003 0.046 -9999 0 -0.46 6 6
mol:Na + -0.047 0.12 -9999 0 -0.3 107 107
mol:ADP -0.002 0.057 -9999 0 -0.34 16 16
GNAT2 -0.007 0.095 -9999 0 -0.53 19 19
RGS9-1/Gbeta5/R9AP -0.022 0.12 -9999 0 -0.32 75 75
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.004 0.06 -9999 0 -0.32 20 20
GRK7 -0.001 0.063 -9999 0 -0.46 11 11
CNGB3 -0.029 0.12 -9999 0 -0.46 42 42
Cone Metarhodopsin II/X-Arrestin -0.001 0.03 -9999 0 -0.32 5 5
mol:Ca2+ -0.049 0.12 -9999 0 -0.35 44 44
Cone PDE6 -0.018 0.1 -9999 0 -0.32 44 44
Cone Metarhodopsin II -0.001 0.044 -9999 0 -0.26 16 16
Na + (4 Units) -0.048 0.12 -9999 0 -0.35 44 44
GNAT2/GDP -0.021 0.11 -9999 0 -0.31 55 55
GNB5 0.007 0.048 -9999 0 -0.58 4 4
mol:GMP (4 units) -0.004 0.058 -9999 0 -0.28 24 24
Cone Transducin -0.017 0.11 -9999 0 -0.34 46 46
SLC24A2 -0.011 0.092 -9999 0 -0.48 22 22
GNB3/GNGT2 -0.02 0.12 -9999 0 -0.39 53 53
GNB3 -0.019 0.12 -9999 0 -0.53 33 33
GNAT2/GTP -0.005 0.07 -9999 0 -0.38 19 19
CNGA3 -0.05 0.17 -9999 0 -0.52 66 66
ARR3 -0.001 0.042 -9999 0 -0.46 5 5
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.047 0.12 -9999 0 -0.3 107 107
mol:Pi -0.022 0.12 -9999 0 -0.32 75 75
Cone CNG Channel -0.053 0.11 -9999 0 -0.32 43 43
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.011 0.092 -9999 0 -0.48 22 22
RGS9 -0.036 0.15 -9999 0 -0.52 52 52
PDE6C 0 0.038 -9999 0 -0.46 4 4
GNGT2 -0.009 0.1 -9999 0 -0.56 21 21
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0.019 -9999 0 -0.46 1 1
Cellular roles of Anthrax toxin

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
ANTXR1 -0.045 0.17 -10000 0 -0.53 62 62
ANTXR2 0.005 0.058 -10000 0 -0.53 7 7
negative regulation of myeloid dendritic cell antigen processing and presentation -0.008 0.022 -10000 0 -0.068 68 68
monocyte activation -0.025 0.13 -10000 0 -0.49 38 38
MAP2K2 -0.004 0.032 -10000 0 -0.76 1 1
MAP2K1 -0.008 0.027 -10000 0 -0.35 2 2
MAP2K7 -0.007 0.022 -10000 0 -0.31 1 1
MAP2K6 -0.012 0.045 -10000 0 -0.32 10 10
CYAA -0.021 0.094 -10000 0 -0.28 68 68
MAP2K4 -0.008 0.029 -10000 0 -0.31 3 3
IL1B -0.04 0.11 -10000 0 -0.28 90 90
Channel -0.021 0.1 -10000 0 -0.3 68 68
NLRP1 -0.02 0.065 -10000 0 -0.28 31 31
CALM1 0.011 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.009 0.025 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.008 0.022 0.068 68 -10000 0 68
MAPK3 -0.007 0.022 -10000 0 -0.31 1 1
MAPK1 -0.007 0.024 -10000 0 -0.38 1 1
PGR -0.041 0.099 -10000 0 -0.29 77 77
PA/Cellular Receptors -0.024 0.11 -10000 0 -0.33 68 68
apoptosis -0.008 0.022 -10000 0 -0.068 68 68
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.019 0.093 -10000 0 -0.27 68 68
macrophage activation 0.007 0.028 -10000 0 -0.33 2 2
TNF -0.017 0.12 -10000 0 -0.54 30 30
VCAM1 -0.025 0.14 -10000 0 -0.49 38 38
platelet activation -0.009 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.002 0.027 0.14 4 -10000 0 4
IL18 -0.008 0.055 -10000 0 -0.25 19 19
negative regulation of macrophage activation -0.008 0.022 -10000 0 -0.068 68 68
LEF -0.008 0.022 -10000 0 -0.069 68 68
CASP1 -0.017 0.041 -10000 0 -0.16 33 33
mol:cAMP -0.009 0.025 -10000 0 -10000 0 0
necrosis -0.008 0.022 -10000 0 -0.068 68 68
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.019 0.095 -10000 0 -0.28 68 68
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.018 0.091 -10000 0 -0.63 10 10
HDAC1 0.008 0.004 -10000 0 -10000 0 0
AES 0.01 0.024 -10000 0 -0.58 1 1
FBXW11 0.011 0 -10000 0 -10000 0 0
DTX1 -0.01 0.11 -10000 0 -0.54 23 23
LRP6/FZD1 0.014 0.038 -10000 0 -0.4 5 5
TLE1 0.007 0.048 -10000 0 -0.58 4 4
AP1 -0.061 0.13 -10000 0 -0.31 108 108
NCSTN 0.011 0 -10000 0 -10000 0 0
ADAM10 0.006 0.054 -10000 0 -0.58 5 5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.036 0.067 -10000 0 -1.3 1 1
NICD/RBPSUH 0.016 0.085 -10000 0 -0.65 9 9
WIF1 -0.18 0.25 -10000 0 -0.5 222 222
NOTCH1 -0.012 0.078 -10000 0 -0.63 9 9
PSENEN 0.01 0.024 -10000 0 -0.58 1 1
KREMEN2 -0.038 0.15 -10000 0 -0.48 60 60
DKK1 -0.15 0.24 -10000 0 -0.51 185 185
beta catenin/beta TrCP1 0.05 0.068 0.25 2 -10000 0 2
APH1B 0.006 0.054 -10000 0 -0.58 5 5
APH1A 0.011 0 -10000 0 -10000 0 0
AXIN1 -0.013 0.047 -10000 0 -0.36 5 5
CtBP/CBP/TCF1/TLE1/AES 0.013 0.053 -10000 0 -0.34 9 9
PSEN1 0.011 0 -10000 0 -10000 0 0
FOS -0.026 0.14 -10000 0 -0.53 41 41
JUN 0.007 0.052 -10000 0 -0.56 5 5
MAP3K7 0.01 0.002 -10000 0 -10000 0 0
CTNNB1 0.047 0.072 0.27 2 -10000 0 2
MAPK3 0.01 0.024 -10000 0 -0.58 1 1
DKK2/LRP6/Kremen 2 -0.069 0.16 -10000 0 -0.32 159 159
HNF1A 0.005 0.057 -10000 0 -0.56 6 6
CTBP1 0.01 0.024 -10000 0 -0.58 1 1
MYC 0.01 0.13 -10000 0 -1.4 5 5
NKD1 -0.13 0.24 -10000 0 -0.52 158 158
FZD1 0.009 0.039 -10000 0 -0.54 3 3
NOTCH1 precursor/Deltex homolog 1 0.006 0.097 -10000 0 -0.59 10 10
apoptosis -0.061 0.13 -10000 0 -0.31 108 108
Delta 1/NOTCHprecursor 0.009 0.096 -10000 0 -0.63 10 10
DLL1 -0.003 0.086 -10000 0 -0.52 16 16
PPARD 0.019 0.058 -10000 0 -1.4 1 1
Gamma Secretase 0.031 0.033 -10000 0 -0.29 6 6
APC -0.028 0.1 -10000 0 -0.47 24 24
DVL1 -0.01 0.053 -10000 0 -0.5 4 4
CSNK2A1 0.012 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.11 0.18 -10000 0 -0.32 225 225
LRP6 0.009 0.034 -10000 0 -0.58 2 2
CSNK1A1 0.01 0.034 -10000 0 -0.58 2 2
NLK 0.011 0.004 -10000 0 -10000 0 0
CCND1 0.019 0.058 -10000 0 -1.4 1 1
WNT1 -0.009 0.087 -10000 0 -0.46 21 21
Axin1/APC/beta catenin 0.025 0.079 -10000 0 -0.42 8 8
DKK2 -0.086 0.21 -10000 0 -0.54 106 106
NOTCH1 precursor/DVL1 -0.017 0.09 -10000 0 -0.66 10 10
GSK3B 0.009 0.034 -10000 0 -0.58 2 2
FRAT1 0.01 0.024 -10000 0 -0.58 1 1
NOTCH/Deltex homolog 1 -0.021 0.092 -10000 0 -0.6 10 10
PPP2R5D 0.059 0.12 0.25 152 -10000 0 152
MAPK1 0.01 0.024 -10000 0 -0.58 1 1
WNT1/LRP6/FZD1 -0.094 0.15 -10000 0 -0.34 89 89
RBPJ 0.01 0.031 -10000 0 -0.52 2 2
CREBBP 0.014 0.002 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.012 0.045 -9999 0 -0.37 8 8
alphaV beta3 Integrin -0.025 0.14 -9999 0 -0.36 74 74
PTK2 -0.026 0.15 -9999 0 -0.52 28 28
IGF1R 0.01 0.024 -9999 0 -0.58 1 1
PI4KB 0.011 0 -9999 0 -10000 0 0
MFGE8 0 0.074 -9999 0 -0.49 13 13
SRC 0.01 0.024 -9999 0 -0.58 1 1
CDKN1B -0.035 0.13 -9999 0 -0.5 29 29
VEGFA 0.011 0.019 -9999 0 -0.46 1 1
ILK -0.034 0.13 -9999 0 -0.49 28 28
ROCK1 0 0.08 -9999 0 -0.58 11 11
AKT1 -0.024 0.12 -9999 0 -0.46 27 27
PTK2B 0.011 0.08 -9999 0 -0.31 28 28
alphaV/beta3 Integrin/JAM-A -0.041 0.15 -9999 0 -0.49 29 29
CBL 0.011 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.001 0.083 -9999 0 -0.34 32 32
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.028 0.13 -9999 0 -0.33 64 64
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.005 0.11 -9999 0 -0.64 10 10
alphaV/beta3 Integrin/Syndecan-1 0.005 0.082 -9999 0 -0.35 30 30
PI4KA 0.011 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.12 0.2 -9999 0 -0.58 68 68
PI4 Kinase 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/Osteopontin -0.1 0.18 -9999 0 -0.32 212 212
RPS6KB1 -0.083 0.21 -9999 0 -0.54 71 71
TLN1 0.01 0.024 -9999 0 -0.58 1 1
MAPK3 -0.065 0.2 -9999 0 -0.64 52 52
GPR124 0.003 0.069 -9999 0 -0.55 9 9
MAPK1 -0.065 0.2 -9999 0 -0.64 52 52
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
alphaV/beta3 Integrin/Tumstatin -0.047 0.14 -9999 0 -0.32 121 121
cell adhesion 0.002 0.092 -9999 0 -0.38 24 24
ANGPTL3 0.002 0.033 -9999 0 -0.46 3 3
VEGFR2 homodimer/VEGFA homodimer/Src 0.018 0.041 -9999 0 -0.31 9 9
IGF-1R heterotetramer 0.01 0.024 -9999 0 -0.58 1 1
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.019 -9999 0 -0.46 1 1
ITGB3 -0.006 0.098 -9999 0 -0.54 19 19
IGF1 -0.073 0.2 -9999 0 -0.52 94 94
RAC1 0.011 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0 0.097 -9999 0 -0.38 34 34
apoptosis 0 0.08 -9999 0 -0.58 11 11
CD47 0.009 0.034 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/CD47 0.004 0.086 -9999 0 -0.36 30 30
VCL 0.009 0.034 -9999 0 -0.58 2 2
alphaV/beta3 Integrin/Del1 -0.025 0.15 -9999 0 -0.42 66 66
CSF1 0.006 0.055 -9999 0 -0.54 6 6
PIK3C2A -0.053 0.18 -9999 0 -0.6 45 45
PI4 Kinase/Pyk2 -0.058 0.12 -9999 0 -0.46 24 24
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.009 0.083 -9999 0 -0.34 26 26
FAK1/Vinculin -0.014 0.12 -9999 0 -0.42 28 28
alphaV beta3/Integrin/ppsTEM5 0 0.098 -9999 0 -0.38 34 34
RHOA 0.01 0.024 -9999 0 -0.58 1 1
VTN -0.051 0.17 -9999 0 -0.5 71 71
BCAR1 0.008 0.044 -9999 0 -0.52 4 4
FGF2 -0.039 0.16 -9999 0 -0.52 56 56
F11R -0.018 0.11 -9999 0 -0.37 56 56
alphaV/beta3 Integrin/Lactadherin -0.001 0.096 -9999 0 -0.39 27 27
alphaV/beta3 Integrin/TGFBR2 0.005 0.082 -9999 0 -0.34 30 30
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.018 0.065 -9999 0 -0.34 17 17
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
alphaV/beta3 Integrin/Talin 0.005 0.075 -9999 0 -0.34 24 24
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.086 0.21 -9999 0 -0.52 109 109
alphaV/beta3 Integrin/Pyk2 0.013 0.081 -9999 0 -0.31 28 28
SDC1 0.01 0.024 -9999 0 -0.58 1 1
VAV3 -0.021 0.12 -9999 0 -0.31 91 91
PTPN11 0.006 0.054 -9999 0 -0.58 5 5
IRS1 0.002 0.072 -9999 0 -0.58 9 9
FAK1/Paxillin -0.014 0.12 -9999 0 -0.4 28 28
cell migration -0.006 0.11 -9999 0 -0.37 27 27
ITGAV 0 0.08 -9999 0 -0.58 11 11
PI3K -0.061 0.13 -9999 0 -0.5 25 25
SPP1 -0.16 0.25 -9999 0 -0.52 194 194
KDR 0.005 0.058 -9999 0 -0.53 7 7
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0.08 -9999 0 -0.58 11 11
COL4A3 -0.073 0.19 -9999 0 -0.51 95 95
angiogenesis -0.065 0.2 -9999 0 -0.66 49 49
Rac1/GTP -0.014 0.12 -9999 0 -0.56 4 4
EDIL3 -0.039 0.16 -9999 0 -0.57 51 51
cell proliferation 0.005 0.081 -9999 0 -0.34 30 30
a4b1 and a4b7 Integrin 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
ITGB1 0.011 0 -9999 0 -10000 0 0
ITGB7 -0.014 0.12 -9999 0 -0.53 28 28
ITGA4 -0.018 0.13 -9999 0 -0.56 30 30
alpha4/beta7 Integrin -0.022 0.13 -9999 0 -0.43 52 52
alpha4/beta1 Integrin -0.004 0.093 -9999 0 -0.41 30 30
FAS signaling pathway (CD95)

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
SPTAN1 0.011 0.058 0.26 16 -0.3 4 20
RFC1 0.011 0.062 0.26 16 -0.38 4 20
PRKDC 0.01 0.061 0.24 22 -0.3 6 28
RIPK1 0.013 0.003 -10000 0 -10000 0 0
CASP7 -0.01 0.051 0.24 6 -0.43 1 7
FASLG/FAS/FADD/FAF1 0.004 0.11 0.22 61 -0.3 31 92
MAP2K4 -0.027 0.13 -10000 0 -0.43 23 23
mol:ceramide -0.027 0.12 -10000 0 -0.39 44 44
GSN 0.006 0.068 0.24 22 -0.29 12 34
FASLG/FAS/FADD/FAF1/Caspase 8 0.001 0.12 -10000 0 -0.36 33 33
FAS -0.001 0.074 -10000 0 -0.56 10 10
BID 0.008 0.05 0.29 13 -0.32 2 15
MAP3K1 -0.006 0.088 0.22 5 -0.3 15 20
MAP3K7 0.01 0.004 -10000 0 -10000 0 0
RB1 0 0.085 0.26 15 -0.35 21 36
CFLAR 0.013 0.003 -10000 0 -10000 0 0
HGF/MET -0.066 0.17 -10000 0 -0.37 136 136
ARHGDIB 0.009 0.06 0.24 21 -0.31 5 26
FADD 0.009 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.006 0.068 0.29 12 -0.24 22 34
NFKB1 -0.043 0.085 -10000 0 -0.32 17 17
MAPK8 -0.045 0.17 -10000 0 -0.45 68 68
DFFA 0.012 0.056 0.24 22 -0.28 3 25
DNA fragmentation during apoptosis 0.012 0.056 0.24 22 -0.28 3 25
FAS/FADD/MET 0.012 0.052 -10000 0 -0.34 12 12
CFLAR/RIP1 0.013 0.007 -10000 0 -10000 0 0
FAIM3 -0.012 0.11 -10000 0 -0.52 27 27
FAF1 0.009 0.008 -10000 0 -10000 0 0
PARP1 0.012 0.056 0.24 22 -0.28 3 25
DFFB 0.012 0.056 0.24 22 -0.28 3 25
CHUK -0.04 0.08 -10000 0 -0.46 6 6
FASLG -0.055 0.18 -10000 0 -0.53 69 69
FAS/FADD 0.006 0.055 -10000 0 -0.41 10 10
HGF -0.037 0.16 -10000 0 -0.54 52 52
LMNA 0.009 0.052 0.23 15 -0.3 3 18
CASP6 0.011 0.054 0.23 25 -0.28 3 28
CASP10 0.008 0.025 -10000 0 -0.58 1 1
CASP3 0.014 0.067 0.28 27 -0.33 3 30
PTPN13 -0.082 0.21 -10000 0 -0.56 98 98
CASP8 0.013 0.067 0.3 27 -0.44 1 28
IL6 -0.16 0.41 -10000 0 -1.3 65 65
MET 0.01 0.031 -10000 0 -0.52 2 2
ICAD/CAD 0.011 0.052 0.24 16 -0.29 2 18
FASLG/FAS/FADD/FAF1/Caspase 10 -0.027 0.12 -10000 0 -0.39 44 44
activation of caspase activity by cytochrome c 0.008 0.05 0.29 13 -0.32 2 15
PAK2 0.011 0.06 0.24 22 -0.39 3 25
BCL2 -0.007 0.1 -10000 0 -0.55 20 20
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.011 0 -10000 0 -10000 0 0
HDAC3 0.011 0 -10000 0 -10000 0 0
VDR 0.01 0.024 -10000 0 -0.58 1 1
Cbp/p300/PCAF 0.01 0.072 -10000 0 -0.37 20 20
EP300 0.007 0.048 -10000 0 -0.58 4 4
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.002 0.079 -10000 0 -0.38 12 12
KAT2B -0.006 0.099 -10000 0 -0.58 17 17
MAPK14 0.011 0 -10000 0 -10000 0 0
AKT1 0.005 0.085 0.21 12 -0.3 15 27
RAR alpha/9cRA/Cyclin H -0.046 0.083 -10000 0 -0.46 5 5
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.006 0.085 -10000 0 -0.38 17 17
CDC2 0 0.002 -10000 0 -10000 0 0
response to UV 0.001 0.003 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.031 0.081 -10000 0 -0.47 1 1
NCOR2 0.008 0.046 -10000 0 -0.55 4 4
VDR/VDR/Vit D3 0.008 0.018 -10000 0 -0.43 1 1
RXRs/RARs/NRIP1/9cRA -0.049 0.17 -10000 0 -0.42 90 90
NCOA2 0.004 0.067 -10000 0 -0.56 8 8
NCOA3 0.01 0.024 -10000 0 -0.58 1 1
NCOA1 0.01 0.024 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.01 0.024 -10000 0 -0.58 1 1
RARG 0.006 0.059 -10000 0 -0.58 6 6
RAR gamma1/9cRA 0.012 0.038 -10000 0 -0.36 6 6
MAPK3 0.011 0.024 -10000 0 -0.58 1 1
MAPK1 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 0.011 0.024 -10000 0 -0.58 1 1
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.058 0.16 -10000 0 -0.43 82 82
RARA -0.039 0.1 -10000 0 -0.25 84 84
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.009 0.094 -10000 0 -0.4 19 19
PRKCA 0.011 0.031 -10000 0 -0.52 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.058 0.17 -10000 0 -0.43 89 89
RXRG -0.071 0.14 -10000 0 -0.34 83 83
RXRA -0.028 0.091 -10000 0 -0.22 83 83
RXRB -0.061 0.13 -10000 0 -0.34 81 81
VDR/Vit D3/DNA 0.008 0.018 -10000 0 -0.43 1 1
RBP1 -0.085 0.2 -10000 0 -0.48 115 115
CRBP1/9-cic-RA -0.061 0.14 -10000 0 -0.35 115 115
RARB -0.004 0.095 -10000 0 -0.54 18 18
PRKCG -0.15 0.24 -10000 0 -0.51 182 182
MNAT1 0.008 0.046 -10000 0 -0.55 4 4
RAR alpha/RXRs -0.042 0.18 -10000 0 -0.43 85 85
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.04 0.15 -10000 0 -0.37 84 84
proteasomal ubiquitin-dependent protein catabolic process -0.017 0.095 -10000 0 -0.36 18 18
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.058 0.17 -10000 0 -0.43 89 89
positive regulation of DNA binding -0.044 0.079 -10000 0 -0.43 5 5
NRIP1 -0.06 0.2 -10000 0 -0.97 13 13
RXRs/RARs -0.06 0.16 -10000 0 -0.42 89 89
RXRs/RXRs/DNA/9cRA -0.066 0.17 -10000 0 -0.44 87 87
PRKACA 0.011 0 -10000 0 -10000 0 0
CDK7 0.008 0.042 -10000 0 -0.58 3 3
TFIIH 0.019 0.044 -10000 0 -0.39 6 6
RAR alpha/9cRA -0.033 0.061 -10000 0 -0.39 4 4
CCNH 0.011 0 -10000 0 -10000 0 0
CREBBP 0.011 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.006 0.042 -10000 0 -0.55 1 1
EPHB forward 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
Ephrin A5/EPHB2 -0.059 0.15 -10000 0 -0.33 128 128
cell-cell adhesion 0.06 0.1 0.42 15 -10000 0 15
Ephrin B/EPHB2/RasGAP 0.008 0.089 -10000 0 -0.32 30 30
ITSN1 0.01 0.024 -10000 0 -0.58 1 1
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
SHC1 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.004 0.082 -10000 0 -0.34 32 32
Ephrin B1/EPHB1 -0.057 0.13 -10000 0 -0.29 139 139
HRAS/GDP -0.058 0.1 -10000 0 -0.43 13 13
Ephrin B/EPHB1/GRB7 -0.051 0.14 -10000 0 -0.34 65 65
Endophilin/SYNJ1 0.006 0.083 -10000 0 -0.3 30 30
KRAS 0.006 0.057 -10000 0 -0.56 6 6
Ephrin B/EPHB1/Src -0.047 0.14 -10000 0 -0.33 60 60
endothelial cell migration 0.021 0.038 -10000 0 -0.36 5 5
GRB2 0.011 0 -10000 0 -10000 0 0
GRB7 0.002 0.066 -10000 0 -0.46 12 12
PAK1 0.01 0.093 -10000 0 -0.6 5 5
HRAS 0.008 0.041 -10000 0 -0.49 4 4
RRAS 0.006 0.087 -10000 0 -0.32 28 28
DNM1 -0.006 0.093 -10000 0 -0.5 20 20
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.046 0.13 -10000 0 -0.31 60 60
lamellipodium assembly -0.06 0.1 -10000 0 -0.42 15 15
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.023 0.1 -10000 0 -0.28 46 46
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
EPHB2 0 0.079 -10000 0 -0.55 12 12
EPHB3 -0.018 0.13 -10000 0 -0.54 32 32
EPHB1 -0.1 0.21 -10000 0 -0.49 138 138
EPHB4 0.011 0 -10000 0 -10000 0 0
mol:GDP -0.024 0.11 -10000 0 -0.36 23 23
Ephrin B/EPHB2 0.002 0.087 -10000 0 -0.33 28 28
Ephrin B/EPHB3 -0.008 0.1 -10000 0 -0.34 39 39
JNK cascade -0.037 0.12 -10000 0 -0.3 51 51
Ephrin B/EPHB1 -0.053 0.13 -10000 0 -0.34 60 60
RAP1/GDP -0.011 0.1 -10000 0 -0.41 8 8
EFNB2 0.01 0.031 -10000 0 -0.52 2 2
EFNB3 -0.021 0.13 -10000 0 -0.52 36 36
EFNB1 0.01 0.024 -10000 0 -0.58 1 1
Ephrin B2/EPHB1-2 -0.051 0.13 -10000 0 -0.27 149 149
RAP1B 0.011 0 -10000 0 -10000 0 0
RAP1A 0.01 0.024 -10000 0 -0.58 1 1
CDC42/GTP -0.065 0.12 -10000 0 -0.47 19 19
Rap1/GTP -0.061 0.1 -10000 0 -0.43 17 17
axon guidance -0.058 0.14 -10000 0 -0.33 128 128
MAPK3 -0.011 0.093 -10000 0 -0.39 9 9
MAPK1 -0.011 0.094 -10000 0 -0.39 10 10
Rac1/GDP -0.016 0.11 -10000 0 -0.38 12 12
actin cytoskeleton reorganization -0.053 0.091 -10000 0 -0.39 17 17
CDC42/GDP -0.018 0.11 -10000 0 -0.39 15 15
PI3K 0.023 0.038 -10000 0 -0.36 5 5
EFNA5 -0.097 0.22 -10000 0 -0.52 122 122
Ephrin B2/EPHB4 0.014 0.019 -10000 0 -0.31 2 2
Ephrin B/EPHB2/Intersectin/N-WASP 0.011 0.073 -10000 0 -0.28 28 28
CDC42 0.006 0.054 -10000 0 -0.58 5 5
RAS family/GTP -0.066 0.12 -10000 0 -0.46 23 23
PTK2 0.016 0.038 -10000 0 -0.57 1 1
MAP4K4 -0.037 0.12 -10000 0 -0.3 51 51
SRC 0.01 0.024 -10000 0 -0.58 1 1
KALRN 0.006 0.054 -10000 0 -0.58 5 5
Intersectin/N-WASP 0.016 0.018 -10000 0 -0.42 1 1
neuron projection morphogenesis -0.009 0.11 -10000 0 -0.4 17 17
MAP2K1 -0.017 0.097 -10000 0 -0.4 10 10
WASL 0.011 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.044 0.13 -10000 0 -0.33 50 50
cell migration -0.014 0.11 -10000 0 -0.44 10 10
NRAS 0.001 0.076 -10000 0 -0.58 10 10
SYNJ1 0.006 0.084 -10000 0 -0.3 30 30
PXN 0.011 0 -10000 0 -10000 0 0
TF -0.046 0.13 -10000 0 -0.44 20 20
HRAS/GTP -0.067 0.11 -10000 0 -0.47 17 17
Ephrin B1/EPHB1-2 -0.05 0.13 -10000 0 -0.27 148 148
cell adhesion mediated by integrin 0.011 0.081 0.32 24 -10000 0 24
RAC1 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.045 0.13 -10000 0 -0.49 15 15
RAC1-CDC42/GTP -0.073 0.12 -10000 0 -0.47 29 29
RASA1 0.009 0.034 -10000 0 -0.58 2 2
RAC1-CDC42/GDP -0.013 0.11 -10000 0 -0.42 9 9
ruffle organization -0.026 0.12 -10000 0 -0.43 16 16
NCK1 0.009 0.034 -10000 0 -0.58 2 2
receptor internalization 0.003 0.095 -10000 0 -0.5 7 7
Ephrin B/EPHB2/KALRN 0.006 0.098 -10000 0 -0.35 30 30
ROCK1 -0.003 0.093 -10000 0 -0.34 39 39
RAS family/GDP -0.048 0.088 -10000 0 -0.4 16 16
Rac1/GTP -0.063 0.11 -10000 0 -0.45 15 15
Ephrin B/EPHB1/Src/Paxillin -0.028 0.1 -10000 0 -0.28 60 60
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 -0.044 0.14 -10000 0 -0.42 61 61
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.024 0.12 0.49 15 -10000 0 15
IL27/IL27R/JAK1 -0.024 0.16 -10000 0 -0.62 17 17
TBX21 -0.046 0.23 -10000 0 -0.56 72 72
IL12B -0.004 0.071 -10000 0 -0.46 14 14
IL12A -0.025 0.11 -10000 0 -0.41 47 47
IL6ST -0.005 0.096 -10000 0 -0.58 16 16
IL27RA/JAK1 0.006 0.095 -10000 0 -1.2 3 3
IL27 -0.006 0.081 -10000 0 -0.46 18 18
TYK2 0.01 0.025 -10000 0 -0.58 1 1
T-helper cell lineage commitment -0.19 0.4 -10000 0 -1.2 62 62
T-helper 2 cell differentiation 0.024 0.12 0.49 15 -10000 0 15
T cell proliferation during immune response 0.024 0.12 0.49 15 -10000 0 15
MAPKKK cascade -0.024 0.12 -10000 0 -0.49 15 15
STAT3 0.011 0 -10000 0 -10000 0 0
STAT2 0.011 0.019 -10000 0 -0.46 1 1
STAT1 0.006 0.051 -10000 0 -0.5 6 6
IL12RB1 -0.034 0.15 -10000 0 -0.54 48 48
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.041 0.22 -10000 0 -0.57 55 55
IL27/IL27R/JAK2/TYK2 -0.024 0.13 -10000 0 -0.49 15 15
positive regulation of T cell mediated cytotoxicity -0.024 0.12 -10000 0 -0.49 15 15
STAT1 (dimer) -0.056 0.24 0.4 20 -0.73 35 55
JAK2 -0.008 0.1 -10000 0 -0.55 21 21
JAK1 0.009 0.042 -10000 0 -0.58 3 3
STAT2 (dimer) -0.018 0.12 -10000 0 -0.49 13 13
T cell proliferation -0.098 0.18 -10000 0 -0.49 56 56
IL12/IL12R/TYK2/JAK2 -0.043 0.14 -10000 0 -0.54 16 16
IL17A -0.19 0.4 -10000 0 -1.3 62 62
mast cell activation 0.024 0.12 0.49 15 -10000 0 15
IFNG -0.011 0.042 -10000 0 -0.11 63 63
T cell differentiation -0.004 0.007 0.014 1 -0.022 61 62
STAT3 (dimer) -0.018 0.12 -10000 0 -0.5 12 12
STAT5A (dimer) -0.018 0.12 -10000 0 -0.48 13 13
STAT4 (dimer) -0.037 0.16 -10000 0 -0.51 36 36
STAT4 -0.027 0.14 -10000 0 -0.56 40 40
T cell activation -0.006 0.01 0.12 3 -10000 0 3
IL27R/JAK2/TYK2 -0.013 0.12 -10000 0 -0.82 7 7
GATA3 -0.026 0.22 -10000 0 -1.3 16 16
IL18 0.003 0.05 -10000 0 -0.39 9 9
positive regulation of mast cell cytokine production -0.017 0.12 -10000 0 -0.49 12 12
IL27/EBI3 -0.026 0.13 -10000 0 -0.39 60 60
IL27RA -0.002 0.096 -10000 0 -1.3 3 3
IL6 -0.15 0.25 -10000 0 -0.53 169 169
STAT5A 0.011 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.005 0.039 0.47 3 -10000 0 3
IL1B -0.043 0.13 -10000 0 -0.38 80 80
EBI3 -0.031 0.15 -10000 0 -0.56 44 44
TNF -0.012 0.09 -10000 0 -0.4 30 30
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.013 0.035 -9999 0 -0.44 3 3
ARNO/beta Arrestin1-2 -0.004 0.07 -9999 0 -10000 0 0
EGFR 0.004 0.063 -9999 0 -0.53 8 8
EPHA2 0.006 0.055 -9999 0 -0.54 6 6
USP6 0.008 0.041 -9999 0 -0.49 4 4
IQSEC1 0.011 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.13 0.19 -9999 0 -0.36 223 223
ARRB2 0.007 0.008 -9999 0 -0.19 1 1
mol:GTP 0.004 0.046 -9999 0 -0.26 12 12
ARRB1 0.009 0.034 -9999 0 -0.58 2 2
FBXO8 0.009 0.034 -9999 0 -0.58 2 2
TSHR -0.013 0.096 -9999 0 -0.46 26 26
EGF -0.18 0.25 -9999 0 -0.51 216 216
somatostatin receptor activity 0 0 -9999 0 -0.001 29 29
ARAP2 -0.006 0.099 -9999 0 -0.58 17 17
mol:GDP -0.033 0.086 -9999 0 -0.3 32 32
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 13 13
ITGA2B -0.044 0.16 -9999 0 -0.5 63 63
ARF6 0.01 0.024 -9999 0 -0.58 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.024 0.045 -9999 0 -0.37 6 6
ADAP1 0.01 0.031 -9999 0 -0.52 2 2
KIF13B 0.009 0.034 -9999 0 -0.58 2 2
HGF/MET -0.02 0.12 -9999 0 -0.39 54 54
PXN 0.011 0 -9999 0 -10000 0 0
ARF6/GTP -0.038 0.093 -9999 0 -0.29 30 30
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.099 0.16 -9999 0 -0.36 93 93
ADRB2 -0.031 0.15 -9999 0 -0.54 45 45
receptor agonist activity 0 0 -9999 0 0 31 31
actin filament binding 0 0 -9999 0 -0.001 35 35
SRC 0.01 0.024 -9999 0 -0.58 1 1
ITGB3 -0.006 0.098 -9999 0 -0.54 19 19
GNAQ 0.005 0.059 -9999 0 -0.58 6 6
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 25 25
ARF6/GDP -0.002 0.1 -9999 0 -0.36 32 32
ARF6/GDP/GULP/ACAP1 -0.06 0.14 -9999 0 -0.39 60 60
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.013 0.1 -9999 0 -0.32 38 38
ACAP1 -0.026 0.14 -9999 0 -0.54 40 40
ACAP2 0.001 0.076 -9999 0 -0.58 10 10
LHCGR/beta Arrestin2 0.001 0.012 -9999 0 -0.26 1 1
EFNA1 0.011 0.019 -9999 0 -0.46 1 1
HGF -0.037 0.16 -9999 0 -0.54 52 52
CYTH3 0.007 0.029 -9999 0 -0.4 3 3
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.009 0.034 -9999 0 -0.58 2 2
fibronectin binding 0 0 -9999 0 0 28 28
endosomal lumen acidification 0 0 -9999 0 0 27 27
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.051 0.18 -9999 0 -0.54 68 68
GNAQ/ARNO 0.01 0.031 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 15 15
MET 0.01 0.031 -9999 0 -0.52 2 2
GNA14 -0.007 0.1 -9999 0 -0.56 19 19
GNA15 -0.008 0.1 -9999 0 -0.54 21 21
GIT1 0.01 0.024 -9999 0 -0.58 1 1
mol:PI-4-5-P2 0 0 -9999 0 -0.001 26 26
GNA11 0.007 0.05 -9999 0 -0.53 5 5
LHCGR 0 0.019 -9999 0 -0.46 1 1
AGTR1 -0.094 0.21 -9999 0 -0.51 118 118
desensitization of G-protein coupled receptor protein signaling pathway 0.001 0.011 -9999 0 -0.26 1 1
IPCEF1/ARNO -0.073 0.12 -9999 0 -0.47 1 1
alphaIIb/beta3 Integrin -0.036 0.13 -9999 0 -0.37 81 81
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.004 0.092 -10000 0 -0.54 17 17
Jak2/Leptin Receptor -0.055 0.13 0.19 1 -0.47 35 36
PTP1B/AKT1 -0.021 0.078 -10000 0 -0.35 11 11
FYN 0.005 0.06 -10000 0 -0.55 7 7
p210 bcr-abl/PTP1B -0.029 0.083 0.17 1 -0.32 18 19
EGFR 0.001 0.064 -10000 0 -0.54 8 8
EGF/EGFR -0.097 0.15 -10000 0 -0.35 107 107
CSF1 0.006 0.055 -10000 0 -0.54 6 6
AKT1 0.01 0.025 -10000 0 -0.59 1 1
INSR 0.009 0.034 -10000 0 -0.58 2 2
PTP1B/N-cadherin -0.07 0.15 -10000 0 -0.36 99 99
Insulin Receptor/Insulin -0.026 0.061 -10000 0 -0.37 6 6
HCK -0.018 0.12 -10000 0 -0.55 31 31
CRK 0.011 0.019 -10000 0 -0.46 1 1
TYK2 -0.022 0.082 -10000 0 -0.36 11 11
EGF -0.18 0.25 -10000 0 -0.51 216 216
YES1 0.004 0.064 -10000 0 -0.58 7 7
CAV1 -0.042 0.1 -10000 0 -0.36 21 21
TXN 0.009 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.02 0.086 -10000 0 -0.37 13 13
cell migration 0.029 0.083 0.32 18 -0.17 1 19
STAT3 0.011 0.001 -10000 0 -10000 0 0
PRLR -0.042 0.17 -10000 0 -0.58 54 54
ITGA2B -0.044 0.16 -10000 0 -0.5 63 63
CSF1R -0.03 0.14 -10000 0 -0.53 45 45
Prolactin Receptor/Prolactin -0.043 0.14 -10000 0 -0.42 71 71
FGR -0.026 0.14 -10000 0 -0.54 40 40
PTP1B/p130 Cas -0.024 0.085 -10000 0 -0.36 13 13
Crk/p130 Cas -0.017 0.084 -10000 0 -0.38 11 11
DOK1 -0.018 0.089 -10000 0 -0.37 20 20
JAK2 -0.047 0.13 -10000 0 -0.42 47 47
Jak2/Leptin Receptor/Leptin -0.055 0.12 -10000 0 -0.46 28 28
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
PTPN1 -0.029 0.084 0.17 1 -0.33 18 19
LYN 0.011 0 -10000 0 -10000 0 0
CDH2 -0.084 0.21 -10000 0 -0.53 104 104
SRC 0 0.059 -10000 0 -1.2 1 1
ITGB3 -0.007 0.098 -10000 0 -0.54 19 19
CAT1/PTP1B -0.081 0.17 -10000 0 -0.49 53 53
CAPN1 0.01 0.025 -10000 0 -0.59 1 1
CSK 0.01 0.024 -10000 0 -0.58 1 1
PI3K -0.022 0.066 -10000 0 -0.46 6 6
mol:H2O2 -0.001 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.05 0.11 -10000 0 -0.45 26 26
negative regulation of transcription -0.046 0.13 -10000 0 -0.41 47 47
FCGR2A -0.022 0.13 -10000 0 -0.54 36 36
FER 0 0.071 -10000 0 -0.54 10 10
alphaIIb/beta3 Integrin -0.038 0.13 -10000 0 -0.37 81 81
BLK -0.12 0.23 -10000 0 -0.52 139 139
Insulin Receptor/Insulin/Shc 0.013 0.031 -10000 0 -0.36 3 3
RHOA 0.01 0.025 -10000 0 -0.59 1 1
LEPR 0 0.079 -10000 0 -0.55 12 12
BCAR1 0.008 0.044 -10000 0 -0.52 4 4
p210 bcr-abl/Grb2 0.011 0 -10000 0 -10000 0 0
mol:NADPH -0.002 0.003 -10000 0 -10000 0 0
TRPV6 -0.083 0.19 -10000 0 -0.52 63 63
PRL -0.013 0.089 -10000 0 -0.45 23 23
SOCS3 -0.003 0.13 -10000 0 -0.9 9 9
SPRY2 0.007 0.043 -10000 0 -0.59 3 3
Insulin Receptor/Insulin/IRS1 0.007 0.058 -10000 0 -0.38 12 12
CSF1/CSF1R -0.038 0.12 -10000 0 -0.42 38 38
Ras protein signal transduction 0.021 0.025 -10000 0 -10000 0 0
IRS1 0.002 0.072 -10000 0 -0.58 9 9
INS -0.002 0.036 -10000 0 -0.5 3 3
LEP -0.024 0.12 -10000 0 -0.46 39 39
STAT5B -0.033 0.09 -10000 0 -0.32 25 25
STAT5A -0.033 0.09 -10000 0 -0.31 26 26
GRB2 0.011 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.03 0.1 -10000 0 -0.4 28 28
CSN2 -0.008 0.06 -10000 0 -10000 0 0
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
LAT -0.033 0.14 -10000 0 -0.57 32 32
YBX1 0.016 0.016 -10000 0 -0.36 1 1
LCK -0.031 0.14 -10000 0 -0.51 48 48
SHC1 0.011 0 -10000 0 -10000 0 0
NOX4 -0.073 0.19 -10000 0 -0.52 92 92
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.011 0.04 -9999 0 -0.31 9 9
ADCY5 -0.058 0.14 -9999 0 -0.32 132 132
ADCY6 0.015 0 -9999 0 -10000 0 0
ADCY7 0.014 0.022 -9999 0 -0.3 3 3
ADCY1 -0.018 0.095 -9999 0 -0.28 66 66
ADCY2 -0.017 0.1 -9999 0 -0.34 54 54
ADCY3 0.015 0.015 -9999 0 -0.36 1 1
ADCY8 0.003 0.042 -9999 0 -0.27 14 14
PRKCE 0.009 0 -9999 0 -10000 0 0
ADCY9 0.014 0.025 -9999 0 -0.33 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.014 0.067 -9999 0 -0.23 22 22
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.022 0.17 -9999 0 -0.63 28 28
MAP3K8 0.009 0.031 -9999 0 -0.52 2 2
FOS -0.023 0.16 -9999 0 -0.59 30 30
PRKCA 0.01 0.031 -9999 0 -0.52 2 2
PTPN7 -0.048 0.17 -9999 0 -0.5 71 71
HRAS 0.008 0.041 -9999 0 -0.49 4 4
PRKCB -0.04 0.16 -9999 0 -0.54 56 56
NRAS 0.001 0.076 -9999 0 -0.58 10 10
RAS family/GTP 0.011 0.069 -9999 0 -0.41 13 13
MAPK3 -0.02 0.14 -9999 0 -0.63 23 23
MAP2K1 -0.007 0.12 -9999 0 -0.42 40 40
ELK1 0.01 0.025 -9999 0 -0.58 1 1
BRAF -0.013 0.12 -9999 0 -0.43 40 40
mol:GTP 0 0.001 -9999 0 -0.005 41 41
MAPK1 -0.02 0.14 -9999 0 -0.63 23 23
RAF1 -0.012 0.11 -9999 0 -0.42 39 39
KRAS 0.006 0.057 -9999 0 -0.56 6 6
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.02 0.2 -10000 0 -0.71 13 13
CRP -0.028 0.2 -10000 0 -0.73 14 14
cell cycle arrest -0.034 0.22 -10000 0 -0.67 30 30
TIMP1 -0.009 0.18 -10000 0 -0.63 11 11
IL6ST -0.002 0.096 -10000 0 -0.58 16 16
Rac1/GDP -0.039 0.17 -10000 0 -0.52 42 42
AP1 0.002 0.12 -10000 0 -0.57 9 9
GAB2 0.01 0.034 -10000 0 -0.58 2 2
TNFSF11 -0.075 0.33 -10000 0 -1 56 56
HSP90B1 0.009 0.14 -10000 0 -1.3 6 6
GAB1 0.012 0.001 -10000 0 -10000 0 0
MAPK14 -0.03 0.16 -10000 0 -0.55 30 30
AKT1 0.037 0.072 -10000 0 -0.73 4 4
FOXO1 0.041 0.07 -10000 0 -0.68 4 4
MAP2K6 -0.036 0.16 -10000 0 -0.48 41 41
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.03 0.18 -10000 0 -0.54 37 37
MITF -0.048 0.17 -10000 0 -0.49 48 48
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.01 0.024 -10000 0 -0.58 1 1
A2M 0.009 0.09 -10000 0 -0.58 9 9
CEBPB 0.013 0.042 -10000 0 -0.48 4 4
GRB2/SOS1/GAB family/SHP2 0 0.089 0.22 1 -0.61 5 6
STAT3 -0.038 0.23 -10000 0 -0.7 31 31
STAT1 -0.009 0.068 -10000 0 -1.1 2 2
CEBPD -0.022 0.2 -10000 0 -0.71 17 17
PIK3CA 0.011 0.034 -10000 0 -0.58 2 2
PI3K 0.016 0.04 -10000 0 -0.42 5 5
JUN 0.006 0.052 -10000 0 -0.56 5 5
PIAS3/MITF -0.041 0.17 -10000 0 -0.51 38 38
MAPK11 -0.037 0.17 -10000 0 -0.57 35 35
STAT3 (dimer)/FOXO1 0.011 0.19 -10000 0 -0.63 13 13
GRB2/SOS1/GAB family -0.059 0.13 0.18 1 -0.54 28 29
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.047 0.17 -10000 0 -0.45 57 57
GRB2 0.012 0.001 -10000 0 -10000 0 0
JAK2 -0.008 0.1 -10000 0 -0.55 21 21
LBP -0.091 0.31 -10000 0 -0.85 64 64
PIK3R1 0.009 0.042 -10000 0 -0.58 3 3
JAK1 0.01 0.042 -10000 0 -0.58 3 3
MYC -0.025 0.21 -10000 0 -0.79 18 18
FGG -0.036 0.22 -10000 0 -0.68 24 24
macrophage differentiation -0.034 0.22 -10000 0 -0.67 30 30
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.063 0.17 -10000 0 -0.45 54 54
JUNB -0.023 0.2 -10000 0 -0.74 16 16
FOS -0.026 0.14 -10000 0 -0.53 41 41
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.039 0.16 -10000 0 -0.46 46 46
STAT1/PIAS1 -0.028 0.16 -10000 0 -0.48 34 34
GRB2/SOS1/GAB family/SHP2/PI3K 0.028 0.075 -10000 0 -0.61 6 6
STAT3 (dimer) -0.037 0.23 -10000 0 -0.7 30 30
PRKCD -0.02 0.19 -10000 0 -0.57 32 32
IL6R -0.005 0.1 -10000 0 -0.56 19 19
SOCS3 -0.034 0.18 -10000 0 -0.63 31 31
gp130 (dimer)/JAK1/JAK1/LMO4 0.013 0.082 -10000 0 -0.36 24 24
Rac1/GTP -0.039 0.18 -10000 0 -0.52 44 44
HCK -0.018 0.12 -10000 0 -0.55 31 31
MAPKKK cascade 0.013 0.094 -10000 0 -0.8 5 5
bone resorption -0.066 0.31 -10000 0 -0.92 56 56
IRF1 -0.02 0.2 -10000 0 -0.7 14 14
mol:GDP -0.048 0.18 -10000 0 -0.51 49 49
SOS1 0.011 0.024 -10000 0 -0.58 1 1
VAV1 -0.049 0.18 -10000 0 -0.52 49 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.04 0.17 -10000 0 -0.59 32 32
PTPN11 -0.011 0.086 -10000 0 -0.91 5 5
IL6/IL6RA -0.081 0.18 -10000 0 -0.38 152 152
gp130 (dimer)/TYK2/TYK2/LMO4 0.011 0.075 -10000 0 -0.34 23 23
gp130 (dimer)/JAK2/JAK2/LMO4 -0.001 0.1 -10000 0 -0.36 41 41
IL6 -0.11 0.22 -10000 0 -0.51 138 138
PIAS3 0.01 0.031 -10000 0 -0.52 2 2
PTPRE 0.006 0.026 -10000 0 -0.57 1 1
PIAS1 0.011 0 -10000 0 -10000 0 0
RAC1 0.012 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.043 0.14 -10000 0 -0.35 72 72
LMO4 0.006 0.062 -10000 0 -0.49 9 9
STAT3 (dimer)/PIAS3 -0.033 0.22 -10000 0 -0.67 31 31
MCL1 0.042 0.063 -10000 0 -0.79 2 2
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.011 0.1 -10000 0 -0.32 47 47
ER alpha/Gai/GDP/Gbeta gamma -0.021 0.14 -10000 0 -0.44 35 35
AKT1 -0.018 0.17 -10000 0 -0.74 30 30
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.02 0.17 -10000 0 -0.78 28 28
mol:Ca2+ -0.023 0.13 -10000 0 -0.43 31 31
IGF1R 0.01 0.024 -10000 0 -0.58 1 1
E2/ER alpha (dimer)/Striatin -0.016 0.098 -10000 0 -0.32 55 55
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis 0.016 0.16 0.7 30 -10000 0 30
RhoA/GTP -0.028 0.086 -10000 0 -0.57 5 5
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.046 0.12 -10000 0 -0.46 32 32
regulation of stress fiber formation -0.009 0.094 0.48 10 -10000 0 10
E2/ERA-ERB (dimer) -0.024 0.11 -10000 0 -0.33 66 66
KRAS 0.006 0.057 -10000 0 -0.56 6 6
G13/GTP -0.012 0.086 -10000 0 -0.29 51 51
pseudopodium formation 0.009 0.094 -10000 0 -0.48 10 10
E2/ER alpha (dimer)/PELP1 -0.013 0.093 -10000 0 -0.32 50 50
GRB2 0.011 0 -10000 0 -10000 0 0
GNG2 0.004 0.063 -10000 0 -0.53 8 8
GNAO1 -0.046 0.16 -10000 0 -0.49 68 68
HRAS 0.008 0.041 -10000 0 -0.49 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.018 0.14 -10000 0 -0.51 31 31
E2/ER beta (dimer) -0.005 0.074 -10000 0 -0.4 20 20
mol:GDP -0.038 0.11 -10000 0 -0.39 42 42
mol:NADP -0.018 0.14 -10000 0 -0.51 31 31
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
mol:IP3 -0.025 0.13 -10000 0 -0.45 31 31
IGF-1R heterotetramer 0.01 0.024 -10000 0 -0.58 1 1
PLCB1 -0.028 0.13 -10000 0 -0.48 29 29
PLCB2 -0.01 0.11 -10000 0 -0.45 26 26
IGF1 -0.073 0.2 -10000 0 -0.52 94 94
mol:L-citrulline -0.018 0.14 -10000 0 -0.51 31 31
RHOA 0.01 0.024 -10000 0 -0.58 1 1
Gai/GDP -0.022 0.15 -10000 0 -0.75 19 19
JNK cascade -0.005 0.073 -10000 0 -0.4 20 20
BCAR1 0.008 0.044 -10000 0 -0.52 4 4
ESR2 -0.007 0.1 -10000 0 -0.54 20 20
GNAQ 0.005 0.059 -10000 0 -0.58 6 6
ESR1 -0.033 0.15 -10000 0 -0.52 49 49
Gq family/GDP/Gbeta gamma 0.003 0.11 -10000 0 -0.52 20 20
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.009 0.068 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.045 0.11 -10000 0 -0.46 31 31
GNAZ -0.012 0.11 -10000 0 -0.55 25 25
E2/ER alpha (dimer) -0.024 0.11 -10000 0 -0.38 49 49
STRN 0.005 0.059 -10000 0 -0.58 6 6
GNAL -0.02 0.12 -10000 0 -0.5 36 36
PELP1 0.01 0.024 -10000 0 -0.58 1 1
MAPK11 -0.005 0.082 -10000 0 -0.33 35 35
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 -0.003 0.089 -10000 0 -0.56 15 15
HBEGF -0.036 0.15 -10000 0 -0.48 38 38
cAMP biosynthetic process -0.044 0.1 -10000 0 -0.27 96 96
SRC -0.015 0.13 -10000 0 -0.44 30 30
PI3K 0.013 0.04 -10000 0 -0.42 5 5
GNB1 0.011 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.037 0.099 -10000 0 -0.38 32 32
SOS1 0.01 0.024 -10000 0 -0.58 1 1
IGF-1R heterotetramer/IGF1 -0.065 0.13 -10000 0 -0.42 51 51
Gs family/GTP -0.044 0.11 -10000 0 -0.28 96 96
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.011 0.069 -10000 0 -0.41 13 13
vasodilation -0.017 0.13 -10000 0 -0.48 31 31
mol:DAG -0.025 0.13 -10000 0 -0.45 31 31
Gs family/GDP/Gbeta gamma -0.045 0.1 -10000 0 -0.38 35 35
MSN 0.008 0.1 -10000 0 -0.52 10 10
Gq family/GTP -0.013 0.11 -10000 0 -0.49 24 24
mol:PI-3-4-5-P3 -0.019 0.17 -10000 0 -0.74 28 28
NRAS 0.001 0.076 -10000 0 -0.58 10 10
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.017 0.13 0.48 31 -10000 0 31
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
RhoA/GDP -0.036 0.1 -10000 0 -0.37 43 43
NOS3 -0.02 0.14 -10000 0 -0.54 31 31
GNA11 0.007 0.05 -10000 0 -0.53 5 5
MAPKKK cascade -0.005 0.14 -10000 0 -0.56 32 32
E2/ER alpha (dimer)/PELP1/Src -0.048 0.12 -10000 0 -0.48 31 31
ruffle organization 0.009 0.094 -10000 0 -0.48 10 10
ROCK2 0.003 0.11 -10000 0 -0.62 9 9
GNA14 -0.007 0.1 -10000 0 -0.56 19 19
GNA15 -0.008 0.1 -10000 0 -0.54 21 21
GNA13 0.009 0.034 -10000 0 -0.58 2 2
MMP9 -0.041 0.16 -10000 0 -0.47 44 44
MMP2 -0.029 0.15 -10000 0 -0.56 25 25
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.011 0 -9999 0 -10000 0 0
VLDLR -0.041 0.16 -9999 0 -0.54 56 56
LRPAP1 0.01 0.024 -9999 0 -0.58 1 1
NUDC 0.011 0.019 -9999 0 -0.46 1 1
RELN/LRP8 -0.045 0.14 -9999 0 -0.35 63 63
CaM/Ca2+ 0.008 0 -9999 0 -10000 0 0
KATNA1 0.01 0.024 -9999 0 -0.58 1 1
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.035 0.12 -9999 0 -0.32 63 63
IQGAP1/CaM 0.015 0.029 -9999 0 -0.39 3 3
DAB1 -0.079 0.2 -9999 0 -0.51 101 101
IQGAP1 0.009 0.039 -9999 0 -0.54 3 3
PLA2G7 -0.022 0.14 -9999 0 -0.56 35 35
CALM1 0.011 0 -9999 0 -10000 0 0
DYNLT1 0.011 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.014 0.036 -9999 0 -0.42 4 4
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.009 0.034 -9999 0 -0.58 2 2
CDK5R1 0.009 0.033 -9999 0 -0.46 3 3
LIS1/Poliovirus Protein 3A 0.014 0 -9999 0 -10000 0 0
CDK5R2 -0.05 0.16 -9999 0 -0.5 69 69
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.13 0.21 -9999 0 -0.37 229 229
YWHAE 0.011 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.025 0.12 -9999 0 -0.42 15 15
MAP1B -0.012 0.052 -9999 0 -0.31 11 11
RAC1 0.017 0.012 -9999 0 -10000 0 0
p35/CDK5 -0.02 0.11 -9999 0 -0.48 3 3
RELN -0.094 0.21 -9999 0 -0.52 118 118
PAFAH/LIS1 0.001 0.085 -9999 0 -0.34 35 35
LIS1/CLIP170 0.021 0.022 -9999 0 -0.35 2 2
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.045 0.081 -9999 0 -0.37 8 8
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.072 0.16 -9999 0 -0.32 130 130
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.033 0.13 -9999 0 -0.45 15 15
LIS1/IQGAP1 0.02 0.025 -9999 0 -0.32 3 3
RHOA 0.016 0.035 -9999 0 -0.81 1 1
PAFAH1B1 0.018 0 -9999 0 -10000 0 0
PAFAH1B3 0.008 0.044 -9999 0 -0.52 4 4
PAFAH1B2 0.007 0.048 -9999 0 -0.58 4 4
MAP1B/LIS1/Dynein heavy chain 0.012 0.036 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.02 0.12 -9999 0 -0.44 10 10
LRP8 0.008 0.042 -9999 0 -0.58 3 3
NDEL1/Katanin 60 -0.026 0.12 -9999 0 -0.42 16 16
P39/CDK5 -0.05 0.14 -9999 0 -0.48 23 23
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.022 0.012 -9999 0 -0.26 1 1
CDK5 -0.027 0.12 -9999 0 -0.59 1 1
PPP2R5D 0.011 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.018 0.019 -9999 0 -0.3 2 2
CSNK2A1 0.011 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.098 0.18 -9999 0 -0.37 138 138
RELN/VLDLR -0.063 0.16 -9999 0 -0.35 96 96
CDC42 0.013 0.057 -9999 0 -0.58 5 5
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.018 -10000 0 -0.43 1 1
GNB1/GNG2 -0.017 0.1 -10000 0 -0.27 76 76
regulation of S phase of mitotic cell cycle -0.001 0.073 -10000 0 -0.27 27 27
GNAO1 -0.046 0.16 -10000 0 -0.49 68 68
HRAS 0.008 0.041 -10000 0 -0.49 4 4
SHBG/T-DHT -0.008 0.061 -10000 0 -0.27 30 30
PELP1 0.01 0.024 -10000 0 -0.58 1 1
AKT1 0.008 0.018 -10000 0 -0.43 1 1
MAP2K1 0 0.089 -10000 0 -0.42 5 5
T-DHT/AR -0.036 0.12 -10000 0 -0.36 71 71
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.006 40 40
GNAI2 0.011 0 -10000 0 -10000 0 0
GNAI3 0.011 0 -10000 0 -10000 0 0
GNAI1 -0.003 0.089 -10000 0 -0.56 15 15
mol:GDP -0.033 0.097 -10000 0 -0.44 23 23
cell proliferation 0 0.12 -10000 0 -0.39 28 28
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
FOS -0.015 0.18 -10000 0 -0.76 29 29
mol:Ca2+ -0.011 0.021 -10000 0 -0.062 66 66
MAPK3 0.001 0.1 -10000 0 -0.47 5 5
MAPK1 0.004 0.062 -10000 0 -0.31 4 4
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
mol:IP3 0 0.001 -10000 0 -0.004 41 41
cAMP biosynthetic process -0.003 0.061 -10000 0 -0.25 30 30
GNG2 0.004 0.063 -10000 0 -0.53 8 8
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 41 41
HRAS/GTP -0.031 0.083 -10000 0 -0.3 24 24
actin cytoskeleton reorganization -0.005 0.046 -10000 0 -0.4 7 7
SRC 0.01 0.024 -10000 0 -0.58 1 1
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 41 41
PI3K 0.012 0.034 -10000 0 -0.36 5 5
apoptosis 0 0.11 0.39 31 -10000 0 31
T-DHT/AR/PELP1 -0.024 0.1 -10000 0 -0.3 72 72
HRAS/GDP -0.032 0.094 -10000 0 -0.42 24 24
CREB1 -0.001 0.12 -10000 0 -0.42 31 31
RAC1-CDC42/GTP -0.004 0.047 -10000 0 -0.41 7 7
AR -0.051 0.16 -10000 0 -0.49 71 71
GNB1 0.011 0 -10000 0 -10000 0 0
RAF1 -0.004 0.089 -10000 0 -0.42 4 4
RAC1-CDC42/GDP -0.03 0.093 -10000 0 -0.41 24 24
T-DHT/AR/PELP1/Src -0.014 0.096 -10000 0 -0.32 26 26
MAP2K2 0.001 0.091 -10000 0 -0.47 4 4
T-DHT/AR/PELP1/Src/PI3K -0.001 0.073 -10000 0 -0.27 27 27
GNAZ -0.012 0.11 -10000 0 -0.55 25 25
SHBG -0.014 0.1 -10000 0 -0.46 30 30
Gi family/GNB1/GNG2/GDP -0.008 0.099 -10000 0 -0.37 21 21
mol:T-DHT 0 0.001 -10000 0 -0.002 33 33
RAC1 0.011 0 -10000 0 -10000 0 0
GNRH1 0.001 0.058 -10000 0 -0.4 12 12
Gi family/GTP -0.023 0.089 -10000 0 -0.24 54 54
CDC42 0.006 0.054 -10000 0 -0.58 5 5
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.008 0.12 -9999 0 -0.42 38 38
CRKL 0.011 0 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
DOCK1 0.01 0.024 -9999 0 -0.58 1 1
ITGA4 -0.018 0.13 -9999 0 -0.56 30 30
alpha4/beta7 Integrin/MAdCAM1 -0.078 0.17 -9999 0 -0.36 112 112
EPO 0 0.053 -9999 0 -0.46 8 8
alpha4/beta7 Integrin -0.022 0.13 -9999 0 -0.43 52 52
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0.019 -9999 0 -0.46 1 1
alpha4/beta1 Integrin -0.004 0.093 -9999 0 -0.41 30 30
EPO/EPOR (dimer) 0.003 0.061 -9999 0 -0.36 16 16
lamellipodium assembly 0.026 0.05 -9999 0 -0.65 2 2
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
PI3K 0.013 0.04 -9999 0 -0.42 5 5
ARF6 0.01 0.024 -9999 0 -0.58 1 1
JAK2 -0.006 0.11 -9999 0 -0.36 41 41
PXN 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
MADCAM1 -0.12 0.23 -9999 0 -0.52 151 151
cell adhesion -0.078 0.17 -9999 0 -0.36 112 112
CRKL/CBL 0.017 0 -9999 0 -10000 0 0
ITGB1 0.011 0 -9999 0 -10000 0 0
SRC -0.007 0.12 -9999 0 -0.42 39 39
ITGB7 -0.014 0.12 -9999 0 -0.53 28 28
RAC1 0.011 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.014 0.13 -9999 0 -0.47 38 38
p130Cas/Crk/Dock1 0.01 0.11 -9999 0 -0.51 18 18
VCAM1 -0.02 0.13 -9999 0 -0.53 35 35
RHOA 0.01 0.024 -9999 0 -0.58 1 1
alpha4/beta1 Integrin/Paxillin/GIT1 0.012 0.075 -9999 0 -0.32 27 27
BCAR1 -0.003 0.12 -9999 0 -0.55 17 17
EPOR 0.004 0.063 -9999 0 -0.5 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.011 0 -9999 0 -10000 0 0
GIT1 0.01 0.024 -9999 0 -0.58 1 1
Rac1/GTP -0.002 0.051 -9999 0 -0.7 2 2
IGF1 pathway

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
NCK2 0.01 0.024 -10000 0 -0.58 1 1
PTK2 0.01 0.024 -10000 0 -0.58 1 1
CRKL -0.022 0.1 -10000 0 -0.3 52 52
GRB2/SOS1/SHC 0.023 0.015 -10000 0 -0.35 1 1
HRAS 0.008 0.041 -10000 0 -0.49 4 4
IRS1/Crk -0.022 0.1 -10000 0 -0.3 53 53
IGF-1R heterotetramer/IGF1/PTP1B -0.029 0.12 -10000 0 -0.34 53 53
AKT1 -0.005 0.094 -10000 0 -0.48 4 4
BAD 0 0.093 -10000 0 -0.46 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.023 0.1 -10000 0 -0.3 53 53
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.025 0.11 -10000 0 -0.3 57 57
RAF1 0.005 0.087 -10000 0 -0.41 5 5
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.014 0.1 -10000 0 -0.29 52 52
YWHAZ 0.008 0.042 -10000 0 -0.58 3 3
IGF-1R heterotetramer/IGF1/IRS1 -0.031 0.11 -10000 0 -0.32 59 59
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
RPS6KB1 -0.008 0.1 -10000 0 -0.5 7 7
GNB2L1 0.011 0.019 -10000 0 -0.46 1 1
positive regulation of MAPKKK cascade 0.003 0.077 -10000 0 -0.36 5 5
PXN 0.011 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
HRAS/GTP -0.034 0.081 -10000 0 -0.49 4 4
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.007 0.097 -10000 0 -0.44 4 4
IGF-1R heterotetramer 0 0.037 -10000 0 -0.66 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck -0.022 0.1 -10000 0 -0.3 53 53
Crk/p130 Cas/Paxillin -0.01 0.097 -10000 0 -0.51 3 3
IGF1R 0 0.038 -10000 0 -0.67 1 1
IGF1 -0.074 0.2 -10000 0 -0.53 94 94
IRS2/Crk -0.019 0.1 -10000 0 -0.29 57 57
PI3K -0.016 0.1 -10000 0 -0.29 56 56
apoptosis -0.005 0.089 0.44 8 -10000 0 8
HRAS/GDP 0.006 0.03 -10000 0 -0.35 4 4
PRKCD -0.015 0.12 -10000 0 -0.39 52 52
RAF1/14-3-3 E 0.012 0.079 -10000 0 -0.37 4 4
BAD/14-3-3 0.005 0.094 -10000 0 -0.47 8 8
PRKCZ -0.006 0.096 -10000 0 -0.48 5 5
Crk/p130 Cas/Paxillin/FAK1 -0.032 0.078 -10000 0 -0.44 9 9
PTPN1 0.01 0.024 -10000 0 -0.58 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.022 0.13 -10000 0 -0.42 52 52
BCAR1 0.008 0.044 -10000 0 -0.52 4 4
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.018 0.11 -10000 0 -0.3 55 55
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.01 0.024 -10000 0 -0.58 1 1
IRS1/NCK2 -0.022 0.1 -10000 0 -0.3 53 53
GRB10 0.007 0.048 -10000 0 -0.58 4 4
PTPN11 -0.025 0.11 -10000 0 -0.3 57 57
IRS1 -0.031 0.11 -10000 0 -0.32 59 59
IRS2 -0.027 0.11 -10000 0 -0.3 60 60
IGF-1R heterotetramer/IGF1 -0.049 0.15 -10000 0 -0.39 94 94
GRB2 0.011 0 -10000 0 -10000 0 0
PDPK1 -0.011 0.098 -10000 0 -0.39 8 8
YWHAE 0.011 0 -10000 0 -10000 0 0
PRKD1 -0.037 0.16 -10000 0 -0.43 75 75
SHC1 0.011 0 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 -0.006 0.072 -9999 0 -0.59 8 8
SVIL 0 0.045 -9999 0 -0.49 4 4
ZNF318 0.032 0.049 -9999 0 -10000 0 0
JMJD2C 0.003 0.02 -9999 0 -0.077 27 27
T-DHT/AR/Ubc9 -0.023 0.11 -9999 0 -0.3 71 71
CARM1 0.009 0.024 -9999 0 -0.58 1 1
PRDX1 0.012 0.025 -9999 0 -0.58 1 1
PELP1 0.014 0.026 -9999 0 -0.58 1 1
CTNNB1 0.005 0.016 -9999 0 -10000 0 0
AKT1 0.016 0.028 -9999 0 -0.58 1 1
PTK2B 0.004 0.037 -9999 0 -0.58 2 2
MED1 0.014 0.046 -9999 0 -0.5 4 4
MAK 0.006 0.12 -9999 0 -0.46 30 30
response to oxidative stress 0.001 0.004 -9999 0 -10000 0 0
HIP1 -0.002 0.063 -9999 0 -0.6 6 6
GSN -0.008 0.076 -9999 0 -0.51 12 12
NCOA2 0.002 0.067 -9999 0 -0.57 8 8
NCOA6 0.004 0.03 -9999 0 -0.58 1 1
DNA-PK 0.04 0.056 -9999 0 -0.45 2 2
NCOA4 0.008 0.034 -9999 0 -0.58 2 2
PIAS3 0.004 0.034 -9999 0 -0.52 2 2
cell proliferation -0.005 0.1 -9999 0 -0.69 8 8
XRCC5 0.015 0.026 -9999 0 -0.57 1 1
UBE3A -0.005 0.057 -9999 0 -0.59 4 4
T-DHT/AR/SNURF -0.077 0.16 -9999 0 -0.33 153 153
FHL2 0.022 0.089 -9999 0 -1.1 2 2
RANBP9 0.004 0.03 -9999 0 -0.58 1 1
JMJD1A -0.006 0.044 -9999 0 -0.11 76 76
CDK6 0.012 0.019 -9999 0 -0.46 1 1
TGFB1I1 -0.002 0.056 -9999 0 -0.52 6 6
T-DHT/AR/CyclinD1 -0.03 0.11 -9999 0 -0.3 72 72
XRCC6 0.016 0.011 -9999 0 -10000 0 0
T-DHT/AR -0.02 0.12 -9999 0 -0.37 36 36
CTDSP1 0.007 0.025 -9999 0 -0.58 1 1
CTDSP2 0.025 0.033 -9999 0 -10000 0 0
BRCA1 0.003 0.031 -9999 0 -0.59 1 1
TCF4 0.009 0.086 -9999 0 -0.52 14 14
CDKN2A -0.064 0.19 -9999 0 -0.5 94 94
SRF 0.022 0.032 -9999 0 -0.45 2 2
NKX3-1 -0.076 0.25 -9999 0 -0.63 80 80
KLK3 -0.16 0.42 -9999 0 -1.4 55 55
TMF1 0.003 0.059 -9999 0 -0.58 6 6
HNRNPA1 0.019 0.018 -9999 0 -10000 0 0
AOF2 -0.009 0.021 -9999 0 -0.069 54 54
APPL1 0.022 0.07 -9999 0 -0.42 12 12
T-DHT/AR/Caspase 8 -0.016 0.11 -9999 0 -0.3 67 67
AR -0.053 0.17 -9999 0 -0.5 71 71
UBA3 0.007 0.025 -9999 0 -0.59 1 1
PATZ1 0.019 0.018 -9999 0 -10000 0 0
PAWR 0.008 0.025 -9999 0 -0.58 1 1
PRKDC 0.013 0.039 -9999 0 -0.52 3 3
PA2G4 0.02 0.021 -9999 0 -10000 0 0
UBE2I 0.011 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.017 0.1 -9999 0 -0.27 72 72
RPS6KA3 -0.002 0.054 -9999 0 -0.59 4 4
T-DHT/AR/ARA70 -0.029 0.11 -9999 0 -0.31 72 72
LATS2 0.017 0.034 -9999 0 -0.49 2 2
T-DHT/AR/PRX1 -0.01 0.11 -9999 0 -0.27 68 68
Cyclin D3/CDK11 p58 0.007 0.031 -9999 0 -0.32 5 5
VAV3 -0.072 0.2 -9999 0 -0.58 78 78
KLK2 -0.027 0.093 -9999 0 -0.47 11 11
CASP8 0.013 0.025 -9999 0 -0.58 1 1
T-DHT/AR/TIF2/CARM1 -0.025 0.11 -9999 0 -0.33 43 43
TMPRSS2 -0.019 0.11 -9999 0 -1.1 3 3
CCND1 0.007 0.026 -9999 0 -0.59 1 1
PIAS1 -0.001 0.031 -9999 0 -10000 0 0
mol:T-DHT -0.003 0.023 -9999 0 -0.072 35 35
CDC2L1 0.001 0.002 -9999 0 -10000 0 0
PIAS4 -0.009 0.053 -9999 0 -0.58 1 1
T-DHT/AR/CDK6 -0.021 0.11 -9999 0 -0.3 70 70
CMTM2 -0.029 0.14 -9999 0 -0.52 47 47
SNURF -0.075 0.2 -9999 0 -0.54 90 90
ZMIZ1 0.008 0.028 -9999 0 -0.44 1 1
CCND3 0.008 0.043 -9999 0 -0.46 5 5
TGIF1 0.019 0.018 -9999 0 -10000 0 0
FKBP4 0.003 0.038 -9999 0 -0.46 3 3
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.009 0.045 -9999 0 -0.37 8 8
PDGFRB -0.005 0.092 -9999 0 -0.54 17 17
SPHK1 -0.045 0.15 -9999 0 -0.8 21 21
mol:S1P -0.044 0.14 -9999 0 -0.69 22 22
S1P1/S1P/Gi -0.047 0.15 -9999 0 -0.39 62 62
GNAO1 -0.047 0.16 -9999 0 -0.49 68 68
PDGFB-D/PDGFRB/PLCgamma1 -0.042 0.15 -9999 0 -0.49 24 24
PLCG1 -0.042 0.15 -9999 0 -0.48 25 25
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.005 0.092 -9999 0 -0.54 17 17
GNAI2 0.01 0.005 -9999 0 -10000 0 0
GNAI3 0.01 0.005 -9999 0 -10000 0 0
GNAI1 -0.005 0.09 -9999 0 -0.56 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.008 0.039 -9999 0 -0.31 8 8
S1P1/S1P -0.02 0.12 -9999 0 -0.49 26 26
negative regulation of cAMP metabolic process -0.046 0.15 -9999 0 -0.38 62 62
MAPK3 -0.061 0.2 -9999 0 -0.56 57 57
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
KDR 0.004 0.059 -9999 0 -0.53 7 7
PLCB2 -0.015 0.11 -9999 0 -0.42 29 29
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.037 0.092 -9999 0 -0.4 26 26
receptor internalization -0.04 0.1 -9999 0 -0.45 26 26
PTGS2 -0.1 0.31 -9999 0 -1 54 54
Rac1/GTP -0.037 0.091 -9999 0 -0.4 26 26
RHOA 0.01 0.024 -9999 0 -0.58 1 1
VEGFA 0.01 0.019 -9999 0 -0.46 1 1
negative regulation of T cell proliferation -0.046 0.15 -9999 0 -0.38 62 62
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.014 0.11 -9999 0 -0.55 25 25
MAPK1 -0.061 0.2 -9999 0 -0.56 57 57
S1P1/S1P/PDGFB-D/PDGFRB -0.021 0.13 -9999 0 -0.42 36 36
ABCC1 0.01 0.025 -9999 0 -0.59 1 1
PDGFR-alpha signaling pathway

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
PDGFRA -0.011 0.11 -9999 0 -0.57 22 22
PDGF/PDGFRA/CRKL 0.001 0.08 -9999 0 -0.4 22 22
positive regulation of JUN kinase activity 0.016 0.063 -9999 0 -0.3 21 21
CRKL 0.011 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.009 0.086 -9999 0 -0.41 26 26
AP1 -0.063 0.21 -9999 0 -0.9 30 30
mol:IP3 0.001 0.086 -9999 0 -0.42 23 23
PLCG1 0.001 0.086 -9999 0 -0.42 23 23
PDGF/PDGFRA/alphaV Integrin -0.007 0.1 -9999 0 -0.42 32 32
RAPGEF1 0.01 0.024 -9999 0 -0.58 1 1
CRK 0.011 0.019 -9999 0 -0.46 1 1
mol:Ca2+ 0.001 0.086 -9999 0 -0.42 23 23
CAV3 -0.002 0.042 -9999 0 -0.46 5 5
CAV1 -0.002 0.082 -9999 0 -0.5 16 16
SHC/Grb2/SOS1 0.017 0.063 -9999 0 -0.3 21 21
PDGF/PDGFRA/Shf -0.032 0.13 -9999 0 -0.38 73 73
FOS -0.03 0.22 -9999 0 -0.89 30 30
JUN -0.008 0.042 -9999 0 -0.44 5 5
oligodendrocyte development -0.007 0.1 -9999 0 -0.42 32 32
GRB2 0.011 0 -9999 0 -10000 0 0
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
mol:DAG 0.001 0.086 -9999 0 -0.42 23 23
PDGF/PDGFRA -0.011 0.11 -9999 0 -0.57 22 22
actin cytoskeleton reorganization 0 0.081 -9999 0 -0.4 23 23
SRF 0.017 0.02 -9999 0 -0.31 2 2
SHC1 0.011 0 -9999 0 -10000 0 0
PI3K 0.007 0.076 -9999 0 -0.35 25 25
PDGF/PDGFRA/Crk/C3G 0.009 0.07 -9999 0 -0.34 22 22
JAK1 0 0.086 -9999 0 -0.41 25 25
ELK1/SRF 0.015 0.069 -9999 0 -0.32 22 22
SHB 0.011 0.019 -9999 0 -0.46 1 1
SHF -0.034 0.14 -9999 0 -0.48 55 55
CSNK2A1 0.005 0.014 -9999 0 -10000 0 0
GO:0007205 0 0.09 -9999 0 -0.44 23 23
SOS1 0.01 0.024 -9999 0 -0.58 1 1
Ras protein signal transduction 0.016 0.063 -9999 0 -0.3 21 21
PDGF/PDGFRA/SHB 0 0.081 -9999 0 -0.4 23 23
PDGF/PDGFRA/Caveolin-1 -0.009 0.1 -9999 0 -0.41 35 35
ITGAV 0 0.08 -9999 0 -0.58 11 11
ELK1 0.005 0.082 -9999 0 -0.39 22 22
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
PDGF/PDGFRA/Crk 0 0.081 -9999 0 -0.4 23 23
JAK-STAT cascade 0 0.085 -9999 0 -0.4 25 25
cell proliferation -0.032 0.13 -9999 0 -0.38 73 73
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.025 0.17 -10000 0 -1.2 11 11
VDR 0.01 0.024 -10000 0 -0.58 1 1
FAM120B 0.01 0.024 -10000 0 -0.58 1 1
RXRs/LXRs/DNA/9cRA 0.025 0.085 -10000 0 -0.58 3 3
RXRs/LXRs/DNA/Oxysterols 0.025 0.12 -10000 0 -0.43 29 29
MED1 0.008 0.044 -10000 0 -0.52 4 4
mol:9cRA 0.002 0.013 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.02 0.12 -10000 0 -0.48 9 9
RXRs/NUR77 0.008 0.091 -10000 0 -0.39 9 9
RXRs/PPAR 0.021 0.058 -10000 0 -0.39 4 4
NCOR2 0.008 0.046 -10000 0 -0.55 4 4
VDR/VDR/Vit D3 0.008 0.018 -10000 0 -0.43 1 1
RARs/VDR/DNA/Vit D3 0.012 0.07 -10000 0 -0.33 18 18
RARA 0.007 0.045 -10000 0 -0.48 5 5
NCOA1 0.01 0.024 -10000 0 -0.58 1 1
VDR/VDR/DNA 0.01 0.024 -10000 0 -0.58 1 1
RARs/RARs/DNA/9cRA 0.008 0.067 -10000 0 -0.28 28 28
RARG 0.005 0.059 -10000 0 -0.58 6 6
RPS6KB1 -0.008 0.081 -10000 0 -0.46 17 17
RARs/THRs/DNA/SMRT -0.022 0.12 -10000 0 -0.28 90 90
THRA 0.008 0.041 -10000 0 -0.49 4 4
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.008 0.018 -10000 0 -0.43 1 1
RXRs/PPAR/9cRA/PGJ2/DNA 0.021 0.073 0.28 8 -0.32 4 12
NR1H4 -0.12 0.22 -10000 0 -0.5 152 152
RXRs/LXRs/DNA 0.034 0.078 -10000 0 -0.72 1 1
NR1H2 0.013 0.027 -10000 0 -0.6 1 1
NR1H3 0.013 0.024 -10000 0 -0.49 1 1
RXRs/VDR/DNA/Vit D3 0.022 0.058 -10000 0 -0.28 5 5
NR4A1 -0.018 0.11 -10000 0 -0.46 37 37
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.032 0.1 -10000 0 -0.26 67 67
RXRG -0.009 0.095 -10000 0 -0.46 25 25
RXR alpha/CCPG 0.018 0.027 -10000 0 -0.42 2 2
RXRA 0.013 0.027 -10000 0 -0.59 1 1
RXRB 0.014 0.012 -10000 0 -10000 0 0
THRB -0.071 0.2 -10000 0 -0.56 86 86
PPARG 0.004 0.064 -10000 0 -0.58 7 7
PPARD 0.01 0.024 -10000 0 -0.58 1 1
TNF 0.003 0.22 -10000 0 -1.1 22 22
mol:Oxysterols 0.002 0.012 -10000 0 -10000 0 0
cholesterol transport 0.025 0.12 -10000 0 -0.42 29 29
PPARA 0.009 0.034 -10000 0 -0.58 2 2
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.005 0.095 -10000 0 -0.54 18 18
RXRs/NUR77/BCL2 0.001 0.07 -10000 0 -0.27 22 22
SREBF1 0.029 0.12 -10000 0 -0.94 3 3
RXRs/RXRs/DNA/9cRA 0.021 0.073 0.28 8 -0.32 4 12
ABCA1 0.019 0.17 -10000 0 -1.1 10 10
RARs/THRs -0.027 0.13 -10000 0 -0.32 88 88
RXRs/FXR -0.052 0.14 -10000 0 -0.33 69 69
BCL2 -0.008 0.1 -10000 0 -0.55 20 20
IL2 signaling events mediated by STAT5

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
GAB2 0.01 0.034 -9999 0 -0.58 2 2
ELF1 -0.018 0.11 -9999 0 -0.36 47 47
CCNA2 0.01 0.024 -9999 0 -0.58 1 1
PIK3CA 0.01 0.034 -9999 0 -0.58 2 2
JAK3 0.001 0.076 -9999 0 -0.53 12 12
PIK3R1 0.009 0.042 -9999 0 -0.58 3 3
JAK1 0.009 0.042 -9999 0 -0.58 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.008 0.14 -9999 0 -0.46 32 32
SHC1 0.012 0.001 -9999 0 -10000 0 0
SP1 -0.009 0.095 -9999 0 -0.35 41 41
IL2RA -0.049 0.23 -9999 0 -0.69 63 63
IL2RB -0.016 0.12 -9999 0 -0.55 30 30
SOS1 0.011 0.024 -9999 0 -0.58 1 1
IL2RG -0.001 0.084 -9999 0 -0.56 13 13
G1/S transition of mitotic cell cycle -0.018 0.19 -9999 0 -0.68 42 42
PTPN11 0.007 0.054 -9999 0 -0.58 5 5
CCND2 -0.034 0.21 -9999 0 -0.78 44 44
LCK -0.03 0.14 -9999 0 -0.51 48 48
GRB2 0.012 0.001 -9999 0 -10000 0 0
IL2 0.002 0.027 -9999 0 -0.46 2 2
CDK6 0.011 0.019 -9999 0 -0.46 1 1
CCND3 0.016 0.12 -9999 0 -0.55 12 12
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.01 0.07 0.25 6 -0.56 4 10
DAPP1 -0.066 0.2 -10000 0 -0.52 67 67
Src family/SYK family/BLNK-LAT/BTK-ITK -0.07 0.23 -10000 0 -0.62 63 63
mol:DAG -0.015 0.11 0.18 2 -0.28 53 55
HRAS 0.008 0.042 -10000 0 -0.49 4 4
RAP1A 0.01 0.026 -10000 0 -0.62 1 1
ARF5/GDP 0.001 0.1 -10000 0 -0.43 24 24
PLCG2 -0.011 0.11 -10000 0 -0.54 24 24
PLCG1 0.01 0.024 -10000 0 -0.58 1 1
ARF5 0.011 0 -10000 0 -10000 0 0
mol:GTP -0.011 0.072 0.23 6 -0.6 4 10
ARF1/GTP -0.01 0.069 0.24 6 -0.56 4 10
RHOA 0.01 0.024 -10000 0 -0.58 1 1
YES1 0.004 0.064 -10000 0 -0.58 7 7
RAP1A/GTP 0.011 0.074 0.22 6 -0.59 4 10
ADAP1 -0.011 0.07 0.22 6 -0.55 5 11
ARAP3 -0.01 0.071 0.23 6 -0.58 4 10
INPPL1 0.01 0.024 -10000 0 -0.58 1 1
PREX1 0.006 0.055 -10000 0 -0.54 6 6
ARHGEF6 -0.005 0.095 -10000 0 -0.54 18 18
ARHGEF7 0.011 0 -10000 0 -10000 0 0
ARF1 0.011 0.019 -10000 0 -0.46 1 1
NRAS 0.002 0.078 -10000 0 -0.59 10 10
FYN 0.005 0.06 -10000 0 -0.55 7 7
ARF6 0.01 0.024 -10000 0 -0.58 1 1
FGR -0.026 0.14 -10000 0 -0.54 40 40
mol:Ca2+ -0.001 0.055 -10000 0 -0.2 2 2
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.044 0.16 -10000 0 -0.52 62 62
ZAP70 -0.036 0.15 -10000 0 -0.53 52 52
mol:IP3 -0.005 0.076 -10000 0 -0.22 22 22
LYN 0.011 0 -10000 0 -10000 0 0
ARF1/GDP 0 0.11 -10000 0 -0.44 24 24
RhoA/GDP -0.021 0.081 0.24 3 -0.47 10 13
PDK1/Src/Hsp90 0.022 0.022 -10000 0 -0.35 2 2
BLNK -0.01 0.11 -10000 0 -0.58 21 21
actin cytoskeleton reorganization 0.014 0.11 0.23 3 -0.48 15 18
SRC 0.01 0.024 -10000 0 -0.58 1 1
PLEKHA2 0.002 0.088 -10000 0 -0.36 32 32
RAC1 0.011 0 -10000 0 -10000 0 0
PTEN 0.004 0.057 -10000 0 -0.56 6 6
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
ARF6/GTP -0.01 0.072 0.25 6 -0.62 4 10
RhoA/GTP 0.016 0.076 0.22 6 -0.63 4 10
Src family/SYK family/BLNK-LAT -0.066 0.2 -10000 0 -0.55 65 65
BLK -0.12 0.23 -10000 0 -0.52 139 139
PDPK1 0.011 0 -10000 0 -10000 0 0
CYTH1 -0.01 0.067 0.22 6 -0.56 4 10
HCK -0.018 0.12 -10000 0 -0.55 31 31
CYTH3 -0.011 0.069 0.22 6 -0.56 4 10
CYTH2 -0.01 0.067 0.22 6 -0.56 4 10
KRAS 0.006 0.059 -10000 0 -0.57 6 6
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.024 0.069 -10000 0 -0.53 5 5
SGK1 -0.01 0.071 0.19 6 -0.6 5 11
INPP5D -0.017 0.12 -10000 0 -0.58 28 28
mol:GDP -0.006 0.11 -10000 0 -0.44 25 25
SOS1 0.01 0.024 -10000 0 -0.58 1 1
SYK 0.011 0.019 -10000 0 -0.46 1 1
ARF6/GDP -0.02 0.081 0.24 3 -0.46 10 13
mol:PI-3-4-5-P3 -0.01 0.074 0.29 6 -0.59 4 10
ARAP3/RAP1A/GTP 0.011 0.075 0.22 6 -0.6 4 10
VAV1 -0.026 0.14 -10000 0 -0.57 38 38
mol:PI-3-4-P2 -0.003 0.097 -10000 0 -0.43 28 28
RAS family/GTP/PI3K Class I 0.012 0.073 -10000 0 -0.38 13 13
PLEKHA1 0.003 0.087 -10000 0 -0.36 31 31
Rac1/GDP 0.001 0.1 -10000 0 -0.43 24 24
LAT -0.01 0.1 -10000 0 -0.51 24 24
Rac1/GTP -0.014 0.14 -10000 0 -0.45 40 40
ITK -0.03 0.096 0.22 5 -0.55 6 11
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.029 0.15 0.21 2 -0.4 53 55
LCK -0.031 0.14 -10000 0 -0.51 48 48
BTK -0.029 0.093 0.22 3 -0.55 6 9
Regulation of Telomerase

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
Telomerase catalytic core complex -0.093 0.28 -9999 0 -1 41 41
RAD9A 0.01 0.024 -9999 0 -0.58 1 1
AP1 -0.014 0.11 -9999 0 -0.39 45 45
IFNAR2 0.011 0.025 -9999 0 -0.58 1 1
AKT1 -0.005 0.059 -9999 0 -0.33 2 2
ER alpha/Oestrogen -0.024 0.11 -9999 0 -0.38 49 49
NFX1/SIN3/HDAC complex 0.033 0.027 -9999 0 -10000 0 0
EGF -0.18 0.25 -9999 0 -0.51 216 216
SMG5 0.01 0.024 -9999 0 -0.58 1 1
SMG6 0.011 0 -9999 0 -10000 0 0
SP3/HDAC2 0.017 0.02 -9999 0 -0.42 1 1
TERT/c-Abl -0.082 0.26 -9999 0 -0.94 40 40
SAP18 0.01 0.019 -9999 0 -0.46 1 1
MRN complex 0.008 0.09 -9999 0 -0.46 19 19
WT1 -0.17 0.26 -9999 0 -0.52 204 204
WRN 0.005 0.062 -9999 0 -0.56 7 7
SP1 0.011 0.025 -9999 0 -0.58 1 1
SP3 0.01 0.025 -9999 0 -0.58 1 1
TERF2IP 0.01 0.024 -9999 0 -0.58 1 1
Telomerase/Nucleolin -0.091 0.22 -9999 0 -0.85 39 39
Mad/Max 0.015 0.027 -9999 0 -0.35 3 3
TERT -0.098 0.29 -9999 0 -1.1 40 40
CCND1 -0.076 0.24 -9999 0 -0.98 32 32
MAX 0.011 0.004 -9999 0 -10000 0 0
RBBP7 0.01 0.024 -9999 0 -0.58 1 1
RBBP4 0.01 0.024 -9999 0 -0.58 1 1
TERF2 0.012 0.009 -9999 0 -10000 0 0
PTGES3 0.009 0.034 -9999 0 -0.58 2 2
SIN3A 0.01 0.024 -9999 0 -0.58 1 1
Telomerase/911 0.019 0.046 -9999 0 -0.5 2 2
CDKN1B -0.019 0.12 -9999 0 -0.36 41 41
RAD1 0.011 0.019 -9999 0 -0.46 1 1
XRCC5 0.01 0.024 -9999 0 -0.58 1 1
XRCC6 0.011 0 -9999 0 -10000 0 0
SAP30 0.009 0.034 -9999 0 -0.58 2 2
TRF2/PARP2 0.017 0.018 -9999 0 -0.38 1 1
UBE3A 0.007 0.049 -9999 0 -0.58 4 4
JUN 0.006 0.052 -9999 0 -0.56 5 5
E6 0 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.006 0.036 -9999 0 -0.43 4 4
FOS -0.026 0.14 -9999 0 -0.53 41 41
IFN-gamma/IRF1 -0.033 0.14 -9999 0 -0.36 87 87
PARP2 0.01 0.024 -9999 0 -0.58 1 1
BLM 0.006 0.057 -9999 0 -0.56 6 6
Telomerase 0.003 0.063 -9999 0 -0.45 6 6
IRF1 0.013 0.028 -9999 0 -0.45 2 2
ESR1 -0.033 0.15 -9999 0 -0.52 49 49
KU/TER 0.016 0.018 -9999 0 -0.42 1 1
ATM/TRF2 0.012 0.048 -9999 0 -0.38 9 9
ubiquitin-dependent protein catabolic process 0.035 0.036 -9999 0 -0.38 2 2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.036 0.037 -9999 0 -0.39 2 2
HDAC1 0.011 0.001 -9999 0 -10000 0 0
HDAC2 0.011 0.008 -9999 0 -10000 0 0
ATM -0.007 0.053 -9999 0 -0.44 9 9
SMAD3 0.003 0.079 -9999 0 -0.4 22 22
ABL1 0.01 0.024 -9999 0 -0.58 1 1
MXD1 0.008 0.036 -9999 0 -0.5 3 3
MRE11A 0.003 0.068 -9999 0 -0.58 8 8
HUS1 0.011 0 -9999 0 -10000 0 0
RPS6KB1 0.006 0.057 -9999 0 -0.56 6 6
TERT/NF kappa B1/14-3-3 -0.086 0.24 -9999 0 -0.97 35 35
NR2F2 0.012 0.007 -9999 0 -10000 0 0
MAPK3 0.01 0.027 -9999 0 -0.35 3 3
MAPK1 0.01 0.027 -9999 0 -0.35 3 3
TGFB1/TGF beta receptor Type II -0.003 0.088 -9999 0 -0.55 15 15
NFKB1 0.01 0.024 -9999 0 -0.58 1 1
HNRNPC 0.011 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.007 0.053 -9999 0 -0.44 9 9
NBN -0.005 0.096 -9999 0 -0.58 16 16
EGFR 0.004 0.063 -9999 0 -0.54 8 8
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.13 0.19 -9999 0 -0.36 223 223
MYC 0.005 0.058 -9999 0 -0.56 6 6
IL2 0.001 0.028 -9999 0 -0.45 2 2
KU 0.016 0.018 -9999 0 -0.42 1 1
RAD50 0.01 0.024 -9999 0 -0.58 1 1
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
TGFB1 -0.003 0.088 -9999 0 -0.55 15 15
TRF2/BLM 0.014 0.04 -9999 0 -0.37 6 6
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.076 0.26 -9999 0 -0.98 37 37
SP1/HDAC2 0.017 0.022 -9999 0 -0.42 1 1
PINX1 0.004 0.064 -9999 0 -0.58 7 7
Telomerase/EST1A -0.091 0.22 -9999 0 -0.85 39 39
Smad3/Myc 0.006 0.076 -9999 0 -0.34 26 26
911 complex 0.022 0.019 -9999 0 -0.31 2 2
IFNG -0.062 0.18 -9999 0 -0.5 86 86
Telomerase/PinX1 -0.093 0.22 -9999 0 -0.84 41 41
Telomerase/AKT1/mTOR/p70S6K 0 0.075 -9999 0 -0.74 2 2
SIN3B 0.01 0.024 -9999 0 -0.58 1 1
YWHAE 0.011 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.091 0.22 -9999 0 -0.84 40 40
response to DNA damage stimulus 0.001 0.017 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.02 0.081 -9999 0 -0.41 16 16
TRF2/WRN 0.013 0.042 -9999 0 -0.36 7 7
Telomerase/hnRNP C1/C2 -0.091 0.22 -9999 0 -0.85 39 39
E2F1 0.009 0.037 -9999 0 -0.5 3 3
ZNFX1 0.011 0.001 -9999 0 -10000 0 0
PIF1 0.007 0.052 -9999 0 -0.56 5 5
NCL 0.011 0 -9999 0 -10000 0 0
DKC1 0.011 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 0.074 0.32 -9999 0 -0.98 17 17
PLK1 0.042 0.073 -9999 0 -1.4 1 1
BIRC5 0.044 0.047 -9999 0 -10000 0 0
HSPA1B 0.06 0.34 -9999 0 -1 21 21
MAP2K1 0.028 0.049 -9999 0 -0.63 2 2
BRCA2 0.057 0.37 -9999 0 -1.2 28 28
FOXM1 0.062 0.38 -9999 0 -1.3 17 17
XRCC1 0.073 0.32 -9999 0 -1 17 17
FOXM1B/p19 -0.12 0.28 -9999 0 -1 35 35
Cyclin D1/CDK4 0.071 0.3 -9999 0 -0.92 14 14
CDC2 0.069 0.33 -9999 0 -1 17 17
TGFA 0.072 0.31 -9999 0 -0.91 17 17
SKP2 0.073 0.32 -9999 0 -1 16 16
CCNE1 0.013 0.034 -9999 0 -0.46 3 3
CKS1B 0.073 0.32 -9999 0 -0.99 17 17
RB1 -0.063 0.18 -9999 0 -0.96 18 18
FOXM1C/SP1 0.062 0.34 -9999 0 -1.1 17 17
AURKB 0.045 0.043 -9999 0 -10000 0 0
CENPF 0.062 0.36 -9999 0 -1.1 24 24
CDK4 0.019 0.012 -9999 0 -10000 0 0
MYC 0.075 0.3 -9999 0 -0.9 19 19
CHEK2 0.029 0.041 -9999 0 -0.63 1 1
ONECUT1 0.068 0.31 -9999 0 -0.97 16 16
CDKN2A -0.074 0.19 -9999 0 -0.51 94 94
LAMA4 0.072 0.33 -9999 0 -1.1 16 16
FOXM1B/HNF6 0.063 0.34 -9999 0 -1.2 16 16
FOS 0.035 0.39 -9999 0 -1 39 39
SP1 0.011 0.024 -9999 0 -0.58 1 1
CDC25B 0.073 0.32 -9999 0 -0.99 16 16
response to radiation 0.016 0.028 -9999 0 -10000 0 0
CENPB 0.073 0.32 -9999 0 -1 18 18
CENPA 0.072 0.33 -9999 0 -1 17 17
NEK2 0.073 0.32 -9999 0 -1 16 16
HIST1H2BA 0.067 0.32 -9999 0 -0.99 16 16
CCNA2 0.014 0.026 -9999 0 -0.59 1 1
EP300 0.007 0.048 -9999 0 -0.58 4 4
CCNB1/CDK1 0.064 0.35 -9999 0 -1.2 17 17
CCNB2 0.071 0.32 -9999 0 -1 18 18
CCNB1 0.071 0.33 -9999 0 -1 17 17
ETV5 0.057 0.36 -9999 0 -1.1 25 25
ESR1 0.035 0.4 -9999 0 -1.1 39 39
CCND1 0.074 0.31 -9999 0 -0.94 15 15
GSK3A 0.028 0.026 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.038 0.049 -9999 0 -0.42 3 3
CDK2 0.014 0.026 -9999 0 -0.59 1 1
G2/M transition of mitotic cell cycle 0.018 0.033 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.089 0.24 -9999 0 -1.1 17 17
GAS1 -0.049 0.51 -9999 0 -1.1 85 85
MMP2 0.035 0.41 -9999 0 -1.2 37 37
RB1/FOXM1C 0.07 0.33 -9999 0 -0.99 22 22
CREBBP 0.011 0 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.077 0.2 -9999 0 -0.51 102 102
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.005 0.056 -9999 0 -0.47 8 8
TCEB1 0.011 0.019 -9999 0 -0.46 1 1
HIF1A/p53 -0.008 0.095 -9999 0 -0.28 56 56
HIF1A 0.013 0.036 -9999 0 -0.25 9 9
COPS5 0.011 0.019 -9999 0 -0.46 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2 0.029 0.042 -9999 0 -0.48 2 2
FIH (dimer) 0.011 0 -9999 0 -10000 0 0
CDKN2A -0.071 0.19 -9999 0 -0.51 94 94
ARNT/IPAS -0.048 0.14 -9999 0 -0.36 103 103
HIF1AN 0.011 0 -9999 0 -10000 0 0
GNB2L1 0.011 0.019 -9999 0 -0.46 1 1
HIF1A/ARNT 0.019 0.04 -9999 0 -0.4 2 2
CUL2 0.011 0 -9999 0 -10000 0 0
OS9 0.011 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.018 0.04 -9999 0 -0.3 9 9
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.019 0.04 -9999 0 -0.4 2 2
PHD1-3/OS9 0.019 0.055 -9999 0 -0.32 10 10
HIF1A/RACK1/Elongin B/Elongin C 0.026 0.055 -9999 0 -0.4 8 8
VHL 0.01 0.024 -9999 0 -0.58 1 1
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
HIF1A/JAB1 0.02 0.036 -9999 0 -0.29 1 1
EGLN3 -0.004 0.089 -9999 0 -0.52 17 17
EGLN2 0.009 0.036 -9999 0 -0.5 3 3
EGLN1 0.011 0 -9999 0 -10000 0 0
TP53 -0.044 0.17 -9999 0 -0.58 56 56
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.027 0.045 -9999 0 -0.86 1 1
ARNT 0.01 0.024 -9999 0 -0.58 1 1
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.01 0.031 -9999 0 -0.52 2 2
HIF1A/p19ARF -0.02 0.1 -9999 0 -0.29 45 45
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 0.009 0.033 -10000 0 -0.46 3 3
mol:Halofuginone 0.004 0.01 -10000 0 -0.23 1 1
ITGA1 0.006 0.054 -10000 0 -0.58 5 5
CDKN1A 0.019 0.048 -10000 0 -0.44 4 4
PRL-3/alpha Tubulin -0.006 0.093 -10000 0 -0.37 36 36
mol:Ca2+ -0.008 0.12 0.3 34 -0.38 39 73
AGT -0.024 0.14 -10000 0 -0.53 39 39
CCNA2 0.02 0.067 -10000 0 -0.89 1 1
TUBA1B 0.011 0 -10000 0 -10000 0 0
EGR1 0.004 0.076 -10000 0 -0.35 25 25
CDK2/Cyclin E1 0.027 0.047 -10000 0 -0.39 4 4
MAPK3 -0.006 0.095 -10000 0 -0.37 37 37
PRL-2 /Rab GGTase beta 0.015 0.031 -10000 0 -0.42 3 3
MAPK1 -0.006 0.095 -10000 0 -0.37 37 37
PTP4A1 0.016 0.07 -10000 0 -0.63 2 2
PTP4A3 -0.021 0.13 -10000 0 -0.52 36 36
PTP4A2 0.011 0 -10000 0 -10000 0 0
ITGB1 -0.005 0.093 -10000 0 -0.37 36 36
SRC 0.01 0.024 -10000 0 -0.58 1 1
RAC1 0.005 0.085 -10000 0 -0.41 20 20
Rab GGTase beta/Rab GGTase alpha 0.014 0.036 -10000 0 -0.42 4 4
PRL-1/ATF-5 0.02 0.066 -10000 0 -0.89 1 1
RABGGTA 0.01 0.024 -10000 0 -0.58 1 1
BCAR1 0.015 0.076 0.3 34 -0.33 2 36
RHOC 0.005 0.085 -10000 0 -0.41 20 20
RHOA 0.004 0.087 -10000 0 -0.41 21 21
cell motility 0.004 0.092 -10000 0 -0.42 21 21
PRL-1/alpha Tubulin 0.02 0.066 -10000 0 -0.89 1 1
PRL-3/alpha1 Integrin -0.01 0.1 -10000 0 -0.38 41 41
ROCK1 0.004 0.093 -10000 0 -0.43 21 21
RABGGTB 0.008 0.042 -10000 0 -0.58 3 3
CDK2 0.01 0.024 -10000 0 -0.58 1 1
mitosis 0.016 0.07 -10000 0 -0.36 11 11
ATF5 0.011 0.019 -10000 0 -0.46 1 1
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0.013 0.1 -10000 0 -0.98 4 4
epithelial cell differentiation -0.049 0.12 -10000 0 -0.54 16 16
ITCH 0.007 0.056 -10000 0 -0.59 5 5
WWP1 0.017 0.11 -10000 0 -1.5 3 3
FYN 0.005 0.06 -10000 0 -0.55 7 7
EGFR 0.004 0.063 -10000 0 -0.53 8 8
PRL -0.013 0.089 -10000 0 -0.46 23 23
neuron projection morphogenesis 0.006 0.12 -10000 0 -0.79 4 4
PTPRZ1 -0.08 0.2 -10000 0 -0.5 102 102
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.005 0.13 -10000 0 -1.1 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.023 0.14 -10000 0 -1.2 3 3
ADAM17 0.011 0.038 -10000 0 -0.63 2 2
ErbB4/ErbB4 0.018 0.1 -10000 0 -1.1 4 4
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0 0.1 -10000 0 -1 4 4
NCOR1 0.01 0.024 -10000 0 -0.58 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.019 0.14 -10000 0 -1 4 4
GRIN2B -0.037 0.16 -10000 0 -0.66 16 16
ErbB4/ErbB2/betacellulin 0.013 0.11 -10000 0 -0.96 4 4
STAT1 0.006 0.051 -10000 0 -0.5 6 6
HBEGF 0.001 0.068 -10000 0 -0.46 13 13
PRLR -0.042 0.17 -10000 0 -0.58 54 54
E4ICDs/ETO2 -0.036 0.15 -10000 0 -0.9 5 5
axon guidance 0.015 0.13 -10000 0 -1.1 4 4
NEDD4 0.008 0.048 -10000 0 -0.57 4 4
Prolactin receptor/Prolactin receptor/Prolactin -0.039 0.14 -10000 0 -0.42 71 71
CBFA2T3 -0.082 0.2 -10000 0 -0.5 108 108
ErbB4/ErbB2/HBEGF 0.015 0.1 -10000 0 -1.1 3 3
MAPK3 0.001 0.12 -10000 0 -0.83 4 4
STAT1 (dimer) 0.016 0.11 -10000 0 -1.1 4 4
MAPK1 0.001 0.12 -10000 0 -0.94 3 3
JAK2 -0.008 0.1 -10000 0 -0.55 21 21
ErbB4/ErbB2/neuregulin 1 beta -0.022 0.14 -10000 0 -0.91 5 5
NRG1 -0.041 0.15 -10000 0 -0.39 88 88
NRG3 -0.003 0.065 -10000 0 -0.46 12 12
NRG2 -0.017 0.1 -10000 0 -0.46 32 32
NRG4 -0.022 0.12 -10000 0 -0.47 38 38
heart development 0.015 0.13 -10000 0 -1.1 4 4
neural crest cell migration -0.022 0.14 -10000 0 -0.87 5 5
ERBB2 0.01 0.06 -10000 0 -0.34 16 16
WWOX/E4ICDs 0.018 0.095 -10000 0 -0.76 6 6
SHC1 0.011 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.003 0.12 -10000 0 -0.98 5 5
apoptosis 0.036 0.096 0.99 4 -10000 0 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.002 0.12 -10000 0 -1.1 4 4
ErbB4/ErbB2/epiregulin -0.074 0.17 -10000 0 -0.53 16 16
ErbB4/ErbB4/betacellulin/betacellulin 0.011 0.11 -10000 0 -0.5 15 15
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.019 0.16 -10000 0 -0.61 20 20
MDM2 0.019 0.1 -10000 0 -1 4 4
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.022 0.14 -10000 0 -0.78 6 6
STAT5A 0.02 0.12 -10000 0 -1.1 4 4
ErbB4/EGFR/neuregulin 1 beta -0.02 0.14 -10000 0 -1.1 4 4
DLG4 0.007 0.048 -10000 0 -0.51 5 5
GRB2/SHC 0.017 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 0.016 0.09 -10000 0 -0.93 4 4
STAT5A (dimer) -0.052 0.13 -10000 0 -0.62 15 15
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.019 0.12 -10000 0 -1.1 4 4
LRIG1 -0.002 0.087 -10000 0 -0.58 13 13
EREG -0.16 0.26 -10000 0 -0.55 187 187
BTC -0.002 0.087 -10000 0 -0.58 13 13
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.015 0.13 -10000 0 -1.2 4 4
ERBB4 0.018 0.1 -10000 0 -1.1 4 4
STAT5B 0.011 0 -10000 0 -10000 0 0
YAP1 0.003 0.086 -10000 0 -1.1 3 3
GRB2 0.011 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.001 0.11 -10000 0 -0.96 4 4
glial cell differentiation -0.016 0.087 0.91 4 -10000 0 4
WWOX 0.009 0.034 -10000 0 -0.58 2 2
cell proliferation -0.015 0.15 -10000 0 -0.78 7 7
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.019 0.12 -9999 0 -0.31 54 54
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.011 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.003 0.12 -9999 0 -0.54 12 12
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.078 -9999 0 -0.37 22 22
antigen processing and presentation of peptide antigen via MHC class I -0.038 0.074 -9999 0 -0.28 20 20
CaM/Ca2+ -0.018 0.11 -9999 0 -0.47 8 8
RAP1A 0.01 0.024 -9999 0 -0.58 1 1
STAT1 (dimer)/SHP2 -0.012 0.12 -9999 0 -0.48 14 14
AKT1 -0.003 0.11 -9999 0 -0.46 12 12
MAP2K1 -0.01 0.12 -9999 0 -0.55 11 11
MAP3K11 -0.014 0.11 -9999 0 -0.42 11 11
IFNGR1 0.008 0.012 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.051 0.12 -9999 0 -0.48 30 30
Rap1/GTP -0.031 0.073 -9999 0 -0.42 5 5
CRKL/C3G 0.016 0.018 -9999 0 -0.42 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.021 0.12 -9999 0 -0.46 11 11
CEBPB -0.008 0.16 -9999 0 -0.48 34 34
STAT3 0.011 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.053 0.22 -9999 0 -0.85 28 28
STAT1 -0.013 0.12 -9999 0 -0.47 14 14
CALM1 0.011 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.065 0.18 -9999 0 -0.51 86 86
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
STAT1 (dimer)/PIAS1 -0.005 0.11 -9999 0 -0.49 11 11
CEBPB/PTGES2/Cbp/p300 -0.039 0.086 -9999 0 -0.41 14 14
mol:Ca2+ -0.021 0.11 -9999 0 -0.3 54 54
MAPK3 -0.005 0.13 -9999 0 -0.68 8 8
STAT1 (dimer) -0.05 0.1 -9999 0 -0.39 20 20
MAPK1 -0.005 0.12 -9999 0 -0.66 8 8
JAK2 -0.011 0.1 -9999 0 -0.56 21 21
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
JAK1 0.005 0.044 -9999 0 -0.6 3 3
CAMK2D 0.007 0.048 -9999 0 -0.58 4 4
DAPK1 -0.012 0.16 -9999 0 -0.54 37 37
SMAD7 0.012 0.059 -9999 0 -0.25 3 3
CBL/CRKL/C3G -0.002 0.1 -9999 0 -0.49 5 5
PI3K -0.041 0.1 -9999 0 -0.5 12 12
IFNG -0.066 0.18 -9999 0 -0.51 86 86
apoptosis -0.012 0.12 -9999 0 -0.4 35 35
CAMK2G 0.011 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.011 0 -9999 0 -10000 0 0
CAMK2A -0.019 0.12 -9999 0 -0.53 33 33
CAMK2B -0.054 0.17 -9999 0 -0.49 76 76
FRAP1 -0.003 0.1 -9999 0 -0.42 12 12
PRKCD -0.002 0.11 -9999 0 -0.46 12 12
RAP1B 0.011 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.038 0.074 -9999 0 -0.28 20 20
PTPN2 0.008 0.042 -9999 0 -0.58 3 3
EP300 0.008 0.048 -9999 0 -0.58 4 4
IRF1 0.001 0.12 -9999 0 -0.49 15 15
STAT1 (dimer)/PIASy -0.005 0.11 -9999 0 -0.5 10 10
SOCS1 -0.047 0.22 -9999 0 -1.4 14 14
mol:GDP -0.03 0.086 -9999 0 -0.46 5 5
CASP1 0.002 0.086 -9999 0 -0.28 36 36
PTGES2 0.007 0.045 -9999 0 -0.48 5 5
IRF9 0.02 0.054 -9999 0 -0.23 4 4
mol:PI-3-4-5-P3 -0.04 0.099 -9999 0 -0.48 12 12
RAP1/GDP -0.031 0.073 -9999 0 -0.43 5 5
CBL -0.012 0.11 -9999 0 -0.47 8 8
MAP3K1 -0.016 0.12 -9999 0 -0.49 14 14
PIAS1 0.011 0 -9999 0 -10000 0 0
PIAS4 0.011 0.024 -9999 0 -0.56 1 1
antigen processing and presentation of peptide antigen via MHC class II -0.038 0.074 -9999 0 -0.28 20 20
PTPN11 -0.019 0.11 -9999 0 -0.31 54 54
CREBBP 0.012 0.001 -9999 0 -10000 0 0
RAPGEF1 0.01 0.024 -9999 0 -0.58 1 1
Nectin adhesion 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
PDGFRB -0.004 0.092 -9999 0 -0.54 17 17
alphaV beta3 Integrin -0.004 0.094 -9999 0 -0.41 29 29
PTK2 -0.027 0.099 -9999 0 -0.43 28 28
positive regulation of JNK cascade -0.017 0.068 -9999 0 -0.31 28 28
CDC42/GDP 0.017 0.11 -9999 0 -0.43 28 28
Rac1/GDP 0.02 0.1 -9999 0 -0.42 27 27
RAP1B 0.011 0 -9999 0 -10000 0 0
RAP1A 0.01 0.024 -9999 0 -0.58 1 1
CTNNB1 0.011 0 -9999 0 -10000 0 0
CDC42/GTP -0.021 0.083 -9999 0 -0.38 28 28
nectin-3/I-afadin -0.003 0.09 -9999 0 -0.42 27 27
RAPGEF1 0.019 0.11 -9999 0 -0.46 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0.12 -9999 0 -0.52 27 27
PDGFB-D/PDGFRB -0.004 0.092 -9999 0 -0.54 17 17
TLN1 0.013 0.059 -9999 0 -0.54 3 3
Rap1/GTP -0.016 0.069 -9999 0 -0.32 27 27
IQGAP1 0.009 0.039 -9999 0 -0.54 3 3
Rap1/GTP/I-afadin 0.02 0.024 -9999 0 -0.32 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.003 0.09 -9999 0 -0.42 27 27
PVR 0.011 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.011 0 -9999 0 -10000 0 0
mol:GDP 0.013 0.13 -9999 0 -0.53 27 27
MLLT4 0.009 0.034 -9999 0 -0.58 2 2
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
PI3K 0.008 0.09 -9999 0 -0.45 4 4
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.014 0.036 -9999 0 -0.42 4 4
positive regulation of lamellipodium assembly -0.026 0.085 -9999 0 -0.3 49 49
PVRL1 0.009 0.034 -9999 0 -0.58 2 2
PVRL3 -0.013 0.12 -9999 0 -0.58 25 25
PVRL2 0.01 0.031 -9999 0 -0.52 2 2
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
CDH1 0.01 0.024 -9999 0 -0.58 1 1
CLDN1 -0.014 0.12 -9999 0 -0.56 26 26
JAM-A/CLDN1 -0.001 0.096 -9999 0 -0.32 48 48
SRC 0.006 0.13 -9999 0 -0.57 27 27
ITGB3 -0.006 0.098 -9999 0 -0.54 19 19
nectin-1(dimer)/I-afadin/I-afadin 0.014 0.036 -9999 0 -0.42 4 4
FARP2 0.016 0.12 -9999 0 -0.5 27 27
RAC1 0.011 0 -9999 0 -10000 0 0
CTNNA1 0.009 0.034 -9999 0 -0.58 2 2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.006 0.078 -9999 0 -0.35 27 27
nectin-1/I-afadin 0.014 0.036 -9999 0 -0.42 4 4
nectin-2/I-afadin 0.014 0.034 -9999 0 -0.4 4 4
RAC1/GTP/IQGAP1/filamentous actin 0.014 0.025 -9999 0 -0.33 3 3
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.005 0.081 -9999 0 -0.35 29 29
CDC42/GTP/IQGAP1/filamentous actin 0.011 0.05 -9999 0 -0.45 6 6
F11R 0.011 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.017 0.068 -9999 0 -0.31 28 28
alphaV/beta3 Integrin/Talin 0.011 0.09 -9999 0 -0.52 7 7
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.014 0.034 -9999 0 -0.4 4 4
nectin-2(dimer)/I-afadin/I-afadin 0.014 0.034 -9999 0 -0.4 4 4
PIP5K1C 0.008 0.059 -9999 0 -0.47 3 3
VAV2 -0.005 0.16 -9999 0 -0.52 49 49
RAP1/GDP -0.022 0.084 -9999 0 -0.39 27 27
ITGAV 0 0.08 -9999 0 -0.58 11 11
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.005 0.08 -9999 0 -0.35 29 29
nectin-3(dimer)/I-afadin/I-afadin -0.003 0.09 -9999 0 -0.42 27 27
Rac1/GTP -0.032 0.1 -9999 0 -0.36 49 49
PTPRM 0.002 0.063 -9999 0 -0.24 27 27
E-cadherin/beta catenin/alpha catenin -0.004 0.037 -9999 0 -0.57 1 1
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.006 0.054 -9999 0 -0.58 5 5
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.046 0.16 -9999 0 -0.49 68 68
CDC42/GTP -0.017 0.11 -9999 0 -0.41 18 18
PLCG1 -0.015 0.11 -9999 0 -0.45 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.011 0 -9999 0 -10000 0 0
GNAI3 0.011 0 -9999 0 -10000 0 0
G12/G13 0.015 0.025 -9999 0 -0.42 2 2
cell migration -0.017 0.1 -9999 0 -0.4 18 18
S1PR5 0 0.076 -9999 0 -0.53 12 12
S1PR4 -0.024 0.14 -9999 0 -0.53 39 39
MAPK3 -0.015 0.11 -9999 0 -0.46 14 14
MAPK1 -0.015 0.11 -9999 0 -0.46 14 14
S1P/S1P5/Gi -0.012 0.096 -9999 0 -0.31 29 29
GNAI1 -0.003 0.089 -9999 0 -0.56 15 15
CDC42/GDP 0.005 0.04 -9999 0 -0.43 5 5
S1P/S1P5/G12 0.009 0.048 -9999 0 -0.32 12 12
RHOA 0.005 0.075 -9999 0 -0.3 27 27
S1P/S1P4/Gi -0.022 0.11 -9999 0 -0.32 49 49
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.012 0.11 -9999 0 -0.55 25 25
S1P/S1P4/G12/G13 0.001 0.08 -9999 0 -0.32 26 26
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.034 -9999 0 -0.58 2 2
CDC42 0.006 0.054 -9999 0 -0.58 5 5
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.011 0.038 -10000 0 -0.36 6 6
RAS family/GTP -0.001 0.096 -10000 0 -0.43 6 6
NFATC4 0.004 0.087 -10000 0 -0.42 4 4
ERBB2IP -0.008 0.11 -10000 0 -0.58 20 20
HSP90 (dimer) 0.01 0.024 -10000 0 -0.58 1 1
mammary gland morphogenesis -0.01 0.1 0.22 6 -0.45 3 9
JUN 0.006 0.1 0.16 3 -0.28 48 51
HRAS 0.008 0.041 -10000 0 -0.49 4 4
DOCK7 -0.003 0.099 -10000 0 -0.4 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.018 0.12 0.23 13 -0.31 51 64
AKT1 0.008 0.018 -10000 0 -0.44 1 1
BAD 0.014 0.031 -10000 0 -0.48 2 2
MAPK10 -0.007 0.082 -10000 0 -0.29 19 19
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.009 0.11 0.24 6 -0.49 3 9
RAF1 0.009 0.098 -10000 0 -0.4 6 6
ErbB2/ErbB3/neuregulin 2 0 0.074 0.23 12 -0.3 5 17
STAT3 0 0.044 -10000 0 -1.1 1 1
cell migration 0.008 0.075 0.16 10 -0.25 17 27
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.001 0.19 -10000 0 -0.59 37 37
FOS 0.003 0.16 -10000 0 -0.42 54 54
NRAS 0.001 0.076 -10000 0 -0.58 10 10
mol:Ca2+ -0.01 0.1 0.22 6 -0.45 3 9
MAPK3 0.004 0.16 -10000 0 -0.51 30 30
MAPK1 0.004 0.15 -10000 0 -0.49 30 30
JAK2 -0.01 0.11 -10000 0 -0.43 10 10
NF2 -0.001 0.004 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.009 0.092 -10000 0 -0.28 50 50
NRG1 -0.067 0.19 -10000 0 -0.53 87 87
GRB2/SOS1 0.016 0.018 -10000 0 -0.42 1 1
MAPK8 0.001 0.096 0.2 7 -0.29 16 23
MAPK9 0.008 0.058 -10000 0 -0.25 4 4
ERBB2 0.005 0.085 0.39 19 -0.34 13 32
ERBB3 0.01 0.024 -10000 0 -0.58 1 1
SHC1 0.011 0.001 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
apoptosis -0.002 0.035 0.82 1 -10000 0 1
STAT3 (dimer) 0.014 0.044 -10000 0 -1 1 1
RNF41 0.016 0.034 -10000 0 -0.32 6 6
FRAP1 0.007 0.016 -10000 0 -0.37 1 1
RAC1-CDC42/GTP -0.027 0.065 -10000 0 -0.33 7 7
ErbB2/ErbB2/HSP90 (dimer) 0.008 0.061 0.26 18 -0.28 13 31
CHRNA1 -0.002 0.18 -10000 0 -0.61 34 34
myelination 0.006 0.086 0.19 5 -0.4 4 9
PPP3CB -0.002 0.093 -10000 0 -0.4 3 3
KRAS 0.006 0.057 -10000 0 -0.56 6 6
RAC1-CDC42/GDP -0.001 0.084 -10000 0 -0.31 5 5
NRG2 -0.017 0.1 -10000 0 -0.46 32 32
mol:GDP -0.009 0.092 -10000 0 -0.28 50 50
SOS1 0.01 0.024 -10000 0 -0.58 1 1
MAP2K2 0.013 0.1 -10000 0 -0.4 10 10
SRC 0.01 0.024 -10000 0 -0.58 1 1
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.005 0.1 -10000 0 -0.42 5 5
MAP2K1 0 0.15 -10000 0 -0.54 16 16
heart morphogenesis -0.01 0.1 0.22 6 -0.45 3 9
RAS family/GDP -0.001 0.096 -10000 0 -0.44 6 6
GRB2 0.011 0.001 -10000 0 -10000 0 0
PRKACA -0.003 0.006 -10000 0 -10000 0 0
CHRNE 0 0.056 -10000 0 -0.18 49 49
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
activation of caspase activity -0.008 0.018 0.44 1 -10000 0 1
nervous system development -0.01 0.1 0.22 6 -0.45 3 9
CDC42 0.006 0.054 -10000 0 -0.58 5 5
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.009 0.036 -9999 0 -0.5 3 3
SPHK1 -0.03 0.14 -9999 0 -0.51 47 47
GNAI2 0.011 0 -9999 0 -10000 0 0
mol:S1P -0.001 0.068 -9999 0 -0.3 23 23
GNAO1 -0.046 0.16 -9999 0 -0.49 68 68
mol:Sphinganine-1-P -0.014 0.11 -9999 0 -0.36 50 50
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.018 0.054 -9999 0 -10000 0 0
GNAI3 0.011 0 -9999 0 -10000 0 0
G12/G13 0.015 0.025 -9999 0 -0.42 2 2
S1PR3 0.005 0.058 -9999 0 -0.53 7 7
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.004 0.058 -9999 0 -0.25 23 23
S1PR5 0 0.076 -9999 0 -0.53 12 12
S1PR4 -0.024 0.14 -9999 0 -0.53 39 39
GNAI1 -0.003 0.089 -9999 0 -0.56 15 15
S1P/S1P5/G12 0.006 0.068 -9999 0 -0.32 9 9
S1P/S1P3/Gq -0.001 0.11 -9999 0 -0.5 15 15
S1P/S1P4/Gi -0.023 0.12 -9999 0 -0.46 21 21
GNAQ 0.005 0.059 -9999 0 -0.58 6 6
GNAZ -0.012 0.11 -9999 0 -0.55 25 25
GNA14 -0.007 0.1 -9999 0 -0.56 19 19
GNA15 -0.008 0.1 -9999 0 -0.54 21 21
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.034 -9999 0 -0.58 2 2
GNA11 0.007 0.05 -9999 0 -0.53 5 5
ABCC1 0.01 0.024 -9999 0 -0.58 1 1
Signaling events mediated by HDAC Class III

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
EP300 0.007 0.048 -10000 0 -0.58 4 4
HDAC4 0.011 0.019 -10000 0 -0.46 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.006 0.09 0.36 36 -10000 0 36
CDKN1A 0.007 0.068 -10000 0 -0.58 5 5
KAT2B -0.006 0.099 -10000 0 -0.58 17 17
BAX 0.01 0.024 -10000 0 -0.58 1 1
FOXO3 0.004 0.041 0.49 4 -10000 0 4
FOXO1 0.009 0.034 -10000 0 -0.58 2 2
FOXO4 0.016 0.029 -10000 0 -0.3 5 5
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.011 0 -10000 0 -10000 0 0
TAT -0.018 0.11 -10000 0 -0.46 33 33
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.004 0.075 -10000 0 -0.42 19 19
PPARGC1A -0.045 0.17 -10000 0 -0.56 58 58
FHL2 0.009 0.034 -10000 0 -0.58 2 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.011 0.041 -10000 0 -0.42 5 5
HIST2H4A -0.006 0.09 -10000 0 -0.36 36 36
SIRT1/FOXO3a 0 0.032 0.29 2 -0.36 3 5
SIRT1 0.004 0.055 -10000 0 -0.58 5 5
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.017 0.04 -10000 0 -0.34 7 7
SIRT1/Histone H1b 0.003 0.067 -10000 0 -0.3 20 20
apoptosis -0.017 0.038 0.35 6 -10000 0 6
SIRT1/PGC1A -0.035 0.11 -10000 0 -0.35 63 63
p53/SIRT1 -0.041 0.13 0.32 4 -0.43 59 63
SIRT1/FOXO4 0.014 0.048 -10000 0 -0.37 8 8
FOXO1/FHL2/SIRT1 0.015 0.043 -10000 0 -0.32 9 9
HIST1H1E 0.003 0.062 -10000 0 -0.31 17 17
SIRT1/p300 0.008 0.061 -10000 0 -0.52 7 7
muscle cell differentiation 0 0.08 0.4 21 -10000 0 21
TP53 -0.047 0.17 -10000 0 -0.58 56 56
KU70/SIRT1/BAX 0.017 0.038 -10000 0 -0.35 6 6
CREBBP 0.011 0 -10000 0 -10000 0 0
MEF2D 0.01 0.024 -10000 0 -0.58 1 1
HIV-1 Tat/SIRT1 -0.011 0.085 -10000 0 -0.33 38 38
ACSS2 0.012 0.044 -10000 0 -0.42 6 6
SIRT1/PCAF/MYOD 0 0.08 -10000 0 -0.4 21 21
Regulation of p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0.014 0.022 -9999 0 -0.36 2 2
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.011 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.001 0.076 -9999 0 -0.58 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.008 0.042 -9999 0 -0.58 3 3
RAC1-CDC42/GTP/PAK family 0.016 0.035 -9999 0 -0.29 5 5
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.004 0.064 -9999 0 -0.58 7 7
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.009 0.034 -9999 0 -0.58 2 2
FYN 0.005 0.06 -9999 0 -0.55 7 7
MAP3K12 0.003 0.068 -9999 0 -0.54 9 9
FGR -0.026 0.14 -9999 0 -0.54 40 40
p38 alpha/TAB1 -0.038 0.087 -9999 0 -0.34 29 29
PRKG1 -0.024 0.14 -9999 0 -0.56 37 37
DUSP8 0.007 0.048 -9999 0 -0.58 4 4
PGK/cGMP/p38 alpha -0.05 0.11 -9999 0 -0.36 48 48
apoptosis -0.037 0.083 -9999 0 -0.33 29 29
RAL/GTP 0.015 0 -9999 0 -10000 0 0
LYN 0.011 0 -9999 0 -10000 0 0
DUSP1 -0.007 0.092 -9999 0 -0.47 22 22
PAK1 0.011 0 -9999 0 -10000 0 0
SRC 0.01 0.024 -9999 0 -0.58 1 1
RAC1/OSM/MEKK3/MKK3 0.027 0.034 -9999 0 -0.37 4 4
TRAF6 0.01 0.024 -9999 0 -0.58 1 1
RAC1 0.011 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.01 0.031 -9999 0 -0.52 2 2
RAC1-CDC42/GTP 0.012 0.034 -9999 0 -0.36 5 5
MAPK11 -0.024 0.14 -9999 0 -0.42 44 44
BLK -0.12 0.23 -9999 0 -0.52 139 139
HCK -0.018 0.12 -9999 0 -0.55 31 31
MAP2K3 0.01 0.024 -9999 0 -0.58 1 1
DUSP16 0.011 0 -9999 0 -10000 0 0
DUSP10 0.009 0.039 -9999 0 -0.54 3 3
TRAF6/MEKK3 0.013 0.024 -9999 0 -0.33 3 3
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.009 0.11 -9999 0 -0.37 30 30
positive regulation of innate immune response -0.021 0.15 -9999 0 -0.46 39 39
LCK -0.031 0.14 -9999 0 -0.51 48 48
p38alpha-beta/MKP7 -0.014 0.14 -9999 0 -0.45 36 36
p38alpha-beta/MKP5 -0.015 0.15 -9999 0 -0.46 37 37
PGK/cGMP -0.018 0.1 -9999 0 -0.41 37 37
PAK2 0.01 0.024 -9999 0 -0.58 1 1
p38alpha-beta/MKP1 -0.022 0.15 -9999 0 -0.44 42 42
CDC42 0.006 0.054 -9999 0 -0.58 5 5
RALB 0.011 0 -9999 0 -10000 0 0
RALA 0.011 0 -9999 0 -10000 0 0
PAK3 0 0.057 -9999 0 -0.46 9 9
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.007 0.048 -10000 0 -0.57 4 4
HSPA8 0.01 0.034 -10000 0 -0.58 2 2
SMAD3/SMAD4/ER alpha -0.034 0.11 0.21 6 -0.36 41 47
AKT1 0.011 0.027 -10000 0 -0.58 1 1
GSC -0.016 0.14 -10000 0 -1.2 5 5
NKX2-5 -0.014 0.085 -10000 0 -0.46 21 21
muscle cell differentiation 0.038 0.091 0.46 15 -10000 0 15
SMAD2-3/SMAD4/SP1 0.024 0.099 -10000 0 -0.42 5 5
SMAD4 -0.001 0.075 -10000 0 -0.56 7 7
CBFB 0.007 0.048 -10000 0 -0.58 4 4
SAP18 0.011 0.019 -10000 0 -0.46 1 1
Cbp/p300/MSG1 -0.036 0.12 -10000 0 -0.34 40 40
SMAD3/SMAD4/VDR -0.007 0.058 -10000 0 -0.41 3 3
MYC 0.006 0.058 -10000 0 -0.55 6 6
CDKN2B -0.011 0.22 -10000 0 -1.4 14 14
AP1 0.01 0.11 -10000 0 -0.48 13 13
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.038 0.055 -10000 0 -0.44 2 2
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.006 0.086 -10000 0 -0.36 11 11
SP3 0.012 0.024 -10000 0 -0.58 1 1
CREB1 0.009 0.034 -10000 0 -0.58 2 2
FOXH1 -0.053 0.17 -10000 0 -0.5 74 74
SMAD3/SMAD4/GR -0.012 0.1 -10000 0 -0.38 29 29
GATA3 -0.026 0.13 -10000 0 -0.54 31 31
SKI/SIN3/HDAC complex/NCoR1 0.036 0.024 -10000 0 -10000 0 0
MEF2C/TIF2 -0.019 0.13 -10000 0 -0.48 22 22
endothelial cell migration 0.036 0.2 1.3 11 -10000 0 11
MAX 0.013 0.01 -10000 0 -10000 0 0
RBBP7 0.01 0.024 -10000 0 -0.58 1 1
RBBP4 0.01 0.024 -10000 0 -0.58 1 1
RUNX2 -0.006 0.097 -10000 0 -0.54 19 19
RUNX3 -0.02 0.12 -10000 0 -0.51 36 36
RUNX1 0.011 0 -10000 0 -10000 0 0
CTBP1 0.01 0.024 -10000 0 -0.58 1 1
NR3C1 -0.013 0.11 -10000 0 -0.52 28 28
VDR 0.01 0.024 -10000 0 -0.58 1 1
CDKN1A 0.028 0.13 -10000 0 -1.2 4 4
KAT2B -0.006 0.099 -10000 0 -0.58 17 17
SMAD2/SMAD2/SMAD4/FOXH1 -0.022 0.13 -10000 0 -0.36 43 43
DCP1A 0.011 0 -10000 0 -10000 0 0
SKI 0.011 0.001 -10000 0 -10000 0 0
SERPINE1 -0.036 0.2 -10000 0 -1.3 11 11
SMAD3/SMAD4/ATF2 0.011 0.076 -10000 0 -0.35 9 9
SMAD3/SMAD4/ATF3 0.003 0.092 -10000 0 -0.36 17 17
SAP30 0.009 0.034 -10000 0 -0.58 2 2
Cbp/p300/PIAS3 0.019 0.04 -10000 0 -0.33 6 6
JUN 0.009 0.11 -10000 0 -0.47 13 13
SMAD3/SMAD4/IRF7 0.009 0.085 -10000 0 -0.41 9 9
TFE3 0.014 0.013 -10000 0 -10000 0 0
COL1A2 -0.047 0.21 -10000 0 -0.69 48 48
mesenchymal cell differentiation -0.001 0.095 0.38 18 -10000 0 18
DLX1 -0.043 0.15 -10000 0 -0.46 65 65
TCF3 0.01 0.024 -10000 0 -0.58 1 1
FOS -0.024 0.14 -10000 0 -0.53 41 41
SMAD3/SMAD4/Max 0.005 0.07 -10000 0 -0.32 12 12
Cbp/p300/SNIP1 0.02 0.031 -10000 0 -0.35 4 4
ZBTB17 0.01 0.026 -10000 0 -0.58 1 1
LAMC1 0.023 0.066 -10000 0 -0.43 1 1
TGIF2/HDAC complex/SMAD3/SMAD4 0.009 0.08 -10000 0 -0.34 17 17
IRF7 0.006 0.057 -10000 0 -0.56 6 6
ESR1 -0.031 0.14 -10000 0 -0.51 49 49
HNF4A 0.004 0.064 -10000 0 -0.58 7 7
MEF2C -0.022 0.13 -10000 0 -0.5 20 20
SMAD2-3/SMAD4 0.013 0.085 -10000 0 -0.4 8 8
Cbp/p300/Src-1 0.019 0.04 -10000 0 -0.43 4 4
IGHV3OR16-13 -0.009 0.05 -10000 0 -0.8 2 2
TGIF2/HDAC complex 0.006 0.054 -10000 0 -0.58 5 5
CREBBP 0.011 0.006 -10000 0 -10000 0 0
SKIL 0 0.08 -10000 0 -0.58 11 11
HDAC1 0.011 0.001 -10000 0 -10000 0 0
HDAC2 0.011 0.001 -10000 0 -10000 0 0
SNIP1 0.011 0.002 -10000 0 -10000 0 0
GCN5L2 0 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.022 0.076 -10000 0 -0.37 3 3
MSG1/HSC70 -0.051 0.14 -10000 0 -0.34 111 111
SMAD2 0.007 0.052 -10000 0 -0.57 4 4
SMAD3 0.001 0.075 -10000 0 -0.57 7 7
SMAD3/E2F4-5/DP1/p107/SMAD4 0.019 0.069 -10000 0 -0.34 4 4
SMAD2/SMAD2/SMAD4 -0.004 0.076 -10000 0 -0.35 24 24
NCOR1 0.01 0.024 -10000 0 -0.58 1 1
NCOA2 0.004 0.067 -10000 0 -0.56 8 8
NCOA1 0.01 0.024 -10000 0 -0.58 1 1
MYOD/E2A 0.007 0.026 -10000 0 -0.35 3 3
SMAD2-3/SMAD4/SP1/MIZ-1 0.031 0.095 -10000 0 -0.41 4 4
IFNB1 0.009 0.082 -10000 0 -0.48 6 6
SMAD3/SMAD4/MEF2C -0.018 0.14 -10000 0 -0.5 22 22
CITED1 -0.08 0.19 -10000 0 -0.49 109 109
SMAD2-3/SMAD4/ARC105 0.021 0.078 -10000 0 -0.38 7 7
RBL1 0.009 0.039 -10000 0 -0.54 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.024 0.1 -10000 0 -0.48 16 16
RUNX1-3/PEBPB2 0.001 0.083 -10000 0 -0.35 19 19
SMAD7 0.027 0.12 -10000 0 -0.69 5 5
MYC/MIZ-1 0.012 0.051 -10000 0 -0.4 7 7
SMAD3/SMAD4 -0.016 0.099 0.31 4 -0.43 14 18
IL10 -0.036 0.2 -10000 0 -0.58 60 60
PIASy/HDAC complex 0.011 0.025 -10000 0 -0.58 1 1
PIAS3 0.009 0.031 -10000 0 -0.52 2 2
CDK2 0.01 0.025 -10000 0 -0.58 1 1
IL5 -0.014 0.13 -10000 0 -0.48 19 19
CDK4 0.011 0.006 -10000 0 -10000 0 0
PIAS4 0.011 0.025 -10000 0 -0.58 1 1
ATF3 -0.004 0.083 -10000 0 -0.46 19 19
SMAD3/SMAD4/SP1 0.014 0.095 -10000 0 -0.37 8 8
FOXG1 -0.063 0.16 -10000 0 -0.48 79 79
FOXO3 0.018 0.025 -10000 0 -0.42 1 1
FOXO1 0.017 0.035 -10000 0 -0.42 3 3
FOXO4 0.017 0.03 -10000 0 -0.42 2 2
heart looping -0.022 0.13 -10000 0 -0.5 20 20
CEBPB 0.008 0.041 -10000 0 -0.49 4 4
SMAD3/SMAD4/DLX1 -0.022 0.12 -10000 0 -0.35 23 23
MYOD1 -0.001 0.026 -10000 0 -0.46 2 2
SMAD3/SMAD4/HNF4 0.008 0.087 -10000 0 -0.37 19 19
SMAD3/SMAD4/GATA3 -0.026 0.14 -10000 0 -0.44 30 30
SnoN/SIN3/HDAC complex/NCoR1 0 0.08 -10000 0 -0.58 11 11
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.008 0.098 -10000 0 -0.42 8 8
SMAD3/SMAD4/SP1-3 0.026 0.087 -10000 0 -0.4 1 1
MED15 0.01 0.024 -10000 0 -0.58 1 1
SP1 0.008 0.044 -10000 0 -0.57 1 1
SIN3B 0.01 0.024 -10000 0 -0.58 1 1
SIN3A 0.01 0.024 -10000 0 -0.58 1 1
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.024 0.13 -10000 0 -0.41 20 20
ITGB5 0.028 0.076 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.036 0.028 -10000 0 -0.46 1 1
SMAD3/SMAD4/AR -0.027 0.13 -10000 0 -0.37 39 39
AR -0.051 0.16 -10000 0 -0.49 71 71
negative regulation of cell growth 0.02 0.08 -10000 0 -0.39 7 7
SMAD3/SMAD4/MYOD 0.005 0.073 -10000 0 -0.33 12 12
E2F5 -0.002 0.087 -10000 0 -0.58 13 13
E2F4 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.006 0.11 -10000 0 -0.38 17 17
SMAD2-3/SMAD4/FOXO1-3a-4 0.025 0.08 -10000 0 -0.34 17 17
TFDP1 0.011 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.011 0.11 -10000 0 -0.48 13 13
SMAD3/SMAD4/RUNX2 0.001 0.096 -10000 0 -0.38 18 18
TGIF2 0.006 0.054 -10000 0 -0.58 5 5
TGIF1 0.011 0 -10000 0 -10000 0 0
ATF2 0.009 0.034 -10000 0 -0.58 2 2
PLK2 and PLK4 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
PLK2 -0.003 0.084 -9999 0 -0.48 18 18
PLK4 0.009 0.034 -9999 0 -0.58 2 2
regulation of centriole replication 0.006 0.069 -9999 0 -0.36 19 19
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.011 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.013 0.073 -9999 0 -0.44 2 2
Syndecan-3/Neurocan 0.004 0.041 -9999 0 -0.6 1 1
POMC -0.026 0.14 -9999 0 -0.52 42 42
EGFR 0.004 0.063 -9999 0 -0.53 8 8
Syndecan-3/EGFR 0.016 0.042 -9999 0 -0.34 6 6
AGRP -0.001 0.05 -9999 0 -0.46 7 7
NCSTN 0.011 0 -9999 0 -10000 0 0
PSENEN 0.01 0.024 -9999 0 -0.58 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.006 0.054 -9999 0 -0.58 5 5
APH1A 0.011 0 -9999 0 -10000 0 0
NCAN -0.004 0.065 -9999 0 -0.46 12 12
long-term memory 0.022 0.041 -9999 0 -0.41 3 3
Syndecan-3/IL8 -0.041 0.12 -9999 0 -0.3 67 67
PSEN1 0.011 0 -9999 0 -10000 0 0
Src/Cortactin 0.016 0.018 -9999 0 -0.42 1 1
FYN 0.005 0.06 -9999 0 -0.55 7 7
limb bud formation -0.002 0.026 -9999 0 -0.62 1 1
MC4R -0.004 0.056 -9999 0 -0.46 9 9
SRC 0.01 0.024 -9999 0 -0.58 1 1
PTN -0.025 0.14 -9999 0 -0.54 39 39
FGFR/FGF/Syndecan-3 -0.002 0.026 -9999 0 -0.63 1 1
neuron projection morphogenesis -0.005 0.073 -9999 0 -0.53 1 1
Syndecan-3/AgRP 0.003 0.036 -9999 0 -0.6 1 1
Syndecan-3/AgRP/MC4R -0.004 0.044 -9999 0 -0.5 2 2
Fyn/Cortactin 0.012 0.044 -9999 0 -0.39 7 7
SDC3 -0.002 0.027 -9999 0 -0.64 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.041 0.12 -9999 0 -0.3 67 67
IL8 -0.11 0.22 -9999 0 -0.52 133 133
Syndecan-3/Fyn/Cortactin 0.023 0.042 -9999 0 -0.42 3 3
Syndecan-3/CASK -0.002 0.025 -9999 0 -0.6 1 1
alpha-MSH/MC4R -0.022 0.11 -9999 0 -0.38 48 48
Gamma Secretase 0.031 0.033 -9999 0 -0.29 6 6
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate -0.014 0.12 -9999 0 -0.46 27 27
PDGFB-D/PDGFRB/SLAP -0.012 0.11 -9999 0 -0.41 41 41
PDGFB-D/PDGFRB/APS/CBL -0.003 0.09 -9999 0 -0.31 45 45
AKT1 0.031 0.066 -9999 0 -0.48 3 3
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.015 0.13 -9999 0 -0.49 26 26
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
FGR -0.041 0.16 -9999 0 -0.59 37 37
mol:Ca2+ -0.005 0.11 -9999 0 -0.6 15 15
MYC 0 0.12 -9999 0 -0.56 17 17
SHC1 0.011 0 -9999 0 -10000 0 0
HRAS/GDP 0.017 0.066 -9999 0 -0.32 15 15
LRP1/PDGFRB/PDGFB 0.007 0.081 -9999 0 -0.4 19 19
GRB10 0.007 0.048 -9999 0 -0.58 4 4
PTPN11 0.006 0.054 -9999 0 -0.58 5 5
GO:0007205 -0.006 0.11 -9999 0 -0.61 15 15
PTEN 0.005 0.059 -9999 0 -0.58 6 6
GRB2 0.011 0 -9999 0 -10000 0 0
GRB7 0.002 0.066 -9999 0 -0.46 12 12
PDGFB-D/PDGFRB/SHP2 0.001 0.078 -9999 0 -0.4 22 22
PDGFB-D/PDGFRB/GRB10 0.002 0.076 -9999 0 -0.39 21 21
cell cycle arrest -0.012 0.11 -9999 0 -0.4 41 41
HRAS 0.008 0.041 -9999 0 -0.49 4 4
HIF1A 0.032 0.077 -9999 0 -0.5 7 7
GAB1 -0.016 0.13 -9999 0 -0.6 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.011 0.12 -9999 0 -0.54 18 18
PDGFB-D/PDGFRB 0.012 0.068 -9999 0 -0.35 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.005 0.068 -9999 0 -0.38 17 17
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.039 0.12 -9999 0 -0.48 27 27
positive regulation of MAPKKK cascade 0.001 0.078 -9999 0 -0.39 22 22
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
mol:IP3 -0.006 0.11 -9999 0 -0.61 15 15
E5 0 0.002 -9999 0 -10000 0 0
CSK 0.01 0.024 -9999 0 -0.58 1 1
PDGFB-D/PDGFRB/GRB7 -0.001 0.084 -9999 0 -0.37 28 28
SHB 0.011 0.019 -9999 0 -0.46 1 1
BLK -0.098 0.21 -9999 0 -0.56 88 88
PTPN2 0.008 0.042 -9999 0 -0.58 3 3
PDGFB-D/PDGFRB/SNX15 0.005 0.068 -9999 0 -0.38 17 17
BCAR1 0.008 0.044 -9999 0 -0.52 4 4
VAV2 -0.019 0.14 -9999 0 -0.6 23 23
CBL 0.011 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.004 0.07 -9999 0 -0.39 18 18
LCK -0.037 0.13 -9999 0 -0.5 37 37
PDGFRB -0.004 0.093 -9999 0 -0.54 17 17
ACP1 0.011 0 -9999 0 -10000 0 0
HCK -0.033 0.15 -9999 0 -0.57 35 35
ABL1 -0.016 0.12 -9999 0 -0.54 20 20
PDGFB-D/PDGFRB/CBL -0.018 0.14 -9999 0 -0.66 17 17
PTPN1 0.01 0.025 -9999 0 -0.59 1 1
SNX15 0.011 0 -9999 0 -10000 0 0
STAT3 0.011 0 -9999 0 -10000 0 0
STAT1 0.006 0.051 -9999 0 -0.5 6 6
cell proliferation 0.002 0.11 -9999 0 -0.49 18 18
SLA -0.013 0.11 -9999 0 -0.52 27 27
actin cytoskeleton reorganization 0.026 0.067 -9999 0 -0.5 3 3
SRC -0.012 0.068 -9999 0 -0.39 16 16
PI3K -0.013 0.059 -9999 0 -0.52 2 2
PDGFB-D/PDGFRB/GRB7/SHC 0.007 0.071 -9999 0 -0.31 28 28
SH2B2 -0.014 0.11 -9999 0 -0.52 29 29
PLCgamma1/SPHK1 -0.016 0.13 -9999 0 -0.51 26 26
LYN -0.01 0.065 -9999 0 -0.38 15 15
LRP1 0.006 0.057 -9999 0 -0.56 6 6
SOS1 0.01 0.024 -9999 0 -0.58 1 1
STAT5B 0.011 0 -9999 0 -10000 0 0
STAT5A 0.011 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.001 0.064 -9999 0 -0.54 2 2
SPHK1 -0.03 0.14 -9999 0 -0.51 47 47
EDG1 0 0.003 -9999 0 -10000 0 0
mol:DAG -0.006 0.11 -9999 0 -0.61 15 15
PLCG1 -0.006 0.12 -9999 0 -0.64 15 15
NHERF/PDGFRB 0.012 0.06 -9999 0 -0.33 16 16
YES1 -0.018 0.099 -9999 0 -0.5 19 19
cell migration 0.012 0.059 -9999 0 -0.33 16 16
SHC/Grb2/SOS1 0.002 0.054 -9999 0 -10000 0 0
SLC9A3R2 0.01 0.024 -9999 0 -0.58 1 1
SLC9A3R1 0.011 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.016 0.064 -9999 0 -0.32 18 18
FYN -0.015 0.087 -9999 0 -0.45 19 19
DOK1 0.015 0.06 -9999 0 -0.32 15 15
HRAS/GTP 0.006 0.03 -9999 0 -0.35 4 4
PDGFB 0.007 0.048 -9999 0 -0.51 5 5
RAC1 -0.009 0.14 -9999 0 -0.6 21 21
PRKCD 0.015 0.061 -9999 0 -0.33 15 15
FER 0.01 0.077 -9999 0 -0.36 19 19
MAPKKK cascade -0.009 0.049 -9999 0 -10000 0 0
RASA1 0.014 0.066 -9999 0 -0.35 16 16
NCK1 0.009 0.034 -9999 0 -0.58 2 2
NCK2 0.01 0.024 -9999 0 -0.58 1 1
p62DOK/Csk 0.021 0.057 -9999 0 -0.29 3 3
PDGFB-D/PDGFRB/SHB 0.005 0.069 -9999 0 -0.38 18 18
chemotaxis -0.016 0.12 -9999 0 -0.52 20 20
STAT1-3-5/STAT1-3-5 -0.01 0.053 -9999 0 -0.55 1 1
Bovine Papilomavirus E5/PDGFRB -0.003 0.068 -9999 0 -0.4 17 17
PTPRJ 0.01 0.024 -9999 0 -0.58 1 1
Regulation of Androgen receptor activity

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
HDAC1 0.016 0.018 -9999 0 -0.43 1 1
SMARCC1 0.002 0.019 -9999 0 -10000 0 0
REL 0.011 0.043 -9999 0 -0.58 3 3
HDAC7 0.027 0.093 -9999 0 -0.51 8 8
JUN 0.004 0.052 -9999 0 -0.56 5 5
EP300 0.007 0.048 -9999 0 -0.58 4 4
KAT2B -0.006 0.099 -9999 0 -0.58 17 17
KAT5 0.011 0.024 -9999 0 -0.58 1 1
MAPK14 0.011 0.06 -9999 0 -0.44 10 10
FOXO1 0.009 0.034 -9999 0 -0.58 2 2
T-DHT/AR 0.024 0.098 -9999 0 -0.52 9 9
MAP2K6 0.001 0.078 -9999 0 -0.59 10 10
BRM/BAF57 0.009 0.041 -9999 0 -0.43 5 5
MAP2K4 0.008 0.042 -9999 0 -0.58 3 3
SMARCA2 0.005 0.049 -9999 0 -0.59 4 4
PDE9A -0.082 0.29 -9999 0 -1.1 44 44
NCOA2 0.003 0.067 -9999 0 -0.56 8 8
CEBPA -0.005 0.098 -9999 0 -0.57 17 17
EHMT2 0.007 0.031 -9999 0 -0.52 2 2
cell proliferation 0.022 0.12 -9999 0 -0.48 18 18
NR0B1 -0.001 0.05 -9999 0 -0.46 7 7
EGR1 -0.011 0.1 -9999 0 -0.5 24 24
RXRs/9cRA 0.004 0.054 -9999 0 -0.24 26 26
AR/RACK1/Src 0.016 0.075 -9999 0 -0.4 9 9
AR/GR -0.01 0.1 -9999 0 -0.35 32 32
GNB2L1 0.011 0.019 -9999 0 -0.46 1 1
PKN1 0.008 0.042 -9999 0 -0.58 3 3
RCHY1 0.01 0.024 -9999 0 -0.58 1 1
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.016 0.037 -9999 0 -0.42 4 4
T-DHT/AR/TIF2/CARM1 0.02 0.085 -9999 0 -0.43 11 11
SRC 0.024 0.06 -9999 0 -0.35 12 12
NR3C1 -0.014 0.12 -9999 0 -0.54 28 28
KLK3 -0.2 0.37 -9999 0 -1 80 80
APPBP2 0.008 0.049 -9999 0 -0.58 4 4
TRIM24 0.009 0.006 -9999 0 -10000 0 0
T-DHT/AR/TIP60 0.018 0.077 -9999 0 -0.43 11 11
TMPRSS2 -0.025 0.14 -9999 0 -0.88 9 9
RXRG -0.013 0.094 -9999 0 -0.46 25 25
mol:9cRA -0.001 0.002 -9999 0 -10000 0 0
RXRA 0.01 0.024 -9999 0 -0.58 1 1
RXRB 0.011 0.001 -9999 0 -10000 0 0
CARM1 0.01 0.024 -9999 0 -0.58 1 1
NR2C2 0.01 0.024 -9999 0 -0.58 1 1
KLK2 0.016 0.1 -9999 0 -0.55 5 5
AR 0 0.083 -9999 0 -0.29 30 30
SENP1 0.01 0.024 -9999 0 -0.58 1 1
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
MDM2 0.012 0.045 -9999 0 -0.52 4 4
SRY 0.002 0.038 -9999 0 -0.45 4 4
GATA2 -0.018 0.13 -9999 0 -0.56 31 31
MYST2 0.011 0.024 -9999 0 -0.58 1 1
HOXB13 -0.097 0.21 -9999 0 -0.5 123 123
T-DHT/AR/RACK1/Src 0.022 0.073 -9999 0 -0.42 8 8
positive regulation of transcription -0.018 0.13 -9999 0 -0.56 31 31
DNAJA1 0.012 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.041 -9999 0 -0.47 3 3
NCOA1 0.011 0.027 -9999 0 -0.62 1 1
SPDEF -0.15 0.25 -9999 0 -0.53 179 179
T-DHT/AR/TIF2 0.014 0.11 -9999 0 -0.68 7 7
T-DHT/AR/Hsp90 0.017 0.074 -9999 0 -0.43 10 10
GSK3B 0.009 0.034 -9999 0 -0.58 2 2
NR2C1 0.011 0.024 -9999 0 -0.58 1 1
mol:T-DHT 0.02 0.063 -9999 0 -0.37 13 13
SIRT1 0.006 0.054 -9999 0 -0.58 5 5
ZMIZ2 0.015 0.027 -9999 0 -0.58 1 1
POU2F1 0.01 0.077 -9999 0 -0.54 10 10
T-DHT/AR/DAX-1 0.009 0.075 -9999 0 -0.42 10 10
CREBBP 0.011 0.001 -9999 0 -10000 0 0
SMARCE1 0.008 0.025 -9999 0 -0.58 1 1
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0.046 -10000 0 -0.34 10 10
MAP4K4 0.019 0.065 -10000 0 -0.51 2 2
BAG4 0.009 0.034 -10000 0 -0.58 2 2
PKC zeta/ceramide -0.023 0.041 0.15 1 -0.2 2 3
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.12 -10000 0 -0.52 30 30
BAX -0.009 0.023 -10000 0 -0.31 1 1
RIPK1 0.011 0 -10000 0 -10000 0 0
AKT1 0.018 0.023 -10000 0 -0.51 1 1
BAD -0.024 0.041 0.16 1 -0.2 2 3
SMPD1 0.012 0.046 -10000 0 -0.2 22 22
RB1 -0.034 0.067 0.16 2 -0.32 20 22
FADD/Caspase 8 0.028 0.062 -10000 0 -0.5 1 1
MAP2K4 -0.021 0.052 -10000 0 -0.31 9 9
NSMAF 0.011 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.018 0.041 -10000 0 -0.31 2 2
EGF -0.18 0.25 -10000 0 -0.51 216 216
mol:ceramide -0.032 0.043 0.16 2 -10000 0 2
MADD 0.011 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.014 0.038 -10000 0 -0.33 7 7
ASAH1 0.011 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.034 0.066 0.16 2 -0.32 20 22
cell proliferation -0.036 0.09 -10000 0 -0.26 57 57
BID 0.009 0.047 -10000 0 -0.33 2 2
MAP3K1 -0.026 0.05 0.16 2 -0.33 6 8
EIF2A -0.021 0.063 -10000 0 -0.32 17 17
TRADD 0.011 0 -10000 0 -10000 0 0
CRADD 0.01 0.024 -10000 0 -0.58 1 1
MAPK3 -0.009 0.039 -10000 0 -0.28 2 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.009 0.039 -10000 0 -0.28 2 2
Cathepsin D/ceramide -0.024 0.041 0.15 1 -0.23 2 3
FADD 0.02 0.062 -10000 0 -0.52 1 1
KSR1 -0.024 0.044 0.16 2 -0.33 2 4
MAPK8 -0.016 0.045 -10000 0 -0.26 5 5
PRKRA -0.024 0.04 0.16 2 -0.2 1 3
PDGFA 0.006 0.052 -10000 0 -0.47 7 7
TRAF2 0.01 0.024 -10000 0 -0.58 1 1
IGF1 -0.073 0.2 -10000 0 -0.52 94 94
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.032 0.042 0.16 2 -10000 0 2
CTSD 0.009 0.036 -10000 0 -0.5 3 3
regulation of nitric oxide biosynthetic process 0.016 0.018 -10000 0 -0.42 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.037 0.096 -10000 0 -0.28 57 57
PRKCD 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.031 -10000 0 -0.52 2 2
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.014 0.038 -10000 0 -0.33 7 7
RelA/NF kappa B1 0.016 0.018 -10000 0 -0.42 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.01 0.024 -10000 0 -0.58 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.015 0.066 -10000 0 -0.56 1 1
TNFR1A/BAG4/TNF-alpha 0.004 0.08 -10000 0 -0.33 32 32
mol:Sphingosine-1-phosphate 0.012 0.046 -10000 0 -0.34 10 10
MAP2K1 -0.012 0.041 -10000 0 -0.29 3 3
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.011 0 -10000 0 -10000 0 0
CYCS -0.016 0.049 0.16 8 -0.23 13 21
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
TNFR1A/BAG4 0.015 0.025 -10000 0 -0.42 2 2
EIF2AK2 -0.026 0.061 -10000 0 -0.31 17 17
TNF-alpha/TNFR1A/FAN 0.006 0.077 -10000 0 -0.35 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.023 0.047 -10000 0 -0.38 3 3
MAP2K2 -0.012 0.039 -10000 0 -0.29 2 2
SMPD3 0.006 0.071 -10000 0 -0.35 14 14
TNF -0.017 0.12 -10000 0 -0.54 30 30
PKC zeta/PAR4 0.015 0.029 -10000 0 -0.39 3 3
mol:PHOSPHOCHOLINE 0.058 0.094 0.23 88 -10000 0 88
NF kappa B1/RelA/I kappa B alpha 0.032 0.029 -10000 0 -0.52 1 1
AIFM1 -0.01 0.038 0.16 8 -0.26 1 9
BCL2 -0.008 0.1 -10000 0 -0.55 20 20
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.006 0.087 0.46 7 -10000 0 7
GNAI2 0.011 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.009 0.048 -10000 0 -0.32 12 12
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.046 0.16 -10000 0 -0.49 68 68
RhoA/GTP -0.005 0.089 -10000 0 -0.47 7 7
negative regulation of cAMP metabolic process -0.011 0.096 -10000 0 -0.3 29 29
GNAZ -0.012 0.11 -10000 0 -0.55 25 25
GNAI3 0.011 0 -10000 0 -10000 0 0
GNA12 0.011 0 -10000 0 -10000 0 0
S1PR5 0 0.076 -10000 0 -0.53 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.012 0.096 -10000 0 -0.31 29 29
RhoA/GDP 0.008 0.018 -10000 0 -0.43 1 1
RHOA 0.01 0.024 -10000 0 -0.58 1 1
GNAI1 -0.003 0.089 -10000 0 -0.56 15 15
Paxillin-dependent events mediated by a4b1

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
CRKL 0.011 0 -10000 0 -10000 0 0
Rac1/GDP 0.003 0.011 -10000 0 -10000 0 0
DOCK1 0.01 0.024 -10000 0 -0.58 1 1
ITGA4 -0.018 0.13 -10000 0 -0.56 30 30
RAC1 0.011 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.022 0.13 -10000 0 -0.43 52 52
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0.019 -10000 0 -0.46 1 1
alpha4/beta1 Integrin 0.005 0.08 -10000 0 -0.34 30 30
alpha4/beta7 Integrin/Paxillin -0.003 0.1 -10000 0 -0.36 38 38
lamellipodium assembly -0.003 0.051 -10000 0 -0.5 5 5
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
PI3K 0.013 0.04 -10000 0 -0.42 5 5
ARF6 0.01 0.024 -10000 0 -0.58 1 1
TLN1 0.01 0.024 -10000 0 -0.58 1 1
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
ARF6/GTP -0.014 0.058 -10000 0 -10000 0 0
cell adhesion 0.017 0.069 -10000 0 -0.29 27 27
CRKL/CBL 0.017 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.011 0.073 -10000 0 -0.32 26 26
ITGB1 0.011 0 -10000 0 -10000 0 0
ITGB7 -0.014 0.12 -10000 0 -0.53 28 28
ARF6/GDP 0.002 0.026 -10000 0 -0.57 1 1
alpha4/beta1 Integrin/Paxillin/VCAM1 0.002 0.12 -10000 0 -0.4 38 38
p130Cas/Crk/Dock1 0.02 0.037 -10000 0 -0.36 5 5
VCAM1 -0.02 0.13 -10000 0 -0.53 35 35
alpha4/beta1 Integrin/Paxillin/Talin 0.018 0.07 -10000 0 -0.29 27 27
alpha4/beta1 Integrin/Paxillin/GIT1 0.018 0.07 -10000 0 -0.29 27 27
BCAR1 0.008 0.044 -10000 0 -0.52 4 4
mol:GDP -0.017 0.069 0.29 27 -10000 0 27
CBL 0.011 0 -10000 0 -10000 0 0
PRKACA 0.011 0 -10000 0 -10000 0 0
GIT1 0.01 0.024 -10000 0 -0.58 1 1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.018 0.07 -10000 0 -0.29 27 27
Rac1/GTP -0.004 0.058 -10000 0 -0.56 5 5
IL2 signaling events mediated by PI3K

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
BCL2L1 0.014 0.1 -10000 0 -0.52 12 12
UGCG 0.01 0.069 -10000 0 -0.84 3 3
AKT1/mTOR/p70S6K/Hsp90/TERT 0.01 0.13 -10000 0 -0.4 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.01 0.068 -10000 0 -0.82 3 3
mol:DAG -0.001 0.009 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.039 0.11 -10000 0 -0.44 31 31
FRAP1 0.017 0.15 -10000 0 -0.51 32 32
FOXO3 0.024 0.13 -10000 0 -0.47 22 22
AKT1 0.018 0.14 -10000 0 -0.48 28 28
GAB2 0.01 0.034 -10000 0 -0.58 2 2
SMPD1 0.013 0.038 -10000 0 -0.6 1 1
SGMS1 0.014 0.028 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.035 -10000 0 -0.36 5 5
CALM1 0.011 0 -10000 0 -10000 0 0
cell proliferation 0.019 0.081 -10000 0 -0.54 4 4
EIF3A 0.01 0.024 -10000 0 -0.58 1 1
PI3K 0.018 0.041 -10000 0 -0.42 5 5
RPS6KB1 0.008 0.096 -10000 0 -0.96 5 5
mol:sphingomyelin -0.001 0.009 -10000 0 -10000 0 0
natural killer cell activation 0 0.001 -10000 0 -0.012 4 4
JAK3 0.003 0.077 -10000 0 -0.53 12 12
PIK3R1 0.011 0.042 -10000 0 -0.58 3 3
JAK1 0.011 0.042 -10000 0 -0.58 3 3
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
MYC 0.021 0.15 -10000 0 -0.65 14 14
MYB 0.006 0.16 -10000 0 -1.2 10 10
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.012 0.14 -10000 0 -0.42 38 38
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.018 0.092 -10000 0 -0.87 5 5
mol:PI-3-4-5-P3 0.012 0.13 -10000 0 -0.41 38 38
Rac1/GDP 0.02 0.032 -10000 0 -0.32 5 5
T cell proliferation 0.017 0.13 -10000 0 -0.44 24 24
SHC1 0.012 0.002 -10000 0 -10000 0 0
RAC1 0.011 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.009 -10000 0 -0.065 9 9
PRKCZ 0.016 0.13 -10000 0 -0.46 24 24
NF kappa B1 p50/RelA -0.038 0.11 -10000 0 -0.46 28 28
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.007 0.11 -10000 0 -0.5 18 18
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
RELA 0.011 0 -10000 0 -10000 0 0
IL2RA -0.044 0.17 -10000 0 -0.55 60 60
IL2RB -0.015 0.12 -10000 0 -0.55 30 30
TERT -0.047 0.17 -10000 0 -0.52 66 66
E2F1 0.014 0.065 -10000 0 -0.42 12 12
SOS1 0.011 0.024 -10000 0 -0.58 1 1
RPS6 0.007 0.045 -10000 0 -0.48 5 5
mol:cAMP -0.002 0.004 0.031 9 -10000 0 9
PTPN11 0.007 0.054 -10000 0 -0.58 5 5
IL2RG 0.001 0.084 -10000 0 -0.56 13 13
actin cytoskeleton organization 0.017 0.13 -10000 0 -0.44 24 24
GRB2 0.012 0.002 -10000 0 -10000 0 0
IL2 0.004 0.027 -10000 0 -0.45 2 2
PIK3CA 0.012 0.034 -10000 0 -0.58 2 2
Rac1/GTP 0.027 0.031 -10000 0 -0.3 5 5
LCK -0.028 0.14 -10000 0 -0.51 48 48
BCL2 0.014 0.18 -10000 0 -0.82 19 19
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.001 0.083 0.58 12 -10000 0 12
PI3K Class IB/PDE3B -0.001 0.083 -10000 0 -0.58 12 12
PDE3B -0.001 0.083 -10000 0 -0.58 12 12
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.022 0.022 -9999 0 -0.35 2 2
SNTA1 0.006 0.055 -9999 0 -0.54 6 6
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.013 0.066 -9999 0 -0.38 16 16
MAPK12 -0.003 0.093 -9999 0 -0.37 23 23
CCND1 0.006 0.042 -9999 0 -0.42 1 1
p38 gamma/SNTA1 0 0.094 -9999 0 -0.37 22 22
MAP2K3 0.01 0.024 -9999 0 -0.58 1 1
PKN1 0.008 0.042 -9999 0 -0.58 3 3
G2/M transition checkpoint -0.003 0.093 -9999 0 -0.36 23 23
MAP2K6 0.009 0.059 -9999 0 -0.32 18 18
MAPT -0.024 0.11 -9999 0 -0.33 52 52
MAPK13 0.017 0.025 -9999 0 -0.42 2 2
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.009 0.042 -9999 0 -0.35 8 8
S1P3 pathway

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
PDGFRB -0.004 0.092 -9999 0 -0.54 17 17
mol:S1P 0 0.005 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.009 0.089 -9999 0 -0.29 36 36
GNAO1 -0.046 0.16 -9999 0 -0.49 68 68
S1P/S1P3/G12/G13 0.018 0.041 -9999 0 -0.31 9 9
AKT1 0 0.097 -9999 0 -0.57 12 12
AKT3 -0.012 0.2 -9999 0 -1.1 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.004 0.092 -9999 0 -0.54 17 17
GNAI2 0.012 0.004 -9999 0 -10000 0 0
GNAI3 0.012 0.004 -9999 0 -10000 0 0
GNAI1 -0.002 0.09 -9999 0 -0.56 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.006 0.06 -9999 0 -0.54 7 7
S1PR2 0.011 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.11 -9999 0 -0.43 18 18
MAPK3 -0.003 0.11 -9999 0 -0.49 13 13
MAPK1 -0.003 0.11 -9999 0 -0.49 13 13
JAK2 -0.011 0.13 -9999 0 -0.46 25 25
CXCR4 -0.016 0.13 -9999 0 -0.48 26 26
FLT1 0.008 0.053 -9999 0 -0.56 5 5
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
Rac1/GDP 0.008 0 -9999 0 -10000 0 0
SRC -0.003 0.11 -9999 0 -0.48 13 13
S1P/S1P3/Gi -0.009 0.11 -9999 0 -0.44 18 18
RAC1 0.011 0 -9999 0 -10000 0 0
RhoA/GTP -0.004 0.1 -9999 0 -0.46 13 13
VEGFA 0.012 0.02 -9999 0 -0.45 1 1
S1P/S1P2/Gi -0.006 0.091 -9999 0 -0.32 21 21
VEGFR1 homodimer/VEGFA homodimer 0.018 0.043 -9999 0 -0.39 6 6
RHOA 0.01 0.024 -9999 0 -0.58 1 1
S1P/S1P3/Gq 0.001 0.097 -9999 0 -0.34 36 36
GNAQ 0.005 0.059 -9999 0 -0.58 6 6
GNAZ -0.012 0.11 -9999 0 -0.55 25 25
G12/G13 0.015 0.025 -9999 0 -0.42 2 2
GNA14 -0.007 0.1 -9999 0 -0.56 19 19
GNA15 -0.008 0.1 -9999 0 -0.54 21 21
GNA12 0.011 0 -9999 0 -10000 0 0
GNA13 0.009 0.034 -9999 0 -0.58 2 2
GNA11 0.007 0.05 -9999 0 -0.53 5 5
Rac1/GTP -0.003 0.1 -9999 0 -0.48 12 12
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.023 0.047 -10000 0 -0.37 6 6
HDAC3 0.011 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.013 0.075 -10000 0 -0.4 19 19
GATA1/HDAC4 0.005 0.055 -10000 0 -0.32 16 16
GATA1/HDAC5 0.004 0.058 -10000 0 -0.33 17 17
GATA2/HDAC5 -0.006 0.098 -10000 0 -0.41 32 32
HDAC5/BCL6/BCoR 0.02 0.03 -10000 0 -0.28 6 6
HDAC9 -0.038 0.16 -10000 0 -0.54 53 53
Glucocorticoid receptor/Hsp90/HDAC6 0.006 0.075 -10000 0 -0.32 29 29
HDAC4/ANKRA2 0.016 0.023 -10000 0 -0.37 2 2
HDAC5/YWHAB 0.016 0.023 -10000 0 -0.37 2 2
NPC/RanGAP1/SUMO1/Ubc9 -0.001 0.095 -10000 0 -0.43 24 24
GATA2 -0.018 0.13 -10000 0 -0.56 31 31
HDAC4/RFXANK 0.014 0.032 -10000 0 -0.37 4 4
BCOR 0.011 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.008 0.046 -10000 0 -0.55 4 4
HDAC5 0.01 0.031 -10000 0 -0.52 2 2
GNB1/GNG2 0.012 0.046 -10000 0 -0.38 8 8
Histones 0.011 0.081 -10000 0 -1.2 1 1
ADRBK1 0.01 0.031 -10000 0 -0.52 2 2
HDAC4 0.011 0.019 -10000 0 -0.46 1 1
XPO1 0 0.08 -10000 0 -0.58 11 11
HDAC5/ANKRA2 0.015 0.029 -10000 0 -0.39 3 3
HDAC4/Ubc9 0.016 0.014 -10000 0 -0.32 1 1
HDAC7 0.01 0.024 -10000 0 -0.58 1 1
HDAC5/14-3-3 E 0.016 0.023 -10000 0 -0.37 2 2
TUBA1B 0.011 0 -10000 0 -10000 0 0
HDAC6 0.011 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.014 0.042 -10000 0 -0.46 4 4
CAMK4 -0.012 0.11 -10000 0 -0.55 25 25
Tubulin/HDAC6 0.004 0.075 -10000 0 -0.29 36 36
SUMO1 -0.008 0.1 -10000 0 -0.58 19 19
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.011 0 -10000 0 -10000 0 0
GATA1 -0.005 0.074 -10000 0 -0.46 15 15
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.011 0 -10000 0 -10000 0 0
NR3C1 -0.014 0.12 -10000 0 -0.54 28 28
SUMO1/HDAC4 0.005 0.1 -10000 0 -0.55 19 19
SRF 0.01 0.027 -10000 0 -0.46 2 2
HDAC4/YWHAB 0.016 0.014 -10000 0 -0.32 1 1
Tubulin -0.005 0.088 -10000 0 -0.35 36 36
HDAC4/14-3-3 E 0.016 0.014 -10000 0 -0.32 1 1
GNB1 0.011 0 -10000 0 -10000 0 0
RANGAP1 0.01 0.031 -10000 0 -0.52 2 2
BCL6/BCoR 0.015 0.027 -10000 0 -0.32 4 4
HDAC4/HDAC3/SMRT (N-CoR2) 0.02 0.031 -10000 0 -0.32 5 5
HDAC4/SRF 0.007 0.075 -10000 0 -0.37 18 18
HDAC4/ER alpha -0.016 0.11 -10000 0 -0.37 50 50
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.011 0.08 -10000 0 -1.2 1 1
cell motility 0.004 0.075 -10000 0 -0.29 36 36
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.011 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.016 0.018 -10000 0 -0.42 1 1
BCL6 0.008 0.038 -10000 0 -0.46 4 4
HDAC4/CaMK II delta B 0.011 0.019 -10000 0 -0.46 1 1
Hsp90/HDAC6 0.016 0.018 -10000 0 -0.42 1 1
ESR1 -0.033 0.15 -10000 0 -0.52 49 49
HDAC6/HDAC11 0.015 0.025 -10000 0 -0.42 2 2
Ran/GTP/Exportin 1 0.006 0.12 -10000 0 -0.68 15 15
NPC -0.003 0.056 -10000 0 -0.31 19 19
MEF2C 0 0.076 -10000 0 -0.53 12 12
RAN 0.011 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0.026 0.049 -10000 0 -0.29 10 10
GNG2 0.004 0.063 -10000 0 -0.53 8 8
NCOR2 0.008 0.046 -10000 0 -0.55 4 4
TUBB2A -0.019 0.12 -10000 0 -0.49 36 36
HDAC11 0.009 0.034 -10000 0 -0.58 2 2
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
RANBP2 -0.007 0.1 -10000 0 -0.57 19 19
ANKRA2 0.01 0.024 -10000 0 -0.58 1 1
RFXANK 0.009 0.039 -10000 0 -0.54 3 3
nuclear import -0.023 0.018 0.32 1 -10000 0 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.011 0 -9999 0 -10000 0 0
HDAC2 0.011 0.001 -9999 0 -10000 0 0
GNB1/GNG2 0.002 0.088 -9999 0 -0.36 28 28
forebrain development -0.003 0.15 -9999 0 -0.51 33 33
GNAO1 -0.046 0.16 -9999 0 -0.49 68 68
SMO/beta Arrestin2 -0.001 0.091 -9999 0 -0.4 29 29
SMO -0.015 0.12 -9999 0 -0.56 29 29
ARRB2 0.012 0.002 -9999 0 -10000 0 0
GLI3/SPOP 0.014 0.099 -9999 0 -0.67 5 5
mol:GTP 0 0.001 -9999 0 -10000 0 0
GSK3B 0.009 0.034 -9999 0 -0.58 2 2
GNAI2 0.012 0.002 -9999 0 -10000 0 0
SIN3/HDAC complex 0.026 0.03 -9999 0 -0.32 4 4
GNAI1 -0.003 0.089 -9999 0 -0.56 15 15
XPO1 0.003 0.08 -9999 0 -0.58 11 11
GLI1/Su(fu) -0.038 0.13 -9999 0 -0.63 14 14
SAP30 0.009 0.034 -9999 0 -0.58 2 2
mol:GDP -0.015 0.12 -9999 0 -0.55 29 29
MIM/GLI2A 0.002 0.092 -9999 0 -0.55 16 16
IFT88 0.007 0.048 -9999 0 -0.58 4 4
GNAI3 0.012 0.002 -9999 0 -10000 0 0
GLI2 0.023 0.06 -9999 0 -0.57 2 2
GLI3 0.008 0.1 -9999 0 -0.32 38 38
CSNK1D 0.011 0 -9999 0 -10000 0 0
CSNK1E 0.011 0 -9999 0 -10000 0 0
SAP18 0.01 0.019 -9999 0 -0.46 1 1
embryonic digit morphogenesis 0.007 0.048 -9999 0 -0.58 4 4
GNG2 0.004 0.063 -9999 0 -0.53 8 8
Gi family/GTP -0.017 0.11 -9999 0 -0.48 16 16
SIN3B 0.01 0.024 -9999 0 -0.58 1 1
SIN3A 0.01 0.024 -9999 0 -0.58 1 1
GLI3/Su(fu) 0.025 0.082 -9999 0 -0.55 5 5
GLI2/Su(fu) 0.03 0.068 -9999 0 -0.4 4 4
FOXA2 -0.037 0.18 -9999 0 -0.95 22 22
neural tube patterning -0.003 0.15 -9999 0 -0.51 33 33
SPOP 0.011 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.019 0.043 -9999 0 -10000 0 0
GNB1 0.011 0 -9999 0 -10000 0 0
CSNK1G2 0.009 0.034 -9999 0 -0.58 2 2
CSNK1G3 0.01 0.024 -9999 0 -0.58 1 1
MTSS1 0.001 0.093 -9999 0 -0.55 16 16
embryonic limb morphogenesis -0.003 0.15 -9999 0 -0.51 33 33
SUFU 0.014 0.048 -9999 0 -10000 0 0
LGALS3 0.009 0.036 -9999 0 -0.5 3 3
catabolic process 0.026 0.11 -9999 0 -0.41 20 20
GLI3A/CBP 0.006 0.066 -9999 0 -0.35 18 18
KIF3A 0 0.08 -9999 0 -0.58 11 11
GLI1 -0.004 0.15 -9999 0 -0.52 33 33
RAB23 0.006 0.055 -9999 0 -0.54 6 6
CSNK1A1 0.009 0.034 -9999 0 -0.58 2 2
IFT172 0.011 0 -9999 0 -10000 0 0
RBBP7 0.01 0.024 -9999 0 -0.58 1 1
Su(fu)/Galectin3 0.017 0.049 -9999 0 -0.37 2 2
GNAZ -0.012 0.11 -9999 0 -0.55 25 25
RBBP4 0.01 0.024 -9999 0 -0.58 1 1
CSNK1G1 0.01 0.024 -9999 0 -0.58 1 1
PIAS1 0.011 0 -9999 0 -10000 0 0
PRKACA 0.011 0 -9999 0 -10000 0 0
GLI2/SPOP 0.027 0.056 -9999 0 -0.54 2 2
STK36 0.014 0.003 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.009 0.1 -9999 0 -0.44 15 15
PTCH1 -0.003 0.17 -9999 0 -0.97 11 11
MIM/GLI1 -0.001 0.17 -9999 0 -0.59 30 30
CREBBP 0.006 0.066 -9999 0 -0.35 18 18
Su(fu)/SIN3/HDAC complex 0.035 0.027 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.011 0 -10000 0 -10000 0 0
NFATC1 0.031 0.061 -10000 0 -0.33 2 2
NFATC2 0.016 0.056 -10000 0 -0.38 4 4
NFATC3 0.018 0.02 -10000 0 -0.41 1 1
YWHAE 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.056 0.14 -10000 0 -0.47 37 37
Exportin 1/Ran/NUP214 0.015 0.051 -10000 0 -0.35 11 11
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.069 0.13 -10000 0 -0.47 40 40
BCL2/BAX 0.002 0.077 -10000 0 -0.4 21 21
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.004 -10000 0 -10000 0 0
CaM/Ca2+ 0.009 0.004 -10000 0 -10000 0 0
BAX 0.01 0.024 -10000 0 -0.58 1 1
MAPK14 0.011 0.003 -10000 0 -10000 0 0
BAD 0.01 0.031 -10000 0 -0.52 2 2
CABIN1/MEF2D -0.048 0.14 -10000 0 -0.45 38 38
Calcineurin A alpha-beta B1/BCL2 -0.008 0.1 -10000 0 -0.55 20 20
FKBP8 0.009 0.034 -10000 0 -0.58 2 2
activation-induced cell death of T cells 0.048 0.13 0.44 38 -10000 0 38
KPNB1 0.011 0 -10000 0 -10000 0 0
KPNA2 0.011 0 -10000 0 -10000 0 0
XPO1 0 0.08 -10000 0 -0.58 11 11
SFN 0.005 0.056 -10000 0 -0.47 8 8
MAP3K8 0.009 0.031 -10000 0 -0.52 2 2
NFAT4/CK1 alpha 0.022 0.046 -10000 0 -0.58 2 2
MEF2D/NFAT1/Cbp/p300 0.026 0.093 -10000 0 -0.42 12 12
CABIN1 -0.057 0.14 -10000 0 -0.48 37 37
CALM1 0.011 0.002 -10000 0 -10000 0 0
RAN 0.011 0 -10000 0 -10000 0 0
MAP3K1 0.005 0.059 -10000 0 -0.58 6 6
CAMK4 -0.012 0.11 -10000 0 -0.55 25 25
mol:Ca2+ 0 0.003 -10000 0 -10000 0 0
MAPK3 0.01 0.024 -10000 0 -0.58 1 1
YWHAH 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.007 0.094 -10000 0 -0.38 36 36
YWHAB 0.011 0 -10000 0 -10000 0 0
MAPK8 0.01 0.024 -10000 0 -0.58 1 1
MAPK9 0.011 0 -10000 0 -10000 0 0
YWHAG 0.011 0 -10000 0 -10000 0 0
FKBP1A 0.011 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.041 0.06 -10000 0 -0.38 1 1
PRKCH 0.005 0.059 -10000 0 -0.58 6 6
CABIN1/Cbp/p300 0.014 0.036 -10000 0 -0.42 4 4
CASP3 0.009 0.034 -10000 0 -0.58 2 2
PIM1 0.011 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.008 0.002 -10000 0 -10000 0 0
apoptosis -0.005 0.037 0.23 1 -0.65 1 2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.032 0.03 -10000 0 -0.38 2 2
PRKCB -0.041 0.16 -10000 0 -0.54 56 56
PRKCE 0.011 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.023 0.018 -10000 0 -0.37 1 1
BAD/BCL-XL 0.016 0.023 -10000 0 -0.37 2 2
PRKCD 0.011 0 -10000 0 -10000 0 0
NUP214 0.011 0 -10000 0 -10000 0 0
PRKCZ 0.009 0.031 -10000 0 -0.52 2 2
PRKCA 0.01 0.031 -10000 0 -0.52 2 2
PRKCG -0.15 0.24 -10000 0 -0.51 182 182
PRKCQ -0.045 0.17 -10000 0 -0.58 57 57
FKBP38/BCL2 0.002 0.079 -10000 0 -0.4 22 22
EP300 0.007 0.048 -10000 0 -0.58 4 4
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.011 0 -10000 0 -10000 0 0
NFATc/JNK1 0.034 0.061 -10000 0 -0.36 1 1
CaM/Ca2+/FKBP38 0.014 0.022 -10000 0 -0.36 2 2
FKBP12/FK506 0.008 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.022 -10000 0 -0.36 2 2
CaM/Ca2+/CAMK IV 0.001 0.071 -10000 0 -0.33 25 25
NFATc/ERK1 0.035 0.059 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.069 0.13 -10000 0 -0.47 39 39
NR4A1 0.017 0.12 -10000 0 -0.42 39 39
GSK3B 0.009 0.034 -10000 0 -0.58 2 2
positive T cell selection 0.018 0.02 -10000 0 -0.41 1 1
NFAT1/CK1 alpha -0.011 0.044 -10000 0 -0.48 3 3
RCH1/ KPNB1 0.017 0 -10000 0 -10000 0 0
YWHAQ 0.011 0 -10000 0 -10000 0 0
PRKACA 0.011 0.003 -10000 0 -10000 0 0
AKAP5 -0.021 0.13 -10000 0 -0.52 36 36
MEF2D 0.01 0.025 -10000 0 -0.59 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.008 0.042 -10000 0 -0.58 3 3
NFATc/p38 alpha 0.034 0.059 -10000 0 -10000 0 0
CREBBP 0.011 0.002 -10000 0 -10000 0 0
BCL2 -0.008 0.1 -10000 0 -0.55 20 20
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.009 0.034 -9999 0 -0.58 2 2
Caspase 8 (4 units) 0.006 0.086 -9999 0 -0.48 6 6
NEF -0.013 0.05 -9999 0 -10000 0 0
NFKBIA 0.009 0.023 -9999 0 -10000 0 0
BIRC3 0.007 0.12 -9999 0 -0.52 30 30
CYCS -0.001 0.11 -9999 0 -0.51 10 10
RIPK1 0.011 0 -9999 0 -10000 0 0
CD247 -0.035 0.16 -9999 0 -0.64 33 33
MAP2K7 0.013 0.083 -9999 0 -0.44 7 7
protein ubiquitination 0.038 0.057 -9999 0 -0.4 3 3
CRADD 0.01 0.024 -9999 0 -0.58 1 1
DAXX 0.011 0 -9999 0 -10000 0 0
FAS 0.002 0.073 -9999 0 -0.56 10 10
BID 0.001 0.097 -9999 0 -0.5 6 6
NF-kappa-B/RelA/I kappa B alpha 0.017 0.065 -9999 0 -0.34 1 1
TRADD 0.011 0 -9999 0 -10000 0 0
MAP3K5 0.009 0.034 -9999 0 -0.58 2 2
CFLAR 0.011 0 -9999 0 -10000 0 0
FADD 0.011 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.017 0.065 -9999 0 -0.34 1 1
MAPK8 0.018 0.082 -9999 0 -0.51 5 5
APAF1 0.008 0.042 -9999 0 -0.58 3 3
TRAF1 0.008 0.038 -9999 0 -0.46 4 4
TRAF2 0.01 0.024 -9999 0 -0.58 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.005 0.1 -9999 0 -0.3 47 47
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.032 0.057 -9999 0 -10000 0 0
CHUK 0.039 0.061 -9999 0 -0.43 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.027 0.049 -9999 0 -0.32 10 10
TCRz/NEF -0.04 0.16 -9999 0 -0.39 82 82
TNF -0.017 0.12 -9999 0 -0.54 30 30
FASLG -0.063 0.23 -9999 0 -0.61 80 80
NFKB1 0.008 0.033 -9999 0 -0.58 1 1
TNFR1A/BAG4/TNF-alpha 0.004 0.08 -9999 0 -0.33 32 32
CASP6 -0.017 0.058 -9999 0 -0.5 4 4
CASP7 0.022 0.13 -9999 0 -0.56 18 18
RELA 0.009 0.023 -9999 0 -10000 0 0
CASP2 0.011 0 -9999 0 -10000 0 0
CASP3 0.022 0.13 -9999 0 -0.55 19 19
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.015 0.025 -9999 0 -0.42 2 2
CASP8 0.01 0.024 -9999 0 -0.58 1 1
CASP9 0.01 0.024 -9999 0 -0.58 1 1
MAP3K14 0.037 0.057 -9999 0 -0.42 1 1
APAF-1/Caspase 9 -0.038 0.1 -9999 0 -0.46 23 23
BCL2 0.015 0.094 -9999 0 -0.46 9 9
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.017 0.093 -9999 0 -0.5 19 19
MDM2/SUMO1 0.004 0.11 -9999 0 -0.58 19 19
HDAC4 0.011 0.019 -9999 0 -0.46 1 1
Ran/GTP/Exportin 1/HDAC1 -0.017 0.093 -9999 0 -0.5 19 19
SUMO1 -0.008 0.1 -9999 0 -0.58 19 19
NPC/RanGAP1/SUMO1 -0.005 0.095 -9999 0 -0.44 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0 0.12 -9999 0 -0.73 15 15
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 -0.007 0.1 -9999 0 -0.57 19 19
SUMO1/HDAC4 0.005 0.1 -9999 0 -0.55 19 19
SUMO1/HDAC1 0.005 0.1 -9999 0 -0.55 19 19
RANGAP1 0.01 0.031 -9999 0 -0.52 2 2
MDM2/SUMO1/SUMO1 0.016 0.072 -9999 0 -0.35 19 19
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 -0.001 0.095 -9999 0 -0.43 24 24
Ran/GTP 0.005 0.088 -9999 0 -0.53 14 14
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.008 0.044 -9999 0 -0.52 4 4
UBE2I 0.011 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.006 0.12 -9999 0 -0.68 15 15
NPC -0.003 0.056 -9999 0 -0.31 19 19
PIAS2 0.01 0.027 -9999 0 -0.46 2 2
PIAS1 0.011 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.015 0.035 -10000 0 -0.54 2 2
CRKL 0.014 0.061 -10000 0 -10000 0 0
mol:PIP3 -0.01 0.054 0.52 6 -10000 0 6
AKT1 0.004 0.038 0.36 6 -0.3 1 7
PTK2B 0.009 0.034 -10000 0 -0.58 2 2
RAPGEF1 0.018 0.06 -10000 0 -0.37 1 1
RANBP10 0.011 0 -10000 0 -10000 0 0
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
HGF/MET/SHIP2 -0.009 0.1 -10000 0 -0.35 38 38
MAP3K5 0.004 0.1 -10000 0 -0.41 14 14
HGF/MET/CIN85/CBL/ENDOPHILINS 0 0.093 -10000 0 -0.32 38 38
AP1 -0.012 0.095 -10000 0 -0.34 45 45
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.011 0 -10000 0 -10000 0 0
apoptosis -0.024 0.16 -10000 0 -0.74 29 29
STAT3 (dimer) 0.011 0.075 -10000 0 -0.41 1 1
GAB1/CRKL/SHP2/PI3K -0.017 0.066 -10000 0 -0.68 3 3
INPP5D -0.017 0.12 -10000 0 -0.58 28 28
CBL/CRK 0.019 0.061 -10000 0 -0.44 1 1
PTPN11 0.006 0.054 -10000 0 -0.58 5 5
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.01 0.024 -10000 0 -0.58 1 1
PTEN 0.005 0.059 -10000 0 -0.58 6 6
ELK1 -0.001 0.025 0.23 2 -0.31 2 4
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.013 0.046 -10000 0 -0.36 3 3
PAK1 0.009 0.035 0.34 6 -0.28 1 7
HGF/MET/RANBP10 -0.008 0.1 -10000 0 -0.32 54 54
HRAS 0.004 0.095 -10000 0 -1.1 1 1
DOCK1 0.018 0.062 -10000 0 -0.53 1 1
GAB1 0.008 0.064 -10000 0 -0.28 2 2
CRK 0.013 0.063 -10000 0 -0.37 2 2
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.008 0.13 -10000 0 -0.49 37 37
JUN 0.007 0.052 -10000 0 -0.56 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.005 0.057 -10000 0 -0.21 38 38
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
cell morphogenesis 0.028 0.091 -10000 0 -0.59 4 4
GRB2/SHC 0.01 0.051 -10000 0 -0.24 2 2
FOS -0.026 0.14 -10000 0 -0.53 41 41
GLMN -0.008 0.046 -10000 0 -0.27 18 18
cell motility -0.001 0.025 0.23 2 -0.31 2 4
HGF/MET/MUC20 -0.016 0.1 -10000 0 -0.33 54 54
cell migration 0.01 0.051 -10000 0 -0.24 2 2
GRB2 0.011 0 -10000 0 -10000 0 0
CBL 0.011 0 -10000 0 -10000 0 0
MET/RANBP10 0.016 0.023 -10000 0 -0.37 2 2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.006 0.076 -10000 0 -0.26 1 1
MET/MUC20 0.007 0.022 -10000 0 -0.38 2 2
RAP1B 0.023 0.058 -10000 0 -0.34 1 1
RAP1A 0.023 0.059 -10000 0 -0.34 1 1
HGF/MET/RANBP9 -0.009 0.1 -10000 0 -0.33 54 54
RAF1 0.01 0.09 -10000 0 -1 1 1
STAT3 0.011 0.076 -10000 0 -0.41 1 1
cell proliferation 0.015 0.097 -10000 0 -0.34 38 38
RPS6KB1 -0.001 0.043 -10000 0 -0.33 5 5
MAPK3 -0.004 0.031 0.67 1 -0.24 1 2
MAPK1 -0.004 0.031 0.67 1 -0.24 1 2
RANBP9 0.01 0.024 -10000 0 -0.58 1 1
MAPK8 0.019 0.089 -10000 0 -0.56 3 3
SRC 0.012 0.074 -10000 0 -0.53 1 1
PI3K 0.007 0.062 -10000 0 -0.39 5 5
MET/Glomulin 0.003 0.042 -10000 0 -0.22 20 20
SOS1 0.01 0.024 -10000 0 -0.58 1 1
MAP2K1 0.015 0.089 -10000 0 -1.1 1 1
MET 0.01 0.031 -10000 0 -0.52 2 2
MAP4K1 -0.002 0.1 -10000 0 -0.44 13 13
PTK2 0.01 0.024 -10000 0 -0.58 1 1
MAP2K2 0.015 0.086 -10000 0 -0.7 2 2
BAD 0.008 0.042 0.34 6 -0.58 1 7
MAP2K4 0.008 0.094 -10000 0 -0.38 13 13
SHP2/GRB2/SOS1/GAB1 -0.016 0.057 -10000 0 -0.47 3 3
INPPL1 0.01 0.024 -10000 0 -0.58 1 1
PXN 0.011 0 -10000 0 -10000 0 0
SH3KBP1 0.01 0.024 -10000 0 -0.58 1 1
HGS 0.002 0.054 -10000 0 -0.25 3 3
PLCgamma1/PKC 0.008 0.018 -10000 0 -0.43 1 1
HGF -0.037 0.16 -10000 0 -0.54 52 52
RASA1 0.009 0.034 -10000 0 -0.58 2 2
NCK1 0.009 0.034 -10000 0 -0.58 2 2
PTPRJ 0.01 0.024 -10000 0 -0.58 1 1
NCK/PLCgamma1 0.008 0.062 -10000 0 -0.32 4 4
PDPK1 -0.003 0.042 0.41 6 -10000 0 6
HGF/MET/SHIP -0.026 0.12 -10000 0 -0.34 81 81
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.01 0.11 -10000 0 -0.57 22 22
HRAS 0.008 0.041 -10000 0 -0.49 4 4
EGFR 0.004 0.063 -10000 0 -0.53 8 8
AKT 0.017 0.077 -10000 0 -0.34 19 19
FOXO3 0.011 0 -10000 0 -10000 0 0
AKT1 0.01 0.024 -10000 0 -0.58 1 1
FOXO1 0.009 0.034 -10000 0 -0.58 2 2
AKT3 -0.012 0.11 -10000 0 -0.51 26 26
FOXO4 0.01 0.024 -10000 0 -0.58 1 1
MET 0.01 0.031 -10000 0 -0.52 2 2
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
PIK3CB 0.008 0.046 -10000 0 -0.55 4 4
NRAS 0.001 0.076 -10000 0 -0.58 10 10
PIK3CG -0.044 0.17 -10000 0 -0.55 58 58
PIK3R3 0.008 0.042 -10000 0 -0.58 3 3
PIK3R2 0.01 0.024 -10000 0 -0.58 1 1
NF1 0.008 0.042 -10000 0 -0.58 3 3
RAS 0.008 0.055 0.21 1 -0.31 8 9
ERBB2 0 0.072 -10000 0 -0.46 14 14
proliferation/survival/translation -0.019 0.045 0.26 7 -0.15 1 8
PI3K 0.009 0.063 0.18 2 -0.27 16 18
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
KRAS 0.006 0.057 -10000 0 -0.56 6 6
FOXO 0.035 0.026 0.16 2 -10000 0 2
AKT2 0.009 0.036 -10000 0 -0.5 3 3
PTEN 0.005 0.059 -10000 0 -0.58 6 6
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.021 0.036 -10000 0 -0.26 10 10
epithelial cell differentiation 0.023 0.023 -10000 0 -0.3 3 3
CYFIP2 0 0.08 -10000 0 -0.58 11 11
ENAH 0.037 0.067 -10000 0 -0.42 6 6
EGFR 0.004 0.063 -10000 0 -0.53 8 8
EPHA2 0.006 0.055 -10000 0 -0.54 6 6
MYO6 0.029 0.022 -10000 0 -0.28 3 3
CTNNB1 0.011 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.014 0.06 -10000 0 -0.38 13 13
AQP5 -0.036 0.098 -10000 0 -0.47 24 24
CTNND1 0.011 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.028 0.025 -10000 0 -0.28 1 1
regulation of calcium-dependent cell-cell adhesion -0.003 0.093 -10000 0 -0.28 47 47
EGF -0.18 0.25 -10000 0 -0.51 216 216
NCKAP1 0.009 0.034 -10000 0 -0.58 2 2
AQP3 -0.021 0.066 -10000 0 -0.47 8 8
cortical microtubule organization 0.023 0.023 -10000 0 -0.3 3 3
GO:0000145 0.026 0.024 -10000 0 -0.26 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.025 0.023 -10000 0 -0.3 3 3
MLLT4 0.009 0.034 -10000 0 -0.58 2 2
ARF6/GDP -0.005 0.039 -10000 0 -0.48 2 2
ARF6 0.01 0.024 -10000 0 -0.58 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.024 0.045 -10000 0 -0.37 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.036 0.025 -10000 0 -10000 0 0
PVRL2 0.01 0.031 -10000 0 -0.52 2 2
ZYX 0.028 0.025 -10000 0 -0.28 1 1
ARF6/GTP 0.027 0.047 -10000 0 -0.39 6 6
CDH1 0.01 0.024 -10000 0 -0.58 1 1
EGFR/EGFR/EGF/EGF -0.084 0.11 -10000 0 -0.48 1 1
RhoA/GDP -0.002 0.023 -10000 0 -0.28 4 4
actin cytoskeleton organization 0.032 0.027 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.01 0.024 -10000 0 -0.58 1 1
GIT1 0.01 0.024 -10000 0 -0.58 1 1
IGF1R 0.01 0.024 -10000 0 -0.58 1 1
IGF1 -0.073 0.2 -10000 0 -0.52 94 94
DIAPH1 -0.014 0.092 -10000 0 -0.62 13 13
Wnt receptor signaling pathway -0.023 0.023 0.3 3 -10000 0 3
RHOA 0.01 0.024 -10000 0 -0.58 1 1
RhoA/GTP -0.005 0.039 -10000 0 -0.48 2 2
CTNNA1 0.009 0.034 -10000 0 -0.58 2 2
VCL 0.032 0.027 -10000 0 -10000 0 0
EFNA1 0.011 0.019 -10000 0 -0.46 1 1
LPP 0.032 0.026 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.004 0.031 -10000 0 -10000 0 0
SEC6/SEC8 -0.003 0.025 -10000 0 -10000 0 0
MGAT3 -0.003 0.094 -10000 0 -0.29 47 47
HGF/MET -0.023 0.072 -10000 0 -10000 0 0
HGF -0.037 0.16 -10000 0 -0.54 52 52
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.021 0.036 -10000 0 -0.26 10 10
actin cable formation 0.051 0.057 -10000 0 -0.4 3 3
KIAA1543 0.031 0.034 -10000 0 -10000 0 0
KIFC3 0.024 0.041 -10000 0 -0.28 9 9
NCK1 0.009 0.034 -10000 0 -0.58 2 2
EXOC3 0.011 0 -10000 0 -10000 0 0
ACTN1 0.029 0.022 -10000 0 -10000 0 0
NCK1/GIT1 0.015 0.031 -10000 0 -0.42 3 3
mol:GDP 0.023 0.023 -10000 0 -0.3 3 3
EXOC4 0.011 0 -10000 0 -10000 0 0
STX4 0.029 0.022 -10000 0 -0.28 3 3
PIP5K1C 0.028 0.025 -10000 0 -0.28 1 1
LIMA1 0.004 0.064 -10000 0 -0.58 7 7
ABI1 0.01 0.024 -10000 0 -0.58 1 1
ROCK1 0.039 0.059 -10000 0 -0.47 4 4
adherens junction assembly 0.038 0.067 -10000 0 -1.1 1 1
IGF-1R heterotetramer/IGF1 -0.038 0.089 -10000 0 -0.55 1 1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.014 0.034 -10000 0 -0.4 4 4
MET 0.01 0.031 -10000 0 -0.52 2 2
PLEKHA7 0.028 0.025 -10000 0 -10000 0 0
mol:GTP 0.023 0.045 -10000 0 -0.37 6 6
establishment of epithelial cell apical/basal polarity 0.045 0.029 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.021 0.036 -10000 0 -0.26 10 10
regulation of cell-cell adhesion 0.032 0.027 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.021 0.036 -10000 0 -0.26 10 10
Insulin 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
CBL/APS/CAP -0.028 0.083 -9999 0 -0.48 5 5
TC10/GTP -0.022 0.071 -9999 0 -0.47 2 2
Insulin Receptor/Insulin/IRS1/Shp2 0.014 0.062 -9999 0 -0.34 17 17
HRAS 0.008 0.041 -9999 0 -0.49 4 4
APS homodimer -0.014 0.11 -9999 0 -0.52 29 29
GRB14 -0.12 0.24 -9999 0 -0.54 142 142
FOXO3 0.002 0.057 -9999 0 -0.66 3 3
AKT1 -0.031 0.12 -9999 0 -0.41 3 3
INSR 0.01 0.034 -9999 0 -0.58 2 2
Insulin Receptor/Insulin 0.027 0.035 -9999 0 -0.6 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.007 0.048 -9999 0 -0.58 4 4
SORBS1 -0.013 0.11 -9999 0 -0.51 28 28
CRK 0.011 0.019 -9999 0 -0.46 1 1
PTPN1 0.024 0.035 -9999 0 -0.59 1 1
CAV1 0.008 0.067 -9999 0 -0.32 17 17
CBL/APS/CAP/Crk-II/C3G 0.006 0.088 -9999 0 -0.31 28 28
Insulin Receptor/Insulin/IRS1/NCK2 0.016 0.054 -9999 0 -0.34 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.009 0.05 -9999 0 -0.3 14 14
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.025 0.048 -9999 0 -0.46 3 3
RPS6KB1 -0.025 0.12 -9999 0 -0.47 4 4
PARD6A 0.007 0.045 -9999 0 -0.48 5 5
CBL 0.011 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.001 0.008 -9999 0 -10000 0 0
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.055 0.093 -9999 0 -0.46 4 4
HRAS/GTP -0.018 0.067 -9999 0 -0.47 3 3
Insulin Receptor 0.01 0.034 -9999 0 -0.58 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.023 0.049 -9999 0 -0.32 9 9
PRKCI -0.019 0.054 -9999 0 -0.59 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.064 0.11 -9999 0 -0.45 3 3
SHC1 0.011 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0.019 0.027 -9999 0 -0.3 4 4
PI3K -0.009 0.05 -9999 0 -0.3 14 14
NCK2 0.01 0.024 -9999 0 -0.58 1 1
RHOQ 0.011 0 -9999 0 -10000 0 0
mol:H2O2 0 0.004 -9999 0 -10000 0 0
HRAS/GDP 0.006 0.03 -9999 0 -0.35 4 4
AKT2 -0.031 0.12 -9999 0 -0.41 5 5
PRKCZ -0.017 0.041 -9999 0 -0.78 1 1
SH2B2 -0.014 0.11 -9999 0 -0.52 29 29
SHC/SHIP 0.006 0.082 -9999 0 -0.3 36 36
F2RL2 -0.034 0.16 -9999 0 -0.56 47 47
TRIP10 0.01 0.024 -9999 0 -0.58 1 1
Insulin Receptor/Insulin/Shc 0.015 0.026 -9999 0 -0.3 3 3
TC10/GTP/CIP4/Exocyst 0.015 0.015 -9999 0 -0.36 1 1
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.027 0.028 -9999 0 -0.3 1 1
RAPGEF1 0.01 0.024 -9999 0 -0.58 1 1
RASA1 0.009 0.034 -9999 0 -0.58 2 2
NCK1 0.009 0.034 -9999 0 -0.58 2 2
CBL/APS/CAP/Crk-II 0 0.092 -9999 0 -0.33 27 27
TC10/GDP 0.008 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.02 0.039 -9999 0 -0.32 7 7
INPP5D -0.001 0.086 -9999 0 -0.32 39 39
SOS1 0.01 0.024 -9999 0 -0.58 1 1
SGK1 -0.012 0.068 -9999 0 -0.93 3 3
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.006 0.054 -9999 0 -0.58 5 5
IRS1 0.002 0.072 -9999 0 -0.58 9 9
p62DOK/RasGAP 0.02 0.028 -9999 0 -0.31 4 4
INS 0 0.036 -9999 0 -0.49 3 3
mol:PI-3-4-P2 -0.001 0.085 -9999 0 -0.32 39 39
GRB2 0.011 0 -9999 0 -10000 0 0
EIF4EBP1 -0.024 0.12 -9999 0 -0.45 5 5
PTPRA 0.012 0.003 -9999 0 -10000 0 0
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
TC10/GTP/CIP4 0.015 0.015 -9999 0 -0.36 1 1
PDPK1 0.011 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.021 0.044 -9999 0 -0.31 3 3
Insulin Receptor/Insulin/IRS1 0.01 0.052 -9999 0 -0.34 12 12
Insulin Receptor/Insulin/IRS3 0.008 0.036 -9999 0 -0.38 5 5
Par3/Par6 0 0.091 -9999 0 -0.31 41 41
Rapid glucocorticoid 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
Gs family/GDP/Gbeta gamma 0 0.076 -10000 0 -0.27 42 42
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.019 -10000 0 -0.32 2 2
GNB1/GNG2 0.011 0.04 -10000 0 -0.32 8 8
GNB1 0.011 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.01 0.069 -10000 0 -0.28 36 36
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 0.005 0.018 0.074 36 -10000 0 36
GNAL -0.02 0.12 -10000 0 -0.5 36 36
GNG2 0.004 0.063 -10000 0 -0.53 8 8
CRH -0.001 0.026 -10000 0 -0.46 2 2
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.006 0.015 -10000 0 -0.36 1 1
MAPK11 0.001 0.04 -10000 0 -0.22 17 17
BARD1 signaling events

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
BARD1/CSTF1 0.012 0.047 -10000 0 -0.42 7 7
ATM 0.002 0.072 -10000 0 -0.58 9 9
UBE2D3 0.011 0 -10000 0 -10000 0 0
PRKDC 0.009 0.039 -10000 0 -0.54 3 3
ATR 0.009 0.034 -10000 0 -0.58 2 2
UBE2L3 0.011 0 -10000 0 -10000 0 0
FANCD2 0.013 0.065 -10000 0 -0.44 10 10
protein ubiquitination 0.02 0.062 -10000 0 -0.33 16 16
XRCC5 0.01 0.024 -10000 0 -0.58 1 1
XRCC6 0.011 0 -10000 0 -10000 0 0
M/R/N Complex 0.008 0.09 -10000 0 -0.46 19 19
MRE11A 0.003 0.068 -10000 0 -0.58 8 8
DNA-PK 0.021 0.035 -10000 0 -0.43 3 3
FA complex/FANCD2/Ubiquitin 0.035 0.058 -10000 0 -0.62 3 3
FANCF 0.005 0.059 -10000 0 -0.58 6 6
BRCA1 0.01 0.024 -10000 0 -0.58 1 1
CCNE1 0.009 0.033 -10000 0 -0.46 3 3
CDK2/Cyclin E1 0.015 0.03 -10000 0 -0.34 4 4
FANCG 0.011 0.019 -10000 0 -0.46 1 1
BRCA1/BACH1/BARD1 0.011 0.05 -10000 0 -0.42 8 8
FANCE 0.011 0 -10000 0 -10000 0 0
FANCC 0.011 0 -10000 0 -10000 0 0
NBN -0.005 0.096 -10000 0 -0.58 16 16
FANCA 0.011 0 -10000 0 -10000 0 0
DNA repair 0.048 0.066 -10000 0 -0.58 4 4
BRCA1/BARD1/ubiquitin 0.011 0.05 -10000 0 -0.42 8 8
BARD1/DNA-PK 0.023 0.049 -10000 0 -0.35 9 9
FANCL 0.008 0.042 -10000 0 -0.58 3 3
mRNA polyadenylation -0.012 0.047 0.42 7 -10000 0 7
BRCA1/BARD1/CTIP/M/R/N Complex 0.005 0.15 -10000 0 -0.74 18 18
BRCA1/BACH1/BARD1/TopBP1 0.018 0.046 -10000 0 -0.35 9 9
BRCA1/BARD1/P53 -0.009 0.11 -10000 0 -0.33 63 63
BARD1/CSTF1/BRCA1 0.018 0.043 -10000 0 -0.35 8 8
BRCA1/BACH1 0.01 0.024 -10000 0 -0.58 1 1
BARD1 0.004 0.064 -10000 0 -0.58 7 7
PCNA 0.011 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.018 0.043 -10000 0 -0.35 8 8
BRCA1/BARD1/UbcH7 0.018 0.043 -10000 0 -0.35 8 8
BRCA1/BARD1/RAD51/PCNA 0.025 0.04 -10000 0 -0.32 8 8
BARD1/DNA-PK/P53 -0.003 0.11 -10000 0 -0.6 3 3
BRCA1/BARD1/Ubiquitin 0.011 0.05 -10000 0 -0.42 8 8
BRCA1/BARD1/CTIP 0.009 0.097 -10000 0 -0.41 25 25
FA complex 0.028 0.052 -10000 0 -1 1 1
BARD1/EWS 0.012 0.047 -10000 0 -0.42 7 7
RBBP8 0.001 0.1 -10000 0 -0.53 19 19
TP53 -0.044 0.17 -10000 0 -0.58 56 56
TOPBP1 0.01 0.024 -10000 0 -0.58 1 1
G1/S transition of mitotic cell cycle 0.009 0.11 0.33 63 -10000 0 63
BRCA1/BARD1 0.023 0.063 -10000 0 -0.33 16 16
CSTF1 0.011 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.003 0.047 -10000 0 -0.43 7 7
CDK2 0.01 0.024 -10000 0 -0.58 1 1
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.011 0 -10000 0 -10000 0 0
RAD50 0.01 0.024 -10000 0 -0.58 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.011 0.05 -10000 0 -0.42 8 8
EWSR1 0.011 0 -10000 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.04 0.083 -9999 0 -0.45 3 3
CRKL 0.02 0.068 -9999 0 -0.42 4 4
mol:DAG 0.026 0.062 -9999 0 -0.33 8 8
HRAS 0.036 0.065 -9999 0 -0.41 4 4
MAPK8 0.019 0.048 -9999 0 -0.32 6 6
RAP1A 0.02 0.071 -9999 0 -0.45 5 5
GAB1 0.02 0.068 -9999 0 -0.42 4 4
MAPK14 0.02 0.046 -9999 0 -0.34 4 4
EPO 0.001 0.054 -9999 0 -0.46 8 8
PLCG1 0.026 0.063 -9999 0 -0.34 8 8
EPOR/TRPC2/IP3 Receptors 0.005 0.064 -9999 0 -0.5 9 9
RAPGEF1 0.01 0.024 -9999 0 -0.58 1 1
EPO/EPOR (dimer)/SOCS3 0.006 0.076 -9999 0 -0.31 30 30
GAB1/SHC/GRB2/SOS1 -0.013 0.052 -9999 0 -0.45 3 3
EPO/EPOR (dimer) 0.006 0.063 -9999 0 -0.36 16 16
IRS2 0.016 0.076 -9999 0 -0.41 5 5
STAT1 0.029 0.081 -9999 0 -0.39 10 10
STAT5B 0.029 0.067 -9999 0 -0.35 7 7
cell proliferation 0.024 0.045 -9999 0 -0.36 2 2
GAB1/SHIP/PIK3R1/SHP2/SHC -0.025 0.082 -9999 0 -0.52 8 8
TEC 0.02 0.068 -9999 0 -0.42 4 4
SOCS3 -0.002 0.082 -9999 0 -0.5 16 16
STAT1 (dimer) 0.029 0.079 -9999 0 -0.38 10 10
JAK2 -0.007 0.1 -9999 0 -0.55 21 21
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
EPO/EPOR (dimer)/JAK2 0.026 0.074 -9999 0 -0.31 19 19
EPO/EPOR 0.006 0.063 -9999 0 -0.36 16 16
LYN 0.012 0.003 -9999 0 -10000 0 0
TEC/VAV2 0.013 0.092 -9999 0 -0.42 7 7
elevation of cytosolic calcium ion concentration 0.005 0.063 -9999 0 -0.5 9 9
SHC1 0.011 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.02 0.053 -9999 0 -0.28 16 16
mol:IP3 0.026 0.062 -9999 0 -0.33 8 8
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.011 0.098 -9999 0 -0.48 6 6
SH2B3 0.011 0.007 -9999 0 -10000 0 0
NFKB1 0.019 0.048 -9999 0 -0.32 6 6
EPO/EPOR (dimer)/JAK2/SOCS3 -0.016 0.061 -9999 0 -0.29 21 21
PTPN6 0.014 0.071 -9999 0 -0.3 19 19
TEC/VAV2/GRB2 0.018 0.09 -9999 0 -0.42 6 6
EPOR 0.005 0.064 -9999 0 -0.5 9 9
INPP5D -0.017 0.12 -9999 0 -0.58 28 28
mol:GDP -0.013 0.053 -9999 0 -0.46 3 3
SOS1 0.01 0.024 -9999 0 -0.58 1 1
PLCG2 -0.011 0.11 -9999 0 -0.54 24 24
CRKL/CBL/C3G 0.031 0.066 -9999 0 -0.47 2 2
VAV2 0.006 0.094 -9999 0 -0.43 7 7
CBL 0.02 0.068 -9999 0 -0.42 4 4
SHC/Grb2/SOS1 -0.014 0.056 -9999 0 -0.41 5 5
STAT5A 0.029 0.067 -9999 0 -0.35 7 7
GRB2 0.011 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.04 0.082 -9999 0 -0.46 4 4
LYN/PLCgamma2 0.001 0.081 -9999 0 -0.39 24 24
PTPN11 0.006 0.054 -9999 0 -0.58 5 5
BTK -0.002 0.11 -9999 0 -0.42 13 13
BCL2 0.025 0.16 -9999 0 -0.83 17 17
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.016 0.079 -9999 0 -0.48 12 12
VEGFR1 homodimer/NRP1 0.008 0.079 -9999 0 -0.48 13 13
mol:DAG 0.015 0.089 -9999 0 -0.64 7 7
VEGFR1 homodimer/NRP1/VEGFR 121 0.014 0.074 -9999 0 -0.45 12 12
CaM/Ca2+ 0.02 0.085 -9999 0 -0.6 7 7
HIF1A 0.007 0.082 -9999 0 -0.54 12 12
GAB1 0.011 0 -9999 0 -10000 0 0
AKT1 0.029 0.094 -9999 0 -0.62 10 10
PLCG1 0.014 0.09 -9999 0 -0.65 7 7
NOS3 0.026 0.11 -9999 0 -0.64 9 9
CBL 0.011 0 -9999 0 -10000 0 0
mol:NO 0.026 0.1 -9999 0 -0.61 9 9
FLT1 0.013 0.09 -9999 0 -0.55 13 13
PGF -0.002 0.078 -9999 0 -0.47 16 16
VEGFR1 homodimer/NRP2/VEGFR121 0.008 0.099 -9999 0 -0.79 4 4
CALM1 0.011 0 -9999 0 -10000 0 0
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
eNOS/Hsp90 0.031 0.1 -9999 0 -0.59 10 10
endothelial cell proliferation 0.004 0.12 -9999 0 -0.73 7 7
mol:Ca2+ 0.015 0.088 -9999 0 -0.63 7 7
MAPK3 0.023 0.081 -9999 0 -0.56 7 7
MAPK1 0.023 0.081 -9999 0 -0.56 7 7
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
PLGF homodimer -0.002 0.078 -9999 0 -0.47 16 16
PRKACA 0.011 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.002 0.082 -9999 0 -0.5 16 16
VEGFA homodimer 0.011 0.019 -9999 0 -0.46 1 1
VEGFR1 homodimer/VEGFA homodimer 0.016 0.08 -9999 0 -0.47 13 13
platelet activating factor biosynthetic process 0.027 0.08 -9999 0 -0.54 7 7
PI3K 0.019 0.098 -9999 0 -0.67 9 9
PRKCA 0.019 0.085 -9999 0 -0.59 7 7
PRKCB -0.008 0.12 -9999 0 -0.6 10 10
VEGFR1 homodimer/PLGF homodimer 0.009 0.094 -9999 0 -0.5 14 14
VEGFA 0.011 0.019 -9999 0 -0.46 1 1
VEGFB 0.011 0 -9999 0 -10000 0 0
mol:IP3 0.015 0.089 -9999 0 -0.64 7 7
RASA1 0.021 0.078 -9999 0 -0.69 5 5
NRP2 -0.014 0.11 -9999 0 -0.5 29 29
VEGFR1 homodimer 0.013 0.09 -9999 0 -0.55 13 13
VEGFB homodimer 0.011 0 -9999 0 -10000 0 0
NCK1 0.009 0.034 -9999 0 -0.58 2 2
eNOS/Caveolin-1 0.025 0.11 -9999 0 -0.64 9 9
PTPN11 0.006 0.054 -9999 0 -0.58 5 5
mol:PI-3-4-5-P3 0.018 0.096 -9999 0 -0.66 9 9
mol:L-citrulline 0.026 0.1 -9999 0 -0.61 9 9
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.013 0.12 -9999 0 -0.67 12 12
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.021 0.081 -9999 0 -0.68 6 6
CD2AP -0.017 0.13 -9999 0 -0.58 29 29
PI3K/GAB1 0.024 0.094 -9999 0 -0.64 9 9
PDPK1 0.022 0.091 -9999 0 -0.62 9 9
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.019 0.091 -9999 0 -0.71 7 7
mol:NADP 0.026 0.1 -9999 0 -0.61 9 9
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
ubiquitin-dependent protein catabolic process 0.012 0.12 -9999 0 -0.66 12 12
VEGFR1 homodimer/NRP2 0.001 0.11 -9999 0 -0.43 23 23
p38 MAPK signaling 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
TRAF6/ASK1 0.01 0.027 -10000 0 -0.44 2 2
TRAF2/ASK1 0.014 0.027 -10000 0 -0.36 3 3
ATM 0.002 0.072 -10000 0 -0.58 9 9
MAP2K3 0.013 0.096 -10000 0 -0.58 12 12
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.015 0.092 -10000 0 -0.54 12 12
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.004 0.083 -10000 0 -0.46 19 19
TXN 0.007 0 -10000 0 -10000 0 0
CALM1 0.011 0 -10000 0 -10000 0 0
GADD45A 0.009 0.034 -10000 0 -0.58 2 2
GADD45B 0.008 0.038 -10000 0 -0.46 4 4
MAP3K1 0.005 0.059 -10000 0 -0.58 6 6
MAP3K6 0.004 0.067 -10000 0 -0.56 8 8
MAP3K7 0.011 0 -10000 0 -10000 0 0
MAP3K4 0.011 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.01 0.055 -10000 0 -0.41 10 10
TAK1/TAB family 0.003 0.021 0.18 3 -10000 0 3
RAC1/OSM/MEKK3 0.02 0.031 -10000 0 -0.4 3 3
TRAF2 0.01 0.024 -10000 0 -0.58 1 1
RAC1/OSM/MEKK3/MKK3 -0.012 0.068 -10000 0 -0.46 12 12
TRAF6 0.006 0.015 -10000 0 -0.36 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.054 0.17 -10000 0 -0.49 76 76
CCM2 0.01 0.031 -10000 0 -0.52 2 2
CaM/Ca2+/CAMKIIB -0.025 0.1 -10000 0 -0.29 76 76
MAPK11 -0.003 0.082 -10000 0 -0.48 17 17
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.016 0.098 -10000 0 -0.33 24 24
OSM/MEKK3 0.014 0.038 -10000 0 -0.51 3 3
TAOK1 0.003 0.078 -10000 0 -0.46 14 14
TAOK2 0.008 0.047 -10000 0 -0.35 10 10
TAOK3 0.009 0.044 -10000 0 -0.35 9 9
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.011 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.009 0.034 -10000 0 -0.58 2 2
MAP3K10 0.007 0.05 -10000 0 -0.53 5 5
MAP3K3 0.009 0.034 -10000 0 -0.58 2 2
TRX/ASK1 0.012 0.021 -10000 0 -0.35 2 2
GADD45/MTK1/MTK1 0.017 0.053 -10000 0 -0.37 3 3
Aurora B signaling

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
Condensin I complex 0.017 0.087 -9999 0 -0.47 15 15
STMN1 0.009 0.07 -9999 0 -0.43 15 15
Aurora B/RasGAP/Survivin 0.025 0.031 -9999 0 -0.48 2 2
Chromosomal passenger complex/Cul3 protein complex -0.012 0.078 -9999 0 -0.39 2 2
BIRC5 0.012 0.019 -9999 0 -0.46 1 1
DES -0.11 0.19 -9999 0 -0.55 93 93
Aurora C/Aurora B/INCENP 0.013 0.061 -9999 0 -0.3 21 21
Aurora B/TACC1 0.012 0.047 -9999 0 -0.34 10 10
Aurora B/PP2A 0.019 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.013 0.012 -9999 0 -0.28 1 1
mitotic metaphase/anaphase transition 0 0.001 -9999 0 -10000 0 0
NDC80 0.009 0.068 -9999 0 -0.43 14 14
Cul3 protein complex -0.057 0.14 -9999 0 -0.36 51 51
KIF2C 0.02 0.023 -9999 0 -0.5 1 1
PEBP1 0.012 0.001 -9999 0 -10000 0 0
KIF20A 0.009 0.034 -9999 0 -0.58 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.018 0.026 -9999 0 -0.43 2 2
SEPT1 -0.008 0.1 -9999 0 -0.53 21 21
SMC2 0.002 0.072 -9999 0 -0.58 9 9
SMC4 -0.004 0.093 -9999 0 -0.58 15 15
NSUN2/NPM1/Nucleolin 0.024 0.03 -9999 0 -10000 0 0
PSMA3 0.011 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.001 -9999 0 -10000 0 0
H3F3B 0.015 0.002 -9999 0 -10000 0 0
AURKB 0.015 0.006 -9999 0 -10000 0 0
AURKC -0.009 0.1 -9999 0 -0.55 21 21
CDCA8 0.012 0.001 -9999 0 -10000 0 0
cytokinesis 0.014 0.038 -9999 0 -10000 0 0
Aurora B/Septin1 0.005 0.056 -9999 0 -10000 0 0
AURKA 0.011 0.001 -9999 0 -10000 0 0
INCENP 0.012 0.001 -9999 0 -10000 0 0
KLHL13 -0.12 0.22 -9999 0 -0.5 148 148
BUB1 0.01 0.024 -9999 0 -0.58 1 1
hSgo1/Aurora B/Survivin 0.022 0.035 -9999 0 -0.33 5 5
EVI5 0.005 0.064 -9999 0 -0.58 7 7
RhoA/GTP -0.001 0.019 -9999 0 -0.34 1 1
SGOL1 0.006 0.054 -9999 0 -0.58 5 5
CENPA 0.023 0.024 -9999 0 -0.26 4 4
NCAPG 0.008 0.042 -9999 0 -0.58 3 3
Aurora B/HC8 Proteasome 0.019 0.004 -9999 0 -10000 0 0
NCAPD2 0.011 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.019 0.019 -9999 0 -0.43 1 1
RHOA 0.01 0.024 -9999 0 -0.58 1 1
NCAPH 0.01 0.024 -9999 0 -0.58 1 1
NPM1 0.012 0.053 -9999 0 -0.47 7 7
RASA1 0.009 0.034 -9999 0 -0.58 2 2
KLHL9 0.01 0.024 -9999 0 -0.58 1 1
mitotic prometaphase 0.001 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.004 -9999 0 -10000 0 0
PPP1CC 0.01 0.024 -9999 0 -0.58 1 1
Centraspindlin 0.027 0.021 -9999 0 -10000 0 0
RhoA/GDP 0.008 0.018 -9999 0 -0.43 1 1
NSUN2 0.017 0.003 -9999 0 -10000 0 0
MYLK -0.005 0.072 -9999 0 -0.24 48 48
KIF23 0.012 0.001 -9999 0 -10000 0 0
VIM 0.014 0.048 -9999 0 -0.37 9 9
RACGAP1 0.012 0.001 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.017 0.003 -9999 0 -10000 0 0
Chromosomal passenger complex 0.028 0.018 -9999 0 -0.22 1 1
Chromosomal passenger complex/EVI5 0.021 0.051 -9999 0 -0.3 7 7
TACC1 0.002 0.073 -9999 0 -0.56 10 10
PPP2R5D 0.011 0 -9999 0 -10000 0 0
CUL3 0.009 0.034 -9999 0 -0.58 2 2
response to DNA damage stimulus 0 0 -9999 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 -0.004 0.094 -9999 0 -0.41 29 29
AKT1 0.053 0.088 -9999 0 -0.54 9 9
PTK2B 0.023 0.096 -9999 0 -0.64 6 6
VEGFR2 homodimer/Frs2 0.021 0.078 -9999 0 -0.55 9 9
CAV1 -0.002 0.082 -9999 0 -0.5 16 16
CALM1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.029 0.076 -9999 0 -0.77 4 4
endothelial cell proliferation 0.046 0.097 -9999 0 -0.5 8 8
mol:Ca2+ 0.034 0.073 -9999 0 -0.66 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.034 0.073 -9999 0 -0.73 4 4
RP11-342D11.1 0.027 0.072 -9999 0 -0.67 4 4
CDH5 0.005 0.055 -9999 0 -0.49 7 7
VEGFA homodimer 0.024 0.054 -9999 0 -0.38 9 9
SHC1 0.011 0 -9999 0 -10000 0 0
SHC2 -0.041 0.16 -9999 0 -0.54 57 57
HRAS/GDP -0.01 0.061 -9999 0 -0.53 6 6
SH2D2A 0.011 0.019 -9999 0 -0.46 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.016 0.077 -9999 0 -0.59 5 5
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.029 0.069 -9999 0 -0.7 4 4
VEGFR1 homodimer 0.007 0.052 -9999 0 -0.56 5 5
SHC/GRB2/SOS1 -0.009 0.065 -9999 0 -0.61 5 5
GRB10 0.033 0.089 -9999 0 -0.68 7 7
PTPN11 0.006 0.054 -9999 0 -0.58 5 5
GRB2 0.011 0 -9999 0 -10000 0 0
PAK1 0.011 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.035 0.083 -9999 0 -0.64 7 7
HRAS 0.008 0.041 -9999 0 -0.49 4 4
VEGF/Rho/ROCK1/Integrin Complex 0.017 0.12 -9999 0 -0.77 10 10
HIF1A 0.002 0.072 -9999 0 -0.58 9 9
FRS2 0.009 0.034 -9999 0 -0.58 2 2
oxygen and reactive oxygen species metabolic process 0.033 0.072 -9999 0 -0.72 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.006 0.096 -9999 0 -0.53 19 19
Nck/Pak 0.015 0.025 -9999 0 -0.42 2 2
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.026 0.077 -9999 0 -0.65 5 5
mol:GDP -0.009 0.063 -9999 0 -0.59 5 5
mol:NADP 0.042 0.086 -9999 0 -0.41 16 16
eNOS/Hsp90 0.045 0.083 -9999 0 -0.48 5 5
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
mol:IP3 0.034 0.074 -9999 0 -0.68 4 4
HIF1A/ARNT 0.01 0.06 -9999 0 -0.46 9 9
SHB 0.011 0.019 -9999 0 -0.46 1 1
VEGFA 0.012 0.02 -9999 0 -0.45 1 1
VEGFC -0.013 0.11 -9999 0 -0.54 26 26
FAK1/Vinculin 0.035 0.11 -9999 0 -0.68 10 10
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.01 0.024 -9999 0 -0.58 1 1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.02 0.1 -9999 0 -0.68 6 6
PTPN6 0.011 0 -9999 0 -10000 0 0
EPAS1 0.015 0.042 -9999 0 -0.4 5 5
mol:L-citrulline 0.042 0.086 -9999 0 -0.41 16 16
ITGAV 0 0.08 -9999 0 -0.58 11 11
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.035 0.073 -9999 0 -0.73 4 4
VEGFR2 homodimer/VEGFA homodimer 0.031 0.079 -9999 0 -0.73 4 4
VEGFR2/3 heterodimer 0.012 0.1 -9999 0 -0.51 17 17
VEGFB 0.011 0 -9999 0 -10000 0 0
MAPK11 0.033 0.085 -9999 0 -0.61 7 7
VEGFR2 homodimer 0.02 0.079 -9999 0 -0.61 8 8
FLT1 0.007 0.052 -9999 0 -0.56 5 5
NEDD4 0.009 0.049 -9999 0 -0.58 4 4
MAPK3 0.027 0.076 -9999 0 -0.52 6 6
MAPK1 0.027 0.076 -9999 0 -0.52 6 6
VEGFA145/NRP2 -0.001 0.082 -9999 0 -0.35 30 30
VEGFR1/2 heterodimer 0.019 0.079 -9999 0 -0.5 12 12
KDR 0.02 0.079 -9999 0 -0.61 8 8
VEGFA165/NRP1/VEGFR2 homodimer 0.023 0.097 -9999 0 -0.64 7 7
SRC 0.01 0.024 -9999 0 -0.58 1 1
platelet activating factor biosynthetic process 0.029 0.078 -9999 0 -0.51 7 7
PI3K 0.045 0.097 -9999 0 -0.64 8 8
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.029 0.071 -9999 0 -0.7 4 4
FES 0.029 0.086 -9999 0 -0.66 5 5
GAB1 -0.011 0.071 -9999 0 -0.66 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.029 0.069 -9999 0 -0.7 4 4
CTNNB1 0.011 0 -9999 0 -10000 0 0
SOS1 0.01 0.024 -9999 0 -0.58 1 1
ARNT 0.01 0.024 -9999 0 -0.58 1 1
eNOS/Caveolin-1 0.04 0.093 -9999 0 -0.5 6 6
VEGFR2 homodimer/VEGFA homodimer/Yes 0.026 0.082 -9999 0 -0.77 4 4
PI3K/GAB1 0.055 0.087 -9999 0 -0.58 7 7
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.037 0.074 -9999 0 -0.68 5 5
PRKACA 0.011 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.005 0.12 -9999 0 -0.67 13 13
HSP90AA1 0.01 0.024 -9999 0 -0.58 1 1
CDC42 0.032 0.086 -9999 0 -0.72 5 5
actin cytoskeleton reorganization 0.029 0.068 -9999 0 -0.69 4 4
PTK2 0.031 0.12 -9999 0 -0.68 11 11
EDG1 0.027 0.072 -9999 0 -0.67 4 4
mol:DAG 0.034 0.074 -9999 0 -0.68 4 4
CaM/Ca2+ 0.037 0.068 -9999 0 -0.62 4 4
MAP2K3 0.038 0.075 -9999 0 -0.63 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.035 0.092 -9999 0 -0.7 7 7
PLCG1 0.034 0.075 -9999 0 -0.69 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.035 0.067 -9999 0 -0.66 4 4
IQGAP1 0.009 0.039 -9999 0 -0.54 3 3
YES1 0.004 0.064 -9999 0 -0.58 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.027 0.08 -9999 0 -0.77 4 4
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.03 0.068 -9999 0 -0.7 4 4
cell migration 0.053 0.098 -9999 0 -0.64 7 7
mol:PI-3-4-5-P3 0.044 0.09 -9999 0 -0.58 8 8
FYN 0.005 0.06 -9999 0 -0.55 7 7
VEGFB/NRP1 0.033 0.068 -9999 0 -0.63 4 4
mol:NO 0.042 0.086 -9999 0 -0.41 16 16
PXN 0.011 0 -9999 0 -10000 0 0
HRAS/GTP -0.01 0.061 -9999 0 -0.53 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.034 0.091 -9999 0 -0.7 7 7
VHL 0.01 0.024 -9999 0 -0.58 1 1
ITGB3 -0.006 0.098 -9999 0 -0.54 19 19
NOS3 0.042 0.096 -9999 0 -0.46 16 16
VEGFR2 homodimer/VEGFA homodimer/Sck 0 0.11 -9999 0 -0.67 5 5
RAC1 0.011 0 -9999 0 -10000 0 0
PRKCA 0.038 0.071 -9999 0 -0.63 4 4
PRKCB 0.012 0.11 -9999 0 -0.59 7 7
VCL 0.009 0.034 -9999 0 -0.58 2 2
VEGFA165/NRP1 0.029 0.072 -9999 0 -0.67 4 4
VEGFR1/2 heterodimer/VEGFA homodimer 0.027 0.077 -9999 0 -0.63 6 6
VEGFA165/NRP2 -0.001 0.082 -9999 0 -0.35 30 30
MAPKKK cascade 0.049 0.082 -9999 0 -0.56 8 8
NRP2 -0.014 0.11 -9999 0 -0.5 29 29
VEGFC homodimer -0.013 0.11 -9999 0 -0.54 26 26
NCK1 0.009 0.034 -9999 0 -0.58 2 2
ROCK1 0 0.08 -9999 0 -0.58 11 11
FAK1/Paxillin 0.036 0.11 -9999 0 -0.64 10 10
MAP3K13 0.034 0.077 -9999 0 -0.67 5 5
PDPK1 0.048 0.081 -9999 0 -0.51 8 8
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.027 0.054 -10000 0 -1.1 1 1
regulation of axonogenesis -0.02 0.045 0.6 2 -10000 0 2
myoblast fusion -0.016 0.032 0.4 2 -10000 0 2
mol:GTP 0.007 0.022 -10000 0 -0.33 2 2
regulation of calcium-dependent cell-cell adhesion 0.005 0.099 0.28 64 -10000 0 64
ARF1/GTP -0.002 0.02 -10000 0 -0.31 2 2
mol:GM1 0.007 0.017 -10000 0 -0.26 2 2
mol:Choline 0.02 0.034 -10000 0 -0.43 3 3
lamellipodium assembly 0.006 0.041 -10000 0 -0.46 2 2
MAPK3 0.02 0.028 -10000 0 -0.34 3 3
ARF6/GTP/NME1/Tiam1 -0.004 0.1 -10000 0 -0.29 64 64
ARF1 0.011 0.019 -10000 0 -0.46 1 1
ARF6/GDP 0.016 0.032 -10000 0 -0.4 2 2
ARF1/GDP 0.025 0.033 -10000 0 -0.36 2 2
ARF6 0.01 0.029 -10000 0 -0.67 1 1
RAB11A 0.011 0 -10000 0 -10000 0 0
TIAM1 -0.042 0.16 -10000 0 -0.52 62 62
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.028 -10000 0 -0.34 3 3
actin filament bundle formation -0.017 0.036 0.52 2 -10000 0 2
KALRN 0.003 0.042 -10000 0 -0.33 7 7
RAB11FIP3/RAB11A 0.016 0.023 -10000 0 -0.37 2 2
RhoA/GDP 0.017 0.036 -10000 0 -0.52 2 2
NME1 0.012 0.019 -10000 0 -0.45 1 1
Rac1/GDP 0.018 0.027 -10000 0 -0.37 2 2
substrate adhesion-dependent cell spreading 0.007 0.022 -10000 0 -0.33 2 2
cortical actin cytoskeleton organization 0.006 0.041 -10000 0 -0.46 2 2
RAC1 0.011 0 -10000 0 -10000 0 0
liver development 0.007 0.022 -10000 0 -0.33 2 2
ARF6/GTP 0.007 0.022 -10000 0 -0.33 2 2
RhoA/GTP -0.002 0.029 -10000 0 -0.68 1 1
mol:GDP 0.006 0.037 -10000 0 -0.4 2 2
ARF6/GTP/RAB11FIP3/RAB11A 0.018 0.025 -10000 0 -0.29 3 3
RHOA 0.01 0.024 -10000 0 -0.58 1 1
PLD1 0.015 0.038 -10000 0 -0.49 3 3
RAB11FIP3 0.01 0.031 -10000 0 -0.52 2 2
tube morphogenesis 0.006 0.041 -10000 0 -0.46 2 2
ruffle organization 0.02 0.045 -10000 0 -0.6 2 2
regulation of epithelial cell migration 0.007 0.022 -10000 0 -0.33 2 2
PLD2 0.017 0.017 -10000 0 -0.34 1 1
PIP5K1A 0.02 0.045 -10000 0 -0.6 2 2
mol:Phosphatidic acid 0.02 0.034 -10000 0 -0.43 3 3
Rac1/GTP 0.006 0.041 -10000 0 -0.46 2 2
Aurora C signaling

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
INCENP 0.011 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.01 0.059 -9999 0 -0.3 21 21
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.003 0.017 -9999 0 -10000 0 0
AURKB 0.011 0 -9999 0 -10000 0 0
AURKC -0.009 0.1 -9999 0 -0.55 21 21
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.016 0.069 -10000 0 -0.35 22 22
Ran/GTP/Exportin 1/HDAC1 -0.013 0.075 -10000 0 -0.4 19 19
NF kappa B1 p50/RelA/I kappa B alpha 0.023 0.071 -10000 0 -0.32 22 22
SUMO1 -0.008 0.1 -10000 0 -0.58 19 19
ZFPM1 -0.003 0.084 -10000 0 -0.49 17 17
NPC/RanGAP1/SUMO1/Ubc9 -0.001 0.095 -10000 0 -0.43 24 24
FKBP3 -0.003 0.09 -10000 0 -0.58 14 14
Histones 0.03 0.038 -10000 0 -10000 0 0
YY1/LSF 0.015 0.06 -10000 0 -0.51 3 3
SMG5 0.01 0.024 -10000 0 -0.58 1 1
RAN 0.011 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.015 0.058 -10000 0 -0.27 21 21
I kappa B alpha/HDAC1 0.018 0.042 -10000 0 -10000 0 0
SAP18 0.011 0.019 -10000 0 -0.46 1 1
RELA 0.018 0.057 -10000 0 -0.24 25 25
HDAC1/Smad7 0.022 0.022 -10000 0 -0.35 2 2
RANGAP1 0.01 0.031 -10000 0 -0.52 2 2
HDAC3/TR2 0.017 0.044 -10000 0 -0.31 1 1
NuRD/MBD3 Complex 0.036 0.031 -10000 0 -0.38 2 2
NF kappa B1 p50/RelA 0.021 0.056 -10000 0 -0.51 1 1
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.018 0.13 -10000 0 -0.56 31 31
GATA1 -0.005 0.074 -10000 0 -0.46 15 15
Mad/Max 0.015 0.026 -10000 0 -0.35 3 3
NuRD/MBD3 Complex/GATA1/Fog1 0.036 0.05 -10000 0 -0.45 3 3
RBBP7 0.01 0.024 -10000 0 -0.58 1 1
NPC -0.003 0.056 -10000 0 -0.31 19 19
RBBP4 0.01 0.024 -10000 0 -0.58 1 1
MAX 0.011 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.011 0 -10000 0 -10000 0 0
NFKBIA 0.013 0.046 -10000 0 -10000 0 0
KAT2B -0.006 0.099 -10000 0 -0.58 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.033 0.025 -10000 0 -10000 0 0
SIN3 complex 0.027 0.03 -10000 0 -0.32 4 4
SMURF1 0.011 0 -10000 0 -10000 0 0
CHD3 0.009 0.034 -10000 0 -0.58 2 2
SAP30 0.009 0.034 -10000 0 -0.58 2 2
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.01 0.024 -10000 0 -0.58 1 1
YY1/HDAC3 0.019 0.059 -10000 0 -0.54 1 1
YY1/HDAC2 0.016 0.054 -10000 0 -0.26 20 20
YY1/HDAC1 0.016 0.054 -10000 0 -0.61 1 1
NuRD/MBD2 Complex (MeCP1) 0.035 0.029 -10000 0 -0.36 1 1
PPARG 0.011 0.08 -10000 0 -0.32 29 29
HDAC8/hEST1B 0.023 0.015 -10000 0 -0.35 1 1
UBE2I 0.011 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -10000 0 -10000 0 0
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.016 0.049 -10000 0 -0.31 3 3
MBD3L2 -0.001 0.019 -10000 0 -0.46 1 1
ubiquitin-dependent protein catabolic process 0.022 0.022 -10000 0 -0.35 2 2
CREBBP 0.011 0 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.038 0.032 -10000 0 -0.37 2 2
HDAC1 0.011 0 -10000 0 -10000 0 0
HDAC3 0.013 0.046 -10000 0 -10000 0 0
HDAC2 0.011 0 -10000 0 -10000 0 0
YY1 0.014 0.062 -10000 0 -0.31 20 20
HDAC8 0.011 0 -10000 0 -10000 0 0
SMAD7 0.009 0.034 -10000 0 -0.58 2 2
NCOR2 0.008 0.046 -10000 0 -0.55 4 4
MXD1 0.009 0.036 -10000 0 -0.5 3 3
STAT3 0.019 0.03 -10000 0 -0.34 4 4
NFKB1 0.01 0.024 -10000 0 -0.58 1 1
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 -0.007 0.1 -10000 0 -0.57 19 19
YY1/LSF/HDAC1 0.021 0.055 -10000 0 -0.47 3 3
YY1/SAP30/HDAC1 0.021 0.053 -10000 0 -0.39 3 3
EP300 0.007 0.048 -10000 0 -0.58 4 4
STAT3 (dimer non-phopshorylated) 0.019 0.03 -10000 0 -0.34 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.046 -10000 0 -10000 0 0
histone deacetylation 0.035 0.029 -10000 0 -0.36 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.023 0.044 -10000 0 -10000 0 0
nuclear export -0.022 0.015 0.35 1 -10000 0 1
PRKACA 0.011 0 -10000 0 -10000 0 0
GATAD2B 0.011 0 -10000 0 -10000 0 0
GATAD2A 0.01 0.024 -10000 0 -0.58 1 1
GATA2/HDAC3 0.001 0.085 -10000 0 -0.33 26 26
GATA1/HDAC1 0.005 0.053 -10000 0 -0.32 15 15
GATA1/HDAC3 0.002 0.057 -10000 0 -0.33 2 2
CHD4 0.011 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.004 0.09 -10000 0 -0.39 30 30
SIN3/HDAC complex/Mad/Max 0.036 0.026 -10000 0 -0.36 1 1
NuRD Complex 0.041 0.038 -10000 0 -0.4 2 2
positive regulation of chromatin silencing 0.028 0.037 -10000 0 -10000 0 0
SIN3B 0.01 0.024 -10000 0 -0.58 1 1
MTA2 0.011 0 -10000 0 -10000 0 0
SIN3A 0.01 0.024 -10000 0 -0.58 1 1
XPO1 0 0.08 -10000 0 -0.58 11 11
SUMO1/HDAC1 0.005 0.1 -10000 0 -0.55 19 19
HDAC complex 0.028 0.02 -10000 0 -0.32 2 2
GATA1/Fog1 -0.005 0.082 -10000 0 -0.35 31 31
FKBP25/HDAC1/HDAC2 0.014 0.057 -10000 0 -0.35 14 14
TNF -0.017 0.12 -10000 0 -0.54 30 30
negative regulation of cell growth 0.036 0.026 -10000 0 -0.36 1 1
NuRD/MBD2/PRMT5 Complex 0.035 0.029 -10000 0 -0.36 1 1
Ran/GTP/Exportin 1 0.006 0.12 -10000 0 -0.68 15 15
NF kappa B/RelA/I kappa B alpha 0.018 0.071 -10000 0 -0.33 21 21
SIN3/HDAC complex/NCoR1 0.034 0.024 -10000 0 -10000 0 0
TFCP2 0.009 0.034 -10000 0 -0.58 2 2
NR2C1 0.01 0.024 -10000 0 -0.58 1 1
MBD3 0.008 0.046 -10000 0 -0.55 4 4
MBD2 0.006 0.054 -10000 0 -0.58 5 5
Canonical NF-kappaB 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
FBXW11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.054 0.058 -9999 0 -0.38 3 3
ERC1 0.009 0.033 -9999 0 -0.46 3 3
RIP2/NOD2 0 0.083 -9999 0 -0.4 24 24
NFKBIA 0.036 0.014 -9999 0 -10000 0 0
BIRC2 -0.002 0.087 -9999 0 -0.58 13 13
IKBKB 0.011 0.019 -9999 0 -0.46 1 1
RIPK2 0.011 0 -9999 0 -10000 0 0
IKBKG 0.02 0.071 -9999 0 -0.46 5 5
IKK complex/A20 0.02 0.088 -9999 0 -0.48 5 5
NEMO/A20/RIP2 0.011 0 -9999 0 -10000 0 0
XPO1 0 0.08 -9999 0 -0.58 11 11
NEMO/ATM 0.021 0.091 -9999 0 -0.53 11 11
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.009 0.051 -9999 0 -0.36 11 11
IKK complex/ELKS -0.015 0.064 -9999 0 -0.52 5 5
BCL10/MALT1/TRAF6 0.017 0.061 -9999 0 -0.49 7 7
NOD2 -0.012 0.11 -9999 0 -0.56 24 24
NFKB1 0.013 0.024 -9999 0 -0.58 1 1
RELA 0.014 0 -9999 0 -10000 0 0
MALT1 0.006 0.054 -9999 0 -0.58 5 5
cIAP1/UbcH5C 0.007 0.064 -9999 0 -0.42 13 13
ATM 0.002 0.072 -9999 0 -0.58 9 9
TNF/TNFR1A -0.004 0.09 -9999 0 -0.39 30 30
TRAF6 0.01 0.024 -9999 0 -0.58 1 1
PRKCA 0.01 0.031 -9999 0 -0.52 2 2
CHUK 0.007 0.048 -9999 0 -0.58 4 4
UBE2D3 0.011 0 -9999 0 -10000 0 0
TNF -0.017 0.12 -9999 0 -0.54 30 30
NF kappa B1 p50/RelA 0.032 0.015 -9999 0 -0.34 1 1
BCL10 0.007 0.048 -9999 0 -0.58 4 4
proteasomal ubiquitin-dependent protein catabolic process 0.036 0.014 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
TNFRSF1A 0.011 0 -9999 0 -10000 0 0
IKK complex 0.029 0.078 -9999 0 -0.61 4 4
CYLD 0.01 0.024 -9999 0 -0.58 1 1
IKK complex/PKC alpha 0.031 0.077 -9999 0 -0.58 4 4
Aurora A signaling

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
Aurora A/GADD45A 0.02 0.025 -9999 0 -0.35 2 2
BIRC5 0.011 0.019 -9999 0 -0.46 1 1
NFKBIA 0.023 0.013 -9999 0 -10000 0 0
CPEB1 -0.052 0.17 -9999 0 -0.54 67 67
AKT1 0.022 0.02 -9999 0 -0.35 1 1
NDEL1 0.011 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.019 0.023 -9999 0 -0.49 1 1
NDEL1/TACC3 0.025 0.015 -9999 0 -10000 0 0
GADD45A 0.009 0.034 -9999 0 -0.58 2 2
GSK3B 0.009 0.033 -9999 0 -0.55 2 2
PAK1/Aurora A 0.021 0.013 -9999 0 -10000 0 0
MDM2 0.008 0.044 -9999 0 -0.52 4 4
JUB 0.011 0 -9999 0 -10000 0 0
TPX2 0.017 0.025 -9999 0 -0.42 2 2
TP53 -0.01 0.11 -9999 0 -0.33 57 57
DLG7 0.015 0.013 -9999 0 -0.2 2 2
AURKAIP1 0.01 0.031 -9999 0 -0.52 2 2
ARHGEF7 0.011 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.026 0.016 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.018 0.023 -9999 0 -0.49 1 1
AURKA 0.019 0.016 -9999 0 -0.24 2 2
AURKB 0.011 0.02 -9999 0 -0.22 4 4
CDC25B 0.023 0.016 -9999 0 -10000 0 0
G2/M transition checkpoint 0.019 0.012 -9999 0 -10000 0 0
mRNA polyadenylation -0.019 0.098 -9999 0 -0.32 44 44
Aurora A/CPEB -0.019 0.099 -9999 0 -0.32 44 44
Aurora A/TACC1/TRAP/chTOG 0.028 0.043 -9999 0 -0.31 8 8
BRCA1 0.01 0.024 -9999 0 -0.58 1 1
centrosome duplication 0.021 0.013 -9999 0 -10000 0 0
regulation of centrosome cycle 0.024 0.015 -9999 0 -10000 0 0
spindle assembly 0.027 0.043 -9999 0 -0.31 8 8
TDRD7 0.011 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.029 0.033 -9999 0 -0.4 3 3
CENPA 0.013 0.034 -9999 0 -0.38 4 4
Aurora A/PP2A 0.021 0.013 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.013 0.049 -9999 0 -0.57 1 1
negative regulation of DNA binding -0.01 0.11 -9999 0 -0.33 57 57
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.016 0.018 -9999 0 -0.42 1 1
RASA1 0.009 0.034 -9999 0 -0.58 2 2
Ajuba/Aurora A 0.019 0.012 -9999 0 -10000 0 0
mitotic prometaphase 0 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.016 -9999 0 -0.24 2 2
TACC1 0.002 0.073 -9999 0 -0.56 10 10
TACC3 0.011 0.019 -9999 0 -0.46 1 1
Aurora A/Antizyme1 0.026 0.021 -9999 0 -0.32 1 1
Aurora A/RasGAP 0.02 0.025 -9999 0 -0.35 2 2
OAZ1 0.011 0 -9999 0 -10000 0 0
RAN 0.011 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.011 0.004 -9999 0 -10000 0 0
GIT1 0.01 0.024 -9999 0 -0.58 1 1
GIT1/beta-PIX/PAK1 0.023 0.015 -9999 0 -0.35 1 1
Importin alpha/Importin beta/TPX2 0.017 0.025 -9999 0 -0.42 2 2
PPP2R5D 0.011 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.026 0.02 -9999 0 -10000 0 0
PAK1 0.011 0 -9999 0 -10000 0 0
CKAP5 0.011 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.009 0.065 -10000 0 -0.86 1 1
oxygen homeostasis 0.005 0.014 -10000 0 -10000 0 0
TCEB2 0.005 0.056 -10000 0 -0.47 8 8
TCEB1 0.011 0.019 -10000 0 -0.46 1 1
VHL/Elongin B/Elongin C/HIF2A -0.015 0.055 -10000 0 -0.46 4 4
EPO 0.074 0.18 -10000 0 -0.59 8 8
FIH (dimer) 0.017 0.012 -10000 0 -10000 0 0
APEX1 0.017 0.014 -10000 0 -10000 0 0
SERPINE1 0.055 0.23 -10000 0 -0.7 18 18
FLT1 -0.013 0.11 -10000 0 -0.91 7 7
ADORA2A 0.069 0.19 -10000 0 -0.7 8 8
germ cell development 0.065 0.21 -10000 0 -0.69 12 12
SLC11A2 0.075 0.19 -10000 0 -0.67 7 7
BHLHE40 0.075 0.19 -10000 0 -0.69 7 7
HIF1AN 0.017 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.021 0.12 -10000 0 -0.44 6 6
ETS1 0.016 0.063 -10000 0 -0.48 9 9
CITED2 -0.006 0.067 -10000 0 -1.1 2 2
KDR -0.014 0.11 -10000 0 -0.87 8 8
PGK1 0.075 0.19 -10000 0 -0.67 7 7
SIRT1 0.007 0.054 -10000 0 -0.58 5 5
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.082 0.22 -10000 0 -0.77 8 8
EPAS1 0.049 0.092 -10000 0 -0.37 5 5
SP1 0.016 0.025 -10000 0 -0.58 1 1
ABCG2 0.043 0.24 -10000 0 -0.76 14 14
EFNA1 0.075 0.19 -10000 0 -0.67 7 7
FXN 0.072 0.19 -10000 0 -0.65 8 8
POU5F1 0.064 0.22 -10000 0 -0.72 12 12
neuron apoptosis -0.08 0.21 0.74 8 -10000 0 8
EP300 0.007 0.048 -10000 0 -0.58 4 4
EGLN3 0.002 0.09 -10000 0 -0.52 17 17
EGLN2 0.015 0.038 -10000 0 -0.49 3 3
EGLN1 0.017 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.018 0.042 -10000 0 -0.31 9 9
VHL 0.01 0.024 -10000 0 -0.58 1 1
ARNT 0.016 0.029 -10000 0 -0.6 1 1
SLC2A1 0.067 0.2 -10000 0 -0.74 7 7
TWIST1 0.046 0.24 -10000 0 -0.68 22 22
ELK1 0.017 0.025 -10000 0 -0.58 1 1
HIF2A/ARNT/Cbp/p300 0.066 0.12 -10000 0 -0.43 4 4
VEGFA 0.075 0.19 -10000 0 -0.67 7 7
CREBBP 0.011 0 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.032 0.026 -9999 0 -0.46 1 1
KLHL20 -0.019 0.053 -9999 0 -0.23 28 28
CYFIP2 0 0.08 -9999 0 -0.58 11 11
Rac1/GDP 0.044 0.04 -9999 0 -0.49 1 1
ENAH 0.026 0.051 -9999 0 -0.48 2 2
AP1M1 0.01 0.024 -9999 0 -0.58 1 1
RAP1B 0.011 0 -9999 0 -10000 0 0
RAP1A 0.01 0.024 -9999 0 -0.58 1 1
CTNNB1 0.011 0 -9999 0 -10000 0 0
CDC42/GTP -0.004 0.032 -9999 0 -0.41 2 2
ABI1/Sra1/Nap1 -0.014 0.04 -9999 0 -0.22 10 10
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.014 0.069 -9999 0 -0.32 18 18
RAPGEF1 0.04 0.033 -9999 0 -0.44 2 2
CTNND1 0.011 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.027 0.026 -9999 0 -0.48 1 1
CRK 0.036 0.028 -9999 0 -0.43 1 1
E-cadherin/gamma catenin/alpha catenin 0.021 0.031 -9999 0 -0.35 4 4
alphaE/beta7 Integrin -0.002 0.086 -9999 0 -0.39 28 28
IQGAP1 0.009 0.039 -9999 0 -0.54 3 3
NCKAP1 0.009 0.034 -9999 0 -0.58 2 2
Rap1/GTP/I-afadin 0.02 0.024 -9999 0 -0.32 3 3
DLG1 0.031 0.033 -9999 0 -0.46 1 1
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.026 -9999 0 -0.26 5 5
MLLT4 0.009 0.034 -9999 0 -0.58 2 2
ARF6/GTP/NME1/Tiam1 -0.01 0.094 -9999 0 -0.28 64 64
PI3K -0.004 0.034 -9999 0 -0.34 5 5
ARF6 0.01 0.024 -9999 0 -0.58 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0.015 0.025 -9999 0 -0.42 2 2
TIAM1 -0.044 0.16 -9999 0 -0.52 62 62
E-cadherin(dimer)/Ca2+ 0.026 0.023 -9999 0 -0.3 3 3
AKT1 -0.003 0.023 -9999 0 -0.23 4 4
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
CDH1 0.01 0.024 -9999 0 -0.58 1 1
RhoA/GDP 0.043 0.041 -9999 0 -0.49 1 1
actin cytoskeleton organization 0.017 0.051 -9999 0 -0.2 6 6
CDC42/GDP 0.041 0.047 -9999 0 -0.42 2 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.019 0.023 -9999 0 -0.26 4 4
ITGB7 -0.014 0.12 -9999 0 -0.53 28 28
RAC1 0.011 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.028 0.024 -9999 0 -0.32 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin 0.019 0.023 -9999 0 -0.3 3 3
mol:GDP 0.04 0.045 -9999 0 -0.46 2 2
CDC42/GTP/IQGAP1 0.011 0.05 -9999 0 -0.45 6 6
JUP 0.01 0.024 -9999 0 -0.58 1 1
p120 catenin/RhoA/GDP 0.035 0.041 -9999 0 -0.49 1 1
RAC1/GTP/IQGAP1 0.014 0.025 -9999 0 -0.33 3 3
PIP5K1C/AP1M1 0.016 0.032 -9999 0 -0.77 1 1
RHOA 0.01 0.024 -9999 0 -0.58 1 1
CDC42 0.006 0.054 -9999 0 -0.58 5 5
CTNNA1 0.009 0.034 -9999 0 -0.58 2 2
positive regulation of S phase of mitotic cell cycle 0.016 0.035 -9999 0 -0.27 1 1
NME1 0.011 0.019 -9999 0 -0.46 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.032 0.028 -9999 0 -0.46 1 1
regulation of cell-cell adhesion -0.004 0.028 -9999 0 -0.35 2 2
WASF2 -0.007 0.021 -9999 0 -10000 0 0
Rap1/GTP -0.003 0.026 -9999 0 -0.44 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.018 0.069 -9999 0 -0.3 21 21
CCND1 0.018 0.042 -9999 0 -0.35 1 1
VAV2 0.008 0.16 -9999 0 -0.68 28 28
RAP1/GDP 0.036 0.036 -9999 0 -0.49 1 1
adherens junction assembly 0.031 0.028 -9999 0 -0.45 1 1
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.01 0.024 -9999 0 -0.58 1 1
PIP5K1C 0.01 0.024 -9999 0 -0.58 1 1
regulation of heterotypic cell-cell adhesion 0.023 0.066 -9999 0 -0.41 1 1
E-cadherin/beta catenin 0 0.022 -9999 0 -0.35 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.032 0.028 -9999 0 -0.46 1 1
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
Rac1/GTP -0.03 0.086 -9999 0 -0.38 27 27
E-cadherin/beta catenin/alpha catenin 0.022 0.027 -9999 0 -0.35 3 3
ITGAE 0.011 0.019 -9999 0 -0.46 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.027 0.027 -9999 0 -0.49 1 1
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.011 0 -10000 0 -10000 0 0
mol:PIP3 -0.004 0.05 0.28 5 -0.29 13 18
FRAP1 0.012 0.017 -10000 0 -10000 0 0
AKT1 0.017 0.048 0.22 5 -0.26 14 19
INSR 0.009 0.034 -10000 0 -0.58 2 2
Insulin Receptor/Insulin 0.005 0.031 -10000 0 -0.32 5 5
mol:GTP -0.006 0.037 -10000 0 -0.54 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.004 0.027 -10000 0 -0.3 3 3
TSC2 0.009 0.031 -10000 0 -0.52 2 2
RHEB/GDP -0.005 0.033 -10000 0 -0.49 1 1
TSC1 0.011 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.008 0.048 -10000 0 -0.34 11 11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.004 0.03 -10000 0 -0.35 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.01 0.024 -10000 0 -0.58 1 1
RPS6KB1 0.017 0.048 0.17 5 -0.4 5 10
MAP3K5 0.007 0.022 -10000 0 -0.38 2 2
PIK3R1 0.008 0.042 -10000 0 -0.58 3 3
apoptosis 0.007 0.022 -10000 0 -0.38 2 2
mol:LY294002 0 0 0.001 1 -0.002 9 10
EIF4B 0.022 0.042 0.17 5 -0.34 5 10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.043 -10000 0 -0.34 4 4
eIF4E/eIF4G1/eIF4A1 -0.001 0.016 -10000 0 -0.25 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.014 0.05 -10000 0 -0.3 14 14
mTOR/RHEB/GTP/Raptor/GBL 0.023 0.024 0.16 5 -0.2 1 6
FKBP1A 0.012 0 -10000 0 -10000 0 0
RHEB/GTP -0.005 0.033 -10000 0 -0.48 1 1
mol:Amino Acids 0 0 0.001 1 -0.002 9 10
FKBP12/Rapamycin 0.009 0.001 -10000 0 -10000 0 0
PDPK1 -0.004 0.044 0.23 5 -0.26 13 18
EIF4E 0.009 0.039 -10000 0 -0.54 3 3
ASK1/PP5C 0.017 0.039 -10000 0 -0.62 2 2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.012 0.031 -10000 0 -0.51 2 2
TSC1/TSC2 0.025 0.045 -10000 0 -0.6 1 1
tumor necrosis factor receptor activity 0 0 0.002 9 -0.001 1 10
RPS6 0.007 0.045 -10000 0 -0.48 5 5
PPP5C 0.011 0 -10000 0 -10000 0 0
EIF4G1 0.011 0 -10000 0 -10000 0 0
IRS1 0.001 0.047 -10000 0 -0.38 9 9
INS -0.002 0.036 -10000 0 -0.5 3 3
PTEN 0.005 0.059 -10000 0 -0.58 6 6
PDK2 -0.005 0.047 0.23 5 -0.27 15 20
EIF4EBP1 0.009 0.044 -10000 0 -1 1 1
PIK3CA 0.009 0.034 -10000 0 -0.58 2 2
PPP2R5D 0.017 0.016 -10000 0 -10000 0 0
peptide biosynthetic process 0.01 0.036 -10000 0 -0.32 4 4
RHEB 0.011 0 -10000 0 -10000 0 0
EIF4A1 0.011 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.003 6 -0.002 6 12
EEF2 0.01 0.036 -10000 0 -0.33 4 4
eIF4E/4E-BP1 0.013 0.047 -10000 0 -0.96 1 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.007 0.048 -9999 0 -0.58 4 4
positive regulation of NF-kappaB transcription factor activity 0.011 0.047 -9999 0 -0.36 9 9
MAP2K4 0.033 0.036 -9999 0 -10000 0 0
IKBKB 0.011 0.019 -9999 0 -0.46 1 1
TNFRSF10B 0.01 0.024 -9999 0 -0.58 1 1
TNFRSF10A 0.011 0 -9999 0 -10000 0 0
SMPD1 0.013 0.029 -9999 0 -0.25 6 6
IKBKG 0.01 0.024 -9999 0 -0.58 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.007 0.043 -9999 0 -0.46 5 5
TRAIL/TRAILR2 0.013 0.04 -9999 0 -0.42 5 5
TRAIL/TRAILR3 -0.004 0.088 -9999 0 -0.36 34 34
TRAIL/TRAILR1 0.014 0.036 -9999 0 -0.42 4 4
TRAIL/TRAILR4 0.011 0.047 -9999 0 -0.36 9 9
TRAIL/TRAILR1/DAP3/GTP 0.02 0.028 -9999 0 -0.32 4 4
IKK complex -0.005 0.038 -9999 0 -0.4 5 5
RIPK1 0.011 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0.008 0 -9999 0 -10000 0 0
MAPK3 0.015 0.04 -9999 0 -0.42 5 5
MAP3K1 0.03 0.03 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.007 0.043 -9999 0 -0.46 5 5
TRADD 0.011 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.011 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.026 -9999 0 -10000 0 0
CFLAR 0.011 0 -9999 0 -10000 0 0
MAPK1 0.015 0.04 -9999 0 -0.42 5 5
TRAIL/TRAILR1/FADD/TRADD/RIP 0.032 0.027 -9999 0 -0.29 4 4
mol:ceramide 0.013 0.028 -9999 0 -0.25 6 6
FADD 0.011 0 -9999 0 -10000 0 0
MAPK8 0.037 0.038 -9999 0 -0.39 1 1
TRAF2 0.01 0.024 -9999 0 -0.58 1 1
TRAILR3 (trimer) -0.014 0.11 -9999 0 -0.49 30 30
CHUK 0.007 0.048 -9999 0 -0.58 4 4
TRAIL/TRAILR1/FADD 0.021 0.031 -9999 0 -0.35 4 4
DAP3 0.011 0 -9999 0 -10000 0 0
CASP10 -0.002 0.036 -9999 0 -0.34 5 5
JNK cascade 0.011 0.047 -9999 0 -0.36 9 9
TRAIL (trimer) 0.007 0.048 -9999 0 -0.58 4 4
TNFRSF10C -0.014 0.11 -9999 0 -0.49 30 30
TRAIL/TRAILR1/DAP3/GTP/FADD 0.025 0.027 -9999 0 -0.3 4 4
TRAIL/TRAILR2/FADD 0.02 0.034 -9999 0 -0.35 5 5
cell death 0.013 0.028 -9999 0 -0.25 6 6
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.028 0.028 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.01 0.024 -9999 0 -0.58 1 1
CASP8 0 0.035 -9999 0 -0.8 1 1
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.031 0.03 -9999 0 -0.29 5 5
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.022 0.072 -10000 0 -0.41 4 4
BAG4 0.009 0.034 -10000 0 -0.58 2 2
BAD 0.018 0.036 -10000 0 -0.4 2 2
NFKBIA 0.011 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.12 -10000 0 -0.52 30 30
BAX 0.018 0.034 -10000 0 -0.52 1 1
EnzymeConsortium:3.1.4.12 0.008 0.019 -10000 0 -0.09 3 3
IKBKB 0.026 0.069 -10000 0 -0.48 2 2
MAP2K2 0.027 0.036 -10000 0 -0.43 1 1
MAP2K1 0.026 0.037 -10000 0 -0.31 2 2
SMPD1 0.012 0.024 -10000 0 -0.24 2 2
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.028 0.068 -10000 0 -0.44 1 1
MAP2K4 0.02 0.048 -10000 0 -0.29 10 10
protein ubiquitination 0.027 0.071 -10000 0 -0.44 4 4
EnzymeConsortium:2.7.1.37 0.029 0.041 -10000 0 -0.3 2 2
response to UV 0 0 -10000 0 -0.002 1 1
RAF1 0.023 0.033 -10000 0 -0.25 2 2
CRADD 0.011 0.024 -10000 0 -0.58 1 1
mol:ceramide 0.014 0.029 -10000 0 -0.2 2 2
I-kappa-B-alpha/RELA/p50/ubiquitin 0.015 0 -10000 0 -10000 0 0
MADD 0.012 0 -10000 0 -10000 0 0
MAP3K1 0.016 0.045 -10000 0 -0.32 7 7
TRADD 0.012 0 -10000 0 -10000 0 0
RELA/p50 0.011 0 -10000 0 -10000 0 0
MAPK3 0.028 0.036 -10000 0 -0.28 2 2
MAPK1 0.028 0.036 -10000 0 -0.28 2 2
p50/RELA/I-kappa-B-alpha 0.017 0 -10000 0 -10000 0 0
FADD 0.022 0.069 -10000 0 -0.39 2 2
KSR1 0.018 0.033 -10000 0 -0.26 3 3
MAPK8 0.024 0.047 -10000 0 -0.28 10 10
TRAF2 0.01 0.024 -10000 0 -0.58 1 1
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.025 0.074 -10000 0 -0.51 3 3
TNF R/SODD 0.015 0.025 -10000 0 -0.42 2 2
TNF -0.016 0.12 -10000 0 -0.54 30 30
CYCS 0.018 0.046 0.13 11 -0.25 8 19
IKBKG 0.026 0.072 -10000 0 -0.51 3 3
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.017 0.072 -10000 0 -0.33 7 7
RELA 0.011 0 -10000 0 -10000 0 0
RIPK1 0.011 0 -10000 0 -10000 0 0
AIFM1 0.022 0.037 0.13 11 -0.35 2 13
TNF/TNF R/SODD 0.004 0.08 -10000 0 -0.33 32 32
TNFRSF1A 0.011 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.031 -10000 0 -0.58 1 1
NSMAF 0.022 0.068 -10000 0 -0.46 1 1
response to hydrogen peroxide 0 0 -10000 0 -0.002 1 1
BCL2 -0.008 0.1 -10000 0 -0.55 20 20
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.015 0.073 -9999 0 -10000 0 0
PLK1 0.054 0.12 -9999 0 -0.88 3 3
CDKN1B 0.095 0.073 -9999 0 -0.41 5 5
FOXO3 0.052 0.12 -9999 0 -0.65 4 4
KAT2B 0.002 0.1 -9999 0 -0.58 17 17
FOXO1/SIRT1 0.001 0.055 -9999 0 -0.37 4 4
CAT 0.056 0.12 -9999 0 -0.73 2 2
CTNNB1 0.011 0 -9999 0 -10000 0 0
AKT1 0.019 0.027 -9999 0 -0.57 1 1
FOXO1 0.022 0.049 -9999 0 -0.28 3 3
MAPK10 0.008 0.083 -9999 0 -0.29 38 38
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.067 0.066 -9999 0 -0.58 2 2
response to oxidative stress 0.009 0.013 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.001 0.088 -9999 0 -0.64 4 4
XPO1 0.001 0.08 -9999 0 -0.58 11 11
EP300 0.008 0.049 -9999 0 -0.58 4 4
BCL2L11 0.026 0.027 -9999 0 -10000 0 0
FOXO1/SKP2 0.023 0.054 -9999 0 -0.43 3 3
mol:GDP 0.009 0.013 -9999 0 -10000 0 0
RAN 0.013 0.001 -9999 0 -10000 0 0
GADD45A 0.08 0.089 -9999 0 -0.88 3 3
YWHAQ 0.011 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.054 0.053 -9999 0 -0.59 3 3
MST1 -0.025 0.15 -9999 0 -0.5 51 51
CSNK1D 0.011 0 -9999 0 -10000 0 0
CSNK1E 0.011 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.043 0.044 -9999 0 -0.45 3 3
YWHAB 0.011 0 -9999 0 -10000 0 0
MAPK8 0.032 0.017 -9999 0 -0.34 1 1
MAPK9 0.032 0.007 -9999 0 -10000 0 0
YWHAG 0.011 0 -9999 0 -10000 0 0
YWHAE 0.011 0 -9999 0 -10000 0 0
YWHAZ 0.008 0.042 -9999 0 -0.58 3 3
SIRT1 0.009 0.056 -9999 0 -0.57 5 5
SOD2 0.094 0.086 -9999 0 -0.63 2 2
RBL2 0.064 0.12 -9999 0 -1.4 2 2
RAL/GDP 0.026 0.01 -9999 0 -10000 0 0
CHUK 0.015 0.05 -9999 0 -0.58 4 4
Ran/GTP 0.012 0.002 -9999 0 -10000 0 0
CSNK1G2 0.009 0.034 -9999 0 -0.58 2 2
RAL/GTP 0.032 0.01 -9999 0 -10000 0 0
CSNK1G1 0.01 0.024 -9999 0 -0.58 1 1
FASLG -0.082 0.36 -9999 0 -1.4 42 42
SKP2 0.008 0.042 -9999 0 -0.58 3 3
USP7 0.013 0.001 -9999 0 -10000 0 0
IKBKB 0.018 0.021 -9999 0 -0.44 1 1
CCNB1 0.056 0.12 -9999 0 -0.73 2 2
FOXO1-3a-4/beta catenin 0.098 0.089 -9999 0 -0.44 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.053 -9999 0 -0.43 3 3
CSNK1A1 0.009 0.034 -9999 0 -0.58 2 2
SGK1 0.008 0.076 -9999 0 -0.48 14 14
CSNK1G3 0.01 0.024 -9999 0 -0.58 1 1
Ran/GTP/Exportin 1 0.014 0.051 -9999 0 -0.36 11 11
ZFAND5 0.068 0.067 -9999 0 -0.72 2 2
SFN 0.005 0.056 -9999 0 -0.47 8 8
CDK2 0.009 0.026 -9999 0 -0.58 1 1
FOXO3A/14-3-3 0.048 0.051 -9999 0 -0.42 4 4
CREBBP 0.01 0.009 -9999 0 -10000 0 0
FBXO32 0.054 0.12 -9999 0 -0.85 1 1
BCL6 0.065 0.099 -9999 0 -0.65 2 2
RALB 0.012 0.001 -9999 0 -10000 0 0
RALA 0.012 0.001 -9999 0 -10000 0 0
YWHAH 0.011 0 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.036 0.057 -10000 0 -0.61 3 3
CLOCK 0.012 0.031 -10000 0 -0.51 2 2
TIMELESS/CRY2 0.033 0.054 -10000 0 -1.2 1 1
DEC1/BMAL1 0.006 0.049 -10000 0 -0.33 12 12
ATR 0.009 0.034 -10000 0 -0.58 2 2
NR1D1 0.031 0.06 -10000 0 -1.3 1 1
ARNTL 0.012 0.034 -10000 0 -0.58 2 2
TIMELESS 0.031 0.058 -10000 0 -0.84 2 2
NPAS2 0.012 0.031 -10000 0 -0.51 2 2
CRY2 0.011 0 -10000 0 -10000 0 0
mol:CO -0.011 0.009 0.12 3 -10000 0 3
CHEK1 0.01 0.024 -10000 0 -0.58 1 1
mol:HEME 0.011 0.009 -10000 0 -0.12 3 3
PER1 0.004 0.063 -10000 0 -0.5 9 9
BMAL/CLOCK/NPAS2 0.033 0.037 -10000 0 -0.35 4 4
BMAL1/CLOCK 0.034 0.067 -10000 0 -0.62 4 4
S phase of mitotic cell cycle 0.036 0.057 -10000 0 -0.61 3 3
TIMELESS/CHEK1/ATR 0.036 0.058 -10000 0 -1.2 1 1
mol:NADPH 0.011 0.009 -10000 0 -0.12 3 3
PER1/TIMELESS 0.029 0.067 -10000 0 -0.93 2 2
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 -0.004 0.059 -10000 0 -0.46 10 10
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.007 0.025 0.26 5 -10000 0 5
BUB1B 0.018 0.029 -10000 0 -0.32 4 4
PLK1 0.015 0.006 -10000 0 -10000 0 0
PLK1S1 0.011 0.019 -10000 0 -0.27 2 2
KIF2A 0.02 0.015 -10000 0 -0.32 1 1
regulation of mitotic centrosome separation 0.015 0.006 -10000 0 -10000 0 0
GOLGA2 0.009 0.034 -10000 0 -0.58 2 2
Hec1/SPC24 0.011 0.068 -10000 0 -0.29 29 29
WEE1 0.017 0.044 -10000 0 -0.51 4 4
cytokinesis 0.022 0.049 -10000 0 -0.28 12 12
PP2A-alpha B56 0.029 0.036 -10000 0 -0.78 1 1
AURKA 0.014 0.004 -10000 0 -10000 0 0
PICH/PLK1 0.021 0.058 -10000 0 -0.3 17 17
CENPE 0.01 0.059 -10000 0 -0.32 18 18
RhoA/GTP 0.008 0.018 -10000 0 -0.43 1 1
positive regulation of microtubule depolymerization 0.02 0.015 -10000 0 -0.31 1 1
PPP2CA 0.011 0 -10000 0 -10000 0 0
FZR1 0.01 0.024 -10000 0 -0.58 1 1
TPX2 0.012 0.016 -10000 0 -0.26 2 2
PAK1 0.011 0 -10000 0 -10000 0 0
SPC24 -0.003 0.089 -10000 0 -0.56 15 15
FBXW11 0.011 0 -10000 0 -10000 0 0
CLSPN 0.013 0.013 -10000 0 -0.3 1 1
GORASP1 0.011 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -0.016 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.008 0.003 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0.001 0.011 1 -10000 0 1
STAG2 0.007 0.048 -10000 0 -0.58 4 4
GRASP65/GM130/RAB1/GTP -0.001 0.018 -10000 0 -0.25 3 3
spindle elongation 0.015 0.006 -10000 0 -10000 0 0
ODF2 0.011 0.001 -10000 0 -10000 0 0
BUB1 -0.001 0.035 -10000 0 -0.86 1 1
TPT1 0.013 0.005 -10000 0 -10000 0 0
CDC25C 0.015 0.004 -10000 0 -10000 0 0
CDC25B 0.01 0.027 -10000 0 -0.45 2 2
SGOL1 0.007 0.025 -10000 0 -0.26 5 5
RHOA 0.01 0.024 -10000 0 -0.58 1 1
CCNB1/CDK1 -0.003 0.025 -10000 0 -0.28 4 4
CDC14B 0.007 0.031 -10000 0 -0.43 3 3
CDC20 0.011 0 -10000 0 -10000 0 0
PLK1/PBIP1 0.01 0.046 -10000 0 -0.3 13 13
mitosis 0 0 -10000 0 -10000 0 0
FBXO5 0.016 0.028 -10000 0 -0.31 4 4
CDC2 0.001 0.001 -10000 0 -10000 0 0
NDC80 -0.003 0.09 -10000 0 -0.58 14 14
metaphase plate congression 0.014 0.006 -10000 0 -10000 0 0
ERCC6L 0.019 0.061 -10000 0 -0.31 17 17
NLP/gamma Tubulin 0.012 0.004 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.013 0.005 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0 -10000 0 -10000 0 0
PPP1R12A 0.007 0.049 -10000 0 -0.58 4 4
interphase 0 0 -10000 0 -10000 0 0
PLK1/PRC1-2 0.026 0.02 -10000 0 -0.3 2 2
GRASP65/GM130/RAB1/GTP/PLK1 0.028 0.023 -10000 0 -0.29 3 3
RAB1A 0.01 0.024 -10000 0 -0.58 1 1
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.017 0.005 -10000 0 -10000 0 0
mitotic prometaphase 0 0.001 0.012 1 -10000 0 1
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.025 -10000 0 -0.4 1 1
microtubule-based process 0.019 0.021 -10000 0 -0.32 2 2
Golgi organization 0.015 0.006 -10000 0 -10000 0 0
Cohesin/SA2 0.015 0.027 -10000 0 -0.31 4 4
PPP1CB/MYPT1 0.012 0.052 -10000 0 -0.48 6 6
KIF20A 0.009 0.034 -10000 0 -0.58 2 2
APC/C/CDC20 0.02 0.006 -10000 0 -10000 0 0
PPP2R1A 0.01 0.024 -10000 0 -0.58 1 1
chromosome segregation 0.01 0.046 -10000 0 -0.29 13 13
PRC1 0.011 0 -10000 0 -10000 0 0
ECT2 0.013 0.051 -10000 0 -0.33 13 13
C13orf34 0.017 0.005 -10000 0 -10000 0 0
NUDC 0.014 0.006 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.018 0.029 -10000 0 -0.32 4 4
spindle assembly 0.015 0.005 -10000 0 -10000 0 0
spindle stabilization 0.011 0.019 -10000 0 -0.27 2 2
APC/C/HCDH1 0.013 0.031 -10000 0 -0.36 4 4
MKLP2/PLK1 0.019 0.021 -10000 0 -0.32 2 2
CCNB1 0.012 0.001 -10000 0 -10000 0 0
PPP1CB 0.008 0.042 -10000 0 -0.59 3 3
BTRC 0.01 0.024 -10000 0 -0.58 1 1
ROCK2 0.012 0.07 -10000 0 -0.48 11 11
TUBG1 0.013 0.003 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.002 0.025 -10000 0 -0.27 4 4
MLF1IP 0 0.065 -10000 0 -0.44 13 13
INCENP 0.011 0.001 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.018 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.025 0.03 -10000 0 -0.32 4 4
CDKN1B 0.024 0.048 -10000 0 -0.52 4 4
CDKN1A 0.022 0.05 -10000 0 -0.41 6 6
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.009 0.039 -10000 0 -0.54 3 3
FOXO3 0.024 0.044 -10000 0 -0.54 3 3
AKT1 -0.005 0.043 -10000 0 -0.57 3 3
BAD 0.01 0.031 -10000 0 -0.52 2 2
AKT3 0.002 0.059 -10000 0 -0.26 26 26
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.024 0.046 -10000 0 -0.47 4 4
AKT1/ASK1 0.023 0.053 -10000 0 -0.58 4 4
BAD/YWHAZ 0.02 0.033 -10000 0 -0.35 4 4
RICTOR -0.009 0.11 -10000 0 -0.58 20 20
RAF1 0.011 0 -10000 0 -10000 0 0
JNK cascade -0.022 0.051 0.55 4 -10000 0 4
TSC1 0.024 0.044 -10000 0 -0.54 3 3
YWHAZ 0.008 0.042 -10000 0 -0.58 3 3
AKT1/RAF1 0.025 0.044 -10000 0 -0.54 3 3
EP300 0.007 0.048 -10000 0 -0.58 4 4
mol:GDP 0.019 0.045 -10000 0 -0.56 3 3
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.023 0.053 -10000 0 -0.54 4 4
YWHAQ 0.011 0 -10000 0 -10000 0 0
TBC1D4 0.015 0.04 -10000 0 -0.34 7 7
MAP3K5 0.009 0.034 -10000 0 -0.58 2 2
MAPKAP1 0.011 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.032 0.03 0.32 3 -10000 0 3
YWHAH 0.011 0 -10000 0 -10000 0 0
AKT1S1 0.024 0.052 -10000 0 -0.63 3 3
CASP9 0.024 0.046 -10000 0 -0.54 3 3
YWHAB 0.011 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.028 0.057 -10000 0 -0.63 4 4
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.022 0.022 -10000 0 -0.35 2 2
YWHAE 0.011 0 -10000 0 -10000 0 0
SRC 0.01 0.024 -10000 0 -0.58 1 1
AKT2/p21CIP1 0.026 0.051 -10000 0 -0.47 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.013 0.014 -10000 0 -10000 0 0
CHUK 0.022 0.058 -10000 0 -0.5 6 6
BAD/BCL-XL 0.035 0.049 -10000 0 -0.58 3 3
mTORC2 0.003 0.062 -10000 0 -0.33 20 20
AKT2 0.013 0.019 -10000 0 -0.35 1 1
FOXO1-3a-4/14-3-3 family 0.042 0.046 -10000 0 -0.52 3 3
PDPK1 0.011 0 -10000 0 -10000 0 0
MDM2 0.022 0.052 -10000 0 -0.49 5 5
MAPKKK cascade -0.025 0.043 0.52 3 -10000 0 3
MDM2/Cbp/p300 0.032 0.057 -10000 0 -0.49 5 5
TSC1/TSC2 0.028 0.051 -10000 0 -0.6 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.03 0.054 -10000 0 -0.47 5 5
glucose import 0.005 0.071 -10000 0 -0.31 18 18
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.021 0.031 -10000 0 -0.34 3 3
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.005 0.072 -10000 0 -0.31 18 18
GSK3A 0.024 0.044 -10000 0 -0.54 3 3
FOXO1 0.023 0.047 -10000 0 -0.54 3 3
GSK3B 0.023 0.054 -10000 0 -0.59 4 4
SFN 0.005 0.056 -10000 0 -0.47 8 8
G1/S transition of mitotic cell cycle 0.028 0.053 -10000 0 -0.57 4 4
p27Kip1/14-3-3 family 0.036 0.029 -10000 0 -0.39 1 1
PRKACA 0.011 0 -10000 0 -10000 0 0
KPNA1 0.009 0.034 -10000 0 -0.58 2 2
HSP90AA1 0.01 0.024 -10000 0 -0.58 1 1
YWHAG 0.011 0 -10000 0 -10000 0 0
RHEB 0.011 0 -10000 0 -10000 0 0
CREBBP 0.011 0 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.015 0.029 -9999 0 -0.39 3 3
FBXW11 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.019 0.033 -9999 0 -0.34 5 5
NF kappa B1 p50/RelA/I kappa B alpha 0.025 0.049 -9999 0 -10000 0 0
NFKBIA 0.009 0.052 -9999 0 -0.22 22 22
MAPK14 0.011 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0.019 -9999 0 -0.31 2 2
ARRB2 0.014 0 -9999 0 -10000 0 0
REL 0.008 0.042 -9999 0 -0.58 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.019 0.031 -9999 0 -0.32 5 5
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.019 -9999 0 -0.31 2 2
PIK3CA 0.009 0.034 -9999 0 -0.58 2 2
NF kappa B1 p50 dimer 0.015 0.023 -9999 0 -0.37 2 2
PIK3R1 0.008 0.042 -9999 0 -0.58 3 3
NFKB1 0.017 0.023 -9999 0 -0.37 2 2
RELA 0.011 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.014 0.053 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.028 0.047 -9999 0 -10000 0 0
SRC 0.01 0.024 -9999 0 -0.58 1 1
PI3K 0.013 0.04 -9999 0 -0.42 5 5
NF kappa B1 p50/RelA 0.014 0.053 -9999 0 -10000 0 0
IKBKB 0.011 0.019 -9999 0 -0.46 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -9999 0 -10000 0 0
SYK 0.011 0.019 -9999 0 -0.46 1 1
I kappa B alpha/PIK3R1 0.013 0.054 -9999 0 -0.29 3 3
cell death 0.027 0.045 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.019 0.033 -9999 0 -0.34 5 5
LCK -0.031 0.14 -9999 0 -0.51 48 48
BCL3 0.009 0.039 -9999 0 -0.54 3 3
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.015 0.11 -10000 0 -0.5 30 30
CLTC 0.024 0.032 -10000 0 -0.7 1 1
calcium ion-dependent exocytosis 0.02 0.022 -10000 0 -0.46 1 1
Dynamin 2/GTP 0.019 0.022 -10000 0 -0.32 2 2
EXOC4 0.011 0 -10000 0 -10000 0 0
CD59 0.022 0.031 -10000 0 -0.7 1 1
CPE -0.038 0.12 -10000 0 -0.32 95 95
CTNNB1 0.011 0 -10000 0 -10000 0 0
membrane fusion 0.02 0.022 -10000 0 -0.45 1 1
CTNND1 0.024 0.021 -10000 0 -0.3 2 2
DNM2 0.01 0.024 -10000 0 -0.58 1 1
mol:PI-4-5-P2 0.024 0.032 -10000 0 -0.5 2 2
TSHR 0 0.062 -10000 0 -0.28 26 26
INS 0.008 0.024 -10000 0 -0.52 1 1
BIN1 0.006 0.054 -10000 0 -0.58 5 5
mol:Choline 0.02 0.022 -10000 0 -0.45 1 1
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.019 -10000 0 -0.31 2 2
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.01 0.024 -10000 0 -0.58 1 1
mol:Ca2+ 0.018 0.022 -10000 0 -0.32 2 2
JUP 0.021 0.032 -10000 0 -0.7 1 1
ASAP2/amphiphysin II 0.017 0.04 -10000 0 -0.32 8 8
ARF6/GTP 0.008 0.018 -10000 0 -0.43 1 1
CDH1 0.021 0.032 -10000 0 -0.7 1 1
clathrin-independent pinocytosis 0.008 0.018 -10000 0 -0.43 1 1
MAPK8IP3 0.005 0.057 -10000 0 -0.51 7 7
positive regulation of endocytosis 0.008 0.018 -10000 0 -0.43 1 1
EXOC2 0.01 0.024 -10000 0 -0.58 1 1
substrate adhesion-dependent cell spreading 0.026 0.065 -10000 0 -0.61 4 4
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.01 0.024 -10000 0 -0.58 1 1
regulation of calcium-dependent cell-cell adhesion 0.002 0.029 0.62 1 -10000 0 1
positive regulation of phagocytosis 0.015 0.015 -10000 0 -0.36 1 1
ARF6/GTP/JIP3 0.011 0.038 -10000 0 -0.31 8 8
ACAP1 0.014 0.032 -10000 0 -0.36 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.009 0.072 -10000 0 -0.7 1 1
clathrin heavy chain/ACAP1 0.027 0.032 -10000 0 -0.66 1 1
JIP4/KLC1 0.021 0.02 -10000 0 -0.32 2 2
EXOC1 0.01 0.024 -10000 0 -0.58 1 1
exocyst 0.026 0.066 -10000 0 -0.62 4 4
RALA/GTP 0.008 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.014 0.022 -10000 0 -0.36 2 2
receptor recycling 0.008 0.018 -10000 0 -0.43 1 1
CTNNA1 0.023 0.028 -10000 0 -0.3 4 4
NME1 0.014 0.019 -10000 0 -0.31 2 2
clathrin coat assembly 0.024 0.031 -10000 0 -0.69 1 1
IL2RA 0.001 0.07 -10000 0 -0.5 2 2
VAMP3 0.015 0.015 -10000 0 -0.36 1 1
GLUT4/clathrin heavy chain/ACAP1 -0.012 0.053 -10000 0 -0.45 2 2
EXOC6 0.008 0.042 -10000 0 -0.58 3 3
PLD1 0.016 0.029 -10000 0 -0.37 3 3
PLD2 0.018 0.008 -10000 0 -10000 0 0
EXOC5 -0.006 0.099 -10000 0 -0.58 17 17
PIP5K1C 0.024 0.032 -10000 0 -0.51 2 2
SDC1 0.021 0.032 -10000 0 -0.7 1 1
ARF6/GDP 0.014 0.019 -10000 0 -0.31 2 2
EXOC7 0.011 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.002 0.03 -10000 0 -0.64 1 1
mol:Phosphatidic acid 0.02 0.022 -10000 0 -0.45 1 1
endocytosis -0.017 0.039 0.32 8 -10000 0 8
SCAMP2 0.011 0 -10000 0 -10000 0 0
ADRB2 0.008 0.08 -10000 0 -0.65 1 1
EXOC3 0.011 0 -10000 0 -10000 0 0
ASAP2 0.009 0.034 -10000 0 -0.58 2 2
Dynamin 2/GDP 0.02 0.022 -10000 0 -0.32 2 2
KLC1 0.011 0 -10000 0 -10000 0 0
AVPR2 0.003 0.083 -10000 0 -0.65 1 1
RALA 0.011 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.031 -10000 0 -0.59 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.004 0.064 -10000 0 -0.58 7 7
SMAD2 0.013 0.023 0.24 1 -0.25 2 3
SMAD3 0.03 0.031 -10000 0 -10000 0 0
SMAD3/SMAD4 0.034 0.03 -10000 0 -10000 0 0
SMAD4/Ubc9/PIASy 0.018 0.043 -10000 0 -0.35 8 8
SMAD2/SMAD2/SMAD4 0.029 0.035 -10000 0 -10000 0 0
PPM1A 0.011 0 -10000 0 -10000 0 0
CALM1 0.011 0 -10000 0 -10000 0 0
SMAD2/SMAD4 0.014 0.041 -10000 0 -0.31 7 7
MAP3K1 0.005 0.059 -10000 0 -0.58 6 6
TRAP-1/SMAD4 0.01 0.053 -10000 0 -0.42 9 9
MAPK3 0.01 0.024 -10000 0 -0.58 1 1
MAPK1 0.01 0.024 -10000 0 -0.58 1 1
NUP214 0.011 0 -10000 0 -10000 0 0
CTDSP1 0.01 0.024 -10000 0 -0.58 1 1
CTDSP2 0.011 0 -10000 0 -10000 0 0
CTDSPL 0.011 0 -10000 0 -10000 0 0
KPNB1 0.011 0 -10000 0 -10000 0 0
TGFBRAP1 0.009 0.034 -10000 0 -0.58 2 2
UBE2I 0.011 0 -10000 0 -10000 0 0
NUP153 0.011 0 -10000 0 -10000 0 0
KPNA2 0.011 0 -10000 0 -10000 0 0
PIAS4 0.01 0.024 -10000 0 -0.58 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.01 0.058 -9999 0 -0.4 4 4
CaM/Ca2+ 0.008 0 -9999 0 -10000 0 0
AKT1 0.01 0.024 -9999 0 -0.58 1 1
AKT2 0.009 0.036 -9999 0 -0.5 3 3
STXBP4 0.005 0.059 -9999 0 -0.58 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.029 0.056 -9999 0 -0.39 3 3
YWHAZ 0.008 0.042 -9999 0 -0.58 3 3
CALM1 0.011 0 -9999 0 -10000 0 0
YWHAQ 0.011 0 -9999 0 -10000 0 0
TBC1D4 0.013 0.047 -9999 0 -0.42 7 7
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.011 0 -9999 0 -10000 0 0
YWHAB 0.011 0 -9999 0 -10000 0 0
SNARE/Synip 0.019 0.038 -9999 0 -0.35 6 6
YWHAG 0.011 0 -9999 0 -10000 0 0
ASIP 0 0.054 -9999 0 -0.46 8 8
PRKCI 0.008 0.042 -9999 0 -0.58 3 3
AS160/CaM/Ca2+ 0.008 0 -9999 0 -10000 0 0
RHOQ 0.011 0 -9999 0 -10000 0 0
GYS1 0.022 0.043 -9999 0 -0.47 4 4
PRKCZ 0.01 0.031 -9999 0 -0.52 2 2
TRIP10 0.01 0.024 -9999 0 -0.58 1 1
TC10/GTP/CIP4/Exocyst 0.015 0.015 -9999 0 -0.36 1 1
AS160/14-3-3 0.033 0.034 -9999 0 -0.34 2 2
VAMP2 0.011 0 -9999 0 -10000 0 0
SLC2A4 0.029 0.06 -9999 0 -0.44 3 3
STX4 0.011 0 -9999 0 -10000 0 0
GSK3B 0.018 0.045 -9999 0 -0.58 3 3
SFN 0.005 0.056 -9999 0 -0.47 8 8
LNPEP 0.003 0.068 -9999 0 -0.58 8 8
YWHAE 0.011 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.035 0.051 -10000 0 -0.41 6 6
adherens junction organization 0.033 0.033 -10000 0 -0.46 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.037 0.051 -10000 0 -0.48 3 3
FMN1 0.028 0.048 -10000 0 -0.41 2 2
mol:IP3 0.03 0.038 -10000 0 -0.49 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.028 0.03 -10000 0 -0.37 2 2
CTNNB1 0.011 0.001 -10000 0 -10000 0 0
AKT1 0.035 0.043 -10000 0 -0.69 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.032 0.039 -10000 0 -0.56 2 2
CTNND1 0.012 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.031 0.036 -10000 0 -0.39 3 3
VASP 0.033 0.029 -10000 0 -0.46 1 1
ZYX 0.032 0.038 -10000 0 -0.74 1 1
JUB 0.033 0.029 -10000 0 -0.46 1 1
EGFR(dimer) 0.029 0.045 -10000 0 -0.33 6 6
E-cadherin/beta catenin-gamma catenin 0.021 0.021 -10000 0 -0.34 2 2
mol:PI-3-4-5-P3 0.03 0.038 -10000 0 -0.3 6 6
PIK3CA 0.01 0.034 -10000 0 -0.58 2 2
PI3K 0.031 0.038 -10000 0 -0.31 6 6
FYN 0.031 0.054 -10000 0 -0.33 7 7
mol:Ca2+ 0.029 0.037 -10000 0 -0.48 1 1
JUP 0.01 0.024 -10000 0 -0.59 1 1
PIK3R1 0.009 0.042 -10000 0 -0.58 3 3
mol:DAG 0.03 0.038 -10000 0 -0.49 1 1
CDH1 0.01 0.024 -10000 0 -0.58 1 1
RhoA/GDP 0.037 0.054 -10000 0 -0.49 4 4
establishment of polarity of embryonic epithelium 0.032 0.028 -10000 0 -0.45 1 1
SRC 0.01 0.024 -10000 0 -0.58 1 1
RAC1 0.011 0 -10000 0 -10000 0 0
RHOA 0.01 0.024 -10000 0 -0.58 1 1
EGFR 0.004 0.063 -10000 0 -0.53 8 8
CASR 0.028 0.044 -10000 0 -0.45 1 1
RhoA/GTP 0.032 0.039 -10000 0 -0.47 2 2
AKT2 0.034 0.047 -10000 0 -0.58 2 2
actin cable formation 0.033 0.047 -10000 0 -0.4 2 2
apoptosis -0.032 0.047 0.37 6 -10000 0 6
CTNNA1 0.01 0.035 -10000 0 -0.58 2 2
mol:GDP 0.032 0.054 -10000 0 -0.52 3 3
PIP5K1A 0.032 0.037 -10000 0 -0.4 3 3
PLCG1 0.03 0.038 -10000 0 -0.5 1 1
Rac1/GTP -0.005 0.036 -10000 0 -0.37 3 3
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex -0.002 0.029 -9999 0 -0.63 1 1
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.021 -9999 0 -0.23 3 3
AP2 0.015 0.03 -9999 0 -0.34 4 4
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.016 0.002 -9999 0 -10000 0 0
CLTB 0.01 0.031 -9999 0 -0.52 2 2
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0.014 -9999 0 -0.26 1 1
CD4 -0.014 0.12 -9999 0 -0.55 27 27
CLTA 0.011 0 -9999 0 -10000 0 0
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
ARFGAP1 0.007 0.026 -9999 0 -0.36 3 3
mol:PI-4-5-P2 -0.001 0.019 -9999 0 -0.32 2 2
ARF1/GTP -0.001 0.012 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.02 0.025 -9999 0 -0.3 3 3
mol:Choline -0.001 0.019 -9999 0 -0.32 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.011 0.019 -9999 0 -0.45 1 1
DDEF1 -0.001 0.019 -9999 0 -0.33 2 2
ARF1/GDP 0.005 0.021 -9999 0 -0.26 3 3
AP2M1 0.011 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.013 0.01 -9999 0 -0.22 1 1
Rac/GTP 0.009 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.02 0.021 -9999 0 -0.25 3 3
ARFIP2 0.01 0.003 -9999 0 -10000 0 0
COPA 0.011 0 -9999 0 -10000 0 0
RAC1 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.02 0.01 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0.008 0.011 -9999 0 -0.26 1 1
GGA3 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.015 0.011 -9999 0 -0.2 1 1
AP2A1 0.008 0.041 -9999 0 -0.49 4 4
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.02 0.028 -9999 0 -0.61 1 1
ARF1/GDP/Membrin 0.015 0.011 -9999 0 -0.19 1 1
Arfaptin 2/Rac/GDP 0.015 0.002 -9999 0 -10000 0 0
CYTH2 0.012 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0.016 0.011 -9999 0 -0.25 1 1
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.008 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.018 0.05 -9999 0 -0.4 1 1
PLD2 -0.001 0.019 -9999 0 -0.32 2 2
ARF-GAP1/v-SNARE 0.007 0.026 -9999 0 -0.36 3 3
PIP5K1A -0.001 0.019 -9999 0 -0.33 2 2
ARF1/GTP/Membrin/GBF1/p115 -0.002 0.019 -9999 0 -0.28 2 2
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.019 -9999 0 -0.32 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.007 0.026 -9999 0 -0.36 3 3
GOSR2 -0.001 0.008 -9999 0 -10000 0 0
USO1 -0.005 0.049 -9999 0 -0.48 6 6
GBF1 -0.001 0.019 -9999 0 -0.42 1 1
ARF1/GTP/Arfaptin 2 0.016 0.011 -9999 0 -0.24 1 1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.005 0.078 -9999 0 -0.35 22 22
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.013 0.04 -9999 0 -0.42 5 5
FBXW11 0.011 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.011 0 -9999 0 -10000 0 0
CHUK 0.007 0.048 -9999 0 -0.58 4 4
NF kappa B2 p100/RelB 0.029 0.051 -9999 0 -0.41 6 6
NFKB1 0.01 0.024 -9999 0 -0.58 1 1
MAP3K14 0.01 0.024 -9999 0 -0.58 1 1
NF kappa B1 p50/RelB 0.014 0.032 -9999 0 -0.37 4 4
RELB 0.009 0.036 -9999 0 -0.5 3 3
NFKB2 0.01 0.031 -9999 0 -0.52 2 2
NF kappa B2 p52/RelB 0.013 0.038 -9999 0 -0.49 3 3
regulation of B cell activation 0.013 0.038 -9999 0 -0.49 3 3
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.022 0.022 -9999 0 -0.35 2 2
E-cadherin/beta catenin 0.016 0.018 -9999 0 -0.42 1 1
CTNNB1 0.011 0 -9999 0 -10000 0 0
JUP 0.01 0.024 -9999 0 -0.58 1 1
CDH1 0.01 0.024 -9999 0 -0.58 1 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 595 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.QG.A5Z2 TCGA.QG.A5Z1 TCGA.QG.A5YX TCGA.QG.A5YW
109_MAP3K5 0.044 0.044 0.044 0.044
47_PPARGC1A 0.011 0.011 0.011 0.011
105_BMP4 0.011 0.011 -0.58 0.011
105_BMP6 0.011 0.011 -0.58 0.011
105_BMP7 0.011 0.011 0.011 0.011
105_BMP2 0.011 0.011 0.011 0.011
131_RELN/VLDLR 0.029 0.029 -0.32 0.029
30_TGFB1/TGF beta receptor Type II 0.011 0.011 0.011 0.011
84_STAT5B -0.14 -0.0064 -0.18 0.037
84_STAT5A -0.14 -0.0064 -0.18 0.037
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/COADREAD-TP/9908691/COADREAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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