PARADIGM pathway analysis of mRNASeq expression data
Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1TD9WQ7
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1TD9WQ7
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 60 significant pathways identified in this analysis.

Table 1.  Get Full Table Top 10 out of 131 pathways in order of significance.

Pathway.Name Avg.Num.Perturbations
Glypican 2 network 309
Aurora B signaling 209
Ephrin A reverse signaling 190
Effects of Botulinum toxin 158
Aurora C signaling 153
TCGA08_retinoblastoma 139
PLK1 signaling events 129
FOXM1 transcription factor network 124
Retinoic acid receptors-mediated signaling 107
Reelin signaling pathway 100
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 669 . 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 ( 669 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Glypican 2 network 0.4619 309 1238 4 -0.17 -1000 1000 -1000 -0.022 -1000
Aurora B signaling 0.3124 209 14034 67 -0.37 0.01 1000 -1000 -0.038 -1000
Ephrin A reverse signaling 0.2840 190 1330 7 -0.099 0 1000 -1000 -0.014 -1000
Effects of Botulinum toxin 0.2362 158 4108 26 -0.2 0.01 1000 -1000 -0.032 -1000
Aurora C signaling 0.2287 153 1075 7 -0.29 0 1000 -1000 -0.023 -1000
TCGA08_retinoblastoma 0.2078 139 1115 8 -0.095 0.06 1000 -1000 -0.012 -1000
PLK1 signaling events 0.1928 129 11027 85 -0.29 0.065 1000 -1000 -0.03 -1000
FOXM1 transcription factor network 0.1854 124 6374 51 -0.39 0.01 1000 -1000 -0.16 -1000
Retinoic acid receptors-mediated signaling 0.1599 107 6243 58 -0.25 0.012 1000 -1000 -0.045 -1000
Reelin signaling pathway 0.1495 100 5612 56 -0.23 0.019 1000 -1000 -0.035 -1000
Syndecan-1-mediated signaling events 0.1390 93 3187 34 -0.13 0.01 1000 -1000 -0.036 -1000
Osteopontin-mediated events 0.1390 93 3555 38 -0.14 0.01 1000 -1000 -0.05 -1000
EGFR-dependent Endothelin signaling events 0.1345 90 1910 21 -0.21 0.01 1000 -1000 -0.032 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.1330 89 7569 85 -0.2 0.01 1000 -1000 -0.045 -1000
IL23-mediated signaling events 0.1300 87 5244 60 -0.44 0.01 1000 -1000 -0.13 -1000
Signaling mediated by p38-alpha and p38-beta 0.1151 77 3420 44 -0.094 0.01 1000 -1000 -0.033 -1000
Visual signal transduction: Rods 0.1121 75 3949 52 -0.2 0.01 1000 -1000 -0.037 -1000
PLK2 and PLK4 events 0.1106 74 223 3 -0.03 -0.01 1000 -1000 -0.005 -1000
Glucocorticoid receptor regulatory network 0.1076 72 8289 114 -0.5 0.25 1000 -1000 -0.041 -1000
TCGA08_p53 0.1076 72 507 7 -0.069 0.034 1000 -1000 -0.005 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1076 72 4913 68 -0.22 0.07 1000 -1000 -0.074 -1000
Thromboxane A2 receptor signaling 0.1046 70 7385 105 -0.23 0.061 1000 -1000 -0.044 -1000
HIF-1-alpha transcription factor network 0.1001 67 5135 76 -0.074 0.063 1000 -1000 -0.054 -1000
Coregulation of Androgen receptor activity 0.0972 65 4986 76 -0.18 0.02 1000 -1000 -0.036 -1000
Ras signaling in the CD4+ TCR pathway 0.0972 65 1112 17 -0.1 0.011 1000 -1000 -0.03 -1000
a4b1 and a4b7 Integrin signaling 0.0957 64 323 5 -0.047 0.005 1000 -1000 -0.022 -1000
Signaling events regulated by Ret tyrosine kinase 0.0957 64 5296 82 -0.094 0.01 1000 -1000 -0.048 -1000
BMP receptor signaling 0.0942 63 5114 81 -0.21 0.039 1000 -1000 -0.05 -1000
PDGFR-alpha signaling pathway 0.0927 62 2766 44 -0.076 0.017 1000 -1000 -0.03 -1000
Rapid glucocorticoid signaling 0.0927 62 1251 20 -0.14 0.012 1000 -1000 -0.019 -1000
BARD1 signaling events 0.0912 61 3505 57 -0.14 0.049 1000 -1000 -0.035 -1000
p75(NTR)-mediated signaling 0.0912 61 7658 125 -0.21 0.01 1000 -1000 -0.049 -1000
amb2 Integrin signaling 0.0912 61 5072 82 -0.12 0.01 1000 -1000 -0.045 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0882 59 2015 34 -0.063 0.01 1000 -1000 -0.032 -1000
Aurora A signaling 0.0867 58 3506 60 -0.21 0.017 1000 -1000 -0.032 -1000
LPA receptor mediated events 0.0852 57 5913 102 -0.21 0.01 1000 -1000 -0.045 -1000
IL12-mediated signaling events 0.0837 56 4881 87 -0.23 0.15 1000 -1000 -0.099 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0837 56 3056 54 -0.13 0.021 1000 -1000 -0.044 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0837 56 2087 37 -0.12 0.01 1000 -1000 -0.032 -1000
Syndecan-4-mediated signaling events 0.0822 55 3711 67 -0.23 0.019 1000 -1000 -0.051 -1000
Signaling events mediated by the Hedgehog family 0.0792 53 2788 52 -0.057 0.049 1000 -1000 -0.04 -1000
Visual signal transduction: Cones 0.0762 51 1966 38 -0.12 0.012 1000 -1000 -0.032 -1000
Arf6 signaling events 0.0732 49 3076 62 -0.21 0.012 1000 -1000 -0.036 -1000
Endothelins 0.0732 49 4737 96 -0.11 0.021 1000 -1000 -0.044 -1000
TCGA08_rtk_signaling 0.0703 47 1233 26 -0.21 0.01 1000 -1000 -0.012 -1000
Cellular roles of Anthrax toxin 0.0673 45 1771 39 -0.042 0.01 1000 -1000 -0.018 -1000
IL1-mediated signaling events 0.0673 45 2847 62 -0.13 0.045 1000 -1000 -0.044 -1000
JNK signaling in the CD4+ TCR pathway 0.0658 44 759 17 -0.16 0.035 1000 -1000 -0.031 -1000
IL4-mediated signaling events 0.0658 44 4006 91 -0.68 0.3 1000 -1000 -0.14 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0658 44 3679 83 -0.24 0.15 1000 -1000 -0.043 -1000
Nongenotropic Androgen signaling 0.0643 43 2247 52 -0.18 0.013 1000 -1000 -0.033 -1000
Glypican 1 network 0.0628 42 2047 48 -0.1 0.024 1000 -1000 -0.023 -1000
Integrins in angiogenesis 0.0628 42 3543 84 -0.069 0.023 1000 -1000 -0.039 -1000
LPA4-mediated signaling events 0.0613 41 495 12 -0.038 0.009 1000 -1000 -0.006 -1000
FAS signaling pathway (CD95) 0.0568 38 1813 47 -0.16 0.026 1000 -1000 -0.031 -1000
IL2 signaling events mediated by STAT5 0.0568 38 849 22 -0.12 0.021 1000 -1000 -0.029 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0568 38 4608 120 -0.17 0.095 1000 -1000 -0.046 -1000
TCR signaling in naïve CD8+ T cells 0.0538 36 3375 93 -0.087 0.056 1000 -1000 -0.047 -1000
Regulation of nuclear SMAD2/3 signaling 0.0523 35 4797 136 -0.19 0.073 1000 -1000 -0.041 -1000
Signaling events mediated by HDAC Class III 0.0508 34 1373 40 -0.087 0.07 1000 -1000 -0.022 -1000
Canonical Wnt signaling pathway 0.0478 32 1658 51 -0.2 0.1 1000 -1000 -0.03 -1000
S1P1 pathway 0.0448 30 1109 36 -0.089 0.01 1000 -1000 -0.031 -1000
Ephrin B reverse signaling 0.0433 29 1426 48 -0.17 0.076 1000 -1000 -0.033 -1000
Fc-epsilon receptor I signaling in mast cells 0.0419 28 2729 97 -0.13 0.026 1000 -1000 -0.047 -1000
S1P5 pathway 0.0404 27 468 17 -0.041 0.026 1000 -1000 -0.033 -1000
IFN-gamma pathway 0.0389 26 1828 68 -0.24 0.056 1000 -1000 -0.05 -1000
Syndecan-3-mediated signaling events 0.0389 26 942 35 -0.21 0.01 1000 -1000 -0.033 -1000
p38 MAPK signaling pathway 0.0389 26 1167 44 -0.11 0.014 1000 -1000 -0.036 -1000
Syndecan-2-mediated signaling events 0.0359 24 1690 69 -0.076 0.031 1000 -1000 -0.025 -1000
Signaling events mediated by PTP1B 0.0359 24 1839 76 -0.2 0.017 1000 -1000 -0.045 -1000
Paxillin-dependent events mediated by a4b1 0.0359 24 875 36 -0.12 0.026 1000 -1000 -0.044 -1000
Insulin-mediated glucose transport 0.0329 22 719 32 -0.13 0.031 1000 -1000 -0.042 -1000
ErbB4 signaling events 0.0314 21 1507 69 -0.21 0.044 1000 -1000 -0.045 -1000
Presenilin action in Notch and Wnt signaling 0.0314 21 1331 61 -0.2 0.038 1000 -1000 -0.044 -1000
Calcium signaling in the CD4+ TCR pathway 0.0314 21 676 31 -0.081 0.01 1000 -1000 -0.049 -1000
VEGFR1 specific signals 0.0314 21 1181 56 -0.17 0.031 1000 -1000 -0.043 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0314 21 701 33 -0.1 0.029 1000 -1000 -0.033 -1000
E-cadherin signaling events 0.0314 21 105 5 -0.011 0.01 1000 -1000 -0.024 -1000
EPO signaling pathway 0.0299 20 1148 55 -0.047 0.048 1000 -1000 -0.044 -1000
IL2 signaling events mediated by PI3K 0.0299 20 1183 58 -0.15 0.017 1000 -1000 -0.057 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0299 20 1521 74 -0.21 0.055 1000 -1000 -0.058 -1000
Caspase cascade in apoptosis 0.0284 19 1477 74 -0.055 0.024 1000 -1000 -0.029 -1000
Regulation of p38-alpha and p38-beta 0.0284 19 1065 54 -0.089 0.011 1000 -1000 -0.036 -1000
Wnt signaling 0.0284 19 135 7 -0.018 0.009 1000 -1000 -0.011 -1000
IL27-mediated signaling events 0.0269 18 937 51 -0.2 0.01 1000 -1000 -0.052 -1000
Regulation of Telomerase 0.0254 17 1759 102 -0.21 0.024 1000 -1000 -0.064 -1000
EPHB forward signaling 0.0224 15 1291 85 -0.17 0.031 1000 -1000 -0.043 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0224 15 1967 125 -0.079 0.041 1000 -1000 -0.055 -1000
S1P3 pathway 0.0224 15 645 42 -0.062 0.023 1000 -1000 -0.036 -1000
E-cadherin signaling in keratinocytes 0.0224 15 674 43 -0.21 0.037 1000 -1000 -0.039 -1000
S1P4 pathway 0.0224 15 388 25 -0.041 0.026 1000 -1000 -0.032 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0224 15 1225 78 -0.11 0.036 1000 -1000 -0.046 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0209 14 757 52 -0.069 0.018 1000 -1000 -0.033 -1000
IL6-mediated signaling events 0.0209 14 1095 75 -0.077 0.048 1000 -1000 -0.087 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0209 14 1256 88 -0.079 0.031 1000 -1000 -0.079 -1000
ErbB2/ErbB3 signaling events 0.0194 13 891 65 -0.057 0.02 1000 -1000 -0.054 -1000
Noncanonical Wnt signaling pathway 0.0194 13 355 26 -0.018 0.026 1000 -1000 -0.044 -1000
FOXA2 and FOXA3 transcription factor networks 0.0194 13 625 46 -0.051 0.03 1000 -1000 -0.075 -1000
Canonical NF-kappaB pathway 0.0179 12 482 39 -0.084 0.052 1000 -1000 -0.051 -1000
Hedgehog signaling events mediated by Gli proteins 0.0179 12 816 65 -0.067 0.058 1000 -1000 -0.046 -1000
TRAIL signaling pathway 0.0179 12 583 48 -0.059 0.038 1000 -1000 -0.037 -1000
BCR signaling pathway 0.0179 12 1261 99 -0.1 0.035 1000 -1000 -0.049 -1000
Insulin Pathway 0.0179 12 916 74 -0.064 0.028 1000 -1000 -0.046 -1000
Signaling events mediated by PRL 0.0179 12 424 34 -0.12 0.028 1000 -1000 -0.022 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0164 11 311 28 -0.063 0.028 1000 -1000 -0.031 -1000
Ceramide signaling pathway 0.0149 10 793 76 -0.031 0.024 1000 -1000 -0.029 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0149 10 460 45 -0.02 0.044 1000 -1000 -0.049 -1000
E-cadherin signaling in the nascent adherens junction 0.0135 9 748 76 -0.017 0.037 1000 -1000 -0.048 -1000
Plasma membrane estrogen receptor signaling 0.0135 9 844 86 -0.073 0.04 1000 -1000 -0.05 -1000
Regulation of Androgen receptor activity 0.0135 9 649 70 -0.085 0.045 1000 -1000 -0.048 -1000
Nectin adhesion pathway 0.0120 8 510 63 -0.064 0.038 1000 -1000 -0.048 -1000
HIF-2-alpha transcription factor network 0.0120 8 358 43 -0.073 0.085 1000 -1000 -0.05 -1000
Signaling mediated by p38-gamma and p38-delta 0.0120 8 121 15 0 0.028 1000 -1000 -0.011 -1000
Atypical NF-kappaB pathway 0.0120 8 252 31 -0.066 0.024 1000 -1000 -0.024 -1000
ceramide signaling pathway 0.0090 6 312 49 -0.02 0.03 1000 -1000 -0.024 -1000
Arf6 trafficking events 0.0090 6 459 71 -0.12 0.034 1000 -1000 -0.037 -1000
Signaling events mediated by HDAC Class II 0.0075 5 448 75 -0.085 0.032 1000 -1000 -0.034 -1000
FoxO family signaling 0.0075 5 353 64 -0.11 0.071 1000 -1000 -0.061 -1000
Class I PI3K signaling events 0.0075 5 378 73 -0.066 0.033 1000 -1000 -0.038 -1000
IGF1 pathway 0.0060 4 236 57 -0.041 0.043 1000 -1000 -0.047 -1000
Circadian rhythm pathway 0.0045 3 73 22 -0.041 0.021 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class I 0.0045 3 406 104 -0.022 0.044 1000 -1000 -0.037 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0030 2 49 23 -0.002 0.036 1000 -1000 -0.04 -1000
PDGFR-beta signaling pathway 0.0030 2 271 97 -0.037 0.048 1000 -1000 -0.043 -1000
Class IB PI3K non-lipid kinase events 0.0030 2 6 3 -0.009 0.009 1000 -1000 -0.007 -1000
Arf6 downstream pathway 0.0015 1 43 43 -0.019 0.02 1000 -1000 -0.025 -1000
Class I PI3K signaling events mediated by Akt 0.0015 1 89 68 -0.029 0.042 1000 -1000 -0.038 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0015 1 41 27 -0.003 0.024 1000 -1000 -0.029 -1000
mTOR signaling pathway 0.0000 0 15 53 -0.008 0.027 1000 -1000 -0.038 -1000
Arf1 pathway 0.0000 0 24 54 -0.004 0.027 1000 -1000 -0.018 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.01 1000 -1000 -0.032 -1000
Total NA 5507 276779 7203 -17 -1000 131000 -131000 -5.3 -131000
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.1 0.17 -9999 0 -0.37 194 194
GPC2 -0.14 0.19 -9999 0 -0.37 268 268
GPC2/Midkine -0.17 0.16 -9999 0 -0.3 388 388
neuron projection morphogenesis -0.17 0.16 -9999 0 -0.29 388 388
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.16 0.11 -9999 0 -0.28 267 267
STMN1 -0.19 0.11 -9999 0 -0.25 525 525
Aurora B/RasGAP/Survivin -0.27 0.17 -9999 0 -0.35 525 525
Chromosomal passenger complex/Cul3 protein complex -0.1 0.091 -9999 0 -0.2 248 248
BIRC5 -0.22 0.19 -9999 0 -0.39 390 390
DES -0.19 0.26 -9999 0 -0.65 150 150
Aurora C/Aurora B/INCENP -0.15 0.088 -9999 0 -0.19 528 528
Aurora B/TACC1 -0.16 0.087 -9999 0 -0.2 525 525
Aurora B/PP2A -0.19 0.1 -9999 0 -0.25 525 525
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.038 0.027 -9999 0 -0.1 1 1
mitotic metaphase/anaphase transition -0.001 0.004 -9999 0 -10000 0 0
NDC80 -0.37 0.19 -9999 0 -0.46 546 546
Cul3 protein complex -0.001 0.016 -9999 0 -0.2 4 4
KIF2C -0.11 0.086 -9999 0 -0.18 395 395
PEBP1 0.003 0.004 -9999 0 -10000 0 0
KIF20A -0.25 0.18 -9999 0 -0.38 455 455
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.19 0.1 -9999 0 -0.25 525 525
SEPT1 0.009 0.015 -9999 0 -0.37 1 1
SMC2 0.01 0 -9999 0 -10000 0 0
SMC4 -0.053 0.14 -9999 0 -0.37 109 109
NSUN2/NPM1/Nucleolin -0.065 0.054 -9999 0 -10000 0 0
PSMA3 0.01 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.002 -9999 0 -10000 0 0
H3F3B -0.098 0.059 -9999 0 -0.24 1 1
AURKB -0.29 0.16 -9999 0 -0.38 525 525
AURKC -0.003 0.069 -9999 0 -0.37 22 22
CDCA8 -0.14 0.19 -9999 0 -0.39 245 245
cytokinesis -0.21 0.16 -9999 0 -0.34 380 380
Aurora B/Septin1 -0.2 0.15 -9999 0 -0.33 359 359
AURKA -0.083 0.17 -9999 0 -0.38 160 160
INCENP 0.003 0.005 -9999 0 -10000 0 0
KLHL13 0.008 0.03 -9999 0 -0.37 4 4
BUB1 -0.25 0.18 -9999 0 -0.38 455 455
hSgo1/Aurora B/Survivin -0.37 0.23 -9999 0 -0.47 528 528
EVI5 0.008 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.22 0.18 -9999 0 -0.36 378 378
SGOL1 -0.24 0.18 -9999 0 -0.37 434 434
CENPA -0.15 0.12 -9999 0 -0.25 368 368
NCAPG -0.31 0.14 -9999 0 -0.37 553 553
Aurora B/HC8 Proteasome -0.19 0.1 -9999 0 -0.25 525 525
NCAPD2 0.004 0.047 -9999 0 -0.37 10 10
Aurora B/PP1-gamma -0.19 0.1 -9999 0 -0.25 525 525
RHOA 0.01 0 -9999 0 -10000 0 0
NCAPH -0.14 0.19 -9999 0 -0.37 262 262
NPM1 -0.087 0.048 -9999 0 -10000 0 0
RASA1 0.01 0 -9999 0 -10000 0 0
KLHL9 0.01 0 -9999 0 -10000 0 0
mitotic prometaphase -0.009 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.19 0.1 -9999 0 -0.25 525 525
PPP1CC 0.01 0 -9999 0 -10000 0 0
Centraspindlin -0.25 0.2 -9999 0 -0.39 395 395
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.087 0.048 -9999 0 -10000 0 0
MYLK -0.098 0.059 -9999 0 -10000 0 0
KIF23 -0.16 0.19 -9999 0 -0.38 289 289
VIM -0.25 0.17 -9999 0 -0.32 534 534
RACGAP1 -0.004 0.056 -9999 0 -0.38 14 14
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.087 0.048 -9999 0 -10000 0 0
Chromosomal passenger complex -0.19 0.14 -9999 0 -0.29 434 434
Chromosomal passenger complex/EVI5 -0.28 0.21 -9999 0 -0.44 390 390
TACC1 0.01 0 -9999 0 -10000 0 0
PPP2R5D 0.01 0 -9999 0 -10000 0 0
CUL3 0.01 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
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 -0.082 0.11 -9999 0 -0.22 254 254
EFNA5 -0.038 0.12 -9999 0 -0.32 96 96
FYN -0.059 0.11 -9999 0 -0.19 254 254
neuron projection morphogenesis -0.082 0.11 -9999 0 -0.22 254 254
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.082 0.12 -9999 0 -0.22 254 254
EPHA5 -0.099 0.16 -9999 0 -0.32 218 218
Effects of Botulinum toxin

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
STX1A -0.11 0.12 -9999 0 -0.22 349 349
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.074 0.1 -9999 0 -0.21 232 232
STXBP1 -0.038 0.12 -9999 0 -0.32 96 96
ACh/CHRNA1 -0.092 0.11 -9999 0 -0.29 136 136
RAB3GAP2/RIMS1/UNC13B -0.058 0.08 -9999 0 -0.17 232 232
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 -0.11 0.16 -9999 0 -0.32 232 232
mol:ACh -0.069 0.067 -9999 0 -0.13 345 345
RAB3GAP2 0.01 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.18 0.17 -9999 0 -0.33 323 323
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.091 0.11 -9999 0 -0.29 136 136
UNC13B 0.01 0 -9999 0 -10000 0 0
CHRNA1 -0.068 0.15 -9999 0 -0.37 136 136
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.17 0.13 -9999 0 -0.27 434 434
SNAP25 -0.11 0.12 -9999 0 -0.22 345 345
VAMP2 0.005 0 -9999 0 -10000 0 0
SYT1 -0.2 0.16 -9999 0 -0.32 431 431
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.11 0.13 -9999 0 -0.22 358 358
STX1A/SNAP25 fragment 1/VAMP2 -0.18 0.17 -9999 0 -0.33 323 323
Aurora C 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
INCENP 0.01 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.15 0.083 -9999 0 -0.19 528 528
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.043 0.024 -9999 0 -10000 0 0
AURKB -0.29 0.16 -9999 0 -0.37 525 525
AURKC -0.003 0.069 -9999 0 -0.37 22 22
TCGA08_retinoblastoma

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
CDKN2B -0.055 0.15 -10000 0 -0.38 111 111
CDKN2C -0.093 0.18 -10000 0 -0.37 193 193
CDKN2A -0.095 0.18 -10000 0 -0.37 195 195
CCND2 0.053 0.073 0.17 147 -10000 0 147
RB1 -0.056 0.073 -10000 0 -0.19 120 120
CDK4 0.06 0.075 0.19 120 -10000 0 120
CDK6 0.057 0.078 0.21 109 -10000 0 109
G1/S progression 0.049 0.078 0.19 120 -10000 0 120
PLK1 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
regulation of centriole-centriole cohesion 0.065 0.05 0.1 434 -10000 0 434
BUB1B -0.096 0.092 -10000 0 -0.19 290 290
PLK1 -0.042 0.053 -10000 0 -0.092 316 316
PLK1S1 -0.018 0.028 -10000 0 -0.095 17 17
KIF2A -0.031 0.048 -10000 0 -0.14 33 33
regulation of mitotic centrosome separation -0.041 0.053 -10000 0 -0.091 316 316
GOLGA2 0.01 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.21 0.15 -10000 0 -0.27 522 522
WEE1 -0.052 0.065 -10000 0 -0.2 22 22
cytokinesis -0.11 0.088 -10000 0 -0.19 267 267
PP2A-alpha B56 -0.02 0.033 -10000 0 -10000 0 0
AURKA -0.027 0.04 -10000 0 -0.097 88 88
PICH/PLK1 -0.13 0.18 -10000 0 -0.35 225 225
CENPE -0.071 0.11 -10000 0 -0.26 148 148
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.03 0.047 -10000 0 -0.14 33 33
PPP2CA 0.01 0 -10000 0 -10000 0 0
FZR1 0.01 0 -10000 0 -10000 0 0
TPX2 -0.031 0.043 -10000 0 -0.1 97 97
PAK1 -0.083 0.15 -10000 0 -0.33 178 178
SPC24 -0.09 0.17 -10000 0 -0.37 174 174
FBXW11 0.01 0 -10000 0 -10000 0 0
CLSPN -0.024 0.044 -10000 0 -0.13 62 62
GORASP1 0.01 0 -10000 0 -10000 0 0
metaphase -0.001 0.004 -10000 0 -0.009 149 149
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.022 0.028 -10000 0 -0.049 313 313
G2 phase of mitotic cell cycle -0.002 0.003 -10000 0 -0.007 87 87
STAG2 0.01 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.011 -10000 0 -10000 0 0
spindle elongation -0.041 0.053 -10000 0 -0.091 316 316
ODF2 0.008 0.004 -10000 0 -10000 0 0
BUB1 -0.038 0.032 -10000 0 -10000 0 0
TPT1 -0.018 0.028 -10000 0 -0.091 26 26
CDC25C -0.051 0.05 -10000 0 -0.14 31 31
CDC25B 0.008 0.015 -10000 0 -0.38 1 1
SGOL1 -0.065 0.05 -10000 0 -0.1 434 434
RHOA 0.01 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.074 0.094 -10000 0 -0.21 168 168
CDC14B 0.008 0.003 -10000 0 -10000 0 0
CDC20 -0.16 0.19 -10000 0 -0.37 298 298
PLK1/PBIP1 -0.11 0.11 -10000 0 -0.23 311 311
mitosis -0.004 0.007 0.014 3 -0.015 157 160
FBXO5 -0.041 0.069 -10000 0 -0.21 74 74
CDC2 -0.005 0.006 -10000 0 -0.011 260 260
NDC80 -0.29 0.16 -10000 0 -0.37 522 522
metaphase plate congression -0.02 0.031 -10000 0 -0.13 1 1
ERCC6L -0.12 0.16 -10000 0 -0.34 209 209
NLP/gamma Tubulin -0.023 0.032 -10000 0 -0.094 42 42
microtubule cytoskeleton organization -0.018 0.028 -10000 0 -0.091 26 26
G2/M transition DNA damage checkpoint 0.001 0.005 0.009 159 -0.009 6 165
PPP1R12A 0.01 0.001 -10000 0 -10000 0 0
interphase 0.001 0.005 0.009 159 -0.009 6 165
PLK1/PRC1-2 -0.15 0.12 -10000 0 -0.23 455 455
GRASP65/GM130/RAB1/GTP/PLK1 -0.025 0.032 -10000 0 -0.13 17 17
RAB1A 0.01 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.029 0.048 -10000 0 -0.17 25 25
mitotic prometaphase -0.001 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.015 0.038 -10000 0 -10000 0 0
microtubule-based process -0.16 0.11 -10000 0 -0.23 455 455
Golgi organization -0.041 0.053 -10000 0 -0.091 316 316
Cohesin/SA2 -0.035 0.039 -10000 0 -0.14 33 33
PPP1CB/MYPT1 0.004 0.007 -10000 0 -10000 0 0
KIF20A -0.25 0.18 -10000 0 -0.37 455 455
APC/C/CDC20 -0.12 0.12 -10000 0 -0.25 303 303
PPP2R1A 0.01 0 -10000 0 -10000 0 0
chromosome segregation -0.11 0.11 -10000 0 -0.22 311 311
PRC1 -0.005 0.074 -10000 0 -0.37 26 26
ECT2 -0.033 0.057 -10000 0 -0.19 37 37
C13orf34 -0.031 0.049 -10000 0 -0.16 31 31
NUDC -0.02 0.031 -10000 0 -0.13 1 1
regulation of attachment of spindle microtubules to kinetochore -0.096 0.091 -10000 0 -0.19 290 290
spindle assembly -0.032 0.044 -10000 0 -0.078 242 242
spindle stabilization -0.018 0.028 -10000 0 -0.095 17 17
APC/C/HCDH1 0.013 0.002 -10000 0 -10000 0 0
MKLP2/PLK1 -0.16 0.12 -10000 0 -0.24 455 455
CCNB1 -0.035 0.12 -10000 0 -0.38 75 75
PPP1CB 0.01 0.001 -10000 0 -10000 0 0
BTRC 0.01 0 -10000 0 -10000 0 0
ROCK2 -0.02 0.041 -10000 0 -0.31 3 3
TUBG1 -0.018 0.028 -10000 0 -0.093 22 22
G2/M transition of mitotic cell cycle -0.075 0.09 -10000 0 -0.21 168 168
MLF1IP -0.12 0.14 -10000 0 -0.27 310 310
INCENP 0.009 0.002 -10000 0 -10000 0 0
FOXM1 transcription factor 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
NFATC3 -0.31 0.45 -9999 0 -0.98 148 148
PLK1 -0.075 0.14 -9999 0 -10000 0 0
BIRC5 -0.15 0.16 -9999 0 -10000 0 0
HSPA1B -0.31 0.45 -9999 0 -0.98 149 149
MAP2K1 0 0.027 -9999 0 -10000 0 0
BRCA2 -0.32 0.47 -9999 0 -1 157 157
FOXM1 -0.37 0.54 -9999 0 -1.2 161 161
XRCC1 -0.31 0.45 -9999 0 -0.98 149 149
FOXM1B/p19 -0.33 0.43 -9999 0 -0.98 162 162
Cyclin D1/CDK4 -0.3 0.44 -9999 0 -0.94 159 159
CDC2 -0.33 0.47 -9999 0 -1 161 161
TGFA -0.27 0.4 -9999 0 -0.87 150 150
SKP2 -0.31 0.45 -9999 0 -0.98 147 147
CCNE1 0.006 0.007 -9999 0 -10000 0 0
CKS1B -0.31 0.45 -9999 0 -1 149 149
RB1 -0.17 0.17 -9999 0 -0.43 82 82
FOXM1C/SP1 -0.36 0.5 -9999 0 -1.1 166 166
AURKB -0.2 0.14 -9999 0 -10000 0 0
CENPF -0.33 0.48 -9999 0 -1 157 157
CDK4 -0.05 0.14 -9999 0 -0.39 96 96
MYC -0.33 0.41 -9999 0 -0.88 168 168
CHEK2 -0.066 0.16 -9999 0 -0.42 113 113
ONECUT1 -0.3 0.44 -9999 0 -0.93 163 163
CDKN2A -0.096 0.18 -9999 0 -0.37 195 195
LAMA4 -0.31 0.46 -9999 0 -1 154 154
FOXM1B/HNF6 -0.34 0.5 -9999 0 -1.1 163 163
FOS -0.31 0.45 -9999 0 -0.99 155 155
SP1 0.009 0.004 -9999 0 -10000 0 0
CDC25B -0.31 0.45 -9999 0 -0.98 149 149
response to radiation -0.011 0.025 -9999 0 -10000 0 0
CENPB -0.31 0.45 -9999 0 -0.98 149 149
CENPA -0.36 0.49 -9999 0 -1.1 165 165
NEK2 -0.34 0.48 -9999 0 -1 159 159
HIST1H2BA -0.31 0.45 -9999 0 -0.99 147 147
CCNA2 -0.13 0.19 -9999 0 -0.39 232 232
EP300 0.01 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.35 0.51 -9999 0 -1.1 158 158
CCNB2 -0.39 0.47 -9999 0 -1.1 165 165
CCNB1 -0.33 0.48 -9999 0 -1 157 157
ETV5 -0.31 0.45 -9999 0 -0.98 149 149
ESR1 -0.31 0.45 -9999 0 -0.98 150 150
CCND1 -0.29 0.43 -9999 0 -0.92 158 158
GSK3A 0.003 0.022 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.13 0.21 -9999 0 -0.39 253 253
CDK2 -0.12 0.18 -9999 0 -0.39 217 217
G2/M transition of mitotic cell cycle -0.014 0.031 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.38 0.42 -9999 0 -1 172 172
GAS1 -0.32 0.47 -9999 0 -1 158 158
MMP2 -0.33 0.47 -9999 0 -1 164 164
RB1/FOXM1C -0.32 0.47 -9999 0 -0.99 168 168
CREBBP 0.01 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.009 0.015 -9999 0 -0.37 1 1
HDAC3 0.01 0 -9999 0 -10000 0 0
VDR -0.005 0.073 -9999 0 -0.35 28 28
Cbp/p300/PCAF 0 0.008 -9999 0 -0.2 1 1
EP300 0.01 0 -9999 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA -0.024 0.038 -9999 0 -10000 0 0
KAT2B 0.009 0.015 -9999 0 -0.37 1 1
MAPK14 0.01 0 -9999 0 -10000 0 0
AKT1 -0.044 0.047 -9999 0 -0.19 4 4
RAR alpha/9cRA/Cyclin H -0.1 0.065 -9999 0 -0.37 5 5
mol:9cRA 0 0 -9999 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.026 0.038 -9999 0 -10000 0 0
CDC2 0 0 -9999 0 -10000 0 0
response to UV 0.001 0 -9999 0 -10000 0 0
RAR alpha/Jnk1 -0.1 0.067 -9999 0 -0.44 5 5
NCOR2 0.01 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.01 0.049 -9999 0 -0.24 28 28
RXRs/RARs/NRIP1/9cRA -0.22 0.16 -9999 0 -0.31 434 434
NCOA2 0.004 0.044 -9999 0 -0.32 12 12
NCOA3 0.01 0 -9999 0 -10000 0 0
NCOA1 0.01 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.005 0.073 -9999 0 -0.35 28 28
RARG 0.008 0.03 -9999 0 -0.37 4 4
RAR gamma1/9cRA -0.001 0.016 -9999 0 -0.21 4 4
MAPK3 0.01 0 -9999 0 -10000 0 0
MAPK1 0.01 0 -9999 0 -10000 0 0
MAPK8 0.008 0.029 -9999 0 -0.32 5 5
mol:Vit D3 0 0 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.24 0.15 -9999 0 -0.33 497 497
RARA -0.13 0.094 -9999 0 -0.19 498 498
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.029 0.046 -9999 0 -0.24 11 11
PRKCA 0.012 0.001 -9999 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.22 0.16 -9999 0 -0.31 497 497
RXRG -0.18 0.14 -9999 0 -0.26 499 499
RXRA -0.1 0.08 -9999 0 -0.38 4 4
RXRB -0.16 0.11 -9999 0 -0.23 497 497
VDR/Vit D3/DNA -0.01 0.049 -9999 0 -0.24 28 28
RBP1 -0.039 0.13 -9999 0 -0.37 86 86
CRBP1/9-cic-RA -0.033 0.087 -9999 0 -0.26 86 86
RARB 0.011 0 -9999 0 -10000 0 0
PRKCG -0.24 0.15 -9999 0 -0.32 497 497
MNAT1 0.009 0.015 -9999 0 -0.37 1 1
RAR alpha/RXRs -0.23 0.17 -9999 0 -0.33 497 497
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.19 0.14 -9999 0 -0.27 434 434
proteasomal ubiquitin-dependent protein catabolic process -0.073 0.069 -9999 0 -0.31 4 4
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.22 0.16 -9999 0 -0.31 497 497
positive regulation of DNA binding -0.1 0.062 -9999 0 -0.35 5 5
NRIP1 -0.2 0.15 -9999 0 -0.42 45 45
RXRs/RARs -0.22 0.16 -9999 0 -0.32 497 497
RXRs/RXRs/DNA/9cRA -0.25 0.15 -9999 0 -0.33 497 497
PRKACA 0.01 0 -9999 0 -10000 0 0
CDK7 0.01 0 -9999 0 -10000 0 0
TFIIH 0 0.008 -9999 0 -0.2 1 1
RAR alpha/9cRA -0.076 0.047 -9999 0 -0.28 5 5
CCNH 0.01 0 -9999 0 -10000 0 0
CREBBP 0.01 0 -9999 0 -10000 0 0
RAR gamma2/9cRA -0.001 0.012 -9999 0 -10000 0 0
Reelin signaling pathway

Figure S10.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S10.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.02 0.063 -9999 0 -0.21 64 64
VLDLR 0.008 0.026 -9999 0 -0.32 4 4
CRKL 0.009 0.015 -9999 0 -0.37 1 1
LRPAP1 0.01 0 -9999 0 -10000 0 0
FYN 0.01 0 -9999 0 -10000 0 0
ITGA3 0.001 0.059 -9999 0 -0.37 16 16
RELN/VLDLR/Fyn -0.07 0.084 -9999 0 -0.17 274 274
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.001 0.013 -9999 0 -10000 0 0
AKT1 -0.081 0.12 -9999 0 -0.31 81 81
MAP2K7 0.01 0 -9999 0 -10000 0 0
RAPGEF1 0.01 0 -9999 0 -10000 0 0
DAB1 -0.057 0.13 -9999 0 -0.32 134 134
RELN/LRP8/DAB1 -0.093 0.1 -9999 0 -0.18 336 336
LRPAP1/LRP8 0 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.084 0.094 -9999 0 -0.27 80 80
DAB1/alpha3/beta1 Integrin -0.076 0.096 -9999 0 -0.28 86 86
long-term memory -0.23 0.18 -9999 0 -0.37 372 372
DAB1/LIS1 -0.075 0.086 -9999 0 -0.27 71 71
DAB1/CRLK/C3G -0.07 0.081 -9999 0 -0.25 72 72
PIK3CA 0.01 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.075 0.086 -9999 0 -0.27 71 71
ARHGEF2 0.01 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.16 0.17 -9999 0 -0.32 348 348
CDK5R1 -0.022 0.098 -9999 0 -0.32 64 64
RELN -0.13 0.16 -9999 0 -0.32 272 272
PIK3R1 0.01 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.069 0.083 -9999 0 -0.17 272 272
GRIN2A/RELN/LRP8/DAB1/Fyn -0.16 0.14 -9999 0 -0.32 268 268
MAPK8 0.007 0.029 -9999 0 -0.32 5 5
RELN/VLDLR/DAB1 -0.094 0.1 -9999 0 -0.18 338 338
ITGB1 0.003 0.051 -9999 0 -0.37 12 12
MAP1B -0.073 0.11 -9999 0 -0.28 80 80
RELN/LRP8 -0.069 0.083 -9999 0 -0.17 272 272
GRIN2B/RELN/LRP8/DAB1/Fyn -0.16 0.14 -9999 0 -0.31 264 264
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.01 0.06 -9999 0 -0.33 21 21
RAP1A -0.041 0.095 -9999 0 -0.24 72 72
PAFAH1B1 0.01 0 -9999 0 -10000 0 0
MAPK8IP1 0.009 0.018 -9999 0 -0.32 2 2
CRLK/C3G 0 0.01 -9999 0 -0.25 1 1
GRIN2B -0.18 0.16 -9999 0 -0.32 375 375
NCK2 0.01 0 -9999 0 -10000 0 0
neuron differentiation -0.062 0.11 -9999 0 -0.29 74 74
neuron adhesion -0.035 0.1 -9999 0 -0.24 87 87
LRP8 0.01 0 -9999 0 -10000 0 0
GSK3B -0.071 0.12 -9999 0 -0.31 72 72
RELN/VLDLR/DAB1/Fyn -0.085 0.095 -9999 0 -0.27 80 80
MAP3K11 0.01 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.092 0.13 -9999 0 -0.21 338 338
CDK5 0.01 0 -9999 0 -10000 0 0
MAPT 0.019 0.038 -9999 0 -0.28 7 7
neuron migration -0.09 0.15 -9999 0 -0.24 278 278
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.063 0.11 -9999 0 -0.29 74 74
RELN/VLDLR -0.06 0.072 -9999 0 -0.14 274 274
Syndecan-1-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
TGFB1 0.009 0.015 -9999 0 -0.37 1 1
CCL5 -0.047 0.14 -9999 0 -0.37 100 100
SDCBP 0.01 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.072 0.11 -9999 0 -0.28 103 103
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 -0.064 0.11 -9999 0 -0.26 106 106
Syndecan-1/Syntenin -0.063 0.11 -9999 0 -0.26 103 103
MAPK3 -0.047 0.1 -9999 0 -0.28 52 52
HGF/MET -0.098 0.11 -9999 0 -0.22 298 298
TGFB1/TGF beta receptor Type II 0.009 0.015 -9999 0 -0.37 1 1
BSG 0.01 0 -9999 0 -10000 0 0
keratinocyte migration -0.063 0.11 -9999 0 -0.26 106 106
Syndecan-1/RANTES -0.089 0.14 -9999 0 -0.33 145 145
Syndecan-1/CD147 -0.056 0.1 -9999 0 -0.25 104 104
Syndecan-1/Syntenin/PIP2 -0.074 0.091 -9999 0 -0.25 103 103
LAMA5 0.008 0.026 -9999 0 -0.37 3 3
positive regulation of cell-cell adhesion -0.073 0.09 -9999 0 -0.25 103 103
MMP7 -0.13 0.18 -9999 0 -0.37 248 248
HGF 0 0.059 -9999 0 -0.34 19 19
Syndecan-1/CASK -0.069 0.11 -9999 0 -0.27 103 103
Syndecan-1/HGF/MET -0.12 0.11 -9999 0 -0.25 204 204
regulation of cell adhesion -0.04 0.098 -9999 0 -0.26 52 52
HPSE -0.073 0.16 -9999 0 -0.37 145 145
positive regulation of cell migration -0.072 0.11 -9999 0 -0.28 103 103
SDC1 -0.073 0.11 -9999 0 -0.28 103 103
Syndecan-1/Collagen -0.072 0.11 -9999 0 -0.28 103 103
PPIB 0.008 0.03 -9999 0 -0.37 4 4
MET -0.13 0.17 -9999 0 -0.32 287 287
PRKACA 0.01 0 -9999 0 -10000 0 0
MMP9 -0.12 0.18 -9999 0 -0.37 220 220
MAPK1 -0.047 0.1 -9999 0 -0.27 53 53
homophilic cell adhesion -0.072 0.11 -9999 0 -0.28 103 103
MMP1 -0.058 0.14 -9999 0 -0.37 112 112
Osteopontin-mediated 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
IKK alpha homodimer -0.037 0.14 -9999 0 -0.29 135 135
NF kappa B1 p50/RelA/I kappa B alpha -0.061 0.12 -9999 0 -0.3 101 101
alphaV/beta3 Integrin/Osteopontin/Src -0.04 0.095 -9999 0 -0.26 102 102
AP1 -0.11 0.17 -9999 0 -0.43 119 119
ILK -0.044 0.14 -9999 0 -0.29 143 143
bone resorption -0.11 0.16 -9999 0 -0.38 148 148
PTK2B 0.008 0.022 -9999 0 -0.32 3 3
PYK2/p130Cas -0.059 0.12 -9999 0 -0.29 104 104
ITGAV 0.01 0.005 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.098 0.12 -9999 0 -0.25 260 260
alphaV/beta3 Integrin/Osteopontin -0.076 0.14 -9999 0 -0.3 168 168
MAP3K1 -0.051 0.15 -9999 0 -0.28 179 179
JUN 0.009 0.002 -9999 0 -10000 0 0
MAPK3 -0.042 0.15 -9999 0 -0.31 135 135
MAPK1 -0.042 0.15 -9999 0 -0.31 135 135
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
MAPK8 -0.046 0.15 -9999 0 -0.29 154 154
ITGB3 -0.064 0.16 -9999 0 -0.38 128 128
NFKBIA -0.035 0.15 -9999 0 -0.3 135 135
FOS 0.001 0.056 -9999 0 -0.35 16 16
CD44 -0.14 0.19 -9999 0 -0.37 259 259
CHUK 0.01 0 -9999 0 -10000 0 0
PLAU -0.067 0.2 -9999 0 -0.5 63 63
NF kappa B1 p50/RelA -0.069 0.12 -9999 0 -0.32 101 101
BCAR1 0.01 0 -9999 0 -10000 0 0
RELA 0.01 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.051 0.1 -9999 0 -0.27 128 128
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.045 0.14 -9999 0 -0.27 172 172
VAV3 -0.042 0.14 -9999 0 -0.27 145 145
MAP3K14 -0.046 0.15 -9999 0 -0.3 143 143
ROCK2 0.009 0.018 -9999 0 -0.32 2 2
SPP1 -0.049 0.14 -9999 0 -0.38 102 102
RAC1 0.01 0 -9999 0 -10000 0 0
Rac1/GTP -0.066 0.11 -9999 0 -0.28 98 98
MMP2 -0.08 0.22 -9999 0 -0.41 177 177
EGFR-dependent Endothelin signaling events

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.01 0 -9999 0 -10000 0 0
EGFR -0.21 0.19 -9999 0 -0.37 377 377
EGF/EGFR -0.12 0.098 -9999 0 -0.18 435 435
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.099 0.085 -9999 0 -0.34 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.034 0.12 -9999 0 -0.37 77 77
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.003 0.07 -9999 0 -0.37 23 23
EGF/EGFR dimer/SHC -0.13 0.11 -9999 0 -0.21 402 402
mol:GDP -0.098 0.085 -9999 0 -0.33 17 17
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.002 0.055 -9999 0 -0.37 14 14
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.087 0.076 -9999 0 -0.3 17 17
SHC1 -0.001 0.064 -9999 0 -0.37 19 19
HRAS/GDP -0.089 0.078 -9999 0 -0.31 17 17
FRAP1 -0.082 0.095 -9999 0 -0.31 18 18
EGF/EGFR dimer -0.15 0.13 -9999 0 -0.26 387 387
SOS1 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.034 0.087 -9999 0 -0.25 90 90
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.092 0.11 -9999 0 -0.21 287 287
CRKL -0.065 0.11 -9999 0 -0.32 11 11
mol:PIP3 -0.01 0.009 -9999 0 -10000 0 0
AKT1 0.004 0.009 -9999 0 -0.19 1 1
PTK2B 0.008 0.022 -9999 0 -0.32 3 3
RAPGEF1 -0.056 0.11 -9999 0 -0.3 11 11
RANBP10 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.078 0.089 -9999 0 -0.17 298 298
MAP3K5 -0.046 0.1 -9999 0 -0.27 13 13
HGF/MET/CIN85/CBL/ENDOPHILINS -0.067 0.077 -9999 0 -0.15 298 298
AP1 -0.018 0.045 -9999 0 -0.22 16 16
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 -0.001 0.064 -9999 0 -0.37 19 19
apoptosis -0.014 0.081 -9999 0 -0.74 7 7
STAT3 (dimer) -0.056 0.1 -9999 0 -0.35 9 9
GAB1/CRKL/SHP2/PI3K -0.069 0.081 -9999 0 -0.29 10 10
INPP5D 0.007 0.033 -9999 0 -0.37 5 5
CBL/CRK -0.056 0.11 -9999 0 -0.3 10 10
PTPN11 0.01 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.01 0 -9999 0 -10000 0 0
PTEN 0.01 0 -9999 0 -10000 0 0
ELK1 -0.049 0.058 -9999 0 -0.13 11 11
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.049 0.057 -9999 0 -0.22 9 9
PAK1 -0.031 0.066 -9999 0 -0.18 1 1
HGF/MET/RANBP10 -0.078 0.089 -9999 0 -0.17 298 298
HRAS -0.2 0.26 -9999 0 -0.5 284 284
DOCK1 -0.056 0.11 -9999 0 -0.3 11 11
GAB1 -0.075 0.12 -9999 0 -0.21 284 284
CRK -0.065 0.11 -9999 0 -0.32 10 10
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.19 0.22 -9999 0 -0.44 288 288
JUN 0.01 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.083 0.095 -9999 0 -0.19 288 288
PIK3R1 0.01 0 -9999 0 -10000 0 0
cell morphogenesis -0.047 0.12 -9999 0 -0.35 10 10
GRB2/SHC -0.061 0.092 -9999 0 -0.16 302 302
FOS 0.001 0.056 -9999 0 -0.35 16 16
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.049 0.058 -9999 0 -0.13 11 11
HGF/MET/MUC20 -0.081 0.092 -9999 0 -0.18 298 298
cell migration -0.06 0.091 -9999 0 -0.16 302 302
GRB2 0.01 0 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
MET/RANBP10 -0.092 0.11 -9999 0 -0.21 287 287
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.057 0.099 -9999 0 -0.34 9 9
MET/MUC20 -0.095 0.11 -9999 0 -0.22 287 287
RAP1B -0.05 0.1 -9999 0 -0.29 11 11
RAP1A -0.048 0.1 -9999 0 -0.29 10 10
HGF/MET/RANBP9 -0.078 0.089 -9999 0 -0.17 298 298
RAF1 -0.18 0.25 -9999 0 -0.47 284 284
STAT3 -0.056 0.1 -9999 0 -0.35 9 9
cell proliferation -0.096 0.16 -9999 0 -0.27 293 293
RPS6KB1 -0.028 0.045 -9999 0 -0.12 7 7
MAPK3 -0.048 0.052 -9999 0 -10000 0 0
MAPK1 -0.048 0.052 -9999 0 -10000 0 0
RANBP9 0.01 0 -9999 0 -10000 0 0
MAPK8 -0.028 0.096 -9999 0 -0.32 13 13
SRC -0.047 0.094 -9999 0 -0.32 9 9
PI3K -0.056 0.09 -9999 0 -0.16 284 284
MET/Glomulin -0.076 0.098 -9999 0 -0.19 287 287
SOS1 0.01 0 -9999 0 -10000 0 0
MAP2K1 -0.16 0.23 -9999 0 -0.43 284 284
MET -0.13 0.17 -9999 0 -0.32 287 287
MAP4K1 -0.055 0.11 -9999 0 -0.28 14 14
PTK2 0.01 0 -9999 0 -10000 0 0
MAP2K2 -0.16 0.23 -9999 0 -0.43 284 284
BAD 0.01 0.009 -9999 0 -0.18 1 1
MAP2K4 -0.037 0.096 -9999 0 -0.26 10 10
SHP2/GRB2/SOS1/GAB1 -0.099 0.11 -9999 0 -0.23 284 284
INPPL1 0.01 0 -9999 0 -10000 0 0
PXN 0.01 0 -9999 0 -10000 0 0
SH3KBP1 0.01 0 -9999 0 -10000 0 0
HGS -0.064 0.094 -9999 0 -0.17 288 288
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF 0 0.059 -9999 0 -0.34 19 19
RASA1 0.01 0 -9999 0 -10000 0 0
NCK1 0.009 0.015 -9999 0 -0.37 1 1
PTPRJ 0.01 0 -9999 0 -10000 0 0
NCK/PLCgamma1 -0.053 0.089 -9999 0 -0.15 285 285
PDPK1 -0.002 0.006 -9999 0 -10000 0 0
HGF/MET/SHIP -0.079 0.089 -9999 0 -0.18 303 303
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.28 0.43 -9999 0 -1 114 114
IL23A -0.3 0.46 -9999 0 -1.1 111 111
NF kappa B1 p50/RelA/I kappa B alpha -0.32 0.38 -9999 0 -0.9 152 152
positive regulation of T cell mediated cytotoxicity -0.31 0.47 -9999 0 -1 152 152
ITGA3 -0.27 0.42 -9999 0 -1 108 108
IL17F -0.18 0.29 -9999 0 -0.65 110 110
IL12B -0.009 0.037 -9999 0 -0.41 2 2
STAT1 (dimer) -0.29 0.45 -9999 0 -0.96 154 154
CD4 -0.27 0.41 -9999 0 -0.97 112 112
IL23 -0.29 0.44 -9999 0 -1.1 111 111
IL23R -0.044 0.081 -9999 0 -10000 0 0
IL1B -0.32 0.5 -9999 0 -1.2 117 117
T-helper cell lineage commitment 0 0 -9999 0 -10000 0 0
IL24 -0.27 0.41 -9999 0 -0.98 108 108
TYK2 0.002 0.018 -9999 0 -10000 0 0
STAT4 -0.17 0.17 -9999 0 -0.32 366 366
STAT3 0.01 0 -9999 0 -10000 0 0
IL18RAP -0.034 0.12 -9999 0 -0.37 77 77
IL12RB1 0.001 0.028 -9999 0 -0.38 2 2
PIK3CA 0.01 0 -9999 0 -10000 0 0
IL12Rbeta1/TYK2 0 0.027 -9999 0 -0.27 2 2
IL23R/JAK2 -0.048 0.1 -9999 0 -10000 0 0
positive regulation of chronic inflammatory response -0.31 0.47 -9999 0 -1 152 152
natural killer cell activation 0.005 0.007 -9999 0 -10000 0 0
JAK2 0.007 0.023 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
NFKB1 0.008 0.003 -9999 0 -10000 0 0
RELA 0.008 0.003 -9999 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.28 0.42 -9999 0 -1 111 111
ALOX12B -0.34 0.5 -9999 0 -1.1 159 159
CXCL1 -0.29 0.44 -9999 0 -1 120 120
T cell proliferation -0.31 0.47 -9999 0 -1 152 152
NFKBIA 0.006 0.03 -9999 0 -0.37 4 4
IL17A -0.14 0.24 -9999 0 -0.51 102 102
PI3K -0.32 0.39 -9999 0 -0.92 153 153
IFNG -0.008 0.019 -9999 0 -0.089 3 3
STAT3 (dimer) -0.31 0.36 -9999 0 -0.88 152 152
IL18R1 -0.002 0.067 -9999 0 -0.36 22 22
IL23/IL23R/JAK2/TYK2/SOCS3 -0.16 0.26 -9999 0 -0.6 86 86
IL18/IL18R -0.027 0.1 -9999 0 -0.25 104 104
macrophage activation -0.018 0.017 -9999 0 -0.043 110 110
TNF -0.31 0.48 -9999 0 -1.2 113 113
STAT3/STAT4 -0.38 0.41 -9999 0 -0.98 167 167
STAT4 (dimer) -0.36 0.46 -9999 0 -1 167 167
IL18 -0.007 0.079 -9999 0 -0.37 30 30
IL19 -0.27 0.41 -9999 0 -0.98 106 106
STAT5A (dimer) -0.29 0.45 -9999 0 -0.96 152 152
STAT1 0.006 0.039 -9999 0 -0.37 7 7
SOCS3 -0.026 0.11 -9999 0 -0.34 70 70
CXCL9 -0.3 0.41 -9999 0 -1 112 112
MPO -0.44 0.57 -9999 0 -1.1 239 239
positive regulation of humoral immune response -0.31 0.47 -9999 0 -1 152 152
IL23/IL23R/JAK2/TYK2 -0.32 0.5 -9999 0 -1.1 152 152
IL6 -0.36 0.52 -9999 0 -1.1 170 170
STAT5A 0.01 0 -9999 0 -10000 0 0
IL2 0.003 0.005 -9999 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.005 0.007 -9999 0 -10000 0 0
CD3E -0.28 0.42 -9999 0 -0.98 117 117
keratinocyte proliferation -0.31 0.47 -9999 0 -1 152 152
NOS2 -0.28 0.42 -9999 0 -1 110 110
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.094 0.32 -9999 0 -0.89 89 89
MKNK1 0.01 0 -9999 0 -10000 0 0
MAPK14 -0.021 0.1 -9999 0 -0.26 98 98
ATF2/c-Jun -0.002 0.081 -9999 0 -0.3 4 4
MAPK11 -0.022 0.1 -9999 0 -0.26 100 100
MITF -0.018 0.12 -9999 0 -0.31 100 100
MAPKAPK5 -0.017 0.12 -9999 0 -0.3 100 100
KRT8 -0.036 0.13 -9999 0 -0.32 104 104
MAPKAPK3 0.01 0 -9999 0 -10000 0 0
MAPKAPK2 0.009 0.015 -9999 0 -0.37 1 1
p38alpha-beta/CK2 -0.03 0.15 -9999 0 -0.37 98 98
CEBPB -0.018 0.12 -9999 0 -0.3 101 101
SLC9A1 -0.018 0.12 -9999 0 -0.3 100 100
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.013 0.12 -9999 0 -0.29 98 98
p38alpha-beta/MNK1 -0.014 0.12 -9999 0 -0.28 98 98
JUN -0.001 0.081 -9999 0 -0.29 4 4
PPARGC1A -0.019 0.13 -9999 0 -0.31 102 102
USF1 -0.017 0.12 -9999 0 -0.3 100 100
RAB5/GDP/GDI1 -0.034 0.076 -9999 0 -0.22 98 98
NOS2 -0.031 0.17 -9999 0 -0.83 13 13
DDIT3 -0.022 0.13 -9999 0 -0.31 100 100
RAB5A 0.01 0 -9999 0 -10000 0 0
HSPB1 -0.012 0.11 -9999 0 -0.24 112 112
p38alpha-beta/HBP1 -0.014 0.12 -9999 0 -0.28 98 98
CREB1 -0.018 0.13 -9999 0 -0.33 100 100
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.006 0.1 -9999 0 -0.24 98 98
RPS6KA4 -0.017 0.12 -9999 0 -0.3 100 100
PLA2G4A -0.009 0.1 -9999 0 -0.24 98 98
GDI1 -0.017 0.12 -9999 0 -0.3 100 100
TP53 -0.041 0.16 -9999 0 -0.38 105 105
RPS6KA5 -0.017 0.12 -9999 0 -0.3 100 100
ESR1 -0.018 0.12 -9999 0 -0.31 100 100
HBP1 0.009 0.015 -9999 0 -0.37 1 1
MEF2C -0.024 0.14 -9999 0 -0.33 100 100
MEF2A -0.017 0.12 -9999 0 -0.3 100 100
EIF4EBP1 -0.027 0.14 -9999 0 -0.34 100 100
KRT19 -0.034 0.14 -9999 0 -0.33 103 103
ELK4 -0.017 0.12 -9999 0 -0.3 100 100
ATF6 -0.017 0.12 -9999 0 -0.3 100 100
ATF1 -0.018 0.13 -9999 0 -0.33 100 100
p38alpha-beta/MAPKAPK2 -0.014 0.12 -9999 0 -0.28 99 99
p38alpha-beta/MAPKAPK3 -0.014 0.12 -9999 0 -0.28 98 98
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.01 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0.01 -9999 0 -0.26 1 1
Metarhodopsin II/Arrestin -0.053 0.083 -9999 0 -0.18 194 194
PDE6G/GNAT1/GTP -0.039 0.082 -9999 0 -0.21 124 124
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.007 0.015 -9999 0 -0.37 1 1
GRK1 0.008 0.015 -9999 0 -0.37 1 1
CNG Channel -0.12 0.11 -9999 0 -0.3 134 134
mol:Na + -0.13 0.098 -9999 0 -0.26 194 194
mol:ADP 0.008 0.015 -9999 0 -0.37 1 1
RGS9-1/Gbeta5/R9AP -0.016 0.055 -9999 0 -0.2 52 52
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.13 0.1 -9999 0 -0.26 194 194
CNGB1 -0.2 0.16 -9999 0 -0.32 405 405
RDH5 -0.02 0.1 -9999 0 -0.37 52 52
SAG 0.001 0.015 -9999 0 -0.37 1 1
mol:Ca2+ -0.11 0.11 -9999 0 -0.25 194 194
Na + (4 Units) -0.12 0.092 -9999 0 -0.24 194 194
RGS9 -0.02 0.1 -9999 0 -0.37 52 52
GNB1/GNGT1 0 0 -9999 0 -10000 0 0
GNAT1/GDP -0.013 0.045 -9999 0 -0.17 49 49
GUCY2D 0 0.049 -9999 0 -0.37 11 11
GNGT1 0 0 -9999 0 -10000 0 0
GUCY2F 0.003 0.036 -9999 0 -0.37 6 6
GNB5 0.01 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.031 0.096 -9999 0 -0.19 155 155
mol:11-cis-retinal -0.02 0.1 -9999 0 -0.37 52 52
mol:cGMP -0.057 0.073 -9999 0 -0.2 19 19
GNB1 0.01 0 -9999 0 -10000 0 0
Rhodopsin -0.08 0.12 -9999 0 -0.24 224 224
SLC24A1 0.01 0 -9999 0 -10000 0 0
CNGA1 0.007 0.03 -9999 0 -0.37 4 4
Metarhodopsin II -0.046 0.072 -9999 0 -0.16 194 194
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.062 0.076 -9999 0 -0.16 98 98
RGS9BP 0.009 0.015 -9999 0 -0.37 1 1
Metarhodopsin II/Transducin -0.043 0.087 -9999 0 -0.18 193 193
GCAP Family/Ca ++ -0.06 0.076 -9999 0 -0.16 258 258
PDE6A/B -0.027 0.076 -9999 0 -0.24 74 74
mol:Pi -0.016 0.055 -9999 0 -0.2 52 52
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0 0.007 -9999 0 -0.19 1 1
PDE6B -0.001 0.06 -9999 0 -0.32 22 22
PDE6A -0.02 0.1 -9999 0 -0.37 52 52
PDE6G -0.061 0.15 -9999 0 -0.37 123 123
RHO -0.088 0.15 -9999 0 -0.32 193 193
PDE6 -0.054 0.085 -9999 0 -0.32 29 29
GUCA1A -0.12 0.16 -9999 0 -0.32 255 255
GC2/GCAP Family -0.06 0.077 -9999 0 -0.17 87 87
GUCA1C 0.002 0.021 -9999 0 -0.37 2 2
GUCA1B 0.009 0.013 -9999 0 -0.32 1 1
PLK2 and PLK4 events

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
PLK2 -0.03 0.11 -9999 0 -0.32 79 79
PLK4 -0.01 0.084 -9999 0 -0.37 34 34
regulation of centriole replication -0.023 0.093 -9999 0 -0.23 110 110
Glucocorticoid receptor regulatory network

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
PCK2 0.008 0.043 0.27 6 -10000 0 6
SMARCC2 0.012 0 -10000 0 -10000 0 0
SMARCC1 0.01 0.021 -10000 0 -0.37 2 2
TBX21 -0.065 0.14 -10000 0 -0.37 76 76
SUMO2 0.01 0.004 -10000 0 -10000 0 0
STAT1 (dimer) 0.006 0.052 -10000 0 -0.43 7 7
FKBP4 0.01 0 -10000 0 -10000 0 0
FKBP5 -0.012 0.088 -10000 0 -0.37 38 38
GR alpha/HSP90/FKBP51/HSP90 0.069 0.1 0.2 193 -0.2 8 201
PRL -0.061 0.094 -10000 0 -0.39 1 1
cortisol/GR alpha (dimer)/TIF2 0.21 0.21 0.44 247 -10000 0 247
RELA -0.053 0.084 -10000 0 -0.21 69 69
FGG 0.21 0.16 0.39 210 -0.3 1 211
GR beta/TIF2 0.085 0.1 0.22 202 -0.22 2 204
IFNG -0.23 0.21 -10000 0 -0.5 179 179
apoptosis 0.023 0.1 0.45 4 -10000 0 4
CREB1 0.009 0.018 -10000 0 -10000 0 0
histone acetylation -0.055 0.11 -10000 0 -0.28 76 76
BGLAP -0.06 0.11 -10000 0 -0.41 5 5
GR/PKAc 0.08 0.09 0.21 136 -10000 0 136
NF kappa B1 p50/RelA -0.09 0.15 -10000 0 -0.35 100 100
SMARCD1 0.012 0 -10000 0 -10000 0 0
MDM2 0.095 0.075 0.18 210 -0.15 2 212
GATA3 -0.071 0.16 -10000 0 -0.37 153 153
AKT1 0 0.016 -10000 0 -0.38 1 1
CSF2 -0.086 0.1 -10000 0 -0.42 5 5
GSK3B 0.01 0.004 -10000 0 -10000 0 0
NR1I3 0.068 0.092 0.45 3 -10000 0 3
CSN2 0.18 0.13 0.33 190 -10000 0 190
BRG1/BAF155/BAF170/BAF60A 0.021 0.018 -10000 0 -0.17 1 1
NFATC1 0.01 0 -10000 0 -10000 0 0
POU2F1 0.009 0.026 -10000 0 -0.37 3 3
CDKN1A -0.036 0.1 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.004 -10000 0 -10000 0 0
SFN -0.008 0.079 -10000 0 -0.37 30 30
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.07 0.1 0.2 198 -0.23 12 210
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.052 0.15 0.43 3 -0.71 20 23
JUN -0.16 0.16 -10000 0 -0.36 183 183
IL4 -0.074 0.11 -10000 0 -0.38 10 10
CDK5R1 -0.022 0.098 -10000 0 -0.32 64 64
PRKACA 0.01 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.049 0.11 0.15 8 -0.28 79 87
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.075 0.096 0.2 196 -0.18 6 202
cortisol/GR alpha (monomer) 0.25 0.24 0.52 245 -10000 0 245
NCOA2 0.004 0.044 -10000 0 -0.32 12 12
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.047 0.078 -10000 0 -0.4 16 16
AP-1/NFAT1-c-4 -0.25 0.24 -10000 0 -0.51 227 227
AFP -0.15 0.14 -10000 0 -0.51 24 24
SUV420H1 0.01 0 -10000 0 -10000 0 0
IRF1 0.13 0.14 0.35 86 -0.38 1 87
TP53 -0.03 0.13 -10000 0 -0.38 67 67
PPP5C 0.01 0 -10000 0 -10000 0 0
KRT17 -0.5 0.48 -10000 0 -0.98 318 318
KRT14 -0.1 0.13 -10000 0 -0.46 13 13
TBP 0.016 0.016 -10000 0 -0.36 1 1
CREBBP 0.022 0.026 -10000 0 -10000 0 0
HDAC1 0.004 0.016 -10000 0 -0.38 1 1
HDAC2 0.01 0 -10000 0 -10000 0 0
AP-1 -0.25 0.24 -10000 0 -0.51 229 229
MAPK14 0.01 0.004 -10000 0 -10000 0 0
MAPK10 0.008 0.026 -10000 0 -0.32 4 4
MAPK11 0.009 0.019 -10000 0 -0.32 2 2
KRT5 -0.34 0.39 -10000 0 -0.81 216 216
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
NCOA1 0.012 0.003 -10000 0 -10000 0 0
STAT1 0.006 0.052 -10000 0 -0.43 7 7
CGA -0.077 0.12 -10000 0 -0.42 13 13
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.11 0.094 0.28 45 -10000 0 45
MAPK3 0.01 0.004 -10000 0 -10000 0 0
MAPK1 0.01 0.004 -10000 0 -10000 0 0
ICAM1 -0.17 0.21 -10000 0 -0.49 133 133
NFKB1 -0.053 0.084 -10000 0 -0.21 64 64
MAPK8 -0.14 0.14 -10000 0 -0.3 211 211
MAPK9 0.01 0.004 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.016 0.1 0.45 4 -10000 0 4
BAX -0.012 0.054 -10000 0 -10000 0 0
POMC -0.13 0.14 -10000 0 -1.3 4 4
EP300 0.022 0.026 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.21 0.21 0.45 228 -0.36 1 229
proteasomal ubiquitin-dependent protein catabolic process 0.07 0.078 0.19 100 -0.14 1 101
SGK1 0.077 0.039 -10000 0 -10000 0 0
IL13 -0.2 0.18 -10000 0 -0.53 59 59
IL6 -0.25 0.34 -10000 0 -0.76 172 172
PRKACG 0.003 0.03 -10000 0 -0.37 4 4
IL5 -0.18 0.16 -10000 0 -0.5 27 27
IL2 -0.23 0.21 -10000 0 -0.5 173 173
CDK5 0.01 0.002 -10000 0 -10000 0 0
PRKACB 0.01 0 -10000 0 -10000 0 0
HSP90AA1 0.01 0 -10000 0 -10000 0 0
IL8 -0.24 0.32 -10000 0 -0.73 164 164
CDK5R1/CDK5 -0.018 0.064 -10000 0 -0.21 64 64
NF kappa B1 p50/RelA/PKAc -0.046 0.11 -10000 0 -0.26 69 69
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.21 0.2 0.42 248 -10000 0 248
SMARCA4 0.012 0 -10000 0 -10000 0 0
chromatin remodeling 0.17 0.11 0.3 203 -10000 0 203
NF kappa B1 p50/RelA/Cbp -0.04 0.12 -10000 0 -0.3 37 37
JUN (dimer) -0.16 0.16 -10000 0 -0.36 182 182
YWHAH 0.004 0.044 -10000 0 -0.32 12 12
VIPR1 -0.22 0.31 -10000 0 -0.66 218 218
NR3C1 0.16 0.13 0.31 211 -10000 0 211
NR4A1 0.012 0.042 -10000 0 -0.36 8 8
TIF2/SUV420H1 -0.004 0.028 -10000 0 -0.21 12 12
MAPKKK cascade 0.023 0.1 0.45 4 -10000 0 4
cortisol/GR alpha (dimer)/Src-1 0.22 0.21 0.45 245 -10000 0 245
PBX1 0.01 0.006 -10000 0 -10000 0 0
POU1F1 0.004 0.008 -10000 0 -10000 0 0
SELE -0.29 0.37 -10000 0 -0.76 225 225
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.17 0.11 0.3 205 -10000 0 205
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.21 0.2 0.42 248 -10000 0 248
mol:cortisol 0.15 0.13 0.3 241 -10000 0 241
MMP1 -0.11 0.12 -10000 0 -0.39 46 46
TCGA08_p53

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
CDKN2A -0.069 0.12 -10000 0 -0.26 195 195
TP53 -0.024 0.049 0.13 13 -0.16 20 33
Senescence -0.024 0.049 0.13 13 -0.16 20 33
Apoptosis -0.024 0.049 0.13 13 -0.16 20 33
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.034 0.069 0.14 183 -0.2 13 196
MDM4 0 0.06 -10000 0 -0.37 17 17
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.002 0.041 -10000 0 -0.35 3 3
NFATC2 -0.027 0.16 -10000 0 -0.55 30 30
NFATC3 -0.027 0.1 -10000 0 -0.23 100 100
CD40LG -0.14 0.33 -10000 0 -0.74 129 129
ITCH -0.051 0.1 -10000 0 -0.34 13 13
CBLB -0.057 0.12 -10000 0 -0.43 23 23
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.15 0.21 -10000 0 -0.57 79 79
JUNB 0.009 0.02 -10000 0 -0.35 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.092 0.11 -10000 0 -0.21 280 280
T cell anergy -0.12 0.17 -10000 0 -0.31 280 280
TLE4 0.005 0.11 -10000 0 -0.43 20 20
Jun/NFAT1-c-4/p21SNFT -0.16 0.31 -10000 0 -0.72 141 141
AP-1/NFAT1-c-4 -0.19 0.34 -10000 0 -0.82 129 129
IKZF1 0.004 0.12 -10000 0 -0.46 20 20
T-helper 2 cell differentiation -0.012 0.13 -10000 0 -0.57 3 3
AP-1/NFAT1 -0.033 0.098 -10000 0 -0.34 34 34
CALM1 -0.038 0.07 -10000 0 -0.22 13 13
EGR2 -0.076 0.31 -10000 0 -0.66 103 103
EGR3 -0.19 0.5 -10000 0 -1.2 138 138
NFAT1/FOXP3 -0.036 0.12 -10000 0 -0.43 36 36
EGR1 -0.001 0.061 -10000 0 -0.33 22 22
JUN 0.004 0.015 -10000 0 -10000 0 0
EGR4 -0.16 0.17 -10000 0 -0.32 332 332
mol:Ca2+ -0.052 0.075 -10000 0 -0.24 13 13
GBP3 -0.05 0.18 -10000 0 -0.44 65 65
FOSL1 -0.065 0.15 -10000 0 -0.37 130 130
NFAT1-c-4/MAF/IRF4 -0.14 0.29 -10000 0 -0.68 143 143
DGKA 0.005 0.11 -10000 0 -0.42 21 21
CREM 0.01 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.15 0.3 -10000 0 -0.71 142 142
CTLA4 -0.015 0.14 -10000 0 -0.43 53 53
NFAT1-c-4 (dimer)/EGR1 -0.16 0.32 -10000 0 -0.74 141 141
NFAT1-c-4 (dimer)/EGR4 -0.22 0.33 -10000 0 -0.82 143 143
FOS -0.005 0.059 -10000 0 -0.37 16 16
IFNG -0.051 0.11 -10000 0 -0.5 12 12
T cell activation -0.016 0.16 -10000 0 -0.52 7 7
MAF 0.01 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.07 0.26 0.56 133 -10000 0 133
TNF -0.19 0.35 -10000 0 -0.77 152 152
FASLG -0.16 0.43 -10000 0 -0.95 138 138
TBX21 -0.013 0.093 -10000 0 -0.38 41 41
BATF3 0.002 0.054 -10000 0 -0.37 14 14
PRKCQ 0.004 0.049 -10000 0 -0.33 14 14
PTPN1 0.005 0.11 -10000 0 -0.44 19 19
NFAT1-c-4/ICER1 -0.15 0.3 -10000 0 -0.71 141 141
GATA3 -0.078 0.16 -10000 0 -0.37 153 153
T-helper 1 cell differentiation -0.036 0.12 -10000 0 -0.49 12 12
IL2RA -0.15 0.2 -10000 0 -0.51 98 98
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.004 0.11 -10000 0 -0.43 21 21
E2F1 0 0.059 -10000 0 -0.44 10 10
PPARG 0.008 0.025 -10000 0 -0.36 3 3
SLC3A2 0.005 0.11 -10000 0 -0.44 18 18
IRF4 0 0.06 -10000 0 -0.37 17 17
PTGS2 -0.15 0.36 -10000 0 -0.8 129 129
CSF2 -0.14 0.33 -10000 0 -0.74 124 124
JunB/Fra1/NFAT1-c-4 -0.17 0.3 -10000 0 -0.69 143 143
IL4 -0.012 0.13 -10000 0 -0.59 3 3
IL5 -0.14 0.33 -10000 0 -0.74 120 120
IL2 -0.017 0.16 -10000 0 -0.53 7 7
IL3 -0.036 0.051 -10000 0 -10000 0 0
RNF128 -0.15 0.22 -10000 0 -0.41 280 280
NFATC1 -0.07 0.26 -10000 0 -0.56 133 133
CDK4 0.022 0.19 0.47 19 -0.41 2 21
PTPRK 0.005 0.11 -10000 0 -0.43 20 20
IL8 -0.17 0.36 -10000 0 -0.78 130 130
POU2F1 0.008 0.026 -10000 0 -0.37 3 3
Thromboxane A2 receptor signaling

Figure S22.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.005 0.021 -10000 0 -0.38 2 2
GNB1/GNG2 -0.076 0.07 -10000 0 -0.17 187 187
AKT1 -0.076 0.09 -10000 0 -0.19 171 171
EGF -0.003 0.07 -10000 0 -0.37 23 23
mol:TXA2 -0.001 0 -10000 0 -10000 0 0
FGR 0.02 0.039 -10000 0 -0.19 8 8
mol:Ca2+ -0.11 0.12 -10000 0 -0.28 170 170
LYN 0.021 0.038 -10000 0 -0.19 7 7
RhoA/GTP -0.05 0.047 -10000 0 -0.12 159 159
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.13 0.14 -10000 0 -0.32 178 178
GNG2 0.009 0.018 -10000 0 -0.32 2 2
ARRB2 0.01 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.028 0.023 -10000 0 -0.26 3 3
G beta5/gamma2 -0.093 0.09 -10000 0 -0.22 177 177
PRKCH -0.12 0.14 -10000 0 -0.32 164 164
DNM1 -0.17 0.17 -10000 0 -0.32 367 367
TXA2/TP beta/beta Arrestin3 -0.087 0.079 -10000 0 -0.19 34 34
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.006 0.073 -10000 0 -0.38 25 25
G12 family/GTP -0.12 0.11 -10000 0 -0.29 169 169
ADRBK1 0.01 0 -10000 0 -10000 0 0
ADRBK2 0.008 0.022 -10000 0 -0.32 3 3
RhoA/GTP/ROCK1 0 0.008 -10000 0 -0.21 1 1
mol:GDP 0.061 0.078 0.24 19 -10000 0 19
mol:NADP 0.009 0.015 -10000 0 -0.38 1 1
RAB11A 0.01 0 -10000 0 -10000 0 0
PRKG1 0.004 0.046 -10000 0 -0.33 12 12
mol:IP3 -0.13 0.15 -10000 0 -0.35 168 168
cell morphogenesis 0 0.008 -10000 0 -0.21 1 1
PLCB2 -0.18 0.19 -10000 0 -0.46 163 163
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.009 0.064 -10000 0 -0.22 12 12
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.019 0.043 -10000 0 -0.21 11 11
RHOA 0.01 0 -10000 0 -10000 0 0
PTGIR 0.002 0.055 -10000 0 -0.38 14 14
PRKCB1 -0.13 0.15 -10000 0 -0.34 165 165
GNAQ 0.01 0 -10000 0 -10000 0 0
mol:L-citrulline 0.009 0.015 -10000 0 -0.38 1 1
TXA2/TXA2-R family -0.19 0.21 -10000 0 -0.5 170 170
LCK -0.009 0.076 -10000 0 -0.25 22 22
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.009 0.035 -10000 0 -0.25 6 6
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.016 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.008 0.034 -10000 0 -0.24 6 6
MAPK14 -0.082 0.097 -10000 0 -0.22 169 169
TGM2/GTP -0.15 0.16 -10000 0 -0.39 169 169
MAPK11 -0.082 0.097 -10000 0 -0.21 173 173
ARHGEF1 -0.063 0.076 -10000 0 -0.17 162 162
GNAI2 0.01 0 -10000 0 -10000 0 0
JNK cascade -0.14 0.16 -10000 0 -0.36 183 183
RAB11/GDP 0.011 0.001 -10000 0 -10000 0 0
ICAM1 -0.11 0.12 -10000 0 -0.27 188 188
cAMP biosynthetic process -0.13 0.14 -10000 0 -0.33 170 170
Gq family/GTP/EBP50 0.022 0.015 -10000 0 -0.17 3 3
actin cytoskeleton reorganization 0 0.008 -10000 0 -0.21 1 1
SRC 0.022 0.036 -10000 0 -0.19 7 7
GNB5 0.01 0 -10000 0 -10000 0 0
GNB1 0.01 0 -10000 0 -10000 0 0
EGF/EGFR -0.002 0.046 -10000 0 -0.18 7 7
VCAM1 -0.13 0.13 -10000 0 -0.3 202 202
TP beta/Gq family/GDP/G beta5/gamma2 0.028 0.023 -10000 0 -0.26 3 3
platelet activation -0.11 0.13 -10000 0 -0.28 169 169
PGI2/IP -0.005 0.037 -10000 0 -0.26 14 14
PRKACA 0.008 0.031 -10000 0 -0.22 2 2
Gq family/GDP/G beta5/gamma2 0.028 0.022 -10000 0 -0.24 3 3
TXA2/TP beta/beta Arrestin2 -0.23 0.2 -10000 0 -0.41 367 367
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.008 0.046 -10000 0 -0.2 20 20
mol:DAG -0.14 0.16 -10000 0 -0.38 164 164
EGFR -0.21 0.19 -10000 0 -0.37 377 377
TXA2/TP alpha -0.17 0.19 -10000 0 -0.44 169 169
Gq family/GTP 0.001 0.014 -10000 0 -0.15 4 4
YES1 0.021 0.037 -10000 0 -0.19 7 7
GNAI2/GTP -0.008 0.032 -10000 0 -0.22 7 7
PGD2/DP -0.01 0.049 -10000 0 -0.26 25 25
SLC9A3R1 0.01 0 -10000 0 -10000 0 0
FYN 0.022 0.036 -10000 0 -0.19 7 7
mol:NO 0.009 0.015 -10000 0 -0.38 1 1
GNA15 0.009 0.02 -10000 0 -0.35 2 2
PGK/cGMP -0.004 0.026 -10000 0 -0.18 13 13
RhoA/GDP 0.011 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.009 0.034 -10000 0 -0.23 8 8
NOS3 0.009 0.015 -10000 0 -0.38 1 1
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA -0.12 0.14 -10000 0 -0.32 164 164
PRKCB -0.15 0.15 -10000 0 -0.35 193 193
PRKCE -0.12 0.14 -10000 0 -0.32 169 169
PRKCD -0.13 0.15 -10000 0 -0.36 164 164
PRKCG -0.17 0.17 -10000 0 -0.4 190 190
muscle contraction -0.18 0.2 -10000 0 -0.46 183 183
PRKCZ -0.14 0.14 -10000 0 -0.32 208 208
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta -0.009 0.036 -10000 0 -0.23 9 9
PRKCQ -0.12 0.14 -10000 0 -0.33 164 164
MAPKKK cascade -0.16 0.18 -10000 0 -0.42 169 169
SELE -0.13 0.15 -10000 0 -0.36 173 173
TP beta/GNAI2/GDP/G beta/gamma -0.008 0.033 -10000 0 -0.23 7 7
ROCK1 0.009 0.015 -10000 0 -0.37 1 1
GNA14 0.009 0.013 -10000 0 -0.32 1 1
chemotaxis -0.22 0.24 -10000 0 -0.59 170 170
GNA12 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0 -10000 0 -10000 0 0
GNA11 0.009 0.018 -10000 0 -0.32 2 2
Rac1/GTP 0.001 0.002 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.005 0.41 -9999 0 -0.8 100 100
HDAC7 0.011 0.003 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.06 0.3 -9999 0 -0.66 94 94
SMAD4 0.011 0.003 -9999 0 -10000 0 0
ID2 0.005 0.41 -9999 0 -0.8 100 100
AP1 -0.002 0.038 -9999 0 -0.24 16 16
ABCG2 0.004 0.41 -9999 0 -0.8 100 100
HIF1A 0.014 0.083 -9999 0 -0.34 6 6
TFF3 -0.009 0.42 -9999 0 -0.82 104 104
GATA2 0.009 0.03 -9999 0 -0.37 4 4
AKT1 0.02 0.082 -9999 0 -0.24 4 4
response to hypoxia 0.008 0.085 -9999 0 -0.16 24 24
MCL1 0.005 0.41 -9999 0 -0.8 100 100
NDRG1 0.004 0.41 -9999 0 -0.8 100 100
SERPINE1 -0.03 0.46 -9999 0 -0.88 116 116
FECH 0.005 0.41 -9999 0 -0.8 100 100
FURIN 0.005 0.41 -9999 0 -0.8 100 100
NCOA2 0.004 0.046 -9999 0 -0.33 12 12
EP300 0.044 0.12 -9999 0 -0.27 27 27
HMOX1 -0.01 0.44 -9999 0 -0.85 107 107
BHLHE40 0.004 0.41 -9999 0 -0.8 100 100
BHLHE41 0.004 0.41 -9999 0 -0.8 101 101
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.012 0.063 -9999 0 -0.32 10 10
ENG 0.063 0.11 -9999 0 -0.4 13 13
JUN 0.011 0.002 -9999 0 -10000 0 0
RORA 0.005 0.41 -9999 0 -0.8 100 100
ABCB1 -0.031 0.063 -9999 0 -10000 0 0
TFRC 0.005 0.41 -9999 0 -0.8 100 100
CXCR4 -0.023 0.45 -9999 0 -0.89 105 105
TF -0.001 0.42 -9999 0 -0.81 103 103
CITED2 0.005 0.41 -9999 0 -0.8 100 100
HIF1A/ARNT -0.074 0.42 -9999 0 -0.89 102 102
LDHA -0.02 0.04 -9999 0 -10000 0 0
ETS1 -0.001 0.42 -9999 0 -0.8 103 103
PGK1 0.005 0.41 -9999 0 -0.8 100 100
NOS2 -0.004 0.42 -9999 0 -0.82 104 104
ITGB2 0.003 0.41 -9999 0 -0.81 100 100
ALDOA 0.005 0.41 -9999 0 -0.8 100 100
Cbp/p300/CITED2 0.003 0.42 -9999 0 -0.83 90 90
FOS 0.002 0.056 -9999 0 -0.35 16 16
HK2 0.001 0.42 -9999 0 -0.81 101 101
SP1 0.017 0.003 -9999 0 -10000 0 0
GCK 0.016 0.3 -9999 0 -1.2 32 32
HK1 0.005 0.41 -9999 0 -0.8 100 100
NPM1 0.005 0.41 -9999 0 -0.8 100 100
EGLN1 0.005 0.41 -9999 0 -0.8 100 100
CREB1 0.016 0 -9999 0 -10000 0 0
PGM1 0.005 0.41 -9999 0 -0.8 100 100
SMAD3 0.011 0.003 -9999 0 -10000 0 0
EDN1 0.056 0.14 -9999 0 -0.46 2 2
IGFBP1 -0.049 0.45 -9999 0 -0.88 109 109
VEGFA 0.017 0.37 -9999 0 -0.71 94 94
HIF1A/JAB1 -0.011 0.036 -9999 0 -0.29 4 4
CP -0.023 0.44 -9999 0 -0.88 104 104
CXCL12 0.004 0.41 -9999 0 -0.8 100 100
COPS5 0.009 0.004 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.003 -9999 0 -10000 0 0
BNIP3 0.005 0.41 -9999 0 -0.8 100 100
EGLN3 0.005 0.41 -9999 0 -0.8 100 100
CA9 -0.033 0.46 -9999 0 -0.88 119 119
TERT -0.057 0.46 -9999 0 -0.86 120 120
ENO1 0.005 0.41 -9999 0 -0.8 100 100
PFKL 0.005 0.41 -9999 0 -0.8 100 100
NCOA1 0.01 0.002 -9999 0 -10000 0 0
ADM -0.008 0.44 -9999 0 -0.85 105 105
ARNT 0.017 0.075 -9999 0 -0.16 4 4
HNF4A -0.013 0.075 -9999 0 -0.33 32 32
ADFP -0.002 0.41 -9999 0 -0.8 101 101
SLC2A1 0.036 0.34 -9999 0 -0.64 76 76
LEP 0 0.41 -9999 0 -0.8 100 100
HIF1A/ARNT/Cbp/p300 -0.065 0.31 -9999 0 -0.68 92 92
EPO 0.032 0.3 -9999 0 -0.62 53 53
CREBBP 0.044 0.12 -9999 0 -0.27 27 27
HIF1A/ARNT/Cbp/p300/HDAC7 -0.064 0.32 -9999 0 -0.69 98 98
PFKFB3 0.005 0.41 -9999 0 -0.8 100 100
NT5E 0.001 0.42 -9999 0 -0.81 101 101
Coregulation of Androgen receptor activity

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
NRIP1 0.009 0.009 -10000 0 -10000 0 0
SVIL 0.005 0.037 -10000 0 -0.37 6 6
ZNF318 0.012 0.023 0.17 12 -10000 0 12
JMJD2C 0 0.012 -10000 0 -0.057 22 22
T-DHT/AR/Ubc9 -0.099 0.12 -10000 0 -0.21 337 337
CARM1 0.01 0.001 -10000 0 -10000 0 0
PRDX1 0.01 0.013 -10000 0 -0.32 1 1
PELP1 0.011 0.003 -10000 0 -10000 0 0
CTNNB1 0.009 0.007 -10000 0 -10000 0 0
AKT1 0.01 0.016 -10000 0 -0.37 1 1
PTK2B 0.008 0.023 -10000 0 -0.32 3 3
MED1 0.011 0.006 -10000 0 -10000 0 0
MAK -0.03 0.12 0.17 11 -0.37 73 84
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.001 0.054 -10000 0 -0.38 13 13
GSN 0.009 0.009 -10000 0 -10000 0 0
NCOA2 0.004 0.044 -10000 0 -0.32 12 12
NCOA6 0.009 0.008 -10000 0 -10000 0 0
DNA-PK 0.005 0.024 0.17 12 -10000 0 12
NCOA4 0.01 0.001 -10000 0 -10000 0 0
PIAS3 0.009 0.007 -10000 0 -10000 0 0
cell proliferation -0.026 0.047 -10000 0 -10000 0 0
XRCC5 0.011 0.005 -10000 0 -10000 0 0
UBE3A 0.008 0.013 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.1 0.12 -10000 0 -0.21 350 350
FHL2 -0.07 0.21 -10000 0 -0.82 45 45
RANBP9 0.009 0.008 -10000 0 -10000 0 0
JMJD1A 0.006 0.02 -10000 0 -0.082 1 1
CDK6 -0.047 0.14 -10000 0 -0.37 100 100
TGFB1I1 -0.1 0.18 -10000 0 -0.38 194 194
T-DHT/AR/CyclinD1 -0.11 0.12 -10000 0 -0.22 369 369
XRCC6 0.011 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.097 0.13 -10000 0 -0.21 340 340
CTDSP1 0.009 0.015 -10000 0 -0.37 1 1
CTDSP2 0.003 0.063 -10000 0 -0.38 17 17
BRCA1 -0.002 0.064 -10000 0 -0.37 19 19
TCF4 0.012 0.01 -10000 0 -10000 0 0
CDKN2A -0.1 0.18 -10000 0 -0.37 195 195
SRF 0.009 0.032 -10000 0 -10000 0 0
NKX3-1 -0.039 0.044 -10000 0 -10000 0 0
KLK3 -0.019 0.18 -10000 0 -1.3 12 12
TMF1 0.009 0.002 -10000 0 -10000 0 0
HNRNPA1 0.011 0.017 -10000 0 -0.37 1 1
AOF2 -0.002 0.009 -10000 0 -0.067 12 12
APPL1 0.02 0.017 -10000 0 -0.25 1 1
T-DHT/AR/Caspase 8 -0.11 0.12 0.1 1 -0.22 346 347
AR -0.18 0.19 -10000 0 -0.37 337 337
UBA3 0.009 0.003 -10000 0 -10000 0 0
PATZ1 0.011 0.008 -10000 0 -10000 0 0
PAWR 0.001 0.057 -10000 0 -0.38 15 15
PRKDC 0.011 0.005 -10000 0 -10000 0 0
PA2G4 0.012 0.01 -10000 0 -10000 0 0
UBE2I 0.01 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.087 0.1 -10000 0 -0.19 337 337
RPS6KA3 0.009 0.009 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.099 0.12 -10000 0 -0.21 337 337
LATS2 0.01 0.022 -10000 0 -0.37 2 2
T-DHT/AR/PRX1 -0.088 0.1 0.12 5 -0.19 338 343
Cyclin D3/CDK11 p58 0 0.002 -10000 0 -10000 0 0
VAV3 -0.026 0.1 -10000 0 -0.33 68 68
KLK2 -0.049 0.062 -10000 0 -0.3 22 22
CASP8 -0.003 0.07 -10000 0 -0.37 23 23
T-DHT/AR/TIF2/CARM1 -0.086 0.1 -10000 0 -0.18 345 345
TMPRSS2 -0.054 0.084 -10000 0 -0.34 37 37
CCND1 -0.016 0.097 -10000 0 -0.38 45 45
PIAS1 0.008 0.013 -10000 0 -10000 0 0
mol:T-DHT -0.002 0.018 -10000 0 -0.058 33 33
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0.007 0.021 -10000 0 -0.14 6 6
T-DHT/AR/CDK6 -0.13 0.14 -10000 0 -0.24 383 383
CMTM2 0.009 0.021 -10000 0 -0.37 2 2
SNURF -0.001 0.06 -10000 0 -0.32 22 22
ZMIZ1 0.009 0.015 -10000 0 -10000 0 0
CCND3 0.01 0.001 -10000 0 -10000 0 0
TGIF1 -0.059 0.15 -10000 0 -0.37 122 122
FKBP4 0.009 0.008 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.032 0.1 -9999 0 -0.29 12 12
MAP3K8 0.003 0.051 -9999 0 -0.38 12 12
FOS -0.04 0.1 -9999 0 -0.23 67 67
PRKCA 0.011 0.002 -9999 0 -10000 0 0
PTPN7 -0.047 0.14 -9999 0 -0.37 101 101
HRAS 0.01 0 -9999 0 -10000 0 0
PRKCB -0.1 0.16 -9999 0 -0.32 225 225
NRAS 0.01 0 -9999 0 -10000 0 0
RAS family/GTP 0 0 -9999 0 -10000 0 0
MAPK3 -0.026 0.075 -9999 0 -0.37 2 2
MAP2K1 -0.082 0.16 -9999 0 -0.31 225 225
ELK1 0.01 0.002 -9999 0 -10000 0 0
BRAF -0.1 0.14 -9999 0 -0.3 225 225
mol:GTP 0 0.001 -9999 0 -0.004 16 16
MAPK1 -0.026 0.075 -9999 0 -0.37 2 2
RAF1 -0.1 0.14 -9999 0 -0.3 225 225
KRAS 0.01 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin 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
ITGB1 0.003 0.051 -9999 0 -0.37 12 12
ITGB7 0.005 0.042 -9999 0 -0.37 8 8
ITGA4 -0.047 0.14 -9999 0 -0.37 99 99
alpha4/beta7 Integrin -0.04 0.096 -9999 0 -0.26 103 103
alpha4/beta1 Integrin -0.041 0.1 -9999 0 -0.27 101 101
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.019 0.026 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.036 0.063 -9999 0 -0.26 23 23
JUN -0.015 0.078 -9999 0 -0.28 17 17
HRAS 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.072 0.1 -9999 0 -0.21 183 183
RAP1A 0.01 0 -9999 0 -10000 0 0
FRS2 0.008 0.026 -9999 0 -0.37 3 3
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.073 0.1 -9999 0 -0.21 185 185
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.065 0.095 -9999 0 -0.19 228 228
RHOA 0.01 0 -9999 0 -10000 0 0
RAP1A/GTP -0.062 0.087 -9999 0 -0.31 33 33
GRB7 0.004 0.033 -9999 0 -0.37 5 5
RET51/GFRalpha1/GDNF -0.072 0.1 -9999 0 -0.21 183 183
MAPKKK cascade -0.053 0.077 -9999 0 -0.27 42 42
BCAR1 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.061 0.093 -9999 0 -0.19 220 220
lamellipodium assembly -0.037 0.062 -9999 0 -0.2 62 62
RET51/GFRalpha1/GDNF/SHC -0.077 0.1 -9999 0 -0.21 199 199
PIK3CA 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.067 0.097 -9999 0 -0.19 234 234
RET9/GFRalpha1/GDNF/Shank3 -0.065 0.097 -9999 0 -0.19 226 226
MAPK3 -0.036 0.096 -9999 0 -0.29 33 33
DOK1 0.008 0.026 -9999 0 -0.37 3 3
DOK6 -0.059 0.14 -9999 0 -0.32 137 137
PXN 0.01 0 -9999 0 -10000 0 0
neurite development -0.037 0.098 -9999 0 -0.28 33 33
DOK5 0.009 0.013 -9999 0 -0.32 1 1
GFRA1 -0.031 0.11 -9999 0 -0.34 79 79
MAPK8 -0.022 0.082 -9999 0 -0.3 17 17
HRAS/GTP -0.059 0.084 -9999 0 -0.3 34 34
tube development -0.059 0.088 -9999 0 -0.19 171 171
MAPK1 -0.036 0.096 -9999 0 -0.29 33 33
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.022 0.07 -9999 0 -0.18 73 73
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
PDLIM7 0.004 0.049 -9999 0 -0.37 11 11
RET51/GFRalpha1/GDNF/Dok6 -0.094 0.11 -9999 0 -0.32 90 90
SHC1 -0.001 0.064 -9999 0 -0.37 19 19
RET51/GFRalpha1/GDNF/Dok4 -0.072 0.1 -9999 0 -0.21 183 183
RET51/GFRalpha1/GDNF/Dok5 -0.072 0.1 -9999 0 -0.21 183 183
PRKCA 0.01 0 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
CREB1 -0.026 0.087 -9999 0 -0.24 60 60
PIK3R1 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.024 0.072 -9999 0 -0.18 76 76
RET51/GFRalpha1/GDNF/Grb7 -0.074 0.1 -9999 0 -0.21 187 187
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.018 0.094 -9999 0 -0.34 53 53
DOK4 0.01 0 -9999 0 -10000 0 0
JNK cascade -0.014 0.077 -9999 0 -0.28 17 17
RET9/GFRalpha1/GDNF/FRS2 -0.062 0.093 -9999 0 -0.19 222 222
SHANK3 0.002 0.049 -9999 0 -0.32 15 15
RASA1 0.01 0 -9999 0 -10000 0 0
NCK1 0.009 0.015 -9999 0 -0.37 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.024 0.072 -9999 0 -0.18 75 75
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.03 0.087 -9999 0 -0.27 29 29
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.03 0.086 -9999 0 -0.21 60 60
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.033 0.092 -9999 0 -0.23 66 66
PI3K -0.022 0.11 -9999 0 -0.28 63 63
SOS1 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.059 0.088 -9999 0 -0.19 171 171
GRB10 0.01 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.027 0.078 -9999 0 -0.23 29 29
RET51/GFRalpha1/GDNF/FRS2 -0.073 0.1 -9999 0 -0.21 185 185
GAB1 0.009 0.015 -9999 0 -0.37 1 1
IRS1 0.01 0 -9999 0 -10000 0 0
IRS2 0.009 0.015 -9999 0 -0.37 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.034 0.092 -9999 0 -0.27 38 38
RET51/GFRalpha1/GDNF/PKC alpha -0.072 0.1 -9999 0 -0.21 183 183
GRB2 0.01 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GDNF -0.081 0.16 -9999 0 -0.37 156 156
RAC1 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.072 0.1 -9999 0 -0.21 183 183
Rac1/GTP -0.042 0.072 -9999 0 -0.25 42 42
RET9/GFRalpha1/GDNF -0.071 0.11 -9999 0 -0.22 220 220
GFRalpha1/GDNF -0.085 0.13 -9999 0 -0.26 220 220
BMP 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
BMP7/BMPR2/BMPR1A-1B/FS -0.02 0.054 -9999 0 -0.16 84 84
SMAD6-7/SMURF1 -0.001 0.011 -9999 0 -0.2 2 2
NOG -0.064 0.15 -9999 0 -0.37 129 129
SMAD9 -0.01 0.022 -9999 0 -0.38 1 1
SMAD4 0.01 0 -9999 0 -10000 0 0
SMAD5 0.007 0.031 -9999 0 -0.23 2 2
BMP7/USAG1 -0.1 0.11 -9999 0 -0.21 326 326
SMAD5/SKI 0.013 0.03 -9999 0 -0.24 1 1
SMAD1 0.035 0.017 -9999 0 -10000 0 0
BMP2 -0.21 0.19 -9999 0 -0.37 382 382
SMAD1/SMAD1/SMAD4 -0.001 0.008 -9999 0 -10000 0 0
BMPR1A 0.01 0 -9999 0 -10000 0 0
BMPR1B 0.009 0.018 -9999 0 -0.32 2 2
BMPR1A-1B/BAMBI -0.001 0.014 -9999 0 -0.18 4 4
AHSG 0.001 0.057 -9999 0 -0.37 15 15
CER1 -0.033 0.11 -9999 0 -0.37 67 67
BMP2-4/CER1 -0.14 0.11 -9999 0 -0.22 445 445
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.005 0.043 -9999 0 -0.24 2 2
BMP2-4 (homodimer) -0.15 0.13 -9999 0 -0.26 387 387
RGMB 0.01 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.002 0.017 -9999 0 -0.18 5 5
RGMA 0.003 0.051 -9999 0 -0.37 12 12
SMURF1 0.01 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.009 0.04 -9999 0 -0.26 2 2
BMP2-4/USAG1 -0.2 0.14 -9999 0 -0.26 515 515
SMAD6/SMURF1/SMAD5 0.013 0.03 -9999 0 -0.24 1 1
SOSTDC1 -0.15 0.17 -9999 0 -0.32 325 325
BMP7/BMPR2/BMPR1A-1B -0.001 0.01 -9999 0 -0.18 1 1
SKI 0.01 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.007 0.033 -9999 0 -0.37 5 5
HFE2 0.007 0.005 -9999 0 -10000 0 0
ZFYVE16 0.01 0 -9999 0 -10000 0 0
MAP3K7 0.01 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.12 0.11 -9999 0 -0.21 391 391
SMAD5/SMAD5/SMAD4 0.013 0.03 -9999 0 -0.24 1 1
MAPK1 0.01 0 -9999 0 -10000 0 0
TAK1/TAB family -0.013 0.018 -9999 0 -0.25 1 1
BMP7 (homodimer) 0.009 0.015 -9999 0 -0.37 1 1
NUP214 0.01 0 -9999 0 -10000 0 0
BMP6/FETUA -0.008 0.043 -9999 0 -0.25 20 20
SMAD1/SKI 0.039 0.016 -9999 0 -10000 0 0
SMAD6 0.009 0.021 -9999 0 -0.37 2 2
CTDSP2 0 0.06 -9999 0 -0.37 17 17
BMP2-4/FETUA -0.13 0.11 -9999 0 -0.22 388 388
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.061 0.14 -9999 0 -0.32 142 142
BMPR2 (homodimer) 0.01 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.001 0.012 -9999 0 -0.21 2 2
CHRDL1 -0.021 0.097 -9999 0 -0.33 61 61
ENDOFIN/SMAD1 0.039 0.016 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.001 0.01 -9999 0 -10000 0 0
SMAD6/SMURF1 0.01 0 -9999 0 -10000 0 0
BAMBI 0.009 0.021 -9999 0 -0.37 2 2
SMURF2 0.01 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.14 0.12 -9999 0 -0.22 414 414
BMP2-4/GREM1 -0.16 0.13 -9999 0 -0.24 442 442
SMAD7 0.01 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 0.006 0.027 -9999 0 -0.35 1 1
SMAD1/SMAD6 0.039 0.016 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.009 0.015 -9999 0 -0.37 1 1
BMP6 0.007 0.033 -9999 0 -0.37 5 5
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.007 0.038 -9999 0 -0.23 2 2
PPM1A 0.01 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.039 0.016 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.01 0 -9999 0 -10000 0 0
PPP1CA 0.01 0 -9999 0 -10000 0 0
XIAP 0.01 0 -9999 0 -10000 0 0
CTDSP1 0.009 0.015 -9999 0 -0.37 1 1
PPP1R15A 0.01 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.02 0.045 -9999 0 -0.25 2 2
CHRD 0.006 0.036 -9999 0 -0.32 8 8
BMPR2 0.01 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.02 0.047 -9999 0 -0.27 2 2
BMP4 -0.001 0.063 -9999 0 -0.37 19 19
FST -0.038 0.13 -9999 0 -0.37 84 84
BMP2-4/NOG -0.16 0.16 -9999 0 -0.28 389 389
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.001 0.009 -9999 0 -0.16 1 1
PDGFR-alpha signaling pathway

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
PDGFRA -0.045 0.14 -9999 0 -0.37 98 98
PDGF/PDGFRA/CRKL -0.035 0.086 -9999 0 -0.24 98 98
positive regulation of JUN kinase activity -0.029 0.062 -9999 0 -0.16 116 116
CRKL 0.009 0.015 -9999 0 -0.37 1 1
PDGF/PDGFRA/Caveolin-3 -0.04 0.094 -9999 0 -0.25 106 106
AP1 -0.028 0.094 -9999 0 -0.75 8 8
mol:IP3 -0.019 0.095 -9999 0 -0.25 98 98
PLCG1 -0.019 0.095 -9999 0 -0.25 98 98
PDGF/PDGFRA/alphaV Integrin -0.035 0.085 -9999 0 -0.24 98 98
RAPGEF1 0.01 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ -0.019 0.095 -9999 0 -0.25 98 98
CAV3 -0.001 0.051 -9999 0 -0.37 12 12
CAV1 -0.052 0.14 -9999 0 -0.37 107 107
SHC/Grb2/SOS1 -0.029 0.062 -9999 0 -0.16 116 116
PDGF/PDGFRA/Shf -0.035 0.085 -9999 0 -0.24 98 98
FOS 0.003 0.1 -9999 0 -0.74 8 8
JUN -0.003 0.008 -9999 0 -10000 0 0
oligodendrocyte development -0.035 0.085 -9999 0 -0.24 98 98
GRB2 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
mol:DAG -0.019 0.095 -9999 0 -0.25 98 98
PDGF/PDGFRA -0.045 0.14 -9999 0 -0.37 98 98
actin cytoskeleton reorganization -0.035 0.085 -9999 0 -0.24 98 98
SRF 0.017 0.004 -9999 0 -10000 0 0
SHC1 -0.001 0.064 -9999 0 -0.37 19 19
PI3K -0.028 0.067 -9999 0 -0.19 97 97
PDGF/PDGFRA/Crk/C3G -0.028 0.067 -9999 0 -0.19 98 98
JAK1 -0.019 0.091 -9999 0 -0.24 98 98
ELK1/SRF 0.008 0.057 -9999 0 -0.17 5 5
SHB 0.01 0 -9999 0 -10000 0 0
SHF 0.01 0 -9999 0 -10000 0 0
CSNK2A1 0.004 0.009 -9999 0 -10000 0 0
GO:0007205 -0.014 0.085 -9999 0 -0.22 98 98
SOS1 0.01 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.029 0.062 -9999 0 -0.16 116 116
PDGF/PDGFRA/SHB -0.035 0.085 -9999 0 -0.24 98 98
PDGF/PDGFRA/Caveolin-1 -0.076 0.12 -9999 0 -0.26 193 193
ITGAV 0.01 0 -9999 0 -10000 0 0
ELK1 -0.003 0.073 -9999 0 -0.18 98 98
PIK3CA 0.01 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.035 0.085 -9999 0 -0.24 98 98
JAK-STAT cascade -0.019 0.091 -9999 0 -0.24 98 98
cell proliferation -0.035 0.085 -9999 0 -0.24 98 98
Rapid glucocorticoid signaling

Figure S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S30.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.035 0.062 -10000 0 -0.14 165 165
MAPK9 0.007 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.092 0.11 -10000 0 -0.22 290 290
GNB1/GNG2 -0.001 0.01 -10000 0 -0.18 2 2
GNB1 0.01 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0 -10000 0 -10000 0 0
Gs family/GTP -0.04 0.071 -10000 0 -0.16 165 165
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 0.012 0.02 0.047 165 -10000 0 165
GNAL -0.073 0.14 -10000 0 -0.32 165 165
GNG2 0.009 0.018 -10000 0 -0.32 2 2
CRH -0.14 0.16 -10000 0 -0.32 290 290
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.022 -10000 0 -0.25 5 5
MAPK11 0.006 0.014 -10000 0 -0.25 2 2
BARD1 signaling 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
BARD1/CSTF1 -0.037 0.089 -10000 0 -0.25 100 100
ATM 0.01 0 -10000 0 -10000 0 0
UBE2D3 0.01 0 -10000 0 -10000 0 0
PRKDC 0.01 0 -10000 0 -10000 0 0
ATR 0.01 0 -10000 0 -10000 0 0
UBE2L3 0.01 0 -10000 0 -10000 0 0
FANCD2 -0.018 0.064 -10000 0 -10000 0 0
protein ubiquitination -0.081 0.13 -10000 0 -0.36 84 84
XRCC5 0.01 0 -10000 0 -10000 0 0
XRCC6 0.01 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.01 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.026 0.055 -10000 0 -0.25 7 7
FANCF 0.01 0 -10000 0 -10000 0 0
BRCA1 -0.001 0.064 -10000 0 -0.37 19 19
CCNE1 0.01 0 -10000 0 -10000 0 0
CDK2/Cyclin E1 -0.082 0.12 -10000 0 -0.25 217 217
FANCG 0.008 0.026 -10000 0 -0.37 3 3
BRCA1/BACH1/BARD1 -0.044 0.11 -10000 0 -0.28 106 106
FANCE 0.01 0 -10000 0 -10000 0 0
FANCC -0.042 0.13 -10000 0 -0.37 91 91
NBN 0.01 0 -10000 0 -10000 0 0
FANCA 0.006 0.036 -10000 0 -0.37 6 6
DNA repair -0.081 0.19 -10000 0 -0.4 150 150
BRCA1/BARD1/ubiquitin -0.044 0.11 -10000 0 -0.28 106 106
BARD1/DNA-PK -0.026 0.062 -10000 0 -0.18 97 97
FANCL 0.01 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.037 0.089 0.25 100 -10000 0 100
BRCA1/BARD1/CTIP/M/R/N Complex 0.006 0.057 -10000 0 -0.24 8 8
BRCA1/BACH1/BARD1/TopBP1 -0.036 0.087 -10000 0 -0.23 106 106
BRCA1/BARD1/P53 -0.049 0.11 -10000 0 -0.23 140 140
BARD1/CSTF1/BRCA1 -0.036 0.087 -10000 0 -0.23 106 106
BRCA1/BACH1 -0.001 0.064 -10000 0 -0.37 19 19
BARD1 -0.047 0.14 -10000 0 -0.37 100 100
PCNA -0.025 0.11 -10000 0 -0.37 61 61
BRCA1/BARD1/UbcH5C -0.036 0.087 -10000 0 -0.23 106 106
BRCA1/BARD1/UbcH7 -0.036 0.087 -10000 0 -0.23 106 106
BRCA1/BARD1/RAD51/PCNA -0.12 0.17 -10000 0 -0.28 273 273
BARD1/DNA-PK/P53 -0.04 0.086 -10000 0 -0.34 29 29
BRCA1/BARD1/Ubiquitin -0.044 0.11 -10000 0 -0.28 106 106
BRCA1/BARD1/CTIP -0.046 0.1 -10000 0 -0.23 130 130
FA complex 0.019 0.035 -10000 0 -0.17 8 8
BARD1/EWS -0.037 0.089 -10000 0 -0.25 100 100
RBBP8 -0.003 0.073 -10000 0 -0.25 53 53
TP53 -0.029 0.12 -10000 0 -0.37 67 67
TOPBP1 0.01 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.049 0.11 0.23 140 -10000 0 140
BRCA1/BARD1 -0.082 0.13 -10000 0 -0.36 84 84
CSTF1 0.01 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.039 0.092 -10000 0 -0.26 100 100
CDK2 -0.12 0.18 -10000 0 -0.37 217 217
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.14 0.19 -10000 0 -0.37 254 254
RAD50 0.01 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.044 0.11 -10000 0 -0.28 106 106
EWSR1 0.01 0 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.012 0.051 -10000 0 -0.22 37 37
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.03 0.065 -10000 0 -0.26 13 13
NGF (dimer)/p75(NTR)/BEX1 -0.043 0.089 -10000 0 -0.21 138 138
NT-4/5 (dimer)/p75(NTR) -0.043 0.1 -10000 0 -0.27 107 107
IKBKB 0.01 0 -10000 0 -10000 0 0
AKT1 -0.005 0.077 -10000 0 -0.31 8 8
IKBKG 0.01 0 -10000 0 -10000 0 0
BDNF -0.17 0.17 -10000 0 -0.32 359 359
MGDIs/NGR/p75(NTR)/LINGO1 -0.075 0.12 -10000 0 -0.23 222 222
FURIN 0.01 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.12 0.11 -10000 0 -0.19 406 406
LINGO1 -0.006 0.07 -10000 0 -0.32 31 31
Sortilin/TRAF6/NRIF 0 0 -10000 0 -10000 0 0
proBDNF (dimer) -0.17 0.17 -10000 0 -0.32 359 359
NTRK1 -0.014 0.093 -10000 0 -0.37 42 42
RTN4R -0.07 0.14 -10000 0 -0.32 160 160
neuron apoptosis -0.083 0.11 -10000 0 -0.28 81 81
IRAK1 0.01 0 -10000 0 -10000 0 0
SHC1 -0.028 0.1 -10000 0 -0.21 141 141
ARHGDIA 0.01 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.035 0.073 -10000 0 -0.19 90 90
MAGEH1 0.008 0.022 -10000 0 -0.32 3 3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.04 0.084 -10000 0 -0.21 94 94
Mammalian IAPs/DIABLO -0.007 0.034 -10000 0 -0.18 17 17
proNGF (dimer) -0.014 0.086 -10000 0 -0.32 48 48
MAGED1 0.01 0 -10000 0 -10000 0 0
APP 0.01 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.009 0.071 -10000 0 -0.37 24 24
ZNF274 0.01 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.031 0.067 -10000 0 -0.18 89 89
NGF -0.014 0.087 -10000 0 -0.32 48 48
cell cycle arrest -0.03 0.072 0.12 9 -0.2 85 94
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.005 0.067 -10000 0 -0.28 9 9
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.035 0.082 -10000 0 -0.22 107 107
NCSTN 0.01 0 -10000 0 -10000 0 0
mol:GTP -0.039 0.082 -10000 0 -0.2 129 129
PSENEN 0.01 0 -10000 0 -10000 0 0
mol:ceramide -0.012 0.081 -10000 0 -0.19 89 89
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.01 0.082 -10000 0 -0.27 28 28
p75(NTR)/beta APP -0.033 0.085 -10000 0 -0.25 89 89
BEX1 0.002 0.049 -10000 0 -0.32 15 15
mol:GDP -0.029 0.091 -10000 0 -0.21 129 129
NGF (dimer) -0.079 0.1 -10000 0 -0.2 250 250
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.066 0.1 -10000 0 -0.25 113 113
PIK3R1 0.01 0 -10000 0 -10000 0 0
RAC1/GTP -0.033 0.07 -10000 0 -0.18 89 89
MYD88 -0.012 0.09 -10000 0 -0.37 39 39
CHUK 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.039 0.083 -10000 0 -0.2 129 129
RHOB 0.01 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.004 0.031 -10000 0 -0.25 10 10
NT3 (dimer) 0.002 0.039 -10000 0 -0.37 7 7
TP53 -0.086 0.11 -10000 0 -0.31 76 76
PRDM4 -0.012 0.082 -10000 0 -0.18 129 129
BDNF (dimer) -0.21 0.14 -10000 0 -0.33 314 314
PIK3CA 0.01 0 -10000 0 -10000 0 0
SORT1 0.01 0 -10000 0 -10000 0 0
activation of caspase activity -0.03 0.065 -10000 0 -0.25 13 13
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.034 0.072 -10000 0 -0.19 89 89
RHOC -0.004 0.073 -10000 0 -0.37 25 25
XIAP 0.01 0 -10000 0 -10000 0 0
MAPK10 -0.043 0.089 -10000 0 -0.25 41 41
DIABLO 0.01 0 -10000 0 -10000 0 0
SMPD2 -0.012 0.082 -10000 0 -0.19 89 89
APH1B 0.01 0 -10000 0 -10000 0 0
APH1A 0.01 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.039 0.083 -10000 0 -0.2 129 129
PSEN1 0.01 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0.01 -10000 0 -0.25 1 1
NT3 (dimer)/p75(NTR) -0.036 0.092 -10000 0 -0.26 93 93
MAPK8 -0.043 0.09 -10000 0 -0.26 41 41
MAPK9 -0.042 0.088 -10000 0 -0.25 37 37
APAF1 0.01 0 -10000 0 -10000 0 0
NTF3 0.002 0.039 -10000 0 -0.37 7 7
NTF4 -0.009 0.071 -10000 0 -0.37 24 24
NDN -0.004 0.066 -10000 0 -0.32 27 27
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.033 0.067 -10000 0 -0.31 14 14
p75 CTF/Sortilin/TRAF6/NRIF 0 0 -10000 0 -10000 0 0
RhoA-B-C/GTP -0.039 0.082 -10000 0 -0.2 129 129
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.091 0.085 -10000 0 -0.23 89 89
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.1 0.093 -10000 0 -0.25 89 89
PRKACB 0.01 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.11 0.11 -10000 0 -0.21 359 359
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.006 0.075 -10000 0 -0.35 30 30
BIRC2 0.01 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.033 0.075 0.13 8 -0.3 20 28
BAD -0.036 0.088 -10000 0 -0.25 40 40
RIPK2 0.008 0.026 -10000 0 -0.37 3 3
NGFR -0.041 0.13 -10000 0 -0.37 89 89
CYCS -0.005 0.077 -10000 0 -0.25 13 13
ADAM17 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.035 0.073 -10000 0 -0.19 92 92
BCL2L11 -0.037 0.089 -10000 0 -0.25 40 40
BDNF (dimer)/p75(NTR) -0.15 0.13 -10000 0 -0.24 406 406
PI3K -0.034 0.072 -10000 0 -0.19 89 89
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.034 0.072 -10000 0 -0.19 89 89
NDNL2 0.01 0 -10000 0 -10000 0 0
YWHAE 0.01 0 -10000 0 -10000 0 0
PRKCI 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.049 0.1 -10000 0 -0.25 129 129
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.034 0.072 -10000 0 -0.19 89 89
TRAF6 0.01 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCZ -0.03 0.11 -10000 0 -0.32 79 79
PLG 0 0.025 -10000 0 -0.37 3 3
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.11 0.12 -10000 0 -0.33 104 104
SQSTM1 0.01 0 -10000 0 -10000 0 0
NGFRAP1 0.01 0 -10000 0 -10000 0 0
CASP3 -0.032 0.083 -10000 0 -0.24 40 40
E2F1 0.004 0.047 -10000 0 -0.37 10 10
CASP9 0.009 0.015 -10000 0 -0.37 1 1
IKK complex -0.037 0.075 -10000 0 -0.3 25 25
NGF (dimer)/TRKA -0.031 0.08 -10000 0 -0.23 89 89
MMP7 -0.13 0.18 -10000 0 -0.37 248 248
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.03 0.065 -10000 0 -0.26 13 13
MMP3 -0.11 0.16 -10000 0 -0.32 239 239
APAF-1/Caspase 9 -0.024 0.049 -10000 0 -0.24 12 12
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.056 0.092 -9999 0 -0.22 155 155
alphaM/beta2 Integrin/GPIbA -0.012 0.035 -9999 0 -0.23 13 13
alphaM/beta2 Integrin/proMMP-9 -0.077 0.1 -9999 0 -0.21 223 223
PLAUR -0.017 0.098 -9999 0 -0.37 47 47
HMGB1 0.003 0.018 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.011 0.034 -9999 0 -0.23 11 11
AGER -0.028 0.1 -9999 0 -0.38 53 53
RAP1A 0.01 0 -9999 0 -10000 0 0
SELPLG 0.009 0.015 -9999 0 -0.37 1 1
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.053 0.086 -9999 0 -0.3 35 35
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.18 -9999 0 -0.37 220 220
CYR61 -0.009 0.081 -9999 0 -0.36 34 34
TLN1 0.01 0 -9999 0 -10000 0 0
Rap1/GTP -0.053 0.068 -9999 0 -0.22 40 40
RHOA 0.01 0 -9999 0 -10000 0 0
P-selectin oligomer -0.001 0.057 -9999 0 -0.37 15 15
MYH2 -0.057 0.095 -9999 0 -0.23 89 89
MST1R 0.008 0.024 -9999 0 -0.34 3 3
leukocyte activation during inflammatory response -0.041 0.069 -9999 0 -0.2 49 49
APOB -0.017 0.09 -9999 0 -0.33 52 52
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.076 0.16 -9999 0 -0.37 150 150
JAM3 0.01 0 -9999 0 -10000 0 0
GP1BA 0.009 0.02 -9999 0 -0.35 2 2
alphaM/beta2 Integrin/CTGF -0.018 0.048 -9999 0 -0.22 32 32
alphaM/beta2 Integrin -0.055 0.09 -9999 0 -0.22 97 97
JAM3 homodimer 0.01 0 -9999 0 -10000 0 0
ICAM2 0.01 0 -9999 0 -10000 0 0
ICAM1 -0.014 0.093 -9999 0 -0.37 42 42
phagocytosis triggered by activation of immune response cell surface activating receptor -0.055 0.089 -9999 0 -0.22 97 97
cell adhesion -0.012 0.035 -9999 0 -0.23 13 13
NFKB1 -0.043 0.16 -9999 0 -0.31 143 143
THY1 0.004 0.044 -9999 0 -0.32 12 12
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.043 0.08 -9999 0 -0.18 155 155
alphaM/beta2 Integrin/LRP/tPA -0.022 0.054 -9999 0 -0.18 67 67
IL6 -0.083 0.24 -9999 0 -0.56 118 118
ITGB2 -0.003 0.048 -9999 0 -0.38 9 9
elevation of cytosolic calcium ion concentration -0.071 0.11 -9999 0 -0.23 195 195
alphaM/beta2 Integrin/JAM2/JAM3 -0.01 0.035 -9999 0 -0.2 19 19
JAM2 0.005 0.042 -9999 0 -0.37 8 8
alphaM/beta2 Integrin/ICAM1 -0.036 0.073 -9999 0 -0.22 52 52
alphaM/beta2 Integrin/uPA/Plg -0.061 0.088 -9999 0 -0.19 196 196
RhoA/GTP -0.06 0.099 -9999 0 -0.24 87 87
positive regulation of phagocytosis -0.042 0.066 -9999 0 -0.29 19 19
Ron/MSP -0.03 0.082 -9999 0 -0.25 81 81
alphaM/beta2 Integrin/uPAR/uPA -0.071 0.11 -9999 0 -0.23 195 195
alphaM/beta2 Integrin/uPAR -0.025 0.064 -9999 0 -0.22 55 55
PLAU -0.099 0.17 -9999 0 -0.37 190 190
PLAT -0.022 0.11 -9999 0 -0.37 56 56
actin filament polymerization -0.055 0.093 -9999 0 -0.22 89 89
MST1 -0.035 0.12 -9999 0 -0.37 78 78
alphaM/beta2 Integrin/lipoprotein(a) -0.042 0.069 -9999 0 -0.21 49 49
TNF -0.054 0.2 -9999 0 -0.55 66 66
RAP1B 0.005 0.044 -9999 0 -0.37 9 9
alphaM/beta2 Integrin/uPA -0.068 0.097 -9999 0 -0.21 194 194
fibrinolysis -0.061 0.087 -9999 0 -0.19 196 196
HCK 0.004 0.049 -9999 0 -0.37 11 11
dendritic cell antigen processing and presentation -0.055 0.089 -9999 0 -0.22 97 97
VTN 0.007 0.031 -9999 0 -0.35 5 5
alphaM/beta2 Integrin/CYR61 -0.021 0.056 -9999 0 -0.22 44 44
LPA -0.048 0.12 -9999 0 -0.32 109 109
LRP1 0.01 0 -9999 0 -10000 0 0
cell migration -0.11 0.14 -9999 0 -0.26 262 262
FN1 -0.045 0.14 -9999 0 -0.37 96 96
alphaM/beta2 Integrin/Thy1 -0.014 0.04 -9999 0 -0.2 23 23
MPO -0.085 0.15 -9999 0 -0.32 189 189
KNG1 -0.003 0.046 -9999 0 -0.37 10 10
RAP1/GDP -0.003 0.024 -9999 0 -0.21 9 9
ROCK1 -0.052 0.095 -9999 0 -0.23 88 88
ELA2 0 0 -9999 0 -10000 0 0
PLG 0 0.025 -9999 0 -0.37 3 3
CTGF -0.002 0.067 -9999 0 -0.37 21 21
alphaM/beta2 Integrin/Hck -0.015 0.053 -9999 0 -0.32 15 15
ITGAM 0.001 0.031 -9999 0 -0.38 3 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.013 0.044 -9999 0 -0.21 24 24
HP -0.1 0.18 -9999 0 -0.37 196 196
leukocyte adhesion -0.041 0.068 -9999 0 -0.24 41 41
SELP -0.001 0.057 -9999 0 -0.37 15 15
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.061 0.11 0.24 172 -10000 0 172
KIRREL -0.022 0.098 -10000 0 -0.38 47 47
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.062 0.11 -10000 0 -0.24 172 172
PLCG1 0.01 0 -10000 0 -10000 0 0
ARRB2 0.01 0 -10000 0 -10000 0 0
WASL 0.01 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.041 0.074 -10000 0 -0.21 37 37
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.026 0.087 -10000 0 -0.19 135 135
FYN -0.03 0.077 -10000 0 -0.16 172 172
mol:Ca2+ -0.041 0.073 -10000 0 -0.33 10 10
mol:DAG -0.041 0.073 -10000 0 -0.33 10 10
NPHS2 -0.007 0.015 -10000 0 -10000 0 0
mol:IP3 -0.041 0.073 -10000 0 -0.33 10 10
regulation of endocytosis -0.036 0.064 -10000 0 -0.29 10 10
Nephrin/NEPH1/podocin/Cholesterol -0.043 0.077 -10000 0 -0.17 172 172
establishment of cell polarity -0.061 0.11 -10000 0 -0.24 172 172
Nephrin/NEPH1/podocin/NCK1-2 -0.036 0.064 -10000 0 -0.28 11 11
Nephrin/NEPH1/beta Arrestin2 -0.022 0.073 -10000 0 -0.29 10 10
NPHS1 -0.063 0.14 -10000 0 -0.33 135 135
Nephrin/NEPH1/podocin -0.04 0.072 -10000 0 -0.16 162 162
TJP1 0.01 0 -10000 0 -10000 0 0
NCK1 0.009 0.015 -10000 0 -0.37 1 1
NCK2 0.01 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.041 0.074 -10000 0 -0.33 10 10
CD2AP 0.01 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.041 0.074 -10000 0 -0.21 37 37
GRB2 0.01 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.026 0.077 -10000 0 -0.2 51 51
cytoskeleton organization -0.028 0.1 -10000 0 -0.21 135 135
Nephrin/NEPH1 -0.041 0.073 -10000 0 -0.16 172 172
Nephrin/NEPH1/ZO-1 -0.045 0.081 -10000 0 -0.18 172 172
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.024 0.08 -9999 0 -0.25 50 50
BIRC5 -0.21 0.19 -9999 0 -0.37 390 390
NFKBIA -0.007 0.054 -9999 0 -0.23 4 4
CPEB1 0.003 0.048 -9999 0 -0.32 14 14
AKT1 -0.006 0.052 -9999 0 -0.31 1 1
NDEL1 0.01 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.019 0.058 -9999 0 -0.26 19 19
NDEL1/TACC3 -0.056 0.11 -9999 0 -0.24 171 171
GADD45A -0.019 0.1 -9999 0 -0.37 50 50
GSK3B 0.01 0.002 -9999 0 -10000 0 0
PAK1/Aurora A -0.058 0.09 -9999 0 -0.18 178 178
MDM2 0.002 0.053 -9999 0 -0.37 13 13
JUB -0.079 0.16 -9999 0 -0.37 155 155
TPX2 -0.062 0.12 -9999 0 -0.25 199 199
TP53 -0.005 0.05 -9999 0 -0.14 58 58
DLG7 -0.014 0.051 -9999 0 -10000 0 0
AURKAIP1 0.01 0 -9999 0 -10000 0 0
ARHGEF7 0.01 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.055 0.12 -9999 0 -0.26 171 171
G2/M transition of mitotic cell cycle -0.019 0.057 -9999 0 -0.26 19 19
AURKA -0.016 0.063 -9999 0 -10000 0 0
AURKB -0.056 0.033 -9999 0 -10000 0 0
CDC25B -0.019 0.052 -9999 0 -0.21 1 1
G2/M transition checkpoint -0.059 0.1 -9999 0 -0.23 155 155
mRNA polyadenylation -0.017 0.05 -9999 0 -0.21 14 14
Aurora A/CPEB -0.017 0.05 -9999 0 -0.22 14 14
Aurora A/TACC1/TRAP/chTOG -0.006 0.037 -9999 0 -10000 0 0
BRCA1 -0.001 0.064 -9999 0 -0.37 19 19
centrosome duplication -0.058 0.089 -9999 0 -0.18 178 178
regulation of centrosome cycle -0.056 0.11 -9999 0 -0.24 171 171
spindle assembly -0.006 0.037 -9999 0 -10000 0 0
TDRD7 0.01 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.11 0.11 -9999 0 -0.26 164 164
CENPA -0.047 0.036 -9999 0 -0.1 160 160
Aurora A/PP2A -0.007 0.05 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.001 0.047 -9999 0 -10000 0 0
negative regulation of DNA binding -0.005 0.05 -9999 0 -0.14 58 58
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.01 0 -9999 0 -10000 0 0
Ajuba/Aurora A -0.059 0.1 -9999 0 -0.23 155 155
mitotic prometaphase 0.017 0.009 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.016 0.063 -9999 0 -10000 0 0
TACC1 0.01 0 -9999 0 -10000 0 0
TACC3 -0.088 0.17 -9999 0 -0.37 171 171
Aurora A/Antizyme1 -0.005 0.043 -9999 0 -10000 0 0
Aurora A/RasGAP -0.007 0.05 -9999 0 -10000 0 0
OAZ1 0.01 0 -9999 0 -10000 0 0
RAN 0.01 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.01 0.002 -9999 0 -10000 0 0
GIT1 0.01 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.045 0.074 -9999 0 -0.17 178 178
Importin alpha/Importin beta/TPX2 -0.062 0.12 -9999 0 -0.25 199 199
PPP2R5D 0.01 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.057 0.13 -9999 0 -0.25 199 199
PAK1 -0.079 0.15 -9999 0 -0.32 178 178
CKAP5 0.01 0 -9999 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.035 0.063 -9999 0 -0.32 8 8
NF kappa B1 p50/RelA/I kappa B alpha -0.047 0.073 -9999 0 -0.22 43 43
AP1 -0.062 0.08 -9999 0 -0.26 57 57
mol:PIP3 -0.13 0.11 -9999 0 -0.27 201 201
AKT1 -0.015 0.039 -9999 0 -0.22 8 8
PTK2B -0.015 0.061 -9999 0 -0.23 21 21
RHOA 0.005 0.04 -9999 0 -0.21 2 2
PIK3CB 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ -0.02 0.076 -9999 0 -0.18 34 34
MAGI3 0.009 0.013 -9999 0 -0.32 1 1
RELA 0.01 0 -9999 0 -10000 0 0
apoptosis -0.065 0.11 -9999 0 -0.21 184 184
HRAS/GDP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization -0.003 0.058 -9999 0 -0.2 25 25
NF kappa B1 p50/RelA -0.055 0.076 -9999 0 -0.25 52 52
endothelial cell migration -0.065 0.15 -9999 0 -0.34 150 150
ADCY4 -0.009 0.09 -9999 0 -0.28 43 43
ADCY5 -0.022 0.11 -9999 0 -0.3 69 69
ADCY6 -0.009 0.09 -9999 0 -0.28 43 43
ADCY7 -0.009 0.09 -9999 0 -0.28 43 43
ADCY1 -0.047 0.12 -9999 0 -0.29 83 83
ADCY2 -0.012 0.098 -9999 0 -0.29 50 50
ADCY3 -0.009 0.09 -9999 0 -0.28 43 43
ADCY8 -0.013 0.098 -9999 0 -0.32 43 43
ADCY9 -0.009 0.09 -9999 0 -0.28 43 43
GSK3B -0.009 0.058 -9999 0 -0.21 21 21
arachidonic acid secretion -0.004 0.086 -9999 0 -0.27 39 39
GNG2 0.009 0.018 -9999 0 -0.32 2 2
TRIP6 0.004 0.035 -9999 0 -10000 0 0
GNAO1 -0.027 0.087 -9999 0 -0.23 39 39
HRAS 0.01 0 -9999 0 -10000 0 0
NFKBIA -0.033 0.1 -9999 0 -0.24 50 50
GAB1 0.009 0.015 -9999 0 -0.37 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.027 0.16 -9999 0 -0.87 24 24
JUN 0.01 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.012 0.028 -9999 0 -0.22 7 7
TIAM1 -0.033 0.19 -9999 0 -1 24 24
PIK3R1 0.01 0 -9999 0 -10000 0 0
mol:IP3 -0.02 0.077 -9999 0 -0.19 34 34
PLCB3 0.008 0.031 -9999 0 -0.19 7 7
FOS 0.001 0.056 -9999 0 -0.35 16 16
positive regulation of mitosis -0.004 0.086 -9999 0 -0.27 39 39
LPA/LPA1-2-3 -0.073 0.092 -9999 0 -0.29 54 54
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0.001 -9999 0 -10000 0 0
BCAR1 0.01 0 -9999 0 -10000 0 0
stress fiber formation -0.025 0.074 -9999 0 -0.26 18 18
GNAZ -0.025 0.083 -9999 0 -0.18 61 61
EGFR/PI3K-beta/Gab1 -0.14 0.11 -9999 0 -0.28 201 201
positive regulation of dendritic cell cytokine production -0.073 0.092 -9999 0 -0.29 54 54
LPA/LPA2/MAGI-3 -0.012 0.029 -9999 0 -0.21 8 8
ARHGEF1 -0.008 0.068 -9999 0 -0.3 7 7
GNAI2 -0.025 0.081 -9999 0 -0.21 32 32
GNAI3 -0.025 0.083 -9999 0 -0.18 72 72
GNAI1 -0.026 0.086 -9999 0 -0.23 37 37
LPA/LPA3 -0.067 0.096 -9999 0 -0.23 158 158
LPA/LPA2 -0.017 0.038 -9999 0 -0.27 7 7
LPA/LPA1 -0.052 0.091 -9999 0 -0.2 175 175
HB-EGF/EGFR -0.18 0.14 -9999 0 -0.25 477 477
HBEGF -0.071 0.13 -9999 0 -0.25 220 220
mol:DAG -0.02 0.077 -9999 0 -0.19 34 34
cAMP biosynthetic process -0.013 0.094 -9999 0 -0.29 45 45
NFKB1 0.01 0 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
GNB1 0.01 0 -9999 0 -10000 0 0
LYN -0.033 0.1 -9999 0 -0.24 48 48
GNAQ -0.043 0.083 -9999 0 -0.18 165 165
LPAR2 0.006 0.039 -9999 0 -0.38 7 7
LPAR3 -0.074 0.14 -9999 0 -0.32 158 158
LPAR1 -0.028 0.086 -9999 0 -0.35 32 32
IL8 -0.13 0.18 -9999 0 -0.41 151 151
PTK2 -0.05 0.095 -9999 0 -0.27 54 54
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.065 0.11 -9999 0 -0.21 184 184
EGFR -0.21 0.19 -9999 0 -0.38 377 377
PLCG1 -0.04 0.093 -9999 0 -0.2 159 159
PLD2 -0.05 0.095 -9999 0 -0.28 50 50
G12/G13 -0.035 0.062 -9999 0 -0.32 7 7
PI3K-beta -0.02 0.041 -9999 0 -0.25 7 7
cell migration -0.029 0.053 -9999 0 -0.25 26 26
SLC9A3R2 0.01 0 -9999 0 -10000 0 0
PXN -0.025 0.075 -9999 0 -0.26 18 18
HRAS/GTP -0.004 0.088 -9999 0 -0.28 39 39
RAC1 0.01 0 -9999 0 -10000 0 0
MMP9 -0.12 0.18 -9999 0 -0.38 220 220
PRKCE -0.002 0.062 -9999 0 -0.32 24 24
PRKCD -0.016 0.075 -9999 0 -0.19 12 12
Gi(beta/gamma) -0.005 0.086 -9999 0 -0.26 44 44
mol:LPA -0.024 0.051 -9999 0 -0.12 143 143
TRIP6/p130 Cas/FAK1/Paxillin -0.055 0.075 -9999 0 -0.25 51 51
MAPKKK cascade -0.004 0.086 -9999 0 -0.27 39 39
contractile ring contraction involved in cytokinesis 0.005 0.04 -9999 0 -0.21 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.043 0.084 -9999 0 -0.18 160 160
GNA15 -0.043 0.084 -9999 0 -0.18 167 167
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
MAPT -0.004 0.059 -9999 0 -0.21 25 25
GNA11 -0.043 0.084 -9999 0 -0.18 161 161
Rac1/GTP -0.028 0.17 -9999 0 -0.92 24 24
MMP2 -0.066 0.15 -9999 0 -0.34 150 150
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.14 0.14 -10000 0 -0.3 221 221
TBX21 -0.14 0.23 -10000 0 -0.77 39 39
B2M -0.029 0.12 -10000 0 -0.37 70 70
TYK2 0.01 0.011 -10000 0 -10000 0 0
IL12RB1 0.009 0.023 -10000 0 -0.36 2 2
GADD45B -0.094 0.18 -10000 0 -0.57 28 28
IL12RB2 -0.23 0.15 -10000 0 -0.32 479 479
GADD45G -0.13 0.2 -10000 0 -0.7 17 17
natural killer cell activation 0.006 0.016 -10000 0 -10000 0 0
RELB 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
IL18 -0.009 0.081 -10000 0 -0.38 30 30
IL2RA -0.094 0.17 -10000 0 -0.37 177 177
IFNG -0.001 0.039 -10000 0 -0.37 7 7
STAT3 (dimer) -0.13 0.2 -10000 0 -0.59 57 57
HLA-DRB5 -0.062 0.15 -10000 0 -0.37 126 126
FASLG -0.14 0.22 -10000 0 -0.76 38 38
NF kappa B2 p52/RelB -0.14 0.2 -10000 0 -0.66 58 58
CD4 0.004 0.051 -10000 0 -0.37 12 12
SOCS1 -0.11 0.18 -10000 0 -0.37 210 210
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.039 0.13 -10000 0 -0.38 85 85
CD3E -0.027 0.12 -10000 0 -0.37 67 67
CD3G -0.024 0.11 -10000 0 -0.38 57 57
IL12Rbeta2/JAK2 -0.15 0.11 -10000 0 -0.22 479 479
CCL3 -0.16 0.29 -10000 0 -1 43 43
CCL4 -0.15 0.28 -10000 0 -1 41 41
HLA-A -0.008 0.083 -10000 0 -0.37 33 33
IL18/IL18R -0.013 0.12 -10000 0 -0.26 104 104
NOS2 -0.11 0.22 -10000 0 -0.84 29 29
IL12/IL12R/TYK2/JAK2/SPHK2 -0.092 0.1 -10000 0 -0.24 71 71
IL1R1 -0.14 0.23 -10000 0 -0.76 38 38
IL4 -0.006 0.016 -10000 0 -10000 0 0
JAK2 0.01 0.011 -10000 0 -10000 0 0
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.012 0.098 -10000 0 -0.4 17 17
RAB7A -0.087 0.17 -10000 0 -0.6 10 10
lysosomal transport -0.083 0.17 -10000 0 -0.57 10 10
FOS -0.071 0.17 -10000 0 -0.8 17 17
STAT4 (dimer) -0.22 0.23 -10000 0 -0.64 77 77
STAT5A (dimer) -0.15 0.2 -10000 0 -0.66 59 59
GZMA -0.14 0.23 -10000 0 -0.71 52 52
GZMB -0.13 0.22 -10000 0 -0.71 47 47
HLX 0.004 0.049 -10000 0 -0.37 11 11
LCK -0.17 0.26 -10000 0 -0.72 80 80
TCR/CD3/MHC II/CD4 -0.026 0.11 -10000 0 -0.28 78 78
IL2/IL2R -0.088 0.16 -10000 0 -0.3 199 199
MAPK14 -0.11 0.19 -10000 0 -0.62 28 28
CCR5 -0.11 0.19 -10000 0 -0.7 22 22
IL1B -0.031 0.11 -10000 0 -0.34 78 78
STAT6 -0.042 0.073 -10000 0 -0.22 21 21
STAT4 -0.17 0.17 -10000 0 -0.32 366 366
STAT3 0.01 0 -10000 0 -10000 0 0
STAT1 0.006 0.039 -10000 0 -0.37 7 7
NFKB1 0.01 0 -10000 0 -10000 0 0
NFKB2 0.01 0 -10000 0 -10000 0 0
IL12B 0.009 0.028 -10000 0 -0.42 2 2
CD8A -0.013 0.086 -10000 0 -0.33 47 47
CD8B 0 0.065 -10000 0 -0.38 19 19
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.15 0.14 0.3 221 -10000 0 221
IL2RB -0.028 0.11 -10000 0 -0.37 66 66
proteasomal ubiquitin-dependent protein catabolic process -0.21 0.21 -10000 0 -0.6 77 77
IL2RG -0.035 0.12 -10000 0 -0.37 79 79
IL12 0.013 0.043 -10000 0 -0.25 13 13
STAT5A 0.01 0 -10000 0 -10000 0 0
CD247 0.006 0.041 -10000 0 -0.32 10 10
IL2 0 0 -10000 0 -10000 0 0
SPHK2 0.01 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.003 0.05 -10000 0 -0.37 11 11
IL12/IL12R/TYK2/JAK2 -0.15 0.24 -10000 0 -0.74 58 58
MAP2K3 -0.11 0.19 -10000 0 -0.6 33 33
RIPK2 0.008 0.026 -10000 0 -0.37 3 3
MAP2K6 -0.11 0.19 -10000 0 -0.62 29 29
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.063 0.15 -10000 0 -0.37 128 128
IL18RAP -0.036 0.12 -10000 0 -0.38 77 77
IL12Rbeta1/TYK2 0.011 0.023 -10000 0 -0.24 2 2
EOMES 0.018 0.044 -10000 0 -10000 0 0
STAT1 (dimer) -0.12 0.2 -10000 0 -0.58 56 56
T cell proliferation -0.1 0.17 -10000 0 -0.5 40 40
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.004 0.068 -10000 0 -0.37 22 22
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.19 0.17 -10000 0 -0.55 66 66
ATF2 -0.095 0.18 -10000 0 -0.59 25 25
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.01 0 -9999 0 -10000 0 0
VLDLR 0.008 0.026 -9999 0 -0.32 4 4
LRPAP1 0.01 0 -9999 0 -10000 0 0
NUDC 0.01 0 -9999 0 -10000 0 0
RELN/LRP8 -0.069 0.083 -9999 0 -0.17 272 272
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.01 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.043 0.084 -9999 0 -0.14 272 272
IQGAP1/CaM -0.003 0.026 -9999 0 -0.25 7 7
DAB1 -0.057 0.13 -9999 0 -0.32 134 134
IQGAP1 0.006 0.039 -9999 0 -0.37 7 7
PLA2G7 0.006 0.038 -9999 0 -0.34 8 8
CALM1 0.01 0 -9999 0 -10000 0 0
DYNLT1 -0.029 0.12 -9999 0 -0.37 67 67
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0 0 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.01 0 -9999 0 -10000 0 0
CDK5R1 -0.022 0.098 -9999 0 -0.32 64 64
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.098 0.16 -9999 0 -0.32 216 216
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.1 0.12 -9999 0 -0.21 338 338
YWHAE 0.01 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.077 0.14 -9999 0 -0.3 151 151
MAP1B 0 0 -9999 0 -10000 0 0
RAC1 -0.001 0.007 -9999 0 -10000 0 0
p35/CDK5 -0.039 0.094 -9999 0 -0.26 49 49
RELN -0.13 0.16 -9999 0 -0.32 272 272
PAFAH/LIS1 0.018 0.022 -9999 0 -0.18 8 8
LIS1/CLIP170 0.021 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.086 0.11 -9999 0 -0.25 174 174
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.088 0.14 -9999 0 -0.37 82 82
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.088 0.15 -9999 0 -0.32 151 151
LIS1/IQGAP1 0.019 0.023 -9999 0 -0.2 7 7
RHOA -0.001 0.007 -9999 0 -10000 0 0
PAFAH1B1 0.018 0 -9999 0 -10000 0 0
PAFAH1B3 0.01 0 -9999 0 -10000 0 0
PAFAH1B2 0.01 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.02 0 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.093 0.12 -9999 0 -0.28 151 151
LRP8 0.01 0 -9999 0 -10000 0 0
NDEL1/Katanin 60 -0.077 0.14 -9999 0 -0.3 151 151
P39/CDK5 -0.074 0.11 -9999 0 -0.26 126 126
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0 -9999 0 -10000 0 0
CDK5 -0.033 0.078 -9999 0 -10000 0 0
PPP2R5D 0.01 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.01 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.081 0.093 -9999 0 -0.28 71 71
RELN/VLDLR -0.06 0.072 -9999 0 -0.14 274 274
CDC42 -0.001 0.007 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 -0.006 0.074 -9999 0 -0.29 13 13
CRKL 0.009 0.015 -9999 0 -0.37 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.01 0 -9999 0 -10000 0 0
ITGA4 -0.047 0.14 -9999 0 -0.37 99 99
alpha4/beta7 Integrin/MAdCAM1 -0.043 0.085 -9999 0 -0.21 104 104
EPO -0.049 0.14 -9999 0 -0.37 100 100
alpha4/beta7 Integrin -0.04 0.096 -9999 0 -0.26 103 103
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.041 0.1 -9999 0 -0.27 101 101
EPO/EPOR (dimer) -0.038 0.09 -9999 0 -0.25 100 100
lamellipodium assembly 0.009 0.013 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
ARF6 0.01 0 -9999 0 -10000 0 0
JAK2 -0.012 0.07 -9999 0 -0.21 40 40
PXN 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
MADCAM1 -0.023 0.099 -9999 0 -0.32 65 65
cell adhesion -0.042 0.085 -9999 0 -0.21 104 104
CRKL/CBL 0 0.01 -9999 0 -0.25 1 1
ITGB1 0.003 0.051 -9999 0 -0.37 12 12
SRC -0.075 0.13 -9999 0 -0.21 283 283
ITGB7 0.005 0.042 -9999 0 -0.37 8 8
RAC1 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.1 0.13 -9999 0 -0.24 283 283
p130Cas/Crk/Dock1 -0.046 0.11 -9999 0 -0.31 55 55
VCAM1 -0.12 0.18 -9999 0 -0.37 231 231
RHOA 0.01 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.029 0.073 -9999 0 -0.19 101 101
BCAR1 -0.063 0.12 -9999 0 -0.19 283 283
EPOR 0.01 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
GIT1 0.01 0 -9999 0 -10000 0 0
Rac1/GTP 0.009 0.013 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.005 0.054 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.036 0.11 -9999 0 -0.41 31 31
positive regulation of JNK cascade -0.078 0.12 -9999 0 -0.34 79 79
Syndecan-4/ADAM12 -0.069 0.15 -9999 0 -0.37 107 107
CCL5 -0.047 0.14 -9999 0 -0.37 100 100
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.01 0 -9999 0 -10000 0 0
ITGA5 -0.042 0.13 -9999 0 -0.37 91 91
SDCBP 0.01 0 -9999 0 -10000 0 0
PLG -0.001 0.025 -9999 0 -0.37 3 3
ADAM12 -0.065 0.15 -9999 0 -0.37 131 131
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.03 0.045 -9999 0 -0.12 95 95
Syndecan-4/Laminin alpha1 -0.046 0.12 -9999 0 -0.41 38 38
Syndecan-4/CXCL12/CXCR4 -0.059 0.14 -9999 0 -0.36 79 79
Syndecan-4/Laminin alpha3 -0.041 0.12 -9999 0 -0.41 40 40
MDK -0.1 0.17 -9999 0 -0.37 194 194
Syndecan-4/FZD7 -0.055 0.13 -9999 0 -0.39 58 58
Syndecan-4/Midkine -0.085 0.16 -9999 0 -0.37 103 103
FZD7 -0.034 0.12 -9999 0 -0.37 77 77
Syndecan-4/FGFR1/FGF -0.053 0.095 -9999 0 -0.39 31 31
THBS1 -0.013 0.089 -9999 0 -0.35 42 42
integrin-mediated signaling pathway -0.14 0.14 -9999 0 -0.36 122 122
positive regulation of MAPKKK cascade -0.078 0.12 -9999 0 -0.34 79 79
Syndecan-4/TACI -0.041 0.11 -9999 0 -0.41 32 32
CXCR4 -0.057 0.15 -9999 0 -0.37 116 116
cell adhesion -0.004 0.062 -9999 0 -0.16 69 69
Syndecan-4/Dynamin -0.036 0.11 -9999 0 -0.41 31 31
Syndecan-4/TSP1 -0.044 0.13 -9999 0 -0.39 54 54
Syndecan-4/GIPC -0.036 0.11 -9999 0 -0.41 31 31
Syndecan-4/RANTES -0.061 0.14 -9999 0 -0.37 68 68
ITGB1 0.003 0.051 -9999 0 -0.37 12 12
LAMA1 -0.013 0.089 -9999 0 -0.37 40 40
LAMA3 -0.005 0.068 -9999 0 -0.33 29 29
RAC1 0.01 0 -9999 0 -10000 0 0
PRKCA 0.019 0.028 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.036 0.11 -9999 0 -0.41 31 31
TFPI -0.16 0.19 -9999 0 -0.37 289 289
F2 0.001 0.026 -9999 0 -0.37 3 3
alpha5/beta1 Integrin -0.038 0.099 -9999 0 -0.28 93 93
positive regulation of cell adhesion -0.044 0.13 -9999 0 -0.39 48 48
ACTN1 0.01 0 -9999 0 -10000 0 0
TNC -0.23 0.19 -9999 0 -0.37 413 413
Syndecan-4/CXCL12 -0.037 0.12 -9999 0 -0.41 33 33
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
CXCL12 0.008 0.03 -9999 0 -0.37 4 4
TNFRSF13B 0.002 0.026 -9999 0 -0.37 3 3
FGF2 0.009 0.015 -9999 0 -0.37 1 1
FGFR1 0.009 0.021 -9999 0 -0.37 2 2
Syndecan-4/PI-4-5-P2 -0.042 0.11 -9999 0 -0.42 31 31
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.045 0.14 -9999 0 -0.38 96 96
cell migration -0.012 0.018 -9999 0 -10000 0 0
PRKCD 0.005 0.036 -9999 0 -0.3 9 9
vasculogenesis -0.042 0.12 -9999 0 -0.38 54 54
SDC4 -0.044 0.12 -9999 0 -0.44 31 31
Syndecan-4/Tenascin C -0.14 0.15 -9999 0 -0.38 122 122
Syndecan-4/PI-4-5-P2/PKC alpha -0.024 0.036 -9999 0 -0.12 2 2
Syndecan-4/Syntenin -0.036 0.11 -9999 0 -0.41 31 31
MMP9 -0.12 0.18 -9999 0 -0.37 220 220
Rac1/GTP -0.019 0.058 -9999 0 -0.17 69 69
cytoskeleton organization -0.035 0.11 -9999 0 -0.4 31 31
GIPC1 0.01 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.11 0.15 -9999 0 -0.37 113 113
Signaling events mediated by the Hedgehog family

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
TGFB2 0.007 0.13 -10000 0 -0.4 53 53
IHH 0.008 0.034 -10000 0 -0.24 3 3
SHH Np/Cholesterol/GAS1 -0.05 0.09 -10000 0 -0.19 171 171
LRPAP1 0.01 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.049 0.089 0.19 171 -10000 0 171
SMO/beta Arrestin2 0.002 0.088 -10000 0 -0.34 11 11
SMO -0.004 0.093 -10000 0 -0.29 38 38
AKT1 0.015 0.048 -10000 0 -0.23 2 2
ARRB2 0.01 0 -10000 0 -10000 0 0
BOC -0.015 0.094 -10000 0 -0.37 43 43
ADRBK1 0.01 0 -10000 0 -10000 0 0
heart looping -0.004 0.092 -10000 0 -0.29 38 38
STIL 0.005 0.09 -10000 0 -0.29 28 28
DHH N/PTCH2 -0.008 0.043 -10000 0 -0.25 21 21
DHH N/PTCH1 0.009 0.086 -10000 0 -0.25 47 47
PIK3CA 0.01 0 -10000 0 -10000 0 0
DHH -0.001 0.064 -10000 0 -0.37 19 19
PTHLH -0.006 0.2 -10000 0 -0.78 36 36
determination of left/right symmetry -0.004 0.092 -10000 0 -0.29 38 38
PIK3R1 0.01 0 -10000 0 -10000 0 0
skeletal system development -0.006 0.19 -10000 0 -0.78 36 36
IHH N/Hhip -0.029 0.1 -10000 0 -0.25 114 114
DHH N/Hhip -0.043 0.091 -10000 0 -0.22 129 129
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.004 0.092 -10000 0 -0.29 38 38
pancreas development -0.047 0.13 -10000 0 -0.32 114 114
HHAT 0.009 0.013 -10000 0 -0.32 1 1
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.057 0.15 -10000 0 -0.37 116 116
somite specification -0.004 0.092 -10000 0 -0.29 38 38
SHH Np/Cholesterol/PTCH1 0.002 0.09 -10000 0 -0.3 25 25
SHH Np/Cholesterol/PTCH2 -0.018 0.051 -10000 0 -0.16 78 78
SHH Np/Cholesterol/Megalin -0.038 0.074 -10000 0 -0.17 151 151
SHH -0.01 0.075 -10000 0 -0.22 77 77
catabolic process 0.011 0.092 -10000 0 -0.29 48 48
SMO/Vitamin D3 -0.011 0.099 -10000 0 -0.32 21 21
SHH Np/Cholesterol/Hhip -0.044 0.078 -10000 0 -0.17 174 174
LRP2 -0.034 0.12 -10000 0 -0.34 86 86
receptor-mediated endocytosis -0.051 0.089 -10000 0 -0.32 35 35
SHH Np/Cholesterol/BOC -0.029 0.065 -10000 0 -0.17 118 118
SHH Np/Cholesterol/CDO -0.02 0.056 -10000 0 -0.16 82 82
mesenchymal cell differentiation 0.044 0.078 0.17 174 -10000 0 174
mol:Vitamin D3 0.004 0.091 -10000 0 -0.29 27 27
IHH N/PTCH2 0.014 0.023 -10000 0 -0.24 3 3
CDON 0.005 0.044 -10000 0 -0.37 9 9
IHH N/PTCH1 0.011 0.092 -10000 0 -0.29 48 48
Megalin/LRPAP1 -0.028 0.074 -10000 0 -0.22 86 86
PTCH2 0.009 0.018 -10000 0 -0.32 2 2
SHH Np/Cholesterol -0.018 0.051 -10000 0 -0.16 77 77
PTCH1 0.011 0.092 -10000 0 -0.29 48 48
HHIP -0.047 0.13 -10000 0 -0.32 114 114
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.015 0.05 -9999 0 -0.18 55 55
RGS9BP 0.009 0.015 -9999 0 -0.37 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.008 0.015 -9999 0 -0.37 1 1
mol:Na + -0.072 0.1 -9999 0 -0.21 229 229
mol:ADP 0.01 0.037 -9999 0 -0.25 13 13
GNAT2 0.008 0.015 -9999 0 -0.37 1 1
RGS9-1/Gbeta5/R9AP -0.016 0.055 -9999 0 -0.2 52 52
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.016 -9999 0 -0.41 1 1
GRK7 0.001 0.051 -9999 0 -0.37 12 12
CNGB3 0.005 0.015 -9999 0 -0.37 1 1
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.068 0.12 -9999 0 -0.23 229 229
Cone PDE6 -0.013 0.047 -9999 0 -0.17 36 36
Cone Metarhodopsin II -0.004 0.026 -9999 0 -0.19 13 13
Na + (4 Units) -0.094 0.11 -9999 0 -0.22 266 266
GNAT2/GDP -0.013 0.047 -9999 0 -0.17 48 48
GNB5 0.01 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.012 0.018 -9999 0 -0.28 2 2
Cone Transducin -0.016 0.053 -9999 0 -0.19 55 55
SLC24A2 -0.058 0.13 -9999 0 -0.32 135 135
GNB3/GNGT2 -0.021 0.071 -9999 0 -0.26 55 55
GNB3 -0.009 0.083 -9999 0 -0.37 33 33
GNAT2/GTP 0 0.01 -9999 0 -0.26 1 1
CNGA3 -0.12 0.18 -9999 0 -0.37 228 228
ARR3 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.073 0.1 -9999 0 -0.21 229 229
mol:Pi -0.016 0.055 -9999 0 -0.2 52 52
Cone CNG Channel -0.055 0.078 -9999 0 -0.23 6 6
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.057 0.13 -9999 0 -0.32 135 135
RGS9 -0.02 0.1 -9999 0 -0.37 52 52
PDE6C 0.004 0.015 -9999 0 -0.37 1 1
GNGT2 -0.003 0.07 -9999 0 -0.37 23 23
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.006 0.015 -9999 0 -0.37 1 1
Arf6 signaling events

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.023 0.059 -9999 0 -0.18 88 88
ARNO/beta Arrestin1-2 -0.003 0.016 -9999 0 -10000 0 0
EGFR -0.21 0.19 -9999 0 -0.37 377 377
EPHA2 0.005 0.042 -9999 0 -0.37 8 8
USP6 0.008 0.029 -9999 0 -0.36 4 4
IQSEC1 0.007 0.029 -9999 0 -0.32 5 5
EGFR/EGFR/EGF/EGF -0.15 0.13 -9999 0 -0.26 387 387
ARRB2 0.009 0.014 -9999 0 -0.13 6 6
mol:GTP -0.002 0.044 -9999 0 -0.11 88 88
ARRB1 0.004 0.043 -9999 0 -0.32 11 11
FBXO8 0.009 0.015 -9999 0 -0.37 1 1
TSHR -0.21 0.19 -9999 0 -0.37 389 389
EGF -0.003 0.07 -9999 0 -0.37 23 23
somatostatin receptor activity 0 0 -9999 0 0 9 9
ARAP2 0.009 0.018 -9999 0 -0.32 2 2
mol:GDP -0.039 0.045 -9999 0 -0.16 11 11
mol:PI-3-4-5-P3 0 0 -9999 0 0 2 2
ITGA2B 0.006 0.034 -9999 0 -0.32 7 7
ARF6 0.01 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.002 0.02 -9999 0 -0.18 9 9
ADAP1 -0.034 0.11 -9999 0 -0.32 88 88
KIF13B 0.01 0 -9999 0 -10000 0 0
HGF/MET -0.098 0.11 -9999 0 -0.22 298 298
PXN 0.01 0 -9999 0 -10000 0 0
ARF6/GTP -0.041 0.044 -9999 0 -0.16 6 6
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.12 0.11 -9999 0 -0.21 392 392
ADRB2 0.01 0 -9999 0 -10000 0 0
receptor agonist activity 0 0 -9999 0 0 4 4
actin filament binding 0 0 -9999 0 0 9 9
SRC 0.01 0 -9999 0 -10000 0 0
ITGB3 -0.064 0.15 -9999 0 -0.37 128 128
GNAQ 0.01 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 6 6
ARF6/GDP 0.012 0.029 -9999 0 -0.22 1 1
ARF6/GDP/GULP/ACAP1 -0.032 0.042 -9999 0 -0.19 14 14
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.035 0.07 -9999 0 -0.18 128 128
ACAP1 0.007 0.033 -9999 0 -0.37 5 5
ACAP2 0.01 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0.005 0.019 -9999 0 -0.19 6 6
EFNA1 0.01 0 -9999 0 -10000 0 0
HGF 0 0.059 -9999 0 -0.35 19 19
CYTH3 0.009 0 -9999 0 -10000 0 0
CYTH2 0.006 0.001 -9999 0 -10000 0 0
NCK1 0.009 0.015 -9999 0 -0.37 1 1
fibronectin binding 0 0 -9999 0 0 8 8
endosomal lumen acidification 0 0 -9999 0 0 10 10
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.002 0.063 -9999 0 -0.33 24 24
GNAQ/ARNO 0.009 0.006 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 4 4
MET -0.13 0.17 -9999 0 -0.32 287 287
GNA14 0.009 0.013 -9999 0 -0.32 1 1
GNA15 0.009 0.02 -9999 0 -0.35 2 2
GIT1 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 0 6 6
GNA11 0.009 0.018 -9999 0 -0.32 2 2
LHCGR 0.002 0.036 -9999 0 -0.37 6 6
AGTR1 -0.014 0.092 -9999 0 -0.37 41 41
desensitization of G-protein coupled receptor protein signaling pathway 0.005 0.019 -9999 0 -0.19 6 6
IPCEF1/ARNO -0.087 0.083 -9999 0 -0.31 13 13
alphaIIb/beta3 Integrin -0.05 0.1 -9999 0 -0.25 134 134
Endothelins

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
AKT1 -0.054 0.14 -10000 0 -0.29 121 121
PTK2B 0.009 0.022 -10000 0 -0.32 3 3
mol:Ca2+ 0.016 0.096 -10000 0 -0.7 6 6
EDN1 -0.029 0.091 -10000 0 -0.33 23 23
EDN3 0 0.059 -10000 0 -0.33 20 20
EDN2 -0.021 0.094 -10000 0 -0.37 44 44
HRAS/GDP -0.024 0.088 -10000 0 -0.25 20 20
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.008 0.065 -10000 0 -0.22 9 9
ADCY4 -0.072 0.15 -10000 0 -0.3 161 161
ADCY5 -0.084 0.17 -10000 0 -0.34 172 172
ADCY6 -0.072 0.15 -10000 0 -0.3 161 161
ADCY7 -0.072 0.15 -10000 0 -0.3 161 161
ADCY1 -0.099 0.17 -10000 0 -0.33 207 207
ADCY2 -0.075 0.16 -10000 0 -0.3 183 183
ADCY3 -0.072 0.15 -10000 0 -0.3 161 161
ADCY8 -0.078 0.16 -10000 0 -0.31 169 169
ADCY9 -0.072 0.15 -10000 0 -0.29 178 178
arachidonic acid secretion -0.001 0.084 -10000 0 -0.34 10 10
ETB receptor/Endothelin-1/Gq/GTP 0.012 0.045 -10000 0 -0.17 1 1
GNAO1 0.004 0.044 -10000 0 -0.32 12 12
HRAS 0.01 0.001 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.044 0.13 0.18 18 -0.36 50 68
ETA receptor/Endothelin-1/Gs/GTP -0.095 0.15 0.17 17 -0.32 161 178
mol:GTP 0.002 0.002 -10000 0 -10000 0 0
COL3A1 -0.11 0.21 -10000 0 -0.38 230 230
EDNRB -0.031 0.11 -10000 0 -0.37 65 65
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.055 0.15 -10000 0 -0.41 52 52
CYSLTR1 -0.055 0.15 -10000 0 -0.41 52 52
SLC9A1 -0.039 0.06 -10000 0 -0.2 40 40
mol:GDP -0.032 0.092 -10000 0 -0.25 34 34
SLC9A3 0.007 0.078 -10000 0 -0.54 6 6
RAF1 -0.023 0.088 -10000 0 -0.28 21 21
JUN 0.021 0.078 -10000 0 -0.49 5 5
JAK2 -0.053 0.14 -10000 0 -0.29 120 120
mol:IP3 0.008 0.064 -10000 0 -0.22 9 9
ETA receptor/Endothelin-1 -0.087 0.16 0.22 13 -0.36 120 133
PLCB1 0.001 0.056 -10000 0 -0.32 19 19
PLCB2 0.009 0.021 -10000 0 -0.37 2 2
ETA receptor/Endothelin-3 -0.057 0.11 -10000 0 -0.3 95 95
FOS -0.009 0.12 -10000 0 -0.76 9 9
Gai/GDP 0.005 0.1 -10000 0 -0.72 12 12
CRK 0.01 0 -10000 0 -10000 0 0
mol:Ca ++ -0.024 0.12 -10000 0 -0.32 46 46
BCAR1 0.01 0 -10000 0 -10000 0 0
PRKCB1 0.008 0.061 -10000 0 -0.2 9 9
GNAQ 0.012 0.002 -10000 0 -10000 0 0
GNAZ 0.009 0.018 -10000 0 -0.32 2 2
GNAL -0.073 0.14 -10000 0 -0.32 165 165
Gs family/GDP -0.079 0.11 -10000 0 -0.27 131 131
ETA receptor/Endothelin-1/Gq/GTP 0.004 0.069 -10000 0 -0.21 10 10
MAPK14 0.021 0.045 -10000 0 -0.18 2 2
TRPC6 0.016 0.1 -10000 0 -0.74 6 6
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.009 0.021 -10000 0 -0.37 2 2
GNAI1 0.006 0.036 -10000 0 -0.32 8 8
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.015 0.048 -10000 0 -0.19 5 5
ETB receptor/Endothelin-2 -0.042 0.097 -10000 0 -0.26 108 108
ETB receptor/Endothelin-3 -0.033 0.081 -10000 0 -0.24 85 85
ETB receptor/Endothelin-1 -0.045 0.098 -10000 0 -0.25 84 84
MAPK3 -0.012 0.11 -10000 0 -0.64 9 9
MAPK1 -0.012 0.11 -10000 0 -0.64 9 9
Rac1/GDP -0.024 0.088 -10000 0 -0.26 19 19
cAMP biosynthetic process -0.096 0.18 -10000 0 -0.33 202 202
MAPK8 0.014 0.086 -10000 0 -0.52 8 8
SRC 0.01 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.007 0.053 -10000 0 -0.26 9 9
p130Cas/CRK/Src/PYK2 -0.029 0.098 -10000 0 -0.34 11 11
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.024 0.088 -10000 0 -0.26 19 19
COL1A2 -0.068 0.17 -10000 0 -0.4 107 107
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.069 0.12 -10000 0 -0.31 117 117
mol:DAG 0.008 0.064 -10000 0 -0.22 9 9
MAP2K2 -0.015 0.095 -10000 0 -0.43 11 11
MAP2K1 -0.015 0.095 -10000 0 -0.42 12 12
EDNRA -0.067 0.15 -10000 0 -0.4 85 85
positive regulation of muscle contraction -0.037 0.12 -10000 0 -0.33 51 51
Gq family/GDP -0.042 0.064 -10000 0 -0.24 16 16
HRAS/GTP -0.032 0.087 -10000 0 -0.24 30 30
PRKCH 0.013 0.061 -10000 0 -0.21 5 5
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA 0.013 0.061 -10000 0 -0.22 4 4
PRKCB -0.03 0.11 -10000 0 -0.24 77 77
PRKCE 0.01 0.071 -10000 0 -0.25 13 13
PRKCD 0.012 0.064 -10000 0 -0.22 7 7
PRKCG -0.069 0.11 -10000 0 -0.23 118 118
regulation of vascular smooth muscle contraction -0.012 0.13 -10000 0 -0.94 8 8
PRKCQ 0.012 0.067 -10000 0 -0.23 12 12
PLA2G4A -0.002 0.087 -10000 0 -0.36 10 10
GNA14 0.011 0.013 -10000 0 -0.32 1 1
GNA15 0.01 0.02 -10000 0 -0.35 2 2
GNA12 0.01 0 -10000 0 -10000 0 0
GNA11 0.01 0.018 -10000 0 -0.32 2 2
Rac1/GTP -0.044 0.13 0.19 18 -0.36 50 68
MMP1 -0.017 0.11 -10000 0 -0.28 51 51
TCGA08_rtk_signaling

Figure S45.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S45.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.046 0.14 -9999 0 -0.37 98 98
HRAS 0.01 0 -9999 0 -10000 0 0
EGFR -0.21 0.19 -9999 0 -0.37 377 377
AKT 0.008 0.017 -9999 0 -0.22 1 1
FOXO3 0.01 0 -9999 0 -10000 0 0
AKT1 0.009 0.015 -9999 0 -0.37 1 1
FOXO1 0.01 0 -9999 0 -10000 0 0
AKT3 0.01 0 -9999 0 -10000 0 0
FOXO4 0.009 0.013 -9999 0 -0.32 1 1
MET -0.13 0.17 -9999 0 -0.32 287 287
PIK3CA 0.01 0 -9999 0 -10000 0 0
PIK3CB 0.01 0 -9999 0 -10000 0 0
NRAS 0.01 0 -9999 0 -10000 0 0
PIK3CG 0.001 0.058 -9999 0 -0.37 16 16
PIK3R3 0.01 0 -9999 0 -10000 0 0
PIK3R2 0.01 0 -9999 0 -10000 0 0
NF1 0.01 0 -9999 0 -10000 0 0
RAS -0.066 0.083 -9999 0 -0.17 222 222
ERBB2 0.005 0.042 -9999 0 -0.37 8 8
proliferation/survival/translation -0.003 0.035 -9999 0 -10000 0 0
PI3K -0.065 0.086 -9999 0 -0.18 222 222
PIK3R1 0.01 0 -9999 0 -10000 0 0
KRAS 0.01 0 -9999 0 -10000 0 0
FOXO 0.01 0.018 -9999 0 -10000 0 0
AKT2 0.01 0 -9999 0 -10000 0 0
PTEN 0.01 0 -9999 0 -10000 0 0
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 -0.012 0.09 -10000 0 -0.37 39 39
ANTXR2 -0.042 0.13 -10000 0 -0.37 90 90
negative regulation of myeloid dendritic cell antigen processing and presentation -0.008 0.018 -10000 0 -0.045 122 122
monocyte activation -0.04 0.1 -10000 0 -0.39 47 47
MAP2K2 -0.003 0.006 -10000 0 -10000 0 0
MAP2K1 -0.006 0.014 -10000 0 -10000 0 0
MAP2K7 -0.006 0.014 -10000 0 -10000 0 0
MAP2K6 -0.006 0.014 -10000 0 -10000 0 0
CYAA -0.024 0.078 -10000 0 -0.18 122 122
MAP2K4 -0.006 0.014 -10000 0 -10000 0 0
IL1B -0.013 0.051 -10000 0 -0.14 78 78
Channel -0.036 0.079 -10000 0 -0.2 122 122
NLRP1 -0.006 0.014 -10000 0 -10000 0 0
CALM1 0.01 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.01 0.021 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.008 0.018 0.045 122 -10000 0 122
MAPK3 -0.006 0.014 -10000 0 -10000 0 0
MAPK1 -0.006 0.014 -10000 0 -10000 0 0
PGR -0.012 0.034 -10000 0 -0.17 26 26
PA/Cellular Receptors -0.04 0.088 -10000 0 -0.22 122 122
apoptosis -0.008 0.018 -10000 0 -0.045 122 122
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.021 0.073 -10000 0 -0.17 122 122
macrophage activation 0.008 0.017 -10000 0 -10000 0 0
TNF -0.02 0.097 -10000 0 -0.33 58 58
VCAM1 -0.04 0.1 -10000 0 -0.39 47 47
platelet activation -0.01 0.021 -10000 0 -10000 0 0
MAPKKK cascade -0.005 0.018 0.064 7 -10000 0 7
IL18 -0.003 0.044 -10000 0 -0.19 30 30
negative regulation of macrophage activation -0.008 0.018 -10000 0 -0.045 122 122
LEF -0.008 0.018 -10000 0 -0.045 122 122
CASP1 -0.007 0.015 -10000 0 -0.066 7 7
mol:cAMP -0.01 0.021 -10000 0 -10000 0 0
necrosis -0.008 0.018 -10000 0 -0.045 122 122
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.034 0.074 -10000 0 -0.19 122 122
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ -0.03 0.11 -9999 0 -0.32 79 79
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.009 0.015 -9999 0 -0.37 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.036 0.056 -9999 0 -0.2 25 25
IRAK/TOLLIP 0.023 0.003 -9999 0 -10000 0 0
IKBKB 0.01 0 -9999 0 -10000 0 0
IKBKG 0.01 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.1 0.13 -9999 0 -0.26 265 265
IL1A -0.007 0.073 -9999 0 -0.33 33 33
IL1B -0.055 0.12 -9999 0 -0.24 190 190
IRAK/TRAF6/p62/Atypical PKCs -0.013 0.035 -9999 0 -10000 0 0
IL1R2 -0.13 0.18 -9999 0 -0.37 241 241
IL1R1 -0.004 0.073 -9999 0 -0.37 25 25
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.008 0.065 -9999 0 -0.22 15 15
TOLLIP 0.01 0 -9999 0 -10000 0 0
TICAM2 0.009 0.013 -9999 0 -0.32 1 1
MAP3K3 0.01 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.045 0.02 -9999 0 -10000 0 0
JUN 0.036 0.004 -9999 0 -10000 0 0
MAP3K7 0.01 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.062 0.098 -9999 0 -0.33 52 52
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.044 0.092 -9999 0 -0.22 116 116
PIK3R1 0.01 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.041 0.086 -9999 0 -0.36 26 26
IL1 beta fragment/IL1R1/IL1RAP -0.074 0.11 -9999 0 -0.24 163 163
NFKB1 0.01 0 -9999 0 -10000 0 0
MAPK8 0.032 0.004 -9999 0 -10000 0 0
IRAK1 0.019 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.031 0.084 -9999 0 -0.24 87 87
IRAK4 0.008 0.03 -9999 0 -0.37 4 4
PRKCI 0.01 0 -9999 0 -10000 0 0
TRAF6 0.01 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.017 0.073 -9999 0 -0.21 32 32
CHUK 0.01 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.074 0.11 -9999 0 -0.24 163 163
IL1 beta/IL1R2 -0.13 0.14 -9999 0 -0.25 342 342
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.054 0.087 -9999 0 -0.3 52 52
IRAK3 -0.004 0.073 -9999 0 -0.37 25 25
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.063 0.1 -9999 0 -0.34 54 54
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.002 0.064 -9999 0 -0.22 17 17
IL1 alpha/IL1R1/IL1RAP -0.038 0.082 -9999 0 -0.2 124 124
RELA 0.01 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.01 0 -9999 0 -10000 0 0
MYD88 -0.012 0.09 -9999 0 -0.37 39 39
IRAK/TRAF6/MEKK3 0.012 0.013 -9999 0 -10000 0 0
IL1RAP -0.032 0.12 -9999 0 -0.37 73 73
UBE2N 0.01 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.049 0.081 -9999 0 -0.28 54 54
CASP1 -0.056 0.14 -9999 0 -0.37 114 114
IL1RN/IL1R2 -0.11 0.13 -9999 0 -0.26 292 292
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.077 0.13 -9999 0 -0.39 73 73
TMEM189-UBE2V1 0.005 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.05 -9999 0 -0.22 3 3
PIK3CA 0.01 0 -9999 0 -10000 0 0
IL1RN -0.025 0.1 -9999 0 -0.34 67 67
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.027 0.003 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.008 0.049 -9999 0 -0.23 23 23
MAP4K1 0.007 0.033 -9999 0 -0.37 5 5
MAP3K8 0.003 0.051 -9999 0 -0.37 12 12
PRKCB -0.1 0.16 -9999 0 -0.32 225 225
DBNL 0.01 0 -9999 0 -10000 0 0
CRKL 0.009 0.015 -9999 0 -0.37 1 1
MAP3K1 0.026 0.042 -9999 0 -0.26 3 3
JUN -0.14 0.24 -9999 0 -0.48 227 227
MAP3K7 0.032 0.025 -9999 0 -0.29 1 1
GRAP2 -0.001 0.064 -9999 0 -0.37 19 19
CRK 0.01 0 -9999 0 -10000 0 0
MAP2K4 0.035 0.032 -9999 0 -0.21 3 3
LAT 0.008 0.025 -9999 0 -0.36 3 3
LCP2 0.008 0.03 -9999 0 -0.37 4 4
MAPK8 -0.16 0.26 -9999 0 -0.51 227 227
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.027 0.027 -9999 0 -0.32 1 1
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.007 0.045 -9999 0 -0.41 5 5
IL4-mediated signaling events

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
BCL2L1 -0.27 0.32 -10000 0 -0.9 54 54
STAT6 (cleaved dimer) -0.33 0.31 -10000 0 -0.83 125 125
IGHG1 -0.11 0.14 -10000 0 -0.38 2 2
IGHG3 -0.27 0.31 -10000 0 -0.83 75 75
AKT1 -0.16 0.2 -10000 0 -0.61 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.13 0.18 -10000 0 -0.63 22 22
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.16 0.19 -10000 0 -0.52 17 17
THY1 -0.28 0.35 -10000 0 -0.98 64 64
MYB -0.028 0.12 -10000 0 -0.37 66 66
HMGA1 0.009 0.015 -10000 0 -0.37 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.22 0.24 -10000 0 -0.6 88 88
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.16 0.19 -10000 0 -0.52 18 18
SP1 0.014 0.007 -10000 0 -10000 0 0
INPP5D 0.007 0.033 -10000 0 -0.37 5 5
SOCS5 0.022 0.014 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.34 0.32 -10000 0 -0.85 127 127
SOCS1 -0.29 0.29 -10000 0 -0.7 144 144
SOCS3 -0.24 0.34 -10000 0 -1 76 76
FCER2 -0.68 0.63 -10000 0 -1.3 347 347
PARP14 -0.021 0.083 -10000 0 -0.38 32 32
CCL17 -0.27 0.32 -10000 0 -0.91 57 57
GRB2 0.01 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.14 0.17 -10000 0 -0.48 34 34
T cell proliferation -0.28 0.33 -10000 0 -0.9 67 67
IL4R/JAK1 -0.28 0.32 -10000 0 -0.89 63 63
EGR2 -0.38 0.4 -10000 0 -1 113 113
JAK2 -0.005 0.025 -10000 0 -10000 0 0
JAK3 -0.001 0.057 -10000 0 -0.32 20 20
PIK3R1 0.01 0 -10000 0 -10000 0 0
JAK1 0.005 0.01 -10000 0 -10000 0 0
COL1A2 -0.12 0.17 -10000 0 -0.51 25 25
CCL26 -0.28 0.33 -10000 0 -0.94 51 51
IL4R -0.29 0.34 -10000 0 -0.94 61 61
PTPN6 0.015 0.034 -10000 0 -0.36 5 5
IL13RA2 -0.45 0.54 -10000 0 -1.2 200 200
IL13RA1 -0.007 0.037 -10000 0 -0.41 3 3
IRF4 -0.098 0.13 -10000 0 -0.5 15 15
ARG1 -0.073 0.12 -10000 0 -10000 0 0
CBL -0.2 0.23 -10000 0 -0.57 83 83
GTF3A 0.01 0.016 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.007 0.041 -10000 0 -0.3 3 3
IRF4/BCL6 -0.048 0.1 -10000 0 -0.48 9 9
CD40LG -0.008 0.073 -10000 0 -0.39 23 23
MAPK14 -0.22 0.25 -10000 0 -0.62 98 98
mitosis -0.16 0.2 -10000 0 -0.58 23 23
STAT6 -0.3 0.35 -10000 0 -0.96 69 69
SPI1 0.008 0.047 -10000 0 -0.37 10 10
RPS6KB1 -0.15 0.19 -10000 0 -0.56 21 21
STAT6 (dimer) -0.3 0.36 -10000 0 -0.96 69 69
STAT6 (dimer)/PARP14 -0.36 0.37 -10000 0 -0.92 113 113
mast cell activation 0.01 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.2 -10000 0 -0.6 32 32
FRAP1 -0.16 0.2 -10000 0 -0.6 24 24
LTA -0.28 0.33 -10000 0 -0.92 63 63
FES 0.009 0.015 -10000 0 -0.37 1 1
T-helper 1 cell differentiation 0.3 0.35 0.95 69 -10000 0 69
CCL11 -0.27 0.31 -10000 0 -0.86 61 61
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.17 0.2 -10000 0 -0.62 25 25
IL2RG -0.038 0.12 -10000 0 -0.38 79 79
IL10 -0.28 0.33 -10000 0 -0.93 60 60
IRS1 0.01 0 -10000 0 -10000 0 0
IRS2 0.009 0.015 -10000 0 -0.37 1 1
IL4 -0.081 0.1 -10000 0 -10000 0 0
IL5 -0.27 0.32 -10000 0 -0.9 56 56
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.24 0.28 -10000 0 -0.73 61 61
COL1A1 -0.17 0.23 -10000 0 -0.74 29 29
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.28 0.32 -10000 0 -0.92 55 55
IL2R gamma/JAK3 -0.031 0.093 -10000 0 -0.25 99 99
TFF3 -0.28 0.33 -10000 0 -0.94 54 54
ALOX15 -0.28 0.33 -10000 0 -0.91 59 59
MYBL1 0.006 0.039 -10000 0 -0.37 7 7
T-helper 2 cell differentiation -0.26 0.29 -10000 0 -0.75 75 75
SHC1 -0.001 0.064 -10000 0 -0.37 19 19
CEBPB 0.012 0.022 -10000 0 -0.37 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.15 0.18 -10000 0 -0.51 12 12
mol:PI-3-4-5-P3 -0.16 0.2 -10000 0 -0.61 23 23
PI3K -0.17 0.21 -10000 0 -0.63 24 24
DOK2 -0.012 0.089 -10000 0 -0.37 38 38
ETS1 0.006 0.07 -10000 0 -0.36 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.12 0.16 -10000 0 -0.46 28 28
ITGB3 -0.29 0.34 -10000 0 -0.92 71 71
PIGR -0.29 0.33 -10000 0 -0.91 65 65
IGHE 0.03 0.034 -10000 0 -10000 0 0
MAPKKK cascade -0.12 0.16 -10000 0 -0.45 28 28
BCL6 0.02 0.012 -10000 0 -10000 0 0
OPRM1 -0.3 0.37 -10000 0 -1 71 71
RETNLB -0.28 0.32 -10000 0 -0.9 56 56
SELP -0.27 0.32 -10000 0 -0.91 59 59
AICDA -0.27 0.31 -10000 0 -0.87 56 56
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.01 0 -10000 0 -10000 0 0
NFATC1 0.021 0.067 -10000 0 -0.26 2 2
NFATC2 0.013 0.05 -10000 0 -0.18 14 14
NFATC3 -0.016 0.095 -10000 0 -0.27 79 79
YWHAE 0.01 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.16 0.16 -10000 0 -0.35 231 231
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.18 0.15 -10000 0 -0.31 324 324
BCL2/BAX 0 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.009 0.001 -10000 0 -10000 0 0
CaM/Ca2+ 0.009 0.001 -10000 0 -10000 0 0
BAX 0.01 0 -10000 0 -10000 0 0
MAPK14 0.01 0.001 -10000 0 -10000 0 0
BAD 0.01 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.15 0.15 -10000 0 -0.33 231 231
Calcineurin A alpha-beta B1/BCL2 0.01 0 -10000 0 -10000 0 0
FKBP8 0.01 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.15 0.15 0.33 231 -10000 0 231
KPNB1 0.01 0 -10000 0 -10000 0 0
KPNA2 0.01 0 -10000 0 -10000 0 0
XPO1 0.01 0 -10000 0 -10000 0 0
SFN -0.008 0.079 -10000 0 -0.37 30 30
MAP3K8 0.003 0.051 -10000 0 -0.38 12 12
NFAT4/CK1 alpha -0.019 0.049 -10000 0 -0.29 5 5
MEF2D/NFAT1/Cbp/p300 -0.01 0.033 -10000 0 -0.28 4 4
CABIN1 -0.16 0.16 -10000 0 -0.36 231 231
CALM1 0.01 0.001 -10000 0 -10000 0 0
RAN 0.01 0 -10000 0 -10000 0 0
MAP3K1 -0.002 0.067 -10000 0 -0.37 21 21
CAMK4 -0.085 0.15 -10000 0 -0.32 190 190
mol:Ca2+ 0.001 0.001 -10000 0 -10000 0 0
MAPK3 0.01 0 -10000 0 -10000 0 0
YWHAH 0.004 0.044 -10000 0 -0.32 12 12
Calcineurin A alpha-beta B1/AKAP79/PKA -0.08 0.1 -10000 0 -0.21 250 250
YWHAB 0.01 0 -10000 0 -10000 0 0
MAPK8 0.008 0.029 -10000 0 -0.32 5 5
MAPK9 0.01 0 -10000 0 -10000 0 0
YWHAG 0.01 0 -10000 0 -10000 0 0
FKBP1A 0.01 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.024 0.07 -10000 0 -0.26 12 12
PRKCH 0.01 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0 0 -10000 0 -10000 0 0
CASP3 0.008 0.03 -10000 0 -0.37 4 4
PIM1 0.008 0.03 -10000 0 -0.37 4 4
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis 0 0 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.028 0.027 -10000 0 -0.2 1 1
PRKCB -0.1 0.16 -10000 0 -0.32 225 225
PRKCE -0.002 0.062 -10000 0 -0.32 24 24
JNK2/NFAT4 -0.009 0.085 -10000 0 -0.24 79 79
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.005 0.039 -10000 0 -0.32 9 9
NUP214 0.01 0 -10000 0 -10000 0 0
PRKCZ -0.029 0.11 -10000 0 -0.32 79 79
PRKCA 0.01 0 -10000 0 -10000 0 0
PRKCG -0.24 0.15 -10000 0 -0.32 497 497
PRKCQ 0.003 0.048 -10000 0 -0.33 14 14
FKBP38/BCL2 0 0 -10000 0 -10000 0 0
EP300 0.01 0.001 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.01 0 -10000 0 -10000 0 0
NFATc/JNK1 0.026 0.064 -10000 0 -0.25 2 2
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.016 0.001 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.05 0.079 -10000 0 -0.18 190 190
NFATc/ERK1 0.026 0.064 -10000 0 -0.24 2 2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.18 0.15 -10000 0 -0.31 324 324
NR4A1 0.038 0.052 -10000 0 -0.37 5 5
GSK3B 0.01 0.001 -10000 0 -10000 0 0
positive T cell selection -0.015 0.094 -10000 0 -0.27 79 79
NFAT1/CK1 alpha -0.009 0.025 -10000 0 -0.17 4 4
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.01 0 -10000 0 -10000 0 0
PRKACA 0.01 0.001 -10000 0 -10000 0 0
AKAP5 -0.12 0.16 -10000 0 -0.32 250 250
MEF2D 0.01 0.013 -10000 0 -0.32 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.01 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.026 0.064 -10000 0 -0.25 2 2
CREBBP 0.01 0.001 -10000 0 -10000 0 0
BCL2 0.01 0 -10000 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 0.009 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.091 0.091 -10000 0 -0.18 338 338
regulation of S phase of mitotic cell cycle -0.029 0.053 -10000 0 -10000 0 0
GNAO1 0.004 0.044 -10000 0 -0.32 12 12
HRAS 0.01 0 -10000 0 -10000 0 0
SHBG/T-DHT 0 0.008 -10000 0 -0.22 1 1
PELP1 0.01 0 -10000 0 -10000 0 0
AKT1 0.009 0.01 -10000 0 -0.26 1 1
MAP2K1 -0.046 0.083 -10000 0 -0.19 7 7
T-DHT/AR -0.13 0.13 -10000 0 -0.26 337 337
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.005 16 16
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.009 0.021 -10000 0 -0.37 2 2
GNAI1 0.006 0.036 -10000 0 -0.32 8 8
mol:GDP -0.059 0.058 -10000 0 -10000 0 0
cell proliferation -0.024 0.084 -10000 0 -0.3 13 13
PIK3CA 0.01 0 -10000 0 -10000 0 0
FOS -0.01 0.094 -10000 0 -0.74 7 7
mol:Ca2+ -0.009 0.011 -10000 0 -0.059 13 13
MAPK3 -0.032 0.082 -10000 0 -0.23 13 13
MAPK1 -0.009 0.044 -10000 0 -0.24 1 1
PIK3R1 0.01 0 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.003 16 16
cAMP biosynthetic process 0.012 0.015 -10000 0 -0.21 1 1
GNG2 0.009 0.018 -10000 0 -0.32 2 2
potassium channel inhibitor activity 0 0.001 -10000 0 -0.003 16 16
HRAS/GTP -0.078 0.077 -10000 0 -0.15 337 337
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.01 0 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.003 16 16
PI3K 0 0 -10000 0 -10000 0 0
apoptosis 0.013 0.069 0.3 13 -10000 0 13
T-DHT/AR/PELP1 -0.1 0.1 -10000 0 -0.21 337 337
HRAS/GDP -0.052 0.052 -10000 0 -10000 0 0
CREB1 -0.014 0.072 -10000 0 -0.32 13 13
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.18 0.19 -10000 0 -0.37 337 337
GNB1 0.01 0 -10000 0 -10000 0 0
RAF1 -0.055 0.086 -10000 0 -0.19 7 7
RAC1-CDC42/GDP -0.047 0.047 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src -0.091 0.09 -10000 0 -0.18 337 337
MAP2K2 -0.046 0.083 -10000 0 -0.19 7 7
T-DHT/AR/PELP1/Src/PI3K -0.029 0.053 -10000 0 -10000 0 0
GNAZ 0.009 0.018 -10000 0 -0.32 2 2
SHBG 0.009 0.015 -10000 0 -0.37 1 1
Gi family/GNB1/GNG2/GDP 0.013 0.051 -10000 0 -0.31 13 13
mol:T-DHT 0 0 -10000 0 -0.003 6 6
RAC1 0.01 0 -10000 0 -10000 0 0
GNRH1 0.007 0.021 -10000 0 -0.26 4 4
Gi family/GTP -0.033 0.04 -10000 0 -0.22 13 13
CDC42 0.01 0 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.001 0.02 -10000 0 -0.24 4 4
fibroblast growth factor receptor signaling pathway -0.001 0.02 -10000 0 -0.24 4 4
LAMA1 -0.013 0.089 -10000 0 -0.37 40 40
PRNP 0.01 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.071 0.1 -10000 0 -0.21 222 222
SMAD2 0.024 0.023 -10000 0 -0.17 8 8
GPC1/PrPc/Cu2+ -0.001 0.011 -10000 0 -0.19 2 2
GPC1/Laminin alpha1 -0.015 0.059 -10000 0 -0.24 42 42
TDGF1 -0.001 0.059 -10000 0 -0.33 21 21
CRIPTO/GPC1 -0.007 0.041 -10000 0 -0.23 22 22
APP/GPC1 -0.001 0.013 -10000 0 -0.23 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.015 0.037 -10000 0 -0.18 23 23
FLT1 0.01 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.003 0.023 -10000 0 -0.2 9 9
SERPINC1 -0.017 0.095 -10000 0 -0.37 44 44
FYN 0.015 0.037 -10000 0 -0.18 22 22
FGR 0.013 0.042 -10000 0 -0.18 28 28
positive regulation of MAPKKK cascade 0.001 0.068 -10000 0 -0.26 24 24
SLIT2 -0.1 0.16 -10000 0 -0.32 220 220
GPC1/NRG -0.043 0.086 -10000 0 -0.21 136 136
NRG1 -0.057 0.13 -10000 0 -0.32 134 134
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.027 0.069 -10000 0 -0.2 87 87
LYN 0.014 0.039 -10000 0 -0.18 25 25
mol:Spermine 0.008 0.014 -10000 0 -0.24 2 2
cell growth -0.001 0.02 -10000 0 -0.24 4 4
BMP signaling pathway -0.009 0.02 0.35 2 -10000 0 2
SRC 0.015 0.037 -10000 0 -0.18 22 22
TGFBR1 0.008 0.03 -10000 0 -0.37 4 4
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.078 0.15 -10000 0 -0.36 151 151
GPC1 0.009 0.02 -10000 0 -0.35 2 2
TGFBR1 (dimer) 0.008 0.03 -10000 0 -0.37 4 4
VEGFA -0.039 0.13 -10000 0 -0.37 86 86
BLK -0.022 0.089 -10000 0 -0.2 125 125
HCK 0.011 0.046 -10000 0 -0.19 33 33
FGF2 0.009 0.015 -10000 0 -0.37 1 1
FGFR1 0.009 0.021 -10000 0 -0.37 2 2
VEGFR1 homodimer 0.01 0 -10000 0 -10000 0 0
TGFBR2 0.008 0.026 -10000 0 -0.37 3 3
cell death -0.001 0.013 -10000 0 -0.23 2 2
ATIII/GPC1 -0.017 0.063 -10000 0 -0.25 46 46
PLA2G2A/GPC1 -0.055 0.1 -10000 0 -0.24 152 152
LCK -0.029 0.097 -10000 0 -0.21 148 148
neuron differentiation -0.043 0.086 -10000 0 -0.21 136 136
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.01 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.008 0.026 -10000 0 -0.37 3 3
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.035 0.088 -9999 0 -0.25 93 93
alphaV beta3 Integrin -0.039 0.08 -9999 0 -0.2 129 129
PTK2 0.005 0.086 -9999 0 -0.26 22 22
IGF1R 0.009 0.015 -9999 0 -0.37 1 1
PI4KB 0.01 0 -9999 0 -10000 0 0
MFGE8 0.009 0.021 -9999 0 -0.37 2 2
SRC 0.01 0 -9999 0 -10000 0 0
CDKN1B -0.014 0.037 -9999 0 -0.49 2 2
VEGFA -0.039 0.13 -9999 0 -0.37 86 86
ILK -0.014 0.037 -9999 0 -0.38 3 3
ROCK1 0.009 0.015 -9999 0 -0.37 1 1
AKT1 -0.012 0.033 -9999 0 -0.36 3 3
PTK2B -0.03 0.12 -9999 0 -0.23 156 156
alphaV/beta3 Integrin/JAM-A -0.033 0.067 -9999 0 -0.16 134 134
CBL 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.04 0.082 -9999 0 -0.21 129 129
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.002 0.018 -9999 0 -0.18 2 2
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.005 0.056 -9999 0 -0.26 2 2
alphaV/beta3 Integrin/Syndecan-1 -0.051 0.11 -9999 0 -0.25 136 136
PI4KA 0.007 0.029 -9999 0 -0.32 5 5
IGF-1R heterotetramer/IGF1/IRS1 -0.051 0.099 -9999 0 -0.3 73 73
PI4 Kinase -0.002 0.018 -9999 0 -0.21 5 5
PIK3CA 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.069 0.13 -9999 0 -0.27 170 170
RPS6KB1 -0.013 0.11 -9999 0 -0.28 73 73
TLN1 0.01 0 -9999 0 -10000 0 0
MAPK3 -0.023 0.046 -9999 0 -0.22 5 5
GPR124 0.009 0.021 -9999 0 -0.37 2 2
MAPK1 -0.023 0.046 -9999 0 -0.22 5 5
PXN 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.053 0.094 -9999 0 -0.21 169 169
cell adhesion -0.029 0.06 -9999 0 -0.3 1 1
ANGPTL3 0.003 0.015 -9999 0 -0.37 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.028 0.071 -9999 0 -0.2 93 93
IGF-1R heterotetramer 0.009 0.015 -9999 0 -0.37 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.008 0.026 -9999 0 -0.37 3 3
ITGB3 -0.064 0.15 -9999 0 -0.37 128 128
IGF1 0.005 0.039 -9999 0 -0.33 9 9
RAC1 0.01 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.039 0.08 -9999 0 -0.2 129 129
apoptosis 0.01 0 -9999 0 -10000 0 0
CD47 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.039 0.079 -9999 0 -0.2 128 128
VCL 0.008 0.03 -9999 0 -0.37 4 4
alphaV/beta3 Integrin/Del1 -0.063 0.1 -9999 0 -0.21 204 204
CSF1 0.004 0.047 -9999 0 -0.37 10 10
PIK3C2A -0.014 0.037 -9999 0 -0.38 3 3
PI4 Kinase/Pyk2 -0.045 0.09 -9999 0 -0.28 70 70
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.059 0.12 -9999 0 -0.26 156 156
FAK1/Vinculin 0.01 0.076 -9999 0 -0.22 22 22
alphaV beta3/Integrin/ppsTEM5 -0.039 0.081 -9999 0 -0.2 129 129
RHOA 0.01 0 -9999 0 -10000 0 0
VTN 0.007 0.031 -9999 0 -0.35 5 5
BCAR1 0.01 0 -9999 0 -10000 0 0
FGF2 0.009 0.015 -9999 0 -0.37 1 1
F11R 0.016 0.025 -9999 0 -0.25 6 6
alphaV/beta3 Integrin/Lactadherin -0.039 0.081 -9999 0 -0.2 129 129
alphaV/beta3 Integrin/TGFBR2 -0.04 0.082 -9999 0 -0.2 129 129
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.021 -9999 0 -0.18 10 10
HSP90AA1 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.035 0.071 -9999 0 -0.18 128 128
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.045 0.14 -9999 0 -0.37 96 96
alphaV/beta3 Integrin/Pyk2 -0.055 0.11 -9999 0 -0.34 67 67
SDC1 -0.013 0.091 -9999 0 -0.37 40 40
VAV3 0.023 0.035 -9999 0 -0.17 12 12
PTPN11 0.01 0 -9999 0 -10000 0 0
IRS1 0.01 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.011 0.074 -9999 0 -0.21 21 21
cell migration 0.017 0.072 -9999 0 -0.26 5 5
ITGAV 0.01 0 -9999 0 -10000 0 0
PI3K -0.028 0.057 -9999 0 -0.29 5 5
SPP1 -0.048 0.14 -9999 0 -0.37 102 102
KDR 0.005 0.042 -9999 0 -0.37 8 8
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0 -9999 0 -10000 0 0
COL4A3 -0.018 0.099 -9999 0 -0.37 50 50
angiogenesis 0.016 0.059 -9999 0 -0.24 4 4
Rac1/GTP -0.014 0.039 -9999 0 -0.28 1 1
EDIL3 -0.038 0.12 -9999 0 -0.32 96 96
cell proliferation -0.039 0.081 -9999 0 -0.2 129 129
LPA4-mediated 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
ADCY4 0.009 0.036 -9999 0 -0.18 24 24
ADCY5 -0.006 0.072 -9999 0 -0.22 63 63
ADCY6 0.009 0.036 -9999 0 -0.18 24 24
ADCY7 0.009 0.036 -9999 0 -0.18 24 24
ADCY1 -0.038 0.092 -9999 0 -0.19 179 179
ADCY2 0.005 0.045 -9999 0 -0.19 34 34
ADCY3 0.009 0.036 -9999 0 -0.18 24 24
ADCY8 0.001 0.055 -9999 0 -0.2 47 47
PRKCE 0.001 0.043 -9999 0 -0.22 24 24
ADCY9 0.009 0.036 -9999 0 -0.18 24 24
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process 0 0.07 -9999 0 -0.29 28 28
FAS signaling pathway (CD95)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.008 0.03 -10000 0 -0.18 1 1
RFC1 0.008 0.03 -10000 0 -0.18 1 1
PRKDC 0.008 0.03 -10000 0 -0.18 1 1
RIPK1 0.011 0.003 -10000 0 -10000 0 0
CASP7 0.009 0.054 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1 0.011 0.053 -10000 0 -10000 0 0
MAP2K4 -0.005 0.11 -10000 0 -0.24 105 105
mol:ceramide 0 0.069 -10000 0 -0.25 1 1
GSN 0.008 0.03 -10000 0 -0.18 1 1
FASLG/FAS/FADD/FAF1/Caspase 8 0.006 0.05 -10000 0 -0.22 1 1
FAS -0.007 0.076 -10000 0 -0.38 27 27
BID 0.011 0.054 -10000 0 -0.2 25 25
MAP3K1 0.009 0.073 -10000 0 -0.27 1 1
MAP3K7 0.008 0.004 -10000 0 -10000 0 0
RB1 0.008 0.03 -10000 0 -0.18 1 1
CFLAR 0.011 0.003 -10000 0 -10000 0 0
HGF/MET -0.078 0.09 -10000 0 -0.18 298 298
ARHGDIB 0.001 0.052 -10000 0 -0.22 24 24
FADD 0.009 0.004 -10000 0 -10000 0 0
actin filament polymerization -0.008 0.03 0.18 1 -10000 0 1
NFKB1 -0.035 0.072 -10000 0 -10000 0 0
MAPK8 -0.027 0.17 -10000 0 -0.41 106 106
DFFA 0.008 0.03 -10000 0 -0.18 1 1
DNA fragmentation during apoptosis 0.008 0.03 -10000 0 -0.18 1 1
FAS/FADD/MET -0.082 0.09 -10000 0 -0.18 311 311
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.085 0.17 -10000 0 -0.37 166 166
FAF1 0.009 0.004 -10000 0 -10000 0 0
PARP1 0.008 0.031 -10000 0 -0.19 2 2
DFFB 0.008 0.03 -10000 0 -0.18 1 1
CHUK -0.03 0.063 -10000 0 -10000 0 0
FASLG -0.006 0.062 -10000 0 -0.37 18 18
FAS/FADD -0.012 0.05 -10000 0 -0.26 27 27
HGF 0 0.059 -10000 0 -0.34 19 19
LMNA -0.005 0.059 -10000 0 -0.22 30 30
CASP6 -0.007 0.063 -10000 0 -0.21 48 48
CASP10 0.009 0.004 -10000 0 -10000 0 0
CASP3 0.009 0.035 -10000 0 -0.21 1 1
PTPN13 0.009 0.015 -10000 0 -0.37 1 1
CASP8 0.026 0.082 0.15 150 -0.25 23 173
IL6 -0.16 0.43 -10000 0 -1.1 106 106
MET -0.13 0.17 -10000 0 -0.32 287 287
ICAD/CAD 0.01 0.03 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 0 0.069 -10000 0 -0.26 1 1
activation of caspase activity by cytochrome c 0.011 0.053 -10000 0 -0.2 25 25
PAK2 0.008 0.03 -10000 0 -0.18 1 1
BCL2 0.01 0.001 -10000 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.011 0 -9999 0 -10000 0 0
ELF1 -0.031 0.076 -9999 0 -10000 0 0
CCNA2 -0.12 0.18 -9999 0 -0.37 232 232
PIK3CA 0.011 0 -9999 0 -10000 0 0
JAK3 0 0.057 -9999 0 -0.32 20 20
PIK3R1 0.01 0 -9999 0 -10000 0 0
JAK1 0.011 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.005 0.088 -9999 0 -0.28 12 12
SHC1 0 0.064 -9999 0 -0.37 19 19
SP1 0.014 0.02 -9999 0 -0.28 1 1
IL2RA -0.062 0.14 -9999 0 -0.29 177 177
IL2RB -0.027 0.11 -9999 0 -0.37 66 66
SOS1 0.01 0 -9999 0 -10000 0 0
IL2RG -0.035 0.12 -9999 0 -0.37 79 79
G1/S transition of mitotic cell cycle -0.031 0.096 -9999 0 -0.44 4 4
PTPN11 0.011 0 -9999 0 -10000 0 0
CCND2 0.021 0.037 -9999 0 -0.33 7 7
LCK -0.065 0.15 -9999 0 -0.37 132 132
GRB2 0.01 0 -9999 0 -10000 0 0
IL2 0.001 0 -9999 0 -10000 0 0
CDK6 -0.048 0.14 -9999 0 -0.37 100 100
CCND3 0.012 0.08 -9999 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.009 0.015 -10000 0 -0.37 1 1
RAS family/GTP/Tiam1 0.007 0.02 -10000 0 -0.21 3 3
NT3 (dimer)/TRKC -0.004 0.035 -10000 0 -0.29 9 9
NT3 (dimer)/TRKB -0.031 0.077 -10000 0 -0.21 96 96
SHC/Grb2/SOS1/GAB1/PI3K 0.026 0.018 -10000 0 -10000 0 0
RAPGEF1 0.01 0 -10000 0 -10000 0 0
BDNF -0.17 0.17 -10000 0 -0.32 359 359
PIK3CA 0.01 0 -10000 0 -10000 0 0
DYNLT1 -0.029 0.12 -10000 0 -0.37 67 67
NTRK1 -0.014 0.093 -10000 0 -0.37 42 42
NTRK2 0.007 0.03 -10000 0 -0.33 5 5
NTRK3 0.008 0.026 -10000 0 -0.32 4 4
NT-4/5 (dimer)/TRKB -0.036 0.084 -10000 0 -0.22 110 110
neuron apoptosis 0.095 0.11 0.34 74 -10000 0 74
SHC 2-3/Grb2 -0.1 0.12 -10000 0 -0.37 74 74
SHC1 -0.001 0.064 -10000 0 -0.37 19 19
SHC2 -0.086 0.083 -10000 0 -0.3 40 40
SHC3 -0.11 0.15 -10000 0 -0.38 106 106
STAT3 (dimer) 0.004 0.044 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.042 0.093 -10000 0 -0.23 125 125
RIN/GDP 0.006 0.052 -10000 0 -0.23 6 6
GIPC1 0.01 0 -10000 0 -10000 0 0
KRAS 0.01 0 -10000 0 -10000 0 0
DNAJA3 -0.028 0.054 -10000 0 -0.22 16 16
RIN/GTP -0.058 0.097 -10000 0 -0.22 174 174
CCND1 0.003 0.079 -10000 0 -0.29 45 45
MAGED1 0.01 0 -10000 0 -10000 0 0
PTPN11 0.01 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.009 0.071 -10000 0 -0.37 24 24
SHC/GRB2/SOS1 -0.006 0.034 -10000 0 -0.2 19 19
GRB2 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.076 0.11 -10000 0 -0.21 243 243
TRKA/NEDD4-2 -0.021 0.07 -10000 0 -0.24 59 59
ELMO1 0.009 0.013 -10000 0 -0.32 1 1
RhoG/GTP/ELMO1/DOCK1 0 0.007 -10000 0 -0.18 1 1
NGF -0.014 0.087 -10000 0 -0.32 48 48
HRAS 0.01 0 -10000 0 -10000 0 0
DOCK1 0.01 0 -10000 0 -10000 0 0
GAB2 0.01 0 -10000 0 -10000 0 0
RIT2 -0.077 0.15 -10000 0 -0.32 174 174
RIT1 0.01 0 -10000 0 -10000 0 0
FRS2 0.008 0.026 -10000 0 -0.37 3 3
DNM1 -0.17 0.17 -10000 0 -0.32 367 367
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.027 0.053 -10000 0 -0.22 16 16
mol:GDP 0.024 0.044 -10000 0 -0.27 4 4
NGF (dimer) -0.014 0.086 -10000 0 -0.32 48 48
RhoG/GDP 0 0.009 -10000 0 -0.22 1 1
RIT1/GDP 0.023 0.032 -10000 0 -0.19 3 3
TIAM1 0.009 0.013 -10000 0 -0.32 1 1
PIK3R1 0.01 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.094 0.085 -10000 0 -0.17 370 370
KIDINS220/CRKL/C3G 0 0.01 -10000 0 -0.25 1 1
SHC/RasGAP -0.007 0.042 -10000 0 -0.25 19 19
FRS2 family/SHP2 -0.001 0.013 -10000 0 -0.2 3 3
SHC/GRB2/SOS1/GAB1 -0.005 0.03 -10000 0 -0.18 20 20
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) 0.002 0.039 -10000 0 -0.37 7 7
RAP1/GDP -0.005 0.019 -10000 0 -0.16 3 3
KIDINS220/CRKL 0.009 0.015 -10000 0 -0.37 1 1
BDNF (dimer) -0.17 0.17 -10000 0 -0.32 359 359
ubiquitin-dependent protein catabolic process -0.029 0.071 -10000 0 -0.19 103 103
Schwann cell development -0.017 0.017 -10000 0 -10000 0 0
EHD4 0.005 0.042 -10000 0 -0.37 8 8
FRS2 family/GRB2/SOS1 -0.001 0.012 -10000 0 -0.18 3 3
FRS2 family/SHP2/CRK family/C3G/GAB2 0.031 0.007 -10000 0 -10000 0 0
RAP1B 0.005 0.044 -10000 0 -0.37 9 9
RAP1A 0.01 0 -10000 0 -10000 0 0
CDC42/GTP -0.062 0.058 -10000 0 -0.31 6 6
ABL1 0.01 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.032 0.031 -10000 0 -10000 0 0
STAT3 0.004 0.044 -10000 0 -10000 0 0
axon guidance -0.06 0.056 -10000 0 -0.3 6 6
MAPK3 -0.049 0.11 -10000 0 -0.28 68 68
MAPK1 -0.049 0.11 -10000 0 -0.28 68 68
CDC42/GDP 0.023 0.032 -10000 0 -0.19 3 3
NTF3 0.002 0.039 -10000 0 -0.37 7 7
NTF4 -0.009 0.071 -10000 0 -0.37 24 24
NGF (dimer)/TRKA/FAIM -0.025 0.064 -10000 0 -0.19 89 89
PI3K 0 0 -10000 0 -10000 0 0
FRS3 0.01 0 -10000 0 -10000 0 0
FAIM 0.01 0 -10000 0 -10000 0 0
GAB1 0.009 0.015 -10000 0 -0.37 1 1
RASGRF1 -0.047 0.094 -10000 0 -0.26 94 94
SOS1 0.01 0 -10000 0 -10000 0 0
MCF2L 0.016 0.031 -10000 0 -0.23 10 10
RGS19 0.01 0 -10000 0 -10000 0 0
CDC42 0.01 0 -10000 0 -10000 0 0
RAS family/GTP 0.009 0.051 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.032 -10000 0 -0.19 3 3
NGF (dimer)/TRKA/GRIT -0.026 0.067 -10000 0 -0.19 89 89
neuron projection morphogenesis -0.001 0.06 -10000 0 -10000 0 0
NGF (dimer)/TRKA/NEDD4-2 -0.029 0.071 -10000 0 -0.19 103 103
MAP2K1 0.026 0.032 -10000 0 -0.16 20 20
NGFR -0.041 0.13 -10000 0 -0.37 89 89
NGF (dimer)/TRKA/GIPC/GAIP -0.11 0.13 -10000 0 -0.32 109 109
RAS family/GTP/PI3K 0.025 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.01 -10000 0 -10000 0 0
NRAS 0.01 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.01 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCZ -0.03 0.11 -10000 0 -0.32 79 79
MAPKKK cascade -0.019 0.14 -10000 0 -0.52 47 47
RASA1 0.01 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.016 0.061 -10000 0 -0.25 42 42
SQSTM1 0.01 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.097 0.094 -10000 0 -0.27 69 69
NGF (dimer)/TRKA/p62/Atypical PKCs -0.035 0.072 -10000 0 -0.31 20 20
MATK -0.092 0.15 -10000 0 -0.32 203 203
NEDD4L 0.001 0.054 -10000 0 -0.32 18 18
RAS family/GDP -0.003 0.017 -10000 0 -0.17 3 3
NGF (dimer)/TRKA -0.031 0.06 -10000 0 -0.24 16 16
Rac1/GTP -0.036 0.051 -10000 0 -0.19 29 29
FRS2 family/SHP2/CRK family -0.001 0.012 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.04 0.087 -10000 0 -0.3 50 50
FYN -0.007 0.12 -10000 0 -0.34 46 46
LAT/GRAP2/SLP76 -0.04 0.095 -10000 0 -0.32 48 48
IKBKB 0.01 0 -10000 0 -10000 0 0
AKT1 0.007 0.093 -10000 0 -0.26 43 43
B2M -0.03 0.12 -10000 0 -0.38 70 70
IKBKG -0.008 0.02 -10000 0 -0.1 11 11
MAP3K8 0.003 0.051 -10000 0 -0.37 12 12
mol:Ca2+ -0.005 0.016 -10000 0 -0.073 18 18
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.001 0.12 -10000 0 -0.34 46 46
TRPV6 -0.087 0.15 -10000 0 -0.33 178 178
CD28 -0.008 0.08 -10000 0 -0.38 30 30
SHC1 -0.012 0.13 -10000 0 -0.35 54 54
receptor internalization -0.012 0.11 -10000 0 -0.3 51 51
PRF1 -0.017 0.13 -10000 0 -0.49 24 24
KRAS 0.01 0 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
COT/AKT1 0.01 0.085 -10000 0 -0.24 39 39
LAT -0.008 0.12 -10000 0 -0.33 48 48
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.04 0.13 -10000 0 -0.38 85 85
CD3E -0.028 0.12 -10000 0 -0.38 67 67
CD3G -0.025 0.11 -10000 0 -0.38 57 57
RASGRP2 0.006 0.011 -10000 0 -10000 0 0
RASGRP1 0.002 0.11 -10000 0 -0.27 63 63
HLA-A -0.009 0.084 -10000 0 -0.38 33 33
RASSF5 0.01 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.04 -10000 0 -0.088 27 27
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.015 0.034 -10000 0 -0.16 16 16
PRKCA -0.01 0.054 -10000 0 -0.18 31 31
GRAP2 -0.001 0.064 -10000 0 -0.37 19 19
mol:IP3 0.005 0.1 0.15 147 -0.28 33 180
EntrezGene:6957 0 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.018 0.097 -10000 0 -0.25 65 65
ORAI1 0.056 0.092 0.21 176 -0.26 2 178
CSK -0.01 0.12 -10000 0 -0.33 49 49
B7 family/CD28 -0.059 0.13 -10000 0 -0.4 65 65
CHUK 0.01 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.016 0.12 -10000 0 -0.36 49 49
PTPN6 -0.015 0.12 -10000 0 -0.35 50 50
VAV1 -0.008 0.12 -10000 0 -0.34 48 48
Monovalent TCR/CD3 -0.017 0.088 -10000 0 -0.24 81 81
CBL 0.01 0 -10000 0 -10000 0 0
LCK -0.016 0.13 -10000 0 -0.34 61 61
PAG1 -0.01 0.12 -10000 0 -0.33 49 49
RAP1A 0.01 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.02 0.13 -10000 0 -0.37 52 52
CD80 -0.014 0.09 -10000 0 -0.38 39 39
CD86 -0.003 0.069 -10000 0 -0.38 22 22
PDK1/CARD11/BCL10/MALT1 -0.018 0.041 -10000 0 -0.19 19 19
HRAS 0.01 0 -10000 0 -10000 0 0
GO:0035030 -0.017 0.13 -10000 0 -0.35 63 63
CD8A -0.014 0.087 -10000 0 -0.33 47 47
CD8B -0.001 0.065 -10000 0 -0.38 19 19
PTPRC 0 0.057 -10000 0 -0.38 15 15
PDK1/PKC theta 0.01 0.11 -10000 0 -0.31 39 39
CSK/PAG1 -0.006 0.11 -10000 0 -0.33 46 46
SOS1 0.01 0 -10000 0 -10000 0 0
peptide-MHC class I -0.026 0.12 -10000 0 -0.34 76 76
GRAP2/SLP76 -0.046 0.11 -10000 0 -0.36 50 50
STIM1 0.029 0.044 0.16 2 -10000 0 2
RAS family/GTP 0.02 0.049 -10000 0 -0.13 15 15
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.013 0.11 -10000 0 -0.31 51 51
mol:DAG -0.023 0.068 0.086 1 -0.25 37 38
RAP1A/GDP 0.009 0.017 -10000 0 -0.051 2 2
PLCG1 0.01 0 -10000 0 -10000 0 0
CD247 0.005 0.041 -10000 0 -0.32 10 10
cytotoxic T cell degranulation -0.016 0.12 -10000 0 -0.47 25 25
RAP1A/GTP -0.001 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.003 0.11 -10000 0 -0.29 46 46
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0 0.12 0.17 114 -0.34 35 149
NRAS 0.01 0 -10000 0 -10000 0 0
ZAP70 0.003 0.052 -10000 0 -0.37 13 13
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.038 0.091 -10000 0 -0.32 44 44
MALT1 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
CD8 heterodimer -0.011 0.075 -10000 0 -0.24 64 64
CARD11 0.009 0.02 -10000 0 -0.35 2 2
PRKCB -0.031 0.074 -10000 0 -0.19 96 96
PRKCE -0.013 0.059 -10000 0 -0.19 42 42
PRKCQ 0.004 0.12 -10000 0 -0.34 43 43
LCP2 0.008 0.03 -10000 0 -0.37 4 4
BCL10 0.01 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.009 0.083 -10000 0 -0.22 42 42
IKK complex 0.008 0.045 -10000 0 -0.09 39 39
RAS family/GDP -0.002 0.005 -10000 0 -10000 0 0
MAP3K14 0.015 0.068 -10000 0 -0.2 28 28
PDPK1 0.009 0.09 -10000 0 -0.25 39 39
TCR/CD3/MHC I/CD8/Fyn -0.021 0.12 -10000 0 -0.35 53 53
Regulation of nuclear SMAD2/3 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
EP300 0.017 0.01 -10000 0 -10000 0 0
HSPA8 0.008 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.006 0.048 0.13 1 -0.2 2 3
AKT1 0.007 0.017 -10000 0 -0.37 1 1
GSC -0.19 0.088 -10000 0 -10000 0 0
NKX2-5 -0.14 0.18 -10000 0 -0.37 261 261
muscle cell differentiation 0.073 0.071 0.27 13 -10000 0 13
SMAD2-3/SMAD4/SP1 -0.008 0.076 -10000 0 -0.26 15 15
SMAD4 -0.014 0.049 -10000 0 -0.19 13 13
CBFB 0.009 0.021 -10000 0 -0.37 2 2
SAP18 0.009 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.021 0.049 -10000 0 -0.2 25 25
SMAD3/SMAD4/VDR 0.028 0.064 -10000 0 -0.26 13 13
MYC -0.12 0.18 -10000 0 -0.37 223 223
CDKN2B 0 0.1 -10000 0 -10000 0 0
AP1 0.023 0.048 -10000 0 -0.25 1 1
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.008 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.011 0.053 -10000 0 -0.25 6 6
SP3 0.012 0 -10000 0 -10000 0 0
CREB1 0.01 0 -10000 0 -10000 0 0
FOXH1 -0.015 0.02 -10000 0 -0.41 1 1
SMAD3/SMAD4/GR 0.008 0.046 -10000 0 -0.2 3 3
GATA3 -0.083 0.17 -10000 0 -0.39 153 153
SKI/SIN3/HDAC complex/NCoR1 0.015 0.019 -10000 0 -10000 0 0
MEF2C/TIF2 -0.086 0.11 -10000 0 -0.35 23 23
endothelial cell migration 0.033 0.13 1.2 3 -10000 0 3
MAX 0.012 0.008 -10000 0 -10000 0 0
RBBP7 0.009 0.001 -10000 0 -10000 0 0
RBBP4 0.009 0.001 -10000 0 -10000 0 0
RUNX2 0.005 0.044 -10000 0 -0.37 9 9
RUNX3 -0.011 0.088 -10000 0 -0.37 37 37
RUNX1 -0.023 0.11 -10000 0 -0.37 57 57
CTBP1 0.01 0 -10000 0 -10000 0 0
NR3C1 0.012 0.008 -10000 0 -10000 0 0
VDR -0.005 0.073 -10000 0 -0.35 28 28
CDKN1A -0.01 0.11 -10000 0 -0.41 1 1
KAT2B 0.012 0.015 -10000 0 -0.37 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.043 0.037 -10000 0 -0.27 1 1
DCP1A 0.01 0 -10000 0 -10000 0 0
SKI 0.009 0.001 -10000 0 -10000 0 0
SERPINE1 -0.034 0.13 -10000 0 -1.2 3 3
SMAD3/SMAD4/ATF2 0.004 0.051 -10000 0 -0.2 6 6
SMAD3/SMAD4/ATF3 0.001 0.062 -10000 0 -0.25 18 18
SAP30 0.009 0.015 -10000 0 -0.37 1 1
Cbp/p300/PIAS3 0.039 0.027 -10000 0 -10000 0 0
JUN 0.023 0.047 -10000 0 -0.25 1 1
SMAD3/SMAD4/IRF7 -0.005 0.071 -10000 0 -0.26 22 22
TFE3 0.002 0.032 -10000 0 -10000 0 0
COL1A2 -0.043 0.1 -10000 0 -0.28 103 103
mesenchymal cell differentiation -0.001 0.062 0.25 19 -10000 0 19
DLX1 -0.11 0.16 -10000 0 -0.32 240 240
TCF3 0.006 0.039 -10000 0 -0.37 7 7
FOS 0.004 0.055 -10000 0 -0.35 16 16
SMAD3/SMAD4/Max 0.008 0.046 -10000 0 -0.2 3 3
Cbp/p300/SNIP1 0.021 0.016 -10000 0 -10000 0 0
ZBTB17 0.012 0.008 -10000 0 -10000 0 0
LAMC1 -0.011 0.13 -10000 0 -0.37 70 70
TGIF2/HDAC complex/SMAD3/SMAD4 -0.008 0.076 -10000 0 -0.24 45 45
IRF7 -0.004 0.073 -10000 0 -0.38 24 24
ESR1 0.01 0.014 -10000 0 -0.33 1 1
HNF4A -0.012 0.071 -10000 0 -0.33 32 32
MEF2C -0.092 0.11 -10000 0 -0.31 38 38
SMAD2-3/SMAD4 -0.025 0.047 -10000 0 -0.21 14 14
Cbp/p300/Src-1 0.028 0.02 -10000 0 -10000 0 0
IGHV3OR16-13 -0.008 0.021 -10000 0 -10000 0 0
TGIF2/HDAC complex -0.009 0.083 -10000 0 -0.37 33 33
CREBBP 0.015 0.006 -10000 0 -10000 0 0
SKIL 0.01 0 -10000 0 -10000 0 0
HDAC1 0.009 0.015 -10000 0 -0.37 1 1
HDAC2 0.009 0.001 -10000 0 -10000 0 0
SNIP1 0.008 0.003 -10000 0 -10000 0 0
GCN5L2 0.006 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.004 0.085 -10000 0 -0.24 58 58
MSG1/HSC70 -0.009 0.05 -10000 0 -0.25 27 27
SMAD2 -0.016 0.017 -10000 0 -10000 0 0
SMAD3 0.005 0.042 -10000 0 -0.16 3 3
SMAD3/E2F4-5/DP1/p107/SMAD4 0.015 0.045 -10000 0 -0.2 5 5
SMAD2/SMAD2/SMAD4 0 0.021 -10000 0 -10000 0 0
NCOR1 0.009 0.001 -10000 0 -10000 0 0
NCOA2 0.004 0.044 -10000 0 -0.32 12 12
NCOA1 0.01 0 -10000 0 -10000 0 0
MYOD/E2A -0.097 0.12 -10000 0 -0.25 257 257
SMAD2-3/SMAD4/SP1/MIZ-1 0 0.071 -10000 0 -0.24 12 12
IFNB1 0.002 0.068 -10000 0 -0.36 9 9
SMAD3/SMAD4/MEF2C -0.082 0.12 -10000 0 -0.31 57 57
CITED1 -0.006 0.075 -10000 0 -0.37 27 27
SMAD2-3/SMAD4/ARC105 -0.018 0.038 -10000 0 -0.19 4 4
RBL1 -0.005 0.074 -10000 0 -0.37 26 26
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.01 0.06 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.029 0.082 -10000 0 -0.24 82 82
SMAD7 0.021 0.071 -10000 0 -10000 0 0
MYC/MIZ-1 -0.075 0.12 -10000 0 -0.25 223 223
SMAD3/SMAD4 0.042 0.1 -10000 0 -0.29 5 5
IL10 -0.054 0.17 -10000 0 -0.4 95 95
PIASy/HDAC complex 0.004 0.006 -10000 0 -10000 0 0
PIAS3 0.012 0.003 -10000 0 -10000 0 0
CDK2 -0.11 0.18 -10000 0 -0.37 217 217
IL5 -0.039 0.13 -10000 0 -0.34 64 64
CDK4 -0.04 0.14 -10000 0 -0.37 96 96
PIAS4 0.004 0.006 -10000 0 -10000 0 0
ATF3 0.005 0.044 -10000 0 -0.37 9 9
SMAD3/SMAD4/SP1 -0.004 0.081 -10000 0 -0.25 29 29
FOXG1 0 0.058 -10000 0 -0.32 21 21
FOXO3 0.014 0.017 -10000 0 -0.25 1 1
FOXO1 0.015 0.017 -10000 0 -0.25 1 1
FOXO4 0.014 0.019 -10000 0 -0.23 2 2
heart looping -0.091 0.11 -10000 0 -0.31 38 38
CEBPB 0.008 0.021 -10000 0 -0.37 2 2
SMAD3/SMAD4/DLX1 -0.066 0.1 -10000 0 -0.23 67 67
MYOD1 -0.14 0.18 -10000 0 -0.37 251 251
SMAD3/SMAD4/HNF4 -0.009 0.065 -10000 0 -0.21 25 25
SMAD3/SMAD4/GATA3 -0.059 0.14 -10000 0 -0.33 99 99
SnoN/SIN3/HDAC complex/NCoR1 0.01 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.013 0.1 -10000 0 -0.28 60 60
SMAD3/SMAD4/SP1-3 0.011 0.072 -10000 0 -0.24 10 10
MED15 0.01 0 -10000 0 -10000 0 0
SP1 0.002 0.03 -10000 0 -10000 0 0
SIN3B 0.009 0.001 -10000 0 -10000 0 0
SIN3A 0.009 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.11 0.11 -10000 0 -0.26 168 168
ITGB5 0.02 0.065 -10000 0 -0.24 1 1
TGIF/SIN3/HDAC complex/CtBP 0.023 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.11 0.13 -10000 0 -0.23 343 343
AR -0.18 0.19 -10000 0 -0.37 337 337
negative regulation of cell growth 0.019 0.045 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.086 0.11 -10000 0 -0.21 263 263
E2F5 -0.004 0.071 -10000 0 -0.37 24 24
E2F4 0.01 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.017 0.028 -10000 0 -0.2 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.008 0.051 -10000 0 -10000 0 0
TFDP1 0.01 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.023 0.051 -10000 0 -0.25 1 1
SMAD3/SMAD4/RUNX2 0.001 0.062 -10000 0 -0.25 19 19
TGIF2 -0.009 0.083 -10000 0 -0.37 33 33
TGIF1 -0.06 0.15 -10000 0 -0.37 122 122
ATF2 0.009 0.013 -10000 0 -0.32 1 1
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.01 0 -10000 0 -10000 0 0
HDAC4 0.01 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.016 0.03 0.25 8 -10000 0 8
CDKN1A -0.029 0.079 -10000 0 -0.21 103 103
KAT2B 0.009 0.015 -10000 0 -0.37 1 1
BAX 0.01 0 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 0.01 0 -10000 0 -10000 0 0
FOXO4 0.018 0.009 -10000 0 -0.21 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.01 0 -10000 0 -10000 0 0
TAT -0.041 0.13 -10000 0 -0.37 87 87
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.087 0.13 -10000 0 -0.25 252 252
PPARGC1A 0.008 0.022 -10000 0 -0.32 3 3
FHL2 -0.013 0.084 -10000 0 -0.32 45 45
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.009 0.02 -10000 0 -10000 0 0
HIST2H4A 0.016 0.031 -10000 0 -0.25 8 8
SIRT1/FOXO3a 0.007 0.016 -10000 0 -10000 0 0
SIRT1 0.01 0.024 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.009 0.022 -10000 0 -0.17 1 1
SIRT1/Histone H1b 0.008 0.025 -10000 0 -10000 0 0
apoptosis -0.009 0.021 -10000 0 -10000 0 0
SIRT1/PGC1A 0.007 0.022 -10000 0 -0.18 3 3
p53/SIRT1 -0.001 0.1 0.18 89 -0.25 67 156
SIRT1/FOXO4 0.009 0.024 -10000 0 -0.17 1 1
FOXO1/FHL2/SIRT1 -0.002 0.045 -10000 0 -0.15 45 45
HIST1H1E 0.016 0.013 -10000 0 -10000 0 0
SIRT1/p300 0.009 0.02 -10000 0 -10000 0 0
muscle cell differentiation 0.07 0.1 0.2 252 -10000 0 252
TP53 -0.029 0.12 -10000 0 -0.37 67 67
KU70/SIRT1/BAX 0.009 0.021 -10000 0 -10000 0 0
CREBBP 0.01 0 -10000 0 -10000 0 0
MEF2D 0.009 0.013 -10000 0 -0.32 1 1
HIV-1 Tat/SIRT1 -0.026 0.089 -10000 0 -0.25 87 87
ACSS2 0.019 0.008 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.07 0.1 -10000 0 -0.2 252 252
Canonical Wnt signaling pathway

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
HDAC1 0.01 0.021 -10000 0 -0.38 1 1
AES 0.01 0.013 -10000 0 -10000 0 0
FBXW11 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.003 0.029 -10000 0 -0.25 9 9
SMAD4 0.01 0 -10000 0 -10000 0 0
DKK2 -0.04 0.12 -10000 0 -0.33 98 98
TLE1 0.01 0.013 -10000 0 -10000 0 0
MACF1 0.011 0 -10000 0 -10000 0 0
CTNNB1 0.092 0.071 0.19 54 -10000 0 54
WIF1 -0.2 0.16 -10000 0 -0.32 417 417
beta catenin/RanBP3 0.062 0.097 0.27 47 -10000 0 47
KREMEN2 0.006 0.04 -10000 0 -0.36 8 8
DKK1 -0.03 0.12 -10000 0 -0.37 71 71
beta catenin/beta TrCP1 0.093 0.067 0.18 54 -10000 0 54
FZD1 0.006 0.042 -10000 0 -0.37 8 8
AXIN2 -0.009 0.036 -10000 0 -10000 0 0
AXIN1 0.011 0.001 -10000 0 -10000 0 0
RAN 0.01 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.023 0.031 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.086 0.039 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.003 0.019 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.058 0.055 -10000 0 -10000 0 0
HNF1A 0.01 0.014 -10000 0 -10000 0 0
CTBP1 0.01 0.014 -10000 0 -10000 0 0
MYC -0.074 0.12 -10000 0 -10000 0 0
RANBP3 0.01 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.027 0.065 -10000 0 -0.18 104 104
NKD1 -0.053 0.14 -10000 0 -0.38 109 109
TCF4 0.01 0.014 -10000 0 -10000 0 0
TCF3 0.006 0.041 -10000 0 -0.37 7 7
WNT1/LRP6/FZD1/Axin1 -0.013 0.042 -10000 0 -0.17 10 10
Ran/GTP 0 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.057 0.084 0.29 25 -10000 0 25
LEF1 0 0.062 -10000 0 -0.37 17 17
DVL1 0.007 0.021 -10000 0 -10000 0 0
CSNK2A1 0.01 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.071 0.049 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.024 0.065 -10000 0 -0.2 79 79
LRP6 0.01 0.015 -10000 0 -0.37 1 1
CSNK1A1 0.011 0.015 -10000 0 -10000 0 0
NLK 0.007 0.005 -10000 0 -10000 0 0
CCND1 -0.022 0.074 -10000 0 -10000 0 0
WNT1 -0.017 0.089 -10000 0 -0.32 52 52
GSK3A 0.011 0.001 -10000 0 -10000 0 0
GSK3B 0.01 0 -10000 0 -10000 0 0
FRAT1 0.01 0 -10000 0 -10000 0 0
PPP2R5D 0.06 0.064 0.2 109 -10000 0 109
APC 0.013 0.046 -10000 0 -0.16 4 4
WNT1/LRP6/FZD1 0.1 0.095 0.18 374 -10000 0 374
CREBBP 0.01 0.014 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.035 0.088 -9999 0 -0.25 93 93
PDGFRB 0.007 0.03 -9999 0 -0.38 4 4
SPHK1 -0.01 0.04 -9999 0 -0.86 1 1
mol:S1P -0.012 0.043 -9999 0 -0.53 2 2
S1P1/S1P/Gi -0.018 0.13 -9999 0 -0.32 98 98
GNAO1 0.004 0.045 -9999 0 -0.33 12 12
PDGFB-D/PDGFRB/PLCgamma1 -0.008 0.12 -9999 0 -0.29 92 92
PLCG1 -0.011 0.13 -9999 0 -0.3 95 95
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.007 0.03 -9999 0 -0.38 4 4
GNAI2 0.01 0.004 -9999 0 -10000 0 0
GNAI3 0.008 0.022 -9999 0 -0.38 2 2
GNAI1 0.005 0.037 -9999 0 -0.33 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.019 0.077 -9999 0 -0.21 93 93
S1P1/S1P -0.035 0.062 -9999 0 -0.32 6 6
negative regulation of cAMP metabolic process -0.017 0.13 -9999 0 -0.31 98 98
MAPK3 -0.034 0.19 -9999 0 -0.49 94 94
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.004 0.042 -9999 0 -0.38 8 8
PLCB2 -0.003 0.072 -9999 0 -0.31 5 5
RAC1 0.01 0 -9999 0 -10000 0 0
RhoA/GTP -0.03 0.053 -9999 0 -0.3 5 5
receptor internalization -0.033 0.059 -9999 0 -0.3 6 6
PTGS2 -0.089 0.33 -9999 0 -0.92 90 90
Rac1/GTP -0.03 0.053 -9999 0 -0.3 5 5
RHOA 0.01 0 -9999 0 -10000 0 0
VEGFA -0.04 0.13 -9999 0 -0.37 86 86
negative regulation of T cell proliferation -0.017 0.13 -9999 0 -0.31 98 98
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.008 0.019 -9999 0 -0.33 2 2
MAPK1 -0.034 0.19 -9999 0 -0.49 94 94
S1P1/S1P/PDGFB-D/PDGFRB -0.007 0.085 -9999 0 -0.36 7 7
ABCC1 0.009 0.016 -9999 0 -0.39 1 1
Ephrin B reverse signaling

Figure S63.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S63.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.009 0.018 -10000 0 -0.32 2 2
EPHB2 0.008 0.021 -10000 0 -0.38 2 2
EFNB1 -0.11 0.12 -10000 0 -0.22 367 367
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.068 0.068 -10000 0 -0.28 21 21
Ephrin B2/EPHB1-2 -0.005 0.03 -10000 0 -0.18 19 19
neuron projection morphogenesis -0.065 0.065 -10000 0 -0.27 21 21
Ephrin B1/EPHB1-2/Tiam1 -0.074 0.078 -10000 0 -0.31 21 21
DNM1 -0.17 0.17 -10000 0 -0.32 367 367
cell-cell signaling -0.001 0.001 -10000 0 -10000 0 0
MAP2K4 0.015 0.007 -10000 0 -10000 0 0
YES1 0.003 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK2 -0.074 0.077 -10000 0 -0.3 21 21
PI3K 0.015 0.007 -10000 0 -10000 0 0
mol:GDP -0.076 0.075 -10000 0 -0.31 21 21
ITGA2B 0.006 0.034 -10000 0 -0.32 7 7
endothelial cell proliferation -0.017 0.057 -10000 0 -0.21 55 55
FYN 0.003 0.005 -10000 0 -10000 0 0
MAP3K7 0.003 0.006 -10000 0 -10000 0 0
FGR 0.001 0.004 -10000 0 -10000 0 0
TIAM1 0.009 0.013 -10000 0 -0.32 1 1
PIK3R1 0.01 0 -10000 0 -10000 0 0
RGS3 0.01 0 -10000 0 -10000 0 0
cell adhesion -0.009 0.071 -10000 0 -0.31 1 1
LYN 0.003 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/Src Family Kinases 0.001 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 -0.002 0.006 -10000 0 -10000 0 0
SRC 0.001 0.003 -10000 0 -10000 0 0
ITGB3 -0.064 0.15 -10000 0 -0.37 128 128
EPHB1 0.001 0.056 -10000 0 -0.35 16 16
EPHB4 -0.021 0.1 -10000 0 -0.37 53 53
RAC1 0.01 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.017 0.057 -10000 0 -0.21 55 55
alphaIIb/beta3 Integrin -0.05 0.1 -10000 0 -0.25 134 134
BLK 0 0.009 -10000 0 -10000 0 0
HCK 0.003 0.006 -10000 0 -10000 0 0
regulation of stress fiber formation 0.076 0.074 0.3 21 -10000 0 21
MAPK8 0.019 0.015 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/RGS3 -0.074 0.077 -10000 0 -0.3 21 21
endothelial cell migration -0.008 0.049 -10000 0 -0.19 8 8
NCK2 0.01 0 -10000 0 -10000 0 0
PTPN13 0.009 0.015 -10000 0 -0.34 1 1
regulation of focal adhesion formation 0.076 0.074 0.3 21 -10000 0 21
chemotaxis 0.076 0.074 0.3 21 -10000 0 21
PIK3CA 0.01 0 -10000 0 -10000 0 0
Rac1/GTP -0.066 0.066 -10000 0 -0.28 21 21
angiogenesis -0.002 0.006 -10000 0 -10000 0 0
LCK -0.003 0.008 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.01 0 -9999 0 -10000 0 0
LAT2 -0.005 0.06 -9999 0 -0.28 8 8
AP1 -0.016 0.039 -9999 0 -0.28 3 3
mol:PIP3 0.003 0.078 -9999 0 -0.31 10 10
IKBKB -0.017 0.068 -9999 0 -0.18 35 35
AKT1 -0.017 0.097 -9999 0 -0.26 54 54
IKBKG -0.017 0.068 -9999 0 -0.18 35 35
MS4A2 -0.003 0.005 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.01 0.001 -9999 0 -10000 0 0
MAP3K1 0.014 0.057 -9999 0 -0.28 5 5
mol:Ca2+ 0.005 0.064 -9999 0 -0.24 10 10
LYN 0.007 0.027 -9999 0 -0.39 3 3
CBLB -0.01 0.063 -9999 0 -0.24 12 12
SHC1 -0.001 0.064 -9999 0 -0.38 19 19
RasGAP/p62DOK -0.002 0.018 -9999 0 -0.18 7 7
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.007 0.033 -9999 0 -0.37 5 5
PLD2 -0.045 0.11 -9999 0 -0.25 93 93
PTPN13 0.008 0.046 -9999 0 -10000 0 0
PTPN11 0.008 0.005 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.017 0.061 -9999 0 -0.21 3 3
SYK 0.003 0.048 -9999 0 -0.38 10 10
GRB2 0.01 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.034 0.062 -9999 0 -0.27 18 18
LAT -0.004 0.058 -9999 0 -0.27 7 7
PAK2 0.014 0.055 -9999 0 -0.28 6 6
NFATC2 -0.032 0.059 -9999 0 -0.24 26 26
HRAS 0.009 0.058 -9999 0 -0.31 6 6
GAB2 0.01 0 -9999 0 -10000 0 0
PLA2G1B 0.026 0.012 -9999 0 -10000 0 0
Fc epsilon R1 -0.084 0.13 -9999 0 -0.25 224 224
Antigen/IgE/Fc epsilon R1 -0.076 0.12 -9999 0 -0.23 224 224
mol:GDP 0.006 0.056 -9999 0 -0.31 6 6
JUN 0.01 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.001 -9999 0 -10000 0 0
FOS 0.001 0.056 -9999 0 -0.35 16 16
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.028 0.049 -9999 0 -0.25 8 8
CHUK -0.017 0.068 -9999 0 -0.18 35 35
KLRG1 -0.009 0.061 -9999 0 -0.2 18 18
VAV1 -0.005 0.061 -9999 0 -0.3 7 7
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.004 0.056 -9999 0 -0.25 7 7
negative regulation of mast cell degranulation -0.004 0.062 -9999 0 -0.29 9 9
BTK -0.02 0.042 -9999 0 -0.27 6 6
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.042 0.09 -9999 0 -0.2 128 128
GAB2/PI3K/SHP2 -0.052 0.085 -9999 0 -0.28 53 53
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.016 0.067 -9999 0 -0.19 57 57
RAF1 0.018 0.015 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.16 -9999 0 -0.4 135 135
FCER1G -0.043 0.13 -9999 0 -0.38 90 90
FCER1A -0.097 0.17 -9999 0 -0.37 187 187
Antigen/IgE/Fc epsilon R1/Fyn -0.068 0.11 -9999 0 -0.2 224 224
MAPK3 0.025 0.012 -9999 0 -10000 0 0
MAPK1 0.025 0.012 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
MAPK8 0.013 0.052 -9999 0 -0.54 5 5
DUSP1 0.008 0.03 -9999 0 -0.37 4 4
NF-kappa-B/RelA -0.021 0.03 -9999 0 -0.16 3 3
actin cytoskeleton reorganization 0.002 0.046 -9999 0 -0.26 1 1
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.018 0.045 -9999 0 -0.32 6 6
FER -0.004 0.056 -9999 0 -0.25 7 7
RELA 0.01 0 -9999 0 -10000 0 0
ITK -0.028 0.076 -9999 0 -0.28 51 51
SOS1 0.01 0 -9999 0 -10000 0 0
PLCG1 0.008 0.06 -9999 0 -0.32 6 6
cytokine secretion -0.016 0.022 -9999 0 -10000 0 0
SPHK1 -0.006 0.06 -9999 0 -0.26 12 12
PTK2 0.002 0.047 -9999 0 -0.27 1 1
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.036 0.065 -9999 0 -0.28 18 18
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG 0.005 0.077 -9999 0 -0.3 9 9
MAP2K2 0.022 0.013 -9999 0 -10000 0 0
MAP2K1 0.022 0.013 -9999 0 -10000 0 0
MAP2K7 0.01 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.027 0.051 -9999 0 -0.25 9 9
MAP2K4 0.016 0.005 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.13 0.17 -9999 0 -0.29 293 293
mol:Choline -0.044 0.11 -9999 0 -0.25 93 93
SHC/Grb2/SOS1 -0.024 0.054 -9999 0 -0.26 20 20
FYN 0.01 0 -9999 0 -10000 0 0
DOK1 0.008 0.026 -9999 0 -0.37 3 3
PXN 0.008 0.045 -9999 0 -10000 0 0
HCLS1 -0.009 0.073 -9999 0 -0.31 20 20
PRKCB -0.031 0.087 -9999 0 -0.24 38 38
FCGR2B -0.1 0.17 -9999 0 -0.37 193 193
IGHE -0.001 0.004 -9999 0 -10000 0 0
KLRG1/SHIP -0.004 0.063 -9999 0 -0.3 9 9
LCP2 0.008 0.03 -9999 0 -0.38 4 4
PLA2G4A -0.006 0.061 -9999 0 -0.26 11 11
RASA1 0.01 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.044 0.11 -9999 0 -0.25 93 93
IKK complex -0.003 0.056 -9999 0 -0.16 10 10
WIPF1 0.009 0.015 -9999 0 -0.37 1 1
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.026 0.063 0.31 12 -10000 0 12
GNAI2 0.01 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.027 0.063 -10000 0 -0.18 101 101
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.044 -10000 0 -0.32 12 12
RhoA/GTP -0.027 0.064 -10000 0 -0.32 12 12
negative regulation of cAMP metabolic process -0.007 0.082 -10000 0 -0.18 109 109
GNAZ 0.009 0.018 -10000 0 -0.32 2 2
GNAI3 0.009 0.021 -10000 0 -0.37 2 2
GNA12 0.01 0 -10000 0 -10000 0 0
S1PR5 -0.041 0.12 -10000 0 -0.32 101 101
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.008 0.083 -10000 0 -0.18 109 109
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
GNAI1 0.006 0.036 -10000 0 -0.32 8 8
IFN-gamma 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.023 0.023 -9999 0 -0.17 3 3
positive regulation of NF-kappaB transcription factor activity -0.001 0.002 -9999 0 -10000 0 0
CRKL 0.009 0.015 -9999 0 -0.37 1 1
STAT1 (dimer)/Cbp/p300 -0.003 0.053 -9999 0 -0.32 7 7
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.008 -9999 0 -0.19 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.063 0.08 -9999 0 -0.21 111 111
CaM/Ca2+ -0.002 0.014 -9999 0 -10000 0 0
RAP1A 0.01 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.032 0.033 -9999 0 -0.19 7 7
AKT1 0.04 0.02 -9999 0 -10000 0 0
MAP2K1 0.034 0.035 -9999 0 -10000 0 0
MAP3K11 0.033 0.021 -9999 0 -10000 0 0
IFNGR1 0.011 0.015 -9999 0 -0.37 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.24 0.17 -9999 0 -0.34 463 463
Rap1/GTP -0.003 0.017 -9999 0 -0.22 1 1
CRKL/C3G 0 0.01 -9999 0 -0.25 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.002 0.016 -9999 0 -10000 0 0
CEBPB 0.056 0.029 -9999 0 -10000 0 0
STAT3 0.01 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.056 0.084 -9999 0 -10000 0 0
STAT1 0.033 0.033 -9999 0 -0.19 7 7
CALM1 0.01 0 -9999 0 -10000 0 0
IFN-gamma (dimer) 0.001 0.038 -9999 0 -0.37 7 7
PIK3CA 0.01 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.037 0.032 -9999 0 -0.19 4 4
CEBPB/PTGES2/Cbp/p300 -0.004 0.017 -9999 0 -0.23 1 1
mol:Ca2+ -0.002 0.015 -9999 0 -0.17 3 3
MAPK3 0.041 0.028 -9999 0 -10000 0 0
STAT1 (dimer) -0.082 0.11 -9999 0 -0.29 111 111
MAPK1 0.041 0.028 -9999 0 -10000 0 0
JAK2 0.011 0.002 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
JAK1 0.011 0.002 -9999 0 -10000 0 0
CAMK2D 0.009 0.013 -9999 0 -0.32 1 1
DAPK1 0.053 0.022 -9999 0 -10000 0 0
SMAD7 -0.016 0.056 -9999 0 -0.13 32 32
CBL/CRKL/C3G -0.001 0.013 -9999 0 -10000 0 0
PI3K -0.001 0.013 -9999 0 -10000 0 0
IFNG 0.001 0.038 -9999 0 -0.37 7 7
apoptosis 0.029 0.025 -9999 0 -10000 0 0
CAMK2G 0.01 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.01 0 -9999 0 -10000 0 0
CAMK2A -0.22 0.15 -9999 0 -0.32 463 463
CAMK2B -0.091 0.15 -9999 0 -0.32 201 201
FRAP1 0.039 0.019 -9999 0 -10000 0 0
PRKCD 0.041 0.02 -9999 0 -10000 0 0
RAP1B 0.005 0.044 -9999 0 -0.37 9 9
negative regulation of cell growth -0.063 0.08 -9999 0 -0.21 111 111
PTPN2 0.01 0 -9999 0 -10000 0 0
EP300 0.01 0.001 -9999 0 -10000 0 0
IRF1 0.003 0.11 -9999 0 -0.39 41 41
STAT1 (dimer)/PIASy 0.022 0.046 -9999 0 -0.23 1 1
SOCS1 -0.075 0.11 -9999 0 -10000 0 0
mol:GDP -0.001 0.012 -9999 0 -10000 0 0
CASP1 -0.035 0.092 -9999 0 -0.22 114 114
PTGES2 0.01 0 -9999 0 -10000 0 0
IRF9 0.039 0.023 -9999 0 -0.2 3 3
mol:PI-3-4-5-P3 -0.001 0.013 -9999 0 -10000 0 0
RAP1/GDP -0.003 0.017 -9999 0 -0.22 1 1
CBL 0.032 0.021 -9999 0 -10000 0 0
MAP3K1 0.028 0.037 -9999 0 -0.16 1 1
PIAS1 0.01 0 -9999 0 -10000 0 0
PIAS4 0.011 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.063 0.08 -9999 0 -0.21 111 111
PTPN11 0.027 0.021 -9999 0 -0.17 3 3
CREBBP 0.01 0.001 -9999 0 -10000 0 0
RAPGEF1 0.01 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.01 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.004 0.023 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.003 0.02 -9999 0 -10000 0 0
POMC 0.008 0.027 -9999 0 -0.34 4 4
EGFR -0.21 0.19 -9999 0 -0.37 377 377
Syndecan-3/EGFR -0.091 0.08 -9999 0 -0.25 2 2
AGRP 0.005 0.03 -9999 0 -0.37 4 4
NCSTN 0.01 0 -9999 0 -10000 0 0
PSENEN 0.01 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.01 0 -9999 0 -10000 0 0
APH1A 0.01 0 -9999 0 -10000 0 0
NCAN 0.003 0.049 -9999 0 -0.34 14 14
long-term memory 0 0.003 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.033 0.061 -9999 0 -0.22 1 1
PSEN1 0.01 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.01 0 -9999 0 -10000 0 0
limb bud formation 0 0.004 -9999 0 -10000 0 0
MC4R -0.082 0.15 -9999 0 -0.32 182 182
SRC 0.01 0 -9999 0 -10000 0 0
PTN -0.001 0.063 -9999 0 -0.37 19 19
FGFR/FGF/Syndecan-3 0 0.004 -9999 0 -10000 0 0
neuron projection morphogenesis -0.005 0.025 -9999 0 -0.24 1 1
Syndecan-3/AgRP -0.001 0.013 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.035 0.057 -9999 0 -0.27 2 2
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 0 0.004 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.032 0.06 -9999 0 -0.22 1 1
IL8 -0.069 0.15 -9999 0 -0.34 149 149
Syndecan-3/Fyn/Cortactin 0 0.003 -9999 0 -10000 0 0
Syndecan-3/CASK 0 0.004 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.059 0.096 -9999 0 -0.21 186 186
Gamma Secretase 0 0 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0 0 -10000 0 -10000 0 0
TRAF2/ASK1 0 0 -10000 0 -10000 0 0
ATM 0.01 0 -10000 0 -10000 0 0
MAP2K3 0.013 0.032 -10000 0 -0.21 2 2
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.014 0.032 -10000 0 -0.25 2 2
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.11 0.18 -10000 0 -0.37 203 203
TXN 0.007 0 -10000 0 -10000 0 0
CALM1 0.01 0 -10000 0 -10000 0 0
GADD45A -0.019 0.1 -10000 0 -0.37 50 50
GADD45B 0.003 0.051 -10000 0 -0.37 12 12
MAP3K1 -0.002 0.067 -10000 0 -0.37 21 21
MAP3K6 0.009 0.015 -10000 0 -0.37 1 1
MAP3K7 0.01 0 -10000 0 -10000 0 0
MAP3K4 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0 0.01 -10000 0 -0.25 1 1
TAK1/TAB family 0 0.007 0.13 2 -10000 0 2
RAC1/OSM/MEKK3 0 0.007 -10000 0 -0.18 1 1
TRAF2 0.01 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.003 0.013 -10000 0 -10000 0 0
TRAF6 0.007 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.09 0.15 -10000 0 -0.32 201 201
CCM2 0.009 0.015 -10000 0 -0.37 1 1
CaM/Ca2+/CAMKIIB -0.053 0.081 -10000 0 -0.18 201 201
MAPK11 0.009 0.018 -10000 0 -0.32 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.045 0.069 -10000 0 -0.15 201 201
OSM/MEKK3 0 0.01 -10000 0 -0.25 1 1
TAOK1 0.009 0.035 -10000 0 -0.24 13 13
TAOK2 0.014 0 -10000 0 -10000 0 0
TAOK3 0.014 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.01 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.01 0 -10000 0 -10000 0 0
MAP3K10 0.008 0.026 -10000 0 -0.32 4 4
MAP3K3 0.01 0 -10000 0 -10000 0 0
TRX/ASK1 0.012 0 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 -0.065 0.09 -10000 0 -0.18 248 248
Syndecan-2-mediated 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
Syndecan-2/Fibronectin -0.013 0.079 -9999 0 -0.21 96 96
EPHB2 0.009 0.021 -9999 0 -0.37 2 2
Syndecan-2/TACI 0.005 0.019 -9999 0 -0.2 4 4
LAMA1 -0.013 0.089 -9999 0 -0.37 40 40
Syndecan-2/alpha2 ITGB1 -0.012 0.044 -9999 0 -0.18 28 28
HRAS 0.01 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0 0.008 -9999 0 -0.21 1 1
ITGA5 -0.042 0.13 -9999 0 -0.37 91 91
BAX 0.031 0.008 -9999 0 -10000 0 0
EPB41 0.005 0.042 -9999 0 -0.37 8 8
positive regulation of cell-cell adhesion 0 0.007 -9999 0 -0.18 1 1
LAMA3 -0.005 0.068 -9999 0 -0.33 29 29
EZR 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.001 0.059 -9999 0 -0.37 16 16
Syndecan-2/MMP2 -0.031 0.094 -9999 0 -0.2 150 150
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.01 0.051 -9999 0 -0.26 26 26
dendrite morphogenesis 0.018 0.015 -9999 0 -0.2 3 3
Syndecan-2/GM-CSF 0 0.008 -9999 0 -0.21 1 1
determination of left/right symmetry 0.015 0.01 -9999 0 -0.25 1 1
Syndecan-2/PKC delta 0.016 0.023 -9999 0 -0.17 10 10
GNB2L1 0.001 0.059 -9999 0 -0.37 16 16
MAPK3 0.019 0.008 -9999 0 -0.18 1 1
MAPK1 0.019 0.008 -9999 0 -0.18 1 1
Syndecan-2/RACK1 -0.004 0.026 -9999 0 -0.16 17 17
NF1 0.01 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.015 0.01 -9999 0 -0.25 1 1
ITGA2 0.001 0.057 -9999 0 -0.37 15 15
MAPK8 0.026 0.019 -9999 0 -0.2 1 1
Syndecan-2/alpha2/beta1 Integrin -0.016 0.049 -9999 0 -0.16 59 59
Syndecan-2/Kininogen 0.002 0.028 -9999 0 -0.2 11 11
ITGB1 0.003 0.051 -9999 0 -0.37 12 12
SRC 0.025 0.028 -9999 0 -0.15 17 17
Syndecan-2/CASK/Protein 4.1 -0.002 0.021 -9999 0 -0.18 9 9
extracellular matrix organization 0.018 0.012 -9999 0 -0.2 2 2
actin cytoskeleton reorganization -0.013 0.079 -9999 0 -0.2 96 96
Syndecan-2/Caveolin-2/Ras -0.004 0.03 -9999 0 -0.19 16 16
Syndecan-2/Laminin alpha3 0.011 0.041 -9999 0 -0.18 29 29
Syndecan-2/RasGAP -0.004 0.024 -9999 0 -0.15 17 17
alpha5/beta1 Integrin -0.038 0.099 -9999 0 -0.28 93 93
PRKCD 0.005 0.039 -9999 0 -0.32 9 9
Syndecan-2 dimer 0.018 0.015 -9999 0 -0.2 3 3
GO:0007205 0.003 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.03 0.027 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
SDCBP 0.01 0 -9999 0 -10000 0 0
TNFRSF13B 0.002 0.026 -9999 0 -0.37 3 3
RASA1 0.01 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.01 0.051 -9999 0 -0.26 26 26
Syndecan-2/Synbindin 0.019 0.009 -9999 0 -0.2 1 1
TGFB1 0.009 0.015 -9999 0 -0.37 1 1
CASP3 0.022 0.028 -9999 0 -0.17 13 13
FN1 -0.045 0.14 -9999 0 -0.37 96 96
Syndecan-2/IL8 -0.026 0.086 -9999 0 -0.18 149 149
SDC2 0.015 0.01 -9999 0 -0.25 1 1
KNG1 -0.003 0.046 -9999 0 -0.37 10 10
Syndecan-2/Neurofibromin 0.019 0.009 -9999 0 -0.2 1 1
TRAPPC4 0.01 0 -9999 0 -10000 0 0
CSF2 0 0 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.019 0.012 -9999 0 -0.2 2 2
Syndecan-2/Syntenin/PI-4-5-P2 0 0.007 -9999 0 -0.18 1 1
Syndecan-2/Ezrin 0 0.007 -9999 0 -0.18 1 1
PRKACA 0.025 0.008 -9999 0 -0.17 1 1
angiogenesis -0.026 0.086 -9999 0 -0.18 149 149
MMP2 -0.076 0.16 -9999 0 -0.37 150 150
IL8 -0.069 0.15 -9999 0 -0.34 149 149
calcineurin-NFAT signaling pathway 0.005 0.019 -9999 0 -0.2 4 4
Signaling events mediated by PTP1B

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
PDGFRB 0.008 0.03 -10000 0 -0.37 4 4
Jak2/Leptin Receptor 0.002 0.057 0.17 50 -0.23 6 56
PTP1B/AKT1 -0.004 0.042 -10000 0 -0.22 1 1
FYN 0.01 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.012 0.046 -10000 0 -10000 0 0
EGFR -0.2 0.19 -10000 0 -0.37 377 377
EGF/EGFR -0.087 0.075 -10000 0 -0.19 135 135
CSF1 0.004 0.047 -10000 0 -0.37 10 10
AKT1 0.01 0.015 -10000 0 -0.37 1 1
INSR 0.01 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.005 0.043 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.005 0.03 -10000 0 -0.19 1 1
HCK 0.004 0.049 -10000 0 -0.37 11 11
CRK 0.01 0 -10000 0 -10000 0 0
TYK2 -0.006 0.043 -10000 0 -10000 0 0
EGF -0.006 0.07 -10000 0 -0.38 23 23
YES1 0.009 0.015 -10000 0 -0.37 1 1
CAV1 -0.025 0.057 -10000 0 -0.19 4 4
TXN 0.007 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.003 0.037 -10000 0 -10000 0 0
cell migration 0.012 0.046 -10000 0 -10000 0 0
STAT3 0.01 0.001 -10000 0 -10000 0 0
PRLR 0.004 0.048 -10000 0 -0.34 13 13
ITGA2B 0.006 0.034 -10000 0 -0.33 7 7
CSF1R 0.007 0.035 -10000 0 -0.37 6 6
Prolactin Receptor/Prolactin -0.001 0.04 -10000 0 -0.23 17 17
FGR 0.006 0.036 -10000 0 -0.37 6 6
PTP1B/p130 Cas -0.005 0.043 -10000 0 -10000 0 0
Crk/p130 Cas -0.003 0.037 -10000 0 -10000 0 0
DOK1 0.002 0.041 -10000 0 -0.2 1 1
JAK2 0.004 0.048 -10000 0 -0.23 8 8
Jak2/Leptin Receptor/Leptin -0.031 0.07 -10000 0 -0.28 23 23
PIK3R1 0.01 0 -10000 0 -10000 0 0
PTPN1 -0.012 0.046 -10000 0 -10000 0 0
LYN 0.008 0.026 -10000 0 -0.37 3 3
CDH2 0.01 0 -10000 0 -10000 0 0
SRC 0.007 0.02 -10000 0 -10000 0 0
ITGB3 -0.064 0.15 -10000 0 -0.37 128 128
CAT1/PTP1B -0.04 0.093 -10000 0 -0.23 63 63
CAPN1 0.01 0.002 -10000 0 -10000 0 0
CSK 0.01 0 -10000 0 -10000 0 0
PI3K -0.008 0.018 -10000 0 -10000 0 0
mol:H2O2 -0.001 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.032 0.076 -10000 0 -0.25 61 61
negative regulation of transcription 0.004 0.048 -10000 0 -0.23 8 8
FCGR2A -0.035 0.12 -10000 0 -0.37 79 79
FER 0.007 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.049 0.1 -10000 0 -0.25 134 134
BLK -0.054 0.14 -10000 0 -0.37 107 107
Insulin Receptor/Insulin/Shc -0.006 0.036 -10000 0 -0.21 20 20
RHOA 0.01 0.002 -10000 0 -10000 0 0
LEPR 0.009 0.026 -10000 0 -0.37 3 3
BCAR1 0.01 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.01 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.002 -10000 0 -10000 0 0
TRPV6 -0.036 0.087 -10000 0 -0.21 66 66
PRL 0 0.029 -10000 0 -0.37 4 4
SOCS3 -0.095 0.33 -10000 0 -1.2 55 55
SPRY2 0.007 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0 0.008 -10000 0 -0.2 1 1
CSF1/CSF1R -0.008 0.046 -10000 0 -0.21 7 7
Ras protein signal transduction 0.017 0.015 -10000 0 -10000 0 0
IRS1 0.01 0 -10000 0 -10000 0 0
INS 0 0.014 -10000 0 -0.37 1 1
LEP 0.004 0.015 -10000 0 -0.37 1 1
STAT5B -0.002 0.045 -10000 0 -0.17 2 2
STAT5A -0.002 0.045 -10000 0 -0.17 2 2
GRB2 0.01 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.006 0.045 -10000 0 -0.22 3 3
CSN2 0.005 0.02 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
LAT 0 0.036 -10000 0 -0.48 1 1
YBX1 0.01 0.046 -10000 0 -0.36 10 10
LCK -0.066 0.15 -10000 0 -0.37 132 132
SHC1 -0.001 0.064 -10000 0 -0.37 19 19
NOX4 -0.12 0.18 -10000 0 -0.38 224 224
Paxillin-dependent events mediated by a4b1

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
CRKL 0.009 0.015 -10000 0 -0.37 1 1
Rac1/GDP 0.006 0.013 -10000 0 -10000 0 0
DOCK1 0.01 0 -10000 0 -10000 0 0
ITGA4 -0.047 0.14 -10000 0 -0.37 99 99
RAC1 0.01 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.04 0.096 -10000 0 -0.26 103 103
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.034 0.083 -10000 0 -0.22 101 101
alpha4/beta7 Integrin/Paxillin -0.028 0.067 -10000 0 -0.18 103 103
lamellipodium assembly 0.007 0.016 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
PI3K 0 0 -10000 0 -10000 0 0
ARF6 0.01 0 -10000 0 -10000 0 0
TLN1 0.01 0 -10000 0 -10000 0 0
PXN 0.018 0 -10000 0 -10000 0 0
PIK3R1 0.01 0 -10000 0 -10000 0 0
ARF6/GTP -0.023 0.059 -10000 0 -0.31 10 10
cell adhesion -0.026 0.066 -10000 0 -0.34 10 10
CRKL/CBL 0 0.01 -10000 0 -0.25 1 1
alpha4/beta1 Integrin/Paxillin -0.029 0.073 -10000 0 -0.19 101 101
ITGB1 0.003 0.051 -10000 0 -0.37 12 12
ITGB7 0.005 0.042 -10000 0 -0.37 8 8
ARF6/GDP 0.006 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.082 0.11 -10000 0 -0.35 55 55
p130Cas/Crk/Dock1 0 0 -10000 0 -10000 0 0
VCAM1 -0.12 0.18 -10000 0 -0.37 231 231
alpha4/beta1 Integrin/Paxillin/Talin -0.026 0.066 -10000 0 -0.34 10 10
alpha4/beta1 Integrin/Paxillin/GIT1 -0.026 0.066 -10000 0 -0.34 10 10
BCAR1 0.01 0 -10000 0 -10000 0 0
mol:GDP 0.026 0.066 0.34 10 -10000 0 10
CBL 0.01 0 -10000 0 -10000 0 0
PRKACA 0.01 0 -10000 0 -10000 0 0
GIT1 0.01 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.026 0.066 -10000 0 -0.34 10 10
Rac1/GTP 0.007 0.017 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.028 0.076 -10000 0 -0.28 35 35
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.009 0.015 -10000 0 -0.37 1 1
AKT2 0.01 0 -10000 0 -10000 0 0
STXBP4 0.004 0.049 -10000 0 -0.37 11 11
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.031 0.12 0.17 170 -0.3 45 215
YWHAZ 0.01 0 -10000 0 -10000 0 0
CALM1 0.01 0 -10000 0 -10000 0 0
YWHAQ 0.01 0 -10000 0 -10000 0 0
TBC1D4 0.018 0.01 -10000 0 -0.25 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.004 0.044 -10000 0 -0.32 12 12
YWHAB 0.01 0 -10000 0 -10000 0 0
SNARE/Synip -0.003 0.026 -10000 0 -0.2 11 11
YWHAG 0.01 0 -10000 0 -10000 0 0
ASIP -0.13 0.18 -10000 0 -0.37 242 242
PRKCI 0.01 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.01 0 -10000 0 -10000 0 0
GYS1 0.025 0.005 -10000 0 -10000 0 0
PRKCZ -0.03 0.11 -10000 0 -0.32 79 79
TRIP10 0 0.06 -10000 0 -0.37 17 17
TC10/GTP/CIP4/Exocyst -0.005 0.033 -10000 0 -0.21 17 17
AS160/14-3-3 0.03 0.031 -10000 0 -0.23 1 1
VAMP2 0.01 0 -10000 0 -10000 0 0
SLC2A4 0.03 0.13 0.2 1 -0.33 45 46
STX4 0.01 0 -10000 0 -10000 0 0
GSK3B 0.02 0.006 -10000 0 -10000 0 0
SFN -0.008 0.079 -10000 0 -0.37 30 30
LNPEP 0.009 0.013 -10000 0 -0.32 1 1
YWHAE 0.01 0 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.016 0.035 -10000 0 -10000 0 0
epithelial cell differentiation -0.009 0.023 -10000 0 -10000 0 0
ITCH 0.014 0.009 -10000 0 -10000 0 0
WWP1 0.02 0.026 -10000 0 -10000 0 0
FYN 0.01 0 -10000 0 -10000 0 0
EGFR -0.21 0.19 -10000 0 -0.37 377 377
PRL -0.001 0.029 -10000 0 -0.37 4 4
neuron projection morphogenesis 0.013 0.069 -10000 0 -0.32 1 1
PTPRZ1 -0.051 0.14 -10000 0 -0.37 106 106
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.029 0.057 -10000 0 -0.27 7 7
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.005 0.057 -10000 0 -0.24 7 7
ADAM17 0.014 0.009 -10000 0 -10000 0 0
ErbB4/ErbB4 0.019 0.031 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.007 0.06 -10000 0 -0.28 22 22
NCOR1 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.031 0.057 -10000 0 -0.26 1 1
GRIN2B -0.046 0.11 -10000 0 -0.27 109 109
ErbB4/ErbB2/betacellulin -0.014 0.044 -10000 0 -0.27 7 7
STAT1 0.006 0.039 -10000 0 -0.37 7 7
HBEGF 0.01 0 -10000 0 -10000 0 0
PRLR 0.003 0.048 -10000 0 -0.34 13 13
E4ICDs/ETO2 0.012 0.048 -10000 0 -0.28 9 9
axon guidance 0.013 0.048 -10000 0 -10000 0 0
NEDD4 -0.037 0.13 -10000 0 -0.37 85 85
Prolactin receptor/Prolactin receptor/Prolactin -0.006 0.037 -10000 0 -0.24 17 17
CBFA2T3 -0.012 0.083 -10000 0 -0.32 44 44
ErbB4/ErbB2/HBEGF -0.006 0.022 -10000 0 -10000 0 0
MAPK3 0.007 0.071 -10000 0 -0.25 6 6
STAT1 (dimer) 0.013 0.041 -10000 0 -10000 0 0
MAPK1 0.007 0.071 -10000 0 -0.25 6 6
JAK2 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.033 0.059 -10000 0 -0.28 2 2
NRG1 -0.027 0.094 -10000 0 -0.22 134 134
NRG3 -0.032 0.11 -10000 0 -0.32 83 83
NRG2 0.009 0.018 -10000 0 -0.32 2 2
NRG4 -0.032 0.11 -10000 0 -0.32 82 82
heart development 0.013 0.048 -10000 0 -10000 0 0
neural crest cell migration -0.01 0.072 -10000 0 -0.28 2 2
ERBB2 0.017 0.031 -10000 0 -0.26 8 8
WWOX/E4ICDs 0.016 0.035 -10000 0 -10000 0 0
SHC1 -0.001 0.064 -10000 0 -0.37 19 19
ErbB4/EGFR/neuregulin 4 -0.12 0.1 -10000 0 -0.32 63 63
apoptosis 0.044 0.11 0.32 83 -10000 0 83
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.015 0.038 -10000 0 -0.27 2 2
ErbB4/ErbB2/epiregulin -0.011 0.039 -10000 0 -0.26 6 6
ErbB4/ErbB4/betacellulin/betacellulin 0.002 0.058 -10000 0 -0.28 9 9
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.008 0.03 -10000 0 -0.26 2 2
MDM2 0.019 0.04 -10000 0 -0.3 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.03 0.059 -10000 0 -0.24 1 1
STAT5A 0.019 0.045 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.12 0.11 -10000 0 -0.31 102 102
DLG4 0.009 0.013 -10000 0 -0.32 1 1
GRB2/SHC -0.007 0.042 -10000 0 -0.25 19 19
E4ICDs/TAB2/NCoR1 -0.008 0.024 -10000 0 -10000 0 0
STAT5A (dimer) -0.009 0.024 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.017 0.044 -10000 0 -10000 0 0
LRIG1 0.009 0.015 -10000 0 -0.37 1 1
EREG -0.004 0.065 -10000 0 -0.37 20 20
BTC -0.01 0.08 -10000 0 -0.37 31 31
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.013 0.048 -10000 0 -10000 0 0
ERBB4 0.019 0.031 -10000 0 -10000 0 0
STAT5B 0.01 0 -10000 0 -10000 0 0
YAP1 -0.001 0.007 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.023 0.05 -10000 0 -0.28 2 2
glial cell differentiation 0.008 0.024 -10000 0 -10000 0 0
WWOX 0.01 0 -10000 0 -10000 0 0
cell proliferation -0.01 0.087 -10000 0 -0.31 4 4
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.044 0.072 -10000 0 -10000 0 0
HDAC1 0.008 0.019 -10000 0 -0.38 1 1
AES 0.011 0.003 -10000 0 -10000 0 0
FBXW11 0.01 0 -10000 0 -10000 0 0
DTX1 0.008 0.026 -10000 0 -0.32 4 4
LRP6/FZD1 -0.003 0.029 -10000 0 -0.25 9 9
TLE1 0.011 0.002 -10000 0 -10000 0 0
AP1 -0.002 0.049 -10000 0 -0.2 9 9
NCSTN 0.01 0 -10000 0 -10000 0 0
ADAM10 0.01 0 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.003 0.046 -10000 0 -10000 0 0
NICD/RBPSUH -0.002 0.011 -10000 0 -10000 0 0
WIF1 -0.2 0.16 -10000 0 -0.32 417 417
NOTCH1 -0.002 0.012 -10000 0 -10000 0 0
PSENEN 0.01 0 -10000 0 -10000 0 0
KREMEN2 0.006 0.04 -10000 0 -0.36 8 8
DKK1 -0.03 0.12 -10000 0 -0.37 71 71
beta catenin/beta TrCP1 0.014 0.037 -10000 0 -10000 0 0
APH1B 0.01 0 -10000 0 -10000 0 0
APH1A 0.01 0 -10000 0 -10000 0 0
AXIN1 -0.003 0.016 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.038 0.031 -10000 0 -10000 0 0
PSEN1 0.01 0 -10000 0 -10000 0 0
FOS 0.001 0.056 -10000 0 -0.35 16 16
JUN 0.01 0 -10000 0 -10000 0 0
MAP3K7 0.011 0.004 -10000 0 -10000 0 0
CTNNB1 0.009 0.039 -10000 0 -10000 0 0
MAPK3 0.01 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.028 0.066 -10000 0 -0.18 104 104
HNF1A 0.011 0.003 -10000 0 -10000 0 0
CTBP1 0.011 0.003 -10000 0 -10000 0 0
MYC -0.068 0.12 -10000 0 -10000 0 0
NKD1 -0.052 0.14 -10000 0 -0.37 109 109
FZD1 0.005 0.042 -10000 0 -0.37 8 8
NOTCH1 precursor/Deltex homolog 1 -0.002 0.01 -10000 0 -10000 0 0
apoptosis -0.002 0.049 -10000 0 -0.2 9 9
Delta 1/NOTCHprecursor -0.044 0.072 -10000 0 -10000 0 0
DLL1 -0.093 0.17 -10000 0 -0.37 180 180
PPARD 0.006 0.019 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.003 0.016 -10000 0 -10000 0 0
DVL1 -0.016 0.016 -10000 0 -10000 0 0
CSNK2A1 0.009 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.024 0.065 -10000 0 -0.2 79 79
LRP6 0.009 0.015 -10000 0 -0.38 1 1
CSNK1A1 0.009 0.002 -10000 0 -10000 0 0
NLK 0.016 0.009 -10000 0 -10000 0 0
CCND1 -0.009 0.068 -10000 0 -10000 0 0
WNT1 -0.018 0.089 -10000 0 -0.32 52 52
Axin1/APC/beta catenin 0.011 0.024 -10000 0 -10000 0 0
DKK2 -0.04 0.12 -10000 0 -0.33 98 98
NOTCH1 precursor/DVL1 -0.002 0.015 -10000 0 -10000 0 0
GSK3B 0.01 0.001 -10000 0 -10000 0 0
FRAT1 0.01 0.002 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.002 0.014 -10000 0 -10000 0 0
PPP2R5D 0.018 0.064 0.16 109 -10000 0 109
MAPK1 0.01 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.11 0.087 -10000 0 -0.3 46 46
RBPJ 0.009 0.015 -10000 0 -0.37 1 1
CREBBP 0.008 0.006 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR 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
NFATC1 0.006 0.02 -9999 0 -10000 0 0
NFATC2 -0.005 0.054 -9999 0 -0.23 32 32
NFATC3 0.006 0.02 -9999 0 -10000 0 0
CD40LG -0.035 0.15 -9999 0 -0.53 28 28
PTGS2 -0.05 0.16 -9999 0 -0.37 73 73
JUNB 0.009 0.02 -9999 0 -0.35 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.007 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.007 -9999 0 -10000 0 0
CALM1 0.008 0.005 -9999 0 -10000 0 0
JUN 0.008 0.006 -9999 0 -10000 0 0
mol:Ca2+ -0.005 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.002 -9999 0 -10000 0 0
FOSL1 -0.065 0.15 -9999 0 -0.37 130 130
CREM 0.01 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.044 0.072 -9999 0 -0.3 29 29
FOS -0.001 0.056 -9999 0 -0.36 16 16
IFNG -0.034 0.14 -9999 0 -0.48 25 25
AP-1/NFAT1-c-4 -0.081 0.12 -9999 0 -0.43 44 44
FASLG -0.034 0.15 -9999 0 -0.45 37 37
NFAT1-c-4/ICER1 -0.026 0.049 -9999 0 -0.25 19 19
IL2RA -0.072 0.19 -9999 0 -0.48 55 55
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.035 0.14 -9999 0 -0.39 37 37
JunB/Fra1/NFAT1-c-4 -0.053 0.084 -9999 0 -0.23 95 95
IL4 -0.035 0.14 -9999 0 -0.39 37 37
IL2 -0.005 0.007 -9999 0 -10000 0 0
IL3 -0.008 0.012 -9999 0 -10000 0 0
FKBP1A 0.01 0 -9999 0 -10000 0 0
BATF3 0.002 0.054 -9999 0 -0.37 14 14
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.008 0.026 -9999 0 -0.37 3 3
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.024 0.017 -9999 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.001 0.015 -9999 0 -0.2 4 4
mol:DAG -0.064 0.1 -9999 0 -0.35 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 -0.024 0.061 -9999 0 -0.36 1 1
CaM/Ca2+ -0.054 0.094 -9999 0 -0.33 1 1
HIF1A 0.014 0.029 -9999 0 -0.36 4 4
GAB1 0.009 0.015 -9999 0 -0.37 1 1
AKT1 -0.027 0.078 -9999 0 -0.26 1 1
PLCG1 -0.065 0.1 -9999 0 -0.35 1 1
NOS3 -0.022 0.076 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
mol:NO -0.021 0.075 -9999 0 -10000 0 0
FLT1 0.023 0.02 -9999 0 -0.24 4 4
PGF -0.17 0.19 -9999 0 -0.37 316 316
VEGFR1 homodimer/NRP2/VEGFR121 -0.025 0.062 -9999 0 -0.36 3 3
CALM1 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
eNOS/Hsp90 -0.015 0.073 -9999 0 -10000 0 0
endothelial cell proliferation -0.078 0.096 -9999 0 -0.25 92 92
mol:Ca2+ -0.064 0.1 -9999 0 -0.35 1 1
MAPK3 -0.044 0.089 -9999 0 -0.3 1 1
MAPK1 -0.044 0.089 -9999 0 -0.3 1 1
PIK3R1 0.01 0 -9999 0 -10000 0 0
PLGF homodimer -0.17 0.19 -9999 0 -0.37 316 316
PRKACA 0.01 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.052 0.14 -9999 0 -0.37 107 107
VEGFA homodimer -0.039 0.13 -9999 0 -0.37 86 86
VEGFR1 homodimer/VEGFA homodimer -0.004 0.077 -9999 0 -0.4 1 1
platelet activating factor biosynthetic process -0.036 0.086 -9999 0 -0.28 1 1
PI3K -0.073 0.077 -9999 0 -0.33 1 1
PRKCA -0.053 0.093 -9999 0 -0.32 1 1
PRKCB -0.081 0.12 -9999 0 -0.3 92 92
VEGFR1 homodimer/PLGF homodimer -0.081 0.11 -9999 0 -0.4 1 1
VEGFA -0.039 0.13 -9999 0 -0.37 86 86
VEGFB 0.01 0 -9999 0 -10000 0 0
mol:IP3 -0.064 0.1 -9999 0 -0.35 1 1
RASA1 0.031 0.015 -9999 0 -10000 0 0
NRP2 0.006 0.036 -9999 0 -0.37 6 6
VEGFR1 homodimer 0.023 0.02 -9999 0 -0.24 4 4
VEGFB homodimer 0.01 0 -9999 0 -10000 0 0
NCK1 0.009 0.015 -9999 0 -0.37 1 1
eNOS/Caveolin-1 -0.042 0.089 -9999 0 -0.26 37 37
PTPN11 0.01 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.072 0.076 -9999 0 -0.32 1 1
mol:L-citrulline -0.021 0.075 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.021 0.053 -9999 0 -0.33 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.023 0.059 -9999 0 -0.36 1 1
CD2AP 0.01 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.066 0.07 -9999 0 -0.31 2 2
PDPK1 -0.045 0.089 -9999 0 -0.3 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.023 0.059 -9999 0 -0.36 1 1
mol:NADP -0.021 0.075 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.02 0.053 -9999 0 -0.33 1 1
VEGFR1 homodimer/NRP2 0.022 0.027 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.016 0.094 -9999 0 -0.36 47 47
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.01 0 -9999 0 -10000 0 0
TCEB1 0.01 0 -9999 0 -10000 0 0
HIF1A/p53 0.005 0.055 -9999 0 -0.15 67 67
HIF1A 0.017 0.014 -9999 0 -0.14 1 1
COPS5 0.01 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0.01 0 -9999 0 -10000 0 0
CDKN2A -0.1 0.18 -9999 0 -0.37 195 195
ARNT/IPAS -0.017 0.061 -9999 0 -0.24 47 47
HIF1AN 0.01 0 -9999 0 -10000 0 0
GNB2L1 0.001 0.059 -9999 0 -0.37 16 16
HIF1A/ARNT 0.023 0.014 -9999 0 -10000 0 0
CUL2 0.01 0 -9999 0 -10000 0 0
OS9 -0.004 0.073 -9999 0 -0.37 25 25
RACK1/Elongin B/Elongin C -0.005 0.031 -9999 0 -0.2 16 16
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.023 0.014 -9999 0 -10000 0 0
PHD1-3/OS9 -0.007 0.033 -9999 0 -0.18 25 25
HIF1A/RACK1/Elongin B/Elongin C -0.004 0.021 -9999 0 -10000 0 0
VHL 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.023 0.014 -9999 0 -10000 0 0
EGLN3 0.01 0 -9999 0 -10000 0 0
EGLN2 0.01 0 -9999 0 -10000 0 0
EGLN1 0.01 0 -9999 0 -10000 0 0
TP53 -0.029 0.12 -9999 0 -0.37 67 67
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.029 0.004 -9999 0 -10000 0 0
ARNT 0.01 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.01 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.028 0.084 -9999 0 -0.16 195 195
E-cadherin 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
E-cadherin/beta catenin-gamma catenin -0.01 0.042 -9999 0 -0.18 35 35
E-cadherin/beta catenin -0.011 0.049 -9999 0 -0.22 34 34
CTNNB1 0.01 0 -9999 0 -10000 0 0
JUP 0.009 0.021 -9999 0 -0.37 2 2
CDH1 -0.008 0.077 -9999 0 -0.34 34 34
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.048 0.039 -10000 0 -10000 0 0
CRKL 0.015 0.058 -10000 0 -0.28 2 2
mol:DAG 0.025 0.047 -10000 0 -0.2 4 4
HRAS 0.031 0.058 -10000 0 -0.26 5 5
MAPK8 0.001 0.07 -10000 0 -0.16 103 103
RAP1A 0.016 0.058 -10000 0 -0.28 2 2
GAB1 0.015 0.058 -10000 0 -0.28 2 2
MAPK14 0.002 0.067 -10000 0 -0.16 103 103
EPO -0.045 0.14 -10000 0 -0.37 100 100
PLCG1 0.025 0.047 -10000 0 -0.2 4 4
EPOR/TRPC2/IP3 Receptors 0.01 0.006 -10000 0 -10000 0 0
RAPGEF1 0.01 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.047 0.083 -10000 0 -0.19 166 166
GAB1/SHC/GRB2/SOS1 -0.018 0.041 -10000 0 -0.28 5 5
EPO/EPOR (dimer) -0.02 0.094 -10000 0 -0.24 100 100
IRS2 0.015 0.058 -10000 0 -0.28 2 2
STAT1 0.031 0.05 -10000 0 -0.21 2 2
STAT5B 0.029 0.048 -10000 0 -0.2 4 4
cell proliferation 0.008 0.065 -10000 0 -0.22 9 9
GAB1/SHIP/PIK3R1/SHP2/SHC -0.017 0.042 -10000 0 -0.25 9 9
TEC 0.014 0.061 -10000 0 -0.29 4 4
SOCS3 -0.026 0.11 -10000 0 -0.34 70 70
STAT1 (dimer) 0.031 0.05 -10000 0 -0.21 2 2
JAK2 0.01 0.006 -10000 0 -10000 0 0
PIK3R1 0.01 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.018 0.064 -10000 0 -0.3 2 2
EPO/EPOR -0.02 0.094 -10000 0 -0.24 100 100
LYN 0.01 0.026 -10000 0 -0.37 3 3
TEC/VAV2 0.02 0.06 -10000 0 -0.27 4 4
elevation of cytosolic calcium ion concentration 0.01 0.006 -10000 0 -10000 0 0
SHC1 -0.001 0.064 -10000 0 -0.37 19 19
EPO/EPOR (dimer)/LYN -0.003 0.078 -10000 0 -0.18 103 103
mol:IP3 0.025 0.047 -10000 0 -0.2 4 4
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.017 0.041 -10000 0 -0.26 6 6
SH2B3 0.009 0.016 -10000 0 -0.37 1 1
NFKB1 0.002 0.067 -10000 0 -0.16 103 103
EPO/EPOR (dimer)/JAK2/SOCS3 -0.029 0.054 0.12 1 -0.17 57 58
PTPN6 0.01 0.06 -10000 0 -0.3 2 2
TEC/VAV2/GRB2 0.024 0.058 -10000 0 -0.26 4 4
EPOR 0.01 0.006 -10000 0 -10000 0 0
INPP5D 0.007 0.033 -10000 0 -0.37 5 5
mol:GDP -0.018 0.042 -10000 0 -0.28 5 5
SOS1 0.01 0 -10000 0 -10000 0 0
PLCG2 0.007 0.033 -10000 0 -0.37 5 5
CRKL/CBL/C3G 0.026 0.055 -10000 0 -0.25 2 2
VAV2 0.016 0.058 -10000 0 -0.28 2 2
CBL 0.016 0.058 -10000 0 -0.28 2 2
SHC/Grb2/SOS1 -0.019 0.045 -10000 0 -0.29 5 5
STAT5A 0.029 0.048 -10000 0 -0.21 1 1
GRB2 0.01 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.042 0.051 -10000 0 -10000 0 0
LYN/PLCgamma2 -0.003 0.035 -10000 0 -0.39 5 5
PTPN11 0.01 0 -10000 0 -10000 0 0
BTK 0.009 0.069 -10000 0 -0.29 9 9
BCL2 0.048 0.039 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.005 0.071 -10000 0 -10000 0 0
UGCG -0.015 0.088 -10000 0 -0.62 13 13
AKT1/mTOR/p70S6K/Hsp90/TERT -0.029 0.082 -10000 0 -0.27 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.01 0.088 -10000 0 -0.61 13 13
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.047 0.063 -10000 0 -0.29 13 13
FRAP1 -0.023 0.099 -10000 0 -0.33 13 13
FOXO3 -0.021 0.099 -10000 0 -0.32 13 13
AKT1 -0.029 0.1 -10000 0 -0.35 13 13
GAB2 0.007 0.005 -10000 0 -10000 0 0
SMPD1 -0.003 0.019 -10000 0 -10000 0 0
SGMS1 -0.003 0.019 -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 0.012 0.008 -10000 0 -10000 0 0
CALM1 0.01 0 -10000 0 -10000 0 0
cell proliferation -0.021 0.076 -10000 0 -0.35 13 13
EIF3A 0.01 0 -10000 0 -10000 0 0
PI3K 0.013 0.009 -10000 0 -10000 0 0
RPS6KB1 0.003 0.029 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.003 -10000 0 -10000 0 0
natural killer cell activation -0.001 0.002 -10000 0 -10000 0 0
JAK3 -0.001 0.057 -10000 0 -0.32 20 20
PIK3R1 0.009 0.006 -10000 0 -10000 0 0
JAK1 0.009 0.005 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
MYC -0.052 0.13 -10000 0 -0.43 6 6
MYB -0.001 0.075 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.022 0.095 -10000 0 -0.3 20 20
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.012 0.035 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.021 0.094 -10000 0 -0.3 20 20
Rac1/GDP 0.015 0.011 -10000 0 -10000 0 0
T cell proliferation -0.028 0.11 -10000 0 -0.31 41 41
SHC1 -0.004 0.064 -10000 0 -0.38 19 19
RAC1 0.01 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.009 -10000 0 -0.027 66 66
PRKCZ -0.03 0.11 -10000 0 -0.32 41 41
NF kappa B1 p50/RelA -0.043 0.062 -10000 0 -0.29 10 10
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.008 0.075 -10000 0 -10000 0 0
HSP90AA1 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
IL2RA -0.096 0.17 -10000 0 -0.38 177 177
IL2RB -0.029 0.11 -10000 0 -0.37 66 66
TERT -0.15 0.19 -10000 0 -0.37 268 268
E2F1 0.004 0.049 -10000 0 -10000 0 0
SOS1 0.007 0.005 -10000 0 -10000 0 0
RPS6 0.004 0.049 -10000 0 -0.37 11 11
mol:cAMP -0.001 0.004 0.013 66 -10000 0 66
PTPN11 0.007 0.005 -10000 0 -10000 0 0
IL2RG -0.037 0.12 -10000 0 -0.37 79 79
actin cytoskeleton organization -0.028 0.11 -10000 0 -0.31 41 41
GRB2 0.007 0.005 -10000 0 -10000 0 0
IL2 0.001 0.003 -10000 0 -10000 0 0
PIK3CA 0.009 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.014 -10000 0 -10000 0 0
LCK -0.067 0.15 -10000 0 -0.37 132 132
BCL2 -0.011 0.086 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.016 0.064 -10000 0 -0.21 26 26
epithelial cell differentiation -0.007 0.031 -10000 0 -0.16 10 10
CYFIP2 0.008 0.026 -10000 0 -0.32 4 4
ENAH 0.044 0.033 -10000 0 -0.18 1 1
EGFR -0.21 0.19 -10000 0 -0.37 377 377
EPHA2 0.005 0.042 -10000 0 -0.37 8 8
MYO6 0.022 0.035 -10000 0 -10000 0 0
CTNNB1 0.01 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.001 0.013 -10000 0 -0.17 4 4
AQP5 -0.086 0.14 -10000 0 -0.35 152 152
CTNND1 0.01 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.035 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.02 0.038 -10000 0 -0.27 2 2
EGF -0.003 0.07 -10000 0 -0.37 23 23
NCKAP1 0.01 0 -10000 0 -10000 0 0
AQP3 -0.072 0.14 -10000 0 -0.36 129 129
cortical microtubule organization -0.007 0.031 -10000 0 -0.16 10 10
GO:0000145 0.021 0.033 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.032 -10000 0 -0.16 10 10
MLLT4 0.01 0 -10000 0 -10000 0 0
ARF6/GDP -0.006 0.025 -10000 0 -0.24 1 1
ARF6 0.01 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.002 0.02 -10000 0 -0.18 9 9
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.028 0.038 -10000 0 -0.2 1 1
PVRL2 0.01 0 -10000 0 -10000 0 0
ZYX 0.016 0.048 -10000 0 -0.3 1 1
ARF6/GTP -0.002 0.018 -10000 0 -10000 0 0
CDH1 -0.008 0.077 -10000 0 -0.34 34 34
EGFR/EGFR/EGF/EGF -0.091 0.081 -10000 0 -0.3 31 31
RhoA/GDP -0.007 0.028 -10000 0 -10000 0 0
actin cytoskeleton organization 0.026 0.036 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.009 0.015 -10000 0 -0.37 1 1
GIT1 0.01 0 -10000 0 -10000 0 0
IGF1R 0.009 0.015 -10000 0 -0.37 1 1
IGF1 0.005 0.039 -10000 0 -0.33 9 9
DIAPH1 -0.003 0.042 -10000 0 -0.54 4 4
Wnt receptor signaling pathway 0.007 0.031 0.16 10 -10000 0 10
RHOA 0.01 0 -10000 0 -10000 0 0
RhoA/GTP -0.006 0.025 -10000 0 -0.24 1 1
CTNNA1 0.01 0 -10000 0 -10000 0 0
VCL 0.026 0.037 -10000 0 -10000 0 0
EFNA1 0.01 0 -10000 0 -10000 0 0
LPP 0.026 0.039 -10000 0 -0.28 1 1
Ephrin A1/EPHA2 -0.008 0.031 -10000 0 -0.28 1 1
SEC6/SEC8 -0.005 0.023 -10000 0 -10000 0 0
MGAT3 0.021 0.038 -10000 0 -0.27 2 2
HGF/MET -0.059 0.073 -10000 0 -0.27 30 30
HGF 0 0.059 -10000 0 -0.34 19 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.016 0.064 -10000 0 -0.22 26 26
actin cable formation 0.055 0.034 -10000 0 -10000 0 0
KIAA1543 0.018 0.051 -10000 0 -0.28 11 11
KIFC3 0.022 0.035 -10000 0 -10000 0 0
NCK1 0.009 0.015 -10000 0 -0.37 1 1
EXOC3 0.01 0 -10000 0 -10000 0 0
ACTN1 0.022 0.035 -10000 0 -10000 0 0
NCK1/GIT1 0 0.01 -10000 0 -0.25 1 1
mol:GDP -0.007 0.031 -10000 0 -0.16 10 10
EXOC4 0.01 0 -10000 0 -10000 0 0
STX4 0.022 0.035 -10000 0 -10000 0 0
PIP5K1C 0.022 0.035 -10000 0 -10000 0 0
LIMA1 -0.1 0.18 -10000 0 -0.37 196 196
ABI1 0.01 0 -10000 0 -10000 0 0
ROCK1 -0.006 0.022 -10000 0 -0.21 1 1
adherens junction assembly 0.007 0.083 -10000 0 -0.3 11 11
IGF-1R heterotetramer/IGF1 -0.008 0.032 -10000 0 -0.27 2 2
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
MET -0.13 0.17 -10000 0 -0.32 287 287
PLEKHA7 0.02 0.042 -10000 0 -0.3 2 2
mol:GTP -0.002 0.02 -10000 0 -0.17 9 9
establishment of epithelial cell apical/basal polarity 0.042 0.032 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.016 0.064 -10000 0 -0.21 26 26
regulation of cell-cell adhesion 0.026 0.036 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.016 0.064 -10000 0 -0.22 26 26
Caspase cascade in apoptosis

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
TOP1 0.013 0.051 -10000 0 -0.21 17 17
ACTA1 0.006 0.062 0.15 14 -0.24 20 34
NUMA1 0.013 0.051 -10000 0 -0.21 17 17
SPTAN1 0.011 0.059 0.15 13 -0.24 18 31
LIMK1 0.011 0.059 0.15 14 -0.24 18 32
BIRC3 -0.006 0.075 -10000 0 -0.35 30 30
BIRC2 0.01 0 -10000 0 -10000 0 0
BAX 0.01 0 -10000 0 -10000 0 0
CASP10 -0.006 0.088 -10000 0 -0.25 70 70
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.01 0 -10000 0 -10000 0 0
PTK2 0.013 0.051 -10000 0 -0.21 17 17
DIABLO 0.01 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.011 0.059 0.15 13 -0.24 18 31
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.01 0 -10000 0 -10000 0 0
GSN 0.011 0.059 0.15 13 -0.24 19 32
MADD 0.009 0.018 -10000 0 -0.32 2 2
TFAP2A -0.055 0.16 -10000 0 -0.61 47 47
BID 0.002 0.052 -10000 0 -0.22 21 21
MAP3K1 0.007 0.028 -10000 0 -10000 0 0
TRADD 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0.01 -10000 0 -0.25 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.004 0.074 0.15 13 -0.28 27 40
CASP9 0.009 0.015 -10000 0 -0.38 1 1
DNA repair -0.007 0.028 -10000 0 -0.14 13 13
neuron apoptosis 0.014 0.025 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.016 0.057 -10000 0 -0.23 17 17
APAF1 0.01 0 -10000 0 -10000 0 0
CASP6 0.017 0.038 -10000 0 -0.25 1 1
TRAF2 0.01 0 -10000 0 -10000 0 0
ICAD/CAD 0.016 0.057 -10000 0 -0.23 17 17
CASP7 -0.001 0.039 0.18 23 -10000 0 23
KRT18 -0.004 0.088 -10000 0 -0.51 19 19
apoptosis -0.017 0.091 0.16 10 -0.26 45 55
DFFA 0.011 0.059 0.15 12 -0.24 18 30
DFFB 0.011 0.059 0.15 13 -0.24 18 31
PARP1 0.007 0.029 0.14 13 -10000 0 13
actin filament polymerization -0.016 0.056 0.22 17 -0.15 3 20
TNF -0.02 0.097 -10000 0 -0.33 58 58
CYCS 0.004 0.039 -10000 0 -0.16 20 20
SATB1 0.022 0.037 -10000 0 -10000 0 0
SLK 0.011 0.059 0.15 12 -0.24 18 30
p15 BID/BAX 0.007 0.046 -10000 0 -0.19 21 21
CASP2 0.021 0.051 -10000 0 -0.24 5 5
JNK cascade -0.007 0.028 -10000 0 -10000 0 0
CASP3 0.005 0.063 0.16 14 -0.26 19 33
LMNB2 0.024 0.038 -10000 0 -0.22 1 1
RIPK1 0.01 0 -10000 0 -10000 0 0
CASP4 -0.046 0.14 -10000 0 -0.37 98 98
Mammalian IAPs/DIABLO -0.007 0.034 -10000 0 -0.17 17 17
negative regulation of DNA binding -0.054 0.15 -10000 0 -0.6 47 47
stress fiber formation 0.011 0.059 0.15 13 -0.24 18 31
GZMB -0.017 0.1 -10000 0 -0.31 70 70
CASP1 -0.028 0.085 -10000 0 -0.19 136 136
LMNB1 0.018 0.04 -10000 0 -0.24 1 1
APP 0.014 0.025 -10000 0 -10000 0 0
TNFRSF1A 0.005 0.044 -10000 0 -0.37 9 9
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0 0.049 -10000 0 -0.26 23 23
VIM -0.023 0.092 0.16 12 -0.26 49 61
LMNA 0.024 0.038 -10000 0 -0.22 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.016 0.053 -10000 0 -0.26 4 4
LRDD 0.009 0.021 -10000 0 -0.37 2 2
SREBF1 0.011 0.059 0.15 12 -0.24 18 30
APAF-1/Caspase 9 -0.001 0.022 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.013 0.05 -10000 0 -0.2 17 17
CFL2 0.016 0.057 0.15 3 -0.23 17 20
GAS2 0.007 0.064 0.15 13 -0.25 20 33
positive regulation of apoptosis 0.023 0.04 -10000 0 -0.23 1 1
PRF1 -0.016 0.097 -10000 0 -0.37 46 46
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.01 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.01 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.081 0.12 -9999 0 -0.19 328 328
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.009 0.015 -9999 0 -0.37 1 1
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.01 0 -9999 0 -10000 0 0
FYN 0.01 0 -9999 0 -10000 0 0
MAP3K12 0.01 0 -9999 0 -10000 0 0
FGR 0.006 0.036 -9999 0 -0.37 6 6
p38 alpha/TAB1 -0.011 0.027 -9999 0 -0.17 3 3
PRKG1 0.004 0.046 -9999 0 -0.33 12 12
DUSP8 -0.007 0.073 -9999 0 -0.32 34 34
PGK/cGMP/p38 alpha -0.011 0.032 -9999 0 -0.19 6 6
apoptosis -0.01 0.026 -9999 0 -0.16 3 3
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.008 0.026 -9999 0 -0.37 3 3
DUSP1 0.008 0.03 -9999 0 -0.37 4 4
PAK1 -0.079 0.15 -9999 0 -0.32 178 178
SRC 0.01 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.001 0.01 -9999 0 -0.18 2 2
TRAF6 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 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 0.009 0.015 -9999 0 -0.37 1 1
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.001 0.051 -9999 0 -0.21 5 5
BLK -0.054 0.14 -9999 0 -0.37 107 107
HCK 0.004 0.049 -9999 0 -0.37 11 11
MAP2K3 0.009 0.015 -9999 0 -0.37 1 1
DUSP16 0.01 0 -9999 0 -10000 0 0
DUSP10 0.009 0.013 -9999 0 -0.32 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.011 0.041 -9999 0 -0.18 3 3
positive regulation of innate immune response 0.005 0.056 -9999 0 -0.24 3 3
LCK -0.066 0.15 -9999 0 -0.37 132 132
p38alpha-beta/MKP7 0.01 0.055 -9999 0 -0.23 3 3
p38alpha-beta/MKP5 0.01 0.055 -9999 0 -0.23 4 4
PGK/cGMP -0.004 0.03 -9999 0 -0.23 12 12
PAK2 0.01 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.009 0.057 -9999 0 -0.22 4 4
CDC42 0.01 0 -9999 0 -10000 0 0
RALB 0.01 0 -9999 0 -10000 0 0
RALA 0.01 0 -9999 0 -10000 0 0
PAK3 -0.089 0.15 -9999 0 -0.32 198 198
Wnt signaling

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
Noncanonical Wnts/FZD 0.009 0.055 -9999 0 -0.18 34 34
FZD6 0.005 0.042 -9999 0 -0.37 8 8
WNT6 0.004 0.046 -9999 0 -0.35 11 11
WNT4 -0.003 0.065 -9999 0 -0.33 26 26
FZD3 0.01 0 -9999 0 -10000 0 0
WNT5A -0.018 0.099 -9999 0 -0.37 48 48
WNT11 0.005 0.041 -9999 0 -0.37 8 8
IL27-mediated signaling events

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.009 0.015 -10000 0 -0.37 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.009 0.046 0.32 2 -10000 0 2
IL27/IL27R/JAK1 -0.052 0.064 -10000 0 -10000 0 0
TBX21 -0.11 0.13 -10000 0 -0.46 41 41
IL12B 0.002 0.021 -10000 0 -0.38 2 2
IL12A 0.005 0.034 -10000 0 -0.26 11 11
IL6ST -0.003 0.051 -10000 0 -0.34 15 15
IL27RA/JAK1 -0.001 0.02 -10000 0 -10000 0 0
IL27 -0.017 0.083 -10000 0 -0.38 33 33
TYK2 0.009 0.002 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.024 0.087 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.009 0.046 0.32 2 -10000 0 2
T cell proliferation during immune response 0.009 0.046 0.32 2 -10000 0 2
MAPKKK cascade -0.009 0.046 -10000 0 -0.32 2 2
STAT3 0.01 0 -10000 0 -10000 0 0
STAT2 0.01 0 -10000 0 -10000 0 0
STAT1 0.002 0.04 -10000 0 -0.38 7 7
IL12RB1 0.009 0.02 -10000 0 -0.35 2 2
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.2 0.16 -10000 0 -0.43 69 69
IL27/IL27R/JAK2/TYK2 -0.009 0.046 -10000 0 -0.33 2 2
positive regulation of T cell mediated cytotoxicity -0.009 0.046 -10000 0 -0.32 2 2
STAT1 (dimer) -0.13 0.13 -10000 0 -0.54 11 11
JAK2 0.009 0.002 -10000 0 -10000 0 0
JAK1 0.007 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.003 0.043 -10000 0 -0.3 2 2
T cell proliferation -0.024 0.068 -10000 0 -0.32 1 1
IL12/IL12R/TYK2/JAK2 0.004 0.024 -10000 0 -10000 0 0
IL17A -0.024 0.087 -10000 0 -10000 0 0
mast cell activation 0.009 0.046 0.32 2 -10000 0 2
IFNG -0.001 0.01 -10000 0 -10000 0 0
T cell differentiation -0.006 0.004 -10000 0 -0.016 15 15
STAT3 (dimer) -0.003 0.043 -10000 0 -0.31 1 1
STAT5A (dimer) -0.003 0.043 -10000 0 -10000 0 0
STAT4 (dimer) -0.081 0.095 -10000 0 -0.36 10 10
STAT4 -0.17 0.17 -10000 0 -0.32 366 366
T cell activation -0.006 0.003 0.042 2 -10000 0 2
IL27R/JAK2/TYK2 -0.008 0.032 -10000 0 -10000 0 0
GATA3 -0.034 0.088 -10000 0 -10000 0 0
IL18 -0.003 0.056 -10000 0 -0.26 30 30
positive regulation of mast cell cytokine production -0.003 0.043 -10000 0 -0.3 1 1
IL27/EBI3 -0.013 0.062 -10000 0 -0.26 37 37
IL27RA 0.002 0.017 -10000 0 -10000 0 0
IL6 -0.054 0.13 -10000 0 -0.33 125 125
STAT5A 0.01 0 -10000 0 -10000 0 0
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.004 0.01 -10000 0 -10000 0 0
IL1B -0.018 0.075 -10000 0 -0.22 78 78
EBI3 0 0.034 -10000 0 -0.39 5 5
TNF -0.012 0.067 -10000 0 -0.23 58 58
Regulation of Telomerase

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
Telomerase catalytic core complex -0.088 0.14 -9999 0 -0.4 14 14
RAD9A 0.01 0 -9999 0 -10000 0 0
AP1 -0.002 0.038 -9999 0 -0.24 16 16
IFNAR2 0.006 0.006 -9999 0 -10000 0 0
AKT1 0.005 0.013 -9999 0 -10000 0 0
ER alpha/Oestrogen 0.001 0.009 -9999 0 -0.22 1 1
NFX1/SIN3/HDAC complex 0.022 0.019 -9999 0 -10000 0 0
EGF -0.005 0.07 -9999 0 -0.37 23 23
SMG5 0.01 0 -9999 0 -10000 0 0
SMG6 0.01 0 -9999 0 -10000 0 0
SP3/HDAC2 0.005 0.008 -9999 0 -10000 0 0
TERT/c-Abl -0.088 0.12 -9999 0 -0.38 11 11
SAP18 0.009 0.002 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.041 0.12 -9999 0 -0.38 75 75
WRN 0.01 0 -9999 0 -10000 0 0
SP1 0.007 0.006 -9999 0 -10000 0 0
SP3 0.006 0.005 -9999 0 -10000 0 0
TERF2IP 0.01 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.082 0.1 -9999 0 -0.35 3 3
Mad/Max 0.004 0.007 -9999 0 -10000 0 0
TERT -0.09 0.14 -9999 0 -0.41 11 11
CCND1 -0.082 0.14 -9999 0 -0.47 11 11
MAX 0.006 0.005 -9999 0 -10000 0 0
RBBP7 0.009 0.002 -9999 0 -10000 0 0
RBBP4 0.009 0.002 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.01 0 -9999 0 -10000 0 0
SIN3A 0.009 0.002 -9999 0 -10000 0 0
Telomerase/911 0.015 0.025 -9999 0 -10000 0 0
CDKN1B 0.003 0.06 -9999 0 -0.4 3 3
RAD1 0.01 0 -9999 0 -10000 0 0
XRCC5 0.01 0 -9999 0 -10000 0 0
XRCC6 0.01 0 -9999 0 -10000 0 0
SAP30 0.008 0.015 -9999 0 -0.38 1 1
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.006 0.005 -9999 0 -10000 0 0
JUN 0.006 0.005 -9999 0 -10000 0 0
E6 -0.002 0.003 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.002 0.004 -9999 0 -10000 0 0
FOS -0.003 0.056 -9999 0 -0.36 16 16
IFN-gamma/IRF1 -0.018 0.068 -9999 0 -0.26 45 45
PARP2 0.01 0 -9999 0 -10000 0 0
BLM -0.026 0.11 -9999 0 -0.37 62 62
Telomerase -0.02 0.044 -9999 0 -10000 0 0
IRF1 -0.015 0.091 -9999 0 -0.37 41 41
ESR1 0.008 0.013 -9999 0 -0.32 1 1
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.024 0.021 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.024 0.021 -9999 0 -10000 0 0
HDAC1 0.008 0.015 -9999 0 -0.38 1 1
HDAC2 0.007 0.006 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.02 0.011 -9999 0 -0.25 1 1
ABL1 0.01 0 -9999 0 -10000 0 0
MXD1 0.006 0.005 -9999 0 -10000 0 0
MRE11A 0.01 0 -9999 0 -10000 0 0
HUS1 0.009 0.015 -9999 0 -0.37 1 1
RPS6KB1 0.01 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.082 0.11 -9999 0 -10000 0 0
NR2F2 0.013 0.02 -9999 0 -0.32 2 2
MAPK3 0.006 0.005 -9999 0 -10000 0 0
MAPK1 0.006 0.005 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.01 0.015 -9999 0 -0.37 1 1
NFKB1 0.01 0 -9999 0 -10000 0 0
HNRNPC 0.01 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.01 0 -9999 0 -10000 0 0
EGFR -0.21 0.19 -9999 0 -0.38 377 377
mol:Oestrogen -0.001 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.15 0.13 -9999 0 -0.26 387 387
MYC -0.12 0.18 -9999 0 -0.38 223 223
IL2 -0.005 0.009 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
TGFB1 0.01 0.015 -9999 0 -0.37 1 1
TRF2/BLM -0.021 0.067 -9999 0 -0.23 62 62
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.08 0.12 -9999 0 -0.37 11 11
SP1/HDAC2 0.01 0.01 -9999 0 -10000 0 0
PINX1 0.01 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.082 0.1 -9999 0 -0.35 3 3
Smad3/Myc -0.052 0.11 -9999 0 -0.2 223 223
911 complex 0 0.008 -9999 0 -0.2 1 1
IFNG 0 0.038 -9999 0 -0.37 7 7
Telomerase/PinX1 -0.082 0.1 -9999 0 -0.35 3 3
Telomerase/AKT1/mTOR/p70S6K -0.004 0.042 -9999 0 -10000 0 0
SIN3B 0.009 0.002 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.082 0.1 -9999 0 -0.35 3 3
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.082 0.1 -9999 0 -0.35 1 1
E2F1 0.001 0.048 -9999 0 -0.38 10 10
ZNFX1 0.009 0.002 -9999 0 -10000 0 0
PIF1 -0.052 0.14 -9999 0 -0.37 107 107
NCL 0.01 0 -9999 0 -10000 0 0
DKC1 0.01 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.026 0.063 -10000 0 -0.18 97 97
cell-cell adhesion 0.016 0.048 0.28 11 -10000 0 11
Ephrin B/EPHB2/RasGAP -0.005 0.027 -10000 0 -0.31 1 1
ITSN1 0.01 0 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
SHC1 -0.001 0.064 -10000 0 -0.37 19 19
Ephrin B1/EPHB3 -0.003 0.029 -10000 0 -0.23 10 10
Ephrin B1/EPHB1 -0.007 0.036 -10000 0 -0.2 23 23
HRAS/GDP -0.016 0.05 -10000 0 -0.28 11 11
Ephrin B/EPHB1/GRB7 -0.009 0.04 -10000 0 -0.36 3 3
Endophilin/SYNJ1 0.024 0.031 -10000 0 -0.29 1 1
KRAS 0.01 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.008 0.036 -10000 0 -0.3 3 3
endothelial cell migration -0.013 0.044 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
GRB7 0.004 0.033 -10000 0 -0.37 5 5
PAK1 0.016 0.052 -10000 0 -0.3 10 10
HRAS 0.01 0 -10000 0 -10000 0 0
RRAS 0.021 0.039 -10000 0 -0.16 13 13
DNM1 -0.17 0.17 -10000 0 -0.32 367 367
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.021 0.04 -10000 0 -0.29 3 3
lamellipodium assembly -0.016 0.048 -10000 0 -0.28 11 11
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.021 0.046 -10000 0 -0.32 6 6
PIK3R1 0.01 0 -10000 0 -10000 0 0
EPHB2 0.009 0.021 -10000 0 -0.37 2 2
EPHB3 0.008 0.03 -10000 0 -0.37 4 4
EPHB1 0.001 0.056 -10000 0 -0.35 16 16
EPHB4 -0.021 0.1 -10000 0 -0.37 53 53
mol:GDP -0.016 0.051 -10000 0 -0.27 12 12
Ephrin B/EPHB2 -0.005 0.028 -10000 0 -0.18 9 9
Ephrin B/EPHB3 -0.006 0.034 -10000 0 -0.21 10 10
JNK cascade 0.024 0.035 -10000 0 -10000 0 0
Ephrin B/EPHB1 -0.008 0.037 -10000 0 -0.19 17 17
RAP1/GDP -0.015 0.045 0.12 1 -0.24 11 12
EFNB2 0.009 0.018 -10000 0 -0.32 2 2
EFNB3 0.004 0.044 -10000 0 -0.32 12 12
EFNB1 0.006 0.039 -10000 0 -0.37 7 7
Ephrin B2/EPHB1-2 -0.005 0.03 -10000 0 -0.18 19 19
RAP1B 0.005 0.044 -10000 0 -0.37 9 9
RAP1A 0.01 0 -10000 0 -10000 0 0
CDC42/GTP -0.007 0.031 -10000 0 -0.28 3 3
Rap1/GTP -0.007 0.029 -10000 0 -0.24 3 3
axon guidance -0.026 0.063 -10000 0 -0.18 97 97
MAPK3 0.031 0.042 -10000 0 -0.28 6 6
MAPK1 0.031 0.042 -10000 0 -0.28 6 6
Rac1/GDP 0.02 0.058 -10000 0 -0.25 12 12
actin cytoskeleton reorganization -0.012 0.037 -10000 0 -0.22 11 11
CDC42/GDP 0.02 0.058 -10000 0 -0.25 12 12
PI3K -0.013 0.044 -10000 0 -10000 0 0
EFNA5 -0.038 0.12 -10000 0 -0.32 96 96
Ephrin B2/EPHB4 -0.017 0.057 -10000 0 -0.21 55 55
Ephrin B/EPHB2/Intersectin/N-WASP 0.024 0.031 -10000 0 -0.17 14 14
CDC42 0.01 0 -10000 0 -10000 0 0
RAS family/GTP -0.006 0.026 -10000 0 -0.23 3 3
PTK2 0.002 0.01 -10000 0 -10000 0 0
MAP4K4 0.024 0.036 -10000 0 -10000 0 0
SRC 0.01 0 -10000 0 -10000 0 0
KALRN 0.002 0.049 -10000 0 -0.32 15 15
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.021 0.066 -10000 0 -0.26 14 14
MAP2K1 0.026 0.044 -10000 0 -0.3 6 6
WASL 0.01 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.006 0.032 -10000 0 -0.18 19 19
cell migration 0.031 0.048 -10000 0 -0.31 6 6
NRAS 0.01 0 -10000 0 -10000 0 0
SYNJ1 0.025 0.031 -10000 0 -0.3 1 1
PXN 0.01 0 -10000 0 -10000 0 0
TF 0.028 0.035 -10000 0 -0.26 4 4
HRAS/GTP -0.007 0.03 -10000 0 -0.26 3 3
Ephrin B1/EPHB1-2 -0.006 0.033 -10000 0 -0.17 25 25
cell adhesion mediated by integrin 0.004 0.031 0.17 18 -10000 0 18
RAC1 0.01 0 -10000 0 -10000 0 0
mol:GTP -0.007 0.033 -10000 0 -0.27 3 3
RAC1-CDC42/GTP -0.007 0.031 -10000 0 -0.28 4 4
RASA1 0.01 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.014 0.043 0.12 1 -0.24 11 12
ruffle organization 0.028 0.062 -10000 0 -0.28 11 11
NCK1 0.009 0.015 -10000 0 -0.37 1 1
receptor internalization 0.007 0.053 -10000 0 -0.27 20 20
Ephrin B/EPHB2/KALRN -0.008 0.035 -10000 0 -0.46 1 1
ROCK1 0.017 0.029 -10000 0 -0.2 11 11
RAS family/GDP -0.012 0.036 -10000 0 -0.24 7 7
Rac1/GTP -0.017 0.051 -10000 0 -0.29 11 11
Ephrin B/EPHB1/Src/Paxillin 0.021 0.04 -10000 0 -0.32 3 3
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.048 0.099 -9999 0 -0.25 128 128
AKT1 0.041 0.053 -9999 0 -10000 0 0
PTK2B -0.014 0.12 -9999 0 -0.31 67 67
VEGFR2 homodimer/Frs2 0.024 0.032 -9999 0 -0.23 8 8
CAV1 -0.052 0.14 -9999 0 -0.37 107 107
CALM1 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.024 0.061 -9999 0 -0.36 3 3
endothelial cell proliferation 0.012 0.084 -9999 0 -0.26 1 1
mol:Ca2+ -0.004 0.087 -9999 0 -0.32 9 9
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.023 0.059 -9999 0 -0.34 6 6
RP11-342D11.1 -0.011 0.087 -9999 0 -0.32 9 9
CDH5 0.006 0.036 -9999 0 -0.37 6 6
VEGFA homodimer -0.023 0.06 -9999 0 -0.18 89 89
SHC1 -0.001 0.064 -9999 0 -0.37 19 19
SHC2 0.01 0 -9999 0 -10000 0 0
HRAS/GDP -0.033 0.064 -9999 0 -0.3 19 19
SH2D2A -0.002 0.064 -9999 0 -0.34 23 23
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.019 0.036 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.028 0.066 -9999 0 -0.37 5 5
VEGFR1 homodimer 0.01 0 -9999 0 -10000 0 0
SHC/GRB2/SOS1 -0.037 0.071 -9999 0 -0.32 19 19
GRB10 -0.004 0.087 -9999 0 -0.32 9 9
PTPN11 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
PAK1 -0.079 0.15 -9999 0 -0.32 178 178
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.022 0.062 -9999 0 -0.35 10 10
HRAS 0.01 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.013 0.054 -9999 0 -10000 0 0
HIF1A 0.008 0.03 -9999 0 -0.37 4 4
FRS2 0.008 0.026 -9999 0 -0.37 3 3
oxygen and reactive oxygen species metabolic process -0.023 0.058 -9999 0 -0.34 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.007 0.08 -9999 0 -0.37 30 30
Nck/Pak -0.057 0.094 -9999 0 -0.21 179 179
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.023 0.059 -9999 0 -0.39 1 1
mol:GDP -0.036 0.069 -9999 0 -0.32 19 19
mol:NADP 0.029 0.059 -9999 0 -10000 0 0
eNOS/Hsp90 0.032 0.057 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
mol:IP3 -0.004 0.088 -9999 0 -0.32 9 9
HIF1A/ARNT -0.002 0.019 -9999 0 -0.25 4 4
SHB 0.01 0 -9999 0 -10000 0 0
VEGFA -0.037 0.13 -9999 0 -0.37 86 86
VEGFC 0.005 0.042 -9999 0 -0.37 8 8
FAK1/Vinculin 0.019 0.078 -9999 0 -0.3 3 3
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.052 0.1 -9999 0 -0.33 66 66
PTPN6 0.007 0.033 -9999 0 -0.37 5 5
EPAS1 0.016 0.019 -9999 0 -10000 0 0
mol:L-citrulline 0.029 0.059 -9999 0 -10000 0 0
ITGAV 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.022 0.055 -9999 0 -0.34 3 3
VEGFR2 homodimer/VEGFA homodimer -0.043 0.077 -9999 0 -0.35 9 9
VEGFR2/3 heterodimer 0.015 0.057 -9999 0 -0.31 8 8
VEGFB 0.01 0 -9999 0 -10000 0 0
MAPK11 0.002 0.082 -9999 0 -0.27 12 12
VEGFR2 homodimer 0.025 0.034 -9999 0 -0.28 8 8
FLT1 0.01 0 -9999 0 -10000 0 0
NEDD4 -0.037 0.13 -9999 0 -0.37 85 85
MAPK3 -0.017 0.099 -9999 0 -0.31 13 13
MAPK1 -0.017 0.099 -9999 0 -0.31 13 13
VEGFA145/NRP2 -0.034 0.088 -9999 0 -0.25 90 90
VEGFR1/2 heterodimer 0.025 0.028 -9999 0 -0.23 8 8
KDR 0.025 0.034 -9999 0 -0.29 8 8
VEGFA165/NRP1/VEGFR2 homodimer -0.038 0.069 -9999 0 -0.33 11 11
SRC 0.01 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.019 0.098 -9999 0 -0.31 13 13
PI3K -0.02 0.038 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.024 0.059 -9999 0 -0.39 1 1
FES -0.005 0.089 -9999 0 -0.32 9 9
GAB1 -0.02 0.039 -9999 0 -0.24 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.023 0.059 -9999 0 -0.39 1 1
CTNNB1 0.01 0 -9999 0 -10000 0 0
SOS1 0.01 0 -9999 0 -10000 0 0
ARNT 0.01 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.008 0.089 -9999 0 -0.31 6 6
VEGFR2 homodimer/VEGFA homodimer/Yes -0.024 0.059 -9999 0 -0.39 1 1
PI3K/GAB1 0.04 0.056 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.049 0.066 -9999 0 -0.3 12 12
PRKACA 0.01 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.012 0.049 -9999 0 -0.39 4 4
HSP90AA1 0.01 0 -9999 0 -10000 0 0
CDC42 -0.004 0.089 -9999 0 -0.32 9 9
actin cytoskeleton reorganization -0.028 0.066 -9999 0 -0.37 5 5
PTK2 0.015 0.079 -9999 0 -0.26 1 1
EDG1 -0.011 0.087 -9999 0 -0.32 9 9
mol:DAG -0.004 0.088 -9999 0 -0.32 9 9
CaM/Ca2+ -0.034 0.061 -9999 0 -0.29 9 9
MAP2K3 0.001 0.087 -9999 0 -0.3 13 13
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.039 0.07 -9999 0 -0.33 9 9
PLCG1 -0.004 0.089 -9999 0 -0.32 9 9
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.021 0.053 -9999 0 -0.36 1 1
IQGAP1 0.006 0.039 -9999 0 -0.37 7 7
YES1 0.009 0.015 -9999 0 -0.37 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.023 0.059 -9999 0 -0.39 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.025 0.061 -9999 0 -0.39 2 2
cell migration 0.039 0.072 -9999 0 -0.42 1 1
mol:PI-3-4-5-P3 -0.019 0.036 -9999 0 -10000 0 0
FYN 0.01 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.004 0.082 -9999 0 -0.3 9 9
mol:NO 0.029 0.059 -9999 0 -10000 0 0
PXN 0.01 0 -9999 0 -10000 0 0
HRAS/GTP -0.033 0.064 -9999 0 -0.29 19 19
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.005 0.089 -9999 0 -0.32 9 9
VHL 0.01 0 -9999 0 -10000 0 0
ITGB3 -0.064 0.15 -9999 0 -0.37 128 128
NOS3 0.029 0.063 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Sck -0.023 0.059 -9999 0 -0.39 1 1
RAC1 0.01 0 -9999 0 -10000 0 0
PRKCA 0.003 0.083 -9999 0 -0.3 9 9
PRKCB -0.028 0.12 -9999 0 -0.29 101 101
VCL 0.008 0.03 -9999 0 -0.37 4 4
VEGFA165/NRP1 -0.011 0.088 -9999 0 -0.33 9 9
VEGFR1/2 heterodimer/VEGFA homodimer -0.023 0.059 -9999 0 -0.39 1 1
VEGFA165/NRP2 -0.034 0.088 -9999 0 -0.25 90 90
MAPKKK cascade -0.032 0.061 -9999 0 -0.29 19 19
NRP2 0.006 0.036 -9999 0 -0.37 6 6
VEGFC homodimer 0.005 0.042 -9999 0 -0.37 8 8
NCK1 0.009 0.015 -9999 0 -0.37 1 1
ROCK1 0.009 0.015 -9999 0 -0.37 1 1
FAK1/Paxillin 0.02 0.075 -9999 0 -10000 0 0
MAP3K13 -0.006 0.09 -9999 0 -0.32 12 12
PDPK1 0.032 0.059 -9999 0 -10000 0 0
S1P3 pathway

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.008 0.03 -9999 0 -0.37 4 4
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.021 0.038 -9999 0 -0.22 11 11
GNAO1 0.005 0.044 -9999 0 -0.32 12 12
S1P/S1P3/G12/G13 -0.034 0.07 -9999 0 -0.18 127 127
AKT1 -0.005 0.017 -9999 0 -10000 0 0
AKT3 0.022 0.041 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.008 0.03 -9999 0 -0.37 4 4
GNAI2 0.011 0 -9999 0 -10000 0 0
GNAI3 0.01 0.021 -9999 0 -0.37 2 2
GNAI1 0.007 0.036 -9999 0 -0.32 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.062 0.15 -9999 0 -0.37 127 127
S1PR2 -0.003 0.069 -9999 0 -0.37 22 22
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.009 0.06 -9999 0 -0.33 9 9
MAPK3 0.015 0.057 -9999 0 -0.3 9 9
MAPK1 0.015 0.057 -9999 0 -0.3 9 9
JAK2 0.002 0.078 -9999 0 -0.35 11 11
CXCR4 -0.016 0.1 -9999 0 -0.27 65 65
FLT1 0.012 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.015 0.057 -9999 0 -0.3 9 9
S1P/S1P3/Gi 0.009 0.061 -9999 0 -0.33 9 9
RAC1 0.01 0 -9999 0 -10000 0 0
RhoA/GTP -0.016 0.042 -9999 0 -0.29 9 9
VEGFA -0.037 0.13 -9999 0 -0.37 86 86
S1P/S1P2/Gi 0.023 0.046 -9999 0 -0.35 5 5
VEGFR1 homodimer/VEGFA homodimer -0.013 0.09 -9999 0 -0.25 86 86
RHOA 0.01 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.004 0.044 -9999 0 -0.16 5 5
GNAQ 0.01 0 -9999 0 -10000 0 0
GNAZ 0.01 0.018 -9999 0 -0.32 2 2
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 0.009 0.013 -9999 0 -0.32 1 1
GNA15 0.009 0.02 -9999 0 -0.35 2 2
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
GNA11 0.009 0.018 -9999 0 -0.32 2 2
Rac1/GTP -0.016 0.042 -9999 0 -0.29 9 9
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.034 0.023 -10000 0 -10000 0 0
adherens junction organization 0.006 0.056 -10000 0 -0.21 24 24
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.053 0.082 -10000 0 -0.22 10 10
FMN1 0.02 0.051 -10000 0 -0.3 10 10
mol:IP3 -0.003 0.016 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.021 0.042 -10000 0 -0.19 24 24
CTNNB1 0.01 0.002 -10000 0 -10000 0 0
AKT1 0.032 0.028 -10000 0 -0.18 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.021 0.063 -10000 0 -0.3 24 24
CTNND1 0.011 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.026 0.04 -10000 0 -0.24 1 1
VASP 0.026 0.041 -10000 0 -0.18 24 24
ZYX 0.02 0.052 -10000 0 -0.3 2 2
JUB -0.015 0.084 -10000 0 -0.32 6 6
EGFR(dimer) -0.074 0.094 -10000 0 -0.29 18 18
E-cadherin/beta catenin-gamma catenin -0.009 0.04 -10000 0 -0.18 35 35
mol:PI-3-4-5-P3 -0.005 0.021 -10000 0 -0.19 1 1
PIK3CA 0.011 0 -10000 0 -10000 0 0
PI3K -0.005 0.022 -10000 0 -0.2 1 1
FYN 0.037 0.022 -10000 0 -10000 0 0
mol:Ca2+ 0.028 0.023 -10000 0 -10000 0 0
JUP 0.009 0.021 -10000 0 -0.37 2 2
PIK3R1 0.011 0 -10000 0 -10000 0 0
mol:DAG -0.003 0.016 -10000 0 -10000 0 0
CDH1 -0.008 0.077 -10000 0 -0.34 34 34
RhoA/GDP -0.053 0.082 -10000 0 -0.22 10 10
establishment of polarity of embryonic epithelium 0.026 0.041 -10000 0 -0.17 24 24
SRC 0.01 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
EGFR -0.21 0.19 -10000 0 -0.37 377 377
CASR 0.031 0.024 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.014 -10000 0 -10000 0 0
AKT2 0.033 0.027 -10000 0 -10000 0 0
actin cable formation 0.025 0.051 -10000 0 -0.3 9 9
apoptosis 0.004 0.019 0.17 1 -10000 0 1
CTNNA1 0.011 0.001 -10000 0 -10000 0 0
mol:GDP -0.061 0.087 -10000 0 -0.22 17 17
PIP5K1A 0.026 0.04 -10000 0 -0.25 1 1
PLCG1 -0.004 0.016 -10000 0 -10000 0 0
Rac1/GTP -0.079 0.07 -10000 0 -0.26 18 18
homophilic cell adhesion 0.001 0 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.004 0.044 -9999 0 -0.32 12 12
CDC42/GTP -0.006 0.032 -9999 0 -0.31 4 4
PLCG1 0.026 0.039 -9999 0 -0.32 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.01 0 -9999 0 -10000 0 0
GNAI3 0.009 0.021 -9999 0 -0.37 2 2
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.006 0.032 -9999 0 -0.3 4 4
S1PR5 -0.041 0.12 -9999 0 -0.32 101 101
S1PR4 0.006 0.038 -9999 0 -0.37 7 7
MAPK3 0.026 0.039 -9999 0 -0.32 4 4
MAPK1 0.026 0.039 -9999 0 -0.32 4 4
S1P/S1P5/Gi -0.008 0.083 -9999 0 -0.18 109 109
GNAI1 0.006 0.036 -9999 0 -0.32 8 8
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.027 0.063 -9999 0 -0.18 101 101
RHOA 0.023 0.019 -9999 0 -0.16 6 6
S1P/S1P4/Gi 0.02 0.041 -9999 0 -0.22 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.009 0.018 -9999 0 -0.32 2 2
S1P/S1P4/G12/G13 -0.002 0.018 -9999 0 -0.18 7 7
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 0.029 0.063 -10000 0 -0.37 15 15
CRKL 0.025 0.064 -10000 0 -0.38 15 15
HRAS 0.009 0.082 -10000 0 -0.34 18 18
mol:PIP3 0.012 0.06 -10000 0 -0.37 15 15
SPRED1 0.01 0 -10000 0 -10000 0 0
SPRED2 0.01 0 -10000 0 -10000 0 0
GAB1 0.021 0.066 -10000 0 -0.41 15 15
FOXO3 0.029 0.058 -10000 0 -0.35 15 15
AKT1 0.024 0.062 -10000 0 -0.38 15 15
BAD 0.029 0.058 -10000 0 -0.35 15 15
megakaryocyte differentiation 0.021 0.065 -10000 0 -0.4 15 15
GSK3B 0.029 0.058 -10000 0 -0.35 15 15
RAF1 0.015 0.071 -10000 0 -0.3 15 15
SHC1 -0.001 0.064 -10000 0 -0.37 19 19
STAT3 0.021 0.066 -10000 0 -0.41 15 15
STAT1 0.027 0.14 -10000 0 -0.91 15 15
HRAS/SPRED1 -0.022 0.052 -10000 0 -0.28 18 18
cell proliferation 0.02 0.067 -10000 0 -0.41 15 15
PIK3CA 0.01 0 -10000 0 -10000 0 0
TEC 0.006 0.039 -10000 0 -0.37 7 7
RPS6KB1 0.021 0.066 -10000 0 -0.41 15 15
HRAS/SPRED2 -0.022 0.052 -10000 0 -0.28 18 18
LYN/TEC/p62DOK -0.008 0.062 -10000 0 -0.38 16 16
MAPK3 0.022 0.054 -10000 0 -0.21 14 14
STAP1 0.008 0.08 -10000 0 -0.36 21 21
GRAP2 -0.001 0.064 -10000 0 -0.37 19 19
JAK2 -0.016 0.12 -10000 0 -0.78 15 15
STAT1 (dimer) 0.027 0.14 -10000 0 -0.89 15 15
mol:Gleevec -0.002 0.003 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.05 0.089 -10000 0 -0.43 17 17
actin filament polymerization 0.013 0.075 -10000 0 -0.41 15 15
LYN 0.008 0.026 -10000 0 -0.37 3 3
STAP1/STAT5A (dimer) 0.019 0.1 -10000 0 -0.57 15 15
PIK3R1 0.01 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.004 0.053 -10000 0 -0.34 15 15
PI3K 0.03 0.063 -10000 0 -0.38 15 15
PTEN 0.01 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR 0.015 0.18 -10000 0 -1.1 15 15
MAPK8 0.02 0.068 -10000 0 -0.42 15 15
STAT3 (dimer) 0.021 0.065 -10000 0 -0.4 15 15
positive regulation of transcription 0.022 0.047 -10000 0 -0.18 14 14
mol:GDP -0.041 0.078 -10000 0 -0.34 25 25
PIK3C2B 0.019 0.068 -10000 0 -0.41 15 15
CBL/CRKL 0.03 0.06 -10000 0 -0.36 15 15
FER 0.021 0.066 -10000 0 -0.41 15 15
SH2B3 0.021 0.066 -10000 0 -0.41 15 15
PDPK1 0.018 0.056 -10000 0 -0.34 15 15
SNAI2 0.016 0.074 -10000 0 -0.43 15 15
positive regulation of cell proliferation 0.028 0.11 -10000 0 -0.69 15 15
KITLG 0.013 0.005 -10000 0 -10000 0 0
cell motility 0.028 0.11 -10000 0 -0.69 15 15
PTPN6 -0.001 0.033 -10000 0 -0.37 5 5
EPOR 0.036 0.045 -10000 0 -10000 0 0
STAT5A (dimer) 0.028 0.092 -10000 0 -0.57 15 15
SOCS1 -0.11 0.18 -10000 0 -0.37 210 210
cell migration 0 0.087 0.47 15 -10000 0 15
SOS1 0.01 0 -10000 0 -10000 0 0
EPO -0.046 0.14 -10000 0 -0.37 100 100
VAV1 0.008 0.025 -10000 0 -0.36 3 3
GRB10 0.021 0.066 -10000 0 -0.41 15 15
PTPN11 0.008 0.003 -10000 0 -10000 0 0
SCF/KIT 0.015 0.069 -10000 0 -0.44 15 15
GO:0007205 -0.002 0.004 -10000 0 -10000 0 0
MAP2K1 0.02 0.059 -10000 0 -0.23 15 15
CBL 0.01 0 -10000 0 -10000 0 0
KIT 0.015 0.18 -10000 0 -1.2 15 15
MAP2K2 0.02 0.059 -10000 0 -0.23 15 15
SHC/Grb2/SOS1 -0.008 0.065 -10000 0 -0.41 15 15
STAT5A 0.028 0.094 -10000 0 -0.59 15 15
GRB2 0.01 0 -10000 0 -10000 0 0
response to radiation 0.016 0.073 -10000 0 -0.42 15 15
SHC/GRAP2 -0.014 0.062 -10000 0 -0.27 35 35
PTPRO 0.021 0.066 -10000 0 -0.41 15 15
SH2B2 0.013 0.076 -10000 0 -0.42 15 15
DOK1 0.008 0.026 -10000 0 -0.37 3 3
MATK 0 0.088 -10000 0 -0.48 15 15
CREBBP 0.029 0.005 -10000 0 -10000 0 0
BCL2 0.036 0.044 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.009 0.019 -9999 0 -10000 0 0
VDR -0.005 0.073 -9999 0 -0.35 28 28
FAM120B 0.009 0.015 -9999 0 -0.37 1 1
RXRs/LXRs/DNA/9cRA 0.003 0.091 -9999 0 -0.24 54 54
RXRs/LXRs/DNA/Oxysterols -0.005 0.12 -9999 0 -0.35 53 53
MED1 0.01 0 -9999 0 -10000 0 0
mol:9cRA -0.002 0.016 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.017 0.048 -9999 0 -0.3 1 1
RXRs/NUR77 0.014 0.053 -9999 0 -0.21 10 10
RXRs/PPAR 0.014 0.052 -9999 0 -0.19 9 9
NCOR2 0.01 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.01 0.049 -9999 0 -0.24 28 28
RARs/VDR/DNA/Vit D3 -0.007 0.036 -9999 0 -0.18 18 18
RARA 0.01 0 -9999 0 -10000 0 0
NCOA1 0.01 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.005 0.073 -9999 0 -0.35 28 28
RARs/RARs/DNA/9cRA -0.001 0.013 -9999 0 -0.17 4 4
RARG 0.008 0.03 -9999 0 -0.37 4 4
RPS6KB1 0.011 0.022 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.017 0.048 -9999 0 -0.3 1 1
THRA 0.01 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.01 0.049 -9999 0 -0.24 28 28
RXRs/PPAR/9cRA/PGJ2/DNA 0.006 0.059 -9999 0 -0.22 9 9
NR1H4 -0.069 0.15 -9999 0 -0.37 135 135
RXRs/LXRs/DNA 0.018 0.068 -9999 0 -0.28 4 4
NR1H2 0.01 0.011 -9999 0 -10000 0 0
NR1H3 0.008 0.028 -9999 0 -0.37 3 3
RXRs/VDR/DNA/Vit D3 0.007 0.062 -9999 0 -0.23 17 17
NR4A1 0.007 0.032 -9999 0 -0.36 5 5
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.013 0.064 -9999 0 -0.19 25 25
RXRG -0.012 0.084 -9999 0 -0.33 44 44
RXR alpha/CCPG 0.014 0.013 -9999 0 -0.25 1 1
RXRA 0.01 0.011 -9999 0 -10000 0 0
RXRB 0.01 0.013 -9999 0 -10000 0 0
THRB -0.011 0.081 -9999 0 -0.32 42 42
PPARG 0.008 0.025 -9999 0 -0.36 3 3
PPARD 0.01 0 -9999 0 -10000 0 0
TNF -0.038 0.24 -9999 0 -0.87 49 49
mol:Oxysterols -0.001 0.014 -9999 0 -10000 0 0
cholesterol transport -0.004 0.12 -9999 0 -0.35 53 53
PPARA 0.01 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.01 0 -9999 0 -10000 0 0
RXRs/NUR77/BCL2 0.01 0.05 -9999 0 -0.17 44 44
SREBF1 0.003 0.11 -9999 0 -0.47 4 4
RXRs/RXRs/DNA/9cRA 0.007 0.059 -9999 0 -0.22 9 9
ABCA1 -0.011 0.13 -9999 0 -0.5 4 4
RARs/THRs -0.009 0.034 -9999 0 -0.31 1 1
RXRs/FXR -0.026 0.092 -9999 0 -0.22 38 38
BCL2 0.01 0 -9999 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.009 0.12 -9999 0 -0.58 2 2
CRP -0.015 0.12 -9999 0 -0.58 2 2
cell cycle arrest -0.02 0.12 -9999 0 -0.57 5 5
TIMP1 -0.031 0.14 -9999 0 -0.51 8 8
IL6ST 0.002 0.05 -9999 0 -0.32 15 15
Rac1/GDP -0.013 0.099 -9999 0 -0.3 31 31
AP1 0.028 0.041 -9999 0 -10000 0 0
GAB2 0.011 0.001 -9999 0 -10000 0 0
TNFSF11 -0.013 0.12 -9999 0 -0.61 3 3
HSP90B1 0.02 0.028 -9999 0 -10000 0 0
GAB1 0.01 0.015 -9999 0 -0.37 1 1
MAPK14 -0.037 0.17 -9999 0 -0.52 64 64
AKT1 0.043 0.011 -9999 0 -10000 0 0
FOXO1 0.048 0.01 -9999 0 -10000 0 0
MAP2K6 -0.03 0.13 -9999 0 -0.37 65 65
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.006 0.1 -9999 0 -0.36 13 13
MITF -0.022 0.1 -9999 0 -0.32 31 31
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.01 0 -9999 0 -10000 0 0
A2M 0.011 0.037 -9999 0 -10000 0 0
CEBPB 0.015 0.021 -9999 0 -0.37 2 2
GRB2/SOS1/GAB family/SHP2 0.011 0.04 -9999 0 -10000 0 0
STAT3 -0.017 0.13 -9999 0 -0.59 5 5
STAT1 0 0.009 -9999 0 -10000 0 0
CEBPD -0.013 0.13 -9999 0 -0.59 4 4
PIK3CA 0.011 0 -9999 0 -10000 0 0
PI3K 0.017 0.002 -9999 0 -10000 0 0
JUN 0.01 0 -9999 0 -10000 0 0
PIAS3/MITF -0.013 0.096 -9999 0 -0.3 30 30
MAPK11 -0.037 0.17 -9999 0 -0.52 65 65
STAT3 (dimer)/FOXO1 0.026 0.11 -9999 0 -0.46 2 2
GRB2/SOS1/GAB family -0.028 0.059 -9999 0 -0.26 10 10
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.017 0.092 -9999 0 -0.28 31 31
GRB2 0.011 0.001 -9999 0 -10000 0 0
JAK2 0.01 0 -9999 0 -10000 0 0
LBP 0.002 0.098 -9999 0 -0.49 1 1
PIK3R1 0.011 0 -9999 0 -10000 0 0
JAK1 0.009 0.006 -9999 0 -10000 0 0
MYC -0.044 0.15 -9999 0 -0.6 5 5
FGG -0.015 0.12 -9999 0 -0.58 2 2
macrophage differentiation -0.02 0.12 -9999 0 -0.57 5 5
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.032 0.064 -9999 0 -0.21 38 38
JUNB -0.01 0.12 -9999 0 -0.7 3 3
FOS 0.001 0.056 -9999 0 -0.35 16 16
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.03 0.11 -9999 0 -0.33 36 36
STAT1/PIAS1 -0.018 0.086 -9999 0 -0.31 13 13
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.016 -9999 0 -10000 0 0
STAT3 (dimer) -0.017 0.13 -9999 0 -0.59 5 5
PRKCD -0.001 0.12 -9999 0 -0.44 8 8
IL6R 0.009 0.006 -9999 0 -10000 0 0
SOCS3 -0.077 0.31 -9999 0 -1.1 57 57
gp130 (dimer)/JAK1/JAK1/LMO4 0.009 0.035 -9999 0 -0.18 9 9
Rac1/GTP -0.029 0.093 -9999 0 -0.3 31 31
HCK 0.003 0.049 -9999 0 -0.37 11 11
MAPKKK cascade 0.026 0.029 -9999 0 -10000 0 0
bone resorption -0.012 0.12 -9999 0 -0.58 3 3
IRF1 -0.015 0.13 -9999 0 -0.59 4 4
mol:GDP -0.022 0.1 -9999 0 -0.32 32 32
SOS1 0.01 0.001 -9999 0 -10000 0 0
VAV1 -0.022 0.1 -9999 0 -0.32 32 32
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.018 0.15 -9999 0 -0.5 57 57
PTPN11 0 0.008 -9999 0 -10000 0 0
IL6/IL6RA -0.034 0.094 -9999 0 -0.23 125 125
gp130 (dimer)/TYK2/TYK2/LMO4 0.008 0.031 -9999 0 -0.17 9 9
gp130 (dimer)/JAK2/JAK2/LMO4 0.008 0.031 -9999 0 -0.17 14 14
IL6 -0.055 0.14 -9999 0 -0.34 125 125
PIAS3 0.01 0 -9999 0 -10000 0 0
PTPRE 0.01 0.011 -9999 0 -10000 0 0
PIAS1 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.028 0.085 -9999 0 -0.22 58 58
LMO4 0.009 0.008 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.056 0.09 -9999 0 -0.53 7 7
MCL1 0.047 0.01 -9999 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.025 0.13 -10000 0 -0.86 5 5
NCK1/PAK1/Dok-R -0.051 0.067 -10000 0 -0.37 8 8
NCK1/Dok-R -0.025 0.088 -10000 0 -0.87 5 5
PIK3CA 0.01 0 -10000 0 -10000 0 0
mol:beta2-estradiol -0.004 0.022 0.22 3 -10000 0 3
RELA 0.01 0 -10000 0 -10000 0 0
SHC1 -0.002 0.064 -10000 0 -0.38 19 19
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 0.001 0.034 0.22 3 -0.35 3 6
TNIP2 0.007 0.033 -10000 0 -0.37 5 5
NF kappa B/RelA -0.016 0.079 -10000 0 -0.85 5 5
FN1 -0.045 0.14 -10000 0 -0.37 96 96
PLD2 0.014 0.096 -10000 0 -0.9 5 5
PTPN11 0.01 0 -10000 0 -10000 0 0
GRB14 -0.063 0.14 -10000 0 -0.32 146 146
ELK1 0.031 0.089 -10000 0 -0.83 5 5
GRB7 0.004 0.033 -10000 0 -0.37 5 5
PAK1 -0.079 0.15 -10000 0 -0.32 178 178
Tie2/Ang1/alpha5/beta1 Integrin -0.059 0.13 -10000 0 -0.68 13 13
CDKN1A -0.051 0.16 -10000 0 -0.54 9 9
ITGA5 -0.042 0.13 -10000 0 -0.37 91 91
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.025 0.088 -10000 0 -0.87 5 5
CRK 0.01 0 -10000 0 -10000 0 0
mol:NO -0.013 0.11 -10000 0 -0.63 5 5
PLG 0.009 0.096 -10000 0 -0.9 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.014 0.12 -10000 0 -0.81 5 5
GRB2 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.002 -10000 0 -10000 0 0
ANGPT2 -0.076 0.14 -10000 0 -0.5 5 5
BMX 0.011 0.097 -10000 0 -0.9 5 5
ANGPT1 -0.006 0.1 -10000 0 -0.75 6 6
tube development -0.043 0.14 -10000 0 -0.64 5 5
ANGPT4 -0.048 0.13 -10000 0 -0.38 94 94
response to hypoxia 0 0.009 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.004 0.1 -10000 0 -0.92 5 5
alpha5/beta1 Integrin -0.038 0.099 -10000 0 -0.28 93 93
FGF2 0.011 0.015 -10000 0 -0.37 1 1
STAT5A (dimer) -0.051 0.16 -10000 0 -0.7 6 6
mol:L-citrulline -0.013 0.11 -10000 0 -0.63 5 5
AGTR1 -0.017 0.094 -10000 0 -0.39 41 41
MAPK14 0.001 0.11 -10000 0 -0.99 5 5
Tie2/SHP2 -0.006 0.053 -10000 0 -0.92 2 2
TEK 0.014 0.066 -10000 0 -1 2 2
RPS6KB1 -0.013 0.12 -10000 0 -0.81 5 5
Angiotensin II/AT1 -0.014 0.068 -10000 0 -0.28 41 41
Tie2/Ang1/GRB2 0.012 0.097 -10000 0 -0.92 5 5
MAPK3 0.026 0.09 -10000 0 -0.84 5 5
MAPK1 0.026 0.09 -10000 0 -0.84 5 5
Tie2/Ang1/GRB7 0.009 0.097 -10000 0 -0.92 5 5
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 0.013 0.096 -10000 0 -0.9 5 5
PI3K -0.021 0.13 -10000 0 -0.96 5 5
FES 0 0.11 -10000 0 -0.98 5 5
Crk/Dok-R -0.025 0.088 -10000 0 -0.87 5 5
Tie2/Ang1/ABIN2 0.011 0.1 -10000 0 -0.95 5 5
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.022 0.12 -10000 0 -0.76 5 5
STAT5A 0.01 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.013 0.12 -10000 0 -0.81 5 5
Tie2/Ang2 -0.06 0.17 -10000 0 -0.86 5 5
Tie2/Ang1 0.008 0.1 -10000 0 -0.96 5 5
FOXO1 -0.03 0.14 -10000 0 -0.78 5 5
ELF1 0.015 0.006 -10000 0 -10000 0 0
ELF2 0.01 0.095 -10000 0 -0.9 5 5
mol:Choline 0.021 0.093 -10000 0 -0.87 5 5
cell migration -0.039 0.055 -10000 0 -0.19 34 34
FYN -0.048 0.15 -10000 0 -0.72 5 5
DOK2 -0.012 0.089 -10000 0 -0.37 38 38
negative regulation of cell cycle -0.047 0.15 -10000 0 -0.48 10 10
ETS1 0.002 0.071 -10000 0 -0.34 26 26
PXN -0.005 0.11 -10000 0 -0.67 5 5
ITGB1 0.003 0.051 -10000 0 -0.37 12 12
NOS3 -0.016 0.12 -10000 0 -0.72 5 5
RAC1 0.01 0 -10000 0 -10000 0 0
TNF -0.017 0.1 -10000 0 -0.34 60 60
MAPKKK cascade 0.021 0.093 -10000 0 -0.87 5 5
RASA1 0.01 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc 0.006 0.1 -10000 0 -0.92 5 5
NCK1 0.009 0.015 -10000 0 -0.37 1 1
vasculogenesis -0.011 0.11 -10000 0 -0.57 5 5
mol:Phosphatidic acid 0.021 0.093 -10000 0 -0.87 5 5
mol:Angiotensin II -0.004 0.007 -10000 0 -10000 0 0
mol:NADP -0.013 0.11 -10000 0 -0.63 5 5
Rac1/GTP -0.05 0.088 -10000 0 -0.76 5 5
MMP2 -0.023 0.12 -10000 0 -0.9 5 5
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.015 0.009 -10000 0 -0.21 1 1
RAS family/GTP -0.033 0.067 -10000 0 -0.31 15 15
NFATC4 0.005 0.065 -10000 0 -0.21 11 11
ERBB2IP 0.009 0.021 -10000 0 -0.38 2 2
HSP90 (dimer) 0.01 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.033 0.063 0.12 1 -0.27 10 11
JUN 0.02 0.056 -10000 0 -0.21 4 4
HRAS 0.01 0.001 -10000 0 -10000 0 0
DOCK7 -0.007 0.073 -10000 0 -0.26 10 10
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.04 0.076 0.12 1 -0.24 35 36
AKT1 0.008 0.011 -10000 0 -0.26 1 1
BAD 0.015 0.009 -10000 0 -0.21 1 1
MAPK10 -0.016 0.031 -10000 0 -0.14 13 13
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.013 0.08 -10000 0 -0.29 10 10
RAF1 0.004 0.083 -10000 0 -0.3 15 15
ErbB2/ErbB3/neuregulin 2 -0.008 0.04 -10000 0 -0.2 20 20
STAT3 0.002 0.003 -10000 0 -10000 0 0
cell migration 0.016 0.051 -10000 0 -0.14 7 7
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation 0.004 0.12 -10000 0 -0.47 5 5
FOS 0.011 0.1 -10000 0 -0.41 10 10
NRAS 0.01 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.033 0.063 0.12 1 -0.27 10 11
MAPK3 0.004 0.11 -10000 0 -0.36 9 9
MAPK1 0.004 0.11 -10000 0 -0.36 9 9
JAK2 -0.007 0.073 -10000 0 -0.26 10 10
NF2 -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.027 0.098 -10000 0 -0.2 145 145
NRG1 -0.057 0.13 -10000 0 -0.32 134 134
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 -0.017 0.094 -10000 0 -0.21 45 45
MAPK9 -0.016 0.03 -10000 0 -0.13 10 10
ERBB2 -0.003 0.03 0.15 2 -0.26 8 10
ERBB3 -0.003 0.061 -10000 0 -0.34 22 22
SHC1 -0.001 0.064 -10000 0 -0.38 19 19
RAC1 0.01 0 -10000 0 -10000 0 0
apoptosis 0.001 0.008 0.18 1 -10000 0 1
STAT3 (dimer) 0.002 0.004 -10000 0 -10000 0 0
RNF41 0.019 0.009 -10000 0 -0.18 1 1
FRAP1 0.007 0.009 -10000 0 -0.21 1 1
RAC1-CDC42/GTP -0.022 0.042 -10000 0 -0.18 10 10
ErbB2/ErbB2/HSP90 (dimer) -0.002 0.024 0.12 2 -0.21 8 10
CHRNA1 -0.003 0.11 -10000 0 -0.39 10 10
myelination 0.006 0.064 -10000 0 -0.21 11 11
PPP3CB -0.006 0.069 -10000 0 -0.24 10 10
KRAS 0.01 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.032 0.076 -10000 0 -0.33 15 15
NRG2 0.009 0.018 -10000 0 -0.32 2 2
mol:GDP -0.027 0.097 -10000 0 -0.2 145 145
SOS1 0.01 0 -10000 0 -10000 0 0
MAP2K2 0.011 0.082 -10000 0 -0.28 15 15
SRC 0.01 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 -0.007 0.073 -10000 0 -0.26 10 10
MAP2K1 -0.008 0.11 -10000 0 -0.36 11 11
heart morphogenesis -0.033 0.063 0.12 1 -0.27 10 11
RAS family/GDP -0.034 0.068 -10000 0 -0.32 15 15
GRB2 0.01 0 -10000 0 -10000 0 0
PRKACA -0.002 0.005 -10000 0 -10000 0 0
CHRNE 0.011 0.019 -10000 0 -0.14 5 5
HSP90AA1 0.01 0 -10000 0 -10000 0 0
activation of caspase activity -0.008 0.011 0.26 1 -10000 0 1
nervous system development -0.033 0.063 0.12 1 -0.27 10 11
CDC42 0.01 0 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.009 0.081 -9999 0 -0.36 33 33
GNB1/GNG2 -0.013 0.04 -9999 0 -0.27 6 6
mol:DAG 0.025 0.049 -9999 0 -0.25 6 6
PLCG1 0.026 0.05 -9999 0 -0.26 6 6
YES1 0.015 0.053 -9999 0 -0.25 7 7
FZD3 0.01 0 -9999 0 -10000 0 0
FZD6 0.005 0.042 -9999 0 -0.37 8 8
G protein 0.025 0.05 -9999 0 -0.26 6 6
MAP3K7 -0.01 0.076 -9999 0 -0.25 32 32
mol:Ca2+ 0.025 0.048 -9999 0 -0.24 6 6
mol:IP3 0.025 0.049 -9999 0 -0.25 6 6
NLK 0 0.003 -9999 0 -10000 0 0
GNB1 0.01 0 -9999 0 -10000 0 0
CAMK2A -0.014 0.081 -9999 0 -0.22 83 83
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD 0.009 0.055 -9999 0 -0.18 34 34
CSNK1A1 0.01 0 -9999 0 -10000 0 0
GNAS 0.016 0.052 -9999 0 -0.31 4 4
GO:0007205 0.025 0.048 -9999 0 -0.25 6 6
WNT6 0.004 0.046 -9999 0 -0.35 11 11
WNT4 -0.003 0.065 -9999 0 -0.33 26 26
NFAT1/CK1 alpha -0.017 0.045 -9999 0 -0.24 13 13
GNG2 0.009 0.018 -9999 0 -0.32 2 2
WNT5A -0.018 0.099 -9999 0 -0.37 48 48
WNT11 0.005 0.041 -9999 0 -0.37 8 8
CDC42 0.021 0.05 -9999 0 -0.29 4 4
FOXA2 and FOXA3 transcription factor networks

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
ACADVL 0.028 0.18 -10000 0 -0.67 11 11
PCK1 0.011 0.15 -10000 0 -0.95 6 6
HNF4A 0.007 0.23 -10000 0 -0.74 29 29
KCNJ11 0.022 0.22 -10000 0 -0.86 19 19
AKT1 0.001 0.11 -10000 0 -0.35 10 10
response to starvation 0.002 0.008 -10000 0 -10000 0 0
DLK1 0.01 0.21 -10000 0 -0.76 14 14
NKX2-1 0.011 0.14 -10000 0 -0.97 3 3
ACADM 0.028 0.18 -10000 0 -0.67 11 11
TAT -0.008 0.14 -10000 0 -10000 0 0
CEBPB 0.01 0.022 -10000 0 -0.37 2 2
CEBPA 0.009 0.033 -10000 0 -0.37 5 5
TTR 0.005 0.12 -10000 0 -0.54 5 5
PKLR 0.023 0.19 -10000 0 -0.68 15 15
APOA1 0.013 0.23 -10000 0 -0.83 13 13
CPT1C 0.027 0.18 -10000 0 -0.67 11 11
ALAS1 0.023 0.12 -10000 0 -10000 0 0
TFRC 0.018 0.15 -10000 0 -10000 0 0
FOXF1 0.002 0.039 0.2 2 -0.37 6 8
NF1 0.016 0 -10000 0 -10000 0 0
HNF1A (dimer) 0.009 0.018 -10000 0 -10000 0 0
CPT1A 0.028 0.18 -10000 0 -0.67 11 11
HMGCS1 0.028 0.18 -10000 0 -0.68 10 10
NR3C1 -0.015 0.043 -10000 0 -10000 0 0
CPT1B 0.027 0.18 -10000 0 -0.69 11 11
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.008 0.016 -10000 0 -10000 0 0
GCK 0.006 0.23 -10000 0 -0.71 38 38
CREB1 0.013 0.021 -10000 0 -0.19 4 4
IGFBP1 -0.035 0.15 -10000 0 -0.54 1 1
PDX1 0.023 0.13 -10000 0 -0.56 1 1
UCP2 0.019 0.19 -10000 0 -0.66 13 13
ALDOB 0.027 0.2 -10000 0 -0.76 14 14
AFP -0.031 0.1 -10000 0 -0.34 33 33
BDH1 0.005 0.23 -10000 0 -0.72 39 39
HADH 0.03 0.19 -10000 0 -0.68 14 14
F2 0.011 0.23 -10000 0 -0.86 11 11
HNF1A 0.009 0.018 -10000 0 -10000 0 0
G6PC 0.01 0.067 -10000 0 -10000 0 0
SLC2A2 0.021 0.13 -10000 0 -10000 0 0
INS 0.017 0.041 -10000 0 -0.39 1 1
FOXA1 -0.027 0.11 0.23 1 -0.38 55 56
FOXA3 -0.051 0.16 -10000 0 -0.38 112 112
FOXA2 0.025 0.23 -10000 0 -0.76 16 16
ABCC8 -0.016 0.3 -10000 0 -0.78 69 69
ALB -0.022 0.11 -10000 0 -0.73 9 9
Canonical NF-kappaB pathway

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
FBXW11 0.012 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.052 0.028 -9999 0 -10000 0 0
ERC1 0.009 0.015 -9999 0 -0.37 1 1
RIP2/NOD2 -0.062 0.11 -9999 0 -0.25 166 166
NFKBIA 0.035 0.028 -9999 0 -0.33 4 4
BIRC2 0.01 0 -9999 0 -10000 0 0
IKBKB 0.01 0 -9999 0 -10000 0 0
RIPK2 0.008 0.026 -9999 0 -0.37 3 3
IKBKG -0.012 0.02 -9999 0 -10000 0 0
IKK complex/A20 -0.018 0.039 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.008 0.026 -9999 0 -0.37 3 3
XPO1 0.01 0 -9999 0 -10000 0 0
NEMO/ATM 0.021 0.034 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.01 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.006 0.013 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.084 0.16 -9999 0 -0.37 163 163
NFKB1 0.012 0.006 -9999 0 -10000 0 0
RELA 0.012 0.006 -9999 0 -10000 0 0
MALT1 0.01 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.01 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.022 0.068 -9999 0 -0.22 67 67
TRAF6 0.01 0 -9999 0 -10000 0 0
PRKCA 0.01 0 -9999 0 -10000 0 0
CHUK 0.01 0 -9999 0 -10000 0 0
UBE2D3 0.01 0 -9999 0 -10000 0 0
TNF -0.02 0.097 -9999 0 -0.33 58 58
NF kappa B1 p50/RelA -0.001 0.014 -9999 0 -0.18 4 4
BCL10 0.01 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.035 0.028 -9999 0 -0.33 4 4
beta TrCP1/SCF ubiquitin ligase complex 0.012 0.006 -9999 0 -10000 0 0
TNFRSF1A 0.005 0.044 -9999 0 -0.37 9 9
IKK complex -0.008 0.014 -9999 0 -10000 0 0
CYLD 0.01 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.006 0.011 -9999 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.009 0.015 -9999 0 -0.38 1 1
HDAC2 0.01 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.041 0.082 -9999 0 -0.2 135 135
forebrain development 0.015 0.076 -9999 0 -0.35 20 20
GNAO1 0.004 0.044 -9999 0 -0.32 12 12
SMO/beta Arrestin2 -0.037 0.11 -9999 0 -0.25 135 135
SMO -0.067 0.15 -9999 0 -0.37 135 135
ARRB2 0.01 0.002 -9999 0 -10000 0 0
GLI3/SPOP 0.046 0.027 -9999 0 -0.21 2 2
mol:GTP 0 0.001 -9999 0 -10000 0 0
GSK3B 0.01 0 -9999 0 -10000 0 0
GNAI2 0.01 0.001 -9999 0 -10000 0 0
SIN3/HDAC complex 0 0.008 -9999 0 -10000 0 0
GNAI1 0.006 0.036 -9999 0 -0.32 8 8
XPO1 0.011 0.002 -9999 0 -10000 0 0
GLI1/Su(fu) -0.016 0.045 -9999 0 -0.33 3 3
SAP30 0.009 0.015 -9999 0 -0.38 1 1
mol:GDP -0.067 0.15 -9999 0 -0.37 135 135
MIM/GLI2A 0.009 0.021 -9999 0 -0.37 2 2
IFT88 0.01 0 -9999 0 -10000 0 0
GNAI3 0.009 0.021 -9999 0 -0.37 2 2
GLI2 0.031 0.019 -9999 0 -10000 0 0
GLI3 0.043 0.029 -9999 0 -0.22 2 2
CSNK1D 0.01 0 -9999 0 -10000 0 0
CSNK1E 0.01 0 -9999 0 -10000 0 0
SAP18 0.01 0 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.01 0 -9999 0 -10000 0 0
GNG2 0.009 0.018 -9999 0 -0.32 2 2
Gi family/GTP 0.002 0.062 -9999 0 -0.31 11 11
SIN3B 0.01 0 -9999 0 -10000 0 0
SIN3A 0.01 0 -9999 0 -10000 0 0
GLI3/Su(fu) 0.035 0.032 -9999 0 -0.24 2 2
GLI2/Su(fu) 0.027 0.045 -9999 0 -10000 0 0
FOXA2 -0.002 0.012 -9999 0 -10000 0 0
neural tube patterning 0.015 0.076 -9999 0 -0.35 20 20
SPOP 0.01 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.006 0.04 -9999 0 -0.17 1 1
GNB1 0.01 0 -9999 0 -10000 0 0
CSNK1G2 0.01 0 -9999 0 -10000 0 0
CSNK1G3 0.01 0 -9999 0 -10000 0 0
MTSS1 0.009 0.021 -9999 0 -0.37 2 2
embryonic limb morphogenesis 0.015 0.076 -9999 0 -0.35 20 20
SUFU 0 0.046 -9999 0 -0.2 1 1
LGALS3 -0.019 0.1 -9999 0 -0.37 51 51
catabolic process 0.058 0.025 -9999 0 -10000 0 0
GLI3A/CBP 0.004 0.056 -9999 0 -0.28 20 20
KIF3A 0.008 0.022 -9999 0 -0.32 3 3
GLI1 0.015 0.077 -9999 0 -0.36 20 20
RAB23 0.01 0 -9999 0 -10000 0 0
CSNK1A1 0.01 0 -9999 0 -10000 0 0
IFT172 0.009 0.013 -9999 0 -0.32 1 1
RBBP7 0.01 0 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.009 0.073 -9999 0 -0.27 27 27
GNAZ 0.009 0.018 -9999 0 -0.32 2 2
RBBP4 0.01 0 -9999 0 -10000 0 0
CSNK1G1 0.01 0 -9999 0 -10000 0 0
PIAS1 0.01 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GLI2/SPOP 0.034 0.017 -9999 0 -10000 0 0
STK36 0.01 0.021 -9999 0 -0.37 2 2
Gi family/GNB1/GNG2/GDP 0.012 0.057 -9999 0 -0.3 11 11
PTCH1 0.018 0.078 -9999 0 -0.53 3 3
MIM/GLI1 0.019 0.074 -9999 0 -0.43 4 4
CREBBP 0.004 0.056 -9999 0 -0.28 20 20
Su(fu)/SIN3/HDAC complex 0.033 0.013 -9999 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.008 0.026 -10000 0 -0.37 3 3
positive regulation of NF-kappaB transcription factor activity -0.004 0.032 -10000 0 -0.25 11 11
MAP2K4 0.034 0.016 -10000 0 -10000 0 0
IKBKB 0.01 0 -10000 0 -10000 0 0
TNFRSF10B -0.007 0.078 -10000 0 -0.37 29 29
TNFRSF10A 0.008 0.024 -10000 0 -0.34 3 3
SMPD1 -0.005 0.022 -10000 0 -0.18 2 2
IKBKG 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.005 0.042 -10000 0 -0.37 8 8
TRAIL/TRAILR2 -0.012 0.056 -10000 0 -0.27 30 30
TRAIL/TRAILR3 -0.046 0.098 -10000 0 -0.25 122 122
TRAIL/TRAILR1 -0.002 0.023 -10000 0 -0.24 6 6
TRAIL/TRAILR4 -0.004 0.032 -10000 0 -0.25 11 11
TRAIL/TRAILR1/DAP3/GTP -0.002 0.016 -10000 0 -0.17 6 6
IKK complex -0.002 0.01 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.017 0.018 -10000 0 -0.25 3 3
MAP3K1 -0.001 0.011 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.005 0.042 -10000 0 -0.37 8 8
TRADD 0.01 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.008 0.023 -10000 0 -0.34 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.013 -10000 0 -10000 0 0
CFLAR 0.01 0 -10000 0 -10000 0 0
MAPK1 0.017 0.018 -10000 0 -0.25 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP -0.001 0.014 -10000 0 -10000 0 0
mol:ceramide 0.01 0.025 -10000 0 -0.18 2 2
FADD 0.01 0 -10000 0 -10000 0 0
MAPK8 0.038 0.016 -10000 0 -10000 0 0
TRAF2 0.01 0 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.059 0.15 -10000 0 -0.37 120 120
CHUK 0.01 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.002 0.018 -10000 0 -0.19 6 6
DAP3 0.01 0 -10000 0 -10000 0 0
CASP10 -0.003 0.024 0.14 2 -0.24 2 4
JNK cascade -0.004 0.032 -10000 0 -0.25 11 11
TRAIL (trimer) 0.008 0.026 -10000 0 -0.37 3 3
TNFRSF10C -0.059 0.15 -10000 0 -0.37 120 120
TRAIL/TRAILR1/DAP3/GTP/FADD -0.001 0.015 -10000 0 -0.16 4 4
TRAIL/TRAILR2/FADD -0.01 0.046 -10000 0 -0.22 30 30
cell death 0.01 0.025 -10000 0 -0.18 2 2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.024 0.024 -10000 0 -0.18 2 2
TRAILR2 (trimer) -0.007 0.078 -10000 0 -0.37 29 29
CASP8 -0.001 0.012 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.008 0.036 -10000 0 -0.34 2 2
BCR signaling pathway

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.02 0.042 -10000 0 -0.22 2 2
IKBKB 0.017 0.024 -10000 0 -0.16 1 1
AKT1 -0.005 0.051 -10000 0 -0.17 11 11
IKBKG 0.02 0.024 -10000 0 -0.17 1 1
CALM1 0.007 0.03 -10000 0 -0.22 1 1
PIK3CA 0.01 0 -10000 0 -10000 0 0
MAP3K1 0.013 0.056 -10000 0 -0.28 4 4
MAP3K7 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.032 -10000 0 -0.22 2 2
DOK1 0.008 0.026 -10000 0 -0.37 3 3
AP-1 0.022 0.028 -10000 0 -10000 0 0
LYN 0.008 0.026 -10000 0 -0.37 3 3
BLNK 0.007 0.031 -10000 0 -0.35 5 5
SHC1 -0.001 0.064 -10000 0 -0.37 19 19
BCR complex -0.024 0.084 -10000 0 -0.29 54 54
CD22 -0.036 0.07 -10000 0 -0.26 24 24
CAMK2G 0.013 0.029 -10000 0 -0.2 1 1
CSNK2A1 0.01 0 -10000 0 -10000 0 0
INPP5D 0.007 0.033 -10000 0 -0.37 5 5
SHC/GRB2/SOS1 -0.02 0.065 -10000 0 -0.34 17 17
GO:0007205 0.001 0.032 -10000 0 -0.22 2 2
SYK 0.004 0.047 -10000 0 -0.37 10 10
ELK1 0.007 0.03 -10000 0 -0.2 2 2
NFATC1 0.009 0.053 -10000 0 -0.25 8 8
B-cell antigen/BCR complex -0.024 0.084 -10000 0 -0.29 54 54
PAG1/CSK 0 0 -10000 0 -10000 0 0
NFKBIB 0.014 0.01 -10000 0 -10000 0 0
HRAS 0.013 0.037 -10000 0 -0.22 3 3
NFKBIA 0.014 0.01 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.016 0.009 -10000 0 -10000 0 0
RasGAP/Csk -0.062 0.1 -10000 0 -0.37 39 39
mol:GDP 0.003 0.03 0.16 1 -0.2 2 3
PTEN 0.01 0 -10000 0 -10000 0 0
CD79B -0.007 0.078 -10000 0 -0.37 29 29
NF-kappa-B/RelA/I kappa B alpha 0.016 0.009 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.002 0.066 -10000 0 -0.32 7 7
PIK3R1 0.01 0 -10000 0 -10000 0 0
mol:IP3 -0.003 0.031 -10000 0 -0.22 2 2
CSK 0.01 0 -10000 0 -10000 0 0
FOS 0.009 0.038 -10000 0 -0.21 4 4
CHUK 0.02 0.024 -10000 0 -0.17 1 1
IBTK 0.01 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.005 0.023 -10000 0 -0.27 2 2
PTPN6 -0.034 0.069 -10000 0 -0.26 26 26
RELA 0.01 0 -10000 0 -10000 0 0
BCL2A1 0.009 0.023 -10000 0 -0.067 6 6
VAV2 -0.026 0.06 -10000 0 -0.32 12 12
ubiquitin-dependent protein catabolic process 0.017 0.01 -10000 0 -10000 0 0
BTK -0.003 0.022 -10000 0 -10000 0 0
CD19 -0.033 0.069 -10000 0 -0.27 34 34
MAP4K1 0.007 0.033 -10000 0 -0.37 5 5
CD72 -0.044 0.13 -10000 0 -0.37 94 94
PAG1 0.01 0 -10000 0 -10000 0 0
MAPK14 0.018 0.051 -10000 0 -0.28 2 2
SH3BP5 0.008 0.022 -10000 0 -0.32 3 3
PIK3AP1 0.005 0.05 0.18 2 -0.3 10 12
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.008 0.052 -10000 0 -0.24 12 12
RAF1 0.018 0.035 -10000 0 -0.23 2 2
RasGAP/p62DOK/SHIP -0.059 0.1 -10000 0 -0.36 40 40
CD79A -0.01 0.086 -10000 0 -0.37 35 35
re-entry into mitotic cell cycle 0.022 0.028 -10000 0 -10000 0 0
RASA1 0.01 0 -10000 0 -10000 0 0
MAPK3 0.028 0.031 -10000 0 -0.2 1 1
MAPK1 0.028 0.031 -10000 0 -0.2 1 1
CD72/SHP1 -0.055 0.11 -10000 0 -0.32 56 56
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 0.017 0.052 -10000 0 -0.28 2 2
actin cytoskeleton organization 0.004 0.065 -10000 0 -0.28 12 12
NF-kappa-B/RelA 0.035 0.019 -10000 0 -10000 0 0
Calcineurin -0.005 0.018 -10000 0 -10000 0 0
PI3K -0.042 0.07 -10000 0 -0.28 26 26
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.007 0.032 0.18 2 -0.22 4 6
SOS1 0.01 0 -10000 0 -10000 0 0
Bam32/HPK1 0.005 0.054 -10000 0 -0.55 2 2
DAPP1 -0.012 0.048 -10000 0 -0.78 1 1
cytokine secretion 0.009 0.051 -10000 0 -0.24 8 8
mol:DAG -0.003 0.031 -10000 0 -0.22 2 2
PLCG2 0.007 0.033 -10000 0 -0.37 5 5
MAP2K1 0.023 0.033 -10000 0 -0.21 2 2
B-cell antigen/BCR complex/FcgammaRIIB -0.078 0.13 -10000 0 -0.25 210 210
mol:PI-3-4-5-P3 -0.034 0.053 -10000 0 -0.21 25 25
ETS1 0.012 0.042 -10000 0 -0.23 5 5
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.02 0.069 -10000 0 -0.39 14 14
B-cell antigen/BCR complex/LYN -0.025 0.05 -10000 0 -0.25 13 13
MALT1 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
RAC1 0.004 0.068 -10000 0 -0.3 12 12
B-cell antigen/BCR complex/LYN/SYK -0.056 0.081 -10000 0 -0.3 30 30
CARD11 0.006 0.034 -10000 0 -0.32 2 2
FCGR2B -0.1 0.17 -10000 0 -0.37 193 193
PPP3CA 0.01 0 -10000 0 -10000 0 0
BCL10 0.01 0 -10000 0 -10000 0 0
IKK complex 0.013 0.015 -10000 0 -10000 0 0
PTPRC 0.001 0.057 -10000 0 -0.37 15 15
PDPK1 -0.007 0.049 -10000 0 -0.16 14 14
PPP3CB 0.01 0 -10000 0 -10000 0 0
PPP3CC 0.01 0 -10000 0 -10000 0 0
POU2F2 0.016 0.008 -10000 0 -0.069 2 2
Insulin Pathway

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.007 0.03 -9999 0 -10000 0 0
TC10/GTP -0.006 0.029 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 0 0.006 -9999 0 -10000 0 0
HRAS 0.01 0 -9999 0 -10000 0 0
APS homodimer -0.007 0.079 -9999 0 -0.37 30 30
GRB14 -0.063 0.14 -9999 0 -0.32 146 146
FOXO3 -0.003 0.006 -9999 0 -10000 0 0
AKT1 0.01 0.057 -9999 0 -10000 0 0
INSR 0.011 0.001 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.01 0 -9999 0 -10000 0 0
SORBS1 0.01 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
PTPN1 0.028 0.006 -9999 0 -10000 0 0
CAV1 -0.009 0.071 -9999 0 -0.17 108 108
CBL/APS/CAP/Crk-II/C3G -0.007 0.033 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 0 0.006 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.005 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.028 0.017 -9999 0 -10000 0 0
RPS6KB1 0.016 0.055 -9999 0 -10000 0 0
PARD6A 0.009 0.013 -9999 0 -0.32 1 1
CBL 0.01 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.007 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.018 0.033 -9999 0 -10000 0 0
HRAS/GTP -0.005 0.023 -9999 0 -10000 0 0
Insulin Receptor 0.011 0.001 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.005 0.028 -9999 0 -0.16 19 19
PRKCI -0.006 0.012 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.024 0.045 -9999 0 -10000 0 0
SHC1 -0.001 0.064 -9999 0 -0.37 19 19
negative regulation of MAPKKK cascade 0 0.009 -9999 0 -10000 0 0
PI3K 0 0.005 -9999 0 -10000 0 0
NCK2 0.01 0 -9999 0 -10000 0 0
RHOQ 0.01 0 -9999 0 -10000 0 0
mol:H2O2 0 0.001 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
AKT2 0.01 0.057 -9999 0 -10000 0 0
PRKCZ -0.052 0.13 -9999 0 -0.4 79 79
SH2B2 -0.007 0.08 -9999 0 -0.37 30 30
SHC/SHIP 0.02 0.034 -9999 0 -0.16 23 23
F2RL2 -0.064 0.15 -9999 0 -0.37 128 128
TRIP10 0 0.06 -9999 0 -0.37 17 17
Insulin Receptor/Insulin/Shc -0.006 0.032 -9999 0 -0.19 20 20
TC10/GTP/CIP4/Exocyst -0.005 0.033 -9999 0 -0.21 17 17
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.005 0.028 -9999 0 -0.16 19 19
RAPGEF1 0.01 0 -9999 0 -10000 0 0
RASA1 0.01 0 -9999 0 -10000 0 0
NCK1 0.009 0.015 -9999 0 -0.37 1 1
CBL/APS/CAP/Crk-II -0.008 0.036 -9999 0 -0.18 30 30
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.005 0.031 -9999 0 -0.18 20 20
INPP5D 0.02 0.018 -9999 0 -0.17 6 6
SOS1 0.01 0 -9999 0 -10000 0 0
SGK1 -0.001 0.002 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
IRS1 0.01 0 -9999 0 -10000 0 0
p62DOK/RasGAP 0 0.009 -9999 0 -10000 0 0
INS 0.002 0.014 -9999 0 -0.37 1 1
mol:PI-3-4-P2 0.02 0.018 -9999 0 -0.16 6 6
GRB2 0.01 0 -9999 0 -10000 0 0
EIF4EBP1 -0.042 0.091 -9999 0 -0.25 39 39
PTPRA 0.011 0.001 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 -0.005 0.033 -9999 0 -0.21 17 17
PDPK1 0.01 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.023 0.019 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0 0.006 -9999 0 -0.16 1 1
Insulin Receptor/Insulin/IRS3 0 0.009 -9999 0 -0.24 1 1
Par3/Par6 -0.036 0.073 -9999 0 -0.17 138 138
Signaling events mediated by PRL

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCNE1 0.01 0 -10000 0 -10000 0 0
mol:Halofuginone 0.004 0 -10000 0 -10000 0 0
ITGA1 -0.028 0.12 -10000 0 -0.37 66 66
CDKN1A 0.016 0.025 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.002 0.019 -10000 0 -0.25 4 4
mol:Ca2+ -0.001 0.022 0.15 4 -0.24 4 8
AGT 0.008 0.028 -10000 0 -0.35 4 4
CCNA2 -0.034 0.091 -10000 0 -0.31 1 1
TUBA1B 0.01 0 -10000 0 -10000 0 0
EGR1 0.012 0.042 -10000 0 -0.21 22 22
CDK2/Cyclin E1 -0.035 0.09 -10000 0 -0.22 1 1
MAPK3 0.016 0.021 -10000 0 -0.25 4 4
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.016 0.021 -10000 0 -0.25 4 4
PTP4A1 0.028 0.012 -10000 0 -10000 0 0
PTP4A3 0.008 0.03 -10000 0 -0.37 4 4
PTP4A2 0.01 0 -10000 0 -10000 0 0
ITGB1 0.012 0.041 -10000 0 -0.25 16 16
SRC 0.01 0 -10000 0 -10000 0 0
RAC1 0.025 0.008 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.027 0.028 -10000 0 -10000 0 0
RABGGTA 0.01 0 -10000 0 -10000 0 0
BCAR1 0.001 0.012 0.15 4 -10000 0 4
RHOC 0.023 0.015 -10000 0 -10000 0 0
RHOA 0.025 0.008 -10000 0 -10000 0 0
cell motility 0.026 0.018 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.027 0.028 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.026 0.078 -10000 0 -0.26 69 69
ROCK1 0.026 0.019 -10000 0 -10000 0 0
RABGGTB 0.01 0 -10000 0 -10000 0 0
CDK2 -0.12 0.18 -10000 0 -0.37 217 217
mitosis 0.028 0.012 -10000 0 -10000 0 0
ATF5 0.01 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.01 0 -9999 0 -10000 0 0
SPHK1 0.006 0.038 -9999 0 -0.37 7 7
GNAI2 0.01 0 -9999 0 -10000 0 0
mol:S1P 0.016 0.015 -9999 0 -0.21 1 1
GNAO1 0.004 0.044 -9999 0 -0.32 12 12
mol:Sphinganine-1-P 0.015 0.027 -9999 0 -0.25 7 7
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.006 0.028 -9999 0 -10000 0 0
GNAI3 0.009 0.021 -9999 0 -0.37 2 2
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 -0.063 0.15 -9999 0 -0.37 127 127
S1PR2 -0.003 0.069 -9999 0 -0.37 22 22
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.001 0.011 -9999 0 -0.18 1 1
S1PR5 -0.041 0.12 -9999 0 -0.32 101 101
S1PR4 0.006 0.038 -9999 0 -0.37 7 7
GNAI1 0.006 0.036 -9999 0 -0.32 8 8
S1P/S1P5/G12 -0.022 0.052 -9999 0 -0.22 2 2
S1P/S1P3/Gq 0.01 0.044 -9999 0 -0.2 1 1
S1P/S1P4/Gi 0.028 0.038 -9999 0 -0.32 5 5
GNAQ 0.01 0 -9999 0 -10000 0 0
GNAZ 0.009 0.018 -9999 0 -0.32 2 2
GNA14 0.009 0.013 -9999 0 -0.32 1 1
GNA15 0.009 0.02 -9999 0 -0.35 2 2
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0 -9999 0 -10000 0 0
GNA11 0.009 0.018 -9999 0 -0.32 2 2
ABCC1 0.009 0.015 -9999 0 -0.37 1 1
Ceramide signaling pathway

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
SPHK2 0.017 0.015 -10000 0 -0.25 2 2
MAP4K4 0.019 0.054 -10000 0 -0.34 3 3
BAG4 0.005 0.039 -10000 0 -0.32 9 9
PKC zeta/ceramide -0.016 0.047 -10000 0 -0.16 61 61
NFKBIA 0.008 0.03 -10000 0 -0.37 4 4
BIRC3 -0.006 0.075 -10000 0 -0.35 30 30
BAX 0.002 0.006 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
AKT1 0.013 0.015 -10000 0 -0.35 1 1
BAD -0.001 0.011 0.11 2 -10000 0 2
SMPD1 0.01 0.039 -10000 0 -0.17 3 3
RB1 -0.001 0.011 0.11 2 -10000 0 2
FADD/Caspase 8 0.024 0.054 -10000 0 -0.34 3 3
MAP2K4 -0.001 0.033 0.11 2 -0.17 21 23
NSMAF 0.01 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.005 0.011 0.11 2 -10000 0 2
EGF -0.003 0.07 -10000 0 -0.37 23 23
mol:ceramide -0.008 0.012 0.11 2 -10000 0 2
MADD 0.009 0.018 -10000 0 -0.32 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.017 0.015 -10000 0 -0.25 2 2
ASAH1 0.01 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.001 0.011 0.1 2 -10000 0 2
cell proliferation -0.004 0.022 -10000 0 -0.21 4 4
BID 0.015 0.04 -10000 0 -10000 0 0
MAP3K1 -0.007 0.035 0.11 2 -0.19 21 23
EIF2A 0.011 0.01 -10000 0 -10000 0 0
TRADD 0.01 0 -10000 0 -10000 0 0
CRADD 0.01 0 -10000 0 -10000 0 0
MAPK3 0.014 0.01 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.014 0.01 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.001 0.011 0.099 2 -10000 0 2
FADD 0.019 0.053 -10000 0 -0.34 3 3
KSR1 -0.001 0.011 0.11 2 -10000 0 2
MAPK8 -0.02 0.071 -10000 0 -0.2 82 82
PRKRA -0.001 0.011 0.11 2 -10000 0 2
PDGFA 0.009 0.021 -10000 0 -0.37 2 2
TRAF2 0.01 0 -10000 0 -10000 0 0
IGF1 0.005 0.039 -10000 0 -0.33 9 9
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.008 0.012 0.11 2 -10000 0 2
CTSD 0.01 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.018 0.027 -10000 0 -0.22 4 4
PRKCD 0.005 0.039 -10000 0 -0.32 9 9
PRKCZ -0.03 0.11 -10000 0 -0.32 79 79
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.017 0.015 -10000 0 -0.25 2 2
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.001 0.057 -10000 0 -0.37 15 15
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.056 -10000 0 -0.37 3 3
TNFR1A/BAG4/TNF-alpha -0.02 0.058 -10000 0 -0.18 74 74
mol:Sphingosine-1-phosphate 0.017 0.015 -10000 0 -0.25 2 2
MAP2K1 0.011 0.01 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
CYCS 0.001 0.008 -10000 0 -10000 0 0
TNFRSF1A 0.005 0.044 -10000 0 -0.37 9 9
NFKB1 0.01 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.006 0.039 -10000 0 -0.24 17 17
EIF2AK2 0.005 0.011 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.018 0.054 -10000 0 -0.18 67 67
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.038 -10000 0 -10000 0 0
MAP2K2 0.011 0.01 -10000 0 -10000 0 0
SMPD3 -0.001 0.077 -10000 0 -0.3 30 30
TNF -0.02 0.097 -10000 0 -0.33 58 58
PKC zeta/PAR4 -0.031 0.08 -10000 0 -0.23 90 90
mol:PHOSPHOCHOLINE -0.009 0.026 0.1 19 -0.098 3 22
NF kappa B1/RelA/I kappa B alpha -0.02 0.051 -10000 0 -0.31 5 5
AIFM1 0.001 0.008 -10000 0 -10000 0 0
BCL2 0.01 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.005 0.039 -9999 0 -0.32 9 9
Caspase 8 (4 units) -0.009 0.034 -9999 0 -0.21 12 12
NEF 0 0.02 -9999 0 -10000 0 0
NFKBIA 0.007 0.035 -9999 0 -0.39 4 4
BIRC3 0.018 0.08 -9999 0 -0.35 30 30
CYCS 0.029 0.037 -9999 0 -0.21 2 2
RIPK1 0.01 0 -9999 0 -10000 0 0
CD247 0.005 0.044 -9999 0 -0.32 10 10
MAP2K7 0.03 0.029 -9999 0 -10000 0 0
protein ubiquitination 0.042 0.039 -9999 0 -10000 0 0
CRADD 0.01 0 -9999 0 -10000 0 0
DAXX 0.01 0 -9999 0 -10000 0 0
FAS -0.006 0.076 -9999 0 -0.37 27 27
BID 0.024 0.038 -9999 0 -0.23 2 2
NF-kappa-B/RelA/I kappa B alpha -0.009 0.042 -9999 0 -0.19 33 33
TRADD 0.01 0 -9999 0 -10000 0 0
MAP3K5 0.01 0 -9999 0 -10000 0 0
CFLAR 0.01 0 -9999 0 -10000 0 0
FADD 0.01 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.009 0.042 -9999 0 -0.19 33 33
MAPK8 0.034 0.03 -9999 0 -10000 0 0
APAF1 0.01 0 -9999 0 -10000 0 0
TRAF1 0.01 0 -9999 0 -10000 0 0
TRAF2 0.01 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.019 0.039 -9999 0 -0.2 6 6
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.034 0.046 -9999 0 -0.21 3 3
CHUK 0.043 0.041 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.012 0.049 -9999 0 -0.34 7 7
TCRz/NEF -0.008 0.039 -9999 0 -0.2 28 28
TNF -0.02 0.097 -9999 0 -0.33 58 58
FASLG 0.006 0.061 -9999 0 -0.33 18 18
NFKB1 0.009 0.016 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.02 0.058 -9999 0 -0.18 74 74
CASP6 -0.005 0.021 -9999 0 -10000 0 0
CASP7 0.044 0.079 -9999 0 -0.36 17 17
RELA 0.009 0.016 -9999 0 -10000 0 0
CASP2 0.009 0.021 -9999 0 -0.37 2 2
CASP3 0.044 0.079 -9999 0 -0.36 17 17
TNFRSF1A 0.005 0.044 -9999 0 -0.37 9 9
TNFR1A/BAG4 -0.006 0.039 -9999 0 -0.24 17 17
CASP8 -0.003 0.07 -9999 0 -0.37 23 23
CASP9 0.009 0.015 -9999 0 -0.37 1 1
MAP3K14 0.039 0.044 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.012 0.049 -9999 0 -0.25 18 18
BCL2 0.038 0.028 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.016 0.072 -9999 0 -0.35 24 24
KLHL20 -0.011 0.035 -9999 0 -0.22 7 7
CYFIP2 0.008 0.026 -9999 0 -0.32 4 4
Rac1/GDP 0.037 0.046 -9999 0 -0.21 8 8
ENAH 0.015 0.073 -9999 0 -0.35 24 24
AP1M1 0.01 0 -9999 0 -10000 0 0
RAP1B 0.005 0.044 -9999 0 -0.37 9 9
RAP1A 0.01 0 -9999 0 -10000 0 0
CTNNB1 0.01 0 -9999 0 -10000 0 0
CDC42/GTP -0.006 0.024 -9999 0 -0.23 1 1
ABI1/Sra1/Nap1 -0.007 0.024 -9999 0 -0.14 8 8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.011 0.04 -9999 0 -0.18 21 21
RAPGEF1 0.028 0.065 -9999 0 -0.3 24 24
CTNND1 0.01 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.015 0.069 -9999 0 -0.37 24 24
CRK 0.023 0.069 -9999 0 -0.33 24 24
E-cadherin/gamma catenin/alpha catenin -0.01 0.042 -9999 0 -0.18 35 35
alphaE/beta7 Integrin -0.004 0.032 -9999 0 -0.25 11 11
IQGAP1 0.006 0.039 -9999 0 -0.37 7 7
NCKAP1 0.01 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.002 0.021 -9999 0 -0.18 9 9
DLG1 0.016 0.073 -9999 0 -0.35 24 24
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.017 -9999 0 -0.16 1 1
MLLT4 0.01 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.001 0.011 -9999 0 -0.17 3 3
PI3K -0.005 0.021 -9999 0 -0.2 1 1
ARF6 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.012 0.052 -9999 0 -0.23 35 35
TIAM1 0.009 0.013 -9999 0 -0.32 1 1
E-cadherin(dimer)/Ca2+ -0.007 0.032 -9999 0 -0.16 10 10
AKT1 -0.003 0.012 -9999 0 -0.12 1 1
PIK3R1 0.01 0 -9999 0 -10000 0 0
CDH1 -0.008 0.077 -9999 0 -0.34 34 34
RhoA/GDP 0.037 0.046 -9999 0 -0.29 1 1
actin cytoskeleton organization -0.008 0.026 -9999 0 -0.16 7 7
CDC42/GDP 0.037 0.046 -9999 0 -0.29 1 1
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.011 0.039 -9999 0 -0.18 24 24
ITGB7 0.005 0.042 -9999 0 -0.37 8 8
RAC1 0.01 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.008 0.034 -9999 0 -0.18 10 10
E-cadherin/Ca2+/beta catenin/alpha catenin -0.008 0.033 -9999 0 -0.15 34 34
mol:GDP 0.034 0.052 -9999 0 -0.24 8 8
CDC42/GTP/IQGAP1 -0.002 0.021 -9999 0 -0.21 7 7
JUP 0.009 0.021 -9999 0 -0.37 2 2
p120 catenin/RhoA/GDP -0.008 0.036 -9999 0 -0.29 1 1
RAC1/GTP/IQGAP1 -0.002 0.021 -9999 0 -0.21 7 7
PIP5K1C/AP1M1 0 0.008 -9999 0 -0.21 1 1
RHOA 0.01 0 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
CTNNA1 0.01 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.014 0.047 -9999 0 -0.15 45 45
NME1 0.009 0.021 -9999 0 -0.37 2 2
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.016 0.072 -9999 0 -0.35 24 24
regulation of cell-cell adhesion -0.005 0.021 -9999 0 -0.2 1 1
WASF2 -0.004 0.012 -9999 0 -10000 0 0
Rap1/GTP -0.007 0.027 -9999 0 -0.26 1 1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.01 0.038 -9999 0 -0.31 1 1
CCND1 0.016 0.057 -9999 0 -0.19 45 45
VAV2 0.025 0.071 -9999 0 -0.33 24 24
RAP1/GDP -0.006 0.032 -9999 0 -0.28 1 1
adherens junction assembly 0.018 0.071 -9999 0 -0.34 24 24
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.01 0 -9999 0 -10000 0 0
PIP5K1C 0.009 0.013 -9999 0 -0.32 1 1
regulation of heterotypic cell-cell adhesion -0.009 0.035 -9999 0 -0.29 1 1
E-cadherin/beta catenin -0.011 0.051 -9999 0 -0.26 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.016 0.073 -9999 0 -0.35 24 24
PIK3CA 0.01 0 -9999 0 -10000 0 0
Rac1/GTP -0.017 0.055 -9999 0 -0.34 8 8
E-cadherin/beta catenin/alpha catenin -0.009 0.039 -9999 0 -0.18 34 34
ITGAE 0.008 0.026 -9999 0 -0.37 3 3
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.015 0.07 -9999 0 -0.37 24 24
Plasma membrane estrogen receptor signaling

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.004 0.026 -10000 0 -0.16 16 16
ER alpha/Gai/GDP/Gbeta gamma 0.029 0.049 -10000 0 -0.32 9 9
AKT1 0.03 0.029 -10000 0 -0.67 1 1
PIK3CA 0.01 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.027 0.029 -10000 0 -0.68 1 1
mol:Ca2+ 0.032 0.025 -10000 0 -0.22 2 2
IGF1R 0.009 0.015 -10000 0 -0.37 1 1
E2/ER alpha (dimer)/Striatin -0.002 0.019 -10000 0 -0.18 8 8
SHC1 -0.001 0.064 -10000 0 -0.37 19 19
apoptosis -0.03 0.028 0.64 1 -10000 0 1
RhoA/GTP 0 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.005 0.032 -10000 0 -0.28 6 6
regulation of stress fiber formation -0.036 0.029 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) -0.005 0.033 -10000 0 -0.21 17 17
KRAS 0.01 0 -10000 0 -10000 0 0
G13/GTP 0 0.006 -10000 0 -0.16 1 1
pseudopodium formation 0.036 0.029 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 0 0.007 -10000 0 -0.18 1 1
GRB2 0.01 0 -10000 0 -10000 0 0
GNG2 0.009 0.018 -10000 0 -0.32 2 2
GNAO1 0.004 0.044 -10000 0 -0.32 12 12
HRAS 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.037 0.035 -10000 0 -0.3 2 2
E2/ER beta (dimer) -0.006 0.04 -10000 0 -0.26 16 16
mol:GDP -0.003 0.019 -10000 0 -0.26 1 1
mol:NADP 0.037 0.035 -10000 0 -0.3 2 2
PIK3R1 0.01 0 -10000 0 -10000 0 0
mol:IP3 0.033 0.026 -10000 0 -0.23 2 2
IGF-1R heterotetramer 0.009 0.015 -10000 0 -0.37 1 1
PLCB1 0.028 0.023 -10000 0 -0.22 3 3
PLCB2 0.029 0.023 -10000 0 -0.24 2 2
IGF1 0.005 0.039 -10000 0 -0.33 9 9
mol:L-citrulline 0.037 0.035 -10000 0 -0.3 2 2
RHOA 0.01 0 -10000 0 -10000 0 0
Gai/GDP -0.013 0.086 -10000 0 -0.64 12 12
JNK cascade -0.006 0.04 -10000 0 -0.26 16 16
BCAR1 0.01 0 -10000 0 -10000 0 0
ESR2 0.001 0.059 -10000 0 -0.37 16 16
GNAQ 0.01 0 -10000 0 -10000 0 0
ESR1 0.009 0.013 -10000 0 -0.32 1 1
Gq family/GDP/Gbeta gamma 0.032 0.023 -10000 0 -0.31 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.03 0.017 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.009 0.046 -10000 0 -0.34 10 10
GNAZ 0.009 0.018 -10000 0 -0.32 2 2
E2/ER alpha (dimer) 0 0.009 -10000 0 -0.22 1 1
STRN 0.006 0.034 -10000 0 -0.32 7 7
GNAL -0.073 0.14 -10000 0 -0.32 165 165
PELP1 0.01 0 -10000 0 -10000 0 0
MAPK11 0.009 0.036 -10000 0 -0.2 18 18
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.009 0.021 -10000 0 -0.37 2 2
GNAI1 0.006 0.036 -10000 0 -0.32 8 8
HBEGF -0.013 0.094 -10000 0 -0.35 18 18
cAMP biosynthetic process -0.037 0.068 -10000 0 -0.15 169 169
SRC 0.034 0.047 -10000 0 -0.34 6 6
PI3K 0 0 -10000 0 -10000 0 0
GNB1 0.01 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.003 0.017 -10000 0 -0.22 1 1
SOS1 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.008 0.04 -10000 0 -0.28 10 10
Gs family/GTP -0.037 0.068 -10000 0 -0.15 169 169
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0 0 -10000 0 -10000 0 0
vasodilation 0.036 0.034 -10000 0 -0.28 2 2
mol:DAG 0.033 0.026 -10000 0 -0.23 2 2
Gs family/GDP/Gbeta gamma -0.026 0.047 -10000 0 -0.2 16 16
MSN 0.037 0.03 -10000 0 -10000 0 0
Gq family/GTP -0.002 0.017 -10000 0 -0.29 1 1
mol:PI-3-4-5-P3 0.027 0.028 -10000 0 -0.66 1 1
NRAS 0.01 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.036 0.034 0.28 2 -10000 0 2
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.003 0.017 -10000 0 -0.24 1 1
NOS3 0.037 0.036 -10000 0 -0.31 2 2
GNA11 0.009 0.018 -10000 0 -0.32 2 2
MAPKKK cascade 0.04 0.043 -10000 0 -0.46 1 1
E2/ER alpha (dimer)/PELP1/Src -0.005 0.034 -10000 0 -0.3 6 6
ruffle organization 0.036 0.029 -10000 0 -10000 0 0
ROCK2 0.038 0.006 -10000 0 -10000 0 0
GNA14 0.009 0.013 -10000 0 -0.32 1 1
GNA15 0.009 0.02 -10000 0 -0.35 2 2
GNA13 0.01 0 -10000 0 -10000 0 0
MMP9 -0.017 0.098 -10000 0 -0.35 19 19
MMP2 0.001 0.089 -10000 0 -0.34 15 15
Regulation of Androgen receptor activity

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
HDAC1 0.017 0.011 -9999 0 -0.25 1 1
SMARCC1 0.012 0.018 -9999 0 -10000 0 0
REL 0.008 0.027 -9999 0 -0.34 4 4
HDAC7 0.028 0.042 -9999 0 -10000 0 0
JUN 0.009 0.002 -9999 0 -10000 0 0
EP300 0.01 0 -9999 0 -10000 0 0
KAT2B 0.009 0.015 -9999 0 -0.37 1 1
KAT5 0.01 0 -9999 0 -10000 0 0
MAPK14 0.019 0.007 -9999 0 -10000 0 0
FOXO1 0.01 0 -9999 0 -10000 0 0
T-DHT/AR 0.028 0.044 -9999 0 -0.23 2 2
MAP2K6 0.011 0.002 -9999 0 -10000 0 0
BRM/BAF57 0 0.002 -9999 0 -10000 0 0
MAP2K4 0.011 0.002 -9999 0 -10000 0 0
SMARCA2 0.009 0.003 -9999 0 -10000 0 0
PDE9A 0.011 0.031 -9999 0 -10000 0 0
NCOA2 0.004 0.044 -9999 0 -0.32 12 12
CEBPA 0.007 0.032 -9999 0 -0.36 5 5
EHMT2 0.01 0.002 -9999 0 -10000 0 0
cell proliferation 0.045 0.049 -9999 0 -10000 0 0
NR0B1 -0.037 0.12 -9999 0 -0.36 85 85
EGR1 -0.002 0.06 -9999 0 -0.33 22 22
RXRs/9cRA -0.01 0.038 -9999 0 -0.15 44 44
AR/RACK1/Src 0.002 0.039 -9999 0 -0.29 1 1
AR/GR -0.012 0.045 -9999 0 -10000 0 0
GNB2L1 0.001 0.059 -9999 0 -0.37 16 16
PKN1 0.01 0.001 -9999 0 -10000 0 0
RCHY1 0.01 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -9999 0 -10000 0 0
MAPK8 0.017 0.021 -9999 0 -0.22 5 5
T-DHT/AR/TIF2/CARM1 0.005 0.038 -9999 0 -0.29 5 5
SRC 0.034 0.017 -9999 0 -0.16 2 2
NR3C1 0.01 0 -9999 0 -10000 0 0
KLK3 -0.037 0.16 -9999 0 -1.1 12 12
APPBP2 0.011 0.002 -9999 0 -10000 0 0
TRIM24 0.008 0.026 -9999 0 -0.37 3 3
T-DHT/AR/TIP60 0.012 0.033 -9999 0 -0.19 2 2
TMPRSS2 -0.003 0.069 -9999 0 -10000 0 0
RXRG -0.012 0.083 -9999 0 -0.33 44 44
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.01 0.001 -9999 0 -10000 0 0
RXRB 0.01 0.001 -9999 0 -10000 0 0
CARM1 0.01 0.001 -9999 0 -10000 0 0
NR2C2 0.01 0 -9999 0 -10000 0 0
KLK2 0.013 0.065 -9999 0 -0.27 19 19
AR -0.019 0.053 -9999 0 -0.14 1 1
SENP1 0.01 0.001 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
MDM2 0.003 0.053 -9999 0 -0.38 13 13
SRY -0.041 0.12 -9999 0 -0.37 78 78
GATA2 0.008 0.03 -9999 0 -0.37 4 4
MYST2 0.01 0.001 -9999 0 -10000 0 0
HOXB13 -0.085 0.16 -9999 0 -0.38 157 157
T-DHT/AR/RACK1/Src 0.016 0.042 -9999 0 -0.3 1 1
positive regulation of transcription 0.008 0.03 -9999 0 -0.37 4 4
DNAJA1 0.011 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.015 -9999 0 -10000 0 0
NCOA1 0.012 0.004 -9999 0 -10000 0 0
SPDEF -0.023 0.098 -9999 0 -0.32 64 64
T-DHT/AR/TIF2 0.024 0.035 -9999 0 -0.25 5 5
T-DHT/AR/Hsp90 0.012 0.033 -9999 0 -0.19 2 2
GSK3B 0.011 0.002 -9999 0 -10000 0 0
NR2C1 0.01 0.001 -9999 0 -10000 0 0
mol:T-DHT 0.03 0.017 -9999 0 -0.18 2 2
SIRT1 0.01 0 -9999 0 -10000 0 0
ZMIZ2 0.011 0.005 -9999 0 -10000 0 0
POU2F1 0.019 0.028 -9999 0 -0.38 3 3
T-DHT/AR/DAX-1 -0.009 0.064 -9999 0 -0.2 30 30
CREBBP 0.01 0.001 -9999 0 -10000 0 0
SMARCE1 0.009 0.003 -9999 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.008 0.03 -9999 0 -0.37 4 4
alphaV beta3 Integrin -0.048 0.099 -9999 0 -0.25 128 128
PTK2 -0.014 0.042 -9999 0 -0.36 6 6
positive regulation of JNK cascade -0.003 0.025 -9999 0 -0.28 5 5
CDC42/GDP 0.037 0.04 -9999 0 -0.37 5 5
Rac1/GDP 0.038 0.04 -9999 0 -0.37 5 5
RAP1B 0.005 0.044 -9999 0 -0.37 9 9
RAP1A 0.01 0 -9999 0 -10000 0 0
CTNNB1 0.01 0 -9999 0 -10000 0 0
CDC42/GTP -0.002 0.031 -9999 0 -0.34 5 5
nectin-3/I-afadin -0.002 0.018 -9999 0 -0.21 5 5
RAPGEF1 0.033 0.044 -9999 0 -0.41 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.028 0.048 -9999 0 -0.47 5 5
PDGFB-D/PDGFRB 0.008 0.03 -9999 0 -0.37 4 4
TLN1 0.026 0.011 -9999 0 -10000 0 0
Rap1/GTP -0.004 0.031 -9999 0 -0.28 6 6
IQGAP1 0.006 0.039 -9999 0 -0.37 7 7
Rap1/GTP/I-afadin -0.002 0.021 -9999 0 -0.18 9 9
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.002 0.018 -9999 0 -0.21 5 5
PVR 0.01 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.01 0 -9999 0 -10000 0 0
mol:GDP 0.036 0.047 -9999 0 -0.45 5 5
MLLT4 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K -0.002 0.016 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.002 0.02 -9999 0 -0.21 6 6
positive regulation of lamellipodium assembly -0.003 0.026 -9999 0 -0.29 5 5
PVRL1 0.007 0.032 -9999 0 -0.32 6 6
PVRL3 0.007 0.029 -9999 0 -0.32 5 5
PVRL2 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
CDH1 -0.008 0.077 -9999 0 -0.34 34 34
CLDN1 0.005 0.041 -9999 0 -0.33 10 10
JAM-A/CLDN1 -0.005 0.026 -9999 0 -0.18 6 6
SRC -0.007 0.046 -9999 0 -0.52 5 5
ITGB3 -0.064 0.15 -9999 0 -0.37 128 128
nectin-1(dimer)/I-afadin/I-afadin -0.002 0.02 -9999 0 -0.21 6 6
FARP2 0.031 0.046 -9999 0 -0.44 5 5
RAC1 0.01 0 -9999 0 -10000 0 0
CTNNA1 0.01 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.001 0.015 -9999 0 -0.17 5 5
nectin-1/I-afadin -0.002 0.02 -9999 0 -0.21 6 6
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin -0.002 0.021 -9999 0 -0.21 7 7
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.003 0.021 -9999 0 -0.17 11 11
CDC42/GTP/IQGAP1/filamentous actin -0.002 0.021 -9999 0 -0.21 7 7
F11R 0.007 0.033 -9999 0 -0.37 5 5
positive regulation of filopodium formation -0.003 0.025 -9999 0 -0.28 5 5
alphaV/beta3 Integrin/Talin 0.001 0.071 -9999 0 -0.25 4 4
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0.021 0.012 -9999 0 -10000 0 0
VAV2 0.031 0.046 -9999 0 -0.45 5 5
RAP1/GDP -0.005 0.035 -9999 0 -0.34 5 5
ITGAV 0.01 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.001 0.015 -9999 0 -0.17 5 5
nectin-3(dimer)/I-afadin/I-afadin -0.002 0.018 -9999 0 -0.21 5 5
Rac1/GTP -0.003 0.031 -9999 0 -0.36 5 5
PTPRM -0.001 0.011 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.007 0.03 -9999 0 -0.26 1 1
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 -0.07 0.11 -10000 0 -10000 0 0
oxygen homeostasis 0.006 0.013 -10000 0 -10000 0 0
TCEB2 0.01 0 -10000 0 -10000 0 0
TCEB1 0.01 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.009 0.027 -10000 0 -10000 0 0
EPO 0.06 0.2 -10000 0 -0.48 41 41
FIH (dimer) 0.017 0.011 -10000 0 -10000 0 0
APEX1 0.015 0.013 -10000 0 -10000 0 0
SERPINE1 0.051 0.23 -10000 0 -0.46 71 71
FLT1 -0.002 0.016 -10000 0 -10000 0 0
ADORA2A 0.079 0.18 -10000 0 -0.45 5 5
germ cell development 0.084 0.17 -10000 0 -0.48 3 3
SLC11A2 0.085 0.17 -10000 0 -0.49 3 3
BHLHE40 0.083 0.18 -10000 0 -0.47 4 4
HIF1AN 0.017 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.028 0.068 -10000 0 -0.24 35 35
ETS1 0.009 0.072 -10000 0 -0.37 23 23
CITED2 -0.002 0.013 -10000 0 -10000 0 0
KDR -0.004 0.032 -10000 0 -10000 0 0
PGK1 0.085 0.17 -10000 0 -0.49 3 3
SIRT1 0.01 0.002 -10000 0 -10000 0 0
response to hypoxia -0.001 0.003 -10000 0 -10000 0 0
HIF2A/ARNT 0.075 0.19 -10000 0 -0.41 37 37
EPAS1 0.058 0.078 -10000 0 -10000 0 0
SP1 0.009 0.012 -10000 0 -10000 0 0
ABCG2 0.085 0.18 -10000 0 -0.54 3 3
EFNA1 0.085 0.17 -10000 0 -0.49 3 3
FXN 0.079 0.18 -10000 0 -0.45 5 5
POU5F1 0.084 0.17 -10000 0 -0.5 3 3
neuron apoptosis -0.073 0.19 0.4 37 -10000 0 37
EP300 0.01 0 -10000 0 -10000 0 0
EGLN3 0.017 0.011 -10000 0 -10000 0 0
EGLN2 0.017 0.011 -10000 0 -10000 0 0
EGLN1 0.017 0.011 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0.01 0 -10000 0 -10000 0 0
ARNT 0.015 0.013 -10000 0 -10000 0 0
SLC2A1 0.079 0.18 -10000 0 -0.45 5 5
TWIST1 0.077 0.18 -10000 0 -0.46 10 10
ELK1 0.016 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.022 0.055 -10000 0 -0.28 1 1
VEGFA 0.066 0.21 -10000 0 -0.47 66 66
CREBBP 0.01 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.016 0.038 -9999 0 -0.17 27 27
SNTA1 0.007 0.032 -9999 0 -0.32 6 6
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.016 0.038 -9999 0 -0.17 27 27
MAPK12 0.024 0.004 -9999 0 -10000 0 0
CCND1 0.014 0.015 -9999 0 -10000 0 0
p38 gamma/SNTA1 0.028 0.005 -9999 0 -10000 0 0
MAP2K3 0.009 0.015 -9999 0 -0.37 1 1
PKN1 0.01 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.024 0.004 -9999 0 -10000 0 0
MAP2K6 0.019 0.005 -9999 0 -10000 0 0
MAPT 0.016 0.042 -9999 0 -0.16 33 33
MAPK13 0.009 0.046 -9999 0 -0.22 27 27
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.013 0.006 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.011 0.052 -9999 0 -0.25 30 30
FBXW11 0.01 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.02 0.015 -9999 0 -0.18 4 4
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.033 -9999 0 -10000 0 0
NFKBIA 0.005 0.038 -9999 0 -0.14 8 8
MAPK14 0.01 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.021 0 -9999 0 -10000 0 0
ARRB2 0.014 0 -9999 0 -10000 0 0
REL 0.008 0.027 -9999 0 -0.34 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.011 0.046 -9999 0 -0.2 30 30
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
NFKB1 0.018 0 -9999 0 -10000 0 0
RELA 0.01 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.012 0.035 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.024 0.032 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.012 0.035 -9999 0 -10000 0 0
IKBKB 0.01 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.01 0 -9999 0 -10000 0 0
SYK 0.004 0.047 -9999 0 -0.37 10 10
I kappa B alpha/PIK3R1 0.01 0.035 -9999 0 -10000 0 0
cell death 0.023 0.031 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.02 0.015 -9999 0 -0.18 4 4
LCK -0.066 0.15 -9999 0 -0.37 132 132
BCL3 -0.007 0.08 -9999 0 -0.37 30 30
ceramide signaling pathway

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
MAP4K4 0.023 0.055 -9999 0 -0.34 3 3
BAG4 0.005 0.039 -9999 0 -0.32 9 9
BAD 0.019 0.022 -9999 0 -10000 0 0
NFKBIA 0.008 0.03 -9999 0 -0.37 4 4
BIRC3 -0.006 0.075 -9999 0 -0.35 30 30
BAX 0.019 0.022 -9999 0 -0.11 3 3
EnzymeConsortium:3.1.4.12 0.007 0.017 -9999 0 -0.085 3 3
IKBKB 0.028 0.053 -9999 0 -0.32 3 3
MAP2K2 0.028 0.024 -9999 0 -10000 0 0
MAP2K1 0.028 0.024 -9999 0 -10000 0 0
SMPD1 0.012 0.017 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.026 0.055 -9999 0 -0.33 3 3
MAP2K4 0.019 0.036 -9999 0 -0.14 21 21
protein ubiquitination 0.029 0.054 -9999 0 -0.32 3 3
EnzymeConsortium:2.7.1.37 0.03 0.029 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -0.001 2 2
RAF1 0.024 0.024 -9999 0 -10000 0 0
CRADD 0.01 0 -9999 0 -10000 0 0
mol:ceramide 0.014 0.023 -9999 0 -0.12 3 3
I-kappa-B-alpha/RELA/p50/ubiquitin -0.001 0.016 -9999 0 -0.21 4 4
MADD 0.009 0.018 -9999 0 -0.32 2 2
MAP3K1 0.014 0.037 -9999 0 -0.14 24 24
TRADD 0.01 0 -9999 0 -10000 0 0
RELA/p50 0.01 0 -9999 0 -10000 0 0
MAPK3 0.03 0.024 -9999 0 -10000 0 0
MAPK1 0.03 0.024 -9999 0 -10000 0 0
p50/RELA/I-kappa-B-alpha -0.002 0.019 -9999 0 -0.25 4 4
FADD 0.023 0.055 -9999 0 -0.34 3 3
KSR1 0.019 0.024 -9999 0 -0.11 3 3
MAPK8 0.023 0.036 -9999 0 -0.16 3 3
TRAF2 0.01 0 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.028 0.053 -9999 0 -0.32 3 3
TNF R/SODD -0.006 0.039 -9999 0 -0.24 17 17
TNF -0.02 0.097 -9999 0 -0.33 58 58
CYCS 0.02 0.022 -9999 0 -10000 0 0
IKBKG 0.028 0.053 -9999 0 -0.32 3 3
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.026 0.044 -9999 0 -0.25 13 13
RELA 0.01 0 -9999 0 -10000 0 0
RIPK1 0.01 0 -9999 0 -10000 0 0
AIFM1 0.02 0.022 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.02 0.058 -9999 0 -0.18 74 74
TNFRSF1A 0.005 0.044 -9999 0 -0.37 9 9
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.019 0.016 -9999 0 -10000 0 0
NSMAF 0.023 0.055 -9999 0 -0.34 3 3
response to hydrogen peroxide 0 0 -9999 0 -0.001 2 2
BCL2 0.01 0 -9999 0 -10000 0 0
Arf6 trafficking events

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.002 0.061 -9999 0 -0.32 23 23
CLTC 0.025 0.01 -9999 0 -0.2 1 1
calcium ion-dependent exocytosis 0.02 0.013 -9999 0 -10000 0 0
Dynamin 2/GTP -0.001 0.01 -9999 0 -0.18 2 2
EXOC4 0.01 0 -9999 0 -10000 0 0
CD59 0.023 0.005 -9999 0 -10000 0 0
CPE 0.015 0.007 -9999 0 -0.18 1 1
CTNNB1 0.01 0 -9999 0 -10000 0 0
membrane fusion 0.021 0.002 -9999 0 -10000 0 0
CTNND1 0.025 0.01 -9999 0 -0.16 2 2
DNM2 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.025 0.011 -9999 0 -0.25 1 1
TSHR -0.12 0.11 -9999 0 -0.21 389 389
INS 0.009 0.005 -9999 0 -10000 0 0
BIN1 0.01 0 -9999 0 -10000 0 0
mol:Choline 0.021 0.002 -9999 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -9999 0 -10000 0 0
mol:GDP 0.014 0.012 -9999 0 -0.21 2 2
membrane depolarization 0 0 -9999 0 -10000 0 0
ARF6 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ -0.001 0.01 -9999 0 -0.18 2 2
JUP 0.022 0.007 -9999 0 -10000 0 0
ASAP2/amphiphysin II 0 0 -9999 0 -10000 0 0
ARF6/GTP 0 0 -9999 0 -10000 0 0
CDH1 0.016 0.031 -9999 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -9999 0 -10000 0 0
MAPK8IP3 0.007 0.032 -9999 0 -0.32 6 6
positive regulation of endocytosis 0 0 -9999 0 -10000 0 0
EXOC2 0.01 0 -9999 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.034 0.003 -9999 0 -10000 0 0
insulin receptor binding 0 0 -9999 0 -10000 0 0
SPAG9 0.01 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.004 0.016 -9999 0 -10000 0 0
positive regulation of phagocytosis 0.015 0 -9999 0 -10000 0 0
ARF6/GTP/JIP3 -0.002 0.017 -9999 0 -0.18 6 6
ACAP1 0.02 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CHRM2 -0.032 0.074 -9999 0 -0.22 2 2
clathrin heavy chain/ACAP1 0.029 0.012 -9999 0 -0.19 1 1
JIP4/KLC1 0 0 -9999 0 -10000 0 0
EXOC1 0.009 0.015 -9999 0 -0.37 1 1
exocyst 0.034 0.003 -9999 0 -10000 0 0
RALA/GTP 0 0 -9999 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -9999 0 -10000 0 0
receptor recycling 0 0 -9999 0 -10000 0 0
CTNNA1 0.025 0.01 -9999 0 -0.16 2 2
NME1 0.014 0.012 -9999 0 -0.21 2 2
clathrin coat assembly 0.025 0.01 -9999 0 -0.2 1 1
IL2RA -0.004 0.042 -9999 0 -10000 0 0
VAMP3 0.015 0 -9999 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.004 0.021 -9999 0 -0.18 1 1
EXOC6 0.01 0 -9999 0 -10000 0 0
PLD1 -0.002 0.022 -9999 0 -0.21 7 7
PLD2 0 0 -9999 0 -10000 0 0
EXOC5 0.01 0 -9999 0 -10000 0 0
PIP5K1C 0.025 0.011 -9999 0 -0.25 1 1
SDC1 0.017 0.023 -9999 0 -10000 0 0
ARF6/GDP 0.013 0.012 -9999 0 -0.21 2 2
EXOC7 0.01 0 -9999 0 -10000 0 0
E-cadherin/beta catenin -0.004 0.017 -9999 0 -10000 0 0
mol:Phosphatidic acid 0.021 0.002 -9999 0 -10000 0 0
endocytosis 0 0 -9999 0 -10000 0 0
SCAMP2 0.01 0 -9999 0 -10000 0 0
ADRB2 0.029 0.01 -9999 0 -0.18 1 1
EXOC3 0.01 0 -9999 0 -10000 0 0
ASAP2 0.01 0 -9999 0 -10000 0 0
Dynamin 2/GDP 0.019 0.011 -9999 0 -0.18 2 2
KLC1 0.01 0 -9999 0 -10000 0 0
AVPR2 0.028 0.012 -9999 0 -0.19 1 1
RALA 0.01 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.014 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0 0.008 -9999 0 -10000 0 0
HDAC3 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.001 0.017 -9999 0 -0.25 3 3
GATA1/HDAC5 -0.001 0.017 -9999 0 -0.25 3 3
GATA2/HDAC5 -0.002 0.019 -9999 0 -0.25 4 4
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 0.01 0 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0 -9999 0 -10000 0 0
GATA2 0.008 0.03 -9999 0 -0.37 4 4
HDAC4/RFXANK -0.002 0.024 -9999 0 -0.25 6 6
BCOR 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.01 0 -9999 0 -10000 0 0
HDAC5 0.01 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.012 -9999 0 -0.21 2 2
Histones 0.032 0 -9999 0 -10000 0 0
ADRBK1 0.01 0 -9999 0 -10000 0 0
HDAC4 0.01 0 -9999 0 -10000 0 0
XPO1 0.01 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.01 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.01 0 -9999 0 -10000 0 0
HDAC6 0.01 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.002 0.024 -9999 0 -0.25 6 6
CAMK4 -0.085 0.15 -9999 0 -0.32 190 190
Tubulin/HDAC6 -0.001 0.011 -9999 0 -0.17 3 3
SUMO1 0.01 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.01 0 -9999 0 -10000 0 0
GATA1 0.005 0.026 -9999 0 -0.37 3 3
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
NR3C1 0.01 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.024 0 -9999 0 -10000 0 0
SRF 0.01 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.001 0.014 -9999 0 -0.21 3 3
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.01 0 -9999 0 -10000 0 0
RANGAP1 0.01 0 -9999 0 -10000 0 0
BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.048 0.076 -9999 0 -0.17 190 190
HDAC4/ER alpha 0 0.008 -9999 0 -0.21 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.032 0 -9999 0 -10000 0 0
cell motility -0.001 0.011 -9999 0 -0.17 3 3
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.01 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.01 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.01 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 0.009 0.013 -9999 0 -0.32 1 1
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.002 0.049 -9999 0 -0.32 15 15
RAN 0.01 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.003 0.019 -9999 0 -10000 0 0
GNG2 0.009 0.018 -9999 0 -0.32 2 2
NCOR2 0.01 0 -9999 0 -10000 0 0
TUBB2A 0.008 0.022 -9999 0 -0.32 3 3
HDAC11 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
RANBP2 0.01 0 -9999 0 -10000 0 0
ANKRA2 0.01 0 -9999 0 -10000 0 0
RFXANK 0.006 0.036 -9999 0 -0.37 6 6
nuclear import 0 0 -9999 0 -10000 0 0
FoxO family signaling

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
G6PC -0.007 0.068 -9999 0 -10000 0 0
PLK1 0 0.15 -9999 0 -10000 0 0
CDKN1B 0.042 0.096 -9999 0 -10000 0 0
FOXO3 0.026 0.11 -9999 0 -10000 0 0
KAT2B 0.012 0.019 -9999 0 -0.36 1 1
FOXO1/SIRT1 -0.023 0.046 -9999 0 -10000 0 0
CAT 0.031 0.1 -9999 0 -10000 0 0
CTNNB1 0.01 0 -9999 0 -10000 0 0
AKT1 0.014 0.02 -9999 0 -0.38 1 1
FOXO1 -0.009 0.066 -9999 0 -10000 0 0
MAPK10 0.027 0.01 -9999 0 -10000 0 0
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
FOXO4 0.07 0.038 -9999 0 -10000 0 0
response to oxidative stress 0.004 0.016 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.007 0.09 -9999 0 -0.37 1 1
XPO1 0.01 0 -9999 0 -10000 0 0
EP300 0.011 0.003 -9999 0 -10000 0 0
BCL2L11 0.02 0.033 -9999 0 -10000 0 0
FOXO1/SKP2 -0.005 0.059 -9999 0 -0.28 1 1
mol:GDP 0.004 0.016 -9999 0 -10000 0 0
RAN 0.011 0.001 -9999 0 -10000 0 0
GADD45A 0.046 0.094 -9999 0 -10000 0 0
YWHAQ 0.01 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.043 0.032 -9999 0 -10000 0 0
MST1 -0.032 0.12 -9999 0 -0.37 78 78
CSNK1D 0.01 0 -9999 0 -10000 0 0
CSNK1E 0.01 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.038 0.038 -9999 0 -0.27 1 1
YWHAB 0.01 0 -9999 0 -10000 0 0
MAPK8 0.028 0.011 -9999 0 -10000 0 0
MAPK9 0.027 0.01 -9999 0 -10000 0 0
YWHAG 0.01 0 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
YWHAZ 0.01 0 -9999 0 -10000 0 0
SIRT1 0.005 0.007 -9999 0 -10000 0 0
SOD2 0.044 0.12 -9999 0 -0.36 7 7
RBL2 0.047 0.083 -9999 0 -10000 0 0
RAL/GDP 0.017 0.014 -9999 0 -10000 0 0
CHUK 0.013 0.012 -9999 0 -10000 0 0
Ran/GTP 0.01 0.003 -9999 0 -10000 0 0
CSNK1G2 0.01 0 -9999 0 -10000 0 0
RAL/GTP 0.024 0.014 -9999 0 -10000 0 0
CSNK1G1 0.01 0 -9999 0 -10000 0 0
FASLG 0.011 0.046 -9999 0 -10000 0 0
SKP2 0.009 0.021 -9999 0 -0.37 2 2
USP7 0.011 0.001 -9999 0 -10000 0 0
IKBKB 0.013 0.012 -9999 0 -10000 0 0
CCNB1 0.019 0.13 -9999 0 -10000 0 0
FOXO1-3a-4/beta catenin -0.015 0.056 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.059 -9999 0 -0.27 1 1
CSNK1A1 0.01 0 -9999 0 -10000 0 0
SGK1 0.013 0.012 -9999 0 -10000 0 0
CSNK1G3 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.017 0.006 -9999 0 -10000 0 0
ZFAND5 0.071 0.035 -9999 0 -10000 0 0
SFN -0.008 0.079 -9999 0 -0.37 30 30
CDK2 -0.11 0.18 -9999 0 -0.37 217 217
FOXO3A/14-3-3 0.038 0.039 -9999 0 -0.24 1 1
CREBBP 0.011 0.006 -9999 0 -10000 0 0
FBXO32 0.027 0.11 -9999 0 -10000 0 0
BCL6 0.047 0.083 -9999 0 -10000 0 0
RALB 0.011 0.001 -9999 0 -10000 0 0
RALA 0.011 0.001 -9999 0 -10000 0 0
YWHAH 0.004 0.044 -9999 0 -0.32 12 12
Class I PI3K signaling events

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
ARF5/GTP -0.003 0.02 -9999 0 -10000 0 0
DAPP1 0.011 0.046 -9999 0 -0.25 5 5
Src family/SYK family/BLNK-LAT/BTK-ITK 0.017 0.058 -9999 0 -0.31 7 7
mol:DAG 0.025 0.043 -9999 0 -0.18 7 7
HRAS 0.01 0.002 -9999 0 -10000 0 0
RAP1A 0.01 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.033 0.014 -9999 0 -0.16 1 1
PLCG2 0.007 0.033 -9999 0 -0.37 5 5
PLCG1 0.01 0 -9999 0 -10000 0 0
ARF5 0.01 0 -9999 0 -10000 0 0
mol:GTP -0.004 0.024 -9999 0 -10000 0 0
ARF1/GTP -0.003 0.018 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
YES1 0.009 0.015 -9999 0 -0.37 1 1
RAP1A/GTP -0.004 0.023 -9999 0 -10000 0 0
ADAP1 -0.006 0.039 -9999 0 -0.28 12 12
ARAP3 -0.004 0.024 -9999 0 -10000 0 0
INPPL1 0.01 0 -9999 0 -10000 0 0
PREX1 0.01 0 -9999 0 -10000 0 0
ARHGEF6 0.006 0.036 -9999 0 -0.37 6 6
ARHGEF7 0.01 0 -9999 0 -10000 0 0
ARF1 0.01 0 -9999 0 -10000 0 0
NRAS 0.01 0.002 -9999 0 -10000 0 0
FYN 0.01 0 -9999 0 -10000 0 0
ARF6 0.01 0 -9999 0 -10000 0 0
FGR 0.006 0.036 -9999 0 -0.37 6 6
mol:Ca2+ 0.02 0.025 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.009 0.013 -9999 0 -0.32 1 1
ZAP70 0.003 0.052 -9999 0 -0.37 13 13
mol:IP3 0.024 0.032 -9999 0 -10000 0 0
LYN 0.008 0.026 -9999 0 -0.37 3 3
ARF1/GDP 0.033 0.014 -9999 0 -0.16 1 1
RhoA/GDP -0.003 0.018 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
BLNK 0.007 0.031 -9999 0 -0.35 5 5
actin cytoskeleton reorganization 0.048 0.022 -9999 0 -10000 0 0
SRC 0.01 0 -9999 0 -10000 0 0
PLEKHA2 0.022 0.019 -9999 0 -0.2 5 5
RAC1 0.01 0 -9999 0 -10000 0 0
PTEN 0.001 0.004 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
ARF6/GTP -0.003 0.02 -9999 0 -10000 0 0
RhoA/GTP -0.004 0.022 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT 0.012 0.056 -9999 0 -0.28 7 7
BLK -0.054 0.14 -9999 0 -0.37 107 107
PDPK1 0.01 0 -9999 0 -10000 0 0
CYTH1 -0.004 0.021 -9999 0 -10000 0 0
HCK 0.004 0.049 -9999 0 -0.37 11 11
CYTH3 -0.004 0.021 -9999 0 -10000 0 0
CYTH2 -0.004 0.021 -9999 0 -10000 0 0
KRAS 0.01 0.002 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.002 0.01 -9999 0 -10000 0 0
SGK1 -0.002 0.011 -9999 0 -10000 0 0
INPP5D 0.007 0.033 -9999 0 -0.37 5 5
mol:GDP 0.029 0.015 -9999 0 -0.18 1 1
SOS1 0.01 0 -9999 0 -10000 0 0
SYK 0.004 0.047 -9999 0 -0.37 10 10
ARF6/GDP -0.003 0.018 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.023 -9999 0 -10000 0 0
ARAP3/RAP1A/GTP -0.004 0.024 -9999 0 -10000 0 0
VAV1 0.008 0.025 -9999 0 -0.36 3 3
mol:PI-3-4-P2 0.016 0.023 -9999 0 -0.25 5 5
RAS family/GTP/PI3K Class I 0.02 0.028 -9999 0 -10000 0 0
PLEKHA1 0.022 0.019 -9999 0 -0.2 5 5
Rac1/GDP 0.033 0.014 -9999 0 -0.16 1 1
LAT 0.008 0.025 -9999 0 -0.36 3 3
Rac1/GTP 0.032 0.013 -9999 0 -0.21 1 1
ITK -0.007 0.033 -9999 0 -0.3 2 2
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.027 0.053 -9999 0 -0.25 7 7
LCK -0.066 0.15 -9999 0 -0.37 132 132
BTK -0.009 0.034 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.01 0 -9999 0 -10000 0 0
PTK2 0.01 0 -9999 0 -10000 0 0
CRKL 0.019 0.021 -9999 0 -0.15 9 9
GRB2/SOS1/SHC -0.006 0.034 -9999 0 -0.2 19 19
HRAS 0.01 0 -9999 0 -10000 0 0
IRS1/Crk 0.019 0.02 -9999 0 -0.15 8 8
IGF-1R heterotetramer/IGF1/PTP1B -0.002 0.02 -9999 0 -0.16 10 10
AKT1 0.034 0.018 -9999 0 -10000 0 0
BAD 0.039 0.018 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.019 0.02 -9999 0 -0.15 8 8
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.018 0.02 -9999 0 -0.15 8 8
RAF1 0.041 0.017 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.002 0.016 -9999 0 -10000 0 0
YWHAZ 0.01 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.013 0.022 -9999 0 -0.16 10 10
PIK3CA 0.01 0 -9999 0 -10000 0 0
RPS6KB1 0.034 0.017 -9999 0 -10000 0 0
GNB2L1 0.001 0.059 -9999 0 -0.37 16 16
positive regulation of MAPKKK cascade 0.035 0.016 -9999 0 -10000 0 0
PXN 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.005 0.026 -9999 0 -0.25 1 1
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.006 0.032 -9999 0 -0.17 19 19
IGF-1R heterotetramer 0.009 0.015 -9999 0 -0.36 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck -0.002 0.017 -9999 0 -0.15 8 8
Crk/p130 Cas/Paxillin -0.002 0.014 -9999 0 -10000 0 0
IGF1R 0.009 0.015 -9999 0 -0.36 1 1
IGF1 0.006 0.04 -9999 0 -0.34 9 9
IRS2/Crk 0.024 0.02 -9999 0 -0.16 1 1
PI3K -0.002 0.016 -9999 0 -10000 0 0
apoptosis -0.041 0.016 -9999 0 -10000 0 0
HRAS/GDP 0 0 -9999 0 -10000 0 0
PRKCD 0.025 0.042 -9999 0 -0.32 8 8
RAF1/14-3-3 E 0.043 0.016 -9999 0 -10000 0 0
BAD/14-3-3 0.043 0.017 -9999 0 -10000 0 0
PRKCZ 0.03 0.022 -9999 0 -0.25 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.001 0.009 -9999 0 -10000 0 0
PTPN1 0.01 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.021 0.038 -9999 0 -0.28 8 8
BCAR1 0.01 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.007 0.036 -9999 0 -0.2 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.01 0 -9999 0 -10000 0 0
IRS1/NCK2 0.019 0.02 -9999 0 -0.15 8 8
GRB10 0.01 0 -9999 0 -10000 0 0
PTPN11 0.019 0.02 -9999 0 -0.15 8 8
IRS1 0.013 0.022 -9999 0 -0.16 10 10
IRS2 0.019 0.021 -9999 0 -0.15 9 9
IGF-1R heterotetramer/IGF1 -0.003 0.028 -9999 0 -0.23 10 10
GRB2 0.01 0 -9999 0 -10000 0 0
PDPK1 0.029 0.018 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
PRKD1 0.025 0.038 -9999 0 -0.26 8 8
SHC1 -0.001 0.064 -9999 0 -0.37 19 19
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 -0.041 0.098 -9999 0 -0.41 1 1
CLOCK 0.005 0.042 -9999 0 -0.32 11 11
TIMELESS/CRY2 -0.001 0.084 -9999 0 -10000 0 0
DEC1/BMAL1 0 0.001 -9999 0 -10000 0 0
ATR 0.01 0 -9999 0 -10000 0 0
NR1D1 0.013 0.049 -9999 0 -10000 0 0
ARNTL 0.01 0.006 -9999 0 -10000 0 0
TIMELESS -0.006 0.093 -9999 0 -10000 0 0
NPAS2 0.009 0.023 -9999 0 -0.33 3 3
CRY2 0.009 0.013 -9999 0 -0.32 1 1
mol:CO -0.002 0.022 -9999 0 -10000 0 0
CHEK1 -0.021 0.1 -9999 0 -0.37 54 54
mol:HEME 0.002 0.022 -9999 0 -10000 0 0
PER1 0.01 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.021 0.034 -9999 0 -0.21 1 1
BMAL1/CLOCK 0.012 0.067 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.041 0.098 -9999 0 -0.41 1 1
TIMELESS/CHEK1/ATR -0.041 0.099 -9999 0 -0.41 1 1
mol:NADPH 0.002 0.022 -9999 0 -10000 0 0
PER1/TIMELESS -0.001 0.084 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.017 0.051 -9999 0 -0.19 47 47
Ran/GTP/Exportin 1/HDAC1 0 0.006 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.063 -9999 0 -0.2 47 47
SUMO1 0.01 0 -9999 0 -10000 0 0
ZFPM1 0.01 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.017 0 -9999 0 -10000 0 0
FKBP3 0.01 0 -9999 0 -10000 0 0
Histones -0.008 0.023 -9999 0 -10000 0 0
YY1/LSF 0.024 0.004 -9999 0 -10000 0 0
SMG5 0.01 0 -9999 0 -10000 0 0
RAN 0.01 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.009 0.052 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.012 0.038 -9999 0 -0.17 1 1
SAP18 0.01 0 -9999 0 -10000 0 0
RELA 0.014 0.051 -9999 0 -0.16 47 47
HDAC1/Smad7 0 0.008 -9999 0 -0.2 1 1
RANGAP1 0.01 0 -9999 0 -10000 0 0
HDAC3/TR2 0.013 0.037 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.037 0.012 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.017 0.046 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.008 0.03 -9999 0 -0.37 4 4
GATA1 0.005 0.026 -9999 0 -0.37 3 3
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.044 0.014 -9999 0 -10000 0 0
RBBP7 0.01 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.01 0 -9999 0 -10000 0 0
MAX 0.01 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.01 0 -9999 0 -10000 0 0
NFKBIA 0.008 0.043 -9999 0 -10000 0 0
KAT2B 0.009 0.015 -9999 0 -0.37 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.034 0.005 -9999 0 -10000 0 0
SIN3 complex 0 0.007 -9999 0 -10000 0 0
SMURF1 0.01 0 -9999 0 -10000 0 0
CHD3 0.008 0.026 -9999 0 -0.32 4 4
SAP30 0.009 0.015 -9999 0 -0.37 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.01 0 -9999 0 -10000 0 0
YY1/HDAC3 0.023 0.035 -9999 0 -10000 0 0
YY1/HDAC2 0.024 0.004 -9999 0 -10000 0 0
YY1/HDAC1 0.024 0.009 -9999 0 -0.19 1 1
NuRD/MBD2 Complex (MeCP1) 0.037 0.012 -9999 0 -10000 0 0
PPARG -0.018 0.056 -9999 0 -0.21 48 48
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.01 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.01 0 -9999 0 -10000 0 0
TNFRSF1A 0.005 0.044 -9999 0 -0.37 9 9
HDAC3/SMRT (N-CoR2) 0.013 0.037 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0.008 -9999 0 -0.2 1 1
CREBBP 0.01 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.039 0.012 -9999 0 -10000 0 0
HDAC1 0.009 0.015 -9999 0 -0.37 1 1
HDAC3 0.009 0.042 -9999 0 -10000 0 0
HDAC2 0.01 0 -9999 0 -10000 0 0
YY1 0.024 0.005 -9999 0 -10000 0 0
HDAC8 0.01 0 -9999 0 -10000 0 0
SMAD7 0.01 0 -9999 0 -10000 0 0
NCOR2 0.01 0 -9999 0 -10000 0 0
MXD1 0.01 0 -9999 0 -10000 0 0
STAT3 0.02 0 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.01 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.009 -9999 0 -10000 0 0
YY1/SAP30/HDAC1 -0.001 0.009 -9999 0 -10000 0 0
EP300 0.01 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.02 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.043 -9999 0 -10000 0 0
histone deacetylation 0.037 0.012 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.021 0.034 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GATAD2B 0.01 0 -9999 0 -10000 0 0
GATAD2A 0.01 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.012 0.039 -9999 0 -0.17 4 4
GATA1/HDAC1 -0.002 0.02 -9999 0 -0.25 4 4
GATA1/HDAC3 0.005 0.039 -9999 0 -0.17 3 3
CHD4 0.01 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.022 0.068 -9999 0 -0.22 67 67
SIN3/HDAC complex/Mad/Max 0.038 0.004 -9999 0 -10000 0 0
NuRD Complex 0.043 0.012 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.007 0.023 -9999 0 -10000 0 0
SIN3B 0.01 0 -9999 0 -10000 0 0
MTA2 0.01 0 -9999 0 -10000 0 0
SIN3A 0.01 0 -9999 0 -10000 0 0
XPO1 0.01 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.023 0.007 -9999 0 -0.16 1 1
HDAC complex 0 0.007 -9999 0 -0.18 1 1
GATA1/Fog1 -0.001 0.017 -9999 0 -0.25 3 3
FKBP25/HDAC1/HDAC2 0 0.008 -9999 0 -0.2 1 1
TNF -0.02 0.097 -9999 0 -0.33 58 58
negative regulation of cell growth 0.037 0.004 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.037 0.012 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.018 0.057 -9999 0 -0.22 47 47
SIN3/HDAC complex/NCoR1 0.036 0.004 -9999 0 -10000 0 0
TFCP2 0.009 0.013 -9999 0 -0.32 1 1
NR2C1 0.01 0 -9999 0 -10000 0 0
MBD3 0.01 0 -9999 0 -10000 0 0
MBD2 0.01 0 -9999 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.01 0 -9999 0 -10000 0 0
SMAD2 0.014 0.012 -9999 0 -10000 0 0
SMAD3 0.03 0.017 -9999 0 -10000 0 0
SMAD3/SMAD4 0.036 0.007 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0 0.002 -9999 0 -10000 0 0
PPM1A 0.01 0 -9999 0 -10000 0 0
CALM1 0.01 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.018 0.01 -9999 0 -10000 0 0
MAP3K1 -0.002 0.067 -9999 0 -0.37 21 21
TRAP-1/SMAD4 -0.002 0.018 -9999 0 -0.21 5 5
MAPK3 0.01 0 -9999 0 -10000 0 0
MAPK1 0.01 0 -9999 0 -10000 0 0
NUP214 0.01 0 -9999 0 -10000 0 0
CTDSP1 0.009 0.015 -9999 0 -0.37 1 1
CTDSP2 0 0.06 -9999 0 -0.37 17 17
CTDSPL 0.01 0 -9999 0 -10000 0 0
KPNB1 0.01 0 -9999 0 -10000 0 0
TGFBRAP1 0.007 0.029 -9999 0 -0.32 5 5
UBE2I 0.01 0 -9999 0 -10000 0 0
NUP153 0.01 0 -9999 0 -10000 0 0
KPNA2 0.01 0 -9999 0 -10000 0 0
PIAS4 0.01 0 -9999 0 -10000 0 0
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate -0.004 0.022 -9999 0 -0.28 1 1
PDGFB-D/PDGFRB/SLAP -0.006 0.038 -9999 0 -0.25 15 15
PDGFB-D/PDGFRB/APS/CBL -0.01 0.045 -9999 0 -0.2 34 34
AKT1 0.045 0.014 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.014 0.029 -9999 0 -0.27 1 1
PIK3CA 0.01 0 -9999 0 -10000 0 0
FGR 0.001 0.016 -9999 0 -10000 0 0
mol:Ca2+ 0.014 0.022 -9999 0 -10000 0 0
MYC -0.037 0.11 -9999 0 -0.34 1 1
SHC1 -0.001 0.064 -9999 0 -0.37 19 19
HRAS/GDP 0.003 0.016 -9999 0 -0.16 1 1
LRP1/PDGFRB/PDGFB -0.001 0.015 -9999 0 -0.2 4 4
GRB10 0.01 0 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
GO:0007205 0.013 0.022 -9999 0 -10000 0 0
PTEN 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
GRB7 0.004 0.033 -9999 0 -0.37 5 5
PDGFB-D/PDGFRB/SHP2 -0.001 0.019 -9999 0 -0.25 4 4
PDGFB-D/PDGFRB/GRB10 -0.001 0.019 -9999 0 -0.25 4 4
cell cycle arrest -0.006 0.037 -9999 0 -0.25 15 15
HRAS 0.01 0 -9999 0 -10000 0 0
HIF1A 0.048 0.018 -9999 0 -10000 0 0
GAB1 0.003 0.039 -9999 0 -0.23 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.005 0.039 -9999 0 -0.24 1 1
PDGFB-D/PDGFRB 0.005 0.019 -9999 0 -0.2 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.001 0.019 -9999 0 -0.25 4 4
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.014 0.032 -9999 0 -0.32 1 1
positive regulation of MAPKKK cascade -0.001 0.019 -9999 0 -0.25 4 4
PIK3R1 0.01 0 -9999 0 -10000 0 0
mol:IP3 0.014 0.022 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.01 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.003 0.032 -9999 0 -0.28 8 8
SHB 0.01 0 -9999 0 -10000 0 0
BLK -0.009 0.026 -9999 0 -10000 0 0
PTPN2 0.007 0.005 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.001 0.019 -9999 0 -0.25 4 4
BCAR1 0.01 0 -9999 0 -10000 0 0
VAV2 -0.003 0.052 -9999 0 -0.28 1 1
CBL 0.01 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.001 0.019 -9999 0 -0.25 4 4
LCK -0.011 0.026 -9999 0 -0.25 1 1
PDGFRB 0.005 0.03 -9999 0 -0.37 4 4
ACP1 0.01 0 -9999 0 -10000 0 0
HCK 0.001 0.018 -9999 0 -0.25 1 1
ABL1 0.008 0.03 -9999 0 -0.21 1 1
PDGFB-D/PDGFRB/CBL 0.004 0.036 -9999 0 -10000 0 0
PTPN1 0.007 0.005 -9999 0 -10000 0 0
SNX15 0.01 0 -9999 0 -10000 0 0
STAT3 0.01 0 -9999 0 -10000 0 0
STAT1 0.006 0.039 -9999 0 -0.37 7 7
cell proliferation -0.034 0.11 -9999 0 -0.32 1 1
SLA 0.004 0.049 -9999 0 -0.37 11 11
actin cytoskeleton reorganization 0.026 0.024 -9999 0 -10000 0 0
SRC 0.002 0.014 -9999 0 -10000 0 0
PI3K -0.001 0.009 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.009 0.049 -9999 0 -0.25 23 23
SH2B2 -0.007 0.08 -9999 0 -0.37 30 30
PLCgamma1/SPHK1 0.015 0.029 -9999 0 -0.28 1 1
LYN 0.002 0.015 -9999 0 -10000 0 0
LRP1 0.01 0 -9999 0 -10000 0 0
SOS1 0.01 0 -9999 0 -10000 0 0
STAT5B 0.01 0 -9999 0 -10000 0 0
STAT5A 0.01 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0 0.014 -9999 0 -10000 0 0
SPHK1 0.006 0.038 -9999 0 -0.37 7 7
EDG1 0 0.001 -9999 0 -10000 0 0
mol:DAG 0.014 0.022 -9999 0 -10000 0 0
PLCG1 0.014 0.022 -9999 0 -10000 0 0
NHERF/PDGFRB -0.001 0.015 -9999 0 -0.2 4 4
YES1 0.002 0.015 -9999 0 -10000 0 0
cell migration -0.001 0.015 -9999 0 -0.2 4 4
SHC/Grb2/SOS1 -0.004 0.032 -9999 0 -0.32 3 3
SLC9A3R2 0.01 0 -9999 0 -10000 0 0
SLC9A3R1 0.01 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.001 0.013 -9999 0 -0.17 4 4
FYN 0.002 0.014 -9999 0 -10000 0 0
DOK1 0.017 0.025 -9999 0 -0.21 6 6
HRAS/GTP 0 0 -9999 0 -10000 0 0
PDGFB 0.01 0 -9999 0 -10000 0 0
RAC1 -0.013 0.077 -9999 0 -0.32 1 1
PRKCD 0.017 0.02 -9999 0 -0.17 4 4
FER 0.017 0.02 -9999 0 -0.17 4 4
MAPKKK cascade -0.005 0.031 -9999 0 -0.32 3 3
RASA1 0.017 0.02 -9999 0 -0.17 4 4
NCK1 0.009 0.015 -9999 0 -0.37 1 1
NCK2 0.01 0 -9999 0 -10000 0 0
p62DOK/Csk 0.016 0.026 -9999 0 -0.33 1 1
PDGFB-D/PDGFRB/SHB -0.001 0.019 -9999 0 -0.25 4 4
chemotaxis 0.008 0.029 -9999 0 -0.21 1 1
STAT1-3-5/STAT1-3-5 -0.002 0.017 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.002 0.02 -9999 0 -0.26 4 4
PTPRJ 0.01 0 -9999 0 -10000 0 0
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.009 0.02 0.35 2 -10000 0 2
PI3K Class IB/PDE3B 0.009 0.02 -10000 0 -0.35 2 2
PDE3B 0.009 0.02 -10000 0 -0.35 2 2
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.015 0.07 -10000 0 -10000 0 0
regulation of axonogenesis -0.019 0.017 -10000 0 -10000 0 0
myoblast fusion -0.004 0.039 0.23 1 -10000 0 1
mol:GTP -0.007 0.024 -10000 0 -0.13 1 1
regulation of calcium-dependent cell-cell adhesion -0.019 0.028 0.18 3 -10000 0 3
ARF1/GTP -0.004 0.015 -10000 0 -10000 0 0
mol:GM1 0.003 0.019 -10000 0 -10000 0 0
mol:Choline 0.016 0.024 -10000 0 -0.16 7 7
lamellipodium assembly -0.009 0.032 -10000 0 -10000 0 0
MAPK3 0.013 0.036 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.02 0.028 -10000 0 -0.18 3 3
ARF1 0.01 0 -10000 0 -10000 0 0
ARF6/GDP 0.004 0.039 -10000 0 -0.23 1 1
ARF1/GDP 0.011 0.035 -10000 0 -0.21 1 1
ARF6 0.005 0.014 -10000 0 -10000 0 0
RAB11A 0.01 0 -10000 0 -10000 0 0
TIAM1 0.01 0.013 -10000 0 -0.32 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.013 0.036 -10000 0 -10000 0 0
actin filament bundle formation 0.009 0.029 0.2 1 -10000 0 1
KALRN -0.007 0.028 -10000 0 -0.29 1 1
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.009 0.029 -10000 0 -0.21 1 1
NME1 0.01 0.021 -10000 0 -0.37 2 2
Rac1/GDP -0.009 0.029 -10000 0 -0.21 1 1
substrate adhesion-dependent cell spreading -0.007 0.024 -10000 0 -0.13 1 1
cortical actin cytoskeleton organization -0.009 0.032 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
liver development -0.007 0.024 -10000 0 -0.13 1 1
ARF6/GTP -0.007 0.024 -10000 0 -0.13 1 1
RhoA/GTP -0.004 0.015 -10000 0 -10000 0 0
mol:GDP -0.009 0.034 -10000 0 -0.23 1 1
ARF6/GTP/RAB11FIP3/RAB11A -0.003 0.011 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
PLD1 0.009 0.028 -10000 0 -0.19 7 7
RAB11FIP3 0.01 0 -10000 0 -10000 0 0
tube morphogenesis -0.009 0.032 -10000 0 -10000 0 0
ruffle organization 0.019 0.017 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.007 0.024 -10000 0 -0.13 1 1
PLD2 0.011 0.019 -10000 0 -10000 0 0
PIP5K1A 0.019 0.017 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.016 0.024 -10000 0 -0.16 7 7
Rac1/GTP -0.009 0.033 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.018 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.03 0.003 -10000 0 -10000 0 0
CDKN1A 0.002 0.065 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.01 0 -10000 0 -10000 0 0
FOXO3 0.03 0.003 -10000 0 -10000 0 0
AKT1 0 0.002 -10000 0 -10000 0 0
BAD 0.01 0 -10000 0 -10000 0 0
AKT3 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.029 0.007 -10000 0 -10000 0 0
AKT1/ASK1 0 0.002 -10000 0 -10000 0 0
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.01 0 -10000 0 -10000 0 0
RAF1 0.01 0 -10000 0 -10000 0 0
JNK cascade 0 0.002 -10000 0 -10000 0 0
TSC1 0.03 0.003 -10000 0 -10000 0 0
YWHAZ 0.01 0 -10000 0 -10000 0 0
AKT1/RAF1 0.029 0.003 -10000 0 -10000 0 0
EP300 0.01 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.03 0.003 -10000 0 -10000 0 0
YWHAQ 0.01 0 -10000 0 -10000 0 0
TBC1D4 0.019 0 -10000 0 -10000 0 0
MAP3K5 0.01 0 -10000 0 -10000 0 0
MAPKAP1 0.01 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.027 0.023 0.17 1 -10000 0 1
YWHAH 0.004 0.044 -10000 0 -0.32 12 12
AKT1S1 0.03 0.003 -10000 0 -10000 0 0
CASP9 0.029 0.008 -10000 0 -10000 0 0
YWHAB 0.01 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.034 0.003 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -10000 0 -10000 0 0
YWHAE 0.01 0 -10000 0 -10000 0 0
SRC 0.01 0 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.022 0.05 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.014 0.001 -10000 0 -10000 0 0
CHUK 0.03 0.003 -10000 0 -10000 0 0
BAD/BCL-XL 0.039 0.003 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0.014 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.042 0.023 -10000 0 -10000 0 0
PDPK1 0.01 0 -10000 0 -10000 0 0
MDM2 0.026 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.029 0.003 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.035 0.023 -10000 0 -10000 0 0
TSC1/TSC2 0.035 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.002 0.017 -10000 0 -10000 0 0
glucose import 0.018 0.031 -10000 0 -0.14 23 23
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.025 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.018 0.031 -10000 0 -0.14 23 23
GSK3A 0.03 0.003 -10000 0 -10000 0 0
FOXO1 0.03 0.003 -10000 0 -10000 0 0
GSK3B 0.03 0.003 -10000 0 -10000 0 0
SFN -0.008 0.079 -10000 0 -0.37 30 30
G1/S transition of mitotic cell cycle 0.035 0.003 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.034 0.019 -10000 0 -10000 0 0
PRKACA 0.01 0 -10000 0 -10000 0 0
KPNA1 0.01 0 -10000 0 -10000 0 0
HSP90AA1 0.01 0 -10000 0 -10000 0 0
YWHAG 0.01 0 -10000 0 -10000 0 0
RHEB 0.01 0 -10000 0 -10000 0 0
CREBBP 0.01 0 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.009 0.015 -9999 0 -0.37 1 1
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
MDM2/SUMO1 0.02 0.025 -9999 0 -0.16 13 13
HDAC4 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0 0.005 -9999 0 -10000 0 0
SUMO1 0.01 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.023 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.01 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.01 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.024 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.023 0.007 -9999 0 -0.16 1 1
RANGAP1 0.01 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 -0.003 0.024 -9999 0 -0.18 13 13
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.017 0 -9999 0 -10000 0 0
Ran/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.002 0.053 -9999 0 -0.37 13 13
UBE2I 0.01 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
PIAS2 0.01 0 -9999 0 -10000 0 0
PIAS1 0.01 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
mTOR signaling 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
GBL 0 0 -9999 0 -10000 0 0
MKNK1 0.01 0 -9999 0 -10000 0 0
mol:PIP3 0 0 -9999 0 -10000 0 0
FRAP1 0.012 0.001 -9999 0 -10000 0 0
AKT1 0.023 0.001 -9999 0 -10000 0 0
INSR 0.01 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0.008 -9999 0 -0.21 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0 0 -9999 0 -10000 0 0
TSC2 0.01 0 -9999 0 -10000 0 0
RHEB/GDP 0 0 -9999 0 -10000 0 0
TSC1 0.01 0 -9999 0 -10000 0 0
Insulin Receptor/IRS1 0.013 0 -9999 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EIF3A 0.01 0 -9999 0 -10000 0 0
RPS6KB1 0.022 0.001 -9999 0 -10000 0 0
MAP3K5 0.008 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
apoptosis 0.008 0 -9999 0 -10000 0 0
mol:LY294002 0 0 -9999 0 -10000 0 0
EIF4B 0.027 0.001 -9999 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.002 0.015 -9999 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
PI3K 0.019 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.025 0.001 -9999 0 -10000 0 0
FKBP1A 0.01 0 -9999 0 -10000 0 0
RHEB/GTP 0 0 -9999 0 -10000 0 0
mol:Amino Acids 0 0 -9999 0 -10000 0 0
FKBP12/Rapamycin 0 0 -9999 0 -10000 0 0
PDPK1 0 0.001 -9999 0 -10000 0 0
EIF4E 0.01 0 -9999 0 -10000 0 0
ASK1/PP5C 0.017 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.014 0 -9999 0 -10000 0 0
TSC1/TSC2 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RPS6 0.004 0.049 -9999 0 -0.37 11 11
PPP5C 0.01 0 -9999 0 -10000 0 0
EIF4G1 0.01 0 -9999 0 -10000 0 0
IRS1 0.007 0 -9999 0 -10000 0 0
INS 0 0.015 -9999 0 -0.37 1 1
PTEN 0.01 0 -9999 0 -10000 0 0
PDK2 0 0.001 -9999 0 -10000 0 0
EIF4EBP1 -0.008 0.024 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
PPP2R5D 0.017 0 -9999 0 -10000 0 0
peptide biosynthetic process 0.013 0.008 -9999 0 -0.18 1 1
RHEB 0.01 0 -9999 0 -10000 0 0
EIF4A1 0.01 0 -9999 0 -10000 0 0
mol:Rapamycin 0 0 -9999 0 -10000 0 0
EEF2 0.013 0.008 -9999 0 -0.18 1 1
eIF4E/4E-BP1 -0.001 0.021 -9999 0 -10000 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.016 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.01 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.02 0 -9999 0 -10000 0 0
CD4 0.003 0.051 -9999 0 -0.37 12 12
CLTA 0.01 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0.009 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.022 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.01 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0.01 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.02 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.01 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.022 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.01 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 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 0.027 0.012 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.009 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.009 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.004 0.027 -9999 0 -0.2 12 12
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -9999 0 0
FBXW11 0.01 0 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.01 0 -9999 0 -9999 0 0
CHUK 0.01 0 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0 0 -9999 0 -9999 0 0
NFKB1 0.01 0 -9999 0 -9999 0 0
MAP3K14 0.01 0 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0 0 -9999 0 -9999 0 0
RELB 0.01 0 -9999 0 -9999 0 0
NFKB2 0.01 0 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -9999 0 0
regulation of B cell activation 0 0 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 669 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WY.A85E TCGA.WY.A85D TCGA.WY.A85C TCGA.WY.A85B
109_MAP3K5 0.043 -0.16 -0.16 -0.16
47_PPARGC1A 0.0099 0.0099 0.0099 0.0099
105_BMP4 0.0099 0.0099 0.0099 0.0099
105_BMP6 0.0099 0.0099 0.0099 0.0099
105_BMP7 0.0099 0.0099 0.0099 0.0099
105_BMP2 -0.37 -0.37 -0.37 -0.37
131_RELN/VLDLR 0 0 0 0
30_TGFB1/TGF beta receptor Type II 0.0098 0.0097 0.012 0.0098
84_STAT5B 0.036 0.035 0.0024 0.0024
84_STAT5A 0.036 0.035 0.0024 0.0024
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/GBMLGG-TP/22312676/GBMLGG-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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