PARADIGM pathway analysis of mRNASeq expression and copy number data
Thyroid Adenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1JD4V8M
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1JD4V8M
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 37 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
Ephrin A reverse signaling 243
Signaling events mediated by Stem cell factor receptor (c-Kit) 167
Signaling events regulated by Ret tyrosine kinase 140
Reelin signaling pathway 125
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 109
Noncanonical Wnt signaling pathway 101
Wnt signaling 100
PDGFR-alpha signaling pathway 94
FOXA2 and FOXA3 transcription factor networks 91
Nongenotropic Androgen signaling 86
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 488 . 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 ( 488 ).

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
Ephrin A reverse signaling 0.4980 243 1702 7 -0.42 0 1000 -1000 -0.005 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3422 167 13071 78 -0.74 0.24 1000 -1000 -0.05 -1000
Signaling events regulated by Ret tyrosine kinase 0.2869 140 11480 82 -0.37 0.027 1000 -1000 -0.063 -1000
Reelin signaling pathway 0.2561 125 7041 56 -0.46 0.06 1000 -1000 -0.037 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2234 109 7434 68 -0.73 0.35 1000 -1000 -0.064 -1000
Noncanonical Wnt signaling pathway 0.2070 101 2644 26 -0.32 0.027 1000 -1000 -0.046 -1000
Wnt signaling 0.2049 100 702 7 -0.32 0.014 1000 -1000 -0.018 -1000
PDGFR-alpha signaling pathway 0.1926 94 4172 44 -0.4 0.043 1000 -1000 -0.039 -1000
FOXA2 and FOXA3 transcription factor networks 0.1865 91 4190 46 -0.85 0.031 1000 -1000 -0.05 -1000
Nongenotropic Androgen signaling 0.1762 86 4509 52 -0.26 0.19 1000 -1000 -0.036 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1557 76 4116 54 -0.46 0.039 1000 -1000 -0.05 -1000
Signaling events mediated by the Hedgehog family 0.1455 71 3719 52 -0.29 0.14 1000 -1000 -0.051 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1352 66 2260 34 -0.1 0.027 1000 -1000 -0.031 -1000
Endothelins 0.1352 66 6393 96 -0.32 0.031 1000 -1000 -0.045 -1000
Calcium signaling in the CD4+ TCR pathway 0.1352 66 2068 31 -0.34 0.027 1000 -1000 -0.036 -1000
HIF-1-alpha transcription factor network 0.1270 62 4747 76 -0.47 0.041 1000 -1000 -0.058 -1000
IL4-mediated signaling events 0.1230 60 5482 91 -1.2 0.55 1000 -1000 -0.06 -1000
Glypican 1 network 0.1230 60 2917 48 -0.3 0.052 1000 -1000 -0.028 -1000
IGF1 pathway 0.1189 58 3318 57 -0.14 0.065 1000 -1000 -0.053 -1000
EPHB forward signaling 0.1148 56 4840 85 -0.24 0.11 1000 -1000 -0.057 -1000
Ephrin B reverse signaling 0.1107 54 2607 48 -0.24 0.12 1000 -1000 -0.032 -1000
Coregulation of Androgen receptor activity 0.1025 50 3812 76 -0.67 0.075 1000 -1000 -0.016 -1000
IL23-mediated signaling events 0.1025 50 3051 60 -0.29 0.027 1000 -1000 -0.056 -1000
BMP receptor signaling 0.0963 47 3887 81 -0.44 0.052 1000 -1000 -0.047 -1000
Glucocorticoid receptor regulatory network 0.0963 47 5469 114 -0.44 0.25 1000 -1000 -0.058 -1000
TCR signaling in naïve CD8+ T cells 0.0943 46 4362 93 -0.15 0.046 1000 -1000 -0.053 -1000
Arf6 signaling events 0.0881 43 2718 62 -0.25 0.061 1000 -1000 -0.032 -1000
Signaling mediated by p38-alpha and p38-beta 0.0840 41 1806 44 -0.22 0.027 1000 -1000 -0.035 -1000
Thromboxane A2 receptor signaling 0.0799 39 4098 105 -0.16 0.05 1000 -1000 -0.042 -1000
Hedgehog signaling events mediated by Gli proteins 0.0717 35 2299 65 -0.58 0.064 1000 -1000 -0.045 -1000
IL6-mediated signaling events 0.0717 35 2684 75 -0.15 0.054 1000 -1000 -0.04 -1000
Ras signaling in the CD4+ TCR pathway 0.0697 34 580 17 -0.11 0.034 1000 -1000 -0.022 -1000
IL12-mediated signaling events 0.0656 32 2868 87 -0.37 0.031 1000 -1000 -0.068 -1000
EGFR-dependent Endothelin signaling events 0.0615 30 642 21 -0.074 0.038 1000 -1000 -0.043 -1000
ErbB2/ErbB3 signaling events 0.0533 26 1707 65 -0.17 0.037 1000 -1000 -0.062 -1000
Plasma membrane estrogen receptor signaling 0.0533 26 2301 86 -0.13 0.049 1000 -1000 -0.062 -1000
Regulation of p38-alpha and p38-beta 0.0512 25 1401 54 -0.36 0.065 1000 -1000 -0.049 -1000
Syndecan-1-mediated signaling events 0.0471 23 795 34 -0.078 0.027 1000 -1000 -0.035 -1000
Osteopontin-mediated events 0.0471 23 908 38 -0.15 0.044 1000 -1000 -0.044 -1000
FAS signaling pathway (CD95) 0.0471 23 1119 47 -0.22 0.042 1000 -1000 -0.033 -1000
Regulation of Androgen receptor activity 0.0471 23 1658 70 -0.44 0.035 1000 -1000 -0.047 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0451 22 1923 85 -0.22 0.13 1000 -1000 -0.048 -1000
IFN-gamma pathway 0.0451 22 1559 68 -0.16 0.035 1000 -1000 -0.053 -1000
BCR signaling pathway 0.0451 22 2195 99 -0.097 0.048 1000 -1000 -0.058 -1000
IL27-mediated signaling events 0.0430 21 1090 51 -0.11 0.044 1000 -1000 -0.039 -1000
LPA receptor mediated events 0.0430 21 2202 102 -0.15 0.035 1000 -1000 -0.066 -1000
Ceramide signaling pathway 0.0410 20 1525 76 -0.15 0.075 1000 -1000 -0.033 -1000
Syndecan-4-mediated signaling events 0.0410 20 1399 67 -0.14 0.039 1000 -1000 -0.047 -1000
Fc-epsilon receptor I signaling in mast cells 0.0389 19 1920 97 -0.15 0.044 1000 -1000 -0.051 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0389 19 1679 88 -0.25 0.039 1000 -1000 -0.062 -1000
Signaling events mediated by PRL 0.0389 19 661 34 -0.084 0.04 1000 -1000 -0.038 -1000
ceramide signaling pathway 0.0348 17 862 49 -0.058 0.039 1000 -1000 -0.035 -1000
amb2 Integrin signaling 0.0328 16 1328 82 -0.21 0.035 1000 -1000 -0.033 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0328 16 840 52 -0.18 0.058 1000 -1000 -0.037 -1000
Integrins in angiogenesis 0.0328 16 1379 84 -0.14 0.055 1000 -1000 -0.052 -1000
Signaling events mediated by PTP1B 0.0307 15 1210 76 -0.19 0.042 1000 -1000 -0.034 -1000
mTOR signaling pathway 0.0307 15 799 53 -0.044 0.03 1000 -1000 -0.042 -1000
VEGFR1 specific signals 0.0307 15 866 56 -0.044 0.058 1000 -1000 -0.05 -1000
LPA4-mediated signaling events 0.0287 14 175 12 -0.054 0.003 1000 -1000 -0.024 -1000
Regulation of nuclear SMAD2/3 signaling 0.0287 14 1915 136 -0.26 0.053 1000 -1000 -0.033 -1000
Visual signal transduction: Cones 0.0287 14 547 38 -0.043 0.043 1000 -1000 -0.018 -1000
JNK signaling in the CD4+ TCR pathway 0.0287 14 249 17 -0.083 0.03 1000 -1000 -0.034 -1000
p75(NTR)-mediated signaling 0.0287 14 1773 125 -0.28 0.07 1000 -1000 -0.071 -1000
IL1-mediated signaling events 0.0287 14 872 62 -0.083 0.061 1000 -1000 -0.055 -1000
TCGA08_rtk_signaling 0.0287 14 378 26 -0.18 0.045 1000 -1000 -0.005 -1000
Insulin Pathway 0.0287 14 1040 74 -0.057 0.066 1000 -1000 -0.047 -1000
Presenilin action in Notch and Wnt signaling 0.0266 13 805 61 -0.15 0.07 1000 -1000 -0.044 -1000
Nectin adhesion pathway 0.0266 13 821 63 -0.1 0.073 1000 -1000 -0.047 -1000
Signaling events mediated by HDAC Class III 0.0266 13 550 40 -0.28 0.046 1000 -1000 -0.019 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0266 13 598 45 -0.058 0.075 1000 -1000 -0.047 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0266 13 1657 120 -0.24 0.074 1000 -1000 -0.047 -1000
FOXM1 transcription factor network 0.0266 13 692 51 -0.22 0.052 1000 -1000 -0.07 -1000
Caspase cascade in apoptosis 0.0246 12 936 74 -0.058 0.045 1000 -1000 -0.03 -1000
ErbB4 signaling events 0.0246 12 880 69 -0.052 0.036 1000 -1000 -0.032 -1000
Syndecan-3-mediated signaling events 0.0246 12 441 35 -0.11 0.069 1000 -1000 -0.03 -1000
IL2 signaling events mediated by PI3K 0.0246 12 706 58 -0.058 0.048 1000 -1000 -0.03 -1000
Rapid glucocorticoid signaling 0.0246 12 254 20 -0.059 0.034 1000 -1000 -0.008 -1000
Cellular roles of Anthrax toxin 0.0225 11 463 39 -0.058 0.027 1000 -1000 -0.02 -1000
Visual signal transduction: Rods 0.0225 11 588 52 -0.069 0.048 1000 -1000 -0.033 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0205 10 292 28 -0.13 0.056 1000 -1000 -0.02 -1000
Syndecan-2-mediated signaling events 0.0205 10 704 69 -0.14 0.05 1000 -1000 -0.033 -1000
BARD1 signaling events 0.0184 9 540 57 -0.041 0.05 1000 -1000 -0.042 -1000
S1P1 pathway 0.0184 9 353 36 -0.062 0.027 1000 -1000 -0.043 -1000
Retinoic acid receptors-mediated signaling 0.0184 9 542 58 -0.036 0.053 1000 -1000 -0.038 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0184 9 734 74 -0.13 0.067 1000 -1000 -0.076 -1000
TCGA08_p53 0.0164 8 61 7 -0.025 0.025 1000 -1000 -0.01 -1000
Class I PI3K signaling events 0.0164 8 615 73 -0.19 0.05 1000 -1000 -0.041 -1000
Regulation of Telomerase 0.0164 8 843 102 -0.19 0.071 1000 -1000 -0.043 -1000
S1P3 pathway 0.0164 8 352 42 -0.13 0.048 1000 -1000 -0.04 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0143 7 649 83 -0.17 0.049 1000 -1000 -0.036 -1000
TCGA08_retinoblastoma 0.0143 7 60 8 -0.033 0.031 1000 -1000 -0.002 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0143 7 249 33 -0.11 0.055 1000 -1000 -0.044 -1000
Class IB PI3K non-lipid kinase events 0.0143 7 21 3 -0.015 0.015 1000 -1000 -0.001 -1000
PLK1 signaling events 0.0123 6 549 85 -0.006 0.049 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class I 0.0123 6 705 104 -0.058 0.062 1000 -1000 -0.032 -1000
a4b1 and a4b7 Integrin signaling 0.0102 5 29 5 0.007 0.034 1000 -1000 0.005 -1000
IL2 signaling events mediated by STAT5 0.0102 5 129 22 -0.028 0.033 1000 -1000 -0.031 -1000
PDGFR-beta signaling pathway 0.0102 5 491 97 -0.14 0.079 1000 -1000 -0.054 -1000
S1P4 pathway 0.0102 5 134 25 -0.003 0.047 1000 -1000 -0.029 -1000
Aurora B signaling 0.0102 5 380 67 -0.32 0.1 1000 -1000 -0.033 -1000
Canonical NF-kappaB pathway 0.0082 4 157 39 -0.058 0.061 1000 -1000 -0.039 -1000
Insulin-mediated glucose transport 0.0082 4 150 32 -0.082 0.05 1000 -1000 -0.029 -1000
Class I PI3K signaling events mediated by Akt 0.0082 4 294 68 -0.082 0.05 1000 -1000 -0.038 -1000
FoxO family signaling 0.0082 4 258 64 -0.082 0.1 1000 -1000 -0.044 -1000
Signaling mediated by p38-gamma and p38-delta 0.0082 4 64 15 -0.002 0.027 1000 -1000 -0.029 -1000
Atypical NF-kappaB pathway 0.0082 4 126 31 -0.018 0.04 1000 -1000 -0.029 -1000
Canonical Wnt signaling pathway 0.0082 4 225 51 -0.038 0.065 1000 -1000 -0.052 -1000
Effects of Botulinum toxin 0.0082 4 124 26 -0.064 0.048 1000 -1000 -0.007 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0082 4 544 125 -0.008 0.07 1000 -1000 -0.058 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0061 3 70 23 -0.016 0.049 1000 -1000 -0.026 -1000
Circadian rhythm pathway 0.0061 3 70 22 -0.016 0.041 1000 -1000 -0.035 -1000
EPO signaling pathway 0.0061 3 168 55 -0.013 0.059 1000 -1000 -0.037 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0061 3 127 37 0 0.063 1000 -1000 -0.031 -1000
S1P5 pathway 0.0061 3 58 17 -0.007 0.032 1000 -1000 -0.016 -1000
HIF-2-alpha transcription factor network 0.0061 3 134 43 -0.16 0.16 1000 -1000 -0.047 -1000
p38 MAPK signaling pathway 0.0061 3 162 44 -0.031 0.049 1000 -1000 -0.029 -1000
Paxillin-dependent events mediated by a4b1 0.0041 2 91 36 -0.053 0.055 1000 -1000 -0.047 -1000
E-cadherin signaling in keratinocytes 0.0041 2 127 43 -0.03 0.051 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class II 0.0020 1 88 75 -0.036 0.074 1000 -1000 -0.026 -1000
Aurora A signaling 0.0020 1 118 60 -0.021 0.055 1000 -1000 -0.026 -1000
TRAIL signaling pathway 0.0020 1 86 48 -0.014 0.075 1000 -1000 -0.041 -1000
E-cadherin signaling in the nascent adherens junction 0.0020 1 126 76 -0.057 0.066 1000 -1000 -0.064 -1000
Arf6 trafficking events 0.0020 1 124 71 -0.048 0.05 1000 -1000 -0.028 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.016 0.027 1000 -1000 -0.017 -1000
Arf6 downstream pathway 0.0000 0 9 43 -0.058 0.046 1000 -1000 -0.023 -1000
Aurora C signaling 0.0000 0 4 7 -0.005 0.046 1000 -1000 -0.015 -1000
Glypican 2 network 0.0000 0 0 4 -0.019 0.016 1000 -1000 -0.008 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 13 27 0 0.066 1000 -1000 -0.034 -1000
E-cadherin signaling events 0.0000 0 0 5 0.026 0.051 1000 -1000 0.001 -1000
Arf1 pathway 0.0000 0 25 54 -0.001 0.051 1000 -1000 -0.018 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.072 1000 -1000 -0.001 -1000
Total NA 3455 199328 7203 -22 8 131000 -131000 -4.9 -131000
Ephrin A reverse signaling

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
MAPKKK cascade -0.32 0.26 -9999 0 -0.48 332 332
EFNA5 -0.071 0.24 -9999 0 -0.67 68 68
FYN -0.29 0.24 -9999 0 -0.44 332 332
neuron projection morphogenesis -0.32 0.26 -9999 0 -0.48 332 332
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.32 0.26 -9999 0 -0.48 332 332
EPHA5 -0.42 0.33 -9999 0 -0.67 306 306
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.22 0.21 0.38 1 -0.39 272 273
CRKL -0.23 0.22 -10000 0 -0.41 277 277
HRAS -0.19 0.19 -10000 0 -0.36 236 236
mol:PIP3 -0.2 0.21 -10000 0 -0.39 251 251
SPRED1 0.027 0.004 -10000 0 -10000 0 0
SPRED2 0.025 0.032 -10000 0 -0.67 1 1
GAB1 -0.24 0.24 -10000 0 -0.44 277 277
FOXO3 -0.19 0.21 0.37 2 -0.37 265 267
AKT1 -0.21 0.22 0.29 2 -0.39 275 277
BAD -0.19 0.21 0.28 2 -0.37 264 266
megakaryocyte differentiation -0.24 0.23 -10000 0 -0.43 286 286
GSK3B -0.19 0.21 0.31 3 -0.37 268 271
RAF1 -0.16 0.16 0.35 1 -0.33 101 102
SHC1 0.025 0.007 -10000 0 -10000 0 0
STAT3 -0.24 0.23 -10000 0 -0.44 271 271
STAT1 -0.59 0.56 -10000 0 -1.1 280 280
HRAS/SPRED1 -0.16 0.16 -10000 0 -0.33 100 100
cell proliferation -0.24 0.24 -10000 0 -0.44 280 280
PIK3CA 0.022 0.055 -10000 0 -0.67 3 3
TEC 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.22 0.23 -10000 0 -0.42 277 277
HRAS/SPRED2 -0.16 0.16 -10000 0 -0.33 99 99
LYN/TEC/p62DOK -0.21 0.24 -10000 0 -0.41 275 275
MAPK3 -0.11 0.12 0.26 5 -0.29 21 26
STAP1 -0.25 0.24 -10000 0 -0.44 277 277
GRAP2 -0.017 0.14 -10000 0 -0.55 31 31
JAK2 -0.49 0.48 -10000 0 -0.89 279 279
STAT1 (dimer) -0.57 0.54 -10000 0 -1 280 280
mol:Gleevec 0.008 0.011 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.21 0.24 -10000 0 -0.42 262 262
actin filament polymerization -0.23 0.23 -10000 0 -0.43 275 275
LYN 0.027 0.005 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.34 0.32 0.35 1 -0.61 278 279
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.19 0.21 -10000 0 -0.38 264 264
PI3K -0.21 0.24 -10000 0 -0.41 273 273
PTEN 0.026 0.018 -10000 0 -0.36 1 1
SCF/KIT/EPO/EPOR -0.7 0.66 -10000 0 -1.3 278 278
MAPK8 -0.24 0.24 -10000 0 -0.44 280 280
STAT3 (dimer) -0.23 0.23 -10000 0 -0.43 271 271
positive regulation of transcription -0.085 0.11 0.3 7 -0.24 19 26
mol:GDP -0.2 0.2 -10000 0 -0.38 239 239
PIK3C2B -0.23 0.23 -10000 0 -0.44 253 253
CBL/CRKL -0.2 0.22 -10000 0 -0.39 273 273
FER -0.24 0.24 -10000 0 -0.44 276 276
SH2B3 -0.24 0.23 -10000 0 -0.44 278 278
PDPK1 -0.19 0.2 0.3 3 -0.36 246 249
SNAI2 -0.24 0.24 -10000 0 -0.44 277 277
positive regulation of cell proliferation -0.41 0.4 -10000 0 -0.74 279 279
KITLG -0.017 0.094 -10000 0 -0.7 8 8
cell motility -0.41 0.4 -10000 0 -0.74 279 279
PTPN6 0.038 0.014 -10000 0 -10000 0 0
EPOR -0.15 0.19 -10000 0 -1.2 5 5
STAT5A (dimer) -0.34 0.33 -10000 0 -0.61 278 278
SOCS1 0.024 0.035 -10000 0 -0.67 1 1
cell migration 0.24 0.23 0.43 273 -10000 0 273
SOS1 0.027 0.005 -10000 0 -10000 0 0
EPO -0.008 0.03 -10000 0 -10000 0 0
VAV1 0.012 0.059 -10000 0 -0.56 3 3
GRB10 -0.24 0.23 -10000 0 -0.44 276 276
PTPN11 0.033 0.033 -10000 0 -0.65 1 1
SCF/KIT -0.25 0.25 -10000 0 -0.46 278 278
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.12 0.13 0.27 3 -0.27 65 68
CBL 0.027 0.005 -10000 0 -10000 0 0
KIT -0.74 0.68 -10000 0 -1.3 278 278
MAP2K2 -0.12 0.13 0.28 2 -0.3 27 29
SHC/Grb2/SOS1 -0.2 0.23 -10000 0 -0.42 241 241
STAT5A -0.34 0.34 -10000 0 -0.63 277 277
GRB2 0.026 0.007 -10000 0 -10000 0 0
response to radiation -0.24 0.24 -10000 0 -0.43 277 277
SHC/GRAP2 0.002 0.11 -10000 0 -0.38 31 31
PTPRO -0.25 0.23 -10000 0 -0.44 286 286
SH2B2 -0.24 0.23 -10000 0 -0.44 275 275
DOK1 0.027 0.005 -10000 0 -10000 0 0
MATK -0.24 0.23 -10000 0 -0.44 273 273
CREBBP -0.043 0.077 -10000 0 -10000 0 0
BCL2 -0.22 0.4 -10000 0 -1.5 39 39
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.061 0.097 -10000 0 -0.66 6 6
Crk/p130 Cas/Paxillin -0.22 0.19 -10000 0 -0.38 250 250
JUN -0.26 0.26 -10000 0 -0.58 152 152
HRAS 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.26 0.29 -10000 0 -0.48 282 282
RAP1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.26 0.29 -10000 0 -0.48 285 285
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.2 0.22 -10000 0 -0.4 267 267
RHOA 0.027 0.004 -10000 0 -10000 0 0
RAP1A/GTP -0.24 0.26 -10000 0 -0.44 279 279
GRB7 0.002 0.054 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.26 0.28 -10000 0 -0.48 278 278
MAPKKK cascade -0.23 0.23 -10000 0 -0.42 276 276
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.25 0.27 -10000 0 -0.46 284 284
lamellipodium assembly -0.19 0.18 -10000 0 -0.35 253 253
RET51/GFRalpha1/GDNF/SHC -0.26 0.28 -10000 0 -0.48 272 272
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
RET9/GFRalpha1/GDNF/SHC -0.2 0.22 -10000 0 -0.39 269 269
RET9/GFRalpha1/GDNF/Shank3 -0.21 0.21 -10000 0 -0.4 269 269
MAPK3 -0.24 0.23 -10000 0 -0.42 277 277
DOK1 0.027 0.005 -10000 0 -10000 0 0
DOK6 -0.082 0.25 -10000 0 -0.67 76 76
PXN 0.027 0.005 -10000 0 -10000 0 0
neurite development -0.26 0.24 -10000 0 -0.53 165 165
DOK5 -0.068 0.24 -10000 0 -0.67 66 66
GFRA1 -0.37 0.34 -10000 0 -0.66 277 277
MAPK8 -0.19 0.2 -10000 0 -0.54 71 71
HRAS/GTP -0.25 0.28 -10000 0 -0.47 282 282
tube development -0.19 0.2 -10000 0 -0.38 254 254
MAPK1 -0.24 0.23 0.32 3 -0.42 279 282
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.16 -10000 0 -0.29 268 268
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PDLIM7 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.3 0.33 -10000 0 -0.53 295 295
SHC1 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.26 0.29 -10000 0 -0.48 284 284
RET51/GFRalpha1/GDNF/Dok5 -0.31 0.33 -10000 0 -0.54 298 298
PRKCA -0.004 0.14 -10000 0 -0.67 21 21
HRAS/GDP 0.019 0.007 -10000 0 -10000 0 0
CREB1 -0.19 0.21 -10000 0 -0.37 251 251
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.14 0.15 -10000 0 -0.29 238 238
RET51/GFRalpha1/GDNF/Grb7 -0.27 0.29 -10000 0 -0.49 282 282
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.1 0.26 -10000 0 -0.65 83 83
DOK4 0.026 0.009 -10000 0 -10000 0 0
JNK cascade -0.25 0.25 -10000 0 -0.56 152 152
RET9/GFRalpha1/GDNF/FRS2 -0.2 0.22 -10000 0 -0.4 268 268
SHANK3 0.02 0.012 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.15 0.16 -10000 0 -0.29 258 258
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.2 0.2 -10000 0 -0.35 281 281
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.2 0.2 -10000 0 -0.35 286 286
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.22 0.26 -10000 0 -0.4 271 271
PI3K -0.3 0.29 -10000 0 -0.55 255 255
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.19 0.21 -10000 0 -0.38 254 254
GRB10 0.026 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.18 0.18 -10000 0 -0.32 263 263
RET51/GFRalpha1/GDNF/FRS2 -0.26 0.29 -10000 0 -0.48 285 285
GAB1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.057 0.23 -10000 0 -0.66 59 59
IRS2 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.22 0.26 -10000 0 -0.4 269 269
RET51/GFRalpha1/GDNF/PKC alpha -0.28 0.3 -10000 0 -0.5 284 284
GRB2 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GDNF -0.007 0.024 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.31 0.32 -10000 0 -0.53 299 299
Rac1/GTP -0.23 0.22 -10000 0 -0.42 250 250
RET9/GFRalpha1/GDNF -0.23 0.23 -10000 0 -0.43 275 275
GFRalpha1/GDNF -0.27 0.26 -10000 0 -0.5 275 275
Reelin signaling pathway

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
CDK5R1/CDK5 0.037 0.013 -10000 0 -10000 0 0
VLDLR -0.004 0.14 -10000 0 -0.66 21 21
CRKL 0.02 0.012 -10000 0 -10000 0 0
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ITGA3 0.025 0.015 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.3 0.23 -10000 0 -0.45 343 343
MAPK8IP1/MKK7/MAP3K11/JNK1 0.06 0.067 -10000 0 -0.38 9 9
AKT1 -0.2 0.15 -10000 0 -0.29 329 329
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.023 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.28 0.22 -10000 0 -0.42 332 332
LRPAP1/LRP8 0.018 0.11 -10000 0 -0.5 19 19
RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.4 332 332
DAB1/alpha3/beta1 Integrin -0.25 0.21 -10000 0 -0.38 321 321
long-term memory -0.26 0.23 -10000 0 -0.4 331 331
DAB1/LIS1 -0.25 0.22 -10000 0 -0.39 326 326
DAB1/CRLK/C3G -0.25 0.21 -10000 0 -0.38 330 330
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
DAB1/NCK2 -0.26 0.22 -10000 0 -0.39 332 332
ARHGEF2 0.025 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.001 0.12 -10000 0 -0.67 16 16
CDK5R1 0.025 0.012 -10000 0 -10000 0 0
RELN -0.46 0.32 -10000 0 -0.67 335 335
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.3 0.24 -10000 0 -0.45 339 339
GRIN2A/RELN/LRP8/DAB1/Fyn -0.26 0.24 -10000 0 -0.41 331 331
MAPK8 0.013 0.095 -10000 0 -0.64 10 10
RELN/VLDLR/DAB1 -0.28 0.21 -10000 0 -0.41 342 342
ITGB1 0.027 0.004 -10000 0 -10000 0 0
MAP1B -0.28 0.21 -10000 0 -0.41 333 333
RELN/LRP8 -0.3 0.24 -10000 0 -0.45 338 338
GRIN2B/RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.4 331 331
PI3K 0.036 0.043 -10000 0 -0.5 3 3
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.037 0.015 -10000 0 -10000 0 0
RAP1A -0.24 0.2 0.57 2 -0.4 135 137
PAFAH1B1 0.026 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.005 -10000 0 -10000 0 0
CRLK/C3G 0.028 0.019 -10000 0 -10000 0 0
GRIN2B -0.005 0.02 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
neuron differentiation -0.13 0.13 -10000 0 -0.43 36 36
neuron adhesion -0.22 0.21 0.45 9 -0.6 28 37
LRP8 -0.001 0.14 -10000 0 -0.67 19 19
GSK3B -0.19 0.14 -10000 0 -0.43 31 31
RELN/VLDLR/DAB1/Fyn -0.26 0.21 -10000 0 -0.39 334 334
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.16 -10000 0 -0.31 332 332
CDK5 0.026 0.006 -10000 0 -10000 0 0
MAPT 0.053 0.17 0.82 20 -0.6 3 23
neuron migration -0.26 0.19 -10000 0 -0.39 313 313
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.13 -10000 0 -0.43 36 36
RELN/VLDLR -0.28 0.24 -10000 0 -0.43 337 337
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.009 0.1 -10000 0 -0.46 15 15
NFATC2 -0.22 0.33 -10000 0 -0.71 123 123
NFATC3 -0.083 0.14 -10000 0 -0.28 120 120
CD40LG -0.62 0.55 -10000 0 -1.1 262 262
ITCH 0.038 0.016 -10000 0 -10000 0 0
CBLB 0.038 0.016 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.44 0.5 -10000 0 -1.2 128 128
JUNB 0.02 0.058 -10000 0 -0.59 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.042 0.018 -10000 0 -0.32 1 1
T cell anergy 0.007 0.073 0.4 5 -0.47 1 6
TLE4 -0.21 0.35 -10000 0 -0.79 109 109
Jun/NFAT1-c-4/p21SNFT -0.55 0.59 -10000 0 -1.1 231 231
AP-1/NFAT1-c-4 -0.7 0.74 -10000 0 -1.3 251 251
IKZF1 -0.16 0.27 -10000 0 -0.66 78 78
T-helper 2 cell differentiation -0.28 0.33 -10000 0 -0.79 112 112
AP-1/NFAT1 -0.32 0.41 -10000 0 -0.74 199 199
CALM1 0.038 0.012 -10000 0 -10000 0 0
EGR2 -0.73 0.78 -10000 0 -1.5 229 229
EGR3 -0.54 0.7 -10000 0 -1.5 139 139
NFAT1/FOXP3 -0.17 0.28 -10000 0 -0.58 121 121
EGR1 -0.12 0.28 -10000 0 -0.67 97 97
JUN -0.13 0.28 -10000 0 -0.66 105 105
EGR4 -0.014 0.14 -10000 0 -0.64 23 23
mol:Ca2+ 0.012 0.009 -10000 0 -0.18 1 1
GBP3 -0.16 0.26 -10000 0 -0.65 73 73
FOSL1 0.006 0.06 -10000 0 -0.51 2 2
NFAT1-c-4/MAF/IRF4 -0.48 0.56 -10000 0 -1 232 232
DGKA -0.15 0.24 -10000 0 -0.58 87 87
CREM 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.49 0.55 -10000 0 -1 232 232
CTLA4 -0.18 0.29 -10000 0 -0.69 91 91
NFAT1-c-4 (dimer)/EGR1 -0.56 0.63 -10000 0 -1.2 225 225
NFAT1-c-4 (dimer)/EGR4 -0.51 0.56 -10000 0 -1 233 233
FOS -0.16 0.3 -10000 0 -0.67 125 125
IFNG -0.37 0.5 -10000 0 -1.1 127 127
T cell activation -0.39 0.39 -10000 0 -0.87 159 159
MAF 0.026 0.006 -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 0.35 0.41 0.74 224 -10000 0 224
TNF -0.54 0.55 -10000 0 -1 250 250
FASLG -0.7 0.76 -10000 0 -1.4 240 240
TBX21 -0.017 0.15 -10000 0 -0.68 21 21
BATF3 0.018 0.043 -10000 0 -0.67 1 1
PRKCQ 0.019 0.068 -10000 0 -0.61 5 5
PTPN1 -0.15 0.25 -10000 0 -0.62 74 74
NFAT1-c-4/ICER1 -0.49 0.55 -10000 0 -1 230 230
GATA3 -0.006 0.14 -10000 0 -0.63 24 24
T-helper 1 cell differentiation -0.35 0.48 -10000 0 -1 128 128
IL2RA -0.4 0.46 -10000 0 -0.97 147 147
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.15 0.25 -10000 0 -0.6 80 80
E2F1 -0.011 0.067 -10000 0 -10000 0 0
PPARG 0.016 0.084 -10000 0 -0.67 7 7
SLC3A2 -0.15 0.25 -10000 0 -0.61 75 75
IRF4 -0.044 0.17 -10000 0 -0.65 33 33
PTGS2 -0.6 0.55 0.5 1 -1.1 248 249
CSF2 -0.61 0.53 -10000 0 -1.1 256 256
JunB/Fra1/NFAT1-c-4 -0.46 0.54 -10000 0 -0.98 225 225
IL4 -0.29 0.35 -10000 0 -0.84 110 110
IL5 -0.59 0.52 -10000 0 -1 250 250
IL2 -0.4 0.4 -10000 0 -0.9 156 156
IL3 -0.07 0.09 -10000 0 -0.86 2 2
RNF128 0.035 0.037 -10000 0 -0.74 1 1
NFATC1 -0.36 0.42 -10000 0 -0.75 223 223
CDK4 0.24 0.25 0.55 136 -10000 0 136
PTPRK -0.15 0.25 -10000 0 -0.57 94 94
IL8 -0.6 0.53 0.5 1 -1.1 252 253
POU2F1 0.025 0.01 -10000 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 -0.091 0.26 -10000 0 -0.67 82 82
GNB1/GNG2 -0.2 0.23 -10000 0 -0.52 114 114
mol:DAG -0.19 0.2 -10000 0 -0.49 109 109
PLCG1 -0.19 0.21 -10000 0 -0.5 109 109
YES1 -0.22 0.22 -10000 0 -0.37 292 292
FZD3 0.027 0.005 -10000 0 -10000 0 0
FZD6 0.027 0.005 -10000 0 -10000 0 0
G protein -0.19 0.22 -10000 0 -0.51 110 110
MAP3K7 -0.16 0.17 0.31 1 -0.41 106 107
mol:Ca2+ -0.18 0.2 -10000 0 -0.47 110 110
mol:IP3 -0.19 0.2 -10000 0 -0.49 109 109
NLK 0 0.054 -10000 0 -0.81 2 2
GNB1 0.026 0.006 -10000 0 -10000 0 0
CAMK2A -0.17 0.18 0.32 1 -0.45 107 108
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.23 0.24 -10000 0 -0.39 294 294
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
GNAS -0.21 0.22 -10000 0 -0.37 291 291
GO:0007205 -0.18 0.19 -10000 0 -0.47 109 109
WNT6 0.021 0.024 -10000 0 -10000 0 0
WNT4 -0.19 0.32 -10000 0 -0.67 152 152
NFAT1/CK1 alpha -0.24 0.24 -10000 0 -0.5 175 175
GNG2 0.025 0.032 -10000 0 -0.67 1 1
WNT5A 0.014 0.094 -10000 0 -0.67 9 9
WNT11 -0.32 0.35 -10000 0 -0.66 247 247
CDC42 -0.2 0.21 -10000 0 -0.51 114 114
Wnt signaling

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
Noncanonical Wnts/FZD -0.23 0.24 -9999 0 -0.39 294 294
FZD6 0.027 0.005 -9999 0 -10000 0 0
WNT6 0.021 0.024 -9999 0 -10000 0 0
WNT4 -0.19 0.32 -9999 0 -0.67 152 152
FZD3 0.027 0.005 -9999 0 -10000 0 0
WNT5A 0.014 0.094 -9999 0 -0.67 9 9
WNT11 -0.32 0.35 -9999 0 -0.66 247 247
PDGFR-alpha signaling pathway

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
PDGFRA -0.2 0.32 -10000 0 -0.68 148 148
PDGF/PDGFRA/CRKL -0.14 0.24 -10000 0 -0.5 149 149
positive regulation of JUN kinase activity -0.073 0.2 -10000 0 -0.38 135 135
CRKL 0.02 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.14 0.24 -10000 0 -0.51 147 147
AP1 -0.4 0.54 -10000 0 -1.2 135 135
mol:IP3 -0.16 0.24 -10000 0 -0.52 146 146
PLCG1 -0.16 0.24 -10000 0 -0.52 146 146
PDGF/PDGFRA/alphaV Integrin -0.14 0.25 -10000 0 -0.51 148 148
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.16 0.24 -10000 0 -0.52 146 146
CAV3 -0.011 0.018 -10000 0 -10000 0 0
CAV1 0.013 0.094 -10000 0 -0.67 9 9
SHC/Grb2/SOS1 -0.073 0.2 -10000 0 -0.39 135 135
PDGF/PDGFRA/Shf -0.14 0.24 -10000 0 -0.5 148 148
FOS -0.4 0.52 0.31 1 -1.2 135 136
JUN -0.14 0.22 -10000 0 -0.57 103 103
oligodendrocyte development -0.14 0.25 -10000 0 -0.51 148 148
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:DAG -0.16 0.24 -10000 0 -0.52 146 146
PDGF/PDGFRA -0.2 0.32 -10000 0 -0.68 148 148
actin cytoskeleton reorganization -0.14 0.24 -10000 0 -0.5 148 148
SRF 0.025 0.013 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
PI3K -0.097 0.22 -10000 0 -0.43 148 148
PDGF/PDGFRA/Crk/C3G -0.096 0.22 -10000 0 -0.42 144 144
JAK1 -0.15 0.24 -10000 0 -0.5 148 148
ELK1/SRF -0.12 0.19 0.32 1 -0.41 140 141
SHB 0.025 0.007 -10000 0 -10000 0 0
SHF 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.043 0.024 -10000 0 -10000 0 0
GO:0007205 -0.17 0.25 -10000 0 -0.54 147 147
SOS1 0.027 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.073 0.2 -10000 0 -0.38 135 135
PDGF/PDGFRA/SHB -0.14 0.24 -10000 0 -0.5 148 148
PDGF/PDGFRA/Caveolin-1 -0.14 0.25 -10000 0 -0.51 149 149
ITGAV 0.024 0.045 -10000 0 -0.67 2 2
ELK1 -0.16 0.22 -10000 0 -0.49 144 144
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
PDGF/PDGFRA/Crk -0.13 0.24 -10000 0 -0.49 146 146
JAK-STAT cascade -0.15 0.24 -10000 0 -0.5 148 148
cell proliferation -0.14 0.24 -10000 0 -0.5 148 148
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.46 0.48 -10000 0 -0.93 218 218
PCK1 -0.3 0.44 -10000 0 -1.3 63 63
HNF4A -0.61 0.6 -10000 0 -1.2 232 232
KCNJ11 -0.44 0.47 -10000 0 -0.99 172 172
AKT1 -0.064 0.14 -10000 0 -0.44 14 14
response to starvation -0.019 0.043 -10000 0 -0.49 2 2
DLK1 -0.44 0.47 -10000 0 -0.98 177 177
NKX2-1 -0.17 0.19 -10000 0 -10000 0 0
ACADM -0.46 0.48 -10000 0 -0.98 190 190
TAT -0.18 0.2 -10000 0 -0.56 16 16
CEBPB 0.027 0.005 -10000 0 -10000 0 0
CEBPA 0.019 0.071 -10000 0 -0.67 5 5
TTR -0.14 0.23 0.72 5 -0.74 24 29
PKLR -0.46 0.48 -10000 0 -0.97 191 191
APOA1 -0.85 0.83 -10000 0 -1.6 237 237
CPT1C -0.47 0.49 -10000 0 -0.94 214 214
ALAS1 -0.16 0.19 -10000 0 -0.63 1 1
TFRC -0.23 0.27 -10000 0 -0.73 37 37
FOXF1 0.014 0.071 -10000 0 -0.67 5 5
NF1 0.031 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.028 0.007 -10000 0 -10000 0 0
CPT1A -0.47 0.48 -10000 0 -0.93 218 218
HMGCS1 -0.46 0.48 -10000 0 -0.95 207 207
NR3C1 0.032 0.011 -10000 0 -10000 0 0
CPT1B -0.47 0.48 -10000 0 -0.95 206 206
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.027 0.006 -10000 0 -10000 0 0
GCK -0.59 0.62 -10000 0 -1.1 244 244
CREB1 0.009 0.065 -10000 0 -0.25 15 15
IGFBP1 -0.16 0.18 -10000 0 -10000 0 0
PDX1 -0.18 0.19 -10000 0 -0.6 3 3
UCP2 -0.47 0.48 -10000 0 -0.98 192 192
ALDOB -0.44 0.47 -10000 0 -0.98 175 175
AFP -0.02 0.087 -10000 0 -0.35 18 18
BDH1 -0.47 0.48 -10000 0 -0.98 191 191
HADH -0.44 0.47 -10000 0 -1 157 157
F2 -0.57 0.58 -10000 0 -1.1 216 216
HNF1A 0.028 0.007 -10000 0 -10000 0 0
G6PC -0.001 0.067 -10000 0 -10000 0 0
SLC2A2 -0.22 0.23 -10000 0 -0.54 1 1
INS -0.022 0.014 -10000 0 -10000 0 0
FOXA1 -0.016 0.096 -10000 0 -0.31 31 31
FOXA3 -0.026 0.12 -10000 0 -0.32 38 38
FOXA2 -0.5 0.54 -10000 0 -1 200 200
ABCC8 -0.69 0.66 -10000 0 -1.3 244 244
ALB -0.064 0.28 -10000 0 -1.1 31 31
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.13 0.22 -10000 0 -0.39 195 195
regulation of S phase of mitotic cell cycle -0.1 0.16 -10000 0 -0.29 196 196
GNAO1 0.003 0.12 -10000 0 -0.67 15 15
HRAS 0.025 0.011 -10000 0 -10000 0 0
SHBG/T-DHT 0.01 0.058 -10000 0 -0.44 8 8
PELP1 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.14 0.2 0.45 5 -0.37 191 196
T-DHT/AR -0.2 0.26 -10000 0 -0.5 202 202
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.005 128 128
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
mol:GDP -0.21 0.26 -10000 0 -0.52 197 197
cell proliferation -0.2 0.26 0.46 11 -0.51 147 158
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
FOS -0.26 0.37 0.45 9 -0.79 145 154
mol:Ca2+ -0.026 0.029 -10000 0 -0.066 104 104
MAPK3 -0.16 0.24 0.5 12 -0.53 83 95
MAPK1 -0.18 0.22 0.31 4 -0.41 175 179
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 127 127
cAMP biosynthetic process 0.017 0.069 0.26 10 -0.41 8 18
GNG2 0.025 0.032 -10000 0 -0.67 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 127 127
HRAS/GTP -0.14 0.2 -10000 0 -0.38 191 191
actin cytoskeleton reorganization 0.037 0.033 -10000 0 -0.36 3 3
SRC 0.026 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 127 127
PI3K 0.033 0.038 -10000 0 -0.44 3 3
apoptosis 0.19 0.25 0.51 150 -0.41 7 157
T-DHT/AR/PELP1 -0.16 0.23 -10000 0 -0.44 196 196
HRAS/GDP -0.2 0.25 -10000 0 -0.5 198 198
CREB1 -0.21 0.27 0.42 7 -0.56 149 156
RAC1-CDC42/GTP 0.047 0.035 -10000 0 -0.36 3 3
AR -0.26 0.34 -10000 0 -0.66 202 202
GNB1 0.026 0.006 -10000 0 -10000 0 0
RAF1 -0.14 0.21 0.5 6 -0.38 191 197
RAC1-CDC42/GDP -0.17 0.25 -10000 0 -0.48 197 197
T-DHT/AR/PELP1/Src -0.14 0.22 -10000 0 -0.41 191 191
MAP2K2 -0.14 0.19 0.43 2 -0.37 187 189
T-DHT/AR/PELP1/Src/PI3K -0.1 0.16 -10000 0 -0.29 196 196
GNAZ 0.02 0.012 -10000 0 -10000 0 0
SHBG 0.014 0.089 -10000 0 -0.67 8 8
Gi family/GNB1/GNG2/GDP -0.033 0.1 -10000 0 -0.45 16 16
mol:T-DHT 0 0.003 0.001 60 -0.005 66 126
RAC1 0.026 0.006 -10000 0 -10000 0 0
GNRH1 0.006 0.033 -10000 0 -0.51 2 2
Gi family/GTP -0.087 0.11 -10000 0 -0.3 47 47
CDC42 0.027 0.005 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.005 -10000 0 -10000 0 0
VLDLR -0.004 0.14 -10000 0 -0.66 21 21
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
NUDC 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.3 0.24 -10000 0 -0.45 338 338
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
KATNA1 0.027 0.004 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.28 0.21 -10000 0 -0.41 328 328
IQGAP1/CaM 0.039 0.008 -10000 0 -10000 0 0
DAB1 0.006 0.023 -10000 0 -10000 0 0
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
PLA2G7 -0.063 0.23 -10000 0 -0.67 63 63
CALM1 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.018 0.11 -10000 0 -0.5 19 19
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.005 -10000 0 -10000 0 0
CDK5R1 0.025 0.012 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.012 0.003 -10000 0 -10000 0 0
CDK5R2 0.001 0.023 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.3 0.23 -10000 0 -0.45 342 342
YWHAE 0.026 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.21 0.18 0.36 5 -0.34 208 213
MAP1B 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.017 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.24 0.19 -10000 0 -0.37 317 317
RELN -0.46 0.32 -10000 0 -0.67 335 335
PAFAH/LIS1 -0.029 0.16 -10000 0 -0.43 63 63
LIS1/CLIP170 0.031 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.17 0.15 -10000 0 -0.48 15 15
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.17 -10000 0 -0.47 44 44
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.23 0.18 0.64 1 -0.35 316 317
LIS1/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
RHOA 0.017 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.016 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.015 -10000 0 -10000 0 0
PAFAH1B2 0.016 0.085 -10000 0 -0.63 8 8
MAP1B/LIS1/Dynein heavy chain 0.031 0.012 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.18 0.29 4 -0.44 36 40
LRP8 -0.001 0.14 -10000 0 -0.67 19 19
NDEL1/Katanin 60 -0.21 0.18 0.29 4 -0.33 315 319
P39/CDK5 -0.25 0.19 -10000 0 -0.37 327 327
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.03 0.01 -10000 0 -10000 0 0
CDK5 -0.26 0.19 -10000 0 -0.39 328 328
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.26 0.21 -10000 0 -0.39 323 323
RELN/VLDLR -0.28 0.24 -10000 0 -0.43 337 337
CDC42 0.017 0.005 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.088 0.21 -10000 0 -0.64 26 26
IHH -0.15 0.31 -10000 0 -0.7 119 119
SHH Np/Cholesterol/GAS1 -0.053 0.16 -10000 0 -0.39 83 83
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.053 0.16 0.39 83 -10000 0 83
SMO/beta Arrestin2 -0.075 0.2 -10000 0 -0.52 16 16
SMO -0.096 0.21 -10000 0 -0.44 113 113
AKT1 -0.016 0.1 -10000 0 -0.61 2 2
ARRB2 0.026 0.007 -10000 0 -10000 0 0
BOC 0.016 0.089 -10000 0 -0.67 8 8
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping -0.094 0.2 -10000 0 -0.43 113 113
STIL -0.065 0.16 -10000 0 -0.54 10 10
DHH N/PTCH2 -0.051 0.2 -10000 0 -0.51 80 80
DHH N/PTCH1 -0.076 0.19 -10000 0 -0.5 19 19
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
DHH 0.021 0.063 -10000 0 -0.67 4 4
PTHLH -0.14 0.31 -10000 0 -1.1 30 30
determination of left/right symmetry -0.094 0.2 -10000 0 -0.43 113 113
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
skeletal system development -0.14 0.3 -10000 0 -1 30 30
IHH N/Hhip -0.29 0.33 -10000 0 -0.59 252 252
DHH N/Hhip -0.17 0.26 -10000 0 -0.5 185 185
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.094 0.2 -10000 0 -0.43 113 113
pancreas development -0.25 0.33 -10000 0 -0.67 184 184
HHAT 0.024 0.032 -10000 0 -0.67 1 1
PI3K 0.036 0.043 -10000 0 -0.5 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.1 0.26 -10000 0 -0.63 94 94
somite specification -0.094 0.2 -10000 0 -0.43 113 113
SHH Np/Cholesterol/PTCH1 -0.07 0.16 -10000 0 -0.5 13 13
SHH Np/Cholesterol/PTCH2 -0.044 0.15 -10000 0 -0.39 73 73
SHH Np/Cholesterol/Megalin -0.08 0.18 -10000 0 -0.38 124 124
SHH -0.005 0.029 -10000 0 -0.5 1 1
catabolic process -0.094 0.2 -10000 0 -0.42 117 117
SMO/Vitamin D3 -0.076 0.18 -10000 0 -0.54 12 12
SHH Np/Cholesterol/Hhip -0.14 0.2 -10000 0 -0.4 166 166
LRP2 -0.16 0.3 -10000 0 -0.66 129 129
receptor-mediated endocytosis -0.14 0.21 -10000 0 -0.61 37 37
SHH Np/Cholesterol/BOC 0.014 0.056 -10000 0 -0.37 9 9
SHH Np/Cholesterol/CDO -0.094 0.18 -10000 0 -0.41 116 116
mesenchymal cell differentiation 0.14 0.2 0.4 166 -10000 0 166
mol:Vitamin D3 -0.065 0.17 -10000 0 -0.52 11 11
IHH N/PTCH2 -0.17 0.29 -10000 0 -0.53 175 175
CDON -0.18 0.32 -10000 0 -0.67 142 142
IHH N/PTCH1 -0.091 0.21 -10000 0 -0.42 121 121
Megalin/LRPAP1 -0.1 0.24 -10000 0 -0.49 129 129
PTCH2 -0.086 0.26 -10000 0 -0.67 79 79
SHH Np/Cholesterol 0.01 0.023 -10000 0 -0.4 1 1
PTCH1 -0.094 0.2 -10000 0 -0.42 117 117
HHIP -0.25 0.33 -10000 0 -0.67 184 184
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.099 0.24 0.53 112 -10000 0 112
KIRREL -0.044 0.19 -10000 0 -0.69 39 39
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.1 0.24 -10000 0 -0.53 112 112
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARRB2 0.026 0.007 -10000 0 -10000 0 0
WASL 0.026 0.006 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.055 0.2 -10000 0 -0.43 103 103
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.057 0.16 -10000 0 -0.35 101 101
FYN -0.062 0.2 0.27 25 -0.4 105 130
mol:Ca2+ -0.055 0.2 -10000 0 -0.43 102 102
mol:DAG -0.054 0.2 -10000 0 -0.43 102 102
NPHS2 -0.005 0.053 -10000 0 -0.73 1 1
mol:IP3 -0.054 0.2 -10000 0 -0.43 102 102
regulation of endocytosis -0.049 0.18 -10000 0 -0.38 101 101
Nephrin/NEPH1/podocin/Cholesterol -0.067 0.2 -10000 0 -0.43 105 105
establishment of cell polarity -0.099 0.24 -10000 0 -0.53 112 112
Nephrin/NEPH1/podocin/NCK1-2 -0.039 0.2 -10000 0 -0.4 102 102
Nephrin/NEPH1/beta Arrestin2 -0.048 0.18 -10000 0 -0.39 101 101
NPHS1 -0.1 0.26 -10000 0 -0.67 83 83
Nephrin/NEPH1/podocin -0.06 0.19 -10000 0 -0.4 105 105
TJP1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.054 0.2 -10000 0 -0.43 102 102
CD2AP 0.027 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.054 0.2 -10000 0 -0.43 101 101
GRB2 0.026 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.077 0.2 0.28 21 -0.41 105 126
cytoskeleton organization -0.081 0.2 -10000 0 -0.45 100 100
Nephrin/NEPH1 -0.071 0.18 -10000 0 -0.39 112 112
Nephrin/NEPH1/ZO-1 -0.068 0.21 -10000 0 -0.45 106 106
Endothelins

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
AKT1 -0.029 0.091 -10000 0 -0.33 26 26
PTK2B 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.28 0.46 1 -0.67 75 76
EDN1 -0.002 0.097 -10000 0 -0.55 8 8
EDN3 -0.31 0.35 -10000 0 -0.67 231 231
EDN2 0.011 0.082 -10000 0 -0.67 6 6
HRAS/GDP -0.11 0.23 0.44 3 -0.48 95 98
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.074 0.15 -10000 0 -0.32 109 109
ADCY4 -0.069 0.14 0.35 1 -0.4 65 66
ADCY5 -0.11 0.2 0.35 1 -0.44 110 111
ADCY6 -0.067 0.14 0.35 1 -0.4 64 65
ADCY7 -0.066 0.14 0.35 1 -0.4 64 65
ADCY1 -0.07 0.15 0.35 1 -0.41 65 66
ADCY2 -0.099 0.18 -10000 0 -0.43 92 92
ADCY3 -0.068 0.15 0.35 1 -0.4 67 68
ADCY8 -0.096 0.15 0.35 1 -0.43 68 69
ADCY9 -0.067 0.14 0.35 1 -0.4 64 65
arachidonic acid secretion -0.19 0.32 0.37 10 -0.6 154 164
ETB receptor/Endothelin-1/Gq/GTP -0.082 0.18 -10000 0 -0.36 117 117
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
HRAS 0.025 0.011 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.031 0.1 -10000 0 -0.32 16 16
ETA receptor/Endothelin-1/Gs/GTP -0.025 0.18 -10000 0 -0.41 71 71
mol:GTP -0.003 0.009 -10000 0 -10000 0 0
COL3A1 -0.034 0.099 -10000 0 -0.44 10 10
EDNRB 0.015 0.079 -10000 0 -0.67 6 6
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.067 0.14 -10000 0 -0.58 24 24
CYSLTR1 -0.036 0.13 -10000 0 -0.65 15 15
SLC9A1 0 0.054 -10000 0 -0.26 9 9
mol:GDP -0.12 0.24 0.4 5 -0.49 102 107
SLC9A3 -0.054 0.21 -10000 0 -0.7 33 33
RAF1 -0.16 0.28 0.44 3 -0.51 157 160
JUN -0.28 0.49 0.45 1 -1.1 125 126
JAK2 -0.03 0.095 -10000 0 -0.41 15 15
mol:IP3 -0.1 0.2 -10000 0 -0.4 127 127
ETA receptor/Endothelin-1 0.014 0.13 -10000 0 -0.4 27 27
PLCB1 0.023 0.032 -10000 0 -0.68 1 1
PLCB2 0.02 0.022 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.23 0.28 -10000 0 -0.52 232 232
FOS -0.27 0.45 0.61 2 -0.98 131 133
Gai/GDP -0.012 0.15 -10000 0 -0.65 22 22
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.18 -10000 0 -0.43 83 83
BCAR1 0.026 0.006 -10000 0 -10000 0 0
PRKCB1 -0.1 0.2 -10000 0 -0.39 130 130
GNAQ 0.015 0.022 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAL -0.059 0.23 -10000 0 -0.65 61 61
Gs family/GDP -0.15 0.25 0.28 1 -0.52 117 118
ETA receptor/Endothelin-1/Gq/GTP -0.087 0.17 -10000 0 -0.36 122 122
MAPK14 -0.07 0.15 -10000 0 -0.37 60 60
TRPC6 -0.16 0.3 0.47 1 -0.71 75 76
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.072 0.16 -10000 0 -0.35 87 87
ETB receptor/Endothelin-2 0.021 0.087 -10000 0 -0.51 12 12
ETB receptor/Endothelin-3 -0.23 0.27 -10000 0 -0.51 234 234
ETB receptor/Endothelin-1 0.015 0.097 -10000 0 -0.53 11 11
MAPK3 -0.24 0.41 0.37 9 -0.84 138 147
MAPK1 -0.29 0.44 0.6 1 -0.94 139 140
Rac1/GDP -0.11 0.22 0.37 1 -0.47 92 93
cAMP biosynthetic process -0.074 0.18 0.47 10 -0.43 66 76
MAPK8 -0.19 0.36 0.48 1 -0.69 119 120
SRC 0.026 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.003 0.076 -10000 0 -0.36 9 9
p130Cas/CRK/Src/PYK2 -0.15 0.28 0.38 11 -0.54 134 145
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.22 0.37 1 -0.48 91 92
COL1A2 -0.005 0.098 -10000 0 -0.46 9 9
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.014 0.084 -10000 0 -0.53 7 7
mol:DAG -0.1 0.2 -10000 0 -0.4 127 127
MAP2K2 -0.19 0.34 0.4 11 -0.66 141 152
MAP2K1 -0.21 0.34 0.42 3 -0.68 145 148
EDNRA 0.002 0.073 -10000 0 -0.23 24 24
positive regulation of muscle contraction -0.023 0.076 0.23 1 -0.35 8 9
Gq family/GDP -0.14 0.28 0.37 2 -0.54 131 133
HRAS/GTP -0.14 0.24 0.31 7 -0.47 129 136
PRKCH -0.1 0.2 0.3 1 -0.41 112 113
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.12 0.22 0.3 1 -0.47 104 105
PRKCB -0.11 0.2 0.3 1 -0.42 113 114
PRKCE -0.11 0.2 -10000 0 -0.45 94 94
PRKCD -0.11 0.19 -10000 0 -0.44 94 94
PRKCG -0.1 0.19 -10000 0 -0.42 109 109
regulation of vascular smooth muscle contraction -0.32 0.52 0.65 2 -1.2 130 132
PRKCQ -0.11 0.2 -10000 0 -0.42 114 114
PLA2G4A -0.21 0.35 0.37 10 -0.66 154 164
GNA14 -0.14 0.28 -10000 0 -0.64 114 114
GNA15 0.006 0.051 -10000 0 -0.67 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA11 0.008 0.086 -10000 0 -0.63 8 8
Rac1/GTP 0.031 0.1 -10000 0 -0.32 16 16
MMP1 -0.034 0.078 0.62 2 -10000 0 2
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.01 0.067 -10000 0 -0.45 9 9
NFATC2 -0.078 0.17 -10000 0 -0.45 82 82
NFATC3 -0.001 0.031 -10000 0 -10000 0 0
CD40LG -0.33 0.36 -10000 0 -0.74 176 176
PTGS2 -0.31 0.35 0.38 1 -0.73 163 164
JUNB 0.02 0.058 -10000 0 -0.59 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.024 -10000 0 -10000 0 0
CaM/Ca2+ 0.007 0.024 -10000 0 -10000 0 0
CALM1 0.018 0.02 -10000 0 -10000 0 0
JUN -0.13 0.28 -10000 0 -0.67 105 105
mol:Ca2+ -0.008 0.019 -10000 0 -0.18 4 4
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.011 -10000 0 -10000 0 0
FOSL1 0.006 0.06 -10000 0 -0.51 2 2
CREM 0.027 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.17 0.24 -10000 0 -0.46 162 162
FOS -0.16 0.3 -10000 0 -0.67 125 125
IFNG -0.33 0.36 0.38 1 -0.72 188 189
AP-1/NFAT1-c-4 -0.34 0.44 -10000 0 -0.83 173 173
FASLG -0.3 0.34 0.38 1 -0.7 171 172
NFAT1-c-4/ICER1 -0.077 0.17 -10000 0 -0.4 89 89
IL2RA -0.31 0.34 -10000 0 -0.69 172 172
FKBP12/FK506 0.02 0.004 -10000 0 -10000 0 0
CSF2 -0.32 0.31 0.38 1 -0.67 178 179
JunB/Fra1/NFAT1-c-4 -0.068 0.17 -10000 0 -0.39 88 88
IL4 -0.3 0.32 0.38 1 -0.66 168 169
IL2 0.003 0.072 -10000 0 -1 2 2
IL3 -0.009 0.054 -10000 0 -0.92 1 1
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
BATF3 0.018 0.043 -10000 0 -0.67 1 1
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.025 0.01 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.18 0.35 0.61 4 -0.78 59 63
HDAC7 0.028 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.23 0.4 -10000 0 -0.77 127 127
SMAD4 0.028 0.005 -10000 0 -10000 0 0
ID2 -0.18 0.34 0.62 3 -0.79 58 61
AP1 -0.19 0.36 -10000 0 -0.71 148 148
ABCG2 -0.19 0.35 0.61 1 -0.82 55 56
HIF1A -0.018 0.073 -10000 0 -0.35 1 1
TFF3 -0.47 0.42 0.62 3 -0.86 191 194
GATA2 0.028 0.01 -10000 0 -10000 0 0
AKT1 -0.052 0.11 -10000 0 -0.22 73 73
response to hypoxia -0.068 0.11 -10000 0 -0.23 92 92
MCL1 -0.18 0.34 0.61 3 -0.78 58 61
NDRG1 -0.18 0.34 0.6 2 -0.81 51 53
SERPINE1 -0.19 0.34 0.61 1 -0.81 52 53
FECH -0.18 0.35 0.61 4 -0.79 58 62
FURIN -0.18 0.35 0.61 4 -0.76 68 72
NCOA2 -0.036 0.2 -10000 0 -0.67 44 44
EP300 -0.1 0.18 -10000 0 -0.34 160 160
HMOX1 -0.2 0.33 0.62 2 -0.79 57 59
BHLHE40 -0.19 0.34 0.62 2 -0.75 72 74
BHLHE41 -0.19 0.34 0.61 1 -0.77 64 65
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.031 0.1 -10000 0 -10000 0 0
ENG 0.012 0.092 0.47 3 -10000 0 3
JUN -0.12 0.28 -10000 0 -0.67 104 104
RORA -0.18 0.35 0.61 4 -0.79 61 65
ABCB1 -0.05 0.16 -10000 0 -1.1 8 8
TFRC -0.19 0.35 0.62 2 -0.81 56 58
CXCR4 -0.18 0.34 0.62 3 -0.81 53 56
TF -0.22 0.4 0.62 2 -0.86 92 94
CITED2 -0.21 0.38 0.61 3 -0.9 67 70
HIF1A/ARNT -0.21 0.38 -10000 0 -0.88 56 56
LDHA -0.032 0.11 -10000 0 -0.69 8 8
ETS1 -0.18 0.34 0.62 3 -0.79 58 61
PGK1 -0.18 0.34 0.61 1 -0.82 49 50
NOS2 -0.19 0.34 0.62 2 -0.78 62 64
ITGB2 -0.18 0.35 0.62 3 -0.82 50 53
ALDOA -0.18 0.34 0.61 1 -0.79 57 58
Cbp/p300/CITED2 -0.29 0.46 -10000 0 -0.95 119 119
FOS -0.15 0.3 -10000 0 -0.67 125 125
HK2 -0.18 0.35 0.62 3 -0.81 54 57
SP1 0.031 0.018 -10000 0 -10000 0 0
GCK -0.39 0.64 -10000 0 -1.4 134 134
HK1 -0.18 0.34 0.62 3 -0.77 63 66
NPM1 -0.18 0.34 0.61 1 -0.78 58 59
EGLN1 -0.18 0.34 0.61 3 -0.81 50 53
CREB1 0.033 0.006 -10000 0 -10000 0 0
PGM1 -0.18 0.34 0.61 3 -0.75 70 73
SMAD3 0.028 0.004 -10000 0 -10000 0 0
EDN1 -0.19 0.29 0.5 1 -0.68 80 81
IGFBP1 -0.19 0.34 0.61 1 -0.76 66 67
VEGFA -0.2 0.35 -10000 0 -0.7 102 102
HIF1A/JAB1 0.005 0.057 -10000 0 -10000 0 0
CP -0.31 0.45 0.62 2 -0.88 146 148
CXCL12 -0.22 0.4 0.62 3 -0.87 83 86
COPS5 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.041 0.008 -10000 0 -10000 0 0
BNIP3 -0.18 0.34 0.62 3 -0.77 62 65
EGLN3 -0.2 0.35 -10000 0 -0.8 65 65
CA9 -0.19 0.34 0.6 2 -0.78 64 66
TERT -0.19 0.34 0.6 1 -0.78 62 63
ENO1 -0.18 0.34 0.61 3 -0.81 53 56
PFKL -0.18 0.34 0.62 3 -0.8 55 58
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.19 0.35 0.62 3 -0.76 75 78
ARNT -0.013 0.071 -10000 0 -0.31 2 2
HNF4A -0.015 0.058 -10000 0 -0.22 3 3
ADFP -0.2 0.33 -10000 0 -0.7 94 94
SLC2A1 -0.19 0.34 -10000 0 -0.69 105 105
LEP -0.19 0.34 0.61 1 -0.78 59 60
HIF1A/ARNT/Cbp/p300 -0.25 0.41 -10000 0 -0.78 136 136
EPO -0.14 0.28 -10000 0 -0.85 25 25
CREBBP -0.079 0.17 -10000 0 -0.33 134 134
HIF1A/ARNT/Cbp/p300/HDAC7 -0.22 0.4 -10000 0 -0.78 119 119
PFKFB3 -0.18 0.34 0.62 3 -0.77 65 68
NT5E -0.19 0.35 0.62 2 -0.83 52 54
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.5 0.39 -10000 0 -1.1 82 82
STAT6 (cleaved dimer) -0.51 0.41 -10000 0 -0.97 150 150
IGHG1 -0.18 0.13 -10000 0 -0.36 29 29
IGHG3 -0.49 0.38 -10000 0 -0.9 161 161
AKT1 -0.27 0.28 0.62 2 -0.81 62 64
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.3 -10000 0 -0.9 57 57
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.3 0.3 -10000 0 -0.73 105 105
THY1 -0.5 0.39 -10000 0 -1.1 91 91
MYB 0.011 0.097 -10000 0 -0.64 10 10
HMGA1 0.027 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.34 0.31 -10000 0 -0.79 98 98
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.28 -10000 0 -0.81 63 63
SP1 0.031 0.009 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
SOCS5 0.041 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.5 0.4 -10000 0 -1 121 121
SOCS1 -0.35 0.26 -10000 0 -0.71 75 75
SOCS3 -0.32 0.35 0.6 2 -1 61 63
FCER2 -0.51 0.42 -10000 0 -1 130 130
PARP14 0.027 0.005 -10000 0 -10000 0 0
CCL17 -0.53 0.42 -10000 0 -1.2 89 89
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.2 -10000 0 -0.66 47 47
T cell proliferation -0.5 0.41 -10000 0 -1.1 100 100
IL4R/JAK1 -0.5 0.4 -10000 0 -1 103 103
EGR2 -0.84 0.68 -10000 0 -1.5 223 223
JAK2 -0.032 0.041 -10000 0 -0.38 2 2
JAK3 -0.011 0.064 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.004 0.021 -10000 0 -10000 0 0
COL1A2 -0.15 0.13 -10000 0 -0.97 2 2
CCL26 -0.5 0.39 -10000 0 -1.1 84 84
IL4R -0.53 0.42 -10000 0 -1.1 97 97
PTPN6 0.04 0.012 -10000 0 -10000 0 0
IL13RA2 -0.6 0.53 -10000 0 -1.4 111 111
IL13RA1 -0.031 0.033 -10000 0 -10000 0 0
IRF4 -0.28 0.48 -10000 0 -1.1 96 96
ARG1 -0.13 0.13 -10000 0 -0.65 6 6
CBL -0.32 0.29 -10000 0 -0.8 79 79
GTF3A 0.025 0.016 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
IL13RA1/JAK2 -0.037 0.047 -10000 0 -0.25 1 1
IRF4/BCL6 -0.26 0.44 -10000 0 -1 95 95
CD40LG -0.066 0.23 -10000 0 -0.64 65 65
MAPK14 -0.33 0.33 -10000 0 -0.89 81 81
mitosis -0.26 0.26 0.62 2 -0.75 63 65
STAT6 -0.56 0.48 -10000 0 -1.1 142 142
SPI1 0.023 0.031 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 0.7 3 -0.7 61 64
STAT6 (dimer) -0.57 0.47 -10000 0 -1.1 142 142
STAT6 (dimer)/PARP14 -0.53 0.43 -10000 0 -1 131 131
mast cell activation 0.014 0.009 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.27 0.3 -10000 0 -0.87 66 66
FRAP1 -0.27 0.28 0.62 2 -0.81 63 65
LTA -0.51 0.4 -10000 0 -1.1 93 93
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.55 0.45 1.1 145 -10000 0 145
CCL11 -0.48 0.38 -10000 0 -1 104 104
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.27 0.3 -10000 0 -0.87 66 66
IL2RG -0.01 0.14 -10000 0 -0.62 21 21
IL10 -0.51 0.42 -10000 0 -1.2 87 87
IRS1 -0.057 0.23 -10000 0 -0.66 59 59
IRS2 0.026 0.006 -10000 0 -10000 0 0
IL4 -0.12 0.089 -10000 0 -10000 0 0
IL5 -0.5 0.39 -10000 0 -1.1 88 88
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.44 0.35 -10000 0 -0.93 98 98
COL1A1 -0.21 0.24 -10000 0 -1.1 22 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.5 0.41 -10000 0 -1.2 74 74
IL2R gamma/JAK3 -0.02 0.12 -10000 0 -0.45 22 22
TFF3 -1.2 0.57 -10000 0 -1.4 393 393
ALOX15 -0.5 0.39 -10000 0 -1.1 78 78
MYBL1 0.026 0.008 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.43 0.35 -10000 0 -0.91 100 100
SHC1 0.025 0.007 -10000 0 -10000 0 0
CEBPB 0.03 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.27 0.28 -10000 0 -0.78 65 65
mol:PI-3-4-5-P3 -0.27 0.28 0.62 2 -0.81 62 64
PI3K -0.28 0.3 0.67 1 -0.88 62 63
DOK2 0.02 0.051 -10000 0 -0.67 2 2
ETS1 0.039 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.19 -10000 0 -0.64 41 41
ITGB3 -0.51 0.42 -10000 0 -1.2 76 76
PIGR -0.53 0.44 -10000 0 -1.3 87 87
IGHE 0.046 0.044 0.24 9 -10000 0 9
MAPKKK cascade -0.2 0.19 0.58 1 -0.62 41 42
BCL6 0.026 0.032 -10000 0 -0.67 1 1
OPRM1 -0.51 0.39 -10000 0 -1.1 88 88
RETNLB -0.51 0.39 -10000 0 -1.1 82 82
SELP -0.5 0.41 -10000 0 -1.1 84 84
AICDA -0.49 0.38 -10000 0 -1.1 70 70
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.052 0.025 -9999 0 -0.44 1 1
fibroblast growth factor receptor signaling pathway 0.052 0.025 -9999 0 -0.44 1 1
LAMA1 -0.02 0.17 -9999 0 -0.66 33 33
PRNP 0.025 0.032 -9999 0 -0.67 1 1
GPC1/SLIT2 -0.042 0.19 -9999 0 -0.5 71 71
SMAD2 0.016 0.038 -9999 0 -0.39 3 3
GPC1/PrPc/Cu2+ 0.034 0.023 -9999 0 -0.44 1 1
GPC1/Laminin alpha1 0.002 0.14 -9999 0 -0.5 33 33
TDGF1 -0.27 0.34 -9999 0 -0.67 207 207
CRIPTO/GPC1 -0.19 0.27 -9999 0 -0.5 205 205
APP/GPC1 0.038 0.011 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.17 0.22 -9999 0 -0.44 203 203
FLT1 0.024 0.032 -9999 0 -0.67 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.047 0.042 -9999 0 -0.43 3 3
SERPINC1 0.02 0.022 -9999 0 -10000 0 0
FYN -0.17 0.22 -9999 0 -0.44 205 205
FGR -0.17 0.22 -9999 0 -0.44 199 199
positive regulation of MAPKKK cascade -0.23 0.26 -9999 0 -0.51 199 199
SLIT2 -0.077 0.25 -9999 0 -0.66 73 73
GPC1/NRG -0.009 0.15 -9999 0 -0.5 42 42
NRG1 -0.035 0.2 -9999 0 -0.66 43 43
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.053 -9999 0 -0.56 3 3
LYN -0.17 0.22 -9999 0 -0.44 200 200
mol:Spermine 0.008 0.004 -9999 0 -10000 0 0
cell growth 0.052 0.025 -9999 0 -0.44 1 1
BMP signaling pathway -0.026 0.008 -9999 0 -10000 0 0
SRC -0.17 0.22 -9999 0 -0.44 202 202
TGFBR1 0.022 0.023 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.18 0.3 -9999 0 -0.67 129 129
GPC1 0.026 0.009 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.022 0.023 -9999 0 -10000 0 0
VEGFA 0.023 0.055 -9999 0 -0.67 3 3
BLK -0.3 0.3 -9999 0 -0.53 270 270
HCK -0.18 0.22 -9999 0 -0.44 202 202
FGF2 0.027 0.004 -9999 0 -10000 0 0
FGFR1 0.025 0.032 -9999 0 -0.67 1 1
VEGFR1 homodimer 0.024 0.032 -9999 0 -0.67 1 1
TGFBR2 0.023 0.055 -9999 0 -0.67 3 3
cell death 0.038 0.011 -9999 0 -10000 0 0
ATIII/GPC1 0.034 0.019 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.12 0.23 -9999 0 -0.5 128 128
LCK -0.18 0.22 -9999 0 -0.44 204 204
neuron differentiation -0.009 0.15 -9999 0 -0.5 42 42
PrPc/Cu2+ 0.019 0.024 -9999 0 -0.5 1 1
APP 0.026 0.005 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.023 0.055 -9999 0 -0.67 3 3
IGF1 pathway

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
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTK2 0.026 0.006 -10000 0 -10000 0 0
CRKL -0.1 0.18 -10000 0 -0.36 152 152
GRB2/SOS1/SHC 0.048 0.02 -10000 0 -10000 0 0
HRAS 0.026 0.011 -10000 0 -10000 0 0
IRS1/Crk -0.093 0.19 -10000 0 -0.36 148 148
IGF-1R heterotetramer/IGF1/PTP1B -0.065 0.19 -10000 0 -0.42 106 106
AKT1 -0.091 0.17 -10000 0 -0.36 103 103
BAD -0.089 0.16 -10000 0 -0.59 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.098 0.18 -10000 0 -0.36 148 148
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.09 0.19 -10000 0 -0.36 152 152
RAF1 -0.069 0.15 0.39 1 -0.54 17 18
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.064 0.19 -10000 0 -0.34 145 145
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.097 0.2 -10000 0 -0.39 153 153
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
RPS6KB1 -0.089 0.16 -10000 0 -0.62 15 15
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.059 0.14 0.32 6 -0.44 16 22
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.071 0.16 -10000 0 -0.35 98 98
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.029 0.17 -10000 0 -0.34 96 96
IGF-1R heterotetramer -0.009 0.058 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.079 0.2 -10000 0 -0.36 152 152
Crk/p130 Cas/Paxillin -0.058 0.19 -10000 0 -0.36 103 103
IGF1R -0.009 0.058 -10000 0 -10000 0 0
IGF1 -0.14 0.29 -10000 0 -0.69 107 107
IRS2/Crk -0.087 0.18 -10000 0 -0.38 103 103
PI3K -0.067 0.2 -10000 0 -0.35 152 152
apoptosis 0.065 0.14 0.5 15 -0.32 2 17
HRAS/GDP 0.019 0.007 -10000 0 -10000 0 0
PRKCD -0.091 0.19 -10000 0 -0.45 105 105
RAF1/14-3-3 E -0.045 0.14 0.33 3 -0.45 17 20
BAD/14-3-3 -0.068 0.16 0.35 3 -0.54 15 18
PRKCZ -0.089 0.17 0.25 1 -0.62 15 16
Crk/p130 Cas/Paxillin/FAK1 -0.059 0.16 -10000 0 -0.54 15 15
PTPN1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.094 0.2 -10000 0 -0.47 107 107
BCAR1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.043 0.18 -10000 0 -0.37 103 103
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.089 0.19 -10000 0 -0.36 152 152
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 -0.1 0.19 -10000 0 -0.36 152 152
IRS1 -0.11 0.2 -10000 0 -0.39 152 152
IRS2 -0.1 0.18 -10000 0 -0.36 152 152
IGF-1R heterotetramer/IGF1 -0.1 0.23 -10000 0 -0.53 107 107
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDPK1 -0.091 0.18 -10000 0 -0.38 106 106
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKD1 -0.091 0.19 -10000 0 -0.45 105 105
SHC1 0.025 0.007 -10000 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.034 0.17 -10000 0 -0.44 70 70
cell-cell adhesion 0.11 0.16 0.32 175 -10000 0 175
Ephrin B/EPHB2/RasGAP 0.065 0.06 -10000 0 -0.37 7 7
ITSN1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
SHC1 0.025 0.007 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.025 0.046 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.14 0.23 -10000 0 -0.43 188 188
HRAS/GDP -0.082 0.16 -10000 0 -0.32 53 53
Ephrin B/EPHB1/GRB7 -0.1 0.22 -10000 0 -0.39 180 180
Endophilin/SYNJ1 0.023 0.073 0.44 6 -0.35 7 13
KRAS 0.027 0.005 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.1 0.22 -10000 0 -0.38 180 180
endothelial cell migration 0.052 0.037 -10000 0 -0.37 3 3
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.002 0.054 -10000 0 -10000 0 0
PAK1 0.024 0.074 0.47 5 -0.35 7 12
HRAS 0.026 0.011 -10000 0 -10000 0 0
RRAS 0.02 0.067 0.44 4 -0.36 6 10
DNM1 0.004 0.12 -10000 0 -0.61 16 16
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.13 0.18 -10000 0 -0.36 180 180
lamellipodium assembly -0.11 0.16 -10000 0 -0.32 175 175
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.088 0.16 -10000 0 -0.29 164 164
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPHB2 0.022 0.055 -10000 0 -0.67 3 3
EPHB3 -0.064 0.072 -10000 0 -10000 0 0
EPHB1 -0.24 0.34 -10000 0 -0.66 189 189
EPHB4 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.074 0.13 0.24 1 -0.37 13 14
Ephrin B/EPHB2 0.051 0.056 -10000 0 -0.37 7 7
Ephrin B/EPHB3 0.059 0.055 -10000 0 -0.42 4 4
JNK cascade -0.13 0.19 -10000 0 -0.37 178 178
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.38 186 186
RAP1/GDP -0.049 0.14 -10000 0 -0.33 12 12
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EFNB3 0.015 0.068 -10000 0 -0.67 4 4
EFNB1 0.026 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.12 0.22 -10000 0 -0.4 188 188
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.088 0.18 -10000 0 -0.33 176 176
Rap1/GTP -0.1 0.17 -10000 0 -0.33 165 165
axon guidance -0.034 0.17 -10000 0 -0.44 70 70
MAPK3 -0.083 0.14 -10000 0 -0.44 9 9
MAPK1 -0.082 0.13 -10000 0 -0.37 15 15
Rac1/GDP -0.06 0.13 -10000 0 -0.35 11 11
actin cytoskeleton reorganization -0.081 0.12 -10000 0 -0.31 7 7
CDC42/GDP -0.059 0.14 0.37 1 -0.35 12 13
PI3K 0.057 0.039 -10000 0 -0.37 3 3
EFNA5 -0.071 0.24 -10000 0 -0.67 68 68
Ephrin B2/EPHB4 0.034 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.026 0.044 -10000 0 -0.31 7 7
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.1 0.16 -10000 0 -0.32 170 170
PTK2 0.043 0.099 0.67 10 -10000 0 10
MAP4K4 -0.13 0.19 -10000 0 -0.38 178 178
SRC 0.026 0.008 -10000 0 -10000 0 0
KALRN 0.027 0.004 -10000 0 -10000 0 0
Intersectin/N-WASP 0.038 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.079 0.14 0.32 5 -0.32 2 7
MAP2K1 -0.084 0.15 -10000 0 -0.28 163 163
WASL 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.11 0.22 -10000 0 -0.4 178 178
cell migration -0.086 0.18 0.58 4 -0.3 163 167
NRAS 0.027 0.005 -10000 0 -10000 0 0
SYNJ1 0.023 0.074 0.45 6 -0.35 7 13
PXN 0.027 0.005 -10000 0 -10000 0 0
TF -0.023 0.13 0.47 3 -0.37 50 53
HRAS/GTP -0.095 0.19 -10000 0 -0.34 175 175
Ephrin B1/EPHB1-2 -0.12 0.22 -10000 0 -0.39 188 188
cell adhesion mediated by integrin -0.007 0.073 0.39 4 -0.3 13 17
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP -0.1 0.2 -10000 0 -0.36 178 178
RAC1-CDC42/GTP -0.14 0.16 -10000 0 -0.35 176 176
RASA1 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.051 0.13 -10000 0 -0.34 11 11
ruffle organization -0.11 0.18 0.58 4 -0.38 6 10
NCK1 0.027 0.004 -10000 0 -10000 0 0
receptor internalization 0.001 0.085 0.41 3 -0.37 17 20
Ephrin B/EPHB2/KALRN 0.065 0.06 -10000 0 -0.37 7 7
ROCK1 -0.023 0.043 -10000 0 -10000 0 0
RAS family/GDP -0.075 0.1 -10000 0 -0.32 4 4
Rac1/GTP -0.12 0.17 -10000 0 -0.34 175 175
Ephrin B/EPHB1/Src/Paxillin -0.094 0.16 -10000 0 -0.3 182 182
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EPHB2 0.021 0.055 -10000 0 -0.67 3 3
EFNB1 -0.002 0.086 -10000 0 -0.47 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.12 0.22 -10000 0 -0.39 187 187
Ephrin B2/EPHB1-2 -0.12 0.22 -10000 0 -0.4 187 187
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.37 187 187
Ephrin B1/EPHB1-2/Tiam1 -0.13 0.23 -10000 0 -0.41 194 194
DNM1 0.004 0.12 -10000 0 -0.63 15 15
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.002 0.095 0.41 1 -0.64 8 9
YES1 0.004 0.11 -10000 0 -0.89 7 7
Ephrin B1/EPHB1-2/NCK2 -0.12 0.21 -10000 0 -0.38 188 188
PI3K 0.024 0.11 -10000 0 -0.83 7 7
mol:GDP -0.13 0.23 -10000 0 -0.41 194 194
ITGA2B -0.04 0.2 -10000 0 -0.66 46 46
endothelial cell proliferation 0.033 0.01 -10000 0 -10000 0 0
FYN 0.003 0.11 -10000 0 -0.86 8 8
MAP3K7 -0.011 0.089 -10000 0 -0.68 8 8
FGR 0.001 0.11 -10000 0 -0.85 8 8
TIAM1 -0.057 0.078 -10000 0 -0.67 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RGS3 0.025 0.008 -10000 0 -10000 0 0
cell adhesion -0.025 0.16 -10000 0 -0.43 55 55
LYN 0.003 0.11 -10000 0 -0.86 8 8
Ephrin B1/EPHB1-2/Src Family Kinases -0.006 0.1 -10000 0 -0.81 8 8
Ephrin B1/EPHB1-2 -0.011 0.093 -10000 0 -0.77 7 7
SRC 0.001 0.11 -10000 0 -0.85 8 8
ITGB3 0.012 0.095 -10000 0 -0.64 10 10
EPHB1 -0.24 0.34 -10000 0 -0.67 189 189
EPHB4 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.023 0.18 -10000 0 -0.52 53 53
BLK -0.049 0.14 -10000 0 -0.92 8 8
HCK 0.002 0.11 -10000 0 -0.85 8 8
regulation of stress fiber formation 0.12 0.21 0.38 188 -10000 0 188
MAPK8 -0.007 0.12 0.36 5 -0.67 12 17
Ephrin B1/EPHB1-2/RGS3 -0.12 0.21 -10000 0 -0.38 188 188
endothelial cell migration -0.007 0.081 0.41 1 -0.62 7 8
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTPN13 0.023 0.091 -10000 0 -0.79 6 6
regulation of focal adhesion formation 0.12 0.21 0.38 188 -10000 0 188
chemotaxis 0.12 0.21 0.38 188 -10000 0 188
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
Rac1/GTP -0.12 0.22 -10000 0 -0.38 187 187
angiogenesis -0.012 0.095 -10000 0 -0.73 8 8
LCK 0 0.12 -10000 0 -0.89 8 8
Coregulation of Androgen receptor activity

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
NRIP1 -0.005 0.052 -10000 0 -0.2 6 6
SVIL -0.002 0.048 -10000 0 -10000 0 0
ZNF318 0.075 0.087 0.21 126 -0.67 1 127
JMJD2C -0.065 0.067 -10000 0 -0.12 275 275
T-DHT/AR/Ubc9 -0.22 0.24 -10000 0 -0.49 202 202
CARM1 0.023 0.009 -10000 0 -10000 0 0
PRDX1 0.029 0.006 -10000 0 -10000 0 0
PELP1 0.032 0.013 -10000 0 -10000 0 0
CTNNB1 0.003 0.04 -10000 0 -10000 0 0
AKT1 0.038 0.02 -10000 0 -10000 0 0
PTK2B 0.008 0.032 -10000 0 -10000 0 0
MED1 0.037 0.021 -10000 0 -10000 0 0
MAK 0.066 0.12 0.22 59 -0.65 7 66
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.006 0.064 -10000 0 -0.67 2 2
GSN 0 0.044 -10000 0 -10000 0 0
NCOA2 -0.039 0.2 -10000 0 -0.67 44 44
NCOA6 -0.003 0.054 -10000 0 -0.67 1 1
DNA-PK 0.074 0.078 -10000 0 -10000 0 0
NCOA4 0.026 0.005 -10000 0 -10000 0 0
PIAS3 0.003 0.038 -10000 0 -10000 0 0
cell proliferation -0.002 0.15 -10000 0 -0.8 10 10
XRCC5 0.037 0.018 -10000 0 -10000 0 0
UBE3A -0.012 0.063 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.25 0.26 -10000 0 -0.52 210 210
FHL2 -0.13 0.33 -10000 0 -1.1 43 43
RANBP9 -0.001 0.046 -10000 0 -10000 0 0
JMJD1A -0.001 0.035 -10000 0 -0.12 34 34
CDK6 0.023 0.055 -10000 0 -0.67 3 3
TGFB1I1 -0.003 0.047 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.24 0.24 -10000 0 -0.5 208 208
XRCC6 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR -0.28 0.26 -10000 0 -0.52 228 228
CTDSP1 0.012 0.023 -10000 0 -10000 0 0
CTDSP2 0.058 0.052 -10000 0 -10000 0 0
BRCA1 -0.003 0.047 -10000 0 -10000 0 0
TCF4 0.048 0.035 -10000 0 -10000 0 0
CDKN2A 0.003 0.083 -10000 0 -10000 0 0
SRF 0.034 0.051 -10000 0 -10000 0 0
NKX3-1 -0.11 0.14 -10000 0 -0.7 11 11
KLK3 -0.38 0.65 -10000 0 -1.4 137 137
TMF1 0.018 0.046 -10000 0 -0.67 2 2
HNRNPA1 0.044 0.029 -10000 0 -10000 0 0
AOF2 -0.02 0.033 -10000 0 -0.072 137 137
APPL1 0.042 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.22 0.24 -10000 0 -0.48 199 199
AR -0.31 0.34 -10000 0 -0.7 202 202
UBA3 0.013 0.023 -10000 0 -10000 0 0
PATZ1 0.033 0.031 -10000 0 -10000 0 0
PAWR 0.02 0.015 -10000 0 -10000 0 0
PRKDC 0.037 0.018 -10000 0 -10000 0 0
PA2G4 0.048 0.037 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.2 0.22 -10000 0 -0.45 201 201
RPS6KA3 -0.003 0.046 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.23 0.24 -10000 0 -0.49 203 203
LATS2 0.04 0.043 -10000 0 -0.67 1 1
T-DHT/AR/PRX1 -0.19 0.22 -10000 0 -0.43 204 204
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.005 0.084 -10000 0 -0.67 6 6
KLK2 -0.67 0.55 -10000 0 -1.1 279 279
CASP8 0.03 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.24 0.27 -10000 0 -0.52 208 208
TMPRSS2 -0.16 0.27 -10000 0 -1.1 33 33
CCND1 0.014 0.03 -10000 0 -10000 0 0
PIAS1 -0.012 0.063 -10000 0 -10000 0 0
mol:T-DHT -0.033 0.039 -10000 0 -0.076 181 181
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.03 0.09 -10000 0 -0.18 116 116
T-DHT/AR/CDK6 -0.22 0.24 -10000 0 -0.49 204 204
CMTM2 0.029 0.012 -10000 0 -10000 0 0
SNURF -0.014 0.16 -10000 0 -0.65 28 28
ZMIZ1 -0.024 0.056 -10000 0 -0.66 1 1
CCND3 0.028 0.004 -10000 0 -10000 0 0
TGIF1 0.044 0.029 -10000 0 -10000 0 0
FKBP4 -0.002 0.045 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 -0.19 0.54 -10000 0 -1.3 78 78
IL23A -0.21 0.56 -10000 0 -1.3 85 85
NF kappa B1 p50/RelA/I kappa B alpha -0.17 0.55 -10000 0 -1.2 82 82
positive regulation of T cell mediated cytotoxicity -0.23 0.62 -10000 0 -1.4 89 89
ITGA3 -0.18 0.51 -10000 0 -1.2 78 78
IL17F -0.1 0.34 0.65 2 -0.74 77 79
IL12B 0.005 0.087 -10000 0 -0.69 5 5
STAT1 (dimer) -0.21 0.59 -10000 0 -1.3 87 87
CD4 -0.18 0.5 -10000 0 -1.2 77 77
IL23 -0.2 0.53 -10000 0 -1.2 86 86
IL23R 0.003 0.11 -10000 0 -0.96 2 2
IL1B -0.22 0.58 -10000 0 -1.4 80 80
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.17 0.5 -10000 0 -1.2 77 77
TYK2 0.015 0.035 -10000 0 -10000 0 0
STAT4 0.004 0.098 -10000 0 -0.58 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
IL18RAP -0.008 0.14 -10000 0 -0.67 20 20
IL12RB1 -0.001 0.076 -10000 0 -0.63 4 4
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
IL12Rbeta1/TYK2 0.015 0.068 -10000 0 -0.48 4 4
IL23R/JAK2 0.01 0.13 -10000 0 -0.87 2 2
positive regulation of chronic inflammatory response -0.23 0.62 -10000 0 -1.4 89 89
natural killer cell activation 0.001 0.009 -10000 0 -0.046 2 2
JAK2 0.015 0.052 -10000 0 -0.38 2 2
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.006 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.18 0.5 -10000 0 -1.1 87 87
ALOX12B -0.18 0.5 -10000 0 -1.2 78 78
CXCL1 -0.2 0.52 -10000 0 -1.2 80 80
T cell proliferation -0.23 0.62 -10000 0 -1.4 89 89
NFKBIA 0.027 0.006 -10000 0 -10000 0 0
IL17A -0.056 0.27 -10000 0 -0.58 65 65
PI3K -0.19 0.55 -10000 0 -1.3 82 82
IFNG -0.014 0.052 0.12 1 -0.13 64 65
STAT3 (dimer) -0.17 0.52 -10000 0 -1.2 79 79
IL18R1 -0.002 0.096 -10000 0 -0.58 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.095 0.34 -10000 0 -0.79 65 65
IL18/IL18R 0 0.15 -10000 0 -0.48 34 34
macrophage activation -0.008 0.021 -10000 0 -0.045 79 79
TNF -0.25 0.61 -10000 0 -1.4 97 97
STAT3/STAT4 -0.2 0.56 -10000 0 -1.3 82 82
STAT4 (dimer) -0.22 0.59 -10000 0 -1.4 84 84
IL18 -0.008 0.11 -10000 0 -0.65 11 11
IL19 -0.17 0.5 -10000 0 -1.2 77 77
STAT5A (dimer) -0.21 0.58 -10000 0 -1.3 86 86
STAT1 0.023 0.023 -10000 0 -10000 0 0
SOCS3 -0.006 0.14 -10000 0 -0.67 22 22
CXCL9 -0.26 0.61 -10000 0 -1.4 104 104
MPO -0.18 0.51 -10000 0 -1.2 79 79
positive regulation of humoral immune response -0.23 0.62 -10000 0 -1.4 89 89
IL23/IL23R/JAK2/TYK2 -0.28 0.75 -10000 0 -1.6 89 89
IL6 -0.29 0.64 -10000 0 -1.3 121 121
STAT5A 0.026 0.007 -10000 0 -10000 0 0
IL2 0.003 0.03 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 -10000 0 -0.046 2 2
CD3E -0.21 0.56 -10000 0 -1.3 86 86
keratinocyte proliferation -0.23 0.62 -10000 0 -1.4 89 89
NOS2 -0.18 0.5 -10000 0 -1.2 78 78
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.16 0.29 -10000 0 -0.48 206 206
SMAD6-7/SMURF1 0.052 0.014 -10000 0 -10000 0 0
NOG -0.019 0.16 -10000 0 -0.67 29 29
SMAD9 -0.19 0.27 -10000 0 -0.54 172 172
SMAD4 0.027 0.004 -10000 0 -10000 0 0
SMAD5 -0.082 0.16 -10000 0 -0.44 29 29
BMP7/USAG1 -0.24 0.27 -10000 0 -0.5 245 245
SMAD5/SKI -0.068 0.17 0.33 2 -0.44 26 28
SMAD1 -0.035 0.094 -10000 0 -0.48 2 2
BMP2 0.001 0.13 -10000 0 -0.67 18 18
SMAD1/SMAD1/SMAD4 -0.02 0.084 -10000 0 -0.53 1 1
BMPR1A 0.027 0.005 -10000 0 -10000 0 0
BMPR1B -0.2 0.32 -10000 0 -0.67 159 159
BMPR1A-1B/BAMBI -0.11 0.23 -10000 0 -0.44 158 158
AHSG -0.004 0.04 -10000 0 -10000 0 0
CER1 -0.014 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.014 0.12 -10000 0 -0.44 28 28
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.065 0.16 -10000 0 -0.54 27 27
BMP2-4 (homodimer) 0.005 0.13 -10000 0 -0.5 29 29
RGMB 0.026 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.086 0.22 -10000 0 -0.4 158 158
RGMA 0.003 0.12 -10000 0 -0.65 17 17
SMURF1 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.078 0.16 -10000 0 -0.46 33 33
BMP2-4/USAG1 -0.22 0.26 -10000 0 -0.46 258 258
SMAD6/SMURF1/SMAD5 -0.066 0.17 0.32 1 -0.43 26 27
SOSTDC1 -0.33 0.34 -10000 0 -0.67 245 245
BMP7/BMPR2/BMPR1A-1B -0.086 0.22 -10000 0 -0.4 156 156
SKI 0.026 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.027 0.007 -10000 0 -10000 0 0
HFE2 -0.003 0.022 -10000 0 -10000 0 0
ZFYVE16 0.026 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.014 0.14 -10000 0 -0.45 38 38
SMAD5/SMAD5/SMAD4 -0.065 0.17 0.33 2 -0.42 30 32
MAPK1 0.02 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.053 0.15 -10000 0 -0.42 28 28
BMP7 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.027 0.032 -10000 0 -10000 0 0
SMAD1/SKI -0.026 0.1 0.33 1 -0.43 3 4
SMAD6 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.021 0.12 -10000 0 -0.45 29 29
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.14 0.29 -10000 0 -0.66 115 115
BMPR2 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.045 0.052 -10000 0 -0.44 5 5
BMPR1A-1B (homodimer) -0.14 0.25 -10000 0 -0.5 158 158
CHRDL1 -0.44 0.32 -10000 0 -0.66 334 334
ENDOFIN/SMAD1 -0.028 0.097 -10000 0 -0.48 2 2
SMAD6-7/SMURF1/SMAD1 -0.011 0.1 -10000 0 -0.58 1 1
SMAD6/SMURF1 0.026 0.006 -10000 0 -10000 0 0
BAMBI 0.019 0.052 -10000 0 -0.67 2 2
SMURF2 0.026 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.3 0.24 -10000 0 -0.46 324 324
BMP2-4/GREM1 -0.082 0.24 -10000 0 -0.47 125 125
SMAD7 0.027 0.004 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.17 0.26 -10000 0 -0.51 171 171
SMAD1/SMAD6 -0.026 0.095 -10000 0 -0.62 1 1
TAK1/SMAD6 0.038 0.01 -10000 0 -10000 0 0
BMP7 0.027 0.005 -10000 0 -10000 0 0
BMP6 0.027 0.007 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.057 0.13 -10000 0 -0.4 29 29
PPM1A 0.027 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.024 0.096 0.31 1 -0.48 2 3
SMAD7/SMURF1 0.038 0.01 -10000 0 -10000 0 0
CTDSPL 0.027 0.004 -10000 0 -10000 0 0
PPP1CA 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.007 -10000 0 -10000 0 0
CTDSP1 0.027 0.005 -10000 0 -10000 0 0
PPP1R15A 0.018 0.071 -10000 0 -0.67 5 5
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.26 -10000 0 -0.64 85 85
CHRD 0.013 0.099 -10000 0 -0.67 10 10
BMPR2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.079 0.16 -10000 0 -0.48 30 30
BMP4 0.008 0.11 -10000 0 -0.64 12 12
FST -0.14 0.29 -10000 0 -0.67 111 111
BMP2-4/NOG -0.006 0.16 -10000 0 -0.44 55 55
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.071 0.21 -10000 0 -0.38 153 153
Glucocorticoid receptor regulatory network

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
PCK2 0.084 0.086 0.36 1 -10000 0 1
SMARCC2 0.025 0.019 -10000 0 -10000 0 0
SMARCC1 0.026 0.018 -10000 0 -10000 0 0
TBX21 -0.12 0.24 -10000 0 -0.78 39 39
SUMO2 0.023 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.03 0.023 -10000 0 -10000 0 0
FKBP4 0.027 0.005 -10000 0 -10000 0 0
FKBP5 0.019 0.072 -10000 0 -0.62 6 6
GR alpha/HSP90/FKBP51/HSP90 0.12 0.11 0.33 49 -0.39 5 54
PRL -0.062 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.18 0.29 0.56 126 -0.46 19 145
RELA -0.029 0.1 -10000 0 -0.26 37 37
FGG 0.16 0.2 0.49 89 -10000 0 89
GR beta/TIF2 0.072 0.2 0.34 63 -0.45 44 107
IFNG -0.36 0.47 -10000 0 -1 136 136
apoptosis -0.013 0.23 0.47 45 -0.52 20 65
CREB1 0.026 0.014 -10000 0 -10000 0 0
histone acetylation -0.076 0.16 -10000 0 -0.43 57 57
BGLAP -0.076 0.13 -10000 0 -0.44 22 22
GR/PKAc 0.11 0.1 0.34 32 -0.33 1 33
NF kappa B1 p50/RelA -0.051 0.18 -10000 0 -0.37 84 84
SMARCD1 0.025 0.019 -10000 0 -10000 0 0
MDM2 0.084 0.097 0.24 99 -10000 0 99
GATA3 -0.003 0.14 -10000 0 -0.63 24 24
AKT1 0.021 0.004 -10000 0 -10000 0 0
CSF2 -0.11 0.14 -10000 0 -0.51 26 26
GSK3B 0.025 0.018 -10000 0 -10000 0 0
NR1I3 0.006 0.23 0.5 34 -0.57 11 45
CSN2 0.13 0.16 0.39 90 -10000 0 90
BRG1/BAF155/BAF170/BAF60A 0.063 0.055 -10000 0 -0.31 7 7
NFATC1 0.015 0.094 -10000 0 -0.67 9 9
POU2F1 0.026 0.01 -10000 0 -10000 0 0
CDKN1A 0.027 0.035 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.013 -10000 0 -10000 0 0
SFN -0.082 0.12 -10000 0 -0.67 13 13
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.13 0.35 41 -0.37 11 52
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.39 0.48 28 -0.83 100 128
JUN -0.24 0.27 -10000 0 -0.57 158 158
IL4 -0.099 0.16 -10000 0 -0.6 24 24
CDK5R1 0.026 0.013 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.26 0.31 -10000 0 -0.64 156 156
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.11 0.34 41 -0.38 4 45
cortisol/GR alpha (monomer) 0.25 0.3 0.64 141 -10000 0 141
NCOA2 -0.036 0.2 -10000 0 -0.67 44 44
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.3 -10000 0 -0.68 126 126
AP-1/NFAT1-c-4 -0.38 0.41 -10000 0 -0.75 226 226
AFP -0.17 0.2 -10000 0 -0.57 56 56
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.14 0.46 39 -10000 0 39
TP53 0.041 0.013 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
KRT17 -0.29 0.34 -10000 0 -0.85 89 89
KRT14 -0.082 0.12 -10000 0 -0.53 2 2
TBP 0.034 0.007 -10000 0 -10000 0 0
CREBBP 0.033 0.048 -10000 0 -0.26 11 11
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.005 -10000 0 -10000 0 0
AP-1 -0.38 0.41 -10000 0 -0.75 226 226
MAPK14 0.027 0.016 -10000 0 -10000 0 0
MAPK10 0.024 0.036 -10000 0 -0.67 1 1
MAPK11 0.017 0.019 -10000 0 -10000 0 0
KRT5 -0.38 0.5 -10000 0 -1 137 137
interleukin-1 receptor activity 0.003 0.003 -10000 0 -10000 0 0
NCOA1 0.029 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.023 -10000 0 -10000 0 0
CGA -0.093 0.14 -10000 0 -0.52 15 15
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.087 0.12 0.33 41 -10000 0 41
MAPK3 0.025 0.016 -10000 0 -10000 0 0
MAPK1 0.02 0.017 -10000 0 -10000 0 0
ICAM1 -0.17 0.24 -10000 0 -0.6 87 87
NFKB1 -0.028 0.099 -10000 0 -0.26 32 32
MAPK8 -0.14 0.18 -10000 0 -0.47 75 75
MAPK9 0.027 0.014 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.017 0.23 0.47 44 -0.55 20 64
BAX 0.04 0.093 0.84 5 -10000 0 5
POMC -0.44 0.63 -10000 0 -1.4 124 124
EP300 0.025 0.045 -10000 0 -0.26 9 9
cortisol/GR alpha (dimer)/p53 0.23 0.24 0.56 137 -10000 0 137
proteasomal ubiquitin-dependent protein catabolic process 0.08 0.13 0.33 81 -10000 0 81
SGK1 0.008 0.22 0.51 1 -1.3 11 12
IL13 -0.21 0.25 -10000 0 -0.73 53 53
IL6 -0.31 0.49 -10000 0 -1.1 117 117
PRKACG -0.009 0.016 -10000 0 -10000 0 0
IL5 -0.18 0.21 -10000 0 -0.65 42 42
IL2 -0.25 0.28 -10000 0 -0.69 93 93
CDK5 0.027 0.008 -10000 0 -10000 0 0
PRKACB 0.025 0.032 -10000 0 -0.67 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
IL8 -0.18 0.29 -10000 0 -0.7 75 75
CDK5R1/CDK5 0.038 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.004 0.14 -10000 0 -0.37 30 30
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.53 136 -10000 0 136
SMARCA4 0.024 0.019 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.15 0.38 86 -0.4 3 89
NF kappa B1 p50/RelA/Cbp -0.013 0.16 -10000 0 -0.4 34 34
JUN (dimer) -0.24 0.27 -10000 0 -0.57 158 158
YWHAH 0.02 0.012 -10000 0 -10000 0 0
VIPR1 -0.21 0.36 -10000 0 -0.96 82 82
NR3C1 0.16 0.19 0.44 106 -10000 0 106
NR4A1 -0.26 0.36 -10000 0 -0.66 203 203
TIF2/SUV420H1 -0.01 0.16 -10000 0 -0.5 44 44
MAPKKK cascade -0.013 0.23 0.47 45 -0.52 20 65
cortisol/GR alpha (dimer)/Src-1 0.23 0.24 0.55 141 -10000 0 141
PBX1 0.024 0.033 -10000 0 -0.67 1 1
POU1F1 0.005 0.022 -10000 0 -10000 0 0
SELE -0.26 0.46 -10000 0 -1.1 93 93
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.15 0.38 86 -0.4 3 89
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.53 136 -10000 0 136
mol:cortisol 0.14 0.19 0.38 140 -10000 0 140
MMP1 -0.1 0.14 -10000 0 -0.9 10 10
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.053 0.25 0.29 19 -0.59 70 89
FYN -0.1 0.32 0.47 1 -0.79 72 73
LAT/GRAP2/SLP76 -0.08 0.25 -10000 0 -0.62 76 76
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 -0.061 0.21 0.49 8 -0.47 75 83
B2M 0.027 0.006 -10000 0 -10000 0 0
IKBKG -0.015 0.056 0.1 5 -0.16 25 30
MAP3K8 0.016 0.085 -10000 0 -0.63 8 8
mol:Ca2+ -0.03 0.042 0.092 5 -0.1 100 105
integrin-mediated signaling pathway 0.034 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.3 0.5 4 -0.72 79 83
TRPV6 -0.1 0.35 1 19 -0.67 100 119
CD28 -0.012 0.15 -10000 0 -0.65 23 23
SHC1 -0.099 0.32 0.31 20 -0.78 73 93
receptor internalization -0.12 0.34 -10000 0 -0.8 83 83
PRF1 -0.1 0.33 -10000 0 -0.89 60 60
KRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.044 0.17 0.47 4 -0.38 74 78
LAT -0.1 0.31 0.3 3 -0.78 75 78
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.049 0.21 -10000 0 -0.64 53 53
CD3E -0.031 0.19 -10000 0 -0.63 42 42
CD3G -0.1 0.26 -10000 0 -0.65 89 89
RASGRP2 -0.004 0.034 0.096 3 -0.18 12 15
RASGRP1 -0.048 0.21 0.5 10 -0.47 74 84
HLA-A 0.026 0.012 -10000 0 -10000 0 0
RASSF5 0.025 0.007 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.034 0.01 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.14 0.32 31 -0.13 42 73
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.047 0.084 -10000 0 -0.25 54 54
PRKCA -0.035 0.12 -10000 0 -0.3 65 65
GRAP2 -0.017 0.14 -10000 0 -0.55 31 31
mol:IP3 -0.03 0.21 0.26 72 -0.44 71 143
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.12 0.35 -10000 0 -0.86 74 74
ORAI1 0.046 0.21 0.7 2 -0.8 15 17
CSK -0.11 0.32 -10000 0 -0.8 75 75
B7 family/CD28 -0.1 0.34 -10000 0 -0.8 79 79
CHUK 0.027 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.13 0.38 -10000 0 -0.95 75 75
PTPN6 -0.11 0.32 0.25 1 -0.8 75 76
VAV1 -0.11 0.31 -10000 0 -0.77 75 75
Monovalent TCR/CD3 -0.12 0.31 -10000 0 -0.6 108 108
CBL 0.027 0.005 -10000 0 -10000 0 0
LCK -0.11 0.33 -10000 0 -0.84 70 70
PAG1 -0.11 0.32 -10000 0 -0.8 74 74
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.13 0.38 -10000 0 -0.94 76 76
CD80 -0.04 0.2 -10000 0 -0.67 46 46
CD86 0.014 0.076 -10000 0 -0.68 5 5
PDK1/CARD11/BCL10/MALT1 -0.039 0.11 -10000 0 -0.29 58 58
HRAS 0.026 0.011 -10000 0 -10000 0 0
GO:0035030 -0.1 0.26 -10000 0 -0.63 79 79
CD8A -0.022 0.18 -10000 0 -0.65 35 35
CD8B -0.05 0.21 -10000 0 -0.65 53 53
PTPRC -0.007 0.14 -10000 0 -0.68 19 19
PDK1/PKC theta -0.074 0.26 0.57 10 -0.59 75 85
CSK/PAG1 -0.1 0.31 -10000 0 -0.79 71 71
SOS1 0.027 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.039 0.014 -10000 0 -10000 0 0
GRAP2/SLP76 -0.099 0.3 -10000 0 -0.75 76 76
STIM1 0.018 0.16 1.2 2 -0.9 9 11
RAS family/GTP 0.01 0.099 0.23 26 -0.18 46 72
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.38 -10000 0 -0.89 83 83
mol:DAG -0.058 0.16 0.14 6 -0.39 74 80
RAP1A/GDP 0.009 0.06 0.18 17 -10000 0 17
PLCG1 0.027 0.005 -10000 0 -10000 0 0
CD247 0 0.13 -10000 0 -0.68 16 16
cytotoxic T cell degranulation -0.097 0.31 -10000 0 -0.83 62 62
RAP1A/GTP -0.001 0.012 -10000 0 -0.068 10 10
mol:PI-3-4-5-P3 -0.08 0.24 0.52 6 -0.57 79 85
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.047 0.26 0.28 66 -0.59 71 137
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 0.001 0.12 -10000 0 -0.65 16 16
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.078 0.24 -10000 0 -0.59 75 75
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
CD8 heterodimer -0.052 0.23 -10000 0 -0.59 70 70
CARD11 -0.018 0.1 -10000 0 -0.67 8 8
PRKCB -0.029 0.12 -10000 0 -0.3 66 66
PRKCE -0.028 0.12 -10000 0 -0.29 66 66
PRKCQ -0.092 0.28 0.56 7 -0.68 76 83
LCP2 0.024 0.019 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.046 0.18 0.51 9 -0.4 75 84
IKK complex 0.018 0.13 0.37 25 -0.13 12 37
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 -0.033 0.12 0.26 3 -0.29 60 63
PDPK1 -0.057 0.2 0.49 9 -0.45 73 82
TCR/CD3/MHC I/CD8/Fyn -0.15 0.42 -10000 0 -0.99 81 81
Arf6 signaling events

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
CENTA1/KIF3B 0.035 0.008 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.018 0.15 -10000 0 -0.71 12 12
EGFR 0.021 0.063 -10000 0 -0.67 4 4
EPHA2 0.026 0.013 -10000 0 -10000 0 0
USP6 0.025 0.013 -10000 0 -10000 0 0
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.043 0.19 -10000 0 -0.5 73 73
ARRB2 -0.036 0.13 -10000 0 -0.39 59 59
mol:GTP 0.024 0.038 0.18 18 -10000 0 18
ARRB1 0.025 0.032 -10000 0 -0.67 1 1
FBXO8 0.027 0.004 -10000 0 -10000 0 0
TSHR 0.024 0.045 -10000 0 -0.67 2 2
EGF -0.074 0.24 -10000 0 -0.66 70 70
somatostatin receptor activity 0 0.001 0.002 14 -0.001 137 151
ARAP2 0.025 0.036 -10000 0 -0.51 2 2
mol:GDP -0.11 0.14 0.27 5 -0.3 118 123
mol:PI-3-4-5-P3 0 0 0.002 11 -0.001 74 85
ITGA2B -0.04 0.2 -10000 0 -0.66 46 46
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.025 -10000 0 -10000 0 0
ADAP1 0.026 0.006 -10000 0 -10000 0 0
KIF13B 0.027 0.005 -10000 0 -10000 0 0
HGF/MET -0.077 0.19 -10000 0 -0.52 69 69
PXN 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.11 0.16 0.47 9 -0.29 147 156
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.02 0.17 -10000 0 -0.43 73 73
ADRB2 0.009 0.11 -10000 0 -0.67 12 12
receptor agonist activity 0 0 0.001 18 0 142 160
actin filament binding 0 0 0.002 15 -0.001 138 153
SRC 0.026 0.008 -10000 0 -10000 0 0
ITGB3 0.012 0.095 -10000 0 -0.64 10 10
GNAQ 0.025 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.005 16 -0.001 68 84
ARF6/GDP -0.007 0.092 0.24 2 -0.45 9 11
ARF6/GDP/GULP/ACAP1 -0.14 0.19 -10000 0 -0.41 112 112
alphaIIb/beta3 Integrin/paxillin/GIT1 0.013 0.15 -10000 0 -0.41 53 53
ACAP1 0.019 0.044 -10000 0 -0.51 2 2
ACAP2 0.027 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.05 0.19 -10000 0 -0.56 59 59
EFNA1 0.025 0.007 -10000 0 -10000 0 0
HGF -0.073 0.24 -10000 0 -0.67 69 69
CYTH3 0.006 0.033 -10000 0 -0.51 2 2
CYTH2 -0.009 0.15 -10000 0 -0.94 13 13
NCK1 0.027 0.004 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 22 0 100 122
endosomal lumen acidification 0 0 0.002 6 -0.001 139 145
microtubule-based process 0 0 -10000 0 0 7 7
GULP1 -0.091 0.26 -10000 0 -0.65 85 85
GNAQ/ARNO 0.004 0.14 -10000 0 -0.86 13 13
mol:Phosphatidic acid 0 0 0.001 13 -10000 0 13
PIP3-E 0 0 0.001 9 0 15 24
MET -0.028 0.071 -10000 0 -10000 0 0
GNA14 -0.13 0.28 -10000 0 -0.63 114 114
GNA15 0.012 0.05 -10000 0 -0.67 1 1
GIT1 0.026 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 0.003 15 -0.001 108 123
GNA11 0.014 0.085 -10000 0 -0.63 8 8
LHCGR -0.074 0.22 -10000 0 -0.67 59 59
AGTR1 -0.25 0.34 -10000 0 -0.67 195 195
desensitization of G-protein coupled receptor protein signaling pathway -0.049 0.19 -10000 0 -0.56 59 59
IPCEF1/ARNO -0.034 0.18 -10000 0 -0.75 13 13
alphaIIb/beta3 Integrin -0.023 0.18 -10000 0 -0.52 53 53
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.091 0.33 -10000 0 -1.1 42 42
MKNK1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.018 0.11 -10000 0 -0.34 34 34
ATF2/c-Jun -0.2 0.35 -10000 0 -0.79 119 119
MAPK11 -0.013 0.097 -10000 0 -0.34 29 29
MITF -0.025 0.12 -10000 0 -0.41 39 39
MAPKAPK5 -0.021 0.12 -10000 0 -0.4 35 35
KRT8 -0.021 0.12 -10000 0 -0.4 35 35
MAPKAPK3 0.027 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.007 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.027 0.15 -10000 0 -0.5 34 34
CEBPB -0.022 0.12 -10000 0 -0.4 37 37
SLC9A1 -0.025 0.12 -10000 0 -0.4 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.076 0.18 -10000 0 -0.42 82 82
p38alpha-beta/MNK1 -0.011 0.13 -10000 0 -0.4 34 34
JUN -0.2 0.34 -10000 0 -0.78 119 119
PPARGC1A -0.22 0.25 -10000 0 -0.45 249 249
USF1 -0.025 0.12 -10000 0 -0.4 40 40
RAB5/GDP/GDI1 -0.037 0.1 -10000 0 -0.34 23 23
NOS2 -0.03 0.12 -10000 0 -0.47 15 15
DDIT3 -0.021 0.12 -10000 0 -0.4 35 35
RAB5A 0.027 0.004 -10000 0 -10000 0 0
HSPB1 -0.017 0.095 0.38 2 -0.33 33 35
p38alpha-beta/HBP1 -0.008 0.12 -10000 0 -0.41 28 28
CREB1 -0.057 0.16 -10000 0 -0.47 42 42
RAB5/GDP 0.02 0.003 -10000 0 -10000 0 0
EIF4E -0.026 0.1 -10000 0 -0.37 29 29
RPS6KA4 -0.023 0.12 -10000 0 -0.41 37 37
PLA2G4A -0.052 0.16 -10000 0 -0.49 49 49
GDI1 -0.021 0.12 -10000 0 -0.42 34 34
TP53 -0.033 0.13 -10000 0 -0.5 30 30
RPS6KA5 -0.065 0.18 -10000 0 -0.45 79 79
ESR1 -0.053 0.19 -10000 0 -0.55 50 50
HBP1 0.026 0.006 -10000 0 -10000 0 0
MEF2C -0.021 0.12 -10000 0 -0.4 36 36
MEF2A -0.027 0.13 -10000 0 -0.41 41 41
EIF4EBP1 -0.056 0.16 -10000 0 -0.46 43 43
KRT19 -0.054 0.17 -10000 0 -0.5 45 45
ELK4 -0.026 0.12 -10000 0 -0.4 40 40
ATF6 -0.025 0.12 -10000 0 -0.4 40 40
ATF1 -0.055 0.16 -10000 0 -0.47 40 40
p38alpha-beta/MAPKAPK2 -0.012 0.13 -10000 0 -0.4 34 34
p38alpha-beta/MAPKAPK3 -0.012 0.13 -10000 0 -0.41 33 33
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.006 0.051 -10000 0 -10000 0 0
GNB1/GNG2 -0.034 0.067 -10000 0 -0.19 69 69
AKT1 0.01 0.13 0.41 22 -0.21 35 57
EGF -0.074 0.24 -10000 0 -0.66 70 70
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.018 0.088 0.36 13 -0.5 3 16
mol:Ca2+ -0.018 0.15 0.38 18 -0.3 71 89
LYN 0.017 0.087 0.36 12 -0.5 3 15
RhoA/GTP -0.01 0.055 -10000 0 -0.14 33 33
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.019 0.17 0.43 18 -0.34 69 87
GNG2 0.025 0.032 -10000 0 -0.67 1 1
ARRB2 0.026 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.031 0.12 0.27 1 -0.59 12 13
G beta5/gamma2 -0.044 0.091 -10000 0 -0.26 69 69
PRKCH -0.025 0.17 0.44 15 -0.36 70 85
DNM1 0.004 0.12 -10000 0 -0.61 16 16
TXA2/TP beta/beta Arrestin3 -0.01 0.12 -10000 0 -0.42 33 33
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.004 0.14 -10000 0 -0.67 21 21
G12 family/GTP -0.036 0.12 -10000 0 -0.31 68 68
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
ADRBK2 0.02 0.012 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.036 0.007 -10000 0 -10000 0 0
mol:GDP 0.05 0.14 0.38 42 -0.35 7 49
mol:NADP 0.026 0.006 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
PRKG1 -0.16 0.31 -10000 0 -0.66 133 133
mol:IP3 -0.029 0.18 0.43 15 -0.38 71 86
cell morphogenesis 0.035 0.007 -10000 0 -10000 0 0
PLCB2 -0.052 0.22 0.46 11 -0.52 71 82
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.076 0.17 0.36 9 -0.33 135 144
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.013 0.082 0.34 10 -0.5 3 13
RHOA 0.027 0.004 -10000 0 -10000 0 0
PTGIR 0.018 0.071 -10000 0 -0.67 5 5
PRKCB1 -0.029 0.17 0.42 14 -0.38 72 86
GNAQ 0.025 0.008 -10000 0 -10000 0 0
mol:L-citrulline 0.026 0.006 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.049 0.23 0.49 14 -0.53 71 85
LCK 0.013 0.1 0.36 13 -0.53 6 19
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.025 0.087 -10000 0 -0.34 19 19
TXA2-R family/G12 family/GDP/G beta/gamma 0.03 0.034 -10000 0 -0.34 2 2
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.029 0.087 -10000 0 -0.33 19 19
MAPK14 -0.006 0.12 0.34 22 -0.23 66 88
TGM2/GTP -0.047 0.18 0.34 5 -0.43 71 76
MAPK11 -0.01 0.13 0.36 21 -0.23 64 85
ARHGEF1 -0.016 0.074 0.17 1 -0.18 63 64
GNAI2 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.027 0.18 0.42 20 -0.39 71 91
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.017 0.15 0.35 22 -0.29 72 94
cAMP biosynthetic process -0.03 0.17 0.43 15 -0.35 71 86
Gq family/GTP/EBP50 -0.045 0.12 0.24 2 -0.23 118 120
actin cytoskeleton reorganization 0.035 0.007 -10000 0 -10000 0 0
SRC 0.015 0.082 0.34 10 -0.5 3 13
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.02 0.13 0.44 15 -0.3 15 30
VCAM1 -0.014 0.15 0.37 18 -0.3 71 89
TP beta/Gq family/GDP/G beta5/gamma2 -0.031 0.12 0.27 1 -0.59 12 13
platelet activation -0.006 0.17 0.46 22 -0.3 69 91
PGI2/IP 0.013 0.053 -10000 0 -0.5 5 5
PRKACA 0.002 0.087 -10000 0 -0.37 22 22
Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.28 1 -0.54 13 14
TXA2/TP beta/beta Arrestin2 0.006 0.1 -10000 0 -0.53 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.001 0.087 -10000 0 -0.37 20 20
mol:DAG -0.035 0.19 0.46 13 -0.42 72 85
EGFR 0.021 0.063 -10000 0 -0.67 4 4
TXA2/TP alpha -0.047 0.22 0.51 13 -0.48 71 84
Gq family/GTP -0.064 0.13 0.22 2 -0.27 132 134
YES1 0.02 0.091 0.37 14 -0.5 3 17
GNAI2/GTP 0.007 0.075 -10000 0 -0.6 3 3
PGD2/DP -0.003 0.11 -10000 0 -0.5 21 21
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.021 0.092 0.36 16 -0.5 3 19
mol:NO 0.026 0.006 -10000 0 -10000 0 0
GNA15 0.012 0.05 -10000 0 -0.67 1 1
PGK/cGMP -0.091 0.21 -10000 0 -0.43 132 132
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.038 0.098 -10000 0 -0.51 7 7
NOS3 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.031 0.18 0.42 18 -0.38 74 92
PRKCB -0.028 0.18 0.42 18 -0.37 71 89
PRKCE -0.032 0.16 0.38 11 -0.37 72 83
PRKCD -0.03 0.17 0.44 12 -0.38 71 83
PRKCG -0.029 0.18 0.41 17 -0.39 68 85
muscle contraction -0.041 0.22 0.5 15 -0.49 71 86
PRKCZ -0.02 0.17 0.41 20 -0.34 70 90
ARR3 -0.002 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.014 0.087 -10000 0 -0.44 8 8
PRKCQ -0.029 0.17 0.41 14 -0.36 73 87
MAPKKK cascade -0.04 0.21 0.47 15 -0.46 71 86
SELE -0.032 0.18 0.36 20 -0.42 71 91
TP beta/GNAI2/GDP/G beta/gamma 0.037 0.095 -10000 0 -0.76 3 3
ROCK1 0.027 0.004 -10000 0 -10000 0 0
GNA14 -0.13 0.28 -10000 0 -0.63 114 114
chemotaxis -0.056 0.26 0.52 14 -0.61 71 85
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.014 0.085 -10000 0 -0.63 8 8
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.046 0.042 -10000 0 -0.82 1 1
forebrain development -0.3 0.28 0.41 2 -0.54 238 240
GNAO1 0.002 0.12 -10000 0 -0.67 15 15
SMO/beta Arrestin2 0.015 0.036 -10000 0 -0.5 1 1
SMO 0.015 0.034 -10000 0 -0.67 1 1
ARRB2 0.021 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.036 0.075 -10000 0 -0.37 3 3
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
GNAI2 0.025 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.064 0.032 -10000 0 -0.4 1 1
GNAI1 0.023 0.032 -10000 0 -0.68 1 1
XPO1 0.016 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.21 0.22 -10000 0 -0.49 134 134
SAP30 0.026 0.032 -10000 0 -0.67 1 1
mol:GDP 0.015 0.034 -10000 0 -0.67 1 1
MIM/GLI2A -0.031 0.067 -10000 0 -10000 0 0
IFT88 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.025 0.006 -10000 0 -10000 0 0
GLI2 0 0.079 0.28 2 -0.38 7 9
GLI3 0.026 0.078 0.28 3 -0.36 5 8
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
SAP18 0.027 0.007 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.025 0.032 -10000 0 -0.67 1 1
Gi family/GTP -0.016 0.069 -10000 0 -0.3 17 17
SIN3B 0.026 0.008 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
GLI3/Su(fu) 0.037 0.067 -10000 0 -0.48 2 2
GLI2/Su(fu) 0.009 0.076 -10000 0 -0.49 3 3
FOXA2 -0.58 0.62 -10000 0 -1.2 237 237
neural tube patterning -0.3 0.28 0.41 2 -0.54 238 240
SPOP 0.026 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.034 0.03 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
MTSS1 -0.031 0.066 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.3 0.28 0.41 2 -0.54 238 240
SUFU 0.018 0.016 -10000 0 -0.23 1 1
LGALS3 -0.025 0.071 -10000 0 -10000 0 0
catabolic process 0.031 0.1 -10000 0 -0.49 5 5
GLI3A/CBP -0.17 0.2 -10000 0 -0.38 240 240
KIF3A 0.026 0.006 -10000 0 -10000 0 0
GLI1 -0.3 0.29 0.41 2 -0.55 237 239
RAB23 0.021 0.063 -10000 0 -0.67 4 4
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
IFT172 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.019 0.05 -10000 0 -10000 0 0
GNAZ 0.019 0.012 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.67 2 2
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GLI2/SPOP 0.01 0.081 -10000 0 -0.41 4 4
STK36 0.016 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.01 0.055 -10000 0 -0.34 4 4
PTCH1 -0.27 0.26 0.58 2 -0.59 131 133
MIM/GLI1 -0.42 0.38 0.35 1 -0.7 265 266
CREBBP -0.17 0.2 -10000 0 -0.38 240 240
Su(fu)/SIN3/HDAC complex 0.035 0.069 -10000 0 -0.53 5 5
IL6-mediated 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
BCL2L1 -0.003 0.2 0.6 5 -0.59 20 25
CRP 0 0.21 0.59 9 -0.59 23 32
cell cycle arrest -0.018 0.21 0.75 1 -0.66 26 27
TIMP1 -0.04 0.22 0.6 3 -0.63 33 36
IL6ST -0.065 0.24 -10000 0 -0.67 65 65
Rac1/GDP -0.051 0.2 0.31 1 -0.52 51 52
AP1 -0.11 0.27 -10000 0 -0.6 93 93
GAB2 0.027 0.005 -10000 0 -10000 0 0
TNFSF11 -0.014 0.19 0.63 4 -0.6 20 24
HSP90B1 0.041 0.053 -10000 0 -0.64 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 -0.095 0.25 -10000 0 -0.67 56 56
AKT1 0.04 0.058 -10000 0 -0.97 1 1
FOXO1 0.039 0.056 -10000 0 -0.91 1 1
MAP2K6 -0.085 0.23 0.24 1 -0.53 72 73
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.036 0.2 0.33 6 -0.51 44 50
MITF -0.074 0.21 -10000 0 -0.38 119 119
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.025 0.008 -10000 0 -10000 0 0
A2M 0.026 0.071 -10000 0 -1.1 2 2
CEBPB 0.033 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.005 0.1 -10000 0 -0.53 7 7
STAT3 -0.027 0.22 0.76 1 -0.7 26 27
STAT1 0.008 0.1 -10000 0 -0.96 5 5
CEBPD -0.005 0.2 0.59 3 -0.58 24 27
PIK3CA 0.024 0.055 -10000 0 -0.67 3 3
PI3K 0.038 0.044 -10000 0 -0.5 3 3
JUN -0.12 0.28 -10000 0 -0.67 104 104
PIAS3/MITF -0.058 0.21 -10000 0 -0.55 48 48
MAPK11 -0.095 0.24 -10000 0 -0.68 51 51
STAT3 (dimer)/FOXO1 0.013 0.17 -10000 0 -0.52 20 20
GRB2/SOS1/GAB family -0.034 0.2 -10000 0 -0.51 42 42
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.077 0.21 -10000 0 -0.37 137 137
GRB2 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.024 0.025 -10000 0 -0.35 2 2
LBP 0.004 0.18 0.56 10 -0.5 20 30
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.026 0.015 -10000 0 -10000 0 0
MYC -0.018 0.25 0.63 3 -0.91 20 23
FGG -0.012 0.19 0.68 3 -0.64 14 17
macrophage differentiation -0.018 0.21 0.75 1 -0.66 26 27
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.076 0.26 -10000 0 -0.45 136 136
JUNB -0.007 0.21 0.6 3 -0.66 23 26
FOS -0.15 0.3 -10000 0 -0.67 125 125
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.073 0.23 -10000 0 -0.38 140 140
STAT1/PIAS1 -0.043 0.21 -10000 0 -0.5 50 50
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.061 -10000 0 -0.54 3 3
STAT3 (dimer) -0.021 0.22 0.76 1 -0.68 26 27
PRKCD -0.024 0.19 0.41 6 -0.56 31 37
IL6R 0.001 0.13 -10000 0 -0.67 17 17
SOCS3 -0.11 0.32 0.43 2 -0.93 51 53
gp130 (dimer)/JAK1/JAK1/LMO4 -0.007 0.17 -10000 0 -0.43 63 63
Rac1/GTP -0.048 0.2 -10000 0 -0.53 48 48
HCK 0.018 0.035 -10000 0 -10000 0 0
MAPKKK cascade 0.023 0.1 0.34 1 -0.6 7 8
bone resorption -0.013 0.19 0.62 4 -0.56 23 27
IRF1 -0.002 0.2 0.64 6 -0.6 18 24
mol:GDP -0.07 0.21 0.25 1 -0.49 65 66
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.071 0.21 0.25 1 -0.5 63 64
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.091 0.25 -10000 0 -0.69 55 55
PTPN11 0.015 0.068 -10000 0 -0.97 2 2
IL6/IL6RA -0.081 0.23 -10000 0 -0.52 101 101
gp130 (dimer)/TYK2/TYK2/LMO4 -0.01 0.16 -10000 0 -0.41 65 65
gp130 (dimer)/JAK2/JAK2/LMO4 -0.013 0.17 -10000 0 -0.43 65 65
IL6 -0.11 0.27 -10000 0 -0.67 90 90
PIAS3 0.026 0.007 -10000 0 -10000 0 0
PTPRE -0.019 0.074 -10000 0 -0.67 1 1
PIAS1 0.027 0.004 -10000 0 -10000 0 0
RAC1 0.027 0.006 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.079 0.21 -10000 0 -0.38 134 134
LMO4 0.028 0.018 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.025 0.21 -10000 0 -0.69 26 26
MCL1 0.054 0.071 -10000 0 -0.82 1 1
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.11 0.22 -10000 0 -0.42 130 130
MAP3K8 0.014 0.085 -10000 0 -0.63 8 8
FOS -0.077 0.17 0.29 3 -0.45 58 61
PRKCA -0.015 0.14 -10000 0 -0.67 21 21
PTPN7 -0.02 0.13 -10000 0 -0.67 16 16
HRAS 0.025 0.011 -10000 0 -10000 0 0
PRKCB -0.006 0.082 -10000 0 -0.68 5 5
NRAS 0.025 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.034 0.031 -10000 0 -10000 0 0
MAPK3 -0.013 0.12 -10000 0 -0.47 20 20
MAP2K1 -0.021 0.14 -10000 0 -0.54 25 25
ELK1 0.012 0.025 -10000 0 -10000 0 0
BRAF -0.016 0.13 -10000 0 -0.52 25 25
mol:GTP -0.002 0.004 -10000 0 -0.006 128 128
MAPK1 -0.099 0.2 -10000 0 -0.41 116 116
RAF1 -0.015 0.12 -10000 0 -0.51 25 25
KRAS 0.026 0.005 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.026 0.14 -10000 0 -0.35 47 47
TBX21 -0.12 0.42 -10000 0 -1.2 55 55
B2M 0.023 0.018 -10000 0 -10000 0 0
TYK2 0.02 0.03 -10000 0 -10000 0 0
IL12RB1 0.004 0.074 -10000 0 -0.6 4 4
GADD45B -0.092 0.39 -10000 0 -1 58 58
IL12RB2 -0.003 0.13 -10000 0 -0.65 17 17
GADD45G -0.088 0.35 -10000 0 -0.95 50 50
natural killer cell activation 0.001 0.019 -10000 0 -10000 0 0
RELB 0.025 0.007 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL18 -0.002 0.11 -10000 0 -0.65 11 11
IL2RA -0.014 0.15 -10000 0 -0.63 25 25
IFNG -0.07 0.22 -10000 0 -0.67 59 59
STAT3 (dimer) -0.078 0.31 -10000 0 -0.78 61 61
HLA-DRB5 -0.009 0.081 -10000 0 -0.67 4 4
FASLG -0.13 0.45 -10000 0 -1.2 59 59
NF kappa B2 p52/RelB -0.098 0.38 -10000 0 -0.94 62 62
CD4 0.011 0.033 -10000 0 -10000 0 0
SOCS1 0.024 0.035 -10000 0 -0.67 1 1
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.063 0.21 -10000 0 -0.63 53 53
CD3E -0.044 0.18 -10000 0 -0.62 42 42
CD3G -0.11 0.26 -10000 0 -0.65 89 89
IL12Rbeta2/JAK2 0.012 0.11 -10000 0 -0.47 19 19
CCL3 -0.11 0.41 -10000 0 -1.2 46 46
CCL4 -0.15 0.49 -10000 0 -1.4 57 57
HLA-A 0.023 0.019 -10000 0 -10000 0 0
IL18/IL18R 0.031 0.16 -10000 0 -0.49 33 33
NOS2 -0.083 0.35 -10000 0 -0.99 44 44
IL12/IL12R/TYK2/JAK2/SPHK2 -0.026 0.14 -10000 0 -0.34 50 50
IL1R1 -0.099 0.37 -10000 0 -1.1 46 46
IL4 0 0.033 -10000 0 -10000 0 0
JAK2 0.018 0.039 -10000 0 -0.37 2 2
EntrezGene:6957 -0.006 0.014 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.21 0.49 -10000 0 -1.1 96 96
RAB7A -0.054 0.3 -10000 0 -0.74 53 53
lysosomal transport -0.049 0.28 -10000 0 -0.7 54 54
FOS -0.37 0.61 -10000 0 -1.2 158 158
STAT4 (dimer) -0.08 0.36 -10000 0 -0.86 62 62
STAT5A (dimer) -0.14 0.4 -10000 0 -0.96 71 71
GZMA -0.11 0.4 -10000 0 -1.2 46 46
GZMB -0.11 0.39 -10000 0 -1.1 49 49
HLX 0.022 0.024 -10000 0 -10000 0 0
LCK -0.12 0.43 -10000 0 -1.1 61 61
TCR/CD3/MHC II/CD4 -0.14 0.29 -10000 0 -0.54 115 115
IL2/IL2R -0.006 0.16 -10000 0 -0.52 36 36
MAPK14 -0.081 0.37 0.46 1 -0.89 64 65
CCR5 -0.089 0.39 -10000 0 -1.1 47 47
IL1B -0.033 0.2 -10000 0 -0.7 38 38
STAT6 -0.006 0.11 -10000 0 -0.46 5 5
STAT4 0.004 0.098 -10000 0 -0.58 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
NFKB2 0.027 0.004 -10000 0 -10000 0 0
IL12B 0.007 0.079 -10000 0 -0.68 5 5
CD8A -0.024 0.18 -10000 0 -0.65 35 35
CD8B -0.053 0.21 -10000 0 -0.64 53 53
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.026 0.14 0.35 47 -10000 0 47
IL2RB 0.004 0.09 -10000 0 -0.57 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.067 0.32 -10000 0 -0.77 62 62
IL2RG -0.011 0.14 -10000 0 -0.62 21 21
IL12 -0.033 0.18 -10000 0 -0.52 55 55
STAT5A 0.026 0.007 -10000 0 -10000 0 0
CD247 -0.012 0.13 -10000 0 -0.68 16 16
IL2 -0.003 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.053 0.22 -10000 0 -0.67 51 51
IL12/IL12R/TYK2/JAK2 -0.14 0.5 -10000 0 -1.2 64 64
MAP2K3 -0.081 0.36 -10000 0 -0.91 58 58
RIPK2 0.027 0.005 -10000 0 -10000 0 0
MAP2K6 -0.088 0.37 -10000 0 -0.92 62 62
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.092 -10000 0 -0.67 7 7
IL18RAP -0.002 0.14 -10000 0 -0.67 20 20
IL12Rbeta1/TYK2 0.025 0.065 -10000 0 -0.45 4 4
EOMES -0.13 0.4 -10000 0 -1.3 48 48
STAT1 (dimer) -0.12 0.35 -10000 0 -0.78 83 83
T cell proliferation -0.048 0.26 -10000 0 -0.62 62 62
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.004 0.096 -10000 0 -0.57 10 10
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.061 0.28 -10000 0 -0.67 65 65
ATF2 -0.084 0.34 0.44 1 -0.79 68 69
EGFR-dependent Endothelin signaling events

Figure S34.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S34.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.011 -9999 0 -10000 0 0
EGFR 0.021 0.063 -9999 0 -0.67 4 4
EGF/EGFR -0.015 0.15 -9999 0 -0.36 75 75
EGF/EGFR dimer/SHC/GRB2/SOS1 0.004 0.16 -9999 0 -0.38 67 67
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.024 0.035 -9999 0 -0.67 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.074 0.24 -9999 0 -0.66 70 70
EGF/EGFR dimer/SHC -0.023 0.17 -9999 0 -0.43 73 73
mol:GDP 0 0.15 -9999 0 -0.38 67 67
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.02 0.071 -9999 0 -0.67 5 5
GRB2/SOS1 0.038 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.013 0.14 -9999 0 -0.35 67 67
SHC1 0.025 0.007 -9999 0 -10000 0 0
HRAS/GDP 0 0.15 -9999 0 -0.36 67 67
FRAP1 -0.05 0.12 -9999 0 -0.36 67 67
EGF/EGFR dimer -0.043 0.19 -9999 0 -0.5 73 73
SOS1 0.027 0.005 -9999 0 -10000 0 0
GRB2 0.026 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.032 0.061 -9999 0 -0.5 6 6
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.004 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.12 -10000 0 -0.36 22 22
NFATC4 -0.019 0.088 0.28 4 -0.28 40 44
ERBB2IP 0.027 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.015 0.11 -10000 0 -0.35 40 40
JUN -0.005 0.094 0.34 10 -0.2 7 17
HRAS 0.025 0.011 -10000 0 -10000 0 0
DOCK7 -0.025 0.1 -10000 0 -0.34 42 42
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.003 0.13 -10000 0 -0.39 42 42
AKT1 0.007 0.006 -10000 0 -10000 0 0
BAD 0.005 0.005 -10000 0 -10000 0 0
MAPK10 -0.009 0.065 0.25 4 -0.39 1 5
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.016 0.12 -10000 0 -0.38 40 40
RAF1 -0.011 0.12 0.33 8 -0.38 22 30
ErbB2/ErbB3/neuregulin 2 -0.026 0.14 -10000 0 -0.41 58 58
STAT3 0.028 0.069 -10000 0 -0.84 3 3
cell migration 0.008 0.11 0.39 21 -0.28 4 25
mol:PI-3-4-5-P3 0 0.004 -10000 0 -10000 0 0
cell proliferation -0.15 0.32 -10000 0 -0.68 115 115
FOS -0.12 0.26 0.35 6 -0.5 151 157
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.11 -10000 0 -0.35 40 40
MAPK3 -0.078 0.24 0.38 3 -0.51 87 90
MAPK1 -0.17 0.3 0.36 1 -0.63 118 119
JAK2 -0.025 0.099 -10000 0 -0.34 39 39
NF2 -0.011 0.11 -10000 0 -0.62 16 16
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.012 0.11 -10000 0 -0.34 43 43
NRG1 -0.035 0.2 -10000 0 -0.66 43 43
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
MAPK8 -0.02 0.11 -10000 0 -0.33 47 47
MAPK9 -0.01 0.062 0.23 3 -0.2 1 4
ERBB2 -0.017 0.006 -10000 0 -10000 0 0
ERBB3 0.016 0.079 -10000 0 -0.62 7 7
SHC1 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.001 0.014 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.068 -10000 0 -0.82 3 3
RNF41 0 0.008 -10000 0 -10000 0 0
FRAP1 0.002 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.017 0.076 -10000 0 -0.25 41 41
ErbB2/ErbB2/HSP90 (dimer) 0.014 0.013 -10000 0 -10000 0 0
CHRNA1 -0.075 0.19 0.33 1 -0.39 106 107
myelination -0.009 0.14 0.52 17 -0.27 40 57
PPP3CB -0.022 0.095 -10000 0 -0.32 40 40
KRAS 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.021 0.11 -10000 0 -0.3 41 41
NRG2 -0.052 0.22 -10000 0 -0.67 53 53
mol:GDP -0.011 0.11 -10000 0 -0.34 43 43
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K2 -0.026 0.12 0.31 5 -0.38 21 26
SRC 0.026 0.008 -10000 0 -10000 0 0
mol:cAMP 0 0.003 -10000 0 -10000 0 0
PTPN11 -0.024 0.1 0.25 1 -0.34 41 42
MAP2K1 -0.074 0.22 -10000 0 -0.59 34 34
heart morphogenesis -0.015 0.11 -10000 0 -0.35 40 40
RAS family/GDP 0.016 0.12 -10000 0 -0.35 21 21
GRB2 0.025 0.007 -10000 0 -10000 0 0
PRKACA -0.011 0.13 -10000 0 -0.65 18 18
CHRNE 0.007 0.037 0.18 12 -0.22 1 13
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.006 -10000 0 -10000 0 0
nervous system development -0.015 0.11 -10000 0 -0.35 40 40
CDC42 0.027 0.005 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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 0.039 0.1 -10000 0 -0.41 23 23
ER alpha/Gai/GDP/Gbeta gamma -0.004 0.14 -10000 0 -0.53 23 23
AKT1 -0.013 0.2 -10000 0 -0.78 28 28
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.009 0.2 -10000 0 -0.79 28 28
mol:Ca2+ -0.096 0.19 -10000 0 -0.42 117 117
IGF1R 0.027 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.02 0.15 -10000 0 -0.45 50 50
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis 0.011 0.19 0.74 28 -10000 0 28
RhoA/GTP 0.006 0.071 -10000 0 -0.34 17 17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas 0.005 0.13 -10000 0 -0.55 19 19
regulation of stress fiber formation 0.009 0.087 0.29 33 -0.28 1 34
E2/ERA-ERB (dimer) 0.005 0.11 -10000 0 -0.43 25 25
KRAS 0.027 0.005 -10000 0 -10000 0 0
G13/GTP 0.009 0.085 -10000 0 -0.36 22 22
pseudopodium formation -0.009 0.087 0.28 1 -0.29 33 34
E2/ER alpha (dimer)/PELP1 0.009 0.094 -10000 0 -0.41 21 21
GRB2 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.025 0.032 -10000 0 -0.67 1 1
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
HRAS 0.026 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.009 0.15 0.47 7 -0.59 22 29
E2/ER beta (dimer) 0.015 0.047 -10000 0 -0.5 4 4
mol:GDP 0.002 0.11 -10000 0 -0.46 24 24
mol:NADP 0.009 0.15 0.47 7 -0.59 22 29
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.1 0.2 -10000 0 -0.44 117 117
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
PLCB1 -0.099 0.2 -10000 0 -0.45 117 117
PLCB2 -0.1 0.21 -10000 0 -0.45 117 117
IGF1 -0.13 0.29 -10000 0 -0.67 107 107
mol:L-citrulline 0.009 0.15 0.47 7 -0.59 22 29
RHOA 0.027 0.004 -10000 0 -10000 0 0
Gai/GDP 0.004 0.15 -10000 0 -0.69 18 18
JNK cascade 0.015 0.047 -10000 0 -0.5 4 4
BCAR1 0.026 0.006 -10000 0 -10000 0 0
ESR2 0.021 0.063 -10000 0 -0.67 4 4
GNAQ 0.025 0.008 -10000 0 -10000 0 0
ESR1 -0.014 0.15 -10000 0 -0.64 23 23
Gq family/GDP/Gbeta gamma -0.057 0.19 -10000 0 -0.65 28 28
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.019 0.098 -10000 0 -0.6 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.003 0.13 -10000 0 -0.54 20 20
GNAZ 0.02 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.01 0.11 -10000 0 -0.48 23 23
STRN -0.016 0.17 -10000 0 -0.66 30 30
GNAL -0.059 0.23 -10000 0 -0.65 61 61
PELP1 0.026 0.007 -10000 0 -10000 0 0
MAPK11 0.009 0.041 -10000 0 -0.43 4 4
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
HBEGF -0.017 0.14 0.38 4 -0.55 20 24
cAMP biosynthetic process -0.04 0.15 -10000 0 -0.38 76 76
SRC -0.004 0.13 -10000 0 -0.5 22 22
PI3K 0.036 0.043 -10000 0 -0.5 3 3
GNB1 0.026 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.03 0.11 -10000 0 -0.43 23 23
SOS1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.07 0.16 -10000 0 -0.49 30 30
Gs family/GTP -0.029 0.16 -10000 0 -0.39 76 76
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.015 -10000 0 -10000 0 0
vasodilation 0.01 0.15 0.46 7 -0.56 22 29
mol:DAG -0.1 0.2 -10000 0 -0.44 117 117
Gs family/GDP/Gbeta gamma -0.026 0.14 -10000 0 -0.35 70 70
MSN -0.01 0.093 0.29 1 -0.32 33 34
Gq family/GTP -0.1 0.22 -10000 0 -0.47 122 122
mol:PI-3-4-5-P3 -0.007 0.19 -10000 0 -0.76 28 28
NRAS 0.027 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.01 0.15 0.56 22 -0.46 7 29
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.019 0.11 -10000 0 -0.44 24 24
NOS3 0.003 0.16 0.42 3 -0.62 22 25
GNA11 0.014 0.085 -10000 0 -0.63 8 8
MAPKKK cascade -0.015 0.18 0.37 1 -0.58 30 31
E2/ER alpha (dimer)/PELP1/Src 0 0.14 -10000 0 -0.57 20 20
ruffle organization -0.009 0.087 0.28 1 -0.29 33 34
ROCK2 -0.004 0.11 0.36 5 -0.34 34 39
GNA14 -0.13 0.28 -10000 0 -0.63 114 114
GNA15 0.012 0.05 -10000 0 -0.67 1 1
GNA13 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.032 0.16 -10000 0 -0.58 24 24
MMP2 -0.004 0.13 0.34 1 -0.58 14 15
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.035 0.01 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.099 -10000 0 -0.67 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.12 0.13 -10000 0 -0.25 250 250
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
MAP3K12 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.014 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.043 0.068 -10000 0 -0.28 10 10
PRKG1 -0.16 0.31 -10000 0 -0.66 133 133
DUSP8 0.02 0.057 -10000 0 -0.67 3 3
PGK/cGMP/p38 alpha -0.1 0.18 -10000 0 -0.37 129 129
apoptosis -0.042 0.065 -10000 0 -0.27 10 10
RAL/GTP 0.035 0.008 -10000 0 -10000 0 0
LYN 0.027 0.005 -10000 0 -10000 0 0
DUSP1 -0.083 0.25 -10000 0 -0.67 76 76
PAK1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.065 0.02 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.01 -10000 0 -10000 0 0
MAPK11 -0.052 0.16 0.41 19 -0.33 32 51
BLK -0.19 0.31 -10000 0 -0.66 143 143
HCK 0.018 0.035 -10000 0 -10000 0 0
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
DUSP16 0.027 0.005 -10000 0 -10000 0 0
DUSP10 0.023 0.034 -10000 0 -0.67 1 1
TRAF6/MEKK3 0.031 0.029 -10000 0 -0.4 2 2
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.01 0.12 0.35 20 -0.3 10 30
positive regulation of innate immune response -0.041 0.17 0.45 20 -0.4 14 34
LCK 0.012 0.082 -10000 0 -0.67 6 6
p38alpha-beta/MKP7 -0.044 0.14 0.34 8 -0.41 10 18
p38alpha-beta/MKP5 -0.036 0.15 0.43 14 -0.44 7 21
PGK/cGMP -0.12 0.23 -10000 0 -0.5 133 133
PAK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.095 0.18 0.31 4 -0.42 63 67
CDC42 0.027 0.005 -10000 0 -10000 0 0
RALB 0.027 0.005 -10000 0 -10000 0 0
RALA 0.026 0.006 -10000 0 -10000 0 0
PAK3 -0.36 0.34 -10000 0 -0.65 272 272
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.017 -10000 0 -10000 0 0
CCL5 -0.017 0.16 -10000 0 -0.67 28 28
SDCBP 0.027 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.036 0.13 -10000 0 -0.42 38 38
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.031 0.14 -10000 0 -0.53 22 22
Syndecan-1/Syntenin -0.029 0.14 0.26 1 -0.51 24 25
MAPK3 -0.029 0.12 -10000 0 -0.49 20 20
HGF/MET -0.077 0.19 -10000 0 -0.52 69 69
TGFB1/TGF beta receptor Type II 0.024 0.017 -10000 0 -10000 0 0
BSG 0.025 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.03 0.13 -10000 0 -0.52 22 22
Syndecan-1/RANTES -0.048 0.18 -10000 0 -0.53 50 50
Syndecan-1/CD147 -0.014 0.14 -10000 0 -0.52 21 21
Syndecan-1/Syntenin/PIP2 -0.029 0.13 -10000 0 -0.5 24 24
LAMA5 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.028 0.13 -10000 0 -0.48 24 24
MMP7 -0.078 0.15 -10000 0 -0.66 25 25
HGF -0.073 0.24 -10000 0 -0.67 69 69
Syndecan-1/CASK -0.043 0.13 -10000 0 -0.41 41 41
Syndecan-1/HGF/MET -0.073 0.2 -10000 0 -0.49 74 74
regulation of cell adhesion -0.031 0.11 -10000 0 -0.5 18 18
HPSE 0.009 0.094 -10000 0 -0.64 9 9
positive regulation of cell migration -0.036 0.13 -10000 0 -0.42 38 38
SDC1 -0.036 0.13 -10000 0 -0.41 41 41
Syndecan-1/Collagen -0.036 0.13 -10000 0 -0.42 38 38
PPIB 0.027 0.004 -10000 0 -10000 0 0
MET -0.028 0.071 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
MMP9 -0.038 0.19 -10000 0 -0.67 38 38
MAPK1 -0.03 0.12 -10000 0 -0.49 21 21
homophilic cell adhesion -0.034 0.13 0.28 1 -0.41 39 40
MMP1 -0.045 0.072 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.002 0.1 -10000 0 -0.38 29 29
NF kappa B1 p50/RelA/I kappa B alpha 0.012 0.1 0.35 3 -0.51 2 5
alphaV/beta3 Integrin/Osteopontin/Src 0.002 0.12 -10000 0 -0.49 24 24
AP1 -0.14 0.3 -10000 0 -0.69 87 87
ILK -0.005 0.11 -10000 0 -0.39 28 28
bone resorption -0.006 0.12 -10000 0 -0.51 8 8
PTK2B 0.027 0.005 -10000 0 -10000 0 0
PYK2/p130Cas 0.044 0.11 -10000 0 -0.37 27 27
ITGAV 0.026 0.045 -10000 0 -0.66 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.014 0.11 -10000 0 -0.49 23 23
alphaV/beta3 Integrin/Osteopontin 0.03 0.12 -10000 0 -0.44 29 29
MAP3K1 -0.006 0.11 -10000 0 -0.4 29 29
JUN -0.12 0.28 -10000 0 -0.67 104 104
MAPK3 -0.02 0.097 -10000 0 -0.37 29 29
MAPK1 -0.022 0.094 -10000 0 -0.37 29 29
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.017 0.12 -10000 0 -0.4 35 35
ITGB3 0.014 0.095 -10000 0 -0.63 10 10
NFKBIA -0.016 0.093 -10000 0 -0.4 11 11
FOS -0.15 0.3 -10000 0 -0.67 125 125
CD44 0.027 0.005 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
PLAU -0.035 0.11 0.52 3 -0.6 1 4
NF kappa B1 p50/RelA 0.023 0.099 -10000 0 -0.5 2 2
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.029 0.086 -10000 0 -0.54 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.006 0.11 -10000 0 -0.4 29 29
VAV3 -0.014 0.11 0.4 1 -0.39 33 34
MAP3K14 -0.011 0.1 -10000 0 -0.4 29 29
ROCK2 -0.006 0.15 -10000 0 -0.66 23 23
SPP1 -0.028 0.15 -10000 0 -0.66 22 22
RAC1 0.026 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.11 -10000 0 -0.36 32 32
MMP2 -0.13 0.24 -10000 0 -0.55 89 89
FAS signaling pathway (CD95)

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
SPTAN1 0.013 0.061 0.24 31 -10000 0 31
RFC1 0.014 0.063 0.24 33 -10000 0 33
PRKDC 0.016 0.069 0.26 35 -10000 0 35
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CASP7 -0.004 0.098 -10000 0 -0.76 6 6
FASLG/FAS/FADD/FAF1 -0.014 0.093 0.24 5 -0.34 29 34
MAP2K4 -0.031 0.17 0.32 2 -0.52 25 27
mol:ceramide -0.02 0.13 -10000 0 -0.43 31 31
GSN 0.013 0.061 0.24 31 -10000 0 31
FASLG/FAS/FADD/FAF1/Caspase 8 -0.019 0.12 -10000 0 -0.43 30 30
FAS 0.019 0.019 -10000 0 -10000 0 0
BID -0.018 0.035 0.28 3 -10000 0 3
MAP3K1 -0.011 0.12 0.27 3 -0.53 10 13
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
RB1 0.013 0.065 0.25 31 -10000 0 31
CFLAR 0.028 0.007 -10000 0 -10000 0 0
HGF/MET -0.019 0.19 -10000 0 -0.46 72 72
ARHGDIB 0.015 0.068 0.25 36 -10000 0 36
FADD 0.019 0.019 -10000 0 -10000 0 0
actin filament polymerization -0.013 0.061 -10000 0 -0.24 31 31
NFKB1 -0.019 0.1 -10000 0 -0.57 3 3
MAPK8 -0.071 0.23 0.4 2 -0.48 98 100
DFFA 0.014 0.063 0.24 33 -10000 0 33
DNA fragmentation during apoptosis 0.014 0.063 0.24 33 -10000 0 33
FAS/FADD/MET 0.042 0.042 -10000 0 -10000 0 0
CFLAR/RIP1 0.042 0.01 -10000 0 -10000 0 0
FAIM3 0.017 0.061 -10000 0 -0.67 3 3
FAF1 0.018 0.021 -10000 0 -10000 0 0
PARP1 0.018 0.079 0.29 34 -10000 0 34
DFFB 0.014 0.063 0.24 33 -10000 0 33
CHUK -0.018 0.091 -10000 0 -0.62 2 2
FASLG -0.03 0.17 -10000 0 -0.68 29 29
FAS/FADD 0.028 0.028 -10000 0 -10000 0 0
HGF -0.073 0.24 -10000 0 -0.67 69 69
LMNA 0.013 0.068 0.25 30 -10000 0 30
CASP6 0.014 0.063 0.24 33 -10000 0 33
CASP10 0.019 0.019 -10000 0 -10000 0 0
CASP3 0.018 0.078 0.3 35 -10000 0 35
PTPN13 0.018 0.077 -10000 0 -0.67 6 6
CASP8 -0.014 0.033 0.4 3 -10000 0 3
IL6 -0.22 0.53 -10000 0 -1.3 100 100
MET -0.028 0.071 -10000 0 -10000 0 0
ICAD/CAD 0.012 0.056 0.22 25 -10000 0 25
FASLG/FAS/FADD/FAF1/Caspase 10 -0.021 0.13 -10000 0 -0.44 31 31
activation of caspase activity by cytochrome c -0.018 0.034 0.28 3 -10000 0 3
PAK2 0.014 0.063 0.24 34 -10000 0 34
BCL2 -0.024 0.18 -10000 0 -0.66 36 36
Regulation of Androgen receptor activity

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
HDAC1 0.009 0.013 -10000 0 -10000 0 0
SMARCC1 0.011 0.013 -10000 0 -10000 0 0
REL -0.013 0.17 -10000 0 -0.66 32 32
HDAC7 -0.07 0.12 -10000 0 -0.51 17 17
JUN -0.12 0.28 -10000 0 -0.67 104 104
EP300 0.02 0.012 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
KAT5 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.015 0.075 -10000 0 -0.52 10 10
FOXO1 0.025 0.007 -10000 0 -10000 0 0
T-DHT/AR -0.068 0.13 -10000 0 -0.52 19 19
MAP2K6 0.004 0.1 -10000 0 -0.68 10 10
BRM/BAF57 0.018 0.033 -10000 0 -10000 0 0
MAP2K4 0.019 0.014 -10000 0 -10000 0 0
SMARCA2 0.013 0.022 -10000 0 -10000 0 0
PDE9A 0.014 0.067 -10000 0 -0.59 1 1
NCOA2 -0.042 0.2 -10000 0 -0.67 44 44
CEBPA 0.019 0.071 -10000 0 -0.67 5 5
EHMT2 0.025 0.005 -10000 0 -10000 0 0
cell proliferation -0.081 0.2 0.56 21 -0.48 21 42
NR0B1 -0.008 0.023 -10000 0 -10000 0 0
EGR1 -0.12 0.28 -10000 0 -0.67 97 97
RXRs/9cRA 0.02 0.072 -10000 0 -0.4 4 4
AR/RACK1/Src -0.13 0.15 0.33 2 -0.56 18 20
AR/GR -0.12 0.18 0.25 5 -0.34 149 154
GNB2L1 0.022 0.008 -10000 0 -10000 0 0
PKN1 0.025 0.007 -10000 0 -10000 0 0
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.005 0.007 -10000 0 -0.015 66 66
MAPK8 -0.014 0.071 -10000 0 -0.51 9 9
T-DHT/AR/TIF2/CARM1 -0.13 0.19 0.34 3 -0.58 46 49
SRC -0.044 0.088 0.24 1 -0.46 16 17
NR3C1 0.026 0.006 -10000 0 -10000 0 0
KLK3 -0.35 0.55 0.38 2 -1.2 138 140
APPBP2 0.024 0.013 -10000 0 -10000 0 0
TRIM24 0.014 0.021 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.07 0.13 0.33 6 -0.56 16 22
TMPRSS2 -0.044 0.28 -10000 0 -1.1 30 30
RXRG -0.1 0.075 -10000 0 -0.67 4 4
mol:9cRA -0.002 0.003 -10000 0 -0.011 8 8
RXRA 0.024 0.008 -10000 0 -10000 0 0
RXRB 0.026 0.004 -10000 0 -10000 0 0
CARM1 0.02 0.009 -10000 0 -10000 0 0
NR2C2 0.012 0.099 -10000 0 -0.67 10 10
KLK2 -0.44 0.38 0.34 2 -0.76 277 279
AR -0.14 0.18 -10000 0 -0.35 196 196
SENP1 0.025 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
MDM2 0.035 0.016 -10000 0 -10000 0 0
SRY 0.009 0.015 0.031 137 -10000 0 137
GATA2 0.027 0.008 -10000 0 -10000 0 0
MYST2 0.001 0.002 -10000 0 -10000 0 0
HOXB13 -0.011 0.034 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.099 0.13 0.33 4 -0.57 16 20
positive regulation of transcription 0.027 0.008 -10000 0 -10000 0 0
DNAJA1 0.024 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.008 -10000 0 -10000 0 0
NCOA1 0.018 0.022 -10000 0 -10000 0 0
SPDEF -0.003 0.048 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.092 0.15 0.28 2 -0.45 47 49
T-DHT/AR/Hsp90 -0.071 0.13 0.33 7 -0.56 16 23
GSK3B 0.025 0.007 -10000 0 -10000 0 0
NR2C1 0.028 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.038 0.092 0.26 1 -0.49 16 17
SIRT1 0.025 0.032 -10000 0 -0.67 1 1
ZMIZ2 0.035 0.017 -10000 0 -10000 0 0
POU2F1 0.032 0.036 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.075 0.13 0.32 6 -0.57 16 22
CREBBP 0.026 0.006 -10000 0 -10000 0 0
SMARCE1 0.012 0.022 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.004 0.056 -10000 0 -10000 0 0
CRKL -0.014 0.091 0.36 1 -0.33 4 5
mol:PIP3 -0.002 0.017 0.33 1 -10000 0 1
AKT1 0.003 0.055 0.37 2 -0.45 3 5
PTK2B 0.027 0.005 -10000 0 -10000 0 0
RAPGEF1 0.001 0.1 0.41 8 -0.4 1 9
RANBP10 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
HGF/MET/SHIP2 -0.014 0.18 -10000 0 -0.45 69 69
MAP3K5 0.011 0.12 0.45 12 -0.4 6 18
HGF/MET/CIN85/CBL/ENDOPHILINS 0.003 0.17 -10000 0 -0.42 65 65
AP1 -0.18 0.33 -10000 0 -0.64 147 147
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
apoptosis -0.22 0.4 0.38 1 -0.81 149 150
STAT3 (dimer) -0.019 0.1 -10000 0 -0.3 24 24
GAB1/CRKL/SHP2/PI3K 0.026 0.11 -10000 0 -0.5 3 3
INPP5D 0.019 0.033 -10000 0 -10000 0 0
CBL/CRK 0.016 0.11 0.5 7 -0.41 1 8
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.35 1 1
ELK1 0.034 0.14 0.42 28 -0.23 4 32
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.006 0.068 -10000 0 -0.23 5 5
PAK1 0.005 0.058 0.35 5 -0.4 2 7
HGF/MET/RANBP10 -0.014 0.18 -10000 0 -0.46 67 67
HRAS -0.02 0.13 -10000 0 -0.54 3 3
DOCK1 0 0.11 0.43 9 -0.4 4 13
GAB1 -0.011 0.096 0.26 1 -0.35 4 5
CRK -0.006 0.097 0.31 4 -0.43 1 5
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.043 0.19 -10000 0 -0.51 69 69
JUN -0.12 0.28 -10000 0 -0.67 104 104
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.03 0.085 -10000 0 -0.24 67 67
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.008 0.13 0.47 6 -0.51 3 9
GRB2/SHC 0.004 0.085 -10000 0 -0.22 23 23
FOS -0.15 0.3 -10000 0 -0.67 125 125
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.033 0.14 0.42 28 -0.23 4 32
HGF/MET/MUC20 -0.065 0.16 -10000 0 -0.45 69 69
cell migration 0.004 0.083 -10000 0 -0.22 23 23
GRB2 0.026 0.007 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.004 0.056 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.015 0.11 -10000 0 -0.3 63 63
MET/MUC20 -0.016 0.046 -10000 0 -10000 0 0
RAP1B 0.011 0.13 0.56 12 -0.37 1 13
RAP1A 0.009 0.11 0.4 11 -0.37 1 12
HGF/MET/RANBP9 -0.013 0.18 -10000 0 -0.46 66 66
RAF1 -0.017 0.12 -10000 0 -0.49 2 2
STAT3 -0.019 0.1 -10000 0 -0.3 24 24
cell proliferation -0.023 0.15 -10000 0 -0.39 59 59
RPS6KB1 0 0.034 -10000 0 -0.22 2 2
MAPK3 -0.022 0.1 0.52 12 -10000 0 12
MAPK1 0.13 0.29 0.61 128 -10000 0 128
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.023 0.17 0.6 17 -0.6 9 26
SRC -0.02 0.1 -10000 0 -0.28 63 63
PI3K 0.003 0.094 -10000 0 -0.39 4 4
MET/Glomulin -0.007 0.044 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K1 -0.011 0.12 0.32 2 -0.46 2 4
MET -0.028 0.071 -10000 0 -10000 0 0
MAP4K1 0.006 0.12 0.48 7 -0.42 6 13
PTK2 0.026 0.006 -10000 0 -10000 0 0
MAP2K2 -0.007 0.12 0.34 1 -0.44 1 2
BAD 0.005 0.058 0.35 5 -0.4 2 7
MAP2K4 0.021 0.14 0.51 19 -0.4 4 23
SHP2/GRB2/SOS1/GAB1 0.018 0.098 -10000 0 -0.38 1 1
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.027 0.005 -10000 0 -10000 0 0
SH3KBP1 0.025 0.007 -10000 0 -10000 0 0
HGS -0.028 0.077 -10000 0 -0.22 64 64
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF -0.073 0.24 -10000 0 -0.67 69 69
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.003 0.099 -10000 0 -0.25 27 27
PDPK1 -0.001 0.048 -10000 0 -0.48 3 3
HGF/MET/SHIP -0.018 0.18 -10000 0 -0.45 69 69
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.01 0.14 -10000 0 -0.36 59 59
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.002 0.12 -10000 0 -0.35 4 4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.035 0.053 -10000 0 -0.29 1 1
antigen processing and presentation of peptide antigen via MHC class I 0.008 0.07 -10000 0 -0.24 4 4
CaM/Ca2+ 0.015 0.13 -10000 0 -0.33 59 59
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.011 0.13 -10000 0 -0.34 59 59
AKT1 -0.016 0.12 0.38 5 -0.32 57 62
MAP2K1 -0.024 0.11 0.29 2 -0.32 57 59
MAP3K11 -0.021 0.12 0.3 5 -0.34 59 64
IFNGR1 0.02 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.018 0.072 -10000 0 -0.44 2 2
Rap1/GTP -0.019 0.093 -10000 0 -0.36 1 1
CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.018 0.15 -10000 0 -0.37 58 58
CEBPB -0.056 0.19 0.52 6 -0.52 36 42
STAT3 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.018 0.16 -10000 0 -0.76 5 5
STAT1 -0.021 0.12 0.3 5 -0.34 59 64
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.064 0.23 -10000 0 -0.67 59 59
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
STAT1 (dimer)/PIAS1 -0.006 0.12 0.3 4 -0.32 59 63
CEBPB/PTGES2/Cbp/p300 -0.023 0.12 -10000 0 -0.39 12 12
mol:Ca2+ 0.008 0.14 -10000 0 -0.35 59 59
MAPK3 -0.008 0.12 -10000 0 -0.65 4 4
STAT1 (dimer) 0.018 0.096 -10000 0 -0.34 3 3
MAPK1 -0.16 0.3 0.44 1 -0.67 117 118
JAK2 0.017 0.035 -10000 0 -0.38 2 2
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
JAK1 0.02 0.025 -10000 0 -10000 0 0
CAMK2D 0.027 0.004 -10000 0 -10000 0 0
DAPK1 -0.039 0.18 0.48 9 -0.6 26 35
SMAD7 0.019 0.065 0.36 8 -10000 0 8
CBL/CRKL/C3G -0.008 0.12 0.3 2 -0.32 41 43
PI3K 0.013 0.13 -10000 0 -0.33 59 59
IFNG -0.064 0.23 -10000 0 -0.67 59 59
apoptosis -0.037 0.15 0.56 4 -0.46 35 39
CAMK2G 0.027 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.007 -10000 0 -10000 0 0
CAMK2A 0.012 0.033 -10000 0 -10000 0 0
CAMK2B 0.021 0.063 -10000 0 -0.67 4 4
FRAP1 -0.023 0.11 0.37 5 -0.3 57 62
PRKCD -0.012 0.13 0.42 9 -0.38 6 15
RAP1B 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.008 0.07 -10000 0 -0.24 4 4
PTPN2 0.027 0.004 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
IRF1 -0.014 0.085 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy -0.01 0.12 0.3 2 -0.32 58 60
SOCS1 0.017 0.12 -10000 0 -1 6 6
mol:GDP -0.009 0.11 0.28 2 -0.3 41 43
CASP1 0.016 0.063 0.35 6 -0.32 2 8
PTGES2 0.025 0.008 -10000 0 -10000 0 0
IRF9 -0.001 0.057 0.34 1 -10000 0 1
mol:PI-3-4-5-P3 -0.001 0.12 -10000 0 -0.32 59 59
RAP1/GDP -0.004 0.1 -10000 0 -0.36 1 1
CBL -0.021 0.12 0.29 6 -0.34 59 65
MAP3K1 -0.022 0.12 0.3 2 -0.34 57 59
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PIAS4 0.025 0.008 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.008 0.07 -10000 0 -0.24 4 4
PTPN11 -0.024 0.12 -10000 0 -0.35 59 59
CREBBP 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN -0.064 0.17 0.44 9 -0.43 36 45
IKBKB 0.011 0.12 0.5 15 -0.32 6 21
AKT1 0.001 0.17 0.52 27 -0.24 14 41
IKBKG -0.001 0.13 0.47 15 -0.36 12 27
CALM1 -0.02 0.092 0.39 3 -0.4 8 11
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
MAP3K1 -0.01 0.16 0.46 11 -0.52 20 31
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.093 0.32 2 -0.42 8 10
DOK1 0.027 0.005 -10000 0 -10000 0 0
AP-1 -0.057 0.15 0.53 11 -0.26 92 103
LYN 0.027 0.005 -10000 0 -10000 0 0
BLNK 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
BCR complex -0.065 0.18 -10000 0 -0.49 61 61
CD22 -0.065 0.17 -10000 0 -0.42 79 79
CAMK2G -0.016 0.09 0.34 4 -0.43 5 9
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.035 0.12 -10000 0 -0.34 54 54
GO:0007205 -0.022 0.095 0.32 2 -0.43 8 10
SYK 0.025 0.008 -10000 0 -10000 0 0
ELK1 -0.017 0.092 0.33 3 -0.47 5 8
NFATC1 -0.036 0.13 0.36 6 -0.42 22 28
B-cell antigen/BCR complex -0.065 0.18 -10000 0 -0.49 61 61
PAG1/CSK 0.038 0.026 -10000 0 -0.5 1 1
NFKBIB 0.019 0.043 0.2 11 -0.13 6 17
HRAS -0.014 0.098 0.35 5 -0.37 7 12
NFKBIA 0.019 0.043 0.2 11 -0.12 8 19
NF-kappa-B/RelA/I kappa B beta 0.024 0.04 0.2 11 -10000 0 11
RasGAP/Csk 0.001 0.17 -10000 0 -0.4 69 69
mol:GDP -0.02 0.092 0.29 2 -0.43 8 10
PTEN 0.026 0.018 -10000 0 -0.35 1 1
CD79B 0.007 0.049 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.024 0.04 0.2 11 -10000 0 11
GRB2 0.026 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.032 0.15 0.44 4 -0.47 19 23
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.021 0.091 0.32 2 -0.42 7 9
CSK 0.027 0.004 -10000 0 -10000 0 0
FOS -0.097 0.18 0.47 8 -0.36 125 133
CHUK 0.008 0.1 0.42 14 -0.4 4 18
IBTK 0.027 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.01 0.1 -10000 0 -0.45 8 8
PTPN6 -0.061 0.16 -10000 0 -0.4 76 76
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.015 0.035 0.17 5 -0.12 10 15
VAV2 -0.051 0.15 -10000 0 -0.63 14 14
ubiquitin-dependent protein catabolic process 0.023 0.043 0.2 11 -0.12 6 17
BTK -0.038 0.24 -10000 0 -0.98 30 30
CD19 -0.056 0.15 -10000 0 -0.4 63 63
MAP4K1 0.009 0.078 -10000 0 -0.67 5 5
CD72 0.025 0.012 -10000 0 -10000 0 0
PAG1 0.025 0.032 -10000 0 -0.67 1 1
MAPK14 -0.003 0.15 0.43 13 -0.46 17 30
SH3BP5 0.027 0.004 -10000 0 -10000 0 0
PIK3AP1 -0.014 0.093 -10000 0 -0.45 8 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.043 0.18 -10000 0 -0.42 70 70
RAF1 -0.012 0.095 0.34 7 -0.4 4 11
RasGAP/p62DOK/SHIP -0.002 0.17 -10000 0 -0.39 68 68
CD79A -0.095 0.22 -10000 0 -0.65 62 62
re-entry into mitotic cell cycle -0.056 0.15 0.53 11 -0.26 91 102
RASA1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.001 0.1 0.39 15 -0.42 2 17
MAPK1 -0.008 0.089 0.36 9 -0.4 2 11
CD72/SHP1 -0.042 0.16 0.28 4 -0.45 39 43
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.01 0.16 0.47 12 -0.49 18 30
actin cytoskeleton organization -0.04 0.14 0.34 2 -0.53 13 15
NF-kappa-B/RelA 0.048 0.072 0.35 11 -0.22 1 12
Calcineurin 0.01 0.089 -10000 0 -0.41 4 4
PI3K -0.058 0.14 -10000 0 -0.45 22 22
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.017 0.097 -10000 0 -0.44 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.019 0.22 -10000 0 -0.92 20 20
DAPP1 -0.04 0.24 -10000 0 -1.1 19 19
cytokine secretion -0.034 0.13 0.36 6 -0.39 22 28
mol:DAG -0.021 0.091 0.32 2 -0.42 7 9
PLCG2 0.026 0.006 -10000 0 -10000 0 0
MAP2K1 -0.01 0.091 0.34 6 -0.46 2 8
B-cell antigen/BCR complex/FcgammaRIIB -0.05 0.18 -10000 0 -0.44 77 77
mol:PI-3-4-5-P3 -0.05 0.097 -10000 0 -0.36 15 15
ETS1 -0.013 0.086 0.34 5 -0.41 4 9
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.015 0.15 -10000 0 -0.38 58 58
B-cell antigen/BCR complex/LYN -0.044 0.16 -10000 0 -0.41 64 64
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
RAC1 -0.044 0.14 0.36 1 -0.57 13 14
B-cell antigen/BCR complex/LYN/SYK -0.033 0.18 -10000 0 -0.43 73 73
CARD11 -0.033 0.11 0.41 3 -0.45 13 16
FCGR2B -0.008 0.15 -10000 0 -0.67 23 23
PPP3CA 0.027 0.004 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.019 0.096 0.45 17 -0.13 4 21
PTPRC -0.006 0.14 -10000 0 -0.67 19 19
PDPK1 -0.026 0.086 0.23 11 -0.25 16 27
PPP3CB 0.027 0.005 -10000 0 -10000 0 0
PPP3CC 0.027 0.005 -10000 0 -10000 0 0
POU2F2 0.019 0.032 0.16 13 -10000 0 13
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.017 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -0.014 1 1
cytokine production during immune response 0.044 0.13 0.43 20 -10000 0 20
IL27/IL27R/JAK1 -0.012 0.17 -10000 0 -0.4 56 56
TBX21 -0.065 0.18 0.39 4 -0.56 29 33
IL12B 0.006 0.073 -10000 0 -0.67 5 5
IL12A -0.048 0.16 -10000 0 -0.5 51 51
IL6ST -0.072 0.24 -10000 0 -0.68 65 65
IL27RA/JAK1 0.019 0.053 0.56 1 -10000 0 1
IL27 0.011 0.027 -10000 0 -10000 0 0
TYK2 0.019 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.047 0.13 -10000 0 -0.49 4 4
T-helper 2 cell differentiation 0.044 0.13 0.43 20 -10000 0 20
T cell proliferation during immune response 0.044 0.13 0.43 20 -10000 0 20
MAPKKK cascade -0.044 0.13 -10000 0 -0.43 20 20
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT2 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
IL12RB1 0.007 0.069 -10000 0 -0.59 4 4
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.057 0.19 0.49 11 -0.53 29 40
IL27/IL27R/JAK2/TYK2 -0.045 0.13 -10000 0 -0.44 20 20
positive regulation of T cell mediated cytotoxicity -0.044 0.13 -10000 0 -0.43 20 20
STAT1 (dimer) -0.024 0.21 0.53 11 -0.56 21 32
JAK2 0.019 0.031 -10000 0 -0.36 2 2
JAK1 0.027 0.008 -10000 0 -10000 0 0
STAT2 (dimer) -0.033 0.14 -10000 0 -0.45 16 16
T cell proliferation -0.11 0.19 -10000 0 -0.44 96 96
IL12/IL12R/TYK2/JAK2 -0.068 0.23 -10000 0 -0.76 34 34
IL17A -0.047 0.13 -10000 0 -0.49 4 4
mast cell activation 0.044 0.13 0.43 20 -10000 0 20
IFNG -0.016 0.051 0.087 5 -0.12 70 75
T cell differentiation -0.004 0.008 0.014 1 -0.022 65 66
STAT3 (dimer) -0.032 0.13 -10000 0 -0.44 16 16
STAT5A (dimer) -0.032 0.13 -10000 0 -0.44 16 16
STAT4 (dimer) -0.038 0.15 0.33 1 -0.44 23 24
STAT4 0.004 0.098 -10000 0 -0.58 11 11
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.024 0.15 -10000 0 -0.39 58 58
GATA3 -0.057 0.3 -10000 0 -1.3 24 24
IL18 -0.012 0.077 -10000 0 -0.48 11 11
positive regulation of mast cell cytokine production -0.031 0.13 -10000 0 -0.43 16 16
IL27/EBI3 -0.028 0.058 -10000 0 -0.26 1 1
IL27RA 0 0.024 -10000 0 -10000 0 0
IL6 -0.11 0.27 -10000 0 -0.67 90 90
STAT5A 0.026 0.007 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -0.023 2 2
IL2 -0.011 0.018 -10000 0 -10000 0 0
IL1B -0.033 0.14 -10000 0 -0.51 38 38
EBI3 -0.049 0.073 -10000 0 -0.36 1 1
TNF -0.054 0.16 -10000 0 -0.51 57 57
LPA receptor mediated events

Figure S46.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S46.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.019 0.13 -10000 0 -0.42 33 33
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.086 0.42 1 -10000 0 1
AP1 -0.15 0.3 -10000 0 -0.55 155 155
mol:PIP3 -0.01 0.091 -10000 0 -0.35 29 29
AKT1 0.03 0.096 0.29 12 -0.56 2 14
PTK2B -0.009 0.086 0.26 1 -0.36 12 13
RHOA 0.014 0.042 0.21 3 -10000 0 3
PIK3CB 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.072 0.27 8 -10000 0 8
MAGI3 0.025 0.032 -10000 0 -0.67 1 1
RELA 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.009 0.1 -10000 0 -0.35 36 36
HRAS/GDP 0.019 0.007 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0 0.1 0.35 11 -0.37 9 20
NF kappa B1 p50/RelA -0.018 0.1 -10000 0 -0.42 10 10
endothelial cell migration -0.016 0.15 -10000 0 -0.52 33 33
ADCY4 -0.029 0.15 -10000 0 -0.51 35 35
ADCY5 -0.055 0.16 -10000 0 -0.54 39 39
ADCY6 -0.029 0.14 -10000 0 -0.51 35 35
ADCY7 -0.03 0.15 -10000 0 -0.52 35 35
ADCY1 -0.032 0.15 -10000 0 -0.5 37 37
ADCY2 -0.05 0.17 -10000 0 -0.54 39 39
ADCY3 -0.029 0.15 -10000 0 -0.52 34 34
ADCY8 -0.037 0.15 -10000 0 -0.52 36 36
ADCY9 -0.03 0.15 -10000 0 -0.52 35 35
GSK3B -0.008 0.084 0.37 2 -0.34 12 14
arachidonic acid secretion -0.029 0.14 -10000 0 -0.44 46 46
GNG2 0.025 0.032 -10000 0 -0.67 1 1
TRIP6 0.024 0.01 -10000 0 -10000 0 0
GNAO1 -0.025 0.15 -10000 0 -0.46 46 46
HRAS 0.026 0.011 -10000 0 -10000 0 0
NFKBIA -0.006 0.094 0.46 5 -0.49 1 6
GAB1 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.016 0.18 -10000 0 -0.79 22 22
JUN -0.12 0.28 -10000 0 -0.67 104 104
LPA/LPA2/NHERF2 0.035 0.017 -10000 0 -10000 0 0
TIAM1 0.001 0.21 -10000 0 -0.92 23 23
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
mol:IP3 -0.011 0.064 0.32 1 -10000 0 1
PLCB3 0.027 0.035 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.67 125 125
positive regulation of mitosis -0.029 0.14 -10000 0 -0.44 46 46
LPA/LPA1-2-3 0.019 0.12 -10000 0 -0.4 29 29
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.006 -10000 0 -10000 0 0
stress fiber formation 0.001 0.1 0.45 2 -0.32 28 30
GNAZ -0.015 0.12 -10000 0 -0.43 34 34
EGFR/PI3K-beta/Gab1 0 0.098 -10000 0 -0.36 29 29
positive regulation of dendritic cell cytokine production 0.018 0.11 -10000 0 -0.4 29 29
LPA/LPA2/MAGI-3 0.034 0.027 -10000 0 -0.45 1 1
ARHGEF1 0.005 0.1 0.36 3 -0.39 23 26
GNAI2 -0.012 0.12 -10000 0 -0.45 33 33
GNAI3 -0.012 0.12 -10000 0 -0.45 33 33
GNAI1 -0.012 0.12 -10000 0 -0.44 34 34
LPA/LPA3 0.015 0.024 -10000 0 -10000 0 0
LPA/LPA2 0.02 0.013 -10000 0 -10000 0 0
LPA/LPA1 -0.015 0.14 -10000 0 -0.47 40 40
HB-EGF/EGFR -0.018 0.13 -10000 0 -0.44 39 39
HBEGF -0.034 0.14 -10000 0 -0.49 38 38
mol:DAG -0.011 0.064 0.32 1 -10000 0 1
cAMP biosynthetic process -0.036 0.17 0.42 10 -0.46 48 58
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN -0.007 0.09 0.36 6 -0.49 1 7
GNAQ 0.016 0.015 -10000 0 -10000 0 0
LPAR2 0.025 0.008 -10000 0 -10000 0 0
LPAR3 0.013 0.033 -10000 0 -10000 0 0
LPAR1 -0.022 0.18 -10000 0 -0.59 40 40
IL8 -0.081 0.17 0.37 1 -0.46 38 39
PTK2 -0.002 0.1 -10000 0 -0.39 26 26
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
CASP3 -0.009 0.1 -10000 0 -0.35 36 36
EGFR 0.021 0.063 -10000 0 -0.67 4 4
PLCG1 -0.012 0.063 -10000 0 -0.29 3 3
PLD2 -0.002 0.1 -10000 0 -0.39 24 24
G12/G13 0.021 0.12 -10000 0 -0.39 32 32
PI3K-beta 0.005 0.088 -10000 0 -0.68 2 2
cell migration 0.019 0.073 -10000 0 -0.27 9 9
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
PXN 0 0.098 0.27 1 -0.33 28 29
HRAS/GTP -0.029 0.15 -10000 0 -0.45 46 46
RAC1 0.026 0.006 -10000 0 -10000 0 0
MMP9 -0.038 0.19 -10000 0 -0.67 38 38
PRKCE 0.02 0.071 -10000 0 -0.67 5 5
PRKCD -0.008 0.085 0.35 9 -10000 0 9
Gi(beta/gamma) -0.024 0.14 -10000 0 -0.5 33 33
mol:LPA 0.002 0.017 -10000 0 -0.19 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.019 0.11 -10000 0 -0.41 15 15
MAPKKK cascade -0.029 0.14 -10000 0 -0.44 46 46
contractile ring contraction involved in cytokinesis 0.017 0.047 0.25 4 -10000 0 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.065 0.15 -10000 0 -0.35 103 103
GNA15 0.013 0.027 -10000 0 -0.36 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
MAPT -0.003 0.094 0.33 8 -0.38 9 17
GNA11 0.011 0.046 -10000 0 -0.33 8 8
Rac1/GTP 0.015 0.19 -10000 0 -0.83 22 22
MMP2 -0.016 0.15 -10000 0 -0.52 33 33
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.016 0.005 -10000 0 -10000 0 0
MAP4K4 -0.015 0.12 -10000 0 -0.5 15 15
BAG4 0.025 0.032 -10000 0 -0.67 1 1
PKC zeta/ceramide -0.019 0.096 -10000 0 -0.29 34 34
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BAX -0.013 0.076 -10000 0 -0.34 20 20
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.028 0.14 0.79 16 -10000 0 16
BAD -0.032 0.088 0.18 1 -0.34 20 21
SMPD1 -0.012 0.09 0.26 6 -0.23 61 67
RB1 -0.032 0.09 0.19 1 -0.41 16 17
FADD/Caspase 8 -0.006 0.12 -10000 0 -0.52 13 13
MAP2K4 -0.019 0.072 0.24 1 -0.39 7 8
NSMAF 0.027 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.023 0.082 0.18 7 -0.4 12 19
EGF -0.074 0.24 -10000 0 -0.66 70 70
mol:ceramide -0.037 0.097 -10000 0 -0.3 37 37
MADD 0.027 0.005 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.015 0.024 -10000 0 -0.5 1 1
ASAH1 0.025 0.032 -10000 0 -0.67 1 1
negative regulation of cell cycle -0.032 0.089 0.19 1 -0.4 16 17
cell proliferation -0.059 0.15 -10000 0 -0.32 103 103
BID -0.15 0.28 -10000 0 -0.59 129 129
MAP3K1 -0.027 0.078 0.19 1 -0.38 13 14
EIF2A -0.029 0.078 -10000 0 -0.47 9 9
TRADD 0.026 0.006 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.014 0.069 -10000 0 -0.37 9 9
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.042 0.085 -10000 0 -0.38 12 12
Cathepsin D/ceramide -0.018 0.093 -10000 0 -0.29 31 31
FADD -0.014 0.12 -10000 0 -0.49 15 15
KSR1 -0.026 0.087 0.18 9 -0.3 26 35
MAPK8 -0.018 0.09 -10000 0 -0.39 17 17
PRKRA -0.034 0.09 -10000 0 -0.37 19 19
PDGFA 0.026 0.006 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
IGF1 -0.13 0.29 -10000 0 -0.67 107 107
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.036 0.096 -10000 0 -0.29 37 37
CTSD 0.026 0.009 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.039 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.062 0.16 -10000 0 -0.35 103 103
PRKCD 0.027 0.004 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.015 0.024 -10000 0 -0.5 1 1
RelA/NF kappa B1 0.039 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.015 0.12 -10000 0 -0.51 16 16
TNFR1A/BAG4/TNF-alpha -0.005 0.16 -10000 0 -0.44 58 58
mol:Sphingosine-1-phosphate 0.016 0.005 -10000 0 -10000 0 0
MAP2K1 -0.022 0.077 -10000 0 -0.39 11 11
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
CYCS -0.006 0.071 0.17 24 -0.25 17 41
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.026 -10000 0 -0.5 1 1
EIF2AK2 -0.031 0.084 -10000 0 -0.49 10 10
TNF-alpha/TNFR1A/FAN -0.004 0.16 -10000 0 -0.44 57 57
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.088 -10000 0 -0.48 7 7
MAP2K2 -0.015 0.066 -10000 0 -0.38 7 7
SMPD3 -0.018 0.1 -10000 0 -0.26 66 66
TNF -0.058 0.22 -10000 0 -0.67 57 57
PKC zeta/PAR4 0.038 0.01 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.016 0.11 0.25 69 -0.25 17 86
NF kappa B1/RelA/I kappa B alpha 0.075 0.023 -10000 0 -10000 0 0
AIFM1 -0.01 0.082 0.17 25 -0.27 24 49
BCL2 -0.024 0.18 -10000 0 -0.66 36 36
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.007 0.1 -10000 0 -0.81 6 6
Syndecan-4/Syndesmos -0.033 0.15 -10000 0 -0.54 38 38
positive regulation of JNK cascade -0.047 0.19 -10000 0 -0.56 40 40
Syndecan-4/ADAM12 -0.042 0.16 -10000 0 -0.54 38 38
CCL5 -0.017 0.16 -10000 0 -0.67 28 28
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
DNM2 0.025 0.008 -10000 0 -10000 0 0
ITGA5 0.027 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
PLG 0.008 0.031 -10000 0 -10000 0 0
ADAM12 -0.01 0.064 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.057 0.03 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.055 0.18 -10000 0 -0.58 37 37
Syndecan-4/CXCL12/CXCR4 -0.049 0.2 -10000 0 -0.6 40 40
Syndecan-4/Laminin alpha3 -0.044 0.17 -10000 0 -0.57 36 36
MDK -0.019 0.068 -10000 0 -10000 0 0
Syndecan-4/FZD7 -0.033 0.16 -10000 0 -0.54 38 38
Syndecan-4/Midkine -0.044 0.16 -10000 0 -0.55 37 37
FZD7 0.022 0.051 -10000 0 -0.51 4 4
Syndecan-4/FGFR1/FGF -0.008 0.15 -10000 0 -0.5 37 37
THBS1 0.016 0.04 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.048 0.16 -10000 0 -0.55 38 38
positive regulation of MAPKKK cascade -0.047 0.19 -10000 0 -0.56 40 40
Syndecan-4/TACI -0.12 0.21 -10000 0 -0.61 37 37
CXCR4 0.026 0.011 -10000 0 -10000 0 0
cell adhesion -0.003 0.072 0.2 5 -0.3 21 26
Syndecan-4/Dynamin -0.033 0.15 -10000 0 -0.54 37 37
Syndecan-4/TSP1 -0.035 0.16 -10000 0 -0.54 38 38
Syndecan-4/GIPC -0.033 0.15 -10000 0 -0.54 37 37
Syndecan-4/RANTES -0.053 0.19 -10000 0 -0.65 38 38
ITGB1 0.027 0.004 -10000 0 -10000 0 0
LAMA1 -0.02 0.17 -10000 0 -0.66 33 33
LAMA3 -0.001 0.13 -10000 0 -0.67 16 16
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.013 0.2 0.76 21 -0.62 21 42
Syndecan-4/alpha-Actinin -0.032 0.15 -10000 0 -0.54 37 37
TFPI -0.011 0.16 -10000 0 -0.66 27 27
F2 0.01 0.029 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.068 0.18 -10000 0 -0.58 37 37
ACTN1 0.026 0.008 -10000 0 -10000 0 0
TNC -0.031 0.09 -10000 0 -0.67 4 4
Syndecan-4/CXCL12 -0.067 0.2 -10000 0 -0.62 40 40
FGF6 -0.016 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
CXCL12 -0.044 0.21 -10000 0 -0.66 50 50
TNFRSF13B -0.14 0.28 -10000 0 -0.67 109 109
FGF2 0.027 0.004 -10000 0 -10000 0 0
FGFR1 0.025 0.032 -10000 0 -0.67 1 1
Syndecan-4/PI-4-5-P2 -0.045 0.15 -10000 0 -0.54 38 38
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.075 0.074 -10000 0 -0.22 2 2
cell migration -0.027 0.012 -10000 0 -10000 0 0
PRKCD 0.026 0.022 -10000 0 -10000 0 0
vasculogenesis -0.033 0.15 -10000 0 -0.52 38 38
SDC4 -0.044 0.16 -10000 0 -0.57 38 38
Syndecan-4/Tenascin C -0.05 0.16 -10000 0 -0.57 38 38
Syndecan-4/PI-4-5-P2/PKC alpha -0.046 0.024 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.032 0.16 -10000 0 -0.54 38 38
MMP9 -0.038 0.19 -10000 0 -0.67 38 38
Rac1/GTP -0.003 0.073 0.2 5 -0.31 21 26
cytoskeleton organization -0.032 0.15 -10000 0 -0.52 38 38
GIPC1 0.025 0.008 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.05 0.18 -10000 0 -0.57 39 39
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.009 -10000 0 -10000 0 0
LAT2 -0.002 0.066 -10000 0 -0.28 2 2
AP1 -0.12 0.25 -10000 0 -0.55 102 102
mol:PIP3 0.028 0.17 0.6 21 -0.38 20 41
IKBKB 0.039 0.17 0.59 27 -0.26 7 34
AKT1 -0.007 0.12 0.31 30 -0.36 25 55
IKBKG 0.041 0.18 0.63 27 -0.26 7 34
MS4A2 -0.014 0.062 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
MAP3K1 0.024 0.11 0.45 12 -0.41 6 18
mol:Ca2+ 0.033 0.16 0.51 29 -0.31 12 41
LYN 0.027 0.011 -10000 0 -10000 0 0
CBLB 0 0.064 -10000 0 -0.27 1 1
SHC1 0.025 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK -0.02 0.16 -10000 0 -0.4 76 76
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
PLD2 -0.009 0.13 0.32 33 -0.37 30 63
PTPN13 0.012 0.13 0.53 1 -0.62 13 14
PTPN11 0.022 0.036 -10000 0 -0.7 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.031 0.16 0.62 21 -0.36 7 28
SYK 0.025 0.012 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0 0.11 -10000 0 -0.37 28 28
LAT -0.003 0.07 -10000 0 -0.32 4 4
PAK2 0.017 0.1 0.33 7 -0.42 9 16
NFATC2 -0.1 0.23 -10000 0 -0.61 82 82
HRAS 0.013 0.1 0.24 2 -0.43 10 12
GAB2 0.027 0.005 -10000 0 -10000 0 0
PLA2G1B 0.005 0.098 -10000 0 -0.69 7 7
Fc epsilon R1 0.008 0.13 -10000 0 -0.45 32 32
Antigen/IgE/Fc epsilon R1 0.01 0.12 -10000 0 -0.41 32 32
mol:GDP 0.003 0.11 -10000 0 -0.47 13 13
JUN -0.12 0.28 -10000 0 -0.67 104 104
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.67 125 125
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.004 0.07 -10000 0 -0.25 9 9
CHUK 0.036 0.16 0.59 25 -0.26 7 32
KLRG1 -0.007 0.077 -10000 0 -0.3 15 15
VAV1 -0.004 0.073 0.21 1 -0.36 6 7
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL 0 0.064 -10000 0 -10000 0 0
negative regulation of mast cell degranulation 0.006 0.081 -10000 0 -0.3 10 10
BTK -0.005 0.12 -10000 0 -0.56 16 16
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.018 0.15 -10000 0 -0.46 40 40
GAB2/PI3K/SHP2 -0.029 0.098 -10000 0 -0.38 29 29
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.001 0.072 -10000 0 -0.26 30 30
RAF1 0.014 0.086 -10000 0 -0.86 4 4
Fc epsilon R1/FcgammaRIIB/SHIP 0.025 0.17 -10000 0 -0.49 42 42
FCER1G 0.018 0.034 -10000 0 -10000 0 0
FCER1A -0.034 0.18 -10000 0 -0.67 33 33
Antigen/IgE/Fc epsilon R1/Fyn 0.024 0.12 -10000 0 -0.38 32 32
MAPK3 0.019 0.092 -10000 0 -0.7 6 6
MAPK1 -0.014 0.11 -10000 0 -0.72 7 7
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0 0.18 -10000 0 -0.63 30 30
DUSP1 -0.083 0.25 -10000 0 -0.67 76 76
NF-kappa-B/RelA 0.015 0.048 0.14 1 -0.18 2 3
actin cytoskeleton reorganization 0.014 0.13 0.37 1 -0.7 10 11
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.024 0.098 -10000 0 -0.46 7 7
FER -0.003 0.071 -10000 0 -0.42 3 3
RELA 0.027 0.005 -10000 0 -10000 0 0
ITK -0.043 0.15 -10000 0 -0.46 54 54
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 0.011 0.12 0.4 8 -0.5 10 18
cytokine secretion 0.005 0.03 -10000 0 -10000 0 0
SPHK1 -0.001 0.066 0.27 1 -0.28 2 3
PTK2 0.014 0.13 0.37 1 -0.75 10 11
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.007 0.11 -10000 0 -0.38 28 28
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.035 0.18 0.66 20 -0.41 11 31
MAP2K2 0.018 0.091 -10000 0 -0.8 4 4
MAP2K1 0.009 0.084 -10000 0 -0.76 5 5
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
KLRG1/SHP2 -0.001 0.082 -10000 0 -0.31 14 14
MAP2K4 -0.006 0.19 -10000 0 -0.85 23 23
Fc epsilon R1/FcgammaRIIB 0.007 0.18 -10000 0 -0.52 42 42
mol:Choline -0.009 0.13 0.32 33 -0.36 30 63
SHC/Grb2/SOS1 0.037 0.077 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
DOK1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.018 0.13 0.46 3 -0.66 10 13
HCLS1 -0.001 0.065 -10000 0 -0.28 2 2
PRKCB 0.036 0.18 0.63 25 -0.32 15 40
FCGR2B -0.008 0.15 -10000 0 -0.67 23 23
IGHE 0.001 0.011 -10000 0 -10000 0 0
KLRG1/SHIP 0.006 0.082 -10000 0 -0.31 10 10
LCP2 0.024 0.019 -10000 0 -10000 0 0
PLA2G4A -0.023 0.12 -10000 0 -0.42 31 31
RASA1 0.026 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.009 0.13 0.32 33 -0.36 30 63
IKK complex 0.044 0.18 0.62 29 -0.21 3 32
WIPF1 0.027 0.005 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.016 0.21 -10000 0 -0.94 21 21
NCK1/PAK1/Dok-R -0.029 0.09 -10000 0 -0.43 21 21
NCK1/Dok-R -0.008 0.26 -10000 0 -1.1 21 21
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
mol:beta2-estradiol 0 0.047 0.23 18 -10000 0 18
RELA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.025 0.008 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
F2 -0.011 0.057 0.27 14 -10000 0 14
TNIP2 0.027 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.007 0.24 -10000 0 -1 21 21
FN1 -0.08 0.066 -10000 0 -10000 0 0
PLD2 -0.029 0.25 -10000 0 -1.2 21 21
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GRB14 0.009 0.11 -10000 0 -0.67 12 12
ELK1 -0.028 0.23 -10000 0 -1 21 21
GRB7 0.002 0.054 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.004 0.26 -10000 0 -1.1 21 21
CDKN1A -0.024 0.16 0.49 4 -0.63 21 25
ITGA5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.008 0.25 -10000 0 -1.1 21 21
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:NO 0.008 0.18 0.57 8 -0.67 21 29
PLG -0.035 0.26 -10000 0 -1.2 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.014 0.2 -10000 0 -0.89 21 21
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.006 -10000 0 -10000 0 0
ANGPT2 -0.1 0.2 0.42 1 -0.79 17 18
BMX -0.039 0.26 -10000 0 -1.2 21 21
ANGPT1 -0.049 0.27 -10000 0 -1.3 19 19
tube development -0.039 0.18 0.48 2 -0.72 21 23
ANGPT4 -0.031 0.19 -10000 0 -0.67 39 39
response to hypoxia -0.004 0.016 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.03 0.28 -10000 0 -1.2 21 21
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
FGF2 0.026 0.004 -10000 0 -10000 0 0
STAT5A (dimer) -0.039 0.19 -10000 0 -0.82 21 21
mol:L-citrulline 0.008 0.18 0.57 8 -0.67 21 29
AGTR1 -0.25 0.34 -10000 0 -0.67 195 195
MAPK14 -0.03 0.26 -10000 0 -1.2 21 21
Tie2/SHP2 -0.005 0.19 -10000 0 -1.2 8 8
TEK 0.003 0.2 -10000 0 -1.4 8 8
RPS6KB1 -0.01 0.2 0.5 2 -0.89 21 23
Angiotensin II/AT1 -0.19 0.26 -10000 0 -0.5 195 195
Tie2/Ang1/GRB2 -0.02 0.27 -10000 0 -1.2 21 21
MAPK3 -0.024 0.23 -10000 0 -1.1 21 21
MAPK1 -0.033 0.23 -10000 0 -1.1 21 21
Tie2/Ang1/GRB7 -0.021 0.27 -10000 0 -1.2 21 21
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.036 0.26 -10000 0 -1.2 21 21
PI3K -0.024 0.24 -10000 0 -1.1 21 21
FES -0.031 0.25 -10000 0 -1.2 21 21
Crk/Dok-R -0.008 0.25 -10000 0 -1.1 22 22
Tie2/Ang1/ABIN2 -0.02 0.27 -10000 0 -1.2 21 21
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.007 0.19 0.5 4 -0.82 21 25
STAT5A 0.026 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.013 0.2 0.48 1 -0.9 21 22
Tie2/Ang2 -0.059 0.23 -10000 0 -1 21 21
Tie2/Ang1 -0.032 0.28 -10000 0 -1.3 21 21
FOXO1 -0.004 0.2 0.56 4 -0.83 21 25
ELF1 0.027 0.053 -10000 0 -0.59 3 3
ELF2 -0.028 0.25 -10000 0 -1.1 21 21
mol:Choline -0.026 0.24 -10000 0 -1.1 21 21
cell migration -0.01 0.057 -10000 0 -0.24 21 21
FYN -0.049 0.2 0.53 1 -0.84 21 22
DOK2 0.02 0.051 -10000 0 -0.67 2 2
negative regulation of cell cycle -0.021 0.15 0.46 5 -0.57 21 26
ETS1 0.025 0.049 -10000 0 -0.24 14 14
PXN 0 0.18 0.59 5 -0.73 21 26
ITGB1 0.027 0.004 -10000 0 -10000 0 0
NOS3 0.001 0.19 0.57 7 -0.77 21 28
RAC1 0.026 0.006 -10000 0 -10000 0 0
TNF -0.06 0.23 -10000 0 -0.59 73 73
MAPKKK cascade -0.026 0.24 -10000 0 -1.1 21 21
RASA1 0.026 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.022 0.27 -10000 0 -1.2 21 21
NCK1 0.027 0.004 -10000 0 -10000 0 0
vasculogenesis 0.011 0.16 0.52 10 -0.6 21 31
mol:Phosphatidic acid -0.026 0.24 -10000 0 -1.1 21 21
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.008 0.18 0.57 8 -0.67 21 29
Rac1/GTP -0.008 0.19 -10000 0 -0.82 21 21
MMP2 -0.034 0.26 -10000 0 -1.2 21 21
Signaling events mediated by PRL

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
CCNE1 0.025 0.008 -10000 0 -10000 0 0
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.016 0.083 -10000 0 -0.67 7 7
CDKN1A -0.007 0.071 -10000 0 -0.61 1 1
PRL-3/alpha Tubulin 0.029 0.033 -10000 0 -10000 0 0
mol:Ca2+ -0.026 0.074 0.24 5 -0.52 9 14
AGT 0.006 0.098 -10000 0 -0.67 9 9
CCNA2 -0.066 0.15 -10000 0 -0.36 96 96
TUBA1B 0.027 0.005 -10000 0 -10000 0 0
EGR1 -0.084 0.2 -10000 0 -0.49 97 97
CDK2/Cyclin E1 0.019 0.076 -10000 0 -0.53 1 1
MAPK3 0.009 0.025 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.04 0.008 -10000 0 -10000 0 0
MAPK1 0.007 0.022 -10000 0 -10000 0 0
PTP4A1 -0.068 0.16 -10000 0 -0.39 97 97
PTP4A3 0.014 0.041 -10000 0 -10000 0 0
PTP4A2 0.027 0.005 -10000 0 -10000 0 0
ITGB1 0.009 0.026 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 -0.011 0.081 -10000 0 -0.37 8 8
Rab GGTase beta/Rab GGTase alpha 0.039 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.049 0.16 -10000 0 -0.36 93 93
RABGGTA 0.027 0.005 -10000 0 -10000 0 0
BCAR1 -0.017 0.006 -10000 0 -10000 0 0
RHOC -0.011 0.083 -10000 0 -0.4 7 7
RHOA -0.01 0.08 -10000 0 -0.38 7 7
cell motility -0.003 0.095 0.3 5 -0.38 8 13
PRL-1/alpha Tubulin -0.048 0.16 -10000 0 -0.36 97 97
PRL-3/alpha1 Integrin 0.021 0.073 -10000 0 -0.52 7 7
ROCK1 -0.005 0.093 0.3 3 -0.4 7 10
RABGGTB 0.027 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.005 -10000 0 -10000 0 0
mitosis -0.068 0.16 -10000 0 -0.38 97 97
ATF5 0.02 0.028 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 -0.016 0.12 -10000 0 -0.44 20 20
BAG4 0.025 0.032 -10000 0 -0.67 1 1
BAD 0.007 0.065 0.34 9 -10000 0 9
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BAX 0.012 0.071 0.24 24 -0.16 1 25
EnzymeConsortium:3.1.4.12 0.001 0.04 0.16 10 -0.1 17 27
IKBKB -0.014 0.12 0.29 1 -0.45 15 16
MAP2K2 0.017 0.095 0.32 26 -0.3 2 28
MAP2K1 0.011 0.084 0.31 20 -0.3 2 22
SMPD1 0.005 0.046 0.24 7 -0.14 3 10
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.011 0.12 -10000 0 -0.45 20 20
MAP2K4 0.017 0.097 0.35 26 -10000 0 26
protein ubiquitination -0.013 0.12 0.32 4 -0.44 17 21
EnzymeConsortium:2.7.1.37 0.017 0.11 0.36 28 -0.3 2 30
response to UV 0 0.002 0.006 27 -0.002 3 30
RAF1 0.011 0.086 0.3 23 -0.31 2 25
CRADD 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide 0.004 0.059 0.22 12 -0.15 16 28
I-kappa-B-alpha/RELA/p50/ubiquitin 0.036 0.008 -10000 0 -10000 0 0
MADD 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.01 0.077 0.32 17 -10000 0 17
TRADD 0.026 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.017 0.088 0.32 22 -0.29 2 24
MAPK1 -0.005 0.091 0.32 17 -0.27 4 21
p50/RELA/I-kappa-B-alpha 0.039 0.009 -10000 0 -10000 0 0
FADD -0.016 0.12 -10000 0 -0.44 19 19
KSR1 0.01 0.081 0.27 24 -0.19 12 36
MAPK8 0.011 0.11 0.38 22 -0.35 9 31
TRAF2 0.025 0.009 -10000 0 -10000 0 0
response to radiation 0 0.001 0.006 13 -10000 0 13
CHUK -0.015 0.12 0.33 1 -0.44 16 17
TNF R/SODD 0.038 0.026 -10000 0 -0.5 1 1
TNF -0.058 0.22 -10000 0 -0.67 57 57
CYCS 0.019 0.081 0.25 28 -0.18 1 29
IKBKG -0.014 0.12 0.38 1 -0.44 15 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.017 0.13 -10000 0 -0.45 22 22
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AIFM1 0.017 0.08 0.25 24 -0.17 3 27
TNF/TNF R/SODD -0.005 0.16 -10000 0 -0.44 58 58
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.006 13 -10000 0 13
CASP8 0.008 0.13 -10000 0 -0.72 14 14
NSMAF -0.015 0.12 -10000 0 -0.45 18 18
response to hydrogen peroxide 0 0.002 0.006 27 -0.002 3 30
BCL2 -0.024 0.18 -10000 0 -0.66 36 36
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.007 0.1 -9999 0 -0.52 11 11
alphaM/beta2 Integrin/GPIbA -0.001 0.12 -9999 0 -0.49 18 18
alphaM/beta2 Integrin/proMMP-9 -0.022 0.16 -9999 0 -0.49 41 41
PLAUR -0.021 0.068 -9999 0 -10000 0 0
HMGB1 0.007 0.036 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.012 0.086 -9999 0 -0.56 5 5
AGER -0.04 0.18 -9999 0 -0.7 32 32
RAP1A 0.027 0.005 -9999 0 -10000 0 0
SELPLG 0.017 0.036 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.039 0.2 -9999 0 -0.46 56 56
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.038 0.19 -9999 0 -0.67 38 38
CYR61 -0.17 0.32 -9999 0 -0.67 140 140
TLN1 0.025 0.007 -9999 0 -10000 0 0
Rap1/GTP 0 0.088 -9999 0 -0.38 8 8
RHOA 0.027 0.004 -9999 0 -10000 0 0
P-selectin oligomer 0.015 0.078 -9999 0 -0.67 6 6
MYH2 -0.03 0.098 -9999 0 -0.4 10 10
MST1R 0.02 0.064 -9999 0 -0.67 4 4
leukocyte activation during inflammatory response 0.012 0.081 -9999 0 -0.49 5 5
APOB 0.006 0.039 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.016 0.079 -9999 0 -0.62 7 7
JAM3 0.027 0.005 -9999 0 -10000 0 0
GP1BA 0.002 0.12 -9999 0 -0.63 15 15
alphaM/beta2 Integrin/CTGF -0.05 0.19 -9999 0 -0.47 72 72
alphaM/beta2 Integrin -0.023 0.089 -9999 0 -0.38 12 12
JAM3 homodimer 0.027 0.005 -9999 0 -10000 0 0
ICAM2 0.026 0.007 -9999 0 -10000 0 0
ICAM1 -0.018 0.067 -9999 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.023 0.09 -9999 0 -0.38 13 13
cell adhesion -0.001 0.12 -9999 0 -0.49 18 18
NFKB1 -0.12 0.26 -9999 0 -0.49 136 136
THY1 0.026 0.011 -9999 0 -10000 0 0
RhoA/GDP 0.02 0.003 -9999 0 -10000 0 0
Lipoprotein(a) 0.021 0.028 -9999 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.025 0.097 -9999 0 -0.47 10 10
IL6 -0.21 0.39 -9999 0 -0.94 97 97
ITGB2 -0.004 0.058 -9999 0 -0.7 1 1
elevation of cytosolic calcium ion concentration -0.02 0.1 -9999 0 -0.51 5 5
alphaM/beta2 Integrin/JAM2/JAM3 0.026 0.095 -9999 0 -0.48 9 9
JAM2 0.02 0.063 -9999 0 -0.67 4 4
alphaM/beta2 Integrin/ICAM1 0.031 0.11 -9999 0 -0.48 9 9
alphaM/beta2 Integrin/uPA/Plg 0.013 0.099 -9999 0 -0.52 5 5
RhoA/GTP -0.025 0.1 -9999 0 -0.38 15 15
positive regulation of phagocytosis -0.007 0.097 -9999 0 -0.57 5 5
Ron/MSP 0.034 0.056 -9999 0 -0.5 5 5
alphaM/beta2 Integrin/uPAR/uPA 0.014 0.11 -9999 0 -0.52 5 5
alphaM/beta2 Integrin/uPAR 0.005 0.095 -9999 0 -0.55 5 5
PLAU -0.041 0.074 -9999 0 -10000 0 0
PLAT 0.019 0.066 -9999 0 -0.67 4 4
actin filament polymerization -0.029 0.095 -9999 0 -0.38 10 10
MST1 0.026 0.032 -9999 0 -0.67 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.017 0.084 -9999 0 -0.5 5 5
TNF -0.17 0.35 -9999 0 -0.91 74 74
RAP1B 0.027 0.005 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.003 0.1 -9999 0 -0.51 6 6
fibrinolysis 0.01 0.097 -9999 0 -0.52 5 5
HCK 0.018 0.035 -9999 0 -10000 0 0
dendritic cell antigen processing and presentation -0.023 0.09 -9999 0 -0.38 13 13
VTN -0.039 0.2 -9999 0 -0.67 44 44
alphaM/beta2 Integrin/CYR61 -0.12 0.23 -9999 0 -0.46 142 142
LPA -0.005 0.026 -9999 0 -10000 0 0
LRP1 0.025 0.032 -9999 0 -0.67 1 1
cell migration -0.031 0.16 -9999 0 -0.48 43 43
FN1 -0.08 0.066 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.013 0.087 -9999 0 -0.56 5 5
MPO 0.013 0.072 -9999 0 -0.67 5 5
KNG1 -0.005 0.037 -9999 0 -10000 0 0
RAP1/GDP 0.035 0.009 -9999 0 -10000 0 0
ROCK1 -0.024 0.097 -9999 0 -0.4 9 9
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.014 0.019 -9999 0 -10000 0 0
CTGF -0.073 0.24 -9999 0 -0.66 71 71
alphaM/beta2 Integrin/Hck 0.009 0.092 -9999 0 -0.51 6 6
ITGAM -0.007 0.081 -9999 0 -0.62 5 5
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.02 0.1 -9999 0 -0.52 10 10
HP -0.022 0.097 -9999 0 -0.67 6 6
leukocyte adhesion -0.031 0.16 -9999 0 -0.46 35 35
SELP 0.015 0.079 -9999 0 -0.67 6 6
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.04 0.13 0.9 7 -10000 0 7
VDR 0.026 0.008 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.006 0.11 -10000 0 -0.41 8 8
RXRs/LXRs/DNA/Oxysterols -0.011 0.15 -10000 0 -0.42 52 52
MED1 0.026 0.007 -10000 0 -10000 0 0
mol:9cRA -0.001 0.019 -10000 0 -0.14 1 1
RARs/THRs/DNA/Src-1 0.02 0.069 -10000 0 -0.3 21 21
RXRs/NUR77 -0.087 0.23 -10000 0 -0.44 131 131
RXRs/PPAR -0.019 0.081 -10000 0 -0.38 11 11
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.006 -10000 0 -10000 0 0
RARs/VDR/DNA/Vit D3 0.048 0.075 -10000 0 -0.38 13 13
RARA 0.026 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.008 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.031 0.072 -10000 0 -0.37 14 14
RARG 0.027 0.005 -10000 0 -10000 0 0
RPS6KB1 0.051 0.12 0.56 27 -10000 0 27
RARs/THRs/DNA/SMRT 0.02 0.069 -10000 0 -0.3 21 21
THRA 0.026 0.007 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.02 0.006 -10000 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA 0.038 0.099 -10000 0 -0.36 8 8
NR1H4 -0.005 0.022 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.058 0.12 -10000 0 -0.5 4 4
NR1H2 0.022 0.024 -10000 0 -10000 0 0
NR1H3 0.023 0.027 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.049 0.081 -10000 0 -0.45 3 3
NR4A1 -0.18 0.32 -10000 0 -0.67 141 141
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.004 0.055 -10000 0 -0.31 3 3
RXRG -0.1 0.076 -10000 0 -0.6 5 5
RXR alpha/CCPG 0.032 0.025 -10000 0 -10000 0 0
RXRA 0.02 0.025 -10000 0 -10000 0 0
RXRB 0.023 0.027 -10000 0 -10000 0 0
THRB 0.013 0.095 -10000 0 -0.64 10 10
PPARG 0.016 0.084 -10000 0 -0.67 7 7
PPARD 0.027 0.003 -10000 0 -10000 0 0
TNF -0.1 0.38 -10000 0 -1.1 58 58
mol:Oxysterols -0.001 0.016 -10000 0 -10000 0 0
cholesterol transport -0.01 0.15 -10000 0 -0.42 52 52
PPARA 0.02 0.012 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.007 0.12 -10000 0 -0.67 14 14
RXRs/NUR77/BCL2 -0.11 0.17 -10000 0 -0.34 154 154
SREBF1 -0.011 0.14 -10000 0 -0.59 4 4
RXRs/RXRs/DNA/9cRA 0.038 0.099 -10000 0 -0.36 8 8
ABCA1 -0.011 0.14 -10000 0 -0.59 4 4
RARs/THRs 0.056 0.098 -10000 0 -0.4 20 20
RXRs/FXR 0.049 0.087 -10000 0 -0.48 3 3
BCL2 -0.024 0.18 -10000 0 -0.66 36 36
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.032 0.07 -10000 0 -0.57 6 6
alphaV beta3 Integrin 0.04 0.079 -10000 0 -0.47 10 10
PTK2 0.013 0.14 0.41 11 -0.56 7 18
IGF1R 0.027 0.004 -10000 0 -10000 0 0
PI4KB 0.025 0.007 -10000 0 -10000 0 0
MFGE8 0.01 0.048 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
CDKN1B -0.028 0.16 -10000 0 -0.53 45 45
VEGFA 0.023 0.055 -10000 0 -0.67 3 3
ILK -0.028 0.16 -10000 0 -0.53 46 46
ROCK1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.03 0.15 -10000 0 -0.5 45 45
PTK2B 0.013 0.089 0.36 1 -0.42 15 16
alphaV/beta3 Integrin/JAM-A 0.007 0.14 -10000 0 -0.39 50 50
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.037 0.077 -10000 0 -0.46 10 10
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.09 0.24 -10000 0 -0.43 152 152
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0 0.093 -10000 0 -0.41 5 5
alphaV/beta3 Integrin/Syndecan-1 0.04 0.079 -10000 0 -0.47 10 10
PI4KA 0.02 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.094 0.23 -10000 0 -0.42 151 151
PI4 Kinase 0.028 0.019 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
alphaV/beta3 Integrin/Osteopontin 0.022 0.12 -10000 0 -0.45 29 29
RPS6KB1 -0.14 0.19 0.42 2 -0.42 112 114
TLN1 0.025 0.007 -10000 0 -10000 0 0
MAPK3 -0.051 0.13 -10000 0 -0.65 11 11
GPR124 0.027 0.005 -10000 0 -10000 0 0
MAPK1 -0.06 0.14 -10000 0 -0.59 18 18
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.028 0.12 -10000 0 -0.52 19 19
cell adhesion 0.031 0.075 -10000 0 -0.46 9 9
ANGPTL3 0.007 0.024 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.064 -10000 0 -0.5 6 6
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
TGFBR2 0.023 0.055 -10000 0 -0.67 3 3
ITGB3 0.012 0.095 -10000 0 -0.64 10 10
IGF1 -0.13 0.29 -10000 0 -0.67 107 107
RAC1 0.026 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.04 0.078 -10000 0 -0.47 10 10
apoptosis 0.024 0.045 -10000 0 -0.67 2 2
CD47 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.04 0.079 -10000 0 -0.47 10 10
VCL 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.034 0.1 -10000 0 -0.48 16 16
CSF1 0.015 0.089 -10000 0 -0.67 8 8
PIK3C2A -0.029 0.17 -10000 0 -0.53 47 47
PI4 Kinase/Pyk2 -0.014 0.12 -10000 0 -0.64 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.095 -10000 0 -0.45 15 15
FAK1/Vinculin 0.023 0.12 0.39 9 -0.45 6 15
alphaV beta3/Integrin/ppsTEM5 0.04 0.078 -10000 0 -0.47 10 10
RHOA 0.027 0.004 -10000 0 -10000 0 0
VTN -0.039 0.2 -10000 0 -0.67 44 44
BCAR1 0.026 0.006 -10000 0 -10000 0 0
FGF2 0.027 0.004 -10000 0 -10000 0 0
F11R 0.016 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.042 0.079 -10000 0 -0.47 10 10
alphaV/beta3 Integrin/TGFBR2 0.038 0.084 -10000 0 -0.44 13 13
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.055 0.072 -10000 0 -0.44 9 9
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.036 0.073 -10000 0 -0.44 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.08 0.066 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.034 0.087 -10000 0 -0.42 15 15
SDC1 0.025 0.014 -10000 0 -10000 0 0
VAV3 0.009 0.08 -10000 0 -0.42 14 14
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
IRS1 -0.057 0.23 -10000 0 -0.66 59 59
FAK1/Paxillin 0.022 0.12 0.35 8 -0.45 6 14
cell migration 0.018 0.11 0.34 6 -0.4 6 12
ITGAV 0.024 0.045 -10000 0 -0.67 2 2
PI3K 0.016 0.14 -10000 0 -0.38 51 51
SPP1 -0.031 0.15 -10000 0 -0.67 22 22
KDR 0.021 0.063 -10000 0 -0.67 4 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.045 -10000 0 -0.67 2 2
COL4A3 0.008 0.11 -10000 0 -0.62 14 14
angiogenesis -0.054 0.15 -10000 0 -0.61 17 17
Rac1/GTP 0.021 0.075 -10000 0 -0.39 14 14
EDIL3 0.007 0.089 -10000 0 -0.67 7 7
cell proliferation 0.037 0.083 -10000 0 -0.44 13 13
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
Jak2/Leptin Receptor -0.004 0.12 0.29 2 -0.38 25 27
PTP1B/AKT1 0.008 0.071 0.32 2 -0.29 5 7
FYN 0.027 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.001 0.082 0.32 10 -0.28 8 18
EGFR 0.015 0.066 -10000 0 -0.68 4 4
EGF/EGFR -0.033 0.16 -10000 0 -0.38 71 71
CSF1 0.015 0.089 -10000 0 -0.67 8 8
AKT1 0.027 0.006 -10000 0 -10000 0 0
INSR 0.026 0.008 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.001 0.11 0.32 6 -0.35 18 24
Insulin Receptor/Insulin 0.018 0.067 -10000 0 -0.32 2 2
HCK 0.018 0.035 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
TYK2 0.009 0.093 0.32 20 -0.3 4 24
EGF -0.074 0.24 -10000 0 -0.67 70 70
YES1 0.027 0.005 -10000 0 -10000 0 0
CAV1 -0.002 0.11 0.4 12 -0.32 8 20
TXN 0.024 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.029 0.14 -10000 0 -0.38 57 57
cell migration -0.001 0.082 0.28 8 -0.32 10 18
STAT3 0.026 0.007 -10000 0 -10000 0 0
PRLR -0.015 0.16 -10000 0 -0.67 25 25
ITGA2B -0.04 0.2 -10000 0 -0.66 46 46
CSF1R 0.024 0.035 -10000 0 -0.67 1 1
Prolactin Receptor/Prolactin 0.001 0.12 -10000 0 -0.5 25 25
FGR 0.025 0.014 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.007 0.072 0.28 3 -0.29 5 8
Crk/p130 Cas 0.014 0.071 -10000 0 -0.35 1 1
DOK1 0.013 0.087 0.37 12 -0.34 3 15
JAK2 -0.011 0.12 0.37 4 -0.39 29 33
Jak2/Leptin Receptor/Leptin -0.01 0.13 -10000 0 -0.5 22 22
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PTPN1 0.001 0.083 0.32 10 -0.28 8 18
LYN 0.027 0.005 -10000 0 -10000 0 0
CDH2 -0.07 0.12 -10000 0 -0.63 15 15
SRC 0.023 0.057 0.32 1 -0.39 5 6
ITGB3 0.011 0.096 -10000 0 -0.64 10 10
CAT1/PTP1B -0.057 0.16 0.38 15 -0.36 44 59
CAPN1 0.027 0.006 -10000 0 -10000 0 0
CSK 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.024 0.078 -10000 0 -0.46 4 4
mol:H2O2 -0.001 0.007 -10000 0 -10000 0 0
STAT3 (dimer) -0.01 0.14 -10000 0 -0.53 22 22
negative regulation of transcription -0.01 0.12 0.37 4 -0.38 29 33
FCGR2A 0.018 0.043 -10000 0 -0.67 1 1
FER 0.021 0.055 -10000 0 -0.68 3 3
alphaIIb/beta3 Integrin -0.024 0.18 -10000 0 -0.52 53 53
BLK -0.19 0.31 -10000 0 -0.66 143 143
Insulin Receptor/Insulin/Shc 0.042 0.018 -10000 0 -10000 0 0
RHOA 0.028 0.006 -10000 0 -10000 0 0
LEPR 0.021 0.06 -10000 0 -0.53 5 5
BCAR1 0.026 0.006 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.007 -10000 0 -10000 0 0
mol:NADPH 0 0.005 -10000 0 -10000 0 0
TRPV6 -0.088 0.18 0.3 6 -0.45 45 51
PRL -0.006 0.02 -10000 0 -10000 0 0
SOCS3 -0.051 0.32 -10000 0 -1.3 30 30
SPRY2 0.022 0.046 -10000 0 -0.68 2 2
Insulin Receptor/Insulin/IRS1 -0.015 0.16 -10000 0 -0.44 58 58
CSF1/CSF1R 0.01 0.095 0.28 1 -0.45 10 11
Ras protein signal transduction 0.027 0.11 0.46 26 -10000 0 26
IRS1 -0.057 0.23 -10000 0 -0.66 59 59
INS 0.011 0.014 -10000 0 -10000 0 0
LEP 0.009 0.032 -10000 0 -10000 0 0
STAT5B 0.003 0.091 0.3 11 -0.28 14 25
STAT5A 0.003 0.091 0.3 11 -0.29 12 23
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.006 0.073 0.28 1 -0.33 6 7
CSN2 0.001 0.063 0.81 1 -10000 0 1
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
LAT 0.02 0.073 0.32 1 -0.45 8 9
YBX1 0.033 0.007 -10000 0 -10000 0 0
LCK 0.012 0.082 -10000 0 -0.67 6 6
SHC1 0.025 0.007 -10000 0 -10000 0 0
NOX4 -0.039 0.074 -10000 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.032 0.11 -10000 0 -0.33 59 59
FRAP1 0.01 0.047 0.36 3 -0.42 1 4
AKT1 -0.027 0.097 -10000 0 -0.28 56 56
INSR 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0.002 0.09 -10000 0 -0.42 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.036 -10000 0 -0.24 1 1
TSC2 0.026 0.006 -10000 0 -10000 0 0
RHEB/GDP -0.002 0.075 -10000 0 -0.38 3 3
TSC1 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.025 0.13 -10000 0 -0.38 60 60
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.016 0.044 -10000 0 -0.27 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.018 0.099 0.39 18 -0.37 3 21
MAP3K5 0.006 0.028 0.18 1 -0.22 6 7
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
apoptosis 0.006 0.029 0.18 1 -0.21 7 8
mol:LY294002 0 0.001 0.001 1 -0.002 73 74
EIF4B 0.023 0.11 0.46 21 -0.32 3 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.026 0.069 0.38 4 -0.33 2 6
eIF4E/eIF4G1/eIF4A1 0.016 0.024 -10000 0 -0.25 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.009 0.13 -10000 0 -0.36 60 60
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.048 0.25 4 -0.24 2 6
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.011 0.081 -10000 0 -0.38 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 73 74
FKBP12/Rapamycin 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.034 0.11 -10000 0 -0.32 57 57
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.025 0.074 -10000 0 -0.5 8 8
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.008 -10000 0 -10000 0 0
TSC1/TSC2 0.004 0.098 0.28 1 -0.46 3 4
tumor necrosis factor receptor activity 0 0.001 0.002 73 -0.001 1 74
RPS6 0.025 0.008 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
EIF4G1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.044 0.14 -10000 0 -0.37 68 68
INS -0.016 0.003 -10000 0 -10000 0 0
PTEN 0.025 0.018 -10000 0 -0.35 1 1
PDK2 -0.031 0.1 0.22 3 -0.31 56 59
EIF4EBP1 0.016 0.097 -10000 0 -0.93 5 5
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
PPP2R5D 0.02 0.075 0.39 13 -0.38 1 14
peptide biosynthetic process 0.013 0.014 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
EIF4A1 0.026 0.007 -10000 0 -10000 0 0
mol:Rapamycin 0 0.002 0.007 27 -0.003 3 30
EEF2 0.013 0.014 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.03 0.089 -10000 0 -0.83 5 5
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.04 -10000 0 -0.81 1 1
VEGFR1 homodimer/NRP1 0.015 0.038 -10000 0 -0.81 1 1
mol:DAG -0.021 0.13 -10000 0 -0.4 48 48
VEGFR1 homodimer/NRP1/VEGFR 121 0.028 0.059 -10000 0 -0.63 3 3
CaM/Ca2+ -0.005 0.12 -10000 0 -0.38 48 48
HIF1A 0.032 0.019 -10000 0 -0.37 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.019 0.13 -10000 0 -0.69 4 4
PLCG1 -0.021 0.13 -10000 0 -0.4 48 48
NOS3 -0.012 0.12 -10000 0 -0.52 3 3
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:NO -0.007 0.12 0.47 3 -0.5 3 6
FLT1 0.02 0.043 -10000 0 -0.91 1 1
PGF -0.042 0.21 -10000 0 -0.66 48 48
VEGFR1 homodimer/NRP2/VEGFR121 0.045 0.062 -10000 0 -0.63 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
eNOS/Hsp90 0.005 0.12 -10000 0 -0.49 3 3
endothelial cell proliferation -0.039 0.15 0.36 2 -0.43 47 49
mol:Ca2+ -0.02 0.13 -10000 0 -0.4 48 48
MAPK3 -0.041 0.13 0.36 2 -0.39 20 22
MAPK1 -0.043 0.13 -10000 0 -0.36 55 55
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PLGF homodimer -0.042 0.21 -10000 0 -0.66 48 48
PRKACA 0.025 0.008 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.013 0.094 -10000 0 -0.67 9 9
VEGFA homodimer 0.023 0.055 -10000 0 -0.67 3 3
VEGFR1 homodimer/VEGFA homodimer 0.031 0.063 -10000 0 -0.68 3 3
platelet activating factor biosynthetic process -0.044 0.12 -10000 0 -0.95 1 1
PI3K 0.017 0.14 -10000 0 -0.39 49 49
PRKCA -0.041 0.14 -10000 0 -0.38 66 66
PRKCB -0.034 0.12 -10000 0 -0.38 52 52
VEGFR1 homodimer/PLGF homodimer -0.012 0.14 -10000 0 -0.44 48 48
VEGFA 0.023 0.055 -10000 0 -0.67 3 3
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.021 0.13 -10000 0 -0.4 48 48
RASA1 0.02 0.038 -10000 0 -0.76 1 1
NRP2 0.015 0.041 -10000 0 -10000 0 0
VEGFR1 homodimer 0.02 0.042 -10000 0 -0.9 1 1
VEGFB homodimer 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.003 0.14 0.55 4 -0.53 6 10
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
mol:PI-3-4-5-P3 0.015 0.14 -10000 0 -0.38 49 49
mol:L-citrulline -0.007 0.12 0.47 3 -0.5 3 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.058 0.062 -10000 0 -0.6 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.061 -10000 0 -0.63 3 3
CD2AP 0.027 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.027 0.14 -10000 0 -0.37 49 49
PDPK1 -0.016 0.13 0.34 3 -0.99 2 5
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.074 -10000 0 -0.74 3 3
mol:NADP -0.007 0.12 0.47 3 -0.5 3 6
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.056 0.06 -10000 0 -0.59 3 3
VEGFR1 homodimer/NRP2 0.026 0.047 -10000 0 -0.81 1 1
LPA4-mediated signaling events

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
ADCY4 0.002 0.045 -10000 0 -0.44 5 5
ADCY5 -0.054 0.15 -10000 0 -0.44 65 65
ADCY6 0.002 0.045 -10000 0 -0.44 5 5
ADCY7 0.001 0.045 -10000 0 -0.44 5 5
ADCY1 -0.002 0.065 -10000 0 -0.49 8 8
ADCY2 -0.038 0.13 -10000 0 -0.44 45 45
ADCY3 0.002 0.045 -10000 0 -0.44 5 5
ADCY8 -0.048 0.053 -10000 0 -0.49 5 5
PRKCE 0.003 0.052 -10000 0 -0.5 5 5
ADCY9 0.001 0.045 -10000 0 -0.44 5 5
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.035 0.096 0.37 6 -0.36 16 22
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.026 0.025 0.37 1 -10000 0 1
HSPA8 0.02 0.057 -10000 0 -0.59 4 4
SMAD3/SMAD4/ER alpha -0.004 0.13 -10000 0 -0.48 21 21
AKT1 0.026 0.006 -10000 0 -10000 0 0
GSC -0.18 0.5 -10000 0 -1.4 69 69
NKX2-5 0.018 0.014 -10000 0 -10000 0 0
muscle cell differentiation -0.009 0.082 0.38 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.038 0.094 -10000 0 -10000 0 0
SMAD4 -0.007 0.071 -10000 0 -0.22 5 5
CBFB 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.025 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.042 0.07 -10000 0 -0.38 4 4
SMAD3/SMAD4/VDR 0.049 0.074 -10000 0 -10000 0 0
MYC 0.011 0.11 -10000 0 -0.65 12 12
CDKN2B -0.019 0.11 -10000 0 -0.51 1 1
AP1 -0.19 0.41 -10000 0 -0.75 149 149
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.028 0.063 -10000 0 -0.5 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.011 0.034 -10000 0 -10000 0 0
SP3 0.029 0.005 -10000 0 -10000 0 0
CREB1 0.027 0.005 -10000 0 -10000 0 0
FOXH1 0.005 0.053 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.02 0.078 -10000 0 -10000 0 0
GATA3 -0.008 0.15 -10000 0 -0.62 24 24
SKI/SIN3/HDAC complex/NCoR1 0.028 0.041 -10000 0 -0.65 1 1
MEF2C/TIF2 -0.033 0.14 0.32 2 -0.4 41 43
endothelial cell migration -0.023 0.079 1.3 1 -10000 0 1
MAX 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.007 -10000 0 -10000 0 0
RBBP4 0.023 0.045 -10000 0 -0.67 2 2
RUNX2 -0.015 0.078 -10000 0 -0.67 2 2
RUNX3 0.013 0.09 -10000 0 -0.67 8 8
RUNX1 -0.038 0.073 -10000 0 -10000 0 0
CTBP1 0.027 0.004 -10000 0 -10000 0 0
NR3C1 0.025 0.006 -10000 0 -10000 0 0
VDR 0.026 0.008 -10000 0 -10000 0 0
CDKN1A 0.019 0.046 -10000 0 -10000 0 0
KAT2B 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.012 0.12 -10000 0 -0.29 38 38
DCP1A 0.027 0.004 -10000 0 -10000 0 0
SKI 0.026 0.006 -10000 0 -10000 0 0
SERPINE1 0.023 0.079 -10000 0 -1.3 1 1
SMAD3/SMAD4/ATF2 0.003 0.12 -10000 0 -0.45 22 22
SMAD3/SMAD4/ATF3 -0.075 0.23 -10000 0 -0.51 103 103
SAP30 0.025 0.032 -10000 0 -0.67 1 1
Cbp/p300/PIAS3 0.049 0.044 -10000 0 -10000 0 0
JUN -0.2 0.4 0.3 1 -0.74 149 150
SMAD3/SMAD4/IRF7 0.024 0.079 -10000 0 -10000 0 0
TFE3 0.03 0.009 -10000 0 -10000 0 0
COL1A2 0.028 0.039 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.015 0.096 0.4 3 -10000 0 3
DLX1 -0.009 0.15 -10000 0 -0.64 26 26
TCF3 0.025 0.008 -10000 0 -10000 0 0
FOS -0.17 0.33 -10000 0 -0.73 125 125
SMAD3/SMAD4/Max 0.019 0.079 -10000 0 -0.25 3 3
Cbp/p300/SNIP1 0.043 0.036 -10000 0 -0.42 1 1
ZBTB17 0.027 0.006 -10000 0 -10000 0 0
LAMC1 0.011 0.059 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.022 0.079 -10000 0 -10000 0 0
IRF7 0.027 0.01 -10000 0 -10000 0 0
ESR1 -0.016 0.15 -10000 0 -0.64 23 23
HNF4A -0.009 0.024 -10000 0 -10000 0 0
MEF2C -0.013 0.1 0.39 3 -0.88 1 4
SMAD2-3/SMAD4 0.011 0.095 -10000 0 -0.29 2 2
Cbp/p300/Src-1 0.047 0.035 -10000 0 -10000 0 0
IGHV3OR16-13 0.001 0.034 -10000 0 -0.34 3 3
TGIF2/HDAC complex 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.03 0.011 -10000 0 -10000 0 0
SKIL 0.026 0.032 -10000 0 -0.67 1 1
HDAC1 0.026 0.005 -10000 0 -10000 0 0
HDAC2 0.026 0.004 -10000 0 -10000 0 0
SNIP1 0.024 0.032 -10000 0 -0.67 1 1
GCN5L2 0.004 0.013 0.2 1 -10000 0 1
SMAD3/SMAD4/TFE3 0.029 0.08 -10000 0 -10000 0 0
MSG1/HSC70 -0.063 0.07 -10000 0 -0.47 8 8
SMAD2 0.011 0.048 -10000 0 -10000 0 0
SMAD3 0.005 0.059 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.066 -10000 0 -0.36 8 8
SMAD2/SMAD2/SMAD4 0.003 0.036 0.23 3 -10000 0 3
NCOR1 0.025 0.007 -10000 0 -10000 0 0
NCOA2 -0.036 0.2 -10000 0 -0.67 44 44
NCOA1 0.027 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.029 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.046 0.093 -10000 0 -10000 0 0
IFNB1 -0.001 0.057 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.004 0.11 -10000 0 -0.62 2 2
CITED1 -0.097 0.079 -10000 0 -0.61 5 5
SMAD2-3/SMAD4/ARC105 0.012 0.085 -10000 0 -10000 0 0
RBL1 0.014 0.094 -10000 0 -0.67 9 9
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.013 0.034 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.048 0.068 -10000 0 -0.45 7 7
SMAD7 -0.088 0.25 -10000 0 -0.52 107 107
MYC/MIZ-1 0.027 0.083 -10000 0 -0.48 12 12
SMAD3/SMAD4 0.023 0.11 0.3 28 -0.52 1 29
IL10 -0.029 0.15 -10000 0 -0.52 33 33
PIASy/HDAC complex 0.017 0.02 -10000 0 -10000 0 0
PIAS3 0.027 0.008 -10000 0 -10000 0 0
CDK2 0.03 0.011 -10000 0 -10000 0 0
IL5 -0.022 0.1 -10000 0 -0.4 22 22
CDK4 0.031 0.012 -10000 0 -10000 0 0
PIAS4 0.017 0.02 -10000 0 -10000 0 0
ATF3 -0.12 0.28 -10000 0 -0.67 104 104
SMAD3/SMAD4/SP1 0.033 0.081 -10000 0 -10000 0 0
FOXG1 0.008 0.042 -10000 0 -0.67 1 1
FOXO3 0.015 0.007 -10000 0 -10000 0 0
FOXO1 0.015 0.008 -10000 0 -10000 0 0
FOXO4 0.015 0.008 -10000 0 -10000 0 0
heart looping -0.013 0.1 0.39 3 -0.87 1 4
CEBPB 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.004 0.14 -10000 0 -0.48 25 25
MYOD1 -0.013 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.016 0.08 -10000 0 -0.3 1 1
SMAD3/SMAD4/GATA3 0 0.14 -10000 0 -0.41 33 33
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.032 -10000 0 -0.67 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.032 0.11 -10000 0 -0.49 7 7
SMAD3/SMAD4/SP1-3 0.053 0.08 -10000 0 -10000 0 0
MED15 0.02 0.012 -10000 0 -10000 0 0
SP1 0.032 0.01 -10000 0 -10000 0 0
SIN3B 0.025 0.008 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.028 0.12 -10000 0 -0.34 6 6
ITGB5 0.015 0.059 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.031 0.034 -10000 0 -0.49 1 1
SMAD3/SMAD4/AR -0.18 0.26 -10000 0 -0.48 196 196
AR -0.26 0.34 -10000 0 -0.66 202 202
negative regulation of cell growth -0.022 0.12 -10000 0 -0.38 9 9
SMAD3/SMAD4/MYOD 0.016 0.08 -10000 0 -0.26 1 1
E2F5 0.025 0.032 -10000 0 -0.67 1 1
E2F4 0.026 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.027 0.097 -10000 0 -0.33 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.014 0.036 -10000 0 -10000 0 0
TFDP1 0.025 0.018 -10000 0 -0.35 1 1
SMAD3/SMAD4/AP1 -0.18 0.42 -10000 0 -0.76 149 149
SMAD3/SMAD4/RUNX2 0.015 0.097 -10000 0 -0.4 3 3
TGIF2 0.027 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.004 -10000 0 -10000 0 0
ATF2 -0.001 0.14 -10000 0 -0.65 20 20
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.03 0.074 -9999 0 -0.38 15 15
RGS9BP -0.013 0.16 -9999 0 -0.66 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.039 0.2 -9999 0 -0.65 46 46
mol:Na + 0.018 0.032 -9999 0 -10000 0 0
mol:ADP -0.043 0.15 -9999 0 -0.5 45 45
GNAT2 0.016 0.02 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.022 0.18 -9999 0 -0.44 70 70
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.028 0.01 -9999 0 -10000 0 0
GRK7 0.005 0.022 -9999 0 -10000 0 0
CNGB3 -0.008 0.017 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0.014 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.028 -9999 0 -10000 0 0
Cone PDE6 -0.004 0.16 -9999 0 -0.4 69 69
Cone Metarhodopsin II -0.01 0.12 -9999 0 -0.39 45 45
Na + (4 Units) 0.024 0.037 -9999 0 -10000 0 0
GNAT2/GDP -0.009 0.16 -9999 0 -0.38 69 69
GNB5 0.027 0.004 -9999 0 -10000 0 0
mol:GMP (4 units) -0.002 0.022 -9999 0 -10000 0 0
Cone Transducin 0.033 0.079 -9999 0 -0.4 15 15
SLC24A2 -0.007 0.03 -9999 0 -10000 0 0
GNB3/GNGT2 0.02 0.095 -9999 0 -0.5 15 15
GNB3 0.006 0.12 -9999 0 -0.67 14 14
GNAT2/GTP 0.018 0.006 -9999 0 -10000 0 0
CNGA3 0.008 0.049 -9999 0 -10000 0 0
ARR3 -0.002 0.02 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel 0.018 0.032 -9999 0 -10000 0 0
mol:Pi -0.022 0.18 -9999 0 -0.44 70 70
Cone CNG Channel 0.043 0.033 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.007 0.03 -9999 0 -10000 0 0
RGS9 -0.041 0.2 -9999 0 -0.67 46 46
PDE6C -0.005 0.02 -9999 0 -10000 0 0
GNGT2 0.023 0.034 -9999 0 -0.67 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H -0.003 0.02 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 0.02 0.12 -10000 0 -0.43 24 24
MAP4K1 0.009 0.078 -10000 0 -0.67 5 5
MAP3K8 0.016 0.085 -10000 0 -0.63 8 8
PRKCB 0.005 0.081 -10000 0 -0.67 5 5
DBNL 0.026 0.006 -10000 0 -10000 0 0
CRKL 0.02 0.012 -10000 0 -10000 0 0
MAP3K1 0.003 0.078 -10000 0 -0.31 23 23
JUN -0.083 0.21 0.37 1 -0.52 51 52
MAP3K7 0.003 0.078 -10000 0 -0.4 8 8
GRAP2 -0.017 0.14 -10000 0 -0.55 31 31
CRK 0.026 0.007 -10000 0 -10000 0 0
MAP2K4 -0.003 0.096 0.38 2 -0.37 16 18
LAT 0.021 0.058 -10000 0 -0.59 4 4
LCP2 0.024 0.019 -10000 0 -10000 0 0
MAPK8 -0.007 0.15 -10000 0 -0.61 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.007 0.082 -10000 0 -0.33 23 23
LAT/GRAP2/SLP76/HPK1/HIP-55 0.03 0.12 -10000 0 -0.42 23 23
p75(NTR)-mediated 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
Sortilin/TRAF6 0.036 0.036 -10000 0 -0.5 2 2
Necdin/E2F1 0 0.077 -10000 0 -0.55 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.057 0.092 -10000 0 -0.4 16 16
NGF (dimer)/p75(NTR)/BEX1 -0.18 0.25 -10000 0 -0.44 221 221
NT-4/5 (dimer)/p75(NTR) -0.011 0.13 -10000 0 -0.52 28 28
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.004 0.097 0.36 1 -0.4 19 20
IKBKG 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.01 0.1 -10000 0 -0.67 10 10
MGDIs/NGR/p75(NTR)/LINGO1 0.023 0.092 -10000 0 -0.44 16 16
FURIN 0.027 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.027 0.11 -10000 0 -0.44 24 24
LINGO1 0.02 0.031 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.031 0.028 -10000 0 -0.35 2 2
proBDNF (dimer) 0.01 0.1 -10000 0 -0.67 10 10
NTRK1 0.01 0.03 -10000 0 -10000 0 0
RTN4R 0.02 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.023 0.13 0.42 13 -0.53 5 18
IRAK1 0.025 0.008 -10000 0 -10000 0 0
SHC1 -0.006 0.09 -10000 0 -0.46 15 15
ARHGDIA 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.069 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.047 0.093 -10000 0 -0.42 16 16
MAGEH1 0.026 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.045 0.1 -10000 0 -0.42 20 20
Mammalian IAPs/DIABLO 0.045 0.094 -10000 0 -0.4 19 19
proNGF (dimer) 0.021 0.056 -10000 0 -0.67 3 3
MAGED1 0.026 0.007 -10000 0 -10000 0 0
APP 0.026 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.11 -10000 0 -0.64 13 13
ZNF274 0.025 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.012 0.085 -10000 0 -0.4 16 16
NGF 0.021 0.056 -10000 0 -0.67 3 3
cell cycle arrest 0.057 0.14 0.46 16 -0.38 16 32
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.07 -10000 0 -0.32 18 18
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.02 0.12 -10000 0 -0.45 30 30
NCSTN 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0.034 0.098 -10000 0 -0.44 18 18
PSENEN 0.025 0.007 -10000 0 -10000 0 0
mol:ceramide 0.003 0.092 -10000 0 -0.42 16 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.019 0.059 -10000 0 -0.38 4 4
p75(NTR)/beta APP 0.005 0.1 -10000 0 -0.5 16 16
BEX1 -0.28 0.34 -10000 0 -0.67 212 212
mol:GDP -0.018 0.088 -10000 0 -0.44 18 18
NGF (dimer) 0.038 0.11 -10000 0 -0.41 26 26
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.035 0.09 -10000 0 -0.41 16 16
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.03 0.083 -10000 0 -0.4 16 16
MYD88 0.027 0.004 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.034 0.098 -10000 0 -0.45 18 18
RHOB 0.027 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.005 0.053 -10000 0 -10000 0 0
NT3 (dimer) -0.018 0.16 -10000 0 -0.67 26 26
TP53 -0.003 0.098 0.35 1 -0.36 24 25
PRDM4 0.001 0.09 -10000 0 -0.42 16 16
BDNF (dimer) 0.007 0.14 -10000 0 -0.44 32 32
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.051 0.089 -10000 0 -0.4 16 16
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.047 0.097 -10000 0 -0.42 18 18
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.007 -10000 0 -10000 0 0
MAPK10 0.015 0.11 0.34 16 -0.4 14 30
DIABLO 0.027 0.005 -10000 0 -10000 0 0
SMPD2 0.003 0.093 -10000 0 -0.42 16 16
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.035 0.096 -10000 0 -0.46 16 16
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.027 -10000 0 -0.5 1 1
NT3 (dimer)/p75(NTR) -0.028 0.15 -10000 0 -0.51 41 41
MAPK8 0.01 0.12 0.34 15 -0.41 14 29
MAPK9 0.011 0.1 0.34 11 -0.39 13 24
APAF1 0.025 0.032 -10000 0 -0.67 1 1
NTF3 -0.018 0.16 -10000 0 -0.67 26 26
NTF4 0.004 0.11 -10000 0 -0.64 13 13
NDN 0.02 0.07 -10000 0 -0.67 5 5
RAC1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.052 0.086 -10000 0 -0.37 17 17
p75 CTF/Sortilin/TRAF6/NRIF 0.059 0.053 -10000 0 -0.52 3 3
RhoA-B-C/GTP 0.033 0.097 -10000 0 -0.44 18 18
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.049 0.11 -10000 0 -0.38 25 25
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.04 0.11 -10000 0 -0.4 26 26
PRKACB 0.025 0.032 -10000 0 -0.67 1 1
proBDNF (dimer)/p75 ECD 0.023 0.086 -10000 0 -0.5 12 12
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.07 0.14 0.48 12 -0.39 16 28
BAD 0.027 0.14 0.44 26 -0.4 15 41
RIPK2 0.027 0.005 -10000 0 -10000 0 0
NGFR -0.016 0.13 -10000 0 -0.67 16 16
CYCS 0.008 0.1 0.36 12 -0.4 16 28
ADAM17 0.024 0.045 -10000 0 -0.67 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.046 0.098 -10000 0 -0.42 18 18
BCL2L11 0.027 0.14 0.43 26 -0.4 15 41
BDNF (dimer)/p75(NTR) -0.008 0.12 -10000 0 -0.5 26 26
PI3K 0.046 0.1 -10000 0 -0.42 19 19
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.049 0.093 -10000 0 -0.42 16 16
NDNL2 0.027 0.004 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.002 0.11 -10000 0 -0.5 18 18
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.047 0.093 -10000 0 -0.42 16 16
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
PLG -0.014 0.019 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.005 0.098 -10000 0 -0.4 25 25
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
NGFRAP1 0.026 0.007 -10000 0 -10000 0 0
CASP3 0.03 0.14 0.43 26 -0.36 15 41
E2F1 -0.017 0.067 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.049 0.075 -10000 0 -0.46 3 3
NGF (dimer)/TRKA 0.028 0.049 -10000 0 -0.51 3 3
MMP7 -0.078 0.15 -10000 0 -0.66 25 25
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.055 0.096 -10000 0 -0.4 18 18
MMP3 -0.017 0.047 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.014 0.096 -10000 0 -0.57 5 5
IL1-mediated signaling events

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
UBC13/UEV1A 0.034 0.008 -9999 0 -10000 0 0
PRKCZ 0.026 0.006 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.013 0.064 -9999 0 -0.38 2 2
IRAK/TOLLIP 0.029 0.011 -9999 0 -10000 0 0
IKBKB 0.027 0.005 -9999 0 -10000 0 0
IKBKG 0.025 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.053 0.2 -9999 0 -0.54 68 68
IL1A -0.031 0.18 -9999 0 -0.66 38 38
IL1B -0.027 0.14 -9999 0 -0.51 39 39
IRAK/TRAF6/p62/Atypical PKCs 0.061 0.038 -9999 0 -0.36 2 2
IL1R2 -0.04 0.19 -9999 0 -0.65 39 39
IL1R1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.005 0.051 -9999 0 -10000 0 0
TOLLIP 0.026 0.005 -9999 0 -10000 0 0
TICAM2 0.019 0.071 -9999 0 -0.67 5 5
MAP3K3 0.026 0.007 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.003 -9999 0 -10000 0 0
IKK complex/ELKS 0.034 0.058 -9999 0 -10000 0 0
JUN -0.083 0.16 -9999 0 -0.37 108 108
MAP3K7 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.037 0.13 -9999 0 -0.38 38 38
IL1 alpha/IL1R1/IL1RAP/MYD88 0.035 0.13 -9999 0 -0.41 37 37
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.047 0.12 -9999 0 -0.38 37 37
IL1 beta fragment/IL1R1/IL1RAP 0.012 0.13 -9999 0 -0.42 38 38
NFKB1 0.027 0.004 -9999 0 -10000 0 0
MAPK8 -0.014 0.086 -9999 0 -0.44 16 16
IRAK1 0.015 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 0.01 0.087 -9999 0 -0.48 11 11
IRAK4 0.027 0.005 -9999 0 -10000 0 0
PRKCI 0.027 0.004 -9999 0 -10000 0 0
TRAF6 0.024 0.045 -9999 0 -0.67 2 2
PI3K 0.036 0.043 -9999 0 -0.5 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.07 -9999 0 -0.38 3 3
CHUK 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.012 0.13 -9999 0 -0.42 38 38
IL1 beta/IL1R2 -0.045 0.19 -9999 0 -0.49 68 68
IRAK/TRAF6/TAK1/TAB1/TAB2 0.035 0.029 -9999 0 -0.36 2 2
NF kappa B1 p50/RelA 0.024 0.11 -9999 0 -0.36 37 37
IRAK3 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.035 0.13 -9999 0 -0.38 40 40
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.006 0.086 -9999 0 -0.29 37 37
IL1 alpha/IL1R1/IL1RAP 0.019 0.13 -9999 0 -0.44 37 37
RELA 0.027 0.005 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.026 0.006 -9999 0 -10000 0 0
MYD88 0.027 0.004 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.042 0.033 -9999 0 -0.38 2 2
IL1RAP -0.011 0.065 -9999 0 -10000 0 0
UBE2N 0.027 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 -0.009 0.11 -9999 0 -0.38 11 11
CASP1 0.023 0.046 -9999 0 -0.67 2 2
IL1RN/IL1R2 -0.039 0.17 -9999 0 -0.54 44 44
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.027 0.13 -9999 0 -0.4 38 38
TMEM189-UBE2V1 -0.004 0.02 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.009 0.072 -9999 0 -0.36 2 2
PIK3CA 0.023 0.055 -9999 0 -0.67 3 3
IL1RN -0.011 0.11 -9999 0 -0.64 11 11
TRAF6/TAK1/TAB1/TAB2 0.045 0.03 -9999 0 -0.37 2 2
MAP2K6 0.006 0.061 -9999 0 -0.36 12 12
TCGA08_rtk_signaling

Figure S65.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S65.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.18 0.32 -10000 0 -0.66 149 149
HRAS 0.026 0.011 -10000 0 -10000 0 0
EGFR 0.021 0.063 -10000 0 -0.67 4 4
AKT 0.015 0.083 0.33 9 -0.21 1 10
FOXO3 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
AKT3 0.025 0.008 -10000 0 -10000 0 0
FOXO4 0.026 0.007 -10000 0 -10000 0 0
MET -0.028 0.071 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
PIK3CB 0.027 0.004 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
PIK3CG 0.009 0.1 -10000 0 -0.67 11 11
PIK3R3 0.027 0.005 -10000 0 -10000 0 0
PIK3R2 0.025 0.008 -10000 0 -10000 0 0
NF1 0.026 0.007 -10000 0 -10000 0 0
RAS -0.031 0.087 -10000 0 -0.17 131 131
ERBB2 0.026 0.007 -10000 0 -10000 0 0
proliferation/survival/translation -0.038 0.06 0.32 7 -0.2 1 8
PI3K -0.016 0.098 0.41 7 -0.18 47 54
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
FOXO 0.045 0.059 0.32 7 -10000 0 7
AKT2 0.025 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.35 1 1
Insulin 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
CBL/APS/CAP -0.003 0.14 -10000 0 -0.37 59 59
TC10/GTP 0.042 0.038 -10000 0 -0.35 3 3
Insulin Receptor/Insulin/IRS1/Shp2 0.001 0.16 -10000 0 -0.42 58 58
HRAS 0.026 0.011 -10000 0 -10000 0 0
APS homodimer 0.026 0.009 -10000 0 -10000 0 0
GRB14 0.009 0.11 -10000 0 -0.67 12 12
FOXO3 0 0.12 -10000 0 -0.65 15 15
AKT1 -0.026 0.14 0.34 6 -0.34 64 70
INSR 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.052 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.026 0.006 -10000 0 -10000 0 0
SORBS1 0.021 0.063 -10000 0 -0.67 4 4
CRK 0.026 0.007 -10000 0 -10000 0 0
PTPN1 0.017 0.027 -10000 0 -10000 0 0
CAV1 -0.035 0.14 -10000 0 -0.39 64 64
CBL/APS/CAP/Crk-II/C3G 0.066 0.048 -10000 0 -0.38 3 3
Insulin Receptor/Insulin/IRS1/NCK2 0.002 0.16 -10000 0 -0.41 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.14 -10000 0 -0.37 60 60
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.006 0.099 -10000 0 -0.4 7 7
RPS6KB1 -0.032 0.12 0.3 3 -0.66 2 5
PARD6A 0.026 0.006 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.017 0.036 -10000 0 -0.52 2 2
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.011 0.13 -10000 0 -0.56 3 3
HRAS/GTP -0.024 0.11 -10000 0 -0.33 46 46
Insulin Receptor 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.015 0.14 -10000 0 -0.39 46 46
PRKCI 0.013 0.073 -10000 0 -0.5 4 4
Insulin Receptor/Insulin/GRB14/PDK1 -0.025 0.14 -10000 0 -0.36 68 68
SHC1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.045 0.046 -10000 0 -0.43 2 2
PI3K 0.004 0.14 -10000 0 -0.38 60 60
NCK2 0.027 0.005 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
mol:H2O2 0.001 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.007 -10000 0 -10000 0 0
AKT2 -0.029 0.14 0.38 7 -0.4 12 19
PRKCZ 0.013 0.072 -10000 0 -0.52 4 4
SH2B2 0.026 0.009 -10000 0 -10000 0 0
SHC/SHIP -0.013 0.13 0.3 1 -0.37 48 49
F2RL2 -0.017 0.083 -10000 0 -0.67 3 3
TRIP10 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.041 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.064 0.031 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.06 0.044 -10000 0 -0.4 3 3
TC10/GDP 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.055 0.025 -10000 0 -10000 0 0
INPP5D -0.031 0.14 0.31 1 -0.39 58 59
SOS1 0.027 0.005 -10000 0 -10000 0 0
SGK1 -0.015 0.16 -10000 0 -0.83 16 16
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
IRS1 -0.057 0.23 -10000 0 -0.66 59 59
p62DOK/RasGAP 0.046 0.047 -10000 0 -0.44 2 2
INS 0.019 0.007 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.031 0.13 0.31 1 -0.38 58 59
GRB2 0.026 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.031 0.12 0.36 3 -0.57 3 6
PTPRA 0.029 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
TC10/GTP/CIP4 0.034 0.011 -10000 0 -10000 0 0
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.008 0.098 -10000 0 -0.29 46 46
Insulin Receptor/Insulin/IRS1 -0.011 0.15 -10000 0 -0.41 58 58
Insulin Receptor/Insulin/IRS3 0.033 0.012 -10000 0 -10000 0 0
Par3/Par6 0.059 0.039 -10000 0 -0.38 2 2
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.005 0.14 -10000 0 -0.69 11 11
HDAC1 0.024 0.008 -10000 0 -10000 0 0
AES 0.024 0.008 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.045 -10000 0 -0.67 2 2
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.055 -10000 0 -0.67 3 3
AP1 -0.13 0.24 -10000 0 -0.46 153 153
NCSTN 0.025 0.007 -10000 0 -10000 0 0
ADAM10 0.011 0.1 -10000 0 -0.67 11 11
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.028 0.076 -10000 0 -0.49 6 6
NICD/RBPSUH 0.005 0.14 -10000 0 -0.64 11 11
WIF1 -0.014 0.045 -10000 0 -10000 0 0
NOTCH1 -0.004 0.13 -10000 0 -0.48 29 29
PSENEN 0.026 0.007 -10000 0 -10000 0 0
KREMEN2 0.016 0.036 -10000 0 -10000 0 0
DKK1 0.001 0.062 -10000 0 -0.67 1 1
beta catenin/beta TrCP1 0.046 0.048 0.28 3 -10000 0 3
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
AXIN1 -0.006 0.083 0.38 1 -0.4 11 12
CtBP/CBP/TCF1/TLE1/AES 0.019 0.032 -10000 0 -0.29 3 3
PSEN1 0.027 0.005 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.67 125 125
JUN -0.12 0.28 -10000 0 -0.67 104 104
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.038 0.063 0.31 12 -10000 0 12
MAPK3 0.026 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.035 0.093 -10000 0 -0.44 17 17
HNF1A 0.026 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.004 -10000 0 -10000 0 0
MYC -0.019 0.25 -10000 0 -1.2 19 19
NKD1 0.006 0.11 -10000 0 -0.67 13 13
FZD1 0.026 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.005 0.14 -10000 0 -0.64 13 13
apoptosis -0.13 0.24 -10000 0 -0.45 153 153
Delta 1/NOTCHprecursor 0.005 0.14 -10000 0 -0.67 11 11
DLL1 0.025 0.032 -10000 0 -0.67 1 1
PPARD 0.021 0.082 -10000 0 -0.84 4 4
Gamma Secretase 0.07 0.03 -10000 0 -10000 0 0
APC 0 0.073 0.33 2 -0.55 3 5
DVL1 0.025 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.05 0.038 -10000 0 -0.49 1 1
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.013 0.007 -10000 0 -10000 0 0
CCND1 0.009 0.13 -10000 0 -0.85 10 10
WNT1 0.018 0.02 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.045 0.096 0.44 11 -0.47 2 13
DKK2 -0.003 0.13 -10000 0 -0.65 19 19
NOTCH1 precursor/DVL1 0.012 0.12 -10000 0 -0.59 11 11
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.026 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.005 0.14 -10000 0 -0.65 13 13
PPP2R5D 0.028 0.058 0.33 13 -0.32 3 16
MAPK1 0.02 0.012 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.065 0.018 -10000 0 -10000 0 0
RBPJ 0.027 0.008 -10000 0 -10000 0 0
CREBBP 0.028 0.008 -10000 0 -10000 0 0
Nectin adhesion 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
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
alphaV beta3 Integrin 0.025 0.086 -10000 0 -0.55 10 10
PTK2 0.011 0.14 -10000 0 -0.53 27 27
positive regulation of JNK cascade 0.014 0.096 -10000 0 -0.32 29 29
CDC42/GDP 0.032 0.14 0.44 1 -0.44 33 34
Rac1/GDP 0.031 0.13 0.28 1 -0.45 27 28
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.024 0.12 -10000 0 -0.4 29 29
nectin-3/I-afadin 0.01 0.12 -10000 0 -0.5 27 27
RAPGEF1 0.013 0.13 0.35 2 -0.5 27 29
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.011 0.15 -10000 0 -0.57 28 28
PDGFB-D/PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
TLN1 -0.004 0.06 -10000 0 -0.78 1 1
Rap1/GTP 0.012 0.094 -10000 0 -0.35 26 26
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.014 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.01 0.12 -10000 0 -0.5 27 27
PVR 0.025 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.025 0.007 -10000 0 -10000 0 0
mol:GDP 0.018 0.17 0.47 1 -0.54 34 35
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
PI3K 0.051 0.12 -10000 0 -0.42 26 26
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.02 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.01 0.11 -10000 0 -0.36 27 27
PVRL1 0.022 0.025 -10000 0 -10000 0 0
PVRL3 -0.012 0.16 -10000 0 -0.66 28 28
PVRL2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
CLDN1 -0.1 0.094 -10000 0 -0.61 10 10
JAM-A/CLDN1 0.042 0.13 -10000 0 -0.41 32 32
SRC 0.007 0.16 -10000 0 -0.64 28 28
ITGB3 0.012 0.095 -10000 0 -0.64 10 10
nectin-1(dimer)/I-afadin/I-afadin 0.036 0.02 -10000 0 -10000 0 0
FARP2 0.02 0.16 -10000 0 -0.54 32 32
RAC1 0.026 0.006 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.024 0.11 -10000 0 -0.44 27 27
nectin-1/I-afadin 0.036 0.02 -10000 0 -10000 0 0
nectin-2/I-afadin 0.038 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.026 0.11 -10000 0 -0.44 27 27
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.008 -10000 0 -10000 0 0
F11R 0.025 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.014 0.096 -10000 0 -0.32 29 29
alphaV/beta3 Integrin/Talin 0.024 0.1 -10000 0 -0.56 10 10
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
PIP5K1C -0.002 0.065 -10000 0 -0.24 27 27
VAV2 0.001 0.18 0.37 1 -0.59 31 32
RAP1/GDP 0.035 0.12 0.28 3 -0.42 28 31
ITGAV 0.024 0.045 -10000 0 -0.67 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.024 0.11 -10000 0 -0.44 27 27
nectin-3(dimer)/I-afadin/I-afadin 0.01 0.12 -10000 0 -0.5 27 27
Rac1/GTP 0.016 0.13 -10000 0 -0.44 27 27
PTPRM 0.001 0.071 -10000 0 -0.27 27 27
E-cadherin/beta catenin/alpha catenin 0.073 0.027 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.02 0.012 -10000 0 -10000 0 0
HDAC4 0.027 0.005 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.013 0.024 0.5 1 -10000 0 1
CDKN1A -0.007 0.012 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
BAX 0.025 0.01 -10000 0 -10000 0 0
FOXO3 -0.004 0.007 -10000 0 -10000 0 0
FOXO1 0.026 0.007 -10000 0 -10000 0 0
FOXO4 0.014 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
TAT 0.011 0.024 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.009 -10000 0 -10000 0 0
PPARGC1A -0.28 0.34 -10000 0 -0.67 213 213
FHL2 -0.029 0.19 -10000 0 -0.67 39 39
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.026 0.03 -10000 0 -0.51 1 1
HIST2H4A 0.013 0.024 -10000 0 -0.51 1 1
SIRT1/FOXO3a 0.038 0.051 -10000 0 -0.43 1 1
SIRT1 0.022 0.032 -10000 0 -0.67 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.046 0.028 -10000 0 -0.44 1 1
SIRT1/Histone H1b -0.005 0.069 -10000 0 -0.31 10 10
apoptosis -0.037 0.032 0.44 1 -10000 0 1
SIRT1/PGC1A -0.17 0.24 -10000 0 -0.44 213 213
p53/SIRT1 0.028 0.027 -10000 0 -0.51 1 1
SIRT1/FOXO4 -0.004 0.064 -10000 0 -0.23 14 14
FOXO1/FHL2/SIRT1 0.009 0.12 -10000 0 -0.4 40 40
HIST1H1E 0.008 0.044 -10000 0 -0.35 7 7
SIRT1/p300 0.026 0.03 -10000 0 -0.51 1 1
muscle cell differentiation -0.029 0.028 0.44 1 -10000 0 1
TP53 0.022 0.007 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.037 0.033 -10000 0 -0.44 1 1
CREBBP 0.026 0.006 -10000 0 -10000 0 0
MEF2D 0.025 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.031 0.029 -10000 0 -0.51 1 1
ACSS2 0.013 0.024 -10000 0 -0.51 1 1
SIRT1/PCAF/MYOD 0.029 0.028 -10000 0 -0.44 1 1
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.025 0.032 -10000 0 -0.67 1 1
Caspase 8 (4 units) 0.025 0.088 -10000 0 -0.41 6 6
NEF -0.011 0.058 -10000 0 -0.23 25 25
NFKBIA 0.021 0.032 -10000 0 -10000 0 0
BIRC3 -0.004 0.15 -10000 0 -0.65 23 23
CYCS -0.006 0.089 0.22 1 -0.38 9 10
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CD247 -0.011 0.15 -10000 0 -0.43 38 38
MAP2K7 0.001 0.16 -10000 0 -0.63 22 22
protein ubiquitination 0.009 0.098 0.36 6 -0.34 4 10
CRADD 0.027 0.005 -10000 0 -10000 0 0
DAXX 0.027 0.003 -10000 0 -10000 0 0
FAS 0.027 0.005 -10000 0 -10000 0 0
BID -0.007 0.095 0.22 1 -0.31 30 31
NF-kappa-B/RelA/I kappa B alpha 0.043 0.079 -10000 0 -0.32 19 19
TRADD 0.026 0.006 -10000 0 -10000 0 0
MAP3K5 0.026 0.032 -10000 0 -0.67 1 1
CFLAR 0.027 0.005 -10000 0 -10000 0 0
FADD 0.027 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.043 0.079 -10000 0 -0.32 19 19
MAPK8 -0.004 0.16 0.35 1 -0.59 23 24
APAF1 0.025 0.032 -10000 0 -0.67 1 1
TRAF1 0.025 0.008 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.002 0.094 -10000 0 -0.32 30 30
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0 0.11 -10000 0 -0.36 18 18
CHUK 0.004 0.096 0.28 3 -0.37 4 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.075 0.03 -10000 0 -0.38 1 1
TCRz/NEF -0.018 0.14 -10000 0 -0.45 41 41
TNF -0.058 0.22 -10000 0 -0.67 57 57
FASLG -0.042 0.21 -10000 0 -0.74 38 38
NFKB1 0.021 0.033 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.005 0.16 -10000 0 -0.44 58 58
CASP6 0.04 0.095 -10000 0 -0.66 5 5
CASP7 0.011 0.15 0.36 3 -0.57 26 29
RELA 0.021 0.033 -10000 0 -0.18 3 3
CASP2 0.026 0.006 -10000 0 -10000 0 0
CASP3 0.011 0.15 0.35 1 -0.56 26 27
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.026 -10000 0 -0.5 1 1
CASP8 0.027 0.005 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
MAP3K14 0.003 0.1 -10000 0 -0.38 7 7
APAF-1/Caspase 9 -0.001 0.12 -10000 0 -0.47 22 22
BCL2 -0.025 0.16 0.34 1 -0.57 23 24
Neurotrophic factor-mediated Trk receptor signaling

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 0.02 0.012 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.002 0.065 -10000 0 -0.23 21 21
NT3 (dimer)/TRKC -0.022 0.14 -10000 0 -0.5 37 37
NT3 (dimer)/TRKB 0.004 0.15 -10000 0 -0.44 45 45
SHC/Grb2/SOS1/GAB1/PI3K 0.03 0.028 -10000 0 -0.28 3 3
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.01 0.1 -10000 0 -0.67 10 10
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.01 0.03 -10000 0 -10000 0 0
NTRK2 0.019 0.065 -10000 0 -0.61 5 5
NTRK3 -0.011 0.11 -10000 0 -0.64 12 12
NT-4/5 (dimer)/TRKB 0.014 0.13 -10000 0 -0.45 32 32
neuron apoptosis -0.011 0.11 0.39 16 -10000 0 16
SHC 2-3/Grb2 0.011 0.12 -10000 0 -0.42 16 16
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.002 0.1 -10000 0 -0.55 10 10
SHC3 -0.005 0.12 -10000 0 -0.46 20 20
STAT3 (dimer) 0.03 0.015 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.002 0.14 -10000 0 -0.43 40 40
RIN/GDP -0.004 0.078 0.3 7 -0.25 6 13
GIPC1 0.025 0.008 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
DNAJA3 -0.005 0.071 -10000 0 -0.38 15 15
RIN/GTP 0.013 0.004 -10000 0 -10000 0 0
CCND1 0.02 0.017 -10000 0 -10000 0 0
MAGED1 0.026 0.007 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.004 0.11 -10000 0 -0.64 13 13
SHC/GRB2/SOS1 0.048 0.02 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.038 0.064 -10000 0 -0.44 7 7
TRKA/NEDD4-2 0.031 0.023 -10000 0 -10000 0 0
ELMO1 -0.24 0.34 -10000 0 -0.67 186 186
RhoG/GTP/ELMO1/DOCK1 -0.15 0.23 -10000 0 -0.44 186 186
NGF 0.021 0.056 -10000 0 -0.67 3 3
HRAS 0.026 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.055 -10000 0 -0.67 3 3
GAB2 0.027 0.005 -10000 0 -10000 0 0
RIT2 -0.009 0.016 -10000 0 -10000 0 0
RIT1 0.025 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
DNM1 0.004 0.12 -10000 0 -0.61 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.12 0.19 -10000 0 -0.35 186 186
mol:GDP -0.013 0.1 0.35 8 -0.35 9 17
NGF (dimer) 0.021 0.056 -10000 0 -0.67 3 3
RhoG/GDP -0.18 0.25 -10000 0 -0.5 186 186
RIT1/GDP -0.003 0.076 0.3 7 -0.26 4 11
TIAM1 -0.057 0.078 -10000 0 -0.67 1 1
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.037 0.088 -10000 0 -0.47 13 13
KIDINS220/CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
SHC/RasGAP 0.037 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.053 0.025 -10000 0 -0.44 1 1
SHC/GRB2/SOS1/GAB1 0.06 0.026 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.005 -10000 0 -10000 0 0
NT3 (dimer) -0.018 0.16 -10000 0 -0.67 26 26
RAP1/GDP -0.005 0.058 -10000 0 -0.23 3 3
KIDINS220/CRKL 0.02 0.012 -10000 0 -10000 0 0
BDNF (dimer) 0.01 0.1 -10000 0 -0.67 10 10
ubiquitin-dependent protein catabolic process 0.045 0.043 -10000 0 -0.44 3 3
Schwann cell development -0.03 0.029 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.065 0.021 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.02 0.037 -10000 0 -0.25 4 4
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.007 0.12 -10000 0 -0.37 43 43
ABL1 0.025 0.008 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.1 -10000 0 -0.5 6 6
STAT3 0.03 0.015 -10000 0 -10000 0 0
axon guidance -0.016 0.11 -10000 0 -0.35 43 43
MAPK3 0.018 0.069 -10000 0 -0.4 7 7
MAPK1 0.01 0.063 -10000 0 -0.4 7 7
CDC42/GDP -0.001 0.079 0.3 7 -0.26 4 11
NTF3 -0.018 0.16 -10000 0 -0.67 26 26
NTF4 0.004 0.11 -10000 0 -0.64 13 13
NGF (dimer)/TRKA/FAIM 0.046 0.043 -10000 0 -0.44 3 3
PI3K 0.036 0.043 -10000 0 -0.5 3 3
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.027 0.004 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
RASGRF1 -0.041 0.083 -10000 0 -0.4 19 19
SOS1 0.027 0.005 -10000 0 -10000 0 0
MCF2L -0.028 0.12 -10000 0 -0.43 36 36
RGS19 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.07 -10000 0 -0.44 3 3
Rac1/GDP -0.004 0.068 0.22 1 -0.24 4 5
NGF (dimer)/TRKA/GRIT 0.026 0.042 -10000 0 -0.44 3 3
neuron projection morphogenesis 0.023 0.088 -10000 0 -0.7 2 2
NGF (dimer)/TRKA/NEDD4-2 0.046 0.043 -10000 0 -0.44 3 3
MAP2K1 0.039 0.058 0.36 4 -10000 0 4
NGFR -0.016 0.13 -10000 0 -0.67 16 16
NGF (dimer)/TRKA/GIPC/GAIP 0.016 0.071 -10000 0 -0.34 15 15
RAS family/GTP/PI3K 0.026 0.027 -10000 0 -0.3 3 3
FRS2 family/SHP2/GRB2/SOS1 0.074 0.032 -10000 0 -0.38 1 1
NRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
MAPKKK cascade 0.021 0.074 -10000 0 -0.54 6 6
RASA1 0.026 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.03 0.024 -10000 0 -10000 0 0
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.048 0.084 -10000 0 -0.44 12 12
NGF (dimer)/TRKA/p62/Atypical PKCs 0.068 0.045 -10000 0 -0.38 3 3
MATK 0.017 0.068 -10000 0 -0.61 5 5
NEDD4L 0.027 0.004 -10000 0 -10000 0 0
RAS family/GDP -0.019 0.042 -10000 0 -0.2 1 1
NGF (dimer)/TRKA 0 0.077 -10000 0 -0.39 16 16
Rac1/GTP -0.11 0.12 -10000 0 -0.26 164 164
FRS2 family/SHP2/CRK family 0.057 0.042 -10000 0 -0.38 1 1
FOXM1 transcription factor network

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
NFATC3 -0.009 0.31 0.79 2 -0.93 11 13
PLK1 0.03 0.095 -10000 0 -0.81 5 5
BIRC5 0.025 0.1 -10000 0 -1.1 3 3
HSPA1B -0.015 0.31 -10000 0 -0.93 11 11
MAP2K1 0.026 0.045 -10000 0 -10000 0 0
BRCA2 -0.018 0.32 0.8 1 -0.99 14 15
FOXM1 -0.041 0.34 -10000 0 -0.97 20 20
XRCC1 -0.006 0.31 -10000 0 -0.92 11 11
FOXM1B/p19 -0.039 0.33 -10000 0 -0.9 24 24
Cyclin D1/CDK4 0.007 0.29 -10000 0 -0.83 11 11
CDC2 -0.019 0.32 -10000 0 -0.87 20 20
TGFA -0.007 0.29 -10000 0 -0.82 11 11
SKP2 -0.011 0.33 0.79 2 -0.98 14 16
CCNE1 0.027 0.011 -10000 0 -10000 0 0
CKS1B -0.004 0.31 0.79 1 -0.92 11 12
RB1 0.029 0.19 -10000 0 -0.71 8 8
FOXM1C/SP1 -0.022 0.33 -10000 0 -0.95 19 19
AURKB 0.01 0.13 -10000 0 -0.86 8 8
CENPF -0.005 0.31 0.79 1 -0.92 11 12
CDK4 0.028 0.019 -10000 0 -10000 0 0
MYC -0.023 0.31 -10000 0 -0.94 16 16
CHEK2 0.02 0.04 -10000 0 -10000 0 0
ONECUT1 -0.005 0.3 -10000 0 -0.89 11 11
CDKN2A -0.034 0.071 -10000 0 -10000 0 0
LAMA4 -0.015 0.31 -10000 0 -0.93 11 11
FOXM1B/HNF6 -0.011 0.32 -10000 0 -1 12 12
FOS -0.22 0.6 0.79 2 -1.2 129 131
SP1 0.026 0.009 -10000 0 -10000 0 0
CDC25B -0.01 0.31 0.8 1 -0.93 11 12
response to radiation 0.007 0.026 -10000 0 -10000 0 0
CENPB -0.01 0.31 0.8 1 -0.93 11 12
CENPA -0.023 0.32 -10000 0 -0.96 14 14
NEK2 -0.005 0.31 0.79 1 -0.92 11 12
HIST1H2BA -0.021 0.31 -10000 0 -0.94 11 11
CCNA2 0.026 0.021 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
CCNB1/CDK1 -0.025 0.33 -10000 0 -1 13 13
CCNB2 -0.017 0.31 -10000 0 -0.93 11 11
CCNB1 -0.016 0.32 0.68 2 -0.94 13 15
ETV5 -0.015 0.31 -10000 0 -0.93 11 11
ESR1 -0.052 0.38 -10000 0 -1.1 28 28
CCND1 0.001 0.3 -10000 0 -0.85 11 11
GSK3A 0.022 0.038 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.052 0.043 -10000 0 -10000 0 0
CDK2 0.028 0.009 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.01 0.032 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.031 0.31 -10000 0 -0.89 18 18
GAS1 -0.16 0.55 0.8 1 -1.2 98 99
MMP2 -0.017 0.34 0.79 2 -1.2 12 14
RB1/FOXM1C 0.001 0.29 -10000 0 -0.89 11 11
CREBBP 0.026 0.006 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.022 0.083 0.32 5 -0.39 11 16
ACTA1 0.01 0.098 0.34 6 -0.43 12 18
NUMA1 0.017 0.093 0.28 6 -0.46 12 18
SPTAN1 0.008 0.094 0.35 6 -0.44 11 17
LIMK1 0.014 0.1 0.45 8 -0.47 9 17
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BIRC2 0.027 0.005 -10000 0 -10000 0 0
BAX 0.025 0.01 -10000 0 -10000 0 0
CASP10 -0.009 0.081 -10000 0 -0.5 11 11
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.007 -10000 0 -10000 0 0
PTK2 0.015 0.095 0.39 2 -0.41 16 18
DIABLO 0.027 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes 0.008 0.093 0.35 6 -0.43 11 17
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
GSN 0.008 0.095 0.34 6 -0.44 11 17
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.044 0.22 -10000 0 -0.61 63 63
BID -0.011 0.059 -10000 0 -0.32 11 11
MAP3K1 0.018 0.041 0.27 3 -10000 0 3
TRADD 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.027 -10000 0 -0.5 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.011 0.1 0.45 8 -0.47 9 17
CASP9 0.026 0.006 -10000 0 -10000 0 0
DNA repair -0.017 0.063 0.5 3 -0.21 19 22
neuron apoptosis 0.009 0.11 -10000 0 -0.55 15 15
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.017 0.1 0.35 4 -0.48 12 16
APAF1 0.025 0.032 -10000 0 -0.67 1 1
CASP6 0.02 0.084 0.34 4 -0.57 4 8
TRAF2 0.025 0.009 -10000 0 -10000 0 0
ICAD/CAD 0.013 0.1 0.4 13 -0.46 9 22
CASP7 0.007 0.098 0.31 22 -0.45 8 30
KRT18 0.021 0.04 -10000 0 -0.44 2 2
apoptosis 0.017 0.097 0.48 4 -0.42 11 15
DFFA 0.01 0.097 0.34 7 -0.44 11 18
DFFB 0.01 0.097 0.34 7 -0.44 11 18
PARP1 0.017 0.064 0.21 19 -0.51 3 22
actin filament polymerization -0.019 0.12 0.44 9 -0.54 11 20
TNF -0.058 0.22 -10000 0 -0.67 57 57
CYCS 0 0.047 0.24 3 -0.22 9 12
SATB1 0.02 0.084 0.52 2 -0.53 4 6
SLK 0.006 0.098 0.37 5 -0.43 13 18
p15 BID/BAX -0.009 0.068 -10000 0 -0.29 11 11
CASP2 -0.015 0.1 0.21 3 -0.37 18 21
JNK cascade -0.018 0.04 -10000 0 -0.27 3 3
CASP3 0.007 0.098 0.32 7 -0.45 12 19
LMNB2 0.005 0.11 0.36 9 -0.42 11 20
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.045 0.094 -10000 0 -0.4 19 19
negative regulation of DNA binding -0.044 0.22 -10000 0 -0.6 63 63
stress fiber formation 0.006 0.097 0.37 5 -0.43 13 18
GZMB -0.005 0.094 -10000 0 -0.58 11 11
CASP1 0.015 0.026 -10000 0 -0.39 2 2
LMNB1 0.019 0.088 0.33 11 -0.31 2 13
APP 0.008 0.11 -10000 0 -0.56 15 15
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to stress 0 0.001 -10000 0 -10000 0 0
CASP8 0.009 0.002 -10000 0 -10000 0 0
VIM 0.019 0.09 0.37 5 -0.42 10 15
LMNA 0.014 0.098 0.35 11 -0.42 5 16
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.014 0.11 -10000 0 -0.4 16 16
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.016 0.1 0.41 10 -0.49 8 18
APAF-1/Caspase 9 0.013 0.063 -10000 0 -0.55 4 4
nuclear fragmentation during apoptosis 0.017 0.092 0.28 6 -0.45 12 18
CFL2 0.018 0.12 0.54 11 -0.45 9 20
GAS2 0.004 0.098 0.3 7 -0.44 13 20
positive regulation of apoptosis 0.015 0.1 0.36 9 -0.37 8 17
PRF1 0.017 0.078 -10000 0 -0.67 6 6
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF 0 0.085 -10000 0 -0.33 3 3
epithelial cell differentiation -0.004 0.098 -10000 0 -0.41 6 6
ITCH 0.036 0.019 -10000 0 -10000 0 0
WWP1 -0.008 0.068 -10000 0 -0.38 1 1
FYN 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.021 0.063 -10000 0 -0.67 4 4
PRL -0.012 0.014 -10000 0 -10000 0 0
neuron projection morphogenesis -0.018 0.11 0.34 3 -0.45 7 10
PTPRZ1 0.002 0.1 -10000 0 -0.67 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC 0.002 0.13 -10000 0 -0.37 36 36
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.037 0.14 -10000 0 -0.42 44 44
ADAM17 0.033 0.049 -10000 0 -0.67 2 2
ErbB4/ErbB4 -0.013 0.086 -10000 0 -0.38 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.028 0.14 -10000 0 -0.44 35 35
NCOR1 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.024 0.13 -10000 0 -0.39 44 44
GRIN2B -0.034 0.12 0.25 2 -0.38 44 46
ErbB4/ErbB2/betacellulin 0.001 0.11 -10000 0 -0.48 15 15
STAT1 0.023 0.023 -10000 0 -10000 0 0
HBEGF 0.018 0.034 -10000 0 -10000 0 0
PRLR -0.015 0.16 -10000 0 -0.67 25 25
E4ICDs/ETO2 -0.001 0.085 -10000 0 -0.39 4 4
axon guidance -0.005 0.071 -10000 0 -0.4 2 2
NEDD4 0.034 0.048 -10000 0 -0.66 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0 0.12 -10000 0 -0.5 25 25
CBFA2T3 0.024 0.033 -10000 0 -0.67 1 1
ErbB4/ErbB2/HBEGF 0.012 0.072 -10000 0 -0.4 3 3
MAPK3 -0.013 0.12 -10000 0 -0.47 7 7
STAT1 (dimer) 0.001 0.084 -10000 0 -0.32 3 3
MAPK1 -0.017 0.11 -10000 0 -0.36 25 25
JAK2 0.024 0.025 -10000 0 -0.35 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.03 0.13 -10000 0 -0.39 41 41
NRG1 -0.026 0.16 -10000 0 -0.52 43 43
NRG3 -0.022 0.18 -10000 0 -0.64 35 35
NRG2 -0.052 0.22 -10000 0 -0.67 53 53
NRG4 0.021 0.02 -10000 0 -10000 0 0
heart development -0.005 0.071 -10000 0 -0.4 2 2
neural crest cell migration -0.03 0.12 -10000 0 -0.39 41 41
ERBB2 0.019 0.035 -10000 0 -0.49 2 2
WWOX/E4ICDs -0.002 0.088 -10000 0 -0.46 3 3
SHC1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.011 0.094 -10000 0 -0.51 4 4
apoptosis 0.021 0.13 0.4 35 -10000 0 35
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.047 0.16 -10000 0 -0.43 56 56
ErbB4/ErbB2/epiregulin 0.013 0.084 -10000 0 -0.42 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.013 0.12 -10000 0 -0.51 16 16
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.006 0.12 -10000 0 -0.36 27 27
MDM2 -0.011 0.077 0.26 2 -0.41 1 3
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.021 0.13 -10000 0 -0.4 42 42
STAT5A 0 0.072 -10000 0 -0.45 1 1
ErbB4/EGFR/neuregulin 1 beta -0.026 0.14 -10000 0 -0.41 46 46
DLG4 0.026 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.035 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.001 0.075 -10000 0 -0.3 3 3
STAT5A (dimer) 0.005 0.11 -10000 0 -0.44 6 6
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.073 -10000 0 -0.38 2 2
LRIG1 0.016 0.085 -10000 0 -0.63 8 8
EREG -0.049 0.069 -10000 0 -10000 0 0
BTC 0.005 0.12 -10000 0 -0.67 15 15
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.005 0.07 -10000 0 -0.4 2 2
ERBB4 -0.013 0.087 -10000 0 -0.38 2 2
STAT5B 0.026 0.007 -10000 0 -10000 0 0
YAP1 0.005 0.066 -10000 0 -0.47 8 8
GRB2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.011 0.071 -10000 0 -0.39 3 3
glial cell differentiation 0.001 0.074 0.3 3 -10000 0 3
WWOX 0.025 0.032 -10000 0 -0.67 1 1
cell proliferation -0.024 0.14 -10000 0 -0.48 17 17
Syndecan-3-mediated signaling events

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
CTTN 0.027 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.027 0.11 -9999 0 -0.34 35 35
Syndecan-3/Neurocan 0.004 0.096 -9999 0 -0.36 29 29
POMC -0.11 0.28 -9999 0 -0.66 98 98
EGFR 0.021 0.063 -9999 0 -0.67 4 4
Syndecan-3/EGFR 0.028 0.04 -9999 0 -0.33 5 5
AGRP 0.003 0.033 -9999 0 -10000 0 0
NCSTN 0.025 0.007 -9999 0 -10000 0 0
PSENEN 0.025 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.027 0.004 -9999 0 -10000 0 0
APH1A 0.025 0.007 -9999 0 -10000 0 0
NCAN -0.026 0.18 -9999 0 -0.66 34 34
long-term memory 0.05 0.029 -9999 0 -0.27 1 1
Syndecan-3/IL8 0.031 0.064 -9999 0 -0.36 10 10
PSEN1 0.027 0.005 -9999 0 -10000 0 0
Src/Cortactin 0.039 0.01 -9999 0 -10000 0 0
FYN 0.027 0.004 -9999 0 -10000 0 0
limb bud formation 0.015 0.006 -9999 0 -10000 0 0
MC4R 0 0.026 -9999 0 -10000 0 0
SRC 0.026 0.008 -9999 0 -10000 0 0
PTN -0.037 0.2 -9999 0 -0.67 44 44
FGFR/FGF/Syndecan-3 0.015 0.006 -9999 0 -10000 0 0
neuron projection morphogenesis -0.023 0.13 -9999 0 -0.33 60 60
Syndecan-3/AgRP 0.031 0.024 -9999 0 -0.31 1 1
Syndecan-3/AgRP/MC4R 0.046 0.029 -9999 0 -0.29 1 1
Fyn/Cortactin 0.039 0.009 -9999 0 -10000 0 0
SDC3 0.015 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.031 0.064 -9999 0 -0.35 10 10
IL8 -0.023 0.11 -9999 0 -0.67 10 10
Syndecan-3/Fyn/Cortactin 0.052 0.03 -9999 0 -0.28 1 1
Syndecan-3/CASK 0.011 0.024 -9999 0 -0.3 1 1
alpha-MSH/MC4R -0.075 0.22 -9999 0 -0.5 97 97
Gamma Secretase 0.069 0.03 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.002 0.1 -10000 0 -0.64 7 7
UGCG -0.057 0.22 -10000 0 -0.64 56 56
AKT1/mTOR/p70S6K/Hsp90/TERT 0.014 0.14 0.46 4 -0.42 21 25
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.058 0.22 -10000 0 -0.62 58 58
mol:DAG -0.01 0.12 -10000 0 -0.77 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.17 -10000 0 -0.44 46 46
FRAP1 -0.015 0.19 0.44 2 -0.51 46 48
FOXO3 -0.002 0.17 0.44 2 -0.64 19 21
AKT1 -0.007 0.18 -10000 0 -0.7 20 20
GAB2 0.027 0.006 -10000 0 -10000 0 0
SMPD1 0.009 0.086 -10000 0 -0.77 5 5
SGMS1 0.001 0.11 -10000 0 -0.64 12 12
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.007 0.036 -10000 0 -0.44 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.029 0.19 0.33 5 -0.53 39 44
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.039 0.045 -10000 0 -0.51 3 3
RPS6KB1 0.016 0.067 -10000 0 -0.82 2 2
mol:sphingomyelin -0.01 0.12 -10000 0 -0.77 12 12
natural killer cell activation 0 0.002 -10000 0 -0.011 7 7
JAK3 -0.01 0.064 -10000 0 -10000 0 0
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.028 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC -0.005 0.21 0.47 4 -0.94 17 21
MYB 0.004 0.18 -10000 0 -1.2 10 10
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.004 0.15 -10000 0 -0.55 21 21
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.043 0.067 -10000 0 -0.74 2 2
mol:PI-3-4-5-P3 -0.003 0.14 -10000 0 -0.54 21 21
Rac1/GDP 0.023 0.036 -10000 0 -0.41 3 3
T cell proliferation -0.003 0.13 -10000 0 -0.52 19 19
SHC1 0.025 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.01 -10000 0 -0.066 10 10
PRKCZ -0.004 0.14 -10000 0 -0.54 19 19
NF kappa B1 p50/RelA 0.012 0.17 -10000 0 -0.51 26 26
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.11 -10000 0 -0.56 12 12
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL2RA -0.014 0.15 -10000 0 -0.63 25 25
IL2RB 0.005 0.091 -10000 0 -0.57 10 10
TERT -0.005 0.022 -10000 0 -10000 0 0
E2F1 0.024 0.068 -10000 0 -0.43 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
RPS6 0.025 0.008 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.031 10 -10000 0 10
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
IL2RG -0.01 0.14 -10000 0 -0.62 21 21
actin cytoskeleton organization -0.003 0.13 -10000 0 -0.52 19 19
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.018 0.013 -10000 0 -10000 0 0
PIK3CA 0.024 0.055 -10000 0 -0.67 3 3
Rac1/GTP 0.048 0.042 -10000 0 -0.39 3 3
LCK 0.014 0.082 -10000 0 -0.67 6 6
BCL2 -0.04 0.27 0.47 4 -0.79 49 53
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.006 0.14 -10000 0 -0.37 59 59
MAPK9 0.008 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.021 -10000 0 -10000 0 0
GNB1/GNG2 0.034 0.023 -10000 0 -0.44 1 1
GNB1 0.026 0.006 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0.001 -10000 0 -10000 0 0
Gs family/GTP -0.034 0.14 -10000 0 -0.39 61 61
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 0.032 0.096 61 -10000 0 61
GNAL -0.059 0.23 -10000 0 -0.65 61 61
GNG2 0.025 0.032 -10000 0 -0.67 1 1
CRH 0 0.038 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0.056 -10000 0 -0.38 10 10
MAPK11 0.006 0.004 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.092 -10000 0 -0.61 10 10
ANTXR2 0.023 0.055 -10000 0 -0.67 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.081 13 13
monocyte activation -0.037 0.16 -10000 0 -0.44 63 63
MAP2K2 -0.009 0.12 -10000 0 -0.54 22 22
MAP2K1 -0.001 0.012 -10000 0 -10000 0 0
MAP2K7 -0.001 0.012 -10000 0 -10000 0 0
MAP2K6 -0.009 0.056 -10000 0 -0.39 10 10
CYAA -0.007 0.057 -10000 0 -0.38 11 11
MAP2K4 -0.001 0.013 0.11 1 -10000 0 1
IL1B -0.026 0.1 0.18 1 -0.35 40 41
Channel 0.024 0.066 -10000 0 -0.4 11 11
NLRP1 -0.002 0.027 0.11 1 -0.38 2 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.011 0.029 -10000 0 -0.51 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.081 13 -10000 0 13
MAPK3 -0.001 0.012 -10000 0 -10000 0 0
MAPK1 -0.001 0.012 -10000 0 -10000 0 0
PGR -0.011 0.055 -10000 0 -0.32 13 13
PA/Cellular Receptors 0.024 0.072 -10000 0 -0.4 13 13
apoptosis -0.002 0.013 -10000 0 -0.081 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.023 0.062 -10000 0 -0.34 13 13
macrophage activation -0.001 0.011 -10000 0 -10000 0 0
TNF -0.058 0.22 -10000 0 -0.67 57 57
VCAM1 -0.038 0.16 -10000 0 -0.44 63 63
platelet activation 0.011 0.029 -10000 0 -0.51 1 1
MAPKKK cascade -0.003 0.029 0.16 2 -0.13 8 10
IL18 -0.009 0.06 -10000 0 -0.32 13 13
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.081 13 13
LEF -0.002 0.013 -10000 0 -0.082 13 13
CASP1 0.001 0.018 -10000 0 -0.096 14 14
mol:cAMP 0.011 0.029 -10000 0 -0.51 1 1
necrosis -0.002 0.013 -10000 0 -0.081 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.023 0.063 -10000 0 -0.38 11 11
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.008 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.026 0.009 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.02 0.049 -10000 0 -0.43 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.001 0.023 -10000 0 -10000 0 0
GRK1 -0.039 0.2 -10000 0 -0.65 46 46
CNG Channel 0.037 0.058 -10000 0 -0.37 7 7
mol:Na + 0.029 0.069 -10000 0 -0.39 9 9
mol:ADP -0.039 0.2 -10000 0 -0.65 46 46
RGS9-1/Gbeta5/R9AP -0.022 0.18 -10000 0 -0.44 70 70
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.041 0.072 -10000 0 -0.4 9 9
CNGB1 0.017 0.03 -10000 0 -10000 0 0
RDH5 -0.069 0.071 -10000 0 -10000 0 0
SAG -0.009 0.017 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.1 0.48 12 -0.38 8 20
Na + (4 Units) 0.022 0.065 -10000 0 -0.37 9 9
RGS9 -0.041 0.2 -10000 0 -0.67 46 46
GNB1/GNGT1 0.029 0.013 -10000 0 -10000 0 0
GNAT1/GDP -0.011 0.16 -10000 0 -0.39 70 70
GUCY2D 0.013 0.077 -10000 0 -0.62 6 6
GNGT1 -0.015 0.013 -10000 0 -10000 0 0
GUCY2F -0.013 0.01 -10000 0 -10000 0 0
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.015 0.044 -10000 0 -0.38 3 3
mol:11-cis-retinal -0.069 0.07 -10000 0 -10000 0 0
mol:cGMP 0.032 0.057 -10000 0 -0.39 6 6
GNB1 0.026 0.006 -10000 0 -10000 0 0
Rhodopsin -0.04 0.055 -10000 0 -10000 0 0
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 0.018 0.072 -10000 0 -0.67 5 5
Metarhodopsin II -0.01 0.12 -10000 0 -0.39 45 45
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.048 0.063 -10000 0 -0.4 8 8
RGS9BP -0.013 0.16 -10000 0 -0.66 27 27
Metarhodopsin II/Transducin 0.013 0.006 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.039 0.036 -10000 0 -0.41 3 3
PDE6A/B 0.031 0.028 -10000 0 -10000 0 0
mol:Pi -0.022 0.18 -10000 0 -0.44 70 70
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.038 0.014 -10000 0 -10000 0 0
PDE6B 0.027 0.004 -10000 0 -10000 0 0
PDE6A 0.012 0.036 -10000 0 -10000 0 0
PDE6G 0.01 0.072 -10000 0 -0.67 4 4
RHO 0.006 0.023 -10000 0 -10000 0 0
PDE6 0.004 0.16 -10000 0 -0.38 70 70
GUCA1A 0.005 0.025 -10000 0 -10000 0 0
GC2/GCAP Family 0.046 0.037 -10000 0 -0.42 2 2
GUCA1C -0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.023 0.055 -10000 0 -0.67 3 3
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.025 0.007 -9999 0 -10000 0 0
SPHK1 0.022 0.023 -9999 0 -10000 0 0
GNAI2 0.027 0.004 -9999 0 -10000 0 0
mol:S1P 0.017 0.007 -9999 0 -10000 0 0
GNAO1 0.004 0.12 -9999 0 -0.67 15 15
mol:Sphinganine-1-P 0.013 0.015 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.056 0.028 -9999 0 -10000 0 0
GNAI3 0.027 0.005 -9999 0 -10000 0 0
G12/G13 0.038 0.011 -9999 0 -10000 0 0
S1PR3 0.025 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.014 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.01 0.018 -9999 0 -0.2 2 2
S1PR5 0.023 0.034 -9999 0 -0.67 1 1
S1PR4 0.024 0.017 -9999 0 -10000 0 0
GNAI1 0.025 0.032 -9999 0 -0.67 1 1
S1P/S1P5/G12 0.043 0.032 -9999 0 -0.38 1 1
S1P/S1P3/Gq -0.055 0.16 -9999 0 -0.3 132 132
S1P/S1P4/Gi 0.003 0.079 -9999 0 -0.32 17 17
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.02 0.012 -9999 0 -10000 0 0
GNA14 -0.13 0.28 -9999 0 -0.63 114 114
GNA15 0.012 0.05 -9999 0 -0.67 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.014 0.085 -9999 0 -0.63 8 8
ABCC1 0.026 0.006 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.036 0.059 -10000 0 -0.36 7 7
EPHB2 0.022 0.055 -10000 0 -0.67 3 3
Syndecan-2/TACI -0.08 0.2 -10000 0 -0.43 112 112
LAMA1 -0.02 0.17 -10000 0 -0.66 33 33
Syndecan-2/alpha2 ITGB1 0.044 0.092 -10000 0 -0.38 19 19
HRAS 0.026 0.011 -10000 0 -10000 0 0
Syndecan-2/CASK 0.006 0.043 -10000 0 -0.33 7 7
ITGA5 0.027 0.005 -10000 0 -10000 0 0
BAX 0.002 0.065 -10000 0 -0.39 12 12
EPB41 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.024 0.041 -10000 0 -0.39 4 4
LAMA3 -0.001 0.13 -10000 0 -0.67 16 16
EZR 0.027 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.023 0.045 -10000 0 -0.67 2 2
Syndecan-2/MMP2 0.021 0.071 -10000 0 -0.44 10 10
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.006 0.056 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.058 -10000 0 -0.38 9 9
Syndecan-2/GM-CSF -0.033 0.056 -10000 0 -0.36 6 6
determination of left/right symmetry 0.009 0.05 -10000 0 -0.38 7 7
Syndecan-2/PKC delta 0.026 0.045 -10000 0 -0.38 5 5
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.03 0.048 -10000 0 -0.4 4 4
MAPK1 -0.024 0.047 -10000 0 -0.4 4 4
Syndecan-2/RACK1 0.038 0.041 -10000 0 -0.37 4 4
NF1 0.026 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.009 0.05 -10000 0 -0.38 7 7
ITGA2 -0.031 0.072 -10000 0 -10000 0 0
MAPK8 0.004 0.074 -10000 0 -0.42 14 14
Syndecan-2/alpha2/beta1 Integrin 0.034 0.12 -10000 0 -0.41 31 31
Syndecan-2/Kininogen 0.016 0.049 -10000 0 -0.33 7 7
ITGB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.022 0.045 0.35 1 -0.35 4 5
Syndecan-2/CASK/Protein 4.1 0.023 0.041 -10000 0 -0.3 7 7
extracellular matrix organization 0.024 0.044 -10000 0 -0.43 4 4
actin cytoskeleton reorganization -0.036 0.059 -10000 0 -0.36 7 7
Syndecan-2/Caveolin-2/Ras 0.039 0.05 -10000 0 -0.39 6 6
Syndecan-2/Laminin alpha3 0.008 0.094 -10000 0 -0.42 21 21
Syndecan-2/RasGAP 0.05 0.043 -10000 0 -0.36 4 4
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.058 -10000 0 -0.38 9 9
GO:0007205 0.003 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.042 -10000 0 -0.35 4 4
RHOA 0.027 0.004 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
TNFRSF13B -0.14 0.28 -10000 0 -0.67 109 109
RASA1 0.026 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin -0.006 0.056 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.026 0.044 -10000 0 -0.35 6 6
TGFB1 0.024 0.017 -10000 0 -10000 0 0
CASP3 0.018 0.044 -10000 0 -0.39 4 4
FN1 -0.08 0.066 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.004 0.085 -10000 0 -0.39 17 17
SDC2 0.009 0.05 -10000 0 -0.38 7 7
KNG1 -0.005 0.037 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.026 0.043 -10000 0 -0.38 5 5
TRAPPC4 0.027 0.005 -10000 0 -10000 0 0
CSF2 -0.078 0.063 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.024 0.044 -10000 0 -0.43 4 4
Syndecan-2/Syntenin/PI-4-5-P2 0.024 0.041 -10000 0 -0.39 4 4
Syndecan-2/Ezrin 0.042 0.043 -10000 0 -0.39 4 4
PRKACA 0.017 0.041 0.19 4 -0.39 4 8
angiogenesis -0.004 0.084 -10000 0 -0.39 17 17
MMP2 0.016 0.079 -10000 0 -0.62 7 7
IL8 -0.023 0.11 -10000 0 -0.67 10 10
calcineurin-NFAT signaling pathway -0.08 0.19 -10000 0 -0.43 112 112
BARD1 signaling events

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.012 0.12 -10000 0 -0.5 23 23
ATM 0.025 0.032 -10000 0 -0.67 1 1
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
PRKDC 0.027 0.005 -10000 0 -10000 0 0
ATR 0.026 0.032 -10000 0 -0.67 1 1
UBE2L3 0.02 0.012 -10000 0 -10000 0 0
FANCD2 0.023 0.026 -10000 0 -0.38 2 2
protein ubiquitination 0.044 0.094 -10000 0 -0.38 20 20
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
M/R/N Complex 0.05 0.034 -10000 0 -0.44 2 2
MRE11A 0.024 0.045 -10000 0 -0.67 2 2
DNA-PK 0.04 0.025 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.007 0.12 -10000 0 -0.49 23 23
FANCF 0.027 0.005 -10000 0 -10000 0 0
BRCA1 0.026 0.007 -10000 0 -10000 0 0
CCNE1 0.025 0.008 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.037 0.012 -10000 0 -10000 0 0
FANCG 0.025 0.007 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.012 0.11 -10000 0 -0.45 26 26
FANCE 0.027 0.003 -10000 0 -10000 0 0
FANCC 0.025 0.008 -10000 0 -10000 0 0
NBN 0.027 0.005 -10000 0 -10000 0 0
FANCA 0.02 0.029 -10000 0 -10000 0 0
DNA repair 0.018 0.089 0.41 2 -0.47 5 7
BRCA1/BARD1/ubiquitin 0.012 0.11 -10000 0 -0.45 26 26
BARD1/DNA-PK 0.029 0.099 -10000 0 -0.39 22 22
FANCL 0.027 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.012 0.12 0.49 23 -10000 0 23
BRCA1/BARD1/CTIP/M/R/N Complex 0.014 0.074 -10000 0 -0.29 22 22
BRCA1/BACH1/BARD1/TopBP1 0.028 0.1 -10000 0 -0.44 20 20
BRCA1/BARD1/P53 0.043 0.099 -10000 0 -0.4 21 21
BARD1/CSTF1/BRCA1 0.029 0.1 -10000 0 -0.44 20 20
BRCA1/BACH1 0.026 0.007 -10000 0 -10000 0 0
BARD1 -0.01 0.15 -10000 0 -0.62 27 27
PCNA 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.029 0.1 -10000 0 -0.44 20 20
BRCA1/BARD1/UbcH7 0.018 0.1 -10000 0 -0.42 21 21
BRCA1/BARD1/RAD51/PCNA 0.043 0.098 -10000 0 -0.4 20 20
BARD1/DNA-PK/P53 0.038 0.096 -10000 0 -0.37 20 20
BRCA1/BARD1/Ubiquitin 0.012 0.11 -10000 0 -0.45 26 26
BRCA1/BARD1/CTIP 0.023 0.094 -10000 0 -0.4 21 21
FA complex 0.028 0.033 -10000 0 -0.24 4 4
BARD1/EWS 0.003 0.12 -10000 0 -0.48 25 25
RBBP8 0.016 0.024 -10000 0 -0.5 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
TOPBP1 0.027 0.004 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.041 0.098 0.4 21 -10000 0 21
BRCA1/BARD1 0.05 0.097 -10000 0 -0.38 20 20
CSTF1 0.027 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.007 0.11 -10000 0 -0.47 27 27
CDK2 0.027 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.026 0.01 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.012 0.11 -10000 0 -0.45 26 26
EWSR1 0.02 0.012 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.03 0.071 -10000 0 -0.57 6 6
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
SPHK1 0.009 0.06 -10000 0 -0.86 2 2
mol:S1P 0.007 0.058 -10000 0 -0.79 2 2
S1P1/S1P/Gi -0.01 0.13 -10000 0 -0.43 35 35
GNAO1 0.001 0.12 -10000 0 -0.68 15 15
PDGFB-D/PDGFRB/PLCgamma1 -0.008 0.12 -10000 0 -0.47 17 17
PLCG1 -0.01 0.12 -10000 0 -0.41 33 33
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
GNAI2 0.025 0.013 -10000 0 -10000 0 0
GNAI3 0.025 0.013 -10000 0 -10000 0 0
GNAI1 0.023 0.034 -10000 0 -0.67 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.001 0.058 -10000 0 -0.49 6 6
S1P1/S1P 0.002 0.071 -10000 0 -0.45 7 7
negative regulation of cAMP metabolic process -0.009 0.13 -10000 0 -0.42 35 35
MAPK3 -0.023 0.17 -10000 0 -0.6 35 35
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.021 0.063 -10000 0 -0.67 4 4
PLCB2 0.013 0.078 0.4 5 -0.49 4 9
RAC1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.008 0.062 -10000 0 -0.46 4 4
receptor internalization 0.002 0.066 -10000 0 -0.42 7 7
PTGS2 -0.062 0.3 0.64 3 -1 43 46
Rac1/GTP 0.009 0.061 -10000 0 -0.46 4 4
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFA 0.022 0.055 -10000 0 -0.67 3 3
negative regulation of T cell proliferation -0.009 0.13 -10000 0 -0.42 35 35
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.015 -10000 0 -10000 0 0
MAPK1 -0.024 0.18 -10000 0 -0.61 37 37
S1P1/S1P/PDGFB-D/PDGFRB 0.011 0.081 -10000 0 -0.44 8 8
ABCC1 0.026 0.006 -10000 0 -10000 0 0
Retinoic acid receptors-mediated 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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.006 -10000 0 -10000 0 0
VDR 0.026 0.008 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.025 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.002 0.07 -10000 0 -0.31 10 10
KAT2B 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.012 0.084 0.25 12 -0.35 15 27
RAR alpha/9cRA/Cyclin H 0.03 0.1 -10000 0 -0.48 7 7
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.012 0.067 0.24 1 -0.35 8 9
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.009 0.1 -10000 0 -0.59 10 10
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.007 0.14 -10000 0 -0.54 25 25
NCOA2 -0.036 0.2 -10000 0 -0.67 44 44
NCOA3 0.027 0.005 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.008 -10000 0 -10000 0 0
RARG 0.027 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.034 0.011 -10000 0 -10000 0 0
MAPK3 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.02 0.012 -10000 0 -10000 0 0
MAPK8 0.014 0.096 -10000 0 -0.64 10 10
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.005 0.13 -10000 0 -0.54 22 22
RARA 0.002 0.083 -10000 0 -0.32 27 27
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.016 0.13 -10000 0 -0.48 26 26
PRKCA -0.002 0.14 -10000 0 -0.67 21 21
RXRs/RARs/NRIP1/9cRA/HDAC1 0.007 0.15 0.4 4 -0.53 26 30
RXRG -0.022 0.088 -10000 0 -0.39 25 25
RXRA 0.004 0.081 -10000 0 -0.32 23 23
RXRB 0.005 0.082 -10000 0 -0.38 21 21
VDR/Vit D3/DNA 0.02 0.006 -10000 0 -10000 0 0
RBP1 0.016 0.084 -10000 0 -0.67 7 7
CRBP1/9-cic-RA 0.012 0.063 -10000 0 -0.5 7 7
RARB 0.009 0.12 -10000 0 -0.67 14 14
PRKCG 0.021 0.014 -10000 0 -10000 0 0
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.012 0.14 -10000 0 -0.57 25 25
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.004 0.13 -10000 0 -0.49 24 24
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.094 0.36 3 -0.43 12 15
RXRs/RARs/NRIP1/9cRA/HDAC3 0.008 0.15 0.42 5 -0.54 25 30
positive regulation of DNA binding 0.019 0.095 -10000 0 -0.36 22 22
NRIP1 0.008 0.14 0.5 1 -0.66 7 8
RXRs/RARs 0.001 0.14 -10000 0 -0.53 27 27
RXRs/RXRs/DNA/9cRA -0.015 0.12 -10000 0 -0.54 23 23
PRKACA 0.025 0.008 -10000 0 -10000 0 0
CDK7 0.026 0.005 -10000 0 -10000 0 0
TFIIH 0.053 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.044 0.074 -10000 0 -0.47 3 3
CCNH 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.049 0.018 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.029 0.008 -10000 0 -10000 0 0
epithelial cell differentiation 0.055 0.016 -10000 0 -10000 0 0
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
ENAH 0.022 0.079 0.46 11 -10000 0 11
EGFR 0.021 0.063 -10000 0 -0.67 4 4
EPHA2 0.026 0.013 -10000 0 -10000 0 0
MYO6 0.031 0.066 0.42 11 -10000 0 11
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.053 0.013 -10000 0 -10000 0 0
AQP5 0.003 0.11 -10000 0 -0.54 18 18
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.047 0.38 7 -10000 0 7
regulation of calcium-dependent cell-cell adhesion -0.011 0.054 0.4 5 -10000 0 5
EGF -0.074 0.24 -10000 0 -0.66 70 70
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
AQP3 -0.042 0.17 -10000 0 -0.53 49 49
cortical microtubule organization 0.055 0.016 -10000 0 -10000 0 0
GO:0000145 0.012 0.047 0.37 7 -10000 0 7
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.061 0.017 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.006 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.025 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.012 0.031 -10000 0 -10000 0 0
PVRL2 0.025 0.007 -10000 0 -10000 0 0
ZYX 0.021 0.021 -10000 0 -10000 0 0
ARF6/GTP 0.067 0.027 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.009 0.14 -10000 0 -0.35 71 71
RhoA/GDP 0.057 0.016 -10000 0 -10000 0 0
actin cytoskeleton organization 0.021 0.051 0.38 8 -10000 0 8
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
IGF1R 0.027 0.004 -10000 0 -10000 0 0
IGF1 -0.13 0.29 -10000 0 -0.67 107 107
DIAPH1 0.05 0.05 -10000 0 -10000 0 0
Wnt receptor signaling pathway -0.055 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.006 0.004 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
VCL 0.021 0.051 0.39 8 -10000 0 8
EFNA1 0.025 0.007 -10000 0 -10000 0 0
LPP 0.01 0.059 0.35 3 -0.36 8 11
Ephrin A1/EPHA2 0.047 0.019 -10000 0 -10000 0 0
SEC6/SEC8 0.014 0.006 -10000 0 -10000 0 0
MGAT3 -0.011 0.055 0.4 5 -10000 0 5
HGF/MET -0.005 0.14 -10000 0 -0.37 63 63
HGF -0.073 0.24 -10000 0 -0.67 69 69
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.029 0.008 -10000 0 -10000 0 0
actin cable formation 0.066 0.13 0.5 29 -0.33 1 30
KIAA1543 0.013 0.053 0.37 8 -0.35 1 9
KIFC3 0.021 0.024 -10000 0 -10000 0 0
NCK1 0.027 0.004 -10000 0 -10000 0 0
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ACTN1 0.024 0.038 0.36 4 -10000 0 4
NCK1/GIT1 0.038 0.01 -10000 0 -10000 0 0
mol:GDP 0.055 0.016 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
STX4 0.021 0.024 -10000 0 -10000 0 0
PIP5K1C 0.024 0.047 0.38 7 -10000 0 7
LIMA1 0.027 0.005 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.044 0.1 0.44 22 -10000 0 22
adherens junction assembly 0.026 0.086 0.46 12 -0.56 1 13
IGF-1R heterotetramer/IGF1 -0.037 0.16 -10000 0 -0.35 101 101
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
MET -0.028 0.071 -10000 0 -10000 0 0
PLEKHA7 0.026 0.053 0.38 8 -0.37 1 9
mol:GTP 0.059 0.024 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.032 0.067 0.48 7 -10000 0 7
cortical actin cytoskeleton stabilization 0.029 0.008 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.021 0.051 0.38 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.029 0.008 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.025 0.041 -10000 0 -10000 0 0
TP53 -0.008 0.037 -10000 0 -0.18 20 20
Senescence -0.008 0.037 -10000 0 -0.18 20 20
Apoptosis -0.008 0.037 -10000 0 -0.18 20 20
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.011 0.025 0.34 1 -10000 0 1
MDM4 0.025 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP 0.026 0.047 0.29 10 -0.35 1 11
DAPP1 -0.036 0.13 0.33 4 -0.47 12 16
Src family/SYK family/BLNK-LAT/BTK-ITK -0.051 0.17 0.29 7 -0.48 27 34
mol:DAG -0.015 0.096 0.35 11 -0.25 15 26
HRAS 0.027 0.012 -10000 0 -10000 0 0
RAP1A 0.028 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.035 0.065 0.35 1 -0.35 4 5
PLCG2 0.026 0.006 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
ARF5 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.048 0.3 10 -10000 0 10
ARF1/GTP 0.004 0.017 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.019 0.017 -10000 0 -10000 0 0
ADAP1 -0.001 0.046 0.29 10 -10000 0 10
ARAP3 0 0.048 0.3 10 -10000 0 10
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PREX1 0.027 0.005 -10000 0 -10000 0 0
ARHGEF6 0.025 0.019 -10000 0 -0.35 1 1
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
ARF1 0.025 0.008 -10000 0 -10000 0 0
NRAS 0.028 0.008 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.065 0.26 14 -10000 0 14
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.057 0.078 -10000 0 -0.67 1 1
ZAP70 0.001 0.12 -10000 0 -0.65 16 16
mol:IP3 -0.012 0.069 0.24 12 -0.19 10 22
LYN 0.027 0.005 -10000 0 -10000 0 0
ARF1/GDP 0.034 0.073 0.3 7 -0.35 6 13
RhoA/GDP 0.038 0.044 0.35 2 -10000 0 2
PDK1/Src/Hsp90 0.05 0.035 -10000 0 -0.44 2 2
BLNK 0.027 0.004 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.034 0.076 0.35 16 -0.3 1 17
SRC 0.026 0.008 -10000 0 -10000 0 0
PLEKHA2 0.005 0.016 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.021 -10000 0 -0.33 1 1
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.025 0.039 0.29 9 -10000 0 9
RhoA/GTP 0.024 0.042 0.3 9 -10000 0 9
Src family/SYK family/BLNK-LAT -0.044 0.14 -10000 0 -0.44 24 24
BLK -0.19 0.31 -10000 0 -0.66 143 143
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
CYTH1 0.002 0.054 0.31 12 -10000 0 12
HCK 0.018 0.035 -10000 0 -10000 0 0
CYTH3 -0.002 0.05 0.29 10 -0.36 1 11
CYTH2 0.003 0.058 0.31 14 -10000 0 14
KRAS 0.028 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.016 0.096 -10000 0 -0.56 11 11
SGK1 0.016 0.11 -10000 0 -0.61 11 11
INPP5D 0.019 0.033 -10000 0 -10000 0 0
mol:GDP 0.027 0.081 0.3 12 -0.32 9 21
SOS1 0.027 0.005 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.03 0.051 0.28 9 -10000 0 9
mol:PI-3-4-5-P3 -0.007 0.015 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.019 0.017 -10000 0 -10000 0 0
VAV1 0.012 0.059 -10000 0 -0.56 3 3
mol:PI-3-4-P2 0.012 0.021 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.044 0.03 0.33 1 -10000 0 1
PLEKHA1 0.005 0.016 -10000 0 -10000 0 0
Rac1/GDP 0.034 0.065 0.35 1 -0.34 5 6
LAT 0.021 0.058 -10000 0 -0.59 4 4
Rac1/GTP 0.018 0.06 0.27 1 -0.48 3 4
ITK -0.039 0.12 0.28 10 -0.36 49 59
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.027 0.12 0.38 9 -0.35 17 26
LCK 0.012 0.082 -10000 0 -0.67 6 6
BTK -0.005 0.067 0.29 13 -0.36 6 19
Regulation of Telomerase

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
Telomerase catalytic core complex -0.001 0.099 0.49 5 -10000 0 5
RAD9A 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.19 0.36 -10000 0 -0.71 148 148
IFNAR2 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.054 -10000 0 -0.24 20 20
ER alpha/Oestrogen -0.009 0.11 -10000 0 -0.48 23 23
NFX1/SIN3/HDAC complex 0.031 0.036 -10000 0 -0.49 1 1
EGF -0.074 0.24 -10000 0 -0.66 70 70
SMG5 0.025 0.007 -10000 0 -10000 0 0
SMG6 0.026 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.008 -10000 0 -10000 0 0
TERT/c-Abl -0.002 0.08 0.47 1 -10000 0 1
SAP18 0.026 0.007 -10000 0 -10000 0 0
MRN complex 0.05 0.034 -10000 0 -0.44 2 2
WT1 0.008 0.045 -10000 0 -10000 0 0
WRN 0.025 0.032 -10000 0 -0.67 1 1
SP1 0.028 0.006 -10000 0 -10000 0 0
SP3 0.027 0.005 -10000 0 -10000 0 0
TERF2IP 0.026 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.012 0.081 -10000 0 -10000 0 0
Mad/Max 0.04 0.009 -10000 0 -10000 0 0
TERT -0.001 0.1 0.5 5 -10000 0 5
CCND1 0.002 0.1 0.56 5 -10000 0 5
MAX 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.007 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.67 2 2
TERF2 0.024 0.009 -10000 0 -10000 0 0
PTGES3 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
Telomerase/911 0.025 0.058 -10000 0 -10000 0 0
CDKN1B -0.028 0.14 -10000 0 -0.42 54 54
RAD1 0.026 0.006 -10000 0 -10000 0 0
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
SAP30 0.026 0.032 -10000 0 -0.67 1 1
TRF2/PARP2 0.037 0.011 -10000 0 -10000 0 0
UBE3A 0.027 0.004 -10000 0 -10000 0 0
JUN -0.12 0.28 -10000 0 -0.67 104 104
E6 0 0 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.003 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.67 125 125
IFN-gamma/IRF1 -0.017 0.17 -10000 0 -0.48 59 59
PARP2 0.027 0.005 -10000 0 -10000 0 0
BLM 0.027 0.008 -10000 0 -10000 0 0
Telomerase 0.015 0.1 0.27 1 -0.48 11 12
IRF1 0.03 0.009 -10000 0 -10000 0 0
ESR1 -0.014 0.15 -10000 0 -0.64 23 23
KU/TER 0.029 0.018 -10000 0 -10000 0 0
ATM/TRF2 0.038 0.025 -10000 0 -0.45 1 1
ubiquitin-dependent protein catabolic process 0.037 0.04 -10000 0 -0.33 3 3
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.038 0.04 -10000 0 -0.34 3 3
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
ATM 0.009 0.023 -10000 0 -0.48 1 1
SMAD3 0.015 0.01 -10000 0 -10000 0 0
ABL1 0.025 0.008 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
MRE11A 0.024 0.045 -10000 0 -0.67 2 2
HUS1 0.026 0.006 -10000 0 -10000 0 0
RPS6KB1 0.026 0.007 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.018 0.08 -10000 0 -10000 0 0
NR2F2 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.002 0.013 -10000 0 -10000 0 0
MAPK1 0.002 0.011 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.024 0.017 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.027 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.023 -10000 0 -0.48 1 1
NBN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.021 0.063 -10000 0 -0.67 4 4
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.042 0.19 -10000 0 -0.5 73 73
MYC 0.011 0.1 -10000 0 -0.64 12 12
IL2 0.02 0.009 -10000 0 -10000 0 0
KU 0.029 0.018 -10000 0 -10000 0 0
RAD50 0.026 0.006 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
TGFB1 0.024 0.017 -10000 0 -10000 0 0
TRF2/BLM 0.037 0.012 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.003 0.084 0.5 2 -10000 0 2
SP1/HDAC2 0.042 0.01 -10000 0 -10000 0 0
PINX1 0.027 0.005 -10000 0 -10000 0 0
Telomerase/EST1A 0.012 0.079 -10000 0 -10000 0 0
Smad3/Myc 0.018 0.069 -10000 0 -0.43 10 10
911 complex 0.052 0.015 -10000 0 -10000 0 0
IFNG -0.06 0.22 -10000 0 -0.66 59 59
Telomerase/PinX1 0.011 0.081 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.014 0.062 0.37 1 -0.42 2 3
SIN3B 0.025 0.008 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.009 0.078 -10000 0 -10000 0 0
response to DNA damage stimulus 0.003 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.071 0.036 -10000 0 -0.38 2 2
TRF2/WRN 0.037 0.026 -10000 0 -0.48 1 1
Telomerase/hnRNP C1/C2 0.011 0.081 -10000 0 -10000 0 0
E2F1 -0.016 0.067 -10000 0 -10000 0 0
ZNFX1 0.027 0.005 -10000 0 -10000 0 0
PIF1 0.018 0.072 -10000 0 -0.67 5 5
NCL 0.027 0.005 -10000 0 -10000 0 0
DKC1 0.025 0.008 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 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 0.025 0.032 -9999 0 -0.67 1 1
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.013 0.053 -9999 0 -0.26 16 16
GNAO1 0.005 0.12 -9999 0 -0.67 15 15
S1P/S1P3/G12/G13 0.048 0.019 -9999 0 -10000 0 0
AKT1 0.023 0.041 -9999 0 -0.35 3 3
AKT3 0.019 0.067 -9999 0 -0.49 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.032 -9999 0 -0.67 1 1
GNAI2 0.029 0.004 -9999 0 -10000 0 0
GNAI3 0.028 0.005 -9999 0 -10000 0 0
GNAI1 0.026 0.032 -9999 0 -0.67 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.026 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.014 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.07 -9999 0 -0.3 15 15
MAPK3 0.003 0.065 -9999 0 -0.39 3 3
MAPK1 0.013 0.058 -9999 0 -0.38 3 3
JAK2 0.006 0.067 -9999 0 -0.4 3 3
CXCR4 0.003 0.065 -9999 0 -0.39 3 3
FLT1 0.027 0.032 -9999 0 -0.67 1 1
RhoA/GDP 0.02 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.004 -9999 0 -10000 0 0
SRC 0.003 0.063 -9999 0 -0.34 3 3
S1P/S1P3/Gi 0.006 0.071 -9999 0 -0.3 15 15
RAC1 0.026 0.006 -9999 0 -10000 0 0
RhoA/GTP 0.01 0.073 -9999 0 -0.38 3 3
VEGFA 0.025 0.055 -9999 0 -0.67 3 3
S1P/S1P2/Gi 0.004 0.074 -9999 0 -0.32 15 15
VEGFR1 homodimer/VEGFA homodimer 0.04 0.057 -9999 0 -0.64 3 3
RHOA 0.027 0.004 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.055 0.15 -9999 0 -0.31 117 117
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.021 0.013 -9999 0 -10000 0 0
G12/G13 0.038 0.011 -9999 0 -10000 0 0
GNA14 -0.13 0.28 -9999 0 -0.63 114 114
GNA15 0.012 0.05 -9999 0 -0.67 1 1
GNA12 0.026 0.006 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.014 0.085 -9999 0 -0.63 8 8
Rac1/GTP 0.01 0.073 -9999 0 -0.38 3 3
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.027 0.005 -10000 0 -10000 0 0
NFATC1 0.035 0.095 0.46 9 -0.38 9 18
NFATC2 -0.022 0.097 0.28 9 -0.27 30 39
NFATC3 0.018 0.01 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.01 0.088 0.28 1 -0.39 11 12
Exportin 1/Ran/NUP214 0.047 0.018 -10000 0 -10000 0 0
mol:DAG -0.002 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0.003 0.1 -10000 0 -0.45 11 11
BCL2/BAX -0.002 0.14 -10000 0 -0.49 36 36
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.02 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.02 -10000 0 -10000 0 0
BAX 0.025 0.01 -10000 0 -10000 0 0
MAPK14 0.025 0.005 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
CABIN1/MEF2D 0.004 0.093 0.4 2 -0.38 10 12
Calcineurin A alpha-beta B1/BCL2 -0.024 0.18 -10000 0 -0.66 36 36
FKBP8 0.025 0.008 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.004 0.092 0.38 10 -0.39 2 12
KPNB1 0.026 0.007 -10000 0 -10000 0 0
KPNA2 0.026 0.007 -10000 0 -10000 0 0
XPO1 0.026 0.005 -10000 0 -10000 0 0
SFN -0.082 0.12 -10000 0 -0.67 13 13
MAP3K8 0.014 0.085 -10000 0 -0.63 8 8
NFAT4/CK1 alpha 0.019 0.029 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.072 0.17 -10000 0 -0.34 108 108
CABIN1 -0.009 0.086 0.28 1 -0.38 10 11
CALM1 0.023 0.009 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
CAMK4 0.013 0.085 -10000 0 -0.67 7 7
mol:Ca2+ -0.004 0.008 -10000 0 -10000 0 0
MAPK3 0.026 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.036 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.01 0.095 -10000 0 -0.64 10 10
MAPK9 0.026 0.006 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.021 0.087 0.37 2 -0.47 3 5
PRKCH 0.027 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.013 0.031 -10000 0 -10000 0 0
CASP3 0.025 0.005 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.012 -10000 0 -10000 0 0
apoptosis 0.01 0.044 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.004 0.053 -10000 0 -0.32 5 5
PRKCB 0.005 0.081 -10000 0 -0.67 5 5
PRKCE 0.02 0.07 -10000 0 -0.67 5 5
JNK2/NFAT4 0.031 0.025 -10000 0 -10000 0 0
BAD/BCL-XL 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.004 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
PRKCZ 0.024 0.007 -10000 0 -10000 0 0
PRKCA -0.004 0.14 -10000 0 -0.67 21 21
PRKCG 0.005 0.023 -10000 0 -10000 0 0
PRKCQ 0.02 0.065 -10000 0 -0.61 5 5
FKBP38/BCL2 -0.001 0.14 -10000 0 -0.49 36 36
EP300 0.01 0.02 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.037 0.1 0.41 7 -0.44 5 12
CaM/Ca2+/FKBP38 0.02 0.025 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.004 -10000 0 -10000 0 0
CSNK1A1 0.005 0.02 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.013 0.062 -10000 0 -0.45 7 7
NFATc/ERK1 0.042 0.081 0.44 3 -0.48 2 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.008 0.1 -10000 0 -0.49 9 9
NR4A1 -0.17 0.29 -10000 0 -0.61 143 143
GSK3B 0.024 0.007 -10000 0 -10000 0 0
positive T cell selection 0.018 0.01 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.023 0.072 -10000 0 -0.31 10 10
RCH1/ KPNB1 0.038 0.01 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.023 0.008 -10000 0 -10000 0 0
AKAP5 0.027 0.005 -10000 0 -10000 0 0
MEF2D 0.014 0.021 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.049 0.094 0.43 10 -0.49 2 12
CREBBP 0.013 0.022 -10000 0 -10000 0 0
BCL2 -0.024 0.18 -10000 0 -0.66 36 36
TCGA08_retinoblastoma

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
CDKN2B -0.033 0.074 -10000 0 -10000 0 0
CDKN2C 0.031 0.019 -10000 0 -10000 0 0
CDKN2A -0.033 0.075 -10000 0 -0.17 6 6
CCND2 0.01 0.023 -10000 0 -10000 0 0
RB1 -0.015 0.049 0.32 2 -0.23 14 16
CDK4 0.014 0.041 0.25 10 -10000 0 10
CDK6 0.015 0.043 0.26 10 -0.16 1 11
G1/S progression 0.015 0.05 0.24 15 -0.32 2 17
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.28 -10000 0 -0.66 96 96
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.013 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/p53 0.033 0.039 0.35 1 -10000 0 1
HIF1A 0.009 0.024 -10000 0 -0.25 2 2
COPS5 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.055 0.052 -10000 0 -0.39 3 3
FIH (dimer) 0.027 0.004 -10000 0 -10000 0 0
CDKN2A -0.032 0.071 -10000 0 -10000 0 0
ARNT/IPAS -0.067 0.21 -10000 0 -0.48 96 96
HIF1AN 0.027 0.004 -10000 0 -10000 0 0
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.032 0.048 0.31 7 -10000 0 7
CUL2 0.027 0.004 -10000 0 -10000 0 0
OS9 0.027 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.052 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.032 0.037 0.28 1 -10000 0 1
PHD1-3/OS9 0.049 0.073 -10000 0 -0.4 11 11
HIF1A/RACK1/Elongin B/Elongin C 0.055 0.04 -10000 0 -10000 0 0
VHL 0.023 0.055 -10000 0 -0.67 3 3
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.036 0.047 0.34 4 -10000 0 4
EGLN3 0.007 0.1 -10000 0 -0.67 10 10
EGLN2 0.025 0.007 -10000 0 -10000 0 0
EGLN1 0.024 0.032 -10000 0 -0.67 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.026 0.076 -10000 0 -0.57 6 6
ARNT 0.025 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.012 -10000 0 -10000 0 0
HIF1A/p19ARF 0.039 0.052 0.32 6 -0.24 2 8
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.015 0.08 0.62 7 -10000 0 7
PI3K Class IB/PDE3B 0.015 0.08 -10000 0 -0.62 7 7
PDE3B 0.015 0.081 -10000 0 -0.62 7 7
PLK1 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
regulation of centriole-centriole cohesion -0.006 0.016 0.12 1 -0.15 2 3
BUB1B 0.014 0.032 0.19 9 -10000 0 9
PLK1 0.012 0.03 0.16 13 -0.1 1 14
PLK1S1 0.015 0.026 0.17 10 -10000 0 10
KIF2A 0.018 0.067 0.32 20 -0.38 1 21
regulation of mitotic centrosome separation 0.012 0.03 0.16 13 -0.1 1 14
GOLGA2 0.025 0.008 -10000 0 -10000 0 0
Hec1/SPC24 0.034 0.037 -10000 0 -10000 0 0
WEE1 0.022 0.046 0.28 6 -0.26 5 11
cytokinesis 0.011 0.062 0.27 8 -0.24 4 12
PP2A-alpha B56 0.048 0.096 -10000 0 -0.55 9 9
AURKA 0.014 0.023 0.17 7 -10000 0 7
PICH/PLK1 0.019 0.015 -10000 0 -10000 0 0
CENPE 0.01 0.052 0.25 11 -0.38 3 14
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.018 0.067 0.32 20 -0.38 1 21
PPP2CA 0.026 0.006 -10000 0 -10000 0 0
FZR1 0.025 0.008 -10000 0 -10000 0 0
TPX2 0.015 0.027 0.17 11 -10000 0 11
PAK1 0.026 0.005 -10000 0 -10000 0 0
SPC24 0.015 0.037 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
CLSPN 0.012 0.028 0.14 1 -0.28 3 4
GORASP1 0.027 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.006 0.023 26 -10000 0 26
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.019 0.085 17 -0.05 1 18
G2 phase of mitotic cell cycle 0 0.004 0.019 13 -10000 0 13
STAG2 0.026 0.007 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.024 0.03 -10000 0 -0.41 2 2
spindle elongation 0.012 0.03 0.16 13 -0.1 1 14
ODF2 0.025 0.008 -10000 0 -10000 0 0
BUB1 0.023 0.1 -10000 0 -0.55 14 14
TPT1 0.004 0.044 0.14 4 -0.18 23 27
CDC25C 0.019 0.025 0.17 8 -10000 0 8
CDC25B 0.027 0.011 -10000 0 -10000 0 0
SGOL1 0.006 0.016 0.15 2 -0.12 1 3
RHOA 0.027 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.042 0.014 -10000 0 -10000 0 0
CDC14B 0.003 0.045 -10000 0 -0.38 6 6
CDC20 0.025 0.017 -10000 0 -10000 0 0
PLK1/PBIP1 0.01 0.019 0.14 3 -10000 0 3
mitosis -0.001 0.003 0.02 3 -10000 0 3
FBXO5 0.013 0.037 0.21 9 -0.34 1 10
CDC2 0.001 0.001 -10000 0 -10000 0 0
NDC80 0.007 0.05 -10000 0 -10000 0 0
metaphase plate congression 0.014 0.025 -10000 0 -0.23 3 3
ERCC6L 0.025 0.014 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.011 0.027 0.13 17 -10000 0 17
microtubule cytoskeleton organization 0.004 0.044 0.14 4 -0.18 23 27
G2/M transition DNA damage checkpoint 0 0.004 0.019 16 -10000 0 16
PPP1R12A 0.027 0.005 -10000 0 -10000 0 0
interphase 0 0.004 0.019 16 -10000 0 16
PLK1/PRC1-2 0.038 0.028 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.049 0.021 -10000 0 -10000 0 0
RAB1A 0.027 0.005 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.01 0.027 0.14 14 -10000 0 14
mitotic prometaphase 0 0.004 0.027 7 -10000 0 7
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.026 -10000 0 -10000 0 0
microtubule-based process 0.023 0.026 -10000 0 -10000 0 0
Golgi organization 0.012 0.03 0.16 13 -0.1 1 14
Cohesin/SA2 0.021 0.021 0.18 3 -10000 0 3
PPP1CB/MYPT1 0.039 0.009 -10000 0 -10000 0 0
KIF20A 0.003 0.054 -10000 0 -10000 0 0
APC/C/CDC20 0.025 0.023 0.16 3 -10000 0 3
PPP2R1A 0.025 0.007 -10000 0 -10000 0 0
chromosome segregation 0.01 0.019 0.13 3 -10000 0 3
PRC1 0.027 0.004 -10000 0 -10000 0 0
ECT2 0.01 0.042 0.22 8 -0.4 2 10
C13orf34 0.01 0.026 0.13 14 -0.081 1 15
NUDC 0.014 0.025 -10000 0 -0.23 3 3
regulation of attachment of spindle microtubules to kinetochore 0.014 0.032 0.19 9 -10000 0 9
spindle assembly 0.014 0.037 0.17 19 -0.079 1 20
spindle stabilization 0.015 0.026 0.17 10 -10000 0 10
APC/C/HCDH1 0.019 0.041 -10000 0 -0.32 6 6
MKLP2/PLK1 0.023 0.026 -10000 0 -10000 0 0
CCNB1 0.027 0.006 -10000 0 -10000 0 0
PPP1CB 0.027 0.005 -10000 0 -10000 0 0
BTRC 0.027 0.004 -10000 0 -10000 0 0
ROCK2 -0.006 0.11 0.22 2 -0.4 31 33
TUBG1 0.015 0.029 0.18 9 -0.16 2 11
G2/M transition of mitotic cell cycle 0.013 0.01 -10000 0 -10000 0 0
MLF1IP 0.007 0.012 -10000 0 -10000 0 0
INCENP 0.024 0.045 -10000 0 -0.67 2 2
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.004 0.16 -10000 0 -0.43 57 57
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.02 0.14 -10000 0 -0.38 56 56
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.026 0.007 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -10000 0 -10000 0 0
FKBP3 0.027 0.005 -10000 0 -10000 0 0
Histones 0.035 0.084 -10000 0 -10000 0 0
YY1/LSF 0.006 0.065 -10000 0 -0.43 4 4
SMG5 0.025 0.007 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.008 0.11 -10000 0 -0.31 55 55
I kappa B alpha/HDAC1 0.01 0.081 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
RELA -0.017 0.11 -10000 0 -0.31 57 57
HDAC1/Smad7 0.051 0.016 -10000 0 -10000 0 0
RANGAP1 0.02 0.012 -10000 0 -10000 0 0
HDAC3/TR2 0.011 0.081 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.031 0.037 -10000 0 -0.44 2 2
NF kappa B1 p50/RelA -0.025 0.12 0.32 1 -0.42 15 16
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 0.027 0.008 -10000 0 -10000 0 0
GATA1 0.012 0.021 -10000 0 -10000 0 0
Mad/Max 0.039 0.008 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.034 0.068 -10000 0 -0.49 5 5
RBBP7 0.025 0.007 -10000 0 -10000 0 0
NPC 0.016 0.003 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.67 2 2
MAX 0.027 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NFKBIA -0.004 0.084 -10000 0 -0.23 56 56
KAT2B 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.029 0.034 -10000 0 -0.55 1 1
SIN3 complex 0.061 0.031 -10000 0 -0.4 1 1
SMURF1 0.026 0.006 -10000 0 -10000 0 0
CHD3 0.026 0.007 -10000 0 -10000 0 0
SAP30 0.025 0.032 -10000 0 -0.67 1 1
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.026 0.007 -10000 0 -10000 0 0
YY1/HDAC3 -0.009 0.08 -10000 0 -0.26 11 11
YY1/HDAC2 0.009 0.054 -10000 0 -0.28 1 1
YY1/HDAC1 0.01 0.053 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.031 0.031 -10000 0 -0.4 1 1
PPARG -0.023 0.14 -10000 0 -0.39 61 61
HDAC8/hEST1B 0.046 0.021 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.011 0.081 -10000 0 -10000 0 0
MBD3L2 -0.015 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.015 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.035 0.062 -10000 0 -0.45 4 4
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 -0.004 0.084 -10000 0 -0.23 56 56
HDAC2 0.027 0.004 -10000 0 -10000 0 0
YY1 0.019 0.012 -10000 0 -10000 0 0
HDAC8 0.026 0.007 -10000 0 -10000 0 0
SMAD7 0.027 0.004 -10000 0 -10000 0 0
NCOR2 0.027 0.005 -10000 0 -10000 0 0
MXD1 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.018 0.012 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.027 0.005 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.019 0.066 -10000 0 -0.4 4 4
YY1/SAP30/HDAC1 0.021 0.057 -10000 0 -0.3 1 1
EP300 0.02 0.012 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.083 -10000 0 -0.23 56 56
histone deacetylation 0.038 0.034 -10000 0 -0.39 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.003 0.074 -10000 0 -0.27 9 9
nuclear export -0.046 0.021 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GATAD2B 0.025 0.007 -10000 0 -10000 0 0
GATAD2A 0.025 0.008 -10000 0 -10000 0 0
GATA2/HDAC3 0.011 0.081 -10000 0 -10000 0 0
GATA1/HDAC1 0.034 0.013 -10000 0 -10000 0 0
GATA1/HDAC3 0.008 0.08 -10000 0 -10000 0 0
CHD4 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.026 0.18 -10000 0 -0.5 57 57
SIN3/HDAC complex/Mad/Max 0.032 0.034 -10000 0 -0.49 1 1
NuRD Complex 0.041 0.052 -10000 0 -0.49 2 2
positive regulation of chromatin silencing 0.033 0.082 -10000 0 -10000 0 0
SIN3B 0.025 0.008 -10000 0 -10000 0 0
MTA2 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
SUMO1/HDAC1 0.014 0.057 -10000 0 -0.27 2 2
HDAC complex 0.062 0.036 -10000 0 -0.39 2 2
GATA1/Fog1 0.034 0.014 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.053 0.014 -10000 0 -10000 0 0
TNF -0.058 0.22 -10000 0 -0.67 57 57
negative regulation of cell growth 0.035 0.035 -10000 0 -0.48 1 1
NuRD/MBD2/PRMT5 Complex 0.031 0.031 -10000 0 -0.4 1 1
Ran/GTP/Exportin 1 0.017 0.052 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.032 0.14 -10000 0 -0.39 57 57
SIN3/HDAC complex/NCoR1 0.031 0.044 -10000 0 -0.44 2 2
TFCP2 0.021 0.063 -10000 0 -0.67 4 4
NR2C1 0.027 0.005 -10000 0 -10000 0 0
MBD3 0.025 0.008 -10000 0 -10000 0 0
MBD2 0.027 0.004 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.027 0.004 -9999 0 -10000 0 0
ITGB7 0.007 0.099 -9999 0 -0.64 10 10
ITGA4 0.02 0.058 -9999 0 -0.67 3 3
alpha4/beta7 Integrin 0.019 0.089 -9999 0 -0.49 13 13
alpha4/beta1 Integrin 0.034 0.046 -9999 0 -0.5 3 3
IL2 signaling events mediated by STAT5

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
GAB2 0.027 0.005 -10000 0 -10000 0 0
ELF1 0.005 0.098 -10000 0 -0.39 26 26
CCNA2 0.024 0.019 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
JAK3 -0.011 0.064 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.005 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.004 0.13 -10000 0 -0.55 17 17
SHC1 0.026 0.008 -10000 0 -10000 0 0
SP1 0.033 0.006 -10000 0 -10000 0 0
IL2RA -0.028 0.2 -10000 0 -0.86 25 25
IL2RB 0.004 0.09 -10000 0 -0.57 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
IL2RG -0.011 0.14 -10000 0 -0.62 21 21
G1/S transition of mitotic cell cycle 0.03 0.063 0.42 5 -0.5 3 8
PTPN11 0.026 0.032 -10000 0 -0.67 1 1
CCND2 0.023 0.005 -10000 0 -10000 0 0
LCK 0.013 0.082 -10000 0 -0.67 6 6
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.02 0.006 -10000 0 -10000 0 0
CDK6 0.022 0.055 -10000 0 -0.67 3 3
CCND3 0.008 0.11 -10000 0 -0.59 9 9
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.024 0.051 0.31 1 -0.66 1 2
PDGFB-D/PDGFRB/SLAP 0.037 0.027 -10000 0 -0.51 1 1
PDGFB-D/PDGFRB/APS/CBL 0.052 0.026 -10000 0 -0.42 1 1
AKT1 0.029 0.087 0.5 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.028 0.053 0.34 1 -0.7 1 2
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
FGR 0.017 0.045 0.36 1 -0.53 2 3
mol:Ca2+ 0.034 0.083 0.41 13 -0.74 1 14
MYC 0.029 0.18 0.58 18 -0.77 14 32
SHC1 0.025 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.034 0.024 -10000 0 -0.37 1 1
LRP1/PDGFRB/PDGFB 0.038 0.04 -10000 0 -0.44 2 2
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GO:0007205 0.034 0.083 0.41 13 -0.75 1 14
PTEN 0.026 0.018 -10000 0 -0.35 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.002 0.054 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.037 0.036 -10000 0 -0.51 2 2
PDGFB-D/PDGFRB/GRB10 0.038 0.027 -10000 0 -0.51 1 1
cell cycle arrest 0.037 0.027 -10000 0 -0.51 1 1
HRAS 0.026 0.011 -10000 0 -10000 0 0
HIF1A 0.023 0.084 0.48 11 -10000 0 11
GAB1 0.029 0.094 0.43 12 -0.56 2 14
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.034 0.11 0.48 17 -0.7 1 18
PDGFB-D/PDGFRB 0.054 0.029 -10000 0 -0.46 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.038 0.027 -10000 0 -0.51 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.032 0.052 -10000 0 -0.67 1 1
positive regulation of MAPKKK cascade 0.037 0.036 -10000 0 -0.51 2 2
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.034 0.083 0.41 13 -0.76 1 14
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.018 0.051 -10000 0 -0.56 1 1
SHB 0.025 0.007 -10000 0 -10000 0 0
BLK -0.14 0.26 -10000 0 -0.55 139 139
PTPN2 0.028 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.038 0.026 -10000 0 -0.49 1 1
BCAR1 0.026 0.006 -10000 0 -10000 0 0
VAV2 0.033 0.11 0.49 14 -0.57 3 17
CBL 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.038 0.027 -10000 0 -0.51 1 1
LCK 0.01 0.081 -10000 0 -0.65 6 6
PDGFRB 0.026 0.033 -10000 0 -0.68 1 1
ACP1 0.027 0.005 -10000 0 -10000 0 0
HCK 0.024 0.031 0.29 1 -0.44 1 2
ABL1 0.026 0.097 0.42 14 -0.58 2 16
PDGFB-D/PDGFRB/CBL 0.023 0.083 0.45 4 -0.64 2 6
PTPN1 0.027 0.005 -10000 0 -10000 0 0
SNX15 0.027 0.005 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.023 -10000 0 -10000 0 0
cell proliferation 0.031 0.17 0.56 19 -0.67 14 33
SLA 0.026 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.033 0.026 -10000 0 -0.37 1 1
SRC 0.018 0.035 0.29 1 -0.45 1 2
PI3K 0.012 0.034 -10000 0 -0.34 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.049 0.028 -10000 0 -0.3 1 1
SH2B2 0.026 0.009 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.029 0.055 0.34 1 -0.74 1 2
LYN 0.018 0.035 -10000 0 -0.44 2 2
LRP1 0.025 0.032 -10000 0 -0.67 1 1
SOS1 0.027 0.005 -10000 0 -10000 0 0
STAT5B 0.026 0.007 -10000 0 -10000 0 0
STAT5A 0.026 0.007 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.079 0.032 -10000 0 -0.38 1 1
SPHK1 0.023 0.023 -10000 0 -10000 0 0
EDG1 0.001 0.005 -10000 0 -10000 0 0
mol:DAG 0.034 0.083 0.41 13 -0.76 1 14
PLCG1 0.034 0.084 0.41 13 -0.79 1 14
NHERF/PDGFRB 0.05 0.028 -10000 0 -0.44 1 1
YES1 0.015 0.057 0.37 1 -0.47 5 6
cell migration 0.049 0.028 -10000 0 -0.44 1 1
SHC/Grb2/SOS1 0.072 0.035 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.062 0.033 -10000 0 -0.4 1 1
FYN 0.016 0.05 0.29 1 -0.44 4 5
DOK1 0.023 0.029 -10000 0 -0.41 1 1
HRAS/GTP 0.019 0.007 -10000 0 -10000 0 0
PDGFB 0.02 0.012 -10000 0 -10000 0 0
RAC1 0.039 0.14 0.55 19 -0.46 11 30
PRKCD 0.023 0.03 -10000 0 -0.41 1 1
FER 0.019 0.043 -10000 0 -0.41 4 4
MAPKKK cascade 0.015 0.056 0.37 1 -10000 0 1
RASA1 0.022 0.027 -10000 0 -0.41 1 1
NCK1 0.027 0.004 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.039 0.029 -10000 0 -0.38 1 1
PDGFB-D/PDGFRB/SHB 0.036 0.028 -10000 0 -0.51 1 1
chemotaxis 0.026 0.096 0.42 14 -0.56 2 16
STAT1-3-5/STAT1-3-5 0.063 0.029 -10000 0 -0.36 1 1
Bovine Papilomavirus E5/PDGFRB 0.019 0.025 -10000 0 -0.51 1 1
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
S1P4 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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
CDC42/GTP 0.007 0.074 -10000 0 -0.3 14 14
PLCG1 -0.002 0.068 -10000 0 -0.32 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.004 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
G12/G13 0.038 0.011 -10000 0 -10000 0 0
cell migration 0.007 0.073 -10000 0 -0.3 14 14
S1PR5 0.023 0.034 -10000 0 -0.67 1 1
S1PR4 0.024 0.017 -10000 0 -10000 0 0
MAPK3 -0.003 0.068 -10000 0 -0.32 14 14
MAPK1 0.009 0.061 -10000 0 -0.31 14 14
S1P/S1P5/Gi -0.001 0.075 -10000 0 -0.32 17 17
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
CDC42/GDP 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.025 -10000 0 -0.44 1 1
RHOA 0.034 0.07 0.41 12 -10000 0 12
S1P/S1P4/Gi 0 0.074 -10000 0 -0.32 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
S1P/S1P4/G12/G13 0.047 0.018 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.018 0.04 -10000 0 -0.25 2 2
STMN1 0.002 0.041 -10000 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.05 0.054 -10000 0 -0.44 1 1
Chromosomal passenger complex/Cul3 protein complex 0.014 0.051 -10000 0 -0.25 11 11
BIRC5 0.014 0.051 -10000 0 -0.68 1 1
DES -0.32 0.3 -10000 0 -0.56 289 289
Aurora C/Aurora B/INCENP 0.054 0.045 -10000 0 -0.45 2 2
Aurora B/TACC1 0.031 0.042 -10000 0 -0.49 1 1
Aurora B/PP2A 0.031 0.043 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 0.006 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.009 0.058 -10000 0 -10000 0 0
Cul3 protein complex 0.038 0.073 -10000 0 -0.41 11 11
KIF2C 0.015 0.028 -10000 0 -0.47 1 1
PEBP1 0.027 0.006 -10000 0 -10000 0 0
KIF20A 0.003 0.054 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.031 0.042 -10000 0 -10000 0 0
SEPT1 0.024 0.02 -10000 0 -10000 0 0
SMC2 0.025 0.008 -10000 0 -10000 0 0
SMC4 0.027 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.017 0.08 -10000 0 -0.54 8 8
PSMA3 0.027 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.012 0.016 -10000 0 -10000 0 0
AURKB 0.003 0.063 -10000 0 -10000 0 0
AURKC 0.02 0.029 -10000 0 -10000 0 0
CDCA8 0.028 0.014 -10000 0 -10000 0 0
cytokinesis -0.017 0.054 -10000 0 -0.36 4 4
Aurora B/Septin1 0.046 0.066 0.27 1 -0.34 5 6
AURKA 0.026 0.005 -10000 0 -10000 0 0
INCENP 0.026 0.046 -10000 0 -0.68 2 2
KLHL13 0.005 0.1 -10000 0 -0.62 12 12
BUB1 -0.026 0.076 -10000 0 -0.67 1 1
hSgo1/Aurora B/Survivin 0.048 0.055 -10000 0 -0.4 1 1
EVI5 0.028 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.051 0.047 -10000 0 -10000 0 0
SGOL1 0.021 0.028 -10000 0 -10000 0 0
CENPA 0.02 0.039 0.2 2 -0.24 3 5
NCAPG 0.013 0.043 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.031 0.043 -10000 0 -10000 0 0
NCAPD2 0.027 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.031 0.043 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
NCAPH 0.006 0.052 -10000 0 -10000 0 0
NPM1 0.012 0.041 -10000 0 -0.3 6 6
RASA1 0.026 0.005 -10000 0 -10000 0 0
KLHL9 0.025 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.031 0.043 -10000 0 -10000 0 0
PPP1CC 0.027 0.005 -10000 0 -10000 0 0
Centraspindlin 0.043 0.048 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
NSUN2 0.012 0.044 -10000 0 -0.31 2 2
MYLK 0.011 0.024 -10000 0 -0.4 1 1
KIF23 0.021 0.033 -10000 0 -10000 0 0
VIM 0.001 0.038 -10000 0 -10000 0 0
RACGAP1 0.028 0.006 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.005 0.081 -10000 0 -0.58 6 6
Chromosomal passenger complex 0.016 0.035 -10000 0 -0.26 3 3
Chromosomal passenger complex/EVI5 0.1 0.066 -10000 0 -0.41 3 3
TACC1 0.025 0.032 -10000 0 -0.67 1 1
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
CUL3 0.027 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Canonical NF-kappaB 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
FBXW11 0.029 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.046 0.067 0.38 1 -10000 0 1
ERC1 0.027 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.022 0.052 -10000 0 -0.5 2 2
NFKBIA 0.022 0.014 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
IKBKB 0.027 0.005 -10000 0 -10000 0 0
RIPK2 0.027 0.005 -10000 0 -10000 0 0
IKBKG 0.033 0.025 -10000 0 -10000 0 0
IKK complex/A20 0.014 0.14 0.33 1 -0.48 6 7
NEMO/A20/RIP2 0.027 0.005 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.033 0.074 -10000 0 -0.56 1 1
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.036 0.008 -10000 0 -10000 0 0
IKK complex/ELKS 0.044 0.068 -10000 0 -0.38 1 1
BCL10/MALT1/TRAF6 0.051 0.034 -10000 0 -0.44 2 2
NOD2 0.004 0.066 -10000 0 -0.67 2 2
NFKB1 0.03 0.004 -10000 0 -10000 0 0
RELA 0.029 0.005 -10000 0 -10000 0 0
MALT1 0.027 0.004 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.039 0.008 -10000 0 -10000 0 0
ATM 0.025 0.032 -10000 0 -0.67 1 1
TNF/TNFR1A -0.026 0.18 -10000 0 -0.5 57 57
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
PRKCA -0.004 0.14 -10000 0 -0.67 21 21
CHUK 0.027 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF -0.058 0.22 -10000 0 -0.67 57 57
NF kappa B1 p50/RelA 0.061 0.016 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.014 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.029 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.047 0.073 -10000 0 -0.4 1 1
CYLD 0.026 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.039 0.1 -10000 0 -0.46 2 2
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.028 0.1 -10000 0 -0.48 8 8
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.026 0.005 -10000 0 -10000 0 0
AKT2 0.025 0.007 -10000 0 -10000 0 0
STXBP4 0.024 0.032 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.024 0.1 0.33 7 -0.5 7 14
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.054 0.18 -10000 0 -0.49 67 67
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.05 0.027 -10000 0 -0.44 1 1
YWHAG 0.026 0.006 -10000 0 -10000 0 0
ASIP 0.005 0.048 -10000 0 -10000 0 0
PRKCI 0.027 0.004 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
GYS1 0.017 0.012 0.25 1 -10000 0 1
PRKCZ 0.026 0.006 -10000 0 -10000 0 0
TRIP10 0.025 0.008 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
AS160/14-3-3 -0.033 0.094 -10000 0 -0.35 15 15
VAMP2 0.026 0.007 -10000 0 -10000 0 0
SLC2A4 0.022 0.11 0.35 5 -0.57 7 12
STX4 0.026 0.006 -10000 0 -10000 0 0
GSK3B 0.023 0.008 -10000 0 -10000 0 0
SFN -0.082 0.12 -10000 0 -0.67 13 13
LNPEP 0.001 0.13 -10000 0 -0.67 18 18
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.016 0.005 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.044 0.016 -10000 0 -10000 0 0
CDKN1B 0.022 0.024 -10000 0 -10000 0 0
CDKN1A 0.02 0.025 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.027 0.005 -10000 0 -10000 0 0
FOXO3 0.022 0.024 -10000 0 -10000 0 0
AKT1 0.021 0.023 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
AKT3 0.013 0.026 -10000 0 -0.39 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.022 0.026 -10000 0 -10000 0 0
AKT1/ASK1 0.038 0.037 -10000 0 -0.33 1 1
BAD/YWHAZ 0.05 0.018 -10000 0 -10000 0 0
RICTOR 0.025 0.032 -10000 0 -0.67 1 1
RAF1 0.027 0.004 -10000 0 -10000 0 0
JNK cascade -0.036 0.035 0.32 1 -10000 0 1
TSC1 0.02 0.025 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.041 0.035 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
mol:GDP 0.022 0.024 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.021 0.023 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.047 0.15 -10000 0 -0.42 64 64
MAP3K5 0.026 0.032 -10000 0 -0.67 1 1
MAPKAP1 0.025 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.012 0.076 0.43 4 -0.32 8 12
YWHAH 0.02 0.012 -10000 0 -10000 0 0
AKT1S1 0.027 0.038 -10000 0 -10000 0 0
CASP9 0.023 0.03 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.044 0.049 0.36 6 -10000 0 6
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.05 0.035 -10000 0 -0.44 2 2
YWHAE 0.026 0.007 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.022 0.029 -10000 0 -0.35 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.017 0.011 -10000 0 -10000 0 0
CHUK 0.022 0.024 -10000 0 -10000 0 0
BAD/BCL-XL 0.046 0.034 0.28 1 -10000 0 1
mTORC2 0.03 0.023 -10000 0 -0.4 1 1
AKT2 0.014 0.026 -10000 0 -0.39 2 2
FOXO1-3a-4/14-3-3 family 0.021 0.081 0.36 9 -0.37 3 12
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
MDM2 0.022 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.04 0.035 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.039 0.034 -10000 0 -10000 0 0
TSC1/TSC2 0.023 0.039 0.28 7 -10000 0 7
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.033 -10000 0 -10000 0 0
glucose import -0.058 0.16 0.21 4 -0.41 78 82
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.028 0.21 2 -10000 0 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.061 0.16 -10000 0 -0.41 78 78
GSK3A 0.026 0.037 -10000 0 -10000 0 0
FOXO1 0.021 0.024 -10000 0 -10000 0 0
GSK3B 0.022 0.024 -10000 0 -10000 0 0
SFN -0.082 0.12 -10000 0 -0.67 13 13
G1/S transition of mitotic cell cycle 0.028 0.043 0.29 3 -10000 0 3
p27Kip1/14-3-3 family 0.017 0.052 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
KPNA1 0.027 0.004 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
YWHAG 0.026 0.006 -10000 0 -10000 0 0
RHEB 0.026 0.006 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.025 0.11 0.66 10 -10000 0 10
PLK1 0.071 0.11 0.6 2 -0.58 4 6
CDKN1B 0.073 0.089 0.47 3 -0.4 1 4
FOXO3 0.069 0.11 -10000 0 -0.58 5 5
KAT2B 0.033 0.018 -10000 0 -10000 0 0
FOXO1/SIRT1 0.018 0.055 0.42 2 -0.39 1 3
CAT 0.065 0.13 -10000 0 -0.96 4 4
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.034 0.018 -10000 0 -10000 0 0
FOXO1 0.017 0.08 0.44 11 -10000 0 11
MAPK10 0.032 0.031 0.2 8 -0.4 1 9
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.068 0.085 0.49 9 -0.51 3 12
response to oxidative stress 0.011 0.011 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.085 0.087 -10000 0 -0.59 4 4
XPO1 0.027 0.005 -10000 0 -10000 0 0
EP300 0.021 0.013 -10000 0 -10000 0 0
BCL2L11 0.027 0.099 -10000 0 -0.64 9 9
FOXO1/SKP2 0.015 0.054 -10000 0 -0.43 3 3
mol:GDP 0.011 0.011 -10000 0 -10000 0 0
RAN 0.028 0.006 -10000 0 -10000 0 0
GADD45A 0.098 0.092 0.45 6 -0.54 4 10
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.002 0.1 -10000 0 -0.48 7 7
MST1 0.031 0.036 -10000 0 -0.66 1 1
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.007 0.11 -10000 0 -0.56 10 10
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.026 0.062 0.21 1 -0.38 9 10
MAPK9 0.03 0.017 0.2 3 -10000 0 3
YWHAG 0.026 0.006 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
SIRT1 0.025 0.036 -10000 0 -0.66 1 1
SOD2 0.1 0.1 0.56 10 -0.62 2 12
RBL2 0.079 0.15 0.57 1 -0.86 7 8
RAL/GDP 0.046 0.014 -10000 0 -10000 0 0
CHUK 0.033 0.018 -10000 0 -10000 0 0
Ran/GTP 0.023 0.005 -10000 0 -10000 0 0
CSNK1G2 0.025 0.008 -10000 0 -10000 0 0
RAL/GTP 0.05 0.015 -10000 0 -10000 0 0
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
FASLG -0.055 0.36 -10000 0 -1.3 34 34
SKP2 0.022 0.055 -10000 0 -0.67 3 3
USP7 0.027 0.006 -10000 0 -10000 0 0
IKBKB 0.032 0.018 -10000 0 -10000 0 0
CCNB1 0.072 0.11 0.6 2 -0.58 3 5
FOXO1-3a-4/beta catenin 0.099 0.097 0.45 6 -0.42 4 10
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.054 -10000 0 -0.43 3 3
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
SGK1 0.017 0.11 -10000 0 -0.67 11 11
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.01 -10000 0 -10000 0 0
ZFAND5 0.076 0.11 0.6 13 -0.44 2 15
SFN -0.082 0.12 -10000 0 -0.67 13 13
CDK2 0.027 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.011 0.1 -10000 0 -0.51 10 10
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FBXO32 0.069 0.11 0.58 1 -0.57 4 5
BCL6 0.085 0.12 0.5 2 -0.75 5 7
RALB 0.028 0.005 -10000 0 -10000 0 0
RALA 0.027 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.008 0.003 -10000 0 -10000 0 0
SNTA1 0.027 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.008 0.004 -10000 0 -10000 0 0
MAPK12 -0.002 0.055 -10000 0 -0.38 10 10
CCND1 0.007 0.046 -10000 0 -0.4 4 4
p38 gamma/SNTA1 0.02 0.067 -10000 0 -0.36 11 11
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
PKN1 0.025 0.008 -10000 0 -10000 0 0
G2/M transition checkpoint 0 0.063 0.21 7 -0.38 11 18
MAP2K6 0.001 0.064 -10000 0 -0.42 11 11
MAPT 0.008 0.048 0.28 6 -0.36 3 9
MAPK13 0.016 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.015 0.019 -10000 0 -0.39 1 1
Atypical NF-kappaB 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
BCL3/RelA 0.037 0.013 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.002 0.11 -10000 0 -0.43 31 31
NF kappa B1 p50/RelA/I kappa B alpha 0.036 0.038 -10000 0 -10000 0 0
NFKBIA 0.014 0.029 -10000 0 -0.24 5 5
MAPK14 0.027 0.003 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.032 0.008 -10000 0 -10000 0 0
ARRB2 0.016 0.005 -10000 0 -10000 0 0
REL -0.018 0.17 -10000 0 -0.66 32 32
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.03 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
NF kappa B1 p50 dimer 0.025 0.023 0.25 5 -10000 0 5
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.017 0.003 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.02 0.038 -10000 0 -0.31 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.04 0.039 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PI3K 0.036 0.043 -10000 0 -0.5 3 3
NF kappa B1 p50/RelA 0.02 0.039 -10000 0 -0.31 5 5
IKBKB 0.027 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.028 0.038 -10000 0 -10000 0 0
cell death 0.038 0.038 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.002 0.11 -10000 0 -0.43 31 31
LCK 0.012 0.082 -10000 0 -0.67 6 6
BCL3 0.025 0.01 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.022 0.23 2 -10000 0 2
AES 0.025 0.018 0.2 1 -10000 0 1
FBXW11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
SMAD4 0.027 0.004 -10000 0 -10000 0 0
DKK2 -0.003 0.13 -10000 0 -0.65 19 19
TLE1 0.021 0.057 -10000 0 -0.66 3 3
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.048 0.089 0.46 16 -10000 0 16
WIF1 -0.013 0.045 -10000 0 -10000 0 0
beta catenin/RanBP3 0.031 0.085 0.38 24 -10000 0 24
KREMEN2 0.016 0.036 -10000 0 -10000 0 0
DKK1 0.001 0.062 -10000 0 -0.67 1 1
beta catenin/beta TrCP1 0.048 0.045 0.38 2 -10000 0 2
FZD1 0.026 0.006 -10000 0 -10000 0 0
AXIN2 -0.029 0.3 0.6 14 -1.4 18 32
AXIN1 0.026 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.03 0.067 -10000 0 -0.51 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.039 0.094 0.3 1 -0.55 4 5
Axin1/APC/GSK3 0.034 0.045 0.34 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.034 0.028 0.32 1 -10000 0 1
HNF1A 0.027 0.021 0.23 1 -10000 0 1
CTBP1 0.027 0.02 0.24 1 -10000 0 1
MYC -0.038 0.24 0.55 5 -1.4 14 19
RANBP3 0.025 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.035 0.093 -10000 0 -0.44 17 17
NKD1 0.006 0.11 -10000 0 -0.67 13 13
TCF4 0.027 0.02 -10000 0 -10000 0 0
TCF3 0.025 0.02 0.23 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.065 0.02 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.022 0.12 0.49 22 -10000 0 22
LEF1 0.023 0.049 0.21 2 -0.63 2 4
DVL1 0.028 0.016 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.038 0.11 -10000 0 -0.52 9 9
DKK1/LRP6/Kremen 2 0.05 0.038 -10000 0 -0.49 1 1
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.02 0.2 1 -10000 0 1
NLK 0.026 0.008 -10000 0 -10000 0 0
CCND1 -0.011 0.082 0.58 2 -0.68 2 4
WNT1 0.023 0.015 -10000 0 -10000 0 0
GSK3A 0.026 0.008 -10000 0 -10000 0 0
GSK3B 0.027 0.004 -10000 0 -10000 0 0
FRAT1 0.027 0.005 -10000 0 -10000 0 0
PPP2R5D 0.032 0.056 0.33 13 -0.28 2 15
APC 0.022 0.039 0.36 3 -0.38 1 4
WNT1/LRP6/FZD1 0.031 0.02 -10000 0 -10000 0 0
CREBBP 0.027 0.02 0.23 1 -10000 0 1
Effects of Botulinum toxin

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
STX1A 0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.036 0.013 -10000 0 -10000 0 0
STXBP1 0.025 0.008 -10000 0 -10000 0 0
ACh/CHRNA1 0.01 0.039 -10000 0 -0.17 3 3
RAB3GAP2/RIMS1/UNC13B 0.048 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.021 0.017 -10000 0 -10000 0 0
mol:ACh 0.002 0.044 0.14 20 -0.14 24 44
RAB3GAP2 0.025 0.008 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.031 0.055 -10000 0 -0.26 1 1
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.01 0.039 -10000 0 -0.17 3 3
UNC13B 0.025 0.008 -10000 0 -10000 0 0
CHRNA1 0.008 0.043 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.039 0.11 -10000 0 -0.48 24 24
SNAP25 -0.015 0.075 -10000 0 -0.34 25 25
VAMP2 0.006 0.001 -10000 0 -10000 0 0
SYT1 -0.064 0.15 -10000 0 -0.67 23 23
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.024 0.009 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.031 0.055 -10000 0 -0.26 1 1
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.025 0.086 -10000 0 -0.55 10 10
AKT1 0.039 0.091 0.39 2 -0.64 5 7
PTK2B 0.018 0.11 0.35 1 -0.79 5 6
VEGFR2 homodimer/Frs2 0.032 0.084 -10000 0 -0.88 4 4
CAV1 0.013 0.094 -10000 0 -0.67 9 9
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.046 0.095 -10000 0 -0.73 6 6
endothelial cell proliferation 0.051 0.15 0.59 18 -0.64 4 22
mol:Ca2+ 0.023 0.09 -10000 0 -0.86 4 4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.06 0.092 -10000 0 -0.87 4 4
RP11-342D11.1 0.012 0.089 -10000 0 -0.86 4 4
CDH5 0.026 0.006 -10000 0 -10000 0 0
VEGFA homodimer 0.059 0.058 -10000 0 -0.49 4 4
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.021 0.055 -10000 0 -0.67 3 3
HRAS/GDP 0.039 0.079 -10000 0 -0.7 4 4
SH2D2A -0.008 0.14 -10000 0 -0.67 21 21
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.056 0.095 -10000 0 -0.65 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.025 0.13 -10000 0 -0.46 27 27
VEGFR1 homodimer 0.024 0.032 -10000 0 -0.67 1 1
SHC/GRB2/SOS1 0.065 0.095 -10000 0 -0.81 4 4
GRB10 0.023 0.089 -10000 0 -0.86 4 4
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.069 0.093 -10000 0 -0.84 4 4
HRAS 0.026 0.011 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.027 0.065 -10000 0 -0.44 5 5
HIF1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.058 0.09 -10000 0 -0.85 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.018 0.077 -10000 0 -0.67 6 6
Nck/Pak 0.039 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.047 0.095 -10000 0 -0.73 6 6
mol:GDP 0.051 0.087 -10000 0 -0.76 4 4
mol:NADP 0.04 0.098 0.46 7 -0.48 6 13
eNOS/Hsp90 0.043 0.08 -10000 0 -0.49 4 4
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.023 0.093 -10000 0 -0.88 4 4
HIF1A/ARNT 0.037 0.012 -10000 0 -10000 0 0
SHB 0.025 0.007 -10000 0 -10000 0 0
VEGFA 0.025 0.055 -10000 0 -0.67 3 3
VEGFC 0.025 0.032 -10000 0 -0.67 1 1
FAK1/Vinculin 0.04 0.1 -10000 0 -0.74 5 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.049 0.12 -10000 0 -0.84 5 5
PTPN6 0.027 0.005 -10000 0 -10000 0 0
EPAS1 0.03 0.057 -10000 0 -0.53 4 4
mol:L-citrulline 0.04 0.098 0.46 7 -0.48 6 13
ITGAV 0.024 0.045 -10000 0 -0.67 2 2
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.058 0.093 -10000 0 -0.77 5 5
VEGFR2 homodimer/VEGFA homodimer 0.049 0.11 -10000 0 -0.98 4 4
VEGFR2/3 heterodimer 0.026 0.11 -10000 0 -0.83 7 7
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.006 0.098 0.38 1 -0.92 4 5
VEGFR2 homodimer 0.019 0.091 -10000 0 -0.97 4 4
FLT1 0.024 0.032 -10000 0 -0.67 1 1
NEDD4 0.026 0.045 -10000 0 -0.67 2 2
MAPK3 0 0.092 0.37 1 -0.82 4 5
MAPK1 -0.005 0.092 0.37 1 -0.83 4 5
VEGFA145/NRP2 0.028 0.053 -10000 0 -0.5 3 3
VEGFR1/2 heterodimer 0.03 0.094 -10000 0 -0.96 4 4
KDR 0.019 0.091 -10000 0 -0.97 4 4
VEGFA165/NRP1/VEGFR2 homodimer 0.053 0.1 -10000 0 -0.91 4 4
SRC 0.026 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.01 0.11 0.38 11 -0.86 4 15
PI3K 0.042 0.098 -10000 0 -0.87 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.047 0.095 -10000 0 -0.73 6 6
FES 0.024 0.097 -10000 0 -0.91 4 4
GAB1 0.029 0.094 -10000 0 -0.86 4 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.046 0.095 -10000 0 -0.73 6 6
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.025 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.039 0.09 0.4 1 -0.54 5 6
VEGFR2 homodimer/VEGFA homodimer/Yes 0.046 0.095 -10000 0 -0.73 6 6
PI3K/GAB1 0.05 0.085 -10000 0 -0.67 4 4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.07 0.092 -10000 0 -0.84 4 4
PRKACA 0.025 0.008 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.04 0.11 -10000 0 -0.74 8 8
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
CDC42 0.022 0.096 -10000 0 -0.91 4 4
actin cytoskeleton reorganization 0.024 0.13 -10000 0 -0.46 27 27
PTK2 0.025 0.1 -10000 0 -0.82 5 5
EDG1 0.012 0.089 -10000 0 -0.86 4 4
mol:DAG 0.023 0.093 -10000 0 -0.88 4 4
CaM/Ca2+ 0.036 0.086 -10000 0 -0.8 4 4
MAP2K3 0.009 0.1 0.37 1 -0.9 4 5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.051 0.1 -10000 0 -0.93 4 4
PLCG1 0.023 0.096 -10000 0 -0.91 4 4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.057 0.094 -10000 0 -0.86 4 4
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.046 0.1 -10000 0 -0.78 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.046 0.095 -10000 0 -0.73 6 6
cell migration 0.046 0.085 0.34 1 -0.66 4 5
mol:PI-3-4-5-P3 0.041 0.087 -10000 0 -0.75 4 4
FYN 0.027 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.027 0.086 -10000 0 -0.81 4 4
mol:NO 0.04 0.098 0.46 7 -0.48 6 13
PXN 0.027 0.005 -10000 0 -10000 0 0
HRAS/GTP 0.021 0.075 -10000 0 -0.71 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.043 0.1 -10000 0 -0.93 4 4
VHL 0.023 0.055 -10000 0 -0.67 3 3
ITGB3 0.012 0.095 -10000 0 -0.64 10 10
NOS3 0.039 0.11 0.49 6 -0.55 6 12
VEGFR2 homodimer/VEGFA homodimer/Sck 0.041 0.1 -10000 0 -0.65 8 8
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.001 0.12 0.36 1 -0.96 4 5
PRKCB 0.005 0.094 0.36 1 -0.81 4 5
VCL 0.027 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.029 0.095 -10000 0 -0.78 5 5
VEGFR1/2 heterodimer/VEGFA homodimer 0.044 0.1 -10000 0 -0.78 6 6
VEGFA165/NRP2 0.028 0.053 -10000 0 -0.5 3 3
MAPKKK cascade 0.053 0.092 0.36 2 -0.71 4 6
NRP2 0.015 0.041 -10000 0 -10000 0 0
VEGFC homodimer 0.025 0.032 -10000 0 -0.67 1 1
NCK1 0.027 0.004 -10000 0 -10000 0 0
ROCK1 0.027 0.004 -10000 0 -10000 0 0
FAK1/Paxillin 0.04 0.1 -10000 0 -0.74 5 5
MAP3K13 0.016 0.12 -10000 0 -0.97 4 4
PDPK1 0.027 0.081 -10000 0 -0.66 5 5
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.027 0.004 -9999 0 -10000 0 0
SMAD2 -0.016 0.044 -9999 0 -0.24 1 1
SMAD3 0.021 0.015 -9999 0 -10000 0 0
SMAD3/SMAD4 0.032 0.05 -9999 0 -0.41 5 5
SMAD4/Ubc9/PIASy 0.049 0.019 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.027 0.063 -9999 0 -0.41 1 1
PPM1A 0.027 0.005 -9999 0 -10000 0 0
CALM1 0.027 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.003 0.054 -9999 0 -0.34 2 2
MAP3K1 0.026 0.005 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.007 0.13 -9999 0 -0.49 30 30
MAPK3 0.026 0.006 -9999 0 -10000 0 0
MAPK1 0.02 0.012 -9999 0 -10000 0 0
NUP214 0.025 0.008 -9999 0 -10000 0 0
CTDSP1 0.027 0.005 -9999 0 -10000 0 0
CTDSP2 0.027 0.005 -9999 0 -10000 0 0
CTDSPL 0.027 0.004 -9999 0 -10000 0 0
KPNB1 0.026 0.007 -9999 0 -10000 0 0
TGFBRAP1 -0.016 0.17 -9999 0 -0.66 30 30
UBE2I 0.026 0.007 -9999 0 -10000 0 0
NUP153 0.026 0.032 -9999 0 -0.67 1 1
KPNA2 0.026 0.007 -9999 0 -10000 0 0
PIAS4 0.025 0.008 -9999 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.04 0.042 -9999 0 -0.45 1 1
CLOCK -0.016 0.17 -9999 0 -0.67 31 31
TIMELESS/CRY2 0.027 0.035 -9999 0 -10000 0 0
DEC1/BMAL1 0.019 0.035 -9999 0 -10000 0 0
ATR 0.026 0.032 -9999 0 -0.67 1 1
NR1D1 0.001 0.039 -9999 0 -10000 0 0
ARNTL 0.014 0.044 -9999 0 -10000 0 0
TIMELESS 0.011 0.03 -9999 0 -10000 0 0
NPAS2 0.027 0.019 -9999 0 -0.35 1 1
CRY2 0.027 0.005 -9999 0 -10000 0 0
mol:CO -0.005 0.009 -9999 0 -10000 0 0
CHEK1 0.027 0.005 -9999 0 -10000 0 0
mol:HEME 0.005 0.009 -9999 0 -10000 0 0
PER1 0.026 0.007 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.025 0.12 -9999 0 -0.44 31 31
BMAL1/CLOCK -0.003 0.11 -9999 0 -0.48 2 2
S phase of mitotic cell cycle 0.04 0.042 -9999 0 -0.45 1 1
TIMELESS/CHEK1/ATR 0.041 0.042 -9999 0 -0.45 1 1
mol:NADPH 0.005 0.009 -9999 0 -10000 0 0
PER1/TIMELESS 0.026 0.033 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.012 0.013 -9999 0 -0.12 1 1
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.031 0.098 -10000 0 -10000 0 0
CRKL 0.014 0.048 0.46 3 -10000 0 3
mol:DAG 0.028 0.047 -10000 0 -10000 0 0
HRAS 0.034 0.064 0.35 6 -10000 0 6
MAPK8 0.012 0.069 -10000 0 -0.43 9 9
RAP1A 0.023 0.063 0.49 5 -10000 0 5
GAB1 0.021 0.053 0.46 3 -10000 0 3
MAPK14 0.02 0.032 -10000 0 -10000 0 0
EPO 0.018 0.023 -10000 0 -10000 0 0
PLCG1 0.028 0.048 -10000 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.023 0.022 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.024 0.1 -10000 0 -0.42 22 22
GAB1/SHC/GRB2/SOS1 0.046 0.044 -10000 0 -10000 0 0
EPO/EPOR (dimer) 0.03 0.028 -10000 0 -10000 0 0
IRS2 0.02 0.055 0.5 3 -10000 0 3
STAT1 0.029 0.071 -10000 0 -10000 0 0
STAT5B 0.028 0.06 -10000 0 -10000 0 0
cell proliferation 0.011 0.077 0.36 6 -0.4 9 15
GAB1/SHIP/PIK3R1/SHP2/SHC 0.036 0.042 -10000 0 -0.4 1 1
TEC 0.021 0.053 0.46 3 -10000 0 3
SOCS3 -0.006 0.14 -10000 0 -0.67 22 22
STAT1 (dimer) 0.029 0.07 -10000 0 -10000 0 0
JAK2 0.026 0.026 -10000 0 -0.34 2 2
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.059 0.054 -10000 0 -10000 0 0
EPO/EPOR 0.03 0.028 -10000 0 -10000 0 0
LYN 0.025 0.014 -10000 0 -10000 0 0
TEC/VAV2 0.031 0.041 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.023 0.021 -10000 0 -10000 0 0
SHC1 0.025 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.049 0.032 -10000 0 -10000 0 0
mol:IP3 0.028 0.047 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.043 0.047 -10000 0 -10000 0 0
SH2B3 0.028 0.008 -10000 0 -10000 0 0
NFKB1 0.02 0.032 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 0 0.06 -10000 0 -0.26 20 20
PTPN6 0.022 0.047 0.31 1 -10000 0 1
TEC/VAV2/GRB2 0.041 0.044 -10000 0 -10000 0 0
EPOR 0.023 0.022 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
mol:GDP 0.046 0.044 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG2 0.026 0.006 -10000 0 -10000 0 0
CRKL/CBL/C3G 0.03 0.043 -10000 0 -10000 0 0
VAV2 0.023 0.059 0.47 5 -10000 0 5
CBL 0.021 0.056 0.45 4 -10000 0 4
SHC/Grb2/SOS1 0.035 0.039 -10000 0 -10000 0 0
STAT5A 0.028 0.06 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.097 -10000 0 -0.42 1 1
LYN/PLCgamma2 0.039 0.01 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
BTK 0.01 0.059 0.26 1 -0.36 6 7
BCL2 -0.013 0.25 -10000 0 -0.9 35 35
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.014 0.066 -9999 0 -0.38 12 12
CRKL 0.02 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.004 -9999 0 -10000 0 0
DOCK1 0.023 0.055 -9999 0 -0.67 3 3
ITGA4 0.02 0.058 -9999 0 -0.67 3 3
alpha4/beta7 Integrin/MAdCAM1 0.047 0.083 -9999 0 -0.4 14 14
EPO 0.004 0.026 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.019 0.089 -9999 0 -0.49 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.026 0.007 -9999 0 -10000 0 0
alpha4/beta1 Integrin 0.034 0.046 -9999 0 -0.5 3 3
EPO/EPOR (dimer) 0.03 0.021 -9999 0 -10000 0 0
lamellipodium assembly 0.02 0.037 -9999 0 -0.4 3 3
PIK3CA 0.023 0.055 -9999 0 -0.67 3 3
PI3K 0.036 0.043 -9999 0 -0.5 3 3
ARF6 0.027 0.005 -9999 0 -10000 0 0
JAK2 0.022 0.045 -9999 0 -0.51 3 3
PXN 0.027 0.005 -9999 0 -10000 0 0
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
MADCAM1 0.006 0.056 -9999 0 -0.67 2 2
cell adhesion 0.045 0.082 -9999 0 -0.4 14 14
CRKL/CBL 0.03 0.018 -9999 0 -10000 0 0
ITGB1 0.027 0.004 -9999 0 -10000 0 0
SRC 0.016 0.066 -9999 0 -0.45 7 7
ITGB7 0.007 0.099 -9999 0 -0.64 10 10
RAC1 0.026 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.069 -9999 0 -0.49 7 7
p130Cas/Crk/Dock1 0.034 0.066 -9999 0 -0.36 10 10
VCAM1 0.018 0.072 -9999 0 -0.67 5 5
RHOA 0.027 0.004 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.038 -9999 0 -0.4 2 2
BCAR1 0.007 0.061 -9999 0 -0.42 7 7
EPOR 0.024 0.017 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.027 0.005 -9999 0 -10000 0 0
GIT1 0.026 0.007 -9999 0 -10000 0 0
Rac1/GTP 0.02 0.038 -9999 0 -0.41 3 3
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.007 0.074 0.47 3 -10000 0 3
GNAI2 0.027 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.025 -10000 0 -0.44 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
RhoA/GTP 0.007 0.076 -10000 0 -0.48 3 3
negative regulation of cAMP metabolic process -0.001 0.074 -10000 0 -0.32 17 17
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
S1PR5 0.023 0.034 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.001 0.075 -10000 0 -0.32 17 17
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.014 0.034 -10000 0 -10000 0 0
oxygen homeostasis 0.011 0.009 -10000 0 -10000 0 0
TCEB2 0.025 0.013 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.1 0.087 -10000 0 -0.53 3 3
EPO 0.12 0.11 -10000 0 -0.91 1 1
FIH (dimer) 0.036 0.012 -10000 0 -10000 0 0
APEX1 0.035 0.015 -10000 0 -10000 0 0
SERPINE1 0.12 0.12 -10000 0 -0.67 3 3
FLT1 0.02 0.12 -10000 0 -0.7 9 9
ADORA2A 0.1 0.12 0.43 1 -0.72 2 3
germ cell development 0.12 0.11 -10000 0 -0.71 2 2
SLC11A2 0.12 0.11 -10000 0 -0.75 2 2
BHLHE40 0.13 0.11 -10000 0 -0.75 2 2
HIF1AN 0.036 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.11 0.096 -10000 0 -0.66 2 2
ETS1 0.037 0.015 -10000 0 -10000 0 0
CITED2 -0.033 0.31 -10000 0 -1.1 37 37
KDR 0.025 0.13 -10000 0 -1 6 6
PGK1 0.12 0.11 -10000 0 -0.75 2 2
SIRT1 0.025 0.032 -10000 0 -0.67 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.16 0.14 -10000 0 -0.94 2 2
EPAS1 0.061 0.069 -10000 0 -0.46 2 2
SP1 0.032 0.007 -10000 0 -10000 0 0
ABCG2 0.12 0.13 -10000 0 -0.88 3 3
EFNA1 0.13 0.11 -10000 0 -0.75 2 2
FXN 0.12 0.12 0.47 3 -0.72 2 5
POU5F1 0.13 0.11 -10000 0 -0.75 2 2
neuron apoptosis -0.16 0.13 0.89 2 -10000 0 2
EP300 0.02 0.012 -10000 0 -10000 0 0
EGLN3 0.017 0.1 -10000 0 -0.66 10 10
EGLN2 0.035 0.014 -10000 0 -10000 0 0
EGLN1 0.034 0.035 -10000 0 -0.67 1 1
VHL/Elongin B/Elongin C 0.049 0.042 -10000 0 -0.45 3 3
VHL 0.023 0.055 -10000 0 -0.67 3 3
ARNT 0.034 0.015 -10000 0 -10000 0 0
SLC2A1 0.14 0.12 0.45 9 -0.72 2 11
TWIST1 0.12 0.14 0.43 2 -0.57 8 10
ELK1 0.022 0.035 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.089 0.098 -10000 0 -0.63 1 1
VEGFA 0.12 0.12 -10000 0 -0.7 4 4
CREBBP 0.026 0.006 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.019 0.03 -10000 0 -0.32 3 3
TRAF2/ASK1 0.032 0.024 -10000 0 -0.44 1 1
ATM 0.025 0.032 -10000 0 -0.67 1 1
MAP2K3 0.036 0.095 0.42 15 -0.38 3 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.095 0.34 14 -0.4 7 21
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.014 0.084 -10000 0 -0.67 7 7
TXN 0.008 0.003 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GADD45B 0.006 0.11 -10000 0 -0.61 15 15
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
MAP3K6 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.026 -10000 0 -0.5 1 1
TAK1/TAB family 0.011 0.032 -10000 0 -0.19 3 3
RAC1/OSM/MEKK3 0.049 0.015 -10000 0 -10000 0 0
TRAF2 0.025 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.036 0.055 -10000 0 -0.39 1 1
TRAF6 0.007 0.026 -10000 0 -0.4 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.021 0.063 -10000 0 -0.67 4 4
CCM2 0.026 0.011 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.031 0.043 -10000 0 -0.44 4 4
MAPK11 0.02 0.012 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.046 0.053 -10000 0 -0.49 4 4
OSM/MEKK3 0.037 0.013 -10000 0 -10000 0 0
TAOK1 -0.031 0.13 -10000 0 -0.4 55 55
TAOK2 0.015 0.019 -10000 0 -0.39 1 1
TAOK3 0.015 0.019 -10000 0 -0.39 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.026 0.032 -10000 0 -0.67 1 1
MAP3K10 0.025 0.007 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.036 -10000 0 -0.42 1 1
GADD45/MTK1/MTK1 0.037 0.091 -10000 0 -0.4 18 18
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
DOCK1 0.023 0.055 -10000 0 -0.67 3 3
ITGA4 0.02 0.058 -10000 0 -0.67 3 3
RAC1 0.026 0.006 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.019 0.089 -10000 0 -0.49 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.048 0.042 -10000 0 -0.44 3 3
alpha4/beta7 Integrin/Paxillin 0.033 0.072 -10000 0 -0.4 12 12
lamellipodium assembly 0.025 0.063 -10000 0 -0.58 4 4
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
PI3K 0.036 0.043 -10000 0 -0.5 3 3
ARF6 0.027 0.005 -10000 0 -10000 0 0
TLN1 0.025 0.007 -10000 0 -10000 0 0
PXN 0.016 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.052 0.035 -10000 0 -0.35 2 2
cell adhesion 0.05 0.04 -10000 0 -0.36 3 3
CRKL/CBL 0.03 0.018 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.041 0.038 -10000 0 -0.4 3 3
ITGB1 0.027 0.004 -10000 0 -10000 0 0
ITGB7 0.007 0.099 -10000 0 -0.64 10 10
ARF6/GDP 0.024 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.049 0.064 -10000 0 -0.43 7 7
p130Cas/Crk/Dock1 0.048 0.041 -10000 0 -0.44 3 3
VCAM1 0.018 0.072 -10000 0 -0.67 5 5
alpha4/beta1 Integrin/Paxillin/Talin 0.052 0.041 -10000 0 -0.37 3 3
alpha4/beta1 Integrin/Paxillin/GIT1 0.055 0.037 -10000 0 -0.38 2 2
BCAR1 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.053 0.036 0.38 2 -10000 0 2
CBL 0.027 0.005 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.052 0.041 -10000 0 -0.37 3 3
Rac1/GTP 0.026 0.072 -10000 0 -0.67 4 4
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.028 0.041 0.29 3 -0.38 3 6
adherens junction organization 0.021 0.04 0.25 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.037 0.049 -10000 0 -0.6 1 1
FMN1 0.008 0.082 -10000 0 -0.34 24 24
mol:IP3 0.027 0.033 -10000 0 -0.33 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.029 0.021 -10000 0 -10000 0 0
CTNNB1 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.033 0.035 0.25 1 -0.32 3 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.035 0.027 -10000 0 -10000 0 0
CTNND1 0.028 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.033 -10000 0 -0.38 2 2
VASP 0.025 0.018 -10000 0 -10000 0 0
ZYX 0.026 0.02 -10000 0 -10000 0 0
JUB 0.025 0.02 -10000 0 -10000 0 0
EGFR(dimer) 0.04 0.044 -10000 0 -0.36 4 4
E-cadherin/beta catenin-gamma catenin 0.051 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.048 0.038 0.25 1 -0.34 3 4
PIK3CA 0.024 0.055 -10000 0 -0.67 3 3
PI3K 0.05 0.039 0.26 1 -0.34 3 4
FYN 0.026 0.036 0.29 3 -10000 0 3
mol:Ca2+ 0.027 0.032 -10000 0 -0.32 3 3
JUP 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:DAG 0.027 0.033 -10000 0 -0.33 3 3
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.038 0.05 -10000 0 -0.6 1 1
establishment of polarity of embryonic epithelium 0.025 0.017 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.021 0.063 -10000 0 -0.67 4 4
CASR 0.018 0.031 -10000 0 -0.31 3 3
RhoA/GTP 0.039 0.032 -10000 0 -0.3 3 3
AKT2 0.031 0.033 -10000 0 -0.32 3 3
actin cable formation 0.006 0.078 -10000 0 -0.33 23 23
apoptosis -0.03 0.043 0.36 3 -0.32 4 7
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
mol:GDP 0.022 0.05 -10000 0 -0.38 6 6
PIP5K1A 0.023 0.033 -10000 0 -0.39 2 2
PLCG1 0.028 0.033 -10000 0 -0.34 3 3
Rac1/GTP 0.049 0.044 -10000 0 -0.34 4 4
homophilic cell adhesion 0.001 0.005 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.063 0.03 -9999 0 -0.38 1 1
HDAC3 0.026 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.035 0.012 -9999 0 -10000 0 0
GATA1/HDAC5 0.034 0.013 -9999 0 -10000 0 0
GATA2/HDAC5 0.038 0.011 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.049 0.028 -9999 0 -0.44 1 1
HDAC9 0.012 0.043 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.051 0.017 -9999 0 -10000 0 0
HDAC4/ANKRA2 0.039 0.01 -9999 0 -10000 0 0
HDAC5/YWHAB 0.038 0.01 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -9999 0 -10000 0 0
GATA2 0.027 0.008 -9999 0 -10000 0 0
HDAC4/RFXANK 0.037 0.014 -9999 0 -10000 0 0
BCOR 0.026 0.007 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.02 0.012 -9999 0 -10000 0 0
HDAC5 0.026 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.037 0.027 -9999 0 -0.5 1 1
Histones 0.008 0.048 -9999 0 -10000 0 0
ADRBK1 0.027 0.005 -9999 0 -10000 0 0
HDAC4 0.027 0.005 -9999 0 -10000 0 0
XPO1 0.027 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.038 0.011 -9999 0 -10000 0 0
HDAC7 0.027 0.005 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
TUBA1B 0.027 0.005 -9999 0 -10000 0 0
HDAC6 0.026 0.007 -9999 0 -10000 0 0
HDAC5/RFXANK 0.036 0.015 -9999 0 -10000 0 0
CAMK4 0.013 0.085 -9999 0 -0.67 7 7
Tubulin/HDAC6 0.047 0.048 -9999 0 -0.39 5 5
SUMO1 0.027 0.005 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.027 0.005 -9999 0 -10000 0 0
GATA1 0.012 0.021 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.026 0.007 -9999 0 -10000 0 0
NR3C1 0.026 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.058 -9999 0 -0.29 1 1
SRF 0.027 0.003 -9999 0 -10000 0 0
HDAC4/YWHAB 0.039 0.009 -9999 0 -10000 0 0
Tubulin 0.034 0.055 -9999 0 -0.5 5 5
HDAC4/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
GNB1 0.026 0.006 -9999 0 -10000 0 0
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
BCL6/BCoR 0.037 0.027 -9999 0 -0.5 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.052 0.014 -9999 0 -10000 0 0
HDAC4/SRF 0.046 0.06 -9999 0 -0.44 7 7
HDAC4/ER alpha 0.008 0.11 -9999 0 -0.49 22 22
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.008 0.047 -9999 0 -10000 0 0
cell motility 0.046 0.048 -9999 0 -0.39 5 5
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
HDAC7/HDAC3 0.039 0.009 -9999 0 -10000 0 0
BCL6 0.026 0.032 -9999 0 -0.67 1 1
HDAC4/CaMK II delta B 0.027 0.005 -9999 0 -10000 0 0
Hsp90/HDAC6 0.037 0.012 -9999 0 -10000 0 0
ESR1 -0.014 0.15 -9999 0 -0.64 23 23
HDAC6/HDAC11 0.038 0.011 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.017 0.052 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
MEF2C 0.025 0.032 -9999 0 -0.67 1 1
RAN 0.026 0.005 -9999 0 -10000 0 0
HDAC4/MEF2C 0.074 0.031 -9999 0 -0.38 1 1
GNG2 0.025 0.032 -9999 0 -0.67 1 1
NCOR2 0.027 0.005 -9999 0 -10000 0 0
TUBB2A 0.02 0.07 -9999 0 -0.67 5 5
HDAC11 0.027 0.004 -9999 0 -10000 0 0
HSP90AA1 0.027 0.005 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
ANKRA2 0.026 0.005 -9999 0 -10000 0 0
RFXANK 0.025 0.012 -9999 0 -10000 0 0
nuclear import -0.036 0.011 -9999 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.03 0.025 -10000 0 -10000 0 0
BIRC5 0.013 0.05 -10000 0 -0.67 1 1
NFKBIA 0.015 0.022 0.25 3 -10000 0 3
CPEB1 -0.021 0.18 -10000 0 -0.64 35 35
AKT1 0.015 0.024 0.25 4 -10000 0 4
NDEL1 0.026 0.007 -10000 0 -10000 0 0
Aurora A/BRCA1 0.027 0.021 -10000 0 -10000 0 0
NDEL1/TACC3 0.043 0.024 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.026 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.03 0.024 -10000 0 -10000 0 0
MDM2 0.027 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.008 0.027 -10000 0 -10000 0 0
TP53 0.025 0.012 -10000 0 -10000 0 0
DLG7 0.012 0.011 -10000 0 -10000 0 0
AURKAIP1 0.026 0.011 -10000 0 -10000 0 0
ARHGEF7 0.026 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.046 0.024 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.026 0.02 -10000 0 -10000 0 0
AURKA 0.02 0.015 -10000 0 -10000 0 0
AURKB 0.013 0.022 -10000 0 -0.16 3 3
CDC25B 0.021 0.011 -10000 0 -10000 0 0
G2/M transition checkpoint 0.01 0.018 -10000 0 -10000 0 0
mRNA polyadenylation -0.001 0.11 -10000 0 -0.4 31 31
Aurora A/CPEB -0.001 0.11 -10000 0 -0.4 31 31
Aurora A/TACC1/TRAP/chTOG 0.054 0.039 -10000 0 -0.37 1 1
BRCA1 0.026 0.007 -10000 0 -10000 0 0
centrosome duplication 0.03 0.024 -10000 0 -10000 0 0
regulation of centrosome cycle 0.042 0.023 -10000 0 -10000 0 0
spindle assembly 0.053 0.038 -10000 0 -0.37 1 1
TDRD7 0.025 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.055 0.033 -10000 0 -0.36 1 1
CENPA 0.016 0.031 -10000 0 -0.25 6 6
Aurora A/PP2A 0.03 0.023 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.021 0.018 -10000 0 -10000 0 0
negative regulation of DNA binding 0.025 0.012 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.037 0.012 -10000 0 -10000 0 0
RASA1 0.026 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A 0.01 0.018 -10000 0 -10000 0 0
mitotic prometaphase -0.004 0.011 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.015 -10000 0 -10000 0 0
TACC1 0.025 0.032 -10000 0 -0.67 1 1
TACC3 0.027 0.008 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.046 0.02 -10000 0 -10000 0 0
Aurora A/RasGAP 0.03 0.024 -10000 0 -10000 0 0
OAZ1 0.025 0.008 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.024 0.01 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.017 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.008 0.027 -10000 0 -10000 0 0
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 0.017 0.03 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
CKAP5 0.027 0.005 -10000 0 -10000 0 0
TRAIL signaling 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
TNFSF10 0.024 0.045 -10000 0 -0.67 2 2
positive regulation of NF-kappaB transcription factor activity 0.037 0.036 -10000 0 -0.5 2 2
MAP2K4 0.027 0.044 -10000 0 -0.37 2 2
IKBKB 0.027 0.005 -10000 0 -10000 0 0
TNFRSF10B 0.027 0.005 -10000 0 -10000 0 0
TNFRSF10A 0.022 0.055 -10000 0 -0.67 3 3
SMPD1 0.015 0.028 -10000 0 -0.39 2 2
IKBKG 0.025 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.027 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR2 0.037 0.036 -10000 0 -0.5 2 2
TRAIL/TRAILR3 0.005 0.062 -10000 0 -0.5 2 2
TRAIL/TRAILR1 0.034 0.056 -10000 0 -0.5 5 5
TRAIL/TRAILR4 0.037 0.036 -10000 0 -0.5 2 2
TRAIL/TRAILR1/DAP3/GTP 0.043 0.048 -10000 0 -0.4 5 5
IKK complex 0.024 0.053 -10000 0 -0.46 1 1
RIPK1 0.027 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.019 0.006 -10000 0 -10000 0 0
MAPK3 0.014 0.034 -10000 0 -0.5 2 2
MAP3K1 0.028 0.046 -10000 0 -0.4 3 3
TRAILR4 (trimer) 0.027 0.005 -10000 0 -10000 0 0
TRADD 0.026 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.022 0.055 -10000 0 -0.67 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.041 -10000 0 -0.34 5 5
CFLAR 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.011 0.034 -10000 0 -0.49 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP 0.072 0.05 -10000 0 -0.38 5 5
mol:ceramide 0.015 0.028 -10000 0 -0.39 2 2
FADD 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.017 0.07 0.28 1 -0.36 10 11
TRAF2 0.025 0.009 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.014 0.066 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.048 0.051 -10000 0 -0.43 5 5
DAP3 0.025 0.007 -10000 0 -10000 0 0
CASP10 0.011 0.035 -10000 0 -0.43 2 2
JNK cascade 0.037 0.036 -10000 0 -0.5 2 2
TRAIL (trimer) 0.024 0.045 -10000 0 -0.67 2 2
TNFRSF10C -0.014 0.066 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.054 0.049 -10000 0 -0.38 5 5
TRAIL/TRAILR2/FADD 0.051 0.033 -10000 0 -0.43 2 2
cell death 0.015 0.028 -10000 0 -0.39 2 2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.03 0.033 -10000 0 -0.42 2 2
TRAILR2 (trimer) 0.027 0.005 -10000 0 -10000 0 0
CASP8 0.012 0.03 -10000 0 -0.58 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.075 0.036 -10000 0 -0.37 2 2
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.03 0.03 -10000 0 -10000 0 0
KLHL20 0.014 0.051 0.2 1 -10000 0 1
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.038 0.042 0.26 3 -10000 0 3
ENAH 0.027 0.027 -10000 0 -10000 0 0
AP1M1 0.025 0.008 -10000 0 -10000 0 0
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.035 0.015 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.031 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.056 0.066 -10000 0 -0.4 9 9
RAPGEF1 0.026 0.034 0.27 1 -10000 0 1
CTNND1 0.027 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.032 0.034 -10000 0 -10000 0 0
CRK 0.026 0.027 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0.051 0.016 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.023 0.077 -10000 0 -0.5 9 9
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.05 0.014 -10000 0 -10000 0 0
DLG1 0.029 0.033 -10000 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.008 0.016 -10000 0 -10000 0 0
MLLT4 0.027 0.004 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.055 0.031 -10000 0 -0.4 1 1
PI3K 0.016 0.022 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.038 0.011 -10000 0 -10000 0 0
TIAM1 -0.057 0.078 -10000 0 -0.67 1 1
E-cadherin(dimer)/Ca2+ 0.061 0.017 -10000 0 -10000 0 0
AKT1 0.018 0.021 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.046 0.067 0.4 9 -10000 0 9
actin cytoskeleton organization 0.013 0.04 0.19 3 -10000 0 3
CDC42/GDP 0.046 0.075 0.46 10 -10000 0 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.023 0.007 -10000 0 -10000 0 0
ITGB7 0.007 0.099 -10000 0 -0.64 10 10
RAC1 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.066 0.019 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.046 0.012 -10000 0 -10000 0 0
mol:GDP 0.036 0.081 0.49 10 -10000 0 10
CDC42/GTP/IQGAP1 0.036 0.008 -10000 0 -10000 0 0
JUP 0.026 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.045 0.043 0.28 1 -10000 0 1
RAC1/GTP/IQGAP1 0.035 0.009 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.037 0.012 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.012 0.036 0.21 4 -10000 0 4
NME1 0.026 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0.029 0.033 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.025 0.011 -10000 0 -10000 0 0
WASF2 0.007 0.022 -10000 0 -10000 0 0
Rap1/GTP 0.042 0.026 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.066 0.066 -10000 0 -0.38 9 9
CCND1 0.013 0.039 0.2 3 -10000 0 3
VAV2 0.007 0.14 -10000 0 -0.53 25 25
RAP1/GDP 0.048 0.039 0.3 4 -10000 0 4
adherens junction assembly 0.029 0.033 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.004 -10000 0 -10000 0 0
PIP5K1C 0.025 0.008 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.054 0.062 -10000 0 -0.36 9 9
E-cadherin/beta catenin 0.015 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC 0.03 0.03 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.67 3 3
Rac1/GTP -0.005 0.075 -10000 0 -0.32 1 1
E-cadherin/beta catenin/alpha catenin 0.053 0.014 -10000 0 -10000 0 0
ITGAE 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.033 0.035 -10000 0 -10000 0 0
Arf6 trafficking events

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.003 0.14 -10000 0 -0.65 20 20
CLTC 0.028 0.022 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.019 0.015 -10000 0 -10000 0 0
Dynamin 2/GTP 0.027 0.01 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
CD59 0.021 0.011 -10000 0 -10000 0 0
CPE 0.01 0.054 -10000 0 -0.43 7 7
CTNNB1 0.027 0.004 -10000 0 -10000 0 0
membrane fusion 0.019 0.012 -10000 0 -10000 0 0
CTNND1 0.022 0.037 0.36 3 -10000 0 3
DNM2 0.025 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.03 0.24 1 -10000 0 1
TSHR 0.015 0.029 -10000 0 -0.44 2 2
INS 0.01 0.058 -10000 0 -0.45 7 7
BIN1 0.027 0.005 -10000 0 -10000 0 0
mol:Choline 0.019 0.012 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.016 0.005 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.027 0.01 -10000 0 -10000 0 0
JUP 0.021 0.009 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.05 0.023 -10000 0 -0.4 1 1
ARF6/GTP 0.02 0.004 -10000 0 -10000 0 0
CDH1 0.021 0.011 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.02 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.009 -10000 0 -10000 0 0
positive regulation of endocytosis 0.02 0.004 -10000 0 -10000 0 0
EXOC2 0.027 0.004 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.033 0.014 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.046 0.025 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.016 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.035 0.01 -10000 0 -10000 0 0
ACAP1 0.023 0.014 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.017 0.01 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.028 0.024 -10000 0 -10000 0 0
JIP4/KLC1 0.049 0.014 -10000 0 -10000 0 0
EXOC1 0.027 0.004 -10000 0 -10000 0 0
exocyst 0.033 0.014 -10000 0 -10000 0 0
RALA/GTP 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.02 0.004 -10000 0 -10000 0 0
CTNNA1 0.02 0.029 0.36 1 -10000 0 1
NME1 0.016 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0.032 0.036 0.34 3 -10000 0 3
IL2RA 0.009 0.052 -10000 0 -0.23 20 20
VAMP3 0.016 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.024 0.071 -10000 0 -0.31 19 19
EXOC6 0.027 0.005 -10000 0 -10000 0 0
PLD1 0.018 0.005 -10000 0 -10000 0 0
PLD2 0.018 0.006 -10000 0 -10000 0 0
EXOC5 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.021 0.012 -10000 0 -10000 0 0
SDC1 0.021 0.012 -10000 0 -10000 0 0
ARF6/GDP 0.025 0.007 -10000 0 -10000 0 0
EXOC7 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.049 0.026 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.019 0.012 -10000 0 -10000 0 0
endocytosis -0.048 0.023 0.4 1 -10000 0 1
SCAMP2 0.027 0.004 -10000 0 -10000 0 0
ADRB2 0.029 0.086 0.41 10 -0.33 10 20
EXOC3 0.026 0.007 -10000 0 -10000 0 0
ASAP2 0.025 0.032 -10000 0 -0.67 1 1
Dynamin 2/GDP 0.03 0.011 -10000 0 -10000 0 0
KLC1 0.027 0.005 -10000 0 -10000 0 0
AVPR2 0.029 0.079 0.41 9 -0.33 9 18
RALA 0.026 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.046 0.026 -10000 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.025 0.017 -9999 0 -9999 0 0
PLK4 0.027 0.004 -9999 0 -9999 0 0
regulation of centriole replication 0.016 0.011 -9999 0 -9999 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.002 0.039 -10000 0 -10000 0 0
regulation of axonogenesis -0.012 0.02 0.27 2 -10000 0 2
myoblast fusion -0.011 0.027 -10000 0 -10000 0 0
mol:GTP 0.009 0.018 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.025 0.062 0.41 1 -10000 0 1
ARF1/GTP 0.03 0.013 -10000 0 -10000 0 0
mol:GM1 0.005 0.011 -10000 0 -10000 0 0
mol:Choline 0.009 0.013 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.026 -10000 0 -10000 0 0
MAPK3 0.009 0.025 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.026 0.063 -10000 0 -0.41 1 1
ARF1 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.011 0.027 -10000 0 -10000 0 0
ARF1/GDP 0.02 0.029 -10000 0 -10000 0 0
ARF6 0.03 0.008 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
TIAM1 -0.058 0.079 -10000 0 -0.67 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.023 -10000 0 -10000 0 0
actin filament bundle formation -0.024 0.029 -10000 0 -10000 0 0
KALRN 0.009 0.02 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.024 0.029 -10000 0 -10000 0 0
NME1 0.025 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.026 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.009 0.018 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.015 0.026 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
liver development 0.009 0.018 -10000 0 -10000 0 0
ARF6/GTP 0.009 0.018 -10000 0 -10000 0 0
RhoA/GTP 0.032 0.011 -10000 0 -10000 0 0
mol:GDP 0.009 0.02 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.046 0.015 -10000 0 -10000 0 0
RHOA 0.027 0.004 -10000 0 -10000 0 0
PLD1 0.013 0.017 -10000 0 -10000 0 0
RAB11FIP3 0.026 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.015 0.026 -10000 0 -10000 0 0
ruffle organization 0.012 0.02 -10000 0 -0.27 2 2
regulation of epithelial cell migration 0.009 0.018 -10000 0 -10000 0 0
PLD2 0.012 0.016 -10000 0 -10000 0 0
PIP5K1A 0.012 0.02 -10000 0 -0.27 2 2
mol:Phosphatidic acid 0.009 0.013 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.026 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.024 0.045 -9999 0 -0.67 2 2
Aurora C/Aurora B/INCENP 0.046 0.042 -9999 0 -0.45 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.009 0.013 -9999 0 -10000 0 0
AURKB -0.005 0.06 -9999 0 -10000 0 0
AURKC 0.02 0.029 -9999 0 -10000 0 0
Glypican 2 network

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
MDK -0.019 0.068 -9999 0 -9999 0 0
GPC2 0.016 0.037 -9999 0 -9999 0 0
GPC2/Midkine -0.004 0.059 -9999 0 -9999 0 0
neuron projection morphogenesis -0.004 0.058 -9999 0 -9999 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 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.001 0.014 -9999 0 -10000 0 0
MDM2/SUMO1 0.015 0.054 -9999 0 -10000 0 0
HDAC4 0.027 0.005 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 0.001 0.013 -9999 0 -10000 0 0
SUMO1 0.027 0.005 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.006 0.036 -9999 0 -0.24 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.012 0.008 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.026 0.005 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.027 0.005 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.058 -9999 0 -0.29 1 1
SUMO1/HDAC1 0.014 0.057 -9999 0 -0.27 2 2
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.066 0.018 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.009 -9999 0 -10000 0 0
Ran/GTP 0.006 0.047 -9999 0 -0.23 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.027 0.005 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.006 0.045 -9999 0 -10000 0 0
NPC 0.016 0.003 -9999 0 -10000 0 0
PIAS2 0.027 0.004 -9999 0 -10000 0 0
PIAS1 0.027 0.004 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.051 0.016 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.039 0.009 -9999 0 -9999 0 0
CTNNB1 0.027 0.004 -9999 0 -9999 0 0
JUP 0.026 0.007 -9999 0 -9999 0 0
CDH1 0.026 0.006 -9999 0 -9999 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 0.011 0.017 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.025 0.033 0.2 1 -0.17 2 3
AP2 0.038 0.011 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.036 0.011 -10000 0 -10000 0 0
CLTB 0.026 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.009 -10000 0 -10000 0 0
CD4 0.022 0.027 -10000 0 -10000 0 0
CLTA 0.025 0.007 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.006 0.024 -10000 0 -0.37 2 2
ARF1/GTP 0.028 0.02 -10000 0 -0.2 2 2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.015 0.007 -10000 0 -10000 0 0
mol:Choline 0.006 0.024 -10000 0 -0.36 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.026 0.009 -10000 0 -10000 0 0
DDEF1 0.007 0.028 -10000 0 -0.37 2 2
ARF1/GDP 0.004 0.017 -10000 0 -10000 0 0
AP2M1 0.027 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.014 0.006 -10000 0 -10000 0 0
Rac/GTP 0.021 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.036 0.015 -10000 0 -10000 0 0
ARFIP2 0.022 0.013 -10000 0 -10000 0 0
COPA 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.034 -10000 0 -0.48 1 1
ARF1/GTP/ARHGAP10 0.018 0.007 -10000 0 -10000 0 0
GGA3 0.026 0.007 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.024 0.022 -10000 0 -0.28 1 1
AP2A1 0.025 0.007 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.008 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.026 0.025 -10000 0 -0.25 2 2
Arfaptin 2/Rac/GDP 0.034 0.011 -10000 0 -10000 0 0
CYTH2 0.028 0.01 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.033 0.014 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.019 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.024 0.025 -10000 0 -10000 0 0
PLD2 0.006 0.024 -10000 0 -0.37 2 2
ARF-GAP1/v-SNARE 0.009 0.002 -10000 0 -10000 0 0
PIP5K1A 0.006 0.025 -10000 0 -0.37 2 2
ARF1/GTP/Membrin/GBF1/p115 0.023 0.02 -10000 0 -0.19 2 2
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.006 0.024 -10000 0 -0.36 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.009 0.002 -10000 0 -10000 0 0
GOSR2 0.014 0.013 -10000 0 -10000 0 0
USO1 0.014 0.013 -10000 0 -10000 0 0
GBF1 0.013 0.024 -10000 0 -0.3 2 2
ARF1/GTP/Arfaptin 2 0.035 0.014 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.051 0.017 -10000 0 -10000 0 0
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 0.038 0.011 -9999 0 -9999 0 0
FBXW11 0.026 0.006 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -9999 0 -9999 0 0
CHUK 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.072 0.027 -9999 0 -9999 0 0
NFKB1 0.027 0.004 -9999 0 -9999 0 0
MAP3K14 0.026 0.007 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.038 0.011 -9999 0 -9999 0 0
RELB 0.025 0.007 -9999 0 -9999 0 0
NFKB2 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.01 -9999 0 -9999 0 0
regulation of B cell activation 0.034 0.01 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 486 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.MK.A4N9 TCGA.MK.A4N7 TCGA.MK.A4N6 TCGA.L6.A4EU
109_MAP3K5 -0.2 0.027 0.027 0.027
47_PPARGC1A -0.67 -0.67 -0.67 0.028
105_BMP4 0.028 -0.12 0.028 0.028
105_BMP6 0.028 0.028 0.028 0.028
105_BMP7 0.028 0.028 0.028 0.028
105_BMP2 0.028 0.028 0.028 0.028
131_RELN/VLDLR -0.4 -0.4 -0.4 -0.4
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.027 0.027
84_STAT5B 0.04 -0.049 0.032 -0.048
84_STAT5A 0.04 -0.049 0.032 -0.048
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/THCA-TP/6044636/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/THCA-TP/6154813/GDAC_Gistic2Report_6156791/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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