PARADIGM pathway analysis of mRNASeq expression and copy number data
Thyroid Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1348JP0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1348JP0
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 35 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 247
Signaling events mediated by Stem cell factor receptor (c-Kit) 168
Reelin signaling pathway 136
Signaling events regulated by Ret tyrosine kinase 136
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 121
PDGFR-alpha signaling pathway 94
FOXA2 and FOXA3 transcription factor networks 88
Nongenotropic Androgen signaling 86
Signaling events mediated by the Hedgehog family 83
Noncanonical Wnt signaling pathway 81
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 501 . 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 ( 501 ).

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 0.4930 247 1731 7 -0.42 0 1000 -1000 -0.011 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3353 168 13123 78 -0.75 0.24 1000 -1000 -0.051 -1000
Reelin signaling pathway 0.2715 136 7635 56 -0.46 0.061 1000 -1000 -0.037 -1000
Signaling events regulated by Ret tyrosine kinase 0.2715 136 11193 82 -0.37 0.027 1000 -1000 -0.065 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2415 121 8258 68 -0.73 0.35 1000 -1000 -0.049 -1000
PDGFR-alpha signaling pathway 0.1876 94 4171 44 -0.4 0.043 1000 -1000 -0.034 -1000
FOXA2 and FOXA3 transcription factor networks 0.1756 88 4052 46 -0.84 0.031 1000 -1000 -0.063 -1000
Nongenotropic Androgen signaling 0.1717 86 4516 52 -0.26 0.19 1000 -1000 -0.034 -1000
Signaling events mediated by the Hedgehog family 0.1657 83 4329 52 -0.29 0.14 1000 -1000 -0.039 -1000
Noncanonical Wnt signaling pathway 0.1617 81 2118 26 -0.33 0.027 1000 -1000 -0.048 -1000
Wnt signaling 0.1537 77 542 7 -0.33 0.014 1000 -1000 -0.025 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1357 68 3677 54 -0.46 0.039 1000 -1000 -0.066 -1000
Calcium signaling in the CD4+ TCR pathway 0.1357 68 2119 31 -0.36 0.027 1000 -1000 -0.049 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1337 67 2311 34 -0.1 0.027 1000 -1000 -0.038 -1000
IL4-mediated signaling events 0.1297 65 5919 91 -1.2 0.57 1000 -1000 -0.064 -1000
Glypican 1 network 0.1257 63 3028 48 -0.3 0.052 1000 -1000 -0.025 -1000
Endothelins 0.1257 63 6054 96 -0.32 0.029 1000 -1000 -0.052 -1000
IGF1 pathway 0.1198 60 3456 57 -0.14 0.063 1000 -1000 -0.057 -1000
Ephrin B reverse signaling 0.1078 54 2592 48 -0.24 0.12 1000 -1000 -0.029 -1000
HIF-1-alpha transcription factor network 0.1058 53 4063 76 -0.49 0.041 1000 -1000 -0.068 -1000
Coregulation of Androgen receptor activity 0.1018 51 3896 76 -0.68 0.076 1000 -1000 -0.024 -1000
BMP receptor signaling 0.0998 50 4056 81 -0.44 0.052 1000 -1000 -0.063 -1000
TCR signaling in naïve CD8+ T cells 0.0978 49 4564 93 -0.16 0.046 1000 -1000 -0.049 -1000
IL23-mediated signaling events 0.0978 49 2994 60 -0.26 0.027 1000 -1000 -0.053 -1000
EPHB forward signaling 0.0958 48 4099 85 -0.24 0.11 1000 -1000 -0.066 -1000
Arf6 signaling events 0.0878 44 2753 62 -0.26 0.062 1000 -1000 -0.039 -1000
Glucocorticoid receptor regulatory network 0.0878 44 5063 114 -0.45 0.26 1000 -1000 -0.055 -1000
IL12-mediated signaling events 0.0798 40 3498 87 -0.36 0.029 1000 -1000 -0.069 -1000
Signaling mediated by p38-alpha and p38-beta 0.0798 40 1789 44 -0.22 0.027 1000 -1000 -0.023 -1000
Thromboxane A2 receptor signaling 0.0719 36 3825 105 -0.16 0.047 1000 -1000 -0.045 -1000
Hedgehog signaling events mediated by Gli proteins 0.0719 36 2377 65 -0.58 0.064 1000 -1000 -0.037 -1000
EGFR-dependent Endothelin signaling events 0.0619 31 669 21 -0.075 0.038 1000 -1000 -0.048 -1000
IL6-mediated signaling events 0.0599 30 2292 75 -0.15 0.054 1000 -1000 -0.043 -1000
Plasma membrane estrogen receptor signaling 0.0519 26 2240 86 -0.14 0.049 1000 -1000 -0.06 -1000
Ras signaling in the CD4+ TCR pathway 0.0519 26 452 17 -0.1 0.041 1000 -1000 -0.028 -1000
ErbB2/ErbB3 signaling events 0.0499 25 1628 65 -0.17 0.037 1000 -1000 -0.062 -1000
Syndecan-1-mediated signaling events 0.0499 25 852 34 -0.079 0.027 1000 -1000 -0.034 -1000
Osteopontin-mediated events 0.0499 25 975 38 -0.15 0.043 1000 -1000 -0.04 -1000
IFN-gamma pathway 0.0499 25 1762 68 -0.17 0.035 1000 -1000 -0.047 -1000
Regulation of p38-alpha and p38-beta 0.0499 25 1396 54 -0.36 0.065 1000 -1000 -0.051 -1000
FAS signaling pathway (CD95) 0.0479 24 1172 47 -0.2 0.042 1000 -1000 -0.035 -1000
Regulation of Androgen receptor activity 0.0479 24 1748 70 -0.45 0.036 1000 -1000 -0.058 -1000
BCR signaling pathway 0.0459 23 2337 99 -0.1 0.048 1000 -1000 -0.059 -1000
Syndecan-4-mediated signaling events 0.0459 23 1545 67 -0.16 0.039 1000 -1000 -0.036 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0439 22 1879 85 -0.22 0.14 1000 -1000 -0.043 -1000
Ceramide signaling pathway 0.0399 20 1559 76 -0.15 0.075 1000 -1000 -0.036 -1000
LPA receptor mediated events 0.0399 20 2078 102 -0.15 0.035 1000 -1000 -0.062 -1000
Fc-epsilon receptor I signaling in mast cells 0.0379 19 1924 97 -0.15 0.044 1000 -1000 -0.054 -1000
Signaling events mediated by PRL 0.0379 19 660 34 -0.087 0.04 1000 -1000 -0.039 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0359 18 1647 88 -0.26 0.039 1000 -1000 -0.066 -1000
ceramide signaling pathway 0.0339 17 842 49 -0.055 0.039 1000 -1000 -0.04 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0339 17 887 52 -0.18 0.057 1000 -1000 -0.032 -1000
Signaling events mediated by PTP1B 0.0319 16 1219 76 -0.19 0.039 1000 -1000 -0.034 -1000
Integrins in angiogenesis 0.0319 16 1420 84 -0.14 0.056 1000 -1000 -0.049 -1000
IL27-mediated signaling events 0.0319 16 862 51 -0.11 0.045 1000 -1000 -0.047 -1000
JNK signaling in the CD4+ TCR pathway 0.0299 15 269 17 -0.084 0.026 1000 -1000 -0.031 -1000
amb2 Integrin signaling 0.0299 15 1284 82 -0.19 0.035 1000 -1000 -0.042 -1000
LPA4-mediated signaling events 0.0279 14 175 12 -0.054 0.004 1000 -1000 -0.028 -1000
Visual signal transduction: Cones 0.0279 14 551 38 -0.043 0.043 1000 -1000 -0.016 -1000
p75(NTR)-mediated signaling 0.0279 14 1848 125 -0.28 0.071 1000 -1000 -0.061 -1000
mTOR signaling pathway 0.0279 14 793 53 -0.042 0.03 1000 -1000 -0.041 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0279 14 659 45 -0.056 0.076 1000 -1000 -0.042 -1000
Insulin Pathway 0.0279 14 1080 74 -0.054 0.065 1000 -1000 -0.045 -1000
VEGFR1 specific signals 0.0279 14 825 56 -0.045 0.058 1000 -1000 -0.053 -1000
Regulation of nuclear SMAD2/3 signaling 0.0259 13 1874 136 -0.26 0.053 1000 -1000 -0.043 -1000
Nectin adhesion pathway 0.0259 13 876 63 -0.11 0.073 1000 -1000 -0.055 -1000
Signaling events mediated by HDAC Class III 0.0259 13 554 40 -0.28 0.047 1000 -1000 -0.023 -1000
IL1-mediated signaling events 0.0259 13 862 62 -0.077 0.062 1000 -1000 -0.044 -1000
Rapid glucocorticoid signaling 0.0259 13 262 20 -0.061 0.034 1000 -1000 -0.006 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0259 13 1650 120 -0.24 0.074 1000 -1000 -0.049 -1000
Caspase cascade in apoptosis 0.0240 12 952 74 -0.056 0.046 1000 -1000 -0.035 -1000
Cellular roles of Anthrax toxin 0.0240 12 469 39 -0.056 0.027 1000 -1000 -0.02 -1000
Presenilin action in Notch and Wnt signaling 0.0240 12 759 61 -0.15 0.07 1000 -1000 -0.054 -1000
IL2 signaling events mediated by PI3K 0.0240 12 725 58 -0.059 0.048 1000 -1000 -0.042 -1000
FOXM1 transcription factor network 0.0240 12 662 51 -0.22 0.051 1000 -1000 -0.087 -1000
Syndecan-3-mediated signaling events 0.0220 11 397 35 -0.11 0.07 1000 -1000 -0.03 -1000
Visual signal transduction: Rods 0.0220 11 601 52 -0.073 0.045 1000 -1000 -0.027 -1000
ErbB4 signaling events 0.0200 10 744 69 -0.052 0.037 1000 -1000 -0.043 -1000
BARD1 signaling events 0.0200 10 576 57 -0.04 0.051 1000 -1000 -0.052 -1000
Syndecan-2-mediated signaling events 0.0200 10 721 69 -0.16 0.05 1000 -1000 -0.036 -1000
S1P1 pathway 0.0200 10 378 36 -0.054 0.027 1000 -1000 -0.037 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0200 10 750 74 -0.13 0.068 1000 -1000 -0.067 -1000
TCGA08_p53 0.0180 9 67 7 -0.025 0.025 1000 -1000 -0.013 -1000
Retinoic acid receptors-mediated signaling 0.0180 9 533 58 -0.037 0.054 1000 -1000 -0.035 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0160 8 690 83 -0.17 0.049 1000 -1000 -0.03 -1000
TCGA08_rtk_signaling 0.0160 8 225 26 -0.18 0.045 1000 -1000 -0.008 -1000
Regulation of Telomerase 0.0160 8 863 102 -0.19 0.071 1000 -1000 -0.05 -1000
S1P3 pathway 0.0160 8 365 42 -0.14 0.048 1000 -1000 -0.04 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0140 7 204 28 -0.14 0.056 1000 -1000 -0.023 -1000
Class I PI3K signaling events 0.0140 7 582 73 -0.19 0.05 1000 -1000 -0.046 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0140 7 249 33 -0.11 0.055 1000 -1000 -0.031 -1000
Class IB PI3K non-lipid kinase events 0.0140 7 21 3 -0.015 0.015 1000 -1000 -0.003 -1000
a4b1 and a4b7 Integrin signaling 0.0120 6 32 5 0.004 0.034 1000 -1000 -0.006 -1000
PLK1 signaling events 0.0120 6 554 85 -0.006 0.049 1000 -1000 -0.035 -1000
IL2 signaling events mediated by STAT5 0.0120 6 135 22 -0.033 0.033 1000 -1000 -0.034 -1000
TCGA08_retinoblastoma 0.0120 6 54 8 -0.035 0.031 1000 -1000 -0.001 -1000
Insulin-mediated glucose transport 0.0100 5 161 32 -0.085 0.05 1000 -1000 -0.022 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0100 5 627 125 -0.008 0.07 1000 -1000 -0.052 -1000
PDGFR-beta signaling pathway 0.0100 5 501 97 -0.15 0.079 1000 -1000 -0.052 -1000
S1P4 pathway 0.0100 5 140 25 -0.003 0.047 1000 -1000 -0.03 -1000
Aurora B signaling 0.0100 5 368 67 -0.32 0.1 1000 -1000 -0.039 -1000
Circadian rhythm pathway 0.0080 4 98 22 -0.017 0.04 1000 -1000 -0.023 -1000
Class I PI3K signaling events mediated by Akt 0.0080 4 304 68 -0.085 0.05 1000 -1000 -0.037 -1000
S1P5 pathway 0.0080 4 72 17 -0.007 0.032 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class I 0.0080 4 510 104 -0.056 0.063 1000 -1000 -0.034 -1000
Atypical NF-kappaB pathway 0.0080 4 126 31 -0.018 0.04 1000 -1000 -0.023 -1000
Canonical Wnt signaling pathway 0.0080 4 219 51 -0.037 0.065 1000 -1000 -0.049 -1000
Effects of Botulinum toxin 0.0080 4 127 26 -0.067 0.048 1000 -1000 -0.01 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0060 3 71 23 -0.016 0.049 1000 -1000 -0.025 -1000
Canonical NF-kappaB pathway 0.0060 3 149 39 -0.056 0.062 1000 -1000 -0.038 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0060 3 137 37 0 0.063 1000 -1000 -0.035 -1000
FoxO family signaling 0.0060 3 246 64 -0.085 0.1 1000 -1000 -0.051 -1000
Signaling mediated by p38-gamma and p38-delta 0.0060 3 53 15 -0.005 0.027 1000 -1000 -0.03 -1000
E-cadherin signaling in keratinocytes 0.0060 3 146 43 -0.03 0.051 1000 -1000 -0.039 -1000
p38 MAPK signaling pathway 0.0060 3 170 44 -0.032 0.049 1000 -1000 -0.025 -1000
Aurora A signaling 0.0040 2 128 60 -0.025 0.055 1000 -1000 -0.022 -1000
EPO signaling pathway 0.0040 2 158 55 -0.015 0.059 1000 -1000 -0.051 -1000
TRAIL signaling pathway 0.0040 2 109 48 -0.014 0.074 1000 -1000 -0.045 -1000
HIF-2-alpha transcription factor network 0.0040 2 126 43 -0.16 0.16 1000 -1000 -0.042 -1000
Paxillin-dependent events mediated by a4b1 0.0040 2 96 36 -0.053 0.055 1000 -1000 -0.04 -1000
E-cadherin signaling in the nascent adherens junction 0.0040 2 156 76 -0.059 0.066 1000 -1000 -0.059 -1000
Signaling events mediated by HDAC Class II 0.0020 1 89 75 -0.036 0.074 1000 -1000 -0.027 -1000
Arf6 trafficking events 0.0020 1 104 71 -0.048 0.05 1000 -1000 -0.024 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.016 0.027 1000 -1000 -0.015 -1000
Arf6 downstream pathway 0.0000 0 9 43 -0.061 0.045 1000 -1000 -0.031 -1000
Aurora C signaling 0.0000 0 4 7 -0.007 0.046 1000 -1000 -0.014 -1000
Glypican 2 network 0.0000 0 3 4 -0.02 0.016 1000 -1000 0.003 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 13 27 0 0.067 1000 -1000 -0.036 -1000
E-cadherin signaling events 0.0000 0 0 5 0.026 0.052 1000 -1000 0.003 -1000
Arf1 pathway 0.0000 0 21 54 -0.001 0.052 1000 -1000 -0.018 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.073 1000 -1000 -0.002 -1000
Total NA 3425 198957 7203 -22 8.1 131000 -131000 -5 -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 -0.48 339 339
EFNA5 -0.071 0.24 -9999 0 -0.67 69 69
FYN -0.3 0.24 -9999 0 -0.45 332 332
neuron projection morphogenesis -0.32 0.26 -9999 0 -0.48 339 339
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.32 0.26 -9999 0 -0.48 339 339
EPHA5 -0.42 0.33 -9999 0 -0.67 313 313
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 -0.39 278 279
CRKL -0.23 0.22 -10000 0 -0.41 285 285
HRAS -0.2 0.19 -10000 0 -0.4 104 104
mol:PIP3 -0.2 0.2 -10000 0 -0.39 254 254
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 -0.44 286 286
FOXO3 -0.19 0.21 0.37 2 -0.37 272 274
AKT1 -0.21 0.22 0.29 2 -0.39 278 280
BAD -0.19 0.2 0.28 1 -0.37 269 270
megakaryocyte differentiation -0.24 0.23 -10000 0 -0.43 295 295
GSK3B -0.19 0.21 0.31 3 -0.37 271 274
RAF1 -0.16 0.16 0.35 1 -0.35 68 69
SHC1 0.025 0.008 -10000 0 -10000 0 0
STAT3 -0.24 0.23 -10000 0 -0.44 280 280
STAT1 -0.6 0.56 -10000 0 -1.1 288 288
HRAS/SPRED1 -0.16 0.16 -10000 0 -0.35 70 70
cell proliferation -0.24 0.24 -10000 0 -0.44 289 289
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
TEC 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.23 0.23 -10000 0 -0.42 286 286
HRAS/SPRED2 -0.16 0.16 -10000 0 -0.35 71 71
LYN/TEC/p62DOK -0.21 0.24 -10000 0 -0.41 284 284
MAPK3 -0.11 0.12 0.26 5 -0.29 19 24
STAP1 -0.25 0.24 -10000 0 -0.45 286 286
GRAP2 -0.02 0.15 -10000 0 -0.56 33 33
JAK2 -0.5 0.48 -10000 0 -0.89 287 287
STAT1 (dimer) -0.58 0.54 -10000 0 -1 288 288
mol:Gleevec 0.008 0.011 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.21 0.24 -10000 0 -0.42 267 267
actin filament polymerization -0.24 0.23 -10000 0 -0.43 284 284
LYN 0.027 0.005 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.34 0.32 0.35 1 -0.61 287 288
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.19 0.21 -10000 0 -0.38 270 270
PI3K -0.21 0.24 -10000 0 -0.41 282 282
PTEN 0.026 0.018 -10000 0 -0.36 1 1
SCF/KIT/EPO/EPOR -0.7 0.66 -10000 0 -1.3 287 287
MAPK8 -0.25 0.24 -10000 0 -0.44 289 289
STAT3 (dimer) -0.23 0.23 -10000 0 -0.43 280 280
positive regulation of transcription -0.086 0.11 0.3 7 -0.24 17 24
mol:GDP -0.2 0.2 -10000 0 -0.38 235 235
PIK3C2B -0.23 0.23 -10000 0 -0.44 261 261
CBL/CRKL -0.21 0.22 -10000 0 -0.39 282 282
FER -0.24 0.24 -10000 0 -0.44 285 285
SH2B3 -0.24 0.23 -10000 0 -0.44 287 287
PDPK1 -0.19 0.2 0.3 3 -0.36 240 243
SNAI2 -0.24 0.24 -10000 0 -0.44 286 286
positive regulation of cell proliferation -0.42 0.4 -10000 0 -0.75 287 287
KITLG -0.017 0.094 -10000 0 -0.71 8 8
cell motility -0.42 0.4 -10000 0 -0.75 287 287
PTPN6 0.039 0.014 -10000 0 -10000 0 0
EPOR -0.16 0.19 -10000 0 -1.2 5 5
STAT5A (dimer) -0.34 0.33 -10000 0 -0.61 287 287
SOCS1 0.023 0.035 -10000 0 -0.67 1 1
cell migration 0.24 0.23 0.43 280 -10000 0 280
SOS1 0.027 0.005 -10000 0 -10000 0 0
EPO -0.008 0.031 -10000 0 -10000 0 0
VAV1 0.011 0.061 -10000 0 -0.57 3 3
GRB10 -0.24 0.23 -10000 0 -0.44 284 284
PTPN11 0.034 0.033 -10000 0 -0.66 1 1
SCF/KIT -0.25 0.25 -10000 0 -0.46 287 287
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.13 0.13 0.27 3 -0.32 17 20
CBL 0.027 0.005 -10000 0 -10000 0 0
KIT -0.75 0.68 -10000 0 -1.3 287 287
MAP2K2 -0.12 0.13 0.28 2 -0.32 17 19
SHC/Grb2/SOS1 -0.2 0.23 -10000 0 -0.42 249 249
STAT5A -0.35 0.34 -10000 0 -0.63 287 287
GRB2 0.026 0.007 -10000 0 -10000 0 0
response to radiation -0.24 0.24 -10000 0 -0.43 286 286
SHC/GRAP2 0 0.11 -10000 0 -0.39 33 33
PTPRO -0.25 0.23 -10000 0 -0.44 295 295
SH2B2 -0.24 0.23 -10000 0 -0.44 284 284
DOK1 0.027 0.005 -10000 0 -10000 0 0
MATK -0.24 0.23 -10000 0 -0.44 280 280
CREBBP -0.043 0.077 -10000 0 -10000 0 0
BCL2 -0.22 0.4 -10000 0 -1.5 42 42
Reelin signaling pathway

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
CDK5R1/CDK5 0.037 0.015 -10000 0 -10000 0 0
VLDLR -0.003 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 -0.45 351 351
MAPK8IP1/MKK7/MAP3K11/JNK1 0.061 0.067 -10000 0 -0.38 9 9
AKT1 -0.2 0.15 -10000 0 -0.3 337 337
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 -0.42 340 340
LRPAP1/LRP8 0.017 0.11 -10000 0 -0.51 20 20
RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.4 340 340
DAB1/alpha3/beta1 Integrin -0.25 0.21 -10000 0 -0.39 327 327
long-term memory -0.26 0.23 -10000 0 -0.4 339 339
DAB1/LIS1 -0.26 0.22 -10000 0 -0.4 333 333
DAB1/CRLK/C3G -0.25 0.21 -10000 0 -0.38 335 335
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
DAB1/NCK2 -0.26 0.22 -10000 0 -0.4 340 340
ARHGEF2 0.026 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 0.014 -10000 0 -10000 0 0
RELN -0.46 0.32 -10000 0 -0.67 343 343
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.3 0.24 -10000 0 -0.45 347 347
GRIN2A/RELN/LRP8/DAB1/Fyn -0.27 0.24 -10000 0 -0.42 339 339
MAPK8 0.013 0.095 -10000 0 -0.64 10 10
RELN/VLDLR/DAB1 -0.28 0.22 -10000 0 -0.41 351 351
ITGB1 0.027 0.004 -10000 0 -10000 0 0
MAP1B -0.28 0.21 -10000 0 -0.41 341 341
RELN/LRP8 -0.3 0.24 -10000 0 -0.45 346 346
GRIN2B/RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.41 339 339
PI3K 0.036 0.043 -10000 0 -0.51 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 0.49 3 -0.38 252 255
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 -0.14 0.13 -10000 0 -0.42 39 39
neuron adhesion -0.22 0.21 0.48 8 -0.64 25 33
LRP8 -0.001 0.14 -10000 0 -0.67 20 20
GSK3B -0.19 0.14 -10000 0 -0.28 337 337
RELN/VLDLR/DAB1/Fyn -0.26 0.21 -10000 0 -0.4 342 342
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.16 -10000 0 -0.31 352 352
CDK5 0.026 0.006 -10000 0 -10000 0 0
MAPT 0.052 0.17 0.82 20 -0.61 3 23
neuron migration -0.26 0.19 -10000 0 -0.39 320 320
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.14 0.13 -10000 0 -0.42 39 39
RELN/VLDLR -0.29 0.24 -10000 0 -0.43 345 345
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.061 0.097 -10000 0 -0.67 6 6
Crk/p130 Cas/Paxillin -0.22 0.19 -10000 0 -0.38 254 254
JUN -0.26 0.26 -10000 0 -0.58 156 156
HRAS 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.26 0.29 -10000 0 -0.49 287 287
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 -0.49 290 290
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 -0.41 265 265
RHOA 0.027 0.003 -10000 0 -10000 0 0
RAP1A/GTP -0.24 0.26 -10000 0 -0.44 284 284
GRB7 0.001 0.057 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.26 0.29 -10000 0 -0.49 283 283
MAPKKK cascade -0.23 0.24 -10000 0 -0.42 280 280
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.25 0.27 -10000 0 -0.46 286 286
lamellipodium assembly -0.19 0.18 -10000 0 -0.35 254 254
RET51/GFRalpha1/GDNF/SHC -0.26 0.29 -10000 0 -0.49 277 277
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
RET9/GFRalpha1/GDNF/SHC -0.2 0.22 -10000 0 -0.41 249 249
RET9/GFRalpha1/GDNF/Shank3 -0.21 0.21 -10000 0 -0.4 273 273
MAPK3 -0.24 0.23 -10000 0 -0.42 282 282
DOK1 0.027 0.005 -10000 0 -10000 0 0
DOK6 -0.083 0.26 -10000 0 -0.67 78 78
PXN 0.027 0.005 -10000 0 -10000 0 0
neurite development -0.26 0.25 -10000 0 -0.53 168 168
DOK5 -0.067 0.24 -10000 0 -0.67 67 67
GFRA1 -0.37 0.34 -10000 0 -0.67 281 281
MAPK8 -0.2 0.2 -10000 0 -0.54 72 72
HRAS/GTP -0.26 0.28 -10000 0 -0.47 287 287
tube development -0.19 0.2 -10000 0 -0.38 258 258
MAPK1 -0.24 0.23 0.32 3 -0.42 283 286
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.16 -10000 0 -0.3 258 258
Rac1/GDP 0.02 0.004 -10000 0 -10000 0 0
SRC 0.027 0.008 -10000 0 -10000 0 0
PDLIM7 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.3 0.34 -10000 0 -0.54 300 300
SHC1 0.025 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.26 0.29 -10000 0 -0.49 289 289
RET51/GFRalpha1/GDNF/Dok5 -0.31 0.34 -10000 0 -0.55 303 303
PRKCA 0.002 0.13 -10000 0 -0.67 17 17
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
CREB1 -0.19 0.21 -10000 0 -0.38 254 254
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.14 0.16 -10000 0 -0.29 242 242
RET51/GFRalpha1/GDNF/Grb7 -0.27 0.29 -10000 0 -0.49 286 286
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.1 0.26 -10000 0 -0.66 85 85
DOK4 0.026 0.009 -10000 0 -10000 0 0
JNK cascade -0.25 0.25 -10000 0 -0.56 156 156
RET9/GFRalpha1/GDNF/FRS2 -0.2 0.22 -10000 0 -0.41 265 265
SHANK3 0.02 0.013 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.15 0.16 -10000 0 -0.3 242 242
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.2 0.21 -10000 0 -0.35 286 286
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.2 0.21 -10000 0 -0.5 85 85
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.22 0.26 -10000 0 -0.4 273 273
PI3K -0.3 0.29 -10000 0 -0.55 259 259
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.19 0.21 -10000 0 -0.38 258 258
GRB10 0.026 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.18 0.18 -10000 0 -0.43 85 85
RET51/GFRalpha1/GDNF/FRS2 -0.26 0.29 -10000 0 -0.49 290 290
GAB1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.054 0.22 -10000 0 -0.67 58 58
IRS2 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.22 0.26 -10000 0 -0.4 273 273
RET51/GFRalpha1/GDNF/PKC alpha -0.27 0.3 -10000 0 -0.5 287 287
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 -0.54 304 304
Rac1/GTP -0.23 0.22 -10000 0 -0.42 254 254
RET9/GFRalpha1/GDNF -0.23 0.23 -10000 0 -0.44 278 278
GFRalpha1/GDNF -0.27 0.27 -10000 0 -0.5 279 279
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 -0.011 0.11 -10000 0 -0.31 34 34
NFATC2 -0.22 0.33 -10000 0 -0.7 135 135
NFATC3 -0.083 0.14 -10000 0 -0.28 127 127
CD40LG -0.63 0.55 -10000 0 -1.1 276 276
ITCH 0.038 0.016 -10000 0 -10000 0 0
CBLB 0.039 0.016 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.46 0.52 -10000 0 -1.1 160 160
JUNB 0.02 0.057 -10000 0 -0.6 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 -0.22 0.36 -10000 0 -0.72 137 137
Jun/NFAT1-c-4/p21SNFT -0.56 0.58 -10000 0 -1.1 247 247
AP-1/NFAT1-c-4 -0.72 0.73 -10000 0 -1.3 271 271
IKZF1 -0.17 0.28 -10000 0 -0.6 111 111
T-helper 2 cell differentiation -0.28 0.33 -10000 0 -0.78 120 120
AP-1/NFAT1 -0.32 0.41 -10000 0 -0.72 214 214
CALM1 0.038 0.012 -10000 0 -10000 0 0
EGR2 -0.73 0.78 -10000 0 -1.5 238 238
EGR3 -0.53 0.68 -10000 0 -1.1 233 233
NFAT1/FOXP3 -0.17 0.28 -10000 0 -0.55 145 145
EGR1 -0.12 0.28 -10000 0 -0.68 101 101
JUN -0.14 0.28 -10000 0 -0.67 108 108
EGR4 -0.016 0.15 -10000 0 -0.66 24 24
mol:Ca2+ 0.012 0.009 -10000 0 -10000 0 0
GBP3 -0.16 0.26 -10000 0 -0.56 121 121
FOSL1 0.005 0.055 -10000 0 -0.36 1 1
NFAT1-c-4/MAF/IRF4 -0.49 0.55 -10000 0 -0.98 247 247
DGKA -0.16 0.25 -10000 0 -0.55 111 111
CREM 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.5 0.55 -10000 0 -0.98 247 247
CTLA4 -0.2 0.31 -10000 0 -0.65 122 122
NFAT1-c-4 (dimer)/EGR1 -0.56 0.63 -10000 0 -1.1 243 243
NFAT1-c-4 (dimer)/EGR4 -0.52 0.55 -10000 0 -1 248 248
FOS -0.16 0.3 -10000 0 -0.68 125 125
IFNG -0.37 0.5 -10000 0 -1.1 143 143
T cell activation -0.39 0.39 -10000 0 -0.88 161 161
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 0.4 0.73 231 -10000 0 231
TNF -0.55 0.54 -10000 0 -1 259 259
FASLG -0.7 0.75 -10000 0 -1.4 250 250
TBX21 -0.02 0.15 -10000 0 -0.69 22 22
BATF3 0.018 0.043 -10000 0 -0.67 1 1
PRKCQ 0.017 0.074 -10000 0 -0.62 6 6
PTPN1 -0.16 0.25 -10000 0 -0.56 107 107
NFAT1-c-4/ICER1 -0.49 0.54 -10000 0 -0.98 244 244
GATA3 -0.006 0.15 -10000 0 -0.64 25 25
T-helper 1 cell differentiation -0.36 0.48 -10000 0 -1 144 144
IL2RA -0.42 0.46 -10000 0 -0.9 184 184
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.16 0.25 -10000 0 -0.55 114 114
E2F1 -0.013 0.07 -10000 0 -10000 0 0
PPARG 0.016 0.084 -10000 0 -0.67 7 7
SLC3A2 -0.16 0.25 -10000 0 -0.55 110 110
IRF4 -0.047 0.18 -10000 0 -0.66 37 37
PTGS2 -0.61 0.54 0.51 1 -1 266 267
CSF2 -0.62 0.52 -10000 0 -1.1 268 268
JunB/Fra1/NFAT1-c-4 -0.46 0.53 -10000 0 -0.96 239 239
IL4 -0.3 0.35 -10000 0 -0.84 116 116
IL5 -0.6 0.52 -10000 0 -1 265 265
IL2 -0.4 0.4 -10000 0 -0.9 158 158
IL3 -0.071 0.089 -10000 0 -0.86 2 2
RNF128 0.035 0.037 -10000 0 -0.75 1 1
NFATC1 -0.35 0.41 -10000 0 -0.73 231 231
CDK4 0.24 0.25 0.55 126 -10000 0 126
PTPRK -0.16 0.25 -10000 0 -0.55 113 113
IL8 -0.61 0.53 0.51 1 -1 269 270
POU2F1 0.026 0.01 -10000 0 -10000 0 0
PDGFR-alpha 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
PDGFRA -0.2 0.32 -10000 0 -0.69 149 149
PDGF/PDGFRA/CRKL -0.14 0.24 -10000 0 -0.5 149 149
positive regulation of JUN kinase activity -0.072 0.2 -10000 0 -0.4 129 129
CRKL 0.02 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.14 0.24 -10000 0 -0.52 147 147
AP1 -0.4 0.54 -10000 0 -1.2 135 135
mol:IP3 -0.16 0.24 -10000 0 -0.53 147 147
PLCG1 -0.16 0.24 -10000 0 -0.53 147 147
PDGF/PDGFRA/alphaV Integrin -0.14 0.25 -10000 0 -0.51 149 149
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 -0.52 147 147
CAV3 -0.011 0.019 -10000 0 -10000 0 0
CAV1 0.014 0.094 -10000 0 -0.67 9 9
SHC/Grb2/SOS1 -0.071 0.2 -10000 0 -0.4 129 129
PDGF/PDGFRA/Shf -0.14 0.24 -10000 0 -0.51 149 149
FOS -0.39 0.52 -10000 0 -1.2 135 135
JUN -0.15 0.22 -10000 0 -0.57 106 106
oligodendrocyte development -0.14 0.25 -10000 0 -0.51 149 149
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:DAG -0.16 0.24 -10000 0 -0.53 147 147
PDGF/PDGFRA -0.2 0.32 -10000 0 -0.69 149 149
actin cytoskeleton reorganization -0.13 0.24 -10000 0 -0.5 149 149
SRF 0.025 0.013 -10000 0 -10000 0 0
SHC1 0.025 0.008 -10000 0 -10000 0 0
PI3K -0.095 0.22 -10000 0 -0.43 149 149
PDGF/PDGFRA/Crk/C3G -0.094 0.22 -10000 0 -0.43 140 140
JAK1 -0.15 0.24 -10000 0 -0.51 149 149
ELK1/SRF -0.12 0.19 0.32 1 -0.41 140 141
SHB 0.026 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 -0.54 148 148
SOS1 0.027 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.072 0.2 -10000 0 -0.4 129 129
PDGF/PDGFRA/SHB -0.14 0.24 -10000 0 -0.5 149 149
PDGF/PDGFRA/Caveolin-1 -0.14 0.26 -10000 0 -0.52 150 150
ITGAV 0.024 0.045 -10000 0 -0.67 2 2
ELK1 -0.16 0.22 -10000 0 -0.49 145 145
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PDGF/PDGFRA/Crk -0.13 0.24 -10000 0 -0.5 147 147
JAK-STAT cascade -0.15 0.24 -10000 0 -0.5 149 149
cell proliferation -0.13 0.24 -10000 0 -0.5 149 149
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.47 0.49 -10000 0 -1 190 190
PCK1 -0.3 0.44 -10000 0 -1.3 65 65
HNF4A -0.61 0.6 -10000 0 -1.2 233 233
KCNJ11 -0.45 0.47 -10000 0 -1 169 169
AKT1 -0.065 0.14 -10000 0 -0.45 12 12
response to starvation -0.018 0.042 -10000 0 -0.49 2 2
DLK1 -0.45 0.47 -10000 0 -1 166 166
NKX2-1 -0.19 0.19 -10000 0 -0.4 152 152
ACADM -0.47 0.48 -10000 0 -1 177 177
TAT -0.18 0.2 -10000 0 -0.69 1 1
CEBPB 0.027 0.005 -10000 0 -10000 0 0
CEBPA 0.019 0.07 -10000 0 -0.67 5 5
TTR -0.14 0.22 0.68 6 -0.74 23 29
PKLR -0.46 0.48 -10000 0 -0.98 192 192
APOA1 -0.84 0.83 -10000 0 -1.7 234 234
CPT1C -0.47 0.49 -10000 0 -1 191 191
ALAS1 -0.16 0.19 -10000 0 -0.63 1 1
TFRC -0.23 0.27 -10000 0 -0.87 19 19
FOXF1 0.02 0.063 -10000 0 -0.67 4 4
NF1 0.031 0.008 -10000 0 -10000 0 0
HNF1A (dimer) 0.028 0.008 -10000 0 -10000 0 0
CPT1A -0.47 0.48 -10000 0 -0.98 200 200
HMGCS1 -0.47 0.48 -10000 0 -1 184 184
NR3C1 0.031 0.012 -10000 0 -10000 0 0
CPT1B -0.47 0.48 -10000 0 -1 175 175
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 -1.2 210 210
CREB1 0.009 0.066 -10000 0 -0.24 16 16
IGFBP1 -0.16 0.18 -10000 0 -10000 0 0
PDX1 -0.18 0.19 -10000 0 -10000 0 0
UCP2 -0.47 0.48 -10000 0 -1 177 177
ALDOB -0.44 0.47 -10000 0 -1 166 166
AFP -0.017 0.085 -10000 0 -0.4 2 2
BDH1 -0.47 0.48 -10000 0 -1 168 168
HADH -0.44 0.47 -10000 0 -1 167 167
F2 -0.58 0.58 -10000 0 -1.2 208 208
HNF1A 0.028 0.008 -10000 0 -10000 0 0
G6PC -0.001 0.067 -10000 0 -10000 0 0
SLC2A2 -0.22 0.23 -10000 0 -0.56 1 1
INS -0.025 0.053 -10000 0 -0.68 3 3
FOXA1 -0.009 0.096 -10000 0 -0.32 28 28
FOXA3 -0.027 0.12 -10000 0 -0.32 38 38
FOXA2 -0.5 0.54 -10000 0 -1.1 187 187
ABCC8 -0.7 0.66 -10000 0 -1.3 250 250
ALB -0.058 0.27 -10000 0 -1.1 30 30
Nongenotropic Androgen signaling

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
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.14 0.22 -10000 0 -0.4 194 194
regulation of S phase of mitotic cell cycle -0.1 0.16 -10000 0 -0.29 200 200
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
HRAS 0.025 0.011 -10000 0 -10000 0 0
SHBG/T-DHT 0.009 0.061 -10000 0 -0.44 9 9
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 -0.37 195 200
T-DHT/AR -0.2 0.26 -10000 0 -0.5 206 206
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 0.003 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.68 1 1
mol:GDP -0.21 0.26 -10000 0 -0.52 203 203
cell proliferation -0.2 0.26 0.46 11 -0.53 139 150
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
FOS -0.26 0.37 0.47 8 -0.84 130 138
mol:Ca2+ -0.026 0.029 -10000 0 -0.066 105 105
MAPK3 -0.16 0.24 0.5 12 -0.53 83 95
MAPK1 -0.18 0.22 0.31 4 -0.42 173 177
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 118 118
cAMP biosynthetic process 0.016 0.071 0.26 10 -0.41 9 19
GNG2 0.025 0.032 -10000 0 -0.67 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 118 118
HRAS/GTP -0.14 0.2 -10000 0 -0.38 195 195
actin cytoskeleton reorganization 0.038 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 -0.004 118 118
PI3K 0.033 0.038 -10000 0 -0.44 3 3
apoptosis 0.19 0.25 0.52 149 -0.41 7 156
T-DHT/AR/PELP1 -0.16 0.23 -10000 0 -0.44 204 204
HRAS/GDP -0.2 0.26 -10000 0 -0.5 202 202
CREB1 -0.21 0.27 0.42 7 -0.56 149 156
RAC1-CDC42/GTP 0.047 0.036 -10000 0 -0.37 3 3
AR -0.26 0.34 -10000 0 -0.67 206 206
GNB1 0.026 0.006 -10000 0 -10000 0 0
RAF1 -0.14 0.21 0.5 6 -0.38 195 201
RAC1-CDC42/GDP -0.17 0.26 -10000 0 -0.48 201 201
T-DHT/AR/PELP1/Src -0.14 0.22 -10000 0 -0.41 195 195
MAP2K2 -0.14 0.19 0.43 2 -0.37 191 193
T-DHT/AR/PELP1/Src/PI3K -0.1 0.16 -10000 0 -0.3 200 200
GNAZ 0.02 0.012 -10000 0 -10000 0 0
SHBG 0.013 0.094 -10000 0 -0.67 9 9
Gi family/GNB1/GNG2/GDP -0.032 0.099 -10000 0 -0.46 16 16
mol:T-DHT 0 0.003 0.001 58 -0.005 67 125
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 48 48
CDC42 0.027 0.005 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.087 0.21 -10000 0 -0.62 30 30
IHH -0.15 0.31 -10000 0 -0.7 119 119
SHH Np/Cholesterol/GAS1 -0.053 0.16 -10000 0 -0.4 84 84
LRPAP1 0.027 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.053 0.16 0.39 84 -10000 0 84
SMO/beta Arrestin2 -0.073 0.2 -10000 0 -0.42 108 108
SMO -0.094 0.21 -10000 0 -0.44 115 115
AKT1 -0.015 0.1 -10000 0 -0.61 2 2
ARRB2 0.026 0.007 -10000 0 -10000 0 0
BOC 0.016 0.088 -10000 0 -0.67 8 8
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping -0.093 0.2 -10000 0 -0.43 116 116
STIL -0.064 0.16 -10000 0 -0.49 14 14
DHH N/PTCH2 -0.05 0.2 -10000 0 -0.51 80 80
DHH N/PTCH1 -0.075 0.19 -10000 0 -0.37 127 127
PIK3CA 0.023 0.054 -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 33 33
determination of left/right symmetry -0.093 0.2 -10000 0 -0.43 116 116
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
skeletal system development -0.13 0.3 -10000 0 -1 33 33
IHH N/Hhip -0.29 0.33 -10000 0 -0.59 258 258
DHH N/Hhip -0.17 0.27 -10000 0 -0.51 190 190
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.093 0.2 -10000 0 -0.43 116 116
pancreas development -0.25 0.33 -10000 0 -0.67 189 189
HHAT 0.024 0.032 -10000 0 -0.67 1 1
PI3K 0.036 0.043 -10000 0 -0.51 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.1 0.26 -10000 0 -0.63 95 95
somite specification -0.093 0.2 -10000 0 -0.43 116 116
SHH Np/Cholesterol/PTCH1 -0.069 0.16 -10000 0 -0.34 105 105
SHH Np/Cholesterol/PTCH2 -0.043 0.15 -10000 0 -0.41 65 65
SHH Np/Cholesterol/Megalin -0.081 0.18 -10000 0 -0.38 126 126
SHH -0.005 0.029 -10000 0 -0.51 1 1
catabolic process -0.092 0.2 -10000 0 -0.4 140 140
SMO/Vitamin D3 -0.074 0.18 -10000 0 -0.38 107 107
SHH Np/Cholesterol/Hhip -0.14 0.2 -10000 0 -0.41 171 171
LRP2 -0.16 0.3 -10000 0 -0.66 131 131
receptor-mediated endocytosis -0.14 0.21 -10000 0 -0.59 43 43
SHH Np/Cholesterol/BOC 0.014 0.056 -10000 0 -0.37 9 9
SHH Np/Cholesterol/CDO -0.095 0.18 -10000 0 -0.38 145 145
mesenchymal cell differentiation 0.14 0.2 0.4 171 -10000 0 171
mol:Vitamin D3 -0.063 0.17 -10000 0 -0.36 70 70
IHH N/PTCH2 -0.17 0.29 -10000 0 -0.54 175 175
CDON -0.18 0.32 -10000 0 -0.67 146 146
IHH N/PTCH1 -0.09 0.21 -10000 0 -0.41 140 140
Megalin/LRPAP1 -0.1 0.24 -10000 0 -0.5 131 131
PTCH2 -0.084 0.26 -10000 0 -0.67 79 79
SHH Np/Cholesterol 0.009 0.023 -10000 0 -0.4 1 1
PTCH1 -0.093 0.2 -10000 0 -0.41 140 140
HHIP -0.25 0.33 -10000 0 -0.67 189 189
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.092 0.26 -10000 0 -0.67 84 84
GNB1/GNG2 -0.2 0.23 -10000 0 -0.53 113 113
mol:DAG -0.19 0.2 -10000 0 -0.49 112 112
PLCG1 -0.19 0.21 -10000 0 -0.51 112 112
YES1 -0.22 0.22 -10000 0 -0.54 116 116
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 0.28 2 -0.42 109 111
mol:Ca2+ -0.18 0.2 -10000 0 -0.47 112 112
mol:IP3 -0.19 0.2 -10000 0 -0.49 112 112
NLK 0 0.054 -10000 0 -0.81 2 2
GNB1 0.026 0.006 -10000 0 -10000 0 0
CAMK2A -0.17 0.19 0.29 2 -0.45 109 111
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.23 0.24 -10000 0 -0.55 125 125
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
GNAS -0.22 0.22 -10000 0 -0.54 114 114
GO:0007205 -0.18 0.2 -10000 0 -0.48 112 112
WNT6 0.02 0.027 -10000 0 -10000 0 0
WNT4 -0.19 0.32 -10000 0 -0.67 156 156
NFAT1/CK1 alpha -0.24 0.24 -10000 0 -0.55 140 140
GNG2 0.025 0.032 -10000 0 -0.67 1 1
WNT5A 0.014 0.094 -10000 0 -0.67 9 9
WNT11 -0.33 0.35 -10000 0 -0.67 252 252
CDC42 -0.2 0.21 -10000 0 -0.52 114 114
Wnt signaling

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
Noncanonical Wnts/FZD -0.23 0.24 -9999 0 -0.55 125 125
FZD6 0.027 0.005 -9999 0 -10000 0 0
WNT6 0.02 0.027 -9999 0 -10000 0 0
WNT4 -0.19 0.32 -9999 0 -0.67 156 156
FZD3 0.027 0.005 -9999 0 -10000 0 0
WNT5A 0.014 0.094 -9999 0 -0.67 9 9
WNT11 -0.33 0.35 -9999 0 -0.67 252 252
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.027 0.005 -10000 0 -10000 0 0
VLDLR -0.003 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 -0.45 346 346
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 -0.42 335 335
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 -0.062 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 0.017 0.11 -10000 0 -0.51 20 20
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.005 -10000 0 -10000 0 0
CDK5R1 0.025 0.014 -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 -0.31 0.23 -10000 0 -0.45 351 351
YWHAE 0.026 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.21 0.19 0.42 3 -0.55 21 24
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 -0.38 324 324
RELN -0.46 0.32 -10000 0 -0.67 343 343
PAFAH/LIS1 -0.027 0.15 -10000 0 -0.44 60 60
LIS1/CLIP170 0.031 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 0.15 -10000 0 -0.48 16 16
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.2 0.17 -10000 0 -0.3 333 333
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.23 0.18 0.64 1 -0.54 27 28
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 0.016 -10000 0 -10000 0 0
PAFAH1B2 0.016 0.084 -10000 0 -0.64 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 0.32 2 -0.56 18 20
LRP8 -0.001 0.14 -10000 0 -0.67 20 20
NDEL1/Katanin 60 -0.21 0.18 0.33 2 -0.57 19 21
P39/CDK5 -0.25 0.19 -10000 0 -0.38 333 333
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.031 0.01 -10000 0 -10000 0 0
CDK5 -0.27 0.19 -10000 0 -0.39 335 335
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 -0.4 331 331
RELN/VLDLR -0.29 0.24 -10000 0 -0.43 345 345
CDC42 0.017 0.006 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.01 0.068 -9999 0 -0.45 9 9
NFATC2 -0.08 0.17 -9999 0 -0.45 84 84
NFATC3 -0.002 0.031 -9999 0 -10000 0 0
CD40LG -0.34 0.37 -9999 0 -0.76 185 185
PTGS2 -0.31 0.35 -9999 0 -0.72 175 175
JUNB 0.02 0.057 -9999 0 -0.6 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.024 -9999 0 -10000 0 0
CaM/Ca2+ 0.007 0.024 -9999 0 -10000 0 0
CALM1 0.017 0.021 -9999 0 -10000 0 0
JUN -0.14 0.29 -9999 0 -0.67 108 108
mol:Ca2+ -0.008 0.02 -9999 0 -0.18 4 4
Calcineurin A alpha-beta B1/FKBP12/FK506 0.014 0.011 -9999 0 -10000 0 0
FOSL1 0.005 0.055 -9999 0 -0.36 1 1
CREM 0.027 0.004 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.18 0.25 -9999 0 -0.47 166 166
FOS -0.16 0.3 -9999 0 -0.68 125 125
IFNG -0.34 0.36 -9999 0 -0.73 195 195
AP-1/NFAT1-c-4 -0.36 0.45 -9999 0 -0.86 178 178
FASLG -0.32 0.35 -9999 0 -0.72 177 177
NFAT1-c-4/ICER1 -0.081 0.17 -9999 0 -0.41 91 91
IL2RA -0.32 0.34 -9999 0 -0.71 177 177
FKBP12/FK506 0.02 0.004 -9999 0 -10000 0 0
CSF2 -0.33 0.32 -9999 0 -0.7 175 175
JunB/Fra1/NFAT1-c-4 -0.071 0.18 -9999 0 -0.4 87 87
IL4 -0.31 0.32 -9999 0 -0.68 174 174
IL2 0.003 0.071 -9999 0 -1 2 2
IL3 -0.009 0.054 -9999 0 -0.92 1 1
FKBP1A 0.027 0.005 -9999 0 -10000 0 0
BATF3 0.018 0.043 -9999 0 -0.67 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.026 0.01 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.1 0.25 0.53 115 -10000 0 115
KIRREL -0.046 0.2 -10000 0 -0.69 41 41
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.1 0.25 -10000 0 -0.53 115 115
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 -0.057 0.21 -10000 0 -0.44 106 106
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.058 0.16 -10000 0 -0.35 103 103
FYN -0.063 0.2 0.28 26 -0.41 106 132
mol:Ca2+ -0.056 0.2 -10000 0 -0.43 105 105
mol:DAG -0.056 0.2 -10000 0 -0.43 105 105
NPHS2 -0.005 0.054 -10000 0 -0.74 1 1
mol:IP3 -0.056 0.2 -10000 0 -0.43 105 105
regulation of endocytosis -0.05 0.18 -10000 0 -0.39 103 103
Nephrin/NEPH1/podocin/Cholesterol -0.068 0.2 -10000 0 -0.43 108 108
establishment of cell polarity -0.1 0.25 -10000 0 -0.53 115 115
Nephrin/NEPH1/podocin/NCK1-2 -0.04 0.2 -10000 0 -0.4 105 105
Nephrin/NEPH1/beta Arrestin2 -0.049 0.18 -10000 0 -0.39 103 103
NPHS1 -0.1 0.26 -10000 0 -0.68 84 84
Nephrin/NEPH1/podocin -0.061 0.19 -10000 0 -0.41 106 106
TJP1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.003 -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 -0.055 0.2 -10000 0 -0.43 105 105
CD2AP 0.027 0.003 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.055 0.2 -10000 0 -0.43 103 103
GRB2 0.026 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.078 0.2 0.28 21 -0.42 107 128
cytoskeleton organization -0.082 0.2 -10000 0 -0.45 102 102
Nephrin/NEPH1 -0.072 0.19 -10000 0 -0.39 115 115
Nephrin/NEPH1/ZO-1 -0.069 0.21 -10000 0 -0.46 106 106
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.52 0.4 -10000 0 -1.2 80 80
STAT6 (cleaved dimer) -0.53 0.41 -10000 0 -0.95 176 176
IGHG1 -0.18 0.13 -10000 0 -0.39 9 9
IGHG3 -0.51 0.38 -10000 0 -0.89 180 180
AKT1 -0.27 0.28 0.62 2 -0.82 60 62
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.23 0.29 -10000 0 -1 48 48
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.31 0.3 -10000 0 -0.76 98 98
THY1 -0.52 0.4 -10000 0 -1.1 90 90
MYB 0.01 0.1 -10000 0 -0.65 11 11
HMGA1 0.027 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.35 0.31 -10000 0 -0.78 104 104
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.28 -10000 0 -0.84 59 59
SP1 0.03 0.012 -10000 0 -10000 0 0
INPP5D 0.019 0.034 -10000 0 -10000 0 0
SOCS5 0.041 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.52 0.41 -10000 0 -0.99 144 144
SOCS1 -0.36 0.26 -10000 0 -0.71 84 84
SOCS3 -0.32 0.33 0.6 2 -1 57 59
FCER2 -0.56 0.46 -10000 0 -1.1 150 150
PARP14 0.026 0.009 -10000 0 -10000 0 0
CCL17 -0.55 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 -0.22 0.2 -10000 0 -0.66 47 47
T cell proliferation -0.51 0.41 -10000 0 -1 122 122
IL4R/JAK1 -0.52 0.4 -10000 0 -1 125 125
EGR2 -0.86 0.68 -10000 0 -1.5 235 235
JAK2 -0.033 0.041 -10000 0 -0.39 2 2
JAK3 -0.012 0.067 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.003 0.021 -10000 0 -10000 0 0
COL1A2 -0.16 0.15 -10000 0 -1.2 3 3
CCL26 -0.52 0.4 -10000 0 -1.1 95 95
IL4R -0.55 0.43 -10000 0 -1.1 122 122
PTPN6 0.041 0.012 -10000 0 -10000 0 0
IL13RA2 -0.62 0.53 -10000 0 -1.3 140 140
IL13RA1 -0.031 0.033 -10000 0 -10000 0 0
IRF4 -0.31 0.5 -10000 0 -1.1 109 109
ARG1 -0.13 0.13 -10000 0 -0.79 3 3
CBL -0.33 0.29 -10000 0 -0.8 81 81
GTF3A 0.024 0.019 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
IL13RA1/JAK2 -0.038 0.047 -10000 0 -0.25 1 1
IRF4/BCL6 -0.28 0.46 -10000 0 -1 109 109
CD40LG -0.081 0.24 -10000 0 -0.64 77 77
MAPK14 -0.34 0.32 -10000 0 -0.88 81 81
mitosis -0.26 0.26 0.62 2 -0.77 61 63
STAT6 -0.58 0.48 -10000 0 -1.1 165 165
SPI1 0.022 0.035 -10000 0 -10000 0 0
RPS6KB1 -0.25 0.25 0.71 3 -0.74 54 57
STAT6 (dimer) -0.59 0.48 -10000 0 -1.1 166 166
STAT6 (dimer)/PARP14 -0.55 0.44 -10000 0 -1 162 162
mast cell activation 0.015 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.28 0.3 -10000 0 -0.91 62 62
FRAP1 -0.28 0.28 0.62 2 -0.82 61 63
LTA -0.53 0.4 -10000 0 -1.1 85 85
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.57 0.46 1 167 -10000 0 167
CCL11 -0.5 0.38 -10000 0 -1.1 95 95
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.3 -10000 0 -0.9 63 63
IL2RG -0.01 0.14 -10000 0 -0.62 21 21
IL10 -0.53 0.42 -10000 0 -1.1 113 113
IRS1 -0.054 0.22 -10000 0 -0.67 58 58
IRS2 0.026 0.006 -10000 0 -10000 0 0
IL4 -0.12 0.09 -10000 0 -10000 0 0
IL5 -0.52 0.4 -10000 0 -1.1 88 88
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.45 0.35 -10000 0 -0.88 124 124
COL1A1 -0.22 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 -0.52 0.42 -10000 0 -1.1 88 88
IL2R gamma/JAK3 -0.021 0.12 -10000 0 -0.51 18 18
TFF3 -1.2 0.58 -10000 0 -1.4 403 403
ALOX15 -0.52 0.4 -10000 0 -1.1 91 91
MYBL1 0.027 0.008 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.45 0.35 -10000 0 -0.88 122 122
SHC1 0.025 0.008 -10000 0 -10000 0 0
CEBPB 0.03 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.28 0.28 -10000 0 -0.87 52 52
mol:PI-3-4-5-P3 -0.28 0.28 0.62 2 -0.83 60 62
PI3K -0.29 0.3 0.68 1 -0.9 60 61
DOK2 0.019 0.052 -10000 0 -0.67 2 2
ETS1 0.04 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.19 0.38 1 -0.66 39 40
ITGB3 -0.53 0.43 -10000 0 -1.2 94 94
PIGR -0.55 0.45 -10000 0 -1.2 100 100
IGHE 0.047 0.044 0.24 9 -10000 0 9
MAPKKK cascade -0.2 0.19 0.48 2 -0.64 39 41
BCL6 0.026 0.032 -10000 0 -0.67 1 1
OPRM1 -0.53 0.4 -10000 0 -1.1 92 92
RETNLB -0.53 0.4 -10000 0 -1.1 85 85
SELP -0.52 0.41 -10000 0 -1.2 85 85
AICDA -0.51 0.38 -10000 0 -1 101 101
Glypican 1 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
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 -0.021 0.18 -9999 0 -0.66 34 34
PRNP 0.025 0.032 -9999 0 -0.67 1 1
GPC1/SLIT2 -0.041 0.19 -9999 0 -0.5 74 74
SMAD2 0.016 0.038 -9999 0 -0.4 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 34 34
TDGF1 -0.27 0.34 -9999 0 -0.67 212 212
CRIPTO/GPC1 -0.19 0.27 -9999 0 -0.5 212 212
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 -0.44 210 210
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 0.019 0.023 -9999 0 -10000 0 0
FYN -0.17 0.23 -9999 0 -0.44 210 210
FGR -0.17 0.22 -9999 0 -0.43 210 210
positive regulation of MAPKKK cascade -0.23 0.26 -9999 0 -0.51 210 210
SLIT2 -0.077 0.25 -9999 0 -0.67 74 74
GPC1/NRG -0.008 0.15 -9999 0 -0.5 43 43
NRG1 -0.033 0.19 -9999 0 -0.66 43 43
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.053 -9999 0 -0.57 3 3
LYN -0.17 0.22 -9999 0 -0.43 210 210
mol:Spermine 0.009 0.004 -9999 0 -10000 0 0
cell growth 0.052 0.025 -9999 0 -0.44 1 1
BMP signaling pathway -0.026 0.009 -9999 0 -10000 0 0
SRC -0.17 0.22 -9999 0 -0.44 210 210
TGFBR1 0.021 0.025 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.18 0.3 -9999 0 -0.67 132 132
GPC1 0.026 0.009 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.021 0.025 -9999 0 -10000 0 0
VEGFA 0.023 0.054 -9999 0 -0.67 3 3
BLK -0.3 0.3 -9999 0 -0.53 283 283
HCK -0.18 0.22 -9999 0 -0.44 210 210
FGF2 0.027 0.004 -9999 0 -10000 0 0
FGFR1 0.026 0.032 -9999 0 -0.67 1 1
VEGFR1 homodimer 0.024 0.032 -9999 0 -0.67 1 1
TGFBR2 0.023 0.054 -9999 0 -0.67 3 3
cell death 0.038 0.011 -9999 0 -10000 0 0
ATIII/GPC1 0.034 0.02 -9999 0 -10000 0 0
PLA2G2A/GPC1 -0.12 0.24 -9999 0 -0.51 132 132
LCK -0.18 0.22 -9999 0 -0.44 215 215
neuron differentiation -0.008 0.15 -9999 0 -0.49 43 43
PrPc/Cu2+ 0.019 0.024 -9999 0 -0.51 1 1
APP 0.027 0.006 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.023 0.054 -9999 0 -0.67 3 3
Endothelins

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
AKT1 -0.03 0.094 -10000 0 -0.45 9 9
PTK2B 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.28 0.47 1 -0.67 77 78
EDN1 -0.003 0.099 -10000 0 -0.53 9 9
EDN3 -0.31 0.35 -10000 0 -0.67 236 236
EDN2 0.011 0.082 -10000 0 -0.67 6 6
HRAS/GDP -0.11 0.23 0.45 3 -0.49 91 94
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.075 0.15 -10000 0 -0.35 84 84
ADCY4 -0.071 0.15 0.35 1 -0.41 66 67
ADCY5 -0.12 0.2 0.35 1 -0.45 112 113
ADCY6 -0.069 0.15 0.35 1 -0.4 65 66
ADCY7 -0.068 0.15 0.35 1 -0.4 66 67
ADCY1 -0.072 0.15 0.35 1 -0.42 66 67
ADCY2 -0.1 0.18 -10000 0 -0.44 92 92
ADCY3 -0.07 0.15 0.35 1 -0.4 69 70
ADCY8 -0.1 0.16 0.35 1 -0.44 68 69
ADCY9 -0.068 0.15 0.35 1 -0.4 65 66
arachidonic acid secretion -0.19 0.32 0.37 10 -0.62 144 154
ETB receptor/Endothelin-1/Gq/GTP -0.084 0.18 -10000 0 -0.37 120 120
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 0.029 0.11 -10000 0 -0.4 8 8
ETA receptor/Endothelin-1/Gs/GTP -0.028 0.18 -10000 0 -0.42 70 70
mol:GTP -0.003 0.009 -10000 0 -10000 0 0
COL3A1 -0.036 0.1 -10000 0 -0.48 9 9
EDNRB 0.015 0.079 -10000 0 -0.68 6 6
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.07 0.15 -10000 0 -0.6 23 23
CYSLTR1 -0.038 0.13 -10000 0 -0.67 15 15
SLC9A1 0 0.055 -10000 0 -0.27 9 9
mol:GDP -0.12 0.24 0.38 6 -0.51 94 100
SLC9A3 -0.055 0.21 -10000 0 -0.71 34 34
RAF1 -0.16 0.28 0.44 3 -0.56 133 136
JUN -0.29 0.49 0.46 1 -1.1 128 129
JAK2 -0.031 0.098 -10000 0 -0.47 11 11
mol:IP3 -0.1 0.2 -10000 0 -0.42 118 118
ETA receptor/Endothelin-1 0.011 0.13 -10000 0 -0.46 17 17
PLCB1 0.024 0.032 -10000 0 -0.68 1 1
PLCB2 0.02 0.025 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.24 0.28 -10000 0 -0.52 237 237
FOS -0.27 0.44 0.62 2 -1 128 130
Gai/GDP -0.011 0.15 -10000 0 -0.65 22 22
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.1 0.19 -10000 0 -0.48 58 58
BCAR1 0.026 0.006 -10000 0 -10000 0 0
PRKCB1 -0.11 0.2 -10000 0 -0.41 118 118
GNAQ 0.015 0.022 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAL -0.061 0.23 -10000 0 -0.66 64 64
Gs family/GDP -0.15 0.25 0.28 1 -0.53 115 116
ETA receptor/Endothelin-1/Gq/GTP -0.09 0.18 -10000 0 -0.37 112 112
MAPK14 -0.071 0.15 -10000 0 -0.38 61 61
TRPC6 -0.16 0.3 0.47 1 -0.71 77 78
GNAI2 0.027 0.003 -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 -0.073 0.16 -10000 0 -0.36 87 87
ETB receptor/Endothelin-2 0.02 0.087 -10000 0 -0.51 12 12
ETB receptor/Endothelin-3 -0.23 0.28 -10000 0 -0.51 239 239
ETB receptor/Endothelin-1 0.014 0.1 -10000 0 -0.55 11 11
MAPK3 -0.24 0.41 0.38 9 -0.87 131 140
MAPK1 -0.29 0.44 0.6 1 -0.98 131 132
Rac1/GDP -0.11 0.22 0.37 1 -0.48 87 88
cAMP biosynthetic process -0.076 0.18 0.49 9 -0.44 67 76
MAPK8 -0.19 0.36 0.48 1 -0.69 122 123
SRC 0.026 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.003 0.076 -10000 0 -0.32 16 16
p130Cas/CRK/Src/PYK2 -0.15 0.29 0.44 7 -0.54 132 139
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.22 0.37 1 -0.49 85 86
COL1A2 -0.007 0.11 -10000 0 -0.59 7 7
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.012 0.085 -10000 0 -0.53 7 7
mol:DAG -0.1 0.2 -10000 0 -0.42 118 118
MAP2K2 -0.19 0.34 0.4 11 -0.68 134 145
MAP2K1 -0.2 0.34 0.5 2 -0.7 138 140
EDNRA 0.001 0.073 -10000 0 -0.37 5 5
positive regulation of muscle contraction -0.024 0.08 -10000 0 -0.39 7 7
Gq family/GDP -0.15 0.28 0.38 1 -0.56 125 126
HRAS/GTP -0.14 0.24 0.33 6 -0.51 106 112
PRKCH -0.11 0.2 -10000 0 -0.45 91 91
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.12 0.22 -10000 0 -0.47 98 98
PRKCB -0.11 0.2 -10000 0 -0.45 94 94
PRKCE -0.11 0.2 -10000 0 -0.47 87 87
PRKCD -0.11 0.2 -10000 0 -0.45 93 93
PRKCG -0.1 0.2 -10000 0 -0.45 89 89
regulation of vascular smooth muscle contraction -0.32 0.52 0.65 2 -1.2 128 130
PRKCQ -0.11 0.2 -10000 0 -0.45 97 97
PLA2G4A -0.21 0.35 0.37 10 -0.69 144 154
GNA14 -0.14 0.29 -10000 0 -0.64 120 120
GNA15 0.007 0.052 -10000 0 -0.68 1 1
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA11 0.008 0.085 -10000 0 -0.64 8 8
Rac1/GTP 0.029 0.11 -10000 0 -0.39 9 9
MMP1 -0.035 0.08 0.62 2 -10000 0 2
IGF1 pathway

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
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 -0.36 151 151
GRB2/SOS1/SHC 0.048 0.02 -10000 0 -10000 0 0
HRAS 0.026 0.011 -10000 0 -10000 0 0
IRS1/Crk -0.091 0.19 -10000 0 -0.36 148 148
IGF-1R heterotetramer/IGF1/PTP1B -0.064 0.2 -10000 0 -0.43 107 107
AKT1 -0.089 0.17 -10000 0 -0.36 104 104
BAD -0.087 0.16 -10000 0 -0.59 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.097 0.18 -10000 0 -0.36 148 148
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.088 0.19 -10000 0 -0.37 152 152
RAF1 -0.068 0.15 0.39 1 -0.55 16 17
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.062 0.19 -10000 0 -0.35 145 145
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.096 0.21 -10000 0 -0.39 153 153
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
RPS6KB1 -0.088 0.17 -10000 0 -0.62 15 15
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.058 0.14 0.32 6 -0.46 14 20
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 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 -0.07 0.16 -10000 0 -0.35 99 99
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.028 0.17 -10000 0 -0.35 97 97
IGF-1R heterotetramer -0.008 0.058 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.077 0.2 -10000 0 -0.36 152 152
Crk/p130 Cas/Paxillin -0.056 0.19 -10000 0 -0.37 104 104
IGF1R -0.008 0.058 -10000 0 -10000 0 0
IGF1 -0.14 0.29 -10000 0 -0.69 108 108
IRS2/Crk -0.085 0.18 -10000 0 -0.35 146 146
PI3K -0.065 0.2 -10000 0 -0.35 152 152
apoptosis 0.063 0.15 0.5 15 -0.4 1 16
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
PRKCD -0.09 0.2 -10000 0 -0.45 106 106
RAF1/14-3-3 E -0.043 0.14 0.33 3 -0.46 16 19
BAD/14-3-3 -0.067 0.16 0.4 2 -0.54 15 17
PRKCZ -0.087 0.17 0.25 1 -0.36 105 106
Crk/p130 Cas/Paxillin/FAK1 -0.057 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 -0.092 0.21 -10000 0 -0.47 108 108
BCAR1 0.026 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.042 0.18 -10000 0 -0.38 104 104
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
IRS1/NCK2 -0.087 0.19 -10000 0 -0.36 152 152
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 -0.098 0.19 -10000 0 -0.36 152 152
IRS1 -0.11 0.2 -10000 0 -0.39 152 152
IRS2 -0.098 0.18 -10000 0 -0.36 152 152
IGF-1R heterotetramer/IGF1 -0.1 0.23 -10000 0 -0.54 108 108
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDPK1 -0.089 0.18 -10000 0 -0.38 107 107
YWHAE 0.026 0.007 -10000 0 -10000 0 0
PRKD1 -0.09 0.2 -10000 0 -0.45 106 106
SHC1 0.025 0.008 -10000 0 -10000 0 0
Ephrin B reverse signaling

Figure S19.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S19.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.026 0.006 -10000 0 -10000 0 0
EPHB2 0.022 0.055 -10000 0 -0.68 3 3
EFNB1 -0.002 0.085 -10000 0 -0.48 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.11 0.22 -10000 0 -0.39 185 185
Ephrin B2/EPHB1-2 -0.12 0.22 -10000 0 -0.4 185 185
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.38 185 185
Ephrin B1/EPHB1-2/Tiam1 -0.13 0.23 -10000 0 -0.42 192 192
DNM1 0.005 0.11 -10000 0 -0.63 15 15
cell-cell signaling -0.001 0.003 -10000 0 -10000 0 0
MAP2K4 -0.002 0.094 0.41 1 -0.65 8 9
YES1 0.004 0.11 -10000 0 -0.89 7 7
Ephrin B1/EPHB1-2/NCK2 -0.12 0.22 -10000 0 -0.39 186 186
PI3K 0.025 0.11 -10000 0 -0.83 7 7
mol:GDP -0.13 0.23 -10000 0 -0.41 192 192
ITGA2B -0.041 0.2 -10000 0 -0.67 48 48
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 0.088 -10000 0 -0.68 8 8
FGR 0.002 0.11 -10000 0 -0.85 8 8
TIAM1 -0.059 0.081 -10000 0 -0.67 1 1
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RGS3 0.025 0.008 -10000 0 -10000 0 0
cell adhesion -0.026 0.16 -10000 0 -0.43 57 57
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 -0.01 0.092 -10000 0 -0.77 7 7
SRC 0.002 0.11 -10000 0 -0.85 8 8
ITGB3 0.011 0.1 -10000 0 -0.65 11 11
EPHB1 -0.24 0.34 -10000 0 -0.67 188 188
EPHB4 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.034 0.011 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.025 0.18 -10000 0 -0.53 55 55
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 0.38 186 -10000 0 186
MAPK8 -0.006 0.12 0.36 5 -0.67 12 17
Ephrin B1/EPHB1-2/RGS3 -0.12 0.21 -10000 0 -0.38 186 186
endothelial cell migration -0.006 0.083 0.4 2 -0.62 7 9
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTPN13 0.024 0.091 -10000 0 -0.79 6 6
regulation of focal adhesion formation 0.12 0.21 0.38 186 -10000 0 186
chemotaxis 0.12 0.21 0.38 186 -10000 0 186
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
Rac1/GTP -0.12 0.22 -10000 0 -0.39 185 185
angiogenesis -0.011 0.094 -10000 0 -0.73 8 8
LCK 0 0.12 -10000 0 -0.9 8 8
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.21 0.33 -10000 0 -0.82 55 55
HDAC7 0.028 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.24 0.4 -10000 0 -0.82 107 107
SMAD4 0.028 0.005 -10000 0 -10000 0 0
ID2 -0.2 0.35 0.62 3 -0.85 45 48
AP1 -0.19 0.37 -10000 0 -0.72 149 149
ABCG2 -0.2 0.35 0.61 1 -0.86 50 51
HIF1A -0.021 0.073 -10000 0 -0.35 1 1
TFF3 -0.49 0.43 0.62 3 -0.92 169 172
GATA2 0.028 0.01 -10000 0 -10000 0 0
AKT1 -0.054 0.11 -10000 0 -0.25 29 29
response to hypoxia -0.071 0.11 -10000 0 -0.24 84 84
MCL1 -0.19 0.34 0.62 2 -0.85 45 47
NDRG1 -0.2 0.34 0.6 2 -0.83 51 53
SERPINE1 -0.2 0.34 0.61 1 -0.86 46 47
FECH -0.2 0.35 0.62 3 -0.86 44 47
FURIN -0.2 0.35 0.62 3 -0.85 46 49
NCOA2 -0.036 0.2 -10000 0 -0.67 45 45
EP300 -0.1 0.18 -10000 0 -0.34 163 163
HMOX1 -0.21 0.33 0.62 2 -0.85 46 48
BHLHE40 -0.2 0.35 0.62 2 -0.85 48 50
BHLHE41 -0.2 0.35 0.61 1 -0.84 49 50
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.029 0.1 -10000 0 -10000 0 0
ENG 0.01 0.092 0.47 3 -10000 0 3
JUN -0.12 0.29 -10000 0 -0.67 107 107
RORA -0.2 0.35 0.62 3 -0.86 46 49
ABCB1 -0.052 0.16 -10000 0 -1.2 8 8
TFRC -0.2 0.35 0.62 2 -0.87 47 49
CXCR4 -0.2 0.35 0.62 3 -0.83 51 54
TF -0.24 0.4 0.62 2 -0.94 75 77
CITED2 -0.22 0.39 0.61 3 -0.95 61 64
HIF1A/ARNT -0.22 0.38 -10000 0 -0.93 48 48
LDHA -0.033 0.11 -10000 0 -0.7 8 8
ETS1 -0.2 0.35 0.62 3 -0.84 49 52
PGK1 -0.2 0.34 0.61 1 -0.86 44 45
NOS2 -0.2 0.35 0.61 2 -0.84 49 51
ITGB2 -0.2 0.35 0.62 3 -0.86 46 49
ALDOA -0.2 0.34 0.61 1 -0.84 49 50
Cbp/p300/CITED2 -0.3 0.46 -10000 0 -0.98 113 113
FOS -0.15 0.3 -10000 0 -0.67 125 125
HK2 -0.2 0.35 0.62 3 -0.84 50 53
SP1 0.032 0.017 -10000 0 -10000 0 0
GCK -0.4 0.64 -10000 0 -1.4 137 137
HK1 -0.2 0.35 0.62 3 -0.84 49 52
NPM1 -0.2 0.34 0.61 1 -0.86 43 44
EGLN1 -0.19 0.34 0.62 2 -0.87 42 44
CREB1 0.033 0.006 -10000 0 -10000 0 0
PGM1 -0.2 0.35 0.62 2 -0.85 46 48
SMAD3 0.028 0.004 -10000 0 -10000 0 0
EDN1 -0.19 0.29 0.5 1 -0.69 76 77
IGFBP1 -0.2 0.34 0.61 1 -0.87 43 44
VEGFA -0.2 0.35 -10000 0 -0.73 91 91
HIF1A/JAB1 0.003 0.058 -10000 0 -10000 0 0
CP -0.32 0.46 0.62 2 -0.95 125 127
CXCL12 -0.24 0.4 0.62 3 -0.93 75 78
COPS5 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.041 0.009 -10000 0 -10000 0 0
BNIP3 -0.2 0.35 0.62 3 -0.84 48 51
EGLN3 -0.21 0.35 -10000 0 -0.86 54 54
CA9 -0.2 0.35 0.6 2 -0.84 51 53
TERT -0.2 0.34 0.6 1 -0.84 50 51
ENO1 -0.2 0.35 0.62 2 -0.85 46 48
PFKL -0.2 0.35 0.62 3 -0.84 49 52
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.21 0.36 0.62 3 -0.85 51 54
ARNT -0.015 0.071 -10000 0 -0.31 2 2
HNF4A -0.015 0.058 -10000 0 -0.22 4 4
ADFP -0.21 0.33 -10000 0 -0.82 55 55
SLC2A1 -0.2 0.35 -10000 0 -0.73 87 87
LEP -0.2 0.34 0.61 1 -0.86 44 45
HIF1A/ARNT/Cbp/p300 -0.26 0.41 -10000 0 -0.84 110 110
EPO -0.14 0.28 -10000 0 -0.91 21 21
CREBBP -0.081 0.17 -10000 0 -0.33 133 133
HIF1A/ARNT/Cbp/p300/HDAC7 -0.23 0.4 -10000 0 -0.82 102 102
PFKFB3 -0.2 0.35 0.62 3 -0.84 48 51
NT5E -0.2 0.36 0.62 2 -0.87 46 48
Coregulation of Androgen receptor activity

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
NRIP1 -0.006 0.053 -10000 0 -0.21 6 6
SVIL -0.003 0.048 -10000 0 -10000 0 0
ZNF318 0.076 0.087 0.26 3 -0.67 1 4
JMJD2C -0.066 0.067 -10000 0 -0.12 285 285
T-DHT/AR/Ubc9 -0.23 0.24 -10000 0 -0.49 209 209
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 0.002 0.04 -10000 0 -10000 0 0
AKT1 0.038 0.021 -10000 0 -10000 0 0
PTK2B 0.007 0.032 -10000 0 -10000 0 0
MED1 0.037 0.021 -10000 0 -10000 0 0
MAK 0.067 0.12 0.26 3 -0.65 7 10
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 -0.001 0.045 -10000 0 -10000 0 0
NCOA2 -0.039 0.2 -10000 0 -0.68 45 45
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 -0.003 0.15 -10000 0 -0.81 10 10
XRCC5 0.037 0.018 -10000 0 -10000 0 0
UBE3A -0.012 0.063 -10000 0 -0.18 1 1
T-DHT/AR/SNURF -0.25 0.26 -10000 0 -0.52 218 218
FHL2 -0.13 0.33 -10000 0 -1.1 45 45
RANBP9 -0.001 0.046 -10000 0 -10000 0 0
JMJD1A -0.006 0.032 -10000 0 -0.13 30 30
CDK6 0.023 0.055 -10000 0 -0.67 3 3
TGFB1I1 -0.003 0.048 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.24 0.24 -10000 0 -0.51 209 209
XRCC6 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR -0.28 0.26 -10000 0 -0.53 234 234
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 0.035 0.051 -10000 0 -10000 0 0
NKX3-1 -0.12 0.1 -10000 0 -0.21 241 241
KLK3 -0.39 0.65 -10000 0 -1.4 142 142
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 -0.072 142 142
APPL1 0.042 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.22 0.24 -10000 0 -0.48 208 208
AR -0.31 0.34 -10000 0 -0.71 206 206
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 0.049 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 -0.45 210 210
RPS6KA3 -0.003 0.046 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.23 0.24 -10000 0 -0.49 212 212
LATS2 0.041 0.043 -10000 0 -0.67 1 1
T-DHT/AR/PRX1 -0.2 0.22 -10000 0 -0.44 203 203
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.005 0.084 -10000 0 -0.68 6 6
KLK2 -0.68 0.55 -10000 0 -1.1 288 288
CASP8 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.24 0.27 -10000 0 -0.53 209 209
TMPRSS2 -0.16 0.27 -10000 0 -1.1 33 33
CCND1 0.013 0.031 -10000 0 -10000 0 0
PIAS1 -0.012 0.063 -10000 0 -10000 0 0
mol:T-DHT -0.034 0.04 -10000 0 -0.079 184 184
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.031 0.09 -10000 0 -0.19 51 51
T-DHT/AR/CDK6 -0.23 0.24 -10000 0 -0.48 216 216
CMTM2 0.029 0.012 -10000 0 -10000 0 0
SNURF -0.014 0.16 -10000 0 -0.65 29 29
ZMIZ1 -0.025 0.057 -10000 0 -0.67 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 0.046 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.16 0.3 -10000 0 -0.48 211 211
SMAD6-7/SMURF1 0.052 0.014 -10000 0 -10000 0 0
NOG -0.02 0.17 -10000 0 -0.67 30 30
SMAD9 -0.18 0.27 -10000 0 -0.54 169 169
SMAD4 0.027 0.005 -10000 0 -10000 0 0
SMAD5 -0.084 0.17 -10000 0 -0.33 115 115
BMP7/USAG1 -0.24 0.27 -10000 0 -0.51 250 250
SMAD5/SKI -0.069 0.17 0.3 4 -0.43 31 35
SMAD1 -0.036 0.094 -10000 0 -0.66 1 1
BMP2 0.001 0.13 -10000 0 -0.67 18 18
SMAD1/SMAD1/SMAD4 -0.021 0.085 -10000 0 -0.53 1 1
BMPR1A 0.027 0.005 -10000 0 -10000 0 0
BMPR1B -0.21 0.33 -10000 0 -0.67 164 164
BMPR1A-1B/BAMBI -0.11 0.24 -10000 0 -0.44 164 164
AHSG -0.005 0.042 -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 -0.066 0.16 -10000 0 -0.54 29 29
BMP2-4 (homodimer) 0.006 0.13 -10000 0 -0.51 29 29
RGMB 0.027 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.088 0.22 -10000 0 -0.4 163 163
RGMA 0.001 0.13 -10000 0 -0.66 19 19
SMURF1 0.026 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.079 0.16 -10000 0 -0.46 34 34
BMP2-4/USAG1 -0.22 0.26 -10000 0 -0.46 263 263
SMAD6/SMURF1/SMAD5 -0.068 0.17 0.32 1 -0.42 29 30
SOSTDC1 -0.33 0.35 -10000 0 -0.67 250 250
BMP7/BMPR2/BMPR1A-1B -0.088 0.22 -10000 0 -0.4 161 161
SKI 0.026 0.006 -10000 0 -10000 0 0
BMP6 (homodimer) 0.026 0.014 -10000 0 -10000 0 0
HFE2 -0.003 0.022 -10000 0 -10000 0 0
ZFYVE16 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.015 0.14 -10000 0 -0.45 38 38
SMAD5/SMAD5/SMAD4 -0.067 0.17 0.3 4 -0.42 31 35
MAPK1 0.02 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.054 0.15 -10000 0 -0.42 29 29
BMP7 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
NUP214 0.025 0.008 -10000 0 -10000 0 0
BMP6/FETUA 0.026 0.034 -10000 0 -10000 0 0
SMAD1/SKI -0.026 0.1 0.34 1 -0.62 1 2
SMAD6 0.027 0.004 -10000 0 -10000 0 0
CTDSP2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.022 0.12 -10000 0 -0.45 29 29
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.14 0.29 -10000 0 -0.66 114 114
BMPR2 (homodimer) 0.027 0.005 -10000 0 -10000 0 0
GADD34/PP1CA 0.046 0.047 -10000 0 -0.44 4 4
BMPR1A-1B (homodimer) -0.14 0.26 -10000 0 -0.51 164 164
CHRDL1 -0.44 0.32 -10000 0 -0.66 341 341
ENDOFIN/SMAD1 -0.029 0.098 -10000 0 -0.62 1 1
SMAD6-7/SMURF1/SMAD1 -0.013 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 0.25 -10000 0 -0.46 331 331
BMP2-4/GREM1 -0.079 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 -0.51 168 168
SMAD1/SMAD6 -0.027 0.096 -10000 0 -0.62 1 1
TAK1/SMAD6 0.039 0.01 -10000 0 -10000 0 0
BMP7 0.027 0.005 -10000 0 -10000 0 0
BMP6 0.026 0.014 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.058 0.13 -10000 0 -0.4 31 31
PPM1A 0.027 0.005 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.025 0.097 0.31 1 -0.62 1 2
SMAD7/SMURF1 0.039 0.01 -10000 0 -10000 0 0
CTDSPL 0.027 0.003 -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 0.02 0.063 -10000 0 -0.67 4 4
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.16 0.26 -10000 0 -0.64 88 88
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 -0.08 0.16 -10000 0 -0.49 32 32
BMP4 0.008 0.11 -10000 0 -0.65 12 12
FST -0.14 0.29 -10000 0 -0.67 112 112
BMP2-4/NOG -0.006 0.16 -10000 0 -0.44 58 58
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.073 0.21 -10000 0 -0.38 158 158
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.057 0.24 0.29 20 -0.59 71 91
FYN -0.1 0.32 0.46 1 -0.78 74 75
LAT/GRAP2/SLP76 -0.083 0.25 -10000 0 -0.63 76 76
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 -0.062 0.21 0.52 10 -0.47 77 87
B2M 0.027 0.006 -10000 0 -10000 0 0
IKBKG -0.016 0.057 0.14 3 -0.16 28 31
MAP3K8 0.018 0.079 -10000 0 -0.63 7 7
mol:Ca2+ -0.03 0.042 0.092 5 -0.11 102 107
integrin-mediated signaling pathway 0.034 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.3 0.46 5 -0.73 78 83
TRPV6 -0.1 0.35 0.99 20 -0.68 103 123
CD28 -0.014 0.15 -10000 0 -0.65 25 25
SHC1 -0.1 0.32 0.3 21 -0.79 74 95
receptor internalization -0.13 0.34 -10000 0 -0.66 118 118
PRF1 -0.11 0.33 -10000 0 -0.89 63 63
KRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.046 0.16 0.4 6 -0.38 77 83
LAT -0.11 0.31 0.3 4 -0.78 76 80
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.048 0.21 -10000 0 -0.64 52 52
CD3E -0.03 0.19 -10000 0 -0.63 42 42
CD3G -0.096 0.26 -10000 0 -0.65 88 88
RASGRP2 -0.004 0.033 0.094 3 -0.18 12 15
RASGRP1 -0.051 0.22 0.54 12 -0.47 76 88
HLA-A 0 0.006 0.063 2 -10000 0 2
RASSF5 0.025 0.008 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.034 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.017 0.14 0.34 30 -0.13 46 76
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.048 0.085 -10000 0 -0.25 60 60
PRKCA -0.035 0.12 -10000 0 -0.29 71 71
GRAP2 -0.02 0.15 -10000 0 -0.56 33 33
mol:IP3 -0.033 0.21 0.26 72 -0.44 74 146
EntrezGene:6957 0 0.005 0.045 2 -10000 0 2
TCR/CD3/MHC I/CD8 -0.13 0.35 -10000 0 -0.88 73 73
ORAI1 0.046 0.21 0.7 2 -0.78 16 18
CSK -0.11 0.32 -10000 0 -0.79 77 77
B7 family/CD28 -0.11 0.35 -10000 0 -0.81 80 80
CHUK 0.027 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.14 0.38 -10000 0 -0.91 82 82
PTPN6 -0.12 0.32 0.24 1 -0.8 76 77
VAV1 -0.11 0.31 0.31 1 -0.78 75 76
Monovalent TCR/CD3 -0.11 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 -0.82 74 74
PAG1 -0.11 0.32 -10000 0 -0.8 77 77
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.14 0.38 -10000 0 -0.9 82 82
CD80 -0.043 0.21 -10000 0 -0.67 49 49
CD86 0.013 0.077 -10000 0 -0.68 5 5
PDK1/CARD11/BCL10/MALT1 -0.042 0.11 -10000 0 -0.29 61 61
HRAS 0.026 0.011 -10000 0 -10000 0 0
GO:0035030 -0.1 0.26 -10000 0 -0.63 81 81
CD8A -0.025 0.18 -10000 0 -0.66 38 38
CD8B -0.052 0.22 -10000 0 -0.65 55 55
PTPRC -0.009 0.14 -10000 0 -0.68 20 20
PDK1/PKC theta -0.076 0.26 0.61 12 -0.59 76 88
CSK/PAG1 -0.11 0.31 -10000 0 -0.78 74 74
SOS1 0.027 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.012 -10000 0 -10000 0 0
GRAP2/SLP76 -0.1 0.3 -10000 0 -0.75 77 77
STIM1 0.019 0.16 1.2 2 -0.9 9 11
RAS family/GTP 0.008 0.098 0.23 25 -0.19 43 68
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.38 -10000 0 -0.72 118 118
mol:DAG -0.059 0.16 0.14 6 -0.4 75 81
RAP1A/GDP 0.008 0.059 0.19 17 -0.066 10 27
PLCG1 0.027 0.005 -10000 0 -10000 0 0
CD247 -0.001 0.13 -10000 0 -0.68 17 17
cytotoxic T cell degranulation -0.1 0.31 -10000 0 -0.83 64 64
RAP1A/GTP -0.001 0.012 -10000 0 -0.067 11 11
mol:PI-3-4-5-P3 -0.083 0.24 0.54 8 -0.58 78 86
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.051 0.26 0.28 67 -0.59 74 141
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 0 0.13 -10000 0 -0.66 17 17
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.082 0.24 -10000 0 -0.59 76 76
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
CD8 heterodimer -0.057 0.24 -10000 0 -0.59 75 75
CARD11 -0.019 0.12 -10000 0 -0.67 11 11
PRKCB -0.032 0.12 -10000 0 -0.3 66 66
PRKCE -0.031 0.12 -10000 0 -0.29 62 62
PRKCQ -0.095 0.29 0.59 9 -0.69 75 84
LCP2 0.024 0.021 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
regulation of survival gene product expression -0.049 0.18 0.51 10 -0.4 76 86
IKK complex 0.018 0.13 0.38 26 -0.13 11 37
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 -0.035 0.12 0.27 4 -0.29 63 67
PDPK1 -0.059 0.2 0.53 11 -0.45 75 86
TCR/CD3/MHC I/CD8/Fyn -0.16 0.41 -10000 0 -1 80 80
IL23-mediated signaling events

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
CCL2 -0.18 0.53 -10000 0 -1.3 77 77
IL23A -0.2 0.54 -10000 0 -1.3 85 85
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.54 -10000 0 -1.2 81 81
positive regulation of T cell mediated cytotoxicity -0.22 0.61 -10000 0 -1.4 88 88
ITGA3 -0.17 0.5 -10000 0 -1.2 76 76
IL17F -0.094 0.33 0.64 2 -0.74 74 76
IL12B 0.003 0.097 -10000 0 -0.7 7 7
STAT1 (dimer) -0.2 0.58 -10000 0 -1.3 84 84
CD4 -0.17 0.49 -10000 0 -1.2 74 74
IL23 -0.19 0.52 -10000 0 -1.2 84 84
IL23R 0.006 0.1 -10000 0 -0.82 2 2
IL1B -0.21 0.56 -10000 0 -1.4 78 78
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.16 0.5 -10000 0 -1.2 74 74
TYK2 0.016 0.035 -10000 0 -10000 0 0
STAT4 0.004 0.099 -10000 0 -0.59 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
IL18RAP -0.012 0.15 -10000 0 -0.68 23 23
IL12RB1 -0.004 0.089 -10000 0 -0.66 6 6
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
IL12Rbeta1/TYK2 0.011 0.078 -10000 0 -0.51 6 6
IL23R/JAK2 0.013 0.13 -10000 0 -0.72 2 2
positive regulation of chronic inflammatory response -0.22 0.61 -10000 0 -1.4 88 88
natural killer cell activation 0.001 0.009 -10000 0 -0.046 2 2
JAK2 0.016 0.052 -10000 0 -0.38 2 2
PIK3R1 0.027 0.005 -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 -0.17 0.49 -10000 0 -1.1 85 85
ALOX12B -0.17 0.49 -10000 0 -1.2 77 77
CXCL1 -0.18 0.52 -10000 0 -1.2 79 79
T cell proliferation -0.22 0.61 -10000 0 -1.4 88 88
NFKBIA 0.027 0.006 -10000 0 -10000 0 0
IL17A -0.051 0.26 -10000 0 -0.58 61 61
PI3K -0.18 0.55 -10000 0 -1.3 79 79
IFNG -0.015 0.053 0.12 1 -0.13 69 70
STAT3 (dimer) -0.16 0.51 -10000 0 -1.2 76 76
IL18R1 -0.002 0.096 -10000 0 -0.59 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.089 0.34 -10000 0 -0.81 61 61
IL18/IL18R -0.004 0.15 -10000 0 -0.49 36 36
macrophage activation -0.008 0.021 -10000 0 -0.045 79 79
TNF -0.24 0.6 -10000 0 -1.4 94 94
STAT3/STAT4 -0.19 0.55 -10000 0 -1.3 78 78
STAT4 (dimer) -0.21 0.58 -10000 0 -1.4 82 82
IL18 -0.009 0.11 -10000 0 -0.65 11 11
IL19 -0.16 0.5 -10000 0 -1.2 75 75
STAT5A (dimer) -0.2 0.57 -10000 0 -1.3 83 83
STAT1 0.023 0.023 -10000 0 -10000 0 0
SOCS3 -0.001 0.14 -10000 0 -0.67 19 19
CXCL9 -0.26 0.62 -10000 0 -1.4 109 109
MPO -0.17 0.5 -10000 0 -1.2 77 77
positive regulation of humoral immune response -0.22 0.61 -10000 0 -1.4 88 88
IL23/IL23R/JAK2/TYK2 -0.26 0.74 -10000 0 -1.6 85 85
IL6 -0.26 0.62 -10000 0 -1.3 112 112
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 -0.2 0.55 -10000 0 -1.3 85 85
keratinocyte proliferation -0.22 0.61 -10000 0 -1.4 88 88
NOS2 -0.17 0.49 -10000 0 -1.2 76 76
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.033 0.17 -10000 0 -0.44 71 71
cell-cell adhesion 0.11 0.16 0.32 172 -10000 0 172
Ephrin B/EPHB2/RasGAP 0.065 0.06 -10000 0 -0.38 7 7
ITSN1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
SHC1 0.025 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.026 0.048 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.14 0.23 -10000 0 -0.43 187 187
HRAS/GDP -0.079 0.16 -10000 0 -0.35 19 19
Ephrin B/EPHB1/GRB7 -0.099 0.23 -10000 0 -0.4 178 178
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 -0.096 0.22 -10000 0 -0.38 179 179
endothelial cell migration 0.052 0.037 -10000 0 -0.37 3 3
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.001 0.057 -10000 0 -10000 0 0
PAK1 0.024 0.075 0.47 5 -0.35 7 12
HRAS 0.026 0.011 -10000 0 -10000 0 0
RRAS 0.021 0.067 0.44 4 -0.36 6 10
DNM1 0.005 0.12 -10000 0 -0.62 16 16
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.12 0.18 -10000 0 -0.37 179 179
lamellipodium assembly -0.11 0.16 -10000 0 -0.32 172 172
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.085 0.16 -10000 0 -0.3 162 162
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
EPHB2 0.022 0.055 -10000 0 -0.67 3 3
EPHB3 -0.067 0.075 -10000 0 -10000 0 0
EPHB1 -0.24 0.34 -10000 0 -0.67 188 188
EPHB4 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.071 0.13 0.25 1 -0.38 13 14
Ephrin B/EPHB2 0.051 0.056 -10000 0 -0.38 7 7
Ephrin B/EPHB3 0.057 0.055 -10000 0 -0.43 4 4
JNK cascade -0.12 0.19 -10000 0 -0.38 176 176
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.38 180 180
RAP1/GDP -0.046 0.14 -10000 0 -0.34 13 13
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 -0.4 187 187
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.084 0.18 -10000 0 -0.38 21 21
Rap1/GTP -0.1 0.17 -10000 0 -0.33 162 162
axon guidance -0.034 0.17 -10000 0 -0.44 71 71
MAPK3 -0.081 0.14 -10000 0 -0.44 10 10
MAPK1 -0.079 0.13 -10000 0 -0.44 10 10
Rac1/GDP -0.057 0.13 -10000 0 -0.35 12 12
actin cytoskeleton reorganization -0.079 0.12 -10000 0 -0.33 4 4
CDC42/GDP -0.054 0.14 0.4 2 -0.35 13 15
PI3K 0.057 0.039 -10000 0 -0.38 3 3
EFNA5 -0.071 0.24 -10000 0 -0.67 69 69
Ephrin B2/EPHB4 0.034 0.011 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.026 0.044 -10000 0 -0.32 7 7
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.1 0.16 -10000 0 -0.41 8 8
PTK2 0.043 0.098 0.67 10 -10000 0 10
MAP4K4 -0.12 0.19 -10000 0 -0.38 176 176
SRC 0.027 0.008 -10000 0 -10000 0 0
KALRN 0.027 0.003 -10000 0 -10000 0 0
Intersectin/N-WASP 0.038 0.01 -10000 0 -10000 0 0
neuron projection morphogenesis -0.076 0.14 0.32 5 -0.32 2 7
MAP2K1 -0.082 0.15 -10000 0 -0.46 11 11
WASL 0.026 0.006 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.11 0.22 -10000 0 -0.4 176 176
cell migration -0.083 0.18 0.58 4 -0.48 13 17
NRAS 0.027 0.005 -10000 0 -10000 0 0
SYNJ1 0.023 0.074 0.45 6 -0.36 7 13
PXN 0.027 0.005 -10000 0 -10000 0 0
TF -0.024 0.13 0.47 3 -0.37 52 55
HRAS/GTP -0.092 0.19 -10000 0 -0.34 173 173
Ephrin B1/EPHB1-2 -0.12 0.22 -10000 0 -0.4 187 187
cell adhesion mediated by integrin -0.007 0.073 0.39 4 -0.35 9 13
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP -0.096 0.2 -10000 0 -0.36 176 176
RAC1-CDC42/GTP -0.14 0.16 -10000 0 -0.37 131 131
RASA1 0.027 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.048 0.14 -10000 0 -0.35 9 9
ruffle organization -0.1 0.18 0.57 5 -0.39 6 11
NCK1 0.027 0.003 -10000 0 -10000 0 0
receptor internalization 0.002 0.085 0.41 3 -0.37 17 20
Ephrin B/EPHB2/KALRN 0.065 0.06 -10000 0 -0.38 7 7
ROCK1 -0.025 0.044 -10000 0 -10000 0 0
RAS family/GDP -0.073 0.1 -10000 0 -0.34 3 3
Rac1/GTP -0.11 0.17 -10000 0 -0.34 172 172
Ephrin B/EPHB1/Src/Paxillin -0.091 0.16 -10000 0 -0.3 181 181
Arf6 signaling events

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
CENTA1/KIF3B 0.035 0.009 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.017 0.15 -10000 0 -0.71 12 12
EGFR 0.019 0.07 -10000 0 -0.67 5 5
EPHA2 0.026 0.013 -10000 0 -10000 0 0
USP6 0.025 0.014 -10000 0 -10000 0 0
IQSEC1 0.027 0.004 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.045 0.2 -10000 0 -0.5 76 76
ARRB2 -0.037 0.13 -10000 0 -0.39 62 62
mol:GTP 0.024 0.037 0.17 20 -10000 0 20
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 -0.68 2 2
EGF -0.076 0.25 -10000 0 -0.67 72 72
somatostatin receptor activity 0 0.001 0.002 14 -0.001 142 156
ARAP2 0.025 0.036 -10000 0 -0.52 2 2
mol:GDP -0.11 0.14 0.27 5 -0.31 111 116
mol:PI-3-4-5-P3 0 0 0.002 11 -0.001 56 67
ITGA2B -0.041 0.2 -10000 0 -0.67 48 48
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.062 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 -0.078 0.19 -10000 0 -0.52 70 70
PXN 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.11 0.16 0.51 8 -0.29 151 159
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.022 0.18 -10000 0 -0.44 74 74
ADRB2 0.011 0.1 -10000 0 -0.68 11 11
receptor agonist activity 0 0 0.001 17 0 149 166
actin filament binding 0 0 0.002 15 -0.001 138 153
SRC 0.026 0.008 -10000 0 -10000 0 0
ITGB3 0.011 0.1 -10000 0 -0.65 11 11
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 -0.006 0.092 0.25 2 -0.46 9 11
ARF6/GDP/GULP/ACAP1 -0.14 0.19 -10000 0 -0.41 120 120
alphaIIb/beta3 Integrin/paxillin/GIT1 0.012 0.16 -10000 0 -0.42 55 55
ACAP1 0.019 0.045 -10000 0 -0.52 2 2
ACAP2 0.027 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.053 0.19 -10000 0 -0.56 62 62
EFNA1 0.025 0.008 -10000 0 -10000 0 0
HGF -0.073 0.24 -10000 0 -0.67 70 70
CYTH3 0.006 0.033 -10000 0 -0.51 2 2
CYTH2 -0.008 0.15 -10000 0 -0.94 13 13
NCK1 0.027 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 21 0 98 119
endosomal lumen acidification 0 0 0.002 6 -0.001 142 148
microtubule-based process 0 0 -10000 0 0 7 7
GULP1 -0.093 0.26 -10000 0 -0.65 88 88
GNAQ/ARNO 0.005 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 10 0 15 25
MET -0.03 0.074 -10000 0 -10000 0 0
GNA14 -0.14 0.29 -10000 0 -0.64 120 120
GNA15 0.013 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 -0.001 101 116
GNA11 0.014 0.085 -10000 0 -0.64 8 8
LHCGR -0.078 0.23 -10000 0 -0.68 62 62
AGTR1 -0.26 0.34 -10000 0 -0.67 201 201
desensitization of G-protein coupled receptor protein signaling pathway -0.053 0.19 -10000 0 -0.56 62 62
IPCEF1/ARNO -0.035 0.18 -10000 0 -0.75 13 13
alphaIIb/beta3 Integrin -0.025 0.18 -10000 0 -0.53 55 55
Glucocorticoid receptor regulatory network

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
PCK2 0.084 0.087 0.36 1 -10000 0 1
SMARCC2 0.026 0.018 -10000 0 -10000 0 0
SMARCC1 0.026 0.018 -10000 0 -10000 0 0
TBX21 -0.12 0.24 -10000 0 -0.77 42 42
SUMO2 0.024 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.03 0.024 -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 0.34 48 -0.42 4 52
PRL -0.062 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.18 0.29 0.57 121 -0.46 20 141
RELA -0.026 0.098 -10000 0 -0.29 19 19
FGG 0.16 0.2 0.51 79 -10000 0 79
GR beta/TIF2 0.073 0.2 0.35 58 -0.45 45 103
IFNG -0.36 0.48 -10000 0 -1 138 138
apoptosis -0.016 0.23 0.51 32 -0.52 21 53
CREB1 0.026 0.014 -10000 0 -10000 0 0
histone acetylation -0.074 0.16 -10000 0 -0.42 60 60
BGLAP -0.077 0.13 -10000 0 -0.53 4 4
GR/PKAc 0.11 0.1 0.36 24 -0.34 1 25
NF kappa B1 p50/RelA -0.044 0.17 -10000 0 -0.45 39 39
SMARCD1 0.026 0.018 -10000 0 -10000 0 0
MDM2 0.085 0.097 0.25 85 -10000 0 85
GATA3 -0.004 0.15 -10000 0 -0.64 25 25
AKT1 0.021 0.004 -10000 0 -10000 0 0
CSF2 -0.12 0.14 -10000 0 -0.6 11 11
GSK3B 0.025 0.018 -10000 0 -10000 0 0
NR1I3 0.003 0.23 0.52 30 -0.57 11 41
CSN2 0.13 0.16 0.41 74 -10000 0 74
BRG1/BAF155/BAF170/BAF60A 0.063 0.054 -10000 0 -0.32 6 6
NFATC1 0.016 0.094 -10000 0 -0.67 9 9
POU2F1 0.026 0.01 -10000 0 -10000 0 0
CDKN1A 0.026 0.034 -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 -0.085 0.13 -10000 0 -0.67 15 15
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.14 0.36 31 -0.37 11 42
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.4 0.49 24 -0.83 104 128
JUN -0.24 0.27 -10000 0 -0.57 170 170
IL4 -0.099 0.16 -10000 0 -0.57 27 27
CDK5R1 0.026 0.015 -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 -0.66 157 157
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.11 0.37 26 -0.38 4 30
cortisol/GR alpha (monomer) 0.26 0.3 0.68 131 -10000 0 131
NCOA2 -0.037 0.2 -10000 0 -0.67 45 45
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.18 0.3 -10000 0 -0.69 126 126
AP-1/NFAT1-c-4 -0.38 0.41 -10000 0 -0.77 219 219
AFP -0.17 0.21 -10000 0 -0.62 41 41
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.14 0.45 48 -10000 0 48
TP53 0.041 0.015 -10000 0 -10000 0 0
PPP5C 0.025 0.008 -10000 0 -10000 0 0
KRT17 -0.29 0.34 -10000 0 -0.85 89 89
KRT14 -0.085 0.12 -10000 0 -0.48 8 8
TBP 0.034 0.007 -10000 0 -10000 0 0
CREBBP 0.036 0.046 -10000 0 -0.26 10 10
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 -0.77 219 219
MAPK14 0.027 0.016 -10000 0 -10000 0 0
MAPK10 0.025 0.035 -10000 0 -0.68 1 1
MAPK11 0.017 0.019 -10000 0 -10000 0 0
KRT5 -0.37 0.49 -10000 0 -1.1 132 132
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 0.024 -10000 0 -10000 0 0
CGA -0.095 0.14 -10000 0 -0.52 14 14
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.094 0.12 0.37 27 -10000 0 27
MAPK3 0.025 0.016 -10000 0 -10000 0 0
MAPK1 0.02 0.017 -10000 0 -10000 0 0
ICAM1 -0.16 0.24 -10000 0 -0.66 67 67
NFKB1 -0.025 0.096 -10000 0 -0.26 32 32
MAPK8 -0.14 0.18 -10000 0 -0.44 95 95
MAPK9 0.027 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.02 0.24 0.51 31 -0.55 21 52
BAX 0.04 0.093 0.85 5 -10000 0 5
POMC -0.45 0.63 -10000 0 -1.6 111 111
EP300 0.027 0.044 -10000 0 -0.26 8 8
cortisol/GR alpha (dimer)/p53 0.23 0.25 0.58 126 -10000 0 126
proteasomal ubiquitin-dependent protein catabolic process 0.08 0.13 0.34 80 -10000 0 80
SGK1 0.013 0.21 0.51 1 -1.3 10 11
IL13 -0.21 0.25 -10000 0 -0.76 47 47
IL6 -0.28 0.48 -10000 0 -1.2 102 102
PRKACG -0.009 0.016 -10000 0 -10000 0 0
IL5 -0.18 0.2 -10000 0 -0.72 28 28
IL2 -0.25 0.28 -10000 0 -0.74 76 76
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 -0.72 73 73
CDK5R1/CDK5 0.038 0.02 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.002 0.14 -10000 0 -0.39 21 21
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.55 128 -10000 0 128
SMARCA4 0.025 0.018 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.15 0.42 65 -0.44 1 66
NF kappa B1 p50/RelA/Cbp -0.006 0.16 -10000 0 -0.42 25 25
JUN (dimer) -0.24 0.27 -10000 0 -0.56 170 170
YWHAH 0.02 0.012 -10000 0 -10000 0 0
VIPR1 -0.22 0.36 -10000 0 -0.96 88 88
NR3C1 0.16 0.19 0.47 96 -10000 0 96
NR4A1 -0.26 0.36 -10000 0 -0.66 210 210
TIF2/SUV420H1 -0.011 0.16 -10000 0 -0.51 45 45
MAPKKK cascade -0.016 0.23 0.51 32 -0.52 21 53
cortisol/GR alpha (dimer)/Src-1 0.23 0.25 0.58 128 -10000 0 128
PBX1 0.025 0.032 -10000 0 -0.67 1 1
POU1F1 0.005 0.022 -10000 0 -10000 0 0
SELE -0.25 0.45 -10000 0 -1.1 88 88
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.15 0.42 65 -0.44 1 66
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.55 128 -10000 0 128
mol:cortisol 0.14 0.19 0.39 134 -10000 0 134
MMP1 -0.1 0.14 -10000 0 -0.87 10 10
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.029 0.14 -10000 0 -0.36 51 51
TBX21 -0.12 0.43 -10000 0 -1.1 60 60
B2M 0.023 0.018 -10000 0 -10000 0 0
TYK2 0.02 0.03 -10000 0 -10000 0 0
IL12RB1 0 0.088 -10000 0 -0.64 6 6
GADD45B -0.096 0.39 -10000 0 -1 57 57
IL12RB2 -0.003 0.13 -10000 0 -0.66 17 17
GADD45G -0.092 0.36 -10000 0 -0.98 50 50
natural killer cell activation 0.001 0.02 0.047 10 -0.04 36 46
RELB 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL18 -0.003 0.11 -10000 0 -0.66 11 11
IL2RA -0.017 0.16 -10000 0 -0.64 28 28
IFNG -0.073 0.23 -10000 0 -0.67 62 62
STAT3 (dimer) -0.081 0.32 -10000 0 -0.8 61 61
HLA-DRB5 -0.005 0.01 -10000 0 -0.022 105 105
FASLG -0.14 0.46 -10000 0 -1.2 64 64
NF kappa B2 p52/RelB -0.1 0.39 -10000 0 -0.96 64 64
CD4 0.011 0.036 -10000 0 -10000 0 0
SOCS1 0.023 0.035 -10000 0 -0.67 1 1
EntrezGene:6955 -0.007 0.015 -10000 0 -0.029 135 135
CD3D -0.061 0.2 -10000 0 -0.64 52 52
CD3E -0.043 0.18 -10000 0 -0.62 42 42
CD3G -0.11 0.26 -10000 0 -0.66 88 88
IL12Rbeta2/JAK2 0.012 0.11 -10000 0 -0.47 19 19
CCL3 -0.12 0.42 -10000 0 -1.2 55 55
CCL4 -0.15 0.49 -10000 0 -1.4 61 61
HLA-A -0.001 0.01 -10000 0 -0.038 27 27
IL18/IL18R 0.027 0.16 -10000 0 -0.49 36 36
NOS2 -0.088 0.36 -10000 0 -0.96 51 51
IL12/IL12R/TYK2/JAK2/SPHK2 -0.029 0.14 -10000 0 -0.34 58 58
IL1R1 -0.1 0.38 -10000 0 -1 53 53
IL4 0 0.034 -10000 0 -10000 0 0
JAK2 0.018 0.04 -10000 0 -0.38 2 2
EntrezGene:6957 -0.006 0.014 -10000 0 -0.027 129 129
TCR/CD3/MHC I/CD8 -0.21 0.49 -10000 0 -1.1 96 96
RAB7A -0.057 0.3 -10000 0 -0.84 37 37
lysosomal transport -0.051 0.29 -10000 0 -0.78 38 38
FOS -0.36 0.61 -10000 0 -1.2 157 157
STAT4 (dimer) -0.085 0.36 -10000 0 -0.88 64 64
STAT5A (dimer) -0.14 0.41 -10000 0 -0.94 81 81
GZMA -0.12 0.4 -10000 0 -1.1 53 53
GZMB -0.11 0.39 -10000 0 -1.1 49 49
HLX 0.022 0.025 -10000 0 -10000 0 0
LCK -0.13 0.43 -10000 0 -1.1 65 65
TCR/CD3/MHC II/CD4 -0.14 0.26 -10000 0 -0.5 120 120
IL2/IL2R -0.007 0.17 -10000 0 -0.55 37 37
MAPK14 -0.085 0.37 -10000 0 -0.93 60 60
CCR5 -0.095 0.4 -10000 0 -1.1 54 54
IL1B -0.025 0.18 -10000 0 -0.71 32 32
STAT6 -0.007 0.11 -10000 0 -0.46 5 5
STAT4 0.004 0.099 -10000 0 -0.59 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 0.004 0.09 -10000 0 -0.68 7 7
CD8A -0.028 0.18 -10000 0 -0.66 38 38
CD8B -0.055 0.21 -10000 0 -0.65 55 55
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.029 0.14 0.35 51 -10000 0 51
IL2RB 0.004 0.09 -10000 0 -0.58 10 10
proteasomal ubiquitin-dependent protein catabolic process -0.072 0.33 -10000 0 -0.78 64 64
IL2RG -0.012 0.14 -10000 0 -0.63 21 21
IL12 -0.037 0.18 -10000 0 -0.53 58 58
STAT5A 0.026 0.007 -10000 0 -10000 0 0
CD247 -0.013 0.13 -10000 0 -0.68 17 17
IL2 -0.003 0.02 -10000 0 -10000 0 0
SPHK2 0.026 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.055 0.22 -10000 0 -0.68 53 53
IL12/IL12R/TYK2/JAK2 -0.14 0.51 -10000 0 -1.2 65 65
MAP2K3 -0.086 0.37 -10000 0 -0.93 59 59
RIPK2 0.027 0.005 -10000 0 -10000 0 0
MAP2K6 -0.093 0.38 -10000 0 -0.92 64 64
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.005 0.011 -10000 0 -0.026 113 113
IL18RAP -0.006 0.15 -10000 0 -0.68 23 23
IL12Rbeta1/TYK2 0.019 0.076 -10000 0 -0.49 6 6
EOMES -0.13 0.4 -10000 0 -1.3 49 49
STAT1 (dimer) -0.12 0.36 -10000 0 -0.79 89 89
T cell proliferation -0.051 0.27 -10000 0 -0.62 65 65
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.005 0.096 -10000 0 -0.58 10 10
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.067 0.28 -10000 0 -0.67 69 69
ATF2 -0.088 0.34 -10000 0 -0.83 62 62
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.083 0.32 -10000 0 -1.2 39 39
MKNK1 0.027 0.005 -10000 0 -10000 0 0
MAPK14 -0.016 0.11 -10000 0 -0.34 37 37
ATF2/c-Jun -0.2 0.36 -10000 0 -0.8 122 122
MAPK11 -0.011 0.095 -10000 0 -0.35 27 27
MITF -0.022 0.12 -10000 0 -0.42 36 36
MAPKAPK5 -0.018 0.11 -10000 0 -0.41 32 32
KRT8 -0.018 0.11 -10000 0 -0.41 32 32
MAPKAPK3 0.027 0.003 -10000 0 -10000 0 0
MAPKAPK2 0.025 0.008 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.027 0.15 -10000 0 -0.48 37 37
CEBPB -0.02 0.12 -10000 0 -0.41 34 34
SLC9A1 -0.022 0.12 -10000 0 -0.41 37 37
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.074 0.19 -10000 0 -0.44 80 80
p38alpha-beta/MNK1 -0.009 0.13 -10000 0 -0.41 32 32
JUN -0.2 0.35 -10000 0 -0.79 122 122
PPARGC1A -0.22 0.25 -10000 0 -0.45 254 254
USF1 -0.023 0.12 -10000 0 -0.41 37 37
RAB5/GDP/GDI1 -0.035 0.1 -10000 0 -0.32 34 34
NOS2 -0.028 0.12 -10000 0 -0.48 16 16
DDIT3 -0.019 0.11 -10000 0 -0.4 33 33
RAB5A 0.027 0.004 -10000 0 -10000 0 0
HSPB1 -0.015 0.092 0.37 2 -0.34 30 32
p38alpha-beta/HBP1 -0.005 0.12 -10000 0 -0.42 26 26
CREB1 -0.054 0.16 -10000 0 -0.46 43 43
RAB5/GDP 0.02 0.003 -10000 0 -10000 0 0
EIF4E -0.024 0.1 -10000 0 -0.38 28 28
RPS6KA4 -0.02 0.12 -10000 0 -0.42 34 34
PLA2G4A -0.05 0.16 -10000 0 -0.48 50 50
GDI1 -0.018 0.12 -10000 0 -0.43 31 31
TP53 -0.031 0.13 -10000 0 -0.5 31 31
RPS6KA5 -0.062 0.18 -10000 0 -0.45 77 77
ESR1 -0.05 0.19 -10000 0 -0.54 52 52
HBP1 0.026 0.006 -10000 0 -10000 0 0
MEF2C -0.019 0.12 -10000 0 -0.41 33 33
MEF2A -0.024 0.12 -10000 0 -0.42 38 38
EIF4EBP1 -0.053 0.15 -10000 0 -0.45 44 44
KRT19 -0.051 0.16 -10000 0 -0.46 50 50
ELK4 -0.023 0.12 -10000 0 -0.41 37 37
ATF6 -0.023 0.12 -10000 0 -0.41 37 37
ATF1 -0.052 0.15 -10000 0 -0.46 41 41
p38alpha-beta/MAPKAPK2 -0.01 0.12 -10000 0 -0.41 32 32
p38alpha-beta/MAPKAPK3 -0.009 0.13 -10000 0 -0.42 32 32
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.005 0.053 -10000 0 -10000 0 0
GNB1/GNG2 -0.032 0.065 -10000 0 -0.19 67 67
AKT1 0.014 0.13 0.4 24 -0.21 18 42
EGF -0.075 0.25 -10000 0 -0.67 72 72
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.021 0.086 0.36 14 -0.5 2 16
mol:Ca2+ -0.014 0.15 0.38 18 -0.3 68 86
LYN 0.02 0.085 0.36 13 -0.5 2 15
RhoA/GTP -0.008 0.054 -10000 0 -0.15 2 2
mol:PGI2 0 0.001 -10000 0 -10000 0 0
SYK -0.015 0.17 0.43 19 -0.34 67 86
GNG2 0.025 0.032 -10000 0 -0.68 1 1
ARRB2 0.026 0.007 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.27 1 -0.59 12 13
G beta5/gamma2 -0.042 0.089 -10000 0 -0.25 67 67
PRKCH -0.021 0.17 0.44 15 -0.36 68 83
DNM1 0.005 0.12 -10000 0 -0.62 16 16
TXA2/TP beta/beta Arrestin3 -0.009 0.12 -10000 0 -0.53 20 20
mol:GTP 0 0.002 -10000 0 -10000 0 0
PTGDR -0.002 0.14 -10000 0 -0.67 20 20
G12 family/GTP -0.033 0.12 -10000 0 -0.31 65 65
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 0.047 0.14 0.39 38 -0.35 7 45
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 -0.67 136 136
mol:IP3 -0.024 0.18 0.44 15 -0.38 69 84
cell morphogenesis 0.036 0.007 -10000 0 -10000 0 0
PLCB2 -0.045 0.22 0.45 12 -0.52 68 80
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.077 0.17 0.36 10 -0.33 140 150
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.015 0.081 0.35 11 -0.5 2 13
RHOA 0.027 0.003 -10000 0 -10000 0 0
PTGIR 0.02 0.063 -10000 0 -0.68 4 4
PRKCB1 -0.024 0.17 0.43 14 -0.38 68 82
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 -0.042 0.23 0.49 14 -0.54 68 82
LCK 0.016 0.098 0.36 14 -0.53 5 19
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.027 0.081 -10000 0 -0.32 17 17
TXA2-R family/G12 family/GDP/G beta/gamma 0.031 0.033 -10000 0 -0.34 2 2
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.032 0.081 -10000 0 -0.32 18 18
MAPK14 -0.003 0.12 0.35 21 -0.23 60 81
TGM2/GTP -0.041 0.18 0.34 6 -0.43 63 69
MAPK11 -0.006 0.13 0.36 22 -0.23 59 81
ARHGEF1 -0.014 0.073 0.17 1 -0.19 37 38
GNAI2 0.027 0.003 -10000 0 -10000 0 0
JNK cascade -0.021 0.18 0.43 19 -0.39 68 87
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.013 0.14 0.38 19 -0.29 69 88
cAMP biosynthetic process -0.025 0.17 0.43 16 -0.36 63 79
Gq family/GTP/EBP50 -0.046 0.12 0.24 2 -0.33 27 29
actin cytoskeleton reorganization 0.036 0.007 -10000 0 -10000 0 0
SRC 0.018 0.08 0.35 11 -0.5 2 13
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.019 0.13 0.43 17 -0.29 14 31
VCAM1 -0.01 0.15 0.36 21 -0.3 69 90
TP beta/Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.27 1 -0.59 12 13
platelet activation -0.002 0.17 0.45 24 -0.3 65 89
PGI2/IP 0.015 0.048 -10000 0 -0.51 4 4
PRKACA 0.005 0.079 -10000 0 -0.35 21 21
Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.28 1 -0.56 12 13
TXA2/TP beta/beta Arrestin2 0.006 0.1 -10000 0 -0.54 16 16
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.001 0.079 -10000 0 -0.35 19 19
mol:DAG -0.029 0.19 0.45 14 -0.43 68 82
EGFR 0.019 0.07 -10000 0 -0.67 5 5
TXA2/TP alpha -0.041 0.22 0.5 14 -0.49 63 77
Gq family/GTP -0.066 0.13 0.22 2 -0.28 122 124
YES1 0.022 0.088 0.37 15 -0.5 2 17
GNAI2/GTP 0.009 0.069 -10000 0 -0.36 7 7
PGD2/DP -0.001 0.1 -10000 0 -0.51 20 20
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
FYN 0.024 0.089 0.36 17 -0.5 2 19
mol:NO 0.026 0.006 -10000 0 -10000 0 0
GNA15 0.013 0.05 -10000 0 -0.67 1 1
PGK/cGMP -0.092 0.21 -10000 0 -0.43 134 134
RhoA/GDP 0.028 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.04 0.091 -10000 0 -0.48 6 6
NOS3 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.024 0.18 0.44 17 -0.38 70 87
PRKCB -0.023 0.18 0.44 17 -0.37 67 84
PRKCE -0.027 0.16 0.37 12 -0.37 69 81
PRKCD -0.025 0.17 0.43 13 -0.38 68 81
PRKCG -0.024 0.18 0.41 18 -0.39 66 84
muscle contraction -0.034 0.22 0.5 15 -0.49 68 83
PRKCZ -0.014 0.17 0.4 22 -0.34 65 87
ARR3 -0.002 0.02 -10000 0 -10000 0 0
TXA2/TP beta 0.016 0.08 -10000 0 -0.33 15 15
PRKCQ -0.024 0.17 0.41 14 -0.36 70 84
MAPKKK cascade -0.034 0.21 0.46 16 -0.46 68 84
SELE -0.027 0.18 0.37 19 -0.42 69 88
TP beta/GNAI2/GDP/G beta/gamma 0.039 0.089 -10000 0 -0.8 2 2
ROCK1 0.027 0.005 -10000 0 -10000 0 0
GNA14 -0.14 0.29 -10000 0 -0.64 120 120
chemotaxis -0.049 0.26 0.55 12 -0.61 69 81
GNA12 0.026 0.006 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.015 0.084 -10000 0 -0.64 8 8
Rac1/GTP 0.019 0.005 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.045 0.042 -10000 0 -0.82 1 1
forebrain development -0.3 0.28 0.37 3 -0.53 246 249
GNAO1 0.002 0.12 -10000 0 -0.67 15 15
SMO/beta Arrestin2 0.015 0.036 -10000 0 -0.51 1 1
SMO 0.016 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 -0.34 6 6
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.003 -10000 0 -10000 0 0
GNAI2 0.025 0.005 -10000 0 -10000 0 0
SIN3/HDAC complex 0.064 0.033 -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 0.21 -10000 0 -0.49 135 135
SAP30 0.026 0.032 -10000 0 -0.67 1 1
mol:GDP 0.016 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 -0.34 11 13
GLI3 0.027 0.078 0.28 3 -0.35 6 9
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) 0.01 0.075 -10000 0 -0.49 3 3
FOXA2 -0.58 0.62 -10000 0 -1.2 242 242
neural tube patterning -0.3 0.28 0.37 3 -0.53 246 249
SPOP 0.026 0.007 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.035 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 0.067 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.3 0.28 0.37 3 -0.53 246 249
SUFU 0.019 0.016 -10000 0 -10000 0 0
LGALS3 -0.023 0.077 -10000 0 -0.67 1 1
catabolic process 0.032 0.1 -10000 0 -0.44 8 8
GLI3A/CBP -0.17 0.2 -10000 0 -0.38 245 245
KIF3A 0.027 0.006 -10000 0 -10000 0 0
GLI1 -0.3 0.28 0.41 2 -0.55 245 247
RAB23 0.022 0.063 -10000 0 -0.67 4 4
CSNK1A1 0.027 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 0.053 -10000 0 -0.4 1 1
GNAZ 0.018 0.012 -10000 0 -10000 0 0
RBBP4 0.025 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 0.011 0.081 -10000 0 -0.36 8 8
STK36 0.016 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.01 0.054 -10000 0 -0.31 6 6
PTCH1 -0.27 0.26 0.58 2 -0.59 135 137
MIM/GLI1 -0.42 0.37 0.35 1 -0.7 270 271
CREBBP -0.17 0.2 -10000 0 -0.38 245 245
Su(fu)/SIN3/HDAC complex 0.036 0.068 -10000 0 -0.53 5 5
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.026 0.011 -9999 0 -10000 0 0
EGFR 0.019 0.07 -9999 0 -0.67 5 5
EGF/EGFR -0.017 0.15 -9999 0 -0.37 78 78
EGF/EGFR dimer/SHC/GRB2/SOS1 0.003 0.16 -9999 0 -0.38 70 70
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 -0.075 0.25 -9999 0 -0.67 72 72
EGF/EGFR dimer/SHC -0.024 0.18 -9999 0 -0.43 76 76
mol:GDP -0.002 0.16 -9999 0 -0.38 70 70
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.019 0.071 -9999 0 -0.67 5 5
GRB2/SOS1 0.038 0.011 -9999 0 -10000 0 0
HRAS/GTP -0.014 0.14 -9999 0 -0.35 70 70
SHC1 0.025 0.008 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.15 -9999 0 -0.36 70 70
FRAP1 -0.052 0.13 -9999 0 -0.36 70 70
EGF/EGFR dimer -0.045 0.2 -9999 0 -0.5 76 76
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 0.062 -9999 0 -0.51 6 6
IL6-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
BCL2L1 0.003 0.19 0.6 5 -0.67 8 13
CRP 0.005 0.2 0.58 9 -0.64 13 22
cell cycle arrest -0.012 0.2 0.75 1 -0.65 25 26
TIMP1 -0.038 0.22 0.56 4 -0.64 31 35
IL6ST -0.065 0.24 -10000 0 -0.67 66 66
Rac1/GDP -0.042 0.2 0.31 1 -0.53 45 46
AP1 -0.11 0.27 -10000 0 -0.6 96 96
GAB2 0.027 0.005 -10000 0 -10000 0 0
TNFSF11 -0.009 0.19 0.63 4 -0.66 10 14
HSP90B1 0.043 0.052 -10000 0 -0.64 1 1
GAB1 0.028 0.004 -10000 0 -10000 0 0
MAPK14 -0.082 0.24 -10000 0 -0.69 49 49
AKT1 0.04 0.06 -10000 0 -0.98 1 1
FOXO1 0.04 0.058 -10000 0 -0.91 1 1
MAP2K6 -0.074 0.23 0.25 1 -0.6 54 55
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.029 0.19 0.34 5 -0.54 37 42
MITF -0.063 0.21 -10000 0 -0.55 50 50
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 0.07 -10000 0 -1.1 2 2
CEBPB 0.033 0.006 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.009 0.093 -10000 0 -0.46 7 7
STAT3 -0.021 0.21 0.76 1 -0.69 25 26
STAT1 0.01 0.097 -10000 0 -0.92 5 5
CEBPD 0 0.19 0.64 2 -0.63 13 15
PIK3CA 0.024 0.055 -10000 0 -0.67 3 3
PI3K 0.038 0.043 -10000 0 -0.51 3 3
JUN -0.12 0.29 -10000 0 -0.67 107 107
PIAS3/MITF -0.048 0.2 0.27 1 -0.56 42 43
MAPK11 -0.085 0.23 -10000 0 -0.7 45 45
STAT3 (dimer)/FOXO1 0.018 0.16 -10000 0 -0.54 14 14
GRB2/SOS1/GAB family -0.025 0.2 -10000 0 -0.55 34 34
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.068 0.21 -10000 0 -0.37 128 128
GRB2 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.024 0.025 -10000 0 -0.36 2 2
LBP 0.008 0.18 0.59 8 -0.56 7 15
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.013 -10000 0 -10000 0 0
MYC -0.013 0.24 0.63 3 -1 15 18
FGG -0.006 0.19 0.68 3 -0.68 9 12
macrophage differentiation -0.012 0.2 0.75 1 -0.65 25 26
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.065 0.25 -10000 0 -0.46 128 128
JUNB -0.001 0.21 0.6 3 -0.76 14 17
FOS -0.15 0.3 -10000 0 -0.67 125 125
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.062 0.22 -10000 0 -0.44 88 88
STAT1/PIAS1 -0.034 0.2 -10000 0 -0.51 45 45
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.062 -10000 0 -0.55 3 3
STAT3 (dimer) -0.015 0.21 0.76 1 -0.68 25 26
PRKCD -0.017 0.19 0.42 6 -0.57 27 33
IL6R 0.003 0.12 -10000 0 -0.67 16 16
SOCS3 -0.095 0.31 0.43 2 -0.93 45 47
gp130 (dimer)/JAK1/JAK1/LMO4 -0.006 0.17 -10000 0 -0.44 64 64
Rac1/GTP -0.04 0.2 -10000 0 -0.55 42 42
HCK 0.016 0.039 -10000 0 -10000 0 0
MAPKKK cascade 0.026 0.1 -10000 0 -0.55 7 7
bone resorption -0.008 0.18 0.63 4 -0.62 10 14
IRF1 0.003 0.19 0.64 6 -0.64 11 17
mol:GDP -0.061 0.2 0.25 1 -0.55 48 49
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.062 0.2 0.25 1 -0.56 48 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.078 0.24 -10000 0 -0.71 48 48
PTPN11 0.014 0.074 -10000 0 -0.87 3 3
IL6/IL6RA -0.07 0.22 -10000 0 -0.52 92 92
gp130 (dimer)/TYK2/TYK2/LMO4 -0.009 0.16 -10000 0 -0.43 59 59
gp130 (dimer)/JAK2/JAK2/LMO4 -0.012 0.17 -10000 0 -0.44 64 64
IL6 -0.095 0.26 -10000 0 -0.68 81 81
PIAS3 0.026 0.007 -10000 0 -10000 0 0
PTPRE -0.025 0.078 -10000 0 -0.68 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 -0.069 0.21 -10000 0 -0.38 126 126
LMO4 0.028 0.016 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.017 0.21 -10000 0 -0.68 25 25
MCL1 0.054 0.072 -10000 0 -0.82 1 1
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.04 0.1 -10000 0 -0.41 22 22
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 29 29
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.009 0.2 -10000 0 -0.79 29 29
mol:Ca2+ -0.098 0.19 -10000 0 -0.43 119 119
IGF1R 0.027 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.019 0.15 -10000 0 -0.45 51 51
SHC1 0.025 0.008 -10000 0 -10000 0 0
apoptosis 0.011 0.19 0.74 29 -10000 0 29
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 -0.54 20 20
regulation of stress fiber formation 0.009 0.088 0.36 5 -0.28 1 6
E2/ERA-ERB (dimer) 0.007 0.11 -10000 0 -0.44 24 24
KRAS 0.027 0.005 -10000 0 -10000 0 0
G13/GTP 0.01 0.085 -10000 0 -0.36 22 22
pseudopodium formation -0.009 0.088 0.28 1 -0.36 5 6
E2/ER alpha (dimer)/PELP1 0.009 0.093 -10000 0 -0.4 22 22
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 -0.58 23 30
E2/ER beta (dimer) 0.017 0.041 -10000 0 -0.51 3 3
mol:GDP 0.003 0.11 -10000 0 -0.47 23 23
mol:NADP 0.009 0.15 0.47 7 -0.58 23 30
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.1 0.2 -10000 0 -0.45 119 119
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
PLCB1 -0.1 0.21 -10000 0 -0.45 121 121
PLCB2 -0.1 0.21 -10000 0 -0.46 120 120
IGF1 -0.13 0.29 -10000 0 -0.67 108 108
mol:L-citrulline 0.009 0.15 0.47 7 -0.58 23 30
RHOA 0.027 0.003 -10000 0 -10000 0 0
Gai/GDP 0.005 0.14 -10000 0 -0.67 20 20
JNK cascade 0.017 0.041 -10000 0 -0.51 3 3
BCAR1 0.026 0.006 -10000 0 -10000 0 0
ESR2 0.023 0.055 -10000 0 -0.67 3 3
GNAQ 0.025 0.008 -10000 0 -10000 0 0
ESR1 -0.013 0.15 -10000 0 -0.65 23 23
Gq family/GDP/Gbeta gamma -0.059 0.19 -10000 0 -0.66 27 27
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.097 -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 -0.49 23 23
STRN -0.016 0.17 -10000 0 -0.66 31 31
GNAL -0.061 0.23 -10000 0 -0.66 64 64
PELP1 0.026 0.007 -10000 0 -10000 0 0
MAPK11 0.01 0.035 -10000 0 -0.43 3 3
GNAI2 0.027 0.003 -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 -0.019 0.14 0.37 3 -0.55 21 24
cAMP biosynthetic process -0.04 0.16 -10000 0 -0.38 78 78
SRC -0.004 0.13 -10000 0 -0.5 22 22
PI3K 0.036 0.043 -10000 0 -0.51 3 3
GNB1 0.026 0.006 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.031 0.11 -10000 0 -0.46 19 19
SOS1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.07 0.16 -10000 0 -0.43 48 48
Gs family/GTP -0.036 0.16 -10000 0 -0.39 78 78
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 -0.55 23 30
mol:DAG -0.1 0.2 -10000 0 -0.45 119 119
Gs family/GDP/Gbeta gamma -0.027 0.14 -10000 0 -0.35 68 68
MSN -0.011 0.094 0.29 1 -0.39 5 6
Gq family/GTP -0.1 0.22 -10000 0 -0.48 122 122
mol:PI-3-4-5-P3 -0.008 0.19 -10000 0 -0.75 29 29
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 0.55 23 -0.46 7 30
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.11 -10000 0 -0.44 23 23
NOS3 0.003 0.15 0.42 3 -0.61 23 26
GNA11 0.015 0.084 -10000 0 -0.64 8 8
MAPKKK cascade -0.015 0.18 0.37 1 -0.58 32 33
E2/ER alpha (dimer)/PELP1/Src 0 0.14 -10000 0 -0.57 20 20
ruffle organization -0.009 0.088 0.28 1 -0.36 5 6
ROCK2 -0.004 0.11 0.36 5 -0.35 35 40
GNA14 -0.14 0.29 -10000 0 -0.64 120 120
GNA15 0.013 0.05 -10000 0 -0.67 1 1
GNA13 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.034 0.16 -10000 0 -0.57 26 26
MMP2 -0.004 0.13 0.34 1 -0.59 14 15
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.1 0.22 -10000 0 -0.51 66 66
MAP3K8 0.015 0.079 -10000 0 -0.63 7 7
FOS -0.075 0.17 0.29 3 -0.44 59 62
PRKCA -0.008 0.13 -10000 0 -0.68 17 17
PTPN7 -0.023 0.13 -10000 0 -0.67 18 18
HRAS 0.025 0.011 -10000 0 -10000 0 0
PRKCB -0.003 0.081 -10000 0 -0.68 5 5
NRAS 0.026 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.022 -10000 0 -10000 0 0
MAPK3 -0.012 0.12 -10000 0 -0.47 22 22
MAP2K1 -0.015 0.13 -10000 0 -0.55 21 21
ELK1 0.013 0.025 -10000 0 -10000 0 0
BRAF -0.011 0.11 -10000 0 -0.52 21 21
mol:GTP -0.002 0.004 -10000 0 -0.007 128 128
MAPK1 -0.1 0.2 -10000 0 -0.5 64 64
RAF1 -0.011 0.11 -10000 0 -0.52 21 21
KRAS 0.026 0.005 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.005 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.005 0.12 -10000 0 -0.37 18 18
NFATC4 -0.018 0.087 0.28 4 -0.28 37 41
ERBB2IP 0.027 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.027 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.014 0.11 -10000 0 -0.35 39 39
JUN -0.005 0.094 0.34 10 -0.21 6 16
HRAS 0.025 0.011 -10000 0 -10000 0 0
DOCK7 -0.024 0.1 -10000 0 -0.34 40 40
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.004 0.12 -10000 0 -0.4 41 41
AKT1 0.007 0.006 -10000 0 -10000 0 0
BAD 0.005 0.004 -10000 0 -10000 0 0
MAPK10 -0.008 0.065 0.25 4 -0.3 2 6
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.015 0.12 -10000 0 -0.38 39 39
RAF1 -0.011 0.12 0.39 4 -0.39 18 22
ErbB2/ErbB3/neuregulin 2 -0.025 0.14 -10000 0 -0.42 59 59
STAT3 0.028 0.069 -10000 0 -0.84 3 3
cell migration 0.007 0.11 0.39 20 -0.28 4 24
mol:PI-3-4-5-P3 0 0.004 -10000 0 -10000 0 0
cell proliferation -0.15 0.32 -10000 0 -0.68 117 117
FOS -0.12 0.26 0.35 6 -0.5 151 157
NRAS 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.014 0.11 -10000 0 -0.35 39 39
MAPK3 -0.077 0.24 0.38 3 -0.52 84 87
MAPK1 -0.17 0.3 0.36 1 -0.64 119 120
JAK2 -0.024 0.098 -10000 0 -0.34 38 38
NF2 -0.011 0.11 -10000 0 -0.62 16 16
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.011 0.11 -10000 0 -0.34 41 41
NRG1 -0.034 0.19 -10000 0 -0.66 43 43
GRB2/SOS1 0.037 0.011 -10000 0 -10000 0 0
MAPK8 -0.019 0.11 -10000 0 -0.33 46 46
MAPK9 -0.009 0.062 0.23 3 -10000 0 3
ERBB2 -0.017 0.006 -10000 0 -10000 0 0
ERBB3 0.016 0.079 -10000 0 -0.63 7 7
SHC1 0.025 0.008 -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 0.067 -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 -0.016 0.076 -10000 0 -0.25 38 38
ErbB2/ErbB2/HSP90 (dimer) 0.014 0.013 -10000 0 -10000 0 0
CHRNA1 -0.075 0.19 0.33 1 -0.4 99 100
myelination -0.008 0.14 0.52 17 -0.28 17 34
PPP3CB -0.021 0.094 -10000 0 -0.32 39 39
KRAS 0.026 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.022 0.1 -10000 0 -0.3 40 40
NRG2 -0.052 0.22 -10000 0 -0.67 54 54
mol:GDP -0.011 0.11 -10000 0 -0.34 41 41
SOS1 0.026 0.005 -10000 0 -10000 0 0
MAP2K2 -0.026 0.12 0.31 5 -0.38 19 24
SRC 0.027 0.008 -10000 0 -10000 0 0
mol:cAMP 0 0.003 -10000 0 -10000 0 0
PTPN11 -0.022 0.1 0.25 1 -0.34 40 41
MAP2K1 -0.073 0.23 -10000 0 -0.63 29 29
heart morphogenesis -0.014 0.11 -10000 0 -0.35 39 39
RAS family/GDP 0.017 0.11 -10000 0 -0.38 14 14
GRB2 0.025 0.007 -10000 0 -10000 0 0
PRKACA -0.011 0.12 -10000 0 -0.65 18 18
CHRNE 0.008 0.037 0.18 12 -0.23 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 -0.014 0.11 -10000 0 -0.35 39 39
CDC42 0.027 0.005 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.024 0.017 -9999 0 -10000 0 0
CCL5 -0.016 0.16 -9999 0 -0.67 28 28
SDCBP 0.027 0.005 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.039 0.13 -9999 0 -0.41 42 42
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.033 0.14 -9999 0 -0.48 29 29
Syndecan-1/Syntenin -0.031 0.14 -9999 0 -0.49 28 28
MAPK3 -0.031 0.12 -9999 0 -0.49 21 21
HGF/MET -0.078 0.19 -9999 0 -0.52 70 70
TGFB1/TGF beta receptor Type II 0.024 0.017 -9999 0 -10000 0 0
BSG 0.025 0.008 -9999 0 -10000 0 0
keratinocyte migration -0.033 0.14 -9999 0 -0.47 29 29
Syndecan-1/RANTES -0.051 0.19 -9999 0 -0.56 46 46
Syndecan-1/CD147 -0.016 0.14 -9999 0 -0.52 22 22
Syndecan-1/Syntenin/PIP2 -0.031 0.14 -9999 0 -0.47 28 28
LAMA5 0.027 0.005 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.031 0.13 -9999 0 -0.46 28 28
MMP7 -0.079 0.16 -9999 0 -0.66 26 26
HGF -0.073 0.24 -9999 0 -0.67 70 70
Syndecan-1/CASK -0.046 0.13 -9999 0 -0.41 45 45
Syndecan-1/HGF/MET -0.076 0.2 -9999 0 -0.49 76 76
regulation of cell adhesion -0.033 0.11 -9999 0 -0.49 19 19
HPSE 0.01 0.094 -9999 0 -0.64 9 9
positive regulation of cell migration -0.039 0.13 -9999 0 -0.41 42 42
SDC1 -0.039 0.13 -9999 0 -0.4 45 45
Syndecan-1/Collagen -0.039 0.13 -9999 0 -0.41 42 42
PPIB 0.027 0.004 -9999 0 -10000 0 0
MET -0.029 0.074 -9999 0 -10000 0 0
PRKACA 0.025 0.008 -9999 0 -10000 0 0
MMP9 -0.043 0.2 -9999 0 -0.67 42 42
MAPK1 -0.032 0.12 -9999 0 -0.49 22 22
homophilic cell adhesion -0.039 0.13 -9999 0 -0.4 43 43
MMP1 -0.045 0.075 -9999 0 -10000 0 0
Osteopontin-mediated 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
IKK alpha homodimer 0.001 0.11 -10000 0 -0.38 31 31
NF kappa B1 p50/RelA/I kappa B alpha 0.01 0.11 0.35 3 -0.51 2 5
alphaV/beta3 Integrin/Osteopontin/Src -0.003 0.12 -10000 0 -0.5 25 25
AP1 -0.14 0.3 -10000 0 -0.67 100 100
ILK -0.006 0.11 -10000 0 -0.4 30 30
bone resorption -0.007 0.13 -10000 0 -0.54 7 7
PTK2B 0.027 0.005 -10000 0 -10000 0 0
PYK2/p130Cas 0.043 0.11 -10000 0 -0.37 31 31
ITGAV 0.026 0.045 -10000 0 -0.67 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.013 0.12 -10000 0 -0.5 24 24
alphaV/beta3 Integrin/Osteopontin 0.027 0.13 -10000 0 -0.44 31 31
MAP3K1 -0.007 0.11 -10000 0 -0.4 31 31
JUN -0.12 0.29 -10000 0 -0.67 107 107
MAPK3 -0.022 0.099 -10000 0 -0.37 31 31
MAPK1 -0.023 0.095 -10000 0 -0.37 30 30
Rac1/GDP 0.02 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.018 0.12 -10000 0 -0.4 37 37
ITGB3 0.013 0.1 -10000 0 -0.64 11 11
NFKBIA -0.018 0.094 -10000 0 -0.36 30 30
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 -0.039 0.11 0.52 3 -0.61 1 4
NF kappa B1 p50/RelA 0.022 0.1 -10000 0 -0.51 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 0.028 0.088 -10000 0 -0.54 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.007 0.11 -10000 0 -0.4 31 31
VAV3 -0.015 0.12 0.4 1 -0.39 35 36
MAP3K14 -0.012 0.11 -10000 0 -0.4 31 31
ROCK2 -0.006 0.15 -10000 0 -0.66 24 24
SPP1 -0.028 0.15 -10000 0 -0.67 23 23
RAC1 0.026 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.11 -10000 0 -0.36 34 34
MMP2 -0.13 0.24 -10000 0 -0.56 91 91
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.009 0.14 -10000 0 -0.36 62 62
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 0.001 0.12 -10000 0 -0.31 44 44
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 0.072 -10000 0 -0.24 4 4
CaM/Ca2+ 0.013 0.14 -10000 0 -0.33 62 62
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.013 0.13 -10000 0 -0.34 62 62
AKT1 -0.017 0.12 0.38 5 -0.32 61 66
MAP2K1 -0.025 0.12 0.29 2 -0.32 60 62
MAP3K11 -0.022 0.13 0.3 5 -0.34 62 67
IFNGR1 0.02 0.026 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.017 0.074 -10000 0 -0.36 5 5
Rap1/GTP -0.02 0.095 -10000 0 -0.31 5 5
CRKL/C3G 0.028 0.019 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.017 0.15 -10000 0 -0.37 61 61
CEBPB -0.059 0.19 0.52 6 -0.53 37 43
STAT3 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.016 0.16 -10000 0 -0.76 5 5
STAT1 -0.023 0.13 0.3 5 -0.34 62 67
CALM1 0.027 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.066 0.23 -10000 0 -0.67 62 62
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
STAT1 (dimer)/PIAS1 -0.006 0.13 0.3 4 -0.32 62 66
CEBPB/PTGES2/Cbp/p300 -0.024 0.12 -10000 0 -0.39 14 14
mol:Ca2+ 0.006 0.14 -10000 0 -0.35 62 62
MAPK3 -0.009 0.12 -10000 0 -0.65 4 4
STAT1 (dimer) 0.017 0.098 -10000 0 -0.33 4 4
MAPK1 -0.17 0.31 0.44 1 -0.67 122 123
JAK2 0.017 0.036 -10000 0 -0.38 2 2
PIK3R1 0.027 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 -0.041 0.18 0.48 9 -0.6 27 36
SMAD7 0.018 0.065 0.42 6 -10000 0 6
CBL/CRKL/C3G -0.009 0.12 0.3 2 -0.32 56 58
PI3K 0.011 0.14 -10000 0 -0.34 62 62
IFNG -0.066 0.23 -10000 0 -0.68 62 62
apoptosis -0.038 0.15 0.56 4 -0.46 37 41
CAMK2G 0.027 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.007 -10000 0 -10000 0 0
CAMK2A 0.011 0.035 -10000 0 -10000 0 0
CAMK2B 0.019 0.07 -10000 0 -0.67 5 5
FRAP1 -0.024 0.11 0.37 5 -0.3 61 66
PRKCD -0.013 0.13 0.42 9 -0.32 60 69
RAP1B 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.008 0.072 -10000 0 -0.24 4 4
PTPN2 0.027 0.004 -10000 0 -10000 0 0
EP300 0.02 0.013 -10000 0 -10000 0 0
IRF1 -0.015 0.086 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy -0.012 0.12 0.3 2 -0.32 61 63
SOCS1 0.018 0.12 -10000 0 -1 6 6
mol:GDP -0.01 0.11 0.28 2 -0.3 56 58
CASP1 0.016 0.064 0.45 4 -0.32 2 6
PTGES2 0.025 0.008 -10000 0 -10000 0 0
IRF9 -0.001 0.058 0.35 1 -10000 0 1
mol:PI-3-4-5-P3 -0.002 0.13 -10000 0 -0.33 62 62
RAP1/GDP -0.006 0.1 -10000 0 -0.31 5 5
CBL -0.022 0.13 0.29 6 -0.34 62 68
MAP3K1 -0.023 0.12 0.3 2 -0.34 60 62
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 0.072 -10000 0 -0.24 4 4
PTPN11 -0.026 0.13 -10000 0 -0.36 62 62
CREBBP 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
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 -0.25 255 255
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 0.026 0.015 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.044 0.068 -10000 0 -0.28 10 10
PRKG1 -0.16 0.31 -10000 0 -0.67 136 136
DUSP8 0.019 0.065 -10000 0 -0.67 4 4
PGK/cGMP/p38 alpha -0.11 0.18 -10000 0 -0.37 132 132
apoptosis -0.042 0.065 -10000 0 -0.27 10 10
RAL/GTP 0.036 0.008 -10000 0 -10000 0 0
LYN 0.027 0.005 -10000 0 -10000 0 0
DUSP1 -0.084 0.26 -10000 0 -0.67 78 78
PAK1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.027 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 -0.054 0.16 0.42 18 -0.33 30 48
BLK -0.19 0.31 -10000 0 -0.67 148 148
HCK 0.017 0.039 -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 -0.011 0.12 0.35 19 -0.33 7 26
positive regulation of innate immune response -0.043 0.17 0.46 19 -0.47 8 27
LCK 0.012 0.082 -10000 0 -0.67 6 6
p38alpha-beta/MKP7 -0.045 0.14 0.34 9 -0.46 7 16
p38alpha-beta/MKP5 -0.037 0.15 0.43 14 -0.45 7 21
PGK/cGMP -0.12 0.23 -10000 0 -0.5 136 136
PAK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.097 0.18 0.31 4 -0.46 45 49
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 -0.66 279 279
FAS signaling pathway (CD95)

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
SPTAN1 0.013 0.062 0.24 32 -10000 0 32
RFC1 0.015 0.064 0.24 35 -10000 0 35
PRKDC 0.017 0.071 0.26 37 -10000 0 37
RIPK1 0.029 0.005 -10000 0 -10000 0 0
CASP7 -0.003 0.095 -10000 0 -0.74 6 6
FASLG/FAS/FADD/FAF1 -0.015 0.096 0.24 5 -0.34 33 38
MAP2K4 -0.027 0.16 0.32 2 -0.5 25 27
mol:ceramide -0.02 0.13 -10000 0 -0.43 35 35
GSN 0.013 0.062 0.24 32 -10000 0 32
FASLG/FAS/FADD/FAF1/Caspase 8 -0.02 0.12 -10000 0 -0.43 33 33
FAS 0.02 0.018 -10000 0 -10000 0 0
BID -0.017 0.036 0.26 4 -10000 0 4
MAP3K1 -0.008 0.12 0.26 4 -0.41 18 22
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
RB1 0.014 0.066 0.25 33 -10000 0 33
CFLAR 0.028 0.006 -10000 0 -10000 0 0
HGF/MET -0.02 0.19 -10000 0 -0.47 73 73
ARHGDIB 0.016 0.069 0.25 38 -10000 0 38
FADD 0.02 0.018 -10000 0 -10000 0 0
actin filament polymerization -0.013 0.062 -10000 0 -0.24 32 32
NFKB1 -0.015 0.098 -10000 0 -0.57 3 3
MAPK8 -0.063 0.22 0.4 2 -0.48 90 92
DFFA 0.015 0.065 0.24 36 -10000 0 36
DNA fragmentation during apoptosis 0.015 0.065 0.24 36 -10000 0 36
FAS/FADD/MET 0.039 0.044 -10000 0 -10000 0 0
CFLAR/RIP1 0.042 0.01 -10000 0 -10000 0 0
FAIM3 0.016 0.061 -10000 0 -0.67 3 3
FAF1 0.019 0.02 -10000 0 -10000 0 0
PARP1 0.019 0.082 0.29 36 -10000 0 36
DFFB 0.015 0.065 0.24 36 -10000 0 36
CHUK -0.015 0.089 -10000 0 -0.62 2 2
FASLG -0.034 0.18 -10000 0 -0.68 33 33
FAS/FADD 0.029 0.026 -10000 0 -10000 0 0
HGF -0.073 0.24 -10000 0 -0.67 70 70
LMNA 0.014 0.07 0.26 28 -10000 0 28
CASP6 0.015 0.064 0.24 35 -10000 0 35
CASP10 0.02 0.018 -10000 0 -10000 0 0
CASP3 0.019 0.08 0.3 37 -0.18 1 38
PTPN13 0.019 0.077 -10000 0 -0.67 6 6
CASP8 -0.012 0.034 0.4 3 -10000 0 3
IL6 -0.2 0.5 -10000 0 -1.3 90 90
MET -0.029 0.074 -10000 0 -10000 0 0
ICAD/CAD 0.014 0.06 0.22 35 -10000 0 35
FASLG/FAS/FADD/FAF1/Caspase 10 -0.02 0.14 -10000 0 -0.43 35 35
activation of caspase activity by cytochrome c -0.017 0.036 0.26 4 -10000 0 4
PAK2 0.015 0.065 0.24 36 -10000 0 36
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
Regulation of Androgen receptor activity

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
HDAC1 0.009 0.013 -10000 0 -10000 0 0
SMARCC1 0.011 0.013 -10000 0 -10000 0 0
REL -0.012 0.17 -10000 0 -0.66 32 32
HDAC7 -0.07 0.12 -10000 0 -0.5 19 19
JUN -0.12 0.29 -10000 0 -0.67 107 107
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 20 20
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 0.015 0.066 -10000 0 -0.59 1 1
NCOA2 -0.043 0.2 -10000 0 -0.68 45 45
CEBPA 0.02 0.07 -10000 0 -0.67 5 5
EHMT2 0.025 0.005 -10000 0 -10000 0 0
cell proliferation -0.082 0.2 0.56 21 -0.48 21 42
NR0B1 -0.008 0.023 -10000 0 -10000 0 0
EGR1 -0.13 0.28 -10000 0 -0.68 101 101
RXRs/9cRA 0.017 0.072 -10000 0 -0.4 4 4
AR/RACK1/Src -0.13 0.15 0.33 2 -0.52 22 24
AR/GR -0.12 0.18 0.25 5 -0.32 199 204
GNB2L1 0.022 0.008 -10000 0 -10000 0 0
PKN1 0.025 0.008 -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 61 61
MAPK8 -0.014 0.071 -10000 0 -0.52 9 9
T-DHT/AR/TIF2/CARM1 -0.13 0.19 0.34 3 -0.57 48 51
SRC -0.044 0.088 0.24 1 -0.47 16 17
NR3C1 0.027 0.006 -10000 0 -10000 0 0
KLK3 -0.36 0.55 -10000 0 -1.2 142 142
APPBP2 0.024 0.012 -10000 0 -10000 0 0
TRIM24 0.013 0.021 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.07 0.13 0.32 7 -0.57 16 23
TMPRSS2 -0.043 0.28 -10000 0 -1.1 30 30
RXRG -0.11 0.076 -10000 0 -0.67 4 4
mol:9cRA -0.002 0.003 -10000 0 -0.012 5 5
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 -0.68 10 10
KLK2 -0.45 0.38 0.34 2 -0.77 287 289
AR -0.14 0.18 -10000 0 -0.35 203 203
SENP1 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
MDM2 0.036 0.016 -10000 0 -10000 0 0
SRY 0.009 0.015 0.031 142 -10000 0 142
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 -0.1 0.13 0.33 4 -0.56 17 21
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 0.049 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.092 0.15 0.28 2 -0.44 51 53
T-DHT/AR/Hsp90 -0.071 0.13 0.32 8 -0.56 16 24
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 0.036 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
BCR signaling 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
JUN -0.067 0.18 0.43 10 -0.4 51 61
IKBKB 0.01 0.12 0.48 16 -0.32 7 23
AKT1 -0.001 0.17 0.55 25 -0.25 14 39
IKBKG -0.002 0.13 0.47 15 -0.34 15 30
CALM1 -0.022 0.093 0.39 3 -0.4 8 11
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
MAP3K1 -0.015 0.17 0.45 12 -0.53 21 33
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.024 0.093 0.32 2 -0.42 8 10
DOK1 0.027 0.005 -10000 0 -10000 0 0
AP-1 -0.058 0.15 0.51 12 -0.27 96 108
LYN 0.027 0.005 -10000 0 -10000 0 0
BLNK 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.025 0.008 -10000 0 -10000 0 0
BCR complex -0.072 0.18 -10000 0 -0.5 67 67
CD22 -0.07 0.18 -10000 0 -0.42 84 84
CAMK2G -0.019 0.09 0.34 4 -0.43 5 9
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
INPP5D 0.019 0.034 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.04 0.12 -10000 0 -0.34 59 59
GO:0007205 -0.025 0.095 0.32 2 -0.43 8 10
SYK 0.025 0.008 -10000 0 -10000 0 0
ELK1 -0.02 0.093 0.31 4 -0.42 7 11
NFATC1 -0.04 0.14 0.36 6 -0.43 25 31
B-cell antigen/BCR complex -0.072 0.18 -10000 0 -0.5 67 67
PAG1/CSK 0.038 0.027 -10000 0 -0.51 1 1
NFKBIB 0.019 0.044 0.19 13 -0.13 6 19
HRAS -0.018 0.096 0.29 4 -0.37 7 11
NFKBIA 0.019 0.044 0.19 13 -0.12 8 21
NF-kappa-B/RelA/I kappa B beta 0.024 0.04 0.19 13 -10000 0 13
RasGAP/Csk -0.028 0.18 -10000 0 -0.4 74 74
mol:GDP -0.023 0.093 0.29 2 -0.41 9 11
PTEN 0.026 0.018 -10000 0 -0.36 1 1
CD79B 0.006 0.052 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.024 0.04 0.19 13 -10000 0 13
GRB2 0.026 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.038 0.16 0.41 5 -0.48 20 25
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.024 0.092 0.32 2 -0.4 8 10
CSK 0.027 0.008 -10000 0 -10000 0 0
FOS -0.098 0.18 0.47 8 -0.37 125 133
CHUK 0.007 0.1 0.42 14 -0.36 6 20
IBTK 0.027 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.013 0.11 -10000 0 -0.45 11 11
PTPN6 -0.065 0.16 -10000 0 -0.48 42 42
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.014 0.036 0.16 6 -0.12 11 17
VAV2 -0.057 0.16 -10000 0 -0.63 16 16
ubiquitin-dependent protein catabolic process 0.022 0.043 0.19 13 -0.12 6 19
BTK -0.037 0.24 -10000 0 -0.98 30 30
CD19 -0.062 0.16 -10000 0 -0.4 69 69
MAP4K1 0.008 0.079 -10000 0 -0.67 5 5
CD72 0.024 0.016 -10000 0 -10000 0 0
PAG1 0.025 0.032 -10000 0 -0.67 1 1
MAPK14 -0.008 0.15 0.42 14 -0.45 21 35
SH3BP5 0.027 0.004 -10000 0 -10000 0 0
PIK3AP1 -0.017 0.094 -10000 0 -0.43 9 9
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.049 0.18 -10000 0 -0.42 79 79
RAF1 -0.015 0.096 0.34 7 -0.39 4 11
RasGAP/p62DOK/SHIP -0.008 0.17 -10000 0 -0.39 74 74
CD79A -0.1 0.23 -10000 0 -0.66 68 68
re-entry into mitotic cell cycle -0.057 0.15 0.5 12 -0.26 96 108
RASA1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.004 0.1 0.38 16 -0.4 2 18
MAPK1 -0.01 0.09 0.36 9 -0.39 2 11
CD72/SHP1 -0.047 0.17 0.28 4 -0.46 41 45
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.014 0.16 0.44 14 -0.46 25 39
actin cytoskeleton organization -0.045 0.14 0.34 2 -0.52 16 18
NF-kappa-B/RelA 0.048 0.073 0.34 12 -0.22 1 13
Calcineurin 0.007 0.09 -10000 0 -0.41 4 4
PI3K -0.063 0.14 -10000 0 -0.45 25 25
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.02 0.097 -10000 0 -0.44 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
Bam32/HPK1 -0.024 0.22 -10000 0 -0.91 21 21
DAPP1 -0.045 0.25 -10000 0 -1.1 20 20
cytokine secretion -0.037 0.13 0.36 6 -0.4 25 31
mol:DAG -0.024 0.092 0.32 2 -0.4 8 10
PLCG2 0.026 0.006 -10000 0 -10000 0 0
MAP2K1 -0.013 0.092 0.33 7 -0.45 2 9
B-cell antigen/BCR complex/FcgammaRIIB -0.057 0.19 -10000 0 -0.44 83 83
mol:PI-3-4-5-P3 -0.053 0.099 -10000 0 -0.36 15 15
ETS1 -0.015 0.086 0.34 5 -0.39 5 10
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.013 0.16 -10000 0 -0.38 64 64
B-cell antigen/BCR complex/LYN -0.05 0.17 -10000 0 -0.42 71 71
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
RAC1 -0.049 0.15 0.36 1 -0.56 16 17
B-cell antigen/BCR complex/LYN/SYK -0.04 0.19 -10000 0 -0.45 68 68
CARD11 -0.037 0.12 0.41 3 -0.44 18 21
FCGR2B -0.009 0.15 -10000 0 -0.67 24 24
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 0.43 18 -0.13 6 24
PTPRC -0.008 0.14 -10000 0 -0.67 20 20
PDPK1 -0.029 0.087 0.23 11 -0.25 17 28
PPP3CB 0.027 0.005 -10000 0 -10000 0 0
PPP3CC 0.027 0.005 -10000 0 -10000 0 0
POU2F2 0.019 0.033 0.16 14 -10000 0 14
Syndecan-4-mediated signaling events

Figure S44.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S44.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.01 0.1 -10000 0 -0.81 6 6
Syndecan-4/Syndesmos -0.041 0.16 -10000 0 -0.54 42 42
positive regulation of JNK cascade -0.054 0.19 -10000 0 -0.55 47 47
Syndecan-4/ADAM12 -0.053 0.16 -10000 0 -0.55 42 42
CCL5 -0.016 0.16 -10000 0 -0.67 28 28
Rac1/GDP 0.02 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 0.007 0.031 -10000 0 -10000 0 0
ADAM12 -0.011 0.067 -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 -0.058 0.03 -10000 0 -0.18 4 4
Syndecan-4/Laminin alpha1 -0.063 0.18 -10000 0 -0.58 42 42
Syndecan-4/CXCL12/CXCR4 -0.057 0.2 -10000 0 -0.59 46 46
Syndecan-4/Laminin alpha3 -0.052 0.17 -10000 0 -0.56 41 41
MDK -0.02 0.076 -10000 0 -0.67 1 1
Syndecan-4/FZD7 -0.041 0.16 -10000 0 -0.55 42 42
Syndecan-4/Midkine -0.053 0.16 -10000 0 -0.56 41 41
FZD7 0.023 0.051 -10000 0 -0.52 4 4
Syndecan-4/FGFR1/FGF -0.014 0.16 -10000 0 -0.51 41 41
THBS1 0.012 0.046 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.059 0.16 -10000 0 -0.55 42 42
positive regulation of MAPKKK cascade -0.054 0.19 -10000 0 -0.55 47 47
Syndecan-4/TACI -0.13 0.21 -10000 0 -0.58 47 47
CXCR4 0.026 0.013 -10000 0 -10000 0 0
cell adhesion -0.009 0.066 0.2 5 -0.31 17 22
Syndecan-4/Dynamin -0.041 0.16 -10000 0 -0.55 41 41
Syndecan-4/TSP1 -0.045 0.16 -10000 0 -0.55 42 42
Syndecan-4/GIPC -0.041 0.16 -10000 0 -0.55 41 41
Syndecan-4/RANTES -0.061 0.2 -10000 0 -0.66 42 42
ITGB1 0.027 0.004 -10000 0 -10000 0 0
LAMA1 -0.021 0.18 -10000 0 -0.66 34 34
LAMA3 -0.001 0.13 -10000 0 -0.67 16 16
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA 0.019 0.19 0.76 21 -0.62 17 38
Syndecan-4/alpha-Actinin -0.04 0.16 -10000 0 -0.55 41 41
TFPI -0.012 0.16 -10000 0 -0.66 28 28
F2 0.01 0.03 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.075 0.18 -10000 0 -0.58 42 42
ACTN1 0.027 0.008 -10000 0 -10000 0 0
TNC -0.033 0.096 -10000 0 -0.67 5 5
Syndecan-4/CXCL12 -0.077 0.2 -10000 0 -0.58 51 51
FGF6 -0.016 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
CXCL12 -0.047 0.22 -10000 0 -0.67 53 53
TNFRSF13B -0.16 0.29 -10000 0 -0.67 121 121
FGF2 0.027 0.004 -10000 0 -10000 0 0
FGFR1 0.026 0.032 -10000 0 -0.67 1 1
Syndecan-4/PI-4-5-P2 -0.051 0.16 -10000 0 -0.55 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.086 0.07 -10000 0 -0.24 1 1
cell migration -0.027 0.012 -10000 0 -10000 0 0
PRKCD 0.026 0.022 -10000 0 -10000 0 0
vasculogenesis -0.043 0.16 -10000 0 -0.53 42 42
SDC4 -0.051 0.16 -10000 0 -0.58 42 42
Syndecan-4/Tenascin C -0.061 0.17 -10000 0 -0.58 42 42
Syndecan-4/PI-4-5-P2/PKC alpha -0.046 0.023 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.04 0.16 -10000 0 -0.55 42 42
MMP9 -0.043 0.2 -10000 0 -0.67 42 42
Rac1/GTP -0.009 0.068 0.2 5 -0.32 17 22
cytoskeleton organization -0.039 0.15 -10000 0 -0.52 42 42
GIPC1 0.025 0.008 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.059 0.18 -10000 0 -0.55 47 47
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.005 0.058 -10000 0 -10000 0 0
CRKL -0.013 0.091 0.36 2 -0.42 1 3
mol:PIP3 -0.002 0.017 0.34 1 -10000 0 1
AKT1 0.003 0.056 0.37 2 -0.45 3 5
PTK2B 0.027 0.005 -10000 0 -10000 0 0
RAPGEF1 0.003 0.1 0.42 8 -0.4 1 9
RANBP10 0.026 0.006 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
HGF/MET/SHIP2 -0.015 0.18 -10000 0 -0.45 70 70
MAP3K5 0.012 0.12 0.44 13 -0.4 6 19
HGF/MET/CIN85/CBL/ENDOPHILINS 0.002 0.17 -10000 0 -0.42 66 66
AP1 -0.18 0.33 -10000 0 -0.65 148 148
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.025 0.008 -10000 0 -10000 0 0
apoptosis -0.22 0.4 0.38 1 -0.81 150 151
STAT3 (dimer) -0.019 0.1 -10000 0 -0.3 24 24
GAB1/CRKL/SHP2/PI3K 0.027 0.11 0.34 1 -0.5 3 4
INPP5D 0.019 0.034 -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 -0.36 1 1
ELK1 0.035 0.14 0.41 30 -0.23 4 34
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.006 0.068 -10000 0 -0.24 4 4
PAK1 0.006 0.058 0.35 5 -0.4 2 7
HGF/MET/RANBP10 -0.015 0.18 -10000 0 -0.45 70 70
HRAS -0.02 0.13 -10000 0 -0.55 3 3
DOCK1 0.001 0.11 0.44 9 -0.4 4 13
GAB1 -0.011 0.097 0.26 1 -0.35 4 5
CRK -0.006 0.098 0.37 2 -0.43 1 3
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.044 0.19 -10000 0 -0.51 70 70
JUN -0.12 0.29 -10000 0 -0.67 107 107
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.031 0.086 -10000 0 -0.24 68 68
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.006 0.13 0.52 5 -0.51 3 8
GRB2/SHC 0.004 0.085 -10000 0 -0.28 1 1
FOS -0.15 0.3 -10000 0 -0.67 125 125
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.034 0.14 0.41 30 -0.23 4 34
HGF/MET/MUC20 -0.065 0.16 -10000 0 -0.45 70 70
cell migration 0.004 0.084 -10000 0 -0.27 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.005 0.057 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.016 0.11 -10000 0 -0.3 64 64
MET/MUC20 -0.017 0.048 -10000 0 -10000 0 0
RAP1B 0.012 0.13 0.55 13 -0.37 1 14
RAP1A 0.009 0.11 0.39 12 -0.37 1 13
HGF/MET/RANBP9 -0.014 0.18 -10000 0 -0.45 70 70
RAF1 -0.018 0.12 -10000 0 -0.46 3 3
STAT3 -0.02 0.11 -10000 0 -0.3 24 24
cell proliferation -0.023 0.15 -10000 0 -0.39 60 60
RPS6KB1 0 0.034 -10000 0 -0.22 2 2
MAPK3 -0.022 0.1 0.52 12 -10000 0 12
MAPK1 0.14 0.29 0.61 134 -10000 0 134
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.024 0.17 0.56 19 -0.54 12 31
SRC -0.021 0.1 -10000 0 -0.3 25 25
PI3K 0.003 0.094 -10000 0 -0.39 4 4
MET/Glomulin -0.007 0.045 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K1 -0.01 0.13 0.43 2 -0.46 2 4
MET -0.029 0.074 -10000 0 -10000 0 0
MAP4K1 0.007 0.12 0.46 8 -0.43 6 14
PTK2 0.026 0.006 -10000 0 -10000 0 0
MAP2K2 -0.006 0.12 0.43 2 -0.44 1 3
BAD 0.006 0.058 0.35 5 -0.4 2 7
MAP2K4 0.022 0.14 0.51 19 -0.4 4 23
SHP2/GRB2/SOS1/GAB1 0.018 0.098 -10000 0 -0.36 1 1
INPPL1 0.027 0.005 -10000 0 -10000 0 0
PXN 0.027 0.005 -10000 0 -10000 0 0
SH3KBP1 0.026 0.007 -10000 0 -10000 0 0
HGS -0.028 0.077 -10000 0 -0.22 65 65
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF -0.073 0.24 -10000 0 -0.67 70 70
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
NCK/PLCgamma1 0.003 0.099 -10000 0 -0.26 27 27
PDPK1 -0.001 0.048 -10000 0 -0.48 3 3
HGF/MET/SHIP -0.018 0.18 -10000 0 -0.46 70 70
Ceramide signaling pathway

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
SPHK2 0.016 0.005 -10000 0 -10000 0 0
MAP4K4 -0.013 0.12 -10000 0 -0.5 15 15
BAG4 0.026 0.032 -10000 0 -0.67 1 1
PKC zeta/ceramide -0.02 0.097 -10000 0 -0.28 38 38
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.15 -10000 0 -0.62 25 25
BAX -0.013 0.075 -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 -0.033 0.088 0.18 1 -0.39 16 17
SMPD1 -0.011 0.089 0.27 6 -0.23 61 67
RB1 -0.033 0.09 0.19 1 -0.46 13 14
FADD/Caspase 8 -0.004 0.12 -10000 0 -0.52 13 13
MAP2K4 -0.02 0.072 0.21 2 -0.37 8 10
NSMAF 0.027 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.024 0.083 0.19 1 -0.41 12 13
EGF -0.075 0.25 -10000 0 -0.67 72 72
mol:ceramide -0.038 0.098 -10000 0 -0.29 40 40
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 0.016 0.024 -10000 0 -0.51 1 1
ASAH1 0.025 0.032 -10000 0 -0.67 1 1
negative regulation of cell cycle -0.033 0.089 0.19 1 -0.45 13 14
cell proliferation -0.059 0.15 -10000 0 -0.33 104 104
BID -0.15 0.28 -10000 0 -0.6 127 127
MAP3K1 -0.028 0.079 0.19 1 -0.28 27 28
EIF2A -0.03 0.078 -10000 0 -0.45 10 10
TRADD 0.026 0.006 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.014 0.07 -10000 0 -0.35 10 10
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.043 0.086 -10000 0 -0.38 13 13
Cathepsin D/ceramide -0.019 0.093 -10000 0 -0.28 34 34
FADD -0.013 0.12 -10000 0 -0.5 15 15
KSR1 -0.027 0.087 0.18 9 -0.29 29 38
MAPK8 -0.019 0.091 -10000 0 -0.37 20 20
PRKRA -0.035 0.091 -10000 0 -0.38 18 18
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 -0.67 108 108
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.037 0.097 -10000 0 -0.29 40 40
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 -0.063 0.16 -10000 0 -0.35 104 104
PRKCD 0.027 0.003 -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 0.016 0.024 -10000 0 -0.51 1 1
RelA/NF kappa B1 0.04 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 -0.013 0.12 -10000 0 -0.51 16 16
TNFR1A/BAG4/TNF-alpha -0.003 0.16 -10000 0 -0.44 57 57
mol:Sphingosine-1-phosphate 0.016 0.005 -10000 0 -10000 0 0
MAP2K1 -0.023 0.078 -10000 0 -0.38 12 12
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
CYCS -0.006 0.072 0.17 26 -0.24 20 46
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 -0.51 1 1
EIF2AK2 -0.032 0.084 -10000 0 -0.47 11 11
TNF-alpha/TNFR1A/FAN -0.002 0.16 -10000 0 -0.44 56 56
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.012 0.088 -10000 0 -0.48 7 7
MAP2K2 -0.015 0.068 -10000 0 -0.36 8 8
SMPD3 -0.016 0.1 -10000 0 -0.26 65 65
TNF -0.056 0.22 -10000 0 -0.67 56 56
PKC zeta/PAR4 0.038 0.011 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.016 0.11 0.25 70 -0.24 19 89
NF kappa B1/RelA/I kappa B alpha 0.075 0.024 -10000 0 -10000 0 0
AIFM1 -0.01 0.082 0.17 26 -0.27 24 50
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.019 0.13 -10000 0 -0.42 33 33
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.087 0.35 2 -10000 0 2
AP1 -0.15 0.3 -10000 0 -0.55 157 157
mol:PIP3 -0.011 0.091 -10000 0 -0.41 9 9
AKT1 0.032 0.097 0.32 5 -0.57 2 7
PTK2B -0.009 0.085 0.26 1 -0.36 12 13
RHOA 0.014 0.042 0.25 1 -10000 0 1
PIK3CB 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.009 0.072 0.27 8 -10000 0 8
MAGI3 0.026 0.032 -10000 0 -0.67 1 1
RELA 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.008 0.1 -10000 0 -0.35 36 36
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0 0.099 0.35 11 -0.37 9 20
NF kappa B1 p50/RelA -0.019 0.1 -10000 0 -0.43 9 9
endothelial cell migration -0.015 0.15 -10000 0 -0.52 33 33
ADCY4 -0.029 0.14 -10000 0 -0.52 34 34
ADCY5 -0.054 0.16 -10000 0 -0.54 39 39
ADCY6 -0.029 0.14 -10000 0 -0.52 34 34
ADCY7 -0.029 0.15 -10000 0 -0.53 34 34
ADCY1 -0.031 0.15 -10000 0 -0.51 36 36
ADCY2 -0.049 0.17 -10000 0 -0.54 39 39
ADCY3 -0.029 0.15 -10000 0 -0.53 33 33
ADCY8 -0.037 0.15 -10000 0 -0.53 35 35
ADCY9 -0.029 0.15 -10000 0 -0.53 34 34
GSK3B -0.007 0.084 0.37 2 -0.34 12 14
arachidonic acid secretion -0.028 0.14 -10000 0 -0.49 36 36
GNG2 0.026 0.032 -10000 0 -0.67 1 1
TRIP6 0.024 0.01 -10000 0 -10000 0 0
GNAO1 -0.024 0.15 -10000 0 -0.47 46 46
HRAS 0.026 0.011 -10000 0 -10000 0 0
NFKBIA -0.005 0.095 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 0.015 0.18 -10000 0 -0.79 22 22
JUN -0.12 0.29 -10000 0 -0.67 107 107
LPA/LPA2/NHERF2 0.035 0.017 -10000 0 -10000 0 0
TIAM1 0 0.21 -10000 0 -0.93 23 23
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.012 0.065 0.32 1 -10000 0 1
PLCB3 0.027 0.034 -10000 0 -10000 0 0
FOS -0.15 0.3 -10000 0 -0.67 125 125
positive regulation of mitosis -0.028 0.14 -10000 0 -0.49 36 36
LPA/LPA1-2-3 0.019 0.12 -10000 0 -0.41 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 0.002 0.1 0.45 2 -0.4 11 13
GNAZ -0.015 0.12 -10000 0 -0.44 33 33
EGFR/PI3K-beta/Gab1 -0.001 0.099 -10000 0 -0.46 7 7
positive regulation of dendritic cell cytokine production 0.018 0.11 -10000 0 -0.4 29 29
LPA/LPA2/MAGI-3 0.035 0.027 -10000 0 -0.45 1 1
ARHGEF1 0.006 0.1 0.36 3 -0.39 23 26
GNAI2 -0.012 0.12 -10000 0 -0.45 33 33
GNAI3 -0.011 0.12 -10000 0 -0.45 33 33
GNAI1 -0.011 0.12 -10000 0 -0.44 34 34
LPA/LPA3 0.015 0.025 -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 -0.022 0.14 -10000 0 -0.44 44 44
HBEGF -0.038 0.14 -10000 0 -0.49 42 42
mol:DAG -0.012 0.065 0.32 1 -10000 0 1
cAMP biosynthetic process -0.035 0.17 0.42 10 -0.47 48 58
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.027 0.008 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN -0.007 0.091 0.36 6 -0.49 1 7
GNAQ 0.016 0.015 -10000 0 -10000 0 0
LPAR2 0.026 0.008 -10000 0 -10000 0 0
LPAR3 0.013 0.034 -10000 0 -10000 0 0
LPAR1 -0.022 0.18 -10000 0 -0.62 38 38
IL8 -0.084 0.17 0.36 1 -0.47 38 39
PTK2 -0.002 0.1 -10000 0 -0.4 25 25
Rac1/GDP 0.02 0.004 -10000 0 -10000 0 0
CASP3 -0.008 0.1 -10000 0 -0.36 36 36
EGFR 0.019 0.07 -10000 0 -0.67 5 5
PLCG1 -0.013 0.064 -10000 0 -0.3 3 3
PLD2 -0.002 0.1 -10000 0 -0.4 24 24
G12/G13 0.022 0.12 -10000 0 -0.4 32 32
PI3K-beta 0.006 0.087 -10000 0 -0.68 2 2
cell migration 0.019 0.072 -10000 0 -0.27 9 9
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
PXN 0.001 0.098 0.27 1 -0.46 7 8
HRAS/GTP -0.028 0.15 -10000 0 -0.5 36 36
RAC1 0.026 0.006 -10000 0 -10000 0 0
MMP9 -0.043 0.2 -10000 0 -0.67 42 42
PRKCE 0.02 0.07 -10000 0 -0.68 5 5
PRKCD -0.008 0.085 0.32 12 -10000 0 12
Gi(beta/gamma) -0.023 0.14 -10000 0 -0.51 33 33
mol:LPA 0.002 0.017 -10000 0 -0.19 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.02 0.11 -10000 0 -0.51 6 6
MAPKKK cascade -0.028 0.14 -10000 0 -0.49 36 36
contractile ring contraction involved in cytokinesis 0.017 0.047 0.27 3 -10000 0 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.068 0.15 -10000 0 -0.35 108 108
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 0.012 0.046 -10000 0 -0.34 7 7
Rac1/GTP 0.014 0.19 -10000 0 -0.83 22 22
MMP2 -0.015 0.15 -10000 0 -0.53 33 33
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.026 0.009 -10000 0 -10000 0 0
LAT2 -0.003 0.066 -10000 0 -0.28 2 2
AP1 -0.12 0.26 -10000 0 -0.55 105 105
mol:PIP3 0.027 0.17 0.62 20 -0.42 11 31
IKBKB 0.039 0.17 0.58 28 -0.26 8 36
AKT1 -0.007 0.12 0.32 26 -0.38 18 44
IKBKG 0.041 0.17 0.62 28 -0.26 7 35
MS4A2 -0.015 0.064 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
MAP3K1 0.024 0.11 0.44 13 -0.4 7 20
mol:Ca2+ 0.033 0.16 0.55 26 -0.32 11 37
LYN 0.027 0.011 -10000 0 -10000 0 0
CBLB -0.001 0.063 -10000 0 -0.26 2 2
SHC1 0.025 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK -0.021 0.17 -10000 0 -0.4 78 78
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.034 -10000 0 -10000 0 0
PLD2 -0.009 0.13 0.32 34 -0.37 30 64
PTPN13 0.012 0.13 0.53 1 -0.62 13 14
PTPN11 0.023 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 0.63 20 -0.38 5 25
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 -0.001 0.11 -10000 0 -0.37 28 28
LAT -0.004 0.069 -10000 0 -0.33 4 4
PAK2 0.017 0.1 0.32 8 -0.4 10 18
NFATC2 -0.11 0.23 -10000 0 -0.61 84 84
HRAS 0.012 0.099 0.26 1 -0.43 10 11
GAB2 0.027 0.005 -10000 0 -10000 0 0
PLA2G1B 0.006 0.096 -10000 0 -0.68 7 7
Fc epsilon R1 0.005 0.13 -10000 0 -0.45 32 32
Antigen/IgE/Fc epsilon R1 0.009 0.12 -10000 0 -0.41 32 32
mol:GDP 0.003 0.11 -10000 0 -0.48 13 13
JUN -0.12 0.29 -10000 0 -0.67 107 107
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 0.003 0.069 -10000 0 -0.24 19 19
CHUK 0.036 0.16 0.58 26 -0.26 7 33
KLRG1 -0.007 0.077 -10000 0 -0.3 14 14
VAV1 -0.005 0.073 0.21 1 -0.36 6 7
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.001 0.063 -10000 0 -10000 0 0
negative regulation of mast cell degranulation 0.006 0.08 -10000 0 -0.3 10 10
BTK -0.006 0.12 -10000 0 -0.54 17 17
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.018 0.15 -10000 0 -0.47 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 0.085 -10000 0 -0.85 4 4
Fc epsilon R1/FcgammaRIIB/SHIP 0.019 0.17 -10000 0 -0.5 42 42
FCER1G 0.018 0.035 -10000 0 -10000 0 0
FCER1A -0.033 0.18 -10000 0 -0.68 33 33
Antigen/IgE/Fc epsilon R1/Fyn 0.025 0.12 -10000 0 -0.38 32 32
MAPK3 0.019 0.091 -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 0.001 0.18 -10000 0 -0.63 31 31
DUSP1 -0.084 0.26 -10000 0 -0.67 78 78
NF-kappa-B/RelA 0.015 0.048 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.015 0.13 0.37 1 -0.71 10 11
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.023 0.098 -10000 0 -0.47 7 7
FER -0.004 0.071 -10000 0 -0.38 4 4
RELA 0.027 0.005 -10000 0 -10000 0 0
ITK -0.042 0.15 -10000 0 -0.47 54 54
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 0.011 0.12 0.4 8 -0.51 10 18
cytokine secretion 0.005 0.03 -10000 0 -10000 0 0
SPHK1 -0.001 0.065 0.27 1 -0.28 2 3
PTK2 0.014 0.13 0.37 1 -0.75 10 11
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.006 0.11 -10000 0 -0.38 27 27
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.035 0.18 0.64 21 -0.41 11 32
MAP2K2 0.019 0.09 -10000 0 -0.79 4 4
MAP2K1 0.01 0.083 -10000 0 -0.76 5 5
MAP2K7 0.025 0.008 -10000 0 -10000 0 0
KLRG1/SHP2 -0.001 0.082 -10000 0 -0.32 13 13
MAP2K4 -0.005 0.19 -10000 0 -0.84 24 24
Fc epsilon R1/FcgammaRIIB 0.007 0.18 -10000 0 -0.53 42 42
mol:Choline -0.009 0.13 0.32 34 -0.37 30 64
SHC/Grb2/SOS1 0.037 0.076 -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 -0.67 10 13
HCLS1 -0.002 0.064 -10000 0 -0.28 2 2
PRKCB 0.036 0.18 0.62 26 -0.34 12 38
FCGR2B -0.009 0.15 -10000 0 -0.67 24 24
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 0.021 -10000 0 -10000 0 0
PLA2G4A -0.023 0.12 -10000 0 -0.42 32 32
RASA1 0.027 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.009 0.13 0.32 34 -0.37 30 64
IKK complex 0.044 0.18 0.61 30 -0.21 2 32
WIPF1 0.027 0.005 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.025 0.008 -10000 0 -10000 0 0
mol:Halofuginone 0.004 0.001 -10000 0 -10000 0 0
ITGA1 0.017 0.083 -10000 0 -0.67 7 7
CDKN1A -0.007 0.071 -10000 0 -0.61 1 1
PRL-3/alpha Tubulin 0.028 0.035 -10000 0 -10000 0 0
mol:Ca2+ -0.024 0.082 0.24 5 -0.52 11 16
AGT 0.003 0.11 -10000 0 -0.67 11 11
CCNA2 -0.067 0.15 -10000 0 -0.37 100 100
TUBA1B 0.027 0.005 -10000 0 -10000 0 0
EGR1 -0.087 0.21 -10000 0 -0.5 101 101
CDK2/Cyclin E1 0.018 0.077 -10000 0 -0.54 1 1
MAPK3 0.008 0.027 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.04 0.007 -10000 0 -10000 0 0
MAPK1 0.007 0.023 -10000 0 -10000 0 0
PTP4A1 -0.07 0.16 -10000 0 -0.39 101 101
PTP4A3 0.013 0.043 -10000 0 -10000 0 0
PTP4A2 0.027 0.005 -10000 0 -10000 0 0
ITGB1 0.008 0.028 -10000 0 -10000 0 0
SRC 0.027 0.008 -10000 0 -10000 0 0
RAC1 -0.011 0.082 -10000 0 -0.61 2 2
Rab GGTase beta/Rab GGTase alpha 0.039 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.054 0.16 -10000 0 -0.37 98 98
RABGGTA 0.027 0.005 -10000 0 -10000 0 0
BCAR1 -0.012 0.014 -10000 0 -10000 0 0
RHOC -0.011 0.083 -10000 0 -0.68 2 2
RHOA -0.011 0.081 -10000 0 -0.61 2 2
cell motility -0.004 0.096 0.33 3 -0.71 2 5
PRL-1/alpha Tubulin -0.05 0.16 -10000 0 -0.36 101 101
PRL-3/alpha1 Integrin 0.021 0.074 -10000 0 -0.52 7 7
ROCK1 -0.005 0.093 0.33 2 -0.72 2 4
RABGGTB 0.027 0.005 -10000 0 -10000 0 0
CDK2 0.027 0.005 -10000 0 -10000 0 0
mitosis -0.07 0.16 -10000 0 -0.39 101 101
ATF5 0.02 0.029 -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 -0.012 0.2 -10000 0 -0.94 20 20
NCK1/PAK1/Dok-R -0.028 0.088 -10000 0 -0.43 20 20
NCK1/Dok-R -0.003 0.25 -10000 0 -1.1 20 20
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
mol:beta2-estradiol 0 0.045 0.23 18 -10000 0 18
RELA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.026 0.008 -10000 0 -10000 0 0
Rac/GDP 0.02 0.004 -10000 0 -10000 0 0
F2 -0.012 0.056 0.27 13 -10000 0 13
TNIP2 0.027 0.004 -10000 0 -10000 0 0
NF kappa B/RelA 0.011 0.23 -10000 0 -1.1 20 20
FN1 -0.085 0.069 -10000 0 -10000 0 0
PLD2 -0.024 0.25 -10000 0 -1.2 20 20
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GRB14 0.006 0.12 -10000 0 -0.67 15 15
ELK1 -0.024 0.22 -10000 0 -1 20 20
GRB7 0.001 0.057 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.007 0.25 -10000 0 -1.1 20 20
CDKN1A -0.022 0.16 0.49 4 -0.63 20 24
ITGA5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.003 0.25 -10000 0 -1.1 21 21
CRK 0.026 0.007 -10000 0 -10000 0 0
mol:NO 0.011 0.17 0.57 8 -0.67 20 28
PLG -0.031 0.25 -10000 0 -1.2 20 20
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.011 0.19 -10000 0 -0.89 20 20
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
ANGPT2 -0.1 0.2 0.42 1 -0.78 17 18
BMX -0.034 0.26 -10000 0 -1.2 20 20
ANGPT1 -0.043 0.26 -10000 0 -1.3 18 18
tube development -0.037 0.17 0.44 4 -0.73 20 24
ANGPT4 -0.034 0.2 -10000 0 -0.67 42 42
response to hypoxia -0.004 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.027 0.27 -10000 0 -1.2 20 20
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
FGF2 0.026 0.004 -10000 0 -10000 0 0
STAT5A (dimer) -0.037 0.19 -10000 0 -0.83 20 20
mol:L-citrulline 0.011 0.17 0.57 8 -0.67 20 28
AGTR1 -0.26 0.34 -10000 0 -0.67 201 201
MAPK14 -0.026 0.25 -10000 0 -1.2 20 20
Tie2/SHP2 -0.003 0.18 -10000 0 -1.2 8 8
TEK 0.005 0.19 -10000 0 -1.4 8 8
RPS6KB1 -0.006 0.2 0.51 2 -0.89 20 22
Angiotensin II/AT1 -0.19 0.26 -10000 0 -0.5 201 201
Tie2/Ang1/GRB2 -0.016 0.26 -10000 0 -1.2 20 20
MAPK3 -0.02 0.22 -10000 0 -1.1 20 20
MAPK1 -0.029 0.22 -10000 0 -1.1 20 20
Tie2/Ang1/GRB7 -0.016 0.26 -10000 0 -1.2 20 20
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.032 0.26 -10000 0 -1.2 20 20
PI3K -0.02 0.23 -10000 0 -1.1 20 20
FES -0.026 0.25 -10000 0 -1.2 20 20
Crk/Dok-R -0.003 0.25 -10000 0 -1.1 21 21
Tie2/Ang1/ABIN2 -0.015 0.26 -10000 0 -1.2 20 20
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.003 0.19 0.5 4 -0.83 20 24
STAT5A 0.026 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.009 0.2 0.48 1 -0.9 20 21
Tie2/Ang2 -0.056 0.22 -10000 0 -1 20 20
Tie2/Ang1 -0.027 0.28 -10000 0 -1.3 20 20
FOXO1 0 0.19 0.56 4 -0.84 20 24
ELF1 0.028 0.053 -10000 0 -0.59 3 3
ELF2 -0.023 0.24 -10000 0 -1.2 20 20
mol:Choline -0.021 0.23 -10000 0 -1.1 20 20
cell migration -0.014 0.055 -10000 0 -0.24 20 20
FYN -0.046 0.19 0.53 1 -0.84 20 21
DOK2 0.019 0.052 -10000 0 -0.67 2 2
negative regulation of cell cycle -0.019 0.15 0.48 4 -0.57 20 24
ETS1 0.026 0.047 -10000 0 -0.24 13 13
PXN 0.003 0.18 0.59 5 -0.73 20 25
ITGB1 0.027 0.004 -10000 0 -10000 0 0
NOS3 0.005 0.19 0.58 7 -0.78 20 27
RAC1 0.026 0.006 -10000 0 -10000 0 0
TNF -0.056 0.23 -10000 0 -0.59 71 71
MAPKKK cascade -0.021 0.23 -10000 0 -1.1 20 20
RASA1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.017 0.26 -10000 0 -1.2 20 20
NCK1 0.027 0.003 -10000 0 -10000 0 0
vasculogenesis 0.014 0.16 0.52 10 -0.6 20 30
mol:Phosphatidic acid -0.021 0.23 -10000 0 -1.1 20 20
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.011 0.17 0.57 8 -0.67 20 28
Rac1/GTP -0.004 0.18 -10000 0 -0.83 20 20
MMP2 -0.029 0.26 -10000 0 -1.2 20 20
ceramide signaling pathway

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
MAP4K4 -0.015 0.12 -10000 0 -0.45 19 19
BAG4 0.026 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 0.013 0.07 0.25 23 -10000 0 23
EnzymeConsortium:3.1.4.12 0.002 0.039 0.16 10 -0.1 17 27
IKBKB -0.013 0.12 0.29 1 -0.45 15 16
MAP2K2 0.018 0.094 0.34 23 -0.3 2 25
MAP2K1 0.011 0.083 0.34 16 -0.3 2 18
SMPD1 0.005 0.045 0.21 9 -0.12 7 16
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.01 0.12 -10000 0 -0.46 18 18
MAP2K4 0.018 0.096 0.35 26 -10000 0 26
protein ubiquitination -0.011 0.12 0.32 4 -0.46 14 18
EnzymeConsortium:2.7.1.37 0.018 0.11 0.38 25 -0.31 2 27
response to UV 0 0.002 0.006 27 -0.002 3 30
RAF1 0.012 0.085 0.31 21 -0.32 2 23
CRADD 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide 0.005 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 0.076 0.31 18 -0.16 10 28
TRADD 0.026 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.018 0.088 0.34 19 -0.29 2 21
MAPK1 -0.005 0.09 0.33 16 -0.27 4 20
p50/RELA/I-kappa-B-alpha 0.039 0.009 -10000 0 -10000 0 0
FADD -0.014 0.12 -10000 0 -0.46 17 17
KSR1 0.01 0.08 0.27 24 -0.28 3 27
MAPK8 0.012 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 -0.014 0.12 0.34 1 -0.45 15 16
TNF R/SODD 0.038 0.026 -10000 0 -0.51 1 1
TNF -0.055 0.22 -10000 0 -0.68 56 56
CYCS 0.02 0.08 0.24 30 -0.18 1 31
IKBKG -0.012 0.12 0.38 1 -0.45 14 15
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.015 0.13 -10000 0 -0.46 20 20
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.028 0.003 -10000 0 -10000 0 0
AIFM1 0.018 0.079 0.25 25 -0.18 2 27
TNF/TNF R/SODD -0.003 0.16 -10000 0 -0.44 57 57
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.006 13 -10000 0 13
CASP8 0.009 0.13 -10000 0 -0.72 14 14
NSMAF -0.014 0.12 -10000 0 -0.45 18 18
response to hydrogen peroxide 0 0.002 0.006 27 -0.002 3 30
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.04 0.12 0.89 7 -10000 0 7
VDR 0.026 0.009 -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 -0.3 41 41
RXRs/LXRs/DNA/Oxysterols -0.01 0.15 -10000 0 -0.42 54 54
MED1 0.026 0.007 -10000 0 -10000 0 0
mol:9cRA -0.001 0.018 -10000 0 -0.14 1 1
RARs/THRs/DNA/Src-1 0.02 0.069 -10000 0 -0.3 21 21
RXRs/NUR77 -0.091 0.24 -10000 0 -0.45 135 135
RXRs/PPAR -0.02 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 0.049 0.074 -10000 0 -0.37 14 14
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 0.009 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.032 0.071 -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 0.021 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 0.036 0.097 -10000 0 -0.44 5 5
NR1H4 -0.004 0.022 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.057 0.12 -10000 0 -0.5 4 4
NR1H2 0.022 0.024 -10000 0 -10000 0 0
NR1H3 0.023 0.026 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.048 0.08 -10000 0 -0.45 3 3
NR4A1 -0.18 0.32 -10000 0 -0.67 146 146
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.003 0.054 -10000 0 -0.31 3 3
RXRG -0.11 0.077 -10000 0 -0.6 5 5
RXR alpha/CCPG 0.032 0.025 -10000 0 -10000 0 0
RXRA 0.021 0.025 -10000 0 -10000 0 0
RXRB 0.023 0.026 -10000 0 -10000 0 0
THRB 0.014 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 -0.097 0.37 -10000 0 -1.1 57 57
mol:Oxysterols 0 0.016 -10000 0 -10000 0 0
cholesterol transport -0.009 0.15 -10000 0 -0.41 54 54
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 -0.34 152 152
SREBF1 -0.011 0.14 -10000 0 -0.53 7 7
RXRs/RXRs/DNA/9cRA 0.037 0.097 -10000 0 -0.44 5 5
ABCA1 -0.01 0.14 -10000 0 -0.51 8 8
RARs/THRs 0.056 0.098 -10000 0 -0.4 20 20
RXRs/FXR 0.047 0.085 -10000 0 -0.48 3 3
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
Signaling events mediated by PTP1B

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
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
Jak2/Leptin Receptor -0.006 0.12 0.29 2 -0.38 26 28
PTP1B/AKT1 0.006 0.071 0.32 2 -0.28 6 8
FYN 0.027 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0 0.082 0.34 9 -0.28 8 17
EGFR 0.013 0.072 -10000 0 -0.68 5 5
EGF/EGFR -0.035 0.16 -10000 0 -0.39 74 74
CSF1 0.016 0.088 -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 -0.004 0.11 0.32 6 -0.35 17 23
Insulin Receptor/Insulin 0.015 0.072 -10000 0 -0.35 4 4
HCK 0.017 0.039 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
TYK2 0.008 0.093 0.33 17 -0.32 3 20
EGF -0.076 0.25 -10000 0 -0.67 72 72
YES1 0.027 0.005 -10000 0 -10000 0 0
CAV1 -0.004 0.11 0.42 11 -0.33 8 19
TXN 0.024 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.029 0.14 -10000 0 -0.39 56 56
cell migration 0 0.082 0.28 8 -0.34 9 17
STAT3 0.026 0.007 -10000 0 -10000 0 0
PRLR -0.014 0.16 -10000 0 -0.67 25 25
ITGA2B -0.042 0.21 -10000 0 -0.67 48 48
CSF1R 0.024 0.035 -10000 0 -0.67 1 1
Prolactin Receptor/Prolactin 0.001 0.12 -10000 0 -0.51 25 25
FGR 0.026 0.015 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.006 0.073 0.3 2 -0.29 5 7
Crk/p130 Cas 0.013 0.071 -10000 0 -0.35 1 1
DOK1 0.012 0.087 0.36 12 -0.34 3 15
JAK2 -0.012 0.12 0.32 6 -0.38 33 39
Jak2/Leptin Receptor/Leptin -0.007 0.13 -10000 0 -0.49 20 20
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
PTPN1 0 0.083 0.34 9 -0.29 8 17
LYN 0.027 0.005 -10000 0 -10000 0 0
CDH2 -0.073 0.12 -10000 0 -0.63 14 14
SRC 0.023 0.057 0.32 1 -0.42 4 5
ITGB3 0.01 0.1 -10000 0 -0.65 11 11
CAT1/PTP1B -0.06 0.16 0.42 12 -0.36 45 57
CAPN1 0.027 0.006 -10000 0 -10000 0 0
CSK 0.027 0.008 -10000 0 -10000 0 0
PI3K 0.021 0.082 -10000 0 -0.42 6 6
mol:H2O2 -0.001 0.007 -10000 0 -10000 0 0
STAT3 (dimer) -0.007 0.13 -10000 0 -0.52 19 19
negative regulation of transcription -0.01 0.12 0.32 6 -0.37 33 39
FCGR2A 0.017 0.045 -10000 0 -0.67 1 1
FER 0.022 0.055 -10000 0 -0.68 3 3
alphaIIb/beta3 Integrin -0.026 0.18 -10000 0 -0.53 55 55
BLK -0.19 0.31 -10000 0 -0.67 148 148
Insulin Receptor/Insulin/Shc 0.039 0.04 -10000 0 -0.42 3 3
RHOA 0.028 0.006 -10000 0 -10000 0 0
LEPR 0.021 0.06 -10000 0 -0.54 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 -0.09 0.18 0.38 3 -0.47 42 45
PRL -0.006 0.019 -10000 0 -10000 0 0
SOCS3 -0.038 0.3 -10000 0 -1.3 26 26
SPRY2 0.022 0.046 -10000 0 -0.68 2 2
Insulin Receptor/Insulin/IRS1 -0.016 0.16 -10000 0 -0.45 60 60
CSF1/CSF1R 0.008 0.095 0.28 1 -0.46 10 11
Ras protein signal transduction 0.026 0.11 0.47 24 -10000 0 24
IRS1 -0.054 0.22 -10000 0 -0.67 58 58
INS 0.007 0.055 -10000 0 -0.67 3 3
LEP 0.009 0.033 -10000 0 -10000 0 0
STAT5B 0.001 0.091 0.3 10 -0.28 14 24
STAT5A 0.001 0.091 0.32 9 -0.28 14 23
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.073 0.28 1 -0.32 7 8
CSN2 0.001 0.062 0.81 1 -10000 0 1
PIK3CA 0.023 0.054 -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 0.008 -10000 0 -10000 0 0
NOX4 -0.041 0.077 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.07 -10000 0 -0.58 6 6
alphaV beta3 Integrin 0.04 0.081 -10000 0 -0.48 11 11
PTK2 0.013 0.14 0.41 11 -0.53 9 20
IGF1R 0.027 0.004 -10000 0 -10000 0 0
PI4KB 0.026 0.007 -10000 0 -10000 0 0
MFGE8 0.009 0.05 -10000 0 -10000 0 0
SRC 0.027 0.008 -10000 0 -10000 0 0
CDKN1B -0.027 0.16 -10000 0 -0.54 45 45
VEGFA 0.023 0.054 -10000 0 -0.67 3 3
ILK -0.027 0.16 -10000 0 -0.53 46 46
ROCK1 0.027 0.005 -10000 0 -10000 0 0
AKT1 -0.029 0.15 -10000 0 -0.5 45 45
PTK2B 0.012 0.09 0.36 1 -0.42 16 17
alphaV/beta3 Integrin/JAM-A 0.007 0.14 -10000 0 -0.4 51 51
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.036 0.08 -10000 0 -0.46 11 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.087 0.24 -10000 0 -0.44 152 152
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.001 0.092 -10000 0 -0.41 5 5
alphaV/beta3 Integrin/Syndecan-1 0.04 0.081 -10000 0 -0.48 11 11
PI4KA 0.02 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.093 0.23 -10000 0 -0.43 152 152
PI4 Kinase 0.028 0.019 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
alphaV/beta3 Integrin/Osteopontin 0.02 0.13 -10000 0 -0.43 35 35
RPS6KB1 -0.14 0.19 0.42 2 -0.43 112 114
TLN1 0.026 0.007 -10000 0 -10000 0 0
MAPK3 -0.051 0.13 -10000 0 -0.64 12 12
GPR124 0.027 0.005 -10000 0 -10000 0 0
MAPK1 -0.06 0.14 -10000 0 -0.58 19 19
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.028 0.12 -10000 0 -0.52 20 20
cell adhesion 0.03 0.078 -10000 0 -0.46 10 10
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 0.02 0.004 -10000 0 -10000 0 0
TGFBR2 0.023 0.054 -10000 0 -0.67 3 3
ITGB3 0.011 0.1 -10000 0 -0.65 11 11
IGF1 -0.13 0.29 -10000 0 -0.67 108 108
RAC1 0.026 0.006 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.039 0.081 -10000 0 -0.47 11 11
apoptosis 0.024 0.044 -10000 0 -0.67 2 2
CD47 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.04 0.081 -10000 0 -0.48 11 11
VCL 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.032 0.1 -10000 0 -0.48 18 18
CSF1 0.016 0.088 -10000 0 -0.67 8 8
PIK3C2A -0.028 0.17 -10000 0 -0.53 47 47
PI4 Kinase/Pyk2 -0.014 0.12 -10000 0 -0.65 3 3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.048 0.097 -10000 0 -0.45 16 16
FAK1/Vinculin 0.024 0.12 0.39 9 -0.45 6 15
alphaV beta3/Integrin/ppsTEM5 0.04 0.081 -10000 0 -0.48 11 11
RHOA 0.027 0.003 -10000 0 -10000 0 0
VTN -0.038 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 0.041 0.082 -10000 0 -0.48 11 11
alphaV/beta3 Integrin/TGFBR2 0.038 0.086 -10000 0 -0.44 14 14
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.056 0.072 -10000 0 -0.44 9 9
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.036 0.075 -10000 0 -0.44 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.085 0.069 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.034 0.089 -10000 0 -0.42 16 16
SDC1 0.026 0.015 -10000 0 -10000 0 0
VAV3 0.009 0.08 -10000 0 -0.43 14 14
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
IRS1 -0.054 0.22 -10000 0 -0.67 58 58
FAK1/Paxillin 0.022 0.12 0.35 8 -0.45 6 14
cell migration 0.018 0.11 0.34 6 -0.41 6 12
ITGAV 0.024 0.045 -10000 0 -0.67 2 2
PI3K 0.016 0.14 -10000 0 -0.38 52 52
SPP1 -0.031 0.15 -10000 0 -0.67 23 23
KDR 0.022 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 -0.63 14 14
angiogenesis -0.054 0.15 -10000 0 -0.55 25 25
Rac1/GTP 0.021 0.075 -10000 0 -0.4 14 14
EDIL3 0.005 0.095 -10000 0 -0.67 8 8
cell proliferation 0.037 0.086 -10000 0 -0.44 14 14
IL27-mediated signaling events

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
TGFB1 0.026 0.018 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.045 0.13 0.48 14 -10000 0 14
IL27/IL27R/JAK1 -0.015 0.17 -10000 0 -0.49 11 11
TBX21 -0.066 0.18 0.39 6 -0.58 28 34
IL12B 0.004 0.085 -10000 0 -0.68 7 7
IL12A -0.049 0.16 -10000 0 -0.5 53 53
IL6ST -0.072 0.24 -10000 0 -0.68 66 66
IL27RA/JAK1 0.02 0.054 0.55 1 -10000 0 1
IL27 0.011 0.028 -10000 0 -10000 0 0
TYK2 0.019 0.021 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.04 0.13 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.045 0.13 0.48 14 -10000 0 14
T cell proliferation during immune response 0.045 0.13 0.48 14 -10000 0 14
MAPKKK cascade -0.045 0.13 -10000 0 -0.48 14 14
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT2 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.024 0.023 -10000 0 -10000 0 0
IL12RB1 0.004 0.082 -10000 0 -0.62 6 6
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.057 0.19 0.48 13 -0.55 27 40
IL27/IL27R/JAK2/TYK2 -0.046 0.13 -10000 0 -0.49 14 14
positive regulation of T cell mediated cytotoxicity -0.045 0.13 -10000 0 -0.48 14 14
STAT1 (dimer) -0.026 0.22 0.52 12 -0.6 17 29
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 -0.47 14 14
T cell proliferation -0.11 0.19 -10000 0 -0.52 55 55
IL12/IL12R/TYK2/JAK2 -0.073 0.24 -10000 0 -0.84 30 30
IL17A -0.04 0.13 -10000 0 -10000 0 0
mast cell activation 0.045 0.13 0.48 14 -10000 0 14
IFNG -0.016 0.051 0.1 3 -0.13 69 72
T cell differentiation -0.004 0.008 -10000 0 -0.022 63 63
STAT3 (dimer) -0.032 0.14 -10000 0 -0.46 13 13
STAT5A (dimer) -0.032 0.14 -10000 0 -0.46 13 13
STAT4 (dimer) -0.039 0.15 -10000 0 -0.48 17 17
STAT4 0.004 0.099 -10000 0 -0.59 11 11
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.025 0.15 -10000 0 -0.52 5 5
GATA3 -0.058 0.3 -10000 0 -1.4 25 25
IL18 -0.012 0.077 -10000 0 -0.49 11 11
positive regulation of mast cell cytokine production -0.032 0.13 -10000 0 -0.46 13 13
IL27/EBI3 -0.031 0.06 -10000 0 -0.26 1 1
IL27RA 0 0.024 -10000 0 -10000 0 0
IL6 -0.096 0.26 -10000 0 -0.67 81 81
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 -0.027 0.13 -10000 0 -0.51 32 32
EBI3 -0.052 0.075 -10000 0 -0.37 1 1
TNF -0.053 0.16 -10000 0 -0.51 56 56
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.018 0.12 -10000 0 -0.46 24 24
MAP4K1 0.008 0.079 -10000 0 -0.67 5 5
MAP3K8 0.018 0.079 -10000 0 -0.63 7 7
PRKCB 0.007 0.08 -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 0.002 0.081 -10000 0 -0.32 25 25
JUN -0.084 0.21 0.37 1 -0.49 63 64
MAP3K7 0.002 0.081 -10000 0 -0.41 9 9
GRAP2 -0.02 0.15 -10000 0 -0.56 33 33
CRK 0.026 0.007 -10000 0 -10000 0 0
MAP2K4 -0.003 0.097 0.34 3 -0.37 17 20
LAT 0.021 0.058 -10000 0 -0.6 4 4
LCP2 0.024 0.021 -10000 0 -10000 0 0
MAPK8 -0.007 0.15 -10000 0 -0.62 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.006 0.085 -10000 0 -0.34 25 25
LAT/GRAP2/SLP76/HPK1/HIP-55 0.026 0.12 -10000 0 -0.44 23 23
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.011 0.1 -10000 0 -0.52 11 11
alphaM/beta2 Integrin/GPIbA 0.001 0.12 -10000 0 -0.49 18 18
alphaM/beta2 Integrin/proMMP-9 -0.023 0.17 -10000 0 -0.5 44 44
PLAUR -0.023 0.071 -10000 0 -10000 0 0
HMGB1 0.009 0.035 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.015 0.085 -10000 0 -0.57 5 5
AGER -0.037 0.18 -10000 0 -0.7 32 32
RAP1A 0.027 0.005 -10000 0 -10000 0 0
SELPLG 0.016 0.039 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.032 0.19 -10000 0 -0.47 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.043 0.2 -10000 0 -0.67 42 42
CYR61 -0.18 0.32 -10000 0 -0.67 144 144
TLN1 0.026 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.001 0.087 -10000 0 -0.37 9 9
RHOA 0.027 0.003 -10000 0 -10000 0 0
P-selectin oligomer 0.015 0.078 -10000 0 -0.67 6 6
MYH2 -0.031 0.097 -10000 0 -0.44 7 7
MST1R 0.02 0.065 -10000 0 -0.67 4 4
leukocyte activation during inflammatory response 0.014 0.081 -10000 0 -0.49 5 5
APOB 0.006 0.04 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.017 0.079 -10000 0 -0.63 7 7
JAM3 0.027 0.005 -10000 0 -10000 0 0
GP1BA 0.002 0.12 -10000 0 -0.63 15 15
alphaM/beta2 Integrin/CTGF -0.051 0.19 -10000 0 -0.47 76 76
alphaM/beta2 Integrin -0.024 0.089 -10000 0 -0.43 9 9
JAM3 homodimer 0.027 0.005 -10000 0 -10000 0 0
ICAM2 0.026 0.007 -10000 0 -10000 0 0
ICAM1 -0.011 0.065 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.024 0.09 -10000 0 -0.42 10 10
cell adhesion 0.001 0.12 -10000 0 -0.49 18 18
NFKB1 -0.11 0.26 0.33 1 -0.51 124 125
THY1 0.026 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.021 0.028 -10000 0 -10000 0 0
alphaM/beta2 Integrin/LRP/tPA 0.026 0.095 -10000 0 -0.48 9 9
IL6 -0.19 0.38 -10000 0 -0.96 88 88
ITGB2 -0.001 0.058 -10000 0 -0.71 1 1
elevation of cytosolic calcium ion concentration -0.02 0.11 -10000 0 -0.52 5 5
alphaM/beta2 Integrin/JAM2/JAM3 0.026 0.094 -10000 0 -0.5 8 8
JAM2 0.021 0.063 -10000 0 -0.67 4 4
alphaM/beta2 Integrin/ICAM1 0.034 0.1 -10000 0 -0.52 8 8
alphaM/beta2 Integrin/uPA/Plg 0.009 0.098 -10000 0 -0.59 4 4
RhoA/GTP -0.026 0.1 -10000 0 -0.45 8 8
positive regulation of phagocytosis -0.007 0.096 -10000 0 -0.63 4 4
Ron/MSP 0.034 0.056 -10000 0 -0.51 5 5
alphaM/beta2 Integrin/uPAR/uPA -0.02 0.11 -10000 0 -0.52 5 5
alphaM/beta2 Integrin/uPAR 0.007 0.094 -10000 0 -0.62 4 4
PLAU -0.045 0.077 -10000 0 -10000 0 0
PLAT 0.02 0.058 -10000 0 -0.67 3 3
actin filament polymerization -0.029 0.095 -10000 0 -0.42 7 7
MST1 0.026 0.032 -10000 0 -0.67 1 1
alphaM/beta2 Integrin/lipoprotein(a) 0.018 0.083 -10000 0 -0.5 5 5
TNF -0.16 0.35 -10000 0 -0.92 73 73
RAP1B 0.027 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.004 0.099 -10000 0 -0.52 6 6
fibrinolysis 0.008 0.097 -10000 0 -0.58 4 4
HCK 0.017 0.039 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.024 0.09 -10000 0 -0.42 10 10
VTN -0.038 0.2 -10000 0 -0.67 44 44
alphaM/beta2 Integrin/CYR61 -0.12 0.23 -10000 0 -0.47 146 146
LPA -0.005 0.026 -10000 0 -10000 0 0
LRP1 0.025 0.032 -10000 0 -0.67 1 1
cell migration -0.031 0.16 -10000 0 -0.5 43 43
FN1 -0.085 0.069 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.016 0.086 -10000 0 -0.56 5 5
MPO 0.012 0.078 -10000 0 -0.67 6 6
KNG1 -0.005 0.038 -10000 0 -10000 0 0
RAP1/GDP 0.035 0.009 -10000 0 -10000 0 0
ROCK1 -0.024 0.098 -10000 0 -0.43 7 7
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.014 0.02 -10000 0 -10000 0 0
CTGF -0.078 0.25 -10000 0 -0.66 76 76
alphaM/beta2 Integrin/Hck 0.011 0.092 -10000 0 -0.57 5 5
ITGAM -0.005 0.081 -10000 0 -0.73 4 4
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.02 0.1 -10000 0 -0.52 10 10
HP -0.023 0.098 -10000 0 -0.67 6 6
leukocyte adhesion -0.025 0.16 -10000 0 -0.54 22 22
SELP 0.015 0.078 -10000 0 -0.67 6 6
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.002 0.045 -10000 0 -0.44 5 5
ADCY5 -0.054 0.15 -10000 0 -0.44 66 66
ADCY6 0.002 0.045 -10000 0 -0.44 5 5
ADCY7 0.002 0.044 -10000 0 -0.44 5 5
ADCY1 -0.002 0.065 -10000 0 -0.49 8 8
ADCY2 -0.038 0.13 -10000 0 -0.45 45 45
ADCY3 0.002 0.045 -10000 0 -0.44 5 5
ADCY8 -0.05 0.054 -10000 0 -0.49 5 5
PRKCE 0.004 0.052 -10000 0 -0.51 5 5
ADCY9 0.002 0.044 -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 -0.37 15 21
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.03 0.074 -9999 0 -0.38 15 15
RGS9BP -0.015 0.16 -9999 0 -0.66 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.038 0.2 -9999 0 -0.65 46 46
mol:Na + 0.017 0.034 -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 -0.45 71 71
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+ -0.01 0.029 -9999 0 -10000 0 0
Cone PDE6 -0.003 0.16 -9999 0 -0.4 70 70
Cone Metarhodopsin II -0.009 0.12 -9999 0 -0.39 46 46
Na + (4 Units) 0.022 0.039 -9999 0 -10000 0 0
GNAT2/GDP -0.008 0.16 -9999 0 -0.39 68 68
GNB5 0.027 0.004 -9999 0 -10000 0 0
mol:GMP (4 units) -0.003 0.022 -9999 0 -10000 0 0
Cone Transducin 0.033 0.079 -9999 0 -0.4 15 15
SLC24A2 -0.008 0.031 -9999 0 -10000 0 0
GNB3/GNGT2 0.021 0.094 -9999 0 -0.51 15 15
GNB3 0.007 0.12 -9999 0 -0.67 14 14
GNAT2/GTP 0.017 0.008 -9999 0 -10000 0 0
CNGA3 0.007 0.052 -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 0.017 0.034 -9999 0 -10000 0 0
mol:Pi -0.022 0.18 -9999 0 -0.45 71 71
Cone CNG Channel 0.043 0.034 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.008 0.031 -9999 0 -10000 0 0
RGS9 -0.039 0.2 -9999 0 -0.67 45 45
PDE6C -0.005 0.02 -9999 0 -10000 0 0
GNGT2 0.023 0.035 -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
p75(NTR)-mediated 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
Sortilin/TRAF6 0.037 0.036 -10000 0 -0.51 2 2
Necdin/E2F1 -0.001 0.078 -10000 0 -0.55 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.057 0.091 -10000 0 -0.4 16 16
NGF (dimer)/p75(NTR)/BEX1 -0.18 0.25 -10000 0 -0.44 228 228
NT-4/5 (dimer)/p75(NTR) -0.012 0.14 -10000 0 -0.52 30 30
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.005 0.097 0.36 1 -0.4 19 20
IKBKG 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.009 0.1 -10000 0 -0.67 11 11
MGDIs/NGR/p75(NTR)/LINGO1 0.023 0.092 -10000 0 -0.45 16 16
FURIN 0.027 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.026 0.11 -10000 0 -0.42 27 27
LINGO1 0.02 0.032 -10000 0 -10000 0 0
Sortilin/TRAF6/NRIF 0.031 0.028 -10000 0 -0.35 2 2
proBDNF (dimer) 0.009 0.1 -10000 0 -0.67 11 11
NTRK1 0.01 0.032 -10000 0 -10000 0 0
RTN4R 0.02 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.022 0.13 0.4 16 -0.42 17 33
IRAK1 0.025 0.008 -10000 0 -10000 0 0
SHC1 -0.006 0.09 -10000 0 -0.45 16 16
ARHGDIA 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.07 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.047 0.092 -10000 0 -0.43 16 16
MAGEH1 0.026 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.045 0.1 -10000 0 -0.41 21 21
Mammalian IAPs/DIABLO 0.046 0.094 -10000 0 -0.4 19 19
proNGF (dimer) 0.022 0.056 -10000 0 -0.67 3 3
MAGED1 0.026 0.007 -10000 0 -10000 0 0
APP 0.027 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.12 -10000 0 -0.65 15 15
ZNF274 0.026 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.012 0.085 -10000 0 -0.4 16 16
NGF 0.022 0.056 -10000 0 -0.67 3 3
cell cycle arrest 0.057 0.14 0.42 19 -0.38 16 35
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.016 0.069 -10000 0 -0.32 18 18
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.018 0.13 -10000 0 -0.45 32 32
NCSTN 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0.034 0.097 -10000 0 -0.45 18 18
PSENEN 0.026 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 -0.36 5 5
p75(NTR)/beta APP 0.005 0.1 -10000 0 -0.51 16 16
BEX1 -0.28 0.35 -10000 0 -0.67 218 218
mol:GDP -0.018 0.088 -10000 0 -0.44 18 18
NGF (dimer) 0.036 0.11 -10000 0 -0.41 27 27
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.034 0.09 -10000 0 -0.41 16 16
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.03 0.083 -10000 0 -0.39 17 17
MYD88 0.027 0.003 -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 0.003 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.004 0.055 -10000 0 -10000 0 0
NT3 (dimer) -0.016 0.15 -10000 0 -0.67 25 25
TP53 -0.003 0.099 0.35 1 -0.36 26 27
PRDM4 0.001 0.09 -10000 0 -0.42 16 16
BDNF (dimer) -0.011 0.14 -10000 0 -0.44 34 34
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
SORT1 0.027 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.051 0.088 -10000 0 -0.4 16 16
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.047 0.097 -10000 0 -0.42 19 19
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 -0.38 18 34
DIABLO 0.027 0.005 -10000 0 -10000 0 0
SMPD2 0.003 0.092 -10000 0 -0.42 16 16
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.026 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.035 0.095 -10000 0 -0.45 17 17
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.026 -10000 0 -0.51 1 1
NT3 (dimer)/p75(NTR) -0.026 0.15 -10000 0 -0.51 40 40
MAPK8 0.01 0.12 0.34 15 -0.39 19 34
MAPK9 0.011 0.1 0.34 10 -0.38 17 27
APAF1 0.025 0.032 -10000 0 -0.67 1 1
NTF3 -0.016 0.16 -10000 0 -0.67 25 25
NTF4 0.002 0.12 -10000 0 -0.65 15 15
NDN 0.02 0.07 -10000 0 -0.67 5 5
RAC1/GDP 0.02 0.004 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.052 0.085 -10000 0 -0.38 17 17
p75 CTF/Sortilin/TRAF6/NRIF 0.06 0.052 -10000 0 -0.52 3 3
RhoA-B-C/GTP 0.033 0.097 -10000 0 -0.45 18 18
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.048 0.11 -10000 0 -0.38 26 26
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.039 0.11 -10000 0 -0.39 29 29
PRKACB 0.025 0.032 -10000 0 -0.67 1 1
proBDNF (dimer)/p75 ECD 0.023 0.089 -10000 0 -0.51 13 13
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 0.071 0.14 0.48 12 -0.38 17 29
BAD 0.027 0.14 0.45 25 -0.4 16 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 0.097 -10000 0 -0.43 18 18
BCL2L11 0.027 0.14 0.44 25 -0.39 16 41
BDNF (dimer)/p75(NTR) -0.009 0.13 -10000 0 -0.51 27 27
PI3K 0.046 0.099 -10000 0 -0.43 19 19
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.049 0.092 -10000 0 -0.43 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 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.002 0.11 -10000 0 -0.51 18 18
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.047 0.092 -10000 0 -0.43 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 0.02 -10000 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.005 0.099 -10000 0 -0.4 26 26
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
NGFRAP1 0.026 0.007 -10000 0 -10000 0 0
CASP3 0.031 0.14 0.44 26 -0.36 16 42
E2F1 -0.019 0.07 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.05 0.075 -10000 0 -0.46 3 3
NGF (dimer)/TRKA 0.027 0.05 -10000 0 -0.51 3 3
MMP7 -0.079 0.16 -10000 0 -0.66 26 26
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.055 0.096 -10000 0 -0.4 18 18
MMP3 -0.017 0.049 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.014 0.095 -10000 0 -0.54 6 6
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.03 0.11 -10000 0 -0.33 58 58
FRAP1 0.01 0.047 0.36 3 -0.42 1 4
AKT1 -0.026 0.096 -10000 0 -0.28 55 55
INSR 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.024 0.037 -10000 0 -0.43 3 3
mol:GTP 0.004 0.089 -10000 0 -0.42 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.007 0.036 -10000 0 -0.24 1 1
TSC2 0.026 0.006 -10000 0 -10000 0 0
RHEB/GDP -0.001 0.074 -10000 0 -0.39 3 3
TSC1 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.023 0.13 -10000 0 -0.37 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 0.019 0.098 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 72 73
EIF4B 0.024 0.11 0.46 21 -0.32 3 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 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 -0.007 0.13 -10000 0 -0.36 59 59
mTOR/RHEB/GTP/Raptor/GBL 0.004 0.047 0.28 3 -0.24 2 5
FKBP1A 0.027 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.012 0.08 -10000 0 -0.38 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 72 73
FKBP12/Rapamycin 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.032 0.11 -10000 0 -0.32 56 56
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.026 0.074 -10000 0 -0.5 8 8
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.008 -10000 0 -10000 0 0
TSC1/TSC2 0.006 0.096 0.28 1 -0.46 3 4
tumor necrosis factor receptor activity 0 0.001 0.002 72 -0.001 1 73
RPS6 0.025 0.008 -10000 0 -10000 0 0
PPP5C 0.025 0.008 -10000 0 -10000 0 0
EIF4G1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.042 0.14 -10000 0 -0.37 67 67
INS -0.02 0.051 -10000 0 -0.67 3 3
PTEN 0.025 0.018 -10000 0 -0.36 1 1
PDK2 -0.029 0.1 0.22 3 -0.31 55 58
EIF4EBP1 0.017 0.096 -10000 0 -0.93 5 5
PIK3CA 0.023 0.055 -10000 0 -0.68 3 3
PPP2R5D 0.02 0.074 0.39 13 -0.38 1 14
peptide biosynthetic process 0.011 0.034 -10000 0 -0.39 3 3
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 0.009 19 -0.003 3 22
EEF2 0.011 0.034 -10000 0 -0.39 3 3
eIF4E/4E-BP1 0.03 0.088 -10000 0 -0.83 5 5
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.026 0.032 -10000 0 -0.67 1 1
Caspase 8 (4 units) 0.023 0.09 -10000 0 -0.41 6 6
NEF -0.014 0.067 -10000 0 -0.25 29 29
NFKBIA 0.021 0.032 -10000 0 -10000 0 0
BIRC3 -0.004 0.15 -10000 0 -0.66 22 22
CYCS -0.008 0.093 0.21 1 -0.31 25 26
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CD247 -0.014 0.15 -10000 0 -0.44 41 41
MAP2K7 -0.001 0.16 0.28 1 -0.6 25 26
protein ubiquitination 0.009 0.099 0.36 6 -0.37 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 -0.009 0.098 0.19 16 -0.31 36 52
NF-kappa-B/RelA/I kappa B alpha 0.043 0.079 -10000 0 -0.33 18 18
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 -0.33 18 18
MAPK8 -0.005 0.16 0.35 1 -0.55 27 28
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 -0.001 0.098 -10000 0 -0.32 35 35
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0 0.11 -10000 0 -0.37 19 19
CHUK 0.005 0.098 0.28 3 -0.4 4 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.076 0.03 -10000 0 -0.38 1 1
TCRz/NEF -0.022 0.15 -10000 0 -0.45 46 46
TNF -0.056 0.22 -10000 0 -0.67 56 56
FASLG -0.048 0.23 -10000 0 -0.77 41 41
NFKB1 0.021 0.033 -10000 0 -0.18 2 2
TNFR1A/BAG4/TNF-alpha -0.003 0.16 -10000 0 -0.44 57 57
CASP6 0.039 0.096 -10000 0 -0.66 5 5
CASP7 0.011 0.15 0.39 2 -0.57 26 28
RELA 0.021 0.033 -10000 0 -10000 0 0
CASP2 0.026 0.006 -10000 0 -10000 0 0
CASP3 0.01 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 -0.51 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 -0.41 6 6
APAF-1/Caspase 9 -0.002 0.12 -10000 0 -0.48 22 22
BCL2 -0.027 0.16 0.34 1 -0.54 26 27
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.004 0.14 -10000 0 -0.37 62 62
TC10/GTP 0.041 0.042 -10000 0 -0.35 4 4
Insulin Receptor/Insulin/IRS1/Shp2 0 0.16 -10000 0 -0.42 60 60
HRAS 0.026 0.011 -10000 0 -10000 0 0
APS homodimer 0.024 0.033 -10000 0 -0.67 1 1
GRB14 0.006 0.12 -10000 0 -0.67 15 15
FOXO3 0.002 0.12 -10000 0 -0.65 14 14
AKT1 -0.028 0.14 0.36 5 -0.34 64 69
INSR 0.027 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.05 0.036 -10000 0 -0.34 3 3
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 0.016 0.039 -10000 0 -0.34 3 3
CAV1 -0.035 0.14 -10000 0 -0.39 66 66
CBL/APS/CAP/Crk-II/C3G 0.065 0.052 -10000 0 -0.38 4 4
Insulin Receptor/Insulin/IRS1/NCK2 0.002 0.16 -10000 0 -0.42 60 60
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.14 -10000 0 -0.37 62 62
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.007 0.1 -10000 0 -0.45 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 0.018 0.036 -10000 0 -0.52 2 2
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.011 0.13 -10000 0 -0.68 2 2
HRAS/GTP -0.024 0.11 -10000 0 -0.34 46 46
Insulin Receptor 0.027 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.015 0.14 -10000 0 -0.39 47 47
PRKCI 0.012 0.075 -10000 0 -0.49 5 5
Insulin Receptor/Insulin/GRB14/PDK1 -0.026 0.14 -10000 0 -0.36 70 70
SHC1 0.025 0.008 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.046 0.046 -10000 0 -0.43 2 2
PI3K 0.004 0.15 -10000 0 -0.38 62 62
NCK2 0.027 0.005 -10000 0 -10000 0 0
RHOQ 0.027 0.005 -10000 0 -10000 0 0
mol:H2O2 0.001 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
AKT2 -0.03 0.14 0.38 7 -0.75 2 9
PRKCZ 0.013 0.074 -10000 0 -0.51 5 5
SH2B2 0.024 0.033 -10000 0 -0.67 1 1
SHC/SHIP -0.013 0.13 0.3 1 -0.37 50 51
F2RL2 -0.018 0.085 -10000 0 -0.67 3 3
TRIP10 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.039 0.037 -10000 0 -0.37 3 3
TC10/GTP/CIP4/Exocyst 0.034 0.011 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.062 0.041 -10000 0 -0.34 2 2
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.059 0.049 -10000 0 -0.4 4 4
TC10/GDP 0.02 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.053 0.041 -10000 0 -0.37 3 3
INPP5D -0.031 0.14 0.31 1 -0.39 60 61
SOS1 0.027 0.005 -10000 0 -10000 0 0
SGK1 -0.013 0.15 -10000 0 -0.83 15 15
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
IRS1 -0.054 0.22 -10000 0 -0.67 58 58
p62DOK/RasGAP 0.046 0.046 -10000 0 -0.44 2 2
INS 0.015 0.054 -10000 0 -0.67 3 3
mol:PI-3-4-P2 -0.031 0.14 0.31 1 -0.38 60 61
GRB2 0.026 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.032 0.12 0.36 3 -0.57 3 6
PTPRA 0.028 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -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 -0.009 0.1 -10000 0 -0.3 47 47
Insulin Receptor/Insulin/IRS1 -0.012 0.15 -10000 0 -0.41 60 60
Insulin Receptor/Insulin/IRS3 0.03 0.043 -10000 0 -0.5 3 3
Par3/Par6 0.058 0.039 -10000 0 -0.38 2 2
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.033 0.04 -10000 0 -0.82 1 1
VEGFR1 homodimer/NRP1 0.015 0.038 -10000 0 -0.82 1 1
mol:DAG -0.022 0.13 -10000 0 -0.4 51 51
VEGFR1 homodimer/NRP1/VEGFR 121 0.028 0.059 -10000 0 -0.64 3 3
CaM/Ca2+ -0.006 0.13 -10000 0 -0.38 51 51
HIF1A 0.033 0.019 -10000 0 -0.37 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.02 0.14 -10000 0 -0.7 4 4
PLCG1 -0.022 0.13 -10000 0 -0.4 51 51
NOS3 -0.012 0.12 -10000 0 -0.81 1 1
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:NO -0.007 0.12 0.47 3 -0.77 1 4
FLT1 0.021 0.042 -10000 0 -0.91 1 1
PGF -0.045 0.21 -10000 0 -0.67 51 51
VEGFR1 homodimer/NRP2/VEGFR121 0.045 0.062 -10000 0 -0.64 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
eNOS/Hsp90 0.005 0.12 -10000 0 -0.74 1 1
endothelial cell proliferation -0.037 0.15 0.36 2 -0.43 47 49
mol:Ca2+ -0.022 0.13 -10000 0 -0.4 51 51
MAPK3 -0.038 0.13 0.36 2 -0.4 16 18
MAPK1 -0.042 0.13 -10000 0 -0.99 1 1
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
PLGF homodimer -0.044 0.21 -10000 0 -0.67 51 51
PRKACA 0.025 0.008 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0.014 0.094 -10000 0 -0.67 9 9
VEGFA homodimer 0.023 0.054 -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 -0.041 0.12 -10000 0 -0.96 1 1
PI3K 0.015 0.14 -10000 0 -0.39 52 52
PRKCA -0.039 0.14 -10000 0 -0.38 63 63
PRKCB -0.034 0.13 -10000 0 -0.38 54 54
VEGFR1 homodimer/PLGF homodimer -0.014 0.15 -10000 0 -0.44 51 51
VEGFA 0.023 0.054 -10000 0 -0.67 3 3
VEGFB 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 -0.022 0.13 -10000 0 -0.4 51 51
RASA1 0.02 0.038 -10000 0 -0.76 1 1
NRP2 0.014 0.043 -10000 0 -10000 0 0
VEGFR1 homodimer 0.02 0.042 -10000 0 -0.91 1 1
VEGFB homodimer 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.002 0.14 0.55 4 -0.62 4 8
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
mol:PI-3-4-5-P3 0.013 0.14 -10000 0 -0.38 52 52
mol:L-citrulline -0.007 0.12 0.47 3 -0.77 1 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.058 0.062 -10000 0 -0.61 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.045 0.061 -10000 0 -0.64 3 3
CD2AP 0.027 0.003 -10000 0 -10000 0 0
PI3K/GAB1 0.025 0.14 -10000 0 -0.37 49 49
PDPK1 -0.017 0.13 0.34 3 -0.99 2 5
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.044 0.074 -10000 0 -0.75 3 3
mol:NADP -0.007 0.12 0.47 3 -0.77 1 4
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.056 0.06 -10000 0 -0.6 3 3
VEGFR1 homodimer/NRP2 0.026 0.047 -10000 0 -0.82 1 1
Regulation of nuclear SMAD2/3 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
EP300 0.025 0.025 0.37 1 -10000 0 1
HSPA8 0.021 0.057 -10000 0 -0.6 4 4
SMAD3/SMAD4/ER alpha -0.003 0.13 -10000 0 -0.48 21 21
AKT1 0.026 0.007 -10000 0 -10000 0 0
GSC -0.17 0.49 -10000 0 -1.4 67 67
NKX2-5 0.002 0.002 -10000 0 -10000 0 0
muscle cell differentiation -0.012 0.081 0.38 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.037 0.096 -10000 0 -10000 0 0
SMAD4 -0.007 0.071 -10000 0 -0.26 1 1
CBFB 0.026 0.006 -10000 0 -10000 0 0
SAP18 0.025 0.007 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.034 0.072 -10000 0 -0.44 3 3
SMAD3/SMAD4/VDR 0.048 0.074 -10000 0 -10000 0 0
MYC 0.012 0.1 -10000 0 -0.65 12 12
CDKN2B -0.021 0.11 -10000 0 -0.51 1 1
AP1 -0.19 0.41 -10000 0 -0.77 149 149
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.029 0.063 -10000 0 -0.51 3 3
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.01 0.035 -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 0.021 0.079 -10000 0 -10000 0 0
GATA3 -0.009 0.15 -10000 0 -0.63 25 25
SKI/SIN3/HDAC complex/NCoR1 0.028 0.041 -10000 0 -0.65 1 1
MEF2C/TIF2 -0.026 0.15 0.32 3 -0.4 42 45
endothelial cell migration -0.022 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 0.024 0.045 -10000 0 -0.67 2 2
RUNX2 -0.015 0.08 -10000 0 -0.67 2 2
RUNX3 0.009 0.1 -10000 0 -0.67 11 11
RUNX1 -0.04 0.076 -10000 0 -10000 0 0
CTBP1 0.027 0.004 -10000 0 -10000 0 0
NR3C1 0.026 0.006 -10000 0 -10000 0 0
VDR 0.026 0.009 -10000 0 -10000 0 0
CDKN1A 0.019 0.047 -10000 0 -10000 0 0
KAT2B 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.014 0.12 -10000 0 -0.34 7 7
DCP1A 0.027 0.003 -10000 0 -10000 0 0
SKI 0.026 0.006 -10000 0 -10000 0 0
SERPINE1 0.022 0.079 -10000 0 -1.3 1 1
SMAD3/SMAD4/ATF2 0.003 0.13 -10000 0 -0.49 20 20
SMAD3/SMAD4/ATF3 -0.079 0.24 -10000 0 -0.51 108 108
SAP30 0.025 0.032 -10000 0 -0.68 1 1
Cbp/p300/PIAS3 0.048 0.044 -10000 0 -10000 0 0
JUN -0.2 0.4 0.3 1 -0.76 149 150
SMAD3/SMAD4/IRF7 0.024 0.08 -10000 0 -10000 0 0
TFE3 0.03 0.009 -10000 0 -10000 0 0
COL1A2 0.026 0.064 -10000 0 -1.1 1 1
mesenchymal cell differentiation -0.014 0.097 0.46 2 -10000 0 2
DLX1 -0.009 0.15 -10000 0 -0.65 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 0.02 0.08 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.042 0.036 -10000 0 -0.42 1 1
ZBTB17 0.028 0.006 -10000 0 -10000 0 0
LAMC1 0.012 0.06 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.022 0.08 -10000 0 -10000 0 0
IRF7 0.027 0.01 -10000 0 -10000 0 0
ESR1 -0.015 0.15 -10000 0 -0.65 23 23
HNF4A -0.009 0.024 -10000 0 -10000 0 0
MEF2C -0.006 0.1 0.38 4 -0.88 1 5
SMAD2-3/SMAD4 0.012 0.095 -10000 0 -0.3 1 1
Cbp/p300/Src-1 0.046 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 0.027 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 0.03 0.08 -10000 0 -10000 0 0
MSG1/HSC70 -0.068 0.07 -10000 0 -0.47 8 8
SMAD2 0.012 0.047 -10000 0 -10000 0 0
SMAD3 0.005 0.06 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.013 0.067 -10000 0 -0.45 4 4
SMAD2/SMAD2/SMAD4 0.004 0.036 0.24 2 -10000 0 2
NCOR1 0.025 0.007 -10000 0 -10000 0 0
NCOA2 -0.037 0.2 -10000 0 -0.67 45 45
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 0.094 -10000 0 -10000 0 0
IFNB1 0 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.009 0.11 -10000 0 -0.61 2 2
CITED1 -0.1 0.081 -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 0.012 0.035 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.043 0.077 -10000 0 -0.43 11 11
SMAD7 -0.087 0.25 -10000 0 -0.55 84 84
MYC/MIZ-1 0.028 0.083 -10000 0 -0.49 12 12
SMAD3/SMAD4 0.022 0.11 0.29 32 -0.52 1 33
IL10 -0.03 0.15 -10000 0 -0.52 35 35
PIASy/HDAC complex 0.018 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 0.11 -10000 0 -0.4 23 23
CDK4 0.031 0.011 -10000 0 -10000 0 0
PIAS4 0.018 0.02 -10000 0 -10000 0 0
ATF3 -0.13 0.29 -10000 0 -0.67 110 110
SMAD3/SMAD4/SP1 0.033 0.083 -10000 0 -10000 0 0
FOXG1 0.007 0.043 -10000 0 -0.68 1 1
FOXO3 0.015 0.008 -10000 0 -10000 0 0
FOXO1 0.014 0.009 -10000 0 -10000 0 0
FOXO4 0.014 0.008 -10000 0 -10000 0 0
heart looping -0.006 0.1 0.38 4 -0.87 1 5
CEBPB 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.003 0.14 -10000 0 -0.49 24 24
MYOD1 -0.013 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.016 0.081 -10000 0 -0.3 1 1
SMAD3/SMAD4/GATA3 0 0.14 -10000 0 -0.42 34 34
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.032 -10000 0 -0.67 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.028 0.12 -10000 0 -0.48 10 10
SMAD3/SMAD4/SP1-3 0.053 0.081 -10000 0 -10000 0 0
MED15 0.02 0.012 -10000 0 -10000 0 0
SP1 0.03 0.015 -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 0.022 0.11 -10000 0 -0.41 3 3
ITGB5 0.015 0.06 -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 -0.48 198 198
AR -0.26 0.34 -10000 0 -0.66 206 206
negative regulation of cell growth -0.023 0.12 -10000 0 -0.44 5 5
SMAD3/SMAD4/MYOD 0.016 0.08 -10000 0 -10000 0 0
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 0.096 -10000 0 -0.37 1 1
SMAD2-3/SMAD4/FOXO1-3a-4 0.013 0.036 -10000 0 -10000 0 0
TFDP1 0.025 0.019 -10000 0 -0.36 1 1
SMAD3/SMAD4/AP1 -0.18 0.43 -10000 0 -0.78 149 149
SMAD3/SMAD4/RUNX2 0.014 0.097 -10000 0 -0.47 2 2
TGIF2 0.027 0.005 -10000 0 -10000 0 0
TGIF1 0.027 0.005 -10000 0 -10000 0 0
ATF2 -0.002 0.14 -10000 0 -0.66 21 21
Nectin adhesion 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
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
alphaV beta3 Integrin 0.025 0.089 -10000 0 -0.52 12 12
PTK2 0.008 0.15 -10000 0 -0.55 27 27
positive regulation of JNK cascade 0.013 0.099 -10000 0 -0.33 31 31
CDC42/GDP 0.029 0.14 0.44 1 -0.45 32 33
Rac1/GDP 0.029 0.14 -10000 0 -0.45 30 30
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.022 0.12 -10000 0 -0.41 30 30
nectin-3/I-afadin 0.007 0.13 -10000 0 -0.51 30 30
RAPGEF1 0.011 0.14 0.35 2 -0.51 29 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.008 0.16 -10000 0 -0.58 29 29
PDGFB-D/PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
TLN1 -0.005 0.061 -10000 0 -0.79 1 1
Rap1/GTP 0.01 0.097 -10000 0 -0.36 28 28
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 0.007 0.13 -10000 0 -0.51 30 30
PVR 0.026 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.026 0.007 -10000 0 -10000 0 0
mol:GDP 0.015 0.17 0.47 1 -0.55 35 36
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PI3K 0.049 0.12 -10000 0 -0.42 29 29
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.037 0.02 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.008 0.11 -10000 0 -0.35 30 30
PVRL1 0.023 0.025 -10000 0 -10000 0 0
PVRL3 -0.016 0.17 -10000 0 -0.66 31 31
PVRL2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
CLDN1 -0.11 0.095 -10000 0 -0.61 10 10
JAM-A/CLDN1 0.037 0.13 -10000 0 -0.43 32 32
SRC 0.004 0.17 -10000 0 -0.65 30 30
ITGB3 0.011 0.1 -10000 0 -0.65 11 11
nectin-1(dimer)/I-afadin/I-afadin 0.037 0.02 -10000 0 -10000 0 0
FARP2 0.018 0.16 -10000 0 -0.55 32 32
RAC1 0.026 0.006 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.022 0.12 -10000 0 -0.44 30 30
nectin-1/I-afadin 0.037 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 0.024 0.12 -10000 0 -0.44 30 30
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.008 -10000 0 -10000 0 0
F11R 0.026 0.007 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.013 0.099 -10000 0 -0.33 31 31
alphaV/beta3 Integrin/Talin 0.023 0.11 -10000 0 -0.55 11 11
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 -0.003 0.066 -10000 0 -0.24 28 28
VAV2 -0.002 0.19 0.37 1 -0.58 35 36
RAP1/GDP 0.033 0.13 0.28 1 -0.42 30 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 0.022 0.12 -10000 0 -0.44 30 30
nectin-3(dimer)/I-afadin/I-afadin 0.007 0.13 -10000 0 -0.51 30 30
Rac1/GTP 0.014 0.14 -10000 0 -0.44 30 30
PTPRM 0 0.073 -10000 0 -0.27 29 29
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 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
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 0.51 1 -10000 0 1
CDKN1A -0.006 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 0.025 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.008 0.01 -10000 0 -10000 0 0
PPARGC1A -0.28 0.35 -10000 0 -0.67 220 220
FHL2 -0.028 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 0.039 0.053 -10000 0 -0.43 1 1
SIRT1 0.022 0.032 -10000 0 -0.68 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.047 0.028 -10000 0 -0.44 1 1
SIRT1/Histone H1b -0.006 0.07 -10000 0 -0.32 10 10
apoptosis -0.036 0.033 0.44 1 -10000 0 1
SIRT1/PGC1A -0.18 0.24 -10000 0 -0.44 219 219
p53/SIRT1 0.028 0.027 -10000 0 -0.51 1 1
SIRT1/FOXO4 -0.004 0.064 -10000 0 -0.31 4 4
FOXO1/FHL2/SIRT1 0.009 0.12 -10000 0 -0.4 40 40
HIST1H1E 0.008 0.047 -10000 0 -0.34 8 8
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 0.023 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 0.026 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.031 0.029 -10000 0 -0.51 1 1
ACSS2 0.014 0.024 -10000 0 -0.51 1 1
SIRT1/PCAF/MYOD 0.029 0.028 -10000 0 -0.45 1 1
IL1-mediated signaling events

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
UBC13/UEV1A 0.02 0.004 -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 0.016 0.06 -9999 0 -0.38 2 2
IRAK/TOLLIP 0.03 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 -0.054 0.21 -9999 0 -0.55 70 70
IL1A -0.029 0.18 -9999 0 -0.67 37 37
IL1B -0.02 0.13 -9999 0 -0.51 33 33
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.038 -9999 0 -0.36 2 2
IL1R2 -0.044 0.19 -9999 0 -0.66 42 42
IL1R1 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.008 0.049 -9999 0 -0.27 1 1
TOLLIP 0.027 0.005 -9999 0 -10000 0 0
TICAM2 0.019 0.07 -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 0.036 0.061 -9999 0 -10000 0 0
JUN -0.077 0.16 -9999 0 -0.37 111 111
MAP3K7 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.042 0.12 -9999 0 -0.38 32 32
IL1 alpha/IL1R1/IL1RAP/MYD88 0.036 0.13 -9999 0 -0.41 36 36
PIK3R1 0.027 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.047 0.12 -9999 0 -0.39 36 36
IL1 beta fragment/IL1R1/IL1RAP 0.018 0.12 -9999 0 -0.42 32 32
NFKB1 0.027 0.004 -9999 0 -10000 0 0
MAPK8 -0.003 0.086 -9999 0 -0.44 16 16
IRAK1 0.016 0.005 -9999 0 -10000 0 0
IL1RN/IL1R1 0.011 0.087 -9999 0 -0.48 11 11
IRAK4 0.027 0.005 -9999 0 -10000 0 0
PRKCI 0.027 0.003 -9999 0 -10000 0 0
TRAF6 0.024 0.045 -9999 0 -0.67 2 2
PI3K 0.036 0.043 -9999 0 -0.51 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.015 0.066 -9999 0 -0.38 3 3
CHUK 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.018 0.12 -9999 0 -0.42 32 32
IL1 beta/IL1R2 -0.042 0.18 -9999 0 -0.48 66 66
IRAK/TRAF6/TAK1/TAB1/TAB2 0.036 0.028 -9999 0 -0.36 2 2
NF kappa B1 p50/RelA 0.029 0.11 -9999 0 -0.36 31 31
IRAK3 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.04 0.12 -9999 0 -0.39 34 34
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.007 0.084 -9999 0 -0.29 36 36
IL1 alpha/IL1R1/IL1RAP 0.02 0.13 -9999 0 -0.44 36 36
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 0.003 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.042 0.032 -9999 0 -0.38 2 2
IL1RAP -0.013 0.068 -9999 0 -10000 0 0
UBE2N 0.027 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 0.009 0.1 -9999 0 -0.34 33 33
CASP1 0.022 0.047 -9999 0 -0.67 2 2
IL1RN/IL1R2 -0.042 0.17 -9999 0 -0.52 50 50
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.033 0.12 -9999 0 -0.4 32 32
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.012 0.07 -9999 0 -0.32 4 4
PIK3CA 0.023 0.054 -9999 0 -0.67 3 3
IL1RN -0.011 0.11 -9999 0 -0.65 11 11
TRAF6/TAK1/TAB1/TAB2 0.037 0.027 -9999 0 -0.37 2 2
MAP2K6 0.01 0.06 -9999 0 -0.36 12 12
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.007 0.14 -10000 0 -0.38 58 58
MAPK9 0.008 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.022 -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 -0.035 0.14 -10000 0 -0.39 64 64
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 64 -10000 0 64
GNAL -0.061 0.23 -10000 0 -0.66 64 64
GNG2 0.025 0.032 -10000 0 -0.67 1 1
CRH 0 0.039 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.001 0.056 -10000 0 -0.38 10 10
MAPK11 0.006 0.004 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.003 0.065 -10000 0 -0.38 2 2
NT3 (dimer)/TRKC -0.022 0.14 -10000 0 -0.5 37 37
NT3 (dimer)/TRKB 0.005 0.14 -10000 0 -0.44 44 44
SHC/Grb2/SOS1/GAB1/PI3K 0.03 0.028 -10000 0 -0.29 3 3
RAPGEF1 0.025 0.008 -10000 0 -10000 0 0
BDNF 0.009 0.1 -10000 0 -0.67 11 11
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
DYNLT1 0.027 0.004 -10000 0 -10000 0 0
NTRK1 0.01 0.032 -10000 0 -10000 0 0
NTRK2 0.019 0.065 -10000 0 -0.61 5 5
NTRK3 -0.013 0.12 -10000 0 -0.65 13 13
NT-4/5 (dimer)/TRKB 0.013 0.13 -10000 0 -0.45 34 34
neuron apoptosis -0.011 0.11 0.38 19 -10000 0 19
SHC 2-3/Grb2 0.011 0.12 -10000 0 -0.41 19 19
SHC1 0.025 0.008 -10000 0 -10000 0 0
SHC2 0.002 0.1 -10000 0 -0.46 15 15
SHC3 -0.005 0.12 -10000 0 -0.42 28 28
STAT3 (dimer) 0.03 0.015 -10000 0 -10000 0 0
NT3 (dimer)/TRKA 0.003 0.14 -10000 0 -0.44 39 39
RIN/GDP -0.005 0.078 0.3 7 -0.27 3 10
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 0.018 -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) 0.002 0.12 -10000 0 -0.65 15 15
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 -0.41 8 8
TRKA/NEDD4-2 0.031 0.025 -10000 0 -10000 0 0
ELMO1 -0.24 0.34 -10000 0 -0.67 190 190
RhoG/GTP/ELMO1/DOCK1 -0.15 0.24 -10000 0 -0.44 190 190
NGF 0.022 0.056 -10000 0 -0.67 3 3
HRAS 0.026 0.011 -10000 0 -10000 0 0
DOCK1 0.023 0.054 -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 0.026 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
DNM1 0.005 0.12 -10000 0 -0.62 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 -0.35 189 189
mol:GDP -0.014 0.1 0.35 8 -0.36 7 15
NGF (dimer) 0.022 0.056 -10000 0 -0.67 3 3
RhoG/GDP -0.18 0.26 -10000 0 -0.51 190 190
RIT1/GDP -0.003 0.076 0.3 7 -0.26 4 11
TIAM1 -0.059 0.081 -10000 0 -0.67 1 1
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB 0.036 0.087 -10000 0 -0.45 15 15
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 0.061 0.026 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.006 -10000 0 -10000 0 0
NT3 (dimer) -0.016 0.15 -10000 0 -0.67 25 25
RAP1/GDP -0.005 0.057 -10000 0 -0.22 4 4
KIDINS220/CRKL 0.02 0.012 -10000 0 -10000 0 0
BDNF (dimer) 0.009 0.1 -10000 0 -0.67 11 11
ubiquitin-dependent protein catabolic process 0.045 0.043 -10000 0 -0.44 3 3
Schwann cell development -0.031 0.028 -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 -0.28 1 1
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.008 0.12 -10000 0 -0.35 46 46
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 -0.008 0.1 -10000 0 -0.49 7 7
STAT3 0.03 0.015 -10000 0 -10000 0 0
axon guidance -0.016 0.11 -10000 0 -0.34 46 46
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 0.078 0.3 7 -0.26 4 11
NTF3 -0.016 0.16 -10000 0 -0.67 25 25
NTF4 0.002 0.12 -10000 0 -0.65 15 15
NGF (dimer)/TRKA/FAIM 0.046 0.043 -10000 0 -0.44 3 3
PI3K 0.036 0.043 -10000 0 -0.51 3 3
FRS3 0.027 0.003 -10000 0 -10000 0 0
FAIM 0.027 0.003 -10000 0 -10000 0 0
GAB1 0.027 0.004 -10000 0 -10000 0 0
RASGRF1 -0.043 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 -0.44 36 36
RGS19 0.026 0.009 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.07 -10000 0 -0.59 1 1
Rac1/GDP -0.005 0.067 0.22 1 -0.25 3 4
NGF (dimer)/TRKA/GRIT 0.026 0.043 -10000 0 -0.44 3 3
neuron projection morphogenesis 0.024 0.088 -10000 0 -0.7 2 2
NGF (dimer)/TRKA/NEDD4-2 0.046 0.043 -10000 0 -0.44 3 3
MAP2K1 0.04 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 0.07 -10000 0 -0.34 15 15
RAS family/GTP/PI3K 0.027 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 0.003 -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 0.027 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.03 0.025 -10000 0 -10000 0 0
SQSTM1 0.026 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.047 0.083 -10000 0 -0.41 14 14
NGF (dimer)/TRKA/p62/Atypical PKCs 0.068 0.046 -10000 0 -0.38 3 3
MATK 0.015 0.069 -10000 0 -0.61 5 5
NEDD4L 0.027 0.004 -10000 0 -10000 0 0
RAS family/GDP -0.02 0.042 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.003 0.077 -10000 0 -0.39 16 16
Rac1/GTP -0.11 0.12 -10000 0 -0.27 136 136
FRS2 family/SHP2/CRK family 0.057 0.043 -10000 0 -0.38 1 1
Caspase cascade in apoptosis

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
TOP1 0.021 0.088 0.32 5 -0.42 12 17
ACTA1 0.008 0.1 0.34 6 -0.48 12 18
NUMA1 0.016 0.097 0.28 6 -0.48 13 19
SPTAN1 0.006 0.1 0.35 6 -0.47 12 18
LIMK1 0.012 0.11 0.45 8 -0.51 10 18
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 -0.011 0.089 -10000 0 -0.54 12 12
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.026 0.007 -10000 0 -10000 0 0
PTK2 0.014 0.099 0.39 2 -0.43 17 19
DIABLO 0.027 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes 0.006 0.1 0.35 6 -0.46 12 18
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
GSN 0.006 0.1 0.37 5 -0.48 12 17
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.042 0.22 -10000 0 -0.61 62 62
BID -0.012 0.061 -10000 0 -0.31 13 13
MAP3K1 0.018 0.042 0.27 3 -0.21 2 5
TRADD 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.038 0.026 -10000 0 -0.51 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.009 0.11 0.45 8 -0.51 10 18
CASP9 0.027 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 0.016 0.11 0.35 4 -0.51 13 17
APAF1 0.025 0.032 -10000 0 -0.67 1 1
CASP6 0.02 0.086 0.39 1 -0.59 4 5
TRAF2 0.025 0.009 -10000 0 -10000 0 0
ICAD/CAD 0.012 0.11 0.4 14 -0.5 10 24
CASP7 0.007 0.097 0.31 22 -0.52 6 28
KRT18 0.021 0.04 -10000 0 -0.44 2 2
apoptosis 0.016 0.1 0.48 4 -0.45 12 16
DFFA 0.008 0.1 0.36 6 -0.49 11 17
DFFB 0.009 0.1 0.36 6 -0.48 12 18
PARP1 0.017 0.064 0.21 19 -0.51 3 22
actin filament polymerization -0.017 0.12 0.47 10 -0.54 11 21
TNF -0.056 0.22 -10000 0 -0.67 56 56
CYCS -0.001 0.048 0.24 3 -0.21 14 17
SATB1 0.02 0.085 0.52 2 -0.55 4 6
SLK 0.004 0.1 0.41 4 -0.47 14 18
p15 BID/BAX -0.011 0.07 -10000 0 -0.29 12 12
CASP2 -0.014 0.1 0.21 3 -0.37 18 21
JNK cascade -0.018 0.041 0.21 2 -0.27 3 5
CASP3 0.005 0.11 0.36 5 -0.49 13 18
LMNB2 0.006 0.11 0.36 9 -0.41 12 21
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.046 0.094 -10000 0 -0.4 19 19
negative regulation of DNA binding -0.041 0.22 -10000 0 -0.6 62 62
stress fiber formation 0.004 0.1 0.41 4 -0.46 14 18
GZMB -0.007 0.1 -10000 0 -0.61 12 12
CASP1 0.015 0.026 -10000 0 -0.39 2 2
LMNB1 0.02 0.087 0.33 11 -0.3 3 14
APP 0.009 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 0.017 0.095 0.45 3 -0.46 10 13
LMNA 0.015 0.097 0.35 11 -0.42 5 16
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.013 0.11 -10000 0 -0.4 16 16
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.014 0.11 0.43 9 -0.53 9 18
APAF-1/Caspase 9 0.013 0.063 -10000 0 -0.55 4 4
nuclear fragmentation during apoptosis 0.016 0.096 0.28 6 -0.47 13 19
CFL2 0.017 0.12 0.54 11 -0.49 10 21
GAS2 0.002 0.1 0.39 3 -0.47 14 17
positive regulation of apoptosis 0.016 0.1 0.36 9 -0.38 7 16
PRF1 0.015 0.089 -10000 0 -0.68 8 8
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.091 -10000 0 -0.61 10 10
ANTXR2 0.023 0.054 -10000 0 -0.67 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.082 13 13
monocyte activation -0.035 0.16 -10000 0 -0.44 62 62
MAP2K2 -0.008 0.11 -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 0.11 1 -0.39 10 11
CYAA -0.007 0.057 -10000 0 -0.35 13 13
MAP2K4 -0.001 0.012 0.11 1 -10000 0 1
IL1B -0.021 0.094 0.18 1 -0.35 34 35
Channel 0.024 0.066 -10000 0 -0.37 13 13
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 0.028 -10000 0 -0.51 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.082 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 -0.012 0.055 -10000 0 -0.32 13 13
PA/Cellular Receptors 0.025 0.072 -10000 0 -0.4 13 13
apoptosis -0.002 0.013 -10000 0 -0.082 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.024 0.062 -10000 0 -0.35 13 13
macrophage activation -0.001 0.011 -10000 0 -10000 0 0
TNF -0.056 0.22 -10000 0 -0.67 56 56
VCAM1 -0.036 0.16 -10000 0 -0.44 62 62
platelet activation 0.011 0.028 -10000 0 -0.51 1 1
MAPKKK cascade -0.003 0.029 0.11 10 -0.13 8 18
IL18 -0.009 0.06 -10000 0 -0.33 13 13
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.082 13 13
LEF -0.002 0.013 -10000 0 -0.082 13 13
CASP1 0.001 0.018 -10000 0 -0.097 14 14
mol:cAMP 0.011 0.029 -10000 0 -0.52 1 1
necrosis -0.002 0.013 -10000 0 -0.082 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.024 0.063 -10000 0 -0.35 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.006 0.14 -10000 0 -0.69 11 11
HDAC1 0.024 0.008 -10000 0 -10000 0 0
AES 0.025 0.008 -10000 0 -10000 0 0
FBXW11 0.027 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 -0.68 3 3
AP1 -0.13 0.24 -10000 0 -0.48 140 140
NCSTN 0.026 0.007 -10000 0 -10000 0 0
ADAM10 0.012 0.1 -10000 0 -0.67 11 11
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.029 0.075 -10000 0 -0.55 4 4
NICD/RBPSUH 0.006 0.13 -10000 0 -0.64 11 11
WIF1 -0.015 0.047 -10000 0 -10000 0 0
NOTCH1 -0.003 0.13 -10000 0 -0.69 10 10
PSENEN 0.026 0.007 -10000 0 -10000 0 0
KREMEN2 0.016 0.037 -10000 0 -10000 0 0
DKK1 -0.001 0.07 -10000 0 -0.67 2 2
beta catenin/beta TrCP1 0.046 0.048 0.29 2 -10000 0 2
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.026 0.007 -10000 0 -10000 0 0
AXIN1 -0.006 0.082 0.38 1 -0.41 10 11
CtBP/CBP/TCF1/TLE1/AES 0.019 0.031 -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 0.29 -10000 0 -0.67 107 107
MAP3K7 0.026 0.004 -10000 0 -10000 0 0
CTNNB1 0.038 0.063 0.31 11 -10000 0 11
MAPK3 0.026 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.034 0.096 -10000 0 -0.45 18 18
HNF1A 0.026 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC -0.017 0.25 -10000 0 -1.2 19 19
NKD1 0.007 0.11 -10000 0 -0.68 13 13
FZD1 0.026 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.006 0.14 -10000 0 -0.64 13 13
apoptosis -0.13 0.24 -10000 0 -0.48 140 140
Delta 1/NOTCHprecursor 0.006 0.14 -10000 0 -0.67 11 11
DLL1 0.025 0.032 -10000 0 -0.67 1 1
PPARD 0.022 0.081 -10000 0 -0.84 4 4
Gamma Secretase 0.07 0.03 -10000 0 -10000 0 0
APC 0 0.074 0.38 1 -0.68 2 3
DVL1 0.025 0.01 -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 0.049 0.044 -10000 0 -0.47 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
NLK 0.014 0.007 -10000 0 -10000 0 0
CCND1 0.01 0.13 -10000 0 -0.85 10 10
WNT1 0.018 0.022 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.045 0.095 0.44 11 -0.61 1 12
DKK2 -0.004 0.14 -10000 0 -0.66 20 20
NOTCH1 precursor/DVL1 0.013 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 0.006 0.14 -10000 0 -0.66 13 13
PPP2R5D 0.027 0.062 0.33 13 -0.38 3 16
MAPK1 0.02 0.012 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.064 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
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.002 0.1 -10000 0 -0.72 5 5
UGCG -0.059 0.22 -10000 0 -0.64 58 58
AKT1/mTOR/p70S6K/Hsp90/TERT 0.013 0.14 0.42 5 -0.41 22 27
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.059 0.22 -10000 0 -0.62 60 60
mol:DAG -0.009 0.12 -10000 0 -0.77 12 12
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.17 -10000 0 -0.46 40 40
FRAP1 -0.017 0.2 0.44 2 -0.51 49 51
FOXO3 -0.003 0.17 0.44 2 -0.62 21 23
AKT1 -0.008 0.18 -10000 0 -0.67 22 22
GAB2 0.027 0.006 -10000 0 -10000 0 0
SMPD1 0.01 0.085 -10000 0 -0.77 5 5
SGMS1 0.002 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 -0.45 3 3
CALM1 0.027 0.005 -10000 0 -10000 0 0
cell proliferation -0.03 0.19 0.33 5 -0.52 42 47
EIF3A 0.027 0.004 -10000 0 -10000 0 0
PI3K 0.039 0.044 -10000 0 -0.52 3 3
RPS6KB1 0.016 0.067 -10000 0 -0.82 2 2
mol:sphingomyelin -0.009 0.12 -10000 0 -0.77 12 12
natural killer cell activation 0 0.002 -10000 0 -0.012 4 4
JAK3 -0.01 0.066 -10000 0 -10000 0 0
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.029 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC -0.006 0.21 0.47 4 -0.95 17 21
MYB 0.002 0.19 -10000 0 -1.2 11 11
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.005 0.15 -10000 0 -0.56 22 22
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.043 0.067 -10000 0 -0.74 2 2
mol:PI-3-4-5-P3 -0.004 0.14 -10000 0 -0.54 22 22
Rac1/GDP 0.023 0.036 -10000 0 -0.41 3 3
T cell proliferation -0.004 0.13 -10000 0 -0.52 20 20
SHC1 0.026 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 11 11
PRKCZ -0.005 0.14 -10000 0 -0.54 20 20
NF kappa B1 p50/RelA 0.01 0.17 -10000 0 -0.5 28 28
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0 0.11 -10000 0 -0.62 10 10
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
IL2RA -0.017 0.16 -10000 0 -0.64 28 28
IL2RB 0.005 0.09 -10000 0 -0.58 10 10
TERT -0.006 0.023 -10000 0 -10000 0 0
E2F1 0.022 0.07 -10000 0 -0.43 11 11
SOS1 0.027 0.005 -10000 0 -10000 0 0
RPS6 0.025 0.008 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.031 11 -10000 0 11
PTPN11 0.025 0.032 -10000 0 -0.68 1 1
IL2RG -0.01 0.14 -10000 0 -0.63 21 21
actin cytoskeleton organization -0.004 0.13 -10000 0 -0.52 20 20
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL2 0.018 0.013 -10000 0 -10000 0 0
PIK3CA 0.025 0.055 -10000 0 -0.68 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 -0.042 0.27 0.47 4 -0.79 51 55
FOXM1 transcription factor network

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
NFATC3 -0.017 0.31 0.78 2 -0.94 11 13
PLK1 0.029 0.095 -10000 0 -0.82 5 5
BIRC5 0.025 0.1 -10000 0 -0.93 4 4
HSPA1B -0.023 0.31 -10000 0 -0.94 11 11
MAP2K1 0.025 0.045 -10000 0 -10000 0 0
BRCA2 -0.025 0.32 0.79 1 -1 14 15
FOXM1 -0.048 0.34 -10000 0 -1.1 13 13
XRCC1 -0.014 0.31 -10000 0 -0.91 12 12
FOXM1B/p19 -0.047 0.33 -10000 0 -0.94 20 20
Cyclin D1/CDK4 0 0.29 -10000 0 -0.85 9 9
CDC2 -0.026 0.32 -10000 0 -0.9 17 17
TGFA -0.014 0.29 -10000 0 -0.84 10 10
SKP2 -0.019 0.32 0.78 2 -0.99 14 16
CCNE1 0.027 0.01 -10000 0 -10000 0 0
CKS1B -0.023 0.31 -10000 0 -0.85 18 18
RB1 0.026 0.19 -10000 0 -0.72 7 7
FOXM1C/SP1 -0.029 0.33 -10000 0 -1 14 14
AURKB 0.008 0.13 -10000 0 -0.8 10 10
CENPF -0.012 0.31 0.78 1 -0.94 10 11
CDK4 0.027 0.019 -10000 0 -10000 0 0
MYC -0.029 0.31 -10000 0 -0.94 16 16
CHEK2 0.02 0.04 -10000 0 -10000 0 0
ONECUT1 -0.012 0.3 -10000 0 -0.9 11 11
CDKN2A -0.033 0.073 -10000 0 -10000 0 0
LAMA4 -0.023 0.31 -10000 0 -0.94 11 11
FOXM1B/HNF6 -0.019 0.32 -10000 0 -1 11 11
FOS -0.22 0.59 0.78 2 -1.2 128 130
SP1 0.027 0.009 -10000 0 -10000 0 0
CDC25B -0.018 0.31 0.79 1 -0.93 11 12
response to radiation 0.006 0.026 -10000 0 -10000 0 0
CENPB -0.018 0.31 0.79 1 -0.94 10 11
CENPA -0.032 0.32 -10000 0 -0.97 15 15
NEK2 -0.012 0.31 0.78 1 -0.94 10 11
HIST1H2BA -0.029 0.31 -10000 0 -0.94 11 11
CCNA2 0.026 0.022 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
CCNB1/CDK1 -0.034 0.33 -10000 0 -1 12 12
CCNB2 -0.025 0.31 -10000 0 -0.95 10 10
CCNB1 -0.024 0.32 -10000 0 -0.97 12 12
ETV5 -0.023 0.31 -10000 0 -0.94 11 11
ESR1 -0.059 0.38 -10000 0 -1.1 28 28
CCND1 -0.006 0.29 -10000 0 -0.88 9 9
GSK3A 0.022 0.038 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.051 0.043 -10000 0 -10000 0 0
CDK2 0.028 0.008 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.009 0.032 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.036 0.31 -10000 0 -0.98 12 12
GAS1 -0.17 0.55 0.79 1 -1.2 99 100
MMP2 -0.024 0.34 0.78 2 -1.2 12 14
RB1/FOXM1C -0.006 0.29 -10000 0 -0.91 10 10
CREBBP 0.026 0.006 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.027 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.027 0.12 -9999 0 -0.34 36 36
Syndecan-3/Neurocan 0.004 0.095 -9999 0 -0.36 29 29
POMC -0.11 0.28 -9999 0 -0.66 101 101
EGFR 0.019 0.07 -9999 0 -0.67 5 5
Syndecan-3/EGFR 0.027 0.044 -9999 0 -0.33 6 6
AGRP 0.003 0.035 -9999 0 -10000 0 0
NCSTN 0.026 0.007 -9999 0 -10000 0 0
PSENEN 0.026 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 0.026 0.007 -9999 0 -10000 0 0
NCAN -0.026 0.17 -9999 0 -0.66 34 34
long-term memory 0.051 0.029 -9999 0 -10000 0 0
Syndecan-3/IL8 0.029 0.066 -9999 0 -0.36 11 11
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 0.028 -9999 0 -10000 0 0
SRC 0.027 0.008 -9999 0 -10000 0 0
PTN -0.038 0.2 -9999 0 -0.67 45 45
FGFR/FGF/Syndecan-3 0.015 0.006 -9999 0 -10000 0 0
neuron projection morphogenesis -0.023 0.13 -9999 0 -0.41 5 5
Syndecan-3/AgRP 0.031 0.023 -9999 0 -0.31 1 1
Syndecan-3/AgRP/MC4R 0.045 0.03 -9999 0 -10000 0 0
Fyn/Cortactin 0.039 0.008 -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 0.029 0.065 -9999 0 -0.36 11 11
IL8 -0.026 0.12 -9999 0 -0.67 11 11
Syndecan-3/Fyn/Cortactin 0.052 0.03 -9999 0 -10000 0 0
Syndecan-3/CASK 0.011 0.023 -9999 0 -0.3 1 1
alpha-MSH/MC4R -0.077 0.22 -9999 0 -0.5 101 101
Gamma Secretase 0.07 0.03 -9999 0 -10000 0 0
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.027 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.009 -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 -0.44 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 -0.038 0.2 -10000 0 -0.65 46 46
CNG Channel 0.036 0.061 -10000 0 -0.38 8 8
mol:Na + 0.028 0.072 -10000 0 -0.39 10 10
mol:ADP -0.038 0.2 -10000 0 -0.65 46 46
RGS9-1/Gbeta5/R9AP -0.022 0.18 -10000 0 -0.45 71 71
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.041 0.075 -10000 0 -0.4 10 10
CNGB1 0.016 0.034 -10000 0 -10000 0 0
RDH5 -0.073 0.074 -10000 0 -10000 0 0
SAG -0.009 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.1 0.48 12 -0.38 10 22
Na + (4 Units) 0.021 0.067 -10000 0 -0.37 10 10
RGS9 -0.039 0.2 -10000 0 -0.67 45 45
GNB1/GNGT1 0.029 0.014 -10000 0 -10000 0 0
GNAT1/GDP -0.01 0.16 -10000 0 -0.39 70 70
GUCY2D 0.013 0.077 -10000 0 -0.62 6 6
GNGT1 -0.015 0.014 -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) 0.014 0.044 -10000 0 -0.38 3 3
mol:11-cis-retinal -0.072 0.074 -10000 0 -10000 0 0
mol:cGMP 0.032 0.057 -10000 0 -0.4 6 6
GNB1 0.026 0.006 -10000 0 -10000 0 0
Rhodopsin -0.043 0.057 -10000 0 -10000 0 0
SLC24A1 0.027 0.004 -10000 0 -10000 0 0
CNGA1 0.017 0.078 -10000 0 -0.67 6 6
Metarhodopsin II -0.009 0.12 -10000 0 -0.39 46 46
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.045 0.065 -10000 0 -0.41 8 8
RGS9BP -0.015 0.16 -10000 0 -0.66 29 29
Metarhodopsin II/Transducin 0.013 0.007 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.038 0.038 -10000 0 -0.41 3 3
PDE6A/B 0.031 0.029 -10000 0 -10000 0 0
mol:Pi -0.022 0.18 -10000 0 -0.45 71 71
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.038 0.016 -10000 0 -10000 0 0
PDE6B 0.027 0.004 -10000 0 -10000 0 0
PDE6A 0.012 0.037 -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 0.17 -10000 0 -0.39 71 71
GUCA1A 0.005 0.025 -10000 0 -10000 0 0
GC2/GCAP Family 0.045 0.038 -10000 0 -0.36 3 3
GUCA1C -0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.023 0.055 -10000 0 -0.67 3 3
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.002 0.086 -10000 0 -0.37 2 2
epithelial cell differentiation -0.004 0.098 -10000 0 -0.41 7 7
ITCH 0.037 0.019 -10000 0 -10000 0 0
WWP1 -0.009 0.07 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.67 5 5
PRL -0.012 0.015 -10000 0 -10000 0 0
neuron projection morphogenesis -0.018 0.11 0.34 3 -0.48 5 8
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 -0.51 6 6
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.037 0.13 -10000 0 -0.42 43 43
ADAM17 0.034 0.049 -10000 0 -0.67 2 2
ErbB4/ErbB4 -0.015 0.088 -10000 0 -0.46 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.029 0.14 -10000 0 -0.45 33 33
NCOR1 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.025 0.13 -10000 0 -0.4 41 41
GRIN2B -0.034 0.12 -10000 0 -0.4 28 28
ErbB4/ErbB2/betacellulin 0 0.11 -10000 0 -0.5 14 14
STAT1 0.023 0.023 -10000 0 -10000 0 0
HBEGF 0.018 0.035 -10000 0 -10000 0 0
PRLR -0.015 0.15 -10000 0 -0.67 25 25
E4ICDs/ETO2 -0.002 0.086 -10000 0 -0.48 2 2
axon guidance -0.006 0.071 -10000 0 -0.47 1 1
NEDD4 0.034 0.048 -10000 0 -0.66 2 2
Prolactin receptor/Prolactin receptor/Prolactin 0.001 0.12 -10000 0 -0.51 25 25
CBFA2T3 0.024 0.034 -10000 0 -0.67 1 1
ErbB4/ErbB2/HBEGF 0.011 0.073 -10000 0 -0.45 2 2
MAPK3 -0.013 0.12 -10000 0 -0.48 6 6
STAT1 (dimer) -0.001 0.086 -10000 0 -0.41 1 1
MAPK1 -0.016 0.11 -10000 0 -0.5 5 5
JAK2 0.024 0.025 -10000 0 -0.36 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.03 0.12 -10000 0 -0.4 38 38
NRG1 -0.025 0.15 -10000 0 -0.52 43 43
NRG3 -0.021 0.17 -10000 0 -0.65 35 35
NRG2 -0.052 0.22 -10000 0 -0.67 54 54
NRG4 0.021 0.021 -10000 0 -10000 0 0
heart development -0.006 0.071 -10000 0 -0.47 1 1
neural crest cell migration -0.03 0.12 -10000 0 -0.39 38 38
ERBB2 0.02 0.035 -10000 0 -0.5 2 2
WWOX/E4ICDs -0.003 0.089 -10000 0 -0.78 1 1
SHC1 0.025 0.008 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.009 0.097 -10000 0 -0.49 5 5
apoptosis 0.022 0.13 0.4 35 -10000 0 35
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.049 0.16 -10000 0 -0.44 55 55
ErbB4/ErbB2/epiregulin 0.01 0.085 -10000 0 -0.42 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.015 0.12 -10000 0 -0.52 16 16
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.005 0.12 -10000 0 -0.45 6 6
MDM2 -0.013 0.078 -10000 0 -0.41 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.021 0.13 -10000 0 -0.4 41 41
STAT5A -0.001 0.072 -10000 0 -0.45 1 1
ErbB4/EGFR/neuregulin 1 beta -0.027 0.14 -10000 0 -0.41 44 44
DLG4 0.026 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.035 0.014 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.002 0.076 -10000 0 -0.38 1 1
STAT5A (dimer) 0.005 0.11 -10000 0 -0.46 4 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.073 -10000 0 -0.45 1 1
LRIG1 0.017 0.084 -10000 0 -0.64 8 8
EREG -0.052 0.072 -10000 0 -10000 0 0
BTC 0.004 0.12 -10000 0 -0.67 16 16
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.006 0.07 -10000 0 -0.48 1 1
ERBB4 -0.014 0.088 -10000 0 -0.46 1 1
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 0.01 0.072 -10000 0 -0.43 2 2
glial cell differentiation 0.002 0.076 0.38 1 -10000 0 1
WWOX 0.025 0.032 -10000 0 -0.67 1 1
cell proliferation -0.024 0.14 -10000 0 -0.57 9 9
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.012 0.12 -10000 0 -0.47 27 27
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 0.096 -10000 0 -0.38 21 21
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.02 0.012 -10000 0 -10000 0 0
M/R/N Complex 0.051 0.034 -10000 0 -0.44 2 2
MRE11A 0.024 0.045 -10000 0 -0.67 2 2
DNA-PK 0.04 0.026 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.008 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 0.026 0.007 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.011 0.12 -10000 0 -0.46 27 27
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 0.031 -10000 0 -10000 0 0
DNA repair 0.018 0.09 0.41 2 -0.47 5 7
BRCA1/BARD1/ubiquitin 0.011 0.12 -10000 0 -0.46 27 27
BARD1/DNA-PK 0.028 0.1 -10000 0 -0.4 23 23
FANCL 0.027 0.005 -10000 0 -10000 0 0
mRNA polyadenylation -0.012 0.12 0.47 27 -10000 0 27
BRCA1/BARD1/CTIP/M/R/N Complex 0.014 0.075 -10000 0 -0.29 23 23
BRCA1/BACH1/BARD1/TopBP1 0.028 0.1 -10000 0 -0.42 24 24
BRCA1/BARD1/P53 0.042 0.1 -10000 0 -0.4 22 22
BARD1/CSTF1/BRCA1 0.028 0.1 -10000 0 -0.42 23 23
BRCA1/BACH1 0.026 0.007 -10000 0 -10000 0 0
BARD1 -0.01 0.15 -10000 0 -0.63 28 28
PCNA 0.027 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.028 0.1 -10000 0 -0.42 24 24
BRCA1/BARD1/UbcH7 0.017 0.1 -10000 0 -0.41 24 24
BRCA1/BARD1/RAD51/PCNA 0.043 0.1 -10000 0 -0.41 21 21
BARD1/DNA-PK/P53 0.037 0.098 -10000 0 -0.38 21 21
BRCA1/BARD1/Ubiquitin 0.011 0.12 -10000 0 -0.46 27 27
BRCA1/BARD1/CTIP 0.023 0.096 -10000 0 -0.4 22 22
FA complex 0.028 0.033 -10000 0 -10000 0 0
BARD1/EWS 0.002 0.12 -10000 0 -0.46 28 28
RBBP8 0.016 0.024 -10000 0 -0.51 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
TOPBP1 0.027 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.04 0.099 0.4 22 -10000 0 22
BRCA1/BARD1 0.05 0.099 -10000 0 -0.38 21 21
CSTF1 0.027 0.005 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.008 0.12 -10000 0 -0.47 28 28
CDK2 0.027 0.005 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.026 0.011 -10000 0 -10000 0 0
RAD50 0.027 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.011 0.12 -10000 0 -0.46 27 27
EWSR1 0.02 0.012 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.038 0.06 -10000 0 -0.4 6 6
EPHB2 0.022 0.055 -10000 0 -0.67 3 3
Syndecan-2/TACI -0.089 0.2 -10000 0 -0.44 121 121
LAMA1 -0.021 0.18 -10000 0 -0.66 34 34
Syndecan-2/alpha2 ITGB1 0.042 0.092 -10000 0 -0.38 19 19
HRAS 0.026 0.011 -10000 0 -10000 0 0
Syndecan-2/CASK 0.007 0.043 -10000 0 -0.33 7 7
ITGA5 0.027 0.005 -10000 0 -10000 0 0
BAX 0.003 0.065 -10000 0 -0.46 1 1
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 -0.48 9 9
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 -0.008 0.059 -10000 0 -10000 0 0
dendrite morphogenesis 0.023 0.057 -10000 0 -0.38 9 9
Syndecan-2/GM-CSF -0.035 0.057 -10000 0 -0.45 4 4
determination of left/right symmetry 0.01 0.05 -10000 0 -0.39 7 7
Syndecan-2/PKC delta 0.026 0.045 -10000 0 -0.33 7 7
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.032 0.049 -10000 0 -0.41 4 4
MAPK1 -0.026 0.048 -10000 0 -0.41 4 4
Syndecan-2/RACK1 0.038 0.041 -10000 0 -0.38 4 4
NF1 0.026 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.01 0.05 -10000 0 -0.39 7 7
ITGA2 -0.034 0.075 -10000 0 -10000 0 0
MAPK8 0.004 0.074 -10000 0 -0.42 14 14
Syndecan-2/alpha2/beta1 Integrin 0.032 0.12 -10000 0 -0.42 32 32
Syndecan-2/Kininogen 0.016 0.05 -10000 0 -0.44 4 4
ITGB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.022 0.045 0.35 1 -0.36 4 5
Syndecan-2/CASK/Protein 4.1 0.023 0.041 -10000 0 -0.35 5 5
extracellular matrix organization 0.024 0.044 -10000 0 -0.43 4 4
actin cytoskeleton reorganization -0.038 0.06 -10000 0 -0.4 6 6
Syndecan-2/Caveolin-2/Ras 0.039 0.05 -10000 0 -0.39 6 6
Syndecan-2/Laminin alpha3 0.009 0.094 -10000 0 -0.42 21 21
Syndecan-2/RasGAP 0.05 0.042 -10000 0 -0.36 4 4
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.003 -10000 0 -10000 0 0
Syndecan-2 dimer 0.023 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 0.003 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
TNFRSF13B -0.16 0.29 -10000 0 -0.67 121 121
RASA1 0.027 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin -0.008 0.059 -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 0.19 5 -0.4 4 9
FN1 -0.085 0.069 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.005 0.087 -10000 0 -0.4 18 18
SDC2 0.01 0.05 -10000 0 -0.39 7 7
KNG1 -0.005 0.038 -10000 0 -10000 0 0
Syndecan-2/Neurofibromin 0.026 0.043 -10000 0 -0.43 4 4
TRAPPC4 0.027 0.005 -10000 0 -10000 0 0
CSF2 -0.082 0.067 -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 -0.4 4 4
Syndecan-2/Ezrin 0.042 0.043 -10000 0 -0.4 4 4
PRKACA 0.017 0.041 -10000 0 -0.4 4 4
angiogenesis -0.005 0.087 -10000 0 -0.39 18 18
MMP2 0.017 0.079 -10000 0 -0.63 7 7
IL8 -0.026 0.12 -10000 0 -0.67 11 11
calcineurin-NFAT signaling pathway -0.089 0.2 -10000 0 -0.44 122 122
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.03 0.071 -10000 0 -0.57 6 6
PDGFRB 0.025 0.032 -10000 0 -0.68 1 1
SPHK1 0.01 0.059 -10000 0 -0.86 2 2
mol:S1P 0.008 0.057 -10000 0 -0.79 2 2
S1P1/S1P/Gi -0.007 0.12 -10000 0 -0.4 39 39
GNAO1 0.002 0.12 -10000 0 -0.68 15 15
PDGFB-D/PDGFRB/PLCgamma1 -0.005 0.12 -10000 0 -0.38 30 30
PLCG1 -0.007 0.12 -10000 0 -0.39 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.032 -10000 0 -0.68 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 0.033 -10000 0 -0.68 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 0.001 0.058 -10000 0 -0.5 6 6
S1P1/S1P 0.004 0.07 -10000 0 -0.45 7 7
negative regulation of cAMP metabolic process -0.006 0.12 -10000 0 -0.39 39 39
MAPK3 -0.019 0.16 -10000 0 -0.56 35 35
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.02 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 -0.68 4 4
PLCB2 0.014 0.077 0.4 5 -0.49 4 9
RAC1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.01 0.06 -10000 0 -0.38 7 7
receptor internalization 0.004 0.065 -10000 0 -0.42 7 7
PTGS2 -0.054 0.29 0.64 3 -0.98 41 44
Rac1/GTP 0.011 0.059 -10000 0 -0.38 7 7
RHOA 0.027 0.003 -10000 0 -10000 0 0
VEGFA 0.023 0.055 -10000 0 -0.67 3 3
negative regulation of T cell proliferation -0.006 0.12 -10000 0 -0.39 39 39
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.019 0.015 -10000 0 -10000 0 0
MAPK1 -0.02 0.17 -10000 0 -0.6 34 34
S1P1/S1P/PDGFB-D/PDGFRB 0.012 0.08 -10000 0 -0.44 8 8
ABCC1 0.026 0.006 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.029 0.009 -10000 0 -10000 0 0
epithelial cell differentiation 0.056 0.016 -10000 0 -10000 0 0
CYFIP2 0.027 0.006 -10000 0 -10000 0 0
ENAH 0.022 0.078 0.46 11 -10000 0 11
EGFR 0.019 0.07 -10000 0 -0.67 5 5
EPHA2 0.026 0.013 -10000 0 -10000 0 0
MYO6 0.031 0.065 0.42 11 -10000 0 11
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.053 0.013 -10000 0 -10000 0 0
AQP5 0.001 0.11 -10000 0 -0.53 19 19
CTNND1 0.027 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.024 0.046 0.38 7 -10000 0 7
regulation of calcium-dependent cell-cell adhesion -0.011 0.054 0.39 5 -10000 0 5
EGF -0.075 0.25 -10000 0 -0.67 72 72
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
AQP3 -0.041 0.17 -10000 0 -0.53 49 49
cortical microtubule organization 0.056 0.016 -10000 0 -10000 0 0
GO:0000145 0.012 0.046 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 0.062 0.025 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.013 0.031 -10000 0 -10000 0 0
PVRL2 0.026 0.007 -10000 0 -10000 0 0
ZYX 0.021 0.021 -10000 0 -10000 0 0
ARF6/GTP 0.068 0.028 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.011 0.14 -10000 0 -0.36 74 74
RhoA/GDP 0.057 0.016 -10000 0 -10000 0 0
actin cytoskeleton organization 0.021 0.05 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 -0.67 108 108
DIAPH1 0.05 0.05 -10000 0 -10000 0 0
Wnt receptor signaling pathway -0.056 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
RhoA/GTP 0.006 0.004 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
VCL 0.021 0.051 0.39 8 -10000 0 8
EFNA1 0.025 0.008 -10000 0 -10000 0 0
LPP 0.011 0.06 0.35 4 -0.36 8 12
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 -0.006 0.15 -10000 0 -0.38 64 64
HGF -0.073 0.24 -10000 0 -0.67 70 70
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.029 0.009 -10000 0 -10000 0 0
actin cable formation 0.068 0.13 0.47 33 -0.33 1 34
KIAA1543 0.013 0.052 0.37 8 -0.35 1 9
KIFC3 0.021 0.023 -10000 0 -10000 0 0
NCK1 0.027 0.003 -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 0.056 0.016 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
STX4 0.022 0.023 -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 0.045 0.1 0.44 22 -10000 0 22
adherens junction assembly 0.027 0.085 0.46 12 -0.56 1 13
IGF-1R heterotetramer/IGF1 -0.036 0.16 -10000 0 -0.36 102 102
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.011 -10000 0 -10000 0 0
MET -0.029 0.074 -10000 0 -10000 0 0
PLEKHA7 0.026 0.052 0.38 8 -0.37 1 9
mol:GTP 0.06 0.024 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.033 0.067 0.48 7 -10000 0 7
cortical actin cytoskeleton stabilization 0.029 0.009 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.021 0.05 0.38 8 -10000 0 8
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.029 0.009 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.025 0.043 -10000 0 -10000 0 0
TP53 -0.009 0.039 -10000 0 -0.18 22 22
Senescence -0.009 0.038 -10000 0 -0.18 22 22
Apoptosis -0.009 0.038 -10000 0 -0.18 22 22
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.011 0.025 0.35 1 -10000 0 1
MDM4 0.025 0.008 -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 0.027 0.006 -10000 0 -10000 0 0
VDR 0.026 0.009 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.026 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 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 0.014 0.083 0.25 14 -0.35 15 29
RAR alpha/9cRA/Cyclin H 0.035 0.097 -10000 0 -0.38 19 19
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.013 0.066 0.25 1 -0.33 10 11
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.011 0.097 -10000 0 -0.36 25 25
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 -0.003 0.13 -10000 0 -0.54 22 22
NCOA2 -0.037 0.2 -10000 0 -0.67 45 45
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 0.009 -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 0.095 -10000 0 -0.64 10 10
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.009 0.12 -10000 0 -0.53 19 19
RARA 0.005 0.075 -10000 0 -0.31 24 24
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.015 0.13 -10000 0 -0.48 25 25
PRKCA 0.004 0.13 -10000 0 -0.67 17 17
RXRs/RARs/NRIP1/9cRA/HDAC1 0.011 0.14 0.4 4 -0.54 23 27
RXRG -0.029 0.079 -10000 0 -0.4 21 21
RXRA 0.007 0.075 -10000 0 -0.3 24 24
RXRB 0.009 0.074 -10000 0 -0.38 17 17
VDR/Vit D3/DNA 0.02 0.006 -10000 0 -10000 0 0
RBP1 0.013 0.094 -10000 0 -0.67 9 9
CRBP1/9-cic-RA 0.01 0.071 -10000 0 -0.51 9 9
RARB 0.009 0.12 -10000 0 -0.67 14 14
PRKCG 0.022 0.014 -10000 0 -10000 0 0
MNAT1 0.027 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.006 0.13 -10000 0 -0.57 22 22
RXRs/RARs/SMRT(N-CoR2)/9cRA 0 0.12 -10000 0 -0.49 21 21
proteasomal ubiquitin-dependent protein catabolic process 0.014 0.09 0.36 3 -0.42 11 14
RXRs/RARs/NRIP1/9cRA/HDAC3 0.012 0.14 0.42 5 -0.54 23 28
positive regulation of DNA binding 0.023 0.088 -10000 0 -0.36 19 19
NRIP1 0.012 0.13 0.5 1 -0.68 6 7
RXRs/RARs 0.005 0.13 -10000 0 -0.54 23 23
RXRs/RXRs/DNA/9cRA -0.011 0.12 -10000 0 -0.55 19 19
PRKACA 0.025 0.008 -10000 0 -10000 0 0
CDK7 0.027 0.005 -10000 0 -10000 0 0
TFIIH 0.054 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.047 0.068 -10000 0 -0.42 3 3
CCNH 0.027 0.005 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.05 0.018 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.027 0.005 -10000 0 -10000 0 0
NFATC1 0.036 0.095 0.46 9 -0.38 9 18
NFATC2 -0.022 0.097 0.28 9 -0.27 31 40
NFATC3 0.018 0.011 -10000 0 -10000 0 0
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.007 0.086 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 0.004 0.098 -10000 0 -0.44 9 9
BCL2/BAX -0.003 0.14 -10000 0 -0.48 38 38
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 0.006 0.091 0.34 3 -0.39 10 13
Calcineurin A alpha-beta B1/BCL2 -0.026 0.18 -10000 0 -0.66 38 38
FKBP8 0.025 0.008 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.006 0.09 0.38 10 -0.34 3 13
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 -0.085 0.13 -10000 0 -0.67 15 15
MAP3K8 0.016 0.079 -10000 0 -0.63 7 7
NFAT4/CK1 alpha 0.019 0.029 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.073 0.17 -10000 0 -0.34 109 109
CABIN1 -0.007 0.084 0.28 1 -0.38 10 11
CALM1 0.024 0.009 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.027 0.005 -10000 0 -10000 0 0
CAMK4 0.013 0.085 -10000 0 -0.67 7 7
mol:Ca2+ -0.004 0.009 -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 0.011 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 -0.41 5 7
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 0.009 0.044 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.054 -10000 0 -0.32 5 5
PRKCB 0.007 0.08 -10000 0 -0.67 5 5
PRKCE 0.02 0.07 -10000 0 -0.67 5 5
JNK2/NFAT4 0.031 0.026 -10000 0 -10000 0 0
BAD/BCL-XL 0.039 0.009 -10000 0 -10000 0 0
PRKCD 0.027 0.003 -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 0.002 0.13 -10000 0 -0.67 17 17
PRKCG 0.005 0.023 -10000 0 -10000 0 0
PRKCQ 0.019 0.072 -10000 0 -0.62 6 6
FKBP38/BCL2 -0.003 0.14 -10000 0 -0.48 38 38
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 0.038 0.1 0.42 7 -0.36 17 24
CaM/Ca2+/FKBP38 0.02 0.026 -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 0.043 0.08 0.44 3 -0.36 9 12
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.008 0.1 -10000 0 -0.45 9 9
NR4A1 -0.17 0.29 -10000 0 -0.61 148 148
GSK3B 0.024 0.007 -10000 0 -10000 0 0
positive T cell selection 0.018 0.011 -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 -0.37 9 19
CREBBP 0.013 0.022 -10000 0 -10000 0 0
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
TCGA08_rtk_signaling

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
PDGFRA -0.18 0.32 -10000 0 -0.67 150 150
HRAS 0.026 0.011 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.67 5 5
AKT 0.015 0.084 0.32 10 -10000 0 10
FOXO3 0.027 0.004 -10000 0 -10000 0 0
AKT1 0.027 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 -0.029 0.074 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PIK3CB 0.027 0.003 -10000 0 -10000 0 0
NRAS 0.027 0.005 -10000 0 -10000 0 0
PIK3CG 0.006 0.12 -10000 0 -0.67 14 14
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 -0.32 5 5
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 0.099 0.39 8 -0.25 13 21
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
KRAS 0.027 0.005 -10000 0 -10000 0 0
FOXO 0.045 0.059 0.31 8 -10000 0 8
AKT2 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.36 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex -0.002 0.099 0.49 5 -10000 0 5
RAD9A 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.19 0.37 -10000 0 -0.72 149 149
IFNAR2 0.028 0.006 -10000 0 -10000 0 0
AKT1 0.007 0.053 -10000 0 -0.24 20 20
ER alpha/Oestrogen -0.009 0.11 -10000 0 -0.48 23 23
NFX1/SIN3/HDAC complex 0.032 0.036 -10000 0 -0.49 1 1
EGF -0.075 0.25 -10000 0 -0.67 72 72
SMG5 0.026 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 -0.003 0.081 0.47 1 -10000 0 1
SAP18 0.026 0.007 -10000 0 -10000 0 0
MRN complex 0.051 0.034 -10000 0 -0.44 2 2
WT1 0.007 0.048 -10000 0 -10000 0 0
WRN 0.026 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 0.041 0.009 -10000 0 -10000 0 0
TERT -0.002 0.1 0.5 5 -10000 0 5
CCND1 0.001 0.1 0.55 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 0.026 0.059 -10000 0 -10000 0 0
CDKN1B -0.029 0.15 -10000 0 -0.42 57 57
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 0.038 0.011 -10000 0 -10000 0 0
UBE3A 0.028 0.004 -10000 0 -10000 0 0
JUN -0.12 0.29 -10000 0 -0.67 107 107
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 -0.023 0.18 -10000 0 -0.48 62 62
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 -0.51 10 11
IRF1 0.03 0.009 -10000 0 -10000 0 0
ESR1 -0.013 0.15 -10000 0 -0.65 23 23
KU/TER 0.029 0.019 -10000 0 -10000 0 0
ATM/TRF2 0.038 0.025 -10000 0 -0.46 1 1
ubiquitin-dependent protein catabolic process 0.038 0.039 -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 0.01 0.023 -10000 0 -0.48 1 1
SMAD3 0.015 0.011 -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 0.017 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 0.02 0.07 -10000 0 -0.67 5 5
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.044 0.2 -10000 0 -0.5 76 76
MYC 0.011 0.1 -10000 0 -0.65 12 12
IL2 0.02 0.009 -10000 0 -10000 0 0
KU 0.029 0.019 -10000 0 -10000 0 0
RAD50 0.027 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 0.038 0.012 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.002 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 0.08 -10000 0 -10000 0 0
Smad3/Myc 0.018 0.069 -10000 0 -0.42 11 11
911 complex 0.052 0.015 -10000 0 -10000 0 0
IFNG -0.062 0.23 -10000 0 -0.67 62 62
Telomerase/PinX1 0.011 0.081 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.014 0.061 0.37 1 -0.42 2 3
SIN3B 0.026 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 0.082 -10000 0 -10000 0 0
E2F1 -0.018 0.071 -10000 0 -10000 0 0
ZNFX1 0.027 0.005 -10000 0 -10000 0 0
PIF1 0.017 0.078 -10000 0 -0.67 6 6
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 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
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 0.02 -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 0.027 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 -0.4 3 3
MAPK1 0.014 0.058 -9999 0 -0.38 3 3
JAK2 0.007 0.067 -9999 0 -0.4 3 3
CXCR4 0.003 0.064 -9999 0 -0.4 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 0.02 0.004 -9999 0 -10000 0 0
SRC 0.003 0.063 -9999 0 -0.34 3 3
S1P/S1P3/Gi 0.006 0.07 -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 17 17
VEGFR1 homodimer/VEGFA homodimer 0.04 0.057 -9999 0 -0.64 3 3
RHOA 0.027 0.003 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.057 0.15 -9999 0 -0.31 122 122
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 -0.14 0.29 -9999 0 -0.64 120 120
GNA15 0.013 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 0.015 0.084 -9999 0 -0.64 8 8
Rac1/GTP 0.01 0.072 -9999 0 -0.38 3 3
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.026 0.007 -9999 0 -10000 0 0
SPHK1 0.022 0.024 -9999 0 -10000 0 0
GNAI2 0.027 0.003 -9999 0 -10000 0 0
mol:S1P 0.017 0.008 -9999 0 -10000 0 0
GNAO1 0.004 0.12 -9999 0 -0.67 15 15
mol:Sphinganine-1-P 0.014 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 0.023 0.02 -9999 0 -10000 0 0
GNAI1 0.025 0.032 -9999 0 -0.67 1 1
S1P/S1P5/G12 0.043 0.031 -9999 0 -0.38 1 1
S1P/S1P3/Gq -0.056 0.16 -9999 0 -0.39 38 38
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 -0.14 0.29 -9999 0 -0.64 120 120
GNA15 0.013 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 0.015 0.084 -9999 0 -0.64 8 8
ABCC1 0.026 0.006 -9999 0 -10000 0 0
Class I PI3K signaling events

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
ARF5/GTP 0.026 0.046 0.29 10 -0.35 1 11
DAPP1 -0.037 0.13 0.33 4 -0.47 12 16
Src family/SYK family/BLNK-LAT/BTK-ITK -0.052 0.17 0.32 2 -0.52 21 23
mol:DAG -0.016 0.095 0.35 11 -0.26 12 23
HRAS 0.027 0.012 -10000 0 -10000 0 0
RAP1A 0.028 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.035 0.064 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 0.003 -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 0.045 0.29 10 -10000 0 10
ARAP3 0 0.047 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 -0.36 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 0.007 -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 0.026 0.015 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.065 0.3 10 -10000 0 10
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.059 0.081 -10000 0 -0.67 1 1
ZAP70 0 0.13 -10000 0 -0.66 17 17
mol:IP3 -0.013 0.069 0.24 11 -0.21 4 15
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 0.039 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 0.4 10 -10000 0 10
SRC 0.027 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 -0.34 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 0.025 0.042 0.3 9 -10000 0 9
Src family/SYK family/BLNK-LAT -0.045 0.14 -10000 0 -0.44 24 24
BLK -0.19 0.31 -10000 0 -0.67 148 148
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
CYTH1 0.002 0.054 0.31 12 -10000 0 12
HCK 0.017 0.039 -10000 0 -10000 0 0
CYTH3 -0.002 0.049 0.29 10 -0.36 1 11
CYTH2 0.003 0.057 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 0.018 0.089 -10000 0 -0.54 10 10
SGK1 0.018 0.098 -10000 0 -0.59 10 10
INPP5D 0.019 0.034 -10000 0 -10000 0 0
mol:GDP 0.026 0.08 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 0.29 8 -10000 0 8
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 0.011 0.061 -10000 0 -0.57 3 3
mol:PI-3-4-P2 0.012 0.021 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.044 0.029 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 -0.6 4 4
Rac1/GTP 0.017 0.059 0.27 1 -0.48 3 4
ITK -0.039 0.12 0.28 9 -0.36 48 57
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.12 0.38 9 -0.36 15 24
LCK 0.012 0.082 -10000 0 -0.67 6 6
BTK -0.005 0.067 0.3 13 -0.36 6 19
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.28 -10000 0 -0.67 97 97
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.014 -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 -0.031 0.074 -10000 0 -10000 0 0
ARNT/IPAS -0.067 0.21 -10000 0 -0.49 97 97
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 0.033 0.038 0.28 1 -10000 0 1
PHD1-3/OS9 0.05 0.073 -10000 0 -0.4 11 11
HIF1A/RACK1/Elongin B/Elongin C 0.055 0.039 -10000 0 -10000 0 0
VHL 0.023 0.054 -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 0.006 0.1 -10000 0 -0.67 10 10
EGLN2 0.026 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 0.075 -10000 0 -0.57 6 6
ARNT 0.026 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 0.037 0.052 0.32 6 -10000 0 6
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.015 0.08 0.63 7 -10000 0 7
PI3K Class IB/PDE3B 0.015 0.08 -10000 0 -0.63 7 7
PDE3B 0.015 0.08 -10000 0 -0.63 7 7
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.027 0.004 -9999 0 -10000 0 0
ITGB7 0.004 0.11 -9999 0 -0.65 12 12
ITGA4 0.02 0.058 -9999 0 -0.67 3 3
alpha4/beta7 Integrin 0.017 0.095 -9999 0 -0.51 14 14
alpha4/beta1 Integrin 0.034 0.046 -9999 0 -0.51 3 3
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 -0.13 3 4
BUB1B 0.014 0.031 0.19 9 -0.15 1 10
PLK1 0.012 0.03 0.16 13 -0.1 1 14
PLK1S1 0.015 0.026 0.18 9 -10000 0 9
KIF2A 0.018 0.067 0.32 20 -0.39 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 0.033 0.036 -10000 0 -10000 0 0
WEE1 0.022 0.046 0.28 6 -0.34 2 8
cytokinesis 0.011 0.062 0.26 9 -0.24 4 13
PP2A-alpha B56 0.048 0.095 -10000 0 -0.55 9 9
AURKA 0.014 0.023 0.17 7 -10000 0 7
PICH/PLK1 0.02 0.015 -10000 0 -10000 0 0
CENPE 0.01 0.051 0.25 11 -0.39 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 0.027 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 0.027 0.005 -10000 0 -10000 0 0
SPC24 0.016 0.037 -10000 0 -10000 0 0
FBXW11 0.027 0.006 -10000 0 -10000 0 0
CLSPN 0.012 0.029 0.13 2 -0.29 3 5
GORASP1 0.027 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.006 0.022 28 -10000 0 28
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.018 0.095 14 -0.05 1 15
G2 phase of mitotic cell cycle 0 0.004 0.018 15 -10000 0 15
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 0.022 0.099 -10000 0 -0.56 13 13
TPT1 0.004 0.045 0.14 5 -0.18 24 29
CDC25C 0.019 0.025 0.18 7 -10000 0 7
CDC25B 0.027 0.011 -10000 0 -10000 0 0
SGOL1 0.006 0.016 0.13 3 -0.12 1 4
RHOA 0.027 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.042 0.015 -10000 0 -10000 0 0
CDC14B 0.003 0.045 -10000 0 -0.38 6 6
CDC20 0.025 0.019 -10000 0 -10000 0 0
PLK1/PBIP1 0.01 0.019 0.12 5 -10000 0 5
mitosis -0.001 0.003 0.02 3 -10000 0 3
FBXO5 0.013 0.037 0.22 8 -0.34 1 9
CDC2 0.002 0.001 0.01 1 -10000 0 1
NDC80 0.009 0.05 -10000 0 -10000 0 0
metaphase plate congression 0.014 0.025 0.14 1 -0.24 3 4
ERCC6L 0.025 0.014 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.011 0.027 0.14 15 -10000 0 15
microtubule cytoskeleton organization 0.004 0.045 0.14 5 -0.18 24 29
G2/M transition DNA damage checkpoint 0 0.004 0.018 17 -10000 0 17
PPP1R12A 0.027 0.005 -10000 0 -10000 0 0
interphase 0 0.004 0.018 17 -10000 0 17
PLK1/PRC1-2 0.038 0.027 -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 0.009 0.027 0.15 13 -10000 0 13
mitotic prometaphase 0 0.004 0.027 7 -10000 0 7
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.026 -10000 0 -10000 0 0
microtubule-based process 0.013 0.031 -10000 0 -10000 0 0
Golgi organization 0.012 0.03 0.16 13 -0.1 1 14
Cohesin/SA2 0.022 0.02 0.18 3 -10000 0 3
PPP1CB/MYPT1 0.04 0.009 -10000 0 -10000 0 0
KIF20A 0.005 0.054 -10000 0 -10000 0 0
APC/C/CDC20 0.025 0.024 0.16 3 -10000 0 3
PPP2R1A 0.026 0.007 -10000 0 -10000 0 0
chromosome segregation 0.01 0.019 0.12 5 -10000 0 5
PRC1 0.027 0.004 -10000 0 -10000 0 0
ECT2 0.01 0.041 0.22 8 -0.4 2 10
C13orf34 0.01 0.026 0.14 13 -0.081 1 14
NUDC 0.014 0.025 0.14 1 -0.24 3 4
regulation of attachment of spindle microtubules to kinetochore 0.014 0.031 0.19 9 -0.14 1 10
spindle assembly 0.014 0.037 0.17 18 -10000 0 18
spindle stabilization 0.015 0.026 0.18 9 -10000 0 9
APC/C/HCDH1 0.019 0.041 -10000 0 -0.35 5 5
MKLP2/PLK1 0.013 0.032 -10000 0 -10000 0 0
CCNB1 0.028 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 -0.41 31 33
TUBG1 0.015 0.028 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 -0.68 2 2
IL2 signaling events mediated by STAT5

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
GAB2 0.027 0.005 -10000 0 -10000 0 0
ELF1 0.004 0.1 -10000 0 -0.39 29 29
CCNA2 0.025 0.02 -10000 0 -10000 0 0
PIK3CA 0.024 0.054 -10000 0 -0.67 3 3
JAK3 -0.012 0.066 -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 0.003 0.13 -10000 0 -0.59 16 16
SHC1 0.026 0.008 -10000 0 -10000 0 0
SP1 0.033 0.006 -10000 0 -10000 0 0
IL2RA -0.033 0.21 -10000 0 -0.87 28 28
IL2RB 0.004 0.09 -10000 0 -0.58 10 10
SOS1 0.027 0.005 -10000 0 -10000 0 0
IL2RG -0.011 0.14 -10000 0 -0.63 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 0.024 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 0.007 0.12 -10000 0 -0.58 10 10
TCGA08_retinoblastoma

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
CDKN2B -0.035 0.077 -10000 0 -10000 0 0
CDKN2C 0.031 0.02 -10000 0 -10000 0 0
CDKN2A -0.032 0.077 -10000 0 -10000 0 0
CCND2 0.011 0.024 -10000 0 -10000 0 0
RB1 -0.016 0.049 0.32 2 -0.24 14 16
CDK4 0.015 0.042 0.26 10 -10000 0 10
CDK6 0.017 0.044 0.26 10 -0.16 1 11
G1/S progression 0.017 0.051 0.24 15 -0.32 2 17
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.029 0.1 -10000 0 -0.46 9 9
CaM/Ca2+ 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
AKT2 0.026 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 0.023 0.1 0.3 10 -0.45 9 19
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 -0.053 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 0.05 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -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 -0.035 0.094 -10000 0 -0.34 17 17
VAMP2 0.026 0.007 -10000 0 -10000 0 0
SLC2A4 0.022 0.11 0.33 6 -0.51 9 15
STX4 0.026 0.006 -10000 0 -10000 0 0
GSK3B 0.024 0.008 -10000 0 -10000 0 0
SFN -0.085 0.13 -10000 0 -0.67 15 15
LNPEP 0.004 0.12 -10000 0 -0.67 16 16
YWHAE 0.026 0.007 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.025 0.089 -10000 0 -0.52 12 12
AKT1 0.04 0.09 0.39 2 -0.61 6 8
PTK2B 0.017 0.11 0.35 1 -0.8 5 6
VEGFR2 homodimer/Frs2 0.032 0.083 -10000 0 -0.88 4 4
CAV1 0.014 0.094 -10000 0 -0.67 9 9
CALM1 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.047 0.094 -10000 0 -0.74 6 6
endothelial cell proliferation 0.054 0.14 0.59 18 -0.64 4 22
mol:Ca2+ 0.023 0.09 -10000 0 -0.64 7 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.061 0.092 -10000 0 -0.77 5 5
RP11-342D11.1 0.012 0.089 -10000 0 -0.64 7 7
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 0.008 -10000 0 -10000 0 0
SHC2 0.021 0.055 -10000 0 -0.67 3 3
HRAS/GDP 0.04 0.079 -10000 0 -0.64 5 5
SH2D2A -0.008 0.14 -10000 0 -0.67 21 21
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.058 0.095 -10000 0 -0.65 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.025 0.13 -10000 0 -0.47 27 27
VEGFR1 homodimer 0.024 0.032 -10000 0 -0.67 1 1
SHC/GRB2/SOS1 0.066 0.095 -10000 0 -0.81 4 4
GRB10 0.024 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 0.07 0.092 -10000 0 -0.84 4 4
HRAS 0.026 0.011 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.028 0.065 -10000 0 -0.41 6 6
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 0.059 0.089 -10000 0 -0.75 5 5
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 0.048 0.094 -10000 0 -0.74 6 6
mol:GDP 0.052 0.086 -10000 0 -0.76 4 4
mol:NADP 0.041 0.097 0.46 7 -0.48 6 13
eNOS/Hsp90 0.044 0.079 -10000 0 -0.5 4 4
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
mol:IP3 0.023 0.093 -10000 0 -0.66 7 7
HIF1A/ARNT 0.037 0.012 -10000 0 -10000 0 0
SHB 0.026 0.007 -10000 0 -10000 0 0
VEGFA 0.025 0.054 -10000 0 -0.67 3 3
VEGFC 0.026 0.032 -10000 0 -0.67 1 1
FAK1/Vinculin 0.041 0.1 -10000 0 -0.74 5 5
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.049 0.12 -10000 0 -0.52 16 16
PTPN6 0.027 0.005 -10000 0 -10000 0 0
EPAS1 0.031 0.056 -10000 0 -0.53 4 4
mol:L-citrulline 0.041 0.097 0.46 7 -0.48 6 13
ITGAV 0.024 0.045 -10000 0 -0.67 2 2
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.059 0.092 -10000 0 -0.77 5 5
VEGFR2 homodimer/VEGFA homodimer 0.05 0.11 -10000 0 -0.73 7 7
VEGFR2/3 heterodimer 0.027 0.11 -10000 0 -0.84 7 7
VEGFB 0.027 0.005 -10000 0 -10000 0 0
MAPK11 0.006 0.098 0.38 1 -0.7 7 8
VEGFR2 homodimer 0.019 0.09 -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 0.002 0.091 0.38 1 -0.73 5 6
MAPK1 -0.003 0.091 0.38 1 -0.74 5 6
VEGFA145/NRP2 0.028 0.054 -10000 0 -0.51 3 3
VEGFR1/2 heterodimer 0.03 0.093 -10000 0 -0.96 4 4
KDR 0.019 0.091 -10000 0 -0.98 4 4
VEGFA165/NRP1/VEGFR2 homodimer 0.054 0.099 -10000 0 -0.67 7 7
SRC 0.027 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.011 0.11 0.38 11 -0.76 5 16
PI3K 0.043 0.098 -10000 0 -0.78 5 5
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.048 0.094 -10000 0 -0.74 6 6
FES 0.024 0.096 -10000 0 -0.68 7 7
GAB1 0.03 0.093 -10000 0 -0.77 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.095 -10000 0 -0.74 6 6
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.026 0.007 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.04 0.09 0.4 1 -0.54 5 6
VEGFR2 homodimer/VEGFA homodimer/Yes 0.047 0.095 -10000 0 -0.74 6 6
PI3K/GAB1 0.052 0.085 -10000 0 -0.62 5 5
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 0.023 0.096 -10000 0 -0.68 7 7
actin cytoskeleton reorganization 0.025 0.13 -10000 0 -0.46 27 27
PTK2 0.026 0.1 -10000 0 -0.75 6 6
EDG1 0.012 0.089 -10000 0 -0.64 7 7
mol:DAG 0.023 0.093 -10000 0 -0.66 7 7
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 0.052 0.1 -10000 0 -0.94 4 4
PLCG1 0.023 0.096 -10000 0 -0.68 7 7
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.058 0.094 -10000 0 -0.7 6 6
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 -0.79 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.047 0.094 -10000 0 -0.74 6 6
cell migration 0.047 0.084 0.34 1 -0.66 4 5
mol:PI-3-4-5-P3 0.042 0.086 -10000 0 -0.68 5 5
FYN 0.027 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.028 0.085 -10000 0 -0.61 7 7
mol:NO 0.041 0.097 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 -0.64 5 5
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.044 0.1 -10000 0 -0.94 4 4
VHL 0.023 0.054 -10000 0 -0.67 3 3
ITGB3 0.011 0.1 -10000 0 -0.65 11 11
NOS3 0.04 0.1 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 0.003 0.12 0.36 1 -0.96 4 5
PRKCB 0.007 0.094 0.36 1 -0.56 9 10
VCL 0.027 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 0.03 0.095 -10000 0 -0.67 7 7
VEGFR1/2 heterodimer/VEGFA homodimer 0.044 0.1 -10000 0 -0.78 6 6
VEGFA165/NRP2 0.028 0.054 -10000 0 -0.51 3 3
MAPKKK cascade 0.054 0.091 0.36 2 -0.71 4 6
NRP2 0.014 0.043 -10000 0 -10000 0 0
VEGFC homodimer 0.026 0.032 -10000 0 -0.67 1 1
NCK1 0.027 0.003 -10000 0 -10000 0 0
ROCK1 0.027 0.005 -10000 0 -10000 0 0
FAK1/Paxillin 0.041 0.1 -10000 0 -0.74 5 5
MAP3K13 0.016 0.12 -10000 0 -0.54 14 14
PDPK1 0.028 0.081 -10000 0 -0.67 5 5
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate 0.025 0.052 0.31 1 -0.67 1 2
PDGFB-D/PDGFRB/SLAP 0.038 0.027 -10000 0 -0.51 1 1
PDGFB-D/PDGFRB/APS/CBL 0.051 0.034 -10000 0 -0.43 2 2
AKT1 0.03 0.087 0.5 11 -0.33 2 13
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.029 0.054 0.34 1 -0.71 1 2
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
FGR 0.018 0.045 0.33 2 -0.54 2 4
mol:Ca2+ 0.034 0.082 0.41 13 -0.74 1 14
MYC 0.03 0.18 0.58 18 -0.77 14 32
SHC1 0.025 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.025 -10000 0 -0.38 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 -0.76 1 14
PTEN 0.026 0.018 -10000 0 -0.36 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.001 0.057 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.038 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 0.024 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 0.5 16 -0.7 1 17
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 0.033 0.053 -10000 0 -0.67 1 1
positive regulation of MAPKKK cascade 0.037 0.036 -10000 0 -0.51 2 2
PIK3R1 0.027 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 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.018 0.052 -10000 0 -0.57 1 1
SHB 0.026 0.007 -10000 0 -10000 0 0
BLK -0.15 0.26 -10000 0 -0.56 144 144
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 0.034 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 0.011 0.08 -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 -0.59 2 16
PDGFB-D/PDGFRB/CBL 0.023 0.083 0.45 4 -0.64 2 6
PTPN1 0.028 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 0.032 0.17 0.56 19 -0.68 14 33
SLA 0.026 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.034 0.027 -10000 0 -0.37 1 1
SRC 0.019 0.035 0.29 1 -0.4 2 3
PI3K 0.012 0.034 -10000 0 -0.35 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.049 0.028 -10000 0 -0.31 1 1
SH2B2 0.024 0.033 -10000 0 -0.67 1 1
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 0.024 -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 0.056 0.37 1 -0.48 5 6
cell migration 0.05 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 -0.48 3 4
DOK1 0.024 0.029 -10000 0 -0.41 1 1
HRAS/GTP 0.019 0.008 -10000 0 -10000 0 0
PDGFB 0.02 0.012 -10000 0 -10000 0 0
RAC1 0.039 0.14 0.54 20 -0.46 11 31
PRKCD 0.024 0.031 -10000 0 -0.42 1 1
FER 0.02 0.043 -10000 0 -0.42 4 4
MAPKKK cascade 0.016 0.056 0.37 1 -10000 0 1
RASA1 0.023 0.028 -10000 0 -0.42 1 1
NCK1 0.027 0.003 -10000 0 -10000 0 0
NCK2 0.027 0.005 -10000 0 -10000 0 0
p62DOK/Csk 0.039 0.03 -10000 0 -0.38 1 1
PDGFB-D/PDGFRB/SHB 0.036 0.028 -10000 0 -0.51 1 1
chemotaxis 0.026 0.095 0.42 14 -0.56 2 16
STAT1-3-5/STAT1-3-5 0.064 0.029 -10000 0 -0.37 1 1
Bovine Papilomavirus E5/PDGFRB 0.019 0.025 -10000 0 -0.52 1 1
PTPRJ 0.027 0.005 -10000 0 -10000 0 0
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.004 0.12 -10000 0 -0.67 15 15
CDC42/GTP 0.008 0.074 -10000 0 -0.3 15 15
PLCG1 -0.002 0.067 -10000 0 -0.31 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.027 0.003 -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 15 15
S1PR5 0.023 0.034 -10000 0 -0.67 1 1
S1PR4 0.023 0.02 -10000 0 -10000 0 0
MAPK3 -0.003 0.068 -10000 0 -0.31 16 16
MAPK1 0.009 0.06 -10000 0 -0.32 14 14
S1P/S1P5/Gi -0.001 0.074 -10000 0 -0.32 18 18
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 0.035 0.07 0.41 12 -10000 0 12
S1P/S1P4/Gi 0 0.073 -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 S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.017 0.041 -10000 0 -0.26 1 1
STMN1 0.001 0.042 -10000 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.053 0.051 -10000 0 -0.44 1 1
Chromosomal passenger complex/Cul3 protein complex 0.014 0.05 -10000 0 -0.31 3 3
BIRC5 0.017 0.048 -10000 0 -0.68 1 1
DES -0.32 0.3 -10000 0 -0.57 289 289
Aurora C/Aurora B/INCENP 0.054 0.044 -10000 0 -0.45 2 2
Aurora B/TACC1 0.029 0.043 -10000 0 -0.5 1 1
Aurora B/PP2A 0.02 0.05 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.011 0.007 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.001 0.002 -10000 0 -10000 0 0
NDC80 -0.008 0.06 0.2 1 -10000 0 1
Cul3 protein complex 0.038 0.073 -10000 0 -0.44 10 10
KIF2C 0.015 0.028 -10000 0 -0.47 1 1
PEBP1 0.027 0.006 -10000 0 -10000 0 0
KIF20A 0.004 0.054 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.02 0.05 -10000 0 -10000 0 0
SEPT1 0.024 0.021 -10000 0 -10000 0 0
SMC2 0.025 0.008 -10000 0 -10000 0 0
SMC4 0.027 0.003 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.017 0.079 0.28 1 -0.54 8 9
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 0.011 0.017 -10000 0 -10000 0 0
AURKB 0.001 0.066 -10000 0 -10000 0 0
AURKC 0.02 0.03 -10000 0 -10000 0 0
CDCA8 0.028 0.016 -10000 0 -10000 0 0
cytokinesis -0.018 0.054 -10000 0 -0.38 3 3
Aurora B/Septin1 0.045 0.066 -10000 0 -0.41 1 1
AURKA 0.027 0.005 -10000 0 -10000 0 0
INCENP 0.026 0.046 -10000 0 -0.68 2 2
KLHL13 0.006 0.1 -10000 0 -0.62 12 12
BUB1 -0.028 0.079 -10000 0 -0.68 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 0.05 0.047 -10000 0 -10000 0 0
SGOL1 0.021 0.029 -10000 0 -10000 0 0
CENPA 0.018 0.041 0.2 2 -0.23 4 6
NCAPG 0.013 0.045 -10000 0 -10000 0 0
Aurora B/HC8 Proteasome 0.02 0.05 -10000 0 -10000 0 0
NCAPD2 0.027 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.019 0.05 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
NCAPH 0.005 0.054 -10000 0 -10000 0 0
NPM1 0.012 0.041 -10000 0 -0.31 3 3
RASA1 0.027 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 0.02 0.05 -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 0.011 0.043 -10000 0 -0.31 3 3
MYLK 0.01 0.025 -10000 0 -0.41 1 1
KIF23 0.021 0.034 -10000 0 -10000 0 0
VIM 0 0.04 -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 0.08 -10000 0 -0.49 9 9
Chromosomal passenger complex 0.015 0.036 -10000 0 -0.26 3 3
Chromosomal passenger complex/EVI5 0.1 0.07 -10000 0 -0.42 3 3
TACC1 0.026 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
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.039 0.042 -9999 0 -0.45 1 1
CLOCK -0.017 0.17 -9999 0 -0.67 32 32
TIMELESS/CRY2 0.026 0.036 -9999 0 -10000 0 0
DEC1/BMAL1 0.016 0.039 -9999 0 -10000 0 0
ATR 0.026 0.032 -9999 0 -0.67 1 1
NR1D1 -0.001 0.042 -9999 0 -10000 0 0
ARNTL 0.01 0.049 -9999 0 -10000 0 0
TIMELESS 0.01 0.032 -9999 0 -10000 0 0
NPAS2 0.027 0.019 -9999 0 -0.36 1 1
CRY2 0.027 0.005 -9999 0 -10000 0 0
mol:CO -0.004 0.009 -9999 0 -10000 0 0
CHEK1 0.027 0.005 -9999 0 -10000 0 0
mol:HEME 0.004 0.009 -9999 0 -10000 0 0
PER1 0.026 0.007 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.023 0.13 -9999 0 -0.44 32 32
BMAL1/CLOCK -0.005 0.11 -9999 0 -0.41 29 29
S phase of mitotic cell cycle 0.039 0.042 -9999 0 -0.45 1 1
TIMELESS/CHEK1/ATR 0.04 0.043 -9999 0 -0.46 1 1
mol:NADPH 0.004 0.009 -9999 0 -10000 0 0
PER1/TIMELESS 0.025 0.034 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.012 0.013 -9999 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 0.021 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 0.022 0.023 -10000 0 -10000 0 0
BAD 0.027 0.005 -10000 0 -10000 0 0
AKT3 0.014 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 0.036 -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 0.021 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 0.023 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.022 0.023 -10000 0 -10000 0 0
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 -0.046 0.15 -10000 0 -0.43 63 63
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 -0.011 0.076 0.3 11 -0.32 8 19
YWHAH 0.02 0.012 -10000 0 -10000 0 0
AKT1S1 0.027 0.038 -10000 0 -10000 0 0
CASP9 0.024 0.031 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.045 0.048 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 0.027 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.022 0.029 -10000 0 -0.36 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 0.047 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 0.019 0.08 0.37 8 -0.36 4 12
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
MDM2 0.023 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.041 0.035 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.039 0.034 -10000 0 -10000 0 0
TSC1/TSC2 0.024 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 -0.057 0.16 -10000 0 -0.42 78 78
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.029 0.21 2 -10000 0 2
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.059 0.16 -10000 0 -0.42 78 78
GSK3A 0.026 0.037 -10000 0 -10000 0 0
FOXO1 0.021 0.025 -10000 0 -10000 0 0
GSK3B 0.022 0.024 -10000 0 -10000 0 0
SFN -0.085 0.13 -10000 0 -0.67 15 15
G1/S transition of mitotic cell cycle 0.029 0.044 0.3 3 -10000 0 3
p27Kip1/14-3-3 family 0.016 0.052 0.26 1 -0.34 5 6
PRKACA 0.025 0.008 -10000 0 -10000 0 0
KPNA1 0.027 0.003 -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
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.007 0.074 0.3 15 -10000 0 15
GNAI2 0.027 0.003 -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 0.075 -10000 0 -0.48 3 3
negative regulation of cAMP metabolic process 0 0.074 -10000 0 -0.32 18 18
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 0.074 -10000 0 -0.32 18 18
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.006 0.16 -10000 0 -0.44 56 56
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.018 0.14 -10000 0 -0.38 55 55
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 0.037 0.083 -10000 0 -10000 0 0
YY1/LSF 0.006 0.065 -10000 0 -0.43 4 4
SMG5 0.026 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.007 0.11 -10000 0 -0.31 54 54
I kappa B alpha/HDAC1 0.011 0.08 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
RELA -0.016 0.11 -10000 0 -0.32 56 56
HDAC1/Smad7 0.052 0.016 -10000 0 -10000 0 0
RANGAP1 0.02 0.012 -10000 0 -10000 0 0
HDAC3/TR2 0.012 0.08 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.031 0.037 -10000 0 -0.44 2 2
NF kappa B1 p50/RelA -0.024 0.12 0.32 1 -0.43 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 0.035 0.067 -10000 0 -0.49 5 5
RBBP7 0.026 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 0.027 0.006 -10000 0 -10000 0 0
NFKBIA -0.003 0.083 -10000 0 -10000 0 0
KAT2B 0.027 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.03 0.034 -10000 0 -0.55 1 1
SIN3 complex 0.061 0.032 -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 0.026 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 -0.008 0.079 -10000 0 -10000 0 0
YY1/HDAC2 0.009 0.054 -10000 0 -0.28 1 1
YY1/HDAC1 0.01 0.054 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.032 0.031 -10000 0 -0.4 1 1
PPARG -0.021 0.14 -10000 0 -0.39 60 60
HDAC8/hEST1B 0.047 0.021 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.012 0.08 -10000 0 -10000 0 0
MBD3L2 -0.015 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.016 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.036 0.061 -10000 0 -0.45 4 4
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 -0.003 0.083 -10000 0 -10000 0 0
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 0.022 0.058 -10000 0 -0.27 2 2
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 -0.003 0.083 -10000 0 -10000 0 0
histone deacetylation 0.038 0.034 -10000 0 -0.39 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.003 0.074 -10000 0 -0.3 1 1
nuclear export -0.046 0.021 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GATAD2B 0.026 0.007 -10000 0 -10000 0 0
GATAD2A 0.025 0.008 -10000 0 -10000 0 0
GATA2/HDAC3 0.012 0.08 -10000 0 -10000 0 0
GATA1/HDAC1 0.035 0.013 -10000 0 -10000 0 0
GATA1/HDAC3 0.009 0.079 -10000 0 -10000 0 0
CHD4 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.024 0.17 -10000 0 -0.51 56 56
SIN3/HDAC complex/Mad/Max 0.032 0.034 -10000 0 -0.49 1 1
NuRD Complex 0.042 0.052 -10000 0 -0.49 2 2
positive regulation of chromatin silencing 0.034 0.081 -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 0.063 0.036 -10000 0 -0.4 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 -0.056 0.22 -10000 0 -0.67 56 56
negative regulation of cell growth 0.036 0.035 -10000 0 -0.48 1 1
NuRD/MBD2/PRMT5 Complex 0.032 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 -0.03 0.14 -10000 0 -0.4 55 55
SIN3/HDAC complex/NCoR1 0.031 0.044 -10000 0 -0.45 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
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 0.027 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.003 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 0.031 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 0.054 -10000 0 -0.67 3 3
NF kappa B1 p50 dimer 0.025 0.023 0.25 5 -10000 0 5
PIK3R1 0.027 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 0.027 0.008 -10000 0 -10000 0 0
PI3K 0.036 0.043 -10000 0 -0.51 3 3
NF kappa B1 p50/RelA 0.021 0.038 -10000 0 -0.31 5 5
IKBKB 0.027 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.027 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 0.003 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 0.25 1 -10000 0 1
AES 0.025 0.018 -10000 0 -10000 0 0
FBXW11 0.027 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 0.005 -10000 0 -10000 0 0
DKK2 -0.003 0.14 -10000 0 -0.66 20 20
TLE1 0.021 0.056 0.22 1 -0.66 3 4
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.049 0.088 0.47 15 -10000 0 15
WIF1 -0.015 0.047 -10000 0 -10000 0 0
beta catenin/RanBP3 0.03 0.084 0.38 23 -10000 0 23
KREMEN2 0.016 0.037 -10000 0 -10000 0 0
DKK1 0 0.07 -10000 0 -0.67 2 2
beta catenin/beta TrCP1 0.049 0.046 0.49 1 -10000 0 1
FZD1 0.027 0.006 -10000 0 -10000 0 0
AXIN2 -0.029 0.3 0.62 12 -1.4 18 30
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 0.066 -10000 0 -0.51 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.04 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 0.029 0.32 1 -10000 0 1
HNF1A 0.027 0.02 0.23 1 -10000 0 1
CTBP1 0.027 0.02 -10000 0 -10000 0 0
MYC -0.037 0.24 0.57 4 -1.4 14 18
RANBP3 0.025 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.034 0.096 -10000 0 -0.45 18 18
NKD1 0.007 0.11 -10000 0 -0.67 13 13
TCF4 0.027 0.019 0.22 1 -10000 0 1
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 0.022 0.049 0.22 1 -0.63 2 3
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 0.04 0.11 -10000 0 -0.53 8 8
DKK1/LRP6/Kremen 2 0.049 0.044 -10000 0 -0.47 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.027 0.019 -10000 0 -10000 0 0
NLK 0.026 0.008 -10000 0 -10000 0 0
CCND1 -0.011 0.082 0.58 2 -0.69 2 4
WNT1 0.022 0.018 -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 0.031 0.058 0.33 13 -0.32 2 15
APC 0.022 0.039 0.36 3 -0.39 1 4
WNT1/LRP6/FZD1 0.032 0.021 -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 0.009 0.044 -10000 0 -0.24 4 4
RAB3GAP2/RIMS1/UNC13B 0.048 0.02 -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 0.018 -10000 0 -10000 0 0
mol:ACh 0.002 0.044 0.14 19 -0.14 24 43
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 0.009 0.044 -10000 0 -0.24 4 4
UNC13B 0.025 0.008 -10000 0 -10000 0 0
CHRNA1 0.008 0.052 -10000 0 -0.67 1 1
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.041 0.11 -10000 0 -0.49 24 24
SNAP25 -0.015 0.075 -10000 0 -0.34 25 25
VAMP2 0.006 0.001 -10000 0 -10000 0 0
SYT1 -0.067 0.16 -10000 0 -0.67 24 24
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
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.027 0.005 -9999 0 -10000 0 0
SMAD2 -0.016 0.044 -9999 0 -0.24 1 1
SMAD3 0.021 0.016 -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 0.064 -9999 0 -0.42 1 1
PPM1A 0.027 0.005 -9999 0 -10000 0 0
CALM1 0.027 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 -0.004 0.055 -9999 0 -0.43 1 1
MAP3K1 0.027 0.005 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.006 0.13 -9999 0 -0.49 31 31
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 0.003 -9999 0 -10000 0 0
KPNB1 0.026 0.007 -9999 0 -10000 0 0
TGFBRAP1 -0.016 0.17 -9999 0 -0.66 31 31
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
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.049 0.065 0.38 1 -10000 0 1
ERC1 0.027 0.005 -10000 0 -10000 0 0
RIP2/NOD2 0.021 0.053 -10000 0 -0.51 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 0.016 0.14 -10000 0 -0.5 5 5
NEMO/A20/RIP2 0.027 0.005 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.034 0.074 -10000 0 -0.56 1 1
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.036 0.008 -10000 0 -10000 0 0
IKK complex/ELKS 0.045 0.067 -10000 0 -0.38 1 1
BCL10/MALT1/TRAF6 0.051 0.034 -10000 0 -0.44 2 2
NOD2 0.003 0.067 -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 -0.024 0.17 -10000 0 -0.51 56 56
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
PRKCA 0.002 0.13 -10000 0 -0.67 17 17
CHUK 0.027 0.004 -10000 0 -10000 0 0
UBE2D3 0.027 0.004 -10000 0 -10000 0 0
TNF -0.056 0.22 -10000 0 -0.67 56 56
NF kappa B1 p50/RelA 0.062 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 0.013 -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 0.048 0.072 -10000 0 -0.4 1 1
CYLD 0.026 0.006 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.044 0.099 -10000 0 -0.47 2 2
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.012 0.07 -9999 0 -0.38 14 14
CRKL 0.02 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.02 0.004 -9999 0 -10000 0 0
DOCK1 0.023 0.054 -9999 0 -0.67 3 3
ITGA4 0.02 0.058 -9999 0 -0.67 3 3
alpha4/beta7 Integrin/MAdCAM1 0.045 0.089 -9999 0 -0.41 16 16
EPO 0.004 0.027 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.017 0.095 -9999 0 -0.51 14 14
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 -0.51 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 0.054 -9999 0 -0.67 3 3
PI3K 0.036 0.043 -9999 0 -0.51 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 0.027 0.005 -9999 0 -10000 0 0
MADCAM1 0.004 0.064 -9999 0 -0.67 3 3
cell adhesion 0.043 0.088 -9999 0 -0.4 16 16
CRKL/CBL 0.03 0.019 -9999 0 -10000 0 0
ITGB1 0.027 0.004 -9999 0 -10000 0 0
SRC 0.016 0.065 -9999 0 -0.45 7 7
ITGB7 0.004 0.11 -9999 0 -0.65 12 12
RAC1 0.026 0.006 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.045 0.068 -9999 0 -0.5 7 7
p130Cas/Crk/Dock1 0.035 0.065 -9999 0 -0.37 10 10
VCAM1 0.019 0.071 -9999 0 -0.67 5 5
RHOA 0.027 0.003 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.063 0.038 -9999 0 -0.4 2 2
BCAR1 0.008 0.061 -9999 0 -0.43 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
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.025 0.11 0.64 11 -10000 0 11
PLK1 0.07 0.12 0.6 2 -0.63 2 4
CDKN1B 0.074 0.09 0.47 3 -0.4 1 4
FOXO3 0.067 0.11 -10000 0 -0.63 4 4
KAT2B 0.032 0.019 -10000 0 -10000 0 0
FOXO1/SIRT1 0.019 0.056 0.42 2 -0.4 1 3
CAT 0.063 0.13 -10000 0 -1.4 2 2
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
AKT1 0.034 0.02 -10000 0 -10000 0 0
FOXO1 0.017 0.08 0.44 11 -10000 0 11
MAPK10 0.033 0.032 -10000 0 -0.41 1 1
mol:GTP 0.002 0.001 -10000 0 -10000 0 0
FOXO4 0.069 0.085 0.49 9 -0.51 3 12
response to oxidative stress 0.01 0.012 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.087 0.087 -10000 0 -0.79 2 2
XPO1 0.027 0.005 -10000 0 -10000 0 0
EP300 0.021 0.013 -10000 0 -10000 0 0
BCL2L11 0.027 0.098 -10000 0 -0.71 6 6
FOXO1/SKP2 0.016 0.055 -10000 0 -0.44 3 3
mol:GDP 0.01 0.012 -10000 0 -10000 0 0
RAN 0.028 0.006 -10000 0 -10000 0 0
GADD45A 0.1 0.091 0.46 6 -0.58 3 9
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0 0.1 -10000 0 -0.44 9 9
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 -0.009 0.11 -10000 0 -0.49 14 14
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.027 0.062 0.21 2 -0.39 9 11
MAPK9 0.031 0.018 -10000 0 -10000 0 0
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 0.026 0.037 -10000 0 -0.67 1 1
SOD2 0.1 0.1 0.58 9 -0.62 2 11
RBL2 0.078 0.15 0.57 1 -1.1 4 5
RAL/GDP 0.046 0.015 -10000 0 -10000 0 0
CHUK 0.032 0.019 -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 0.016 -10000 0 -10000 0 0
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
FASLG -0.07 0.38 -10000 0 -1.4 39 39
SKP2 0.022 0.055 -10000 0 -0.67 3 3
USP7 0.028 0.006 -10000 0 -10000 0 0
IKBKB 0.032 0.02 -10000 0 -10000 0 0
CCNB1 0.07 0.11 0.6 2 -0.63 2 4
FOXO1-3a-4/beta catenin 0.1 0.099 0.44 7 -0.42 4 11
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.055 -10000 0 -0.43 3 3
CSNK1A1 0.027 0.006 -10000 0 -10000 0 0
SGK1 0.018 0.1 -10000 0 -0.67 10 10
CSNK1G3 0.026 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.041 0.01 -10000 0 -10000 0 0
ZFAND5 0.077 0.11 0.6 13 -0.44 2 15
SFN -0.085 0.13 -10000 0 -0.67 15 15
CDK2 0.027 0.005 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.008 0.1 -10000 0 -0.47 13 13
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FBXO32 0.067 0.11 0.59 1 -0.6 3 4
BCL6 0.084 0.12 0.57 1 -0.82 4 5
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 S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.009 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 0.009 0.004 -10000 0 -10000 0 0
MAPK12 -0.004 0.053 -10000 0 -0.39 9 9
CCND1 0.004 0.037 -10000 0 -0.33 4 4
p38 gamma/SNTA1 0.018 0.065 -10000 0 -0.38 10 10
MAP2K3 0.026 0.007 -10000 0 -10000 0 0
PKN1 0.025 0.008 -10000 0 -10000 0 0
G2/M transition checkpoint -0.005 0.056 -10000 0 -0.39 10 10
MAP2K6 -0.003 0.062 -10000 0 -0.44 10 10
MAPT 0.009 0.052 0.32 7 -0.37 3 10
MAPK13 0.016 0.005 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.008 0.002 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
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 0.036 0.052 -10000 0 -0.36 7 7
FMN1 0.008 0.082 -10000 0 -0.35 24 24
mol:IP3 0.028 0.032 -10000 0 -0.33 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.029 0.022 -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 0.036 0.028 -10000 0 -10000 0 0
CTNND1 0.028 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.023 0.032 -10000 0 -0.38 2 2
VASP 0.025 0.018 -10000 0 -10000 0 0
ZYX 0.026 0.021 -10000 0 -10000 0 0
JUB 0.025 0.02 -10000 0 -10000 0 0
EGFR(dimer) 0.039 0.048 -10000 0 -0.36 5 5
E-cadherin/beta catenin-gamma catenin 0.051 0.016 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.049 0.038 0.25 1 -0.34 3 4
PIK3CA 0.025 0.055 -10000 0 -0.68 3 3
PI3K 0.05 0.039 0.26 1 -0.35 3 4
FYN 0.026 0.036 0.29 3 -0.29 3 6
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 0.028 0.032 -10000 0 -0.33 3 3
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.037 0.053 -10000 0 -0.36 7 7
establishment of polarity of embryonic epithelium 0.025 0.018 -10000 0 -10000 0 0
SRC 0.027 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
EGFR 0.019 0.07 -10000 0 -0.67 5 5
CASR 0.018 0.031 -10000 0 -0.32 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 -0.34 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 0.052 -10000 0 -0.38 7 7
PIP5K1A 0.023 0.033 -10000 0 -0.39 2 2
PLCG1 0.028 0.033 -10000 0 -0.34 3 3
Rac1/GTP 0.048 0.047 -10000 0 -0.33 5 5
homophilic cell adhesion 0.001 0.005 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.037 0.094 0.41 16 -0.38 3 19
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.095 0.34 14 -0.38 8 22
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 0.027 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 -0.51 1 1
TAK1/TAB family 0.011 0.033 -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 0.037 0.055 -10000 0 -0.33 2 2
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 0.019 0.07 -10000 0 -0.67 5 5
CCM2 0.026 0.011 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.031 0.048 -10000 0 -0.44 5 5
MAPK11 0.02 0.013 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.045 0.056 -10000 0 -0.48 5 5
OSM/MEKK3 0.037 0.014 -10000 0 -10000 0 0
TAOK1 -0.032 0.13 -10000 0 -0.4 57 57
TAOK2 0.015 0.019 -10000 0 -0.39 1 1
TAOK3 0.016 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 0.026 0.007 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.037 -10000 0 -0.43 1 1
GADD45/MTK1/MTK1 0.038 0.091 -10000 0 -0.4 18 18
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.03 0.025 -10000 0 -10000 0 0
BIRC5 0.016 0.047 -10000 0 -0.67 1 1
NFKBIA 0.015 0.022 0.25 3 -10000 0 3
CPEB1 -0.025 0.18 -10000 0 -0.65 38 38
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 0.044 0.024 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.009 -10000 0 -10000 0 0
PAK1/Aurora A 0.03 0.025 -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 0.028 -10000 0 -10000 0 0
TP53 0.026 0.012 -10000 0 -10000 0 0
DLG7 0.013 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 0.047 0.024 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.027 0.021 -10000 0 -10000 0 0
AURKA 0.021 0.016 -10000 0 -10000 0 0
AURKB 0.012 0.023 -10000 0 -0.16 3 3
CDC25B 0.021 0.012 -10000 0 -10000 0 0
G2/M transition checkpoint 0.01 0.018 -10000 0 -10000 0 0
mRNA polyadenylation -0.003 0.11 -10000 0 -0.4 34 34
Aurora A/CPEB -0.003 0.11 -10000 0 -0.4 34 34
Aurora A/TACC1/TRAP/chTOG 0.055 0.039 -10000 0 -0.38 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 0.043 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 0.033 -10000 0 -0.25 7 7
Aurora A/PP2A 0.031 0.024 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.022 0.02 -10000 0 -10000 0 0
negative regulation of DNA binding 0.026 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 0.027 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 0.021 0.016 -10000 0 -10000 0 0
TACC1 0.026 0.032 -10000 0 -0.67 1 1
TACC3 0.026 0.011 -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 0.027 0.005 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA 0.025 0.01 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.05 0.018 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.008 0.028 -10000 0 -10000 0 0
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
Aurora A/TPX2 0.018 0.031 -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
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.031 0.099 -10000 0 -10000 0 0
CRKL 0.014 0.048 0.46 3 -10000 0 3
mol:DAG 0.028 0.048 -10000 0 -10000 0 0
HRAS 0.035 0.064 0.36 5 -10000 0 5
MAPK8 0.013 0.069 -10000 0 -0.44 9 9
RAP1A 0.023 0.063 0.49 5 -10000 0 5
GAB1 0.021 0.054 0.46 3 -10000 0 3
MAPK14 0.021 0.033 -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 0.028 0.093 -10000 0 -0.41 19 19
GAB1/SHC/GRB2/SOS1 0.047 0.045 -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 0.072 -10000 0 -10000 0 0
STAT5B 0.027 0.061 -10000 0 -10000 0 0
cell proliferation 0.012 0.077 0.36 6 -0.41 9 15
GAB1/SHIP/PIK3R1/SHP2/SHC 0.036 0.042 -10000 0 -0.41 1 1
TEC 0.021 0.054 0.46 3 -10000 0 3
SOCS3 -0.001 0.14 -10000 0 -0.67 19 19
STAT1 (dimer) 0.029 0.071 -10000 0 -10000 0 0
JAK2 0.026 0.027 -10000 0 -0.34 2 2
PIK3R1 0.027 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 0.032 0.042 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.023 0.022 -10000 0 -10000 0 0
SHC1 0.025 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.049 0.032 -10000 0 -10000 0 0
mol:IP3 0.028 0.048 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.043 0.048 -10000 0 -10000 0 0
SH2B3 0.028 0.008 -10000 0 -10000 0 0
NFKB1 0.021 0.033 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 0.002 0.057 -10000 0 -0.27 16 16
PTPN6 0.022 0.048 0.31 1 -10000 0 1
TEC/VAV2/GRB2 0.042 0.045 -10000 0 -10000 0 0
EPOR 0.023 0.022 -10000 0 -10000 0 0
INPP5D 0.019 0.034 -10000 0 -10000 0 0
mol:GDP 0.047 0.045 -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 0.022 0.056 0.45 4 -10000 0 4
SHC/Grb2/SOS1 0.035 0.039 -10000 0 -10000 0 0
STAT5A 0.027 0.061 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
STAT5 (dimer) 0.039 0.098 -10000 0 -0.42 1 1
LYN/PLCgamma2 0.039 0.011 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
BTK 0.01 0.059 -10000 0 -0.36 6 6
BCL2 -0.015 0.26 -10000 0 -0.9 37 37
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.023 0.055 -10000 0 -0.67 3 3
positive regulation of NF-kappaB transcription factor activity 0.036 0.043 -10000 0 -0.51 3 3
MAP2K4 0.027 0.046 -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 0.023 0.055 -10000 0 -0.67 3 3
SMPD1 0.015 0.03 -10000 0 -0.34 3 3
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 0.036 0.043 -10000 0 -0.51 3 3
TRAIL/TRAILR3 0.004 0.067 -10000 0 -0.51 3 3
TRAIL/TRAILR1 0.033 0.061 -10000 0 -0.51 6 6
TRAIL/TRAILR4 0.036 0.043 -10000 0 -0.51 3 3
TRAIL/TRAILR1/DAP3/GTP 0.042 0.052 -10000 0 -0.4 6 6
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 0.013 0.041 -10000 0 -0.51 3 3
MAP3K1 0.027 0.047 -10000 0 -0.37 4 4
TRAILR4 (trimer) 0.027 0.005 -10000 0 -10000 0 0
TRADD 0.026 0.006 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.023 0.054 -10000 0 -0.67 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.028 0.043 -10000 0 -0.33 6 6
CFLAR 0.027 0.005 -10000 0 -10000 0 0
MAPK1 0.01 0.041 -10000 0 -0.5 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.071 0.054 -10000 0 -0.38 6 6
mol:ceramide 0.015 0.03 -10000 0 -0.34 3 3
FADD 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.016 0.071 0.28 1 -0.36 10 11
TRAF2 0.025 0.009 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.014 0.068 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.048 0.055 -10000 0 -0.44 6 6
DAP3 0.025 0.008 -10000 0 -10000 0 0
CASP10 0.01 0.04 -10000 0 -0.43 3 3
JNK cascade 0.036 0.043 -10000 0 -0.51 3 3
TRAIL (trimer) 0.023 0.055 -10000 0 -0.67 3 3
TNFRSF10C -0.014 0.068 -10000 0 -10000 0 0
TRAIL/TRAILR1/DAP3/GTP/FADD 0.053 0.052 -10000 0 -0.38 6 6
TRAIL/TRAILR2/FADD 0.051 0.04 -10000 0 -0.43 3 3
cell death 0.015 0.03 -10000 0 -0.34 3 3
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.03 0.035 -10000 0 -0.37 3 3
TRAILR2 (trimer) 0.027 0.005 -10000 0 -10000 0 0
CASP8 0.011 0.032 -10000 0 -0.58 1 1
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.074 0.041 -10000 0 -0.38 3 3
HIF-2-alpha transcription factor network

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
MMP14 0.015 0.034 -10000 0 -10000 0 0
oxygen homeostasis 0.011 0.009 -10000 0 -10000 0 0
TCEB2 0.025 0.014 -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 -0.54 3 3
EPO 0.12 0.11 -10000 0 -0.91 1 1
FIH (dimer) 0.037 0.012 -10000 0 -10000 0 0
APEX1 0.035 0.015 -10000 0 -10000 0 0
SERPINE1 0.12 0.12 -10000 0 -0.75 2 2
FLT1 -0.002 0.12 -10000 0 -0.7 9 9
ADORA2A 0.1 0.12 0.43 1 -0.72 2 3
germ cell development 0.13 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 0.037 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.11 0.096 -10000 0 -0.66 2 2
ETS1 0.038 0.015 -10000 0 -10000 0 0
CITED2 -0.036 0.31 -10000 0 -1.1 40 40
KDR 0.004 0.13 -10000 0 -1 6 6
PGK1 0.12 0.11 -10000 0 -0.99 1 1
SIRT1 0.026 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 -0.95 2 2
EPAS1 0.061 0.069 -10000 0 -0.46 2 2
SP1 0.033 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 0.62 1 -0.72 2 3
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 0.016 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 -0.68 1 1
VHL/Elongin B/Elongin C 0.05 0.042 -10000 0 -0.46 3 3
VHL 0.023 0.054 -10000 0 -0.67 3 3
ARNT 0.034 0.015 -10000 0 -10000 0 0
SLC2A1 0.14 0.12 0.49 5 -0.72 2 7
TWIST1 0.13 0.14 0.46 1 -0.6 6 7
ELK1 0.022 0.036 -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
Paxillin-dependent events mediated by a4b1

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.009 -10000 0 -10000 0 0
DOCK1 0.023 0.054 -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 0.017 0.095 -10000 0 -0.51 14 14
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 0.032 0.077 -10000 0 -0.41 14 14
lamellipodium assembly 0.025 0.063 -10000 0 -0.58 4 4
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PI3K 0.036 0.043 -10000 0 -0.51 3 3
ARF6 0.027 0.005 -10000 0 -10000 0 0
TLN1 0.026 0.007 -10000 0 -10000 0 0
PXN 0.016 0.005 -10000 0 -10000 0 0
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.053 0.035 -10000 0 -0.35 2 2
cell adhesion 0.051 0.04 -10000 0 -0.37 3 3
CRKL/CBL 0.03 0.019 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.042 0.038 -10000 0 -0.4 3 3
ITGB1 0.027 0.004 -10000 0 -10000 0 0
ITGB7 0.004 0.11 -10000 0 -0.65 12 12
ARF6/GDP 0.024 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.05 0.064 -10000 0 -0.43 7 7
p130Cas/Crk/Dock1 0.048 0.041 -10000 0 -0.44 3 3
VCAM1 0.019 0.071 -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 0.071 -10000 0 -0.67 4 4
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.03 0.029 -10000 0 -10000 0 0
KLHL20 0.013 0.051 0.2 1 -10000 0 1
CYFIP2 0.027 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.039 0.042 0.26 2 -10000 0 2
ENAH 0.028 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 0.003 -10000 0 -10000 0 0
CDC42/GTP 0.035 0.016 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.008 0.032 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.055 0.072 -10000 0 -0.4 11 11
RAPGEF1 0.026 0.033 0.27 1 -10000 0 1
CTNND1 0.027 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.033 0.034 -10000 0 -0.31 1 1
CRK 0.026 0.026 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0.051 0.016 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.021 0.084 -10000 0 -0.51 11 11
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 0.053 0.03 -10000 0 -0.4 1 1
PI3K 0.017 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 -0.059 0.081 -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 0.027 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.046 0.067 0.44 7 -10000 0 7
actin cytoskeleton organization 0.012 0.041 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 0.008 -10000 0 -10000 0 0
ITGB7 0.004 0.11 -10000 0 -0.65 12 12
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 0.48 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 0.046 0.043 -10000 0 -10000 0 0
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 0.003 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
CTNNA1 0.027 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.012 0.037 0.2 5 -10000 0 5
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 0.027 0.24 2 -10000 0 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.064 0.072 -10000 0 -0.38 11 11
CCND1 0.012 0.04 0.19 4 -10000 0 4
VAV2 0.006 0.14 -10000 0 -0.51 33 33
RAP1/GDP 0.048 0.039 0.3 5 -10000 0 5
adherens junction assembly 0.029 0.032 -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 0.053 0.068 -10000 0 -0.37 11 11
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 0.029 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
Rac1/GTP -0.006 0.076 -10000 0 -0.31 10 10
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 0.034 -10000 0 -0.32 1 1
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.063 0.03 -9999 0 -0.39 1 1
HDAC3 0.027 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.035 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 0.05 0.028 -9999 0 -0.44 1 1
HDAC9 0.012 0.045 -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 0.013 -9999 0 -10000 0 0
HDAC5 0.026 0.007 -9999 0 -10000 0 0
GNB1/GNG2 0.037 0.027 -9999 0 -0.51 1 1
Histones 0.007 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 -0.4 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 0.027 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 -0.51 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 -0.51 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0.053 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 -0.48 23 23
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.007 0.048 -9999 0 -10000 0 0
cell motility 0.046 0.048 -9999 0 -0.4 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 -0.013 0.15 -9999 0 -0.65 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 0.027 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 0.027 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
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 -0.66 20 20
CLTC 0.029 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 0.022 0.011 -10000 0 -10000 0 0
CPE 0.011 0.05 -10000 0 -0.44 6 6
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
membrane fusion 0.02 0.013 -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 0.023 0.031 0.24 1 -10000 0 1
TSHR 0.015 0.029 -10000 0 -0.44 2 2
INS 0.007 0.073 -10000 0 -0.48 10 10
BIN1 0.027 0.005 -10000 0 -10000 0 0
mol:Choline 0.02 0.013 -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 0.01 -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 -0.047 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 0.024 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 0.029 0.024 -10000 0 -10000 0 0
JIP4/KLC1 0.05 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 0.033 0.036 0.34 3 -10000 0 3
IL2RA 0.008 0.055 -10000 0 -10000 0 0
VAMP3 0.016 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.024 0.071 -10000 0 -0.32 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 0.02 0.013 -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 0.03 0.084 0.41 10 -0.33 9 19
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 0.081 0.46 7 -0.33 10 17
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 0.018 -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 -0.004 0.042 -10000 0 -10000 0 0
regulation of axonogenesis -0.011 0.021 0.27 2 -10000 0 2
myoblast fusion -0.01 0.028 -10000 0 -10000 0 0
mol:GTP 0.009 0.019 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.024 0.063 0.41 1 -10000 0 1
ARF1/GTP 0.03 0.014 -10000 0 -10000 0 0
mol:GM1 0.004 0.012 -10000 0 -10000 0 0
mol:Choline 0.008 0.014 -10000 0 -10000 0 0
lamellipodium assembly 0.015 0.027 -10000 0 -10000 0 0
MAPK3 0.008 0.027 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.024 0.064 -10000 0 -0.42 1 1
ARF1 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.01 0.028 -10000 0 -10000 0 0
ARF1/GDP 0.02 0.03 -10000 0 -10000 0 0
ARF6 0.03 0.009 -10000 0 -10000 0 0
RAB11A 0.027 0.004 -10000 0 -10000 0 0
TIAM1 -0.061 0.082 -10000 0 -0.67 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.025 -10000 0 -10000 0 0
actin filament bundle formation -0.023 0.03 -10000 0 -10000 0 0
KALRN 0.009 0.021 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0.038 0.011 -10000 0 -10000 0 0
RhoA/GDP 0.023 0.03 -10000 0 -10000 0 0
NME1 0.026 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.027 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.008 0.019 -10000 0 -10000 0 0
cortical actin cytoskeleton organization 0.015 0.027 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
liver development 0.008 0.019 -10000 0 -10000 0 0
ARF6/GTP 0.009 0.019 -10000 0 -10000 0 0
RhoA/GTP 0.031 0.012 -10000 0 -10000 0 0
mol:GDP 0.008 0.021 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A 0.045 0.016 -10000 0 -10000 0 0
RHOA 0.027 0.003 -10000 0 -10000 0 0
PLD1 0.012 0.018 -10000 0 -10000 0 0
RAB11FIP3 0.026 0.007 -10000 0 -10000 0 0
tube morphogenesis 0.015 0.027 -10000 0 -10000 0 0
ruffle organization 0.011 0.021 -10000 0 -0.27 2 2
regulation of epithelial cell migration 0.008 0.019 -10000 0 -10000 0 0
PLD2 0.012 0.017 -10000 0 -10000 0 0
PIP5K1A 0.011 0.021 -10000 0 -0.27 2 2
mol:Phosphatidic acid 0.008 0.014 -10000 0 -10000 0 0
Rac1/GTP 0.015 0.027 -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 0.041 -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 0.014 -9999 0 -10000 0 0
AURKB -0.007 0.063 -9999 0 -10000 0 0
AURKC 0.02 0.03 -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 -0.02 0.076 -9999 0 -0.67 1 1
GPC2 0.016 0.038 -9999 0 -10000 0 0
GPC2/Midkine -0.004 0.061 -9999 0 -0.3 1 1
neuron projection morphogenesis -0.004 0.061 -9999 0 -0.3 1 1
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 0.007 0.035 -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 0.027 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 0.067 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 0.048 -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 0.046 -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 0.052 0.016 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.039 0.009 -9999 0 -9999 0 0
CTNNB1 0.027 0.003 -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 0.034 0.2 2 -10000 0 2
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 0.027 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 0.021 0.03 -10000 0 -10000 0 0
CLTA 0.026 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 -10000 0 0
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 -0.37 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 0.005 0.017 -10000 0 -10000 0 0
AP2M1 0.027 0.003 -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 0.007 -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 0.026 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.033 -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 0.008 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.019 0.009 -10000 0 -10000 0 0
ARF1/GDP/Membrin 0.026 0.024 -10000 0 -0.31 1 1
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 0.02 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 0.025 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 0.024 -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 -0.37 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 0.052 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 0.027 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 0.027 0.006 -9999 0 -9999 0 0
CHUK 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.073 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 0.026 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 497 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.QD.A8IV TCGA.MK.A84Z TCGA.MK.A4N9 TCGA.MK.A4N7
109_MAP3K5 -0.065 0.053 -0.2 0.025
47_PPARGC1A 0.028 0 -0.67 -0.67
105_BMP4 0.028 0.028 0.028 -0.13
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 0.064 -0.22 -0.4 -0.4
30_TGFB1/TGF beta receptor Type II 0.027 0.027 0.027 0.028
84_STAT5B 0.04 0.053 0.04 -0.05
84_STAT5A 0.04 0.053 0.04 -0.05
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/19438636/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/THCA-TP/19775582/GDAC_Gistic2Report_19781945/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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