PARADIGM pathway analysis of mRNASeq expression and copy number data
Thyroid Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C18C9V6S
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C18C9V6S
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 249
Signaling events mediated by Stem cell factor receptor (c-Kit) 168
Signaling events regulated by Ret tyrosine kinase 144
Reelin signaling pathway 132
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 108
Wnt signaling 102
PDGFR-alpha signaling pathway 96
FOXA2 and FOXA3 transcription factor networks 93
Noncanonical Wnt signaling pathway 89
Nongenotropic Androgen signaling 87
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 0.4970 249 1748 7 -0.42 0 1000 -1000 -0.002 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3353 168 13118 78 -0.75 0.24 1000 -1000 -0.055 -1000
Signaling events regulated by Ret tyrosine kinase 0.2874 144 11820 82 -0.37 0.027 1000 -1000 -0.058 -1000
Reelin signaling pathway 0.2635 132 7428 56 -0.46 0.061 1000 -1000 -0.036 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2156 108 7368 68 -0.73 0.35 1000 -1000 -0.076 -1000
Wnt signaling 0.2036 102 720 7 -0.33 0.014 1000 -1000 -0.024 -1000
PDGFR-alpha signaling pathway 0.1916 96 4234 44 -0.4 0.043 1000 -1000 -0.037 -1000
FOXA2 and FOXA3 transcription factor networks 0.1856 93 4280 46 -0.84 0.031 1000 -1000 -0.059 -1000
Noncanonical Wnt signaling pathway 0.1776 89 2323 26 -0.33 0.027 1000 -1000 -0.05 -1000
Nongenotropic Androgen signaling 0.1737 87 4525 52 -0.26 0.19 1000 -1000 -0.035 -1000
Signaling events mediated by the Hedgehog family 0.1697 85 4439 52 -0.29 0.14 1000 -1000 -0.04 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1477 74 4008 54 -0.46 0.039 1000 -1000 -0.055 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1357 68 2317 34 -0.1 0.027 1000 -1000 -0.031 -1000
Calcium signaling in the CD4+ TCR pathway 0.1317 66 2060 31 -0.35 0.027 1000 -1000 -0.032 -1000
Endothelins 0.1277 64 6174 96 -0.32 0.03 1000 -1000 -0.045 -1000
IGF1 pathway 0.1257 63 3615 57 -0.14 0.063 1000 -1000 -0.039 -1000
Glypican 1 network 0.1238 62 3015 48 -0.3 0.052 1000 -1000 -0.024 -1000
IL4-mediated signaling events 0.1158 58 5344 91 -1.2 0.57 1000 -1000 -0.08 -1000
Ephrin B reverse signaling 0.1058 53 2554 48 -0.24 0.12 1000 -1000 -0.036 -1000
Coregulation of Androgen receptor activity 0.1038 52 4007 76 -0.68 0.076 1000 -1000 -0.025 -1000
TCR signaling in naïve CD8+ T cells 0.1018 51 4796 93 -0.16 0.046 1000 -1000 -0.044 -1000
HIF-1-alpha transcription factor network 0.0998 50 3863 76 -0.49 0.041 1000 -1000 -0.053 -1000
BMP receptor signaling 0.0998 50 4097 81 -0.45 0.052 1000 -1000 -0.048 -1000
IL23-mediated signaling events 0.0978 49 2994 60 -0.27 0.027 1000 -1000 -0.056 -1000
Glucocorticoid receptor regulatory network 0.0938 47 5442 114 -0.45 0.26 1000 -1000 -0.057 -1000
Arf6 signaling events 0.0878 44 2771 62 -0.26 0.061 1000 -1000 -0.033 -1000
IL12-mediated signaling events 0.0798 40 3551 87 -0.36 0.029 1000 -1000 -0.074 -1000
Signaling mediated by p38-alpha and p38-beta 0.0778 39 1729 44 -0.22 0.027 1000 -1000 -0.033 -1000
Thromboxane A2 receptor signaling 0.0739 37 3901 105 -0.16 0.047 1000 -1000 -0.045 -1000
Hedgehog signaling events mediated by Gli proteins 0.0739 37 2423 65 -0.58 0.064 1000 -1000 -0.031 -1000
EPHB forward signaling 0.0699 35 3022 85 -0.24 0.11 1000 -1000 -0.074 -1000
EGFR-dependent Endothelin signaling events 0.0619 31 669 21 -0.075 0.038 1000 -1000 -0.04 -1000
Ras signaling in the CD4+ TCR pathway 0.0579 29 507 17 -0.1 0.035 1000 -1000 -0.028 -1000
IL6-mediated signaling events 0.0559 28 2106 75 -0.15 0.054 1000 -1000 -0.041 -1000
Regulation of p38-alpha and p38-beta 0.0519 26 1430 54 -0.36 0.065 1000 -1000 -0.048 -1000
Osteopontin-mediated events 0.0499 25 973 38 -0.15 0.043 1000 -1000 -0.034 -1000
Plasma membrane estrogen receptor signaling 0.0499 25 2190 86 -0.13 0.049 1000 -1000 -0.057 -1000
ErbB2/ErbB3 signaling events 0.0479 24 1584 65 -0.16 0.037 1000 -1000 -0.052 -1000
Syndecan-1-mediated signaling events 0.0479 24 835 34 -0.078 0.027 1000 -1000 -0.038 -1000
FAS signaling pathway (CD95) 0.0479 24 1156 47 -0.2 0.042 1000 -1000 -0.037 -1000
BCR signaling pathway 0.0479 24 2449 99 -0.1 0.048 1000 -1000 -0.052 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0459 23 2025 85 -0.22 0.14 1000 -1000 -0.045 -1000
Regulation of Androgen receptor activity 0.0459 23 1669 70 -0.45 0.036 1000 -1000 -0.053 -1000
IFN-gamma pathway 0.0439 22 1521 68 -0.17 0.035 1000 -1000 -0.055 -1000
LPA receptor mediated events 0.0439 22 2296 102 -0.15 0.035 1000 -1000 -0.057 -1000
Syndecan-4-mediated signaling events 0.0439 22 1522 67 -0.16 0.039 1000 -1000 -0.041 -1000
Ceramide signaling pathway 0.0399 20 1578 76 -0.15 0.075 1000 -1000 -0.042 -1000
Fc-epsilon receptor I signaling in mast cells 0.0379 19 1890 97 -0.15 0.044 1000 -1000 -0.061 -1000
amb2 Integrin signaling 0.0359 18 1491 82 -0.19 0.035 1000 -1000 -0.034 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0359 18 1625 88 -0.26 0.039 1000 -1000 -0.065 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0339 17 928 52 -0.18 0.057 1000 -1000 -0.044 -1000
Integrins in angiogenesis 0.0339 17 1479 84 -0.14 0.056 1000 -1000 -0.047 -1000
IL27-mediated signaling events 0.0339 17 903 51 -0.11 0.045 1000 -1000 -0.042 -1000
JNK signaling in the CD4+ TCR pathway 0.0319 16 278 17 -0.084 0.028 1000 -1000 -0.03 -1000
Signaling events mediated by PTP1B 0.0319 16 1248 76 -0.19 0.039 1000 -1000 -0.034 -1000
ceramide signaling pathway 0.0319 16 831 49 -0.056 0.039 1000 -1000 -0.042 -1000
mTOR signaling pathway 0.0299 15 799 53 -0.043 0.03 1000 -1000 -0.041 -1000
LPA4-mediated signaling events 0.0279 14 177 12 -0.054 0.004 1000 -1000 -0.022 -1000
Regulation of nuclear SMAD2/3 signaling 0.0279 14 1913 136 -0.26 0.053 1000 -1000 -0.04 -1000
Visual signal transduction: Cones 0.0279 14 551 38 -0.042 0.043 1000 -1000 -0.013 -1000
p75(NTR)-mediated signaling 0.0279 14 1830 125 -0.28 0.071 1000 -1000 -0.067 -1000
Nectin adhesion pathway 0.0279 14 886 63 -0.11 0.073 1000 -1000 -0.053 -1000
Insulin Pathway 0.0279 14 1042 74 -0.056 0.065 1000 -1000 -0.048 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0279 14 1682 120 -0.24 0.074 1000 -1000 -0.046 -1000
Presenilin action in Notch and Wnt signaling 0.0259 13 817 61 -0.15 0.07 1000 -1000 -0.048 -1000
Signaling events mediated by HDAC Class III 0.0259 13 557 40 -0.28 0.046 1000 -1000 -0.02 -1000
IL1-mediated signaling events 0.0259 13 850 62 -0.076 0.061 1000 -1000 -0.047 -1000
Syndecan-3-mediated signaling events 0.0259 13 471 35 -0.12 0.07 1000 -1000 -0.019 -1000
Rapid glucocorticoid signaling 0.0259 13 266 20 -0.062 0.034 1000 -1000 -0.007 -1000
FOXM1 transcription factor network 0.0259 13 676 51 -0.22 0.051 1000 -1000 -0.076 -1000
Caspase cascade in apoptosis 0.0240 12 939 74 -0.057 0.046 1000 -1000 -0.041 -1000
Cellular roles of Anthrax toxin 0.0240 12 470 39 -0.057 0.027 1000 -1000 -0.027 -1000
IL2 signaling events mediated by PI3K 0.0240 12 738 58 -0.059 0.048 1000 -1000 -0.032 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0240 12 551 45 -0.057 0.076 1000 -1000 -0.053 -1000
ErbB4 signaling events 0.0220 11 776 69 -0.052 0.037 1000 -1000 -0.042 -1000
Visual signal transduction: Rods 0.0220 11 598 52 -0.072 0.045 1000 -1000 -0.028 -1000
BARD1 signaling events 0.0200 10 577 57 -0.04 0.05 1000 -1000 -0.038 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0200 10 301 28 -0.13 0.056 1000 -1000 -0.018 -1000
Syndecan-2-mediated signaling events 0.0200 10 697 69 -0.16 0.05 1000 -1000 -0.047 -1000
S1P1 pathway 0.0200 10 362 36 -0.053 0.027 1000 -1000 -0.038 -1000
TCGA08_rtk_signaling 0.0200 10 263 26 -0.18 0.045 1000 -1000 -0.007 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0200 10 750 74 -0.13 0.067 1000 -1000 -0.069 -1000
S1P3 pathway 0.0200 10 427 42 -0.13 0.048 1000 -1000 -0.026 -1000
Signaling events mediated by PRL 0.0200 10 373 34 -0.086 0.04 1000 -1000 -0.046 -1000
TCGA08_p53 0.0180 9 67 7 -0.024 0.025 1000 -1000 -0.011 -1000
Retinoic acid receptors-mediated signaling 0.0160 8 515 58 -0.037 0.053 1000 -1000 -0.041 -1000
Class I PI3K signaling events 0.0160 8 615 73 -0.19 0.05 1000 -1000 -0.034 -1000
Regulation of Telomerase 0.0160 8 870 102 -0.19 0.071 1000 -1000 -0.039 -1000
VEGFR1 specific signals 0.0160 8 464 56 -0.044 0.058 1000 -1000 -0.058 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0140 7 252 33 -0.11 0.055 1000 -1000 -0.024 -1000
Class IB PI3K non-lipid kinase events 0.0140 7 21 3 -0.015 0.015 1000 -1000 0 -1000
a4b1 and a4b7 Integrin signaling 0.0120 6 33 5 0.004 0.034 1000 -1000 -0.001 -1000
PLK1 signaling events 0.0120 6 546 85 -0.006 0.049 1000 -1000 -0.039 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0120 6 573 83 -0.17 0.049 1000 -1000 -0.038 -1000
IL2 signaling events mediated by STAT5 0.0120 6 136 22 -0.033 0.033 1000 -1000 -0.033 -1000
TCGA08_retinoblastoma 0.0120 6 55 8 -0.035 0.031 1000 -1000 -0.003 -1000
S1P4 pathway 0.0100 5 141 25 -0.003 0.047 1000 -1000 -0.025 -1000
Aurora B signaling 0.0100 5 371 67 -0.32 0.1 1000 -1000 -0.045 -1000
Insulin-mediated glucose transport 0.0080 4 148 32 -0.085 0.05 1000 -1000 -0.034 -1000
Class I PI3K signaling events mediated by Akt 0.0080 4 303 68 -0.085 0.05 1000 -1000 -0.034 -1000
Signaling events mediated by HDAC Class I 0.0080 4 470 104 -0.057 0.062 1000 -1000 -0.037 -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 4 230 51 -0.037 0.065 1000 -1000 -0.041 -1000
Effects of Botulinum toxin 0.0080 4 122 26 -0.067 0.048 1000 -1000 -0.009 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0080 4 615 125 -0.01 0.07 1000 -1000 -0.055 -1000
PDGFR-beta signaling pathway 0.0080 4 482 97 -0.14 0.079 1000 -1000 -0.058 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0060 3 72 23 -0.016 0.049 1000 -1000 -0.03 -1000
Canonical NF-kappaB pathway 0.0060 3 154 39 -0.057 0.061 1000 -1000 -0.032 -1000
Circadian rhythm pathway 0.0060 3 83 22 -0.017 0.04 1000 -1000 -0.026 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0060 3 139 37 0 0.063 1000 -1000 -0.031 -1000
S1P5 pathway 0.0060 3 58 17 -0.007 0.032 1000 -1000 -0.021 -1000
HIF-2-alpha transcription factor network 0.0060 3 130 43 -0.16 0.16 1000 -1000 -0.053 -1000
FoxO family signaling 0.0060 3 253 64 -0.085 0.1 1000 -1000 -0.042 -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 3 137 43 -0.03 0.051 1000 -1000 -0.039 -1000
p38 MAPK signaling pathway 0.0060 3 169 44 -0.031 0.049 1000 -1000 -0.025 -1000
Aurora A signaling 0.0040 2 130 60 -0.024 0.055 1000 -1000 -0.022 -1000
EPO signaling pathway 0.0040 2 162 55 -0.015 0.059 1000 -1000 -0.035 -1000
TRAIL signaling pathway 0.0040 2 110 48 -0.014 0.074 1000 -1000 -0.039 -1000
Paxillin-dependent events mediated by a4b1 0.0040 2 98 36 -0.053 0.055 1000 -1000 -0.037 -1000
Signaling events mediated by HDAC Class II 0.0020 1 89 75 -0.036 0.074 1000 -1000 -0.023 -1000
E-cadherin signaling in the nascent adherens junction 0.0020 1 141 76 -0.059 0.066 1000 -1000 -0.058 -1000
Arf6 trafficking events 0.0020 1 105 71 -0.048 0.05 1000 -1000 -0.027 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.016 0.027 1000 -1000 -0.016 -1000
Arf6 downstream pathway 0.0000 0 9 43 -0.06 0.045 1000 -1000 -0.024 -1000
Aurora C signaling 0.0000 0 4 7 -0.007 0.045 1000 -1000 -0.015 -1000
Glypican 2 network 0.0000 0 3 4 -0.02 0.016 1000 -1000 0.007 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 12 27 0 0.066 1000 -1000 -0.035 -1000
E-cadherin signaling events 0.0000 0 0 5 0.026 0.051 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 0.072 1000 -1000 0 -1000
Total NA 3447 198495 7203 -22 8 131000 -131000 -4.9 -131000
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.32 0.26 -9999 0 -0.48 341 341
EFNA5 -0.071 0.24 -9999 0 -0.67 69 69
FYN -0.3 0.24 -9999 0 -0.44 341 341
neuron projection morphogenesis -0.32 0.26 -9999 0 -0.48 341 341
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.32 0.26 -9999 0 -0.48 341 341
EPHA5 -0.42 0.33 -9999 0 -0.67 315 315
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 -0.39 279 280
CRKL -0.23 0.22 -10000 0 -0.41 285 285
HRAS -0.2 0.19 -10000 0 -0.4 107 107
mol:PIP3 -0.2 0.2 -10000 0 -0.39 255 255
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 -0.44 287 287
FOXO3 -0.19 0.21 0.37 2 -0.37 247 249
AKT1 -0.21 0.22 0.29 2 -0.39 274 276
BAD -0.19 0.2 0.28 1 -0.37 244 245
megakaryocyte differentiation -0.24 0.23 -10000 0 -0.43 296 296
GSK3B -0.19 0.21 0.31 3 -0.37 247 250
RAF1 -0.16 0.16 0.35 1 -0.35 71 72
SHC1 0.025 0.007 -10000 0 -10000 0 0
STAT3 -0.24 0.23 -10000 0 -0.44 280 280
STAT1 -0.6 0.56 -10000 0 -1.1 289 289
HRAS/SPRED1 -0.16 0.16 -10000 0 -0.35 70 70
cell proliferation -0.24 0.24 -10000 0 -0.44 290 290
PIK3CA 0.022 0.054 -10000 0 -0.68 3 3
TEC 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.23 0.23 -10000 0 -0.42 287 287
HRAS/SPRED2 -0.16 0.16 -10000 0 -0.35 71 71
LYN/TEC/p62DOK -0.21 0.24 -10000 0 -0.41 285 285
MAPK3 -0.11 0.12 0.26 5 -0.29 20 25
STAP1 -0.25 0.24 -10000 0 -0.45 287 287
GRAP2 -0.019 0.15 -10000 0 -0.56 33 33
JAK2 -0.5 0.48 -10000 0 -0.89 288 288
STAT1 (dimer) -0.58 0.54 -10000 0 -1 289 289
mol:Gleevec 0.008 0.011 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.21 0.24 -10000 0 -0.42 270 270
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 -0.61 288 289
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 -0.41 278 278
PTEN 0.026 0.018 -10000 0 -0.36 1 1
SCF/KIT/EPO/EPOR -0.7 0.66 -10000 0 -1.3 288 288
MAPK8 -0.25 0.24 -10000 0 -0.44 290 290
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 19 26
mol:GDP -0.2 0.2 -10000 0 -0.38 241 241
PIK3C2B -0.23 0.23 -10000 0 -0.44 262 262
CBL/CRKL -0.21 0.22 -10000 0 -0.39 282 282
FER -0.24 0.24 -10000 0 -0.44 286 286
SH2B3 -0.24 0.23 -10000 0 -0.44 288 288
PDPK1 -0.19 0.2 0.3 3 -0.36 252 255
SNAI2 -0.24 0.24 -10000 0 -0.44 287 287
positive regulation of cell proliferation -0.41 0.4 -10000 0 -0.75 288 288
KITLG -0.017 0.093 -10000 0 -0.71 8 8
cell motility -0.41 0.4 -10000 0 -0.75 288 288
PTPN6 0.038 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 -0.61 288 288
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 -0.44 285 285
PTPN11 0.034 0.033 -10000 0 -0.66 1 1
SCF/KIT -0.25 0.25 -10000 0 -0.46 288 288
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.13 0.13 0.27 3 -0.3 27 30
CBL 0.027 0.005 -10000 0 -10000 0 0
KIT -0.75 0.68 -10000 0 -1.3 288 288
MAP2K2 -0.12 0.13 0.28 2 -0.3 26 28
SHC/Grb2/SOS1 -0.2 0.23 -10000 0 -0.42 250 250
STAT5A -0.35 0.34 -10000 0 -0.63 288 288
GRB2 0.026 0.007 -10000 0 -10000 0 0
response to radiation -0.24 0.24 -10000 0 -0.43 287 287
SHC/GRAP2 0 0.11 -10000 0 -0.39 33 33
PTPRO -0.25 0.23 -10000 0 -0.44 296 296
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
Signaling events regulated by Ret tyrosine kinase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.061 0.097 -10000 0 -0.67 6 6
Crk/p130 Cas/Paxillin -0.22 0.19 -10000 0 -0.38 256 256
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 -0.49 288 288
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 -0.49 291 291
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.2 0.22 -10000 0 -0.4 272 272
RHOA 0.027 0.003 -10000 0 -10000 0 0
RAP1A/GTP -0.24 0.26 -10000 0 -0.44 286 286
GRB7 0.001 0.056 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.26 0.29 -10000 0 -0.49 284 284
MAPKKK cascade -0.23 0.24 -10000 0 -0.42 283 283
BCAR1 0.026 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.25 0.27 -10000 0 -0.46 287 287
lamellipodium assembly -0.19 0.18 -10000 0 -0.35 260 260
RET51/GFRalpha1/GDNF/SHC -0.26 0.28 -10000 0 -0.49 278 278
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
RET9/GFRalpha1/GDNF/SHC -0.2 0.22 -10000 0 -0.39 272 272
RET9/GFRalpha1/GDNF/Shank3 -0.21 0.21 -10000 0 -0.4 275 275
MAPK3 -0.24 0.23 -10000 0 -0.42 283 283
DOK1 0.027 0.005 -10000 0 -10000 0 0
DOK6 -0.083 0.25 -10000 0 -0.67 78 78
PXN 0.027 0.005 -10000 0 -10000 0 0
neurite development -0.26 0.25 -10000 0 -0.45 284 284
DOK5 -0.067 0.24 -10000 0 -0.67 67 67
GFRA1 -0.37 0.34 -10000 0 -0.67 282 282
MAPK8 -0.19 0.2 -10000 0 -0.49 92 92
HRAS/GTP -0.25 0.28 -10000 0 -0.47 289 289
tube development -0.19 0.2 -10000 0 -0.38 259 259
MAPK1 -0.24 0.23 0.32 3 -0.42 285 288
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.16 -10000 0 -0.3 259 259
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PDLIM7 0.026 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.3 0.34 -10000 0 -0.54 301 301
SHC1 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.26 0.29 -10000 0 -0.49 290 290
RET51/GFRalpha1/GDNF/Dok5 -0.31 0.34 -10000 0 -0.55 304 304
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 -0.38 256 256
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.14 0.16 -10000 0 -0.29 243 243
RET51/GFRalpha1/GDNF/Grb7 -0.27 0.29 -10000 0 -0.49 288 288
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 -0.4 273 273
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 -0.3 244 244
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.2 0.21 -10000 0 -0.35 287 287
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.2 0.2 -10000 0 -0.35 292 292
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.22 0.26 -10000 0 -0.4 277 277
PI3K -0.3 0.29 -10000 0 -0.55 263 263
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.19 0.21 -10000 0 -0.38 259 259
GRB10 0.026 0.006 -10000 0 -10000 0 0
activation of MAPKK activity -0.18 0.18 -10000 0 -0.32 268 268
RET51/GFRalpha1/GDNF/FRS2 -0.26 0.29 -10000 0 -0.48 291 291
GAB1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.056 0.22 -10000 0 -0.67 59 59
IRS2 0.026 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.22 0.26 -10000 0 -0.4 275 275
RET51/GFRalpha1/GDNF/PKC alpha -0.27 0.3 -10000 0 -0.5 289 289
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 -0.54 305 305
Rac1/GTP -0.23 0.22 -10000 0 -0.42 259 259
RET9/GFRalpha1/GDNF -0.23 0.23 -10000 0 -0.44 280 280
GFRalpha1/GDNF -0.27 0.27 -10000 0 -0.5 280 280
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.037 0.015 -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 -0.45 352 352
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 -0.42 341 341
LRPAP1/LRP8 0.017 0.11 -10000 0 -0.51 20 20
RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.4 341 341
DAB1/alpha3/beta1 Integrin -0.25 0.21 -10000 0 -0.39 329 329
long-term memory -0.26 0.23 -10000 0 -0.4 340 340
DAB1/LIS1 -0.25 0.22 -10000 0 -0.39 334 334
DAB1/CRLK/C3G -0.25 0.21 -10000 0 -0.38 336 336
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
DAB1/NCK2 -0.26 0.22 -10000 0 -0.4 341 341
ARHGEF2 0.025 0.007 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.001 0.12 -10000 0 -0.67 16 16
CDK5R1 0.025 0.014 -10000 0 -10000 0 0
RELN -0.46 0.32 -10000 0 -0.67 344 344
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.3 0.24 -10000 0 -0.45 348 348
GRIN2A/RELN/LRP8/DAB1/Fyn -0.27 0.24 -10000 0 -0.42 340 340
MAPK8 0.013 0.095 -10000 0 -0.64 10 10
RELN/VLDLR/DAB1 -0.28 0.22 -10000 0 -0.41 352 352
ITGB1 0.027 0.004 -10000 0 -10000 0 0
MAP1B -0.28 0.21 -10000 0 -0.41 342 342
RELN/LRP8 -0.3 0.24 -10000 0 -0.45 347 347
GRIN2B/RELN/LRP8/DAB1/Fyn -0.26 0.22 -10000 0 -0.4 340 340
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 -0.36 321 324
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 0.44 10 -0.6 29 39
LRP8 -0.001 0.14 -10000 0 -0.67 20 20
GSK3B -0.19 0.14 -10000 0 -0.43 32 32
RELN/VLDLR/DAB1/Fyn -0.26 0.21 -10000 0 -0.39 348 348
MAP3K11 0.027 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.21 0.16 -10000 0 -0.31 341 341
CDK5 0.026 0.006 -10000 0 -10000 0 0
MAPT 0.052 0.17 0.82 20 -0.6 3 23
neuron migration -0.26 0.19 -10000 0 -0.39 322 322
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 -0.42 355 355
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 -0.43 18 18
NFATC2 -0.22 0.33 -10000 0 -0.72 124 124
NFATC3 -0.083 0.14 -10000 0 -0.3 68 68
CD40LG -0.63 0.55 -10000 0 -1.1 268 268
ITCH 0.038 0.016 -10000 0 -10000 0 0
CBLB 0.038 0.016 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.46 0.52 -10000 0 -1.2 134 134
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 -0.8 110 110
Jun/NFAT1-c-4/p21SNFT -0.56 0.58 -10000 0 -1.1 232 232
AP-1/NFAT1-c-4 -0.71 0.73 -10000 0 -1.3 251 251
IKZF1 -0.17 0.28 -10000 0 -0.67 81 81
T-helper 2 cell differentiation -0.28 0.33 -10000 0 -0.88 87 87
AP-1/NFAT1 -0.32 0.41 -10000 0 -0.76 195 195
CALM1 0.038 0.012 -10000 0 -10000 0 0
EGR2 -0.73 0.78 -10000 0 -1.5 235 235
EGR3 -0.53 0.67 -10000 0 -1.5 123 123
NFAT1/FOXP3 -0.17 0.28 -10000 0 -0.58 126 126
EGR1 -0.12 0.28 -10000 0 -0.68 101 101
JUN -0.13 0.28 -10000 0 -0.67 107 107
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 -0.61 95 95
FOSL1 0.005 0.055 -10000 0 -0.36 1 1
NFAT1-c-4/MAF/IRF4 -0.49 0.55 -10000 0 -0.99 238 238
DGKA -0.15 0.25 -10000 0 -0.6 82 82
CREM 0.027 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.5 0.54 -10000 0 -1 241 241
CTLA4 -0.19 0.31 -10000 0 -0.71 102 102
NFAT1-c-4 (dimer)/EGR1 -0.56 0.62 -10000 0 -1.2 232 232
NFAT1-c-4 (dimer)/EGR4 -0.52 0.55 -10000 0 -1 241 241
FOS -0.16 0.3 -10000 0 -0.68 125 125
IFNG -0.37 0.5 -10000 0 -1.1 133 133
T cell activation -0.39 0.39 -10000 0 -0.86 166 166
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 0.73 228 -10000 0 228
TNF -0.55 0.54 -10000 0 -1 254 254
FASLG -0.7 0.75 -10000 0 -1.4 249 249
TBX21 -0.02 0.15 -10000 0 -0.68 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 -0.63 76 76
NFAT1-c-4/ICER1 -0.49 0.54 -10000 0 -1 238 238
GATA3 -0.006 0.15 -10000 0 -0.64 25 25
T-helper 1 cell differentiation -0.36 0.48 -10000 0 -1.1 133 133
IL2RA -0.42 0.46 -10000 0 -1 134 134
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.15 0.25 -10000 0 -0.64 71 71
E2F1 -0.013 0.07 -10000 0 -10000 0 0
PPARG 0.016 0.083 -10000 0 -0.67 7 7
SLC3A2 -0.16 0.25 -10000 0 -0.59 90 90
IRF4 -0.047 0.18 -10000 0 -0.66 37 37
PTGS2 -0.6 0.54 0.51 1 -1.1 244 245
CSF2 -0.62 0.52 -10000 0 -1.1 259 259
JunB/Fra1/NFAT1-c-4 -0.46 0.53 -10000 0 -0.97 229 229
IL4 -0.3 0.35 -10000 0 -0.94 86 86
IL5 -0.6 0.52 -10000 0 -1.1 247 247
IL2 -0.4 0.4 -10000 0 -0.89 164 164
IL3 -0.072 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 -0.74 228 228
CDK4 0.24 0.25 0.61 67 -10000 0 67
PTPRK -0.15 0.25 -10000 0 -0.62 76 76
IL8 -0.61 0.53 -10000 0 -1.1 242 242
POU2F1 0.025 0.01 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.23 0.24 -9999 0 -0.4 302 302
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 -0.67 253 253
PDGFR-alpha signaling pathway

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
PDGFRA -0.2 0.32 -10000 0 -0.69 149 149
PDGF/PDGFRA/CRKL -0.14 0.24 -10000 0 -0.5 150 150
positive regulation of JUN kinase activity -0.072 0.2 -10000 0 -0.38 145 145
CRKL 0.02 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.14 0.24 -10000 0 -0.51 149 149
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 -0.51 150 150
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 0.093 -10000 0 -0.67 9 9
SHC/Grb2/SOS1 -0.071 0.2 -10000 0 -0.38 145 145
PDGF/PDGFRA/Shf -0.13 0.24 -10000 0 -0.51 149 149
FOS -0.39 0.52 -10000 0 -1.2 135 135
JUN -0.14 0.22 -10000 0 -0.57 106 106
oligodendrocyte development -0.14 0.25 -10000 0 -0.51 150 150
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:DAG -0.16 0.24 -10000 0 -0.53 147 147
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 0.007 -10000 0 -10000 0 0
PI3K -0.095 0.22 -10000 0 -0.43 149 149
PDGF/PDGFRA/Crk/C3G -0.093 0.22 -10000 0 -0.42 146 146
JAK1 -0.15 0.24 -10000 0 -0.51 149 149
ELK1/SRF -0.12 0.19 0.32 1 -0.41 141 142
SHB 0.025 0.007 -10000 0 -10000 0 0
SHF 0.027 0.008 -10000 0 -10000 0 0
CSNK2A1 0.043 0.024 -10000 0 -10000 0 0
GO:0007205 -0.17 0.25 -10000 0 -0.54 148 148
SOS1 0.027 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.072 0.2 -10000 0 -0.38 145 145
PDGF/PDGFRA/SHB -0.13 0.24 -10000 0 -0.5 149 149
PDGF/PDGFRA/Caveolin-1 -0.14 0.25 -10000 0 -0.51 151 151
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 -0.49 149 149
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 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
ACADVL -0.47 0.48 -10000 0 -0.93 228 228
PCK1 -0.3 0.44 -10000 0 -1.3 63 63
HNF4A -0.61 0.6 -10000 0 -1.2 234 234
KCNJ11 -0.45 0.47 -10000 0 -1 173 173
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 -0.98 183 183
NKX2-1 -0.19 0.19 -10000 0 -0.39 173 173
ACADM -0.47 0.48 -10000 0 -0.94 221 221
TAT -0.18 0.2 -10000 0 -0.55 18 18
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 0.65 7 -0.69 31 38
PKLR -0.46 0.48 -10000 0 -0.98 194 194
APOA1 -0.84 0.83 -10000 0 -1.7 236 236
CPT1C -0.47 0.49 -10000 0 -1 194 194
ALAS1 -0.16 0.19 -10000 0 -0.63 1 1
TFRC -0.23 0.27 -10000 0 -0.88 18 18
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 0.007 -10000 0 -10000 0 0
CPT1A -0.47 0.48 -10000 0 -1 195 195
HMGCS1 -0.47 0.48 -10000 0 -0.99 195 195
NR3C1 0.031 0.012 -10000 0 -10000 0 0
CPT1B -0.47 0.48 -10000 0 -1 191 191
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 -1.2 218 218
CREB1 0.009 0.065 -10000 0 -0.24 16 16
IGFBP1 -0.16 0.18 -10000 0 -10000 0 0
PDX1 -0.18 0.19 -10000 0 -0.61 3 3
UCP2 -0.48 0.48 -10000 0 -1 195 195
ALDOB -0.45 0.47 -10000 0 -1 172 172
AFP -0.016 0.084 -10000 0 -0.4 2 2
BDH1 -0.47 0.48 -10000 0 -0.98 199 199
HADH -0.44 0.47 -10000 0 -1 174 174
F2 -0.58 0.58 -10000 0 -1.2 194 194
HNF1A 0.028 0.007 -10000 0 -10000 0 0
G6PC 0 0.067 -10000 0 -10000 0 0
SLC2A2 -0.22 0.23 -10000 0 -10000 0 0
INS -0.025 0.053 -10000 0 -0.68 3 3
FOXA1 -0.009 0.096 -10000 0 -0.34 21 21
FOXA3 -0.027 0.12 -10000 0 -0.39 18 18
FOXA2 -0.5 0.54 -10000 0 -1.1 202 202
ABCC8 -0.7 0.66 -10000 0 -1.3 255 255
ALB -0.058 0.27 -10000 0 -1.1 30 30
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.092 0.26 -10000 0 -0.67 84 84
GNB1/GNG2 -0.2 0.23 -10000 0 -0.53 115 115
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 -0.52 123 123
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 -0.51 112 112
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 -0.4 302 302
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
GNAS -0.22 0.22 -10000 0 -0.53 121 121
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 -0.54 147 147
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 -0.67 253 253
CDC42 -0.2 0.21 -10000 0 -0.51 116 116
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.14 0.22 -10000 0 -0.4 191 191
regulation of S phase of mitotic cell cycle -0.1 0.16 -10000 0 -0.29 201 201
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 -0.37 196 201
T-DHT/AR -0.2 0.26 -10000 0 -0.5 207 207
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 -0.52 141 152
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 -0.41 180 184
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 116 116
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 -0.004 116 116
HRAS/GTP -0.14 0.2 -10000 0 -0.38 196 196
actin cytoskeleton reorganization 0.037 0.033 -10000 0 -0.36 3 3
SRC 0.026 0.01 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 116 116
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 -0.5 203 203
CREB1 -0.21 0.27 0.42 7 -0.56 149 156
RAC1-CDC42/GTP 0.047 0.035 -10000 0 -0.37 3 3
AR -0.26 0.34 -10000 0 -0.67 207 207
GNB1 0.026 0.006 -10000 0 -10000 0 0
RAF1 -0.14 0.21 0.5 6 -0.38 196 202
RAC1-CDC42/GDP -0.17 0.26 -10000 0 -0.48 202 202
T-DHT/AR/PELP1/Src -0.14 0.22 -10000 0 -0.41 196 196
MAP2K2 -0.14 0.19 0.43 2 -0.37 192 194
T-DHT/AR/PELP1/Src/PI3K -0.1 0.16 -10000 0 -0.3 201 201
GNAZ 0.02 0.012 -10000 0 -10000 0 0
SHBG 0.013 0.093 -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 56 -0.005 67 123
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 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
TGFB2 -0.088 0.21 -10000 0 -0.62 31 31
IHH -0.15 0.31 -10000 0 -0.7 121 121
SHH Np/Cholesterol/GAS1 -0.053 0.16 -10000 0 -0.4 83 83
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 -0.074 0.2 -10000 0 -0.42 110 110
SMO -0.095 0.21 -10000 0 -0.44 118 118
AKT1 -0.016 0.1 -10000 0 -0.61 2 2
ARRB2 0.026 0.007 -10000 0 -10000 0 0
BOC 0.016 0.088 -10000 0 -0.67 8 8
ADRBK1 0.027 0.005 -10000 0 -10000 0 0
heart looping -0.094 0.2 -10000 0 -0.43 118 118
STIL -0.065 0.16 0.27 1 -0.49 14 15
DHH N/PTCH2 -0.051 0.2 -10000 0 -0.51 81 81
DHH N/PTCH1 -0.076 0.19 -10000 0 -0.37 129 129
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 32 32
determination of left/right symmetry -0.094 0.2 -10000 0 -0.43 118 118
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
skeletal system development -0.14 0.3 -10000 0 -1 32 32
IHH N/Hhip -0.29 0.33 -10000 0 -0.59 260 260
DHH N/Hhip -0.17 0.27 -10000 0 -0.51 191 191
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.094 0.2 -10000 0 -0.43 118 118
pancreas development -0.25 0.33 -10000 0 -0.67 190 190
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 -0.094 0.2 -10000 0 -0.43 118 118
SHH Np/Cholesterol/PTCH1 -0.07 0.16 -10000 0 -0.34 108 108
SHH Np/Cholesterol/PTCH2 -0.043 0.15 -10000 0 -0.38 80 80
SHH Np/Cholesterol/Megalin -0.081 0.18 -10000 0 -0.41 107 107
SHH -0.005 0.029 -10000 0 -0.51 1 1
catabolic process -0.093 0.2 -10000 0 -0.4 142 142
SMO/Vitamin D3 -0.075 0.18 -10000 0 -0.38 109 109
SHH Np/Cholesterol/Hhip -0.14 0.2 -10000 0 -0.39 190 190
LRP2 -0.16 0.3 -10000 0 -0.66 132 132
receptor-mediated endocytosis -0.14 0.21 -10000 0 -0.6 42 42
SHH Np/Cholesterol/BOC 0.014 0.056 -10000 0 -0.37 9 9
SHH Np/Cholesterol/CDO -0.095 0.18 -10000 0 -0.38 143 143
mesenchymal cell differentiation 0.14 0.2 0.39 190 -10000 0 190
mol:Vitamin D3 -0.064 0.17 -10000 0 -0.34 108 108
IHH N/PTCH2 -0.17 0.29 -10000 0 -0.53 179 179
CDON -0.18 0.32 -10000 0 -0.67 147 147
IHH N/PTCH1 -0.091 0.21 -10000 0 -0.41 142 142
Megalin/LRPAP1 -0.1 0.24 -10000 0 -0.5 132 132
PTCH2 -0.085 0.26 -10000 0 -0.67 80 80
SHH Np/Cholesterol 0.009 0.023 -10000 0 -0.4 1 1
PTCH1 -0.094 0.2 -10000 0 -0.4 142 142
HHIP -0.25 0.33 -10000 0 -0.67 190 190
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 -0.45 347 347
CaM/Ca2+ 0.02 0.003 -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 -0.42 336 336
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 -0.061 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 -0.3 0.23 -10000 0 -0.45 352 352
YWHAE 0.026 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.21 0.19 0.35 6 -0.5 27 33
MAP1B 0.007 0.002 -10000 0 -10000 0 0
RAC1 0.017 0.005 -10000 0 -10000 0 0
p35/CDK5 -0.24 0.19 -10000 0 -0.37 325 325
RELN -0.46 0.32 -10000 0 -0.67 344 344
PAFAH/LIS1 -0.027 0.15 -10000 0 -0.43 63 63
LIS1/CLIP170 0.031 0.009 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.18 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 -0.36 322 323
LIS1/IQGAP1 0.031 0.009 -10000 0 -10000 0 0
RHOA 0.017 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.016 0.005 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.015 -10000 0 -10000 0 0
PAFAH1B2 0.016 0.084 -10000 0 -0.64 8 8
MAP1B/LIS1/Dynein heavy chain 0.031 0.011 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.2 0.18 0.32 2 -0.55 19 21
LRP8 -0.001 0.14 -10000 0 -0.67 20 20
NDEL1/Katanin 60 -0.21 0.18 0.31 3 -0.54 22 25
P39/CDK5 -0.25 0.19 -10000 0 -0.38 335 335
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.031 0.01 -10000 0 -10000 0 0
CDK5 -0.27 0.19 -10000 0 -0.39 336 336
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 -0.4 332 332
RELN/VLDLR -0.29 0.24 -10000 0 -0.42 355 355
CDC42 0.017 0.006 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.1 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 -0.056 0.2 -10000 0 -0.43 106 106
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.057 0.16 -10000 0 -0.35 103 103
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 -0.055 0.2 -10000 0 -0.43 105 105
NPHS2 -0.005 0.053 -10000 0 -0.74 1 1
mol:IP3 -0.055 0.2 -10000 0 -0.43 105 105
regulation of endocytosis -0.05 0.18 -10000 0 -0.39 104 104
Nephrin/NEPH1/podocin/Cholesterol -0.068 0.2 -10000 0 -0.43 110 110
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 -0.39 104 104
NPHS1 -0.1 0.26 -10000 0 -0.68 84 84
Nephrin/NEPH1/podocin -0.061 0.19 -10000 0 -0.41 108 108
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 -0.077 0.2 0.28 21 -0.41 108 129
cytoskeleton organization -0.081 0.2 -10000 0 -0.45 102 102
Nephrin/NEPH1 -0.071 0.18 -10000 0 -0.4 111 111
Nephrin/NEPH1/ZO-1 -0.069 0.21 -10000 0 -0.45 109 109
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.011 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 -0.76 187 187
PTGS2 -0.31 0.35 -9999 0 -0.73 171 171
JUNB 0.02 0.057 -9999 0 -0.6 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.007 0.025 -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 0.28 -9999 0 -0.68 107 107
mol:Ca2+ -0.008 0.019 -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 -0.49 142 142
FOS -0.16 0.3 -9999 0 -0.68 125 125
IFNG -0.34 0.36 -9999 0 -0.74 186 186
AP-1/NFAT1-c-4 -0.35 0.45 -9999 0 -0.86 178 178
FASLG -0.32 0.35 -9999 0 -0.73 171 171
NFAT1-c-4/ICER1 -0.08 0.17 -9999 0 -0.41 91 91
IL2RA -0.32 0.34 -9999 0 -0.72 172 172
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 83 83
IL4 -0.3 0.32 -9999 0 -0.69 166 166
IL2 0.003 0.071 -9999 0 -1 2 2
IL3 -0.009 0.053 -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 0.025 0.01 -9999 0 -10000 0 0
Endothelins

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
AKT1 -0.03 0.094 -10000 0 -0.47 8 8
PTK2B 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.28 0.47 1 -0.67 76 77
EDN1 -0.004 0.099 -10000 0 -0.56 8 8
EDN3 -0.31 0.35 -10000 0 -0.67 237 237
EDN2 0.011 0.082 -10000 0 -0.67 6 6
HRAS/GDP -0.11 0.23 0.45 3 -0.49 92 95
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.075 0.15 -10000 0 -0.34 90 90
ADCY4 -0.071 0.15 0.35 1 -0.41 66 67
ADCY5 -0.12 0.2 0.35 1 -0.45 113 114
ADCY6 -0.069 0.15 0.35 1 -0.41 65 66
ADCY7 -0.069 0.15 0.35 1 -0.4 66 67
ADCY1 -0.073 0.16 0.35 1 -0.42 67 68
ADCY2 -0.1 0.18 -10000 0 -0.44 92 92
ADCY3 -0.071 0.15 0.35 1 -0.4 70 71
ADCY8 -0.1 0.16 0.35 1 -0.44 69 70
ADCY9 -0.069 0.15 0.35 1 -0.4 66 67
arachidonic acid secretion -0.18 0.32 0.36 11 -0.61 151 162
ETB receptor/Endothelin-1/Gq/GTP -0.084 0.18 -10000 0 -0.37 122 122
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 0.03 0.11 -10000 0 -0.4 8 8
ETA receptor/Endothelin-1/Gs/GTP -0.028 0.18 -10000 0 -0.42 71 71
mol:GTP -0.003 0.009 -10000 0 -10000 0 0
COL3A1 -0.036 0.1 -10000 0 -0.49 8 8
EDNRB 0.015 0.078 -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 0.35 8 -0.51 95 103
SLC9A3 -0.054 0.21 0.37 1 -0.69 37 38
RAF1 -0.16 0.28 0.44 3 -0.54 141 144
JUN -0.28 0.49 0.46 1 -1.1 126 127
JAK2 -0.031 0.098 -10000 0 -0.47 11 11
mol:IP3 -0.1 0.2 -10000 0 -0.4 128 128
ETA receptor/Endothelin-1 0.012 0.13 -10000 0 -0.55 10 10
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 -0.52 238 238
FOS -0.27 0.44 0.61 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 -0.49 54 54
BCAR1 0.026 0.006 -10000 0 -10000 0 0
PRKCB1 -0.11 0.2 -10000 0 -0.41 121 121
GNAQ 0.015 0.022 -10000 0 -10000 0 0
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAL -0.062 0.23 -10000 0 -0.66 65 65
Gs family/GDP -0.15 0.25 0.28 1 -0.52 119 120
ETA receptor/Endothelin-1/Gq/GTP -0.089 0.18 -10000 0 -0.37 118 118
MAPK14 -0.07 0.15 -10000 0 -0.36 71 71
TRPC6 -0.16 0.3 0.47 1 -0.71 76 77
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 -0.35 92 92
ETB receptor/Endothelin-2 0.02 0.087 -10000 0 -0.51 12 12
ETB receptor/Endothelin-3 -0.23 0.28 -10000 0 -0.51 240 240
ETB receptor/Endothelin-1 0.014 0.099 -10000 0 -0.55 11 11
MAPK3 -0.24 0.41 0.38 9 -0.86 134 143
MAPK1 -0.28 0.44 0.6 1 -0.96 136 137
Rac1/GDP -0.11 0.22 0.3 3 -0.48 90 93
cAMP biosynthetic process -0.077 0.18 0.49 9 -0.46 59 68
MAPK8 -0.19 0.36 0.48 1 -0.74 105 106
SRC 0.026 0.008 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.003 0.076 -10000 0 -0.31 17 17
p130Cas/CRK/Src/PYK2 -0.15 0.28 0.39 10 -0.54 133 143
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.22 0.37 1 -0.48 87 88
COL1A2 -0.007 0.11 -10000 0 -0.62 6 6
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.013 0.084 -10000 0 -0.53 7 7
mol:DAG -0.1 0.2 -10000 0 -0.4 128 128
MAP2K2 -0.19 0.34 0.39 12 -0.68 135 147
MAP2K1 -0.2 0.34 0.43 3 -0.68 142 145
EDNRA 0.001 0.073 -10000 0 -0.37 5 5
positive regulation of muscle contraction -0.024 0.079 -10000 0 -0.41 6 6
Gq family/GDP -0.14 0.28 0.38 1 -0.55 131 132
HRAS/GTP -0.14 0.24 0.3 8 -0.5 112 120
PRKCH -0.11 0.2 -10000 0 -0.44 94 94
RAC1 0.026 0.006 -10000 0 -10000 0 0
PRKCA -0.11 0.22 -10000 0 -0.47 100 100
PRKCB -0.11 0.2 -10000 0 -0.45 98 98
PRKCE -0.11 0.2 -10000 0 -0.46 95 95
PRKCD -0.11 0.2 -10000 0 -0.44 94 94
PRKCG -0.1 0.19 -10000 0 -0.43 100 100
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 -0.67 151 161
GNA14 -0.14 0.29 -10000 0 -0.64 120 120
GNA15 0.006 0.052 -10000 0 -0.67 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 0.03 0.11 -10000 0 -0.4 8 8
MMP1 -0.034 0.079 0.93 1 -10000 0 1
IGF1 pathway

Figure S16.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S16.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.027 0.005 -10000 0 -10000 0 0
PTK2 0.026 0.006 -10000 0 -10000 0 0
CRKL -0.1 0.18 -10000 0 -0.36 152 152
GRB2/SOS1/SHC 0.048 0.02 -10000 0 -10000 0 0
HRAS 0.026 0.011 -10000 0 -10000 0 0
IRS1/Crk -0.091 0.19 -10000 0 -0.36 149 149
IGF-1R heterotetramer/IGF1/PTP1B -0.063 0.2 -10000 0 -0.43 107 107
AKT1 -0.089 0.17 -10000 0 -0.36 106 106
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 -0.36 149 149
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.089 0.19 -10000 0 -0.37 153 153
RAF1 -0.068 0.15 0.39 1 -0.54 17 18
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.062 0.19 -10000 0 -0.35 146 146
YWHAZ 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.096 0.2 -10000 0 -0.39 154 154
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
RPS6KB1 -0.088 0.16 -10000 0 -0.36 103 103
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.058 0.14 0.32 6 -0.45 16 22
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
HRAS/GTP -0.07 0.16 -10000 0 -0.35 99 99
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.028 0.17 -10000 0 -0.35 99 99
IGF-1R heterotetramer -0.008 0.058 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.077 0.2 -10000 0 -0.36 153 153
Crk/p130 Cas/Paxillin -0.057 0.19 -10000 0 -0.33 148 148
IGF1R -0.009 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 -0.34 149 149
PI3K -0.065 0.2 -10000 0 -0.35 153 153
apoptosis 0.063 0.14 0.5 15 -0.4 1 16
HRAS/GDP 0.019 0.008 -10000 0 -10000 0 0
PRKCD -0.089 0.19 -10000 0 -0.45 107 107
RAF1/14-3-3 E -0.043 0.14 0.33 3 -0.46 17 20
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 0.2 -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 -0.36 153 153
GRB10 0.026 0.006 -10000 0 -10000 0 0
PTPN11 -0.098 0.19 -10000 0 -0.36 153 153
IRS1 -0.11 0.2 -10000 0 -0.39 154 154
IRS2 -0.098 0.18 -10000 0 -0.36 154 154
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 -0.089 0.19 -10000 0 -0.45 107 107
SHC1 0.025 0.007 -10000 0 -10000 0 0
Glypican 1 network

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
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 -0.51 72 72
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 -0.67 214 214
CRIPTO/GPC1 -0.2 0.27 -9999 0 -0.51 212 212
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 -0.44 209 209
FLT1 0.024 0.032 -9999 0 -0.67 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.047 0.041 -9999 0 -0.43 3 3
SERPINC1 0.019 0.023 -9999 0 -10000 0 0
FYN -0.18 0.23 -9999 0 -0.44 211 211
FGR -0.17 0.22 -9999 0 -0.44 205 205
positive regulation of MAPKKK cascade -0.23 0.26 -9999 0 -0.51 207 207
SLIT2 -0.077 0.25 -9999 0 -0.66 74 74
GPC1/NRG -0.008 0.15 -9999 0 -0.5 42 42
NRG1 -0.033 0.19 -9999 0 -0.66 43 43
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.052 -9999 0 -0.57 3 3
LYN -0.17 0.22 -9999 0 -0.44 210 210
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 -0.44 209 209
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 -0.54 278 278
HCK -0.18 0.22 -9999 0 -0.44 211 211
FGF2 0.027 0.004 -9999 0 -10000 0 0
FGFR1 0.025 0.032 -9999 0 -0.67 1 1
VEGFR1 homodimer 0.024 0.032 -9999 0 -0.67 1 1
TGFBR2 0.023 0.054 -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 -0.44 217 217
neuron differentiation -0.008 0.15 -9999 0 -0.5 42 42
PrPc/Cu2+ 0.019 0.024 -9999 0 -0.51 1 1
APP 0.026 0.006 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.023 0.054 -9999 0 -0.67 3 3
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.52 0.4 -10000 0 -1.1 84 84
STAT6 (cleaved dimer) -0.53 0.41 -10000 0 -1 149 149
IGHG1 -0.18 0.13 -10000 0 -0.38 15 15
IGHG3 -0.5 0.38 -10000 0 -0.92 159 159
AKT1 -0.27 0.28 0.62 2 -0.88 50 52
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 -0.85 68 68
THY1 -0.52 0.4 -10000 0 -1.1 96 96
MYB 0.01 0.1 -10000 0 -0.64 11 11
HMGA1 0.027 0.003 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.35 0.31 -10000 0 -0.87 78 78
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.28 0.28 -10000 0 -0.95 44 44
SP1 0.03 0.011 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
SOCS5 0.041 0.018 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.52 0.41 -10000 0 -1 124 124
SOCS1 -0.36 0.26 -10000 0 -0.73 73 73
SOCS3 -0.32 0.33 0.6 2 -1 56 58
FCER2 -0.56 0.46 -10000 0 -1.1 146 146
PARP14 0.026 0.009 -10000 0 -10000 0 0
CCL17 -0.55 0.42 -10000 0 -1.1 104 104
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.2 -10000 0 -0.72 37 37
T cell proliferation -0.51 0.41 -10000 0 -1.1 93 93
IL4R/JAK1 -0.51 0.4 -10000 0 -1.1 90 90
EGR2 -0.86 0.68 -10000 0 -1.5 236 236
JAK2 -0.033 0.041 -10000 0 -0.39 2 2
JAK3 -0.012 0.066 -10000 0 -10000 0 0
PIK3R1 0.026 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 -1.2 81 81
IL4R -0.55 0.42 -10000 0 -1.2 89 89
PTPN6 0.04 0.012 -10000 0 -10000 0 0
IL13RA2 -0.62 0.53 -10000 0 -1.3 136 136
IL13RA1 -0.031 0.033 -10000 0 -10000 0 0
IRF4 -0.31 0.5 -10000 0 -1.2 98 98
ARG1 -0.13 0.13 -10000 0 -0.73 4 4
CBL -0.33 0.29 -10000 0 -0.83 73 73
GTF3A 0.024 0.018 -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 -1.1 96 96
CD40LG -0.082 0.24 -10000 0 -0.64 78 78
MAPK14 -0.34 0.32 -10000 0 -0.96 67 67
mitosis -0.26 0.26 0.62 2 -0.81 51 53
STAT6 -0.58 0.48 -10000 0 -1.1 147 147
SPI1 0.022 0.035 -10000 0 -10000 0 0
RPS6KB1 -0.25 0.25 0.71 3 -0.77 47 50
STAT6 (dimer) -0.58 0.48 -10000 0 -1.1 147 147
STAT6 (dimer)/PARP14 -0.55 0.44 -10000 0 -1.1 140 140
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 -0.99 51 51
FRAP1 -0.28 0.28 0.62 2 -0.88 51 53
LTA -0.53 0.4 -10000 0 -1.1 106 106
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.57 0.46 1.1 147 -10000 0 147
CCL11 -0.5 0.38 -10000 0 -1.1 82 82
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.28 0.3 -10000 0 -0.99 51 51
IL2RG -0.01 0.14 -10000 0 -0.62 21 21
IL10 -0.53 0.42 -10000 0 -1.2 87 87
IRS1 -0.056 0.22 -10000 0 -0.67 59 59
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 83 83
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.45 0.35 -10000 0 -0.96 93 93
COL1A1 -0.22 0.24 -10000 0 -1 26 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.52 0.41 -10000 0 -1.2 71 71
IL2R gamma/JAK3 -0.021 0.12 -10000 0 -0.5 19 19
TFF3 -1.2 0.58 -10000 0 -1.4 403 403
ALOX15 -0.52 0.4 -10000 0 -1.1 89 89
MYBL1 0.026 0.008 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.45 0.35 -10000 0 -0.94 95 95
SHC1 0.025 0.007 -10000 0 -10000 0 0
CEBPB 0.03 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.28 0.28 -10000 0 -0.98 40 40
mol:PI-3-4-5-P3 -0.27 0.28 0.62 2 -0.88 50 52
PI3K -0.29 0.3 0.67 1 -0.97 50 51
DOK2 0.019 0.052 -10000 0 -0.67 2 2
ETS1 0.039 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.2 0.19 -10000 0 -0.71 32 32
ITGB3 -0.53 0.43 -10000 0 -1.2 88 88
PIGR -0.55 0.45 -10000 0 -1.3 90 90
IGHE 0.047 0.044 0.24 9 -10000 0 9
MAPKKK cascade -0.2 0.19 0.59 1 -0.69 32 33
BCL6 0.026 0.032 -10000 0 -0.67 1 1
OPRM1 -0.53 0.4 -10000 0 -1.1 86 86
RETNLB -0.53 0.4 -10000 0 -1.1 85 85
SELP -0.52 0.41 -10000 0 -1.1 90 90
AICDA -0.5 0.38 -10000 0 -1 116 116
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 0.021 0.055 -10000 0 -0.68 3 3
EFNB1 -0.002 0.085 -10000 0 -0.51 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.11 0.22 -10000 0 -0.4 184 184
Ephrin B2/EPHB1-2 -0.12 0.22 -10000 0 -0.4 182 182
neuron projection morphogenesis -0.12 0.21 -10000 0 -0.38 184 184
Ephrin B1/EPHB1-2/Tiam1 -0.13 0.23 -10000 0 -0.42 186 186
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 0.024 0.11 -10000 0 -0.83 7 7
mol:GDP -0.13 0.23 -10000 0 -0.42 187 187
ITGA2B -0.042 0.21 -10000 0 -0.67 49 49
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 0.026 0.005 -10000 0 -10000 0 0
RGS3 0.025 0.008 -10000 0 -10000 0 0
cell adhesion -0.027 0.16 -10000 0 -0.48 37 37
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 -0.64 11 11
EPHB1 -0.24 0.34 -10000 0 -0.67 189 189
EPHB4 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.033 0.01 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.026 0.18 -10000 0 -0.53 56 56
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 0.38 4 -0.7 11 15
Ephrin B1/EPHB1-2/RGS3 -0.12 0.21 -10000 0 -0.38 186 186
endothelial cell migration -0.006 0.082 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 -0.39 184 184
angiogenesis -0.011 0.094 -10000 0 -0.73 8 8
LCK 0 0.12 -10000 0 -0.9 8 8
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 -0.006 0.053 -10000 0 -0.21 3 3
SVIL -0.003 0.048 -10000 0 -10000 0 0
ZNF318 0.076 0.088 0.21 97 -0.67 1 98
JMJD2C -0.066 0.067 -10000 0 -0.12 285 285
T-DHT/AR/Ubc9 -0.23 0.24 -10000 0 -0.49 210 210
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 0.22 67 -0.65 7 74
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.007 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 -0.002 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 -0.52 219 219
FHL2 -0.13 0.33 -10000 0 -1.2 42 42
RANBP9 -0.002 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 0.047 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.24 0.24 -10000 0 -0.49 219 219
XRCC6 0.028 0.023 -10000 0 -10000 0 0
T-DHT/AR -0.28 0.26 -10000 0 -0.53 235 235
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 0.004 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 -0.22 237 237
KLK3 -0.39 0.65 -10000 0 -1.4 143 143
TMF1 0.017 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 -0.072 143 143
APPL1 0.042 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.22 0.24 -10000 0 -0.49 204 204
AR -0.31 0.34 -10000 0 -0.71 207 207
UBA3 0.012 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 -0.44 211 211
RPS6KA3 -0.003 0.046 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.23 0.24 -10000 0 -0.49 211 211
LATS2 0.041 0.043 -10000 0 -0.67 1 1
T-DHT/AR/PRX1 -0.2 0.22 -10000 0 -0.44 205 205
Cyclin D3/CDK11 p58 0.022 0.005 -10000 0 -10000 0 0
VAV3 -0.005 0.083 -10000 0 -0.68 6 6
KLK2 -0.68 0.55 -10000 0 -1.1 291 291
CASP8 0.031 0.009 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.24 0.27 -10000 0 -0.53 213 213
TMPRSS2 -0.16 0.27 -10000 0 -1.1 31 31
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 -0.079 183 183
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.031 0.091 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.23 0.24 -10000 0 -0.49 212 212
CMTM2 0.029 0.012 -10000 0 -10000 0 0
SNURF -0.014 0.16 -10000 0 -0.65 29 29
ZMIZ1 -0.025 0.056 -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
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.058 0.24 0.29 20 -0.59 72 92
FYN -0.1 0.32 0.46 1 -0.76 79 80
LAT/GRAP2/SLP76 -0.084 0.25 -10000 0 -0.62 78 78
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 -0.063 0.21 0.52 10 -0.46 81 91
B2M 0.027 0.006 -10000 0 -10000 0 0
IKBKG -0.016 0.057 0.14 3 -0.16 34 37
MAP3K8 0.018 0.078 -10000 0 -0.63 7 7
mol:Ca2+ -0.03 0.042 0.092 5 -0.11 100 105
integrin-mediated signaling pathway 0.034 0.01 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.3 0.46 5 -0.72 81 86
TRPV6 -0.1 0.35 0.99 20 -0.68 103 123
CD28 -0.015 0.15 -10000 0 -0.65 25 25
SHC1 -0.1 0.32 0.3 21 -0.75 81 102
receptor internalization -0.13 0.35 -10000 0 -0.66 119 119
PRF1 -0.11 0.33 -10000 0 -0.88 65 65
KRAS 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
COT/AKT1 -0.046 0.17 0.4 6 -0.37 81 87
LAT -0.11 0.31 0.3 4 -0.76 81 85
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.049 0.21 -10000 0 -0.64 53 53
CD3E -0.031 0.19 -10000 0 -0.63 42 42
CD3G -0.097 0.26 -10000 0 -0.65 89 89
RASGRP2 -0.004 0.033 0.094 3 -0.18 12 15
RASGRP1 -0.051 0.22 0.56 11 -0.47 77 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 0.01 -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 49 79
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.049 0.085 -10000 0 -0.25 61 61
PRKCA -0.036 0.12 -10000 0 -0.29 76 76
GRAP2 -0.019 0.15 -10000 0 -0.56 33 33
mol:IP3 -0.033 0.21 0.26 72 -0.44 75 147
EntrezGene:6957 0 0.005 0.045 2 -10000 0 2
TCR/CD3/MHC I/CD8 -0.13 0.35 -10000 0 -0.85 77 77
ORAI1 0.046 0.21 0.7 2 -0.78 16 18
CSK -0.12 0.32 -10000 0 -0.79 79 79
B7 family/CD28 -0.11 0.35 -10000 0 -0.7 104 104
CHUK 0.027 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.14 0.38 -10000 0 -0.89 85 85
PTPN6 -0.12 0.32 0.23 2 -0.78 80 82
VAV1 -0.11 0.31 0.31 1 -0.76 80 81
Monovalent TCR/CD3 -0.12 0.32 -10000 0 -0.61 109 109
CBL 0.027 0.005 -10000 0 -10000 0 0
LCK -0.11 0.33 -10000 0 -0.79 79 79
PAG1 -0.12 0.32 -10000 0 -0.79 78 78
RAP1A 0.027 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.14 0.38 -10000 0 -0.88 86 86
CD80 -0.042 0.21 -10000 0 -0.67 49 49
CD86 0.013 0.076 -10000 0 -0.68 5 5
PDK1/CARD11/BCL10/MALT1 -0.042 0.11 -10000 0 -0.28 69 69
HRAS 0.026 0.011 -10000 0 -10000 0 0
GO:0035030 -0.1 0.26 -10000 0 -0.56 104 104
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 77 89
CSK/PAG1 -0.11 0.31 -10000 0 -0.78 75 75
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 -0.74 79 79
STIM1 0.019 0.16 1.2 2 -0.9 9 11
RAS family/GTP 0.008 0.098 0.23 26 -0.18 47 73
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.14 0.39 -10000 0 -0.72 119 119
mol:DAG -0.06 0.16 0.14 6 -0.4 76 82
RAP1A/GDP 0.008 0.059 0.19 17 -0.065 19 36
PLCG1 0.027 0.005 -10000 0 -10000 0 0
CD247 -0.003 0.13 -10000 0 -0.68 18 18
cytotoxic T cell degranulation -0.1 0.31 -10000 0 -0.79 72 72
RAP1A/GTP -0.001 0.012 -10000 0 -0.067 11 11
mol:PI-3-4-5-P3 -0.084 0.25 0.54 8 -0.57 81 89
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.052 0.26 0.28 66 -0.58 76 142
NRAS 0.027 0.005 -10000 0 -10000 0 0
ZAP70 -0.002 0.13 -10000 0 -0.66 18 18
GRB2/SOS1 0.038 0.011 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.083 0.24 -10000 0 -0.59 77 77
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 0.23 -10000 0 -0.6 73 73
CARD11 -0.019 0.12 -10000 0 -0.67 11 11
PRKCB -0.032 0.12 -10000 0 -0.29 69 69
PRKCE -0.031 0.12 -10000 0 -0.28 73 73
PRKCQ -0.095 0.29 0.59 9 -0.68 78 87
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 0.48 11 -0.39 79 90
IKK complex 0.018 0.13 0.37 27 -0.12 35 62
RAS family/GDP -0.005 0.011 -10000 0 -10000 0 0
MAP3K14 -0.035 0.12 0.27 4 -0.28 73 77
PDPK1 -0.059 0.2 0.53 11 -0.44 81 92
TCR/CD3/MHC I/CD8/Fyn -0.16 0.41 -10000 0 -1 82 82
HIF-1-alpha transcription factor network

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
PKM2 -0.21 0.33 -10000 0 -0.82 53 53
HDAC7 0.028 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.24 0.4 -10000 0 -0.83 103 103
SMAD4 0.028 0.005 -10000 0 -10000 0 0
ID2 -0.2 0.35 0.62 3 -0.87 42 45
AP1 -0.19 0.37 -10000 0 -0.72 149 149
ABCG2 -0.2 0.35 0.61 1 -0.87 48 49
HIF1A -0.021 0.073 -10000 0 -0.35 1 1
TFF3 -0.49 0.43 0.62 3 -0.95 152 155
GATA2 0.028 0.01 -10000 0 -10000 0 0
AKT1 -0.054 0.11 -10000 0 -0.29 8 8
response to hypoxia -0.071 0.11 -10000 0 -0.23 95 95
MCL1 -0.19 0.34 0.62 2 -0.86 42 44
NDRG1 -0.2 0.34 0.61 1 -0.86 44 45
SERPINE1 -0.2 0.34 0.61 1 -0.87 44 45
FECH -0.2 0.35 0.62 3 -0.86 43 46
FURIN -0.2 0.35 0.62 3 -0.85 46 49
NCOA2 -0.036 0.2 -10000 0 -0.67 45 45
EP300 -0.11 0.18 -10000 0 -0.36 139 139
HMOX1 -0.21 0.33 0.64 1 -0.86 44 45
BHLHE40 -0.2 0.35 0.62 2 -0.85 48 50
BHLHE41 -0.2 0.35 0.61 1 -0.87 43 44
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.029 0.1 -10000 0 -10000 0 0
ENG 0.01 0.091 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 -0.88 45 47
CXCR4 -0.2 0.35 0.62 3 -0.84 48 51
TF -0.24 0.4 0.62 2 -0.95 72 74
CITED2 -0.22 0.39 0.62 2 -0.95 61 63
HIF1A/ARNT -0.22 0.38 -10000 0 -0.95 44 44
LDHA -0.034 0.11 -10000 0 -0.65 10 10
ETS1 -0.2 0.35 0.62 2 -0.87 42 44
PGK1 -0.2 0.34 0.61 1 -0.86 44 45
NOS2 -0.2 0.35 0.62 2 -0.86 45 47
ITGB2 -0.2 0.35 0.62 3 -0.86 46 49
ALDOA -0.2 0.34 0.61 1 -0.86 44 45
Cbp/p300/CITED2 -0.3 0.46 -10000 0 -1 105 105
FOS -0.15 0.3 -10000 0 -0.67 125 125
HK2 -0.2 0.35 0.62 2 -0.87 44 46
SP1 0.032 0.017 -10000 0 -10000 0 0
GCK -0.4 0.64 -10000 0 -1.4 138 138
HK1 -0.2 0.35 0.62 3 -0.85 46 49
NPM1 -0.2 0.34 0.61 1 -0.87 41 42
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 -0.86 44 46
SMAD3 0.028 0.004 -10000 0 -10000 0 0
EDN1 -0.19 0.29 0.49 1 -0.71 69 70
IGFBP1 -0.2 0.34 0.61 1 -0.87 42 43
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 0.45 0.62 2 -0.95 124 126
CXCL12 -0.24 0.4 0.62 3 -0.97 65 68
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 -0.85 46 49
EGLN3 -0.21 0.35 -10000 0 -0.87 51 51
CA9 -0.2 0.35 0.61 1 -0.85 49 50
TERT -0.2 0.34 -10000 0 -0.86 44 44
ENO1 -0.2 0.35 0.62 2 -0.85 46 48
PFKL -0.2 0.35 0.62 3 -0.87 41 44
NCOA1 0.027 0.005 -10000 0 -10000 0 0
ADM -0.21 0.35 0.62 3 -0.86 48 51
ARNT -0.016 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 53 53
SLC2A1 -0.2 0.35 -10000 0 -0.73 85 85
LEP -0.2 0.34 0.61 1 -0.87 43 44
HIF1A/ARNT/Cbp/p300 -0.26 0.41 -10000 0 -0.85 105 105
EPO -0.14 0.28 -10000 0 -0.85 26 26
CREBBP -0.082 0.17 -10000 0 -0.33 130 130
HIF1A/ARNT/Cbp/p300/HDAC7 -0.23 0.4 -10000 0 -0.85 91 91
PFKFB3 -0.2 0.35 0.62 3 -0.85 46 49
NT5E -0.2 0.35 0.62 2 -0.87 46 48
BMP receptor signaling

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
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 -0.55 163 163
SMAD4 0.027 0.005 -10000 0 -10000 0 0
SMAD5 -0.084 0.17 -10000 0 -0.31 157 157
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 0.041 -10000 0 -10000 0 0
CER1 -0.014 0.009 -10000 0 -10000 0 0
BMP2-4/CER1 0.014 0.11 -10000 0 -0.44 29 29
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 0.026 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 -0.087 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 0.026 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 0.31 3 -0.42 31 34
MAPK1 0.02 0.012 -10000 0 -10000 0 0
TAK1/TAB family -0.054 0.15 -10000 0 -0.42 30 30
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 -0.48 2 3
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 -0.45 0.32 -10000 0 -0.66 343 343
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 -0.46 333 333
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 -0.52 162 162
SMAD1/SMAD6 -0.027 0.096 -10000 0 -0.62 1 1
TAK1/SMAD6 0.038 0.01 -10000 0 -10000 0 0
BMP7 0.027 0.005 -10000 0 -10000 0 0
BMP6 0.026 0.014 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.057 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 0.038 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 0.098 -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 -0.45 37 37
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 -0.072 0.21 -10000 0 -0.38 158 158
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 0.54 -10000 0 -1.3 78 78
IL23A -0.2 0.55 -10000 0 -1.3 83 83
NF kappa B1 p50/RelA/I kappa B alpha -0.16 0.54 -10000 0 -1.2 80 80
positive regulation of T cell mediated cytotoxicity -0.22 0.61 -10000 0 -1.4 86 86
ITGA3 -0.17 0.5 -10000 0 -1.2 76 76
IL17F -0.095 0.33 0.64 2 -0.74 75 77
IL12B 0.003 0.097 -10000 0 -0.7 7 7
STAT1 (dimer) -0.2 0.58 -10000 0 -1.3 85 85
CD4 -0.17 0.49 -10000 0 -1.2 75 75
IL23 -0.19 0.53 -10000 0 -1.2 83 83
IL23R 0.005 0.1 -10000 0 -0.82 2 2
IL1B -0.21 0.57 -10000 0 -1.4 79 79
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 0.098 -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 86 86
natural killer cell activation 0.001 0.009 -10000 0 -0.046 2 2
JAK2 0.016 0.051 -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 -0.19 0.52 -10000 0 -1.2 82 82
T cell proliferation -0.22 0.61 -10000 0 -1.4 86 86
NFKBIA 0.027 0.006 -10000 0 -10000 0 0
IL17A -0.051 0.27 -10000 0 -0.58 63 63
PI3K -0.18 0.55 -10000 0 -1.3 78 78
IFNG -0.015 0.053 0.12 1 -0.13 67 68
STAT3 (dimer) -0.16 0.51 -10000 0 -1.2 77 77
IL18R1 -0.002 0.096 -10000 0 -0.59 10 10
IL23/IL23R/JAK2/TYK2/SOCS3 -0.089 0.34 -10000 0 -0.81 62 62
IL18/IL18R -0.004 0.15 -10000 0 -0.49 35 35
macrophage activation -0.008 0.021 -10000 0 -0.045 79 79
TNF -0.24 0.6 -10000 0 -1.4 95 95
STAT3/STAT4 -0.19 0.55 -10000 0 -1.3 80 80
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 74 74
STAT5A (dimer) -0.2 0.57 -10000 0 -1.3 83 83
STAT1 0.023 0.024 -10000 0 -10000 0 0
SOCS3 -0.001 0.13 -10000 0 -0.67 19 19
CXCL9 -0.26 0.62 -10000 0 -1.4 110 110
MPO -0.17 0.5 -10000 0 -1.2 79 79
positive regulation of humoral immune response -0.22 0.61 -10000 0 -1.4 86 86
IL23/IL23R/JAK2/TYK2 -0.26 0.74 -10000 0 -1.7 85 85
IL6 -0.27 0.62 -10000 0 -1.3 113 113
STAT5A 0.026 0.007 -10000 0 -10000 0 0
IL2 0.003 0.029 -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 86 86
keratinocyte proliferation -0.22 0.61 -10000 0 -1.4 86 86
NOS2 -0.17 0.49 -10000 0 -1.2 75 75
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.084 0.087 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 -0.76 43 43
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 0.33 56 -0.39 5 61
PRL -0.062 0.1 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.18 0.29 0.54 148 -0.45 21 169
RELA -0.025 0.098 -10000 0 -0.28 21 21
FGG 0.16 0.2 0.47 105 -10000 0 105
GR beta/TIF2 0.072 0.2 0.33 73 -0.45 45 118
IFNG -0.36 0.48 -10000 0 -1.1 126 126
apoptosis -0.015 0.23 0.5 38 -0.53 20 58
CREB1 0.026 0.014 -10000 0 -10000 0 0
histone acetylation -0.074 0.16 -10000 0 -0.47 46 46
BGLAP -0.076 0.13 -10000 0 -0.49 13 13
GR/PKAc 0.11 0.1 0.36 25 -0.34 1 26
NF kappa B1 p50/RelA -0.043 0.17 -10000 0 -0.4 57 57
SMARCD1 0.026 0.018 -10000 0 -10000 0 0
MDM2 0.084 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 -0.56 17 17
GSK3B 0.025 0.018 -10000 0 -10000 0 0
NR1I3 0.004 0.23 0.51 34 -0.69 5 39
CSN2 0.13 0.16 0.39 90 -10000 0 90
BRG1/BAF155/BAF170/BAF60A 0.063 0.053 -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 0.34 45 -0.37 12 57
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.12 0.4 0.48 30 -0.83 104 134
JUN -0.24 0.27 -10000 0 -0.57 163 163
IL4 -0.099 0.16 -10000 0 -0.67 16 16
CDK5R1 0.025 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 -0.68 148 148
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.11 0.35 37 -0.38 4 41
cortisol/GR alpha (monomer) 0.26 0.3 0.64 151 -10000 0 151
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 -0.78 215 215
AFP -0.17 0.21 -10000 0 -0.66 30 30
SUV420H1 0.027 0.005 -10000 0 -10000 0 0
IRF1 0.14 0.14 0.46 43 -10000 0 43
TP53 0.041 0.015 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
KRT17 -0.29 0.34 -10000 0 -0.72 133 133
KRT14 -0.084 0.12 -10000 0 -0.51 4 4
TBP 0.034 0.007 -10000 0 -10000 0 0
CREBBP 0.035 0.046 -10000 0 -0.29 1 1
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 -0.78 216 216
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 -0.38 0.49 -10000 0 -1.1 128 128
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 -0.094 0.14 -10000 0 -0.52 14 14
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.093 0.12 0.36 31 -10000 0 31
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 -0.62 77 77
NFKB1 -0.024 0.096 -10000 0 -0.25 33 33
MAPK8 -0.14 0.18 -10000 0 -0.46 83 83
MAPK9 0.027 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.019 0.24 0.5 35 -0.55 21 56
BAX 0.04 0.093 0.85 5 -10000 0 5
POMC -0.45 0.63 -10000 0 -1.2 160 160
EP300 0.026 0.044 -10000 0 -0.29 1 1
cortisol/GR alpha (dimer)/p53 0.23 0.25 0.57 139 -10000 0 139
proteasomal ubiquitin-dependent protein catabolic process 0.08 0.13 0.34 79 -10000 0 79
SGK1 0.012 0.21 0.51 1 -1.3 10 11
IL13 -0.21 0.25 -10000 0 -0.73 53 53
IL6 -0.28 0.47 -10000 0 -1.1 103 103
PRKACG -0.009 0.016 -10000 0 -10000 0 0
IL5 -0.18 0.21 -10000 0 -0.7 32 32
IL2 -0.25 0.28 -10000 0 -0.65 117 117
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 -0.17 0.29 -10000 0 -0.74 68 68
CDK5R1/CDK5 0.038 0.02 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.002 0.14 -10000 0 -0.38 25 25
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.53 141 -10000 0 141
SMARCA4 0.024 0.018 -10000 0 -10000 0 0
chromatin remodeling 0.14 0.15 0.39 84 -0.44 1 85
NF kappa B1 p50/RelA/Cbp -0.006 0.15 -10000 0 -0.43 23 23
JUN (dimer) -0.24 0.27 -10000 0 -0.57 163 163
YWHAH 0.02 0.012 -10000 0 -10000 0 0
VIPR1 -0.21 0.36 -10000 0 -0.88 102 102
NR3C1 0.16 0.19 0.45 106 -10000 0 106
NR4A1 -0.26 0.36 -10000 0 -0.66 212 212
TIF2/SUV420H1 -0.011 0.16 -10000 0 -0.51 45 45
MAPKKK cascade -0.015 0.23 0.5 38 -0.53 20 58
cortisol/GR alpha (dimer)/Src-1 0.23 0.25 0.55 152 -10000 0 152
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 93 93
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.14 0.15 0.39 83 -0.44 1 84
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.23 0.23 0.53 141 -10000 0 141
mol:cortisol 0.14 0.19 0.38 150 -10000 0 150
MMP1 -0.1 0.14 -10000 0 -0.87 10 10
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 -0.044 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 0.18 18 -10000 0 18
ARRB1 0.025 0.032 -10000 0 -0.67 1 1
FBXO8 0.027 0.004 -10000 0 -10000 0 0
TSHR 0.024 0.045 -10000 0 -0.67 2 2
EGF -0.075 0.24 -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 -0.31 113 118
mol:PI-3-4-5-P3 0 0 0.002 11 -0.001 75 86
ITGA2B -0.042 0.21 -10000 0 -0.67 49 49
ARF6 0.027 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.061 0.025 -10000 0 -10000 0 0
ADAP1 0.026 0.006 -10000 0 -10000 0 0
KIF13B 0.027 0.005 -10000 0 -10000 0 0
HGF/MET -0.078 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 76 76
ADRB2 0.011 0.1 -10000 0 -0.67 11 11
receptor agonist activity 0 0 0.001 18 0 138 156
actin filament binding 0 0 0.002 15 -0.001 140 155
SRC 0.026 0.008 -10000 0 -10000 0 0
ITGB3 0.011 0.1 -10000 0 -0.64 11 11
GNAQ 0.025 0.008 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.004 17 -0.001 70 87
ARF6/GDP -0.006 0.091 0.24 2 -0.46 9 11
ARF6/GDP/GULP/ACAP1 -0.14 0.19 -10000 0 -0.42 108 108
alphaIIb/beta3 Integrin/paxillin/GIT1 0.011 0.16 -10000 0 -0.42 56 56
ACAP1 0.018 0.045 -10000 0 -0.52 2 2
ACAP2 0.027 0.004 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 -0.052 0.19 -10000 0 -0.56 62 62
EFNA1 0.025 0.007 -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 22 0 98 120
endosomal lumen acidification 0 0 0.002 6 -0.001 147 153
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 12 22
MET -0.03 0.073 -10000 0 -10000 0 0
GNA14 -0.13 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 -0.001 108 123
GNA11 0.014 0.084 -10000 0 -0.64 8 8
LHCGR -0.077 0.23 -10000 0 -0.67 62 62
AGTR1 -0.26 0.34 -10000 0 -0.67 202 202
desensitization of G-protein coupled receptor protein signaling pathway -0.051 0.19 -10000 0 -0.56 62 62
IPCEF1/ARNO -0.035 0.18 -10000 0 -0.75 13 13
alphaIIb/beta3 Integrin -0.026 0.18 -10000 0 -0.53 56 56
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.029 0.14 -10000 0 -0.36 51 51
TBX21 -0.12 0.43 -10000 0 -1.2 58 58
B2M 0.023 0.017 -10000 0 -10000 0 0
TYK2 0.019 0.03 -10000 0 -10000 0 0
IL12RB1 0 0.088 -10000 0 -0.64 6 6
GADD45B -0.095 0.39 -10000 0 -1 56 56
IL12RB2 -0.003 0.13 -10000 0 -0.66 17 17
GADD45G -0.091 0.36 -10000 0 -0.98 50 50
natural killer cell activation 0.001 0.02 0.047 10 -0.04 35 45
RELB 0.025 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 -0.004 0.01 -10000 0 -0.022 105 105
FASLG -0.14 0.46 -10000 0 -1.2 62 62
NF kappa B2 p52/RelB -0.1 0.38 -10000 0 -0.97 63 63
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 -0.029 138 138
CD3D -0.063 0.2 -10000 0 -0.64 53 53
CD3E -0.043 0.18 -10000 0 -0.62 42 42
CD3G -0.11 0.26 -10000 0 -0.66 89 89
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 62 62
HLA-A -0.001 0.01 -10000 0 -0.036 30 30
IL18/IL18R 0.027 0.16 -10000 0 -0.49 36 36
NOS2 -0.087 0.35 -10000 0 -1 47 47
IL12/IL12R/TYK2/JAK2/SPHK2 -0.029 0.14 -10000 0 -0.36 49 49
IL1R1 -0.1 0.38 -10000 0 -1.1 48 48
IL4 0 0.034 -10000 0 -10000 0 0
JAK2 0.018 0.039 -10000 0 -0.38 2 2
EntrezGene:6957 -0.006 0.014 -10000 0 -0.027 132 132
TCR/CD3/MHC I/CD8 -0.21 0.49 -10000 0 -1.1 97 97
RAB7A -0.057 0.3 -10000 0 -0.76 53 53
lysosomal transport -0.051 0.28 -10000 0 -0.71 53 53
FOS -0.36 0.6 -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 -0.95 79 79
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 -0.43 158 158
IL2/IL2R -0.007 0.17 -10000 0 -0.54 37 37
MAPK14 -0.084 0.37 -10000 0 -0.93 60 60
CCR5 -0.095 0.4 -10000 0 -1.1 49 49
IL1B -0.026 0.18 -10000 0 -0.7 33 33
STAT6 -0.007 0.11 -10000 0 -0.46 5 5
STAT4 0.004 0.098 -10000 0 -0.59 11 11
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.023 0.024 -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 -0.65 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 -0.071 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 -0.015 0.13 -10000 0 -0.68 18 18
IL2 -0.003 0.02 -10000 0 -10000 0 0
SPHK2 0.025 0.007 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.055 0.22 -10000 0 -0.68 53 53
IL12/IL12R/TYK2/JAK2 -0.14 0.5 -10000 0 -1.2 65 65
MAP2K3 -0.085 0.37 -10000 0 -0.93 59 59
RIPK2 0.027 0.005 -10000 0 -10000 0 0
MAP2K6 -0.092 0.38 -10000 0 -0.93 63 63
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.005 0.011 -10000 0 -0.026 114 114
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 -0.8 88 88
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 0.004 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 68 68
ATF2 -0.088 0.34 0.44 1 -0.82 64 65
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.083 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 -0.35 33 33
ATF2/c-Jun -0.2 0.36 -10000 0 -0.81 120 120
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 -0.024 0.15 -10000 0 -0.51 32 32
CEBPB -0.019 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 -0.8 120 120
PPARGC1A -0.22 0.25 -10000 0 -0.45 255 255
USF1 -0.023 0.12 -10000 0 -0.41 37 37
RAB5/GDP/GDI1 -0.035 0.1 -10000 0 -0.35 23 23
NOS2 -0.027 0.12 -10000 0 -0.49 12 12
DDIT3 -0.019 0.11 -10000 0 -0.41 32 32
RAB5A 0.027 0.004 -10000 0 -10000 0 0
HSPB1 -0.014 0.092 0.37 2 -0.37 19 21
p38alpha-beta/HBP1 -0.005 0.12 -10000 0 -0.42 26 26
CREB1 -0.053 0.16 -10000 0 -0.48 40 40
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 49 49
GDI1 -0.018 0.12 -10000 0 -0.43 31 31
TP53 -0.03 0.13 -10000 0 -0.5 31 31
RPS6KA5 -0.061 0.18 -10000 0 -0.45 77 77
ESR1 -0.05 0.19 -10000 0 -0.56 48 48
HBP1 0.026 0.006 -10000 0 -10000 0 0
MEF2C -0.018 0.11 -10000 0 -0.41 33 33
MEF2A -0.024 0.12 -10000 0 -0.42 38 38
EIF4EBP1 -0.053 0.15 -10000 0 -0.46 41 41
KRT19 -0.051 0.16 -10000 0 -0.5 43 43
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 -0.47 38 38
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 S29.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.005 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 -0.23 5 29
EGF -0.075 0.24 -10000 0 -0.67 72 72
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.021 0.085 0.36 14 -0.5 2 16
mol:Ca2+ -0.014 0.15 0.38 19 -0.3 69 88
LYN 0.02 0.084 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 -0.014 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 -0.031 0.12 0.27 1 -0.59 12 13
G beta5/gamma2 -0.042 0.089 -10000 0 -0.25 67 67
PRKCH -0.02 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 -0.032 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 -0.67 137 137
mol:IP3 -0.024 0.18 0.43 16 -0.38 69 85
cell morphogenesis 0.035 0.007 -10000 0 -10000 0 0
PLCB2 -0.045 0.22 0.45 12 -0.52 69 81
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.076 0.17 0.36 10 -0.33 140 150
mol:PDG2 0 0.001 -10000 0 -10000 0 0
HCK 0.015 0.08 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 -0.041 0.23 0.48 15 -0.53 68 83
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 -0.68 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.031 0.033 -10000 0 -0.36 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.032 0.081 -10000 0 -0.67 2 2
MAPK14 -0.003 0.12 0.34 22 -0.23 61 83
TGM2/GTP -0.04 0.18 0.34 6 -0.43 63 69
MAPK11 -0.006 0.13 0.36 22 -0.23 58 80
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 0.42 21 -0.39 68 89
RAB11/GDP 0.027 0.006 -10000 0 -10000 0 0
ICAM1 -0.013 0.14 0.36 22 -0.29 69 91
cAMP biosynthetic process -0.025 0.17 0.43 16 -0.36 64 80
Gq family/GTP/EBP50 -0.046 0.12 0.24 2 -0.23 120 122
actin cytoskeleton reorganization 0.035 0.007 -10000 0 -10000 0 0
SRC 0.018 0.079 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 0.37 19 -0.3 69 88
TP beta/Gq family/GDP/G beta5/gamma2 -0.031 0.12 0.27 1 -0.59 12 13
platelet activation -0.001 0.17 0.45 24 -0.3 66 90
PGI2/IP 0.015 0.047 -10000 0 -0.51 4 4
PRKACA 0.005 0.078 -10000 0 -0.35 21 21
Gq family/GDP/G beta5/gamma2 -0.032 0.12 0.28 1 -0.54 13 14
TXA2/TP beta/beta Arrestin2 0.006 0.1 -10000 0 -0.54 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 -0.04 0.22 0.5 14 -0.49 65 79
Gq family/GTP -0.065 0.13 0.22 2 -0.27 137 139
YES1 0.022 0.088 0.37 15 -0.5 2 17
GNAI2/GTP 0.009 0.069 -10000 0 -0.6 2 2
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 -0.093 0.21 -10000 0 -0.43 136 136
RhoA/GDP 0.027 0.004 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.04 0.091 -10000 0 -0.8 2 2
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 0.43 18 -0.38 70 88
PRKCB -0.023 0.17 0.42 19 -0.37 68 87
PRKCE -0.027 0.16 0.37 12 -0.37 69 81
PRKCD -0.025 0.17 0.43 13 -0.38 69 82
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 -0.37 9 9
PRKCQ -0.024 0.17 0.4 15 -0.36 69 84
MAPKKK cascade -0.033 0.2 0.46 16 -0.46 68 84
SELE -0.026 0.18 0.35 22 -0.42 69 91
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 -0.13 0.29 -10000 0 -0.64 120 120
chemotaxis -0.048 0.26 0.51 15 -0.61 69 84
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 S30.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC2 0.028 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.045 0.042 -10000 0 -0.82 1 1
forebrain development -0.3 0.28 0.37 3 -0.53 251 254
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 0.015 0.034 -10000 0 -0.67 1 1
ARRB2 0.021 0.008 -10000 0 -10000 0 0
GLI3/SPOP 0.036 0.075 -10000 0 -0.37 3 3
mol:GTP -0.002 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.003 -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 -0.49 136 136
SAP30 0.026 0.032 -10000 0 -0.67 1 1
mol:GDP 0.015 0.034 -10000 0 -0.67 1 1
MIM/GLI2A -0.031 0.067 -10000 0 -10000 0 0
IFT88 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.025 0.006 -10000 0 -10000 0 0
GLI2 0 0.079 0.28 2 -0.33 12 14
GLI3 0.027 0.078 0.28 3 -0.36 5 8
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
SAP18 0.026 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 -0.43 3 3
GLI2/Su(fu) 0.01 0.075 -10000 0 -0.39 6 6
FOXA2 -0.58 0.62 -10000 0 -1.2 244 244
neural tube patterning -0.3 0.28 0.37 3 -0.53 251 254
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 -0.53 251 254
SUFU 0.018 0.016 -10000 0 -0.24 1 1
LGALS3 -0.023 0.077 -10000 0 -0.67 1 1
catabolic process 0.032 0.1 0.29 1 -0.44 8 9
GLI3A/CBP -0.17 0.2 -10000 0 -0.38 245 245
KIF3A 0.026 0.006 -10000 0 -10000 0 0
GLI1 -0.3 0.28 0.37 3 -0.54 251 254
RAB23 0.022 0.063 -10000 0 -0.67 4 4
CSNK1A1 0.026 0.006 -10000 0 -10000 0 0
IFT172 0.027 0.005 -10000 0 -10000 0 0
RBBP7 0.026 0.008 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.019 0.052 -10000 0 -0.33 2 2
GNAZ 0.018 0.012 -10000 0 -10000 0 0
RBBP4 0.024 0.045 -10000 0 -0.67 2 2
CSNK1G1 0.027 0.004 -10000 0 -10000 0 0
PIAS1 0.027 0.004 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GLI2/SPOP 0.011 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 -0.34 4 4
PTCH1 -0.27 0.26 0.58 2 -0.59 139 141
MIM/GLI1 -0.42 0.37 0.34 1 -0.68 285 286
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
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.033 0.17 -10000 0 -0.44 71 71
cell-cell adhesion 0.11 0.16 0.38 6 -10000 0 6
Ephrin B/EPHB2/RasGAP 0.065 0.06 -10000 0 -0.38 7 7
ITSN1 0.026 0.005 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
SHC1 0.025 0.007 -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 -0.43 186 186
HRAS/GDP -0.079 0.16 -10000 0 -0.42 3 3
Ephrin B/EPHB1/GRB7 -0.099 0.23 -10000 0 -0.4 179 179
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 -0.097 0.22 -10000 0 -0.38 180 180
endothelial cell migration 0.052 0.037 -10000 0 -0.37 3 3
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.001 0.056 -10000 0 -10000 0 0
PAK1 0.024 0.074 0.47 5 -0.35 7 12
HRAS 0.026 0.011 -10000 0 -10000 0 0
RRAS 0.02 0.067 0.44 4 -0.36 6 10
DNM1 0.005 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 -0.38 6 6
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.085 0.16 -10000 0 -0.42 18 18
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPHB2 0.022 0.054 -10000 0 -0.67 3 3
EPHB3 -0.067 0.075 -10000 0 -10000 0 0
EPHB1 -0.24 0.34 -10000 0 -0.67 189 189
EPHB4 0.026 0.006 -10000 0 -10000 0 0
mol:GDP -0.071 0.13 -10000 0 -0.38 10 10
Ephrin B/EPHB2 0.051 0.056 -10000 0 -0.38 7 7
Ephrin B/EPHB3 0.058 0.055 -10000 0 -0.43 4 4
JNK cascade -0.12 0.19 -10000 0 -0.38 177 177
Ephrin B/EPHB1 -0.11 0.21 -10000 0 -0.38 180 180
RAP1/GDP -0.046 0.14 -10000 0 -0.41 2 2
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 -0.4 182 182
RAP1B 0.027 0.005 -10000 0 -10000 0 0
RAP1A 0.027 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.085 0.18 -10000 0 -0.45 5 5
Rap1/GTP -0.1 0.17 -10000 0 -0.44 7 7
axon guidance -0.033 0.17 -10000 0 -0.44 71 71
MAPK3 -0.081 0.14 -10000 0 -0.46 9 9
MAPK1 -0.079 0.13 -10000 0 -0.44 10 10
Rac1/GDP -0.058 0.13 -10000 0 -0.38 5 5
actin cytoskeleton reorganization -0.079 0.12 -10000 0 -0.34 3 3
CDC42/GDP -0.055 0.14 0.4 2 -0.38 5 7
PI3K 0.057 0.038 -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 -0.36 3 3
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.1 0.16 -10000 0 -0.42 7 7
PTK2 0.043 0.098 0.67 10 -10000 0 10
MAP4K4 -0.12 0.19 -10000 0 -0.38 177 177
SRC 0.026 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 -10000 0 5
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 -0.4 177 177
cell migration -0.083 0.18 0.58 4 -0.49 12 16
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 -0.023 0.13 0.47 3 -0.38 44 47
HRAS/GTP -0.092 0.19 -10000 0 -0.41 11 11
Ephrin B1/EPHB1-2 -0.12 0.22 -10000 0 -0.4 177 177
cell adhesion mediated by integrin -0.007 0.073 0.39 4 -0.52 4 8
RAC1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP -0.097 0.2 -10000 0 -0.36 175 175
RAC1-CDC42/GTP -0.14 0.16 -10000 0 -0.37 127 127
RASA1 0.027 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.048 0.14 -10000 0 -0.4 2 2
ruffle organization -0.1 0.18 0.57 5 -0.48 1 6
NCK1 0.027 0.003 -10000 0 -10000 0 0
receptor internalization 0.002 0.085 0.41 3 -0.39 11 14
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 2 2
Rac1/GTP -0.11 0.17 -10000 0 -0.4 6 6
Ephrin B/EPHB1/Src/Paxillin -0.091 0.16 -10000 0 -0.3 182 182
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 0.034 -9999 0 -0.67 1 1
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.075 0.24 -9999 0 -0.67 72 72
EGF/EGFR dimer/SHC -0.024 0.17 -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 0.007 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.15 -9999 0 -0.36 70 70
FRAP1 -0.051 0.13 -9999 0 -0.36 70 70
EGF/EGFR dimer -0.044 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
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.1 0.22 -10000 0 -0.51 65 65
MAP3K8 0.015 0.079 -10000 0 -0.63 7 7
FOS -0.075 0.17 0.3 2 -0.44 59 61
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 0.035 0.031 -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 -0.099 0.2 -10000 0 -0.41 121 121
RAF1 -0.01 0.11 -10000 0 -0.52 21 21
KRAS 0.026 0.005 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.003 0.19 0.6 5 -0.65 10 15
CRP 0.006 0.2 0.59 9 -0.67 10 19
cell cycle arrest -0.011 0.2 0.75 1 -0.66 23 24
TIMP1 -0.036 0.22 0.6 3 -0.7 21 24
IL6ST -0.064 0.24 -10000 0 -0.67 66 66
Rac1/GDP -0.041 0.2 0.31 1 -0.55 42 43
AP1 -0.11 0.27 -10000 0 -0.6 92 92
GAB2 0.027 0.005 -10000 0 -10000 0 0
TNFSF11 -0.008 0.19 0.63 4 -0.68 8 12
HSP90B1 0.043 0.052 -10000 0 -0.64 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 -0.082 0.24 -10000 0 -0.71 46 46
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 -10000 0 -0.63 50 50
mol:GTP 0 0.003 -10000 0 -10000 0 0
MAP2K4 -0.028 0.19 0.35 3 -0.58 29 32
MITF -0.063 0.21 -10000 0 -0.58 44 44
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 -0.49 6 6
STAT3 -0.021 0.21 0.76 1 -0.7 24 25
STAT1 0.01 0.097 -10000 0 -0.92 5 5
CEBPD 0.001 0.19 0.64 2 -0.63 13 15
PIK3CA 0.024 0.054 -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 -0.047 0.2 -10000 0 -0.57 40 40
MAPK11 -0.084 0.23 -10000 0 -0.72 43 43
STAT3 (dimer)/FOXO1 0.019 0.16 -10000 0 -0.54 15 15
GRB2/SOS1/GAB family -0.025 0.2 -10000 0 -0.61 26 26
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.068 0.21 -10000 0 -0.46 72 72
GRB2 0.026 0.007 -10000 0 -10000 0 0
JAK2 0.024 0.025 -10000 0 -0.36 2 2
LBP 0.009 0.18 0.61 7 -0.56 6 13
PIK3R1 0.027 0.006 -10000 0 -10000 0 0
JAK1 0.027 0.013 -10000 0 -10000 0 0
MYC -0.012 0.24 0.63 3 -1 15 18
FGG -0.006 0.19 0.68 3 -0.67 10 13
macrophage differentiation -0.011 0.2 0.75 1 -0.66 23 24
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.064 0.25 -10000 0 -0.46 128 128
JUNB -0.001 0.2 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 -0.061 0.22 -10000 0 -0.59 48 48
STAT1/PIAS1 -0.034 0.2 -10000 0 -0.57 35 35
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.062 -10000 0 -0.55 3 3
STAT3 (dimer) -0.014 0.21 0.76 1 -0.69 23 24
PRKCD -0.016 0.19 0.43 5 -0.6 23 28
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 -0.039 0.2 -10000 0 -0.56 40 40
HCK 0.016 0.038 -10000 0 -10000 0 0
MAPKKK cascade 0.026 0.099 0.34 1 -0.58 6 7
bone resorption -0.007 0.18 0.63 4 -0.63 9 13
IRF1 0.004 0.19 0.64 6 -0.65 10 16
mol:GDP -0.06 0.2 0.25 1 -0.55 47 48
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.061 0.2 0.25 1 -0.56 47 48
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 -0.069 0.22 -10000 0 -0.52 92 92
gp130 (dimer)/TYK2/TYK2/LMO4 -0.009 0.16 -10000 0 -0.41 66 66
gp130 (dimer)/JAK2/JAK2/LMO4 -0.012 0.17 -10000 0 -0.43 66 66
IL6 -0.094 0.26 -10000 0 -0.68 81 81
PIAS3 0.026 0.007 -10000 0 -10000 0 0
PTPRE -0.025 0.077 -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 -0.39 117 117
LMO4 0.028 0.016 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.016 0.21 -10000 0 -0.7 22 22
MCL1 0.054 0.072 -10000 0 -0.82 1 1
Regulation of p38-alpha and p38-beta

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
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 0.098 -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 -0.25 256 256
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.027 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
FYN 0.027 0.004 -10000 0 -10000 0 0
MAP3K12 0.027 0.005 -10000 0 -10000 0 0
FGR 0.025 0.015 -10000 0 -10000 0 0
p38 alpha/TAB1 -0.043 0.068 -10000 0 -0.28 10 10
PRKG1 -0.16 0.31 -10000 0 -0.67 137 137
DUSP8 0.019 0.065 -10000 0 -0.67 4 4
PGK/cGMP/p38 alpha -0.11 0.18 -10000 0 -0.37 133 133
apoptosis -0.042 0.065 -10000 0 -0.27 10 10
RAL/GTP 0.035 0.008 -10000 0 -10000 0 0
LYN 0.027 0.005 -10000 0 -10000 0 0
DUSP1 -0.083 0.25 -10000 0 -0.67 78 78
PAK1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.065 0.02 -10000 0 -10000 0 0
TRAF6 0.024 0.045 -10000 0 -0.67 2 2
RAC1 0.026 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.026 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.035 0.01 -10000 0 -10000 0 0
MAPK11 -0.053 0.15 0.41 19 -0.33 32 51
BLK -0.19 0.31 -10000 0 -0.67 148 148
HCK 0.017 0.038 -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 -0.3 10 29
positive regulation of innate immune response -0.043 0.16 0.46 19 -0.4 14 33
LCK 0.012 0.082 -10000 0 -0.67 6 6
p38alpha-beta/MKP7 -0.044 0.14 0.34 9 -0.46 7 16
p38alpha-beta/MKP5 -0.037 0.15 0.46 12 -0.45 7 19
PGK/cGMP -0.12 0.23 -10000 0 -0.5 137 137
PAK2 0.027 0.004 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.096 0.18 0.31 4 -0.42 64 68
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 -0.66 280 280
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.34 4 -0.46 3 7
alphaV/beta3 Integrin/Osteopontin/Src -0.003 0.12 -10000 0 -0.5 25 25
AP1 -0.14 0.3 -10000 0 -0.7 89 89
ILK -0.005 0.11 -10000 0 -0.4 30 30
bone resorption -0.007 0.13 -10000 0 -0.46 12 12
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 0.028 0.12 -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 -0.021 0.098 -10000 0 -0.37 31 31
MAPK1 -0.022 0.095 -10000 0 -0.37 30 30
Rac1/GDP 0.019 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 0.099 -10000 0 -0.64 11 11
NFKBIA -0.017 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 -0.038 0.11 0.52 3 -0.49 3 6
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
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.04 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+ -0.097 0.19 -10000 0 -0.43 121 121
IGF1R 0.027 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.02 0.15 -10000 0 -0.45 51 51
SHC1 0.025 0.007 -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 0.1 -10000 0 -0.44 24 24
KRAS 0.027 0.005 -10000 0 -10000 0 0
G13/GTP 0.01 0.084 -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 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 -0.1 0.2 -10000 0 -0.44 121 121
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 -0.46 121 121
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 0.054 -10000 0 -0.67 3 3
GNAQ 0.025 0.008 -10000 0 -10000 0 0
ESR1 -0.014 0.14 -10000 0 -0.65 23 23
Gq family/GDP/Gbeta gamma -0.059 0.19 -10000 0 -0.65 28 28
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.097 -10000 0 -0.57 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC 0.003 0.13 -10000 0 -0.54 20 20
GNAZ 0.02 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.01 0.11 -10000 0 -0.48 23 23
STRN -0.016 0.17 -10000 0 -0.66 31 31
GNAL -0.062 0.23 -10000 0 -0.66 65 65
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 0.41 2 -0.54 21 23
cAMP biosynthetic process -0.041 0.16 -10000 0 -0.38 80 80
SRC -0.004 0.13 -10000 0 -0.51 21 21
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 -0.069 0.16 -10000 0 -0.43 48 48
Gs family/GTP -0.031 0.16 -10000 0 -0.39 80 80
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 -0.44 121 121
Gs family/GDP/Gbeta gamma -0.027 0.14 -10000 0 -0.45 23 23
MSN -0.01 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 -0.007 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 0.004 0.15 0.49 2 -0.61 23 25
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 0.001 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 -0.36 19 24
GNA14 -0.13 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
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.29 12 16
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 -0.4 1 11
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 0.27 3 -0.39 1 4
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.014 0.12 -10000 0 -0.38 39 39
RAF1 -0.01 0.12 0.32 9 -0.38 19 28
ErbB2/ErbB3/neuregulin 2 -0.025 0.14 -10000 0 -0.41 60 60
STAT3 0.028 0.069 -10000 0 -0.84 3 3
cell migration 0.008 0.11 0.4 19 -0.3 3 22
mol:PI-3-4-5-P3 0 0.004 -10000 0 -10000 0 0
cell proliferation -0.15 0.32 -10000 0 -0.69 116 116
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 -0.076 0.24 0.38 3 -0.52 84 87
MAPK1 -0.16 0.3 0.36 1 -0.64 119 120
JAK2 -0.023 0.098 -10000 0 -0.34 37 37
NF2 -0.01 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 -0.033 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 45 45
MAPK9 -0.008 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 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
apoptosis 0.001 0.014 -10000 0 -10000 0 0
STAT3 (dimer) 0.028 0.067 -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 0.075 -10000 0 -0.25 37 37
ErbB2/ErbB2/HSP90 (dimer) 0.014 0.013 -10000 0 -10000 0 0
CHRNA1 -0.074 0.19 0.33 1 -0.4 93 94
myelination -0.008 0.14 0.52 17 -0.31 1 18
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 -0.051 0.22 -10000 0 -0.67 54 54
mol:GDP -0.01 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 20 25
SRC 0.026 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 39 40
MAP2K1 -0.073 0.23 0.36 1 -0.6 33 34
heart morphogenesis -0.014 0.11 -10000 0 -0.35 39 39
RAS family/GDP 0.017 0.11 -10000 0 -0.36 18 18
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 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
TGFB1 0.024 0.017 -10000 0 -10000 0 0
CCL5 -0.018 0.16 -10000 0 -0.67 29 29
SDCBP 0.027 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.038 0.13 -10000 0 -0.41 42 42
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.033 0.14 -10000 0 -0.52 23 23
Syndecan-1/Syntenin -0.031 0.14 0.25 1 -0.49 28 29
MAPK3 -0.031 0.12 -10000 0 -0.49 21 21
HGF/MET -0.078 0.19 -10000 0 -0.52 70 70
TGFB1/TGF beta receptor Type II 0.024 0.017 -10000 0 -10000 0 0
BSG 0.025 0.008 -10000 0 -10000 0 0
keratinocyte migration -0.032 0.14 -10000 0 -0.52 23 23
Syndecan-1/RANTES -0.051 0.19 -10000 0 -0.59 42 42
Syndecan-1/CD147 -0.016 0.14 -10000 0 -0.52 22 22
Syndecan-1/Syntenin/PIP2 -0.031 0.14 -10000 0 -0.47 28 28
LAMA5 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.03 0.13 -10000 0 -0.46 28 28
MMP7 -0.078 0.16 -10000 0 -0.66 26 26
HGF -0.072 0.24 -10000 0 -0.67 70 70
Syndecan-1/CASK -0.045 0.13 -10000 0 -0.4 45 45
Syndecan-1/HGF/MET -0.075 0.2 -10000 0 -0.5 73 73
regulation of cell adhesion -0.033 0.11 -10000 0 -0.49 19 19
HPSE 0.01 0.093 -10000 0 -0.64 9 9
positive regulation of cell migration -0.038 0.13 -10000 0 -0.41 42 42
SDC1 -0.038 0.13 -10000 0 -0.4 45 45
Syndecan-1/Collagen -0.038 0.13 -10000 0 -0.41 42 42
PPIB 0.027 0.004 -10000 0 -10000 0 0
MET -0.03 0.073 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
MMP9 -0.043 0.2 -10000 0 -0.67 42 42
MAPK1 -0.032 0.12 -10000 0 -0.49 22 22
homophilic cell adhesion -0.038 0.13 -10000 0 -0.4 43 43
MMP1 -0.044 0.075 -10000 0 -10000 0 0
FAS signaling pathway (CD95)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPTAN1 0.013 0.062 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 -0.019 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 -0.42 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 0.27 3 -0.57 8 11
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 -0.019 0.19 -10000 0 -0.48 70 70
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 -0.062 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 0.04 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 -0.52 3 3
FASLG -0.034 0.18 -10000 0 -0.68 33 33
FAS/FADD 0.029 0.026 -10000 0 -10000 0 0
HGF -0.072 0.24 -10000 0 -0.67 70 70
LMNA 0.014 0.07 0.25 34 -10000 0 34
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 -10000 0 37
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 -0.03 0.073 -10000 0 -10000 0 0
ICAD/CAD 0.014 0.06 0.23 27 -10000 0 27
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 -0.66 38 38
BCR signaling pathway

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
JUN -0.067 0.18 0.43 10 -0.41 46 56
IKBKB 0.01 0.12 0.48 16 -0.32 7 23
AKT1 -0.002 0.17 0.55 25 -0.24 15 40
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+ -0.025 0.093 0.32 2 -0.4 9 11
DOK1 0.027 0.005 -10000 0 -10000 0 0
AP-1 -0.058 0.15 0.51 12 -0.26 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 0.007 -10000 0 -10000 0 0
BCR complex -0.072 0.18 -10000 0 -0.5 68 68
CD22 -0.07 0.18 -10000 0 -0.42 85 85
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 0.033 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.04 0.12 -10000 0 -0.34 60 60
GO:0007205 -0.025 0.095 0.32 2 -0.42 9 11
SYK 0.025 0.008 -10000 0 -10000 0 0
ELK1 -0.02 0.093 0.29 5 -0.42 7 12
NFATC1 -0.041 0.14 0.36 6 -0.43 25 31
B-cell antigen/BCR complex -0.072 0.18 -10000 0 -0.5 68 68
PAG1/CSK 0.038 0.026 -10000 0 -0.51 1 1
NFKBIB 0.019 0.044 0.19 13 -0.13 6 19
HRAS -0.017 0.099 0.35 5 -0.34 9 14
NFKBIA 0.019 0.044 0.19 13 -0.12 8 21
NF-kappa-B/RelA/I kappa B beta 0.023 0.04 0.2 12 -10000 0 12
RasGAP/Csk -0.006 0.18 -10000 0 -0.4 75 75
mol:GDP -0.023 0.093 0.29 2 -0.4 10 12
PTEN 0.026 0.018 -10000 0 -0.36 1 1
CD79B 0.006 0.051 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha 0.023 0.04 0.2 12 -10000 0 12
GRB2 0.026 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.038 0.16 0.41 5 -0.39 60 65
PIK3R1 0.026 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 -0.37 126 134
CHUK 0.007 0.1 0.42 14 -0.38 5 19
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 -0.4 83 83
RELA 0.027 0.005 -10000 0 -10000 0 0
BCL2A1 0.014 0.036 0.17 5 -0.12 11 16
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 70 70
MAP4K1 0.008 0.079 -10000 0 -0.67 5 5
CD72 0.024 0.015 -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 -0.42 10 10
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.05 0.18 -10000 0 -0.42 80 80
RAF1 -0.015 0.097 0.34 7 -0.35 6 13
RasGAP/p62DOK/SHIP -0.008 0.17 -10000 0 -0.39 75 75
CD79A -0.1 0.23 -10000 0 -0.66 69 69
re-entry into mitotic cell cycle -0.057 0.15 0.5 12 -0.26 98 110
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 -0.048 0.17 0.31 1 -0.46 42 43
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MAPK8 -0.014 0.16 0.46 13 -0.46 25 38
actin cytoskeleton organization -0.046 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 0.091 -10000 0 -0.41 4 4
PI3K -0.063 0.14 -10000 0 -0.44 26 26
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.02 0.098 -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 84 84
mol:PI-3-4-5-P3 -0.055 0.098 -10000 0 -0.33 22 22
ETS1 -0.015 0.086 0.36 4 -0.42 4 8
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.009 0.16 -10000 0 -0.38 65 65
B-cell antigen/BCR complex/LYN -0.051 0.17 -10000 0 -0.42 72 72
MALT1 0.027 0.004 -10000 0 -10000 0 0
TRAF6 0.024 0.044 -10000 0 -0.67 2 2
RAC1 -0.05 0.15 0.36 1 -0.56 16 17
B-cell antigen/BCR complex/LYN/SYK -0.04 0.19 -10000 0 -0.43 82 82
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 0.018 0.095 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 0.032 0.17 11 -10000 0 11
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.005 0.057 -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 0.055 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 -0.014 0.18 -10000 0 -0.45 70 70
MAP3K5 0.012 0.12 0.44 13 -0.43 4 17
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 0.007 -10000 0 -10000 0 0
apoptosis -0.22 0.4 -10000 0 -0.81 149 149
STAT3 (dimer) -0.019 0.1 -10000 0 -0.28 63 63
GAB1/CRKL/SHP2/PI3K 0.027 0.11 0.34 1 -0.5 3 4
INPP5D 0.019 0.033 -10000 0 -10000 0 0
CBL/CRK 0.016 0.11 0.5 7 -0.41 1 8
PTPN11 0.025 0.032 -10000 0 -0.67 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.005 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.36 1 1
ELK1 0.035 0.14 0.41 30 -0.26 2 32
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.006 0.068 -10000 0 -0.24 5 5
PAK1 0.006 0.058 0.35 5 -0.4 2 7
HGF/MET/RANBP10 -0.015 0.18 -10000 0 -0.46 68 68
HRAS -0.02 0.13 -10000 0 -0.55 3 3
DOCK1 0.001 0.11 0.46 8 -0.47 2 10
GAB1 -0.011 0.097 -10000 0 -0.36 3 3
CRK -0.005 0.098 0.37 2 -0.43 1 3
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.043 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 0.085 -10000 0 -0.24 68 68
PIK3R1 0.026 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 -0.23 23 23
FOS -0.15 0.3 -10000 0 -0.67 125 125
GLMN 0.004 0.001 -10000 0 -10000 0 0
cell motility 0.034 0.14 0.41 30 -0.26 2 32
HGF/MET/MUC20 -0.065 0.16 -10000 0 -0.45 70 70
cell migration 0.004 0.083 -10000 0 -0.22 23 23
GRB2 0.026 0.007 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
MET/RANBP10 -0.005 0.057 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.015 0.11 -10000 0 -0.3 64 64
MET/MUC20 -0.017 0.048 -10000 0 -10000 0 0
RAP1B 0.012 0.13 0.54 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 -0.017 0.12 -10000 0 -0.46 3 3
STAT3 -0.019 0.1 -10000 0 -0.28 63 63
cell proliferation -0.023 0.15 -10000 0 -0.39 60 60
RPS6KB1 0 0.033 -10000 0 -0.22 2 2
MAPK3 -0.022 0.1 0.52 12 -10000 0 12
MAPK1 0.14 0.29 0.6 137 -10000 0 137
RANBP9 0.027 0.003 -10000 0 -10000 0 0
MAPK8 0.024 0.17 0.58 18 -0.6 9 27
SRC -0.02 0.1 -10000 0 -0.28 64 64
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 0.12 0.39 3 -0.46 2 5
MET -0.03 0.073 -10000 0 -10000 0 0
MAP4K1 0.007 0.12 0.48 7 -0.43 6 13
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 0.057 0.35 5 -0.4 2 7
MAP2K4 0.022 0.14 0.51 19 -0.42 3 22
SHP2/GRB2/SOS1/GAB1 0.018 0.097 -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 0.025 0.007 -10000 0 -10000 0 0
HGS -0.028 0.077 -10000 0 -0.24 26 26
PLCgamma1/PKC 0.02 0.004 -10000 0 -10000 0 0
HGF -0.072 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 -0.24 67 67
PDPK1 -0.001 0.048 -10000 0 -0.48 3 3
HGF/MET/SHIP -0.018 0.18 -10000 0 -0.45 70 70
Regulation of Androgen receptor activity

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
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 -0.069 0.12 -10000 0 -0.53 16 16
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 -0.54 17 17
MAP2K6 0.004 0.099 -10000 0 -0.68 10 10
BRM/BAF57 0.017 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 0.019 0.07 -10000 0 -0.67 5 5
EHMT2 0.025 0.005 -10000 0 -10000 0 0
cell proliferation -0.082 0.2 0.57 20 -0.48 21 41
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 -0.56 18 20
AR/GR -0.12 0.18 0.28 2 -0.34 153 155
GNB2L1 0.022 0.008 -10000 0 -10000 0 0
PKN1 0.025 0.007 -10000 0 -10000 0 0
RCHY1 0.027 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity -0.005 0.007 -10000 0 -0.017 47 47
MAPK8 -0.014 0.071 -10000 0 -0.52 9 9
T-DHT/AR/TIF2/CARM1 -0.13 0.19 0.34 3 -0.58 47 50
SRC -0.044 0.087 0.24 1 -0.46 16 17
NR3C1 0.026 0.006 -10000 0 -10000 0 0
KLK3 -0.36 0.55 0.39 1 -1.2 144 145
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 0.33 6 -0.57 16 22
TMPRSS2 -0.043 0.27 -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 -0.013 2 2
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 0.098 -10000 0 -0.68 10 10
KLK2 -0.45 0.38 0.34 2 -0.76 289 291
AR -0.14 0.18 -10000 0 -0.35 201 201
SENP1 0.025 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 0.032 143 -10000 0 143
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 -0.57 16 20
positive regulation of transcription 0.027 0.008 -10000 0 -10000 0 0
DNAJA1 0.024 0.014 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.008 -10000 0 -10000 0 0
NCOA1 0.018 0.022 -10000 0 -10000 0 0
SPDEF -0.003 0.049 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.092 0.15 0.28 2 -0.45 48 50
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 -0.037 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
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 -0.44 1 1
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 0.071 -10000 0 -0.26 2 2
CaM/Ca2+ 0.014 0.13 -10000 0 -0.33 62 62
RAP1A 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.012 0.13 -10000 0 -0.34 62 62
AKT1 -0.017 0.12 0.38 5 -0.37 7 12
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 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.017 0.074 -10000 0 -0.44 2 2
Rap1/GTP -0.02 0.094 -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 -0.57 28 34
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 -0.71 6 6
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 -0.35 2 2
MAPK1 -0.17 0.31 0.44 1 -0.66 127 128
JAK2 0.017 0.036 -10000 0 -0.38 2 2
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
JAK1 0.019 0.025 -10000 0 -10000 0 0
CAMK2D 0.027 0.004 -10000 0 -10000 0 0
DAPK1 -0.04 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 44 46
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 36 40
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 -0.35 7 12
PRKCD -0.013 0.13 0.42 9 -0.37 8 17
RAP1B 0.027 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.008 0.071 -10000 0 -0.26 2 2
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 -0.011 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 -0.31 45 47
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 -0.005 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 0.071 -10000 0 -0.26 2 2
PTPN11 -0.025 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
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.019 0.12 -10000 0 -0.42 33 33
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.086 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 -0.35 30 30
AKT1 0.032 0.096 0.3 9 -0.57 2 11
PTK2B -0.009 0.085 0.26 1 -0.32 17 18
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 0.025 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 -0.42 10 10
endothelial cell migration -0.015 0.15 -10000 0 -0.52 33 33
ADCY4 -0.028 0.14 -10000 0 -0.52 35 35
ADCY5 -0.054 0.16 -10000 0 -0.53 41 41
ADCY6 -0.028 0.14 -10000 0 -0.52 35 35
ADCY7 -0.029 0.15 -10000 0 -0.52 35 35
ADCY1 -0.031 0.15 -10000 0 -0.51 37 37
ADCY2 -0.048 0.16 -10000 0 -0.52 42 42
ADCY3 -0.028 0.15 -10000 0 -0.53 34 34
ADCY8 -0.037 0.15 -10000 0 -0.5 39 39
ADCY9 -0.029 0.15 -10000 0 -0.52 35 35
GSK3B -0.007 0.084 0.37 2 -0.34 12 14
arachidonic acid secretion -0.028 0.14 -10000 0 -0.44 47 47
GNG2 0.025 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 0.4 7 -0.49 1 8
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 -0.92 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 -0.44 47 47
LPA/LPA1-2-3 0.019 0.12 -10000 0 -0.38 33 33
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 -0.32 28 30
GNAZ -0.014 0.12 -10000 0 -0.44 34 34
EGFR/PI3K-beta/Gab1 -0.001 0.098 -10000 0 -0.36 30 30
positive regulation of dendritic cell cytokine production 0.018 0.11 -10000 0 -0.38 33 33
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 -0.011 0.12 -10000 0 -0.45 33 33
GNAI3 -0.011 0.12 -10000 0 -0.44 35 35
GNAI1 -0.011 0.12 -10000 0 -0.43 35 35
LPA/LPA3 0.015 0.024 -10000 0 -0.14 1 1
LPA/LPA2 0.02 0.013 -10000 0 -10000 0 0
LPA/LPA1 -0.014 0.14 -10000 0 -0.47 40 40
HB-EGF/EGFR -0.022 0.14 -10000 0 -0.44 45 45
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 -0.034 0.16 0.42 10 -0.46 49 59
NFKB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
GNB1 0.026 0.006 -10000 0 -10000 0 0
LYN -0.007 0.091 0.35 7 -0.4 2 9
GNAQ 0.016 0.015 -10000 0 -10000 0 0
LPAR2 0.025 0.008 -10000 0 -10000 0 0
LPAR3 0.013 0.034 -10000 0 -10000 0 0
LPAR1 -0.021 0.18 -10000 0 -0.6 40 40
IL8 -0.083 0.17 0.36 1 -0.47 38 39
PTK2 -0.002 0.1 -10000 0 -0.38 28 28
Rac1/GDP 0.019 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 -0.25 6 6
PLD2 -0.001 0.1 -10000 0 -0.37 28 28
G12/G13 0.022 0.11 -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 -0.24 17 17
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
PXN 0.001 0.097 0.27 1 -0.33 28 29
HRAS/GTP -0.028 0.14 -10000 0 -0.45 47 47
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 -0.67 5 5
PRKCD -0.008 0.085 0.35 9 -10000 0 9
Gi(beta/gamma) -0.023 0.14 -10000 0 -0.5 34 34
mol:LPA 0.002 0.016 -10000 0 -0.19 2 2
TRIP6/p130 Cas/FAK1/Paxillin 0.02 0.11 -10000 0 -0.38 26 26
MAPKKK cascade -0.028 0.14 -10000 0 -0.44 47 47
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 -0.067 0.15 -10000 0 -0.34 117 117
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 -0.33 8 8
Rac1/GTP 0.015 0.19 -10000 0 -0.83 22 22
MMP2 -0.015 0.15 -10000 0 -0.53 33 33
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.009 0.1 -10000 0 -0.74 7 7
Syndecan-4/Syndesmos -0.039 0.16 -10000 0 -0.54 42 42
positive regulation of JNK cascade -0.053 0.19 -10000 0 -0.56 44 44
Syndecan-4/ADAM12 -0.049 0.16 -10000 0 -0.55 42 42
CCL5 -0.018 0.16 -10000 0 -0.67 29 29
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
DNM2 0.025 0.008 -10000 0 -10000 0 0
ITGA5 0.027 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
PLG 0.008 0.031 -10000 0 -10000 0 0
ADAM12 -0.011 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 -0.061 0.18 -10000 0 -0.58 41 41
Syndecan-4/CXCL12/CXCR4 -0.056 0.2 -10000 0 -0.6 44 44
Syndecan-4/Laminin alpha3 -0.05 0.17 -10000 0 -0.57 40 40
MDK -0.02 0.076 -10000 0 -0.67 1 1
Syndecan-4/FZD7 -0.039 0.16 -10000 0 -0.55 42 42
Syndecan-4/Midkine -0.051 0.16 -10000 0 -0.56 41 41
FZD7 0.022 0.051 -10000 0 -0.52 4 4
Syndecan-4/FGFR1/FGF -0.013 0.16 -10000 0 -0.51 41 41
THBS1 0.012 0.046 -10000 0 -10000 0 0
integrin-mediated signaling pathway -0.055 0.16 -10000 0 -0.55 42 42
positive regulation of MAPKKK cascade -0.053 0.19 -10000 0 -0.56 44 44
Syndecan-4/TACI -0.13 0.21 -10000 0 -0.61 42 42
CXCR4 0.026 0.013 -10000 0 -10000 0 0
cell adhesion -0.008 0.066 0.2 5 -0.31 17 22
Syndecan-4/Dynamin -0.039 0.16 -10000 0 -0.55 41 41
Syndecan-4/TSP1 -0.042 0.16 -10000 0 -0.55 42 42
Syndecan-4/GIPC -0.039 0.16 -10000 0 -0.55 41 41
Syndecan-4/RANTES -0.06 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 -0.038 0.16 -10000 0 -0.55 41 41
TFPI -0.012 0.16 -10000 0 -0.66 28 28
F2 0.01 0.029 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.009 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.074 0.18 -10000 0 -0.58 41 41
ACTN1 0.026 0.008 -10000 0 -10000 0 0
TNC -0.033 0.096 -10000 0 -0.67 5 5
Syndecan-4/CXCL12 -0.075 0.2 -10000 0 -0.62 44 44
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 -0.67 122 122
FGF2 0.027 0.004 -10000 0 -10000 0 0
FGFR1 0.025 0.032 -10000 0 -0.67 1 1
Syndecan-4/PI-4-5-P2 -0.05 0.15 -10000 0 -0.55 42 42
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 -0.084 0.071 -10000 0 -0.22 2 2
cell migration -0.027 0.012 -10000 0 -10000 0 0
PRKCD 0.026 0.021 -10000 0 -10000 0 0
vasculogenesis -0.04 0.16 -10000 0 -0.53 42 42
SDC4 -0.05 0.16 -10000 0 -0.58 42 42
Syndecan-4/Tenascin C -0.057 0.17 -10000 0 -0.57 42 42
Syndecan-4/PI-4-5-P2/PKC alpha -0.046 0.023 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.038 0.16 -10000 0 -0.55 42 42
MMP9 -0.043 0.2 -10000 0 -0.67 42 42
Rac1/GTP -0.009 0.067 0.2 5 -0.32 17 22
cytoskeleton organization -0.037 0.15 -10000 0 -0.52 42 42
GIPC1 0.025 0.008 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.057 0.18 -10000 0 -0.57 43 43
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.016 0.005 -10000 0 -10000 0 0
MAP4K4 -0.014 0.12 -10000 0 -0.5 15 15
BAG4 0.025 0.032 -10000 0 -0.67 1 1
PKC zeta/ceramide -0.02 0.097 -10000 0 -0.28 37 37
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.14 -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 -10000 0 -0.34 21 21
SMPD1 -0.012 0.089 0.27 6 -0.23 61 67
RB1 -0.033 0.09 0.19 1 -0.29 35 36
FADD/Caspase 8 -0.005 0.12 -10000 0 -0.52 13 13
MAP2K4 -0.02 0.072 0.24 1 -0.37 8 9
NSMAF 0.027 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.024 0.082 -10000 0 -0.41 12 12
EGF -0.075 0.24 -10000 0 -0.67 72 72
mol:ceramide -0.037 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 -0.28 35 36
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 0.085 -10000 0 -0.38 13 13
Cathepsin D/ceramide -0.019 0.093 -10000 0 -0.27 37 37
FADD -0.013 0.12 -10000 0 -0.5 15 15
KSR1 -0.027 0.087 0.18 7 -0.31 26 33
MAPK8 -0.019 0.091 -10000 0 -0.37 20 20
PRKRA -0.035 0.091 -10000 0 -0.29 35 35
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 -0.062 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 0.039 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.014 0.12 -10000 0 -0.51 16 16
TNFR1A/BAG4/TNF-alpha -0.004 0.16 -10000 0 -0.44 58 58
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 0.071 0.17 25 -0.24 18 43
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 -0.003 0.16 -10000 0 -0.44 57 57
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.012 0.087 -10000 0 -0.48 7 7
MAP2K2 -0.015 0.068 -10000 0 -0.38 7 7
SMPD3 -0.017 0.1 -10000 0 -0.33 26 26
TNF -0.057 0.22 -10000 0 -0.67 57 57
PKC zeta/PAR4 0.038 0.011 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.016 0.11 0.25 70 -0.25 17 87
NF kappa B1/RelA/I kappa B alpha 0.075 0.024 -10000 0 -10000 0 0
AIFM1 -0.01 0.082 0.17 25 -0.26 26 51
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
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 -0.26 4 4
AP1 -0.11 0.26 -10000 0 -0.55 104 104
mol:PIP3 0.027 0.17 0.62 20 -0.41 12 32
IKBKB 0.039 0.17 0.58 28 -0.27 6 34
AKT1 -0.007 0.12 0.32 26 -0.46 6 32
IKBKG 0.041 0.17 0.62 28 -0.26 7 35
MS4A2 -0.014 0.064 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.68 3 3
MAP3K1 0.024 0.11 0.44 13 -0.41 6 19
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 0.063 -10000 0 -0.27 1 1
SHC1 0.025 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK -0.021 0.16 -10000 0 -0.4 78 78
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.033 -10000 0 -10000 0 0
PLD2 -0.009 0.13 0.32 34 -0.37 29 63
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 0.62 21 -0.38 5 26
SYK 0.025 0.012 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0 0.1 -10000 0 -0.37 27 27
LAT -0.003 0.069 -10000 0 -0.33 4 4
PAK2 0.017 0.1 0.32 8 -0.43 8 16
NFATC2 -0.1 0.23 -10000 0 -0.61 84 84
HRAS 0.012 0.099 0.24 2 -0.43 10 12
GAB2 0.027 0.005 -10000 0 -10000 0 0
PLA2G1B 0.006 0.096 -10000 0 -0.68 7 7
Fc epsilon R1 0.007 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 0.1 -10000 0 -0.46 14 14
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 -0.26 8 8
CHUK 0.037 0.16 0.58 26 -0.27 6 32
KLRG1 -0.007 0.077 -10000 0 -0.3 15 15
VAV1 -0.004 0.073 0.21 1 -0.36 6 7
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL 0 0.063 -10000 0 -10000 0 0
negative regulation of mast cell degranulation 0.007 0.08 -10000 0 -0.3 10 10
BTK -0.005 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 28 28
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.001 0.072 -10000 0 -0.27 29 29
RAF1 0.014 0.084 -10000 0 -0.85 4 4
Fc epsilon R1/FcgammaRIIB/SHIP 0.021 0.17 -10000 0 -0.51 41 41
FCER1G 0.018 0.036 -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 0.09 -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 -0.083 0.25 -10000 0 -0.67 78 78
NF-kappa-B/RelA 0.015 0.047 -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 0.024 0.098 -10000 0 -0.47 7 7
FER -0.003 0.07 -10000 0 -0.43 3 3
RELA 0.027 0.005 -10000 0 -10000 0 0
ITK -0.043 0.15 -10000 0 -0.47 55 55
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 0.012 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 0.66 20 -0.42 10 30
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 14 14
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 -0.008 0.13 0.32 34 -0.37 29 63
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 0.019 0.13 0.46 3 -0.67 10 13
HCLS1 -0.001 0.064 -10000 0 -0.28 2 2
PRKCB 0.036 0.18 0.64 25 -0.34 12 37
FCGR2B -0.009 0.15 -10000 0 -0.67 24 24
IGHE 0.001 0.011 -10000 0 -10000 0 0
KLRG1/SHIP 0.007 0.081 -10000 0 -0.31 10 10
LCP2 0.024 0.021 -10000 0 -10000 0 0
PLA2G4A -0.022 0.12 -10000 0 -0.42 31 31
RASA1 0.027 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.008 0.13 0.32 34 -0.37 29 63
IKK complex 0.044 0.18 0.61 30 -0.21 2 32
WIPF1 0.027 0.005 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.01 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 -0.44 54 54
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 55 55
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 0.025 0.007 -10000 0 -10000 0 0
Rap1/GTP 0 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 -0.03 0.097 -10000 0 -0.36 15 15
MST1R 0.02 0.064 -10000 0 -0.67 4 4
leukocyte activation during inflammatory response 0.014 0.08 -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 -0.05 0.19 -10000 0 -0.47 77 77
alphaM/beta2 Integrin -0.023 0.089 -10000 0 -0.3 26 26
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 0.089 -10000 0 -0.31 24 24
cell adhesion 0.001 0.12 -10000 0 -0.49 18 18
NFKB1 -0.11 0.26 0.33 1 -0.5 131 132
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 -0.002 0.058 -10000 0 -0.29 5 5
elevation of cytosolic calcium ion concentration -0.02 0.11 -10000 0 -0.3 19 19
alphaM/beta2 Integrin/JAM2/JAM3 0.026 0.094 -10000 0 -0.47 9 9
JAM2 0.021 0.063 -10000 0 -0.67 4 4
alphaM/beta2 Integrin/ICAM1 0.034 0.1 -10000 0 -0.49 9 9
alphaM/beta2 Integrin/uPA/Plg 0.013 0.098 -10000 0 -0.48 6 6
RhoA/GTP -0.025 0.1 -10000 0 -0.31 40 40
positive regulation of phagocytosis -0.006 0.096 -10000 0 -0.46 8 8
Ron/MSP 0.034 0.056 -10000 0 -0.51 5 5
alphaM/beta2 Integrin/uPAR/uPA -0.02 0.11 -10000 0 -0.3 19 19
alphaM/beta2 Integrin/uPAR 0.007 0.094 -10000 0 -0.29 18 18
PLAU -0.044 0.076 -10000 0 -10000 0 0
PLAT 0.02 0.058 -10000 0 -0.67 3 3
actin filament polymerization -0.029 0.094 -10000 0 -0.35 14 14
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 74 74
RAP1B 0.027 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.004 0.099 -10000 0 -0.35 12 12
fibrinolysis 0.008 0.097 -10000 0 -0.47 6 6
HCK 0.017 0.038 -10000 0 -10000 0 0
dendritic cell antigen processing and presentation -0.024 0.089 -10000 0 -0.31 24 24
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 -0.48 46 46
FN1 -0.084 0.068 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.016 0.086 -10000 0 -0.5 6 6
MPO 0.012 0.077 -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 -0.023 0.097 -10000 0 -0.4 9 9
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 -0.35 12 12
ITGAM -0.005 0.08 -10000 0 -0.55 6 6
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.019 0.1 -10000 0 -0.48 12 12
HP -0.023 0.098 -10000 0 -0.67 6 6
leukocyte adhesion -0.025 0.16 -10000 0 -0.45 38 38
SELP 0.015 0.078 -10000 0 -0.67 6 6
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 21 21
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 0.019 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 -0.084 0.068 -10000 0 -10000 0 0
PLD2 -0.025 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 0.056 -10000 0 -10000 0 0
PAK1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin 0.008 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 -0.004 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 0.005 -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 -0.044 0.26 -10000 0 -1.3 18 18
tube development -0.037 0.17 0.49 2 -0.73 20 22
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 -0.67 202 202
MAPK14 -0.026 0.25 -10000 0 -1.2 20 20
Tie2/SHP2 -0.003 0.18 -10000 0 -1.2 8 8
TEK 0.004 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 -0.5 202 202
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 -0.027 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 -0.01 0.2 0.48 1 -0.9 20 21
Tie2/Ang2 -0.057 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 -0.024 0.24 -10000 0 -1.2 20 20
mol:Choline -0.022 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 0.046 -10000 0 -10000 0 0
PXN 0.003 0.18 0.59 5 -0.73 20 25
ITGB1 0.027 0.004 -10000 0 -10000 0 0
NOS3 0.004 0.19 0.58 7 -0.78 20 27
RAC1 0.026 0.006 -10000 0 -10000 0 0
TNF -0.058 0.23 -10000 0 -0.66 61 61
MAPKKK cascade -0.022 0.23 -10000 0 -1.1 20 20
RASA1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.018 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 -0.022 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 -0.005 0.18 -10000 0 -0.83 20 20
MMP2 -0.03 0.26 -10000 0 -1.2 20 20
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.04 0.12 0.89 7 -10000 0 7
VDR 0.026 0.008 -10000 0 -10000 0 0
FAM120B 0.027 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.006 0.11 -10000 0 -0.3 42 42
RXRs/LXRs/DNA/Oxysterols -0.01 0.15 -10000 0 -0.42 52 52
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 -0.09 0.23 -10000 0 -0.45 136 136
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 0.048 0.074 -10000 0 -0.38 13 13
RARA 0.026 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.026 0.008 -10000 0 -10000 0 0
RARs/RARs/DNA/9cRA 0.032 0.071 -10000 0 -0.38 13 13
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 0.037 0.098 -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 -0.22 47 47
RXR alpha/CCPG 0.032 0.025 -10000 0 -10000 0 0
RXRA 0.02 0.025 -10000 0 -10000 0 0
RXRB 0.023 0.026 -10000 0 -10000 0 0
THRB 0.014 0.095 -10000 0 -0.64 10 10
PPARG 0.016 0.083 -10000 0 -0.67 7 7
PPARD 0.027 0.003 -10000 0 -10000 0 0
TNF -0.099 0.38 -10000 0 -1.1 58 58
mol:Oxysterols -0.001 0.016 -10000 0 -10000 0 0
cholesterol transport -0.01 0.15 -10000 0 -0.42 52 52
PPARA 0.02 0.012 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.007 0.12 -10000 0 -0.67 14 14
RXRs/NUR77/BCL2 -0.11 0.17 -10000 0 -0.34 161 161
SREBF1 -0.011 0.14 -10000 0 -0.59 4 4
RXRs/RXRs/DNA/9cRA 0.037 0.098 -10000 0 -0.44 5 5
ABCA1 -0.01 0.14 -10000 0 -0.59 4 4
RARs/THRs 0.056 0.098 -10000 0 -0.4 20 20
RXRs/FXR 0.048 0.086 -10000 0 -0.48 3 3
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.033 0.069 -10000 0 -0.58 6 6
alphaV beta3 Integrin 0.039 0.081 -10000 0 -0.47 11 11
PTK2 0.013 0.14 0.41 11 -0.5 11 22
IGF1R 0.027 0.004 -10000 0 -10000 0 0
PI4KB 0.025 0.007 -10000 0 -10000 0 0
MFGE8 0.009 0.05 -10000 0 -10000 0 0
SRC 0.026 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 0.079 -10000 0 -0.46 11 11
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.088 0.24 -10000 0 -0.43 153 153
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 -0.47 11 11
PI4KA 0.02 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.093 0.23 -10000 0 -0.43 153 153
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 -0.4 152 154
TLN1 0.025 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 -0.57 20 20
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.028 0.12 -10000 0 -0.52 20 20
cell adhesion 0.03 0.077 -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 0.019 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 -0.64 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 0.08 -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 -0.47 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 0.015 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 0.096 -10000 0 -0.45 16 16
FAK1/Vinculin 0.024 0.12 0.39 9 -0.41 9 18
alphaV beta3/Integrin/ppsTEM5 0.04 0.081 -10000 0 -0.47 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 0.081 -10000 0 -0.47 11 11
alphaV/beta3 Integrin/TGFBR2 0.037 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 -0.084 0.068 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 0.034 0.089 -10000 0 -0.42 16 16
SDC1 0.025 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 -0.056 0.22 -10000 0 -0.67 59 59
FAK1/Paxillin 0.022 0.12 0.35 8 -0.41 9 17
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 -0.03 0.15 -10000 0 -0.67 23 23
KDR 0.021 0.063 -10000 0 -0.67 4 4
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.024 0.044 -10000 0 -0.67 2 2
COL4A3 0.008 0.11 -10000 0 -0.63 14 14
angiogenesis -0.054 0.15 -10000 0 -0.52 32 32
Rac1/GTP 0.021 0.074 -10000 0 -0.4 14 14
EDIL3 0.005 0.094 -10000 0 -0.67 8 8
cell proliferation 0.037 0.085 -10000 0 -0.44 14 14
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.017 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -0.014 1 1
cytokine production during immune response 0.045 0.13 0.48 15 -10000 0 15
IL27/IL27R/JAK1 -0.015 0.17 -10000 0 -0.49 11 11
TBX21 -0.065 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 0.02 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.039 0.13 -10000 0 -0.49 3 3
T-helper 2 cell differentiation 0.045 0.13 0.48 15 -10000 0 15
T cell proliferation during immune response 0.045 0.13 0.48 15 -10000 0 15
MAPKKK cascade -0.045 0.13 -10000 0 -0.48 15 15
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT2 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.023 0.024 -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 -0.54 27 40
IL27/IL27R/JAK2/TYK2 -0.045 0.13 -10000 0 -0.48 15 15
positive regulation of T cell mediated cytotoxicity -0.045 0.13 -10000 0 -0.48 15 15
STAT1 (dimer) -0.026 0.22 0.52 12 -0.59 18 30
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 -0.48 13 13
T cell proliferation -0.11 0.19 -10000 0 -0.51 59 59
IL12/IL12R/TYK2/JAK2 -0.073 0.24 -10000 0 -0.83 31 31
IL17A -0.04 0.13 -10000 0 -0.49 3 3
mast cell activation 0.045 0.13 0.48 15 -10000 0 15
IFNG -0.016 0.051 0.1 3 -0.13 69 72
T cell differentiation -0.004 0.008 0.014 1 -0.022 69 70
STAT3 (dimer) -0.032 0.13 -10000 0 -0.46 14 14
STAT5A (dimer) -0.032 0.13 -10000 0 -0.46 14 14
STAT4 (dimer) -0.039 0.15 0.33 1 -0.46 20 21
STAT4 0.004 0.098 -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 -0.47 11 11
GATA3 -0.058 0.3 -10000 0 -1.3 25 25
IL18 -0.012 0.077 -10000 0 -0.49 11 11
positive regulation of mast cell cytokine production -0.031 0.13 -10000 0 -0.45 14 14
IL27/EBI3 -0.03 0.06 -10000 0 -0.26 1 1
IL27RA 0 0.024 -10000 0 -10000 0 0
IL6 -0.095 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 -0.028 0.13 -10000 0 -0.51 33 33
EBI3 -0.052 0.075 -10000 0 -0.37 1 1
TNF -0.053 0.16 -10000 0 -0.51 57 57
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.018 0.12 -10000 0 -0.45 25 25
MAP4K1 0.008 0.079 -10000 0 -0.67 5 5
MAP3K8 0.018 0.078 -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 0.08 -10000 0 -0.32 25 25
JUN -0.084 0.21 0.37 1 -0.51 54 55
MAP3K7 0.002 0.08 -10000 0 -0.32 26 26
GRAP2 -0.019 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 -0.006 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 0.028 0.12 -10000 0 -0.44 23 23
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
Jak2/Leptin Receptor -0.006 0.12 0.32 1 -0.4 23 24
PTP1B/AKT1 0.006 0.071 0.32 2 -0.29 5 7
FYN 0.027 0.004 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0 0.082 0.31 11 -0.28 9 20
EGFR 0.013 0.072 -10000 0 -0.68 5 5
EGF/EGFR -0.035 0.16 0.24 1 -0.39 74 75
CSF1 0.015 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 -0.003 0.11 0.32 6 -0.33 20 26
Insulin Receptor/Insulin 0.015 0.072 -10000 0 -0.35 4 4
HCK 0.017 0.038 -10000 0 -10000 0 0
CRK 0.026 0.007 -10000 0 -10000 0 0
TYK2 0.008 0.093 0.31 21 -0.29 5 26
EGF -0.075 0.25 -10000 0 -0.67 72 72
YES1 0.027 0.005 -10000 0 -10000 0 0
CAV1 -0.004 0.11 0.4 12 -0.32 10 22
TXN 0.024 0.011 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.03 0.14 -10000 0 -0.39 57 57
cell migration 0 0.082 0.28 9 -0.31 11 20
STAT3 0.026 0.007 -10000 0 -10000 0 0
PRLR -0.014 0.15 -10000 0 -0.67 25 25
ITGA2B -0.043 0.21 -10000 0 -0.67 49 49
CSF1R 0.023 0.035 -10000 0 -0.67 1 1
Prolactin Receptor/Prolactin 0.001 0.12 -10000 0 -0.51 25 25
FGR 0.025 0.015 -10000 0 -10000 0 0
PTP1B/p130 Cas 0.006 0.073 0.28 3 -0.27 8 11
Crk/p130 Cas 0.013 0.071 -10000 0 -0.29 4 4
DOK1 0.012 0.087 0.36 12 -0.34 3 15
JAK2 -0.012 0.12 0.37 4 -0.38 30 34
Jak2/Leptin Receptor/Leptin -0.007 0.13 -10000 0 -0.49 19 19
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
PTPN1 0 0.083 0.31 11 -0.28 9 20
LYN 0.027 0.005 -10000 0 -10000 0 0
CDH2 -0.072 0.12 -10000 0 -0.63 14 14
SRC 0.023 0.057 0.32 1 -0.39 5 6
ITGB3 0.01 0.1 -10000 0 -0.65 11 11
CAT1/PTP1B -0.06 0.16 0.4 14 -0.36 46 60
CAPN1 0.027 0.005 -10000 0 -10000 0 0
CSK 0.027 0.008 -10000 0 -10000 0 0
PI3K 0.021 0.082 -10000 0 -0.48 4 4
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 0.37 4 -0.38 30 34
FCGR2A 0.017 0.045 -10000 0 -0.67 1 1
FER 0.021 0.055 -10000 0 -0.68 3 3
alphaIIb/beta3 Integrin -0.027 0.18 -10000 0 -0.53 56 56
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 0.34 4 -0.45 46 50
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 61 61
CSF1/CSF1R 0.008 0.095 0.28 1 -0.46 10 11
Ras protein signal transduction 0.026 0.11 0.46 26 -10000 0 26
IRS1 -0.056 0.22 -10000 0 -0.67 59 59
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 0.29 11 -0.28 14 25
STAT5A 0.001 0.091 0.29 11 -0.28 14 25
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.073 0.28 1 -0.33 6 7
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 0.072 0.32 1 -0.45 8 9
YBX1 0.033 0.007 -10000 0 -10000 0 0
LCK 0.012 0.082 -10000 0 -0.67 6 6
SHC1 0.025 0.007 -10000 0 -10000 0 0
NOX4 -0.041 0.076 -10000 0 -10000 0 0
ceramide signaling 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
MAP4K4 -0.015 0.12 -10000 0 -0.44 20 20
BAG4 0.025 0.032 -10000 0 -0.67 1 1
BAD 0.007 0.065 0.34 9 -10000 0 9
NFKBIA 0.027 0.005 -10000 0 -10000 0 0
BIRC3 -0.01 0.14 -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 0.017 0.094 0.34 23 -0.3 2 25
MAP2K1 0.011 0.083 0.31 20 -0.3 2 22
SMPD1 0.005 0.045 0.22 8 -0.14 3 11
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.01 0.12 -10000 0 -0.46 18 18
MAP2K4 0.017 0.096 0.35 26 -10000 0 26
protein ubiquitination -0.012 0.12 0.32 4 -0.44 17 21
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 0.004 0.059 0.22 12 -0.16 13 25
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 -10000 0 18
TRADD 0.026 0.006 -10000 0 -10000 0 0
RELA/p50 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.017 0.088 0.33 20 -0.29 2 22
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 -0.45 18 18
KSR1 0.01 0.08 0.28 23 -0.33 2 25
MAPK8 0.011 0.11 0.38 22 -0.35 9 31
TRAF2 0.025 0.009 -10000 0 -10000 0 0
response to radiation 0 0.001 0.006 13 -10000 0 13
CHUK -0.014 0.12 0.33 1 -0.44 16 17
TNF R/SODD 0.038 0.026 -10000 0 -0.51 1 1
TNF -0.056 0.22 -10000 0 -0.68 57 57
CYCS 0.02 0.08 0.26 26 -0.18 1 27
IKBKG -0.013 0.12 0.38 1 -0.45 15 16
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.016 0.13 -10000 0 -0.46 20 20
RELA 0.027 0.005 -10000 0 -10000 0 0
RIPK1 0.027 0.003 -10000 0 -10000 0 0
AIFM1 0.018 0.079 0.25 24 -0.18 2 26
TNF/TNF R/SODD -0.004 0.16 -10000 0 -0.44 58 58
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
response to heat 0 0.001 0.006 13 -10000 0 13
CASP8 0.009 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
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.027 0.005 -10000 0 -10000 0 0
mol:PIP3 -0.031 0.11 -10000 0 -0.33 59 59
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 0.003 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 0.075 -10000 0 -0.39 3 3
TSC1 0.025 0.008 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.024 0.13 -10000 0 -0.38 60 60
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.016 0.044 -10000 0 -0.27 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.027 0.004 -10000 0 -10000 0 0
RPS6KB1 0.018 0.098 0.39 18 -0.37 3 21
MAP3K5 0.006 0.028 0.18 1 -0.22 6 7
PIK3R1 0.027 0.005 -10000 0 -10000 0 0
apoptosis 0.006 0.029 0.18 1 -0.21 7 8
mol:LY294002 0 0.001 0.001 1 -0.002 73 74
EIF4B 0.023 0.11 0.46 21 -0.32 3 24
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.027 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 -0.008 0.13 -10000 0 -0.36 60 60
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 0.081 -10000 0 -0.38 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 73 74
FKBP12/Rapamycin 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.033 0.11 -10000 0 -0.32 57 57
EIF4E 0.027 0.004 -10000 0 -10000 0 0
ASK1/PP5C 0.026 0.073 -10000 0 -0.51 7 7
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.008 -10000 0 -10000 0 0
TSC1/TSC2 0.005 0.097 0.28 1 -0.46 3 4
tumor necrosis factor receptor activity 0 0.001 0.002 73 -0.001 1 74
RPS6 0.025 0.007 -10000 0 -10000 0 0
PPP5C 0.025 0.007 -10000 0 -10000 0 0
EIF4G1 0.027 0.004 -10000 0 -10000 0 0
IRS1 -0.043 0.14 -10000 0 -0.38 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 -0.03 0.1 0.22 3 -0.31 56 59
EIF4EBP1 0.016 0.096 -10000 0 -0.93 5 5
PIK3CA 0.023 0.054 -10000 0 -0.68 3 3
PPP2R5D 0.019 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
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 0.044 -10000 0 -0.44 5 5
ADCY5 -0.054 0.15 -10000 0 -0.44 66 66
ADCY6 0.002 0.044 -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 -0.44 46 46
ADCY3 0.002 0.044 -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 0.095 0.37 6 -0.36 16 22
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.025 0.025 0.37 1 -10000 0 1
HSPA8 0.02 0.057 -10000 0 -0.6 4 4
SMAD3/SMAD4/ER alpha -0.002 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 -0.31 1 1
SMAD4 -0.006 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 0.035 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 -0.02 0.11 -10000 0 -0.49 2 2
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 0.078 1.3 1 -10000 0 1
MAX 0.026 0.005 -10000 0 -10000 0 0
RBBP7 0.025 0.007 -10000 0 -10000 0 0
RBBP4 0.023 0.045 -10000 0 -0.67 2 2
RUNX2 -0.015 0.079 -10000 0 -0.67 2 2
RUNX3 0.009 0.1 -10000 0 -0.67 11 11
RUNX1 -0.039 0.076 -10000 0 -10000 0 0
CTBP1 0.027 0.004 -10000 0 -10000 0 0
NR3C1 0.025 0.006 -10000 0 -10000 0 0
VDR 0.026 0.008 -10000 0 -10000 0 0
CDKN1A 0.019 0.047 -10000 0 -10000 0 0
KAT2B 0.029 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.015 0.12 -10000 0 -0.3 31 31
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 -0.078 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 -0.76 148 149
SMAD3/SMAD4/IRF7 0.025 0.08 -10000 0 -10000 0 0
TFE3 0.03 0.009 -10000 0 -10000 0 0
COL1A2 0.026 0.063 -10000 0 -1.1 1 1
mesenchymal cell differentiation -0.014 0.096 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 0.027 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 0.14 -10000 0 -0.65 23 23
HNF4A -0.008 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 -0.29 2 2
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 0.029 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 -0.067 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 0.066 -10000 0 -0.41 5 5
SMAD2/SMAD2/SMAD4 0.004 0.036 0.23 3 -10000 0 3
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 0.01 0.11 -10000 0 -0.61 2 2
CITED1 -0.1 0.08 -10000 0 -0.61 5 5
SMAD2-3/SMAD4/ARC105 0.013 0.085 -10000 0 -10000 0 0
RBL1 0.014 0.093 -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 0.044 0.077 -10000 0 -0.45 10 10
SMAD7 -0.086 0.25 -10000 0 -0.54 96 96
MYC/MIZ-1 0.028 0.083 -10000 0 -0.51 11 11
SMAD3/SMAD4 0.021 0.11 0.29 30 -0.52 1 31
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 0.03 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 -0.29 1 1
FOXG1 0.007 0.042 -10000 0 -0.68 1 1
FOXO3 0.015 0.008 -10000 0 -10000 0 0
FOXO1 0.014 0.008 -10000 0 -10000 0 0
FOXO4 0.014 0.008 -10000 0 -10000 0 0
heart looping -0.006 0.099 0.38 4 -0.86 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 0.017 0.081 -10000 0 -0.3 1 1
SMAD3/SMAD4/GATA3 0 0.14 -10000 0 -0.42 32 32
SnoN/SIN3/HDAC complex/NCoR1 0.026 0.031 -10000 0 -0.67 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.029 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 0.031 0.012 -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 -0.34 6 6
ITGB5 0.016 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 -0.48 199 199
AR -0.26 0.34 -10000 0 -0.66 207 207
negative regulation of cell growth -0.022 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 0.018 -10000 0 -0.36 1 1
SMAD3/SMAD4/AP1 -0.18 0.42 -10000 0 -0.78 148 148
SMAD3/SMAD4/RUNX2 0.015 0.097 -10000 0 -0.46 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
Visual signal transduction: Cones

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
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 -0.042 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 0.006 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 0.028 -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) 0.023 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) -0.002 0.022 -9999 0 -10000 0 0
Cone Transducin 0.033 0.078 -9999 0 -0.4 15 15
SLC24A2 -0.007 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 0.051 -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 + -0.007 0.03 -9999 0 -10000 0 0
RGS9 -0.038 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 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
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 -0.44 229 229
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 0.027 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 0.031 -10000 0 -10000 0 0
RTN4R 0.02 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.022 0.13 0.46 10 -0.45 10 20
IRAK1 0.025 0.008 -10000 0 -10000 0 0
SHC1 -0.006 0.089 0.19 4 -0.45 16 20
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 0.093 -10000 0 -0.4 19 19
proNGF (dimer) 0.021 0.056 -10000 0 -0.67 3 3
MAGED1 0.026 0.007 -10000 0 -10000 0 0
APP 0.026 0.006 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.12 -10000 0 -0.65 15 15
ZNF274 0.025 0.007 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.012 0.084 -10000 0 -0.4 16 16
NGF 0.021 0.056 -10000 0 -0.67 3 3
cell cycle arrest 0.057 0.14 0.42 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 0.12 -10000 0 -0.45 32 32
NCSTN 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0.034 0.097 -10000 0 -0.45 18 18
PSENEN 0.025 0.007 -10000 0 -10000 0 0
mol:ceramide 0.003 0.092 -10000 0 -0.42 16 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.019 0.059 -10000 0 -0.38 4 4
p75(NTR)/beta APP 0.005 0.1 -10000 0 -0.51 16 16
BEX1 -0.28 0.35 -10000 0 -0.67 219 219
mol:GDP -0.018 0.087 -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 0.089 -10000 0 -0.41 16 16
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.031 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 0.035 0.097 -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 -0.43 18 18
RHOC 0.027 0.005 -10000 0 -10000 0 0
XIAP 0.026 0.007 -10000 0 -10000 0 0
MAPK10 0.016 0.11 0.34 16 -0.4 15 31
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 0.025 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.036 0.095 -10000 0 -0.45 17 17
PSEN1 0.027 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 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 -0.41 16 31
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 0.15 -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 0.019 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 0.059 0.052 -10000 0 -0.52 3 3
RhoA-B-C/GTP 0.033 0.096 -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 -0.4 27 27
PRKACB 0.025 0.032 -10000 0 -0.67 1 1
proBDNF (dimer)/p75 ECD 0.023 0.088 -10000 0 -0.51 13 13
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.01 0.14 -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 -0.39 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) -0.008 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 -0.42 17 17
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 0.03 0.14 0.43 25 -0.36 16 41
E2F1 -0.019 0.07 -10000 0 -10000 0 0
CASP9 0.027 0.005 -10000 0 -10000 0 0
IKK complex 0.05 0.074 -10000 0 -0.46 3 3
NGF (dimer)/TRKA 0.027 0.049 -10000 0 -0.51 3 3
MMP7 -0.078 0.16 -10000 0 -0.66 26 26
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.055 0.095 -10000 0 -0.4 18 18
MMP3 -0.017 0.048 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.014 0.095 -10000 0 -0.58 5 5
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
alphaV beta3 Integrin 0.025 0.089 -10000 0 -0.55 11 11
PTK2 0.008 0.15 -10000 0 -0.53 30 30
positive regulation of JNK cascade 0.013 0.099 -10000 0 -0.33 31 31
CDC42/GDP 0.029 0.14 0.44 1 -0.44 34 35
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 -0.4 31 31
nectin-3/I-afadin 0.007 0.13 -10000 0 -0.51 30 30
RAPGEF1 0.011 0.14 0.35 2 -0.5 29 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.008 0.16 -10000 0 -0.58 30 30
PDGFB-D/PDGFRB 0.025 0.032 -10000 0 -0.67 1 1
TLN1 -0.004 0.061 -10000 0 -0.78 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 0.025 0.007 -10000 0 -10000 0 0
Necl-5(dimer) 0.025 0.007 -10000 0 -10000 0 0
mol:GDP 0.015 0.17 0.47 1 -0.55 36 37
MLLT4 0.027 0.004 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
PI3K 0.048 0.12 -10000 0 -0.42 29 29
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.036 0.02 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly 0.008 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 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
CLDN1 -0.11 0.095 -10000 0 -0.61 10 10
JAM-A/CLDN1 0.038 0.13 -10000 0 -0.42 35 35
SRC 0.004 0.17 -10000 0 -0.64 31 31
ITGB3 0.011 0.1 -10000 0 -0.64 11 11
nectin-1(dimer)/I-afadin/I-afadin 0.036 0.02 -10000 0 -10000 0 0
FARP2 0.018 0.16 -10000 0 -0.54 32 32
RAC1 0.026 0.006 -10000 0 -10000 0 0
CTNNA1 0.026 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.022 0.12 -10000 0 -0.44 30 30
nectin-1/I-afadin 0.036 0.02 -10000 0 -10000 0 0
nectin-2/I-afadin 0.038 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.035 0.009 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.024 0.12 -10000 0 -0.44 30 30
CDC42/GTP/IQGAP1/filamentous actin 0.036 0.008 -10000 0 -10000 0 0
F11R 0.025 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 -10000 0 -0.42 30 30
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
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 -0.005 0.14 -10000 0 -0.37 63 63
TC10/GTP 0.041 0.042 -10000 0 -0.35 4 4
Insulin Receptor/Insulin/IRS1/Shp2 -0.001 0.16 -10000 0 -0.42 61 61
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 0.001 0.12 -10000 0 -0.65 14 14
AKT1 -0.029 0.14 0.36 5 -0.75 2 7
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 -0.036 0.14 -10000 0 -0.39 67 67
CBL/APS/CAP/Crk-II/C3G 0.065 0.052 -10000 0 -0.38 4 4
Insulin Receptor/Insulin/IRS1/NCK2 0.001 0.16 -10000 0 -0.41 61 61
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.14 -10000 0 -0.37 63 63
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.007 0.1 -10000 0 -0.43 8 8
RPS6KB1 -0.033 0.12 0.32 2 -0.66 2 4
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 0.026 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.012 0.13 -10000 0 -0.68 2 2
HRAS/GTP -0.024 0.11 -10000 0 -0.34 47 47
Insulin Receptor 0.027 0.01 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.014 0.14 -10000 0 -0.39 48 48
PRKCI 0.012 0.075 -10000 0 -0.49 5 5
Insulin Receptor/Insulin/GRB14/PDK1 -0.027 0.14 -10000 0 -0.36 71 71
SHC1 0.025 0.007 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.045 0.046 -10000 0 -0.43 2 2
PI3K 0.003 0.15 -10000 0 -0.38 63 63
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 -0.031 0.14 0.38 7 -0.4 12 19
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 -0.019 0.084 -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 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.052 0.041 -10000 0 -0.37 3 3
INPP5D -0.032 0.14 0.31 1 -0.39 61 62
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 -0.056 0.22 -10000 0 -0.67 59 59
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 61 62
GRB2 0.026 0.007 -10000 0 -10000 0 0
EIF4EBP1 -0.033 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 48 48
Insulin Receptor/Insulin/IRS1 -0.013 0.15 -10000 0 -0.41 61 61
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
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.02 0.012 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.003 0.065 -10000 0 -0.28 6 6
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 0.031 -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 -0.01 0.11 0.38 18 -10000 0 18
SHC 2-3/Grb2 0.011 0.12 -10000 0 -0.42 18 18
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.002 0.1 -10000 0 -0.55 10 10
SHC3 -0.005 0.12 -10000 0 -0.46 21 21
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 -0.004 0.077 0.3 7 -0.26 4 11
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 -0.44 7 7
TRKA/NEDD4-2 0.031 0.024 -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 0.021 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 0.025 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 -0.35 193 193
mol:GDP -0.013 0.1 0.35 8 -0.36 7 15
NGF (dimer) 0.021 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 0.026 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 0.06 0.025 -10000 0 -10000 0 0
RIT1/GTP 0.019 0.005 -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 -0.03 0.028 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.065 0.02 -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 45 45
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 45 45
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 0.15 -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 -0.042 0.083 -10000 0 -0.38 22 22
SOS1 0.027 0.005 -10000 0 -10000 0 0
MCF2L -0.028 0.12 -10000 0 -0.44 36 36
RGS19 0.026 0.008 -10000 0 -10000 0 0
CDC42 0.027 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.069 -10000 0 -0.48 2 2
Rac1/GDP -0.005 0.067 0.22 1 -0.25 3 4
NGF (dimer)/TRKA/GRIT 0.025 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 0.045 0.043 -10000 0 -0.44 3 3
MAP2K1 0.039 0.058 0.36 4 -10000 0 4
NGFR -0.016 0.13 -10000 0 -0.67 16 16
NGF (dimer)/TRKA/GIPC/GAIP 0.016 0.07 -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 0.031 -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 0.073 -10000 0 -0.52 7 7
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 0.045 -10000 0 -0.38 3 3
MATK 0.015 0.068 -10000 0 -0.61 5 5
NEDD4L 0.027 0.004 -10000 0 -10000 0 0
RAS family/GDP -0.019 0.042 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.003 0.076 -10000 0 -0.37 18 18
Rac1/GTP -0.11 0.12 -10000 0 -0.26 169 169
FRS2 family/SHP2/CRK family 0.057 0.043 -10000 0 -0.38 1 1
Presenilin action in Notch and Wnt 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
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 0.024 0.008 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.045 -10000 0 -0.67 2 2
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
TLE1 0.02 0.055 -10000 0 -0.68 3 3
AP1 -0.13 0.24 -10000 0 -0.46 154 154
NCSTN 0.025 0.007 -10000 0 -10000 0 0
ADAM10 0.011 0.1 -10000 0 -0.67 11 11
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.029 0.075 -10000 0 -0.55 4 4
NICD/RBPSUH 0.006 0.13 -10000 0 -0.64 11 11
WIF1 -0.015 0.046 -10000 0 -10000 0 0
NOTCH1 -0.003 0.13 -10000 0 -0.49 29 29
PSENEN 0.026 0.007 -10000 0 -10000 0 0
KREMEN2 0.016 0.038 -10000 0 -10000 0 0
DKK1 -0.001 0.07 -10000 0 -0.67 2 2
beta catenin/beta TrCP1 0.046 0.047 0.28 3 -10000 0 3
APH1B 0.027 0.004 -10000 0 -10000 0 0
APH1A 0.025 0.007 -10000 0 -10000 0 0
AXIN1 -0.006 0.082 0.38 1 -0.4 11 12
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 0.3 13 -10000 0 13
MAPK3 0.026 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.034 0.095 -10000 0 -0.44 19 19
HNF1A 0.026 0.005 -10000 0 -10000 0 0
CTBP1 0.026 0.004 -10000 0 -10000 0 0
MYC -0.017 0.25 -10000 0 -1.2 19 19
NKD1 0.007 0.11 -10000 0 -0.67 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 -0.46 154 154
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 0.073 0.33 2 -0.55 3 5
DVL1 0.025 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.048 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 0.41 13 -0.47 2 15
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 0.003 -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 0.061 0.33 13 -0.35 4 17
MAPK1 0.02 0.012 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.065 0.017 -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
Signaling events mediated by HDAC Class III

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
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 -0.67 221 221
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 0.046 0.028 -10000 0 -0.44 1 1
SIRT1/Histone H1b -0.006 0.07 -10000 0 -0.31 10 10
apoptosis -0.036 0.032 0.44 1 -10000 0 1
SIRT1/PGC1A -0.18 0.24 -10000 0 -0.44 221 221
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 0.046 -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 0.022 0.007 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.037 0.033 -10000 0 -0.44 1 1
CREBBP 0.026 0.006 -10000 0 -10000 0 0
MEF2D 0.025 0.007 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.031 0.028 -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 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
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 -0.055 0.21 -9999 0 -0.53 74 74
IL1A -0.03 0.18 -9999 0 -0.67 38 38
IL1B -0.021 0.14 -9999 0 -0.51 34 34
IRAK/TRAF6/p62/Atypical PKCs 0.061 0.037 -9999 0 -0.36 2 2
IL1R2 -0.043 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 0.026 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 0.002 -9999 0 -10000 0 0
IKK complex/ELKS 0.036 0.061 -9999 0 -10000 0 0
JUN -0.076 0.16 -9999 0 -0.37 111 111
MAP3K7 0.027 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.041 0.12 -9999 0 -0.39 33 33
IL1 alpha/IL1R1/IL1RAP/MYD88 0.035 0.13 -9999 0 -0.41 37 37
PIK3R1 0.026 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.047 0.12 -9999 0 -0.39 37 37
IL1 beta fragment/IL1R1/IL1RAP 0.017 0.12 -9999 0 -0.42 33 33
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 0.086 -9999 0 -0.51 10 10
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 0.017 0.12 -9999 0 -0.42 33 33
IL1 beta/IL1R2 -0.042 0.18 -9999 0 -0.48 67 67
IRAK/TRAF6/TAK1/TAB1/TAB2 0.036 0.028 -9999 0 -0.36 2 2
NF kappa B1 p50/RelA 0.028 0.11 -9999 0 -0.36 32 32
IRAK3 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.039 0.12 -9999 0 -0.39 35 35
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.006 0.085 -9999 0 -0.29 37 37
IL1 alpha/IL1R1/IL1RAP 0.019 0.13 -9999 0 -0.44 37 37
RELA 0.027 0.005 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.026 0.006 -9999 0 -10000 0 0
MYD88 0.027 0.003 -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 0.008 0.1 -9999 0 -0.39 10 10
CASP1 0.022 0.047 -9999 0 -0.67 2 2
IL1RN/IL1R2 -0.041 0.17 -9999 0 -0.54 47 47
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.032 0.12 -9999 0 -0.4 33 33
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.011 0.071 -9999 0 -0.36 2 2
PIK3CA 0.023 0.054 -9999 0 -0.67 3 3
IL1RN -0.011 0.11 -9999 0 -0.64 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
Syndecan-3-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
CTTN 0.027 0.005 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.027 0.12 -9999 0 -0.33 42 42
Syndecan-3/Neurocan 0.004 0.095 -9999 0 -0.34 33 33
POMC -0.12 0.28 -9999 0 -0.66 102 102
EGFR 0.019 0.07 -9999 0 -0.67 5 5
Syndecan-3/EGFR 0.027 0.043 -9999 0 -0.33 6 6
AGRP 0.003 0.034 -9999 0 -10000 0 0
NCSTN 0.025 0.007 -9999 0 -10000 0 0
PSENEN 0.025 0.007 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.027 0.004 -9999 0 -10000 0 0
APH1A 0.025 0.007 -9999 0 -10000 0 0
NCAN -0.025 0.17 -9999 0 -0.66 34 34
long-term memory 0.05 0.029 -9999 0 -0.27 1 1
Syndecan-3/IL8 0.03 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 0.027 -9999 0 -10000 0 0
SRC 0.026 0.008 -9999 0 -10000 0 0
PTN -0.037 0.2 -9999 0 -0.67 45 45
FGFR/FGF/Syndecan-3 0.015 0.006 -9999 0 -10000 0 0
neuron projection morphogenesis -0.022 0.13 -9999 0 -0.34 63 63
Syndecan-3/AgRP 0.031 0.024 -9999 0 -0.31 1 1
Syndecan-3/AgRP/MC4R 0.045 0.03 -9999 0 -0.29 1 1
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 -0.28 1 1
Syndecan-3/CASK 0.011 0.023 -9999 0 -0.26 2 2
alpha-MSH/MC4R -0.078 0.22 -9999 0 -0.5 102 102
Gamma Secretase 0.07 0.03 -9999 0 -10000 0 0
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 -0.008 0.14 -10000 0 -0.38 59 59
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 -0.036 0.14 -10000 0 -0.39 65 65
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 0.013 0.033 0.096 65 -10000 0 65
GNAL -0.062 0.23 -10000 0 -0.66 65 65
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 0.055 -10000 0 -0.38 10 10
MAPK11 0.006 0.004 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.016 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 -1.1 3 3
HSPA1B -0.022 0.31 -10000 0 -0.94 11 11
MAP2K1 0.025 0.044 -10000 0 -10000 0 0
BRCA2 -0.025 0.32 0.79 1 -1 14 15
FOXM1 -0.047 0.34 -10000 0 -1 17 17
XRCC1 -0.014 0.31 -10000 0 -0.92 11 11
FOXM1B/p19 -0.046 0.33 -10000 0 -0.91 23 23
Cyclin D1/CDK4 0.001 0.29 -10000 0 -0.83 11 11
CDC2 -0.026 0.32 -10000 0 -0.89 18 18
TGFA -0.013 0.29 -10000 0 -0.83 11 11
SKP2 -0.018 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 -0.66 9 9
FOXM1C/SP1 -0.028 0.33 -10000 0 -1 14 14
AURKB 0.008 0.13 -10000 0 -0.87 8 8
CENPF -0.011 0.31 0.78 1 -0.93 11 12
CDK4 0.027 0.019 -10000 0 -10000 0 0
MYC -0.028 0.31 -10000 0 -0.94 16 16
CHEK2 0.02 0.039 -10000 0 -10000 0 0
ONECUT1 -0.011 0.3 -10000 0 -0.9 11 11
CDKN2A -0.033 0.073 -10000 0 -10000 0 0
LAMA4 -0.022 0.31 -10000 0 -0.94 11 11
FOXM1B/HNF6 -0.018 0.32 -10000 0 -1 11 11
FOS -0.22 0.59 0.78 2 -1.2 128 130
SP1 0.026 0.009 -10000 0 -10000 0 0
CDC25B -0.017 0.31 0.79 1 -0.93 11 12
response to radiation 0.006 0.025 -10000 0 -10000 0 0
CENPB -0.017 0.31 0.79 1 -0.93 11 12
CENPA -0.031 0.32 -10000 0 -0.97 15 15
NEK2 -0.012 0.31 0.78 1 -0.94 10 11
HIST1H2BA -0.028 0.31 -10000 0 -0.94 11 11
CCNA2 0.026 0.023 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
CCNB1/CDK1 -0.033 0.33 -10000 0 -1.1 11 11
CCNB2 -0.024 0.31 -10000 0 -0.94 11 11
CCNB1 -0.024 0.32 -10000 0 -0.98 11 11
ETV5 -0.022 0.31 -10000 0 -0.94 11 11
ESR1 -0.058 0.38 -10000 0 -1.1 28 28
CCND1 -0.006 0.29 -10000 0 -0.86 11 11
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 -0.96 13 13
GAS1 -0.17 0.54 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 -0.89 11 11
CREBBP 0.026 0.006 -10000 0 -10000 0 0
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 0.02 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 0.37 5 -0.49 11 16
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 -0.48 11 17
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 0.35 6 -0.48 12 18
MADD 0.027 0.005 -10000 0 -10000 0 0
TFAP2A -0.043 0.22 -10000 0 -0.61 63 63
BID -0.012 0.061 -10000 0 -0.32 12 12
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 0.026 0.006 -10000 0 -10000 0 0
DNA repair -0.017 0.063 0.42 4 -0.21 19 23
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 0.32 20 -0.57 5 25
KRT18 0.021 0.04 -10000 0 -0.44 2 2
apoptosis 0.015 0.1 0.48 4 -0.47 10 14
DFFA 0.008 0.1 0.36 6 -0.49 11 17
DFFB 0.009 0.1 0.36 6 -0.49 11 17
PARP1 0.017 0.064 0.21 19 -0.43 4 23
actin filament polymerization -0.017 0.12 0.47 10 -0.54 11 21
TNF -0.057 0.22 -10000 0 -0.67 57 57
CYCS -0.001 0.048 0.28 2 -0.23 8 10
SATB1 0.02 0.085 0.52 2 -0.55 4 6
SLK 0.004 0.1 0.41 4 -0.48 13 17
p15 BID/BAX -0.01 0.07 -10000 0 -0.35 7 7
CASP2 -0.014 0.1 0.21 4 -0.37 18 22
JNK cascade -0.018 0.041 0.21 2 -0.27 3 5
CASP3 0.005 0.1 0.34 6 -0.5 12 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 -0.042 0.22 -10000 0 -0.6 63 63
stress fiber formation 0.004 0.1 0.41 4 -0.47 13 17
GZMB -0.007 0.1 -10000 0 -0.61 12 12
CASP1 0.015 0.026 -10000 0 -0.39 2 2
LMNB1 0.019 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 -0.4 6 17
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 -0.48 10 21
GAS2 0.002 0.1 0.36 4 -0.47 14 18
positive regulation of apoptosis 0.016 0.1 0.36 9 -0.36 9 18
PRF1 0.015 0.089 -10000 0 -0.67 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 -0.036 0.16 -10000 0 -0.44 63 63
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 -0.38 11 11
MAP2K4 -0.001 0.012 0.11 1 -10000 0 1
IL1B -0.022 0.095 0.18 1 -0.35 35 36
Channel 0.024 0.066 -10000 0 -0.37 13 13
NLRP1 -0.002 0.027 -10000 0 -0.38 2 2
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 -0.057 0.22 -10000 0 -0.67 57 57
VCAM1 -0.036 0.16 -10000 0 -0.44 63 63
platelet activation 0.011 0.028 -10000 0 -0.51 1 1
MAPKKK cascade -0.003 0.029 0.11 10 -0.1 19 29
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 -0.17 3 3
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 0.062 -10000 0 -0.35 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.002 0.1 -10000 0 -0.68 6 6
UGCG -0.058 0.22 -10000 0 -0.64 58 58
AKT1/mTOR/p70S6K/Hsp90/TERT 0.013 0.14 0.42 5 -0.41 23 28
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 -0.43 49 49
FRAP1 -0.016 0.19 0.44 2 -0.5 51 53
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 -0.51 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 0.065 -10000 0 -10000 0 0
PIK3R1 0.028 0.006 -10000 0 -10000 0 0
JAK1 0.028 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
MYC -0.006 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 0.042 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 -0.003 0.13 -10000 0 -0.52 20 20
SHC1 0.025 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.01 -10000 0 -0.066 11 11
PRKCZ -0.005 0.14 -10000 0 -0.54 20 20
NF kappa B1 p50/RelA 0.011 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 0.007 -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 -0.003 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 0.013 0.082 -10000 0 -0.67 6 6
BCL2 -0.042 0.27 0.47 4 -0.79 51 55
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.025 0.032 -10000 0 -0.67 1 1
Caspase 8 (4 units) 0.023 0.09 -10000 0 -0.48 4 4
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 -0.65 23 23
CYCS -0.008 0.093 -10000 0 -0.47 4 4
RIPK1 0.027 0.003 -10000 0 -10000 0 0
CD247 -0.016 0.16 -10000 0 -0.76 18 18
MAP2K7 -0.001 0.16 -10000 0 -0.63 22 22
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 -0.01 0.098 -10000 0 -0.41 10 10
NF-kappa-B/RelA/I kappa B alpha 0.043 0.078 -10000 0 -0.32 19 19
TRADD 0.026 0.006 -10000 0 -10000 0 0
MAP3K5 0.026 0.032 -10000 0 -0.67 1 1
CFLAR 0.027 0.005 -10000 0 -10000 0 0
FADD 0.027 0.005 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.043 0.079 -10000 0 -0.33 19 19
MAPK8 -0.005 0.16 0.35 1 -0.61 21 22
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 33 33
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0 0.11 -10000 0 -0.43 9 9
CHUK 0.005 0.098 0.28 3 -0.4 4 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.076 0.029 -10000 0 -0.38 1 1
TCRz/NEF -0.023 0.15 -10000 0 -0.45 47 47
TNF -0.057 0.22 -10000 0 -0.67 57 57
FASLG -0.049 0.23 -10000 0 -0.76 42 42
NFKB1 0.021 0.033 -10000 0 -0.18 2 2
TNFR1A/BAG4/TNF-alpha -0.004 0.16 -10000 0 -0.44 58 58
CASP6 0.039 0.096 -10000 0 -0.66 5 5
CASP7 0.01 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 -0.58 22 23
ErbB4 signaling events

Figure S75.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S75.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.014 -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 0.033 0.049 -10000 0 -0.67 2 2
ErbB4/ErbB4 -0.015 0.088 -10000 0 -0.38 2 2
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.029 0.14 -10000 0 -0.45 34 34
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 -0.001 0.11 -10000 0 -0.49 15 15
STAT1 0.023 0.024 -10000 0 -10000 0 0
HBEGF 0.018 0.034 -10000 0 -10000 0 0
PRLR -0.015 0.15 -10000 0 -0.67 25 25
E4ICDs/ETO2 -0.003 0.086 -10000 0 -0.43 3 3
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 0.12 -10000 0 -0.51 25 25
CBFA2T3 0.024 0.033 -10000 0 -0.67 1 1
ErbB4/ErbB2/HBEGF 0.01 0.073 -10000 0 -0.4 3 3
MAPK3 -0.013 0.12 -10000 0 -0.48 6 6
STAT1 (dimer) -0.002 0.086 -10000 0 -0.36 2 2
MAPK1 -0.017 0.11 -10000 0 -0.47 6 6
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 -0.024 0.15 -10000 0 -0.52 42 42
NRG3 -0.021 0.17 -10000 0 -0.65 35 35
NRG2 -0.051 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 -0.55 2 2
SHC1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 0.008 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 56 56
ErbB4/ErbB2/epiregulin 0.01 0.085 -10000 0 -0.42 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.016 0.12 -10000 0 -0.51 17 17
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 0.005 0.12 -10000 0 -0.37 25 25
MDM2 -0.013 0.078 0.26 2 -0.41 1 3
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.021 0.13 -10000 0 -0.4 41 41
STAT5A -0.001 0.071 -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 -0.45 5 5
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.072 -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 -0.015 0.088 -10000 0 -0.38 2 2
STAT5B 0.026 0.007 -10000 0 -10000 0 0
YAP1 0.005 0.066 -10000 0 -0.47 8 8
GRB2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.01 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
Visual signal transduction: Rods

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
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 0.06 -10000 0 -0.38 8 8
mol:Na + 0.028 0.071 -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 0.033 -10000 0 -10000 0 0
RDH5 -0.072 0.073 -10000 0 -10000 0 0
SAG -0.009 0.018 -10000 0 -10000 0 0
mol:Ca2+ -0.008 0.1 0.5 11 -0.38 9 20
Na + (4 Units) 0.021 0.067 -10000 0 -0.37 10 10
RGS9 -0.038 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 0.073 -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 -0.042 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 0.064 -10000 0 -0.4 8 8
RGS9BP -0.015 0.16 -10000 0 -0.66 29 29
Metarhodopsin II/Transducin 0.013 0.006 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.038 0.038 -10000 0 -0.41 3 3
PDE6A/B 0.031 0.028 -10000 0 -10000 0 0
mol:Pi -0.022 0.18 -10000 0 -0.45 71 71
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.037 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 0.16 -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 -0.42 2 2
GUCA1C -0.016 0.002 -10000 0 -10000 0 0
GUCA1B 0.023 0.055 -10000 0 -0.67 3 3
BARD1 signaling events

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
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 0.05 0.034 -10000 0 -0.44 2 2
MRE11A 0.024 0.045 -10000 0 -0.67 2 2
DNA-PK 0.04 0.026 -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 0.025 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 0.019 0.031 -10000 0 -10000 0 0
DNA repair 0.018 0.09 0.41 2 -0.45 6 8
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 -0.011 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 0.097 -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 0.098 -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 0.013 -10000 0 -10000 0 0
RAD50 0.026 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
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.025 0.007 -9999 0 -10000 0 0
SPHK1 0.022 0.023 -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 0.017 -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 -0.3 135 135
S1P/S1P4/Gi 0.003 0.079 -9999 0 -0.32 17 17
GNAQ 0.025 0.008 -9999 0 -10000 0 0
GNAZ 0.02 0.012 -9999 0 -10000 0 0
GNA14 -0.13 0.29 -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
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.038 0.059 -10000 0 -0.4 6 6
EPHB2 0.022 0.054 -10000 0 -0.67 3 3
Syndecan-2/TACI -0.09 0.2 -10000 0 -0.44 122 122
LAMA1 -0.021 0.18 -10000 0 -0.66 34 34
Syndecan-2/alpha2 ITGB1 0.043 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 -0.43 4 4
ITGA5 0.027 0.005 -10000 0 -10000 0 0
BAX 0.003 0.064 -10000 0 -0.46 1 1
EPB41 0.027 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.024 0.04 -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 0.058 -10000 0 -10000 0 0
dendrite morphogenesis 0.023 0.057 -10000 0 -0.43 7 7
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 -0.43 4 4
GNB2L1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.031 0.048 -10000 0 -0.41 4 4
MAPK1 -0.025 0.047 -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 -0.033 0.074 -10000 0 -10000 0 0
MAPK8 0.004 0.074 -10000 0 -0.43 13 13
Syndecan-2/alpha2/beta1 Integrin 0.033 0.12 -10000 0 -0.41 32 32
Syndecan-2/Kininogen 0.016 0.049 -10000 0 -0.44 4 4
ITGB1 0.027 0.004 -10000 0 -10000 0 0
SRC 0.022 0.044 0.35 1 -0.36 4 5
Syndecan-2/CASK/Protein 4.1 0.023 0.041 -10000 0 -0.4 4 4
extracellular matrix organization 0.024 0.044 -10000 0 -0.43 4 4
actin cytoskeleton reorganization -0.038 0.059 -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 -0.43 20 20
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 0.057 -10000 0 -0.43 7 7
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 0.041 -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 -0.67 122 122
RASA1 0.027 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin -0.008 0.058 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.026 0.044 -10000 0 -0.43 4 4
TGFB1 0.024 0.017 -10000 0 -10000 0 0
CASP3 0.018 0.044 -10000 0 -0.39 4 4
FN1 -0.084 0.068 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.005 0.087 -10000 0 -0.43 15 15
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 -0.081 0.066 -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 -0.39 4 4
angiogenesis -0.005 0.086 -10000 0 -0.43 15 15
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 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
VEGFR2 homodimer/VEGFA homodimer 0.03 0.07 -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 -0.46 15 15
PLCG1 -0.007 0.12 -10000 0 -0.4 30 30
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 0.012 -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 -0.59 32 32
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.019 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.003 -10000 0 -10000 0 0
KDR 0.021 0.063 -10000 0 -0.68 4 4
PLCB2 0.014 0.077 0.37 6 -0.4 7 13
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 -0.053 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 0.054 -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 0.013 0.079 -10000 0 -0.44 8 8
ABCC1 0.026 0.006 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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
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 -0.03 0.073 -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 0.086 -10000 0 -0.19 43 43
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 0.026 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 0.025 0.007 -10000 0 -10000 0 0
PTEN 0.026 0.018 -10000 0 -0.36 1 1
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 0.008 -10000 0 -10000 0 0
epithelial cell differentiation 0.055 0.016 -10000 0 -10000 0 0
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
ENAH 0.022 0.078 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 0.002 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 0.4 5 -10000 0 5
EGF -0.075 0.24 -10000 0 -0.67 72 72
NCKAP1 0.027 0.005 -10000 0 -10000 0 0
AQP3 -0.04 0.17 -10000 0 -0.53 49 49
cortical microtubule organization 0.055 0.016 -10000 0 -10000 0 0
GO:0000145 0.012 0.046 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 0.061 0.025 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.013 0.03 -10000 0 -10000 0 0
PVRL2 0.025 0.007 -10000 0 -10000 0 0
ZYX 0.021 0.02 -10000 0 -10000 0 0
ARF6/GTP 0.067 0.027 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.011 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 0.049 -10000 0 -10000 0 0
Wnt receptor signaling pathway -0.055 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 0.026 0.006 -10000 0 -10000 0 0
VCL 0.021 0.051 0.39 8 -10000 0 8
EFNA1 0.025 0.007 -10000 0 -10000 0 0
LPP 0.011 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 -0.005 0.14 -10000 0 -0.38 64 64
HGF -0.072 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 0.067 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 0.055 0.016 -10000 0 -10000 0 0
EXOC4 0.026 0.006 -10000 0 -10000 0 0
STX4 0.021 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 0.044 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 -0.03 0.073 -10000 0 -10000 0 0
PLEKHA7 0.026 0.052 0.38 8 -0.37 1 9
mol:GTP 0.059 0.024 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.033 0.067 0.48 7 -10000 0 7
cortical actin cytoskeleton stabilization 0.029 0.008 -10000 0 -10000 0 0
regulation of cell-cell adhesion 0.021 0.05 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
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.04 -9999 0 -0.35 3 3
AKT3 0.019 0.067 -9999 0 -0.48 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.025 0.032 -9999 0 -0.67 1 1
GNAI2 0.029 0.004 -9999 0 -10000 0 0
GNAI3 0.028 0.005 -9999 0 -10000 0 0
GNAI1 0.026 0.032 -9999 0 -0.67 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.026 0.008 -9999 0 -10000 0 0
S1PR2 0.024 0.014 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.006 0.07 -9999 0 -0.3 16 16
MAPK3 0.003 0.065 -9999 0 -0.29 15 15
MAPK1 0.014 0.058 -9999 0 -0.28 15 15
JAK2 0.007 0.067 -9999 0 -0.4 3 3
CXCR4 0.003 0.064 -9999 0 -0.29 15 15
FLT1 0.027 0.032 -9999 0 -0.67 1 1
RhoA/GDP 0.02 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.004 -9999 0 -10000 0 0
SRC 0.003 0.063 -9999 0 -0.28 15 15
S1P/S1P3/Gi 0.006 0.07 -9999 0 -0.3 16 16
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 0.054 -9999 0 -0.67 3 3
S1P/S1P2/Gi 0.004 0.074 -9999 0 -0.32 16 16
VEGFR1 homodimer/VEGFA homodimer 0.04 0.056 -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 -0.13 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 -0.28 15 15
Signaling events mediated by PRL

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
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 0.034 -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 -0.41 4 4
TUBA1B 0.027 0.005 -10000 0 -10000 0 0
EGR1 -0.086 0.21 -10000 0 -0.5 101 101
CDK2/Cyclin E1 0.018 0.077 -10000 0 -0.54 1 1
MAPK3 0.009 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 -0.39 100 100
PTP4A3 0.013 0.043 -10000 0 -10000 0 0
PTP4A2 0.027 0.005 -10000 0 -10000 0 0
ITGB1 0.008 0.027 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 -0.011 0.082 -10000 0 -0.37 8 8
Rab GGTase beta/Rab GGTase alpha 0.039 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.054 0.16 -10000 0 -0.41 3 3
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 -0.01 0.081 -10000 0 -0.61 2 2
cell motility -0.004 0.095 0.31 4 -0.71 2 6
PRL-1/alpha Tubulin -0.05 0.16 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.021 0.073 -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 -0.069 0.16 -10000 0 -0.39 100 100
ATF5 0.02 0.029 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.024 0.043 -10000 0 -10000 0 0
TP53 -0.009 0.038 -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 S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.027 0.005 -10000 0 -10000 0 0
HDAC3 0.026 0.006 -10000 0 -10000 0 0
VDR 0.026 0.008 -10000 0 -10000 0 0
Cbp/p300/PCAF 0.04 0.026 -10000 0 -10000 0 0
EP300 0.02 0.012 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.003 0.069 -10000 0 -0.32 9 9
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 -0.36 14 28
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 -0.35 8 9
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.011 0.097 -10000 0 -0.57 10 10
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.02 0.006 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.003 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 0.008 -10000 0 -10000 0 0
RARG 0.027 0.005 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.034 0.011 -10000 0 -10000 0 0
MAPK3 0.027 0.006 -10000 0 -10000 0 0
MAPK1 0.02 0.012 -10000 0 -10000 0 0
MAPK8 0.014 0.095 -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 0.012 0.14 0.38 5 -0.54 23 28
RXRG -0.028 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 0.021 0.015 -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 0.087 -10000 0 -0.36 19 19
NRIP1 0.013 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 -0.01 0.11 -10000 0 -0.55 19 19
PRKACA 0.025 0.008 -10000 0 -10000 0 0
CDK7 0.026 0.005 -10000 0 -10000 0 0
TFIIH 0.053 0.012 -10000 0 -10000 0 0
RAR alpha/9cRA 0.047 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 0.049 0.018 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.026 0.046 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 0.29 7 -0.47 29 36
mol:DAG -0.016 0.095 0.35 11 -0.25 15 26
HRAS 0.027 0.012 -10000 0 -10000 0 0
RAP1A 0.028 0.007 -10000 0 -10000 0 0
ARF5/GDP 0.035 0.064 0.28 2 -0.35 4 6
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 0.025 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 -0.002 0.13 -10000 0 -0.66 18 18
mol:IP3 -0.013 0.069 0.24 11 -0.2 7 18
LYN 0.027 0.005 -10000 0 -10000 0 0
ARF1/GDP 0.034 0.072 0.3 7 -0.35 6 13
RhoA/GDP 0.039 0.043 0.35 2 -10000 0 2
PDK1/Src/Hsp90 0.05 0.034 -10000 0 -0.44 2 2
BLNK 0.027 0.004 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.034 0.076 0.35 16 -0.3 1 17
SRC 0.026 0.008 -10000 0 -10000 0 0
PLEKHA2 0.005 0.016 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.023 0.021 -10000 0 -0.34 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 0.024 0.041 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 0.038 -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 0.088 -10000 0 -0.54 10 10
SGK1 0.018 0.098 -10000 0 -0.56 11 11
INPP5D 0.019 0.033 -10000 0 -10000 0 0
mol:GDP 0.027 0.08 0.29 13 -0.32 9 22
SOS1 0.027 0.005 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.03 0.05 0.28 9 -10000 0 9
mol:PI-3-4-5-P3 -0.007 0.015 -10000 0 -10000 0 0
ARAP3/RAP1A/GTP 0.019 0.017 -10000 0 -10000 0 0
VAV1 0.011 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 49 58
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.028 0.12 0.38 9 -0.35 16 25
LCK 0.012 0.082 -10000 0 -0.67 6 6
BTK -0.005 0.066 0.3 13 -0.36 6 19
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.001 0.099 0.49 5 -10000 0 5
RAD9A 0.027 0.005 -10000 0 -10000 0 0
AP1 -0.19 0.37 -10000 0 -0.72 149 149
IFNAR2 0.027 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 0.24 -10000 0 -0.67 72 72
SMG5 0.025 0.007 -10000 0 -10000 0 0
SMG6 0.026 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.041 0.008 -10000 0 -10000 0 0
TERT/c-Abl -0.003 0.081 0.47 1 -10000 0 1
SAP18 0.026 0.007 -10000 0 -10000 0 0
MRN complex 0.05 0.034 -10000 0 -0.44 2 2
WT1 0.007 0.047 -10000 0 -10000 0 0
WRN 0.025 0.032 -10000 0 -0.67 1 1
SP1 0.028 0.006 -10000 0 -10000 0 0
SP3 0.027 0.005 -10000 0 -10000 0 0
TERF2IP 0.026 0.006 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.012 0.081 -10000 0 -10000 0 0
Mad/Max 0.04 0.009 -10000 0 -10000 0 0
TERT -0.001 0.1 0.5 5 -10000 0 5
CCND1 0.002 0.099 0.53 6 -10000 0 6
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 0.058 -10000 0 -0.29 3 3
CDKN1B -0.029 0.14 -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 0.037 0.011 -10000 0 -10000 0 0
UBE3A 0.027 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 -0.022 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 -0.46 13 14
IRF1 0.03 0.009 -10000 0 -10000 0 0
ESR1 -0.013 0.14 -10000 0 -0.65 23 23
KU/TER 0.029 0.019 -10000 0 -10000 0 0
ATM/TRF2 0.038 0.024 -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 0.009 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 0.018 0.08 -10000 0 -10000 0 0
NR2F2 0.026 0.004 -10000 0 -10000 0 0
MAPK3 0.002 0.013 -10000 0 -10000 0 0
MAPK1 0.002 0.011 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.024 0.017 -10000 0 -10000 0 0
NFKB1 0.027 0.004 -10000 0 -10000 0 0
HNRNPC 0.027 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.023 -10000 0 -0.48 1 1
NBN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.02 0.07 -10000 0 -0.67 5 5
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.043 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 0.026 0.006 -10000 0 -10000 0 0
HSP90AA1 0.027 0.005 -10000 0 -10000 0 0
TGFB1 0.024 0.017 -10000 0 -10000 0 0
TRF2/BLM 0.037 0.012 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.002 0.084 0.5 2 -10000 0 2
SP1/HDAC2 0.042 0.009 -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 0.068 -10000 0 -0.43 10 10
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 0.01 0.078 -10000 0 -10000 0 0
response to DNA damage stimulus 0.003 0.019 -10000 0 -0.14 1 1
MRN complex/TRF2/Rap1 0.071 0.036 -10000 0 -0.38 2 2
TRF2/WRN 0.037 0.025 -10000 0 -0.48 1 1
Telomerase/hnRNP C1/C2 0.012 0.081 -10000 0 -10000 0 0
E2F1 -0.018 0.07 -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
VEGFR1 specific signals

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
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 -0.72 1 1
HIF1A 0.033 0.019 -10000 0 -0.37 1 1
GAB1 0.027 0.004 -10000 0 -10000 0 0
AKT1 -0.019 0.13 -10000 0 -1 2 2
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 0.02 0.042 -10000 0 -0.91 1 1
PGF -0.044 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 -0.56 9 11
mol:Ca2+ -0.021 0.13 -10000 0 -0.4 51 51
MAPK3 -0.038 0.13 0.36 2 -0.98 1 3
MAPK1 -0.041 0.13 -10000 0 -0.98 1 1
PIK3R1 0.026 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 0.093 -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 -0.95 1 1
PI3K 0.015 0.14 -10000 0 -1.1 1 1
PRKCA -0.039 0.14 -10000 0 -1 1 1
PRKCB -0.034 0.13 -10000 0 -0.46 10 10
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 -1 1 1
mol:L-citrulline -0.007 0.12 0.47 3 -0.77 1 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.058 0.061 -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 -1 1 1
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
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.28 -10000 0 -0.67 98 98
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.025 0.013 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
HIF1A/p53 0.033 0.039 0.35 1 -10000 0 1
HIF1A 0.009 0.024 -10000 0 -0.25 2 2
COPS5 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.054 0.052 -10000 0 -0.39 3 3
FIH (dimer) 0.027 0.004 -10000 0 -10000 0 0
CDKN2A -0.031 0.073 -10000 0 -10000 0 0
ARNT/IPAS -0.067 0.21 -10000 0 -0.49 98 98
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 0.037 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 0.025 0.007 -10000 0 -10000 0 0
EGLN1 0.024 0.032 -10000 0 -0.67 1 1
TP53 0.026 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.026 0.075 -10000 0 -0.54 7 7
ARNT 0.025 0.007 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.02 0.012 -10000 0 -10000 0 0
HIF1A/p19ARF 0.038 0.052 0.32 6 -10000 0 6
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.015 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 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
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 0.016 0.095 -9999 0 -0.49 15 15
alpha4/beta1 Integrin 0.034 0.046 -9999 0 -0.51 3 3
PLK1 signaling events

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.006 0.016 0.12 1 -0.15 2 3
BUB1B 0.014 0.031 0.19 9 -10000 0 9
PLK1 0.012 0.03 0.16 13 -0.1 1 14
PLK1S1 0.015 0.026 0.17 10 -10000 0 10
KIF2A 0.018 0.067 0.32 20 -0.39 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 0.037 -10000 0 -10000 0 0
WEE1 0.022 0.046 0.31 4 -0.34 2 6
cytokinesis 0.011 0.062 0.26 9 -0.23 6 15
PP2A-alpha B56 0.048 0.095 -10000 0 -0.57 8 8
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 0.26 10 -0.39 3 13
RhoA/GTP 0.02 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.018 0.066 0.32 20 -0.38 1 21
PPP2CA 0.026 0.006 -10000 0 -10000 0 0
FZR1 0.025 0.008 -10000 0 -10000 0 0
TPX2 0.015 0.027 0.17 11 -10000 0 11
PAK1 0.026 0.005 -10000 0 -10000 0 0
SPC24 0.015 0.037 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
CLSPN 0.012 0.029 0.14 1 -0.29 3 4
GORASP1 0.027 0.004 -10000 0 -10000 0 0
metaphase 0.001 0.006 0.023 27 -10000 0 27
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 0.02 12 -10000 0 12
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 -0.55 14 14
TPT1 0.004 0.045 0.14 4 -0.18 24 28
CDC25C 0.019 0.025 0.17 8 -10000 0 8
CDC25B 0.027 0.011 -10000 0 -10000 0 0
SGOL1 0.006 0.016 0.15 2 -0.12 1 3
RHOA 0.027 0.003 -10000 0 -10000 0 0
CCNB1/CDK1 0.042 0.014 -10000 0 -10000 0 0
CDC14B 0.003 0.045 -10000 0 -0.38 6 6
CDC20 0.025 0.019 -10000 0 -10000 0 0
PLK1/PBIP1 0.01 0.019 0.14 3 -10000 0 3
mitosis -0.001 0.003 0.019 5 -10000 0 5
FBXO5 0.013 0.037 0.21 9 -0.34 1 10
CDC2 0.002 0.001 0.011 1 -10000 0 1
NDC80 0.009 0.049 -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 4 -0.18 24 28
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 0.14 14 -10000 0 14
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 0.021 0.02 0.18 3 -10000 0 3
PPP1CB/MYPT1 0.04 0.009 -10000 0 -10000 0 0
KIF20A 0.005 0.053 -10000 0 -10000 0 0
APC/C/CDC20 0.025 0.024 0.18 2 -10000 0 2
PPP2R1A 0.025 0.007 -10000 0 -10000 0 0
chromosome segregation 0.01 0.019 0.14 3 -10000 0 3
PRC1 0.027 0.004 -10000 0 -10000 0 0
ECT2 0.01 0.041 0.21 9 -0.4 2 11
C13orf34 0.01 0.026 0.13 14 -0.081 1 15
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 -10000 0 9
spindle assembly 0.014 0.037 0.17 18 -10000 0 18
spindle stabilization 0.015 0.026 0.17 10 -10000 0 10
APC/C/HCDH1 0.019 0.041 -10000 0 -0.32 6 6
MKLP2/PLK1 0.013 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 -0.42 30 32
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
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.027 0.005 -10000 0 -10000 0 0
NFATC1 0.036 0.094 0.46 9 -0.38 9 18
NFATC2 -0.022 0.097 0.29 8 -0.27 30 38
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 -0.4 10 11
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 0.097 -10000 0 -0.43 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 0.078 -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 -0.45 26 26
CABIN1 -0.007 0.084 0.28 1 -0.4 9 10
CALM1 0.023 0.009 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
CAMK4 0.013 0.085 -10000 0 -0.67 7 7
mol:Ca2+ -0.004 0.008 -10000 0 -10000 0 0
MAPK3 0.026 0.006 -10000 0 -10000 0 0
YWHAH 0.02 0.012 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.036 0.012 -10000 0 -10000 0 0
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.011 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 -0.47 3 5
PRKCH 0.027 0.005 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.013 0.031 -10000 0 -10000 0 0
CASP3 0.025 0.005 -10000 0 -10000 0 0
PIM1 0.027 0.003 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.012 -10000 0 -10000 0 0
apoptosis 0.009 0.044 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.053 -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 0.024 -10000 0 -10000 0 0
PRKCQ 0.019 0.072 -10000 0 -0.62 6 6
FKBP38/BCL2 -0.002 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 0.41 7 -0.44 5 12
CaM/Ca2+/FKBP38 0.02 0.025 -10000 0 -10000 0 0
FKBP12/FK506 0.02 0.004 -10000 0 -10000 0 0
CSNK1A1 0.005 0.02 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.013 0.062 -10000 0 -0.45 7 7
NFATc/ERK1 0.043 0.08 0.44 3 -0.48 2 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.009 0.1 -10000 0 -0.44 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 -0.36 6 6
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 0.093 0.43 10 -0.41 4 14
CREBBP 0.013 0.022 -10000 0 -10000 0 0
BCL2 -0.026 0.18 -10000 0 -0.67 38 38
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 0.024 0.021 -10000 0 -10000 0 0
PIK3CA 0.024 0.054 -10000 0 -0.67 3 3
JAK3 -0.012 0.065 -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 -0.57 17 17
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 0.023 0.005 -10000 0 -10000 0 0
LCK 0.012 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 0.054 -10000 0 -0.67 3 3
CCND3 0.008 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 -0.18 1 1
CCND2 0.011 0.024 -10000 0 -10000 0 0
RB1 -0.016 0.049 0.32 2 -0.24 14 16
CDK4 0.014 0.042 0.26 10 -10000 0 10
CDK6 0.016 0.043 0.26 10 -0.16 1 11
G1/S progression 0.016 0.05 0.24 15 -0.32 2 17
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 16 16
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 0.072 -10000 0 -0.29 16 16
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 15 15
MAPK1 0.009 0.06 -10000 0 -0.31 15 15
S1P/S1P5/Gi -0.001 0.074 -10000 0 -0.32 17 17
GNAI1 0.025 0.032 -10000 0 -0.67 1 1
CDC42/GDP 0.02 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.032 0.025 -10000 0 -0.44 1 1
RHOA 0.035 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 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
Condensin I complex 0.017 0.041 -10000 0 -0.25 2 2
STMN1 0.001 0.042 -10000 0 -10000 0 0
Aurora B/RasGAP/Survivin 0.052 0.051 -10000 0 -0.44 1 1
Chromosomal passenger complex/Cul3 protein complex 0.014 0.05 -10000 0 -0.25 11 11
BIRC5 0.017 0.048 -10000 0 -0.68 1 1
DES -0.32 0.3 -10000 0 -0.57 286 286
Aurora C/Aurora B/INCENP 0.054 0.045 -10000 0 -0.45 2 2
Aurora B/TACC1 0.03 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 -10000 0 -10000 0 0
Cul3 protein complex 0.038 0.072 -10000 0 -0.44 10 10
KIF2C 0.015 0.027 -10000 0 -0.47 1 1
PEBP1 0.027 0.006 -10000 0 -10000 0 0
KIF20A 0.004 0.053 -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 -10000 0 -0.54 8 8
PSMA3 0.027 0.005 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.003 -10000 0 -10000 0 0
H3F3B 0.011 0.017 -10000 0 -10000 0 0
AURKB 0.001 0.065 -10000 0 -10000 0 0
AURKC 0.02 0.03 -10000 0 -10000 0 0
CDCA8 0.027 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 -0.38 2 2
AURKA 0.026 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 0.078 -10000 0 -0.68 1 1
hSgo1/Aurora B/Survivin 0.047 0.056 -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 0.03 -10000 0 -10000 0 0
CENPA 0.019 0.04 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 0.04 -10000 0 -0.32 2 2
RASA1 0.027 0.005 -10000 0 -10000 0 0
KLHL9 0.025 0.007 -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 -0.4 1 1
KIF23 0.021 0.034 -10000 0 -10000 0 0
VIM 0 0.039 -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 -0.51 8 8
Chromosomal passenger complex 0.015 0.036 -10000 0 -0.26 3 3
Chromosomal passenger complex/EVI5 0.1 0.069 -10000 0 -0.42 3 3
TACC1 0.025 0.032 -10000 0 -0.67 1 1
PPP2R5D 0.027 0.003 -10000 0 -10000 0 0
CUL3 0.027 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.029 0.1 -10000 0 -0.5 7 7
CaM/Ca2+ 0.02 0.003 -10000 0 -10000 0 0
AKT1 0.027 0.005 -10000 0 -10000 0 0
AKT2 0.025 0.007 -10000 0 -10000 0 0
STXBP4 0.024 0.032 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.023 0.1 0.34 6 -0.5 7 13
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 -0.052 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 0.004 0.05 -10000 0 -10000 0 0
PRKCI 0.027 0.003 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.02 0.003 -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 -0.034 0.094 -10000 0 -0.35 15 15
VAMP2 0.026 0.007 -10000 0 -10000 0 0
SLC2A4 0.022 0.11 0.35 5 -0.57 7 12
STX4 0.026 0.006 -10000 0 -10000 0 0
GSK3B 0.024 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
Class I PI3K signaling events mediated by Akt

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
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 0.023 -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 0.034 0.32 1 -10000 0 1
TSC1 0.021 0.024 -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 0.36 6 -0.32 8 14
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 0.034 -10000 0 -0.44 2 2
YWHAE 0.026 0.007 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
AKT2/p21CIP1 0.022 0.029 -10000 0 -0.32 2 2
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 0.023 -10000 0 -10000 0 0
BAD/BCL-XL 0.046 0.034 0.28 1 -10000 0 1
mTORC2 0.03 0.023 -10000 0 -0.4 1 1
AKT2 0.014 0.026 -10000 0 -0.39 2 2
FOXO1-3a-4/14-3-3 family 0.02 0.08 0.37 8 -0.36 4 12
PDPK1 0.023 0.045 -10000 0 -0.67 2 2
MDM2 0.022 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.041 0.035 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.039 0.034 -10000 0 -10000 0 0
TSC1/TSC2 0.023 0.039 0.3 4 -10000 0 4
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.033 -10000 0 -10000 0 0
glucose import -0.056 0.16 0.21 5 -0.41 78 83
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.026 0.029 0.2 3 -10000 0 3
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
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.005 0.16 -10000 0 -0.44 57 57
Ran/GTP/Exportin 1/HDAC1 0.007 0.002 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.019 0.14 -10000 0 -0.38 56 56
SUMO1 0.027 0.005 -10000 0 -10000 0 0
ZFPM1 0.026 0.007 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.013 0.009 -10000 0 -10000 0 0
FKBP3 0.027 0.005 -10000 0 -10000 0 0
Histones 0.036 0.083 -10000 0 -10000 0 0
YY1/LSF 0.006 0.065 -10000 0 -0.43 4 4
SMG5 0.025 0.007 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.007 0.11 -10000 0 -0.31 55 55
I kappa B alpha/HDAC1 0.011 0.081 -10000 0 -10000 0 0
SAP18 0.026 0.007 -10000 0 -10000 0 0
RELA -0.016 0.11 -10000 0 -0.47 14 14
HDAC1/Smad7 0.051 0.016 -10000 0 -10000 0 0
RANGAP1 0.02 0.012 -10000 0 -10000 0 0
HDAC3/TR2 0.012 0.081 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.031 0.037 -10000 0 -0.44 2 2
NF kappa B1 p50/RelA -0.024 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 0.026 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 0.029 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 0.053 -10000 0 -0.28 1 1
NuRD/MBD2 Complex (MeCP1) 0.032 0.031 -10000 0 -0.4 1 1
PPARG -0.022 0.14 -10000 0 -0.39 59 59
HDAC8/hEST1B 0.046 0.021 -10000 0 -10000 0 0
UBE2I 0.026 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.027 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.012 0.081 -10000 0 -10000 0 0
MBD3L2 -0.015 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.051 0.015 -10000 0 -10000 0 0
CREBBP 0.026 0.006 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.036 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 0.021 0.058 -10000 0 -0.31 1 1
EP300 0.02 0.012 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.018 0.012 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 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 -10000 0 0
nuclear export -0.046 0.021 -10000 0 -10000 0 0
PRKACA 0.025 0.008 -10000 0 -10000 0 0
GATAD2B 0.025 0.007 -10000 0 -10000 0 0
GATAD2A 0.025 0.008 -10000 0 -10000 0 0
GATA2/HDAC3 0.012 0.081 -10000 0 -10000 0 0
GATA1/HDAC1 0.034 0.013 -10000 0 -10000 0 0
GATA1/HDAC3 0.009 0.08 -10000 0 -10000 0 0
CHD4 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.025 0.17 -10000 0 -0.51 57 57
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 -0.31 1 1
HDAC complex 0.062 0.036 -10000 0 -0.39 2 2
GATA1/Fog1 0.034 0.014 -10000 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0.053 0.014 -10000 0 -10000 0 0
TNF -0.057 0.22 -10000 0 -0.67 57 57
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 56 56
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 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
BCL3/RelA 0.037 0.013 -10000 0 -10000 0 0
FBXW11 0.026 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.003 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 0.03 0.011 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.032 0.008 -10000 0 -10000 0 0
PIK3CA 0.023 0.054 -10000 0 -0.67 3 3
NF kappa B1 p50 dimer 0.025 0.023 0.25 5 -10000 0 5
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
NFKB1 0.017 0.003 -10000 0 -10000 0 0
RELA 0.027 0.005 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.02 0.038 -10000 0 -0.31 5 5
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.04 0.039 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
PI3K 0.036 0.043 -10000 0 -0.51 3 3
NF kappa B1 p50/RelA 0.02 0.038 -10000 0 -0.31 5 5
IKBKB 0.027 0.005 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -10000 0 -10000 0 0
SYK 0.025 0.008 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.028 0.038 -10000 0 -10000 0 0
cell death 0.038 0.038 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.003 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 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
HDAC1 0.027 0.022 0.25 1 -10000 0 1
AES 0.025 0.018 0.2 1 -10000 0 1
FBXW11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.039 0.009 -10000 0 -10000 0 0
SMAD4 0.027 0.005 -10000 0 -10000 0 0
DKK2 -0.003 0.14 -10000 0 -0.66 20 20
TLE1 0.021 0.056 -10000 0 -0.66 3 3
MACF1 0.027 0.005 -10000 0 -10000 0 0
CTNNB1 0.048 0.088 0.46 16 -10000 0 16
WIF1 -0.014 0.047 -10000 0 -10000 0 0
beta catenin/RanBP3 0.03 0.084 0.38 24 -10000 0 24
KREMEN2 0.016 0.038 -10000 0 -10000 0 0
DKK1 -0.001 0.07 -10000 0 -0.67 2 2
beta catenin/beta TrCP1 0.048 0.045 0.49 1 -10000 0 1
FZD1 0.026 0.006 -10000 0 -10000 0 0
AXIN2 -0.029 0.3 0.57 18 -1.4 18 36
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 0.093 0.3 1 -0.55 4 5
Axin1/APC/GSK3 0.034 0.045 0.34 4 -10000 0 4
Axin1/APC/GSK3/beta catenin/Macf1 0.034 0.028 0.32 1 -10000 0 1
HNF1A 0.027 0.02 0.21 2 -10000 0 2
CTBP1 0.027 0.02 0.24 1 -10000 0 1
MYC -0.037 0.24 0.55 5 -1.4 14 19
RANBP3 0.025 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.034 0.095 -10000 0 -0.44 19 19
NKD1 0.007 0.11 -10000 0 -0.67 13 13
TCF4 0.027 0.019 -10000 0 -10000 0 0
TCF3 0.025 0.02 0.23 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.065 0.02 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.021 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 0.039 0.11 -10000 0 -0.52 9 9
DKK1/LRP6/Kremen 2 0.048 0.044 -10000 0 -0.47 2 2
LRP6 0.027 0.005 -10000 0 -10000 0 0
CSNK1A1 0.026 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 -0.68 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 0.031 0.021 -10000 0 -10000 0 0
CREBBP 0.027 0.02 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.009 0.002 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.036 0.013 -10000 0 -10000 0 0
STXBP1 0.025 0.008 -10000 0 -10000 0 0
ACh/CHRNA1 0.01 0.044 -10000 0 -0.46 1 1
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 -0.46 1 1
UNC13B 0.025 0.007 -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 -0.48 25 25
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
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.025 0.089 -10000 0 -0.55 11 11
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 0.093 -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 -0.69 6 6
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 -0.44 5 5
SHC1 0.025 0.007 -10000 0 -10000 0 0
SHC2 0.021 0.055 -10000 0 -0.67 3 3
HRAS/GDP 0.04 0.078 -10000 0 -0.64 5 5
SH2D2A -0.01 0.14 -10000 0 -0.67 22 22
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS 0.058 0.095 -10000 0 -0.65 4 4
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.024 0.13 -10000 0 -0.46 28 28
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 0.088 -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 -0.44 5 5
HIF1A 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.058 0.089 -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 0.047 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 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.023 0.092 -10000 0 -0.71 6 6
HIF1A/ARNT 0.037 0.012 -10000 0 -10000 0 0
SHB 0.025 0.007 -10000 0 -10000 0 0
VEGFA 0.025 0.054 -10000 0 -0.67 3 3
VEGFC 0.025 0.032 -10000 0 -0.67 1 1
FAK1/Vinculin 0.04 0.1 0.33 1 -0.69 6 7
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 0.048 0.12 -10000 0 -0.52 16 16
PTPN6 0.027 0.005 -10000 0 -10000 0 0
EPAS1 0.03 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 0.044 -10000 0 -0.67 2 2
MAPK3 0.003 0.091 0.38 1 -0.73 5 6
MAPK1 -0.003 0.09 0.38 1 -0.74 5 6
VEGFA145/NRP2 0.027 0.054 -10000 0 -0.51 3 3
VEGFR1/2 heterodimer 0.03 0.093 -10000 0 -0.96 4 4
KDR 0.019 0.09 -10000 0 -0.98 4 4
VEGFA165/NRP1/VEGFR2 homodimer 0.054 0.099 -10000 0 -0.8 5 5
SRC 0.026 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.011 0.11 0.38 11 -0.86 4 15
PI3K 0.042 0.097 -10000 0 -0.87 4 4
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.048 0.094 -10000 0 -0.74 6 6
FES 0.024 0.096 -10000 0 -0.73 6 6
GAB1 0.03 0.093 -10000 0 -0.77 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.047 0.094 -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 0.025 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 0.094 -10000 0 -0.74 6 6
PI3K/GAB1 0.051 0.084 -10000 0 -0.62 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.07 0.092 -10000 0 -0.68 6 6
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 -0.73 6 6
actin cytoskeleton reorganization 0.024 0.13 -10000 0 -0.46 28 28
PTK2 0.026 0.1 0.32 1 -0.75 6 7
EDG1 0.012 0.089 -10000 0 -0.64 7 7
mol:DAG 0.023 0.092 -10000 0 -0.71 6 6
CaM/Ca2+ 0.036 0.085 -10000 0 -0.8 4 4
MAP2K3 0.01 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 -0.73 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.057 0.093 -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 -0.76 4 4
FYN 0.027 0.004 -10000 0 -10000 0 0
VEGFB/NRP1 0.028 0.085 -10000 0 -0.81 4 4
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 -0.71 4 4
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 -0.64 11 11
NOS3 0.04 0.1 0.49 6 -0.55 6 12
VEGFR2 homodimer/VEGFA homodimer/Sck 0.041 0.099 -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 0.093 0.36 1 -0.81 4 5
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 0.027 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 0.025 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 -0.69 6 6
MAP3K13 0.016 0.12 -10000 0 -0.54 14 14
PDPK1 0.028 0.081 -10000 0 -0.66 5 5
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.025 0.052 0.31 1 -0.66 1 2
PDGFB-D/PDGFRB/SLAP 0.037 0.027 -10000 0 -0.51 1 1
PDGFB-D/PDGFRB/APS/CBL 0.051 0.034 -10000 0 -0.43 2 2
AKT1 0.03 0.086 0.5 11 -10000 0 11
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.029 0.053 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 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.035 0.024 -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 0.082 0.43 11 -0.76 1 12
PTEN 0.026 0.018 -10000 0 -0.36 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.001 0.056 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.037 0.036 -10000 0 -0.51 2 2
PDGFB-D/PDGFRB/GRB10 0.038 0.026 -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 0.083 0.48 11 -10000 0 11
GAB1 0.029 0.094 0.45 11 -0.78 1 12
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 0.026 -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 0.026 0.005 -10000 0 -10000 0 0
mol:IP3 0.034 0.083 0.43 11 -0.76 1 12
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.011 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.017 0.052 -10000 0 -0.57 1 1
SHB 0.025 0.007 -10000 0 -10000 0 0
BLK -0.14 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 0.026 -10000 0 -0.51 1 1
LCK 0.011 0.08 -10000 0 -0.65 6 6
PDGFRB 0.026 0.032 -10000 0 -0.68 1 1
ACP1 0.027 0.005 -10000 0 -10000 0 0
HCK 0.024 0.031 -10000 0 -0.44 1 1
ABL1 0.026 0.096 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 0.024 -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 -10000 0 -0.45 1 1
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 0.023 -10000 0 -10000 0 0
EDG1 0.001 0.005 -10000 0 -10000 0 0
mol:DAG 0.034 0.083 0.43 11 -0.76 1 12
PLCG1 0.034 0.084 0.44 11 -0.79 1 12
NHERF/PDGFRB 0.05 0.028 -10000 0 -0.44 1 1
YES1 0.015 0.056 0.37 1 -0.51 4 5
cell migration 0.049 0.028 -10000 0 -0.44 1 1
SHC/Grb2/SOS1 0.072 0.035 -10000 0 -10000 0 0
SLC9A3R2 0.026 0.006 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.062 0.033 -10000 0 -0.4 1 1
FYN 0.016 0.05 -10000 0 -0.53 2 2
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 0.55 19 -0.46 11 30
PRKCD 0.024 0.03 -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
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
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 0.063 -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 -0.34 2 2
MAP3K1 0.026 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 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
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 0.013 -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 0.015 0.14 0.33 1 -0.48 6 7
NEMO/A20/RIP2 0.027 0.005 -10000 0 -10000 0 0
XPO1 0.027 0.005 -10000 0 -10000 0 0
NEMO/ATM 0.034 0.074 -10000 0 -0.44 2 2
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 -0.025 0.17 -10000 0 -0.51 57 57
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 -0.057 0.22 -10000 0 -0.67 57 57
NF kappa B1 p50/RelA 0.061 0.016 -10000 0 -10000 0 0
BCL10 0.027 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.022 0.013 -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
Circadian rhythm pathway

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
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 0.027 0.035 -9999 0 -10000 0 0
DEC1/BMAL1 0.017 0.039 -9999 0 -10000 0 0
ATR 0.026 0.032 -9999 0 -0.67 1 1
NR1D1 0 0.041 -9999 0 -10000 0 0
ARNTL 0.01 0.049 -9999 0 -10000 0 0
TIMELESS 0.01 0.031 -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 -0.005 0.009 -9999 0 -10000 0 0
CHEK1 0.027 0.005 -9999 0 -10000 0 0
mol:HEME 0.005 0.009 -9999 0 -10000 0 0
PER1 0.026 0.007 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.023 0.12 -9999 0 -0.44 32 32
BMAL1/CLOCK -0.005 0.11 -9999 0 -0.44 14 14
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 0.005 0.009 -9999 0 -10000 0 0
PER1/TIMELESS 0.026 0.033 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.012 0.013 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.012 0.07 -9999 0 -0.38 14 14
CRKL 0.02 0.012 -9999 0 -10000 0 0
Rac1/GDP 0.019 0.004 -9999 0 -10000 0 0
DOCK1 0.023 0.054 -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 0.026 -9999 0 -10000 0 0
alpha4/beta7 Integrin 0.016 0.095 -9999 0 -0.49 15 15
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 0.026 0.005 -9999 0 -10000 0 0
MADCAM1 0.004 0.064 -9999 0 -0.67 3 3
cell adhesion 0.043 0.087 -9999 0 -0.4 16 16
CRKL/CBL 0.029 0.018 -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 -0.49 7 7
p130Cas/Crk/Dock1 0.035 0.065 -9999 0 -0.37 10 10
VCAM1 0.018 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 -0.34 3 3
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
S1P5 pathway

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.007 0.074 0.47 3 -10000 0 3
GNAI2 0.027 0.003 -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 17 17
GNAZ 0.02 0.012 -10000 0 -10000 0 0
GNAI3 0.027 0.005 -10000 0 -10000 0 0
GNA12 0.026 0.006 -10000 0 -10000 0 0
S1PR5 0.023 0.034 -10000 0 -0.67 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.001 0.074 -10000 0 -0.32 17 17
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
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 0.015 0.034 -10000 0 -10000 0 0
oxygen homeostasis 0.011 0.009 -10000 0 -10000 0 0
TCEB2 0.025 0.013 -10000 0 -10000 0 0
TCEB1 0.027 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.1 0.087 -10000 0 -0.54 3 3
EPO 0.12 0.11 -10000 0 -0.68 2 2
FIH (dimer) 0.036 0.012 -10000 0 -10000 0 0
APEX1 0.035 0.015 -10000 0 -10000 0 0
SERPINE1 0.12 0.12 -10000 0 -0.67 3 3
FLT1 -0.002 0.12 -10000 0 -0.88 4 4
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 -0.75 2 2
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 0.032 0.007 -10000 0 -10000 0 0
ABCG2 0.12 0.13 -10000 0 -0.78 4 4
EFNA1 0.13 0.11 -10000 0 -0.75 2 2
FXN 0.12 0.12 0.51 2 -0.72 2 4
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 0.049 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 0.47 6 -0.72 2 8
TWIST1 0.12 0.14 0.44 2 -0.57 8 10
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
FoxO family signaling

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
G6PC 0.025 0.11 0.62 12 -10000 0 12
PLK1 0.069 0.11 0.6 2 -0.71 1 3
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 0.033 0.02 -10000 0 -10000 0 0
FOXO1 0.017 0.08 0.44 11 -10000 0 11
MAPK10 0.033 0.032 0.2 4 -0.41 1 5
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 -0.43 3 3
mol:GDP 0.01 0.012 -10000 0 -10000 0 0
RAN 0.028 0.006 -10000 0 -10000 0 0
GADD45A 0.099 0.09 0.47 5 -0.58 3 8
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0 0.1 -10000 0 -0.48 7 7
MST1 0.031 0.036 -10000 0 -0.66 1 1
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.02 0.012 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.008 0.11 -10000 0 -0.56 10 10
YWHAB 0.027 0.005 -10000 0 -10000 0 0
MAPK8 0.027 0.062 0.2 6 -0.39 9 15
MAPK9 0.031 0.018 0.2 4 -10000 0 4
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 0.56 10 -0.62 2 12
RBL2 0.078 0.15 0.5 2 -0.89 7 9
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 0.054 -10000 0 -0.67 3 3
USP7 0.027 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 -0.71 1 3
FOXO1-3a-4/beta catenin 0.099 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 0.026 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 0.076 0.1 0.57 15 -0.44 2 17
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 -0.51 10 10
CREBBP 0.026 0.006 -10000 0 -10000 0 0
FBXO32 0.067 0.11 0.59 1 -0.63 2 3
BCL6 0.083 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 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
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 -0.37 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 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
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 -0.34 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 0.035 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 0.048 0.038 0.25 1 -0.34 3 4
PIK3CA 0.024 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 -10000 0 3
mol:Ca2+ 0.027 0.032 -10000 0 -0.32 3 3
JUP 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.007 -10000 0 -10000 0 0
mol:DAG 0.028 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 -0.61 1 1
establishment of polarity of embryonic epithelium 0.025 0.018 -10000 0 -10000 0 0
SRC 0.026 0.008 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
RHOA 0.027 0.003 -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 0.077 -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 S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.019 0.03 -10000 0 -0.32 3 3
TRAF2/ASK1 0.032 0.024 -10000 0 -0.44 1 1
ATM 0.025 0.032 -10000 0 -0.67 1 1
MAP2K3 0.036 0.094 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 -0.4 7 21
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.014 0.083 -10000 0 -0.67 7 7
TXN 0.008 0.003 -10000 0 -10000 0 0
CALM1 0.027 0.005 -10000 0 -10000 0 0
GADD45A 0.027 0.005 -10000 0 -10000 0 0
GADD45B 0.006 0.11 -10000 0 -0.61 15 15
MAP3K1 0.026 0.005 -10000 0 -10000 0 0
MAP3K6 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
MAP3K4 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.038 0.026 -10000 0 -0.51 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 -0.031 0.13 -10000 0 -0.4 57 57
TAOK2 0.015 0.019 -10000 0 -0.39 1 1
TAOK3 0.016 0.018 -10000 0 -0.39 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.027 0.003 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.026 0.032 -10000 0 -0.67 1 1
MAP3K10 0.025 0.007 -10000 0 -10000 0 0
MAP3K3 0.026 0.007 -10000 0 -10000 0 0
TRX/ASK1 0.017 0.036 -10000 0 -0.43 1 1
GADD45/MTK1/MTK1 0.038 0.091 -10000 0 -0.4 18 18
Aurora A signaling

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
Aurora A/GADD45A 0.03 0.025 -10000 0 -10000 0 0
BIRC5 0.015 0.047 -10000 0 -0.67 1 1
NFKBIA 0.015 0.022 0.25 3 -10000 0 3
CPEB1 -0.024 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 0.024 -10000 0 -10000 0 0
MDM2 0.027 0.005 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.008 0.028 -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 0.046 0.024 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.027 0.02 -10000 0 -10000 0 0
AURKA 0.021 0.015 -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 -0.39 35 35
Aurora A/CPEB -0.002 0.11 -10000 0 -0.4 35 35
Aurora A/TACC1/TRAP/chTOG 0.055 0.038 -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 0.042 0.023 -10000 0 -10000 0 0
spindle assembly 0.053 0.038 -10000 0 -0.37 1 1
TDRD7 0.025 0.008 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.055 0.033 -10000 0 -0.36 1 1
CENPA 0.016 0.033 -10000 0 -0.25 7 7
Aurora A/PP2A 0.03 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 0.015 -10000 0 -10000 0 0
TACC1 0.025 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 0.017 -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 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
BCL2L1 0.031 0.099 -10000 0 -10000 0 0
CRKL 0.014 0.047 0.46 3 -10000 0 3
mol:DAG 0.028 0.047 -10000 0 -10000 0 0
HRAS 0.034 0.064 0.35 6 -10000 0 6
MAPK8 0.013 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 0.071 -10000 0 -10000 0 0
STAT5B 0.027 0.061 -10000 0 -10000 0 0
cell proliferation 0.012 0.077 0.34 7 -0.41 9 16
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 0.13 -10000 0 -0.67 19 19
STAT1 (dimer) 0.029 0.071 -10000 0 -10000 0 0
JAK2 0.026 0.026 -10000 0 -0.34 2 2
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.059 0.054 -10000 0 -10000 0 0
EPO/EPOR 0.03 0.028 -10000 0 -10000 0 0
LYN 0.025 0.014 -10000 0 -10000 0 0
TEC/VAV2 0.032 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 0.007 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.049 0.032 -10000 0 -10000 0 0
mol:IP3 0.028 0.047 -10000 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.043 0.047 -10000 0 -10000 0 0
SH2B3 0.028 0.008 -10000 0 -10000 0 0
NFKB1 0.021 0.033 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2/SOCS3 0.002 0.056 -10000 0 -0.26 18 18
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 0.033 -10000 0 -10000 0 0
mol:GDP 0.046 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 0.097 -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 0.25 -10000 0 -0.9 37 37
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
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 0.054 -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 0.066 -10000 0 -0.51 3 3
TRAIL/TRAILR1 0.033 0.06 -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 -0.4 2 2
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 0.067 -10000 0 -10000 0 0
CHUK 0.027 0.004 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.047 0.055 -10000 0 -0.44 6 6
DAP3 0.025 0.007 -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 0.05 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
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 0.016 0.095 -10000 0 -0.49 15 15
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 0.062 -10000 0 -0.53 5 5
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 0.025 0.007 -10000 0 -10000 0 0
PXN 0.016 0.005 -10000 0 -10000 0 0
PIK3R1 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.052 0.035 -10000 0 -0.35 2 2
cell adhesion 0.05 0.04 -10000 0 -0.37 3 3
CRKL/CBL 0.029 0.018 -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 0.063 -10000 0 -0.43 7 7
p130Cas/Crk/Dock1 0.048 0.041 -10000 0 -0.44 3 3
VCAM1 0.018 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
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.062 0.03 -9999 0 -0.38 1 1
HDAC3 0.026 0.006 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0.007 0.002 -9999 0 -10000 0 0
GATA1/HDAC4 0.035 0.012 -9999 0 -10000 0 0
GATA1/HDAC5 0.034 0.013 -9999 0 -10000 0 0
GATA2/HDAC5 0.038 0.01 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR 0.049 0.028 -9999 0 -0.44 1 1
HDAC9 0.012 0.045 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 0.051 0.016 -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 0.008 0.048 -9999 0 -10000 0 0
ADRBK1 0.027 0.005 -9999 0 -10000 0 0
HDAC4 0.027 0.005 -9999 0 -10000 0 0
XPO1 0.027 0.005 -9999 0 -10000 0 0
HDAC5/ANKRA2 0.038 0.011 -9999 0 -10000 0 0
HDAC4/Ubc9 0.038 0.011 -9999 0 -10000 0 0
HDAC7 0.027 0.005 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0.038 0.011 -9999 0 -10000 0 0
TUBA1B 0.027 0.005 -9999 0 -10000 0 0
HDAC6 0.026 0.007 -9999 0 -10000 0 0
HDAC5/RFXANK 0.036 0.015 -9999 0 -10000 0 0
CAMK4 0.013 0.085 -9999 0 -0.67 7 7
Tubulin/HDAC6 0.047 0.048 -9999 0 -0.4 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 0.026 0.006 -9999 0 -10000 0 0
SUMO1/HDAC4 0.014 0.058 -9999 0 -0.29 1 1
SRF 0.027 0.003 -9999 0 -10000 0 0
HDAC4/YWHAB 0.039 0.009 -9999 0 -10000 0 0
Tubulin 0.034 0.055 -9999 0 -0.51 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) 0.052 0.014 -9999 0 -10000 0 0
HDAC4/SRF 0.046 0.06 -9999 0 -0.44 7 7
HDAC4/ER alpha 0.008 0.11 -9999 0 -0.48 23 23
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.008 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 -0.014 0.14 -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 0.026 0.005 -9999 0 -10000 0 0
RFXANK 0.025 0.012 -9999 0 -10000 0 0
nuclear import -0.036 0.011 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.03 0.029 -10000 0 -10000 0 0
KLHL20 0.013 0.051 0.2 1 -10000 0 1
CYFIP2 0.026 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.039 0.042 0.26 1 -10000 0 1
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 -10000 0 -10000 0 0
CTNND1 0.027 0.005 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.033 0.034 -10000 0 -10000 0 0
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 0.083 -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 0.054 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 0.026 0.005 -10000 0 -10000 0 0
CDH1 0.026 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.046 0.067 0.47 6 -10000 0 6
actin cytoskeleton organization 0.012 0.041 0.19 3 -10000 0 3
CDC42/GDP 0.046 0.075 0.48 9 -10000 0 9
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 0.08 0.54 8 -10000 0 8
CDC42/GTP/IQGAP1 0.036 0.008 -10000 0 -10000 0 0
JUP 0.026 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.045 0.043 -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 0.026 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 -10000 0 -10000 0 0
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 -0.52 30 30
RAP1/GDP 0.048 0.039 0.32 3 -10000 0 3
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 0.067 -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 -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 0.01 0.054 -10000 0 -0.44 7 7
CTNNB1 0.027 0.003 -10000 0 -10000 0 0
membrane fusion 0.018 0.006 -10000 0 -10000 0 0
CTNND1 0.022 0.036 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 0.018 0.006 -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 0.003 -10000 0 -10000 0 0
CDH1 0.021 0.011 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.02 0.003 -10000 0 -10000 0 0
MAPK8IP3 0.026 0.009 -10000 0 -10000 0 0
positive regulation of endocytosis 0.02 0.003 -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 0.049 0.014 -10000 0 -10000 0 0
EXOC1 0.027 0.004 -10000 0 -10000 0 0
exocyst 0.033 0.014 -10000 0 -10000 0 0
RALA/GTP 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.035 0.01 -10000 0 -10000 0 0
receptor recycling 0.02 0.003 -10000 0 -10000 0 0
CTNNA1 0.02 0.029 0.36 1 -10000 0 1
NME1 0.016 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0.032 0.036 0.34 3 -10000 0 3
IL2RA 0.008 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 0.018 0.006 -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 0.08 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 0.025 -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 -0.012 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 0.013 -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 0.025 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 -0.06 0.081 -10000 0 -0.67 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.024 -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 0.025 0.007 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.027 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.009 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 0.009 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 0.017 -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 0.012 0.021 -10000 0 -0.27 2 2
regulation of epithelial cell migration 0.009 0.019 -10000 0 -10000 0 0
PLD2 0.012 0.017 -10000 0 -10000 0 0
PIP5K1A 0.012 0.021 -10000 0 -0.27 2 2
mol:Phosphatidic acid 0.008 0.013 -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 0.045 0.042 -9999 0 -0.45 2 2
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B 0.009 0.014 -9999 0 -10000 0 0
AURKB -0.007 0.062 -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 0.037 -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 -0.31 1 1
RANGAP1 0.02 0.012 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.066 0.018 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.013 0.009 -9999 0 -10000 0 0
Ran/GTP 0.006 0.047 -9999 0 -0.23 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.027 0.005 -9999 0 -10000 0 0
UBE2I 0.026 0.007 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.006 0.046 -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 0.051 0.016 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.039 0.009 -9999 0 -9999 0 0
CTNNB1 0.027 0.003 -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 0.026 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.021 0.009 -10000 0 -10000 0 0
CD4 0.021 0.03 -10000 0 -10000 0 0
CLTA 0.025 0.007 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
ARFGAP1 0.009 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.006 0.024 -10000 0 -0.37 2 2
ARF1/GTP 0.028 0.02 -10000 0 -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 0.027 -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 0.025 0.007 -10000 0 -10000 0 0
RAC1 0.026 0.006 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.014 0.033 -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 0.007 -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 0.019 0.004 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.025 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 0.026 0.006 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.026 0.006 -9999 0 -9999 0 0
CHUK 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.072 0.027 -9999 0 -9999 0 0
NFKB1 0.027 0.004 -9999 0 -9999 0 0
MAP3K14 0.026 0.007 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.038 0.011 -9999 0 -9999 0 0
RELB 0.025 0.007 -9999 0 -9999 0 0
NFKB2 0.027 0.004 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.034 0.01 -9999 0 -9999 0 0
regulation of B cell activation 0.034 0.01 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 499 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 0.026
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 0.027
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/11493761/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/THCA-TP/11541722/Gistic2_Analysis_11542109/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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