PARADIGM pathway analysis of mRNASeq expression data
Thyroid Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1MC8X4F
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1MC8X4F
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 49 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Ephrin A reverse signaling 247
Signaling events mediated by Stem cell factor receptor (c-Kit) 160
Signaling events regulated by Ret tyrosine kinase 149
TCGA08_retinoblastoma 139
Reelin signaling pathway 122
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 112
Wnt signaling 105
PDGFR-alpha signaling pathway 100
Noncanonical Wnt signaling pathway 99
IL4-mediated signaling events 91
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 486 . 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 ( 486 ).

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 0.5082 247 1733 7 -0.52 0 1000 -1000 -0.03 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.3292 160 12543 78 -0.8 0.24 1000 -1000 -0.071 -1000
Signaling events regulated by Ret tyrosine kinase 0.3066 149 12243 82 -0.46 0.013 1000 -1000 -0.079 -1000
TCGA08_retinoblastoma 0.2860 139 1118 8 -0.13 0.073 1000 -1000 -0.018 -1000
Reelin signaling pathway 0.2510 122 6841 56 -0.6 0.033 1000 -1000 -0.082 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2305 112 7677 68 -0.9 0.37 1000 -1000 -0.12 -1000
Wnt signaling 0.2160 105 735 7 -0.41 0.013 1000 -1000 -0.019 -1000
PDGFR-alpha signaling pathway 0.2058 100 4416 44 -0.51 0.033 1000 -1000 -0.062 -1000
Noncanonical Wnt signaling pathway 0.2037 99 2594 26 -0.41 0.013 1000 -1000 -0.079 -1000
IL4-mediated signaling events 0.1872 91 8297 91 -1.3 0.66 1000 -1000 -0.13 -1000
FOXA2 and FOXA3 transcription factor networks 0.1852 90 4181 46 -0.92 0.021 1000 -1000 -0.044 -1000
Nongenotropic Androgen signaling 0.1749 85 4452 52 -0.34 0.16 1000 -1000 -0.064 -1000
Signaling events mediated by the Hedgehog family 0.1667 81 4212 52 -0.38 0.2 1000 -1000 -0.082 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.1605 78 4250 54 -0.6 0.028 1000 -1000 -0.093 -1000
Calcium signaling in the CD4+ TCR pathway 0.1564 76 2385 31 -0.53 0.013 1000 -1000 -0.082 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.1481 72 2475 34 -0.17 0.013 1000 -1000 -0.067 -1000
Glypican 1 network 0.1296 63 3067 48 -0.38 0.028 1000 -1000 -0.042 -1000
Ephrin B reverse signaling 0.1276 62 3018 48 -0.31 0.19 1000 -1000 -0.068 -1000
Endothelins 0.1235 60 5798 96 -0.4 0.013 1000 -1000 -0.083 -1000
IGF1 pathway 0.1173 57 3249 57 -0.2 0.059 1000 -1000 -0.092 -1000
HIF-1-alpha transcription factor network 0.1132 55 4180 76 -0.57 0.042 1000 -1000 -0.099 -1000
Glucocorticoid receptor regulatory network 0.1111 54 6179 114 -0.57 0.37 1000 -1000 -0.07 -1000
TCR signaling in naïve CD8+ T cells 0.1111 54 5080 93 -0.2 0.089 1000 -1000 -0.075 -1000
IL23-mediated signaling events 0.1111 54 3299 60 -0.34 0.021 1000 -1000 -0.15 -1000
BMP receptor signaling 0.1070 52 4263 81 -0.58 0.026 1000 -1000 -0.085 -1000
Glypican 2 network 0.1049 51 207 4 -0.087 -0.01 1000 -1000 -0.022 -1000
Coregulation of Androgen receptor activity 0.0988 48 3664 76 -0.77 0.061 1000 -1000 -0.06 -1000
Arf6 signaling events 0.0967 47 2918 62 -0.32 0.021 1000 -1000 -0.061 -1000
Syndecan-1-mediated signaling events 0.0947 46 1590 34 -0.2 0.013 1000 -1000 -0.057 -1000
EPHB forward signaling 0.0926 45 3836 85 -0.31 0.15 1000 -1000 -0.094 -1000
IL12-mediated signaling events 0.0802 39 3420 87 -0.41 0.023 1000 -1000 -0.12 -1000
Signaling mediated by p38-alpha and p38-beta 0.0802 39 1751 44 -0.23 0.013 1000 -1000 -0.055 -1000
Hedgehog signaling events mediated by Gli proteins 0.0782 38 2522 65 -0.66 0.061 1000 -1000 -0.071 -1000
amb2 Integrin signaling 0.0782 38 3128 82 -0.24 0.013 1000 -1000 -0.081 -1000
IL6-mediated signaling events 0.0761 37 2799 75 -0.21 0.059 1000 -1000 -0.083 -1000
Syndecan-4-mediated signaling events 0.0741 36 2426 67 -0.24 0.013 1000 -1000 -0.088 -1000
Thromboxane A2 receptor signaling 0.0679 33 3506 105 -0.21 0.032 1000 -1000 -0.068 -1000
EGFR-dependent Endothelin signaling events 0.0658 32 679 21 -0.11 0.013 1000 -1000 -0.068 -1000
Osteopontin-mediated events 0.0638 31 1202 38 -0.26 0.013 1000 -1000 -0.092 -1000
FAS signaling pathway (CD95) 0.0617 30 1416 47 -0.26 0.029 1000 -1000 -0.047 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0597 29 2483 85 -0.28 0.013 1000 -1000 -0.08 -1000
Ras signaling in the CD4+ TCR pathway 0.0576 28 479 17 -0.095 0.013 1000 -1000 -0.046 -1000
Plasma membrane estrogen receptor signaling 0.0556 27 2354 86 -0.18 0.02 1000 -1000 -0.077 -1000
Regulation of Androgen receptor activity 0.0556 27 1893 70 -0.48 0.034 1000 -1000 -0.057 -1000
Syndecan-2-mediated signaling events 0.0535 26 1831 69 -0.22 0.038 1000 -1000 -0.059 -1000
Regulation of p38-alpha and p38-beta 0.0535 26 1414 54 -0.47 0.013 1000 -1000 -0.058 -1000
ErbB2/ErbB3 signaling events 0.0514 25 1675 65 -0.13 0.027 1000 -1000 -0.064 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0514 25 1323 52 -0.28 0.054 1000 -1000 -0.064 -1000
Visual signal transduction: Rods 0.0514 25 1340 52 -0.2 0.016 1000 -1000 -0.088 -1000
LPA receptor mediated events 0.0494 24 2527 102 -0.25 0.031 1000 -1000 -0.085 -1000
JNK signaling in the CD4+ TCR pathway 0.0473 23 404 17 -0.1 0.02 1000 -1000 -0.061 -1000
Integrins in angiogenesis 0.0473 23 1979 84 -0.24 0.033 1000 -1000 -0.099 -1000
BCR signaling pathway 0.0473 23 2364 99 -0.19 0.023 1000 -1000 -0.093 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0473 23 2033 88 -0.32 0.028 1000 -1000 -0.12 -1000
Signaling events mediated by PTP1B 0.0432 21 1664 76 -0.25 0.021 1000 -1000 -0.079 -1000
p75(NTR)-mediated signaling 0.0432 21 2701 125 -0.36 0.066 1000 -1000 -0.094 -1000
Effects of Botulinum toxin 0.0432 21 556 26 -0.16 0.019 1000 -1000 -0.059 -1000
IL27-mediated signaling events 0.0432 21 1111 51 -0.17 0.065 1000 -1000 -0.1 -1000
Regulation of nuclear SMAD2/3 signaling 0.0412 20 2767 136 -0.34 0.066 1000 -1000 -0.072 -1000
Aurora C signaling 0.0391 19 138 7 -0.059 0 1000 -1000 -0.042 -1000
Nectin adhesion pathway 0.0391 19 1205 63 -0.26 0.033 1000 -1000 -0.078 -1000
VEGFR1 specific signals 0.0391 19 1111 56 -0.07 0.041 1000 -1000 -0.077 -1000
Visual signal transduction: Cones 0.0370 18 715 38 -0.091 0.013 1000 -1000 -0.057 -1000
IL1-mediated signaling events 0.0370 18 1167 62 -0.12 0.066 1000 -1000 -0.093 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0370 18 2247 120 -0.31 0.042 1000 -1000 -0.076 -1000
FOXM1 transcription factor network 0.0370 18 952 51 -0.19 0.046 1000 -1000 -0.14 -1000
ErbB4 signaling events 0.0350 17 1239 69 -0.14 0.057 1000 -1000 -0.08 -1000
Fc-epsilon receptor I signaling in mast cells 0.0350 17 1741 97 -0.21 0.031 1000 -1000 -0.09 -1000
TCGA08_rtk_signaling 0.0350 17 459 26 -0.25 0.024 1000 -1000 -0.021 -1000
Insulin-mediated glucose transport 0.0329 16 525 32 -0.21 0.042 1000 -1000 -0.062 -1000
Aurora B signaling 0.0329 16 1094 67 -0.38 0.014 1000 -1000 -0.07 -1000
Syndecan-3-mediated signaling events 0.0309 15 550 35 -0.16 0.013 1000 -1000 -0.07 -1000
Rapid glucocorticoid signaling 0.0309 15 318 20 -0.092 0.015 1000 -1000 -0.033 -1000
LPA4-mediated signaling events 0.0288 14 178 12 -0.12 0.016 1000 -1000 -0.023 -1000
IFN-gamma pathway 0.0288 14 1014 68 -0.1 0.042 1000 -1000 -0.092 -1000
IL2 signaling events mediated by STAT5 0.0288 14 328 22 -0.067 0.039 1000 -1000 -0.045 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0288 14 467 33 -0.16 0.035 1000 -1000 -0.061 -1000
Class IB PI3K non-lipid kinase events 0.0288 14 42 3 -0.003 -1000 1000 -1000 -0.016 -1000
Presenilin action in Notch and Wnt signaling 0.0267 13 828 61 -0.21 0.043 1000 -1000 -0.081 -1000
Ceramide signaling pathway 0.0267 13 1012 76 -0.18 0.024 1000 -1000 -0.065 -1000
Signaling events mediated by HDAC Class III 0.0267 13 540 40 -0.35 0.024 1000 -1000 -0.041 -1000
IL2 signaling events mediated by PI3K 0.0267 13 795 58 -0.065 0.031 1000 -1000 -0.079 -1000
Insulin Pathway 0.0267 13 1021 74 -0.081 0.038 1000 -1000 -0.09 -1000
Signaling events mediated by PRL 0.0267 13 471 34 -0.11 0.013 1000 -1000 -0.037 -1000
a4b1 and a4b7 Integrin signaling 0.0226 11 59 5 -0.03 0.004 1000 -1000 -0.042 -1000
Cellular roles of Anthrax toxin 0.0226 11 438 39 -0.091 0.019 1000 -1000 -0.026 -1000
Regulation of Telomerase 0.0226 11 1164 102 -0.28 0.053 1000 -1000 -0.097 -1000
mTOR signaling pathway 0.0206 10 543 53 -0.044 0.021 1000 -1000 -0.057 -1000
Retinoic acid receptors-mediated signaling 0.0206 10 591 58 -0.12 0.033 1000 -1000 -0.073 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0206 10 478 45 -0.091 0.039 1000 -1000 -0.087 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0206 10 809 74 -0.18 0.086 1000 -1000 -0.092 -1000
Class I PI3K signaling events 0.0206 10 797 73 -0.25 0.023 1000 -1000 -0.074 -1000
Caspase cascade in apoptosis 0.0185 9 715 74 -0.091 0.029 1000 -1000 -0.054 -1000
BARD1 signaling events 0.0185 9 568 57 -0.033 0.054 1000 -1000 -0.058 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0185 9 827 83 -0.21 0.052 1000 -1000 -0.08 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0165 8 249 28 -0.18 0.031 1000 -1000 -0.051 -1000
Class I PI3K signaling events mediated by Akt 0.0165 8 556 68 -0.21 0.052 1000 -1000 -0.061 -1000
ceramide signaling pathway 0.0165 8 438 49 -0.091 0.031 1000 -1000 -0.045 -1000
S1P3 pathway 0.0165 8 364 42 -0.18 0.049 1000 -1000 -0.06 -1000
TRAIL signaling pathway 0.0144 7 377 48 -0.078 0.047 1000 -1000 -0.072 -1000
S1P1 pathway 0.0144 7 256 36 -0.037 0.032 1000 -1000 -0.059 -1000
Arf6 downstream pathway 0.0123 6 284 43 -0.18 0.093 1000 -1000 -0.045 -1000
Signaling events mediated by HDAC Class I 0.0123 6 675 104 -0.091 0.059 1000 -1000 -0.072 -1000
FoxO family signaling 0.0123 6 417 64 -0.21 0.16 1000 -1000 -0.071 -1000
Canonical NF-kappaB pathway 0.0103 5 225 39 -0.091 0.071 1000 -1000 -0.087 -1000
Circadian rhythm pathway 0.0103 5 127 22 -0.06 0.013 1000 -1000 -0.062 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0103 5 206 37 -0.031 0.039 1000 -1000 -0.059 -1000
EPO signaling pathway 0.0082 4 224 55 -0.037 0.062 1000 -1000 -0.099 -1000
Atypical NF-kappaB pathway 0.0082 4 149 31 -0.038 0.047 1000 -1000 -0.052 -1000
Canonical Wnt signaling pathway 0.0082 4 223 51 -0.047 0.068 1000 -1000 -0.058 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0082 4 533 125 -0.034 0.087 1000 -1000 -0.091 -1000
E-cadherin signaling in the nascent adherens junction 0.0082 4 379 76 -0.17 0.074 1000 -1000 -0.085 -1000
PLK1 signaling events 0.0062 3 317 85 -0.043 0.033 1000 -1000 -0.043 -1000
S1P5 pathway 0.0062 3 66 17 -0.017 0.022 1000 -1000 -0.06 -1000
HIF-2-alpha transcription factor network 0.0062 3 138 43 -0.2 0.2 1000 -1000 -0.081 -1000
Signaling mediated by p38-gamma and p38-delta 0.0062 3 48 15 0 0.032 1000 -1000 -0.033 -1000
Paxillin-dependent events mediated by a4b1 0.0062 3 130 36 -0.03 0.024 1000 -1000 -0.07 -1000
PDGFR-beta signaling pathway 0.0062 3 364 97 -0.18 0.064 1000 -1000 -0.087 -1000
S1P4 pathway 0.0062 3 90 25 -0.017 0.032 1000 -1000 -0.058 -1000
p38 MAPK signaling pathway 0.0062 3 144 44 -0.038 0.026 1000 -1000 -0.066 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0041 2 59 23 -0.036 0.049 1000 -1000 -0.076 -1000
Signaling events mediated by HDAC Class II 0.0041 2 180 75 -0.049 0.035 1000 -1000 -0.063 -1000
Aurora A signaling 0.0041 2 166 60 -0.049 0.038 1000 -1000 -0.057 -1000
E-cadherin signaling in keratinocytes 0.0041 2 115 43 -0.004 0.053 1000 -1000 -0.067 -1000
PLK2 and PLK4 events 0.0021 1 5 3 0.01 0.022 1000 -1000 -0.018 -1000
Arf6 trafficking events 0.0021 1 76 71 -0.02 0.046 1000 -1000 -0.077 -1000
TCGA08_p53 0.0000 0 0 7 -0.085 0.054 1000 -1000 -0.011 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.032 1000 -1000 -0.058 -1000
E-cadherin signaling events 0.0000 0 0 5 0 0.013 1000 -1000 -0.04 -1000
Arf1 pathway 0.0000 0 31 54 -0.005 0.036 1000 -1000 -0.041 -1000
Alternative NF-kappaB pathway 0.0000 0 2 13 -0.001 0.013 1000 -1000 -0.056 -1000
Total NA 3998 221006 7203 -30 -990 131000 -131000 -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 -0.43 0.31 -9999 0 -0.61 338 338
EFNA5 -0.12 0.3 -9999 0 -0.82 74 74
FYN -0.38 0.3 -9999 0 -0.56 338 338
neuron projection morphogenesis -0.43 0.31 -9999 0 -0.61 338 338
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.43 0.32 -9999 0 -0.62 338 338
EPHA5 -0.52 0.4 -9999 0 -0.82 307 307
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 -0.21 0.22 -10000 0 -0.4 282 282
CRKL -0.22 0.24 -10000 0 -0.42 275 275
HRAS -0.19 0.21 -10000 0 -0.52 38 38
mol:PIP3 -0.22 0.22 -10000 0 -0.41 275 275
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.012 0.038 -10000 0 -0.82 1 1
GAB1 -0.24 0.25 -10000 0 -0.45 275 275
FOXO3 -0.19 0.22 -10000 0 -0.38 275 275
AKT1 -0.22 0.23 -10000 0 -0.42 275 275
BAD -0.19 0.22 -10000 0 -0.38 275 275
megakaryocyte differentiation -0.25 0.25 -10000 0 -0.45 283 283
GSK3B -0.19 0.22 -10000 0 -0.38 275 275
RAF1 -0.15 0.18 -10000 0 -0.46 23 23
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.24 0.25 -10000 0 -0.45 275 275
STAT1 -0.59 0.59 -10000 0 -1.1 276 276
HRAS/SPRED1 -0.17 0.14 -10000 0 -0.45 25 25
cell proliferation -0.24 0.25 -10000 0 -0.45 278 278
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.24 0.25 -10000 0 -0.45 275 275
HRAS/SPRED2 -0.17 0.15 -10000 0 -0.45 27 27
LYN/TEC/p62DOK -0.23 0.21 -10000 0 -0.41 275 275
MAPK3 -0.094 0.13 -10000 0 -0.32 21 21
STAP1 -0.26 0.25 -10000 0 -0.47 275 275
GRAP2 -0.042 0.2 -10000 0 -0.78 34 34
JAK2 -0.51 0.45 -10000 0 -0.9 276 276
STAT1 (dimer) -0.57 0.57 -10000 0 -1.1 276 276
mol:Gleevec 0.008 0.01 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.24 0.21 -10000 0 -0.42 278 278
actin filament polymerization -0.23 0.24 -10000 0 -0.44 275 275
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.35 0.34 -10000 0 -0.64 275 275
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.21 0.19 -10000 0 -0.37 274 274
PI3K -0.22 0.24 -10000 0 -0.42 276 276
PTEN 0.012 0.038 -10000 0 -0.82 1 1
SCF/KIT/EPO/EPOR -0.74 0.72 -10000 0 -1.4 275 275
MAPK8 -0.24 0.26 -10000 0 -0.46 278 278
STAT3 (dimer) -0.23 0.24 -10000 0 -0.44 275 275
positive regulation of transcription -0.075 0.11 -10000 0 -0.26 15 15
mol:GDP -0.23 0.19 -10000 0 -0.55 42 42
PIK3C2B -0.24 0.25 -10000 0 -0.45 275 275
CBL/CRKL -0.2 0.22 -10000 0 -0.39 275 275
FER -0.24 0.25 -10000 0 -0.45 276 276
SH2B3 -0.24 0.25 -10000 0 -0.45 275 275
PDPK1 -0.2 0.21 -10000 0 -0.37 276 276
SNAI2 -0.24 0.26 -10000 0 -0.46 276 276
positive regulation of cell proliferation -0.41 0.42 -10000 0 -0.77 276 276
KITLG -0.004 0.1 -10000 0 -0.86 7 7
cell motility -0.41 0.42 -10000 0 -0.77 276 276
PTPN6 0.02 0.018 -10000 0 -10000 0 0
EPOR -0.14 0.18 -10000 0 -0.67 2 2
STAT5A (dimer) -0.33 0.35 -10000 0 -0.63 276 276
SOCS1 0.009 0.048 -10000 0 -0.42 5 5
cell migration 0.24 0.25 0.45 278 -10000 0 278
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.005 0.041 -10000 0 -0.33 7 7
VAV1 -0.013 0.1 -10000 0 -0.36 34 34
GRB10 -0.24 0.25 -10000 0 -0.45 275 275
PTPN11 0.02 0.039 -10000 0 -0.81 1 1
SCF/KIT -0.26 0.26 -10000 0 -0.48 275 275
GO:0007205 0.011 0.013 -10000 0 -10000 0 0
MAP2K1 -0.11 0.15 -10000 0 -0.35 21 21
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.8 0.75 -10000 0 -1.5 275 275
MAP2K2 -0.11 0.15 -10000 0 -0.35 21 21
SHC/Grb2/SOS1 -0.23 0.21 -10000 0 -0.41 275 275
STAT5A -0.35 0.36 -10000 0 -0.65 276 276
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.24 0.25 -10000 0 -0.45 276 276
SHC/GRAP2 -0.042 0.16 -10000 0 -0.63 31 31
PTPRO -0.25 0.25 -10000 0 -0.46 283 283
SH2B2 -0.24 0.25 -10000 0 -0.45 275 275
DOK1 0.013 0 -10000 0 -10000 0 0
MATK -0.24 0.25 -10000 0 -0.46 278 278
CREBBP 0.018 0.021 -10000 0 -10000 0 0
BCL2 -0.22 0.42 -10000 0 -1.6 35 35
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 -0.09 0.069 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.26 0.2 -9999 0 -0.51 118 118
JUN -0.32 0.31 -9999 0 -0.68 170 170
HRAS 0.012 0.021 -9999 0 -0.31 2 2
RET51/GFRalpha1/GDNF/GRB10 -0.39 0.32 -9999 0 -0.61 303 303
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.39 0.32 -9999 0 -0.61 303 303
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.3 0.25 -9999 0 -0.51 277 277
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.35 0.29 -9999 0 -0.55 303 303
GRB7 -0.042 0.12 -9999 0 -0.31 82 82
RET51/GFRalpha1/GDNF -0.39 0.32 -9999 0 -0.61 303 303
MAPKKK cascade -0.31 0.26 -9999 0 -0.49 303 303
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.35 0.31 -9999 0 -0.58 289 289
lamellipodium assembly -0.24 0.18 -9999 0 -0.38 278 278
RET51/GFRalpha1/GDNF/SHC -0.39 0.32 -9999 0 -0.61 303 303
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
RET9/GFRalpha1/GDNF/SHC -0.29 0.25 -9999 0 -0.51 277 277
RET9/GFRalpha1/GDNF/Shank3 -0.29 0.25 -9999 0 -0.51 277 277
MAPK3 -0.32 0.29 -9999 0 -0.51 303 303
DOK1 0.013 0 -9999 0 -10000 0 0
DOK6 -0.12 0.3 -9999 0 -0.82 76 76
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.31 0.29 -9999 0 -0.67 129 129
DOK5 -0.1 0.29 -9999 0 -0.82 66 66
GFRA1 -0.46 0.41 -9999 0 -0.82 278 278
MAPK8 -0.24 0.23 -9999 0 -0.59 91 91
HRAS/GTP -0.36 0.3 -9999 0 -0.57 303 303
tube development -0.27 0.24 -9999 0 -0.48 277 277
MAPK1 -0.32 0.29 -9999 0 -0.51 303 303
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.18 0.18 -9999 0 -0.34 277 277
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
PDLIM7 0.01 0.033 -9999 0 -0.31 5 5
RET51/GFRalpha1/GDNF/Dok6 -0.44 0.38 -9999 0 -0.67 314 314
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.39 0.32 -9999 0 -0.61 303 303
RET51/GFRalpha1/GDNF/Dok5 -0.46 0.39 -9999 0 -0.69 315 315
PRKCA -0.028 0.18 -9999 0 -0.82 24 24
HRAS/GDP -0.001 0.014 -9999 0 -10000 0 0
CREB1 -0.24 0.24 -9999 0 -0.43 277 277
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.18 0.18 -9999 0 -0.34 277 277
RET51/GFRalpha1/GDNF/Grb7 -0.42 0.33 -9999 0 -0.64 303 303
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.17 0.32 -9999 0 -0.64 136 136
DOK4 0.013 0.015 -9999 0 -0.31 1 1
JNK cascade -0.31 0.3 -9999 0 -0.65 177 177
RET9/GFRalpha1/GDNF/FRS2 -0.29 0.25 -9999 0 -0.51 277 277
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.18 0.18 -9999 0 -0.34 277 277
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.25 0.24 -9999 0 -0.41 303 303
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.25 0.24 -9999 0 -0.41 303 303
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.29 0.31 -9999 0 -0.47 303 303
PI3K -0.37 0.34 -9999 0 -0.62 278 278
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.27 0.24 -9999 0 -0.48 277 277
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.22 0.21 -9999 0 -0.38 277 277
RET51/GFRalpha1/GDNF/FRS2 -0.39 0.32 -9999 0 -0.61 303 303
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.081 0.26 -9999 0 -0.82 55 55
IRS2 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.29 0.31 -9999 0 -0.47 303 303
RET51/GFRalpha1/GDNF/PKC alpha -0.41 0.36 -9999 0 -0.64 305 305
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.002 0.041 -9999 0 -0.31 8 8
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.44 0.37 -9999 0 -0.67 314 314
Rac1/GTP -0.29 0.23 -9999 0 -0.46 278 278
RET9/GFRalpha1/GDNF -0.32 0.28 -9999 0 -0.56 277 277
GFRalpha1/GDNF -0.37 0.32 -9999 0 -0.64 277 277
TCGA08_retinoblastoma

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
CDKN2B -0.12 0.16 -10000 0 -0.32 202 202
CDKN2C 0.027 0.036 -10000 0 -0.32 2 2
CDKN2A -0.13 0.16 -10000 0 -0.32 206 206
CCND2 0.07 0.073 0.17 141 -10000 0 141
RB1 -0.069 0.072 -10000 0 -0.17 141 141
CDK4 0.07 0.072 0.17 142 -10000 0 142
CDK6 0.073 0.077 0.18 141 -0.18 2 143
G1/S progression 0.061 0.08 0.17 141 -10000 0 141
Reelin signaling pathway

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
CDK5R1/CDK5 -0.001 0.013 -9999 0 -10000 0 0
VLDLR -0.023 0.17 -9999 0 -0.82 21 21
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
ITGA3 0.01 0.033 -9999 0 -0.31 5 5
RELN/VLDLR/Fyn -0.42 0.26 -9999 0 -0.57 361 361
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.009 0.062 -9999 0 -0.46 9 9
AKT1 -0.24 0.18 -9999 0 -0.33 362 362
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 0.006 0.016 -9999 0 -0.31 1 1
RELN/LRP8/DAB1 -0.39 0.25 -9999 0 -0.53 360 360
LRPAP1/LRP8 -0.027 0.13 -9999 0 -0.63 21 21
RELN/LRP8/DAB1/Fyn -0.37 0.24 -9999 0 -0.5 360 360
DAB1/alpha3/beta1 Integrin -0.35 0.23 -9999 0 -0.84 36 36
long-term memory -0.37 0.25 -9999 0 -0.49 362 362
DAB1/LIS1 -0.36 0.24 -9999 0 -0.48 365 365
DAB1/CRLK/C3G -0.35 0.23 -9999 0 -0.88 32 32
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
DAB1/NCK2 -0.36 0.24 -9999 0 -0.48 365 365
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.023 0.16 -9999 0 -0.64 27 27
CDK5R1 0.012 0.021 -9999 0 -0.31 2 2
RELN -0.6 0.37 -9999 0 -0.82 356 356
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.42 0.26 -9999 0 -0.57 360 360
GRIN2A/RELN/LRP8/DAB1/Fyn -0.38 0.26 -9999 0 -0.51 362 362
MAPK8 -0.002 0.11 -9999 0 -0.82 9 9
RELN/VLDLR/DAB1 -0.39 0.25 -9999 0 -0.53 361 361
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.37 0.26 -9999 0 -0.5 365 365
RELN/LRP8 -0.42 0.26 -9999 0 -0.57 360 360
GRIN2B/RELN/LRP8/DAB1/Fyn -0.37 0.23 -9999 0 -0.5 360 360
PI3K -0.004 0.049 -9999 0 -0.63 3 3
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.02 -9999 0 -10000 0 0
RAP1A -0.31 0.23 -9999 0 -0.82 30 30
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0 -9999 0 -10000 0 0
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.003 0.016 -9999 0 -0.31 1 1
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.16 0.14 -9999 0 -0.53 22 22
neuron adhesion -0.28 0.23 -9999 0 -0.74 34 34
LRP8 -0.023 0.17 -9999 0 -0.82 21 21
GSK3B -0.22 0.17 -9999 0 -0.62 18 18
RELN/VLDLR/DAB1/Fyn -0.37 0.23 -9999 0 -0.5 361 361
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.26 0.18 -9999 0 -0.36 362 362
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT 0.033 0.089 -9999 0 -0.33 20 20
neuron migration -0.3 0.22 -9999 0 -0.42 357 357
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.16 0.14 -9999 0 -0.53 22 22
RELN/VLDLR -0.4 0.27 -9999 0 -0.54 365 365
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.043 0.16 -10000 0 -0.54 33 33
NFATC2 -0.24 0.38 -10000 0 -0.81 124 124
NFATC3 -0.083 0.13 -10000 0 -10000 0 0
CD40LG -0.74 0.57 -10000 0 -1.2 260 260
ITCH 0.051 0.015 -10000 0 -10000 0 0
CBLB 0.051 0.015 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.53 0.52 -10000 0 -1.2 142 142
JUNB 0.003 0.092 -10000 0 -0.82 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.015 -10000 0 -0.34 1 1
T cell anergy 0.025 0.065 -10000 0 -0.49 1 1
TLE4 -0.25 0.44 -10000 0 -0.91 128 128
Jun/NFAT1-c-4/p21SNFT -0.66 0.61 -10000 0 -1.2 237 237
AP-1/NFAT1-c-4 -0.9 0.79 -10000 0 -1.6 251 251
IKZF1 -0.18 0.34 -10000 0 -0.72 107 107
T-helper 2 cell differentiation -0.32 0.35 -10000 0 -0.82 125 125
AP-1/NFAT1 -0.42 0.49 -10000 0 -0.9 214 214
CALM1 0.029 0.009 -10000 0 -10000 0 0
EGR2 -0.8 0.86 -10000 0 -1.7 223 223
EGR3 -0.58 0.75 -10000 0 -1.7 127 127
NFAT1/FOXP3 -0.22 0.33 -10000 0 -0.71 122 122
EGR1 -0.16 0.34 -10000 0 -0.82 103 103
JUN -0.19 0.35 -10000 0 -0.83 109 109
EGR4 -0.035 0.18 -10000 0 -0.71 30 30
mol:Ca2+ 0.016 0.01 -10000 0 -10000 0 0
GBP3 -0.17 0.32 -10000 0 -0.69 103 103
FOSL1 -0.028 0.12 -10000 0 -0.33 59 59
NFAT1-c-4/MAF/IRF4 -0.57 0.56 -10000 0 -1.1 224 224
DGKA -0.16 0.3 -10000 0 -0.71 80 80
CREM 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.56 0.56 -10000 0 -1.1 236 236
CTLA4 -0.24 0.38 -10000 0 -0.82 111 111
NFAT1-c-4 (dimer)/EGR1 -0.64 0.67 -10000 0 -1.3 234 234
NFAT1-c-4 (dimer)/EGR4 -0.58 0.57 -10000 0 -1.1 238 238
FOS -0.22 0.37 -10000 0 -0.83 129 129
IFNG -0.43 0.54 -10000 0 -1.1 159 159
T cell activation -0.44 0.43 -10000 0 -0.98 155 155
MAF 0.013 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.37 0.42 0.82 177 -10000 0 177
TNF -0.6 0.58 -10000 0 -1.1 236 236
FASLG -0.75 0.79 -10000 0 -1.5 242 242
TBX21 -0.038 0.18 -10000 0 -0.72 30 30
BATF3 -0.006 0.082 -10000 0 -0.33 27 27
PRKCQ 0.004 0.085 -10000 0 -0.82 5 5
PTPN1 -0.16 0.3 -10000 0 -0.68 91 91
NFAT1-c-4/ICER1 -0.55 0.56 -10000 0 -1.1 234 234
GATA3 -0.03 0.19 -10000 0 -0.78 27 27
T-helper 1 cell differentiation -0.41 0.52 -10000 0 -1 160 160
IL2RA -0.48 0.46 -10000 0 -1 152 152
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.16 0.3 -10000 0 -0.72 75 75
E2F1 -0.081 0.15 -10000 0 -0.3 152 152
PPARG -0.003 0.11 -10000 0 -0.59 13 13
SLC3A2 -0.16 0.3 -10000 0 -0.75 67 67
IRF4 -0.1 0.23 -10000 0 -0.45 120 120
PTGS2 -0.71 0.57 -10000 0 -1.2 253 253
CSF2 -0.78 0.54 -10000 0 -1.2 265 265
JunB/Fra1/NFAT1-c-4 -0.54 0.54 -10000 0 -1.1 210 210
IL4 -0.33 0.37 -10000 0 -0.88 122 122
IL5 -0.69 0.54 -10000 0 -1.2 248 248
IL2 -0.45 0.44 -10000 0 -1 154 154
IL3 -0.097 0.062 -10000 0 -10000 0 0
RNF128 0.049 0.042 -10000 0 -0.88 1 1
NFATC1 -0.37 0.43 -10000 0 -0.82 177 177
CDK4 0.22 0.24 0.69 18 -10000 0 18
PTPRK -0.16 0.3 -10000 0 -0.66 99 99
IL8 -0.72 0.55 -10000 0 -1.2 250 250
POU2F1 0.013 0.015 -10000 0 -0.31 1 1
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.28 0.28 -9999 0 -0.47 302 302
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 0.005 0.049 -9999 0 -0.31 11 11
WNT4 -0.26 0.39 -9999 0 -0.81 162 162
FZD3 0.013 0 -9999 0 -10000 0 0
WNT5A -0.005 0.12 -9999 0 -0.78 11 11
WNT11 -0.41 0.42 -9999 0 -0.82 249 249
PDGFR-alpha signaling pathway

Figure S8.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S8.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.26 0.39 -9999 0 -0.84 154 154
PDGF/PDGFRA/CRKL -0.2 0.29 -9999 0 -0.63 154 154
positive regulation of JUN kinase activity -0.15 0.22 -9999 0 -0.48 154 154
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.21 0.3 -9999 0 -0.64 154 154
AP1 -0.51 0.63 -9999 0 -1.5 136 136
mol:IP3 -0.2 0.31 -9999 0 -0.65 154 154
PLCG1 -0.2 0.31 -9999 0 -0.65 154 154
PDGF/PDGFRA/alphaV Integrin -0.2 0.3 -9999 0 -0.63 155 155
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.2 0.31 -9999 0 -0.65 154 154
CAV3 -0.001 0.029 -9999 0 -0.31 4 4
CAV1 -0.009 0.14 -9999 0 -0.82 13 13
SHC/Grb2/SOS1 -0.15 0.23 -9999 0 -0.49 154 154
PDGF/PDGFRA/Shf -0.2 0.29 -9999 0 -0.63 154 154
FOS -0.46 0.61 -9999 0 -1.4 136 136
JUN -0.17 0.29 -9999 0 -0.7 109 109
oligodendrocyte development -0.2 0.3 -9999 0 -0.63 155 155
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG -0.2 0.31 -9999 0 -0.65 154 154
PDGF/PDGFRA -0.26 0.39 -9999 0 -0.84 154 154
actin cytoskeleton reorganization -0.2 0.29 -9999 0 -0.63 154 154
SRF 0.033 0.012 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K -0.17 0.25 -9999 0 -0.54 157 157
PDGF/PDGFRA/Crk/C3G -0.17 0.25 -9999 0 -0.54 154 154
JAK1 -0.19 0.3 -9999 0 -0.63 154 154
ELK1/SRF -0.13 0.24 -9999 0 -0.49 154 154
SHB 0.013 0 -9999 0 -10000 0 0
SHF 0.013 0.015 -9999 0 -0.31 1 1
CSNK2A1 0.028 0.027 -9999 0 -10000 0 0
GO:0007205 -0.2 0.32 -9999 0 -0.66 154 154
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.15 0.22 -9999 0 -0.48 154 154
PDGF/PDGFRA/SHB -0.2 0.29 -9999 0 -0.63 154 154
PDGF/PDGFRA/Caveolin-1 -0.21 0.32 -9999 0 -0.66 157 157
ITGAV 0.01 0.054 -9999 0 -0.82 2 2
ELK1 -0.18 0.28 -9999 0 -0.6 154 154
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
PDGF/PDGFRA/Crk -0.2 0.29 -9999 0 -0.63 154 154
JAK-STAT cascade -0.19 0.3 -9999 0 -0.63 154 154
cell proliferation -0.2 0.29 -9999 0 -0.63 154 154
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 -0.13 0.32 -9999 0 -0.82 83 83
GNB1/GNG2 -0.26 0.24 -9999 0 -0.6 124 124
mol:DAG -0.21 0.24 -9999 0 -0.55 118 118
PLCG1 -0.22 0.25 -9999 0 -0.57 118 118
YES1 -0.25 0.27 -9999 0 -0.43 302 302
FZD3 0.013 0 -9999 0 -10000 0 0
FZD6 0.013 0 -9999 0 -10000 0 0
G protein -0.24 0.22 -9999 0 -0.58 118 118
MAP3K7 -0.17 0.2 -9999 0 -0.45 116 116
mol:Ca2+ -0.2 0.23 -9999 0 -0.53 118 118
mol:IP3 -0.21 0.24 -9999 0 -0.55 118 118
NLK -0.01 0.01 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.19 0.22 -9999 0 -0.48 129 129
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.28 0.28 -9999 0 -0.47 302 302
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.25 0.27 -9999 0 -0.62 125 125
GO:0007205 -0.21 0.23 -9999 0 -0.54 116 116
WNT6 0.005 0.049 -9999 0 -0.31 11 11
WNT4 -0.26 0.39 -9999 0 -0.81 162 162
NFAT1/CK1 alpha -0.3 0.25 -9999 0 -0.62 150 150
GNG2 0.012 0.038 -9999 0 -0.82 1 1
WNT5A -0.005 0.12 -9999 0 -0.78 11 11
WNT11 -0.41 0.42 -9999 0 -0.82 249 249
CDC42 -0.23 0.25 -9999 0 -0.59 123 123
IL4-mediated signaling events

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
BCL2L1 -0.59 0.44 -10000 0 -1.2 129 129
STAT6 (cleaved dimer) -0.64 0.44 -10000 0 -1 251 251
IGHG1 -0.2 0.14 -10000 0 -0.36 22 22
IGHG3 -0.58 0.42 -10000 0 -0.96 221 221
AKT1 -0.32 0.26 -10000 0 -0.72 76 76
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.26 0.26 -10000 0 -0.75 55 55
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.35 0.28 -10000 0 -0.75 100 100
THY1 -0.59 0.44 -10000 0 -1.1 159 159
MYB -0.008 0.12 -10000 0 -0.63 16 16
HMGA1 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.41 0.31 -10000 0 -0.74 167 167
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.32 0.26 -10000 0 -0.74 67 67
SP1 0.02 0.006 -10000 0 -10000 0 0
INPP5D -0.003 0.071 -10000 0 -0.31 24 24
SOCS5 0.03 0.013 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.62 0.44 -10000 0 -1 231 231
SOCS1 -0.4 0.29 -10000 0 -0.74 118 118
SOCS3 -0.38 0.36 -10000 0 -1 69 69
FCER2 -0.58 0.42 -10000 0 -1 179 179
PARP14 0.013 0.004 -10000 0 -10000 0 0
CCL17 -0.66 0.48 -10000 0 -1.1 199 199
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.26 0.21 -10000 0 -0.66 49 49
T cell proliferation -0.6 0.46 -10000 0 -1.1 183 183
IL4R/JAK1 -0.59 0.44 -10000 0 -1.1 163 163
EGR2 -0.93 0.73 -10000 0 -1.6 238 238
JAK2 -0.017 0.045 -10000 0 -0.86 1 1
JAK3 -0.065 0.14 -10000 0 -0.31 120 120
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.002 0.008 -10000 0 -10000 0 0
COL1A2 -0.19 0.15 -10000 0 -0.54 33 33
CCL26 -0.61 0.45 -10000 0 -1.1 169 169
IL4R -0.63 0.47 -10000 0 -1.1 168 168
PTPN6 0.028 0.009 -10000 0 -10000 0 0
IL13RA2 -0.7 0.57 -10000 0 -1.3 174 174
IL13RA1 -0.016 0.024 -10000 0 -10000 0 0
IRF4 -0.34 0.48 -10000 0 -1.2 92 92
ARG1 -0.14 0.11 -10000 0 -10000 0 0
CBL -0.38 0.3 -10000 0 -0.73 136 136
GTF3A 0.016 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
IL13RA1/JAK2 -0.024 0.045 -10000 0 -0.68 1 1
IRF4/BCL6 -0.31 0.44 -10000 0 -1.1 88 88
CD40LG -0.12 0.3 -10000 0 -0.8 78 78
MAPK14 -0.39 0.32 -10000 0 -0.78 130 130
mitosis -0.3 0.24 -10000 0 -0.67 76 76
STAT6 -0.67 0.51 -10000 0 -1.1 214 214
SPI1 0.002 0.071 -10000 0 -0.31 24 24
RPS6KB1 -0.29 0.24 -10000 0 -0.68 60 60
STAT6 (dimer) -0.67 0.51 -10000 0 -1.1 214 214
STAT6 (dimer)/PARP14 -0.63 0.47 -10000 0 -1.1 197 197
mast cell activation 0.016 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.32 0.28 -10000 0 -0.73 82 82
FRAP1 -0.32 0.26 -10000 0 -0.72 76 76
LTA -0.61 0.46 -10000 0 -1.1 169 169
FES 0.013 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.66 0.5 1.1 215 -10000 0 215
CCL11 -0.58 0.43 -10000 0 -1.1 161 161
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.32 0.27 -10000 0 -0.7 90 90
IL2RG -0.043 0.19 -10000 0 -0.55 52 52
IL10 -0.61 0.47 -10000 0 -1.1 170 170
IRS1 -0.081 0.26 -10000 0 -0.82 55 55
IRS2 0.013 0 -10000 0 -10000 0 0
IL4 -0.14 0.096 -10000 0 -10000 0 0
IL5 -0.6 0.44 -10000 0 -1.1 161 161
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.48 0.33 -10000 0 -0.84 163 163
COL1A1 -0.26 0.24 -10000 0 -0.82 20 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.59 0.45 -10000 0 -1.2 128 128
IL2R gamma/JAK3 -0.08 0.18 -10000 0 -0.52 52 52
TFF3 -1.3 0.61 -10000 0 -1.6 393 393
ALOX15 -0.6 0.44 -10000 0 -1.1 159 159
MYBL1 0.013 0.015 -10000 0 -0.31 1 1
T-helper 2 cell differentiation -0.51 0.36 -10000 0 -0.86 194 194
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.018 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.3 0.26 -10000 0 -0.71 66 66
mol:PI-3-4-5-P3 -0.32 0.26 -10000 0 -0.72 76 76
PI3K -0.33 0.28 -10000 0 -0.77 76 76
DOK2 0 0.076 -10000 0 -0.38 16 16
ETS1 0.03 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.24 0.21 -10000 0 -0.65 48 48
ITGB3 -0.61 0.47 -10000 0 -1.2 156 156
PIGR -0.64 0.5 -10000 0 -1.2 169 169
IGHE 0.051 0.035 -10000 0 -10000 0 0
MAPKKK cascade -0.24 0.2 -10000 0 -0.64 48 48
BCL6 0.012 0.038 -10000 0 -0.82 1 1
OPRM1 -0.6 0.44 -10000 0 -1.1 155 155
RETNLB -0.6 0.44 -10000 0 -1.1 159 159
SELP -0.6 0.46 -10000 0 -1.1 151 151
AICDA -0.58 0.42 -10000 0 -1.1 141 141
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.51 0.55 -9999 0 -1.1 203 203
PCK1 -0.34 0.5 -9999 0 -1.4 72 72
HNF4A -0.67 0.66 -9999 0 -1.3 240 240
KCNJ11 -0.48 0.55 -9999 0 -1.1 189 189
AKT1 -0.04 0.12 -9999 0 -0.38 13 13
response to starvation -0.018 0.034 -9999 0 -10000 0 0
DLK1 -0.49 0.54 -9999 0 -1.1 185 185
NKX2-1 -0.16 0.21 -9999 0 -10000 0 0
ACADM -0.51 0.55 -9999 0 -1.1 205 205
TAT -0.2 0.22 -9999 0 -0.63 20 20
CEBPB 0.013 0.005 -9999 0 -10000 0 0
CEBPA 0.005 0.085 -9999 0 -0.82 5 5
TTR -0.19 0.22 -9999 0 -0.76 31 31
PKLR -0.52 0.55 -9999 0 -1.1 186 186
APOA1 -0.92 0.89 -9999 0 -1.7 245 245
CPT1C -0.53 0.55 -9999 0 -1.1 216 216
ALAS1 -0.16 0.21 -9999 0 -10000 0 0
TFRC -0.26 0.3 -9999 0 -0.76 36 36
FOXF1 -0.011 0.093 -9999 0 -0.76 7 7
NF1 0.021 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.015 0.007 -9999 0 -10000 0 0
CPT1A -0.51 0.55 -9999 0 -1.1 190 190
HMGCS1 -0.51 0.55 -9999 0 -1.1 211 211
NR3C1 0.019 0.016 -9999 0 -10000 0 0
CPT1B -0.51 0.55 -9999 0 -1.1 186 186
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.005 -9999 0 -10000 0 0
GCK -0.66 0.7 -9999 0 -1.3 226 226
CREB1 0 0.053 -9999 0 -10000 0 0
IGFBP1 -0.18 0.2 -9999 0 -0.55 11 11
PDX1 -0.18 0.21 -9999 0 -0.61 1 1
UCP2 -0.51 0.55 -9999 0 -1.1 187 187
ALDOB -0.48 0.54 -9999 0 -1.1 188 188
AFP -0.048 0.11 -9999 0 -0.51 6 6
BDH1 -0.51 0.55 -9999 0 -1.1 192 192
HADH -0.48 0.54 -9999 0 -1.1 184 184
F2 -0.63 0.64 -9999 0 -1.3 203 203
HNF1A 0.015 0.007 -9999 0 -10000 0 0
G6PC -0.006 0.09 -9999 0 -10000 0 0
SLC2A2 -0.23 0.26 -9999 0 -0.65 3 3
INS -0.008 0.018 -9999 0 -10000 0 0
FOXA1 -0.06 0.15 -9999 0 -0.54 13 13
FOXA3 -0.075 0.17 -9999 0 -0.49 35 35
FOXA2 -0.55 0.61 -9999 0 -1.2 204 204
ABCC8 -0.78 0.76 -9999 0 -1.4 258 258
ALB -0.1 0.32 -9999 0 -1.3 30 30
Nongenotropic Androgen signaling

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
PTK2 0.012 0.001 -10000 0 -10000 0 0
GNB1/GNG2 -0.21 0.25 -10000 0 -0.51 205 205
regulation of S phase of mitotic cell cycle -0.13 0.18 -10000 0 -0.34 206 206
GNAO1 -0.017 0.15 -10000 0 -0.72 20 20
HRAS 0.011 0.021 -10000 0 -0.32 2 2
SHBG/T-DHT -0.008 0.072 -10000 0 -0.56 8 8
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0.001 -10000 0 -10000 0 0
MAP2K1 -0.17 0.24 -10000 0 -0.44 204 204
T-DHT/AR -0.27 0.32 -10000 0 -0.64 204 204
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.005 128 128
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.038 -10000 0 -0.82 1 1
mol:GDP -0.26 0.31 -10000 0 -0.62 204 204
cell proliferation -0.2 0.28 -10000 0 -0.65 88 88
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
FOS -0.25 0.4 -10000 0 -0.89 129 129
mol:Ca2+ -0.027 0.031 -10000 0 -0.071 93 93
MAPK3 -0.18 0.26 -10000 0 -0.46 205 205
MAPK1 -0.084 0.13 -10000 0 -0.31 78 78
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 129 129
cAMP biosynthetic process 0.016 0.076 -10000 0 -0.53 8 8
GNG2 0.012 0.038 -10000 0 -0.82 1 1
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 129 129
HRAS/GTP -0.2 0.23 -10000 0 -0.47 204 204
actin cytoskeleton reorganization -0.003 0.035 -10000 0 -0.44 3 3
SRC 0.012 0.015 -10000 0 -0.32 1 1
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 129 129
PI3K -0.003 0.043 -10000 0 -0.55 3 3
apoptosis 0.16 0.25 0.53 129 -10000 0 129
T-DHT/AR/PELP1 -0.23 0.28 -10000 0 -0.56 204 204
HRAS/GDP -0.25 0.29 -10000 0 -0.59 205 205
CREB1 -0.18 0.28 -10000 0 -0.57 129 129
RAC1-CDC42/GTP -0.003 0.035 -10000 0 -0.45 3 3
AR -0.34 0.41 -10000 0 -0.83 204 204
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.18 0.24 -10000 0 -0.46 204 204
RAC1-CDC42/GDP -0.24 0.28 -10000 0 -0.56 204 204
T-DHT/AR/PELP1/Src -0.22 0.25 -10000 0 -0.51 204 204
MAP2K2 -0.17 0.24 -10000 0 -0.44 204 204
T-DHT/AR/PELP1/Src/PI3K -0.13 0.19 -10000 0 -0.34 206 206
GNAZ 0.013 0 -10000 0 -10000 0 0
SHBG 0 0.11 -10000 0 -0.82 8 8
Gi family/GNB1/GNG2/GDP -0.02 0.12 -10000 0 -0.55 16 16
mol:T-DHT 0 0.001 0.002 77 -0.003 50 127
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.009 0.043 -10000 0 -0.5 3 3
Gi family/GTP -0.095 0.12 -10000 0 -0.48 17 17
CDC42 0.013 0 -10000 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.11 0.26 -10000 0 -0.69 36 36
IHH -0.21 0.37 -10000 0 -0.84 122 122
SHH Np/Cholesterol/GAS1 -0.11 0.21 -10000 0 -0.52 98 98
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.11 0.21 0.51 98 -10000 0 98
SMO/beta Arrestin2 -0.098 0.24 -10000 0 -0.49 125 125
SMO -0.11 0.26 -10000 0 -0.52 126 126
AKT1 -0.028 0.12 -10000 0 -0.66 2 2
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC -0.002 0.11 -10000 0 -0.82 9 9
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.11 0.25 -10000 0 -0.51 126 126
STIL -0.08 0.2 -10000 0 -0.61 18 18
DHH N/PTCH2 -0.11 0.24 -10000 0 -0.64 81 81
DHH N/PTCH1 -0.1 0.23 -10000 0 -0.46 129 129
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
DHH 0.006 0.076 -10000 0 -0.82 4 4
PTHLH -0.16 0.37 -10000 0 -1.2 36 36
determination of left/right symmetry -0.11 0.25 -10000 0 -0.51 126 126
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.16 0.37 -10000 0 -1.2 36 36
IHH N/Hhip -0.38 0.4 -10000 0 -0.74 256 256
DHH N/Hhip -0.25 0.31 -10000 0 -0.64 188 188
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.11 0.25 -10000 0 -0.51 126 126
pancreas development -0.31 0.4 -10000 0 -0.82 188 188
HHAT 0.012 0.038 -10000 0 -0.82 1 1
PI3K -0.004 0.049 -10000 0 -0.63 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.15 0.33 -10000 0 -0.82 97 97
somite specification -0.11 0.25 -10000 0 -0.51 126 126
SHH Np/Cholesterol/PTCH1 -0.09 0.21 -10000 0 -0.62 18 18
SHH Np/Cholesterol/PTCH2 -0.089 0.19 -10000 0 -0.52 80 80
SHH Np/Cholesterol/Megalin -0.14 0.23 -10000 0 -0.52 128 128
SHH 0.007 0.05 -10000 0 -0.63 1 1
catabolic process -0.12 0.25 -10000 0 -0.51 125 125
SMO/Vitamin D3 -0.094 0.22 -10000 0 -0.66 18 18
SHH Np/Cholesterol/Hhip -0.2 0.25 -10000 0 -0.51 187 187
LRP2 -0.2 0.37 -10000 0 -0.82 127 127
receptor-mediated endocytosis -0.2 0.24 -10000 0 -0.72 48 48
SHH Np/Cholesterol/BOC -0.015 0.078 -10000 0 -0.52 10 10
SHH Np/Cholesterol/CDO -0.15 0.23 -10000 0 -0.52 141 141
mesenchymal cell differentiation 0.2 0.24 0.51 187 -10000 0 187
mol:Vitamin D3 -0.09 0.21 -10000 0 -0.63 18 18
IHH N/PTCH2 -0.23 0.35 -10000 0 -0.67 179 179
CDON -0.23 0.38 -10000 0 -0.82 140 140
IHH N/PTCH1 -0.12 0.25 -10000 0 -0.52 125 125
Megalin/LRPAP1 -0.16 0.28 -10000 0 -0.63 127 127
PTCH2 -0.12 0.31 -10000 0 -0.82 79 79
SHH Np/Cholesterol -0.006 0.036 -10000 0 -0.51 1 1
PTCH1 -0.12 0.25 -10000 0 -0.52 125 125
HHIP -0.31 0.4 -10000 0 -0.82 188 188
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR -0.023 0.17 -9999 0 -0.82 21 21
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.42 0.26 -9999 0 -0.57 360 360
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.37 0.26 -9999 0 -0.52 360 360
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.006 0.016 -9999 0 -0.31 1 1
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.1 0.29 -9999 0 -0.82 66 66
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.027 0.13 -9999 0 -0.63 21 21
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 0.012 0.021 -9999 0 -0.31 2 2
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 0.004 0.021 -9999 0 -0.31 2 2
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.42 0.26 -9999 0 -0.57 361 361
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.28 0.21 -9999 0 -0.73 17 17
MAP1B 0 0.005 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.32 0.23 -9999 0 -0.45 360 360
RELN -0.6 0.37 -9999 0 -0.82 356 356
PAFAH/LIS1 -0.05 0.2 -9999 0 -0.55 66 66
LIS1/CLIP170 0.028 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.22 0.14 -9999 0 -0.55 17 17
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.25 0.19 -9999 0 -0.34 366 366
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.3 0.22 -9999 0 -0.42 360 360
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.024 0 -9999 0 -10000 0 0
PAFAH1B3 0.011 0.03 -9999 0 -0.31 4 4
PAFAH1B2 -0.002 0.11 -9999 0 -0.82 9 9
MAP1B/LIS1/Dynein heavy chain 0.027 0.003 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.28 0.17 -9999 0 -0.69 17 17
LRP8 -0.023 0.17 -9999 0 -0.82 21 21
NDEL1/Katanin 60 -0.28 0.21 -9999 0 -0.73 17 17
P39/CDK5 -0.32 0.23 -9999 0 -0.45 360 360
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.34 0.24 -9999 0 -0.48 360 360
PPP2R5D 0.013 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.36 0.23 -9999 0 -0.49 361 361
RELN/VLDLR -0.4 0.27 -9999 0 -0.54 365 365
CDC42 0 0 -9999 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.011 0.081 -9999 0 -0.56 9 9
NFATC2 -0.1 0.22 -9999 0 -0.58 83 83
NFATC3 0 0.027 -9999 0 -10000 0 0
CD40LG -0.44 0.41 -9999 0 -0.87 197 197
PTGS2 -0.42 0.4 -9999 0 -0.85 185 185
JUNB 0.003 0.092 -9999 0 -0.82 6 6
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.005 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.005 0.015 -9999 0 -10000 0 0
CALM1 0.008 0.008 -9999 0 -10000 0 0
JUN -0.18 0.35 -9999 0 -0.83 109 109
mol:Ca2+ -0.01 0.012 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.004 -9999 0 -10000 0 0
FOSL1 -0.028 0.12 -9999 0 -0.33 59 59
CREM 0.013 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.26 0.28 -9999 0 -0.59 168 168
FOS -0.22 0.37 -9999 0 -0.83 129 129
IFNG -0.44 0.4 -9999 0 -0.85 203 203
AP-1/NFAT1-c-4 -0.53 0.51 -9999 0 -0.98 222 222
FASLG -0.42 0.39 -9999 0 -0.83 189 189
NFAT1-c-4/ICER1 -0.11 0.2 -9999 0 -0.5 90 90
IL2RA -0.41 0.38 -9999 0 -0.83 182 182
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.48 0.36 -9999 0 -0.77 254 254
JunB/Fra1/NFAT1-c-4 -0.13 0.2 -9999 0 -0.51 92 92
IL4 -0.4 0.36 -9999 0 -0.8 180 180
IL2 -0.012 0.026 -9999 0 -10000 0 0
IL3 -0.032 0.03 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 -0.006 0.082 -9999 0 -0.33 27 27
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.015 -9999 0 -0.31 1 1
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.17 0.3 0.69 117 -10000 0 117
KIRREL -0.068 0.24 -10000 0 -0.85 40 40
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.17 0.3 -10000 0 -0.69 117 117
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.13 0.24 -10000 0 -0.54 117 117
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.076 0.2 -10000 0 -0.41 117 117
FYN -0.11 0.24 -10000 0 -0.51 117 117
mol:Ca2+ -0.13 0.24 -10000 0 -0.53 117 117
mol:DAG -0.13 0.24 -10000 0 -0.54 117 117
NPHS2 -0.017 0.053 -10000 0 -0.9 1 1
mol:IP3 -0.13 0.24 -10000 0 -0.54 117 117
regulation of endocytosis -0.12 0.21 -10000 0 -0.48 117 117
Nephrin/NEPH1/podocin/Cholesterol -0.13 0.24 -10000 0 -0.55 117 117
establishment of cell polarity -0.17 0.3 -10000 0 -0.69 117 117
Nephrin/NEPH1/podocin/NCK1-2 -0.12 0.22 -10000 0 -0.49 117 117
Nephrin/NEPH1/beta Arrestin2 -0.11 0.22 -10000 0 -0.48 117 117
NPHS1 -0.16 0.32 -10000 0 -0.83 90 90
Nephrin/NEPH1/podocin -0.12 0.23 -10000 0 -0.51 117 117
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.13 0.24 -10000 0 -0.54 117 117
CD2AP 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.13 0.24 -10000 0 -0.54 117 117
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.11 0.24 -10000 0 -0.51 121 121
cytoskeleton organization -0.1 0.26 -10000 0 -0.54 117 117
Nephrin/NEPH1 -0.13 0.24 -10000 0 -0.53 117 117
Nephrin/NEPH1/ZO-1 -0.14 0.26 -10000 0 -0.57 117 117
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 -0.001 0.026 -10000 0 -0.55 1 1
fibroblast growth factor receptor signaling pathway -0.001 0.026 -10000 0 -0.54 1 1
LAMA1 -0.049 0.22 -10000 0 -0.81 37 37
PRNP 0.012 0.038 -10000 0 -0.82 1 1
GPC1/SLIT2 -0.097 0.23 -10000 0 -0.63 73 73
SMAD2 0.028 0.049 -10000 0 -0.49 3 3
GPC1/PrPc/Cu2+ -0.001 0.026 -10000 0 -0.55 1 1
GPC1/Laminin alpha1 -0.048 0.17 -10000 0 -0.63 36 36
TDGF1 -0.34 0.41 -10000 0 -0.82 204 204
CRIPTO/GPC1 -0.27 0.31 -10000 0 -0.63 204 204
APP/GPC1 0 0.009 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.21 0.28 -10000 0 -0.54 204 204
FLT1 0.012 0.038 -10000 0 -0.82 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.008 0.049 -10000 0 -0.55 3 3
SERPINC1 0.007 0.042 -10000 0 -0.31 8 8
FYN -0.21 0.28 -10000 0 -0.54 204 204
FGR -0.21 0.28 -10000 0 -0.54 204 204
positive regulation of MAPKKK cascade -0.28 0.32 -10000 0 -0.62 206 206
SLIT2 -0.11 0.3 -10000 0 -0.8 76 76
GPC1/NRG -0.061 0.18 -10000 0 -0.63 46 46
NRG1 -0.067 0.24 -10000 0 -0.8 48 48
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.005 0.059 -10000 0 -0.71 3 3
LYN -0.21 0.28 -10000 0 -0.54 204 204
mol:Spermine 0.012 0.01 -10000 0 -10000 0 0
cell growth -0.001 0.026 -10000 0 -0.54 1 1
BMP signaling pathway -0.013 0.015 0.31 1 -10000 0 1
SRC -0.21 0.28 -10000 0 -0.55 204 204
TGFBR1 0.005 0.051 -10000 0 -0.31 12 12
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.25 0.37 -10000 0 -0.69 184 184
GPC1 0.013 0.015 -10000 0 -0.31 1 1
TGFBR1 (dimer) 0.005 0.051 -10000 0 -0.31 12 12
VEGFA 0.008 0.066 -10000 0 -0.82 3 3
BLK -0.38 0.38 -10000 0 -0.67 278 278
HCK -0.22 0.28 -10000 0 -0.55 204 204
FGF2 0.013 0 -10000 0 -10000 0 0
FGFR1 0.012 0.038 -10000 0 -0.82 1 1
VEGFR1 homodimer 0.012 0.038 -10000 0 -0.82 1 1
TGFBR2 0.008 0.066 -10000 0 -0.82 3 3
cell death 0 0.009 -10000 0 -10000 0 0
ATIII/GPC1 -0.004 0.027 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.2 0.28 -10000 0 -0.63 135 135
LCK -0.23 0.28 -10000 0 -0.55 209 209
neuron differentiation -0.061 0.18 -10000 0 -0.63 46 46
PrPc/Cu2+ -0.001 0.029 -10000 0 -0.64 1 1
APP 0.013 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.008 0.065 -10000 0 -0.82 3 3
Ephrin B reverse signaling

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
EFNB2 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.066 -10000 0 -0.83 3 3
EFNB1 -0.001 0.12 -10000 0 -0.63 17 17
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.25 0.25 -10000 0 -0.53 204 204
Ephrin B2/EPHB1-2 -0.2 0.25 -10000 0 -0.5 191 191
neuron projection morphogenesis -0.24 0.23 -10000 0 -0.5 204 204
Ephrin B1/EPHB1-2/Tiam1 -0.27 0.27 -10000 0 -0.57 204 204
DNM1 -0.017 0.15 -10000 0 -0.8 18 18
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.006 0.084 -10000 0 -0.8 5 5
YES1 -0.008 0.1 -10000 0 -1 5 5
Ephrin B1/EPHB1-2/NCK2 -0.19 0.25 -10000 0 -0.47 204 204
PI3K 0.004 0.11 -10000 0 -1.1 5 5
mol:GDP -0.27 0.26 -10000 0 -0.56 204 204
ITGA2B -0.074 0.26 -10000 0 -0.82 51 51
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.008 0.1 -10000 0 -1 5 5
MAP3K7 -0.011 0.086 -10000 0 -0.85 5 5
FGR -0.01 0.1 -10000 0 -1 5 5
TIAM1 -0.17 0.16 -10000 0 -0.32 276 276
PIK3R1 0.013 0 -10000 0 -10000 0 0
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.043 0.21 -10000 0 -0.54 63 63
LYN -0.008 0.1 -10000 0 -1 5 5
Ephrin B1/EPHB1-2/Src Family Kinases -0.012 0.099 -10000 0 -0.98 5 5
Ephrin B1/EPHB1-2 -0.018 0.093 -10000 0 -0.92 5 5
SRC -0.01 0.1 -10000 0 -1 5 5
ITGB3 -0.014 0.15 -10000 0 -0.82 16 16
EPHB1 -0.31 0.41 -10000 0 -0.82 189 189
EPHB4 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.086 0.23 -10000 0 -0.68 61 61
BLK -0.065 0.14 -10000 0 -1.1 5 5
HCK -0.011 0.1 -10000 0 -1 5 5
regulation of stress fiber formation 0.19 0.24 0.47 204 -10000 0 204
MAPK8 0.006 0.12 -10000 0 -0.78 10 10
Ephrin B1/EPHB1-2/RGS3 -0.19 0.25 -10000 0 -0.47 204 204
endothelial cell migration -0.005 0.076 -10000 0 -0.74 5 5
NCK2 0.013 0 -10000 0 -10000 0 0
PTPN13 0.006 0.098 -10000 0 -0.94 5 5
regulation of focal adhesion formation 0.19 0.24 0.47 204 -10000 0 204
chemotaxis 0.19 0.24 0.47 204 -10000 0 204
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
Rac1/GTP -0.25 0.24 -10000 0 -0.52 204 204
angiogenesis -0.018 0.092 -10000 0 -0.91 5 5
LCK -0.013 0.11 -10000 0 -1.1 5 5
Endothelins

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
AKT1 -0.05 0.14 -9999 0 -0.53 10 10
PTK2B 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.13 0.28 -9999 0 -0.7 59 59
EDN1 -0.043 0.12 -9999 0 -0.74 7 7
EDN3 -0.4 0.42 -9999 0 -0.82 239 239
EDN2 -0.016 0.12 -9999 0 -0.4 34 34
HRAS/GDP -0.1 0.24 -9999 0 -0.54 78 78
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.082 0.18 -9999 0 -0.39 90 90
ADCY4 -0.095 0.19 -9999 0 -0.5 68 68
ADCY5 -0.16 0.25 -9999 0 -0.56 114 114
ADCY6 -0.095 0.19 -9999 0 -0.5 68 68
ADCY7 -0.095 0.19 -9999 0 -0.5 68 68
ADCY1 -0.1 0.2 -9999 0 -0.52 70 70
ADCY2 -0.14 0.24 -9999 0 -0.55 102 102
ADCY3 -0.095 0.19 -9999 0 -0.5 68 68
ADCY8 -0.2 0.2 -9999 0 -0.54 94 94
ADCY9 -0.095 0.19 -9999 0 -0.5 68 68
arachidonic acid secretion -0.17 0.32 -9999 0 -0.65 131 131
ETB receptor/Endothelin-1/Gq/GTP -0.093 0.21 -9999 0 -0.43 115 115
GNAO1 -0.017 0.15 -9999 0 -0.72 20 20
HRAS 0.01 0.021 -9999 0 -0.31 2 2
ETA receptor/Endothelin-1/G12/GTP -0.013 0.16 -9999 0 -0.51 9 9
ETA receptor/Endothelin-1/Gs/GTP -0.081 0.22 -9999 0 -0.53 69 69
mol:GTP -0.003 0.009 -9999 0 -10000 0 0
COL3A1 -0.067 0.17 -9999 0 -0.5 38 38
EDNRB 0.004 0.087 -9999 0 -0.84 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
CYSLTR2 -0.16 0.24 -9999 0 -0.64 52 52
CYSLTR1 -0.059 0.17 -9999 0 -0.75 14 14
SLC9A1 -0.021 0.075 -9999 0 -0.3 6 6
mol:GDP -0.12 0.25 -9999 0 -0.56 88 88
SLC9A3 -0.045 0.19 -9999 0 -0.79 20 20
RAF1 -0.15 0.3 -9999 0 -0.58 124 124
JUN -0.28 0.51 -9999 0 -1.2 117 117
JAK2 -0.052 0.14 -9999 0 -0.54 10 10
mol:IP3 -0.11 0.22 -9999 0 -0.49 101 101
ETA receptor/Endothelin-1 -0.034 0.2 -9999 0 -0.52 19 19
PLCB1 0.009 0.039 -9999 0 -0.83 1 1
PLCB2 0.005 0.043 -9999 0 -0.32 8 8
ETA receptor/Endothelin-3 -0.33 0.34 -9999 0 -0.66 238 238
FOS -0.26 0.48 -9999 0 -1 130 130
Gai/GDP -0.003 0.13 -9999 0 -0.66 16 16
CRK 0.013 0.001 -9999 0 -10000 0 0
mol:Ca ++ -0.12 0.23 -9999 0 -0.6 51 51
BCAR1 0.013 0.002 -9999 0 -10000 0 0
PRKCB1 -0.11 0.22 -9999 0 -0.48 102 102
GNAQ 0.011 0.008 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNAL -0.092 0.28 -9999 0 -0.82 61 61
Gs family/GDP -0.18 0.25 -9999 0 -0.57 118 118
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.21 -9999 0 -0.45 101 101
MAPK14 -0.061 0.17 -9999 0 -0.46 33 33
TRPC6 -0.14 0.3 -9999 0 -0.75 58 58
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
GNAI1 0.012 0.038 -9999 0 -0.82 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.073 0.18 -9999 0 -0.4 83 83
ETB receptor/Endothelin-2 -0.026 0.1 -9999 0 -0.64 11 11
ETB receptor/Endothelin-3 -0.32 0.32 -9999 0 -0.64 240 240
ETB receptor/Endothelin-1 -0.018 0.12 -9999 0 -0.63 11 11
MAPK3 -0.23 0.44 -9999 0 -0.89 136 136
MAPK1 -0.23 0.44 -9999 0 -0.89 135 135
Rac1/GDP -0.1 0.24 -9999 0 -0.54 74 74
cAMP biosynthetic process -0.14 0.21 -9999 0 -0.54 78 78
MAPK8 -0.17 0.34 -9999 0 -0.69 105 105
SRC 0.012 0.015 -9999 0 -0.32 1 1
ETB receptor/Endothelin-1/Gi/GTP 0.009 0.078 -9999 0 -0.36 7 7
p130Cas/CRK/Src/PYK2 -0.13 0.29 -9999 0 -0.62 91 91
mol:K + 0 0 -9999 0 -10000 0 0
G12/GDP -0.1 0.24 -9999 0 -0.53 79 79
COL1A2 -0.036 0.16 -9999 0 -0.53 16 16
EntrezGene:2778 0 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-2 -0.029 0.11 -9999 0 -0.63 8 8
mol:DAG -0.11 0.22 -9999 0 -0.49 101 101
MAP2K2 -0.18 0.35 -9999 0 -0.69 138 138
MAP2K1 -0.18 0.35 -9999 0 -0.69 138 138
EDNRA -0.037 0.098 -9999 0 -0.55 4 4
positive regulation of muscle contraction -0.035 0.12 -9999 0 -0.49 8 8
Gq family/GDP -0.19 0.29 -9999 0 -0.66 112 112
HRAS/GTP -0.13 0.26 -9999 0 -0.57 94 94
PRKCH -0.1 0.22 -9999 0 -0.51 83 83
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.12 0.26 -9999 0 -0.55 98 98
PRKCB -0.12 0.23 -9999 0 -0.52 89 89
PRKCE -0.1 0.23 -9999 0 -0.52 84 84
PRKCD -0.1 0.22 -9999 0 -0.51 83 83
PRKCG -0.1 0.22 -9999 0 -0.51 83 83
regulation of vascular smooth muscle contraction -0.3 0.56 -9999 0 -1.2 130 130
PRKCQ -0.1 0.23 -9999 0 -0.51 86 86
PLA2G4A -0.19 0.36 -9999 0 -0.72 131 131
GNA14 -0.18 0.36 -9999 0 -0.83 112 112
GNA15 -0.015 0.093 -9999 0 -0.33 37 37
GNA12 0.013 0 -9999 0 -10000 0 0
GNA11 -0.005 0.11 -9999 0 -0.82 9 9
Rac1/GTP -0.013 0.16 -9999 0 -0.53 8 8
MMP1 -0.098 0.16 -9999 0 -10000 0 0
IGF1 pathway

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
NCK2 0.013 0 -10000 0 -10000 0 0
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.13 0.24 -10000 0 -0.45 156 156
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.012 0.021 -10000 0 -0.31 2 2
IRS1/Crk -0.13 0.24 -10000 0 -0.46 156 156
IGF-1R heterotetramer/IGF1/PTP1B -0.13 0.22 -10000 0 -0.53 113 113
AKT1 -0.091 0.22 -10000 0 -0.78 15 15
BAD -0.077 0.2 -10000 0 -0.71 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.13 0.24 -10000 0 -0.45 156 156
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.13 0.24 -10000 0 -0.46 156 156
RAF1 -0.068 0.19 -10000 0 -0.66 15 15
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.14 0.21 -10000 0 -0.46 113 113
YWHAZ 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.16 0.24 -10000 0 -0.5 156 156
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
RPS6KB1 -0.091 0.22 -10000 0 -0.78 15 15
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.059 0.16 -10000 0 -0.54 15 15
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.12 0.19 -10000 0 -0.73 13 13
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.1 0.18 -10000 0 -0.42 113 113
IGF-1R heterotetramer -0.019 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.15 0.22 -10000 0 -0.46 156 156
Crk/p130 Cas/Paxillin -0.13 0.2 -10000 0 -0.44 113 113
IGF1R -0.019 0.048 -10000 0 -10000 0 0
IGF1 -0.2 0.36 -10000 0 -0.82 119 119
IRS2/Crk -0.11 0.23 -10000 0 -0.43 156 156
PI3K -0.14 0.22 -10000 0 -0.47 114 114
apoptosis 0.059 0.18 0.58 15 -10000 0 15
HRAS/GDP -0.001 0.014 -10000 0 -10000 0 0
PRKCD -0.11 0.24 -10000 0 -0.53 113 113
RAF1/14-3-3 E -0.05 0.17 -10000 0 -0.54 15 15
BAD/14-3-3 -0.063 0.19 -10000 0 -0.63 15 15
PRKCZ -0.091 0.22 -10000 0 -0.78 15 15
Crk/p130 Cas/Paxillin/FAK1 -0.1 0.16 -10000 0 -0.64 15 15
PTPN1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.12 0.26 -10000 0 -0.57 113 113
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.11 0.19 -10000 0 -0.46 113 113
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.13 0.24 -10000 0 -0.45 156 156
GRB10 0.013 0 -10000 0 -10000 0 0
PTPN11 -0.13 0.24 -10000 0 -0.46 156 156
IRS1 -0.15 0.25 -10000 0 -0.5 156 156
IRS2 -0.13 0.24 -10000 0 -0.45 156 156
IGF-1R heterotetramer/IGF1 -0.17 0.28 -10000 0 -0.66 113 113
GRB2 0.013 0 -10000 0 -10000 0 0
PDPK1 -0.1 0.23 -10000 0 -0.45 114 114
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKD1 -0.11 0.24 -10000 0 -0.53 114 114
SHC1 0.013 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.18 0.42 -9999 0 -0.96 51 51
HDAC7 0.015 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.28 0.34 -9999 0 -0.82 105 105
SMAD4 0.015 0.003 -9999 0 -10000 0 0
ID2 -0.18 0.42 -9999 0 -0.94 56 56
AP1 -0.29 0.45 -9999 0 -0.92 152 152
ABCG2 -0.19 0.42 -9999 0 -0.95 57 57
HIF1A -0.008 0.068 -9999 0 -10000 0 0
TFF3 -0.57 0.52 -9999 0 -1 193 193
GATA2 0.014 0.015 -9999 0 -0.31 1 1
AKT1 -0.038 0.1 -9999 0 -10000 0 0
response to hypoxia -0.059 0.11 -9999 0 -0.24 20 20
MCL1 -0.18 0.42 -9999 0 -0.96 50 50
NDRG1 -0.18 0.42 -9999 0 -0.95 54 54
SERPINE1 -0.2 0.43 -9999 0 -0.96 56 56
FECH -0.18 0.42 -9999 0 -0.92 61 61
FURIN -0.18 0.42 -9999 0 -0.93 58 58
NCOA2 -0.061 0.24 -9999 0 -0.82 44 44
EP300 -0.062 0.18 -9999 0 -0.33 112 112
HMOX1 -0.19 0.42 -9999 0 -0.93 62 62
BHLHE40 -0.19 0.43 -9999 0 -0.94 62 62
BHLHE41 -0.19 0.42 -9999 0 -1 46 46
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.017 0.036 -9999 0 -10000 0 0
ENG 0.042 0.092 -9999 0 -10000 0 0
JUN -0.17 0.35 -9999 0 -0.82 109 109
RORA -0.19 0.42 -9999 0 -0.98 50 50
ABCB1 -0.077 0.19 -9999 0 -1.4 8 8
TFRC -0.19 0.42 -9999 0 -0.95 57 57
CXCR4 -0.18 0.42 -9999 0 -0.93 61 61
TF -0.23 0.49 -9999 0 -1.1 83 83
CITED2 -0.22 0.47 -9999 0 -1 70 70
HIF1A/ARNT -0.29 0.38 -9999 0 -1 66 66
LDHA -0.039 0.049 -9999 0 -10000 0 0
ETS1 -0.18 0.42 -9999 0 -0.96 51 51
PGK1 -0.18 0.42 -9999 0 -0.99 44 44
NOS2 -0.2 0.43 -9999 0 -0.98 55 55
ITGB2 -0.19 0.42 -9999 0 -0.95 61 61
ALDOA -0.18 0.42 -9999 0 -0.96 50 50
Cbp/p300/CITED2 -0.32 0.51 -9999 0 -1.1 103 103
FOS -0.21 0.37 -9999 0 -0.82 129 129
HK2 -0.19 0.42 -9999 0 -0.94 58 58
SP1 0.022 0.008 -9999 0 -10000 0 0
GCK -0.39 0.72 -9999 0 -1.5 136 136
HK1 -0.18 0.42 -9999 0 -0.94 56 56
NPM1 -0.18 0.42 -9999 0 -0.95 53 53
EGLN1 -0.18 0.42 -9999 0 -0.97 51 51
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.18 0.42 -9999 0 -0.94 56 56
SMAD3 0.015 0.003 -9999 0 -10000 0 0
EDN1 -0.16 0.32 -9999 0 -0.73 67 67
IGFBP1 -0.2 0.42 -9999 0 -0.94 60 60
VEGFA -0.16 0.38 -9999 0 -0.76 74 74
HIF1A/JAB1 -0.011 0.02 -9999 0 -10000 0 0
CP -0.35 0.55 -9999 0 -1 147 147
CXCL12 -0.23 0.49 -9999 0 -1 84 84
COPS5 0.014 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0.003 -9999 0 -10000 0 0
BNIP3 -0.18 0.42 -9999 0 -0.94 56 56
EGLN3 -0.2 0.44 -9999 0 -0.97 64 64
CA9 -0.2 0.42 -9999 0 -0.94 62 62
TERT -0.2 0.42 -9999 0 -0.94 60 60
ENO1 -0.18 0.42 -9999 0 -0.94 56 56
PFKL -0.18 0.42 -9999 0 -0.94 56 56
NCOA1 0.014 0 -9999 0 -10000 0 0
ADM -0.22 0.44 -9999 0 -0.97 63 63
ARNT -0.009 0.067 -9999 0 -10000 0 0
HNF4A -0.026 0.065 -9999 0 -0.35 10 10
ADFP -0.2 0.41 -9999 0 -0.92 66 66
SLC2A1 -0.15 0.38 -9999 0 -0.75 73 73
LEP -0.2 0.42 -9999 0 -0.96 56 56
HIF1A/ARNT/Cbp/p300 -0.29 0.36 -9999 0 -0.86 105 105
EPO -0.14 0.33 -9999 0 -0.91 28 28
CREBBP -0.062 0.18 -9999 0 -0.32 126 126
HIF1A/ARNT/Cbp/p300/HDAC7 -0.28 0.34 -9999 0 -0.82 102 102
PFKFB3 -0.18 0.42 -9999 0 -0.93 63 63
NT5E -0.19 0.43 -9999 0 -0.97 55 55
Glucocorticoid receptor regulatory 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
PCK2 0.045 0.094 -10000 0 -10000 0 0
SMARCC2 0.013 0.014 -10000 0 -10000 0 0
SMARCC1 0.013 0.014 -10000 0 -10000 0 0
TBX21 -0.16 0.28 -10000 0 -0.86 46 46
SUMO2 0.014 0.013 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.05 -10000 0 -0.31 11 11
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 0.001 0.1 -10000 0 -0.82 7 7
GR alpha/HSP90/FKBP51/HSP90 0.13 0.13 0.36 35 -0.49 7 42
PRL -0.089 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.25 0.31 0.59 152 -0.49 21 173
RELA -0.036 0.088 -10000 0 -10000 0 0
FGG 0.24 0.19 0.52 106 -10000 0 106
GR beta/TIF2 0.085 0.23 0.35 71 -0.56 44 115
IFNG -0.5 0.51 -10000 0 -1 178 178
apoptosis 0.036 0.24 0.52 54 -0.56 2 56
CREB1 0.011 0.023 -10000 0 -10000 0 0
histone acetylation -0.072 0.17 -10000 0 -0.42 55 55
BGLAP -0.099 0.15 -10000 0 -0.52 15 15
GR/PKAc 0.13 0.1 0.36 25 -0.41 1 26
NF kappa B1 p50/RelA -0.074 0.16 -10000 0 -0.45 32 32
SMARCD1 0.013 0.014 -10000 0 -10000 0 0
MDM2 0.12 0.094 0.27 102 -10000 0 102
GATA3 -0.027 0.19 -10000 0 -0.78 27 27
AKT1 0 0 -10000 0 -10000 0 0
CSF2 -0.21 0.16 -10000 0 -0.58 33 33
GSK3B 0.014 0.013 -10000 0 -10000 0 0
NR1I3 0.063 0.23 0.51 41 -0.78 4 45
CSN2 0.2 0.14 0.43 74 -10000 0 74
BRG1/BAF155/BAF170/BAF60A 0.017 0.049 -10000 0 -10000 0 0
NFATC1 0 0.11 -10000 0 -0.82 9 9
POU2F1 0.013 0.015 -10000 0 -0.3 1 1
CDKN1A 0.023 0.055 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.012 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 312 312
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.046 0.16 0.35 14 -0.48 14 28
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.074 0.44 0.49 42 -0.88 103 145
JUN -0.33 0.3 -10000 0 -0.71 160 160
IL4 -0.13 0.18 -10000 0 -0.65 25 25
CDK5R1 0.012 0.022 -10000 0 -0.32 2 2
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.37 0.41 -10000 0 -0.82 185 185
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.12 0.35 31 -0.47 6 37
cortisol/GR alpha (monomer) 0.37 0.3 0.71 171 -10000 0 171
NCOA2 -0.062 0.24 -10000 0 -0.82 44 44
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.26 0.36 -10000 0 -0.85 129 129
AP-1/NFAT1-c-4 -0.56 0.48 -10000 0 -0.98 231 231
AFP -0.22 0.22 -10000 0 -0.7 30 30
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.2 0.15 0.45 73 -10000 0 73
TP53 0.032 0.023 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.48 0.37 -10000 0 -0.82 189 189
KRT14 -0.24 0.18 -10000 0 -0.63 16 16
TBP 0.022 0.009 -10000 0 -10000 0 0
CREBBP 0.064 0.066 -10000 0 -10000 0 0
HDAC1 0.011 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.013 -10000 0 -10000 0 0
AP-1 -0.57 0.49 -10000 0 -0.98 232 232
MAPK14 0.014 0.012 -10000 0 -10000 0 0
MAPK10 0.013 0.04 -10000 0 -0.83 1 1
MAPK11 0.014 0.013 -10000 0 -10000 0 0
KRT5 -0.55 0.53 -10000 0 -1.2 162 162
interleukin-1 receptor activity 0.017 0.013 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 0.015 0.05 -10000 0 -0.31 11 11
CGA -0.13 0.16 -10000 0 -0.54 24 24
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.24 0.14 0.41 121 -10000 0 121
MAPK3 0.014 0.012 -10000 0 -10000 0 0
MAPK1 0.014 0.012 -10000 0 -10000 0 0
ICAM1 -0.26 0.27 -10000 0 -0.65 115 115
NFKB1 -0.038 0.097 -10000 0 -0.31 12 12
MAPK8 -0.19 0.2 -10000 0 -0.52 93 93
MAPK9 0.014 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.03 0.24 0.52 54 -0.58 2 56
BAX 0.028 0.032 -10000 0 -10000 0 0
POMC -0.54 0.69 -10000 0 -1.5 138 138
EP300 0.065 0.067 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.33 0.24 0.6 165 -10000 0 165
proteasomal ubiquitin-dependent protein catabolic process 0.088 0.071 0.24 32 -10000 0 32
SGK1 0.1 0.24 -10000 0 -1.4 11 11
IL13 -0.3 0.25 -10000 0 -0.74 77 77
IL6 -0.41 0.54 -10000 0 -1.2 127 127
PRKACG 0.002 0.005 -10000 0 -10000 0 0
IL5 -0.26 0.2 -10000 0 -0.68 52 52
IL2 -0.36 0.27 -10000 0 -0.8 92 92
CDK5 0.013 0.007 -10000 0 -10000 0 0
PRKACB 0.012 0.038 -10000 0 -0.82 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.27 0.32 -10000 0 -0.74 99 99
CDK5R1/CDK5 0.007 0.023 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.032 0.12 -10000 0 -0.56 3 3
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.56 160 -10000 0 160
SMARCA4 0.013 0.014 -10000 0 -10000 0 0
chromatin remodeling 0.2 0.15 0.42 94 -10000 0 94
NF kappa B1 p50/RelA/Cbp 0.018 0.16 -10000 0 -0.52 5 5
JUN (dimer) -0.33 0.3 -10000 0 -0.71 160 160
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.24 0.41 -10000 0 -1.1 82 82
NR3C1 0.22 0.19 0.5 111 -10000 0 111
NR4A1 -0.31 0.41 -10000 0 -0.76 206 206
TIF2/SUV420H1 -0.057 0.18 -10000 0 -0.63 44 44
MAPKKK cascade 0.036 0.24 0.52 54 -0.56 2 56
cortisol/GR alpha (dimer)/Src-1 0.32 0.24 0.6 163 -10000 0 163
PBX1 0.012 0.038 -10000 0 -0.82 1 1
POU1F1 0.007 0.008 -10000 0 -10000 0 0
SELE -0.35 0.51 -10000 0 -1.2 105 105
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.2 0.15 0.43 90 -10000 0 90
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.31 0.22 0.56 160 -10000 0 160
mol:cortisol 0.21 0.19 0.4 188 -10000 0 188
MMP1 -0.22 0.15 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.12 0.23 -10000 0 -0.62 77 77
FYN -0.11 0.35 -10000 0 -0.8 85 85
LAT/GRAP2/SLP76 -0.12 0.27 -10000 0 -0.66 87 87
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.054 0.22 -10000 0 -0.47 89 89
B2M 0.013 0.006 -10000 0 -10000 0 0
IKBKG -0.031 0.05 -10000 0 -0.18 11 11
MAP3K8 0 0.11 -10000 0 -0.82 8 8
mol:Ca2+ -0.031 0.051 -10000 0 -0.12 107 107
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.1 0.33 -10000 0 -0.73 91 91
TRPV6 -0.18 0.34 -10000 0 -0.8 110 110
CD28 -0.043 0.19 -10000 0 -0.59 45 45
SHC1 -0.12 0.35 -10000 0 -0.8 86 86
receptor internalization -0.14 0.38 -10000 0 -0.83 95 95
PRF1 -0.12 0.36 -10000 0 -0.89 73 73
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 -0.037 0.18 -10000 0 -0.38 88 88
LAT -0.12 0.35 -10000 0 -0.81 86 86
EntrezGene:6955 0 0.003 -10000 0 -10000 0 0
CD3D -0.096 0.27 -10000 0 -0.72 73 73
CD3E -0.072 0.25 -10000 0 -0.76 54 54
CD3G -0.15 0.33 -10000 0 -0.79 97 97
RASGRP2 0 0.031 -10000 0 -0.19 6 6
RASGRP1 -0.05 0.22 -10000 0 -0.47 91 91
HLA-A 0.011 0.022 -10000 0 -0.31 2 2
RASSF5 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.068 -10000 0 -0.12 64 64
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.056 0.09 -10000 0 -0.25 64 64
PRKCA -0.062 0.14 -10000 0 -0.32 84 84
GRAP2 -0.042 0.2 -10000 0 -0.78 34 34
mol:IP3 -0.051 0.23 0.28 84 -0.46 87 171
EntrezGene:6957 0 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.16 0.43 -10000 0 -0.97 83 83
ORAI1 0.089 0.16 0.39 102 -10000 0 102
CSK -0.12 0.36 -10000 0 -0.82 86 86
B7 family/CD28 -0.2 0.35 -10000 0 -0.75 113 113
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.16 0.43 -10000 0 -0.96 91 91
PTPN6 -0.12 0.36 -10000 0 -0.84 85 85
VAV1 -0.12 0.35 -10000 0 -0.79 90 90
Monovalent TCR/CD3 -0.16 0.41 -10000 0 -0.74 121 121
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.12 0.37 -10000 0 -0.83 87 87
PAG1 -0.12 0.36 -10000 0 -0.82 86 86
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.16 0.43 -10000 0 -0.96 90 90
CD80 -0.07 0.25 -10000 0 -0.81 49 49
CD86 -0.009 0.1 -10000 0 -0.42 24 24
PDK1/CARD11/BCL10/MALT1 -0.069 0.11 -10000 0 -0.29 71 71
HRAS 0.012 0.021 -10000 0 -0.31 2 2
GO:0035030 -0.11 0.3 -10000 0 -0.64 97 97
CD8A -0.049 0.22 -10000 0 -0.83 36 36
CD8B -0.092 0.27 -10000 0 -0.74 69 69
PTPRC -0.034 0.18 -10000 0 -0.59 37 37
PDK1/PKC theta -0.069 0.27 -10000 0 -0.6 87 87
CSK/PAG1 -0.11 0.35 -10000 0 -0.83 80 80
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.015 0.018 -10000 0 -10000 0 0
GRAP2/SLP76 -0.15 0.32 -10000 0 -0.78 90 90
STIM1 0.047 0.082 -10000 0 -10000 0 0
RAS family/GTP 0.008 0.092 -10000 0 -0.18 52 52
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.16 0.43 -10000 0 -0.93 95 95
mol:DAG -0.071 0.18 -10000 0 -0.41 88 88
RAP1A/GDP 0.006 0.03 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.023 0.16 -10000 0 -0.64 27 27
cytotoxic T cell degranulation -0.11 0.34 -10000 0 -0.81 77 77
RAP1A/GTP -0.003 0.009 -10000 0 -0.07 5 5
mol:PI-3-4-5-P3 -0.074 0.26 -10000 0 -0.57 91 91
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.081 0.29 0.3 78 -0.62 88 166
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.022 0.16 -10000 0 -0.62 27 27
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.12 0.26 -10000 0 -0.63 88 88
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.01 0.054 -10000 0 -0.82 2 2
CD8 heterodimer -0.11 0.3 -10000 0 -0.77 74 74
CARD11 -0.072 0.17 -10000 0 -0.35 115 115
PRKCB -0.059 0.13 -10000 0 -0.32 79 79
PRKCE -0.052 0.12 -10000 0 -0.3 72 72
PRKCQ -0.092 0.31 -10000 0 -0.7 88 88
LCP2 0.009 0.039 -10000 0 -0.31 7 7
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.04 0.19 -10000 0 -0.4 89 89
IKK complex 0.013 0.069 -10000 0 -0.12 38 38
RAS family/GDP -0.005 0.01 -10000 0 -10000 0 0
MAP3K14 -0.017 0.14 -10000 0 -0.3 74 74
PDPK1 -0.048 0.21 -10000 0 -0.45 87 87
TCR/CD3/MHC I/CD8/Fyn -0.17 0.46 -10000 0 -1.1 85 85
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 -0.22 0.56 -10000 0 -1.3 76 76
IL23A -0.23 0.57 -10000 0 -1.3 86 86
NF kappa B1 p50/RelA/I kappa B alpha -0.3 0.48 -10000 0 -1.2 88 88
positive regulation of T cell mediated cytotoxicity -0.26 0.62 -10000 0 -1.4 88 88
ITGA3 -0.21 0.52 -10000 0 -1.2 79 79
IL17F -0.11 0.35 -10000 0 -0.75 73 73
IL12B -0.001 0.1 -10000 0 -0.63 9 9
STAT1 (dimer) -0.24 0.59 -10000 0 -1.3 87 87
CD4 -0.2 0.51 -10000 0 -1.2 82 82
IL23 -0.24 0.54 -10000 0 -1.2 83 83
IL23R -0.005 0.1 -10000 0 -10000 0 0
IL1B -0.24 0.6 -10000 0 -1.4 80 80
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.2 0.51 -10000 0 -1.2 82 82
TYK2 0.014 0.023 -10000 0 -10000 0 0
STAT4 -0.025 0.14 -10000 0 -0.45 40 40
STAT3 0.013 0 -10000 0 -10000 0 0
IL18RAP -0.027 0.17 -10000 0 -0.8 23 23
IL12RB1 -0.021 0.12 -10000 0 -0.37 44 44
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
IL12Rbeta1/TYK2 -0.009 0.093 -10000 0 -0.68 4 4
IL23R/JAK2 -0.002 0.13 -10000 0 -0.68 1 1
positive regulation of chronic inflammatory response -0.26 0.62 -10000 0 -1.4 88 88
natural killer cell activation 0.001 0.009 0.036 1 -10000 0 1
JAK2 0.021 0.048 -10000 0 -0.86 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
NFKB1 0.011 0.038 -10000 0 -0.83 1 1
RELA 0.013 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.22 0.51 -10000 0 -1.1 85 85
ALOX12B -0.22 0.52 -10000 0 -1.2 87 87
CXCL1 -0.23 0.54 -10000 0 -1.2 83 83
T cell proliferation -0.26 0.62 -10000 0 -1.4 88 88
NFKBIA 0.013 0.004 -10000 0 -10000 0 0
IL17A -0.063 0.28 -10000 0 -0.59 58 58
PI3K -0.31 0.49 -10000 0 -1.2 88 88
IFNG -0.02 0.055 -10000 0 -0.13 74 74
STAT3 (dimer) -0.29 0.45 -10000 0 -1.2 86 86
IL18R1 -0.031 0.15 -10000 0 -0.43 47 47
IL23/IL23R/JAK2/TYK2/SOCS3 -0.1 0.33 -10000 0 -0.76 55 55
IL18/IL18R -0.068 0.18 -10000 0 -0.56 47 47
macrophage activation -0.015 0.018 -10000 0 -0.045 85 85
TNF -0.28 0.63 -10000 0 -1.4 99 99
STAT3/STAT4 -0.32 0.5 -10000 0 -1.3 91 91
STAT4 (dimer) -0.26 0.59 -10000 0 -1.3 91 91
IL18 -0.039 0.16 -10000 0 -0.41 58 58
IL19 -0.2 0.51 -10000 0 -1.2 77 77
STAT5A (dimer) -0.24 0.59 -10000 0 -1.3 88 88
STAT1 0.006 0.049 -10000 0 -0.31 11 11
SOCS3 -0.034 0.19 -10000 0 -0.8 28 28
CXCL9 -0.3 0.64 -10000 0 -1.4 110 110
MPO -0.2 0.52 -10000 0 -1.2 86 86
positive regulation of humoral immune response -0.26 0.62 -10000 0 -1.4 88 88
IL23/IL23R/JAK2/TYK2 -0.3 0.75 -10000 0 -1.6 88 88
IL6 -0.34 0.66 -10000 0 -1.4 124 124
STAT5A 0.013 0 -10000 0 -10000 0 0
IL2 0.001 0.017 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.001 0.009 0.036 1 -10000 0 1
CD3E -0.24 0.58 -10000 0 -1.3 92 92
keratinocyte proliferation -0.26 0.62 -10000 0 -1.4 88 88
NOS2 -0.21 0.51 -10000 0 -1.2 77 77
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.27 0.33 -9999 0 -0.6 217 217
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.049 0.21 -9999 0 -0.7 42 42
SMAD9 -0.22 0.28 -9999 0 -0.59 165 165
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.096 0.2 -9999 0 -0.37 161 161
BMP7/USAG1 -0.33 0.32 -9999 0 -0.63 253 253
SMAD5/SKI -0.085 0.2 -9999 0 -0.53 28 28
SMAD1 0.019 0.045 -9999 0 -10000 0 0
BMP2 -0.021 0.17 -9999 0 -0.82 20 20
SMAD1/SMAD1/SMAD4 -0.001 0.001 -9999 0 -10000 0 0
BMPR1A 0.013 0 -9999 0 -10000 0 0
BMPR1B -0.26 0.39 -9999 0 -0.82 161 161
BMPR1A-1B/BAMBI -0.19 0.26 -9999 0 -0.56 161 161
AHSG -0.018 0.085 -9999 0 -0.31 37 37
CER1 0 0.003 -9999 0 -10000 0 0
BMP2-4/CER1 -0.04 0.14 -9999 0 -0.55 33 33
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.078 0.2 -9999 0 -0.63 32 32
BMP2-4 (homodimer) -0.046 0.16 -9999 0 -0.63 33 33
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.5 161 161
RGMA -0.018 0.16 -9999 0 -0.82 18 18
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.089 0.19 -9999 0 -0.58 29 29
BMP2-4/USAG1 -0.32 0.3 -9999 0 -0.58 269 269
SMAD6/SMURF1/SMAD5 -0.085 0.2 -9999 0 -0.53 28 28
SOSTDC1 -0.42 0.42 -9999 0 -0.82 254 254
BMP7/BMPR2/BMPR1A-1B -0.16 0.23 -9999 0 -0.5 161 161
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.013 0.015 -9999 0 -0.31 1 1
HFE2 0.001 0.033 -9999 0 -0.31 5 5
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.05 0.16 -9999 0 -0.56 42 42
SMAD5/SMAD5/SMAD4 -0.085 0.2 -9999 0 -0.53 28 28
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.094 0.14 -9999 0 -0.49 29 29
BMP7 (homodimer) 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.016 0.056 -9999 0 -0.4 1 1
SMAD1/SKI 0.026 0.043 -9999 0 -10000 0 0
SMAD6 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.052 0.15 -9999 0 -0.57 33 33
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.21 0.36 -9999 0 -0.73 143 143
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA -0.008 0.065 -9999 0 -0.55 7 7
BMPR1A-1B (homodimer) -0.21 0.3 -9999 0 -0.63 161 161
CHRDL1 -0.58 0.38 -9999 0 -0.82 345 345
ENDOFIN/SMAD1 0.026 0.043 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.006 0.008 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.002 0.08 -9999 0 -0.37 19 19
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.42 0.28 -9999 0 -0.59 351 351
BMP2-4/GREM1 -0.18 0.28 -9999 0 -0.61 135 135
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.19 0.28 -9999 0 -0.55 165 165
SMAD1/SMAD6 0.026 0.043 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 0.013 0 -9999 0 -10000 0 0
BMP6 0.013 0.015 -9999 0 -0.31 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.067 0.16 -9999 0 -0.5 29 29
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.026 0.043 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.001 0.1 -9999 0 -0.82 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.2 0.32 -9999 0 -0.79 86 86
CHRD -0.004 0.12 -9999 0 -0.82 10 10
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.095 0.2 -9999 0 -0.62 29 29
BMP4 -0.014 0.14 -9999 0 -0.64 20 20
FST -0.2 0.36 -9999 0 -0.79 127 127
BMP2-4/NOG -0.078 0.19 -9999 0 -0.55 65 65
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.15 0.22 -9999 0 -0.46 161 161
Glypican 2 network

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
MDK -0.087 0.15 -9999 0 -0.31 149 149
GPC2 -0.01 0.083 -9999 0 -0.31 34 34
GPC2/Midkine -0.076 0.11 -9999 0 -0.4 12 12
neuron projection morphogenesis -0.076 0.11 -9999 0 -0.4 12 12
Coregulation of Androgen receptor activity

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
NRIP1 -0.015 0.064 -10000 0 -0.36 13 13
SVIL -0.006 0.031 -10000 0 -10000 0 0
ZNF318 0.061 0.093 0.22 8 -0.82 1 9
JMJD2C -0.064 0.069 -10000 0 -0.12 276 276
T-DHT/AR/Ubc9 -0.28 0.3 -10000 0 -0.62 204 204
CARM1 0.012 0.003 -10000 0 -10000 0 0
PRDX1 0.015 0.004 -10000 0 -10000 0 0
PELP1 0.02 0.011 -10000 0 -10000 0 0
CTNNB1 -0.002 0.023 -10000 0 -10000 0 0
AKT1 0.026 0.019 -10000 0 -10000 0 0
PTK2B 0.004 0.015 -10000 0 -10000 0 0
MED1 0.025 0.019 -10000 0 -10000 0 0
MAK 0.052 0.13 -10000 0 -0.8 6 6
response to oxidative stress 0.002 0.004 -10000 0 -10000 0 0
HIP1 -0.01 0.061 -10000 0 -0.82 2 2
GSN -0.006 0.03 -10000 0 -10000 0 0
NCOA2 -0.064 0.24 -10000 0 -0.82 44 44
NCOA6 -0.007 0.047 -10000 0 -0.82 1 1
DNA-PK 0.058 0.084 0.26 1 -10000 0 1
NCOA4 0.011 0.004 -10000 0 -10000 0 0
PIAS3 -0.002 0.023 -10000 0 -10000 0 0
cell proliferation -0.011 0.15 -10000 0 -1.1 6 6
XRCC5 0.025 0.018 -10000 0 -10000 0 0
UBE3A -0.016 0.047 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.31 0.33 -10000 0 -0.67 211 211
FHL2 -0.16 0.36 -10000 0 -1.3 39 39
RANBP9 -0.005 0.029 -10000 0 -10000 0 0
JMJD1A 0.002 0.037 -10000 0 -0.12 36 36
CDK6 0.009 0.066 -10000 0 -0.82 3 3
TGFB1I1 -0.006 0.031 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.3 0.3 -10000 0 -0.63 207 207
XRCC6 0.025 0.018 -10000 0 -10000 0 0
T-DHT/AR -0.33 0.32 -10000 0 -0.64 230 230
CTDSP1 0.009 0.006 -10000 0 -10000 0 0
CTDSP2 0.046 0.05 -10000 0 -10000 0 0
BRCA1 -0.006 0.031 -10000 0 -10000 0 0
TCF4 0.035 0.034 -10000 0 -10000 0 0
CDKN2A -0.11 0.16 -10000 0 -0.31 140 140
SRF 0.028 0.039 -10000 0 -10000 0 0
NKX3-1 -0.13 0.15 -10000 0 -1.3 4 4
KLK3 -0.44 0.71 -10000 0 -1.6 137 137
TMF1 0.006 0.054 -10000 0 -0.82 2 2
HNRNPA1 0.031 0.028 -10000 0 -10000 0 0
AOF2 -0.022 0.034 -10000 0 -0.075 137 137
APPL1 0.052 0.042 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.28 0.29 -10000 0 -0.61 204 204
AR -0.38 0.42 -10000 0 -0.87 204 204
UBA3 0.009 0.006 -10000 0 -10000 0 0
PATZ1 0.031 0.028 -10000 0 -10000 0 0
PAWR 0.009 0.006 -10000 0 -10000 0 0
PRKDC 0.025 0.018 -10000 0 -10000 0 0
PA2G4 0.036 0.036 -10000 0 -10000 0 0
UBE2I 0.013 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.25 0.28 -10000 0 -0.57 204 204
RPS6KA3 -0.006 0.03 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.28 0.3 -10000 0 -0.62 204 204
LATS2 0.029 0.047 -10000 0 -0.82 1 1
T-DHT/AR/PRX1 -0.24 0.28 -10000 0 -0.56 204 204
Cyclin D3/CDK11 p58 0 0.003 -10000 0 -10000 0 0
VAV3 -0.012 0.094 -10000 0 -0.83 6 6
KLK2 -0.77 0.63 -10000 0 -1.3 275 275
CASP8 0.017 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.31 0.34 -10000 0 -0.67 210 210
TMPRSS2 -0.19 0.32 -10000 0 -1.2 35 35
CCND1 0.001 0.049 -10000 0 -0.31 11 11
PIAS1 -0.016 0.047 -10000 0 -10000 0 0
mol:T-DHT -0.031 0.041 -10000 0 -0.082 162 162
CDC2L1 0.001 0.002 -10000 0 -10000 0 0
PIAS4 -0.036 0.077 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.28 0.3 -10000 0 -0.62 206 206
CMTM2 0.014 0.027 -10000 0 -0.31 3 3
SNURF -0.032 0.19 -10000 0 -0.82 26 26
ZMIZ1 -0.013 0.051 -10000 0 -0.81 1 1
CCND3 0.014 0.002 -10000 0 -10000 0 0
TGIF1 0.031 0.028 -10000 0 -10000 0 0
FKBP4 -0.005 0.029 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.043 0.11 -9999 0 -0.47 13 13
EGFR 0.006 0.076 -9999 0 -0.82 4 4
EPHA2 0.011 0.026 -9999 0 -0.31 3 3
USP6 0.011 0.026 -9999 0 -0.31 3 3
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.096 0.22 -9999 0 -0.63 72 72
ARRB2 -0.044 0.15 -9999 0 -0.45 59 59
mol:GTP 0.021 0.012 -9999 0 -10000 0 0
ARRB1 0.012 0.038 -9999 0 -0.82 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR 0.01 0.054 -9999 0 -0.82 2 2
EGF -0.11 0.29 -9999 0 -0.78 74 74
somatostatin receptor activity 0 0 -9999 0 -0.001 133 133
ARAP2 0.01 0.054 -9999 0 -0.82 2 2
mol:GDP -0.12 0.15 -9999 0 -0.31 129 129
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 64 64
ITGA2B -0.074 0.26 -9999 0 -0.82 51 51
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.01 -9999 0 -10000 0 0
ADAP1 0.013 0 -9999 0 -10000 0 0
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.17 0.24 -9999 0 -0.69 74 74
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.12 0.15 -9999 0 -0.31 134 134
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.083 0.19 -9999 0 -0.55 72 72
ADRB2 -0.009 0.14 -9999 0 -0.82 13 13
receptor agonist activity 0 0 -9999 0 0 137 137
actin filament binding 0 0 -9999 0 -0.001 131 131
SRC 0.013 0.015 -9999 0 -0.31 1 1
ITGB3 -0.014 0.15 -9999 0 -0.82 16 16
GNAQ 0.013 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 -9999 0 -0.001 120 120
ARF6/GDP 0.001 0.069 -9999 0 -0.32 3 3
ARF6/GDP/GULP/ACAP1 -0.19 0.2 -9999 0 -0.5 118 118
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.068 0.19 -9999 0 -0.54 61 61
ACAP1 0.001 0.075 -9999 0 -0.38 15 15
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.081 0.22 -9999 0 -0.68 59 59
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.11 0.3 -9999 0 -0.82 74 74
CYTH3 0.009 0.042 -9999 0 -0.64 2 2
CYTH2 0.008 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 110 110
endosomal lumen acidification 0 0 -9999 0 -0.001 137 137
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.14 0.32 -9999 0 -0.82 90 90
GNAQ/ARNO 0.009 0.009 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 19 19
MET -0.11 0.16 -9999 0 -0.31 180 180
GNA14 -0.18 0.35 -9999 0 -0.82 112 112
GNA15 -0.013 0.093 -9999 0 -0.33 37 37
GIT1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 130 130
GNA11 -0.002 0.11 -9999 0 -0.82 9 9
LHCGR -0.098 0.27 -9999 0 -0.77 66 66
AGTR1 -0.32 0.41 -9999 0 -0.82 196 196
desensitization of G-protein coupled receptor protein signaling pathway -0.081 0.22 -9999 0 -0.68 59 59
IPCEF1/ARNO -0.056 0.16 -9999 0 -0.43 72 72
alphaIIb/beta3 Integrin -0.086 0.23 -9999 0 -0.68 61 61
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.008 0.042 -9999 0 -0.31 8 8
CCL5 -0.045 0.21 -9999 0 -0.72 39 39
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.1 0.16 -9999 0 -0.49 48 48
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.092 0.16 -9999 0 -0.61 24 24
Syndecan-1/Syntenin -0.092 0.16 -9999 0 -0.61 24 24
MAPK3 -0.069 0.14 -9999 0 -0.6 19 19
HGF/MET -0.17 0.24 -9999 0 -0.69 74 74
TGFB1/TGF beta receptor Type II 0.008 0.042 -9999 0 -0.31 8 8
BSG 0.013 0.015 -9999 0 -0.31 1 1
keratinocyte migration -0.091 0.15 -9999 0 -0.6 24 24
Syndecan-1/RANTES -0.12 0.22 -9999 0 -0.66 53 53
Syndecan-1/CD147 -0.081 0.15 -9999 0 -0.62 21 21
Syndecan-1/Syntenin/PIP2 -0.099 0.14 -9999 0 -0.62 22 22
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.097 0.14 -9999 0 -0.57 24 24
MMP7 -0.18 0.22 -9999 0 -0.37 242 242
HGF -0.11 0.3 -9999 0 -0.82 74 74
Syndecan-1/CASK -0.1 0.16 -9999 0 -0.47 48 48
Syndecan-1/HGF/MET -0.2 0.24 -9999 0 -0.65 87 87
regulation of cell adhesion -0.059 0.14 -9999 0 -0.58 19 19
HPSE -0.017 0.14 -9999 0 -0.51 28 28
positive regulation of cell migration -0.1 0.16 -9999 0 -0.49 48 48
SDC1 -0.11 0.16 -9999 0 -0.49 48 48
Syndecan-1/Collagen -0.1 0.16 -9999 0 -0.49 48 48
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.11 0.16 -9999 0 -0.31 180 180
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.082 0.24 -9999 0 -0.57 79 79
MAPK1 -0.069 0.14 -9999 0 -0.6 19 19
homophilic cell adhesion -0.1 0.16 -9999 0 -0.48 48 48
MMP1 -0.14 0.16 -9999 0 -0.31 233 233
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.088 0.2 -10000 0 -0.56 76 76
cell-cell adhesion 0.15 0.19 0.55 10 -10000 0 10
Ephrin B/EPHB2/RasGAP -0.014 0.068 -10000 0 -0.46 10 10
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.1 0.081 -10000 0 -10000 0 0
Ephrin B1/EPHB1 -0.22 0.27 -10000 0 -0.55 189 189
HRAS/GDP -0.14 0.17 -10000 0 -0.5 12 12
Ephrin B/EPHB1/GRB7 -0.21 0.25 -10000 0 -0.51 194 194
Endophilin/SYNJ1 0.025 0.072 -10000 0 -0.43 10 10
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.19 0.23 -10000 0 -0.47 194 194
endothelial cell migration -0.003 0.037 -10000 0 -0.47 3 3
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 -0.042 0.12 -10000 0 -0.31 82 82
PAK1 0.034 0.073 -10000 0 -0.43 10 10
HRAS 0.012 0.021 -10000 0 -0.31 2 2
RRAS 0.025 0.074 -10000 0 -0.44 10 10
DNM1 -0.017 0.15 -10000 0 -0.8 18 18
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.16 0.24 -10000 0 -0.45 194 194
lamellipodium assembly -0.15 0.19 -10000 0 -0.55 10 10
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.11 0.18 -10000 0 -0.33 189 189
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.066 -10000 0 -0.82 3 3
EPHB3 -0.19 0.16 -10000 0 -0.31 296 296
EPHB1 -0.31 0.41 -10000 0 -0.82 189 189
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.071 0.18 -10000 0 -0.51 7 7
Ephrin B/EPHB2 -0.014 0.07 -10000 0 -0.47 10 10
Ephrin B/EPHB3 -0.086 0.087 -10000 0 -0.57 7 7
JNK cascade -0.15 0.24 -10000 0 -0.46 191 191
Ephrin B/EPHB1 -0.2 0.24 -10000 0 -0.48 194 194
RAP1/GDP -0.055 0.16 -10000 0 -0.53 3 3
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.01 0.12 -10000 0 -0.46 24 24
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.2 0.25 -10000 0 -0.51 191 191
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.16 0.19 -10000 0 -0.58 10 10
Rap1/GTP -0.15 0.19 -10000 0 -0.56 10 10
axon guidance -0.088 0.2 -10000 0 -0.56 76 76
MAPK3 -0.08 0.16 -10000 0 -0.38 10 10
MAPK1 -0.08 0.16 -10000 0 -0.53 2 2
Rac1/GDP -0.047 0.17 -10000 0 -0.46 7 7
actin cytoskeleton reorganization -0.11 0.13 -10000 0 -0.55 3 3
CDC42/GDP -0.047 0.17 -10000 0 -0.46 7 7
PI3K -0.003 0.037 -10000 0 -0.47 3 3
EFNA5 -0.12 0.3 -10000 0 -0.82 74 74
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.029 0.055 -10000 0 -0.33 10 10
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.15 0.18 -10000 0 -0.54 11 11
PTK2 0.042 0.052 -10000 0 -10000 0 0
MAP4K4 -0.16 0.25 -10000 0 -0.46 191 191
SRC 0.013 0.015 -10000 0 -0.31 1 1
KALRN 0.013 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.071 0.18 -10000 0 -0.55 3 3
MAP2K1 -0.093 0.17 -10000 0 -0.41 10 10
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.2 0.24 -10000 0 -0.5 191 191
cell migration -0.089 0.19 -10000 0 -0.44 10 10
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 0.026 0.073 -10000 0 -0.44 10 10
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.021 0.17 -10000 0 -0.45 60 60
HRAS/GTP -0.17 0.2 -10000 0 -0.59 11 11
Ephrin B1/EPHB1-2 -0.2 0.25 -10000 0 -0.51 191 191
cell adhesion mediated by integrin 0.013 0.075 0.5 7 -10000 0 7
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.18 0.22 -10000 0 -0.44 196 196
RAC1-CDC42/GTP -0.21 0.21 -10000 0 -0.49 146 146
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.055 0.16 -10000 0 -0.53 3 3
ruffle organization -0.12 0.22 -10000 0 -0.56 10 10
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization 0.017 0.12 -10000 0 -0.46 25 25
Ephrin B/EPHB2/KALRN -0.014 0.068 -10000 0 -0.46 10 10
ROCK1 -0.074 0.081 -10000 0 -10000 0 0
RAS family/GDP -0.085 0.11 -10000 0 -0.52 3 3
Rac1/GTP -0.16 0.2 -10000 0 -0.6 10 10
Ephrin B/EPHB1/Src/Paxillin -0.11 0.18 -10000 0 -0.34 194 194
IL12-mediated signaling events

Figure S31.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S31.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.023 0.16 -10000 0 -0.47 27 27
TBX21 -0.12 0.44 -10000 0 -1.1 61 61
B2M 0.012 0.008 -10000 0 -10000 0 0
TYK2 0.016 0.02 -10000 0 -10000 0 0
IL12RB1 -0.018 0.12 -10000 0 -0.37 44 44
GADD45B -0.089 0.38 -10000 0 -1 52 52
IL12RB2 -0.017 0.16 -10000 0 -0.75 21 21
GADD45G -0.072 0.34 -10000 0 -0.86 54 54
natural killer cell activation 0.003 0.022 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.035 0.16 -10000 0 -0.41 58 58
IL2RA -0.047 0.2 -10000 0 -0.58 49 49
IFNG -0.11 0.28 -10000 0 -0.72 78 78
STAT3 (dimer) -0.071 0.32 -10000 0 -0.74 65 65
HLA-DRB5 -0.041 0.13 -10000 0 -0.35 70 70
FASLG -0.13 0.47 -10000 0 -1.2 64 64
NF kappa B2 p52/RelB -0.17 0.32 -10000 0 -0.9 63 63
CD4 0.001 0.057 -10000 0 -0.32 15 15
SOCS1 0.009 0.048 -10000 0 -0.42 5 5
EntrezGene:6955 -0.007 0.015 -10000 0 -10000 0 0
CD3D -0.1 0.27 -10000 0 -0.72 73 73
CD3E -0.075 0.25 -10000 0 -0.75 54 54
CD3G -0.15 0.33 -10000 0 -0.8 97 97
IL12Rbeta2/JAK2 -0.002 0.13 -10000 0 -0.64 19 19
CCL3 -0.1 0.43 -10000 0 -1.1 55 55
CCL4 -0.15 0.52 -10000 0 -1.4 63 63
HLA-A 0.011 0.022 -10000 0 -0.31 2 2
IL18/IL18R -0.032 0.2 -10000 0 -0.57 46 46
NOS2 -0.086 0.34 -10000 0 -0.9 47 47
IL12/IL12R/TYK2/JAK2/SPHK2 -0.021 0.15 -10000 0 -0.44 27 27
IL1R1 -0.085 0.37 -10000 0 -0.95 54 54
IL4 0 0.027 -10000 0 -0.34 1 1
JAK2 0.014 0.044 -10000 0 -0.86 1 1
EntrezGene:6957 -0.006 0.015 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.24 0.56 -10000 0 -1.1 106 106
RAB7A -0.039 0.29 -10000 0 -0.67 55 55
lysosomal transport -0.034 0.28 -10000 0 -0.64 55 55
FOS -0.41 0.65 -10000 0 -1.3 162 162
STAT4 (dimer) -0.076 0.35 -10000 0 -0.83 61 61
STAT5A (dimer) -0.22 0.36 -10000 0 -0.87 93 93
GZMA -0.1 0.41 -10000 0 -1.1 55 55
GZMB -0.099 0.39 -10000 0 -1 53 53
HLX 0.004 0.055 -10000 0 -0.31 14 14
LCK -0.11 0.43 -10000 0 -0.98 69 69
TCR/CD3/MHC II/CD4 -0.19 0.35 -10000 0 -0.62 135 135
IL2/IL2R -0.081 0.22 -10000 0 -0.67 47 47
MAPK14 -0.067 0.35 -10000 0 -0.8 64 64
CCR5 -0.096 0.41 -10000 0 -1.2 43 43
IL1B -0.053 0.24 -10000 0 -0.83 40 40
STAT6 -0.003 0.11 -10000 0 -10000 0 0
STAT4 -0.025 0.14 -10000 0 -0.45 40 40
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.049 -10000 0 -0.31 11 11
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B -0.001 0.096 -10000 0 -0.58 10 10
CD8A -0.05 0.22 -10000 0 -0.83 36 36
CD8B -0.093 0.27 -10000 0 -0.73 69 69
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.023 0.16 0.46 27 -10000 0 27
IL2RB -0.015 0.13 -10000 0 -0.51 26 26
proteasomal ubiquitin-dependent protein catabolic process -0.064 0.32 -10000 0 -0.75 61 61
IL2RG -0.047 0.19 -10000 0 -0.55 52 52
IL12 -0.057 0.22 -10000 0 -0.64 56 56
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.026 0.16 -10000 0 -0.64 27 27
IL2 0.004 0.006 -10000 0 -10000 0 0
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.075 0.26 -10000 0 -0.8 54 54
IL12/IL12R/TYK2/JAK2 -0.12 0.48 -10000 0 -1.1 69 69
MAP2K3 -0.069 0.35 -10000 0 -0.79 64 64
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 -0.076 0.36 -10000 0 -0.82 64 64
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.026 0.13 -10000 0 -0.4 44 44
IL18RAP -0.023 0.18 -10000 0 -0.8 23 23
IL12Rbeta1/TYK2 -0.003 0.093 -10000 0 -0.64 4 4
EOMES -0.14 0.43 -10000 0 -1.5 43 43
STAT1 (dimer) -0.13 0.37 -10000 0 -0.77 94 94
T cell proliferation -0.047 0.27 -10000 0 -0.61 58 58
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.027 0.15 -10000 0 -0.42 47 47
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.14 0.25 -10000 0 -0.69 61 61
ATF2 -0.069 0.33 -10000 0 -0.75 62 62
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.11 0.39 -9999 0 -1.3 43 43
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.035 0.11 -9999 0 -0.39 19 19
ATF2/c-Jun -0.22 0.42 -9999 0 -0.96 112 112
MAPK11 -0.035 0.11 -9999 0 -0.39 19 19
MITF -0.028 0.13 -9999 0 -0.4 43 43
MAPKAPK5 -0.028 0.13 -9999 0 -0.4 43 43
KRT8 -0.028 0.13 -9999 0 -0.48 19 19
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.048 0.17 -9999 0 -0.52 43 43
CEBPB -0.028 0.13 -9999 0 -0.4 43 43
SLC9A1 -0.028 0.13 -9999 0 -0.4 43 43
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.07 0.19 -9999 0 -0.46 60 60
p38alpha-beta/MNK1 -0.025 0.14 -9999 0 -0.5 19 19
JUN -0.21 0.42 -9999 0 -0.95 112 112
PPARGC1A -0.23 0.25 -9999 0 -0.46 252 252
USF1 -0.028 0.13 -9999 0 -0.4 43 43
RAB5/GDP/GDI1 -0.038 0.084 -9999 0 -0.35 18 18
NOS2 -0.048 0.16 -9999 0 -0.66 8 8
DDIT3 -0.031 0.14 -9999 0 -0.41 43 43
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.012 0.11 -9999 0 -0.39 19 19
p38alpha-beta/HBP1 -0.025 0.14 -9999 0 -0.5 19 19
CREB1 -0.048 0.16 -9999 0 -0.46 43 43
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.015 0.12 -9999 0 -0.44 18 18
RPS6KA4 -0.028 0.13 -9999 0 -0.4 43 43
PLA2G4A -0.049 0.2 -9999 0 -0.61 44 44
GDI1 -0.028 0.13 -9999 0 -0.4 43 43
TP53 -0.037 0.16 -9999 0 -0.5 43 43
RPS6KA5 -0.076 0.2 -9999 0 -0.46 86 86
ESR1 -0.065 0.21 -9999 0 -0.55 56 56
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.029 0.14 -9999 0 -0.4 44 44
MEF2A -0.029 0.14 -9999 0 -0.4 44 44
EIF4EBP1 -0.048 0.16 -9999 0 -0.45 44 44
KRT19 -0.1 0.21 -9999 0 -0.55 55 55
ELK4 -0.028 0.13 -9999 0 -0.4 43 43
ATF6 -0.028 0.13 -9999 0 -0.4 43 43
ATF1 -0.049 0.16 -9999 0 -0.47 44 44
p38alpha-beta/MAPKAPK2 -0.025 0.14 -9999 0 -0.5 19 19
p38alpha-beta/MAPKAPK3 -0.025 0.14 -9999 0 -0.5 19 19
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.002 0.047 -9999 0 -1 1 1
forebrain development -0.32 0.28 -9999 0 -0.56 254 254
GNAO1 -0.02 0.15 -9999 0 -0.72 20 20
SMO/beta Arrestin2 0.011 0.032 -9999 0 -0.63 1 1
SMO 0.006 0.038 -9999 0 -0.82 1 1
ARRB2 0.008 0.007 -9999 0 -10000 0 0
GLI3/SPOP 0.044 0.056 -9999 0 -10000 0 0
mol:GTP -0.002 0.003 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.01 0.006 -9999 0 -10000 0 0
SIN3/HDAC complex 0.009 0.029 -9999 0 -0.5 1 1
GNAI1 0.008 0.039 -9999 0 -0.83 1 1
XPO1 0.008 0.008 -9999 0 -10000 0 0
GLI1/Su(fu) -0.24 0.19 -9999 0 -0.51 134 134
SAP30 0.012 0.038 -9999 0 -0.82 1 1
mol:GDP 0.006 0.038 -9999 0 -0.82 1 1
MIM/GLI2A -0.007 0.043 -9999 0 -0.31 1 1
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.01 0.006 -9999 0 -10000 0 0
GLI2 0.033 0.062 -9999 0 -10000 0 0
GLI3 0.039 0.059 -9999 0 -0.3 13 13
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0 -9999 0 -10000 0 0
GNG2 0.012 0.038 -9999 0 -0.82 1 1
Gi family/GTP 0.008 0.071 -9999 0 -0.33 18 18
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.029 0.05 -9999 0 -10000 0 0
GLI2/Su(fu) 0.023 0.059 -9999 0 -10000 0 0
FOXA2 -0.66 0.66 -9999 0 -1.3 235 235
neural tube patterning -0.32 0.28 -9999 0 -0.56 254 254
SPOP 0.013 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.018 0.022 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 -0.007 0.043 -9999 0 -0.31 1 1
embryonic limb morphogenesis -0.32 0.28 -9999 0 -0.56 254 254
SUFU 0.016 0.021 -9999 0 -10000 0 0
LGALS3 -0.1 0.16 -9999 0 -0.31 173 173
catabolic process 0.061 0.069 -9999 0 -0.39 2 2
GLI3A/CBP -0.2 0.2 -9999 0 -0.38 255 255
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.33 0.29 -9999 0 -0.57 254 254
RAB23 0.006 0.076 -9999 0 -0.82 4 4
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.013 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.035 0.079 -9999 0 -0.4 1 1
GNAZ 0.01 0.006 -9999 0 -10000 0 0
RBBP4 0.009 0.065 -9999 0 -0.82 3 3
CSNK1G1 0.013 0 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.038 0.058 -9999 0 -10000 0 0
STK36 0.008 0.008 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.013 0.063 -9999 0 -0.42 2 2
PTCH1 -0.28 0.27 -9999 0 -0.62 134 134
MIM/GLI1 -0.45 0.39 -9999 0 -0.76 247 247
CREBBP -0.2 0.2 -9999 0 -0.38 255 255
Su(fu)/SIN3/HDAC complex 0.056 0.027 -9999 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.043 0.12 -9999 0 -0.46 28 28
alphaM/beta2 Integrin/GPIbA -0.054 0.14 -9999 0 -0.51 35 35
alphaM/beta2 Integrin/proMMP-9 -0.092 0.19 -9999 0 -0.56 61 61
PLAUR -0.088 0.15 -9999 0 -0.31 151 151
HMGB1 0.002 0.024 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.034 0.099 -9999 0 -0.43 20 20
AGER -0.059 0.22 -9999 0 -0.8 37 37
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.007 0.079 -9999 0 -0.31 30 30
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.12 0.19 -9999 0 -0.62 44 44
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.082 0.24 -9999 0 -0.57 79 79
CYR61 -0.24 0.38 -9999 0 -0.82 147 147
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.072 0.09 -9999 0 -0.46 8 8
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.003 0.1 -9999 0 -0.59 13 13
MYH2 -0.1 0.12 -9999 0 -0.4 38 38
MST1R 0.001 0.096 -9999 0 -0.65 9 9
leukocyte activation during inflammatory response -0.04 0.093 -9999 0 -0.46 10 10
APOB -0.011 0.079 -9999 0 -0.31 31 31
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.001 0.1 -9999 0 -0.67 10 10
JAM3 0.013 0 -9999 0 -10000 0 0
GP1BA -0.019 0.15 -9999 0 -0.63 24 24
alphaM/beta2 Integrin/CTGF -0.11 0.22 -9999 0 -0.57 88 88
alphaM/beta2 Integrin -0.095 0.11 -9999 0 -0.35 46 46
JAM3 homodimer 0.013 0 -9999 0 -10000 0 0
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 -0.083 0.15 -9999 0 -0.31 143 143
phagocytosis triggered by activation of immune response cell surface activating receptor -0.094 0.11 -9999 0 -0.35 46 46
cell adhesion -0.053 0.14 -9999 0 -0.51 35 35
NFKB1 -0.13 0.3 -9999 0 -0.74 59 59
THY1 0.011 0.03 -9999 0 -0.31 4 4
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.014 0.051 -9999 0 -0.34 3 3
alphaM/beta2 Integrin/LRP/tPA -0.034 0.1 -9999 0 -0.58 10 10
IL6 -0.23 0.46 -9999 0 -1.1 101 101
ITGB2 -0.018 0.086 -9999 0 -0.34 28 28
elevation of cytosolic calcium ion concentration -0.14 0.16 -9999 0 -0.5 42 42
alphaM/beta2 Integrin/JAM2/JAM3 -0.031 0.1 -9999 0 -0.6 9 9
JAM2 0.006 0.077 -9999 0 -0.72 5 5
alphaM/beta2 Integrin/ICAM1 -0.068 0.12 -9999 0 -0.5 22 22
alphaM/beta2 Integrin/uPA/Plg -0.098 0.12 -9999 0 -0.51 20 20
RhoA/GTP -0.11 0.12 -9999 0 -0.42 40 40
positive regulation of phagocytosis -0.07 0.12 -9999 0 -0.49 17 17
Ron/MSP -0.011 0.077 -9999 0 -0.63 7 7
alphaM/beta2 Integrin/uPAR/uPA -0.14 0.16 -9999 0 -0.5 42 42
alphaM/beta2 Integrin/uPAR -0.084 0.13 -9999 0 -0.46 33 33
PLAU -0.14 0.16 -9999 0 -0.31 225 225
PLAT 0.001 0.086 -9999 0 -0.48 12 12
actin filament polymerization -0.1 0.11 -9999 0 -0.38 38 38
MST1 0.011 0.041 -9999 0 -0.57 2 2
alphaM/beta2 Integrin/lipoprotein(a) -0.04 0.095 -9999 0 -0.51 8 8
TNF -0.18 0.4 -9999 0 -0.98 79 79
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.11 0.13 -9999 0 -0.44 38 38
fibrinolysis -0.097 0.12 -9999 0 -0.51 20 20
HCK -0.008 0.08 -9999 0 -0.31 31 31
dendritic cell antigen processing and presentation -0.094 0.11 -9999 0 -0.35 46 46
VTN -0.069 0.24 -9999 0 -0.76 52 52
alphaM/beta2 Integrin/CYR61 -0.2 0.28 -9999 0 -0.59 154 154
LPA -0.003 0.046 -9999 0 -0.31 10 10
LRP1 0.012 0.038 -9999 0 -0.82 1 1
cell migration -0.088 0.2 -9999 0 -0.57 57 57
FN1 -0.22 0.15 -9999 0 -0.31 350 350
alphaM/beta2 Integrin/Thy1 -0.035 0.1 -9999 0 -0.42 21 21
MPO -0.001 0.096 -9999 0 -0.65 9 9
KNG1 -0.014 0.077 -9999 0 -0.31 30 30
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.095 0.12 -9999 0 -0.39 37 37
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.003 0.035 -9999 0 -0.31 6 6
CTGF -0.11 0.3 -9999 0 -0.82 71 71
alphaM/beta2 Integrin/Hck -0.044 0.12 -9999 0 -0.47 30 30
ITGAM -0.023 0.11 -9999 0 -0.39 30 30
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.045 0.13 -9999 0 -0.52 26 26
HP -0.082 0.16 -9999 0 -0.34 131 131
leukocyte adhesion -0.091 0.16 -9999 0 -0.61 26 26
SELP -0.003 0.11 -9999 0 -0.59 13 13
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.057 0.21 -10000 0 -0.71 14 14
CRP -0.063 0.22 -10000 0 -0.7 19 19
cell cycle arrest -0.08 0.24 -10000 0 -0.73 32 32
TIMP1 -0.16 0.22 -10000 0 -0.59 44 44
IL6ST -0.11 0.29 -10000 0 -0.82 69 69
Rac1/GDP -0.088 0.25 -10000 0 -0.62 60 60
AP1 -0.19 0.32 -10000 0 -0.7 122 122
GAB2 0.014 0.001 -10000 0 -10000 0 0
TNFSF11 -0.099 0.23 -10000 0 -0.68 21 21
HSP90B1 0.022 0.043 -10000 0 -10000 0 0
GAB1 0.014 0 -10000 0 -10000 0 0
MAPK14 -0.099 0.3 -10000 0 -0.81 55 55
AKT1 0.053 0.057 -10000 0 -1.1 1 1
FOXO1 0.059 0.053 -10000 0 -0.98 1 1
MAP2K6 -0.1 0.29 -10000 0 -0.72 63 63
mol:GTP 0 0.001 -10000 0 -10000 0 0
MAP2K4 -0.076 0.24 -10000 0 -0.65 45 45
MITF -0.09 0.26 -10000 0 -0.62 62 62
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.013 0 -10000 0 -10000 0 0
A2M 0.025 0.006 -10000 0 -10000 0 0
CEBPB 0.022 0.002 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.023 0.086 -10000 0 -0.49 1 1
STAT3 -0.093 0.25 -10000 0 -0.79 32 32
STAT1 -0.011 0.023 -10000 0 -10000 0 0
CEBPD -0.057 0.21 -10000 0 -0.69 17 17
PIK3CA 0.01 0.066 -10000 0 -0.82 3 3
PI3K 0.019 0.051 -10000 0 -0.63 3 3
JUN -0.18 0.35 -10000 0 -0.82 109 109
PIAS3/MITF -0.078 0.25 -10000 0 -0.62 54 54
MAPK11 -0.099 0.3 -10000 0 -0.81 55 55
STAT3 (dimer)/FOXO1 -0.008 0.2 0.43 1 -0.58 22 23
GRB2/SOS1/GAB family -0.11 0.2 -10000 0 -0.69 32 32
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.12 0.26 -10000 0 -0.56 84 84
GRB2 0.014 0 -10000 0 -10000 0 0
JAK2 0.012 0.038 -10000 0 -0.82 1 1
LBP -0.061 0.2 -10000 0 -0.59 18 18
PIK3R1 0.015 0 -10000 0 -10000 0 0
JAK1 0.014 0.005 -10000 0 -10000 0 0
MYC -0.072 0.27 -10000 0 -0.86 31 31
FGG -0.066 0.22 -10000 0 -0.68 22 22
macrophage differentiation -0.08 0.24 -10000 0 -0.73 32 32
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.18 0.29 -10000 0 -0.57 153 153
JUNB -0.063 0.23 -10000 0 -0.75 25 25
FOS -0.21 0.37 -10000 0 -0.82 129 129
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.1 0.28 -10000 0 -0.58 84 84
STAT1/PIAS1 -0.083 0.24 -10000 0 -0.55 67 67
GRB2/SOS1/GAB family/SHP2/PI3K 0.038 0.061 -10000 0 -0.59 3 3
STAT3 (dimer) -0.089 0.24 -10000 0 -0.76 32 32
PRKCD -0.064 0.23 -10000 0 -0.64 39 39
IL6R -0.015 0.15 -10000 0 -0.82 17 17
SOCS3 -0.12 0.37 -10000 0 -1 53 53
gp130 (dimer)/JAK1/JAK1/LMO4 -0.058 0.2 -10000 0 -0.55 69 69
Rac1/GTP -0.11 0.24 -10000 0 -0.62 60 60
HCK -0.008 0.08 -10000 0 -0.31 31 31
MAPKKK cascade 0.01 0.077 -10000 0 -0.98 1 1
bone resorption -0.095 0.22 -10000 0 -0.64 23 23
IRF1 -0.057 0.21 -10000 0 -0.64 28 28
mol:GDP -0.1 0.26 -10000 0 -0.62 67 67
SOS1 0.013 0.001 -10000 0 -10000 0 0
VAV1 -0.1 0.27 -10000 0 -0.64 67 67
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.11 0.3 -10000 0 -0.8 57 57
PTPN11 -0.011 0.059 -10000 0 -1.2 1 1
IL6/IL6RA -0.15 0.29 -10000 0 -0.66 108 108
gp130 (dimer)/TYK2/TYK2/LMO4 -0.065 0.2 -10000 0 -0.55 69 69
gp130 (dimer)/JAK2/JAK2/LMO4 -0.066 0.2 -10000 0 -0.55 69 69
IL6 -0.17 0.33 -10000 0 -0.72 123 123
PIAS3 0.013 0 -10000 0 -10000 0 0
PTPRE -0.083 0.15 -10000 0 -0.32 128 128
PIAS1 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.1 0.27 -10000 0 -0.46 137 137
LMO4 0.012 0.01 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.11 0.23 0.38 1 -0.78 32 33
MCL1 0.059 0.048 -10000 0 -0.88 1 1
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.081 0.063 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.13 0.18 -9999 0 -0.65 40 40
positive regulation of JNK cascade -0.17 0.2 -9999 0 -0.61 69 69
Syndecan-4/ADAM12 -0.17 0.18 -9999 0 -0.65 41 41
CCL5 -0.045 0.21 -9999 0 -0.72 39 39
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG 0 0.035 -9999 0 -0.31 4 4
ADAM12 -0.068 0.14 -9999 0 -0.31 121 121
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.065 0.045 -9999 0 -0.23 4 4
Syndecan-4/Laminin alpha1 -0.17 0.21 -9999 0 -0.68 49 49
Syndecan-4/CXCL12/CXCR4 -0.17 0.23 -9999 0 -0.65 69 69
Syndecan-4/Laminin alpha3 -0.15 0.19 -9999 0 -0.66 45 45
MDK -0.087 0.15 -9999 0 -0.31 149 149
Syndecan-4/FZD7 -0.14 0.18 -9999 0 -0.64 42 42
Syndecan-4/Midkine -0.18 0.19 -9999 0 -0.65 41 41
FZD7 0.006 0.076 -9999 0 -0.82 4 4
Syndecan-4/FGFR1/FGF -0.13 0.16 -9999 0 -0.6 41 41
THBS1 -0.011 0.086 -9999 0 -0.31 36 36
integrin-mediated signaling pathway -0.18 0.19 -9999 0 -0.66 40 40
positive regulation of MAPKKK cascade -0.17 0.2 -9999 0 -0.61 69 69
Syndecan-4/TACI -0.24 0.26 -9999 0 -0.64 120 120
CXCR4 0.012 0.021 -9999 0 -0.31 2 2
cell adhesion -0.073 0.094 -9999 0 -0.44 24 24
Syndecan-4/Dynamin -0.13 0.18 -9999 0 -0.65 40 40
Syndecan-4/TSP1 -0.14 0.18 -9999 0 -0.65 40 40
Syndecan-4/GIPC -0.13 0.18 -9999 0 -0.65 40 40
Syndecan-4/RANTES -0.16 0.22 -9999 0 -0.74 48 48
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.049 0.22 -9999 0 -0.81 37 37
LAMA3 -0.025 0.16 -9999 0 -0.59 31 31
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.013 0.18 -9999 0 -0.75 24 24
Syndecan-4/alpha-Actinin -0.13 0.18 -9999 0 -0.65 40 40
TFPI -0.035 0.2 -9999 0 -0.82 28 28
F2 -0.006 0.05 -9999 0 -0.31 12 12
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.17 0.21 -9999 0 -0.67 54 54
ACTN1 0.013 0.015 -9999 0 -0.31 1 1
TNC -0.12 0.17 -9999 0 -0.82 4 4
Syndecan-4/CXCL12 -0.18 0.24 -9999 0 -0.68 70 70
FGF6 0 0.001 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.08 0.26 -9999 0 -0.82 54 54
TNFRSF13B -0.19 0.35 -9999 0 -0.79 121 121
FGF2 0.013 0 -9999 0 -10000 0 0
FGFR1 0.012 0.038 -9999 0 -0.82 1 1
Syndecan-4/PI-4-5-P2 -0.14 0.18 -9999 0 -0.66 40 40
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.32 331 331
cell migration -0.021 0.017 -9999 0 -10000 0 0
PRKCD 0.008 0.015 -9999 0 -10000 0 0
vasculogenesis -0.14 0.17 -9999 0 -0.62 40 40
SDC4 -0.15 0.19 -9999 0 -0.7 40 40
Syndecan-4/Tenascin C -0.19 0.2 -9999 0 -0.7 40 40
Syndecan-4/PI-4-5-P2/PKC alpha -0.051 0.035 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.13 0.18 -9999 0 -0.65 40 40
MMP9 -0.084 0.24 -9999 0 -0.57 79 79
Rac1/GTP -0.075 0.096 -9999 0 -0.46 24 24
cytoskeleton organization -0.13 0.17 -9999 0 -0.62 40 40
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.16 0.21 -9999 0 -0.65 58 58
Thromboxane A2 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
TGM2 -0.034 0.11 -10000 0 -0.32 67 67
GNB1/GNG2 -0.045 0.068 -10000 0 -0.2 48 48
AKT1 -0.014 0.1 -10000 0 -0.21 47 47
EGF -0.11 0.29 -10000 0 -0.78 74 74
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.03 0.078 -10000 0 -0.65 2 2
mol:Ca2+ -0.045 0.15 -10000 0 -0.31 76 76
LYN 0.032 0.077 -10000 0 -0.65 2 2
RhoA/GTP -0.031 0.045 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.045 0.16 -10000 0 -0.35 73 73
GNG2 0.012 0.038 -10000 0 -0.82 1 1
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.025 0.12 -10000 0 -0.54 11 11
G beta5/gamma2 -0.061 0.092 -10000 0 -0.27 48 48
PRKCH -0.053 0.16 -10000 0 -0.36 74 74
DNM1 -0.017 0.15 -10000 0 -0.8 18 18
TXA2/TP beta/beta Arrestin3 -0.013 0.057 -10000 0 -0.3 17 17
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.025 0.17 -10000 0 -0.82 22 22
G12 family/GTP -0.078 0.11 -10000 0 -0.31 73 73
ADRBK1 0.013 0 -10000 0 -10000 0 0
ADRBK2 0.013 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.1 0.36 16 -10000 0 16
mol:NADP 0.013 0 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.21 0.37 -10000 0 -0.82 131 131
mol:IP3 -0.06 0.18 -10000 0 -0.39 76 76
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.089 0.23 -10000 0 -0.53 76 76
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.098 0.2 -10000 0 -0.4 143 143
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.023 0.082 -10000 0 -0.65 2 2
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.003 0.092 -10000 0 -0.82 6 6
PRKCB1 -0.061 0.17 -10000 0 -0.39 76 76
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline 0.013 0 -10000 0 -10000 0 0
TXA2/TXA2-R family -0.086 0.23 -10000 0 -0.54 77 77
LCK 0.022 0.097 -10000 0 -0.55 7 7
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.02 0.091 -10000 0 -0.97 2 2
TXA2-R family/G12 family/GDP/G beta/gamma 0.028 0.031 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.019 0.09 -10000 0 -0.96 2 2
MAPK14 -0.02 0.11 -10000 0 -0.23 45 45
TGM2/GTP -0.073 0.2 -10000 0 -0.43 76 76
MAPK11 -0.02 0.11 -10000 0 -0.23 47 47
ARHGEF1 -0.016 0.089 -10000 0 -0.19 17 17
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.058 0.18 -10000 0 -0.39 77 77
RAB11/GDP 0.013 0.001 -10000 0 -10000 0 0
ICAM1 -0.052 0.15 -10000 0 -0.3 82 82
cAMP biosynthetic process -0.06 0.17 -10000 0 -0.36 76 76
Gq family/GTP/EBP50 -0.043 0.12 -10000 0 -0.25 119 119
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.031 0.077 -10000 0 -0.65 2 2
GNB5 0.013 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.018 0.1 -10000 0 -0.31 16 16
VCAM1 -0.039 0.14 -10000 0 -0.3 76 76
TP beta/Gq family/GDP/G beta5/gamma2 -0.025 0.12 -10000 0 -0.54 11 11
platelet activation -0.027 0.15 -10000 0 -0.3 72 72
PGI2/IP -0.008 0.071 -10000 0 -0.64 6 6
PRKACA -0.002 0.11 -10000 0 -0.43 26 26
Gq family/GDP/G beta5/gamma2 -0.027 0.12 -10000 0 -0.5 11 11
TXA2/TP beta/beta Arrestin2 -0.025 0.12 -10000 0 -0.66 17 17
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.006 0.11 -10000 0 -0.41 26 26
mol:DAG -0.069 0.19 -10000 0 -0.43 76 76
EGFR 0.006 0.076 -10000 0 -0.82 4 4
TXA2/TP alpha -0.083 0.22 -10000 0 -0.49 76 76
Gq family/GTP -0.075 0.13 -10000 0 -0.3 119 119
YES1 0.032 0.077 -10000 0 -0.65 2 2
GNAI2/GTP -0.017 0.078 -10000 0 -0.8 2 2
PGD2/DP -0.029 0.13 -10000 0 -0.64 22 22
SLC9A3R1 0.012 0.021 -10000 0 -0.31 2 2
FYN 0.032 0.077 -10000 0 -0.65 2 2
mol:NO 0.013 0 -10000 0 -10000 0 0
GNA15 -0.013 0.093 -10000 0 -0.33 37 37
PGK/cGMP -0.15 0.25 -10000 0 -0.56 131 131
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.032 0.1 -10000 0 -0.66 6 6
NOS3 0.013 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.065 0.18 -10000 0 -0.4 79 79
PRKCB -0.063 0.17 -10000 0 -0.38 77 77
PRKCE -0.055 0.17 -10000 0 -0.38 74 74
PRKCD -0.056 0.17 -10000 0 -0.39 74 74
PRKCG -0.06 0.18 -10000 0 -0.4 74 74
muscle contraction -0.075 0.22 -10000 0 -0.49 77 77
PRKCZ -0.045 0.16 -10000 0 -0.35 73 73
ARR3 0.004 0.006 -10000 0 -10000 0 0
TXA2/TP beta -0.02 0.092 -10000 0 -0.98 2 2
PRKCQ -0.054 0.17 -10000 0 -0.36 77 77
MAPKKK cascade -0.076 0.21 -10000 0 -0.47 77 77
SELE -0.059 0.18 -10000 0 -0.43 74 74
TP beta/GNAI2/GDP/G beta/gamma -0.019 0.095 -10000 0 -1.1 2 2
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.18 0.35 -10000 0 -0.82 112 112
chemotaxis -0.099 0.26 -10000 0 -0.62 76 76
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 -0.002 0.11 -10000 0 -0.82 9 9
Rac1/GTP 0 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS 0.012 0.021 -9999 0 -0.31 2 2
EGFR 0.006 0.076 -9999 0 -0.82 4 4
EGF/EGFR -0.076 0.17 -9999 0 -0.46 78 78
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.07 0.16 -9999 0 -0.46 72 72
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.01 0.046 -9999 0 -0.44 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 74 74
EGF/EGFR dimer/SHC -0.083 0.19 -9999 0 -0.55 72 72
mol:GDP -0.069 0.16 -9999 0 -0.46 72 72
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.003 0.087 -9999 0 -0.68 7 7
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.064 0.15 -9999 0 -0.42 72 72
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.065 0.15 -9999 0 -0.43 72 72
FRAP1 -0.034 0.17 -9999 0 -0.44 72 72
EGF/EGFR dimer -0.096 0.22 -9999 0 -0.63 72 72
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.01 0.072 -9999 0 -0.63 6 6
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.034 0.15 -9999 0 -0.48 38 38
NF kappa B1 p50/RelA/I kappa B alpha -0.056 0.12 -9999 0 -0.55 9 9
alphaV/beta3 Integrin/Osteopontin/Src -0.067 0.15 -9999 0 -0.62 24 24
AP1 -0.26 0.35 -9999 0 -0.84 112 112
ILK -0.034 0.16 -9999 0 -0.5 38 38
bone resorption -0.048 0.16 -9999 0 -0.67 12 12
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.054 0.13 -9999 0 -0.46 38 38
ITGAV 0.01 0.054 -9999 0 -0.82 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.027 0.13 -9999 0 -0.63 21 21
alphaV/beta3 Integrin/Osteopontin -0.072 0.16 -9999 0 -0.57 38 38
MAP3K1 -0.035 0.16 -9999 0 -0.51 38 38
JUN -0.17 0.35 -9999 0 -0.82 109 109
MAPK3 -0.035 0.15 -9999 0 -0.47 38 38
MAPK1 -0.035 0.15 -9999 0 -0.47 38 38
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAPK8 -0.032 0.17 -9999 0 -0.52 43 43
ITGB3 -0.014 0.15 -9999 0 -0.82 16 16
NFKBIA -0.028 0.15 -9999 0 -0.46 38 38
FOS -0.21 0.37 -9999 0 -0.82 129 129
CD44 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.11 0.18 -9999 0 -0.68 6 6
NF kappa B1 p50/RelA -0.062 0.11 -9999 0 -0.55 8 8
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.023 0.13 -9999 0 -0.69 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.034 0.16 -9999 0 -0.51 38 38
VAV3 -0.029 0.16 -9999 0 -0.49 43 43
MAP3K14 -0.042 0.16 -9999 0 -0.51 38 38
ROCK2 -0.023 0.17 -9999 0 -0.82 21 21
SPP1 -0.082 0.2 -9999 0 -0.42 108 108
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.056 0.13 -9999 0 -0.44 43 43
MMP2 -0.18 0.29 -9999 0 -0.67 99 99
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 0.024 0.077 0.29 35 -10000 0 35
RFC1 0.024 0.077 0.29 35 -10000 0 35
PRKDC 0.024 0.077 0.29 35 -10000 0 35
RIPK1 0.014 0.004 -10000 0 -10000 0 0
CASP7 -0.013 0.044 0.2 3 -10000 0 3
FASLG/FAS/FADD/FAF1 -0.028 0.1 0.26 4 -0.37 32 36
MAP2K4 -0.023 0.16 -10000 0 -0.4 35 35
mol:ceramide -0.022 0.14 -10000 0 -0.48 33 33
GSN 0.024 0.077 0.29 35 -10000 0 35
FASLG/FAS/FADD/FAF1/Caspase 8 -0.019 0.13 -10000 0 -0.47 32 32
FAS 0.011 0.006 -10000 0 -10000 0 0
BID -0.033 0.08 0.32 3 -10000 0 3
MAP3K1 0.004 0.097 -10000 0 -0.28 15 15
MAP3K7 0.01 0.006 -10000 0 -10000 0 0
RB1 0.023 0.078 0.29 34 -0.32 1 35
CFLAR 0.014 0.004 -10000 0 -10000 0 0
HGF/MET -0.15 0.22 -10000 0 -0.62 76 76
ARHGDIB 0.021 0.081 0.29 35 -10000 0 35
FADD 0.011 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.024 0.077 -10000 0 -0.29 35 35
NFKB1 -0.053 0.093 -10000 0 -0.32 16 16
MAPK8 -0.058 0.22 -10000 0 -0.45 102 102
DFFA 0.024 0.077 0.29 35 -10000 0 35
DNA fragmentation during apoptosis 0.024 0.077 0.29 35 -10000 0 35
FAS/FADD/MET -0.059 0.077 -10000 0 -10000 0 0
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.002 0.088 -10000 0 -0.39 20 20
FAF1 0.011 0.007 -10000 0 -10000 0 0
PARP1 0.024 0.077 0.29 35 -10000 0 35
DFFB 0.024 0.077 0.29 35 -10000 0 35
CHUK -0.045 0.082 -10000 0 -0.73 1 1
FASLG -0.058 0.22 -10000 0 -0.66 50 50
FAS/FADD 0 0.001 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.82 74 74
LMNA 0.022 0.07 0.26 35 -10000 0 35
CASP6 0.024 0.077 0.29 35 -10000 0 35
CASP10 0.011 0.006 -10000 0 -10000 0 0
CASP3 0.029 0.094 0.35 38 -10000 0 38
PTPN13 0.005 0.084 -10000 0 -0.82 5 5
CASP8 0.008 0.044 0.46 3 -10000 0 3
IL6 -0.26 0.56 -10000 0 -1.4 98 98
MET -0.11 0.16 -10000 0 -0.31 180 180
ICAD/CAD 0.023 0.072 0.27 35 -10000 0 35
FASLG/FAS/FADD/FAF1/Caspase 10 -0.022 0.15 -10000 0 -0.49 33 33
activation of caspase activity by cytochrome c -0.033 0.08 0.32 3 -10000 0 3
PAK2 0.024 0.077 0.29 35 -10000 0 35
BCL2 -0.047 0.22 -10000 0 -0.82 35 35
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.075 0.098 -10000 0 -10000 0 0
CRKL -0.032 0.11 -10000 0 -0.33 26 26
mol:PIP3 -0.019 0.033 0.69 1 -10000 0 1
AKT1 0.001 0.04 0.45 1 -0.53 2 3
PTK2B 0.013 0 -10000 0 -10000 0 0
RAPGEF1 -0.023 0.11 -10000 0 -10000 0 0
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
HGF/MET/SHIP2 -0.14 0.21 -10000 0 -0.6 74 74
MAP3K5 -0.019 0.11 -10000 0 -0.48 5 5
HGF/MET/CIN85/CBL/ENDOPHILINS -0.12 0.19 -10000 0 -0.55 74 74
AP1 -0.28 0.42 -10000 0 -0.87 152 152
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.26 0.4 -10000 0 -0.85 152 152
STAT3 (dimer) -0.041 0.13 -10000 0 -0.34 74 74
GAB1/CRKL/SHP2/PI3K -0.043 0.095 -10000 0 -0.7 2 2
INPP5D -0.003 0.071 -10000 0 -0.31 24 24
CBL/CRK -0.023 0.11 -10000 0 -10000 0 0
PTPN11 0.012 0.038 -10000 0 -0.82 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.038 -10000 0 -0.82 1 1
ELK1 -0.049 0.062 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.04 0.073 -10000 0 -0.24 27 27
PAK1 0.009 0.038 0.42 1 -0.5 2 3
HGF/MET/RANBP10 -0.14 0.21 -10000 0 -0.6 74 74
HRAS -0.06 0.16 -10000 0 -0.43 74 74
DOCK1 -0.026 0.12 -10000 0 -0.55 4 4
GAB1 -0.042 0.12 -10000 0 -0.3 74 74
CRK -0.032 0.11 -10000 0 -0.33 26 26
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.11 0.21 -10000 0 -0.6 74 74
JUN -0.17 0.35 -10000 0 -0.82 109 109
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.072 0.1 -10000 0 -0.29 74 74
PIK3R1 0.013 0 -10000 0 -10000 0 0
cell morphogenesis -0.012 0.14 -10000 0 -0.65 2 2
GRB2/SHC -0.039 0.097 -10000 0 -0.3 26 26
FOS -0.21 0.37 -10000 0 -0.82 129 129
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.049 0.062 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.14 0.21 -10000 0 -0.61 74 74
cell migration -0.055 0.085 -10000 0 -0.3 26 26
GRB2 0.013 0 -10000 0 -10000 0 0
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.075 0.098 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.052 0.14 -10000 0 -0.36 74 74
MET/MUC20 -0.079 0.1 -10000 0 -0.21 180 180
RAP1B -0.013 0.1 -10000 0 -10000 0 0
RAP1A -0.013 0.1 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.14 0.21 -10000 0 -0.6 74 74
RAF1 -0.049 0.16 -10000 0 -0.45 27 27
STAT3 -0.041 0.13 -10000 0 -0.34 74 74
cell proliferation -0.049 0.18 -10000 0 -0.45 74 74
RPS6KB1 -0.015 0.04 -10000 0 -10000 0 0
MAPK3 -0.05 0.057 -10000 0 -10000 0 0
MAPK1 -0.05 0.057 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.007 0.13 -10000 0 -0.59 13 13
SRC -0.041 0.13 -10000 0 -0.39 26 26
PI3K -0.042 0.1 -10000 0 -0.32 29 29
MET/Glomulin -0.059 0.094 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.038 0.14 -10000 0 -0.42 27 27
MET -0.11 0.16 -10000 0 -0.31 180 180
MAP4K1 -0.028 0.12 -10000 0 -0.34 30 30
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.038 0.14 -10000 0 -0.42 27 27
BAD 0.009 0.038 0.42 1 -0.5 2 3
MAP2K4 -0.01 0.1 -10000 0 -0.43 5 5
SHP2/GRB2/SOS1/GAB1 -0.058 0.091 -10000 0 -0.38 1 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.013 0 -10000 0 -10000 0 0
HGS -0.049 0.1 -10000 0 -0.26 74 74
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.11 0.3 -10000 0 -0.82 74 74
RASA1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.013 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.042 0.11 -10000 0 -0.33 26 26
PDPK1 -0.009 0.044 0.52 1 -0.58 2 3
HGF/MET/SHIP -0.15 0.21 -10000 0 -0.6 74 74
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.095 0.22 -9999 0 -0.54 44 44
MAP3K8 -0.003 0.11 -9999 0 -0.83 8 8
FOS -0.059 0.17 -9999 0 -0.5 35 35
PRKCA -0.031 0.18 -9999 0 -0.83 24 24
PTPN7 -0.044 0.17 -9999 0 -0.46 57 57
HRAS 0.011 0.021 -9999 0 -0.32 2 2
PRKCB -0.03 0.13 -9999 0 -0.36 52 52
NRAS 0.013 0.002 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.009 -9999 0 -10000 0 0
MAPK3 -0.031 0.12 -9999 0 -0.42 28 28
MAP2K1 -0.027 0.16 -9999 0 -0.59 28 28
ELK1 0.008 0.011 -9999 0 -10000 0 0
BRAF -0.046 0.14 -9999 0 -0.57 28 28
mol:GTP -0.001 0.003 -9999 0 -0.006 128 128
MAPK1 -0.031 0.12 -9999 0 -0.52 17 17
RAF1 -0.046 0.14 -9999 0 -0.57 28 28
KRAS 0.013 0.002 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.036 0.12 -10000 0 -0.51 27 27
ER alpha/Gai/GDP/Gbeta gamma 0.005 0.15 -10000 0 -0.48 36 36
AKT1 -0.016 0.21 -10000 0 -0.86 26 26
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.015 0.21 -10000 0 -0.87 26 26
mol:Ca2+ -0.099 0.23 -10000 0 -0.5 114 114
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.072 0.18 -10000 0 -0.58 52 52
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.013 0.2 0.81 26 -10000 0 26
RhoA/GTP -0.027 0.091 -10000 0 -0.41 24 24
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.037 0.13 -10000 0 -0.59 24 24
regulation of stress fiber formation -0.013 0.12 0.47 4 -10000 0 4
E2/ERA-ERB (dimer) -0.042 0.14 -10000 0 -0.57 27 27
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.035 0.11 -10000 0 -0.51 24 24
pseudopodium formation 0.013 0.12 -10000 0 -0.47 4 4
E2/ER alpha (dimer)/PELP1 -0.038 0.12 -10000 0 -0.55 24 24
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.012 0.038 -10000 0 -0.82 1 1
GNAO1 -0.017 0.15 -10000 0 -0.72 20 20
HRAS 0.012 0.021 -10000 0 -0.31 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.011 0.15 -10000 0 -0.58 26 26
E2/ER beta (dimer) -0.005 0.058 -10000 0 -0.64 4 4
mol:GDP -0.037 0.13 -10000 0 -0.56 27 27
mol:NADP 0.011 0.15 -10000 0 -0.58 26 26
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.1 0.24 -10000 0 -0.52 114 114
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.11 0.24 -10000 0 -0.54 114 114
PLCB2 -0.11 0.25 -10000 0 -0.54 113 113
IGF1 -0.18 0.35 -10000 0 -0.8 119 119
mol:L-citrulline 0.011 0.15 -10000 0 -0.58 26 26
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.027 0.14 -10000 0 -0.78 16 16
JNK cascade -0.005 0.058 -10000 0 -0.64 4 4
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 0.006 0.076 -10000 0 -0.82 4 4
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.049 0.19 -10000 0 -0.54 55 55
Gq family/GDP/Gbeta gamma -0.055 0.17 -10000 0 -0.53 22 22
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.02 0.082 -10000 0 -0.36 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.037 0.13 -10000 0 -0.59 24 24
GNAZ 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.045 0.14 -10000 0 -0.64 24 24
STRN -0.038 0.2 -10000 0 -0.82 30 30
GNAL -0.092 0.28 -10000 0 -0.82 61 61
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.015 0.052 -10000 0 -0.55 4 4
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.038 -10000 0 -0.82 1 1
HBEGF -0.005 0.16 -10000 0 -0.52 29 29
cAMP biosynthetic process -0.09 0.19 -10000 0 -0.48 84 84
SRC 0.013 0.14 -10000 0 -0.5 25 25
PI3K -0.004 0.049 -10000 0 -0.63 3 3
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.032 0.12 -10000 0 -0.5 27 27
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.18 -10000 0 -0.53 39 39
Gs family/GTP -0.092 0.19 -10000 0 -0.49 84 84
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.009 -10000 0 -10000 0 0
vasodilation 0.012 0.14 -10000 0 -0.55 26 26
mol:DAG -0.1 0.24 -10000 0 -0.52 114 114
Gs family/GDP/Gbeta gamma -0.074 0.16 -10000 0 -0.41 84 84
MSN 0.012 0.12 -10000 0 -0.52 4 4
Gq family/GTP -0.15 0.24 -10000 0 -0.57 113 113
mol:PI-3-4-5-P3 -0.013 0.2 -10000 0 -0.83 26 26
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.012 0.14 0.55 26 -10000 0 26
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.034 0.12 -10000 0 -0.52 27 27
NOS3 0.01 0.16 -10000 0 -0.62 26 26
GNA11 -0.002 0.11 -10000 0 -0.82 9 9
MAPKKK cascade -0.009 0.2 -10000 0 -0.55 52 52
E2/ER alpha (dimer)/PELP1/Src -0.04 0.14 -10000 0 -0.62 24 24
ruffle organization 0.013 0.12 -10000 0 -0.47 4 4
ROCK2 0.002 0.13 -10000 0 -0.44 21 21
GNA14 -0.18 0.35 -10000 0 -0.82 112 112
GNA15 -0.013 0.093 -10000 0 -0.33 37 37
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.027 0.19 -10000 0 -0.52 46 46
MMP2 0.014 0.15 -10000 0 -0.49 29 29
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.005 -9999 0 -10000 0 0
SMARCC1 0.013 0.014 -9999 0 -10000 0 0
REL -0.033 0.2 -9999 0 -0.82 30 30
HDAC7 -0.031 0.14 -9999 0 -0.63 15 15
JUN -0.18 0.35 -9999 0 -0.82 109 109
EP300 0.013 0.001 -9999 0 -10000 0 0
KAT2B 0.013 0.001 -9999 0 -10000 0 0
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.002 0.095 -9999 0 -0.64 10 10
FOXO1 0.012 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.044 0.15 -9999 0 -0.65 17 17
MAP2K6 -0.009 0.12 -9999 0 -0.78 11 11
BRM/BAF57 -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 0.009 0.007 -9999 0 -10000 0 0
SMARCA2 0.009 0.007 -9999 0 -10000 0 0
PDE9A 0.011 0.057 -9999 0 -10000 0 0
NCOA2 -0.069 0.24 -9999 0 -0.83 44 44
CEBPA 0.006 0.084 -9999 0 -0.82 5 5
EHMT2 0.009 0.006 -9999 0 -10000 0 0
cell proliferation -0.067 0.15 -9999 0 -0.54 15 15
NR0B1 -0.002 0.041 -9999 0 -0.31 8 8
EGR1 -0.17 0.34 -9999 0 -0.83 103 103
RXRs/9cRA -0.13 0.059 -9999 0 -0.5 4 4
AR/RACK1/Src -0.11 0.16 -9999 0 -0.66 17 17
AR/GR -0.13 0.2 -9999 0 -0.37 126 126
GNB2L1 0.007 0.007 -9999 0 -10000 0 0
PKN1 0.013 0.001 -9999 0 -10000 0 0
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity -0.006 0.005 -9999 0 -10000 0 0
MAPK8 0 0.089 -9999 0 -0.64 9 9
T-DHT/AR/TIF2/CARM1 -0.12 0.23 -9999 0 -0.69 52 52
SRC -0.003 0.11 -9999 0 -0.54 17 17
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.4 0.57 -9999 0 -1.3 139 139
APPBP2 0.013 0.004 -9999 0 -10000 0 0
TRIM24 0.009 0.007 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.053 0.14 -9999 0 -0.66 17 17
TMPRSS2 -0.06 0.32 -9999 0 -1.2 32 32
RXRG -0.28 0.12 -9999 0 -0.32 430 430
mol:9cRA -0.002 0.002 -9999 0 -10000 0 0
RXRA 0.012 0.001 -9999 0 -10000 0 0
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.007 0.007 -9999 0 -10000 0 0
NR2C2 -0.003 0.11 -9999 0 -0.82 9 9
KLK2 -0.48 0.43 -9999 0 -0.83 284 284
AR -0.15 0.22 -9999 0 -0.38 206 206
SENP1 0.012 0.002 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.022 0.014 -9999 0 -10000 0 0
SRY 0.009 0.015 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
MYST2 0.014 0.002 -9999 0 -10000 0 0
HOXB13 -0.015 0.054 -9999 0 -0.32 13 13
T-DHT/AR/RACK1/Src -0.076 0.15 -9999 0 -0.66 17 17
positive regulation of transcription 0.013 0.015 -9999 0 -0.31 1 1
DNAJA1 0.013 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.005 -9999 0 -10000 0 0
NCOA1 0.013 0.009 -9999 0 -10000 0 0
SPDEF -0.027 0.1 -9999 0 -0.32 53 53
T-DHT/AR/TIF2 -0.053 0.16 -9999 0 -0.45 46 46
T-DHT/AR/Hsp90 -0.055 0.14 -9999 0 -0.66 17 17
GSK3B 0.01 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.005 0.12 -9999 0 -0.57 17 17
SIRT1 0.011 0.038 -9999 0 -0.82 1 1
ZMIZ2 0.023 0.015 -9999 0 -10000 0 0
POU2F1 0.031 0.02 -9999 0 -0.3 1 1
T-DHT/AR/DAX-1 -0.074 0.14 -9999 0 -0.67 17 17
CREBBP 0.013 0.001 -9999 0 -10000 0 0
SMARCE1 0.009 0.007 -9999 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.12 0.1 -9999 0 -0.65 7 7
EPHB2 0.008 0.066 -9999 0 -0.82 3 3
Syndecan-2/TACI -0.13 0.25 -9999 0 -0.56 118 118
LAMA1 -0.049 0.22 -9999 0 -0.81 37 37
Syndecan-2/alpha2 ITGB1 -0.072 0.11 -9999 0 -0.47 24 24
HRAS 0.012 0.021 -9999 0 -0.31 2 2
Syndecan-2/CASK -0.008 0.066 -9999 0 -0.55 7 7
ITGA5 0.013 0 -9999 0 -10000 0 0
BAX 0.025 0.097 -9999 0 -0.75 1 1
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.007 0.059 -9999 0 -0.5 7 7
LAMA3 -0.025 0.16 -9999 0 -0.59 31 31
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.008 0.066 -9999 0 -0.82 3 3
Syndecan-2/MMP2 0.008 0.1 -9999 0 -0.58 13 13
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.079 0.099 -9999 0 -10000 0 0
dendrite morphogenesis 0.014 0.081 -9999 0 -0.54 10 10
Syndecan-2/GM-CSF -0.11 0.099 -9999 0 -0.57 7 7
determination of left/right symmetry 0.012 0.078 -9999 0 -0.63 7 7
Syndecan-2/PKC delta 0.018 0.068 -9999 0 -0.54 7 7
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.087 0.092 -9999 0 -0.51 7 7
MAPK1 -0.087 0.092 -9999 0 -0.51 7 7
Syndecan-2/RACK1 -0.007 0.056 -9999 0 -0.47 7 7
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.012 0.078 -9999 0 -0.63 7 7
ITGA2 -0.12 0.16 -9999 0 -0.31 191 191
MAPK8 0.018 0.1 -9999 0 -0.55 16 16
Syndecan-2/alpha2/beta1 Integrin -0.087 0.14 -9999 0 -0.51 40 40
Syndecan-2/Kininogen -0.007 0.079 -9999 0 -0.55 7 7
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.031 0.058 -9999 0 -0.44 7 7
Syndecan-2/CASK/Protein 4.1 -0.007 0.06 -9999 0 -0.5 7 7
extracellular matrix organization 0.015 0.071 -9999 0 -0.54 7 7
actin cytoskeleton reorganization -0.12 0.1 -9999 0 -0.65 7 7
Syndecan-2/Caveolin-2/Ras -0.011 0.077 -9999 0 -0.55 9 9
Syndecan-2/Laminin alpha3 -0.008 0.13 -9999 0 -0.55 24 24
Syndecan-2/RasGAP -0.007 0.053 -9999 0 -0.44 7 7
alpha5/beta1 Integrin 0 0 -9999 0 -10000 0 0
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.014 0.081 -9999 0 -0.55 10 10
GO:0007205 0.004 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.057 -9999 0 -0.42 7 7
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.19 0.35 -9999 0 -0.79 121 121
RASA1 0.013 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin -0.079 0.099 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.018 0.068 -9999 0 -0.54 7 7
TGFB1 0.008 0.042 -9999 0 -0.31 8 8
CASP3 0.027 0.063 -9999 0 -0.49 7 7
FN1 -0.22 0.15 -9999 0 -0.31 350 350
Syndecan-2/IL8 -0.037 0.12 -9999 0 -0.55 17 17
SDC2 0.012 0.078 -9999 0 -0.63 7 7
KNG1 -0.014 0.077 -9999 0 -0.31 30 30
Syndecan-2/Neurofibromin 0.018 0.068 -9999 0 -0.54 7 7
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.21 0.15 -9999 0 -0.31 329 329
Syndecan-2/TGFB1 0.015 0.071 -9999 0 -0.54 7 7
Syndecan-2/Syntenin/PI-4-5-P2 -0.007 0.06 -9999 0 -0.5 7 7
Syndecan-2/Ezrin -0.007 0.059 -9999 0 -0.49 7 7
PRKACA 0.027 0.063 -9999 0 -0.49 7 7
angiogenesis -0.037 0.12 -9999 0 -0.54 17 17
MMP2 -0.001 0.1 -9999 0 -0.67 10 10
IL8 -0.081 0.18 -9999 0 -0.36 124 124
calcineurin-NFAT signaling pathway -0.12 0.25 -9999 0 -0.56 118 118
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.005 0.12 -9999 0 -0.78 11 11
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.15 0.15 -9999 0 -0.28 281 281
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
MAP3K12 0.013 0 -9999 0 -10000 0 0
FGR 0.011 0.03 -9999 0 -0.31 4 4
p38 alpha/TAB1 -0.047 0.068 -9999 0 -0.3 6 6
PRKG1 -0.21 0.37 -9999 0 -0.82 131 131
DUSP8 0.002 0.083 -9999 0 -0.82 4 4
PGK/cGMP/p38 alpha -0.16 0.2 -9999 0 -0.47 134 134
apoptosis -0.046 0.066 -9999 0 -0.29 6 6
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.013 0 -9999 0 -10000 0 0
DUSP1 -0.12 0.31 -9999 0 -0.82 78 78
PAK1 0.013 0 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
RAC1/OSM/MEKK3/MKK3 0 0.006 -9999 0 -10000 0 0
TRAF6 0.01 0.054 -9999 0 -0.82 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.013 0.015 -9999 0 -0.31 1 1
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 -0.06 0.13 -9999 0 -0.37 15 15
BLK -0.25 0.38 -9999 0 -0.76 164 164
HCK -0.008 0.08 -9999 0 -0.31 31 31
MAP2K3 0.013 0 -9999 0 -10000 0 0
DUSP16 0.013 0 -9999 0 -10000 0 0
DUSP10 0.01 0.043 -9999 0 -0.48 3 3
TRAF6/MEKK3 -0.002 0.033 -9999 0 -0.51 2 2
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.027 0.092 -9999 0 -0.34 5 5
positive regulation of innate immune response -0.059 0.14 -9999 0 -0.41 12 12
LCK -0.01 0.11 -9999 0 -0.44 25 25
p38alpha-beta/MKP7 -0.049 0.13 -9999 0 -0.47 5 5
p38alpha-beta/MKP5 -0.05 0.13 -9999 0 -0.48 7 7
PGK/cGMP -0.17 0.28 -9999 0 -0.64 131 131
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.11 0.2 -9999 0 -0.49 74 74
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.47 0.41 -9999 0 -0.82 281 281
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.021 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.042 0.1 -9999 0 -0.38 21 21
NFATC4 -0.001 0.11 -9999 0 -0.34 17 17
ERBB2IP 0.014 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.013 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.047 0.13 -9999 0 -0.41 55 55
JUN 0.002 0.096 -9999 0 -0.27 12 12
HRAS 0.011 0.021 -9999 0 -0.32 2 2
DOCK7 -0.016 0.14 -9999 0 -0.38 58 58
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.056 0.16 -9999 0 -0.49 55 55
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.023 0.064 -9999 0 -0.32 3 3
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.026 0.15 -9999 0 -0.44 55 55
RAF1 -0.004 0.13 -9999 0 -0.4 21 21
ErbB2/ErbB3/neuregulin 2 -0.069 0.18 -9999 0 -0.52 64 64
STAT3 0 0.003 -9999 0 -10000 0 0
cell migration 0.022 0.083 -9999 0 -0.31 5 5
mol:PI-3-4-5-P3 0 0.002 -9999 0 -10000 0 0
cell proliferation -0.13 0.33 -9999 0 -0.68 114 114
FOS -0.11 0.28 -9999 0 -0.52 152 152
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.047 0.13 -9999 0 -0.41 55 55
MAPK3 -0.084 0.25 -9999 0 -0.5 111 111
MAPK1 -0.084 0.25 -9999 0 -0.5 110 110
JAK2 -0.014 0.14 -9999 0 -0.38 56 56
NF2 -0.002 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.016 0.13 -9999 0 -0.38 55 55
NRG1 -0.069 0.24 -9999 0 -0.8 48 48
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.014 0.13 -9999 0 -0.35 63 63
MAPK9 -0.023 0.062 -9999 0 -0.26 2 2
ERBB2 0 0 -9999 0 -10000 0 0
ERBB3 -0.008 0.12 -9999 0 -0.74 12 12
SHC1 0.013 0.002 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
apoptosis 0.003 0.01 -9999 0 -10000 0 0
STAT3 (dimer) 0 0.003 -9999 0 -10000 0 0
RNF41 0.027 0.008 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.033 0.088 -9999 0 -0.38 2 2
ErbB2/ErbB2/HSP90 (dimer) 0 0 -9999 0 -10000 0 0
CHRNA1 -0.057 0.2 -9999 0 -0.39 93 93
myelination 0.008 0.11 -9999 0 -0.32 25 25
PPP3CB -0.012 0.13 -9999 0 -0.36 55 55
KRAS 0.013 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP -0.025 0.11 -9999 0 -0.65 2 2
NRG2 -0.082 0.26 -9999 0 -0.8 57 57
mol:GDP -0.016 0.13 -9999 0 -0.37 55 55
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.006 0.14 -9999 0 -0.41 21 21
SRC 0.013 0.015 -9999 0 -0.31 1 1
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.015 0.14 -9999 0 -0.38 56 56
MAP2K1 -0.077 0.23 -9999 0 -0.58 33 33
heart morphogenesis -0.047 0.13 -9999 0 -0.41 55 55
RAS family/GDP -0.036 0.1 -9999 0 -0.64 2 2
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.003 0.009 -9999 0 -10000 0 0
CHRNE 0.01 0.034 -9999 0 -0.13 17 17
HSP90AA1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.047 0.13 -9999 0 -0.41 55 55
CDC42 0.013 0 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.038 0.038 -9999 0 -10000 0 0
VDR 0.013 0.015 -9999 0 -10000 0 0
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.059 0.11 -9999 0 -0.35 48 48
RXRs/LXRs/DNA/Oxysterols -0.049 0.16 -9999 0 -0.46 58 58
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA 0 0.017 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.022 0.083 -9999 0 -0.34 23 23
RXRs/NUR77 -0.26 0.25 -9999 0 -0.63 145 145
RXRs/PPAR -0.055 0.065 -9999 0 -0.4 11 11
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0 0.01 -9999 0 -10000 0 0
RARs/VDR/DNA/Vit D3 -0.013 0.078 -9999 0 -0.48 13 13
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -9999 0 -10000 0 0
RARs/RARs/DNA/9cRA -0.012 0.077 -9999 0 -0.48 13 13
RARG 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.054 0.031 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.022 0.083 -9999 0 -0.34 23 23
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0 0.01 -9999 0 -10000 0 0
RXRs/PPAR/9cRA/PGJ2/DNA -0.12 0.083 -9999 0 -0.53 5 5
NR1H4 0 0.036 -9999 0 -0.31 6 6
RXRs/LXRs/DNA -0.098 0.093 -9999 0 -0.58 4 4
NR1H2 0.016 0.012 -9999 0 -10000 0 0
NR1H3 0.015 0.014 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.11 0.068 -9999 0 -0.52 4 4
NR4A1 -0.23 0.38 -9999 0 -0.82 143 143
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.048 0.049 -9999 0 -0.33 4 4
RXRG -0.28 0.12 -9999 0 -0.32 430 430
RXR alpha/CCPG 0.021 0.01 -9999 0 -10000 0 0
RXRA 0.015 0.012 -9999 0 -10000 0 0
RXRB 0.015 0.014 -9999 0 -10000 0 0
THRB -0.006 0.12 -9999 0 -0.82 11 11
PPARG -0.003 0.11 -9999 0 -0.59 13 13
PPARD 0.013 0 -9999 0 -10000 0 0
TNF -0.14 0.42 -9999 0 -1.3 58 58
mol:Oxysterols 0.001 0.016 -9999 0 -10000 0 0
cholesterol transport -0.048 0.15 -9999 0 -0.46 58 58
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.009 0.14 -9999 0 -0.82 13 13
RXRs/NUR77/BCL2 -0.19 0.2 -9999 0 -0.45 167 167
SREBF1 -0.038 0.14 -9999 0 -0.62 3 3
RXRs/RXRs/DNA/9cRA -0.12 0.083 -9999 0 -0.53 5 5
ABCA1 -0.037 0.14 -9999 0 -0.62 3 3
RARs/THRs -0.023 0.1 -9999 0 -0.48 23 23
RXRs/FXR -0.12 0.072 -9999 0 -0.56 4 4
BCL2 -0.047 0.22 -9999 0 -0.82 35 35
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP -0.001 0.017 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.001 0.011 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.018 0.071 -9999 0 -0.56 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.003 0.026 -9999 0 -0.31 3 3
GRK1 -0.067 0.24 -9999 0 -0.81 47 47
CNG Channel -0.028 0.085 -9999 0 -0.51 9 9
mol:Na + -0.023 0.081 -9999 0 -0.48 8 8
mol:ADP -0.067 0.24 -9999 0 -0.81 47 47
RGS9-1/Gbeta5/R9AP -0.091 0.21 -9999 0 -0.56 79 79
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.023 0.084 -9999 0 -0.53 5 5
CNGB1 0 0.062 -9999 0 -0.31 18 18
RDH5 -0.2 0.16 -9999 0 -0.31 315 315
SAG 0.002 0.015 -9999 0 -0.31 1 1
mol:Ca2+ 0.016 0.088 -9999 0 -0.8 1 1
Na + (4 Units) -0.021 0.075 -9999 0 -0.77 1 1
RGS9 -0.077 0.26 -9999 0 -0.8 54 54
GNB1/GNGT1 -0.003 0.026 -9999 0 -10000 0 0
GNAT1/GDP -0.08 0.18 -9999 0 -0.49 79 79
GUCY2D -0.011 0.11 -9999 0 -0.43 26 26
GNGT1 -0.005 0.04 -9999 0 -0.31 8 8
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.002 0.074 -9999 0 -0.48 5 5
mol:11-cis-retinal -0.2 0.16 -9999 0 -0.31 315 315
mol:cGMP -0.016 0.071 -9999 0 -0.48 9 9
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.13 0.099 -9999 0 -10000 0 0
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 0.001 0.09 -9999 0 -0.57 10 10
Metarhodopsin II -0.049 0.15 -9999 0 -0.52 46 46
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.017 0.075 -9999 0 -0.51 9 9
RGS9BP -0.037 0.2 -9999 0 -0.82 29 29
Metarhodopsin II/Transducin 0.01 0.016 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.005 0.043 -9999 0 -0.52 3 3
PDE6A/B -0.012 0.048 -9999 0 -10000 0 0
mol:Pi -0.091 0.21 -9999 0 -0.56 79 79
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.003 0.024 -9999 0 -0.3 1 1
PDE6B 0.013 0 -9999 0 -10000 0 0
PDE6A -0.008 0.077 -9999 0 -0.31 29 29
PDE6G -0.017 0.12 -9999 0 -0.82 5 5
RHO 0.006 0.016 -9999 0 -0.31 1 1
PDE6 -0.092 0.18 -9999 0 -0.48 82 82
GUCA1A 0.004 0.03 -9999 0 -0.31 4 4
GC2/GCAP Family -0.005 0.043 -9999 0 -0.52 3 3
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.008 0.067 -9999 0 -0.7 4 4
LPA receptor mediated events

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
GNB1/GNG2 -0.047 0.16 -9999 0 -0.54 41 41
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.051 -9999 0 -0.6 1 1
AP1 -0.25 0.36 -9999 0 -0.68 178 178
mol:PIP3 -0.042 0.13 -9999 0 -0.64 8 8
AKT1 -0.029 0.098 -9999 0 -0.58 5 5
PTK2B -0.001 0.087 -9999 0 -0.27 42 42
RHOA 0.031 0.047 -9999 0 -0.26 1 1
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.005 0.073 -9999 0 -0.32 1 1
MAGI3 0.012 0.038 -9999 0 -0.82 1 1
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.016 0.14 -9999 0 -0.45 41 41
HRAS/GDP -0.001 0.014 -9999 0 -0.21 2 2
positive regulation of microtubule depolymerization 0.008 0.089 -9999 0 -0.36 9 9
NF kappa B1 p50/RelA -0.047 0.12 -9999 0 -0.55 13 13
endothelial cell migration -0.03 0.21 -9999 0 -0.64 43 43
ADCY4 -0.017 0.2 -9999 0 -0.61 42 42
ADCY5 -0.049 0.22 -9999 0 -0.65 45 45
ADCY6 -0.017 0.2 -9999 0 -0.61 42 42
ADCY7 -0.017 0.2 -9999 0 -0.61 42 42
ADCY1 -0.02 0.2 -9999 0 -0.62 42 42
ADCY2 -0.041 0.22 -9999 0 -0.66 43 43
ADCY3 -0.017 0.2 -9999 0 -0.61 42 42
ADCY8 -0.059 0.2 -9999 0 -0.63 45 45
ADCY9 -0.017 0.2 -9999 0 -0.61 42 42
GSK3B 0.008 0.083 -9999 0 -0.3 13 13
arachidonic acid secretion -0.01 0.19 -9999 0 -0.57 42 42
GNG2 0.012 0.038 -9999 0 -0.82 1 1
TRIP6 0.026 0.008 -9999 0 -10000 0 0
GNAO1 -0.043 0.21 -9999 0 -0.6 56 56
HRAS 0.012 0.021 -9999 0 -0.31 2 2
NFKBIA 0.01 0.079 -9999 0 -10000 0 0
GAB1 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.033 0.098 -9999 0 -0.97 5 5
JUN -0.17 0.35 -9999 0 -0.82 109 109
LPA/LPA2/NHERF2 -0.001 0.007 -9999 0 -10000 0 0
TIAM1 -0.043 0.12 -9999 0 -1.2 5 5
PIK3R1 0.014 0.001 -9999 0 -10000 0 0
mol:IP3 0.004 0.074 -9999 0 -0.32 1 1
PLCB3 0.03 0.008 -9999 0 -10000 0 0
FOS -0.21 0.37 -9999 0 -0.82 129 129
positive regulation of mitosis -0.01 0.19 -9999 0 -0.57 42 42
LPA/LPA1-2-3 -0.053 0.16 -9999 0 -0.54 41 41
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation 0.002 0.11 -9999 0 -0.35 41 41
GNAZ -0.023 0.18 -9999 0 -0.57 43 43
EGFR/PI3K-beta/Gab1 -0.044 0.13 -9999 0 -0.68 8 8
positive regulation of dendritic cell cytokine production -0.052 0.15 -9999 0 -0.54 41 41
LPA/LPA2/MAGI-3 -0.002 0.028 -9999 0 -0.59 1 1
ARHGEF1 -0.003 0.15 -9999 0 -0.49 41 41
GNAI2 -0.023 0.18 -9999 0 -0.57 43 43
GNAI3 -0.023 0.18 -9999 0 -0.57 43 43
GNAI1 -0.024 0.18 -9999 0 -0.57 44 44
LPA/LPA3 -0.01 0.043 -9999 0 -0.21 20 20
LPA/LPA2 -0.001 0.01 -9999 0 -10000 0 0
LPA/LPA1 -0.059 0.19 -9999 0 -0.66 43 43
HB-EGF/EGFR -0.053 0.17 -9999 0 -0.54 46 46
HBEGF -0.06 0.19 -9999 0 -0.62 42 42
mol:DAG 0.004 0.074 -9999 0 -0.32 1 1
cAMP biosynthetic process -0.03 0.2 -9999 0 -0.56 55 55
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
SRC 0.013 0.015 -9999 0 -0.31 1 1
GNB1 0.014 0.001 -9999 0 -10000 0 0
LYN 0.01 0.079 -9999 0 -10000 0 0
GNAQ 0.019 0.028 -9999 0 -10000 0 0
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 -0.003 0.065 -9999 0 -0.31 20 20
LPAR1 -0.055 0.24 -9999 0 -0.84 41 41
IL8 -0.13 0.2 -9999 0 -0.46 69 69
PTK2 -0.012 0.16 -9999 0 -0.5 41 41
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.016 0.14 -9999 0 -0.45 41 41
EGFR 0.006 0.076 -9999 0 -0.82 4 4
PLCG1 -0.015 0.084 -9999 0 -0.29 13 13
PLD2 -0.012 0.16 -9999 0 -0.5 41 41
G12/G13 -0.047 0.15 -9999 0 -0.53 41 41
PI3K-beta -0.034 0.12 -9999 0 -0.71 5 5
cell migration -0.016 0.059 -9999 0 -0.25 10 10
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
PXN 0.002 0.12 -9999 0 -0.36 41 41
HRAS/GTP -0.012 0.19 -9999 0 -0.59 42 42
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.082 0.24 -9999 0 -0.57 79 79
PRKCE 0.007 0.076 -9999 0 -0.82 4 4
PRKCD 0.012 0.071 -9999 0 -10000 0 0
Gi(beta/gamma) -0.011 0.19 -9999 0 -0.58 42 42
mol:LPA 0.003 0.018 -9999 0 -0.22 2 2
TRIP6/p130 Cas/FAK1/Paxillin -0.032 0.13 -9999 0 -0.45 41 41
MAPKKK cascade -0.01 0.19 -9999 0 -0.57 42 42
contractile ring contraction involved in cytokinesis 0.031 0.047 -9999 0 -0.26 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.085 0.2 -9999 0 -0.44 112 112
GNA15 0.009 0.054 -9999 0 -0.43 1 1
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT 0.008 0.091 -9999 0 -0.41 6 6
GNA11 0.011 0.067 -9999 0 -0.43 9 9
Rac1/GTP -0.034 0.1 -9999 0 -1 5 5
MMP2 -0.031 0.21 -9999 0 -0.65 43 43
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.054 0.16 -9999 0 -0.55 40 40
MAP4K1 -0.019 0.12 -9999 0 -0.41 37 37
MAP3K8 0 0.11 -9999 0 -0.82 8 8
PRKCB -0.027 0.13 -9999 0 -0.36 52 52
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.014 0.11 -9999 0 -0.56 5 5
JUN -0.1 0.24 -9999 0 -0.51 119 119
MAP3K7 0.014 0.11 -9999 0 -0.56 5 5
GRAP2 -0.042 0.2 -9999 0 -0.78 34 34
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.02 0.11 -9999 0 -0.52 7 7
LAT 0.006 0.077 -9999 0 -0.72 5 5
LCP2 0.009 0.039 -9999 0 -0.31 7 7
MAPK8 -0.001 0.14 -9999 0 -0.76 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.11 -9999 0 -0.37 32 32
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.05 0.15 -9999 0 -0.52 40 40
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 -0.008 0.077 -9999 0 -0.73 5 5
alphaV beta3 Integrin -0.02 0.11 -9999 0 -0.61 16 16
PTK2 0.014 0.16 -9999 0 -0.56 17 17
IGF1R 0.013 0 -9999 0 -10000 0 0
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 -0.025 0.1 -9999 0 -0.31 57 57
SRC 0.013 0.015 -9999 0 -0.31 1 1
CDKN1B -0.064 0.18 -9999 0 -0.61 45 45
VEGFA 0.008 0.066 -9999 0 -0.82 3 3
ILK -0.064 0.18 -9999 0 -0.61 45 45
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.059 0.17 -9999 0 -0.57 45 45
PTK2B 0.018 0.12 -9999 0 -0.52 21 21
alphaV/beta3 Integrin/JAM-A -0.062 0.16 -9999 0 -0.49 60 60
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.021 0.11 -9999 0 -0.61 16 16
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.17 0.26 -9999 0 -0.54 156 156
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.002 0.11 -9999 0 -0.54 4 4
alphaV/beta3 Integrin/Syndecan-1 -0.021 0.11 -9999 0 -0.61 16 16
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.24 0.25 -9999 0 -0.62 115 115
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
alphaV/beta3 Integrin/Osteopontin -0.072 0.16 -9999 0 -0.58 38 38
RPS6KB1 -0.21 0.24 -9999 0 -0.58 115 115
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.096 0.16 -9999 0 -0.78 16 16
GPR124 0.013 0 -9999 0 -10000 0 0
MAPK1 -0.096 0.16 -9999 0 -0.78 16 16
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.037 0.16 -9999 0 -0.63 28 28
cell adhesion -0.031 0.11 -9999 0 -0.56 16 16
ANGPTL3 0.005 0.026 -9999 0 -0.31 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.007 0.068 -9999 0 -0.64 5 5
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.008 0.066 -9999 0 -0.82 3 3
ITGB3 -0.014 0.15 -9999 0 -0.82 16 16
IGF1 -0.18 0.35 -9999 0 -0.8 119 119
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.02 0.11 -9999 0 -0.6 16 16
apoptosis 0.01 0.053 -9999 0 -0.82 2 2
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.02 0.11 -9999 0 -0.61 16 16
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.04 0.14 -9999 0 -0.63 23 23
CSF1 0 0.11 -9999 0 -0.82 8 8
PIK3C2A -0.066 0.18 -9999 0 -0.61 46 46
PI4 Kinase/Pyk2 -0.055 0.14 -9999 0 -0.78 4 4
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.024 0.12 -9999 0 -0.56 21 21
FAK1/Vinculin 0.023 0.13 -9999 0 -0.49 9 9
alphaV beta3/Integrin/ppsTEM5 -0.02 0.11 -9999 0 -0.61 16 16
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.069 0.24 -9999 0 -0.76 52 52
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 0.013 0 -9999 0 -10000 0 0
F11R 0.024 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.038 0.12 -9999 0 -0.61 16 16
alphaV/beta3 Integrin/TGFBR2 -0.023 0.12 -9999 0 -0.63 18 18
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.01 0.077 -9999 0 -0.55 9 9
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.019 0.1 -9999 0 -0.56 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.22 0.15 -9999 0 -0.31 350 350
alphaV/beta3 Integrin/Pyk2 -0.023 0.11 -9999 0 -0.53 21 21
SDC1 0.011 0.03 -9999 0 -0.31 4 4
VAV3 0.026 0.099 -9999 0 -0.53 14 14
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
IRS1 -0.081 0.26 -9999 0 -0.82 55 55
FAK1/Paxillin 0.023 0.13 -9999 0 -0.49 9 9
cell migration 0.033 0.12 -9999 0 -0.44 9 9
ITGAV 0.01 0.054 -9999 0 -0.82 2 2
PI3K -0.058 0.16 -9999 0 -0.94 4 4
SPP1 -0.082 0.2 -9999 0 -0.42 108 108
KDR 0.008 0.066 -9999 0 -0.82 3 3
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0.053 -9999 0 -0.82 2 2
COL4A3 -0.012 0.14 -9999 0 -0.82 15 15
angiogenesis -0.086 0.18 -9999 0 -0.61 37 37
Rac1/GTP -0.014 0.084 -9999 0 -0.48 14 14
EDIL3 -0.024 0.14 -9999 0 -0.43 41 41
cell proliferation -0.023 0.12 -9999 0 -0.62 18 18
BCR signaling pathway

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
JUN -0.11 0.18 -9999 0 -0.45 62 62
IKBKB -0.018 0.071 -9999 0 -0.36 3 3
AKT1 -0.04 0.1 -9999 0 -0.27 21 21
IKBKG -0.016 0.074 -9999 0 -0.33 5 5
CALM1 -0.034 0.085 -9999 0 -0.35 2 2
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
MAP3K1 -0.072 0.18 -9999 0 -0.65 16 16
MAP3K7 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.044 0.089 -9999 0 -0.38 2 2
DOK1 0.013 0 -9999 0 -10000 0 0
AP-1 -0.082 0.13 -9999 0 -0.28 108 108
LYN 0.013 0 -9999 0 -10000 0 0
BLNK 0.013 0 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
BCR complex -0.17 0.24 -9999 0 -0.52 135 135
CD22 -0.15 0.22 -9999 0 -0.51 104 104
CAMK2G -0.025 0.081 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 24 24
SHC/GRB2/SOS1 -0.095 0.15 -9999 0 -10000 0 0
GO:0007205 -0.045 0.09 -9999 0 -0.38 2 2
SYK 0.013 0 -9999 0 -10000 0 0
ELK1 -0.035 0.086 -9999 0 -0.36 2 2
NFATC1 -0.068 0.16 -9999 0 -0.55 19 19
B-cell antigen/BCR complex -0.17 0.24 -9999 0 -0.52 135 135
PAG1/CSK -0.001 0.029 -9999 0 -0.63 1 1
NFKBIB 0.002 0.028 -9999 0 -0.11 3 3
HRAS -0.037 0.099 -9999 0 -0.35 2 2
NFKBIA 0.003 0.027 -9999 0 -0.11 3 3
NF-kappa-B/RelA/I kappa B beta 0.009 0.024 -9999 0 -0.2 1 1
RasGAP/Csk -0.14 0.2 -9999 0 -0.49 94 94
mol:GDP -0.04 0.083 -9999 0 -0.36 2 2
PTEN 0.012 0.038 -9999 0 -0.82 1 1
CD79B -0.028 0.11 -9999 0 -0.31 62 62
NF-kappa-B/RelA/I kappa B alpha 0.009 0.024 -9999 0 -0.2 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.085 0.18 -9999 0 -0.43 72 72
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.051 0.087 -9999 0 -0.38 2 2
CSK 0.013 0 -9999 0 -10000 0 0
FOS -0.14 0.21 -9999 0 -0.47 129 129
CHUK -0.016 0.074 -9999 0 -0.35 4 4
IBTK 0.013 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.066 0.094 -9999 0 -0.49 8 8
PTPN6 -0.14 0.21 -9999 0 -0.6 51 51
RELA 0.013 0 -9999 0 -10000 0 0
BCL2A1 0.005 0.035 -9999 0 -0.13 18 18
VAV2 -0.13 0.18 -9999 0 -0.84 11 11
ubiquitin-dependent protein catabolic process 0.008 0.027 -9999 0 -0.11 3 3
BTK -0.019 0.16 -9999 0 -1.2 8 8
CD19 -0.15 0.2 -9999 0 -0.45 98 98
MAP4K1 -0.019 0.12 -9999 0 -0.41 37 37
CD72 0.012 0.021 -9999 0 -0.31 2 2
PAG1 0.012 0.038 -9999 0 -0.82 1 1
MAPK14 -0.054 0.16 -9999 0 -0.52 16 16
SH3BP5 0.013 0 -9999 0 -10000 0 0
PIK3AP1 -0.034 0.088 -9999 0 -10000 0 0
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.06 0.17 -9999 0 -0.43 71 71
RAF1 -0.027 0.094 -9999 0 -10000 0 0
RasGAP/p62DOK/SHIP -0.14 0.19 -9999 0 -0.47 93 93
CD79A -0.19 0.3 -9999 0 -0.52 183 183
re-entry into mitotic cell cycle -0.08 0.13 -9999 0 -0.28 108 108
RASA1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.008 0.083 -9999 0 -10000 0 0
MAPK1 -0.008 0.083 -9999 0 -10000 0 0
CD72/SHP1 -0.1 0.21 -9999 0 -0.58 46 46
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAPK8 -0.061 0.17 -9999 0 -0.53 24 24
actin cytoskeleton organization -0.085 0.18 -9999 0 -0.68 11 11
NF-kappa-B/RelA 0.023 0.045 -9999 0 -0.2 1 1
Calcineurin -0.035 0.059 -9999 0 -10000 0 0
PI3K -0.13 0.16 -9999 0 -0.54 29 29
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.054 0.085 -9999 0 -0.34 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.11 0.24 -9999 0 -1 21 21
DAPP1 -0.13 0.26 -9999 0 -1.2 18 18
cytokine secretion -0.063 0.15 -9999 0 -0.5 19 19
mol:DAG -0.051 0.087 -9999 0 -0.38 2 2
PLCG2 0.013 0 -9999 0 -10000 0 0
MAP2K1 -0.017 0.089 -9999 0 -10000 0 0
B-cell antigen/BCR complex/FcgammaRIIB -0.17 0.23 -9999 0 -0.58 94 94
mol:PI-3-4-5-P3 -0.095 0.12 -9999 0 -0.38 23 23
ETS1 -0.015 0.076 -9999 0 -10000 0 0
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.17 -9999 0 -0.46 74 74
B-cell antigen/BCR complex/LYN -0.12 0.2 -9999 0 -0.49 81 81
MALT1 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.054 -9999 0 -0.82 2 2
RAC1 -0.091 0.19 -9999 0 -0.75 11 11
B-cell antigen/BCR complex/LYN/SYK -0.15 0.22 -9999 0 -0.55 81 81
CARD11 -0.074 0.12 -9999 0 -0.51 12 12
FCGR2B -0.029 0.18 -9999 0 -0.82 23 23
PPP3CA 0.013 0 -9999 0 -10000 0 0
BCL10 0.013 0 -9999 0 -10000 0 0
IKK complex 0.001 0.035 -9999 0 -0.14 2 2
PTPRC -0.033 0.17 -9999 0 -0.59 37 37
PDPK1 -0.043 0.1 -9999 0 -0.27 21 21
PPP3CB 0.013 0 -9999 0 -10000 0 0
PPP3CC 0.013 0 -9999 0 -10000 0 0
POU2F2 0.009 0.024 -9999 0 -0.089 1 1
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.01 0.22 -10000 0 -0.96 21 21
NCK1/PAK1/Dok-R -0.028 0.091 -10000 0 -0.43 21 21
NCK1/Dok-R -0.068 0.24 -10000 0 -1.2 21 21
PIK3CA 0.008 0.065 -10000 0 -0.82 3 3
mol:beta2-estradiol -0.003 0.047 0.25 15 -10000 0 15
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.014 0.001 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.01 0.069 0.26 4 -0.33 11 15
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.06 0.23 -10000 0 -1.1 21 21
FN1 -0.22 0.15 -10000 0 -0.31 350 350
PLD2 0 0.27 -10000 0 -1.2 21 21
PTPN11 0.012 0.038 -10000 0 -0.82 1 1
GRB14 -0.011 0.14 -10000 0 -0.82 14 14
ELK1 0.015 0.24 -10000 0 -1.1 21 21
GRB7 -0.042 0.12 -10000 0 -0.31 82 82
PAK1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.24 -10000 0 -1.2 21 21
CDKN1A -0.011 0.17 -10000 0 -0.64 21 21
ITGA5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.068 0.24 -10000 0 -1.2 21 21
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO 0.026 0.17 -10000 0 -0.69 21 21
PLG -0.009 0.27 -10000 0 -1.2 21 21
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.009 0.21 -10000 0 -0.92 21 21
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
ANGPT2 -0.11 0.22 -10000 0 -0.72 25 25
BMX -0.015 0.29 -10000 0 -1.3 21 21
ANGPT1 -0.039 0.29 -10000 0 -1.5 18 18
tube development -0.018 0.19 -10000 0 -0.73 21 21
ANGPT4 -0.06 0.23 -10000 0 -0.74 48 48
response to hypoxia 0 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.019 0.3 -10000 0 -1.3 21 21
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 0.012 0.001 -10000 0 -10000 0 0
STAT5A (dimer) -0.021 0.21 -10000 0 -0.84 21 21
mol:L-citrulline 0.026 0.17 -10000 0 -0.69 21 21
AGTR1 -0.32 0.41 -10000 0 -0.82 196 196
MAPK14 -0.012 0.27 -10000 0 -1.2 21 21
Tie2/SHP2 -0.025 0.15 -10000 0 -1.4 5 5
TEK 0.016 0.17 -10000 0 -1.5 5 5
RPS6KB1 0.01 0.21 -10000 0 -0.92 21 21
Angiotensin II/AT1 -0.25 0.32 -10000 0 -0.64 196 196
Tie2/Ang1/GRB2 -0.005 0.28 -10000 0 -1.3 21 21
MAPK3 0.011 0.25 -10000 0 -1.1 21 21
MAPK1 0.011 0.25 -10000 0 -1.1 21 21
Tie2/Ang1/GRB7 -0.03 0.29 -10000 0 -1.3 21 21
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
MAPK8 -0.008 0.29 -10000 0 -1.3 21 21
PI3K -0.005 0.25 -10000 0 -1.1 21 21
FES -0.011 0.27 -10000 0 -1.2 21 21
Crk/Dok-R -0.068 0.24 -10000 0 -1.2 21 21
Tie2/Ang1/ABIN2 -0.005 0.28 -10000 0 -1.3 21 21
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.014 0.2 -10000 0 -0.84 21 21
STAT5A 0.014 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.01 0.21 -10000 0 -0.92 21 21
Tie2/Ang2 -0.04 0.24 -10000 0 -1 21 21
Tie2/Ang1 -0.012 0.3 -10000 0 -1.4 21 21
FOXO1 0.021 0.2 -10000 0 -0.85 21 21
ELF1 0.015 0.079 -10000 0 -0.85 4 4
ELF2 -0.004 0.27 -10000 0 -1.2 21 21
mol:Choline 0.003 0.26 -10000 0 -1.2 21 21
cell migration -0.024 0.056 -10000 0 -0.25 9 9
FYN -0.024 0.21 -10000 0 -0.84 21 21
DOK2 0 0.076 -10000 0 -0.38 16 16
negative regulation of cell cycle -0.008 0.16 -10000 0 -0.58 21 21
ETS1 0.016 0.045 -10000 0 -10000 0 0
PXN 0.022 0.18 -10000 0 -0.74 21 21
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.022 0.19 -10000 0 -0.79 21 21
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.089 0.28 -10000 0 -0.78 64 64
MAPKKK cascade 0.003 0.26 -10000 0 -1.2 21 21
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.009 0.28 -10000 0 -1.3 21 21
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.028 0.15 -10000 0 -0.61 21 21
mol:Phosphatidic acid 0.003 0.26 -10000 0 -1.2 21 21
mol:Angiotensin II 0.001 0.001 -10000 0 -10000 0 0
mol:NADP 0.026 0.17 -10000 0 -0.69 21 21
Rac1/GTP -0.051 0.18 -10000 0 -0.85 21 21
MMP2 -0.007 0.28 -10000 0 -1.3 21 21
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 0.012 0.038 -10000 0 -0.82 1 1
Jak2/Leptin Receptor -0.023 0.096 -10000 0 -0.39 15 15
PTP1B/AKT1 -0.003 0.064 -10000 0 -0.31 4 4
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.012 0.071 -10000 0 -0.33 5 5
EGFR 0.005 0.076 -10000 0 -0.83 4 4
EGF/EGFR -0.083 0.18 -10000 0 -0.5 72 72
CSF1 0 0.11 -10000 0 -0.82 8 8
AKT1 0.014 0.001 -10000 0 -10000 0 0
INSR 0.014 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.1 0.12 -10000 0 -0.46 19 19
Insulin Receptor/Insulin -0.013 0.041 -10000 0 -10000 0 0
HCK -0.008 0.08 -10000 0 -0.31 31 31
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.003 0.067 -10000 0 -0.36 2 2
EGF -0.11 0.29 -10000 0 -0.79 74 74
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.017 0.099 -10000 0 -0.39 5 5
TXN 0.011 0.016 -10000 0 -0.32 1 1
PTP1B/IRS1/GRB2 -0.053 0.17 -10000 0 -0.5 56 56
cell migration 0.012 0.071 0.33 5 -10000 0 5
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.046 0.2 -10000 0 -0.61 47 47
ITGA2B -0.075 0.26 -10000 0 -0.82 51 51
CSF1R 0.008 0.05 -10000 0 -0.4 6 6
Prolactin Receptor/Prolactin -0.041 0.15 -10000 0 -0.64 27 27
FGR 0.011 0.03 -10000 0 -0.31 4 4
PTP1B/p130 Cas -0.004 0.066 -10000 0 -0.32 4 4
Crk/p130 Cas 0.001 0.061 -10000 0 -0.35 2 2
DOK1 0.006 0.063 -10000 0 -0.37 1 1
JAK2 -0.012 0.089 -10000 0 -0.37 14 14
Jak2/Leptin Receptor/Leptin -0.056 0.14 -10000 0 -0.58 28 28
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.012 0.071 -10000 0 -0.33 5 5
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.19 0.2 -10000 0 -0.34 279 279
SRC 0.012 0.03 -10000 0 -10000 0 0
ITGB3 -0.016 0.15 -10000 0 -0.83 16 16
CAT1/PTP1B -0.09 0.15 -10000 0 -0.38 63 63
CAPN1 0.013 0.003 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.015 0.055 -10000 0 -0.61 3 3
mol:H2O2 0 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.055 0.15 -10000 0 -0.63 27 27
negative regulation of transcription -0.011 0.089 -10000 0 -0.37 14 14
FCGR2A -0.007 0.084 -10000 0 -0.33 28 28
FER 0.007 0.066 -10000 0 -0.83 3 3
alphaIIb/beta3 Integrin -0.085 0.23 -10000 0 -0.68 61 61
BLK -0.25 0.38 -10000 0 -0.76 164 164
Insulin Receptor/Insulin/Shc 0 0.001 -10000 0 -10000 0 0
RHOA 0.013 0.003 -10000 0 -10000 0 0
LEPR 0.004 0.086 -10000 0 -0.67 7 7
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH 0 0.004 -10000 0 -10000 0 0
TRPV6 -0.12 0.19 -10000 0 -0.45 65 65
PRL 0.001 0.016 -10000 0 -0.31 1 1
SOCS3 -0.07 0.35 -10000 0 -1.5 27 27
SPRY2 0.009 0.056 -10000 0 -0.66 3 3
Insulin Receptor/Insulin/IRS1 -0.063 0.18 -10000 0 -0.56 55 55
CSF1/CSF1R -0.009 0.096 -10000 0 -0.52 10 10
Ras protein signal transduction 0.02 0.023 -10000 0 -10000 0 0
IRS1 -0.081 0.26 -10000 0 -0.82 55 55
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.007 0.065 -10000 0 -0.31 21 21
STAT5B -0.007 0.07 -10000 0 -0.26 10 10
STAT5A -0.007 0.07 -10000 0 -0.26 10 10
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.005 0.069 -10000 0 -0.35 5 5
CSN2 -0.007 0.056 -10000 0 -10000 0 0
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
LAT 0.002 0.066 -10000 0 -0.54 5 5
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.01 0.11 -10000 0 -0.44 25 25
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.13 0.16 -10000 0 -0.31 213 213
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.003 0.04 -10000 0 -0.63 2 2
Necdin/E2F1 -0.069 0.12 -10000 0 -0.76 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.036 0.1 -10000 0 -0.49 20 20
NGF (dimer)/p75(NTR)/BEX1 -0.29 0.28 -10000 0 -0.57 230 230
NT-4/5 (dimer)/p75(NTR) -0.075 0.18 -10000 0 -0.67 35 35
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 -0.004 0.12 -10000 0 -0.49 23 23
IKBKG 0.013 0 -10000 0 -10000 0 0
BDNF -0.013 0.14 -10000 0 -0.6 21 21
MGDIs/NGR/p75(NTR)/LINGO1 -0.05 0.12 -10000 0 -0.54 21 21
FURIN 0.013 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.058 0.14 -10000 0 -0.55 31 31
LINGO1 -0.003 0.072 -10000 0 -0.31 25 25
Sortilin/TRAF6/NRIF -0.002 0.026 -10000 0 -0.4 2 2
proBDNF (dimer) -0.013 0.14 -10000 0 -0.6 21 21
NTRK1 -0.002 0.061 -10000 0 -0.31 18 18
RTN4R 0.013 0 -10000 0 -10000 0 0
neuron apoptosis -0.011 0.13 -10000 0 -0.48 29 29
IRAK1 0.013 0 -10000 0 -10000 0 0
SHC1 -0.021 0.13 -10000 0 -0.57 20 20
ARHGDIA 0.013 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.04 0.11 -10000 0 -0.52 20 20
MAGEH1 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.045 0.12 -10000 0 -0.52 25 25
Mammalian IAPs/DIABLO -0.028 0.11 -10000 0 -0.5 25 25
proNGF (dimer) 0.006 0.07 -10000 0 -0.57 6 6
MAGED1 0.013 0 -10000 0 -10000 0 0
APP 0.013 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.02 0.15 -10000 0 -0.64 25 25
ZNF274 0.013 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.037 0.1 -10000 0 -0.49 20 20
NGF 0.006 0.07 -10000 0 -0.57 6 6
cell cycle arrest 0.042 0.16 -10000 0 -0.47 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.008 0.086 -10000 0 -0.35 22 22
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.065 0.16 -10000 0 -0.58 37 37
NCSTN 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.047 0.12 -10000 0 -0.57 21 21
PSENEN 0.013 0 -10000 0 -10000 0 0
mol:ceramide -0.01 0.12 -10000 0 -0.51 20 20
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.071 -10000 0 -0.44 2 2
p75(NTR)/beta APP -0.051 0.13 -10000 0 -0.63 18 18
BEX1 -0.36 0.42 -10000 0 -0.82 215 215
mol:GDP -0.032 0.13 -10000 0 -0.58 20 20
NGF (dimer) -0.095 0.13 -10000 0 -0.51 30 30
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.043 0.11 -10000 0 -0.52 18 18
PIK3R1 0.013 0 -10000 0 -10000 0 0
RAC1/GTP -0.039 0.11 -10000 0 -0.5 20 20
MYD88 0.013 0 -10000 0 -10000 0 0
CHUK 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.047 0.13 -10000 0 -0.57 21 21
RHOB 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 -0.063 0.094 -10000 0 -10000 0 0
NT3 (dimer) -0.05 0.2 -10000 0 -0.62 48 48
TP53 -0.006 0.13 -10000 0 -0.45 31 31
PRDM4 -0.011 0.12 -10000 0 -0.52 20 20
BDNF (dimer) -0.13 0.16 -10000 0 -0.54 39 39
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
SORT1 0.013 0 -10000 0 -10000 0 0
activation of caspase activity -0.036 0.1 -10000 0 -0.48 20 20
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.042 0.12 -10000 0 -0.52 22 22
RHOC 0.013 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
MAPK10 0.023 0.12 -10000 0 -0.45 20 20
DIABLO 0.013 0 -10000 0 -10000 0 0
SMPD2 -0.011 0.12 -10000 0 -0.52 20 20
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.046 0.12 -10000 0 -0.57 20 20
PSEN1 0.013 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.029 -10000 0 -0.63 1 1
NT3 (dimer)/p75(NTR) -0.096 0.2 -10000 0 -0.66 46 46
MAPK8 0.018 0.13 -10000 0 -0.46 20 20
MAPK9 0.023 0.12 -10000 0 -0.44 19 19
APAF1 0.012 0.038 -10000 0 -0.82 1 1
NTF3 -0.05 0.2 -10000 0 -0.62 48 48
NTF4 -0.02 0.16 -10000 0 -0.64 25 25
NDN 0.005 0.084 -10000 0 -0.82 5 5
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.033 0.096 -10000 0 -0.45 21 21
p75 CTF/Sortilin/TRAF6/NRIF -0.004 0.054 -10000 0 -0.66 3 3
RhoA-B-C/GTP -0.046 0.12 -10000 0 -0.56 21 21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.048 0.12 -10000 0 -0.48 31 31
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.053 0.13 -10000 0 -0.52 31 31
PRKACB 0.012 0.038 -10000 0 -0.82 1 1
proBDNF (dimer)/p75 ECD -0.022 0.11 -10000 0 -0.63 14 14
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.68 35 35
BIRC2 0.013 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.066 0.17 0.24 185 -0.47 20 205
BAD 0.029 0.12 -10000 0 -0.44 20 20
RIPK2 0.013 0 -10000 0 -10000 0 0
NGFR -0.062 0.19 -10000 0 -0.42 84 84
CYCS -0.001 0.12 -10000 0 -0.48 20 20
ADAM17 0.01 0.054 -10000 0 -0.82 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.042 0.12 -10000 0 -0.52 22 22
BCL2L11 0.029 0.12 -10000 0 -0.44 20 20
BDNF (dimer)/p75(NTR) -0.07 0.17 -10000 0 -0.63 31 31
PI3K -0.043 0.12 -10000 0 -0.53 23 23
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.04 0.11 -10000 0 -0.52 20 20
NDNL2 0.013 0 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.056 0.14 -10000 0 -0.66 20 20
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.04 0.11 -10000 0 -0.52 20 20
TRAF6 0.01 0.054 -10000 0 -0.82 2 2
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
PLG -0.003 0.035 -10000 0 -0.31 6 6
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.017 0.14 -10000 0 -0.49 31 31
SQSTM1 0.013 0 -10000 0 -10000 0 0
NGFRAP1 0.013 0 -10000 0 -10000 0 0
CASP3 0.03 0.11 -10000 0 -0.4 20 20
E2F1 -0.089 0.15 -10000 0 -0.31 152 152
CASP9 0.013 0 -10000 0 -10000 0 0
IKK complex -0.014 0.059 -10000 0 -0.54 3 3
NGF (dimer)/TRKA -0.013 0.064 -10000 0 -0.64 3 3
MMP7 -0.18 0.22 -10000 0 -0.37 242 242
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.038 0.11 -10000 0 -0.49 22 22
MMP3 -0.039 0.11 -10000 0 -0.31 67 67
APAF-1/Caspase 9 -0.041 0.11 -10000 0 -0.61 7 7
Effects of Botulinum toxin

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
STX1A 0.012 0 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.001 0.013 -9999 0 -10000 0 0
STXBP1 0.013 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.015 0.064 -9999 0 -0.23 9 9
RAB3GAP2/RIMS1/UNC13B -0.001 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 0.01 0.021 -9999 0 -0.31 2 2
mol:ACh -0.007 0.041 -9999 0 -0.15 29 29
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.015 0.063 -9999 0 -0.23 9 9
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.018 0.093 -9999 0 -0.31 44 44
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.11 0.16 -9999 0 -0.24 217 217
SNAP25 -0.032 0.097 -9999 0 -0.38 29 29
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.16 0.23 -9999 0 -0.38 217 217
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.019 0 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.014 0.044 -9999 0 -10000 0 0
IL27-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
TGFB1 0.01 0.042 -10000 0 -0.31 8 8
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.065 0.14 0.54 9 -10000 0 9
IL27/IL27R/JAK1 -0.12 0.19 -10000 0 -0.68 6 6
TBX21 -0.091 0.22 -10000 0 -0.66 30 30
IL12B -0.005 0.091 -10000 0 -0.63 8 8
IL12A -0.06 0.2 -10000 0 -0.64 51 51
IL6ST -0.11 0.29 -10000 0 -0.83 69 69
IL27RA/JAK1 0.013 0.026 -10000 0 -10000 0 0
IL27 0.002 0.037 -10000 0 -0.32 6 6
TYK2 0.012 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.062 0.16 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.065 0.14 0.54 9 -10000 0 9
T cell proliferation during immune response 0.065 0.14 0.54 9 -10000 0 9
MAPKKK cascade -0.065 0.14 -10000 0 -0.54 9 9
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.006 0.049 -10000 0 -0.32 11 11
IL12RB1 -0.022 0.12 -10000 0 -0.36 44 44
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.09 0.21 -10000 0 -0.66 27 27
IL27/IL27R/JAK2/TYK2 -0.065 0.15 -10000 0 -0.55 9 9
positive regulation of T cell mediated cytotoxicity -0.065 0.14 -10000 0 -0.54 9 9
STAT1 (dimer) -0.12 0.24 0.52 16 -0.8 12 28
JAK2 0.012 0.039 -10000 0 -0.84 1 1
JAK1 0.014 0.002 -10000 0 -10000 0 0
STAT2 (dimer) -0.054 0.14 -10000 0 -0.54 7 7
T cell proliferation -0.16 0.24 -10000 0 -0.62 59 59
IL12/IL12R/TYK2/JAK2 -0.055 0.17 -10000 0 -0.68 14 14
IL17A -0.063 0.16 -10000 0 -10000 0 0
mast cell activation 0.065 0.14 0.54 9 -10000 0 9
IFNG -0.02 0.048 -10000 0 -0.13 65 65
T cell differentiation -0.005 0.008 -10000 0 -0.022 55 55
STAT3 (dimer) -0.054 0.14 -10000 0 -0.54 7 7
STAT5A (dimer) -0.054 0.14 -10000 0 -0.54 7 7
STAT4 (dimer) -0.074 0.16 -10000 0 -0.52 21 21
STAT4 -0.025 0.14 -10000 0 -0.45 40 40
T cell activation -0.012 0.006 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.063 0.18 -10000 0 -0.72 4 4
GATA3 -0.044 0.34 -10000 0 -1.5 25 25
IL18 -0.025 0.12 -10000 0 -0.64 11 11
positive regulation of mast cell cytokine production -0.053 0.14 -10000 0 -0.53 7 7
IL27/EBI3 -0.097 0.12 -10000 0 -0.44 6 6
IL27RA 0.004 0.027 -10000 0 -10000 0 0
IL6 -0.17 0.33 -10000 0 -0.82 97 97
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.002 0.013 -10000 0 -10000 0 0
IL1B -0.042 0.18 -10000 0 -0.64 38 38
EBI3 -0.14 0.17 -10000 0 -0.32 232 232
TNF -0.07 0.21 -10000 0 -0.6 64 64
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 0.02 0.015 -10000 0 -10000 0 0
HSPA8 0.004 0.076 -10000 0 -0.82 4 4
SMAD3/SMAD4/ER alpha -0.053 0.14 -10000 0 -0.58 25 25
AKT1 0.008 0.011 -10000 0 -10000 0 0
GSC -0.21 0.56 -10000 0 -1.6 71 71
NKX2-5 0.002 0.029 -10000 0 -0.31 4 4
muscle cell differentiation 0.026 0.051 0.44 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.005 0.08 -10000 0 -10000 0 0
SMAD4 -0.012 0.06 -10000 0 -10000 0 0
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.012 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.12 0.078 -10000 0 -0.55 5 5
SMAD3/SMAD4/VDR 0.01 0.044 -10000 0 -10000 0 0
MYC 0 0.14 -10000 0 -0.82 13 13
CDKN2B -0.076 0.14 -10000 0 -10000 0 0
AP1 -0.26 0.51 -10000 0 -0.94 152 152
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.032 0.056 -10000 0 -0.71 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.001 0.063 -10000 0 -10000 0 0
SP3 0.016 0.002 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.011 0.074 -10000 0 -0.31 21 21
SMAD3/SMAD4/GR -0.017 0.045 -10000 0 -10000 0 0
GATA3 -0.032 0.19 -10000 0 -0.78 27 27
SKI/SIN3/HDAC complex/NCoR1 0.04 0.029 -10000 0 -10000 0 0
MEF2C/TIF2 -0.045 0.17 -10000 0 -0.52 38 38
endothelial cell migration -0.009 0.1 1.4 1 -10000 0 1
MAX 0.013 0.006 -10000 0 -10000 0 0
RBBP7 0.012 0.004 -10000 0 -10000 0 0
RBBP4 0.007 0.066 -10000 0 -0.82 3 3
RUNX2 -0.076 0.15 -10000 0 -0.32 129 129
RUNX3 -0.007 0.12 -10000 0 -0.6 16 16
RUNX1 -0.13 0.16 -10000 0 -0.31 213 213
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.013 0.006 -10000 0 -10000 0 0
VDR 0.013 0.015 -10000 0 -10000 0 0
CDKN1A 0.023 0.073 -10000 0 -10000 0 0
KAT2B 0.016 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.038 0.094 -10000 0 -0.44 3 3
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.012 0.004 -10000 0 -10000 0 0
SERPINE1 0.009 0.1 -10000 0 -1.4 1 1
SMAD3/SMAD4/ATF2 -0.038 0.12 -10000 0 -0.59 18 18
SMAD3/SMAD4/ATF3 -0.16 0.26 -10000 0 -0.63 114 114
SAP30 0.01 0.038 -10000 0 -0.83 1 1
Cbp/p300/PIAS3 0.033 0.045 -10000 0 -10000 0 0
JUN -0.25 0.5 -10000 0 -0.93 152 152
SMAD3/SMAD4/IRF7 -0.017 0.045 -10000 0 -10000 0 0
TFE3 0.019 0.006 -10000 0 -10000 0 0
COL1A2 -0.002 0.092 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.066 0.095 0.46 4 -10000 0 4
DLX1 -0.033 0.19 -10000 0 -0.82 27 27
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.22 0.4 -10000 0 -0.89 129 129
SMAD3/SMAD4/Max -0.017 0.045 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.006 0.041 -10000 0 -0.55 2 2
ZBTB17 0.021 0.012 -10000 0 -10000 0 0
LAMC1 0.026 0.053 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.017 0.043 -10000 0 -10000 0 0
IRF7 0.014 0.016 -10000 0 -0.31 1 1
ESR1 -0.05 0.19 -10000 0 -0.54 55 55
HNF4A -0.003 0.045 -10000 0 -0.31 10 10
MEF2C 0.004 0.099 -10000 0 -1 1 1
SMAD2-3/SMAD4 -0.032 0.055 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.025 0.031 -10000 0 -10000 0 0
IGHV3OR16-13 -0.016 0.024 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.018 0.01 -10000 0 -10000 0 0
SKIL 0.012 0.038 -10000 0 -0.82 1 1
HDAC1 0.012 0.004 -10000 0 -10000 0 0
HDAC2 0.012 0.004 -10000 0 -10000 0 0
SNIP1 0.008 0.054 -10000 0 -0.82 2 2
GCN5L2 0.006 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.011 0.045 -10000 0 -10000 0 0
MSG1/HSC70 -0.18 0.1 -10000 0 -0.68 9 9
SMAD2 -0.003 0.04 -10000 0 -10000 0 0
SMAD3 -0.005 0.047 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.01 0.075 -10000 0 -0.36 13 13
SMAD2/SMAD2/SMAD4 0.014 0.028 -10000 0 -10000 0 0
NCOR1 0.012 0.004 -10000 0 -10000 0 0
NCOA2 -0.062 0.24 -10000 0 -0.82 44 44
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A -0.002 0.018 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.014 0.077 -10000 0 -10000 0 0
IFNB1 0.014 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.006 0.099 -10000 0 -1 1 1
CITED1 -0.26 0.14 -10000 0 -0.32 403 403
SMAD2-3/SMAD4/ARC105 -0.022 0.046 -10000 0 -10000 0 0
RBL1 -0.007 0.13 -10000 0 -0.82 12 12
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.006 0.082 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.081 0.11 -10000 0 -0.49 14 14
SMAD7 -0.1 0.28 -10000 0 -0.59 101 101
MYC/MIZ-1 0.013 0.11 -10000 0 -0.63 13 13
SMAD3/SMAD4 0.064 0.1 0.31 42 -0.35 1 43
IL10 -0.026 0.19 -10000 0 -0.62 38 38
PIASy/HDAC complex 0.007 0.01 -10000 0 -10000 0 0
PIAS3 0.016 0.005 -10000 0 -10000 0 0
CDK2 0.018 0.011 -10000 0 -10000 0 0
IL5 -0.016 0.14 -10000 0 -0.5 26 26
CDK4 0.019 0.012 -10000 0 -10000 0 0
PIAS4 0.007 0.01 -10000 0 -10000 0 0
ATF3 -0.19 0.35 -10000 0 -0.79 121 121
SMAD3/SMAD4/SP1 -0.015 0.054 -10000 0 -10000 0 0
FOXG1 -0.003 0.072 -10000 0 -0.39 13 13
FOXO3 0.017 0.015 -10000 0 -10000 0 0
FOXO1 0.017 0.015 -10000 0 -10000 0 0
FOXO4 0.017 0.015 -10000 0 -10000 0 0
heart looping 0.004 0.098 -10000 0 -1 1 1
CEBPB 0.009 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.05 0.14 -10000 0 -0.6 27 27
MYOD1 -0.002 0.029 -10000 0 -0.31 4 4
SMAD3/SMAD4/HNF4 -0.024 0.052 -10000 0 -0.4 1 1
SMAD3/SMAD4/GATA3 -0.051 0.14 -10000 0 -0.54 30 30
SnoN/SIN3/HDAC complex/NCoR1 0.012 0.038 -10000 0 -0.82 1 1
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.075 0.11 -10000 0 -0.55 11 11
SMAD3/SMAD4/SP1-3 0.006 0.056 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.015 0.022 -10000 0 -10000 0 0
SIN3B 0.012 0.004 -10000 0 -10000 0 0
SIN3A 0.012 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.017 0.095 -10000 0 -0.52 2 2
ITGB5 0.036 0.059 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.042 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.26 0.29 -10000 0 -0.6 204 204
AR -0.34 0.41 -10000 0 -0.82 204 204
negative regulation of cell growth -0.04 0.13 -10000 0 -0.46 8 8
SMAD3/SMAD4/MYOD -0.023 0.049 -10000 0 -10000 0 0
E2F5 0.012 0.038 -10000 0 -0.82 1 1
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.013 0.066 -10000 0 -0.36 2 2
SMAD2-3/SMAD4/FOXO1-3a-4 0.001 0.067 -10000 0 -10000 0 0
TFDP1 0.012 0.038 -10000 0 -0.82 1 1
SMAD3/SMAD4/AP1 -0.27 0.51 -10000 0 -0.96 152 152
SMAD3/SMAD4/RUNX2 -0.066 0.096 -10000 0 -0.47 4 4
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 -0.018 0.16 -10000 0 -0.82 18 18
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.01 0.054 -9999 0 -0.82 2 2
Aurora C/Aurora B/INCENP -0.039 0.077 -9999 0 -0.39 8 8
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.011 0.02 -9999 0 -10000 0 0
AURKB -0.059 0.14 -9999 0 -0.31 107 107
AURKC -0.001 0.067 -9999 0 -0.31 21 21
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
alphaV beta3 Integrin -0.023 0.13 -9999 0 -0.7 16 16
PTK2 -0.04 0.15 -9999 0 -0.61 28 28
positive regulation of JNK cascade -0.02 0.081 -9999 0 -0.34 28 28
CDC42/GDP 0.031 0.13 -9999 0 -0.47 28 28
Rac1/GDP 0.033 0.12 -9999 0 -0.46 28 28
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.025 0.1 -9999 0 -0.43 28 28
nectin-3/I-afadin -0.036 0.15 -9999 0 -0.63 28 28
RAPGEF1 0.024 0.14 -9999 0 -0.54 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0.16 -9999 0 -0.63 28 28
PDGFB-D/PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
TLN1 0.019 0.075 -9999 0 -0.94 1 1
Rap1/GTP -0.022 0.086 -9999 0 -0.37 28 28
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.036 0.15 -9999 0 -0.63 28 28
PVR 0.013 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.013 0 -9999 0 -10000 0 0
mol:GDP 0.025 0.16 -9999 0 -0.59 28 28
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
PI3K -0.03 0.13 -9999 0 -0.51 29 29
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.005 0.033 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.021 0.085 -9999 0 -0.36 28 28
PVRL1 0.005 0.053 -9999 0 -0.31 13 13
PVRL3 -0.035 0.2 -9999 0 -0.82 28 28
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
CLDN1 -0.26 0.15 -9999 0 -0.33 396 396
JAM-A/CLDN1 -0.14 0.14 -9999 0 -0.58 38 38
SRC -0.043 0.17 -9999 0 -0.72 28 28
ITGB3 -0.014 0.15 -9999 0 -0.82 16 16
nectin-1(dimer)/I-afadin/I-afadin -0.005 0.033 -9999 0 -10000 0 0
FARP2 0.019 0.15 -9999 0 -0.58 28 28
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.031 0.13 -9999 0 -0.55 28 28
nectin-1/I-afadin -0.005 0.033 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.036 0.13 -9999 0 -0.55 28 28
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.02 0.081 -9999 0 -0.34 28 28
alphaV/beta3 Integrin/Talin 0.016 0.14 -9999 0 -0.61 16 16
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0.011 0.08 -9999 0 -1 1 1
VAV2 0.018 0.15 -9999 0 -0.59 28 28
RAP1/GDP -0.025 0.1 -9999 0 -0.43 28 28
ITGAV 0.01 0.054 -9999 0 -0.82 2 2
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.031 0.13 -9999 0 -0.55 28 28
nectin-3(dimer)/I-afadin/I-afadin -0.036 0.15 -9999 0 -0.63 28 28
Rac1/GTP -0.026 0.1 -9999 0 -0.44 28 28
PTPRM -0.018 0.082 -9999 0 -0.32 28 28
E-cadherin/beta catenin/alpha catenin -0.003 0.016 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.032 0.044 -9999 0 -0.93 1 1
VEGFR1 homodimer/NRP1 -0.002 0.042 -9999 0 -0.94 1 1
mol:DAG -0.012 0.16 -9999 0 -0.49 49 49
VEGFR1 homodimer/NRP1/VEGFR 121 -0.005 0.068 -9999 0 -0.78 3 3
CaM/Ca2+ -0.004 0.15 -9999 0 -0.46 49 49
HIF1A 0.021 0.018 -9999 0 -0.38 1 1
GAB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.009 0.16 -9999 0 -1.1 2 2
PLCG1 -0.012 0.16 -9999 0 -0.5 49 49
NOS3 0.017 0.15 -9999 0 -0.43 49 49
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.018 0.15 -9999 0 -0.42 49 49
FLT1 0.031 0.048 -9999 0 -1 1 1
PGF -0.07 0.25 -9999 0 -0.81 49 49
VEGFR1 homodimer/NRP2/VEGFR121 -0.014 0.075 -9999 0 -0.77 3 3
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
eNOS/Hsp90 0.025 0.14 -9999 0 -0.81 1 1
endothelial cell proliferation -0.029 0.19 -9999 0 -0.52 50 50
mol:Ca2+ -0.011 0.16 -9999 0 -0.49 49 49
MAPK3 -0.017 0.18 -9999 0 -0.44 71 71
MAPK1 -0.017 0.18 -9999 0 -0.48 24 24
PIK3R1 0.013 0 -9999 0 -10000 0 0
PLGF homodimer -0.07 0.25 -9999 0 -0.81 49 49
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.009 0.14 -9999 0 -0.82 13 13
VEGFA homodimer 0.008 0.065 -9999 0 -0.82 3 3
VEGFR1 homodimer/VEGFA homodimer 0.029 0.074 -9999 0 -0.82 3 3
platelet activating factor biosynthetic process -0.009 0.17 -9999 0 -0.96 2 2
PI3K -0.05 0.15 -9999 0 -0.47 51 51
PRKCA -0.027 0.19 -9999 0 -0.47 71 71
PRKCB -0.022 0.17 -9999 0 -0.47 53 53
VEGFR1 homodimer/PLGF homodimer -0.025 0.18 -9999 0 -0.55 49 49
VEGFA 0.008 0.066 -9999 0 -0.82 3 3
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.012 0.16 -9999 0 -0.49 49 49
RASA1 0.041 0.041 -9999 0 -0.86 1 1
NRP2 -0.012 0.088 -9999 0 -0.31 38 38
VEGFR1 homodimer 0.031 0.048 -9999 0 -1 1 1
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.013 0.16 -9999 0 -0.8 4 4
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
mol:PI-3-4-5-P3 -0.049 0.15 -9999 0 -0.46 51 51
mol:L-citrulline 0.018 0.15 -9999 0 -0.42 49 49
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.004 0.064 -9999 0 -0.73 3 3
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.005 0.067 -9999 0 -0.77 3 3
CD2AP 0.013 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.047 0.14 -9999 0 -0.69 3 3
PDPK1 0.001 0.16 -9999 0 -0.45 51 51
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.006 0.084 -9999 0 -0.9 3 3
mol:NADP 0.018 0.15 -9999 0 -0.42 49 49
HSP90AA1 0.013 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.004 0.062 -9999 0 -0.71 3 3
VEGFR1 homodimer/NRP2 0.018 0.065 -9999 0 -0.93 1 1
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.017 0.087 -9999 0 -0.48 16 16
RGS9BP -0.037 0.2 -9999 0 -0.82 29 29
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.067 0.24 -9999 0 -0.81 47 47
mol:Na + -0.021 0.057 -9999 0 -10000 0 0
mol:ADP -0.044 0.19 -9999 0 -0.64 46 46
GNAT2 0.009 0.022 -9999 0 -0.31 2 2
RGS9-1/Gbeta5/R9AP -0.091 0.21 -9999 0 -0.56 79 79
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.011 -9999 0 -10000 0 0
GRK7 0.007 0.007 -9999 0 -10000 0 0
CNGB3 0.003 0.005 -9999 0 -10000 0 0
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.014 0.063 -9999 0 -0.3 2 2
Cone PDE6 -0.08 0.18 -9999 0 -0.48 79 79
Cone Metarhodopsin II -0.049 0.15 -9999 0 -0.52 46 46
Na + (4 Units) -0.025 0.057 -9999 0 -0.3 2 2
GNAT2/GDP -0.079 0.18 -9999 0 -0.48 79 79
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.011 0.015 -9999 0 -10000 0 0
Cone Transducin -0.018 0.091 -9999 0 -0.5 16 16
SLC24A2 -0.009 0.063 -9999 0 -0.31 20 20
GNB3/GNGT2 -0.022 0.11 -9999 0 -0.63 16 16
GNB3 -0.013 0.14 -9999 0 -0.79 16 16
GNAT2/GTP -0.001 0.014 -9999 0 -0.21 2 2
CNGA3 -0.027 0.11 -9999 0 -0.31 60 60
ARR3 0.004 0.006 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.021 0.057 -9999 0 -10000 0 0
mol:Pi -0.091 0.21 -9999 0 -0.56 79 79
Cone CNG Channel -0.017 0.043 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.009 0.063 -9999 0 -0.31 20 20
RGS9 -0.077 0.26 -9999 0 -0.8 54 54
PDE6C 0.003 0.016 -9999 0 -0.31 1 1
GNGT2 0.01 0.046 -9999 0 -0.44 4 4
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.004 0.006 -9999 0 -10000 0 0
IL1-mediated signaling events

Figure S64.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S64.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.03 0.068 -9999 0 -0.32 8 8
IRAK/TOLLIP 0.029 0.004 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.12 0.25 -9999 0 -0.67 75 75
IL1A -0.055 0.22 -9999 0 -0.79 41 41
IL1B -0.033 0.18 -9999 0 -0.64 40 40
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.027 -9999 0 -0.43 2 2
IL1R2 -0.083 0.24 -9999 0 -0.59 77 77
IL1R1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.005 0.069 -9999 0 -0.3 1 1
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.005 0.084 -9999 0 -0.82 5 5
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.066 0.028 -9999 0 -10000 0 0
JUN -0.072 0.22 -9999 0 -0.43 120 120
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.068 0.14 -9999 0 -0.47 42 42
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.074 0.14 -9999 0 -0.51 38 38
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.067 0.13 -9999 0 -0.48 38 38
IL1 beta fragment/IL1R1/IL1RAP -0.078 0.15 -9999 0 -0.53 39 39
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAPK8 0.021 0.11 -9999 0 -0.51 17 17
IRAK1 0.023 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.045 0.12 -9999 0 -0.63 11 11
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
TRAF6 0.01 0.054 -9999 0 -0.82 2 2
PI3K -0.004 0.049 -9999 0 -0.63 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.003 0.088 -9999 0 -0.34 8 8
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.078 0.15 -9999 0 -0.53 39 39
IL1 beta/IL1R2 -0.1 0.23 -9999 0 -0.61 74 74
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.028 -9999 0 -0.44 2 2
NF kappa B1 p50/RelA -0.058 0.12 -9999 0 -0.55 8 8
IRAK3 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.07 0.14 -9999 0 -0.48 44 44
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.016 0.1 -9999 0 -0.34 38 38
IL1 alpha/IL1R1/IL1RAP -0.085 0.16 -9999 0 -0.55 41 41
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.013 0 -9999 0 -10000 0 0
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.022 0.035 -9999 0 -0.47 2 2
IL1RAP -0.073 0.14 -9999 0 -0.31 128 128
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.054 0.12 -9999 0 -0.5 12 12
CASP1 0.008 0.059 -9999 0 -0.52 5 5
IL1RN/IL1R2 -0.11 0.22 -9999 0 -0.63 61 61
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.07 0.14 -9999 0 -0.5 39 39
TMEM189-UBE2V1 0.004 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.002 0.081 -9999 0 -0.34 4 4
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
IL1RN -0.055 0.17 -9999 0 -0.38 85 85
TRAF6/TAK1/TAB1/TAB2 -0.002 0.03 -9999 0 -0.46 2 2
MAP2K6 0.022 0.074 -9999 0 -0.44 12 12
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.065 0.082 -10000 0 -0.34 22 22
NT3 (dimer)/TRKC -0.09 0.19 -10000 0 -0.68 40 40
NT3 (dimer)/TRKB -0.086 0.18 -10000 0 -0.58 50 50
SHC/Grb2/SOS1/GAB1/PI3K 0.038 0.029 -10000 0 -0.33 3 3
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.013 0.14 -10000 0 -0.6 21 21
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 -0.002 0.061 -10000 0 -0.31 18 18
NTRK2 0.005 0.084 -10000 0 -0.82 5 5
NTRK3 -0.056 0.17 -10000 0 -0.39 84 84
NT-4/5 (dimer)/TRKB -0.068 0.16 -10000 0 -0.58 40 40
neuron apoptosis 0.04 0.092 0.42 15 -10000 0 15
SHC 2-3/Grb2 -0.043 0.1 -10000 0 -0.46 15 15
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.03 0.092 -10000 0 -0.64 6 6
SHC3 -0.047 0.1 -10000 0 -0.55 12 12
STAT3 (dimer) 0.018 0.024 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.087 0.18 -10000 0 -0.58 45 45
RIN/GDP -0.009 0.063 -10000 0 -0.28 2 2
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.032 0.092 -10000 0 -0.44 19 19
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.026 0.044 -10000 0 -10000 0 0
MAGED1 0.013 0 -10000 0 -10000 0 0
PTPN11 0.012 0.038 -10000 0 -0.82 1 1
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.02 0.15 -10000 0 -0.64 25 25
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.019 0.082 -10000 0 -0.55 9 9
TRKA/NEDD4-2 -0.007 0.038 -10000 0 -10000 0 0
ELMO1 -0.31 0.41 -10000 0 -0.82 189 189
RhoG/GTP/ELMO1/DOCK1 -0.22 0.28 -10000 0 -0.56 190 190
NGF 0.006 0.07 -10000 0 -0.57 6 6
HRAS 0.012 0.021 -10000 0 -0.31 2 2
DOCK1 0.006 0.076 -10000 0 -0.82 4 4
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 0.002 0.005 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 -0.017 0.15 -10000 0 -0.8 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.2 0.23 -10000 0 -0.47 205 205
mol:GDP -0.016 0.09 -10000 0 -0.4 4 4
NGF (dimer) 0.006 0.07 -10000 0 -0.57 6 6
RhoG/GDP -0.25 0.31 -10000 0 -0.64 189 189
RIT1/GDP -0.004 0.063 -10000 0 -0.28 2 2
TIAM1 -0.17 0.16 -10000 0 -0.32 276 276
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.022 0.11 -10000 0 -0.61 15 15
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.025 -10000 0 -0.55 1 1
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.05 0.2 -10000 0 -0.62 48 48
RAP1/GDP -0.018 0.042 -10000 0 -10000 0 0
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.013 0.14 -10000 0 -0.6 21 21
ubiquitin-dependent protein catabolic process -0.01 0.053 -10000 0 -0.55 3 3
Schwann cell development -0.042 0.032 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.042 0.017 -10000 0 -0.32 1 1
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.067 0.15 -10000 0 -0.47 52 52
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.007 0.037 -10000 0 -10000 0 0
STAT3 0.018 0.024 -10000 0 -10000 0 0
axon guidance -0.064 0.14 -10000 0 -0.45 52 52
MAPK3 0.014 0.081 -10000 0 -0.5 9 9
MAPK1 0.014 0.081 -10000 0 -0.5 9 9
CDC42/GDP -0.004 0.063 -10000 0 -0.28 2 2
NTF3 -0.05 0.2 -10000 0 -0.62 48 48
NTF4 -0.02 0.16 -10000 0 -0.64 25 25
NGF (dimer)/TRKA/FAIM -0.01 0.053 -10000 0 -0.55 3 3
PI3K -0.004 0.049 -10000 0 -0.63 3 3
FRS3 0.013 0 -10000 0 -10000 0 0
FAIM 0.013 0 -10000 0 -10000 0 0
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.13 0.11 -10000 0 -0.48 27 27
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.053 0.18 -10000 0 -0.59 39 39
RGS19 0.013 0 -10000 0 -10000 0 0
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.048 -10000 0 -0.42 1 1
Rac1/GDP -0.004 0.063 -10000 0 -0.28 2 2
NGF (dimer)/TRKA/GRIT -0.011 0.055 -10000 0 -0.56 3 3
neuron projection morphogenesis 0 0.095 -10000 0 -0.52 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.01 0.053 -10000 0 -0.55 3 3
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.062 0.19 -10000 0 -0.42 84 84
NGF (dimer)/TRKA/GIPC/GAIP 0.019 0.079 -10000 0 -0.35 19 19
RAS family/GTP/PI3K 0.03 0.032 -10000 0 -0.37 3 3
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.021 -10000 0 -0.46 1 1
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.057 -10000 0 -0.61 3 3
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.007 0.038 -10000 0 -10000 0 0
SQSTM1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.02 0.1 -10000 0 -0.56 15 15
NGF (dimer)/TRKA/p62/Atypical PKCs -0.008 0.043 -10000 0 -0.47 3 3
MATK -0.002 0.1 -10000 0 -0.82 6 6
NEDD4L 0.013 0 -10000 0 -10000 0 0
RAS family/GDP -0.015 0.042 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.036 0.099 -10000 0 -0.45 23 23
Rac1/GTP -0.19 0.15 -10000 0 -0.35 193 193
FRS2 family/SHP2/CRK family -0.001 0.021 -10000 0 -0.46 1 1
FOXM1 transcription factor network

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
NFATC3 0.046 0.35 -9999 0 -0.92 14 14
PLK1 0.043 0.07 -9999 0 -10000 0 0
BIRC5 0.024 0.12 -9999 0 -1.6 1 1
HSPA1B 0.045 0.35 -9999 0 -0.92 14 14
MAP2K1 0.032 0.038 -9999 0 -10000 0 0
BRCA2 0.04 0.36 -9999 0 -0.98 17 17
FOXM1 0.034 0.39 -9999 0 -0.99 22 22
XRCC1 0.046 0.35 -9999 0 -0.92 14 14
FOXM1B/p19 -0.098 0.31 -9999 0 -0.87 30 30
Cyclin D1/CDK4 0.033 0.34 -9999 0 -0.86 14 14
CDC2 0.039 0.37 -9999 0 -0.88 22 22
TGFA 0.016 0.35 -9999 0 -0.85 17 17
SKP2 0.038 0.37 -9999 0 -0.98 17 17
CCNE1 0.016 0.01 -9999 0 -10000 0 0
CKS1B 0.046 0.35 -9999 0 -0.92 14 14
RB1 -0.054 0.11 -9999 0 -1.2 1 1
FOXM1C/SP1 0.03 0.37 -9999 0 -0.97 21 21
AURKB -0.004 0.12 -9999 0 -10000 0 0
CENPF 0.04 0.36 -9999 0 -0.95 14 14
CDK4 0.019 0.015 -9999 0 -10000 0 0
MYC 0.038 0.36 -9999 0 -0.92 21 21
CHEK2 0.032 0.038 -9999 0 -10000 0 0
ONECUT1 0.029 0.35 -9999 0 -0.88 17 17
CDKN2A -0.13 0.16 -9999 0 -0.32 169 169
LAMA4 0.046 0.35 -9999 0 -0.92 14 14
FOXM1B/HNF6 0.022 0.37 -9999 0 -1 17 17
FOS -0.19 0.66 -9999 0 -1.2 130 130
SP1 0.014 0.005 -9999 0 -10000 0 0
CDC25B 0.045 0.35 -9999 0 -0.92 14 14
response to radiation 0.015 0.035 -9999 0 -10000 0 0
CENPB 0.046 0.35 -9999 0 -0.92 14 14
CENPA 0.033 0.37 -9999 0 -0.96 19 19
NEK2 0.036 0.36 -9999 0 -0.94 17 17
HIST1H2BA 0.037 0.35 -9999 0 -0.92 14 14
CCNA2 0.01 0.047 -9999 0 -0.33 9 9
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.033 0.38 -9999 0 -1 14 14
CCNB2 0.042 0.36 -9999 0 -0.95 14 14
CCNB1 0.041 0.37 -9999 0 -0.96 14 14
ETV5 0.045 0.35 -9999 0 -0.92 15 15
ESR1 -0.005 0.44 -9999 0 -1.1 36 36
CCND1 0.035 0.34 -9999 0 -0.88 14 14
GSK3A 0.03 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.036 0.05 -9999 0 -10000 0 0
CDK2 0.016 0.01 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.017 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.13 0.23 -9999 0 -0.88 22 22
GAS1 -0.13 0.62 -9999 0 -1.2 105 105
MMP2 0.036 0.38 -9999 0 -1.1 17 17
RB1/FOXM1C 0.043 0.34 -9999 0 -0.93 14 14
CREBBP 0.013 0 -9999 0 -10000 0 0
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.013 0.093 -10000 0 -0.35 5 5
epithelial cell differentiation -0.048 0.1 -10000 0 -0.47 11 11
ITCH 0.024 0.02 -10000 0 -10000 0 0
WWP1 0 0.079 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
EGFR 0.006 0.076 -10000 0 -0.82 4 4
PRL 0.001 0.015 -10000 0 -0.31 1 1
neuron projection morphogenesis 0.003 0.14 -10000 0 -0.51 10 10
PTPRZ1 -0.016 0.13 -10000 0 -0.82 11 11
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.059 0.13 -10000 0 -0.45 47 47
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.044 0.17 -10000 0 -0.53 48 48
ADAM17 0.02 0.058 -10000 0 -0.82 2 2
ErbB4/ErbB4 -0.01 0.1 -10000 0 -0.52 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.044 0.17 -10000 0 -0.56 37 37
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.068 0.15 -10000 0 -0.5 47 47
GRIN2B -0.029 0.16 -10000 0 -0.47 47 47
ErbB4/ErbB2/betacellulin -0.036 0.11 -10000 0 -0.63 13 13
STAT1 0.006 0.049 -10000 0 -0.31 11 11
HBEGF -0.003 0.072 -10000 0 -0.31 25 25
PRLR -0.047 0.2 -10000 0 -0.61 47 47
E4ICDs/ETO2 -0.005 0.091 -10000 0 -0.57 2 2
axon guidance -0.001 0.087 -10000 0 -0.44 3 3
NEDD4 0.02 0.057 -10000 0 -0.81 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.045 0.15 -10000 0 -0.64 27 27
CBFA2T3 0.011 0.041 -10000 0 -0.57 2 2
ErbB4/ErbB2/HBEGF -0.029 0.061 -10000 0 -0.58 2 2
MAPK3 -0.006 0.15 -10000 0 -0.53 11 11
STAT1 (dimer) -0.007 0.09 -10000 0 -0.45 1 1
MAPK1 -0.006 0.15 -10000 0 -0.53 11 11
JAK2 0.012 0.038 -10000 0 -0.82 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.068 0.15 -10000 0 -0.5 47 47
NRG1 -0.036 0.2 -10000 0 -0.65 47 47
NRG3 -0.049 0.22 -10000 0 -0.82 36 36
NRG2 -0.082 0.26 -10000 0 -0.8 57 57
NRG4 0.007 0.039 -10000 0 -0.31 7 7
heart development -0.001 0.087 -10000 0 -0.44 3 3
neural crest cell migration -0.034 0.16 -10000 0 -0.49 47 47
ERBB2 0.028 0.043 -10000 0 -0.62 2 2
WWOX/E4ICDs -0.005 0.093 -10000 0 -0.95 1 1
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.036 0.085 -10000 0 -0.66 4 4
apoptosis 0.057 0.14 0.46 37 -10000 0 37
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.066 0.19 -10000 0 -0.56 55 55
ErbB4/ErbB2/epiregulin -0.078 0.087 -10000 0 -0.55 3 3
ErbB4/ErbB4/betacellulin/betacellulin -0.018 0.13 -10000 0 -0.64 14 14
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.061 0.12 -10000 0 -0.47 28 28
MDM2 0.001 0.087 -10000 0 -0.46 1 1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.063 0.15 -10000 0 -0.5 47 47
STAT5A 0.007 0.082 -10000 0 -0.44 2 2
ErbB4/EGFR/neuregulin 1 beta -0.072 0.16 -10000 0 -0.51 50 50
DLG4 0.013 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.032 0.063 -10000 0 -0.43 1 1
STAT5A (dimer) -0.05 0.11 -10000 0 -0.51 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.006 0.08 -10000 0 -0.44 2 2
LRIG1 0 0.11 -10000 0 -0.82 8 8
EREG -0.14 0.16 -10000 0 -0.31 225 225
BTC -0.009 0.14 -10000 0 -0.82 13 13
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.001 0.087 -10000 0 -0.44 3 3
ERBB4 -0.01 0.1 -10000 0 -0.52 1 1
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 -0.01 0.02 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.025 0.057 -10000 0 -0.51 2 2
glial cell differentiation 0.032 0.063 0.42 1 -10000 0 1
WWOX 0.012 0.038 -10000 0 -0.82 1 1
cell proliferation -0.023 0.17 -10000 0 -0.46 54 54
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0.015 -9999 0 -0.31 1 1
LAT2 -0.019 0.1 -9999 0 -0.38 5 5
AP1 -0.2 0.28 -9999 0 -0.63 127 127
mol:PIP3 -0.017 0.15 -9999 0 -0.52 14 14
IKBKB 0.002 0.093 -9999 0 -0.29 12 12
AKT1 -0.018 0.14 -9999 0 -0.59 6 6
IKBKG 0.002 0.093 -9999 0 -0.29 12 12
MS4A2 -0.066 0.14 -9999 0 -0.32 113 113
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.83 3 3
MAP3K1 0.01 0.1 -9999 0 -0.46 7 7
mol:Ca2+ -0.009 0.12 -9999 0 -0.38 14 14
LYN 0.01 0.007 -9999 0 -10000 0 0
CBLB -0.011 0.09 -9999 0 -0.38 2 2
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.081 0.18 -9999 0 -0.5 78 78
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D -0.003 0.071 -9999 0 -0.31 24 24
PLD2 -0.05 0.15 -9999 0 -0.45 42 42
PTPN13 -0.002 0.1 -9999 0 -0.59 5 5
PTPN11 0.011 0.04 -9999 0 -0.86 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.018 0.1 -9999 0 -0.37 4 4
SYK 0.01 0.007 -9999 0 -10000 0 0
GRB2 0.013 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.064 0.13 -9999 0 -0.54 14 14
LAT -0.015 0.1 -9999 0 -0.43 8 8
PAK2 0.001 0.11 -9999 0 -0.51 8 8
NFATC2 -0.15 0.28 -9999 0 -0.76 83 83
HRAS -0.008 0.12 -9999 0 -0.56 8 8
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.031 0.017 -9999 0 -10000 0 0
Fc epsilon R1 -0.1 0.17 -9999 0 -0.51 54 54
Antigen/IgE/Fc epsilon R1 -0.092 0.16 -9999 0 -0.49 48 48
mol:GDP -0.017 0.13 -9999 0 -0.54 12 12
JUN -0.17 0.35 -9999 0 -0.82 109 109
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
FOS -0.21 0.37 -9999 0 -0.82 129 129
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.045 0.08 -9999 0 -0.38 4 4
CHUK 0.002 0.093 -9999 0 -0.29 11 11
KLRG1 -0.023 0.11 -9999 0 -0.41 14 14
VAV1 -0.023 0.12 -9999 0 -0.49 9 9
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.011 0.09 -9999 0 -0.38 2 2
negative regulation of mast cell degranulation -0.021 0.11 -9999 0 -0.4 11 11
BTK -0.048 0.11 -9999 0 -0.61 11 11
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.049 0.19 -9999 0 -0.53 44 44
GAB2/PI3K/SHP2 -0.067 0.13 -9999 0 -0.66 6 6
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.019 0.096 -9999 0 -0.3 22 22
RAF1 0.018 0.021 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.2 -9999 0 -0.58 57 57
FCER1G -0.009 0.083 -9999 0 -0.32 32 32
FCER1A -0.078 0.23 -9999 0 -0.56 76 76
Antigen/IgE/Fc epsilon R1/Fyn -0.082 0.14 -9999 0 -0.48 42 42
MAPK3 0.029 0.017 -9999 0 -10000 0 0
MAPK1 0.029 0.017 -9999 0 -10000 0 0
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAPK8 0.007 0.1 -9999 0 -0.69 9 9
DUSP1 -0.12 0.31 -9999 0 -0.82 78 78
NF-kappa-B/RelA -0.019 0.044 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.005 0.084 -9999 0 -0.38 1 1
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.043 0.1 -9999 0 -0.63 7 7
FER -0.014 0.099 -9999 0 -0.45 6 6
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.074 0.18 -9999 0 -0.53 61 61
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.013 0.13 -9999 0 -0.57 10 10
cytokine secretion -0.014 0.032 -9999 0 -10000 0 0
SPHK1 -0.015 0.094 -9999 0 -0.39 4 4
PTK2 -0.006 0.086 -9999 0 -0.39 1 1
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.067 0.14 -9999 0 -0.56 12 12
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.012 0.15 -9999 0 -0.5 13 13
MAP2K2 0.025 0.018 -9999 0 -10000 0 0
MAP2K1 0.025 0.018 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.048 0.095 -9999 0 -0.45 11 11
MAP2K4 0.021 0.008 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.11 0.21 -9999 0 -0.62 54 54
mol:Choline -0.049 0.15 -9999 0 -0.44 42 42
SHC/Grb2/SOS1 -0.032 0.066 -9999 0 -0.39 1 1
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.013 0 -9999 0 -10000 0 0
PXN 0.003 0.082 -9999 0 -0.36 1 1
HCLS1 -0.013 0.094 -9999 0 -0.4 4 4
PRKCB -0.011 0.12 -9999 0 -0.38 21 21
FCGR2B -0.029 0.18 -9999 0 -0.82 23 23
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.021 0.11 -9999 0 -0.4 11 11
LCP2 0.009 0.039 -9999 0 -0.32 7 7
PLA2G4A -0.042 0.16 -9999 0 -0.52 34 34
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.049 0.15 -9999 0 -0.44 42 42
IKK complex 0.018 0.076 -9999 0 -0.23 2 2
WIPF1 0.013 0 -9999 0 -10000 0 0
TCGA08_rtk_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
PDGFRA -0.25 0.39 -10000 0 -0.82 154 154
HRAS 0.012 0.021 -10000 0 -0.31 2 2
EGFR 0.006 0.076 -10000 0 -0.82 4 4
AKT 0.018 0.025 0.21 1 -10000 0 1
FOXO3 0.013 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
AKT3 0.013 0 -10000 0 -10000 0 0
FOXO4 0.013 0 -10000 0 -10000 0 0
MET -0.11 0.16 -10000 0 -0.31 180 180
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
PIK3CB 0.013 0 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
PIK3CG -0.011 0.13 -10000 0 -0.67 17 17
PIK3R3 0.012 0.038 -10000 0 -0.82 1 1
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.013 0 -10000 0 -10000 0 0
RAS -0.061 0.099 -10000 0 -0.26 43 43
ERBB2 0.013 0 -10000 0 -10000 0 0
proliferation/survival/translation -0.024 0.024 0.19 1 -0.17 1 2
PI3K -0.041 0.096 0.23 1 -0.22 49 50
PIK3R1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
FOXO 0.024 0.026 0.2 1 -10000 0 1
AKT2 0.013 0 -10000 0 -10000 0 0
PTEN 0.012 0.038 -10000 0 -0.82 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.004 0.076 -10000 0 -0.36 7 7
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.013 0 -10000 0 -10000 0 0
AKT2 0.013 0 -10000 0 -10000 0 0
STXBP4 0.012 0.038 -10000 0 -0.82 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.041 0.077 0.26 2 -10000 0 2
YWHAZ 0.013 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.065 0.22 -10000 0 -0.63 66 66
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
SNARE/Synip -0.001 0.025 -10000 0 -0.55 1 1
YWHAG 0.013 0 -10000 0 -10000 0 0
ASIP -0.03 0.11 -10000 0 -0.31 62 62
PRKCI 0.013 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.013 0 -10000 0 -10000 0 0
GYS1 0.034 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
TRIP10 0.013 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 -0.038 0.1 -10000 0 -0.26 56 56
VAMP2 0.013 0 -10000 0 -10000 0 0
SLC2A4 0.042 0.081 0.26 2 -10000 0 2
STX4 0.013 0 -10000 0 -10000 0 0
GSK3B 0.028 0 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 312 312
LNPEP -0.014 0.15 -10000 0 -0.82 16 16
YWHAE 0.013 0 -10000 0 -10000 0 0
Aurora B signaling

Figure S71.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S71.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0 0.078 -9999 0 -10000 0 0
STMN1 -0.021 0.094 -9999 0 -0.39 1 1
Aurora B/RasGAP/Survivin -0.025 0.11 -9999 0 -0.55 1 1
Chromosomal passenger complex/Cul3 protein complex 0.007 0.071 -9999 0 -0.29 14 14
BIRC5 -0.017 0.1 -9999 0 -0.33 42 42
DES -0.38 0.3 -9999 0 -0.61 298 298
Aurora C/Aurora B/INCENP -0.016 0.088 -9999 0 -0.48 4 4
Aurora B/TACC1 -0.021 0.081 -9999 0 -0.71 1 1
Aurora B/PP2A -0.025 0.091 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.005 0.026 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.05 0.15 -9999 0 -0.39 60 60
Cul3 protein complex -0.018 0.088 -9999 0 -0.55 12 12
KIF2C 0 0.042 -9999 0 -0.16 1 1
PEBP1 0.011 0.005 -9999 0 -10000 0 0
KIF20A -0.043 0.12 -9999 0 -0.31 80 80
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.025 0.091 -9999 0 -10000 0 0
SEPT1 0.008 0.042 -9999 0 -0.31 8 8
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.007 0.045 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.002 -9999 0 -10000 0 0
H3F3B -0.007 0.055 -9999 0 -10000 0 0
AURKB -0.05 0.14 -9999 0 -0.31 107 107
AURKC -0.001 0.067 -9999 0 -0.31 21 21
CDCA8 0.01 0.027 -9999 0 -0.33 3 3
cytokinesis -0.066 0.082 -9999 0 -0.43 5 5
Aurora B/Septin1 -0.027 0.1 -9999 0 -0.44 7 7
AURKA 0.012 0.002 -9999 0 -10000 0 0
INCENP 0.009 0.055 -9999 0 -0.84 2 2
KLHL13 -0.017 0.14 -9999 0 -0.55 26 26
BUB1 -0.1 0.16 -9999 0 -0.32 170 170
hSgo1/Aurora B/Survivin -0.026 0.12 -9999 0 -0.44 18 18
EVI5 0.014 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.031 0.072 -9999 0 -0.36 3 3
SGOL1 0.001 0.062 -9999 0 -0.31 18 18
CENPA -0.008 0.069 -9999 0 -0.24 6 6
NCAPG -0.018 0.097 -9999 0 -0.31 47 47
Aurora B/HC8 Proteasome -0.025 0.091 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.025 0.091 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.034 0.12 -9999 0 -0.31 71 71
NPM1 -0.012 0.048 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
KLHL9 0.013 0 -9999 0 -10000 0 0
mitotic prometaphase -0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.025 0.091 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.035 0.08 -9999 0 -0.35 18 18
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.012 0.048 -9999 0 -10000 0 0
MYLK -0.007 0.055 -9999 0 -10000 0 0
KIF23 -0.004 0.073 -9999 0 -0.32 25 25
VIM -0.02 0.093 -9999 0 -10000 0 0
RACGAP1 0.013 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.012 0.048 -9999 0 -10000 0 0
Chromosomal passenger complex -0.013 0.083 -9999 0 -0.26 18 18
Chromosomal passenger complex/EVI5 0.011 0.12 -9999 0 -0.48 6 6
TACC1 0.012 0.038 -9999 0 -0.82 1 1
PPP2R5D 0.013 0 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.042 0.12 -9999 0 -0.42 47 47
Syndecan-3/Neurocan -0.035 0.12 -9999 0 -0.47 35 35
POMC -0.16 0.34 -9999 0 -0.81 102 102
EGFR 0.006 0.076 -9999 0 -0.82 4 4
Syndecan-3/EGFR -0.004 0.042 -9999 0 -0.46 4 4
AGRP -0.004 0.059 -9999 0 -0.31 17 17
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.013 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.013 0 -9999 0 -10000 0 0
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN -0.051 0.22 -9999 0 -0.77 39 39
long-term memory 0 0.005 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.039 0.081 -9999 0 -0.46 10 10
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0 0.009 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.008 -9999 0 -10000 0 0
MC4R 0.001 0.039 -9999 0 -0.31 7 7
SRC 0.013 0.015 -9999 0 -0.31 1 1
PTN -0.068 0.25 -9999 0 -0.81 48 48
FGFR/FGF/Syndecan-3 -0.001 0.008 -9999 0 -10000 0 0
neuron projection morphogenesis -0.07 0.15 -9999 0 -0.61 3 3
Syndecan-3/AgRP -0.005 0.023 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.006 0.025 -9999 0 -10000 0 0
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.001 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.038 0.08 -9999 0 -0.46 10 10
IL8 -0.081 0.18 -9999 0 -0.36 124 124
Syndecan-3/Fyn/Cortactin -0.001 0.006 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.007 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.13 0.26 -9999 0 -0.64 99 99
Gamma Secretase 0 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.061 0.16 -10000 0 -0.48 62 62
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.007 0.054 -10000 0 -0.21 31 31
GNB1/GNG2 -0.001 0.025 -10000 0 -0.55 1 1
GNB1 0.013 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.065 0.17 -10000 0 -0.52 61 61
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.015 0.039 0.12 61 -10000 0 61
GNAL -0.092 0.28 -10000 0 -0.82 61 61
GNG2 0.012 0.038 -10000 0 -0.82 1 1
CRH -0.013 0.079 -10000 0 -0.31 31 31
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0 0.063 -10000 0 -0.46 9 9
MAPK11 0.009 0 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.016 0.052 -9999 0 -0.55 4 4
ADCY5 -0.058 0.2 -9999 0 -0.56 65 65
ADCY6 0.016 0.052 -9999 0 -0.55 4 4
ADCY7 0.016 0.052 -9999 0 -0.55 4 4
ADCY1 0.01 0.078 -9999 0 -0.57 8 8
ADCY2 -0.04 0.18 -9999 0 -0.57 46 46
ADCY3 0.016 0.052 -9999 0 -0.55 4 4
ADCY8 -0.12 0.099 -9999 0 -0.7 4 4
PRKCE 0.007 0.059 -9999 0 -0.64 4 4
ADCY9 0.016 0.052 -9999 0 -0.55 4 4
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.056 0.1 -9999 0 -0.37 31 31
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.027 0.16 -9999 0 -0.44 64 64
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.049 0.12 -9999 0 -0.75 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.01 0.037 -9999 0 -0.65 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.024 0.061 -9999 0 -0.3 2 2
CaM/Ca2+ -0.056 0.14 -9999 0 -0.4 64 64
RAP1A 0.013 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.02 0.16 -9999 0 -0.41 64 64
AKT1 -0.002 0.15 -9999 0 -0.62 3 3
MAP2K1 -0.005 0.15 -9999 0 -0.38 63 63
MAP3K11 -0.017 0.16 -9999 0 -0.41 64 64
IFNGR1 0.009 0.014 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.024 0.067 -9999 0 -0.64 1 1
Rap1/GTP -0.041 0.1 -9999 0 -0.6 1 1
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.063 0.16 -9999 0 -0.46 63 63
CEBPB 0.017 0.18 -9999 0 -0.82 5 5
STAT3 0.013 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.059 0.15 -9999 0 -1.1 2 2
STAT1 -0.019 0.16 -9999 0 -0.41 64 64
CALM1 0.013 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.1 0.28 -9999 0 -0.72 78 78
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
STAT1 (dimer)/PIAS1 -0.01 0.15 -9999 0 -0.48 5 5
CEBPB/PTGES2/Cbp/p300 -0.035 0.082 -9999 0 -0.44 5 5
mol:Ca2+ -0.06 0.15 -9999 0 -0.43 64 64
MAPK3 0.01 0.14 -9999 0 -0.53 5 5
STAT1 (dimer) -0.03 0.08 -9999 0 -0.42 2 2
MAPK1 0.01 0.14 -9999 0 -0.53 5 5
JAK2 0.008 0.042 -9999 0 -0.88 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.009 0.014 -9999 0 -10000 0 0
CAMK2D 0.013 0 -9999 0 -10000 0 0
DAPK1 0.015 0.18 -9999 0 -0.66 24 24
SMAD7 0.041 0.056 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.05 0.12 -9999 0 -0.76 1 1
PI3K -0.056 0.14 -9999 0 -0.52 8 8
IFNG -0.1 0.28 -9999 0 -0.72 78 78
apoptosis 0.013 0.13 -9999 0 -0.45 24 24
CAMK2G 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.004 0.068 -9999 0 -0.31 22 22
CAMK2B 0.005 0.084 -9999 0 -0.82 5 5
FRAP1 0 0.14 -9999 0 -0.57 3 3
PRKCD -0.002 0.15 -9999 0 -0.63 3 3
RAP1B 0.013 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.024 0.061 -9999 0 -0.3 2 2
PTPN2 0.013 0 -9999 0 -10000 0 0
EP300 0.014 0 -9999 0 -10000 0 0
IRF1 0.029 0.12 -9999 0 -0.47 2 2
STAT1 (dimer)/PIASy -0.054 0.13 -9999 0 -0.48 5 5
SOCS1 0.001 0.074 -9999 0 -1.5 1 1
mol:GDP -0.048 0.12 -9999 0 -0.71 1 1
CASP1 0.039 0.062 -9999 0 -0.35 2 2
PTGES2 0.013 0 -9999 0 -10000 0 0
IRF9 0.042 0.058 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.055 0.14 -9999 0 -0.5 8 8
RAP1/GDP -0.041 0.1 -9999 0 -0.6 1 1
CBL -0.017 0.16 -9999 0 -0.41 64 64
MAP3K1 -0.016 0.16 -9999 0 -0.41 64 64
PIAS1 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.024 0.061 -9999 0 -0.3 2 2
PTPN11 -0.027 0.16 -9999 0 -0.43 64 64
CREBBP 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.014 0 -9999 0 -10000 0 0
ELF1 -0.014 0.12 -9999 0 -0.44 30 30
CCNA2 0.007 0.044 -9999 0 -0.31 9 9
PIK3CA 0.009 0.066 -9999 0 -0.82 3 3
JAK3 -0.067 0.14 -9999 0 -0.31 120 120
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.018 0.15 -9999 0 -0.56 19 19
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.022 0 -9999 0 -10000 0 0
IL2RA -0.043 0.25 -9999 0 -0.98 30 30
IL2RB -0.014 0.13 -9999 0 -0.51 26 26
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.046 0.19 -9999 0 -0.55 52 52
G1/S transition of mitotic cell cycle 0.039 0.054 -9999 0 -0.59 3 3
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
CCND2 0.033 0 -9999 0 -10000 0 0
LCK -0.009 0.11 -9999 0 -0.44 25 25
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.005 0.006 -9999 0 -10000 0 0
CDK6 0.008 0.066 -9999 0 -0.82 3 3
CCND3 0.028 0.13 -9999 0 -0.64 7 7
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.16 0.34 -9999 0 -0.82 102 102
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.026 -9999 0 -0.31 3 3
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.023 -9999 0 -10000 0 0
HIF1A 0.022 0.024 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.004 0.041 -9999 0 -0.51 3 3
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.13 0.16 -9999 0 -0.31 208 208
ARNT/IPAS -0.13 0.26 -9999 0 -0.63 102 102
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.023 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.012 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.023 -9999 0 -10000 0 0
PHD1-3/OS9 -0.018 0.088 -9999 0 -0.54 12 12
HIF1A/RACK1/Elongin B/Elongin C -0.003 0.017 -9999 0 -10000 0 0
VHL 0.008 0.066 -9999 0 -0.82 3 3
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.029 0.023 -9999 0 -10000 0 0
EGLN3 -0.017 0.14 -9999 0 -0.51 28 28
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.01 0.054 -9999 0 -0.82 2 2
TP53 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.051 -9999 0 -0.6 3 3
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.032 0.074 -9999 0 -0.29 1 1
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.003 0.11 0.57 14 -10000 0 14
PI3K Class IB/PDE3B -0.003 0.11 -10000 0 -0.57 14 14
PDE3B -0.003 0.11 -10000 0 -0.57 14 14
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.018 0.12 -10000 0 -0.79 11 11
HDAC1 0.002 0.009 -10000 0 -10000 0 0
AES 0.012 0.002 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 0.001 0.1 -10000 0 -0.82 7 7
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.007 0.065 -10000 0 -0.82 3 3
AP1 -0.14 0.26 -10000 0 -0.49 162 162
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 -0.006 0.12 -10000 0 -0.82 11 11
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.054 -10000 0 -0.34 1 1
NICD/RBPSUH -0.017 0.11 -10000 0 -0.74 11 11
WIF1 -0.033 0.1 -10000 0 -10000 0 0
NOTCH1 -0.017 0.11 -10000 0 -0.77 11 11
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.01 0.085 -10000 0 -0.31 35 35
DKK1 -0.043 0.13 -10000 0 -0.82 2 2
beta catenin/beta TrCP1 0.036 0.037 -10000 0 -10000 0 0
APH1B 0.013 0 -10000 0 -10000 0 0
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0 0.036 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.024 0.037 -10000 0 -0.35 2 2
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.21 0.37 -10000 0 -0.82 129 129
JUN -0.17 0.35 -10000 0 -0.82 109 109
MAP3K7 0.012 0.003 -10000 0 -10000 0 0
CTNNB1 0.029 0.04 0.24 13 -10000 0 13
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.037 0.12 -10000 0 -0.56 20 20
HNF1A 0.012 0.002 -10000 0 -10000 0 0
CTBP1 0.012 0.002 -10000 0 -10000 0 0
MYC -0.015 0.25 -10000 0 -1.5 13 13
NKD1 -0.013 0.14 -10000 0 -0.73 17 17
FZD1 0.013 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.023 0.12 -10000 0 -0.62 18 18
apoptosis -0.14 0.26 -10000 0 -0.48 162 162
Delta 1/NOTCHprecursor -0.017 0.12 -10000 0 -0.76 11 11
DLL1 0.011 0.041 -10000 0 -0.57 2 2
PPARD 0.024 0.017 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.001 0.06 -10000 0 -1.1 1 1
DVL1 0.003 0.01 -10000 0 -10000 0 0
CSNK2A1 0.014 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.003 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.039 0.081 -10000 0 -0.63 2 2
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.014 0.002 -10000 0 -10000 0 0
NLK 0.015 0.008 -10000 0 -10000 0 0
CCND1 0.019 0.043 -10000 0 -10000 0 0
WNT1 0.01 0.021 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.043 0.051 -10000 0 -0.67 1 1
DKK2 -0.028 0.17 -10000 0 -0.65 30 30
NOTCH1 precursor/DVL1 -0.012 0.097 -10000 0 -0.65 11 11
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.024 0.12 -10000 0 -0.64 18 18
PPP2R5D 0.011 0.063 0.37 14 -10000 0 14
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.016 0.044 -10000 0 -10000 0 0
RBPJ 0.013 0.015 -10000 0 -0.31 1 1
CREBBP 0.017 0.004 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.024 0 -10000 0 -10000 0 0
MAP4K4 -0.003 0.14 -10000 0 -0.7 11 11
BAG4 0.012 0.038 -10000 0 -0.82 1 1
PKC zeta/ceramide -0.018 0.04 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.036 0.19 -10000 0 -0.68 35 35
BAX -0.005 0.019 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.023 0.008 -10000 0 -10000 0 0
BAD -0.017 0.04 -10000 0 -10000 0 0
SMPD1 -0.006 0.096 -10000 0 -0.26 58 58
RB1 -0.018 0.046 -10000 0 -0.5 1 1
FADD/Caspase 8 0.009 0.14 -10000 0 -0.66 11 11
MAP2K4 -0.009 0.038 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.011 0.05 -10000 0 -0.52 2 2
EGF -0.11 0.29 -10000 0 -0.78 74 74
mol:ceramide -0.028 0.043 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.023 0.03 -10000 0 -0.63 1 1
ASAH1 0.012 0.038 -10000 0 -0.82 1 1
negative regulation of cell cycle -0.018 0.045 -10000 0 -0.49 1 1
cell proliferation -0.1 0.16 -10000 0 -0.39 114 114
BID -0.017 0.093 -10000 0 -0.4 11 11
MAP3K1 -0.017 0.04 -10000 0 -10000 0 0
EIF2A 0 0.036 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 0.002 0.047 -10000 0 -0.47 2 2
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.002 0.047 -10000 0 -0.47 2 2
Cathepsin D/ceramide -0.018 0.04 -10000 0 -10000 0 0
FADD -0.003 0.14 -10000 0 -0.7 11 11
KSR1 -0.019 0.053 -10000 0 -0.55 2 2
MAPK8 -0.009 0.056 -10000 0 -0.31 9 9
PRKRA -0.017 0.04 -10000 0 -10000 0 0
PDGFA 0.013 0 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.18 0.35 -10000 0 -0.8 119 119
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.042 -10000 0 -10000 0 0
CTSD 0.013 0.015 -10000 0 -0.31 1 1
regulation of nitric oxide biosynthetic process -0.001 0.029 -10000 0 -0.63 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.087 0.19 -10000 0 -0.42 114 114
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.023 0.03 -10000 0 -0.63 1 1
RelA/NF kappa B1 -0.001 0.029 -10000 0 -0.63 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.013 0.15 -10000 0 -0.75 11 11
TNFR1A/BAG4/TNF-alpha -0.068 0.18 -10000 0 -0.55 59 59
mol:Sphingosine-1-phosphate 0.024 0 -10000 0 -10000 0 0
MAP2K1 -0.002 0.048 -10000 0 -0.49 2 2
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.004 0.051 0.18 26 -10000 0 26
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
TNFR1A/BAG4 -0.001 0.029 -10000 0 -0.63 1 1
EIF2AK2 -0.009 0.038 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.067 0.18 -10000 0 -0.55 58 58
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.015 0.08 -10000 0 -0.33 11 11
MAP2K2 -0.002 0.048 -10000 0 -0.49 2 2
SMPD3 -0.012 0.12 -10000 0 -0.3 63 63
TNF -0.091 0.27 -10000 0 -0.78 64 64
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.022 0.11 0.28 68 -10000 0 68
NF kappa B1/RelA/I kappa B alpha -0.001 0.021 -10000 0 -0.46 1 1
AIFM1 0.003 0.051 0.18 26 -10000 0 26
BCL2 -0.047 0.22 -10000 0 -0.82 35 35
Signaling events mediated by HDAC Class III

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
EP300 0.013 0 -10000 0 -10000 0 0
HDAC4 0.013 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.021 0.03 0.63 1 -10000 0 1
CDKN1A -0.007 0.039 -10000 0 -10000 0 0
KAT2B 0.013 0 -10000 0 -10000 0 0
BAX 0.013 0.015 -10000 0 -0.31 1 1
FOXO3 0 0.007 -10000 0 -10000 0 0
FOXO1 0.013 0 -10000 0 -10000 0 0
FOXO4 0.024 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT 0.006 0.03 -10000 0 -0.31 4 4
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.011 0.02 -10000 0 -10000 0 0
PPARGC1A -0.35 0.42 -10000 0 -0.82 211 211
FHL2 -0.054 0.23 -10000 0 -0.82 39 39
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.001 0.031 -10000 0 -0.63 1 1
HIST2H4A 0.021 0.03 -10000 0 -0.63 1 1
SIRT1/FOXO3a 0.001 0.027 -10000 0 -0.56 1 1
SIRT1 0.001 0.04 -10000 0 -0.82 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.001 0.028 -10000 0 -0.55 1 1
SIRT1/Histone H1b -0.005 0.051 -10000 0 -0.33 10 10
apoptosis -0.001 0.028 0.54 1 -10000 0 1
SIRT1/PGC1A -0.24 0.28 -10000 0 -0.56 211 211
p53/SIRT1 0.005 0.045 -10000 0 -0.63 1 1
SIRT1/FOXO4 0.001 0.028 -10000 0 -0.53 1 1
FOXO1/FHL2/SIRT1 -0.039 0.14 -10000 0 -0.51 40 40
HIST1H1E 0.015 0.054 -10000 0 -0.37 9 9
SIRT1/p300 0.001 0.031 -10000 0 -0.63 1 1
muscle cell differentiation 0 0.031 0.55 1 -10000 0 1
TP53 0.003 0.013 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.001 0.029 -10000 0 -0.55 1 1
CREBBP 0.013 0 -10000 0 -10000 0 0
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.001 0.036 -10000 0 -0.63 1 1
ACSS2 0.021 0.03 -10000 0 -0.63 1 1
SIRT1/PCAF/MYOD 0 0.031 -10000 0 -0.56 1 1
IL2 signaling events mediated by PI3K

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
BCL2L1 0.011 0.12 -10000 0 -0.88 2 2
UGCG -0.04 0.17 -10000 0 -0.82 21 21
AKT1/mTOR/p70S6K/Hsp90/TERT 0.02 0.13 -10000 0 -0.41 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.019 0.17 -10000 0 -0.8 21 21
mol:DAG 0 0.004 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.059 0.14 -10000 0 -0.46 35 35
FRAP1 0.002 0.2 -10000 0 -0.49 50 50
FOXO3 0.02 0.16 -10000 0 -0.6 18 18
AKT1 0.01 0.18 -10000 0 -0.59 24 24
GAB2 0.013 0.004 -10000 0 -10000 0 0
SMPD1 -0.005 0.023 -10000 0 -10000 0 0
SGMS1 -0.005 0.023 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.046 -10000 0 -0.56 3 3
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.001 0.16 -10000 0 -0.47 31 31
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.02 0.053 -10000 0 -0.64 3 3
RPS6KB1 0.017 0.041 -10000 0 -10000 0 0
mol:sphingomyelin 0 0.004 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -0.012 5 5
JAK3 -0.065 0.14 -10000 0 -0.31 120 120
PIK3R1 0.015 0.005 -10000 0 -10000 0 0
JAK1 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.012 0.038 -10000 0 -0.82 1 1
MYC 0.007 0.22 -10000 0 -0.94 18 18
MYB -0.016 0.2 -10000 0 -1.3 10 10
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.008 0.16 -10000 0 -0.55 25 25
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.031 0.038 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.009 0.16 -10000 0 -0.53 25 25
Rac1/GDP 0.024 0.043 -10000 0 -0.51 3 3
T cell proliferation 0.018 0.15 -10000 0 -0.51 21 21
SHC1 0.013 0.004 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.004 0.011 -10000 0 -0.051 16 16
PRKCZ 0.017 0.15 -10000 0 -0.54 21 21
NF kappa B1 p50/RelA -0.058 0.14 -10000 0 -0.45 35 35
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.001 0.13 -10000 0 -0.6 11 11
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.047 0.2 -10000 0 -0.58 49 49
IL2RB -0.013 0.13 -10000 0 -0.51 26 26
TERT 0 0.033 -10000 0 -0.31 5 5
E2F1 -0.005 0.076 -10000 0 -0.45 10 10
SOS1 0.013 0.004 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP -0.002 0.005 0.024 16 -10000 0 16
PTPN11 0.011 0.038 -10000 0 -0.83 1 1
IL2RG -0.045 0.19 -10000 0 -0.55 52 52
actin cytoskeleton organization 0.018 0.15 -10000 0 -0.51 21 21
GRB2 0.013 0.004 -10000 0 -10000 0 0
IL2 0.007 0.007 -10000 0 -10000 0 0
PIK3CA 0.01 0.066 -10000 0 -0.83 3 3
Rac1/GTP 0.031 0.043 -10000 0 -0.49 3 3
LCK -0.008 0.11 -10000 0 -0.43 25 25
BCL2 -0.025 0.28 -10000 0 -0.82 47 47
Insulin 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
CBL/APS/CAP -0.053 0.14 -9999 0 -0.44 58 58
TC10/GTP -0.004 0.038 -9999 0 -0.42 4 4
Insulin Receptor/Insulin/IRS1/Shp2 -0.059 0.17 -9999 0 -0.52 55 55
HRAS 0.012 0.021 -9999 0 -0.31 2 2
APS homodimer 0.013 0.015 -9999 0 -0.31 1 1
GRB14 -0.011 0.14 -9999 0 -0.82 14 14
FOXO3 -0.025 0.11 -9999 0 -0.72 11 11
AKT1 -0.01 0.16 -9999 0 -0.89 2 2
INSR 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.013 0 -9999 0 -10000 0 0
SORBS1 0.006 0.076 -9999 0 -0.82 4 4
CRK 0.013 0 -9999 0 -10000 0 0
PTPN1 0.038 0 -9999 0 -10000 0 0
CAV1 -0.042 0.18 -9999 0 -0.48 68 68
CBL/APS/CAP/Crk-II/C3G -0.004 0.042 -9999 0 -0.46 4 4
Insulin Receptor/Insulin/IRS1/NCK2 -0.058 0.16 -9999 0 -0.51 55 55
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.053 0.15 -9999 0 -0.46 57 57
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.005 0.1 -9999 0 -10000 0 0
RPS6KB1 0 0.15 -9999 0 -0.76 2 2
PARD6A 0.013 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.054 0.13 -9999 0 -0.78 2 2
HRAS/GTP -0.048 0.12 -9999 0 -0.5 3 3
Insulin Receptor 0.015 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.054 0.15 -9999 0 -0.48 55 55
PRKCI -0.014 0.034 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.062 0.16 -9999 0 -0.43 71 71
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PI3K -0.054 0.15 -9999 0 -0.46 57 57
NCK2 0.013 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.014 -9999 0 -10000 0 0
AKT2 -0.01 0.16 -9999 0 -0.89 2 2
PRKCZ -0.014 0.034 -9999 0 -10000 0 0
SH2B2 0.013 0.015 -9999 0 -0.31 1 1
SHC/SHIP -0.026 0.16 -9999 0 -0.45 55 55
F2RL2 -0.081 0.16 -9999 0 -0.32 135 135
TRIP10 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.004 0.045 -9999 0 -0.5 4 4
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0 0 -9999 0 -10000 0 0
INPP5D -0.036 0.16 -9999 0 -0.49 55 55
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.027 0.16 -9999 0 -1 11 11
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
IRS1 -0.081 0.26 -9999 0 -0.82 55 55
p62DOK/RasGAP 0 0 -9999 0 -10000 0 0
INS 0.003 0 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.036 0.16 -9999 0 -0.48 55 55
GRB2 0.013 0 -9999 0 -10000 0 0
EIF4EBP1 -0.001 0.15 -9999 0 -0.64 4 4
PTPRA 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.01 0.054 -9999 0 -0.82 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.006 0.12 -9999 0 -0.33 55 55
Insulin Receptor/Insulin/IRS1 -0.059 0.16 -9999 0 -0.52 55 55
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.036 0.064 -9999 0 -0.47 3 3
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 0.013 0 -9999 0 -10000 0 0
mol:Halofuginone 0.005 0.002 -9999 0 -10000 0 0
ITGA1 0.003 0.092 -9999 0 -0.82 6 6
CDKN1A -0.013 0.088 -9999 0 -10000 0 0
PRL-3/alpha Tubulin -0.016 0.055 -9999 0 -10000 0 0
mol:Ca2+ -0.013 0.11 -9999 0 -0.65 9 9
AGT -0.019 0.13 -9999 0 -0.45 34 34
CCNA2 -0.062 0.2 -9999 0 -0.59 4 4
TUBA1B 0.013 0 -9999 0 -10000 0 0
EGR1 -0.11 0.27 -9999 0 -0.63 103 103
CDK2/Cyclin E1 0.004 0.077 -9999 0 -10000 0 0
MAPK3 0.006 0.061 -9999 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -9999 0 -10000 0 0
MAPK1 0.006 0.061 -9999 0 -10000 0 0
PTP4A1 -0.071 0.21 -9999 0 -0.48 103 103
PTP4A3 -0.013 0.089 -9999 0 -0.31 39 39
PTP4A2 0.013 0 -9999 0 -10000 0 0
ITGB1 0.006 0.061 -9999 0 -10000 0 0
SRC 0.013 0.015 -9999 0 -0.31 1 1
RAC1 -0.016 0.092 -9999 0 -0.25 13 13
Rab GGTase beta/Rab GGTase alpha 0 0 -9999 0 -10000 0 0
PRL-1/ATF-5 -0.067 0.2 -9999 0 -0.59 4 4
RABGGTA 0.013 0 -9999 0 -10000 0 0
BCAR1 0.012 0.04 -9999 0 -10000 0 0
RHOC -0.016 0.092 -9999 0 -10000 0 0
RHOA -0.016 0.092 -9999 0 -10000 0 0
cell motility -0.014 0.098 -9999 0 -0.26 13 13
PRL-1/alpha Tubulin -0.061 0.2 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin -0.024 0.09 -9999 0 -0.66 6 6
ROCK1 -0.015 0.099 -9999 0 -0.27 13 13
RABGGTB 0.013 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
mitosis -0.071 0.21 -9999 0 -0.48 103 103
ATF5 0 0.065 -9999 0 -0.31 20 20
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.02 0.14 -9999 0 -0.51 31 31
ITGA4 0.004 0.069 -9999 0 -0.41 11 11
alpha4/beta7 Integrin -0.03 0.12 -9999 0 -0.62 15 15
alpha4/beta1 Integrin -0.006 0.049 -9999 0 -0.63 2 2
Cellular roles of Anthrax toxin

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
ANTXR1 -0.004 0.12 -10000 0 -0.82 10 10
ANTXR2 0.008 0.066 -10000 0 -0.82 3 3
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.016 -10000 0 -0.1 13 13
monocyte activation -0.049 0.17 -10000 0 -0.48 62 62
MAP2K2 -0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.002 0.014 -10000 0 -10000 0 0
MAP2K7 -0.002 0.014 -10000 0 -10000 0 0
MAP2K6 -0.013 0.073 -10000 0 -0.5 10 10
CYAA 0.003 0.081 -10000 0 -0.48 13 13
MAP2K4 -0.002 0.014 -10000 0 -10000 0 0
IL1B -0.025 0.14 -10000 0 -0.47 40 40
Channel -0.014 0.083 -10000 0 -0.51 13 13
NLRP1 -0.004 0.034 -10000 0 -0.49 2 2
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.016 0.1 13 -10000 0 13
MAPK3 -0.002 0.014 -10000 0 -10000 0 0
MAPK1 -0.002 0.014 -10000 0 -10000 0 0
PGR -0.024 0.089 -10000 0 -0.47 16 16
PA/Cellular Receptors -0.015 0.089 -10000 0 -0.55 13 13
apoptosis -0.003 0.016 -10000 0 -0.1 13 13
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.004 0.08 -10000 0 -0.48 13 13
macrophage activation 0.019 0.015 -10000 0 -10000 0 0
TNF -0.091 0.27 -10000 0 -0.78 64 64
VCAM1 -0.05 0.18 -10000 0 -0.49 62 62
platelet activation -0.003 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.013 0.024 0.11 10 -10000 0 10
IL18 -0.01 0.086 -10000 0 -0.42 14 14
negative regulation of macrophage activation -0.003 0.016 -10000 0 -0.1 13 13
LEF -0.003 0.017 -10000 0 -0.1 13 13
CASP1 -0.004 0.02 -10000 0 -0.22 2 2
mol:cAMP -0.003 0.019 -10000 0 -10000 0 0
necrosis -0.003 0.016 -10000 0 -0.1 13 13
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.013 0.079 -10000 0 -0.49 13 13
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.023 0.092 -9999 0 -0.51 1 1
RAD9A 0.013 0 -9999 0 -10000 0 0
AP1 -0.28 0.45 -9999 0 -0.92 152 152
IFNAR2 0.014 0.003 -9999 0 -10000 0 0
AKT1 -0.001 0.071 -9999 0 -0.29 24 24
ER alpha/Oestrogen -0.044 0.14 -9999 0 -0.4 55 55
NFX1/SIN3/HDAC complex 0.047 0.026 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 74 74
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.007 0.011 -9999 0 -10000 0 0
TERT/c-Abl -0.035 0.068 -9999 0 -0.48 1 1
SAP18 0.014 0 -9999 0 -10000 0 0
MRN complex -0.003 0.043 -9999 0 -0.55 3 3
WT1 -0.025 0.1 -9999 0 -0.31 53 53
WRN 0.012 0.038 -9999 0 -0.82 1 1
SP1 0.015 0.003 -9999 0 -10000 0 0
SP3 0.014 0.002 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.029 0.053 -9999 0 -10000 0 0
Mad/Max 0.006 0.01 -9999 0 -10000 0 0
TERT -0.023 0.093 -9999 0 -0.52 1 1
CCND1 -0.015 0.092 -9999 0 -0.57 1 1
MAX 0.014 0.002 -9999 0 -10000 0 0
RBBP7 0.014 0 -9999 0 -10000 0 0
RBBP4 0.008 0.066 -9999 0 -0.82 3 3
TERF2 0 0.005 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.014 0 -9999 0 -10000 0 0
Telomerase/911 0.036 0.019 -9999 0 -10000 0 0
CDKN1B -0.04 0.19 -9999 0 -0.52 63 63
RAD1 0.013 0 -9999 0 -10000 0 0
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.012 0.038 -9999 0 -0.82 1 1
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.001 -9999 0 -10000 0 0
JUN -0.17 0.35 -9999 0 -0.82 109 109
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.003 0.006 -9999 0 -10000 0 0
FOS -0.21 0.37 -9999 0 -0.82 129 129
IFN-gamma/IRF1 -0.086 0.21 -9999 0 -0.61 64 64
PARP2 0.013 0 -9999 0 -10000 0 0
BLM 0.013 0.015 -9999 0 -10000 0 0
Telomerase 0.014 0.072 -9999 0 -0.48 5 5
IRF1 0.018 0.015 -9999 0 -0.3 1 1
ESR1 -0.049 0.19 -9999 0 -0.54 55 55
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.025 -9999 0 -0.56 1 1
ubiquitin-dependent protein catabolic process 0.052 0.027 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.053 0.027 -9999 0 -10000 0 0
HDAC1 0.014 0 -9999 0 -10000 0 0
HDAC2 0.015 0.003 -9999 0 -10000 0 0
ATM -0.001 0.026 -9999 0 -0.56 1 1
SMAD3 0.02 0.029 -9999 0 -10000 0 0
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.014 0.002 -9999 0 -10000 0 0
MRE11A 0.008 0.066 -9999 0 -0.82 3 3
HUS1 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.013 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.031 0.065 -9999 0 -10000 0 0
NR2F2 0.012 0.002 -9999 0 -10000 0 0
MAPK3 0.017 0.006 -9999 0 -10000 0 0
MAPK1 0.017 0.006 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.008 0.042 -9999 0 -0.31 8 8
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.025 -9999 0 -0.56 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR 0.007 0.076 -9999 0 -0.82 4 4
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.096 0.22 -9999 0 -0.63 72 72
MYC -0.009 0.14 -9999 0 -0.82 13 13
IL2 0.006 0.007 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
TGFB1 0.008 0.042 -9999 0 -0.31 8 8
TRF2/BLM 0 0.009 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.018 0.078 -9999 0 -10000 0 0
SP1/HDAC2 0.022 0.007 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.029 0.053 -9999 0 -10000 0 0
Smad3/Myc 0.009 0.097 -9999 0 -0.56 13 13
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.1 0.28 -9999 0 -0.71 78 78
Telomerase/PinX1 -0.029 0.053 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.021 0.037 -9999 0 -10000 0 0
SIN3B 0.014 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.029 0.053 -9999 0 -10000 0 0
response to DNA damage stimulus 0.003 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.003 0.036 -9999 0 -0.45 3 3
TRF2/WRN -0.001 0.027 -9999 0 -0.59 1 1
Telomerase/hnRNP C1/C2 -0.029 0.053 -9999 0 -10000 0 0
E2F1 -0.088 0.15 -9999 0 -0.31 152 152
ZNFX1 0.014 0 -9999 0 -10000 0 0
PIF1 0.002 0.089 -9999 0 -0.6 9 9
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.013 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.042 0.12 0.33 1 -0.36 57 58
FRAP1 0.008 0.026 -10000 0 -10000 0 0
AKT1 -0.035 0.1 0.25 1 -0.66 3 4
INSR 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.026 0.077 -10000 0 -0.51 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.007 0.022 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.022 0.065 -10000 0 -0.46 3 3
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.033 0.14 -10000 0 -0.42 55 55
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.009 0.027 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.01 0.06 -10000 0 -0.35 3 3
MAP3K5 0.011 0.021 -10000 0 -0.45 1 1
PIK3R1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.011 0.021 -10000 0 -0.45 1 1
mol:LY294002 0 0.001 0.001 1 -0.002 54 55
EIF4B 0.018 0.054 -10000 0 -0.34 2 2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.013 0.039 -10000 0 -0.32 2 2
eIF4E/eIF4G1/eIF4A1 -0.001 0.008 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.023 0.14 -10000 0 -0.39 57 57
mTOR/RHEB/GTP/Raptor/GBL 0.021 0.04 0.18 1 -0.28 2 3
FKBP1A 0.013 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.022 0.064 -10000 0 -0.45 3 3
mol:Amino Acids 0 0.001 0.001 1 -0.002 54 55
FKBP12/Rapamycin 0 0.001 -10000 0 -10000 0 0
PDPK1 -0.039 0.12 0.26 1 -0.34 57 58
EIF4E 0.013 0 -10000 0 -10000 0 0
ASK1/PP5C 0.016 0.034 -10000 0 -0.62 1 1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.028 0.083 -10000 0 -0.56 3 3
tumor necrosis factor receptor activity 0 0.001 0.002 54 -0.001 1 55
RPS6 0.013 0 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
EIF4G1 0.013 0 -10000 0 -10000 0 0
IRS1 -0.044 0.15 -10000 0 -0.46 55 55
INS 0 0 -10000 0 -10000 0 0
PTEN 0.011 0.038 -10000 0 -0.82 1 1
PDK2 -0.037 0.11 0.26 1 -0.32 57 58
EIF4EBP1 0.012 0.01 -10000 0 -10000 0 0
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
PPP2R5D 0.015 0.025 -10000 0 -10000 0 0
peptide biosynthetic process 0.018 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.013 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 0.004 1 -0.004 3 4
EEF2 0.018 0 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.019 0.008 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.013 0 -10000 0 -10000 0 0
HDAC3 0.013 0 -10000 0 -10000 0 0
VDR 0.013 0.015 -10000 0 -10000 0 0
Cbp/p300/PCAF 0 0 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.033 0.06 -10000 0 -0.34 6 6
KAT2B 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0 -10000 0 -10000 0 0
AKT1 0.011 0.085 0.24 6 -0.41 14 20
RAR alpha/9cRA/Cyclin H -0.024 0.095 -10000 0 -0.41 24 24
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.029 0.067 -10000 0 -0.38 7 7
CDC2 0 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.002 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.015 0.11 -10000 0 -0.72 9 9
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0 0.01 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA -0.021 0.16 -10000 0 -0.62 27 27
NCOA2 -0.062 0.24 -10000 0 -0.82 44 44
NCOA3 0.013 0 -10000 0 -10000 0 0
NCOA1 0.013 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.013 0.015 -10000 0 -10000 0 0
RARG 0.014 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0.014 0.002 -10000 0 -10000 0 0
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.11 -10000 0 -0.82 9 9
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.039 0.15 -10000 0 -0.66 24 24
RARA 0.006 0.093 -10000 0 -0.33 31 31
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0 0.14 -10000 0 -0.4 32 32
PRKCA -0.025 0.18 -10000 0 -0.82 24 24
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.032 0.16 -10000 0 -0.64 27 27
RXRG -0.12 0.11 -10000 0 -0.53 28 28
RXRA 0.012 0.095 -10000 0 -0.34 31 31
RXRB 0.003 0.1 -10000 0 -0.44 24 24
VDR/Vit D3/DNA 0 0.01 -10000 0 -10000 0 0
RBP1 -0.003 0.11 -10000 0 -0.65 12 12
CRBP1/9-cic-RA -0.012 0.084 -10000 0 -0.5 12 12
RARB -0.007 0.14 -10000 0 -0.82 13 13
PRKCG 0.008 0.022 -10000 0 -0.31 2 2
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs -0.028 0.17 -10000 0 -0.67 27 27
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.009 0.14 -10000 0 -0.54 27 27
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.088 -10000 0 -0.49 7 7
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.032 0.16 -10000 0 -0.64 27 27
positive regulation of DNA binding -0.023 0.089 -10000 0 -0.38 24 24
NRIP1 -0.027 0.15 -10000 0 -0.62 20 20
RXRs/RARs -0.04 0.16 -10000 0 -0.64 27 27
RXRs/RXRs/DNA/9cRA -0.051 0.15 -10000 0 -0.68 24 24
PRKACA 0.013 0 -10000 0 -10000 0 0
CDK7 0.013 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.013 0.054 -10000 0 -0.53 2 2
CCNH 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-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
BAG4 0.012 0.038 -9999 0 -0.82 1 1
Caspase 8 (4 units) -0.021 0.06 -9999 0 -10000 0 0
NEF -0.011 0.054 -9999 0 -10000 0 0
NFKBIA 0.009 0.029 -9999 0 -10000 0 0
BIRC3 -0.005 0.2 -9999 0 -0.81 26 26
CYCS -0.005 0.1 -9999 0 -0.4 5 5
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.035 0.18 -9999 0 -0.78 23 23
MAP2K7 0.025 0.079 -9999 0 -10000 0 0
protein ubiquitination 0.039 0.087 -9999 0 -10000 0 0
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.013 0 -9999 0 -10000 0 0
BID -0.014 0.1 -9999 0 -0.42 5 5
NF-kappa-B/RelA/I kappa B alpha -0.022 0.08 -9999 0 -0.53 1 1
TRADD 0.013 0 -9999 0 -10000 0 0
MAP3K5 0.012 0.038 -9999 0 -0.82 1 1
CFLAR 0.013 0 -9999 0 -10000 0 0
FADD 0.013 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.022 0.081 -9999 0 -0.35 26 26
MAPK8 0.024 0.096 -9999 0 -0.42 9 9
APAF1 0.012 0.038 -9999 0 -0.82 1 1
TRAF1 0.013 0 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.011 0.095 -9999 0 -0.31 27 27
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.024 0.1 -9999 0 -0.36 11 11
CHUK 0.039 0.092 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.001 0.021 -9999 0 -0.46 1 1
TCRz/NEF -0.057 0.17 -9999 0 -0.52 49 49
TNF -0.091 0.27 -9999 0 -0.78 64 64
FASLG -0.066 0.28 -9999 0 -0.84 49 49
NFKB1 0.007 0.048 -9999 0 -0.82 1 1
TNFR1A/BAG4/TNF-alpha -0.068 0.18 -9999 0 -0.55 59 59
CASP6 -0.004 0.045 -9999 0 -10000 0 0
CASP7 0.03 0.17 -9999 0 -0.62 25 25
RELA 0.009 0.029 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.03 0.17 -9999 0 -0.62 25 25
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.029 -9999 0 -0.63 1 1
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.032 0.099 -9999 0 -0.37 2 2
APAF-1/Caspase 9 -0.046 0.12 -9999 0 -0.52 25 25
BCL2 -0.001 0.15 -9999 0 -0.41 41 41
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.033 0 -9999 0 -10000 0 0
epithelial cell differentiation 0 0 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
ENAH 0.071 0.009 -9999 0 -10000 0 0
EGFR 0.006 0.076 -9999 0 -0.82 4 4
EPHA2 0.011 0.026 -9999 0 -0.31 3 3
MYO6 0.041 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 0 0 -9999 0 -10000 0 0
AQP5 -0.04 0.13 -9999 0 -0.59 26 26
CTNND1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.04 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.038 0.074 -9999 0 -10000 0 0
EGF -0.11 0.29 -9999 0 -0.78 74 74
NCKAP1 0.013 0 -9999 0 -10000 0 0
AQP3 -0.075 0.2 -9999 0 -0.59 61 61
cortical microtubule organization 0 0 -9999 0 -10000 0 0
GO:0000145 0.039 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GDP 0 0.005 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.001 0.01 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.049 0.032 -9999 0 -10000 0 0
PVRL2 0.013 0 -9999 0 -10000 0 0
ZYX 0.041 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.009 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.064 0.15 -9999 0 -0.43 72 72
RhoA/GDP 0 0 -9999 0 -10000 0 0
actin cytoskeleton organization 0.047 0 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
IGF1R 0.013 0 -9999 0 -10000 0 0
IGF1 -0.18 0.35 -9999 0 -0.8 119 119
DIAPH1 0 0.002 -9999 0 -10000 0 0
Wnt receptor signaling pathway 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0 0.005 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
VCL 0.047 0 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
LPP 0.041 0.057 -9999 0 -0.43 7 7
Ephrin A1/EPHA2 -0.001 0.008 -9999 0 -10000 0 0
SEC6/SEC8 0 0 -9999 0 -10000 0 0
MGAT3 -0.038 0.075 -9999 0 -10000 0 0
HGF/MET -0.1 0.16 -9999 0 -0.47 74 74
HGF -0.11 0.3 -9999 0 -0.82 74 74
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.033 0 -9999 0 -10000 0 0
actin cable formation 0.086 0.02 -9999 0 -10000 0 0
KIAA1543 0.047 0.021 -9999 0 -0.42 1 1
KIFC3 0.041 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
EXOC3 0.013 0 -9999 0 -10000 0 0
ACTN1 0.04 0.007 -9999 0 -10000 0 0
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
EXOC4 0.013 0 -9999 0 -10000 0 0
STX4 0.041 0 -9999 0 -10000 0 0
PIP5K1C 0.041 0 -9999 0 -10000 0 0
LIMA1 0.013 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
ROCK1 0 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.064 0.02 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.1 0.18 -9999 0 -0.43 113 113
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET -0.11 0.16 -9999 0 -0.31 180 180
PLEKHA7 0.04 0.022 -9999 0 -0.45 1 1
mol:GTP -0.001 0.01 -9999 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.067 0 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.033 0 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.047 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.033 0 -9999 0 -10000 0 0
Class I PI3K signaling events

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.001 0.034 0.3 1 -0.53 1 2
DAPP1 -0.053 0.14 -10000 0 -0.46 14 14
Src family/SYK family/BLNK-LAT/BTK-ITK -0.058 0.18 -10000 0 -0.49 31 31
mol:DAG -0.005 0.096 -10000 0 -0.28 15 15
HRAS 0.013 0.021 -10000 0 -0.31 2 2
RAP1A 0.014 0.001 -10000 0 -10000 0 0
ARF5/GDP 0.023 0.035 -10000 0 -0.46 1 1
PLCG2 0.013 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
ARF5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.014 0.27 1 -10000 0 1
ARF1/GTP -0.001 0.022 0.28 1 -10000 0 1
RHOA 0.013 0 -10000 0 -10000 0 0
YES1 0.013 0 -10000 0 -10000 0 0
RAP1A/GTP 0 0.013 -10000 0 -10000 0 0
ADAP1 0 0.013 0.26 1 -10000 0 1
ARAP3 0 0.014 0.27 1 -10000 0 1
INPPL1 0.013 0 -10000 0 -10000 0 0
PREX1 0.013 0 -10000 0 -10000 0 0
ARHGEF6 0.012 0.038 -10000 0 -0.82 1 1
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.014 0.001 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
FGR 0.011 0.03 -10000 0 -0.31 4 4
mol:Ca2+ 0.007 0.054 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.17 0.16 -10000 0 -0.32 276 276
ZAP70 -0.022 0.16 -10000 0 -0.62 27 27
mol:IP3 0.005 0.072 -10000 0 -10000 0 0
LYN 0.013 0 -10000 0 -10000 0 0
ARF1/GDP 0.023 0.035 -10000 0 -0.46 1 1
RhoA/GDP -0.001 0.019 0.28 1 -10000 0 1
PDK1/Src/Hsp90 -0.003 0.036 -10000 0 -0.55 2 2
BLNK 0.013 0 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.038 0.038 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
PLEKHA2 0.023 0.041 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.002 0.036 -10000 0 -0.8 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP 0 0.015 0.3 1 -10000 0 1
RhoA/GTP 0 0.013 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.049 0.16 -10000 0 -0.61 13 13
BLK -0.25 0.38 -10000 0 -0.76 164 164
PDPK1 0.01 0.054 -10000 0 -0.82 2 2
CYTH1 0 0.013 -10000 0 -10000 0 0
HCK -0.008 0.08 -10000 0 -0.31 31 31
CYTH3 -0.002 0.034 0.26 1 -0.49 2 3
CYTH2 0 0.013 -10000 0 -10000 0 0
KRAS 0.014 0.001 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.014 0.095 -10000 0 -0.62 11 11
SGK1 -0.015 0.11 0.24 1 -0.69 11 12
INPP5D -0.003 0.071 -10000 0 -0.31 24 24
mol:GDP 0.015 0.037 -10000 0 -0.49 1 1
SOS1 0.013 0 -10000 0 -10000 0 0
SYK 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.02 0.29 1 -10000 0 1
mol:PI-3-4-5-P3 0 0.018 0.36 1 -10000 0 1
ARAP3/RAP1A/GTP 0 0.013 -10000 0 -10000 0 0
VAV1 -0.013 0.1 -10000 0 -0.36 34 34
mol:PI-3-4-P2 0.013 0.049 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0 0.006 -10000 0 -10000 0 0
PLEKHA1 0.023 0.041 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.035 -10000 0 -0.46 1 1
LAT 0.006 0.077 -10000 0 -0.72 5 5
Rac1/GTP -0.006 0.055 -10000 0 -0.47 2 2
ITK -0.056 0.14 -10000 0 -0.44 60 60
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.014 0.13 -10000 0 -0.4 15 15
LCK -0.01 0.11 -10000 0 -0.44 25 25
BTK -0.013 0.061 -10000 0 -0.43 8 8
Caspase cascade in apoptosis

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
TOP1 0.019 0.092 -10000 0 -0.46 12 12
ACTA1 0.01 0.12 -10000 0 -0.59 12 12
NUMA1 0.019 0.092 -10000 0 -0.46 12 12
SPTAN1 0.015 0.12 -10000 0 -0.61 11 11
LIMK1 0.015 0.12 -10000 0 -0.64 10 10
BIRC3 -0.036 0.19 -10000 0 -0.68 35 35
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.013 0.015 -10000 0 -0.31 1 1
CASP10 0 0.12 -10000 0 -0.62 14 14
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 0.019 0.092 -10000 0 -0.46 12 12
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.015 0.11 -10000 0 -0.59 11 11
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN 0.015 0.12 -10000 0 -0.64 10 10
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.057 0.22 -10000 0 -0.65 60 60
BID -0.011 0.068 -10000 0 -0.31 12 12
MAP3K1 0.014 0.042 -10000 0 -0.23 3 3
TRADD 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.029 -10000 0 -0.63 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.012 0.12 -10000 0 -0.61 11 11
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair -0.016 0.052 0.17 2 -0.23 22 24
neuron apoptosis 0.023 0.015 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.021 0.11 -10000 0 -0.61 10 10
APAF1 0.012 0.038 -10000 0 -0.82 1 1
CASP6 0.022 0.064 -10000 0 -0.4 5 5
TRAF2 0.013 0 -10000 0 -10000 0 0
ICAD/CAD 0.022 0.11 -10000 0 -0.61 10 10
CASP7 0.009 0.08 0.34 25 -10000 0 25
KRT18 0.017 0.018 -10000 0 -10000 0 0
apoptosis 0.026 0.11 -10000 0 -0.56 12 12
DFFA 0.015 0.12 -10000 0 -0.61 11 11
DFFB 0.015 0.12 -10000 0 -0.61 11 11
PARP1 0.016 0.052 0.23 22 -0.17 2 24
actin filament polymerization -0.023 0.11 0.58 10 -10000 0 10
TNF -0.091 0.27 -10000 0 -0.78 64 64
CYCS 0.005 0.045 -10000 0 -0.22 12 12
SATB1 0.029 0.061 -10000 0 -0.4 4 4
SLK 0.012 0.13 -10000 0 -0.64 13 13
p15 BID/BAX -0.002 0.06 -10000 0 -0.35 4 4
CASP2 0.006 0.12 -10000 0 -0.46 11 11
JNK cascade -0.014 0.042 0.23 3 -10000 0 3
CASP3 0.007 0.12 -10000 0 -0.62 12 12
LMNB2 0.021 0.076 -10000 0 -0.32 4 4
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.013 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.028 0.11 -10000 0 -0.5 25 25
negative regulation of DNA binding -0.056 0.22 -10000 0 -0.64 60 60
stress fiber formation 0.012 0.12 -10000 0 -0.62 13 13
GZMB -0.013 0.14 -10000 0 -0.71 14 14
CASP1 0.016 0.032 -10000 0 -0.45 2 2
LMNB1 0.02 0.077 -10000 0 -0.32 4 4
APP 0.024 0.015 -10000 0 -10000 0 0
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.012 0 -10000 0 -10000 0 0
VIM 0.022 0.1 0.26 12 -0.51 10 22
LMNA 0.021 0.076 -10000 0 -0.32 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.003 0.12 -10000 0 -0.49 11 11
LRDD 0.013 0 -10000 0 -10000 0 0
SREBF1 0.014 0.12 -10000 0 -0.64 10 10
APAF-1/Caspase 9 0.005 0.042 -10000 0 -0.4 1 1
nuclear fragmentation during apoptosis 0.019 0.091 -10000 0 -0.46 12 12
CFL2 0.022 0.11 -10000 0 -0.6 10 10
GAS2 0.01 0.13 -10000 0 -0.58 16 16
positive regulation of apoptosis 0.023 0.079 -10000 0 -0.31 4 4
PRF1 -0.002 0.11 -10000 0 -0.72 10 10
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.032 0.14 -10000 0 -0.63 25 25
ATM 0.012 0.038 -10000 0 -0.82 1 1
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
ATR 0.012 0.038 -10000 0 -0.82 1 1
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.026 0.03 -10000 0 -0.44 2 2
protein ubiquitination -0.025 0.1 -10000 0 -0.46 26 26
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex -0.003 0.043 -10000 0 -0.55 3 3
MRE11A 0.008 0.066 -10000 0 -0.82 3 3
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.002 0.012 -10000 0 -10000 0 0
FANCF 0.013 0 -10000 0 -10000 0 0
BRCA1 0.013 0 -10000 0 -10000 0 0
CCNE1 0.013 0 -10000 0 -10000 0 0
CDK2/Cyclin E1 0 0 -10000 0 -10000 0 0
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.032 0.14 -10000 0 -0.63 25 25
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.013 0 -10000 0 -10000 0 0
NBN 0.013 0 -10000 0 -10000 0 0
FANCA -0.001 0.068 -10000 0 -0.31 22 22
DNA repair 0.054 0.099 -10000 0 -0.41 1 1
BRCA1/BARD1/ubiquitin -0.032 0.14 -10000 0 -0.63 25 25
BARD1/DNA-PK -0.026 0.11 -10000 0 -0.5 25 25
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.032 0.14 0.63 25 -10000 0 25
BRCA1/BARD1/CTIP/M/R/N Complex 0.021 0.089 -10000 0 -0.58 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.028 0.12 -10000 0 -0.55 25 25
BRCA1/BARD1/P53 -0.027 0.11 -10000 0 -0.5 26 26
BARD1/CSTF1/BRCA1 -0.028 0.12 -10000 0 -0.55 25 25
BRCA1/BACH1 0.013 0 -10000 0 -10000 0 0
BARD1 -0.03 0.18 -10000 0 -0.82 25 25
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.028 0.12 -10000 0 -0.55 25 25
BRCA1/BARD1/UbcH7 -0.028 0.12 -10000 0 -0.55 25 25
BRCA1/BARD1/RAD51/PCNA -0.026 0.11 -10000 0 -0.5 25 25
BARD1/DNA-PK/P53 -0.024 0.1 -10000 0 -0.46 25 25
BRCA1/BARD1/Ubiquitin -0.032 0.14 -10000 0 -0.63 25 25
BRCA1/BARD1/CTIP -0.027 0.11 -10000 0 -0.5 26 26
FA complex 0.038 0.024 -10000 0 -0.26 1 1
BARD1/EWS -0.032 0.14 -10000 0 -0.63 25 25
RBBP8 0.023 0.03 -10000 0 -0.63 1 1
TP53 0.013 0 -10000 0 -10000 0 0
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.026 0.11 0.49 26 -10000 0 26
BRCA1/BARD1 -0.025 0.1 -10000 0 -0.46 26 26
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.033 0.14 -10000 0 -0.64 25 25
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.012 0.021 -10000 0 -0.31 2 2
RAD50 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.032 0.14 -10000 0 -0.63 25 25
EWSR1 0.013 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.046 0.06 -10000 0 -0.38 8 8
NFATC2 -0.018 0.095 -10000 0 -0.29 26 26
NFATC3 0.018 0.012 -10000 0 -10000 0 0
YWHAE 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.011 0.092 -10000 0 -0.59 4 4
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.002 0.004 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.026 0.097 -10000 0 -0.59 9 9
BCL2/BAX -0.046 0.16 -10000 0 -0.63 35 35
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.01 -10000 0 -10000 0 0
CaM/Ca2+ 0.006 0.01 -10000 0 -10000 0 0
BAX 0.013 0.015 -10000 0 -0.31 1 1
MAPK14 0.01 0.006 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.015 0.088 -10000 0 -0.57 4 4
Calcineurin A alpha-beta B1/BCL2 -0.047 0.22 -10000 0 -0.82 35 35
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.015 0.086 0.56 4 -10000 0 4
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.013 0 -10000 0 -10000 0 0
XPO1 0.013 0.001 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 312 312
MAP3K8 -0.004 0.11 -10000 0 -0.82 8 8
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.12 0.16 -10000 0 -0.49 22 22
CABIN1 0.011 0.093 -10000 0 -0.6 4 4
CALM1 0.01 0.006 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
MAP3K1 0.013 0 -10000 0 -10000 0 0
CAMK4 -0.005 0.11 -10000 0 -0.54 16 16
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.006 0.11 -10000 0 -0.82 9 9
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
FKBP1A 0.013 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.006 0.05 -10000 0 -10000 0 0
PRKCH 0.013 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.004 -10000 0 -10000 0 0
CASP3 0.01 0.006 -10000 0 -10000 0 0
PIM1 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.014 0.05 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.004 0.047 -10000 0 -10000 0 0
PRKCB -0.027 0.13 -10000 0 -0.36 52 52
PRKCE 0.006 0.076 -10000 0 -0.82 4 4
JNK2/NFAT4 0.022 0.014 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.013 0 -10000 0 -10000 0 0
NUP214 0.013 0.001 -10000 0 -10000 0 0
PRKCZ 0.01 0.006 -10000 0 -10000 0 0
PRKCA -0.028 0.18 -10000 0 -0.82 24 24
PRKCG 0.005 0.022 -10000 0 -0.31 2 2
PRKCQ 0.005 0.084 -10000 0 -0.82 5 5
FKBP38/BCL2 -0.045 0.16 -10000 0 -0.63 35 35
EP300 0.01 0.007 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
NFATc/JNK1 0.033 0.086 -10000 0 -0.4 9 9
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.01 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.011 0.071 -10000 0 -0.56 7 7
NFATc/ERK1 0.052 0.056 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.025 0.096 -10000 0 -0.58 9 9
NR4A1 -0.18 0.36 -10000 0 -0.73 144 144
GSK3B 0.01 0.006 -10000 0 -10000 0 0
positive T cell selection 0.018 0.012 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.036 0.062 -10000 0 -0.41 4 4
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.01 0.006 -10000 0 -10000 0 0
AKAP5 0.013 0 -10000 0 -10000 0 0
MEF2D 0.01 0.007 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.041 0.062 -10000 0 -10000 0 0
CREBBP 0.01 0.007 -10000 0 -10000 0 0
BCL2 -0.047 0.22 -10000 0 -0.82 35 35
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 0.006 0.049 -9999 0 -0.31 11 11
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.022 0.016 -9999 0 -10000 0 0
GNAO1 -0.017 0.15 -9999 0 -0.72 20 20
mol:Sphinganine-1-P 0.019 0.034 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.002 0.014 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.013 0 -9999 0 -10000 0 0
S1PR2 0.01 0.033 -9999 0 -0.31 5 5
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.002 0.011 -9999 0 -10000 0 0
S1PR5 0.007 0.054 -9999 0 -0.38 8 8
S1PR4 0.01 0.033 -9999 0 -0.31 5 5
GNAI1 0.012 0.038 -9999 0 -0.82 1 1
S1P/S1P5/G12 -0.004 0.028 -9999 0 -0.49 1 1
S1P/S1P3/Gq -0.048 0.15 -9999 0 -0.4 23 23
S1P/S1P4/Gi 0.031 0.068 -9999 0 -0.32 17 17
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNA14 -0.18 0.35 -9999 0 -0.82 112 112
GNA15 -0.013 0.093 -9999 0 -0.33 37 37
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.002 0.11 -9999 0 -0.82 9 9
ABCC1 0.013 0 -9999 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.024 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.039 0.016 -10000 0 -10000 0 0
CDKN1A 0.033 0.032 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
FOXO3 0.039 0.016 -10000 0 -10000 0 0
AKT1 -0.001 0.015 -10000 0 -0.28 1 1
BAD 0.013 0 -10000 0 -10000 0 0
AKT3 0.016 0.03 -10000 0 -0.45 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.039 0.016 -10000 0 -10000 0 0
AKT1/ASK1 -0.002 0.023 -10000 0 -0.43 1 1
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0.012 0.038 -10000 0 -0.82 1 1
RAF1 0.013 0 -10000 0 -10000 0 0
JNK cascade 0.002 0.023 0.42 1 -10000 0 1
TSC1 0.039 0.016 -10000 0 -10000 0 0
YWHAZ 0.013 0 -10000 0 -10000 0 0
AKT1/RAF1 0.038 0.016 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.032 0.017 -10000 0 -0.28 1 1
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.039 0.016 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 -0.052 0.2 -10000 0 -0.55 66 66
MAP3K5 0.012 0.038 -10000 0 -0.82 1 1
MAPKAP1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.011 0.035 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
AKT1S1 0.039 0.016 -10000 0 -10000 0 0
CASP9 0.039 0.016 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.045 0.015 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 -0.003 0.036 -10000 0 -0.55 2 2
YWHAE 0.013 0 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
AKT2/p21CIP1 -0.005 0.03 -10000 0 -0.37 2 2
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.019 0.006 -10000 0 -10000 0 0
CHUK 0.039 0.016 -10000 0 -10000 0 0
BAD/BCL-XL 0.052 0.015 -10000 0 -10000 0 0
mTORC2 -0.001 0.023 -10000 0 -0.51 1 1
AKT2 0.016 0.03 -10000 0 -0.45 2 2
FOXO1-3a-4/14-3-3 family 0.025 0.041 -10000 0 -10000 0 0
PDPK1 0.01 0.054 -10000 0 -0.82 2 2
MDM2 0.039 0.016 -10000 0 -10000 0 0
MAPKKK cascade -0.038 0.016 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.051 0.015 -10000 0 -10000 0 0
TSC1/TSC2 0.046 0.016 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.011 -10000 0 -10000 0 0
glucose import -0.06 0.21 -10000 0 -0.52 80 80
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.033 0.012 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.06 0.21 -10000 0 -0.53 80 80
GSK3A 0.039 0.016 -10000 0 -10000 0 0
FOXO1 0.039 0.016 -10000 0 -10000 0 0
GSK3B 0.039 0.016 -10000 0 -10000 0 0
SFN -0.21 0.19 -10000 0 -0.34 312 312
G1/S transition of mitotic cell cycle 0.046 0.016 -10000 0 -10000 0 0
p27Kip1/14-3-3 family -0.001 0.052 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
KPNA1 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0 -10000 0 -10000 0 0
RHEB 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.004 0.13 -10000 0 -0.56 11 11
BAG4 0.012 0.038 -10000 0 -0.82 1 1
BAD 0.017 0.046 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.037 0.19 -10000 0 -0.68 35 35
BAX 0.017 0.047 -10000 0 -0.22 1 1
EnzymeConsortium:3.1.4.12 0.004 0.034 -10000 0 -0.12 11 11
IKBKB 0.013 0.12 -10000 0 -0.52 11 11
MAP2K2 0.027 0.057 -10000 0 -0.37 2 2
MAP2K1 0.027 0.057 -10000 0 -0.37 2 2
SMPD1 0.01 0.034 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.013 0.13 -10000 0 -0.54 11 11
MAP2K4 0.024 0.047 -10000 0 -10000 0 0
protein ubiquitination 0.014 0.12 -10000 0 -0.53 11 11
EnzymeConsortium:2.7.1.37 0.031 0.062 -10000 0 -0.37 2 2
response to UV 0 0.001 -10000 0 -0.002 13 13
RAF1 0.022 0.057 -10000 0 -0.4 2 2
CRADD 0.014 0 -10000 0 -10000 0 0
mol:ceramide 0.01 0.048 -10000 0 -0.17 11 11
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.017 0.047 -10000 0 -10000 0 0
TRADD 0.014 0 -10000 0 -10000 0 0
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.03 0.056 -10000 0 -0.36 2 2
MAPK1 0.03 0.056 -10000 0 -0.36 2 2
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.004 0.13 -10000 0 -0.56 11 11
KSR1 0.016 0.057 -10000 0 -0.43 2 2
MAPK8 0.023 0.077 -10000 0 -0.44 9 9
TRAF2 0.013 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.013 0.12 -10000 0 -0.52 11 11
TNF R/SODD -0.001 0.029 -10000 0 -0.63 1 1
TNF -0.091 0.27 -10000 0 -0.78 64 64
CYCS 0.027 0.056 0.16 29 -10000 0 29
IKBKG 0.013 0.12 -10000 0 -0.52 11 11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.004 0.14 -10000 0 -0.45 25 25
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.027 0.056 0.16 29 -10000 0 29
TNF/TNF R/SODD -0.068 0.18 -10000 0 -0.55 59 59
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.033 -10000 0 -10000 0 0
NSMAF 0.005 0.13 -10000 0 -0.55 11 11
response to hydrogen peroxide 0 0.001 -10000 0 -0.002 13 13
BCL2 -0.047 0.22 -10000 0 -0.82 35 35
S1P3 pathway

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.026 0.058 -9999 0 -0.33 1 1
GNAO1 -0.015 0.15 -9999 0 -0.72 20 20
S1P/S1P3/G12/G13 0 0 -9999 0 -10000 0 0
AKT1 -0.005 0.029 -9999 0 -0.47 1 1
AKT3 0.049 0.05 -9999 0 -0.56 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
GNAI2 0.015 0 -9999 0 -10000 0 0
GNAI3 0.015 0 -9999 0 -10000 0 0
GNAI1 0.013 0.038 -9999 0 -0.82 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.015 0 -9999 0 -10000 0 0
S1PR2 0.01 0.033 -9999 0 -0.31 5 5
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.036 0.067 -9999 0 -0.32 16 16
MAPK3 0.042 0.064 -9999 0 -10000 0 0
MAPK1 0.042 0.064 -9999 0 -10000 0 0
JAK2 0.046 0.065 -9999 0 -0.43 1 1
CXCR4 0.042 0.065 -9999 0 -10000 0 0
FLT1 0.015 0.038 -9999 0 -0.82 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.042 0.064 -9999 0 -10000 0 0
S1P/S1P3/Gi 0.036 0.068 -9999 0 -0.32 16 16
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.01 0.052 -9999 0 -10000 0 0
VEGFA 0.011 0.066 -9999 0 -0.82 3 3
S1P/S1P2/Gi 0.03 0.068 -9999 0 -0.32 16 16
VEGFR1 homodimer/VEGFA homodimer 0.024 0.068 -9999 0 -0.8 3 3
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.065 0.17 -9999 0 -0.35 119 119
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.015 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 -0.18 0.35 -9999 0 -0.82 112 112
GNA15 -0.013 0.093 -9999 0 -0.33 37 37
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 -0.002 0.11 -9999 0 -0.82 9 9
Rac1/GTP -0.01 0.052 -9999 0 -10000 0 0
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.008 0.067 -9999 0 -0.7 4 4
positive regulation of NF-kappaB transcription factor activity -0.004 0.05 -9999 0 -0.63 3 3
MAP2K4 0.047 0.031 -9999 0 -0.3 3 3
IKBKB 0.013 0 -9999 0 -10000 0 0
TNFRSF10B 0.013 0 -9999 0 -10000 0 0
TNFRSF10A 0.008 0.066 -9999 0 -0.82 3 3
SMPD1 -0.002 0.023 -9999 0 -0.29 3 3
IKBKG 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.004 0.05 -9999 0 -0.63 3 3
TRAIL/TRAILR3 -0.06 0.1 -9999 0 -0.68 3 3
TRAIL/TRAILR1 -0.008 0.07 -9999 0 -0.63 6 6
TRAIL/TRAILR4 -0.004 0.05 -9999 0 -0.63 3 3
TRAIL/TRAILR1/DAP3/GTP -0.007 0.056 -9999 0 -0.5 6 6
IKK complex -0.002 0.017 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.02 0.052 -9999 0 -0.63 3 3
MAP3K1 -0.003 0.028 -9999 0 -0.32 3 3
TRAILR4 (trimer) 0.013 0 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.008 0.065 -9999 0 -0.82 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.035 0.041 -9999 0 -0.33 6 6
CFLAR 0.013 0 -9999 0 -10000 0 0
MAPK1 0.02 0.052 -9999 0 -0.63 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP -0.006 0.051 -9999 0 -0.46 6 6
mol:ceramide -0.002 0.023 -9999 0 -0.29 3 3
FADD 0.013 0 -9999 0 -10000 0 0
MAPK8 0.045 0.077 -9999 0 -0.47 9 9
TRAF2 0.013 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.077 0.15 -9999 0 -0.31 135 135
CHUK 0.013 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.007 0.061 -9999 0 -0.55 6 6
DAP3 0.013 0 -9999 0 -10000 0 0
CASP10 -0.005 0.046 -9999 0 -0.52 3 3
JNK cascade -0.004 0.05 -9999 0 -0.63 3 3
TRAIL (trimer) 0.008 0.067 -9999 0 -0.7 4 4
TNFRSF10C -0.078 0.15 -9999 0 -0.31 135 135
TRAIL/TRAILR1/DAP3/GTP/FADD -0.006 0.052 -9999 0 -0.47 6 6
TRAIL/TRAILR2/FADD -0.004 0.043 -9999 0 -0.55 3 3
cell death 0.019 0.025 -9999 0 -0.29 3 3
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.037 0.029 -9999 0 -0.33 3 3
TRAILR2 (trimer) 0.013 0 -9999 0 -10000 0 0
CASP8 0.001 0.013 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.003 0.037 -9999 0 -0.46 3 3
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.008 0.077 -9999 0 -0.74 5 5
PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
SPHK1 -0.008 0.022 -9999 0 -10000 0 0
mol:S1P -0.009 0.026 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.013 0.15 -9999 0 -0.67 11 11
GNAO1 -0.017 0.15 -9999 0 -0.73 20 20
PDGFB-D/PDGFRB/PLCgamma1 0.023 0.14 -9999 0 -0.57 11 11
PLCG1 0.02 0.14 -9999 0 -0.64 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.012 0.038 -9999 0 -0.82 1 1
GNAI2 0.013 0.005 -9999 0 -10000 0 0
GNAI3 0.013 0.005 -9999 0 -10000 0 0
GNAI1 0.012 0.038 -9999 0 -0.83 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.012 0.07 -9999 0 -0.64 5 5
S1P1/S1P -0.016 0.064 -9999 0 -0.51 5 5
negative regulation of cAMP metabolic process 0.014 0.15 -9999 0 -0.65 11 11
MAPK3 0.006 0.2 -9999 0 -0.59 44 44
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.008 0.066 -9999 0 -0.82 3 3
PLCB2 0.031 0.07 -9999 0 -0.44 5 5
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.013 0.052 -9999 0 -0.42 5 5
receptor internalization -0.015 0.059 -9999 0 -0.47 5 5
PTGS2 -0.037 0.34 -9999 0 -1.1 44 44
Rac1/GTP -0.013 0.052 -9999 0 -0.42 5 5
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.008 0.066 -9999 0 -0.82 3 3
negative regulation of T cell proliferation 0.014 0.15 -9999 0 -0.65 11 11
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0.005 -9999 0 -10000 0 0
MAPK1 0.006 0.2 -9999 0 -0.59 44 44
S1P1/S1P/PDGFB-D/PDGFRB 0.032 0.086 -9999 0 -0.51 6 6
ABCC1 0.014 0.002 -9999 0 -10000 0 0
Arf6 downstream 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
PLAUR -0.06 0.13 -10000 0 -10000 0 0
regulation of axonogenesis -0.01 0.037 0.32 2 -10000 0 2
myoblast fusion 0.023 0.052 -10000 0 -10000 0 0
mol:GTP -0.026 0.039 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.093 0.11 0.52 1 -10000 0 1
ARF1/GTP -0.015 0.023 -10000 0 -10000 0 0
mol:GM1 -0.011 0.033 -10000 0 -10000 0 0
mol:Choline 0.012 0.029 -10000 0 -10000 0 0
lamellipodium assembly -0.002 0.064 -10000 0 -10000 0 0
MAPK3 -0.017 0.065 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.094 0.11 -10000 0 -0.52 1 1
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.023 0.052 -10000 0 -10000 0 0
ARF1/GDP 0.005 0.059 -10000 0 -10000 0 0
ARF6 -0.001 0.023 -10000 0 -10000 0 0
RAB11A 0.013 0 -10000 0 -10000 0 0
TIAM1 -0.18 0.17 -10000 0 -0.32 276 276
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 -0.017 0.065 -10000 0 -10000 0 0
actin filament bundle formation 0.025 0.038 -10000 0 -10000 0 0
KALRN -0.005 0.051 -10000 0 -10000 0 0
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.025 0.038 -10000 0 -10000 0 0
NME1 0.011 0.007 -10000 0 -10000 0 0
Rac1/GDP -0.025 0.038 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.026 0.039 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.002 0.064 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
liver development -0.026 0.039 -10000 0 -10000 0 0
ARF6/GTP -0.026 0.039 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.023 -10000 0 -10000 0 0
mol:GDP -0.01 0.065 -10000 0 -10000 0 0
ARF6/GTP/RAB11FIP3/RAB11A -0.01 0.014 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0.001 0.033 -10000 0 -10000 0 0
RAB11FIP3 0.013 0 -10000 0 -10000 0 0
tube morphogenesis -0.002 0.064 -10000 0 -10000 0 0
ruffle organization 0.01 0.037 -10000 0 -0.32 2 2
regulation of epithelial cell migration -0.026 0.039 -10000 0 -10000 0 0
PLD2 0.001 0.033 -10000 0 -10000 0 0
PIP5K1A 0.01 0.037 -10000 0 -0.33 2 2
mol:Phosphatidic acid 0.012 0.029 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.064 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.062 0.16 -9999 0 -0.5 59 59
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.049 0.14 -9999 0 -0.42 59 59
SUMO1 0.013 0 -9999 0 -10000 0 0
ZFPM1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
FKBP3 0.013 0 -9999 0 -10000 0 0
Histones -0.025 0.067 -9999 0 -10000 0 0
YY1/LSF 0.028 0.051 -9999 0 -0.53 4 4
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.013 0.13 -9999 0 -0.37 58 58
I kappa B alpha/HDAC1 0 0.091 -9999 0 -10000 0 0
SAP18 0.013 0 -9999 0 -10000 0 0
RELA -0.003 0.12 -9999 0 -0.32 58 58
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
HDAC3/TR2 0 0.091 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.049 0.02 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.002 0.11 -9999 0 -0.29 59 59
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
GATA1 0.009 0.006 -9999 0 -10000 0 0
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.059 0.022 -9999 0 -10000 0 0
RBBP7 0.013 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.008 0.066 -9999 0 -0.82 3 3
MAX 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NFKBIA -0.008 0.1 -9999 0 -0.28 58 58
KAT2B 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.044 0.027 -9999 0 -10000 0 0
SIN3 complex -0.001 0.022 -9999 0 -0.5 1 1
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.012 0.038 -9999 0 -0.82 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.013 0 -9999 0 -10000 0 0
YY1/HDAC3 0.014 0.085 -9999 0 -10000 0 0
YY1/HDAC2 0.033 0 -9999 0 -10000 0 0
YY1/HDAC1 0.033 0 -9999 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.049 0.02 -9999 0 -10000 0 0
PPARG -0.061 0.16 -9999 0 -0.46 63 63
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0 0.091 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.013 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.053 0.022 -9999 0 -10000 0 0
HDAC1 0.013 0 -9999 0 -10000 0 0
HDAC3 -0.008 0.1 -9999 0 -10000 0 0
HDAC2 0.013 0 -9999 0 -10000 0 0
YY1 0.032 0 -9999 0 -10000 0 0
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.013 0 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
MXD1 0.013 0 -9999 0 -10000 0 0
STAT3 0.028 0 -9999 0 -10000 0 0
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.004 0.044 -9999 0 -0.48 4 4
YY1/SAP30/HDAC1 -0.001 0.022 -9999 0 -0.48 1 1
EP300 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.027 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.1 -9999 0 -0.28 58 58
histone deacetylation 0.049 0.02 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.011 0.085 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GATAD2B 0.013 0 -9999 0 -10000 0 0
GATAD2A 0.013 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.001 0.091 -9999 0 -10000 0 0
GATA1/HDAC1 0 0 -9999 0 -10000 0 0
GATA1/HDAC3 -0.01 0.09 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.078 0.2 -9999 0 -0.63 58 58
SIN3/HDAC complex/Mad/Max 0.049 0.023 -9999 0 -10000 0 0
NuRD Complex 0.058 0.022 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.025 0.066 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -10000 0 0
HDAC complex -0.003 0.039 -9999 0 -0.5 3 3
GATA1/Fog1 0 0 -9999 0 -10000 0 0
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.091 0.27 -9999 0 -0.78 64 64
negative regulation of cell growth 0.049 0.023 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.049 0.02 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.053 0.14 -9999 0 -0.44 58 58
SIN3/HDAC complex/NCoR1 0.046 0.026 -9999 0 -10000 0 0
TFCP2 0.006 0.076 -9999 0 -0.82 4 4
NR2C1 0.013 0 -9999 0 -10000 0 0
MBD3 0.013 0 -9999 0 -10000 0 0
MBD2 0.013 0 -9999 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.039 0.022 -9999 0 -10000 0 0
PLK1 0.11 0.11 -9999 0 -0.73 1 1
CDKN1B 0.15 0.048 -9999 0 -0.39 1 1
FOXO3 0.11 0.11 -9999 0 -0.62 3 3
KAT2B 0.025 0.01 -9999 0 -10000 0 0
FOXO1/SIRT1 0.009 0.038 -9999 0 -0.59 1 1
CAT 0.1 0.15 -9999 0 -1.4 3 3
CTNNB1 0.013 0 -9999 0 -10000 0 0
AKT1 0.028 0.011 -9999 0 -10000 0 0
FOXO1 0.042 0.015 -9999 0 -10000 0 0
MAPK10 0.043 0.026 -9999 0 -0.51 1 1
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.063 -9999 0 -0.48 4 4
response to oxidative stress 0.015 0.013 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.011 0.087 -9999 0 -0.72 3 3
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.015 0.002 -9999 0 -10000 0 0
BCL2L11 0.041 0.027 -9999 0 -10000 0 0
FOXO1/SKP2 0.039 0.051 -9999 0 -0.5 4 4
mol:GDP 0.015 0.013 -9999 0 -10000 0 0
RAN 0.015 0.001 -9999 0 -10000 0 0
GADD45A 0.13 0.062 -9999 0 -0.72 1 1
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.041 0.041 -9999 0 -10000 0 0
MST1 0.023 0.042 -9999 0 -0.55 2 2
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.009 0.064 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.035 0.072 -9999 0 -0.49 9 9
MAPK9 0.044 0.007 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.006 0.042 -9999 0 -0.82 1 1
SOD2 0.16 0.073 -9999 0 -0.79 1 1
RBL2 0.11 0.15 -9999 0 -1.4 4 4
RAL/GDP 0.033 0.012 -9999 0 -10000 0 0
CHUK 0.025 0.01 -9999 0 -10000 0 0
Ran/GTP 0.015 0.002 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.043 0.01 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.068 0.4 -9999 0 -1.5 33 33
SKP2 0.006 0.076 -9999 0 -0.82 4 4
USP7 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.025 0.01 -9999 0 -10000 0 0
CCNB1 0.11 0.1 -9999 0 -0.73 1 1
FOXO1-3a-4/beta catenin -0.003 0.05 -9999 0 -0.42 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.05 -9999 0 -0.5 4 4
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.006 0.13 -9999 0 -0.82 11 11
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.026 0.003 -9999 0 -10000 0 0
ZFAND5 0.11 0.053 -9999 0 -0.47 1 1
SFN -0.21 0.19 -9999 0 -0.34 312 312
CDK2 0.014 0.003 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.017 0.062 -9999 0 -0.32 4 4
CREBBP 0.014 0.003 -9999 0 -10000 0 0
FBXO32 0.11 0.11 -9999 0 -0.73 1 1
BCL6 0.12 0.1 -9999 0 -0.94 2 2
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.071 0.056 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.028 0.078 -9999 0 -0.63 2 2
NFKBIA 0.049 0.024 -9999 0 -0.47 1 1
BIRC2 0.013 0 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
RIPK2 0.013 0 -9999 0 -10000 0 0
IKBKG -0.005 0.021 -9999 0 -10000 0 0
IKK complex/A20 -0.05 0.13 -9999 0 -0.64 2 2
NEMO/A20/RIP2 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.042 0.039 -9999 0 -0.43 1 1
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.002 0.014 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.002 0.035 -9999 0 -0.55 2 2
NOD2 -0.032 0.12 -9999 0 -0.33 64 64
NFKB1 0.015 0.038 -9999 0 -0.82 1 1
RELA 0.017 0 -9999 0 -10000 0 0
MALT1 0.013 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.012 0.038 -9999 0 -0.82 1 1
TNF/TNFR1A -0.078 0.2 -9999 0 -0.63 58 58
TRAF6 0.01 0.054 -9999 0 -0.82 2 2
PRKCA -0.028 0.18 -9999 0 -0.82 24 24
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.091 0.27 -9999 0 -0.78 64 64
NF kappa B1 p50/RelA -0.001 0.024 -9999 0 -0.53 1 1
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.049 0.024 -9999 0 -0.47 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex -0.003 0.016 -9999 0 -10000 0 0
CYLD 0.013 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.021 0.087 -9999 0 -0.54 1 1
Circadian rhythm 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
chromatin modification -0.027 0.048 -9999 0 -0.63 1 1
CLOCK -0.039 0.2 -9999 0 -0.83 29 29
TIMELESS/CRY2 -0.006 0.065 -9999 0 -10000 0 0
DEC1/BMAL1 -0.021 0.064 -9999 0 -10000 0 0
ATR 0.012 0.038 -9999 0 -0.82 1 1
NR1D1 -0.06 0.13 -9999 0 -10000 0 0
ARNTL -0.02 0.096 -9999 0 -0.32 46 46
TIMELESS -0.014 0.074 -9999 0 -10000 0 0
NPAS2 0.009 0.041 -9999 0 -0.56 2 2
CRY2 0.013 0 -9999 0 -10000 0 0
mol:CO 0.008 0.031 -9999 0 -10000 0 0
CHEK1 0.013 0 -9999 0 -10000 0 0
mol:HEME -0.008 0.031 -9999 0 -10000 0 0
PER1 0.013 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 -0.03 0.15 -9999 0 -0.56 30 30
BMAL1/CLOCK -0.056 0.15 -9999 0 -0.62 15 15
S phase of mitotic cell cycle -0.027 0.048 -9999 0 -0.63 1 1
TIMELESS/CHEK1/ATR -0.027 0.048 -9999 0 -0.64 1 1
mol:NADPH -0.008 0.031 -9999 0 -10000 0 0
PER1/TIMELESS -0.006 0.065 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 0 0.015 -9999 0 -0.31 1 1
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.011 0.086 -9999 0 -0.44 14 14
CRKL 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.006 0.076 -9999 0 -0.82 4 4
ITGA4 0.004 0.069 -9999 0 -0.41 11 11
alpha4/beta7 Integrin/MAdCAM1 -0.031 0.097 -9999 0 -0.5 16 16
EPO 0.002 0.039 -9999 0 -0.31 7 7
alpha4/beta7 Integrin -0.03 0.12 -9999 0 -0.62 15 15
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.006 0.049 -9999 0 -0.63 2 2
EPO/EPOR (dimer) -0.007 0.037 -9999 0 -10000 0 0
lamellipodium assembly -0.002 0.038 -9999 0 -0.47 3 3
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
PI3K -0.004 0.049 -9999 0 -0.63 3 3
ARF6 0.013 0 -9999 0 -10000 0 0
JAK2 0.024 0.048 -9999 0 -0.5 3 3
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
MADCAM1 -0.011 0.091 -9999 0 -0.35 29 29
cell adhesion -0.031 0.097 -9999 0 -0.49 16 16
CRKL/CBL 0 0 -9999 0 -10000 0 0
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.022 0.08 -9999 0 -0.56 7 7
ITGB7 -0.02 0.14 -9999 0 -0.51 31 31
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.014 0.082 -9999 0 -0.62 7 7
p130Cas/Crk/Dock1 0.039 0.081 -9999 0 -0.82 1 1
VCAM1 -0.001 0.099 -9999 0 -0.57 12 12
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.004 0.036 -9999 0 -0.5 2 2
BCAR1 0.03 0.076 -9999 0 -0.52 7 7
EPOR 0.007 0.046 -9999 0 -0.31 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.002 0.039 -9999 0 -0.48 3 3
EPO signaling 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
BCL2L1 0.053 0.1 -9999 0 -10000 0 0
CRKL 0.038 0.045 -9999 0 -0.53 1 1
mol:DAG 0.042 0.049 -9999 0 -10000 0 0
HRAS 0.062 0.042 -9999 0 -10000 0 0
MAPK8 0.021 0.086 -9999 0 -0.57 9 9
RAP1A 0.038 0.045 -9999 0 -0.53 1 1
GAB1 0.038 0.045 -9999 0 -0.53 1 1
MAPK14 0.03 0.031 -9999 0 -10000 0 0
EPO 0.005 0.038 -9999 0 -0.3 7 7
PLCG1 0.042 0.05 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.009 0.047 -9999 0 -0.32 10 10
RAPGEF1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.037 0.13 -9999 0 -0.57 27 27
GAB1/SHC/GRB2/SOS1 -0.005 0.025 -9999 0 -0.46 1 1
EPO/EPOR (dimer) 0.013 0.042 -9999 0 -10000 0 0
IRS2 0.038 0.045 -9999 0 -0.53 1 1
STAT1 0.042 0.076 -9999 0 -10000 0 0
STAT5B 0.043 0.064 -9999 0 -10000 0 0
cell proliferation 0.028 0.081 -9999 0 -0.53 9 9
GAB1/SHIP/PIK3R1/SHP2/SHC -0.008 0.034 -9999 0 -10000 0 0
TEC 0.038 0.045 -9999 0 -0.53 1 1
SOCS3 -0.034 0.19 -9999 0 -0.8 28 28
STAT1 (dimer) 0.042 0.076 -9999 0 -10000 0 0
JAK2 0.013 0.039 -9999 0 -0.84 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.043 0.051 -9999 0 -0.57 1 1
EPO/EPOR 0.013 0.042 -9999 0 -10000 0 0
LYN 0.014 0.004 -9999 0 -10000 0 0
TEC/VAV2 0.046 0.044 -9999 0 -0.51 1 1
elevation of cytosolic calcium ion concentration 0.009 0.047 -9999 0 -0.32 10 10
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.028 0.036 -9999 0 -10000 0 0
mol:IP3 0.042 0.049 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.01 0.033 -9999 0 -0.48 1 1
SH2B3 0.014 0.005 -9999 0 -10000 0 0
NFKB1 0.029 0.039 -9999 0 -0.5 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.019 0.069 -9999 0 -0.29 28 28
PTPN6 0.031 0.047 -9999 0 -0.56 1 1
TEC/VAV2/GRB2 0.051 0.043 -9999 0 -0.49 1 1
EPOR 0.009 0.047 -9999 0 -0.32 10 10
INPP5D -0.003 0.071 -9999 0 -0.31 24 24
mol:GDP -0.005 0.025 -9999 0 -0.47 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.013 0 -9999 0 -10000 0 0
CRKL/CBL/C3G 0.051 0.043 -9999 0 -0.49 1 1
VAV2 0.038 0.045 -9999 0 -0.53 1 1
CBL 0.038 0.045 -9999 0 -0.53 1 1
SHC/Grb2/SOS1 -0.006 0.028 -9999 0 -0.49 1 1
STAT5A 0.043 0.064 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
STAT5 (dimer) 0.053 0.097 -9999 0 -10000 0 0
LYN/PLCgamma2 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
BTK 0.021 0.088 -9999 0 -0.5 8 8
BCL2 0.004 0.28 -9999 0 -0.98 35 35
Atypical NF-kappaB 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
BCL3/RelA 0 0.009 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.008 0.14 -9999 0 -0.56 30 30
NF kappa B1 p50/RelA/I kappa B alpha 0.044 0.039 -9999 0 -0.42 1 1
NFKBIA 0.025 0.037 -9999 0 -0.28 6 6
MAPK14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.027 0.026 -9999 0 -0.55 1 1
ARRB2 0.018 0 -9999 0 -10000 0 0
REL -0.038 0.2 -9999 0 -0.82 30 30
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.026 0.027 -9999 0 -0.55 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.027 0.026 -9999 0 -0.55 1 1
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
NF kappa B1 p50 dimer 0.02 0.03 -9999 0 -0.63 1 1
PIK3R1 0.013 0 -9999 0 -10000 0 0
NFKB1 0.023 0.03 -9999 0 -0.63 1 1
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.031 0.038 -9999 0 -0.27 6 6
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.047 0.038 -9999 0 -0.4 1 1
SRC 0.013 0.015 -9999 0 -0.31 1 1
PI3K -0.004 0.049 -9999 0 -0.63 3 3
NF kappa B1 p50/RelA 0.031 0.039 -9999 0 -0.27 6 6
IKBKB 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/PIK3R1 0.03 0.035 -9999 0 -10000 0 0
cell death -0.004 0.028 -9999 0 -0.38 1 1
NF kappa B1 p105/c-Rel -0.008 0.14 -9999 0 -0.56 30 30
LCK -0.01 0.11 -9999 0 -0.44 25 25
BCL3 0.013 0.015 -9999 0 -0.31 1 1
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.006 0.023 -10000 0 -10000 0 0
AES 0.005 0.02 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.013 0 -10000 0 -10000 0 0
DKK2 -0.028 0.17 -10000 0 -0.65 30 30
TLE1 0 0.066 -10000 0 -0.8 3 3
MACF1 0.014 0 -10000 0 -10000 0 0
CTNNB1 0.047 0.04 -10000 0 -10000 0 0
WIF1 -0.034 0.1 -10000 0 -10000 0 0
beta catenin/RanBP3 0.022 0.091 0.37 26 -10000 0 26
KREMEN2 -0.01 0.085 -10000 0 -0.31 35 35
DKK1 -0.043 0.13 -10000 0 -0.82 2 2
beta catenin/beta TrCP1 0.052 0.038 -10000 0 -10000 0 0
FZD1 0.014 0.001 -10000 0 -10000 0 0
AXIN2 -0.047 0.31 -10000 0 -1.6 18 18
AXIN1 0.014 0 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.019 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.063 0.044 -10000 0 -0.41 1 1
Axin1/APC/GSK3 0.007 0.031 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.059 0.018 -10000 0 -10000 0 0
HNF1A 0.006 0.021 -10000 0 -10000 0 0
CTBP1 0.006 0.021 -10000 0 -10000 0 0
MYC -0.032 0.26 -10000 0 -1.6 13 13
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.037 0.12 -10000 0 -0.56 20 20
NKD1 -0.013 0.14 -10000 0 -0.73 17 17
TCF4 0.006 0.021 -10000 0 -10000 0 0
TCF3 0.006 0.021 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0 0.008 -10000 0 -10000 0 0
Ran/GTP 0.001 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.029 0.12 0.48 27 -10000 0 27
LEF1 -0.002 0.066 -10000 0 -0.42 9 9
DVL1 0.018 0.027 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.068 0.074 -10000 0 -0.5 3 3
DKK1/LRP6/Kremen 2 -0.039 0.081 -10000 0 -0.63 2 2
LRP6 0.014 0.001 -10000 0 -10000 0 0
CSNK1A1 0.006 0.023 -10000 0 -10000 0 0
NLK 0.014 0.004 -10000 0 -10000 0 0
CCND1 0 0.074 -10000 0 -0.64 2 2
WNT1 0.01 0.021 -10000 0 -10000 0 0
GSK3A 0.014 0.001 -10000 0 -10000 0 0
GSK3B 0.014 0 -10000 0 -10000 0 0
FRAT1 0.013 0 -10000 0 -10000 0 0
PPP2R5D 0.03 0.06 0.37 14 -10000 0 14
APC 0.039 0.026 -10000 0 -0.47 1 1
WNT1/LRP6/FZD1 0.035 0.036 -10000 0 -10000 0 0
CREBBP 0.006 0.021 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.023 0.13 -9999 0 -0.7 16 16
AKT1 0.085 0.085 -9999 0 -0.69 4 4
PTK2B 0.036 0.13 -9999 0 -0.94 5 5
VEGFR2 homodimer/Frs2 0.032 0.087 -9999 0 -1.1 3 3
CAV1 -0.009 0.14 -9999 0 -0.82 13 13
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.009 0.098 -9999 0 -0.87 5 5
endothelial cell proliferation 0.076 0.1 -9999 0 -0.63 4 4
mol:Ca2+ 0.052 0.097 -9999 0 -0.72 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.008 0.093 -9999 0 -0.82 5 5
RP11-342D11.1 0.043 0.096 -9999 0 -0.73 6 6
CDH5 0.013 0 -9999 0 -10000 0 0
VEGFA homodimer -0.006 0.063 -9999 0 -0.59 5 5
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0.008 0.066 -9999 0 -0.82 3 3
HRAS/GDP -0.008 0.077 -9999 0 -0.76 4 4
SH2D2A -0.033 0.18 -9999 0 -0.64 34 34
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.007 0.064 -9999 0 -0.72 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.034 0.14 -9999 0 -0.56 27 27
VEGFR1 homodimer 0.012 0.038 -9999 0 -0.82 1 1
SHC/GRB2/SOS1 -0.009 0.09 -9999 0 -1 3 3
GRB10 0.052 0.097 -9999 0 -1 3 3
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.008 0.089 -9999 0 -0.79 5 5
HRAS 0.012 0.021 -9999 0 -0.31 2 2
VEGF/Rho/ROCK1/Integrin Complex 0.04 0.079 -9999 0 -0.52 5 5
HIF1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.008 0.089 -9999 0 -0.8 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.005 0.084 -9999 0 -0.82 5 5
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.009 0.098 -9999 0 -0.87 5 5
mol:GDP -0.008 0.082 -9999 0 -0.93 3 3
mol:NADP 0.078 0.062 -9999 0 -0.58 3 3
eNOS/Hsp90 0.08 0.058 -9999 0 -0.54 3 3
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.052 0.1 -9999 0 -0.75 6 6
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
VEGFA 0.011 0.065 -9999 0 -0.82 3 3
VEGFC 0.012 0.038 -9999 0 -0.82 1 1
FAK1/Vinculin 0.059 0.11 -9999 0 -0.68 7 7
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.025 0.13 -9999 0 -0.58 21 21
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 0.02 0.061 -9999 0 -0.65 3 3
mol:L-citrulline 0.078 0.062 -9999 0 -0.58 3 3
ITGAV 0.01 0.054 -9999 0 -0.82 2 2
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.008 0.093 -9999 0 -0.82 5 5
VEGFR2 homodimer/VEGFA homodimer -0.011 0.11 -9999 0 -0.85 6 6
VEGFR2/3 heterodimer 0.027 0.12 -9999 0 -0.95 6 6
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.054 0.1 -9999 0 -0.77 6 6
VEGFR2 homodimer 0.031 0.096 -9999 0 -1.2 3 3
FLT1 0.012 0.038 -9999 0 -0.82 1 1
NEDD4 0.012 0.054 -9999 0 -0.82 2 2
MAPK3 0.044 0.1 -9999 0 -0.83 4 4
MAPK1 0.044 0.1 -9999 0 -0.83 4 4
VEGFA145/NRP2 -0.019 0.072 -9999 0 -0.63 3 3
VEGFR1/2 heterodimer 0.031 0.1 -9999 0 -1.2 3 3
KDR 0.031 0.096 -9999 0 -1.2 3 3
VEGFA165/NRP1/VEGFR2 homodimer -0.017 0.1 -9999 0 -1.2 3 3
SRC 0.013 0.015 -9999 0 -0.31 1 1
platelet activating factor biosynthetic process 0.046 0.1 -9999 0 -1 3 3
PI3K -0.01 0.089 -9999 0 -0.96 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.009 0.098 -9999 0 -0.87 5 5
FES 0.052 0.11 -9999 0 -1.1 3 3
GAB1 -0.008 0.087 -9999 0 -0.99 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.009 0.098 -9999 0 -0.87 5 5
CTNNB1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.07 0.09 -9999 0 -0.63 3 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.009 0.098 -9999 0 -0.87 5 5
PI3K/GAB1 0.087 0.079 -9999 0 -0.72 3 3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.008 0.089 -9999 0 -1 3 3
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.012 0.11 -9999 0 -0.83 7 7
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 0.052 0.11 -9999 0 -1.1 3 3
actin cytoskeleton reorganization -0.033 0.14 -9999 0 -0.55 27 27
PTK2 0.053 0.12 -9999 0 -0.76 7 7
EDG1 0.043 0.096 -9999 0 -0.73 6 6
mol:DAG 0.052 0.1 -9999 0 -0.75 6 6
CaM/Ca2+ -0.008 0.083 -9999 0 -0.94 3 3
MAP2K3 0.052 0.12 -9999 0 -1.1 3 3
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.01 0.1 -9999 0 -1.2 3 3
PLCG1 0.052 0.11 -9999 0 -1.1 3 3
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.009 0.094 -9999 0 -0.82 5 5
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.01 0.11 -9999 0 -0.94 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.009 0.098 -9999 0 -0.87 5 5
cell migration 0.083 0.094 -9999 0 -0.72 3 3
mol:PI-3-4-5-P3 -0.009 0.077 -9999 0 -0.82 3 3
FYN 0.013 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.008 0.084 -9999 0 -0.68 6 6
mol:NO 0.078 0.062 -9999 0 -0.58 3 3
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.008 0.077 -9999 0 -0.76 4 4
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.051 0.11 -9999 0 -1.2 3 3
VHL 0.008 0.066 -9999 0 -0.82 3 3
ITGB3 -0.014 0.15 -9999 0 -0.82 16 16
NOS3 0.08 0.071 -9999 0 -0.69 3 3
VEGFR2 homodimer/VEGFA homodimer/Sck -0.012 0.1 -9999 0 -0.72 8 8
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.035 0.15 -9999 0 -1.2 3 3
PRKCB 0.039 0.11 -9999 0 -0.94 3 3
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.042 0.1 -9999 0 -0.77 6 6
VEGFR1/2 heterodimer/VEGFA homodimer -0.01 0.11 -9999 0 -0.94 5 5
VEGFA165/NRP2 -0.019 0.072 -9999 0 -0.63 3 3
MAPKKK cascade -0.008 0.076 -9999 0 -0.85 3 3
NRP2 -0.012 0.088 -9999 0 -0.31 38 38
VEGFC homodimer 0.012 0.038 -9999 0 -0.82 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.059 0.11 -9999 0 -0.68 7 7
MAP3K13 0.044 0.13 -9999 0 -1.2 3 3
PDPK1 0.077 0.087 -9999 0 -0.74 4 4
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.044 0.007 -9999 0 -10000 0 0
KLHL20 -0.009 0.021 -9999 0 -10000 0 0
CYFIP2 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.074 0.009 -9999 0 -10000 0 0
ENAH 0.044 0.007 -9999 0 -10000 0 0
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP 0 0.002 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.001 0.014 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.017 0.08 -9999 0 -0.5 12 12
RAPGEF1 0.058 0.006 -9999 0 -10000 0 0
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -9999 0 -10000 0 0
CRK 0.052 0.006 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin 0 0 -9999 0 -10000 0 0
alphaE/beta7 Integrin -0.023 0.1 -9999 0 -0.63 12 12
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 0.045 0.002 -9999 0 -10000 0 0
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.016 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.08 0.072 -9999 0 -0.5 1 1
PI3K -0.002 0.021 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin 0 0 -9999 0 -10000 0 0
TIAM1 -0.17 0.16 -9999 0 -0.32 276 276
E-cadherin(dimer)/Ca2+ 0 0 -9999 0 -10000 0 0
AKT1 -0.001 0.012 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 0.013 0 -9999 0 -10000 0 0
RhoA/GDP 0.074 0.009 -9999 0 -10000 0 0
actin cytoskeleton organization -0.007 0.016 -9999 0 -10000 0 0
CDC42/GDP 0.074 0.009 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.027 0 -9999 0 -10000 0 0
ITGB7 -0.02 0.14 -9999 0 -0.51 31 31
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
mol:GDP 0.072 0.01 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0 0.002 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.013 0.032 -9999 0 -0.15 10 10
NME1 0.013 0 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.044 0.007 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0 0.002 -9999 0 -10000 0 0
WASF2 0.002 0.008 -9999 0 -10000 0 0
Rap1/GTP 0 0.003 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.016 0.075 -9999 0 -0.46 12 12
CCND1 0.015 0.038 -9999 0 -0.18 10 10
VAV2 0.056 0.007 -9999 0 -10000 0 0
RAP1/GDP 0 0.004 -9999 0 -10000 0 0
adherens junction assembly 0.045 0.001 -9999 0 -10000 0 0
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.015 0.07 -9999 0 -0.44 12 12
E-cadherin/beta catenin 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.044 0.009 -9999 0 -10000 0 0
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
Rac1/GTP -0.017 0.033 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin 0 0 -9999 0 -10000 0 0
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -9999 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.01 0.018 -9999 0 -10000 0 0
BUB1B 0.017 0.028 -9999 0 -10000 0 0
PLK1 0.017 0.012 -9999 0 -0.098 3 3
PLK1S1 0.015 0.007 -9999 0 -10000 0 0
KIF2A 0.023 0.03 -9999 0 -0.59 1 1
regulation of mitotic centrosome separation 0.017 0.012 -9999 0 -0.098 3 3
GOLGA2 0.013 0 -9999 0 -10000 0 0
Hec1/SPC24 -0.002 0.076 -9999 0 -0.28 16 16
WEE1 0.022 0.011 -9999 0 -10000 0 0
cytokinesis 0.001 0.07 -9999 0 -0.31 3 3
PP2A-alpha B56 -0.018 0.059 -9999 0 -0.73 3 3
AURKA 0.016 0.009 -9999 0 -10000 0 0
PICH/PLK1 0.033 0.019 -9999 0 -10000 0 0
CENPE 0.019 0.049 -9999 0 -0.53 3 3
RhoA/GTP 0 0 -9999 0 -10000 0 0
positive regulation of microtubule depolymerization 0.023 0.029 -9999 0 -0.58 1 1
PPP2CA 0.013 0 -9999 0 -10000 0 0
FZR1 0.013 0 -9999 0 -10000 0 0
TPX2 0.009 0.021 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
SPC24 -0.009 0.081 -9999 0 -0.31 32 32
FBXW11 0.013 0 -9999 0 -10000 0 0
CLSPN 0.005 0.035 -9999 0 -0.35 2 2
GORASP1 0.013 0 -9999 0 -10000 0 0
metaphase 0.001 0.001 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NLP 0.009 0.007 -9999 0 -0.066 3 3
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
STAG2 0.013 0 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.001 0.003 -9999 0 -10000 0 0
spindle elongation 0.017 0.012 -9999 0 -0.098 3 3
ODF2 0.013 0.001 -9999 0 -10000 0 0
BUB1 -0.027 0.068 -9999 0 -0.8 3 3
TPT1 0.015 0.007 -9999 0 -10000 0 0
CDC25C 0.011 0.023 -9999 0 -10000 0 0
CDC25B 0.012 0.026 -9999 0 -0.31 3 3
SGOL1 0.01 0.018 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 0.005 0.013 -9999 0 -10000 0 0
CDC14B 0.005 0.067 -9999 0 -0.65 5 5
CDC20 0.009 0.039 -9999 0 -0.31 7 7
PLK1/PBIP1 0.002 0.023 -9999 0 -0.16 2 2
mitosis 0 0.002 -9999 0 -0.022 3 3
FBXO5 0.021 0.021 -9999 0 -0.4 1 1
CDC2 0.001 0.001 -9999 0 -10000 0 0
NDC80 -0.034 0.12 -9999 0 -0.31 70 70
metaphase plate congression 0.015 0.007 -9999 0 -10000 0 0
ERCC6L 0.007 0.016 -9999 0 -10000 0 0
NLP/gamma Tubulin 0.013 0.009 -9999 0 -0.077 3 3
microtubule cytoskeleton organization 0.015 0.007 -9999 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -9999 0 -0.011 3 3
PPP1R12A 0.013 0 -9999 0 -10000 0 0
interphase 0 0.001 -9999 0 -0.011 3 3
PLK1/PRC1-2 0.004 0.061 -9999 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0 0.004 -9999 0 -10000 0 0
RAB1A 0.013 0 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
Aurora A/BORA 0.018 0.039 -9999 0 -0.48 3 3
mitotic prometaphase 0 0.001 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.034 -9999 0 -0.32 2 2
microtubule-based process -0.005 0.065 -9999 0 -10000 0 0
Golgi organization 0.017 0.012 -9999 0 -0.098 3 3
Cohesin/SA2 -0.001 0.005 -9999 0 -10000 0 0
PPP1CB/MYPT1 0 0 -9999 0 -10000 0 0
KIF20A -0.043 0.12 -9999 0 -0.31 84 84
APC/C/CDC20 0.021 0.024 -9999 0 -10000 0 0
PPP2R1A 0.013 0 -9999 0 -10000 0 0
chromosome segregation 0.002 0.023 -9999 0 -0.16 2 2
PRC1 0.013 0 -9999 0 -10000 0 0
ECT2 0.022 0.039 -9999 0 -0.56 2 2
C13orf34 0.018 0.04 -9999 0 -0.48 3 3
NUDC 0.015 0.007 -9999 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.017 0.027 -9999 0 -10000 0 0
spindle assembly 0.017 0.011 -9999 0 -0.092 3 3
spindle stabilization 0.015 0.007 -9999 0 -10000 0 0
APC/C/HCDH1 0.013 0.058 -9999 0 -0.56 5 5
MKLP2/PLK1 -0.005 0.065 -9999 0 -10000 0 0
CCNB1 0.014 0.001 -9999 0 -10000 0 0
PPP1CB 0.013 0 -9999 0 -10000 0 0
BTRC 0.013 0 -9999 0 -10000 0 0
ROCK2 0.001 0.11 -9999 0 -0.52 21 21
TUBG1 0.015 0.007 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.001 0.009 -9999 0 -10000 0 0
MLF1IP 0.007 0.034 -9999 0 -0.22 11 11
INCENP 0.009 0.054 -9999 0 -0.83 2 2
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.012 0.055 0.38 1 -10000 0 1
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.032 -10000 0 -0.55 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.017 0.15 -10000 0 -0.72 20 20
RhoA/GTP -0.012 0.056 -10000 0 -0.39 1 1
negative regulation of cAMP metabolic process 0.022 0.071 -10000 0 -0.33 17 17
GNAZ 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 0.007 0.054 -10000 0 -0.38 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.022 0.071 -10000 0 -0.34 17 17
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.012 0.038 -10000 0 -0.82 1 1
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.001 0.023 -10000 0 -10000 0 0
oxygen homeostasis 0.016 0.011 -10000 0 -10000 0 0
TCEB2 0.011 0.026 -10000 0 -0.31 3 3
TCEB1 0.013 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.011 0.074 -10000 0 -0.7 4 4
EPO 0.18 0.14 -10000 0 -0.8 2 2
FIH (dimer) 0.029 0.011 -10000 0 -10000 0 0
APEX1 0.027 0.011 -10000 0 -10000 0 0
SERPINE1 0.18 0.17 -10000 0 -0.8 3 3
FLT1 -0.002 0.072 -10000 0 -1.6 1 1
ADORA2A 0.19 0.14 -10000 0 -0.86 2 2
germ cell development 0.19 0.14 -10000 0 -0.85 2 2
SLC11A2 0.19 0.15 -10000 0 -0.89 2 2
BHLHE40 0.18 0.16 -10000 0 -0.89 2 2
HIF1AN 0.029 0.011 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.003 0.076 -10000 0 -0.97 2 2
ETS1 0.03 0.002 -10000 0 -10000 0 0
CITED2 -0.09 0.32 -10000 0 -1.2 37 37
KDR -0.007 0.11 -10000 0 -1.4 3 3
PGK1 0.19 0.15 -10000 0 -0.89 2 2
SIRT1 0.012 0.038 -10000 0 -0.82 1 1
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.2 0.16 -10000 0 -1.2 2 2
EPAS1 0.11 0.1 -10000 0 -0.63 3 3
SP1 0.022 0.002 -10000 0 -10000 0 0
ABCG2 0.19 0.16 -10000 0 -0.88 4 4
EFNA1 0.19 0.15 -10000 0 -0.89 2 2
FXN 0.19 0.14 -10000 0 -0.86 2 2
POU5F1 0.19 0.15 -10000 0 -0.9 2 2
neuron apoptosis -0.2 0.16 1.1 2 -10000 0 2
EP300 0.013 0 -10000 0 -10000 0 0
EGLN3 -0.002 0.14 -10000 0 -0.5 28 28
EGLN2 0.029 0.011 -10000 0 -10000 0 0
EGLN1 0.025 0.056 -10000 0 -0.82 2 2
VHL/Elongin B/Elongin C -0.004 0.048 -10000 0 -0.6 3 3
VHL 0.008 0.066 -10000 0 -0.82 3 3
ARNT 0.027 0.011 -10000 0 -10000 0 0
SLC2A1 0.19 0.14 -10000 0 -0.86 2 2
TWIST1 0.18 0.18 -10000 0 -0.65 11 11
ELK1 0.015 0.026 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.001 0.067 -10000 0 -0.76 2 2
VEGFA 0.19 0.16 -10000 0 -0.84 4 4
CREBBP 0.013 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.032 0 -9999 0 -10000 0 0
SNTA1 0.013 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.032 0.009 -9999 0 -10000 0 0
MAPK12 0.02 0.078 -9999 0 -0.48 11 11
CCND1 0.017 0.034 -9999 0 -0.25 1 1
p38 gamma/SNTA1 0.025 0.073 -9999 0 -0.46 10 10
MAP2K3 0.013 0 -9999 0 -10000 0 0
PKN1 0.013 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.02 0.077 -9999 0 -0.48 11 11
MAP2K6 0.013 0.083 -9999 0 -0.53 11 11
MAPT 0.024 0.045 -9999 0 -0.4 3 3
MAPK13 0.024 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.017 0.021 -9999 0 -0.45 1 1
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.006 -10000 0 -10000 0 0
DOCK1 0.006 0.076 -10000 0 -0.82 4 4
ITGA4 0.004 0.069 -10000 0 -0.41 11 11
RAC1 0.013 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.03 0.12 -10000 0 -0.62 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.005 0.041 -10000 0 -0.55 2 2
alpha4/beta7 Integrin/Paxillin -0.022 0.088 -10000 0 -0.5 14 14
lamellipodium assembly -0.004 0.058 -10000 0 -0.54 5 5
PIK3CA 0.008 0.066 -10000 0 -0.82 3 3
PI3K -0.004 0.049 -10000 0 -0.63 3 3
ARF6 0.013 0 -10000 0 -10000 0 0
TLN1 0.013 0 -10000 0 -10000 0 0
PXN 0.024 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
ARF6/GTP -0.004 0.03 -10000 0 -0.42 2 2
cell adhesion -0.004 0.033 -10000 0 -0.46 2 2
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.004 0.036 -10000 0 -0.5 2 2
ITGB1 0.013 0 -10000 0 -10000 0 0
ITGB7 -0.02 0.14 -10000 0 -0.51 31 31
ARF6/GDP 0.001 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.011 0.07 -10000 0 -0.53 7 7
p130Cas/Crk/Dock1 -0.004 0.049 -10000 0 -0.55 4 4
VCAM1 -0.001 0.099 -10000 0 -0.57 12 12
alpha4/beta1 Integrin/Paxillin/Talin -0.004 0.033 -10000 0 -0.46 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 -0.004 0.033 -10000 0 -0.46 2 2
BCAR1 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.004 0.033 0.46 2 -10000 0 2
CBL 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
GIT1 0.013 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.004 0.033 -10000 0 -0.46 2 2
Rac1/GTP -0.005 0.068 -10000 0 -0.63 5 5
PDGFR-beta 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
S1P1/Sphingosine-1-phosphate -0.001 0.04 -9999 0 -0.74 1 1
PDGFB-D/PDGFRB/SLAP -0.002 0.03 -9999 0 -0.64 1 1
PDGFB-D/PDGFRB/APS/CBL -0.001 0.026 -9999 0 -0.55 1 1
AKT1 0.059 0.044 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.024 0.051 -9999 0 -0.79 1 1
PIK3CA 0.008 0.066 -9999 0 -0.82 3 3
FGR 0.002 0.029 -9999 0 -0.56 1 1
mol:Ca2+ 0.02 0.049 -9999 0 -0.82 1 1
MYC 0.018 0.15 -9999 0 -0.84 14 14
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.011 0.029 -9999 0 -0.45 1 1
LRP1/PDGFRB/PDGFB -0.002 0.035 -9999 0 -0.55 2 2
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.012 0.038 -9999 0 -0.82 1 1
GO:0007205 0.02 0.049 -9999 0 -0.85 1 1
PTEN 0.012 0.038 -9999 0 -0.82 1 1
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 -0.042 0.12 -9999 0 -0.31 82 82
PDGFB-D/PDGFRB/SHP2 -0.003 0.041 -9999 0 -0.64 2 2
PDGFB-D/PDGFRB/GRB10 -0.001 0.029 -9999 0 -0.64 1 1
cell cycle arrest -0.002 0.03 -9999 0 -0.63 1 1
HRAS 0.012 0.021 -9999 0 -0.31 2 2
HIF1A 0.064 0.04 -9999 0 -10000 0 0
GAB1 0.013 0.064 -9999 0 -0.87 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.02 0.06 -9999 0 -0.78 1 1
PDGFB-D/PDGFRB 0.012 0.031 -9999 0 -0.57 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.001 0.029 -9999 0 -0.64 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.001 0.048 -9999 0 -0.75 1 1
positive regulation of MAPKKK cascade -0.002 0.041 -9999 0 -0.64 2 2
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.02 0.05 -9999 0 -0.86 1 1
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.013 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.036 0.084 -9999 0 -0.8 1 1
SHB 0.013 0 -9999 0 -10000 0 0
BLK -0.18 0.28 -9999 0 -0.62 143 143
PTPN2 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.001 0.029 -9999 0 -0.64 1 1
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 0.017 0.071 -9999 0 -0.87 1 1
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.001 0.029 -9999 0 -0.64 1 1
LCK -0.008 0.088 -9999 0 -0.73 6 6
PDGFRB 0.012 0.038 -9999 0 -0.83 1 1
ACP1 0.013 0 -9999 0 -10000 0 0
HCK 0.005 0.035 -9999 0 -0.55 1 1
ABL1 0.009 0.061 -9999 0 -0.83 1 1
PDGFB-D/PDGFRB/CBL 0.009 0.068 -9999 0 -0.95 1 1
PTPN1 0.014 0.002 -9999 0 -10000 0 0
SNX15 0.013 0 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
STAT1 0.006 0.049 -9999 0 -0.31 11 11
cell proliferation 0.02 0.13 -9999 0 -0.73 14 14
SLA 0.013 0.015 -9999 0 -0.31 1 1
actin cytoskeleton reorganization 0.052 0.025 -9999 0 -10000 0 0
SRC 0.005 0.029 -9999 0 -0.56 1 1
PI3K -0.004 0.041 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.028 0.066 -9999 0 -0.7 1 1
SH2B2 0.013 0.015 -9999 0 -0.31 1 1
PLCgamma1/SPHK1 0.024 0.053 -9999 0 -0.83 1 1
LYN 0.006 0.029 -9999 0 -0.56 1 1
LRP1 0.012 0.038 -9999 0 -0.82 1 1
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.013 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0 0.021 -9999 0 -0.45 1 1
SPHK1 0.007 0.049 -9999 0 -0.31 11 11
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.02 0.05 -9999 0 -0.86 1 1
PLCG1 0.02 0.052 -9999 0 -0.9 1 1
NHERF/PDGFRB -0.002 0.027 -9999 0 -0.55 1 1
YES1 0.003 0.028 -9999 0 -0.56 1 1
cell migration -0.002 0.027 -9999 0 -0.54 1 1
SHC/Grb2/SOS1 0 0.021 -9999 0 -0.45 1 1
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0.021 -9999 0 -0.31 2 2
NHERF1-2/PDGFRB/PTEN -0.003 0.033 -9999 0 -0.5 2 2
FYN 0.006 0.029 -9999 0 -0.56 1 1
DOK1 0.034 0.025 -9999 0 -0.5 1 1
HRAS/GTP -0.001 0.014 -9999 0 -10000 0 0
PDGFB 0.013 0 -9999 0 -10000 0 0
RAC1 0.027 0.09 -9999 0 -0.44 14 14
PRKCD 0.034 0.025 -9999 0 -0.51 1 1
FER 0.031 0.05 -9999 0 -0.51 4 4
MAPKKK cascade -0.001 0.021 -9999 0 -0.44 1 1
RASA1 0.034 0.025 -9999 0 -0.51 1 1
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.017 0.03 -9999 0 -0.46 1 1
PDGFB-D/PDGFRB/SHB -0.001 0.029 -9999 0 -0.64 1 1
chemotaxis 0.01 0.06 -9999 0 -0.79 1 1
STAT1-3-5/STAT1-3-5 -0.003 0.023 -9999 0 -0.43 1 1
Bovine Papilomavirus E5/PDGFRB 0.001 0.03 -9999 0 -0.65 1 1
PTPRJ 0.013 0 -9999 0 -10000 0 0
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.017 0.15 -9999 0 -0.72 20 20
CDC42/GTP -0.011 0.054 -9999 0 -0.32 1 1
PLCG1 0.03 0.065 -9999 0 -0.33 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.011 0.053 -9999 0 -0.32 1 1
S1PR5 0.007 0.054 -9999 0 -0.38 8 8
S1PR4 0.01 0.033 -9999 0 -0.31 5 5
MAPK3 0.03 0.065 -9999 0 -0.31 17 17
MAPK1 0.03 0.065 -9999 0 -0.33 1 1
S1P/S1P5/Gi 0.022 0.071 -9999 0 -0.34 17 17
GNAI1 0.012 0.038 -9999 0 -0.82 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.004 0.032 -9999 0 -0.55 1 1
RHOA 0.032 0.016 -9999 0 -10000 0 0
S1P/S1P4/Gi 0.023 0.069 -9999 0 -0.33 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 -0.001 0.014 -9999 0 -10000 0 0
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.002 0.031 -9999 0 -0.39 3 3
TRAF2/ASK1 -0.001 0.025 -9999 0 -0.55 1 1
ATM 0.012 0.038 -9999 0 -0.82 1 1
MAP2K3 0.026 0.057 -9999 0 -0.53 2 2
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.025 0.078 -9999 0 -0.44 6 6
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G -0.001 0.1 -9999 0 -0.67 10 10
TXN 0.009 0.006 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GADD45B -0.014 0.15 -9999 0 -0.82 16 16
MAP3K1 0.013 0 -9999 0 -10000 0 0
MAP3K6 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
MAP3K4 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.001 0.029 -9999 0 -0.63 1 1
TAK1/TAB family -0.001 0.014 -9999 0 -0.22 2 2
RAC1/OSM/MEKK3 0 0.006 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.008 0.033 -9999 0 -0.47 1 1
TRAF6 0.007 0.03 -9999 0 -0.46 2 2
RAC1 0.013 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B 0.005 0.084 -9999 0 -0.82 5 5
CCM2 0.013 0.015 -9999 0 -0.31 1 1
CaM/Ca2+/CAMKIIB -0.006 0.056 -9999 0 -0.55 5 5
MAPK11 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.006 0.064 -9999 0 -0.6 5 5
OSM/MEKK3 0 0.009 -9999 0 -10000 0 0
TAOK1 -0.038 0.16 -9999 0 -0.46 57 57
TAOK2 0.017 0.021 -9999 0 -0.45 1 1
TAOK3 0.017 0.021 -9999 0 -0.45 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.012 0.038 -9999 0 -0.82 1 1
MAP3K10 0.013 0 -9999 0 -10000 0 0
MAP3K3 0.013 0 -9999 0 -10000 0 0
TRX/ASK1 0.015 0.026 -9999 0 -0.55 1 1
GADD45/MTK1/MTK1 -0.023 0.1 -9999 0 -0.49 22 22
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.045 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.049 0.02 -9999 0 -0.39 1 1
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.001 0.019 -9999 0 -0.42 1 1
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.022 0 -9999 0 -10000 0 0
MAP3K1 0.013 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.036 0.15 -9999 0 -0.63 28 28
MAPK3 0.013 0 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
KPNB1 0.013 0 -9999 0 -10000 0 0
TGFBRAP1 -0.035 0.2 -9999 0 -0.82 28 28
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.012 0.038 -9999 0 -0.82 1 1
KPNA2 0.013 0 -9999 0 -10000 0 0
PIAS4 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.001 0.022 -9999 0 -0.5 1 1
HDAC3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC5 0 0 -9999 0 -10000 0 0
GATA2/HDAC5 0 0.009 -9999 0 -10000 0 0
HDAC5/BCL6/BCoR -0.001 0.025 -9999 0 -0.55 1 1
HDAC9 -0.018 0.097 -9999 0 -0.31 47 47
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
GATA2 0.013 0.015 -9999 0 -0.31 1 1
HDAC4/RFXANK -0.001 0.013 -9999 0 -10000 0 0
BCOR 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.013 0 -9999 0 -10000 0 0
HDAC5 0.013 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.029 -9999 0 -0.63 1 1
Histones 0.035 0.024 -9999 0 -10000 0 0
ADRBK1 0.013 0 -9999 0 -10000 0 0
HDAC4 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.013 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.013 0 -9999 0 -10000 0 0
HDAC6 0.013 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.013 -9999 0 -10000 0 0
CAMK4 -0.005 0.11 -9999 0 -0.54 16 16
Tubulin/HDAC6 -0.006 0.055 -9999 0 -0.55 5 5
SUMO1 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
GATA1 0.009 0.006 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
NR3C1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -10000 0 0
SRF 0.013 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.006 0.064 -9999 0 -0.63 5 5
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
RANGAP1 0.013 0 -9999 0 -10000 0 0
BCL6/BCoR -0.001 0.029 -9999 0 -0.63 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.011 0.068 -9999 0 -0.55 7 7
HDAC4/ER alpha -0.044 0.14 -9999 0 -0.63 24 24
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.035 0.024 -9999 0 -10000 0 0
cell motility -0.006 0.055 -9999 0 -0.54 5 5
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.012 0.038 -9999 0 -0.82 1 1
HDAC4/CaMK II delta B 0.013 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.049 0.19 -9999 0 -0.54 55 55
HDAC6/HDAC11 0 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.012 0.038 -9999 0 -0.82 1 1
RAN 0.013 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.001 0.021 -9999 0 -0.46 1 1
GNG2 0.012 0.038 -9999 0 -0.82 1 1
NCOR2 0.013 0 -9999 0 -10000 0 0
TUBB2A 0.005 0.084 -9999 0 -0.82 5 5
HDAC11 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
ANKRA2 0.013 0 -9999 0 -10000 0 0
RFXANK 0.012 0.021 -9999 0 -0.31 2 2
nuclear import 0 0 -9999 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.028 0.007 -9999 0 -10000 0 0
BIRC5 -0.016 0.098 -9999 0 -0.33 42 42
NFKBIA 0.032 0.008 -9999 0 -10000 0 0
CPEB1 -0.049 0.22 -9999 0 -0.82 36 36
AKT1 0.032 0.008 -9999 0 -10000 0 0
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.003 0.011 -9999 0 -10000 0 0
NDEL1/TACC3 0.003 0.013 -9999 0 -10000 0 0
GADD45A 0.013 0 -9999 0 -10000 0 0
GSK3B 0.013 0.005 -9999 0 -10000 0 0
PAK1/Aurora A 0.028 0.007 -9999 0 -10000 0 0
MDM2 0.013 0 -9999 0 -10000 0 0
JUB 0.012 0.038 -9999 0 -0.82 1 1
TPX2 0.002 0.068 -9999 0 -10000 0 0
TP53 0.031 0.006 -9999 0 -10000 0 0
DLG7 0.021 0.008 -9999 0 -10000 0 0
AURKAIP1 0.012 0.021 -9999 0 -0.31 2 2
ARHGEF7 0.013 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.003 0.014 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.003 0.011 -9999 0 -10000 0 0
AURKA 0.026 0.011 -9999 0 -10000 0 0
AURKB -0.014 0.027 -9999 0 -0.14 3 3
CDC25B 0.007 0.018 -9999 0 -10000 0 0
G2/M transition checkpoint 0.002 0.025 -9999 0 -0.5 1 1
mRNA polyadenylation -0.035 0.13 -9999 0 -0.5 36 36
Aurora A/CPEB -0.035 0.13 -9999 0 -0.5 36 36
Aurora A/TACC1/TRAP/chTOG 0.003 0.026 -9999 0 -0.47 1 1
BRCA1 0.013 0 -9999 0 -10000 0 0
centrosome duplication 0.028 0.007 -9999 0 -10000 0 0
regulation of centrosome cycle 0.002 0.011 -9999 0 -10000 0 0
spindle assembly 0.002 0.024 -9999 0 -0.46 1 1
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.01 0.036 -9999 0 -0.45 1 1
CENPA -0.009 0.026 -9999 0 -0.26 3 3
Aurora A/PP2A 0.028 0.007 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.038 0.008 -9999 0 -10000 0 0
negative regulation of DNA binding 0.031 0.006 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
Ajuba/Aurora A 0.002 0.025 -9999 0 -0.5 1 1
mitotic prometaphase 0.005 0.01 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.011 -9999 0 -10000 0 0
TACC1 0.012 0.038 -9999 0 -0.82 1 1
TACC3 0.013 0.015 -9999 0 -0.31 1 1
Aurora A/Antizyme1 0.003 0.016 -9999 0 -10000 0 0
Aurora A/RasGAP 0.028 0.007 -9999 0 -10000 0 0
OAZ1 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.005 -9999 0 -10000 0 0
GIT1 0.013 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.002 0.068 -9999 0 -10000 0 0
PPP2R5D 0.013 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.019 0.05 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
CKAP5 0.013 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.051 0.039 -10000 0 -0.44 3 3
adherens junction organization 0.041 0.037 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.053 0.057 -10000 0 -0.74 1 1
FMN1 0.022 0.11 -10000 0 -0.44 25 25
mol:IP3 -0.003 0.032 -10000 0 -0.41 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.04 0.012 -10000 0 -10000 0 0
CTNNB1 0.013 0 -10000 0 -10000 0 0
AKT1 0.049 0.035 -10000 0 -0.4 3 3
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.046 0.006 -10000 0 -10000 0 0
CTNND1 0.014 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.036 -10000 0 -0.49 2 2
VASP 0.047 0.011 -10000 0 -10000 0 0
ZYX 0.047 0.011 -10000 0 -10000 0 0
JUB 0.046 0.025 -10000 0 -0.43 1 1
EGFR(dimer) 0.042 0.048 -10000 0 -0.47 4 4
E-cadherin/beta catenin-gamma catenin 0 0.003 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.033 -10000 0 -0.43 3 3
PIK3CA 0.009 0.066 -10000 0 -0.82 3 3
PI3K -0.003 0.034 -10000 0 -0.44 3 3
FYN 0.05 0.035 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.031 -10000 0 -0.4 3 3
JUP 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.001 -10000 0 -10000 0 0
mol:DAG -0.003 0.032 -10000 0 -0.41 3 3
CDH1 0.013 0 -10000 0 -10000 0 0
RhoA/GDP 0.053 0.057 -10000 0 -0.74 1 1
establishment of polarity of embryonic epithelium 0.046 0.011 -10000 0 -10000 0 0
SRC 0.013 0.015 -10000 0 -0.31 1 1
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR 0.006 0.076 -10000 0 -0.82 4 4
CASR 0.042 0.038 -10000 0 -0.38 3 3
RhoA/GTP -0.002 0.028 -10000 0 -0.36 3 3
AKT2 0.049 0.035 -10000 0 -0.4 3 3
actin cable formation 0.029 0.1 -10000 0 -0.42 25 25
apoptosis 0.003 0.032 0.41 3 -10000 0 3
CTNNA1 0.014 0.001 -10000 0 -10000 0 0
mol:GDP 0.047 0.061 -10000 0 -0.48 6 6
PIP5K1A 0.045 0.037 -10000 0 -0.5 2 2
PLCG1 -0.003 0.033 -10000 0 -0.42 3 3
Rac1/GTP -0.004 0.039 -10000 0 -0.42 4 4
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.01 0.033 -9999 0 -0.31 5 5
PLK4 0.013 0 -9999 0 -10000 0 0
regulation of centriole replication 0.022 0.023 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.02 0.16 -10000 0 -0.73 22 22
CLTC 0.034 0 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.029 0 -10000 0 -10000 0 0
Dynamin 2/GTP 0 0 -10000 0 -10000 0 0
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.031 0 -10000 0 -10000 0 0
CPE 0.011 0.073 -10000 0 -0.56 8 8
CTNNB1 0.013 0 -10000 0 -10000 0 0
membrane fusion 0.028 0 -10000 0 -10000 0 0
CTNND1 0.034 0 -10000 0 -10000 0 0
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.035 0 -10000 0 -10000 0 0
TSHR 0.018 0.037 -10000 0 -0.56 2 2
INS 0.013 0 -10000 0 -10000 0 0
BIN1 0.013 0 -10000 0 -10000 0 0
mol:Choline 0.028 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.02 0 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
JUP 0.031 0 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.001 0.023 -10000 0 -0.5 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.031 0 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.013 0.015 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.013 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.046 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.013 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0 0 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0.008 -10000 0 -10000 0 0
ACAP1 0.027 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.001 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.04 0.002 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.046 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.034 0 -10000 0 -10000 0 0
NME1 0.02 0 -10000 0 -10000 0 0
clathrin coat assembly 0.034 0 -10000 0 -10000 0 0
IL2RA 0.011 0.07 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.016 0.077 -10000 0 -0.41 18 18
EXOC6 0.013 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.035 0 -10000 0 -10000 0 0
SDC1 0.03 0.008 -10000 0 -10000 0 0
ARF6/GDP 0.019 0 -10000 0 -10000 0 0
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.028 0 -10000 0 -10000 0 0
endocytosis 0.001 0.023 0.5 1 -10000 0 1
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.028 0.077 -10000 0 -0.44 13 13
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.012 0.038 -10000 0 -0.82 1 1
Dynamin 2/GDP 0.027 0 -10000 0 -10000 0 0
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 0.031 0.068 -10000 0 -0.44 10 10
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0 0 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.085 0.11 -9999 0 -9999 0 0
TP53 -0.028 0.033 -9999 0 -9999 0 0
Senescence -0.028 0.033 -9999 0 -9999 0 0
Apoptosis -0.028 0.033 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 0.054 0.062 -9999 0 -9999 0 0
MDM4 0.013 0 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.032 0 -9999 0 -9999 0 0
HDAC4 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.013 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.018 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.031 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.013 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.013 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -9999 0 0
RANGAP1 0.013 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.013 0 -9999 0 -9999 0 0
UBE2I 0.013 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.013 0 -9999 0 -9999 0 0
PIAS1 0.013 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 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 0 -9999 0 -9999 0 0
E-cadherin/beta catenin 0 0 -9999 0 -9999 0 0
CTNNB1 0.013 0 -9999 0 -9999 0 0
JUP 0.013 0 -9999 0 -9999 0 0
CDH1 0.013 0 -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 0.001 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.021 0.015 -9999 0 -0.21 2 2
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.003 -9999 0 -10000 0 0
CLTB 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.027 0 -9999 0 -10000 0 0
CD4 0.003 0.057 -9999 0 -0.31 15 15
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.027 -9999 0 -0.43 2 2
ARF1/GTP -0.001 0.016 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.029 0 -9999 0 -10000 0 0
mol:Choline -0.002 0.027 -9999 0 -0.42 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 -0.002 0.028 -9999 0 -0.43 2 2
ARF1/GDP 0 0.007 -9999 0 -10000 0 0
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0.001 -9999 0 -10000 0 0
Rac/GTP 0 0.001 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0.002 -9999 0 -10000 0 0
ARFIP2 0 0.005 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.027 0.008 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin -0.001 0.01 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.029 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin -0.001 0.009 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.004 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0.002 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.036 0.014 -9999 0 -10000 0 0
PLD2 -0.002 0.027 -9999 0 -0.43 2 2
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A -0.002 0.028 -9999 0 -0.43 2 2
ARF1/GTP/Membrin/GBF1/p115 -0.001 0.015 -9999 0 -0.24 2 2
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.027 -9999 0 -0.42 2 2
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 -0.001 0.011 -9999 0 -10000 0 0
USO1 -0.001 0.011 -9999 0 -10000 0 0
GBF1 -0.001 0.011 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.003 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.005 0.027 -9999 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 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0 0 -9999 0 -10000 0 0
NFKB1 0.012 0.038 -9999 0 -0.82 1 1
MAP3K14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.001 0.029 -9999 0 -0.63 1 1
RELB 0.013 0 -9999 0 -10000 0 0
NFKB2 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB 0 0 -9999 0 -10000 0 0
regulation of B cell activation 0 0 -9999 0 -10000 0 0
Inferred Pathway Levels Matrix

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

pid_entity TCGA.MK.A4N9 TCGA.MK.A4N7 TCGA.MK.A4N6 TCGA.L6.A4EU
109_MAP3K5 -0.28 -0.017 -0.017 -0.017
47_PPARGC1A -0.82 -0.82 -0.82 0.013
105_BMP4 0.013 -0.31 0.013 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 0.013 0.013 0.013 0.013
105_BMP2 0.013 0.013 0.013 0.013
131_RELN/VLDLR -0.5 -0.5 -0.5 -0.5
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.013 0.013
84_STAT5B 0.047 -0.097 0 -0.097
84_STAT5A 0.047 -0.097 0 -0.097
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/3353350/THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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