PARADIGM pathway analysis of mRNASeq expression data
Kidney Renal Clear Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C18K783Q
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C18K783Q
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 48 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
TCGA08_retinoblastoma 258
HIF-1-alpha transcription factor network 201
Nephrin/Neph1 signaling in the kidney podocyte 183
TCR signaling in naïve CD8+ T cells 148
TCGA08_p53 146
Syndecan-4-mediated signaling events 120
Aurora B signaling 119
FOXA2 and FOXA3 transcription factor networks 117
IL12-mediated signaling events 116
Glypican 1 network 106
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 533 . 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 ( 533 ).

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
TCGA08_retinoblastoma 0.4841 258 2071 8 -0.84 0.22 1000 -1000 -0.042 -1000
HIF-1-alpha transcription factor network 0.3771 201 15296 76 -1.3 0.026 1000 -1000 -0.18 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.3433 183 6222 34 -0.6 0.016 1000 -1000 -0.11 -1000
TCR signaling in naïve CD8+ T cells 0.2777 148 13797 93 -0.66 0.33 1000 -1000 -0.11 -1000
TCGA08_p53 0.2739 146 1027 7 -0.65 0.31 1000 -1000 -0.019 -1000
Syndecan-4-mediated signaling events 0.2251 120 8066 67 -0.64 0.11 1000 -1000 -0.14 -1000
Aurora B signaling 0.2233 119 8035 67 -0.4 0.016 1000 -1000 -0.11 -1000
FOXA2 and FOXA3 transcription factor networks 0.2195 117 5395 46 -1.2 0.025 1000 -1000 -0.095 -1000
IL12-mediated signaling events 0.2176 116 10111 87 -0.69 0.16 1000 -1000 -0.14 -1000
Glypican 1 network 0.1989 106 5123 48 -0.56 0.045 1000 -1000 -0.078 -1000
FOXM1 transcription factor network 0.1970 105 5382 51 -0.82 0.04 1000 -1000 -0.2 -1000
PDGFR-alpha signaling pathway 0.1951 104 4618 44 -0.27 0.034 1000 -1000 -0.096 -1000
amb2 Integrin signaling 0.1576 84 6888 82 -0.55 0.016 1000 -1000 -0.12 -1000
IL4-mediated signaling events 0.1463 78 7117 91 -0.84 0.54 1000 -1000 -0.17 -1000
Caspase cascade in apoptosis 0.1445 77 5751 74 -0.32 0.16 1000 -1000 -0.093 -1000
JNK signaling in the CD4+ TCR pathway 0.1445 77 1318 17 -0.41 0.016 1000 -1000 -0.092 -1000
EGFR-dependent Endothelin signaling events 0.1388 74 1567 21 -0.67 0.016 1000 -1000 -0.11 -1000
Aurora C signaling 0.1332 71 499 7 -0.39 0.012 1000 -1000 -0.064 -1000
VEGFR1 specific signals 0.1332 71 3991 56 -0.47 0.046 1000 -1000 -0.12 -1000
Glypican 2 network 0.1313 70 281 4 -0.12 -1000 1000 -1000 -0.052 -1000
Syndecan-1-mediated signaling events 0.1257 67 2303 34 -0.41 0.016 1000 -1000 -0.11 -1000
BMP receptor signaling 0.1182 63 5108 81 -0.69 0.016 1000 -1000 -0.13 -1000
HIF-2-alpha transcription factor network 0.1144 61 2637 43 -0.76 0.34 1000 -1000 -0.12 -1000
IL23-mediated signaling events 0.1144 61 3673 60 -0.39 0.021 1000 -1000 -0.19 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.1144 61 2013 33 -0.83 0.016 1000 -1000 -0.089 -1000
Signaling events mediated by the Hedgehog family 0.0957 51 2691 52 -0.44 0.12 1000 -1000 -0.11 -1000
Fc-epsilon receptor I signaling in mast cells 0.0901 48 4663 97 -0.32 0.04 1000 -1000 -0.13 -1000
IL27-mediated signaling events 0.0844 45 2319 51 -0.62 0.074 1000 -1000 -0.096 -1000
S1P1 pathway 0.0807 43 1551 36 -0.38 0.018 1000 -1000 -0.092 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0788 42 2877 68 -0.55 0.063 1000 -1000 -0.17 -1000
Ephrin A reverse signaling 0.0769 41 292 7 -0.059 0 1000 -1000 -0.052 -1000
Effects of Botulinum toxin 0.0769 41 1091 26 -0.36 0.016 1000 -1000 -0.092 -1000
Arf6 signaling events 0.0750 40 2485 62 -0.67 0.016 1000 -1000 -0.086 -1000
Calcium signaling in the CD4+ TCR pathway 0.0713 38 1194 31 -0.46 0.016 1000 -1000 -0.16 -1000
p75(NTR)-mediated signaling 0.0675 36 4581 125 -0.41 0.016 1000 -1000 -0.15 -1000
IL2 signaling events mediated by PI3K 0.0657 35 2030 58 -0.43 0.032 1000 -1000 -0.11 -1000
LPA4-mediated signaling events 0.0638 34 417 12 -0.16 0.026 1000 -1000 -0.041 -1000
IL2 signaling events mediated by STAT5 0.0638 34 751 22 -0.44 0.038 1000 -1000 -0.081 -1000
Coregulation of Androgen receptor activity 0.0582 31 2356 76 -0.92 0.033 1000 -1000 -0.073 -1000
PLK1 signaling events 0.0582 31 2656 85 -0.38 0.016 1000 -1000 -0.08 -1000
Integrins in angiogenesis 0.0582 31 2613 84 -0.38 0.04 1000 -1000 -0.13 -1000
BCR signaling pathway 0.0582 31 3154 99 -0.34 0.035 1000 -1000 -0.14 -1000
Glucocorticoid receptor regulatory network 0.0563 30 3429 114 -0.41 0.16 1000 -1000 -0.098 -1000
Regulation of Telomerase 0.0563 30 3129 102 -0.67 0.051 1000 -1000 -0.14 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0544 29 2279 78 -0.32 0.045 1000 -1000 -0.11 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0525 28 1541 54 -0.65 0.031 1000 -1000 -0.13 -1000
EPO signaling pathway 0.0525 28 1566 55 -0.29 0.018 1000 -1000 -0.13 -1000
IL6-mediated signaling events 0.0507 27 2091 75 -0.29 0.076 1000 -1000 -0.13 -1000
Reelin signaling pathway 0.0450 24 1392 56 -0.24 0.016 1000 -1000 -0.12 -1000
Visual signal transduction: Rods 0.0450 24 1256 52 -0.29 0.016 1000 -1000 -0.12 -1000
Signaling events mediated by PTP1B 0.0432 23 1765 76 -0.67 0.049 1000 -1000 -0.12 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0432 23 2094 88 -0.31 0.075 1000 -1000 -0.16 -1000
Aurora A signaling 0.0413 22 1323 60 -0.24 0.053 1000 -1000 -0.11 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0413 22 1005 45 -0.57 0.062 1000 -1000 -0.13 -1000
Syndecan-2-mediated signaling events 0.0394 21 1454 69 -0.55 0.053 1000 -1000 -0.1 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0394 21 2530 120 -0.16 0.14 1000 -1000 -0.11 -1000
Endothelins 0.0338 18 1780 96 -0.35 0.086 1000 -1000 -0.1 -1000
Wnt signaling 0.0338 18 127 7 -0.068 0.016 1000 -1000 -0.085 -1000
Class I PI3K signaling events 0.0338 18 1325 73 -0.47 0.036 1000 -1000 -0.11 -1000
Regulation of nuclear SMAD2/3 signaling 0.0319 17 2404 136 -0.45 0.1 1000 -1000 -0.13 -1000
Presenilin action in Notch and Wnt signaling 0.0319 17 1039 61 -0.19 0.092 1000 -1000 -0.11 -1000
S1P3 pathway 0.0319 17 720 42 -0.37 0.062 1000 -1000 -0.089 -1000
Thromboxane A2 receptor signaling 0.0300 16 1776 105 -0.67 0.067 1000 -1000 -0.11 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0300 16 610 37 -0.29 0.026 1000 -1000 -0.13 -1000
LPA receptor mediated events 0.0300 16 1665 102 -0.4 0.06 1000 -1000 -0.13 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0281 15 426 28 -0.14 0.023 1000 -1000 -0.081 -1000
Ceramide signaling pathway 0.0281 15 1164 76 -0.67 0.23 1000 -1000 -0.091 -1000
FoxO family signaling 0.0281 15 997 64 -0.57 0.12 1000 -1000 -0.11 -1000
PLK2 and PLK4 events 0.0263 14 44 3 -0.016 0.011 1000 -1000 -0.036 -1000
E-cadherin signaling events 0.0263 14 71 5 -0.023 0.016 1000 -1000 -0.07 -1000
IFN-gamma pathway 0.0244 13 887 68 -0.37 0.018 1000 -1000 -0.13 -1000
FAS signaling pathway (CD95) 0.0244 13 647 47 -0.42 0.028 1000 -1000 -0.075 -1000
Canonical Wnt signaling pathway 0.0244 13 713 51 -0.19 0.096 1000 -1000 -0.088 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0244 13 1729 125 -0.39 0.043 1000 -1000 -0.15 -1000
Regulation of Androgen receptor activity 0.0244 13 932 70 -0.96 0.04 1000 -1000 -0.094 -1000
Nongenotropic Androgen signaling 0.0225 12 639 52 -0.18 0.071 1000 -1000 -0.086 -1000
ErbB4 signaling events 0.0206 11 796 69 -0.18 0.1 1000 -1000 -0.13 -1000
S1P5 pathway 0.0206 11 197 17 -0.14 0.046 1000 -1000 -0.074 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0206 11 836 74 -0.67 0.099 1000 -1000 -0.14 -1000
S1P4 pathway 0.0206 11 287 25 -0.14 0.033 1000 -1000 -0.075 -1000
Visual signal transduction: Cones 0.0169 9 363 38 -0.041 0.016 1000 -1000 -0.095 -1000
Noncanonical Wnt signaling pathway 0.0169 9 254 26 -0.12 0.016 1000 -1000 -0.13 -1000
a4b1 and a4b7 Integrin signaling 0.0169 9 48 5 -0.02 0.016 1000 -1000 -0.051 -1000
TCGA08_rtk_signaling 0.0169 9 238 26 -0.28 0.041 1000 -1000 -0.033 -1000
Signaling events regulated by Ret tyrosine kinase 0.0150 8 692 82 -0.064 0.025 1000 -1000 -0.13 -1000
Class IB PI3K non-lipid kinase events 0.0150 8 24 3 -0.003 0.003 1000 -1000 -0.021 -1000
Signaling events mediated by PRL 0.0131 7 245 34 -0.055 0.045 1000 -1000 -0.091 -1000
Canonical NF-kappaB pathway 0.0113 6 268 39 -0.19 0.075 1000 -1000 -0.12 -1000
Insulin-mediated glucose transport 0.0113 6 192 32 -0.083 0.068 1000 -1000 -0.099 -1000
Signaling events mediated by HDAC Class III 0.0113 6 242 40 -0.058 0.032 1000 -1000 -0.066 -1000
IL1-mediated signaling events 0.0113 6 400 62 -0.09 0.059 1000 -1000 -0.14 -1000
Ephrin B reverse signaling 0.0113 6 335 48 -0.03 0.031 1000 -1000 -0.1 -1000
Signaling mediated by p38-alpha and p38-beta 0.0113 6 271 44 -0.046 0.049 1000 -1000 -0.069 -1000
Plasma membrane estrogen receptor signaling 0.0113 6 540 86 -0.16 0.07 1000 -1000 -0.13 -1000
p38 MAPK signaling pathway 0.0113 6 276 44 -0.099 0.049 1000 -1000 -0.1 -1000
ErbB2/ErbB3 signaling events 0.0094 5 387 65 -0.13 0.059 1000 -1000 -0.1 -1000
Arf6 downstream pathway 0.0094 5 225 43 -0.033 0.033 1000 -1000 -0.057 -1000
Signaling mediated by p38-gamma and p38-delta 0.0094 5 85 15 0 0.036 1000 -1000 -0.049 -1000
Syndecan-3-mediated signaling events 0.0094 5 209 35 -0.039 0.016 1000 -1000 -0.12 -1000
E-cadherin signaling in the nascent adherens junction 0.0094 5 407 76 -0.026 0.067 1000 -1000 -0.12 -1000
Arf6 trafficking events 0.0094 5 413 71 -0.12 0.058 1000 -1000 -0.11 -1000
Ras signaling in the CD4+ TCR pathway 0.0094 5 85 17 -0.037 0.055 1000 -1000 -0.064 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0075 4 363 85 -0.037 0.079 1000 -1000 -0.11 -1000
EPHB forward signaling 0.0075 4 376 85 -0.075 0.069 1000 -1000 -0.14 -1000
BARD1 signaling events 0.0056 3 217 57 -0.17 0.044 1000 -1000 -0.1 -1000
Osteopontin-mediated events 0.0056 3 123 38 -0.03 0.096 1000 -1000 -0.15 -1000
Cellular roles of Anthrax toxin 0.0056 3 119 39 -0.022 0.027 1000 -1000 -0.042 -1000
Paxillin-dependent events mediated by a4b1 0.0056 3 138 36 -0.026 0.031 1000 -1000 -0.1 -1000
PDGFR-beta signaling pathway 0.0056 3 386 97 -0.058 0.087 1000 -1000 -0.12 -1000
E-cadherin signaling in keratinocytes 0.0056 3 133 43 -0.29 0.054 1000 -1000 -0.12 -1000
Hedgehog signaling events mediated by Gli proteins 0.0038 2 134 65 -0.06 0.093 1000 -1000 -0.097 -1000
ceramide signaling pathway 0.0038 2 131 49 -0.12 0.054 1000 -1000 -0.074 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0038 2 119 52 -0.031 0.093 1000 -1000 -0.11 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0038 2 181 83 -0.083 0.081 1000 -1000 -0.11 -1000
Signaling events mediated by HDAC Class I 0.0038 2 216 104 -0.029 0.063 1000 -1000 -0.1 -1000
Retinoic acid receptors-mediated signaling 0.0038 2 128 58 -0.025 0.062 1000 -1000 -0.11 -1000
Regulation of p38-alpha and p38-beta 0.0038 2 150 54 -0.041 0.073 1000 -1000 -0.094 -1000
Insulin Pathway 0.0038 2 200 74 -0.034 0.055 1000 -1000 -0.14 -1000
Signaling events mediated by HDAC Class II 0.0019 1 127 75 -0.027 0.051 1000 -1000 -0.092 -1000
Circadian rhythm pathway 0.0019 1 33 22 -0.019 0.064 1000 -1000 -0.089 -1000
mTOR signaling pathway 0.0019 1 102 53 -0.01 0.044 1000 -1000 -0.087 -1000
Class I PI3K signaling events mediated by Akt 0.0019 1 103 68 -0.083 0.059 1000 -1000 -0.1 -1000
Nectin adhesion pathway 0.0019 1 92 63 -0.016 0.078 1000 -1000 -0.11 -1000
Atypical NF-kappaB pathway 0.0019 1 55 31 -0.02 0.037 1000 -1000 -0.1 -1000
IGF1 pathway 0.0019 1 110 57 -0.065 0.071 1000 -1000 -0.14 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 2 23 -0.001 0.062 1000 -1000 -0.11 -1000
TRAIL signaling pathway 0.0000 0 32 48 -0.002 0.07 1000 -1000 -0.095 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.039 1000 -1000 -0.082 -1000
Rapid glucocorticoid signaling 0.0000 0 16 20 -0.006 0.016 1000 -1000 -0.065 -1000
Arf1 pathway 0.0000 0 31 54 -0.01 0.043 1000 -1000 -0.078 -1000
Alternative NF-kappaB pathway 0.0000 0 10 13 -0.005 0.016 1000 -1000 -0.11 -1000
Total NA 4180 224701 7203 -40 -990 131000 -131000 -14 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.011 0.099 -10000 0 -0.87 7 7
CDKN2C 0.079 0.017 -10000 0 -10000 0 0
CDKN2A -0.84 0.17 -10000 0 -0.87 513 513
CCND2 0.18 0.049 0.47 7 -10000 0 7
RB1 -0.2 0.051 -10000 0 -0.21 512 512
CDK4 0.22 0.052 0.22 512 -10000 0 512
CDK6 0.2 0.055 0.51 7 -0.18 1 8
G1/S progression 0.2 0.054 0.21 512 -10000 0 512
HIF-1-alpha transcription factor network

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
PKM2 -0.98 0.53 -9999 0 -1.4 305 305
HDAC7 0.014 0.005 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.68 0.33 -9999 0 -0.94 277 277
SMAD4 0.017 0 -9999 0 -10000 0 0
ID2 -0.98 0.53 -9999 0 -1.4 301 301
AP1 -0.014 0.087 -9999 0 -0.56 13 13
ABCG2 -0.98 0.53 -9999 0 -1.4 310 310
HIF1A -0.1 0.068 -9999 0 -0.89 2 2
TFF3 -0.99 0.53 -9999 0 -1.4 308 308
GATA2 -0.001 0.12 -9999 0 -0.74 13 13
AKT1 -0.093 0.053 -9999 0 -10000 0 0
response to hypoxia -0.13 0.058 -9999 0 -10000 0 0
MCL1 -0.98 0.53 -9999 0 -1.4 300 300
NDRG1 -0.98 0.53 -9999 0 -1.4 301 301
SERPINE1 -1 0.56 -9999 0 -1.4 308 308
FECH -0.98 0.53 -9999 0 -1.4 306 306
FURIN -0.98 0.53 -9999 0 -1.4 301 301
NCOA2 -0.004 0.11 -9999 0 -0.74 11 11
EP300 -0.1 0.075 -9999 0 -0.36 7 7
HMOX1 -1 0.54 -9999 0 -1.4 308 308
BHLHE40 -0.98 0.53 -9999 0 -1.4 302 302
BHLHE41 -1.1 0.58 -9999 0 -1.5 320 320
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.08 0.056 -9999 0 -0.6 2 2
ENG -0.059 0.064 -9999 0 -10000 0 0
JUN 0.016 0.003 -9999 0 -10000 0 0
RORA -0.98 0.53 -9999 0 -1.4 306 306
ABCB1 -0.3 0.42 -9999 0 -1.3 70 70
TFRC -0.98 0.53 -9999 0 -1.4 306 306
CXCR4 -1.1 0.59 -9999 0 -1.5 325 325
TF -1 0.58 -9999 0 -1.4 320 320
CITED2 -0.98 0.53 -9999 0 -1.4 301 301
HIF1A/ARNT -1.3 0.85 -9999 0 -1.8 343 343
LDHA -0.086 0.062 -9999 0 -0.85 2 2
ETS1 -0.98 0.53 -9999 0 -1.4 301 301
PGK1 -0.98 0.53 -9999 0 -1.4 302 302
NOS2 -0.98 0.53 -9999 0 -1.4 304 304
ITGB2 -1 0.56 -9999 0 -1.4 316 316
ALDOA -0.98 0.53 -9999 0 -1.4 301 301
Cbp/p300/CITED2 -0.98 0.53 -9999 0 -1.4 302 302
FOS -0.002 0.12 -9999 0 -0.75 13 13
HK2 -1.2 0.58 -9999 0 -1.5 393 393
SP1 0.021 0.029 -9999 0 -10000 0 0
GCK -0.18 0.18 -9999 0 -1.1 10 10
HK1 -0.98 0.53 -9999 0 -1.4 299 299
NPM1 -0.98 0.53 -9999 0 -1.4 301 301
EGLN1 -0.98 0.53 -9999 0 -1.4 300 300
CREB1 0.026 0.002 -9999 0 -10000 0 0
PGM1 -0.98 0.53 -9999 0 -1.4 305 305
SMAD3 0.017 0 -9999 0 -10000 0 0
EDN1 -0.092 0.17 -9999 0 -0.8 19 19
IGFBP1 -1 0.57 -9999 0 -1.4 312 312
VEGFA -0.77 0.41 -9999 0 -1.2 240 240
HIF1A/JAB1 -0.055 0.047 -9999 0 -0.69 2 2
CP -1.2 0.59 -9999 0 -1.5 386 386
CXCL12 -0.99 0.53 -9999 0 -1.4 309 309
COPS5 0.011 0.008 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.98 0.53 -9999 0 -1.4 301 301
EGLN3 -1.3 0.51 -9999 0 -1.5 413 413
CA9 -1.3 0.48 -9999 0 -1.5 426 426
TERT -1 0.55 -9999 0 -1.4 317 317
ENO1 -0.98 0.53 -9999 0 -1.4 300 300
PFKL -0.98 0.53 -9999 0 -1.4 306 306
NCOA1 0.015 0.003 -9999 0 -10000 0 0
ADM -1.1 0.57 -9999 0 -1.4 321 321
ARNT -0.1 0.047 -9999 0 -10000 0 0
HNF4A -0.042 0.21 -9999 0 -0.74 44 44
ADFP -0.99 0.53 -9999 0 -1.3 340 340
SLC2A1 -0.63 0.34 -9999 0 -1 144 144
LEP -1 0.55 -9999 0 -1.4 308 308
HIF1A/ARNT/Cbp/p300 -0.71 0.34 -9999 0 -0.94 302 302
EPO -0.61 0.4 -9999 0 -1.1 187 187
CREBBP -0.099 0.074 -9999 0 -0.36 2 2
HIF1A/ARNT/Cbp/p300/HDAC7 -0.75 0.38 -9999 0 -1 300 300
PFKFB3 -0.98 0.53 -9999 0 -1.4 301 301
NT5E -0.98 0.53 -9999 0 -1.4 301 301
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.48 0.26 0.62 415 -10000 0 415
KIRREL -0.056 0.11 -10000 0 -0.81 10 10
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.48 0.26 -10000 0 -0.62 415 415
PLCG1 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.038 -10000 0 -0.86 1 1
WASL 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.52 0.31 -10000 0 -0.83 230 230
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.41 0.26 -10000 0 -0.66 230 230
FYN -0.49 0.3 -10000 0 -0.79 230 230
mol:Ca2+ -0.52 0.3 -10000 0 -0.82 230 230
mol:DAG -0.52 0.3 -10000 0 -0.83 230 230
NPHS2 -0.4 0.38 -10000 0 -0.8 254 254
mol:IP3 -0.52 0.3 -10000 0 -0.83 230 230
regulation of endocytosis -0.46 0.28 -10000 0 -0.74 230 230
Nephrin/NEPH1/podocin/Cholesterol -0.53 0.31 -10000 0 -0.65 434 434
establishment of cell polarity -0.48 0.26 -10000 0 -0.62 415 415
Nephrin/NEPH1/podocin/NCK1-2 -0.48 0.29 -10000 0 -0.78 230 230
Nephrin/NEPH1/beta Arrestin2 -0.47 0.28 -10000 0 -0.76 230 230
NPHS1 -0.6 0.32 -10000 0 -0.78 412 412
Nephrin/NEPH1/podocin -0.5 0.29 -10000 0 -0.8 230 230
TJP1 0.016 0 -10000 0 -10000 0 0
NCK1 0.014 0.033 -10000 0 -0.74 1 1
NCK2 0.016 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.52 0.31 -10000 0 -0.83 230 230
CD2AP 0.016 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.52 0.31 -10000 0 -0.83 230 230
GRB2 0.016 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.48 0.3 -10000 0 -0.78 230 230
cytoskeleton organization -0.52 0.32 -10000 0 -0.84 230 230
Nephrin/NEPH1 -0.36 0.2 -10000 0 -0.46 415 415
Nephrin/NEPH1/ZO-1 -0.39 0.21 -10000 0 -0.54 230 230
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.34 0.33 -10000 0 -0.68 237 237
FYN -0.41 0.49 -10000 0 -0.91 245 245
LAT/GRAP2/SLP76 -0.36 0.38 -10000 0 -0.75 244 244
IKBKB 0.016 0 -10000 0 -10000 0 0
AKT1 -0.25 0.29 -10000 0 -0.54 244 244
B2M 0.009 0.009 -10000 0 -10000 0 0
IKBKG -0.079 0.072 -10000 0 -0.19 83 83
MAP3K8 0.012 0.054 -10000 0 -0.86 2 2
mol:Ca2+ -0.11 0.045 -10000 0 -0.14 348 348
integrin-mediated signaling pathway -0.02 0.1 -10000 0 -0.58 18 18
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.41 0.45 -10000 0 -0.85 255 255
TRPV6 -0.66 0.26 -10000 0 -0.76 461 461
CD28 -0.057 0.23 -10000 0 -0.87 40 40
SHC1 -0.44 0.49 -10000 0 -0.93 249 249
receptor internalization -0.51 0.56 -10000 0 -1.1 253 253
PRF1 -0.48 0.59 -10000 0 -1.1 235 235
KRAS 0.016 0 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
COT/AKT1 -0.18 0.22 -10000 0 -0.41 226 226
LAT -0.5 0.53 -10000 0 -1 262 262
EntrezGene:6955 -0.003 0.005 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 241 241
CD3E -0.34 0.44 -10000 0 -0.87 215 215
CD3G -0.33 0.43 -10000 0 -0.87 205 205
RASGRP2 -0.023 0.029 -10000 0 -0.14 3 3
RASGRP1 -0.23 0.27 -10000 0 -0.51 238 238
HLA-A 0.005 0.055 -10000 0 -0.87 2 2
RASSF5 -0.014 0.16 -10000 0 -0.86 18 18
RAP1A/GTP/RAPL -0.02 0.11 -10000 0 -0.59 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP -0.036 0.081 -10000 0 -0.13 4 4
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.15 0.13 -10000 0 -0.34 103 103
PRKCA -0.14 0.17 -10000 0 -0.31 214 214
GRAP2 -0.042 0.22 -10000 0 -0.86 35 35
mol:IP3 -0.16 0.34 0.26 165 -0.5 225 390
EntrezGene:6957 -0.003 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.52 0.63 -10000 0 -1.1 260 260
ORAI1 0.33 0.13 0.38 460 -10000 0 460
CSK -0.45 0.51 -10000 0 -0.97 248 248
B7 family/CD28 -0.51 0.51 -10000 0 -1 247 247
CHUK 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.56 0.62 -10000 0 -1.2 255 255
PTPN6 -0.43 0.52 -10000 0 -0.98 243 243
VAV1 -0.48 0.53 -10000 0 -1 258 258
Monovalent TCR/CD3 -0.45 0.53 -10000 0 -0.99 242 242
CBL 0.014 0.033 -10000 0 -0.74 1 1
LCK -0.44 0.53 -10000 0 -0.98 243 243
PAG1 -0.46 0.51 -10000 0 -0.97 249 249
RAP1A 0.016 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.53 0.63 -10000 0 -1.2 247 247
CD80 -0.18 0.36 -10000 0 -0.87 117 117
CD86 -0.13 0.32 -10000 0 -0.87 82 82
PDK1/CARD11/BCL10/MALT1 -0.18 0.17 -10000 0 -0.41 117 117
HRAS 0.014 0.038 -10000 0 -0.86 1 1
GO:0035030 -0.35 0.41 -10000 0 -0.77 247 247
CD8A -0.38 0.44 -10000 0 -0.87 236 236
CD8B -0.3 0.42 -10000 0 -0.87 187 187
PTPRC -0.083 0.27 -10000 0 -0.87 56 56
PDK1/PKC theta -0.32 0.36 -10000 0 -0.68 246 246
CSK/PAG1 -0.44 0.49 -10000 0 -0.95 242 242
SOS1 0.016 0 -10000 0 -10000 0 0
peptide-MHC class I -0.003 0.041 -10000 0 -0.68 2 2
GRAP2/SLP76 -0.43 0.44 -10000 0 -0.88 246 246
STIM1 0.17 0.064 -10000 0 -10000 0 0
RAS family/GTP -0.064 0.11 -10000 0 -0.19 8 8
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.59 0.65 -10000 0 -1.2 253 253
mol:DAG -0.2 0.26 -10000 0 -0.46 239 239
RAP1A/GDP -0.014 0.035 -10000 0 -10000 0 0
PLCG1 0.016 0 -10000 0 -10000 0 0
CD247 -0.28 0.41 -10000 0 -0.87 174 174
cytotoxic T cell degranulation -0.44 0.55 -10000 0 -0.99 246 246
RAP1A/GTP -0.008 0.008 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.31 0.35 -10000 0 -0.66 253 253
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.26 0.44 0.3 108 -0.7 238 346
NRAS 0.016 0 -10000 0 -10000 0 0
ZAP70 -0.47 0.44 -10000 0 -0.86 296 296
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.38 0.35 -10000 0 -0.73 246 246
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
CD8 heterodimer -0.49 0.56 -10000 0 -1.1 242 242
CARD11 -0.17 0.36 -10000 0 -0.86 110 110
PRKCB -0.14 0.17 -10000 0 -0.31 212 212
PRKCE -0.14 0.17 -10000 0 -0.32 187 187
PRKCQ -0.39 0.42 -10000 0 -0.8 254 254
LCP2 -0.038 0.21 -10000 0 -0.86 33 33
BCL10 0.016 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.2 0.24 -10000 0 -0.45 243 243
IKK complex -0.028 0.084 -10000 0 -10000 0 0
RAS family/GDP -0.011 0.012 -10000 0 -0.11 1 1
MAP3K14 -0.13 0.18 -10000 0 -0.32 151 151
PDPK1 -0.23 0.27 -10000 0 -0.5 239 239
TCR/CD3/MHC I/CD8/Fyn -0.55 0.65 -10000 0 -1.2 244 244
TCGA08_p53

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
CDKN2A -0.65 0.13 -10000 0 -0.68 513 513
TP53 -0.17 0.037 -10000 0 -10000 0 0
Senescence -0.17 0.037 -10000 0 -10000 0 0
Apoptosis -0.17 0.037 -10000 0 -10000 0 0
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.31 0.062 0.32 513 -10000 0 513
MDM4 0.014 0.038 -10000 0 -0.86 1 1
Syndecan-4-mediated signaling events

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
PTK2 -0.054 0.14 -9999 0 -0.54 39 39
Syndecan-4/Syndesmos -0.46 0.39 -9999 0 -0.84 236 236
positive regulation of JNK cascade -0.53 0.37 -9999 0 -0.84 287 287
Syndecan-4/ADAM12 -0.56 0.49 -9999 0 -1 260 260
CCL5 -0.35 0.43 -9999 0 -0.86 224 224
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.016 0 -9999 0 -10000 0 0
ITGA5 -0.049 0.23 -9999 0 -0.86 39 39
SDCBP 0.016 0 -9999 0 -10000 0 0
PLG -0.36 0.37 -9999 0 -0.72 274 274
ADAM12 -0.22 0.39 -9999 0 -0.86 142 142
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.1 0.071 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.47 0.4 -9999 0 -0.86 238 238
Syndecan-4/CXCL12/CXCR4 -0.59 0.43 -9999 0 -0.94 287 287
Syndecan-4/Laminin alpha3 -0.46 0.39 -9999 0 -0.85 241 241
MDK -0.049 0.23 -9999 0 -0.86 39 39
Syndecan-4/FZD7 -0.46 0.39 -9999 0 -0.84 237 237
Syndecan-4/Midkine -0.49 0.41 -9999 0 -0.88 249 249
FZD7 0.014 0.033 -9999 0 -0.74 1 1
Syndecan-4/FGFR1/FGF -0.43 0.33 -9999 0 -0.76 239 239
THBS1 0.011 0.057 -9999 0 -0.74 3 3
integrin-mediated signaling pathway -0.44 0.36 -9999 0 -0.79 242 242
positive regulation of MAPKKK cascade -0.53 0.37 -9999 0 -0.84 287 287
Syndecan-4/TACI -0.5 0.42 -9999 0 -0.9 249 249
CXCR4 -0.29 0.42 -9999 0 -0.86 186 186
cell adhesion -0.007 0.12 -9999 0 -0.51 15 15
Syndecan-4/Dynamin -0.46 0.39 -9999 0 -0.84 236 236
Syndecan-4/TSP1 -0.46 0.39 -9999 0 -0.84 238 238
Syndecan-4/GIPC -0.46 0.39 -9999 0 -0.84 237 237
Syndecan-4/RANTES -0.64 0.46 -9999 0 -1 294 294
ITGB1 0.016 0 -9999 0 -10000 0 0
LAMA1 -0.006 0.13 -9999 0 -0.75 15 15
LAMA3 0.004 0.1 -9999 0 -0.86 7 7
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA 0.11 0.066 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.46 0.39 -9999 0 -0.84 237 237
TFPI 0.002 0.11 -9999 0 -0.81 9 9
F2 -0.32 0.42 -9999 0 -0.87 199 199
alpha5/beta1 Integrin -0.049 0.17 -9999 0 -0.66 39 39
positive regulation of cell adhesion -0.45 0.38 -9999 0 -0.82 243 243
ACTN1 0.013 0.05 -9999 0 -0.8 2 2
TNC -0.004 0.12 -9999 0 -0.74 14 14
Syndecan-4/CXCL12 -0.47 0.39 -9999 0 -0.84 242 242
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
CXCL12 -0.001 0.11 -9999 0 -0.74 12 12
TNFRSF13B -0.072 0.26 -9999 0 -0.86 52 52
FGF2 0.008 0.075 -9999 0 -0.77 5 5
FGFR1 0.016 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.47 0.39 -9999 0 -0.85 236 236
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.039 0.22 -9999 0 -0.83 39 39
cell migration -0.03 0.022 -9999 0 -10000 0 0
PRKCD 0.024 0.045 -9999 0 -0.85 1 1
vasculogenesis -0.44 0.36 -9999 0 -0.79 238 238
SDC4 -0.5 0.43 -9999 0 -0.93 236 236
Syndecan-4/Tenascin C -0.47 0.39 -9999 0 -0.84 242 242
Syndecan-4/PI-4-5-P2/PKC alpha -0.079 0.055 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.46 0.39 -9999 0 -0.84 236 236
MMP9 -0.4 0.44 -9999 0 -0.86 251 251
Rac1/GTP -0.008 0.12 -9999 0 -0.53 15 15
cytoskeleton organization -0.43 0.36 -9999 0 -0.79 236 236
GIPC1 0.014 0.033 -9999 0 -0.74 1 1
Syndecan-4/TFPI -0.47 0.39 -9999 0 -0.85 240 240
Aurora B 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
Condensin I complex -0.24 0.32 -9999 0 -0.68 163 163
STMN1 -0.29 0.34 -9999 0 -0.66 248 248
Aurora B/RasGAP/Survivin -0.4 0.48 -9999 0 -0.87 253 253
Chromosomal passenger complex/Cul3 protein complex -0.16 0.23 -9999 0 -0.49 151 151
BIRC5 -0.25 0.41 -9999 0 -0.89 154 154
DES -0.38 0.34 -9999 0 -0.6 316 316
Aurora C/Aurora B/INCENP -0.24 0.28 -9999 0 -0.53 249 249
Aurora B/TACC1 -0.26 0.3 -9999 0 -0.57 248 248
Aurora B/PP2A -0.3 0.34 -9999 0 -0.66 248 248
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.072 0.09 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.008 -9999 0 -10000 0 0
NDC80 -0.4 0.5 -9999 0 -0.89 253 253
Cul3 protein complex -0.015 0.083 -9999 0 -0.47 17 17
KIF2C -0.15 0.18 -9999 0 -0.34 200 200
PEBP1 0.007 0.008 -9999 0 -10000 0 0
KIF20A -0.38 0.44 -9999 0 -0.86 238 238
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.3 0.34 -9999 0 -0.66 249 249
SEPT1 -0.096 0.29 -9999 0 -0.86 68 68
SMC2 0.016 0 -9999 0 -10000 0 0
SMC4 0.016 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.18 0.24 -9999 0 -0.45 195 195
PSMA3 0.016 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.003 0.004 -9999 0 -10000 0 0
H3F3B -0.17 0.21 -9999 0 -0.39 248 248
AURKB -0.4 0.44 -9999 0 -0.87 248 248
AURKC 0.012 0.054 -9999 0 -0.86 2 2
CDCA8 -0.026 0.17 -9999 0 -0.89 20 20
cytokinesis -0.34 0.37 -9999 0 -0.75 216 216
Aurora B/Septin1 -0.36 0.42 -9999 0 -0.83 210 210
AURKA 0.002 0.094 -9999 0 -0.87 6 6
INCENP 0.008 0.009 -9999 0 -10000 0 0
KLHL13 -0.008 0.13 -9999 0 -0.74 17 17
BUB1 -0.37 0.44 -9999 0 -0.86 232 232
hSgo1/Aurora B/Survivin -0.39 0.48 -9999 0 -0.85 254 254
EVI5 0.01 0.008 -9999 0 -10000 0 0
RhoA/GTP -0.31 0.34 -9999 0 -0.72 194 194
SGOL1 -0.014 0.16 -9999 0 -0.86 18 18
CENPA -0.29 0.35 -9999 0 -0.63 255 255
NCAPG -0.27 0.41 -9999 0 -0.86 176 176
Aurora B/HC8 Proteasome -0.3 0.34 -9999 0 -0.66 248 248
NCAPD2 0.016 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.3 0.34 -9999 0 -0.66 248 248
RHOA 0.016 0 -9999 0 -10000 0 0
NCAPH -0.13 0.33 -9999 0 -0.86 89 89
NPM1 -0.21 0.24 -9999 0 -0.47 248 248
RASA1 0.014 0.033 -9999 0 -0.74 1 1
KLHL9 0.016 0 -9999 0 -10000 0 0
mitotic prometaphase -0.01 0.011 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.3 0.34 -9999 0 -0.66 248 248
PPP1CC 0.016 0 -9999 0 -10000 0 0
Centraspindlin -0.34 0.38 -9999 0 -0.78 201 201
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 -0.21 0.24 -9999 0 -0.47 248 248
MYLK -0.17 0.21 -9999 0 -0.39 248 248
KIF23 -0.006 0.11 -9999 0 -0.88 8 8
VIM -0.34 0.4 -9999 0 -0.73 263 263
RACGAP1 0.004 0.055 -9999 0 -0.88 2 2
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.21 0.24 -9999 0 -0.47 248 248
Chromosomal passenger complex -0.34 0.41 -9999 0 -0.76 240 240
Chromosomal passenger complex/EVI5 -0.36 0.48 -9999 0 -1 149 149
TACC1 0.016 0 -9999 0 -10000 0 0
PPP2R5D 0.016 0 -9999 0 -10000 0 0
CUL3 0.016 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.44 0.47 -9999 0 -1.2 113 113
PCK1 -0.93 0.71 -9999 0 -1.4 310 310
HNF4A -0.57 0.57 -9999 0 -1.4 138 138
KCNJ11 -0.44 0.5 -9999 0 -1.3 100 100
AKT1 -0.17 0.18 -9999 0 -10000 0 0
response to starvation -0.02 0.038 -9999 0 -10000 0 0
DLK1 -0.55 0.57 -9999 0 -1.3 165 165
NKX2-1 -0.056 0.21 -9999 0 -0.84 4 4
ACADM -0.44 0.47 -9999 0 -1.1 126 126
TAT -0.51 0.35 -9999 0 -0.92 168 168
CEBPB -0.024 0.14 -9999 0 -0.92 12 12
CEBPA -0.019 0.12 -9999 0 -0.9 10 10
TTR -0.88 0.48 -9999 0 -1.2 336 336
PKLR -0.5 0.56 -9999 0 -1.3 124 124
APOA1 -0.55 0.56 -9999 0 -1.3 136 136
CPT1C -0.44 0.47 -9999 0 -1.2 115 115
ALAS1 -0.17 0.19 -9999 0 -10000 0 0
TFRC -0.62 0.42 -9999 0 -1 225 225
FOXF1 -0.001 0.12 -9999 0 -0.84 10 10
NF1 0.025 0.001 -9999 0 -10000 0 0
HNF1A (dimer) -0.003 0.085 -9999 0 -0.79 5 5
CPT1A -0.44 0.47 -9999 0 -1.2 110 110
HMGCS1 -0.44 0.47 -9999 0 -1.1 121 121
NR3C1 0.003 0.065 -9999 0 -0.96 1 1
CPT1B -0.46 0.49 -9999 0 -1.2 120 120
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.017 0.005 -9999 0 -10000 0 0
GCK -0.45 0.48 -9999 0 -1.2 118 118
CREB1 -0.028 0.066 -9999 0 -10000 0 0
IGFBP1 -0.31 0.42 -9999 0 -1 120 120
PDX1 -0.19 0.22 -9999 0 -1 6 6
UCP2 -0.44 0.47 -9999 0 -1.2 114 114
ALDOB -0.94 0.62 -9999 0 -1.3 361 361
AFP -0.7 0.49 -9999 0 -0.97 327 327
BDH1 -0.59 0.57 -9999 0 -1.2 184 184
HADH -0.43 0.48 -9999 0 -1.2 102 102
F2 -0.65 0.62 -9999 0 -1.3 191 191
HNF1A -0.003 0.086 -9999 0 -0.79 5 5
G6PC -0.81 0.66 -9999 0 -1.5 255 255
SLC2A2 -0.32 0.48 -9999 0 -1.7 48 48
INS 0.009 0.055 -9999 0 -10000 0 0
FOXA1 -0.36 0.38 -9999 0 -0.97 134 134
FOXA3 -0.61 0.37 -9999 0 -0.9 296 296
FOXA2 -0.51 0.56 -9999 0 -1.3 123 123
ABCC8 -0.44 0.49 -9999 0 -1.2 101 101
ALB -1.2 0.48 -9999 0 -1.4 461 461
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.16 0.26 -10000 0 -0.52 137 137
TBX21 -0.54 0.67 -10000 0 -1.2 246 246
B2M 0.011 0.009 -10000 0 -10000 0 0
TYK2 0.012 0.021 -10000 0 -10000 0 0
IL12RB1 -0.26 0.42 -10000 0 -0.9 160 160
GADD45B -0.29 0.42 -10000 0 -0.8 170 170
IL12RB2 -0.11 0.31 -10000 0 -0.87 76 76
GADD45G -0.3 0.43 -10000 0 -0.79 187 187
natural killer cell activation -0.01 0.03 -10000 0 -10000 0 0
RELB 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL18 0.003 0.1 -10000 0 -0.87 7 7
IL2RA -0.16 0.35 -10000 0 -0.86 105 105
IFNG -0.38 0.44 -10000 0 -0.86 239 239
STAT3 (dimer) -0.37 0.46 -10000 0 -0.86 217 217
HLA-DRB5 -0.036 0.21 -10000 0 -0.86 32 32
FASLG -0.6 0.7 -10000 0 -1.3 239 239
NF kappa B2 p52/RelB -0.51 0.53 -10000 0 -1.1 220 220
CD4 0.002 0.11 -10000 0 -0.86 9 9
SOCS1 0.006 0.093 -10000 0 -0.86 6 6
EntrezGene:6955 -0.002 0.009 -10000 0 -10000 0 0
CD3D -0.38 0.44 -10000 0 -0.87 241 241
CD3E -0.34 0.43 -10000 0 -0.87 215 215
CD3G -0.32 0.43 -10000 0 -0.87 205 205
IL12Rbeta2/JAK2 -0.084 0.25 -10000 0 -0.68 76 76
CCL3 -0.48 0.63 -10000 0 -1.2 198 198
CCL4 -0.5 0.66 -10000 0 -1.2 220 220
HLA-A 0.007 0.054 -10000 0 -0.86 2 2
IL18/IL18R -0.12 0.3 -10000 0 -0.6 149 149
NOS2 -0.36 0.49 -10000 0 -0.92 191 191
IL12/IL12R/TYK2/JAK2/SPHK2 -0.16 0.26 -10000 0 -0.56 100 100
IL1R1 -0.44 0.59 -10000 0 -1.1 190 190
IL4 0.013 0.031 -10000 0 -10000 0 0
JAK2 0.012 0.021 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.69 0.81 -10000 0 -1.4 262 262
RAB7A -0.23 0.37 -10000 0 -0.69 135 135
lysosomal transport -0.22 0.36 -10000 0 -0.65 136 136
FOS -0.37 0.5 -10000 0 -0.94 207 207
STAT4 (dimer) -0.4 0.53 -10000 0 -0.96 217 217
STAT5A (dimer) -0.65 0.61 -10000 0 -1.2 255 255
GZMA -0.56 0.7 -10000 0 -1.3 234 234
GZMB -0.53 0.67 -10000 0 -1.2 236 236
HLX -0.091 0.29 -10000 0 -0.86 65 65
LCK -0.51 0.69 -10000 0 -1.2 222 222
TCR/CD3/MHC II/CD4 -0.37 0.47 -10000 0 -0.86 232 232
IL2/IL2R -0.41 0.42 -10000 0 -0.71 308 308
MAPK14 -0.3 0.44 -10000 0 -0.79 189 189
CCR5 -0.45 0.59 -10000 0 -1.1 204 204
IL1B 0.002 0.095 -10000 0 -0.86 6 6
STAT6 -0.083 0.15 -10000 0 -10000 0 0
STAT4 -0.035 0.21 -10000 0 -0.86 31 31
STAT3 0.016 0 -10000 0 -10000 0 0
STAT1 0.014 0.038 -10000 0 -0.86 1 1
NFKB1 0.014 0.033 -10000 0 -0.74 1 1
NFKB2 0.016 0 -10000 0 -10000 0 0
IL12B -0.092 0.29 -10000 0 -0.89 62 62
CD8A -0.38 0.44 -10000 0 -0.87 236 236
CD8B -0.3 0.42 -10000 0 -0.87 187 187
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.16 0.26 0.51 137 -10000 0 137
IL2RB -0.44 0.44 -10000 0 -0.86 274 274
proteasomal ubiquitin-dependent protein catabolic process -0.36 0.47 -10000 0 -0.85 217 217
IL2RG -0.04 0.21 -10000 0 -0.86 34 34
IL12 -0.07 0.24 -10000 0 -0.71 63 63
STAT5A 0.016 0 -10000 0 -10000 0 0
CD247 -0.27 0.41 -10000 0 -0.87 174 174
IL2 -0.007 0.12 -10000 0 -0.86 10 10
SPHK2 0.013 0.046 -10000 0 -0.74 2 2
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.01 0.046 -10000 0 -0.91 1 1
IL12/IL12R/TYK2/JAK2 -0.57 0.77 -10000 0 -1.4 222 222
MAP2K3 -0.3 0.44 -10000 0 -0.8 191 191
RIPK2 0.014 0.038 -10000 0 -0.86 1 1
MAP2K6 -0.3 0.44 -10000 0 -0.8 191 191
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.01 0.076 -10000 0 -0.86 4 4
IL18RAP -0.21 0.39 -10000 0 -0.87 137 137
IL12Rbeta1/TYK2 -0.2 0.34 -10000 0 -0.72 160 160
EOMES -0.29 0.37 -10000 0 -0.74 215 215
STAT1 (dimer) -0.44 0.51 -10000 0 -0.95 239 239
T cell proliferation -0.26 0.37 -10000 0 -0.66 200 200
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.002 0.1 -10000 0 -0.8 8 8
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.36 0.33 -10000 0 -0.74 201 201
ATF2 -0.27 0.41 -10000 0 -0.75 167 167
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.006 0.052 -10000 0 -0.49 6 6
fibroblast growth factor receptor signaling pathway -0.005 0.052 -10000 0 -0.49 6 6
LAMA1 -0.006 0.13 -10000 0 -0.75 15 15
PRNP 0.016 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.12 0.23 -10000 0 -0.56 119 119
SMAD2 0.045 0.02 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ -0.001 0.021 -10000 0 -0.48 1 1
GPC1/Laminin alpha1 -0.017 0.096 -10000 0 -0.56 16 16
TDGF1 -0.56 0.32 -10000 0 -0.74 401 401
CRIPTO/GPC1 -0.42 0.24 -10000 0 -0.56 401 401
APP/GPC1 -0.002 0.034 -10000 0 -0.56 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.35 0.22 -10000 0 -0.47 401 401
FLT1 0.007 0.085 -10000 0 -0.86 5 5
GPC1/TGFB/TGFBR1/TGFBR2 -0.001 0.02 -10000 0 -0.47 1 1
SERPINC1 -0.053 0.22 -10000 0 -0.76 46 46
FYN -0.35 0.22 -10000 0 -0.47 401 401
FGR -0.35 0.22 -10000 0 -0.48 401 401
positive regulation of MAPKKK cascade -0.36 0.24 -10000 0 -0.67 66 66
SLIT2 -0.15 0.32 -10000 0 -0.74 118 118
GPC1/NRG -0.019 0.1 -10000 0 -0.56 18 18
NRG1 -0.008 0.13 -10000 0 -0.74 17 17
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.26 0.3 -10000 0 -0.58 240 240
LYN -0.35 0.22 -10000 0 -0.47 401 401
mol:Spermine 0.014 0.025 -10000 0 -0.57 1 1
cell growth -0.005 0.052 -10000 0 -0.49 6 6
BMP signaling pathway -0.014 0.033 0.74 1 -10000 0 1
SRC -0.35 0.22 -10000 0 -0.47 401 401
TGFBR1 0.016 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.06 0.24 -10000 0 -0.86 43 43
GPC1 0.014 0.033 -10000 0 -0.74 1 1
TGFBR1 (dimer) 0.016 0 -10000 0 -10000 0 0
VEGFA -0.38 0.44 -10000 0 -0.86 239 239
BLK -0.38 0.26 -10000 0 -0.51 406 406
HCK -0.38 0.24 -10000 0 -0.5 412 412
FGF2 0.008 0.075 -10000 0 -0.77 5 5
FGFR1 0.016 0 -10000 0 -10000 0 0
VEGFR1 homodimer 0.007 0.084 -10000 0 -0.86 5 5
TGFBR2 0.016 0 -10000 0 -10000 0 0
cell death -0.002 0.034 -10000 0 -0.55 2 2
ATIII/GPC1 -0.05 0.16 -10000 0 -0.57 47 47
PLA2G2A/GPC1 -0.055 0.18 -10000 0 -0.66 44 44
LCK -0.37 0.24 -10000 0 -0.49 409 409
neuron differentiation -0.019 0.1 -10000 0 -0.55 18 18
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.014 0.033 -10000 0 -0.74 1 1
TGFBR2 (dimer) 0.016 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.18 0.67 -10000 0 -1.2 119 119
PLK1 -0.098 0.4 -10000 0 -0.8 129 129
BIRC5 -0.13 0.43 -10000 0 -0.79 154 154
HSPA1B -0.18 0.67 -10000 0 -1.2 119 119
MAP2K1 0.04 0.047 -10000 0 -10000 0 0
BRCA2 -0.19 0.68 -10000 0 -1.2 121 121
FOXM1 -0.37 0.99 -10000 0 -1.9 128 128
XRCC1 -0.18 0.67 -10000 0 -1.2 117 117
FOXM1B/p19 -0.49 0.49 0.5 1 -1.2 133 134
Cyclin D1/CDK4 -0.18 0.61 -10000 0 -1.1 106 106
CDC2 -0.21 0.72 -10000 0 -1.3 127 127
TGFA -0.16 0.6 -10000 0 -1.1 108 108
SKP2 -0.18 0.67 -10000 0 -1.2 120 120
CCNE1 0.002 0.11 -10000 0 -0.88 8 8
CKS1B -0.18 0.67 -10000 0 -1.2 119 119
RB1 -0.19 0.26 -10000 0 -0.7 91 91
FOXM1C/SP1 -0.28 0.77 -10000 0 -1.5 124 124
AURKB -0.25 0.46 -10000 0 -0.74 248 248
CENPF -0.21 0.71 -10000 0 -1.3 121 121
CDK4 0.02 0.022 -10000 0 -10000 0 0
MYC -0.15 0.6 -10000 0 -1.1 118 118
CHEK2 0.037 0.075 -10000 0 -0.91 2 2
ONECUT1 -0.19 0.65 -10000 0 -1.2 120 120
CDKN2A -0.82 0.17 -10000 0 -0.86 513 513
LAMA4 -0.28 0.69 -10000 0 -1.3 126 126
FOXM1B/HNF6 -0.27 0.79 -10000 0 -1.5 120 120
FOS -0.2 0.68 -10000 0 -1.2 122 122
SP1 0.016 0.005 -10000 0 -10000 0 0
CDC25B -0.18 0.68 -10000 0 -1.2 119 119
response to radiation 0.014 0.05 -10000 0 -10000 0 0
CENPB -0.18 0.67 -10000 0 -1.2 119 119
CENPA -0.28 0.77 -10000 0 -1.4 146 146
NEK2 -0.24 0.75 -10000 0 -1.4 134 134
HIST1H2BA -0.19 0.67 -10000 0 -1.2 119 119
CCNA2 -0.15 0.35 -10000 0 -0.88 102 102
EP300 0.014 0.033 -10000 0 -0.74 1 1
CCNB1/CDK1 -0.27 0.8 -10000 0 -1.5 123 123
CCNB2 -0.24 0.75 -10000 0 -1.4 131 131
CCNB1 -0.21 0.72 -10000 0 -1.3 120 120
ETV5 -0.18 0.67 -10000 0 -1.2 119 119
ESR1 -0.19 0.68 -10000 0 -1.2 120 120
CCND1 -0.17 0.63 -10000 0 -1.1 108 108
GSK3A 0.036 0.041 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.08 0.28 -10000 0 -0.64 103 103
CDK2 0.015 0.015 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.015 0.059 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 -0.42 0.58 -10000 0 -1.4 134 134
GAS1 -0.23 0.7 -10000 0 -1.2 133 133
MMP2 -0.19 0.68 -10000 0 -1.2 119 119
RB1/FOXM1C -0.21 0.67 -10000 0 -1.2 118 118
CREBBP 0.016 0 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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
PDGFRA -0.27 0.37 -9999 0 -0.74 205 205
PDGF/PDGFRA/CRKL -0.21 0.26 -9999 0 -0.54 205 205
positive regulation of JUN kinase activity -0.16 0.2 -9999 0 -0.52 1 1
CRKL 0.016 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.22 0.27 -9999 0 -0.55 208 208
AP1 -0.16 0.24 -9999 0 -1.2 13 13
mol:IP3 -0.19 0.29 -9999 0 -0.55 205 205
PLCG1 -0.19 0.29 -9999 0 -0.55 205 205
PDGF/PDGFRA/alphaV Integrin -0.21 0.26 -9999 0 -0.54 205 205
RAPGEF1 0.016 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.29 -9999 0 -0.55 205 205
CAV3 0 0.065 -9999 0 -0.86 3 3
CAV1 -0.045 0.22 -9999 0 -0.86 37 37
SHC/Grb2/SOS1 -0.16 0.2 -9999 0 -0.52 1 1
PDGF/PDGFRA/Shf -0.21 0.26 -9999 0 -0.54 206 206
FOS -0.12 0.27 -9999 0 -1.2 13 13
JUN -0.013 0.017 -9999 0 -10000 0 0
oligodendrocyte development -0.21 0.26 -9999 0 -0.54 205 205
GRB2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
mol:DAG -0.19 0.29 -9999 0 -0.55 205 205
PDGF/PDGFRA -0.27 0.37 -9999 0 -0.74 205 205
actin cytoskeleton reorganization -0.21 0.26 -9999 0 -0.54 205 205
SRF 0.034 0.009 -9999 0 -10000 0 0
SHC1 0.014 0.038 -9999 0 -0.86 1 1
PI3K -0.18 0.22 -9999 0 -0.45 206 206
PDGF/PDGFRA/Crk/C3G -0.17 0.22 -9999 0 -0.45 205 205
JAK1 -0.19 0.28 -9999 0 -0.54 205 205
ELK1/SRF -0.15 0.19 -9999 0 -10000 0 0
SHB 0.016 0 -9999 0 -10000 0 0
SHF 0.014 0.033 -9999 0 -0.74 1 1
CSNK2A1 0.017 0.022 -9999 0 -10000 0 0
GO:0007205 -0.19 0.29 -9999 0 -0.56 205 205
SOS1 0.016 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.16 0.2 -9999 0 -0.52 1 1
PDGF/PDGFRA/SHB -0.21 0.26 -9999 0 -0.54 205 205
PDGF/PDGFRA/Caveolin-1 -0.25 0.29 -9999 0 -0.57 234 234
ITGAV 0.016 0 -9999 0 -10000 0 0
ELK1 -0.16 0.26 -9999 0 -0.49 205 205
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
PDGF/PDGFRA/Crk -0.21 0.26 -9999 0 -0.54 205 205
JAK-STAT cascade -0.19 0.28 -9999 0 -0.54 205 205
cell proliferation -0.21 0.26 -9999 0 -0.54 206 206
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.14 0.28 -9999 0 -0.67 109 109
alphaM/beta2 Integrin/GPIbA -0.13 0.28 -9999 0 -0.67 104 104
alphaM/beta2 Integrin/proMMP-9 -0.39 0.43 -9999 0 -0.74 281 281
PLAUR -0.029 0.19 -9999 0 -0.86 27 27
HMGB1 0.015 0.013 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.13 0.28 -9999 0 -0.67 103 103
AGER -0.14 0.34 -9999 0 -0.86 95 95
RAP1A 0.016 0 -9999 0 -10000 0 0
SELPLG -0.04 0.22 -9999 0 -0.86 34 34
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.23 0.33 -9999 0 -0.94 62 62
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 251 251
CYR61 0.007 0.08 -9999 0 -0.74 6 6
TLN1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP -0.25 0.2 -9999 0 -0.56 115 115
RHOA 0.016 0 -9999 0 -10000 0 0
P-selectin oligomer -0.02 0.16 -9999 0 -0.74 25 25
MYH2 -0.34 0.26 -9999 0 -0.64 191 191
MST1R 0.005 0.09 -9999 0 -0.78 7 7
leukocyte activation during inflammatory response -0.27 0.35 -9999 0 -0.63 223 223
APOB -0.26 0.4 -9999 0 -0.86 169 169
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.004 0.098 -9999 0 -0.84 7 7
JAM3 0.016 0 -9999 0 -10000 0 0
GP1BA 0.014 0.033 -9999 0 -0.74 1 1
alphaM/beta2 Integrin/CTGF -0.14 0.29 -9999 0 -0.68 105 105
alphaM/beta2 Integrin -0.3 0.25 -9999 0 -0.53 230 230
JAM3 homodimer 0.016 0 -9999 0 -10000 0 0
ICAM2 0.016 0 -9999 0 -10000 0 0
ICAM1 -0.002 0.12 -9999 0 -0.86 11 11
phagocytosis triggered by activation of immune response cell surface activating receptor -0.3 0.24 -9999 0 -0.52 230 230
cell adhesion -0.13 0.28 -9999 0 -0.67 104 104
NFKB1 -0.18 0.36 -9999 0 -0.94 63 63
THY1 0.014 0.033 -9999 0 -0.74 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.19 0.28 -9999 0 -0.59 170 170
alphaM/beta2 Integrin/LRP/tPA -0.13 0.27 -9999 0 -0.62 105 105
IL6 -0.2 0.41 -9999 0 -0.91 101 101
ITGB2 -0.15 0.34 -9999 0 -0.86 100 100
elevation of cytosolic calcium ion concentration -0.15 0.29 -9999 0 -0.64 121 121
alphaM/beta2 Integrin/JAM2/JAM3 -0.12 0.26 -9999 0 -0.62 103 103
JAM2 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/ICAM1 -0.13 0.28 -9999 0 -0.85 41 41
alphaM/beta2 Integrin/uPA/Plg -0.34 0.34 -9999 0 -0.85 109 109
RhoA/GTP -0.36 0.27 -9999 0 -0.68 190 190
positive regulation of phagocytosis -0.25 0.27 -9999 0 -0.7 107 107
Ron/MSP -0.017 0.1 -9999 0 -0.62 15 15
alphaM/beta2 Integrin/uPAR/uPA -0.15 0.3 -9999 0 -0.64 121 121
alphaM/beta2 Integrin/uPAR -0.16 0.32 -9999 0 -0.7 120 120
PLAU 0.003 0.098 -9999 0 -0.74 9 9
PLAT -0.004 0.12 -9999 0 -0.74 14 14
actin filament polymerization -0.33 0.24 -9999 0 -0.6 191 191
MST1 0.003 0.1 -9999 0 -0.85 8 8
alphaM/beta2 Integrin/lipoprotein(a) -0.27 0.36 -9999 0 -0.64 223 223
TNF -0.15 0.34 -9999 0 -0.84 67 67
RAP1B 0.016 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.14 0.28 -9999 0 -0.66 108 108
fibrinolysis -0.34 0.33 -9999 0 -0.84 109 109
HCK -0.032 0.2 -9999 0 -0.86 29 29
dendritic cell antigen processing and presentation -0.3 0.24 -9999 0 -0.52 230 230
VTN -0.1 0.28 -9999 0 -0.75 82 82
alphaM/beta2 Integrin/CYR61 -0.14 0.28 -9999 0 -0.66 109 109
LPA 0.003 0.066 -9999 0 -0.86 3 3
LRP1 0.016 0 -9999 0 -10000 0 0
cell migration -0.37 0.4 -9999 0 -0.69 282 282
FN1 -0.049 0.23 -9999 0 -0.86 39 39
alphaM/beta2 Integrin/Thy1 -0.13 0.28 -9999 0 -0.67 104 104
MPO -0.013 0.15 -9999 0 -0.86 17 17
KNG1 -0.55 0.32 -9999 0 -0.74 396 396
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.33 0.26 -9999 0 -0.63 181 181
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.38 0.38 -9999 0 -0.74 274 274
CTGF 0.006 0.086 -9999 0 -0.74 7 7
alphaM/beta2 Integrin/Hck -0.16 0.35 -9999 0 -0.79 107 107
ITGAM -0.021 0.18 -9999 0 -0.86 22 22
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.17 0.34 -9999 0 -0.74 111 111
HP -0.2 0.38 -9999 0 -0.86 133 133
leukocyte adhesion -0.18 0.27 -9999 0 -0.82 51 51
SELP -0.02 0.16 -9999 0 -0.74 25 25
IL4-mediated signaling events

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
BCL2L1 -0.48 0.48 -10000 0 -1.2 114 114
STAT6 (cleaved dimer) -0.58 0.49 -10000 0 -1.2 180 180
IGHG1 -0.17 0.18 -10000 0 -0.69 11 11
IGHG3 -0.48 0.46 -10000 0 -1.1 136 136
AKT1 -0.28 0.33 -10000 0 -0.84 86 86
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.24 0.31 -10000 0 -0.81 89 89
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.27 0.3 -10000 0 -0.8 65 65
THY1 -0.48 0.48 -10000 0 -1.2 114 114
MYB -0.21 0.39 -10000 0 -0.86 139 139
HMGA1 0.014 0.038 -10000 0 -0.86 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.39 0.42 -10000 0 -0.96 131 131
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.3 -10000 0 -0.8 65 65
SP1 0.022 0.015 -10000 0 -10000 0 0
INPP5D 0.009 0.076 -10000 0 -0.86 4 4
SOCS5 0.026 0.017 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.56 0.48 -10000 0 -1.2 153 153
SOCS1 -0.33 0.34 -10000 0 -0.81 82 82
SOCS3 -0.3 0.34 -10000 0 -0.9 78 78
FCER2 -0.41 0.44 -10000 0 -1.1 85 85
PARP14 0.016 0.004 -10000 0 -10000 0 0
CCL17 -0.5 0.5 -10000 0 -1.2 123 123
GRB2 0.016 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.22 0.28 -10000 0 -0.79 54 54
T cell proliferation -0.5 0.51 -10000 0 -1.2 130 130
IL4R/JAK1 -0.48 0.47 -10000 0 -1.2 114 114
EGR2 -0.49 0.5 -10000 0 -1.2 111 111
JAK2 0.006 0.023 -10000 0 -10000 0 0
JAK3 -0.16 0.35 -10000 0 -0.86 107 107
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
JAK1 0.007 0.015 -10000 0 -10000 0 0
COL1A2 -0.21 0.3 -10000 0 -0.89 67 67
CCL26 -0.49 0.49 -10000 0 -1.2 114 114
IL4R -0.51 0.51 -10000 0 -1.2 117 117
PTPN6 0.027 0.012 -10000 0 -10000 0 0
IL13RA2 -0.56 0.56 -10000 0 -1.3 141 141
IL13RA1 0.006 0.023 -10000 0 -10000 0 0
IRF4 -0.27 0.42 -10000 0 -0.96 127 127
ARG1 -0.18 0.26 -10000 0 -0.76 52 52
CBL -0.36 0.4 -10000 0 -0.94 116 116
GTF3A 0.01 0.03 -10000 0 -10000 0 0
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
IL13RA1/JAK2 -0.007 0.043 -10000 0 -10000 0 0
IRF4/BCL6 -0.26 0.37 -10000 0 -0.93 115 115
CD40LG -0.078 0.29 -10000 0 -0.91 57 57
MAPK14 -0.35 0.39 -10000 0 -0.94 113 113
mitosis -0.26 0.31 -10000 0 -0.78 86 86
STAT6 -0.55 0.56 -10000 0 -1.3 125 125
SPI1 -0.1 0.3 -10000 0 -0.86 73 73
RPS6KB1 -0.24 0.3 -10000 0 -0.77 74 74
STAT6 (dimer) -0.56 0.56 -10000 0 -1.3 125 125
STAT6 (dimer)/PARP14 -0.51 0.51 -10000 0 -1.2 124 124
mast cell activation 0.012 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.3 0.36 -10000 0 -0.89 100 100
FRAP1 -0.28 0.33 -10000 0 -0.84 86 86
LTA -0.6 0.56 -10000 0 -1.3 155 155
FES 0.013 0.046 -10000 0 -0.74 2 2
T-helper 1 cell differentiation 0.54 0.54 1.3 125 -10000 0 125
CCL11 -0.69 0.6 -10000 0 -1.3 231 231
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.29 0.34 -10000 0 -0.86 96 96
IL2RG -0.035 0.21 -10000 0 -0.85 34 34
IL10 -0.5 0.5 -10000 0 -1.2 115 115
IRS1 0.01 0.065 -10000 0 -0.74 4 4
IRS2 0.003 0.11 -10000 0 -0.86 8 8
IL4 -0.11 0.12 -10000 0 -10000 0 0
IL5 -0.49 0.48 -10000 0 -1.2 111 111
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.39 0.37 -10000 0 -0.88 107 107
COL1A1 -0.41 0.43 -10000 0 -0.92 205 205
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.48 0.48 -10000 0 -1.2 97 97
IL2R gamma/JAK3 -0.16 0.36 -10000 0 -0.83 111 111
TFF3 -0.5 0.5 -10000 0 -1.2 126 126
ALOX15 -0.49 0.48 -10000 0 -1.2 111 111
MYBL1 -0.044 0.22 -10000 0 -0.86 36 36
T-helper 2 cell differentiation -0.43 0.41 -10000 0 -0.97 130 130
SHC1 0.014 0.038 -10000 0 -0.86 1 1
CEBPB 0 0.13 -10000 0 -0.87 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.29 -10000 0 -0.78 68 68
mol:PI-3-4-5-P3 -0.28 0.33 -10000 0 -0.84 86 86
PI3K -0.3 0.36 -10000 0 -0.91 86 86
DOK2 -0.035 0.2 -10000 0 -0.86 31 31
ETS1 0.028 0.014 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.21 0.27 -10000 0 -0.77 54 54
ITGB3 -0.49 0.49 -10000 0 -1.2 115 115
PIGR -0.84 0.7 -10000 0 -1.4 274 274
IGHE 0.028 0.089 0.29 14 -0.37 4 18
MAPKKK cascade -0.2 0.26 -10000 0 -0.75 54 54
BCL6 0.014 0.004 -10000 0 -10000 0 0
OPRM1 -0.49 0.48 -10000 0 -1.2 111 111
RETNLB -0.49 0.48 -10000 0 -1.2 114 114
SELP -0.51 0.52 -10000 0 -1.3 119 119
AICDA -0.62 0.54 -10000 0 -1.2 184 184
Caspase cascade in apoptosis

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
TOP1 -0.13 0.26 -10000 0 -0.49 172 172
ACTA1 -0.19 0.35 -10000 0 -0.67 173 173
NUMA1 -0.13 0.26 -10000 0 -0.49 172 172
SPTAN1 -0.19 0.35 -10000 0 -0.66 172 172
LIMK1 -0.19 0.35 -10000 0 -0.66 173 173
BIRC3 -0.12 0.31 -10000 0 -0.86 80 80
BIRC2 0.012 0.007 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
CASP10 -0.28 0.46 -10000 0 -0.86 190 190
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.016 0 -10000 0 -10000 0 0
PTK2 -0.13 0.26 -10000 0 -0.49 172 172
DIABLO 0.016 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.18 0.34 -10000 0 -0.65 172 172
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
GSN -0.19 0.35 -10000 0 -0.66 172 172
MADD 0.016 0 -10000 0 -10000 0 0
TFAP2A -0.3 0.28 -10000 0 -0.54 294 294
BID -0.09 0.17 -10000 0 -0.31 190 190
MAP3K1 -0.044 0.11 -10000 0 -0.22 78 78
TRADD 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.19 0.35 -10000 0 -0.66 170 170
CASP9 0.016 0.001 -10000 0 -10000 0 0
DNA repair 0.014 0.094 -10000 0 -0.21 35 35
neuron apoptosis 0.011 0.044 -10000 0 -0.61 1 1
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.17 0.34 -10000 0 -0.63 172 172
APAF1 0.016 0.001 -10000 0 -10000 0 0
CASP6 -0.05 0.15 -10000 0 -0.39 28 28
TRAF2 0.016 0 -10000 0 -10000 0 0
ICAD/CAD -0.17 0.34 -10000 0 -0.77 105 105
CASP7 0.05 0.12 0.34 80 -10000 0 80
KRT18 -0.002 0.046 -10000 0 -0.3 2 2
apoptosis -0.17 0.32 -10000 0 -0.7 113 113
DFFA -0.19 0.35 -10000 0 -0.66 172 172
DFFB -0.19 0.35 -10000 0 -0.66 172 172
PARP1 -0.014 0.094 0.21 35 -10000 0 35
actin filament polymerization 0.16 0.32 0.72 106 -10000 0 106
TNF 0.003 0.1 -10000 0 -0.8 8 8
CYCS -0.069 0.13 -10000 0 -0.28 105 105
SATB1 -0.037 0.15 -10000 0 -0.48 3 3
SLK -0.19 0.35 -10000 0 -0.66 172 172
p15 BID/BAX -0.073 0.15 -10000 0 -0.32 105 105
CASP2 0.031 0.088 -10000 0 -0.42 1 1
JNK cascade 0.044 0.11 0.22 78 -10000 0 78
CASP3 -0.21 0.37 -10000 0 -0.71 172 172
LMNB2 0.011 0.085 -10000 0 -0.39 4 4
RIPK1 0.016 0 -10000 0 -10000 0 0
CASP4 0.016 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO -0.078 0.19 -10000 0 -0.52 80 80
negative regulation of DNA binding -0.29 0.28 -10000 0 -0.54 294 294
stress fiber formation -0.18 0.35 -10000 0 -0.65 172 172
GZMB -0.32 0.5 -10000 0 -0.97 190 190
CASP1 0.023 0 -10000 0 -10000 0 0
LMNB1 0.009 0.089 -10000 0 -0.37 7 7
APP 0.011 0.045 -10000 0 -0.62 1 1
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.015 0 -10000 0 -10000 0 0
VIM -0.17 0.31 -10000 0 -0.56 175 175
LMNA 0.011 0.085 -10000 0 -0.39 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.005 0.09 -10000 0 -0.41 7 7
LRDD 0.003 0.1 -10000 0 -0.85 8 8
SREBF1 -0.19 0.35 -10000 0 -0.66 173 173
APAF-1/Caspase 9 -0.01 0.062 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis -0.13 0.26 -10000 0 -0.48 172 172
CFL2 -0.17 0.34 -10000 0 -0.75 106 106
GAS2 -0.2 0.36 -10000 0 -0.66 177 177
positive regulation of apoptosis 0.015 0.085 -10000 0 -0.38 4 4
PRF1 -0.2 0.38 -10000 0 -0.86 132 132
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.41 0.54 -9999 0 -0.9 245 245
MAP4K1 -0.34 0.43 -9999 0 -0.86 218 218
MAP3K8 0.012 0.054 -9999 0 -0.86 2 2
PRKCB 0.008 0.08 -9999 0 -0.81 5 5
DBNL 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
MAP3K1 -0.15 0.29 -9999 0 -0.62 124 124
JUN 0 0.087 -9999 0 -0.6 6 6
MAP3K7 -0.15 0.29 -9999 0 -0.62 124 124
GRAP2 -0.042 0.22 -9999 0 -0.86 35 35
CRK 0.016 0 -9999 0 -10000 0 0
MAP2K4 -0.14 0.28 -9999 0 -0.59 124 124
LAT -0.23 0.39 -9999 0 -0.86 148 148
LCP2 -0.039 0.21 -9999 0 -0.86 33 33
MAPK8 -0.012 0.092 -9999 0 -0.64 6 6
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.2 0.29 -9999 0 -0.66 124 124
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.39 0.51 -9999 0 -1.2 124 124
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.014 0.038 -9999 0 -0.86 1 1
EGFR 0.001 0.11 -9999 0 -0.85 9 9
EGF/EGFR -0.37 0.16 -9999 0 -0.86 27 27
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.36 0.14 -9999 0 -0.89 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.012 0.054 -9999 0 -0.86 2 2
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.67 0.23 -9999 0 -0.74 480 480
EGF/EGFR dimer/SHC -0.44 0.16 -9999 0 -0.48 481 481
mol:GDP -0.36 0.13 -9999 0 -0.87 9 9
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.014 0.16 -9999 0 -0.86 18 18
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.32 0.12 -9999 0 -0.81 10 10
SHC1 0.014 0.038 -9999 0 -0.86 1 1
HRAS/GDP -0.33 0.13 -9999 0 -0.82 10 10
FRAP1 -0.34 0.14 -9999 0 -0.85 9 9
EGF/EGFR dimer -0.51 0.18 -9999 0 -0.56 481 481
SOS1 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.025 0.12 -9999 0 -0.66 20 20
Aurora C 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
INCENP 0.016 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.25 0.27 -9999 0 -0.53 249 249
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.063 0.068 -9999 0 -10000 0 0
AURKB -0.39 0.44 -9999 0 -0.86 248 248
AURKC 0.012 0.054 -9999 0 -0.86 2 2
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer -0.008 0.071 -9999 0 -0.68 5 5
VEGFR1 homodimer/NRP1 -0.008 0.072 -9999 0 -0.62 7 7
mol:DAG -0.26 0.29 -9999 0 -0.52 294 294
VEGFR1 homodimer/NRP1/VEGFR 121 -0.24 0.27 -9999 0 -0.54 240 240
CaM/Ca2+ -0.27 0.25 -9999 0 -0.92 7 7
HIF1A 0.02 0.057 -9999 0 -0.72 2 2
GAB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.22 0.21 -9999 0 -0.94 6 6
PLCG1 -0.26 0.29 -9999 0 -0.52 294 294
NOS3 -0.18 0.24 -9999 0 -0.85 6 6
CBL 0.014 0.033 -9999 0 -0.74 1 1
mol:NO -0.17 0.24 -9999 0 -0.8 6 6
FLT1 0.031 0.086 -9999 0 -0.71 7 7
PGF -0.47 0.44 -9999 0 -0.86 293 293
VEGFR1 homodimer/NRP2/VEGFR121 -0.24 0.27 -9999 0 -0.53 245 245
CALM1 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
eNOS/Hsp90 -0.16 0.23 -9999 0 -0.76 6 6
endothelial cell proliferation -0.2 0.26 -9999 0 -0.82 9 9
mol:Ca2+ -0.26 0.29 -9999 0 -0.52 294 294
MAPK3 -0.21 0.26 -9999 0 -0.88 6 6
MAPK1 -0.21 0.26 -9999 0 -0.83 7 7
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
PLGF homodimer -0.47 0.44 -9999 0 -0.86 293 293
PRKACA 0.016 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.045 0.22 -9999 0 -0.86 37 37
VEGFA homodimer -0.38 0.44 -9999 0 -0.86 239 239
VEGFR1 homodimer/VEGFA homodimer -0.26 0.29 -9999 0 -0.58 240 240
platelet activating factor biosynthetic process -0.2 0.25 -9999 0 -0.85 6 6
PI3K -0.27 0.25 -9999 0 -0.99 7 7
PRKCA -0.23 0.27 -9999 0 -0.89 7 7
PRKCB -0.24 0.28 -9999 0 -0.9 9 9
VEGFR1 homodimer/PLGF homodimer -0.32 0.29 -9999 0 -0.58 294 294
VEGFA -0.38 0.44 -9999 0 -0.86 239 239
VEGFB 0.016 0 -9999 0 -10000 0 0
mol:IP3 -0.26 0.29 -9999 0 -0.52 294 294
RASA1 0.046 0.077 -9999 0 -0.65 6 6
NRP2 0.004 0.1 -9999 0 -0.86 7 7
VEGFR1 homodimer 0.031 0.086 -9999 0 -0.7 7 7
VEGFB homodimer 0.016 0 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.74 1 1
eNOS/Caveolin-1 -0.19 0.26 -9999 0 -0.8 31 31
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.27 0.25 -9999 0 -0.96 7 7
mol:L-citrulline -0.17 0.24 -9999 0 -0.8 6 6
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.22 0.25 -9999 0 -0.94 6 6
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.24 0.27 -9999 0 -0.53 241 241
CD2AP 0.016 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.25 0.23 -9999 0 -0.99 6 6
PDPK1 -0.22 0.27 -9999 0 -0.94 7 7
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.24 0.27 -9999 0 -0.52 240 240
mol:NADP -0.17 0.24 -9999 0 -0.8 6 6
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.22 0.25 -9999 0 -0.92 6 6
VEGFR1 homodimer/NRP2 -0.015 0.095 -9999 0 -0.61 12 12
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.049 0.23 -9999 0 -0.86 39 39
GPC2 -0.087 0.28 -9999 0 -0.86 62 62
GPC2/Midkine -0.12 0.28 -9999 0 -0.73 90 90
neuron projection morphogenesis -0.12 0.28 -9999 0 -0.73 90 90
Syndecan-1-mediated signaling events

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
TGFB1 0.007 0.085 -9999 0 -0.86 5 5
CCL5 -0.35 0.43 -9999 0 -0.86 224 224
SDCBP 0.016 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.22 0.23 -9999 0 -0.59 94 94
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 -0.2 0.22 -9999 0 -0.56 95 95
Syndecan-1/Syntenin -0.2 0.22 -9999 0 -0.55 94 94
MAPK3 -0.16 0.2 -9999 0 -0.7 15 15
HGF/MET -0.032 0.15 -9999 0 -0.66 26 26
TGFB1/TGF beta receptor Type II 0.007 0.084 -9999 0 -0.86 5 5
BSG 0.014 0.038 -9999 0 -0.86 1 1
keratinocyte migration -0.2 0.21 -9999 0 -0.55 95 95
Syndecan-1/RANTES -0.41 0.33 -9999 0 -0.68 280 280
Syndecan-1/CD147 -0.2 0.18 -9999 0 -0.53 89 89
Syndecan-1/Syntenin/PIP2 -0.21 0.19 -9999 0 -0.54 94 94
LAMA5 0.013 0.05 -9999 0 -0.8 2 2
positive regulation of cell-cell adhesion -0.21 0.18 -9999 0 -0.52 94 94
MMP7 -0.13 0.3 -9999 0 -0.75 99 99
HGF -0.019 0.17 -9999 0 -0.8 23 23
Syndecan-1/CASK -0.21 0.22 -9999 0 -0.56 94 94
Syndecan-1/HGF/MET -0.23 0.22 -9999 0 -0.58 104 104
regulation of cell adhesion -0.15 0.2 -9999 0 -0.67 15 15
HPSE 0.013 0.046 -9999 0 -0.74 2 2
positive regulation of cell migration -0.22 0.23 -9999 0 -0.59 94 94
SDC1 -0.22 0.23 -9999 0 -0.59 94 94
Syndecan-1/Collagen -0.22 0.23 -9999 0 -0.59 94 94
PPIB 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.085 -9999 0 -0.86 5 5
PRKACA 0.016 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 251 251
MAPK1 -0.16 0.2 -9999 0 -0.7 15 15
homophilic cell adhesion -0.22 0.22 -9999 0 -0.58 94 94
MMP1 -0.15 0.34 -9999 0 -0.83 106 106
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.59 0.31 -9999 0 -0.85 285 285
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.12 0.31 -9999 0 -0.84 85 85
SMAD9 -0.065 0.086 -9999 0 -0.57 11 11
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD5 -0.18 0.17 -9999 0 -0.51 19 19
BMP7/USAG1 -0.69 0.34 -9999 0 -0.8 462 462
SMAD5/SKI -0.17 0.16 -9999 0 -0.5 15 15
SMAD1 0.002 0.041 -9999 0 -10000 0 0
BMP2 0.01 0.068 -9999 0 -0.77 4 4
SMAD1/SMAD1/SMAD4 0 0.001 -9999 0 -10000 0 0
BMPR1A 0.016 0 -9999 0 -10000 0 0
BMPR1B -0.51 0.35 -9999 0 -0.74 367 367
BMPR1A-1B/BAMBI -0.33 0.22 -9999 0 -0.48 371 371
AHSG -0.014 0.13 -9999 0 -0.86 13 13
CER1 0.004 0.007 -9999 0 -10000 0 0
BMP2-4/CER1 -0.007 0.057 -9999 0 -0.5 7 7
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.11 -9999 0 -0.49 19 19
BMP2-4 (homodimer) -0.008 0.065 -9999 0 -0.57 7 7
RGMB 0.012 0.054 -9999 0 -0.86 2 2
BMP6/BMPR2/BMPR1A-1B -0.3 0.2 -9999 0 -0.78 5 5
RGMA 0.009 0.073 -9999 0 -0.74 5 5
SMURF1 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.15 0.15 -9999 0 -0.56 19 19
BMP2-4/USAG1 -0.31 0.24 -9999 0 -0.48 343 343
SMAD6/SMURF1/SMAD5 -0.17 0.16 -9999 0 -0.5 15 15
SOSTDC1 -0.47 0.36 -9999 0 -0.74 342 342
BMP7/BMPR2/BMPR1A-1B -0.58 0.3 -9999 0 -0.85 264 264
SKI 0.016 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.004 0.092 -9999 0 -0.74 8 8
HFE2 -0.019 0.16 -9999 0 -0.86 19 19
ZFYVE16 0.016 0 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.017 0.097 -9999 0 -0.55 16 16
SMAD5/SMAD5/SMAD4 -0.17 0.16 -9999 0 -0.58 3 3
MAPK1 0.016 0 -9999 0 -10000 0 0
TAK1/TAB family -0.13 0.1 -9999 0 -0.5 15 15
BMP7 (homodimer) -0.5 0.35 -9999 0 -0.74 358 358
NUP214 0.016 0 -9999 0 -10000 0 0
BMP6/FETUA -0.025 0.12 -9999 0 -0.62 21 21
SMAD1/SKI 0.012 0.039 -9999 0 -10000 0 0
SMAD6 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.02 0.1 -9999 0 -0.55 20 20
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.18 0.33 -9999 0 -0.75 134 134
BMPR2 (homodimer) 0.016 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.38 0.26 -9999 0 -0.56 367 367
CHRDL1 -0.38 0.38 -9999 0 -0.74 277 277
ENDOFIN/SMAD1 0.012 0.039 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0.005 0.004 -9999 0 -10000 0 0
SMAD6/SMURF1 0.016 0 -9999 0 -10000 0 0
BAMBI 0.004 0.092 -9999 0 -0.74 8 8
SMURF2 0.014 0.033 -9999 0 -0.74 1 1
BMP2-4/CHRDL1 -0.25 0.24 -9999 0 -0.48 279 279
BMP2-4/GREM1 -0.13 0.22 -9999 0 -0.63 13 13
SMAD7 0.016 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.038 0.09 -9999 0 -0.56 9 9
SMAD1/SMAD6 0.012 0.039 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.5 0.35 -9999 0 -0.74 358 358
BMP6 0.004 0.092 -9999 0 -0.74 8 8
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.12 0.12 -9999 0 -0.46 19 19
PPM1A 0.016 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.011 0.042 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
PPP1CA 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
PPP1R15A 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.2 0.19 -9999 0 -0.59 65 65
CHRD -0.001 0.11 -9999 0 -0.78 11 11
BMPR2 0.016 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.17 0.13 -9999 0 -0.58 19 19
BMP4 0.011 0.057 -9999 0 -0.74 3 3
FST -0.075 0.25 -9999 0 -0.76 62 62
BMP2-4/NOG -0.095 0.21 -9999 0 -0.56 91 91
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.54 0.29 -9999 0 -0.8 264 264
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.03 0.088 -10000 0 -0.71 8 8
oxygen homeostasis -0.001 0.015 -10000 0 -10000 0 0
TCEB2 0.011 0.063 -10000 0 -0.82 3 3
TCEB1 0.016 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.23 0.14 -10000 0 -0.57 6 6
EPO -0.4 0.41 -10000 0 -0.9 153 153
FIH (dimer) 0.014 0.02 -10000 0 -10000 0 0
APEX1 0.013 0.013 -10000 0 -10000 0 0
SERPINE1 -0.34 0.41 -10000 0 -0.93 120 120
FLT1 -0.019 0.077 -10000 0 -0.76 5 5
ADORA2A -0.3 0.34 -10000 0 -0.82 83 83
germ cell development -0.41 0.44 -10000 0 -0.93 177 177
SLC11A2 -0.29 0.34 -10000 0 -0.81 83 83
BHLHE40 -0.29 0.34 -10000 0 -0.81 83 83
HIF1AN 0.014 0.02 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.3 0.22 -10000 0 -0.56 146 146
ETS1 0.037 0.004 -10000 0 -10000 0 0
CITED2 -0.023 0.056 -10000 0 -1.2 1 1
KDR -0.015 0.065 -10000 0 -1.4 1 1
PGK1 -0.29 0.34 -10000 0 -0.81 83 83
SIRT1 0.014 0.005 -10000 0 -10000 0 0
response to hypoxia -0.002 0.005 -10000 0 -10000 0 0
HIF2A/ARNT -0.35 0.42 -10000 0 -1 83 83
EPAS1 -0.27 0.19 -10000 0 -0.46 162 162
SP1 0.026 0.006 -10000 0 -10000 0 0
ABCG2 -0.29 0.34 -10000 0 -0.81 84 84
EFNA1 -0.29 0.34 -10000 0 -0.81 84 84
FXN -0.3 0.34 -10000 0 -0.82 83 83
POU5F1 -0.43 0.47 -10000 0 -1 177 177
neuron apoptosis 0.34 0.4 0.96 83 -10000 0 83
EP300 0.014 0.033 -10000 0 -0.74 1 1
EGLN3 -0.76 0.29 -10000 0 -0.87 469 469
EGLN2 0.011 0.016 -10000 0 -10000 0 0
EGLN1 0.014 0.02 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.004 0.045 -10000 0 -0.52 4 4
VHL 0.014 0.033 -10000 0 -0.74 1 1
ARNT 0.013 0.014 -10000 0 -10000 0 0
SLC2A1 -0.32 0.37 -10000 0 -0.9 85 85
TWIST1 -0.31 0.34 -10000 0 -0.83 86 86
ELK1 0.026 0.001 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.26 0.2 -10000 0 -0.56 84 84
VEGFA -0.47 0.49 -10000 0 -0.99 199 199
CREBBP 0.016 0 -10000 0 -10000 0 0
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 -0.25 0.47 -10000 0 -1.1 70 70
IL23A -0.24 0.47 -10000 0 -1.1 55 55
NF kappa B1 p50/RelA/I kappa B alpha -0.32 0.39 -10000 0 -1 79 79
positive regulation of T cell mediated cytotoxicity -0.28 0.52 -10000 0 -1.1 91 91
ITGA3 -0.24 0.46 -10000 0 -1.1 55 55
IL17F -0.15 0.34 -10000 0 -0.74 36 36
IL12B -0.085 0.29 -10000 0 -0.88 62 62
STAT1 (dimer) -0.27 0.5 -10000 0 -1.1 89 89
CD4 -0.24 0.47 -10000 0 -1.1 66 66
IL23 -0.27 0.48 -10000 0 -1.1 70 70
IL23R -0.012 0.15 -10000 0 -0.8 10 10
IL1B -0.25 0.48 -10000 0 -1.1 67 67
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.24 0.47 -10000 0 -1.1 65 65
TYK2 0.016 0.024 -10000 0 -10000 0 0
STAT4 -0.035 0.21 -10000 0 -0.86 31 31
STAT3 0.016 0.001 -10000 0 -10000 0 0
IL18RAP -0.22 0.39 -10000 0 -0.88 137 137
IL12RB1 -0.25 0.42 -10000 0 -0.89 160 160
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
IL12Rbeta1/TYK2 -0.2 0.33 -10000 0 -0.7 160 160
IL23R/JAK2 -0.011 0.16 -10000 0 -0.78 9 9
positive regulation of chronic inflammatory response -0.28 0.52 -10000 0 -1.1 91 91
natural killer cell activation 0.002 0.012 0.063 10 -10000 0 10
JAK2 0.021 0.034 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
NFKB1 0.01 0.033 -10000 0 -0.73 1 1
RELA 0.012 0.009 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.26 0.46 -10000 0 -1.1 70 70
ALOX12B -0.3 0.5 -10000 0 -1.1 85 85
CXCL1 -0.28 0.52 -10000 0 -1.1 83 83
T cell proliferation -0.28 0.52 -10000 0 -1.1 91 91
NFKBIA 0.012 0.009 -10000 0 -10000 0 0
IL17A -0.099 0.29 -10000 0 -0.61 3 3
PI3K -0.33 0.4 -10000 0 -1 91 91
IFNG -0.052 0.069 0.13 4 -0.12 221 225
STAT3 (dimer) -0.31 0.38 -10000 0 -1 78 78
IL18R1 -0.003 0.1 -10000 0 -0.8 8 8
IL23/IL23R/JAK2/TYK2/SOCS3 -0.18 0.38 -10000 0 -0.79 87 87
IL18/IL18R -0.17 0.28 -10000 0 -0.61 149 149
macrophage activation -0.017 0.018 -10000 0 -0.045 10 10
TNF -0.25 0.49 -10000 0 -1.1 68 68
STAT3/STAT4 -0.35 0.43 -10000 0 -1.1 96 96
STAT4 (dimer) -0.3 0.53 -10000 0 -1.2 89 89
IL18 -0.002 0.099 -10000 0 -0.86 7 7
IL19 -0.25 0.46 -10000 0 -1 67 67
STAT5A (dimer) -0.27 0.5 -10000 0 -1.1 88 88
STAT1 0.014 0.038 -10000 0 -0.86 1 1
SOCS3 0.009 0.076 -10000 0 -0.86 4 4
CXCL9 -0.39 0.59 -10000 0 -1.1 165 165
MPO -0.25 0.48 -10000 0 -1.1 70 70
positive regulation of humoral immune response -0.28 0.52 -10000 0 -1.1 91 91
IL23/IL23R/JAK2/TYK2 -0.3 0.54 -10000 0 -1.2 90 90
IL6 -0.3 0.53 -10000 0 -1.2 93 93
STAT5A 0.016 0 -10000 0 -10000 0 0
IL2 -0.016 0.12 -10000 0 -0.86 10 10
positive regulation of tyrosine phosphorylation of STAT protein 0.002 0.012 0.063 10 -10000 0 10
CD3E -0.38 0.6 -10000 0 -1.1 166 166
keratinocyte proliferation -0.28 0.52 -10000 0 -1.1 91 91
NOS2 -0.25 0.47 -10000 0 -1.1 71 71
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.007 0.13 -9999 0 -0.77 15 15
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.063 -9999 0 -0.82 3 3
TCEB1 0.016 0 -9999 0 -10000 0 0
HIF1A/p53 -0.08 0.047 -9999 0 -0.39 1 1
HIF1A -0.099 0.039 -9999 0 -0.42 1 1
COPS5 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.038 -9999 0 -0.48 2 2
FIH (dimer) 0.016 0 -9999 0 -10000 0 0
CDKN2A -0.83 0.17 -9999 0 -0.86 513 513
ARNT/IPAS -0.016 0.097 -9999 0 -0.58 15 15
HIF1AN 0.016 0 -9999 0 -10000 0 0
GNB2L1 0.014 0.038 -9999 0 -0.86 1 1
HIF1A/ARNT -0.08 0.047 -9999 0 -0.39 1 1
CUL2 0.016 0 -9999 0 -10000 0 0
OS9 0.016 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.004 0.048 -9999 0 -0.55 4 4
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 -0.08 0.047 -9999 0 -0.39 1 1
PHD1-3/OS9 -0.46 0.17 -9999 0 -0.52 467 467
HIF1A/RACK1/Elongin B/Elongin C -0.067 0.049 -9999 0 -0.54 4 4
VHL 0.014 0.033 -9999 0 -0.74 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
HIF1A/JAB1 -0.08 0.047 -9999 0 -0.39 1 1
EGLN3 -0.76 0.28 -9999 0 -0.86 469 469
EGLN2 0.016 0 -9999 0 -10000 0 0
EGLN1 0.016 0 -9999 0 -10000 0 0
TP53 0.016 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.003 0.038 -9999 0 -0.61 1 1
ARNT 0.016 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.016 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.55 0.11 -9999 0 -0.57 513 513
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.24 0.26 -10000 0 -0.74 32 32
IHH -0.096 0.23 -10000 0 -0.82 47 47
SHH Np/Cholesterol/GAS1 -0.036 0.12 -10000 0 -0.45 43 43
LRPAP1 0.016 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.036 0.12 0.45 43 -10000 0 43
SMO/beta Arrestin2 -0.14 0.15 -10000 0 -0.6 34 34
SMO -0.13 0.19 -10000 0 -0.63 33 33
AKT1 -0.04 0.092 -10000 0 -0.46 1 1
ARRB2 0.014 0.038 -10000 0 -0.86 1 1
BOC 0.016 0 -10000 0 -10000 0 0
ADRBK1 0.016 0 -10000 0 -10000 0 0
heart looping -0.13 0.19 -10000 0 -0.62 33 33
STIL -0.093 0.16 -10000 0 -0.67 10 10
DHH N/PTCH2 -0.044 0.16 -10000 0 -0.63 37 37
DHH N/PTCH1 -0.16 0.16 -10000 0 -0.62 37 37
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
DHH -0.002 0.11 -10000 0 -0.74 12 12
PTHLH -0.44 0.41 -10000 0 -0.74 328 328
determination of left/right symmetry -0.13 0.19 -10000 0 -0.62 33 33
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
skeletal system development -0.43 0.4 -10000 0 -0.73 328 328
IHH N/Hhip -0.2 0.31 -10000 0 -0.65 164 164
DHH N/Hhip -0.15 0.26 -10000 0 -0.57 142 142
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.13 0.19 -10000 0 -0.62 33 33
pancreas development -0.18 0.33 -10000 0 -0.75 133 133
HHAT 0.016 0 -10000 0 -10000 0 0
PI3K -0.002 0.034 -10000 0 -0.56 2 2
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.031 0.18 -10000 0 -0.74 33 33
somite specification -0.13 0.19 -10000 0 -0.62 33 33
SHH Np/Cholesterol/PTCH1 -0.13 0.14 -10000 0 -0.55 36 36
SHH Np/Cholesterol/PTCH2 -0.034 0.13 -10000 0 -0.5 36 36
SHH Np/Cholesterol/Megalin -0.047 0.15 -10000 0 -0.48 52 52
SHH 0.018 0.085 -10000 0 -0.57 11 11
catabolic process -0.15 0.19 -10000 0 -0.65 32 32
SMO/Vitamin D3 -0.11 0.18 -10000 0 -0.58 36 36
SHH Np/Cholesterol/Hhip -0.12 0.2 -10000 0 -0.46 139 139
LRP2 -0.05 0.21 -10000 0 -0.74 46 46
receptor-mediated endocytosis -0.15 0.18 -10000 0 -0.62 44 44
SHH Np/Cholesterol/BOC -0.009 0.063 -10000 0 -0.44 11 11
SHH Np/Cholesterol/CDO -0.069 0.18 -10000 0 -0.52 70 70
mesenchymal cell differentiation 0.12 0.2 0.45 139 -10000 0 139
mol:Vitamin D3 -0.11 0.17 -10000 0 -0.56 36 36
IHH N/PTCH2 -0.081 0.21 -10000 0 -0.62 70 70
CDON -0.083 0.28 -10000 0 -0.86 60 60
IHH N/PTCH1 -0.16 0.19 -10000 0 -0.66 32 32
Megalin/LRPAP1 -0.048 0.16 -10000 0 -0.56 46 46
PTCH2 -0.026 0.19 -10000 0 -0.86 25 25
SHH Np/Cholesterol -0.009 0.065 -10000 0 -0.45 11 11
PTCH1 -0.15 0.19 -10000 0 -0.65 32 32
HHIP -0.18 0.33 -10000 0 -0.75 133 133
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.016 0 -9999 0 -10000 0 0
LAT2 -0.16 0.23 -9999 0 -0.7 62 62
AP1 -0.16 0.21 -9999 0 -0.56 89 89
mol:PIP3 -0.23 0.34 -9999 0 -0.7 145 145
IKBKB -0.086 0.16 -9999 0 -0.34 75 75
AKT1 -0.16 0.21 -9999 0 -0.72 22 22
IKBKG -0.086 0.16 -9999 0 -0.34 84 84
MS4A2 -0.18 0.36 -9999 0 -0.86 117 117
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.011 0.033 -9999 0 -0.75 1 1
MAP3K1 -0.12 0.26 -9999 0 -0.59 89 89
mol:Ca2+ -0.16 0.24 -9999 0 -0.48 138 138
LYN 0.011 0.009 -9999 0 -10000 0 0
CBLB -0.12 0.15 -9999 0 -0.54 21 21
SHC1 0.014 0.038 -9999 0 -0.86 1 1
RasGAP/p62DOK -0.002 0.03 -9999 0 -0.48 2 2
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.009 0.076 -9999 0 -0.86 4 4
PLD2 -0.17 0.28 -9999 0 -0.56 100 100
PTPN13 -0.068 0.16 -9999 0 -0.49 21 21
PTPN11 0.014 0.006 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.043 0.17 -9999 0 -0.4 12 12
SYK 0.008 0.047 -9999 0 -0.75 2 2
GRB2 0.015 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.29 0.32 -9999 0 -0.76 141 141
LAT -0.25 0.29 -9999 0 -0.65 158 158
PAK2 -0.15 0.29 -9999 0 -0.64 115 115
NFATC2 -0.07 0.1 -9999 0 -0.68 5 5
HRAS -0.18 0.32 -9999 0 -0.7 124 124
GAB2 0.016 0 -9999 0 -10000 0 0
PLA2G1B 0.039 0.027 -9999 0 -10000 0 0
Fc epsilon R1 -0.25 0.32 -9999 0 -0.62 217 217
Antigen/IgE/Fc epsilon R1 -0.24 0.3 -9999 0 -0.58 217 217
mol:GDP -0.2 0.35 -9999 0 -0.77 129 129
JUN 0.016 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.033 -9999 0 -0.74 1 1
FOS -0.003 0.12 -9999 0 -0.75 13 13
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.12 0.16 -9999 0 -0.57 21 21
CHUK -0.086 0.16 -9999 0 -0.34 73 73
KLRG1 -0.12 0.15 -9999 0 -0.55 21 21
VAV1 -0.2 0.32 -9999 0 -0.69 136 136
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.12 0.15 -9999 0 -0.55 22 22
negative regulation of mast cell degranulation -0.11 0.15 -9999 0 -0.56 23 23
BTK -0.18 0.24 -9999 0 -0.58 114 114
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.17 0.22 -9999 0 -0.58 85 85
GAB2/PI3K/SHP2 -0.18 0.24 -9999 0 -0.82 22 22
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.12 0.15 -9999 0 -0.55 21 21
RAF1 0.026 0.027 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.3 0.39 -9999 0 -0.87 122 122
FCER1G -0.15 0.34 -9999 0 -0.87 98 98
FCER1A -0.021 0.16 -9999 0 -0.77 22 22
Antigen/IgE/Fc epsilon R1/Fyn -0.22 0.28 -9999 0 -0.54 203 203
MAPK3 0.04 0.025 -9999 0 -10000 0 0
MAPK1 0.04 0.025 -9999 0 -10000 0 0
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
MAPK8 -0.012 0.079 -9999 0 -0.58 2 2
DUSP1 0.014 0.038 -9999 0 -0.86 1 1
NF-kappa-B/RelA -0.069 0.074 -9999 0 -0.33 1 1
actin cytoskeleton reorganization -0.073 0.16 -9999 0 -0.48 21 21
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.22 0.29 -9999 0 -0.72 116 116
FER -0.12 0.15 -9999 0 -0.55 23 23
RELA 0.016 0 -9999 0 -10000 0 0
ITK -0.14 0.19 -9999 0 -0.42 165 165
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG1 -0.2 0.36 -9999 0 -0.76 131 131
cytokine secretion -0.051 0.053 -9999 0 -10000 0 0
SPHK1 -0.16 0.22 -9999 0 -0.64 60 60
PTK2 -0.076 0.16 -9999 0 -0.5 21 21
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.24 0.31 -9999 0 -0.77 110 110
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.18 0.31 -9999 0 -0.68 110 110
MAP2K2 0.034 0.031 -9999 0 -0.42 1 1
MAP2K1 0.035 0.024 -9999 0 -10000 0 0
MAP2K7 0.016 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.11 0.15 -9999 0 -0.53 21 21
MAP2K4 0.017 0.015 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.32 0.4 -9999 0 -0.72 229 229
mol:Choline -0.17 0.28 -9999 0 -0.55 100 100
SHC/Grb2/SOS1 -0.1 0.14 -9999 0 -0.52 16 16
FYN 0.016 0 -9999 0 -10000 0 0
DOK1 0.016 0 -9999 0 -10000 0 0
PXN -0.061 0.15 -9999 0 -0.46 17 17
HCLS1 -0.13 0.19 -9999 0 -0.68 31 31
PRKCB -0.14 0.23 -9999 0 -0.48 117 117
FCGR2B -0.14 0.34 -9999 0 -0.86 96 96
IGHE -0.005 0.01 -9999 0 -10000 0 0
KLRG1/SHIP -0.11 0.15 -9999 0 -0.57 23 23
LCP2 -0.039 0.21 -9999 0 -0.87 33 33
PLA2G4A -0.12 0.16 -9999 0 -0.54 27 27
RASA1 0.014 0.033 -9999 0 -0.74 1 1
mol:Phosphatidic acid -0.17 0.28 -9999 0 -0.55 100 100
IKK complex -0.046 0.13 -9999 0 -0.28 1 1
WIPF1 0.016 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.009 0.085 -10000 0 -0.86 5 5
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.074 0.2 0.6 34 -0.44 3 37
IL27/IL27R/JAK1 -0.079 0.35 0.58 1 -0.86 58 59
TBX21 -0.21 0.41 0.5 1 -0.72 184 185
IL12B -0.093 0.28 -10000 0 -0.87 62 62
IL12A 0.008 0.031 -10000 0 -0.68 1 1
IL6ST -0.016 0.14 -10000 0 -0.75 19 19
IL27RA/JAK1 0.011 0.062 -10000 0 -0.7 1 1
IL27 -0.043 0.21 -10000 0 -0.88 32 32
TYK2 0.011 0.012 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.025 0.13 -10000 0 -0.74 2 2
T-helper 2 cell differentiation 0.074 0.2 0.6 34 -0.44 3 37
T cell proliferation during immune response 0.074 0.2 0.6 34 -0.44 3 37
MAPKKK cascade -0.074 0.2 0.44 3 -0.6 34 37
STAT3 0.016 0 -10000 0 -10000 0 0
STAT2 0.016 0 -10000 0 -10000 0 0
STAT1 0.015 0.039 -10000 0 -0.86 1 1
IL12RB1 -0.25 0.4 -10000 0 -0.87 160 160
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.16 0.35 0.5 1 -0.7 108 109
IL27/IL27R/JAK2/TYK2 -0.078 0.2 0.44 3 -0.61 34 37
positive regulation of T cell mediated cytotoxicity -0.074 0.2 0.44 3 -0.6 34 37
STAT1 (dimer) -0.064 0.51 0.54 126 -0.98 73 199
JAK2 0.011 0.012 -10000 0 -10000 0 0
JAK1 0.017 0.006 -10000 0 -10000 0 0
STAT2 (dimer) -0.08 0.18 0.39 3 -0.62 25 28
T cell proliferation -0.12 0.25 0.4 1 -0.68 58 59
IL12/IL12R/TYK2/JAK2 -0.17 0.27 -10000 0 -0.68 62 62
IL17A -0.025 0.13 -10000 0 -0.74 2 2
mast cell activation 0.074 0.2 0.6 34 -0.44 3 37
IFNG -0.04 0.066 0.13 3 -0.11 239 242
T cell differentiation -0.011 0.011 0.03 3 -0.026 142 145
STAT3 (dimer) -0.08 0.18 0.39 3 -0.62 24 27
STAT5A (dimer) -0.08 0.18 0.39 3 -0.61 26 29
STAT4 (dimer) -0.11 0.24 0.39 2 -0.76 44 46
STAT4 -0.035 0.21 -10000 0 -0.86 31 31
T cell activation -0.012 0.007 0.1 1 -10000 0 1
IL27R/JAK2/TYK2 -0.043 0.1 -10000 0 -0.71 1 1
GATA3 -0.62 0.68 -10000 0 -1.3 264 264
IL18 0.005 0.079 -10000 0 -0.68 7 7
positive regulation of mast cell cytokine production -0.08 0.18 0.38 3 -0.61 24 27
IL27/EBI3 -0.12 0.33 -10000 0 -0.83 86 86
IL27RA -0.003 0.063 -10000 0 -0.76 1 1
IL6 -0.087 0.28 -10000 0 -0.81 67 67
STAT5A 0.016 0 -10000 0 -10000 0 0
monocyte differentiation -0.002 0.003 -10000 0 -10000 0 0
IL2 0.001 0.086 -10000 0 -0.59 10 10
IL1B 0.006 0.071 -10000 0 -0.66 6 6
EBI3 -0.12 0.31 -10000 0 -0.88 76 76
TNF 0.004 0.078 -10000 0 -0.62 8 8
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.67 239 239
PDGFRB 0.016 0.004 -9999 0 -10000 0 0
SPHK1 -0.031 0.1 -9999 0 -0.36 45 45
mol:S1P -0.024 0.096 -9999 0 -0.36 16 16
S1P1/S1P/Gi -0.047 0.14 -9999 0 -0.51 14 14
GNAO1 0.01 0.083 -9999 0 -0.84 5 5
PDGFB-D/PDGFRB/PLCgamma1 -0.055 0.087 -9999 0 -0.63 2 2
PLCG1 -0.028 0.13 -9999 0 -0.5 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0.004 -9999 0 -10000 0 0
GNAI2 0.018 0.005 -9999 0 -10000 0 0
GNAI3 0.015 0.006 -9999 0 -10000 0 0
GNAI1 0.011 0.057 -9999 0 -0.75 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.24 0.3 -9999 0 -0.58 239 239
S1P1/S1P -0.21 0.21 -9999 0 -0.42 240 240
negative regulation of cAMP metabolic process -0.046 0.14 -9999 0 -0.5 14 14
MAPK3 -0.038 0.16 -9999 0 -0.57 26 26
calcium-dependent phospholipase C activity 0 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 0.014 0.033 -9999 0 -0.74 1 1
PLCB2 -0.2 0.26 -9999 0 -0.6 78 78
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.17 0.17 -9999 0 -0.51 24 24
receptor internalization -0.19 0.2 -9999 0 -0.39 240 240
PTGS2 -0.048 0.24 -9999 0 -0.99 27 27
Rac1/GTP -0.17 0.17 -9999 0 -0.51 23 23
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFA -0.38 0.44 -9999 0 -0.86 239 239
negative regulation of T cell proliferation -0.046 0.14 -9999 0 -0.5 14 14
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.057 -9999 0 -0.74 3 3
MAPK1 -0.038 0.16 -9999 0 -0.57 26 26
S1P1/S1P/PDGFB-D/PDGFRB -0.17 0.24 -9999 0 -0.63 24 24
ABCC1 0.016 0.002 -9999 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.19 0.35 -10000 0 -1.1 70 70
NFATC2 -0.082 0.24 -10000 0 -0.75 23 23
NFATC3 -0.021 0.064 -10000 0 -10000 0 0
CD40LG -0.24 0.44 -10000 0 -1.2 59 59
ITCH 0.054 0.057 -10000 0 -10000 0 0
CBLB 0.054 0.057 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.55 0.56 -10000 0 -1.2 207 207
JUNB 0.013 0.046 -10000 0 -0.74 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.011 0.057 -10000 0 -10000 0 0
T cell anergy 0.023 0.093 -10000 0 -0.6 1 1
TLE4 -0.032 0.18 -10000 0 -0.79 7 7
Jun/NFAT1-c-4/p21SNFT -0.24 0.28 -10000 0 -1 26 26
AP-1/NFAT1-c-4 -0.3 0.37 -10000 0 -1.2 39 39
IKZF1 -0.13 0.36 -10000 0 -0.89 92 92
T-helper 2 cell differentiation -0.35 0.28 -10000 0 -0.76 88 88
AP-1/NFAT1 -0.095 0.17 -10000 0 -0.7 14 14
CALM1 0.029 0.036 -10000 0 -10000 0 0
EGR2 -0.11 0.29 -10000 0 -1.3 10 10
EGR3 -0.11 0.29 -10000 0 -1.4 9 9
NFAT1/FOXP3 -0.28 0.4 -10000 0 -0.94 118 118
EGR1 0 0.11 -10000 0 -0.74 12 12
JUN 0.006 0.022 -10000 0 -10000 0 0
EGR4 0.004 0.084 -10000 0 -0.86 5 5
mol:Ca2+ 0.011 0.04 -10000 0 -10000 0 0
GBP3 -0.036 0.19 -10000 0 -0.81 11 11
FOSL1 -0.029 0.19 -10000 0 -0.86 27 27
NFAT1-c-4/MAF/IRF4 -0.26 0.36 -10000 0 -0.94 87 87
DGKA -0.036 0.2 -10000 0 -0.97 9 9
CREM 0.015 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.17 0.22 -10000 0 -1.1 9 9
CTLA4 -0.44 0.59 -10000 0 -1 243 243
NFAT1-c-4 (dimer)/EGR1 -0.17 0.24 -10000 0 -1.1 14 14
NFAT1-c-4 (dimer)/EGR4 -0.17 0.23 -10000 0 -1.1 10 10
FOS -0.013 0.12 -10000 0 -0.75 13 13
IFNG -0.5 0.52 -10000 0 -1 241 241
T cell activation -0.05 0.22 -10000 0 -0.86 14 14
MAF 0.016 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 0.063 0.2 0.85 4 -10000 0 4
TNF -0.097 0.28 -10000 0 -1.1 14 14
FASLG -0.33 0.47 -10000 0 -1.1 35 35
TBX21 -0.3 0.44 -10000 0 -0.93 174 174
BATF3 -0.06 0.25 -10000 0 -0.86 46 46
PRKCQ -0.034 0.13 -10000 0 -0.74 16 16
PTPN1 -0.032 0.18 -10000 0 -0.74 9 9
NFAT1-c-4/ICER1 -0.17 0.22 -10000 0 -1.1 8 8
GATA3 -0.36 0.38 -10000 0 -0.74 264 264
T-helper 1 cell differentiation -0.48 0.5 -10000 0 -0.99 241 241
IL2RA -0.38 0.46 -10000 0 -1.1 131 131
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.032 0.18 -10000 0 -0.76 8 8
E2F1 -0.081 0.28 -10000 0 -0.85 64 64
PPARG 0.016 0.001 -10000 0 -10000 0 0
SLC3A2 -0.032 0.18 -10000 0 -0.82 6 6
IRF4 -0.18 0.36 -10000 0 -0.86 118 118
PTGS2 -0.21 0.4 -10000 0 -1.1 35 35
CSF2 -0.21 0.4 -10000 0 -1.1 34 34
JunB/Fra1/NFAT1-c-4 -0.18 0.23 -10000 0 -1 12 12
IL4 -0.37 0.29 -10000 0 -0.8 85 85
IL5 -0.2 0.38 -10000 0 -1 26 26
IL2 -0.051 0.23 -10000 0 -0.88 14 14
IL3 -0.049 0.049 -10000 0 -10000 0 0
RNF128 0.034 0.16 -10000 0 -0.78 19 19
NFATC1 -0.064 0.2 -10000 0 -0.85 4 4
CDK4 0.035 0.18 -10000 0 -10000 0 0
PTPRK -0.033 0.18 -10000 0 -0.81 8 8
IL8 -0.22 0.42 -10000 0 -1.1 42 42
POU2F1 0.016 0.003 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.057 0.17 -9999 0 -0.52 58 58
EFNA5 -0.059 0.23 -9999 0 -0.75 52 52
FYN -0.027 0.16 -9999 0 -0.47 58 58
neuron projection morphogenesis -0.057 0.17 -9999 0 -0.52 58 58
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.057 0.17 -9999 0 -0.53 58 58
EPHA5 -0.008 0.11 -9999 0 -0.86 8 8
Effects of Botulinum toxin

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
STX1A 0.008 0.071 -9999 0 -0.66 6 6
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.02 0.11 -9999 0 -0.66 16 16
STXBP1 0.014 0.033 -9999 0 -0.74 1 1
ACh/CHRNA1 -0.27 0.31 -9999 0 -0.63 229 229
RAB3GAP2/RIMS1/UNC13B -0.017 0.098 -9999 0 -0.57 16 16
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 -0.014 0.15 -9999 0 -0.86 16 16
mol:ACh -0.01 0.053 -9999 0 -0.13 83 83
RAB3GAP2 0.016 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.039 0.099 -9999 0 -0.62 4 4
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.27 0.31 -9999 0 -0.62 229 229
UNC13B 0.016 0 -9999 0 -10000 0 0
CHRNA1 -0.36 0.43 -9999 0 -0.86 229 229
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.082 0.2 -9999 0 -0.53 86 86
SNAP25 -0.04 0.12 -9999 0 -0.33 79 79
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.11 0.28 -9999 0 -0.74 86 86
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.007 0.063 -9999 0 -0.56 7 7
STX1A/SNAP25 fragment 1/VAMP2 -0.039 0.099 -9999 0 -0.62 4 4
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.004 0.042 -9999 0 -0.48 4 4
ARNO/beta Arrestin1-2 -0.019 0.064 -9999 0 -10000 0 0
EGFR 0.001 0.11 -9999 0 -0.85 9 9
EPHA2 0.014 0.033 -9999 0 -0.74 1 1
USP6 0.014 0.038 -9999 0 -0.86 1 1
IQSEC1 0.015 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.51 0.18 -9999 0 -0.56 481 481
ARRB2 -0.017 0.11 -9999 0 -0.39 42 42
mol:GTP -0.011 0.048 -9999 0 -0.23 2 2
ARRB1 0.016 0 -9999 0 -10000 0 0
FBXO8 0.016 0 -9999 0 -10000 0 0
TSHR -0.085 0.28 -9999 0 -0.86 61 61
EGF -0.67 0.23 -9999 0 -0.74 480 480
somatostatin receptor activity 0 0 -9999 0 -0.001 17 17
ARAP2 0.013 0.046 -9999 0 -0.74 2 2
mol:GDP -0.057 0.095 -9999 0 -0.34 24 24
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 11 11
ITGA2B -0.015 0.16 -9999 0 -0.86 19 19
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.034 -9999 0 -0.52 1 1
ADAP1 0.01 0.065 -9999 0 -0.74 4 4
KIF13B 0.016 0 -9999 0 -10000 0 0
HGF/MET -0.032 0.15 -9999 0 -0.66 26 26
PXN 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.088 0.091 -9999 0 -0.34 22 22
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.43 0.16 -9999 0 -0.48 481 481
ADRB2 0.013 0.046 -9999 0 -0.74 2 2
receptor agonist activity 0 0 -9999 0 0 14 14
actin filament binding 0 0 -9999 0 -0.001 19 19
SRC 0.016 0 -9999 0 -10000 0 0
ITGB3 0.007 0.08 -9999 0 -0.74 6 6
GNAQ 0.015 0.001 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 11 11
ARF6/GDP -0.069 0.14 -9999 0 -0.4 6 6
ARF6/GDP/GULP/ACAP1 -0.23 0.26 -9999 0 -0.53 207 207
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.023 0.11 -9999 0 -0.55 18 18
ACAP1 -0.32 0.43 -9999 0 -0.86 204 204
ACAP2 0.016 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.046 0.16 -9999 0 -0.59 42 42
EFNA1 0.014 0.038 -9999 0 -0.86 1 1
HGF -0.02 0.17 -9999 0 -0.8 23 23
CYTH3 0.015 0 -9999 0 -10000 0 0
CYTH2 0.01 0.001 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.74 1 1
fibronectin binding 0 0 -9999 0 -0.001 13 13
endosomal lumen acidification 0 0 -9999 0 -0.001 22 22
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.011 0.14 -9999 0 -0.75 19 19
GNAQ/ARNO 0.009 0.01 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 2 2
MET 0.007 0.085 -9999 0 -0.86 5 5
GNA14 0.004 0.092 -9999 0 -0.74 8 8
GNA15 -0.009 0.14 -9999 0 -0.86 15 15
GIT1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 12 12
GNA11 0.011 0.057 -9999 0 -0.74 3 3
LHCGR -0.061 0.23 -9999 0 -0.86 41 41
AGTR1 -0.026 0.17 -9999 0 -0.74 29 29
desensitization of G-protein coupled receptor protein signaling pathway -0.046 0.16 -9999 0 -0.59 42 42
IPCEF1/ARNO -0.34 0.12 -9999 0 -0.81 8 8
alphaIIb/beta3 Integrin -0.03 0.14 -9999 0 -0.66 24 24
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.013 0.047 -9999 0 -10000 0 0
NFATC2 -0.019 0.073 -9999 0 -0.59 5 5
NFATC3 -0.013 0.047 -9999 0 -10000 0 0
CD40LG -0.3 0.42 -9999 0 -0.94 103 103
PTGS2 -0.29 0.39 -9999 0 -0.86 96 96
JUNB 0.013 0.046 -9999 0 -0.74 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.02 0.018 -9999 0 -10000 0 0
CaM/Ca2+ -0.02 0.018 -9999 0 -10000 0 0
CALM1 0.006 0.013 -9999 0 -10000 0 0
JUN 0.006 0.013 -9999 0 -10000 0 0
mol:Ca2+ -0.02 0.019 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 -0.002 0.003 -9999 0 -10000 0 0
FOSL1 -0.029 0.19 -9999 0 -0.86 27 27
CREM 0.015 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.19 0.2 -9999 0 -0.74 37 37
FOS -0.013 0.12 -9999 0 -0.76 13 13
IFNG -0.43 0.52 -9999 0 -0.98 227 227
AP-1/NFAT1-c-4 -0.41 0.41 -9999 0 -1.1 94 94
FASLG -0.46 0.52 -9999 0 -0.98 229 229
NFAT1-c-4/ICER1 -0.081 0.086 -9999 0 -0.6 4 4
IL2RA -0.34 0.44 -9999 0 -1 107 107
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.28 0.38 -9999 0 -0.86 94 94
JunB/Fra1/NFAT1-c-4 -0.096 0.13 -9999 0 -0.68 9 9
IL4 -0.28 0.37 -9999 0 -0.83 91 91
IL2 -0.012 0.11 -9999 0 -0.77 10 10
IL3 -0.028 0.026 -9999 0 -10000 0 0
FKBP1A 0.016 0 -9999 0 -10000 0 0
BATF3 -0.06 0.25 -9999 0 -0.86 46 46
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.016 0.003 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.001 0.024 -9999 0 -0.56 1 1
Necdin/E2F1 -0.083 0.22 -9999 0 -0.68 65 65
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.078 0.2 -9999 0 -0.98 8 8
NGF (dimer)/p75(NTR)/BEX1 -0.26 0.3 -9999 0 -0.55 253 253
NT-4/5 (dimer)/p75(NTR) -0.053 0.18 -9999 0 -0.67 42 42
IKBKB 0.016 0 -9999 0 -10000 0 0
AKT1 -0.032 0.22 -9999 0 -0.95 9 9
IKBKG 0.016 0 -9999 0 -10000 0 0
BDNF -0.1 0.3 -9999 0 -0.86 71 71
MGDIs/NGR/p75(NTR)/LINGO1 -0.071 0.2 -9999 0 -0.61 62 62
FURIN 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.12 0.25 -9999 0 -0.61 100 100
LINGO1 -0.022 0.18 -9999 0 -0.86 23 23
Sortilin/TRAF6/NRIF -0.001 0.014 -9999 0 -10000 0 0
proBDNF (dimer) -0.1 0.3 -9999 0 -0.86 71 71
NTRK1 -0.044 0.2 -9999 0 -0.75 41 41
RTN4R 0.004 0.098 -9999 0 -0.84 7 7
neuron apoptosis -0.065 0.23 -9999 0 -0.67 31 31
IRAK1 0.016 0 -9999 0 -10000 0 0
SHC1 -0.059 0.24 -9999 0 -0.62 78 78
ARHGDIA 0.014 0.033 -9999 0 -0.74 1 1
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.084 0.21 -9999 0 -0.57 76 76
MAGEH1 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.086 0.21 -9999 0 -0.58 77 77
Mammalian IAPs/DIABLO -0.078 0.19 -9999 0 -0.52 80 80
proNGF (dimer) -0.065 0.25 -9999 0 -0.86 49 49
MAGED1 0.014 0.038 -9999 0 -0.86 1 1
APP 0.014 0.033 -9999 0 -0.74 1 1
NT-4/5 (dimer) -0.004 0.092 -9999 0 -0.86 6 6
ZNF274 0.016 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.079 0.2 -9999 0 -0.54 76 76
NGF -0.065 0.25 -9999 0 -0.86 49 49
cell cycle arrest -0.013 0.25 -9999 0 -0.59 59 59
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.044 0.11 -9999 0 -0.57 8 8
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.046 0.16 -9999 0 -0.58 42 42
NCSTN 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.09 0.23 -9999 0 -0.62 77 77
PSENEN 0.016 0 -9999 0 -10000 0 0
mol:ceramide -0.044 0.22 -9999 0 -0.57 76 76
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.034 0.085 -9999 0 -0.44 8 8
p75(NTR)/beta APP -0.046 0.17 -9999 0 -0.66 37 37
BEX1 -0.26 0.37 -9999 0 -0.74 195 195
mol:GDP -0.071 0.24 -9999 0 -0.64 77 77
NGF (dimer) -0.34 0.3 -9999 0 -0.84 90 90
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.065 0.18 -9999 0 -0.56 62 62
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
RAC1/GTP -0.08 0.2 -9999 0 -0.56 76 76
MYD88 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.091 0.23 -9999 0 -0.63 77 77
RHOB 0.016 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.08 0.22 -9999 0 -0.66 64 64
NT3 (dimer) 0.005 0.09 -9999 0 -0.78 7 7
TP53 -0.041 0.22 -9999 0 -0.91 8 8
PRDM4 -0.044 0.22 -9999 0 -0.57 76 76
BDNF (dimer) -0.41 0.36 -9999 0 -0.87 143 143
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
SORT1 0.014 0.033 -9999 0 -0.74 1 1
activation of caspase activity -0.077 0.19 -9999 0 -0.96 8 8
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.084 0.21 -9999 0 -0.57 76 76
RHOC 0.016 0 -9999 0 -10000 0 0
XIAP 0.016 0 -9999 0 -10000 0 0
MAPK10 -0.023 0.21 -9999 0 -0.63 23 23
DIABLO 0.016 0 -9999 0 -10000 0 0
SMPD2 -0.044 0.22 -9999 0 -0.57 76 76
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.092 0.23 -9999 0 -0.63 78 78
PSEN1 0.016 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.052 0.18 -9999 0 -0.66 42 42
MAPK8 -0.021 0.2 -9999 0 -0.63 22 22
MAPK9 -0.02 0.2 -9999 0 -0.63 22 22
APAF1 0.016 0 -9999 0 -10000 0 0
NTF3 0.005 0.09 -9999 0 -0.78 7 7
NTF4 -0.004 0.092 -9999 0 -0.86 6 6
NDN 0.011 0.057 -9999 0 -0.74 3 3
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.071 0.18 -9999 0 -0.91 8 8
p75 CTF/Sortilin/TRAF6/NRIF -0.001 0.018 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.09 0.23 -9999 0 -0.62 77 77
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.098 0.21 -9999 0 -0.52 98 98
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.1 0.23 -9999 0 -0.56 98 98
PRKACB 0.016 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.088 0.22 -9999 0 -0.66 71 71
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.12 0.31 -9999 0 -0.86 80 80
BIRC2 0.016 0 -9999 0 -10000 0 0
neuron projection morphogenesis 0.008 0.24 -9999 0 -0.88 9 9
BAD -0.01 0.2 -9999 0 -0.59 22 22
RIPK2 0.014 0.038 -9999 0 -0.86 1 1
NGFR -0.044 0.22 -9999 0 -0.86 36 36
CYCS -0.033 0.22 -9999 0 -0.54 77 77
ADAM17 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.084 0.21 -9999 0 -0.57 77 77
BCL2L11 -0.009 0.2 -9999 0 -0.59 22 22
BDNF (dimer)/p75(NTR) -0.13 0.28 -9999 0 -0.7 100 100
PI3K -0.084 0.21 -9999 0 -0.58 76 76
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.084 0.21 -9999 0 -0.57 76 76
NDNL2 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.1 0.26 -9999 0 -0.72 77 77
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.085 0.21 -9999 0 -0.57 77 77
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.057 -9999 0 -0.74 3 3
PLG -0.38 0.38 -9999 0 -0.74 274 274
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.12 0.23 -9999 0 -0.67 44 44
SQSTM1 0.016 0 -9999 0 -10000 0 0
NGFRAP1 0.016 0 -9999 0 -10000 0 0
CASP3 -0.004 0.18 -9999 0 -0.53 22 22
E2F1 -0.09 0.28 -9999 0 -0.86 64 64
CASP9 0.016 0 -9999 0 -10000 0 0
IKK complex -0.069 0.14 -9999 0 -0.59 13 13
NGF (dimer)/TRKA -0.1 0.24 -9999 0 -0.63 88 88
MMP7 -0.13 0.3 -9999 0 -0.75 99 99
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.078 0.2 -9999 0 -0.98 8 8
MMP3 -0.069 0.25 -9999 0 -0.86 47 47
APAF-1/Caspase 9 -0.11 0.17 -9999 0 -0.69 11 11
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.12 0.24 -10000 0 -0.77 35 35
UGCG -0.024 0.055 -10000 0 -0.77 2 2
AKT1/mTOR/p70S6K/Hsp90/TERT -0.078 0.19 -10000 0 -0.48 57 57
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide -0.009 0.064 -10000 0 -0.76 2 2
mol:DAG -0.004 0.006 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.11 0.16 -10000 0 -0.56 36 36
FRAP1 -0.082 0.23 -10000 0 -0.61 51 51
FOXO3 -0.073 0.22 -10000 0 -0.66 33 33
AKT1 -0.09 0.24 -10000 0 -0.64 52 52
GAB2 0.016 0.003 -10000 0 -10000 0 0
SMPD1 -0.021 0.03 -10000 0 -10000 0 0
SGMS1 -0.021 0.03 -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 0.026 0.032 -10000 0 -0.48 2 2
CALM1 0.016 0 -10000 0 -10000 0 0
cell proliferation -0.022 0.1 -10000 0 -0.49 2 2
EIF3A 0.016 0 -10000 0 -10000 0 0
PI3K -0.002 0.034 -10000 0 -0.55 2 2
RPS6KB1 -0.026 0.087 -10000 0 -10000 0 0
mol:sphingomyelin -0.004 0.006 -10000 0 -10000 0 0
natural killer cell activation 0 0.002 -10000 0 -10000 0 0
JAK3 -0.16 0.35 -10000 0 -0.86 107 107
PIK3R1 0.017 0.033 -10000 0 -0.74 1 1
JAK1 0.018 0.004 -10000 0 -10000 0 0
NFKB1 0.014 0.033 -10000 0 -0.74 1 1
MYC -0.075 0.23 -10000 0 -0.66 37 37
MYB -0.18 0.34 -10000 0 -0.74 139 139
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.12 0.26 -10000 0 -0.68 63 63
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.034 0.067 -10000 0 -0.47 2 2
mol:PI-3-4-5-P3 -0.11 0.25 -10000 0 -0.65 63 63
Rac1/GDP 0.02 0.033 -10000 0 -0.43 2 2
T cell proliferation -0.093 0.23 -10000 0 -0.59 65 65
SHC1 0.014 0.038 -10000 0 -0.86 1 1
RAC1 0.015 0.002 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.008 0.026 -10000 0 -0.05 139 139
PRKCZ -0.099 0.25 -10000 0 -0.62 65 65
NF kappa B1 p50/RelA -0.1 0.16 -10000 0 -0.56 34 34
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.14 0.26 -10000 0 -0.58 103 103
HSP90AA1 0.016 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
IL2RA -0.16 0.35 -10000 0 -0.86 105 105
IL2RB -0.43 0.44 -10000 0 -0.86 274 274
TERT -0.11 0.3 -10000 0 -0.86 75 75
E2F1 -0.099 0.2 -10000 0 -0.37 177 177
SOS1 0.016 0.003 -10000 0 -10000 0 0
RPS6 0.012 0.054 -10000 0 -0.86 2 2
mol:cAMP 0.003 0.013 0.025 139 -10000 0 139
PTPN11 0.016 0.003 -10000 0 -10000 0 0
IL2RG -0.038 0.21 -10000 0 -0.86 34 34
actin cytoskeleton organization -0.093 0.23 -10000 0 -0.59 65 65
GRB2 0.016 0.003 -10000 0 -10000 0 0
IL2 -0.004 0.12 -10000 0 -0.86 10 10
PIK3CA 0.017 0.033 -10000 0 -0.74 1 1
Rac1/GTP 0.032 0.034 -10000 0 -0.4 2 2
LCK -0.017 0.17 -10000 0 -0.85 22 22
BCL2 -0.049 0.18 -10000 0 -0.52 28 28
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.026 0.022 -9999 0 -0.48 1 1
ADCY5 0.006 0.1 -9999 0 -0.48 22 22
ADCY6 0.026 0.041 -9999 0 -0.92 1 1
ADCY7 0.009 0.1 -9999 0 -0.58 16 16
ADCY1 0.013 0.084 -9999 0 -0.5 14 14
ADCY2 -0.13 0.27 -9999 0 -0.58 141 141
ADCY3 0.026 0.022 -9999 0 -0.48 1 1
ADCY8 -0.16 0.28 -9999 0 -0.59 165 165
PRKCE 0.014 0.025 -9999 0 -0.57 1 1
ADCY9 0.026 0.022 -9999 0 -0.48 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.092 0.17 -9999 0 -0.5 54 54
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0 -9999 0 -10000 0 0
ELF1 -0.045 0.14 -9999 0 -0.72 1 1
CCNA2 -0.15 0.34 -9999 0 -0.86 102 102
PIK3CA 0.015 0.033 -9999 0 -0.74 1 1
JAK3 -0.16 0.35 -9999 0 -0.86 107 107
PIK3R1 0.015 0.033 -9999 0 -0.74 1 1
JAK1 0.017 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.1 0.25 -9999 0 -0.66 59 59
SHC1 0.015 0.038 -9999 0 -0.86 1 1
SP1 0.025 0.022 -9999 0 -10000 0 0
IL2RA -0.12 0.32 -9999 0 -0.77 106 106
IL2RB -0.44 0.44 -9999 0 -0.86 274 274
SOS1 0.017 0 -9999 0 -10000 0 0
IL2RG -0.039 0.21 -9999 0 -0.86 34 34
G1/S transition of mitotic cell cycle -0.044 0.2 -9999 0 -0.55 13 13
PTPN11 0.017 0 -9999 0 -10000 0 0
CCND2 0.038 0.05 -9999 0 -0.78 2 2
LCK -0.019 0.17 -9999 0 -0.85 22 22
GRB2 0.017 0 -9999 0 -10000 0 0
IL2 -0.006 0.12 -9999 0 -0.86 10 10
CDK6 0.014 0.033 -9999 0 -0.74 1 1
CCND3 -0.074 0.21 -9999 0 -0.72 17 17
Coregulation of Androgen receptor activity

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
NRIP1 0.013 0.035 -9999 0 -0.78 1 1
SVIL 0.015 0.007 -9999 0 -10000 0 0
ZNF318 0.016 0.023 -9999 0 -10000 0 0
JMJD2C -0.001 0.022 -9999 0 -0.11 19 19
T-DHT/AR/Ubc9 -0.078 0.11 -9999 0 -0.54 26 26
CARM1 0.015 0.003 -9999 0 -10000 0 0
PRDX1 0.016 0.001 -9999 0 -10000 0 0
PELP1 0.016 0.003 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
AKT1 0.017 0.006 -9999 0 -10000 0 0
PTK2B 0.015 0.003 -9999 0 -10000 0 0
MED1 0.013 0.009 -9999 0 -10000 0 0
MAK 0.014 0.044 -9999 0 -0.86 1 1
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.009 0.068 -9999 0 -0.77 4 4
GSN 0.015 0.008 -9999 0 -10000 0 0
NCOA2 0 0.11 -9999 0 -0.74 11 11
NCOA6 0.016 0.003 -9999 0 -10000 0 0
DNA-PK 0.005 0.026 -9999 0 -10000 0 0
NCOA4 0.015 0.002 -9999 0 -10000 0 0
PIAS3 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.028 0.036 -9999 0 -0.61 1 1
XRCC5 0.016 0.005 -9999 0 -10000 0 0
UBE3A 0.014 0.013 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.094 0.15 -9999 0 -0.59 39 39
FHL2 -0.04 0.11 -9999 0 -1.1 5 5
RANBP9 0.016 0.003 -9999 0 -10000 0 0
JMJD1A -0.12 0.056 -9999 0 -0.14 460 460
CDK6 0.014 0.033 -9999 0 -0.74 1 1
TGFB1I1 0.013 0.039 -9999 0 -0.86 1 1
T-DHT/AR/CyclinD1 -0.1 0.15 -9999 0 -0.59 46 46
XRCC6 0.016 0.005 -9999 0 -10000 0 0
T-DHT/AR -0.15 0.12 -9999 0 -0.58 26 26
CTDSP1 0.015 0.003 -9999 0 -10000 0 0
CTDSP2 0.015 0.017 -9999 0 -10000 0 0
BRCA1 0.015 0.007 -9999 0 -10000 0 0
TCF4 0.014 0.013 -9999 0 -10000 0 0
CDKN2A -0.83 0.17 -9999 0 -0.86 513 513
SRF 0.026 0.012 -9999 0 -10000 0 0
NKX3-1 -0.19 0.07 -9999 0 -10000 0 0
KLK3 0.024 0.15 -9999 0 -0.7 21 21
TMF1 0.015 0.003 -9999 0 -10000 0 0
HNRNPA1 0.014 0.013 -9999 0 -10000 0 0
AOF2 -0.001 0.01 -9999 0 -10000 0 0
APPL1 0.033 0.013 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.077 0.11 -9999 0 -0.54 26 26
AR -0.07 0.16 -9999 0 -0.78 26 26
UBA3 0.015 0.003 -9999 0 -10000 0 0
PATZ1 0.014 0.013 -9999 0 -10000 0 0
PAWR 0.014 0.033 -9999 0 -0.74 1 1
PRKDC 0.016 0.005 -9999 0 -10000 0 0
PA2G4 0.014 0.012 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.069 0.1 -9999 0 -0.5 26 26
RPS6KA3 0.013 0.035 -9999 0 -0.78 1 1
T-DHT/AR/ARA70 -0.078 0.11 -9999 0 -0.54 26 26
LATS2 0.014 0.011 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.069 0.1 -9999 0 -0.49 26 26
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 -0.004 0.12 -9999 0 -0.74 14 14
KLK2 -0.085 0.14 -9999 0 -0.8 19 19
CASP8 0.016 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.069 0.13 -9999 0 -0.56 32 32
TMPRSS2 -0.92 0.35 -9999 0 -1.1 460 460
CCND1 -0.018 0.17 -9999 0 -0.86 20 20
PIAS1 0.014 0.013 -9999 0 -10000 0 0
mol:T-DHT -0.062 0.027 -9999 0 -0.072 449 449
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.013 0.019 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.078 0.11 -9999 0 -0.56 26 26
CMTM2 -0.004 0.13 -9999 0 -0.86 12 12
SNURF -0.009 0.13 -9999 0 -0.74 17 17
ZMIZ1 -0.031 0.022 -9999 0 -10000 0 0
CCND3 0.016 0.001 -9999 0 -10000 0 0
TGIF1 0.014 0.013 -9999 0 -10000 0 0
FKBP4 0.016 0.003 -9999 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.001 0.056 0.29 18 -10000 0 18
BUB1B -0.022 0.12 -10000 0 -0.5 26 26
PLK1 -0.011 0.058 -10000 0 -0.2 10 10
PLK1S1 0.001 0.031 -10000 0 -10000 0 0
KIF2A -0.003 0.072 -10000 0 -0.56 4 4
regulation of mitotic centrosome separation -0.012 0.058 -10000 0 -0.2 10 10
GOLGA2 0.016 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.18 0.33 -10000 0 -0.72 129 129
WEE1 -0.001 0.055 -10000 0 -0.28 7 7
cytokinesis -0.2 0.27 -10000 0 -0.5 238 238
PP2A-alpha B56 -0.14 0.16 -10000 0 -10000 0 0
AURKA -0.002 0.044 -10000 0 -0.3 6 6
PICH/PLK1 -0.044 0.16 -10000 0 -0.82 19 19
CENPE -0.062 0.21 -10000 0 -0.62 62 62
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.003 0.071 -10000 0 -0.55 4 4
PPP2CA 0.016 0 -10000 0 -10000 0 0
FZR1 0.014 0.033 -10000 0 -0.74 1 1
TPX2 -0.049 0.12 -10000 0 -0.25 127 127
PAK1 0.016 0.002 -10000 0 -10000 0 0
SPC24 -0.075 0.27 -10000 0 -0.86 55 55
FBXW11 0.016 0 -10000 0 -10000 0 0
CLSPN -0.025 0.096 -10000 0 -0.28 60 60
GORASP1 0.016 0 -10000 0 -10000 0 0
metaphase -0.004 0.009 -10000 0 -0.02 129 129
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.006 0.031 -10000 0 -0.098 10 10
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.014 6 6
STAG2 0.016 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.013 -10000 0 -10000 0 0
spindle elongation -0.012 0.058 -10000 0 -0.2 10 10
ODF2 0.016 0.002 -10000 0 -10000 0 0
BUB1 -0.16 0.19 -10000 0 -0.45 10 10
TPT1 0.001 0.031 -10000 0 -10000 0 0
CDC25C -0.13 0.17 -10000 0 -0.31 242 242
CDC25B 0.007 0.086 -10000 0 -0.88 5 5
SGOL1 0.001 0.057 -10000 0 -0.29 18 18
RHOA 0.016 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.023 0.1 -10000 0 -0.74 9 9
CDC14B 0.016 0.002 -10000 0 -10000 0 0
CDC20 -0.055 0.24 -10000 0 -0.86 43 43
PLK1/PBIP1 -0.041 0.12 -10000 0 -0.59 19 19
mitosis -0.001 0.004 0.03 6 -10000 0 6
FBXO5 0.003 0.044 -10000 0 -0.21 2 2
CDC2 -0.001 0.004 -10000 0 -0.023 9 9
NDC80 -0.17 0.36 -10000 0 -0.86 112 112
metaphase plate congression -0.004 0.041 -10000 0 -10000 0 0
ERCC6L -0.036 0.16 -10000 0 -0.81 19 19
NLP/gamma Tubulin -0.003 0.034 -10000 0 -0.12 5 5
microtubule cytoskeleton organization 0.001 0.031 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0.016 0.002 -10000 0 -10000 0 0
interphase 0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.25 0.29 -10000 0 -0.56 238 238
GRASP65/GM130/RAB1/GTP/PLK1 -0.013 0.027 -10000 0 -10000 0 0
RAB1A 0.016 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.007 0.038 -10000 0 -10000 0 0
mitotic prometaphase -0.003 0.005 -10000 0 -0.012 121 121
proteasomal ubiquitin-dependent protein catabolic process -0.012 0.042 -10000 0 -10000 0 0
microtubule-based process -0.24 0.3 -10000 0 -0.58 238 238
Golgi organization -0.012 0.058 -10000 0 -0.2 10 10
Cohesin/SA2 -0.024 0.044 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A -0.38 0.44 -10000 0 -0.86 238 238
APC/C/CDC20 -0.044 0.18 -10000 0 -0.64 43 43
PPP2R1A 0.016 0 -10000 0 -10000 0 0
chromosome segregation -0.04 0.11 -10000 0 -0.58 19 19
PRC1 0.006 0.093 -10000 0 -0.86 6 6
ECT2 0.001 0.053 -10000 0 -10000 0 0
C13orf34 0.004 0.042 -10000 0 -10000 0 0
NUDC -0.004 0.041 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.022 0.12 -10000 0 -0.5 26 26
spindle assembly -0.006 0.047 -10000 0 -0.16 8 8
spindle stabilization 0.001 0.031 -10000 0 -10000 0 0
APC/C/HCDH1 -0.001 0.021 -10000 0 -0.49 1 1
MKLP2/PLK1 -0.25 0.31 -10000 0 -0.59 238 238
CCNB1 0.002 0.11 -10000 0 -0.87 8 8
PPP1CB 0.016 0.002 -10000 0 -10000 0 0
BTRC 0.016 0 -10000 0 -10000 0 0
ROCK2 0.004 0.058 -10000 0 -0.48 4 4
TUBG1 0.001 0.031 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.025 0.097 -10000 0 -0.71 9 9
MLF1IP -0.012 0.13 -10000 0 -0.69 19 19
INCENP 0.009 0.008 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.3 0.33 -9999 0 -0.67 239 239
alphaV beta3 Integrin -0.01 0.074 -9999 0 -0.53 10 10
PTK2 -0.15 0.23 -9999 0 -0.55 48 48
IGF1R 0.016 0 -9999 0 -10000 0 0
PI4KB 0.016 0 -9999 0 -10000 0 0
MFGE8 0.014 0.038 -9999 0 -0.86 1 1
SRC 0.016 0 -9999 0 -10000 0 0
CDKN1B -0.084 0.19 -9999 0 -0.52 82 82
VEGFA -0.38 0.44 -9999 0 -0.86 239 239
ILK -0.084 0.19 -9999 0 -0.52 82 82
ROCK1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.077 0.17 -9999 0 -0.49 74 74
PTK2B -0.19 0.27 -9999 0 -0.48 239 239
alphaV/beta3 Integrin/JAM-A -0.07 0.15 -9999 0 -0.52 10 10
CBL 0.014 0.033 -9999 0 -0.74 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.22 0.24 -9999 0 -0.47 254 254
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.009 0.066 -9999 0 -0.52 6 6
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.13 0.14 -9999 0 -0.47 46 46
alphaV/beta3 Integrin/Syndecan-1 -0.011 0.07 -9999 0 -0.47 12 12
PI4KA 0.016 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.047 0.14 -9999 0 -0.8 4 4
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
alphaV/beta3 Integrin/Osteopontin -0.009 0.064 -9999 0 -0.47 10 10
RPS6KB1 -0.043 0.13 -9999 0 -0.73 4 4
TLN1 0.016 0 -9999 0 -10000 0 0
MAPK3 -0.044 0.1 -9999 0 -0.69 5 5
GPR124 0.011 0.066 -9999 0 -0.86 3 3
MAPK1 -0.044 0.1 -9999 0 -0.69 5 5
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
alphaV/beta3 Integrin/Tumstatin -0.057 0.16 -9999 0 -0.49 63 63
cell adhesion -0.17 0.18 -9999 0 -0.83 1 1
ANGPTL3 -0.34 0.38 -9999 0 -0.74 248 248
VEGFR2 homodimer/VEGFA homodimer/Src -0.26 0.29 -9999 0 -0.58 239 239
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.016 0 -9999 0 -10000 0 0
ITGB3 0.007 0.08 -9999 0 -0.74 6 6
IGF1 0.006 0.093 -9999 0 -0.86 6 6
RAC1 0.016 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.009 0.065 -9999 0 -0.5 9 9
apoptosis 0.016 0 -9999 0 -10000 0 0
CD47 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.005 0.05 -9999 0 -0.47 6 6
VCL 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.019 0.099 -9999 0 -0.52 19 19
CSF1 0.014 0.033 -9999 0 -0.74 1 1
PIK3C2A -0.086 0.2 -9999 0 -0.53 83 83
PI4 Kinase/Pyk2 -0.23 0.24 -9999 0 -0.75 47 47
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.24 0.26 -9999 0 -0.52 239 239
FAK1/Vinculin -0.11 0.18 -9999 0 -0.56 3 3
alphaV beta3/Integrin/ppsTEM5 -0.009 0.066 -9999 0 -0.51 9 9
RHOA 0.016 0 -9999 0 -10000 0 0
VTN -0.1 0.28 -9999 0 -0.75 82 82
BCAR1 0.014 0.033 -9999 0 -0.74 1 1
FGF2 0.008 0.075 -9999 0 -0.77 5 5
F11R 0.025 0.059 -9999 0 -0.58 5 5
alphaV/beta3 Integrin/Lactadherin -0.006 0.056 -9999 0 -0.49 7 7
alphaV/beta3 Integrin/TGFBR2 -0.005 0.05 -9999 0 -0.47 6 6
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.002 0.041 -9999 0 -0.85 1 1
HSP90AA1 0.016 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.005 0.046 -9999 0 -0.43 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.049 0.23 -9999 0 -0.86 39 39
alphaV/beta3 Integrin/Pyk2 -0.22 0.24 -9999 0 -0.88 1 1
SDC1 0.007 0.08 -9999 0 -0.74 6 6
VAV3 0.04 0.082 -9999 0 -0.79 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.065 -9999 0 -0.74 4 4
FAK1/Paxillin -0.11 0.18 -9999 0 -0.56 3 3
cell migration -0.091 0.17 -9999 0 -0.52 2 2
ITGAV 0.016 0 -9999 0 -10000 0 0
PI3K -0.062 0.14 -9999 0 -1.1 1 1
SPP1 0.01 0.065 -9999 0 -0.74 4 4
KDR 0.014 0.033 -9999 0 -0.74 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.016 0 -9999 0 -10000 0 0
COL4A3 -0.068 0.24 -9999 0 -0.74 59 59
angiogenesis 0.002 0.15 -9999 0 -0.8 3 3
Rac1/GTP -0.011 0.066 -9999 0 -0.72 1 1
EDIL3 -0.005 0.13 -9999 0 -0.78 14 14
cell proliferation -0.005 0.05 -9999 0 -0.47 6 6
BCR signaling 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
JUN -0.054 0.16 -10000 0 -0.42 34 34
IKBKB -0.023 0.1 -10000 0 -10000 0 0
AKT1 -0.023 0.12 -10000 0 -0.31 9 9
IKBKG -0.022 0.11 -10000 0 -0.3 3 3
CALM1 -0.042 0.1 -10000 0 -0.5 3 3
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
MAP3K1 -0.11 0.25 -10000 0 -0.63 73 73
MAP3K7 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.054 0.11 -10000 0 -0.5 4 4
DOK1 0.016 0 -10000 0 -10000 0 0
AP-1 -0.011 0.09 -10000 0 -10000 0 0
LYN 0.016 0 -10000 0 -10000 0 0
BLNK 0.014 0.033 -10000 0 -0.74 1 1
SHC1 0.014 0.038 -10000 0 -0.86 1 1
BCR complex -0.17 0.29 -10000 0 -0.68 131 131
CD22 -0.15 0.23 -10000 0 -0.67 51 51
CAMK2G -0.029 0.098 -10000 0 -0.49 2 2
CSNK2A1 0.016 0 -10000 0 -10000 0 0
INPP5D 0.009 0.076 -10000 0 -0.86 4 4
SHC/GRB2/SOS1 -0.1 0.19 -10000 0 -0.85 4 4
GO:0007205 -0.055 0.11 -10000 0 -0.5 4 4
SYK 0.013 0.046 -10000 0 -0.74 2 2
ELK1 -0.042 0.1 -10000 0 -0.51 3 3
NFATC1 -0.07 0.2 -10000 0 -0.51 58 58
B-cell antigen/BCR complex -0.17 0.29 -10000 0 -0.68 131 131
PAG1/CSK -0.002 0.041 -10000 0 -0.66 2 2
NFKBIB 0.005 0.039 -10000 0 -0.13 1 1
HRAS -0.037 0.12 -10000 0 -0.49 4 4
NFKBIA 0.005 0.038 -10000 0 -0.14 1 1
NF-kappa-B/RelA/I kappa B beta 0.013 0.032 -10000 0 -0.18 1 1
RasGAP/Csk -0.21 0.32 -10000 0 -0.99 47 47
mol:GDP -0.05 0.1 0.29 1 -0.47 4 5
PTEN 0.016 0 -10000 0 -10000 0 0
CD79B 0.011 0.066 -10000 0 -0.86 3 3
NF-kappa-B/RelA/I kappa B alpha 0.014 0.032 -10000 0 -0.19 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.078 0.22 -10000 0 -0.57 65 65
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
mol:IP3 -0.066 0.1 -10000 0 -0.51 4 4
CSK 0.016 0 -10000 0 -10000 0 0
FOS -0.04 0.11 -10000 0 -0.48 6 6
CHUK -0.022 0.11 -10000 0 -10000 0 0
IBTK 0.016 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.12 0.2 -10000 0 -0.56 63 63
PTPN6 -0.14 0.21 -10000 0 -0.68 39 39
RELA 0.016 0 -10000 0 -10000 0 0
BCL2A1 -0.01 0.068 -10000 0 -0.14 108 108
VAV2 -0.17 0.28 -10000 0 -0.8 75 75
ubiquitin-dependent protein catabolic process 0.011 0.037 -10000 0 -0.12 1 1
BTK -0.086 0.17 0.46 1 -0.42 107 108
CD19 -0.19 0.32 -10000 0 -0.89 79 79
MAP4K1 -0.34 0.43 -10000 0 -0.86 218 218
CD72 -0.19 0.37 -10000 0 -0.86 124 124
PAG1 0.012 0.054 -10000 0 -0.86 2 2
MAPK14 -0.084 0.21 -10000 0 -0.53 64 64
SH3BP5 0.014 0.033 -10000 0 -0.74 1 1
PIK3AP1 -0.037 0.11 -10000 0 -0.54 6 6
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.11 0.23 -10000 0 -0.57 79 79
RAF1 -0.025 0.11 -10000 0 -0.53 2 2
RasGAP/p62DOK/SHIP -0.2 0.31 -10000 0 -0.97 48 48
CD79A -0.2 0.38 -10000 0 -0.86 131 131
re-entry into mitotic cell cycle -0.012 0.089 -10000 0 -10000 0 0
RASA1 0.014 0.033 -10000 0 -0.74 1 1
MAPK3 -0.001 0.099 -10000 0 -10000 0 0
MAPK1 -0.001 0.099 -10000 0 -0.42 2 2
CD72/SHP1 -0.23 0.33 -10000 0 -0.82 101 101
NFKB1 0.014 0.033 -10000 0 -0.74 1 1
MAPK8 -0.085 0.21 -10000 0 -0.52 69 69
actin cytoskeleton organization -0.095 0.26 -10000 0 -0.66 69 69
NF-kappa-B/RelA 0.035 0.059 -10000 0 -10000 0 0
Calcineurin -0.042 0.07 -10000 0 -10000 0 0
PI3K -0.14 0.22 -10000 0 -0.6 71 71
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.061 0.1 -10000 0 -0.55 4 4
SOS1 0.016 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.27 0.32 -10000 0 -0.74 137 137
DAPP1 -0.11 0.18 -10000 0 -0.61 36 36
cytokine secretion -0.064 0.19 -10000 0 -0.47 58 58
mol:DAG -0.066 0.1 -10000 0 -0.51 4 4
PLCG2 0.003 0.1 -10000 0 -0.82 8 8
MAP2K1 -0.013 0.11 -10000 0 -0.48 2 2
B-cell antigen/BCR complex/FcgammaRIIB -0.24 0.37 -10000 0 -0.72 180 180
mol:PI-3-4-5-P3 -0.097 0.15 -10000 0 -0.4 67 67
ETS1 -0.017 0.092 -10000 0 -10000 0 0
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.12 0.22 -10000 0 -0.98 3 3
B-cell antigen/BCR complex/LYN -0.14 0.21 -10000 0 -0.59 63 63
MALT1 0.016 0 -10000 0 -10000 0 0
TRAF6 0.016 0 -10000 0 -10000 0 0
RAC1 -0.1 0.28 -10000 0 -0.72 69 69
B-cell antigen/BCR complex/LYN/SYK -0.16 0.25 -10000 0 -0.67 64 64
CARD11 -0.14 0.26 -10000 0 -0.62 110 110
FCGR2B -0.14 0.34 -10000 0 -0.86 96 96
PPP3CA 0.016 0 -10000 0 -10000 0 0
BCL10 0.016 0 -10000 0 -10000 0 0
IKK complex 0.005 0.047 -10000 0 -10000 0 0
PTPRC -0.077 0.27 -10000 0 -0.86 56 56
PDPK1 -0.06 0.1 -10000 0 -0.31 9 9
PPP3CB 0.016 0 -10000 0 -10000 0 0
PPP3CC 0.016 0 -10000 0 -10000 0 0
POU2F2 0.001 0.057 -10000 0 -0.14 66 66
Glucocorticoid receptor regulatory network

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
PCK2 0.019 0.11 -10000 0 -1.4 1 1
SMARCC2 0.018 0 -10000 0 -10000 0 0
SMARCC1 0.018 0 -10000 0 -10000 0 0
TBX21 -0.25 0.41 -10000 0 -0.82 179 179
SUMO2 0.011 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.025 0.053 -10000 0 -1.2 1 1
FKBP4 0.016 0 -10000 0 -10000 0 0
FKBP5 0.004 0.098 -10000 0 -0.84 7 7
GR alpha/HSP90/FKBP51/HSP90 0.056 0.13 0.39 5 -0.57 8 13
PRL -0.015 0.11 -10000 0 -0.56 1 1
cortisol/GR alpha (dimer)/TIF2 0.13 0.29 0.57 83 -0.62 2 85
RELA 0.005 0.076 -10000 0 -10000 0 0
FGG -0.14 0.43 0.58 12 -0.72 155 167
GR beta/TIF2 0.051 0.14 0.43 5 -0.52 10 15
IFNG -0.41 0.44 -10000 0 -0.83 242 242
apoptosis -0.093 0.21 -10000 0 -0.65 10 10
CREB1 -0.014 0.1 -10000 0 -0.38 13 13
histone acetylation 0.02 0.13 0.39 10 -0.44 7 17
BGLAP -0.009 0.13 -10000 0 -0.74 3 3
GR/PKAc 0.066 0.1 0.4 2 -0.6 1 3
NF kappa B1 p50/RelA 0.011 0.14 -10000 0 -0.56 8 8
SMARCD1 0.018 0 -10000 0 -10000 0 0
MDM2 0.047 0.093 0.31 12 -10000 0 12
GATA3 -0.35 0.38 -10000 0 -0.74 264 264
AKT1 0 0.005 -10000 0 -10000 0 0
CSF2 -0.027 0.15 -10000 0 -0.68 17 17
GSK3B 0.011 0.007 -10000 0 -10000 0 0
NR1I3 -0.057 0.22 -10000 0 -0.82 13 13
CSN2 0.045 0.19 0.5 4 -0.66 1 5
BRG1/BAF155/BAF170/BAF60A 0.004 0.014 -10000 0 -10000 0 0
NFATC1 0.018 0.005 -10000 0 -10000 0 0
POU2F1 0.019 0.005 -10000 0 -10000 0 0
CDKN1A 0.05 0.052 -10000 0 -0.72 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.083 0.27 -10000 0 -0.83 62 62
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.003 0.21 0.39 1 -0.58 25 26
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.058 0.22 -10000 0 -0.85 13 13
JUN -0.22 0.25 -10000 0 -0.61 94 94
IL4 -0.024 0.12 -10000 0 -0.63 1 1
CDK5R1 0.012 0.007 -10000 0 -10000 0 0
PRKACA 0.016 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.25 0.26 0.31 1 -0.7 81 82
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.062 0.12 0.39 3 -0.6 4 7
cortisol/GR alpha (monomer) 0.15 0.34 0.65 99 -0.8 1 100
NCOA2 0 0.11 -10000 0 -0.74 11 11
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.054 0.14 -10000 0 -0.82 13 13
AP-1/NFAT1-c-4 -0.32 0.34 -10000 0 -0.81 112 112
AFP -0.35 0.56 -10000 0 -1.4 112 112
SUV420H1 0.016 0 -10000 0 -10000 0 0
IRF1 0.085 0.15 0.51 8 -0.62 1 9
TP53 0.044 0.021 -10000 0 -10000 0 0
PPP5C 0.016 0 -10000 0 -10000 0 0
KRT17 -0.25 0.41 -10000 0 -1.1 71 71
KRT14 -0.15 0.3 -10000 0 -0.83 81 81
TBP 0.028 0.01 -10000 0 -10000 0 0
CREBBP 0.049 0.082 -10000 0 -10000 0 0
HDAC1 0.01 0.008 -10000 0 -10000 0 0
HDAC2 0.011 0.014 -10000 0 -10000 0 0
AP-1 -0.33 0.34 -10000 0 -0.82 115 115
MAPK14 0.012 0.007 -10000 0 -10000 0 0
MAPK10 0.005 0.074 -10000 0 -0.75 5 5
MAPK11 0.008 0.055 -10000 0 -0.88 2 2
KRT5 -0.27 0.39 -10000 0 -0.93 111 111
interleukin-1 receptor activity 0 0.011 -10000 0 -10000 0 0
NCOA1 0.019 0.002 -10000 0 -10000 0 0
STAT1 0.025 0.053 -10000 0 -1.2 1 1
CGA -0.13 0.37 -10000 0 -1.2 52 52
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.091 0.15 0.45 35 -10000 0 35
MAPK3 0.012 0.007 -10000 0 -10000 0 0
MAPK1 0.012 0.007 -10000 0 -10000 0 0
ICAM1 -0.049 0.23 -10000 0 -0.76 29 29
NFKB1 0.003 0.085 -10000 0 -0.9 1 1
MAPK8 -0.14 0.2 -10000 0 -0.49 65 65
MAPK9 0.012 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.098 0.22 -10000 0 -0.68 10 10
BAX 0.052 0.028 -10000 0 -10000 0 0
POMC -0.037 0.17 -10000 0 -0.86 6 6
EP300 0.047 0.087 -10000 0 -0.6 1 1
cortisol/GR alpha (dimer)/p53 0.16 0.29 0.58 92 -0.7 1 93
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.071 0.28 2 -10000 0 2
SGK1 0.1 0.098 -10000 0 -10000 0 0
IL13 -0.36 0.28 -10000 0 -0.81 92 92
IL6 -0.12 0.38 -10000 0 -0.98 75 75
PRKACG 0.004 0.007 -10000 0 -10000 0 0
IL5 -0.29 0.21 -10000 0 -0.71 46 46
IL2 -0.17 0.25 -10000 0 -0.86 26 26
CDK5 0.012 0.007 -10000 0 -10000 0 0
PRKACB 0.016 0 -10000 0 -10000 0 0
HSP90AA1 0.016 0 -10000 0 -10000 0 0
IL8 -0.077 0.3 -10000 0 -0.92 44 44
CDK5R1/CDK5 0 0.003 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc 0.027 0.1 -10000 0 -0.62 1 1
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.26 0.56 73 -0.65 1 74
SMARCA4 0.018 0 -10000 0 -10000 0 0
chromatin remodeling 0.1 0.15 0.41 34 -10000 0 34
NF kappa B1 p50/RelA/Cbp 0.066 0.14 -10000 0 -0.93 1 1
JUN (dimer) -0.21 0.25 -10000 0 -0.61 94 94
YWHAH 0.016 0 -10000 0 -10000 0 0
VIPR1 -0.057 0.22 -10000 0 -1 16 16
NR3C1 0.081 0.19 0.5 32 -0.95 1 33
NR4A1 0.002 0.13 -10000 0 -0.73 16 16
TIF2/SUV420H1 -0.011 0.079 -10000 0 -0.56 11 11
MAPKKK cascade -0.093 0.21 -10000 0 -0.65 10 10
cortisol/GR alpha (dimer)/Src-1 0.15 0.28 0.58 85 -0.8 1 86
PBX1 -0.003 0.13 -10000 0 -0.74 16 16
POU1F1 0.009 0.009 -10000 0 -10000 0 0
SELE -0.095 0.36 -10000 0 -1.3 39 39
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.1 0.15 0.41 34 -10000 0 34
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.26 0.56 73 -0.65 1 74
mol:cortisol 0.064 0.2 0.38 87 -0.26 14 101
MMP1 -0.23 0.4 -10000 0 -0.98 106 106
Regulation of Telomerase

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
Telomerase catalytic core complex -0.24 0.28 -9999 0 -0.84 79 79
RAD9A 0.016 0 -9999 0 -10000 0 0
AP1 -0.014 0.087 -9999 0 -0.56 13 13
IFNAR2 0.015 0.007 -9999 0 -10000 0 0
AKT1 0.013 0.069 -9999 0 -0.43 10 10
ER alpha/Oestrogen -0.006 0.057 -9999 0 -0.59 5 5
NFX1/SIN3/HDAC complex 0.044 0.055 -9999 0 -10000 0 0
EGF -0.67 0.23 -9999 0 -0.74 480 480
SMG5 0.016 0 -9999 0 -10000 0 0
SMG6 0.016 0 -9999 0 -10000 0 0
SP3/HDAC2 0 0 -9999 0 -10000 0 0
TERT/c-Abl -0.22 0.26 -9999 0 -0.79 77 77
SAP18 0.013 0.006 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.34 0.38 -9999 0 -0.74 248 248
WRN 0.016 0 -9999 0 -10000 0 0
SP1 0.015 0.007 -9999 0 -10000 0 0
SP3 0.014 0.006 -9999 0 -10000 0 0
TERF2IP 0.016 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.18 0.23 -9999 0 -0.72 66 66
Mad/Max 0 0 -9999 0 -10000 0 0
TERT -0.24 0.29 -9999 0 -0.88 79 79
CCND1 -0.22 0.27 -9999 0 -0.78 87 87
MAX 0.014 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.006 -9999 0 -10000 0 0
RBBP4 0.012 0.033 -9999 0 -0.74 1 1
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.016 0 -9999 0 -10000 0 0
SIN3A 0.013 0.006 -9999 0 -10000 0 0
Telomerase/911 0.004 0.029 -9999 0 -10000 0 0
CDKN1B -0.22 0.3 -9999 0 -0.55 239 239
RAD1 0.016 0 -9999 0 -10000 0 0
XRCC5 0.016 0 -9999 0 -10000 0 0
XRCC6 0.016 0 -9999 0 -10000 0 0
SAP30 -0.018 0.16 -9999 0 -0.86 19 19
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.014 0.006 -9999 0 -10000 0 0
JUN 0.014 0.006 -9999 0 -10000 0 0
E6 -0.001 0.003 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0 0 -9999 0 -10000 0 0
FOS -0.005 0.12 -9999 0 -0.75 13 13
IFN-gamma/IRF1 -0.29 0.32 -9999 0 -0.65 239 239
PARP2 0.016 0 -9999 0 -10000 0 0
BLM -0.004 0.13 -9999 0 -0.86 12 12
Telomerase -0.021 0.16 -9999 0 -0.39 47 47
IRF1 0.016 0.039 -9999 0 -0.86 1 1
ESR1 0.006 0.076 -9999 0 -0.77 5 5
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.021 -9999 0 -0.49 1 1
ubiquitin-dependent protein catabolic process 0.051 0.051 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex -0.007 0.033 -9999 0 -10000 0 0
HDAC1 0.013 0.006 -9999 0 -10000 0 0
HDAC2 0.015 0.007 -9999 0 -10000 0 0
ATM -0.001 0.023 -9999 0 -0.52 1 1
SMAD3 0.025 0.067 -9999 0 -0.66 5 5
ABL1 0.016 0 -9999 0 -10000 0 0
MXD1 0.014 0.006 -9999 0 -10000 0 0
MRE11A 0.016 0 -9999 0 -10000 0 0
HUS1 0.016 0 -9999 0 -10000 0 0
RPS6KB1 0.016 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.17 0.25 -9999 0 -0.74 74 74
NR2F2 0.01 0.012 -9999 0 -10000 0 0
MAPK3 0.009 0.094 -9999 0 -0.67 10 10
MAPK1 0.009 0.094 -9999 0 -0.67 10 10
TGFB1/TGF beta receptor Type II 0.008 0.084 -9999 0 -0.86 5 5
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
HNRNPC 0.016 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.023 -9999 0 -0.52 1 1
NBN 0.016 0 -9999 0 -10000 0 0
EGFR 0.001 0.11 -9999 0 -0.85 9 9
mol:Oestrogen -0.001 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.51 0.18 -9999 0 -0.57 481 481
MYC -0.021 0.17 -9999 0 -0.86 21 21
IL2 -0.008 0.12 -9999 0 -0.86 10 10
KU 0 0 -9999 0 -10000 0 0
RAD50 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
TGFB1 0.008 0.084 -9999 0 -0.86 5 5
TRF2/BLM -0.014 0.093 -9999 0 -0.62 12 12
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.21 0.26 -9999 0 -0.78 77 77
SP1/HDAC2 0.007 0.014 -9999 0 -10000 0 0
PINX1 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.18 0.23 -9999 0 -0.72 66 66
Smad3/Myc -0.021 0.13 -9999 0 -0.59 25 25
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.37 0.43 -9999 0 -0.85 239 239
Telomerase/PinX1 -0.18 0.23 -9999 0 -0.72 66 66
Telomerase/AKT1/mTOR/p70S6K -0.012 0.079 -9999 0 -0.53 2 2
SIN3B 0.013 0.006 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.18 0.23 -9999 0 -0.72 65 65
response to DNA damage stimulus 0.004 0.006 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.004 -9999 0 -10000 0 0
TRF2/WRN 0 0.004 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.18 0.23 -9999 0 -0.72 66 66
E2F1 -0.091 0.29 -9999 0 -0.87 64 64
ZNFX1 0.013 0.006 -9999 0 -10000 0 0
PIF1 -0.14 0.33 -9999 0 -0.86 93 93
NCL 0.016 0 -9999 0 -10000 0 0
DKC1 0.016 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.18 0.27 -10000 0 -0.54 96 96
CRKL 0.016 0.12 -10000 0 -0.67 5 5
HRAS -0.043 0.18 -10000 0 -0.51 41 41
mol:PIP3 -0.005 0.11 -10000 0 -0.44 24 24
SPRED1 0.016 0 -10000 0 -10000 0 0
SPRED2 0.014 0.033 -10000 0 -0.74 1 1
GAB1 0.005 0.12 -10000 0 -0.49 24 24
FOXO3 0.022 0.11 -10000 0 -0.59 5 5
AKT1 0.012 0.12 -10000 0 -0.45 24 24
BAD 0.021 0.11 -10000 0 -0.59 6 6
megakaryocyte differentiation -0.074 0.22 -10000 0 -0.45 117 117
GSK3B 0.022 0.11 -10000 0 -0.59 5 5
RAF1 -0.012 0.15 -10000 0 -0.54 3 3
SHC1 0.014 0.038 -10000 0 -0.86 1 1
STAT3 0.005 0.12 -10000 0 -0.49 24 24
STAT1 -0.02 0.25 -10000 0 -1 24 24
HRAS/SPRED1 -0.068 0.12 -10000 0 -0.43 19 19
cell proliferation 0.004 0.13 -10000 0 -0.51 24 24
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
TEC 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.006 0.12 -10000 0 -0.48 26 26
HRAS/SPRED2 -0.068 0.12 -10000 0 -0.43 20 20
LYN/TEC/p62DOK -0.02 0.1 -10000 0 -0.66 5 5
MAPK3 0.011 0.12 -10000 0 -0.37 2 2
STAP1 -0.32 0.22 -10000 0 -0.42 406 406
GRAP2 -0.042 0.22 -10000 0 -0.86 35 35
JAK2 -0.07 0.2 -10000 0 -0.9 24 24
STAT1 (dimer) -0.018 0.24 -10000 0 -1 24 24
mol:Gleevec -0.002 0.005 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.13 0.22 -10000 0 -0.55 49 49
actin filament polymerization -0.002 0.14 -10000 0 -0.49 30 30
LYN 0.016 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.3 0.23 -10000 0 -0.88 33 33
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
CBL/CRKL/GRB2 -0.016 0.095 -10000 0 -0.59 5 5
PI3K -0.022 0.11 -10000 0 -0.45 25 25
PTEN 0.016 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.13 0.35 -10000 0 -1.3 26 26
MAPK8 0.003 0.13 -10000 0 -0.52 24 24
STAT3 (dimer) 0.005 0.12 -10000 0 -0.48 24 24
positive regulation of transcription 0.014 0.098 -10000 0 -0.31 1 1
mol:GDP -0.11 0.19 -10000 0 -0.62 44 44
PIK3C2B 0.005 0.12 -10000 0 -0.49 24 24
CBL/CRKL 0.024 0.11 -10000 0 -0.62 5 5
FER 0.003 0.13 -10000 0 -0.5 26 26
SH2B3 0.005 0.12 -10000 0 -0.49 24 24
PDPK1 0.005 0.1 -10000 0 -0.4 25 25
SNAI2 0.004 0.13 -10000 0 -0.5 24 24
positive regulation of cell proliferation -0.003 0.19 -10000 0 -0.7 31 31
KITLG 0 0.11 -10000 0 -0.76 10 10
cell motility -0.003 0.19 -10000 0 -0.7 31 31
PTPN6 0.008 0.011 -10000 0 -10000 0 0
EPOR 0.039 0.073 -10000 0 -10000 0 0
STAT5A (dimer) 0.001 0.16 -10000 0 -0.59 32 32
SOCS1 0.006 0.093 -10000 0 -0.86 6 6
cell migration 0.045 0.2 0.5 72 -10000 0 72
SOS1 0.016 0 -10000 0 -10000 0 0
EPO -0.29 0.42 -10000 0 -0.86 187 187
VAV1 -0.19 0.37 -10000 0 -0.86 125 125
GRB10 0.005 0.12 -10000 0 -0.49 24 24
PTPN11 0.008 0.01 -10000 0 -10000 0 0
SCF/KIT -0.037 0.12 -10000 0 -0.47 33 33
GO:0007205 -0.001 0.006 -10000 0 -10000 0 0
MAP2K1 0.005 0.13 -10000 0 -0.42 2 2
CBL 0.014 0.033 -10000 0 -0.74 1 1
KIT -0.016 0.29 -10000 0 -1.2 31 31
MAP2K2 0.004 0.13 -10000 0 -0.42 2 2
SHC/Grb2/SOS1 -0.021 0.1 -10000 0 -0.66 5 5
STAT5A 0 0.17 -10000 0 -0.61 32 32
GRB2 0.016 0 -10000 0 -10000 0 0
response to radiation 0.004 0.13 -10000 0 -0.49 24 24
SHC/GRAP2 -0.045 0.17 -10000 0 -0.66 36 36
PTPRO -0.076 0.22 -10000 0 -0.46 117 117
SH2B2 -0.002 0.14 -10000 0 -0.5 30 30
DOK1 0.016 0 -10000 0 -10000 0 0
MATK -0.046 0.2 -10000 0 -0.52 72 72
CREBBP 0.044 0.012 -10000 0 -10000 0 0
BCL2 0.041 0.071 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.016 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
NUDC 0.016 0 -9999 0 -10000 0 0
RELN/LRP8 -0.16 0.22 -9999 0 -0.48 179 179
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.016 0.001 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.11 0.22 -9999 0 -0.52 6 6
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.011 0.14 -9999 0 -0.86 13 13
IQGAP1 0.016 0 -9999 0 -10000 0 0
PLA2G7 -0.65 0.38 -9999 0 -0.86 404 404
CALM1 0.016 0 -9999 0 -10000 0 0
DYNLT1 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.001 0.029 -9999 0 -0.66 1 1
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.016 0 -9999 0 -10000 0 0
CDK5R1 0.016 0.001 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 -0.099 0.29 -9999 0 -0.86 67 67
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.17 0.24 -9999 0 -0.49 190 190
YWHAE 0.016 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.16 -9999 0 -0.59 16 16
MAP1B -0.001 0.02 -9999 0 -0.33 2 2
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.12 0.17 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.74 178 178
PAFAH/LIS1 -0.44 0.25 -9999 0 -0.57 404 404
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.098 0.12 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.1 0.14 -9999 0 -0.69 1 1
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.13 0.19 -9999 0 -0.64 16 16
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.031 0 -9999 0 -10000 0 0
PAFAH1B3 0.014 0.033 -9999 0 -0.74 1 1
PAFAH1B2 0.014 0.033 -9999 0 -0.74 1 1
MAP1B/LIS1/Dynein heavy chain -0.001 0.013 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.12 0.15 -9999 0 -0.56 16 16
LRP8 0.014 0.038 -9999 0 -0.86 1 1
NDEL1/Katanin 60 -0.13 0.16 -9999 0 -0.59 16 16
P39/CDK5 -0.18 0.22 -9999 0 -0.86 16 16
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.094 0.21 -9999 0 -0.48 6 6
PPP2R5D 0.016 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.016 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.14 0.2 -9999 0 -0.89 1 1
RELN/VLDLR -0.14 0.2 -9999 0 -0.52 6 6
CDC42 0 0 -9999 0 -10000 0 0
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.02 0.18 -9999 0 -10000 0 0
CRKL -0.094 0.22 -9999 0 -10000 0 0
mol:DAG -0.12 0.17 -9999 0 -10000 0 0
HRAS -0.11 0.15 -9999 0 -0.7 1 1
MAPK8 -0.14 0.26 -9999 0 -0.48 187 187
RAP1A -0.094 0.22 -9999 0 -10000 0 0
GAB1 -0.094 0.22 -9999 0 -10000 0 0
MAPK14 -0.13 0.25 -9999 0 -0.48 187 187
EPO -0.29 0.42 -9999 0 -0.85 187 187
PLCG1 -0.13 0.17 -9999 0 -10000 0 0
EPOR/TRPC2/IP3 Receptors 0.007 0.019 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.2 0.27 -9999 0 -0.55 188 188
GAB1/SHC/GRB2/SOS1 -0.12 0.16 -9999 0 -10000 0 0
EPO/EPOR (dimer) -0.23 0.31 -9999 0 -0.65 187 187
IRS2 -0.1 0.23 -9999 0 -0.88 2 2
STAT1 -0.065 0.21 -9999 0 -10000 0 0
STAT5B -0.07 0.21 -9999 0 -10000 0 0
cell proliferation -0.12 0.24 -9999 0 -0.85 1 1
GAB1/SHIP/PIK3R1/SHP2/SHC -0.11 0.15 -9999 0 -0.71 1 1
TEC -0.094 0.22 -9999 0 -10000 0 0
SOCS3 0.009 0.076 -9999 0 -0.86 4 4
STAT1 (dimer) -0.063 0.21 -9999 0 -10000 0 0
JAK2 0.006 0.018 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
EPO/EPOR (dimer)/JAK2 -0.1 0.24 -9999 0 -10000 0 0
EPO/EPOR -0.23 0.31 -9999 0 -0.65 187 187
LYN 0.018 0.001 -9999 0 -10000 0 0
TEC/VAV2 -0.081 0.22 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.007 0.019 -9999 0 -10000 0 0
SHC1 0.014 0.038 -9999 0 -0.86 1 1
EPO/EPOR (dimer)/LYN -0.16 0.28 -9999 0 -0.54 187 187
mol:IP3 -0.12 0.17 -9999 0 -10000 0 0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.13 0.18 -9999 0 -0.79 3 3
SH2B3 0.006 0.018 -9999 0 -10000 0 0
NFKB1 -0.14 0.26 -9999 0 -0.48 187 187
EPO/EPOR (dimer)/JAK2/SOCS3 -0.11 0.15 -9999 0 -0.53 3 3
PTPN6 -0.11 0.23 -9999 0 -10000 0 0
TEC/VAV2/GRB2 -0.12 0.17 -9999 0 -10000 0 0
EPOR 0.007 0.019 -9999 0 -10000 0 0
INPP5D 0.009 0.076 -9999 0 -0.86 4 4
mol:GDP -0.12 0.16 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
PLCG2 0.003 0.1 -9999 0 -0.82 8 8
CRKL/CBL/C3G -0.12 0.17 -9999 0 -0.73 1 1
VAV2 -0.094 0.22 -9999 0 -10000 0 0
CBL -0.095 0.22 -9999 0 -0.8 1 1
SHC/Grb2/SOS1 -0.12 0.17 -9999 0 -10000 0 0
STAT5A -0.07 0.21 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
STAT5 (dimer) -0.045 0.21 -9999 0 -10000 0 0
LYN/PLCgamma2 -0.009 0.076 -9999 0 -0.62 8 8
PTPN11 0.016 0 -9999 0 -10000 0 0
BTK -0.2 0.29 -9999 0 -0.88 30 30
BCL2 -0.02 0.18 -9999 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.3 -9999 0 -0.76 40 40
CRP -0.2 0.39 -9999 0 -0.91 90 90
cell cycle arrest -0.18 0.35 -9999 0 -0.8 79 79
TIMP1 -0.15 0.33 -9999 0 -0.77 70 70
IL6ST -0.015 0.14 -9999 0 -0.74 19 19
Rac1/GDP -0.14 0.26 -9999 0 -0.6 91 91
AP1 0.021 0.1 -9999 0 -0.55 3 3
GAB2 0.011 0.008 -9999 0 -10000 0 0
TNFSF11 -0.19 0.37 -9999 0 -0.91 61 61
HSP90B1 0.004 0.087 -9999 0 -10000 0 0
GAB1 0.014 0.006 -9999 0 -10000 0 0
MAPK14 0.014 0.14 -9999 0 -0.72 5 5
AKT1 0.06 0.034 -9999 0 -10000 0 0
FOXO1 0.076 0.023 -9999 0 -10000 0 0
MAP2K6 -0.02 0.14 -9999 0 -0.7 6 6
mol:GTP -0.001 0.003 -9999 0 -10000 0 0
MAP2K4 -0.14 0.27 -9999 0 -0.65 70 70
MITF -0.026 0.14 -9999 0 -0.69 5 5
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.016 0 -9999 0 -10000 0 0
A2M 0.028 0.005 -9999 0 -10000 0 0
CEBPB 0.003 0.13 -9999 0 -0.86 12 12
GRB2/SOS1/GAB family/SHP2 0 0.069 -9999 0 -10000 0 0
STAT3 -0.18 0.36 -9999 0 -0.85 75 75
STAT1 -0.005 0.025 -9999 0 -0.49 1 1
CEBPD -0.14 0.3 -9999 0 -0.78 34 34
PIK3CA 0.017 0.033 -9999 0 -0.74 1 1
PI3K -0.002 0.034 -9999 0 -0.55 2 2
JUN 0.01 0.008 -9999 0 -10000 0 0
PIAS3/MITF -0.02 0.13 -9999 0 -0.71 4 4
MAPK11 0.013 0.14 -9999 0 -0.78 6 6
STAT3 (dimer)/FOXO1 -0.072 0.27 -9999 0 -0.65 16 16
GRB2/SOS1/GAB family -0.048 0.11 -9999 0 -0.66 4 4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.04 0.16 -9999 0 -0.65 13 13
GRB2 0.014 0.006 -9999 0 -10000 0 0
JAK2 0.016 0 -9999 0 -10000 0 0
LBP -0.29 0.44 -9999 0 -0.88 165 165
PIK3R1 0.016 0.033 -9999 0 -0.74 1 1
JAK1 0.015 0.006 -9999 0 -10000 0 0
MYC -0.15 0.32 -9999 0 -0.81 44 44
FGG -0.27 0.43 -9999 0 -0.89 123 123
macrophage differentiation -0.18 0.35 -9999 0 -0.8 79 79
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.07 0.17 -9999 0 -0.56 34 34
JUNB -0.14 0.3 -9999 0 -0.77 34 34
FOS -0.009 0.12 -9999 0 -0.75 13 13
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.037 0.15 -9999 0 -0.48 22 22
STAT1/PIAS1 -0.049 0.16 -9999 0 -0.51 20 20
GRB2/SOS1/GAB family/SHP2/PI3K 0.022 0.038 -9999 0 -10000 0 0
STAT3 (dimer) -0.18 0.36 -9999 0 -0.84 79 79
PRKCD -0.15 0.3 -9999 0 -0.72 58 58
IL6R 0.015 0.006 -9999 0 -10000 0 0
SOCS3 0.028 0.14 -9999 0 -0.69 7 7
gp130 (dimer)/JAK1/JAK1/LMO4 -0.005 0.093 -9999 0 -0.47 15 15
Rac1/GTP -0.18 0.23 -9999 0 -0.61 97 97
HCK -0.033 0.2 -9999 0 -0.86 29 29
MAPKKK cascade 0.025 0.061 -9999 0 -10000 0 0
bone resorption -0.18 0.35 -9999 0 -0.84 63 63
IRF1 -0.14 0.3 -9999 0 -0.76 40 40
mol:GDP -0.15 0.27 -9999 0 -0.6 102 102
SOS1 0.01 0.008 -9999 0 -10000 0 0
VAV1 -0.15 0.27 -9999 0 -0.61 102 102
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 0.01 0.13 -9999 0 -0.72 4 4
PTPN11 -0.004 0.012 -9999 0 -10000 0 0
IL6/IL6RA -0.078 0.21 -9999 0 -0.63 67 67
gp130 (dimer)/TYK2/TYK2/LMO4 -0.014 0.088 -9999 0 -0.47 19 19
gp130 (dimer)/JAK2/JAK2/LMO4 -0.014 0.088 -9999 0 -0.47 19 19
IL6 -0.092 0.28 -9999 0 -0.82 67 67
PIAS3 0.016 0 -9999 0 -10000 0 0
PTPRE 0.016 0.04 -9999 0 -0.81 1 1
PIAS1 0.016 0 -9999 0 -10000 0 0
RAC1 0.015 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.036 0.13 -9999 0 -0.45 15 15
LMO4 0.012 0.014 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.22 0.29 -9999 0 -0.8 65 65
MCL1 0.075 0.022 -9999 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0 0 -9999 0 -10000 0 0
VLDLR 0.016 0 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
LRPAP1 0.016 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ITGA3 0.012 0.054 -9999 0 -0.86 2 2
RELN/VLDLR/Fyn -0.16 0.22 -9999 0 -0.48 178 178
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.004 0.045 -9999 0 -0.8 1 1
AKT1 -0.067 0.16 -9999 0 -0.57 2 2
MAP2K7 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
DAB1 -0.011 0.14 -9999 0 -0.86 13 13
RELN/LRP8/DAB1 -0.16 0.22 -9999 0 -0.45 191 191
LRPAP1/LRP8 -0.001 0.029 -9999 0 -0.66 1 1
RELN/LRP8/DAB1/Fyn -0.15 0.2 -9999 0 -0.52 19 19
DAB1/alpha3/beta1 Integrin -0.13 0.18 -9999 0 -0.82 1 1
long-term memory -0.2 0.24 -9999 0 -0.88 24 24
DAB1/LIS1 -0.14 0.18 -9999 0 -0.85 1 1
DAB1/CRLK/C3G -0.13 0.17 -9999 0 -0.82 1 1
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
DAB1/NCK2 -0.14 0.18 -9999 0 -0.86 1 1
ARHGEF2 0.016 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.1 0.3 -9999 0 -0.83 76 76
CDK5R1 0.016 0.001 -9999 0 -10000 0 0
RELN -0.24 0.36 -9999 0 -0.74 178 178
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
RELN/LRP8/Fyn -0.16 0.22 -9999 0 -0.48 179 179
GRIN2A/RELN/LRP8/DAB1/Fyn -0.21 0.25 -9999 0 -0.62 77 77
MAPK8 0.013 0.046 -9999 0 -0.74 2 2
RELN/VLDLR/DAB1 -0.16 0.22 -9999 0 -0.45 190 190
ITGB1 0.016 0 -9999 0 -10000 0 0
MAP1B -0.15 0.2 -9999 0 -0.51 19 19
RELN/LRP8 -0.16 0.22 -9999 0 -0.48 179 179
GRIN2B/RELN/LRP8/DAB1/Fyn -0.15 0.2 -9999 0 -0.9 2 2
PI3K -0.002 0.034 -9999 0 -0.56 2 2
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.002 0.041 -9999 0 -0.66 2 2
RAP1A -0.11 0.17 -9999 0 -0.75 1 1
PAFAH1B1 0.016 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0.046 -9999 0 -0.74 2 2
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B 0.008 0.054 -9999 0 -0.86 2 2
NCK2 0.016 0 -9999 0 -10000 0 0
neuron differentiation -0.03 0.12 -9999 0 -0.53 3 3
neuron adhesion -0.05 0.19 -9999 0 -0.7 1 1
LRP8 0.014 0.038 -9999 0 -0.86 1 1
GSK3B -0.053 0.15 -9999 0 -0.53 2 2
RELN/VLDLR/DAB1/Fyn -0.15 0.2 -9999 0 -0.52 18 18
MAP3K11 0.014 0.033 -9999 0 -0.74 1 1
RELN/VLDLR/DAB1/P13K -0.11 0.15 -9999 0 -0.61 2 2
CDK5 0.016 0 -9999 0 -10000 0 0
MAPT 0.016 0.082 -9999 0 -0.69 6 6
neuron migration -0.06 0.21 -9999 0 -0.61 1 1
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.03 0.12 -9999 0 -0.54 3 3
RELN/VLDLR -0.14 0.2 -9999 0 -0.52 6 6
Visual signal transduction: Rods

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
mol:K + 0.016 0 -9999 0 -10000 0 0
GNAT1/GTP -0.01 0.082 -9999 0 -0.68 8 8
Metarhodopsin II/Arrestin -0.018 0.1 -9999 0 -0.59 16 16
PDE6G/GNAT1/GTP -0.014 0.086 -9999 0 -0.56 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.007 0.11 -9999 0 -0.86 8 8
GRK1 0.003 0.006 -9999 0 -10000 0 0
CNG Channel -0.11 0.21 -9999 0 -0.94 12 12
mol:Na + -0.11 0.21 -9999 0 -0.81 22 22
mol:ADP 0.003 0.006 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.035 0.13 -9999 0 -0.5 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.12 0.22 -9999 0 -0.85 22 22
CNGB1 -0.008 0.12 -9999 0 -0.86 11 11
RDH5 -0.003 0.13 -9999 0 -0.83 12 12
SAG 0.001 0.038 -9999 0 -0.86 1 1
mol:Ca2+ -0.069 0.22 -9999 0 -0.78 22 22
Na + (4 Units) -0.1 0.2 -9999 0 -0.74 22 22
RGS9 -0.008 0.14 -9999 0 -0.81 15 15
GNB1/GNGT1 -0.23 0.32 -9999 0 -0.66 183 183
GNAT1/GDP -0.038 0.13 -9999 0 -0.53 16 16
GUCY2D -0.031 0.19 -9999 0 -0.86 26 26
GNGT1 -0.29 0.42 -9999 0 -0.86 183 183
GUCY2F 0.002 0.005 -9999 0 -10000 0 0
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.038 0.15 -9999 0 -0.59 29 29
mol:11-cis-retinal -0.003 0.13 -9999 0 -0.83 12 12
mol:cGMP -0.04 0.14 -9999 0 -0.58 14 14
GNB1 0.016 0 -9999 0 -10000 0 0
Rhodopsin -0.033 0.14 -9999 0 -0.65 27 27
SLC24A1 0.016 0 -9999 0 -10000 0 0
CNGA1 -0.13 0.3 -9999 0 -0.74 100 100
Metarhodopsin II -0.016 0.091 -9999 0 -0.55 15 15
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.043 0.15 -9999 0 -0.56 39 39
RGS9BP -0.017 0.15 -9999 0 -0.74 23 23
Metarhodopsin II/Transducin -0.12 0.16 -9999 0 -0.62 11 11
GCAP Family/Ca ++ -0.017 0.098 -9999 0 -0.56 16 16
PDE6A/B -0.035 0.15 -9999 0 -0.66 28 28
mol:Pi -0.035 0.13 -9999 0 -0.49 38 38
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.19 0.27 -9999 0 -0.55 186 186
PDE6B 0.007 0.08 -9999 0 -0.74 6 6
PDE6A -0.024 0.18 -9999 0 -0.86 23 23
PDE6G 0.008 0.075 -9999 0 -0.77 5 5
RHO -0.015 0.14 -9999 0 -0.86 15 15
PDE6 -0.056 0.16 -9999 0 -0.82 8 8
GUCA1A -0.01 0.12 -9999 0 -0.86 10 10
GC2/GCAP Family -0.017 0.098 -9999 0 -0.57 14 14
GUCA1C 0.001 0.046 -9999 0 -0.74 2 2
GUCA1B 0.007 0.085 -9999 0 -0.86 5 5
Signaling events mediated by PTP1B

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
PDGFRB 0.016 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.048 0.1 -10000 0 -0.46 10 10
PTP1B/AKT1 -0.032 0.047 -10000 0 -0.41 2 2
FYN 0.016 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.049 0.053 -10000 0 -0.37 6 6
EGFR -0.013 0.11 -10000 0 -0.87 9 9
EGF/EGFR -0.37 0.14 -10000 0 -0.41 477 477
CSF1 0.014 0.033 -10000 0 -0.74 1 1
AKT1 0.016 0.001 -10000 0 -10000 0 0
INSR 0.016 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.05 0.091 -10000 0 -0.45 20 20
Insulin Receptor/Insulin -0.008 0.035 -10000 0 -10000 0 0
HCK -0.032 0.2 -10000 0 -0.86 29 29
CRK 0.016 0 -10000 0 -10000 0 0
TYK2 -0.035 0.05 -10000 0 -0.41 3 3
EGF -0.67 0.23 -10000 0 -0.74 480 480
YES1 0.016 0 -10000 0 -10000 0 0
CAV1 -0.15 0.1 -10000 0 -0.42 40 40
TXN 0.002 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.033 0.055 -10000 0 -0.45 6 6
cell migration 0.049 0.053 0.37 6 -10000 0 6
STAT3 0.015 0.002 -10000 0 -10000 0 0
PRLR -0.087 0.26 -10000 0 -0.74 71 71
ITGA2B -0.019 0.16 -10000 0 -0.86 19 19
CSF1R 0.004 0.1 -10000 0 -0.86 7 7
Prolactin Receptor/Prolactin -0.075 0.19 -10000 0 -0.56 71 71
FGR 0.011 0.066 -10000 0 -0.86 3 3
PTP1B/p130 Cas -0.036 0.052 -10000 0 -0.44 2 2
Crk/p130 Cas -0.03 0.042 -10000 0 -0.42 1 1
DOK1 -0.019 0.046 -10000 0 -0.38 2 2
JAK2 -0.054 0.11 -10000 0 -0.42 17 17
Jak2/Leptin Receptor/Leptin -0.054 0.13 -10000 0 -0.58 11 11
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
PTPN1 -0.049 0.053 -10000 0 -0.37 6 6
LYN 0.016 0 -10000 0 -10000 0 0
CDH2 -0.01 0.14 -10000 0 -0.74 18 18
SRC 0 0.021 -10000 0 -10000 0 0
ITGB3 0.003 0.08 -10000 0 -0.74 6 6
CAT1/PTP1B -0.23 0.13 -10000 0 -0.58 36 36
CAPN1 0.002 0.006 -10000 0 -10000 0 0
CSK 0.016 0 -10000 0 -10000 0 0
PI3K 0.008 0.043 -10000 0 -0.63 1 1
mol:H2O2 -0.007 0.002 -10000 0 -10000 0 0
STAT3 (dimer) -0.036 0.13 -10000 0 -0.71 5 5
negative regulation of transcription -0.053 0.11 -10000 0 -0.41 17 17
FCGR2A -0.024 0.18 -10000 0 -0.86 24 24
FER -0.001 0.046 -10000 0 -0.75 2 2
alphaIIb/beta3 Integrin -0.03 0.14 -10000 0 -0.66 24 24
BLK -0.041 0.21 -10000 0 -0.86 34 34
Insulin Receptor/Insulin/Shc -0.001 0.026 -10000 0 -0.59 1 1
RHOA 0.002 0.006 -10000 0 -10000 0 0
LEPR 0.014 0.004 -10000 0 -10000 0 0
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
p210 bcr-abl/Grb2 0.016 0 -10000 0 -10000 0 0
mol:NADPH -0.007 0.003 -10000 0 -10000 0 0
TRPV6 -0.22 0.15 -10000 0 -0.55 62 62
PRL 0.004 0.007 -10000 0 -10000 0 0
SOCS3 0.025 0.067 -10000 0 -0.73 4 4
SPRY2 0.002 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.004 0.042 -10000 0 -0.49 4 4
CSF1/CSF1R -0.037 0.075 -10000 0 -0.53 10 10
Ras protein signal transduction 0.039 0.016 -10000 0 -10000 0 0
IRS1 0.01 0.065 -10000 0 -0.74 4 4
INS 0.001 0.001 -10000 0 -10000 0 0
LEP -0.073 0.26 -10000 0 -0.86 51 51
STAT5B -0.045 0.068 -10000 0 -0.46 5 5
STAT5A -0.045 0.068 -10000 0 -0.46 5 5
GRB2 0.016 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.035 0.05 -10000 0 -0.41 3 3
CSN2 -0.008 0.069 -10000 0 -10000 0 0
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
LAT -0.1 0.17 -10000 0 -0.36 119 119
YBX1 0.003 0.008 -10000 0 -10000 0 0
LCK -0.02 0.17 -10000 0 -0.85 22 22
SHC1 0.014 0.038 -10000 0 -0.86 1 1
NOX4 -0.006 0.073 -10000 0 -0.75 5 5
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.084 0.31 -10000 0 -0.9 30 30
NCK1/PAK1/Dok-R -0.083 0.11 -10000 0 -0.42 27 27
NCK1/Dok-R -0.083 0.26 -10000 0 -1 32 32
PIK3CA 0.005 0.033 -10000 0 -0.74 1 1
mol:beta2-estradiol -0.006 0.038 0.32 5 -10000 0 5
RELA 0.016 0 -10000 0 -10000 0 0
SHC1 0.007 0.039 -10000 0 -0.87 1 1
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.31 0.42 -10000 0 -0.85 199 199
TNIP2 0.016 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.057 0.23 -10000 0 -0.96 31 31
FN1 -0.049 0.23 -10000 0 -0.86 39 39
PLD2 0.033 0.3 -10000 0 -1.1 31 31
PTPN11 0.016 0 -10000 0 -10000 0 0
GRB14 -0.024 0.17 -10000 0 -0.74 28 28
ELK1 0.061 0.27 -10000 0 -0.96 31 31
GRB7 0.004 0.092 -10000 0 -0.74 8 8
PAK1 0.016 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.11 0.29 -10000 0 -1 43 43
CDKN1A -0.11 0.31 -10000 0 -0.68 20 20
ITGA5 -0.049 0.23 -10000 0 -0.86 39 39
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.083 0.26 -10000 0 -1 32 32
CRK 0.016 0 -10000 0 -10000 0 0
mol:NO -0.049 0.26 -10000 0 -0.65 30 30
PLG -0.19 0.34 -10000 0 -1.2 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.12 0.21 -10000 0 -0.84 30 30
GRB2 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.007 0.034 -10000 0 -0.74 1 1
ANGPT2 -0.2 0.38 -10000 0 -0.65 169 169
BMX -0.037 0.34 -10000 0 -1.1 31 31
ANGPT1 0.075 0.19 -10000 0 -1.2 8 8
tube development -0.13 0.34 -10000 0 -0.74 25 25
ANGPT4 -0.018 0.15 -10000 0 -0.87 16 16
response to hypoxia -0.003 0.017 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.024 0.32 -10000 0 -1.2 31 31
alpha5/beta1 Integrin -0.049 0.17 -10000 0 -0.66 39 39
FGF2 0.01 0.077 -10000 0 -0.76 5 5
STAT5A (dimer) -0.15 0.36 -10000 0 -0.85 26 26
mol:L-citrulline -0.049 0.26 -10000 0 -0.65 30 30
AGTR1 -0.036 0.17 -10000 0 -0.75 29 29
MAPK14 -0.003 0.31 -10000 0 -1.1 30 30
Tie2/SHP2 -0.061 0.25 -10000 0 -1.1 29 29
TEK -0.046 0.29 -10000 0 -1.2 29 29
RPS6KB1 -0.047 0.28 -10000 0 -0.86 30 30
Angiotensin II/AT1 -0.043 0.13 -10000 0 -0.58 29 29
Tie2/Ang1/GRB2 -0.004 0.3 -10000 0 -1.1 31 31
MAPK3 0.045 0.27 -10000 0 -0.99 31 31
MAPK1 0.045 0.27 -10000 0 -0.99 31 31
Tie2/Ang1/GRB7 -0.009 0.31 -10000 0 -1.2 31 31
NFKB1 0.014 0.033 -10000 0 -0.74 1 1
MAPK8 0.031 0.3 -10000 0 -1.1 31 31
PI3K -0.07 0.32 -10000 0 -1 30 30
FES -0.008 0.31 -10000 0 -1.1 31 31
Crk/Dok-R -0.082 0.26 -10000 0 -1 31 31
Tie2/Ang1/ABIN2 -0.004 0.3 -10000 0 -1.1 31 31
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.073 0.29 -10000 0 -0.8 30 30
STAT5A 0.016 0.001 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.047 0.28 -10000 0 -0.86 30 30
Tie2/Ang2 -0.19 0.4 -10000 0 -1 26 26
Tie2/Ang1 0.024 0.33 -10000 0 -1.2 31 31
FOXO1 -0.11 0.31 -10000 0 -0.8 30 30
ELF1 0.023 0.035 -10000 0 -0.73 1 1
ELF2 0.029 0.3 -10000 0 -1.1 31 31
mol:Choline 0.035 0.28 -10000 0 -1 31 31
cell migration -0.055 0.071 -10000 0 -10000 0 0
FYN -0.15 0.36 -10000 0 -0.85 25 25
DOK2 -0.035 0.2 -10000 0 -0.86 31 31
negative regulation of cell cycle -0.095 0.3 -10000 0 -0.61 20 20
ETS1 0.028 0.037 -10000 0 -10000 0 0
PXN -0.025 0.25 -10000 0 -0.7 30 30
ITGB1 0.016 0 -10000 0 -10000 0 0
NOS3 -0.06 0.28 -10000 0 -0.74 30 30
RAC1 0.016 0 -10000 0 -10000 0 0
TNF 0.009 0.1 -10000 0 -0.79 8 8
MAPKKK cascade 0.035 0.28 -10000 0 -1 31 31
RASA1 0.014 0.033 -10000 0 -0.74 1 1
Tie2/Ang1/Shc -0.003 0.3 -10000 0 -1.1 31 31
NCK1 0.014 0.033 -10000 0 -0.74 1 1
vasculogenesis -0.04 0.24 -10000 0 -0.58 30 30
mol:Phosphatidic acid 0.035 0.28 -10000 0 -1 31 31
mol:Angiotensin II -0.016 0.022 -10000 0 -10000 0 0
mol:NADP -0.049 0.26 -10000 0 -0.65 30 30
Rac1/GTP -0.13 0.19 -10000 0 -0.8 30 30
MMP2 0.026 0.3 -10000 0 -1.1 31 31
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.019 0.045 -9999 0 -10000 0 0
BIRC5 -0.24 0.4 -9999 0 -0.86 154 154
NFKBIA 0.047 0.039 -9999 0 -10000 0 0
CPEB1 -0.14 0.31 -9999 0 -0.76 109 109
AKT1 0.047 0.039 -9999 0 -10000 0 0
NDEL1 0.016 0 -9999 0 -10000 0 0
Aurora A/BRCA1 0.017 0.04 -9999 0 -10000 0 0
NDEL1/TACC3 0.016 0.074 -9999 0 -0.74 4 4
GADD45A 0.016 0 -9999 0 -10000 0 0
GSK3B 0.013 0.019 -9999 0 -10000 0 0
PAK1/Aurora A 0.019 0.045 -9999 0 -10000 0 0
MDM2 0.016 0 -9999 0 -10000 0 0
JUB 0.011 0.057 -9999 0 -0.74 3 3
TPX2 -0.14 0.3 -9999 0 -0.67 127 127
TP53 0.024 0.036 -9999 0 -10000 0 0
DLG7 0.019 0.043 -9999 0 -10000 0 0
AURKAIP1 0.011 0.06 -9999 0 -0.78 3 3
ARHGEF7 0.016 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.017 0.078 -9999 0 -0.77 4 4
G2/M transition of mitotic cell cycle 0.017 0.04 -9999 0 -10000 0 0
AURKA 0.026 0.054 -9999 0 -10000 0 0
AURKB -0.14 0.15 -9999 0 -0.29 248 248
CDC25B 0.017 0.061 -9999 0 -0.58 2 2
G2/M transition checkpoint 0.014 0.052 -9999 0 -0.43 3 3
mRNA polyadenylation -0.075 0.19 -9999 0 -0.44 109 109
Aurora A/CPEB -0.076 0.19 -9999 0 -0.44 109 109
Aurora A/TACC1/TRAP/chTOG 0.023 0.044 -9999 0 -10000 0 0
BRCA1 0.016 0 -9999 0 -10000 0 0
centrosome duplication 0.019 0.045 -9999 0 -10000 0 0
regulation of centrosome cycle -0.006 0.064 -9999 0 -0.73 4 4
spindle assembly -0.002 0.022 -9999 0 -10000 0 0
TDRD7 0.016 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.14 0.21 -9999 0 -0.73 7 7
CENPA -0.12 0.14 -9999 0 -0.3 171 171
Aurora A/PP2A 0.019 0.045 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.053 0.035 -9999 0 -10000 0 0
negative regulation of DNA binding 0.025 0.036 -9999 0 -10000 0 0
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.014 0.033 -9999 0 -0.74 1 1
Ajuba/Aurora A 0.015 0.053 -9999 0 -0.44 3 3
mitotic prometaphase 0.037 0.04 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.042 0.049 -9999 0 -10000 0 0
TACC1 0.016 0 -9999 0 -10000 0 0
TACC3 0.009 0.076 -9999 0 -0.86 4 4
Aurora A/Antizyme1 0.017 0.06 -9999 0 -0.52 2 2
Aurora A/RasGAP 0.018 0.049 -9999 0 -0.47 1 1
OAZ1 0.014 0.038 -9999 0 -0.86 1 1
RAN 0.016 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.019 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.14 0.3 -9999 0 -0.66 127 127
PPP2R5D 0.016 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.086 0.24 -9999 0 -0.52 127 127
PAK1 0.016 0 -9999 0 -10000 0 0
CKAP5 0.016 0 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.014 0.033 -9999 0 -0.74 1 1
Caspase 8 (4 units) -0.096 0.092 -9999 0 -10000 0 0
NEF -0.057 0.084 -9999 0 -10000 0 0
NFKBIA 0.002 0.044 -9999 0 -10000 0 0
BIRC3 -0.068 0.3 -9999 0 -0.79 80 80
CYCS -0.077 0.14 -9999 0 -0.43 1 1
RIPK1 0.016 0 -9999 0 -10000 0 0
CD247 -0.37 0.48 -9999 0 -1 174 174
MAP2K7 -0.04 0.11 -9999 0 -10000 0 0
protein ubiquitination 0.061 0.07 -9999 0 -0.44 1 1
CRADD 0.016 0 -9999 0 -10000 0 0
DAXX 0.016 0 -9999 0 -10000 0 0
FAS 0.016 0 -9999 0 -10000 0 0
BID -0.091 0.15 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha -0.049 0.12 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
MAP3K5 0.016 0 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
FADD 0.016 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.05 0.12 -9999 0 -10000 0 0
MAPK8 -0.029 0.1 -9999 0 -0.51 1 1
APAF1 0.016 0 -9999 0 -10000 0 0
TRAF1 0.014 0.038 -9999 0 -0.86 1 1
TRAF2 0.016 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.13 0.13 -9999 0 -10000 0 0
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.048 0.066 -9999 0 -10000 0 0
CHUK 0.062 0.074 -9999 0 -0.49 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0 0 -9999 0 -10000 0 0
TCRz/NEF -0.4 0.44 -9999 0 -0.74 284 284
TNF 0.003 0.1 -9999 0 -0.8 8 8
FASLG -0.57 0.61 -9999 0 -1.1 284 284
NFKB1 0 0.054 -9999 0 -0.73 1 1
TNFR1A/BAG4/TNF-alpha -0.009 0.067 -9999 0 -0.52 9 9
CASP6 -0.047 0.052 -9999 0 -10000 0 0
CASP7 -0.058 0.21 -9999 0 -0.55 50 50
RELA 0.002 0.044 -9999 0 -10000 0 0
CASP2 0.016 0 -9999 0 -10000 0 0
CASP3 -0.058 0.21 -9999 0 -0.55 50 50
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.001 0.024 -9999 0 -0.56 1 1
CASP8 0.016 0 -9999 0 -10000 0 0
CASP9 0.016 0 -9999 0 -10000 0 0
MAP3K14 0.054 0.079 -9999 0 -0.53 3 3
APAF-1/Caspase 9 -0.12 0.18 -9999 0 -0.56 54 54
BCL2 -0.017 0.099 -9999 0 -0.46 1 1
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin -0.042 0.15 -9999 0 -0.58 39 39
EPHB2 0 0.11 -9999 0 -0.76 11 11
Syndecan-2/TACI -0.056 0.17 -9999 0 -0.58 52 52
LAMA1 -0.006 0.13 -9999 0 -0.75 15 15
Syndecan-2/alpha2 ITGB1 -0.01 0.067 -9999 0 -0.49 7 7
HRAS 0.014 0.038 -9999 0 -0.86 1 1
Syndecan-2/CASK 0 0 -9999 0 -10000 0 0
ITGA5 -0.049 0.23 -9999 0 -0.86 39 39
BAX 0.053 0.028 -9999 0 -10000 0 0
EPB41 0.016 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0 -9999 0 -10000 0 0
LAMA3 0.004 0.1 -9999 0 -0.86 7 7
EZR 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.001 0.11 -9999 0 -0.85 9 9
Syndecan-2/MMP2 -0.007 0.064 -9999 0 -0.56 7 7
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.005 0.054 -9999 0 -0.56 5 5
dendrite morphogenesis -0.01 0.07 -9999 0 -0.49 11 11
Syndecan-2/GM-CSF -0.016 0.095 -9999 0 -0.58 15 15
determination of left/right symmetry 0.027 0 -9999 0 -10000 0 0
Syndecan-2/PKC delta -0.001 0.025 -9999 0 -0.58 1 1
GNB2L1 0.014 0.038 -9999 0 -0.86 1 1
MAPK3 0.022 0.093 -9999 0 -0.52 15 15
MAPK1 0.022 0.093 -9999 0 -0.52 15 15
Syndecan-2/RACK1 -0.002 0.03 -9999 0 -0.5 2 2
NF1 0.016 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.027 0 -9999 0 -10000 0 0
ITGA2 0.009 0.073 -9999 0 -0.74 5 5
MAPK8 0.045 0.031 -9999 0 -0.46 2 2
Syndecan-2/alpha2/beta1 Integrin -0.015 0.08 -9999 0 -0.65 2 2
Syndecan-2/Kininogen -0.35 0.21 -9999 0 -0.48 396 396
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.048 0.031 -9999 0 -0.46 2 2
Syndecan-2/CASK/Protein 4.1 0 0 -9999 0 -10000 0 0
extracellular matrix organization -0.005 0.055 -9999 0 -0.57 5 5
actin cytoskeleton reorganization -0.042 0.15 -9999 0 -0.57 39 39
Syndecan-2/Caveolin-2/Ras -0.01 0.07 -9999 0 -0.51 10 10
Syndecan-2/Laminin alpha3 -0.008 0.066 -9999 0 -0.58 7 7
Syndecan-2/RasGAP -0.003 0.043 -9999 0 -0.67 2 2
alpha5/beta1 Integrin -0.049 0.17 -9999 0 -0.66 39 39
PRKCD 0.014 0.038 -9999 0 -0.86 1 1
Syndecan-2 dimer -0.01 0.07 -9999 0 -0.49 11 11
GO:0007205 0.005 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.002 0.04 -9999 0 -0.83 1 1
RHOA 0.016 0 -9999 0 -10000 0 0
SDCBP 0.016 0 -9999 0 -10000 0 0
TNFRSF13B -0.072 0.26 -9999 0 -0.86 52 52
RASA1 0.014 0.033 -9999 0 -0.74 1 1
alpha2/beta1 Integrin -0.005 0.054 -9999 0 -0.56 5 5
Syndecan-2/Synbindin 0 0 -9999 0 -10000 0 0
TGFB1 0.007 0.085 -9999 0 -0.86 5 5
CASP3 0.043 0.024 -9999 0 -0.52 1 1
FN1 -0.049 0.23 -9999 0 -0.86 39 39
Syndecan-2/IL8 -0.035 0.14 -9999 0 -0.56 34 34
SDC2 0.027 0 -9999 0 -10000 0 0
KNG1 -0.55 0.32 -9999 0 -0.74 396 396
Syndecan-2/Neurofibromin 0 0 -9999 0 -10000 0 0
TRAPPC4 0.016 0 -9999 0 -10000 0 0
CSF2 -0.017 0.14 -9999 0 -0.86 15 15
Syndecan-2/TGFB1 -0.005 0.056 -9999 0 -0.58 5 5
Syndecan-2/Syntenin/PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0 0 -9999 0 -10000 0 0
PRKACA 0.044 0 -9999 0 -10000 0 0
angiogenesis -0.035 0.14 -9999 0 -0.55 34 34
MMP2 0.004 0.098 -9999 0 -0.84 7 7
IL8 -0.039 0.21 -9999 0 -0.84 34 34
calcineurin-NFAT signaling pathway -0.056 0.17 -9999 0 -0.57 52 52
Neurotrophic factor-mediated Trk receptor 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
CRKL 0.016 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.015 0.058 -10000 0 -0.62 1 1
NT3 (dimer)/TRKC -0.04 0.15 -10000 0 -0.6 35 35
NT3 (dimer)/TRKB -0.13 0.24 -10000 0 -0.54 132 132
SHC/Grb2/SOS1/GAB1/PI3K -0.002 0.021 -10000 0 -10000 0 0
RAPGEF1 0.016 0 -10000 0 -10000 0 0
BDNF -0.1 0.3 -10000 0 -0.86 71 71
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
DYNLT1 0.016 0 -10000 0 -10000 0 0
NTRK1 -0.044 0.2 -10000 0 -0.75 41 41
NTRK2 -0.13 0.3 -10000 0 -0.74 100 100
NTRK3 -0.029 0.18 -10000 0 -0.74 31 31
NT-4/5 (dimer)/TRKB -0.13 0.25 -10000 0 -0.55 130 130
neuron apoptosis 0.14 0.18 0.56 51 -10000 0 51
SHC 2-3/Grb2 -0.15 0.2 -10000 0 -0.63 51 51
SHC1 0.014 0.038 -10000 0 -0.86 1 1
SHC2 -0.097 0.14 -10000 0 -0.46 48 48
SHC3 -0.16 0.24 -10000 0 -0.59 101 101
STAT3 (dimer) 0.013 0.067 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.082 0.2 -10000 0 -0.55 79 79
RIN/GDP 0.049 0.064 -10000 0 -0.32 1 1
GIPC1 0.014 0.033 -10000 0 -0.74 1 1
KRAS 0.016 0 -10000 0 -10000 0 0
DNAJA3 -0.069 0.14 -10000 0 -0.63 13 13
RIN/GTP -0.001 0.029 -10000 0 -0.68 1 1
CCND1 0.01 0.16 -10000 0 -0.78 20 20
MAGED1 0.014 0.038 -10000 0 -0.86 1 1
PTPN11 0.016 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.004 0.092 -10000 0 -0.86 6 6
SHC/GRB2/SOS1 -0.001 0.025 -10000 0 -0.57 1 1
GRB2 0.016 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.15 0.27 -10000 0 -0.59 131 131
TRKA/NEDD4-2 -0.044 0.16 -10000 0 -0.57 41 41
ELMO1 0.012 0.054 -10000 0 -0.86 2 2
RhoG/GTP/ELMO1/DOCK1 -0.003 0.041 -10000 0 -0.55 3 3
NGF -0.065 0.25 -10000 0 -0.86 49 49
HRAS 0.014 0.038 -10000 0 -0.86 1 1
DOCK1 0.014 0.033 -10000 0 -0.74 1 1
GAB2 0.016 0 -10000 0 -10000 0 0
RIT2 0.002 0.038 -10000 0 -0.86 1 1
RIT1 0.016 0 -10000 0 -10000 0 0
FRS2 0.016 0 -10000 0 -10000 0 0
DNM1 -0.006 0.14 -10000 0 -0.86 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.068 0.14 -10000 0 -0.59 15 15
mol:GDP 0.063 0.086 -10000 0 -0.48 2 2
NGF (dimer) -0.065 0.25 -10000 0 -0.86 49 49
RhoG/GDP -0.003 0.041 -10000 0 -0.68 2 2
RIT1/GDP 0.055 0.062 -10000 0 -0.31 1 1
TIAM1 0.014 0.033 -10000 0 -0.74 1 1
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
BDNF (dimer)/TRKB -0.16 0.26 -10000 0 -0.55 159 159
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.002 0.037 -10000 0 -0.61 2 2
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 -0.001 0.023 -10000 0 -0.52 1 1
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) 0.005 0.09 -10000 0 -0.78 7 7
RAP1/GDP -0.008 0.031 -10000 0 -10000 0 0
KIDINS220/CRKL 0.016 0 -10000 0 -10000 0 0
BDNF (dimer) -0.1 0.3 -10000 0 -0.86 71 71
ubiquitin-dependent protein catabolic process -0.09 0.2 -10000 0 -0.54 88 88
Schwann cell development -0.026 0.032 -10000 0 -10000 0 0
EHD4 0.016 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 0 -10000 0 -10000 0 0
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.24 -10000 0 -0.81 31 31
ABL1 0.016 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.049 0.078 -10000 0 -10000 0 0
STAT3 0.013 0.067 -10000 0 -10000 0 0
axon guidance -0.14 0.22 -10000 0 -0.76 31 31
MAPK3 -0.098 0.26 -10000 0 -0.58 96 96
MAPK1 -0.098 0.26 -10000 0 -0.58 96 96
CDC42/GDP 0.055 0.062 -10000 0 -0.31 1 1
NTF3 0.005 0.09 -10000 0 -0.78 7 7
NTF4 -0.004 0.092 -10000 0 -0.86 6 6
NGF (dimer)/TRKA/FAIM -0.089 0.2 -10000 0 -0.54 88 88
PI3K -0.002 0.034 -10000 0 -0.56 2 2
FRS3 0.016 0 -10000 0 -10000 0 0
FAIM 0.016 0 -10000 0 -10000 0 0
GAB1 0.016 0 -10000 0 -10000 0 0
RASGRF1 -0.079 0.16 -10000 0 -0.61 24 24
SOS1 0.016 0 -10000 0 -10000 0 0
MCF2L 0.001 0.14 -10000 0 -0.52 35 35
RGS19 0.016 0 -10000 0 -10000 0 0
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP 0.049 0.066 -10000 0 -10000 0 0
Rac1/GDP 0.055 0.062 -10000 0 -10000 0 0
NGF (dimer)/TRKA/GRIT -0.091 0.21 -10000 0 -0.55 88 88
neuron projection morphogenesis -0.021 0.14 -10000 0 -0.54 13 13
NGF (dimer)/TRKA/NEDD4-2 -0.09 0.21 -10000 0 -0.55 88 88
MAP2K1 0.053 0.023 -10000 0 -10000 0 0
NGFR -0.044 0.22 -10000 0 -0.86 36 36
NGF (dimer)/TRKA/GIPC/GAIP -0.055 0.12 -10000 0 -0.62 4 4
RAS family/GTP/PI3K -0.002 0.029 -10000 0 -0.6 1 1
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.016 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.057 -10000 0 -0.74 3 3
MAPKKK cascade -0.094 0.18 -10000 0 -0.55 58 58
RASA1 0.014 0.033 -10000 0 -0.74 1 1
TRKA/c-Abl -0.043 0.15 -10000 0 -0.56 41 41
SQSTM1 0.016 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.15 0.24 -10000 0 -0.59 70 70
NGF (dimer)/TRKA/p62/Atypical PKCs -0.077 0.18 -10000 0 -0.51 52 52
MATK -0.072 0.26 -10000 0 -0.86 53 53
NEDD4L 0.014 0.033 -10000 0 -0.74 1 1
RAS family/GDP -0.008 0.031 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.074 0.15 -10000 0 -0.47 38 38
Rac1/GTP -0.044 0.084 -10000 0 -0.4 8 8
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Endothelins

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
AKT1 0.008 0.22 -10000 0 -0.88 3 3
PTK2B 0.016 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.083 0.13 -10000 0 -0.83 3 3
EDN1 -0.015 0.19 -10000 0 -0.78 18 18
EDN3 -0.018 0.15 -10000 0 -0.86 17 17
EDN2 -0.091 0.28 -10000 0 -0.82 68 68
HRAS/GDP 0.052 0.17 -10000 0 -0.64 12 12
ETA receptor/Endothelin-1/Gq/GTP/PLC beta 0.021 0.16 -10000 0 -0.48 18 18
ADCY4 0.01 0.17 -10000 0 -0.74 3 3
ADCY5 -0.007 0.2 -10000 0 -0.69 14 14
ADCY6 0.009 0.17 -10000 0 -0.74 3 3
ADCY7 -0.005 0.19 -10000 0 -0.72 7 7
ADCY1 -0.001 0.18 -10000 0 -0.74 4 4
ADCY2 -0.12 0.27 -10000 0 -0.7 31 31
ADCY3 0.01 0.17 -10000 0 -0.74 3 3
ADCY8 -0.16 0.28 -10000 0 -0.74 35 35
ADCY9 0.01 0.17 -10000 0 -0.74 3 3
arachidonic acid secretion 0.076 0.15 -10000 0 -0.53 10 10
ETB receptor/Endothelin-1/Gq/GTP 0.034 0.11 -10000 0 -0.46 12 12
GNAO1 0.008 0.082 -10000 0 -0.84 5 5
HRAS 0.014 0.038 -10000 0 -0.86 1 1
ETA receptor/Endothelin-1/G12/GTP -0.013 0.22 0.38 74 -0.82 3 77
ETA receptor/Endothelin-1/Gs/GTP -0.013 0.21 0.36 74 -0.79 3 77
mol:GTP 0.004 0.002 -10000 0 -10000 0 0
COL3A1 -0.042 0.34 -10000 0 -0.95 53 53
EDNRB 0.007 0.068 -10000 0 -0.78 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.043 0.3 -10000 0 -0.75 51 51
CYSLTR1 0.008 0.22 -10000 0 -0.84 4 4
SLC9A1 -0.014 0.11 -10000 0 -0.39 2 2
mol:GDP 0.045 0.18 -10000 0 -0.64 14 14
SLC9A3 -0.35 0.3 -10000 0 -0.66 152 152
RAF1 0.047 0.17 -10000 0 -0.61 14 14
JUN 0.086 0.12 -10000 0 -0.57 1 1
JAK2 0.008 0.22 -10000 0 -0.88 3 3
mol:IP3 0.018 0.17 -10000 0 -0.56 18 18
ETA receptor/Endothelin-1 -0.026 0.27 0.45 74 -0.65 19 93
PLCB1 0.001 0.11 -10000 0 -0.74 11 11
PLCB2 -0.078 0.27 -10000 0 -0.86 58 58
ETA receptor/Endothelin-3 -0.021 0.15 -10000 0 -0.68 19 19
FOS 0.06 0.2 -10000 0 -0.84 16 16
Gai/GDP 0.039 0.069 -10000 0 -0.62 1 1
CRK 0.016 0.001 -10000 0 -10000 0 0
mol:Ca ++ 0.003 0.24 -10000 0 -0.77 16 16
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
PRKCB1 0.019 0.16 -10000 0 -0.54 18 18
GNAQ 0.02 0.004 -10000 0 -10000 0 0
GNAZ 0.011 0.057 -10000 0 -0.74 3 3
GNAL 0.016 0 -10000 0 -10000 0 0
Gs family/GDP -0.044 0.11 -10000 0 -0.59 12 12
ETA receptor/Endothelin-1/Gq/GTP 0.044 0.14 -10000 0 -0.48 11 11
MAPK14 0.024 0.13 -10000 0 -0.56 10 10
TRPC6 0.083 0.14 -10000 0 -0.89 3 3
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.057 -10000 0 -0.74 3 3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta 0.014 0.14 -10000 0 -0.52 15 15
ETB receptor/Endothelin-2 -0.086 0.21 -10000 0 -0.62 71 71
ETB receptor/Endothelin-3 -0.028 0.12 -10000 0 -0.66 20 20
ETB receptor/Endothelin-1 -0.032 0.16 -10000 0 -0.62 19 19
MAPK3 0.06 0.19 -10000 0 -0.72 17 17
MAPK1 0.06 0.19 -10000 0 -0.72 17 17
Rac1/GDP 0.052 0.17 -10000 0 -0.71 8 8
cAMP biosynthetic process -0.061 0.19 -10000 0 -0.6 14 14
MAPK8 0.078 0.13 -10000 0 -0.58 3 3
SRC 0.016 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.03 0.09 -10000 0 -0.57 3 3
p130Cas/CRK/Src/PYK2 0.072 0.17 -10000 0 -0.67 10 10
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP 0.052 0.17 -10000 0 -0.65 10 10
COL1A2 -0.1 0.33 -10000 0 -0.9 65 65
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.081 0.23 -10000 0 -0.63 70 70
mol:DAG 0.018 0.17 -10000 0 -0.56 18 18
MAP2K2 0.057 0.18 -10000 0 -0.66 12 12
MAP2K1 0.058 0.17 -10000 0 -0.66 11 11
EDNRA -0.007 0.14 -10000 0 -0.98 2 2
positive regulation of muscle contraction 0.019 0.19 -10000 0 -0.78 3 3
Gq family/GDP -0.035 0.14 -10000 0 -0.7 16 16
HRAS/GTP 0.036 0.17 -10000 0 -0.63 14 14
PRKCH 0.029 0.16 -10000 0 -0.58 13 13
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.029 0.16 -10000 0 -0.57 14 14
PRKCB 0.024 0.18 -10000 0 -0.67 15 15
PRKCE 0.028 0.16 -10000 0 -0.62 11 11
PRKCD 0.028 0.16 -10000 0 -0.6 12 12
PRKCG 0.003 0.2 -10000 0 -0.63 29 29
regulation of vascular smooth muscle contraction 0.059 0.23 -10000 0 -0.96 16 16
PRKCQ 0.016 0.18 -10000 0 -0.63 19 19
PLA2G4A 0.076 0.16 -10000 0 -0.57 10 10
GNA14 0.008 0.093 -10000 0 -0.74 8 8
GNA15 -0.006 0.14 -10000 0 -0.86 15 15
GNA12 0.016 0 -10000 0 -10000 0 0
GNA11 0.014 0.057 -10000 0 -0.74 3 3
Rac1/GTP -0.013 0.22 0.38 74 -0.82 3 77
MMP1 -0.14 0.37 -10000 0 -0.85 106 106
Wnt signaling

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
Noncanonical Wnts/FZD -0.064 0.13 -9999 0 -0.6 8 8
FZD6 0.016 0 -9999 0 -10000 0 0
WNT6 -0.017 0.17 -9999 0 -0.86 20 20
WNT4 -0.068 0.24 -9999 0 -0.75 58 58
FZD3 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.057 -9999 0 -0.74 3 3
WNT11 -0.04 0.2 -9999 0 -0.76 38 38
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.001 0.017 -9999 0 -10000 0 0
DAPP1 0.03 0.11 -9999 0 -0.54 9 9
Src family/SYK family/BLNK-LAT/BTK-ITK -0.14 0.26 -9999 0 -0.72 57 57
mol:DAG -0.071 0.15 -9999 0 -0.31 78 78
HRAS 0.015 0.038 -9999 0 -0.86 1 1
RAP1A 0.017 0.001 -9999 0 -10000 0 0
ARF5/GDP 0.019 0.073 -9999 0 -10000 0 0
PLCG2 0.003 0.1 -9999 0 -0.82 8 8
PLCG1 0.016 0 -9999 0 -10000 0 0
ARF5 0.016 0 -9999 0 -10000 0 0
mol:GTP -0.001 0.019 -9999 0 -0.43 1 1
ARF1/GTP -0.001 0.017 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.001 0.018 -9999 0 -0.42 1 1
ADAP1 -0.003 0.036 -9999 0 -10000 0 0
ARAP3 -0.001 0.018 -9999 0 -0.42 1 1
INPPL1 0.016 0 -9999 0 -10000 0 0
PREX1 0.016 0 -9999 0 -10000 0 0
ARHGEF6 0.016 0 -9999 0 -10000 0 0
ARHGEF7 0.016 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
NRAS 0.017 0.001 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
FGR 0.011 0.066 -9999 0 -0.86 3 3
mol:Ca2+ -0.023 0.077 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.014 0.033 -9999 0 -0.74 1 1
ZAP70 -0.47 0.44 -9999 0 -0.86 296 296
mol:IP3 -0.037 0.1 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
ARF1/GDP 0.019 0.073 -9999 0 -10000 0 0
RhoA/GDP -0.004 0.017 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.02 -9999 0 -0.47 1 1
BLNK 0.014 0.033 -9999 0 -0.74 1 1
actin cytoskeleton reorganization 0.045 0.081 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PLEKHA2 0.036 0.053 -9999 0 -0.57 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
PTEN 0 0.002 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
ARF6/GTP -0.001 0.017 -9999 0 -10000 0 0
RhoA/GTP -0.001 0.017 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.2 0.24 -9999 0 -0.56 132 132
BLK -0.041 0.21 -9999 0 -0.86 34 34
PDPK1 0.014 0.033 -9999 0 -0.74 1 1
CYTH1 -0.001 0.017 -9999 0 -10000 0 0
HCK -0.032 0.2 -9999 0 -0.86 29 29
CYTH3 -0.001 0.017 -9999 0 -10000 0 0
CYTH2 -0.001 0.017 -9999 0 -10000 0 0
KRAS 0.017 0.001 -9999 0 -10000 0 0
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.001 0.024 -9999 0 -0.54 1 1
SGK1 -0.001 0.026 -9999 0 -0.6 1 1
INPP5D 0.009 0.076 -9999 0 -0.86 4 4
mol:GDP 0.01 0.077 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
SYK 0.013 0.046 -9999 0 -0.74 2 2
ARF6/GDP -0.004 0.016 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.019 -9999 0 -0.43 1 1
ARAP3/RAP1A/GTP -0.001 0.019 -9999 0 -0.43 1 1
VAV1 -0.19 0.37 -9999 0 -0.86 125 125
mol:PI-3-4-P2 0.025 0.06 -9999 0 -0.66 4 4
RAS family/GTP/PI3K Class I -0.001 0.019 -9999 0 -0.44 1 1
PLEKHA1 0.036 0.053 -9999 0 -0.57 4 4
Rac1/GDP 0.019 0.073 -9999 0 -10000 0 0
LAT -0.23 0.39 -9999 0 -0.86 148 148
Rac1/GTP 0 0.1 -9999 0 -10000 0 0
ITK -0.14 0.21 -9999 0 -0.46 165 165
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.11 0.2 -9999 0 -0.46 78 78
LCK -0.02 0.17 -9999 0 -0.85 22 22
BTK -0.095 0.18 -9999 0 -0.46 110 110
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.014 0.034 -10000 0 -0.73 1 1
HSPA8 0.016 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.02 0.089 -10000 0 -0.52 4 4
AKT1 0.02 0.007 -10000 0 -10000 0 0
GSC -0.027 0.22 -10000 0 -0.76 44 44
NKX2-5 -0.046 0.21 -10000 0 -0.86 34 34
muscle cell differentiation 0.034 0.11 0.58 9 -10000 0 9
SMAD2-3/SMAD4/SP1 0.043 0.08 -10000 0 -10000 0 0
SMAD4 0.032 0.03 -10000 0 -10000 0 0
CBFB 0.016 0 -10000 0 -10000 0 0
SAP18 0.015 0.004 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.003 0.046 -10000 0 -0.57 2 2
SMAD3/SMAD4/VDR 0.01 0.05 -10000 0 -10000 0 0
MYC -0.033 0.17 -10000 0 -0.86 21 21
CDKN2B 0.055 0.092 -10000 0 -0.68 6 6
AP1 0.064 0.073 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.012 0.049 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.051 0.069 -10000 0 -0.53 1 1
SP3 0.02 0 -10000 0 -10000 0 0
CREB1 0.016 0 -10000 0 -10000 0 0
FOXH1 -0.061 0.25 -10000 0 -0.88 46 46
SMAD3/SMAD4/GR 0.01 0.044 -10000 0 -0.6 1 1
GATA3 -0.36 0.38 -10000 0 -0.74 264 264
SKI/SIN3/HDAC complex/NCoR1 0.054 0.044 -10000 0 -10000 0 0
MEF2C/TIF2 -0.076 0.2 -10000 0 -0.88 16 16
endothelial cell migration 0.096 0.26 0.73 76 -10000 0 76
MAX 0.019 0.016 -10000 0 -10000 0 0
RBBP7 0.015 0.004 -10000 0 -10000 0 0
RBBP4 0.014 0.033 -10000 0 -0.74 1 1
RUNX2 -0.007 0.14 -10000 0 -0.86 14 14
RUNX3 -0.36 0.44 -10000 0 -0.86 229 229
RUNX1 -0.047 0.23 -10000 0 -0.86 38 38
CTBP1 0.016 0 -10000 0 -10000 0 0
NR3C1 0.017 0.042 -10000 0 -0.87 1 1
VDR 0.011 0.057 -10000 0 -0.74 3 3
CDKN1A 0.083 0.074 -10000 0 -0.64 2 2
KAT2B 0.013 0.033 -10000 0 -0.74 1 1
SMAD2/SMAD2/SMAD4/FOXH1 -0.054 0.18 -10000 0 -0.61 46 46
DCP1A 0.016 0 -10000 0 -10000 0 0
SKI 0.015 0.004 -10000 0 -10000 0 0
SERPINE1 -0.098 0.26 -10000 0 -0.74 76 76
SMAD3/SMAD4/ATF2 0.007 0.037 -10000 0 -0.48 1 1
SMAD3/SMAD4/ATF3 0.004 0.057 -10000 0 -0.48 5 5
SAP30 -0.016 0.16 -10000 0 -0.86 19 19
Cbp/p300/PIAS3 0.007 0.035 -10000 0 -10000 0 0
JUN 0.075 0.071 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 -0.012 0.11 -10000 0 -0.56 18 18
TFE3 0.021 0.012 -10000 0 -10000 0 0
COL1A2 -0.092 0.25 -10000 0 -0.75 67 67
mesenchymal cell differentiation 0.007 0.1 0.59 14 -10000 0 14
DLX1 -0.45 0.44 -10000 0 -0.86 284 284
TCF3 0.016 0 -10000 0 -10000 0 0
FOS 0.007 0.12 -10000 0 -0.74 13 13
SMAD3/SMAD4/Max 0.011 0.035 -10000 0 -10000 0 0
Cbp/p300/SNIP1 -0.001 0.02 -10000 0 -0.46 1 1
ZBTB17 -0.001 0.044 -10000 0 -0.71 2 2
LAMC1 0.071 0.042 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.008 0.031 -10000 0 -10000 0 0
IRF7 -0.013 0.16 -10000 0 -0.85 19 19
ESR1 0.001 0.077 -10000 0 -0.76 5 5
HNF4A -0.047 0.21 -10000 0 -0.74 44 44
MEF2C -0.007 0.22 -10000 0 -0.8 20 20
SMAD2-3/SMAD4 0.005 0.031 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.005 0.028 -10000 0 -10000 0 0
IGHV3OR16-13 -0.05 0.054 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.016 0 -10000 0 -10000 0 0
CREBBP 0.015 0.008 -10000 0 -10000 0 0
SKIL 0.016 0 -10000 0 -10000 0 0
HDAC1 0.015 0.004 -10000 0 -10000 0 0
HDAC2 0.015 0.004 -10000 0 -10000 0 0
SNIP1 0.015 0.005 -10000 0 -10000 0 0
GCN5L2 -0.002 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.01 0.036 -10000 0 -10000 0 0
MSG1/HSC70 0.002 0.043 -10000 0 -0.67 2 2
SMAD2 0.022 0.019 -10000 0 -10000 0 0
SMAD3 0.032 0.027 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.062 0.033 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.024 0.032 -10000 0 -0.52 1 1
NCOR1 0.015 0.004 -10000 0 -10000 0 0
NCOA2 0 0.11 -10000 0 -0.74 11 11
NCOA1 0.016 0 -10000 0 -10000 0 0
MYOD/E2A -0.036 0.15 -10000 0 -0.66 29 29
SMAD2-3/SMAD4/SP1/MIZ-1 0.077 0.084 -10000 0 -10000 0 0
IFNB1 0.045 0.11 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.009 0.21 -10000 0 -0.9 11 11
CITED1 0.011 0.054 -10000 0 -0.86 2 2
SMAD2-3/SMAD4/ARC105 0.007 0.03 -10000 0 -10000 0 0
RBL1 0.016 0.001 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.076 0.067 -10000 0 -0.58 1 1
RUNX1-3/PEBPB2 -0.29 0.32 -10000 0 -0.61 251 251
SMAD7 0.1 0.079 -10000 0 -10000 0 0
MYC/MIZ-1 -0.027 0.13 -10000 0 -0.65 23 23
SMAD3/SMAD4 -0.021 0.12 -10000 0 -10000 0 0
IL10 -0.2 0.31 -10000 0 -0.98 32 32
PIASy/HDAC complex 0.018 0.01 -10000 0 -10000 0 0
PIAS3 0.014 0.006 -10000 0 -10000 0 0
CDK2 0.015 0.008 -10000 0 -10000 0 0
IL5 -0.17 0.25 -10000 0 -0.75 15 15
CDK4 0.015 0.009 -10000 0 -10000 0 0
PIAS4 0.018 0.009 -10000 0 -10000 0 0
ATF3 0.009 0.073 -10000 0 -0.74 5 5
SMAD3/SMAD4/SP1 -0.012 0.053 -10000 0 -10000 0 0
FOXG1 -0.025 0.17 -10000 0 -0.86 20 20
FOXO3 0.036 0.01 -10000 0 -10000 0 0
FOXO1 0.036 0.009 -10000 0 -10000 0 0
FOXO4 0.036 0.009 -10000 0 -10000 0 0
heart looping -0.007 0.22 -10000 0 -0.79 20 20
CEBPB -0.002 0.13 -10000 0 -0.86 12 12
SMAD3/SMAD4/DLX1 -0.31 0.3 -10000 0 -0.58 284 284
MYOD1 -0.041 0.2 -10000 0 -0.86 29 29
SMAD3/SMAD4/HNF4 -0.033 0.14 -10000 0 -0.51 28 28
SMAD3/SMAD4/GATA3 -0.23 0.25 -10000 0 -0.8 17 17
SnoN/SIN3/HDAC complex/NCoR1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.23 0.28 -10000 0 -0.79 32 32
SMAD3/SMAD4/SP1-3 -0.005 0.043 -10000 0 -10000 0 0
MED15 0.016 0 -10000 0 -10000 0 0
SP1 0.013 0.049 -10000 0 -10000 0 0
SIN3B 0.015 0.004 -10000 0 -10000 0 0
SIN3A 0.015 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.078 0.22 -10000 0 -0.83 25 25
ITGB5 0.085 0.064 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.053 0.043 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.015 0.11 -10000 0 -0.5 22 22
AR -0.021 0.16 -10000 0 -0.74 26 26
negative regulation of cell growth 0.065 0.066 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.024 0.14 -10000 0 -0.6 29 29
E2F5 0.014 0.033 -10000 0 -0.74 1 1
E2F4 0.016 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.043 0.15 -10000 0 -0.67 13 13
SMAD2-3/SMAD4/FOXO1-3a-4 0.076 0.045 -10000 0 -10000 0 0
TFDP1 0.016 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.008 0.067 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 -0.007 0.1 -10000 0 -0.59 14 14
TGIF2 0.016 0 -10000 0 -10000 0 0
TGIF1 0.016 0 -10000 0 -10000 0 0
ATF2 0.014 0.033 -10000 0 -0.74 1 1
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.001 0.028 -10000 0 -0.66 1 1
HDAC1 0.003 0.011 -10000 0 -10000 0 0
AES 0.005 0.008 -10000 0 -10000 0 0
FBXW11 0.016 0 -10000 0 -10000 0 0
DTX1 -0.053 0.22 -10000 0 -0.74 48 48
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.015 0.002 -10000 0 -10000 0 0
AP1 -0.096 0.16 -10000 0 -0.34 151 151
NCSTN 0.016 0 -10000 0 -10000 0 0
ADAM10 0.014 0.033 -10000 0 -0.74 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.011 0.067 -10000 0 -0.45 1 1
NICD/RBPSUH -0.001 0.027 -10000 0 -0.64 1 1
WIF1 0.001 0.075 -10000 0 -0.76 5 5
NOTCH1 -0.001 0.029 -10000 0 -0.68 1 1
PSENEN 0.016 0 -10000 0 -10000 0 0
KREMEN2 -0.091 0.28 -10000 0 -0.86 64 64
DKK1 -0.019 0.17 -10000 0 -0.82 22 22
beta catenin/beta TrCP1 0.084 0.084 -10000 0 -10000 0 0
APH1B 0.016 0 -10000 0 -10000 0 0
APH1A 0.016 0 -10000 0 -10000 0 0
AXIN1 -0.011 0.035 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.008 0.048 -10000 0 -10000 0 0
PSEN1 0.016 0 -10000 0 -10000 0 0
FOS -0.003 0.12 -10000 0 -0.75 13 13
JUN 0.016 0 -10000 0 -10000 0 0
MAP3K7 0.002 0.008 -10000 0 -10000 0 0
CTNNB1 0.08 0.091 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.095 0.22 -10000 0 -0.57 89 89
HNF1A -0.002 0.072 -10000 0 -0.74 5 5
CTBP1 0.005 0.008 -10000 0 -10000 0 0
MYC 0.002 0.15 -10000 0 -0.73 21 21
NKD1 -0.19 0.34 -10000 0 -0.74 142 142
FZD1 0.016 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.036 0.11 -10000 0 -0.64 1 1
apoptosis -0.096 0.16 -10000 0 -0.34 151 151
Delta 1/NOTCHprecursor -0.001 0.027 -10000 0 -0.64 1 1
DLL1 0.016 0 -10000 0 -10000 0 0
PPARD 0.029 0.023 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC -0.011 0.035 -10000 0 -10000 0 0
DVL1 -0.005 0.032 -10000 0 -0.47 2 2
CSNK2A1 0.015 0.004 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.004 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.091 0.22 -10000 0 -0.61 79 79
LRP6 0.016 0 -10000 0 -10000 0 0
CSNK1A1 0.015 0.004 -10000 0 -10000 0 0
NLK 0.015 0.013 -10000 0 -10000 0 0
CCND1 0.003 0.15 -10000 0 -0.73 20 20
WNT1 -0.026 0.18 -10000 0 -0.86 25 25
Axin1/APC/beta catenin 0.081 0.052 -10000 0 -10000 0 0
DKK2 -0.026 0.18 -10000 0 -0.82 26 26
NOTCH1 precursor/DVL1 -0.003 0.033 -10000 0 -0.58 1 1
GSK3B 0.012 0.007 -10000 0 -10000 0 0
FRAT1 0.012 0.007 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.036 0.11 -10000 0 -0.66 1 1
PPP2R5D 0.092 0.16 0.35 141 -10000 0 141
MAPK1 0.016 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.029 0.12 -10000 0 -0.52 26 26
RBPJ 0.016 0 -10000 0 -10000 0 0
CREBBP 0.019 0.006 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.002 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.04 0.044 -9999 0 -10000 0 0
GNAO1 0.01 0.082 -9999 0 -0.84 5 5
S1P/S1P3/G12/G13 -0.001 0.019 -9999 0 -0.43 1 1
AKT1 -0.002 0.012 -9999 0 -10000 0 0
AKT3 -0.025 0.1 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
GNAI2 0.018 0 -9999 0 -10000 0 0
GNAI3 0.018 0 -9999 0 -10000 0 0
GNAI1 0.013 0.057 -9999 0 -0.74 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.017 0.033 -9999 0 -0.74 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.054 0.048 -9999 0 -0.53 1 1
MAPK3 0.062 0.046 -9999 0 -0.5 1 1
MAPK1 0.062 0.046 -9999 0 -0.5 1 1
JAK2 -0.024 0.13 -9999 0 -0.48 2 2
CXCR4 -0.12 0.26 -9999 0 -0.47 187 187
FLT1 0.011 0.085 -9999 0 -0.86 5 5
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.062 0.046 -9999 0 -0.5 1 1
S1P/S1P3/Gi 0.054 0.049 -9999 0 -0.54 1 1
RAC1 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.005 0.035 -9999 0 -0.49 1 1
VEGFA -0.37 0.44 -9999 0 -0.86 239 239
S1P/S1P2/Gi 0.049 0.043 -9999 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer -0.28 0.35 -9999 0 -0.67 240 240
RHOA 0.016 0 -9999 0 -10000 0 0
S1P/S1P3/Gq 0.027 0.075 -9999 0 -0.6 1 1
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.013 0.057 -9999 0 -0.74 3 3
G12/G13 0 0 -9999 0 -10000 0 0
GNA14 0.004 0.092 -9999 0 -0.74 8 8
GNA15 -0.009 0.14 -9999 0 -0.86 15 15
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.011 0.057 -9999 0 -0.74 3 3
Rac1/GTP -0.005 0.035 -9999 0 -0.49 1 1
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.004 0.12 -10000 0 -0.86 11 11
GNB1/GNG2 -0.034 0.063 -10000 0 -0.22 14 14
AKT1 0.055 0.1 -10000 0 -0.25 1 1
EGF -0.67 0.23 -10000 0 -0.74 480 480
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.032 0.08 -10000 0 -0.61 2 2
mol:Ca2+ 0.042 0.14 -10000 0 -0.33 28 28
LYN -0.029 0.071 -10000 0 -10000 0 0
RhoA/GTP -0.017 0.037 -10000 0 -0.19 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK 0.051 0.15 -10000 0 -0.37 25 25
GNG2 0.016 0 -10000 0 -10000 0 0
ARRB2 0.014 0.038 -10000 0 -0.86 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 0.029 0.079 -10000 0 -0.42 8 8
G beta5/gamma2 -0.044 0.083 -10000 0 -0.3 16 16
PRKCH 0.043 0.15 -10000 0 -0.39 21 21
DNM1 -0.006 0.14 -10000 0 -0.86 13 13
TXA2/TP beta/beta Arrestin3 -0.014 0.045 -10000 0 -0.27 13 13
mol:GTP 0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.11 0.31 -10000 0 -0.86 77 77
G12 family/GTP -0.042 0.091 -10000 0 -0.32 25 25
ADRBK1 0.016 0 -10000 0 -10000 0 0
ADRBK2 0.016 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP -0.031 0.11 0.31 12 -10000 0 12
mol:NADP 0.016 0 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
PRKG1 -0.006 0.12 -10000 0 -0.74 15 15
mol:IP3 0.038 0.17 -10000 0 -0.42 28 28
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 0.029 0.22 -10000 0 -0.58 28 28
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.054 0.13 -10000 0 -0.6 15 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.051 0.12 -10000 0 -0.6 9 9
RHOA 0.016 0 -10000 0 -10000 0 0
PTGIR 0.013 0.05 -10000 0 -0.8 2 2
PRKCB1 0.038 0.16 -10000 0 -0.38 42 42
GNAQ 0.016 0 -10000 0 -10000 0 0
mol:L-citrulline 0.016 0 -10000 0 -10000 0 0
TXA2/TXA2-R family 0.037 0.21 -10000 0 -0.53 44 44
LCK -0.045 0.12 -10000 0 -0.6 13 13
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.04 0.096 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma 0.028 0.036 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.04 0.095 -10000 0 -10000 0 0
MAPK14 0.055 0.11 -10000 0 -0.31 1 1
TGM2/GTP 0.037 0.19 -10000 0 -0.48 30 30
MAPK11 0.054 0.11 -10000 0 -0.35 3 3
ARHGEF1 0.042 0.088 -10000 0 -0.32 1 1
GNAI2 0.016 0 -10000 0 -10000 0 0
JNK cascade 0.045 0.17 -10000 0 -0.39 44 44
RAB11/GDP 0.015 0.002 -10000 0 -10000 0 0
ICAM1 0.045 0.13 -10000 0 -0.35 20 20
cAMP biosynthetic process 0.035 0.16 -10000 0 -0.38 32 32
Gq family/GTP/EBP50 0.025 0.062 -10000 0 -0.34 3 3
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.029 0.071 -10000 0 -10000 0 0
GNB5 0.016 0 -10000 0 -10000 0 0
GNB1 0.016 0 -10000 0 -10000 0 0
EGF/EGFR -0.085 0.1 -10000 0 -0.41 15 15
VCAM1 0.044 0.14 -10000 0 -0.34 26 26
TP beta/Gq family/GDP/G beta5/gamma2 0.029 0.079 -10000 0 -0.42 8 8
platelet activation 0.067 0.15 -10000 0 -0.34 15 15
PGI2/IP -0.002 0.038 -10000 0 -0.62 2 2
PRKACA -0.051 0.12 -10000 0 -0.34 79 79
Gq family/GDP/G beta5/gamma2 0.024 0.079 -10000 0 -0.41 8 8
TXA2/TP beta/beta Arrestin2 -0.015 0.065 -10000 0 -0.4 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.013 0.12 -10000 0 -10000 0 0
mol:DAG 0.038 0.18 -10000 0 -0.44 42 42
EGFR 0.001 0.11 -10000 0 -0.85 9 9
TXA2/TP alpha 0.034 0.21 -10000 0 -0.54 32 32
Gq family/GTP -0.006 0.055 -10000 0 -0.29 8 8
YES1 -0.029 0.071 -10000 0 -10000 0 0
GNAI2/GTP -0.034 0.082 -10000 0 -10000 0 0
PGD2/DP -0.098 0.24 -10000 0 -0.68 77 77
SLC9A3R1 0.016 0 -10000 0 -10000 0 0
FYN -0.029 0.071 -10000 0 -10000 0 0
mol:NO 0.016 0 -10000 0 -10000 0 0
GNA15 -0.009 0.14 -10000 0 -0.86 15 15
PGK/cGMP -0.014 0.08 -10000 0 -0.48 15 15
RhoA/GDP 0.015 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.046 0.11 -10000 0 -0.71 1 1
NOS3 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
PRKCA 0.043 0.15 -10000 0 -0.39 21 21
PRKCB 0.041 0.16 -10000 0 -0.43 22 22
PRKCE 0.044 0.16 -10000 0 -0.41 19 19
PRKCD 0.042 0.16 -10000 0 -0.41 22 22
PRKCG 0.03 0.18 -10000 0 -0.49 33 33
muscle contraction 0.043 0.2 -10000 0 -0.49 44 44
PRKCZ 0.05 0.15 -10000 0 -0.37 27 27
ARR3 0.004 0.007 -10000 0 -10000 0 0
TXA2/TP beta -0.039 0.093 -10000 0 -10000 0 0
PRKCQ 0.036 0.16 -10000 0 -0.43 23 23
MAPKKK cascade 0.036 0.19 -10000 0 -0.49 29 29
SELE 0.038 0.15 -10000 0 -0.42 38 38
TP beta/GNAI2/GDP/G beta/gamma -0.037 0.09 -10000 0 -10000 0 0
ROCK1 0.016 0 -10000 0 -10000 0 0
GNA14 0.004 0.092 -10000 0 -0.74 8 8
chemotaxis 0.037 0.23 -10000 0 -0.61 43 43
GNA12 0.016 0 -10000 0 -10000 0 0
GNA13 0.016 0 -10000 0 -10000 0 0
GNA11 0.011 0.057 -10000 0 -0.74 3 3
Rac1/GTP 0 0 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.025 0.095 -9999 0 -0.52 16 16
CRKL 0.016 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.014 0.033 -9999 0 -0.74 1 1
ITGA4 -0.011 0.15 -9999 0 -0.86 16 16
alpha4/beta7 Integrin/MAdCAM1 -0.027 0.12 -9999 0 -0.52 28 28
EPO -0.29 0.42 -9999 0 -0.86 187 187
alpha4/beta7 Integrin -0.02 0.11 -9999 0 -0.66 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.02 0.11 -9999 0 -0.66 16 16
EPO/EPOR (dimer) -0.23 0.32 -9999 0 -0.66 187 187
lamellipodium assembly 0 0.035 -9999 0 -0.53 2 2
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
PI3K -0.002 0.034 -9999 0 -0.56 2 2
ARF6 0.016 0 -9999 0 -10000 0 0
JAK2 -0.12 0.17 -9999 0 -0.66 6 6
PXN 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
MADCAM1 -0.007 0.13 -9999 0 -0.86 12 12
cell adhesion -0.027 0.12 -9999 0 -0.52 28 28
CRKL/CBL -0.001 0.024 -9999 0 -0.56 1 1
ITGB1 0.016 0 -9999 0 -10000 0 0
SRC 0.015 0.13 -9999 0 -0.52 25 25
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.031 0.13 -9999 0 -0.56 30 30
p130Cas/Crk/Dock1 -0.024 0.1 -9999 0 -0.8 1 1
VCAM1 -0.006 0.13 -9999 0 -0.82 14 14
RHOA 0.016 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.016 0.089 -9999 0 -0.52 16 16
BCAR1 0.026 0.12 -9999 0 -0.89 1 1
EPOR 0.016 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0.033 -9999 0 -0.74 1 1
GIT1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.036 -9999 0 -0.55 2 2
LPA receptor mediated events

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
GNB1/GNG2 -0.021 0.088 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.038 -9999 0 -10000 0 0
AP1 -0.03 0.1 -9999 0 -0.52 2 2
mol:PIP3 -0.026 0.091 -9999 0 -0.54 1 1
AKT1 -0.014 0.058 -9999 0 -10000 0 0
PTK2B 0.032 0.059 -9999 0 -0.28 1 1
RHOA 0.036 0.037 -9999 0 -10000 0 0
PIK3CB 0.015 0 -9999 0 -10000 0 0
mol:Ca2+ 0.05 0.052 -9999 0 -0.45 2 2
MAGI3 0.011 0.057 -9999 0 -0.74 3 3
RELA 0.016 0 -9999 0 -10000 0 0
apoptosis -0.022 0.085 -9999 0 -0.37 27 27
HRAS/GDP -0.001 0.029 -9999 0 -0.68 1 1
positive regulation of microtubule depolymerization 0.046 0.069 -9999 0 -0.41 1 1
NF kappa B1 p50/RelA -0.019 0.073 -9999 0 -10000 0 0
endothelial cell migration 0.005 0.14 -9999 0 -0.54 30 30
ADCY4 0.031 0.12 -9999 0 -0.47 25 25
ADCY5 0.022 0.13 -9999 0 -0.49 28 28
ADCY6 0.031 0.12 -9999 0 -0.47 25 25
ADCY7 0.026 0.12 -9999 0 -0.48 25 25
ADCY1 0.026 0.13 -9999 0 -0.48 26 26
ADCY2 -0.019 0.14 -9999 0 -0.51 26 26
ADCY3 0.031 0.12 -9999 0 -0.47 25 25
ADCY8 -0.027 0.14 -9999 0 -0.48 25 25
ADCY9 0.031 0.12 -9999 0 -0.47 25 25
GSK3B 0.042 0.057 -9999 0 -10000 0 0
arachidonic acid secretion 0.038 0.11 -9999 0 -0.44 23 23
GNG2 0.015 0 -9999 0 -10000 0 0
TRIP6 0.001 0.008 -9999 0 -10000 0 0
GNAO1 0.007 0.12 -9999 0 -0.48 28 28
HRAS 0.014 0.038 -9999 0 -0.86 1 1
NFKBIA 0.06 0.062 -9999 0 -10000 0 0
GAB1 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.001 0.053 -9999 0 -0.86 2 2
JUN 0.016 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.002 0.023 -9999 0 -0.48 1 1
TIAM1 -0.002 0.062 -9999 0 -1 2 2
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
mol:IP3 0.05 0.053 -9999 0 -0.46 2 2
PLCB3 0.037 0.023 -9999 0 -0.43 1 1
FOS -0.003 0.12 -9999 0 -0.75 13 13
positive regulation of mitosis 0.038 0.11 -9999 0 -0.44 23 23
LPA/LPA1-2-3 -0.025 0.1 -9999 0 -0.44 27 27
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.033 -9999 0 -0.74 1 1
stress fiber formation 0.039 0.076 -9999 0 -10000 0 0
GNAZ 0.009 0.12 -9999 0 -0.48 26 26
EGFR/PI3K-beta/Gab1 -0.027 0.094 -9999 0 -0.57 1 1
positive regulation of dendritic cell cytokine production -0.025 0.099 -9999 0 -0.44 27 27
LPA/LPA2/MAGI-3 -0.004 0.037 -9999 0 -0.48 3 3
ARHGEF1 0.03 0.095 -9999 0 -0.49 1 1
GNAI2 0.012 0.11 -9999 0 -0.46 23 23
GNAI3 0.012 0.11 -9999 0 -0.46 23 23
GNAI1 0.009 0.12 -9999 0 -0.48 26 26
LPA/LPA3 -0.007 0.06 -9999 0 -0.67 4 4
LPA/LPA2 -0.002 0.014 -9999 0 -10000 0 0
LPA/LPA1 -0.028 0.12 -9999 0 -0.5 30 30
HB-EGF/EGFR -0.28 0.29 -9999 0 -0.58 257 257
HBEGF -0.3 0.35 -9999 0 -0.66 251 251
mol:DAG 0.05 0.053 -9999 0 -0.46 2 2
cAMP biosynthetic process 0.019 0.12 -9999 0 -0.46 25 25
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
SRC 0.016 0 -9999 0 -10000 0 0
GNB1 0.015 0 -9999 0 -10000 0 0
LYN 0.06 0.062 -9999 0 -10000 0 0
GNAQ -0.004 0.035 -9999 0 -0.4 4 4
LPAR2 0.016 0 -9999 0 -10000 0 0
LPAR3 0.003 0.076 -9999 0 -0.86 4 4
LPAR1 -0.013 0.15 -9999 0 -0.73 23 23
IL8 -0.078 0.2 -9999 0 -0.49 44 44
PTK2 0.024 0.1 -9999 0 -0.48 4 4
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.022 0.085 -9999 0 -0.37 27 27
EGFR 0 0.11 -9999 0 -0.85 9 9
PLCG1 0.019 0.055 -9999 0 -0.38 5 5
PLD2 0.024 0.1 -9999 0 -0.48 4 4
G12/G13 -0.021 0.088 -9999 0 -0.42 23 23
PI3K-beta -0.016 0.067 -9999 0 -10000 0 0
cell migration -0.009 0.034 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.033 -9999 0 -0.74 1 1
PXN 0.039 0.077 -9999 0 -10000 0 0
HRAS/GTP -0.026 0.098 -9999 0 -0.45 23 23
RAC1 0.016 0 -9999 0 -10000 0 0
MMP9 -0.4 0.44 -9999 0 -0.86 251 251
PRKCE 0.013 0.033 -9999 0 -0.74 1 1
PRKCD 0.058 0.055 -9999 0 -0.45 1 1
Gi(beta/gamma) -0.026 0.097 -9999 0 -0.44 25 25
mol:LPA 0.003 0.025 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.018 0.08 -9999 0 -10000 0 0
MAPKKK cascade 0.038 0.11 -9999 0 -0.44 23 23
contractile ring contraction involved in cytokinesis 0.036 0.037 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.01 0.06 -9999 0 -0.4 12 12
GNA15 -0.015 0.078 -9999 0 -0.42 18 18
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
MAPT 0.046 0.07 -9999 0 -0.42 1 1
GNA11 -0.006 0.045 -9999 0 -0.39 7 7
Rac1/GTP -0.002 0.056 -9999 0 -0.91 2 2
MMP2 0.005 0.14 -9999 0 -0.54 30 30
Sphingosine 1-phosphate (S1P) pathway

Figure S66.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S66.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0.046 -9999 0 -0.74 2 2
SPHK1 -0.058 0.24 -9999 0 -0.86 45 45
GNAI2 0.016 0 -9999 0 -10000 0 0
mol:S1P 0.001 0.095 -9999 0 -0.31 47 47
GNAO1 0.008 0.082 -9999 0 -0.84 5 5
mol:Sphinganine-1-P -0.03 0.2 -9999 0 -0.66 47 47
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.017 0.056 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0.014 0.033 -9999 0 -0.74 1 1
S1PR2 0.016 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.023 0.075 -9999 0 -0.29 2 2
S1PR5 -0.14 0.33 -9999 0 -0.86 93 93
S1PR4 -0.034 0.2 -9999 0 -0.86 30 30
GNAI1 0.011 0.057 -9999 0 -0.74 3 3
S1P/S1P5/G12 -0.11 0.21 -9999 0 -0.54 93 93
S1P/S1P3/Gq 0.023 0.1 -9999 0 -0.44 16 16
S1P/S1P4/Gi 0.022 0.098 -9999 0 -0.38 13 13
GNAQ 0.016 0 -9999 0 -10000 0 0
GNAZ 0.011 0.057 -9999 0 -0.74 3 3
GNA14 0.004 0.092 -9999 0 -0.74 8 8
GNA15 -0.009 0.14 -9999 0 -0.86 15 15
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
GNA11 0.011 0.057 -9999 0 -0.74 3 3
ABCC1 0.016 0 -9999 0 -10000 0 0
Ceramide signaling pathway

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
SPHK2 0.027 0.044 -10000 0 -0.56 3 3
MAP4K4 0.026 0.093 -10000 0 -0.48 1 1
BAG4 0.014 0.033 -10000 0 -0.74 1 1
PKC zeta/ceramide -0.098 0.046 -10000 0 -0.48 3 3
NFKBIA 0.016 0 -10000 0 -10000 0 0
BIRC3 -0.12 0.31 -10000 0 -0.86 80 80
BAX -0.042 0.018 -10000 0 -10000 0 0
RIPK1 0.016 0 -10000 0 -10000 0 0
AKT1 0.046 0.008 -10000 0 -10000 0 0
BAD -0.098 0.043 -10000 0 -0.45 2 2
SMPD1 0.027 0.041 -10000 0 -0.28 1 1
RB1 -0.096 0.037 -10000 0 -10000 0 0
FADD/Caspase 8 0.04 0.087 -10000 0 -10000 0 0
MAP2K4 -0.08 0.035 -10000 0 -10000 0 0
NSMAF 0.016 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.084 0.056 -10000 0 -0.59 4 4
EGF -0.67 0.23 -10000 0 -0.74 480 480
mol:ceramide -0.11 0.039 0.2 2 -10000 0 2
MADD 0.016 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.03 0.025 -10000 0 -0.56 1 1
ASAH1 0.016 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.095 0.037 -10000 0 -10000 0 0
cell proliferation -0.052 0.059 -10000 0 -0.46 10 10
BID -0.011 0.065 -10000 0 -0.34 1 1
MAP3K1 -0.096 0.037 -10000 0 -10000 0 0
EIF2A -0.067 0.034 -10000 0 -10000 0 0
TRADD 0.016 0 -10000 0 -10000 0 0
CRADD 0.016 0 -10000 0 -10000 0 0
MAPK3 -0.065 0.052 -10000 0 -0.54 4 4
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.065 0.052 -10000 0 -0.54 4 4
Cathepsin D/ceramide -0.097 0.035 -10000 0 -0.26 1 1
FADD 0.026 0.093 -10000 0 -0.48 1 1
KSR1 -0.1 0.059 -10000 0 -0.63 4 4
MAPK8 -0.076 0.041 -10000 0 -0.35 4 4
PRKRA -0.096 0.037 -10000 0 -10000 0 0
PDGFA 0.014 0.033 -10000 0 -0.74 1 1
TRAF2 0.016 0 -10000 0 -10000 0 0
IGF1 0.006 0.093 -10000 0 -0.86 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.039 0.2 2 -10000 0 2
CTSD 0.014 0.033 -10000 0 -0.74 1 1
regulation of nitric oxide biosynthetic process -0.001 0.024 -10000 0 -0.55 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.055 0.065 -10000 0 -0.5 10 10
PRKCD 0.014 0.038 -10000 0 -0.86 1 1
PRKCZ 0.011 0.057 -10000 0 -0.74 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.03 0.025 -10000 0 -0.56 1 1
RelA/NF kappa B1 -0.001 0.024 -10000 0 -0.56 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0.033 -10000 0 -0.74 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.033 0.077 -10000 0 -0.51 1 1
TNFR1A/BAG4/TNF-alpha -0.009 0.067 -10000 0 -0.52 9 9
mol:Sphingosine-1-phosphate 0.027 0.044 -10000 0 -0.56 3 3
MAP2K1 -0.07 0.054 -10000 0 -0.55 4 4
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.016 0 -10000 0 -10000 0 0
CYCS -0.063 0.023 -10000 0 -0.23 1 1
TNFRSF1A 0.016 0 -10000 0 -10000 0 0
NFKB1 0.014 0.033 -10000 0 -0.74 1 1
TNFR1A/BAG4 -0.001 0.024 -10000 0 -0.56 1 1
EIF2AK2 -0.08 0.035 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.008 0.064 -10000 0 -0.52 8 8
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.016 0.037 -10000 0 -10000 0 0
MAP2K2 -0.071 0.053 -10000 0 -0.55 4 4
SMPD3 0.026 0.051 -10000 0 -0.33 2 2
TNF 0.003 0.1 -10000 0 -0.8 8 8
PKC zeta/PAR4 -0.004 0.048 -10000 0 -0.56 4 4
mol:PHOSPHOCHOLINE 0.23 0.083 0.26 482 -10000 0 482
NF kappa B1/RelA/I kappa B alpha -0.004 0.038 -10000 0 -10000 0 0
AIFM1 -0.063 0.025 -10000 0 -0.23 1 1
BCL2 0.016 0 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC -0.57 0.68 -9999 0 -1.3 250 250
PLK1 -0.12 0.37 -9999 0 -0.8 93 93
CDKN1B 0.062 0.16 -9999 0 -10000 0 0
FOXO3 -0.035 0.23 -9999 0 -0.66 14 14
KAT2B 0.012 0.04 -9999 0 -0.78 1 1
FOXO1/SIRT1 -0.14 0.21 -9999 0 -10000 0 0
CAT -0.024 0.22 -9999 0 -0.89 7 7
CTNNB1 0.016 0 -9999 0 -10000 0 0
AKT1 -0.007 0.038 -9999 0 -10000 0 0
FOXO1 -0.16 0.23 -9999 0 -0.41 250 250
MAPK10 0.033 0.049 -9999 0 -0.43 5 5
mol:GTP 0.003 0.001 -9999 0 -10000 0 0
FOXO4 0.11 0.048 -9999 0 -10000 0 0
response to oxidative stress -0.028 0.045 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.029 0.2 -9999 0 -0.62 7 7
XPO1 0.017 0 -9999 0 -10000 0 0
EP300 -0.006 0.042 -9999 0 -0.74 1 1
BCL2L11 0.013 0.044 -9999 0 -10000 0 0
FOXO1/SKP2 -0.14 0.21 -9999 0 -0.4 3 3
mol:GDP -0.028 0.045 -9999 0 -10000 0 0
RAN 0.018 0.001 -9999 0 -10000 0 0
GADD45A 0.12 0.098 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.031 0.085 -9999 0 -10000 0 0
MST1 0.001 0.11 -9999 0 -0.86 8 8
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.043 0.095 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
MAPK8 0.036 0.034 -9999 0 -0.43 2 2
MAPK9 0.037 0.019 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
SIRT1 0.035 0.028 -9999 0 -10000 0 0
SOD2 0.015 0.2 -9999 0 -0.71 6 6
RBL2 0.025 0.17 -9999 0 -1.3 1 1
RAL/GDP 0.009 0.024 -9999 0 -10000 0 0
CHUK 0.014 0.02 -9999 0 -10000 0 0
Ran/GTP 0.017 0.003 -9999 0 -10000 0 0
CSNK1G2 0.014 0.033 -9999 0 -0.74 1 1
RAL/GTP 0.024 0.026 -9999 0 -10000 0 0
CSNK1G1 0.016 0 -9999 0 -10000 0 0
FASLG -0.34 0.39 -9999 0 -0.73 265 265
SKP2 0.016 0 -9999 0 -10000 0 0
USP7 0.018 0.001 -9999 0 -10000 0 0
IKBKB 0.014 0.02 -9999 0 -10000 0 0
CCNB1 -0.027 0.23 -9999 0 -0.95 9 9
FOXO1-3a-4/beta catenin -0.069 0.1 -9999 0 -0.43 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.14 0.21 -9999 0 -0.4 3 3
CSNK1A1 0.016 0 -9999 0 -10000 0 0
SGK1 0.014 0.02 -9999 0 -10000 0 0
CSNK1G3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.014 -9999 0 -10000 0 0
ZFAND5 0.11 0.044 -9999 0 -10000 0 0
SFN -0.083 0.27 -9999 0 -0.83 62 62
CDK2 -0.019 0.041 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.014 0.099 -9999 0 -10000 0 0
CREBBP -0.019 0.041 -9999 0 -10000 0 0
FBXO32 -0.024 0.22 -9999 0 -0.79 8 8
BCL6 0.027 0.16 -9999 0 -10000 0 0
RALB 0.018 0 -9999 0 -10000 0 0
RALA 0.018 0 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.016 0.16 -9999 0 -0.86 19 19
PLK4 0.011 0.066 -9999 0 -0.86 3 3
regulation of centriole replication 0.002 0.14 -9999 0 -0.66 22 22
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.022 0.1 -9999 0 -0.49 24 24
E-cadherin/beta catenin -0.023 0.11 -9999 0 -0.56 22 22
CTNNB1 0.016 0 -9999 0 -10000 0 0
JUP 0.011 0.057 -9999 0 -0.74 3 3
CDH1 -0.016 0.15 -9999 0 -0.74 22 22
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.19 0.22 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.15 0.17 -9999 0 -1.2 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.026 0.029 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.1 0.091 -9999 0 -0.37 1 1
CaM/Ca2+ -0.18 0.2 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.18 0.2 -9999 0 -1 1 1
AKT1 -0.16 0.17 -9999 0 -10000 0 0
MAP2K1 -0.12 0.22 -9999 0 -10000 0 0
MAP3K11 -0.14 0.23 -9999 0 -0.8 1 1
IFNGR1 0.001 0.019 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.27 0.29 -9999 0 -0.73 117 117
Rap1/GTP -0.13 0.14 -9999 0 -10000 0 0
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.21 0.23 -9999 0 -10000 0 0
CEBPB -0.067 0.2 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.19 0.21 -9999 0 -1 2 2
STAT1 -0.14 0.23 -9999 0 -1 1 1
CALM1 0.016 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.37 0.43 -9999 0 -0.85 239 239
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
STAT1 (dimer)/PIAS1 -0.17 0.19 -9999 0 -0.95 1 1
CEBPB/PTGES2/Cbp/p300 -0.074 0.084 -9999 0 -0.47 1 1
mol:Ca2+ -0.19 0.21 -9999 0 -10000 0 0
MAPK3 -0.087 0.2 -9999 0 -10000 0 0
STAT1 (dimer) -0.14 0.12 -9999 0 -0.54 1 1
MAPK1 -0.087 0.2 -9999 0 -10000 0 0
JAK2 0.001 0.019 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
JAK1 0.001 0.019 -9999 0 -10000 0 0
CAMK2D 0.016 0 -9999 0 -10000 0 0
DAPK1 -0.024 0.15 -9999 0 -0.63 3 3
SMAD7 -0.02 0.082 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.16 0.18 -9999 0 -10000 0 0
PI3K -0.17 0.19 -9999 0 -10000 0 0
IFNG -0.37 0.43 -9999 0 -0.85 239 239
apoptosis -0.036 0.12 -9999 0 -0.44 3 3
CAMK2G 0.016 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.24 0.36 -9999 0 -0.74 180 180
CAMK2B -0.098 0.27 -9999 0 -0.75 79 79
FRAP1 -0.1 0.2 -9999 0 -10000 0 0
PRKCD -0.12 0.21 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.1 0.091 -9999 0 -0.37 1 1
PTPN2 0.016 0 -9999 0 -10000 0 0
EP300 0.015 0.033 -9999 0 -0.74 1 1
IRF1 -0.057 0.18 -9999 0 -0.66 3 3
STAT1 (dimer)/PIASy -0.17 0.19 -9999 0 -0.95 1 1
SOCS1 0.011 0.082 -9999 0 -0.73 6 6
mol:GDP -0.15 0.17 -9999 0 -10000 0 0
CASP1 -0.02 0.082 -9999 0 -10000 0 0
PTGES2 0.013 0.046 -9999 0 -0.74 2 2
IRF9 0.018 0.076 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.17 0.18 -9999 0 -10000 0 0
RAP1/GDP -0.13 0.14 -9999 0 -10000 0 0
CBL -0.15 0.23 -9999 0 -10000 0 0
MAP3K1 -0.14 0.23 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PIAS4 0.015 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.1 0.091 -9999 0 -0.37 1 1
PTPN11 -0.16 0.24 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.012 0.043 -10000 0 -10000 0 0
RFC1 0.012 0.043 -10000 0 -10000 0 0
PRKDC 0.012 0.043 -10000 0 -10000 0 0
RIPK1 0.015 0.004 -10000 0 -10000 0 0
CASP7 -0.023 0.066 0.25 7 -10000 0 7
FASLG/FAS/FADD/FAF1 -0.13 0.16 -10000 0 -0.35 22 22
MAP2K4 -0.084 0.16 -10000 0 -0.43 23 23
mol:ceramide -0.15 0.2 -10000 0 -0.48 32 32
GSN 0.012 0.043 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 8 -0.17 0.18 -10000 0 -0.44 22 22
FAS 0.015 0.006 -10000 0 -10000 0 0
BID 0.018 0.066 -10000 0 -10000 0 0
MAP3K1 -0.035 0.1 -10000 0 -10000 0 0
MAP3K7 0.014 0.005 -10000 0 -10000 0 0
RB1 0.012 0.043 -10000 0 -10000 0 0
CFLAR 0.015 0.004 -10000 0 -10000 0 0
HGF/MET -0.036 0.14 -10000 0 -0.57 33 33
ARHGDIB 0.012 0.043 -10000 0 -10000 0 0
FADD 0.015 0.006 -10000 0 -10000 0 0
actin filament polymerization -0.012 0.043 -10000 0 -10000 0 0
NFKB1 -0.065 0.077 -10000 0 -0.71 1 1
MAPK8 -0.084 0.18 -10000 0 -0.53 25 25
DFFA 0.012 0.043 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.012 0.043 -10000 0 -10000 0 0
FAS/FADD/MET -0.005 0.055 -10000 0 -0.57 5 5
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.045 0.22 -10000 0 -0.86 37 37
FAF1 0.015 0.006 -10000 0 -10000 0 0
PARP1 0.012 0.043 -10000 0 -10000 0 0
DFFB 0.012 0.043 -10000 0 -10000 0 0
CHUK -0.052 0.067 -10000 0 -0.65 1 1
FASLG -0.42 0.44 -10000 0 -0.86 265 265
FAS/FADD 0 0 -10000 0 -10000 0 0
HGF -0.019 0.17 -10000 0 -0.8 23 23
LMNA 0.01 0.047 -10000 0 -0.52 1 1
CASP6 0.012 0.043 -10000 0 -10000 0 0
CASP10 0.015 0.006 -10000 0 -10000 0 0
CASP3 0.014 0.05 -10000 0 -10000 0 0
PTPN13 0.003 0.098 -10000 0 -0.74 9 9
CASP8 0.028 0.1 0.4 37 -10000 0 37
IL6 -0.13 0.34 -10000 0 -0.96 67 67
MET 0.007 0.085 -10000 0 -0.86 5 5
ICAD/CAD 0.012 0.042 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.15 0.2 -10000 0 -0.49 32 32
activation of caspase activity by cytochrome c 0.018 0.066 -10000 0 -10000 0 0
PAK2 0.012 0.042 -10000 0 -10000 0 0
BCL2 0.016 0.001 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.005 0.019 -10000 0 -10000 0 0
AES 0.005 0.016 -10000 0 -10000 0 0
FBXW11 0.016 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 0.016 0 -10000 0 -10000 0 0
DKK2 -0.026 0.18 -10000 0 -0.82 26 26
TLE1 0.005 0.016 -10000 0 -10000 0 0
MACF1 0.016 0.001 -10000 0 -10000 0 0
CTNNB1 0.048 0.1 -10000 0 -0.45 1 1
WIF1 -0.001 0.075 -10000 0 -0.77 5 5
beta catenin/RanBP3 0.004 0.11 0.35 20 -10000 0 20
KREMEN2 -0.091 0.28 -10000 0 -0.86 64 64
DKK1 -0.019 0.17 -10000 0 -0.82 22 22
beta catenin/beta TrCP1 0.056 0.094 -10000 0 -10000 0 0
FZD1 0.016 0.001 -10000 0 -10000 0 0
AXIN2 0.009 0.099 -10000 0 -1.4 2 2
AXIN1 0.016 0.004 -10000 0 -10000 0 0
RAN 0.016 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.002 0.018 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.072 0.064 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.04 0.083 0.25 2 -10000 0 2
Axin1/APC/GSK3/beta catenin/Macf1 0.059 0.1 -10000 0 -10000 0 0
HNF1A -0.002 0.074 -10000 0 -0.74 5 5
CTBP1 0.005 0.017 -10000 0 -10000 0 0
MYC -0.01 0.15 -10000 0 -0.75 21 21
RANBP3 0.016 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.096 0.22 -10000 0 -0.57 89 89
NKD1 -0.19 0.33 -10000 0 -0.74 142 142
TCF4 0.005 0.017 -10000 0 -10000 0 0
TCF3 0.005 0.017 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.024 0.11 -10000 0 -0.52 25 25
Ran/GTP 0 0.001 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.02 0.11 0.52 3 -10000 0 3
LEF1 -0.021 0.15 -10000 0 -0.86 16 16
DVL1 0.004 0.034 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.082 0.07 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.091 0.22 -10000 0 -0.61 79 79
LRP6 0.016 0.002 -10000 0 -10000 0 0
CSNK1A1 0.005 0.019 -10000 0 -10000 0 0
NLK 0.016 0.005 -10000 0 -10000 0 0
CCND1 -0.009 0.15 -10000 0 -0.75 20 20
WNT1 -0.026 0.18 -10000 0 -0.86 25 25
GSK3A 0.016 0.004 -10000 0 -10000 0 0
GSK3B 0.016 0.002 -10000 0 -10000 0 0
FRAT1 0.015 0.004 -10000 0 -10000 0 0
PPP2R5D 0.096 0.15 0.35 141 -10000 0 141
APC -0.005 0.11 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.012 0.063 0.27 5 -10000 0 5
CREBBP 0.005 0.017 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.006 0.059 -9999 0 -0.56 6 6
AKT1 -0.054 0.2 -9999 0 -0.71 3 3
PTK2B -0.16 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/Frs2 -0.002 0.04 -9999 0 -0.83 1 1
CAV1 -0.045 0.22 -9999 0 -0.86 37 37
CALM1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.23 0.25 -9999 0 -1.2 1 1
endothelial cell proliferation -0.04 0.19 -9999 0 -0.69 1 1
mol:Ca2+ -0.16 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.21 0.24 -9999 0 -1.2 1 1
RP11-342D11.1 -0.17 0.26 -9999 0 -1.1 1 1
CDH5 0.014 0.038 -9999 0 -0.86 1 1
VEGFA homodimer -0.23 0.26 -9999 0 -0.52 239 239
SHC1 0.014 0.038 -9999 0 -0.86 1 1
SHC2 0.006 0.089 -9999 0 -0.82 6 6
HRAS/GDP -0.17 0.19 -9999 0 -0.82 2 2
SH2D2A -0.27 0.41 -9999 0 -0.86 172 172
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.14 0.15 -9999 0 -0.78 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.39 0.33 -9999 0 -1 66 66
VEGFR1 homodimer 0.007 0.084 -9999 0 -0.86 5 5
SHC/GRB2/SOS1 -0.19 0.2 -9999 0 -1.1 1 1
GRB10 -0.16 0.26 -9999 0 -1.1 1 1
PTPN11 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
PAK1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.2 0.22 -9999 0 -1 2 2
HRAS 0.014 0.038 -9999 0 -0.86 1 1
VEGF/Rho/ROCK1/Integrin Complex -0.086 0.094 -9999 0 -0.58 1 1
HIF1A 0.013 0.046 -9999 0 -0.74 2 2
FRS2 0.016 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.21 0.23 -9999 0 -1.2 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.016 0 -9999 0 -10000 0 0
Nck/Pak -0.001 0.024 -9999 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.23 0.25 -9999 0 -1.2 1 1
mol:GDP -0.18 0.2 -9999 0 -1 1 1
mol:NADP -0.063 0.19 -9999 0 -0.62 1 1
eNOS/Hsp90 -0.052 0.18 -9999 0 -0.57 1 1
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
mol:IP3 -0.16 0.27 -9999 0 -1.1 1 1
HIF1A/ARNT -0.002 0.034 -9999 0 -0.56 2 2
SHB 0.016 0 -9999 0 -10000 0 0
VEGFA -0.37 0.44 -9999 0 -0.86 239 239
VEGFC 0.014 0.038 -9999 0 -0.86 1 1
FAK1/Vinculin -0.1 0.22 -9999 0 -0.99 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.22 0.24 -9999 0 -1.2 1 1
PTPN6 0.016 0 -9999 0 -10000 0 0
EPAS1 0.026 0.036 -9999 0 -0.71 1 1
mol:L-citrulline -0.063 0.19 -9999 0 -0.62 1 1
ITGAV 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.21 0.24 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer -0.22 0.25 -9999 0 -1.2 1 1
VEGFR2/3 heterodimer -0.002 0.04 -9999 0 -0.83 1 1
VEGFB 0.016 0 -9999 0 -10000 0 0
MAPK11 -0.15 0.26 -9999 0 -0.83 2 2
VEGFR2 homodimer 0.043 0.049 -9999 0 -0.72 2 2
FLT1 0.007 0.085 -9999 0 -0.86 5 5
NEDD4 0.015 0.046 -9999 0 -0.74 2 2
MAPK3 -0.14 0.25 -9999 0 -0.76 2 2
MAPK1 -0.14 0.25 -9999 0 -0.76 2 2
VEGFA145/NRP2 -0.3 0.33 -9999 0 -0.66 244 244
VEGFR1/2 heterodimer -0.008 0.068 -9999 0 -0.61 6 6
KDR 0.043 0.049 -9999 0 -0.73 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.21 0.23 -9999 0 -1.2 2 2
SRC 0.016 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.14 0.25 -9999 0 -0.77 2 2
PI3K -0.16 0.18 -9999 0 -0.78 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.23 0.25 -9999 0 -1.2 1 1
FES -0.17 0.27 -9999 0 -1 2 2
GAB1 -0.16 0.19 -9999 0 -0.8 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.23 0.25 -9999 0 -1.2 1 1
CTNNB1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
ARNT 0.016 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.081 0.2 -9999 0 -0.61 12 12
VEGFR2 homodimer/VEGFA homodimer/Yes -0.23 0.25 -9999 0 -1.2 1 1
PI3K/GAB1 -0.054 0.19 -9999 0 -0.69 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.2 0.22 -9999 0 -1.1 1 1
PRKACA 0.016 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.043 -9999 0 -0.64 2 2
HSP90AA1 0.016 0 -9999 0 -10000 0 0
CDC42 -0.16 0.27 -9999 0 -1.2 1 1
actin cytoskeleton reorganization -0.39 0.33 -9999 0 -1 66 66
PTK2 -0.12 0.24 -9999 0 -1.1 1 1
EDG1 -0.17 0.26 -9999 0 -1.1 1 1
mol:DAG -0.16 0.27 -9999 0 -1.1 1 1
CaM/Ca2+ -0.18 0.2 -9999 0 -1 1 1
MAP2K3 -0.14 0.26 -9999 0 -1.1 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.21 0.23 -9999 0 -1.2 1 1
PLCG1 -0.16 0.27 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.21 0.24 -9999 0 -1.2 1 1
IQGAP1 0.016 0 -9999 0 -10000 0 0
YES1 0.016 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.23 0.25 -9999 0 -1.2 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.23 0.25 -9999 0 -0.5 239 239
cell migration -0.053 0.2 -9999 0 -0.77 1 1
mol:PI-3-4-5-P3 -0.15 0.17 -9999 0 -0.7 6 6
FYN 0.016 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.19 0.21 -9999 0 -1 1 1
mol:NO -0.063 0.19 -9999 0 -0.62 1 1
PXN 0.016 0 -9999 0 -10000 0 0
HRAS/GTP -0.17 0.19 -9999 0 -0.82 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.21 0.23 -9999 0 -1.2 1 1
VHL 0.014 0.033 -9999 0 -0.74 1 1
ITGB3 0.007 0.08 -9999 0 -0.74 6 6
NOS3 -0.073 0.2 -9999 0 -0.73 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck -0.23 0.26 -9999 0 -0.87 6 6
RAC1 0.016 0 -9999 0 -10000 0 0
PRKCA -0.14 0.25 -9999 0 -1 1 1
PRKCB -0.14 0.25 -9999 0 -0.96 2 2
VCL 0.016 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.21 0.24 -9999 0 -1.2 1 1
VEGFR1/2 heterodimer/VEGFA homodimer -0.23 0.26 -9999 0 -1.1 5 5
VEGFA165/NRP2 -0.3 0.33 -9999 0 -0.66 244 244
MAPKKK cascade -0.16 0.18 -9999 0 -0.8 2 2
NRP2 0.004 0.1 -9999 0 -0.86 7 7
VEGFC homodimer 0.014 0.038 -9999 0 -0.86 1 1
NCK1 0.014 0.033 -9999 0 -0.74 1 1
ROCK1 0.016 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.1 0.22 -9999 0 -0.99 1 1
MAP3K13 -0.16 0.27 -9999 0 -1.2 1 1
PDPK1 -0.072 0.2 -9999 0 -0.65 6 6
Regulation of Androgen receptor activity

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
HDAC1 0.03 0.002 -9999 0 -10000 0 0
SMARCC1 0.026 0.01 -9999 0 -10000 0 0
REL 0.008 0.065 -9999 0 -0.74 4 4
HDAC7 -0.098 0.088 -9999 0 -0.66 3 3
JUN 0.015 0.003 -9999 0 -10000 0 0
EP300 0.014 0.033 -9999 0 -0.74 1 1
KAT2B 0.014 0.033 -9999 0 -0.74 1 1
KAT5 0.016 0 -9999 0 -10000 0 0
MAPK14 0.001 0.046 -9999 0 -0.59 3 3
FOXO1 0.016 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.11 0.091 -9999 0 -0.68 4 4
MAP2K6 -0.002 0.058 -9999 0 -0.76 3 3
BRM/BAF57 0 0 -9999 0 -10000 0 0
MAP2K4 0.002 0.006 -9999 0 -10000 0 0
SMARCA2 0.015 0.003 -9999 0 -10000 0 0
PDE9A -0.12 0.13 -9999 0 -1.3 4 4
NCOA2 0 0.11 -9999 0 -0.74 11 11
CEBPA -0.001 0.12 -9999 0 -0.86 10 10
EHMT2 0.015 0.003 -9999 0 -10000 0 0
cell proliferation -0.093 0.098 -9999 0 -0.55 2 2
NR0B1 -0.051 0.21 -9999 0 -0.86 34 34
EGR1 -0.002 0.11 -9999 0 -0.74 12 12
RXRs/9cRA -0.004 0.047 -9999 0 -0.54 4 4
AR/RACK1/Src -0.016 0.064 -9999 0 -0.57 2 2
AR/GR 0 0.087 -9999 0 -0.69 4 4
GNB2L1 0.014 0.038 -9999 0 -0.86 1 1
PKN1 0.015 0.003 -9999 0 -10000 0 0
RCHY1 0.016 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.002 0.037 -9999 0 -0.57 2 2
T-DHT/AR/TIF2/CARM1 -0.022 0.098 -9999 0 -0.7 7 7
SRC 0.003 0.049 -9999 0 -10000 0 0
NR3C1 0.014 0.038 -9999 0 -0.86 1 1
KLK3 -0.052 0.19 -9999 0 -0.71 27 27
APPBP2 0.002 0.006 -9999 0 -10000 0 0
TRIM24 0.015 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.026 0.057 -9999 0 -0.57 4 4
TMPRSS2 -0.96 0.38 -9999 0 -1.1 460 460
RXRG 0.006 0.076 -9999 0 -0.86 4 4
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.016 0.001 -9999 0 -10000 0 0
RXRB 0.016 0.001 -9999 0 -10000 0 0
CARM1 0.015 0.003 -9999 0 -10000 0 0
NR2C2 0.014 0.033 -9999 0 -0.74 1 1
KLK2 -0.025 0.14 -9999 0 -0.63 22 22
AR -0.011 0.089 -9999 0 -0.43 14 14
SENP1 0.016 0.001 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
MDM2 0.013 0.009 -9999 0 -10000 0 0
SRY 0.002 0.007 -9999 0 -10000 0 0
GATA2 -0.003 0.12 -9999 0 -0.74 13 13
MYST2 0.016 0.001 -9999 0 -10000 0 0
HOXB13 -0.16 0.34 -9999 0 -0.86 104 104
T-DHT/AR/RACK1/Src -0.016 0.062 -9999 0 -0.59 2 2
positive regulation of transcription -0.003 0.12 -9999 0 -0.74 13 13
DNAJA1 0.002 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.002 -9999 0 -10000 0 0
NCOA1 0.024 0.005 -9999 0 -10000 0 0
SPDEF -0.17 0.36 -9999 0 -0.86 114 114
T-DHT/AR/TIF2 0.018 0.076 -9999 0 -0.66 4 4
T-DHT/AR/Hsp90 -0.028 0.056 -9999 0 -0.57 4 4
GSK3B 0.002 0.005 -9999 0 -10000 0 0
NR2C1 0.016 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.011 0.053 -9999 0 -0.49 4 4
SIRT1 0.015 0.003 -9999 0 -10000 0 0
ZMIZ2 0.014 0.008 -9999 0 -10000 0 0
POU2F1 0.005 0.015 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.067 0.14 -9999 0 -0.6 29 29
CREBBP 0.015 0.003 -9999 0 -10000 0 0
SMARCE1 0.015 0.003 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

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
PTK2 0.015 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.021 0.093 -10000 0 -0.43 26 26
regulation of S phase of mitotic cell cycle -0.015 0.069 -10000 0 -0.62 1 1
GNAO1 0.008 0.082 -10000 0 -0.84 5 5
HRAS 0.014 0.038 -10000 0 -0.86 1 1
SHBG/T-DHT -0.05 0.15 -10000 0 -0.49 54 54
PELP1 0.016 0.001 -10000 0 -10000 0 0
AKT1 0.015 0 -10000 0 -10000 0 0
MAP2K1 0.046 0.092 -10000 0 -10000 0 0
T-DHT/AR -0.028 0.12 -10000 0 -0.57 26 26
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -0.007 13 13
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.057 -10000 0 -0.74 3 3
mol:GDP -0.027 0.12 -10000 0 -0.55 26 26
cell proliferation 0.071 0.11 -10000 0 -0.64 4 4
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
FOS 0.056 0.14 -10000 0 -0.81 13 13
mol:Ca2+ -0.003 0.014 -10000 0 -0.11 4 4
MAPK3 0.062 0.1 -10000 0 -0.57 4 4
MAPK1 0.044 0.054 -10000 0 -0.29 4 4
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
mol:IP3 0 0.001 -10000 0 -0.004 13 13
cAMP biosynthetic process -0.045 0.15 -10000 0 -0.48 54 54
GNG2 0.016 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 13 13
HRAS/GTP -0.02 0.086 -10000 0 -0.45 4 4
actin cytoskeleton reorganization -0.001 0.023 -10000 0 -10000 0 0
SRC 0.016 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 13 13
PI3K -0.002 0.03 -10000 0 -0.48 2 2
apoptosis -0.06 0.094 0.43 12 -10000 0 12
T-DHT/AR/PELP1 -0.024 0.1 -10000 0 -0.48 26 26
HRAS/GDP -0.026 0.12 -10000 0 -0.52 27 27
CREB1 0.061 0.1 -10000 0 -0.47 12 12
RAC1-CDC42/GTP -0.001 0.023 -10000 0 -10000 0 0
AR -0.021 0.16 -10000 0 -0.74 26 26
GNB1 0.016 0 -10000 0 -10000 0 0
RAF1 0.035 0.094 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.024 0.11 -10000 0 -0.49 26 26
T-DHT/AR/PELP1/Src -0.021 0.094 -10000 0 -0.46 4 4
MAP2K2 0.046 0.094 -10000 0 -10000 0 0
T-DHT/AR/PELP1/Src/PI3K -0.015 0.069 -10000 0 -0.62 1 1
GNAZ 0.011 0.057 -10000 0 -0.74 3 3
SHBG -0.061 0.23 -10000 0 -0.74 54 54
Gi family/GNB1/GNG2/GDP -0.008 0.044 -10000 0 -0.45 2 2
mol:T-DHT 0 0 -10000 0 -0.003 9 9
RAC1 0.016 0 -10000 0 -10000 0 0
GNRH1 -0.18 0.31 -10000 0 -0.68 148 148
Gi family/GTP -0.013 0.058 -10000 0 -0.48 4 4
CDC42 0.016 0 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.11 0.07 -10000 0 -10000 0 0
epithelial cell differentiation -0.052 0.11 -10000 0 -0.56 1 1
ITCH 0.055 0.017 -10000 0 -10000 0 0
WWP1 -0.097 0.066 -10000 0 -10000 0 0
FYN 0.016 0 -10000 0 -10000 0 0
EGFR 0.001 0.11 -10000 0 -0.85 9 9
PRL 0.006 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis -0.019 0.08 -10000 0 -10000 0 0
PTPRZ1 -0.082 0.25 -10000 0 -0.75 65 65
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.053 0.074 -10000 0 -0.65 1 1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.084 0.094 -10000 0 -0.57 10 10
ADAM17 0.055 0.017 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.14 0.085 -10000 0 -0.46 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.1 -10000 0 -0.63 12 12
NCOR1 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.076 0.078 -10000 0 -0.71 1 1
GRIN2B -0.057 0.091 -10000 0 -0.61 3 3
ErbB4/ErbB2/betacellulin -0.13 0.16 -10000 0 -0.51 74 74
STAT1 0.014 0.038 -10000 0 -0.86 1 1
HBEGF 0.016 0 -10000 0 -10000 0 0
PRLR -0.085 0.26 -10000 0 -0.74 71 71
E4ICDs/ETO2 -0.11 0.079 -10000 0 -0.7 2 2
axon guidance -0.017 0.071 -10000 0 -10000 0 0
NEDD4 0.052 0.051 -10000 0 -0.72 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.075 0.19 -10000 0 -0.56 71 71
CBFA2T3 0.012 0.054 -10000 0 -0.86 2 2
ErbB4/ErbB2/HBEGF -0.064 0.038 -10000 0 -0.51 1 1
MAPK3 -0.03 0.082 -10000 0 -0.6 1 1
STAT1 (dimer) -0.11 0.072 -10000 0 -0.54 1 1
MAPK1 -0.03 0.082 -10000 0 -0.6 1 1
JAK2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.077 0.081 -10000 0 -0.53 11 11
NRG1 0.035 0.11 -10000 0 -0.56 17 17
NRG3 -0.004 0.13 -10000 0 -0.86 12 12
NRG2 -0.001 0.12 -10000 0 -0.85 10 10
NRG4 -0.055 0.22 -10000 0 -0.76 47 47
heart development -0.017 0.071 -10000 0 -10000 0 0
neural crest cell migration -0.077 0.08 -10000 0 -0.52 11 11
ERBB2 0.052 0.039 -10000 0 -0.56 2 2
WWOX/E4ICDs -0.11 0.074 -10000 0 -0.7 1 1
SHC1 0.014 0.038 -10000 0 -0.86 1 1
ErbB4/EGFR/neuregulin 4 -0.14 0.15 -10000 0 -0.56 51 51
apoptosis 0.1 0.063 0.44 1 -10000 0 1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.12 0.088 -10000 0 -0.53 10 10
ErbB4/ErbB2/epiregulin -0.098 0.13 -10000 0 -0.57 35 35
ErbB4/ErbB4/betacellulin/betacellulin -0.18 0.19 -10000 0 -0.58 82 82
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.13 0.14 -10000 0 -0.72 1 1
MDM2 -0.1 0.073 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.054 0.078 -10000 0 -0.66 1 1
STAT5A -0.005 0.067 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.085 0.1 -10000 0 -0.62 8 8
DLG4 0.016 0 -10000 0 -10000 0 0
GRB2/SHC -0.001 0.029 -10000 0 -0.66 1 1
E4ICDs/TAB2/NCoR1 -0.1 0.048 -10000 0 -10000 0 0
STAT5A (dimer) -0.055 0.12 -10000 0 -0.62 1 1
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.007 0.064 -10000 0 -10000 0 0
LRIG1 0.016 0 -10000 0 -10000 0 0
EREG -0.041 0.21 -10000 0 -0.86 34 34
BTC -0.1 0.27 -10000 0 -0.74 82 82
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.017 0.072 -10000 0 -10000 0 0
ERBB4 -0.14 0.085 -10000 0 -0.46 1 1
STAT5B 0.016 0 -10000 0 -10000 0 0
YAP1 -0.034 0.016 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.1 0.13 -10000 0 -0.52 37 37
glial cell differentiation 0.1 0.047 -10000 0 -10000 0 0
WWOX 0.014 0.038 -10000 0 -0.86 1 1
cell proliferation -0.077 0.16 -10000 0 -0.67 8 8
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.046 0.093 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.1 0.22 -9999 0 -0.59 93 93
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 0.008 0.082 -9999 0 -0.84 5 5
RhoA/GTP -0.046 0.094 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process -0.015 0.13 -9999 0 -10000 0 0
GNAZ 0.011 0.057 -9999 0 -0.74 3 3
GNAI3 0.016 0 -9999 0 -10000 0 0
GNA12 0.016 0 -9999 0 -10000 0 0
S1PR5 -0.14 0.33 -9999 0 -0.86 93 93
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.053 0.11 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
GNAI1 0.011 0.057 -9999 0 -0.74 3 3
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.012 0.058 -9999 0 -10000 0 0
epithelial cell differentiation -0.016 0.079 -9999 0 -10000 0 0
CYFIP2 0.004 0.092 -9999 0 -0.74 8 8
ENAH 0.078 0.065 -9999 0 -10000 0 0
EGFR 0.001 0.11 -9999 0 -0.85 9 9
EPHA2 0.014 0.033 -9999 0 -0.74 1 1
MYO6 0.032 0.096 -9999 0 -0.78 2 2
CTNNB1 0.016 0 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.057 -9999 0 -0.47 8 8
AQP5 -0.17 0.24 -9999 0 -0.52 161 161
CTNND1 0.016 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.034 0.083 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.018 0.12 -9999 0 -0.84 1 1
EGF -0.67 0.23 -9999 0 -0.74 480 480
NCKAP1 0.016 0 -9999 0 -10000 0 0
AQP3 -0.05 0.16 -9999 0 -0.58 39 39
cortical microtubule organization -0.016 0.079 -9999 0 -10000 0 0
GO:0000145 0.034 0.079 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.017 0.08 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GDP -0.014 0.062 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.003 0.034 -9999 0 -0.52 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.05 0.084 -9999 0 -0.57 1 1
PVRL2 0.016 0 -9999 0 -10000 0 0
ZYX 0.034 0.084 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.031 -9999 0 -10000 0 0
CDH1 -0.016 0.15 -9999 0 -0.74 22 22
EGFR/EGFR/EGF/EGF -0.34 0.14 -9999 0 -0.77 28 28
RhoA/GDP -0.015 0.073 -9999 0 -10000 0 0
actin cytoskeleton organization 0.042 0.092 -9999 0 -0.71 2 2
IGF-1R heterotetramer 0.016 0 -9999 0 -10000 0 0
GIT1 0.016 0 -9999 0 -10000 0 0
IGF1R 0.016 0 -9999 0 -10000 0 0
IGF1 0.006 0.093 -9999 0 -0.86 6 6
DIAPH1 -0.01 0.085 -9999 0 -0.69 8 8
Wnt receptor signaling pathway 0.016 0.079 -9999 0 -10000 0 0
RHOA 0.016 0 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.063 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
VCL 0.042 0.094 -9999 0 -0.74 2 2
EFNA1 0.014 0.038 -9999 0 -0.86 1 1
LPP 0.043 0.089 -9999 0 -0.8 1 1
Ephrin A1/EPHA2 -0.016 0.074 -9999 0 -10000 0 0
SEC6/SEC8 -0.013 0.062 -9999 0 -10000 0 0
MGAT3 0.018 0.12 -9999 0 -0.86 1 1
HGF/MET -0.036 0.13 -9999 0 -0.95 4 4
HGF -0.019 0.17 -9999 0 -0.8 23 23
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.012 0.059 -9999 0 -10000 0 0
actin cable formation 0.099 0.07 -9999 0 -10000 0 0
KIAA1543 0.036 0.12 -9999 0 -0.85 6 6
KIFC3 0.034 0.086 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.74 1 1
EXOC3 0.016 0 -9999 0 -10000 0 0
ACTN1 0.033 0.093 -9999 0 -0.86 1 1
NCK1/GIT1 -0.001 0.024 -9999 0 -0.56 1 1
mol:GDP -0.016 0.079 -9999 0 -10000 0 0
EXOC4 0.016 0 -9999 0 -10000 0 0
STX4 0.034 0.084 -9999 0 -10000 0 0
PIP5K1C 0.034 0.084 -9999 0 -10000 0 0
LIMA1 0.016 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
ROCK1 -0.012 0.054 -9999 0 -10000 0 0
adherens junction assembly 0.058 0.12 -9999 0 -0.79 7 7
IGF-1R heterotetramer/IGF1 -0.019 0.083 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
MET 0.007 0.085 -9999 0 -0.86 5 5
PLEKHA7 0.031 0.1 -9999 0 -0.78 3 3
mol:GTP -0.003 0.034 -9999 0 -0.52 1 1
establishment of epithelial cell apical/basal polarity 0.07 0.076 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.012 0.058 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.042 0.092 -9999 0 -0.71 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.012 0.059 -9999 0 -10000 0 0
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.008 0.082 -9999 0 -0.84 5 5
CDC42/GTP -0.018 0.063 -9999 0 -10000 0 0
PLCG1 0.033 0.08 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.016 0 -9999 0 -10000 0 0
GNAI3 0.016 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
cell migration -0.018 0.062 -9999 0 -10000 0 0
S1PR5 -0.14 0.33 -9999 0 -0.86 93 93
S1PR4 -0.034 0.2 -9999 0 -0.86 30 30
MAPK3 0.033 0.08 -9999 0 -10000 0 0
MAPK1 0.033 0.08 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.053 0.11 -9999 0 -10000 0 0
GNAI1 0.011 0.057 -9999 0 -0.74 3 3
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.1 0.22 -9999 0 -0.59 93 93
RHOA 0.013 0.12 -9999 0 -0.49 30 30
S1P/S1P4/Gi -0.021 0.072 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.057 -9999 0 -0.74 3 3
S1P/S1P4/G12/G13 -0.03 0.12 -9999 0 -0.53 30 30
GNA12 0.016 0 -9999 0 -10000 0 0
GNA13 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.031 0.12 -9999 0 -0.51 33 33
RGS9BP -0.017 0.15 -9999 0 -0.74 23 23
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.003 0.006 -9999 0 -10000 0 0
mol:Na + -0.012 0.084 -9999 0 -0.59 11 11
mol:ADP 0.012 0.043 -9999 0 -0.68 2 2
GNAT2 0.014 0.005 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.035 0.13 -9999 0 -0.5 38 38
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.001 0.025 -9999 0 -0.59 1 1
GRK7 0.008 0.054 -9999 0 -0.86 2 2
CNGB3 -0.007 0.11 -9999 0 -0.86 8 8
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.009 0.11 -9999 0 -0.64 15 15
Cone PDE6 -0.033 0.12 -9999 0 -0.58 5 5
Cone Metarhodopsin II -0.002 0.034 -9999 0 -0.55 2 2
Na + (4 Units) -0.018 0.11 -9999 0 -0.64 15 15
GNAT2/GDP -0.03 0.11 -9999 0 -0.5 9 9
GNB5 0.016 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.015 0.043 -9999 0 -0.54 3 3
Cone Transducin -0.033 0.13 -9999 0 -0.54 33 33
SLC24A2 -0.008 0.099 -9999 0 -0.86 7 7
GNB3/GNGT2 -0.041 0.16 -9999 0 -0.66 33 33
GNB3 -0.038 0.21 -9999 0 -0.86 32 32
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0 0.065 -9999 0 -0.86 3 3
ARR3 0.004 0.007 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.012 0.085 -9999 0 -0.6 11 11
mol:Pi -0.035 0.13 -9999 0 -0.49 38 38
Cone CNG Channel -0.013 0.083 -9999 0 -0.52 13 13
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.008 0.099 -9999 0 -0.86 7 7
RGS9 -0.008 0.14 -9999 0 -0.81 15 15
PDE6C 0.004 0.054 -9999 0 -0.86 2 2
GNGT2 0.014 0.038 -9999 0 -0.86 1 1
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.003 0.038 -9999 0 -0.86 1 1
Noncanonical Wnt signaling pathway

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
NFATC2 0.008 0.078 -9999 0 -0.79 5 5
GNB1/GNG2 -0.054 0.11 -9999 0 -0.53 8 8
mol:DAG 0.009 0.13 -9999 0 -10000 0 0
PLCG1 0.009 0.13 -9999 0 -10000 0 0
YES1 -0.011 0.14 -9999 0 -0.56 8 8
FZD3 0.016 0 -9999 0 -10000 0 0
FZD6 0.016 0 -9999 0 -10000 0 0
G protein -0.05 0.1 -9999 0 -10000 0 0
MAP3K7 -0.096 0.22 -9999 0 -0.55 40 40
mol:Ca2+ 0.01 0.12 -9999 0 -10000 0 0
mol:IP3 0.009 0.13 -9999 0 -10000 0 0
NLK -0.007 0.009 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CAMK2A -0.12 0.24 -9999 0 -0.6 50 50
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.064 0.13 -9999 0 -0.6 8 8
CSNK1A1 0.016 0 -9999 0 -10000 0 0
GNAS -0.011 0.14 -9999 0 -0.56 8 8
GO:0007205 0.01 0.13 -9999 0 -10000 0 0
WNT6 -0.017 0.17 -9999 0 -0.86 20 20
WNT4 -0.068 0.24 -9999 0 -0.75 58 58
NFAT1/CK1 alpha -0.051 0.1 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
WNT5A 0.011 0.057 -9999 0 -0.74 3 3
WNT11 -0.04 0.2 -9999 0 -0.76 38 38
CDC42 0 0.14 -9999 0 -0.52 8 8
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.016 0 -9999 0 -10000 0 0
ITGB7 0.016 0 -9999 0 -10000 0 0
ITGA4 -0.011 0.15 -9999 0 -0.86 16 16
alpha4/beta7 Integrin -0.02 0.11 -9999 0 -0.66 16 16
alpha4/beta1 Integrin -0.02 0.11 -9999 0 -0.66 16 16
TCGA08_rtk_signaling

Figure S84.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S84.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.28 0.37 -9999 0 -0.74 205 205
HRAS 0.014 0.038 -9999 0 -0.86 1 1
EGFR 0.001 0.11 -9999 0 -0.85 9 9
AKT 0.035 0.029 -9999 0 -10000 0 0
FOXO3 0.016 0 -9999 0 -10000 0 0
AKT1 0.016 0 -9999 0 -10000 0 0
FOXO1 0.016 0 -9999 0 -10000 0 0
AKT3 0.016 0 -9999 0 -10000 0 0
FOXO4 0.016 0 -9999 0 -10000 0 0
MET 0.007 0.085 -9999 0 -0.86 5 5
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
PIK3CB 0.016 0 -9999 0 -10000 0 0
NRAS 0.016 0 -9999 0 -10000 0 0
PIK3CG 0.011 0.066 -9999 0 -0.86 3 3
PIK3R3 0.016 0 -9999 0 -10000 0 0
PIK3R2 0.016 0 -9999 0 -10000 0 0
NF1 0.016 0 -9999 0 -10000 0 0
RAS -0.041 0.097 -9999 0 -0.38 5 5
ERBB2 0.013 0.046 -9999 0 -0.74 2 2
proliferation/survival/translation -0.041 0.013 -9999 0 -10000 0 0
PI3K -0.022 0.091 -9999 0 -0.29 6 6
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
KRAS 0.016 0 -9999 0 -10000 0 0
FOXO 0.041 0.034 -9999 0 -10000 0 0
AKT2 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.012 0.036 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.036 0.096 -9999 0 -0.48 7 7
JUN 0.025 0.12 -9999 0 -0.56 8 8
HRAS 0.014 0.038 -9999 0 -0.86 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.052 0.16 -9999 0 -0.7 11 11
RAP1A 0.016 0 -9999 0 -10000 0 0
FRS2 0.016 0 -9999 0 -10000 0 0
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.052 0.16 -9999 0 -0.7 11 11
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.041 0.13 -9999 0 -0.46 47 47
RHOA 0.016 0 -9999 0 -10000 0 0
RAP1A/GTP -0.046 0.14 -9999 0 -0.82 5 5
GRB7 0.004 0.092 -9999 0 -0.74 8 8
RET51/GFRalpha1/GDNF -0.052 0.16 -9999 0 -0.7 11 11
MAPKKK cascade -0.041 0.12 -9999 0 -0.7 6 6
BCAR1 0.014 0.033 -9999 0 -0.74 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.04 0.13 -9999 0 -0.46 46 46
lamellipodium assembly -0.034 0.091 -9999 0 -0.44 7 7
RET51/GFRalpha1/GDNF/SHC -0.053 0.16 -9999 0 -0.69 12 12
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
RET9/GFRalpha1/GDNF/SHC -0.038 0.13 -9999 0 -0.46 44 44
RET9/GFRalpha1/GDNF/Shank3 -0.037 0.12 -9999 0 -0.46 43 43
MAPK3 0.006 0.14 -9999 0 -0.77 5 5
DOK1 0.016 0 -9999 0 -10000 0 0
DOK6 -0.001 0.11 -9999 0 -0.74 12 12
PXN 0.016 0 -9999 0 -10000 0 0
neurite development -0.042 0.12 -9999 0 -0.73 5 5
DOK5 -0.006 0.13 -9999 0 -0.76 15 15
GFRA1 -0.042 0.2 -9999 0 -0.75 40 40
MAPK8 0.015 0.12 -9999 0 -0.6 8 8
HRAS/GTP -0.048 0.14 -9999 0 -0.83 6 6
tube development -0.034 0.12 -9999 0 -0.5 6 6
MAPK1 0.006 0.14 -9999 0 -0.77 5 5
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.024 0.082 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PDLIM7 0.009 0.076 -9999 0 -0.86 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.057 0.17 -9999 0 -0.86 12 12
SHC1 0.014 0.038 -9999 0 -0.86 1 1
RET51/GFRalpha1/GDNF/Dok4 -0.052 0.16 -9999 0 -0.7 11 11
RET51/GFRalpha1/GDNF/Dok5 -0.064 0.19 -9999 0 -0.8 19 19
PRKCA 0.016 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.029 -9999 0 -0.68 1 1
CREB1 -0.032 0.098 -9999 0 -0.53 5 5
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.025 0.083 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Grb7 -0.058 0.18 -9999 0 -0.79 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.012 0.14 -9999 0 -0.76 19 19
DOK4 0.016 0 -9999 0 -10000 0 0
JNK cascade 0.025 0.11 -9999 0 -0.54 8 8
RET9/GFRalpha1/GDNF/FRS2 -0.037 0.12 -9999 0 -0.46 43 43
SHANK3 0.016 0 -9999 0 -10000 0 0
RASA1 0.014 0.033 -9999 0 -0.74 1 1
NCK1 0.014 0.033 -9999 0 -0.74 1 1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.025 0.083 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.034 0.1 -9999 0 -0.6 5 5
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.035 0.11 -9999 0 -0.6 6 6
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.036 0.11 -9999 0 -0.76 5 5
PI3K -0.051 0.14 -9999 0 -0.73 7 7
SOS1 0.016 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.034 0.12 -9999 0 -0.5 6 6
GRB10 0.016 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.03 0.092 -9999 0 -0.52 5 5
RET51/GFRalpha1/GDNF/FRS2 -0.052 0.16 -9999 0 -0.7 11 11
GAB1 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.065 -9999 0 -0.74 4 4
IRS2 0.003 0.11 -9999 0 -0.86 8 8
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.036 0.11 -9999 0 -0.76 5 5
RET51/GFRalpha1/GDNF/PKC alpha -0.052 0.16 -9999 0 -0.7 11 11
GRB2 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GDNF 0.001 0.065 -9999 0 -0.86 3 3
RAC1 0.016 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.055 0.16 -9999 0 -0.72 12 12
Rac1/GTP -0.04 0.11 -9999 0 -0.54 7 7
RET9/GFRalpha1/GDNF -0.041 0.14 -9999 0 -0.51 43 43
GFRalpha1/GDNF -0.047 0.16 -9999 0 -0.58 43 43
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.003 0.099 0.8 8 -10000 0 8
PI3K Class IB/PDE3B 0.003 0.1 -10000 0 -0.8 8 8
PDE3B 0.003 0.1 -10000 0 -0.8 8 8
Signaling events mediated by PRL

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
CCNE1 0.003 0.11 -10000 0 -0.86 8 8
mol:Halofuginone 0.007 0.001 -10000 0 -10000 0 0
ITGA1 0.016 0 -10000 0 -10000 0 0
CDKN1A 0.04 0.035 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.024 0.12 -10000 0 -0.66 19 19
mol:Ca2+ -0.016 0.16 0.4 19 -0.65 25 44
AGT -0.024 0.18 -10000 0 -0.82 25 25
CCNA2 -0.055 0.23 -10000 0 -0.88 7 7
TUBA1B 0.016 0 -10000 0 -10000 0 0
EGR1 0.02 0.086 -10000 0 -0.55 12 12
CDK2/Cyclin E1 -0.01 0.063 -10000 0 -0.49 8 8
MAPK3 0.006 0.13 -10000 0 -0.66 19 19
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.006 0.13 -10000 0 -0.66 19 19
PTP4A1 0.041 0.069 -10000 0 -10000 0 0
PTP4A3 -0.016 0.16 -10000 0 -0.86 19 19
PTP4A2 0.016 0 -10000 0 -10000 0 0
ITGB1 0.006 0.13 -10000 0 -0.66 19 19
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.03 0.062 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha -0.002 0.034 -10000 0 -0.56 2 2
PRL-1/ATF-5 0.042 0.075 -10000 0 -10000 0 0
RABGGTA 0.013 0.046 -10000 0 -0.74 2 2
BCAR1 0.013 0.079 0.4 19 -0.57 1 20
RHOC 0.03 0.062 -10000 0 -10000 0 0
RHOA 0.03 0.062 -10000 0 -10000 0 0
cell motility 0.036 0.064 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.045 0.064 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.024 0.12 -10000 0 -0.66 19 19
ROCK1 0.036 0.064 -10000 0 -10000 0 0
RABGGTB 0.016 0 -10000 0 -10000 0 0
CDK2 0.016 0 -10000 0 -10000 0 0
mitosis 0.041 0.068 -10000 0 -10000 0 0
ATF5 0.011 0.066 -10000 0 -0.86 3 3
Canonical NF-kappaB 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
FBXW11 0.02 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.075 0.074 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.15 0.28 -9999 0 -0.67 123 123
NFKBIA 0.063 0.02 -9999 0 -10000 0 0
BIRC2 0.016 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
RIPK2 0.014 0.038 -9999 0 -0.86 1 1
IKBKG -0.046 0.084 -9999 0 -10000 0 0
IKK complex/A20 -0.04 0.079 -9999 0 -0.58 2 2
NEMO/A20/RIP2 0.014 0.038 -9999 0 -0.86 1 1
XPO1 0.016 0 -9999 0 -10000 0 0
NEMO/ATM -0.042 0.077 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.034 0.062 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.19 0.37 -9999 0 -0.86 123 123
NFKB1 0.019 0.033 -9999 0 -0.73 1 1
RELA 0.02 0 -9999 0 -10000 0 0
MALT1 0.016 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.014 0.033 -9999 0 -0.74 1 1
TNF/TNFR1A -0.009 0.075 -9999 0 -0.61 8 8
TRAF6 0.016 0 -9999 0 -10000 0 0
PRKCA 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
UBE2D3 0.016 0 -9999 0 -10000 0 0
TNF 0.003 0.1 -9999 0 -0.8 8 8
NF kappa B1 p50/RelA -0.001 0.02 -9999 0 -10000 0 0
BCL10 0.016 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.063 0.02 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
IKK complex -0.038 0.069 -9999 0 -10000 0 0
CYLD 0.016 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.035 0.063 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.006 0.034 -10000 0 -10000 0 0
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.016 0 -10000 0 -10000 0 0
AKT2 0.016 0 -10000 0 -10000 0 0
STXBP4 0.016 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.066 0.09 0.32 36 -0.36 1 37
YWHAZ 0.016 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
TBC1D4 0.031 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
YWHAB 0.016 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
ASIP -0.072 0.26 -10000 0 -0.86 51 51
PRKCI 0.016 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.016 0 -10000 0 -10000 0 0
GYS1 0.043 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.057 -10000 0 -0.74 3 3
TRIP10 0.016 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.033 0.083 -10000 0 -10000 0 0
VAMP2 0.016 0 -10000 0 -10000 0 0
SLC2A4 0.068 0.094 0.33 36 -0.4 1 37
STX4 0.016 0 -10000 0 -10000 0 0
GSK3B 0.034 0 -10000 0 -10000 0 0
SFN -0.083 0.27 -10000 0 -0.83 62 62
LNPEP 0.013 0.046 -10000 0 -0.74 2 2
YWHAE 0.016 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.014 0.033 -10000 0 -0.74 1 1
HDAC4 0.016 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.025 0.043 0.67 2 -10000 0 2
CDKN1A -0.002 0.04 -10000 0 -0.65 2 2
KAT2B 0.014 0.033 -10000 0 -0.74 1 1
BAX 0.016 0 -10000 0 -10000 0 0
FOXO3 0.001 0.023 0.53 1 -10000 0 1
FOXO1 0.016 0 -10000 0 -10000 0 0
FOXO4 0.03 0.016 -10000 0 -0.33 1 1
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
TAT -0.005 0.12 -10000 0 -0.86 11 11
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.017 0.16 -10000 0 -0.66 30 30
PPARGC1A -0.058 0.22 -10000 0 -0.74 52 52
FHL2 0.008 0.075 -10000 0 -0.77 5 5
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0 0.008 -10000 0 -10000 0 0
HIST2H4A 0.025 0.043 -10000 0 -0.67 2 2
SIRT1/FOXO3a 0.001 0.016 0.32 1 -10000 0 1
SIRT1 0.001 0.01 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.008 -10000 0 -10000 0 0
SIRT1/Histone H1b 0 0.019 -10000 0 -10000 0 0
apoptosis 0 0.008 -10000 0 -10000 0 0
SIRT1/PGC1A -0.047 0.14 -10000 0 -0.48 52 52
p53/SIRT1 0.001 0.023 0.38 2 -10000 0 2
SIRT1/FOXO4 0 0.015 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.004 0.045 -10000 0 -0.46 5 5
HIST1H1E 0.029 0.022 -10000 0 -0.32 2 2
SIRT1/p300 -0.001 0.025 -10000 0 -0.56 1 1
muscle cell differentiation 0.032 0.13 0.57 30 -10000 0 30
TP53 0.001 0.01 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0 0.008 -10000 0 -10000 0 0
CREBBP 0.016 0 -10000 0 -10000 0 0
MEF2D 0.016 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.013 0.095 -10000 0 -0.67 11 11
ACSS2 0.027 0.005 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD -0.032 0.13 -10000 0 -0.57 30 30
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.057 -9999 0 -0.74 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.004 0.029 -9999 0 -10000 0 0
IRAK/TOLLIP 0 0 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
IKBKG 0.016 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.086 0.22 -9999 0 -0.62 74 74
IL1A -0.009 0.14 -9999 0 -0.86 14 14
IL1B 0.023 0.072 -9999 0 -0.65 6 6
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.026 -9999 0 -10000 0 0
IL1R2 -0.078 0.26 -9999 0 -0.79 62 62
IL1R1 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.003 0.025 -9999 0 -10000 0 0
TOLLIP 0.016 0 -9999 0 -10000 0 0
TICAM2 0.016 0.001 -9999 0 -10000 0 0
MAP3K3 0.016 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.039 0.046 -9999 0 -10000 0 0
JUN 0.059 0.037 -9999 0 -10000 0 0
MAP3K7 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.01 0.068 -9999 0 -0.77 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.017 0.094 -9999 0 -0.52 17 17
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.016 0.087 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP -0.009 0.068 -9999 0 -0.52 8 8
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
MAPK8 0.05 0.039 -9999 0 -10000 0 0
IRAK1 0.03 0.006 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.021 0.12 -9999 0 -0.66 17 17
IRAK4 0.016 0 -9999 0 -10000 0 0
PRKCI 0.016 0 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
PI3K -0.002 0.034 -9999 0 -0.56 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.031 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.009 0.068 -9999 0 -0.52 8 8
IL1 beta/IL1R2 -0.066 0.17 -9999 0 -0.51 68 68
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.009 0.069 -9999 0 -1 1 1
IRAK3 0.016 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.008 0.06 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.009 0.05 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP -0.019 0.1 -9999 0 -0.57 18 18
RELA 0.016 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.016 0 -9999 0 -10000 0 0
MYD88 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
IL1RAP 0.009 0.073 -9999 0 -0.83 4 4
UBE2N 0.016 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.007 0.048 -9999 0 -10000 0 0
CASP1 0.016 0 -9999 0 -10000 0 0
IL1RN/IL1R2 -0.09 0.22 -9999 0 -0.62 77 77
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.009 0.063 -9999 0 -10000 0 0
TMEM189-UBE2V1 0.007 0.008 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.006 0.034 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
IL1RN -0.012 0.15 -9999 0 -0.86 17 17
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.042 0.032 -9999 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.016 0 -10000 0 -10000 0 0
EPHB2 0 0.11 -10000 0 -0.76 11 11
EFNB1 0.014 0.11 -10000 0 -0.66 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.022 0.11 -10000 0 -0.78 5 5
Ephrin B2/EPHB1-2 -0.013 0.085 -10000 0 -0.53 13 13
neuron projection morphogenesis -0.021 0.1 -10000 0 -0.75 5 5
Ephrin B1/EPHB1-2/Tiam1 -0.024 0.12 -10000 0 -0.79 6 6
DNM1 -0.006 0.14 -10000 0 -0.86 13 13
cell-cell signaling 0.001 0.001 -10000 0 -10000 0 0
MAP2K4 0.023 0.091 -10000 0 -0.67 9 9
YES1 -0.015 0.12 -10000 0 -0.89 9 9
Ephrin B1/EPHB1-2/NCK2 -0.024 0.11 -10000 0 -0.87 4 4
PI3K -0.011 0.096 -10000 0 -0.69 10 10
mol:GDP -0.024 0.12 -10000 0 -0.78 6 6
ITGA2B -0.015 0.16 -10000 0 -0.86 19 19
endothelial cell proliferation 0 0 -10000 0 -10000 0 0
FYN -0.015 0.12 -10000 0 -0.89 9 9
MAP3K7 -0.012 0.092 -10000 0 -0.71 9 9
FGR -0.015 0.12 -10000 0 -0.88 9 9
TIAM1 0.014 0.033 -10000 0 -0.74 1 1
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
RGS3 0.016 0 -10000 0 -10000 0 0
cell adhesion 0.016 0.15 -10000 0 -0.56 26 26
LYN -0.015 0.12 -10000 0 -0.89 9 9
Ephrin B1/EPHB1-2/Src Family Kinases -0.015 0.11 -10000 0 -0.84 9 9
Ephrin B1/EPHB1-2 -0.015 0.1 -10000 0 -0.78 9 9
SRC -0.014 0.11 -10000 0 -0.88 9 9
ITGB3 0.007 0.08 -10000 0 -0.74 6 6
EPHB1 0.009 0.071 -10000 0 -0.8 4 4
EPHB4 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.03 0.14 -10000 0 -0.66 24 24
BLK -0.022 0.12 -10000 0 -0.88 9 9
HCK -0.021 0.12 -10000 0 -0.93 9 9
regulation of stress fiber formation 0.023 0.11 0.85 4 -10000 0 4
MAPK8 0.031 0.091 -10000 0 -0.63 9 9
Ephrin B1/EPHB1-2/RGS3 -0.024 0.11 -10000 0 -0.79 5 5
endothelial cell migration -0.009 0.079 -10000 0 -0.61 9 9
NCK2 0.016 0 -10000 0 -10000 0 0
PTPN13 -0.01 0.11 -10000 0 -0.85 9 9
regulation of focal adhesion formation 0.023 0.11 0.85 4 -10000 0 4
chemotaxis 0.023 0.11 0.78 5 -10000 0 5
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
Rac1/GTP -0.022 0.11 -10000 0 -0.78 5 5
angiogenesis -0.015 0.1 -10000 0 -0.77 9 9
LCK -0.019 0.12 -10000 0 -0.9 9 9
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 0.006 0.26 -9999 0 -1.1 27 27
MKNK1 0.016 0 -9999 0 -10000 0 0
MAPK14 0.023 0.074 -9999 0 -0.44 1 1
ATF2/c-Jun 0.043 0.065 -9999 0 -0.61 1 1
MAPK11 0.019 0.091 -9999 0 -0.69 3 3
MITF 0.042 0.094 -9999 0 -0.46 2 2
MAPKAPK5 0.042 0.094 -9999 0 -0.46 2 2
KRT8 0.041 0.095 -9999 0 -0.46 2 2
MAPKAPK3 0.016 0 -9999 0 -10000 0 0
MAPKAPK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 0.03 0.12 -9999 0 -0.65 3 3
CEBPB 0.033 0.11 -9999 0 -0.55 1 1
SLC9A1 0.042 0.094 -9999 0 -0.46 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 0.049 0.098 -9999 0 -0.68 2 2
p38alpha-beta/MNK1 -0.021 0.079 -9999 0 -0.53 3 3
JUN 0.044 0.065 -9999 0 -0.6 1 1
PPARGC1A 0 0.16 -9999 0 -0.38 54 54
USF1 0.042 0.094 -9999 0 -0.46 2 2
RAB5/GDP/GDI1 -0.014 0.053 -9999 0 -0.41 1 1
NOS2 0.036 0.14 -9999 0 -0.87 8 8
DDIT3 0.04 0.098 -9999 0 -0.4 5 5
RAB5A 0.016 0 -9999 0 -10000 0 0
HSPB1 0.045 0.095 -9999 0 -0.65 4 4
p38alpha-beta/HBP1 -0.021 0.079 -9999 0 -0.53 3 3
CREB1 0.048 0.097 -9999 0 -0.55 1 1
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E 0.046 0.083 -9999 0 -0.54 1 1
RPS6KA4 0.042 0.094 -9999 0 -0.46 2 2
PLA2G4A 0.04 0.11 -9999 0 -0.74 4 4
GDI1 0.042 0.094 -9999 0 -0.46 2 2
TP53 0.044 0.12 -9999 0 -0.56 3 3
RPS6KA5 0.042 0.094 -9999 0 -0.55 1 1
ESR1 0.038 0.1 -9999 0 -0.57 3 3
HBP1 0.016 0 -9999 0 -10000 0 0
MEF2C 0.042 0.094 -9999 0 -0.55 1 1
MEF2A 0.042 0.094 -9999 0 -0.46 2 2
EIF4EBP1 0.041 0.1 -9999 0 -0.47 4 4
KRT19 -0.046 0.21 -9999 0 -0.4 109 109
ELK4 0.042 0.094 -9999 0 -0.46 2 2
ATF6 0.042 0.094 -9999 0 -0.46 2 2
ATF1 0.048 0.097 -9999 0 -0.55 1 1
p38alpha-beta/MAPKAPK2 -0.021 0.079 -9999 0 -0.53 3 3
p38alpha-beta/MAPKAPK3 -0.021 0.079 -9999 0 -0.53 3 3
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.01 0.067 -10000 0 -0.5 6 6
ER alpha/Gai/GDP/Gbeta gamma 0.053 0.057 -10000 0 -10000 0 0
AKT1 0.045 0.08 -10000 0 -0.8 4 4
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.04 0.08 -10000 0 -0.73 5 5
mol:Ca2+ -0.015 0.19 -10000 0 -0.46 67 67
IGF1R 0.016 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.008 0.07 -10000 0 -0.55 8 8
SHC1 0.014 0.038 -10000 0 -0.86 1 1
apoptosis -0.045 0.076 0.68 5 -10000 0 5
RhoA/GTP -0.004 0.039 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.008 0.048 -10000 0 -10000 0 0
regulation of stress fiber formation -0.066 0.053 0.54 2 -10000 0 2
E2/ERA-ERB (dimer) -0.012 0.08 -10000 0 -0.54 12 12
KRAS 0.016 0 -10000 0 -10000 0 0
G13/GTP -0.004 0.045 -10000 0 -0.46 5 5
pseudopodium formation 0.066 0.053 -10000 0 -0.54 2 2
E2/ER alpha (dimer)/PELP1 -0.005 0.049 -10000 0 -0.5 5 5
GRB2 0.016 0 -10000 0 -10000 0 0
GNG2 0.016 0 -10000 0 -10000 0 0
GNAO1 0.008 0.082 -10000 0 -0.84 5 5
HRAS 0.014 0.038 -10000 0 -0.86 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.062 0.064 -10000 0 -0.46 5 5
E2/ER beta (dimer) -0.008 0.074 -10000 0 -0.64 7 7
mol:GDP -0.01 0.062 -10000 0 -0.41 12 12
mol:NADP 0.062 0.064 -10000 0 -0.46 5 5
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
mol:IP3 -0.018 0.19 -10000 0 -0.49 63 63
IGF-1R heterotetramer 0.016 0 -10000 0 -10000 0 0
PLCB1 -0.025 0.1 -10000 0 -0.56 12 12
PLCB2 -0.067 0.17 -10000 0 -0.48 68 68
IGF1 0.006 0.093 -10000 0 -0.86 6 6
mol:L-citrulline 0.062 0.064 -10000 0 -0.46 5 5
RHOA 0.016 0 -10000 0 -10000 0 0
Gai/GDP -0.007 0.047 -10000 0 -0.63 1 1
JNK cascade -0.008 0.073 -10000 0 -0.64 7 7
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
ESR2 0.005 0.096 -10000 0 -0.83 7 7
GNAQ 0.016 0 -10000 0 -10000 0 0
ESR1 0.008 0.075 -10000 0 -0.77 5 5
Gq family/GDP/Gbeta gamma -0.016 0.076 -10000 0 -0.59 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.051 0.035 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.008 0.049 -10000 0 -10000 0 0
GNAZ 0.011 0.057 -10000 0 -0.74 3 3
E2/ER alpha (dimer) -0.006 0.057 -10000 0 -0.59 5 5
STRN 0.01 0.065 -10000 0 -0.74 4 4
GNAL 0.016 0 -10000 0 -10000 0 0
PELP1 0.016 0 -10000 0 -10000 0 0
MAPK11 0.015 0.076 -10000 0 -0.56 9 9
GNAI2 0.016 0 -10000 0 -10000 0 0
GNAI3 0.016 0 -10000 0 -10000 0 0
GNAI1 0.011 0.057 -10000 0 -0.74 3 3
HBEGF -0.042 0.14 -10000 0 -0.51 6 6
cAMP biosynthetic process -0.01 0.065 -10000 0 -0.43 12 12
SRC 0.062 0.054 -10000 0 -10000 0 0
PI3K -0.002 0.034 -10000 0 -0.56 2 2
GNB1 0.016 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.008 0.054 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.01 0.051 -10000 0 -10000 0 0
Gs family/GTP -0.01 0.066 -10000 0 -0.44 12 12
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.023 -10000 0 -0.53 1 1
vasodilation 0.062 0.062 -10000 0 -0.44 5 5
mol:DAG -0.018 0.19 -10000 0 -0.49 63 63
Gs family/GDP/Gbeta gamma -0.008 0.049 -10000 0 -10000 0 0
MSN 0.068 0.057 -10000 0 -0.59 2 2
Gq family/GTP -0.019 0.082 -10000 0 -0.49 11 11
mol:PI-3-4-5-P3 0.04 0.077 -10000 0 -0.7 5 5
NRAS 0.016 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.062 0.062 0.44 5 -10000 0 5
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.009 0.058 -10000 0 -0.44 5 5
NOS3 0.063 0.067 -10000 0 -0.48 5 5
GNA11 0.011 0.057 -10000 0 -0.74 3 3
MAPKKK cascade 0.07 0.075 -10000 0 -0.58 5 5
E2/ER alpha (dimer)/PELP1/Src -0.008 0.049 -10000 0 -10000 0 0
ruffle organization 0.066 0.053 -10000 0 -0.54 2 2
ROCK2 -0.006 0.055 -10000 0 -0.68 2 2
GNA14 0.004 0.092 -10000 0 -0.74 8 8
GNA15 -0.009 0.14 -10000 0 -0.86 15 15
GNA13 0.016 0 -10000 0 -10000 0 0
MMP9 -0.16 0.25 -10000 0 -0.66 8 8
MMP2 0.064 0.083 -10000 0 -0.66 3 3
p38 MAPK signaling pathway

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
TRAF6/ASK1 0 0 -10000 0 -10000 0 0
TRAF2/ASK1 0 0 -10000 0 -10000 0 0
ATM 0.014 0.033 -10000 0 -0.74 1 1
MAP2K3 0.038 0.044 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.049 0.045 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.002 0.12 -10000 0 -0.85 11 11
TXN 0.011 0 -10000 0 -10000 0 0
CALM1 0.016 0 -10000 0 -10000 0 0
GADD45A 0.016 0 -10000 0 -10000 0 0
GADD45B 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.016 0 -10000 0 -10000 0 0
MAP3K6 0.014 0.033 -10000 0 -0.74 1 1
MAP3K7 0.016 0 -10000 0 -10000 0 0
MAP3K4 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.001 0.024 -10000 0 -0.56 1 1
TAK1/TAB family 0.001 0.012 0.2 2 -10000 0 2
RAC1/OSM/MEKK3 0 0 -10000 0 -10000 0 0
TRAF2 0.016 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.004 0.014 -10000 0 -10000 0 0
TRAF6 0.011 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.099 0.27 -10000 0 -0.75 79 79
CCM2 0.016 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.073 0.18 -10000 0 -0.49 79 79
MAPK11 0.012 0.054 -10000 0 -0.86 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.066 0.16 -10000 0 -0.44 79 79
OSM/MEKK3 0 0 -10000 0 -10000 0 0
TAOK1 0.016 0.053 -10000 0 -0.41 8 8
TAOK2 0.022 0.019 -10000 0 -0.41 1 1
TAOK3 0.022 0.019 -10000 0 -0.41 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.016 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.016 0 -10000 0 -10000 0 0
MAP3K10 0.014 0.033 -10000 0 -0.74 1 1
MAP3K3 0.016 0 -10000 0 -10000 0 0
TRX/ASK1 0 0 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 -0.01 0.069 -10000 0 -0.5 10 10
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.028 0.003 -10000 0 -10000 0 0
RAS family/GTP -0.015 0.073 -10000 0 -0.72 3 3
NFATC4 0.047 0.076 -10000 0 -0.54 2 2
ERBB2IP 0.008 0.008 -10000 0 -10000 0 0
HSP90 (dimer) 0.016 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.017 0.077 -10000 0 -0.64 1 1
JUN 0.037 0.079 -10000 0 -0.41 2 2
HRAS 0.013 0.038 -10000 0 -0.86 1 1
DOCK7 0.02 0.091 -10000 0 -0.62 2 2
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.022 0.1 -10000 0 -0.87 2 2
AKT1 0.016 0.002 -10000 0 -10000 0 0
BAD 0.026 0.035 -10000 0 -0.54 2 2
MAPK10 -0.01 0.044 -10000 0 -0.39 1 1
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.019 0.083 -10000 0 -0.72 1 1
RAF1 0.039 0.094 -10000 0 -0.68 3 3
ErbB2/ErbB3/neuregulin 2 -0.019 0.095 -10000 0 -0.48 21 21
STAT3 0 0.002 -10000 0 -10000 0 0
cell migration 0.059 0.056 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.086 0.26 -10000 0 -0.6 9 9
FOS -0.035 0.19 -10000 0 -0.48 15 15
NRAS 0.015 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.017 0.077 -10000 0 -0.64 1 1
MAPK3 -0.056 0.21 -10000 0 -0.56 8 8
MAPK1 -0.056 0.21 -10000 0 -0.56 8 8
JAK2 0.021 0.087 -10000 0 -0.6 1 1
NF2 -0.001 0.002 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.006 0.089 -10000 0 -0.82 2 2
NRG1 -0.015 0.13 -10000 0 -0.74 17 17
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 0.024 0.086 -10000 0 -0.47 3 3
MAPK9 -0.008 0.036 -10000 0 -10000 0 0
ERBB2 -0.002 0.035 -10000 0 -0.57 2 2
ERBB3 -0.004 0.097 -10000 0 -0.74 9 9
SHC1 0.008 0.039 -10000 0 -0.86 1 1
RAC1 0.016 0 -10000 0 -10000 0 0
apoptosis 0.002 0.022 0.35 2 -10000 0 2
STAT3 (dimer) 0 0.002 -10000 0 -10000 0 0
RNF41 0.038 0.005 -10000 0 -10000 0 0
FRAP1 0.014 0.002 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.012 0.052 -10000 0 -0.42 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.002 0.03 -10000 0 -0.49 2 2
CHRNA1 -0.13 0.28 -10000 0 -0.45 229 229
myelination 0.05 0.074 -10000 0 -0.48 2 2
PPP3CB 0.02 0.082 -10000 0 -0.55 1 1
KRAS 0.015 0.001 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.014 0.068 -10000 0 -0.72 2 2
NRG2 -0.001 0.12 -10000 0 -0.85 10 10
mol:GDP 0.007 0.089 -10000 0 -0.81 2 2
SOS1 0.009 0.008 -10000 0 -10000 0 0
MAP2K2 0.046 0.096 -10000 0 -0.63 3 3
SRC 0.016 0 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 0.02 0.087 -10000 0 -0.6 1 1
MAP2K1 -0.039 0.18 -10000 0 -0.57 8 8
heart morphogenesis -0.017 0.077 -10000 0 -0.64 1 1
RAS family/GDP -0.014 0.073 -10000 0 -0.72 3 3
GRB2 0.009 0.008 -10000 0 -10000 0 0
PRKACA -0.001 0.005 -10000 0 -10000 0 0
CHRNE 0.021 0.026 -10000 0 -0.24 2 2
HSP90AA1 0.016 0 -10000 0 -10000 0 0
activation of caspase activity -0.016 0.002 -10000 0 -10000 0 0
nervous system development -0.017 0.077 -10000 0 -0.64 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.02 0.17 -10000 0 -0.71 27 27
regulation of axonogenesis -0.033 0.034 -10000 0 -10000 0 0
myoblast fusion 0.016 0.07 0.32 27 -10000 0 27
mol:GTP -0.01 0.043 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.01 0.047 0.49 2 -10000 0 2
ARF1/GTP -0.007 0.029 -10000 0 -10000 0 0
mol:GM1 0.007 0.035 -10000 0 -10000 0 0
mol:Choline 0.033 0.031 -10000 0 -10000 0 0
lamellipodium assembly -0.016 0.073 -10000 0 -0.33 27 27
MAPK3 0.024 0.068 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.01 0.047 -10000 0 -0.5 2 2
ARF1 0.016 0 -10000 0 -10000 0 0
ARF6/GDP -0.016 0.07 -10000 0 -0.32 27 27
ARF1/GDP 0.02 0.07 -10000 0 -10000 0 0
ARF6 0.009 0.024 -10000 0 -10000 0 0
RAB11A 0.016 0 -10000 0 -10000 0 0
TIAM1 0.016 0.033 -10000 0 -0.74 1 1
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.024 0.068 -10000 0 -10000 0 0
actin filament bundle formation 0.014 0.062 -10000 0 -10000 0 0
KALRN -0.012 0.055 -10000 0 -10000 0 0
RAB11FIP3/RAB11A -0.001 0.024 -10000 0 -0.56 1 1
RhoA/GDP -0.014 0.062 -10000 0 -10000 0 0
NME1 0.016 0.038 -10000 0 -0.86 1 1
Rac1/GDP -0.014 0.062 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading -0.01 0.043 -10000 0 -10000 0 0
cortical actin cytoskeleton organization -0.016 0.074 -10000 0 -0.33 27 27
RAC1 0.016 0 -10000 0 -10000 0 0
liver development -0.01 0.043 -10000 0 -10000 0 0
ARF6/GTP -0.01 0.043 -10000 0 -10000 0 0
RhoA/GTP -0.007 0.029 -10000 0 -10000 0 0
mol:GDP -0.016 0.071 -10000 0 -0.32 27 27
ARF6/GTP/RAB11FIP3/RAB11A -0.006 0.029 -10000 0 -0.45 1 1
RHOA 0.016 0 -10000 0 -10000 0 0
PLD1 0.021 0.035 -10000 0 -10000 0 0
RAB11FIP3 0.014 0.033 -10000 0 -0.74 1 1
tube morphogenesis -0.016 0.073 -10000 0 -0.33 27 27
ruffle organization 0.033 0.034 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.01 0.043 -10000 0 -10000 0 0
PLD2 0.021 0.035 -10000 0 -10000 0 0
PIP5K1A 0.033 0.034 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.033 0.031 -10000 0 -10000 0 0
Rac1/GTP -0.016 0.074 -10000 0 -0.33 27 27
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.035 0.056 -9999 0 -0.49 6 6
SNTA1 0.013 0.05 -9999 0 -0.8 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.036 0.049 -9999 0 -0.47 5 5
MAPK12 0.029 0.084 -9999 0 -0.49 13 13
CCND1 0.014 0.07 -9999 0 -0.3 20 20
p38 gamma/SNTA1 0.033 0.088 -9999 0 -0.51 11 11
MAP2K3 0.016 0 -9999 0 -10000 0 0
PKN1 0.016 0 -9999 0 -10000 0 0
G2/M transition checkpoint 0.029 0.083 -9999 0 -0.49 13 13
MAP2K6 0.03 0.041 -9999 0 -0.47 3 3
MAPT 0.032 0.068 -9999 0 -0.49 6 6
MAPK13 0.025 0.057 -9999 0 -0.56 5 5
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.022 0.018 -9999 0 -0.39 1 1
Syndecan-3-mediated signaling events

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
CTTN 0.016 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.013 0.068 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.013 0.077 -9999 0 -0.48 14 14
POMC 0.012 0.05 -9999 0 -0.8 2 2
EGFR 0.001 0.11 -9999 0 -0.85 9 9
Syndecan-3/EGFR -0.009 0.064 -9999 0 -0.47 10 10
AGRP 0.007 0.047 -9999 0 -0.74 2 2
NCSTN 0.016 0 -9999 0 -10000 0 0
PSENEN 0.016 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.016 0 -9999 0 -10000 0 0
APH1A 0.016 0 -9999 0 -10000 0 0
NCAN -0.01 0.14 -9999 0 -0.86 13 13
long-term memory -0.001 0.016 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.031 0.12 -9999 0 -0.47 35 35
PSEN1 0.016 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.018 -9999 0 -0.43 1 1
MC4R -0.01 0.11 -9999 0 -0.86 9 9
SRC 0.016 0 -9999 0 -10000 0 0
PTN -0.012 0.14 -9999 0 -0.75 19 19
FGFR/FGF/Syndecan-3 -0.001 0.019 -9999 0 -0.43 1 1
neuron projection morphogenesis -0.023 0.09 -9999 0 -10000 0 0
Syndecan-3/AgRP -0.002 0.03 -9999 0 -0.4 3 3
Syndecan-3/AgRP/MC4R -0.01 0.066 -9999 0 -0.47 9 9
Fyn/Cortactin 0 0 -9999 0 -10000 0 0
SDC3 -0.001 0.019 -9999 0 -0.43 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.03 0.12 -9999 0 -0.46 35 35
IL8 -0.039 0.21 -9999 0 -0.84 34 34
Syndecan-3/Fyn/Cortactin -0.001 0.016 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.018 -9999 0 -0.41 1 1
alpha-MSH/MC4R -0.014 0.094 -9999 0 -0.66 11 11
Gamma Secretase 0 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.021 0.1 -9999 0 -0.51 22 22
KLHL20 -0.013 0.046 -9999 0 -0.35 2 2
CYFIP2 0.004 0.092 -9999 0 -0.74 8 8
Rac1/GDP 0.067 0.076 -9999 0 -10000 0 0
ENAH -0.021 0.1 -9999 0 -0.51 22 22
AP1M1 0.016 0 -9999 0 -10000 0 0
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.015 0.003 -9999 0 -10000 0 0
CDC42/GTP -0.01 0.047 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.01 0.036 -9999 0 -0.22 7 7
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.017 0.084 -9999 0 -10000 0 0
RAPGEF1 0.053 0.099 -9999 0 -10000 0 0
CTNND1 0.016 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.022 0.11 -9999 0 -0.53 22 22
CRK 0.042 0.11 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin -0.022 0.1 -9999 0 -0.49 24 24
alphaE/beta7 Integrin 0 0 -9999 0 -10000 0 0
IQGAP1 0.016 0 -9999 0 -10000 0 0
NCKAP1 0.016 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
DLG1 -0.021 0.1 -9999 0 -0.51 22 22
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.035 -9999 0 -10000 0 0
MLLT4 0.016 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.002 0.03 -9999 0 -0.48 2 2
PI3K -0.01 0.044 -9999 0 -10000 0 0
ARF6 0.016 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.026 0.12 -9999 0 -0.57 24 24
TIAM1 0.014 0.033 -9999 0 -0.74 1 1
E-cadherin(dimer)/Ca2+ -0.017 0.08 -9999 0 -10000 0 0
AKT1 -0.005 0.025 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
CDH1 -0.016 0.15 -9999 0 -0.74 22 22
RhoA/GDP 0.067 0.076 -9999 0 -10000 0 0
actin cytoskeleton organization -0.01 0.034 -9999 0 -0.24 2 2
CDC42/GDP 0.067 0.076 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.014 0.068 -9999 0 -0.32 24 24
ITGB7 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.017 0.084 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin -0.017 0.082 -9999 0 -0.41 22 22
mol:GDP 0.063 0.087 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.011 0.057 -9999 0 -0.74 3 3
p120 catenin/RhoA/GDP -0.012 0.06 -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 0.016 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.035 0.063 -9999 0 -0.26 20 20
NME1 0.014 0.038 -9999 0 -0.86 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.021 0.1 -9999 0 -0.51 22 22
regulation of cell-cell adhesion -0.009 0.041 -9999 0 -10000 0 0
WASF2 -0.005 0.018 -9999 0 -10000 0 0
Rap1/GTP -0.011 0.054 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.018 0.086 -9999 0 -0.8 1 1
CCND1 -0.016 0.065 -9999 0 -0.33 20 20
VAV2 0.049 0.1 -9999 0 -10000 0 0
RAP1/GDP -0.011 0.056 -9999 0 -10000 0 0
adherens junction assembly 0.032 0.11 -9999 0 -0.49 22 22
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.016 0 -9999 0 -10000 0 0
PIP5K1C 0.016 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.017 0.081 -9999 0 -0.77 1 1
E-cadherin/beta catenin -0.019 0.09 -9999 0 -0.45 22 22
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.021 0.1 -9999 0 -0.51 22 22
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
Rac1/GTP -0.021 0.072 -9999 0 -0.6 1 1
E-cadherin/beta catenin/alpha catenin -0.019 0.094 -9999 0 -0.47 22 22
ITGAE 0.016 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.023 0.11 -9999 0 -0.55 22 22
Arf6 trafficking events

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
SLC2A4 -0.003 0.12 -10000 0 -0.81 12 12
CLTC 0.043 0.014 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.036 0.001 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.023 -10000 0 -0.53 1 1
EXOC4 0.016 0 -10000 0 -10000 0 0
CD59 0.039 0.009 -10000 0 -10000 0 0
CPE 0 0.12 -10000 0 -0.58 22 22
CTNNB1 0.016 0 -10000 0 -10000 0 0
membrane fusion 0 0 -10000 0 -10000 0 0
CTNND1 0.042 0.023 -10000 0 -0.49 1 1
DNM2 0.016 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.006 -10000 0 -10000 0 0
TSHR -0.045 0.2 -10000 0 -0.59 61 61
INS 0.016 0.002 -10000 0 -10000 0 0
BIN1 0.016 0 -10000 0 -10000 0 0
mol:Choline 0 0 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.026 -10000 0 -0.58 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.016 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.023 -10000 0 -0.53 1 1
JUP 0.037 0.023 -10000 0 -10000 0 0
ASAP2/amphiphysin II -0.001 0.019 -10000 0 -0.43 1 1
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.027 0.056 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 -0.049 0.23 -10000 0 -0.86 39 39
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.016 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.058 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.016 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.007 0.035 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.025 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 -0.043 0.15 -10000 0 -0.59 39 39
ACAP1 -0.019 0.025 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.032 0.015 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.042 0.017 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.016 0 -10000 0 -10000 0 0
exocyst 0 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 0.042 0.023 -10000 0 -0.49 1 1
NME1 0.024 0.026 -10000 0 -0.59 1 1
clathrin coat assembly 0.042 0.014 -10000 0 -10000 0 0
IL2RA -0.015 0.11 -10000 0 -10000 0 0
VAMP3 0.025 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.009 0.06 -10000 0 -0.43 7 7
EXOC6 0.016 0 -10000 0 -10000 0 0
PLD1 0 0 -10000 0 -10000 0 0
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.016 0 -10000 0 -10000 0 0
PIP5K1C 0.044 0.006 -10000 0 -10000 0 0
SDC1 0.036 0.031 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.025 -10000 0 -0.58 1 1
EXOC7 0.016 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.007 0.036 -10000 0 -10000 0 0
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
endocytosis 0.001 0.019 0.43 1 -10000 0 1
SCAMP2 0.016 0 -10000 0 -10000 0 0
ADRB2 0.049 0.029 -10000 0 -0.37 2 2
EXOC3 0.016 0 -10000 0 -10000 0 0
ASAP2 0.014 0.033 -10000 0 -0.74 1 1
Dynamin 2/GDP -0.001 0.023 -10000 0 -0.53 1 1
KLC1 0.016 0 -10000 0 -10000 0 0
AVPR2 -0.12 0.21 -10000 0 -0.37 220 220
RALA 0.016 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.006 0.03 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1 0.049 0.12 -9999 0 -0.68 5 5
MAP3K8 0.013 0.054 -9999 0 -0.86 2 2
FOS 0.041 0.11 -9999 0 -0.57 5 5
PRKCA 0.017 0.003 -9999 0 -10000 0 0
PTPN7 -0.037 0.21 -9999 0 -0.86 34 34
HRAS 0.014 0.038 -9999 0 -0.86 1 1
PRKCB 0.009 0.081 -9999 0 -0.82 5 5
NRAS 0.016 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.001 0.023 -9999 0 -0.53 1 1
MAPK3 0.029 0.085 -9999 0 -0.52 3 3
MAP2K1 0.055 0.055 -9999 0 -0.48 5 5
ELK1 0.017 0.003 -9999 0 -10000 0 0
BRAF -0.004 0.043 -9999 0 -0.46 4 4
mol:GTP 0 0.001 -9999 0 -0.006 12 12
MAPK1 0.029 0.085 -9999 0 -0.52 3 3
RAF1 -0.004 0.043 -9999 0 -0.44 5 5
KRAS 0.016 0.001 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.006 0.064 -9999 0 -0.66 5 5
CRKL 0.04 0.064 -9999 0 -0.46 2 2
mol:PIP3 -0.03 0.003 -9999 0 -10000 0 0
AKT1 0 0.019 -9999 0 -0.44 1 1
PTK2B 0.016 0 -9999 0 -10000 0 0
RAPGEF1 0.049 0.061 -9999 0 -0.43 2 2
RANBP10 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
HGF/MET/SHIP2 -0.028 0.13 -9999 0 -0.57 26 26
MAP3K5 -0.025 0.12 -9999 0 -0.41 1 1
HGF/MET/CIN85/CBL/ENDOPHILINS -0.026 0.12 -9999 0 -0.61 15 15
AP1 -0.014 0.08 -9999 0 -0.51 13 13
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.014 0.038 -9999 0 -0.86 1 1
apoptosis 0.004 0.11 -9999 0 -0.7 12 12
STAT3 (dimer) 0.041 0.077 -9999 0 -0.53 3 3
GAB1/CRKL/SHP2/PI3K -0.011 0.054 -9999 0 -0.58 2 2
INPP5D 0.009 0.076 -9999 0 -0.86 4 4
CBL/CRK 0.047 0.067 -9999 0 -0.51 3 3
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.016 0 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
ELK1 0.001 0.029 -9999 0 -0.29 5 5
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.008 0.038 -9999 0 -0.34 2 2
PAK1 0.01 0.018 -9999 0 -0.41 1 1
HGF/MET/RANBP10 -0.028 0.13 -9999 0 -0.57 26 26
HRAS 0.032 0.096 -9999 0 -0.71 3 3
DOCK1 0.049 0.067 -9999 0 -0.51 3 3
GAB1 0.031 0.067 -9999 0 -0.44 3 3
CRK 0.04 0.064 -9999 0 -0.46 2 2
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.022 0.1 -9999 0 -0.54 14 14
JUN 0.016 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.013 0.059 -9999 0 -0.4 5 5
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
cell morphogenesis 0.079 0.083 -9999 0 -0.65 2 2
GRB2/SHC -0.011 0.056 -9999 0 -0.54 3 3
FOS -0.003 0.12 -9999 0 -0.75 13 13
GLMN 0 0 -9999 0 -10000 0 0
cell motility 0.001 0.029 -9999 0 -0.29 5 5
HGF/MET/MUC20 -0.028 0.13 -9999 0 -0.58 26 26
cell migration -0.011 0.055 -9999 0 -0.52 3 3
GRB2 0.016 0 -9999 0 -10000 0 0
CBL 0.014 0.033 -9999 0 -0.74 1 1
MET/RANBP10 -0.006 0.064 -9999 0 -0.66 5 5
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.015 0.071 -9999 0 -0.58 3 3
MET/MUC20 -0.006 0.065 -9999 0 -0.68 5 5
RAP1B 0.058 0.058 -9999 0 -10000 0 0
RAP1A 0.058 0.058 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.028 0.13 -9999 0 -0.57 26 26
RAF1 0.041 0.092 -9999 0 -0.66 3 3
STAT3 -0.014 0.065 -9999 0 -0.54 3 3
cell proliferation 0.055 0.1 -9999 0 -0.62 4 4
RPS6KB1 -0.004 0.019 -9999 0 -10000 0 0
MAPK3 -0.006 0.026 -9999 0 -0.27 5 5
MAPK1 -0.006 0.026 -9999 0 -0.27 5 5
RANBP9 0.016 0 -9999 0 -10000 0 0
MAPK8 0.011 0.1 -9999 0 -0.56 2 2
SRC 0.042 0.077 -9999 0 -0.54 3 3
PI3K -0.012 0.06 -9999 0 -0.53 4 4
MET/Glomulin 0.009 0.06 -9999 0 -0.61 5 5
SOS1 0.016 0 -9999 0 -10000 0 0
MAP2K1 0.05 0.086 -9999 0 -0.6 3 3
MET 0.007 0.085 -9999 0 -0.86 5 5
MAP4K1 -0.037 0.12 -9999 0 -0.42 6 6
PTK2 0.016 0 -9999 0 -10000 0 0
MAP2K2 0.05 0.088 -9999 0 -0.6 3 3
BAD 0.008 0.044 -9999 0 -0.66 2 2
MAP2K4 -0.012 0.11 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.011 0.055 -9999 0 -0.57 2 2
INPPL1 0.016 0 -9999 0 -10000 0 0
PXN 0.016 0 -9999 0 -10000 0 0
SH3KBP1 0.016 0 -9999 0 -10000 0 0
HGS -0.011 0.053 -9999 0 -0.49 2 2
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.019 0.17 -9999 0 -0.8 23 23
RASA1 0.014 0.033 -9999 0 -0.74 1 1
NCK1 0.014 0.033 -9999 0 -0.74 1 1
PTPRJ 0.016 0 -9999 0 -10000 0 0
NCK/PLCgamma1 -0.012 0.058 -9999 0 -0.53 3 3
PDPK1 -0.014 0.021 -9999 0 -0.49 1 1
HGF/MET/SHIP -0.032 0.14 -9999 0 -0.59 29 29
EPHB forward 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
Ephrin A5/EPHB2 -0.058 0.16 -10000 0 -0.49 63 63
cell-cell adhesion 0.014 0.074 0.63 3 -10000 0 3
Ephrin B/EPHB2/RasGAP -0.015 0.08 -10000 0 -0.8 1 1
ITSN1 0.016 0 -10000 0 -10000 0 0
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
SHC1 0.014 0.038 -10000 0 -0.86 1 1
Ephrin B1/EPHB3 -0.013 0.079 -10000 0 -0.49 14 14
Ephrin B1/EPHB1 -0.004 0.046 -10000 0 -0.53 4 4
HRAS/GDP -0.009 0.055 -10000 0 -10000 0 0
Ephrin B/EPHB1/GRB7 -0.015 0.076 -10000 0 -10000 0 0
Endophilin/SYNJ1 0.035 0.086 -10000 0 -0.74 1 1
KRAS 0.016 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.009 0.06 -10000 0 -10000 0 0
endothelial cell migration -0.001 0.024 -10000 0 -10000 0 0
GRB2 0.016 0 -10000 0 -10000 0 0
GRB7 0.004 0.092 -10000 0 -0.74 8 8
PAK1 0.047 0.084 -10000 0 -0.75 1 1
HRAS 0.014 0.038 -10000 0 -0.86 1 1
RRAS 0.036 0.087 -10000 0 -0.76 1 1
DNM1 -0.006 0.14 -10000 0 -0.86 13 13
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.042 0.065 -10000 0 -10000 0 0
lamellipodium assembly -0.014 0.074 -10000 0 -0.63 3 3
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.006 0.038 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
EPHB2 0 0.11 -10000 0 -0.76 11 11
EPHB3 -0.004 0.12 -10000 0 -0.75 14 14
EPHB1 0.01 0.071 -10000 0 -0.8 4 4
EPHB4 0.016 0 -10000 0 -10000 0 0
mol:GDP -0.004 0.061 -10000 0 -10000 0 0
Ephrin B/EPHB2 -0.015 0.08 -10000 0 -0.6 3 3
Ephrin B/EPHB3 -0.017 0.088 -10000 0 -0.71 3 3
JNK cascade 0.04 0.086 -10000 0 -0.78 2 2
Ephrin B/EPHB1 -0.009 0.062 -10000 0 -0.5 2 2
RAP1/GDP -0.003 0.053 -10000 0 -10000 0 0
EFNB2 0.016 0 -10000 0 -10000 0 0
EFNB3 0.004 0.092 -10000 0 -0.74 8 8
EFNB1 0.016 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.013 0.085 -10000 0 -0.53 13 13
RAP1B 0.016 0 -10000 0 -10000 0 0
RAP1A 0.016 0 -10000 0 -10000 0 0
CDC42/GTP -0.016 0.082 -10000 0 -0.7 3 3
Rap1/GTP -0.014 0.074 -10000 0 -0.64 3 3
axon guidance -0.058 0.16 -10000 0 -0.49 63 63
MAPK3 0.065 0.042 -10000 0 -10000 0 0
MAPK1 0.065 0.042 -10000 0 -10000 0 0
Rac1/GDP -0.004 0.056 -10000 0 -10000 0 0
actin cytoskeleton reorganization -0.011 0.059 -10000 0 -0.49 2 2
CDC42/GDP -0.004 0.056 -10000 0 -10000 0 0
PI3K -0.002 0.025 -10000 0 -10000 0 0
EFNA5 -0.059 0.23 -10000 0 -0.75 52 52
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.01 0.056 -10000 0 -0.6 1 1
CDC42 0.016 0 -10000 0 -10000 0 0
RAS family/GTP -0.015 0.077 -10000 0 -0.64 4 4
PTK2 0.003 0.017 -10000 0 -10000 0 0
MAP4K4 0.04 0.087 -10000 0 -0.79 2 2
SRC 0.016 0 -10000 0 -10000 0 0
KALRN 0.016 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.011 0.059 -10000 0 -0.5 1 1
MAP2K1 0.056 0.044 -10000 0 -10000 0 0
WASL 0.016 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.013 0.085 -10000 0 -0.63 6 6
cell migration 0.066 0.05 -10000 0 -10000 0 0
NRAS 0.016 0 -10000 0 -10000 0 0
SYNJ1 0.035 0.088 -10000 0 -0.76 1 1
PXN 0.016 0 -10000 0 -10000 0 0
TF -0.075 0.23 -10000 0 -0.79 3 3
HRAS/GTP -0.016 0.086 -10000 0 -0.71 4 4
Ephrin B1/EPHB1-2 -0.013 0.085 -10000 0 -0.53 13 13
cell adhesion mediated by integrin 0.01 0.064 0.46 8 -10000 0 8
RAC1 0.016 0 -10000 0 -10000 0 0
mol:GTP -0.017 0.087 -10000 0 -0.74 3 3
RAC1-CDC42/GTP -0.022 0.099 -10000 0 -0.77 5 5
RASA1 0.014 0.033 -10000 0 -0.74 1 1
RAC1-CDC42/GDP -0.003 0.053 -10000 0 -10000 0 0
ruffle organization 0.069 0.09 -10000 0 -0.64 3 3
NCK1 0.014 0.033 -10000 0 -0.74 1 1
receptor internalization 0.033 0.12 -10000 0 -0.77 2 2
Ephrin B/EPHB2/KALRN -0.014 0.079 -10000 0 -0.8 1 1
ROCK1 0.022 0.076 -10000 0 -0.44 14 14
RAS family/GDP -0.011 0.059 -10000 0 -0.53 1 1
Rac1/GTP -0.015 0.079 -10000 0 -0.68 3 3
Ephrin B/EPHB1/Src/Paxillin -0.006 0.042 -10000 0 -10000 0 0
BARD1 signaling events

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
BARD1/CSTF1 -0.004 0.048 -10000 0 -0.56 4 4
ATM 0.014 0.033 -10000 0 -0.74 1 1
UBE2D3 0.016 0 -10000 0 -10000 0 0
PRKDC 0.016 0 -10000 0 -10000 0 0
ATR 0.016 0 -10000 0 -10000 0 0
UBE2L3 0.016 0 -10000 0 -10000 0 0
FANCD2 0.034 0.019 -10000 0 -0.4 1 1
protein ubiquitination -0.011 0.074 -10000 0 -0.87 1 1
XRCC5 0.016 0 -10000 0 -10000 0 0
XRCC6 0.016 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.016 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.033 0.067 -10000 0 -0.52 1 1
FANCF 0.016 0 -10000 0 -10000 0 0
BRCA1 0.016 0 -10000 0 -10000 0 0
CCNE1 0.003 0.11 -10000 0 -0.86 8 8
CDK2/Cyclin E1 -0.01 0.081 -10000 0 -0.66 8 8
FANCG 0.016 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.004 0.048 -10000 0 -0.56 4 4
FANCE 0.014 0.038 -10000 0 -0.86 1 1
FANCC 0.016 0 -10000 0 -10000 0 0
NBN 0.016 0 -10000 0 -10000 0 0
FANCA -0.17 0.36 -10000 0 -0.86 110 110
DNA repair 0.044 0.13 -10000 0 -0.67 5 5
BRCA1/BARD1/ubiquitin -0.004 0.048 -10000 0 -0.56 4 4
BARD1/DNA-PK -0.003 0.037 -10000 0 -10000 0 0
FANCL 0.016 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.004 0.048 0.55 4 -10000 0 4
BRCA1/BARD1/CTIP/M/R/N Complex -0.004 0.041 -10000 0 -0.78 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.004 0.041 -10000 0 -0.47 4 4
BRCA1/BARD1/P53 -0.003 0.037 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 -0.004 0.041 -10000 0 -0.47 4 4
BRCA1/BACH1 0.016 0 -10000 0 -10000 0 0
BARD1 0.01 0.065 -10000 0 -0.74 4 4
PCNA 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.004 0.041 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 -0.004 0.041 -10000 0 -0.47 4 4
BRCA1/BARD1/RAD51/PCNA -0.017 0.091 -10000 0 -0.52 14 14
BARD1/DNA-PK/P53 -0.003 0.034 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.004 0.048 -10000 0 -0.56 4 4
BRCA1/BARD1/CTIP -0.005 0.052 -10000 0 -0.85 1 1
FA complex -0.056 0.11 -10000 0 -0.57 1 1
BARD1/EWS -0.004 0.048 -10000 0 -0.56 4 4
RBBP8 0.029 0.045 -10000 0 -1 1 1
TP53 0.016 0 -10000 0 -10000 0 0
TOPBP1 0.016 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.003 0.036 -10000 0 -10000 0 0
BRCA1/BARD1 -0.011 0.075 -10000 0 -0.89 1 1
CSTF1 0.016 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.004 0.049 -10000 0 -0.57 4 4
CDK2 0.016 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.007 0.14 -10000 0 -0.86 14 14
RAD50 0.016 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.004 0.048 -10000 0 -0.56 4 4
EWSR1 0.016 0 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer -0.011 0.063 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.011 0.059 -9999 0 -0.67 1 1
alphaV/beta3 Integrin/Osteopontin/Src -0.004 0.047 -9999 0 -0.54 4 4
AP1 -0.019 0.092 -9999 0 -0.69 6 6
ILK 0.06 0.065 -9999 0 -10000 0 0
bone resorption -0.026 0.1 -9999 0 -0.72 4 4
PTK2B 0.016 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.008 0.053 -9999 0 -10000 0 0
ITGAV 0.022 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.03 0.14 -9999 0 -0.65 25 25
alphaV/beta3 Integrin/Osteopontin -0.009 0.061 -9999 0 -0.48 2 2
MAP3K1 0.06 0.065 -9999 0 -10000 0 0
JUN 0.016 0.002 -9999 0 -10000 0 0
MAPK3 0.072 0.081 -9999 0 -10000 0 0
MAPK1 0.072 0.081 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
MAPK8 0.072 0.078 -9999 0 -0.77 2 2
ITGB3 0.014 0.08 -9999 0 -0.73 6 6
NFKBIA 0.085 0.081 -9999 0 -10000 0 0
FOS -0.002 0.12 -9999 0 -0.75 13 13
CD44 -0.019 0.17 -9999 0 -0.86 21 21
CHUK 0.016 0 -9999 0 -10000 0 0
PLAU 0.084 0.17 -9999 0 -1.1 9 9
NF kappa B1 p50/RelA -0.012 0.06 -9999 0 -0.64 1 1
BCAR1 0.014 0.033 -9999 0 -0.74 1 1
RELA 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.006 0.057 -9999 0 -0.54 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.057 0.07 -9999 0 -10000 0 0
VAV3 0.055 0.1 -9999 0 -0.78 1 1
MAP3K14 0.059 0.082 -9999 0 -0.5 4 4
ROCK2 0.01 0.065 -9999 0 -0.74 4 4
SPP1 0.017 0.065 -9999 0 -0.73 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
Rac1/GTP -0.016 0.075 -9999 0 -0.71 1 1
MMP2 0.096 0.13 -9999 0 -0.74 7 7
Cellular roles of Anthrax toxin

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
ANTXR1 0.014 0.033 -10000 0 -0.74 1 1
ANTXR2 0.014 0.033 -10000 0 -0.74 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0.006 -10000 0 -0.093 2 2
monocyte activation 0.006 0.083 -10000 0 -0.37 21 21
MAP2K2 -0.002 0.034 -10000 0 -0.8 1 1
MAP2K1 0 0.005 -10000 0 -10000 0 0
MAP2K7 0 0.005 -10000 0 -10000 0 0
MAP2K6 -0.003 0.032 -10000 0 -0.43 3 3
CYAA 0.02 0.027 -10000 0 -0.42 2 2
MAP2K4 0 0.005 -10000 0 -10000 0 0
IL1B 0.017 0.059 -10000 0 -0.49 6 6
Channel -0.002 0.027 -10000 0 -0.44 2 2
NLRP1 -0.005 0.051 -10000 0 -0.52 5 5
CALM1 0.016 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0.006 0.093 2 -10000 0 2
MAPK3 0 0.005 -10000 0 -10000 0 0
MAPK1 0 0.005 -10000 0 -10000 0 0
PGR -0.015 0.08 -10000 0 -0.44 18 18
PA/Cellular Receptors -0.002 0.03 -10000 0 -0.48 2 2
apoptosis 0 0.006 -10000 0 -0.093 2 2
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.002 0.025 -10000 0 -0.42 2 2
macrophage activation 0.027 0.005 -10000 0 -10000 0 0
TNF 0.003 0.1 -10000 0 -0.8 8 8
VCAM1 -0.015 0.08 -10000 0 -0.37 21 21
platelet activation 0 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.022 0.01 -10000 0 -10000 0 0
IL18 0.016 0.065 -10000 0 -0.52 7 7
negative regulation of macrophage activation 0 0.006 -10000 0 -0.093 2 2
LEF 0 0.006 -10000 0 -0.094 2 2
CASP1 -0.002 0.023 -10000 0 -0.23 5 5
mol:cAMP 0 0.007 -10000 0 -10000 0 0
necrosis 0 0.006 -10000 0 -0.093 2 2
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.002 0.026 -10000 0 -0.42 2 2
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.016 0 -10000 0 -10000 0 0
Rac1/GDP 0.002 0.013 -10000 0 -10000 0 0
DOCK1 0.014 0.033 -10000 0 -0.74 1 1
ITGA4 -0.011 0.15 -10000 0 -0.86 16 16
RAC1 0.016 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.02 0.11 -10000 0 -0.66 16 16
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.017 0.098 -10000 0 -0.57 16 16
alpha4/beta7 Integrin/Paxillin -0.016 0.089 -10000 0 -0.52 16 16
lamellipodium assembly -0.001 0.043 -10000 0 -0.77 1 1
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
PI3K -0.002 0.034 -10000 0 -0.56 2 2
ARF6 0.016 0 -10000 0 -10000 0 0
TLN1 0.016 0 -10000 0 -10000 0 0
PXN 0.031 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
ARF6/GTP -0.013 0.075 -10000 0 -10000 0 0
cell adhesion -0.014 0.082 -10000 0 -10000 0 0
CRKL/CBL -0.001 0.024 -10000 0 -0.56 1 1
alpha4/beta1 Integrin/Paxillin -0.016 0.089 -10000 0 -0.52 16 16
ITGB1 0.016 0 -10000 0 -10000 0 0
ITGB7 0.016 0 -10000 0 -10000 0 0
ARF6/GDP 0.002 0.013 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.026 0.11 -10000 0 -10000 0 0
p130Cas/Crk/Dock1 -0.002 0.029 -10000 0 -0.47 2 2
VCAM1 -0.006 0.13 -10000 0 -0.82 14 14
alpha4/beta1 Integrin/Paxillin/Talin -0.015 0.083 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.015 0.083 -10000 0 -0.49 16 16
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
mol:GDP 0.014 0.082 0.48 16 -10000 0 16
CBL 0.014 0.033 -10000 0 -0.74 1 1
PRKACA 0.016 0 -10000 0 -10000 0 0
GIT1 0.016 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.015 0.083 -10000 0 -10000 0 0
Rac1/GTP -0.001 0.05 -10000 0 -0.93 1 1
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate -0.036 0.12 -9999 0 -0.42 45 45
PDGFB-D/PDGFRB/SLAP -0.033 0.14 -9999 0 -0.67 26 26
PDGFB-D/PDGFRB/APS/CBL -0.008 0.069 -9999 0 -0.56 8 8
AKT1 -0.002 0.022 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.012 0.14 -9999 0 -0.44 45 45
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
FGR -0.004 0.029 -9999 0 -10000 0 0
mol:Ca2+ 0.038 0.041 -9999 0 -10000 0 0
MYC 0.041 0.14 -9999 0 -0.58 21 21
SHC1 0.014 0.038 -9999 0 -0.86 1 1
HRAS/GDP -0.002 0.038 -9999 0 -0.88 1 1
LRP1/PDGFRB/PDGFB 0 0 -9999 0 -10000 0 0
GRB10 0.016 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
GO:0007205 0.038 0.041 -9999 0 -10000 0 0
PTEN 0.016 0 -9999 0 -10000 0 0
GRB2 0.016 0 -9999 0 -10000 0 0
GRB7 0.004 0.092 -9999 0 -0.74 8 8
PDGFB-D/PDGFRB/SHP2 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0 0 -9999 0 -10000 0 0
cell cycle arrest -0.033 0.14 -9999 0 -0.67 26 26
HRAS 0.014 0.038 -9999 0 -0.86 1 1
HIF1A 0.087 0.04 -9999 0 -0.59 1 1
GAB1 0.032 0.077 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.035 0.083 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.012 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0 0 -9999 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.039 0.12 -9999 0 -0.48 19 19
positive regulation of MAPKKK cascade 0 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
mol:IP3 0.038 0.042 -9999 0 -10000 0 0
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.015 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.008 0.068 -9999 0 -0.56 8 8
SHB 0.016 0 -9999 0 -10000 0 0
BLK -0.023 0.087 -9999 0 -0.46 2 2
PTPN2 0.016 0.003 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0.033 -9999 0 -0.74 1 1
VAV2 0.034 0.089 -9999 0 -10000 0 0
CBL 0.014 0.033 -9999 0 -0.74 1 1
PDGFB-D/PDGFRB/DEP1 0 0 -9999 0 -10000 0 0
LCK -0.017 0.081 -9999 0 -0.5 6 6
PDGFRB 0.015 0.006 -9999 0 -10000 0 0
ACP1 0.016 0 -9999 0 -10000 0 0
HCK -0.02 0.082 -9999 0 -10000 0 0
ABL1 0.033 0.06 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/CBL 0.032 0.071 -9999 0 -10000 0 0
PTPN1 0.016 0.003 -9999 0 -10000 0 0
SNX15 0.016 0 -9999 0 -10000 0 0
STAT3 0.016 0 -9999 0 -10000 0 0
STAT1 0.014 0.038 -9999 0 -0.86 1 1
cell proliferation 0.042 0.13 -9999 0 -0.52 21 21
SLA -0.027 0.19 -9999 0 -0.86 26 26
actin cytoskeleton reorganization 0.001 0.025 -9999 0 -10000 0 0
SRC -0.002 0.014 -9999 0 -10000 0 0
PI3K -0.002 0.024 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.008 0.063 -9999 0 -0.49 9 9
SH2B2 0.004 0.1 -9999 0 -0.86 7 7
PLCgamma1/SPHK1 0.011 0.14 -9999 0 -0.45 45 45
LYN -0.001 0.014 -9999 0 -10000 0 0
LRP1 0.016 0 -9999 0 -10000 0 0
SOS1 0.016 0 -9999 0 -10000 0 0
STAT5B 0.016 0 -9999 0 -10000 0 0
STAT5A 0.016 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.001 0.023 -9999 0 -10000 0 0
SPHK1 -0.058 0.24 -9999 0 -0.86 45 45
EDG1 0.001 0.003 -9999 0 -10000 0 0
mol:DAG 0.038 0.042 -9999 0 -10000 0 0
PLCG1 0.038 0.042 -9999 0 -10000 0 0
NHERF/PDGFRB -0.001 0.02 -9999 0 -0.47 1 1
YES1 -0.001 0.014 -9999 0 -10000 0 0
cell migration -0.001 0.02 -9999 0 -0.47 1 1
SHC/Grb2/SOS1 -0.001 0.02 -9999 0 -10000 0 0
SLC9A3R2 0.014 0.033 -9999 0 -0.74 1 1
SLC9A3R1 0.016 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.001 0.018 -9999 0 -10000 0 0
FYN -0.001 0.014 -9999 0 -10000 0 0
DOK1 0.044 0.009 -9999 0 -10000 0 0
HRAS/GTP -0.001 0.029 -9999 0 -0.68 1 1
PDGFB 0.016 0 -9999 0 -10000 0 0
RAC1 0.044 0.1 -9999 0 -0.52 2 2
PRKCD 0.042 0.028 -9999 0 -0.53 1 1
FER 0.041 0.032 -9999 0 -0.44 2 2
MAPKKK cascade 0 0.021 -9999 0 -10000 0 0
RASA1 0.042 0.025 -9999 0 -10000 0 0
NCK1 0.014 0.033 -9999 0 -0.74 1 1
NCK2 0.016 0 -9999 0 -10000 0 0
p62DOK/Csk 0.007 0.018 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0 0 -9999 0 -10000 0 0
chemotaxis 0.033 0.059 -9999 0 -10000 0 0
STAT1-3-5/STAT1-3-5 -0.001 0.02 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0 0 -9999 0 -10000 0 0
PTPRJ 0.016 0 -9999 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.057 0.052 -10000 0 -0.45 1 1
adherens junction organization 0.039 0.08 -10000 0 -0.53 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.06 -10000 0 -10000 0 0
FMN1 0.021 0.12 -10000 0 -0.66 2 2
mol:IP3 -0.008 0.04 -10000 0 -0.47 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.065 -10000 0 -0.71 1 1
CTNNB1 0.001 0.006 -10000 0 -10000 0 0
AKT1 0.054 0.056 -10000 0 -0.5 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.014 0.11 -10000 0 -0.55 17 17
CTNND1 0.016 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.044 0.074 -10000 0 -0.56 2 2
VASP 0.045 0.072 -10000 0 -0.66 1 1
ZYX 0.045 0.072 -10000 0 -0.66 1 1
JUB 0.042 0.079 -10000 0 -0.58 2 2
EGFR(dimer) -0.02 0.082 -10000 0 -0.48 9 9
E-cadherin/beta catenin-gamma catenin -0.021 0.1 -10000 0 -0.47 24 24
mol:PI-3-4-5-P3 -0.01 0.047 -10000 0 -0.54 1 1
PIK3CA 0.015 0.033 -10000 0 -0.74 1 1
PI3K -0.01 0.048 -10000 0 -0.55 1 1
FYN -0.23 0.13 -10000 0 -0.61 2 2
mol:Ca2+ -0.008 0.039 -10000 0 -0.46 1 1
JUP -0.003 0.056 -10000 0 -0.74 3 3
PIK3R1 0.015 0.033 -10000 0 -0.74 1 1
mol:DAG -0.008 0.04 -10000 0 -0.47 1 1
CDH1 -0.03 0.15 -10000 0 -0.74 22 22
RhoA/GDP -0.013 0.06 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.044 0.071 -10000 0 -0.64 1 1
SRC 0.016 0 -10000 0 -10000 0 0
RAC1 0.016 0 -10000 0 -10000 0 0
RHOA 0.016 0 -10000 0 -10000 0 0
EGFR 0.001 0.11 -10000 0 -0.85 9 9
CASR -0.29 0.15 -10000 0 -0.54 18 18
RhoA/GTP -0.007 0.034 -10000 0 -10000 0 0
AKT2 0.054 0.056 -10000 0 -0.5 1 1
actin cable formation 0.031 0.12 -10000 0 -0.63 2 2
apoptosis 0.009 0.043 0.48 1 -10000 0 1
CTNNA1 0.016 0.004 -10000 0 -10000 0 0
mol:GDP -0.015 0.065 -10000 0 -10000 0 0
PIP5K1A 0.044 0.075 -10000 0 -0.58 2 2
PLCG1 -0.008 0.041 -10000 0 -0.49 1 1
Rac1/GTP -0.018 0.073 -10000 0 -0.6 1 1
homophilic cell adhesion 0.002 0.001 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.016 0.001 -9999 0 -10000 0 0
HDAC2 0.015 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.02 -9999 0 -10000 0 0
forebrain development 0.055 0.094 -9999 0 -0.5 2 2
GNAO1 0.008 0.083 -9999 0 -0.84 5 5
SMO/beta Arrestin2 -0.002 0.038 -9999 0 -0.61 2 2
SMO 0.016 0.033 -9999 0 -0.74 1 1
ARRB2 0.014 0.038 -9999 0 -0.86 1 1
GLI3/SPOP 0.061 0.024 -9999 0 -10000 0 0
mol:GTP 0.001 0.002 -9999 0 -10000 0 0
GSK3B 0.016 0 -9999 0 -10000 0 0
GNAI2 0.016 0.004 -9999 0 -10000 0 0
SIN3/HDAC complex -0.019 0.097 -9999 0 -0.52 19 19
GNAI1 0.011 0.057 -9999 0 -0.74 3 3
XPO1 0.019 0.005 -9999 0 -10000 0 0
GLI1/Su(fu) -0.013 0.061 -9999 0 -10000 0 0
SAP30 -0.016 0.16 -9999 0 -0.86 19 19
mol:GDP 0.016 0.033 -9999 0 -0.74 1 1
MIM/GLI2A 0.023 0.008 -9999 0 -10000 0 0
IFT88 0.014 0.033 -9999 0 -0.74 1 1
GNAI3 0.016 0.004 -9999 0 -10000 0 0
GLI2 0.057 0.032 -9999 0 -10000 0 0
GLI3 0.055 0.026 -9999 0 -10000 0 0
CSNK1D 0.016 0 -9999 0 -10000 0 0
CSNK1E 0.016 0 -9999 0 -10000 0 0
SAP18 0.016 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.014 0.033 -9999 0 -0.74 1 1
GNG2 0.016 0 -9999 0 -10000 0 0
Gi family/GTP 0.044 0.051 -9999 0 -0.55 1 1
SIN3B 0.015 0.001 -9999 0 -10000 0 0
SIN3A 0.016 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.074 0.034 -9999 0 -10000 0 0
GLI2/Su(fu) 0.074 0.037 -9999 0 -10000 0 0
FOXA2 -0.06 0.22 -9999 0 -0.83 38 38
neural tube patterning 0.055 0.094 -9999 0 -0.5 2 2
SPOP 0.016 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 -0.001 0.013 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0.033 -9999 0 -0.74 1 1
CSNK1G3 0.016 0 -9999 0 -10000 0 0
MTSS1 0.023 0.008 -9999 0 -10000 0 0
embryonic limb morphogenesis 0.055 0.094 -9999 0 -0.5 2 2
SUFU 0.038 0.021 -9999 0 -10000 0 0
LGALS3 -0.006 0.14 -9999 0 -0.86 13 13
catabolic process 0.093 0.031 -9999 0 -10000 0 0
GLI3A/CBP 0.017 0.056 -9999 0 -10000 0 0
KIF3A 0.016 0 -9999 0 -10000 0 0
GLI1 0.055 0.095 -9999 0 -0.51 2 2
RAB23 0.016 0 -9999 0 -10000 0 0
CSNK1A1 0.016 0 -9999 0 -10000 0 0
IFT172 0.016 0 -9999 0 -10000 0 0
RBBP7 0.015 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 -0.014 0.084 -9999 0 -0.54 13 13
GNAZ 0.011 0.057 -9999 0 -0.74 3 3
RBBP4 0.014 0.033 -9999 0 -0.74 1 1
CSNK1G1 0.016 0 -9999 0 -10000 0 0
PIAS1 0.016 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GLI2/SPOP 0.061 0.029 -9999 0 -10000 0 0
STK36 0.019 0.005 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.052 0.047 -9999 0 -0.48 1 1
PTCH1 0.062 0.099 -9999 0 -1.1 1 1
MIM/GLI1 0.052 0.15 -9999 0 -0.71 1 1
CREBBP 0.017 0.056 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.056 0.048 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.028 0.1 -9999 0 -10000 0 0
BAG4 0.014 0.033 -9999 0 -0.74 1 1
BAD 0.03 0.045 -9999 0 -0.42 2 2
NFKBIA 0.016 0 -9999 0 -10000 0 0
BIRC3 -0.12 0.31 -9999 0 -0.86 80 80
BAX 0.032 0.036 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.012 0.027 -9999 0 -0.099 1 1
IKBKB 0.038 0.095 -9999 0 -10000 0 0
MAP2K2 0.047 0.052 -9999 0 -0.38 4 4
MAP2K1 0.047 0.05 -9999 0 -0.38 4 4
SMPD1 0.019 0.027 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 0.038 0.097 -9999 0 -10000 0 0
MAP2K4 0.041 0.035 -9999 0 -10000 0 0
protein ubiquitination 0.04 0.096 -9999 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.054 0.051 -9999 0 -0.38 4 4
response to UV 0.001 0 -9999 0 -10000 0 0
RAF1 0.039 0.052 -9999 0 -0.41 4 4
CRADD 0.016 0.001 -9999 0 -10000 0 0
mol:ceramide 0.022 0.037 -9999 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -9999 0 -10000 0 0
MADD 0.016 0.001 -9999 0 -10000 0 0
MAP3K1 0.032 0.036 -9999 0 -10000 0 0
TRADD 0.016 0.001 -9999 0 -10000 0 0
RELA/p50 0.016 0 -9999 0 -10000 0 0
MAPK3 0.05 0.05 -9999 0 -0.37 4 4
MAPK1 0.05 0.05 -9999 0 -0.37 4 4
p50/RELA/I-kappa-B-alpha 0 0 -9999 0 -10000 0 0
FADD 0.028 0.1 -9999 0 -10000 0 0
KSR1 0.03 0.055 -9999 0 -0.45 4 4
MAPK8 0.048 0.04 -9999 0 -10000 0 0
TRAF2 0.016 0.001 -9999 0 -10000 0 0
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.038 0.095 -9999 0 -10000 0 0
TNF R/SODD -0.001 0.024 -9999 0 -0.56 1 1
TNF 0.004 0.1 -9999 0 -0.8 8 8
CYCS 0.033 0.038 -9999 0 -10000 0 0
IKBKG 0.038 0.095 -9999 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.018 0.1 -9999 0 -0.44 1 1
RELA 0.016 0 -9999 0 -10000 0 0
RIPK1 0.016 0.001 -9999 0 -10000 0 0
AIFM1 0.033 0.037 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.009 0.067 -9999 0 -0.52 9 9
TNFRSF1A 0.016 0.001 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.029 0.029 -9999 0 -10000 0 0
NSMAF 0.029 0.098 -9999 0 -10000 0 0
response to hydrogen peroxide 0.001 0 -9999 0 -10000 0 0
BCL2 0.016 0 -9999 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.005 0.071 -9999 0 -0.73 5 5
VDR 0.011 0.057 -9999 0 -0.74 3 3
FAM120B 0.016 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.077 0.05 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.087 0.062 -9999 0 -10000 0 0
MED1 0.016 0 -9999 0 -10000 0 0
mol:9cRA 0.009 0.008 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.019 0.072 -9999 0 -10000 0 0
RXRs/NUR77 -0.007 0.087 -9999 0 -0.51 1 1
RXRs/PPAR 0.058 0.029 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.003 0.042 -9999 0 -0.57 3 3
RARs/VDR/DNA/Vit D3 -0.004 0.039 -9999 0 -10000 0 0
RARA 0.016 0 -9999 0 -10000 0 0
NCOA1 0.016 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.011 0.057 -9999 0 -0.74 3 3
RARs/RARs/DNA/9cRA -0.001 0.025 -9999 0 -0.41 2 2
RARG 0.016 0 -9999 0 -10000 0 0
RPS6KB1 -0.001 0.034 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.019 0.072 -9999 0 -10000 0 0
THRA 0.014 0.033 -9999 0 -0.74 1 1
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.003 0.042 -9999 0 -0.57 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.005 0.056 -9999 0 -0.5 4 4
NR1H4 -0.009 0.13 -9999 0 -0.75 17 17
RXRs/LXRs/DNA 0.008 0.056 -9999 0 -10000 0 0
NR1H2 0.023 0.033 -9999 0 -0.73 1 1
NR1H3 0.025 0.006 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.005 0.052 -9999 0 -10000 0 0
NR4A1 -0.006 0.13 -9999 0 -0.75 15 15
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.041 0.067 -9999 0 -0.41 2 2
RXRG 0.015 0.076 -9999 0 -0.85 4 4
RXR alpha/CCPG 0 0.004 -9999 0 -10000 0 0
RXRA 0.024 0.004 -9999 0 -10000 0 0
RXRB 0.025 0.006 -9999 0 -10000 0 0
THRB -0.031 0.18 -9999 0 -0.74 33 33
PPARG 0.016 0 -9999 0 -10000 0 0
PPARD 0.016 0 -9999 0 -10000 0 0
TNF 0.084 0.13 -9999 0 -0.87 8 8
mol:Oxysterols 0.009 0.007 -9999 0 -10000 0 0
cholesterol transport 0.086 0.061 -9999 0 -10000 0 0
PPARA 0.016 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.013 0.046 -9999 0 -0.74 2 2
RXRs/NUR77/BCL2 -0.01 0.054 -9999 0 -10000 0 0
SREBF1 0.093 0.064 -9999 0 -0.66 1 1
RXRs/RXRs/DNA/9cRA 0.005 0.056 -9999 0 -0.5 4 4
ABCA1 0.092 0.071 -9999 0 -0.66 2 2
RARs/THRs -0.026 0.098 -9999 0 -10000 0 0
RXRs/FXR -0.008 0.091 -9999 0 -0.5 5 5
BCL2 0.016 0 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.016 0 -10000 0 -10000 0 0
NFATC1 0.075 0.027 -10000 0 -10000 0 0
NFATC2 0.052 0.036 -10000 0 -0.32 2 2
NFATC3 0.029 0.039 -10000 0 -0.48 3 3
YWHAE 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.032 0.072 -10000 0 -0.46 4 4
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0.001 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.012 0.053 -10000 0 -0.52 2 2
BCL2/BAX 0 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.001 -10000 0 -10000 0 0
CaM/Ca2+ 0 0.001 -10000 0 -10000 0 0
BAX 0.016 0 -10000 0 -10000 0 0
MAPK14 0.016 0.003 -10000 0 -10000 0 0
BAD 0.013 0.05 -10000 0 -0.8 2 2
CABIN1/MEF2D 0.038 0.067 -10000 0 -0.43 4 4
Calcineurin A alpha-beta B1/BCL2 0.016 0 -10000 0 -10000 0 0
FKBP8 0.014 0.033 -10000 0 -0.74 1 1
activation-induced cell death of T cells -0.037 0.067 0.43 4 -10000 0 4
KPNB1 0.016 0 -10000 0 -10000 0 0
KPNA2 0.016 0 -10000 0 -10000 0 0
XPO1 0.016 0 -10000 0 -10000 0 0
SFN -0.083 0.27 -10000 0 -0.83 62 62
MAP3K8 0.013 0.054 -10000 0 -0.86 2 2
NFAT4/CK1 alpha -0.002 0.023 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.011 0.056 -10000 0 -10000 0 0
CABIN1 0.032 0.072 -10000 0 -0.47 4 4
CALM1 0.016 0.003 -10000 0 -10000 0 0
RAN 0.016 0 -10000 0 -10000 0 0
MAP3K1 0.016 0 -10000 0 -10000 0 0
CAMK4 0.013 0.046 -10000 0 -0.74 2 2
mol:Ca2+ 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.016 0 -10000 0 -10000 0 0
YWHAH 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.002 0.034 -10000 0 -0.56 2 2
YWHAB 0.016 0 -10000 0 -10000 0 0
MAPK8 0.013 0.046 -10000 0 -0.74 2 2
MAPK9 0.016 0 -10000 0 -10000 0 0
YWHAG 0.016 0 -10000 0 -10000 0 0
FKBP1A 0.016 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.002 0.028 -10000 0 -10000 0 0
PRKCH 0.016 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.001 0.024 -10000 0 -0.55 1 1
CASP3 0.016 0.003 -10000 0 -10000 0 0
PIM1 0.016 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.001 0.019 -10000 0 -0.39 1 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.076 -10000 0 -0.47 2 2
PRKCB 0.008 0.08 -10000 0 -0.81 5 5
PRKCE 0.014 0.033 -10000 0 -0.74 1 1
JNK2/NFAT4 -0.002 0.033 -10000 0 -0.44 3 3
BAD/BCL-XL -0.002 0.037 -10000 0 -0.61 2 2
PRKCD 0.014 0.038 -10000 0 -0.86 1 1
NUP214 0.016 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.057 -10000 0 -0.75 3 3
PRKCA 0.016 0 -10000 0 -10000 0 0
PRKCG -0.03 0.18 -10000 0 -0.86 23 23
PRKCQ -0.007 0.13 -10000 0 -0.74 16 16
FKBP38/BCL2 -0.001 0.024 -10000 0 -0.56 1 1
EP300 0.015 0.033 -10000 0 -0.74 1 1
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.016 0 -10000 0 -10000 0 0
NFATc/JNK1 0.079 0.037 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 -0.001 0.022 -10000 0 -0.5 1 1
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.027 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.002 0.029 -10000 0 -0.48 2 2
NFATc/ERK1 0.081 0.025 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.013 0.053 -10000 0 -0.52 2 2
NR4A1 0.073 0.13 -10000 0 -0.67 15 15
GSK3B 0.016 0.003 -10000 0 -10000 0 0
positive T cell selection 0.029 0.039 -10000 0 -0.48 3 3
NFAT1/CK1 alpha -0.003 0.02 -10000 0 -10000 0 0
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.016 0 -10000 0 -10000 0 0
PRKACA 0.016 0.003 -10000 0 -10000 0 0
AKAP5 0.013 0.046 -10000 0 -0.74 2 2
MEF2D 0.016 0.003 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.08 0.028 -10000 0 -10000 0 0
CREBBP 0.016 0.003 -10000 0 -10000 0 0
BCL2 0.016 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.008 0.058 -9999 0 -0.55 1 1
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.006 0.047 -9999 0 -0.54 1 1
SUMO1 0.016 0 -9999 0 -10000 0 0
ZFPM1 0.011 0.057 -9999 0 -0.74 3 3
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
FKBP3 0.016 0 -9999 0 -10000 0 0
Histones -0.003 0.021 -9999 0 -10000 0 0
YY1/LSF -0.001 0.031 -9999 0 -0.72 1 1
SMG5 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 -0.005 0.039 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 -0.003 0.027 -9999 0 -10000 0 0
SAP18 0.016 0 -9999 0 -10000 0 0
RELA 0.046 0.042 -9999 0 -10000 0 0
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
HDAC3/TR2 -0.003 0.027 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.062 0.025 -9999 0 -0.46 1 1
NF kappa B1 p50/RelA 0.048 0.047 -9999 0 -0.64 1 1
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.003 0.12 -9999 0 -0.74 13 13
GATA1 -0.021 0.17 -9999 0 -0.86 21 21
Mad/Max 0 0 -9999 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.008 0.045 -9999 0 -0.53 2 2
RBBP7 0.016 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.014 0.033 -9999 0 -0.74 1 1
MAX 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.016 0 -9999 0 -10000 0 0
NFKBIA -0.004 0.031 -9999 0 -10000 0 0
KAT2B 0.014 0.033 -9999 0 -0.74 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex -0.008 0.038 -9999 0 -10000 0 0
SIN3 complex -0.019 0.097 -9999 0 -0.52 19 19
SMURF1 0.016 0 -9999 0 -10000 0 0
CHD3 0.016 0 -9999 0 -10000 0 0
SAP30 -0.016 0.16 -9999 0 -0.86 19 19
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.016 0 -9999 0 -10000 0 0
YY1/HDAC3 -0.004 0.036 -9999 0 -0.64 1 1
YY1/HDAC2 -0.001 0.031 -9999 0 -0.72 1 1
YY1/HDAC1 -0.001 0.031 -9999 0 -0.72 1 1
NuRD/MBD2 Complex (MeCP1) 0.063 0.01 -9999 0 -10000 0 0
PPARG -0.006 0.046 -9999 0 -0.39 4 4
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
TNFRSF1A 0.016 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.003 0.027 -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 0.016 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.001 0.024 -9999 0 -0.52 1 1
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 -0.004 0.031 -9999 0 -10000 0 0
HDAC2 0.016 0 -9999 0 -10000 0 0
YY1 0.039 0.037 -9999 0 -0.81 1 1
HDAC8 0.016 0 -9999 0 -10000 0 0
SMAD7 0.016 0 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
MXD1 0.016 0 -9999 0 -10000 0 0
STAT3 0.034 0.019 -9999 0 -0.4 1 1
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.001 0.029 -9999 0 -0.67 1 1
YY1/SAP30/HDAC1 -0.019 0.098 -9999 0 -0.52 20 20
EP300 0.014 0.033 -9999 0 -0.74 1 1
STAT3 (dimer non-phopshorylated) 0.033 0.019 -9999 0 -0.4 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.004 0.031 -9999 0 -10000 0 0
histone deacetylation 0.063 0.01 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.003 0.026 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
GATAD2B 0.016 0 -9999 0 -10000 0 0
GATAD2A 0.016 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.014 0.07 -9999 0 -0.42 13 13
GATA1/HDAC1 -0.026 0.13 -9999 0 -0.66 21 21
GATA1/HDAC3 -0.024 0.1 -9999 0 -0.52 21 21
CHD4 0.016 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.009 0.075 -9999 0 -0.61 8 8
SIN3/HDAC complex/Mad/Max 0.056 0.041 -9999 0 -10000 0 0
NuRD Complex -0.001 0.019 -9999 0 -0.41 1 1
positive regulation of chromatin silencing -0.003 0.021 -9999 0 -10000 0 0
SIN3B 0.016 0 -9999 0 -10000 0 0
MTA2 0.016 0 -9999 0 -10000 0 0
SIN3A 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.018 -9999 0 -10000 0 0
GATA1/Fog1 -0.029 0.14 -9999 0 -0.65 24 24
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF 0.003 0.1 -9999 0 -0.8 8 8
negative regulation of cell growth 0.056 0.04 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.063 0.01 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.006 0.044 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.053 0.041 -9999 0 -10000 0 0
TFCP2 0.016 0 -9999 0 -10000 0 0
NR2C1 0.016 0 -9999 0 -10000 0 0
MBD3 0.013 0.05 -9999 0 -0.8 2 2
MBD2 0.016 0 -9999 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -9999 0 -10000 0 0
HDAC3 0.016 0 -9999 0 -10000 0 0
VDR 0.011 0.057 -9999 0 -0.74 3 3
Cbp/p300/PCAF -0.002 0.039 -9999 0 -0.91 1 1
EP300 0.014 0.033 -9999 0 -0.74 1 1
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.056 0.034 -9999 0 -0.43 1 1
KAT2B 0.014 0.033 -9999 0 -0.74 1 1
MAPK14 0.016 0 -9999 0 -10000 0 0
AKT1 0.03 0.038 -9999 0 -10000 0 0
RAR alpha/9cRA/Cyclin H -0.009 0.038 -9999 0 -10000 0 0
mol:9cRA 0 0 -9999 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.052 0.036 -9999 0 -0.48 1 1
CDC2 0.001 0.001 -9999 0 -10000 0 0
response to UV 0.002 0.001 -9999 0 -10000 0 0
RAR alpha/Jnk1 -0.011 0.053 -9999 0 -0.58 2 2
NCOR2 0.016 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.003 0.042 -9999 0 -0.57 3 3
RXRs/RARs/NRIP1/9cRA 0.062 0.082 -9999 0 -0.52 1 1
NCOA2 0 0.11 -9999 0 -0.74 11 11
NCOA3 0.016 0 -9999 0 -10000 0 0
NCOA1 0.016 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.011 0.057 -9999 0 -0.74 3 3
RARG 0.017 0.001 -9999 0 -10000 0 0
RAR gamma1/9cRA 0 0 -9999 0 -10000 0 0
MAPK3 0.017 0.001 -9999 0 -10000 0 0
MAPK1 0.016 0 -9999 0 -10000 0 0
MAPK8 0.015 0.046 -9999 0 -0.74 2 2
mol:Vit D3 0 0 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.018 0.073 -9999 0 -10000 0 0
RARA 0.025 0.06 -9999 0 -0.27 2 2
negative regulation of phosphoinositide 3-kinase cascade 0 0 -9999 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.046 0.065 -9999 0 -0.44 5 5
PRKCA 0.021 0.001 -9999 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.054 0.083 -9999 0 -0.57 1 1
RXRG 0.013 0.09 -9999 0 -0.38 27 27
RXRA 0.036 0.056 -9999 0 -10000 0 0
RXRB 0.017 0.083 -9999 0 -0.37 23 23
VDR/Vit D3/DNA -0.003 0.042 -9999 0 -0.57 3 3
RBP1 0.009 0.073 -9999 0 -0.83 4 4
CRBP1/9-cic-RA -0.005 0.056 -9999 0 -0.65 4 4
RARB 0.016 0.046 -9999 0 -0.74 2 2
PRKCG -0.025 0.18 -9999 0 -0.86 23 23
MNAT1 0.016 0 -9999 0 -10000 0 0
RAR alpha/RXRs 0.053 0.084 -9999 0 -10000 0 0
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.06 0.074 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.056 0.047 -9999 0 -0.33 1 1
RXRs/RARs/NRIP1/9cRA/HDAC3 0.054 0.083 -9999 0 -0.57 1 1
positive regulation of DNA binding -0.008 0.037 -9999 0 -10000 0 0
NRIP1 0.053 0.091 -9999 0 -1.2 1 1
RXRs/RARs 0.046 0.081 -9999 0 -0.41 1 1
RXRs/RXRs/DNA/9cRA -0.017 0.073 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
CDK7 0.016 0 -9999 0 -10000 0 0
TFIIH 0 0 -9999 0 -10000 0 0
RAR alpha/9cRA -0.006 0.026 -9999 0 -10000 0 0
CCNH 0.016 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
RAR gamma2/9cRA 0 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.016 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.011 0.057 -9999 0 -0.74 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family -0.006 0.037 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.016 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 0.016 0 -9999 0 -10000 0 0
FYN 0.016 0 -9999 0 -10000 0 0
MAP3K12 0.014 0.033 -9999 0 -0.74 1 1
FGR 0.011 0.066 -9999 0 -0.86 3 3
p38 alpha/TAB1 -0.012 0.037 -9999 0 -10000 0 0
PRKG1 -0.006 0.12 -9999 0 -0.74 15 15
DUSP8 0.014 0.033 -9999 0 -0.74 1 1
PGK/cGMP/p38 alpha -0.02 0.064 -9999 0 -0.43 3 3
apoptosis -0.012 0.036 -9999 0 -10000 0 0
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.016 0 -9999 0 -10000 0 0
DUSP1 0.014 0.038 -9999 0 -0.86 1 1
PAK1 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0 -9999 0 -10000 0 0
TRAF6 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 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 0.016 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.056 0.084 -9999 0 -0.42 2 2
BLK -0.041 0.21 -9999 0 -0.86 34 34
HCK -0.032 0.2 -9999 0 -0.86 29 29
MAP2K3 0.016 0 -9999 0 -10000 0 0
DUSP16 0.016 0 -9999 0 -10000 0 0
DUSP10 0.011 0.066 -9999 0 -0.86 3 3
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.057 0.065 -9999 0 -0.34 2 2
positive regulation of innate immune response 0.067 0.091 -9999 0 -0.44 2 2
LCK -0.02 0.17 -9999 0 -0.85 22 22
p38alpha-beta/MKP7 0.073 0.087 -9999 0 -10000 0 0
p38alpha-beta/MKP5 0.07 0.092 -9999 0 -10000 0 0
PGK/cGMP -0.016 0.094 -9999 0 -0.57 15 15
PAK2 0.016 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.072 0.089 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
RALB 0.016 0 -9999 0 -10000 0 0
RALA 0.016 0 -9999 0 -10000 0 0
PAK3 -0.007 0.14 -9999 0 -0.83 14 14
Insulin 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
CBL/APS/CAP -0.01 0.064 -9999 0 -10000 0 0
TC10/GTP -0.007 0.054 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/Shp2 -0.003 0.038 -9999 0 -10000 0 0
HRAS 0.014 0.038 -9999 0 -0.86 1 1
APS homodimer 0.004 0.1 -9999 0 -0.86 7 7
GRB14 -0.024 0.17 -9999 0 -0.74 28 28
FOXO3 -0.003 0.012 -9999 0 -10000 0 0
AKT1 -0.021 0.084 -9999 0 -0.66 2 2
INSR 0.018 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 0.016 0 -9999 0 -10000 0 0
SORBS1 0.014 0.033 -9999 0 -0.74 1 1
CRK 0.016 0 -9999 0 -10000 0 0
PTPN1 0.049 0.001 -9999 0 -10000 0 0
CAV1 -0.005 0.14 -9999 0 -0.51 37 37
CBL/APS/CAP/Crk-II/C3G -0.008 0.06 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1/NCK2 -0.003 0.038 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.004 0.04 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.002 0.023 -9999 0 -10000 0 0
RPS6KB1 0.055 0.094 -9999 0 -0.58 2 2
PARD6A 0.011 0.057 -9999 0 -0.74 3 3
CBL 0.014 0.033 -9999 0 -0.74 1 1
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.002 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.018 0.073 -9999 0 -0.58 2 2
HRAS/GTP -0.007 0.055 -9999 0 -0.73 1 1
Insulin Receptor 0.018 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.004 0.041 -9999 0 -10000 0 0
PRKCI -0.005 0.019 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.023 0.091 -9999 0 -0.72 2 2
SHC1 0.014 0.038 -9999 0 -0.86 1 1
negative regulation of MAPKKK cascade -0.001 0.035 -9999 0 -0.82 1 1
PI3K -0.004 0.041 -9999 0 -10000 0 0
NCK2 0.016 0 -9999 0 -10000 0 0
RHOQ 0.016 0 -9999 0 -10000 0 0
mol:H2O2 0 0 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.029 -9999 0 -0.68 1 1
AKT2 -0.021 0.084 -9999 0 -0.66 2 2
PRKCZ -0.008 0.055 -9999 0 -0.69 3 3
SH2B2 0.004 0.1 -9999 0 -0.86 7 7
SHC/SHIP -0.007 0.062 -9999 0 -0.86 1 1
F2RL2 -0.034 0.2 -9999 0 -0.86 30 30
TRIP10 0.016 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.001 0.024 -9999 0 -0.55 1 1
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.001 0.022 -9999 0 -10000 0 0
RAPGEF1 0.016 0 -9999 0 -10000 0 0
RASA1 0.014 0.033 -9999 0 -0.74 1 1
NCK1 0.014 0.033 -9999 0 -0.74 1 1
CBL/APS/CAP/Crk-II -0.008 0.065 -9999 0 -0.52 7 7
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.001 0.023 -9999 0 -0.54 1 1
INPP5D 0.029 0.067 -9999 0 -0.61 4 4
SOS1 0.016 0 -9999 0 -10000 0 0
SGK1 -0.001 0.006 -9999 0 -10000 0 0
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.016 0 -9999 0 -10000 0 0
IRS1 0.01 0.065 -9999 0 -0.74 4 4
p62DOK/RasGAP -0.001 0.036 -9999 0 -0.83 1 1
INS 0.005 0.001 -9999 0 -10000 0 0
mol:PI-3-4-P2 0.029 0.066 -9999 0 -0.6 4 4
GRB2 0.016 0 -9999 0 -10000 0 0
EIF4EBP1 0.031 0.15 -9999 0 -0.73 6 6
PTPRA 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.014 0.033 -9999 0 -0.74 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos -0.003 0.028 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.003 0.039 -9999 0 -0.45 4 4
Insulin Receptor/Insulin/IRS3 0 0 -9999 0 -10000 0 0
Par3/Par6 -0.03 0.12 -9999 0 -0.5 30 30
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.001 0.018 -9999 0 -10000 0 0
HDAC3 0.016 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.026 0.13 -9999 0 -0.66 21 21
GATA1/HDAC5 -0.027 0.13 -9999 0 -0.66 22 22
GATA2/HDAC5 -0.015 0.089 -9999 0 -0.56 14 14
HDAC5/BCL6/BCoR -0.001 0.02 -9999 0 -0.47 1 1
HDAC9 0.016 0 -9999 0 -10000 0 0
Glucocorticoid receptor/Hsp90/HDAC6 -0.001 0.025 -9999 0 -0.57 1 1
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB -0.001 0.024 -9999 0 -0.56 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0 -9999 0 -10000 0 0
GATA2 -0.003 0.12 -9999 0 -0.74 13 13
HDAC4/RFXANK -0.001 0.029 -9999 0 -0.66 1 1
BCOR 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.014 0.033 -9999 0 -0.74 1 1
HDAC5 0.014 0.033 -9999 0 -0.74 1 1
GNB1/GNG2 0 0 -9999 0 -10000 0 0
Histones -0.003 0.039 -9999 0 -0.83 1 1
ADRBK1 0.016 0 -9999 0 -10000 0 0
HDAC4 0.016 0 -9999 0 -10000 0 0
XPO1 0.016 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 -0.001 0.024 -9999 0 -0.56 1 1
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.016 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E -0.001 0.024 -9999 0 -0.56 1 1
TUBA1B 0.016 0 -9999 0 -10000 0 0
HDAC6 0.016 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.002 0.037 -9999 0 -0.61 2 2
CAMK4 0.013 0.046 -9999 0 -0.74 2 2
Tubulin/HDAC6 -0.001 0.02 -9999 0 -0.47 1 1
SUMO1 0.016 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
GATA1 -0.021 0.17 -9999 0 -0.86 21 21
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.016 0 -9999 0 -10000 0 0
NR3C1 0.014 0.038 -9999 0 -0.86 1 1
SUMO1/HDAC4 0 0 -9999 0 -10000 0 0
SRF 0.016 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin -0.001 0.024 -9999 0 -0.56 1 1
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
RANGAP1 0.016 0 -9999 0 -10000 0 0
BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.002 0.029 -9999 0 -0.47 2 2
HDAC4/ER alpha -0.005 0.056 -9999 0 -0.58 5 5
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.051 0.042 -9999 0 -0.82 1 1
cell motility -0.001 0.02 -9999 0 -0.47 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.016 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.016 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.016 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 0.008 0.075 -9999 0 -0.77 5 5
HDAC6/HDAC11 -0.002 0.034 -9999 0 -0.56 2 2
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.016 0 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
HDAC4/MEF2C 0 0 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
NCOR2 0.016 0 -9999 0 -10000 0 0
TUBB2A 0.014 0.033 -9999 0 -0.74 1 1
HDAC11 0.013 0.046 -9999 0 -0.74 2 2
HSP90AA1 0.016 0 -9999 0 -10000 0 0
RANBP2 0.016 0 -9999 0 -10000 0 0
ANKRA2 0.016 0 -9999 0 -10000 0 0
RFXANK 0.014 0.038 -9999 0 -0.86 1 1
nuclear import 0.001 0.017 -9999 0 -10000 0 0
Circadian rhythm 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
chromatin modification -0.001 0.016 -10000 0 -10000 0 0
CLOCK 0.019 0.033 -10000 0 -0.74 1 1
TIMELESS/CRY2 0.056 0.025 -10000 0 -10000 0 0
DEC1/BMAL1 -0.001 0.029 -10000 0 -0.66 1 1
ATR 0.016 0 -10000 0 -10000 0 0
NR1D1 0.053 0.069 -10000 0 -1 2 2
ARNTL 0.02 0.003 -10000 0 -10000 0 0
TIMELESS 0.055 0.028 -10000 0 -10000 0 0
NPAS2 0.006 0.1 -10000 0 -0.74 10 10
CRY2 0.016 0 -10000 0 -10000 0 0
mol:CO -0.019 0.009 0.12 2 -10000 0 2
CHEK1 0.016 0 -10000 0 -10000 0 0
mol:HEME 0.019 0.009 -10000 0 -0.12 2 2
PER1 0.016 0 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.044 0.073 -10000 0 -0.46 11 11
BMAL1/CLOCK 0.064 0.055 -10000 0 -0.82 1 1
S phase of mitotic cell cycle -0.001 0.016 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.001 0.016 -10000 0 -10000 0 0
mol:NADPH 0.019 0.009 -10000 0 -0.12 2 2
PER1/TIMELESS 0.056 0.025 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.001 0.038 -10000 0 -0.86 1 1
mTOR signaling pathway

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.016 0 -10000 0 -10000 0 0
mol:PIP3 -0.004 0.036 -10000 0 -0.4 2 2
FRAP1 0.02 0.012 -10000 0 -10000 0 0
AKT1 -0.004 0.036 -10000 0 -0.47 2 2
INSR 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.028 -10000 0 -0.46 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.009 -10000 0 -10000 0 0
TSC2 0.016 0 -10000 0 -10000 0 0
RHEB/GDP -0.002 0.025 -10000 0 -0.42 1 1
TSC1 0.016 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.018 0.035 -10000 0 -0.39 4 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.011 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.016 0 -10000 0 -10000 0 0
RPS6KB1 0.036 0.024 -10000 0 -0.33 1 1
MAP3K5 0.014 0.001 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
apoptosis 0.014 0.001 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.002 4 4
EIF4B 0.044 0.021 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.003 0.031 -10000 0 -0.45 2 2
eIF4E/eIF4G1/eIF4A1 0 0.004 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.004 0.038 -10000 0 -0.36 6 6
mTOR/RHEB/GTP/Raptor/GBL 0.042 0.018 -10000 0 -0.24 1 1
FKBP1A 0.016 0.001 -10000 0 -10000 0 0
RHEB/GTP -0.002 0.024 -10000 0 -0.41 1 1
mol:Amino Acids 0 0 -10000 0 -0.002 4 4
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.004 0.043 -10000 0 -0.74 1 1
EIF4E 0.016 0 -10000 0 -10000 0 0
ASK1/PP5C 0.027 0.008 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.023 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.003 0.03 -10000 0 -0.5 1 1
tumor necrosis factor receptor activity 0 0 0.002 4 -10000 0 4
RPS6 0.012 0.054 -10000 0 -0.86 2 2
PPP5C 0.016 0 -10000 0 -10000 0 0
EIF4G1 0.016 0 -10000 0 -10000 0 0
IRS1 0.008 0.037 -10000 0 -0.42 4 4
INS 0 0.001 -10000 0 -10000 0 0
PTEN 0.015 0 -10000 0 -10000 0 0
PDK2 -0.003 0.033 -10000 0 -0.37 2 2
EIF4EBP1 -0.01 0.1 -10000 0 -0.46 28 28
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
PPP2R5D 0.029 0.011 -10000 0 -10000 0 0
peptide biosynthetic process 0.023 0.001 -10000 0 -10000 0 0
RHEB 0.016 0 -10000 0 -10000 0 0
EIF4A1 0.016 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -0.004 1 1
EEF2 0.023 0.001 -10000 0 -10000 0 0
eIF4E/4E-BP1 0.001 0.094 -10000 0 -0.4 28 28
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.031 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ -0.002 0.029 -9999 0 -0.52 1 1
CDKN1B 0.05 0.007 -9999 0 -10000 0 0
CDKN1A 0.048 0.032 -9999 0 -0.47 2 2
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.016 0 -9999 0 -10000 0 0
FOXO3 0.05 0.007 -9999 0 -10000 0 0
AKT1 0 0.006 -9999 0 -10000 0 0
BAD 0.013 0.05 -9999 0 -0.8 2 2
AKT3 0.022 0.019 -9999 0 -0.41 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.05 0.007 -9999 0 -10000 0 0
AKT1/ASK1 0 0.005 -9999 0 -10000 0 0
BAD/YWHAZ -0.002 0.032 -9999 0 -0.52 2 2
RICTOR 0.016 0 -9999 0 -10000 0 0
RAF1 0.016 0 -9999 0 -10000 0 0
JNK cascade 0 0.005 -9999 0 -10000 0 0
TSC1 0.05 0.007 -9999 0 -10000 0 0
YWHAZ 0.016 0 -9999 0 -10000 0 0
AKT1/RAF1 0.048 0.007 -9999 0 -10000 0 0
EP300 0.014 0.033 -9999 0 -0.74 1 1
mol:GDP 0 0.006 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.05 0.007 -9999 0 -10000 0 0
YWHAQ 0.016 0 -9999 0 -10000 0 0
TBC1D4 0.033 0.016 -9999 0 -0.34 1 1
MAP3K5 0.016 0 -9999 0 -10000 0 0
MAPKAP1 0.016 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.041 0.052 -9999 0 -10000 0 0
YWHAH 0.016 0 -9999 0 -10000 0 0
AKT1S1 0.05 0.007 -9999 0 -10000 0 0
CASP9 0.05 0.007 -9999 0 -10000 0 0
YWHAB 0.016 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.057 0.007 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.02 -9999 0 -0.47 1 1
YWHAE 0.016 0 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
AKT2/p21CIP1 -0.002 0.03 -9999 0 -0.44 2 2
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.024 0.002 -9999 0 -10000 0 0
CHUK 0.05 0.007 -9999 0 -10000 0 0
BAD/BCL-XL -0.002 0.028 -9999 0 -0.56 1 1
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.022 0.019 -9999 0 -0.41 1 1
FOXO1-3a-4/14-3-3 family 0.059 0.059 -9999 0 -10000 0 0
PDPK1 0.014 0.033 -9999 0 -0.74 1 1
MDM2 0.05 0.007 -9999 0 -10000 0 0
MAPKKK cascade -0.048 0.007 -9999 0 -10000 0 0
MDM2/Cbp/p300 -0.001 0.021 -9999 0 -10000 0 0
TSC1/TSC2 0.059 0.007 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.02 -9999 0 -0.46 1 1
glucose import 0.03 0.079 -9999 0 -0.48 12 12
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.043 0.005 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 0.03 0.079 -9999 0 -0.48 12 12
GSK3A 0.05 0.007 -9999 0 -10000 0 0
FOXO1 0.05 0.007 -9999 0 -10000 0 0
GSK3B 0.05 0.007 -9999 0 -10000 0 0
SFN -0.083 0.27 -9999 0 -0.83 62 62
G1/S transition of mitotic cell cycle 0.059 0.007 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.036 0.078 -9999 0 -10000 0 0
PRKACA 0.016 0 -9999 0 -10000 0 0
KPNA1 0.016 0 -9999 0 -10000 0 0
HSP90AA1 0.016 0 -9999 0 -10000 0 0
YWHAG 0.016 0 -9999 0 -10000 0 0
RHEB 0.016 0 -9999 0 -10000 0 0
CREBBP 0.016 0 -9999 0 -10000 0 0
Nectin adhesion pathway

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
PDGFRB 0.016 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.006 0.059 -9999 0 -0.56 6 6
PTK2 -0.005 0.045 -9999 0 -0.77 1 1
positive regulation of JNK cascade -0.003 0.027 -9999 0 -0.37 1 1
CDC42/GDP 0.076 0.041 -9999 0 -0.51 1 1
Rac1/GDP 0.078 0.04 -9999 0 -0.5 1 1
RAP1B 0.016 0 -9999 0 -10000 0 0
RAP1A 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.016 0 -9999 0 -10000 0 0
CDC42/GTP -0.003 0.033 -9999 0 -0.46 1 1
nectin-3/I-afadin -0.003 0.042 -9999 0 -0.56 3 3
RAPGEF1 0.073 0.044 -9999 0 -0.59 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.066 0.049 -9999 0 -0.57 3 3
PDGFB-D/PDGFRB 0.016 0 -9999 0 -10000 0 0
TLN1 0.045 0.018 -9999 0 -10000 0 0
Rap1/GTP -0.002 0.025 -9999 0 -0.39 1 1
IQGAP1 0.016 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 -0.003 0.042 -9999 0 -0.56 3 3
PVR 0.016 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.016 0 -9999 0 -10000 0 0
mol:GDP 0.077 0.049 -9999 0 -0.53 3 3
MLLT4 0.016 0 -9999 0 -10000 0 0
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
PI3K -0.004 0.038 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.002 0.025 -9999 0 -0.39 1 1
PVRL1 0.016 0 -9999 0 -10000 0 0
PVRL3 0.011 0.057 -9999 0 -0.74 3 3
PVRL2 0.016 0 -9999 0 -10000 0 0
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
CDH1 -0.016 0.15 -9999 0 -0.74 22 22
CLDN1 0.008 0.078 -9999 0 -0.79 5 5
JAM-A/CLDN1 -0.007 0.055 -9999 0 -0.52 2 2
SRC -0.004 0.049 -9999 0 -0.64 3 3
ITGB3 0.007 0.08 -9999 0 -0.74 6 6
nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
FARP2 0.068 0.053 -9999 0 -0.53 4 4
RAC1 0.016 0 -9999 0 -10000 0 0
CTNNA1 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.003 0.035 -9999 0 -0.47 3 3
nectin-1/I-afadin 0 0 -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 -0.003 0.035 -9999 0 -0.47 3 3
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.016 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.003 0.027 -9999 0 -0.37 1 1
alphaV/beta3 Integrin/Talin -0.005 0.043 -9999 0 -0.57 1 1
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 -0.001 0.017 -9999 0 -10000 0 0
VAV2 0.068 0.047 -9999 0 -0.54 3 3
RAP1/GDP -0.003 0.03 -9999 0 -0.46 1 1
ITGAV 0.016 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.003 0.035 -9999 0 -0.47 3 3
nectin-3(dimer)/I-afadin/I-afadin -0.003 0.042 -9999 0 -0.56 3 3
Rac1/GTP -0.003 0.031 -9999 0 -0.48 1 1
PTPRM -0.001 0.02 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.015 0.073 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.016 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

Figure S124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.002 0.041 -9999 0 -0.66 2 2
FBXW11 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.004 0.046 -9999 0 -0.47 5 5
NF kappa B1 p50/RelA/I kappa B alpha -0.008 0.038 -9999 0 -10000 0 0
NFKBIA 0.028 0.055 -9999 0 -10000 0 0
MAPK14 0.016 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 -0.001 0.02 -9999 0 -0.47 1 1
ARRB2 0.022 0.018 -9999 0 -0.39 1 1
REL 0.01 0.065 -9999 0 -0.74 4 4
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.003 0.041 -9999 0 -0.54 3 3
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA -0.001 0.02 -9999 0 -0.47 1 1
PIK3CA 0.014 0.033 -9999 0 -0.74 1 1
NF kappa B1 p50 dimer 0.025 0.025 -9999 0 -0.56 1 1
PIK3R1 0.014 0.033 -9999 0 -0.74 1 1
NFKB1 0.03 0.025 -9999 0 -0.56 1 1
RELA 0.016 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.037 0.054 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.008 0.036 -9999 0 -10000 0 0
SRC 0.016 0 -9999 0 -10000 0 0
PI3K -0.002 0.034 -9999 0 -0.56 2 2
NF kappa B1 p50/RelA 0.037 0.054 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.016 0 -9999 0 -10000 0 0
SYK 0.013 0.046 -9999 0 -0.74 2 2
I kappa B alpha/PIK3R1 0.034 0.054 -9999 0 -0.39 1 1
cell death -0.008 0.035 -9999 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.004 0.046 -9999 0 -0.47 5 5
LCK -0.02 0.17 -9999 0 -0.85 22 22
BCL3 0.012 0.054 -9999 0 -0.86 2 2
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.016 0 -10000 0 -10000 0 0
PTK2 0.016 0 -10000 0 -10000 0 0
CRKL 0.029 0.055 -10000 0 -0.41 6 6
GRB2/SOS1/SHC -0.001 0.025 -10000 0 -0.57 1 1
HRAS 0.014 0.038 -10000 0 -0.86 1 1
IRS1/Crk -0.007 0.05 -10000 0 -0.41 6 6
IGF-1R heterotetramer/IGF1/PTP1B -0.006 0.055 -10000 0 -0.52 6 6
AKT1 0.054 0.061 -10000 0 -0.71 1 1
BAD 0.062 0.071 -10000 0 -1 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.029 0.055 -10000 0 -0.41 6 6
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.007 0.051 -10000 0 -0.41 6 6
RAF1 0.067 0.057 -10000 0 -0.7 1 1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.006 0.047 -10000 0 -10000 0 0
YWHAZ 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.008 0.056 -10000 0 -0.45 6 6
PIK3CA 0.014 0.033 -10000 0 -0.74 1 1
RPS6KB1 0.054 0.061 -10000 0 -0.71 1 1
GNB2L1 0.014 0.038 -10000 0 -0.86 1 1
positive regulation of MAPKKK cascade 0.059 0.049 -10000 0 -0.56 1 1
PXN 0.016 0 -10000 0 -10000 0 0
PIK3R1 0.014 0.033 -10000 0 -0.74 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.007 0.048 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.006 0.048 -10000 0 -0.5 1 1
IGF-1R heterotetramer 0.015 0.012 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.007 0.051 -10000 0 -0.41 6 6
Crk/p130 Cas/Paxillin -0.007 0.046 -10000 0 -10000 0 0
IGF1R 0.015 0.012 -10000 0 -10000 0 0
IGF1 0.006 0.092 -10000 0 -0.85 6 6
IRS2/Crk 0.029 0.082 -10000 0 -0.48 8 8
PI3K -0.008 0.052 -10000 0 -10000 0 0
apoptosis -0.065 0.059 0.79 1 -10000 0 1
HRAS/GDP -0.001 0.029 -10000 0 -0.68 1 1
PRKCD 0.05 0.056 -10000 0 -0.82 1 1
RAF1/14-3-3 E 0.071 0.05 -10000 0 -0.57 1 1
BAD/14-3-3 0.068 0.064 -10000 0 -0.89 1 1
PRKCZ 0.052 0.068 -10000 0 -0.71 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.006 0.043 -10000 0 -0.56 1 1
PTPN1 0.016 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 0.042 0.047 -10000 0 -10000 0 0
BCAR1 0.014 0.033 -10000 0 -0.74 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.006 0.053 -10000 0 -0.55 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.016 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.007 0.05 -10000 0 -10000 0 0
GRB10 0.016 0 -10000 0 -10000 0 0
PTPN11 0.029 0.055 -10000 0 -0.41 6 6
IRS1 0.018 0.059 -10000 0 -0.45 6 6
IRS2 0.02 0.086 -10000 0 -0.47 14 14
IGF-1R heterotetramer/IGF1 -0.008 0.069 -10000 0 -0.66 6 6
GRB2 0.016 0 -10000 0 -10000 0 0
PDPK1 0.045 0.064 -10000 0 -0.76 1 1
YWHAE 0.016 0 -10000 0 -10000 0 0
PRKD1 0.05 0.049 -10000 0 -10000 0 0
SHC1 0.014 0.038 -10000 0 -0.86 1 1
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.016 0 -9999 0 -10000 0 0
SMAD2 0.019 0 -9999 0 -10000 0 0
SMAD3 0.056 0 -9999 0 -10000 0 0
SMAD3/SMAD4 0.062 0 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy 0 0 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0 0 -9999 0 -10000 0 0
PPM1A 0.016 0 -9999 0 -10000 0 0
CALM1 0.016 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.027 0 -9999 0 -10000 0 0
MAP3K1 0.016 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.001 0.024 -9999 0 -0.56 1 1
MAPK3 0.016 0 -9999 0 -10000 0 0
MAPK1 0.016 0 -9999 0 -10000 0 0
NUP214 0.016 0 -9999 0 -10000 0 0
CTDSP1 0.016 0 -9999 0 -10000 0 0
CTDSP2 0.016 0 -9999 0 -10000 0 0
CTDSPL 0.016 0 -9999 0 -10000 0 0
KPNB1 0.016 0 -9999 0 -10000 0 0
TGFBRAP1 0.014 0.033 -9999 0 -0.74 1 1
UBE2I 0.016 0 -9999 0 -10000 0 0
NUP153 0.016 0 -9999 0 -10000 0 0
KPNA2 0.016 0 -9999 0 -10000 0 0
PIAS4 0.016 0 -9999 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 0.014 0.033 -9999 0 -0.74 1 1
positive regulation of NF-kappaB transcription factor activity -0.001 0.024 -9999 0 -0.55 1 1
MAP2K4 0.063 0.017 -9999 0 -10000 0 0
IKBKB 0.016 0 -9999 0 -10000 0 0
TNFRSF10B 0.014 0.038 -9999 0 -0.86 1 1
TNFRSF10A 0.014 0.033 -9999 0 -0.74 1 1
SMPD1 -0.001 0.016 -9999 0 -0.27 2 2
IKBKG 0.016 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR2 -0.002 0.037 -9999 0 -0.61 2 2
TRAIL/TRAILR3 -0.002 0.037 -9999 0 -0.61 2 2
TRAIL/TRAILR1 -0.002 0.034 -9999 0 -0.56 2 2
TRAIL/TRAILR4 -0.001 0.024 -9999 0 -0.56 1 1
TRAIL/TRAILR1/DAP3/GTP -0.002 0.027 -9999 0 -0.43 2 2
IKK complex -0.001 0.009 -9999 0 -10000 0 0
RIPK1 0.016 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 0.03 0.025 -9999 0 -0.55 1 1
MAP3K1 -0.001 0.014 -9999 0 -10000 0 0
TRAILR4 (trimer) 0.016 0 -9999 0 -10000 0 0
TRADD 0.016 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.014 0.033 -9999 0 -0.74 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.018 -9999 0 -10000 0 0
CFLAR 0.016 0 -9999 0 -10000 0 0
MAPK1 0.03 0.025 -9999 0 -0.55 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP -0.001 0.024 -9999 0 -10000 0 0
mol:ceramide -0.001 0.016 -9999 0 -0.26 2 2
FADD 0.016 0 -9999 0 -10000 0 0
MAPK8 0.07 0.03 -9999 0 -10000 0 0
TRAF2 0.016 0 -9999 0 -10000 0 0
TRAILR3 (trimer) 0.014 0.038 -9999 0 -0.86 1 1
CHUK 0.016 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.002 0.029 -9999 0 -0.47 2 2
DAP3 0.016 0 -9999 0 -10000 0 0
CASP10 -0.002 0.024 -9999 0 -0.45 1 1
JNK cascade -0.001 0.024 -9999 0 -0.55 1 1
TRAIL (trimer) 0.014 0.033 -9999 0 -0.74 1 1
TNFRSF10C 0.014 0.038 -9999 0 -0.86 1 1
TRAIL/TRAILR1/DAP3/GTP/FADD -0.002 0.024 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD -0.002 0.032 -9999 0 -0.52 2 2
cell death -0.001 0.016 -9999 0 -0.26 2 2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.017 -9999 0 -10000 0 0
TRAILR2 (trimer) 0.014 0.038 -9999 0 -0.86 1 1
CASP8 0 0.007 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.002 0.027 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0 0 -9999 0 -9999 0 0
HDAC4 0.016 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.016 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.023 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.039 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.016 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.016 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0 0 -9999 0 -9999 0 0
RANGAP1 0.016 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 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 0.016 0 -9999 0 -9999 0 0
UBE2I 0.016 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 0.016 0 -9999 0 -9999 0 0
PIAS1 0.016 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0 0 -9999 0 -10000 0 0
MAPK9 0.011 0 -9999 0 -10000 0 0
adrenocorticotropin secretion -0.004 0.072 -9999 0 -0.68 6 6
GNB1/GNG2 0 0 -9999 0 -10000 0 0
GNB1 0.016 0 -9999 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
MAPK14 0.011 0 -9999 0 -10000 0 0
Gs family/GTP 0 0 -9999 0 -10000 0 0
EntrezGene:2778 0 0 -9999 0 -10000 0 0
vasopressin secretion 0 0 -9999 0 -10000 0 0
G-protein coupled receptor activity 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
glutamate secretion 0 0 -9999 0 -10000 0 0
GNAL 0.016 0 -9999 0 -10000 0 0
GNG2 0.016 0 -9999 0 -10000 0 0
CRH -0.006 0.092 -9999 0 -0.86 6 6
mol:cortisol 0 0 -9999 0 -10000 0 0
MAPK8 0.01 0.027 -9999 0 -0.42 2 2
MAPK11 0.01 0.025 -9999 0 -0.4 2 2
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 -0.001 0.022 -9999 0 -0.51 1 1
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.027 0.009 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0.002 -9999 0 -10000 0 0
CLTB 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0.001 -9999 0 -10000 0 0
CD4 0.001 0.11 -9999 0 -0.86 9 9
CLTA 0.016 0 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
ARFGAP1 0.014 0.025 -9999 0 -0.57 1 1
mol:PI-4-5-P2 -0.001 0.017 -9999 0 -0.38 1 1
ARF1/GTP 0 0.009 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.001 0.02 -9999 0 -0.46 1 1
mol:Choline -0.001 0.016 -9999 0 -0.38 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.016 0 -9999 0 -10000 0 0
DDEF1 -0.001 0.017 -9999 0 -0.38 1 1
ARF1/GDP -0.001 0.02 -9999 0 -0.46 1 1
AP2M1 0.016 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 -0.001 0.018 -9999 0 -0.42 1 1
ARFIP2 0 0.003 -9999 0 -10000 0 0
COPA 0.016 0 -9999 0 -10000 0 0
RAC1 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.034 0.005 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0.001 -9999 0 -10000 0 0
GGA3 0.016 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0.005 -9999 0 -10000 0 0
AP2A1 0.016 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.01 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0.005 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0.003 -9999 0 -10000 0 0
CYTH2 0.016 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 0.043 0.034 -9999 0 -10000 0 0
PLD2 -0.001 0.016 -9999 0 -0.38 1 1
ARF-GAP1/v-SNARE 0.014 0.025 -9999 0 -0.57 1 1
PIP5K1A -0.001 0.017 -9999 0 -0.38 1 1
ARF1/GTP/Membrin/GBF1/p115 0 0.009 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.001 0.016 -9999 0 -0.38 1 1
KDEL Receptor/Ligand/ARF-GAP1 0.014 0.025 -9999 0 -0.57 1 1
GOSR2 0 0.007 -9999 0 -10000 0 0
USO1 0 0.007 -9999 0 -10000 0 0
GBF1 0 0.007 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0.002 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.01 0.074 -9999 0 -0.57 9 9
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 -0.005 0.057 -9999 0 -0.66 4 4
FBXW11 0.016 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 0.016 0 -9999 0 -10000 0 0
CHUK 0.016 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.004 0.042 -9999 0 -10000 0 0
NFKB1 0.014 0.033 -9999 0 -0.74 1 1
MAP3K14 0.009 0.076 -9999 0 -0.86 4 4
NF kappa B1 p50/RelB -0.001 0.024 -9999 0 -0.56 1 1
RELB 0.016 0 -9999 0 -10000 0 0
NFKB2 0.016 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 533 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.T7.A92I TCGA.MW.A4EC TCGA.MM.A84U TCGA.MM.A564
109_MAP3K5 0.074 0.074 -0.13 0.074
47_PPARGC1A 0.016 0.016 0.016 0.016
105_BMP4 0.016 0.016 0.016 0.016
105_BMP6 0.016 0.016 0.016 0.016
105_BMP7 0.016 -6.4e-15 -0.74 -0.74
105_BMP2 0.016 0.016 0.016 0.016
131_RELN/VLDLR -0.42 -0.42 0 -0.42
30_TGFB1/TGF beta receptor Type II 0.015 0.015 0.015 0.021
84_STAT5B -0.03 -0.031 -0.14 -0.14
84_STAT5A -0.03 -0.031 -0.14 -0.14
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/KIRC-TP/14527250/KIRC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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