PARADIGM pathway analysis of mRNASeq expression and copy number data
Lung Squamous Cell Carcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1RV0M1D
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1RV0M1D
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 31 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
Angiopoietin receptor Tie2-mediated signaling 159
Signaling events mediated by the Hedgehog family 137
Endothelins 90
Fc-epsilon receptor I signaling in mast cells 61
Thromboxane A2 receptor signaling 59
Aurora B signaling 57
IL4-mediated signaling events 55
amb2 Integrin signaling 55
Signaling mediated by p38-alpha and p38-beta 54
TCGA08_retinoblastoma 54
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 482 . 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 ( 482 ).

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
Angiopoietin receptor Tie2-mediated signaling 0.3299 159 14047 88 -0.72 0.076 1000 -1000 -0.06 -1000
Signaling events mediated by the Hedgehog family 0.2842 137 7132 52 -0.44 0.23 1000 -1000 -0.034 -1000
Endothelins 0.1867 90 8700 96 -0.37 0.11 1000 -1000 -0.061 -1000
Fc-epsilon receptor I signaling in mast cells 0.1266 61 5920 97 -0.15 0.023 1000 -1000 -0.061 -1000
Thromboxane A2 receptor signaling 0.1224 59 6241 105 -0.2 0.056 1000 -1000 -0.039 -1000
Aurora B signaling 0.1183 57 3827 67 -0.3 0.29 1000 -1000 -0.044 -1000
IL4-mediated signaling events 0.1141 55 5024 91 -0.8 0.48 1000 -1000 -0.12 -1000
amb2 Integrin signaling 0.1141 55 4520 82 -0.51 0.036 1000 -1000 -0.052 -1000
Signaling mediated by p38-alpha and p38-beta 0.1120 54 2419 44 -0.11 0.022 1000 -1000 -0.033 -1000
TCGA08_retinoblastoma 0.1120 54 433 8 -0.01 0.098 1000 -1000 -0.003 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.1058 51 2672 52 -0.26 0.048 1000 -1000 -0.049 -1000
Aurora C signaling 0.1017 49 349 7 0 0.15 1000 -1000 -0.02 -1000
Signaling events regulated by Ret tyrosine kinase 0.0871 42 3507 82 -0.11 0.055 1000 -1000 -0.057 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0788 38 3006 78 -0.16 0.051 1000 -1000 -0.046 -1000
BMP receptor signaling 0.0768 37 3050 81 -0.27 0.15 1000 -1000 -0.044 -1000
Nongenotropic Androgen signaling 0.0768 37 1924 52 -0.11 0.077 1000 -1000 -0.04 -1000
PLK1 signaling events 0.0726 35 2998 85 -0.028 0.16 1000 -1000 -0.023 -1000
Integrins in angiogenesis 0.0705 34 2878 84 -0.34 0.13 1000 -1000 -0.054 -1000
Calcium signaling in the CD4+ TCR pathway 0.0705 34 1067 31 -0.17 0.024 1000 -1000 -0.057 -1000
Arf6 signaling events 0.0664 32 1995 62 -0.14 0.043 1000 -1000 -0.029 -1000
IL6-mediated signaling events 0.0622 30 2278 75 -0.47 0.05 1000 -1000 -0.048 -1000
Reelin signaling pathway 0.0602 29 1651 56 -0.071 0.059 1000 -1000 -0.041 -1000
Canonical Wnt signaling pathway 0.0602 29 1520 51 -0.34 0.16 1000 -1000 -0.05 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0581 28 3593 125 -0.13 0.051 1000 -1000 -0.053 -1000
Glypican 2 network 0.0560 27 110 4 0.028 0.059 1000 -1000 0.011 -1000
Presenilin action in Notch and Wnt signaling 0.0539 26 1635 61 -0.34 0.16 1000 -1000 -0.044 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0539 26 1769 68 -0.18 0.04 1000 -1000 -0.092 -1000
IL23-mediated signaling events 0.0539 26 1602 60 -0.2 0.023 1000 -1000 -0.099 -1000
Coregulation of Androgen receptor activity 0.0519 25 1916 76 -0.33 0.097 1000 -1000 -0.032 -1000
FOXA2 and FOXA3 transcription factor networks 0.0519 25 1181 46 -0.7 0.11 1000 -1000 -0.1 -1000
Syndecan-3-mediated signaling events 0.0519 25 889 35 -0.25 0.055 1000 -1000 -0.022 -1000
Visual signal transduction: Cones 0.0498 24 931 38 -0.041 0.13 1000 -1000 -0.026 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0498 24 2111 85 -0.1 0.031 1000 -1000 -0.047 -1000
FOXM1 transcription factor network 0.0498 24 1229 51 0.022 0.36 1000 -1000 -0.13 -1000
LPA4-mediated signaling events 0.0477 23 284 12 -0.1 0 1000 -1000 -0.027 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0477 23 774 33 -0.17 0.097 1000 -1000 -0.032 -1000
HIF-1-alpha transcription factor network 0.0456 22 1699 76 -0.11 0.14 1000 -1000 -0.094 -1000
Glucocorticoid receptor regulatory network 0.0456 22 2528 114 -0.33 0.078 1000 -1000 -0.056 -1000
TCR signaling in naïve CD8+ T cells 0.0456 22 2105 93 -0.062 0.032 1000 -1000 -0.058 -1000
Regulation of Androgen receptor activity 0.0456 22 1582 70 -0.36 0.15 1000 -1000 -0.05 -1000
IL12-mediated signaling events 0.0436 21 1871 87 -0.18 0.043 1000 -1000 -0.074 -1000
Syndecan-1-mediated signaling events 0.0436 21 737 34 -0.093 0.15 1000 -1000 -0.046 -1000
Plasma membrane estrogen receptor signaling 0.0436 21 1871 86 -0.11 0.038 1000 -1000 -0.056 -1000
ErbB4 signaling events 0.0415 20 1422 69 -0.13 0.16 1000 -1000 -0.047 -1000
Nectin adhesion pathway 0.0415 20 1295 63 -0.033 0.12 1000 -1000 -0.05 -1000
Wnt signaling 0.0415 20 145 7 0.006 0.057 1000 -1000 -0.009 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0394 19 1039 54 -0.071 0.073 1000 -1000 -0.043 -1000
Glypican 1 network 0.0394 19 927 48 -0.14 0.087 1000 -1000 -0.034 -1000
S1P1 pathway 0.0394 19 700 36 -0.1 0.022 1000 -1000 -0.047 -1000
FAS signaling pathway (CD95) 0.0373 18 853 47 -0.2 0.063 1000 -1000 -0.034 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0373 18 2168 120 -0.14 0.061 1000 -1000 -0.043 -1000
Caspase cascade in apoptosis 0.0332 16 1228 74 -0.069 0.085 1000 -1000 -0.047 -1000
JNK signaling in the CD4+ TCR pathway 0.0332 16 281 17 -0.035 0.031 1000 -1000 -0.037 -1000
Noncanonical Wnt signaling pathway 0.0332 16 418 26 -0.054 0.057 1000 -1000 -0.039 -1000
TCGA08_p53 0.0332 16 116 7 -0.029 0.022 1000 -1000 -0.014 -1000
Visual signal transduction: Rods 0.0332 16 845 52 -0.041 0.094 1000 -1000 -0.036 -1000
p75(NTR)-mediated signaling 0.0290 14 1857 125 -0.048 0.15 1000 -1000 -0.069 -1000
PDGFR-alpha signaling pathway 0.0290 14 620 44 -0.13 0.046 1000 -1000 -0.038 -1000
Ephrin B reverse signaling 0.0290 14 681 48 -0.058 0.063 1000 -1000 -0.03 -1000
IGF1 pathway 0.0290 14 850 57 -0.056 0.059 1000 -1000 -0.049 -1000
Ras signaling in the CD4+ TCR pathway 0.0290 14 239 17 -0.017 0.031 1000 -1000 -0.026 -1000
Signaling events mediated by PTP1B 0.0270 13 1046 76 -0.048 0.057 1000 -1000 -0.034 -1000
S1P4 pathway 0.0270 13 326 25 -0.028 0.032 1000 -1000 -0.03 -1000
Osteopontin-mediated events 0.0249 12 469 38 -0.046 0.13 1000 -1000 -0.05 -1000
Aurora A signaling 0.0249 12 721 60 -0.039 0.21 1000 -1000 -0.024 -1000
Effects of Botulinum toxin 0.0249 12 333 26 -0.036 0.031 1000 -1000 -0.016 -1000
BCR signaling pathway 0.0249 12 1189 99 -0.088 0.053 1000 -1000 -0.066 -1000
EGFR-dependent Endothelin signaling events 0.0249 12 263 21 -0.025 0.049 1000 -1000 -0.041 -1000
HIF-2-alpha transcription factor network 0.0228 11 474 43 -0.075 0.078 1000 -1000 -0.056 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0228 11 852 74 -0.14 0.049 1000 -1000 -0.067 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0207 10 306 28 -0.11 0.043 1000 -1000 -0.027 -1000
Hedgehog signaling events mediated by Gli proteins 0.0207 10 702 65 -0.53 0.055 1000 -1000 -0.055 -1000
mTOR signaling pathway 0.0207 10 537 53 -0.018 0.089 1000 -1000 -0.038 -1000
Syndecan-4-mediated signaling events 0.0207 10 693 67 -0.032 0.087 1000 -1000 -0.047 -1000
Regulation of nuclear SMAD2/3 signaling 0.0187 9 1356 136 -0.21 0.15 1000 -1000 -0.05 -1000
Syndecan-2-mediated signaling events 0.0187 9 645 69 -0.032 0.087 1000 -1000 -0.04 -1000
Retinoic acid receptors-mediated signaling 0.0187 9 543 58 -0.16 0.045 1000 -1000 -0.035 -1000
LPA receptor mediated events 0.0187 9 957 102 -0.061 0.041 1000 -1000 -0.062 -1000
ErbB2/ErbB3 signaling events 0.0166 8 538 65 -0.039 0.033 1000 -1000 -0.049 -1000
Cellular roles of Anthrax toxin 0.0166 8 348 39 -0.062 0.022 1000 -1000 -0.022 -1000
IL2 signaling events mediated by PI3K 0.0166 8 487 58 -0.018 0.12 1000 -1000 -0.04 -1000
Regulation of p38-alpha and p38-beta 0.0166 8 442 54 -0.044 0.053 1000 -1000 -0.047 -1000
IL27-mediated signaling events 0.0166 8 448 51 -0.069 0.029 1000 -1000 -0.047 -1000
IL2 signaling events mediated by STAT5 0.0166 8 176 22 0.006 0.077 1000 -1000 -0.037 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0145 7 326 45 -0.02 0.051 1000 -1000 -0.05 -1000
EPHB forward signaling 0.0145 7 673 85 -0.042 0.085 1000 -1000 -0.067 -1000
Insulin Pathway 0.0145 7 533 74 -0.09 0.061 1000 -1000 -0.062 -1000
PDGFR-beta signaling pathway 0.0145 7 708 97 -0.047 0.065 1000 -1000 -0.059 -1000
E-cadherin signaling in keratinocytes 0.0145 7 332 43 -0.05 0.064 1000 -1000 -0.036 -1000
IFN-gamma pathway 0.0124 6 475 68 -0.026 0.067 1000 -1000 -0.058 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0124 6 553 83 -0.069 0.041 1000 -1000 -0.035 -1000
TCGA08_rtk_signaling 0.0124 6 181 26 -0.062 0.08 1000 -1000 -0.008 -1000
Class I PI3K signaling events 0.0124 6 468 73 -0.031 0.042 1000 -1000 -0.045 -1000
S1P3 pathway 0.0124 6 260 42 -0.11 0.042 1000 -1000 -0.039 -1000
Signaling events mediated by PRL 0.0124 6 218 34 -0.036 0.063 1000 -1000 -0.05 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0104 5 173 34 -0.032 0.051 1000 -1000 -0.029 -1000
EPO signaling pathway 0.0104 5 281 55 -0.001 0.06 1000 -1000 -0.045 -1000
Ceramide signaling pathway 0.0104 5 417 76 -0.011 0.06 1000 -1000 -0.04 -1000
TRAIL signaling pathway 0.0104 5 252 48 -0.036 0.06 1000 -1000 -0.033 -1000
Signaling events mediated by HDAC Class II 0.0083 4 302 75 -0.036 0.056 1000 -1000 -0.031 -1000
BARD1 signaling events 0.0083 4 234 57 -0.042 0.088 1000 -1000 -0.043 -1000
Ephrin A reverse signaling 0.0083 4 34 7 0 0.03 1000 -1000 -0.007 -1000
Signaling events mediated by HDAC Class III 0.0083 4 190 40 -0.078 0.041 1000 -1000 -0.031 -1000
IL1-mediated signaling events 0.0083 4 286 62 -0.021 0.042 1000 -1000 -0.043 -1000
ceramide signaling pathway 0.0083 4 226 49 0 0.033 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class I 0.0083 4 514 104 -0.043 0.055 1000 -1000 -0.032 -1000
E-cadherin signaling in the nascent adherens junction 0.0083 4 310 76 -0.014 0.06 1000 -1000 -0.057 -1000
VEGFR1 specific signals 0.0083 4 256 56 -0.13 0.057 1000 -1000 -0.053 -1000
Arf6 downstream pathway 0.0062 3 136 43 -0.044 0.045 1000 -1000 -0.027 -1000
Insulin-mediated glucose transport 0.0062 3 107 32 -0.009 0.043 1000 -1000 -0.032 -1000
Class I PI3K signaling events mediated by Akt 0.0062 3 212 68 -0.034 0.047 1000 -1000 -0.037 -1000
FoxO family signaling 0.0062 3 254 64 -0.023 0.072 1000 -1000 -0.073 -1000
Paxillin-dependent events mediated by a4b1 0.0062 3 115 36 -0.041 0.042 1000 -1000 -0.028 -1000
Arf6 trafficking events 0.0062 3 250 71 -0.052 0.04 1000 -1000 -0.031 -1000
Regulation of Telomerase 0.0062 3 365 102 -0.042 0.068 1000 -1000 -0.046 -1000
p38 MAPK signaling pathway 0.0062 3 146 44 -0.003 0.054 1000 -1000 -0.029 -1000
Canonical NF-kappaB pathway 0.0041 2 108 39 -0.006 0.046 1000 -1000 -0.025 -1000
a4b1 and a4b7 Integrin signaling 0.0041 2 14 5 0.018 0.029 1000 -1000 0.008 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0041 2 89 37 -0.013 0.052 1000 -1000 -0.034 -1000
Signaling mediated by p38-gamma and p38-delta 0.0041 2 34 15 -0.011 0.022 1000 -1000 -0.036 -1000
Circadian rhythm pathway 0.0021 1 29 22 -0.006 0.048 1000 -1000 -0.032 -1000
S1P5 pathway 0.0021 1 23 17 -0.015 0.03 1000 -1000 -0.018 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0021 1 52 27 -0.009 0.053 1000 -1000 -0.036 -1000
Rapid glucocorticoid signaling 0.0021 1 31 20 -0.011 0.024 1000 -1000 -0.013 -1000
Class IB PI3K non-lipid kinase events 0.0021 1 3 3 -0.021 0.021 1000 -1000 -0.01 -1000
Arf1 pathway 0.0021 1 76 54 -0.005 0.031 1000 -1000 -0.017 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 10 23 0.003 0.043 1000 -1000 -0.027 -1000
PLK2 and PLK4 events 0.0000 0 1 3 -0.009 0.022 1000 -1000 -0.03 -1000
Atypical NF-kappaB pathway 0.0000 0 11 31 -0.008 0.023 1000 -1000 -0.027 -1000
E-cadherin signaling events 0.0000 0 0 5 0.021 0.041 1000 -1000 0.009 -1000
Alternative NF-kappaB pathway 0.0000 0 4 13 0 0.06 1000 -1000 0 -1000
Total NA 2435 157382 7203 -14 9.6 131000 -131000 -5.5 -131000
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.53 0.5 -10000 0 -0.97 263 263
NCK1/PAK1/Dok-R -0.25 0.21 -10000 0 -0.44 263 263
NCK1/Dok-R -0.61 0.63 -10000 0 -1.1 261 261
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
mol:beta2-estradiol 0.063 0.098 0.24 112 -10000 0 112
RELA 0.023 0.001 -10000 0 -10000 0 0
SHC1 0.02 0.005 -10000 0 -10000 0 0
Rac/GDP 0.017 0.003 -10000 0 -10000 0 0
F2 0.076 0.12 0.27 115 -10000 0 115
TNIP2 0.021 0.006 -10000 0 -10000 0 0
NF kappa B/RelA -0.56 0.58 -10000 0 -1.1 261 261
FN1 0.01 0.084 -10000 0 -0.56 10 10
PLD2 -0.64 0.65 -10000 0 -1.2 260 260
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GRB14 -0.014 0.14 0.24 1 -0.56 30 31
ELK1 -0.57 0.56 -10000 0 -1.1 263 263
GRB7 0.025 0.033 0.38 4 -10000 0 4
PAK1 0.023 0.017 0.38 1 -10000 0 1
Tie2/Ang1/alpha5/beta1 Integrin -0.59 0.62 -10000 0 -1.1 261 261
CDKN1A -0.37 0.33 -10000 0 -0.66 262 262
ITGA5 0.023 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.62 0.64 -10000 0 -1.2 262 262
CRK 0.022 0.006 -10000 0 -10000 0 0
mol:NO -0.38 0.35 -10000 0 -0.69 263 263
PLG -0.65 0.65 -10000 0 -1.2 260 260
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.5 0.47 -10000 0 -0.91 263 263
GRB2 0.022 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.006 -10000 0 -10000 0 0
ANGPT2 -0.31 0.33 -10000 0 -0.71 158 158
BMX -0.7 0.68 -10000 0 -1.3 261 261
ANGPT1 -0.36 0.56 -10000 0 -1.3 116 116
tube development -0.42 0.37 -10000 0 -0.75 262 262
ANGPT4 -0.24 0.28 -10000 0 -0.56 205 205
response to hypoxia -0.037 0.033 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.68 0.68 -10000 0 -1.3 261 261
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
FGF2 0.007 0.095 -10000 0 -0.56 13 13
STAT5A (dimer) -0.49 0.44 -10000 0 -0.87 262 262
mol:L-citrulline -0.38 0.35 -10000 0 -0.69 263 263
AGTR1 -0.14 0.25 -10000 0 -0.56 126 126
MAPK14 -0.7 0.67 -10000 0 -1.3 263 263
Tie2/SHP2 -0.58 0.6 -10000 0 -1.2 236 236
TEK -0.64 0.66 -10000 0 -1.3 236 236
RPS6KB1 -0.51 0.47 -10000 0 -0.93 263 263
Angiotensin II/AT1 -0.1 0.19 -10000 0 -0.41 126 126
Tie2/Ang1/GRB2 -0.66 0.68 -10000 0 -1.2 261 261
MAPK3 -0.58 0.57 -10000 0 -1.1 259 259
MAPK1 -0.58 0.57 -10000 0 -1.1 260 260
Tie2/Ang1/GRB7 -0.66 0.68 -10000 0 -1.2 261 261
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.65 0.65 -10000 0 -1.2 261 261
PI3K -0.63 0.59 -10000 0 -1.2 263 263
FES -0.69 0.66 -10000 0 -1.3 263 263
Crk/Dok-R -0.62 0.64 -10000 0 -1.2 262 262
Tie2/Ang1/ABIN2 -0.66 0.68 -10000 0 -1.2 261 261
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.47 0.43 -10000 0 -0.85 263 263
STAT5A 0.023 0.004 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.5 0.47 -10000 0 -0.92 263 263
Tie2/Ang2 -0.6 0.55 -10000 0 -1.1 262 262
Tie2/Ang1 -0.72 0.74 -10000 0 -1.3 261 261
FOXO1 -0.47 0.44 -10000 0 -0.86 263 263
ELF1 -0.037 0.068 -10000 0 -10000 0 0
ELF2 -0.65 0.66 -10000 0 -1.2 261 261
mol:Choline -0.6 0.6 -10000 0 -1.1 260 260
cell migration -0.13 0.12 -10000 0 -0.24 263 263
FYN -0.49 0.44 -10000 0 -0.87 262 262
DOK2 -0.02 0.15 -10000 0 -0.56 33 33
negative regulation of cell cycle -0.33 0.3 -10000 0 -0.6 263 263
ETS1 -0.067 0.14 -10000 0 -0.29 113 113
PXN -0.41 0.38 -10000 0 -0.75 263 263
ITGB1 0.022 0.004 -10000 0 -10000 0 0
NOS3 -0.44 0.41 -10000 0 -0.8 263 263
RAC1 0.022 0.004 -10000 0 -10000 0 0
TNF -0.067 0.14 0.25 1 -0.29 107 108
MAPKKK cascade -0.6 0.6 -10000 0 -1.1 260 260
RASA1 0.021 0.006 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.66 0.68 -10000 0 -1.2 260 260
NCK1 0.019 0.008 -10000 0 -10000 0 0
vasculogenesis -0.34 0.31 -10000 0 -0.61 263 263
mol:Phosphatidic acid -0.6 0.6 -10000 0 -1.1 260 260
mol:Angiotensin II 0 0.001 -10000 0 -10000 0 0
mol:NADP -0.38 0.35 -10000 0 -0.69 263 263
Rac1/GTP -0.47 0.44 -10000 0 -0.86 263 263
MMP2 -0.65 0.65 -10000 0 -1.2 260 260
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.16 0.23 -10000 0 -0.74 29 29
IHH -0.31 0.31 -10000 0 -0.59 261 261
SHH Np/Cholesterol/GAS1 -0.029 0.12 0.2 1 -0.33 66 67
LRPAP1 0.021 0.006 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.029 0.12 0.33 66 -0.2 1 67
SMO/beta Arrestin2 -0.2 0.23 -10000 0 -0.4 249 249
SMO -0.22 0.23 -10000 0 -0.42 255 255
AKT1 -0.11 0.16 -10000 0 -0.57 30 30
ARRB2 0.022 0.006 -10000 0 -10000 0 0
BOC 0.019 0.041 0.24 2 -0.56 2 4
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
heart looping -0.22 0.23 -10000 0 -0.41 255 255
STIL -0.18 0.19 -10000 0 -0.5 64 64
DHH N/PTCH2 0 0.12 -10000 0 -0.4 37 37
DHH N/PTCH1 -0.18 0.21 -10000 0 -0.34 284 284
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
DHH -0.023 0.15 -10000 0 -0.56 34 34
PTHLH -0.2 0.26 -10000 0 -0.74 28 28
determination of left/right symmetry -0.22 0.23 -10000 0 -0.41 255 255
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
skeletal system development -0.2 0.26 -10000 0 -0.74 28 28
IHH N/Hhip -0.44 0.29 -10000 0 -0.58 370 370
DHH N/Hhip -0.28 0.23 -10000 0 -0.44 305 305
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.22 0.23 -10000 0 -0.41 255 255
pancreas development -0.34 0.28 -10000 0 -0.56 294 294
HHAT 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.014 0.07 -10000 0 -0.56 7 7
somite specification -0.22 0.23 -10000 0 -0.41 255 255
SHH Np/Cholesterol/PTCH1 -0.18 0.2 -10000 0 -0.39 136 136
SHH Np/Cholesterol/PTCH2 -0.026 0.12 0.2 1 -0.33 62 63
SHH Np/Cholesterol/Megalin -0.19 0.2 -10000 0 -0.36 261 261
SHH -0.06 0.13 0.3 1 -0.42 59 60
catabolic process -0.18 0.21 -10000 0 -0.36 271 271
SMO/Vitamin D3 -0.2 0.22 -10000 0 -0.38 255 255
SHH Np/Cholesterol/Hhip -0.23 0.2 -10000 0 -0.37 302 302
LRP2 -0.27 0.29 -10000 0 -0.56 241 241
receptor-mediated endocytosis -0.32 0.26 -10000 0 -0.58 201 201
SHH Np/Cholesterol/BOC -0.023 0.11 -10000 0 -0.33 52 52
SHH Np/Cholesterol/CDO -0.027 0.12 0.2 1 -0.32 64 65
mesenchymal cell differentiation 0.23 0.19 0.36 302 -10000 0 302
mol:Vitamin D3 -0.18 0.2 -10000 0 -0.47 85 85
IHH N/PTCH2 -0.19 0.21 -10000 0 -0.37 259 259
CDON 0.016 0.06 -10000 0 -0.56 5 5
IHH N/PTCH1 -0.18 0.22 -10000 0 -0.36 271 271
Megalin/LRPAP1 -0.19 0.22 -10000 0 -0.41 241 241
PTCH2 0.02 0.048 0.24 2 -0.56 3 5
SHH Np/Cholesterol -0.033 0.11 -10000 0 -0.32 59 59
PTCH1 -0.18 0.21 -10000 0 -0.36 271 271
HHIP -0.34 0.28 -10000 0 -0.56 294 294
Endothelins

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
AKT1 -0.099 0.15 -10000 0 -0.41 74 74
PTK2B 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.28 -10000 0 -0.83 48 48
EDN1 -0.093 0.17 -10000 0 -0.46 65 65
EDN3 -0.05 0.18 0.24 13 -0.56 48 61
EDN2 0.043 0.11 0.24 64 -0.56 7 71
HRAS/GDP -0.22 0.25 -10000 0 -0.56 136 136
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.1 0.18 -10000 0 -0.44 82 82
ADCY4 -0.098 0.16 -10000 0 -0.38 88 88
ADCY5 -0.1 0.17 -10000 0 -0.4 90 90
ADCY6 -0.083 0.14 -10000 0 -0.36 69 69
ADCY7 -0.08 0.14 -10000 0 -0.36 68 68
ADCY1 -0.082 0.14 -10000 0 -0.36 69 69
ADCY2 -0.071 0.15 0.25 8 -0.38 64 72
ADCY3 -0.082 0.14 -10000 0 -0.36 70 70
ADCY8 -0.15 0.18 -10000 0 -0.36 179 179
ADCY9 -0.083 0.14 -10000 0 -0.36 70 70
arachidonic acid secretion -0.19 0.24 -10000 0 -0.49 156 156
ETB receptor/Endothelin-1/Gq/GTP -0.27 0.27 -10000 0 -0.43 297 297
GNAO1 0.021 0.031 0.24 2 -0.56 1 3
HRAS 0.022 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.076 0.15 -10000 0 -0.38 71 71
ETA receptor/Endothelin-1/Gs/GTP -0.075 0.15 -10000 0 -0.36 76 76
mol:GTP -0.001 0.003 -10000 0 -10000 0 0
COL3A1 -0.1 0.15 -10000 0 -0.41 67 67
EDNRB -0.3 0.29 -10000 0 -0.56 265 265
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.11 0.18 -10000 0 -0.47 72 72
CYSLTR1 -0.15 0.24 -10000 0 -0.58 96 96
SLC9A1 -0.055 0.096 -10000 0 -0.27 59 59
mol:GDP -0.24 0.27 -10000 0 -0.6 141 141
SLC9A3 -0.37 0.37 -10000 0 -0.72 195 195
RAF1 -0.23 0.27 -10000 0 -0.58 151 151
JUN -0.14 0.24 -10000 0 -0.74 39 39
JAK2 -0.098 0.15 -10000 0 -0.41 74 74
mol:IP3 -0.21 0.25 -10000 0 -0.54 143 143
ETA receptor/Endothelin-1 -0.11 0.18 -10000 0 -0.44 92 92
PLCB1 0.021 0.006 -10000 0 -10000 0 0
PLCB2 0.01 0.076 -10000 0 -0.56 8 8
ETA receptor/Endothelin-3 -0.071 0.14 -10000 0 -0.42 58 58
FOS -0.24 0.32 -10000 0 -0.76 102 102
Gai/GDP -0.091 0.29 -10000 0 -0.86 54 54
CRK 0.021 0.005 -10000 0 -10000 0 0
mol:Ca ++ -0.26 0.28 -10000 0 -0.62 150 150
BCAR1 0.022 0.006 -10000 0 -10000 0 0
PRKCB1 -0.2 0.24 -10000 0 -0.52 143 143
GNAQ 0.017 0.03 -10000 0 -0.56 1 1
GNAZ 0.016 0.06 -10000 0 -0.56 5 5
GNAL 0.018 0.046 -10000 0 -0.56 3 3
Gs family/GDP -0.21 0.24 -10000 0 -0.54 135 135
ETA receptor/Endothelin-1/Gq/GTP -0.12 0.2 -10000 0 -0.41 123 123
MAPK14 -0.22 0.23 -10000 0 -0.5 156 156
TRPC6 -0.16 0.3 -10000 0 -0.92 46 46
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.23 0.24 -10000 0 -0.51 166 166
ETB receptor/Endothelin-2 -0.22 0.23 0.27 1 -0.42 272 273
ETB receptor/Endothelin-3 -0.26 0.24 -10000 0 -0.44 289 289
ETB receptor/Endothelin-1 -0.28 0.24 -10000 0 -0.46 288 288
MAPK3 -0.25 0.32 -10000 0 -0.68 139 139
MAPK1 -0.25 0.32 -10000 0 -0.68 137 137
Rac1/GDP -0.21 0.25 -10000 0 -0.56 134 134
cAMP biosynthetic process -0.091 0.16 0.25 7 -0.43 54 61
MAPK8 -0.17 0.3 -10000 0 -0.72 79 79
SRC 0.022 0.004 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.17 0.16 -10000 0 -0.31 215 215
p130Cas/CRK/Src/PYK2 -0.23 0.28 -10000 0 -0.61 135 135
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.21 0.25 -10000 0 -0.56 134 134
COL1A2 -0.26 0.22 -10000 0 -0.54 122 122
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.014 0.12 0.27 3 -0.37 20 23
mol:DAG -0.21 0.25 -10000 0 -0.54 143 143
MAP2K2 -0.24 0.28 -10000 0 -0.6 149 149
MAP2K1 -0.24 0.28 -10000 0 -0.6 148 148
EDNRA -0.051 0.098 -10000 0 -0.33 31 31
positive regulation of muscle contraction -0.084 0.13 -10000 0 -0.37 63 63
Gq family/GDP -0.19 0.27 -10000 0 -0.58 129 129
HRAS/GTP -0.23 0.27 -10000 0 -0.57 149 149
PRKCH -0.2 0.24 -10000 0 -0.54 130 130
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA -0.2 0.24 0.21 2 -0.54 131 133
PRKCB -0.22 0.26 -10000 0 -0.56 139 139
PRKCE -0.2 0.24 0.21 1 -0.53 130 131
PRKCD -0.2 0.24 -10000 0 -0.54 130 130
PRKCG -0.21 0.24 -10000 0 -0.55 133 133
regulation of vascular smooth muscle contraction -0.28 0.38 -10000 0 -0.92 99 99
PRKCQ -0.22 0.26 -10000 0 -0.58 143 143
PLA2G4A -0.21 0.26 -10000 0 -0.54 156 156
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
GNA15 0.02 0.009 -10000 0 -10000 0 0
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA11 0.02 0.009 -10000 0 -10000 0 0
Rac1/GTP -0.077 0.15 -10000 0 -0.38 71 71
MMP1 0.11 0.11 0.38 26 -10000 0 26
Fc-epsilon receptor I signaling in mast 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
PPAP2A 0.021 0.006 -10000 0 -10000 0 0
LAT2 -0.11 0.21 -10000 0 -0.46 97 97
AP1 -0.11 0.26 -10000 0 -0.56 92 92
mol:PIP3 -0.13 0.23 0.24 8 -0.52 90 98
IKBKB -0.061 0.14 0.2 12 -0.3 73 85
AKT1 -0.056 0.21 0.41 19 -0.44 53 72
IKBKG -0.07 0.13 0.18 9 -0.3 74 83
MS4A2 -0.11 0.24 -10000 0 -0.56 106 106
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.012 0.011 -10000 0 -10000 0 0
MAP3K1 -0.029 0.22 0.29 34 -0.48 56 90
mol:Ca2+ -0.096 0.17 0.22 9 -0.38 90 99
LYN 0.012 0.043 -10000 0 -0.58 2 2
CBLB -0.1 0.2 -10000 0 -0.44 92 92
SHC1 0.022 0.005 -10000 0 -10000 0 0
RasGAP/p62DOK -0.002 0.11 -10000 0 -0.33 50 50
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
PLD2 -0.14 0.21 0.34 12 -0.39 168 180
PTPN13 -0.1 0.21 -10000 0 -0.65 30 30
PTPN11 0.007 0.028 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.039 0.18 0.33 20 -0.36 50 70
SYK 0.015 0.019 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.14 0.23 -10000 0 -0.51 102 102
LAT -0.11 0.2 -10000 0 -0.44 97 97
PAK2 -0.037 0.24 0.25 95 -0.54 58 153
NFATC2 -0.13 0.26 -10000 0 -0.76 63 63
HRAS -0.11 0.25 0.23 8 -0.58 76 84
GAB2 0.008 0.091 -10000 0 -0.56 12 12
PLA2G1B -0.084 0.25 -10000 0 -0.92 39 39
Fc epsilon R1 -0.14 0.26 -10000 0 -0.46 175 175
Antigen/IgE/Fc epsilon R1 -0.13 0.24 -10000 0 -0.42 175 175
mol:GDP -0.12 0.26 0.27 1 -0.61 81 82
JUN 0.022 0.004 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
FOS -0.043 0.18 -10000 0 -0.56 53 53
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.11 0.21 -10000 0 -0.46 99 99
CHUK -0.072 0.13 0.19 7 -0.3 72 79
KLRG1 -0.11 0.19 -10000 0 -0.43 86 86
VAV1 -0.11 0.21 -10000 0 -0.45 97 97
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.11 0.2 -10000 0 -0.44 96 96
negative regulation of mast cell degranulation -0.088 0.19 -10000 0 -0.48 62 62
BTK -0.14 0.29 -10000 0 -0.67 83 83
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.14 0.25 -10000 0 -0.43 155 155
GAB2/PI3K/SHP2 -0.12 0.16 -10000 0 -0.4 96 96
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.11 0.2 -10000 0 -0.39 126 126
RAF1 -0.048 0.28 -10000 0 -0.96 39 39
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.25 -10000 0 -0.41 175 175
FCER1G 0.001 0.099 -10000 0 -0.58 13 13
FCER1A -0.15 0.26 -10000 0 -0.57 132 132
Antigen/IgE/Fc epsilon R1/Fyn -0.12 0.24 -10000 0 -0.4 175 175
MAPK3 -0.047 0.26 -10000 0 -0.9 39 39
MAPK1 -0.048 0.26 -10000 0 -0.9 39 39
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.05 0.25 -10000 0 -0.86 34 34
DUSP1 -0.044 0.18 -10000 0 -0.56 53 53
NF-kappa-B/RelA -0.038 0.083 -10000 0 -0.19 56 56
actin cytoskeleton reorganization -0.1 0.22 -10000 0 -0.59 48 48
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.091 0.2 -10000 0 -0.52 62 62
FER -0.11 0.2 -10000 0 -0.44 97 97
RELA 0.023 0.001 -10000 0 -10000 0 0
ITK -0.066 0.15 -10000 0 -0.43 59 59
SOS1 0.023 0.004 -10000 0 -10000 0 0
PLCG1 -0.12 0.26 0.27 2 -0.6 81 83
cytokine secretion -0.03 0.058 -10000 0 -0.17 8 8
SPHK1 -0.11 0.2 -10000 0 -0.44 96 96
PTK2 -0.1 0.23 -10000 0 -0.71 31 31
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.14 0.25 -10000 0 -0.53 103 103
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.13 0.23 0.25 8 -0.51 93 101
MAP2K2 -0.05 0.26 -10000 0 -0.9 39 39
MAP2K1 -0.05 0.26 -10000 0 -0.9 39 39
MAP2K7 0.022 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.086 0.19 0.22 2 -0.47 62 64
MAP2K4 -0.036 0.27 -10000 0 -1 32 32
Fc epsilon R1/FcgammaRIIB -0.12 0.26 -10000 0 -0.43 176 176
mol:Choline -0.14 0.21 0.34 12 -0.38 168 180
SHC/Grb2/SOS1 -0.079 0.2 -10000 0 -0.51 61 61
FYN 0.022 0.027 -10000 0 -0.56 1 1
DOK1 0.022 0.004 -10000 0 -10000 0 0
PXN -0.099 0.21 -10000 0 -0.66 28 28
HCLS1 -0.1 0.2 -10000 0 -0.44 91 91
PRKCB -0.1 0.18 0.22 7 -0.42 79 86
FCGR2B 0.014 0.065 -10000 0 -0.56 6 6
IGHE -0.003 0.009 -10000 0 -10000 0 0
KLRG1/SHIP -0.09 0.19 -10000 0 -0.49 62 62
LCP2 0.014 0.065 -10000 0 -0.56 6 6
PLA2G4A -0.11 0.2 -10000 0 -0.45 98 98
RASA1 0.021 0.006 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.14 0.21 0.34 12 -0.38 168 180
IKK complex -0.043 0.11 0.18 11 -0.23 56 67
WIPF1 0.023 0.003 -10000 0 -10000 0 0
Thromboxane A2 receptor signaling

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
TGM2 -0.025 0.16 -10000 0 -0.56 38 38
GNB1/GNG2 -0.067 0.093 -10000 0 -0.19 158 158
AKT1 -0.061 0.12 0.19 1 -0.25 40 41
EGF 0.015 0.072 0.24 3 -0.56 7 10
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.026 0.1 0.25 2 -0.37 28 30
mol:Ca2+ -0.097 0.16 -10000 0 -0.31 168 168
LYN -0.014 0.071 0.25 2 -0.37 9 11
RhoA/GTP -0.038 0.07 -10000 0 -0.13 137 137
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.11 0.18 -10000 0 -0.35 161 161
GNG2 0.016 0.06 -10000 0 -0.56 5 5
ARRB2 0.022 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.04 0.14 -10000 0 -0.58 18 18
G beta5/gamma2 -0.086 0.13 -10000 0 -0.26 154 154
PRKCH -0.12 0.19 -10000 0 -0.36 164 164
DNM1 0.023 0.014 0.24 2 -10000 0 2
TXA2/TP beta/beta Arrestin3 0.011 0.066 -10000 0 -0.58 5 5
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.009 0.084 -10000 0 -0.56 10 10
G12 family/GTP -0.097 0.16 -10000 0 -0.31 161 161
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
ADRBK2 0.022 0.005 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.027 0.01 -10000 0 -10000 0 0
mol:GDP 0.056 0.12 0.38 29 -10000 0 29
mol:NADP 0.02 0.038 -10000 0 -0.56 2 2
RAB11A 0.023 0.003 -10000 0 -10000 0 0
PRKG1 -0.022 0.15 -10000 0 -0.56 36 36
mol:IP3 -0.12 0.21 -10000 0 -0.39 168 168
cell morphogenesis 0.027 0.01 -10000 0 -10000 0 0
PLCB2 -0.18 0.28 -10000 0 -0.54 168 168
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.015 0.081 0.25 2 -0.32 17 19
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.015 0.076 0.25 2 -0.41 9 11
RHOA 0.021 0.007 -10000 0 -10000 0 0
PTGIR 0.008 0.091 -10000 0 -0.56 12 12
PRKCB1 -0.12 0.2 -10000 0 -0.39 167 167
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
mol:L-citrulline 0.02 0.038 -10000 0 -0.56 2 2
TXA2/TXA2-R family -0.18 0.28 -10000 0 -0.54 165 165
LCK -0.013 0.072 0.25 2 -0.39 8 10
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.009 0.078 -10000 0 -0.34 17 17
TXA2-R family/G12 family/GDP/G beta/gamma -0.003 0.11 -10000 0 -0.45 23 23
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.012 0.077 -10000 0 -0.34 17 17
MAPK14 -0.073 0.12 -10000 0 -0.24 156 156
TGM2/GTP -0.15 0.24 -10000 0 -0.45 168 168
MAPK11 -0.071 0.12 0.31 1 -0.24 153 154
ARHGEF1 -0.055 0.095 -10000 0 -0.18 152 152
GNAI2 0.021 0.007 -10000 0 -10000 0 0
JNK cascade -0.12 0.2 -10000 0 -0.4 165 165
RAB11/GDP 0.023 0.003 -10000 0 -10000 0 0
ICAM1 -0.097 0.17 -10000 0 -0.32 163 163
cAMP biosynthetic process -0.12 0.19 -10000 0 -0.36 168 168
Gq family/GTP/EBP50 -0.036 0.099 0.24 3 -0.36 8 11
actin cytoskeleton reorganization 0.027 0.01 -10000 0 -10000 0 0
SRC -0.012 0.069 0.25 2 -0.41 6 8
GNB5 0.023 0.003 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
EGF/EGFR -0.008 0.096 0.25 8 -0.32 19 27
VCAM1 -0.091 0.15 -10000 0 -0.3 163 163
TP beta/Gq family/GDP/G beta5/gamma2 -0.04 0.14 -10000 0 -0.58 18 18
platelet activation -0.096 0.16 0.32 1 -0.31 157 158
PGI2/IP 0.005 0.067 -10000 0 -0.41 12 12
PRKACA -0.002 0.08 -10000 0 -0.37 19 19
Gq family/GDP/G beta5/gamma2 -0.04 0.13 -10000 0 -0.52 21 21
TXA2/TP beta/beta Arrestin2 0.008 0.049 -10000 0 -0.38 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.011 0.077 -10000 0 -0.36 19 19
mol:DAG -0.14 0.23 -10000 0 -0.44 165 165
EGFR 0.022 0.084 0.37 11 -0.56 6 17
TXA2/TP alpha -0.16 0.26 -10000 0 -0.5 168 168
Gq family/GTP -0.058 0.12 -10000 0 -0.25 114 114
YES1 -0.013 0.069 0.25 2 -0.38 7 9
GNAI2/GTP -0.006 0.07 -10000 0 -0.34 14 14
PGD2/DP 0.006 0.062 -10000 0 -0.37 12 12
SLC9A3R1 0.025 0.024 0.27 4 -10000 0 4
FYN -0.014 0.072 0.25 2 -0.41 7 9
mol:NO 0.02 0.038 -10000 0 -0.56 2 2
GNA15 0.022 0.004 -10000 0 -10000 0 0
PGK/cGMP -0.002 0.1 -10000 0 -0.36 38 38
RhoA/GDP 0.021 0.007 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.003 0.14 -10000 0 -0.37 47 47
NOS3 0.02 0.038 -10000 0 -0.56 2 2
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA -0.11 0.19 -10000 0 -0.36 163 163
PRKCB -0.12 0.2 -10000 0 -0.38 165 165
PRKCE -0.11 0.19 0.27 1 -0.37 154 155
PRKCD -0.12 0.2 -10000 0 -0.39 163 163
PRKCG -0.13 0.21 -10000 0 -0.4 162 162
muscle contraction -0.16 0.26 -10000 0 -0.5 166 166
PRKCZ -0.11 0.18 -10000 0 -0.35 162 162
ARR3 -0.011 0.016 -10000 0 -10000 0 0
TXA2/TP beta 0.009 0.081 -10000 0 -0.36 17 17
PRKCQ -0.13 0.2 -10000 0 -0.39 169 169
MAPKKK cascade -0.16 0.25 -10000 0 -0.48 167 167
SELE -0.12 0.2 -10000 0 -0.4 162 162
TP beta/GNAI2/GDP/G beta/gamma 0.02 0.092 -10000 0 -0.46 11 11
ROCK1 0.023 0.003 -10000 0 -10000 0 0
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
chemotaxis -0.2 0.31 -10000 0 -0.62 163 163
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
GNA11 0.022 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.003 -10000 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.059 0.09 0.28 15 -0.31 9 24
STMN1 0.013 0.06 -10000 0 -0.21 6 6
Aurora B/RasGAP/Survivin 0.22 0.15 0.33 285 -0.2 6 291
Chromosomal passenger complex/Cul3 protein complex 0.042 0.081 0.22 6 -0.33 10 16
BIRC5 0.21 0.086 0.25 405 -0.3 1 406
DES -0.3 0.31 -10000 0 -0.64 99 99
Aurora C/Aurora B/INCENP 0.12 0.091 0.3 1 -0.35 1 2
Aurora B/TACC1 0.094 0.094 0.17 120 -0.18 19 139
Aurora B/PP2A 0.12 0.1 -10000 0 -0.19 21 21
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.019 0.031 0.13 4 -10000 0 4
mitotic metaphase/anaphase transition -0.003 0.005 -10000 0 -10000 0 0
NDC80 -0.012 0.11 0.35 20 -0.22 19 39
Cul3 protein complex 0.04 0.032 0.25 2 -10000 0 2
KIF2C 0.071 0.087 0.14 82 -0.36 12 94
PEBP1 0.021 0.006 -10000 0 -10000 0 0
KIF20A 0.12 0.13 0.24 233 -0.29 14 247
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.12 0.099 -10000 0 -0.18 14 14
SEPT1 0.023 0.01 0.24 1 -10000 0 1
SMC2 0.023 0.004 -10000 0 -10000 0 0
SMC4 0.016 0.011 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.074 0.18 0.29 3 -0.57 30 33
PSMA3 0.022 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.003 -10000 0 -10000 0 0
H3F3B 0.045 0.062 0.18 7 -0.22 19 26
AURKB 0.16 0.14 0.25 322 -0.29 22 344
AURKC 0.021 0.029 0.24 1 -0.56 1 2
CDCA8 0.084 0.1 0.25 128 -0.3 1 129
cytokinesis 0.05 0.12 0.24 8 -0.4 23 31
Aurora B/Septin1 0.13 0.14 0.31 16 -0.39 20 36
AURKA 0.028 0.049 0.25 21 -10000 0 21
INCENP 0.024 0.009 -10000 0 -10000 0 0
KLHL13 0.029 0.041 0.27 12 -10000 0 12
BUB1 0.043 0.068 0.25 45 -10000 0 45
hSgo1/Aurora B/Survivin 0.27 0.2 0.39 311 -0.24 28 339
EVI5 0.026 0.006 -10000 0 -10000 0 0
RhoA/GTP 0.1 0.097 0.26 55 -0.28 7 62
SGOL1 0.11 0.14 0.24 226 -0.29 22 248
CENPA 0.083 0.082 0.21 19 -0.25 8 27
NCAPG 0.056 0.089 0.24 81 -0.29 4 85
Aurora B/HC8 Proteasome 0.12 0.1 -10000 0 -0.2 19 19
NCAPD2 0.022 0.017 0.38 1 -10000 0 1
Aurora B/PP1-gamma 0.13 0.1 -10000 0 -0.2 13 13
RHOA 0.021 0.007 -10000 0 -10000 0 0
NCAPH 0.14 0.11 0.24 242 -10000 0 242
NPM1 0.019 0.19 -10000 0 -0.66 27 27
RASA1 0.021 0.006 -10000 0 -10000 0 0
KLHL9 0.019 0.009 -10000 0 -10000 0 0
mitotic prometaphase -0.002 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.1 -10000 0 -0.19 19 19
PPP1CC 0.023 0.002 -10000 0 -10000 0 0
Centraspindlin 0.11 0.11 0.27 73 -0.31 8 81
RhoA/GDP 0.015 0.005 -10000 0 -10000 0 0
NSUN2 0.064 0.12 0.23 2 -0.35 26 28
MYLK 0.052 0.071 0.17 43 -0.22 19 62
KIF23 0.069 0.089 0.25 94 -10000 0 94
VIM 0.005 0.092 0.28 3 -0.31 22 25
RACGAP1 0.026 0.008 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.037 0.14 -10000 0 -0.46 27 27
Chromosomal passenger complex 0.068 0.083 0.19 21 -0.28 15 36
Chromosomal passenger complex/EVI5 0.29 0.17 0.39 306 -0.29 1 307
TACC1 0.018 0.028 -10000 0 -0.56 1 1
PPP2R5D 0.022 0.004 -10000 0 -10000 0 0
CUL3 0.022 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.42 0.53 -10000 0 -1.2 105 105
STAT6 (cleaved dimer) -0.43 0.54 -10000 0 -1.2 114 114
IGHG1 -0.13 0.18 -10000 0 -0.74 3 3
IGHG3 -0.42 0.51 -10000 0 -1.2 110 110
AKT1 -0.21 0.3 -10000 0 -0.95 35 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.27 -10000 0 -1 26 26
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.21 0.32 -10000 0 -1 35 35
THY1 -0.43 0.53 -10000 0 -1.2 105 105
MYB 0.027 0.054 0.24 15 -0.56 2 17
HMGA1 0.024 0.018 0.24 3 -10000 0 3
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.24 0.33 -10000 0 -0.75 73 73
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.32 -10000 0 -1 34 34
SP1 0.027 0.004 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
SOCS5 0.019 0.03 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.43 0.54 -10000 0 -1.2 111 111
SOCS1 -0.28 0.34 -10000 0 -0.75 107 107
SOCS3 -0.21 0.28 -10000 0 -0.93 20 20
FCER2 -0.4 0.51 -10000 0 -1.2 92 92
PARP14 0.021 0.009 -10000 0 -10000 0 0
CCL17 -0.5 0.61 -10000 0 -1.4 125 125
GRB2 0.022 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.26 -10000 0 -0.83 35 35
T cell proliferation -0.43 0.54 -10000 0 -1.2 109 109
IL4R/JAK1 -0.43 0.53 -10000 0 -1.2 106 106
EGR2 -0.45 0.55 -10000 0 -1.3 111 111
JAK2 -0.018 0.048 -10000 0 -10000 0 0
JAK3 0.026 0.009 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
JAK1 0.001 0.026 -10000 0 -10000 0 0
COL1A2 -0.11 0.16 -10000 0 -0.56 1 1
CCL26 -0.43 0.53 -10000 0 -1.2 106 106
IL4R -0.45 0.57 -10000 0 -1.3 106 106
PTPN6 0.026 0.022 -10000 0 -10000 0 0
IL13RA2 -0.45 0.56 -10000 0 -1.3 114 114
IL13RA1 -0.018 0.05 -10000 0 -10000 0 0
IRF4 -0.2 0.38 -10000 0 -0.92 86 86
ARG1 -0.12 0.22 -10000 0 -0.8 25 25
CBL -0.23 0.31 -10000 0 -0.74 62 62
GTF3A 0.028 0.012 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.017 0.068 -10000 0 -10000 0 0
IRF4/BCL6 -0.16 0.32 -10000 0 -0.79 80 80
CD40LG -0.075 0.22 -10000 0 -0.56 82 82
MAPK14 -0.23 0.31 -10000 0 -0.84 41 41
mitosis -0.2 0.28 -10000 0 -0.87 35 35
STAT6 -0.5 0.66 -10000 0 -1.5 110 110
SPI1 -0.014 0.15 -10000 0 -0.56 32 32
RPS6KB1 -0.19 0.27 -10000 0 -0.84 33 33
STAT6 (dimer) -0.5 0.67 -10000 0 -1.5 110 110
STAT6 (dimer)/PARP14 -0.45 0.58 -10000 0 -1.4 106 106
mast cell activation 0.009 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.23 0.34 -10000 0 -0.93 54 54
FRAP1 -0.21 0.3 -10000 0 -0.95 35 35
LTA -0.43 0.53 -10000 0 -1.2 106 106
FES 0.021 0.027 -10000 0 -0.56 1 1
T-helper 1 cell differentiation 0.48 0.61 1.4 110 -10000 0 110
CCL11 -0.42 0.52 -10000 0 -1.2 109 109
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.19 0.3 -10000 0 -1 30 30
IL2RG 0.019 0.07 -10000 0 -0.55 7 7
IL10 -0.43 0.53 -10000 0 -1.2 106 106
IRS1 0.022 0.004 -10000 0 -10000 0 0
IRS2 0.018 0.046 -10000 0 -0.56 3 3
IL4 -0.14 0.27 -10000 0 -1.1 29 29
IL5 -0.44 0.53 -10000 0 -1.2 106 106
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.36 0.46 -10000 0 -0.98 114 114
COL1A1 -0.14 0.26 -10000 0 -1 20 20
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.44 0.55 -10000 0 -1.3 105 105
IL2R gamma/JAK3 0.029 0.055 -10000 0 -0.41 7 7
TFF3 -0.48 0.6 -10000 0 -1.4 111 111
ALOX15 -0.64 0.73 -10000 0 -1.5 181 181
MYBL1 0.023 0.011 0.24 1 -10000 0 1
T-helper 2 cell differentiation -0.48 0.51 -10000 0 -1.1 151 151
SHC1 0.022 0.005 -10000 0 -10000 0 0
CEBPB 0.025 0.006 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.2 0.31 -10000 0 -1 31 31
mol:PI-3-4-5-P3 -0.21 0.3 -10000 0 -0.95 35 35
PI3K -0.22 0.33 -10000 0 -1.1 35 35
DOK2 -0.02 0.15 -10000 0 -0.56 33 33
ETS1 0.009 0.083 -10000 0 -0.53 10 10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.15 0.23 -10000 0 -0.74 29 29
ITGB3 -0.44 0.55 -10000 0 -1.3 107 107
PIGR -0.8 0.78 -10000 0 -1.5 253 253
IGHE 0.045 0.052 0.2 11 -10000 0 11
MAPKKK cascade -0.15 0.22 -10000 0 -0.72 29 29
BCL6 0.013 0.011 -10000 0 -10000 0 0
OPRM1 -0.44 0.53 -10000 0 -1.2 106 106
RETNLB -0.42 0.53 -10000 0 -1.2 102 102
SELP -0.58 0.7 -10000 0 -1.5 147 147
AICDA -0.41 0.51 -10000 0 -1.2 104 104
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.014 0.16 -10000 0 -0.52 40 40
alphaM/beta2 Integrin/GPIbA -0.015 0.16 -10000 0 -0.51 41 41
alphaM/beta2 Integrin/proMMP-9 -0.005 0.16 -10000 0 -0.5 39 39
PLAUR 0.022 0.004 -10000 0 -10000 0 0
HMGB1 0.014 0.021 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.013 0.15 -10000 0 -0.5 39 39
AGER -0.51 0.18 -10000 0 -0.57 427 427
RAP1A 0.022 0.005 -10000 0 -10000 0 0
SELPLG -0.014 0.14 -10000 0 -0.56 30 30
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.35 0.2 -10000 0 -0.4 426 426
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.033 0.047 0.24 24 -10000 0 24
CYR61 -0.004 0.12 -10000 0 -0.56 22 22
TLN1 0.021 0.007 -10000 0 -10000 0 0
Rap1/GTP -0.15 0.26 -10000 0 -0.53 113 113
RHOA 0.021 0.007 -10000 0 -10000 0 0
P-selectin oligomer -0.11 0.24 -10000 0 -0.56 105 105
MYH2 -0.24 0.3 -10000 0 -0.61 146 146
MST1R -0.008 0.13 -10000 0 -0.56 24 24
leukocyte activation during inflammatory response -0.02 0.16 -10000 0 -0.42 59 59
APOB -0.014 0.14 0.24 4 -0.56 27 31
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.017 0.053 -10000 0 -0.56 4 4
JAM3 0.022 0.005 -10000 0 -10000 0 0
GP1BA 0.016 0.055 0.24 1 -0.56 4 5
alphaM/beta2 Integrin/CTGF -0.024 0.18 -10000 0 -0.53 47 47
alphaM/beta2 Integrin -0.2 0.31 -10000 0 -0.62 118 118
JAM3 homodimer 0.022 0.005 -10000 0 -10000 0 0
ICAM2 -0.013 0.14 -10000 0 -0.56 29 29
ICAM1 -0.024 0.16 -10000 0 -0.56 38 38
phagocytosis triggered by activation of immune response cell surface activating receptor -0.18 0.31 -10000 0 -0.6 118 118
cell adhesion -0.016 0.16 -10000 0 -0.51 41 41
NFKB1 -0.36 0.23 -10000 0 -0.72 108 108
THY1 0.022 0.004 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.005 -10000 0 -10000 0 0
Lipoprotein(a) 0.012 0.093 0.24 1 -0.35 27 28
alphaM/beta2 Integrin/LRP/tPA 0 0.15 0.26 4 -0.47 39 43
IL6 -0.39 0.32 -10000 0 -0.93 106 106
ITGB2 -0.007 0.11 -10000 0 -0.57 17 17
elevation of cytosolic calcium ion concentration 0.005 0.15 -10000 0 -0.46 39 39
alphaM/beta2 Integrin/JAM2/JAM3 -0.048 0.21 -10000 0 -0.47 82 82
JAM2 -0.059 0.2 -10000 0 -0.56 66 66
alphaM/beta2 Integrin/ICAM1 -0.028 0.21 -10000 0 -0.46 80 80
alphaM/beta2 Integrin/uPA/Plg 0.006 0.16 -10000 0 -0.47 39 39
RhoA/GTP -0.23 0.31 -10000 0 -0.65 127 127
positive regulation of phagocytosis -0.13 0.24 -10000 0 -0.58 77 77
Ron/MSP 0.007 0.1 -10000 0 -0.42 24 24
alphaM/beta2 Integrin/uPAR/uPA 0.007 0.16 -10000 0 -0.47 39 39
alphaM/beta2 Integrin/uPAR -0.013 0.16 -10000 0 -0.51 39 39
PLAU 0.036 0.054 0.24 30 -10000 0 30
PLAT 0.025 0.036 0.33 6 -10000 0 6
actin filament polymerization -0.23 0.27 -10000 0 -0.57 149 149
MST1 0.021 0.012 0.24 1 -10000 0 1
alphaM/beta2 Integrin/lipoprotein(a) -0.017 0.17 -10000 0 -0.42 59 59
TNF -0.34 0.23 -10000 0 -0.71 101 101
RAP1B 0.022 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.005 0.16 0.26 1 -0.51 39 40
fibrinolysis 0.004 0.15 -10000 0 -0.46 39 39
HCK 0.017 0.053 -10000 0 -0.56 4 4
dendritic cell antigen processing and presentation -0.18 0.31 -10000 0 -0.6 118 118
VTN -0.2 0.28 0.24 2 -0.56 183 185
alphaM/beta2 Integrin/CYR61 -0.029 0.19 -10000 0 -0.53 52 52
LPA 0.02 0.049 0.25 18 -10000 0 18
LRP1 0.023 0.002 -10000 0 -10000 0 0
cell migration -0.017 0.15 -10000 0 -0.48 40 40
FN1 0.01 0.084 -10000 0 -0.56 10 10
alphaM/beta2 Integrin/Thy1 -0.013 0.16 -10000 0 -0.51 39 39
MPO -0.001 0.11 -10000 0 -0.56 19 19
KNG1 0.007 0.052 0.31 12 -10000 0 12
RAP1/GDP 0.029 0.009 -10000 0 -10000 0 0
ROCK1 -0.2 0.28 -10000 0 -0.62 119 119
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.005 0.027 0.24 3 -10000 0 3
CTGF 0.004 0.1 -10000 0 -0.56 15 15
alphaM/beta2 Integrin/Hck -0.014 0.16 -10000 0 -0.5 38 38
ITGAM -0.032 0.16 -10000 0 -0.57 38 38
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.093 0.27 -10000 0 -0.49 120 120
HP -0.15 0.26 -10000 0 -0.56 138 138
leukocyte adhesion -0.34 0.23 -10000 0 -0.61 142 142
SELP -0.11 0.24 -10000 0 -0.56 105 105
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.35 -10000 0 -1.1 49 49
MKNK1 0.022 0.004 -10000 0 -10000 0 0
MAPK14 -0.014 0.13 -10000 0 -0.32 65 65
ATF2/c-Jun -0.021 0.097 -10000 0 -0.4 5 5
MAPK11 -0.016 0.13 -10000 0 -0.32 69 69
MITF -0.04 0.15 -10000 0 -0.38 76 76
MAPKAPK5 -0.031 0.14 -10000 0 -0.37 72 72
KRT8 -0.031 0.14 -10000 0 -0.37 71 71
MAPKAPK3 0.021 0.007 -10000 0 -10000 0 0
MAPKAPK2 0.022 0.004 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.029 0.19 -10000 0 -0.48 66 66
CEBPB -0.031 0.14 -10000 0 -0.36 71 71
SLC9A1 -0.033 0.15 -10000 0 -0.38 70 70
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.027 0.14 -10000 0 -0.36 65 65
p38alpha-beta/MNK1 -0.008 0.16 -10000 0 -0.39 65 65
JUN -0.019 0.097 -10000 0 -0.4 5 5
PPARGC1A -0.11 0.24 -10000 0 -0.45 131 131
USF1 -0.03 0.14 -10000 0 -0.36 69 69
RAB5/GDP/GDI1 -0.017 0.11 -10000 0 -0.28 61 61
NOS2 -0.065 0.28 -10000 0 -1.1 28 28
DDIT3 -0.031 0.14 -10000 0 -0.36 71 71
RAB5A 0.021 0.007 -10000 0 -10000 0 0
HSPB1 -0.028 0.12 0.27 7 -0.31 63 70
p38alpha-beta/HBP1 -0.008 0.16 -10000 0 -0.39 63 63
CREB1 -0.032 0.15 -10000 0 -0.39 69 69
RAB5/GDP 0.016 0.005 -10000 0 -10000 0 0
EIF4E -0.031 0.13 -10000 0 -0.35 60 60
RPS6KA4 -0.031 0.14 -10000 0 -0.37 71 71
PLA2G4A -0.033 0.14 0.27 1 -0.36 62 63
GDI1 -0.028 0.14 -10000 0 -0.37 67 67
TP53 -0.051 0.18 -10000 0 -0.47 69 69
RPS6KA5 -0.031 0.14 -10000 0 -0.37 70 70
ESR1 -0.049 0.18 -10000 0 -0.41 84 84
HBP1 0.022 0.005 -10000 0 -10000 0 0
MEF2C -0.038 0.15 -10000 0 -0.38 74 74
MEF2A -0.031 0.14 -10000 0 -0.37 70 70
EIF4EBP1 -0.03 0.15 -10000 0 -0.39 66 66
KRT19 -0.037 0.16 -10000 0 -0.39 74 74
ELK4 -0.03 0.14 -10000 0 -0.37 70 70
ATF6 -0.03 0.14 -10000 0 -0.36 69 69
ATF1 -0.032 0.15 -10000 0 -0.38 69 69
p38alpha-beta/MAPKAPK2 -0.009 0.16 -10000 0 -0.39 66 66
p38alpha-beta/MAPKAPK3 -0.012 0.16 -10000 0 -0.39 66 66
TCGA08_retinoblastoma

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
CDKN2B 0.016 0.04 -10000 0 -0.44 3 3
CDKN2C 0.023 0.02 -10000 0 -10000 0 0
CDKN2A 0.098 0.14 0.24 201 -0.28 18 219
CCND2 -0.01 0.056 0.24 5 -0.38 7 12
RB1 -0.006 0.083 0.43 6 -0.24 35 41
CDK4 -0.004 0.072 0.25 19 -0.43 6 25
CDK6 -0.004 0.072 0.25 19 -0.44 6 25
G1/S progression 0.033 0.11 0.21 102 -0.43 6 108
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.019 0.069 0.59 2 -10000 0 2
VDR 0.022 0.027 -10000 0 -0.56 1 1
FAM120B 0.023 0.004 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.12 0.15 -10000 0 -0.42 21 21
RXRs/LXRs/DNA/Oxysterols -0.1 0.14 -10000 0 -0.48 19 19
MED1 0.022 0.004 -10000 0 -10000 0 0
mol:9cRA 0.001 0.007 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.002 0.072 -10000 0 -0.27 18 18
RXRs/NUR77 -0.18 0.22 -10000 0 -0.37 255 255
RXRs/PPAR -0.15 0.17 -10000 0 -0.3 249 249
NCOR2 0.022 0.027 -10000 0 -0.56 1 1
VDR/VDR/Vit D3 0.016 0.02 -10000 0 -0.41 1 1
RARs/VDR/DNA/Vit D3 0.047 0.03 -10000 0 -0.3 2 2
RARA 0.022 0.004 -10000 0 -10000 0 0
NCOA1 0.023 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.022 0.027 -10000 0 -0.56 1 1
RARs/RARs/DNA/9cRA 0.036 0.022 -10000 0 -0.29 1 1
RARG 0.023 0.002 -10000 0 -10000 0 0
RPS6KB1 0.038 0.08 0.67 6 -10000 0 6
RARs/THRs/DNA/SMRT -0.001 0.074 -10000 0 -0.28 19 19
THRA 0.022 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.02 -10000 0 -0.41 1 1
RXRs/PPAR/9cRA/PGJ2/DNA -0.14 0.18 -10000 0 -0.32 231 231
NR1H4 -0.001 0.03 0.24 4 -10000 0 4
RXRs/LXRs/DNA -0.12 0.19 -10000 0 -0.31 230 230
NR1H2 0.023 0.012 -10000 0 -10000 0 0
NR1H3 0.024 0.011 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.12 0.18 -10000 0 -0.31 228 228
NR4A1 -0.057 0.2 -10000 0 -0.56 65 65
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.1 0.12 -10000 0 -0.23 230 230
RXRG -0.26 0.29 -10000 0 -0.56 233 233
RXR alpha/CCPG 0.033 0.012 -10000 0 -10000 0 0
RXRA 0.023 0.011 -10000 0 -10000 0 0
RXRB 0.023 0.012 -10000 0 -10000 0 0
THRB 0.002 0.1 -10000 0 -0.56 16 16
PPARG -0.041 0.18 -10000 0 -0.56 51 51
PPARD 0.023 0.004 -10000 0 -10000 0 0
TNF -0.11 0.2 -10000 0 -1.1 12 12
mol:Oxysterols 0.002 0.007 -10000 0 -10000 0 0
cholesterol transport -0.1 0.14 -10000 0 -0.48 19 19
PPARA 0.022 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.02 0.027 -10000 0 -0.56 1 1
RXRs/NUR77/BCL2 -0.16 0.18 -10000 0 -0.31 256 256
SREBF1 -0.091 0.13 -10000 0 -0.55 10 10
RXRs/RXRs/DNA/9cRA -0.14 0.18 -10000 0 -0.32 231 231
ABCA1 -0.092 0.13 -10000 0 -0.55 10 10
RARs/THRs 0.048 0.071 -10000 0 -0.31 16 16
RXRs/FXR -0.13 0.19 -10000 0 -0.33 231 231
BCL2 0.023 0.011 0.24 1 -10000 0 1
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.023 0.002 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.12 0.088 0.3 1 -0.36 1 2
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.004 0.023 -10000 0 -0.42 1 1
AURKB 0.15 0.14 0.24 322 -0.29 22 344
AURKC 0.021 0.029 0.24 1 -0.56 1 2
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.023 0.094 -10000 0 -0.43 17 17
Crk/p130 Cas/Paxillin -0.052 0.12 -10000 0 -0.3 51 51
JUN -0.019 0.12 0.27 7 -0.35 6 13
HRAS 0.022 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.005 0.16 0.28 21 -0.34 74 95
RAP1A 0.022 0.005 -10000 0 -10000 0 0
FRS2 0.022 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.016 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.007 0.17 0.36 4 -0.34 78 82
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.023 0.16 0.24 18 -0.33 85 103
RHOA 0.021 0.007 -10000 0 -10000 0 0
RAP1A/GTP -0.01 0.15 0.32 3 -0.3 79 82
GRB7 0.025 0.033 0.38 4 -10000 0 4
RET51/GFRalpha1/GDNF -0.008 0.17 0.27 20 -0.34 78 98
MAPKKK cascade -0.027 0.14 0.28 2 -0.31 67 69
BCAR1 0.022 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.022 0.16 0.24 19 -0.33 85 104
lamellipodium assembly -0.038 0.12 -10000 0 -0.28 53 53
RET51/GFRalpha1/GDNF/SHC -0.009 0.16 0.28 19 -0.34 76 95
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.022 0.16 0.24 18 -0.33 80 98
RET9/GFRalpha1/GDNF/Shank3 -0.023 0.16 0.24 17 -0.34 84 101
MAPK3 -0.044 0.13 0.33 1 -0.29 79 80
DOK1 0.022 0.004 -10000 0 -10000 0 0
DOK6 -0.025 0.16 -10000 0 -0.56 39 39
PXN 0.023 0.002 -10000 0 -10000 0 0
neurite development -0.049 0.13 0.32 1 -0.38 17 18
DOK5 0.02 0.048 0.24 2 -0.56 3 5
GFRA1 -0.11 0.24 -10000 0 -0.56 108 108
MAPK8 -0.033 0.12 0.28 7 -0.34 8 15
HRAS/GTP -0.019 0.16 0.33 3 -0.33 69 72
tube development -0.021 0.16 0.24 18 -0.32 84 102
MAPK1 -0.041 0.13 0.27 2 -0.29 73 75
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.033 0.12 -10000 0 -0.26 83 83
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
PDLIM7 0.021 0.006 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.024 0.2 0.36 4 -0.36 100 104
SHC1 0.022 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.008 0.17 0.28 20 -0.34 79 99
RET51/GFRalpha1/GDNF/Dok5 -0.01 0.17 0.4 4 -0.34 81 85
PRKCA 0.02 0.038 -10000 0 -0.56 2 2
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
CREB1 -0.038 0.13 0.27 3 -0.29 77 80
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.035 0.12 -10000 0 -0.27 82 82
RET51/GFRalpha1/GDNF/Grb7 -0.006 0.17 0.37 5 -0.33 79 84
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.03 0.041 0.25 16 -10000 0 16
DOK4 0.022 0.005 -10000 0 -10000 0 0
JNK cascade -0.018 0.12 0.26 7 -0.34 6 13
RET9/GFRalpha1/GDNF/FRS2 -0.02 0.16 0.24 19 -0.33 82 101
SHANK3 0.021 0.027 -10000 0 -0.56 1 1
RASA1 0.021 0.006 -10000 0 -10000 0 0
NCK1 0.019 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.033 0.12 -10000 0 -0.26 78 78
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.029 0.12 0.33 1 -0.26 74 75
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.033 0.12 0.28 2 -0.27 76 78
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.026 0.12 0.28 2 -0.26 72 74
PI3K -0.039 0.18 0.28 9 -0.39 65 74
SOS1 0.023 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.015 0.16 0.24 17 -0.32 84 101
GRB10 0.022 0.005 -10000 0 -10000 0 0
activation of MAPKK activity -0.027 0.11 0.31 1 -0.3 1 2
RET51/GFRalpha1/GDNF/FRS2 -0.007 0.17 0.37 4 -0.34 79 83
GAB1 0.022 0.006 -10000 0 -10000 0 0
IRS1 0.022 0.004 -10000 0 -10000 0 0
IRS2 0.018 0.046 -10000 0 -0.56 3 3
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.03 0.12 -10000 0 -0.27 70 70
RET51/GFRalpha1/GDNF/PKC alpha -0.01 0.17 0.37 4 -0.34 82 86
GRB2 0.022 0.004 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GDNF 0.055 0.1 0.28 77 -10000 0 77
RAC1 0.022 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.008 0.17 0.37 4 -0.33 81 85
Rac1/GTP -0.033 0.14 -10000 0 -0.33 53 53
RET9/GFRalpha1/GDNF -0.034 0.17 0.24 20 -0.35 90 110
GFRalpha1/GDNF -0.043 0.2 0.27 20 -0.37 109 129
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.025 0.14 0.32 2 -0.39 49 51
CRKL -0.038 0.14 0.2 1 -0.41 52 53
HRAS -0.031 0.14 -10000 0 -0.4 47 47
mol:PIP3 -0.006 0.14 -10000 0 -0.35 53 53
SPRED1 0.023 0.003 -10000 0 -10000 0 0
SPRED2 0.022 0.006 -10000 0 -10000 0 0
GAB1 -0.039 0.15 -10000 0 -0.42 60 60
FOXO3 -0.025 0.14 -10000 0 -0.38 55 55
AKT1 -0.027 0.15 -10000 0 -0.39 61 61
BAD -0.026 0.14 -10000 0 -0.37 56 56
megakaryocyte differentiation -0.056 0.17 -10000 0 -0.43 74 74
GSK3B -0.007 0.15 0.31 4 -0.38 48 52
RAF1 -0.021 0.12 0.25 2 -0.33 42 44
SHC1 0.022 0.005 -10000 0 -10000 0 0
STAT3 -0.041 0.15 -10000 0 -0.42 61 61
STAT1 -0.11 0.36 -10000 0 -1 60 60
HRAS/SPRED1 -0.012 0.13 -10000 0 -0.33 44 44
cell proliferation -0.039 0.14 -10000 0 -0.41 61 61
PIK3CA 0.012 0.011 -10000 0 -10000 0 0
TEC 0.018 0.046 -10000 0 -0.56 3 3
RPS6KB1 -0.032 0.15 -10000 0 -0.4 62 62
HRAS/SPRED2 -0.013 0.12 -10000 0 -0.33 42 42
LYN/TEC/p62DOK -0.01 0.16 -10000 0 -0.42 51 51
MAPK3 -0.016 0.095 0.22 3 -0.3 17 20
STAP1 -0.053 0.17 -10000 0 -0.43 73 73
GRAP2 -0.006 0.12 -10000 0 -0.56 23 23
JAK2 -0.095 0.32 -10000 0 -0.91 60 60
STAT1 (dimer) -0.11 0.35 -10000 0 -1 60 60
mol:Gleevec 0.001 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.013 0.16 -10000 0 -0.41 57 57
actin filament polymerization -0.04 0.14 -10000 0 -0.4 59 59
LYN 0.02 0.038 -10000 0 -0.56 2 2
STAP1/STAT5A (dimer) -0.079 0.24 -10000 0 -0.65 63 63
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.014 0.14 -10000 0 -0.38 50 50
PI3K -0.02 0.12 -10000 0 -0.4 30 30
PTEN 0.021 0.006 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.12 0.42 -10000 0 -1.2 60 60
MAPK8 -0.04 0.15 -10000 0 -0.42 61 61
STAT3 (dimer) -0.04 0.14 -10000 0 -0.41 61 61
positive regulation of transcription -0.012 0.08 0.2 3 -0.24 16 19
mol:GDP -0.029 0.15 -10000 0 -0.4 52 52
PIK3C2B -0.039 0.15 -10000 0 -0.42 59 59
CBL/CRKL -0.024 0.14 -10000 0 -0.39 52 52
FER -0.039 0.15 -10000 0 -0.42 60 60
SH2B3 -0.043 0.15 -10000 0 -0.42 62 62
PDPK1 -0.003 0.13 -10000 0 -0.33 51 51
SNAI2 -0.04 0.15 -10000 0 -0.41 60 60
positive regulation of cell proliferation -0.083 0.27 -10000 0 -0.76 61 61
KITLG 0.017 0.022 -10000 0 -10000 0 0
cell motility -0.083 0.27 -10000 0 -0.76 61 61
PTPN6 0.022 0.011 -10000 0 -10000 0 0
EPOR -0.031 0.18 -10000 0 -0.84 12 12
STAT5A (dimer) -0.065 0.22 -10000 0 -0.62 62 62
SOCS1 0.021 0.027 -10000 0 -0.56 1 1
cell migration 0.051 0.16 0.41 72 -10000 0 72
SOS1 0.023 0.004 -10000 0 -10000 0 0
EPO 0.019 0.03 0.24 6 -10000 0 6
VAV1 0.019 0.046 -10000 0 -0.56 3 3
GRB10 -0.039 0.14 -10000 0 -0.4 61 61
PTPN11 0.023 0.007 -10000 0 -10000 0 0
SCF/KIT -0.04 0.16 -10000 0 -0.44 61 61
GO:0007205 0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.018 0.097 0.23 3 -0.31 15 18
CBL 0.022 0.004 -10000 0 -10000 0 0
KIT -0.16 0.46 -10000 0 -1.2 69 69
MAP2K2 -0.018 0.097 0.23 3 -0.31 16 19
SHC/Grb2/SOS1 -0.008 0.15 -10000 0 -0.4 52 52
STAT5A -0.066 0.23 -10000 0 -0.65 60 60
GRB2 0.022 0.004 -10000 0 -10000 0 0
response to radiation -0.039 0.14 -10000 0 -0.4 60 60
SHC/GRAP2 0.009 0.096 -10000 0 -0.42 23 23
PTPRO -0.057 0.18 -10000 0 -0.44 74 74
SH2B2 -0.041 0.14 -10000 0 -0.41 59 59
DOK1 0.022 0.004 -10000 0 -10000 0 0
MATK -0.052 0.16 -10000 0 -0.42 72 72
CREBBP 0.017 0.045 -10000 0 -10000 0 0
BCL2 -0.039 0.22 -10000 0 -0.98 16 16
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS 0.069 0.15 0.31 25 -0.32 42 67
SMAD6-7/SMURF1 0.002 0.12 -10000 0 -0.36 44 44
NOG 0.001 0.11 0.24 1 -0.56 17 18
SMAD9 -0.088 0.22 -10000 0 -0.53 90 90
SMAD4 0.022 0.005 -10000 0 -10000 0 0
SMAD5 -0.04 0.14 -10000 0 -0.45 32 32
BMP7/USAG1 -0.016 0.22 0.27 2 -0.43 94 96
SMAD5/SKI -0.039 0.16 0.31 1 -0.46 40 41
SMAD1 0.008 0.062 -10000 0 -0.62 2 2
BMP2 -0.05 0.19 -10000 0 -0.56 59 59
SMAD1/SMAD1/SMAD4 -0.016 0.11 -10000 0 -0.46 6 6
BMPR1A 0.022 0.005 -10000 0 -10000 0 0
BMPR1B -0.022 0.15 -10000 0 -0.56 36 36
BMPR1A-1B/BAMBI 0.011 0.11 0.25 1 -0.36 38 39
AHSG 0.018 0.063 0.35 15 -10000 0 15
CER1 -0.008 0.024 0.24 1 -0.29 1 2
BMP2-4/CER1 -0.017 0.14 -10000 0 -0.37 62 62
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.04 0.15 -10000 0 -0.44 40 40
BMP2-4 (homodimer) -0.031 0.16 -10000 0 -0.43 65 65
RGMB 0.021 0.006 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B 0.014 0.12 -10000 0 -0.34 45 45
RGMA 0.047 0.073 0.26 51 -10000 0 51
SMURF1 0.022 0.006 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.032 0.12 -10000 0 -0.42 27 27
BMP2-4/USAG1 -0.084 0.21 -10000 0 -0.4 133 133
SMAD6/SMURF1/SMAD5 -0.036 0.16 0.33 2 -0.45 41 43
SOSTDC1 -0.087 0.23 0.24 1 -0.56 90 91
BMP7/BMPR2/BMPR1A-1B 0.051 0.14 0.26 1 -0.34 41 42
SKI 0.022 0.005 -10000 0 -10000 0 0
BMP6 (homodimer) 0.009 0.087 -10000 0 -0.56 11 11
HFE2 -0.003 0.025 0.24 2 -10000 0 2
ZFYVE16 0.021 0.006 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/CHRD -0.019 0.12 0.25 1 -0.38 41 42
SMAD5/SMAD5/SMAD4 -0.038 0.16 0.33 2 -0.46 41 43
MAPK1 0.022 0.006 -10000 0 -10000 0 0
TAK1/TAB family -0.018 0.12 -10000 0 -0.38 26 26
BMP7 (homodimer) 0.086 0.13 0.24 159 -0.49 8 167
NUP214 0.023 0.003 -10000 0 -10000 0 0
BMP6/FETUA 0.017 0.07 0.27 10 -0.33 11 21
SMAD1/SKI 0.006 0.086 -10000 0 -0.53 4 4
SMAD6 -0.04 0.18 -10000 0 -0.56 51 51
CTDSP2 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/FETUA -0.011 0.13 0.25 12 -0.37 42 54
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.15 0.11 0.24 283 -0.29 2 285
BMPR2 (homodimer) 0.022 0.004 -10000 0 -10000 0 0
GADD34/PP1CA 0.042 0.015 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.003 0.12 -10000 0 -0.42 36 36
CHRDL1 -0.27 0.29 -10000 0 -0.56 242 242
ENDOFIN/SMAD1 0.008 0.085 -10000 0 -0.53 4 4
SMAD6-7/SMURF1/SMAD1 -0.008 0.12 -10000 0 -0.46 8 8
SMAD6/SMURF1 0.022 0.006 -10000 0 -10000 0 0
BAMBI 0.021 0.043 0.31 2 -0.56 2 4
SMURF2 0.023 0.003 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.2 0.24 -10000 0 -0.4 256 256
BMP2-4/GREM1 0.051 0.19 0.25 1 -0.39 63 64
SMAD7 0.021 0.027 -10000 0 -0.56 1 1
SMAD8A/SMAD8A/SMAD4 -0.088 0.23 -10000 0 -0.51 97 97
SMAD1/SMAD6 0.006 0.086 -10000 0 -0.54 4 4
TAK1/SMAD6 0.032 0.009 -10000 0 -10000 0 0
BMP7 0.087 0.13 0.24 159 -0.49 8 167
BMP6 0.009 0.088 -10000 0 -0.56 11 11
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.026 0.12 -10000 0 -0.38 33 33
PPM1A 0.022 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.006 0.085 -10000 0 -0.5 4 4
SMAD7/SMURF1 0.03 0.023 -10000 0 -0.42 1 1
CTDSPL 0.021 0.007 -10000 0 -10000 0 0
PPP1CA 0.023 0.004 -10000 0 -10000 0 0
XIAP 0.023 0.003 -10000 0 -10000 0 0
CTDSP1 0.022 0.004 -10000 0 -10000 0 0
PPP1R15A 0.022 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.038 0.15 -10000 0 -0.44 38 38
CHRD 0.011 0.042 0.38 1 -0.56 2 3
BMPR2 0.022 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.039 0.13 0.2 1 -0.44 28 29
BMP4 0.012 0.08 0.24 1 -0.56 9 10
FST 0.049 0.092 0.24 70 -0.33 7 77
BMP2-4/NOG -0.025 0.16 -10000 0 -0.39 74 74
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.058 0.13 -10000 0 -0.32 35 35
Nongenotropic Androgen signaling

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
PTK2 -0.004 0.002 -10000 0 -10000 0 0
GNB1/GNG2 -0.038 0.15 -10000 0 -0.32 100 100
regulation of S phase of mitotic cell cycle -0.035 0.095 -10000 0 -0.27 50 50
GNAO1 0.021 0.031 0.24 2 -0.56 1 3
HRAS 0.022 0.004 -10000 0 -10000 0 0
SHBG/T-DHT 0.015 0.004 -10000 0 -10000 0 0
PELP1 0.021 0.006 -10000 0 -10000 0 0
AKT1 -0.004 0.003 -10000 0 -10000 0 0
MAP2K1 -0.073 0.12 -10000 0 -0.3 83 83
T-DHT/AR -0.073 0.17 -10000 0 -0.41 100 100
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 54 54
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
mol:GDP -0.081 0.16 -10000 0 -0.38 100 100
cell proliferation -0.099 0.17 -10000 0 -0.44 69 69
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
FOS -0.11 0.26 -10000 0 -0.79 58 58
mol:Ca2+ -0.01 0.024 -10000 0 -0.074 37 37
MAPK3 -0.091 0.15 -10000 0 -0.43 36 36
MAPK1 -0.044 0.099 -10000 0 -0.34 24 24
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 54 54
cAMP biosynthetic process 0.003 0.017 -10000 0 -10000 0 0
GNG2 0.016 0.06 -10000 0 -0.56 5 5
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 54 54
HRAS/GTP -0.037 0.14 -10000 0 -0.3 97 97
actin cytoskeleton reorganization 0.017 0.018 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 54 54
PI3K 0.015 0.016 -10000 0 -10000 0 0
apoptosis 0.077 0.16 0.44 64 -10000 0 64
T-DHT/AR/PELP1 -0.051 0.16 -10000 0 -0.36 98 98
HRAS/GDP -0.068 0.16 -10000 0 -0.37 99 99
CREB1 -0.083 0.17 -10000 0 -0.47 64 64
RAC1-CDC42/GTP 0.022 0.023 -10000 0 -10000 0 0
AR -0.099 0.24 -10000 0 -0.56 98 98
GNB1 0.021 0.027 -10000 0 -0.56 1 1
RAF1 -0.072 0.12 0.2 1 -0.3 94 95
RAC1-CDC42/GDP -0.026 0.17 -10000 0 -0.36 95 95
T-DHT/AR/PELP1/Src -0.04 0.15 -10000 0 -0.33 97 97
MAP2K2 -0.073 0.12 -10000 0 -0.29 88 88
T-DHT/AR/PELP1/Src/PI3K -0.036 0.095 -10000 0 -0.27 50 50
GNAZ 0.016 0.06 -10000 0 -0.56 5 5
SHBG 0.02 0.01 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.035 0.17 -10000 0 -0.6 28 28
mol:T-DHT 0 0.001 0.002 2 -0.002 35 37
RAC1 0.022 0.004 -10000 0 -10000 0 0
GNRH1 -0.005 0.019 -10000 0 -0.41 1 1
Gi family/GTP -0.033 0.092 -10000 0 -0.33 25 25
CDC42 0.022 0.005 -10000 0 -10000 0 0
PLK1 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
regulation of centriole-centriole cohesion -0.009 0.055 0.16 39 -10000 0 39
BUB1B 0.025 0.03 0.11 2 -0.21 3 5
PLK1 0.01 0.018 0.08 6 -0.086 1 7
PLK1S1 0.01 0.022 -10000 0 -0.18 4 4
KIF2A 0.007 0.019 0.22 2 -10000 0 2
regulation of mitotic centrosome separation 0.01 0.018 0.08 6 -0.086 1 7
GOLGA2 0.023 0.003 -10000 0 -10000 0 0
Hec1/SPC24 0.12 0.11 0.23 220 -0.28 1 221
WEE1 0.008 0.061 -10000 0 -0.34 12 12
cytokinesis 0.021 0.076 0.19 5 -0.27 19 24
PP2A-alpha B56 0.057 0.051 -10000 0 -0.5 2 2
AURKA 0.013 0.025 0.14 3 -0.19 3 6
PICH/PLK1 0.036 0.053 0.24 9 -0.22 1 10
CENPE 0.003 0.026 0.25 2 -0.19 1 3
RhoA/GTP 0.015 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.02 0.22 2 -10000 0 2
PPP2CA 0.021 0.006 -10000 0 -10000 0 0
FZR1 0.022 0.004 -10000 0 -10000 0 0
TPX2 0.057 0.042 0.16 36 -10000 0 36
PAK1 0.023 0.016 0.37 1 -10000 0 1
SPC24 0.087 0.1 0.24 142 -0.29 2 144
FBXW11 0.021 0.006 -10000 0 -10000 0 0
CLSPN 0.013 0.047 -10000 0 -0.22 14 14
GORASP1 0.021 0.007 -10000 0 -10000 0 0
metaphase 0 0.002 0.014 6 -0.012 2 8
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.004 0.01 0.043 7 -10000 0 7
G2 phase of mitotic cell cycle -0.001 0.002 0.011 8 -10000 0 8
STAG2 0.023 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.028 0.16 -10000 0 -0.53 41 41
spindle elongation 0.01 0.018 0.08 6 -0.086 1 7
ODF2 0.023 0.004 -10000 0 -10000 0 0
BUB1 0.036 0.056 -10000 0 -0.55 2 2
TPT1 -0.003 0.051 -10000 0 -0.19 33 33
CDC25C 0.045 0.1 0.2 2 -0.29 34 36
CDC25B 0.021 0.011 -10000 0 -10000 0 0
SGOL1 0.009 0.055 -10000 0 -0.16 39 39
RHOA 0.021 0.007 -10000 0 -10000 0 0
CCNB1/CDK1 0.04 0.055 -10000 0 -0.22 2 2
CDC14B -0.005 0.003 -10000 0 -10000 0 0
CDC20 0.16 0.11 0.24 302 -0.29 4 306
PLK1/PBIP1 0.004 0.012 -10000 0 -10000 0 0
mitosis -0.002 0.004 0.022 4 -0.018 15 19
FBXO5 0.007 0.021 0.14 3 -10000 0 3
CDC2 0.001 0.003 0.008 2 -0.011 7 9
NDC80 0.1 0.12 0.26 165 -0.29 1 166
metaphase plate congression 0.003 0.051 -10000 0 -0.23 21 21
ERCC6L 0.033 0.056 0.2 9 -0.26 1 10
NLP/gamma Tubulin 0.006 0.015 0.078 1 -0.099 2 3
microtubule cytoskeleton organization -0.003 0.051 -10000 0 -0.19 33 33
G2/M transition DNA damage checkpoint -0.001 0.002 0.011 3 -10000 0 3
PPP1R12A 0.023 0.002 -10000 0 -10000 0 0
interphase -0.001 0.002 0.011 3 -10000 0 3
PLK1/PRC1-2 0.11 0.1 0.2 233 -0.18 8 241
GRASP65/GM130/RAB1/GTP/PLK1 0.038 0.021 -10000 0 -10000 0 0
RAB1A 0.022 0.006 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.007 0.015 0.074 6 -10000 0 6
mitotic prometaphase 0 0.004 0.018 21 -10000 0 21
proteasomal ubiquitin-dependent protein catabolic process 0.01 0.1 -10000 0 -0.46 17 17
microtubule-based process 0.09 0.087 0.17 232 -0.17 12 244
Golgi organization 0.01 0.018 0.08 6 -0.086 1 7
Cohesin/SA2 0.023 0.015 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.033 0.006 -10000 0 -10000 0 0
KIF20A 0.12 0.13 0.24 233 -0.29 14 247
APC/C/CDC20 0.11 0.08 0.17 296 -0.16 4 300
PPP2R1A 0.022 0.004 -10000 0 -10000 0 0
chromosome segregation 0.004 0.012 -10000 0 -10000 0 0
PRC1 0.046 0.072 0.26 48 -10000 0 48
ECT2 0.1 0.11 0.22 215 -10000 0 215
C13orf34 0.008 0.015 0.07 6 -10000 0 6
NUDC 0.003 0.051 -10000 0 -0.23 21 21
regulation of attachment of spindle microtubules to kinetochore 0.024 0.03 0.11 2 -0.21 3 5
spindle assembly 0.008 0.017 0.083 6 -10000 0 6
spindle stabilization 0.01 0.022 -10000 0 -0.18 4 4
APC/C/HCDH1 0.019 0.004 -10000 0 -10000 0 0
MKLP2/PLK1 0.09 0.087 0.17 232 -0.17 12 244
CCNB1 0.046 0.074 0.24 54 -0.3 2 56
PPP1CB 0.023 0.004 -10000 0 -10000 0 0
BTRC 0.022 0.005 -10000 0 -10000 0 0
ROCK2 0.006 0.047 -10000 0 -0.28 3 3
TUBG1 0.008 0.025 -10000 0 -0.18 7 7
G2/M transition of mitotic cell cycle 0.006 0.029 -10000 0 -0.22 2 2
MLF1IP -0.006 0.011 -10000 0 -10000 0 0
INCENP 0.023 0.002 -10000 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.009 0.096 -10000 0 -0.4 24 24
alphaV beta3 Integrin 0.026 0.084 -10000 0 -0.37 19 19
PTK2 -0.17 0.19 0.39 2 -0.55 54 56
IGF1R 0.022 0.004 -10000 0 -10000 0 0
PI4KB 0.022 0.006 -10000 0 -10000 0 0
MFGE8 0.023 0.003 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
CDKN1B -0.18 0.25 -10000 0 -0.49 180 180
VEGFA 0.022 0.004 -10000 0 -10000 0 0
ILK -0.18 0.26 -10000 0 -0.5 182 182
ROCK1 0.023 0.003 -10000 0 -10000 0 0
AKT1 -0.17 0.23 -10000 0 -0.46 177 177
PTK2B -0.019 0.097 0.35 3 -0.35 25 28
alphaV/beta3 Integrin/JAM-A -0.097 0.18 -10000 0 -0.33 171 171
CBL 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.037 0.054 -10000 0 -0.36 8 8
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.045 0.065 -10000 0 -0.33 13 13
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.096 0.16 -10000 0 -0.43 51 51
alphaV/beta3 Integrin/Syndecan-1 0.036 0.056 -10000 0 -0.36 9 9
PI4KA 0.022 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.017 0.11 -10000 0 -0.36 35 35
PI4 Kinase 0.03 0.011 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.1 0.098 0.25 1 -0.37 8 9
RPS6KB1 -0.037 0.098 0.32 1 -0.49 10 11
TLN1 0.021 0.007 -10000 0 -10000 0 0
MAPK3 -0.084 0.17 -10000 0 -0.61 31 31
GPR124 0.019 0.009 -10000 0 -10000 0 0
MAPK1 -0.081 0.17 -10000 0 -0.61 31 31
PXN 0.023 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.21 0.2 -10000 0 -0.37 285 285
cell adhesion 0.026 0.051 -10000 0 -0.34 7 7
ANGPTL3 0.007 0.029 0.24 4 -10000 0 4
VEGFR2 homodimer/VEGFA homodimer/Src 0.023 0.084 -10000 0 -0.36 21 21
IGF-1R heterotetramer 0.022 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
TGFBR2 -0.011 0.13 -10000 0 -0.56 26 26
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
IGF1 0.005 0.1 0.24 1 -0.56 15 16
RAC1 0.022 0.004 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.032 0.049 -10000 0 -0.36 6 6
apoptosis 0.023 0.003 -10000 0 -10000 0 0
CD47 0.019 0.028 -10000 0 -0.56 1 1
alphaV/beta3 Integrin/CD47 0.033 0.053 -10000 0 -0.36 7 7
VCL 0.022 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.016 0.1 -10000 0 -0.38 28 28
CSF1 0.017 0.053 -10000 0 -0.56 4 4
PIK3C2A -0.18 0.25 -10000 0 -0.5 182 182
PI4 Kinase/Pyk2 -0.098 0.17 -10000 0 -0.52 25 25
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.029 0.1 -10000 0 -0.37 25 25
FAK1/Vinculin -0.13 0.16 0.36 2 -0.43 52 54
alphaV beta3/Integrin/ppsTEM5 0.032 0.049 -10000 0 -0.36 6 6
RHOA 0.021 0.007 -10000 0 -10000 0 0
VTN -0.2 0.28 0.24 2 -0.56 183 185
BCAR1 0.022 0.005 -10000 0 -10000 0 0
FGF2 0.006 0.095 -10000 0 -0.56 13 13
F11R -0.019 0.064 -10000 0 -0.42 12 12
alphaV/beta3 Integrin/Lactadherin 0.038 0.053 -10000 0 -0.36 8 8
alphaV/beta3 Integrin/TGFBR2 0.011 0.12 -10000 0 -0.41 29 29
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.05 0.037 -10000 0 -0.33 3 3
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.033 0.047 -10000 0 -0.33 7 7
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.01 0.084 -10000 0 -0.56 10 10
alphaV/beta3 Integrin/Pyk2 0.019 0.096 -10000 0 -0.35 25 25
SDC1 0.021 0.027 -10000 0 -0.56 1 1
VAV3 -0.013 0.04 -10000 0 -0.31 4 4
PTPN11 0.023 0.002 -10000 0 -10000 0 0
IRS1 0.022 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.14 0.16 0.32 3 -0.43 52 55
cell migration -0.12 0.14 0.29 4 -0.4 48 52
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PI3K -0.058 0.14 -10000 0 -0.32 79 79
SPP1 0.13 0.12 0.24 246 -0.29 6 252
KDR -0.008 0.13 -10000 0 -0.56 24 24
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.023 0.003 -10000 0 -10000 0 0
COL4A3 -0.34 0.28 -10000 0 -0.56 292 292
angiogenesis -0.11 0.19 -10000 0 -0.62 32 32
Rac1/GTP 0.019 0.037 -10000 0 -0.29 4 4
EDIL3 -0.006 0.12 -10000 0 -0.56 22 22
cell proliferation 0.011 0.12 -10000 0 -0.41 29 29
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.004 0.036 -10000 0 -0.43 1 1
NFATC2 -0.051 0.13 -10000 0 -0.38 62 62
NFATC3 -0.003 0.03 -10000 0 -10000 0 0
CD40LG -0.17 0.29 0.34 2 -0.64 110 112
PTGS2 -0.15 0.27 0.34 2 -0.61 96 98
JUNB 0.021 0.027 -10000 0 -0.56 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.003 0.024 -10000 0 -10000 0 0
CaM/Ca2+ 0.003 0.024 -10000 0 -10000 0 0
CALM1 0.011 0.022 -10000 0 -10000 0 0
JUN 0.011 0.023 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.012 -10000 0 -10000 0 0
FOSL1 0.024 0.014 0.24 2 -10000 0 2
CREM 0.022 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.056 0.17 -10000 0 -0.46 45 45
FOS -0.054 0.18 -10000 0 -0.57 53 53
IFNG -0.13 0.23 0.34 1 -0.54 83 84
AP-1/NFAT1-c-4 -0.14 0.28 -10000 0 -0.64 85 85
FASLG -0.13 0.25 0.34 2 -0.59 79 81
NFAT1-c-4/ICER1 -0.049 0.14 -10000 0 -0.36 61 61
IL2RA -0.13 0.23 0.34 1 -0.55 83 84
FKBP12/FK506 0.016 0.003 -10000 0 -10000 0 0
CSF2 -0.15 0.27 0.34 2 -0.59 105 107
JunB/Fra1/NFAT1-c-4 -0.041 0.14 -10000 0 -0.36 59 59
IL4 -0.13 0.23 0.33 2 -0.54 83 85
IL2 -0.027 0.2 -10000 0 -0.92 22 22
IL3 -0.045 0.19 -10000 0 -0.79 25 25
FKBP1A 0.022 0.005 -10000 0 -10000 0 0
BATF3 0.022 0.004 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.022 0.006 -10000 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B 0.016 0.063 -10000 0 -0.36 12 12
ARNO/beta Arrestin1-2 -0.11 0.22 -10000 0 -0.61 52 52
EGFR 0.022 0.084 0.37 11 -0.56 6 17
EPHA2 0.018 0.046 -10000 0 -0.56 3 3
USP6 0.022 0.006 -10000 0 -10000 0 0
IQSEC1 0.021 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.023 0.084 0.27 8 -0.44 12 20
ARRB2 0.007 0.004 -10000 0 -10000 0 0
mol:GTP 0.037 0.061 0.13 56 -0.17 9 65
ARRB1 -0.085 0.23 -10000 0 -0.56 88 88
FBXO8 0.021 0.006 -10000 0 -10000 0 0
TSHR 0.027 0.04 0.24 16 -10000 0 16
EGF 0.015 0.073 0.24 3 -0.56 7 10
somatostatin receptor activity 0 0 0.001 5 -0.001 91 96
ARAP2 0.02 0.027 -10000 0 -0.56 1 1
mol:GDP -0.091 0.16 0.2 1 -0.35 102 103
mol:PI-3-4-5-P3 0 0 0.001 4 -0.001 59 63
ITGA2B 0.005 0.099 -10000 0 -0.56 14 14
ARF6 0.022 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.039 -10000 0 -0.33 3 3
ADAP1 0.014 0.07 -10000 0 -0.56 7 7
KIF13B 0.015 0.06 -10000 0 -0.56 5 5
HGF/MET -0.056 0.18 0.27 1 -0.41 96 97
PXN 0.023 0.002 -10000 0 -10000 0 0
ARF6/GTP -0.084 0.14 0.24 5 -0.3 98 103
EGFR/EGFR/EGF/EGF/ARFGEP100 0.033 0.076 0.25 8 -0.38 12 20
ADRB2 -0.12 0.25 -10000 0 -0.56 115 115
receptor agonist activity 0 0 0 6 0 90 96
actin filament binding 0 0 0.001 1 -0.001 96 97
SRC 0.022 0.004 -10000 0 -10000 0 0
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
EFA6/PI-4-5-P2 0 0.001 0.001 9 -0.001 61 70
ARF6/GDP -0.019 0.17 0.24 10 -0.51 35 45
ARF6/GDP/GULP/ACAP1 -0.073 0.16 -10000 0 -0.38 69 69
alphaIIb/beta3 Integrin/paxillin/GIT1 0.039 0.082 -10000 0 -0.33 22 22
ACAP1 0.021 0.029 0.24 1 -0.56 1 2
ACAP2 0.014 0.011 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.018 0.2 1 -10000 0 1
EFNA1 0.022 0.005 -10000 0 -10000 0 0
HGF -0.093 0.23 -10000 0 -0.56 94 94
CYTH3 -0.004 0.003 -10000 0 -10000 0 0
CYTH2 -0.015 0.17 -10000 0 -1 14 14
NCK1 0.019 0.008 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 8 0 80 88
endosomal lumen acidification 0 0 0.001 22 -0.001 63 85
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.014 0.07 -10000 0 -0.56 7 7
GNAQ/ARNO -0.002 0.17 -10000 0 -0.95 14 14
mol:Phosphatidic acid 0 0 0 1 -10000 0 1
PIP3-E 0 0 0 4 0 10 14
MET 0.02 0.041 0.38 1 -0.56 2 3
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
GNA15 0.022 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 8 -0.001 73 81
GNA11 0.022 0.004 -10000 0 -10000 0 0
LHCGR -0.005 0.021 0.24 1 -10000 0 1
AGTR1 -0.14 0.25 -10000 0 -0.56 126 126
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.018 0.2 1 -10000 0 1
IPCEF1/ARNO 0.005 0.16 -10000 0 -0.86 15 15
alphaIIb/beta3 Integrin 0.013 0.094 -10000 0 -0.42 22 22
IL6-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
BCL2L1 -0.15 0.23 -10000 0 -0.63 24 24
CRP -0.15 0.23 -10000 0 -0.6 36 36
cell cycle arrest -0.18 0.26 -10000 0 -0.64 51 51
TIMP1 -0.12 0.21 -10000 0 -0.61 17 17
IL6ST -0.009 0.098 -10000 0 -0.56 14 14
Rac1/GDP -0.069 0.16 -10000 0 -0.42 51 51
AP1 0.039 0.15 -10000 0 -0.49 7 7
GAB2 0.015 0.092 -10000 0 -0.56 12 12
TNFSF11 -0.16 0.23 -10000 0 -0.58 41 41
HSP90B1 -0.002 0.089 -10000 0 -0.75 5 5
GAB1 0.026 0.01 -10000 0 -10000 0 0
MAPK14 -0.046 0.14 -10000 0 -0.57 17 17
AKT1 0.04 0.07 0.29 6 -0.35 3 9
FOXO1 0.039 0.068 0.28 6 -0.34 3 9
MAP2K6 -0.058 0.14 -10000 0 -0.4 47 47
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
MAP2K4 -0.092 0.17 -10000 0 -0.45 52 52
MITF -0.067 0.15 -10000 0 -0.4 57 57
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.022 0.004 -10000 0 -10000 0 0
A2M -0.43 0.65 -10000 0 -1.4 157 157
CEBPB 0.026 0.004 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.028 0.12 0.26 4 -0.44 13 17
STAT3 -0.19 0.27 -10000 0 -0.69 46 46
STAT1 -0.005 0.1 -10000 0 -0.88 6 6
CEBPD -0.16 0.24 -10000 0 -0.73 16 16
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
PI3K 0.017 0.018 -10000 0 -10000 0 0
JUN 0.022 0.004 -10000 0 -10000 0 0
PIAS3/MITF -0.061 0.15 -10000 0 -0.39 54 54
MAPK11 -0.045 0.14 -10000 0 -0.58 17 17
STAT3 (dimer)/FOXO1 -0.2 0.3 0.4 1 -0.62 113 114
GRB2/SOS1/GAB family 0.003 0.16 -10000 0 -0.48 20 20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.051 0.16 -10000 0 -0.38 62 62
GRB2 0.027 0.008 -10000 0 -10000 0 0
JAK2 0.02 0.007 -10000 0 -10000 0 0
LBP -0.095 0.19 -10000 0 -0.62 9 9
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
JAK1 0.014 0.019 -10000 0 -10000 0 0
MYC -0.14 0.24 -10000 0 -0.6 29 29
FGG -0.47 0.54 -10000 0 -1 224 224
macrophage differentiation -0.18 0.26 -10000 0 -0.64 51 51
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.034 0.16 -10000 0 -0.36 73 73
JUNB -0.15 0.23 -10000 0 -0.59 36 36
FOS -0.043 0.18 -10000 0 -0.56 53 53
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.066 0.16 -10000 0 -0.41 59 59
STAT1/PIAS1 -0.07 0.16 -10000 0 -0.4 56 56
GRB2/SOS1/GAB family/SHP2/PI3K 0.039 0.069 -10000 0 -0.35 5 5
STAT3 (dimer) -0.18 0.27 -10000 0 -0.68 47 47
PRKCD -0.11 0.2 0.35 3 -0.5 47 50
IL6R 0.001 0.088 -10000 0 -0.56 11 11
SOCS3 -0.032 0.15 0.64 1 -0.76 9 10
gp130 (dimer)/JAK1/JAK1/LMO4 0.013 0.077 -10000 0 -0.35 14 14
Rac1/GTP -0.078 0.17 -10000 0 -0.44 52 52
HCK 0.018 0.053 -10000 0 -0.56 4 4
MAPKKK cascade 0.048 0.13 -10000 0 -0.51 10 10
bone resorption -0.15 0.22 -10000 0 -0.56 41 41
IRF1 -0.16 0.23 -10000 0 -0.58 42 42
mol:GDP -0.071 0.15 -10000 0 -0.42 51 51
SOS1 0.03 0.011 -10000 0 -10000 0 0
VAV1 -0.071 0.16 -10000 0 -0.43 51 51
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.035 0.16 -10000 0 -0.6 24 24
PTPN11 0.008 0.055 -10000 0 -0.77 2 2
IL6/IL6RA -0.056 0.18 -10000 0 -0.43 80 80
gp130 (dimer)/TYK2/TYK2/LMO4 0.017 0.073 -10000 0 -0.35 14 14
gp130 (dimer)/JAK2/JAK2/LMO4 0.016 0.072 -10000 0 -0.35 14 14
IL6 -0.083 0.21 -10000 0 -0.56 76 76
PIAS3 0.022 0.004 -10000 0 -10000 0 0
PTPRE 0.02 0.042 -10000 0 -0.56 2 2
PIAS1 0.023 0.003 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.058 0.15 -10000 0 -0.35 78 78
LMO4 0.009 0.026 0.22 1 -10000 0 1
STAT3 (dimer)/PIAS3 -0.17 0.26 -10000 0 -0.66 47 47
MCL1 0.05 0.08 0.4 4 -10000 0 4
Reelin signaling pathway

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
CDK5R1/CDK5 0.036 0.022 0.18 9 -10000 0 9
VLDLR 0.019 0.028 -10000 0 -0.56 1 1
CRKL 0.022 0.006 -10000 0 -10000 0 0
LRPAP1 0.021 0.006 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.56 1 1
ITGA3 0.016 0.06 -10000 0 -0.56 5 5
RELN/VLDLR/Fyn -0.024 0.15 -10000 0 -0.35 78 78
MAPK8IP1/MKK7/MAP3K11/JNK1 0.059 0.03 -10000 0 -0.31 1 1
AKT1 -0.024 0.081 0.19 1 -0.26 36 37
MAP2K7 0.022 0.005 -10000 0 -10000 0 0
RAPGEF1 0.023 0.004 -10000 0 -10000 0 0
DAB1 0.028 0.06 0.25 30 -10000 0 30
RELN/LRP8/DAB1 -0.012 0.14 0.3 1 -0.33 77 78
LRPAP1/LRP8 0.032 0.014 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.002 0.14 0.3 1 -0.31 76 77
DAB1/alpha3/beta1 Integrin -0.01 0.13 -10000 0 -0.29 71 71
long-term memory -0.013 0.16 0.31 2 -0.33 85 87
DAB1/LIS1 0.002 0.13 0.28 1 -0.3 73 74
DAB1/CRLK/C3G -0.005 0.12 -10000 0 -0.29 63 63
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
DAB1/NCK2 0.003 0.14 0.28 1 -0.3 74 75
ARHGEF2 0.022 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.004 0.13 0.24 23 -0.56 22 45
CDK5R1 0.027 0.029 0.24 9 -10000 0 9
RELN -0.071 0.22 0.24 3 -0.56 77 80
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.021 0.15 -10000 0 -0.36 77 77
GRIN2A/RELN/LRP8/DAB1/Fyn -0.003 0.17 0.31 2 -0.34 89 91
MAPK8 0.022 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.015 0.14 0.34 2 -0.32 75 77
ITGB1 0.022 0.004 -10000 0 -10000 0 0
MAP1B -0.049 0.12 0.28 2 -0.31 75 77
RELN/LRP8 -0.022 0.15 -10000 0 -0.35 77 77
GRIN2B/RELN/LRP8/DAB1/Fyn 0.007 0.14 0.31 2 -0.32 71 73
PI3K 0.017 0.017 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.043 -10000 0 -0.37 5 5
RAP1A -0.04 0.12 0.33 8 -0.29 46 54
PAFAH1B1 0.022 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.022 0.029 0.24 1 -0.56 1 2
CRLK/C3G 0.032 0.009 -10000 0 -10000 0 0
GRIN2B 0 0.029 0.24 4 -10000 0 4
NCK2 0.023 0.002 -10000 0 -10000 0 0
neuron differentiation -0.012 0.093 0.19 2 -0.37 10 12
neuron adhesion -0.041 0.12 0.32 10 -0.33 1 11
LRP8 0.024 0.018 0.24 3 -10000 0 3
GSK3B -0.022 0.072 -10000 0 -0.28 17 17
RELN/VLDLR/DAB1/Fyn -0.006 0.14 0.33 2 -0.31 74 76
MAP3K11 0.023 0.001 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.022 0.09 -10000 0 -0.28 38 38
CDK5 0.022 0.004 -10000 0 -10000 0 0
MAPT 0.001 0.1 0.74 6 -0.52 6 12
neuron migration -0.015 0.13 0.25 5 -0.34 32 37
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.012 0.094 0.19 2 -0.37 10 12
RELN/VLDLR -0.011 0.14 -10000 0 -0.32 75 75
Canonical Wnt signaling pathway

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
HDAC1 0.023 0.016 -10000 0 -10000 0 0
AES 0.023 0.013 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.031 0.011 -10000 0 -10000 0 0
SMAD4 0.022 0.005 -10000 0 -10000 0 0
DKK2 -0.076 0.22 -10000 0 -0.56 80 80
TLE1 0.022 0.012 -10000 0 -10000 0 0
MACF1 0.02 0.038 -10000 0 -0.56 2 2
CTNNB1 0.089 0.13 0.29 35 -0.39 6 41
WIF1 -0.34 0.28 0.24 1 -0.56 295 296
beta catenin/RanBP3 0.008 0.1 0.42 17 -0.44 1 18
KREMEN2 0.16 0.12 0.24 305 -0.29 6 311
DKK1 0.021 0.094 0.25 21 -0.56 9 30
beta catenin/beta TrCP1 0.097 0.12 0.29 31 -0.36 5 36
FZD1 0.022 0.006 -10000 0 -10000 0 0
AXIN2 -0.037 0.28 0.56 9 -1.4 17 26
AXIN1 0.023 0.005 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.026 0.11 -10000 0 -0.57 11 11
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.055 0.13 -10000 0 -0.56 13 13
Axin1/APC/GSK3 0.055 0.077 0.27 7 -0.34 2 9
Axin1/APC/GSK3/beta catenin/Macf1 0.048 0.1 0.3 8 -0.44 2 10
HNF1A 0.027 0.031 0.24 8 -10000 0 8
CTBP1 0.021 0.014 -10000 0 -10000 0 0
MYC 0.057 0.18 0.57 49 -10000 0 49
RANBP3 0.022 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.029 0.2 -10000 0 -0.39 75 75
NKD1 -0.023 0.16 0.24 4 -0.56 38 42
TCF4 0.021 0.03 -10000 0 -0.56 1 1
TCF3 0.023 0.013 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.053 0.024 -10000 0 -10000 0 0
Ran/GTP 0.017 0.002 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.004 0.11 0.39 17 -0.4 14 31
LEF1 0.023 0.017 0.24 1 -10000 0 1
DVL1 0.054 0.08 -10000 0 -0.52 4 4
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.051 0.16 -10000 0 -0.63 14 14
DKK1/LRP6/Kremen 2 0.12 0.11 0.32 15 -0.39 9 24
LRP6 0.022 0.006 -10000 0 -10000 0 0
CSNK1A1 0.022 0.015 -10000 0 -10000 0 0
NLK 0.021 0.009 -10000 0 -10000 0 0
CCND1 0.062 0.26 0.57 66 -1.4 6 72
WNT1 0.022 0.017 0.24 2 -10000 0 2
GSK3A 0.023 0.005 -10000 0 -10000 0 0
GSK3B 0.02 0.008 -10000 0 -10000 0 0
FRAT1 0.02 0.027 -10000 0 -0.56 1 1
PPP2R5D 0.067 0.087 0.32 37 -0.37 1 38
APC 0.019 0.063 0.35 5 -10000 0 5
WNT1/LRP6/FZD1 0.14 0.12 0.23 270 -10000 0 270
CREBBP 0.022 0.013 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.026 0.058 -10000 0 -0.42 8 8
AKT1 -0.006 0.18 0.37 9 -0.55 30 39
PTK2B -0.062 0.19 0.39 4 -0.69 25 29
VEGFR2 homodimer/Frs2 -0.059 0.2 -10000 0 -0.47 78 78
CAV1 -0.13 0.26 -10000 0 -0.56 125 125
CALM1 0.022 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.043 0.19 -10000 0 -0.44 76 76
endothelial cell proliferation -0.011 0.19 0.39 13 -0.53 31 44
mol:Ca2+ -0.043 0.18 0.36 3 -0.67 22 25
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.03 0.19 -10000 0 -0.43 67 67
RP11-342D11.1 -0.059 0.17 -10000 0 -0.68 22 22
CDH5 -0.086 0.23 -10000 0 -0.56 88 88
VEGFA homodimer 0.051 0.022 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
SHC2 0.02 0.038 -10000 0 -0.56 2 2
HRAS/GDP -0.027 0.15 -10000 0 -0.57 22 22
SH2D2A 0.021 0.027 -10000 0 -0.56 1 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.024 0.18 -10000 0 -0.56 31 31
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.041 0.19 -10000 0 -0.43 75 75
VEGFR1 homodimer 0.022 0.006 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.015 0.17 -10000 0 -0.63 22 22
GRB10 -0.043 0.18 0.36 2 -0.67 22 24
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
PAK1 0.023 0.017 0.38 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.077 0.25 -10000 0 -0.68 50 50
HRAS 0.022 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.037 0.13 -10000 0 -0.42 33 33
HIF1A 0.022 0.004 -10000 0 -10000 0 0
FRS2 0.022 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.03 0.18 -10000 0 -0.43 67 67
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 -0.005 0.12 -10000 0 -0.56 21 21
Nck/Pak 0.028 0.013 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.043 0.19 -10000 0 -0.44 78 78
mol:GDP -0.022 0.16 -10000 0 -0.6 22 22
mol:NADP -0.016 0.17 0.39 7 -0.49 32 39
eNOS/Hsp90 -0.008 0.16 0.39 6 -0.46 32 38
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:IP3 -0.043 0.18 0.36 3 -0.68 22 25
HIF1A/ARNT 0.031 0.01 -10000 0 -10000 0 0
SHB 0.021 0.007 -10000 0 -10000 0 0
VEGFA 0.023 0.004 -10000 0 -10000 0 0
VEGFC 0.019 0.038 -10000 0 -0.56 2 2
FAK1/Vinculin -0.042 0.21 0.38 5 -0.65 35 40
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.036 0.2 -10000 0 -0.45 73 73
PTPN6 0.021 0.006 -10000 0 -10000 0 0
EPAS1 -0.078 0.23 -10000 0 -0.56 85 85
mol:L-citrulline -0.016 0.17 0.39 7 -0.49 32 39
ITGAV 0.023 0.003 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.03 0.18 -10000 0 -0.43 67 67
VEGFR2 homodimer/VEGFA homodimer -0.041 0.19 -10000 0 -0.45 69 69
VEGFR2/3 heterodimer -0.074 0.22 -10000 0 -0.48 90 90
VEGFB 0.023 0.002 -10000 0 -10000 0 0
MAPK11 -0.046 0.18 0.4 4 -0.6 29 33
VEGFR2 homodimer -0.076 0.22 -10000 0 -0.53 78 78
FLT1 0.022 0.006 -10000 0 -10000 0 0
NEDD4 0.024 0.003 -10000 0 -10000 0 0
MAPK3 -0.05 0.18 0.42 7 -0.62 25 32
MAPK1 -0.049 0.18 0.42 7 -0.62 25 32
VEGFA145/NRP2 0.031 0.032 -10000 0 -0.4 2 2
VEGFR1/2 heterodimer -0.06 0.2 -10000 0 -0.46 79 79
KDR -0.076 0.22 -10000 0 -0.54 78 78
VEGFA165/NRP1/VEGFR2 homodimer -0.037 0.18 -10000 0 -0.71 22 22
SRC 0.022 0.004 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.047 0.18 0.44 7 -0.63 25 32
PI3K -0.037 0.16 -10000 0 -0.63 22 22
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.039 0.18 -10000 0 -0.44 67 67
FES -0.047 0.19 0.36 1 -0.71 22 23
GAB1 -0.047 0.18 -10000 0 -0.65 26 26
VEGFR2 homodimer/VEGFA homodimer/Src -0.042 0.19 -10000 0 -0.43 77 77
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
SOS1 0.023 0.004 -10000 0 -10000 0 0
ARNT 0.022 0.006 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.071 0.2 0.34 3 -0.48 57 60
VEGFR2 homodimer/VEGFA homodimer/Yes -0.043 0.19 -10000 0 -0.44 74 74
PI3K/GAB1 -0.008 0.17 -10000 0 -0.55 25 25
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.02 0.17 -10000 0 -0.63 21 21
PRKACA 0.022 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.06 0.21 -10000 0 -0.46 84 84
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
CDC42 -0.045 0.18 0.36 3 -0.69 22 25
actin cytoskeleton reorganization -0.041 0.18 -10000 0 -0.43 75 75
PTK2 -0.06 0.22 0.35 4 -0.65 41 45
EDG1 -0.059 0.17 -10000 0 -0.68 22 22
mol:DAG -0.043 0.18 0.36 3 -0.68 22 25
CaM/Ca2+ -0.033 0.17 -10000 0 -0.63 22 22
MAP2K3 -0.048 0.14 -10000 0 -0.57 22 22
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.036 0.18 -10000 0 -0.7 22 22
PLCG1 -0.045 0.18 0.36 3 -0.69 22 25
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.031 0.18 -10000 0 -0.43 65 65
IQGAP1 0.023 0.003 -10000 0 -10000 0 0
YES1 0.022 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.043 0.19 -10000 0 -0.44 77 77
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.042 0.19 -10000 0 -0.44 73 73
cell migration -0.056 0.21 0.42 5 -0.59 41 46
mol:PI-3-4-5-P3 -0.034 0.15 -10000 0 -0.58 22 22
FYN 0.022 0.027 -10000 0 -0.56 1 1
VEGFB/NRP1 -0.039 0.17 -10000 0 -0.64 22 22
mol:NO -0.016 0.17 0.39 7 -0.49 32 39
PXN 0.023 0.002 -10000 0 -10000 0 0
HRAS/GTP -0.039 0.15 -10000 0 -0.57 22 22
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.044 0.18 -10000 0 -0.7 22 22
VHL 0.021 0.007 -10000 0 -10000 0 0
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
NOS3 -0.022 0.19 0.4 7 -0.57 32 39
VEGFR2 homodimer/VEGFA homodimer/Sck -0.044 0.19 -10000 0 -0.44 77 77
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA -0.055 0.17 0.35 3 -0.64 23 26
PRKCB -0.068 0.19 0.39 4 -0.66 26 30
VCL 0.022 0.005 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.039 0.18 -10000 0 -0.41 69 69
VEGFR1/2 heterodimer/VEGFA homodimer -0.044 0.19 -10000 0 -0.44 74 74
VEGFA165/NRP2 0.031 0.032 -10000 0 -0.4 2 2
MAPKKK cascade -0.037 0.15 -10000 0 -0.57 22 22
NRP2 0.02 0.038 -10000 0 -0.56 2 2
VEGFC homodimer 0.019 0.038 -10000 0 -0.56 2 2
NCK1 0.019 0.008 -10000 0 -10000 0 0
ROCK1 0.023 0.003 -10000 0 -10000 0 0
FAK1/Paxillin -0.042 0.22 0.41 6 -0.64 36 42
MAP3K13 -0.039 0.15 -10000 0 -0.6 22 22
PDPK1 -0.036 0.13 -10000 0 -0.52 22 22
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.028 0.038 0.28 10 -9999 0 10
GPC2 0.059 0.089 0.26 72 -9999 0 72
GPC2/Midkine 0.059 0.065 0.28 14 -9999 0 14
neuron projection morphogenesis 0.058 0.065 0.28 14 -9999 0 14
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.031 0.064 -10000 0 -0.38 11 11
HDAC1 0.021 0.005 -10000 0 -10000 0 0
AES 0.022 0.004 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
DTX1 0.024 0.014 0.24 2 -10000 0 2
LRP6/FZD1 0.03 0.011 -10000 0 -10000 0 0
TLE1 0.022 0.004 -10000 0 -10000 0 0
AP1 -0.052 0.15 -10000 0 -0.35 82 82
NCSTN 0.022 0.005 -10000 0 -10000 0 0
ADAM10 0.023 0.003 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.008 0.17 -10000 0 -0.76 21 21
NICD/RBPSUH 0.027 0.063 -10000 0 -0.37 11 11
WIF1 -0.34 0.28 0.24 1 -0.56 295 296
NOTCH1 0.012 0.057 -10000 0 -0.39 9 9
PSENEN 0.021 0.007 -10000 0 -10000 0 0
KREMEN2 0.16 0.12 0.24 305 -0.29 6 311
DKK1 0.021 0.094 0.25 21 -0.56 9 30
beta catenin/beta TrCP1 -0.002 0.11 0.27 1 -0.41 13 14
APH1B 0.023 0.003 -10000 0 -10000 0 0
APH1A 0.022 0.006 -10000 0 -10000 0 0
AXIN1 -0.001 0.079 0.27 1 -0.52 7 8
CtBP/CBP/TCF1/TLE1/AES 0.009 0.036 -10000 0 -10000 0 0
PSEN1 0.022 0.005 -10000 0 -10000 0 0
FOS -0.043 0.18 -10000 0 -0.56 53 53
JUN 0.022 0.004 -10000 0 -10000 0 0
MAP3K7 0.022 0.003 -10000 0 -10000 0 0
CTNNB1 -0.01 0.11 0.26 2 -0.43 14 16
MAPK3 0.023 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.029 0.2 -10000 0 -0.39 75 75
HNF1A 0.026 0.028 0.24 8 -10000 0 8
CTBP1 0.021 0.007 -10000 0 -10000 0 0
MYC 0.021 0.019 -10000 0 -10000 0 0
NKD1 -0.023 0.16 0.24 4 -0.56 38 42
FZD1 0.022 0.006 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.03 0.065 -10000 0 -0.38 11 11
apoptosis -0.052 0.15 -10000 0 -0.34 82 82
Delta 1/NOTCHprecursor 0.029 0.064 -10000 0 -0.38 11 11
DLL1 0.023 0.004 -10000 0 -10000 0 0
PPARD 0.006 0.14 -10000 0 -0.95 9 9
Gamma Secretase 0.055 0.028 -10000 0 -10000 0 0
APC -0.018 0.11 0.27 1 -0.44 23 24
DVL1 -0.045 0.091 -10000 0 -0.36 27 27
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.12 0.11 0.32 15 -0.39 9 24
LRP6 0.022 0.006 -10000 0 -10000 0 0
CSNK1A1 0.022 0.006 -10000 0 -10000 0 0
NLK 0.009 0.004 -10000 0 -10000 0 0
CCND1 0.003 0.15 -10000 0 -1.4 6 6
WNT1 0.018 0.02 0.24 2 -10000 0 2
Axin1/APC/beta catenin -0.016 0.14 0.28 4 -0.46 26 30
DKK2 -0.076 0.22 -10000 0 -0.56 80 80
NOTCH1 precursor/DVL1 -0.028 0.11 -10000 0 -0.52 15 15
GSK3B 0.02 0.007 -10000 0 -10000 0 0
FRAT1 0.02 0.027 -10000 0 -0.56 1 1
NOTCH/Deltex homolog 1 0.032 0.065 -10000 0 -0.38 11 11
PPP2R5D 0.013 0.097 0.28 37 -0.44 6 43
MAPK1 0.022 0.006 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.18 0.18 -10000 0 -0.33 270 270
RBPJ 0.021 0.006 -10000 0 -10000 0 0
CREBBP 0.023 0.006 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.031 0.035 0.25 12 -10000 0 12
NFATC2 -0.047 0.24 -10000 0 -0.6 64 64
NFATC3 0.013 0.063 -10000 0 -0.27 8 8
CD40LG -0.18 0.36 -10000 0 -0.93 65 65
ITCH -0.02 0.099 -10000 0 -10000 0 0
CBLB -0.019 0.096 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.1 0.28 -10000 0 -0.82 45 45
JUNB 0.021 0.027 -10000 0 -0.56 1 1
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.023 0.12 -10000 0 -0.3 75 75
T cell anergy -0.052 0.16 0.25 2 -0.41 70 72
TLE4 -0.036 0.18 -10000 0 -0.6 24 24
Jun/NFAT1-c-4/p21SNFT -0.052 0.27 -10000 0 -0.94 24 24
AP-1/NFAT1-c-4 -0.13 0.38 -10000 0 -1.1 36 36
IKZF1 -0.039 0.2 -10000 0 -0.74 24 24
T-helper 2 cell differentiation -0.076 0.26 -10000 0 -0.76 42 42
AP-1/NFAT1 -0.071 0.22 -10000 0 -0.49 61 61
CALM1 -0.004 0.076 -10000 0 -10000 0 0
EGR2 -0.064 0.28 -10000 0 -1 24 24
EGR3 -0.066 0.28 -10000 0 -1.1 22 22
NFAT1/FOXP3 -0.011 0.18 -10000 0 -0.5 38 38
EGR1 0.012 0.071 -10000 0 -0.56 7 7
JUN 0.004 0.034 -10000 0 -10000 0 0
EGR4 0.027 0.039 0.26 11 -10000 0 11
mol:Ca2+ -0.023 0.067 -10000 0 -0.27 2 2
GBP3 -0.051 0.22 -10000 0 -0.7 34 34
FOSL1 0.024 0.014 0.24 2 -10000 0 2
NFAT1-c-4/MAF/IRF4 -0.036 0.26 -10000 0 -0.94 23 23
DGKA -0.034 0.17 -10000 0 -0.58 23 23
CREM 0.022 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.081 0.28 -10000 0 -0.9 29 29
CTLA4 -0.025 0.15 -10000 0 -0.54 20 20
NFAT1-c-4 (dimer)/EGR1 -0.047 0.27 -10000 0 -1 22 22
NFAT1-c-4 (dimer)/EGR4 -0.04 0.26 -10000 0 -0.92 24 24
FOS -0.06 0.18 -10000 0 -0.57 53 53
IFNG -0.12 0.32 -10000 0 -0.94 48 48
T cell activation -0.068 0.19 -10000 0 -0.73 16 16
MAF 0.022 0.005 -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 0.032 0.16 0.72 15 -10000 0 15
TNF -0.065 0.25 -10000 0 -0.88 28 28
FASLG -0.13 0.42 -10000 0 -1.4 37 37
TBX21 -0.035 0.18 -10000 0 -0.56 48 48
BATF3 0.022 0.004 -10000 0 -10000 0 0
PRKCQ -0.028 0.16 -10000 0 -0.57 40 40
PTPN1 -0.034 0.17 -10000 0 -0.6 21 21
NFAT1-c-4/ICER1 -0.044 0.25 -10000 0 -0.92 23 23
GATA3 0.008 0.097 0.24 3 -0.56 13 16
T-helper 1 cell differentiation -0.11 0.31 -10000 0 -0.91 48 48
IL2RA -0.097 0.28 -10000 0 -0.79 49 49
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.032 0.17 -10000 0 -0.57 23 23
E2F1 0.025 0.005 -10000 0 -10000 0 0
PPARG -0.041 0.18 -10000 0 -0.56 51 51
SLC3A2 -0.034 0.17 -10000 0 -0.6 20 20
IRF4 0.015 0.065 -10000 0 -0.56 6 6
PTGS2 -0.16 0.34 -10000 0 -0.89 57 57
CSF2 -0.16 0.34 -10000 0 -0.92 50 50
JunB/Fra1/NFAT1-c-4 -0.034 0.25 -10000 0 -0.91 22 22
IL4 -0.079 0.27 -10000 0 -0.8 42 42
IL5 -0.14 0.3 -10000 0 -0.93 35 35
IL2 -0.069 0.2 -10000 0 -0.76 15 15
IL3 -0.043 0.17 -10000 0 -0.81 17 17
RNF128 -0.085 0.24 -10000 0 -0.64 77 77
NFATC1 -0.032 0.16 -10000 0 -0.72 15 15
CDK4 0.04 0.14 0.61 8 -10000 0 8
PTPRK -0.033 0.17 -10000 0 -0.6 20 20
IL8 -0.14 0.31 -10000 0 -0.94 35 35
POU2F1 0.022 0.006 -10000 0 -10000 0 0
IL23-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
CCL2 -0.1 0.42 -10000 0 -1.1 46 46
IL23A -0.081 0.39 -10000 0 -1.2 27 27
NF kappa B1 p50/RelA/I kappa B alpha -0.072 0.4 -10000 0 -1.1 39 39
positive regulation of T cell mediated cytotoxicity -0.1 0.45 -10000 0 -1.2 48 48
ITGA3 -0.093 0.4 -10000 0 -1.1 43 43
IL17F -0.002 0.28 -10000 0 -0.7 33 33
IL12B 0.02 0.04 -10000 0 -10000 0 0
STAT1 (dimer) -0.099 0.43 -10000 0 -1.1 46 46
CD4 -0.09 0.42 -10000 0 -1.2 42 42
IL23 -0.073 0.38 -10000 0 -1.2 27 27
IL23R -0.003 0.17 -10000 0 -0.88 14 14
IL1B -0.091 0.41 -10000 0 -1.2 36 36
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.084 0.38 -10000 0 -1.1 36 36
TYK2 0.016 0.034 -10000 0 -10000 0 0
STAT4 0.013 0.075 -10000 0 -0.56 8 8
STAT3 0.023 0.004 -10000 0 -10000 0 0
IL18RAP -0.004 0.12 -10000 0 -0.56 22 22
IL12RB1 -0.017 0.14 -10000 0 -0.59 28 28
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.002 0.12 -10000 0 -0.44 28 28
IL23R/JAK2 0.013 0.17 -10000 0 -0.84 11 11
positive regulation of chronic inflammatory response -0.1 0.45 -10000 0 -1.2 48 48
natural killer cell activation 0 0.006 -10000 0 -10000 0 0
JAK2 0.02 0.04 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
NFKB1 0.021 0.011 -10000 0 -10000 0 0
RELA 0.022 0.011 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.067 0.36 -10000 0 -1.1 28 28
ALOX12B -0.082 0.38 -10000 0 -1.1 37 37
CXCL1 -0.11 0.44 -10000 0 -1.2 48 48
T cell proliferation -0.1 0.45 -10000 0 -1.2 48 48
NFKBIA 0.021 0.011 -10000 0 -10000 0 0
IL17A 0.007 0.23 -10000 0 -0.56 25 25
PI3K -0.098 0.38 -10000 0 -1.1 37 37
IFNG -0.001 0.035 0.1 3 -0.12 21 24
STAT3 (dimer) -0.09 0.36 -10000 0 -1.1 35 35
IL18R1 0.017 0.059 -10000 0 -0.56 5 5
IL23/IL23R/JAK2/TYK2/SOCS3 -0.061 0.31 -10000 0 -0.87 39 39
IL18/IL18R 0.023 0.11 -10000 0 -0.42 24 24
macrophage activation -0.004 0.018 0.033 1 -0.045 24 25
TNF -0.096 0.42 -10000 0 -1.3 33 33
STAT3/STAT4 -0.091 0.42 -10000 0 -1.1 45 45
STAT4 (dimer) -0.1 0.43 -10000 0 -1.2 46 46
IL18 0.019 0.046 -10000 0 -0.56 3 3
IL19 -0.085 0.38 -10000 0 -1.1 37 37
STAT5A (dimer) -0.1 0.43 -10000 0 -1.1 47 47
STAT1 0.022 0.004 -10000 0 -10000 0 0
SOCS3 0.02 0.038 -10000 0 -0.56 2 2
CXCL9 -0.1 0.42 -10000 0 -1.2 44 44
MPO -0.11 0.44 -10000 0 -1.2 52 52
positive regulation of humoral immune response -0.1 0.45 -10000 0 -1.2 48 48
IL23/IL23R/JAK2/TYK2 -0.12 0.51 -10000 0 -1.3 46 46
IL6 -0.2 0.56 -10000 0 -1.2 94 94
STAT5A 0.023 0.004 -10000 0 -10000 0 0
IL2 0.008 0.022 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0.006 -10000 0 -10000 0 0
CD3E -0.096 0.4 -10000 0 -1.1 41 41
keratinocyte proliferation -0.1 0.45 -10000 0 -1.2 48 48
NOS2 -0.12 0.46 -10000 0 -1.2 59 59
Coregulation of Androgen receptor activity

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
NRIP1 0.022 0.006 -10000 0 -10000 0 0
SVIL 0.022 0.004 -10000 0 -10000 0 0
ZNF318 0.022 0.005 -10000 0 -10000 0 0
JMJD2C 0.006 0.012 0.049 4 -10000 0 4
T-DHT/AR/Ubc9 -0.08 0.16 -10000 0 -0.38 98 98
CARM1 0.022 0.005 -10000 0 -10000 0 0
PRDX1 0.022 0.004 -10000 0 -10000 0 0
PELP1 0.022 0.006 -10000 0 -10000 0 0
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.022 0.005 -10000 0 -10000 0 0
PTK2B 0.021 0.007 -10000 0 -10000 0 0
MED1 0.022 0.004 -10000 0 -10000 0 0
MAK -0.017 0.15 -10000 0 -0.56 32 32
response to oxidative stress 0 0 -10000 0 -10000 0 0
HIP1 0.023 0.004 -10000 0 -10000 0 0
GSN 0.023 0.003 -10000 0 -10000 0 0
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
NCOA6 0.022 0.004 -10000 0 -10000 0 0
DNA-PK 0.043 0.013 -10000 0 -10000 0 0
NCOA4 0.022 0.005 -10000 0 -10000 0 0
PIAS3 0.022 0.004 -10000 0 -10000 0 0
cell proliferation -0.075 0.22 -10000 0 -0.78 40 40
XRCC5 0.022 0.004 -10000 0 -10000 0 0
UBE3A 0.023 0.004 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.09 0.18 -10000 0 -0.4 107 107
FHL2 -0.029 0.073 -10000 0 -10000 0 0
RANBP9 0.022 0.004 -10000 0 -10000 0 0
JMJD1A -0.037 0.064 -10000 0 -0.13 153 153
CDK6 0.023 0.024 0.38 2 -10000 0 2
TGFB1I1 0.023 0.003 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.074 0.16 0.26 1 -0.38 92 93
XRCC6 0.022 0.004 -10000 0 -10000 0 0
T-DHT/AR -0.098 0.19 -10000 0 -0.41 98 98
CTDSP1 0.022 0.004 -10000 0 -10000 0 0
CTDSP2 0.022 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.004 -10000 0 -10000 0 0
TCF4 0.021 0.027 -10000 0 -0.56 1 1
CDKN2A 0.097 0.14 0.24 201 -0.3 18 219
SRF 0.026 0.006 -10000 0 -10000 0 0
NKX3-1 -0.11 0.18 -10000 0 -0.59 31 31
KLK3 0.011 0.046 -10000 0 -10000 0 0
TMF1 0.021 0.007 -10000 0 -10000 0 0
HNRNPA1 0.023 0.002 -10000 0 -10000 0 0
AOF2 0 0.001 -10000 0 -10000 0 0
APPL1 -0.009 0.004 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.079 0.16 -10000 0 -0.38 97 97
AR -0.12 0.24 -10000 0 -0.58 98 98
UBA3 0.021 0.007 -10000 0 -10000 0 0
PATZ1 0.022 0.005 -10000 0 -10000 0 0
PAWR 0.023 0.002 -10000 0 -10000 0 0
PRKDC 0.022 0.005 -10000 0 -10000 0 0
PA2G4 0.023 0.002 -10000 0 -10000 0 0
UBE2I 0.022 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.071 0.15 -10000 0 -0.35 97 97
RPS6KA3 0.022 0.004 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.08 0.16 -10000 0 -0.38 98 98
LATS2 0.02 0.027 -10000 0 -0.56 1 1
T-DHT/AR/PRX1 -0.072 0.15 -10000 0 -0.35 98 98
Cyclin D3/CDK11 p58 0.016 0.003 -10000 0 -10000 0 0
VAV3 0.021 0.027 -10000 0 -0.56 1 1
KLK2 -0.037 0.093 -10000 0 -0.46 8 8
CASP8 0.022 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.062 0.16 -10000 0 -0.35 95 95
TMPRSS2 -0.33 0.47 -10000 0 -0.99 156 156
CCND1 0.013 0.067 0.38 1 -0.56 6 7
PIAS1 0.023 0.003 -10000 0 -10000 0 0
mol:T-DHT -0.016 0.03 -10000 0 -0.066 114 114
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.023 0.004 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.074 0.16 0.25 2 -0.38 92 94
CMTM2 -0.049 0.19 -10000 0 -0.56 57 57
SNURF 0.005 0.099 -10000 0 -0.56 14 14
ZMIZ1 -0.004 0.051 -10000 0 -0.62 1 1
CCND3 0.022 0.004 -10000 0 -10000 0 0
TGIF1 0.022 0.005 -10000 0 -10000 0 0
FKBP4 0.022 0.017 0.38 1 -10000 0 1
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.22 0.27 -10000 0 -0.76 31 31
PCK1 -0.11 0.17 -10000 0 -0.7 7 7
HNF4A -0.25 0.34 -10000 0 -0.91 55 55
KCNJ11 -0.23 0.31 -10000 0 -0.87 30 30
AKT1 -0.015 0.096 -10000 0 -0.44 1 1
response to starvation -0.008 0.03 -10000 0 -0.19 3 3
DLK1 -0.21 0.29 -10000 0 -0.74 32 32
NKX2-1 -0.7 0.7 -10000 0 -1.4 249 249
ACADM -0.21 0.27 -10000 0 -0.76 32 32
TAT -0.12 0.2 -10000 0 -0.72 18 18
CEBPB 0.023 0.004 -10000 0 -10000 0 0
CEBPA 0.021 0.028 -10000 0 -0.56 1 1
TTR -0.028 0.18 0.71 1 -0.7 17 18
PKLR -0.21 0.27 -10000 0 -0.76 29 29
APOA1 -0.36 0.5 -10000 0 -1.3 69 69
CPT1C -0.22 0.27 -10000 0 -0.76 31 31
ALAS1 -0.11 0.17 -10000 0 -0.55 4 4
TFRC -0.093 0.2 -10000 0 -0.76 10 10
FOXF1 0.046 0.18 0.24 45 -0.45 45 90
NF1 0.026 0.004 -10000 0 -10000 0 0
HNF1A (dimer) 0.035 0.032 0.26 8 -10000 0 8
CPT1A -0.2 0.28 -10000 0 -0.76 29 29
HMGCS1 -0.18 0.28 -10000 0 -0.76 23 23
NR3C1 0.026 0.008 -10000 0 -10000 0 0
CPT1B -0.21 0.27 -10000 0 -0.76 32 32
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.03 0.012 -10000 0 -10000 0 0
GCK -0.21 0.27 -10000 0 -0.76 31 31
CREB1 0.026 0.008 -10000 0 -10000 0 0
IGFBP1 -0.1 0.16 -10000 0 -0.59 8 8
PDX1 -0.1 0.17 -10000 0 -0.93 1 1
UCP2 -0.21 0.27 -10000 0 -0.76 31 31
ALDOB -0.22 0.28 -10000 0 -0.76 22 22
AFP 0.045 0.077 0.36 1 -10000 0 1
BDH1 -0.12 0.27 0.54 1 -0.75 25 26
HADH -0.21 0.28 -10000 0 -0.76 22 22
F2 -0.28 0.36 -10000 0 -0.95 42 42
HNF1A 0.035 0.032 0.26 8 -10000 0 8
G6PC 0.022 0.06 -10000 0 -10000 0 0
SLC2A2 -0.094 0.18 -10000 0 -0.77 2 2
INS -0.023 0.006 -10000 0 -10000 0 0
FOXA1 0.11 0.12 0.27 86 -0.37 10 96
FOXA3 0.03 0.1 0.37 4 -0.55 13 17
FOXA2 -0.25 0.33 -10000 0 -0.82 33 33
ABCC8 -0.22 0.3 -10000 0 -0.81 37 37
ALB 0.045 0.075 0.32 2 -10000 0 2
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.02 0.008 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.029 0.08 -10000 0 -0.31 19 19
Syndecan-3/Neurocan 0.026 0.073 0.24 2 -0.36 10 12
POMC 0.039 0.081 0.25 42 -0.56 3 45
EGFR 0.022 0.084 0.37 11 -0.56 6 17
Syndecan-3/EGFR 0.019 0.072 0.26 9 -0.32 14 23
AGRP -0.25 0.28 -10000 0 -0.56 208 208
NCSTN 0.022 0.005 -10000 0 -10000 0 0
PSENEN 0.021 0.007 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.023 0.003 -10000 0 -10000 0 0
APH1A 0.022 0.006 -10000 0 -10000 0 0
NCAN 0.029 0.063 0.24 33 -0.29 1 34
long-term memory 0.026 0.065 -10000 0 -0.35 11 11
Syndecan-3/IL8 0.021 0.072 0.24 3 -0.36 12 15
PSEN1 0.022 0.005 -10000 0 -10000 0 0
Src/Cortactin 0.028 0.013 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.56 1 1
limb bud formation 0.001 0.056 -10000 0 -0.38 10 10
MC4R 0.026 0.052 0.25 21 -10000 0 21
SRC 0.022 0.004 -10000 0 -10000 0 0
PTN 0.012 0.086 0.24 3 -0.56 10 13
FGFR/FGF/Syndecan-3 0.001 0.057 -10000 0 -0.39 10 10
neuron projection morphogenesis 0.028 0.093 0.27 9 -0.35 8 17
Syndecan-3/AgRP -0.12 0.16 -10000 0 -0.3 178 178
Syndecan-3/AgRP/MC4R -0.1 0.16 0.32 1 -0.29 177 178
Fyn/Cortactin 0.028 0.024 -10000 0 -0.42 1 1
SDC3 0.001 0.057 -10000 0 -0.39 10 10
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.021 0.071 0.24 3 -0.35 12 15
IL8 0.026 0.064 0.26 16 -0.56 3 19
Syndecan-3/Fyn/Cortactin 0.027 0.067 -10000 0 -0.36 11 11
Syndecan-3/CASK -0.001 0.057 -10000 0 -0.35 12 12
alpha-MSH/MC4R 0.049 0.066 0.28 6 -0.42 3 9
Gamma Secretase 0.055 0.028 -10000 0 -10000 0 0
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.027 0.063 0.22 2 -0.31 14 16
RGS9BP 0.008 0.084 -10000 0 -0.56 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 -0.004 0.031 0.38 2 -10000 0 2
mol:Na + 0.093 0.072 0.24 10 -0.16 2 12
mol:ADP -0.005 0.053 0.33 11 -10000 0 11
GNAT2 0.018 0.013 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.009 0.14 -10000 0 -0.37 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.009 -10000 0 -10000 0 0
GRK7 0.028 0.061 0.3 21 -10000 0 21
CNGB3 0.13 0.12 0.24 235 -0.29 2 237
Cone Metarhodopsin II/X-Arrestin 0.014 0.002 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.078 0.22 29 -10000 0 29
Cone PDE6 0.005 0.12 -10000 0 -0.32 54 54
Cone Metarhodopsin II 0.027 0.036 0.22 10 -10000 0 10
Na + (4 Units) 0.11 0.096 0.29 49 -0.18 2 51
GNAT2/GDP 0.002 0.12 -10000 0 -0.32 58 58
GNB5 0.023 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) -0.005 0.045 -10000 0 -10000 0 0
Cone Transducin 0.03 0.067 0.24 2 -0.32 14 16
SLC24A2 0.057 0.098 0.25 87 -0.29 4 91
GNB3/GNGT2 0.02 0.081 0.27 2 -0.42 14 16
GNB3 0.026 0.034 0.27 8 -10000 0 8
GNAT2/GTP 0.016 0.004 -10000 0 -10000 0 0
CNGA3 0.011 0.027 0.31 2 -10000 0 2
ARR3 -0.011 0.016 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.094 0.073 0.24 10 -0.16 2 12
mol:Pi -0.009 0.14 -10000 0 -0.36 58 58
Cone CNG Channel 0.081 0.064 -10000 0 -10000 0 0
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.057 0.097 0.25 87 -0.29 4 91
RGS9 -0.041 0.18 -10000 0 -0.56 52 52
PDE6C -0.008 0.017 -10000 0 -10000 0 0
GNGT2 0.003 0.1 -10000 0 -0.56 16 16
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H -0.011 0.015 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.031 0.032 0.27 1 -0.42 2 3
CRKL -0.051 0.18 0.31 2 -0.61 31 33
mol:PIP3 0.011 0.014 -10000 0 -10000 0 0
AKT1 0.012 0.041 -10000 0 -10000 0 0
PTK2B 0.021 0.007 -10000 0 -10000 0 0
RAPGEF1 -0.049 0.17 0.3 2 -0.58 31 33
RANBP10 0.022 0.005 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.035 0.16 0.25 1 -0.36 89 90
MAP3K5 -0.044 0.17 0.29 2 -0.55 33 35
HGF/MET/CIN85/CBL/ENDOPHILINS -0.023 0.16 -10000 0 -0.33 92 92
AP1 -0.026 0.12 -10000 0 -0.37 53 53
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
apoptosis -0.1 0.3 -10000 0 -0.78 76 76
STAT3 (dimer) -0.042 0.12 -10000 0 -0.36 22 22
GAB1/CRKL/SHP2/PI3K -0.021 0.14 -10000 0 -0.52 23 23
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
CBL/CRK -0.045 0.17 -10000 0 -0.58 31 31
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.022 0.004 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
ELK1 -0.003 0.078 0.31 19 -0.21 2 21
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.028 0.09 -10000 0 -0.3 23 23
PAK1 0.013 0.048 0.39 1 -10000 0 1
HGF/MET/RANBP10 -0.035 0.16 0.25 1 -0.36 92 93
HRAS -0.057 0.16 -10000 0 -0.59 17 17
DOCK1 -0.049 0.17 0.34 1 -0.58 30 31
GAB1 -0.058 0.18 -10000 0 -0.64 31 31
CRK -0.057 0.17 -10000 0 -0.62 30 30
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.088 0.22 -10000 0 -0.5 98 98
JUN 0.022 0.004 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.036 0.091 0.18 1 -0.22 93 94
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
cell morphogenesis 0.017 0.16 0.3 25 -0.42 18 43
GRB2/SHC -0.007 0.092 -10000 0 -0.28 9 9
FOS -0.043 0.18 -10000 0 -0.56 53 53
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility -0.003 0.077 0.31 19 -0.21 2 21
HGF/MET/MUC20 -0.046 0.15 0.24 1 -0.35 93 94
cell migration -0.008 0.09 -10000 0 -0.28 9 9
GRB2 0.022 0.004 -10000 0 -10000 0 0
CBL 0.022 0.004 -10000 0 -10000 0 0
MET/RANBP10 0.03 0.032 0.27 1 -0.42 2 3
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.037 0.12 -10000 0 -0.28 80 80
MET/MUC20 0.015 0.03 0.25 1 -0.41 2 3
RAP1B -0.041 0.16 0.32 5 -0.53 31 36
RAP1A -0.048 0.16 0.28 2 -0.54 30 32
HGF/MET/RANBP9 -0.035 0.16 0.25 1 -0.36 90 91
RAF1 -0.052 0.16 -10000 0 -0.58 15 15
STAT3 -0.042 0.12 -10000 0 -0.36 22 22
cell proliferation -0.056 0.16 0.25 4 -0.38 75 79
RPS6KB1 -0.005 0.041 -10000 0 -0.28 2 2
MAPK3 -0.004 0.1 0.69 8 -10000 0 8
MAPK1 -0.001 0.11 0.69 9 -10000 0 9
RANBP9 0.022 0.004 -10000 0 -10000 0 0
MAPK8 -0.024 0.16 0.29 3 -0.5 32 35
SRC -0.045 0.11 -10000 0 -0.34 18 18
PI3K 0 0.064 -10000 0 -0.2 30 30
MET/Glomulin 0.014 0.034 0.27 1 -0.36 2 3
SOS1 0.023 0.004 -10000 0 -10000 0 0
MAP2K1 -0.051 0.14 -10000 0 -0.55 14 14
MET 0.02 0.041 0.38 1 -0.56 2 3
MAP4K1 -0.047 0.18 0.29 3 -0.59 34 37
PTK2 0.021 0.006 -10000 0 -10000 0 0
MAP2K2 -0.051 0.15 -10000 0 -0.55 14 14
BAD 0.01 0.04 -10000 0 -10000 0 0
MAP2K4 -0.041 0.15 0.28 2 -0.5 31 33
SHP2/GRB2/SOS1/GAB1 -0.032 0.16 -10000 0 -0.54 30 30
INPPL1 0.022 0.005 -10000 0 -10000 0 0
PXN 0.023 0.002 -10000 0 -10000 0 0
SH3KBP1 0.02 0.038 -10000 0 -0.56 2 2
HGS -0.036 0.084 0.16 1 -0.2 90 91
PLCgamma1/PKC 0.017 0.003 -10000 0 -10000 0 0
HGF -0.093 0.23 -10000 0 -0.56 94 94
RASA1 0.021 0.006 -10000 0 -10000 0 0
NCK1 0.019 0.008 -10000 0 -10000 0 0
PTPRJ 0.021 0.027 -10000 0 -0.56 1 1
NCK/PLCgamma1 -0.01 0.093 -10000 0 -0.22 72 72
PDPK1 0.009 0.021 -10000 0 -10000 0 0
HGF/MET/SHIP -0.036 0.16 0.25 1 -0.36 93 94
FOXM1 transcription factor network

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
NFATC3 0.28 0.23 0.61 3 -1.2 2 5
PLK1 0.12 0.094 -10000 0 -10000 0 0
BIRC5 0.15 0.071 -10000 0 -10000 0 0
HSPA1B 0.28 0.24 0.69 5 -1.2 2 7
MAP2K1 0.071 0.042 -10000 0 -10000 0 0
BRCA2 0.28 0.24 0.62 1 -1.2 2 3
FOXM1 0.3 0.27 0.65 11 -1.4 3 14
XRCC1 0.28 0.24 0.67 10 -1.2 2 12
FOXM1B/p19 0.16 0.27 0.62 9 -1.3 3 12
Cyclin D1/CDK4 0.24 0.25 0.62 16 -1.1 3 19
CDC2 0.29 0.25 0.61 15 -1.3 2 17
TGFA 0.26 0.23 0.57 20 -0.98 3 23
SKP2 0.32 0.26 0.7 46 -1.1 2 48
CCNE1 0.088 0.11 0.29 105 -10000 0 105
CKS1B 0.29 0.24 0.7 16 -1.2 2 18
RB1 0.16 0.2 0.45 40 -0.84 5 45
FOXM1C/SP1 0.28 0.24 -10000 0 -1.4 2 2
AURKB 0.1 0.18 -10000 0 -0.8 10 10
CENPF 0.3 0.24 0.71 12 -1.2 2 14
CDK4 0.043 0.026 0.39 1 -10000 0 1
MYC 0.23 0.22 0.54 14 -1 2 16
CHEK2 0.068 0.043 -10000 0 -10000 0 0
ONECUT1 0.28 0.24 0.59 26 -1.1 3 29
CDKN2A 0.077 0.14 0.22 201 -0.32 18 219
LAMA4 0.27 0.26 0.69 3 -1.2 6 9
FOXM1B/HNF6 0.28 0.26 0.65 10 -1.4 3 13
FOS 0.18 0.45 0.7 7 -0.96 52 59
SP1 0.024 0.002 -10000 0 -10000 0 0
CDC25B 0.29 0.24 0.69 15 -1.2 2 17
response to radiation 0.041 0.03 -10000 0 -10000 0 0
CENPB 0.29 0.24 0.71 12 -1.2 2 14
CENPA 0.31 0.24 0.71 12 -1.2 2 14
NEK2 0.31 0.24 0.68 17 -1.2 2 19
HIST1H2BA 0.28 0.24 0.65 8 -1.2 2 10
CCNA2 0.088 0.1 0.26 123 -0.28 2 125
EP300 0.022 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.28 0.25 0.64 1 -1.5 2 3
CCNB2 0.3 0.24 0.63 7 -1.2 2 9
CCNB1 0.29 0.25 0.63 8 -1.3 2 10
ETV5 0.36 0.29 0.71 81 -1.1 5 86
ESR1 0.25 0.34 0.71 5 -1.1 20 25
CCND1 0.22 0.25 0.6 9 -1.2 3 12
GSK3A 0.059 0.037 -10000 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.15 0.11 0.3 134 -10000 0 134
CDK2 0.033 0.013 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.05 0.036 -10000 0 -10000 0 0
FOXM1B/Cbp/p300 0.25 0.24 -10000 0 -1.2 3 3
GAS1 0.27 0.28 0.64 5 -1.1 8 13
MMP2 0.28 0.26 0.7 2 -1.2 5 7
RB1/FOXM1C 0.24 0.26 0.6 25 -1.2 3 28
CREBBP 0.022 0.005 -10000 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.029 0.087 -10000 0 -0.37 29 29
ADCY5 -0.036 0.099 -10000 0 -0.36 39 39
ADCY6 -0.009 0.022 -10000 0 -0.36 2 2
ADCY7 -0.008 0.016 -10000 0 -0.35 1 1
ADCY1 -0.009 0.028 -10000 0 -0.36 3 3
ADCY2 -0.011 0.083 0.27 15 -0.36 16 31
ADCY3 -0.008 0.016 -10000 0 -0.35 1 1
ADCY8 -0.1 0.15 -10000 0 -0.36 126 126
PRKCE -0.006 0.019 -10000 0 -0.41 1 1
ADCY9 -0.009 0.023 -10000 0 -0.36 2 2
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.018 0.13 0.27 30 -0.29 19 49
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.17 0.27 -10000 0 -0.56 154 154
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.022 0.004 -10000 0 -10000 0 0
TCEB1 0.022 0.005 -10000 0 -10000 0 0
HIF1A/p53 0.011 0.068 0.25 1 -0.27 22 23
HIF1A -0.004 0.049 -10000 0 -0.27 15 15
COPS5 0.022 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.058 0.025 -10000 0 -10000 0 0
FIH (dimer) 0.022 0.005 -10000 0 -10000 0 0
CDKN2A 0.097 0.14 0.24 201 -0.3 18 219
ARNT/IPAS -0.11 0.2 -10000 0 -0.42 141 141
HIF1AN 0.022 0.005 -10000 0 -10000 0 0
GNB2L1 0.021 0.006 -10000 0 -10000 0 0
HIF1A/ARNT 0.009 0.066 -10000 0 -0.28 20 20
CUL2 0.022 0.004 -10000 0 -10000 0 0
OS9 0.023 0.003 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.041 0.016 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.011 0.066 -10000 0 -0.28 21 21
PHD1-3/OS9 0.068 0.052 0.26 2 -10000 0 2
HIF1A/RACK1/Elongin B/Elongin C 0.031 0.064 -10000 0 -0.28 6 6
VHL 0.021 0.007 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.012 0.064 0.25 1 -0.28 17 18
EGLN3 0.054 0.079 0.24 70 -10000 0 70
EGLN2 0.021 0.006 -10000 0 -10000 0 0
EGLN1 0.022 0.004 -10000 0 -10000 0 0
TP53 0.022 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A -0.018 0.18 -10000 0 -0.59 40 40
ARNT 0.022 0.006 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.022 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.055 0.11 0.23 22 -0.31 23 45
HIF-1-alpha transcription factor network

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
PKM2 0.016 0.3 0.48 1 -0.89 28 29
HDAC7 0.023 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.09 0.3 -10000 0 -0.82 17 17
SMAD4 0.022 0.009 -10000 0 -10000 0 0
ID2 0.015 0.3 0.48 1 -0.89 28 29
AP1 -0.024 0.14 -10000 0 -0.42 53 53
ABCG2 -0.02 0.35 0.48 1 -0.89 45 46
HIF1A 0.02 0.074 -10000 0 -0.28 4 4
TFF3 -0.009 0.34 -10000 0 -0.89 39 39
GATA2 -0.04 0.17 -10000 0 -0.56 46 46
AKT1 0.02 0.069 -10000 0 -10000 0 0
response to hypoxia 0.003 0.065 -10000 0 -0.27 7 7
MCL1 0.008 0.29 0.48 1 -0.88 27 28
NDRG1 0.015 0.29 0.48 1 -0.89 25 26
SERPINE1 0.016 0.29 0.48 1 -0.88 26 27
FECH 0.015 0.3 0.48 1 -0.89 27 28
FURIN 0.016 0.3 0.48 1 -0.89 27 28
NCOA2 0.022 0.027 -10000 0 -0.56 1 1
EP300 0.022 0.074 -10000 0 -0.28 6 6
HMOX1 0.015 0.3 0.48 1 -0.89 27 28
BHLHE40 0.013 0.29 0.48 1 -0.88 28 29
BHLHE41 0.01 0.31 0.48 1 -0.96 26 27
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.065 0.13 -10000 0 -0.41 7 7
ENG 0.015 0.12 0.35 2 -0.59 7 9
JUN 0.018 0.017 -10000 0 -10000 0 0
RORA 0.016 0.3 0.48 1 -0.88 28 29
ABCB1 -0.11 0.39 -10000 0 -1.1 60 60
TFRC -0.016 0.26 -10000 0 -0.85 25 25
CXCR4 0.017 0.3 0.48 1 -0.88 28 29
TF 0.007 0.3 -10000 0 -0.88 30 30
CITED2 0.011 0.31 0.48 1 -0.92 28 29
HIF1A/ARNT 0.14 0.4 0.65 1 -1 27 28
LDHA 0.021 0.14 -10000 0 -0.79 10 10
ETS1 0.009 0.32 0.48 1 -0.97 28 29
PGK1 0.015 0.3 0.48 1 -0.89 28 29
NOS2 0.006 0.33 0.48 1 -0.91 34 35
ITGB2 0.004 0.32 -10000 0 -0.93 33 33
ALDOA 0.017 0.3 0.48 1 -0.89 28 29
Cbp/p300/CITED2 0.027 0.32 -10000 0 -0.97 24 24
FOS -0.047 0.18 -10000 0 -0.57 53 53
HK2 0.016 0.3 0.48 1 -0.89 28 29
SP1 0.008 0.051 -10000 0 -0.2 1 1
GCK 0.037 0.11 -10000 0 -10000 0 0
HK1 0.016 0.3 0.48 1 -0.88 28 29
NPM1 0.014 0.3 0.48 1 -0.88 28 29
EGLN1 0.014 0.29 0.48 1 -0.89 27 28
CREB1 0.026 0.004 -10000 0 -10000 0 0
PGM1 0.015 0.3 0.48 1 -0.88 28 29
SMAD3 0.023 0.008 -10000 0 -10000 0 0
EDN1 -0.1 0.38 0.42 1 -1.1 51 52
IGFBP1 0.015 0.3 0.47 1 -0.88 28 29
VEGFA 0.026 0.23 -10000 0 -0.71 15 15
HIF1A/JAB1 0.031 0.058 -10000 0 -0.3 1 1
CP -0.008 0.29 0.48 1 -0.91 30 31
CXCL12 -0.004 0.34 0.48 1 -0.99 35 36
COPS5 0.023 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.033 0.014 -10000 0 -10000 0 0
BNIP3 0.016 0.3 0.48 1 -0.89 28 29
EGLN3 0.026 0.3 0.47 2 -0.89 28 30
CA9 0.082 0.34 0.52 7 -0.93 26 33
TERT 0.056 0.3 0.51 8 -0.87 25 33
ENO1 0.015 0.3 0.48 1 -0.88 28 29
PFKL 0.014 0.3 -10000 0 -0.88 28 28
NCOA1 0.023 0.004 -10000 0 -10000 0 0
ADM 0.015 0.3 0.48 1 -0.88 28 29
ARNT 0.021 0.07 -10000 0 -0.28 2 2
HNF4A 0.028 0.031 0.26 8 -10000 0 8
ADFP 0.005 0.29 -10000 0 -0.88 29 29
SLC2A1 0.083 0.27 0.43 1 -0.7 21 22
LEP 0.029 0.31 0.48 1 -0.89 27 28
HIF1A/ARNT/Cbp/p300 0.087 0.3 -10000 0 -0.84 18 18
EPO 0.053 0.19 -10000 0 -0.71 5 5
CREBBP 0.021 0.078 -10000 0 -0.31 7 7
HIF1A/ARNT/Cbp/p300/HDAC7 0.12 0.32 -10000 0 -0.85 16 16
PFKFB3 0.015 0.3 0.48 1 -0.88 28 29
NT5E 0.015 0.3 0.48 1 -0.9 28 29
Glucocorticoid receptor regulatory network

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
PCK2 -0.01 0.092 0.32 1 -0.46 3 4
SMARCC2 0.024 0.002 -10000 0 -10000 0 0
SMARCC1 0.022 0.007 -10000 0 -10000 0 0
TBX21 -0.07 0.3 0.54 3 -0.9 49 52
SUMO2 0.022 0.007 -10000 0 -10000 0 0
STAT1 (dimer) 0.026 0.005 -10000 0 -10000 0 0
FKBP4 0.022 0.017 0.38 1 -10000 0 1
FKBP5 0.023 0.004 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.009 0.11 0.32 8 -10000 0 8
PRL 0.017 0.094 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0 0.26 0.52 42 -0.4 36 78
RELA -0.062 0.13 -10000 0 -0.29 62 62
FGG -0.25 0.34 0.47 13 -0.6 203 216
GR beta/TIF2 -0.001 0.12 0.31 19 -0.33 1 20
IFNG 0.03 0.19 -10000 0 -0.96 7 7
apoptosis -0.008 0.11 0.5 2 -0.54 5 7
CREB1 0.026 0.011 -10000 0 -10000 0 0
histone acetylation 0.001 0.11 0.32 1 -0.36 13 14
BGLAP 0.023 0.11 -10000 0 -0.53 1 1
GR/PKAc 0.009 0.11 0.34 4 -10000 0 4
NF kappa B1 p50/RelA -0.12 0.24 -10000 0 -0.41 161 161
SMARCD1 0.024 0.002 -10000 0 -10000 0 0
MDM2 0.003 0.08 0.24 20 -10000 0 20
GATA3 0.01 0.097 0.24 3 -0.56 13 16
AKT1 0.019 0.005 -10000 0 -10000 0 0
CSF2 -0.12 0.36 -10000 0 -1.2 49 49
GSK3B 0.02 0.01 -10000 0 -10000 0 0
NR1I3 0.001 0.12 0.61 2 -0.69 1 3
CSN2 -0.051 0.17 0.37 17 -0.36 42 59
BRG1/BAF155/BAF170/BAF60A 0.056 0.02 -10000 0 -10000 0 0
NFATC1 0.021 0.027 -10000 0 -0.56 1 1
POU2F1 0.023 0.007 -10000 0 -10000 0 0
CDKN1A 0.009 0.042 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0 0.004 -10000 0 -10000 0 0
SFN 0.04 0.072 0.24 45 -0.38 3 48
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.025 0.12 0.32 7 -10000 0 7
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.01 0.14 0.51 2 -0.81 9 11
JUN 0.041 0.1 0.38 2 -0.42 4 6
IL4 0.01 0.11 0.32 1 -0.43 5 6
CDK5R1 0.027 0.03 0.24 9 -10000 0 9
PRKACA 0.022 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.13 0.15 -10000 0 -0.4 78 78
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.015 0.11 0.32 8 -10000 0 8
cortisol/GR alpha (monomer) -0.007 0.3 0.6 43 -0.46 42 85
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.001 0.2 -10000 0 -0.55 53 53
AP-1/NFAT1-c-4 0.074 0.19 0.38 2 -0.53 8 10
AFP 0.044 0.095 -10000 0 -10000 0 0
SUV420H1 0.022 0.004 -10000 0 -10000 0 0
IRF1 -0.001 0.14 0.4 11 -0.39 4 15
TP53 0.031 0.008 -10000 0 -10000 0 0
PPP5C 0.022 0.004 -10000 0 -10000 0 0
KRT17 0.069 0.18 -10000 0 -0.62 6 6
KRT14 0.045 0.14 0.46 1 -0.9 2 3
TBP 0.027 0.004 -10000 0 -10000 0 0
CREBBP -0.013 0.045 0.34 1 -10000 0 1
HDAC1 0.021 0.005 -10000 0 -10000 0 0
HDAC2 0.03 0.023 -10000 0 -10000 0 0
AP-1 0.074 0.19 0.38 2 -0.53 8 10
MAPK14 0.022 0.008 -10000 0 -10000 0 0
MAPK10 0.013 0.07 -10000 0 -0.56 7 7
MAPK11 0.021 0.008 -10000 0 -10000 0 0
KRT5 0.072 0.18 -10000 0 -0.72 5 5
interleukin-1 receptor activity 0.007 0.023 -10000 0 -10000 0 0
NCOA1 0.023 0.004 -10000 0 -10000 0 0
STAT1 0.026 0.005 -10000 0 -10000 0 0
CGA 0.016 0.11 -10000 0 -0.54 1 1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 -0.035 0.19 0.47 35 -0.35 14 49
MAPK3 0.022 0.008 -10000 0 -10000 0 0
MAPK1 0.021 0.008 -10000 0 -10000 0 0
ICAM1 -0.14 0.39 -10000 0 -1.1 59 59
NFKB1 -0.059 0.13 -10000 0 -0.25 97 97
MAPK8 0.034 0.14 0.28 5 -0.37 17 22
MAPK9 0.02 0.009 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.01 0.11 0.5 2 -0.57 5 7
BAX 0.007 0.043 -10000 0 -10000 0 0
POMC -0.025 0.2 0.48 4 -0.9 8 12
EP300 -0.013 0.046 0.34 1 -10000 0 1
cortisol/GR alpha (dimer)/p53 0 0.25 0.53 37 -0.41 32 69
proteasomal ubiquitin-dependent protein catabolic process -0.008 0.069 0.24 12 -0.2 1 13
SGK1 -0.005 0.075 -10000 0 -10000 0 0
IL13 0.012 0.16 -10000 0 -0.65 9 9
IL6 -0.21 0.48 -10000 0 -1.1 93 93
PRKACG -0.01 0.019 0.24 1 -10000 0 1
IL5 0.01 0.14 -10000 0 -0.68 4 4
IL2 0.027 0.16 -10000 0 -0.64 5 5
CDK5 0.022 0.005 -10000 0 -10000 0 0
PRKACB 0.022 0.004 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
IL8 -0.07 0.24 -10000 0 -0.68 34 34
CDK5R1/CDK5 0.035 0.023 0.18 9 -10000 0 9
NF kappa B1 p50/RelA/PKAc -0.065 0.2 -10000 0 -0.44 56 56
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.008 0.24 0.5 41 -0.38 32 73
SMARCA4 0.023 0.004 -10000 0 -10000 0 0
chromatin remodeling -0.001 0.14 0.36 16 -0.39 1 17
NF kappa B1 p50/RelA/Cbp -0.091 0.2 0.37 1 -0.48 58 59
JUN (dimer) 0.041 0.1 0.38 2 -0.41 4 6
YWHAH 0.022 0.005 -10000 0 -10000 0 0
VIPR1 -0.29 0.46 -10000 0 -0.92 164 164
NR3C1 -0.01 0.17 0.45 21 -10000 0 21
NR4A1 -0.055 0.2 -10000 0 -0.56 68 68
TIF2/SUV420H1 0.031 0.022 -10000 0 -0.42 1 1
MAPKKK cascade -0.008 0.11 0.5 2 -0.54 5 7
cortisol/GR alpha (dimer)/Src-1 0.003 0.26 0.52 41 -0.4 38 79
PBX1 0.021 0.038 -10000 0 -0.56 2 2
POU1F1 0.004 0.027 0.24 3 -10000 0 3
SELE -0.33 0.56 -10000 0 -1.1 149 149
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A -0.001 0.14 0.37 16 -0.39 1 17
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.008 0.24 0.5 41 -0.38 32 73
mol:cortisol -0.012 0.16 0.33 46 -0.24 46 92
MMP1 0.078 0.11 -10000 0 -0.59 4 4
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.014 0.17 0.3 13 -0.58 25 38
FYN -0.012 0.22 0.31 15 -0.74 31 46
LAT/GRAP2/SLP76 -0.007 0.18 0.25 6 -0.61 31 37
IKBKB 0.022 0.018 0.38 1 -10000 0 1
AKT1 -0.005 0.15 0.25 17 -0.46 33 50
B2M 0.021 0.012 -10000 0 -10000 0 0
IKBKG 0.003 0.044 0.097 11 -0.14 18 29
MAP3K8 0.021 0.027 -10000 0 -0.56 1 1
mol:Ca2+ -0.013 0.016 0.087 2 -0.088 8 10
integrin-mediated signaling pathway 0.029 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.018 0.21 0.31 11 -0.69 33 44
TRPV6 0.003 0.16 1.1 7 -0.56 8 15
CD28 0.018 0.054 -10000 0 -0.57 4 4
SHC1 -0.012 0.21 0.29 16 -0.74 27 43
receptor internalization -0.025 0.22 0.22 4 -0.71 36 40
PRF1 -0.062 0.33 -10000 0 -1.1 42 42
KRAS 0.021 0.006 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
COT/AKT1 0.009 0.12 0.24 15 -0.37 31 46
LAT -0.015 0.2 0.27 7 -0.75 26 33
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D 0.011 0.082 -10000 0 -0.57 9 9
CD3E 0.012 0.077 -10000 0 -0.57 8 8
CD3G -0.012 0.14 -10000 0 -0.57 28 28
RASGRP2 -0.017 0.061 -10000 0 -0.17 63 63
RASGRP1 -0.006 0.14 0.26 13 -0.45 30 43
HLA-A 0.02 0.029 -10000 0 -0.57 1 1
RASSF5 0.022 0.004 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.029 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.059 0.15 28 -0.13 21 49
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.06 -10000 0 -0.24 22 22
PRKCA -0.001 0.087 0.16 13 -0.29 25 38
GRAP2 -0.006 0.12 -10000 0 -0.56 23 23
mol:IP3 -0.017 0.12 0.24 5 -0.45 29 34
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.026 0.19 -10000 0 -0.73 26 26
ORAI1 -0.012 0.12 -10000 0 -0.95 7 7
CSK -0.016 0.2 0.27 7 -0.75 27 34
B7 family/CD28 -0.012 0.23 -10000 0 -0.82 29 29
CHUK 0.022 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.035 0.23 0.25 1 -0.89 27 28
PTPN6 -0.015 0.21 0.26 4 -0.75 27 31
VAV1 -0.017 0.21 0.27 6 -0.76 27 33
Monovalent TCR/CD3 -0.022 0.17 -10000 0 -0.52 35 35
CBL 0.022 0.004 -10000 0 -10000 0 0
LCK -0.013 0.22 0.31 13 -0.79 28 41
PAG1 -0.015 0.21 0.28 9 -0.76 26 35
RAP1A 0.022 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.034 0.24 0.3 2 -0.89 27 29
CD80 0.002 0.1 -10000 0 -0.57 15 15
CD86 0.013 0.066 -10000 0 -0.57 6 6
PDK1/CARD11/BCL10/MALT1 -0.008 0.076 -10000 0 -0.29 22 22
HRAS 0.022 0.004 -10000 0 -10000 0 0
GO:0035030 -0.028 0.17 0.24 1 -0.64 29 30
CD8A 0.013 0.072 -10000 0 -0.57 7 7
CD8B 0.01 0.092 0.24 4 -0.57 11 15
PTPRC -0.013 0.14 -10000 0 -0.57 29 29
PDK1/PKC theta -0.018 0.18 0.28 11 -0.55 35 46
CSK/PAG1 -0.014 0.2 0.29 10 -0.72 26 36
SOS1 0.023 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.03 0.033 -10000 0 -0.55 1 1
GRAP2/SLP76 -0.01 0.21 0.29 3 -0.7 33 36
STIM1 -0.003 0.029 -10000 0 -10000 0 0
RAS family/GTP 0.022 0.073 0.19 25 -0.19 17 42
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.029 0.24 0.23 3 -0.77 36 39
mol:DAG -0.027 0.11 -10000 0 -0.4 29 29
RAP1A/GDP 0.009 0.028 0.083 17 -0.067 5 22
PLCG1 0.022 0.004 -10000 0 -10000 0 0
CD247 0.008 0.089 -10000 0 -0.57 11 11
cytotoxic T cell degranulation -0.055 0.31 -10000 0 -0.98 42 42
RAP1A/GTP -0.006 0.023 -10000 0 -0.065 60 60
mol:PI-3-4-5-P3 -0.008 0.18 0.27 18 -0.55 33 51
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.015 0.17 0.25 5 -0.6 28 33
NRAS 0.022 0.005 -10000 0 -10000 0 0
ZAP70 0.013 0.075 -10000 0 -0.56 8 8
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.018 0.17 -10000 0 -0.6 29 29
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.023 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.018 0.1 -10000 0 -0.55 13 13
CARD11 0.022 0.033 0.31 2 -0.56 1 3
PRKCB -0.008 0.1 0.16 13 -0.32 35 48
PRKCE -0.005 0.084 0.16 5 -0.28 27 32
PRKCQ -0.023 0.2 0.3 10 -0.62 37 47
LCP2 0.014 0.065 -10000 0 -0.56 6 6
BCL10 0.022 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0 0.13 0.23 20 -0.39 32 52
IKK complex 0.014 0.059 0.15 33 -0.12 18 51
RAS family/GDP -0.001 0.01 -10000 0 -10000 0 0
MAP3K14 0.004 0.094 0.18 16 -0.3 25 41
PDPK1 -0.003 0.14 0.24 18 -0.43 32 50
TCR/CD3/MHC I/CD8/Fyn -0.03 0.23 -10000 0 -0.84 28 28
Regulation of Androgen receptor activity

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
HDAC1 -0.01 0.003 -10000 0 -10000 0 0
SMARCC1 0.004 0.023 -10000 0 -10000 0 0
REL 0.021 0.007 -10000 0 -10000 0 0
HDAC7 -0.069 0.11 0.22 1 -0.32 16 17
JUN 0.022 0.004 -10000 0 -10000 0 0
EP300 0.022 0.004 -10000 0 -10000 0 0
KAT2B 0.02 0.027 -10000 0 -0.56 1 1
KAT5 0.023 0.001 -10000 0 -10000 0 0
MAPK14 -0.007 0.024 -10000 0 -10000 0 0
FOXO1 0.022 0.006 -10000 0 -10000 0 0
T-DHT/AR -0.056 0.13 -10000 0 -0.32 37 37
MAP2K6 0.007 0.026 0.22 1 -10000 0 1
BRM/BAF57 0.029 0.023 -10000 0 -0.42 1 1
MAP2K4 0.007 0.024 -10000 0 -10000 0 0
SMARCA2 0.019 0.028 -10000 0 -0.56 1 1
PDE9A -0.085 0.23 -10000 0 -0.95 21 21
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
CEBPA 0.02 0.027 -10000 0 -0.56 1 1
EHMT2 0.023 0.004 -10000 0 -10000 0 0
cell proliferation -0.08 0.17 0.4 5 -0.47 37 42
NR0B1 0.072 0.12 0.24 146 -0.29 7 153
EGR1 0.013 0.07 -10000 0 -0.56 7 7
RXRs/9cRA -0.14 0.18 -10000 0 -0.32 231 231
AR/RACK1/Src -0.027 0.078 0.35 2 -10000 0 2
AR/GR -0.045 0.12 -10000 0 -0.28 88 88
GNB2L1 0.021 0.007 -10000 0 -10000 0 0
PKN1 0.022 0.005 -10000 0 -10000 0 0
RCHY1 0.022 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -10000 0 -10000 0 0
MAPK8 -0.007 0.023 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.018 0.082 0.28 1 -0.33 2 3
SRC -0.027 0.037 0.2 3 -10000 0 3
NR3C1 0.021 0.006 -10000 0 -10000 0 0
KLK3 -0.041 0.13 0.34 2 -0.43 16 18
APPBP2 0.007 0.025 -10000 0 -10000 0 0
TRIM24 0.023 0.004 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.032 0.077 0.25 3 -0.3 1 4
TMPRSS2 -0.36 0.52 -10000 0 -1.1 159 159
RXRG -0.27 0.29 -10000 0 -0.56 233 233
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.022 0.004 -10000 0 -10000 0 0
RXRB 0.022 0.004 -10000 0 -10000 0 0
CARM1 0.023 0.005 -10000 0 -10000 0 0
NR2C2 0.021 0.006 -10000 0 -10000 0 0
KLK2 -0.014 0.075 0.35 2 -0.36 1 3
AR -0.062 0.12 -10000 0 -0.31 84 84
SENP1 0.023 0.002 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
MDM2 0.023 0.017 0.38 1 -10000 0 1
SRY 0 0.001 -10000 0 -10000 0 0
GATA2 -0.036 0.17 -10000 0 -0.56 46 46
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.15 0.12 0.24 281 -10000 0 281
T-DHT/AR/RACK1/Src -0.026 0.079 0.3 4 -10000 0 4
positive regulation of transcription -0.036 0.17 -10000 0 -0.56 46 46
DNAJA1 0.007 0.024 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.013 0.01 0.22 1 -10000 0 1
NCOA1 0.031 0.021 -10000 0 -10000 0 0
SPDEF -0.047 0.19 0.24 4 -0.56 58 62
T-DHT/AR/TIF2 -0.024 0.09 0.38 1 -0.38 15 16
T-DHT/AR/Hsp90 -0.03 0.076 0.28 2 -0.3 1 3
GSK3B 0.017 0.013 -10000 0 -10000 0 0
NR2C1 0.023 0.002 -10000 0 -10000 0 0
mol:T-DHT -0.029 0.035 -10000 0 -10000 0 0
SIRT1 0.022 0.005 -10000 0 -10000 0 0
ZMIZ2 0.022 0.005 -10000 0 -10000 0 0
POU2F1 -0.012 0.061 -10000 0 -0.18 1 1
T-DHT/AR/DAX-1 -0.018 0.11 0.25 8 -0.31 2 10
CREBBP 0.022 0.005 -10000 0 -10000 0 0
SMARCE1 0.022 0.004 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 0.007 0.12 -10000 0 -0.38 26 26
TBX21 -0.12 0.47 -10000 0 -1.3 56 56
B2M 0.022 0.01 -10000 0 -10000 0 0
TYK2 0.014 0.031 -10000 0 -10000 0 0
IL12RB1 -0.019 0.14 -10000 0 -0.59 28 28
GADD45B -0.067 0.36 -10000 0 -1.1 43 43
IL12RB2 0.037 0.075 0.25 37 -0.28 1 38
GADD45G -0.051 0.32 -10000 0 -1 33 33
natural killer cell activation 0 0.017 -10000 0 -10000 0 0
RELB 0.023 0.017 0.38 1 -10000 0 1
RELA 0.023 0.001 -10000 0 -10000 0 0
IL18 0.016 0.05 -10000 0 -0.57 3 3
IL2RA 0.021 0.042 0.24 3 -0.56 2 5
IFNG 0.016 0.056 0.24 2 -0.56 4 6
STAT3 (dimer) -0.049 0.29 -10000 0 -0.78 48 48
HLA-DRB5 -0.038 0.17 -10000 0 -0.56 45 45
FASLG -0.08 0.39 -10000 0 -1.2 42 42
NF kappa B2 p52/RelB -0.059 0.34 -10000 0 -0.89 53 53
CD4 0.001 0.095 -10000 0 -0.56 13 13
SOCS1 0.021 0.027 -10000 0 -0.56 1 1
EntrezGene:6955 -0.002 0.009 -10000 0 -10000 0 0
CD3D 0.006 0.081 -10000 0 -0.56 9 9
CD3E 0.007 0.077 -10000 0 -0.56 8 8
CD3G -0.017 0.14 -10000 0 -0.57 28 28
IL12Rbeta2/JAK2 0.035 0.065 -10000 0 -10000 0 0
CCL3 -0.066 0.34 -10000 0 -1 40 40
CCL4 -0.07 0.35 -10000 0 -1 40 40
HLA-A 0.021 0.028 -10000 0 -0.56 1 1
IL18/IL18R 0.029 0.12 -10000 0 -0.44 24 24
NOS2 -0.094 0.42 -10000 0 -1.1 57 57
IL12/IL12R/TYK2/JAK2/SPHK2 0.008 0.12 -10000 0 -0.39 24 24
IL1R1 -0.064 0.33 -10000 0 -0.94 46 46
IL4 -0.007 0.031 -10000 0 -10000 0 0
JAK2 0.013 0.029 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.044 0.27 -10000 0 -1.1 23 23
RAB7A -0.021 0.28 -10000 0 -0.81 37 37
lysosomal transport -0.016 0.27 -10000 0 -0.76 37 37
FOS -0.18 0.47 -10000 0 -1.1 83 83
STAT4 (dimer) -0.054 0.33 0.42 1 -0.9 49 50
STAT5A (dimer) -0.062 0.34 -10000 0 -0.92 50 50
GZMA -0.071 0.35 -10000 0 -1.1 39 39
GZMB -0.072 0.36 -10000 0 -1.1 40 40
HLX 0.022 0.004 -10000 0 -10000 0 0
LCK -0.075 0.37 -10000 0 -0.97 53 53
TCR/CD3/MHC II/CD4 -0.079 0.28 -10000 0 -0.75 47 47
IL2/IL2R 0.043 0.073 -10000 0 -0.45 8 8
MAPK14 -0.057 0.35 -10000 0 -0.99 44 44
CCR5 -0.075 0.36 -10000 0 -1.2 37 37
IL1B 0.001 0.096 -10000 0 -0.59 11 11
STAT6 0.006 0.091 -10000 0 -10000 0 0
STAT4 0.013 0.075 -10000 0 -0.56 8 8
STAT3 0.023 0.004 -10000 0 -10000 0 0
STAT1 0.022 0.004 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
NFKB2 0.022 0.005 -10000 0 -10000 0 0
IL12B 0.013 0.029 -10000 0 -10000 0 0
CD8A 0.014 0.071 -10000 0 -0.57 7 7
CD8B 0.011 0.092 0.24 4 -0.57 11 15
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.007 0.12 0.38 26 -10000 0 26
IL2RB 0.019 0.046 -10000 0 -0.56 3 3
proteasomal ubiquitin-dependent protein catabolic process -0.043 0.3 0.42 1 -0.8 49 50
IL2RG 0.014 0.07 -10000 0 -0.56 7 7
IL12 0.012 0.06 -10000 0 -0.42 6 6
STAT5A 0.023 0.004 -10000 0 -10000 0 0
CD247 0.003 0.09 -10000 0 -0.57 11 11
IL2 0.001 0.02 -10000 0 -10000 0 0
SPHK2 0.022 0.004 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.004 0.07 -10000 0 -0.57 6 6
IL12/IL12R/TYK2/JAK2 -0.099 0.4 -10000 0 -1.1 53 53
MAP2K3 -0.065 0.36 -10000 0 -1 45 45
RIPK2 0.022 0.005 -10000 0 -10000 0 0
MAP2K6 -0.055 0.34 -10000 0 -0.98 43 43
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.027 0.15 -10000 0 -0.56 36 36
IL18RAP -0.006 0.12 -10000 0 -0.57 22 22
IL12Rbeta1/TYK2 -0.004 0.12 -10000 0 -0.45 28 28
EOMES -0.06 0.25 -10000 0 -0.82 36 36
STAT1 (dimer) -0.043 0.28 -10000 0 -0.74 49 49
T cell proliferation -0.028 0.24 0.43 1 -0.64 46 47
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.014 0.063 -10000 0 -0.57 5 5
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.047 0.27 -10000 0 -0.72 48 48
ATF2 -0.048 0.31 -10000 0 -0.9 43 43
Syndecan-1-mediated signaling events

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
TGFB1 0.022 0.005 -10000 0 -10000 0 0
CCL5 0.012 0.079 -10000 0 -0.56 9 9
SDCBP 0.022 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.023 0.065 0.26 7 -0.39 3 10
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.03 0.073 0.26 6 -0.35 4 10
Syndecan-1/Syntenin 0.031 0.071 0.26 6 -0.35 4 10
MAPK3 0.024 0.065 0.24 6 -0.34 3 9
HGF/MET -0.056 0.18 0.27 1 -0.41 96 97
TGFB1/TGF beta receptor Type II 0.022 0.005 -10000 0 -10000 0 0
BSG 0.022 0.004 -10000 0 -10000 0 0
keratinocyte migration 0.029 0.072 0.26 6 -0.35 4 10
Syndecan-1/RANTES 0.025 0.09 0.26 6 -0.4 10 16
Syndecan-1/CD147 0.042 0.072 0.26 6 -0.36 3 9
Syndecan-1/Syntenin/PIP2 0.029 0.068 0.24 6 -0.33 4 10
LAMA5 0.021 0.027 -10000 0 -0.56 1 1
positive regulation of cell-cell adhesion 0.028 0.066 0.24 6 -0.33 4 10
MMP7 0.02 0.092 0.24 20 -0.56 9 29
HGF -0.093 0.23 -10000 0 -0.56 94 94
Syndecan-1/CASK 0.014 0.065 0.2 6 -0.31 6 12
Syndecan-1/HGF/MET -0.02 0.15 0.29 3 -0.42 21 24
regulation of cell adhesion 0.014 0.062 0.24 6 -0.36 2 8
HPSE 0.022 0.005 -10000 0 -10000 0 0
positive regulation of cell migration 0.023 0.065 0.26 7 -0.39 3 10
SDC1 0.025 0.06 0.24 6 -0.42 2 8
Syndecan-1/Collagen 0.023 0.065 0.26 7 -0.39 3 10
PPIB 0.023 0.003 -10000 0 -10000 0 0
MET 0.02 0.041 0.38 1 -0.56 2 3
PRKACA 0.022 0.005 -10000 0 -10000 0 0
MMP9 0.033 0.047 0.24 24 -10000 0 24
MAPK1 0.02 0.063 0.22 4 -0.34 3 7
homophilic cell adhesion 0.023 0.068 0.25 9 -0.38 3 12
MMP1 0.15 0.11 0.24 292 -0.29 3 295
Plasma membrane estrogen receptor signaling

Figure S43.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.03 0.087 -10000 0 -0.34 22 22
ER alpha/Gai/GDP/Gbeta gamma -0.038 0.19 -10000 0 -0.57 41 41
AKT1 -0.025 0.2 -10000 0 -0.83 26 26
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.02 0.2 -10000 0 -0.83 26 26
mol:Ca2+ -0.094 0.18 -10000 0 -0.42 105 105
IGF1R 0.022 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.014 0.077 -10000 0 -0.35 20 20
SHC1 0.022 0.005 -10000 0 -10000 0 0
apoptosis 0.022 0.19 0.78 26 -10000 0 26
RhoA/GTP 0.006 0.058 -10000 0 -0.28 18 18
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.009 0.16 -10000 0 -0.51 32 32
regulation of stress fiber formation 0.009 0.069 0.45 1 -0.24 4 5
E2/ERA-ERB (dimer) 0.014 0.076 -10000 0 -0.34 20 20
KRAS 0.021 0.006 -10000 0 -10000 0 0
G13/GTP 0.014 0.069 -10000 0 -0.31 20 20
pseudopodium formation -0.009 0.069 0.24 4 -0.45 1 5
E2/ER alpha (dimer)/PELP1 0.013 0.077 -10000 0 -0.35 20 20
GRB2 0.022 0.004 -10000 0 -10000 0 0
GNG2 0.016 0.06 -10000 0 -0.56 5 5
GNAO1 0.021 0.031 0.24 2 -0.56 1 3
HRAS 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.025 0.18 -10000 0 -0.55 38 38
E2/ER beta (dimer) 0.016 0.004 -10000 0 -10000 0 0
mol:GDP -0.004 0.087 -10000 0 -0.4 21 21
mol:NADP -0.025 0.18 -10000 0 -0.55 38 38
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:IP3 -0.098 0.19 -10000 0 -0.44 105 105
IGF-1R heterotetramer 0.022 0.004 -10000 0 -10000 0 0
PLCB1 -0.091 0.19 -10000 0 -0.44 103 103
PLCB2 -0.098 0.2 -10000 0 -0.45 110 110
IGF1 0.005 0.1 0.24 1 -0.56 15 16
mol:L-citrulline -0.025 0.18 -10000 0 -0.55 38 38
RHOA 0.021 0.007 -10000 0 -10000 0 0
Gai/GDP -0.042 0.21 -10000 0 -0.62 54 54
JNK cascade 0.016 0.003 -10000 0 -10000 0 0
BCAR1 0.022 0.005 -10000 0 -10000 0 0
ESR2 0.022 0.005 -10000 0 -10000 0 0
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
ESR1 -0.002 0.12 -10000 0 -0.56 20 20
Gq family/GDP/Gbeta gamma -0.069 0.2 -10000 0 -0.66 34 34
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.014 0.075 -10000 0 -0.48 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.008 0.16 -10000 0 -0.5 34 34
GNAZ 0.016 0.06 -10000 0 -0.56 5 5
E2/ER alpha (dimer) -0.001 0.086 -10000 0 -0.4 21 21
STRN 0.023 0.004 -10000 0 -10000 0 0
GNAL 0.018 0.046 -10000 0 -0.56 3 3
PELP1 0.022 0.006 -10000 0 -10000 0 0
MAPK11 0.01 0.003 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
HBEGF -0.038 0.19 0.31 5 -0.61 35 40
cAMP biosynthetic process 0.01 0.067 -10000 0 -0.3 19 19
SRC -0.036 0.18 0.26 2 -0.55 38 40
PI3K 0.017 0.017 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
G13/GDP/Gbeta gamma 0.017 0.097 -10000 0 -0.4 21 21
SOS1 0.023 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.027 0.12 -10000 0 -0.43 31 31
Gs family/GTP 0.016 0.069 -10000 0 -0.31 19 19
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.038 0.016 -10000 0 -10000 0 0
vasodilation -0.023 0.17 -10000 0 -0.51 39 39
mol:DAG -0.098 0.19 -10000 0 -0.44 105 105
Gs family/GDP/Gbeta gamma 0.001 0.09 -10000 0 -0.39 19 19
MSN -0.01 0.072 0.25 4 -0.49 1 5
Gq family/GTP -0.092 0.21 -10000 0 -0.46 113 113
mol:PI-3-4-5-P3 -0.018 0.19 -10000 0 -0.8 26 26
NRAS 0.022 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.023 0.17 0.51 39 -10000 0 39
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.087 -10000 0 -0.38 21 21
NOS3 -0.028 0.19 -10000 0 -0.59 38 38
GNA11 0.022 0.004 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.16 0.32 1 -0.63 26 27
E2/ER alpha (dimer)/PELP1/Src -0.016 0.17 -10000 0 -0.51 38 38
ruffle organization -0.009 0.069 0.24 4 -0.45 1 5
ROCK2 -0.007 0.075 0.26 4 -0.27 13 17
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
GNA15 0.022 0.004 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
MMP9 -0.03 0.17 0.34 5 -0.59 27 32
MMP2 -0.03 0.17 0.42 1 -0.6 28 29
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.046 0.11 -10000 0 -0.4 12 12
epithelial cell differentiation -0.024 0.089 -10000 0 -0.41 5 5
ITCH 0.038 0.021 -10000 0 -10000 0 0
WWP1 -0.04 0.081 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.56 1 1
EGFR 0.022 0.084 0.37 11 -0.56 6 17
PRL 0.002 0.037 0.24 8 -10000 0 8
neuron projection morphogenesis -0.032 0.078 0.42 1 -0.36 4 5
PTPRZ1 0.16 0.14 0.24 312 -0.49 8 320
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.011 0.09 -10000 0 -0.39 4 4
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.037 0.084 -10000 0 -0.37 10 10
ADAM17 0.037 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.056 0.095 -10000 0 -0.3 6 6
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.18 -10000 0 -0.4 113 113
NCOR1 0.022 0.005 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.032 0.088 -10000 0 -0.36 11 11
GRIN2B -0.036 0.081 -10000 0 -0.39 5 5
ErbB4/ErbB2/betacellulin -0.043 0.11 -10000 0 -0.36 32 32
STAT1 0.022 0.004 -10000 0 -10000 0 0
HBEGF 0.006 0.095 -10000 0 -0.56 13 13
PRLR 0.018 0.1 0.3 20 -0.56 10 30
E4ICDs/ETO2 -0.042 0.1 -10000 0 -0.36 7 7
axon guidance -0.038 0.073 -10000 0 -0.43 2 2
NEDD4 0.038 0.022 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin 0.025 0.079 0.29 7 -0.42 10 17
CBFA2T3 0.015 0.065 -10000 0 -0.56 6 6
ErbB4/ErbB2/HBEGF -0.028 0.089 -10000 0 -0.35 12 12
MAPK3 -0.024 0.082 -10000 0 -0.37 4 4
STAT1 (dimer) -0.039 0.093 -10000 0 -10000 0 0
MAPK1 -0.023 0.08 -10000 0 -0.37 4 4
JAK2 0.02 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.035 0.083 -10000 0 -0.35 10 10
NRG1 -0.005 0.069 -10000 0 -0.42 12 12
NRG3 -0.13 0.25 -10000 0 -0.56 116 116
NRG2 -0.039 0.17 -10000 0 -0.56 46 46
NRG4 0.048 0.072 0.24 57 -0.29 1 58
heart development -0.038 0.073 -10000 0 -0.43 2 2
neural crest cell migration -0.034 0.082 -10000 0 -0.35 10 10
ERBB2 0.008 0.029 0.31 2 -10000 0 2
WWOX/E4ICDs -0.037 0.092 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.019 0.12 0.29 2 -0.43 4 6
apoptosis 0.16 0.24 0.51 128 -10000 0 128
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.07 0.14 -10000 0 -0.4 45 45
ErbB4/ErbB2/epiregulin -0.073 0.15 -10000 0 -0.36 81 81
ErbB4/ErbB4/betacellulin/betacellulin -0.062 0.13 -10000 0 -0.4 35 35
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.021 0.11 0.37 1 -0.43 8 9
MDM2 -0.043 0.09 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.022 0.073 -10000 0 -0.35 10 10
STAT5A -0.038 0.07 -10000 0 -0.41 2 2
ErbB4/EGFR/neuregulin 1 beta -0.028 0.1 0.28 2 -0.42 13 15
DLG4 0.022 0.006 -10000 0 -10000 0 0
GRB2/SHC 0.032 0.009 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.037 0.085 -10000 0 -10000 0 0
STAT5A (dimer) -0.021 0.098 -10000 0 -0.5 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.027 0.078 -10000 0 -0.41 2 2
LRIG1 0.02 0.027 -10000 0 -0.56 1 1
EREG -0.079 0.23 0.25 14 -0.56 87 101
BTC -0.022 0.15 -10000 0 -0.56 35 35
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.038 0.072 -10000 0 -0.43 2 2
ERBB4 -0.056 0.095 -10000 0 -0.3 6 6
STAT5B 0.023 0.004 -10000 0 -10000 0 0
YAP1 -0.01 0.076 -10000 0 -0.52 9 9
GRB2 0.022 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.014 0.092 0.33 2 -10000 0 2
glial cell differentiation 0.037 0.085 -10000 0 -10000 0 0
WWOX 0.022 0.006 -10000 0 -10000 0 0
cell proliferation -0.06 0.13 0.55 1 -0.42 29 30
Nectin adhesion pathway

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
PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
alphaV beta3 Integrin 0.026 0.058 -10000 0 -0.42 8 8
PTK2 0.011 0.14 -10000 0 -0.46 29 29
positive regulation of JNK cascade 0.001 0.1 -10000 0 -0.32 34 34
CDC42/GDP 0.018 0.14 -10000 0 -0.43 36 36
Rac1/GDP 0.017 0.14 -10000 0 -0.42 35 35
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
CDC42/GTP 0.009 0.13 -10000 0 -0.4 33 33
nectin-3/I-afadin 0 0.11 -10000 0 -0.41 32 32
RAPGEF1 0.001 0.14 0.28 1 -0.47 31 32
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.005 0.16 -10000 0 -0.53 32 32
PDGFB-D/PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
TLN1 -0.033 0.1 -10000 0 -0.42 24 24
Rap1/GTP -0.001 0.1 -10000 0 -0.34 29 29
IQGAP1 0.023 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.013 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0 0.11 -10000 0 -0.41 32 32
PVR 0.022 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.022 0.005 -10000 0 -10000 0 0
mol:GDP 0.003 0.17 -10000 0 -0.52 37 37
MLLT4 0.023 0.003 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.018 0.07 -10000 0 -0.31 12 12
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.1 0.077 0.27 1 -0.2 1 2
positive regulation of lamellipodium assembly 0.006 0.11 -10000 0 -0.34 33 33
PVRL1 0.12 0.11 0.24 228 -0.29 1 229
PVRL3 -0.019 0.15 -10000 0 -0.56 32 32
PVRL2 0.022 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
CDH1 0.022 0.005 -10000 0 -10000 0 0
CLDN1 0.065 0.12 0.31 84 -0.56 2 86
JAM-A/CLDN1 0.041 0.1 0.26 28 -0.33 15 43
SRC -0.01 0.17 -10000 0 -0.59 32 32
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
nectin-1(dimer)/I-afadin/I-afadin 0.1 0.077 0.27 1 -0.2 1 2
FARP2 0.002 0.18 -10000 0 -0.53 34 34
RAC1 0.022 0.004 -10000 0 -10000 0 0
CTNNA1 0.021 0.006 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.013 0.1 -10000 0 -0.36 32 32
nectin-1/I-afadin 0.1 0.077 0.27 1 -0.2 1 2
nectin-2/I-afadin 0.032 0.008 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.03 0.007 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.063 0.14 -10000 0 -0.37 31 31
CDC42/GTP/IQGAP1/filamentous actin 0.029 0.008 -10000 0 -10000 0 0
F11R 0.022 0.006 -10000 0 -10000 0 0
positive regulation of filopodium formation 0.001 0.1 -10000 0 -0.32 34 34
alphaV/beta3 Integrin/Talin 0.006 0.13 0.27 3 -0.45 22 25
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.008 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.032 0.008 -10000 0 -10000 0 0
PIP5K1C -0.032 0.11 -10000 0 -0.33 47 47
VAV2 0.004 0.18 -10000 0 -0.53 36 36
RAP1/GDP 0.017 0.13 -10000 0 -0.4 33 33
ITGAV 0.023 0.003 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.013 0.1 -10000 0 -0.36 32 32
nectin-3(dimer)/I-afadin/I-afadin 0 0.11 -10000 0 -0.41 32 32
Rac1/GTP 0.011 0.14 -10000 0 -0.41 33 33
PTPRM -0.029 0.12 -10000 0 -0.35 50 50
E-cadherin/beta catenin/alpha catenin 0.1 0.064 -10000 0 -10000 0 0
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.022 0.005 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD 0.009 0.075 0.28 1 -0.29 19 20
FZD6 0.022 0.005 -10000 0 -10000 0 0
WNT6 0.057 0.084 0.24 80 -0.29 1 81
WNT4 0.019 0.057 0.24 4 -0.56 4 8
FZD3 0.021 0.007 -10000 0 -10000 0 0
WNT5A 0.024 0.032 0.24 8 -0.29 1 9
WNT11 0.006 0.11 0.25 10 -0.56 17 27
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.022 0.005 -10000 0 -10000 0 0
VLDLR 0.019 0.028 -10000 0 -0.56 1 1
LRPAP1 0.021 0.006 -10000 0 -10000 0 0
NUDC 0.022 0.005 -10000 0 -10000 0 0
RELN/LRP8 -0.022 0.15 -10000 0 -0.35 77 77
CaM/Ca2+ 0.016 0.004 -10000 0 -10000 0 0
KATNA1 0.023 0.003 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.055 0.12 -10000 0 -0.32 77 77
IQGAP1/CaM 0.032 0.009 -10000 0 -10000 0 0
DAB1 0.028 0.06 0.25 30 -10000 0 30
IQGAP1 0.023 0.003 -10000 0 -10000 0 0
PLA2G7 0.018 0.053 -10000 0 -0.56 4 4
CALM1 0.022 0.005 -10000 0 -10000 0 0
DYNLT1 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.032 0.014 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.023 0.002 -10000 0 -10000 0 0
CDK5R1 0.027 0.029 0.24 9 -10000 0 9
LIS1/Poliovirus Protein 3A -0.007 0.002 -10000 0 -10000 0 0
CDK5R2 0.073 0.099 0.24 120 -0.29 2 122
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.018 0.15 0.36 2 -0.36 75 77
YWHAE 0.022 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.017 0.12 0.34 1 -0.31 10 11
MAP1B 0.005 0.01 0.21 1 -10000 0 1
RAC1 0.009 0.004 -10000 0 -10000 0 0
p35/CDK5 -0.048 0.12 0.18 19 -0.29 77 96
RELN -0.071 0.22 0.24 3 -0.56 77 80
PAFAH/LIS1 0.019 0.031 -10000 0 -0.35 3 3
LIS1/CLIP170 0.021 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.011 0.097 -10000 0 -0.29 4 4
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.037 0.13 -10000 0 -0.41 22 22
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.035 0.12 0.25 3 -0.28 75 78
LIS1/IQGAP1 0.021 0.008 -10000 0 -10000 0 0
RHOA 0.009 0.004 -10000 0 -10000 0 0
PAFAH1B1 -0.009 0.003 -10000 0 -10000 0 0
PAFAH1B3 0.024 0.025 0.33 3 -10000 0 3
PAFAH1B2 0.022 0.004 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.015 0.027 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.01 0.12 0.33 1 -0.32 9 10
LRP8 0.024 0.018 0.24 3 -10000 0 3
NDEL1/Katanin 60 -0.02 0.12 0.34 1 -0.32 11 12
P39/CDK5 -0.02 0.14 0.31 6 -0.3 74 80
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.021 0.008 -10000 0 -10000 0 0
CDK5 -0.055 0.12 0.18 16 -0.31 77 93
PPP2R5D 0.022 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.019 0.007 -10000 0 -10000 0 0
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.008 0.13 0.28 3 -0.31 68 71
RELN/VLDLR -0.011 0.14 -10000 0 -0.32 75 75
CDC42 0.009 0.004 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.029 0.075 -10000 0 -0.36 13 13
fibroblast growth factor receptor signaling pathway 0.029 0.074 -10000 0 -0.35 13 13
LAMA1 0.087 0.11 0.25 138 -0.29 1 139
PRNP 0.022 0.005 -10000 0 -10000 0 0
GPC1/SLIT2 -0.058 0.18 -10000 0 -0.42 94 94
SMAD2 -0.031 0.072 -10000 0 -0.32 24 24
GPC1/PrPc/Cu2+ 0.035 0.029 -10000 0 -10000 0 0
GPC1/Laminin alpha1 0.084 0.085 0.32 23 -10000 0 23
TDGF1 0.013 0.026 0.24 2 -0.29 1 3
CRIPTO/GPC1 0.037 0.037 -10000 0 -0.2 1 1
APP/GPC1 0.039 0.034 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.013 0.012 -10000 0 -10000 0 0
FLT1 0.022 0.006 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.024 0.099 -10000 0 -0.36 25 25
SERPINC1 0.014 0.031 0.24 6 -10000 0 6
FYN -0.015 0.019 -10000 0 -0.32 1 1
FGR -0.033 0.08 -10000 0 -0.35 27 27
positive regulation of MAPKKK cascade -0.019 0.11 0.29 3 -0.39 18 21
SLIT2 -0.094 0.23 -10000 0 -0.56 94 94
GPC1/NRG 0.026 0.079 -10000 0 -0.42 12 12
NRG1 0.006 0.091 -10000 0 -0.56 12 12
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.049 0.033 -10000 0 -10000 0 0
LYN -0.015 0.025 -10000 0 -0.35 2 2
mol:Spermine -0.008 0.011 -10000 0 -10000 0 0
cell growth 0.029 0.074 -10000 0 -0.35 13 13
BMP signaling pathway -0.033 0.047 -10000 0 -0.24 24 24
SRC -0.014 0.013 -10000 0 -10000 0 0
TGFBR1 0.022 0.004 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.14 0.26 0.24 2 -0.56 131 133
GPC1 0.033 0.047 0.24 24 -10000 0 24
TGFBR1 (dimer) 0.022 0.004 -10000 0 -10000 0 0
VEGFA 0.022 0.004 -10000 0 -10000 0 0
BLK -0.017 0.052 -10000 0 -0.36 9 9
HCK -0.016 0.034 -10000 0 -0.36 4 4
FGF2 0.006 0.095 -10000 0 -0.56 13 13
FGFR1 0.017 0.028 -10000 0 -0.56 1 1
VEGFR1 homodimer 0.022 0.006 -10000 0 -10000 0 0
TGFBR2 -0.011 0.13 -10000 0 -0.56 26 26
cell death 0.039 0.034 -10000 0 -10000 0 0
ATIII/GPC1 0.039 0.037 -10000 0 -10000 0 0
PLA2G2A/GPC1 -0.089 0.2 -10000 0 -0.42 131 131
LCK -0.015 0.02 -10000 0 -0.36 1 1
neuron differentiation 0.026 0.079 -10000 0 -0.41 12 12
PrPc/Cu2+ 0.016 0.004 -10000 0 -10000 0 0
APP 0.022 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) -0.011 0.13 -10000 0 -0.56 26 26
S1P1 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
VEGFR2 homodimer/VEGFA homodimer 0.004 0.097 -10000 0 -0.41 24 24
PDGFRB 0.02 0.028 -10000 0 -0.56 1 1
SPHK1 0 0.054 -10000 0 -0.73 2 2
mol:S1P -0.004 0.053 -10000 0 -0.64 2 2
S1P1/S1P/Gi -0.05 0.16 -10000 0 -0.43 60 60
GNAO1 0.017 0.034 0.23 2 -0.56 1 3
PDGFB-D/PDGFRB/PLCgamma1 -0.032 0.15 0.25 4 -0.38 60 64
PLCG1 -0.051 0.15 -10000 0 -0.4 61 61
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.028 -10000 0 -0.56 1 1
GNAI2 0.016 0.016 -10000 0 -10000 0 0
GNAI3 0.018 0.015 -10000 0 -10000 0 0
GNAI1 0.017 0.031 -10000 0 -0.57 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.025 0.075 -10000 0 -0.35 23 23
S1P1/S1P -0.019 0.082 -10000 0 -0.31 22 22
negative regulation of cAMP metabolic process -0.048 0.16 -10000 0 -0.42 60 60
MAPK3 -0.072 0.21 -10000 0 -0.56 66 66
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.005 -10000 0 -10000 0 0
KDR -0.011 0.13 -10000 0 -0.56 24 24
PLCB2 -0.01 0.093 0.28 4 -0.34 10 14
RAC1 0.022 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.013 0.073 -10000 0 -0.27 22 22
receptor internalization -0.018 0.077 -10000 0 -0.29 22 22
PTGS2 -0.1 0.33 -10000 0 -0.97 55 55
Rac1/GTP -0.013 0.073 -10000 0 -0.28 21 21
RHOA 0.021 0.007 -10000 0 -10000 0 0
VEGFA 0.019 0.013 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.048 0.16 -10000 0 -0.42 60 60
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.012 0.061 -10000 0 -0.56 5 5
MAPK1 -0.066 0.2 -10000 0 -0.54 64 64
S1P1/S1P/PDGFB-D/PDGFRB -0.01 0.095 -10000 0 -0.33 22 22
ABCC1 0.019 0.017 0.24 1 -10000 0 1
FAS signaling pathway (CD95)

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
SPTAN1 -0.008 0.022 0.24 1 -0.19 3 4
RFC1 -0.006 0.027 0.22 4 -0.19 4 8
PRKDC -0.003 0.044 0.22 14 -0.19 4 18
RIPK1 0.024 0.006 -10000 0 -10000 0 0
CASP7 -0.017 0.13 0.45 1 -0.63 18 19
FASLG/FAS/FADD/FAF1 -0.006 0.066 0.22 5 -0.29 18 23
MAP2K4 -0.022 0.15 0.3 5 -0.44 24 29
mol:ceramide -0.019 0.1 -10000 0 -0.38 21 21
GSN -0.008 0.022 0.24 1 -10000 0 1
FASLG/FAS/FADD/FAF1/Caspase 8 -0.008 0.09 -10000 0 -0.36 21 21
FAS 0.012 0.033 -10000 0 -0.58 1 1
BID -0.014 0.056 0.52 4 -10000 0 4
MAP3K1 0.008 0.14 0.34 6 -0.46 23 29
MAP3K7 0.017 0.015 -10000 0 -10000 0 0
RB1 -0.007 0.023 0.23 2 -10000 0 2
CFLAR 0.024 0.005 -10000 0 -10000 0 0
HGF/MET -0.038 0.16 0.25 1 -0.36 93 94
ARHGDIB 0 0.052 0.22 21 -0.19 4 25
FADD 0.013 0.018 -10000 0 -10000 0 0
actin filament polymerization 0.018 0.045 -10000 0 -0.24 1 1
NFKB1 -0.032 0.14 -10000 0 -0.65 15 15
MAPK8 -0.051 0.2 0.36 2 -0.44 82 84
DFFA -0.007 0.027 0.23 2 -0.19 6 8
DNA fragmentation during apoptosis -0.015 0.048 0.22 4 -10000 0 4
FAS/FADD/MET 0.025 0.044 0.26 1 -0.36 3 4
CFLAR/RIP1 0.034 0.011 -10000 0 -10000 0 0
FAIM3 0.019 0.054 0.24 1 -0.56 4 5
FAF1 0.014 0.022 -10000 0 -10000 0 0
PARP1 -0.006 0.035 0.22 6 -10000 0 6
DFFB -0.006 0.031 0.22 4 -10000 0 4
CHUK -0.029 0.12 -10000 0 -0.61 14 14
FASLG -0.009 0.12 -10000 0 -0.56 19 19
FAS/FADD 0.018 0.033 -10000 0 -0.44 1 1
HGF -0.093 0.23 -10000 0 -0.56 94 94
LMNA -0.011 0.043 0.19 9 -10000 0 9
CASP6 -0.006 0.027 0.23 3 -10000 0 3
CASP10 0.013 0.033 -10000 0 -0.56 1 1
CASP3 -0.003 0.018 0.25 2 -10000 0 2
PTPN13 0.017 0.053 -10000 0 -0.56 4 4
CASP8 -0.015 0.047 0.46 4 -10000 0 4
IL6 -0.2 0.5 -10000 0 -1.2 90 90
MET 0.02 0.041 0.38 1 -0.56 2 3
ICAD/CAD -0.008 0.032 0.25 4 -10000 0 4
FASLG/FAS/FADD/FAF1/Caspase 10 -0.02 0.1 -10000 0 -0.38 21 21
activation of caspase activity by cytochrome c -0.014 0.056 0.52 4 -10000 0 4
PAK2 0.063 0.11 0.22 149 -10000 0 149
BCL2 0.023 0.011 0.24 1 -10000 0 1
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.022 0.006 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.041 0.094 -10000 0 -0.27 23 23
NT3 (dimer)/TRKC -0.095 0.2 -10000 0 -0.41 138 138
NT3 (dimer)/TRKB 0.042 0.13 0.32 2 -0.38 30 32
SHC/Grb2/SOS1/GAB1/PI3K 0.009 0.023 -10000 0 -10000 0 0
RAPGEF1 0.023 0.004 -10000 0 -10000 0 0
BDNF -0.048 0.19 -10000 0 -0.56 58 58
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
DYNLT1 0.023 0.003 -10000 0 -10000 0 0
NTRK1 0.014 0.065 -10000 0 -0.56 6 6
NTRK2 0.023 0.17 0.24 76 -0.56 28 104
NTRK3 -0.14 0.26 0.24 2 -0.56 135 137
NT-4/5 (dimer)/TRKB 0.045 0.13 0.29 4 -0.39 32 36
neuron apoptosis 0.042 0.18 0.43 46 -10000 0 46
SHC 2-3/Grb2 -0.047 0.19 -10000 0 -0.48 46 46
SHC1 0.022 0.005 -10000 0 -10000 0 0
SHC2 0.005 0.12 -10000 0 -0.42 18 18
SHC3 -0.075 0.23 -10000 0 -0.53 85 85
STAT3 (dimer) 0.022 0.044 -10000 0 -0.36 6 6
NT3 (dimer)/TRKA 0.043 0.07 0.25 1 -0.36 9 10
RIN/GDP -0.027 0.096 0.29 6 -0.26 8 14
GIPC1 0.022 0.005 -10000 0 -10000 0 0
KRAS 0.021 0.006 -10000 0 -10000 0 0
DNAJA3 0.029 0.059 0.23 1 -0.25 5 6
RIN/GTP 0.013 0.003 -10000 0 -10000 0 0
CCND1 0.001 0.094 0.37 1 -0.82 6 7
MAGED1 0.023 0.004 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.014 0.07 -10000 0 -0.56 7 7
SHC/GRB2/SOS1 0.042 0.014 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.016 0.1 0.25 1 -0.35 31 32
TRKA/NEDD4-2 0.026 0.051 -10000 0 -0.42 6 6
ELMO1 0.012 0.075 -10000 0 -0.56 8 8
RhoG/GTP/ELMO1/DOCK1 0.022 0.051 -10000 0 -0.35 8 8
NGF 0.013 0.078 0.29 3 -0.56 8 11
HRAS 0.022 0.004 -10000 0 -10000 0 0
DOCK1 0.022 0.005 -10000 0 -10000 0 0
GAB2 0.008 0.091 -10000 0 -0.56 12 12
RIT2 -0.015 0.01 -10000 0 -10000 0 0
RIT1 0.022 0.005 -10000 0 -10000 0 0
FRS2 0.022 0.005 -10000 0 -10000 0 0
DNM1 0.023 0.014 0.24 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.036 0.068 0.22 1 -0.26 9 10
mol:GDP -0.043 0.13 0.36 6 -0.36 18 24
NGF (dimer) 0.013 0.078 0.28 3 -0.56 8 11
RhoG/GDP 0.009 0.056 -10000 0 -0.36 10 10
RIT1/GDP -0.025 0.091 0.26 5 -0.26 9 14
TIAM1 0.022 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.005 0.18 0.25 1 -0.41 73 74
KIDINS220/CRKL/C3G 0.032 0.009 -10000 0 -10000 0 0
SHC/RasGAP 0.03 0.012 -10000 0 -10000 0 0
FRS2 family/SHP2 0.043 0.013 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.051 0.021 -10000 0 -10000 0 0
RIT1/GTP 0.016 0.004 -10000 0 -10000 0 0
NT3 (dimer) 0.016 0.061 0.24 2 -0.56 5 7
RAP1/GDP -0.027 0.074 -10000 0 -0.23 8 8
KIDINS220/CRKL 0.022 0.006 -10000 0 -10000 0 0
BDNF (dimer) -0.048 0.19 -10000 0 -0.56 58 58
ubiquitin-dependent protein catabolic process 0.03 0.07 0.25 1 -0.36 14 15
Schwann cell development -0.04 0.031 -10000 0 -10000 0 0
EHD4 0.023 0.003 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.053 0.019 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.012 0.054 -10000 0 -0.25 12 12
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.097 0.21 0.23 3 -0.36 165 168
ABL1 0.023 0.003 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.015 0.094 -10000 0 -0.38 11 11
STAT3 0.022 0.044 -10000 0 -0.36 6 6
axon guidance -0.1 0.2 -10000 0 -0.34 166 166
MAPK3 -0.027 0.086 0.18 17 -0.32 30 47
MAPK1 -0.026 0.084 0.2 1 -0.32 29 30
CDC42/GDP -0.023 0.097 0.28 7 -0.26 10 17
NTF3 0.016 0.061 0.24 2 -0.56 5 7
NTF4 0.014 0.07 -10000 0 -0.56 7 7
NGF (dimer)/TRKA/FAIM 0.026 0.068 0.25 1 -0.36 12 13
PI3K 0.017 0.017 -10000 0 -10000 0 0
FRS3 0.022 0.004 -10000 0 -10000 0 0
FAIM 0.019 0.009 -10000 0 -10000 0 0
GAB1 0.022 0.006 -10000 0 -10000 0 0
RASGRF1 -0.13 0.15 -10000 0 -0.31 134 134
SOS1 0.023 0.004 -10000 0 -10000 0 0
MCF2L -0.11 0.16 0.25 1 -0.36 127 128
RGS19 0.023 0.004 -10000 0 -10000 0 0
CDC42 0.022 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.024 0.081 0.38 1 -0.44 3 4
Rac1/GDP -0.024 0.094 0.25 5 -0.25 12 17
NGF (dimer)/TRKA/GRIT 0.018 0.067 0.24 1 -0.35 14 15
neuron projection morphogenesis 0.032 0.13 -10000 0 -0.77 9 9
NGF (dimer)/TRKA/NEDD4-2 0.03 0.071 0.25 1 -0.36 14 15
MAP2K1 0 0.053 0.35 1 -10000 0 1
NGFR 0.041 0.063 0.25 40 -10000 0 40
NGF (dimer)/TRKA/GIPC/GAIP 0.012 0.051 -10000 0 -0.28 12 12
RAS family/GTP/PI3K 0.009 0.01 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.061 0.022 -10000 0 -10000 0 0
NRAS 0.022 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
PRKCI 0.013 0.011 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
MAPKKK cascade -0.027 0.14 -10000 0 -0.57 24 24
RASA1 0.021 0.006 -10000 0 -10000 0 0
TRKA/c-Abl 0.026 0.051 -10000 0 -0.42 6 6
SQSTM1 0.021 0.007 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC 0.007 0.17 0.26 1 -0.38 69 70
NGF (dimer)/TRKA/p62/Atypical PKCs 0.026 0.061 -10000 0 -0.31 9 9
MATK 0 0.11 -10000 0 -0.56 18 18
NEDD4L 0.022 0.005 -10000 0 -10000 0 0
RAS family/GDP -0.039 0.058 -10000 0 -0.2 7 7
NGF (dimer)/TRKA 0.005 0.049 0.19 1 -0.26 8 9
Rac1/GTP -0.11 0.1 -10000 0 -0.27 77 77
FRS2 family/SHP2/CRK family 0.057 0.026 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 -0.024 0.15 0.28 1 -0.52 30 31
ACTA1 -0.035 0.15 0.26 2 -0.54 29 31
NUMA1 -0.027 0.15 0.28 1 -0.52 32 33
SPTAN1 -0.038 0.15 0.3 1 -0.54 29 30
LIMK1 -0.036 0.15 0.3 1 -0.52 30 31
BIRC3 0.015 0.065 -10000 0 -0.56 6 6
BIRC2 0.022 0.004 -10000 0 -10000 0 0
BAX 0.022 0.004 -10000 0 -10000 0 0
CASP10 -0.03 0.095 -10000 0 -0.45 21 21
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.023 0.003 -10000 0 -10000 0 0
PTK2 -0.025 0.15 0.26 1 -0.53 29 30
DIABLO 0.023 0.002 -10000 0 -10000 0 0
apoptotic nuclear changes -0.037 0.14 0.29 1 -0.52 29 30
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
GSN -0.039 0.15 0.29 1 -0.54 29 30
MADD 0.023 0.004 -10000 0 -10000 0 0
TFAP2A 0.084 0.18 -10000 0 -0.7 21 21
BID -0.007 0.05 -10000 0 -0.26 17 17
MAP3K1 -0.037 0.16 -10000 0 -0.57 34 34
TRADD 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.007 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.029 0.15 0.3 1 -0.54 27 28
CASP9 0.022 0.005 -10000 0 -10000 0 0
DNA repair 0.002 0.048 0.23 6 -0.18 1 7
neuron apoptosis -0.01 0.14 -10000 0 -0.71 17 17
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.034 0.16 0.29 1 -0.59 28 29
APAF1 0.023 0.002 -10000 0 -10000 0 0
CASP6 -0.03 0.21 -10000 0 -1 18 18
TRAF2 0.022 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.037 0.14 0.33 3 -0.53 28 31
CASP7 -0.004 0.066 0.32 5 -0.25 11 16
KRT18 0.009 0.045 -10000 0 -0.62 1 1
apoptosis -0.04 0.16 0.41 1 -0.58 30 31
DFFA -0.038 0.15 0.3 1 -0.53 30 31
DFFB -0.037 0.15 0.3 1 -0.54 29 30
PARP1 -0.002 0.048 0.18 1 -0.23 6 7
actin filament polymerization 0.032 0.14 0.49 28 -0.3 7 35
TNF 0.011 0.084 0.24 1 -0.56 10 11
CYCS -0.003 0.061 0.2 4 -0.26 15 19
SATB1 -0.031 0.19 -10000 0 -0.92 19 19
SLK -0.038 0.15 0.32 1 -0.53 29 30
p15 BID/BAX 0.006 0.066 0.2 3 -0.29 11 14
CASP2 0.007 0.052 0.2 1 -0.38 2 3
JNK cascade 0.036 0.16 0.57 34 -10000 0 34
CASP3 -0.038 0.16 0.32 1 -0.56 30 31
LMNB2 -0.004 0.12 0.24 2 -0.46 20 22
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CASP4 0.021 0.027 -10000 0 -0.56 1 1
Mammalian IAPs/DIABLO 0.052 0.045 -10000 0 -0.33 6 6
negative regulation of DNA binding 0.085 0.18 -10000 0 -0.68 21 21
stress fiber formation -0.037 0.14 0.31 1 -0.52 29 30
GZMB -0.033 0.11 -10000 0 -0.52 22 22
CASP1 0.008 0.041 -10000 0 -0.58 2 2
LMNB1 -0.023 0.18 0.24 2 -0.55 35 37
APP -0.01 0.15 -10000 0 -0.73 17 17
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.004 0.002 -10000 0 -10000 0 0
VIM -0.039 0.16 0.4 1 -0.57 32 33
LMNA 0.004 0.095 0.24 2 -0.41 15 17
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.01 0.057 -10000 0 -0.3 5 5
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.037 0.15 0.3 1 -0.53 30 31
APAF-1/Caspase 9 -0.009 0.14 -10000 0 -0.64 20 20
nuclear fragmentation during apoptosis -0.026 0.15 0.27 1 -0.51 32 33
CFL2 -0.033 0.14 0.3 7 -0.51 28 35
GAS2 -0.069 0.17 -10000 0 -0.43 67 67
positive regulation of apoptosis -0.007 0.14 0.25 2 -0.54 21 23
PRF1 -0.001 0.11 -10000 0 -0.56 19 19
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.024 0.097 -10000 0 -0.35 26 26
MAP4K1 0.016 0.053 -10000 0 -0.56 4 4
MAP3K8 0.021 0.027 -10000 0 -0.56 1 1
PRKCB -0.005 0.12 -10000 0 -0.56 23 23
DBNL 0.022 0.005 -10000 0 -10000 0 0
CRKL 0.022 0.006 -10000 0 -10000 0 0
MAP3K1 0 0.082 -10000 0 -0.34 18 18
JUN -0.035 0.2 -10000 0 -0.66 41 41
MAP3K7 -0.007 0.092 -10000 0 -0.32 27 27
GRAP2 -0.006 0.12 -10000 0 -0.56 23 23
CRK 0.022 0.006 -10000 0 -10000 0 0
MAP2K4 0.002 0.098 0.24 6 -0.52 9 15
LAT 0.023 0.003 -10000 0 -10000 0 0
LCP2 0.014 0.065 -10000 0 -0.56 6 6
MAPK8 -0.034 0.21 -10000 0 -0.7 41 41
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.001 0.096 -10000 0 -0.32 31 31
LAT/GRAP2/SLP76/HPK1/HIP-55 0.031 0.094 -10000 0 -0.33 25 25
Noncanonical Wnt signaling pathway

Figure S54.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S54.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.054 0.2 -10000 0 -0.56 62 62
GNB1/GNG2 0.016 0.095 0.26 1 -0.34 9 10
mol:DAG -0.005 0.078 0.22 2 -0.32 9 11
PLCG1 -0.005 0.08 0.22 2 -0.33 9 11
YES1 -0.004 0.072 0.24 3 -0.28 18 21
FZD3 0.021 0.007 -10000 0 -10000 0 0
FZD6 0.022 0.005 -10000 0 -10000 0 0
G protein 0.012 0.092 -10000 0 -0.36 7 7
MAP3K7 -0.028 0.096 0.19 2 -0.34 25 27
mol:Ca2+ -0.004 0.077 0.22 2 -0.31 9 11
mol:IP3 -0.005 0.078 0.22 2 -0.32 9 11
NLK 0.004 0.082 -10000 0 -0.79 5 5
GNB1 0.021 0.027 -10000 0 -0.56 1 1
CAMK2A -0.021 0.1 0.2 2 -0.35 28 30
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD 0.009 0.075 0.28 1 -0.29 19 20
CSNK1A1 0.021 0.006 -10000 0 -10000 0 0
GNAS -0.004 0.072 0.22 3 -0.28 18 21
GO:0007205 -0.012 0.076 0.22 2 -0.32 9 11
WNT6 0.057 0.084 0.24 80 -0.29 1 81
WNT4 0.019 0.057 0.24 4 -0.56 4 8
NFAT1/CK1 alpha -0.016 0.14 0.28 1 -0.42 22 23
GNG2 0.016 0.06 -10000 0 -0.56 5 5
WNT5A 0.024 0.032 0.24 8 -0.29 1 9
WNT11 0.006 0.11 0.25 10 -0.56 17 27
CDC42 -0.005 0.068 0.25 2 -0.39 4 6
TCGA08_p53

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
CDKN2A -0.029 0.058 0.3 6 -0.21 18 24
TP53 -0.001 0.045 -10000 0 -0.18 23 23
Senescence -0.001 0.045 -10000 0 -0.18 23 23
Apoptosis -0.001 0.045 -10000 0 -0.18 23 23
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.003 0.074 0.32 17 -0.21 6 23
MDM4 0.022 0.004 -10000 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.023 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.016 0.021 0.16 7 -0.2 1 8
Metarhodopsin II/Arrestin 0.023 0.013 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.021 0.054 -10000 0 -0.33 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.008 0.037 0.24 7 -0.29 1 8
GRK1 -0.004 0.031 0.38 2 -10000 0 2
CNG Channel 0.027 0.08 -10000 0 -0.29 23 23
mol:Na + 0.06 0.059 -10000 0 -10000 0 0
mol:ADP -0.004 0.031 0.38 2 -10000 0 2
RGS9-1/Gbeta5/R9AP -0.009 0.14 -10000 0 -0.37 58 58
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.076 0.07 0.26 21 -10000 0 21
CNGB1 0.041 0.064 0.24 43 -10000 0 43
RDH5 0.02 0.038 -10000 0 -0.56 2 2
SAG -0.013 0.014 -10000 0 -10000 0 0
mol:Ca2+ -0.003 0.088 0.35 13 -10000 0 13
Na + (4 Units) 0.046 0.044 -10000 0 -10000 0 0
RGS9 -0.041 0.18 -10000 0 -0.56 52 52
GNB1/GNGT1 0.077 0.079 0.27 18 -0.42 1 19
GNAT1/GDP 0 0.12 -10000 0 -0.32 58 58
GUCY2D 0.02 0.009 -10000 0 -10000 0 0
GNGT1 0.094 0.11 0.26 147 -10000 0 147
GUCY2F -0.005 0.019 -10000 0 -10000 0 0
GNB5 0.023 0.003 -10000 0 -10000 0 0
mol:GMP (4 units) 0 0.071 -10000 0 -0.3 23 23
mol:11-cis-retinal 0.02 0.038 -10000 0 -0.56 2 2
mol:cGMP 0.064 0.063 0.28 3 -10000 0 3
GNB1 0.021 0.027 -10000 0 -0.56 1 1
Rhodopsin 0.027 0.032 -10000 0 -0.42 2 2
SLC24A1 0.023 0.003 -10000 0 -10000 0 0
CNGA1 0.024 0.025 0.24 6 -10000 0 6
Metarhodopsin II 0.022 0.017 0.22 2 -10000 0 2
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.074 0.064 -10000 0 -10000 0 0
RGS9BP 0.008 0.084 -10000 0 -0.56 10 10
Metarhodopsin II/Transducin 0.024 0.045 0.17 14 -0.27 1 15
GCAP Family/Ca ++ 0.065 0.06 -10000 0 -10000 0 0
PDE6A/B 0.016 0.081 -10000 0 -0.41 15 15
mol:Pi -0.009 0.14 -10000 0 -0.36 58 58
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.072 0.071 0.24 18 -0.33 1 19
PDE6B 0.017 0.054 0.24 1 -0.56 4 5
PDE6A 0.008 0.089 0.24 2 -0.56 11 13
PDE6G 0.013 0.075 -10000 0 -0.56 8 8
RHO 0 0.025 0.24 2 -10000 0 2
PDE6 -0.004 0.15 -10000 0 -0.34 68 68
GUCA1A 0.077 0.1 0.24 126 -0.29 2 128
GC2/GCAP Family 0.074 0.063 -10000 0 -10000 0 0
GUCA1C -0.016 0.006 -10000 0 -10000 0 0
GUCA1B 0.022 0.005 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.027 0.047 -10000 0 -0.37 6 6
Necdin/E2F1 0.027 0.047 -10000 0 -0.42 5 5
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.059 0.076 -10000 0 -0.32 13 13
NGF (dimer)/p75(NTR)/BEX1 0.015 0.14 0.29 5 -0.36 48 53
NT-4/5 (dimer)/p75(NTR) 0.038 0.071 0.27 2 -0.42 7 9
IKBKB 0.022 0.018 0.38 1 -10000 0 1
AKT1 0.053 0.11 0.32 6 -0.32 6 12
IKBKG 0.023 0.004 -10000 0 -10000 0 0
BDNF -0.048 0.19 -10000 0 -0.56 58 58
MGDIs/NGR/p75(NTR)/LINGO1 0.064 0.061 0.32 7 -0.36 1 8
FURIN 0.023 0.003 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0 0.15 0.25 2 -0.36 61 63
LINGO1 0.043 0.063 0.24 43 -10000 0 43
Sortilin/TRAF6/NRIF 0.021 0.033 -10000 0 -0.29 4 4
proBDNF (dimer) -0.048 0.19 -10000 0 -0.56 58 58
NTRK1 0.014 0.065 -10000 0 -0.56 6 6
RTN4R 0.021 0.029 0.24 1 -0.56 1 2
neuron apoptosis -0.046 0.15 0.3 1 -0.52 19 20
IRAK1 0.023 0.004 -10000 0 -10000 0 0
SHC1 -0.019 0.051 0.23 3 -0.37 8 11
ARHGDIA 0.022 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.015 0.005 -10000 0 -10000 0 0
Gamma Secretase 0.055 0.028 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.054 0.077 0.26 2 -0.33 13 15
MAGEH1 0.023 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.05 0.089 0.26 3 -0.35 17 20
Mammalian IAPs/DIABLO 0.052 0.045 -10000 0 -0.33 6 6
proNGF (dimer) 0.013 0.078 0.28 3 -0.56 8 11
MAGED1 0.023 0.004 -10000 0 -10000 0 0
APP 0.022 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.014 0.07 -10000 0 -0.56 7 7
ZNF274 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.017 0.051 0.2 3 -0.32 8 11
NGF 0.013 0.078 0.29 3 -0.56 8 11
cell cycle arrest -0.015 0.07 0.21 9 -0.3 13 22
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.015 0.048 -10000 0 -0.26 7 7
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.049 0.065 0.25 2 -0.36 7 9
NCSTN 0.022 0.005 -10000 0 -10000 0 0
mol:GTP 0.047 0.068 0.25 3 -0.36 8 11
PSENEN 0.021 0.007 -10000 0 -10000 0 0
mol:ceramide -0.021 0.06 0.18 9 -0.33 13 22
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.01 0.036 0.24 1 -0.22 5 6
p75(NTR)/beta APP 0.044 0.043 0.27 2 -10000 0 2
BEX1 -0.021 0.17 0.24 20 -0.56 41 61
mol:GDP -0.015 0.05 0.22 3 -0.36 8 11
NGF (dimer) 0.043 0.082 -10000 0 -0.35 16 16
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.073 0.06 0.32 7 -0.33 1 8
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
RAC1/GTP 0.041 0.06 0.22 3 -0.31 8 11
MYD88 0.021 0.007 -10000 0 -10000 0 0
CHUK 0.022 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.048 0.069 0.25 3 -0.37 8 11
RHOB 0.021 0.027 -10000 0 -0.56 1 1
RHOA 0.021 0.007 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.032 0.008 -10000 0 -10000 0 0
NT3 (dimer) 0.016 0.061 0.24 2 -0.56 5 7
TP53 -0.048 0.11 0.33 2 -0.31 61 63
PRDM4 -0.02 0.061 0.18 11 -0.33 13 24
BDNF (dimer) 0.062 0.18 0.31 14 -0.36 63 77
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
SORT1 0.016 0.06 -10000 0 -0.56 5 5
activation of caspase activity 0.053 0.073 -10000 0 -0.31 13 13
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.054 0.078 0.26 3 -0.33 13 16
RHOC 0.022 0.005 -10000 0 -10000 0 0
XIAP 0.023 0.003 -10000 0 -10000 0 0
MAPK10 -0.032 0.1 0.32 5 -0.35 15 20
DIABLO 0.023 0.002 -10000 0 -10000 0 0
SMPD2 -0.021 0.06 0.18 9 -0.33 13 22
APH1B 0.023 0.003 -10000 0 -10000 0 0
APH1A 0.022 0.006 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.044 0.08 0.25 3 -0.36 13 16
PSEN1 0.022 0.005 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.033 0.007 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.038 0.063 0.27 1 -0.42 5 6
MAPK8 -0.029 0.098 0.29 5 -0.32 14 19
MAPK9 -0.029 0.096 0.35 2 -0.33 14 16
APAF1 0.023 0.001 -10000 0 -10000 0 0
NTF3 0.016 0.061 0.24 2 -0.56 5 7
NTF4 0.014 0.07 -10000 0 -0.56 7 7
NDN 0.016 0.06 -10000 0 -0.56 5 5
RAC1/GDP 0.017 0.003 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.051 0.062 -10000 0 -0.3 9 9
p75 CTF/Sortilin/TRAF6/NRIF 0.048 0.041 -10000 0 -0.33 4 4
RhoA-B-C/GTP 0.046 0.068 0.25 3 -0.36 8 11
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.019 0.14 -10000 0 -0.32 61 61
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.013 0.14 0.26 2 -0.34 61 63
PRKACB 0.022 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.021 0.14 -10000 0 -0.41 58 58
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.015 0.065 -10000 0 -0.56 6 6
BIRC2 0.022 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.004 0.075 0.22 4 -0.32 13 17
BAD -0.031 0.1 0.3 6 -0.35 9 15
RIPK2 0.022 0.005 -10000 0 -10000 0 0
NGFR 0.041 0.063 0.25 40 -10000 0 40
CYCS -0.02 0.058 -10000 0 -0.31 12 12
ADAM17 0.022 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.056 0.068 0.26 3 -0.34 8 11
BCL2L11 -0.03 0.1 0.3 5 -0.35 9 14
BDNF (dimer)/p75(NTR) -0.011 0.16 0.27 2 -0.42 58 60
PI3K 0.03 0.065 0.26 1 -0.34 6 7
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.054 0.078 0.26 3 -0.33 13 16
NDNL2 0.023 0.003 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
PRKCI 0.013 0.011 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.037 0.075 0.27 3 -0.42 8 11
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.054 0.078 0.26 3 -0.33 13 16
TRAF6 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
PLG -0.005 0.027 0.24 3 -10000 0 3
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.03 0.12 0.21 2 -0.32 67 69
SQSTM1 0.021 0.007 -10000 0 -10000 0 0
NGFRAP1 0.023 0.003 -10000 0 -10000 0 0
CASP3 -0.031 0.1 0.27 7 -0.33 13 20
E2F1 0.022 0.005 -10000 0 -10000 0 0
CASP9 0.022 0.005 -10000 0 -10000 0 0
IKK complex 0.046 0.082 -10000 0 -0.34 8 8
NGF (dimer)/TRKA 0.019 0.078 0.27 1 -0.41 14 15
MMP7 0.02 0.092 0.24 20 -0.56 9 29
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.059 0.076 -10000 0 -0.32 13 13
MMP3 0.15 0.11 0.24 284 -0.29 3 287
APAF-1/Caspase 9 -0.035 0.05 -10000 0 -0.3 8 8
PDGFR-alpha signaling pathway

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
PDGFRA 0.01 0.06 0.36 1 -0.57 4 5
PDGF/PDGFRA/CRKL 0.021 0.043 0.25 1 -0.35 4 5
positive regulation of JUN kinase activity 0.044 0.04 -10000 0 -0.31 4 4
CRKL 0.022 0.006 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.048 0.16 0.25 1 -0.4 78 79
AP1 -0.11 0.31 0.3 1 -0.96 54 55
mol:IP3 -0.015 0.043 0.3 1 -0.44 3 4
PLCG1 -0.015 0.043 0.3 1 -0.44 3 4
PDGF/PDGFRA/alphaV Integrin 0.021 0.047 0.25 1 -0.41 4 5
RAPGEF1 0.023 0.004 -10000 0 -10000 0 0
CRK 0.022 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.015 0.043 0.3 1 -0.44 3 4
CAV3 -0.09 0.19 -10000 0 -0.56 69 69
CAV1 -0.13 0.26 -10000 0 -0.56 125 125
SHC/Grb2/SOS1 0.046 0.041 -10000 0 -0.32 4 4
PDGF/PDGFRA/Shf 0.022 0.046 0.25 1 -0.4 4 5
FOS -0.11 0.3 -10000 0 -0.94 54 54
JUN -0.022 0.025 -10000 0 -10000 0 0
oligodendrocyte development 0.021 0.047 0.25 1 -0.41 4 5
GRB2 0.022 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:DAG -0.015 0.043 0.3 1 -0.44 3 4
PDGF/PDGFRA 0.01 0.06 0.36 1 -0.57 4 5
actin cytoskeleton reorganization 0.02 0.046 0.25 1 -0.4 4 5
SRF -0.005 0.014 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
PI3K 0.017 0.037 0.24 1 -0.35 2 3
PDGF/PDGFRA/Crk/C3G 0.031 0.043 0.24 1 -0.32 4 5
JAK1 -0.012 0.04 0.28 1 -0.4 4 5
ELK1/SRF -0.011 0.051 0.17 1 -0.35 3 4
SHB 0.021 0.007 -10000 0 -10000 0 0
SHF 0.023 0.003 -10000 0 -10000 0 0
CSNK2A1 0.024 0.02 -10000 0 -10000 0 0
GO:0007205 -0.012 0.044 0.3 1 -0.46 3 4
SOS1 0.023 0.004 -10000 0 -10000 0 0
Ras protein signal transduction 0.044 0.04 -10000 0 -0.31 4 4
PDGF/PDGFRA/SHB 0.021 0.046 0.25 1 -0.4 4 5
PDGF/PDGFRA/Caveolin-1 -0.094 0.2 0.25 1 -0.42 128 129
ITGAV 0.023 0.003 -10000 0 -10000 0 0
ELK1 -0.017 0.047 0.23 2 -0.41 3 5
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.021 0.045 0.25 1 -0.39 4 5
JAK-STAT cascade -0.012 0.04 0.28 1 -0.4 4 5
cell proliferation 0.021 0.046 0.25 1 -0.4 4 5
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.02 0.027 -10000 0 -0.56 1 1
EPHB2 0.026 0.028 0.24 8 -10000 0 8
EFNB1 -0.004 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.063 0.054 0.29 1 -10000 0 1
Ephrin B2/EPHB1-2 0.052 0.057 0.24 16 -0.33 1 17
neuron projection morphogenesis 0.044 0.04 0.22 1 -10000 0 1
Ephrin B1/EPHB1-2/Tiam1 0.06 0.057 0.25 18 -10000 0 18
DNM1 0.024 0.015 0.24 2 -10000 0 2
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.02 0.1 0.24 1 -0.44 25 26
YES1 -0.023 0.16 -10000 0 -0.66 26 26
Ephrin B1/EPHB1-2/NCK2 0.06 0.058 0.25 18 -10000 0 18
PI3K -0.001 0.092 -10000 0 -0.43 16 16
mol:GDP 0.058 0.056 0.24 16 -10000 0 16
ITGA2B 0.005 0.099 -10000 0 -0.56 14 14
endothelial cell proliferation 0.027 0.02 -10000 0 -0.35 1 1
FYN -0.022 0.16 -10000 0 -0.66 26 26
MAP3K7 -0.021 0.11 0.23 1 -0.46 26 27
FGR -0.03 0.16 -10000 0 -0.68 25 25
TIAM1 0.022 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
RGS3 0.022 0.004 -10000 0 -10000 0 0
cell adhesion -0.016 0.099 -10000 0 -0.41 17 17
LYN -0.023 0.16 -10000 0 -0.66 26 26
Ephrin B1/EPHB1-2/Src Family Kinases -0.023 0.14 -10000 0 -0.6 26 26
Ephrin B1/EPHB1-2 -0.02 0.11 -10000 0 -0.51 24 24
SRC -0.02 0.15 -10000 0 -0.65 26 26
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
EPHB1 0.053 0.089 0.28 59 -10000 0 59
EPHB4 0.022 0.006 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.027 0.02 -10000 0 -0.36 1 1
alphaIIb/beta3 Integrin 0.013 0.094 -10000 0 -0.42 22 22
BLK -0.025 0.16 -10000 0 -0.67 25 25
HCK -0.022 0.15 -10000 0 -0.65 26 26
regulation of stress fiber formation -0.058 0.056 -10000 0 -0.24 18 18
MAPK8 -0.019 0.097 0.28 1 -0.42 24 25
Ephrin B1/EPHB1-2/RGS3 0.06 0.057 0.25 18 -10000 0 18
endothelial cell migration -0.01 0.099 0.39 1 -0.37 25 26
NCK2 0.023 0.002 -10000 0 -10000 0 0
PTPN13 0.016 0.064 -10000 0 -0.67 4 4
regulation of focal adhesion formation -0.058 0.056 -10000 0 -0.24 18 18
chemotaxis -0.058 0.056 -10000 0 -0.24 18 18
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.054 0.048 0.26 1 -10000 0 1
angiogenesis -0.021 0.12 -10000 0 -0.5 25 25
LCK -0.02 0.15 -10000 0 -0.67 25 25
IGF1 pathway

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
NCK2 0.023 0.002 -10000 0 -10000 0 0
PTK2 0.021 0.006 -10000 0 -10000 0 0
CRKL 0.003 0.049 -10000 0 -0.3 12 12
GRB2/SOS1/SHC 0.042 0.014 -10000 0 -10000 0 0
HRAS 0.022 0.004 -10000 0 -10000 0 0
IRS1/Crk 0.011 0.053 -10000 0 -0.29 13 13
IGF-1R heterotetramer/IGF1/PTP1B 0.033 0.063 -10000 0 -0.34 12 12
AKT1 0.057 0.095 0.22 18 -0.27 4 22
BAD 0.052 0.091 0.21 18 -0.26 4 22
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.002 0.05 -10000 0 -0.29 13 13
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.016 0.054 -10000 0 -0.3 13 13
RAF1 0.054 0.12 0.28 10 -0.43 9 19
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.042 0.058 -10000 0 -0.29 12 12
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.019 0.059 -10000 0 -0.3 15 15
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
RPS6KB1 0.059 0.097 0.22 21 -0.27 4 25
GNB2L1 0.021 0.006 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade 0.054 0.1 0.27 18 -0.34 4 22
PXN 0.023 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.018 0.044 -10000 0 -0.27 9 9
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.054 0.055 -10000 0 -0.28 9 9
IGF-1R heterotetramer 0.021 0.02 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck 0.031 0.058 -10000 0 -0.3 13 13
Crk/p130 Cas/Paxillin 0.037 0.056 -10000 0 -0.27 13 13
IGF1R 0.021 0.02 -10000 0 -10000 0 0
IGF1 0.007 0.1 0.27 1 -0.57 15 16
IRS2/Crk 0.009 0.053 -10000 0 -0.29 14 14
PI3K 0.022 0.045 -10000 0 -0.29 4 4
apoptosis -0.056 0.092 -10000 0 -0.26 14 14
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
PRKCD -0.001 0.068 -10000 0 -0.37 14 14
RAF1/14-3-3 E 0.054 0.13 0.28 12 -0.37 11 23
BAD/14-3-3 0.058 0.096 0.27 14 -10000 0 14
PRKCZ 0.056 0.096 0.17 192 -0.27 4 196
Crk/p130 Cas/Paxillin/FAK1 0.054 0.062 -10000 0 -10000 0 0
PTPN1 0.022 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.001 0.073 -10000 0 -0.39 14 14
BCAR1 0.022 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.044 0.055 -10000 0 -0.3 9 9
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.023 0.004 -10000 0 -10000 0 0
IRS1/NCK2 0.018 0.056 -10000 0 -0.3 13 13
GRB10 0.022 0.005 -10000 0 -10000 0 0
PTPN11 0.002 0.051 -10000 0 -0.3 13 13
IRS1 0.005 0.058 -10000 0 -0.32 13 13
IRS2 0.001 0.054 -10000 0 -0.3 14 14
IGF-1R heterotetramer/IGF1 0.02 0.079 -10000 0 -0.4 15 15
GRB2 0.022 0.004 -10000 0 -10000 0 0
PDPK1 0.058 0.098 0.17 191 -0.28 4 195
YWHAE 0.022 0.006 -10000 0 -10000 0 0
PRKD1 -0.012 0.095 -10000 0 -0.38 25 25
SHC1 0.022 0.005 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.017 0.15 -10000 0 -0.38 52 52
MAP3K8 0.017 0.03 -10000 0 -0.56 1 1
FOS -0.013 0.12 -10000 0 -0.5 13 13
PRKCA 0.015 0.041 -10000 0 -0.56 2 2
PTPN7 0.017 0.036 0.38 1 -0.56 1 2
HRAS 0.022 0.004 -10000 0 -10000 0 0
PRKCB -0.01 0.12 -10000 0 -0.56 23 23
NRAS 0.022 0.005 -10000 0 -10000 0 0
RAS family/GTP 0.031 0.026 -10000 0 -10000 0 0
MAPK3 0.001 0.095 -10000 0 -0.6 8 8
MAP2K1 -0.016 0.12 -10000 0 -0.45 27 27
ELK1 0.016 0.02 -10000 0 -10000 0 0
BRAF -0.012 0.1 -10000 0 -0.44 24 24
mol:GTP -0.001 0.002 -10000 0 -0.005 54 54
MAPK1 0.002 0.089 -10000 0 -0.47 9 9
RAF1 -0.015 0.11 -10000 0 -0.48 24 24
KRAS 0.021 0.006 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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 0.02 0.027 -10000 0 -0.56 1 1
Jak2/Leptin Receptor -0.018 0.15 -10000 0 -0.44 37 37
PTP1B/AKT1 0.001 0.086 0.24 1 -0.32 20 21
FYN 0.022 0.027 -10000 0 -0.56 1 1
p210 bcr-abl/PTP1B -0.01 0.09 0.21 3 -0.32 24 27
EGFR 0.02 0.085 0.36 11 -0.57 6 17
EGF/EGFR 0.004 0.1 0.24 9 -0.33 28 37
CSF1 0.017 0.053 -10000 0 -0.56 4 4
AKT1 0.022 0.007 -10000 0 -10000 0 0
INSR 0.022 0.006 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.005 0.096 0.23 8 -0.32 21 29
Insulin Receptor/Insulin 0.014 0.086 -10000 0 -0.33 12 12
HCK 0.017 0.053 -10000 0 -0.56 4 4
CRK 0.022 0.006 -10000 0 -10000 0 0
TYK2 -0.011 0.085 0.2 4 -0.32 20 24
EGF 0.015 0.074 0.24 3 -0.57 7 10
YES1 0.022 0.006 -10000 0 -10000 0 0
CAV1 -0.048 0.14 0.22 5 -0.41 34 39
TXN 0.023 0.005 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 0.012 0.09 0.24 1 -0.34 14 15
cell migration 0.01 0.09 0.32 24 -0.21 3 27
STAT3 0.023 0.004 -10000 0 -10000 0 0
PRLR 0.018 0.1 0.3 20 -0.56 10 30
ITGA2B 0.005 0.099 -10000 0 -0.56 14 14
CSF1R 0.014 0.065 -10000 0 -0.56 6 6
Prolactin Receptor/Prolactin 0.025 0.079 0.29 7 -0.42 10 17
FGR -0.011 0.14 -10000 0 -0.56 27 27
PTP1B/p130 Cas 0.003 0.087 0.24 1 -0.32 19 20
Crk/p130 Cas 0.012 0.089 0.24 1 -0.31 17 18
DOK1 -0.01 0.1 0.32 1 -0.34 30 31
JAK2 -0.015 0.14 0.29 2 -0.44 40 42
Jak2/Leptin Receptor/Leptin 0.03 0.12 0.28 1 -0.39 15 16
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
PTPN1 -0.01 0.091 0.21 3 -0.32 24 27
LYN 0.02 0.038 -10000 0 -0.56 2 2
CDH2 0.034 0.061 0.25 27 -0.56 1 28
SRC 0.012 0.08 -10000 0 -0.63 6 6
ITGB3 0.013 0.075 -10000 0 -0.56 8 8
CAT1/PTP1B -0.02 0.15 0.31 4 -0.43 37 41
CAPN1 0.023 0.003 -10000 0 -10000 0 0
CSK 0.023 0.002 -10000 0 -10000 0 0
PI3K 0.01 0.066 -10000 0 -0.34 5 5
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.029 0.11 0.26 1 -0.37 13 14
negative regulation of transcription -0.015 0.14 0.29 2 -0.43 40 42
FCGR2A 0.011 0.079 -10000 0 -0.56 9 9
FER 0.021 0.007 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.012 0.095 -10000 0 -0.42 22 22
BLK 0.014 0.087 0.24 12 -0.56 9 21
Insulin Receptor/Insulin/Shc 0.039 0.013 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
LEPR -0.01 0.13 -10000 0 -0.56 27 27
BCAR1 0.022 0.005 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.022 0.004 -10000 0 -10000 0 0
mol:NADPH 0 0.002 -10000 0 -10000 0 0
TRPV6 -0.017 0.14 0.28 2 -0.43 32 34
PRL 0.005 0.036 0.24 8 -10000 0 8
SOCS3 0.015 0.11 -10000 0 -1.2 4 4
SPRY2 0.018 0.047 -10000 0 -0.57 3 3
Insulin Receptor/Insulin/IRS1 0.04 0.012 -10000 0 -10000 0 0
CSF1/CSF1R 0.006 0.1 0.24 1 -0.36 21 22
Ras protein signal transduction 0.011 0.1 0.59 13 -10000 0 13
IRS1 0.022 0.004 -10000 0 -10000 0 0
INS 0.011 0.015 -10000 0 -10000 0 0
LEP 0.057 0.085 0.24 83 -0.29 1 84
STAT5B -0.008 0.12 0.32 1 -0.36 30 31
STAT5A -0.008 0.12 0.32 1 -0.36 30 31
GRB2 0.022 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.087 0.24 1 -0.32 19 20
CSN2 0.018 0.069 0.49 1 -10000 0 1
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
LAT 0.002 0.1 -10000 0 -0.52 15 15
YBX1 0.026 0.005 -10000 0 -10000 0 0
LCK 0.021 0.027 -10000 0 -0.56 1 1
SHC1 0.022 0.005 -10000 0 -10000 0 0
NOX4 0.023 0.017 0.38 1 -10000 0 1
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.031 0.24 2 -0.56 1 3
CDC42/GTP -0.008 0.097 -10000 0 -0.29 33 33
PLCG1 -0.014 0.086 -10000 0 -0.3 30 30
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
G12/G13 0.032 0.008 -10000 0 -10000 0 0
cell migration -0.008 0.095 -10000 0 -0.28 33 33
S1PR5 0.024 0.036 0.24 6 -0.56 1 7
S1PR4 -0.023 0.16 -10000 0 -0.56 37 37
MAPK3 -0.012 0.084 -10000 0 -0.29 29 29
MAPK1 -0.011 0.08 -10000 0 -0.3 26 26
S1P/S1P5/Gi 0.017 0.037 -10000 0 -0.26 1 1
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
CDC42/GDP 0.016 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.03 0.024 -10000 0 -0.35 1 1
RHOA -0.028 0.086 0.19 15 -0.3 35 50
S1P/S1P4/Gi -0.006 0.089 -10000 0 -0.3 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.016 0.06 -10000 0 -0.56 5 5
S1P/S1P4/G12/G13 0.012 0.098 -10000 0 -0.32 35 35
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
CDC42 0.022 0.005 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.007 0.061 -10000 0 -0.32 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.009 0.071 0.31 3 -0.34 1 4
alphaV/beta3 Integrin/Osteopontin/Src 0.11 0.084 0.27 1 -0.19 5 6
AP1 0.005 0.12 -10000 0 -0.5 3 3
ILK -0.015 0.06 -10000 0 -0.34 8 8
bone resorption -0.014 0.059 -10000 0 -0.31 4 4
PTK2B 0.021 0.007 -10000 0 -10000 0 0
PYK2/p130Cas 0.1 0.095 0.29 2 -0.31 8 10
ITGAV 0.025 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.031 0.022 -10000 0 -0.42 1 1
alphaV/beta3 Integrin/Osteopontin 0.11 0.099 0.26 1 -0.37 8 9
MAP3K1 -0.016 0.059 0.21 1 -0.34 8 9
JUN 0.022 0.005 -10000 0 -10000 0 0
MAPK3 -0.016 0.057 0.38 1 -0.32 8 9
MAPK1 -0.015 0.057 0.38 1 -0.32 8 9
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.023 0.056 0.22 6 -0.33 8 14
ITGB3 0.015 0.075 -10000 0 -0.56 8 8
NFKBIA -0.009 0.052 0.35 1 -0.32 7 8
FOS -0.043 0.18 -10000 0 -0.56 53 53
CD44 0.021 0.027 -10000 0 -0.56 1 1
CHUK 0.022 0.005 -10000 0 -10000 0 0
PLAU 0.002 0.071 0.48 1 -10000 0 1
NF kappa B1 p50/RelA 0.009 0.075 -10000 0 -10000 0 0
BCAR1 0.022 0.005 -10000 0 -10000 0 0
RELA 0.023 0.001 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.03 0.058 -10000 0 -0.41 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.017 0.059 -10000 0 -0.34 8 8
VAV3 -0.024 0.062 0.24 7 -0.35 8 15
MAP3K14 -0.013 0.06 -10000 0 -0.34 8 8
ROCK2 0.022 0.004 -10000 0 -10000 0 0
SPP1 0.13 0.12 0.24 246 -0.28 6 252
RAC1 0.022 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.016 0.058 -10000 0 -0.33 8 8
MMP2 -0.046 0.1 0.31 1 -0.63 4 5
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.022 0.034 -10000 0 -10000 0 0
BIRC5 0.21 0.085 0.24 405 -0.29 1 406
NFKBIA -0.023 0.026 0.24 1 -10000 0 1
CPEB1 -0.014 0.14 -10000 0 -0.56 29 29
AKT1 -0.023 0.024 -10000 0 -10000 0 0
NDEL1 0.022 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.02 0.03 -10000 0 -10000 0 0
NDEL1/TACC3 -0.009 0.041 -10000 0 -10000 0 0
GADD45A 0.022 0.004 -10000 0 -10000 0 0
GSK3B -0.02 0.02 -10000 0 -10000 0 0
PAK1/Aurora A -0.021 0.036 0.31 1 -10000 0 1
MDM2 0.023 0.017 0.38 1 -10000 0 1
JUB 0 0 -10000 0 -10000 0 0
TPX2 -0.022 0.089 0.31 31 -10000 0 31
TP53 -0.01 0.045 0.22 1 -0.24 1 2
DLG7 -0.022 0.023 -10000 0 -10000 0 0
AURKAIP1 0.022 0.005 -10000 0 -10000 0 0
ARHGEF7 0.022 0.006 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.01 0.044 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.02 0.03 -10000 0 -10000 0 0
AURKA -0.025 0.031 0.2 2 -10000 0 2
AURKB 0.08 0.061 0.14 52 -0.17 5 57
CDC25B -0.012 0.024 -10000 0 -0.3 1 1
G2/M transition checkpoint -0.021 0.023 -10000 0 -10000 0 0
mRNA polyadenylation -0.039 0.081 -10000 0 -0.33 29 29
Aurora A/CPEB -0.039 0.082 -10000 0 -0.34 29 29
Aurora A/TACC1/TRAP/chTOG -0.006 0.048 -10000 0 -0.3 1 1
BRCA1 0.023 0.003 -10000 0 -10000 0 0
centrosome duplication -0.021 0.036 0.31 1 -10000 0 1
regulation of centrosome cycle -0.009 0.041 -10000 0 -10000 0 0
spindle assembly -0.007 0.047 -10000 0 -0.29 1 1
TDRD7 0.022 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.083 0.27 7 -10000 0 7
CENPA 0.1 0.052 0.18 52 -10000 0 52
Aurora A/PP2A -0.022 0.034 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.012 0.032 0.24 1 -10000 0 1
negative regulation of DNA binding -0.01 0.045 0.22 1 -0.24 1 2
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.032 0.009 -10000 0 -10000 0 0
RASA1 0.021 0.006 -10000 0 -10000 0 0
Ajuba/Aurora A -0.021 0.024 -10000 0 -10000 0 0
mitotic prometaphase -0.02 0.03 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.025 0.031 0.2 2 -10000 0 2
TACC1 0.018 0.028 -10000 0 -0.56 1 1
TACC3 0.022 0.02 0.31 2 -10000 0 2
Aurora A/Antizyme1 -0.012 0.044 -10000 0 -10000 0 0
Aurora A/RasGAP -0.019 0.03 -10000 0 -10000 0 0
OAZ1 0.022 0.004 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.022 0.019 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.043 0.017 0.25 1 -10000 0 1
Importin alpha/Importin beta/TPX2 -0.022 0.089 0.3 31 -10000 0 31
PPP2R5D 0.022 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 -0.018 0.083 0.21 29 -10000 0 29
PAK1 0.023 0.017 0.38 1 -10000 0 1
CKAP5 0.022 0.004 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.005 0.005 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B -0.012 0.13 -10000 0 -0.4 46 46
STXBP1 0.019 0.046 -10000 0 -0.56 3 3
ACh/CHRNA1 0.014 0.053 0.19 8 -0.29 8 16
RAB3GAP2/RIMS1/UNC13B 0.003 0.12 -10000 0 -0.36 41 41
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 -0.036 0.17 0.24 1 -0.56 45 46
mol:ACh 0 0.032 0.095 10 -0.15 10 20
RAB3GAP2 0.022 0.004 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0 0.098 -10000 0 -0.28 41 41
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.014 0.053 0.19 8 -0.29 8 16
UNC13B 0.018 0.038 -10000 0 -0.56 2 2
CHRNA1 0.02 0.067 0.24 9 -0.56 5 14
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.021 0.041 0.18 16 -0.15 3 19
SNAP25 -0.002 0.042 -10000 0 -0.3 9 9
VAMP2 0.003 0.001 -10000 0 -10000 0 0
SYT1 0.031 0.041 0.25 16 -10000 0 16
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.018 0.03 -10000 0 -0.36 3 3
STX1A/SNAP25 fragment 1/VAMP2 0 0.098 -10000 0 -0.28 41 41
BCR 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
JUN -0.01 0.11 0.54 1 -0.41 19 20
IKBKB 0.027 0.078 0.3 5 -0.31 4 9
AKT1 0.048 0.11 0.24 62 -0.24 9 71
IKBKG 0.024 0.068 0.26 3 -0.29 5 8
CALM1 -0.006 0.094 0.26 1 -0.41 14 15
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
MAP3K1 -0.005 0.14 0.51 1 -0.57 17 18
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.096 0.28 1 -0.42 15 16
DOK1 0.022 0.004 -10000 0 -10000 0 0
AP-1 -0.017 0.078 -10000 0 -0.26 11 11
LYN 0.019 0.038 -10000 0 -0.56 2 2
BLNK 0.021 0.027 -10000 0 -0.56 1 1
SHC1 0.022 0.005 -10000 0 -10000 0 0
BCR complex 0.022 0.087 0.34 1 -0.44 14 15
CD22 -0.039 0.16 0.26 1 -0.62 25 26
CAMK2G -0.006 0.09 0.31 2 -0.38 14 16
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
SHC/GRB2/SOS1 0.015 0.06 -10000 0 -0.34 8 8
GO:0007205 -0.006 0.1 0.28 1 -0.43 16 17
SYK 0.022 0.004 -10000 0 -10000 0 0
ELK1 -0.009 0.098 0.26 1 -0.42 15 16
NFATC1 -0.015 0.1 0.38 2 -0.48 13 15
B-cell antigen/BCR complex 0.022 0.087 0.34 1 -0.44 14 15
PAG1/CSK 0.028 0.046 -10000 0 -0.42 5 5
NFKBIB 0.022 0.043 0.16 4 -0.12 17 21
HRAS -0.007 0.091 0.25 1 -0.4 12 13
NFKBIA 0.022 0.042 0.16 4 -0.12 19 23
NF-kappa-B/RelA/I kappa B beta 0.026 0.037 0.17 3 -10000 0 3
RasGAP/Csk 0.046 0.085 0.31 1 -0.36 16 17
mol:GDP -0.009 0.1 0.27 1 -0.42 17 18
PTEN 0.021 0.006 -10000 0 -10000 0 0
CD79B 0.019 0.047 0.24 1 -0.56 3 4
NF-kappa-B/RelA/I kappa B alpha 0.026 0.037 0.17 3 -10000 0 3
GRB2 0.022 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.008 0.14 0.33 1 -0.55 18 19
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:IP3 -0.005 0.095 0.28 1 -0.42 15 16
CSK 0.023 0.002 -10000 0 -10000 0 0
FOS -0.037 0.12 0.33 2 -0.42 18 20
CHUK 0.014 0.087 0.28 2 -0.3 14 16
IBTK 0.023 0.003 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.014 0.094 -10000 0 -0.46 7 7
PTPN6 -0.038 0.15 0.25 1 -0.6 23 24
RELA 0.023 0.002 -10000 0 -10000 0 0
BCL2A1 0.017 0.032 0.16 3 -0.12 2 5
VAV2 -0.014 0.13 -10000 0 -0.67 12 12
ubiquitin-dependent protein catabolic process 0.024 0.043 0.16 4 -0.12 18 22
BTK -0.088 0.32 -10000 0 -1.1 46 46
CD19 -0.019 0.12 0.26 2 -0.64 12 14
MAP4K1 0.016 0.053 -10000 0 -0.56 4 4
CD72 0.021 0.012 0.24 1 -10000 0 1
PAG1 0.016 0.06 -10000 0 -0.56 5 5
MAPK14 -0.003 0.12 0.66 1 -0.48 16 17
SH3BP5 0.015 0.06 -10000 0 -0.56 5 5
PIK3AP1 -0.004 0.11 0.3 1 -0.55 13 14
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.01 0.15 -10000 0 -0.61 19 19
RAF1 -0.008 0.083 0.23 1 -0.38 10 11
RasGAP/p62DOK/SHIP 0.045 0.084 -10000 0 -0.36 15 15
CD79A 0.012 0.1 0.24 13 -0.56 13 26
re-entry into mitotic cell cycle -0.017 0.078 -10000 0 -0.25 12 12
RASA1 0.021 0.006 -10000 0 -10000 0 0
MAPK3 -0.009 0.073 0.25 1 -0.37 5 6
MAPK1 -0.003 0.079 0.26 5 -0.38 4 9
CD72/SHP1 -0.006 0.15 0.33 2 -0.55 22 24
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.003 0.12 0.49 1 -0.48 16 17
actin cytoskeleton organization -0.009 0.11 0.29 1 -0.58 11 12
NF-kappa-B/RelA 0.053 0.073 0.31 3 -0.2 2 5
Calcineurin 0.016 0.09 -10000 0 -0.43 7 7
PI3K -0.017 0.092 -10000 0 -0.42 16 16
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.003 0.092 0.32 1 -0.42 14 15
SOS1 0.023 0.004 -10000 0 -10000 0 0
Bam32/HPK1 -0.012 0.19 -10000 0 -0.7 26 26
DAPP1 -0.029 0.2 -10000 0 -0.79 25 25
cytokine secretion -0.013 0.099 0.37 2 -0.44 13 15
mol:DAG -0.005 0.095 0.28 1 -0.42 15 16
PLCG2 0.022 0.005 -10000 0 -10000 0 0
MAP2K1 -0.009 0.079 0.26 1 -0.37 8 9
B-cell antigen/BCR complex/FcgammaRIIB 0.029 0.09 0.32 1 -0.41 16 17
mol:PI-3-4-5-P3 0.002 0.084 0.24 1 -0.34 9 10
ETS1 -0.013 0.096 0.29 2 -0.39 16 18
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.047 0.083 0.31 1 -0.35 15 16
B-cell antigen/BCR complex/LYN -0.011 0.13 0.28 2 -0.59 15 17
MALT1 0.022 0.005 -10000 0 -10000 0 0
TRAF6 0.022 0.004 -10000 0 -10000 0 0
RAC1 -0.011 0.12 -10000 0 -0.63 11 11
B-cell antigen/BCR complex/LYN/SYK 0.012 0.16 0.34 2 -0.55 23 25
CARD11 -0.007 0.1 0.26 2 -0.43 15 17
FCGR2B 0.014 0.065 -10000 0 -0.56 6 6
PPP3CA 0.022 0.005 -10000 0 -10000 0 0
BCL10 0.022 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.049 0.16 22 -0.12 3 25
PTPRC -0.013 0.14 -10000 0 -0.56 29 29
PDPK1 0.03 0.093 0.22 50 -0.24 7 57
PPP3CB 0.022 0.005 -10000 0 -10000 0 0
PPP3CC 0.02 0.007 -10000 0 -10000 0 0
POU2F2 0.02 0.026 0.16 2 -10000 0 2
EGFR-dependent Endothelin signaling events

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.022 0.004 -10000 0 -10000 0 0
EGFR 0.022 0.084 0.37 11 -0.56 6 17
EGF/EGFR 0.004 0.12 -10000 0 -0.33 46 46
EGF/EGFR dimer/SHC/GRB2/SOS1 0.049 0.073 -10000 0 -0.34 12 12
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.018 0.046 -10000 0 -0.56 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.015 0.072 0.24 3 -0.56 7 10
EGF/EGFR dimer/SHC 0.033 0.076 0.25 7 -0.38 12 19
mol:GDP 0.044 0.071 -10000 0 -0.33 12 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.025 0.16 -10000 0 -0.56 39 39
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.029 0.061 -10000 0 -0.31 12 12
SHC1 0.022 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.042 0.067 -10000 0 -0.32 12 12
FRAP1 -0.018 0.054 0.16 7 -0.32 12 19
EGF/EGFR dimer 0.024 0.083 0.27 8 -0.44 12 20
SOS1 0.023 0.004 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.009 0.13 -10000 0 -0.42 42 42
HIF-2-alpha transcription factor network

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
MMP14 0.017 0.12 -10000 0 -0.69 13 13
oxygen homeostasis 0.002 0.009 -10000 0 -10000 0 0
TCEB2 0.022 0.004 -10000 0 -10000 0 0
TCEB1 0.022 0.005 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.012 0.13 0.29 6 -0.35 15 21
EPO 0.035 0.16 0.43 2 -0.47 5 7
FIH (dimer) 0.019 0.019 -10000 0 -10000 0 0
APEX1 0.023 0.023 -10000 0 -10000 0 0
SERPINE1 0.022 0.17 0.4 3 -0.5 5 8
FLT1 -0.033 0.23 -10000 0 -0.8 30 30
ADORA2A 0.008 0.16 0.38 4 -0.48 7 11
germ cell development 0.023 0.17 0.4 3 -0.5 8 11
SLC11A2 0.023 0.17 0.4 2 -0.5 6 8
BHLHE40 0.021 0.17 0.42 2 -0.49 6 8
HIF1AN 0.019 0.019 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.027 0.15 0.34 4 -0.4 11 15
ETS1 0.011 0.089 -10000 0 -0.57 10 10
CITED2 0.006 0.17 -10000 0 -1 11 11
KDR -0.066 0.32 -10000 0 -1 45 45
PGK1 0.023 0.17 0.4 3 -0.5 6 9
SIRT1 0.022 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT 0.078 0.22 0.49 3 -0.54 10 13
EPAS1 -0.017 0.12 0.26 7 -0.36 26 33
SP1 0.026 0.003 -10000 0 -10000 0 0
ABCG2 -0.018 0.25 0.42 2 -0.62 54 56
EFNA1 0.019 0.17 0.41 1 -0.5 6 7
FXN 0.008 0.16 0.36 4 -0.47 8 12
POU5F1 0.022 0.17 0.4 3 -0.51 8 11
neuron apoptosis -0.075 0.22 0.52 10 -0.48 3 13
EP300 0.022 0.004 -10000 0 -10000 0 0
EGLN3 0.053 0.082 0.24 70 -10000 0 70
EGLN2 0.018 0.02 -10000 0 -10000 0 0
EGLN1 0.02 0.019 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.041 0.016 -10000 0 -10000 0 0
VHL 0.021 0.007 -10000 0 -10000 0 0
ARNT 0.024 0.023 -10000 0 -10000 0 0
SLC2A1 0.023 0.18 0.38 9 -0.47 9 18
TWIST1 0.019 0.17 0.4 9 -0.5 5 14
ELK1 0.024 0.014 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.029 0.15 0.37 2 -0.4 10 12
VEGFA 0.022 0.17 0.4 2 -0.5 6 8
CREBBP 0.022 0.005 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.018 0.007 -10000 0 -10000 0 0
epithelial cell differentiation 0.044 0.016 -10000 0 -10000 0 0
CYFIP2 0.009 0.084 -10000 0 -0.56 10 10
ENAH 0.008 0.068 0.25 12 -10000 0 12
EGFR 0.022 0.084 0.37 11 -0.56 6 17
EPHA2 0.018 0.046 -10000 0 -0.56 3 3
MYO6 -0.008 0.025 -10000 0 -10000 0 0
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.033 0.057 -10000 0 -0.36 8 8
AQP5 -0.14 0.23 -10000 0 -0.48 140 140
CTNND1 0.023 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.009 0.023 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.086 0.13 -10000 0 -0.29 129 129
EGF 0.015 0.072 0.24 3 -0.56 7 10
NCKAP1 0.023 0.003 -10000 0 -10000 0 0
AQP3 -0.061 0.17 -10000 0 -0.48 65 65
cortical microtubule organization 0.044 0.016 -10000 0 -10000 0 0
GO:0000145 -0.009 0.022 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.049 0.018 -10000 0 -10000 0 0
MLLT4 0.023 0.003 -10000 0 -10000 0 0
ARF6/GDP -0.019 0.023 -10000 0 -0.28 3 3
ARF6 0.022 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.043 0.039 -10000 0 -0.33 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.001 0.009 -10000 0 -10000 0 0
PVRL2 0.022 0.004 -10000 0 -10000 0 0
ZYX -0.009 0.024 -10000 0 -10000 0 0
ARF6/GTP 0.046 0.041 -10000 0 -0.31 3 3
CDH1 0.022 0.005 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.031 0.062 -10000 0 -0.32 12 12
RhoA/GDP 0.045 0.017 -10000 0 -10000 0 0
actin cytoskeleton organization -0.011 0.021 -10000 0 -10000 0 0
IGF-1R heterotetramer 0.022 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
IGF1R 0.022 0.004 -10000 0 -10000 0 0
IGF1 0.005 0.1 0.24 1 -0.56 15 16
DIAPH1 -0.016 0.17 -10000 0 -0.57 21 21
Wnt receptor signaling pathway -0.044 0.016 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.019 0.023 -10000 0 -0.28 3 3
CTNNA1 0.021 0.006 -10000 0 -10000 0 0
VCL -0.011 0.021 -10000 0 -10000 0 0
EFNA1 0.022 0.005 -10000 0 -10000 0 0
LPP -0.008 0.015 -10000 0 -10000 0 0
Ephrin A1/EPHA2 0.036 0.031 -10000 0 -0.3 3 3
SEC6/SEC8 -0.016 0.01 -10000 0 -10000 0 0
MGAT3 -0.087 0.13 -10000 0 -0.3 129 129
HGF/MET -0.025 0.13 -10000 0 -0.29 93 93
HGF -0.093 0.23 -10000 0 -0.56 94 94
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.018 0.007 -10000 0 -10000 0 0
actin cable formation 0.046 0.1 0.32 25 -10000 0 25
KIAA1543 -0.01 0.02 -10000 0 -10000 0 0
KIFC3 -0.01 0.024 -10000 0 -10000 0 0
NCK1 0.019 0.008 -10000 0 -10000 0 0
EXOC3 0.018 0.009 -10000 0 -10000 0 0
ACTN1 -0.009 0.025 -10000 0 -10000 0 0
NCK1/GIT1 0.028 0.013 -10000 0 -10000 0 0
mol:GDP 0.044 0.016 -10000 0 -10000 0 0
EXOC4 0.023 0.004 -10000 0 -10000 0 0
STX4 -0.009 0.025 -10000 0 -10000 0 0
PIP5K1C -0.009 0.023 -10000 0 -10000 0 0
LIMA1 0.023 0.002 -10000 0 -10000 0 0
ABI1 0.022 0.004 -10000 0 -10000 0 0
ROCK1 0.017 0.086 0.3 19 -10000 0 19
adherens junction assembly -0.013 0.093 0.3 2 -0.71 6 8
IGF-1R heterotetramer/IGF1 0.03 0.057 -10000 0 -0.29 13 13
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.032 0.008 -10000 0 -10000 0 0
MET 0.02 0.041 0.38 1 -0.56 2 3
PLEKHA7 -0.01 0.022 -10000 0 -10000 0 0
mol:GTP 0.041 0.038 -10000 0 -0.33 3 3
establishment of epithelial cell apical/basal polarity 0.022 0.083 0.34 7 -10000 0 7
cortical actin cytoskeleton stabilization 0.018 0.007 -10000 0 -10000 0 0
regulation of cell-cell adhesion -0.011 0.021 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.018 0.007 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.022 0.004 -10000 0 -10000 0 0
SPHK1 0.022 0.004 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
mol:S1P 0.011 0.003 -10000 0 -10000 0 0
GNAO1 0.021 0.031 0.24 2 -0.56 1 3
mol:Sphinganine-1-P -0.01 0.002 -10000 0 -10000 0 0
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.043 0.032 -10000 0 -10000 0 0
GNAI3 0.022 0.005 -10000 0 -10000 0 0
G12/G13 0.032 0.008 -10000 0 -10000 0 0
S1PR3 0.022 0.004 -10000 0 -10000 0 0
S1PR2 0.022 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.003 0.024 -10000 0 -0.2 3 3
S1PR5 0.024 0.036 0.24 6 -0.56 1 7
S1PR4 -0.023 0.16 -10000 0 -0.56 37 37
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
S1P/S1P5/G12 0.033 0.037 -10000 0 -0.23 3 3
S1P/S1P3/Gq -0.049 0.13 -10000 0 -0.28 109 109
S1P/S1P4/Gi -0.004 0.092 -10000 0 -0.31 28 28
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
GNAZ 0.016 0.06 -10000 0 -0.56 5 5
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
GNA15 0.022 0.004 -10000 0 -10000 0 0
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
GNA11 0.022 0.004 -10000 0 -10000 0 0
ABCC1 0.023 0.01 0.24 1 -10000 0 1
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.024 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.033 0.048 0.25 1 -0.36 6 7
forebrain development -0.1 0.16 -10000 0 -0.57 17 17
GNAO1 0.015 0.033 0.24 2 -0.57 1 3
SMO/beta Arrestin2 0.007 0.03 0.24 1 -10000 0 1
SMO 0.004 0.032 0.37 2 -10000 0 2
ARRB2 0.005 0.019 -10000 0 -10000 0 0
GLI3/SPOP 0.024 0.095 -10000 0 -0.41 9 9
mol:GTP -0.003 0.004 -10000 0 -10000 0 0
GSK3B 0.02 0.007 -10000 0 -10000 0 0
GNAI2 0.014 0.013 -10000 0 -10000 0 0
SIN3/HDAC complex 0.055 0.022 -10000 0 -10000 0 0
GNAI1 0.015 0.029 -10000 0 -0.57 1 1
XPO1 -0.001 0.024 -10000 0 -10000 0 0
GLI1/Su(fu) -0.1 0.16 -10000 0 -0.59 18 18
SAP30 0.022 0.007 -10000 0 -10000 0 0
mol:GDP 0.004 0.032 0.37 2 -10000 0 2
MIM/GLI2A -0.042 0.069 -10000 0 -10000 0 0
IFT88 0.022 0.006 -10000 0 -10000 0 0
GNAI3 0.016 0.012 -10000 0 -10000 0 0
GLI2 0.016 0.076 0.28 1 -0.38 7 8
GLI3 0.013 0.098 0.34 1 -0.43 10 11
CSNK1D 0.022 0.004 -10000 0 -10000 0 0
CSNK1E 0.022 0.004 -10000 0 -10000 0 0
SAP18 0.023 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.022 0.006 -10000 0 -10000 0 0
GNG2 0.016 0.06 -10000 0 -0.56 5 5
Gi family/GTP -0.01 0.052 -10000 0 -0.28 6 6
SIN3B 0.023 0.005 -10000 0 -10000 0 0
SIN3A 0.024 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) 0.011 0.11 0.32 1 -0.45 15 16
GLI2/Su(fu) 0.01 0.092 0.24 1 -0.41 12 13
FOXA2 -0.53 0.56 -10000 0 -1.1 242 242
neural tube patterning -0.1 0.16 -10000 0 -0.57 17 17
SPOP 0.023 0.003 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.007 0.046 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
CSNK1G2 0.022 0.004 -10000 0 -10000 0 0
CSNK1G3 0.021 0.006 -10000 0 -10000 0 0
MTSS1 -0.042 0.069 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.1 0.16 -10000 0 -0.57 17 17
SUFU 0.004 0.016 -10000 0 -10000 0 0
LGALS3 0.022 0.005 -10000 0 -10000 0 0
catabolic process 0.025 0.13 -10000 0 -0.49 16 16
GLI3A/CBP 0.005 0.03 -10000 0 -0.36 1 1
KIF3A 0.021 0.006 -10000 0 -10000 0 0
GLI1 -0.11 0.16 -10000 0 -0.6 16 16
RAB23 0.023 0.004 -10000 0 -10000 0 0
CSNK1A1 0.021 0.006 -10000 0 -10000 0 0
IFT172 0.023 0.004 -10000 0 -10000 0 0
RBBP7 0.023 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.01 0.041 -10000 0 -10000 0 0
GNAZ 0.01 0.06 -10000 0 -0.56 5 5
RBBP4 0.023 0.004 -10000 0 -10000 0 0
CSNK1G1 0.023 0.003 -10000 0 -10000 0 0
PIAS1 0.023 0.003 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0.022 0.083 -10000 0 -0.36 12 12
STK36 -0.001 0.025 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.011 0.067 -10000 0 -0.35 11 11
PTCH1 -0.1 0.17 -10000 0 -0.78 12 12
MIM/GLI1 -0.22 0.28 -10000 0 -0.51 213 213
CREBBP 0.005 0.03 -10000 0 -0.36 1 1
Su(fu)/SIN3/HDAC complex 0.007 0.088 -10000 0 -0.36 19 19
mTOR 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.022 0.004 -10000 0 -10000 0 0
mol:PIP3 -0.006 0.019 -10000 0 -10000 0 0
FRAP1 0.047 0.056 0.27 1 -0.43 1 2
AKT1 0.054 0.079 0.18 19 -10000 0 19
INSR 0.022 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0.079 0.076 0.26 19 -10000 0 19
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit 0.006 0.013 -10000 0 -10000 0 0
TSC2 0.022 0.004 -10000 0 -10000 0 0
RHEB/GDP 0.008 0.018 -10000 0 -10000 0 0
TSC1 0.023 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.019 0.034 -10000 0 -0.18 11 11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.014 0.023 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.022 0.004 -10000 0 -10000 0 0
RPS6KB1 0.073 0.077 0.25 24 -0.3 1 25
MAP3K5 0.001 0.027 0.19 3 -0.18 7 10
PIK3R1 0.022 0.007 -10000 0 -10000 0 0
apoptosis 0.001 0.027 0.19 3 -0.18 7 10
mol:LY294002 0 0 -10000 0 -0.001 13 13
EIF4B 0.068 0.074 0.24 25 -0.27 1 26
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.071 0.064 0.24 14 -10000 0 14
eIF4E/eIF4G1/eIF4A1 0.008 0.017 -10000 0 -0.27 1 1
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.015 0.028 -10000 0 -0.18 3 3
mTOR/RHEB/GTP/Raptor/GBL 0.055 0.067 0.19 42 -10000 0 42
FKBP1A 0.023 0.005 -10000 0 -10000 0 0
RHEB/GTP 0.062 0.059 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 13 13
FKBP12/Rapamycin 0.019 0.005 -10000 0 -10000 0 0
PDPK1 -0.003 0.032 0.16 12 -10000 0 12
EIF4E 0.022 0.005 -10000 0 -10000 0 0
ASK1/PP5C 0.05 0.084 -10000 0 -0.52 8 8
mTOR/RHEB/GTP/Raptor/GBL/eIF4E -0.006 0.063 -10000 0 -0.87 1 1
TSC1/TSC2 0.089 0.083 0.28 21 -10000 0 21
tumor necrosis factor receptor activity 0 0 0.001 13 -10000 0 13
RPS6 0.021 0.007 -10000 0 -10000 0 0
PPP5C 0.022 0.004 -10000 0 -10000 0 0
EIF4G1 0.013 0.012 -10000 0 -10000 0 0
IRS1 0.005 0.033 -10000 0 -0.19 13 13
INS -0.018 0.003 -10000 0 -10000 0 0
PTEN 0.02 0.006 -10000 0 -10000 0 0
PDK2 -0.003 0.031 0.16 12 -10000 0 12
EIF4EBP1 0.007 0.18 -10000 0 -1 12 12
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PPP2R5D 0.047 0.06 0.28 3 -0.39 1 4
peptide biosynthetic process -0.013 0.013 0.18 2 -10000 0 2
RHEB 0.023 0.004 -10000 0 -10000 0 0
EIF4A1 0.022 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0.001 0.002 0.003 217 -10000 0 217
EEF2 -0.013 0.013 0.18 2 -10000 0 2
eIF4E/4E-BP1 0.012 0.16 -10000 0 -0.93 12 12
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.015 0.14 -10000 0 -0.57 20 20
Syndecan-4/Syndesmos 0.019 0.094 -10000 0 -0.66 5 5
positive regulation of JNK cascade 0.007 0.12 -10000 0 -0.57 9 9
Syndecan-4/ADAM12 0.048 0.12 0.35 1 -0.68 5 6
CCL5 0.012 0.079 -10000 0 -0.56 9 9
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
DNM2 0.022 0.004 -10000 0 -10000 0 0
ITGA5 0.023 0.002 -10000 0 -10000 0 0
SDCBP 0.022 0.005 -10000 0 -10000 0 0
PLG 0.018 0.022 0.23 3 -10000 0 3
ADAM12 0.078 0.099 0.24 127 -0.29 2 129
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.022 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.032 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.052 0.12 -10000 0 -0.68 5 5
Syndecan-4/CXCL12/CXCR4 0.007 0.13 -10000 0 -0.61 9 9
Syndecan-4/Laminin alpha3 0.011 0.097 -10000 0 -0.6 5 5
MDK 0.028 0.038 0.28 10 -10000 0 10
Syndecan-4/FZD7 0.019 0.093 -10000 0 -0.63 5 5
Syndecan-4/Midkine 0.02 0.098 0.35 4 -0.63 5 9
FZD7 0.023 0.017 0.38 1 -10000 0 1
Syndecan-4/FGFR1/FGF 0.014 0.097 -10000 0 -0.6 5 5
THBS1 0.015 0.065 -10000 0 -0.56 6 6
integrin-mediated signaling pathway 0.019 0.094 -10000 0 -0.64 5 5
positive regulation of MAPKKK cascade 0.007 0.12 -10000 0 -0.57 9 9
Syndecan-4/TACI 0.02 0.099 -10000 0 -0.66 5 5
CXCR4 0.023 0.003 -10000 0 -10000 0 0
cell adhesion 0.006 0.054 0.19 5 -0.29 13 18
Syndecan-4/Dynamin 0.018 0.094 -10000 0 -0.66 5 5
Syndecan-4/TSP1 0.015 0.11 -10000 0 -0.66 8 8
Syndecan-4/GIPC 0.018 0.094 -10000 0 -0.66 5 5
Syndecan-4/RANTES 0.012 0.1 -10000 0 -0.62 7 7
ITGB1 0.022 0.004 -10000 0 -10000 0 0
LAMA1 0.087 0.11 0.25 138 -0.29 1 139
LAMA3 0.008 0.088 -10000 0 -0.56 11 11
RAC1 0.022 0.004 -10000 0 -10000 0 0
PRKCA 0.006 0.11 0.74 10 -0.5 1 11
Syndecan-4/alpha-Actinin 0.019 0.094 -10000 0 -0.66 5 5
TFPI -0.024 0.16 -10000 0 -0.56 38 38
F2 0.026 0.038 0.24 14 -10000 0 14
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
positive regulation of cell adhesion 0.014 0.1 -10000 0 -0.6 5 5
ACTN1 0.022 0.005 -10000 0 -10000 0 0
TNC 0.025 0.039 0.24 8 -0.56 1 9
Syndecan-4/CXCL12 -0.003 0.13 -10000 0 -0.62 10 10
FGF6 -0.017 0.006 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
CXCL12 -0.021 0.15 -10000 0 -0.56 35 35
TNFRSF13B 0.019 0.061 0.24 8 -0.56 4 12
FGF2 0.006 0.095 -10000 0 -0.56 13 13
FGFR1 0.017 0.028 -10000 0 -0.56 1 1
Syndecan-4/PI-4-5-P2 0.001 0.088 -10000 0 -0.66 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.008 0.082 -10000 0 -0.54 10 10
cell migration -0.018 0.01 -10000 0 -10000 0 0
PRKCD 0.018 0.014 -10000 0 -10000 0 0
vasculogenesis 0.015 0.1 -10000 0 -0.63 8 8
SDC4 0.01 0.083 -10000 0 -0.69 4 4
Syndecan-4/Tenascin C 0.019 0.097 -10000 0 -0.67 5 5
Syndecan-4/PI-4-5-P2/PKC alpha -0.026 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.018 0.092 -10000 0 -0.63 5 5
MMP9 0.033 0.047 0.23 24 -10000 0 24
Rac1/GTP 0.006 0.055 0.19 5 -0.3 13 18
cytoskeleton organization 0.018 0.091 -10000 0 -0.63 5 5
GIPC1 0.022 0.005 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.004 0.13 -10000 0 -0.69 8 8
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.023 0.006 -10000 0 -10000 0 0
HSPA8 0.022 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.016 0.099 -10000 0 -0.4 20 20
AKT1 0.014 0.03 -10000 0 -10000 0 0
GSC 0.019 0.077 -10000 0 -10000 0 0
NKX2-5 0.11 0.14 0.24 221 -0.29 23 244
muscle cell differentiation -0.029 0.098 0.47 6 -10000 0 6
SMAD2-3/SMAD4/SP1 0.054 0.071 -10000 0 -10000 0 0
SMAD4 0.017 0.038 -10000 0 -10000 0 0
CBFB 0.022 0.005 -10000 0 -10000 0 0
SAP18 0.022 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.043 0.025 -10000 0 -0.36 1 1
SMAD3/SMAD4/VDR 0.053 0.051 -10000 0 -0.31 1 1
MYC 0.022 0.014 -10000 0 -10000 0 0
CDKN2B -0.21 0.47 -10000 0 -1.6 43 43
AP1 0 0.11 -10000 0 -0.33 11 11
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.036 0.065 -10000 0 -0.38 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.011 0.1 -10000 0 -0.34 34 34
SP3 0.024 0.003 -10000 0 -10000 0 0
CREB1 0.023 0.003 -10000 0 -10000 0 0
FOXH1 0.046 0.074 0.28 41 -10000 0 41
SMAD3/SMAD4/GR 0.034 0.047 -10000 0 -10000 0 0
GATA3 0.008 0.097 0.24 2 -0.51 15 17
SKI/SIN3/HDAC complex/NCoR1 -0.001 0.086 -10000 0 -0.35 22 22
MEF2C/TIF2 -0.007 0.096 0.28 2 -0.61 6 8
endothelial cell migration -0.02 0.037 -10000 0 -10000 0 0
MAX 0.021 0.004 -10000 0 -10000 0 0
RBBP7 0.022 0.005 -10000 0 -10000 0 0
RBBP4 0.022 0.004 -10000 0 -10000 0 0
RUNX2 0.023 0.004 -10000 0 -10000 0 0
RUNX3 0.022 0.005 -10000 0 -10000 0 0
RUNX1 0.022 0.005 -10000 0 -10000 0 0
CTBP1 0.021 0.007 -10000 0 -10000 0 0
NR3C1 0.021 0.006 -10000 0 -10000 0 0
VDR 0.022 0.027 -10000 0 -0.56 1 1
CDKN1A 0.014 0.052 -10000 0 -0.5 1 1
KAT2B 0.02 0.027 -10000 0 -0.56 1 1
SMAD2/SMAD2/SMAD4/FOXH1 0.057 0.066 0.28 5 -10000 0 5
DCP1A 0.021 0.007 -10000 0 -10000 0 0
SKI 0.022 0.005 -10000 0 -10000 0 0
SERPINE1 0.02 0.037 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF2 0.036 0.048 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.037 0.047 -10000 0 -10000 0 0
SAP30 0.021 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.043 0.017 -10000 0 -10000 0 0
JUN -0.009 0.1 -10000 0 -0.32 10 10
SMAD3/SMAD4/IRF7 0.038 0.05 -10000 0 -10000 0 0
TFE3 0.026 0.004 -10000 0 -10000 0 0
COL1A2 0.026 0.029 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.036 0.048 -10000 0 -10000 0 0
DLX1 0.15 0.12 0.24 273 -0.29 1 274
TCF3 0.022 0.004 -10000 0 -10000 0 0
FOS -0.041 0.18 -10000 0 -0.56 53 53
SMAD3/SMAD4/Max 0.034 0.048 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.043 0.014 -10000 0 -10000 0 0
ZBTB17 0.022 0.007 -10000 0 -10000 0 0
LAMC1 0.014 0.034 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.036 0.048 -10000 0 -10000 0 0
IRF7 0.023 0.004 -10000 0 -10000 0 0
ESR1 -0.003 0.12 -10000 0 -0.56 20 20
HNF4A 0.021 0.034 0.26 8 -10000 0 8
MEF2C -0.006 0.096 0.37 3 -0.59 6 9
SMAD2-3/SMAD4 0.036 0.061 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.043 0.015 -10000 0 -10000 0 0
IGHV3OR16-13 0.005 0.037 -10000 0 -0.35 5 5
TGIF2/HDAC complex 0.022 0.004 -10000 0 -10000 0 0
CREBBP 0.022 0.006 -10000 0 -10000 0 0
SKIL 0.013 0.011 -10000 0 -10000 0 0
HDAC1 0.022 0.004 -10000 0 -10000 0 0
HDAC2 0.023 0.002 -10000 0 -10000 0 0
SNIP1 0.023 0.017 0.38 1 -10000 0 1
GCN5L2 0 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.042 0.049 -10000 0 -10000 0 0
MSG1/HSC70 0.032 0.023 -10000 0 -0.42 1 1
SMAD2 0.017 0.03 -10000 0 -10000 0 0
SMAD3 0.016 0.036 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.016 0.036 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.005 0.065 0.2 1 -0.4 8 9
NCOR1 0.022 0.005 -10000 0 -10000 0 0
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
NCOA1 0.023 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.05 0.056 0.27 1 -0.19 3 4
SMAD2-3/SMAD4/SP1/MIZ-1 0.062 0.076 -10000 0 -10000 0 0
IFNB1 0.009 0.03 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.025 0.1 -10000 0 -0.58 6 6
CITED1 0.021 0.029 0.24 1 -0.56 1 2
SMAD2-3/SMAD4/ARC105 0.044 0.062 -10000 0 -10000 0 0
RBL1 0.022 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.026 0.16 -10000 0 -0.52 41 41
RUNX1-3/PEBPB2 0.042 0.014 -10000 0 -10000 0 0
SMAD7 0.004 0.11 -10000 0 -0.92 1 1
MYC/MIZ-1 0.032 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4 0.012 0.039 -10000 0 -10000 0 0
IL10 0.001 0.077 -10000 0 -0.46 6 6
PIASy/HDAC complex 0.02 0.011 -10000 0 -10000 0 0
PIAS3 0.022 0.004 -10000 0 -10000 0 0
CDK2 0.023 0.003 -10000 0 -10000 0 0
IL5 0 0.071 -10000 0 -0.37 5 5
CDK4 0.024 0.017 0.38 1 -10000 0 1
PIAS4 0.02 0.011 -10000 0 -10000 0 0
ATF3 0.022 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1 0.043 0.055 -10000 0 -10000 0 0
FOXG1 0.027 0.079 0.25 50 -0.29 1 51
FOXO3 0.002 0.032 -10000 0 -10000 0 0
FOXO1 0.003 0.029 -10000 0 -10000 0 0
FOXO4 0.002 0.032 -10000 0 -10000 0 0
heart looping -0.006 0.095 0.36 3 -0.59 6 9
CEBPB 0.017 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.11 0.094 0.26 7 -10000 0 7
MYOD1 0.032 0.089 0.24 66 -0.29 3 69
SMAD3/SMAD4/HNF4 0.038 0.053 0.27 1 -10000 0 1
SMAD3/SMAD4/GATA3 0.027 0.089 -10000 0 -0.38 15 15
SnoN/SIN3/HDAC complex/NCoR1 0.013 0.011 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.051 0.054 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.055 0.056 -10000 0 -10000 0 0
MED15 0.022 0.006 -10000 0 -10000 0 0
SP1 0.023 0.015 -10000 0 -10000 0 0
SIN3B 0.022 0.005 -10000 0 -10000 0 0
SIN3A 0.023 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.11 0.12 0.35 15 -0.36 5 20
ITGB5 0.014 0.039 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.004 0.075 -10000 0 -0.32 19 19
SMAD3/SMAD4/AR -0.048 0.17 -10000 0 -0.38 97 97
AR -0.099 0.24 -10000 0 -0.56 98 98
negative regulation of cell growth 0.014 0.047 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.052 0.073 0.27 1 -10000 0 1
E2F5 0.022 0.005 -10000 0 -10000 0 0
E2F4 0.022 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.066 0.063 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.012 0.11 -10000 0 -0.37 39 39
TFDP1 0.024 0.029 0.38 3 -10000 0 3
SMAD3/SMAD4/AP1 0.014 0.11 -10000 0 -0.33 10 10
SMAD3/SMAD4/RUNX2 0.036 0.048 -10000 0 -10000 0 0
TGIF2 0.022 0.004 -10000 0 -10000 0 0
TGIF1 0.022 0.005 -10000 0 -10000 0 0
ATF2 0.023 0.003 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

Figure S76.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S76.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.012 0.062 -10000 0 -0.38 11 11
EPHB2 0.026 0.028 0.24 8 -10000 0 8
Syndecan-2/TACI 0.018 0.049 -10000 0 -0.35 7 7
LAMA1 0.087 0.11 0.25 138 -0.29 1 139
Syndecan-2/alpha2 ITGB1 0.033 0.056 -10000 0 -0.3 11 11
HRAS 0.022 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK 0.004 0.028 -10000 0 -0.35 3 3
ITGA5 0.023 0.002 -10000 0 -10000 0 0
BAX -0.006 0.02 -10000 0 -10000 0 0
EPB41 0.022 0.005 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.018 0.027 -10000 0 -0.32 3 3
LAMA3 0.008 0.088 -10000 0 -0.56 11 11
EZR 0.023 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.006 0.095 -10000 0 -0.56 13 13
Syndecan-2/MMP2 0.016 0.049 -10000 0 -0.4 6 6
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.031 0.01 -10000 0 -10000 0 0
dendrite morphogenesis 0.022 0.032 -10000 0 -0.35 2 2
Syndecan-2/GM-CSF -0.013 0.11 -10000 0 -0.35 42 42
determination of left/right symmetry 0.006 0.033 -10000 0 -0.41 3 3
Syndecan-2/PKC delta 0.018 0.029 -10000 0 -0.34 3 3
GNB2L1 0.021 0.006 -10000 0 -10000 0 0
MAPK3 -0.016 0.1 0.19 17 -0.32 42 59
MAPK1 -0.016 0.098 0.19 14 -0.32 40 54
Syndecan-2/RACK1 0.029 0.028 -10000 0 -0.29 3 3
NF1 0.023 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.006 0.033 -10000 0 -0.41 3 3
ITGA2 0.021 0.006 -10000 0 -10000 0 0
MAPK8 0.003 0.027 -10000 0 -0.34 3 3
Syndecan-2/alpha2/beta1 Integrin 0.077 0.074 0.26 15 -0.29 3 18
Syndecan-2/Kininogen 0.016 0.036 0.26 6 -10000 0 6
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC 0.015 0.04 -10000 0 -0.29 2 2
Syndecan-2/CASK/Protein 4.1 0.017 0.027 -10000 0 -0.32 3 3
extracellular matrix organization 0.019 0.03 -10000 0 -0.34 3 3
actin cytoskeleton reorganization 0.012 0.062 -10000 0 -0.38 11 11
Syndecan-2/Caveolin-2/Ras 0.022 0.063 -10000 0 -0.35 12 12
Syndecan-2/Laminin alpha3 0.011 0.061 -10000 0 -0.35 13 13
Syndecan-2/RasGAP 0.038 0.03 -10000 0 -0.27 3 3
alpha5/beta1 Integrin 0.033 0.007 -10000 0 -10000 0 0
PRKCD 0.021 0.007 -10000 0 -10000 0 0
Syndecan-2 dimer 0.022 0.033 -10000 0 -0.35 2 2
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.025 -10000 0 -0.28 2 2
RHOA 0.021 0.007 -10000 0 -10000 0 0
SDCBP 0.022 0.005 -10000 0 -10000 0 0
TNFRSF13B 0.019 0.061 0.24 8 -0.56 4 12
RASA1 0.021 0.006 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.031 0.01 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.019 0.03 -10000 0 -0.35 3 3
TGFB1 0.022 0.005 -10000 0 -10000 0 0
CASP3 0.013 0.042 0.19 18 -0.3 3 21
FN1 0.01 0.084 -10000 0 -0.56 10 10
Syndecan-2/IL8 0.022 0.052 0.26 2 -0.36 6 8
SDC2 0.006 0.033 -10000 0 -0.41 3 3
KNG1 0.007 0.052 0.31 12 -10000 0 12
Syndecan-2/Neurofibromin 0.02 0.03 -10000 0 -0.35 3 3
TRAPPC4 0.022 0.004 -10000 0 -10000 0 0
CSF2 -0.032 0.16 -10000 0 -0.56 42 42
Syndecan-2/TGFB1 0.019 0.03 -10000 0 -0.34 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.018 0.027 -10000 0 -0.32 3 3
Syndecan-2/Ezrin 0.03 0.029 -10000 0 -0.3 3 3
PRKACA 0.015 0.046 0.19 22 -0.31 3 25
angiogenesis 0.021 0.052 0.26 2 -0.36 6 8
MMP2 0.017 0.053 -10000 0 -0.56 4 4
IL8 0.026 0.064 0.26 16 -0.56 3 19
calcineurin-NFAT signaling pathway 0.018 0.049 -10000 0 -0.35 7 7
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.004 -10000 0 -10000 0 0
HDAC3 0.022 0.006 -10000 0 -10000 0 0
VDR 0.022 0.027 -10000 0 -0.56 1 1
Cbp/p300/PCAF 0.04 0.025 -10000 0 -0.36 1 1
EP300 0.022 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.017 0.056 0.25 1 -0.36 8 9
KAT2B 0.02 0.027 -10000 0 -0.56 1 1
MAPK14 0.023 0.004 -10000 0 -10000 0 0
AKT1 -0.009 0.057 -10000 0 -0.28 3 3
RAR alpha/9cRA/Cyclin H 0.038 0.047 -10000 0 -0.32 2 2
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.001 0.088 -10000 0 -0.37 19 19
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.021 0.031 -10000 0 -0.23 3 3
NCOR2 0.022 0.027 -10000 0 -0.56 1 1
VDR/VDR/Vit D3 0.016 0.02 -10000 0 -0.41 1 1
RXRs/RARs/NRIP1/9cRA -0.035 0.11 0.31 1 -0.56 12 13
NCOA2 0.021 0.027 -10000 0 -0.56 1 1
NCOA3 0.023 0.004 -10000 0 -10000 0 0
NCOA1 0.023 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.022 0.027 -10000 0 -0.56 1 1
RARG 0.023 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.03 0.007 -10000 0 -10000 0 0
MAPK3 0.023 0.003 -10000 0 -10000 0 0
MAPK1 0.022 0.006 -10000 0 -10000 0 0
MAPK8 0.023 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.029 0.097 -10000 0 -0.49 8 8
RARA 0.015 0.025 0.2 1 -0.21 4 5
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0 0.089 0.18 1 -0.34 24 25
PRKCA 0.022 0.038 -10000 0 -0.56 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.046 0.13 0.4 1 -0.56 16 17
RXRG -0.16 0.18 -10000 0 -0.34 230 230
RXRA 0.013 0.031 -10000 0 -0.33 2 2
RXRB 0.018 0.035 0.25 1 -0.26 5 6
VDR/Vit D3/DNA 0.016 0.02 -10000 0 -0.41 1 1
RBP1 0.028 0.051 0.28 17 -10000 0 17
CRBP1/9-cic-RA 0.02 0.034 0.19 17 -10000 0 17
RARB 0.021 0.027 -10000 0 -0.56 1 1
PRKCG 0.036 0.062 0.24 32 -0.29 3 35
MNAT1 0.022 0.005 -10000 0 -10000 0 0
RAR alpha/RXRs -0.041 0.1 -10000 0 -0.51 13 13
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.024 0.097 0.26 2 -0.48 12 14
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.1 0.28 2 -0.37 27 29
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.047 0.13 0.4 1 -0.56 17 18
positive regulation of DNA binding 0.029 0.041 -10000 0 -0.31 2 2
NRIP1 -0.044 0.12 0.49 1 -0.6 11 12
RXRs/RARs -0.05 0.14 -10000 0 -0.53 22 22
RXRs/RXRs/DNA/9cRA -0.039 0.09 -10000 0 -0.45 11 11
PRKACA 0.022 0.005 -10000 0 -10000 0 0
CDK7 0.021 0.006 -10000 0 -10000 0 0
TFIIH 0.042 0.014 -10000 0 -10000 0 0
RAR alpha/9cRA 0.045 0.037 -10000 0 -10000 0 0
CCNH 0.021 0.006 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.04 0.016 -10000 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.034 0.065 -10000 0 -0.41 8 8
NF kappa B1 p50/RelA/I kappa B alpha -0.001 0.079 -10000 0 -0.34 7 7
AP1 -0.004 0.11 -10000 0 -0.3 56 56
mol:PIP3 0 0.05 -10000 0 -0.32 9 9
AKT1 0.004 0.095 0.28 7 -0.4 4 11
PTK2B -0.022 0.091 -10000 0 -0.38 15 15
RHOA -0.018 0.089 -10000 0 -0.32 34 34
PIK3CB 0.019 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.03 0.07 0.18 1 -0.32 10 11
MAGI3 0.022 0.005 -10000 0 -10000 0 0
RELA 0.023 0.001 -10000 0 -10000 0 0
apoptosis 0.009 0.044 0.19 1 -0.3 8 9
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.007 0.1 0.26 6 -0.35 14 20
NF kappa B1 p50/RelA -0.005 0.08 -10000 0 -0.36 8 8
endothelial cell migration 0.007 0.067 -10000 0 -0.72 4 4
ADCY4 -0.004 0.078 -10000 0 -0.43 7 7
ADCY5 -0.009 0.074 -10000 0 -0.68 2 2
ADCY6 0.007 0.058 -10000 0 -0.42 4 4
ADCY7 0.007 0.055 -10000 0 -0.37 5 5
ADCY1 0.006 0.056 -10000 0 -0.87 1 1
ADCY2 0.002 0.066 0.21 1 -0.87 1 2
ADCY3 0.007 0.056 -10000 0 -0.37 5 5
ADCY8 -0.047 0.11 -10000 0 -0.51 7 7
ADCY9 0.007 0.06 -10000 0 -0.54 3 3
GSK3B -0.003 0.1 0.19 34 -0.4 10 44
arachidonic acid secretion 0.004 0.063 -10000 0 -0.4 7 7
GNG2 0.016 0.059 -10000 0 -0.56 5 5
TRIP6 0.015 0.008 -10000 0 -10000 0 0
GNAO1 0.009 0.041 -10000 0 -0.36 5 5
HRAS 0.022 0.004 -10000 0 -10000 0 0
NFKBIA -0.02 0.076 -10000 0 -0.34 11 11
GAB1 0.022 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.011 0.15 -10000 0 -0.82 16 16
JUN 0.022 0.004 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.028 0.029 -10000 0 -0.35 2 2
TIAM1 -0.006 0.18 -10000 0 -0.94 16 16
PIK3R1 0.021 0.007 -10000 0 -10000 0 0
mol:IP3 -0.028 0.069 0.18 1 -0.33 9 10
PLCB3 0.011 0.033 0.18 8 -0.32 2 10
FOS -0.043 0.18 -10000 0 -0.56 53 53
positive regulation of mitosis 0.004 0.063 -10000 0 -0.4 7 7
LPA/LPA1-2-3 0.041 0.055 0.24 1 -0.32 8 9
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.022 0.005 -10000 0 -10000 0 0
stress fiber formation -0.003 0.069 -10000 0 -0.4 7 7
GNAZ 0.006 0.052 -10000 0 -0.35 9 9
EGFR/PI3K-beta/Gab1 0.01 0.055 -10000 0 -0.33 9 9
positive regulation of dendritic cell cytokine production 0.039 0.054 0.24 1 -0.32 8 9
LPA/LPA2/MAGI-3 0.028 0.014 -10000 0 -10000 0 0
ARHGEF1 0.01 0.049 0.35 1 -0.31 4 5
GNAI2 0.009 0.037 -10000 0 -0.35 4 4
GNAI3 0.01 0.037 -10000 0 -0.35 4 4
GNAI1 0.01 0.048 -10000 0 -0.43 4 4
LPA/LPA3 0.017 0.047 0.18 10 -0.41 4 14
LPA/LPA2 0.017 0.012 -10000 0 -10000 0 0
LPA/LPA1 0.017 0.043 -10000 0 -0.41 4 4
HB-EGF/EGFR 0.011 0.085 0.26 8 -0.37 18 26
HBEGF -0.022 0.067 -10000 0 -0.42 13 13
mol:DAG -0.028 0.069 0.18 1 -0.33 9 10
cAMP biosynthetic process -0.004 0.068 0.23 2 -0.43 4 6
NFKB1 0.022 0.005 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.027 -10000 0 -0.57 1 1
LYN -0.019 0.081 0.26 2 -0.37 11 13
GNAQ 0.009 0.036 0.19 1 -0.32 5 6
LPAR2 0.022 0.005 -10000 0 -10000 0 0
LPAR3 0.022 0.063 0.25 10 -0.56 4 14
LPAR1 0.022 0.038 -10000 0 -0.32 4 4
IL8 -0.017 0.12 0.29 3 -0.4 20 23
PTK2 0.004 0.049 -10000 0 -0.34 5 5
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
CASP3 0.009 0.044 0.19 1 -0.31 8 9
EGFR 0.022 0.084 0.37 11 -0.56 6 17
PLCG1 -0.021 0.071 0.16 4 -0.26 16 20
PLD2 0.005 0.051 -10000 0 -0.34 5 5
G12/G13 0.041 0.039 -10000 0 -0.32 4 4
PI3K-beta -0.008 0.077 -10000 0 -0.37 9 9
cell migration 0.013 0.057 0.18 1 -0.25 13 14
SLC9A3R2 0.02 0.038 -10000 0 -0.56 2 2
PXN -0.003 0.071 -10000 0 -0.41 7 7
HRAS/GTP 0.003 0.064 -10000 0 -0.42 7 7
RAC1 0.022 0.004 -10000 0 -10000 0 0
MMP9 0.033 0.047 0.24 24 -10000 0 24
PRKCE 0.02 0.027 -10000 0 -0.56 1 1
PRKCD -0.028 0.065 -10000 0 -0.31 9 9
Gi(beta/gamma) 0.008 0.068 -10000 0 -0.56 4 4
mol:LPA 0 0.015 -10000 0 -0.18 3 3
TRIP6/p130 Cas/FAK1/Paxillin 0.02 0.063 0.26 1 -0.43 3 4
MAPKKK cascade 0.004 0.063 -10000 0 -0.4 7 7
contractile ring contraction involved in cytokinesis -0.023 0.099 -10000 0 -0.32 40 40
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.061 0.14 -10000 0 -0.31 108 108
GNA15 0.01 0.033 0.19 1 -0.32 4 5
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.022 0.003 -10000 0 -10000 0 0
MAPT -0.007 0.1 0.26 6 -0.36 14 20
GNA11 0.01 0.033 0.19 1 -0.32 4 5
Rac1/GTP 0.011 0.16 -10000 0 -0.86 16 16
MMP2 0.007 0.068 -10000 0 -0.72 4 4
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 -0.007 0.006 -10000 0 -10000 0 0
RAS family/GTP 0.029 0.061 -10000 0 -0.29 3 3
NFATC4 -0.013 0.058 0.28 4 -0.25 3 7
ERBB2IP 0.021 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0.022 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis 0.009 0.059 -10000 0 -0.3 11 11
JUN 0.014 0.06 0.24 2 -0.45 1 3
HRAS 0.022 0.004 -10000 0 -10000 0 0
DOCK7 -0.016 0.062 0.29 1 -0.29 11 12
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.027 0.057 -10000 0 -0.32 10 10
AKT1 -0.004 0.006 -10000 0 -10000 0 0
BAD -0.007 0.004 -10000 0 -10000 0 0
MAPK10 -0.011 0.054 0.21 4 -0.25 7 11
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.01 0.063 -10000 0 -0.32 11 11
RAF1 0.019 0.075 0.28 9 -0.36 1 10
ErbB2/ErbB3/neuregulin 2 -0.008 0.1 0.21 2 -0.34 42 44
STAT3 0.009 0.12 -10000 0 -0.8 10 10
cell migration -0.006 0.055 0.26 6 -0.27 2 8
mol:PI-3-4-5-P3 0 0.001 -10000 0 -10000 0 0
cell proliferation -0.016 0.17 0.36 2 -0.52 19 21
FOS -0.031 0.19 0.32 3 -0.48 61 64
NRAS 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.009 0.059 -10000 0 -0.3 11 11
MAPK3 -0.006 0.14 0.35 2 -0.53 14 16
MAPK1 -0.008 0.15 0.35 2 -0.53 17 19
JAK2 -0.017 0.057 -10000 0 -0.29 11 11
NF2 -0.005 0.084 -10000 0 -0.57 10 10
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.011 0.052 0.18 2 -0.28 10 12
NRG1 0.006 0.092 -10000 0 -0.56 12 12
GRB2/SOS1 0.032 0.008 -10000 0 -10000 0 0
MAPK8 0.003 0.066 0.24 1 -0.29 11 12
MAPK9 -0.01 0.043 0.21 3 -10000 0 3
ERBB2 -0.016 0.021 0.29 2 -10000 0 2
ERBB3 0.023 0.003 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
apoptosis 0.005 0.017 -10000 0 -0.17 3 3
STAT3 (dimer) 0.01 0.12 -10000 0 -0.79 10 10
RNF41 -0.01 0.007 -10000 0 -10000 0 0
FRAP1 -0.003 0.003 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.024 0.034 -10000 0 -0.22 11 11
ErbB2/ErbB2/HSP90 (dimer) -0.014 0.018 0.21 2 -10000 0 2
CHRNA1 0.003 0.13 0.32 2 -0.5 10 12
myelination -0.003 0.074 0.31 10 -0.25 2 12
PPP3CB -0.015 0.058 0.28 1 -0.28 11 12
KRAS 0.021 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.032 0.057 -10000 0 -0.26 9 9
NRG2 -0.039 0.17 -10000 0 -0.56 46 46
mol:GDP 0.011 0.052 0.18 2 -0.28 10 12
SOS1 0.023 0.004 -10000 0 -10000 0 0
MAP2K2 0.012 0.078 0.27 9 -0.39 1 10
SRC 0.022 0.004 -10000 0 -10000 0 0
mol:cAMP 0 0.001 -10000 0 -10000 0 0
PTPN11 -0.015 0.063 0.28 1 -0.29 11 12
MAP2K1 -0.011 0.15 0.37 1 -0.5 16 17
heart morphogenesis 0.009 0.059 -10000 0 -0.3 11 11
RAS family/GDP 0.033 0.062 -10000 0 -0.3 2 2
GRB2 0.022 0.004 -10000 0 -10000 0 0
PRKACA -0.003 0.091 -10000 0 -0.59 11 11
CHRNE 0.007 0.017 0.081 1 -0.21 1 2
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.004 0.006 -10000 0 -10000 0 0
nervous system development 0.009 0.059 -10000 0 -0.3 11 11
CDC42 0.022 0.005 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.02 0.038 -10000 0 -0.56 2 2
ANTXR2 0.015 0.065 -10000 0 -0.56 6 6
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.01 -10000 0 -0.08 7 7
monocyte activation -0.009 0.1 -10000 0 -0.38 32 32
MAP2K2 -0.007 0.11 -10000 0 -0.58 16 16
MAP2K1 -0.005 0.009 -10000 0 -0.11 1 1
MAP2K7 -0.005 0.008 -10000 0 -0.11 1 1
MAP2K6 -0.005 0.011 0.12 1 -0.11 2 3
CYAA -0.011 0.046 -10000 0 -0.4 6 6
MAP2K4 -0.005 0.008 -10000 0 -0.11 1 1
IL1B -0.009 0.056 0.17 4 -0.3 14 18
Channel 0.021 0.053 -10000 0 -0.42 6 6
NLRP1 -0.006 0.027 -10000 0 -0.34 3 3
CALM1 0.022 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.068 -10000 0 -0.4 13 13
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.01 0.08 7 -10000 0 7
MAPK3 -0.005 0.009 -10000 0 -0.11 2 2
MAPK1 -0.005 0.009 -10000 0 -0.11 1 1
PGR -0.062 0.12 -10000 0 -0.31 91 91
PA/Cellular Receptors 0.022 0.057 -10000 0 -0.46 6 6
apoptosis -0.002 0.01 -10000 0 -0.08 7 7
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.021 0.05 -10000 0 -0.36 7 7
macrophage activation -0.007 0.009 -10000 0 -10000 0 0
TNF 0.011 0.084 0.24 1 -0.56 10 11
VCAM1 -0.007 0.1 -10000 0 -0.38 30 30
platelet activation -0.003 0.068 -10000 0 -0.4 13 13
MAPKKK cascade 0 0.023 0.13 2 -0.17 3 5
IL18 -0.005 0.035 -10000 0 -0.27 6 6
negative regulation of macrophage activation -0.002 0.01 -10000 0 -0.08 7 7
LEF -0.002 0.01 -10000 0 -0.081 7 7
CASP1 -0.003 0.024 -10000 0 -0.15 7 7
mol:cAMP -0.003 0.068 -10000 0 -0.4 13 13
necrosis -0.002 0.01 -10000 0 -0.08 7 7
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.021 0.051 -10000 0 -0.4 6 6
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 0.041 0.075 -10000 0 -0.56 2 2
UGCG 0.014 0.092 -10000 0 -0.7 7 7
AKT1/mTOR/p70S6K/Hsp90/TERT 0.075 0.11 0.29 14 -0.45 10 24
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.016 0.09 -10000 0 -0.69 7 7
mol:DAG -0.018 0.16 -10000 0 -0.8 18 18
CaM/Ca2+/Calcineurin A alpha-beta B1 0.051 0.096 0.33 1 -0.42 7 8
FRAP1 0.049 0.11 0.36 1 -0.47 8 9
FOXO3 0.045 0.11 0.36 3 -0.44 10 13
AKT1 0.048 0.11 0.37 1 -0.47 10 11
GAB2 0.008 0.091 -10000 0 -0.56 12 12
SMPD1 0.004 0.12 -10000 0 -0.7 14 14
SGMS1 0.001 0.13 -10000 0 -0.65 17 17
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 -0.003 0.003 -10000 0 -10000 0 0
CALM1 0.022 0.005 -10000 0 -10000 0 0
cell proliferation 0.033 0.11 0.29 2 -0.46 17 19
EIF3A 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.018 0.019 -10000 0 -10000 0 0
RPS6KB1 0.025 0.044 -10000 0 -0.82 1 1
mol:sphingomyelin -0.018 0.16 -10000 0 -0.8 18 18
natural killer cell activation 0 0 -10000 0 -10000 0 0
JAK3 0.023 0.005 -10000 0 -10000 0 0
PIK3R1 0.023 0.007 -10000 0 -10000 0 0
JAK1 0.024 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MYC 0.062 0.12 0.4 5 -0.49 4 9
MYB 0.018 0.086 -10000 0 -1.2 2 2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.04 0.091 -10000 0 -0.44 9 9
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.046 0.045 -10000 0 -0.74 1 1
mol:PI-3-4-5-P3 0.043 0.092 -10000 0 -0.45 8 8
Rac1/GDP 0.01 0.01 -10000 0 -10000 0 0
T cell proliferation 0.043 0.087 0.26 2 -0.46 6 8
SHC1 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.003 0.006 0.022 15 -0.064 2 17
PRKCZ 0.042 0.088 -10000 0 -0.48 6 6
NF kappa B1 p50/RelA 0.063 0.099 -10000 0 -0.46 5 5
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.008 0.054 -10000 0 -0.47 5 5
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
RELA 0.023 0.001 -10000 0 -10000 0 0
IL2RA 0.021 0.042 0.24 3 -0.56 2 5
IL2RB 0.02 0.046 -10000 0 -0.56 3 3
TERT 0.12 0.14 0.28 187 -0.29 1 188
E2F1 0.025 0.038 -10000 0 -0.41 3 3
SOS1 0.023 0.004 -10000 0 -10000 0 0
RPS6 0.021 0.007 -10000 0 -10000 0 0
mol:cAMP -0.001 0.003 0.03 2 -0.012 15 17
PTPN11 0.023 0.002 -10000 0 -10000 0 0
IL2RG 0.016 0.07 -10000 0 -0.56 7 7
actin cytoskeleton organization 0.043 0.087 0.26 2 -0.46 6 8
GRB2 0.023 0.004 -10000 0 -10000 0 0
IL2 0.021 0.006 -10000 0 -10000 0 0
PIK3CA 0.013 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.023 0.024 -10000 0 -10000 0 0
LCK 0.023 0.027 -10000 0 -0.56 1 1
BCL2 0.046 0.091 0.33 2 -0.46 3 5
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.03 0.007 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.023 0.01 0.24 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.022 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.006 0.017 -10000 0 -0.21 1 1
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.022 0.006 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.023 0.003 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.56 1 1
MAP3K12 0.023 0.002 -10000 0 -10000 0 0
FGR -0.011 0.14 -10000 0 -0.56 27 27
p38 alpha/TAB1 -0.029 0.089 -10000 0 -0.36 25 25
PRKG1 -0.022 0.15 -10000 0 -0.56 36 36
DUSP8 0.014 0.07 -10000 0 -0.56 7 7
PGK/cGMP/p38 alpha -0.01 0.13 -10000 0 -0.34 44 44
apoptosis -0.028 0.085 -10000 0 -0.35 24 24
RAL/GTP 0.03 0.007 -10000 0 -10000 0 0
LYN 0.02 0.038 -10000 0 -0.56 2 2
DUSP1 -0.044 0.18 -10000 0 -0.56 53 53
PAK1 0.023 0.017 0.38 1 -10000 0 1
SRC 0.022 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.053 0.019 -10000 0 -10000 0 0
TRAF6 0.023 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.022 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.029 0.008 -10000 0 -10000 0 0
MAPK11 0.013 0.11 0.29 5 -0.36 16 21
BLK 0.014 0.087 0.24 12 -0.56 9 21
HCK 0.017 0.053 -10000 0 -0.56 4 4
MAP2K3 0.022 0.006 -10000 0 -10000 0 0
DUSP16 0.022 0.005 -10000 0 -10000 0 0
DUSP10 0.021 0.027 -10000 0 -0.56 1 1
TRAF6/MEKK3 0.028 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.007 0.12 0.27 4 -0.41 22 26
positive regulation of innate immune response 0.012 0.13 0.32 5 -0.43 22 27
LCK 0.021 0.027 -10000 0 -0.56 1 1
p38alpha-beta/MKP7 0.019 0.12 0.36 3 -0.42 20 23
p38alpha-beta/MKP5 0.019 0.12 0.26 2 -0.43 19 21
PGK/cGMP -0.016 0.11 -10000 0 -0.4 37 37
PAK2 0.014 0.011 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.007 0.15 0.43 2 -0.42 31 33
CDC42 0.022 0.005 -10000 0 -10000 0 0
RALB 0.023 0.003 -10000 0 -10000 0 0
RALA 0.022 0.005 -10000 0 -10000 0 0
PAK3 0.012 0.056 0.24 1 -0.56 4 5
IL27-mediated signaling events

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
TGFB1 0.025 0.008 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.011 0.097 0.42 10 -10000 0 10
IL27/IL27R/JAK1 0.029 0.087 -10000 0 -0.41 3 3
TBX21 -0.048 0.16 -10000 0 -0.5 38 38
IL12B 0.021 0.008 -10000 0 -10000 0 0
IL12A -0.003 0.046 -10000 0 -0.41 6 6
IL6ST 0.002 0.1 -10000 0 -0.57 14 14
IL27RA/JAK1 0.015 0.033 -10000 0 -10000 0 0
IL27 0.017 0.015 -10000 0 -10000 0 0
TYK2 0.022 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.027 0.14 -10000 0 -0.78 1 1
T-helper 2 cell differentiation 0.011 0.097 0.42 10 -10000 0 10
T cell proliferation during immune response 0.011 0.097 0.42 10 -10000 0 10
MAPKKK cascade -0.011 0.097 -10000 0 -0.42 10 10
STAT3 0.023 0.004 -10000 0 -10000 0 0
STAT2 0.023 0.002 -10000 0 -10000 0 0
STAT1 0.02 0.011 -10000 0 -10000 0 0
IL12RB1 -0.012 0.14 -10000 0 -0.56 28 28
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.024 0.099 -10000 0 -0.44 5 5
IL27/IL27R/JAK2/TYK2 -0.011 0.098 -10000 0 -0.44 9 9
positive regulation of T cell mediated cytotoxicity -0.011 0.097 -10000 0 -0.42 10 10
STAT1 (dimer) 0.014 0.14 0.5 3 -0.56 6 9
JAK2 0.02 0.009 -10000 0 -10000 0 0
JAK1 0.02 0.011 -10000 0 -10000 0 0
STAT2 (dimer) -0.004 0.1 -10000 0 -0.42 11 11
T cell proliferation -0.06 0.14 -10000 0 -0.5 20 20
IL12/IL12R/TYK2/JAK2 -0.061 0.25 -10000 0 -0.8 44 44
IL17A -0.027 0.14 -10000 0 -0.79 1 1
mast cell activation 0.011 0.097 0.42 10 -10000 0 10
IFNG 0.002 0.029 -10000 0 -0.11 16 16
T cell differentiation -0.002 0.005 -10000 0 -0.02 14 14
STAT3 (dimer) -0.004 0.1 -10000 0 -0.41 11 11
STAT5A (dimer) -0.004 0.1 -10000 0 -0.41 11 11
STAT4 (dimer) -0.008 0.11 -10000 0 -0.46 9 9
STAT4 0.013 0.075 -10000 0 -0.56 8 8
T cell activation -0.005 0.003 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.022 0.07 -10000 0 -10000 0 0
GATA3 -0.042 0.23 0.57 2 -1.3 14 16
IL18 -0.001 0.033 -10000 0 -0.41 3 3
positive regulation of mast cell cytokine production -0.004 0.1 -10000 0 -0.41 11 11
IL27/EBI3 0.029 0.024 -10000 0 -0.19 1 1
IL27RA 0.003 0.024 -10000 0 -10000 0 0
IL6 -0.069 0.21 -10000 0 -0.56 76 76
STAT5A 0.023 0.004 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.011 0.023 -10000 0 -10000 0 0
IL1B -0.008 0.062 -10000 0 -0.41 11 11
EBI3 0.02 0.031 0.24 1 -0.56 1 2
TNF -0.007 0.059 -10000 0 -0.41 10 10
IL2 signaling events mediated by STAT5

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
GAB2 0.008 0.091 -10000 0 -0.56 12 12
ELF1 0.025 0.02 -10000 0 -0.36 1 1
CCNA2 0.077 0.1 0.24 123 -0.29 2 125
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
JAK3 0.022 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
JAK1 0.023 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.037 0.095 -10000 0 -0.46 8 8
SHC1 0.022 0.005 -10000 0 -10000 0 0
SP1 0.024 0.031 -10000 0 -0.36 3 3
IL2RA 0.01 0.047 -10000 0 -0.68 2 2
IL2RB 0.019 0.046 -10000 0 -0.56 3 3
SOS1 0.023 0.004 -10000 0 -10000 0 0
IL2RG 0.015 0.07 -10000 0 -0.56 7 7
G1/S transition of mitotic cell cycle 0.037 0.089 0.36 1 -0.68 2 3
PTPN11 0.023 0.002 -10000 0 -10000 0 0
CCND2 0.006 0.065 -10000 0 -0.82 3 3
LCK 0.022 0.027 -10000 0 -0.56 1 1
GRB2 0.023 0.004 -10000 0 -10000 0 0
IL2 0.019 0.006 -10000 0 -10000 0 0
CDK6 0.023 0.024 0.38 2 -10000 0 2
CCND3 0.038 0.095 0.4 3 -0.53 3 6
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.019 0.009 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.028 0.07 -10000 0 -0.29 4 4
NEF -0.005 0.038 -10000 0 -0.2 15 15
NFKBIA 0.022 0.015 -10000 0 -10000 0 0
BIRC3 0.012 0.07 -10000 0 -0.54 6 6
CYCS 0.01 0.067 0.2 6 -0.28 12 18
RIPK1 0.022 0.004 -10000 0 -10000 0 0
CD247 0.003 0.1 -10000 0 -0.39 24 24
MAP2K7 0.009 0.15 0.3 2 -0.61 19 21
protein ubiquitination 0.021 0.073 0.32 3 -0.39 2 5
CRADD 0.023 0.002 -10000 0 -10000 0 0
DAXX 0.022 0.004 -10000 0 -10000 0 0
FAS 0.02 0.027 -10000 0 -0.56 1 1
BID 0.013 0.068 0.18 14 -0.28 15 29
NF-kappa-B/RelA/I kappa B alpha 0.044 0.037 -10000 0 -0.29 5 5
TRADD 0.022 0.005 -10000 0 -10000 0 0
MAP3K5 0.023 0.003 -10000 0 -10000 0 0
CFLAR 0.022 0.004 -10000 0 -10000 0 0
FADD 0.02 0.008 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.044 0.037 -10000 0 -0.29 5 5
MAPK8 0.009 0.14 0.29 2 -0.58 18 20
APAF1 0.023 0.001 -10000 0 -10000 0 0
TRAF1 0.023 0.003 -10000 0 -10000 0 0
TRAF2 0.022 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.012 0.07 -10000 0 -0.29 19 19
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.014 0.076 -10000 0 -0.44 4 4
CHUK 0.022 0.076 0.33 3 -0.42 2 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.051 0.034 -10000 0 -0.31 1 1
TCRz/NEF -0.002 0.1 -10000 0 -0.42 24 24
TNF 0.011 0.084 0.24 1 -0.56 10 11
FASLG -0.02 0.15 -10000 0 -0.62 25 25
NFKB1 0.023 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.027 0.056 -10000 0 -0.36 8 8
CASP6 0.02 0.12 -10000 0 -0.51 14 14
CASP7 0.017 0.11 0.34 4 -0.46 12 16
RELA 0.023 0.017 -10000 0 -0.17 1 1
CASP2 0.023 0.004 -10000 0 -10000 0 0
CASP3 0.011 0.11 0.34 4 -0.47 11 15
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.015 -10000 0 -10000 0 0
CASP8 0.022 0.004 -10000 0 -10000 0 0
CASP9 0.022 0.005 -10000 0 -10000 0 0
MAP3K14 0.022 0.08 -10000 0 -0.41 4 4
APAF-1/Caspase 9 0.013 0.07 -10000 0 -0.4 6 6
BCL2 0.007 0.12 0.28 3 -0.53 17 20
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 0.029 0.027 -10000 0 -0.35 1 1
cell-cell adhesion 0.018 0.018 0.27 1 -10000 0 1
Ephrin B/EPHB2/RasGAP 0.06 0.036 -10000 0 -0.31 1 1
ITSN1 0.022 0.004 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.025 0.043 0.24 15 -10000 0 15
Ephrin B1/EPHB1 0.046 0.054 0.24 18 -10000 0 18
HRAS/GDP -0.024 0.09 -10000 0 -0.3 2 2
Ephrin B/EPHB1/GRB7 0.066 0.058 -10000 0 -0.31 1 1
Endophilin/SYNJ1 -0.011 0.026 -10000 0 -0.29 1 1
KRAS 0.021 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.065 0.056 -10000 0 -0.31 1 1
endothelial cell migration 0.023 0.029 -10000 0 -0.31 1 1
GRB2 0.022 0.004 -10000 0 -10000 0 0
GRB7 0.025 0.033 0.38 4 -10000 0 4
PAK1 0.005 0.07 0.36 3 -0.3 2 5
HRAS 0.022 0.004 -10000 0 -10000 0 0
RRAS -0.011 0.025 -10000 0 -0.3 1 1
DNM1 0.023 0.014 0.24 2 -10000 0 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.009 0.069 0.35 2 -0.3 1 3
lamellipodium assembly -0.018 0.018 -10000 0 -0.27 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.022 0.043 0.26 1 -0.26 2 3
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
EPHB2 0.026 0.028 0.24 8 -10000 0 8
EPHB3 0.026 0.067 0.36 18 -10000 0 18
EPHB1 0.053 0.089 0.28 59 -10000 0 59
EPHB4 0.022 0.006 -10000 0 -10000 0 0
mol:GDP -0.039 0.07 -10000 0 -0.32 2 2
Ephrin B/EPHB2 0.049 0.031 -10000 0 -0.31 1 1
Ephrin B/EPHB3 0.034 0.048 -10000 0 -0.31 1 1
JNK cascade 0.036 0.13 0.35 62 -10000 0 62
Ephrin B/EPHB1 0.056 0.053 0.24 12 -0.31 1 13
RAP1/GDP -0.029 0.086 -10000 0 -0.31 2 2
EFNB2 0.02 0.027 -10000 0 -0.56 1 1
EFNB3 0.023 0.015 0.24 2 -10000 0 2
EFNB1 0.023 0.003 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.052 0.057 0.24 16 -0.33 1 17
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.04 0.045 -10000 0 -0.32 1 1
Rap1/GTP 0.012 0.026 -10000 0 -0.28 1 1
axon guidance 0.029 0.027 -10000 0 -0.35 1 1
MAPK3 0.011 0.04 0.24 3 -10000 0 3
MAPK1 0.011 0.043 0.24 4 -10000 0 4
Rac1/GDP -0.037 0.084 -10000 0 -0.32 2 2
actin cytoskeleton reorganization -0.038 0.044 -10000 0 -0.26 1 1
CDC42/GDP -0.038 0.084 -10000 0 -0.32 2 2
PI3K 0.025 0.031 -10000 0 -0.31 1 1
EFNA5 0.02 0.027 -10000 0 -0.56 1 1
Ephrin B2/EPHB4 0.027 0.02 -10000 0 -0.35 1 1
Ephrin B/EPHB2/Intersectin/N-WASP 0.016 0.034 -10000 0 -0.26 1 1
CDC42 0.022 0.005 -10000 0 -10000 0 0
RAS family/GTP -0.019 0.019 -10000 0 -0.27 1 1
PTK2 0.027 0.14 0.54 31 -10000 0 31
MAP4K4 0.036 0.13 0.35 62 -10000 0 62
SRC 0.022 0.004 -10000 0 -10000 0 0
KALRN 0.018 0.038 -10000 0 -0.56 2 2
Intersectin/N-WASP 0.032 0.008 -10000 0 -10000 0 0
neuron projection morphogenesis 0.017 0.097 0.29 42 -10000 0 42
MAP2K1 0.014 0.04 0.24 1 -10000 0 1
WASL 0.023 0.004 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.058 0.048 0.29 2 -10000 0 2
cell migration 0.013 0.075 0.37 4 -10000 0 4
NRAS 0.022 0.005 -10000 0 -10000 0 0
SYNJ1 -0.011 0.026 -10000 0 -0.3 1 1
PXN 0.023 0.002 -10000 0 -10000 0 0
TF -0.014 0.04 0.2 1 -0.29 5 6
HRAS/GTP 0.042 0.036 -10000 0 -0.28 1 1
Ephrin B1/EPHB1-2 0.056 0.056 0.24 18 -10000 0 18
cell adhesion mediated by integrin -0.02 0.051 0.31 1 -0.22 3 4
RAC1 0.022 0.004 -10000 0 -10000 0 0
mol:GTP 0.045 0.041 -10000 0 -0.3 1 1
RAC1-CDC42/GTP -0.014 0.02 -10000 0 -0.28 1 1
RASA1 0.021 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.03 0.087 -10000 0 -0.31 2 2
ruffle organization 0.012 0.082 0.35 9 -10000 0 9
NCK1 0.019 0.008 -10000 0 -10000 0 0
receptor internalization -0.013 0.025 0.2 1 -0.29 1 2
Ephrin B/EPHB2/KALRN 0.054 0.045 -10000 0 -0.3 3 3
ROCK1 0.085 0.085 0.18 211 -10000 0 211
RAS family/GDP -0.042 0.046 -10000 0 -0.28 1 1
Rac1/GTP -0.018 0.02 -10000 0 -0.28 1 1
Ephrin B/EPHB1/Src/Paxillin 0.02 0.043 -10000 0 -0.26 1 1
Insulin Pathway

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
CBL/APS/CAP 0.008 0.098 -10000 0 -0.3 40 40
TC10/GTP 0.006 0.091 -10000 0 -0.29 36 36
Insulin Receptor/Insulin/IRS1/Shp2 0.054 0.018 -10000 0 -10000 0 0
HRAS 0.022 0.004 -10000 0 -10000 0 0
APS homodimer 0.022 0.005 -10000 0 -10000 0 0
GRB14 -0.014 0.14 0.24 1 -0.56 30 31
FOXO3 0.032 0.055 -10000 0 -0.54 3 3
AKT1 0.045 0.11 0.3 5 -10000 0 5
INSR 0.024 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.044 0.024 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.022 0.005 -10000 0 -10000 0 0
SORBS1 -0.038 0.18 -10000 0 -0.56 49 49
CRK 0.022 0.006 -10000 0 -10000 0 0
PTPN1 0.001 0.034 -10000 0 -10000 0 0
CAV1 -0.09 0.14 -10000 0 -0.31 125 125
CBL/APS/CAP/Crk-II/C3G 0.023 0.11 -10000 0 -0.31 39 39
Insulin Receptor/Insulin/IRS1/NCK2 0.054 0.018 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.023 0.024 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.018 0.057 -10000 0 -0.38 4 4
RPS6KB1 0.038 0.11 0.29 5 -10000 0 5
PARD6A 0.022 0.005 -10000 0 -10000 0 0
CBL 0.022 0.004 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.017 0.007 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc 0.048 0.089 -10000 0 -10000 0 0
HRAS/GTP -0.019 0.017 -10000 0 -0.28 1 1
Insulin Receptor 0.024 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.059 0.025 -10000 0 -10000 0 0
PRKCI 0.008 0.034 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.002 0.067 -10000 0 -0.29 21 21
SHC1 0.022 0.005 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.033 0.021 -10000 0 -10000 0 0
PI3K 0.028 0.029 -10000 0 -10000 0 0
NCK2 0.023 0.002 -10000 0 -10000 0 0
RHOQ 0.022 0.006 -10000 0 -10000 0 0
mol:H2O2 0 0.004 -10000 0 -10000 0 0
HRAS/GDP 0.017 0.003 -10000 0 -10000 0 0
AKT2 0.04 0.11 0.3 8 -0.28 19 27
PRKCZ 0.004 0.048 -10000 0 -10000 0 0
SH2B2 0.022 0.005 -10000 0 -10000 0 0
SHC/SHIP 0.021 0.021 -10000 0 -0.3 1 1
F2RL2 0.05 0.098 0.24 78 -0.36 8 86
TRIP10 0.022 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.04 0.015 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.059 0.025 -10000 0 -10000 0 0
RAPGEF1 0.023 0.004 -10000 0 -10000 0 0
RASA1 0.021 0.006 -10000 0 -10000 0 0
NCK1 0.019 0.008 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.013 0.11 -10000 0 -0.33 40 40
TC10/GDP 0.016 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.051 0.021 -10000 0 -10000 0 0
INPP5D -0.011 0.022 -10000 0 -0.32 1 1
SOS1 0.023 0.004 -10000 0 -10000 0 0
SGK1 0.001 0.056 -10000 0 -0.6 4 4
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
IRS1 0.022 0.004 -10000 0 -10000 0 0
p62DOK/RasGAP 0.033 0.022 -10000 0 -10000 0 0
INS 0.019 0.008 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.011 0.022 -10000 0 -0.32 1 1
GRB2 0.022 0.004 -10000 0 -10000 0 0
EIF4EBP1 0.038 0.11 0.31 13 -10000 0 13
PTPRA 0.023 0.006 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.029 0.009 -10000 0 -10000 0 0
PDPK1 0.022 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.017 0.022 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.041 0.014 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.032 0.011 -10000 0 -10000 0 0
Par3/Par6 0.061 0.057 -10000 0 -0.31 1 1
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate 0.002 0.095 0.25 1 -0.36 21 22
PDGFB-D/PDGFRB/SLAP 0.008 0.1 -10000 0 -0.43 23 23
PDGFB-D/PDGFRB/APS/CBL 0.04 0.024 -10000 0 -0.36 1 1
AKT1 0.065 0.1 0.32 22 -10000 0 22
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.005 0.11 -10000 0 -0.39 24 24
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
FGR -0.047 0.19 0.32 1 -0.6 46 47
mol:Ca2+ -0.006 0.12 -10000 0 -0.44 25 25
MYC 0.02 0.11 0.37 2 -0.4 5 7
SHC1 0.022 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.026 0.035 -10000 0 -0.3 1 1
LRP1/PDGFRB/PDGFB 0.041 0.024 -10000 0 -0.36 1 1
GRB10 0.022 0.005 -10000 0 -10000 0 0
PTPN11 0.023 0.002 -10000 0 -10000 0 0
GO:0007205 -0.006 0.12 -10000 0 -0.45 25 25
PTEN 0.021 0.006 -10000 0 -10000 0 0
GRB2 0.022 0.004 -10000 0 -10000 0 0
GRB7 0.025 0.033 0.38 4 -10000 0 4
PDGFB-D/PDGFRB/SHP2 0.031 0.022 -10000 0 -0.42 1 1
PDGFB-D/PDGFRB/GRB10 0.03 0.023 -10000 0 -0.42 1 1
cell cycle arrest 0.008 0.099 -10000 0 -0.43 23 23
HRAS 0.022 0.004 -10000 0 -10000 0 0
HIF1A 0.057 0.095 0.28 27 -10000 0 27
GAB1 -0.004 0.11 -10000 0 -0.42 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.002 0.1 0.28 2 -0.38 17 19
PDGFB-D/PDGFRB 0.042 0.025 -10000 0 -0.37 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.031 0.023 -10000 0 -0.42 1 1
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.006 0.077 -10000 0 -0.4 6 6
positive regulation of MAPKKK cascade 0.031 0.022 -10000 0 -0.42 1 1
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
mol:IP3 -0.006 0.12 -10000 0 -0.45 25 25
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.022 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.033 0.032 0.27 4 -0.42 1 5
SHB 0.021 0.007 -10000 0 -10000 0 0
BLK -0.047 0.17 -10000 0 -0.47 59 59
PTPN2 0.022 0.006 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.031 0.023 -10000 0 -0.42 1 1
BCAR1 0.022 0.005 -10000 0 -10000 0 0
VAV2 -0.004 0.12 0.27 1 -0.46 20 21
CBL 0.022 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.03 0.032 -10000 0 -0.42 2 2
LCK -0.009 0.11 0.32 1 -0.54 17 18
PDGFRB 0.021 0.028 -10000 0 -0.57 1 1
ACP1 0.023 0.004 -10000 0 -10000 0 0
HCK 0.001 0.084 0.32 1 -0.61 6 7
ABL1 -0.005 0.11 0.23 1 -0.4 22 23
PDGFB-D/PDGFRB/CBL -0.008 0.14 -10000 0 -0.49 25 25
PTPN1 0.023 0.005 -10000 0 -10000 0 0
SNX15 0.023 0.001 -10000 0 -10000 0 0
STAT3 0.023 0.004 -10000 0 -10000 0 0
STAT1 0.022 0.004 -10000 0 -10000 0 0
cell proliferation 0.02 0.1 0.33 3 -0.36 6 9
SLA -0.007 0.12 -10000 0 -0.56 23 23
actin cytoskeleton reorganization 0.024 0.08 0.33 5 -0.3 1 6
SRC 0.005 0.069 0.31 1 -0.65 3 4
PI3K -0.011 0.018 -10000 0 -0.28 1 1
PDGFB-D/PDGFRB/GRB7/SHC 0.043 0.027 0.26 4 -10000 0 4
SH2B2 0.022 0.005 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.005 0.11 -10000 0 -0.41 24 24
LYN 0 0.088 0.3 1 -0.57 8 9
LRP1 0.023 0.002 -10000 0 -10000 0 0
SOS1 0.023 0.004 -10000 0 -10000 0 0
STAT5B 0.023 0.004 -10000 0 -10000 0 0
STAT5A 0.023 0.004 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.05 0.037 -10000 0 -0.31 1 1
SPHK1 0.022 0.005 -10000 0 -10000 0 0
EDG1 0 0.002 -10000 0 -10000 0 0
mol:DAG -0.006 0.12 -10000 0 -0.45 25 25
PLCG1 -0.007 0.12 -10000 0 -0.46 25 25
NHERF/PDGFRB 0.041 0.038 0.26 1 -0.31 4 5
YES1 0 0.077 -10000 0 -0.53 7 7
cell migration 0.041 0.038 0.25 1 -0.31 4 5
SHC/Grb2/SOS1 0.057 0.03 -10000 0 -10000 0 0
SLC9A3R2 0.02 0.038 -10000 0 -0.56 2 2
SLC9A3R1 0.025 0.024 0.27 4 -10000 0 4
NHERF1-2/PDGFRB/PTEN 0.049 0.038 -10000 0 -0.32 3 3
FYN 0.003 0.073 -10000 0 -0.58 5 5
DOK1 -0.003 0.04 -10000 0 -0.34 1 1
HRAS/GTP 0.017 0.003 -10000 0 -10000 0 0
PDGFB 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.001 0.12 0.29 1 -0.46 14 15
PRKCD -0.001 0.042 -10000 0 -0.34 1 1
FER -0.001 0.042 0.18 2 -0.34 1 3
MAPKKK cascade 0.006 0.069 0.37 6 -10000 0 6
RASA1 -0.001 0.042 -10000 0 -0.34 1 1
NCK1 0.019 0.008 -10000 0 -10000 0 0
NCK2 0.023 0.002 -10000 0 -10000 0 0
p62DOK/Csk 0.027 0.034 -10000 0 -0.31 1 1
PDGFB-D/PDGFRB/SHB 0.03 0.024 -10000 0 -0.42 1 1
chemotaxis -0.004 0.11 0.23 1 -0.39 22 23
STAT1-3-5/STAT1-3-5 0.048 0.028 -10000 0 -0.3 1 1
Bovine Papilomavirus E5/PDGFRB 0.015 0.02 -10000 0 -0.42 1 1
PTPRJ 0.021 0.027 -10000 0 -0.56 1 1
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.047 0.078 0.21 6 -0.27 7 13
adherens junction organization 0.015 0.098 0.21 1 -0.42 16 17
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.063 0.089 0.28 5 -0.26 7 12
FMN1 0.009 0.1 -10000 0 -0.36 21 21
mol:IP3 0.003 0.038 -10000 0 -0.24 3 3
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.03 0.08 -10000 0 -0.41 10 10
CTNNB1 0.022 0.007 -10000 0 -10000 0 0
AKT1 0.002 0.042 -10000 0 -0.25 5 5
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.003 0.15 -10000 0 -0.72 16 16
CTNND1 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.022 0.078 -10000 0 -0.38 10 10
VASP 0.027 0.072 -10000 0 -0.38 7 7
ZYX 0.026 0.079 -10000 0 -0.4 10 10
JUB 0.026 0.082 -10000 0 -0.34 15 15
EGFR(dimer) 0.034 0.098 0.27 9 -0.36 14 23
E-cadherin/beta catenin-gamma catenin 0.038 0.015 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.011 0.051 -10000 0 -0.26 10 10
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.011 0.052 -10000 0 -0.26 10 10
FYN 0.041 0.08 0.21 4 -0.29 5 9
mol:Ca2+ 0.003 0.037 -10000 0 -0.24 3 3
JUP 0.024 0.005 -10000 0 -10000 0 0
PIK3R1 0.024 0.008 -10000 0 -10000 0 0
mol:DAG 0.001 0.035 -10000 0 -0.24 3 3
CDH1 0.023 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.064 0.088 0.27 6 -0.27 4 10
establishment of polarity of embryonic epithelium 0.026 0.073 -10000 0 -0.37 8 8
SRC 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
EGFR 0.022 0.084 0.37 11 -0.56 6 17
CASR 0.039 0.076 0.2 4 -0.23 3 7
RhoA/GTP 0.061 0.069 -10000 0 -10000 0 0
AKT2 0.002 0.043 -10000 0 -0.25 9 9
actin cable formation 0.007 0.098 0.23 4 -0.34 20 24
apoptosis -0.05 0.085 0.3 8 -0.22 8 16
CTNNA1 0.025 0.008 -10000 0 -10000 0 0
mol:GDP 0.051 0.088 0.24 8 -0.28 6 14
PIP5K1A 0.023 0.078 -10000 0 -0.4 9 9
PLCG1 0.001 0.036 -10000 0 -0.25 3 3
Rac1/GTP 0.039 0.093 0.29 4 -0.33 14 18
homophilic cell adhesion 0.003 0.004 -10000 0 -10000 0 0
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.042 0.045 -10000 0 -0.3 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.022 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.038 0.044 -10000 0 -0.28 1 1
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.04 0.022 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I 0.002 0.034 -10000 0 -0.23 1 1
CaM/Ca2+ 0.042 0.045 -10000 0 -0.28 4 4
RAP1A 0.022 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.024 0.042 -10000 0 -0.29 3 3
AKT1 0.067 0.098 0.3 19 -0.26 2 21
MAP2K1 -0.008 0.048 0.27 1 -0.28 4 5
MAP3K11 -0.006 0.048 0.27 1 -0.29 4 5
IFNGR1 0.024 0.008 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.006 0.13 -10000 0 -0.39 39 39
Rap1/GTP -0.019 0.021 -10000 0 -10000 0 0
CRKL/C3G 0.032 0.009 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.053 0.045 -10000 0 -0.31 4 4
CEBPB -0.013 0.15 0.29 1 -0.48 30 31
STAT3 0.023 0.004 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.037 0.13 -10000 0 -0.7 13 13
STAT1 -0.004 0.046 0.28 1 -0.29 3 4
CALM1 0.022 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.017 0.057 0.26 2 -0.56 4 6
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.024 0.046 0.27 1 -0.28 3 4
CEBPB/PTGES2/Cbp/p300 0.002 0.095 -10000 0 -0.39 8 8
mol:Ca2+ 0.04 0.043 -10000 0 -0.3 4 4
MAPK3 -0.004 0.11 -10000 0 -0.66 9 9
STAT1 (dimer) 0.006 0.047 -10000 0 -0.31 1 1
MAPK1 -0.005 0.11 -10000 0 -0.62 8 8
JAK2 0.021 0.01 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
JAK1 0.023 0.009 -10000 0 -10000 0 0
CAMK2D 0.022 0.005 -10000 0 -10000 0 0
DAPK1 -0.026 0.17 0.25 1 -0.6 35 36
SMAD7 0.032 0.05 0.16 19 -0.3 1 20
CBL/CRKL/C3G 0.033 0.043 -10000 0 -0.27 3 3
PI3K 0.023 0.039 -10000 0 -0.28 2 2
IFNG 0.017 0.057 0.26 2 -0.57 4 6
apoptosis -0.01 0.13 -10000 0 -0.43 34 34
CAMK2G 0.022 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.022 0.004 -10000 0 -10000 0 0
CAMK2A -0.014 0.14 -10000 0 -0.56 29 29
CAMK2B 0.047 0.075 0.25 55 -0.29 1 56
FRAP1 0.062 0.092 0.27 22 -0.25 2 24
PRKCD 0.066 0.1 0.3 20 -0.26 2 22
RAP1B 0.022 0.005 -10000 0 -10000 0 0
negative regulation of cell growth 0.002 0.034 -10000 0 -0.23 1 1
PTPN2 0.022 0.005 -10000 0 -10000 0 0
EP300 0.022 0.004 -10000 0 -10000 0 0
IRF1 0.003 0.05 0.33 2 -0.33 1 3
STAT1 (dimer)/PIASy 0.022 0.045 0.27 1 -0.28 3 4
SOCS1 -0.006 0.17 -10000 0 -1 13 13
mol:GDP 0.029 0.041 -10000 0 -0.26 3 3
CASP1 0.033 0.052 0.16 20 -0.26 2 22
PTGES2 0.023 0.003 -10000 0 -10000 0 0
IRF9 0.01 0.047 0.2 3 -0.19 1 4
mol:PI-3-4-5-P3 0.016 0.032 -10000 0 -0.27 2 2
RAP1/GDP 0.026 0.033 -10000 0 -10000 0 0
CBL -0.005 0.048 0.27 1 -0.29 4 5
MAP3K1 -0.006 0.047 0.27 1 -0.29 4 5
PIAS1 0.023 0.003 -10000 0 -10000 0 0
PIAS4 0.022 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II 0.002 0.034 -10000 0 -0.23 1 1
PTPN11 0.005 0.051 0.29 1 -0.3 4 5
CREBBP 0.022 0.005 -10000 0 -10000 0 0
RAPGEF1 0.023 0.004 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.022 0.006 -10000 0 -10000 0 0
NFATC1 0.026 0.078 0.29 4 -0.36 4 8
NFATC2 -0.022 0.098 0.18 3 -0.28 38 41
NFATC3 0.012 0.009 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.024 0.13 0.28 1 -0.43 31 32
Exportin 1/Ran/NUP214 0.041 0.015 -10000 0 -10000 0 0
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.004 0.12 -10000 0 -0.41 26 26
BCL2/BAX 0.033 0.011 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.014 -10000 0 -10000 0 0
CaM/Ca2+ 0.012 0.014 -10000 0 -10000 0 0
BAX 0.022 0.004 -10000 0 -10000 0 0
MAPK14 0.022 0.005 -10000 0 -10000 0 0
BAD 0.023 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D -0.013 0.12 -10000 0 -0.43 28 28
Calcineurin A alpha-beta B1/BCL2 0.023 0.011 0.24 1 -10000 0 1
FKBP8 0.022 0.005 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.012 0.12 0.42 28 -10000 0 28
KPNB1 0.023 0.003 -10000 0 -10000 0 0
KPNA2 0.023 0.004 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
SFN 0.04 0.072 0.24 45 -0.38 3 48
MAP3K8 0.017 0.029 -10000 0 -0.56 1 1
NFAT4/CK1 alpha 0.017 0.022 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.022 0.15 -10000 0 -0.33 61 61
CABIN1 -0.023 0.13 0.28 1 -0.44 30 31
CALM1 0.017 0.015 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
MAP3K1 0.021 0.006 -10000 0 -10000 0 0
CAMK4 0.019 0.038 -10000 0 -0.56 2 2
mol:Ca2+ -0.002 0.005 -10000 0 -10000 0 0
MAPK3 0.023 0.003 -10000 0 -10000 0 0
YWHAH 0.022 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.03 0.03 -10000 0 -0.42 2 2
YWHAB 0.023 0.004 -10000 0 -10000 0 0
MAPK8 0.018 0.013 -10000 0 -10000 0 0
MAPK9 0.021 0.007 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
FKBP1A 0.022 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.013 0.095 0.28 1 -0.39 6 7
PRKCH 0.022 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.023 0.025 -10000 0 -10000 0 0
CASP3 0.02 0.007 -10000 0 -10000 0 0
PIM1 0.022 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.012 0.009 -10000 0 -10000 0 0
apoptosis 0.015 0.009 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.041 -10000 0 -0.26 5 5
PRKCB -0.005 0.12 -10000 0 -0.56 23 23
PRKCE 0.021 0.027 -10000 0 -0.56 1 1
JNK2/NFAT4 0.024 0.026 -10000 0 -10000 0 0
BAD/BCL-XL 0.032 0.009 -10000 0 -10000 0 0
PRKCD 0.021 0.007 -10000 0 -10000 0 0
NUP214 0.022 0.003 -10000 0 -10000 0 0
PRKCZ 0.018 0.013 -10000 0 -10000 0 0
PRKCA 0.02 0.038 -10000 0 -0.56 2 2
PRKCG 0.027 0.065 0.24 32 -0.29 3 35
PRKCQ -0.027 0.16 -10000 0 -0.56 40 40
FKBP38/BCL2 0.032 0.011 -10000 0 -10000 0 0
EP300 0.016 0.017 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.022 0.005 -10000 0 -10000 0 0
NFATc/JNK1 0.035 0.077 0.33 2 -0.36 3 5
CaM/Ca2+/FKBP38 0.023 0.019 -10000 0 -10000 0 0
FKBP12/FK506 0.016 0.003 -10000 0 -10000 0 0
CSNK1A1 0.005 0.013 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.02 0.032 -10000 0 -0.28 3 3
NFATc/ERK1 0.038 0.078 0.33 2 -0.36 3 5
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.001 0.12 -10000 0 -0.42 27 27
NR4A1 -0.069 0.21 0.26 1 -0.55 70 71
GSK3B 0.017 0.013 -10000 0 -10000 0 0
positive T cell selection 0.012 0.009 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.012 0.074 0.16 1 -0.32 12 13
RCH1/ KPNB1 0.033 0.007 -10000 0 -10000 0 0
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
PRKACA 0.021 0.005 -10000 0 -10000 0 0
AKAP5 0.02 0.038 -10000 0 -0.56 2 2
MEF2D 0.016 0.018 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
NFATc/p38 alpha 0.036 0.076 0.26 1 -0.36 3 4
CREBBP 0.016 0.017 -10000 0 -10000 0 0
BCL2 0.023 0.011 0.24 1 -10000 0 1
TCGA08_rtk_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
PDGFRA 0.017 0.056 0.38 1 -0.56 4 5
HRAS 0.022 0.004 -10000 0 -10000 0 0
EGFR 0.022 0.084 0.37 11 -0.56 6 17
AKT 0.065 0.076 0.28 15 -0.28 1 16
FOXO3 0.023 0.003 -10000 0 -10000 0 0
AKT1 0.022 0.005 -10000 0 -10000 0 0
FOXO1 0.022 0.006 -10000 0 -10000 0 0
AKT3 0.021 0.027 -10000 0 -0.56 1 1
FOXO4 0.023 0.003 -10000 0 -10000 0 0
MET 0.02 0.041 0.38 1 -0.56 2 3
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PIK3CB 0.019 0.009 -10000 0 -10000 0 0
NRAS 0.022 0.005 -10000 0 -10000 0 0
PIK3CG -0.026 0.16 -10000 0 -0.56 39 39
PIK3R3 0.022 0.004 -10000 0 -10000 0 0
PIK3R2 0.022 0.005 -10000 0 -10000 0 0
NF1 0.023 0.003 -10000 0 -10000 0 0
RAS 0.023 0.05 0.2 11 -0.19 11 22
ERBB2 0.024 0.023 0.38 2 -10000 0 2
proliferation/survival/translation -0.062 0.07 0.27 3 -0.26 9 12
PI3K 0.048 0.076 0.24 34 -0.22 5 39
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
KRAS 0.021 0.006 -10000 0 -10000 0 0
FOXO 0.08 0.063 0.24 25 -10000 0 25
AKT2 0.021 0.007 -10000 0 -10000 0 0
PTEN 0.021 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.009 0.05 -10000 0 -10000 0 0
DAPP1 -0.011 0.12 0.25 3 -0.41 28 31
Src family/SYK family/BLNK-LAT/BTK-ITK -0.024 0.17 0.32 1 -0.56 33 34
mol:DAG -0.003 0.084 0.19 12 -0.24 26 38
HRAS 0.024 0.008 -10000 0 -10000 0 0
RAP1A 0.023 0.008 -10000 0 -10000 0 0
ARF5/GDP 0.016 0.082 -10000 0 -0.36 12 12
PLCG2 0.022 0.005 -10000 0 -10000 0 0
PLCG1 0.022 0.004 -10000 0 -10000 0 0
ARF5 0.023 0.003 -10000 0 -10000 0 0
mol:GTP -0.008 0.046 -10000 0 -0.27 3 3
ARF1/GTP -0.004 0.041 0.23 1 -0.28 3 4
RHOA 0.021 0.007 -10000 0 -10000 0 0
YES1 0.022 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.008 0.048 -10000 0 -0.27 3 3
ADAP1 -0.013 0.055 -10000 0 -0.28 9 9
ARAP3 -0.008 0.046 -10000 0 -0.27 3 3
INPPL1 0.022 0.005 -10000 0 -10000 0 0
PREX1 0.015 0.065 -10000 0 -0.56 6 6
ARHGEF6 0.003 0.1 -10000 0 -0.56 16 16
ARHGEF7 0.022 0.006 -10000 0 -10000 0 0
ARF1 0.022 0.004 -10000 0 -10000 0 0
NRAS 0.023 0.009 -10000 0 -10000 0 0
FYN 0.022 0.027 -10000 0 -0.56 1 1
ARF6 0.022 0.005 -10000 0 -10000 0 0
FGR -0.011 0.14 -10000 0 -0.56 27 27
mol:Ca2+ 0 0.05 0.27 2 -10000 0 2
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.022 0.004 -10000 0 -10000 0 0
ZAP70 0.013 0.075 -10000 0 -0.56 8 8
mol:IP3 -0.002 0.065 0.18 16 -0.19 10 26
LYN 0.02 0.038 -10000 0 -0.56 2 2
ARF1/GDP 0.014 0.083 -10000 0 -0.36 13 13
RhoA/GDP 0.023 0.059 -10000 0 -0.32 2 2
PDK1/Src/Hsp90 0.042 0.014 -10000 0 -10000 0 0
BLNK 0.021 0.027 -10000 0 -0.56 1 1
actin cytoskeleton reorganization 0.004 0.088 0.26 5 -0.43 6 11
SRC 0.022 0.004 -10000 0 -10000 0 0
PLEKHA2 -0.009 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
PTEN 0.019 0.013 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.011 0.047 -10000 0 -0.26 3 3
RhoA/GTP -0.009 0.048 -10000 0 -0.26 3 3
Src family/SYK family/BLNK-LAT -0.01 0.12 -10000 0 -0.44 21 21
BLK 0.014 0.087 0.24 12 -0.56 9 21
PDPK1 0.022 0.004 -10000 0 -10000 0 0
CYTH1 -0.01 0.045 -10000 0 -0.26 3 3
HCK 0.017 0.053 -10000 0 -0.56 4 4
CYTH3 -0.01 0.045 -10000 0 -0.26 3 3
CYTH2 -0.01 0.045 -10000 0 -0.26 3 3
KRAS 0.022 0.009 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.014 0.032 -10000 0 -10000 0 0
SGK1 0.019 0.033 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
mol:GDP 0.002 0.084 -10000 0 -0.34 16 16
SOS1 0.023 0.004 -10000 0 -10000 0 0
SYK 0.022 0.004 -10000 0 -10000 0 0
ARF6/GDP -0.005 0.058 0.21 1 -0.33 2 3
mol:PI-3-4-5-P3 -0.009 0.043 -10000 0 -0.27 3 3
ARAP3/RAP1A/GTP -0.008 0.048 -10000 0 -0.27 3 3
VAV1 0.019 0.046 -10000 0 -0.56 3 3
mol:PI-3-4-P2 -0.01 0.019 -10000 0 -0.42 1 1
RAS family/GTP/PI3K Class I 0.035 0.046 -10000 0 -0.27 3 3
PLEKHA1 -0.011 0.016 -10000 0 -0.36 1 1
Rac1/GDP 0.013 0.083 -10000 0 -0.36 12 12
LAT 0.023 0.003 -10000 0 -10000 0 0
Rac1/GTP 0 0.094 -10000 0 -0.4 18 18
ITK -0.024 0.074 -10000 0 -0.3 24 24
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.011 0.11 0.28 4 -0.34 27 31
LCK 0.021 0.027 -10000 0 -0.56 1 1
BTK -0.031 0.083 -10000 0 -0.29 35 35
S1P3 pathway

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
PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
mol:S1P 0.001 0.001 -10000 0 -10000 0 0
S1P1/S1P/Gi 0.003 0.055 -10000 0 -0.26 13 13
GNAO1 0.022 0.031 0.24 2 -0.56 1 3
S1P/S1P3/G12/G13 0.042 0.012 -10000 0 -10000 0 0
AKT1 0.013 0.08 -10000 0 -0.45 13 13
AKT3 0.018 0.078 -10000 0 -1.2 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.027 -10000 0 -0.56 1 1
GNAI2 0.022 0.007 -10000 0 -10000 0 0
GNAI3 0.023 0.005 -10000 0 -10000 0 0
GNAI1 0.022 0.027 -10000 0 -0.56 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.023 0.005 -10000 0 -10000 0 0
S1PR2 0.022 0.004 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.02 0.039 -10000 0 -0.26 1 1
MAPK3 0.01 0.043 -10000 0 -10000 0 0
MAPK1 0.009 0.037 -10000 0 -10000 0 0
JAK2 0.013 0.049 -10000 0 -0.27 1 1
CXCR4 0.01 0.042 -10000 0 -0.25 1 1
FLT1 0.023 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.005 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
SRC 0.01 0.043 -10000 0 -10000 0 0
S1P/S1P3/Gi 0.02 0.039 -10000 0 -0.26 1 1
RAC1 0.022 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.021 0.054 -10000 0 -10000 0 0
VEGFA 0.024 0.004 -10000 0 -10000 0 0
S1P/S1P2/Gi 0.02 0.034 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.035 0.011 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.047 0.12 -10000 0 -0.27 109 109
GNAQ 0.021 0.027 -10000 0 -0.56 1 1
GNAZ 0.016 0.06 -10000 0 -0.56 5 5
G12/G13 0.032 0.008 -10000 0 -10000 0 0
GNA14 -0.11 0.24 -10000 0 -0.56 108 108
GNA15 0.022 0.004 -10000 0 -10000 0 0
GNA12 0.022 0.005 -10000 0 -10000 0 0
GNA13 0.023 0.003 -10000 0 -10000 0 0
GNA11 0.022 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.017 0.057 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.079 0.11 0.28 105 -10000 0 105
mol:Halofuginone 0.002 0 -10000 0 -10000 0 0
ITGA1 0.016 0.053 -10000 0 -0.56 4 4
CDKN1A 0.009 0.039 -10000 0 -0.31 6 6
PRL-3/alpha Tubulin 0.031 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.036 0.085 -10000 0 -0.42 22 22
AGT -0.005 0.12 0.24 1 -0.56 23 24
CCNA2 -0.014 0.05 0.39 2 -10000 0 2
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
EGR1 0.004 0.05 -10000 0 -0.41 7 7
CDK2/Cyclin E1 0.063 0.099 0.33 4 -0.34 4 8
MAPK3 -0.009 0.003 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.033 0.007 -10000 0 -10000 0 0
MAPK1 -0.009 0.003 -10000 0 -10000 0 0
PTP4A1 -0.009 0.035 -10000 0 -10000 0 0
PTP4A3 0.021 0.006 -10000 0 -10000 0 0
PTP4A2 0.022 0.004 -10000 0 -10000 0 0
ITGB1 -0.009 0.003 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
RAC1 0.01 0.03 -10000 0 -0.31 3 3
Rab GGTase beta/Rab GGTase alpha 0.032 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 0.021 0.056 -10000 0 -10000 0 0
RABGGTA 0.022 0.005 -10000 0 -10000 0 0
BCAR1 -0.017 0.006 -10000 0 -10000 0 0
RHOC 0.006 0.047 -10000 0 -0.31 9 9
RHOA 0.004 0.053 -10000 0 -0.31 12 12
cell motility 0.011 0.065 -10000 0 -0.37 2 2
PRL-1/alpha Tubulin 0.019 0.053 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.025 0.043 -10000 0 -0.36 5 5
ROCK1 0.018 0.052 -10000 0 -0.37 2 2
RABGGTB 0.022 0.004 -10000 0 -10000 0 0
CDK2 0.023 0.002 -10000 0 -10000 0 0
mitosis -0.009 0.035 -10000 0 -10000 0 0
ATF5 0.026 0.026 0.24 7 -10000 0 7
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.032 0.06 0.34 7 -0.24 1 8
KIRREL 0.016 0.07 -10000 0 -0.56 7 7
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.032 0.06 0.24 1 -0.34 7 8
PLCG1 0.022 0.004 -10000 0 -10000 0 0
ARRB2 0.022 0.006 -10000 0 -10000 0 0
WASL 0.023 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.05 0.055 0.32 1 -0.34 4 5
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.013 0.036 -10000 0 -0.3 2 2
FYN 0.009 0.078 0.28 17 -0.37 4 21
mol:Ca2+ 0.048 0.05 0.32 1 -0.28 3 4
mol:DAG 0.049 0.051 0.32 1 -0.29 3 4
NPHS2 -0.004 0.031 0.26 3 -10000 0 3
mol:IP3 0.049 0.051 0.32 1 -0.29 3 4
regulation of endocytosis 0.039 0.052 -10000 0 -0.34 4 4
Nephrin/NEPH1/podocin/Cholesterol 0.037 0.052 0.31 1 -0.34 4 5
establishment of cell polarity 0.032 0.06 0.24 1 -0.34 7 8
Nephrin/NEPH1/podocin/NCK1-2 0.051 0.057 0.32 1 -0.32 4 5
Nephrin/NEPH1/beta Arrestin2 0.042 0.054 -10000 0 -0.35 4 4
NPHS1 0.024 0.059 0.27 23 -10000 0 23
Nephrin/NEPH1/podocin 0.039 0.056 0.31 1 -0.37 4 5
TJP1 0.023 0.003 -10000 0 -10000 0 0
NCK1 0.019 0.008 -10000 0 -10000 0 0
NCK2 0.023 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.05 0.051 0.32 1 -0.29 3 4
CD2AP 0.022 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.049 0.054 0.32 1 -0.35 3 4
GRB2 0.022 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.009 0.099 0.28 15 -0.36 18 33
cytoskeleton organization 0.004 0.042 0.2 1 -0.36 2 3
Nephrin/NEPH1 0.027 0.046 0.2 1 -0.32 4 5
Nephrin/NEPH1/ZO-1 0.041 0.053 -10000 0 -0.35 4 4
EPO signaling 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
BCL2L1 0.041 0.054 0.34 2 -10000 0 2
CRKL 0.023 0.063 0.3 9 -0.28 2 11
mol:DAG 0.025 0.041 -10000 0 -0.33 1 1
HRAS 0.015 0.077 0.28 17 -10000 0 17
MAPK8 0.004 0.053 0.19 13 -0.34 1 14
RAP1A 0.024 0.063 0.3 9 -0.28 2 11
GAB1 0.024 0.062 0.3 8 -0.27 2 10
MAPK14 0.005 0.055 0.21 3 -0.34 1 4
EPO 0.026 0.028 0.26 6 -10000 0 6
PLCG1 0.026 0.041 -10000 0 -0.34 1 1
EPOR/TRPC2/IP3 Receptors 0.026 0.01 -10000 0 -10000 0 0
RAPGEF1 0.023 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.044 0.037 -10000 0 -0.37 2 2
GAB1/SHC/GRB2/SOS1 0.047 0.049 0.26 5 -10000 0 5
EPO/EPOR (dimer) 0.036 0.024 0.23 1 -10000 0 1
IRS2 0.02 0.066 0.3 8 -0.28 5 13
STAT1 0.031 0.04 -10000 0 -10000 0 0
STAT5B 0.029 0.041 -10000 0 -0.33 1 1
cell proliferation 0.001 0.054 0.2 11 -0.32 1 12
GAB1/SHIP/PIK3R1/SHP2/SHC 0.036 0.038 -10000 0 -10000 0 0
TEC 0.021 0.067 0.3 8 -0.29 5 13
SOCS3 0.02 0.038 -10000 0 -0.56 2 2
STAT1 (dimer) 0.03 0.04 -10000 0 -10000 0 0
JAK2 0.023 0.011 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.06 0.05 0.33 1 -0.29 2 3
EPO/EPOR 0.036 0.024 0.23 1 -10000 0 1
LYN 0.02 0.038 -10000 0 -0.56 2 2
TEC/VAV2 0.034 0.064 0.27 6 -0.35 5 11
elevation of cytosolic calcium ion concentration 0.026 0.01 -10000 0 -10000 0 0
SHC1 0.022 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.046 0.034 -10000 0 -0.28 2 2
mol:IP3 0.025 0.041 -10000 0 -0.33 1 1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP 0.042 0.062 0.3 7 -0.28 4 11
SH2B3 0.024 0.039 -10000 0 -0.56 2 2
NFKB1 0.005 0.055 0.18 20 -0.34 1 21
EPO/EPOR (dimer)/JAK2/SOCS3 0.009 0.034 0.26 2 -0.2 6 8
PTPN6 0.016 0.046 0.3 1 -0.29 2 3
TEC/VAV2/GRB2 0.042 0.063 0.27 6 -0.36 4 10
EPOR 0.026 0.01 -10000 0 -10000 0 0
INPP5D 0.021 0.027 -10000 0 -0.56 1 1
mol:GDP 0.047 0.049 0.26 5 -10000 0 5
SOS1 0.023 0.004 -10000 0 -10000 0 0
PLCG2 0.022 0.005 -10000 0 -10000 0 0
CRKL/CBL/C3G 0.045 0.053 0.27 6 -0.27 1 7
VAV2 0.022 0.067 0.3 8 -0.31 4 12
CBL 0.024 0.064 0.3 9 -0.28 2 11
SHC/Grb2/SOS1 0.03 0.03 -10000 0 -0.27 1 1
STAT5A 0.029 0.041 -10000 0 -0.33 1 1
GRB2 0.022 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.044 0.046 -10000 0 -10000 0 0
LYN/PLCgamma2 0.03 0.03 -10000 0 -0.41 2 2
PTPN11 0.023 0.002 -10000 0 -10000 0 0
BTK -0.001 0.1 0.3 7 -0.31 32 39
BCL2 0.042 0.056 0.35 1 -10000 0 1
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.011 0.026 -10000 0 -0.42 2 2
MAP4K4 0.005 0.063 -10000 0 -0.47 2 2
BAG4 0.019 0.009 -10000 0 -10000 0 0
PKC zeta/ceramide 0.014 0.031 -10000 0 -0.18 8 8
NFKBIA 0.022 0.005 -10000 0 -10000 0 0
BIRC3 0.015 0.065 -10000 0 -0.56 6 6
BAX -0.001 0.061 -10000 0 -0.34 14 14
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AKT1 0.012 0.12 0.65 15 -10000 0 15
BAD -0.004 0.032 0.18 2 -0.18 9 11
SMPD1 0.007 0.055 0.21 4 -0.26 3 7
RB1 -0.003 0.032 0.18 3 -0.18 8 11
FADD/Caspase 8 0.024 0.082 -10000 0 -0.45 3 3
MAP2K4 -0.005 0.032 0.18 4 -10000 0 4
NSMAF 0.022 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.002 0.043 0.2 12 -10000 0 12
EGF 0.015 0.072 0.24 3 -0.56 7 10
mol:ceramide -0.001 0.033 0.17 2 -0.19 10 12
MADD 0.023 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.01 0.025 -10000 0 -0.39 2 2
ASAH1 0.02 0.007 -10000 0 -10000 0 0
negative regulation of cell cycle -0.003 0.032 0.18 3 -0.18 8 11
cell proliferation 0.011 0.059 -10000 0 -0.26 13 13
BID -0.001 0.13 -10000 0 -0.61 17 17
MAP3K1 -0.003 0.032 0.18 3 -0.18 9 12
EIF2A 0.049 0.095 0.3 19 -10000 0 19
TRADD 0.022 0.005 -10000 0 -10000 0 0
CRADD 0.023 0.002 -10000 0 -10000 0 0
MAPK3 -0.001 0.042 0.25 3 -10000 0 3
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.001 0.041 0.28 2 -10000 0 2
Cathepsin D/ceramide 0.013 0.033 0.17 1 -0.18 9 10
FADD 0.004 0.057 -10000 0 -0.47 2 2
KSR1 0.001 0.043 0.19 12 -0.18 9 21
MAPK8 -0.004 0.047 -10000 0 -0.26 3 3
PRKRA 0.002 0.043 0.19 14 -0.18 8 22
PDGFA 0.02 0.038 -10000 0 -0.56 2 2
TRAF2 0.022 0.004 -10000 0 -10000 0 0
IGF1 0.005 0.1 0.24 1 -0.56 15 16
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.001 0.033 0.17 2 -0.19 10 12
CTSD 0.022 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.032 0.008 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.012 0.063 -10000 0 -0.28 13 13
PRKCD 0.021 0.007 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.01 0.025 -10000 0 -0.39 2 2
RelA/NF kappa B1 0.033 0.008 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.023 0.002 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.006 0.055 -10000 0 -0.49 2 2
TNFR1A/BAG4/TNF-alpha 0.027 0.056 -10000 0 -0.36 8 8
mol:Sphingosine-1-phosphate -0.011 0.026 -10000 0 -0.41 2 2
MAP2K1 -0.004 0.041 0.25 3 -10000 0 3
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.023 0.001 -10000 0 -10000 0 0
CYCS -0.001 0.041 -10000 0 -0.2 10 10
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.015 -10000 0 -10000 0 0
EIF2AK2 0.002 0.047 0.19 20 -10000 0 20
TNF-alpha/TNFR1A/FAN 0.034 0.053 -10000 0 -0.36 7 7
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.013 0.078 -10000 0 -0.38 11 11
MAP2K2 -0.004 0.042 0.25 3 -10000 0 3
SMPD3 0.003 0.076 0.2 2 -0.29 20 22
TNF 0.011 0.084 0.24 1 -0.56 10 11
PKC zeta/PAR4 0.032 0.008 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.005 0.042 0.24 7 -0.18 4 11
NF kappa B1/RelA/I kappa B alpha 0.06 0.023 -10000 0 -10000 0 0
AIFM1 -0.001 0.037 -10000 0 -0.18 7 7
BCL2 0.023 0.011 0.24 1 -10000 0 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.013 0.011 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0.008 0.056 -10000 0 -0.26 15 15
MAP2K4 0.013 0.029 -10000 0 -10000 0 0
IKBKB 0.022 0.018 0.38 1 -10000 0 1
TNFRSF10B 0.02 0.007 -10000 0 -10000 0 0
TNFRSF10A 0.019 0.028 -10000 0 -0.56 1 1
SMPD1 0.006 0.005 -10000 0 -10000 0 0
IKBKG 0.023 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.002 0.1 -10000 0 -0.56 15 15
TRAIL/TRAILR2 0.018 0.017 -10000 0 -10000 0 0
TRAIL/TRAILR3 -0.01 0.095 -10000 0 -0.27 47 47
TRAIL/TRAILR1 0.016 0.027 -10000 0 -0.42 1 1
TRAIL/TRAILR4 0.008 0.056 -10000 0 -0.26 15 15
TRAIL/TRAILR1/DAP3/GTP 0.022 0.028 -10000 0 -0.33 1 1
IKK complex 0.006 0.032 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.016 0.004 -10000 0 -10000 0 0
MAPK3 -0.006 0.005 -10000 0 -10000 0 0
MAP3K1 0.016 0.029 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.002 0.1 -10000 0 -0.56 15 15
TRADD 0.022 0.005 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.019 0.028 -10000 0 -0.56 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.008 0.027 -10000 0 -0.29 2 2
CFLAR 0.022 0.004 -10000 0 -10000 0 0
MAPK1 -0.005 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP 0.029 0.038 -10000 0 -0.31 1 1
mol:ceramide 0.006 0.005 -10000 0 -10000 0 0
FADD 0.02 0.008 -10000 0 -10000 0 0
MAPK8 0.044 0.054 0.28 1 -10000 0 1
TRAF2 0.022 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) -0.036 0.17 -10000 0 -0.56 46 46
CHUK 0.022 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.02 0.03 -10000 0 -0.36 1 1
DAP3 0.022 0.005 -10000 0 -10000 0 0
CASP10 0.06 0.094 0.37 14 -10000 0 14
JNK cascade 0.008 0.056 -10000 0 -0.26 15 15
TRAIL (trimer) 0.013 0.011 -10000 0 -10000 0 0
TNFRSF10C -0.036 0.17 -10000 0 -0.56 46 46
TRAIL/TRAILR1/DAP3/GTP/FADD 0.023 0.032 -10000 0 -0.31 1 1
TRAIL/TRAILR2/FADD 0.021 0.023 -10000 0 -10000 0 0
cell death 0.006 0.005 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.009 0.018 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.02 0.007 -10000 0 -10000 0 0
CASP8 -0.006 0.083 -10000 0 -0.48 13 13
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.03 0.034 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.047 0.045 -10000 0 -0.33 5 5
HDAC3 0.022 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.01 0.004 -10000 0 -10000 0 0
GATA1/HDAC4 -0.007 0.13 -10000 0 -0.41 42 42
GATA1/HDAC5 -0.007 0.13 -10000 0 -0.41 42 42
GATA2/HDAC5 -0.012 0.13 -10000 0 -0.42 44 44
HDAC5/BCL6/BCoR 0.027 0.023 -10000 0 -10000 0 0
HDAC9 0.022 0.03 0.24 2 -0.56 1 3
Glucocorticoid receptor/Hsp90/HDAC6 0.042 0.015 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.031 0.01 -10000 0 -10000 0 0
HDAC5/YWHAB 0.033 0.008 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.01 0.003 -10000 0 -10000 0 0
GATA2 -0.036 0.17 -10000 0 -0.56 46 46
HDAC4/RFXANK 0.032 0.009 -10000 0 -10000 0 0
BCOR 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.022 0.005 -10000 0 -10000 0 0
HDAC5 0.022 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.026 0.051 -10000 0 -0.42 6 6
Histones 0.017 0.038 -10000 0 -0.26 3 3
ADRBK1 0.022 0.004 -10000 0 -10000 0 0
HDAC4 0.022 0.004 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.031 0.011 -10000 0 -10000 0 0
HDAC4/Ubc9 0.032 0.008 -10000 0 -10000 0 0
HDAC7 0.023 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.031 0.01 -10000 0 -10000 0 0
TUBA1B 0.023 0.002 -10000 0 -10000 0 0
HDAC6 0.023 0.003 -10000 0 -10000 0 0
HDAC5/RFXANK 0.032 0.008 -10000 0 -10000 0 0
CAMK4 0.019 0.038 -10000 0 -0.56 2 2
Tubulin/HDAC6 0.044 0.011 -10000 0 -10000 0 0
SUMO1 0.022 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.023 0.004 -10000 0 -10000 0 0
GATA1 -0.034 0.16 -10000 0 -0.56 42 42
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
NR3C1 0.021 0.006 -10000 0 -10000 0 0
SUMO1/HDAC4 0.032 0.03 -10000 0 -0.24 1 1
SRF 0.022 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.033 0.007 -10000 0 -10000 0 0
Tubulin 0.033 0.007 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.032 0.009 -10000 0 -10000 0 0
GNB1 0.021 0.027 -10000 0 -0.56 1 1
RANGAP1 0.022 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.02 0.017 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.042 0.022 -10000 0 -0.34 1 1
HDAC4/SRF 0.04 0.031 -10000 0 -0.36 2 2
HDAC4/ER alpha 0.014 0.09 -10000 0 -0.41 20 20
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.017 0.038 -10000 0 -0.26 3 3
cell motility 0.044 0.011 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.022 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.032 0.009 -10000 0 -10000 0 0
BCL6 0.014 0.011 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.022 0.004 -10000 0 -10000 0 0
Hsp90/HDAC6 0.032 0.008 -10000 0 -10000 0 0
ESR1 -0.002 0.12 -10000 0 -0.56 20 20
HDAC6/HDAC11 0.031 0.01 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.03 -10000 0 -10000 0 0
NPC 0.014 0.001 -10000 0 -10000 0 0
MEF2C 0.014 0.065 -10000 0 -0.56 6 6
RAN 0.023 0.002 -10000 0 -10000 0 0
HDAC4/MEF2C 0.056 0.05 -10000 0 -0.3 7 7
GNG2 0.016 0.06 -10000 0 -0.56 5 5
NCOR2 0.022 0.027 -10000 0 -0.56 1 1
TUBB2A 0.022 0.004 -10000 0 -10000 0 0
HDAC11 0.021 0.006 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
ANKRA2 0.021 0.006 -10000 0 -10000 0 0
RFXANK 0.022 0.005 -10000 0 -10000 0 0
nuclear import -0.026 0.009 -10000 0 -10000 0 0
BARD1 signaling 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
BARD1/CSTF1 0.033 0.007 -10000 0 -10000 0 0
ATM 0.023 0.004 -10000 0 -10000 0 0
UBE2D3 0.022 0.005 -10000 0 -10000 0 0
PRKDC 0.022 0.005 -10000 0 -10000 0 0
ATR 0.018 0.009 -10000 0 -10000 0 0
UBE2L3 0.022 0.006 -10000 0 -10000 0 0
FANCD2 0.012 0.008 -10000 0 -10000 0 0
protein ubiquitination 0.08 0.059 -10000 0 -10000 0 0
XRCC5 0.022 0.004 -10000 0 -10000 0 0
XRCC6 0.022 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.041 0.016 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
DNA-PK 0.043 0.013 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.011 0.1 0.3 1 -0.55 11 12
FANCF 0.022 0.004 -10000 0 -10000 0 0
BRCA1 0.023 0.003 -10000 0 -10000 0 0
CCNE1 0.079 0.11 0.28 105 -10000 0 105
CDK2/Cyclin E1 0.07 0.075 0.27 31 -10000 0 31
FANCG 0.022 0.024 0.38 2 -10000 0 2
BRCA1/BACH1/BARD1 0.033 0.007 -10000 0 -10000 0 0
FANCE 0.023 0.004 -10000 0 -10000 0 0
FANCC 0.023 0.004 -10000 0 -10000 0 0
NBN 0.022 0.005 -10000 0 -10000 0 0
FANCA 0.023 0.02 0.31 2 -10000 0 2
DNA repair 0.017 0.082 0.29 9 -0.42 5 14
BRCA1/BARD1/ubiquitin 0.033 0.007 -10000 0 -10000 0 0
BARD1/DNA-PK 0.054 0.017 -10000 0 -10000 0 0
FANCL 0.022 0.017 0.38 1 -10000 0 1
mRNA polyadenylation -0.033 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.02 0.029 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 0.039 0.018 -10000 0 -10000 0 0
BRCA1/BARD1/P53 0.044 0.026 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 0.044 0.011 -10000 0 -10000 0 0
BRCA1/BACH1 0.023 0.003 -10000 0 -10000 0 0
BARD1 0.022 0.004 -10000 0 -10000 0 0
PCNA 0.022 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.043 0.013 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 0.042 0.014 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA 0.069 0.048 -10000 0 -10000 0 0
BARD1/DNA-PK/P53 0.06 0.024 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin 0.033 0.007 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP 0.033 0.012 -10000 0 -10000 0 0
FA complex 0.032 0.042 0.41 1 -0.26 2 3
BARD1/EWS 0.032 0.009 -10000 0 -10000 0 0
RBBP8 -0.009 0.003 -10000 0 -10000 0 0
TP53 0.022 0.006 -10000 0 -10000 0 0
TOPBP1 0.02 0.008 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.042 0.025 -10000 0 -10000 0 0
BRCA1/BARD1 0.088 0.063 -10000 0 -10000 0 0
CSTF1 0.023 0.003 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.017 0.003 -10000 0 -10000 0 0
CDK2 0.023 0.002 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.052 0.074 0.24 64 -10000 0 64
RAD50 0.021 0.006 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.033 0.007 -10000 0 -10000 0 0
EWSR1 0.022 0.005 -10000 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.03 0.032 0.24 1 -0.36 1 2
EFNA5 0.02 0.027 -10000 0 -0.56 1 1
FYN 0.001 0.033 0.18 6 -0.32 2 8
neuron projection morphogenesis 0.03 0.032 0.24 1 -0.36 1 2
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.03 0.033 0.24 1 -0.36 1 2
EPHA5 0.019 0.052 0.25 19 -10000 0 19
Signaling events mediated by HDAC Class III

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
EP300 0.022 0.004 -10000 0 -10000 0 0
HDAC4 0.022 0.004 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.01 0.016 -10000 0 -0.3 1 1
CDKN1A -0.009 0.003 -10000 0 -10000 0 0
KAT2B 0.02 0.027 -10000 0 -0.56 1 1
BAX 0.022 0.004 -10000 0 -10000 0 0
FOXO3 -0.004 0.003 -10000 0 -10000 0 0
FOXO1 0.022 0.006 -10000 0 -10000 0 0
FOXO4 0.011 0.003 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.022 0.004 -10000 0 -10000 0 0
TAT 0.017 0.025 0.31 2 -10000 0 2
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.019 0.029 0.31 1 -0.42 1 2
PPARGC1A -0.078 0.22 -10000 0 -0.56 81 81
FHL2 0.025 0.02 0.24 4 -10000 0 4
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.03 0.009 -10000 0 -10000 0 0
HIST2H4A -0.01 0.016 0.3 1 -10000 0 1
SIRT1/FOXO3a 0.011 0.031 -10000 0 -0.2 9 9
SIRT1 0.02 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.041 0.014 -10000 0 -10000 0 0
SIRT1/Histone H1b 0.021 0.035 -10000 0 -0.2 2 2
apoptosis -0.041 0.013 -10000 0 -10000 0 0
SIRT1/PGC1A -0.042 0.14 -10000 0 -0.35 81 81
p53/SIRT1 0.025 0.008 -10000 0 -10000 0 0
SIRT1/FOXO4 0.019 0.032 -10000 0 -0.21 1 1
FOXO1/FHL2/SIRT1 0.04 0.017 -10000 0 -10000 0 0
HIST1H1E 0.014 0.015 0.16 2 -10000 0 2
SIRT1/p300 0.03 0.009 -10000 0 -10000 0 0
muscle cell differentiation -0.014 0.038 0.36 1 -10000 0 1
TP53 0.02 0.005 -10000 0 -10000 0 0
KU70/SIRT1/BAX 0.041 0.013 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
MEF2D 0.022 0.005 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.031 0.015 0.27 1 -10000 0 1
ACSS2 -0.01 0.003 -10000 0 -10000 0 0
SIRT1/PCAF/MYOD 0.014 0.038 -10000 0 -0.36 1 1
IL1-mediated signaling events

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
UBC13/UEV1A 0.032 0.006 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.021 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0 0.056 -10000 0 -0.38 3 3
IRAK/TOLLIP 0.023 0.007 -10000 0 -10000 0 0
IKBKB 0.022 0.018 0.38 1 -10000 0 1
IKBKG 0.023 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 0.029 0.1 0.3 2 -0.42 19 21
IL1A 0.009 0.12 0.24 20 -0.56 19 39
IL1B -0.021 0.066 -10000 0 -0.41 13 13
IRAK/TRAF6/p62/Atypical PKCs 0.03 0.032 -10000 0 -10000 0 0
IL1R2 0.034 0.049 0.24 24 -10000 0 24
IL1R1 0.022 0.027 -10000 0 -0.56 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.027 0.063 0.28 2 -0.28 3 5
TOLLIP 0.022 0.004 -10000 0 -10000 0 0
TICAM2 0.015 0.06 -10000 0 -0.56 5 5
MAP3K3 0.023 0.003 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.015 0.002 -10000 0 -10000 0 0
IKK complex/ELKS 0.034 0.053 0.38 1 -0.33 1 2
JUN -0.011 0.036 0.31 1 -10000 0 1
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.021 0.053 -10000 0 -0.3 9 9
IL1 alpha/IL1R1/IL1RAP/MYD88 0.025 0.076 -10000 0 -0.35 12 12
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.031 0.076 -10000 0 -0.33 12 12
IL1 beta fragment/IL1R1/IL1RAP 0.013 0.053 -10000 0 -0.33 9 9
NFKB1 0.022 0.005 -10000 0 -10000 0 0
MAPK8 -0.008 0.039 0.33 1 -10000 0 1
IRAK1 -0.013 0.004 -10000 0 -10000 0 0
IL1RN/IL1R1 0.033 0.044 0.27 1 -0.58 2 3
IRAK4 0.023 0.003 -10000 0 -10000 0 0
PRKCI 0.013 0.011 -10000 0 -10000 0 0
TRAF6 0.023 0.004 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0 0.057 -10000 0 -0.33 5 5
CHUK 0.022 0.005 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.013 0.053 -10000 0 -0.33 9 9
IL1 beta/IL1R2 0.026 0.073 0.27 3 -0.36 13 16
IRAK/TRAF6/TAK1/TAB1/TAB2 0.029 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.016 0.048 -10000 0 -0.28 9 9
IRAK3 0.008 0.091 -10000 0 -0.56 12 12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.021 0.065 -10000 0 -0.3 13 13
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.003 0.063 -10000 0 -0.32 13 13
IL1 alpha/IL1R1/IL1RAP 0.019 0.078 -10000 0 -0.38 12 12
RELA 0.023 0.001 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.021 0.007 -10000 0 -10000 0 0
MYD88 0.021 0.007 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.039 0.022 -10000 0 -10000 0 0
IL1RAP 0.014 0.011 -10000 0 -10000 0 0
UBE2N 0.023 0.002 -10000 0 -10000 0 0
IRAK/TRAF6 0.007 0.051 -10000 0 -10000 0 0
CASP1 0.02 0.038 -10000 0 -0.56 2 2
IL1RN/IL1R2 0.041 0.048 0.29 3 -0.42 2 5
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.019 0.054 -10000 0 -0.31 9 9
TMEM189-UBE2V1 0.011 0.019 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.001 0.072 -10000 0 -0.33 13 13
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
IL1RN 0.023 0.045 0.27 4 -0.56 2 6
TRAF6/TAK1/TAB1/TAB2 0.042 0.011 -10000 0 -10000 0 0
MAP2K6 -0.005 0.042 0.34 1 -10000 0 1
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.007 0.08 -10000 0 -0.43 7 7
BAG4 0.019 0.009 -10000 0 -10000 0 0
BAD 0.002 0.032 0.15 2 -10000 0 2
NFKBIA 0.022 0.005 -10000 0 -10000 0 0
BIRC3 0.015 0.065 -10000 0 -0.56 6 6
BAX 0.003 0.03 0.13 1 -10000 0 1
EnzymeConsortium:3.1.4.12 0.004 0.022 0.077 1 -0.093 6 7
IKBKB 0.018 0.09 0.29 4 -0.46 5 9
MAP2K2 0.003 0.037 0.18 9 -10000 0 9
MAP2K1 0.002 0.039 0.2 8 -10000 0 8
SMPD1 0.003 0.028 -10000 0 -0.15 3 3
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.033 0.099 0.26 13 -0.49 4 17
MAP2K4 0.003 0.026 0.17 1 -10000 0 1
protein ubiquitination 0.011 0.083 0.25 1 -0.42 6 7
EnzymeConsortium:2.7.1.37 0.001 0.04 0.19 8 -10000 0 8
response to UV 0 0 0.002 9 -10000 0 9
RAF1 0.005 0.037 0.18 9 -10000 0 9
CRADD 0.023 0.002 -10000 0 -10000 0 0
mol:ceramide 0.005 0.033 0.13 2 -0.14 6 8
I-kappa-B-alpha/RELA/p50/ubiquitin 0.03 0.007 -10000 0 -10000 0 0
MADD 0.023 0.004 -10000 0 -10000 0 0
MAP3K1 0.004 0.029 0.16 2 -10000 0 2
TRADD 0.022 0.005 -10000 0 -10000 0 0
RELA/p50 0.023 0.001 -10000 0 -10000 0 0
MAPK3 0.003 0.042 0.19 8 -0.21 1 9
MAPK1 0.003 0.04 0.19 7 -10000 0 7
p50/RELA/I-kappa-B-alpha 0.033 0.008 -10000 0 -10000 0 0
FADD 0.029 0.099 0.26 12 -0.55 3 15
KSR1 0.005 0.039 0.17 10 -10000 0 10
MAPK8 0.001 0.028 0.16 3 -10000 0 3
TRAF2 0.022 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK 0.008 0.076 -10000 0 -0.45 5 5
TNF R/SODD 0.026 0.015 -10000 0 -10000 0 0
TNF 0.011 0.084 0.24 1 -0.56 10 11
CYCS 0.002 0.036 0.2 1 -0.22 2 3
IKBKG 0.009 0.079 0.26 1 -0.42 5 6
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.01 0.083 -10000 0 -0.47 6 6
RELA 0.023 0.001 -10000 0 -10000 0 0
RIPK1 0.022 0.004 -10000 0 -10000 0 0
AIFM1 0.002 0.032 0.13 1 -0.18 1 2
TNF/TNF R/SODD 0.027 0.056 -10000 0 -0.36 8 8
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.018 0.072 -10000 0 -0.52 7 7
NSMAF 0.011 0.079 0.29 2 -0.46 5 7
response to hydrogen peroxide 0 0 0.002 9 -10000 0 9
BCL2 0.023 0.011 0.24 1 -10000 0 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.032 0.074 -10000 0 -0.37 8 8
Ran/GTP/Exportin 1/HDAC1 -0.01 0.004 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.015 0.083 -10000 0 -0.34 10 10
SUMO1 0.022 0.004 -10000 0 -10000 0 0
ZFPM1 0.021 0.027 -10000 0 -0.56 1 1
NPC/RanGAP1/SUMO1/Ubc9 0.01 0.003 -10000 0 -10000 0 0
FKBP3 0.022 0.005 -10000 0 -10000 0 0
Histones 0.04 0.065 -10000 0 -10000 0 0
YY1/LSF 0.012 0.064 -10000 0 -0.29 5 5
SMG5 0.022 0.005 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 0.012 0.041 -10000 0 -0.28 8 8
I kappa B alpha/HDAC1 0.019 0.057 -10000 0 -0.26 1 1
SAP18 0.022 0.006 -10000 0 -10000 0 0
RELA 0.018 0.049 -10000 0 -0.44 1 1
HDAC1/Smad7 0.04 0.024 -10000 0 -0.36 1 1
RANGAP1 0.022 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.017 0.062 -10000 0 -0.26 1 1
NuRD/MBD3 Complex 0.024 0.043 -10000 0 -0.36 3 3
NF kappa B1 p50/RelA 0.015 0.078 -10000 0 -0.36 5 5
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.036 0.17 -10000 0 -0.56 46 46
GATA1 -0.034 0.16 -10000 0 -0.56 42 42
Mad/Max 0.032 0.009 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.003 0.094 -10000 0 -0.38 10 10
RBBP7 0.022 0.005 -10000 0 -10000 0 0
NPC 0.014 0.001 -10000 0 -10000 0 0
RBBP4 0.022 0.004 -10000 0 -10000 0 0
MAX 0.022 0.005 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
NFKBIA 0.011 0.032 -10000 0 -0.21 8 8
KAT2B 0.02 0.027 -10000 0 -0.56 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0.014 0.032 -10000 0 -0.36 1 1
SIN3 complex 0.052 0.02 -10000 0 -10000 0 0
SMURF1 0.022 0.006 -10000 0 -10000 0 0
CHD3 0.022 0.006 -10000 0 -10000 0 0
SAP30 0.021 0.006 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.022 0.005 -10000 0 -10000 0 0
YY1/HDAC3 0.011 0.061 -10000 0 -0.35 7 7
YY1/HDAC2 0.013 0.063 -10000 0 -0.3 5 5
YY1/HDAC1 0.014 0.062 -10000 0 -0.29 5 5
NuRD/MBD2 Complex (MeCP1) 0.024 0.035 -10000 0 -0.25 1 1
PPARG -0.021 0.13 -10000 0 -0.34 55 55
HDAC8/hEST1B 0.043 0.013 -10000 0 -10000 0 0
UBE2I 0.022 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.006 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.017 0.064 -10000 0 -0.36 2 2
MBD3L2 -0.018 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.04 0.024 -10000 0 -0.36 1 1
CREBBP 0.022 0.005 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.019 0.064 -10000 0 -0.32 8 8
HDAC1 0.022 0.004 -10000 0 -10000 0 0
HDAC3 0.011 0.032 -10000 0 -0.21 8 8
HDAC2 0.023 0.002 -10000 0 -10000 0 0
YY1 0.012 0.011 -10000 0 -0.2 1 1
HDAC8 0.023 0.002 -10000 0 -10000 0 0
SMAD7 0.021 0.027 -10000 0 -0.56 1 1
NCOR2 0.022 0.027 -10000 0 -0.56 1 1
MXD1 0.022 0.005 -10000 0 -10000 0 0
STAT3 0.015 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.025 0.062 -10000 0 -0.26 5 5
YY1/SAP30/HDAC1 0.025 0.059 -10000 0 -0.27 4 4
EP300 0.022 0.004 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.015 0.005 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.032 -10000 0 -0.21 8 8
histone deacetylation 0.024 0.035 -10000 0 -0.25 1 1
STAT3 (dimer non-phopshorylated)/HDAC3 0.015 0.034 -10000 0 -0.25 1 1
nuclear export -0.043 0.013 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GATAD2B 0.022 0.005 -10000 0 -10000 0 0
GATAD2A 0.022 0.004 -10000 0 -10000 0 0
GATA2/HDAC3 -0.017 0.12 -10000 0 -0.35 44 44
GATA1/HDAC1 -0.008 0.13 -10000 0 -0.41 42 42
GATA1/HDAC3 -0.014 0.12 -10000 0 -0.33 41 41
CHD4 0.021 0.006 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.022 0.061 -10000 0 -0.42 8 8
SIN3/HDAC complex/Mad/Max 0.011 0.057 -10000 0 -0.28 11 11
NuRD Complex 0.021 0.059 -10000 0 -0.34 3 3
positive regulation of chromatin silencing 0.037 0.064 -10000 0 -10000 0 0
SIN3B 0.022 0.005 -10000 0 -10000 0 0
MTA2 0.023 0.002 -10000 0 -10000 0 0
SIN3A 0.023 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
SUMO1/HDAC1 0.032 0.03 -10000 0 -0.26 1 1
HDAC complex 0.055 0.016 -10000 0 -10000 0 0
GATA1/Fog1 -0.009 0.13 -10000 0 -0.41 43 43
FKBP25/HDAC1/HDAC2 0.043 0.013 -10000 0 -10000 0 0
TNF 0.011 0.084 0.24 1 -0.56 10 11
negative regulation of cell growth 0.011 0.056 -10000 0 -0.27 11 11
NuRD/MBD2/PRMT5 Complex 0.024 0.035 -10000 0 -0.25 1 1
Ran/GTP/Exportin 1 0.03 0.03 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.005 0.066 -10000 0 -0.34 11 11
SIN3/HDAC complex/NCoR1 -0.002 0.079 -10000 0 -0.32 20 20
TFCP2 0.023 0.002 -10000 0 -10000 0 0
NR2C1 0.023 0.002 -10000 0 -10000 0 0
MBD3 0.021 0.027 -10000 0 -0.56 1 1
MBD2 0.022 0.005 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.01 0.091 -10000 0 -0.34 26 26
KLHL20 0.016 0.059 0.17 1 -0.25 9 10
CYFIP2 0.009 0.084 -10000 0 -0.56 10 10
Rac1/GDP 0.011 0.07 0.27 1 -10000 0 1
ENAH -0.01 0.096 -10000 0 -0.34 29 29
AP1M1 0.022 0.005 -10000 0 -10000 0 0
RAP1B 0.022 0.005 -10000 0 -10000 0 0
RAP1A 0.022 0.005 -10000 0 -10000 0 0
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
CDC42/GTP 0.015 0.029 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.01 0.037 -10000 0 -0.2 9 9
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.051 0.026 -10000 0 -0.33 1 1
RAPGEF1 -0.005 0.08 -10000 0 -0.32 1 1
CTNND1 0.023 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.007 0.1 -10000 0 -0.34 29 29
CRK -0.004 0.073 -10000 0 -0.33 6 6
E-cadherin/gamma catenin/alpha catenin 0.043 0.014 -10000 0 -10000 0 0
alphaE/beta7 Integrin 0.031 0.022 -10000 0 -0.42 1 1
IQGAP1 0.023 0.003 -10000 0 -10000 0 0
NCKAP1 0.023 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.04 0.013 -10000 0 -10000 0 0
DLG1 -0.002 0.066 -10000 0 -0.34 13 13
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.007 0.011 -10000 0 -10000 0 0
MLLT4 0.023 0.003 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.041 0.013 -10000 0 -10000 0 0
PI3K -0.009 0.014 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.032 0.009 -10000 0 -10000 0 0
TIAM1 0.022 0.004 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.049 0.018 -10000 0 -10000 0 0
AKT1 0.004 0.031 0.13 1 -10000 0 1
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
CDH1 0.022 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.066 0.27 1 -10000 0 1
actin cytoskeleton organization 0.015 0.048 0.17 5 -0.18 8 13
CDC42/GDP 0.014 0.069 0.25 2 -10000 0 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.015 0.005 -10000 0 -10000 0 0
ITGB7 0.022 0.027 -10000 0 -0.56 1 1
RAC1 0.022 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.053 0.019 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin 0.037 0.013 -10000 0 -10000 0 0
mol:GDP 0 0.075 0.28 1 -10000 0 1
CDC42/GTP/IQGAP1 0.029 0.008 -10000 0 -10000 0 0
JUP 0.023 0.003 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.022 0.065 0.27 1 -10000 0 1
RAC1/GTP/IQGAP1 0.03 0.007 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.032 0.008 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
CDC42 0.022 0.005 -10000 0 -10000 0 0
CTNNA1 0.021 0.006 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.01 0.042 0.15 7 -0.24 6 13
NME1 0.023 0.01 0.24 1 -10000 0 1
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.007 0.092 -10000 0 -0.34 25 25
regulation of cell-cell adhesion 0.009 0.024 -10000 0 -10000 0 0
WASF2 0.007 0.026 -10000 0 -10000 0 0
Rap1/GTP 0.017 0.039 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.06 0.028 -10000 0 -0.31 1 1
CCND1 0.01 0.05 0.16 6 -0.3 6 12
VAV2 -0.013 0.13 -10000 0 -0.65 10 10
RAP1/GDP 0.019 0.054 0.25 1 -10000 0 1
adherens junction assembly -0.007 0.09 -10000 0 -0.33 25 25
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.022 0.004 -10000 0 -10000 0 0
PIP5K1C 0.022 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.044 0.026 -10000 0 -0.3 1 1
E-cadherin/beta catenin 0.01 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.009 0.093 -10000 0 -0.34 25 25
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
Rac1/GTP -0.014 0.079 -10000 0 -0.41 11 11
E-cadherin/beta catenin/alpha catenin 0.042 0.015 -10000 0 -10000 0 0
ITGAE 0.022 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.007 0.1 -10000 0 -0.35 29 29
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.024 0.008 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 0.009 0.003 -10000 0 -10000 0 0
mol:DAG -0.01 0.02 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0.022 0.008 -10000 0 -10000 0 0
CaM/Ca2+ 0.019 0.021 -10000 0 -10000 0 0
HIF1A 0.026 0.005 -10000 0 -10000 0 0
GAB1 0.022 0.006 -10000 0 -10000 0 0
AKT1 0.054 0.078 0.31 3 -10000 0 3
PLCG1 -0.01 0.02 -10000 0 -10000 0 0
NOS3 0.036 0.052 0.31 1 -10000 0 1
CBL 0.022 0.004 -10000 0 -10000 0 0
mol:NO 0.041 0.075 0.42 6 -0.39 2 8
FLT1 0.012 0.004 -10000 0 -10000 0 0
PGF 0.033 0.049 0.24 24 -10000 0 24
VEGFR1 homodimer/NRP2/VEGFR121 0.033 0.027 -10000 0 -0.33 1 1
CALM1 0.022 0.005 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
eNOS/Hsp90 0.043 0.072 0.3 1 -0.38 3 4
endothelial cell proliferation 0.006 0.057 -10000 0 -10000 0 0
mol:Ca2+ -0.01 0.02 -10000 0 -10000 0 0
MAPK3 -0.011 0.038 0.34 3 -10000 0 3
MAPK1 -0.01 0.041 0.34 4 -10000 0 4
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
PLGF homodimer 0.033 0.049 0.24 24 -10000 0 24
PRKACA 0.022 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.13 0.26 -10000 0 -0.56 125 125
VEGFA homodimer 0.022 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.024 0.008 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.012 0.04 0.33 4 -10000 0 4
PI3K 0.028 0.035 -10000 0 -10000 0 0
PRKCA -0.012 0.023 -10000 0 -0.29 1 1
PRKCB -0.024 0.062 -10000 0 -0.31 16 16
VEGFR1 homodimer/PLGF homodimer 0.03 0.033 -10000 0 -10000 0 0
VEGFA 0.022 0.004 -10000 0 -10000 0 0
VEGFB 0.023 0.002 -10000 0 -10000 0 0
mol:IP3 -0.01 0.02 -10000 0 -10000 0 0
RASA1 -0.008 0.02 -10000 0 -10000 0 0
NRP2 0.02 0.038 -10000 0 -0.56 2 2
VEGFR1 homodimer 0.012 0.004 -10000 0 -10000 0 0
VEGFB homodimer 0.023 0.002 -10000 0 -10000 0 0
NCK1 0.019 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.028 0.15 0.46 4 -0.44 12 16
PTPN11 0.023 0.002 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.027 0.034 -10000 0 -10000 0 0
mol:L-citrulline 0.041 0.075 0.42 6 -0.39 2 8
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.046 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.03 0.017 -10000 0 -10000 0 0
CD2AP 0.022 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.035 0.04 -10000 0 -10000 0 0
PDPK1 0.057 0.088 0.34 2 -10000 0 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.036 0.013 -10000 0 -10000 0 0
mol:NADP 0.041 0.075 0.42 6 -0.39 2 8
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.045 0.017 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.022 0.026 -10000 0 -0.34 2 2
Arf6 downstream 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
PLAUR 0.017 0.019 -10000 0 -10000 0 0
regulation of axonogenesis -0.004 0.024 0.24 3 -0.17 3 6
myoblast fusion -0.026 0.035 0.34 1 -10000 0 1
mol:GTP 0.016 0.028 -10000 0 -0.15 11 11
regulation of calcium-dependent cell-cell adhesion -0.044 0.028 -10000 0 -10000 0 0
ARF1/GTP 0.027 0.028 -10000 0 -10000 0 0
mol:GM1 0.007 0.021 -10000 0 -10000 0 0
mol:Choline 0.004 0.02 0.23 3 -10000 0 3
lamellipodium assembly 0.008 0.046 -10000 0 -0.33 7 7
MAPK3 0.017 0.018 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.045 0.029 -10000 0 -10000 0 0
ARF1 0.022 0.004 -10000 0 -10000 0 0
ARF6/GDP 0.026 0.036 -10000 0 -0.34 1 1
ARF1/GDP 0.025 0.047 -10000 0 -0.27 3 3
ARF6 0.03 0.012 -10000 0 -10000 0 0
RAB11A 0.023 0.003 -10000 0 -10000 0 0
TIAM1 0.023 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.017 0.018 -10000 0 -10000 0 0
actin filament bundle formation -0.025 0.043 0.25 3 -10000 0 3
KALRN 0.008 0.027 -10000 0 -0.31 3 3
RAB11FIP3/RAB11A 0.033 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.025 0.044 -10000 0 -0.25 3 3
NME1 0.024 0.012 0.25 1 -10000 0 1
Rac1/GDP 0.026 0.045 -10000 0 -0.25 3 3
substrate adhesion-dependent cell spreading 0.016 0.028 -10000 0 -0.15 11 11
cortical actin cytoskeleton organization 0.008 0.046 -10000 0 -0.33 7 7
RAC1 0.022 0.004 -10000 0 -10000 0 0
liver development 0.016 0.028 -10000 0 -0.15 11 11
ARF6/GTP 0.016 0.028 -10000 0 -0.15 11 11
RhoA/GTP 0.026 0.025 -10000 0 -10000 0 0
mol:GDP 0.007 0.029 -10000 0 -0.21 8 8
ARF6/GTP/RAB11FIP3/RAB11A 0.04 0.028 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
PLD1 0.009 0.028 0.28 3 -10000 0 3
RAB11FIP3 0.022 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.008 0.046 -10000 0 -0.33 7 7
ruffle organization 0.004 0.024 0.17 3 -0.24 3 6
regulation of epithelial cell migration 0.016 0.028 -10000 0 -0.15 11 11
PLD2 0.015 0.018 -10000 0 -10000 0 0
PIP5K1A 0.004 0.024 0.17 3 -0.24 3 6
mol:Phosphatidic acid 0.004 0.02 0.23 3 -10000 0 3
Rac1/GTP 0.008 0.047 -10000 0 -0.34 7 7
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.045 0.11 -10000 0 -0.38 12 12
CaM/Ca2+ 0.016 0.004 -10000 0 -10000 0 0
AKT1 0.022 0.005 -10000 0 -10000 0 0
AKT2 0.021 0.007 -10000 0 -10000 0 0
STXBP4 0.023 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.032 0.12 0.25 5 -0.38 18 23
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
CALM1 0.022 0.005 -10000 0 -10000 0 0
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
TBC1D4 -0.009 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.022 0.005 -10000 0 -10000 0 0
YWHAB 0.023 0.004 -10000 0 -10000 0 0
SNARE/Synip 0.043 0.014 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
ASIP 0.008 0.025 0.24 2 -10000 0 2
PRKCI 0.013 0.011 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.016 0.004 -10000 0 -10000 0 0
RHOQ 0.022 0.006 -10000 0 -10000 0 0
GYS1 0.005 0.003 -10000 0 -10000 0 0
PRKCZ 0.022 0.005 -10000 0 -10000 0 0
TRIP10 0.022 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.029 0.009 -10000 0 -10000 0 0
AS160/14-3-3 0.018 0.04 -10000 0 -0.34 1 1
VAMP2 0.022 0.006 -10000 0 -10000 0 0
SLC2A4 0.031 0.12 0.27 3 -0.42 18 21
STX4 0.023 0.003 -10000 0 -10000 0 0
GSK3B 0.013 0.007 -10000 0 -10000 0 0
SFN 0.04 0.072 0.24 45 -0.38 3 48
LNPEP 0.021 0.006 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.009 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.032 0.014 -10000 0 -10000 0 0
CDKN1B 0.018 0.063 -10000 0 -0.42 5 5
CDKN1A 0.015 0.049 -10000 0 -0.34 6 6
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.022 0.005 -10000 0 -10000 0 0
FOXO3 0.014 0.057 -10000 0 -0.42 5 5
AKT1 0.005 0.052 -10000 0 -0.39 7 7
BAD 0.023 0.002 -10000 0 -10000 0 0
AKT3 0.01 0.017 -10000 0 -0.35 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.013 0.057 -10000 0 -0.37 8 8
AKT1/ASK1 0.031 0.064 -10000 0 -0.37 7 7
BAD/YWHAZ 0.042 0.014 -10000 0 -10000 0 0
RICTOR 0.018 0.009 -10000 0 -10000 0 0
RAF1 0.021 0.006 -10000 0 -10000 0 0
JNK cascade -0.03 0.062 0.36 7 -10000 0 7
TSC1 0.012 0.057 -10000 0 -0.37 8 8
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
AKT1/RAF1 0.034 0.067 -10000 0 -0.59 2 2
EP300 0.022 0.004 -10000 0 -10000 0 0
mol:GDP 0.006 0.055 -10000 0 -0.38 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.016 0.035 -10000 0 -0.29 4 4
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
TBC1D4 0.003 0.001 -10000 0 -10000 0 0
MAP3K5 0.023 0.003 -10000 0 -10000 0 0
MAPKAP1 0.023 0.003 -10000 0 -10000 0 0
negative regulation of cell cycle -0.025 0.068 0.37 6 -0.28 1 7
YWHAH 0.022 0.005 -10000 0 -10000 0 0
AKT1S1 0.015 0.046 -10000 0 -0.37 4 4
CASP9 0.014 0.045 -10000 0 -0.35 5 5
YWHAB 0.023 0.004 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.072 0.3 2 -0.58 2 4
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.042 0.014 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
AKT2/p21CIP1 0.012 0.055 0.25 1 -0.42 4 5
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.009 0.052 -10000 0 -0.34 8 8
CHUK 0.015 0.043 -10000 0 -0.37 4 4
BAD/BCL-XL 0.034 0.065 -10000 0 -0.58 2 2
mTORC2 0.023 0.012 -10000 0 -10000 0 0
AKT2 0.01 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.031 0.088 0.35 1 -0.48 6 7
PDPK1 0.022 0.004 -10000 0 -10000 0 0
MDM2 0.016 0.063 -10000 0 -0.4 6 6
MAPKKK cascade -0.034 0.066 0.57 2 -10000 0 2
MDM2/Cbp/p300 0.047 0.073 0.3 1 -0.54 2 3
TSC1/TSC2 0.012 0.054 0.24 3 -0.57 2 5
proteasomal ubiquitin-dependent protein catabolic process 0.045 0.07 0.29 1 -0.51 2 3
glucose import -0.004 0.028 0.2 2 -0.31 3 5
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.014 0.047 -10000 0 -0.35 4 4
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.005 0.025 -10000 0 -0.32 3 3
GSK3A 0.016 0.048 -10000 0 -0.35 5 5
FOXO1 0.015 0.05 -10000 0 -0.6 2 2
GSK3B 0.025 0.072 -10000 0 -0.5 3 3
SFN 0.04 0.072 0.24 45 -0.38 3 48
G1/S transition of mitotic cell cycle 0.034 0.074 0.28 6 -0.59 1 7
p27Kip1/14-3-3 family 0.027 0.056 -10000 0 -0.54 2 2
PRKACA 0.022 0.005 -10000 0 -10000 0 0
KPNA1 0.02 0.007 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
YWHAG 0.022 0.004 -10000 0 -10000 0 0
RHEB 0.022 0.004 -10000 0 -10000 0 0
CREBBP 0.022 0.005 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.003 0.047 -10000 0 -10000 0 0
PLK1 0.067 0.12 -10000 0 -0.78 2 2
CDKN1B 0.071 0.11 0.3 4 -0.38 9 13
FOXO3 0.07 0.11 0.34 1 -0.78 3 4
KAT2B 0.027 0.032 -10000 0 -0.56 1 1
FOXO1/SIRT1 0.02 0.036 -10000 0 -10000 0 0
CAT 0.051 0.14 -10000 0 -1.1 3 3
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
AKT1 0.03 0.017 -10000 0 -10000 0 0
FOXO1 0.008 0.044 -10000 0 -10000 0 0
MAPK10 0.018 0.05 0.19 15 -0.3 7 22
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.036 0.061 0.33 2 -10000 0 2
response to oxidative stress 0.01 0.01 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.071 0.1 -10000 0 -0.69 2 2
XPO1 0.021 0.007 -10000 0 -10000 0 0
EP300 0.023 0.005 -10000 0 -10000 0 0
BCL2L11 0.033 0.044 -10000 0 -0.78 1 1
FOXO1/SKP2 0.017 0.04 0.25 2 -10000 0 2
mol:GDP 0.01 0.01 -10000 0 -10000 0 0
RAN 0.024 0.002 -10000 0 -10000 0 0
GADD45A 0.049 0.15 -10000 0 -0.64 15 15
YWHAQ 0.022 0.004 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.014 0.12 -10000 0 -0.46 21 21
MST1 0.028 0.02 0.24 1 -10000 0 1
CSNK1D 0.022 0.004 -10000 0 -10000 0 0
CSNK1E 0.022 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.017 0.089 -10000 0 -0.42 11 11
YWHAB 0.023 0.004 -10000 0 -10000 0 0
MAPK8 0.023 0.032 0.19 15 -10000 0 15
MAPK9 0.022 0.033 0.19 17 -10000 0 17
YWHAG 0.022 0.004 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
YWHAZ 0.022 0.005 -10000 0 -10000 0 0
SIRT1 0.021 0.013 -10000 0 -10000 0 0
SOD2 0.062 0.1 0.49 1 -0.62 2 3
RBL2 0.038 0.2 -10000 0 -0.84 20 20
RAL/GDP 0.038 0.013 -10000 0 -10000 0 0
CHUK 0.029 0.016 -10000 0 -10000 0 0
Ran/GTP 0.019 0.002 -10000 0 -10000 0 0
CSNK1G2 0.022 0.004 -10000 0 -10000 0 0
RAL/GTP 0.04 0.012 -10000 0 -10000 0 0
CSNK1G1 0.023 0.003 -10000 0 -10000 0 0
FASLG -0.023 0.28 -10000 0 -1.3 21 21
SKP2 0.02 0.027 0.33 3 -10000 0 3
USP7 0.023 0.005 -10000 0 -10000 0 0
IKBKB 0.028 0.024 0.38 1 -10000 0 1
CCNB1 0.062 0.11 -10000 0 -0.78 2 2
FOXO1-3a-4/beta catenin 0.072 0.092 0.42 2 -0.39 1 3
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.04 0.25 2 -10000 0 2
CSNK1A1 0.021 0.006 -10000 0 -10000 0 0
SGK1 0.03 0.016 -10000 0 -10000 0 0
CSNK1G3 0.021 0.006 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.031 0.01 -10000 0 -10000 0 0
ZFAND5 0.031 0.067 0.36 3 -10000 0 3
SFN 0.04 0.072 0.24 45 -0.38 3 48
CDK2 0.023 0.003 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.026 0.091 -10000 0 -0.43 10 10
CREBBP 0.022 0.005 -10000 0 -10000 0 0
FBXO32 0.066 0.13 0.47 2 -0.7 3 5
BCL6 0.054 0.1 -10000 0 -0.69 1 1
RALB 0.023 0.003 -10000 0 -10000 0 0
RALA 0.023 0.005 -10000 0 -10000 0 0
YWHAH 0.022 0.005 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

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
CRKL 0.022 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.022 0.01 -10000 0 -10000 0 0
DOCK1 0.022 0.005 -10000 0 -10000 0 0
ITGA4 0.018 0.053 -10000 0 -0.56 4 4
RAC1 0.022 0.004 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.046 -10000 0 -0.42 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.039 0.039 -10000 0 -0.36 4 4
alpha4/beta7 Integrin/Paxillin 0.031 0.038 -10000 0 -0.33 5 5
lamellipodium assembly -0.013 0.1 -10000 0 -0.39 30 30
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
TLN1 0.021 0.007 -10000 0 -10000 0 0
PXN -0.01 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
ARF6/GTP 0.04 0.035 -10000 0 -0.29 4 4
cell adhesion 0.038 0.034 -10000 0 -0.3 3 3
CRKL/CBL 0.032 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.031 0.035 -10000 0 -0.33 4 4
ITGB1 0.022 0.004 -10000 0 -10000 0 0
ITGB7 0.022 0.027 -10000 0 -0.56 1 1
ARF6/GDP 0.022 0.01 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.041 0.053 -10000 0 -0.42 5 5
p130Cas/Crk/Dock1 0.042 0.015 -10000 0 -10000 0 0
VCAM1 0.02 0.049 0.24 3 -0.56 3 6
alpha4/beta1 Integrin/Paxillin/Talin 0.039 0.035 -10000 0 -0.31 3 3
alpha4/beta1 Integrin/Paxillin/GIT1 0.042 0.036 -10000 0 -0.31 4 4
BCAR1 0.022 0.005 -10000 0 -10000 0 0
mol:GDP -0.041 0.035 0.31 4 -10000 0 4
CBL 0.022 0.004 -10000 0 -10000 0 0
PRKACA 0.022 0.005 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.039 0.035 -10000 0 -0.31 3 3
Rac1/GTP -0.015 0.11 -10000 0 -0.43 30 30
Arf6 trafficking events

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
SLC2A4 0.018 0.046 -10000 0 -0.56 3 3
CLTC 0.02 0.07 -10000 0 -0.38 12 12
calcium ion-dependent exocytosis 0.006 0.024 -10000 0 -0.24 2 2
Dynamin 2/GTP 0.02 0.007 -10000 0 -10000 0 0
EXOC4 0.023 0.004 -10000 0 -10000 0 0
CD59 0.004 0.04 -10000 0 -0.33 6 6
CPE 0.009 0.017 -10000 0 -0.36 1 1
CTNNB1 0.021 0.007 -10000 0 -10000 0 0
membrane fusion 0.007 0.015 -10000 0 -10000 0 0
CTNND1 -0.005 0.036 0.18 18 -10000 0 18
DNM2 0.022 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.005 0.042 0.21 4 -0.3 4 8
TSHR 0.012 0.017 -10000 0 -10000 0 0
INS 0 0.11 -10000 0 -0.55 17 17
BIN1 0.02 0.038 -10000 0 -0.56 2 2
mol:Choline 0.007 0.015 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.01 0.005 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0.02 0.007 -10000 0 -10000 0 0
JUP 0.003 0.043 -10000 0 -0.34 7 7
ASAP2/amphiphysin II 0.039 0.026 -10000 0 -0.32 2 2
ARF6/GTP 0.016 0.004 -10000 0 -10000 0 0
CDH1 0.005 0.034 -10000 0 -0.34 4 4
clathrin-independent pinocytosis 0.016 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.022 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.016 0.004 -10000 0 -10000 0 0
EXOC2 0.022 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.006 0.043 -10000 0 -0.32 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.023 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.032 0.054 0.32 5 -10000 0 5
positive regulation of phagocytosis 0.01 0.003 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.029 0.008 -10000 0 -10000 0 0
ACAP1 0.009 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.039 0.095 -10000 0 -0.41 8 8
clathrin heavy chain/ACAP1 0.005 0.054 0.24 3 -0.34 7 10
JIP4/KLC1 0.04 0.013 -10000 0 -10000 0 0
EXOC1 0.021 0.006 -10000 0 -10000 0 0
exocyst 0.011 0.037 -10000 0 -0.32 3 3
RALA/GTP 0.016 0.003 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.029 0.008 -10000 0 -10000 0 0
receptor recycling 0.016 0.004 -10000 0 -10000 0 0
CTNNA1 -0.005 0.034 0.18 16 -10000 0 16
NME1 0.01 0.005 -10000 0 -10000 0 0
clathrin coat assembly 0.022 0.071 -10000 0 -0.37 12 12
IL2RA 0.005 0.036 -10000 0 -0.32 5 5
VAMP3 0.01 0.003 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.029 0.064 -10000 0 -0.31 10 10
EXOC6 0.022 0.005 -10000 0 -10000 0 0
PLD1 0.007 0.015 0.18 3 -10000 0 3
PLD2 0.009 0.008 -10000 0 -10000 0 0
EXOC5 0.022 0.005 -10000 0 -10000 0 0
PIP5K1C 0.004 0.037 -10000 0 -0.31 4 4
SDC1 0.003 0.045 -10000 0 -0.34 7 7
ARF6/GDP 0.019 0.006 -10000 0 -10000 0 0
EXOC7 0.022 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.034 0.056 -10000 0 -0.32 5 5
mol:Phosphatidic acid 0.007 0.015 -10000 0 -10000 0 0
endocytosis -0.038 0.026 0.32 2 -10000 0 2
SCAMP2 0.023 0.002 -10000 0 -10000 0 0
ADRB2 -0.052 0.14 0.3 1 -0.43 13 14
EXOC3 0.018 0.009 -10000 0 -10000 0 0
ASAP2 0.022 0.004 -10000 0 -10000 0 0
Dynamin 2/GDP 0.023 0.008 -10000 0 -10000 0 0
KLC1 0.022 0.005 -10000 0 -10000 0 0
AVPR2 -0.045 0.14 0.23 4 -0.31 54 58
RALA 0.022 0.005 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.028 0.052 -10000 0 -0.31 3 3
Regulation of Telomerase

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
Telomerase catalytic core complex 0.057 0.11 0.44 3 -0.56 2 5
RAD9A 0.023 0.004 -10000 0 -10000 0 0
AP1 -0.015 0.14 -10000 0 -0.41 53 53
IFNAR2 0.025 0.007 -10000 0 -10000 0 0
AKT1 0.008 0.057 -10000 0 -0.48 3 3
ER alpha/Oestrogen 0 0.086 -10000 0 -0.4 21 21
NFX1/SIN3/HDAC complex 0.012 0.06 -10000 0 -0.29 11 11
EGF 0.016 0.072 0.24 3 -0.56 7 10
SMG5 0.022 0.005 -10000 0 -10000 0 0
SMG6 0.022 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.011 -10000 0 -10000 0 0
TERT/c-Abl 0.061 0.1 0.47 1 -0.53 2 3
SAP18 0.022 0.006 -10000 0 -10000 0 0
MRN complex 0.041 0.016 -10000 0 -10000 0 0
WT1 0.037 0.051 0.25 26 -10000 0 26
WRN 0.021 0.007 -10000 0 -10000 0 0
SP1 0.027 0.008 -10000 0 -10000 0 0
SP3 0.024 0.006 -10000 0 -10000 0 0
TERF2IP 0.022 0.005 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.062 0.094 -10000 0 -0.49 2 2
Mad/Max 0.035 0.012 -10000 0 -10000 0 0
TERT 0.057 0.11 0.44 3 -0.57 2 5
CCND1 0.068 0.18 0.47 4 -1.1 6 10
MAX 0.023 0.007 -10000 0 -10000 0 0
RBBP7 0.023 0.005 -10000 0 -10000 0 0
RBBP4 0.023 0.004 -10000 0 -10000 0 0
TERF2 0.019 0.008 -10000 0 -10000 0 0
PTGES3 0.023 0.002 -10000 0 -10000 0 0
SIN3A 0.023 0.003 -10000 0 -10000 0 0
Telomerase/911 0.045 0.074 0.32 1 -0.5 3 4
CDKN1B 0.012 0.034 -10000 0 -0.35 4 4
RAD1 0.018 0.009 -10000 0 -10000 0 0
XRCC5 0.022 0.004 -10000 0 -10000 0 0
XRCC6 0.022 0.004 -10000 0 -10000 0 0
SAP30 0.022 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.03 0.011 -10000 0 -10000 0 0
UBE3A 0.024 0.005 -10000 0 -10000 0 0
JUN 0.023 0.006 -10000 0 -10000 0 0
E6 0.001 0.002 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.005 -10000 0 -10000 0 0
FOS -0.042 0.18 -10000 0 -0.56 53 53
IFN-gamma/IRF1 0.034 0.044 -10000 0 -0.41 4 4
PARP2 0.022 0.005 -10000 0 -10000 0 0
BLM 0.028 0.036 0.27 10 -10000 0 10
Telomerase 0.024 0.059 0.33 1 -10000 0 1
IRF1 0.025 0.007 -10000 0 -10000 0 0
ESR1 -0.001 0.12 -10000 0 -0.56 20 20
KU/TER 0.032 0.008 -10000 0 -10000 0 0
ATM/TRF2 0.032 0.009 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.017 0.056 -10000 0 -0.3 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.017 0.057 -10000 0 -0.3 4 4
HDAC1 0.023 0.004 -10000 0 -10000 0 0
HDAC2 0.026 0.007 -10000 0 -10000 0 0
ATM 0.011 0.012 -10000 0 -10000 0 0
SMAD3 -0.011 0.004 -10000 0 -10000 0 0
ABL1 0.023 0.003 -10000 0 -10000 0 0
MXD1 0.023 0.007 -10000 0 -10000 0 0
MRE11A 0.022 0.004 -10000 0 -10000 0 0
HUS1 0.022 0.005 -10000 0 -10000 0 0
RPS6KB1 0.023 0.003 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.064 0.12 -10000 0 -0.58 4 4
NR2F2 0.019 0.007 -10000 0 -10000 0 0
MAPK3 0 0.013 -10000 0 -10000 0 0
MAPK1 0 0.013 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.005 -10000 0 -10000 0 0
HNRNPC 0.022 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.011 0.012 -10000 0 -10000 0 0
NBN 0.022 0.005 -10000 0 -10000 0 0
EGFR 0.023 0.084 0.37 11 -0.56 6 17
mol:Oestrogen 0.001 0.001 -10000 0 -10000 0 0
EGF/EGFR 0.026 0.084 0.27 8 -0.44 12 20
MYC 0.022 0.009 -10000 0 -10000 0 0
IL2 0.023 0.01 -10000 0 -10000 0 0
KU 0.032 0.008 -10000 0 -10000 0 0
RAD50 0.021 0.006 -10000 0 -10000 0 0
HSP90AA1 0.022 0.005 -10000 0 -10000 0 0
TGFB1 0.021 0.005 -10000 0 -10000 0 0
TRF2/BLM 0.034 0.024 0.25 2 -10000 0 2
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.068 0.1 -10000 0 -0.54 2 2
SP1/HDAC2 0.042 0.013 -10000 0 -10000 0 0
PINX1 0.02 0.008 -10000 0 -10000 0 0
Telomerase/EST1A 0.061 0.093 -10000 0 -0.54 1 1
Smad3/Myc 0.019 0.008 -10000 0 -10000 0 0
911 complex 0.035 0.021 -10000 0 -10000 0 0
IFNG 0.021 0.055 0.25 2 -0.56 4 6
Telomerase/PinX1 0.056 0.093 -10000 0 -0.54 1 1
Telomerase/AKT1/mTOR/p70S6K 0.023 0.093 0.24 1 -0.5 10 11
SIN3B 0.023 0.005 -10000 0 -10000 0 0
YWHAE 0.022 0.006 -10000 0 -10000 0 0
Telomerase/EST1B 0.06 0.092 -10000 0 -0.56 1 1
response to DNA damage stimulus 0.004 0.015 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.056 0.024 -10000 0 -10000 0 0
TRF2/WRN 0.029 0.014 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.059 0.094 -10000 0 -0.48 2 2
E2F1 0.025 0.008 -10000 0 -10000 0 0
ZNFX1 0.023 0.004 -10000 0 -10000 0 0
PIF1 0.043 0.064 0.24 45 -10000 0 45
NCL 0.022 0.004 -10000 0 -10000 0 0
DKC1 0.023 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.017 0.01 -10000 0 -10000 0 0
TRAF2/ASK1 0.03 0.007 -10000 0 -10000 0 0
ATM 0.023 0.004 -10000 0 -10000 0 0
MAP2K3 -0.001 0.091 -10000 0 -0.35 17 17
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0 0.078 0.21 1 -0.36 12 13
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.017 0.053 -10000 0 -0.56 4 4
TXN 0.005 0.001 -10000 0 -10000 0 0
CALM1 0.022 0.005 -10000 0 -10000 0 0
GADD45A 0.022 0.004 -10000 0 -10000 0 0
GADD45B 0.006 0.095 -10000 0 -0.56 13 13
MAP3K1 0.021 0.006 -10000 0 -10000 0 0
MAP3K6 0.022 0.005 -10000 0 -10000 0 0
MAP3K7 0.023 0.003 -10000 0 -10000 0 0
MAP3K4 0.023 0.003 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.032 0.008 -10000 0 -10000 0 0
TAK1/TAB family -0.003 0.02 -10000 0 -0.14 7 7
RAC1/OSM/MEKK3 0.042 0.011 -10000 0 -10000 0 0
TRAF2 0.022 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.017 0.078 -10000 0 -0.32 9 9
TRAF6 0.005 0.001 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.047 0.075 0.25 55 -0.29 1 56
CCM2 0.022 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.044 0.046 0.24 4 -0.16 1 5
MAPK11 0.022 0.005 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.054 0.046 0.24 4 -10000 0 4
OSM/MEKK3 0.032 0.008 -10000 0 -10000 0 0
TAOK1 0.01 0.011 -10000 0 -0.22 1 1
TAOK2 0.011 0.002 -10000 0 -10000 0 0
TAOK3 0.011 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.023 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.023 0.003 -10000 0 -10000 0 0
MAP3K10 0.022 0.018 0.38 1 -10000 0 1
MAP3K3 0.023 0.003 -10000 0 -10000 0 0
TRX/ASK1 0.019 0.014 -10000 0 -10000 0 0
GADD45/MTK1/MTK1 0.037 0.071 -10000 0 -0.33 16 16
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.023 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.034 0.087 0.24 2 -0.33 10 12
ERC1 0.021 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.03 0.023 -10000 0 -0.42 1 1
NFKBIA -0.006 0.018 0.2 3 -10000 0 3
BIRC2 0.022 0.004 -10000 0 -10000 0 0
IKBKB 0.022 0.018 0.38 1 -10000 0 1
RIPK2 0.022 0.005 -10000 0 -10000 0 0
IKBKG 0.017 0.026 -10000 0 -10000 0 0
IKK complex/A20 0.025 0.1 -10000 0 -0.42 10 10
NEMO/A20/RIP2 0.022 0.005 -10000 0 -10000 0 0
XPO1 0.021 0.007 -10000 0 -10000 0 0
NEMO/ATM 0.017 0.096 -10000 0 -0.37 21 21
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
Exportin 1/RanGTP 0.028 0.009 -10000 0 -10000 0 0
IKK complex/ELKS 0.021 0.085 -10000 0 -0.4 9 9
BCL10/MALT1/TRAF6 0.043 0.013 -10000 0 -10000 0 0
NOD2 0.021 0.027 -10000 0 -0.56 1 1
NFKB1 0.023 0.005 -10000 0 -10000 0 0
RELA 0.024 0.002 -10000 0 -10000 0 0
MALT1 0.022 0.005 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.032 0.009 -10000 0 -10000 0 0
ATM 0.023 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.022 0.061 -10000 0 -0.42 8 8
TRAF6 0.023 0.004 -10000 0 -10000 0 0
PRKCA 0.02 0.038 -10000 0 -0.56 2 2
CHUK 0.022 0.005 -10000 0 -10000 0 0
UBE2D3 0.022 0.005 -10000 0 -10000 0 0
TNF 0.011 0.084 0.24 1 -0.56 10 11
NF kappa B1 p50/RelA 0.046 0.016 -10000 0 -10000 0 0
BCL10 0.022 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.006 0.017 0.2 3 -10000 0 3
beta TrCP1/SCF ubiquitin ligase complex 0.022 0.007 -10000 0 -10000 0 0
TNFRSF1A 0.021 0.006 -10000 0 -10000 0 0
IKK complex 0.025 0.094 -10000 0 -0.38 16 16
CYLD 0.022 0.005 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.032 0.098 -10000 0 -0.46 10 10
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.022 0.004 -9999 0 -10000 0 0
ITGB7 0.022 0.027 -9999 0 -0.56 1 1
ITGA4 0.018 0.053 -9999 0 -0.56 4 4
alpha4/beta7 Integrin 0.029 0.046 -9999 0 -0.42 5 5
alpha4/beta1 Integrin 0.029 0.042 -9999 0 -0.42 4 4
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.013 0.035 -10000 0 -0.32 5 5
CRKL 0.022 0.006 -10000 0 -10000 0 0
Rac1/GDP 0.017 0.003 -10000 0 -10000 0 0
DOCK1 0.022 0.005 -10000 0 -10000 0 0
ITGA4 0.018 0.053 -10000 0 -0.56 4 4
alpha4/beta7 Integrin/MAdCAM1 0.048 0.044 -10000 0 -0.31 5 5
EPO 0.017 0.03 0.24 6 -10000 0 6
alpha4/beta7 Integrin 0.029 0.046 -10000 0 -0.42 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.022 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.029 0.042 -10000 0 -0.42 4 4
EPO/EPOR (dimer) 0.032 0.02 -10000 0 -10000 0 0
lamellipodium assembly 0.045 0.12 -10000 0 -0.56 11 11
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
ARF6 0.022 0.005 -10000 0 -10000 0 0
JAK2 0.015 0.029 -10000 0 -0.33 3 3
PXN 0.023 0.002 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
MADCAM1 0.02 0.022 0.24 3 -10000 0 3
cell adhesion 0.047 0.043 -10000 0 -0.31 5 5
CRKL/CBL 0.032 0.009 -10000 0 -10000 0 0
ITGB1 0.022 0.004 -10000 0 -10000 0 0
SRC -0.012 0.055 -10000 0 -0.47 4 4
ITGB7 0.022 0.027 -10000 0 -0.56 1 1
RAC1 0.022 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.038 0.058 -10000 0 -0.48 5 5
p130Cas/Crk/Dock1 0.024 0.05 -10000 0 -0.46 3 3
VCAM1 0.02 0.049 0.24 3 -0.56 3 6
RHOA 0.021 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.052 0.038 -10000 0 -0.32 4 4
BCAR1 -0.013 0.053 -10000 0 -0.44 4 4
EPOR 0.022 0.004 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.022 0.004 -10000 0 -10000 0 0
GIT1 0.023 0.003 -10000 0 -10000 0 0
Rac1/GTP 0.045 0.12 -10000 0 -0.58 11 11
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.011 0.004 -10000 0 -10000 0 0
SNTA1 0.022 0.005 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.011 0.004 -10000 0 -10000 0 0
MAPK12 -0.003 0.002 -10000 0 -10000 0 0
CCND1 0.004 0.051 -10000 0 -0.42 6 6
p38 gamma/SNTA1 0.021 0.04 0.28 2 -10000 0 2
MAP2K3 0.022 0.006 -10000 0 -10000 0 0
PKN1 0.022 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint 0.003 0.035 0.2 14 -10000 0 14
MAP2K6 0.003 0.002 -10000 0 -10000 0 0
MAPT 0.002 0.057 0.25 4 -0.3 8 12
MAPK13 -0.009 0.003 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.01 0.003 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.036 0.024 -10000 0 -10000 0 0
CLOCK 0.022 0.007 -10000 0 -10000 0 0
TIMELESS/CRY2 0.032 0.018 -10000 0 -10000 0 0
DEC1/BMAL1 0.039 0.035 -10000 0 -10000 0 0
ATR 0.018 0.009 -10000 0 -10000 0 0
NR1D1 0.014 0.006 -10000 0 -10000 0 0
ARNTL 0.024 0.005 -10000 0 -10000 0 0
TIMELESS 0.014 0.006 -10000 0 -10000 0 0
NPAS2 0.024 0.002 -10000 0 -10000 0 0
CRY2 0.022 0.004 -10000 0 -10000 0 0
mol:CO -0.006 0 -10000 0 -10000 0 0
CHEK1 0.023 0.011 0.24 1 -10000 0 1
mol:HEME 0.006 0 -10000 0 -10000 0 0
PER1 0.019 0.038 -10000 0 -0.56 2 2
BMAL/CLOCK/NPAS2 0.048 0.018 -10000 0 -10000 0 0
BMAL1/CLOCK 0.022 0.05 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.036 0.024 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.036 0.024 -10000 0 -10000 0 0
mol:NADPH 0.006 0 -10000 0 -10000 0 0
PER1/TIMELESS 0.031 0.026 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.015 0.057 0.24 26 -10000 0 26
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.015 0.054 0.24 2 -10000 0 2
GNAI2 0.021 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 0.03 0.024 -10000 0 -0.35 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.031 0.24 2 -0.56 1 3
RhoA/GTP 0.016 0.055 -10000 0 -0.25 2 2
negative regulation of cAMP metabolic process 0.017 0.037 -10000 0 -0.26 1 1
GNAZ 0.016 0.06 -10000 0 -0.56 5 5
GNAI3 0.022 0.005 -10000 0 -10000 0 0
GNA12 0.022 0.005 -10000 0 -10000 0 0
S1PR5 0.024 0.036 0.24 6 -0.56 1 7
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.017 0.037 -10000 0 -0.26 1 1
RhoA/GDP 0.015 0.005 -10000 0 -10000 0 0
RHOA 0.021 0.007 -10000 0 -10000 0 0
GNAI1 0.021 0.027 -10000 0 -0.56 1 1
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.022 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.009 0.007 -10000 0 -10000 0 0
MDM2/SUMO1 0.031 0.033 0.24 1 -0.26 1 2
HDAC4 0.022 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.009 0.006 -10000 0 -10000 0 0
SUMO1 0.022 0.004 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.008 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 0.005 0.002 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.023 0.002 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.023 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.032 0.03 -10000 0 -0.24 1 1
SUMO1/HDAC1 0.032 0.03 -10000 0 -0.26 1 1
RANGAP1 0.022 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.053 0.022 0.26 1 -10000 0 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.01 0.003 -10000 0 -10000 0 0
Ran/GTP 0.022 0.029 -10000 0 -0.19 3 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.023 0.017 0.38 1 -10000 0 1
UBE2I 0.022 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.034 0.056 0.19 43 -10000 0 43
NPC 0.014 0.001 -10000 0 -10000 0 0
PIAS2 0.022 0.005 -10000 0 -10000 0 0
PIAS1 0.023 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.031 0.049 -10000 0 -0.34 7 7
MAPK9 0.005 0.002 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.01 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.024 0.044 -10000 0 -0.35 6 6
GNB1 0.021 0.027 -10000 0 -0.56 1 1
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.005 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.012 0.027 -10000 0 -0.27 4 4
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.002 0.007 0.071 4 -10000 0 4
GNAL 0.018 0.046 -10000 0 -0.56 3 3
GNG2 0.016 0.06 -10000 0 -0.56 5 5
CRH -0.011 0.019 0.24 1 -10000 0 1
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.005 0.001 -10000 0 -10000 0 0
MAPK11 0.005 0.001 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.021 0.027 0.56 1 -10000 0 1
PI3K Class IB/PDE3B 0.021 0.027 -10000 0 -0.56 1 1
PDE3B 0.021 0.027 -10000 0 -0.56 1 1
Arf1 pathway

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
coatomer protein complex 0.004 0.018 -10000 0 -10000 0 0
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.012 0.032 0.13 9 -0.17 3 12
AP2 0.019 0.021 0.27 1 -10000 0 1
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.03 0.009 -10000 0 -10000 0 0
CLTB 0.021 0.006 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.012 0.006 -10000 0 -10000 0 0
CD4 0.006 0.095 -10000 0 -0.56 13 13
CLTA 0.021 0.007 -10000 0 -10000 0 0
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.005 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.004 0.009 -10000 0 -10000 0 0
ARF1/GTP 0.026 0.011 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.006 0.003 -10000 0 -10000 0 0
mol:Choline 0.004 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.023 0.008 -10000 0 -10000 0 0
DDEF1 0.003 0.009 -10000 0 -10000 0 0
ARF1/GDP 0.002 0.015 -10000 0 -10000 0 0
AP2M1 0.013 0.02 0.38 1 -10000 0 1
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization 0.009 0.005 -10000 0 -10000 0 0
Rac/GTP 0.017 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.031 0.011 -10000 0 -10000 0 0
ARFIP2 0.018 0.013 -10000 0 -10000 0 0
COPA 0.022 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.004 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.01 0.033 -10000 0 -0.2 6 6
ARF1/GTP/ARHGAP10 0.015 0.007 -10000 0 -10000 0 0
GGA3 0.022 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.019 0.021 -10000 0 -0.24 2 2
AP2A1 0.022 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0.042 -10000 0 -0.21 10 10
ARF1/GDP/Membrin 0.02 0.024 -10000 0 -0.24 3 3
Arfaptin 2/Rac/GDP 0.029 0.009 -10000 0 -10000 0 0
CYTH2 0.024 0.006 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.029 0.011 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.017 0.003 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.007 0.028 -10000 0 -0.24 4 4
PLD2 0.004 0.009 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.005 0.001 -10000 0 -10000 0 0
PIP5K1A 0.004 0.009 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.014 0.019 -10000 0 -10000 0 0
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.004 0.009 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.005 0.001 -10000 0 -10000 0 0
GOSR2 0.008 0.022 -10000 0 -0.32 2 2
USO1 0.006 0.037 -10000 0 -0.32 6 6
GBF1 0.002 0.051 -10000 0 -0.32 12 12
ARF1/GTP/Arfaptin 2 0.03 0.012 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.018 0.047 0.25 1 -0.36 3 4
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.022 0.005 -9999 0 -10000 0 0
SMAD2 0.003 0.042 -9999 0 -0.25 3 3
SMAD3 0.02 0.028 -9999 0 -10000 0 0
SMAD3/SMAD4 0.025 0.055 -9999 0 -0.48 3 3
SMAD4/Ubc9/PIASy 0.043 0.014 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.039 0.053 -9999 0 -10000 0 0
PPM1A 0.022 0.004 -9999 0 -10000 0 0
CALM1 0.022 0.005 -9999 0 -10000 0 0
SMAD2/SMAD4 0.011 0.051 -9999 0 -0.25 4 4
MAP3K1 0.021 0.006 -9999 0 -10000 0 0
TRAP-1/SMAD4 0.033 0.008 -9999 0 -10000 0 0
MAPK3 0.023 0.003 -9999 0 -10000 0 0
MAPK1 0.022 0.006 -9999 0 -10000 0 0
NUP214 0.023 0.003 -9999 0 -10000 0 0
CTDSP1 0.022 0.004 -9999 0 -10000 0 0
CTDSP2 0.023 0.003 -9999 0 -10000 0 0
CTDSPL 0.021 0.007 -9999 0 -10000 0 0
KPNB1 0.023 0.003 -9999 0 -10000 0 0
TGFBRAP1 0.023 0.002 -9999 0 -10000 0 0
UBE2I 0.022 0.004 -9999 0 -10000 0 0
NUP153 0.022 0.004 -9999 0 -10000 0 0
KPNA2 0.023 0.004 -9999 0 -10000 0 0
PIAS4 0.022 0.004 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.021 0.006 -10000 0 -9999 0 0
PLK4 0.022 0.011 0.24 1 -9999 0 1
regulation of centriole replication -0.009 0.004 -10000 0 -9999 0 0
Atypical NF-kappaB pathway

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
BCL3/RelA 0.033 0.007 -10000 0 -10000 0 0
FBXW11 0.021 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.019 0.01 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.021 0.039 -10000 0 -10000 0 0
NFKBIA 0.01 0.022 -10000 0 -0.22 1 1
MAPK14 0.023 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0.02 0.009 -10000 0 -10000 0 0
ARRB2 0.01 0.003 -10000 0 -10000 0 0
REL 0.021 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0.02 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0.021 0.008 -10000 0 -10000 0 0
PIK3CA 0.012 0.012 -10000 0 -10000 0 0
NF kappa B1 p50 dimer 0.017 0.029 0.42 2 -10000 0 2
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
NFKB1 -0.008 0.027 0.58 1 -10000 0 1
RELA 0.023 0.001 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.017 0.035 0.24 1 -0.23 1 2
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.021 0.044 -10000 0 -10000 0 0
SRC 0.022 0.004 -10000 0 -10000 0 0
PI3K 0.017 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.017 0.035 0.25 1 -0.23 1 2
IKBKB 0.022 0.018 0.38 1 -10000 0 1
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.006 -10000 0 -10000 0 0
SYK 0.022 0.004 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 0.023 0.034 -10000 0 -0.25 1 1
cell death 0.02 0.042 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel 0.019 0.01 -10000 0 -10000 0 0
LCK 0.021 0.027 -10000 0 -0.56 1 1
BCL3 0.022 0.005 -10000 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.041 0.015 -9999 0 -9999 0 0
E-cadherin/beta catenin 0.031 0.011 -9999 0 -9999 0 0
CTNNB1 0.021 0.007 -9999 0 -9999 0 0
JUP 0.023 0.003 -9999 0 -9999 0 0
CDH1 0.022 0.005 -9999 0 -9999 0 0
Alternative NF-kappaB pathway

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.032 0.009 -10000 0 -9999 0 0
FBXW11 0.021 0.006 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.006 -10000 0 -9999 0 0
CHUK 0.022 0.005 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.06 0.025 -10000 0 -9999 0 0
NFKB1 0.022 0.005 -10000 0 -9999 0 0
MAP3K14 0.023 0.004 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.032 0.014 0.27 1 -9999 0 1
RELB 0.023 0.017 0.38 1 -9999 0 1
NFKB2 0.022 0.005 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.029 0.013 0.24 1 -9999 0 1
regulation of B cell activation 0.029 0.013 0.24 1 -9999 0 1
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 478 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.O2.A5IB TCGA.O2.A52W TCGA.O2.A52V TCGA.O2.A52S
109_MAP3K5 -0.17 0.021 0.021 -0.18
47_PPARGC1A 0 0.023 0.023 -0.56
105_BMP4 0.023 0.023 0.023 0.023
105_BMP6 0.023 0.023 0.023 0.023
105_BMP7 0.023 0.24 0.24 0.023
105_BMP2 -0.56 0.023 0.023 0.023
131_RELN/VLDLR 0.06 0.06 0.06 -0.33
30_TGFB1/TGF beta receptor Type II 0.028 0.021 0.021 0.021
84_STAT5B -0.34 0.024 0.024 -0.074
84_STAT5A -0.34 0.024 0.024 -0.074
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/LUSC-TP/4433379/LUSC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Gistic2/LUSC-TP/4426209/Gistic2_Analysis_4426266/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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