PARADIGM pathway analysis of mRNASeq expression and copy number data
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C18C9VNM
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 25 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
Nephrin/Neph1 signaling in the kidney podocyte 129
Angiopoietin receptor Tie2-mediated signaling 98
EGFR-dependent Endothelin signaling events 89
FOXA2 and FOXA3 transcription factor networks 76
PDGFR-alpha signaling pathway 63
Thromboxane A2 receptor signaling 50
Signaling mediated by p38-alpha and p38-beta 41
Glypican 1 network 38
BMP receptor signaling 33
Signaling events mediated by Stem cell factor receptor (c-Kit) 33
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 290 . 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 ( 290 ).

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
Nephrin/Neph1 signaling in the kidney podocyte 0.4448 129 4392 34 -0.45 0.028 1000 -1000 -0.037 -1000
Angiopoietin receptor Tie2-mediated signaling 0.3379 98 8667 88 -0.9 0.094 1000 -1000 -0.074 -1000
EGFR-dependent Endothelin signaling events 0.3069 89 1872 21 -0.56 0.038 1000 -1000 -0.042 -1000
FOXA2 and FOXA3 transcription factor networks 0.2621 76 3532 46 -1.1 0.031 1000 -1000 -0.11 -1000
PDGFR-alpha signaling pathway 0.2172 63 2808 44 -0.25 0.038 1000 -1000 -0.048 -1000
Thromboxane A2 receptor signaling 0.1724 50 5336 105 -0.56 0.097 1000 -1000 -0.048 -1000
Signaling mediated by p38-alpha and p38-beta 0.1414 41 1818 44 -0.17 0.027 1000 -1000 -0.034 -1000
Glypican 1 network 0.1310 38 1844 48 -0.33 0.051 1000 -1000 -0.033 -1000
BMP receptor signaling 0.1138 33 2682 81 -0.37 0.055 1000 -1000 -0.056 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1138 33 2606 78 -0.27 0.063 1000 -1000 -0.062 -1000
Endothelins 0.1069 31 3036 96 -0.61 0.034 1000 -1000 -0.054 -1000
Arf6 signaling events 0.1000 29 1805 62 -0.56 0.059 1000 -1000 -0.037 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1000 29 3706 125 -0.14 0.062 1000 -1000 -0.066 -1000
IL4-mediated signaling events 0.0931 27 2471 91 -0.87 0.52 1000 -1000 -0.1 -1000
Integrins in angiogenesis 0.0828 24 2095 84 -0.41 0.058 1000 -1000 -0.044 -1000
Signaling events mediated by PTP1B 0.0793 23 1773 76 -0.56 0.084 1000 -1000 -0.035 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0793 23 1598 68 -0.48 0.087 1000 -1000 -0.078 -1000
amb2 Integrin signaling 0.0759 22 1816 82 -0.37 0.036 1000 -1000 -0.036 -1000
Ceramide signaling pathway 0.0759 22 1736 76 -0.56 0.2 1000 -1000 -0.047 -1000
S1P1 pathway 0.0724 21 765 36 -0.16 0.027 1000 -1000 -0.045 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0724 21 2556 120 -0.23 0.12 1000 -1000 -0.052 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0690 20 1483 74 -0.56 0.064 1000 -1000 -0.073 -1000
FoxO family signaling 0.0552 16 1065 64 -0.86 0.063 1000 -1000 -0.065 -1000
Plasma membrane estrogen receptor signaling 0.0552 16 1431 86 -0.14 0.048 1000 -1000 -0.053 -1000
Ephrin A reverse signaling 0.0517 15 105 7 -0.032 0 1000 -1000 -0.019 -1000
Signaling events mediated by the Hedgehog family 0.0483 14 743 52 -0.036 0.04 1000 -1000 -0.039 -1000
Glucocorticoid receptor regulatory network 0.0483 14 1684 114 -0.57 0.14 1000 -1000 -0.06 -1000
Signaling events regulated by Ret tyrosine kinase 0.0483 14 1197 82 -0.064 0.028 1000 -1000 -0.06 -1000
TCR signaling in naïve CD8+ T cells 0.0448 13 1211 93 -0.2 0.11 1000 -1000 -0.053 -1000
E-cadherin signaling events 0.0448 13 65 5 -0.025 0.027 1000 -1000 0.001 -1000
LPA4-mediated signaling events 0.0414 12 148 12 -0.14 0.007 1000 -1000 -0.032 -1000
Coregulation of Androgen receptor activity 0.0414 12 981 76 -0.64 0.05 1000 -1000 -0.033 -1000
Syndecan-3-mediated signaling events 0.0414 12 450 35 -0.096 0.075 1000 -1000 -0.025 -1000
Nongenotropic Androgen signaling 0.0414 12 667 52 -0.11 0.045 1000 -1000 -0.042 -1000
TCGA08_rtk_signaling 0.0379 11 291 26 -0.22 0.062 1000 -1000 -0.009 -1000
S1P3 pathway 0.0379 11 483 42 -0.11 0.039 1000 -1000 -0.036 -1000
Caspase cascade in apoptosis 0.0345 10 792 74 -0.42 0.066 1000 -1000 -0.041 -1000
p75(NTR)-mediated signaling 0.0345 10 1346 125 -0.36 0.075 1000 -1000 -0.079 -1000
EPHB forward signaling 0.0345 10 859 85 -0.15 0.075 1000 -1000 -0.075 -1000
Calcium signaling in the CD4+ TCR pathway 0.0345 10 314 31 -0.11 0.028 1000 -1000 -0.038 -1000
E-cadherin signaling in keratinocytes 0.0345 10 447 43 -0.22 0.043 1000 -1000 -0.041 -1000
ErbB4 signaling events 0.0310 9 637 69 -0.22 0.087 1000 -1000 -0.046 -1000
Osteopontin-mediated events 0.0310 9 353 38 -0.065 0.048 1000 -1000 -0.048 -1000
Reelin signaling pathway 0.0310 9 517 56 -0.12 0.071 1000 -1000 -0.042 -1000
IL27-mediated signaling events 0.0310 9 490 51 -1 0.25 1000 -1000 -0.051 -1000
IL6-mediated signaling events 0.0310 9 739 75 -0.22 0.041 1000 -1000 -0.054 -1000
E-cadherin signaling in the nascent adherens junction 0.0310 9 728 76 -0.032 0.048 1000 -1000 -0.058 -1000
IL23-mediated signaling events 0.0310 9 570 60 -0.061 0.04 1000 -1000 -0.094 -1000
Regulation of nuclear SMAD2/3 signaling 0.0276 8 1192 136 -0.48 0.095 1000 -1000 -0.049 -1000
Syndecan-1-mediated signaling events 0.0276 8 275 34 -0.037 0.028 1000 -1000 -0.049 -1000
Noncanonical Wnt signaling pathway 0.0276 8 215 26 -0.14 0.027 1000 -1000 -0.055 -1000
HIF-1-alpha transcription factor network 0.0276 8 637 76 -0.1 0.086 1000 -1000 -0.089 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0276 8 746 85 -0.1 0.11 1000 -1000 -0.049 -1000
Presenilin action in Notch and Wnt signaling 0.0276 8 531 61 -0.15 0.083 1000 -1000 -0.053 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0276 8 453 52 -0.24 0.084 1000 -1000 -0.04 -1000
Effects of Botulinum toxin 0.0276 8 232 26 -0.17 0.045 1000 -1000 -0.02 -1000
Regulation of Telomerase 0.0276 8 870 102 -0.56 0.068 1000 -1000 -0.061 -1000
Visual signal transduction: Rods 0.0276 8 447 52 -0.15 0.053 1000 -1000 -0.046 -1000
Regulation of Androgen receptor activity 0.0276 8 594 70 -0.75 0.044 1000 -1000 -0.055 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0241 7 200 28 -0.11 0.044 1000 -1000 -0.025 -1000
ceramide signaling pathway 0.0241 7 375 49 0 0.041 1000 -1000 -0.049 -1000
Regulation of p38-alpha and p38-beta 0.0241 7 402 54 -0.14 0.065 1000 -1000 -0.053 -1000
Syndecan-4-mediated signaling events 0.0241 7 484 67 -0.35 0.092 1000 -1000 -0.046 -1000
PDGFR-beta signaling pathway 0.0241 7 772 97 -0.032 0.059 1000 -1000 -0.061 -1000
Cellular roles of Anthrax toxin 0.0207 6 243 39 -0.15 0.036 1000 -1000 -0.028 -1000
IFN-gamma pathway 0.0207 6 425 68 -0.25 0.066 1000 -1000 -0.06 -1000
Class IB PI3K non-lipid kinase events 0.0207 6 18 3 -0.012 0.012 1000 -1000 -0.008 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0172 5 318 54 -0.059 0.047 1000 -1000 -0.048 -1000
Syndecan-2-mediated signaling events 0.0172 5 363 69 -0.37 0.054 1000 -1000 -0.046 -1000
Fc-epsilon receptor I signaling in mast cells 0.0172 5 565 97 -0.065 0.049 1000 -1000 -0.063 -1000
PLK1 signaling events 0.0172 5 431 85 -0.008 0.054 1000 -1000 -0.037 -1000
IL1-mediated signaling events 0.0172 5 336 62 -0.14 0.072 1000 -1000 -0.048 -1000
S1P5 pathway 0.0172 5 86 17 -0.012 0.027 1000 -1000 -0.015 -1000
Ephrin B reverse signaling 0.0172 5 279 48 -0.019 0.039 1000 -1000 -0.034 -1000
TCGA08_p53 0.0172 5 39 7 -0.035 0.028 1000 -1000 -0.011 -1000
Canonical Wnt signaling pathway 0.0172 5 272 51 -0.15 0.078 1000 -1000 -0.057 -1000
Wnt signaling 0.0172 5 41 7 -0.003 0.027 1000 -1000 -0.025 -1000
Arf6 trafficking events 0.0172 5 377 71 -0.25 0.047 1000 -1000 -0.036 -1000
BCR signaling pathway 0.0172 5 574 99 -0.043 0.062 1000 -1000 -0.066 -1000
Ras signaling in the CD4+ TCR pathway 0.0172 5 101 17 -0.006 0.042 1000 -1000 -0.036 -1000
ErbB2/ErbB3 signaling events 0.0138 4 281 65 -0.059 0.048 1000 -1000 -0.057 -1000
IL12-mediated signaling events 0.0138 4 368 87 -0.16 0.06 1000 -1000 -0.086 -1000
Nectin adhesion pathway 0.0138 4 267 63 -0.025 0.054 1000 -1000 -0.054 -1000
LPA receptor mediated events 0.0138 4 448 102 -0.07 0.062 1000 -1000 -0.074 -1000
IGF1 pathway 0.0138 4 232 57 -0.022 0.065 1000 -1000 -0.045 -1000
S1P4 pathway 0.0138 4 118 25 -0.012 0.053 1000 -1000 -0.029 -1000
mTOR signaling pathway 0.0103 3 199 53 -0.017 0.048 1000 -1000 -0.04 -1000
Class I PI3K signaling events mediated by Akt 0.0103 3 229 68 -0.03 0.055 1000 -1000 -0.037 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0103 3 271 83 -0.23 0.048 1000 -1000 -0.041 -1000
FAS signaling pathway (CD95) 0.0103 3 153 47 -0.12 0.04 1000 -1000 -0.043 -1000
Class I PI3K signaling events 0.0103 3 232 73 -0.021 0.048 1000 -1000 -0.051 -1000
Signaling events mediated by PRL 0.0103 3 111 34 -0.037 0.04 1000 -1000 -0.05 -1000
FOXM1 transcription factor network 0.0103 3 159 51 -0.093 0.046 1000 -1000 -0.099 -1000
Aurora B signaling 0.0103 3 245 67 -0.24 0.049 1000 -1000 -0.047 -1000
Signaling events mediated by HDAC Class II 0.0069 2 158 75 -0.1 0.071 1000 -1000 -0.031 -1000
BARD1 signaling events 0.0069 2 167 57 -0.049 0.06 1000 -1000 -0.047 -1000
Hedgehog signaling events mediated by Gli proteins 0.0069 2 175 65 -0.012 0.066 1000 -1000 -0.045 -1000
EPO signaling pathway 0.0069 2 162 55 -0.003 0.075 1000 -1000 -0.048 -1000
Insulin-mediated glucose transport 0.0069 2 68 32 -0.03 0.049 1000 -1000 -0.038 -1000
HIF-2-alpha transcription factor network 0.0069 2 128 43 -0.18 0.096 1000 -1000 -0.057 -1000
Signaling mediated by p38-gamma and p38-delta 0.0069 2 43 15 -0.01 0.028 1000 -1000 -0.038 -1000
IL2 signaling events mediated by PI3K 0.0069 2 149 58 -0.015 0.062 1000 -1000 -0.047 -1000
Insulin Pathway 0.0069 2 211 74 -0.024 0.071 1000 -1000 -0.047 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0069 2 87 33 -0.054 0.068 1000 -1000 -0.031 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0034 1 25 23 -0.01 0.048 1000 -1000 -0.035 -1000
JNK signaling in the CD4+ TCR pathway 0.0034 1 24 17 0.014 0.045 1000 -1000 -0.038 -1000
Arf6 downstream pathway 0.0034 1 67 43 -0.044 0.045 1000 -1000 -0.039 -1000
Signaling events mediated by HDAC Class I 0.0034 1 166 104 -0.1 0.067 1000 -1000 -0.036 -1000
Retinoic acid receptors-mediated signaling 0.0034 1 110 58 -0.033 0.058 1000 -1000 -0.052 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0034 1 69 45 0 0.077 1000 -1000 -0.058 -1000
TCGA08_retinoblastoma 0.0034 1 10 8 -0.053 0.032 1000 -1000 -0.003 -1000
VEGFR1 specific signals 0.0034 1 89 56 -0.012 0.064 1000 -1000 -0.063 -1000
Canonical NF-kappaB pathway 0.0000 0 19 39 0 0.061 1000 -1000 -0.04 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.009 0.026 1000 -1000 -0.017 -1000
Visual signal transduction: Cones 0.0000 0 29 38 -0.018 0.055 1000 -1000 -0.019 -1000
Circadian rhythm pathway 0.0000 0 6 22 -0.009 0.059 1000 -1000 -0.047 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0.027 0.04 1000 -1000 0.003 -1000
Aurora A signaling 0.0000 0 19 60 -0.009 0.062 1000 -1000 -0.028 -1000
Aurora C signaling 0.0000 0 0 7 -0.02 0.028 1000 -1000 -0.014 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0000 0 5 37 -0.01 0.063 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class III 0.0000 0 16 40 -0.049 0.05 1000 -1000 -0.024 -1000
TRAIL signaling pathway 0.0000 0 5 48 0 0.07 1000 -1000 -0.051 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 1 36 -0.054 0.057 1000 -1000 -0.046 -1000
Atypical NF-kappaB pathway 0.0000 0 22 31 0 0.04 1000 -1000 -0.031 -1000
Glypican 2 network 0.0000 0 0 4 -0.005 -0.001 1000 -1000 0 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 2 27 0 0.062 1000 -1000 -0.039 -1000
IL2 signaling events mediated by STAT5 0.0000 0 13 22 0.007 0.041 1000 -1000 -0.053 -1000
Rapid glucocorticoid signaling 0.0000 0 9 20 -0.004 0.034 1000 -1000 -0.006 -1000
p38 MAPK signaling pathway 0.0000 0 35 44 0 0.055 1000 -1000 -0.031 -1000
Arf1 pathway 0.0000 0 25 54 -0.001 0.048 1000 -1000 -0.025 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.075 1000 -1000 0 -1000
Total NA 1522 97030 7203 -24 8 131000 -131000 -5.8 -131000
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.37 0.28 0.55 195 -10000 0 195
KIRREL -0.11 0.19 -10000 0 -0.69 26 26
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.37 0.28 -10000 0 -0.55 195 195
PLCG1 0.026 0.007 -10000 0 -10000 0 0
ARRB2 0.026 0.01 -10000 0 -10000 0 0
WASL 0.022 0.012 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.38 0.3 -10000 0 -0.54 212 212
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.32 0.25 -10000 0 -0.47 188 188
FYN -0.38 0.27 0.26 1 -0.51 212 213
mol:Ca2+ -0.37 0.3 -10000 0 -0.53 206 206
mol:DAG -0.38 0.3 -10000 0 -0.54 206 206
NPHS2 -0.29 0.31 -10000 0 -0.69 107 107
mol:IP3 -0.38 0.3 -10000 0 -0.54 206 206
regulation of endocytosis -0.34 0.27 -10000 0 -0.48 207 207
Nephrin/NEPH1/podocin/Cholesterol -0.39 0.3 -10000 0 -0.54 212 212
establishment of cell polarity -0.37 0.28 -10000 0 -0.55 195 195
Nephrin/NEPH1/podocin/NCK1-2 -0.35 0.29 -10000 0 -0.5 210 210
Nephrin/NEPH1/beta Arrestin2 -0.35 0.28 -10000 0 -0.49 207 207
NPHS1 -0.45 0.31 -10000 0 -0.67 187 187
Nephrin/NEPH1/podocin -0.37 0.28 -10000 0 -0.51 212 212
TJP1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.006 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.38 0.3 -10000 0 -0.54 206 206
CD2AP 0.026 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.38 0.3 -10000 0 -0.54 206 206
GRB2 0.026 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.45 0.3 0.28 1 -0.57 229 230
cytoskeleton organization -0.39 0.3 -10000 0 -0.58 184 184
Nephrin/NEPH1 -0.27 0.22 -10000 0 -0.41 191 191
Nephrin/NEPH1/ZO-1 -0.3 0.24 -10000 0 -0.46 191 191
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 -0.56 0.53 -10000 0 -1 164 164
NCK1/PAK1/Dok-R -0.25 0.21 -10000 0 -0.44 163 163
NCK1/Dok-R -0.7 0.7 -10000 0 -1.3 163 163
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.082 0.11 0.24 95 -10000 0 95
RELA 0.028 0.002 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
Rac/GDP 0.016 0.009 -10000 0 -10000 0 0
F2 0.094 0.12 0.26 91 -10000 0 91
TNIP2 0.027 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.63 0.63 -10000 0 -1.2 162 162
FN1 0.02 0.028 -10000 0 -10000 0 0
PLD2 -0.74 0.72 -10000 0 -1.3 163 163
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GRB14 -0.017 0.17 -10000 0 -0.62 20 20
ELK1 -0.63 0.6 -10000 0 -1.1 163 163
GRB7 0.026 0.007 -10000 0 -10000 0 0
PAK1 0.028 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.67 0.68 -10000 0 -1.2 163 163
CDKN1A -0.37 0.35 -10000 0 -0.68 152 152
ITGA5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.7 0.7 -10000 0 -1.3 163 163
CRK 0.026 0.008 -10000 0 -10000 0 0
mol:NO -0.37 0.38 -10000 0 -0.69 164 164
PLG -0.9 0.69 -10000 0 -1.5 163 163
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.52 0.49 -10000 0 -0.94 164 164
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.004 -10000 0 -10000 0 0
ANGPT2 -0.27 0.31 -10000 0 -0.74 66 66
BMX -0.75 0.72 -10000 0 -1.3 163 163
ANGPT1 -0.47 0.63 -10000 0 -1.4 95 95
tube development -0.43 0.4 -10000 0 -0.77 164 164
ANGPT4 0.012 0.023 -10000 0 -10000 0 0
response to hypoxia -0.039 0.034 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.79 0.77 -10000 0 -1.4 163 163
alpha5/beta1 Integrin 0.039 0.01 -10000 0 -10000 0 0
FGF2 0.022 0.059 -10000 0 -0.53 3 3
STAT5A (dimer) -0.49 0.47 -10000 0 -0.9 160 160
mol:L-citrulline -0.37 0.38 -10000 0 -0.69 164 164
AGTR1 -0.17 0.3 -10000 0 -0.64 87 87
MAPK14 -0.76 0.71 -10000 0 -1.3 164 164
Tie2/SHP2 -0.62 0.62 -10000 0 -1.2 148 148
TEK -0.69 0.7 -10000 0 -1.4 148 148
RPS6KB1 -0.52 0.5 -10000 0 -0.95 164 164
Angiotensin II/AT1 -0.13 0.23 -10000 0 -0.48 87 87
Tie2/Ang1/GRB2 -0.77 0.77 -10000 0 -1.4 163 163
MAPK3 -0.65 0.63 -10000 0 -1.2 162 162
MAPK1 -0.66 0.63 -10000 0 -1.2 163 163
Tie2/Ang1/GRB7 -0.77 0.77 -10000 0 -1.4 163 163
NFKB1 0.027 0.006 -10000 0 -10000 0 0
MAPK8 -0.75 0.73 -10000 0 -1.3 163 163
PI3K -0.67 0.64 -10000 0 -1.2 164 164
FES -0.75 0.71 -10000 0 -1.3 164 164
Crk/Dok-R -0.7 0.69 -10000 0 -1.3 162 162
Tie2/Ang1/ABIN2 -0.78 0.77 -10000 0 -1.4 163 163
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.48 0.46 -10000 0 -0.88 164 164
STAT5A 0.026 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.53 0.5 -10000 0 -0.96 164 164
Tie2/Ang2 -0.64 0.6 -10000 0 -1.1 162 162
Tie2/Ang1 -0.85 0.84 -10000 0 -1.5 163 163
FOXO1 -0.49 0.47 -10000 0 -0.89 164 164
ELF1 -0.044 0.074 -10000 0 -10000 0 0
ELF2 -0.76 0.73 -10000 0 -1.4 163 163
mol:Choline -0.69 0.66 -10000 0 -1.2 163 163
cell migration -0.14 0.12 -10000 0 -0.24 163 163
FYN -0.51 0.47 -10000 0 -0.9 164 164
DOK2 0.018 0.047 -10000 0 -0.64 1 1
negative regulation of cell cycle -0.33 0.32 -10000 0 -0.62 152 152
ETS1 -0.071 0.12 -10000 0 -0.25 86 86
PXN -0.42 0.4 -10000 0 -0.77 163 163
ITGB1 0.027 0.005 -10000 0 -10000 0 0
NOS3 -0.44 0.44 -10000 0 -0.8 164 164
RAC1 0.022 0.012 -10000 0 -10000 0 0
TNF -0.08 0.14 -10000 0 -0.27 91 91
MAPKKK cascade -0.69 0.66 -10000 0 -1.2 163 163
RASA1 0.027 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.78 0.77 -10000 0 -1.4 163 163
NCK1 0.027 0.006 -10000 0 -10000 0 0
vasculogenesis -0.33 0.34 -10000 0 -0.61 164 164
mol:Phosphatidic acid -0.69 0.66 -10000 0 -1.2 163 163
mol:Angiotensin II 0 0.001 -10000 0 -10000 0 0
mol:NADP -0.37 0.38 -10000 0 -0.69 164 164
Rac1/GTP -0.47 0.45 -10000 0 -0.86 164 164
MMP2 -0.74 0.72 -10000 0 -1.3 163 163
EGFR-dependent Endothelin signaling events

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
HRAS 0.028 0.003 -9999 0 -10000 0 0
EGFR 0.022 0.012 -9999 0 -10000 0 0
EGF/EGFR -0.28 0.14 -9999 0 -0.36 191 191
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.26 0.15 -9999 0 -0.36 177 177
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.001 0.13 -9999 0 -0.64 12 12
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.56 0.21 -9999 0 -0.63 258 258
EGF/EGFR dimer/SHC -0.32 0.15 -9999 0 -0.36 254 254
mol:GDP -0.26 0.14 -9999 0 -0.36 177 177
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.024 0.041 -9999 0 -0.64 1 1
GRB2/SOS1 0.038 0.012 -9999 0 -10000 0 0
HRAS/GTP -0.24 0.13 -9999 0 -0.34 177 177
SHC1 0.027 0.005 -9999 0 -10000 0 0
HRAS/GDP -0.25 0.14 -9999 0 -0.34 177 177
FRAP1 -0.26 0.12 -9999 0 -0.35 177 177
EGF/EGFR dimer -0.37 0.17 -9999 0 -0.42 258 258
SOS1 0.027 0.005 -9999 0 -10000 0 0
GRB2 0.026 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.014 0.11 -9999 0 -0.48 13 13
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.47 0.37 -10000 0 -0.92 95 95
PCK1 -1.1 0.67 -10000 0 -1.5 189 189
HNF4A -0.54 0.48 -10000 0 -1.2 75 75
KCNJ11 -0.5 0.37 -10000 0 -0.97 91 91
AKT1 -0.26 0.16 -10000 0 -0.45 71 71
response to starvation -0.004 0.014 -10000 0 -10000 0 0
DLK1 -0.51 0.39 -10000 0 -1 89 89
NKX2-1 -0.13 0.14 0.28 1 -0.39 17 18
ACADM -0.48 0.36 -10000 0 -0.92 95 95
TAT -0.44 0.23 -10000 0 -0.73 74 74
CEBPB -0.042 0.049 -10000 0 -10000 0 0
CEBPA -0.048 0.061 -10000 0 -0.44 2 2
TTR -0.74 0.4 -10000 0 -1.1 125 125
PKLR -0.59 0.52 -10000 0 -1.3 94 94
APOA1 -0.6 0.53 -10000 0 -1.3 84 84
CPT1C -0.49 0.38 -10000 0 -0.95 98 98
ALAS1 -0.21 0.15 -10000 0 -0.62 4 4
TFRC -0.58 0.29 -10000 0 -0.86 116 116
FOXF1 0.021 0.056 -10000 0 -0.64 2 2
NF1 0.031 0.008 -10000 0 -10000 0 0
HNF1A (dimer) -0.057 0.096 -10000 0 -0.52 6 6
CPT1A -0.48 0.36 -10000 0 -0.92 94 94
HMGCS1 -0.47 0.36 -10000 0 -0.93 92 92
NR3C1 0.018 0.048 -10000 0 -0.2 1 1
CPT1B -0.47 0.37 -10000 0 -0.92 97 97
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.027 0.009 -10000 0 -10000 0 0
GCK -0.44 0.38 -10000 0 -0.94 85 85
CREB1 -0.094 0.079 -10000 0 -0.28 5 5
IGFBP1 -0.26 0.35 -10000 0 -1.4 21 21
PDX1 -0.26 0.19 -10000 0 -0.78 12 12
UCP2 -0.48 0.37 -10000 0 -0.93 95 95
ALDOB -1.1 0.37 -10000 0 -1.2 269 269
AFP -0.46 0.33 -10000 0 -0.91 70 70
BDH1 -0.47 0.37 -10000 0 -0.93 92 92
HADH -0.5 0.38 -10000 0 -0.96 93 93
F2 -0.56 0.46 -10000 0 -1.2 72 72
HNF1A -0.057 0.096 -10000 0 -0.52 6 6
G6PC -1 0.59 -10000 0 -1.4 197 197
SLC2A2 -0.46 0.55 -10000 0 -1.7 46 46
INS -0.009 0.049 -10000 0 -10000 0 0
FOXA1 -0.21 0.11 -10000 0 -0.27 175 175
FOXA3 -0.45 0.22 -10000 0 -0.51 234 234
FOXA2 -0.57 0.42 -10000 0 -1.1 101 101
ABCC8 -0.5 0.37 -10000 0 -0.97 93 93
ALB -1 0.37 -10000 0 -1.1 254 254
PDGFR-alpha signaling pathway

Figure S5.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S5.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.23 0.32 -10000 0 -0.64 109 109
PDGF/PDGFRA/CRKL -0.15 0.24 -10000 0 -0.47 108 108
positive regulation of JUN kinase activity -0.087 0.2 -10000 0 -0.37 91 91
CRKL 0.026 0.007 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.16 0.24 -10000 0 -0.46 109 109
AP1 -0.25 0.38 -10000 0 -1.1 43 43
mol:IP3 -0.17 0.24 -10000 0 -0.47 107 107
PLCG1 -0.17 0.24 -10000 0 -0.47 107 107
PDGF/PDGFRA/alphaV Integrin -0.15 0.24 -10000 0 -0.46 109 109
RAPGEF1 0.027 0.006 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.17 0.24 -10000 0 -0.47 107 107
CAV3 -0.009 0.018 -10000 0 -10000 0 0
CAV1 0.021 0.013 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.087 0.2 -10000 0 -0.37 91 91
PDGF/PDGFRA/Shf -0.15 0.25 -10000 0 -0.47 108 108
FOS -0.25 0.37 0.32 1 -1.1 43 44
JUN -0.033 0.026 -10000 0 -10000 0 0
oligodendrocyte development -0.15 0.24 -10000 0 -0.46 109 109
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
mol:DAG -0.17 0.24 -10000 0 -0.47 107 107
PDGF/PDGFRA -0.23 0.32 -10000 0 -0.64 109 109
actin cytoskeleton reorganization -0.15 0.24 -10000 0 -0.47 108 108
SRF 0.018 0.011 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
PI3K -0.11 0.22 -10000 0 -0.4 101 101
PDGF/PDGFRA/Crk/C3G -0.11 0.21 -10000 0 -0.4 99 99
JAK1 -0.16 0.23 -10000 0 -0.47 105 105
ELK1/SRF -0.13 0.18 -10000 0 -0.38 93 93
SHB 0.027 0.005 -10000 0 -10000 0 0
SHF 0.027 0.005 -10000 0 -10000 0 0
CSNK2A1 0.038 0.02 -10000 0 -10000 0 0
GO:0007205 -0.18 0.24 -10000 0 -0.49 109 109
SOS1 0.027 0.005 -10000 0 -10000 0 0
Ras protein signal transduction -0.087 0.2 -10000 0 -0.37 91 91
PDGF/PDGFRA/SHB -0.15 0.25 -10000 0 -0.47 108 108
PDGF/PDGFRA/Caveolin-1 -0.14 0.22 -10000 0 -0.41 107 107
ITGAV 0.028 0.003 -10000 0 -10000 0 0
ELK1 -0.17 0.21 -10000 0 -0.44 107 107
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.15 0.24 -10000 0 -0.45 109 109
JAK-STAT cascade -0.16 0.23 -10000 0 -0.47 105 105
cell proliferation -0.15 0.24 -10000 0 -0.47 108 108
Thromboxane A2 receptor 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
TGM2 0.018 0.028 -10000 0 -10000 0 0
GNB1/GNG2 -0.097 0.09 -10000 0 -0.18 141 141
AKT1 -0.092 0.13 0.21 3 -0.33 20 23
EGF -0.56 0.21 -10000 0 -0.63 258 258
mol:TXA2 -0.001 0.001 -10000 0 -10000 0 0
FGR -0.019 0.08 -10000 0 -0.3 12 12
mol:Ca2+ -0.14 0.17 -10000 0 -0.3 128 128
LYN -0.018 0.074 -10000 0 -0.29 12 12
RhoA/GTP -0.057 0.068 -10000 0 -0.14 9 9
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.16 0.19 -10000 0 -0.34 146 146
GNG2 0.026 0.006 -10000 0 -10000 0 0
ARRB2 0.026 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.043 0.13 -10000 0 -0.49 12 12
G beta5/gamma2 -0.12 0.12 -10000 0 -0.24 143 143
PRKCH -0.17 0.2 -10000 0 -0.35 141 141
DNM1 -0.008 0.061 -10000 0 -0.64 1 1
TXA2/TP beta/beta Arrestin3 0.006 0.025 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.026 0.007 -10000 0 -10000 0 0
G12 family/GTP -0.14 0.15 -10000 0 -0.3 105 105
ADRBK1 0.028 0.002 -10000 0 -10000 0 0
ADRBK2 0.026 0.008 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.033 0.012 -10000 0 -10000 0 0
mol:GDP 0.097 0.14 0.41 29 -10000 0 29
mol:NADP 0.003 0.11 -10000 0 -0.64 8 8
RAB11A 0.028 0.004 -10000 0 -10000 0 0
PRKG1 -0.14 0.29 -10000 0 -0.63 73 73
mol:IP3 -0.18 0.21 -10000 0 -0.38 129 129
cell morphogenesis 0.033 0.012 -10000 0 -10000 0 0
PLCB2 -0.24 0.28 -10000 0 -0.52 129 129
mol:cGMP -0.001 0.001 -10000 0 -10000 0 0
BLK -0.02 0.072 -10000 0 -0.29 10 10
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.023 0.074 -10000 0 -0.31 10 10
RHOA 0.027 0.006 -10000 0 -10000 0 0
PTGIR 0.023 0.055 -10000 0 -0.64 2 2
PRKCB1 -0.18 0.21 -10000 0 -0.37 147 147
GNAQ 0.027 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.003 0.11 -10000 0 -0.64 8 8
TXA2/TXA2-R family -0.25 0.28 -10000 0 -0.52 146 146
LCK -0.018 0.075 -10000 0 -0.29 10 10
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.005 0.096 -10000 0 -0.32 21 21
TXA2-R family/G12 family/GDP/G beta/gamma -0.019 0.13 -10000 0 -0.42 27 27
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.01 0.09 -10000 0 -0.32 16 16
MAPK14 -0.11 0.13 0.18 1 -0.23 115 116
TGM2/GTP -0.2 0.23 -10000 0 -0.42 117 117
MAPK11 -0.1 0.13 0.18 1 -0.23 116 117
ARHGEF1 -0.081 0.091 -10000 0 -0.18 95 95
GNAI2 0.026 0.007 -10000 0 -10000 0 0
JNK cascade -0.18 0.21 -10000 0 -0.38 146 146
RAB11/GDP 0.029 0.004 -10000 0 -10000 0 0
ICAM1 -0.13 0.16 -10000 0 -0.28 145 145
cAMP biosynthetic process -0.16 0.19 -10000 0 -0.35 121 121
Gq family/GTP/EBP50 -0.039 0.1 -10000 0 -0.22 58 58
actin cytoskeleton reorganization 0.033 0.012 -10000 0 -10000 0 0
SRC -0.018 0.069 -10000 0 -0.44 1 1
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.025 0.008 -10000 0 -10000 0 0
EGF/EGFR -0.11 0.081 0.25 1 -0.29 29 30
VCAM1 -0.14 0.16 -10000 0 -0.29 146 146
TP beta/Gq family/GDP/G beta5/gamma2 -0.043 0.13 -10000 0 -0.49 12 12
platelet activation -0.14 0.17 0.25 1 -0.3 122 123
PGI2/IP 0.017 0.041 -10000 0 -0.48 2 2
PRKACA 0.016 0.027 -10000 0 -0.31 2 2
Gq family/GDP/G beta5/gamma2 -0.037 0.12 -10000 0 -0.41 15 15
TXA2/TP beta/beta Arrestin2 0.002 0.056 -10000 0 -0.44 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.017 0.098 -10000 0 -0.36 21 21
mol:DAG -0.2 0.23 -10000 0 -0.42 147 147
EGFR 0.022 0.012 -10000 0 -10000 0 0
TXA2/TP alpha -0.22 0.26 -10000 0 -0.48 122 122
Gq family/GTP -0.05 0.12 -10000 0 -0.26 66 66
YES1 -0.018 0.075 -10000 0 -0.29 12 12
GNAI2/GTP -0.003 0.086 -10000 0 -0.31 18 18
PGD2/DP 0.019 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
FYN -0.018 0.075 -10000 0 -0.29 12 12
mol:NO 0.003 0.11 -10000 0 -0.64 8 8
GNA15 0.02 0.027 -10000 0 -10000 0 0
PGK/cGMP -0.08 0.18 -10000 0 -0.37 79 79
RhoA/GDP 0.027 0.007 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.022 0.096 -10000 0 -0.34 16 16
NOS3 0.003 0.11 -10000 0 -0.64 8 8
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCA -0.16 0.19 0.28 2 -0.35 132 134
PRKCB -0.16 0.2 0.28 2 -0.36 132 134
PRKCE -0.17 0.2 0.27 1 -0.36 146 147
PRKCD -0.18 0.21 -10000 0 -0.38 142 142
PRKCG -0.19 0.21 -10000 0 -0.39 146 146
muscle contraction -0.23 0.26 -10000 0 -0.48 146 146
PRKCZ -0.16 0.19 -10000 0 -0.34 145 145
ARR3 -0.008 0.019 -10000 0 -10000 0 0
TXA2/TP beta 0.003 0.098 -10000 0 -0.33 21 21
PRKCQ -0.18 0.2 -10000 0 -0.36 145 145
MAPKKK cascade -0.21 0.24 -10000 0 -0.44 145 145
SELE -0.2 0.22 -10000 0 -0.41 146 146
TP beta/GNAI2/GDP/G beta/gamma 0.024 0.098 -10000 0 -0.33 18 18
ROCK1 0.026 0.007 -10000 0 -10000 0 0
GNA14 -0.11 0.27 -10000 0 -0.62 60 60
chemotaxis -0.29 0.32 -10000 0 -0.6 146 146
GNA12 0.022 0.011 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.012 0.1 -10000 0 -0.64 7 7
Rac1/GTP 0.015 0.008 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.17 0.44 -10000 0 -1.1 47 47
MKNK1 0.026 0.007 -10000 0 -10000 0 0
MAPK14 -0.03 0.15 -10000 0 -0.34 48 48
ATF2/c-Jun -0.032 0.12 -10000 0 -0.44 9 9
MAPK11 -0.029 0.15 -10000 0 -0.34 51 51
MITF -0.043 0.17 -10000 0 -0.4 51 51
MAPKAPK5 -0.046 0.17 -10000 0 -0.39 53 53
KRT8 -0.047 0.17 -10000 0 -0.4 53 53
MAPKAPK3 0.026 0.007 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.055 0.24 -10000 0 -0.54 48 48
CEBPB -0.046 0.17 -10000 0 -0.39 52 52
SLC9A1 -0.051 0.18 -10000 0 -0.41 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.043 0.17 -10000 0 -0.39 49 49
p38alpha-beta/MNK1 -0.03 0.2 -10000 0 -0.44 48 48
JUN -0.034 0.12 -10000 0 -0.44 9 9
PPARGC1A -0.057 0.19 -10000 0 -0.42 58 58
USF1 -0.051 0.18 -10000 0 -0.4 56 56
RAB5/GDP/GDI1 -0.033 0.13 -10000 0 -0.46 9 9
NOS2 -0.094 0.32 -10000 0 -1.2 21 21
DDIT3 -0.046 0.17 -10000 0 -0.39 53 53
RAB5A 0.027 0.006 -10000 0 -10000 0 0
HSPB1 0.005 0.17 0.28 44 -0.34 39 83
p38alpha-beta/HBP1 -0.033 0.19 -10000 0 -0.45 38 38
CREB1 -0.058 0.19 -10000 0 -0.43 57 57
RAB5/GDP 0.02 0.004 -10000 0 -10000 0 0
EIF4E -0.05 0.17 -10000 0 -0.41 43 43
RPS6KA4 -0.049 0.18 -10000 0 -0.39 56 56
PLA2G4A -0.062 0.19 -10000 0 -0.44 48 48
GDI1 -0.049 0.18 -10000 0 -0.39 56 56
TP53 -0.071 0.21 -10000 0 -0.51 49 49
RPS6KA5 -0.057 0.19 -10000 0 -0.42 57 57
ESR1 -0.071 0.22 -10000 0 -0.45 63 63
HBP1 0.022 0.012 -10000 0 -10000 0 0
MEF2C -0.05 0.17 -10000 0 -0.39 56 56
MEF2A -0.051 0.18 -10000 0 -0.4 56 56
EIF4EBP1 -0.059 0.19 -10000 0 -0.43 57 57
KRT19 -0.083 0.22 -10000 0 -0.44 68 68
ELK4 -0.052 0.18 -10000 0 -0.4 56 56
ATF6 -0.051 0.18 -10000 0 -0.4 56 56
ATF1 -0.057 0.19 -10000 0 -0.42 57 57
p38alpha-beta/MAPKAPK2 -0.031 0.2 -10000 0 -0.44 48 48
p38alpha-beta/MAPKAPK3 -0.027 0.2 -10000 0 -0.44 45 45
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.047 0.045 -10000 0 -0.42 2 2
fibroblast growth factor receptor signaling pathway 0.047 0.044 -10000 0 -0.41 2 2
LAMA1 0.006 0.099 -10000 0 -0.59 7 7
PRNP 0.027 0.006 -10000 0 -10000 0 0
GPC1/SLIT2 -0.069 0.21 -10000 0 -0.46 62 62
SMAD2 0.017 0.02 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ 0.035 0.011 -10000 0 -10000 0 0
GPC1/Laminin alpha1 0.021 0.078 -10000 0 -0.45 7 7
TDGF1 -0.33 0.32 -10000 0 -0.63 148 148
CRIPTO/GPC1 -0.23 0.26 -10000 0 -0.48 148 148
APP/GPC1 0.037 0.014 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.21 0.2 -10000 0 -0.41 145 145
FLT1 0.022 0.056 -10000 0 -0.64 2 2
GPC1/TGFB/TGFBR1/TGFBR2 0.051 0.017 -10000 0 -10000 0 0
SERPINC1 -0.076 0.23 -10000 0 -0.62 43 43
FYN -0.21 0.2 -10000 0 -0.41 145 145
FGR -0.21 0.21 -10000 0 -0.42 145 145
positive regulation of MAPKKK cascade -0.22 0.24 0.4 4 -0.44 149 153
SLIT2 -0.11 0.27 -10000 0 -0.61 62 62
GPC1/NRG 0.03 0.064 -10000 0 -0.48 4 4
NRG1 0.015 0.081 -10000 0 -0.58 5 5
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.044 -10000 0 -0.42 2 2
LYN -0.21 0.2 -10000 0 -0.41 144 144
mol:Spermine 0.007 0.004 -10000 0 -10000 0 0
cell growth 0.047 0.044 -10000 0 -0.41 2 2
BMP signaling pathway -0.027 0.008 -10000 0 -10000 0 0
SRC -0.21 0.2 -10000 0 -0.42 139 139
TGFBR1 0.027 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.005 0.029 -10000 0 -10000 0 0
GPC1 0.027 0.008 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.027 0.006 -10000 0 -10000 0 0
VEGFA 0.025 0.013 -10000 0 -10000 0 0
BLK -0.21 0.2 -10000 0 -0.42 143 143
HCK -0.21 0.2 -10000 0 -0.42 139 139
FGF2 0.021 0.059 -10000 0 -0.54 3 3
FGFR1 0.027 0.006 -10000 0 -10000 0 0
VEGFR1 homodimer 0.022 0.055 -10000 0 -0.64 2 2
TGFBR2 0.027 0.006 -10000 0 -10000 0 0
cell death 0.037 0.014 -10000 0 -10000 0 0
ATIII/GPC1 -0.038 0.18 -10000 0 -0.48 41 41
PLA2G2A/GPC1 0.027 0.025 -10000 0 -10000 0 0
LCK -0.21 0.21 -10000 0 -0.42 145 145
neuron differentiation 0.03 0.064 -10000 0 -0.48 4 4
PrPc/Cu2+ 0.02 0.004 -10000 0 -10000 0 0
APP 0.026 0.007 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.027 0.006 -10000 0 -10000 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.37 0.3 -10000 0 -0.52 212 212
SMAD6-7/SMURF1 0.039 0.037 -10000 0 -0.42 1 1
NOG 0.016 0.058 -10000 0 -0.64 2 2
SMAD9 -0.087 0.18 -10000 0 -0.59 28 28
SMAD4 0.026 0.008 -10000 0 -10000 0 0
SMAD5 -0.18 0.18 -10000 0 -0.46 40 40
BMP7/USAG1 -0.21 0.28 -10000 0 -0.51 125 125
SMAD5/SKI -0.17 0.18 0.25 1 -0.44 41 42
SMAD1 -0.037 0.096 -10000 0 -0.49 7 7
BMP2 0.027 0.006 -10000 0 -10000 0 0
SMAD1/SMAD1/SMAD4 -0.032 0.091 -10000 0 -0.42 7 7
BMPR1A 0.028 0.004 -10000 0 -10000 0 0
BMPR1B -0.36 0.32 -10000 0 -0.63 169 169
BMPR1A-1B/BAMBI -0.22 0.23 -10000 0 -0.42 165 165
AHSG 0 0.026 -10000 0 -10000 0 0
CER1 -0.001 0.022 -10000 0 -10000 0 0
BMP2-4/CER1 0.045 0.019 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.15 -10000 0 -0.44 30 30
BMP2-4 (homodimer) 0.037 0.013 -10000 0 -10000 0 0
RGMB 0.028 0.004 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.2 0.22 -10000 0 -0.39 164 164
RGMA -0.055 0.22 -10000 0 -0.61 37 37
SMURF1 0.022 0.012 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.15 0.15 -10000 0 -0.4 36 36
BMP2-4/USAG1 -0.05 0.17 -10000 0 -0.41 51 51
SMAD6/SMURF1/SMAD5 -0.15 0.17 -10000 0 -0.47 30 30
SOSTDC1 -0.11 0.25 -10000 0 -0.64 51 51
BMP7/BMPR2/BMPR1A-1B -0.31 0.25 -10000 0 -0.46 201 201
SKI 0.025 0.008 -10000 0 -10000 0 0
BMP6 (homodimer) 0.02 0.068 -10000 0 -0.64 3 3
HFE2 0.013 0.022 -10000 0 -10000 0 0
ZFYVE16 0.027 0.004 -10000 0 -10000 0 0
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/CHRD 0.024 0.11 -10000 0 -0.41 15 15
SMAD5/SMAD5/SMAD4 -0.17 0.18 0.25 1 -0.44 42 43
MAPK1 0.026 0.008 -10000 0 -10000 0 0
TAK1/TAB family -0.11 0.14 -10000 0 -0.37 24 24
BMP7 (homodimer) -0.19 0.31 -10000 0 -0.64 91 91
NUP214 0.027 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.026 0.056 -10000 0 -0.49 3 3
SMAD1/SKI -0.03 0.11 0.28 1 -0.48 8 9
SMAD6 0.025 0.039 -10000 0 -0.64 1 1
CTDSP2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.044 0.023 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.16 0.29 -10000 0 -0.63 80 80
BMPR2 (homodimer) 0.028 0.004 -10000 0 -10000 0 0
GADD34/PP1CA 0.055 0.01 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.26 0.25 -10000 0 -0.47 169 169
CHRDL1 -0.24 0.32 -10000 0 -0.64 114 114
ENDOFIN/SMAD1 -0.035 0.11 0.28 1 -0.49 8 9
SMAD6-7/SMURF1/SMAD1 -0.029 0.1 -10000 0 -0.48 7 7
SMAD6/SMURF1 0.022 0.012 -10000 0 -10000 0 0
BAMBI 0.024 0.04 -10000 0 -0.64 1 1
SMURF2 0.026 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.13 0.22 -10000 0 -0.42 105 105
BMP2-4/GREM1 -0.075 0.2 -10000 0 -0.42 73 73
SMAD7 0.026 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.083 0.19 -10000 0 -0.58 30 30
SMAD1/SMAD6 -0.035 0.1 -10000 0 -0.49 8 8
TAK1/SMAD6 0.031 0.018 -10000 0 -10000 0 0
BMP7 -0.19 0.31 -10000 0 -0.64 91 91
BMP6 0.02 0.068 -10000 0 -0.64 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.12 0.14 -10000 0 -0.39 33 33
PPM1A 0.026 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.037 0.1 -10000 0 -0.47 8 8
SMAD7/SMURF1 0.03 0.019 -10000 0 -10000 0 0
CTDSPL 0.027 0.006 -10000 0 -10000 0 0
PPP1CA 0.028 0.002 -10000 0 -10000 0 0
XIAP 0.028 0 -10000 0 -10000 0 0
CTDSP1 0.027 0.005 -10000 0 -10000 0 0
PPP1R15A 0.028 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.25 0.27 -10000 0 -0.62 77 77
CHRD -0.012 0.16 -10000 0 -0.64 17 17
BMPR2 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.16 0.16 -10000 0 -0.42 38 38
BMP4 0.027 0.006 -10000 0 -10000 0 0
FST -0.14 0.27 -10000 0 -0.64 64 64
BMP2-4/NOG 0.044 0.044 -10000 0 -0.42 2 2
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.27 0.24 -10000 0 -0.44 166 166
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.059 0.17 -10000 0 -0.42 49 49
CRKL -0.058 0.19 -10000 0 -0.44 50 50
HRAS -0.026 0.16 -10000 0 -0.42 19 19
mol:PIP3 -0.045 0.18 -10000 0 -0.41 47 47
SPRED1 0.027 0.005 -10000 0 -10000 0 0
SPRED2 0.027 0.004 -10000 0 -10000 0 0
GAB1 -0.058 0.2 -10000 0 -0.46 51 51
FOXO3 -0.036 0.21 0.27 4 -0.41 51 55
AKT1 -0.038 0.22 0.29 4 -0.43 60 64
BAD -0.035 0.21 0.27 4 -0.41 52 56
megakaryocyte differentiation -0.099 0.22 -10000 0 -0.44 77 77
GSK3B -0.03 0.21 0.4 6 -0.41 52 58
RAF1 -0.022 0.13 0.29 1 -0.35 12 13
SHC1 0.027 0.005 -10000 0 -10000 0 0
STAT3 -0.059 0.19 -10000 0 -0.45 50 50
STAT1 -0.14 0.4 -10000 0 -0.99 50 50
HRAS/SPRED1 -0.011 0.14 -10000 0 -0.36 14 14
cell proliferation -0.064 0.2 -10000 0 -0.46 53 53
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
TEC 0.027 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.046 0.21 -10000 0 -0.45 51 51
HRAS/SPRED2 -0.01 0.14 -10000 0 -0.36 12 12
LYN/TEC/p62DOK -0.021 0.2 -10000 0 -0.44 50 50
MAPK3 -0.009 0.11 0.31 6 -0.28 5 11
STAP1 -0.26 0.24 -10000 0 -0.4 190 190
GRAP2 0.022 0.02 -10000 0 -10000 0 0
JAK2 -0.12 0.34 -10000 0 -0.86 50 50
STAT1 (dimer) -0.13 0.39 -10000 0 -0.97 50 50
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.027 0.19 -10000 0 -0.44 42 42
actin filament polymerization -0.066 0.18 -10000 0 -0.45 48 48
LYN 0.027 0.005 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.27 0.28 -10000 0 -0.71 59 59
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.03 0.17 -10000 0 -0.4 47 47
PI3K -0.022 0.2 -10000 0 -0.43 49 49
PTEN 0.027 0.004 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.16 0.47 -10000 0 -1.2 50 50
MAPK8 -0.066 0.2 -10000 0 -0.47 53 53
STAT3 (dimer) -0.058 0.18 -10000 0 -0.44 50 50
positive regulation of transcription -0.004 0.094 0.29 6 -0.23 5 11
mol:GDP -0.029 0.16 -10000 0 -0.39 39 39
PIK3C2B -0.058 0.2 -10000 0 -0.46 50 50
CBL/CRKL -0.043 0.18 -10000 0 -0.42 50 50
FER -0.059 0.2 -10000 0 -0.46 50 50
SH2B3 -0.058 0.19 -10000 0 -0.46 50 50
PDPK1 -0.031 0.16 0.31 6 -0.38 40 46
SNAI2 -0.091 0.23 -10000 0 -0.46 67 67
positive regulation of cell proliferation -0.095 0.3 -10000 0 -0.74 50 50
KITLG 0.013 0.074 -10000 0 -0.66 3 3
cell motility -0.095 0.3 -10000 0 -0.74 50 50
PTPN6 0.028 0.011 -10000 0 -10000 0 0
EPOR -0.007 0.14 -10000 0 -1.1 1 1
STAT5A (dimer) -0.078 0.26 -10000 0 -0.62 50 50
SOCS1 0.023 0.04 -10000 0 -0.64 1 1
cell migration 0.063 0.2 0.46 52 -10000 0 52
SOS1 0.027 0.005 -10000 0 -10000 0 0
EPO 0.012 0.023 -10000 0 -10000 0 0
VAV1 0 0.059 -10000 0 -0.64 1 1
GRB10 -0.068 0.19 -10000 0 -0.46 48 48
PTPN11 0.028 0.009 -10000 0 -10000 0 0
SCF/KIT -0.061 0.21 -10000 0 -0.49 51 51
GO:0007205 0.002 0.009 -10000 0 -10000 0 0
MAP2K1 -0.012 0.12 0.33 5 -0.31 5 10
CBL 0.027 0.005 -10000 0 -10000 0 0
KIT -0.19 0.51 -10000 0 -1.3 50 50
MAP2K2 -0.014 0.12 0.33 5 -0.31 5 10
SHC/Grb2/SOS1 -0.02 0.19 -10000 0 -0.43 46 46
STAT5A -0.082 0.26 -10000 0 -0.64 50 50
GRB2 0.026 0.007 -10000 0 -10000 0 0
response to radiation -0.088 0.22 -10000 0 -0.45 67 67
SHC/GRAP2 0.034 0.02 -10000 0 -10000 0 0
PTPRO -0.1 0.23 -10000 0 -0.45 77 77
SH2B2 -0.067 0.19 -10000 0 -0.46 48 48
DOK1 0.026 0.012 -10000 0 -10000 0 0
MATK -0.065 0.2 -10000 0 -0.47 52 52
CREBBP 0.023 0.05 -10000 0 -10000 0 0
BCL2 -0.049 0.23 -10000 0 -1.1 8 8
Endothelins

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
AKT1 -0.013 0.14 0.26 4 -0.41 18 22
PTK2B 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.3 0.45 -10000 0 -0.93 90 90
EDN1 0.021 0.082 -10000 0 -0.63 1 1
EDN3 0.011 0.024 -10000 0 -10000 0 0
EDN2 -0.002 0.13 -10000 0 -0.57 13 13
HRAS/GDP -0.12 0.21 0.28 2 -0.48 49 51
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.099 0.19 -10000 0 -0.4 59 59
ADCY4 -0.035 0.15 -10000 0 -0.46 22 22
ADCY5 -0.03 0.14 -10000 0 -0.39 25 25
ADCY6 -0.013 0.11 -10000 0 -0.38 13 13
ADCY7 -0.011 0.1 -10000 0 -0.38 10 10
ADCY1 -0.13 0.2 -10000 0 -0.39 92 92
ADCY2 -0.034 0.11 -10000 0 -0.39 15 15
ADCY3 -0.013 0.11 -10000 0 -0.38 13 13
ADCY8 -0.016 0.11 -10000 0 -0.38 13 13
ADCY9 -0.01 0.1 -10000 0 -0.38 10 10
arachidonic acid secretion -0.18 0.27 -10000 0 -0.58 66 66
ETB receptor/Endothelin-1/Gq/GTP -0.064 0.15 -10000 0 -0.33 59 59
GNAO1 -0.012 0.15 -10000 0 -0.64 16 16
HRAS 0.027 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.009 0.13 0.36 10 -0.42 10 20
ETA receptor/Endothelin-1/Gs/GTP 0.014 0.14 0.34 16 -0.38 16 32
mol:GTP -0.004 0.008 -10000 0 -10000 0 0
COL3A1 -0.023 0.17 -10000 0 -0.57 18 18
EDNRB 0.024 0.041 -10000 0 -0.64 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.039 0.19 -10000 0 -0.57 26 26
CYSLTR1 -0.013 0.14 -10000 0 -0.47 14 14
SLC9A1 -0.002 0.099 -10000 0 -0.34 13 13
mol:GDP -0.14 0.22 0.28 2 -0.49 56 58
SLC9A3 -0.61 0.37 -10000 0 -0.73 234 234
RAF1 -0.15 0.22 0.28 1 -0.51 58 59
JUN -0.17 0.28 -10000 0 -0.68 44 44
JAK2 -0.013 0.14 0.26 4 -0.43 15 19
mol:IP3 -0.12 0.2 -10000 0 -0.45 58 58
ETA receptor/Endothelin-1 0.012 0.18 0.43 16 -0.42 28 44
PLCB1 -0.062 0.22 -10000 0 -0.64 38 38
PLCB2 0.01 0.036 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 0.01 0.12 -10000 0 -0.47 12 12
FOS -0.2 0.35 -10000 0 -0.9 50 50
Gai/GDP -0.067 0.26 -10000 0 -0.76 33 33
CRK 0.025 0.008 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.21 -10000 0 -0.53 39 39
BCAR1 0.026 0.008 -10000 0 -10000 0 0
PRKCB1 -0.12 0.2 -10000 0 -0.44 60 60
GNAQ 0.014 0.023 -10000 0 -10000 0 0
GNAZ 0.026 0.008 -10000 0 -10000 0 0
GNAL 0.024 0.04 -10000 0 -0.64 1 1
Gs family/GDP -0.12 0.2 0.26 1 -0.46 53 54
ETA receptor/Endothelin-1/Gq/GTP -0.089 0.21 -10000 0 -0.45 54 54
MAPK14 -0.081 0.14 -10000 0 -0.42 23 23
TRPC6 -0.32 0.49 -10000 0 -1 90 90
GNAI2 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.018 0.056 -10000 0 -0.64 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.081 0.15 -10000 0 -0.35 49 49
ETB receptor/Endothelin-2 0.015 0.1 -10000 0 -0.42 14 14
ETB receptor/Endothelin-3 0.033 0.035 -10000 0 -0.48 1 1
ETB receptor/Endothelin-1 0.034 0.073 -10000 0 -0.52 2 2
MAPK3 -0.19 0.31 -10000 0 -0.76 52 52
MAPK1 -0.2 0.34 -10000 0 -0.83 52 52
Rac1/GDP -0.11 0.2 0.28 2 -0.48 41 43
cAMP biosynthetic process -0.078 0.16 0.29 5 -0.43 32 37
MAPK8 -0.2 0.34 -10000 0 -0.77 55 55
SRC 0.026 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.001 0.085 -10000 0 -0.32 12 12
p130Cas/CRK/Src/PYK2 -0.18 0.26 0.29 2 -0.56 69 71
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.2 0.28 2 -0.48 40 42
COL1A2 -0.005 0.11 -10000 0 -0.47 6 6
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.008 0.16 -10000 0 -0.48 24 24
mol:DAG -0.12 0.2 -10000 0 -0.45 58 58
MAP2K2 -0.16 0.25 -10000 0 -0.59 56 56
MAP2K1 -0.16 0.25 0.28 1 -0.59 56 57
EDNRA -0.007 0.16 -10000 0 -0.66 12 12
positive regulation of muscle contraction 0.025 0.15 0.38 6 -0.4 10 16
Gq family/GDP -0.14 0.25 0.29 1 -0.53 63 64
HRAS/GTP -0.14 0.21 -10000 0 -0.48 60 60
PRKCH -0.12 0.2 -10000 0 -0.47 49 49
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCA -0.11 0.19 0.32 1 -0.46 46 47
PRKCB -0.1 0.19 0.23 1 -0.45 45 46
PRKCE -0.12 0.2 -10000 0 -0.47 48 48
PRKCD -0.11 0.19 -10000 0 -0.47 46 46
PRKCG -0.13 0.2 -10000 0 -0.48 50 50
regulation of vascular smooth muscle contraction -0.24 0.4 -10000 0 -1 50 50
PRKCQ -0.12 0.2 -10000 0 -0.47 55 55
PLA2G4A -0.2 0.31 -10000 0 -0.65 66 66
GNA14 -0.12 0.26 -10000 0 -0.63 60 60
GNA15 0.011 0.032 -10000 0 -10000 0 0
GNA12 0.022 0.011 -10000 0 -10000 0 0
GNA11 0.002 0.1 -10000 0 -0.64 7 7
Rac1/GTP 0.009 0.13 0.36 10 -0.39 13 23
MMP1 -0.058 0.24 0.26 2 -0.98 18 20
Arf6 signaling events

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
CENTA1/KIF3B 0.029 0.016 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 0.028 0.088 -10000 0 -0.8 3 3
EGFR 0.022 0.012 -10000 0 -10000 0 0
EPHA2 0.025 0.008 -10000 0 -10000 0 0
USP6 0.022 0.021 -10000 0 -10000 0 0
IQSEC1 0.027 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.37 0.17 -10000 0 -0.42 258 258
ARRB2 0.007 0.011 -10000 0 -10000 0 0
mol:GTP 0.027 0.052 0.19 18 -10000 0 18
ARRB1 0.026 0.039 -10000 0 -0.64 1 1
FBXO8 0.027 0.006 -10000 0 -10000 0 0
TSHR 0.017 0.021 -10000 0 -10000 0 0
EGF -0.56 0.21 -10000 0 -0.63 258 258
somatostatin receptor activity 0 0 0.001 5 -0.001 87 92
ARAP2 0.027 0.006 -10000 0 -10000 0 0
mol:GDP -0.073 0.14 0.25 1 -0.27 59 60
mol:PI-3-4-5-P3 0 0 0.001 5 -0.001 43 48
ITGA2B 0.019 0.026 -10000 0 -10000 0 0
ARF6 0.026 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.059 0.028 -10000 0 -10000 0 0
ADAP1 0.022 0.011 -10000 0 -10000 0 0
KIF13B 0.027 0.006 -10000 0 -10000 0 0
HGF/MET 0.01 0.094 -10000 0 -0.44 11 11
PXN 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.14 0.25 5 -0.29 88 93
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.31 0.16 -10000 0 -0.37 242 242
ADRB2 0.021 0.026 -10000 0 -10000 0 0
receptor agonist activity 0 0 0 7 0 66 73
actin filament binding 0 0 0.001 4 -0.001 87 91
SRC 0.026 0.009 -10000 0 -10000 0 0
ITGB3 -0.006 0.14 -10000 0 -0.64 13 13
GNAQ 0.026 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 27 -0.001 44 71
ARF6/GDP -0.039 0.12 0.27 2 -0.48 14 16
ARF6/GDP/GULP/ACAP1 -0.054 0.14 0.25 1 -0.39 12 13
alphaIIb/beta3 Integrin/paxillin/GIT1 0.043 0.095 -10000 0 -0.38 13 13
ACAP1 0.012 0.036 -10000 0 -10000 0 0
ACAP2 0.027 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.013 0.021 -10000 0 -10000 0 0
EFNA1 0.027 0.005 -10000 0 -10000 0 0
HGF -0.004 0.13 -10000 0 -0.64 11 11
CYTH3 0.006 0.003 -10000 0 -10000 0 0
CYTH2 0.008 0.1 -10000 0 -0.98 3 3
NCK1 0.027 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0 30 0 51 81
endosomal lumen acidification 0 0 0.001 3 -0.001 89 92
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.028 0.004 -10000 0 -10000 0 0
GNAQ/ARNO 0.023 0.096 -10000 0 -0.91 3 3
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 12 12
MET 0.017 0.023 -10000 0 -10000 0 0
GNA14 -0.11 0.27 -10000 0 -0.62 60 60
GNA15 0.02 0.027 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 9 -0.001 50 59
GNA11 0.011 0.1 -10000 0 -0.64 7 7
LHCGR -0.006 0.033 -10000 0 -10000 0 0
AGTR1 -0.18 0.3 -10000 0 -0.64 87 87
desensitization of G-protein coupled receptor protein signaling pathway 0.013 0.021 -10000 0 -10000 0 0
IPCEF1/ARNO -0.24 0.13 -10000 0 -0.91 3 3
alphaIIb/beta3 Integrin 0.008 0.11 -10000 0 -0.48 13 13
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.013 0.11 -10000 0 -0.48 13 13
AKT1 -0.065 0.24 0.36 6 -0.59 45 51
PTK2B -0.1 0.27 0.34 1 -0.68 48 49
VEGFR2 homodimer/Frs2 -0.11 0.31 -10000 0 -0.77 51 51
CAV1 0.021 0.013 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.087 0.3 -10000 0 -0.73 49 49
endothelial cell proliferation -0.036 0.25 0.52 12 -0.54 46 58
mol:Ca2+ -0.096 0.26 -10000 0 -0.66 49 49
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.074 0.27 -10000 0 -0.66 49 49
RP11-342D11.1 -0.11 0.26 -10000 0 -0.67 49 49
CDH5 0.026 0.007 -10000 0 -10000 0 0
VEGFA homodimer 0.062 0.026 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
SHC2 0.021 0.058 -10000 0 -0.64 2 2
HRAS/GDP -0.063 0.24 -10000 0 -0.59 49 49
SH2D2A 0.017 0.032 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.046 0.25 0.32 1 -0.57 49 50
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.09 0.3 -10000 0 -0.73 50 50
VEGFR1 homodimer 0.022 0.055 -10000 0 -0.64 2 2
SHC/GRB2/SOS1 -0.052 0.27 -10000 0 -0.65 49 49
GRB10 -0.093 0.25 -10000 0 -0.63 49 49
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
PAK1 0.028 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.058 0.28 -10000 0 -0.67 48 48
HRAS 0.028 0.003 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.057 0.16 -10000 0 -0.38 46 46
HIF1A 0.026 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.074 0.27 -10000 0 -0.65 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.011 0.1 -10000 0 -0.64 7 7
Nck/Pak 0.04 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.087 0.3 -10000 0 -0.74 49 49
mol:GDP -0.06 0.26 -10000 0 -0.62 49 49
mol:NADP -0.048 0.21 0.32 4 -0.49 48 52
eNOS/Hsp90 -0.032 0.21 0.33 2 -0.46 46 48
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 -0.098 0.26 -10000 0 -0.67 49 49
HIF1A/ARNT 0.039 0.011 -10000 0 -10000 0 0
SHB 0.027 0.005 -10000 0 -10000 0 0
VEGFA 0.027 0.013 -10000 0 -10000 0 0
VEGFC 0.026 0.011 -10000 0 -10000 0 0
FAK1/Vinculin -0.097 0.28 0.41 2 -0.67 52 54
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.089 0.3 -10000 0 -0.64 60 60
PTPN6 0.027 0.006 -10000 0 -10000 0 0
EPAS1 -0.04 0.17 -10000 0 -0.39 51 51
mol:L-citrulline -0.048 0.21 0.32 4 -0.49 48 52
ITGAV 0.028 0.003 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.07 0.28 -10000 0 -0.69 49 49
VEGFR2 homodimer/VEGFA homodimer -0.083 0.3 -10000 0 -0.73 49 49
VEGFR2/3 heterodimer -0.12 0.32 -10000 0 -0.77 55 55
VEGFB 0.028 0.002 -10000 0 -10000 0 0
MAPK11 -0.11 0.27 -10000 0 -0.7 50 50
VEGFR2 homodimer -0.14 0.34 -10000 0 -0.85 52 52
FLT1 0.022 0.056 -10000 0 -0.64 2 2
NEDD4 0.029 0.005 -10000 0 -10000 0 0
MAPK3 -0.091 0.23 0.34 1 -0.6 47 48
MAPK1 -0.092 0.24 0.33 2 -0.6 48 50
VEGFA145/NRP2 0.036 0.034 -10000 0 -0.46 1 1
VEGFR1/2 heterodimer -0.11 0.32 -10000 0 -0.79 51 51
KDR -0.14 0.34 -10000 0 -0.86 52 52
VEGFA165/NRP1/VEGFR2 homodimer -0.075 0.28 -10000 0 -0.68 49 49
SRC 0.026 0.009 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.083 0.25 0.36 6 -0.62 48 54
PI3K -0.087 0.28 -10000 0 -0.7 47 47
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.087 0.3 -10000 0 -0.73 49 49
FES -0.1 0.28 -10000 0 -0.7 49 49
GAB1 -0.091 0.28 -10000 0 -0.71 49 49
VEGFR2 homodimer/VEGFA homodimer/Src -0.085 0.29 -10000 0 -0.72 49 49
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.027 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.042 0.19 0.33 3 -0.48 32 35
VEGFR2 homodimer/VEGFA homodimer/Yes -0.089 0.3 -10000 0 -0.73 49 49
PI3K/GAB1 -0.068 0.25 -10000 0 -0.6 48 48
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.06 0.28 -10000 0 -0.69 48 48
PRKACA 0.028 0.002 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.099 0.31 -10000 0 -0.74 53 53
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
CDC42 -0.1 0.27 -10000 0 -0.7 49 49
actin cytoskeleton reorganization -0.089 0.29 -10000 0 -0.72 50 50
PTK2 -0.11 0.29 -10000 0 -0.74 49 49
EDG1 -0.11 0.26 -10000 0 -0.67 49 49
mol:DAG -0.098 0.26 -10000 0 -0.67 49 49
CaM/Ca2+ -0.078 0.25 -10000 0 -0.62 49 49
MAP2K3 -0.1 0.26 -10000 0 -0.67 48 48
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.045 0.29 -10000 0 -0.66 49 49
PLCG1 -0.1 0.27 -10000 0 -0.68 49 49
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.069 0.28 -10000 0 -0.69 49 49
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
YES1 0.026 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.087 0.3 -10000 0 -0.73 49 49
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.088 0.3 -10000 0 -0.73 49 49
cell migration -0.068 0.24 0.32 1 -0.56 50 51
mol:PI-3-4-5-P3 -0.078 0.26 -10000 0 -0.64 47 47
FYN 0.027 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 -0.088 0.25 -10000 0 -0.64 49 49
mol:NO -0.048 0.21 0.32 4 -0.49 48 52
PXN 0.027 0.005 -10000 0 -10000 0 0
HRAS/GTP -0.079 0.23 -10000 0 -0.59 49 49
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.085 0.26 -10000 0 -0.66 49 49
VHL 0.027 0.006 -10000 0 -10000 0 0
ITGB3 -0.006 0.14 -10000 0 -0.64 13 13
NOS3 -0.059 0.24 0.34 3 -0.56 48 51
VEGFR2 homodimer/VEGFA homodimer/Sck -0.09 0.3 -10000 0 -0.73 50 50
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCA -0.095 0.24 -10000 0 -0.62 48 48
PRKCB -0.096 0.24 -10000 0 -0.64 45 45
VCL 0.028 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.091 0.27 -10000 0 -0.68 49 49
VEGFR1/2 heterodimer/VEGFA homodimer -0.09 0.3 -10000 0 -0.75 49 49
VEGFA165/NRP2 0.036 0.034 -10000 0 -0.46 1 1
MAPKKK cascade -0.07 0.22 -10000 0 -0.57 46 46
NRP2 0.024 0.041 -10000 0 -0.64 1 1
VEGFC homodimer 0.026 0.011 -10000 0 -10000 0 0
NCK1 0.027 0.006 -10000 0 -10000 0 0
ROCK1 0.026 0.007 -10000 0 -10000 0 0
FAK1/Paxillin -0.1 0.28 0.34 1 -0.67 52 53
MAP3K13 -0.1 0.28 -10000 0 -0.71 49 49
PDPK1 -0.076 0.22 -10000 0 -0.57 45 45
IL4-mediated signaling events

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.47 0.44 -10000 0 -1.2 53 53
STAT6 (cleaved dimer) -0.47 0.45 -10000 0 -1.1 67 67
IGHG1 -0.16 0.14 -10000 0 -0.43 5 5
IGHG3 -0.46 0.43 -10000 0 -1.1 64 64
AKT1 -0.21 0.22 -10000 0 -0.77 14 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.14 0.15 -10000 0 -0.64 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.24 -10000 0 -0.83 18 18
THY1 -0.74 0.67 -10000 0 -1.5 118 118
MYB 0.002 0.045 -10000 0 -10000 0 0
HMGA1 0.024 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.26 0.23 -10000 0 -0.64 33 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.24 -10000 0 -0.87 15 15
SP1 0.031 0.011 -10000 0 -10000 0 0
INPP5D 0.024 0.02 -10000 0 -10000 0 0
SOCS5 0.038 0.02 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.46 0.46 -10000 0 -1.2 60 60
SOCS1 -0.31 0.28 -10000 0 -0.74 50 50
SOCS3 -0.22 0.21 -10000 0 -0.8 4 4
FCER2 -0.35 0.33 -10000 0 -0.88 47 47
PARP14 0.027 0.006 -10000 0 -10000 0 0
CCL17 -0.47 0.44 -10000 0 -1.2 53 53
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.2 -10000 0 -0.74 13 13
T cell proliferation -0.46 0.45 -10000 0 -1.2 58 58
IL4R/JAK1 -0.46 0.45 -10000 0 -1.2 56 56
EGR2 -0.53 0.55 -10000 0 -1.4 64 64
JAK2 -0.031 0.04 -10000 0 -10000 0 0
JAK3 0.011 0.045 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
JAK1 0.001 0.023 -10000 0 -10000 0 0
COL1A2 -0.14 0.14 -10000 0 -10000 0 0
CCL26 -0.44 0.46 -10000 0 -1.2 55 55
IL4R -0.49 0.47 -10000 0 -1.3 56 56
PTPN6 0.038 0.015 -10000 0 -10000 0 0
IL13RA2 -0.87 0.65 -10000 0 -1.4 163 163
IL13RA1 -0.031 0.041 -10000 0 -10000 0 0
IRF4 -0.094 0.17 -10000 0 -0.8 11 11
ARG1 -0.13 0.14 -10000 0 -0.98 1 1
CBL -0.25 0.22 -10000 0 -0.62 28 28
GTF3A 0.028 0.015 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.037 0.055 -10000 0 -10000 0 0
IRF4/BCL6 -0.084 0.16 -10000 0 -0.76 11 11
CD40LG 0.027 0.025 -10000 0 -10000 0 0
MAPK14 -0.24 0.22 -10000 0 -0.65 22 22
mitosis -0.2 0.21 -10000 0 -0.72 14 14
STAT6 -0.54 0.53 -10000 0 -1.3 62 62
SPI1 0.01 0.041 -10000 0 -10000 0 0
RPS6KB1 -0.18 0.21 0.52 1 -0.69 14 15
STAT6 (dimer) -0.53 0.53 -10000 0 -1.3 62 62
STAT6 (dimer)/PARP14 -0.49 0.49 -10000 0 -1.2 61 61
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.19 -10000 0 -0.64 11 11
FRAP1 -0.2 0.22 -10000 0 -0.77 14 14
LTA -0.48 0.44 -10000 0 -1.2 56 56
FES 0.025 0.039 -10000 0 -0.64 1 1
T-helper 1 cell differentiation 0.52 0.51 1.3 62 -10000 0 62
CCL11 -0.55 0.54 -10000 0 -1.3 78 78
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.19 -10000 0 -0.65 11 11
IL2RG 0.029 0.021 -10000 0 -10000 0 0
IL10 -0.47 0.44 -10000 0 -1.2 56 56
IRS1 0.017 0.081 -10000 0 -0.58 5 5
IRS2 0.026 0.01 -10000 0 -10000 0 0
IL4 -0.11 0.13 -10000 0 -0.93 3 3
IL5 -0.48 0.44 -10000 0 -1.2 56 56
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.4 0.37 -10000 0 -0.93 61 61
COL1A1 -0.17 0.2 -10000 0 -0.95 9 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.47 0.46 -10000 0 -1.2 54 54
IL2R gamma/JAK3 0.024 0.043 -10000 0 -10000 0 0
TFF3 -0.59 0.59 -10000 0 -1.4 77 77
ALOX15 -0.47 0.44 -10000 0 -1.2 53 53
MYBL1 0.022 0.024 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.39 0.37 -10000 0 -0.92 65 65
SHC1 0.027 0.005 -10000 0 -10000 0 0
CEBPB 0.024 0.021 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.24 -10000 0 -0.97 13 13
mol:PI-3-4-5-P3 -0.2 0.22 -10000 0 -0.77 14 14
PI3K -0.21 0.24 -10000 0 -0.82 14 14
DOK2 0.018 0.047 -10000 0 -0.64 1 1
ETS1 0.037 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.17 0.19 -10000 0 -0.75 11 11
ITGB3 -0.5 0.48 -10000 0 -1.2 66 66
PIGR -0.51 0.49 -10000 0 -1.3 64 64
IGHE 0.043 0.051 0.18 21 -10000 0 21
MAPKKK cascade -0.17 0.19 0.46 1 -0.73 11 12
BCL6 0.026 0.008 -10000 0 -10000 0 0
OPRM1 -0.48 0.44 -10000 0 -1.2 60 60
RETNLB -0.47 0.44 -10000 0 -1.2 53 53
SELP -0.52 0.53 -10000 0 -1.4 60 60
AICDA -0.46 0.43 -10000 0 -1.2 54 54
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.053 0.2 -10000 0 -0.48 50 50
alphaV beta3 Integrin 0.023 0.11 -10000 0 -0.4 16 16
PTK2 -0.13 0.24 0.48 5 -0.56 40 45
IGF1R 0.028 0.004 -10000 0 -10000 0 0
PI4KB 0.027 0.005 -10000 0 -10000 0 0
MFGE8 0.028 0.004 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
CDKN1B -0.11 0.23 -10000 0 -0.52 67 67
VEGFA 0.025 0.013 -10000 0 -10000 0 0
ILK -0.12 0.23 -10000 0 -0.53 68 68
ROCK1 0.026 0.007 -10000 0 -10000 0 0
AKT1 -0.11 0.22 -10000 0 -0.5 67 67
PTK2B -0.055 0.16 -10000 0 -0.37 55 55
alphaV/beta3 Integrin/JAM-A -0.066 0.19 -10000 0 -0.38 77 77
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.26 0.22 -10000 0 -0.41 194 194
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.05 0.085 -10000 0 -0.38 10 10
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.11 0.19 -10000 0 -0.48 38 38
alphaV/beta3 Integrin/Syndecan-1 0.027 0.1 -10000 0 -0.42 14 14
PI4KA 0.026 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.021 0.12 -10000 0 -0.35 23 23
PI4 Kinase 0.038 0.012 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.021 0.11 -10000 0 -0.4 16 16
RPS6KB1 -0.037 0.095 -10000 0 -0.34 22 22
TLN1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.058 0.15 -10000 0 -0.53 19 19
GPR124 0.025 0.04 -10000 0 -0.64 1 1
MAPK1 -0.06 0.15 -10000 0 -0.5 23 23
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.006 0.15 -10000 0 -0.46 24 24
cell adhesion -0.21 0.19 -10000 0 -0.35 170 170
ANGPTL3 -0.41 0.3 -10000 0 -0.62 190 190
VEGFR2 homodimer/VEGFA homodimer/Src -0.028 0.17 -10000 0 -0.42 44 44
IGF-1R heterotetramer 0.028 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.009 -10000 0 -10000 0 0
TGFBR2 0.027 0.006 -10000 0 -10000 0 0
ITGB3 -0.006 0.14 -10000 0 -0.64 13 13
IGF1 0.013 0.095 -10000 0 -0.64 6 6
RAC1 0.022 0.012 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.026 0.099 -10000 0 -0.4 14 14
apoptosis 0.028 0.003 -10000 0 -10000 0 0
CD47 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.028 0.099 -10000 0 -0.42 13 13
VCL 0.028 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.034 0.19 -10000 0 -0.43 48 48
CSF1 0.021 0.056 -10000 0 -0.64 2 2
PIK3C2A -0.12 0.23 -10000 0 -0.53 68 68
PI4 Kinase/Pyk2 -0.12 0.21 -10000 0 -0.38 102 102
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.032 0.18 -10000 0 -0.4 56 56
FAK1/Vinculin -0.093 0.2 0.45 5 -0.43 40 45
alphaV beta3/Integrin/ppsTEM5 0.027 0.1 -10000 0 -0.4 14 14
RHOA 0.027 0.006 -10000 0 -10000 0 0
VTN -0.13 0.28 -10000 0 -0.63 67 67
BCAR1 0.026 0.008 -10000 0 -10000 0 0
FGF2 0.021 0.059 -10000 0 -0.54 3 3
F11R 0.009 0.043 -10000 0 -0.48 2 2
alphaV/beta3 Integrin/Lactadherin 0.028 0.099 -10000 0 -0.42 13 13
alphaV/beta3 Integrin/TGFBR2 0.027 0.099 -10000 0 -0.42 13 13
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.058 0.045 -10000 0 -0.38 2 2
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.026 0.091 -10000 0 -0.38 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.02 0.028 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.04 0.17 -10000 0 -0.37 55 55
SDC1 0.025 0.04 -10000 0 -0.64 1 1
VAV3 0.021 0.06 0.36 1 -0.36 3 4
PTPN11 0.027 0.005 -10000 0 -10000 0 0
IRS1 0.017 0.081 -10000 0 -0.58 5 5
FAK1/Paxillin -0.1 0.19 0.33 2 -0.44 38 40
cell migration -0.095 0.17 0.28 4 -0.4 38 42
ITGAV 0.028 0.003 -10000 0 -10000 0 0
PI3K -0.052 0.19 -10000 0 -0.35 76 76
SPP1 0.017 0.062 -10000 0 -0.54 3 3
KDR -0.09 0.25 -10000 0 -0.63 51 51
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.028 0.003 -10000 0 -10000 0 0
COL4A3 -0.006 0.14 -10000 0 -0.62 15 15
angiogenesis -0.08 0.18 -10000 0 -0.53 22 22
Rac1/GTP 0.024 0.046 -10000 0 -0.34 2 2
EDIL3 -0.068 0.23 -10000 0 -0.64 39 39
cell proliferation 0.027 0.098 -10000 0 -0.41 13 13
Signaling events mediated by PTP1B

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
PDGFRB 0.004 0.12 -10000 0 -0.64 10 10
Jak2/Leptin Receptor -0.15 0.18 -10000 0 -0.37 81 81
PTP1B/AKT1 -0.071 0.11 0.23 3 -0.33 27 30
FYN 0.027 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.084 0.12 0.23 4 -0.36 29 33
EGFR -0.014 0.017 -10000 0 -10000 0 0
EGF/EGFR -0.3 0.14 0.23 1 -0.38 204 205
CSF1 0.021 0.056 -10000 0 -0.64 2 2
AKT1 0.027 0.007 -10000 0 -10000 0 0
INSR 0.028 0.003 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.091 0.15 0.23 3 -0.42 35 38
Insulin Receptor/Insulin -0.046 0.1 0.25 1 -0.34 12 13
HCK 0.013 0.051 -10000 0 -0.64 1 1
CRK 0.026 0.008 -10000 0 -10000 0 0
TYK2 -0.082 0.11 0.23 3 -0.35 27 30
EGF -0.56 0.21 -10000 0 -0.63 258 258
YES1 0.026 0.008 -10000 0 -10000 0 0
CAV1 -0.14 0.13 0.23 5 -0.36 35 40
TXN 0.02 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.088 0.11 -10000 0 -0.38 27 27
cell migration 0.084 0.12 0.36 29 -0.23 4 33
STAT3 0.026 0.007 -10000 0 -10000 0 0
PRLR -0.22 0.32 -10000 0 -0.64 109 109
ITGA2B 0.017 0.026 -10000 0 -10000 0 0
CSF1R 0.021 0.044 -10000 0 -0.64 1 1
Prolactin Receptor/Prolactin -0.16 0.25 -10000 0 -0.48 109 109
FGR 0.02 0.044 -10000 0 -0.64 1 1
PTP1B/p130 Cas -0.082 0.11 0.26 1 -0.35 27 28
Crk/p130 Cas -0.081 0.1 0.27 1 -0.35 24 25
DOK1 -0.073 0.12 0.29 5 -0.36 25 30
JAK2 -0.16 0.2 0.24 1 -0.36 113 114
Jak2/Leptin Receptor/Leptin -0.089 0.11 -10000 0 -0.4 16 16
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
PTPN1 -0.084 0.12 0.23 4 -0.36 29 33
LYN 0.027 0.005 -10000 0 -10000 0 0
CDH2 -0.005 0.14 -10000 0 -0.64 13 13
SRC -0.017 0.1 -10000 0 -0.63 6 6
ITGB3 -0.008 0.14 -10000 0 -0.64 13 13
CAT1/PTP1B -0.19 0.2 0.32 6 -0.44 62 68
CAPN1 0.026 0.003 -10000 0 -10000 0 0
CSK 0.028 0.004 -10000 0 -10000 0 0
PI3K -0.045 0.096 -10000 0 -0.38 6 6
mol:H2O2 -0.005 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.081 0.098 -10000 0 -0.4 12 12
negative regulation of transcription -0.16 0.19 0.24 1 -0.35 114 115
FCGR2A 0.022 0.023 -10000 0 -10000 0 0
FER 0.021 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.005 0.11 -10000 0 -0.48 13 13
BLK 0.016 0.027 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.048 0.013 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
LEPR 0.025 0.021 -10000 0 -0.32 1 1
BCAR1 0.026 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.007 -10000 0 -10000 0 0
mol:NADPH -0.006 0.003 -10000 0 -10000 0 0
TRPV6 -0.15 0.22 0.34 2 -0.51 40 42
PRL -0.01 0.018 -10000 0 -10000 0 0
SOCS3 0.028 0.1 -10000 0 -1.1 2 2
SPRY2 0.024 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.04 0.058 -10000 0 -0.42 4 4
CSF1/CSF1R -0.082 0.11 -10000 0 -0.36 27 27
Ras protein signal transduction 0.056 0.12 0.47 21 -10000 0 21
IRS1 0.017 0.081 -10000 0 -0.58 5 5
INS -0.007 0.019 -10000 0 -10000 0 0
LEP 0.001 0.033 -10000 0 -10000 0 0
STAT5B -0.11 0.13 0.24 2 -0.36 37 39
STAT5A -0.11 0.13 0.24 2 -0.36 37 39
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.093 0.12 -10000 0 -0.36 37 37
CSN2 -0.061 0.11 -10000 0 -0.62 4 4
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
LAT -0.021 0.1 0.26 1 -0.55 8 9
YBX1 0.029 0.009 -10000 0 -10000 0 0
LCK 0.023 0.018 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
NOX4 -0.045 0.2 -10000 0 -0.64 30 30
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.02 0.031 -10000 0 -10000 0 0
NFATC2 -0.003 0.19 -10000 0 -0.58 20 20
NFATC3 -0.01 0.11 -10000 0 -0.29 36 36
CD40LG -0.15 0.39 -10000 0 -0.97 44 44
ITCH 0.023 0.047 -10000 0 -0.27 7 7
CBLB 0.024 0.047 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.075 0.24 -10000 0 -0.83 9 9
JUNB 0.028 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.031 0.056 -10000 0 -0.32 7 7
T cell anergy 0.015 0.078 -10000 0 -0.41 7 7
TLE4 -0.004 0.13 -10000 0 -0.46 9 9
Jun/NFAT1-c-4/p21SNFT -0.08 0.39 -10000 0 -0.95 41 41
AP-1/NFAT1-c-4 -0.14 0.48 -10000 0 -1.1 46 46
IKZF1 -0.003 0.11 -10000 0 -0.44 10 10
T-helper 2 cell differentiation -0.43 0.3 -10000 0 -0.78 80 80
AP-1/NFAT1 -0.031 0.2 -10000 0 -0.47 32 32
CALM1 0.031 0.036 -10000 0 -10000 0 0
EGR2 -0.17 0.52 -10000 0 -1.5 34 34
EGR3 -0.2 0.57 -10000 0 -1.5 45 45
NFAT1/FOXP3 0.015 0.14 -10000 0 -0.42 17 17
EGR1 -0.025 0.18 -10000 0 -0.64 23 23
JUN 0.022 0.022 -10000 0 -10000 0 0
EGR4 0.019 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0.005 0.03 -10000 0 -0.18 7 7
GBP3 -0.003 0.13 -10000 0 -0.42 17 17
FOSL1 0.022 0.057 -10000 0 -0.64 2 2
NFAT1-c-4/MAF/IRF4 -0.072 0.38 -10000 0 -0.94 40 40
DGKA -0.003 0.13 -10000 0 -0.42 17 17
CREM 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.085 0.39 -10000 0 -0.97 41 41
CTLA4 -0.01 0.11 -10000 0 -0.42 8 8
NFAT1-c-4 (dimer)/EGR1 -0.11 0.44 -10000 0 -1.1 41 41
NFAT1-c-4 (dimer)/EGR4 -0.088 0.39 -10000 0 -0.98 41 41
FOS -0.069 0.23 -10000 0 -0.6 43 43
IFNG -0.026 0.15 -10000 0 -0.66 4 4
T cell activation -0.075 0.23 -10000 0 -0.7 18 18
MAF 0.026 0.008 -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 0.087 0.29 0.74 45 -10000 0 45
TNF -0.13 0.38 -10000 0 -0.96 42 42
FASLG -0.2 0.56 -10000 0 -1.4 50 50
TBX21 0.022 0.024 -10000 0 -10000 0 0
BATF3 0.027 0.009 -10000 0 -10000 0 0
PRKCQ 0.013 0.097 -10000 0 -0.59 7 7
PTPN1 -0.001 0.13 -10000 0 -0.42 17 17
NFAT1-c-4/ICER1 -0.089 0.39 -10000 0 -0.97 41 41
GATA3 -0.48 0.28 -10000 0 -0.63 222 222
T-helper 1 cell differentiation -0.025 0.15 -10000 0 -0.65 4 4
IL2RA -0.067 0.24 -10000 0 -0.78 11 11
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.003 0.13 -10000 0 -0.48 7 7
E2F1 0.003 0.047 -10000 0 -10000 0 0
PPARG 0.026 0.009 -10000 0 -10000 0 0
SLC3A2 -0.002 0.13 -10000 0 -0.5 6 6
IRF4 0.017 0.047 -10000 0 -0.64 1 1
PTGS2 -0.2 0.46 -10000 0 -1.1 51 51
CSF2 -0.15 0.39 -10000 0 -0.99 41 41
JunB/Fra1/NFAT1-c-4 -0.072 0.39 -10000 0 -0.95 41 41
IL4 -0.45 0.32 -10000 0 -0.84 74 74
IL5 -0.15 0.39 -10000 0 -0.98 42 42
IL2 -0.077 0.23 -10000 0 -0.71 18 18
IL3 -0.022 0.14 -10000 0 -0.81 6 6
RNF128 0.014 0.12 -10000 0 -0.72 7 7
NFATC1 -0.088 0.29 -10000 0 -0.74 45 45
CDK4 0.045 0.18 0.5 21 -10000 0 21
PTPRK -0.002 0.13 -10000 0 -0.46 9 9
IL8 -0.16 0.39 -10000 0 -0.97 44 44
POU2F1 0.027 0.006 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.016 0.057 -10000 0 -10000 0 0
alphaM/beta2 Integrin/GPIbA 0.013 0.062 -10000 0 -0.47 1 1
alphaM/beta2 Integrin/proMMP-9 -0.012 0.07 -10000 0 -0.41 2 2
PLAUR 0.02 0.027 -10000 0 -10000 0 0
HMGB1 0.018 0.031 -10000 0 -0.17 1 1
alphaM/beta2 Integrin/Talin 0.015 0.056 -10000 0 -10000 0 0
AGER 0.011 0.04 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
SELPLG 0.016 0.033 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.014 0.1 -10000 0 -0.31 14 14
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.019 0.073 -10000 0 -0.64 2 2
CYR61 0.009 0.1 -10000 0 -0.54 9 9
TLN1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.13 0.14 -10000 0 -0.4 37 37
RHOA 0.027 0.006 -10000 0 -10000 0 0
P-selectin oligomer -0.03 0.18 -10000 0 -0.6 26 26
MYH2 -0.2 0.19 -10000 0 -0.54 40 40
MST1R 0.014 0.053 -10000 0 -0.48 2 2
leukocyte activation during inflammatory response -0.017 0.12 -10000 0 -0.37 26 26
APOB -0.017 0.15 -10000 0 -0.64 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.024 0.016 -10000 0 -10000 0 0
JAM3 0.025 0.039 -10000 0 -0.64 1 1
GP1BA 0.023 0.04 -10000 0 -0.64 1 1
alphaM/beta2 Integrin/CTGF 0.006 0.082 -10000 0 -0.4 6 6
alphaM/beta2 Integrin -0.16 0.16 -10000 0 -0.38 60 60
JAM3 homodimer 0.025 0.039 -10000 0 -0.64 1 1
ICAM2 0.026 0.008 -10000 0 -10000 0 0
ICAM1 0.027 0.011 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.16 0.15 -10000 0 -0.39 55 55
cell adhesion 0.013 0.062 -10000 0 -0.47 1 1
NFKB1 -0.03 0.17 0.35 1 -0.5 27 28
THY1 -0.21 0.32 -10000 0 -0.63 105 105
RhoA/GDP 0.02 0.005 -10000 0 -10000 0 0
Lipoprotein(a) -0.018 0.13 -10000 0 -0.41 29 29
alphaM/beta2 Integrin/LRP/tPA -0.006 0.13 -10000 0 -0.38 23 23
IL6 -0.069 0.23 -10000 0 -0.73 29 29
ITGB2 0 0.046 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.016 0.088 -10000 0 -0.39 7 7
alphaM/beta2 Integrin/JAM2/JAM3 0.028 0.074 -10000 0 -0.39 3 3
JAM2 0.018 0.071 -10000 0 -0.56 4 4
alphaM/beta2 Integrin/ICAM1 0.036 0.071 -10000 0 -0.38 2 2
alphaM/beta2 Integrin/uPA/Plg -0.21 0.22 -10000 0 -0.4 153 153
RhoA/GTP -0.2 0.2 -10000 0 -0.48 57 57
positive regulation of phagocytosis -0.12 0.12 -10000 0 -0.36 30 30
Ron/MSP 0.027 0.053 -10000 0 -0.48 2 2
alphaM/beta2 Integrin/uPAR/uPA 0.018 0.09 -10000 0 -0.4 7 7
alphaM/beta2 Integrin/uPAR 0.012 0.06 -10000 0 -10000 0 0
PLAU 0.011 0.1 -10000 0 -0.64 7 7
PLAT -0.037 0.19 -10000 0 -0.61 29 29
actin filament polymerization -0.19 0.18 -10000 0 -0.52 40 40
MST1 0.024 0.04 -10000 0 -0.64 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.015 0.13 -10000 0 -0.38 26 26
TNF -0.035 0.17 0.34 1 -0.64 15 16
RAP1B 0.027 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.004 0.088 -10000 0 -0.43 7 7
fibrinolysis -0.21 0.21 -10000 0 -0.4 153 153
HCK 0.013 0.051 -10000 0 -0.64 1 1
dendritic cell antigen processing and presentation -0.16 0.15 -10000 0 -0.39 55 55
VTN -0.13 0.28 -10000 0 -0.63 67 67
alphaM/beta2 Integrin/CYR61 0.005 0.082 -10000 0 -0.35 7 7
LPA -0.034 0.14 -10000 0 -0.64 14 14
LRP1 0.027 0.005 -10000 0 -10000 0 0
cell migration -0.013 0.063 -10000 0 -0.38 2 2
FN1 0.02 0.028 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.14 0.21 -10000 0 -0.41 101 101
MPO 0.018 0.025 -10000 0 -10000 0 0
KNG1 -0.37 0.31 -10000 0 -0.64 164 164
RAP1/GDP 0.035 0.011 -10000 0 -10000 0 0
ROCK1 -0.19 0.19 -10000 0 -0.54 39 39
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.36 0.31 -10000 0 -0.63 162 162
CTGF 0.012 0.097 -10000 0 -0.59 7 7
alphaM/beta2 Integrin/Hck 0.01 0.068 -10000 0 -0.47 1 1
ITGAM 0.006 0.041 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.002 0.12 -10000 0 -0.38 17 17
HP 0.009 0.036 -10000 0 -10000 0 0
leukocyte adhesion -0.13 0.21 -10000 0 -0.4 95 95
SELP -0.03 0.18 -10000 0 -0.6 26 26
Ceramide signaling 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
SPHK2 0.01 0.01 -10000 0 -10000 0 0
MAP4K4 0.015 0.047 -10000 0 -0.33 1 1
BAG4 0.027 0.006 -10000 0 -10000 0 0
PKC zeta/ceramide -0.11 0.09 -10000 0 -0.27 60 60
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.02 0.027 -10000 0 -10000 0 0
BAX -0.045 0.048 -10000 0 -0.37 3 3
RIPK1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.018 0.043 0.7 1 -10000 0 1
BAD -0.12 0.084 -10000 0 -0.27 60 60
SMPD1 0.01 0.053 0.2 5 -0.24 5 10
RB1 -0.12 0.085 -10000 0 -0.27 59 59
FADD/Caspase 8 0.014 0.06 -10000 0 -10000 0 0
MAP2K4 -0.1 0.081 0.21 1 -0.26 50 51
NSMAF 0.027 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.098 0.082 0.21 1 -0.26 46 47
EGF -0.56 0.21 -10000 0 -0.63 258 258
mol:ceramide -0.12 0.089 -10000 0 -0.29 60 60
MADD 0.028 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.01 -10000 0 -10000 0 0
ASAH1 0.027 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.11 0.085 -10000 0 -0.27 59 59
cell proliferation -0.088 0.083 -10000 0 -0.24 48 48
BID -0.054 0.19 -10000 0 -0.68 23 23
MAP3K1 -0.12 0.084 -10000 0 -0.27 59 59
EIF2A -0.099 0.081 0.24 1 -0.25 52 53
TRADD 0.026 0.007 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.091 0.078 0.18 1 -0.24 46 47
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.099 0.08 0.2 1 -0.24 46 47
Cathepsin D/ceramide -0.11 0.088 -10000 0 -0.27 60 60
FADD 0.015 0.042 -10000 0 -10000 0 0
KSR1 -0.11 0.084 0.18 2 -0.27 49 51
MAPK8 -0.11 0.093 -10000 0 -0.26 69 69
PRKRA -0.12 0.085 0.19 1 -0.27 59 60
PDGFA 0.02 0.017 -10000 0 -10000 0 0
TRAF2 0.027 0.006 -10000 0 -10000 0 0
IGF1 0.013 0.095 -10000 0 -0.64 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.12 0.088 -10000 0 -0.28 60 60
CTSD 0.027 0.007 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.04 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.093 0.089 -10000 0 -0.26 47 47
PRKCD 0.026 0.007 -10000 0 -10000 0 0
PRKCZ 0.025 0.008 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.01 -10000 0 -10000 0 0
RelA/NF kappa B1 0.04 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.016 0.044 -10000 0 -0.35 1 1
TNFR1A/BAG4/TNF-alpha 0.041 0.054 -10000 0 -0.42 3 3
mol:Sphingosine-1-phosphate 0.01 0.01 -10000 0 -10000 0 0
MAP2K1 -0.095 0.08 0.2 1 -0.25 46 47
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.028 0.002 -10000 0 -10000 0 0
CYCS -0.05 0.042 -10000 0 -0.23 2 2
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.012 -10000 0 -10000 0 0
EIF2AK2 -0.11 0.085 0.18 2 -0.26 59 61
TNF-alpha/TNFR1A/FAN 0.041 0.054 -10000 0 -0.42 3 3
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.021 0.077 -10000 0 -0.4 6 6
MAP2K2 -0.095 0.08 0.2 1 -0.25 46 47
SMPD3 0.011 0.035 -10000 0 -10000 0 0
TNF 0.014 0.071 -10000 0 -0.64 3 3
PKC zeta/PAR4 0.036 0.014 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.2 0.083 0.24 204 -10000 0 204
NF kappa B1/RelA/I kappa B alpha 0.07 0.031 -10000 0 -10000 0 0
AIFM1 -0.067 0.063 -10000 0 -0.17 60 60
BCL2 0.026 0.008 -10000 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.058 0.2 -10000 0 -0.48 50 50
PDGFRB 0.004 0.12 -10000 0 -0.64 10 10
SPHK1 -0.011 0.049 -10000 0 -0.61 1 1
mol:S1P -0.011 0.053 -10000 0 -0.51 1 1
S1P1/S1P/Gi -0.077 0.19 -10000 0 -0.45 46 46
GNAO1 -0.017 0.15 -10000 0 -0.64 16 16
PDGFB-D/PDGFRB/PLCgamma1 -0.057 0.19 0.36 3 -0.42 44 47
PLCG1 -0.072 0.17 0.25 1 -0.44 41 42
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.12 -10000 0 -0.64 10 10
GNAI2 0.021 0.019 -10000 0 -10000 0 0
GNAI3 0.021 0.018 -10000 0 -10000 0 0
GNAI1 0.013 0.057 -10000 0 -0.64 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.072 0.16 -10000 0 -0.41 50 50
S1P1/S1P -0.063 0.14 -10000 0 -0.36 32 32
negative regulation of cAMP metabolic process -0.075 0.18 -10000 0 -0.44 46 46
MAPK3 -0.096 0.24 0.34 6 -0.57 48 54
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.005 -10000 0 -10000 0 0
KDR -0.094 0.25 -10000 0 -0.64 51 51
PLCB2 -0.052 0.14 0.34 2 -0.37 16 18
RAC1 0.022 0.012 -10000 0 -10000 0 0
RhoA/GTP -0.051 0.12 -10000 0 -0.31 32 32
receptor internalization -0.062 0.13 -10000 0 -0.33 37 37
PTGS2 -0.16 0.4 0.51 2 -1 49 51
Rac1/GTP -0.046 0.11 -10000 0 -0.31 28 28
RHOA 0.027 0.006 -10000 0 -10000 0 0
VEGFA 0.022 0.017 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.075 0.18 -10000 0 -0.44 46 46
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.018 -10000 0 -10000 0 0
MAPK1 -0.12 0.25 -10000 0 -0.59 56 56
S1P1/S1P/PDGFB-D/PDGFRB -0.058 0.17 0.29 3 -0.39 36 39
ABCC1 0.025 0.009 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.026 0.007 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.037 0.1 -10000 0 -0.29 13 13
NT3 (dimer)/TRKC -0.098 0.24 -10000 0 -0.5 73 73
NT3 (dimer)/TRKB -0.17 0.25 -10000 0 -0.44 129 129
SHC/Grb2/SOS1/GAB1/PI3K 0.028 0.013 -10000 0 -10000 0 0
RAPGEF1 0.027 0.006 -10000 0 -10000 0 0
BDNF 0.013 0.037 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.006 -10000 0 -10000 0 0
NTRK1 -0.11 0.26 -10000 0 -0.63 56 56
NTRK2 -0.23 0.32 -10000 0 -0.63 113 113
NTRK3 -0.084 0.25 -10000 0 -0.64 48 48
NT-4/5 (dimer)/TRKB -0.14 0.22 -10000 0 -0.4 116 116
neuron apoptosis 0.12 0.17 0.45 34 -10000 0 34
SHC 2-3/Grb2 -0.12 0.18 -10000 0 -0.5 34 34
SHC1 0.027 0.005 -10000 0 -10000 0 0
SHC2 -0.11 0.16 -10000 0 -0.46 30 30
SHC3 -0.13 0.2 -10000 0 -0.52 40 40
STAT3 (dimer) 0.03 0.025 -10000 0 -0.37 1 1
NT3 (dimer)/TRKA -0.091 0.23 -10000 0 -0.45 80 80
RIN/GDP -0.024 0.11 0.31 8 -0.28 12 20
GIPC1 0.028 0.002 -10000 0 -10000 0 0
KRAS 0.027 0.006 -10000 0 -10000 0 0
DNAJA3 -0.053 0.12 -10000 0 -0.29 55 55
RIN/GTP 0.012 0.006 -10000 0 -10000 0 0
CCND1 0.016 0.053 -10000 0 -0.88 1 1
MAGED1 0.028 0.003 -10000 0 -10000 0 0
PTPN11 0.027 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.001 0.033 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.018 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.061 0.2 -10000 0 -0.42 64 64
TRKA/NEDD4-2 -0.063 0.2 -10000 0 -0.46 57 57
ELMO1 0.022 0.011 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.029 0.016 -10000 0 -10000 0 0
NGF 0.007 0.11 -10000 0 -0.64 8 8
HRAS 0.028 0.003 -10000 0 -10000 0 0
DOCK1 0.028 0.004 -10000 0 -10000 0 0
GAB2 0.028 0.003 -10000 0 -10000 0 0
RIT2 -0.013 0.014 -10000 0 -10000 0 0
RIT1 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
DNM1 -0.008 0.061 -10000 0 -0.64 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.044 0.13 -10000 0 -0.29 53 53
mol:GDP -0.043 0.16 0.38 8 -0.41 15 23
NGF (dimer) 0.007 0.11 -10000 0 -0.64 8 8
RhoG/GDP 0.016 0.009 -10000 0 -10000 0 0
RIT1/GDP -0.021 0.12 0.31 8 -0.29 10 18
TIAM1 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.14 0.22 -10000 0 -0.42 109 109
KIDINS220/CRKL/C3G 0.037 0.013 -10000 0 -10000 0 0
SHC/RasGAP 0.04 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2 0.051 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.062 0.025 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.004 -10000 0 -10000 0 0
NT3 (dimer) -0.047 0.2 -10000 0 -0.64 31 31
RAP1/GDP -0.026 0.085 -10000 0 -0.25 9 9
KIDINS220/CRKL 0.026 0.007 -10000 0 -10000 0 0
BDNF (dimer) 0.013 0.037 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.053 0.19 -10000 0 -0.41 62 62
Schwann cell development -0.034 0.033 -10000 0 -10000 0 0
EHD4 0.027 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.061 0.026 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.025 0.036 -10000 0 -0.25 2 2
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.19 0.24 -10000 0 -0.4 146 146
ABL1 0.027 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.012 -10000 0 -10000 0 0
Rap1/GTP -0.064 0.14 -10000 0 -0.44 18 18
STAT3 0.03 0.025 -10000 0 -0.37 1 1
axon guidance -0.19 0.22 -10000 0 -0.38 146 146
MAPK3 -0.074 0.16 -10000 0 -0.39 53 53
MAPK1 -0.08 0.16 -10000 0 -0.39 63 63
CDC42/GDP -0.018 0.12 0.3 9 -0.3 9 18
NTF3 -0.048 0.21 -10000 0 -0.64 31 31
NTF4 -0.001 0.033 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM -0.048 0.19 -10000 0 -0.42 56 56
PI3K 0.04 0.009 -10000 0 -10000 0 0
FRS3 0.027 0.006 -10000 0 -10000 0 0
FAIM 0.027 0.008 -10000 0 -10000 0 0
GAB1 0.027 0.006 -10000 0 -10000 0 0
RASGRF1 -0.058 0.13 -10000 0 -0.3 59 59
SOS1 0.027 0.005 -10000 0 -10000 0 0
MCF2L -0.099 0.2 -10000 0 -0.44 69 69
RGS19 0.025 0.013 -10000 0 -10000 0 0
CDC42 0.026 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.011 0.094 -10000 0 -0.41 7 7
Rac1/GDP -0.023 0.1 0.27 4 -0.29 10 14
NGF (dimer)/TRKA/GRIT -0.063 0.19 -10000 0 -0.41 63 63
neuron projection morphogenesis -0.033 0.14 -10000 0 -0.73 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.052 0.19 -10000 0 -0.41 62 62
MAP2K1 0.03 0.063 0.39 5 -10000 0 5
NGFR 0.012 0.095 -10000 0 -0.64 6 6
NGF (dimer)/TRKA/GIPC/GAIP -0.05 0.14 -10000 0 -0.31 57 57
RAS family/GTP/PI3K 0.024 0.01 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.071 0.031 -10000 0 -10000 0 0
NRAS 0.027 0.006 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.012 -10000 0 -10000 0 0
PRKCI 0.027 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCZ 0.025 0.008 -10000 0 -10000 0 0
MAPKKK cascade -0.14 0.27 -10000 0 -0.57 75 75
RASA1 0.027 0.004 -10000 0 -10000 0 0
TRKA/c-Abl -0.061 0.2 -10000 0 -0.47 56 56
SQSTM1 0.025 0.017 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.11 0.22 -10000 0 -0.38 109 109
NGF (dimer)/TRKA/p62/Atypical PKCs -0.021 0.18 -10000 0 -0.37 56 56
MATK 0.013 0.073 -10000 0 -0.64 3 3
NEDD4L 0.025 0.022 -10000 0 -0.33 1 1
RAS family/GDP -0.04 0.066 -10000 0 -0.23 9 9
NGF (dimer)/TRKA -0.055 0.14 -10000 0 -0.31 59 59
Rac1/GTP -0.053 0.098 -10000 0 -0.29 23 23
FRS2 family/SHP2/CRK family 0.067 0.033 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.001 0.081 -10000 0 -0.28 22 22
epithelial cell differentiation 0.021 0.11 -10000 0 -0.36 22 22
CYFIP2 0.025 0.039 -10000 0 -0.64 1 1
ENAH 0 0.13 0.52 11 -10000 0 11
EGFR 0.022 0.012 -10000 0 -10000 0 0
EPHA2 0.025 0.008 -10000 0 -10000 0 0
MYO6 0.001 0.12 0.34 8 -0.35 22 30
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.052 0.031 -10000 0 -0.42 1 1
AQP5 -0.07 0.19 -10000 0 -0.56 31 31
CTNND1 0.028 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.003 0.12 0.34 9 -0.34 22 31
regulation of calcium-dependent cell-cell adhesion -0.024 0.15 0.35 6 -0.38 36 42
EGF -0.56 0.21 -10000 0 -0.63 258 258
NCKAP1 0.028 0.004 -10000 0 -10000 0 0
AQP3 -0.17 0.27 -10000 0 -0.56 88 88
cortical microtubule organization 0.021 0.11 -10000 0 -0.36 22 22
GO:0000145 -0.015 0.11 0.33 9 -0.33 22 31
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.026 0.11 -10000 0 -0.36 22 22
MLLT4 0.027 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.035 0.077 -10000 0 -10000 0 0
ARF6 0.027 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.059 0.028 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.012 0.096 0.34 2 -0.32 20 22
PVRL2 0.028 0.003 -10000 0 -10000 0 0
ZYX -0.007 0.1 0.35 3 -0.35 20 23
ARF6/GTP 0.064 0.032 -10000 0 -10000 0 0
CDH1 -0.025 0.18 -10000 0 -0.64 22 22
EGFR/EGFR/EGF/EGF -0.27 0.16 -10000 0 -0.37 185 185
RhoA/GDP 0.024 0.11 -10000 0 -0.34 22 22
actin cytoskeleton organization -0.016 0.11 0.33 8 -0.34 22 30
IGF-1R heterotetramer 0.028 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
IGF1R 0.028 0.004 -10000 0 -10000 0 0
IGF1 0.013 0.095 -10000 0 -0.64 6 6
DIAPH1 0.035 0.11 -10000 0 -0.54 4 4
Wnt receptor signaling pathway -0.021 0.11 0.36 22 -10000 0 22
RHOA 0.027 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.035 0.078 -10000 0 -10000 0 0
CTNNA1 0.027 0.005 -10000 0 -10000 0 0
VCL -0.017 0.11 0.33 8 -0.34 22 30
EFNA1 0.027 0.005 -10000 0 -10000 0 0
LPP -0.023 0.1 0.34 3 -0.33 22 25
Ephrin A1/EPHA2 0.016 0.1 -10000 0 -0.33 22 22
SEC6/SEC8 -0.013 0.086 -10000 0 -0.32 20 20
MGAT3 -0.025 0.15 0.35 6 -0.38 36 42
HGF/MET -0.002 0.12 -10000 0 -0.36 26 26
HGF -0.004 0.13 -10000 0 -0.64 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.001 0.081 -10000 0 -0.28 22 22
actin cable formation 0.03 0.15 0.56 14 -0.29 1 15
KIAA1543 -0.016 0.12 0.33 9 -0.33 23 32
KIFC3 -0.015 0.096 -10000 0 -0.35 22 22
NCK1 0.027 0.006 -10000 0 -10000 0 0
EXOC3 0.027 0.005 -10000 0 -10000 0 0
ACTN1 0.003 0.12 0.34 9 -0.34 22 31
NCK1/GIT1 0.038 0.012 -10000 0 -10000 0 0
mol:GDP 0.021 0.11 -10000 0 -0.36 22 22
EXOC4 0.022 0.012 -10000 0 -10000 0 0
STX4 -0.014 0.097 -10000 0 -0.35 22 22
PIP5K1C 0.003 0.12 0.34 9 -0.35 22 31
LIMA1 0.027 0.005 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
ROCK1 0.002 0.15 0.54 12 -10000 0 12
adherens junction assembly 0.006 0.13 0.4 13 -0.35 1 14
IGF-1R heterotetramer/IGF1 0.01 0.11 -10000 0 -0.34 27 27
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.039 0.01 -10000 0 -10000 0 0
MET 0.017 0.023 -10000 0 -10000 0 0
PLEKHA7 0.002 0.12 0.34 9 -0.34 23 32
mol:GTP 0.057 0.027 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.003 0.11 0.32 3 -10000 0 3
cortical actin cytoskeleton stabilization 0.001 0.081 -10000 0 -0.28 22 22
regulation of cell-cell adhesion -0.016 0.11 0.33 8 -0.34 22 30
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.001 0.081 -10000 0 -0.28 22 22
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.86 0.61 -10000 0 -1.3 196 196
PLK1 0.044 0.098 -10000 0 -10000 0 0
CDKN1B -0.068 0.12 -10000 0 -0.35 8 8
FOXO3 0.046 0.05 -10000 0 -10000 0 0
KAT2B 0.035 0.009 -10000 0 -10000 0 0
FOXO1/SIRT1 -0.29 0.25 -10000 0 -0.44 187 187
CAT 0.034 0.074 -10000 0 -10000 0 0
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
AKT1 -0.029 0.049 -10000 0 -0.18 4 4
FOXO1 -0.31 0.27 -10000 0 -0.47 195 195
MAPK10 0.033 0.076 0.3 1 -10000 0 1
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.057 0.089 0.36 3 -10000 0 3
response to oxidative stress -0.034 0.035 -10000 0 -0.16 6 6
FOXO3A/SIRT1 0.063 0.083 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
EP300 -0.037 0.051 -10000 0 -0.19 6 6
BCL2L11 0.028 0.061 -10000 0 -0.68 2 2
FOXO1/SKP2 -0.28 0.25 -10000 0 -0.44 185 185
mol:GDP -0.034 0.035 -10000 0 -0.16 6 6
RAN 0.028 0.005 -10000 0 -10000 0 0
GADD45A 0.047 0.17 0.36 1 -0.58 17 18
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.045 0.12 -10000 0 -0.47 13 13
MST1 0.032 0.041 -10000 0 -0.64 1 1
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.026 0.008 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.016 0.13 -10000 0 -0.55 11 11
YWHAB 0.026 0.007 -10000 0 -10000 0 0
MAPK8 0.028 0.081 0.3 1 -10000 0 1
MAPK9 0.033 0.075 0.3 1 -10000 0 1
YWHAG 0.022 0.011 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
YWHAZ 0.027 0.004 -10000 0 -10000 0 0
SIRT1 0.03 0.006 -10000 0 -10000 0 0
SOD2 -0.075 0.14 -10000 0 -0.53 4 4
RBL2 0.056 0.084 -10000 0 -0.76 1 1
RAL/GDP -0.001 0.032 -10000 0 -10000 0 0
CHUK 0.036 0.006 -10000 0 -10000 0 0
Ran/GTP 0.023 0.004 -10000 0 -10000 0 0
CSNK1G2 0.028 0.003 -10000 0 -10000 0 0
RAL/GTP 0.003 0.031 -10000 0 -10000 0 0
CSNK1G1 0.028 0.004 -10000 0 -10000 0 0
FASLG 0.005 0.13 -10000 0 -0.75 8 8
SKP2 0.027 0.005 -10000 0 -10000 0 0
USP7 0.027 0.008 -10000 0 -10000 0 0
IKBKB 0.035 0.008 -10000 0 -10000 0 0
CCNB1 0.035 0.075 -10000 0 -10000 0 0
FOXO1-3a-4/beta catenin -0.053 0.13 0.36 1 -0.41 1 2
proteasomal ubiquitin-dependent protein catabolic process -0.28 0.25 -10000 0 -0.44 185 185
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
SGK1 0.035 0.008 -10000 0 -10000 0 0
CSNK1G3 0.027 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.01 -10000 0 -10000 0 0
ZFAND5 0.054 0.082 0.46 1 -10000 0 1
SFN -0.03 0.09 -10000 0 -0.58 5 5
CDK2 -0.055 0.062 -10000 0 -0.22 4 4
FOXO3A/14-3-3 -0.007 0.12 -10000 0 -0.57 8 8
CREBBP -0.051 0.06 -10000 0 -0.25 1 1
FBXO32 0.037 0.074 -10000 0 -10000 0 0
BCL6 0.056 0.093 -10000 0 -0.68 2 2
RALB 0.029 0.003 -10000 0 -10000 0 0
RALA 0.023 0.012 -10000 0 -10000 0 0
YWHAH 0.026 0.008 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 0.037 0.092 -10000 0 -0.36 13 13
ER alpha/Gai/GDP/Gbeta gamma -0.053 0.22 -10000 0 -0.59 30 30
AKT1 -0.037 0.24 -10000 0 -0.8 25 25
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.035 0.25 -10000 0 -0.82 25 25
mol:Ca2+ -0.13 0.22 -10000 0 -0.49 63 63
IGF1R 0.028 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.005 0.11 -10000 0 -0.38 21 21
SHC1 0.027 0.005 -10000 0 -10000 0 0
apoptosis 0.034 0.23 0.76 25 -10000 0 25
RhoA/GTP 0.006 0.072 -10000 0 -0.33 11 11
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.018 0.19 -10000 0 -0.56 23 23
regulation of stress fiber formation 0.007 0.095 0.27 15 -0.35 6 21
E2/ERA-ERB (dimer) 0.011 0.097 -10000 0 -0.36 17 17
KRAS 0.027 0.006 -10000 0 -10000 0 0
G13/GTP 0.013 0.084 -10000 0 -0.3 17 17
pseudopodium formation -0.007 0.095 0.35 6 -0.27 15 21
E2/ER alpha (dimer)/PELP1 0.012 0.094 -10000 0 -0.35 17 17
GRB2 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.027 0.006 -10000 0 -10000 0 0
GNAO1 -0.012 0.15 -10000 0 -0.64 16 16
HRAS 0.028 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.02 0.22 0.36 2 -0.57 29 31
E2/ER beta (dimer) 0.019 0.006 -10000 0 -10000 0 0
mol:GDP -0.008 0.11 -10000 0 -0.41 17 17
mol:NADP -0.02 0.22 0.36 2 -0.57 29 31
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 -0.14 0.23 -10000 0 -0.51 63 63
IGF-1R heterotetramer 0.028 0.004 -10000 0 -10000 0 0
PLCB1 -0.13 0.24 -10000 0 -0.47 84 84
PLCB2 -0.096 0.21 -10000 0 -0.49 60 60
IGF1 0.013 0.095 -10000 0 -0.64 6 6
mol:L-citrulline -0.02 0.22 0.36 2 -0.57 29 31
RHOA 0.027 0.006 -10000 0 -10000 0 0
Gai/GDP -0.038 0.22 -10000 0 -0.68 27 27
JNK cascade 0.019 0.006 -10000 0 -10000 0 0
BCAR1 0.026 0.008 -10000 0 -10000 0 0
ESR2 0.026 0.009 -10000 0 -10000 0 0
GNAQ 0.027 0.006 -10000 0 -10000 0 0
ESR1 -0.008 0.14 -10000 0 -0.56 17 17
Gq family/GDP/Gbeta gamma -0.058 0.18 -10000 0 -0.59 15 15
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.002 0.16 -10000 0 -0.77 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.016 0.19 0.28 1 -0.54 25 26
GNAZ 0.026 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.006 0.11 -10000 0 -0.42 17 17
STRN 0.016 0.087 -10000 0 -0.64 5 5
GNAL 0.024 0.04 -10000 0 -0.64 1 1
PELP1 0.026 0.008 -10000 0 -10000 0 0
MAPK11 0.013 0.006 -10000 0 -10000 0 0
GNAI2 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.018 0.056 -10000 0 -0.64 2 2
HBEGF -0.024 0.21 0.41 12 -0.56 26 38
cAMP biosynthetic process 0.007 0.082 -10000 0 -0.34 14 14
SRC -0.049 0.2 -10000 0 -0.61 24 24
PI3K 0.04 0.009 -10000 0 -10000 0 0
GNB1 0.025 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.02 0.1 -10000 0 -0.4 13 13
SOS1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.042 0.15 -10000 0 -0.46 23 23
Gs family/GTP 0.014 0.085 -10000 0 -0.34 14 14
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.017 -10000 0 -10000 0 0
vasodilation -0.017 0.2 0.36 2 -0.54 29 31
mol:DAG -0.14 0.23 -10000 0 -0.51 63 63
Gs family/GDP/Gbeta gamma 0 0.096 -10000 0 -0.36 16 16
MSN -0.009 0.099 0.36 6 -0.29 15 21
Gq family/GTP -0.089 0.22 -10000 0 -0.51 60 60
mol:PI-3-4-5-P3 -0.032 0.24 -10000 0 -0.78 25 25
NRAS 0.027 0.006 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.017 0.2 0.54 29 -0.36 2 31
GRB2/SOS1 0.038 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.11 -10000 0 -0.39 17 17
NOS3 -0.024 0.23 0.36 2 -0.61 29 31
GNA11 0.012 0.1 -10000 0 -0.64 7 7
MAPKKK cascade -0.018 0.22 0.37 4 -0.61 29 33
E2/ER alpha (dimer)/PELP1/Src -0.021 0.2 0.3 1 -0.56 26 27
ruffle organization -0.007 0.095 0.35 6 -0.27 15 21
ROCK2 -0.007 0.11 0.38 6 -0.32 16 22
GNA14 -0.11 0.27 -10000 0 -0.62 60 60
GNA15 0.02 0.027 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.045 0.2 0.38 4 -0.56 26 30
MMP2 -0.032 0.2 0.26 1 -0.58 23 24
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.004 0.12 -9999 0 -0.42 21 21
EFNA5 -0.022 0.17 -9999 0 -0.64 21 21
FYN -0.032 0.1 -9999 0 -0.38 21 21
neuron projection morphogenesis -0.004 0.12 -9999 0 -0.42 21 21
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.004 0.12 -9999 0 -0.42 21 21
EPHA5 -0.009 0.023 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

Figure S26.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S26.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.002 0.11 -10000 0 -0.38 3 3
IHH -0.032 0.21 -10000 0 -0.66 28 28
SHH Np/Cholesterol/GAS1 -0.002 0.086 -10000 0 -0.32 18 18
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.002 0.085 0.32 18 -10000 0 18
SMO/beta Arrestin2 -0.007 0.13 -10000 0 -0.41 21 21
SMO -0.015 0.13 -10000 0 -0.43 22 22
AKT1 -0.011 0.13 -10000 0 -0.58 8 8
ARRB2 0.026 0.01 -10000 0 -10000 0 0
BOC 0.027 0.005 -10000 0 -10000 0 0
ADRBK1 0.028 0.002 -10000 0 -10000 0 0
heart looping -0.016 0.13 -10000 0 -0.42 22 22
STIL 0.021 0.12 0.26 1 -0.3 21 22
DHH N/PTCH2 0.004 0.12 -10000 0 -0.48 18 18
DHH N/PTCH1 -0.019 0.15 -10000 0 -0.36 45 45
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
DHH -0.018 0.16 -10000 0 -0.64 18 18
PTHLH -0.014 0.14 -10000 0 -0.48 3 3
determination of left/right symmetry -0.016 0.13 -10000 0 -0.42 22 22
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
skeletal system development -0.013 0.14 -10000 0 -0.48 3 3
IHH N/Hhip -0.026 0.17 -10000 0 -0.45 39 39
DHH N/Hhip -0.015 0.16 -10000 0 -0.52 26 26
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.016 0.13 -10000 0 -0.42 22 22
pancreas development -0.004 0.13 -10000 0 -0.64 11 11
HHAT 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.04 0.009 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.008 0.15 -10000 0 -0.6 16 16
somite specification -0.016 0.13 -10000 0 -0.42 22 22
SHH Np/Cholesterol/PTCH1 -0.006 0.097 -10000 0 -0.31 25 25
SHH Np/Cholesterol/PTCH2 0.014 0.043 -10000 0 -0.38 3 3
SHH Np/Cholesterol/Megalin -0.021 0.12 -10000 0 -0.39 28 28
SHH 0.005 0.051 -10000 0 -0.48 3 3
catabolic process -0.007 0.12 -10000 0 -0.38 28 28
SMO/Vitamin D3 -0.009 0.11 -10000 0 -0.37 22 22
SHH Np/Cholesterol/Hhip 0 0.083 -10000 0 -0.36 14 14
LRP2 -0.034 0.19 -10000 0 -0.63 27 27
receptor-mediated endocytosis -0.036 0.16 -10000 0 -0.54 16 16
SHH Np/Cholesterol/BOC 0.016 0.043 -10000 0 -0.38 3 3
SHH Np/Cholesterol/CDO 0.015 0.044 -10000 0 -0.38 3 3
mesenchymal cell differentiation 0 0.082 0.35 14 -10000 0 14
mol:Vitamin D3 0.029 0.13 -10000 0 -0.31 25 25
IHH N/PTCH2 -0.005 0.14 -10000 0 -0.42 28 28
CDON 0.026 0.012 -10000 0 -10000 0 0
IHH N/PTCH1 0.001 0.13 -10000 0 -0.38 28 28
Megalin/LRPAP1 -0.007 0.15 -10000 0 -0.47 27 27
PTCH2 0.025 0.014 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.008 0.041 -10000 0 -0.38 3 3
PTCH1 -0.007 0.12 -10000 0 -0.38 28 28
HHIP -0.004 0.13 -10000 0 -0.64 11 11
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.043 0.098 -10000 0 -0.95 2 2
SMARCC2 0.028 0.005 -10000 0 -10000 0 0
SMARCC1 0.028 0.007 -10000 0 -10000 0 0
TBX21 -0.045 0.077 0.38 1 -0.41 1 2
SUMO2 0.018 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.032 0.015 -10000 0 -10000 0 0
FKBP4 0.027 0.006 -10000 0 -10000 0 0
FKBP5 0.013 0.095 -10000 0 -0.64 6 6
GR alpha/HSP90/FKBP51/HSP90 0.076 0.088 0.32 3 -0.36 6 9
PRL -0.036 0.079 -10000 0 -0.57 1 1
cortisol/GR alpha (dimer)/TIF2 0.095 0.21 0.48 19 -0.44 10 29
RELA -0.085 0.12 -10000 0 -0.28 27 27
FGG 0.094 0.13 0.44 9 -10000 0 9
GR beta/TIF2 0.032 0.17 0.3 6 -0.45 26 32
IFNG -0.1 0.16 -10000 0 -0.61 7 7
apoptosis -0.051 0.22 -10000 0 -0.61 22 22
CREB1 0.019 0.058 -10000 0 -0.34 7 7
histone acetylation -0.032 0.068 -10000 0 -0.34 1 1
BGLAP -0.037 0.075 -10000 0 -0.47 1 1
GR/PKAc 0.097 0.062 0.33 2 -10000 0 2
NF kappa B1 p50/RelA -0.15 0.2 -10000 0 -0.44 47 47
SMARCD1 0.029 0.005 -10000 0 -10000 0 0
MDM2 0.047 0.055 0.22 8 -10000 0 8
GATA3 -0.48 0.28 -10000 0 -0.63 222 222
AKT1 0.023 0.015 0.21 1 -10000 0 1
CSF2 -0.034 0.056 -10000 0 -10000 0 0
GSK3B 0.019 0.019 -10000 0 -10000 0 0
NR1I3 -0.051 0.25 0.58 1 -0.77 17 18
CSN2 0.077 0.11 0.36 8 -10000 0 8
BRG1/BAF155/BAF170/BAF60A 0.071 0.022 -10000 0 -10000 0 0
NFATC1 0.027 0.009 -10000 0 -10000 0 0
POU2F1 0.028 0.006 -10000 0 -10000 0 0
CDKN1A 0.016 0.052 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.03 0.09 -10000 0 -0.58 5 5
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.06 0.11 0.33 1 -0.36 9 10
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.072 0.28 0.49 2 -0.81 28 30
JUN -0.083 0.15 -10000 0 -0.49 21 21
IL4 -0.044 0.074 -10000 0 -10000 0 0
CDK5R1 0.025 0.009 -10000 0 -10000 0 0
PRKACA 0.028 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.054 0.15 0.23 11 -0.39 33 44
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.089 0.086 0.32 3 -0.32 6 9
cortisol/GR alpha (monomer) 0.14 0.18 0.55 18 -10000 0 18
NCOA2 -0.033 0.19 -10000 0 -0.64 26 26
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.072 0.23 -10000 0 -0.61 41 41
AP-1/NFAT1-c-4 -0.13 0.24 -10000 0 -0.67 28 28
AFP -0.19 0.43 -10000 0 -1.4 32 32
SUV420H1 0.028 0.003 -10000 0 -10000 0 0
IRF1 0.086 0.086 0.43 2 -10000 0 2
TP53 0.038 0.016 -10000 0 -10000 0 0
PPP5C 0.028 0.003 -10000 0 -10000 0 0
KRT17 -0.16 0.32 -10000 0 -1.1 25 25
KRT14 -0.05 0.062 -10000 0 -10000 0 0
TBP 0.033 0.007 -10000 0 -10000 0 0
CREBBP 0.029 0.011 -10000 0 -10000 0 0
HDAC1 0.025 0.007 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
AP-1 -0.13 0.24 -10000 0 -0.67 28 28
MAPK14 0.019 0.019 -10000 0 -10000 0 0
MAPK10 0.019 0.018 -10000 0 -10000 0 0
MAPK11 0.017 0.019 -10000 0 -10000 0 0
KRT5 -0.12 0.22 -10000 0 -1 9 9
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 0.029 0.01 -10000 0 -10000 0 0
STAT1 0.032 0.015 -10000 0 -10000 0 0
CGA -0.073 0.19 -10000 0 -1.2 7 7
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.014 0.067 0.4 1 -10000 0 1
MAPK3 0.019 0.018 -10000 0 -10000 0 0
MAPK1 0.018 0.019 -10000 0 -10000 0 0
ICAM1 -0.15 0.18 -10000 0 -0.53 21 21
NFKB1 -0.08 0.11 -10000 0 -0.28 23 23
MAPK8 -0.078 0.13 -10000 0 -0.41 19 19
MAPK9 0.019 0.018 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.056 0.23 -10000 0 -0.62 26 26
BAX 0.021 0.044 -10000 0 -10000 0 0
POMC -0.2 0.27 -10000 0 -0.74 25 25
EP300 0.029 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.14 0.16 0.48 15 -10000 0 15
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.074 0.32 13 -10000 0 13
SGK1 0.04 0.072 -10000 0 -10000 0 0
IL13 -0.4 0.25 -10000 0 -0.68 95 95
IL6 -0.2 0.36 -10000 0 -1.1 33 33
PRKACG -0.009 0.019 -10000 0 -10000 0 0
IL5 -0.33 0.21 -10000 0 -0.6 59 59
IL2 -0.12 0.17 -10000 0 -0.66 10 10
CDK5 0.021 0.012 -10000 0 -10000 0 0
PRKACB 0.026 0.007 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
IL8 -0.16 0.19 -10000 0 -0.53 31 31
CDK5R1/CDK5 0.028 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.09 0.18 -10000 0 -0.42 24 24
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.13 0.15 0.48 14 -10000 0 14
SMARCA4 0.029 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.092 0.091 0.35 9 -10000 0 9
NF kappa B1 p50/RelA/Cbp -0.088 0.18 -10000 0 -0.43 22 22
JUN (dimer) -0.083 0.15 -10000 0 -0.49 21 21
YWHAH 0.026 0.008 -10000 0 -10000 0 0
VIPR1 -0.084 0.21 0.32 1 -0.96 14 15
NR3C1 0.084 0.11 0.4 9 -10000 0 9
NR4A1 -0.24 0.33 -10000 0 -0.64 116 116
TIF2/SUV420H1 -0.007 0.15 -10000 0 -0.48 26 26
MAPKKK cascade -0.051 0.22 -10000 0 -0.61 22 22
cortisol/GR alpha (dimer)/Src-1 0.14 0.16 0.49 16 -10000 0 16
PBX1 0.014 0.095 -10000 0 -0.64 6 6
POU1F1 0.005 0.023 -10000 0 -10000 0 0
SELE -0.57 0.58 -10000 0 -1.1 147 147
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.092 0.091 0.35 9 -10000 0 9
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.13 0.15 0.48 14 -10000 0 14
mol:cortisol 0.069 0.097 0.3 20 -10000 0 20
MMP1 -0.11 0.33 -10000 0 -1.1 27 27
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.003 0.09 -10000 0 -0.38 12 12
Crk/p130 Cas/Paxillin -0.03 0.11 -10000 0 -0.33 20 20
JUN -0.026 0.11 -10000 0 -0.42 9 9
HRAS 0.028 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.002 0.14 -10000 0 -0.39 29 29
RAP1A 0.027 0.006 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.004 0.15 -10000 0 -0.4 34 34
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.01 0.12 -10000 0 -0.38 22 22
RHOA 0.027 0.006 -10000 0 -10000 0 0
RAP1A/GTP 0.007 0.13 -10000 0 -0.35 32 32
GRB7 0.026 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.006 0.15 -10000 0 -0.4 34 34
MAPKKK cascade -0.011 0.12 -10000 0 -0.35 30 30
BCAR1 0.026 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.004 0.13 -10000 0 -0.4 25 25
lamellipodium assembly -0.021 0.099 -10000 0 -0.3 22 22
RET51/GFRalpha1/GDNF/SHC 0.005 0.15 -10000 0 -0.4 34 34
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.011 0.12 -10000 0 -0.38 22 22
RET9/GFRalpha1/GDNF/Shank3 0.009 0.11 -10000 0 -0.38 22 22
MAPK3 -0.048 0.1 -10000 0 -0.33 32 32
DOK1 0.026 0.012 -10000 0 -10000 0 0
DOK6 -0.064 0.22 -10000 0 -0.62 40 40
PXN 0.027 0.005 -10000 0 -10000 0 0
neurite development -0.056 0.12 -10000 0 -0.43 10 10
DOK5 0.019 0.068 -10000 0 -0.64 3 3
GFRA1 -0.027 0.18 -10000 0 -0.62 23 23
MAPK8 -0.026 0.11 -10000 0 -0.43 10 10
HRAS/GTP 0.004 0.15 -10000 0 -0.39 32 32
tube development 0.017 0.11 -10000 0 -0.36 19 19
MAPK1 -0.038 0.12 0.34 3 -0.34 32 35
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.002 0.079 -10000 0 -0.29 19 19
Rac1/GDP 0.016 0.009 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
PDLIM7 0.027 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.037 0.2 -10000 0 -0.4 61 61
SHC1 0.027 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.005 0.14 -10000 0 -0.39 32 32
RET51/GFRalpha1/GDNF/Dok5 0.002 0.15 -10000 0 -0.39 33 33
PRKCA 0.026 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.002 -10000 0 -10000 0 0
CREB1 -0.011 0.1 -10000 0 -0.34 22 22
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.005 0.089 -10000 0 -0.31 21 21
RET51/GFRalpha1/GDNF/Grb7 0.006 0.14 -10000 0 -0.39 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.005 0.14 -10000 0 -0.62 14 14
DOK4 0.026 0.007 -10000 0 -10000 0 0
JNK cascade -0.025 0.11 -10000 0 -0.41 9 9
RET9/GFRalpha1/GDNF/FRS2 0.01 0.11 -10000 0 -0.38 22 22
SHANK3 0.026 0.008 -10000 0 -10000 0 0
RASA1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.004 0.083 -10000 0 -0.3 19 19
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.012 0.11 -10000 0 -0.3 32 32
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.016 0.11 -10000 0 -0.31 34 34
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.016 0.11 -10000 0 -0.32 32 32
PI3K -0.029 0.16 -10000 0 -0.45 25 25
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.02 0.11 -10000 0 -0.36 19 19
GRB10 0.022 0.011 -10000 0 -10000 0 0
activation of MAPKK activity -0.01 0.093 -10000 0 -0.3 15 15
RET51/GFRalpha1/GDNF/FRS2 0.005 0.15 -10000 0 -0.4 32 32
GAB1 0.027 0.006 -10000 0 -10000 0 0
IRS1 0.017 0.081 -10000 0 -0.58 5 5
IRS2 0.026 0.01 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.019 0.12 -10000 0 -0.32 34 34
RET51/GFRalpha1/GDNF/PKC alpha 0.005 0.14 -10000 0 -0.39 31 31
GRB2 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.028 0.002 -10000 0 -10000 0 0
GDNF -0.007 0.019 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.002 0.16 -10000 0 -0.41 37 37
Rac1/GTP -0.021 0.12 -10000 0 -0.36 21 21
RET9/GFRalpha1/GDNF -0.006 0.12 -10000 0 -0.41 23 23
GFRalpha1/GDNF -0.008 0.14 -10000 0 -0.47 23 23
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.019 0.086 -10000 0 -0.34 5 5
FYN 0.008 0.11 0.35 6 -0.43 5 11
LAT/GRAP2/SLP76 0.021 0.09 0.29 2 -0.35 5 7
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.017 0.12 0.36 18 -0.32 9 27
B2M 0.028 0.006 -10000 0 -10000 0 0
IKBKG 0.013 0.046 0.13 10 -10000 0 10
MAP3K8 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.057 0.048 -10000 0 -0.1 149 149
integrin-mediated signaling pathway 0.033 0.015 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.009 0.13 0.38 11 -0.43 6 17
TRPV6 -0.2 0.57 0.81 58 -0.64 160 218
CD28 0.02 0.046 -10000 0 -0.64 1 1
SHC1 0.003 0.097 0.31 3 -0.39 6 9
receptor internalization 0.004 0.098 0.21 1 -0.38 11 12
PRF1 0.01 0.12 -10000 0 -0.62 6 6
KRAS 0.027 0.006 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
COT/AKT1 0.027 0.11 0.34 18 -0.3 3 21
LAT 0.009 0.1 0.37 5 -0.4 6 11
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D 0.011 0.04 -10000 0 -10000 0 0
CD3E 0.017 0.05 -10000 0 -0.64 1 1
CD3G 0.022 0.024 -10000 0 -10000 0 0
RASGRP2 0.002 0.022 0.1 1 -0.16 3 4
RASGRP1 0.016 0.13 0.36 17 -0.34 9 26
HLA-A 0.001 0.002 -10000 0 -10000 0 0
RASSF5 0.024 0.017 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.034 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.037 0.087 0.25 22 -0.11 1 23
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.009 0.038 -10000 0 -0.19 2 2
PRKCA 0.007 0.057 0.2 6 -0.23 2 8
GRAP2 0.022 0.02 -10000 0 -10000 0 0
mol:IP3 0.11 0.14 0.24 128 -0.32 3 131
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.011 0.054 -10000 0 -0.4 2 2
ORAI1 0.047 0.38 0.66 5 -0.65 57 62
CSK 0.003 0.093 0.26 3 -0.39 6 9
B7 family/CD28 0.029 0.097 0.28 2 -0.36 2 4
CHUK 0.028 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.002 0.098 0.26 1 -0.41 7 8
PTPN6 -0.002 0.09 0.29 2 -0.38 6 8
VAV1 -0.003 0.1 0.28 4 -0.45 6 10
Monovalent TCR/CD3 0.012 0.036 -10000 0 -0.29 2 2
CBL 0.027 0.005 -10000 0 -10000 0 0
LCK 0.003 0.11 0.36 5 -0.38 10 15
PAG1 0.002 0.093 0.25 3 -0.4 5 8
RAP1A 0.027 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.001 0.098 0.27 3 -0.4 7 10
CD80 0.014 0.035 -10000 0 -10000 0 0
CD86 0.007 0.042 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.005 0.048 -10000 0 -0.22 2 2
HRAS 0.028 0.003 -10000 0 -10000 0 0
GO:0035030 -0.003 0.076 0.24 2 -0.32 2 4
CD8A 0.019 0.031 -10000 0 -10000 0 0
CD8B 0.021 0.028 -10000 0 -10000 0 0
PTPRC 0.022 0.043 -10000 0 -0.64 1 1
PDK1/PKC theta 0.021 0.15 0.46 19 -0.37 6 25
CSK/PAG1 0.003 0.09 0.27 4 -0.38 5 9
SOS1 0.027 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.022 0.006 -10000 0 -10000 0 0
GRAP2/SLP76 0.02 0.097 -10000 0 -0.39 5 5
STIM1 0.061 0.13 -10000 0 -0.82 3 3
RAS family/GTP 0.033 0.082 0.26 17 -0.18 3 20
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.003 0.1 -10000 0 -0.39 11 11
mol:DAG 0.026 0.082 0.15 4 -0.29 4 8
RAP1A/GDP 0.023 0.046 0.15 18 -10000 0 18
PLCG1 0.027 0.007 -10000 0 -10000 0 0
CD247 0.023 0.023 -10000 0 -10000 0 0
cytotoxic T cell degranulation 0.01 0.11 -10000 0 -0.6 6 6
RAP1A/GTP 0.001 0.008 -10000 0 -0.06 3 3
mol:PI-3-4-5-P3 0.011 0.12 0.37 11 -0.37 6 17
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.1 0.16 0.27 108 -0.39 4 112
NRAS 0.027 0.006 -10000 0 -10000 0 0
ZAP70 0.014 0.036 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.012 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.006 0.093 0.27 2 -0.39 5 7
MALT1 0.026 0.008 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.03 0.037 -10000 0 -10000 0 0
CARD11 -0.002 0.043 -10000 0 -10000 0 0
PRKCB 0.005 0.052 0.18 3 -0.23 2 5
PRKCE 0.008 0.056 0.21 5 -0.25 1 6
PRKCQ 0.009 0.13 0.4 12 -0.41 6 18
LCP2 0.024 0.018 -10000 0 -10000 0 0
BCL10 0.026 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression 0.018 0.12 0.34 18 -0.27 9 27
IKK complex 0.044 0.12 0.35 27 -10000 0 27
RAS family/GDP 0.002 0.007 -10000 0 -10000 0 0
MAP3K14 0.009 0.065 0.22 8 -0.24 2 10
PDPK1 0.023 0.13 0.4 19 -0.3 6 25
TCR/CD3/MHC I/CD8/Fyn 0.003 0.11 -10000 0 -0.54 5 5
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.013 0.12 -9999 0 -0.42 21 21
E-cadherin/beta catenin -0.003 0.14 -9999 0 -0.48 22 22
CTNNB1 0.027 0.006 -9999 0 -10000 0 0
JUP 0.026 0.007 -9999 0 -10000 0 0
CDH1 -0.025 0.18 -9999 0 -0.64 22 22
LPA4-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
ADCY4 -0.029 0.097 -10000 0 -0.42 17 17
ADCY5 -0.028 0.094 -10000 0 -0.42 16 16
ADCY6 -0.005 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.008 -10000 0 -10000 0 0
ADCY1 -0.14 0.19 -10000 0 -0.41 96 96
ADCY2 -0.027 0.029 -10000 0 -0.42 1 1
ADCY3 -0.005 0.001 -10000 0 -10000 0 0
ADCY8 -0.008 0.007 -10000 0 -10000 0 0
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.005 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.031 0.1 0.3 10 -0.26 8 18
Coregulation of Androgen receptor activity

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
NRIP1 0.026 0.007 -9999 0 -10000 0 0
SVIL 0.027 0.005 -9999 0 -10000 0 0
ZNF318 0.026 0.007 -9999 0 -10000 0 0
JMJD2C 0.001 0.005 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.061 0.1 -9999 0 -0.44 12 12
CARM1 0.028 0.003 -9999 0 -10000 0 0
PRDX1 0.026 0.007 -9999 0 -10000 0 0
PELP1 0.026 0.008 -9999 0 -10000 0 0
CTNNB1 0.027 0.007 -9999 0 -10000 0 0
AKT1 0.026 0.007 -9999 0 -10000 0 0
PTK2B 0.027 0.006 -9999 0 -10000 0 0
MED1 0.026 0.007 -9999 0 -10000 0 0
MAK 0.022 0.021 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.018 0.056 -9999 0 -0.64 2 2
GSN 0.027 0.006 -9999 0 -10000 0 0
NCOA2 -0.033 0.19 -9999 0 -0.64 26 26
NCOA6 0.027 0.006 -9999 0 -10000 0 0
DNA-PK 0.05 0.018 -9999 0 -10000 0 0
NCOA4 0.027 0.005 -9999 0 -10000 0 0
PIAS3 0.027 0.007 -9999 0 -10000 0 0
cell proliferation -0.045 0.11 -9999 0 -0.49 14 14
XRCC5 0.027 0.005 -9999 0 -10000 0 0
UBE3A 0.028 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.083 0.13 -9999 0 -0.44 26 26
FHL2 -0.04 0.08 -9999 0 -0.59 1 1
RANBP9 0.027 0.006 -9999 0 -10000 0 0
JMJD1A -0.088 0.071 -9999 0 -0.14 185 185
CDK6 0.022 0.012 -9999 0 -10000 0 0
TGFB1I1 0.014 0.087 -9999 0 -0.64 5 5
T-DHT/AR/CyclinD1 -0.065 0.1 -9999 0 -0.44 13 13
XRCC6 0.026 0.008 -9999 0 -10000 0 0
T-DHT/AR -0.12 0.13 -9999 0 -0.46 12 12
CTDSP1 0.027 0.005 -9999 0 -10000 0 0
CTDSP2 0.027 0.005 -9999 0 -10000 0 0
BRCA1 0.025 0.013 -9999 0 -10000 0 0
TCF4 0.026 0.008 -9999 0 -10000 0 0
CDKN2A -0.054 0.044 -9999 0 -10000 0 0
SRF 0.032 0.008 -9999 0 -10000 0 0
NKX3-1 -0.16 0.12 -9999 0 -0.24 193 193
KLK3 0.014 0.038 -9999 0 -10000 0 0
TMF1 0.027 0.006 -9999 0 -10000 0 0
HNRNPA1 0.027 0.005 -9999 0 -10000 0 0
AOF2 0 0.001 -9999 0 -10000 0 0
APPL1 0.013 0.005 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.063 0.1 -9999 0 -0.44 12 12
AR -0.065 0.13 -9999 0 -0.66 12 12
UBA3 0.027 0.006 -9999 0 -10000 0 0
PATZ1 0.026 0.008 -9999 0 -10000 0 0
PAWR 0.027 0.005 -9999 0 -10000 0 0
PRKDC 0.027 0.005 -9999 0 -10000 0 0
PA2G4 0.027 0.005 -9999 0 -10000 0 0
UBE2I 0.026 0.008 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.054 0.093 -9999 0 -0.4 12 12
RPS6KA3 0.028 0.003 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.063 0.1 -9999 0 -0.44 12 12
LATS2 0.027 0.006 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.056 0.091 -9999 0 -0.4 12 12
Cyclin D3/CDK11 p58 0.02 0.005 -9999 0 -10000 0 0
VAV3 0.024 0.04 -9999 0 -0.64 1 1
KLK2 -0.056 0.06 -9999 0 -0.37 3 3
CASP8 0.028 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.083 0.16 -9999 0 -0.47 34 34
TMPRSS2 -0.64 0.49 -9999 0 -1 185 185
CCND1 0.025 0.039 -9999 0 -0.64 1 1
PIAS1 0.028 0.004 -9999 0 -10000 0 0
mol:T-DHT -0.043 0.034 -9999 0 -0.069 182 182
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.028 0.004 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.051 0.098 -9999 0 -0.42 12 12
CMTM2 0.018 0.027 -9999 0 -10000 0 0
SNURF -0.01 0.14 -9999 0 -0.62 14 14
ZMIZ1 -0.037 0.051 -9999 0 -10000 0 0
CCND3 0.027 0.006 -9999 0 -10000 0 0
TGIF1 0.026 0.008 -9999 0 -10000 0 0
FKBP4 0.027 0.006 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.028 0.004 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.049 0.17 -9999 0 -0.35 66 66
Syndecan-3/Neurocan -0.006 0.11 -9999 0 -0.36 23 23
POMC 0.019 0.071 -9999 0 -0.56 4 4
EGFR 0.022 0.012 -9999 0 -10000 0 0
Syndecan-3/EGFR -0.006 0.1 -9999 0 -0.36 23 23
AGRP 0.013 0.021 -9999 0 -10000 0 0
NCSTN 0.027 0.005 -9999 0 -10000 0 0
PSENEN 0.028 0.002 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.025 0.039 -9999 0 -0.64 1 1
APH1A 0.027 0.005 -9999 0 -10000 0 0
NCAN 0.007 0.034 -9999 0 -10000 0 0
long-term memory 0.017 0.1 -9999 0 -0.34 23 23
Syndecan-3/IL8 -0.013 0.1 -9999 0 -0.35 24 24
PSEN1 0.026 0.007 -9999 0 -10000 0 0
Src/Cortactin 0.039 0.012 -9999 0 -10000 0 0
FYN 0.027 0.005 -9999 0 -10000 0 0
limb bud formation -0.012 0.097 -9999 0 -0.38 19 19
MC4R -0.007 0.021 -9999 0 -10000 0 0
SRC 0.026 0.009 -9999 0 -10000 0 0
PTN -0.096 0.25 -9999 0 -0.64 50 50
FGFR/FGF/Syndecan-3 -0.012 0.098 -9999 0 -0.38 19 19
neuron projection morphogenesis -0.042 0.18 -9999 0 -0.34 61 61
Syndecan-3/AgRP -0.002 0.1 -9999 0 -0.36 21 21
Syndecan-3/AgRP/MC4R 0.006 0.1 -9999 0 -0.35 21 21
Fyn/Cortactin 0.04 0.009 -9999 0 -10000 0 0
SDC3 -0.012 0.099 -9999 0 -0.38 19 19
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.012 0.1 -9999 0 -0.35 24 24
IL8 0 0.059 -9999 0 -0.64 1 1
Syndecan-3/Fyn/Cortactin 0.017 0.11 -9999 0 -0.34 23 23
Syndecan-3/CASK -0.017 0.1 -9999 0 -0.36 23 23
alpha-MSH/MC4R 0.025 0.057 -9999 0 -0.42 4 4
Gamma Secretase 0.075 0.035 -9999 0 -0.36 1 1
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.007 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.087 -10000 0 -0.38 12 12
regulation of S phase of mitotic cell cycle 0.011 0.062 -10000 0 -0.29 11 11
GNAO1 -0.012 0.15 -10000 0 -0.64 16 16
HRAS 0.026 0.009 -10000 0 -10000 0 0
SHBG/T-DHT 0.007 0.061 -10000 0 -0.31 9 9
PELP1 0.025 0.008 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.022 0.081 -10000 0 -0.32 11 11
T-DHT/AR -0.003 0.1 -10000 0 -0.48 12 12
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.009 43 43
GNAI2 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.018 0.056 -10000 0 -0.64 2 2
mol:GDP -0.016 0.1 -10000 0 -0.49 12 12
cell proliferation -0.041 0.16 0.32 4 -0.44 32 36
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
FOS -0.11 0.3 0.32 1 -0.8 43 44
mol:Ca2+ -0.005 0.02 -10000 0 -0.069 17 17
MAPK3 -0.019 0.13 0.34 7 -0.4 4 11
MAPK1 -0.043 0.16 0.22 1 -0.5 23 24
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.005 43 43
cAMP biosynthetic process -0.002 0.067 0.24 7 -0.3 8 15
GNG2 0.027 0.006 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 43 43
HRAS/GTP 0.022 0.085 -10000 0 -0.35 11 11
actin cytoskeleton reorganization 0.03 0.021 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 43 43
PI3K 0.036 0.008 -10000 0 -10000 0 0
apoptosis 0.045 0.17 0.46 34 -0.28 2 36
T-DHT/AR/PELP1 0.015 0.088 -10000 0 -0.4 12 12
HRAS/GDP -0.002 0.1 -10000 0 -0.47 12 12
CREB1 -0.05 0.18 0.35 1 -0.5 34 35
RAC1-CDC42/GTP 0.037 0.026 -10000 0 -10000 0 0
AR -0.002 0.13 -10000 0 -0.64 12 12
GNB1 0.025 0.008 -10000 0 -10000 0 0
RAF1 -0.004 0.083 -10000 0 -0.34 11 11
RAC1-CDC42/GDP 0.011 0.1 -10000 0 -0.47 11 11
T-DHT/AR/PELP1/Src 0.029 0.086 -10000 0 -0.37 12 12
MAP2K2 -0.023 0.081 -10000 0 -0.32 12 12
T-DHT/AR/PELP1/Src/PI3K 0.011 0.062 -10000 0 -0.29 11 11
GNAZ 0.026 0.008 -10000 0 -10000 0 0
SHBG 0.009 0.096 -10000 0 -0.5 9 9
Gi family/GNB1/GNG2/GDP -0.028 0.15 -10000 0 -0.47 23 23
mol:T-DHT -0.001 0.003 0.001 1 -0.006 40 41
RAC1 0.022 0.012 -10000 0 -10000 0 0
GNRH1 -0.005 0.023 -10000 0 -10000 0 0
Gi family/GTP -0.017 0.075 -10000 0 -0.25 15 15
CDC42 0.026 0.008 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.22 0.32 -10000 0 -0.62 109 109
HRAS 0.028 0.003 -10000 0 -10000 0 0
EGFR 0.022 0.012 -10000 0 -10000 0 0
AKT 0.034 0.1 0.24 31 -10000 0 31
FOXO3 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.007 -10000 0 -10000 0 0
FOXO1 0.027 0.006 -10000 0 -10000 0 0
AKT3 0.027 0.006 -10000 0 -10000 0 0
FOXO4 0.028 0.002 -10000 0 -10000 0 0
MET 0.017 0.023 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
PIK3CB 0.027 0.006 -10000 0 -10000 0 0
NRAS 0.027 0.006 -10000 0 -10000 0 0
PIK3CG 0.018 0.042 -10000 0 -0.64 1 1
PIK3R3 0.026 0.007 -10000 0 -10000 0 0
PIK3R2 0.028 0.002 -10000 0 -10000 0 0
NF1 0.026 0.007 -10000 0 -10000 0 0
RAS -0.027 0.077 -10000 0 -0.16 66 66
ERBB2 0.026 0.007 -10000 0 -10000 0 0
proliferation/survival/translation -0.029 0.048 0.24 2 -10000 0 2
PI3K 0.009 0.11 0.24 34 -0.2 11 45
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
KRAS 0.027 0.006 -10000 0 -10000 0 0
FOXO 0.062 0.085 0.23 37 -10000 0 37
AKT2 0.028 0.002 -10000 0 -10000 0 0
PTEN 0.028 0.004 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.004 0.12 -9999 0 -0.64 10 10
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.003 0.072 -9999 0 -0.28 14 14
GNAO1 -0.011 0.15 -9999 0 -0.64 16 16
S1P/S1P3/G12/G13 0.013 0.1 -9999 0 -0.38 15 15
AKT1 -0.027 0.17 -9999 0 -0.5 29 29
AKT3 -0.001 0.12 -9999 0 -0.59 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.12 -9999 0 -0.64 10 10
GNAI2 0.028 0.007 -9999 0 -10000 0 0
GNAI3 0.028 0.006 -9999 0 -10000 0 0
GNAI1 0.018 0.056 -9999 0 -0.64 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.024 0.18 -9999 0 -0.62 23 23
S1PR2 0.028 0.002 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.011 0.14 -9999 0 -0.34 31 31
MAPK3 -0.014 0.12 -9999 0 -0.48 9 9
MAPK1 -0.008 0.12 -9999 0 -0.34 25 25
JAK2 -0.014 0.14 -9999 0 -0.47 14 14
CXCR4 -0.02 0.13 -9999 0 -0.34 28 28
FLT1 0.024 0.056 -9999 0 -0.64 2 2
RhoA/GDP 0.02 0.005 -9999 0 -10000 0 0
Rac1/GDP 0.016 0.009 -9999 0 -10000 0 0
SRC -0.015 0.13 -9999 0 -0.5 9 9
S1P/S1P3/Gi -0.011 0.14 -9999 0 -0.34 31 31
RAC1 0.022 0.012 -9999 0 -10000 0 0
RhoA/GTP -0.006 0.13 -9999 0 -0.33 28 28
VEGFA 0.027 0.013 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.012 0.092 -9999 0 -0.32 12 12
VEGFR1 homodimer/VEGFA homodimer 0.039 0.046 -9999 0 -0.48 2 2
RHOA 0.027 0.006 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.071 0.18 -9999 0 -0.34 76 76
GNAQ 0.027 0.006 -9999 0 -10000 0 0
GNAZ 0.027 0.008 -9999 0 -10000 0 0
G12/G13 0.031 0.018 -9999 0 -10000 0 0
GNA14 -0.11 0.27 -9999 0 -0.62 60 60
GNA15 0.02 0.027 -9999 0 -10000 0 0
GNA12 0.022 0.011 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.012 0.1 -9999 0 -0.64 7 7
Rac1/GTP -0.015 0.12 -9999 0 -0.34 25 25
Caspase cascade in apoptosis

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
TOP1 0.01 0.092 -10000 0 -0.44 9 9
ACTA1 -0.007 0.055 -10000 0 -0.49 1 1
NUMA1 0.009 0.095 -10000 0 -0.44 9 9
SPTAN1 -0.008 0.054 0.27 1 -0.48 1 2
LIMK1 0.03 0.094 0.27 2 -0.48 1 3
BIRC3 0.02 0.027 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
BAX 0.027 0.009 -10000 0 -10000 0 0
CASP10 -0.011 0.013 -10000 0 -10000 0 0
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0 -10000 0 -10000 0 0
PTK2 0.004 0.14 -10000 0 -0.62 10 10
DIABLO 0.027 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.008 0.054 0.27 1 -0.48 1 2
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
GSN -0.008 0.054 0.28 1 -0.49 1 2
MADD 0.028 0.004 -10000 0 -10000 0 0
TFAP2A -0.42 0.28 -10000 0 -0.53 223 223
BID 0.005 0.007 -10000 0 -10000 0 0
MAP3K1 0.006 0.052 -10000 0 -0.45 3 3
TRADD 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.014 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.001 0.067 0.28 1 -0.48 1 2
CASP9 0.026 0.008 -10000 0 -10000 0 0
DNA repair 0.001 0.055 0.26 10 -10000 0 10
neuron apoptosis -0.014 0.17 -10000 0 -0.63 18 18
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.078 -10000 0 -0.41 7 7
APAF1 0.027 0.005 -10000 0 -10000 0 0
CASP6 0.006 0.21 -10000 0 -0.96 12 12
TRAF2 0.027 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.007 0.049 -10000 0 -0.47 1 1
CASP7 -0.001 0.038 -10000 0 -0.27 2 2
KRT18 0.022 0.048 -10000 0 -0.48 1 1
apoptosis -0.008 0.1 -10000 0 -0.49 10 10
DFFA -0.006 0.049 -10000 0 -0.48 1 1
DFFB -0.005 0.051 -10000 0 -0.48 1 1
PARP1 -0.001 0.056 -10000 0 -0.26 10 10
actin filament polymerization -0.029 0.086 0.44 1 -0.26 2 3
TNF 0.014 0.071 -10000 0 -0.64 3 3
CYCS 0.014 0.025 0.17 1 -10000 0 1
SATB1 0.008 0.2 0.37 5 -0.9 12 17
SLK -0.008 0.052 -10000 0 -0.47 1 1
p15 BID/BAX 0.01 0.042 -10000 0 -10000 0 0
CASP2 0.037 0.094 0.21 49 -0.33 1 50
JNK cascade -0.006 0.051 0.44 3 -10000 0 3
CASP3 -0.007 0.056 -10000 0 -0.39 2 2
LMNB2 0.043 0.14 0.29 11 -0.52 8 19
RIPK1 0.027 0.006 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.066 0.019 -10000 0 -10000 0 0
negative regulation of DNA binding -0.41 0.27 -10000 0 -0.52 223 223
stress fiber formation -0.008 0.051 -10000 0 -0.46 1 1
GZMB 0.007 0.021 -10000 0 -10000 0 0
CASP1 0.015 0.005 -10000 0 -10000 0 0
LMNB1 0.043 0.14 0.29 11 -0.52 8 19
APP -0.014 0.17 -10000 0 -0.64 18 18
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.001 -10000 0 -10000 0 0
VIM -0.005 0.11 -10000 0 -0.5 11 11
LMNA 0.038 0.16 0.29 11 -0.61 10 21
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.009 0.058 -10000 0 -0.35 1 1
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.002 0.069 0.28 1 -0.48 1 2
APAF-1/Caspase 9 -0.022 0.16 -10000 0 -0.6 21 21
nuclear fragmentation during apoptosis 0.009 0.093 -10000 0 -0.44 9 9
CFL2 0.029 0.087 0.26 2 -0.45 1 3
GAS2 -0.014 0.071 -10000 0 -0.43 5 5
positive regulation of apoptosis 0.045 0.15 0.3 11 -0.57 9 20
PRF1 0.025 0.017 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.039 0.01 -10000 0 -10000 0 0
Necdin/E2F1 -0.02 0.13 -10000 0 -0.42 23 23
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.054 0.096 -10000 0 -0.39 11 11
NGF (dimer)/p75(NTR)/BEX1 -0.001 0.15 -10000 0 -0.4 32 32
NT-4/5 (dimer)/p75(NTR) 0.017 0.078 -10000 0 -0.49 6 6
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.01 0.096 0.35 4 -0.39 10 14
IKBKG 0.028 0.002 -10000 0 -10000 0 0
BDNF 0.013 0.037 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.03 0.087 -10000 0 -0.4 10 10
FURIN 0.028 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.029 0.075 -10000 0 -0.43 6 6
LINGO1 0.016 0.087 -10000 0 -0.64 5 5
Sortilin/TRAF6/NRIF 0.034 0.025 -10000 0 -0.33 1 1
proBDNF (dimer) 0.013 0.037 -10000 0 -10000 0 0
NTRK1 -0.11 0.26 -10000 0 -0.63 56 56
RTN4R 0.024 0.016 -10000 0 -10000 0 0
neuron apoptosis 0.005 0.11 0.32 1 -0.48 5 6
IRAK1 0.028 0.002 -10000 0 -10000 0 0
SHC1 -0.004 0.092 -10000 0 -0.43 12 12
ARHGDIA 0.026 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.005 -10000 0 -10000 0 0
Gamma Secretase 0.075 0.035 -10000 0 -0.36 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.043 0.098 -10000 0 -0.41 11 11
MAGEH1 0.027 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.014 0.16 -10000 0 -0.45 25 25
Mammalian IAPs/DIABLO 0.066 0.019 -10000 0 -10000 0 0
proNGF (dimer) 0.007 0.11 -10000 0 -0.64 8 8
MAGED1 0.028 0.003 -10000 0 -10000 0 0
APP 0.026 0.007 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.001 0.033 -10000 0 -10000 0 0
ZNF274 0.028 0.002 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.018 0.085 -10000 0 -0.39 11 11
NGF 0.007 0.11 -10000 0 -0.64 8 8
cell cycle arrest -0.011 0.094 0.34 2 -0.37 11 13
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.015 0.067 -10000 0 -0.3 11 11
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.032 0.072 -10000 0 -0.42 6 6
NCSTN 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0.028 0.1 -10000 0 -0.41 13 13
PSENEN 0.028 0.002 -10000 0 -10000 0 0
mol:ceramide 0.005 0.094 -10000 0 -0.41 11 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.01 0.062 -10000 0 -0.38 2 2
p75(NTR)/beta APP 0.025 0.075 -10000 0 -0.48 6 6
BEX1 -0.018 0.17 -10000 0 -0.64 19 19
mol:GDP -0.014 0.09 -10000 0 -0.41 13 13
NGF (dimer) -0.22 0.22 -10000 0 -0.41 162 162
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.046 0.082 -10000 0 -0.38 9 9
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
RAC1/GTP 0.018 0.084 -10000 0 -0.37 11 11
MYD88 0.027 0.006 -10000 0 -10000 0 0
CHUK 0.028 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.029 0.1 -10000 0 -0.41 13 13
RHOB 0.027 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.015 0.04 -10000 0 -10000 0 0
NT3 (dimer) -0.047 0.2 -10000 0 -0.64 31 31
TP53 -0.018 0.056 -10000 0 -0.36 6 6
PRDM4 0.003 0.091 -10000 0 -0.41 11 11
BDNF (dimer) -0.22 0.21 -10000 0 -0.4 160 160
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
SORT1 0.027 0.006 -10000 0 -10000 0 0
activation of caspase activity 0.048 0.093 -10000 0 -0.39 11 11
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.043 0.098 -10000 0 -0.41 11 11
RHOC 0.027 0.006 -10000 0 -10000 0 0
XIAP 0.028 0 -10000 0 -10000 0 0
MAPK10 0.018 0.099 0.25 5 -0.42 6 11
DIABLO 0.027 0.005 -10000 0 -10000 0 0
SMPD2 0.005 0.095 -10000 0 -0.41 11 11
APH1B 0.025 0.039 -10000 0 -0.64 1 1
APH1A 0.027 0.005 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.029 0.1 -10000 0 -0.41 13 13
PSEN1 0.026 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.036 0.014 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.028 0.17 -10000 0 -0.46 37 37
MAPK8 0.013 0.1 0.25 4 -0.42 6 10
MAPK9 0.017 0.099 0.25 5 -0.42 6 11
APAF1 0.027 0.005 -10000 0 -10000 0 0
NTF3 -0.048 0.21 -10000 0 -0.64 31 31
NTF4 -0.001 0.033 -10000 0 -10000 0 0
NDN -0.024 0.18 -10000 0 -0.61 23 23
RAC1/GDP 0.016 0.009 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.045 0.09 -10000 0 -0.37 11 11
p75 CTF/Sortilin/TRAF6/NRIF 0.066 0.021 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.028 0.1 -10000 0 -0.41 13 13
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.061 0.07 -10000 0 -0.38 6 6
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.051 0.07 -10000 0 -0.4 6 6
PRKACB 0.026 0.007 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.027 0.033 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.02 0.027 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.023 0.12 0.27 2 -0.45 14 16
BAD 0.016 0.11 0.26 6 -0.43 5 11
RIPK2 0.027 0.004 -10000 0 -10000 0 0
NGFR 0.012 0.095 -10000 0 -0.64 6 6
CYCS 0 0.087 0.36 1 -0.39 11 12
ADAM17 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.043 0.098 -10000 0 -0.41 11 11
BCL2L11 0.017 0.11 0.28 7 -0.43 5 12
BDNF (dimer)/p75(NTR) 0.016 0.081 -10000 0 -0.5 6 6
PI3K 0.044 0.094 -10000 0 -0.42 10 10
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.043 0.098 -10000 0 -0.41 11 11
NDNL2 0.027 0.005 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
PRKCI 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.013 0.11 -10000 0 -0.48 13 13
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.043 0.098 -10000 0 -0.41 11 11
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCZ 0.025 0.008 -10000 0 -10000 0 0
PLG -0.36 0.31 -10000 0 -0.63 162 162
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.002 0.087 -10000 0 -0.41 11 11
SQSTM1 0.025 0.017 -10000 0 -10000 0 0
NGFRAP1 0.028 0 -10000 0 -10000 0 0
CASP3 0.016 0.1 0.26 7 -0.39 5 12
E2F1 -0.002 0.047 -10000 0 -10000 0 0
CASP9 0.026 0.008 -10000 0 -10000 0 0
IKK complex -0.028 0.17 -10000 0 -0.43 13 13
NGF (dimer)/TRKA -0.075 0.21 -10000 0 -0.47 63 63
MMP7 -0.013 0.096 -10000 0 -0.64 5 5
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.053 0.098 -10000 0 -0.39 11 11
MMP3 -0.012 0.026 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.003 0.068 -10000 0 -0.55 1 1
EPHB forward signaling

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
Ephrin A5/EPHB2 0 0.12 -10000 0 -0.41 21 21
cell-cell adhesion 0.022 0.055 0.31 9 -10000 0 9
Ephrin B/EPHB2/RasGAP 0.053 0.08 -10000 0 -0.36 8 8
ITSN1 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.083 0.2 -10000 0 -0.41 77 77
Ephrin B1/EPHB1 0.029 0.048 -10000 0 -0.41 3 3
HRAS/GDP 0.009 0.074 -10000 0 -0.34 5 5
Ephrin B/EPHB1/GRB7 0.051 0.09 -10000 0 -0.36 11 11
Endophilin/SYNJ1 0.006 0.074 -10000 0 -0.34 9 9
KRAS 0.027 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.05 0.091 -10000 0 -0.36 11 11
endothelial cell migration 0.044 0.027 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.026 0.007 -10000 0 -10000 0 0
PAK1 -0.005 0.089 0.35 6 -0.35 8 14
HRAS 0.028 0.003 -10000 0 -10000 0 0
RRAS 0.008 0.078 -10000 0 -0.35 9 9
DNM1 -0.008 0.061 -10000 0 -0.64 1 1
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.004 0.077 0.35 1 -0.35 11 12
lamellipodium assembly -0.022 0.055 -10000 0 -0.31 9 9
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.059 -10000 0 -0.27 3 3
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
EPHB2 0.024 0.015 -10000 0 -10000 0 0
EPHB3 -0.15 0.3 -10000 0 -0.64 77 77
EPHB1 0.017 0.07 -10000 0 -0.64 3 3
EPHB4 0.022 0.012 -10000 0 -10000 0 0
mol:GDP 0.039 0.12 0.35 21 -0.35 7 28
Ephrin B/EPHB2 0.04 0.077 -10000 0 -0.36 9 9
Ephrin B/EPHB3 -0.065 0.2 -10000 0 -0.38 77 77
JNK cascade 0.016 0.069 0.35 8 -0.36 3 11
Ephrin B/EPHB1 0.037 0.086 -10000 0 -0.36 11 11
RAP1/GDP 0.075 0.13 0.34 19 -0.32 6 25
EFNB2 0.027 0.006 -10000 0 -10000 0 0
EFNB3 -0.003 0.12 -10000 0 -0.61 10 10
EFNB1 0.028 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.039 0.049 -10000 0 -0.38 3 3
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.021 0.081 -10000 0 -0.36 7 7
Rap1/GTP 0.007 0.066 -10000 0 -10000 0 0
axon guidance 0 0.12 -10000 0 -0.41 21 21
MAPK3 0.004 0.054 -10000 0 -10000 0 0
MAPK1 0.004 0.055 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.097 0.32 3 -0.33 6 9
actin cytoskeleton reorganization -0.007 0.05 -10000 0 -10000 0 0
CDC42/GDP 0.073 0.13 0.35 21 -0.33 6 27
PI3K 0.049 0.03 -10000 0 -10000 0 0
EFNA5 -0.022 0.17 -10000 0 -0.64 21 21
Ephrin B2/EPHB4 0.028 0.017 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.007 0.062 -10000 0 -0.29 10 10
CDC42 0.026 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.066 -10000 0 -10000 0 0
PTK2 -0.002 0.045 0.52 2 -10000 0 2
MAP4K4 0.016 0.07 0.36 8 -0.36 3 11
SRC 0.026 0.009 -10000 0 -10000 0 0
KALRN 0.027 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.03 0.019 -10000 0 -10000 0 0
neuron projection morphogenesis 0.059 0.15 0.36 48 -10000 0 48
MAP2K1 0.008 0.057 -10000 0 -10000 0 0
WASL 0.022 0.012 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.057 0.052 -10000 0 -0.38 3 3
cell migration 0.036 0.12 0.42 12 -10000 0 12
NRAS 0.027 0.006 -10000 0 -10000 0 0
SYNJ1 0.006 0.075 -10000 0 -0.34 9 9
PXN 0.027 0.005 -10000 0 -10000 0 0
TF -0.018 0.074 -10000 0 -0.33 11 11
HRAS/GTP 0.031 0.076 -10000 0 -0.33 10 10
Ephrin B1/EPHB1-2 0.039 0.05 -10000 0 -0.38 3 3
cell adhesion mediated by integrin 0.051 0.1 0.4 9 -10000 0 9
RAC1 0.022 0.012 -10000 0 -10000 0 0
mol:GTP 0.033 0.079 -10000 0 -0.34 10 10
RAC1-CDC42/GTP -0.076 0.14 -10000 0 -0.48 8 8
RASA1 0.027 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.032 0.096 0.32 3 -0.32 5 8
ruffle organization 0.04 0.15 0.33 50 -10000 0 50
NCK1 0.027 0.006 -10000 0 -10000 0 0
receptor internalization -0.02 0.073 -10000 0 -0.33 10 10
Ephrin B/EPHB2/KALRN 0.053 0.08 -10000 0 -0.36 8 8
ROCK1 -0.086 0.18 -10000 0 -0.38 76 76
RAS family/GDP -0.01 0.05 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.064 -10000 0 -0.33 9 9
Ephrin B/EPHB1/Src/Paxillin 0.012 0.063 -10000 0 -0.28 11 11
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.007 0.023 -10000 0 -10000 0 0
NFATC2 -0.021 0.11 -10000 0 -0.41 20 20
NFATC3 0.009 0.021 -10000 0 -10000 0 0
CD40LG -0.057 0.18 0.35 3 -0.51 16 19
PTGS2 -0.11 0.26 0.35 3 -0.63 49 52
JUNB 0.028 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.019 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.019 -10000 0 -10000 0 0
CALM1 0.022 0.017 -10000 0 -10000 0 0
JUN 0.022 0.017 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.006 -10000 0 -10000 0 0
FOSL1 0.022 0.057 -10000 0 -0.64 2 2
CREM 0.027 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.003 0.12 -10000 0 -0.42 6 6
FOS -0.069 0.23 -10000 0 -0.6 43 43
IFNG -0.057 0.17 0.35 3 -0.52 16 19
AP-1/NFAT1-c-4 -0.045 0.21 -10000 0 -0.59 16 16
FASLG -0.061 0.18 0.35 3 -0.51 16 19
NFAT1-c-4/ICER1 -0.006 0.1 -10000 0 -0.35 19 19
IL2RA -0.06 0.17 0.35 3 -0.51 15 18
FKBP12/FK506 0.02 0.004 -10000 0 -10000 0 0
CSF2 -0.059 0.18 0.35 3 -0.52 15 18
JunB/Fra1/NFAT1-c-4 0.004 0.11 -10000 0 -0.34 21 21
IL4 -0.06 0.17 0.35 3 -0.51 16 19
IL2 -0.023 0.18 -10000 0 -0.86 12 12
IL3 -0.008 0.13 -10000 0 -0.66 11 11
FKBP1A 0.027 0.006 -10000 0 -10000 0 0
BATF3 0.026 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.027 0.006 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.009 0.053 -10000 0 -10000 0 0
adherens junction organization -0.004 0.098 0.26 4 -0.29 22 26
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.015 0.056 -10000 0 -10000 0 0
FMN1 -0.023 0.12 -10000 0 -0.32 34 34
mol:IP3 0.008 0.052 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0.088 -10000 0 -0.28 22 22
CTNNB1 0.027 0.008 -10000 0 -10000 0 0
AKT1 0.014 0.067 0.28 2 -10000 0 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.029 0.14 -10000 0 -0.48 22 22
CTNND1 0.03 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.082 -10000 0 -10000 0 0
VASP -0.003 0.084 -10000 0 -0.28 1 1
ZYX -0.006 0.08 -10000 0 -0.27 20 20
JUB -0.002 0.084 -10000 0 -0.27 22 22
EGFR(dimer) 0.009 0.088 -10000 0 -0.27 20 20
E-cadherin/beta catenin-gamma catenin 0.014 0.12 -10000 0 -0.4 21 21
mol:PI-3-4-5-P3 0.03 0.075 0.25 1 -10000 0 1
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
PI3K 0.031 0.076 0.26 1 -10000 0 1
FYN -0.19 0.14 -10000 0 -0.39 23 23
mol:Ca2+ 0.008 0.052 -10000 0 -10000 0 0
JUP 0.027 0.008 -10000 0 -10000 0 0
PIK3R1 0.029 0.007 -10000 0 -10000 0 0
mol:DAG 0.008 0.052 -10000 0 -10000 0 0
CDH1 -0.025 0.18 -10000 0 -0.64 22 22
RhoA/GDP 0.043 0.078 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium -0.003 0.083 -10000 0 -0.27 1 1
SRC 0.026 0.009 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
EGFR 0.022 0.012 -10000 0 -10000 0 0
CASR -0.22 0.16 -10000 0 -0.33 179 179
RhoA/GTP 0.021 0.053 -10000 0 -10000 0 0
AKT2 0.015 0.069 0.28 2 -10000 0 2
actin cable formation -0.023 0.12 -10000 0 -0.36 16 16
apoptosis -0.026 0.096 -10000 0 -0.36 12 12
CTNNA1 0.029 0.008 -10000 0 -10000 0 0
mol:GDP 0.002 0.049 -10000 0 -10000 0 0
PIP5K1A -0.003 0.084 -10000 0 -10000 0 0
PLCG1 0.008 0.053 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.085 -10000 0 -10000 0 0
homophilic cell adhesion 0.001 0.007 -10000 0 -10000 0 0
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.1 0.1 -10000 0 -0.48 2 2
epithelial cell differentiation -0.15 0.17 -10000 0 -0.37 85 85
ITCH 0.055 0.023 -10000 0 -10000 0 0
WWP1 -0.086 0.078 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.022 0.012 -10000 0 -10000 0 0
PRL -0.011 0.016 -10000 0 -10000 0 0
neuron projection morphogenesis -0.054 0.083 0.33 1 -0.4 2 3
PTPRZ1 -0.006 0.078 -10000 0 -0.64 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.057 0.089 -10000 0 -0.43 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.081 0.081 -10000 0 -0.42 4 4
ADAM17 0.056 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.11 0.1 -10000 0 -0.3 6 6
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.1 0.1 -10000 0 -0.47 4 4
NCOR1 0.026 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.072 0.083 -10000 0 -0.4 4 4
GRIN2B -0.076 0.074 -10000 0 -0.39 4 4
ErbB4/ErbB2/betacellulin -0.075 0.1 -10000 0 -0.45 9 9
STAT1 0.026 0.014 -10000 0 -10000 0 0
HBEGF 0.023 0.055 -10000 0 -0.64 2 2
PRLR -0.22 0.32 -10000 0 -0.64 109 109
E4ICDs/ETO2 -0.094 0.095 -10000 0 -10000 0 0
axon guidance -0.056 0.062 -10000 0 -10000 0 0
NEDD4 0.056 0.022 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.16 0.25 -10000 0 -0.48 109 109
CBFA2T3 0.025 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF -0.064 0.081 -10000 0 -0.52 1 1
MAPK3 -0.061 0.075 -10000 0 -0.41 2 2
STAT1 (dimer) -0.098 0.095 -10000 0 -10000 0 0
MAPK1 -0.06 0.075 -10000 0 -0.41 2 2
JAK2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.069 0.084 -10000 0 -0.4 4 4
NRG1 0.022 0.063 -10000 0 -0.43 5 5
NRG3 0.015 0.071 -10000 0 -0.64 3 3
NRG2 0.021 0.06 -10000 0 -0.54 3 3
NRG4 0.022 0.026 -10000 0 -0.33 1 1
heart development -0.056 0.062 -10000 0 -10000 0 0
neural crest cell migration -0.068 0.083 -10000 0 -0.4 4 4
ERBB2 0.029 0.015 -10000 0 -10000 0 0
WWOX/E4ICDs -0.094 0.095 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.066 0.095 -10000 0 -0.4 1 1
apoptosis 0.086 0.094 0.42 6 -10000 0 6
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.1 0.098 -10000 0 -0.38 3 3
ErbB4/ErbB2/epiregulin -0.076 0.079 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin -0.11 0.12 -10000 0 -0.51 11 11
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.21 0.2 -10000 0 -0.44 109 109
MDM2 -0.098 0.094 0.25 4 -10000 0 4
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.052 0.072 -10000 0 -0.4 4 4
STAT5A -0.049 0.064 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.055 0.084 -10000 0 -0.4 4 4
DLG4 0.026 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.013 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.088 0.086 -10000 0 -10000 0 0
STAT5A (dimer) -0.16 0.18 -10000 0 -0.4 84 84
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.048 0.065 -10000 0 -10000 0 0
LRIG1 0.026 0.009 -10000 0 -10000 0 0
EREG -0.026 0.051 -10000 0 -10000 0 0
BTC 0 0.13 -10000 0 -0.61 12 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.056 0.062 -10000 0 -10000 0 0
ERBB4 -0.11 0.1 -10000 0 -0.31 6 6
STAT5B 0.026 0.007 -10000 0 -10000 0 0
YAP1 -0.03 0.09 -10000 0 -0.53 8 8
GRB2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.065 0.077 -10000 0 -0.33 1 1
glial cell differentiation 0.087 0.085 -10000 0 -10000 0 0
WWOX 0.025 0.008 -10000 0 -10000 0 0
cell proliferation -0.06 0.11 0.69 1 -0.41 11 12
Osteopontin-mediated events

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
IKK alpha homodimer 0.014 0.09 -10000 0 -0.34 15 15
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.12 0.36 16 -0.37 2 18
alphaV/beta3 Integrin/Osteopontin/Src 0.036 0.051 -10000 0 -0.39 3 3
AP1 -0.002 0.17 -10000 0 -0.53 11 11
ILK 0.011 0.097 -10000 0 -0.36 15 15
bone resorption 0.016 0.11 0.33 3 -0.36 16 19
PTK2B 0.027 0.006 -10000 0 -10000 0 0
PYK2/p130Cas 0.048 0.1 -10000 0 -0.34 15 15
ITGAV 0.029 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.025 0.071 -10000 0 -0.48 5 5
alphaV/beta3 Integrin/Osteopontin 0.032 0.11 -10000 0 -0.4 15 15
MAP3K1 0.009 0.098 -10000 0 -0.37 15 15
JUN 0.027 0.007 -10000 0 -10000 0 0
MAPK3 -0.008 0.085 -10000 0 -0.34 15 15
MAPK1 -0.009 0.084 -10000 0 -0.34 15 15
Rac1/GDP 0.016 0.009 -10000 0 -10000 0 0
NFKB1 0.027 0.006 -10000 0 -10000 0 0
MAPK8 0.001 0.11 0.38 2 -0.39 15 17
ITGB3 -0.005 0.14 -10000 0 -0.63 13 13
NFKBIA -0.011 0.086 -10000 0 -0.34 15 15
FOS -0.065 0.22 -10000 0 -0.59 43 43
CD44 0.021 0.026 -10000 0 -10000 0 0
CHUK 0.028 0.004 -10000 0 -10000 0 0
PLAU -0.002 0.21 0.49 5 -1.1 7 12
NF kappa B1 p50/RelA 0.038 0.1 -10000 0 -10000 0 0
BCAR1 0.026 0.008 -10000 0 -10000 0 0
RELA 0.028 0.002 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.017 0.11 -10000 0 -0.47 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.009 0.098 -10000 0 -0.37 15 15
VAV3 0.003 0.1 0.38 2 -0.34 16 18
MAP3K14 0 0.091 -10000 0 -0.37 15 15
ROCK2 0.016 0.087 -10000 0 -0.64 5 5
SPP1 0.019 0.063 -10000 0 -0.53 3 3
RAC1 0.022 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.007 0.08 0.34 1 -0.32 11 12
MMP2 -0.026 0.12 0.31 1 -0.44 10 11
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.031 0.019 -10000 0 -10000 0 0
VLDLR 0.026 0.007 -10000 0 -10000 0 0
CRKL 0.026 0.007 -10000 0 -10000 0 0
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
ITGA3 0.021 0.024 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.004 0.1 -10000 0 -0.41 15 15
MAPK8IP1/MKK7/MAP3K11/JNK1 0.071 0.058 -10000 0 -0.36 4 4
AKT1 -0.012 0.066 -10000 0 -0.29 15 15
MAP2K7 0.028 0.002 -10000 0 -10000 0 0
RAPGEF1 0.027 0.006 -10000 0 -10000 0 0
DAB1 -0.002 0.025 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.008 0.094 -10000 0 -0.37 15 15
LRPAP1/LRP8 0.037 0.015 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.007 0.093 -10000 0 -0.37 14 14
DAB1/alpha3/beta1 Integrin 0.017 0.088 -10000 0 -0.35 14 14
long-term memory -0.054 0.17 -10000 0 -0.38 52 52
DAB1/LIS1 0.027 0.093 -10000 0 -0.35 14 14
DAB1/CRLK/C3G 0.018 0.087 -10000 0 -0.34 14 14
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
DAB1/NCK2 0.029 0.095 -10000 0 -0.36 14 14
ARHGEF2 0.027 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.12 0.27 -10000 0 -0.64 61 61
CDK5R1 0.026 0.009 -10000 0 -10000 0 0
RELN -0.036 0.15 -10000 0 -0.64 15 15
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.005 0.1 -10000 0 -0.4 15 15
GRIN2A/RELN/LRP8/DAB1/Fyn -0.05 0.18 -10000 0 -0.39 53 53
MAPK8 0.017 0.081 -10000 0 -0.58 5 5
RELN/VLDLR/DAB1 -0.009 0.095 -10000 0 -0.38 15 15
ITGB1 0.027 0.005 -10000 0 -10000 0 0
MAP1B 0.01 0.11 -10000 0 -0.37 14 14
RELN/LRP8 -0.005 0.1 -10000 0 -0.4 15 15
GRIN2B/RELN/LRP8/DAB1/Fyn 0.024 0.097 -10000 0 -0.37 14 14
PI3K 0.04 0.009 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.033 0.023 -10000 0 -10000 0 0
RAP1A 0.006 0.11 0.33 1 -0.33 13 14
PAFAH1B1 0.026 0.008 -10000 0 -10000 0 0
MAPK8IP1 0.028 0.004 -10000 0 -10000 0 0
CRLK/C3G 0.037 0.013 -10000 0 -10000 0 0
GRIN2B 0.004 0.025 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
neuron differentiation 0.014 0.083 -10000 0 -0.36 6 6
neuron adhesion 0.014 0.12 0.32 12 -0.34 1 13
LRP8 0.025 0.014 -10000 0 -10000 0 0
GSK3B -0.015 0.063 -10000 0 -0.28 14 14
RELN/VLDLR/DAB1/Fyn 0.005 0.094 -10000 0 -0.36 15 15
MAP3K11 0.028 0.002 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.007 0.072 -10000 0 -0.3 15 15
CDK5 0.022 0.011 -10000 0 -10000 0 0
MAPT 0.016 0.2 0.69 16 -0.58 10 26
neuron migration 0.015 0.12 0.36 2 -0.37 14 16
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.014 0.083 -10000 0 -0.36 6 6
RELN/VLDLR 0.022 0.098 -10000 0 -0.38 14 14
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.028 0.01 -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 0.002 0.11 0.36 1 -10000 0 1
IL27/IL27R/JAK1 0.11 0.21 -10000 0 -10000 0 0
TBX21 0.061 0.15 0.47 3 -10000 0 3
IL12B 0.015 0.02 -10000 0 -10000 0 0
IL12A 0.005 0.006 -10000 0 -10000 0 0
IL6ST -0.069 0.24 -10000 0 -0.64 44 44
IL27RA/JAK1 0.04 0.032 -10000 0 -10000 0 0
IL27 0.021 0.025 -10000 0 -10000 0 0
TYK2 0.03 0.004 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.001 0.11 -10000 0 -0.48 2 2
T-helper 2 cell differentiation 0.002 0.11 0.36 1 -10000 0 1
T cell proliferation during immune response 0.002 0.11 0.36 1 -10000 0 1
MAPKKK cascade -0.002 0.11 -10000 0 -0.36 1 1
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT2 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.031 0.015 -10000 0 -10000 0 0
IL12RB1 0.021 0.026 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.05 0.16 0.36 4 -0.46 3 7
IL27/IL27R/JAK2/TYK2 -0.002 0.11 -10000 0 -0.37 1 1
positive regulation of T cell mediated cytotoxicity -0.002 0.11 -10000 0 -0.36 1 1
STAT1 (dimer) 0.25 0.3 0.49 162 -10000 0 162
JAK2 0.028 0.007 -10000 0 -10000 0 0
JAK1 0.031 0.009 -10000 0 -10000 0 0
STAT2 (dimer) 0.013 0.12 -10000 0 -10000 0 0
T cell proliferation -0.028 0.13 -10000 0 -0.5 7 7
IL12/IL12R/TYK2/JAK2 0.035 0.085 -10000 0 -0.7 3 3
IL17A -0.012 0.1 -10000 0 -0.48 2 2
mast cell activation 0.002 0.11 0.36 1 -10000 0 1
IFNG 0.008 0.023 -10000 0 -10000 0 0
T cell differentiation 0.001 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.014 0.11 -10000 0 -10000 0 0
STAT5A (dimer) 0.014 0.11 -10000 0 -10000 0 0
STAT4 (dimer) 0.012 0.12 -10000 0 -10000 0 0
STAT4 0.019 0.029 -10000 0 -10000 0 0
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.008 0.15 -10000 0 -10000 0 0
GATA3 -1 0.56 0.69 1 -1.3 222 223
IL18 0.006 0.008 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production 0.014 0.11 -10000 0 -10000 0 0
IL27/EBI3 0.033 0.051 -10000 0 -0.48 1 1
IL27RA 0.016 0.021 -10000 0 -10000 0 0
IL6 -0.03 0.17 -10000 0 -0.64 20 20
STAT5A 0.026 0.007 -10000 0 -10000 0 0
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.019 0.016 -10000 0 -10000 0 0
IL1B -0.001 0.064 -10000 0 -0.48 5 5
EBI3 0.018 0.055 -10000 0 -0.63 1 1
TNF -0.001 0.051 -10000 0 -0.48 3 3
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.011 0.16 0.5 1 -10000 0 1
CRP -0.018 0.16 0.56 1 -10000 0 1
cell cycle arrest -0.022 0.16 -10000 0 -0.54 4 4
TIMP1 -0.013 0.15 -10000 0 -10000 0 0
IL6ST -0.073 0.24 -10000 0 -0.64 44 44
Rac1/GDP -0.048 0.14 -10000 0 -0.5 10 10
AP1 -0.029 0.16 -10000 0 -0.57 6 6
GAB2 0.028 0.004 -10000 0 -10000 0 0
TNFSF11 -0.019 0.15 -10000 0 -10000 0 0
HSP90B1 0.031 0.04 -10000 0 -10000 0 0
GAB1 0.027 0.006 -10000 0 -10000 0 0
MAPK14 -0.033 0.14 -10000 0 -0.55 8 8
AKT1 0.031 0.029 -10000 0 -10000 0 0
FOXO1 0.033 0.033 -10000 0 -10000 0 0
MAP2K6 -0.046 0.14 -10000 0 -0.46 13 13
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.043 0.13 0.34 1 -0.5 8 9
MITF -0.053 0.14 -10000 0 -0.41 24 24
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.028 0.002 -10000 0 -10000 0 0
A2M 0.009 0.15 -10000 0 -1.2 4 4
CEBPB 0.018 0.027 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.002 0.092 -10000 0 -0.43 5 5
STAT3 -0.027 0.16 -10000 0 -0.58 4 4
STAT1 0.01 0.04 -10000 0 -0.58 1 1
CEBPD -0.015 0.15 0.5 1 -10000 0 1
PIK3CA 0.028 0.005 -10000 0 -10000 0 0
PI3K 0.041 0.01 -10000 0 -10000 0 0
JUN 0.026 0.007 -10000 0 -10000 0 0
PIAS3/MITF -0.03 0.15 -10000 0 -0.51 11 11
MAPK11 -0.032 0.14 -10000 0 -0.55 8 8
STAT3 (dimer)/FOXO1 -0.027 0.14 -10000 0 -10000 0 0
GRB2/SOS1/GAB family -0.007 0.15 -10000 0 -0.52 8 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.047 0.15 -10000 0 -0.37 35 35
GRB2 0.026 0.008 -10000 0 -10000 0 0
JAK2 0.026 0.007 -10000 0 -10000 0 0
LBP -0.22 0.44 -10000 0 -0.9 81 81
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
JAK1 0.027 0.009 -10000 0 -10000 0 0
MYC -0.015 0.15 0.5 1 -10000 0 1
FGG -0.021 0.15 -10000 0 -10000 0 0
macrophage differentiation -0.022 0.16 -10000 0 -0.54 4 4
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.027 0.18 -10000 0 -0.38 49 49
JUNB -0.016 0.15 -10000 0 -10000 0 0
FOS -0.066 0.22 -10000 0 -0.59 43 43
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.051 0.15 -10000 0 -0.39 29 29
STAT1/PIAS1 -0.029 0.15 -10000 0 -0.42 16 16
GRB2/SOS1/GAB family/SHP2/PI3K 0.033 0.03 -10000 0 -10000 0 0
STAT3 (dimer) -0.024 0.16 -10000 0 -0.56 4 4
PRKCD -0.008 0.16 0.33 2 -0.51 4 6
IL6R 0.026 0.04 -10000 0 -0.64 1 1
SOCS3 -0.024 0.15 -10000 0 -0.64 7 7
gp130 (dimer)/JAK1/JAK1/LMO4 -0.017 0.17 -10000 0 -0.41 44 44
Rac1/GTP -0.047 0.14 -10000 0 -0.52 9 9
HCK 0.013 0.05 -10000 0 -0.64 1 1
MAPKKK cascade 0.014 0.096 -10000 0 -0.53 4 4
bone resorption -0.017 0.15 -10000 0 -10000 0 0
IRF1 -0.015 0.16 0.56 1 -10000 0 1
mol:GDP -0.06 0.14 -10000 0 -0.42 22 22
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.061 0.14 -10000 0 -0.42 22 22
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.046 0.16 -10000 0 -0.54 14 14
PTPN11 0.013 0.02 -10000 0 -10000 0 0
IL6/IL6RA -0.007 0.13 -10000 0 -0.46 21 21
gp130 (dimer)/TYK2/TYK2/LMO4 -0.017 0.17 -10000 0 -0.41 44 44
gp130 (dimer)/JAK2/JAK2/LMO4 -0.019 0.17 -10000 0 -0.41 44 44
IL6 -0.028 0.17 -10000 0 -0.64 20 20
PIAS3 0.027 0.006 -10000 0 -10000 0 0
PTPRE 0.024 0.01 -10000 0 -10000 0 0
PIAS1 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.051 0.14 -10000 0 -0.33 51 51
LMO4 0.027 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.023 0.17 -10000 0 -0.6 4 4
MCL1 0.035 0.033 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.021 0.15 -10000 0 -0.51 22 22
KLHL20 0.018 0.085 0.2 2 -0.29 2 4
CYFIP2 0.025 0.039 -10000 0 -0.64 1 1
Rac1/GDP -0.003 0.11 0.32 5 -0.32 19 24
ENAH -0.023 0.15 -10000 0 -0.51 22 22
AP1M1 0.028 0.002 -10000 0 -10000 0 0
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.005 0.078 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.016 0.041 -10000 0 -0.19 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.027 0.12 -10000 0 -0.38 21 21
RAPGEF1 -0.018 0.13 -10000 0 -0.45 21 21
CTNND1 0.028 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.017 0.15 -10000 0 -0.53 22 22
CRK -0.024 0.14 -10000 0 -0.48 21 21
E-cadherin/gamma catenin/alpha catenin 0.014 0.12 -10000 0 -0.41 22 22
alphaE/beta7 Integrin 0.038 0.012 -10000 0 -10000 0 0
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
NCKAP1 0.028 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.018 -10000 0 -10000 0 0
DLG1 -0.023 0.15 -10000 0 -0.51 22 22
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.008 0.054 -10000 0 -0.21 1 1
MLLT4 0.027 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.044 0.022 -10000 0 -10000 0 0
PI3K -0.007 0.07 -10000 0 -10000 0 0
ARF6 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.002 0.14 -10000 0 -0.47 22 22
TIAM1 0.026 0.007 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.026 0.11 -10000 0 -0.36 22 22
AKT1 0 0.046 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
CDH1 -0.025 0.18 -10000 0 -0.64 22 22
RhoA/GDP 0.011 0.12 0.34 8 -0.32 21 29
actin cytoskeleton organization 0.022 0.072 0.18 10 -0.21 2 12
CDC42/GDP 0.02 0.14 0.41 13 -0.32 21 34
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.004 0.081 -10000 0 -0.28 22 22
ITGB7 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.029 0.12 -10000 0 -0.38 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin 0.013 0.11 -10000 0 -0.36 22 22
mol:GDP 0.003 0.15 0.41 14 -0.38 21 35
CDC42/GTP/IQGAP1 0.035 0.011 -10000 0 -10000 0 0
JUP 0.026 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.011 0.12 0.28 5 -0.33 21 26
RAC1/GTP/IQGAP1 0.029 0.016 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.041 0.004 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
CDC42 0.026 0.008 -10000 0 -10000 0 0
CTNNA1 0.027 0.005 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.028 0.073 0.25 14 -0.27 1 15
NME1 0.025 0.012 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.023 0.15 -10000 0 -0.51 22 22
regulation of cell-cell adhesion 0 0.066 -10000 0 -10000 0 0
WASF2 0.012 0.033 -10000 0 -10000 0 0
Rap1/GTP 0.009 0.091 -10000 0 -0.3 4 4
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.037 0.12 -10000 0 -0.36 21 21
CCND1 0.027 0.071 0.24 10 -0.34 1 11
VAV2 -0.032 0.19 -10000 0 -0.5 35 35
RAP1/GDP 0.016 0.1 0.3 5 -0.32 6 11
adherens junction assembly -0.022 0.14 -10000 0 -0.5 22 22
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.028 0.003 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.024 0.11 -10000 0 -0.35 21 21
E-cadherin/beta catenin -0.021 0.11 -10000 0 -0.42 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.023 0.15 -10000 0 -0.51 22 22
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.022 0.1 -10000 0 -0.4 5 5
E-cadherin/beta catenin/alpha catenin 0.014 0.12 -10000 0 -0.42 22 22
ITGAE 0.026 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.018 0.16 -10000 0 -0.54 22 22
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.019 0.3 -10000 0 -0.95 16 16
IL23A -0.026 0.3 -10000 0 -0.97 14 14
NF kappa B1 p50/RelA/I kappa B alpha 0.005 0.29 -10000 0 -0.92 15 15
positive regulation of T cell mediated cytotoxicity -0.023 0.31 -10000 0 -0.95 18 18
ITGA3 -0.012 0.28 -10000 0 -0.88 14 14
IL17F 0.001 0.22 0.49 3 -0.62 12 15
IL12B 0.022 0.04 -10000 0 -10000 0 0
STAT1 (dimer) -0.019 0.3 -10000 0 -0.94 17 17
CD4 -0.014 0.28 -10000 0 -0.89 14 14
IL23 -0.015 0.3 -10000 0 -0.95 14 14
IL23R -0.01 0.18 -10000 0 -0.75 11 11
IL1B -0.031 0.32 -10000 0 -1 17 17
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.021 0.28 -10000 0 -0.89 15 15
TYK2 0.024 0.031 -10000 0 -10000 0 0
STAT4 0.019 0.029 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
IL18RAP 0.014 0.036 -10000 0 -10000 0 0
IL12RB1 0.017 0.04 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.029 0.045 -10000 0 -10000 0 0
IL23R/JAK2 0.01 0.17 -10000 0 -0.73 7 7
positive regulation of chronic inflammatory response -0.023 0.31 -10000 0 -0.95 18 18
natural killer cell activation -0.001 0.006 -10000 0 -10000 0 0
JAK2 0.026 0.038 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
NFKB1 0.028 0.007 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.012 0.28 -10000 0 -0.91 14 14
ALOX12B -0.013 0.28 -10000 0 -0.87 13 13
CXCL1 -0.05 0.33 -10000 0 -1 23 23
T cell proliferation -0.023 0.31 -10000 0 -0.95 18 18
NFKBIA 0.027 0.007 -10000 0 -10000 0 0
IL17A 0.014 0.18 0.37 1 -0.49 9 10
PI3K -0.008 0.29 -10000 0 -0.91 15 15
IFNG 0.001 0.028 0.12 1 -0.11 7 8
STAT3 (dimer) -0.001 0.28 -10000 0 -0.86 14 14
IL18R1 0.026 0.039 -10000 0 -0.64 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 0.006 0.19 -10000 0 -0.63 3 3
IL18/IL18R 0.04 0.045 -10000 0 -0.42 1 1
macrophage activation -0.002 0.015 -10000 0 -0.044 4 4
TNF -0.029 0.3 -10000 0 -0.98 17 17
STAT3/STAT4 -0.013 0.28 -10000 0 -0.89 15 15
STAT4 (dimer) -0.021 0.3 -10000 0 -0.94 17 17
IL18 0.025 0.015 -10000 0 -10000 0 0
IL19 -0.024 0.28 -10000 0 -0.89 15 15
STAT5A (dimer) -0.022 0.29 -10000 0 -0.91 16 16
STAT1 0.026 0.014 -10000 0 -10000 0 0
SOCS3 0.023 0.041 -10000 0 -0.64 1 1
CXCL9 -0.024 0.28 -10000 0 -0.9 16 16
MPO -0.011 0.28 -10000 0 -0.87 13 13
positive regulation of humoral immune response -0.023 0.31 -10000 0 -0.95 18 18
IL23/IL23R/JAK2/TYK2 -0.025 0.31 -10000 0 -1 17 17
IL6 -0.048 0.42 -10000 0 -1.1 32 32
STAT5A 0.026 0.007 -10000 0 -10000 0 0
IL2 0.004 0.024 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.006 -10000 0 -10000 0 0
CD3E -0.025 0.29 -10000 0 -0.93 15 15
keratinocyte proliferation -0.023 0.31 -10000 0 -0.95 18 18
NOS2 -0.061 0.39 -10000 0 -1 31 31
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.022 0.018 -10000 0 -10000 0 0
HSPA8 0.025 0.039 -10000 0 -0.62 1 1
SMAD3/SMAD4/ER alpha 0.026 0.11 -10000 0 -0.43 13 13
AKT1 0.028 0.008 -10000 0 -10000 0 0
GSC -0.002 0.087 -10000 0 -10000 0 0
NKX2-5 0.001 0 -10000 0 -10000 0 0
muscle cell differentiation -0.036 0.071 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.089 0.041 -10000 0 -10000 0 0
SMAD4 0.029 0.027 -10000 0 -10000 0 0
CBFB 0.026 0.007 -10000 0 -10000 0 0
SAP18 0.027 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.043 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.067 0.062 -10000 0 -0.34 2 2
MYC 0.024 0.015 -10000 0 -10000 0 0
CDKN2B -0.003 0.12 -10000 0 -0.5 10 10
AP1 0.003 0.12 -10000 0 -0.33 16 16
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.015 0.11 -10000 0 -0.47 8 8
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.017 0.046 -10000 0 -10000 0 0
SP3 0.029 0.004 -10000 0 -10000 0 0
CREB1 0.027 0.004 -10000 0 -10000 0 0
FOXH1 0.023 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.056 0.042 -10000 0 -10000 0 0
GATA3 -0.48 0.28 -10000 0 -0.63 222 222
SKI/SIN3/HDAC complex/NCoR1 0.023 0.074 -10000 0 -0.43 6 6
MEF2C/TIF2 0.008 0.11 -10000 0 -0.35 25 25
endothelial cell migration 0.042 0.28 1.3 13 -10000 0 13
MAX 0.028 0.013 -10000 0 -10000 0 0
RBBP7 0.028 0.003 -10000 0 -10000 0 0
RBBP4 0.026 0.008 -10000 0 -10000 0 0
RUNX2 0.024 0.018 -10000 0 -10000 0 0
RUNX3 0.013 0.035 -10000 0 -10000 0 0
RUNX1 0.018 0.028 -10000 0 -10000 0 0
CTBP1 0.027 0.005 -10000 0 -10000 0 0
NR3C1 0.029 0.012 -10000 0 -10000 0 0
VDR 0.018 0.078 -10000 0 -0.64 4 4
CDKN1A 0.023 0.08 -10000 0 -10000 0 0
KAT2B 0.025 0.012 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.063 0.026 -10000 0 -10000 0 0
DCP1A 0.026 0.007 -10000 0 -10000 0 0
SKI 0.025 0.009 -10000 0 -10000 0 0
SERPINE1 -0.043 0.28 -10000 0 -1.3 13 13
SMAD3/SMAD4/ATF2 0.054 0.04 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.034 0.1 -10000 0 -0.44 11 11
SAP30 0.026 0.011 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.043 0.03 -10000 0 -10000 0 0
JUN -0.008 0.11 -10000 0 -0.33 1 1
SMAD3/SMAD4/IRF7 0.055 0.041 -10000 0 -10000 0 0
TFE3 0.028 0.022 -10000 0 -10000 0 0
COL1A2 0.027 0.042 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.052 0.039 -10000 0 -10000 0 0
DLX1 0.012 0.032 -10000 0 -10000 0 0
TCF3 0.028 0.003 -10000 0 -10000 0 0
FOS -0.052 0.22 -10000 0 -0.64 36 36
SMAD3/SMAD4/Max 0.055 0.044 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.043 0.027 -10000 0 -10000 0 0
ZBTB17 0.024 0.008 -10000 0 -10000 0 0
LAMC1 0.024 0.029 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.055 0.038 -10000 0 -10000 0 0
IRF7 0.028 0.007 -10000 0 -10000 0 0
ESR1 -0.009 0.14 -10000 0 -0.57 17 17
HNF4A -0.046 0.21 -10000 0 -0.64 31 31
MEF2C 0.026 0.033 0.3 2 -10000 0 2
SMAD2-3/SMAD4 0.06 0.042 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.043 0.027 -10000 0 -10000 0 0
IGHV3OR16-13 0.007 0.048 -10000 0 -0.35 5 5
TGIF2/HDAC complex 0.027 0.006 -10000 0 -10000 0 0
CREBBP 0.024 0.013 -10000 0 -10000 0 0
SKIL 0.027 0.005 -10000 0 -10000 0 0
HDAC1 0.026 0.008 -10000 0 -10000 0 0
HDAC2 0.027 0.006 -10000 0 -10000 0 0
SNIP1 0.026 0.008 -10000 0 -10000 0 0
GCN5L2 -0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.059 0.047 -10000 0 -10000 0 0
MSG1/HSC70 0.038 0.032 -10000 0 -0.47 1 1
SMAD2 0.03 0.009 -10000 0 -10000 0 0
SMAD3 0.028 0.028 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.031 0.026 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.001 0.069 0.29 2 -0.41 4 6
NCOR1 0.026 0.008 -10000 0 -10000 0 0
NCOA2 -0.033 0.19 -10000 0 -0.64 26 26
NCOA1 0.027 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.032 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.095 0.049 -10000 0 -10000 0 0
IFNB1 0.016 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.058 0.038 -10000 0 -10000 0 0
CITED1 0.025 0.015 -10000 0 -10000 0 0
SMAD2-3/SMAD4/ARC105 0.071 0.045 -10000 0 -10000 0 0
RBL1 0.027 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.025 0.05 -10000 0 -0.32 1 1
RUNX1-3/PEBPB2 0.027 0.041 -10000 0 -10000 0 0
SMAD7 0.021 0.11 -10000 0 -10000 0 0
MYC/MIZ-1 0.033 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.003 0.1 -10000 0 -0.45 12 12
IL10 -0.28 0.17 -10000 0 -0.38 209 209
PIASy/HDAC complex 0.029 0.008 -10000 0 -10000 0 0
PIAS3 0.024 0.013 -10000 0 -10000 0 0
CDK2 0.025 0.013 -10000 0 -10000 0 0
IL5 -0.28 0.17 -10000 0 -0.38 209 209
CDK4 0.025 0.013 -10000 0 -10000 0 0
PIAS4 0.029 0.008 -10000 0 -10000 0 0
ATF3 -0.003 0.14 -10000 0 -0.62 13 13
SMAD3/SMAD4/SP1 0.066 0.042 -10000 0 -10000 0 0
FOXG1 -0.006 0.026 -10000 0 -10000 0 0
FOXO3 0.015 0.007 -10000 0 -10000 0 0
FOXO1 0.016 0.006 -10000 0 -10000 0 0
FOXO4 0.016 0.006 -10000 0 -10000 0 0
heart looping 0.026 0.033 0.3 2 -10000 0 2
CEBPB 0.024 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.05 0.043 -10000 0 -10000 0 0
MYOD1 -0.013 0.018 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.004 0.16 -10000 0 -0.43 31 31
SMAD3/SMAD4/GATA3 -0.31 0.2 -10000 0 -0.43 215 215
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.063 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.085 0.039 -10000 0 -10000 0 0
MED15 0.026 0.007 -10000 0 -10000 0 0
SP1 0.033 0.008 -10000 0 -10000 0 0
SIN3B 0.028 0.002 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.064 0.026 -10000 0 -10000 0 0
ITGB5 0.032 0.033 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.02 0.074 -10000 0 -0.54 4 4
SMAD3/SMAD4/AR 0.034 0.11 -10000 0 -0.44 12 12
AR -0.001 0.13 -10000 0 -0.64 12 12
negative regulation of cell growth 0.019 0.06 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.048 0.041 -10000 0 -10000 0 0
E2F5 0.027 0.005 -10000 0 -10000 0 0
E2F4 0.026 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.078 0.039 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.032 0.02 -10000 0 -10000 0 0
TFDP1 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.023 0.13 -10000 0 -0.33 3 3
SMAD3/SMAD4/RUNX2 0.053 0.04 -10000 0 -10000 0 0
TGIF2 0.027 0.006 -10000 0 -10000 0 0
TGIF1 0.026 0.008 -10000 0 -10000 0 0
ATF2 0.028 0.004 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

Figure S50.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S50.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.009 -10000 0 -10000 0 0
CCL5 0.015 0.032 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.03 0.12 0.25 2 -0.36 21 23
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 -0.027 0.12 -10000 0 -0.47 8 8
Syndecan-1/Syntenin -0.023 0.12 0.23 1 -0.47 8 9
MAPK3 -0.023 0.11 -10000 0 -0.56 4 4
HGF/MET 0.01 0.094 -10000 0 -0.44 11 11
TGFB1/TGF beta receptor Type II 0.027 0.009 -10000 0 -10000 0 0
BSG 0.028 0.002 -10000 0 -10000 0 0
keratinocyte migration -0.026 0.11 -10000 0 -0.46 8 8
Syndecan-1/RANTES -0.027 0.12 -10000 0 -0.46 8 8
Syndecan-1/CD147 -0.006 0.12 -10000 0 -0.57 5 5
Syndecan-1/Syntenin/PIP2 -0.023 0.12 -10000 0 -0.46 8 8
LAMA5 0.026 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.023 0.11 -10000 0 -0.45 8 8
MMP7 -0.013 0.096 -10000 0 -0.64 5 5
HGF -0.004 0.13 -10000 0 -0.64 11 11
Syndecan-1/CASK -0.037 0.11 -10000 0 -0.34 22 22
Syndecan-1/HGF/MET -0.022 0.13 -10000 0 -0.48 11 11
regulation of cell adhesion -0.03 0.099 -10000 0 -0.55 4 4
HPSE -0.004 0.14 -10000 0 -0.64 13 13
positive regulation of cell migration -0.03 0.12 0.25 2 -0.36 21 23
SDC1 -0.031 0.12 -10000 0 -0.35 23 23
Syndecan-1/Collagen -0.03 0.12 0.25 2 -0.36 21 23
PPIB 0.028 0.004 -10000 0 -10000 0 0
MET 0.017 0.023 -10000 0 -10000 0 0
PRKACA 0.028 0.002 -10000 0 -10000 0 0
MMP9 -0.019 0.073 -10000 0 -0.64 2 2
MAPK1 -0.023 0.11 -10000 0 -0.54 5 5
homophilic cell adhesion -0.032 0.12 0.25 2 -0.35 21 23
MMP1 -0.023 0.16 -10000 0 -0.64 18 18
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.022 0.17 -9999 0 -0.64 20 20
GNB1/GNG2 0.019 0.1 -9999 0 -0.42 3 3
mol:DAG -0.005 0.079 -9999 0 -0.43 2 2
PLCG1 -0.005 0.081 -9999 0 -0.45 2 2
YES1 -0.012 0.084 -9999 0 -0.39 5 5
FZD3 0.027 0.006 -9999 0 -10000 0 0
FZD6 0.027 0.004 -9999 0 -10000 0 0
G protein 0.021 0.096 -9999 0 -0.45 2 2
MAP3K7 -0.13 0.16 -9999 0 -0.42 17 17
mol:Ca2+ -0.004 0.078 -9999 0 -0.42 2 2
mol:IP3 -0.005 0.079 -9999 0 -0.43 2 2
NLK 0 0.07 -9999 0 -0.82 2 2
GNB1 0.025 0.008 -9999 0 -10000 0 0
CAMK2A -0.14 0.17 -9999 0 -0.34 104 104
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.001 0.09 -9999 0 -0.31 19 19
CSNK1A1 0.027 0.004 -9999 0 -10000 0 0
GNAS -0.01 0.08 -9999 0 -0.39 5 5
GO:0007205 -0.013 0.076 -9999 0 -0.43 2 2
WNT6 0.021 0.042 -9999 0 -0.64 1 1
WNT4 0.005 0.11 -9999 0 -0.6 9 9
NFAT1/CK1 alpha -0.009 0.12 -9999 0 -0.46 3 3
GNG2 0.027 0.006 -9999 0 -10000 0 0
WNT5A 0.012 0.037 -9999 0 -10000 0 0
WNT11 -0.003 0.13 -9999 0 -0.64 12 12
CDC42 -0.011 0.076 -9999 0 -0.41 3 3
HIF-1-alpha transcription factor network

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
PKM2 0.015 0.26 -10000 0 -0.9 9 9
HDAC7 0.028 0.005 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.083 0.25 -10000 0 -0.73 4 4
SMAD4 0.027 0.008 -10000 0 -10000 0 0
ID2 0.028 0.27 -10000 0 -0.93 8 8
AP1 -0.03 0.17 -10000 0 -0.47 37 37
ABCG2 0.024 0.27 -10000 0 -0.92 9 9
HIF1A 0.025 0.066 -10000 0 -10000 0 0
TFF3 -0.037 0.34 -10000 0 -0.97 15 15
GATA2 -0.1 0.27 -10000 0 -0.64 57 57
AKT1 0.03 0.065 -10000 0 -10000 0 0
response to hypoxia 0.01 0.055 -10000 0 -10000 0 0
MCL1 0.027 0.26 -10000 0 -0.97 7 7
NDRG1 0.026 0.26 -10000 0 -0.93 8 8
SERPINE1 -0.018 0.27 -10000 0 -0.96 11 11
FECH 0.023 0.26 -10000 0 -0.92 8 8
FURIN 0.027 0.27 -10000 0 -0.97 7 7
NCOA2 -0.032 0.19 -10000 0 -0.64 26 26
EP300 0.035 0.079 -10000 0 -0.34 2 2
HMOX1 0.02 0.27 -10000 0 -0.97 8 8
BHLHE40 0.023 0.26 -10000 0 -0.96 7 7
BHLHE41 0.021 0.26 -10000 0 -0.96 7 7
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.079 0.1 -10000 0 -10000 0 0
ENG 0.037 0.082 0.34 1 -10000 0 1
JUN 0.027 0.008 -10000 0 -10000 0 0
RORA 0.026 0.27 -10000 0 -0.93 8 8
ABCB1 -0.052 0.26 -10000 0 -1.1 16 16
TFRC 0.025 0.26 -10000 0 -0.99 6 6
CXCR4 0.027 0.27 -10000 0 -0.93 8 8
TF 0.018 0.27 -10000 0 -0.94 7 7
CITED2 0.028 0.27 -10000 0 -0.93 8 8
HIF1A/ARNT 0.08 0.33 -10000 0 -1.1 8 8
LDHA 0.016 0.1 -10000 0 -0.72 3 3
ETS1 0.025 0.27 -10000 0 -0.97 7 7
PGK1 0.027 0.27 -10000 0 -0.93 8 8
NOS2 0.004 0.3 -10000 0 -0.91 15 15
ITGB2 0.015 0.26 -10000 0 -0.93 8 8
ALDOA 0.022 0.26 -10000 0 -0.92 7 7
Cbp/p300/CITED2 0.046 0.27 -10000 0 -0.96 6 6
FOS -0.064 0.22 -10000 0 -0.59 43 43
HK2 0.011 0.27 -10000 0 -0.95 8 8
SP1 0.025 0.036 -10000 0 -10000 0 0
GCK 0.032 0.15 -10000 0 -0.68 2 2
HK1 0.027 0.27 -10000 0 -0.97 7 7
NPM1 0.026 0.26 -10000 0 -0.97 7 7
EGLN1 0.026 0.26 -10000 0 -0.93 8 8
CREB1 0.033 0.005 -10000 0 -10000 0 0
PGM1 0.025 0.26 -10000 0 -0.93 8 8
SMAD3 0.029 0.004 -10000 0 -10000 0 0
EDN1 -0.064 0.25 -10000 0 -0.71 24 24
IGFBP1 -0.031 0.28 -10000 0 -0.89 12 12
VEGFA 0.059 0.21 0.49 2 -0.65 2 4
HIF1A/JAB1 0.039 0.052 -10000 0 -10000 0 0
CP -0.003 0.3 -10000 0 -0.87 13 13
CXCL12 -0.015 0.34 -10000 0 -0.87 24 24
COPS5 0.028 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.013 -10000 0 -10000 0 0
BNIP3 0.028 0.27 -10000 0 -0.97 7 7
EGLN3 0.027 0.27 -10000 0 -0.97 7 7
CA9 0.01 0.27 -10000 0 -0.95 8 8
TERT 0.019 0.26 -10000 0 -0.96 7 7
ENO1 0.026 0.26 -10000 0 -0.93 8 8
PFKL 0.02 0.26 -10000 0 -0.93 8 8
NCOA1 0.028 0.005 -10000 0 -10000 0 0
ADM 0.024 0.27 -10000 0 -0.97 8 8
ARNT 0.026 0.064 -10000 0 -10000 0 0
HNF4A -0.043 0.21 -10000 0 -0.64 31 31
ADFP 0.015 0.26 -10000 0 -0.9 9 9
SLC2A1 0.057 0.21 0.49 2 -0.65 2 4
LEP -0.01 0.24 -10000 0 -0.98 6 6
HIF1A/ARNT/Cbp/p300 0.075 0.25 -10000 0 -0.73 5 5
EPO -0.001 0.2 -10000 0 -0.74 5 5
CREBBP 0.037 0.068 -10000 0 -0.32 1 1
HIF1A/ARNT/Cbp/p300/HDAC7 0.086 0.25 -10000 0 -0.74 2 2
PFKFB3 0.027 0.26 -10000 0 -0.93 8 8
NT5E 0.027 0.27 -10000 0 -1 7 7
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.026 0.024 -10000 0 -10000 0 0
CRKL 0.026 0.13 0.3 3 -0.43 13 16
mol:PIP3 0.002 0.012 -10000 0 -10000 0 0
AKT1 0.012 0.053 -10000 0 -10000 0 0
PTK2B 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.027 0.12 0.3 4 -0.4 13 17
RANBP10 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.023 0.087 -10000 0 -0.42 9 9
MAP3K5 0.033 0.12 0.31 9 -0.39 13 22
HGF/MET/CIN85/CBL/ENDOPHILINS 0.037 0.084 -10000 0 -0.38 9 9
AP1 -0.007 0.15 -10000 0 -0.38 36 36
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.1 0.34 -10000 0 -0.78 51 51
STAT3 (dimer) 0.006 0.061 -10000 0 -0.36 1 1
GAB1/CRKL/SHP2/PI3K 0.052 0.12 -10000 0 -0.4 13 13
INPP5D 0.024 0.02 -10000 0 -10000 0 0
CBL/CRK 0.05 0.14 0.39 10 -0.41 13 23
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.007 -10000 0 -10000 0 0
PTEN 0.028 0.004 -10000 0 -10000 0 0
ELK1 0.088 0.16 0.34 79 -10000 0 79
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.003 0.049 -10000 0 -0.25 2 2
PAK1 0.011 0.05 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.022 0.084 -10000 0 -0.42 8 8
HRAS -0.008 0.1 -10000 0 -0.47 5 5
DOCK1 0.025 0.12 0.3 4 -0.41 13 17
GAB1 0.021 0.13 0.23 1 -0.45 13 14
CRK 0.034 0.14 0.38 9 -0.43 13 22
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.12 -10000 0 -0.5 11 11
JUN 0.026 0.007 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0 0.044 -10000 0 -0.23 9 9
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
cell morphogenesis 0.031 0.11 0.39 5 -10000 0 5
GRB2/SHC 0.031 0.057 -10000 0 -0.26 1 1
FOS -0.065 0.22 -10000 0 -0.59 43 43
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.087 0.16 0.34 79 -10000 0 79
HGF/MET/MUC20 0.01 0.082 -10000 0 -0.38 11 11
cell migration 0.023 0.049 -10000 0 -0.26 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.027 0.024 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.012 0.057 -10000 0 -0.29 7 7
MET/MUC20 0.013 0.015 -10000 0 -10000 0 0
RAP1B 0.031 0.13 0.38 9 -0.38 13 22
RAP1A 0.025 0.11 0.28 4 -0.37 13 17
HGF/MET/RANBP9 0.021 0.086 -10000 0 -0.41 9 9
RAF1 0.018 0.12 0.32 3 -0.54 2 5
STAT3 0.006 0.061 -10000 0 -0.36 1 1
cell proliferation 0.026 0.092 -10000 0 -0.38 6 6
RPS6KB1 0.007 0.026 -10000 0 -0.28 1 1
MAPK3 0.058 0.15 0.49 9 -10000 0 9
MAPK1 0.11 0.23 0.64 31 -10000 0 31
RANBP9 0.027 0.006 -10000 0 -10000 0 0
MAPK8 0.04 0.15 0.46 10 -0.5 7 17
SRC 0.001 0.055 -10000 0 -0.34 1 1
PI3K 0.032 0.057 -10000 0 -10000 0 0
MET/Glomulin 0.007 0.031 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K1 0.026 0.12 0.34 6 -0.5 2 8
MET 0.017 0.023 -10000 0 -10000 0 0
MAP4K1 0.036 0.13 0.32 9 -0.42 13 22
PTK2 0.027 0.004 -10000 0 -10000 0 0
MAP2K2 0.025 0.12 0.34 6 -0.5 2 8
BAD 0.011 0.05 -10000 0 -10000 0 0
MAP2K4 0.04 0.14 0.39 15 -0.36 13 28
SHP2/GRB2/SOS1/GAB1 0.014 0.097 -10000 0 -0.38 12 12
INPPL1 0.028 0.003 -10000 0 -10000 0 0
PXN 0.027 0.005 -10000 0 -10000 0 0
SH3KBP1 0.028 0.002 -10000 0 -10000 0 0
HGS -0.002 0.038 -10000 0 -0.21 8 8
PLCgamma1/PKC 0.02 0.005 -10000 0 -10000 0 0
HGF -0.004 0.13 -10000 0 -0.64 11 11
RASA1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.006 -10000 0 -10000 0 0
PTPRJ 0.028 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 0.026 0.053 -10000 0 -0.23 8 8
PDPK1 0.015 0.057 -10000 0 -10000 0 0
HGF/MET/SHIP 0.019 0.087 -10000 0 -0.38 11 11
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.001 0.13 -10000 0 -0.5 4 4
HDAC1 0.023 0.007 -10000 0 -10000 0 0
AES 0.027 0.003 -10000 0 -10000 0 0
FBXW11 0.027 0.005 -10000 0 -10000 0 0
DTX1 0.013 0.095 -10000 0 -0.64 6 6
LRP6/FZD1 0.031 0.019 -10000 0 -10000 0 0
TLE1 0.026 0.006 -10000 0 -10000 0 0
AP1 -0.11 0.2 -10000 0 -0.37 96 96
NCSTN 0.027 0.005 -10000 0 -10000 0 0
ADAM10 0.027 0.007 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.035 0.067 -10000 0 -0.55 1 1
NICD/RBPSUH 0.025 0.093 -10000 0 -0.38 8 8
WIF1 0.009 0.025 -10000 0 -10000 0 0
NOTCH1 0.016 0.077 -10000 0 -0.39 9 9
PSENEN 0.028 0.002 -10000 0 -10000 0 0
KREMEN2 0.013 0.032 -10000 0 -10000 0 0
DKK1 0.014 0.028 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.063 0.11 0.32 3 -10000 0 3
APH1B 0.025 0.039 -10000 0 -0.64 1 1
APH1A 0.027 0.005 -10000 0 -10000 0 0
AXIN1 -0.005 0.052 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.011 0.053 -10000 0 -0.39 4 4
PSEN1 0.027 0.007 -10000 0 -10000 0 0
FOS -0.065 0.22 -10000 0 -0.59 43 43
JUN 0.026 0.007 -10000 0 -10000 0 0
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.054 0.11 0.28 8 -0.29 2 10
MAPK3 0.026 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.038 0.042 -10000 0 -0.42 1 1
HNF1A 0.017 0.078 -10000 0 -0.64 4 4
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC 0.019 0.098 -10000 0 -0.79 4 4
NKD1 -0.15 0.29 -10000 0 -0.64 76 76
FZD1 0.021 0.014 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.016 0.11 -10000 0 -0.5 3 3
apoptosis -0.11 0.2 -10000 0 -0.37 96 96
Delta 1/NOTCHprecursor -0.001 0.13 -10000 0 -0.43 9 9
DLL1 -0.024 0.17 -10000 0 -0.58 23 23
PPARD -0.011 0.18 -10000 0 -0.78 15 15
Gamma Secretase 0.075 0.035 -10000 0 -0.36 1 1
APC -0.01 0.078 -10000 0 -0.57 3 3
DVL1 0.016 0.018 -10000 0 -10000 0 0
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.036 0.035 -10000 0 -10000 0 0
LRP6 0.027 0.006 -10000 0 -10000 0 0
CSNK1A1 0.028 0.004 -10000 0 -10000 0 0
NLK 0.011 0.005 -10000 0 -10000 0 0
CCND1 0.018 0.12 -10000 0 -0.96 4 4
WNT1 0.012 0.033 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.053 0.11 0.36 9 -0.49 2 11
DKK2 0.021 0.042 -10000 0 -0.64 1 1
NOTCH1 precursor/DVL1 0.016 0.12 -10000 0 -0.5 8 8
GSK3B 0.027 0.006 -10000 0 -10000 0 0
FRAT1 0.027 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.019 0.11 -10000 0 -0.5 3 3
PPP2R5D 0.083 0.16 0.32 72 -0.35 12 84
MAPK1 0.026 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.046 0.036 -10000 0 -10000 0 0
RBPJ 0.027 0.006 -10000 0 -10000 0 0
CREBBP 0.028 0.009 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.023 0.077 -10000 0 -10000 0 0
VDR 0.018 0.078 -10000 0 -0.64 4 4
FAM120B 0.027 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.037 0.035 -10000 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.037 0.052 -10000 0 -0.38 3 3
MED1 0.026 0.007 -10000 0 -10000 0 0
mol:9cRA 0.004 0.006 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.018 0.058 -10000 0 -0.28 10 10
RXRs/NUR77 -0.11 0.22 -10000 0 -0.38 114 114
RXRs/PPAR 0.028 0.018 -10000 0 -10000 0 0
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.013 0.058 -10000 0 -0.48 4 4
RARs/VDR/DNA/Vit D3 0.054 0.05 -10000 0 -0.36 3 3
RARA 0.026 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.018 0.078 -10000 0 -0.64 4 4
RARs/RARs/DNA/9cRA 0.046 0.019 -10000 0 -10000 0 0
RARG 0.027 0.008 -10000 0 -10000 0 0
RPS6KB1 0.043 0.13 0.53 20 -10000 0 20
RARs/THRs/DNA/SMRT 0.018 0.06 -10000 0 -0.28 11 11
THRA 0.026 0.007 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.013 0.058 -10000 0 -0.48 4 4
RXRs/PPAR/9cRA/PGJ2/DNA 0.054 0.029 -10000 0 -10000 0 0
NR1H4 0.018 0.078 -10000 0 -0.64 4 4
RXRs/LXRs/DNA 0.084 0.044 -10000 0 -10000 0 0
NR1H2 0.031 0.009 -10000 0 -10000 0 0
NR1H3 0.031 0.01 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.055 0.058 -10000 0 -0.37 4 4
NR4A1 -0.24 0.33 -10000 0 -0.64 115 115
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.012 0.06 -10000 0 -0.32 8 8
RXRG 0.021 0.014 -10000 0 -10000 0 0
RXR alpha/CCPG 0.04 0.014 -10000 0 -10000 0 0
RXRA 0.029 0.011 -10000 0 -10000 0 0
RXRB 0.03 0.011 -10000 0 -10000 0 0
THRB 0.001 0.13 -10000 0 -0.64 11 11
PPARG 0.026 0.009 -10000 0 -10000 0 0
PPARD 0.027 0.006 -10000 0 -10000 0 0
TNF 0.021 0.12 -10000 0 -1.1 3 3
mol:Oxysterols 0.004 0.005 -10000 0 -10000 0 0
cholesterol transport 0.035 0.056 -10000 0 -0.38 3 3
PPARA 0.026 0.008 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.027 0.006 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 -0.11 0.17 -10000 0 -0.31 114 114
SREBF1 0.026 0.049 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.054 0.029 -10000 0 -10000 0 0
ABCA1 0.032 0.045 -10000 0 -10000 0 0
RARs/THRs 0.057 0.088 -10000 0 -0.36 11 11
RXRs/FXR 0.061 0.055 -10000 0 -0.36 3 3
BCL2 0.026 0.008 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.006 0.006 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.032 0.021 -10000 0 -10000 0 0
STXBP1 0.027 0.006 -10000 0 -10000 0 0
ACh/CHRNA1 -0.007 0.043 -10000 0 -0.14 1 1
RAB3GAP2/RIMS1/UNC13B 0.045 0.024 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.003 0.028 -10000 0 -10000 0 0
mol:ACh 0.019 0.045 0.092 62 -0.14 1 63
RAB3GAP2 0.027 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.029 0.036 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.007 0.043 -10000 0 -0.14 1 1
UNC13B 0.027 0.005 -10000 0 -10000 0 0
CHRNA1 -0.049 0.045 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.1 0.21 -10000 0 -0.42 83 83
SNAP25 -0.007 0.023 -10000 0 -0.32 1 1
VAMP2 0.005 0.001 -10000 0 -10000 0 0
SYT1 -0.17 0.3 -10000 0 -0.64 83 83
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.019 0.013 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.029 0.036 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.15 0.13 -9999 0 -0.6 6 6
RAD9A 0.028 0.007 -9999 0 -10000 0 0
AP1 -0.031 0.17 -9999 0 -0.47 37 37
IFNAR2 0.026 0.008 -9999 0 -10000 0 0
AKT1 0.004 0.055 -9999 0 -0.23 13 13
ER alpha/Oestrogen -0.006 0.11 -9999 0 -0.42 17 17
NFX1/SIN3/HDAC complex 0.013 0.087 -9999 0 -0.49 5 5
EGF -0.56 0.21 -9999 0 -0.63 258 258
SMG5 0.027 0.005 -9999 0 -10000 0 0
SMG6 0.026 0.008 -9999 0 -10000 0 0
SP3/HDAC2 0.04 0.01 -9999 0 -10000 0 0
TERT/c-Abl -0.14 0.12 -9999 0 -0.59 5 5
SAP18 0.027 0.006 -9999 0 -10000 0 0
MRN complex 0.051 0.031 -9999 0 -0.42 1 1
WT1 -0.34 0.33 -9999 0 -0.63 159 159
WRN 0.027 0.006 -9999 0 -10000 0 0
SP1 0.027 0.006 -9999 0 -10000 0 0
SP3 0.028 0.004 -9999 0 -10000 0 0
TERF2IP 0.026 0.008 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.13 0.12 -9999 0 -0.72 2 2
Mad/Max 0.039 0.012 -9999 0 -10000 0 0
TERT -0.15 0.13 -9999 0 -0.65 5 5
CCND1 -0.14 0.13 -9999 0 -0.88 3 3
MAX 0.027 0.007 -9999 0 -10000 0 0
RBBP7 0.028 0.002 -9999 0 -10000 0 0
RBBP4 0.026 0.007 -9999 0 -10000 0 0
TERF2 0.023 0.01 -9999 0 -10000 0 0
PTGES3 0.027 0.005 -9999 0 -10000 0 0
SIN3A 0.028 0.004 -9999 0 -10000 0 0
Telomerase/911 0.021 0.038 -9999 0 -10000 0 0
CDKN1B 0.017 0.016 -9999 0 -10000 0 0
RAD1 0.028 0.004 -9999 0 -10000 0 0
XRCC5 0.027 0.005 -9999 0 -10000 0 0
XRCC6 0.026 0.008 -9999 0 -10000 0 0
SAP30 0.026 0.011 -9999 0 -10000 0 0
TRF2/PARP2 0.035 0.015 -9999 0 -10000 0 0
UBE3A 0.027 0.005 -9999 0 -10000 0 0
JUN 0.026 0.007 -9999 0 -10000 0 0
E6 0 0.001 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.004 -9999 0 -10000 0 0
FOS -0.065 0.22 -9999 0 -0.59 43 43
IFN-gamma/IRF1 0.038 0.024 -9999 0 -10000 0 0
PARP2 0.026 0.007 -9999 0 -10000 0 0
BLM 0.02 0.027 -9999 0 -10000 0 0
Telomerase -0.027 0.12 -9999 0 -0.77 5 5
IRF1 0.031 0.005 -9999 0 -10000 0 0
ESR1 -0.008 0.14 -9999 0 -0.56 17 17
KU/TER 0.038 0.012 -9999 0 -10000 0 0
ATM/TRF2 0.038 0.013 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.017 0.081 -9999 0 -0.44 4 4
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.017 0.083 -9999 0 -0.45 4 4
HDAC1 0.026 0.007 -9999 0 -10000 0 0
HDAC2 0.027 0.006 -9999 0 -10000 0 0
ATM 0.01 0.003 -9999 0 -10000 0 0
SMAD3 0.013 0.006 -9999 0 -10000 0 0
ABL1 0.027 0.006 -9999 0 -10000 0 0
MXD1 0.028 0.004 -9999 0 -10000 0 0
MRE11A 0.027 0.005 -9999 0 -10000 0 0
HUS1 0.022 0.012 -9999 0 -10000 0 0
RPS6KB1 0.026 0.008 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.11 0.13 -9999 0 -0.56 8 8
NR2F2 0.027 0.004 -9999 0 -10000 0 0
MAPK3 -0.004 0.013 -9999 0 -10000 0 0
MAPK1 -0.004 0.014 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.027 0.009 -9999 0 -10000 0 0
NFKB1 0.027 0.006 -9999 0 -10000 0 0
HNRNPC 0.026 0.007 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.003 -9999 0 -10000 0 0
NBN 0.027 0.005 -9999 0 -10000 0 0
EGFR 0.022 0.012 -9999 0 -10000 0 0
mol:Oestrogen 0 0 -9999 0 -10000 0 0
EGF/EGFR -0.37 0.17 -9999 0 -0.42 258 258
MYC 0.026 0.015 -9999 0 -10000 0 0
IL2 0.016 0.016 -9999 0 -10000 0 0
KU 0.038 0.012 -9999 0 -10000 0 0
RAD50 0.025 0.039 -9999 0 -0.64 1 1
HSP90AA1 0.026 0.007 -9999 0 -10000 0 0
TGFB1 0.027 0.009 -9999 0 -10000 0 0
TRF2/BLM 0.031 0.026 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.14 0.12 -9999 0 -0.68 3 3
SP1/HDAC2 0.039 0.012 -9999 0 -10000 0 0
PINX1 0.027 0.006 -9999 0 -10000 0 0
Telomerase/EST1A -0.13 0.12 -9999 0 -0.72 2 2
Smad3/Myc 0.029 0.012 -9999 0 -10000 0 0
911 complex 0.044 0.025 -9999 0 -10000 0 0
IFNG 0.02 0.026 -9999 0 -10000 0 0
Telomerase/PinX1 -0.13 0.12 -9999 0 -0.7 2 2
Telomerase/AKT1/mTOR/p70S6K -0.032 0.1 -9999 0 -0.52 7 7
SIN3B 0.028 0.002 -9999 0 -10000 0 0
YWHAE 0.026 0.008 -9999 0 -10000 0 0
Telomerase/EST1B -0.13 0.12 -9999 0 -0.7 2 2
response to DNA damage stimulus 0.001 0.019 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.068 0.037 -9999 0 -0.36 1 1
TRF2/WRN 0.036 0.014 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.13 0.12 -9999 0 -0.7 2 2
E2F1 -0.001 0.047 -9999 0 -10000 0 0
ZNFX1 0.027 0.007 -9999 0 -10000 0 0
PIF1 0.017 0.032 -9999 0 -10000 0 0
NCL 0.027 0.005 -9999 0 -10000 0 0
DKC1 0.028 0.002 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.028 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.007 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.025 0.011 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.02 0.059 -10000 0 -0.42 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.007 0.02 -10000 0 -10000 0 0
GRK1 -0.008 0.02 -10000 0 -10000 0 0
CNG Channel -0.063 0.17 -10000 0 -0.35 68 68
mol:Na + -0.063 0.16 -10000 0 -0.35 60 60
mol:ADP -0.008 0.02 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.04 0.066 -10000 0 -0.42 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.056 0.17 -10000 0 -0.36 60 60
CNGB1 0.009 0.026 -10000 0 -10000 0 0
RDH5 0.015 0.061 -10000 0 -0.64 2 2
SAG -0.016 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.075 0.17 0.4 12 -0.34 53 65
Na + (4 Units) -0.063 0.15 -10000 0 -0.34 60 60
RGS9 0.013 0.08 -10000 0 -0.64 4 4
GNB1/GNGT1 0.02 0.027 -10000 0 -10000 0 0
GNAT1/GDP 0.043 0.061 -10000 0 -0.37 5 5
GUCY2D 0.006 0.036 -10000 0 -10000 0 0
GNGT1 0.001 0.031 -10000 0 -10000 0 0
GUCY2F -0.015 0.012 -10000 0 -10000 0 0
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.01 0.058 -10000 0 -0.36 6 6
mol:11-cis-retinal 0.015 0.061 -10000 0 -0.64 2 2
mol:cGMP 0.027 0.037 -10000 0 -10000 0 0
GNB1 0.025 0.008 -10000 0 -10000 0 0
Rhodopsin 0.025 0.05 -10000 0 -0.48 2 2
SLC24A1 0.028 0.004 -10000 0 -10000 0 0
CNGA1 -0.15 0.29 -10000 0 -0.62 78 78
Metarhodopsin II 0.024 0.011 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.04 0.04 -10000 0 -10000 0 0
RGS9BP 0.024 0.04 -10000 0 -0.64 1 1
Metarhodopsin II/Transducin 0.005 0.024 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.04 0.02 -10000 0 -10000 0 0
PDE6A/B 0.032 0.039 -10000 0 -0.36 2 2
mol:Pi 0.039 0.066 -10000 0 -0.42 5 5
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.025 0.029 -10000 0 -10000 0 0
PDE6B 0.022 0.046 -10000 0 -0.48 2 2
PDE6A 0.014 0.024 -10000 0 -10000 0 0
PDE6G 0.013 0.088 -10000 0 -0.64 5 5
RHO 0.003 0.024 -10000 0 -10000 0 0
PDE6 0.053 0.092 -10000 0 -0.39 10 10
GUCA1A -0.003 0.024 -10000 0 -10000 0 0
GC2/GCAP Family 0.05 0.024 -10000 0 -10000 0 0
GUCA1C 0.007 0.023 -10000 0 -10000 0 0
GUCA1B 0.026 0.009 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.013 0.005 -10000 0 -10000 0 0
SMARCC1 0.007 0.042 -10000 0 -0.65 1 1
REL 0.015 0.087 -10000 0 -0.64 5 5
HDAC7 -0.11 0.11 -10000 0 -0.46 3 3
JUN 0.026 0.007 -10000 0 -10000 0 0
EP300 0.026 0.008 -10000 0 -10000 0 0
KAT2B 0.027 0.006 -10000 0 -10000 0 0
KAT5 0.028 0.002 -10000 0 -10000 0 0
MAPK14 -0.015 0.025 -10000 0 -10000 0 0
FOXO1 0.027 0.006 -10000 0 -10000 0 0
T-DHT/AR -0.11 0.13 -10000 0 -0.48 3 3
MAP2K6 -0.005 0.025 -10000 0 -10000 0 0
BRM/BAF57 0.036 0.014 -10000 0 -10000 0 0
MAP2K4 -0.005 0.025 -10000 0 -10000 0 0
SMARCA2 0.026 0.007 -10000 0 -10000 0 0
PDE9A -0.18 0.21 -10000 0 -0.77 13 13
NCOA2 -0.033 0.19 -10000 0 -0.64 26 26
CEBPA 0.017 0.049 -10000 0 -0.64 1 1
EHMT2 0.027 0.006 -10000 0 -10000 0 0
cell proliferation -0.15 0.21 0.52 9 -0.5 34 43
NR0B1 -0.009 0.041 -10000 0 -10000 0 0
EGR1 -0.026 0.18 -10000 0 -0.64 23 23
RXRs/9cRA 0.044 0.016 -10000 0 -10000 0 0
AR/RACK1/Src -0.035 0.089 0.32 3 -0.39 3 6
AR/GR -0.014 0.091 0.24 8 -0.31 12 20
GNB2L1 0.027 0.005 -10000 0 -10000 0 0
PKN1 0.028 0.002 -10000 0 -10000 0 0
RCHY1 0.027 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.023 0.058 -10000 0 -0.4 5 5
T-DHT/AR/TIF2/CARM1 -0.058 0.16 0.33 6 -0.47 25 31
SRC -0.041 0.05 0.2 2 -0.39 2 4
NR3C1 0.027 0.004 -10000 0 -10000 0 0
KLK3 -0.064 0.16 0.33 1 -0.45 17 18
APPBP2 -0.005 0.026 -10000 0 -10000 0 0
TRIM24 0.022 0.012 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.04 0.095 0.29 8 -0.37 5 13
TMPRSS2 -0.75 0.53 -10000 0 -1.1 185 185
RXRG -0.004 0.022 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.027 0.006 -10000 0 -10000 0 0
RXRB 0.027 0.006 -10000 0 -10000 0 0
CARM1 0.028 0.003 -10000 0 -10000 0 0
NR2C2 0.021 0.059 -10000 0 -0.54 3 3
KLK2 -0.043 0.13 0.33 7 -0.44 10 17
AR -0.029 0.074 -10000 0 -0.33 14 14
SENP1 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
MDM2 0.027 0.006 -10000 0 -10000 0 0
SRY 0 0.001 -10000 0 -10000 0 0
GATA2 -0.1 0.26 -10000 0 -0.64 57 57
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.006 0.044 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.035 0.096 0.35 4 -0.4 3 7
positive regulation of transcription -0.1 0.26 -10000 0 -0.64 57 57
DNAJA1 -0.005 0.027 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.007 -10000 0 -10000 0 0
NCOA1 0.034 0.015 -10000 0 -10000 0 0
SPDEF 0.015 0.029 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.035 0.12 0.29 5 -0.45 8 13
T-DHT/AR/Hsp90 -0.036 0.094 0.29 8 -0.38 4 12
GSK3B 0.024 0.008 -10000 0 -10000 0 0
NR2C1 0.027 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.046 0.05 -10000 0 -0.42 2 2
SIRT1 0.028 0.004 -10000 0 -10000 0 0
ZMIZ2 0.022 0.012 -10000 0 -10000 0 0
POU2F1 -0.05 0.067 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.047 0.096 0.3 7 -0.38 5 12
CREBBP 0.026 0.008 -10000 0 -10000 0 0
SMARCE1 0.026 0.007 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) 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
SPHK2 0.028 0.003 -9999 0 -10000 0 0
SPHK1 -0.023 0.052 -9999 0 -10000 0 0
GNAI2 0.026 0.007 -9999 0 -10000 0 0
mol:S1P 0.002 0.013 -9999 0 -10000 0 0
GNAO1 -0.012 0.15 -9999 0 -0.64 16 16
mol:Sphinganine-1-P -0.017 0.032 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.044 0.032 -9999 0 -10000 0 0
GNAI3 0.027 0.006 -9999 0 -10000 0 0
G12/G13 0.031 0.018 -9999 0 -10000 0 0
S1PR3 -0.025 0.18 -9999 0 -0.62 23 23
S1PR2 0.028 0.002 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0 0.014 -9999 0 -10000 0 0
S1PR5 0.019 0.069 -9999 0 -0.64 3 3
S1PR4 0.026 0.016 -9999 0 -10000 0 0
GNAI1 0.018 0.056 -9999 0 -0.64 2 2
S1P/S1P5/G12 0.032 0.05 -9999 0 -0.35 3 3
S1P/S1P3/Gq -0.071 0.18 -9999 0 -0.34 74 74
S1P/S1P4/Gi 0.008 0.097 -9999 0 -0.32 12 12
GNAQ 0.027 0.006 -9999 0 -10000 0 0
GNAZ 0.026 0.008 -9999 0 -10000 0 0
GNA14 -0.11 0.27 -9999 0 -0.62 60 60
GNA15 0.02 0.027 -9999 0 -10000 0 0
GNA12 0.022 0.011 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.012 0.1 -9999 0 -0.64 7 7
ABCC1 0.026 0.008 -9999 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.006 0.085 -10000 0 -0.41 6 6
BAG4 0.027 0.006 -10000 0 -10000 0 0
BAD 0.01 0.044 0.2 6 -0.18 1 7
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.02 0.027 -10000 0 -10000 0 0
BAX 0.01 0.043 0.2 6 -0.18 1 7
EnzymeConsortium:3.1.4.12 0.009 0.032 0.13 8 -0.09 6 14
IKBKB 0.011 0.088 0.27 2 -0.38 6 8
MAP2K2 0.019 0.077 0.26 20 -10000 0 20
MAP2K1 0.02 0.076 0.26 20 -10000 0 20
SMPD1 0.01 0.035 0.15 6 -0.16 2 8
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.013 0.084 -10000 0 -0.38 6 6
MAP2K4 0.019 0.074 0.29 15 -10000 0 15
protein ubiquitination 0.015 0.098 0.34 5 -0.4 6 11
EnzymeConsortium:2.7.1.37 0.022 0.089 0.31 20 -10000 0 20
response to UV 0 0.001 0.004 20 -10000 0 20
RAF1 0.022 0.079 0.27 20 -0.18 1 21
CRADD 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide 0.012 0.046 0.2 7 -0.16 2 9
I-kappa-B-alpha/RELA/p50/ubiquitin 0.036 0.009 -10000 0 -10000 0 0
MADD 0.028 0.004 -10000 0 -10000 0 0
MAP3K1 0.012 0.049 0.25 6 -0.18 1 7
TRADD 0.026 0.008 -10000 0 -10000 0 0
RELA/p50 0.028 0.002 -10000 0 -10000 0 0
MAPK3 0.022 0.074 0.25 20 -10000 0 20
MAPK1 0.015 0.081 0.26 19 -10000 0 19
p50/RELA/I-kappa-B-alpha 0.039 0.01 -10000 0 -10000 0 0
FADD 0.006 0.081 -10000 0 -0.39 6 6
KSR1 0.02 0.069 0.25 17 -0.18 1 18
MAPK8 0.012 0.077 0.28 14 -0.28 3 17
TRAF2 0.027 0.006 -10000 0 -10000 0 0
response to radiation 0 0.001 0.004 8 -10000 0 8
CHUK 0.014 0.089 0.27 4 -0.39 6 10
TNF R/SODD 0.038 0.012 -10000 0 -10000 0 0
TNF 0.015 0.071 -10000 0 -0.64 3 3
CYCS 0.026 0.055 0.2 11 -10000 0 11
IKBKG 0.013 0.091 0.27 4 -0.39 6 10
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.009 0.086 -10000 0 -0.43 6 6
RELA 0.028 0.002 -10000 0 -10000 0 0
RIPK1 0.027 0.006 -10000 0 -10000 0 0
AIFM1 0.013 0.042 0.18 7 -10000 0 7
TNF/TNF R/SODD 0.041 0.054 -10000 0 -0.42 3 3
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
response to heat 0 0.001 0.004 8 -10000 0 8
CASP8 0.023 0.073 -10000 0 -0.49 5 5
NSMAF 0.006 0.081 -10000 0 -0.4 5 5
response to hydrogen peroxide 0 0.001 0.004 20 -10000 0 20
BCL2 0.026 0.008 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.033 0.013 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.013 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.026 0.008 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.008 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
MAP3K12 0.027 0.005 -10000 0 -10000 0 0
FGR 0.02 0.044 -10000 0 -0.64 1 1
p38 alpha/TAB1 -0.026 0.084 -10000 0 -0.38 12 12
PRKG1 -0.14 0.28 -10000 0 -0.63 73 73
DUSP8 0.028 0.003 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha -0.048 0.16 -10000 0 -0.32 58 58
apoptosis -0.025 0.08 -10000 0 -0.36 12 12
RAL/GTP 0.03 0.016 -10000 0 -10000 0 0
LYN 0.027 0.005 -10000 0 -10000 0 0
DUSP1 0.025 0.039 -10000 0 -0.64 1 1
PAK1 0.028 0.003 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.052 0.033 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.012 -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 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.026 0.018 -10000 0 -10000 0 0
MAPK11 0.05 0.15 0.36 22 -0.43 10 32
BLK 0.016 0.027 -10000 0 -10000 0 0
HCK 0.013 0.051 -10000 0 -0.64 1 1
MAP2K3 0.026 0.008 -10000 0 -10000 0 0
DUSP16 0.027 0.006 -10000 0 -10000 0 0
DUSP10 0.018 0.03 -10000 0 -10000 0 0
TRAF6/MEKK3 0.033 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.045 0.14 0.33 20 -0.44 10 30
positive regulation of innate immune response 0.058 0.18 0.41 22 -0.48 11 33
LCK 0.023 0.018 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.054 0.15 0.35 14 -0.49 9 23
p38alpha-beta/MKP5 0.065 0.17 0.41 19 -0.48 9 28
PGK/cGMP -0.1 0.21 -10000 0 -0.47 73 73
PAK2 0.027 0.006 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.061 0.16 0.4 16 -0.49 9 25
CDC42 0.026 0.008 -10000 0 -10000 0 0
RALB 0.028 0.003 -10000 0 -10000 0 0
RALA 0.022 0.011 -10000 0 -10000 0 0
PAK3 0.018 0.02 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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
PTK2 -0.02 0.087 -10000 0 -0.69 3 3
Syndecan-4/Syndesmos -0.14 0.15 -10000 0 -0.49 6 6
positive regulation of JNK cascade -0.17 0.18 -10000 0 -0.55 19 19
Syndecan-4/ADAM12 -0.15 0.16 -10000 0 -0.49 6 6
CCL5 0.015 0.032 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.009 -10000 0 -10000 0 0
DNM2 0.028 0.002 -10000 0 -10000 0 0
ITGA5 0.027 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
PLG -0.35 0.31 -10000 0 -0.61 163 163
ADAM12 0.016 0.034 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.054 0.032 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.15 0.17 -10000 0 -0.55 10 10
Syndecan-4/CXCL12/CXCR4 -0.18 0.18 -10000 0 -0.59 18 18
Syndecan-4/Laminin alpha3 -0.15 0.16 -10000 0 -0.51 5 5
MDK 0 0.047 -10000 0 -10000 0 0
Syndecan-4/FZD7 -0.15 0.16 -10000 0 -0.52 10 10
Syndecan-4/Midkine -0.15 0.16 -10000 0 -0.53 4 4
FZD7 0.009 0.11 -10000 0 -0.64 8 8
Syndecan-4/FGFR1/FGF -0.14 0.16 -10000 0 -0.56 4 4
THBS1 0.004 0.12 -10000 0 -0.58 11 11
integrin-mediated signaling pathway -0.14 0.16 -10000 0 -0.5 7 7
positive regulation of MAPKKK cascade -0.17 0.18 -10000 0 -0.55 19 19
Syndecan-4/TACI -0.15 0.15 -10000 0 -0.51 5 5
CXCR4 0.02 0.027 -10000 0 -10000 0 0
cell adhesion 0.025 0.035 0.2 8 -10000 0 8
Syndecan-4/Dynamin -0.14 0.16 -10000 0 -0.53 4 4
Syndecan-4/TSP1 -0.16 0.17 -10000 0 -0.58 10 10
Syndecan-4/GIPC -0.14 0.16 -10000 0 -0.53 4 4
Syndecan-4/RANTES -0.15 0.15 -10000 0 -0.53 4 4
ITGB1 0.027 0.005 -10000 0 -10000 0 0
LAMA1 0.006 0.099 -10000 0 -0.59 7 7
LAMA3 -0.003 0.047 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCA 0.092 0.2 0.83 19 -10000 0 19
Syndecan-4/alpha-Actinin -0.14 0.16 -10000 0 -0.53 4 4
TFPI 0.025 0.04 -10000 0 -0.64 1 1
F2 0.015 0.037 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.01 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.16 -10000 0 -0.54 10 10
ACTN1 0.026 0.007 -10000 0 -10000 0 0
TNC 0.011 0.081 -10000 0 -0.64 4 4
Syndecan-4/CXCL12 -0.18 0.18 -10000 0 -0.6 19 19
FGF6 -0.016 0.009 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
CXCL12 -0.054 0.22 -10000 0 -0.62 36 36
TNFRSF13B 0.005 0.029 -10000 0 -10000 0 0
FGF2 0.021 0.059 -10000 0 -0.54 3 3
FGFR1 0.027 0.006 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.15 0.14 -10000 0 -0.49 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.035 -10000 0 -10000 0 0
cell migration -0.019 0.01 -10000 0 -10000 0 0
PRKCD 0.029 0.02 -10000 0 -10000 0 0
vasculogenesis -0.15 0.16 -10000 0 -0.56 10 10
SDC4 -0.15 0.15 -10000 0 -0.52 6 6
Syndecan-4/Tenascin C -0.15 0.16 -10000 0 -0.54 6 6
Syndecan-4/PI-4-5-P2/PKC alpha -0.043 0.025 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.14 0.16 -10000 0 -0.49 6 6
MMP9 -0.014 0.071 -10000 0 -0.63 2 2
Rac1/GTP 0.025 0.036 0.2 7 -10000 0 7
cytoskeleton organization -0.14 0.15 -10000 0 -0.47 6 6
GIPC1 0.028 0.002 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.14 0.16 -10000 0 -0.56 4 4
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.002 0.1 -10000 0 -0.46 11 11
PDGFB-D/PDGFRB/SLAP 0.018 0.097 -10000 0 -0.48 10 10
PDGFB-D/PDGFRB/APS/CBL 0.028 0.081 -10000 0 -0.37 10 10
AKT1 0.023 0.14 0.51 17 -10000 0 17
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.004 0.12 -10000 0 -0.5 11 11
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
FGR -0.032 0.14 0.34 1 -0.44 24 25
mol:Ca2+ 0.008 0.13 0.32 5 -0.51 13 18
MYC 0.048 0.13 0.44 9 -0.45 1 10
SHC1 0.027 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.077 -10000 0 -0.34 10 10
LRP1/PDGFRB/PDGFB 0.033 0.09 -10000 0 -0.41 11 11
GRB10 0.022 0.011 -10000 0 -10000 0 0
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GO:0007205 0.007 0.13 0.31 5 -0.52 13 18
PTEN 0.028 0.004 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.022 0.095 -10000 0 -0.48 10 10
PDGFB-D/PDGFRB/GRB10 0.017 0.085 -10000 0 -0.41 10 10
cell cycle arrest 0.018 0.097 -10000 0 -0.48 10 10
HRAS 0.028 0.003 -10000 0 -10000 0 0
HIF1A 0.021 0.14 0.49 17 -10000 0 17
GAB1 0.005 0.13 0.35 5 -0.49 12 17
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.006 0.12 0.35 7 -0.46 11 18
PDGFB-D/PDGFRB 0.035 0.088 -10000 0 -0.42 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.022 0.095 -10000 0 -0.48 10 10
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.003 0.093 -10000 0 -0.45 10 10
positive regulation of MAPKKK cascade 0.022 0.095 -10000 0 -0.48 10 10
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 0.007 0.14 0.32 5 -0.52 13 18
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.022 0.089 -10000 0 -0.43 10 10
SHB 0.027 0.005 -10000 0 -10000 0 0
BLK -0.013 0.11 -10000 0 -0.4 19 19
PTPN2 0.027 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.023 0.095 -10000 0 -0.48 10 10
BCAR1 0.026 0.008 -10000 0 -10000 0 0
VAV2 0.009 0.14 0.36 6 -0.5 11 17
CBL 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.023 0.095 -10000 0 -0.48 10 10
LCK -0.026 0.14 0.34 1 -0.44 20 21
PDGFRB 0.005 0.12 -10000 0 -0.64 10 10
ACP1 0.027 0.005 -10000 0 -10000 0 0
HCK -0.002 0.084 -10000 0 -0.4 11 11
ABL1 0.005 0.13 0.32 6 -0.44 14 20
PDGFB-D/PDGFRB/CBL 0.002 0.14 0.29 3 -0.55 13 16
PTPN1 0.027 0.007 -10000 0 -10000 0 0
SNX15 0.028 0.002 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.026 0.014 -10000 0 -10000 0 0
cell proliferation 0.048 0.13 0.41 11 -0.38 2 13
SLA 0.023 0.023 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.03 0.086 0.34 7 -0.34 8 15
SRC 0.001 0.077 -10000 0 -0.39 10 10
PI3K 0.003 0.055 -10000 0 -0.33 7 7
PDGFB-D/PDGFRB/GRB7/SHC 0.037 0.081 -10000 0 -0.37 10 10
SH2B2 0.022 0.012 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.003 0.12 -10000 0 -0.52 11 11
LYN -0.003 0.09 -10000 0 -0.39 14 14
LRP1 0.027 0.005 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
STAT5B 0.026 0.007 -10000 0 -10000 0 0
STAT5A 0.026 0.007 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.059 0.078 -10000 0 -0.35 8 8
SPHK1 -0.023 0.052 -10000 0 -10000 0 0
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.007 0.14 0.32 5 -0.52 13 18
PLCG1 0.007 0.14 0.32 5 -0.54 13 18
NHERF/PDGFRB 0.037 0.077 -10000 0 -0.37 9 9
YES1 -0.029 0.16 0.33 1 -0.51 26 27
cell migration 0.036 0.076 -10000 0 -0.37 9 9
SHC/Grb2/SOS1 0.057 0.079 -10000 0 -0.35 8 8
SLC9A3R2 0.026 0.008 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.049 0.075 -10000 0 -0.38 7 7
FYN -0.011 0.11 -10000 0 -0.4 19 19
DOK1 0.008 0.081 -10000 0 -0.38 10 10
HRAS/GTP 0.021 0.002 -10000 0 -10000 0 0
PDGFB 0.023 0.04 -10000 0 -0.64 1 1
RAC1 0.047 0.15 0.42 11 -0.47 8 19
PRKCD 0.008 0.077 -10000 0 -0.38 9 9
FER 0.011 0.083 -10000 0 -0.38 10 10
MAPKKK cascade 0.003 0.1 0.41 9 -0.34 8 17
RASA1 0.011 0.083 -10000 0 -0.38 10 10
NCK1 0.027 0.006 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.022 0.078 -10000 0 -0.36 10 10
PDGFB-D/PDGFRB/SHB 0.022 0.095 -10000 0 -0.48 10 10
chemotaxis 0.005 0.13 0.32 6 -0.43 14 20
STAT1-3-5/STAT1-3-5 0.047 0.071 -10000 0 -0.34 8 8
Bovine Papilomavirus E5/PDGFRB 0.003 0.091 -10000 0 -0.48 10 10
PTPRJ 0.028 0.004 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.027 0.004 -10000 0 -10000 0 0
ANTXR2 0.027 0.006 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0 -10000 0 -10000 0 0
monocyte activation -0.015 0.11 -10000 0 -0.35 27 27
MAP2K2 0.011 0.058 -10000 0 -0.56 3 3
MAP2K1 -0.003 0.001 -10000 0 -10000 0 0
MAP2K7 -0.003 0.001 -10000 0 -10000 0 0
MAP2K6 -0.002 0.001 -10000 0 -10000 0 0
CYAA -0.004 0.001 -10000 0 -10000 0 0
MAP2K4 -0.002 0.001 -10000 0 -10000 0 0
IL1B -0.001 0.051 0.24 1 -0.33 5 6
Channel 0.034 0.009 -10000 0 -10000 0 0
NLRP1 -0.003 0.003 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.008 0.089 -10000 0 -0.38 16 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0 -10000 0 -10000 0 0
MAPK3 -0.002 0.001 -10000 0 -10000 0 0
MAPK1 -0.002 0.001 -10000 0 -10000 0 0
PGR -0.15 0.17 -10000 0 -0.35 119 119
PA/Cellular Receptors 0.036 0.009 -10000 0 -10000 0 0
apoptosis -0.001 0 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.033 0.009 -10000 0 -10000 0 0
macrophage activation -0.004 0.002 -10000 0 -10000 0 0
TNF 0.014 0.071 -10000 0 -0.64 3 3
VCAM1 -0.007 0.094 -10000 0 -0.33 21 21
platelet activation -0.008 0.089 -10000 0 -0.38 16 16
MAPKKK cascade -0.007 0.031 -10000 0 -0.13 16 16
IL18 0.004 0.023 -10000 0 -10000 0 0
negative regulation of macrophage activation -0.001 0 -10000 0 -10000 0 0
LEF -0.001 0 -10000 0 -10000 0 0
CASP1 0.001 0.002 -10000 0 -10000 0 0
mol:cAMP -0.008 0.09 -10000 0 -0.38 16 16
necrosis -0.001 0 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.033 0.009 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.059 0.029 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.026 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.049 0.037 0.3 3 -10000 0 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.054 0.026 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.042 0.081 -10000 0 -0.23 1 1
CaM/Ca2+ 0.059 0.031 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.027 0.026 -10000 0 -10000 0 0
AKT1 0.017 0.068 0.35 8 -10000 0 8
MAP2K1 0.009 0.052 0.29 8 -10000 0 8
MAP3K11 0.022 0.053 0.29 9 -10000 0 9
IFNGR1 0.029 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.15 0.24 -10000 0 -0.44 114 114
Rap1/GTP 0.017 0.016 -10000 0 -10000 0 0
CRKL/C3G 0.037 0.013 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.066 0.035 -10000 0 -10000 0 0
CEBPB 0.024 0.11 0.38 8 -0.57 1 9
STAT3 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.062 0.1 -10000 0 -1.1 2 2
STAT1 0.02 0.051 0.29 8 -10000 0 8
CALM1 0.027 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.016 0.028 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.034 0.051 0.29 8 -10000 0 8
CEBPB/PTGES2/Cbp/p300 0.031 0.06 -10000 0 -0.35 1 1
mol:Ca2+ 0.056 0.028 -10000 0 -10000 0 0
MAPK3 0.021 0.052 -10000 0 -0.57 1 1
STAT1 (dimer) -0.044 0.12 -10000 0 -0.31 1 1
MAPK1 -0.026 0.21 0.42 1 -0.69 24 25
JAK2 0.029 0.01 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
JAK1 0.028 0.01 -10000 0 -10000 0 0
CAMK2D 0.027 0.006 -10000 0 -10000 0 0
DAPK1 0.024 0.08 0.34 7 -10000 0 7
SMAD7 -0.009 0.069 0.27 7 -10000 0 7
CBL/CRKL/C3G 0.046 0.052 0.29 9 -10000 0 9
PI3K 0.057 0.031 -10000 0 -10000 0 0
IFNG 0.016 0.028 -10000 0 -10000 0 0
apoptosis -0.008 0.1 0.27 1 -0.42 11 12
CAMK2G 0.028 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.007 -10000 0 -10000 0 0
CAMK2A -0.25 0.31 -10000 0 -0.64 113 113
CAMK2B 0.002 0.083 -10000 0 -0.64 4 4
FRAP1 0.006 0.066 0.34 8 -10000 0 8
PRKCD 0.012 0.053 0.3 6 -10000 0 6
RAP1B 0.027 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.042 0.081 -10000 0 -0.23 1 1
PTPN2 0.026 0.008 -10000 0 -10000 0 0
EP300 0.026 0.008 -10000 0 -10000 0 0
IRF1 0.022 0.071 0.45 4 -0.38 1 5
STAT1 (dimer)/PIASy 0.032 0.05 0.29 8 -10000 0 8
SOCS1 0.018 0.11 -10000 0 -1.3 2 2
mol:GDP 0.042 0.049 0.27 9 -10000 0 9
CASP1 -0.008 0.071 0.26 9 -10000 0 9
PTGES2 0.027 0.006 -10000 0 -10000 0 0
IRF9 0.031 0.054 0.26 9 -10000 0 9
mol:PI-3-4-5-P3 0.042 0.023 -10000 0 -10000 0 0
RAP1/GDP 0.038 0.021 -10000 0 -10000 0 0
CBL 0.021 0.053 0.29 9 -10000 0 9
MAP3K1 0.021 0.051 0.29 8 -10000 0 8
PIAS1 0.028 0.004 -10000 0 -10000 0 0
PIAS4 0.028 0.003 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.042 0.081 -10000 0 -0.23 1 1
PTPN11 0.013 0.02 -10000 0 -10000 0 0
CREBBP 0.026 0.008 -10000 0 -10000 0 0
RAPGEF1 0.027 0.006 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

Figure S67.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S67.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.012 0.096 0.64 6 -10000 0 6
PI3K Class IB/PDE3B 0.012 0.096 -10000 0 -0.64 6 6
PDE3B 0.012 0.096 -10000 0 -0.64 6 6
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.007 -10000 0 -10000 0 0
VLDLR 0.026 0.007 -10000 0 -10000 0 0
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
NUDC 0.026 0.008 -10000 0 -10000 0 0
RELN/LRP8 -0.005 0.1 -10000 0 -0.4 15 15
CaM/Ca2+ 0.02 0.005 -10000 0 -10000 0 0
KATNA1 0.027 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.02 0.12 -10000 0 -0.38 14 14
IQGAP1/CaM 0.039 0.01 -10000 0 -10000 0 0
DAB1 -0.002 0.025 -10000 0 -10000 0 0
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
PLA2G7 -0.059 0.04 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
DYNLT1 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.037 0.015 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.005 -10000 0 -10000 0 0
CDK5R1 0.026 0.009 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.01 0.003 -10000 0 -10000 0 0
CDK5R2 -0.006 0.044 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.01 0.1 -10000 0 -0.42 15 15
YWHAE 0.026 0.008 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.039 0.15 0.31 49 -0.34 2 51
MAP1B 0.006 0.003 -10000 0 -10000 0 0
RAC1 0.011 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.012 0.081 -10000 0 -0.34 14 14
RELN -0.036 0.15 -10000 0 -0.64 15 15
PAFAH/LIS1 -0.028 0.027 -10000 0 -10000 0 0
LIS1/CLIP170 0.028 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.006 0.068 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.008 0.088 -10000 0 -0.3 15 15
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.012 0.089 0.3 6 -0.33 13 19
LIS1/IQGAP1 0.028 0.011 -10000 0 -10000 0 0
RHOA 0.013 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.013 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.027 0.007 -10000 0 -10000 0 0
PAFAH1B2 0.025 0.04 -10000 0 -0.64 1 1
MAP1B/LIS1/Dynein heavy chain 0.026 0.019 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.047 0.14 0.31 49 -0.35 1 50
LRP8 0.025 0.014 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.038 0.15 0.31 49 -0.34 3 52
P39/CDK5 -0.026 0.081 -10000 0 -0.35 14 14
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.012 -10000 0 -10000 0 0
CDK5 -0.028 0.08 -10000 0 -0.36 14 14
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.024 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.004 0.093 -10000 0 -0.36 15 15
RELN/VLDLR 0.022 0.098 -10000 0 -0.38 14 14
CDC42 0.013 0.006 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.024 0.019 -10000 0 -10000 0 0
EPHB2 0.024 0.015 -10000 0 -10000 0 0
Syndecan-2/TACI 0.021 0.017 -10000 0 -10000 0 0
LAMA1 0.006 0.099 -10000 0 -0.59 7 7
Syndecan-2/alpha2 ITGB1 0.045 0.046 -10000 0 -0.36 3 3
HRAS 0.028 0.003 -10000 0 -10000 0 0
Syndecan-2/CASK 0.009 0.003 -10000 0 -10000 0 0
ITGA5 0.027 0.005 -10000 0 -10000 0 0
BAX 0.001 0.044 -10000 0 -10000 0 0
EPB41 0.026 0.008 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.027 0.006 -10000 0 -10000 0 0
LAMA3 -0.003 0.047 -10000 0 -10000 0 0
EZR 0.027 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.02 0.016 -10000 0 -10000 0 0
Syndecan-2/MMP2 0.026 0.013 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.034 0.054 -10000 0 -0.48 3 3
dendrite morphogenesis 0.026 0.012 -10000 0 -10000 0 0
Syndecan-2/GM-CSF 0.024 0.01 -10000 0 -10000 0 0
determination of left/right symmetry 0.013 0.004 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.028 0.009 -10000 0 -10000 0 0
GNB2L1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.012 0.013 -10000 0 -10000 0 0
MAPK1 0.013 0.016 -10000 0 -10000 0 0
Syndecan-2/RACK1 0.042 0.011 -10000 0 -10000 0 0
NF1 0.026 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.013 0.004 -10000 0 -10000 0 0
ITGA2 0.021 0.068 -10000 0 -0.64 3 3
MAPK8 0.005 0.05 -10000 0 -0.4 4 4
Syndecan-2/alpha2/beta1 Integrin 0.04 0.073 -10000 0 -0.36 8 8
Syndecan-2/Kininogen -0.22 0.21 -10000 0 -0.41 163 163
ITGB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.019 0.022 -10000 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.025 0.009 -10000 0 -10000 0 0
extracellular matrix organization 0.029 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.024 0.019 -10000 0 -10000 0 0
Syndecan-2/Caveolin-2/Ras 0.034 0.022 -10000 0 -10000 0 0
Syndecan-2/Laminin alpha3 0.009 0.03 -10000 0 -10000 0 0
Syndecan-2/RasGAP 0.054 0.015 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.01 -10000 0 -10000 0 0
PRKCD 0.026 0.007 -10000 0 -10000 0 0
Syndecan-2 dimer 0.026 0.013 -10000 0 -10000 0 0
GO:0007205 0.002 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.019 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
TNFRSF13B 0.005 0.029 -10000 0 -10000 0 0
RASA1 0.027 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.034 0.054 -10000 0 -0.48 3 3
Syndecan-2/Synbindin 0.029 0.008 -10000 0 -10000 0 0
TGFB1 0.027 0.009 -10000 0 -10000 0 0
CASP3 0.015 0.012 0.19 1 -10000 0 1
FN1 0.02 0.028 -10000 0 -10000 0 0
Syndecan-2/IL8 0.012 0.038 -10000 0 -0.41 1 1
SDC2 0.013 0.004 -10000 0 -10000 0 0
KNG1 -0.37 0.31 -10000 0 -0.64 164 164
Syndecan-2/Neurofibromin 0.028 0.01 -10000 0 -10000 0 0
TRAPPC4 0.027 0.005 -10000 0 -10000 0 0
CSF2 0.002 0.024 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.029 0.009 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.027 0.006 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.042 0.014 -10000 0 -10000 0 0
PRKACA 0.016 0.012 0.19 1 -10000 0 1
angiogenesis 0.012 0.038 -10000 0 -0.41 1 1
MMP2 0.024 0.016 -10000 0 -10000 0 0
IL8 0 0.059 -10000 0 -0.64 1 1
calcineurin-NFAT signaling pathway 0.021 0.016 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.028 0.004 -10000 0 -10000 0 0
LAT2 -0.011 0.058 -10000 0 -0.36 3 3
AP1 -0.007 0.15 -10000 0 -0.47 15 15
mol:PIP3 0.041 0.15 0.48 16 -0.45 2 18
IKBKB 0.038 0.12 0.42 16 -0.24 2 18
AKT1 -0.021 0.082 0.34 6 -0.33 1 7
IKBKG 0.037 0.12 0.4 16 -0.24 2 18
MS4A2 -0.003 0.056 -10000 0 -0.5 1 1
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.096 0.33 10 -0.39 4 14
mol:Ca2+ 0.039 0.13 0.44 16 -0.34 2 18
LYN 0.028 0.007 -10000 0 -10000 0 0
CBLB -0.008 0.06 -10000 0 -0.36 3 3
SHC1 0.027 0.005 -10000 0 -10000 0 0
RasGAP/p62DOK 0.049 0.021 -10000 0 -10000 0 0
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.02 -10000 0 -10000 0 0
PLD2 -0.027 0.066 0.34 2 -0.35 7 9
PTPN13 0.014 0.12 0.4 1 -0.85 4 5
PTPN11 0.025 0.013 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.014 0.11 0.4 13 -0.37 4 17
SYK 0.025 0.041 -10000 0 -0.65 1 1
GRB2 0.026 0.008 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.007 0.083 -10000 0 -0.42 3 3
LAT -0.009 0.06 -10000 0 -0.36 3 3
PAK2 0.006 0.099 0.33 10 -0.4 5 15
NFATC2 -0.042 0.15 -10000 0 -0.57 21 21
HRAS 0.002 0.092 0.29 7 -0.43 5 12
GAB2 0.028 0.003 -10000 0 -10000 0 0
PLA2G1B -0.001 0.13 -10000 0 -0.84 7 7
Fc epsilon R1 -0.004 0.09 -10000 0 -0.43 8 8
Antigen/IgE/Fc epsilon R1 0.001 0.084 -10000 0 -0.39 8 8
mol:GDP -0.004 0.088 -10000 0 -0.49 5 5
JUN 0.026 0.007 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
FOS -0.065 0.22 -10000 0 -0.59 43 43
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.002 0.066 -10000 0 -0.34 4 4
CHUK 0.037 0.12 0.4 16 -0.24 2 18
KLRG1 -0.009 0.056 -10000 0 -0.32 3 3
VAV1 -0.016 0.07 -10000 0 -0.41 4 4
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.008 0.061 -10000 0 -0.36 3 3
negative regulation of mast cell degranulation 0.008 0.064 0.22 1 -0.3 3 4
BTK 0 0.082 -10000 0 -0.51 4 4
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.004 0.071 -10000 0 -0.34 8 8
GAB2/PI3K/SHP2 -0.024 0.06 -10000 0 -0.34 7 7
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0.003 0.048 -10000 0 -0.24 8 8
RAF1 0.002 0.14 -10000 0 -0.89 7 7
Fc epsilon R1/FcgammaRIIB/SHIP 0.014 0.1 -10000 0 -0.41 8 8
FCER1G -0.003 0.049 -10000 0 -10000 0 0
FCER1A 0.007 0.11 -10000 0 -0.65 8 8
Antigen/IgE/Fc epsilon R1/Fyn 0.03 0.08 -10000 0 -0.37 8 8
MAPK3 0.002 0.13 -10000 0 -0.81 7 7
MAPK1 -0.007 0.14 -10000 0 -0.9 7 7
NFKB1 0.027 0.006 -10000 0 -10000 0 0
MAPK8 0.01 0.15 -10000 0 -0.63 12 12
DUSP1 0.025 0.039 -10000 0 -0.64 1 1
NF-kappa-B/RelA 0.02 0.046 0.15 4 -10000 0 4
actin cytoskeleton reorganization 0.016 0.13 -10000 0 -0.9 4 4
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.01 0.083 -10000 0 -0.43 4 4
FER -0.008 0.061 -10000 0 -0.36 3 3
RELA 0.028 0.002 -10000 0 -10000 0 0
ITK 0.005 0.026 -10000 0 -0.21 3 3
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 0.011 0.1 0.34 8 -0.46 5 13
cytokine secretion 0.009 0.029 -10000 0 -10000 0 0
SPHK1 -0.022 0.06 -10000 0 -0.36 3 3
PTK2 0.015 0.14 -10000 0 -0.98 4 4
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.002 0.082 -10000 0 -0.46 2 2
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.034 0.14 0.44 15 -0.43 2 17
MAP2K2 -0.002 0.13 -10000 0 -0.83 7 7
MAP2K1 -0.002 0.13 -10000 0 -0.83 7 7
MAP2K7 0.028 0.002 -10000 0 -10000 0 0
KLRG1/SHP2 0.005 0.06 -10000 0 -0.28 3 3
MAP2K4 0.011 0.14 -10000 0 -0.79 9 9
Fc epsilon R1/FcgammaRIIB 0.008 0.1 -10000 0 -0.43 8 8
mol:Choline -0.027 0.065 0.34 2 -0.35 7 9
SHC/Grb2/SOS1 0.042 0.072 -10000 0 -0.32 3 3
FYN 0.027 0.005 -10000 0 -10000 0 0
DOK1 0.026 0.012 -10000 0 -10000 0 0
PXN 0.02 0.14 0.38 8 -0.86 4 12
HCLS1 -0.008 0.061 -10000 0 -0.36 3 3
PRKCB 0.041 0.13 0.45 16 -0.33 2 18
FCGR2B -0.007 0.061 -10000 0 -0.64 1 1
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP 0.008 0.065 -10000 0 -0.31 3 3
LCP2 0.025 0.018 -10000 0 -10000 0 0
PLA2G4A -0.011 0.077 -10000 0 -0.41 7 7
RASA1 0.027 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.027 0.065 0.34 2 -0.35 7 9
IKK complex 0.035 0.11 0.39 16 -10000 0 16
WIPF1 0.027 0.007 -10000 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.003 0.032 0.15 7 -0.13 6 13
BUB1B 0.008 0.036 0.14 6 -0.18 1 7
PLK1 0.009 0.03 0.12 12 -10000 0 12
PLK1S1 0.014 0.025 0.12 10 -10000 0 10
KIF2A 0.008 0.037 0.27 3 -10000 0 3
regulation of mitotic centrosome separation 0.009 0.03 0.12 12 -10000 0 12
GOLGA2 0.027 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.026 0.043 -10000 0 -10000 0 0
WEE1 0.016 0.053 -10000 0 -0.32 5 5
cytokinesis 0.004 0.058 0.23 4 -0.22 1 5
PP2A-alpha B56 0.054 0.058 -10000 0 -0.5 3 3
AURKA 0.012 0.02 0.12 2 -10000 0 2
PICH/PLK1 0.011 0.025 -10000 0 -10000 0 0
CENPE 0.006 0.032 0.23 2 -10000 0 2
RhoA/GTP 0.02 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.037 0.27 3 -10000 0 3
PPP2CA 0.027 0.004 -10000 0 -10000 0 0
FZR1 0.028 0.003 -10000 0 -10000 0 0
TPX2 0.01 0.027 0.12 11 -10000 0 11
PAK1 0.028 0.004 -10000 0 -10000 0 0
SPC24 0.006 0.042 -10000 0 -10000 0 0
FBXW11 0.027 0.005 -10000 0 -10000 0 0
CLSPN -0.007 0.068 -10000 0 -0.24 22 22
GORASP1 0.027 0.006 -10000 0 -10000 0 0
metaphase 0.001 0.005 0.019 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.004 0.017 0.066 12 -10000 0 12
G2 phase of mitotic cell cycle 0 0.003 0.011 8 -10000 0 8
STAG2 0.028 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.09 -10000 0 -0.52 8 8
spindle elongation 0.009 0.03 0.12 12 -10000 0 12
ODF2 0.027 0.006 -10000 0 -10000 0 0
BUB1 0.02 0.059 -10000 0 -0.53 3 3
TPT1 0.005 0.044 0.1 2 -0.2 11 13
CDC25C 0.007 0.038 -10000 0 -0.3 3 3
CDC25B 0.027 0.01 -10000 0 -10000 0 0
SGOL1 0.003 0.032 0.13 6 -0.15 7 13
RHOA 0.027 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.039 0.026 -10000 0 -10000 0 0
CDC14B 0.006 0.003 -10000 0 -10000 0 0
CDC20 0.015 0.032 -10000 0 -10000 0 0
PLK1/PBIP1 0.007 0.026 0.11 5 -10000 0 5
mitosis -0.002 0.002 -10000 0 -10000 0 0
FBXO5 0.006 0.03 0.12 5 -10000 0 5
CDC2 0.001 0.001 -10000 0 -10000 0 0
NDC80 0.015 0.032 -10000 0 -10000 0 0
metaphase plate congression -0.006 0.074 -10000 0 -0.24 25 25
ERCC6L 0.016 0.028 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.009 0.025 0.11 10 -0.11 1 11
microtubule cytoskeleton organization 0.005 0.044 0.1 2 -0.2 11 13
G2/M transition DNA damage checkpoint 0 0.002 0.012 3 -10000 0 3
PPP1R12A 0.028 0.006 -10000 0 -10000 0 0
interphase 0 0.002 0.012 3 -10000 0 3
PLK1/PRC1-2 0.02 0.044 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.047 0.027 -10000 0 -10000 0 0
RAB1A 0.027 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.008 0.025 0.1 13 -10000 0 13
mitotic prometaphase 0.001 0.005 0.017 25 -10000 0 25
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.037 -10000 0 -0.29 3 3
microtubule-based process 0.009 0.037 0.14 1 -10000 0 1
Golgi organization 0.009 0.03 0.12 12 -10000 0 12
Cohesin/SA2 0.025 0.023 -10000 0 -10000 0 0
PPP1CB/MYPT1 0.039 0.011 -10000 0 -10000 0 0
KIF20A -0.008 0.05 -10000 0 -10000 0 0
APC/C/CDC20 0.023 0.029 0.14 1 -10000 0 1
PPP2R1A 0.028 0.003 -10000 0 -10000 0 0
chromosome segregation 0.007 0.026 0.11 5 -10000 0 5
PRC1 0.024 0.02 -10000 0 -10000 0 0
ECT2 0.014 0.057 0.27 11 -10000 0 11
C13orf34 0.007 0.024 0.097 12 -10000 0 12
NUDC -0.006 0.074 -10000 0 -0.24 25 25
regulation of attachment of spindle microtubules to kinetochore 0.008 0.036 0.14 6 -0.18 1 7
spindle assembly 0.011 0.036 0.13 16 -10000 0 16
spindle stabilization 0.014 0.025 0.12 10 -10000 0 10
APC/C/HCDH1 0.025 0.006 -10000 0 -10000 0 0
MKLP2/PLK1 0.009 0.037 0.14 1 -10000 0 1
CCNB1 0.027 0.013 -10000 0 -10000 0 0
PPP1CB 0.028 0.005 -10000 0 -10000 0 0
BTRC 0.028 0.004 -10000 0 -10000 0 0
ROCK2 0.005 0.082 0.27 1 -0.36 11 12
TUBG1 0.012 0.027 0.13 6 -0.23 1 7
G2/M transition of mitotic cell cycle 0.007 0.019 -10000 0 -10000 0 0
MLF1IP 0.002 0.017 -10000 0 -10000 0 0
INCENP 0.028 0.002 -10000 0 -10000 0 0
IL1-mediated signaling events

Figure S72.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S72.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.02 0.004 -9999 0 -10000 0 0
PRKCZ 0.025 0.008 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.027 0.006 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.019 0.043 -9999 0 -10000 0 0
IRAK/TOLLIP 0.031 0.007 -9999 0 -10000 0 0
IKBKB 0.027 0.005 -9999 0 -10000 0 0
IKBKG 0.028 0.002 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.1 0.22 -9999 0 -0.48 74 74
IL1A 0.01 0.037 -9999 0 -10000 0 0
IL1B 0.004 0.065 -9999 0 -0.48 5 5
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.032 -9999 0 -10000 0 0
IL1R2 -0.14 0.29 -9999 0 -0.64 74 74
IL1R1 0.028 0.003 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.015 0.036 -9999 0 -10000 0 0
TOLLIP 0.028 0.003 -9999 0 -10000 0 0
TICAM2 0.025 0.04 -9999 0 -0.64 1 1
MAP3K3 0.026 0.008 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.003 -9999 0 -10000 0 0
IKK complex/ELKS 0.034 0.047 -9999 0 -10000 0 0
JUN -0.009 0.033 -9999 0 -0.31 2 2
MAP3K7 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.062 0.054 -9999 0 -0.35 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88 0.063 0.022 -9999 0 -10000 0 0
PIK3R1 0.028 0.004 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.072 0.027 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP 0.035 0.055 -9999 0 -0.38 4 4
NFKB1 0.027 0.006 -9999 0 -10000 0 0
MAPK8 -0.008 0.035 -9999 0 -0.33 2 2
IRAK1 0.015 0.003 -9999 0 -10000 0 0
IL1RN/IL1R1 0.035 0.026 -9999 0 -10000 0 0
IRAK4 0.027 0.005 -9999 0 -10000 0 0
PRKCI 0.027 0.005 -9999 0 -10000 0 0
TRAF6 0.028 0.004 -9999 0 -10000 0 0
PI3K 0.04 0.009 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.02 0.041 -9999 0 -10000 0 0
CHUK 0.028 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.035 0.055 -9999 0 -0.38 4 4
IL1 beta/IL1R2 -0.088 0.2 -9999 0 -0.42 77 77
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.012 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.046 0.05 -9999 0 -0.33 4 4
IRAK3 0.026 0.01 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.06 0.056 -9999 0 -0.35 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.026 0.015 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP 0.04 0.036 -9999 0 -10000 0 0
RELA 0.028 0.002 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.025 0.017 -9999 0 -10000 0 0
MYD88 0.027 0.006 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.047 0.021 -9999 0 -10000 0 0
IL1RAP 0.026 0.012 -9999 0 -10000 0 0
UBE2N 0.027 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 0.03 0.041 -9999 0 -0.31 3 3
CASP1 0.026 0.012 -9999 0 -10000 0 0
IL1RN/IL1R2 -0.097 0.23 -9999 0 -0.48 73 73
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.049 0.054 -9999 0 -0.36 4 4
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.022 0.044 -9999 0 -10000 0 0
PIK3CA 0.027 0.005 -9999 0 -10000 0 0
IL1RN 0.02 0.032 -9999 0 -0.33 1 1
TRAF6/TAK1/TAB1/TAB2 0.038 0.011 -9999 0 -10000 0 0
MAP2K6 0.015 0.02 -9999 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.011 0.093 0.28 15 -10000 0 15
GNAI2 0.026 0.007 -10000 0 -10000 0 0
S1P/S1P5/G12 0.024 0.049 -10000 0 -0.41 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.012 0.15 -10000 0 -0.64 16 16
RhoA/GTP 0.012 0.095 -10000 0 -0.28 15 15
negative regulation of cAMP metabolic process 0.005 0.095 -10000 0 -0.3 16 16
GNAZ 0.026 0.008 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNA12 0.022 0.011 -10000 0 -10000 0 0
S1PR5 0.019 0.069 -10000 0 -0.64 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.005 0.096 -10000 0 -0.31 16 16
RhoA/GDP 0.02 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.018 0.056 -10000 0 -0.64 2 2
Ephrin B reverse signaling

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
EFNB2 0.027 0.006 -10000 0 -10000 0 0
EPHB2 0.024 0.015 -10000 0 -10000 0 0
EFNB1 -0.008 0.041 -10000 0 -0.48 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.034 0.056 -10000 0 -0.35 3 3
Ephrin B2/EPHB1-2 0.039 0.049 -10000 0 -0.38 3 3
neuron projection morphogenesis 0.011 0.051 -10000 0 -0.33 3 3
Ephrin B1/EPHB1-2/Tiam1 0.017 0.065 -10000 0 -0.37 4 4
DNM1 -0.008 0.061 -10000 0 -0.64 1 1
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.001 0.087 -10000 0 -0.38 11 11
YES1 -0.01 0.13 -10000 0 -0.62 12 12
Ephrin B1/EPHB1-2/NCK2 0.02 0.066 -10000 0 -0.37 4 4
PI3K 0.026 0.088 -10000 0 -0.39 12 12
mol:GDP 0.016 0.064 -10000 0 -0.37 4 4
ITGA2B 0.019 0.026 -10000 0 -10000 0 0
endothelial cell proliferation 0.028 0.016 -10000 0 -10000 0 0
FYN -0.009 0.13 -10000 0 -0.62 12 12
MAP3K7 -0.005 0.07 -10000 0 -0.42 8 8
FGR -0.009 0.13 -10000 0 -0.62 12 12
TIAM1 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
RGS3 0.027 0.006 -10000 0 -10000 0 0
cell adhesion -0.004 0.11 -10000 0 -0.36 22 22
LYN -0.007 0.13 -10000 0 -0.62 12 12
Ephrin B1/EPHB1-2/Src Family Kinases -0.011 0.11 -10000 0 -0.55 12 12
Ephrin B1/EPHB1-2 -0.007 0.084 -10000 0 -0.45 10 10
SRC -0.006 0.12 -10000 0 -0.6 12 12
ITGB3 -0.006 0.14 -10000 0 -0.64 13 13
EPHB1 0.017 0.07 -10000 0 -0.64 3 3
EPHB4 0.022 0.012 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.017 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.008 0.11 -10000 0 -0.48 13 13
BLK -0.006 0.13 -10000 0 -0.61 12 12
HCK -0.007 0.12 -10000 0 -0.59 12 12
regulation of stress fiber formation -0.019 0.064 0.36 4 -10000 0 4
MAPK8 -0.006 0.099 0.28 2 -0.38 14 16
Ephrin B1/EPHB1-2/RGS3 0.02 0.066 -10000 0 -0.37 4 4
endothelial cell migration 0.03 0.096 0.42 1 -0.32 8 9
NCK2 0.028 0.003 -10000 0 -10000 0 0
PTPN13 0.028 0.008 -10000 0 -10000 0 0
regulation of focal adhesion formation -0.019 0.064 0.36 4 -10000 0 4
chemotaxis -0.019 0.065 0.37 4 -10000 0 4
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.051 -10000 0 -0.34 3 3
angiogenesis -0.009 0.091 -10000 0 -0.44 12 12
LCK -0.008 0.13 -10000 0 -0.62 12 12
TCGA08_p53

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
CDKN2A -0.035 0.024 -10000 0 -10000 0 0
TP53 -0.01 0.034 -10000 0 -0.2 9 9
Senescence -0.01 0.035 -10000 0 -0.19 10 10
Apoptosis -0.01 0.035 -10000 0 -0.19 10 10
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.028 0.058 0.33 10 -10000 0 10
MDM4 0.027 0.006 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.023 0.008 -10000 0 -10000 0 0
AES 0.025 0.005 -10000 0 -10000 0 0
FBXW11 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.032 0.019 -10000 0 -10000 0 0
SMAD4 0.026 0.008 -10000 0 -10000 0 0
DKK2 0.021 0.042 -10000 0 -0.64 1 1
TLE1 0.024 0.007 -10000 0 -10000 0 0
MACF1 0.027 0.008 -10000 0 -10000 0 0
CTNNB1 0.067 0.11 0.42 12 -0.35 1 13
WIF1 0.008 0.025 -10000 0 -10000 0 0
beta catenin/RanBP3 0.007 0.051 0.35 1 -10000 0 1
KREMEN2 0.013 0.032 -10000 0 -10000 0 0
DKK1 0.015 0.027 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.075 0.097 0.4 10 -10000 0 10
FZD1 0.022 0.014 -10000 0 -10000 0 0
AXIN2 0.047 0.15 0.6 16 -10000 0 16
AXIN1 0.026 0.008 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.028 0.055 -10000 0 -0.57 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.015 0.14 0.29 1 -0.57 7 8
Axin1/APC/GSK3 0.049 0.075 0.3 2 -0.42 1 3
Axin1/APC/GSK3/beta catenin/Macf1 0.054 0.078 0.38 3 -0.37 1 4
HNF1A 0.015 0.078 -10000 0 -0.64 4 4
CTBP1 0.024 0.006 -10000 0 -10000 0 0
MYC 0.012 0.055 0.6 1 -10000 0 1
RANBP3 0.028 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.039 0.042 -10000 0 -0.42 1 1
NKD1 -0.15 0.29 -10000 0 -0.64 76 76
TCF4 0.023 0.008 -10000 0 -10000 0 0
TCF3 0.025 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.05 0.033 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.028 0.096 0.42 1 -0.4 7 8
LEF1 -0.029 0.18 -10000 0 -0.64 23 23
DVL1 0.022 0.046 -10000 0 -0.56 1 1
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.041 0.1 0.33 2 -0.47 2 4
DKK1/LRP6/Kremen 2 0.036 0.035 -10000 0 -10000 0 0
LRP6 0.027 0.006 -10000 0 -10000 0 0
CSNK1A1 0.025 0.006 -10000 0 -10000 0 0
NLK 0.027 0.008 -10000 0 -10000 0 0
CCND1 0.007 0.1 0.9 1 -1.4 1 2
WNT1 0.014 0.032 -10000 0 -10000 0 0
GSK3A 0.029 0.004 -10000 0 -10000 0 0
GSK3B 0.027 0.006 -10000 0 -10000 0 0
FRAT1 0.027 0.004 -10000 0 -10000 0 0
PPP2R5D 0.078 0.16 0.31 73 -0.33 9 82
APC 0.064 0.12 0.5 12 -10000 0 12
WNT1/LRP6/FZD1 0.017 0.024 -10000 0 -10000 0 0
CREBBP 0.023 0.008 -10000 0 -10000 0 0
Wnt 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
Noncanonical Wnts/FZD -0.001 0.09 -9999 0 -0.31 19 19
FZD6 0.027 0.004 -9999 0 -10000 0 0
WNT6 0.021 0.042 -9999 0 -0.64 1 1
WNT4 0.005 0.11 -9999 0 -0.6 9 9
FZD3 0.027 0.006 -9999 0 -10000 0 0
WNT5A 0.012 0.037 -9999 0 -10000 0 0
WNT11 -0.003 0.13 -9999 0 -0.64 12 12
Arf6 trafficking 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
SLC2A4 0.021 0.046 -10000 0 -0.48 2 2
CLTC 0.013 0.093 -10000 0 -0.38 14 14
calcium ion-dependent exocytosis 0.022 0.052 -10000 0 -0.26 4 4
Dynamin 2/GTP 0.025 0.011 -10000 0 -10000 0 0
EXOC4 0.022 0.012 -10000 0 -10000 0 0
CD59 0.009 0.079 -10000 0 -0.32 14 14
CPE 0.013 0.008 -10000 0 -10000 0 0
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
membrane fusion 0.026 0.038 -10000 0 -10000 0 0
CTNND1 0.024 0.045 -10000 0 -10000 0 0
DNM2 0.028 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.015 0.061 -10000 0 -0.29 5 5
TSHR 0.009 0.012 -10000 0 -10000 0 0
INS 0.01 0.063 -10000 0 -0.48 4 4
BIN1 0.023 0.055 -10000 0 -0.64 2 2
mol:Choline 0.026 0.038 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.007 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.024 0.011 -10000 0 -10000 0 0
JUP 0.007 0.078 -10000 0 -0.32 14 14
ASAP2/amphiphysin II 0.045 0.046 -10000 0 -0.38 3 3
ARF6/GTP 0.02 0.005 -10000 0 -10000 0 0
CDH1 -0.008 0.12 -10000 0 -0.42 14 14
clathrin-independent pinocytosis 0.02 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.024 0.017 -10000 0 -10000 0 0
positive regulation of endocytosis 0.02 0.005 -10000 0 -10000 0 0
EXOC2 0.027 0.006 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.011 0.052 -10000 0 -0.31 5 5
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.026 0.008 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.019 0.11 0.48 7 -10000 0 7
positive regulation of phagocytosis 0.014 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.032 0.016 -10000 0 -10000 0 0
ACAP1 0.027 0.047 -10000 0 -0.22 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.005 0.074 -10000 0 -0.32 14 14
clathrin heavy chain/ACAP1 0.019 0.083 0.26 1 -0.38 5 6
JIP4/KLC1 0.047 0.019 -10000 0 -10000 0 0
EXOC1 0.027 0.006 -10000 0 -10000 0 0
exocyst 0.011 0.052 -10000 0 -0.31 5 5
RALA/GTP 0.016 0.009 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.033 0.013 -10000 0 -10000 0 0
receptor recycling 0.02 0.005 -10000 0 -10000 0 0
CTNNA1 0.021 0.041 -10000 0 -10000 0 0
NME1 0.013 0.007 -10000 0 -10000 0 0
clathrin coat assembly 0.02 0.099 0.25 4 -0.37 14 18
IL2RA 0.007 0.081 -10000 0 -0.33 14 14
VAMP3 0.014 0.005 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.025 0.079 -10000 0 -0.37 5 5
EXOC6 0.028 0.004 -10000 0 -10000 0 0
PLD1 0.011 0.012 -10000 0 -10000 0 0
PLD2 0.01 0.012 -10000 0 -10000 0 0
EXOC5 0.027 0.006 -10000 0 -10000 0 0
PIP5K1C 0.015 0.061 -10000 0 -0.3 5 5
SDC1 0.008 0.08 -10000 0 -0.32 14 14
ARF6/GDP 0.023 0.01 -10000 0 -10000 0 0
EXOC7 0.026 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.02 0.12 -10000 0 -0.5 7 7
mol:Phosphatidic acid 0.026 0.038 -10000 0 -10000 0 0
endocytosis -0.044 0.045 0.37 3 -10000 0 3
SCAMP2 0.028 0.004 -10000 0 -10000 0 0
ADRB2 0.023 0.11 0.32 8 -0.43 5 13
EXOC3 0.027 0.005 -10000 0 -10000 0 0
ASAP2 0.025 0.039 -10000 0 -0.64 1 1
Dynamin 2/GDP 0.028 0.012 -10000 0 -10000 0 0
KLC1 0.026 0.007 -10000 0 -10000 0 0
AVPR2 -0.25 0.17 0.28 2 -0.34 170 172
RALA 0.022 0.011 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.017 0.11 0.33 1 -0.47 7 8
BCR signaling pathway

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
JUN 0.011 0.12 0.35 3 -0.46 9 12
IKBKB 0.029 0.091 0.29 7 -0.33 2 9
AKT1 0.013 0.094 0.31 17 -10000 0 17
IKBKG 0.034 0.08 0.29 7 -0.27 3 10
CALM1 0.002 0.088 0.36 1 -0.4 6 7
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.033 0.12 0.38 5 -0.46 7 12
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0.092 -10000 0 -0.4 7 7
DOK1 0.026 0.012 -10000 0 -10000 0 0
AP-1 -0.01 0.094 0.24 4 -0.26 13 17
LYN 0.027 0.005 -10000 0 -10000 0 0
BLNK 0.004 0.12 -10000 0 -0.64 10 10
SHC1 0.027 0.005 -10000 0 -10000 0 0
BCR complex 0.02 0.063 -10000 0 -0.42 4 4
CD22 -0.002 0.065 -10000 0 -0.51 3 3
CAMK2G -0.001 0.085 0.34 1 -0.39 5 6
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
INPP5D 0.024 0.02 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.011 0.073 -10000 0 -0.37 8 8
GO:0007205 0 0.093 -10000 0 -0.4 7 7
SYK 0.024 0.04 -10000 0 -0.64 1 1
ELK1 -0.001 0.091 0.25 1 -0.4 6 7
NFATC1 0 0.082 0.34 4 -0.4 2 6
B-cell antigen/BCR complex 0.02 0.063 -10000 0 -0.42 4 4
PAG1/CSK 0.04 0.008 -10000 0 -10000 0 0
NFKBIB 0.027 0.051 0.16 9 -0.13 14 23
HRAS 0.004 0.083 0.27 1 -0.44 3 4
NFKBIA 0.027 0.05 0.16 9 -0.12 13 22
NF-kappa-B/RelA/I kappa B beta 0.031 0.045 0.16 8 -10000 0 8
RasGAP/Csk 0.051 0.063 -10000 0 -0.36 3 3
mol:GDP 0.001 0.092 -10000 0 -0.4 7 7
PTEN 0.028 0.004 -10000 0 -10000 0 0
CD79B 0.021 0.056 -10000 0 -0.64 2 2
NF-kappa-B/RelA/I kappa B alpha 0.032 0.044 0.16 8 -10000 0 8
GRB2 0.026 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.019 0.1 0.45 2 -0.51 2 4
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 -0.001 0.092 -10000 0 -0.41 7 7
CSK 0.028 0.004 -10000 0 -10000 0 0
FOS -0.043 0.14 -10000 0 -0.44 18 18
CHUK 0.03 0.088 0.29 7 -0.28 4 11
IBTK 0.027 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.044 0.1 0.31 4 -0.39 3 7
PTPN6 -0.007 0.061 -10000 0 -0.56 2 2
RELA 0.028 0.002 -10000 0 -10000 0 0
BCL2A1 0.019 0.031 0.15 3 -10000 0 3
VAV2 -0.001 0.072 -10000 0 -0.49 3 3
ubiquitin-dependent protein catabolic process 0.029 0.05 0.16 9 -0.12 13 22
BTK 0.01 0.077 -10000 0 -0.89 2 2
CD19 -0.002 0.062 -10000 0 -0.51 3 3
MAP4K1 0.014 0.036 -10000 0 -10000 0 0
CD72 0.02 0.028 -10000 0 -10000 0 0
PAG1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.033 0.11 0.34 6 -0.39 7 13
SH3BP5 0.004 0.12 -10000 0 -0.64 10 10
PIK3AP1 0.001 0.098 -10000 0 -0.42 8 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.01 0.12 -10000 0 -0.49 14 14
RAF1 0.006 0.08 0.29 2 -0.42 3 5
RasGAP/p62DOK/SHIP 0.048 0.065 -10000 0 -0.35 3 3
CD79A 0.01 0.064 -10000 0 -0.64 2 2
re-entry into mitotic cell cycle -0.01 0.093 0.24 4 -0.25 14 18
RASA1 0.027 0.004 -10000 0 -10000 0 0
MAPK3 0.016 0.09 0.33 10 -0.33 2 12
MAPK1 0.005 0.07 0.26 2 -0.35 3 5
CD72/SHP1 0.014 0.077 0.34 2 -0.53 2 4
NFKB1 0.027 0.006 -10000 0 -10000 0 0
MAPK8 0.027 0.11 0.34 6 -0.4 8 14
actin cytoskeleton organization 0.034 0.1 0.33 5 -0.43 3 8
NF-kappa-B/RelA 0.062 0.085 0.27 10 -10000 0 10
Calcineurin 0.03 0.087 0.32 1 -0.39 3 4
PI3K 0.002 0.059 -10000 0 -0.39 2 2
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.004 0.095 0.25 7 -0.43 8 15
SOS1 0.027 0.005 -10000 0 -10000 0 0
Bam32/HPK1 0.008 0.16 -10000 0 -0.65 14 14
DAPP1 -0.01 0.17 -10000 0 -0.72 14 14
cytokine secretion 0.001 0.079 0.34 4 -0.37 2 6
mol:DAG -0.001 0.092 -10000 0 -0.41 7 7
PLCG2 -0.003 0.13 -10000 0 -0.64 12 12
MAP2K1 0.006 0.076 0.28 2 -0.39 3 5
B-cell antigen/BCR complex/FcgammaRIIB 0.006 0.072 -10000 0 -0.42 4 4
mol:PI-3-4-5-P3 -0.016 0.048 0.24 1 -0.31 1 2
ETS1 -0.003 0.079 0.33 1 -0.36 5 6
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.05 0.094 -10000 0 -0.4 9 9
B-cell antigen/BCR complex/LYN 0.008 0.067 -10000 0 -0.52 3 3
MALT1 0.026 0.008 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.034 0.1 0.33 2 -0.45 3 5
B-cell antigen/BCR complex/LYN/SYK 0.035 0.078 -10000 0 -0.55 2 2
CARD11 0.028 0.11 0.31 6 -0.45 3 9
FCGR2B -0.007 0.061 -10000 0 -0.64 1 1
PPP3CA 0.027 0.006 -10000 0 -10000 0 0
BCL10 0.026 0.007 -10000 0 -10000 0 0
IKK complex 0.023 0.052 0.18 14 -0.12 2 16
PTPRC 0.022 0.043 -10000 0 -0.64 1 1
PDPK1 -0.013 0.037 0.21 2 -10000 0 2
PPP3CB 0.028 0.004 -10000 0 -10000 0 0
PPP3CC 0.027 0.006 -10000 0 -10000 0 0
POU2F2 0.024 0.031 0.15 3 -10000 0 3
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.001 0.18 -10000 0 -0.54 16 16
MAP3K8 0.025 0.011 -10000 0 -10000 0 0
FOS 0.009 0.13 0.26 2 -0.47 12 14
PRKCA 0.02 0.018 -10000 0 -10000 0 0
PTPN7 0.017 0.046 -10000 0 -0.65 1 1
HRAS 0.027 0.007 -10000 0 -10000 0 0
PRKCB 0.019 0.022 -10000 0 -10000 0 0
NRAS 0.026 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.028 -10000 0 -10000 0 0
MAPK3 0.02 0.09 -10000 0 -0.46 8 8
MAP2K1 0.03 0.043 -10000 0 -10000 0 0
ELK1 0.019 0.024 -10000 0 -10000 0 0
BRAF 0.013 0.018 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 43 43
MAPK1 -0.006 0.14 -10000 0 -0.49 18 18
RAF1 0.016 0.023 -10000 0 -0.23 1 1
KRAS 0.026 0.006 -10000 0 -10000 0 0
ErbB2/ErbB3 signaling events

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).

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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 -0.004 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.034 0.069 -10000 0 -0.34 2 2
NFATC4 -0.008 0.075 0.31 8 -0.3 2 10
ERBB2IP 0.027 0.006 -10000 0 -10000 0 0
HSP90 (dimer) 0.026 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis 0.011 0.059 -10000 0 -0.33 7 7
JUN 0.016 0.058 0.28 1 -10000 0 1
HRAS 0.027 0.003 -10000 0 -10000 0 0
DOCK7 -0.016 0.06 0.28 1 -0.32 6 7
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.033 0.068 -10000 0 -0.37 7 7
AKT1 0.007 0.005 -10000 0 -10000 0 0
BAD -0.004 0.005 -10000 0 -10000 0 0
MAPK10 0.012 0.061 0.19 8 -10000 0 8
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.013 0.064 -10000 0 -0.36 7 7
RAF1 0.008 0.071 0.35 2 -0.37 1 3
ErbB2/ErbB3/neuregulin 2 0.025 0.057 -10000 0 -0.39 5 5
STAT3 0.03 0.053 -10000 0 -0.83 1 1
cell migration 0.025 0.088 0.31 14 -10000 0 14
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.034 0.16 0.36 1 -0.56 9 10
FOS -0.059 0.19 0.3 2 -0.5 44 46
NRAS 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.059 -10000 0 -0.33 7 7
MAPK3 -0.007 0.1 0.33 2 -10000 0 2
MAPK1 -0.036 0.18 0.35 2 -0.67 13 15
JAK2 -0.016 0.061 0.28 1 -0.32 7 8
NF2 0.009 0.038 -10000 0 -0.62 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.013 0.067 -10000 0 -0.32 8 8
NRG1 0.015 0.081 -10000 0 -0.58 5 5
GRB2/SOS1 0.038 0.012 -10000 0 -10000 0 0
MAPK8 0.013 0.074 0.25 1 -0.3 7 8
MAPK9 0.011 0.059 0.19 7 -10000 0 7
ERBB2