PARADIGM pathway analysis of mRNASeq expression data
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
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 (2015): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C10V8C08
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 30 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 134
EGFR-dependent Endothelin signaling events 113
Angiopoietin receptor Tie2-mediated signaling 101
FOXA2 and FOXA3 transcription factor networks 92
PDGFR-alpha signaling pathway 66
Thromboxane A2 receptor signaling 55
Signaling mediated by p38-alpha and p38-beta 50
Glypican 1 network 39
Endothelins 39
BMP receptor signaling 37
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 0.4621 134 4557 34 -0.3 0.01 1000 -1000 -0.015 -1000
EGFR-dependent Endothelin signaling events 0.3897 113 2380 21 -0.4 0.015 1000 -1000 -0.014 -1000
Angiopoietin receptor Tie2-mediated signaling 0.3483 101 8891 88 -0.8 0.087 1000 -1000 -0.047 -1000
FOXA2 and FOXA3 transcription factor networks 0.3172 92 4273 46 -1 0.013 1000 -1000 -0.055 -1000
PDGFR-alpha signaling pathway 0.2276 66 2922 44 -0.2 0.021 1000 -1000 -0.019 -1000
Thromboxane A2 receptor signaling 0.1897 55 5837 105 -0.4 0.075 1000 -1000 -0.034 -1000
Signaling mediated by p38-alpha and p38-beta 0.1724 50 2217 44 -0.17 0.01 1000 -1000 -0.023 -1000
Glypican 1 network 0.1345 39 1909 48 -0.23 0.02 1000 -1000 -0.017 -1000
Endothelins 0.1345 39 3801 96 -0.53 0.02 1000 -1000 -0.029 -1000
BMP receptor signaling 0.1276 37 3056 81 -0.26 0.02 1000 -1000 -0.039 -1000
Arf6 signaling events 0.1207 35 2186 62 -0.4 0.025 1000 -1000 -0.02 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1172 34 2660 78 -0.2 0.058 1000 -1000 -0.047 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1103 32 4013 125 -0.11 0.025 1000 -1000 -0.033 -1000
FOXM1 transcription factor network 0.1069 31 1618 51 -0.031 0.24 1000 -1000 -0.082 -1000
HIF-1-alpha transcription factor network 0.1034 30 2338 76 -0.082 0.21 1000 -1000 -0.052 -1000
Integrins in angiogenesis 0.1000 29 2438 84 -0.29 0.023 1000 -1000 -0.028 -1000
IL4-mediated signaling events 0.0966 28 2613 91 -0.74 0.41 1000 -1000 -0.14 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0897 26 1803 68 -0.37 0.061 1000 -1000 -0.056 -1000
amb2 Integrin signaling 0.0793 23 1922 82 -0.26 0.013 1000 -1000 -0.022 -1000
S1P1 pathway 0.0793 23 846 36 -0.17 0.01 1000 -1000 -0.02 -1000
Signaling events mediated by PTP1B 0.0724 21 1622 76 -0.4 0.072 1000 -1000 -0.026 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0724 21 1591 74 -0.4 0.028 1000 -1000 -0.04 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0724 21 2534 120 -0.16 0.091 1000 -1000 -0.033 -1000
Glucocorticoid receptor regulatory network 0.0621 18 2059 114 -0.47 0.098 1000 -1000 -0.038 -1000
TCR signaling in naïve CD8+ T cells 0.0586 17 1616 93 -0.31 0.17 1000 -1000 -0.04 -1000
Signaling events regulated by Ret tyrosine kinase 0.0552 16 1319 82 -0.057 0.01 1000 -1000 -0.04 -1000
Ephrin A reverse signaling 0.0517 15 105 7 -0.023 0.002 1000 -1000 -0.007 -1000
FoxO family signaling 0.0517 15 1002 64 -0.8 0.073 1000 -1000 -0.035 -1000
Nongenotropic Androgen signaling 0.0517 15 781 52 -0.1 0.048 1000 -1000 -0.02 -1000
Plasma membrane estrogen receptor signaling 0.0517 15 1324 86 -0.1 0.027 1000 -1000 -0.04 -1000
LPA4-mediated signaling events 0.0483 14 179 12 -0.12 0.005 1000 -1000 -0.009 -1000
Calcium signaling in the CD4+ TCR pathway 0.0483 14 436 31 -0.058 0.016 1000 -1000 -0.037 -1000
S1P3 pathway 0.0483 14 608 42 -0.085 0.015 1000 -1000 -0.035 -1000
E-cadherin signaling in keratinocytes 0.0483 14 620 43 -0.15 0.011 1000 -1000 -0.016 -1000
E-cadherin signaling events 0.0483 14 72 5 -0.027 0.01 1000 -1000 -0.002 -1000
Signaling events mediated by the Hedgehog family 0.0414 12 665 52 -0.032 0.015 1000 -1000 -0.029 -1000
IL27-mediated signaling events 0.0414 12 630 51 -0.92 0.34 1000 -1000 -0.03 -1000
IL6-mediated signaling events 0.0414 12 905 75 -0.19 0.035 1000 -1000 -0.038 -1000
Syndecan-1-mediated signaling events 0.0379 11 402 34 -0.021 0.019 1000 -1000 -0.022 -1000
p75(NTR)-mediated signaling 0.0379 11 1444 125 -0.25 0.028 1000 -1000 -0.039 -1000
TCGA08_rtk_signaling 0.0379 11 304 26 -0.16 0.021 1000 -1000 -0.004 -1000
E-cadherin signaling in the nascent adherens junction 0.0379 11 871 76 -0.027 0.019 1000 -1000 -0.033 -1000
Coregulation of Androgen receptor activity 0.0345 10 787 76 -0.54 0.017 1000 -1000 -0.028 -1000
IL12-mediated signaling events 0.0345 10 938 87 -0.092 0.089 1000 -1000 -0.091 -1000
EPHB forward signaling 0.0345 10 903 85 -0.12 0.044 1000 -1000 -0.035 -1000
ErbB4 signaling events 0.0310 9 624 69 -0.16 0.078 1000 -1000 -0.02 -1000
Osteopontin-mediated events 0.0310 9 360 38 -0.058 0.016 1000 -1000 -0.022 -1000
Noncanonical Wnt signaling pathway 0.0310 9 249 26 -0.071 0.016 1000 -1000 -0.019 -1000
S1P5 pathway 0.0310 9 153 17 -0.029 0.01 1000 -1000 -0.014 -1000
S1P4 pathway 0.0310 9 225 25 -0.029 0.019 1000 -1000 -0.016 -1000
Regulation of nuclear SMAD2/3 signaling 0.0276 8 1196 136 -0.33 0.048 1000 -1000 -0.031 -1000
Presenilin action in Notch and Wnt signaling 0.0276 8 496 61 -0.12 0.074 1000 -1000 -0.039 -1000
Ceramide signaling pathway 0.0276 8 680 76 -0.4 0.18 1000 -1000 -0.025 -1000
Reelin signaling pathway 0.0276 8 499 56 -0.095 0.034 1000 -1000 -0.015 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0276 8 464 52 -0.18 0.04 1000 -1000 -0.026 -1000
Regulation of Telomerase 0.0276 8 836 102 -0.39 0.027 1000 -1000 -0.042 -1000
Visual signal transduction: Rods 0.0276 8 465 52 -0.11 0.016 1000 -1000 -0.015 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0241 7 217 28 -0.085 0.038 1000 -1000 -0.018 -1000
Fc-epsilon receptor I signaling in mast cells 0.0241 7 698 97 -0.058 0.063 1000 -1000 -0.039 -1000
IL23-mediated signaling events 0.0241 7 458 60 -0.013 0.093 1000 -1000 -0.067 -1000
Regulation of Androgen receptor activity 0.0241 7 536 70 -0.66 0.016 1000 -1000 -0.036 -1000
Caspase cascade in apoptosis 0.0207 6 470 74 -0.37 0.027 1000 -1000 -0.018 -1000
Effects of Botulinum toxin 0.0207 6 177 26 -0.12 0.016 1000 -1000 -0.012 -1000
Wnt signaling 0.0207 6 42 7 -0.009 0.01 1000 -1000 -0.013 -1000
Syndecan-4-mediated signaling events 0.0207 6 442 67 -0.24 0.035 1000 -1000 -0.02 -1000
Class IB PI3K non-lipid kinase events 0.0207 6 18 3 0 0 1000 -1000 -0.002 -1000
Syndecan-2-mediated signaling events 0.0172 5 379 69 -0.26 0.023 1000 -1000 -0.015 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0172 5 432 85 -0.091 0.022 1000 -1000 -0.024 -1000
IL1-mediated signaling events 0.0172 5 358 62 -0.11 0.027 1000 -1000 -0.026 -1000
BCR signaling pathway 0.0172 5 565 99 -0.031 0.041 1000 -1000 -0.037 -1000
PDGFR-beta signaling pathway 0.0172 5 554 97 -0.007 0.031 1000 -1000 -0.031 -1000
Ras signaling in the CD4+ TCR pathway 0.0172 5 92 17 -0.021 0.015 1000 -1000 -0.02 -1000
Syndecan-3-mediated signaling events 0.0138 4 143 35 -0.091 0.028 1000 -1000 -0.017 -1000
Regulation of p38-alpha and p38-beta 0.0138 4 221 54 -0.1 0.039 1000 -1000 -0.032 -1000
LPA receptor mediated events 0.0138 4 454 102 -0.085 0.051 1000 -1000 -0.036 -1000
ErbB2/ErbB3 signaling events 0.0103 3 225 65 -0.005 0.11 1000 -1000 -0.024 -1000
Cellular roles of Anthrax toxin 0.0103 3 142 39 -0.091 0.013 1000 -1000 -0.01 -1000
IFN-gamma pathway 0.0103 3 251 68 -0.17 0.033 1000 -1000 -0.041 -1000
Nectin adhesion pathway 0.0103 3 228 63 -0.027 0.023 1000 -1000 -0.035 -1000
HIF-2-alpha transcription factor network 0.0103 3 137 43 -0.16 0.084 1000 -1000 -0.043 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0103 3 291 83 -0.18 0.021 1000 -1000 -0.03 -1000
Canonical Wnt signaling pathway 0.0103 3 196 51 -0.12 0.074 1000 -1000 -0.03 -1000
IGF1 pathway 0.0103 3 223 57 -0.011 0.024 1000 -1000 -0.024 -1000
Insulin Pathway 0.0103 3 224 74 -0.021 0.029 1000 -1000 -0.027 -1000
Signaling events mediated by HDAC Class II 0.0069 2 171 75 -0.083 0.028 1000 -1000 -0.015 -1000
BARD1 signaling events 0.0069 2 161 57 -0.018 0.039 1000 -1000 -0.026 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0069 2 152 54 -0.017 0.035 1000 -1000 -0.03 -1000
FAS signaling pathway (CD95) 0.0069 2 117 47 -0.089 0.015 1000 -1000 -0.029 -1000
Signaling mediated by p38-gamma and p38-delta 0.0069 2 32 15 -0.002 0.012 1000 -1000 -0.01 -1000
IL2 signaling events mediated by PI3K 0.0069 2 152 58 -0.007 0.063 1000 -1000 -0.031 -1000
Class I PI3K signaling events 0.0069 2 159 73 -0.015 0.036 1000 -1000 -0.026 -1000
VEGFR1 specific signals 0.0069 2 117 56 0 0.027 1000 -1000 -0.03 -1000
Aurora B signaling 0.0069 2 184 67 -0.21 0.032 1000 -1000 -0.024 -1000
Hedgehog signaling events mediated by Gli proteins 0.0034 1 98 65 -0.029 0.028 1000 -1000 -0.037 -1000
mTOR signaling pathway 0.0034 1 70 53 -0.002 0.017 1000 -1000 -0.025 -1000
Ephrin B reverse signaling 0.0034 1 87 48 -0.013 0.02 1000 -1000 -0.014 -1000
Signaling events mediated by HDAC Class I 0.0034 1 159 104 -0.083 0.028 1000 -1000 -0.03 -1000
Retinoic acid receptors-mediated signaling 0.0034 1 80 58 -0.031 0.029 1000 -1000 -0.025 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0034 1 62 33 -0.038 0.029 1000 -1000 -0.022 -1000
Signaling events mediated by PRL 0.0034 1 53 34 -0.018 0.015 1000 -1000 -0.023 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 10 23 0.002 0.026 1000 -1000 -0.023 -1000
Canonical NF-kappaB pathway 0.0000 0 6 39 0 0.035 1000 -1000 -0.028 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.008 0.01 1000 -1000 -0.006 -1000
Visual signal transduction: Cones 0.0000 0 28 38 0 0.017 1000 -1000 -0.012 -1000
Circadian rhythm pathway 0.0000 0 8 22 -0.007 0.026 1000 -1000 -0.027 -1000
JNK signaling in the CD4+ TCR pathway 0.0000 0 12 17 0.008 0.028 1000 -1000 -0.018 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0.01 0.015 1000 -1000 -0.002 -1000
Aurora A signaling 0.0000 0 12 60 0 0.025 1000 -1000 -0.015 -1000
Arf6 downstream pathway 0.0000 0 0 43 -0.027 0.028 1000 -1000 -0.027 -1000
Aurora C signaling 0.0000 0 0 7 0 0.01 1000 -1000 -0.01 -1000
EPO signaling pathway 0.0000 0 45 55 -0.015 0.035 1000 -1000 -0.027 -1000
PLK1 signaling events 0.0000 0 58 85 -0.009 0.031 1000 -1000 -0.023 -1000
Insulin-mediated glucose transport 0.0000 0 8 32 -0.007 0.02 1000 -1000 -0.019 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 9 68 -0.026 0.032 1000 -1000 -0.022 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0000 0 5 37 0 0.029 1000 -1000 -0.016 -1000
Signaling events mediated by HDAC Class III 0.0000 0 18 40 -0.018 0.018 1000 -1000 -0.009 -1000
TRAIL signaling pathway 0.0000 0 3 48 0 0.029 1000 -1000 -0.023 -1000
ceramide signaling pathway 0.0000 0 17 49 0 0.025 1000 -1000 -0.023 -1000
TCGA08_p53 0.0000 0 0 7 0 0.01 1000 -1000 -0.001 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 2 36 -0.024 0.025 1000 -1000 -0.019 -1000
Atypical NF-kappaB pathway 0.0000 0 20 31 0 0.023 1000 -1000 -0.018 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0000 0 12 45 0.002 0.047 1000 -1000 -0.035 -1000
Glypican 2 network 0.0000 0 0 4 0.005 0.007 1000 -1000 -0.003 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 3 27 -0.001 0.025 1000 -1000 -0.02 -1000
IL2 signaling events mediated by STAT5 0.0000 0 0 22 0.004 0.048 1000 -1000 -0.035 -1000
Arf6 trafficking events 0.0000 0 11 71 -0.16 0.019 1000 -1000 -0.022 -1000
TCGA08_retinoblastoma 0.0000 0 5 8 -0.035 0.033 1000 -1000 -0.001 -1000
Rapid glucocorticoid signaling 0.0000 0 9 20 -0.001 0.013 1000 -1000 -0.007 -1000
p38 MAPK signaling pathway 0.0000 0 19 44 -0.001 0.023 1000 -1000 -0.025 -1000
Arf1 pathway 0.0000 0 0 54 0 0.019 1000 -1000 -0.019 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.029 1000 -1000 -0.002 -1000
Total NA 1624 102591 7203 -19 5.4 131000 -131000 -3.5 -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 0.25 0.18 0.36 195 -10000 0 195
KIRREL -0.075 0.13 -10000 0 -0.48 27 27
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.25 0.18 -10000 0 -0.37 195 195
PLCG1 0.01 0 -10000 0 -10000 0 0
ARRB2 0.01 0.001 -10000 0 -10000 0 0
WASL 0.01 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.24 0.18 -10000 0 -0.33 216 216
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.25 0.19 -10000 0 -0.34 216 216
FYN -0.23 0.17 -10000 0 -0.32 216 216
mol:Ca2+ -0.24 0.18 -10000 0 -0.33 216 216
mol:DAG -0.24 0.18 -10000 0 -0.33 216 216
NPHS2 -0.2 0.22 -10000 0 -0.48 109 109
mol:IP3 -0.24 0.18 -10000 0 -0.33 216 216
regulation of endocytosis -0.22 0.16 -10000 0 -0.3 216 216
Nephrin/NEPH1/podocin/Cholesterol -0.25 0.18 -10000 0 -0.33 216 216
establishment of cell polarity -0.25 0.18 -10000 0 -0.36 195 195
Nephrin/NEPH1/podocin/NCK1-2 -0.22 0.17 -10000 0 -0.3 216 216
Nephrin/NEPH1/beta Arrestin2 -0.22 0.17 -10000 0 -0.3 216 216
NPHS1 -0.3 0.22 -10000 0 -0.47 187 187
Nephrin/NEPH1/podocin -0.24 0.17 -10000 0 -0.32 216 216
TJP1 0.01 0 -10000 0 -10000 0 0
NCK1 0.01 0 -10000 0 -10000 0 0
NCK2 0.01 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.24 0.18 -10000 0 -0.33 216 216
CD2AP 0.01 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.24 0.18 -10000 0 -0.33 216 216
GRB2 0.01 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.28 0.19 -10000 0 -0.35 235 235
cytoskeleton organization -0.29 0.21 -10000 0 -0.39 216 216
Nephrin/NEPH1 -0.17 0.13 -10000 0 -0.26 195 195
Nephrin/NEPH1/ZO-1 -0.19 0.15 -10000 0 -0.29 195 195
EGFR-dependent Endothelin signaling events

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
HRAS 0.01 0 -9999 0 -10000 0 0
EGFR 0.01 0 -9999 0 -10000 0 0
EGF/EGFR -0.2 0.078 -9999 0 -0.22 264 264
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.19 0.073 -9999 0 -0.22 261 261
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.01 0.093 -9999 0 -0.44 13 13
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.4 0.14 -9999 0 -0.44 261 261
EGF/EGFR dimer/SHC -0.23 0.083 -9999 0 -0.26 261 261
mol:GDP -0.19 0.072 -9999 0 -0.21 261 261
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.008 0.026 -9999 0 -0.44 1 1
GRB2/SOS1 0.015 0 -9999 0 -10000 0 0
HRAS/GTP -0.18 0.065 -9999 0 -0.2 261 261
SHC1 0.01 0 -9999 0 -10000 0 0
HRAS/GDP -0.18 0.068 -9999 0 -0.2 261 261
FRAP1 -0.18 0.064 -9999 0 -0.2 261 261
EGF/EGFR dimer -0.28 0.097 -9999 0 -0.31 261 261
SOS1 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.001 0.07 -9999 0 -0.31 14 14
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.54 0.52 -10000 0 -0.98 166 166
NCK1/PAK1/Dok-R -0.25 0.22 -10000 0 -0.44 166 166
NCK1/Dok-R -0.66 0.65 -10000 0 -1.2 166 166
PIK3CA 0.011 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.082 0.11 0.23 96 -10000 0 96
RELA 0.01 0 -10000 0 -10000 0 0
SHC1 0.008 0.002 -10000 0 -10000 0 0
Rac/GDP 0.007 0 -10000 0 -10000 0 0
F2 0.087 0.11 0.24 96 -10000 0 96
TNIP2 0.01 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.6 0.59 -10000 0 -1.1 166 166
FN1 0.009 0.003 -10000 0 -10000 0 0
PLD2 -0.7 0.68 -10000 0 -1.2 166 166
PTPN11 0.01 0 -10000 0 -10000 0 0
GRB14 -0.021 0.11 -10000 0 -0.44 20 20
ELK1 -0.61 0.58 -10000 0 -1.1 166 166
GRB7 0.01 0 -10000 0 -10000 0 0
PAK1 0.01 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.64 0.63 -10000 0 -1.1 166 166
CDKN1A -0.36 0.34 -10000 0 -0.65 165 165
ITGA5 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.66 0.65 -10000 0 -1.2 166 166
CRK 0.01 0 -10000 0 -10000 0 0
mol:NO -0.38 0.37 -10000 0 -0.7 166 166
PLG -0.8 0.66 -10000 0 -1.3 166 166
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.51 0.48 -10000 0 -0.92 166 166
GRB2 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.008 0.002 -10000 0 -10000 0 0
ANGPT2 -0.26 0.28 -10000 0 -0.58 108 108
BMX -0.7 0.68 -10000 0 -1.2 166 166
ANGPT1 -0.44 0.57 -10000 0 -1.2 96 96
tube development -0.42 0.39 -10000 0 -0.74 166 166
ANGPT4 0.006 0.006 -10000 0 -10000 0 0
response to hypoxia -0.037 0.034 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.73 0.71 -10000 0 -1.3 166 166
alpha5/beta1 Integrin 0.015 0 -10000 0 -10000 0 0
FGF2 0.006 0.045 -10000 0 -0.44 3 3
STAT5A (dimer) -0.48 0.46 -10000 0 -0.86 166 166
mol:L-citrulline -0.38 0.37 -10000 0 -0.7 166 166
AGTR1 -0.13 0.21 -10000 0 -0.44 91 91
MAPK14 -0.72 0.68 -10000 0 -1.3 166 166
Tie2/SHP2 -0.58 0.57 -10000 0 -1.1 149 149
TEK -0.64 0.63 -10000 0 -1.2 149 149
RPS6KB1 -0.52 0.49 -10000 0 -0.93 166 166
Angiotensin II/AT1 -0.091 0.15 -10000 0 -0.31 91 91
Tie2/Ang1/GRB2 -0.72 0.71 -10000 0 -1.3 166 166
MAPK3 -0.62 0.6 -10000 0 -1.1 166 166
MAPK1 -0.62 0.6 -10000 0 -1.1 166 166
Tie2/Ang1/GRB7 -0.72 0.71 -10000 0 -1.3 166 166
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 -0.7 0.68 -10000 0 -1.2 166 166
PI3K -0.64 0.62 -10000 0 -1.2 166 166
FES -0.71 0.68 -10000 0 -1.3 166 166
Crk/Dok-R -0.66 0.65 -10000 0 -1.2 166 166
Tie2/Ang1/ABIN2 -0.72 0.71 -10000 0 -1.3 166 166
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.47 0.45 -10000 0 -0.85 166 166
STAT5A 0.01 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.52 0.49 -10000 0 -0.93 166 166
Tie2/Ang2 -0.6 0.57 -10000 0 -1.1 166 166
Tie2/Ang1 -0.78 0.77 -10000 0 -1.4 166 166
FOXO1 -0.48 0.46 -10000 0 -0.86 166 166
ELF1 -0.048 0.056 -10000 0 -10000 0 0
ELF2 -0.7 0.68 -10000 0 -1.2 166 166
mol:Choline -0.65 0.62 -10000 0 -1.2 166 166
cell migration -0.14 0.12 -10000 0 -0.24 166 166
FYN -0.48 0.46 -10000 0 -0.86 166 166
DOK2 0.008 0.026 -10000 0 -0.44 1 1
negative regulation of cell cycle -0.32 0.31 -10000 0 -0.59 166 166
ETS1 -0.076 0.11 -10000 0 -0.23 96 96
PXN -0.41 0.39 -10000 0 -0.75 166 166
ITGB1 0.01 0 -10000 0 -10000 0 0
NOS3 -0.44 0.43 -10000 0 -0.81 166 166
RAC1 0.01 0 -10000 0 -10000 0 0
TNF -0.076 0.11 -10000 0 -0.24 94 94
MAPKKK cascade -0.65 0.62 -10000 0 -1.2 166 166
RASA1 0.01 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.72 0.72 -10000 0 -1.3 166 166
NCK1 0.01 0 -10000 0 -10000 0 0
vasculogenesis -0.34 0.33 -10000 0 -0.62 166 166
mol:Phosphatidic acid -0.65 0.62 -10000 0 -1.2 166 166
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP -0.38 0.37 -10000 0 -0.7 166 166
Rac1/GTP -0.48 0.44 -10000 0 -0.86 166 166
MMP2 -0.7 0.68 -10000 0 -1.2 166 166
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 -0.45 0.33 -10000 0 -0.83 105 105
PCK1 -1 0.61 -10000 0 -1.4 187 187
HNF4A -0.51 0.42 -10000 0 -1 91 91
KCNJ11 -0.48 0.33 -10000 0 -0.86 103 103
AKT1 -0.26 0.13 -10000 0 -0.39 113 113
response to starvation -0.003 0.012 -10000 0 -0.14 1 1
DLK1 -0.49 0.34 -10000 0 -0.88 105 105
NKX2-1 -0.14 0.14 -10000 0 -0.47 5 5
ACADM -0.46 0.33 -10000 0 -0.82 107 107
TAT -0.43 0.2 -10000 0 -0.6 133 133
CEBPB -0.039 0.034 -10000 0 -10000 0 0
CEBPA -0.033 0.039 -10000 0 -0.44 1 1
TTR -0.69 0.37 -10000 0 -0.82 215 215
PKLR -0.54 0.44 -10000 0 -1 109 109
APOA1 -0.59 0.48 -10000 0 -1.2 96 96
CPT1C -0.46 0.34 -10000 0 -0.86 103 103
ALAS1 -0.22 0.13 -10000 0 -10000 0 0
TFRC -0.58 0.28 -10000 0 -0.73 193 193
FOXF1 0.006 0.038 -10000 0 -0.44 2 2
NF1 0.013 0 -10000 0 -10000 0 0
HNF1A (dimer) -0.053 0.072 -10000 0 -0.25 14 14
CPT1A -0.45 0.33 -10000 0 -0.83 105 105
HMGCS1 -0.45 0.33 -10000 0 -0.83 104 104
NR3C1 0.007 0.04 -10000 0 -0.17 1 1
CPT1B -0.45 0.33 -10000 0 -0.82 106 106
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.012 0.009 -10000 0 -10000 0 0
GCK -0.45 0.33 -10000 0 -0.83 105 105
CREB1 -0.09 0.065 -10000 0 -0.18 59 59
IGFBP1 -0.27 0.32 -10000 0 -1.3 21 21
PDX1 -0.26 0.16 -10000 0 -0.54 41 41
UCP2 -0.46 0.33 -10000 0 -0.83 105 105
ALDOB -0.94 0.32 -10000 0 -1 275 275
AFP -0.4 0.27 -10000 0 -0.56 136 136
BDH1 -0.46 0.33 -10000 0 -0.83 106 106
HADH -0.48 0.33 -10000 0 -0.86 103 103
F2 -0.54 0.42 -10000 0 -1.1 95 95
HNF1A -0.053 0.072 -10000 0 -0.25 14 14
G6PC -0.94 0.54 -10000 0 -1.3 197 197
SLC2A2 -0.45 0.48 -10000 0 -1.2 65 65
INS 0.003 0.038 0.15 6 -10000 0 6
FOXA1 -0.18 0.1 -10000 0 -0.23 205 205
FOXA3 -0.4 0.16 -10000 0 -0.42 268 268
FOXA2 -0.56 0.37 -10000 0 -0.93 116 116
ABCC8 -0.48 0.33 -10000 0 -0.87 101 101
ALB -0.84 0.29 -10000 0 -0.93 256 256
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 -0.17 0.22 -9999 0 -0.45 109 109
PDGF/PDGFRA/CRKL -0.11 0.16 -9999 0 -0.31 109 109
positive regulation of JUN kinase activity -0.072 0.12 -9999 0 -0.23 109 109
CRKL 0.01 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.11 0.15 -9999 0 -0.31 109 109
AP1 -0.2 0.34 -9999 0 -0.96 44 44
mol:IP3 -0.12 0.16 -9999 0 -0.33 109 109
PLCG1 -0.12 0.16 -9999 0 -0.33 109 109
PDGF/PDGFRA/alphaV Integrin -0.11 0.16 -9999 0 -0.31 109 109
RAPGEF1 0.01 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ -0.12 0.16 -9999 0 -0.33 109 109
CAV3 0.002 0.004 -9999 0 -10000 0 0
CAV1 0.01 0.001 -9999 0 -10000 0 0
SHC/Grb2/SOS1 -0.072 0.12 -9999 0 -0.23 109 109
PDGF/PDGFRA/Shf -0.11 0.16 -9999 0 -0.31 109 109
FOS -0.2 0.33 -9999 0 -0.95 44 44
JUN -0.018 0.026 -9999 0 -10000 0 0
oligodendrocyte development -0.11 0.16 -9999 0 -0.31 109 109
GRB2 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
mol:DAG -0.12 0.16 -9999 0 -0.33 109 109
PDGF/PDGFRA -0.17 0.22 -9999 0 -0.45 109 109
actin cytoskeleton reorganization -0.11 0.16 -9999 0 -0.31 109 109
SRF 0.015 0.009 -9999 0 -10000 0 0
SHC1 0.01 0 -9999 0 -10000 0 0
PI3K -0.085 0.13 -9999 0 -0.26 109 109
PDGF/PDGFRA/Crk/C3G -0.085 0.13 -9999 0 -0.26 109 109
JAK1 -0.11 0.15 -9999 0 -0.31 109 109
ELK1/SRF -0.089 0.13 -9999 0 -0.25 109 109
SHB 0.01 0 -9999 0 -10000 0 0
SHF 0.01 0 -9999 0 -10000 0 0
CSNK2A1 0.021 0.017 -9999 0 -10000 0 0
GO:0007205 -0.13 0.18 -9999 0 -0.36 109 109
SOS1 0.01 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.072 0.12 -9999 0 -0.23 109 109
PDGF/PDGFRA/SHB -0.11 0.16 -9999 0 -0.31 109 109
PDGF/PDGFRA/Caveolin-1 -0.11 0.16 -9999 0 -0.31 109 109
ITGAV 0.01 0 -9999 0 -10000 0 0
ELK1 -0.12 0.16 -9999 0 -0.31 109 109
PIK3CA 0.01 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.11 0.16 -9999 0 -0.31 109 109
JAK-STAT cascade -0.11 0.15 -9999 0 -0.31 109 109
cell proliferation -0.11 0.16 -9999 0 -0.31 109 109
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 0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 -0.091 0.087 -10000 0 -0.18 148 148
AKT1 -0.08 0.12 0.24 1 -0.19 148 149
EGF -0.4 0.14 -10000 0 -0.44 261 261
mol:TXA2 -0.001 0.001 -10000 0 -10000 0 0
FGR -0.006 0.052 -10000 0 -0.48 1 1
mol:Ca2+ -0.13 0.17 0.29 1 -0.29 148 149
LYN -0.005 0.048 -10000 0 -0.31 1 1
RhoA/GTP -0.06 0.065 -10000 0 -0.12 148 148
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.15 0.19 0.3 1 -0.32 148 149
GNG2 0.01 0 -10000 0 -10000 0 0
ARRB2 0.01 0.001 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.02 0.079 -10000 0 -0.32 8 8
G beta5/gamma2 -0.12 0.12 -10000 0 -0.23 148 148
PRKCH -0.15 0.19 0.3 1 -0.34 148 149
DNM1 0.005 0.027 -10000 0 -0.44 1 1
TXA2/TP beta/beta Arrestin3 0.002 0.016 -10000 0 -0.19 1 1
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.009 0.001 -10000 0 -10000 0 0
G12 family/GTP -0.15 0.14 -10000 0 -0.29 148 148
ADRBK1 0.01 0 -10000 0 -10000 0 0
ADRBK2 0.01 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.012 0.001 -10000 0 -10000 0 0
mol:GDP 0.075 0.11 0.3 15 -0.19 1 16
mol:NADP -0.006 0.082 -10000 0 -0.44 10 10
RAB11A 0.01 0 -10000 0 -10000 0 0
PRKG1 -0.1 0.2 -10000 0 -0.44 73 73
mol:IP3 -0.16 0.2 0.31 1 -0.36 148 149
cell morphogenesis 0.012 0.001 -10000 0 -10000 0 0
PLCB2 -0.22 0.26 0.33 1 -0.48 148 149
mol:cGMP -0.001 0.001 -10000 0 -10000 0 0
BLK -0.006 0.048 -10000 0 -0.31 1 1
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.007 0.052 -10000 0 -0.48 1 1
RHOA 0.01 0 -10000 0 -10000 0 0
PTGIR 0.006 0.037 -10000 0 -0.44 2 2
PRKCB1 -0.16 0.2 0.3 1 -0.36 148 149
GNAQ 0.01 0 -10000 0 -10000 0 0
mol:L-citrulline -0.006 0.082 -10000 0 -0.44 10 10
TXA2/TXA2-R family -0.23 0.28 0.34 1 -0.5 148 149
LCK -0.005 0.048 -10000 0 -0.31 1 1
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.001 0.055 -10000 0 -0.37 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.012 0.019 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.003 0.056 -10000 0 -0.37 1 1
MAPK14 -0.094 0.13 0.25 1 -0.22 148 149
TGM2/GTP -0.18 0.22 0.32 1 -0.39 148 149
MAPK11 -0.094 0.13 0.25 1 -0.22 148 149
ARHGEF1 -0.074 0.1 0.19 1 -0.17 148 149
GNAI2 0.01 0 -10000 0 -10000 0 0
JNK cascade -0.17 0.21 0.32 1 -0.37 148 149
RAB11/GDP 0.011 0.001 -10000 0 -10000 0 0
ICAM1 -0.12 0.16 0.24 2 -0.27 148 150
cAMP biosynthetic process -0.15 0.19 0.28 1 -0.33 148 149
Gq family/GTP/EBP50 -0.031 0.079 -10000 0 -0.17 66 66
actin cytoskeleton reorganization 0.012 0.001 -10000 0 -10000 0 0
SRC -0.005 0.048 -10000 0 -0.31 1 1
GNB5 0.01 0 -10000 0 -10000 0 0
GNB1 0.01 0 -10000 0 -10000 0 0
EGF/EGFR -0.081 0.052 -10000 0 -0.21 21 21
VCAM1 -0.12 0.16 0.21 4 -0.27 146 150
TP beta/Gq family/GDP/G beta5/gamma2 -0.02 0.079 -10000 0 -0.32 8 8
platelet activation -0.12 0.17 0.3 1 -0.29 148 149
PGI2/IP 0.005 0.026 -10000 0 -0.31 2 2
PRKACA 0.007 0.019 -10000 0 -0.22 2 2
Gq family/GDP/G beta5/gamma2 -0.02 0.069 -10000 0 -0.28 8 8
TXA2/TP beta/beta Arrestin2 0.006 0.03 -10000 0 -0.46 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.009 0.062 -10000 0 -0.23 21 21
mol:DAG -0.18 0.23 0.32 1 -0.4 148 149
EGFR 0.01 0 -10000 0 -10000 0 0
TXA2/TP alpha -0.2 0.25 0.33 1 -0.44 148 149
Gq family/GTP -0.038 0.093 -10000 0 -0.2 67 67
YES1 -0.005 0.048 -10000 0 -0.31 1 1
GNAI2/GTP -0.008 0.053 -10000 0 -0.35 1 1
PGD2/DP 0.007 0.001 -10000 0 -10000 0 0
SLC9A3R1 0.01 0 -10000 0 -10000 0 0
FYN -0.005 0.048 -10000 0 -0.31 1 1
mol:NO -0.006 0.082 -10000 0 -0.44 10 10
GNA15 0.009 0.002 -10000 0 -10000 0 0
PGK/cGMP -0.065 0.13 -10000 0 -0.27 79 79
RhoA/GDP 0.011 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.009 0.055 -10000 0 -0.31 1 1
NOS3 -0.006 0.082 -10000 0 -0.44 10 10
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA -0.15 0.19 0.3 1 -0.34 148 149
PRKCB -0.15 0.19 0.3 1 -0.34 148 149
PRKCE -0.16 0.2 0.3 1 -0.34 148 149
PRKCD -0.17 0.21 0.3 1 -0.37 148 149
PRKCG -0.16 0.2 0.3 1 -0.35 148 149
muscle contraction -0.21 0.26 0.33 1 -0.45 148 149
PRKCZ -0.14 0.19 0.3 1 -0.32 148 149
ARR3 0.002 0.004 -10000 0 -10000 0 0
TXA2/TP beta -0.001 0.058 -10000 0 -0.21 15 15
PRKCQ -0.16 0.2 0.3 1 -0.34 148 149
MAPKKK cascade -0.2 0.24 0.32 1 -0.42 148 149
SELE -0.18 0.21 0.28 1 -0.38 148 149
TP beta/GNAI2/GDP/G beta/gamma 0.01 0.058 -10000 0 -0.37 1 1
ROCK1 0.01 0 -10000 0 -10000 0 0
GNA14 -0.085 0.18 -10000 0 -0.44 61 61
chemotaxis -0.27 0.32 0.36 1 -0.58 148 149
GNA12 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0.001 -10000 0 -10000 0 0
GNA11 -0.001 0.069 -10000 0 -0.44 7 7
Rac1/GTP 0.006 0.001 -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 0.39 -9999 0 -0.87 63 63
MKNK1 0.01 0 -9999 0 -10000 0 0
MAPK14 -0.051 0.14 -9999 0 -0.3 63 63
ATF2/c-Jun -0.037 0.11 -9999 0 -0.4 8 8
MAPK11 -0.051 0.14 -9999 0 -0.3 63 63
MITF -0.063 0.16 -9999 0 -0.36 64 64
MAPKAPK5 -0.062 0.16 -9999 0 -0.36 63 63
KRT8 -0.062 0.16 -9999 0 -0.36 63 63
MAPKAPK3 0.01 0 -9999 0 -10000 0 0
MAPKAPK2 0.01 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.078 0.2 -9999 0 -0.45 63 63
CEBPB -0.062 0.16 -9999 0 -0.36 63 63
SLC9A1 -0.062 0.16 -9999 0 -0.36 63 63
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.059 0.16 -9999 0 -0.35 63 63
p38alpha-beta/MNK1 -0.055 0.17 -9999 0 -0.36 63 63
JUN -0.037 0.11 -9999 0 -0.4 8 8
PPARGC1A -0.07 0.17 -9999 0 -0.37 68 68
USF1 -0.062 0.16 -9999 0 -0.36 63 63
RAB5/GDP/GDI1 -0.043 0.12 -9999 0 -0.27 63 63
NOS2 -0.11 0.29 -9999 0 -1.1 21 21
DDIT3 -0.062 0.16 -9999 0 -0.36 63 63
RAB5A 0.01 0 -9999 0 -10000 0 0
HSPB1 -0.049 0.13 -9999 0 -0.3 62 62
p38alpha-beta/HBP1 -0.055 0.17 -9999 0 -0.36 63 63
CREB1 -0.068 0.18 -9999 0 -0.39 63 63
RAB5/GDP 0.007 0 -9999 0 -10000 0 0
EIF4E -0.055 0.14 -9999 0 -0.32 63 63
RPS6KA4 -0.062 0.16 -9999 0 -0.36 63 63
PLA2G4A -0.061 0.16 -9999 0 -0.34 64 64
GDI1 -0.062 0.16 -9999 0 -0.36 63 63
TP53 -0.082 0.2 -9999 0 -0.45 63 63
RPS6KA5 -0.067 0.17 -9999 0 -0.37 65 65
ESR1 -0.082 0.19 -9999 0 -0.39 73 73
HBP1 0.01 0 -9999 0 -10000 0 0
MEF2C -0.062 0.16 -9999 0 -0.36 63 63
MEF2A -0.062 0.16 -9999 0 -0.36 63 63
EIF4EBP1 -0.068 0.18 -9999 0 -0.39 63 63
KRT19 -0.09 0.19 -9999 0 -0.36 83 83
ELK4 -0.062 0.16 -9999 0 -0.36 63 63
ATF6 -0.062 0.16 -9999 0 -0.36 63 63
ATF1 -0.068 0.18 -9999 0 -0.39 63 63
p38alpha-beta/MAPKAPK2 -0.055 0.17 -9999 0 -0.36 63 63
p38alpha-beta/MAPKAPK3 -0.055 0.17 -9999 0 -0.36 63 63
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 0.017 0.028 -9999 0 -0.26 3 3
fibroblast growth factor receptor signaling pathway 0.017 0.028 -9999 0 -0.26 3 3
LAMA1 -0.003 0.074 -9999 0 -0.44 8 8
PRNP 0.01 0 -9999 0 -10000 0 0
GPC1/SLIT2 -0.055 0.13 -9999 0 -0.31 62 62
SMAD2 0.012 0.004 -9999 0 -10000 0 0
GPC1/PrPc/Cu2+ 0.013 0.001 -9999 0 -10000 0 0
GPC1/Laminin alpha1 0.005 0.051 -9999 0 -0.3 8 8
TDGF1 -0.23 0.22 -9999 0 -0.44 150 150
CRIPTO/GPC1 -0.16 0.16 -9999 0 -0.31 150 150
APP/GPC1 0.015 0.001 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.13 0.13 -9999 0 -0.26 150 150
FLT1 0.007 0.037 -9999 0 -0.44 2 2
GPC1/TGFB/TGFBR1/TGFBR2 0.02 0.001 -9999 0 -10000 0 0
SERPINC1 -0.06 0.16 -9999 0 -0.44 44 44
FYN -0.13 0.13 -9999 0 -0.26 150 150
FGR -0.13 0.13 -9999 0 -0.26 150 150
positive regulation of MAPKKK cascade -0.14 0.16 -9999 0 -0.3 149 149
SLIT2 -0.087 0.18 -9999 0 -0.44 62 62
GPC1/NRG 0.009 0.04 -9999 0 -0.29 5 5
NRG1 0.002 0.059 -9999 0 -0.44 5 5
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.018 0.023 -9999 0 -0.26 2 2
LYN -0.13 0.13 -9999 0 -0.26 150 150
mol:Spermine 0.005 0 -9999 0 -10000 0 0
cell growth 0.017 0.028 -9999 0 -0.26 3 3
BMP signaling pathway -0.01 0.001 -9999 0 -10000 0 0
SRC -0.13 0.13 -9999 0 -0.26 149 149
TGFBR1 0.01 0 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A 0.004 0.005 -9999 0 -10000 0 0
GPC1 0.01 0.001 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.01 0 -9999 0 -10000 0 0
VEGFA 0.01 0.001 -9999 0 -10000 0 0
BLK -0.13 0.13 -9999 0 -0.25 150 150
HCK -0.13 0.13 -9999 0 -0.25 150 150
FGF2 0.005 0.046 -9999 0 -0.44 3 3
FGFR1 0.01 0 -9999 0 -10000 0 0
VEGFR1 homodimer 0.007 0.037 -9999 0 -0.44 2 2
TGFBR2 0.01 0 -9999 0 -10000 0 0
cell death 0.014 0.001 -9999 0 -10000 0 0
ATIII/GPC1 -0.036 0.12 -9999 0 -0.31 44 44
PLA2G2A/GPC1 0.01 0.004 -9999 0 -10000 0 0
LCK -0.13 0.13 -9999 0 -0.25 150 150
neuron differentiation 0.009 0.04 -9999 0 -0.29 5 5
PrPc/Cu2+ 0.007 0 -9999 0 -10000 0 0
APP 0.01 0 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.01 0 -9999 0 -10000 0 0
Endothelins

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
AKT1 0.019 0.11 0.27 16 -0.26 24 40
PTK2B 0.009 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.25 0.43 -10000 0 -0.91 81 81
EDN1 0.008 0.069 0.21 15 -0.45 1 16
EDN3 0.007 0.005 -10000 0 -10000 0 0
EDN2 -0.01 0.093 -10000 0 -0.44 13 13
HRAS/GDP -0.079 0.17 -10000 0 -0.35 66 66
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.075 0.15 0.18 4 -0.32 61 65
ADCY4 0.004 0.11 0.21 7 -0.25 36 43
ADCY5 0.005 0.11 0.21 9 -0.24 32 41
ADCY6 0.017 0.092 0.21 9 -0.23 18 27
ADCY7 0.015 0.091 0.21 9 -0.23 18 27
ADCY1 -0.076 0.14 0.21 2 -0.24 107 109
ADCY2 -0.005 0.067 -10000 0 -0.22 15 15
ADCY3 0.017 0.092 0.21 9 -0.23 18 27
ADCY8 0.01 0.089 0.2 9 -0.22 24 33
ADCY9 0.017 0.092 0.21 9 -0.22 20 29
arachidonic acid secretion -0.14 0.26 -10000 0 -0.48 85 85
ETB receptor/Endothelin-1/Gq/GTP -0.048 0.12 -10000 0 -0.26 55 55
GNAO1 -0.029 0.13 -10000 0 -0.44 25 25
HRAS 0.009 0.001 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.008 0.11 0.32 16 -0.24 24 40
ETA receptor/Endothelin-1/Gs/GTP 0.006 0.1 0.3 16 -0.23 25 41
mol:GTP -0.004 0.007 -10000 0 -10000 0 0
COL3A1 0.01 0.13 0.28 14 -0.41 14 28
EDNRB 0.01 0.028 -10000 0 -0.44 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.008 0.15 0.3 14 -0.43 23 37
CYSLTR1 0.02 0.12 0.28 14 -0.32 12 26
SLC9A1 0.001 0.068 0.19 15 -0.2 8 23
mol:GDP -0.086 0.18 -10000 0 -0.36 68 68
SLC9A3 -0.53 0.33 -10000 0 -0.62 240 240
RAF1 -0.1 0.21 -10000 0 -0.39 79 79
JUN -0.13 0.25 -10000 0 -0.52 64 64
JAK2 0.019 0.11 0.27 16 -0.26 24 40
mol:IP3 -0.087 0.16 -10000 0 -0.35 66 66
ETA receptor/Endothelin-1 0.005 0.14 0.39 16 -0.32 24 40
PLCB1 -0.054 0.16 -10000 0 -0.44 40 40
PLCB2 0.006 0.006 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.002 0.077 0.16 12 -0.3 12 24
FOS -0.16 0.34 -10000 0 -0.87 48 48
Gai/GDP -0.056 0.22 -10000 0 -0.75 25 25
CRK 0.009 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.068 0.18 0.26 4 -0.38 48 52
BCAR1 0.01 0.001 -10000 0 -10000 0 0
PRKCB1 -0.084 0.16 -10000 0 -0.34 67 67
GNAQ 0.003 0.012 -10000 0 -10000 0 0
GNAZ 0.01 0 -10000 0 -10000 0 0
GNAL 0.008 0.026 -10000 0 -0.44 1 1
Gs family/GDP -0.082 0.16 -10000 0 -0.33 67 67
ETA receptor/Endothelin-1/Gq/GTP -0.06 0.16 0.21 4 -0.33 55 59
MAPK14 -0.063 0.12 -10000 0 -0.26 59 59
TRPC6 -0.27 0.46 -10000 0 -0.98 81 81
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.007 0.037 -10000 0 -0.44 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.068 0.12 -10000 0 -0.27 60 60
ETB receptor/Endothelin-2 0 0.069 -10000 0 -0.31 14 14
ETB receptor/Endothelin-3 0.012 0.02 -10000 0 -0.31 1 1
ETB receptor/Endothelin-1 0.012 0.054 0.17 6 -0.36 2 8
MAPK3 -0.15 0.31 -10000 0 -0.73 54 54
MAPK1 -0.15 0.31 -10000 0 -0.73 54 54
Rac1/GDP -0.078 0.17 -10000 0 -0.34 66 66
cAMP biosynthetic process -0.046 0.13 0.23 2 -0.31 34 36
MAPK8 -0.15 0.29 -10000 0 -0.57 82 82
SRC 0.009 0.001 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.002 0.069 -10000 0 -0.22 16 16
p130Cas/CRK/Src/PYK2 -0.13 0.24 -10000 0 -0.45 94 94
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.078 0.17 -10000 0 -0.34 66 66
COL1A2 0.016 0.1 0.28 9 -0.4 4 13
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.014 0.1 0.16 9 -0.31 24 33
mol:DAG -0.087 0.16 -10000 0 -0.35 66 66
MAP2K2 -0.12 0.25 -10000 0 -0.52 64 64
MAP2K1 -0.12 0.25 -10000 0 -0.52 64 64
EDNRA -0.008 0.11 0.21 15 -0.36 17 32
positive regulation of muscle contraction 0.015 0.098 0.23 15 -0.23 24 39
Gq family/GDP -0.11 0.18 -10000 0 -0.4 63 63
HRAS/GTP -0.089 0.18 -10000 0 -0.36 68 68
PRKCH -0.082 0.16 -10000 0 -0.35 60 60
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCA -0.082 0.16 -10000 0 -0.35 60 60
PRKCB -0.081 0.16 -10000 0 -0.34 67 67
PRKCE -0.081 0.16 -10000 0 -0.35 60 60
PRKCD -0.082 0.16 -10000 0 -0.35 60 60
PRKCG -0.069 0.16 0.19 1 -0.33 58 59
regulation of vascular smooth muscle contraction -0.19 0.39 -10000 0 -1 48 48
PRKCQ -0.087 0.17 -10000 0 -0.34 68 68
PLA2G4A -0.16 0.29 -10000 0 -0.52 85 85
GNA14 -0.091 0.18 -10000 0 -0.45 61 61
GNA15 0.004 0.009 -10000 0 -10000 0 0
GNA12 0.01 0 -10000 0 -10000 0 0
GNA11 -0.007 0.069 -10000 0 -0.44 7 7
Rac1/GTP 0.008 0.11 0.32 16 -0.24 24 40
MMP1 -0.032 0.19 -10000 0 -0.74 18 18
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.24 0.18 -9999 0 -0.31 223 223
SMAD6-7/SMURF1 0.019 0.016 -9999 0 -0.26 1 1
NOG 0.004 0.045 -9999 0 -0.44 3 3
SMAD9 -0.057 0.093 -9999 0 -0.48 10 10
SMAD4 0.01 0 -9999 0 -10000 0 0
SMAD5 -0.13 0.12 -9999 0 -0.32 24 24
BMP7/USAG1 -0.14 0.18 -9999 0 -0.34 127 127
SMAD5/SKI -0.12 0.12 -9999 0 -0.31 24 24
SMAD1 -0.013 0.026 -9999 0 -10000 0 0
BMP2 0.01 0 -9999 0 -10000 0 0
SMAD1/SMAD1/SMAD4 -0.015 0.016 -9999 0 -10000 0 0
BMPR1A 0.01 0 -9999 0 -10000 0 0
BMPR1B -0.26 0.22 -9999 0 -0.44 172 172
BMPR1A-1B/BAMBI -0.15 0.14 -9999 0 -0.26 173 173
AHSG 0.004 0.005 -9999 0 -10000 0 0
CER1 0.003 0.005 -9999 0 -10000 0 0
BMP2-4/CER1 0.016 0.003 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.11 0.11 -9999 0 -0.36 22 22
BMP2-4 (homodimer) 0.015 0 -9999 0 -10000 0 0
RGMB 0.01 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.13 0.13 -9999 0 -0.24 173 173
RGMA -0.048 0.15 -9999 0 -0.44 37 37
SMURF1 0.01 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.12 0.11 -9999 0 -0.2 170 170
BMP2-4/USAG1 -0.034 0.1 -9999 0 -0.26 52 52
SMAD6/SMURF1/SMAD5 -0.12 0.12 -9999 0 -0.31 24 24
SOSTDC1 -0.073 0.17 -9999 0 -0.44 52 52
BMP7/BMPR2/BMPR1A-1B -0.2 0.15 -9999 0 -0.28 219 219
SKI 0.01 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.005 0.045 -9999 0 -0.44 3 3
HFE2 0.007 0.004 -9999 0 -10000 0 0
ZFYVE16 0.01 0 -9999 0 -10000 0 0
MAP3K7 0.01 0 -9999 0 -10000 0 0
BMP2-4/CHRD 0.001 0.071 -9999 0 -0.26 20 20
SMAD5/SMAD5/SMAD4 -0.12 0.12 -9999 0 -0.31 24 24
MAPK1 0.01 0 -9999 0 -10000 0 0
TAK1/TAB family -0.1 0.099 -9999 0 -0.3 22 22
BMP7 (homodimer) -0.14 0.21 -9999 0 -0.44 93 93
NUP214 0.01 0 -9999 0 -10000 0 0
BMP6/FETUA 0.007 0.03 -9999 0 -0.28 3 3
SMAD1/SKI -0.01 0.027 -9999 0 -10000 0 0
SMAD6 0.008 0.026 -9999 0 -0.44 1 1
CTDSP2 0.01 0 -9999 0 -10000 0 0
BMP2-4/FETUA 0.016 0.004 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.12 0.2 -9999 0 -0.44 81 81
BMPR2 (homodimer) 0.01 0 -9999 0 -10000 0 0
GADD34/PP1CA 0.02 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.18 0.16 -9999 0 -0.31 172 172
CHRDL1 -0.17 0.22 -9999 0 -0.44 115 115
ENDOFIN/SMAD1 -0.01 0.027 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.005 0.032 -9999 0 -0.22 1 1
SMAD6/SMURF1 0.01 0 -9999 0 -10000 0 0
BAMBI 0.008 0.026 -9999 0 -0.44 1 1
SMURF2 0.01 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.091 0.14 -9999 0 -0.26 115 115
BMP2-4/GREM1 -0.059 0.12 -9999 0 -0.26 81 81
SMAD7 0.01 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.05 0.089 -9999 0 -0.45 10 10
SMAD1/SMAD6 -0.01 0.027 -9999 0 -10000 0 0
TAK1/SMAD6 0.015 0 -9999 0 -10000 0 0
BMP7 -0.14 0.21 -9999 0 -0.44 93 93
BMP6 0.005 0.046 -9999 0 -0.44 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.11 0.1 -9999 0 -0.32 22 22
PPM1A 0.01 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.01 0.027 -9999 0 -10000 0 0
SMAD7/SMURF1 0.015 0 -9999 0 -10000 0 0
CTDSPL 0.01 0 -9999 0 -10000 0 0
PPP1CA 0.01 0 -9999 0 -10000 0 0
XIAP 0.01 0 -9999 0 -10000 0 0
CTDSP1 0.01 0 -9999 0 -10000 0 0
PPP1R15A 0.01 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.19 0.2 -9999 0 -0.29 198 198
CHRD -0.021 0.11 -9999 0 -0.44 20 20
BMPR2 0.01 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.12 -9999 0 -0.21 185 185
BMP4 0.01 0 -9999 0 -10000 0 0
FST -0.094 0.19 -9999 0 -0.44 65 65
BMP2-4/NOG 0.016 0.028 -9999 0 -0.26 3 3
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.19 0.14 -9999 0 -0.26 219 219
Arf6 signaling events

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
CENTA1/KIF3B 0.013 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 0.011 0.013 -9999 0 -10000 0 0
EGFR 0.01 0 -9999 0 -10000 0 0
EPHA2 0.01 0.001 -9999 0 -10000 0 0
USP6 0.009 0.002 -9999 0 -10000 0 0
IQSEC1 0.01 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.28 0.097 -9999 0 -0.31 261 261
ARRB2 0.005 0.002 -9999 0 -10000 0 0
mol:GTP 0.01 0.004 -9999 0 -10000 0 0
ARRB1 0.008 0.026 -9999 0 -0.44 1 1
FBXO8 0.01 0 -9999 0 -10000 0 0
TSHR 0.008 0.004 -9999 0 -10000 0 0
EGF -0.4 0.14 -9999 0 -0.44 261 261
somatostatin receptor activity 0 0 -9999 0 -0.001 116 116
ARAP2 0.01 0 -9999 0 -10000 0 0
mol:GDP -0.076 0.082 -9999 0 -0.19 89 89
mol:PI-3-4-5-P3 0 0 -9999 0 0 97 97
ITGA2B 0.009 0.003 -9999 0 -10000 0 0
ARF6 0.01 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.025 0.001 -9999 0 -10000 0 0
ADAP1 0.01 0 -9999 0 -10000 0 0
KIF13B 0.01 0 -9999 0 -10000 0 0
HGF/MET -0.005 0.07 -9999 0 -0.28 17 17
PXN 0.01 0 -9999 0 -10000 0 0
ARF6/GTP -0.11 0.095 -9999 0 -0.22 113 113
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.23 0.083 -9999 0 -0.26 261 261
ADRB2 0.009 0.002 -9999 0 -10000 0 0
receptor agonist activity 0 0 -9999 0 0 116 116
actin filament binding 0 0 -9999 0 0 116 116
SRC 0.01 0.001 -9999 0 -10000 0 0
ITGB3 -0.012 0.096 -9999 0 -0.44 14 14
GNAQ 0.009 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 110 110
ARF6/GDP -0.015 0.037 -9999 0 -10000 0 0
ARF6/GDP/GULP/ACAP1 -0.059 0.075 -9999 0 -0.21 31 31
alphaIIb/beta3 Integrin/paxillin/GIT1 0.011 0.055 -9999 0 -0.23 14 14
ACAP1 0.008 0.003 -9999 0 -10000 0 0
ACAP2 0.01 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0.005 0.004 -9999 0 -10000 0 0
EFNA1 0.01 0 -9999 0 -10000 0 0
HGF -0.017 0.11 -9999 0 -0.44 17 17
CYTH3 0.004 0 -9999 0 -10000 0 0
CYTH2 0.005 0.002 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 64 64
endosomal lumen acidification 0 0 -9999 0 0 116 116
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.01 0.001 -9999 0 -10000 0 0
GNAQ/ARNO 0.009 0.003 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 0 1 1
PIP3-E 0 0 -9999 0 0 85 85
MET 0.008 0.003 -9999 0 -10000 0 0
GNA14 -0.085 0.18 -9999 0 -0.44 61 61
GNA15 0.009 0.002 -9999 0 -10000 0 0
GIT1 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 113 113
GNA11 -0.001 0.069 -9999 0 -0.44 7 7
LHCGR 0.004 0.005 -9999 0 -10000 0 0
AGTR1 -0.13 0.21 -9999 0 -0.44 91 91
desensitization of G-protein coupled receptor protein signaling pathway 0.005 0.004 -9999 0 -10000 0 0
IPCEF1/ARNO -0.17 0.063 -9999 0 -10000 0 0
alphaIIb/beta3 Integrin -0.003 0.069 -9999 0 -0.31 14 14
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.041 0.15 -10000 0 -0.37 50 50
CRKL -0.055 0.16 -10000 0 -0.4 50 50
HRAS -0.04 0.14 -10000 0 -0.33 50 50
mol:PIP3 -0.053 0.15 -10000 0 -0.37 50 50
SPRED1 0.01 0 -10000 0 -10000 0 0
SPRED2 0.01 0 -10000 0 -10000 0 0
GAB1 -0.059 0.17 -10000 0 -0.42 50 50
FOXO3 -0.045 0.14 -10000 0 -0.36 50 50
AKT1 -0.05 0.16 -10000 0 -0.39 50 50
BAD -0.045 0.14 -10000 0 -0.36 50 50
megakaryocyte differentiation -0.085 0.18 -10000 0 -0.46 50 50
GSK3B -0.045 0.14 -10000 0 -0.36 50 50
RAF1 -0.018 0.12 -10000 0 -0.27 50 50
SHC1 0.01 0 -10000 0 -10000 0 0
STAT3 -0.059 0.17 -10000 0 -0.42 50 50
STAT1 -0.14 0.36 -10000 0 -0.93 50 50
HRAS/SPRED1 -0.018 0.12 -10000 0 -0.27 50 50
cell proliferation -0.061 0.17 -10000 0 -0.42 50 50
PIK3CA 0.01 0 -10000 0 -10000 0 0
TEC 0.01 0 -10000 0 -10000 0 0
RPS6KB1 -0.055 0.17 -10000 0 -0.41 51 51
HRAS/SPRED2 -0.018 0.12 -10000 0 -0.27 50 50
LYN/TEC/p62DOK -0.043 0.16 -10000 0 -0.39 50 50
MAPK3 -0.007 0.089 -10000 0 -0.2 50 50
STAP1 -0.19 0.19 -10000 0 -0.53 51 51
GRAP2 0.009 0.002 -10000 0 -10000 0 0
JAK2 -0.11 0.31 -10000 0 -0.79 50 50
STAT1 (dimer) -0.13 0.36 -10000 0 -0.91 50 50
mol:Gleevec 0.002 0.006 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.049 0.16 -10000 0 -0.39 50 50
actin filament polymerization -0.057 0.16 -10000 0 -0.41 50 50
LYN 0.01 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.2 0.24 -10000 0 -0.68 50 50
PIK3R1 0.01 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.04 0.15 -10000 0 -0.36 50 50
PI3K -0.044 0.16 -10000 0 -0.39 51 51
PTEN 0.01 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.16 0.44 -10000 0 -1.1 50 50
MAPK8 -0.062 0.17 -10000 0 -0.43 50 50
STAT3 (dimer) -0.057 0.16 -10000 0 -0.41 50 50
positive regulation of transcription -0.004 0.075 -10000 0 -0.16 50 50
mol:GDP -0.041 0.14 -10000 0 -0.35 50 50
PIK3C2B -0.059 0.17 -10000 0 -0.42 50 50
CBL/CRKL -0.046 0.15 -10000 0 -0.38 50 50
FER -0.059 0.17 -10000 0 -0.42 50 50
SH2B3 -0.059 0.17 -10000 0 -0.42 50 50
PDPK1 -0.048 0.14 -10000 0 -0.35 50 50
SNAI2 -0.078 0.18 -10000 0 -0.45 50 50
positive regulation of cell proliferation -0.099 0.28 -10000 0 -0.7 50 50
KITLG 0.001 0.05 -10000 0 -0.46 3 3
cell motility -0.099 0.28 -10000 0 -0.7 50 50
PTPN6 0.012 0.009 -10000 0 -10000 0 0
EPOR -0.025 0.11 -10000 0 -10000 0 0
STAT5A (dimer) -0.079 0.23 -10000 0 -0.58 50 50
SOCS1 0.007 0.037 -10000 0 -0.44 2 2
cell migration 0.058 0.16 0.41 50 -10000 0 50
SOS1 0.01 0 -10000 0 -10000 0 0
EPO 0.004 0.01 -10000 0 -10000 0 0
VAV1 0.006 0.027 -10000 0 -0.44 1 1
GRB10 -0.059 0.17 -10000 0 -0.42 50 50
PTPN11 0.012 0.006 -10000 0 -10000 0 0
SCF/KIT -0.063 0.17 -10000 0 -0.44 51 51
GO:0007205 0.003 0.009 -10000 0 -10000 0 0
MAP2K1 -0.011 0.097 -10000 0 -0.22 50 50
CBL 0.01 0 -10000 0 -10000 0 0
KIT -0.18 0.46 -10000 0 -1.2 50 50
MAP2K2 -0.011 0.097 -10000 0 -0.22 50 50
SHC/Grb2/SOS1 -0.043 0.16 -10000 0 -0.39 50 50
STAT5A -0.082 0.24 -10000 0 -0.6 50 50
GRB2 0.01 0 -10000 0 -10000 0 0
response to radiation -0.076 0.18 -10000 0 -0.44 50 50
SHC/GRAP2 0.014 0.003 -10000 0 -10000 0 0
PTPRO -0.087 0.19 -10000 0 -0.47 50 50
SH2B2 -0.059 0.17 -10000 0 -0.42 50 50
DOK1 0.01 0.001 -10000 0 -10000 0 0
MATK -0.06 0.16 -10000 0 -0.42 50 50
CREBBP 0.001 0.043 -10000 0 -10000 0 0
BCL2 -0.023 0.11 -10000 0 -10000 0 0
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 -0.001 0.069 -9999 0 -0.31 14 14
AKT1 -0.065 0.2 -9999 0 -0.49 53 53
PTK2B -0.085 0.2 -9999 0 -0.45 65 65
VEGFR2 homodimer/Frs2 -0.094 0.24 -9999 0 -0.6 53 53
CAV1 0.01 0.001 -9999 0 -10000 0 0
CALM1 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.081 0.22 -9999 0 -0.55 53 53
endothelial cell proliferation -0.057 0.19 -9999 0 -0.46 53 53
mol:Ca2+ -0.077 0.2 -9999 0 -0.51 53 53
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.071 0.21 -9999 0 -0.52 53 53
RP11-342D11.1 -0.082 0.2 -9999 0 -0.51 53 53
CDH5 0.01 0 -9999 0 -10000 0 0
VEGFA homodimer 0.025 0.003 -9999 0 -10000 0 0
SHC1 0.01 0 -9999 0 -10000 0 0
SHC2 0.006 0.037 -9999 0 -0.44 2 2
HRAS/GDP -0.064 0.18 -9999 0 -0.44 53 53
SH2D2A 0.009 0.003 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.061 0.21 -9999 0 -0.47 55 55
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.083 0.22 -9999 0 -0.55 53 53
VEGFR1 homodimer 0.007 0.037 -9999 0 -0.44 2 2
SHC/GRB2/SOS1 -0.06 0.2 -9999 0 -0.48 53 53
GRB10 -0.077 0.2 -9999 0 -0.51 53 53
PTPN11 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
PAK1 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.065 0.21 -9999 0 -0.5 53 53
HRAS 0.01 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.05 0.14 -9999 0 -0.32 53 53
HIF1A 0.01 0 -9999 0 -10000 0 0
FRS2 0.01 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.071 0.21 -9999 0 -0.52 53 53
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.001 0.069 -9999 0 -0.44 7 7
Nck/Pak 0.015 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.081 0.22 -9999 0 -0.55 53 53
mol:GDP -0.063 0.19 -9999 0 -0.47 53 53
mol:NADP -0.057 0.18 -9999 0 -0.42 55 55
eNOS/Hsp90 -0.049 0.17 -9999 0 -0.39 55 55
PIK3R1 0.01 0 -9999 0 -10000 0 0
mol:IP3 -0.078 0.2 -9999 0 -0.51 53 53
HIF1A/ARNT 0.015 0 -9999 0 -10000 0 0
SHB 0.01 0 -9999 0 -10000 0 0
VEGFA 0.01 0.001 -9999 0 -10000 0 0
VEGFC 0.01 0.001 -9999 0 -10000 0 0
FAK1/Vinculin -0.086 0.23 -9999 0 -0.56 53 53
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.083 0.22 -9999 0 -0.47 65 65
PTPN6 0.01 0 -9999 0 -10000 0 0
EPAS1 -0.048 0.14 -9999 0 -0.33 53 53
mol:L-citrulline -0.057 0.18 -9999 0 -0.42 55 55
ITGAV 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.071 0.21 -9999 0 -0.52 53 53
VEGFR2 homodimer/VEGFA homodimer -0.078 0.22 -9999 0 -0.55 53 53
VEGFR2/3 heterodimer -0.1 0.25 -9999 0 -0.6 56 56
VEGFB 0.01 0 -9999 0 -10000 0 0
MAPK11 -0.083 0.21 -9999 0 -0.53 53 53
VEGFR2 homodimer -0.11 0.27 -9999 0 -0.68 53 53
FLT1 0.007 0.037 -9999 0 -0.44 2 2
NEDD4 0.01 0 -9999 0 -10000 0 0
MAPK3 -0.072 0.19 -9999 0 -0.47 53 53
MAPK1 -0.072 0.19 -9999 0 -0.47 53 53
VEGFA145/NRP2 0.014 0.019 -9999 0 -0.31 1 1
VEGFR1/2 heterodimer -0.095 0.24 -9999 0 -0.61 53 53
KDR -0.11 0.27 -9999 0 -0.68 53 53
VEGFA165/NRP1/VEGFR2 homodimer -0.07 0.21 -9999 0 -0.5 54 54
SRC 0.01 0.001 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.074 0.19 -9999 0 -0.48 53 53
PI3K -0.075 0.22 -9999 0 -0.55 53 53
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.081 0.22 -9999 0 -0.55 53 53
FES -0.08 0.21 -9999 0 -0.52 53 53
GAB1 -0.082 0.23 -9999 0 -0.56 53 53
VEGFR2 homodimer/VEGFA homodimer/Src -0.081 0.22 -9999 0 -0.55 53 53
CTNNB1 0.01 0 -9999 0 -10000 0 0
SOS1 0.01 0 -9999 0 -10000 0 0
ARNT 0.01 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.049 0.17 -9999 0 -0.39 55 55
VEGFR2 homodimer/VEGFA homodimer/Yes -0.081 0.22 -9999 0 -0.55 53 53
PI3K/GAB1 -0.065 0.21 -9999 0 -0.51 53 53
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.065 0.21 -9999 0 -0.5 53 53
PRKACA 0.01 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.087 0.23 -9999 0 -0.55 56 56
HSP90AA1 0.01 0 -9999 0 -10000 0 0
CDC42 -0.079 0.21 -9999 0 -0.52 53 53
actin cytoskeleton reorganization -0.082 0.22 -9999 0 -0.55 53 53
PTK2 -0.097 0.24 -9999 0 -0.6 53 53
EDG1 -0.082 0.2 -9999 0 -0.51 53 53
mol:DAG -0.078 0.2 -9999 0 -0.51 53 53
CaM/Ca2+ -0.068 0.19 -9999 0 -0.47 53 53
MAP2K3 -0.077 0.2 -9999 0 -0.5 53 53
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.071 0.21 -9999 0 -0.52 53 53
PLCG1 -0.079 0.21 -9999 0 -0.52 53 53
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.072 0.21 -9999 0 -0.52 53 53
IQGAP1 0.01 0 -9999 0 -10000 0 0
YES1 0.01 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.081 0.22 -9999 0 -0.55 53 53
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.081 0.22 -9999 0 -0.55 53 53
cell migration -0.069 0.2 -9999 0 -0.5 53 53
mol:PI-3-4-5-P3 -0.069 0.21 -9999 0 -0.51 53 53
FYN 0.01 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.072 0.19 -9999 0 -0.48 53 53
mol:NO -0.057 0.18 -9999 0 -0.42 55 55
PXN 0.01 0 -9999 0 -10000 0 0
HRAS/GTP -0.081 0.17 -9999 0 -0.44 53 53
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.073 0.21 -9999 0 -0.52 53 53
VHL 0.01 0 -9999 0 -10000 0 0
ITGB3 -0.012 0.096 -9999 0 -0.44 14 14
NOS3 -0.066 0.2 -9999 0 -0.47 55 55
VEGFR2 homodimer/VEGFA homodimer/Sck -0.081 0.22 -9999 0 -0.53 55 55
RAC1 0.01 0 -9999 0 -10000 0 0
PRKCA -0.073 0.19 -9999 0 -0.48 53 53
PRKCB -0.073 0.19 -9999 0 -0.48 53 53
VCL 0.01 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.077 0.2 -9999 0 -0.51 53 53
VEGFR1/2 heterodimer/VEGFA homodimer -0.082 0.23 -9999 0 -0.56 53 53
VEGFA165/NRP2 0.014 0.019 -9999 0 -0.31 1 1
MAPKKK cascade -0.057 0.18 -9999 0 -0.44 53 53
NRP2 0.008 0.026 -9999 0 -0.44 1 1
VEGFC homodimer 0.01 0.001 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
ROCK1 0.01 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.086 0.23 -9999 0 -0.56 53 53
MAP3K13 -0.081 0.21 -9999 0 -0.53 53 53
PDPK1 -0.061 0.19 -9999 0 -0.45 53 53
FOXM1 transcription factor network

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
NFATC3 0.22 0.32 0.79 37 -0.97 1 38
PLK1 0.075 0.13 0.4 30 -10000 0 30
BIRC5 0.099 0.14 0.45 9 -10000 0 9
HSPA1B 0.22 0.32 0.78 38 -0.97 1 39
MAP2K1 0.056 0.067 0.2 40 -10000 0 40
BRCA2 0.22 0.33 0.79 40 -0.97 1 41
FOXM1 0.18 0.35 0.9 32 -0.8 6 38
XRCC1 0.22 0.32 0.78 38 -0.97 1 39
FOXM1B/p19 -0.031 0.14 -10000 0 -0.86 2 2
Cyclin D1/CDK4 0.2 0.3 0.69 39 -0.9 2 41
CDC2 0.23 0.34 0.8 46 -0.73 6 52
TGFA 0.2 0.3 0.72 38 -0.76 2 40
SKP2 0.22 0.32 0.78 38 -0.97 1 39
CCNE1 0.017 0.013 -10000 0 -10000 0 0
CKS1B 0.22 0.32 0.78 39 -0.97 1 40
RB1 -0.024 0.06 -10000 0 -10000 0 0
FOXM1C/SP1 0.2 0.31 0.71 38 -0.75 6 44
AURKB 0.12 0.14 0.39 33 -10000 0 33
CENPF 0.23 0.34 0.84 40 -0.97 1 41
CDK4 0.026 0.026 -10000 0 -10000 0 0
MYC 0.2 0.29 0.7 38 -0.86 1 39
CHEK2 0.055 0.066 0.2 35 -10000 0 35
ONECUT1 0.2 0.31 0.72 37 -0.82 2 39
CDKN2A -0.004 0.023 -10000 0 -0.13 6 6
LAMA4 0.23 0.33 0.8 37 -0.97 1 38
FOXM1B/HNF6 0.2 0.32 0.73 36 -0.93 2 38
FOS 0.11 0.49 0.78 39 -1 32 71
SP1 0.011 0.001 -10000 0 -10000 0 0
CDC25B 0.22 0.33 0.78 39 -0.97 1 40
response to radiation 0.04 0.054 0.15 45 -10000 0 45
CENPB 0.22 0.32 0.78 39 -0.97 1 40
CENPA 0.24 0.35 0.82 46 -0.97 1 47
NEK2 0.24 0.35 0.82 46 -0.97 1 47
HIST1H2BA 0.22 0.32 0.77 39 -0.97 1 40
CCNA2 0.014 0.012 -10000 0 -10000 0 0
EP300 0.01 0 -10000 0 -10000 0 0
CCNB1/CDK1 0.21 0.34 0.82 39 -1.1 1 40
CCNB2 0.24 0.35 0.82 45 -0.97 1 46
CCNB1 0.23 0.35 0.84 39 -1 1 40
ETV5 0.22 0.32 0.79 36 -0.97 1 37
ESR1 0.18 0.41 0.79 36 -1.1 13 49
CCND1 0.21 0.32 0.74 39 -0.93 2 41
GSK3A 0.049 0.056 0.17 34 -10000 0 34
Cyclin A-E1/CDK1-2 0.04 0.044 0.18 9 -10000 0 9
CDK2 0.02 0.015 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.048 0.066 0.17 52 -10000 0 52
FOXM1B/Cbp/p300 0.026 0.18 -10000 0 -0.73 6 6
GAS1 0.18 0.42 0.78 38 -1 15 53
MMP2 0.22 0.33 0.78 39 -1.1 2 41
RB1/FOXM1C 0.2 0.3 0.71 37 -0.9 2 39
CREBBP 0.01 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 0.19 0.27 0.6 42 -0.73 3 45
HDAC7 0.012 0.007 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.052 0.16 -10000 0 -0.56 3 3
SMAD4 0.01 0 -10000 0 -10000 0 0
ID2 0.19 0.27 0.6 42 -0.73 3 45
AP1 -0.033 0.12 -10000 0 -0.31 44 44
ABCG2 0.19 0.27 0.6 42 -0.73 3 45
HIF1A 0.055 0.067 0.19 12 -10000 0 12
TFF3 0.16 0.31 0.6 40 -0.8 5 45
GATA2 -0.082 0.18 -10000 0 -0.44 60 60
AKT1 0.068 0.074 0.19 43 -10000 0 43
response to hypoxia 0.042 0.068 0.15 47 -0.12 3 50
MCL1 0.19 0.27 0.6 42 -0.73 3 45
NDRG1 0.19 0.27 0.6 42 -0.73 3 45
SERPINE1 0.18 0.29 0.6 40 -0.79 6 46
FECH 0.19 0.27 0.6 42 -0.73 3 45
FURIN 0.19 0.27 0.6 42 -0.73 3 45
NCOA2 -0.029 0.13 -10000 0 -0.44 26 26
EP300 0.12 0.12 0.3 64 -10000 0 64
HMOX1 0.16 0.26 0.59 27 -0.7 4 31
BHLHE40 0.19 0.27 0.6 42 -0.73 3 45
BHLHE41 0.15 0.26 0.59 31 -0.73 3 34
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.046 0.073 -10000 0 -10000 0 0
ENG 0.1 0.095 0.26 41 -10000 0 41
JUN 0.01 0.003 -10000 0 -10000 0 0
RORA 0.19 0.27 0.6 42 -0.73 3 45
ABCB1 -0.036 0.16 -10000 0 -0.79 11 11
TFRC 0.19 0.27 0.6 42 -0.73 3 45
CXCR4 0.16 0.26 0.59 30 -0.73 3 33
TF 0.18 0.27 0.6 41 -0.73 3 44
CITED2 0.19 0.27 0.6 42 -0.73 3 45
HIF1A/ARNT 0.03 0.18 -10000 0 -0.8 3 3
LDHA -0.005 0.017 -10000 0 -10000 0 0
ETS1 0.19 0.27 0.6 42 -0.73 3 45
PGK1 0.19 0.27 0.6 42 -0.73 3 45
NOS2 0.18 0.29 0.6 42 -0.82 5 47
ITGB2 0.12 0.24 0.58 20 -0.73 3 23
ALDOA 0.19 0.27 0.6 42 -0.73 3 45
Cbp/p300/CITED2 0.15 0.24 0.53 23 -0.72 3 26
FOS -0.058 0.16 -10000 0 -0.44 44 44
HK2 0.03 0.17 0.58 3 -0.73 3 6
SP1 0.004 0.043 -10000 0 -0.19 12 12
GCK 0.15 0.16 0.47 20 -10000 0 20
HK1 0.19 0.27 0.6 42 -0.73 3 45
NPM1 0.19 0.27 0.6 42 -0.73 3 45
EGLN1 0.19 0.27 0.6 42 -0.73 3 45
CREB1 0.013 0 -10000 0 -10000 0 0
PGM1 0.19 0.27 0.6 42 -0.73 3 45
SMAD3 0.01 0 -10000 0 -10000 0 0
EDN1 0.037 0.22 0.52 3 -0.56 15 18
IGFBP1 0.17 0.28 0.6 38 -0.7 5 43
VEGFA 0.21 0.22 0.52 42 -0.52 2 44
HIF1A/JAB1 0.011 0.027 -10000 0 -10000 0 0
CP 0.15 0.28 0.59 29 -0.7 6 35
CXCL12 0.18 0.3 0.6 42 -0.72 9 51
COPS5 0.011 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4 0.015 0 -10000 0 -10000 0 0
BNIP3 0.19 0.27 0.6 42 -0.73 3 45
EGLN3 0.17 0.26 0.59 34 -0.73 3 37
CA9 0.039 0.17 0.58 3 -0.68 3 6
TERT 0.14 0.25 0.58 27 -0.7 3 30
ENO1 0.19 0.27 0.6 42 -0.73 3 45
PFKL 0.19 0.27 0.6 42 -0.73 3 45
NCOA1 0.01 0.001 -10000 0 -10000 0 0
ADM 0.19 0.27 0.6 41 -0.73 3 44
ARNT 0.055 0.067 0.19 12 -10000 0 12
HNF4A -0.036 0.14 -10000 0 -0.44 31 31
ADFP 0.17 0.26 0.57 36 -0.73 3 39
SLC2A1 0.2 0.21 0.51 38 -0.52 2 40
LEP 0.14 0.25 0.57 25 -0.73 3 28
HIF1A/ARNT/Cbp/p300 0.075 0.18 -10000 0 -0.58 3 3
EPO 0.17 0.23 0.54 19 -0.85 1 20
CREBBP 0.12 0.12 0.32 51 -10000 0 51
HIF1A/ARNT/Cbp/p300/HDAC7 0.077 0.18 -10000 0 -0.56 3 3
PFKFB3 0.19 0.27 0.6 42 -0.73 3 45
NT5E 0.19 0.28 0.6 42 -0.79 3 45
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.045 0.12 -9999 0 -0.31 53 53
alphaV beta3 Integrin 0.003 0.065 -9999 0 -0.26 17 17
PTK2 -0.1 0.17 -9999 0 -0.35 72 72
IGF1R 0.01 0 -9999 0 -10000 0 0
PI4KB 0.01 0 -9999 0 -10000 0 0
MFGE8 0.01 0 -9999 0 -10000 0 0
SRC 0.01 0.001 -9999 0 -10000 0 0
CDKN1B -0.1 0.18 -9999 0 -0.41 74 74
VEGFA 0.01 0.001 -9999 0 -10000 0 0
ILK -0.1 0.18 -9999 0 -0.41 74 74
ROCK1 0.01 0 -9999 0 -10000 0 0
AKT1 -0.092 0.17 -9999 0 -0.38 74 74
PTK2B -0.037 0.1 -9999 0 -0.22 65 65
alphaV/beta3 Integrin/JAM-A -0.05 0.11 -9999 0 -0.22 83 83
CBL 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.18 0.14 -9999 0 -0.26 200 200
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.016 0.049 -9999 0 -0.23 11 11
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.084 0.14 -9999 0 -0.24 114 114
alphaV/beta3 Integrin/Syndecan-1 0.005 0.061 -9999 0 -0.25 15 15
PI4KA 0.01 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0 0.066 -9999 0 -0.2 26 26
PI4 Kinase 0.015 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.003 0.065 -9999 0 -0.26 17 17
RPS6KB1 0.002 0.066 -9999 0 -0.19 26 26
TLN1 0.01 0 -9999 0 -10000 0 0
MAPK3 -0.039 0.11 -9999 0 -0.4 17 17
GPR124 0.008 0.026 -9999 0 -0.44 1 1
MAPK1 -0.039 0.11 -9999 0 -0.4 17 17
PXN 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.008 0.09 -9999 0 -0.29 26 26
cell adhesion -0.15 0.12 -9999 0 -0.23 196 196
ANGPTL3 -0.29 0.21 -9999 0 -0.44 193 193
VEGFR2 homodimer/VEGFA homodimer/Src -0.031 0.11 -9999 0 -0.26 53 53
IGF-1R heterotetramer 0.01 0 -9999 0 -10000 0 0
Rac1/GDP 0.007 0 -9999 0 -10000 0 0
TGFBR2 0.01 0 -9999 0 -10000 0 0
ITGB3 -0.012 0.096 -9999 0 -0.44 14 14
IGF1 0 0.064 -9999 0 -0.44 6 6
RAC1 0.01 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0.005 0.061 -9999 0 -0.26 15 15
apoptosis 0.01 0 -9999 0 -10000 0 0
CD47 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.006 0.06 -9999 0 -0.26 14 14
VCL 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.032 0.12 -9999 0 -0.28 50 50
CSF1 0.007 0.037 -9999 0 -0.44 2 2
PIK3C2A -0.1 0.18 -9999 0 -0.41 74 74
PI4 Kinase/Pyk2 -0.082 0.13 -9999 0 -0.22 116 116
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.034 0.11 -9999 0 -0.24 65 65
FAK1/Vinculin -0.083 0.14 -9999 0 -0.29 72 72
alphaV beta3/Integrin/ppsTEM5 0.005 0.062 -9999 0 -0.26 15 15
RHOA 0.01 0 -9999 0 -10000 0 0
VTN -0.11 0.2 -9999 0 -0.44 74 74
BCAR1 0.01 0 -9999 0 -10000 0 0
FGF2 0.005 0.046 -9999 0 -0.44 3 3
F11R 0.006 0.032 -9999 0 -0.31 3 3
alphaV/beta3 Integrin/Lactadherin 0.006 0.06 -9999 0 -0.26 14 14
alphaV/beta3 Integrin/TGFBR2 0.006 0.06 -9999 0 -0.26 14 14
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.023 0.021 -9999 0 -0.23 2 2
HSP90AA1 0.01 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.006 0.054 -9999 0 -0.23 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.009 0.003 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.033 0.1 -9999 0 -0.22 65 65
SDC1 0.008 0.026 -9999 0 -0.44 1 1
VAV3 0.011 0.024 -9999 0 -0.22 3 3
PTPN11 0.01 0 -9999 0 -10000 0 0
IRS1 0.002 0.059 -9999 0 -0.44 5 5
FAK1/Paxillin -0.083 0.14 -9999 0 -0.29 72 72
cell migration -0.075 0.13 -9999 0 -0.26 72 72
ITGAV 0.01 0 -9999 0 -10000 0 0
PI3K -0.042 0.11 -9999 0 -0.2 83 83
SPP1 0.005 0.046 -9999 0 -0.44 3 3
KDR -0.072 0.17 -9999 0 -0.44 53 53
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.01 0 -9999 0 -10000 0 0
COL4A3 -0.013 0.1 -9999 0 -0.44 15 15
angiogenesis -0.058 0.13 -9999 0 -0.42 18 18
Rac1/GTP 0.016 0.022 -9999 0 -0.2 3 3
EDIL3 -0.053 0.16 -9999 0 -0.44 40 40
cell proliferation 0.006 0.059 -9999 0 -0.26 14 14
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.38 0.48 0.65 1 -1.2 51 52
STAT6 (cleaved dimer) -0.41 0.42 -10000 0 -0.96 87 87
IGHG1 -0.12 0.18 0.42 5 -0.36 19 24
IGHG3 -0.37 0.46 0.56 2 -0.93 88 90
AKT1 -0.15 0.23 0.48 3 -0.5 16 19
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.1 0.18 0.44 3 -0.44 1 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.16 0.23 0.46 4 -0.5 21 25
THY1 -0.61 0.7 0.65 1 -1.4 112 113
MYB 0.007 0.004 -10000 0 -10000 0 0
HMGA1 0.01 0.001 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.19 0.28 0.53 6 -0.56 47 53
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.16 0.23 0.46 4 -0.5 19 23
SP1 0.015 0.012 -10000 0 -10000 0 0
INPP5D 0.009 0.002 -10000 0 -10000 0 0
SOCS5 0.017 0.021 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.36 0.48 0.54 3 -1.1 55 58
SOCS1 -0.24 0.32 0.5 3 -0.72 52 55
SOCS3 -0.16 0.25 0.49 3 -1.3 1 4
FCER2 -0.27 0.37 0.65 4 -0.8 52 56
PARP14 0.011 0.006 -10000 0 -10000 0 0
CCL17 -0.36 0.49 0.68 2 -1.2 50 52
GRB2 0.01 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.13 0.2 0.42 5 -0.41 10 15
T cell proliferation -0.36 0.48 0.59 2 -1.2 51 53
IL4R/JAK1 -0.38 0.48 -10000 0 -1.1 52 52
EGR2 -0.43 0.58 0.69 2 -1.4 60 62
JAK2 -0.017 0.042 0.15 2 -10000 0 2
JAK3 0.012 0.007 -10000 0 -10000 0 0
PIK3R1 0.01 0 -10000 0 -10000 0 0
JAK1 0.008 0.017 -10000 0 -10000 0 0
COL1A2 -0.11 0.17 0.45 2 -10000 0 2
CCL26 -0.38 0.48 0.68 2 -1.2 51 53
IL4R -0.4 0.51 0.72 2 -1.2 52 54
PTPN6 0.018 0.016 -10000 0 -10000 0 0
IL13RA2 -0.74 0.66 0.65 1 -1.3 161 162
IL13RA1 -0.017 0.042 0.15 2 -10000 0 2
IRF4 -0.046 0.15 0.49 1 -1.3 1 2
ARG1 -0.078 0.15 0.47 2 -10000 0 2
CBL -0.18 0.26 0.49 5 -0.53 47 52
GTF3A 0.019 0.019 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.018 0.062 0.2 5 -10000 0 5
IRF4/BCL6 -0.053 0.12 -10000 0 -1.2 1 1
CD40LG 0.016 0.017 -10000 0 -10000 0 0
MAPK14 -0.18 0.26 0.49 5 -0.55 36 41
mitosis -0.14 0.23 0.45 4 -0.48 16 20
STAT6 -0.42 0.56 0.76 3 -1.2 67 70
SPI1 0.01 0.009 -10000 0 -10000 0 0
RPS6KB1 -0.14 0.22 0.46 3 -0.47 9 12
STAT6 (dimer) -0.42 0.56 0.76 3 -1.2 67 70
STAT6 (dimer)/PARP14 -0.4 0.51 0.59 2 -1.1 68 70
mast cell activation 0.008 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.15 0.23 0.46 5 -0.5 11 16
FRAP1 -0.15 0.23 0.48 3 -0.5 16 19
LTA -0.37 0.49 0.7 3 -1.2 51 54
FES 0.008 0.026 -10000 0 -0.44 1 1
T-helper 1 cell differentiation 0.41 0.55 1.1 75 -0.73 4 79
CCL11 -0.47 0.57 -10000 0 -1.2 81 81
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.22 0.46 4 -0.49 12 16
IL2RG 0.014 0.006 -10000 0 -10000 0 0
IL10 -0.37 0.48 0.73 2 -1.1 52 54
IRS1 0.002 0.059 -10000 0 -0.44 5 5
IRS2 0.01 0.001 -10000 0 -10000 0 0
IL4 -0.083 0.14 0.43 3 -10000 0 3
IL5 -0.38 0.48 0.64 1 -1.2 51 52
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.3 0.39 0.62 4 -0.86 53 57
COL1A1 -0.11 0.2 0.5 5 -10000 0 5
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.48 -10000 0 -1.2 51 51
IL2R gamma/JAK3 0.014 0.01 -10000 0 -10000 0 0
TFF3 -0.48 0.61 0.64 2 -1.4 75 77
ALOX15 -0.38 0.48 0.65 1 -1.2 50 51
MYBL1 0.009 0.002 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.3 0.38 0.56 4 -0.87 53 57
SHC1 0.01 0 -10000 0 -10000 0 0
CEBPB 0.012 0.008 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.15 0.23 0.45 4 -0.48 19 23
mol:PI-3-4-5-P3 -0.15 0.23 0.48 3 -0.5 16 19
PI3K -0.15 0.24 0.48 3 -0.52 16 19
DOK2 0.008 0.026 -10000 0 -0.44 1 1
ETS1 0.015 0.022 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.12 0.19 0.4 5 -0.39 6 11
ITGB3 -0.41 0.52 0.65 1 -1.2 60 61
PIGR -0.4 0.51 0.74 1 -1.2 59 60
IGHE 0.031 0.045 0.12 1 -0.14 3 4
MAPKKK cascade -0.11 0.19 0.4 5 -0.38 6 11
BCL6 0.008 0.005 -10000 0 -10000 0 0
OPRM1 -0.38 0.48 0.64 1 -1.2 50 51
RETNLB -0.38 0.48 -10000 0 -1.2 50 50
SELP -0.43 0.56 0.65 1 -1.4 55 56
AICDA -0.35 0.46 0.64 1 -1.1 51 52
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.016 0.016 -10000 0 -10000 0 0
NFATC2 0.002 0.16 -10000 0 -0.44 17 17
NFATC3 -0.019 0.11 -10000 0 -0.26 45 45
CD40LG -0.094 0.4 0.43 3 -0.91 48 51
ITCH 0.012 0.037 -10000 0 -0.22 7 7
CBLB 0.012 0.037 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.075 0.21 -10000 0 -0.58 25 25
JUNB 0.01 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.045 -10000 0 -0.27 7 7
T cell anergy -0.002 0.061 -10000 0 -0.36 7 7
TLE4 0.014 0.11 -10000 0 -0.4 5 5
Jun/NFAT1-c-4/p21SNFT -0.1 0.38 -10000 0 -0.88 50 50
AP-1/NFAT1-c-4 -0.15 0.45 0.43 1 -1.1 49 50
IKZF1 0.01 0.11 0.27 1 -0.4 5 6
T-helper 2 cell differentiation -0.35 0.31 -10000 0 -0.7 87 87
AP-1/NFAT1 -0.029 0.16 0.23 2 -0.35 42 44
CALM1 0.012 0.027 -10000 0 -0.16 7 7
EGR2 -0.13 0.52 0.46 1 -1.2 49 50
EGR3 -0.16 0.55 0.46 1 -1.3 49 50
NFAT1/FOXP3 0.004 0.11 -10000 0 -0.4 5 5
EGR1 -0.024 0.12 -10000 0 -0.44 23 23
JUN 0.017 0.02 -10000 0 -10000 0 0
EGR4 0.007 0.008 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.026 -10000 0 -0.16 7 7
GBP3 0.014 0.11 -10000 0 -0.4 5 5
FOSL1 0.007 0.037 -10000 0 -0.44 2 2
NFAT1-c-4/MAF/IRF4 -0.1 0.37 -10000 0 -0.87 50 50
DGKA 0.01 0.11 -10000 0 -0.4 5 5
CREM 0.01 0.002 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.11 0.38 -10000 0 -0.9 50 50
CTLA4 -0.001 0.082 -10000 0 -0.33 5 5
NFAT1-c-4 (dimer)/EGR1 -0.12 0.41 -10000 0 -0.97 50 50
NFAT1-c-4 (dimer)/EGR4 -0.11 0.38 -10000 0 -0.91 50 50
FOS -0.052 0.17 -10000 0 -0.44 44 44
IFNG -0.039 0.14 -10000 0 -0.55 6 6
T cell activation -0.037 0.24 0.41 1 -0.62 27 28
MAF 0.01 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.061 0.31 0.71 50 -0.43 1 51
TNF -0.099 0.37 -10000 0 -0.86 51 51
FASLG -0.15 0.56 -10000 0 -1.3 50 50
TBX21 0.014 0.013 -10000 0 -10000 0 0
BATF3 0.01 0.001 -10000 0 -10000 0 0
PRKCQ 0.002 0.075 -10000 0 -0.44 8 8
PTPN1 0.014 0.11 -10000 0 -0.4 5 5
NFAT1-c-4/ICER1 -0.11 0.38 -10000 0 -0.9 50 50
GATA3 -0.34 0.19 -10000 0 -0.44 225 225
T-helper 1 cell differentiation -0.034 0.14 -10000 0 -0.54 6 6
IL2RA -0.076 0.21 -10000 0 -0.55 33 33
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.013 0.11 -10000 0 -0.4 5 5
E2F1 0.009 0.006 -10000 0 -10000 0 0
PPARG 0.01 0.001 -10000 0 -10000 0 0
SLC3A2 0.014 0.11 -10000 0 -0.4 5 5
IRF4 0.008 0.026 -10000 0 -0.44 1 1
PTGS2 -0.12 0.46 0.47 7 -0.96 55 62
CSF2 -0.094 0.41 0.49 5 -0.9 49 54
JunB/Fra1/NFAT1-c-4 -0.099 0.37 -10000 0 -0.87 50 50
IL4 -0.37 0.33 -10000 0 -0.74 86 86
IL5 -0.09 0.41 0.46 7 -0.91 48 55
IL2 -0.038 0.24 0.41 1 -0.63 26 27
IL3 -0.03 0.053 -10000 0 -10000 0 0
RNF128 0.004 0.085 -10000 0 -0.54 7 7
NFATC1 -0.062 0.31 0.43 1 -0.71 50 51
CDK4 0.044 0.21 0.53 28 -10000 0 28
PTPRK 0.014 0.11 -10000 0 -0.4 5 5
IL8 -0.14 0.38 0.42 1 -0.9 49 50
POU2F1 0.01 0 -10000 0 -10000 0 0
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.01 0.029 -10000 0 -0.26 1 1
alphaM/beta2 Integrin/GPIbA 0.01 0.025 -10000 0 -10000 0 0
alphaM/beta2 Integrin/proMMP-9 0.002 0.037 -10000 0 -0.26 4 4
PLAUR 0.009 0.002 -10000 0 -10000 0 0
HMGB1 0.006 0.019 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.011 0.024 -10000 0 -10000 0 0
AGER 0.005 0.018 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
SELPLG 0.009 0.003 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.001 0.061 -10000 0 -0.18 25 25
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0 0.052 -10000 0 -0.44 4 4
CYR61 -0.004 0.078 -10000 0 -0.44 9 9
TLN1 0.01 0 -10000 0 -10000 0 0
Rap1/GTP -0.1 0.1 -10000 0 -0.33 33 33
RHOA 0.01 0 -10000 0 -10000 0 0
P-selectin oligomer -0.034 0.13 -10000 0 -0.44 28 28
MYH2 -0.15 0.14 -10000 0 -0.4 44 44
MST1R 0.006 0.037 -10000 0 -0.44 2 2
leukocyte activation during inflammatory response -0.012 0.07 -10000 0 -0.22 26 26
APOB -0.015 0.099 -10000 0 -0.44 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.008 0.026 -10000 0 -0.44 1 1
JAM3 0.008 0.026 -10000 0 -0.44 1 1
GP1BA 0.008 0.026 -10000 0 -0.44 1 1
alphaM/beta2 Integrin/CTGF 0.004 0.047 -10000 0 -0.25 7 7
alphaM/beta2 Integrin -0.12 0.12 -10000 0 -0.33 44 44
JAM3 homodimer 0.008 0.026 -10000 0 -0.44 1 1
ICAM2 0.01 0 -10000 0 -10000 0 0
ICAM1 0.01 0.001 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.12 0.12 -10000 0 -0.33 44 44
cell adhesion 0.01 0.025 -10000 0 -10000 0 0
NFKB1 0.007 0.12 0.22 1 -0.32 28 29
THY1 -0.15 0.22 -10000 0 -0.44 105 105
RhoA/GDP 0.007 0 -10000 0 -10000 0 0
Lipoprotein(a) -0.019 0.081 -10000 0 -0.26 29 29
alphaM/beta2 Integrin/LRP/tPA -0.008 0.075 -10000 0 -0.23 27 27
IL6 -0.022 0.22 0.27 2 -0.62 31 33
ITGB2 0.004 0.018 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.008 0.046 -10000 0 -0.24 7 7
alphaM/beta2 Integrin/JAM2/JAM3 0.011 0.041 -10000 0 -0.24 5 5
JAM2 0.004 0.052 -10000 0 -0.44 4 4
alphaM/beta2 Integrin/ICAM1 0.013 0.035 -10000 0 -0.23 3 3
alphaM/beta2 Integrin/uPA/Plg -0.12 0.12 -10000 0 -0.23 151 151
RhoA/GTP -0.16 0.15 -10000 0 -0.27 133 133
positive regulation of phagocytosis -0.074 0.087 -10000 0 -0.26 32 32
Ron/MSP 0.01 0.033 -10000 0 -0.31 3 3
alphaM/beta2 Integrin/uPAR/uPA 0.009 0.047 -10000 0 -0.24 7 7
alphaM/beta2 Integrin/uPAR 0.011 0.024 -10000 0 -10000 0 0
PLAU -0.001 0.069 -10000 0 -0.44 7 7
PLAT -0.035 0.14 -10000 0 -0.44 29 29
actin filament polymerization -0.14 0.14 -10000 0 -0.38 44 44
MST1 0.008 0.026 -10000 0 -0.44 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.011 0.071 -10000 0 -0.22 26 26
TNF 0.009 0.12 -10000 0 -0.33 26 26
RAP1B 0.01 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.004 0.05 -10000 0 -0.27 7 7
fibrinolysis -0.12 0.12 -10000 0 -0.23 151 151
HCK 0.007 0.026 -10000 0 -0.44 1 1
dendritic cell antigen processing and presentation -0.12 0.12 -10000 0 -0.33 44 44
VTN -0.11 0.2 -10000 0 -0.44 74 74
alphaM/beta2 Integrin/CYR61 0.003 0.05 -10000 0 -0.25 8 8
LPA -0.018 0.095 -10000 0 -0.44 14 14
LRP1 0.01 0 -10000 0 -10000 0 0
cell migration 0.002 0.037 -10000 0 -0.23 5 5
FN1 0.009 0.003 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.084 0.13 -10000 0 -0.26 101 101
MPO 0.009 0.003 -10000 0 -10000 0 0
KNG1 -0.26 0.22 -10000 0 -0.44 169 169
RAP1/GDP 0.013 0 -10000 0 -10000 0 0
ROCK1 -0.15 0.14 -10000 0 -0.42 40 40
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.25 0.22 -10000 0 -0.44 164 164
CTGF -0.001 0.069 -10000 0 -0.44 7 7
alphaM/beta2 Integrin/Hck 0.01 0.03 -10000 0 -0.31 1 1
ITGAM 0.005 0.018 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.009 0.078 -10000 0 -0.24 28 28
HP 0.007 0.004 -10000 0 -10000 0 0
leukocyte adhesion -0.081 0.13 -10000 0 -0.25 89 89
SELP -0.034 0.13 -10000 0 -0.44 28 28
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 -0.048 0.12 -9999 0 -0.31 53 53
PDGFRB -0.007 0.083 -9999 0 -0.44 10 10
SPHK1 -0.01 0.028 -9999 0 -10000 0 0
mol:S1P -0.014 0.037 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.077 0.18 -9999 0 -0.39 63 63
GNAO1 -0.032 0.13 -9999 0 -0.45 25 25
PDGFB-D/PDGFRB/PLCgamma1 -0.078 0.16 -9999 0 -0.35 64 64
PLCG1 -0.069 0.17 -9999 0 -0.37 62 62
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.007 0.083 -9999 0 -0.44 10 10
GNAI2 0.007 0.009 -9999 0 -10000 0 0
GNAI3 0.007 0.008 -9999 0 -10000 0 0
GNAI1 0.004 0.038 -9999 0 -0.44 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.046 0.1 -9999 0 -0.26 53 53
S1P1/S1P -0.042 0.099 -9999 0 -0.25 29 29
negative regulation of cAMP metabolic process -0.075 0.18 -9999 0 -0.38 63 63
MAPK3 -0.1 0.24 -9999 0 -0.56 58 58
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.007 0 -9999 0 -10000 0 0
RhoA/GDP 0.007 0 -9999 0 -10000 0 0
KDR -0.075 0.17 -9999 0 -0.44 53 53
PLCB2 -0.037 0.09 -9999 0 -0.24 22 22
RAC1 0.01 0 -9999 0 -10000 0 0
RhoA/GTP -0.045 0.081 -9999 0 -0.23 22 22
receptor internalization -0.049 0.088 -9999 0 -0.23 29 29
PTGS2 -0.17 0.38 -9999 0 -0.99 50 50
Rac1/GTP -0.045 0.081 -9999 0 -0.22 28 28
RHOA 0.01 0 -9999 0 -10000 0 0
VEGFA 0.008 0.006 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.075 0.18 -9999 0 -0.38 63 63
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.007 0.008 -9999 0 -10000 0 0
MAPK1 -0.1 0.24 -9999 0 -0.56 58 58
S1P1/S1P/PDGFB-D/PDGFRB -0.059 0.11 -9999 0 -0.29 29 29
ABCC1 0.007 0.007 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.006 0.082 -10000 0 -0.44 10 10
Jak2/Leptin Receptor -0.12 0.12 -10000 0 -0.27 111 111
PTP1B/AKT1 -0.062 0.054 -10000 0 -0.22 22 22
FYN 0.01 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.072 0.06 -10000 0 -0.25 22 22
EGFR -0.009 0.006 -10000 0 -10000 0 0
EGF/EGFR -0.23 0.079 -10000 0 -0.25 265 265
CSF1 0.007 0.037 -10000 0 -0.44 2 2
AKT1 0.01 0 -10000 0 -10000 0 0
INSR 0.01 0 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.076 0.08 -10000 0 -0.29 30 30
Insulin Receptor/Insulin -0.044 0.043 -10000 0 -0.2 5 5
HCK 0.007 0.026 -10000 0 -0.44 1 1
CRK 0.01 0 -10000 0 -10000 0 0
TYK2 -0.067 0.057 -10000 0 -0.24 22 22
EGF -0.4 0.14 -10000 0 -0.45 261 261
YES1 0.01 0 -10000 0 -10000 0 0
CAV1 -0.14 0.058 -10000 0 -0.25 32 32
TXN 0.004 0.002 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.066 0.064 -10000 0 -0.24 26 26
cell migration 0.072 0.06 0.25 22 -10000 0 22
STAT3 0.009 0 -10000 0 -10000 0 0
PRLR -0.16 0.22 -10000 0 -0.44 111 111
ITGA2B 0.008 0.003 -10000 0 -10000 0 0
CSF1R 0.008 0.026 -10000 0 -0.44 1 1
Prolactin Receptor/Prolactin -0.12 0.16 -10000 0 -0.31 111 111
FGR 0.008 0.026 -10000 0 -0.44 1 1
PTP1B/p130 Cas -0.067 0.057 -10000 0 -0.24 22 22
Crk/p130 Cas -0.062 0.056 -10000 0 -0.23 22 22
DOK1 -0.061 0.062 -10000 0 -0.23 25 25
JAK2 -0.13 0.13 -10000 0 -0.29 112 112
Jak2/Leptin Receptor/Leptin -0.071 0.066 -10000 0 -0.27 11 11
PIK3R1 0.01 0 -10000 0 -10000 0 0
PTPN1 -0.072 0.06 -10000 0 -0.25 22 22
LYN 0.01 0 -10000 0 -10000 0 0
CDH2 -0.01 0.093 -10000 0 -0.44 13 13
SRC -0.02 0.023 -10000 0 -10000 0 0
ITGB3 -0.013 0.097 -10000 0 -0.44 14 14
CAT1/PTP1B -0.16 0.089 -10000 0 -0.33 22 22
CAPN1 0.008 0.001 -10000 0 -10000 0 0
CSK 0.01 0 -10000 0 -10000 0 0
PI3K -0.039 0.041 -10000 0 -0.24 1 1
mol:H2O2 -0.004 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.065 0.062 -10000 0 -0.25 11 11
negative regulation of transcription -0.13 0.13 -10000 0 -0.28 112 112
FCGR2A 0.009 0.002 -10000 0 -10000 0 0
FER 0.004 0.002 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.005 0.07 -10000 0 -0.31 14 14
BLK 0.008 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.013 0.002 -10000 0 -10000 0 0
RHOA 0.008 0.001 -10000 0 -10000 0 0
LEPR 0.009 0.026 -10000 0 -0.44 1 1
BCAR1 0.01 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.01 0 -10000 0 -10000 0 0
mol:NADPH -0.005 0.002 -10000 0 -10000 0 0
TRPV6 -0.12 0.089 -10000 0 -0.22 12 12
PRL 0.001 0.004 -10000 0 -10000 0 0
SOCS3 0.015 0.075 -10000 0 -1.2 1 1
SPRY2 0.007 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.008 0.036 -10000 0 -0.26 5 5
CSF1/CSF1R -0.063 0.061 -10000 0 -0.24 23 23
Ras protein signal transduction 0.026 0.017 -10000 0 -10000 0 0
IRS1 0.002 0.059 -10000 0 -0.44 5 5
INS 0 0.002 -10000 0 -10000 0 0
LEP 0.005 0.005 -10000 0 -10000 0 0
STAT5B -0.091 0.073 -10000 0 -0.25 29 29
STAT5A -0.091 0.073 -10000 0 -0.25 29 29
GRB2 0.01 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.074 0.069 -10000 0 -0.25 31 31
CSN2 -0.038 0.071 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
LAT -0.018 0.024 -10000 0 -10000 0 0
YBX1 0.011 0.001 -10000 0 -10000 0 0
LCK 0.01 0.001 -10000 0 -10000 0 0
SHC1 0.01 0 -10000 0 -10000 0 0
NOX4 -0.04 0.14 -10000 0 -0.45 30 30
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 -0.005 0.063 -10000 0 -0.22 24 24
epithelial cell differentiation 0.002 0.065 -10000 0 -0.22 24 24
CYFIP2 0.008 0.026 -10000 0 -0.44 1 1
ENAH 0.002 0.043 -10000 0 -10000 0 0
EGFR 0.01 0 -10000 0 -10000 0 0
EPHA2 0.01 0.001 -10000 0 -10000 0 0
MYO6 -0.006 0.06 -10000 0 -0.2 24 24
CTNNB1 0.01 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.019 0.016 -10000 0 -0.26 1 1
AQP5 -0.05 0.15 -10000 0 -0.44 33 33
CTNND1 0.01 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.006 0.059 -10000 0 -0.2 24 24
regulation of calcium-dependent cell-cell adhesion -0.024 0.089 -10000 0 -0.23 44 44
EGF -0.4 0.14 -10000 0 -0.44 261 261
NCKAP1 0.01 0 -10000 0 -10000 0 0
AQP3 -0.16 0.22 -10000 0 -0.44 107 107
cortical microtubule organization 0.002 0.065 -10000 0 -0.22 24 24
GO:0000145 -0.008 0.056 -10000 0 -0.19 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.003 0.066 -10000 0 -0.22 24 24
MLLT4 0.01 0 -10000 0 -10000 0 0
ARF6/GDP -0.015 0.049 -10000 0 -0.18 24 24
ARF6 0.01 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.025 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.003 0.056 -10000 0 -0.19 24 24
PVRL2 0.01 0 -10000 0 -10000 0 0
ZYX -0.006 0.06 -10000 0 -0.2 24 24
ARF6/GTP 0.028 0.002 -10000 0 -10000 0 0
CDH1 -0.027 0.12 -10000 0 -0.44 24 24
EGFR/EGFR/EGF/EGF -0.19 0.08 -10000 0 -0.21 266 266
RhoA/GDP 0.003 0.062 -10000 0 -0.2 24 24
actin cytoskeleton organization -0.006 0.059 -10000 0 -0.2 24 24
IGF-1R heterotetramer 0.01 0 -10000 0 -10000 0 0
GIT1 0.01 0 -10000 0 -10000 0 0
IGF1R 0.01 0 -10000 0 -10000 0 0
IGF1 0 0.064 -10000 0 -0.44 6 6
DIAPH1 0.019 0.035 -10000 0 -0.55 1 1
Wnt receptor signaling pathway -0.002 0.065 0.22 24 -10000 0 24
RHOA 0.01 0 -10000 0 -10000 0 0
RhoA/GTP -0.015 0.049 -10000 0 -0.18 24 24
CTNNA1 0.01 0 -10000 0 -10000 0 0
VCL -0.006 0.06 -10000 0 -0.2 24 24
EFNA1 0.01 0 -10000 0 -10000 0 0
LPP -0.006 0.057 -10000 0 -0.2 24 24
Ephrin A1/EPHA2 0.001 0.059 -10000 0 -0.2 24 24
SEC6/SEC8 -0.015 0.051 -10000 0 -0.18 24 24
MGAT3 -0.024 0.09 -10000 0 -0.23 44 44
HGF/MET -0.012 0.077 -10000 0 -0.21 33 33
HGF -0.017 0.11 -10000 0 -0.44 17 17
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.005 0.064 -10000 0 -0.22 24 24
actin cable formation 0.011 0.041 -10000 0 -10000 0 0
KIAA1543 -0.006 0.058 -10000 0 -0.2 25 25
KIFC3 -0.006 0.06 -10000 0 -0.2 24 24
NCK1 0.01 0 -10000 0 -10000 0 0
EXOC3 0.01 0 -10000 0 -10000 0 0
ACTN1 -0.006 0.06 -10000 0 -0.2 24 24
NCK1/GIT1 0.015 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.065 -10000 0 -0.22 24 24
EXOC4 0.01 0 -10000 0 -10000 0 0
STX4 -0.006 0.06 -10000 0 -0.2 24 24
PIP5K1C -0.006 0.06 -10000 0 -0.2 24 24
LIMA1 0.01 0 -10000 0 -10000 0 0
ABI1 0.01 0 -10000 0 -10000 0 0
ROCK1 0.001 0.049 -10000 0 -10000 0 0
adherens junction assembly 0 0.056 -10000 0 -0.22 1 1
IGF-1R heterotetramer/IGF1 -0.004 0.066 -10000 0 -0.2 30 30
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.015 0 -10000 0 -10000 0 0
MET 0.009 0.003 -10000 0 -10000 0 0
PLEKHA7 -0.006 0.061 -10000 0 -0.2 25 25
mol:GTP 0.024 0.001 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0 0.054 -10000 0 -0.18 24 24
cortical actin cytoskeleton stabilization -0.005 0.063 -10000 0 -0.22 24 24
regulation of cell-cell adhesion -0.006 0.059 -10000 0 -0.2 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.005 0.064 -10000 0 -0.22 24 24
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.01 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.026 0.072 -10000 0 -0.23 6 6
NT3 (dimer)/TRKC -0.073 0.15 -10000 0 -0.33 73 73
NT3 (dimer)/TRKB -0.12 0.16 -10000 0 -0.28 137 137
SHC/Grb2/SOS1/GAB1/PI3K 0.017 0 -10000 0 -10000 0 0
RAPGEF1 0.01 0 -10000 0 -10000 0 0
BDNF 0.008 0.003 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
DYNLT1 0.01 0 -10000 0 -10000 0 0
NTRK1 -0.079 0.18 -10000 0 -0.44 56 56
NTRK2 -0.16 0.22 -10000 0 -0.44 113 113
NTRK3 -0.065 0.17 -10000 0 -0.44 48 48
NT-4/5 (dimer)/TRKB -0.097 0.14 -10000 0 -0.26 119 119
neuron apoptosis 0.091 0.13 0.36 33 -10000 0 33
SHC 2-3/Grb2 -0.097 0.14 -10000 0 -0.39 33 33
SHC1 0.01 0 -10000 0 -10000 0 0
SHC2 -0.093 0.12 -10000 0 -0.38 29 29
SHC3 -0.1 0.15 -10000 0 -0.44 32 32
STAT3 (dimer) 0.013 0.02 -10000 0 -0.32 1 1
NT3 (dimer)/TRKA -0.07 0.15 -10000 0 -0.3 82 82
RIN/GDP -0.024 0.058 -10000 0 -0.18 7 7
GIPC1 0.01 0 -10000 0 -10000 0 0
KRAS 0.01 0 -10000 0 -10000 0 0
DNAJA3 -0.044 0.1 -10000 0 -0.22 67 67
RIN/GTP 0.001 0.002 -10000 0 -10000 0 0
CCND1 0.011 0.041 -10000 0 -0.68 1 1
MAGED1 0.01 0 -10000 0 -10000 0 0
PTPN11 0.01 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.005 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.02 0 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.045 0.12 -10000 0 -0.26 66 66
TRKA/NEDD4-2 -0.05 0.13 -10000 0 -0.31 57 57
ELMO1 0.01 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.013 0 -10000 0 -10000 0 0
NGF -0.003 0.074 -10000 0 -0.44 8 8
HRAS 0.01 0 -10000 0 -10000 0 0
DOCK1 0.01 0 -10000 0 -10000 0 0
GAB2 0.01 0 -10000 0 -10000 0 0
RIT2 0.001 0.003 -10000 0 -10000 0 0
RIT1 0.01 0 -10000 0 -10000 0 0
FRS2 0.01 0 -10000 0 -10000 0 0
DNM1 0.005 0.027 -10000 0 -0.44 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.01 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.039 0.1 -10000 0 -0.21 67 67
mol:GDP -0.034 0.082 -10000 0 -0.24 15 15
NGF (dimer) -0.003 0.074 -10000 0 -0.44 8 8
RhoG/GDP 0.007 0 -10000 0 -10000 0 0
RIT1/GDP -0.021 0.06 -10000 0 -0.18 7 7
TIAM1 0.01 0 -10000 0 -10000 0 0
PIK3R1 0.01 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.088 0.13 -10000 0 -0.25 113 113
KIDINS220/CRKL/C3G 0.015 0 -10000 0 -10000 0 0
SHC/RasGAP 0.015 0 -10000 0 -10000 0 0
FRS2 family/SHP2 0.02 0.002 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.025 0 -10000 0 -10000 0 0
RIT1/GTP 0.007 0 -10000 0 -10000 0 0
NT3 (dimer) -0.039 0.14 -10000 0 -0.44 31 31
RAP1/GDP -0.02 0.05 -10000 0 -0.16 7 7
KIDINS220/CRKL 0.01 0 -10000 0 -10000 0 0
BDNF (dimer) 0.008 0.003 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.043 0.12 -10000 0 -0.26 64 64
Schwann cell development -0.028 0.025 -10000 0 -10000 0 0
EHD4 0.01 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.025 0.003 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.018 0.002 -10000 0 -10000 0 0
RAP1B 0.01 0 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.14 -10000 0 -0.24 142 142
ABL1 0.01 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.015 0 -10000 0 -10000 0 0
Rap1/GTP -0.028 0.06 -10000 0 -10000 0 0
STAT3 0.013 0.02 -10000 0 -0.32 1 1
axon guidance -0.11 0.13 -10000 0 -0.23 142 142
MAPK3 -0.04 0.11 -10000 0 -0.23 66 66
MAPK1 -0.04 0.11 -10000 0 -0.23 66 66
CDC42/GDP -0.021 0.06 -10000 0 -0.18 7 7
NTF3 -0.039 0.14 -10000 0 -0.44 31 31
NTF4 0.005 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM -0.042 0.12 -10000 0 -0.26 63 63
PI3K 0.015 0 -10000 0 -10000 0 0
FRS3 0.01 0.001 -10000 0 -10000 0 0
FAIM 0.01 0.001 -10000 0 -10000 0 0
GAB1 0.01 0 -10000 0 -10000 0 0
RASGRF1 -0.045 0.1 -10000 0 -0.22 66 66
SOS1 0.01 0 -10000 0 -10000 0 0
MCF2L -0.062 0.13 -10000 0 -0.28 73 73
RGS19 0.01 0.001 -10000 0 -10000 0 0
CDC42 0.01 0 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.043 -10000 0 -10000 0 0
Rac1/GDP -0.021 0.06 -10000 0 -0.18 7 7
NGF (dimer)/TRKA/GRIT -0.048 0.11 -10000 0 -0.26 63 63
neuron projection morphogenesis -0.036 0.1 -10000 0 -0.46 4 4
NGF (dimer)/TRKA/NEDD4-2 -0.043 0.12 -10000 0 -0.26 64 64
MAP2K1 0.013 0 -10000 0 -10000 0 0
NGFR -0.003 0.074 -10000 0 -0.44 8 8
NGF (dimer)/TRKA/GIPC/GAIP -0.037 0.094 -10000 0 -0.22 49 49
RAS family/GTP/PI3K 0.014 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.029 0.003 -10000 0 -10000 0 0
NRAS 0.01 0 -10000 0 -10000 0 0
GRB2/SOS1 0.015 0 -10000 0 -10000 0 0
PRKCI 0.01 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCZ 0.01 0 -10000 0 -10000 0 0
MAPKKK cascade -0.12 0.22 -10000 0 -0.53 63 63
RASA1 0.01 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.049 0.13 -10000 0 -0.31 56 56
SQSTM1 0.009 0.002 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.075 0.12 -10000 0 -0.23 113 113
NGF (dimer)/TRKA/p62/Atypical PKCs -0.026 0.1 -10000 0 -0.22 61 61
MATK 0.004 0.046 -10000 0 -0.44 3 3
NEDD4L 0.008 0.026 -10000 0 -0.44 1 1
RAS family/GDP -0.026 0.043 -10000 0 -0.15 7 7
NGF (dimer)/TRKA -0.047 0.11 -10000 0 -0.23 67 67
Rac1/GTP -0.049 0.072 -10000 0 -0.21 30 30
FRS2 family/SHP2/CRK family 0.029 0.003 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.01 0.087 0.26 1 -0.78 3 4
SMARCC2 0.011 0 -10000 0 -10000 0 0
SMARCC1 0.011 0 -10000 0 -10000 0 0
TBX21 -0.002 0.068 -10000 0 -0.31 5 5
SUMO2 0.006 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.013 0.002 -10000 0 -10000 0 0
FKBP4 0.01 0 -10000 0 -10000 0 0
FKBP5 0 0.064 -10000 0 -0.44 6 6
GR alpha/HSP90/FKBP51/HSP90 0.042 0.073 0.21 10 -0.22 5 15
PRL -0.029 0.075 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.067 0.18 0.42 25 -0.34 5 30
RELA -0.07 0.1 -10000 0 -0.23 30 30
FGG 0.074 0.13 0.37 19 -10000 0 19
GR beta/TIF2 0.015 0.12 0.24 10 -0.28 26 36
IFNG -0.065 0.16 -10000 0 -0.43 25 25
apoptosis -0.06 0.21 0.36 2 -0.5 39 41
CREB1 0.002 0.052 -10000 0 -0.32 7 7
histone acetylation -0.019 0.072 -10000 0 -0.28 7 7
BGLAP -0.013 0.074 -10000 0 -0.39 1 1
GR/PKAc 0.048 0.061 0.21 9 -10000 0 9
NF kappa B1 p50/RelA -0.12 0.18 -10000 0 -0.3 125 125
SMARCD1 0.011 0 -10000 0 -10000 0 0
MDM2 0.038 0.058 0.17 22 -10000 0 22
GATA3 -0.34 0.19 -10000 0 -0.44 225 225
AKT1 0.009 0.016 0.16 3 -10000 0 3
CSF2 -0.029 0.061 -10000 0 -0.4 1 1
GSK3B 0.006 0.008 -10000 0 -10000 0 0
NR1I3 -0.057 0.22 0.37 1 -0.67 20 21
CSN2 0.073 0.12 0.32 16 -10000 0 16
BRG1/BAF155/BAF170/BAF60A 0.029 0 -10000 0 -10000 0 0
NFATC1 0.011 0.002 -10000 0 -10000 0 0
POU2F1 0.01 0.004 -10000 0 -10000 0 0
CDKN1A 0.021 0.029 -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 -0.002 0.058 -10000 0 -0.44 5 5
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.025 0.071 0.21 5 -0.26 6 11
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.075 0.26 0.36 1 -0.72 30 31
JUN -0.045 0.16 0.26 3 -0.38 37 40
IL4 -0.017 0.074 -10000 0 -0.34 2 2
CDK5R1 0.007 0.005 -10000 0 -10000 0 0
PRKACA 0.01 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.019 0.098 0.22 13 -0.28 20 33
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.047 0.069 0.21 9 -0.2 4 13
cortisol/GR alpha (monomer) 0.098 0.18 0.49 24 -10000 0 24
NCOA2 -0.031 0.13 -10000 0 -0.44 26 26
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.05 0.17 -10000 0 -0.44 44 44
AP-1/NFAT1-c-4 -0.065 0.22 0.32 3 -0.52 35 38
AFP -0.15 0.41 -10000 0 -1.3 32 32
SUV420H1 0.01 0 -10000 0 -10000 0 0
IRF1 0.061 0.094 0.35 5 -10000 0 5
TP53 0.021 0.013 -10000 0 -10000 0 0
PPP5C 0.01 0 -10000 0 -10000 0 0
KRT17 -0.1 0.3 -10000 0 -1 21 21
KRT14 -0.034 0.08 -10000 0 -0.36 1 1
TBP 0.014 0 -10000 0 -10000 0 0
CREBBP 0.006 0.017 -10000 0 -10000 0 0
HDAC1 0.009 0.001 -10000 0 -10000 0 0
HDAC2 0.009 0.002 -10000 0 -10000 0 0
AP-1 -0.065 0.22 0.32 3 -0.52 35 38
MAPK14 0.006 0.008 -10000 0 -10000 0 0
MAPK10 0.006 0.008 -10000 0 -10000 0 0
MAPK11 0.006 0.008 -10000 0 -10000 0 0
KRT5 -0.08 0.22 -10000 0 -0.65 21 21
interleukin-1 receptor activity -0.001 0.002 -10000 0 -10000 0 0
NCOA1 0.01 0.009 -10000 0 -10000 0 0
STAT1 0.013 0.002 -10000 0 -10000 0 0
CGA -0.039 0.17 -10000 0 -0.95 8 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.009 0.061 0.27 2 -10000 0 2
MAPK3 0.006 0.008 -10000 0 -10000 0 0
MAPK1 0.006 0.008 -10000 0 -10000 0 0
ICAM1 -0.12 0.18 -10000 0 -0.44 31 31
NFKB1 -0.07 0.1 -10000 0 -0.24 25 25
MAPK8 -0.036 0.13 -10000 0 -0.31 31 31
MAPK9 0.006 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.068 0.21 0.37 2 -0.53 39 41
BAX 0.019 0.022 -10000 0 -10000 0 0
POMC -0.16 0.24 -10000 0 -0.7 20 20
EP300 0.006 0.017 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.097 0.16 0.44 23 -10000 0 23
proteasomal ubiquitin-dependent protein catabolic process 0.026 0.047 0.16 7 -10000 0 7
SGK1 0.029 0.036 -10000 0 -10000 0 0
IL13 -0.31 0.24 -10000 0 -0.61 73 73
IL6 -0.19 0.34 -10000 0 -1 33 33
PRKACG 0.002 0.004 -10000 0 -10000 0 0
IL5 -0.27 0.2 -10000 0 -0.54 62 62
IL2 -0.067 0.16 -10000 0 -0.46 19 19
CDK5 0.007 0.005 -10000 0 -10000 0 0
PRKACB 0.01 0 -10000 0 -10000 0 0
HSP90AA1 0.01 0 -10000 0 -10000 0 0
IL8 -0.11 0.19 -10000 0 -0.46 28 28
CDK5R1/CDK5 0.01 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.072 0.14 -10000 0 -0.32 25 25
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.093 0.15 0.4 26 -10000 0 26
SMARCA4 0.011 0 -10000 0 -10000 0 0
chromatin remodeling 0.069 0.095 0.3 12 -10000 0 12
NF kappa B1 p50/RelA/Cbp -0.082 0.14 -10000 0 -0.32 31 31
JUN (dimer) -0.045 0.16 0.26 3 -0.37 38 41
YWHAH 0.01 0 -10000 0 -10000 0 0
VIPR1 -0.032 0.17 -10000 0 -0.73 15 15
NR3C1 0.058 0.1 0.29 20 -10000 0 20
NR4A1 -0.18 0.23 -10000 0 -0.44 123 123
TIF2/SUV420H1 -0.015 0.093 -10000 0 -0.31 26 26
MAPKKK cascade -0.06 0.21 0.36 2 -0.5 39 41
cortisol/GR alpha (dimer)/Src-1 0.092 0.16 0.42 26 -10000 0 26
PBX1 0.001 0.064 -10000 0 -0.44 6 6
POU1F1 0.005 0.006 -10000 0 -10000 0 0
SELE -0.47 0.5 -10000 0 -0.95 149 149
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.069 0.096 0.3 12 -10000 0 12
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.093 0.15 0.4 26 -10000 0 26
mol:cortisol 0.048 0.1 0.26 26 -10000 0 26
MMP1 -0.083 0.27 -10000 0 -1.1 18 18
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.035 0.026 -10000 0 -0.26 1 1
FYN 0.051 0.065 0.28 13 -0.41 1 14
LAT/GRAP2/SLP76 0.036 0.03 -10000 0 -0.25 1 1
IKBKB 0.01 0 -10000 0 -10000 0 0
AKT1 0.067 0.076 0.25 29 -0.29 1 30
B2M 0.011 0.003 -10000 0 -10000 0 0
IKBKG 0.012 0.013 -10000 0 -0.086 1 1
MAP3K8 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ -0.03 0.022 -10000 0 -0.047 172 172
integrin-mediated signaling pathway 0.013 0.002 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.075 0.087 0.31 23 -0.38 1 24
TRPV6 -0.31 0.2 0.23 2 -0.44 206 208
CD28 0.008 0.026 -10000 0 -0.44 1 1
SHC1 0.045 0.051 0.24 10 -0.3 1 11
receptor internalization 0.027 0.026 0.2 2 -0.22 1 3
PRF1 0.043 0.056 0.37 4 -10000 0 4
KRAS 0.01 0 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
COT/AKT1 0.064 0.068 0.23 29 -0.23 1 30
LAT 0.049 0.052 0.25 8 -0.3 1 9
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D 0.009 0.004 -10000 0 -10000 0 0
CD3E 0.008 0.027 -10000 0 -0.44 1 1
CD3G 0.01 0.003 -10000 0 -10000 0 0
RASGRP2 0.015 0.019 0.066 10 -0.16 2 12
RASGRP1 0.072 0.086 0.27 29 -0.28 2 31
HLA-A 0.011 0.003 -10000 0 -10000 0 0
RASSF5 0.01 0.001 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.013 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.051 0.048 0.13 47 -0.072 1 48
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.001 0.009 -10000 0 -0.14 1 1
PRKCA 0.04 0.035 0.13 17 -0.2 1 18
GRAP2 0.009 0.002 -10000 0 -10000 0 0
mol:IP3 0.14 0.098 0.2 198 -0.29 1 199
EntrezGene:6957 0.002 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.017 0.019 0.17 2 -10000 0 2
ORAI1 0.17 0.11 0.24 206 -0.16 2 208
CSK 0.041 0.044 0.22 6 -0.3 1 7
B7 family/CD28 0.027 0.029 0.27 1 -10000 0 1
CHUK 0.01 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.02 0.025 -10000 0 -0.33 1 1
PTPN6 0.033 0.036 0.24 3 -0.31 1 4
VAV1 0.043 0.054 0.28 3 -0.48 1 4
Monovalent TCR/CD3 0.011 0.015 -10000 0 -0.23 1 1
CBL 0.01 0 -10000 0 -10000 0 0
LCK 0.051 0.066 0.28 13 -0.4 1 14
PAG1 0.041 0.044 0.22 7 -0.3 1 8
RAP1A 0.01 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.021 0.025 -10000 0 -0.32 1 1
CD80 0.009 0.004 -10000 0 -10000 0 0
CD86 0.008 0.004 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.001 0.01 -10000 0 -0.17 1 1
HRAS 0.01 0 -10000 0 -10000 0 0
GO:0035030 0.022 0.027 0.25 1 -10000 0 1
CD8A 0.01 0.003 -10000 0 -10000 0 0
CD8B 0.01 0.003 -10000 0 -10000 0 0
PTPRC 0.009 0.027 -10000 0 -0.44 1 1
PDK1/PKC theta 0.073 0.088 0.29 26 -0.34 1 27
CSK/PAG1 0.035 0.036 0.23 3 -0.29 1 4
SOS1 0.01 0 -10000 0 -10000 0 0
peptide-MHC class I 0.017 0.005 -10000 0 -10000 0 0
GRAP2/SLP76 0.035 0.028 -10000 0 -0.29 1 1
STIM1 0.08 0.053 -10000 0 -10000 0 0
RAS family/GTP 0.05 0.051 0.17 29 -10000 0 29
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.024 0.022 0.2 1 -0.22 1 2
mol:DAG 0.047 0.044 0.097 9 -0.27 1 10
RAP1A/GDP 0.023 0.022 0.072 32 -10000 0 32
PLCG1 0.01 0 -10000 0 -10000 0 0
CD247 0.01 0.003 -10000 0 -10000 0 0
cytotoxic T cell degranulation 0.043 0.056 0.37 4 -10000 0 4
RAP1A/GTP 0 0.005 -10000 0 -0.058 2 2
mol:PI-3-4-5-P3 0.072 0.083 0.27 29 -0.33 1 30
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.15 0.11 0.22 200 -0.37 1 201
NRAS 0.01 0 -10000 0 -10000 0 0
ZAP70 0.009 0.003 -10000 0 -10000 0 0
GRB2/SOS1 0.015 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.035 0.038 -10000 0 -0.39 1 1
MALT1 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
CD8 heterodimer 0.015 0.005 -10000 0 -10000 0 0
CARD11 0.007 0.004 -10000 0 -10000 0 0
PRKCB 0.04 0.035 0.13 18 -0.2 1 19
PRKCE 0.04 0.035 0.13 17 -0.2 1 18
PRKCQ 0.074 0.091 0.31 24 -0.38 1 25
LCP2 0.009 0.002 -10000 0 -10000 0 0
BCL10 0.01 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.064 0.073 0.24 29 -0.25 1 30
IKK complex 0.05 0.052 0.14 47 -10000 0 47
RAS family/GDP 0 0.002 -10000 0 -10000 0 0
MAP3K14 0.055 0.06 0.2 29 -0.18 1 30
PDPK1 0.067 0.076 0.25 29 -0.27 1 30
TCR/CD3/MHC I/CD8/Fyn 0.021 0.027 -10000 0 -0.4 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.002 0.029 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.029 0.075 -9999 0 -0.24 23 23
JUN -0.016 0.077 -9999 0 -0.29 6 6
HRAS 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.012 0.086 -9999 0 -0.24 36 36
RAP1A 0.01 0 -9999 0 -10000 0 0
FRS2 0.01 0 -9999 0 -10000 0 0
RAP1A/GDP 0.007 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.012 0.085 -9999 0 -0.24 36 36
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.006 0.067 -9999 0 -0.23 23 23
RHOA 0.01 0 -9999 0 -10000 0 0
RAP1A/GTP -0.009 0.077 -9999 0 -0.21 36 36
GRB7 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.012 0.086 -9999 0 -0.24 36 36
MAPKKK cascade -0.012 0.079 -9999 0 -0.22 34 34
BCAR1 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.01 0.078 -9999 0 -0.25 26 26
lamellipodium assembly -0.013 0.076 -9999 0 -0.23 23 23
RET51/GFRalpha1/GDNF/SHC -0.012 0.086 -9999 0 -0.24 36 36
PIK3CA 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.006 0.067 -9999 0 -0.23 23 23
RET9/GFRalpha1/GDNF/Shank3 -0.006 0.067 -9999 0 -0.23 23 23
MAPK3 -0.013 0.073 -9999 0 -0.2 36 36
DOK1 0.01 0.001 -9999 0 -10000 0 0
DOK6 -0.057 0.16 -9999 0 -0.44 43 43
PXN 0.01 0 -9999 0 -10000 0 0
neurite development -0.024 0.08 -9999 0 -0.29 8 8
DOK5 0.005 0.046 -9999 0 -0.44 3 3
GFRA1 -0.026 0.12 -9999 0 -0.44 23 23
MAPK8 -0.017 0.081 -9999 0 -0.22 38 38
HRAS/GTP -0.013 0.088 -9999 0 -0.25 34 34
tube development -0.004 0.063 -9999 0 -0.22 23 23
MAPK1 -0.013 0.073 -9999 0 -0.2 36 36
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.007 0.062 -9999 0 -0.22 23 23
Rac1/GDP 0.007 0 -9999 0 -10000 0 0
SRC 0.01 0.001 -9999 0 -10000 0 0
PDLIM7 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.041 0.12 -9999 0 -0.24 72 72
SHC1 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.012 0.086 -9999 0 -0.24 36 36
RET51/GFRalpha1/GDNF/Dok5 -0.015 0.089 -9999 0 -0.24 39 39
PRKCA 0.01 0 -9999 0 -10000 0 0
HRAS/GDP 0.007 0 -9999 0 -10000 0 0
CREB1 -0.012 0.078 -9999 0 -0.26 23 23
PIK3R1 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.007 0.062 -9999 0 -0.22 23 23
RET51/GFRalpha1/GDNF/Grb7 -0.012 0.086 -9999 0 -0.24 36 36
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.012 0.096 -9999 0 -0.44 14 14
DOK4 0.01 0 -9999 0 -10000 0 0
JNK cascade -0.014 0.076 -9999 0 -0.28 6 6
RET9/GFRalpha1/GDNF/FRS2 -0.006 0.067 -9999 0 -0.23 23 23
SHANK3 0.01 0 -9999 0 -10000 0 0
RASA1 0.01 0 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.007 0.062 -9999 0 -0.22 23 23
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.015 0.079 -9999 0 -0.22 36 36
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.015 0.078 -9999 0 -0.22 34 34
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.015 0.081 -9999 0 -0.22 36 36
PI3K -0.018 0.11 -9999 0 -0.34 23 23
SOS1 0.01 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0 0.064 -9999 0 -0.22 23 23
GRB10 0.01 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.012 0.067 -9999 0 -0.21 23 23
RET51/GFRalpha1/GDNF/FRS2 -0.012 0.086 -9999 0 -0.24 36 36
GAB1 0.01 0 -9999 0 -10000 0 0
IRS1 0.002 0.059 -9999 0 -0.44 5 5
IRS2 0.01 0.001 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.015 0.081 -9999 0 -0.22 36 36
RET51/GFRalpha1/GDNF/PKC alpha -0.012 0.086 -9999 0 -0.24 36 36
GRB2 0.01 0 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
GDNF 0.002 0.004 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.017 0.095 -9999 0 -0.25 39 39
Rac1/GTP -0.014 0.09 -9999 0 -0.27 23 23
RET9/GFRalpha1/GDNF -0.013 0.073 -9999 0 -0.26 23 23
GFRalpha1/GDNF -0.017 0.086 -9999 0 -0.31 23 23
Ephrin A reverse signaling

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
MAPKKK cascade -0.011 0.069 -9999 0 -0.26 21 21
EFNA5 -0.023 0.12 -9999 0 -0.44 21 21
FYN -0.009 0.062 -9999 0 -0.23 21 21
neuron projection morphogenesis -0.011 0.069 -9999 0 -0.26 21 21
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.011 0.069 -9999 0 -0.26 21 21
EPHA5 0.002 0.004 -9999 0 -10000 0 0
FoxO family signaling

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
G6PC -0.8 0.56 -10000 0 -1.2 197 197
PLK1 0.083 0.078 -10000 0 -10000 0 0
CDKN1B -0.048 0.1 -10000 0 -10000 0 0
FOXO3 0.068 0.057 -10000 0 -10000 0 0
KAT2B 0.022 0.01 -10000 0 -10000 0 0
FOXO1/SIRT1 -0.26 0.19 -10000 0 -0.39 197 197
CAT 0.072 0.058 -10000 0 -10000 0 0
CTNNB1 0.01 0 -10000 0 -10000 0 0
AKT1 -0.021 0.032 -10000 0 -10000 0 0
FOXO1 -0.28 0.2 -10000 0 -0.42 197 197
MAPK10 0.001 0.015 -10000 0 -10000 0 0
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.02 0.033 -10000 0 -10000 0 0
response to oxidative stress -0.026 0.03 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.071 0.052 -10000 0 -10000 0 0
XPO1 0.01 0 -10000 0 -10000 0 0
EP300 -0.034 0.031 -10000 0 -10000 0 0
BCL2L11 0.022 0.015 -10000 0 -10000 0 0
FOXO1/SKP2 -0.25 0.19 -10000 0 -0.38 197 197
mol:GDP -0.026 0.03 -10000 0 -10000 0 0
RAN 0.01 0 -10000 0 -10000 0 0
GADD45A 0.061 0.035 -10000 0 -10000 0 0
YWHAQ 0.01 0 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.027 0.053 -10000 0 -10000 0 0
MST1 0.02 0.028 -10000 0 -0.42 1 1
CSNK1D 0.01 0 -10000 0 -10000 0 0
CSNK1E 0.01 0 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.032 0.039 -10000 0 -0.25 5 5
YWHAB 0.01 0 -10000 0 -10000 0 0
MAPK8 -0.003 0.034 -10000 0 -0.23 5 5
MAPK9 0.001 0.015 -10000 0 -10000 0 0
YWHAG 0.01 0 -10000 0 -10000 0 0
YWHAE 0.01 0 -10000 0 -10000 0 0
YWHAZ 0.01 0 -10000 0 -10000 0 0
SIRT1 0.009 0.008 -10000 0 -10000 0 0
SOD2 -0.055 0.12 0.31 1 -10000 0 1
RBL2 0.065 0.049 -10000 0 -10000 0 0
RAL/GDP -0.003 0.021 -10000 0 -10000 0 0
CHUK 0.022 0.01 -10000 0 -10000 0 0
Ran/GTP 0.009 0.001 -10000 0 -10000 0 0
CSNK1G2 0.01 0 -10000 0 -10000 0 0
RAL/GTP 0.001 0.02 -10000 0 -10000 0 0
CSNK1G1 0.01 0 -10000 0 -10000 0 0
FASLG 0.039 0.056 -10000 0 -10000 0 0
SKP2 0.01 0 -10000 0 -10000 0 0
USP7 0.01 0 -10000 0 -10000 0 0
IKBKB 0.022 0.01 -10000 0 -10000 0 0
CCNB1 0.073 0.061 -10000 0 -10000 0 0
FOXO1-3a-4/beta catenin -0.053 0.11 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.25 0.19 -10000 0 -0.38 197 197
CSNK1A1 0.01 0 -10000 0 -10000 0 0
SGK1 0.022 0.01 -10000 0 -10000 0 0
CSNK1G3 0.01 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.016 0.002 -10000 0 -10000 0 0
ZFAND5 0.022 0.029 -10000 0 -10000 0 0
SFN -0.002 0.058 -10000 0 -0.44 5 5
CDK2 -0.054 0.045 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.047 0.037 -10000 0 -10000 0 0
CREBBP -0.054 0.045 -10000 0 -10000 0 0
FBXO32 0.073 0.061 -10000 0 -10000 0 0
BCL6 0.066 0.05 -10000 0 -10000 0 0
RALB 0.01 0 -10000 0 -10000 0 0
RALA 0.01 0 -10000 0 -10000 0 0
YWHAH 0.01 0 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.004 0 -10000 0 -10000 0 0
GNB1/GNG2 0.008 0.05 -10000 0 -0.23 12 12
regulation of S phase of mitotic cell cycle 0.003 0.045 -10000 0 -0.21 12 12
GNAO1 -0.029 0.13 -10000 0 -0.44 25 25
HRAS 0.009 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.002 0.047 -10000 0 -0.26 9 9
PELP1 0.009 0.001 -10000 0 -10000 0 0
AKT1 0.005 0 -10000 0 -10000 0 0
MAP2K1 -0.013 0.059 -10000 0 -0.21 11 11
T-DHT/AR -0.008 0.064 -10000 0 -0.31 12 12
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 44 44
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.007 0.037 -10000 0 -0.44 2 2
mol:GDP -0.01 0.074 -10000 0 -0.37 12 12
cell proliferation -0.048 0.14 -10000 0 -0.38 44 44
PIK3CA 0.01 0 -10000 0 -10000 0 0
FOS -0.1 0.28 -10000 0 -0.76 44 44
mol:Ca2+ -0.005 0.019 -10000 0 -0.055 29 29
MAPK3 -0.032 0.1 -10000 0 -0.26 43 43
MAPK1 -0.021 0.075 -10000 0 -0.19 44 44
PIK3R1 0.01 0 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.004 44 44
cAMP biosynthetic process -0.004 0.045 -10000 0 -0.24 9 9
GNG2 0.01 0 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.004 44 44
HRAS/GTP 0.001 0.05 -10000 0 -0.21 12 12
actin cytoskeleton reorganization 0.015 0.001 -10000 0 -10000 0 0
SRC 0.009 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.004 44 44
PI3K 0.013 0 -10000 0 -10000 0 0
apoptosis 0.048 0.15 0.4 44 -10000 0 44
T-DHT/AR/PELP1 -0.001 0.055 -10000 0 -0.26 12 12
HRAS/GDP -0.005 0.072 -10000 0 -0.35 12 12
CREB1 -0.052 0.16 -10000 0 -0.42 44 44
RAC1-CDC42/GTP 0.019 0.001 -10000 0 -10000 0 0
AR -0.009 0.09 -10000 0 -0.44 12 12
GNB1 0.01 0 -10000 0 -10000 0 0
RAF1 -0.008 0.053 -10000 0 -0.21 11 11
RAC1-CDC42/GDP 0.003 0.07 -10000 0 -0.33 12 12
T-DHT/AR/PELP1/Src 0.004 0.051 -10000 0 -0.23 12 12
MAP2K2 -0.013 0.059 -10000 0 -0.21 11 11
T-DHT/AR/PELP1/Src/PI3K 0.003 0.045 -10000 0 -0.21 12 12
GNAZ 0.01 0 -10000 0 -10000 0 0
SHBG -0.004 0.078 -10000 0 -0.44 9 9
Gi family/GNB1/GNG2/GDP -0.012 0.088 -10000 0 -0.29 25 25
mol:T-DHT 0 0.001 -10000 0 -0.002 42 42
RAC1 0.01 0 -10000 0 -10000 0 0
GNRH1 0.003 0.002 -10000 0 -10000 0 0
Gi family/GTP -0.012 0.057 -10000 0 -0.17 27 27
CDC42 0.01 0 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.009 0.057 -10000 0 -0.22 17 17
ER alpha/Gai/GDP/Gbeta gamma -0.025 0.13 -10000 0 -0.34 37 37
AKT1 -0.029 0.18 -10000 0 -0.74 17 17
PIK3CA 0.01 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.029 0.18 -10000 0 -0.75 17 17
mol:Ca2+ -0.09 0.17 -10000 0 -0.38 63 63
IGF1R 0.01 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.007 0.072 -10000 0 -0.26 22 22
SHC1 0.01 0 -10000 0 -10000 0 0
apoptosis 0.027 0.17 0.7 17 -10000 0 17
RhoA/GTP -0.002 0.047 -10000 0 -0.19 17 17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.016 0.12 -10000 0 -0.42 17 17
regulation of stress fiber formation 0 0.046 0.16 22 -10000 0 22
E2/ERA-ERB (dimer) -0.003 0.064 -10000 0 -0.26 17 17
KRAS 0.01 0 -10000 0 -10000 0 0
G13/GTP -0.002 0.058 -10000 0 -0.23 17 17
pseudopodium formation 0 0.046 -10000 0 -0.16 22 22
E2/ER alpha (dimer)/PELP1 -0.003 0.064 -10000 0 -0.26 17 17
GRB2 0.01 0 -10000 0 -10000 0 0
GNG2 0.01 0 -10000 0 -10000 0 0
GNAO1 -0.029 0.13 -10000 0 -0.44 25 25
HRAS 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.024 0.14 -10000 0 -0.51 19 19
E2/ER beta (dimer) 0.007 0 -10000 0 -10000 0 0
mol:GDP -0.007 0.082 -10000 0 -0.34 17 17
mol:NADP -0.024 0.14 -10000 0 -0.51 19 19
PIK3R1 0.01 0 -10000 0 -10000 0 0
mol:IP3 -0.093 0.18 -10000 0 -0.39 63 63
IGF-1R heterotetramer 0.01 0 -10000 0 -10000 0 0
PLCB1 -0.1 0.18 -10000 0 -0.41 63 63
PLCB2 -0.073 0.16 -10000 0 -0.37 61 61
IGF1 0 0.064 -10000 0 -0.44 6 6
mol:L-citrulline -0.024 0.14 -10000 0 -0.51 19 19
RHOA 0.01 0 -10000 0 -10000 0 0
Gai/GDP -0.04 0.19 -10000 0 -0.64 25 25
JNK cascade 0.007 0 -10000 0 -10000 0 0
BCAR1 0.01 0 -10000 0 -10000 0 0
ESR2 0.01 0.001 -10000 0 -10000 0 0
GNAQ 0.01 0 -10000 0 -10000 0 0
ESR1 -0.017 0.11 -10000 0 -0.44 17 17
Gq family/GDP/Gbeta gamma -0.033 0.1 -10000 0 -0.38 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.002 0.062 -10000 0 -0.27 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.016 0.12 -10000 0 -0.42 17 17
GNAZ 0.01 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.011 0.075 -10000 0 -0.31 17 17
STRN 0.002 0.059 -10000 0 -0.44 5 5
GNAL 0.008 0.026 -10000 0 -0.44 1 1
PELP1 0.01 0 -10000 0 -10000 0 0
MAPK11 0.008 0 -10000 0 -10000 0 0
GNAI2 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNAI1 0.007 0.037 -10000 0 -0.44 2 2
HBEGF -0.004 0.12 -10000 0 -0.31 33 33
cAMP biosynthetic process -0.002 0.052 -10000 0 -0.21 18 18
SRC -0.023 0.13 -10000 0 -0.32 37 37
PI3K 0.015 0 -10000 0 -10000 0 0
GNB1 0.01 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.004 0.075 -10000 0 -0.3 17 17
SOS1 0.01 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.035 0.097 -10000 0 -0.35 19 19
Gs family/GTP 0 0.054 -10000 0 -0.21 18 18
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.019 0 -10000 0 -10000 0 0
vasodilation -0.023 0.14 -10000 0 -0.49 19 19
mol:DAG -0.093 0.18 -10000 0 -0.39 63 63
Gs family/GDP/Gbeta gamma -0.004 0.071 -10000 0 -0.29 17 17
MSN -0.001 0.048 -10000 0 -0.17 22 22
Gq family/GTP -0.077 0.17 -10000 0 -0.4 61 61
mol:PI-3-4-5-P3 -0.027 0.18 -10000 0 -0.72 17 17
NRAS 0.01 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.023 0.14 0.49 19 -10000 0 19
GRB2/SOS1 0.015 0 -10000 0 -10000 0 0
RhoA/GDP -0.001 0.08 -10000 0 -0.32 17 17
NOS3 -0.026 0.15 -10000 0 -0.54 19 19
GNA11 -0.001 0.069 -10000 0 -0.44 7 7
MAPKKK cascade -0.021 0.15 -10000 0 -0.51 22 22
E2/ER alpha (dimer)/PELP1/Src -0.018 0.12 -10000 0 -0.44 17 17
ruffle organization 0 0.046 -10000 0 -0.16 22 22
ROCK2 -0.001 0.052 -10000 0 -0.18 22 22
GNA14 -0.085 0.18 -10000 0 -0.44 61 61
GNA15 0.009 0.002 -10000 0 -10000 0 0
GNA13 0.01 0.001 -10000 0 -10000 0 0
MMP9 0.002 0.13 -10000 0 -0.3 33 33
MMP2 -0.019 0.12 -10000 0 -0.31 37 37
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 -0.01 0.063 -9999 0 -0.26 17 17
ADCY5 -0.01 0.063 -9999 0 -0.26 17 17
ADCY6 0.005 0 -9999 0 -10000 0 0
ADCY7 0.005 0.001 -9999 0 -10000 0 0
ADCY1 -0.12 0.13 -9999 0 -0.26 140 140
ADCY2 0.001 0.016 -9999 0 -0.26 1 1
ADCY3 0.005 0 -9999 0 -10000 0 0
ADCY8 0.004 0.002 -9999 0 -10000 0 0
PRKCE 0.005 0 -9999 0 -10000 0 0
ADCY9 0.005 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.006 0.049 -9999 0 -0.16 4 4
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.016 0.031 0.15 5 -10000 0 5
NFATC2 -0.005 0.079 0.15 5 -0.26 22 27
NFATC3 0.016 0.031 0.15 5 -10000 0 5
CD40LG -0.016 0.17 0.35 15 -0.39 26 41
PTGS2 -0.043 0.24 0.35 19 -0.5 48 67
JUNB 0.01 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.006 0.012 -10000 0 -10000 0 0
CaM/Ca2+ 0.006 0.012 -10000 0 -10000 0 0
CALM1 0.01 0.011 -10000 0 -10000 0 0
JUN 0.01 0.011 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.007 0.006 -10000 0 -10000 0 0
FOSL1 0.007 0.037 -10000 0 -0.44 2 2
CREM 0.01 0 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.008 0.075 -10000 0 -0.23 14 14
FOS -0.058 0.16 -10000 0 -0.44 44 44
IFNG -0.029 0.16 0.32 7 -0.39 26 33
AP-1/NFAT1-c-4 -0.048 0.16 -10000 0 -0.44 26 26
FASLG -0.033 0.15 0.37 3 -0.39 26 29
NFAT1-c-4/ICER1 0.001 0.073 -10000 0 -0.22 19 19
IL2RA -0.033 0.15 0.32 9 -0.39 26 35
FKBP12/FK506 0.007 0 -10000 0 -10000 0 0
CSF2 -0.023 0.17 0.36 11 -0.39 26 37
JunB/Fra1/NFAT1-c-4 0.003 0.075 -10000 0 -0.21 21 21
IL4 -0.031 0.16 0.35 5 -0.39 26 31
IL2 -0.004 0.01 -10000 0 -10000 0 0
IL3 -0.007 0.016 -10000 0 -10000 0 0
FKBP1A 0.01 0 -10000 0 -10000 0 0
BATF3 0.01 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.01 0 -10000 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.006 0.082 -9999 0 -0.44 10 10
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.004 0.06 -9999 0 -0.19 27 27
GNAO1 -0.028 0.13 -9999 0 -0.44 25 25
S1P/S1P3/G12/G13 0 0.068 -9999 0 -0.23 23 23
AKT1 -0.016 0.11 -9999 0 -0.57 10 10
AKT3 -0.003 0.064 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.006 0.082 -9999 0 -0.44 10 10
GNAI2 0.01 0 -9999 0 -10000 0 0
GNAI3 0.01 0 -9999 0 -10000 0 0
GNAI1 0.007 0.037 -9999 0 -0.44 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.025 0.12 -9999 0 -0.44 23 23
S1PR2 0.01 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.021 0.11 -9999 0 -0.25 42 42
MAPK3 -0.02 0.1 -9999 0 -0.24 42 42
MAPK1 -0.02 0.1 -9999 0 -0.46 7 7
JAK2 -0.016 0.11 -9999 0 -0.25 41 41
CXCR4 -0.021 0.1 -9999 0 -0.24 41 41
FLT1 0.008 0.037 -9999 0 -0.44 2 2
RhoA/GDP 0.007 0 -9999 0 -10000 0 0
Rac1/GDP 0.007 0 -9999 0 -10000 0 0
SRC -0.02 0.1 -9999 0 -0.24 42 42
S1P/S1P3/Gi -0.022 0.11 -9999 0 -0.26 42 42
RAC1 0.01 0 -9999 0 -10000 0 0
RhoA/GTP -0.015 0.099 -9999 0 -0.49 6 6
VEGFA 0.011 0.001 -9999 0 -10000 0 0
S1P/S1P2/Gi -0.003 0.066 -9999 0 -0.21 27 27
VEGFR1 homodimer/VEGFA homodimer 0.015 0.027 -9999 0 -0.31 2 2
RHOA 0.01 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.057 0.13 -9999 0 -0.26 74 74
GNAQ 0.01 0 -9999 0 -10000 0 0
GNAZ 0.01 0 -9999 0 -10000 0 0
G12/G13 0.015 0.001 -9999 0 -10000 0 0
GNA14 -0.085 0.18 -9999 0 -0.44 61 61
GNA15 0.009 0.002 -9999 0 -10000 0 0
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0.001 -9999 0 -10000 0 0
GNA11 -0.001 0.069 -9999 0 -0.44 7 7
Rac1/GTP -0.015 0.099 -9999 0 -0.23 42 42
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.007 0.037 -9999 0 -10000 0 0
adherens junction organization -0.008 0.069 -9999 0 -0.23 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.011 0.037 -9999 0 -10000 0 0
FMN1 -0.017 0.083 -9999 0 -0.22 40 40
mol:IP3 0.005 0.038 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.005 0.068 -9999 0 -0.23 24 24
CTNNB1 0.01 0.002 -9999 0 -10000 0 0
AKT1 0.006 0.045 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.031 0.1 -9999 0 -0.38 24 24
CTNND1 0.01 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 -0.003 0.064 -9999 0 -0.22 24 24
VASP -0.003 0.065 -9999 0 -0.22 24 24
ZYX -0.003 0.065 -9999 0 -0.22 24 24
JUB -0.003 0.065 -9999 0 -0.22 24 24
EGFR(dimer) 0.001 0.066 -9999 0 -0.22 24 24
E-cadherin/beta catenin-gamma catenin -0.002 0.072 -9999 0 -0.24 24 24
mol:PI-3-4-5-P3 0.008 0.048 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K 0.008 0.049 -9999 0 -10000 0 0
FYN -0.13 0.088 -9999 0 -0.28 15 15
mol:Ca2+ 0.005 0.037 -9999 0 -10000 0 0
JUP 0.01 0.002 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
mol:DAG 0.005 0.038 -9999 0 -10000 0 0
CDH1 -0.028 0.12 -9999 0 -0.44 24 24
RhoA/GDP 0.011 0.037 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium -0.003 0.064 -9999 0 -0.22 24 24
SRC 0.01 0.001 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
EGFR 0.01 0 -9999 0 -10000 0 0
CASR -0.15 0.095 -9999 0 -0.2 213 213
RhoA/GTP 0.009 0.036 -9999 0 -10000 0 0
AKT2 0.006 0.045 -9999 0 -10000 0 0
actin cable formation -0.015 0.081 -9999 0 -0.21 40 40
apoptosis -0.005 0.043 -9999 0 -10000 0 0
CTNNA1 0.01 0.001 -9999 0 -10000 0 0
mol:GDP 0.006 0.038 -9999 0 -10000 0 0
PIP5K1A -0.003 0.065 -9999 0 -0.22 24 24
PLCG1 0.005 0.038 -9999 0 -10000 0 0
Rac1/GTP 0.005 0.063 -9999 0 -0.2 24 24
homophilic cell adhesion 0 0.001 -9999 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.003 0.077 -9999 0 -0.26 24 24
E-cadherin/beta catenin -0.012 0.089 -9999 0 -0.31 24 24
CTNNB1 0.01 0 -9999 0 -10000 0 0
JUP 0.01 0 -9999 0 -10000 0 0
CDH1 -0.027 0.12 -9999 0 -0.44 24 24
Signaling events mediated by the Hedgehog family

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
TGFB2 0.005 0.075 -10000 0 -10000 0 0
IHH -0.03 0.14 -10000 0 -0.47 28 28
SHH Np/Cholesterol/GAS1 -0.004 0.062 -10000 0 -0.23 20 20
LRPAP1 0.01 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.004 0.061 0.23 20 -10000 0 20
SMO/beta Arrestin2 -0.003 0.1 -10000 0 -0.32 23 23
SMO -0.01 0.11 -10000 0 -0.33 25 25
AKT1 0.008 0.053 -10000 0 -0.26 1 1
ARRB2 0.01 0.001 -10000 0 -10000 0 0
BOC 0.01 0 -10000 0 -10000 0 0
ADRBK1 0.01 0 -10000 0 -10000 0 0
heart looping -0.009 0.1 -10000 0 -0.33 25 25
STIL 0.001 0.063 -10000 0 -10000 0 0
DHH N/PTCH2 -0.007 0.08 -10000 0 -0.31 19 19
DHH N/PTCH1 -0.014 0.097 -10000 0 -0.24 43 43
PIK3CA 0.01 0 -10000 0 -10000 0 0
DHH -0.02 0.11 -10000 0 -0.44 19 19
PTHLH -0.006 0.097 -10000 0 -10000 0 0
determination of left/right symmetry -0.009 0.1 -10000 0 -0.33 25 25
PIK3R1 0.01 0 -10000 0 -10000 0 0
skeletal system development -0.006 0.096 -10000 0 -10000 0 0
IHH N/Hhip -0.023 0.1 -10000 0 -0.29 39 39
DHH N/Hhip -0.02 0.1 -10000 0 -0.34 27 27
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.009 0.1 -10000 0 -0.33 25 25
pancreas development -0.008 0.086 -10000 0 -0.44 11 11
HHAT 0.01 0 -10000 0 -10000 0 0
PI3K 0.015 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.017 0.11 -10000 0 -0.44 17 17
somite specification -0.009 0.1 -10000 0 -0.33 25 25
SHH Np/Cholesterol/PTCH1 0.002 0.068 -10000 0 -10000 0 0
SHH Np/Cholesterol/PTCH2 0.01 0.025 -10000 0 -0.23 3 3
SHH Np/Cholesterol/Megalin -0.012 0.077 -10000 0 -0.24 29 29
SHH 0.006 0.032 -10000 0 -0.31 3 3
catabolic process -0.003 0.085 -10000 0 -0.27 25 25
SMO/Vitamin D3 -0.001 0.087 -10000 0 -0.26 23 23
SHH Np/Cholesterol/Hhip 0 0.053 -10000 0 -0.23 14 14
LRP2 -0.032 0.13 -10000 0 -0.44 27 27
receptor-mediated endocytosis -0.018 0.11 -10000 0 -0.44 10 10
SHH Np/Cholesterol/BOC 0.01 0.025 -10000 0 -0.23 3 3
SHH Np/Cholesterol/CDO 0.01 0.025 -10000 0 -0.23 3 3
mesenchymal cell differentiation 0 0.052 0.23 14 -10000 0 14
mol:Vitamin D3 0.004 0.07 -10000 0 -10000 0 0
IHH N/PTCH2 -0.01 0.085 -10000 0 -0.27 28 28
CDON 0.01 0.001 -10000 0 -10000 0 0
IHH N/PTCH1 0.001 0.087 -10000 0 -0.27 25 25
Megalin/LRPAP1 -0.016 0.094 -10000 0 -0.31 27 27
PTCH2 0.01 0.001 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.005 0.025 -10000 0 -0.24 3 3
PTCH1 -0.003 0.085 -10000 0 -0.27 25 25
HHIP -0.008 0.086 -10000 0 -0.44 11 11
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0.002 -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 -0.076 0.089 -10000 0 -10000 0 0
IL27/IL27R/JAK1 0.2 0.17 0.42 7 -10000 0 7
TBX21 0.21 0.15 0.36 100 -10000 0 100
IL12B 0.006 0.006 -10000 0 -10000 0 0
IL12A 0.005 0.002 -10000 0 -10000 0 0
IL6ST -0.043 0.16 -10000 0 -0.43 44 44
IL27RA/JAK1 0.065 0.037 -10000 0 -10000 0 0
IL27 0.02 0.011 -10000 0 -10000 0 0
TYK2 0.018 0.006 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.024 0.082 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.076 0.089 -10000 0 -10000 0 0
T cell proliferation during immune response -0.076 0.089 -10000 0 -10000 0 0
MAPKKK cascade 0.076 0.089 -10000 0 -10000 0 0
STAT3 0.01 0 -10000 0 -10000 0 0
STAT2 0.01 0 -10000 0 -10000 0 0
STAT1 0.02 0.007 -10000 0 -10000 0 0
IL12RB1 0.009 0.003 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.07 0.12 0.35 5 -0.38 1 6
IL27/IL27R/JAK2/TYK2 0.076 0.089 -10000 0 -10000 0 0
positive regulation of T cell mediated cytotoxicity 0.076 0.089 -10000 0 -10000 0 0
STAT1 (dimer) 0.34 0.26 0.52 188 -10000 0 188
JAK2 0.014 0.004 -10000 0 -10000 0 0
JAK1 0.02 0.007 -10000 0 -10000 0 0
STAT2 (dimer) 0.066 0.092 -10000 0 -10000 0 0
T cell proliferation 0.054 0.11 -10000 0 -0.35 4 4
IL12/IL12R/TYK2/JAK2 0.027 0.038 -10000 0 -10000 0 0
IL17A -0.023 0.081 -10000 0 -10000 0 0
mast cell activation -0.076 0.089 -10000 0 -10000 0 0
IFNG 0.023 0.026 0.084 17 -10000 0 17
T cell differentiation 0 0.002 -10000 0 -10000 0 0
STAT3 (dimer) 0.066 0.092 -10000 0 -10000 0 0
STAT5A (dimer) 0.066 0.092 -10000 0 -10000 0 0
STAT4 (dimer) 0.06 0.09 -10000 0 -10000 0 0
STAT4 0.009 0.003 -10000 0 -10000 0 0
T cell activation -0.006 0.004 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.007 0.079 -10000 0 -10000 0 0
GATA3 -0.92 0.5 -10000 0 -1.2 225 225
IL18 0.005 0.001 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production 0.066 0.091 -10000 0 -10000 0 0
IL27/EBI3 0.035 0.03 -10000 0 -0.3 1 1
IL27RA 0.023 0.029 -10000 0 -10000 0 0
IL6 -0.036 0.14 -10000 0 -0.44 29 29
STAT5A 0.01 0 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.001 0.007 -10000 0 -10000 0 0
IL1B -0.001 0.041 -10000 0 -0.31 5 5
EBI3 0.02 0.029 -10000 0 -0.43 1 1
TNF 0.001 0.032 -10000 0 -0.31 3 3
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.02 0.15 -10000 0 -0.51 1 1
CRP 0.022 0.16 0.44 2 -0.51 1 3
cell cycle arrest 0.012 0.16 0.4 8 -0.55 2 10
TIMP1 0.035 0.16 0.46 6 -0.49 1 7
IL6ST -0.054 0.16 -10000 0 -0.44 44 44
Rac1/GDP 0.003 0.12 0.24 9 -0.3 18 27
AP1 -0.017 0.12 -10000 0 -0.29 12 12
GAB2 0.01 0.002 -10000 0 -10000 0 0
TNFSF11 0.022 0.16 0.44 4 -0.51 1 5
HSP90B1 0.018 0.046 -10000 0 -10000 0 0
GAB1 0.01 0.001 -10000 0 -10000 0 0
MAPK14 -0.028 0.11 -10000 0 -0.46 7 7
AKT1 0.023 0.014 -10000 0 -10000 0 0
FOXO1 0.024 0.013 -10000 0 -10000 0 0
MAP2K6 -0.024 0.12 -10000 0 -0.32 18 18
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
MAP2K4 0.019 0.13 0.3 11 -0.38 7 18
MITF -0.02 0.12 0.2 4 -0.3 22 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.01 0 -10000 0 -10000 0 0
A2M 0 0.1 -10000 0 -1.2 2 2
CEBPB 0.006 0.011 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.002 0.058 -10000 0 -10000 0 0
STAT3 0.003 0.16 0.4 8 -0.58 2 10
STAT1 0.011 0.015 -10000 0 -10000 0 0
CEBPD 0.02 0.15 -10000 0 -0.51 1 1
PIK3CA 0.01 0 -10000 0 -10000 0 0
PI3K 0.016 0.001 -10000 0 -10000 0 0
JUN 0.009 0.001 -10000 0 -10000 0 0
PIAS3/MITF -0.016 0.12 -10000 0 -0.3 18 18
MAPK11 -0.028 0.11 -10000 0 -0.46 7 7
STAT3 (dimer)/FOXO1 0.02 0.15 0.38 8 -0.46 3 11
GRB2/SOS1/GAB family -0.023 0.1 -10000 0 -0.42 7 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.035 0.12 -10000 0 -0.26 40 40
GRB2 0.01 0.001 -10000 0 -10000 0 0
JAK2 0.01 0 -10000 0 -10000 0 0
LBP -0.19 0.43 0.45 2 -0.85 82 84
PIK3R1 0.01 0 -10000 0 -10000 0 0
JAK1 0.012 0.004 -10000 0 -10000 0 0
MYC 0.021 0.15 -10000 0 -0.51 1 1
FGG 0.023 0.16 0.44 8 -0.51 1 9
macrophage differentiation 0.012 0.16 0.4 8 -0.55 2 10
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.025 0.11 -10000 0 -0.23 60 60
JUNB 0.02 0.15 -10000 0 -0.5 1 1
FOS -0.059 0.16 -10000 0 -0.44 44 44
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.022 0.13 0.2 4 -0.32 22 26
STAT1/PIAS1 -0.008 0.12 0.23 8 -0.32 16 24
GRB2/SOS1/GAB family/SHP2/PI3K 0.021 0.015 -10000 0 -10000 0 0
STAT3 (dimer) 0.007 0.16 0.4 8 -0.56 2 10
PRKCD 0.03 0.14 0.35 11 -0.41 4 15
IL6R 0.01 0.027 -10000 0 -0.44 1 1
SOCS3 -0.03 0.12 -10000 0 -0.56 6 6
gp130 (dimer)/JAK1/JAK1/LMO4 -0.013 0.1 -10000 0 -0.25 44 44
Rac1/GTP -0.012 0.11 0.23 4 -0.3 18 22
HCK 0.007 0.026 -10000 0 -0.44 1 1
MAPKKK cascade 0.012 0.051 -10000 0 -10000 0 0
bone resorption 0.024 0.15 0.43 4 -0.49 1 5
IRF1 0.02 0.15 -10000 0 -0.51 1 1
mol:GDP -0.012 0.12 0.23 8 -0.31 20 28
SOS1 0.01 0.002 -10000 0 -10000 0 0
VAV1 -0.015 0.12 0.23 8 -0.31 20 28
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.034 0.11 -10000 0 -0.5 7 7
PTPN11 0.011 0.016 -10000 0 -10000 0 0
IL6/IL6RA -0.015 0.099 -10000 0 -0.3 30 30
gp130 (dimer)/TYK2/TYK2/LMO4 -0.015 0.1 -10000 0 -0.25 44 44
gp130 (dimer)/JAK2/JAK2/LMO4 -0.015 0.1 -10000 0 -0.25 44 44
IL6 -0.032 0.14 -10000 0 -0.44 29 29
PIAS3 0.01 0 -10000 0 -10000 0 0
PTPRE 0.002 0.013 -10000 0 -10000 0 0
PIAS1 0.01 0 -10000 0 -10000 0 0
RAC1 0.01 0.001 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.038 0.12 -10000 0 -0.26 49 49
LMO4 0.014 0.009 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 0 0.15 0.36 4 -0.52 4 8
MCL1 0.025 0.013 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0.001 -9999 0 -10000 0 0
CCL5 0.009 0.003 -9999 0 -10000 0 0
SDCBP 0.01 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.013 0.1 -9999 0 -0.24 29 29
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 0.015 0.095 -9999 0 -0.26 17 17
Syndecan-1/Syntenin 0.015 0.095 -9999 0 -0.26 17 17
MAPK3 0.018 0.088 -9999 0 -0.44 4 4
HGF/MET -0.005 0.07 -9999 0 -0.28 17 17
TGFB1/TGF beta receptor Type II 0.01 0.001 -9999 0 -10000 0 0
BSG 0.01 0 -9999 0 -10000 0 0
keratinocyte migration 0.015 0.094 -9999 0 -0.26 17 17
Syndecan-1/RANTES 0.011 0.093 -9999 0 -0.26 18 18
Syndecan-1/CD147 0.019 0.093 -9999 0 -0.26 17 17
Syndecan-1/Syntenin/PIP2 0.012 0.091 -9999 0 -0.26 17 17
LAMA5 0.01 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.012 0.089 -9999 0 -0.25 17 17
MMP7 -0.001 0.058 -9999 0 -0.44 5 5
HGF -0.017 0.11 -9999 0 -0.44 17 17
Syndecan-1/CASK -0.021 0.081 -9999 0 -0.23 29 29
Syndecan-1/HGF/MET 0.005 0.11 -9999 0 -0.28 22 22
regulation of cell adhesion 0.018 0.086 -9999 0 -0.43 4 4
HPSE -0.011 0.093 -9999 0 -0.44 13 13
positive regulation of cell migration 0.013 0.1 -9999 0 -0.24 29 29
SDC1 -0.001 0.094 -9999 0 -0.24 29 29
Syndecan-1/Collagen 0.013 0.1 -9999 0 -0.24 29 29
PPIB 0.01 0 -9999 0 -10000 0 0
MET 0.009 0.003 -9999 0 -10000 0 0
PRKACA 0.01 0 -9999 0 -10000 0 0
MMP9 0 0.052 -9999 0 -0.44 4 4
MAPK1 0.018 0.088 -9999 0 -0.44 4 4
homophilic cell adhesion 0.013 0.099 -9999 0 -0.24 29 29
MMP1 -0.019 0.11 -9999 0 -0.44 18 18
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.015 0 -10000 0 -10000 0 0
Necdin/E2F1 -0.014 0.083 -10000 0 -0.29 23 23
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.015 0.059 -10000 0 -0.23 15 15
NGF (dimer)/p75(NTR)/BEX1 -0.013 0.092 -10000 0 -0.26 34 34
NT-4/5 (dimer)/p75(NTR) 0.002 0.051 -10000 0 -0.3 8 8
IKBKB 0.01 0 -10000 0 -10000 0 0
AKT1 0.001 0.055 -10000 0 -0.23 15 15
IKBKG 0.01 0 -10000 0 -10000 0 0
BDNF 0.008 0.003 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.007 0.061 -10000 0 -0.28 12 12
FURIN 0.01 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.011 0.041 -10000 0 -0.23 8 8
LINGO1 0.002 0.059 -10000 0 -0.44 5 5
Sortilin/TRAF6/NRIF 0.012 0.012 -10000 0 -0.19 1 1
proBDNF (dimer) 0.008 0.003 -10000 0 -10000 0 0
NTRK1 -0.079 0.18 -10000 0 -0.44 56 56
RTN4R 0.01 0.001 -10000 0 -10000 0 0
neuron apoptosis 0.023 0.053 -10000 0 -0.38 1 1
IRAK1 0.01 0 -10000 0 -10000 0 0
SHC1 -0.004 0.064 -10000 0 -0.27 15 15
ARHGDIA 0.01 0 -10000 0 -10000 0 0
RhoA/GTP 0.007 0 -10000 0 -10000 0 0
Gamma Secretase 0.028 0.014 -10000 0 -0.22 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.011 0.062 -10000 0 -0.25 15 15
MAGEH1 0.01 0.001 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.009 0.1 -10000 0 -0.27 33 33
Mammalian IAPs/DIABLO 0.024 0.006 -10000 0 -10000 0 0
proNGF (dimer) -0.003 0.074 -10000 0 -0.44 8 8
MAGED1 0.01 0 -10000 0 -10000 0 0
APP 0.01 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.005 0.005 -10000 0 -10000 0 0
ZNF274 0.01 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.005 0.056 -10000 0 -0.23 15 15
NGF -0.003 0.074 -10000 0 -0.44 8 8
cell cycle arrest 0.004 0.058 0.2 1 -0.2 15 16
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.004 0.056 -10000 0 -0.23 15 15
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.008 0.044 -10000 0 -0.25 8 8
NCSTN 0.01 0 -10000 0 -10000 0 0
mol:GTP 0.004 0.066 -10000 0 -0.27 15 15
PSENEN 0.01 0 -10000 0 -10000 0 0
mol:ceramide -0.001 0.059 -10000 0 -0.24 15 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.007 0.048 -10000 0 -0.37 1 1
p75(NTR)/beta APP 0.006 0.053 -10000 0 -0.31 8 8
BEX1 -0.02 0.11 -10000 0 -0.44 19 19
mol:GDP -0.009 0.064 -10000 0 -0.28 15 15
NGF (dimer) -0.12 0.13 -10000 0 -0.23 167 167
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.013 0.056 -10000 0 -0.25 12 12
PIK3R1 0.01 0 -10000 0 -10000 0 0
RAC1/GTP 0.004 0.057 -10000 0 -0.23 15 15
MYD88 0.01 0 -10000 0 -10000 0 0
CHUK 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.005 0.066 -10000 0 -0.27 15 15
RHOB 0.01 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.011 0.007 -10000 0 -10000 0 0
NT3 (dimer) -0.039 0.14 -10000 0 -0.44 31 31
TP53 0.016 0.039 -10000 0 -0.2 5 5
PRDM4 -0.001 0.059 -10000 0 -0.25 15 15
BDNF (dimer) -0.12 0.12 -10000 0 -0.22 156 156
PIK3CA 0.01 0 -10000 0 -10000 0 0
SORT1 0.01 0 -10000 0 -10000 0 0
activation of caspase activity 0.013 0.058 -10000 0 -0.23 15 15
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.011 0.062 -10000 0 -0.25 15 15
RHOC 0.01 0 -10000 0 -10000 0 0
XIAP 0.01 0 -10000 0 -10000 0 0
MAPK10 0.013 0.059 -10000 0 -0.28 5 5
DIABLO 0.01 0 -10000 0 -10000 0 0
SMPD2 -0.001 0.059 -10000 0 -0.25 15 15
APH1B 0.008 0.026 -10000 0 -0.44 1 1
APH1A 0.01 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.005 0.066 -10000 0 -0.27 15 15
PSEN1 0.01 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.015 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.029 0.12 -10000 0 -0.32 37 37
MAPK8 0.01 0.065 -10000 0 -0.28 5 5
MAPK9 0.013 0.059 -10000 0 -0.28 5 5
APAF1 0.01 0 -10000 0 -10000 0 0
NTF3 -0.039 0.14 -10000 0 -0.44 31 31
NTF4 0.005 0.005 -10000 0 -10000 0 0
NDN -0.026 0.12 -10000 0 -0.44 23 23
RAC1/GDP 0.007 0 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.013 0.054 -10000 0 -0.21 15 15
p75 CTF/Sortilin/TRAF6/NRIF 0.025 0 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.004 0.066 -10000 0 -0.27 15 15
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.019 0.037 -10000 0 -0.22 5 5
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.016 0.038 -10000 0 -0.2 8 8
PRKACB 0.01 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.013 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.009 0.002 -10000 0 -10000 0 0
BIRC2 0.01 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.009 0.088 0.15 18 -0.3 16 34
BAD 0.013 0.061 -10000 0 -0.29 5 5
RIPK2 0.01 0 -10000 0 -10000 0 0
NGFR -0.003 0.074 -10000 0 -0.44 8 8
CYCS 0.001 0.055 -10000 0 -0.23 15 15
ADAM17 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.011 0.062 -10000 0 -0.25 15 15
BCL2L11 0.013 0.061 -10000 0 -0.26 8 8
BDNF (dimer)/p75(NTR) 0.005 0.048 -10000 0 -0.28 8 8
PI3K 0.011 0.061 -10000 0 -0.25 15 15
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.011 0.062 -10000 0 -0.25 15 15
NDNL2 0.01 0 -10000 0 -10000 0 0
YWHAE 0.01 0 -10000 0 -10000 0 0
PRKCI 0.01 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.003 0.077 -10000 0 -0.33 15 15
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.011 0.062 -10000 0 -0.25 15 15
TRAF6 0.01 0 -10000 0 -10000 0 0
RAC1 0.01 0 -10000 0 -10000 0 0
PRKCZ 0.01 0 -10000 0 -10000 0 0
PLG -0.25 0.22 -10000 0 -0.44 164 164
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 0 0.057 -10000 0 -0.24 14 14
SQSTM1 0.009 0.002 -10000 0 -10000 0 0
NGFRAP1 0.01 0 -10000 0 -10000 0 0
CASP3 0.013 0.058 -10000 0 -0.24 8 8
E2F1 0.007 0.004 -10000 0 -10000 0 0
CASP9 0.01 0 -10000 0 -10000 0 0
IKK complex -0.024 0.099 -10000 0 -0.31 10 10
NGF (dimer)/TRKA -0.058 0.14 -10000 0 -0.31 63 63
MMP7 -0.001 0.058 -10000 0 -0.44 5 5
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.015 0.059 -10000 0 -0.23 15 15
MMP3 0.002 0.004 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.009 0.04 -10000 0 -0.34 1 1
TCGA08_rtk_signaling

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
PDGFRA -0.16 0.22 -9999 0 -0.44 109 109
HRAS 0.01 0 -9999 0 -10000 0 0
EGFR 0.01 0 -9999 0 -10000 0 0
AKT 0.017 0.015 -9999 0 -10000 0 0
FOXO3 0.01 0 -9999 0 -10000 0 0
AKT1 0.01 0 -9999 0 -10000 0 0
FOXO1 0.01 0 -9999 0 -10000 0 0
AKT3 0.01 0 -9999 0 -10000 0 0
FOXO4 0.01 0 -9999 0 -10000 0 0
MET 0.009 0.003 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
PIK3CB 0.01 0.001 -9999 0 -10000 0 0
NRAS 0.01 0 -9999 0 -10000 0 0
PIK3CG 0.007 0.037 -9999 0 -0.44 2 2
PIK3R3 0.01 0 -9999 0 -10000 0 0
PIK3R2 0.01 0 -9999 0 -10000 0 0
NF1 0.01 0 -9999 0 -10000 0 0
RAS -0.035 0.07 -9999 0 -0.13 97 97
ERBB2 0.01 0 -9999 0 -10000 0 0
proliferation/survival/translation -0.015 0.012 -9999 0 -10000 0 0
PI3K -0.032 0.068 -9999 0 -0.12 96 96
PIK3R1 0.01 0 -9999 0 -10000 0 0
KRAS 0.01 0 -9999 0 -10000 0 0
FOXO 0.021 0.017 -9999 0 -10000 0 0
AKT2 0.01 0 -9999 0 -10000 0 0
PTEN 0.01 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.018 0.12 -9999 0 -0.41 24 24
KLHL20 0.006 0.045 -9999 0 -0.14 24 24
CYFIP2 0.008 0.026 -9999 0 -0.44 1 1
Rac1/GDP 0.001 0.073 -9999 0 -0.24 24 24
ENAH -0.018 0.12 -9999 0 -0.41 24 24
AP1M1 0.01 0 -9999 0 -10000 0 0
RAP1B 0.01 0 -9999 0 -10000 0 0
RAP1A 0.01 0 -9999 0 -10000 0 0
CTNNB1 0.01 0 -9999 0 -10000 0 0
CDC42/GTP 0.002 0.052 -9999 0 -0.17 24 24
ABI1/Sra1/Nap1 -0.008 0.028 -9999 0 -0.19 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.004 0.071 -9999 0 -0.23 24 24
RAPGEF1 -0.014 0.1 -9999 0 -0.36 24 24
CTNND1 0.01 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.019 0.12 -9999 0 -0.42 24 24
CRK -0.016 0.11 -9999 0 -0.38 24 24
E-cadherin/gamma catenin/alpha catenin -0.003 0.077 -9999 0 -0.26 24 24
alphaE/beta7 Integrin 0.015 0 -9999 0 -10000 0 0
IQGAP1 0.01 0 -9999 0 -10000 0 0
NCKAP1 0.01 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.019 0 -9999 0 -10000 0 0
DLG1 -0.018 0.12 -9999 0 -0.41 24 24
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.011 0.035 -9999 0 -0.13 24 24
MLLT4 0.01 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.019 0.002 -9999 0 -10000 0 0
PI3K -0.013 0.044 -9999 0 -0.16 24 24
ARF6 0.01 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.012 0.089 -9999 0 -0.31 24 24
TIAM1 0.01 0 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.003 0.066 -9999 0 -0.22 24 24
AKT1 0.004 0.03 -9999 0 -0.11 1 1
PIK3R1 0.01 0 -9999 0 -10000 0 0
CDH1 -0.027 0.12 -9999 0 -0.44 24 24
RhoA/GDP 0 0.073 -9999 0 -0.24 24 24
actin cytoskeleton organization 0.006 0.034 -9999 0 -0.2 1 1
CDC42/GDP 0 0.073 -9999 0 -0.24 24 24
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.008 0.064 -9999 0 -0.22 24 24
ITGB7 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.004 0.071 -9999 0 -0.23 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin -0.002 0.065 -9999 0 -0.22 24 24
mol:GDP -0.006 0.082 -9999 0 -0.28 24 24
CDC42/GTP/IQGAP1 0.013 0 -9999 0 -10000 0 0
JUP 0.01 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP 0.002 0.074 -9999 0 -0.25 24 24
RAC1/GTP/IQGAP1 0.013 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.015 0 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
CTNNA1 0.01 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.006 0.026 -9999 0 -0.23 1 1
NME1 0.01 0.001 -9999 0 -10000 0 0
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.018 0.12 -9999 0 -0.41 24 24
regulation of cell-cell adhesion -0.013 0.042 -9999 0 -0.15 24 24
WASF2 0.004 0.018 -9999 0 -0.1 1 1
Rap1/GTP 0.004 0.058 -9999 0 -0.19 24 24
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.009 0.068 -9999 0 -0.22 24 24
CCND1 0.006 0.031 -9999 0 -0.29 1 1
VAV2 -0.011 0.11 -9999 0 -0.38 24 24
RAP1/GDP 0.004 0.063 -9999 0 -0.21 24 24
adherens junction assembly -0.017 0.11 -9999 0 -0.4 24 24
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.01 0 -9999 0 -10000 0 0
PIP5K1C 0.01 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.007 0.064 -9999 0 -0.21 24 24
E-cadherin/beta catenin -0.019 0.09 -9999 0 -0.32 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.018 0.12 -9999 0 -0.41 24 24
PIK3CA 0.01 0 -9999 0 -10000 0 0
Rac1/GTP -0.018 0.062 -9999 0 -0.22 24 24
E-cadherin/beta catenin/alpha catenin -0.003 0.077 -9999 0 -0.26 24 24
ITGAE 0.01 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.02 0.12 -9999 0 -0.43 24 24
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.011 0.003 -10000 0 -10000 0 0
SVIL 0.011 0.003 -10000 0 -10000 0 0
ZNF318 0.007 0.007 -10000 0 -10000 0 0
JMJD2C 0.005 0.015 0.056 22 -10000 0 22
T-DHT/AR/Ubc9 -0.052 0.066 -10000 0 -0.28 12 12
CARM1 0.01 0 -10000 0 -10000 0 0
PRDX1 0.01 0 -10000 0 -10000 0 0
PELP1 0.009 0.001 -10000 0 -10000 0 0
CTNNB1 0.01 0.002 -10000 0 -10000 0 0
AKT1 0.009 0.004 -10000 0 -10000 0 0
PTK2B 0.01 0.002 -10000 0 -10000 0 0
MED1 0.009 0.003 -10000 0 -10000 0 0
MAK 0.007 0.007 -10000 0 -10000 0 0
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.008 0.037 -10000 0 -0.44 2 2
GSN 0.011 0.003 -10000 0 -10000 0 0
NCOA2 -0.03 0.13 -10000 0 -0.44 26 26
NCOA6 0.011 0.003 -10000 0 -10000 0 0
DNA-PK 0.017 0.008 -10000 0 -10000 0 0
NCOA4 0.01 0 -10000 0 -10000 0 0
PIAS3 0.01 0.002 -10000 0 -10000 0 0
cell proliferation -0.027 0.025 -10000 0 -10000 0 0
XRCC5 0.009 0.003 -10000 0 -10000 0 0
UBE3A 0.011 0.004 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.066 0.086 -10000 0 -0.29 27 27
FHL2 -0.04 0.063 -10000 0 -0.86 1 1
RANBP9 0.011 0.003 -10000 0 -10000 0 0
JMJD1A -0.084 0.068 -10000 0 -0.14 186 186
CDK6 0.01 0 -10000 0 -10000 0 0
TGFB1I1 0.003 0.059 -10000 0 -0.44 5 5
T-DHT/AR/CyclinD1 -0.052 0.069 -10000 0 -0.28 13 13
XRCC6 0.009 0.003 -10000 0 -10000 0 0
T-DHT/AR -0.097 0.099 -10000 0 -0.3 12 12
CTDSP1 0.01 0.001 -10000 0 -10000 0 0
CTDSP2 0.008 0.005 -10000 0 -10000 0 0
BRCA1 0.011 0.003 -10000 0 -10000 0 0
TCF4 0.008 0.004 -10000 0 -10000 0 0
CDKN2A 0.002 0.004 -10000 0 -10000 0 0
SRF 0.012 0.009 -10000 0 -0.14 1 1
NKX3-1 -0.14 0.11 -10000 0 -10000 0 0
KLK3 0.003 0.043 -10000 0 -10000 0 0
TMF1 0.01 0.001 -10000 0 -10000 0 0
HNRNPA1 0.009 0.004 -10000 0 -10000 0 0
AOF2 0.001 0.003 -10000 0 -10000 0 0
APPL1 0.008 0.005 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.052 0.066 -10000 0 -0.28 12 12
AR -0.051 0.091 -10000 0 -0.45 12 12
UBA3 0.01 0.001 -10000 0 -10000 0 0
PATZ1 0.009 0.004 -10000 0 -10000 0 0
PAWR 0.01 0.001 -10000 0 -10000 0 0
PRKDC 0.009 0.003 -10000 0 -10000 0 0
PA2G4 0.009 0.004 -10000 0 -10000 0 0
UBE2I 0.01 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.045 0.06 -10000 0 -0.25 12 12
RPS6KA3 0.011 0.003 -10000 0 -10000 0 0
T-DHT/AR/ARA70 -0.051 0.067 -10000 0 -0.28 12 12
LATS2 0.009 0.003 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.046 0.06 -10000 0 -0.26 12 12
Cyclin D3/CDK11 p58 0.007 0.001 -10000 0 -10000 0 0
VAV3 0.009 0.026 -10000 0 -0.44 1 1
KLK2 -0.044 0.041 -10000 0 -10000 0 0
CASP8 0.01 0.001 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.063 0.099 -10000 0 -0.3 34 34
TMPRSS2 -0.54 0.41 -10000 0 -0.85 186 186
CCND1 0.009 0.026 -10000 0 -0.44 1 1
PIAS1 0.011 0.004 -10000 0 -10000 0 0
mol:T-DHT -0.038 0.033 -10000 0 -0.065 171 171
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.012 0.006 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.052 0.066 -10000 0 -0.28 12 12
CMTM2 0.009 0.003 -10000 0 -10000 0 0
SNURF -0.015 0.099 -10000 0 -0.44 15 15
ZMIZ1 -0.032 0.035 -10000 0 -10000 0 0
CCND3 0.01 0.001 -10000 0 -10000 0 0
TGIF1 0.009 0.004 -10000 0 -10000 0 0
FKBP4 0.011 0.003 -10000 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.033 0.091 0.26 25 -0.29 3 28
TBX21 0.077 0.23 0.61 17 -0.65 9 26
B2M 0.012 0.004 -10000 0 -10000 0 0
TYK2 0.02 0.03 0.15 3 -10000 0 3
IL12RB1 0.016 0.024 0.16 1 -10000 0 1
GADD45B 0.073 0.21 0.55 15 -0.59 10 25
IL12RB2 0.005 0.053 0.16 3 -0.45 3 6
GADD45G 0.071 0.22 0.59 11 -1 3 14
natural killer cell activation 0.012 0.029 0.13 7 -10000 0 7
RELB 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
IL18 0.014 0.013 -10000 0 -10000 0 0
IL2RA 0.009 0.003 -10000 0 -10000 0 0
IFNG 0.006 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.058 0.19 0.46 19 -0.57 9 28
HLA-DRB5 0.003 0.039 -10000 0 -0.45 2 2
FASLG 0.081 0.24 0.63 17 -0.65 9 26
NF kappa B2 p52/RelB -0.003 0.15 -10000 0 -0.64 9 9
CD4 0.006 0.01 -10000 0 -10000 0 0
SOCS1 0.007 0.037 -10000 0 -0.44 2 2
EntrezGene:6955 -0.001 0.01 -10000 0 -10000 0 0
CD3D 0.005 0.011 -10000 0 -10000 0 0
CD3E 0.005 0.029 -10000 0 -0.45 1 1
CD3G 0.006 0.012 -10000 0 -10000 0 0
IL12Rbeta2/JAK2 0.013 0.053 0.22 6 -0.33 3 9
CCL3 0.08 0.25 0.58 22 -0.7 9 31
CCL4 0.08 0.24 0.63 17 -0.65 9 26
HLA-A 0.012 0.004 -10000 0 -10000 0 0
IL18/IL18R 0.042 0.052 0.2 11 -0.25 1 12
NOS2 0.024 0.36 0.59 15 -1.1 22 37
IL12/IL12R/TYK2/JAK2/SPHK2 0.034 0.088 0.26 24 -0.3 2 26
IL1R1 0.074 0.23 0.61 13 -0.65 9 22
IL4 -0.01 0.029 -10000 0 -0.13 7 7
JAK2 0.02 0.03 0.13 7 -10000 0 7
EntrezGene:6957 -0.001 0.009 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.015 0.033 -10000 0 -10000 0 0
RAB7A 0.079 0.2 0.54 12 -0.62 3 15
lysosomal transport 0.079 0.19 0.52 14 -0.59 3 17
FOS -0.092 0.46 0.47 11 -1.1 44 55
STAT4 (dimer) 0.088 0.21 0.49 25 -0.57 9 34
STAT5A (dimer) -0.021 0.15 -10000 0 -0.64 9 9
GZMA 0.079 0.22 0.61 16 -0.61 9 25
GZMB 0.077 0.22 0.62 14 -0.61 9 23
HLX 0.01 0.001 -10000 0 -10000 0 0
LCK 0.074 0.24 0.55 25 -0.68 9 34
TCR/CD3/MHC II/CD4 -0.013 0.083 -10000 0 -0.21 32 32
IL2/IL2R 0.017 0.008 -10000 0 -10000 0 0
MAPK14 0.078 0.22 0.55 15 -0.58 11 26
CCR5 0.082 0.22 0.57 22 -0.54 9 31
IL1B 0.012 0.067 0.15 3 -0.44 5 8
STAT6 0.045 0.097 0.28 21 -0.23 2 23
STAT4 0.009 0.003 -10000 0 -10000 0 0
STAT3 0.01 0 -10000 0 -10000 0 0
STAT1 0.01 0.001 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
NFKB2 0.01 0 -10000 0 -10000 0 0
IL12B 0.016 0.029 0.16 2 -10000 0 2
CD8A 0.01 0.004 -10000 0 -10000 0 0
CD8B 0.01 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.033 0.091 0.29 3 -0.26 25 28
IL2RB 0.009 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.089 0.2 0.49 25 -0.53 9 34
IL2RG 0.009 0.002 -10000 0 -10000 0 0
IL12 0.03 0.048 0.2 11 -10000 0 11
STAT5A 0.01 0 -10000 0 -10000 0 0
CD247 0.007 0.011 -10000 0 -10000 0 0
IL2 0.003 0.005 -10000 0 -10000 0 0
SPHK2 0.01 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.019 0.03 0.16 1 -10000 0 1
IL12/IL12R/TYK2/JAK2 0.034 0.2 0.56 5 -0.72 9 14
MAP2K3 0.076 0.22 0.52 19 -0.58 10 29
RIPK2 0.01 0 -10000 0 -10000 0 0
MAP2K6 0.076 0.22 0.53 17 -0.58 10 27
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.029 -10000 0 -0.45 1 1
IL18RAP 0.01 0.012 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.023 0.033 0.17 3 -10000 0 3
EOMES 0.001 0.04 -10000 0 -10000 0 0
STAT1 (dimer) 0.051 0.18 0.44 15 -0.55 9 24
T cell proliferation 0.077 0.19 0.45 24 -0.47 9 33
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.012 0.029 -10000 0 -0.44 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.042 0.12 -10000 0 -0.48 15 15
ATF2 0.076 0.21 0.5 17 -0.54 11 28
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.007 0.071 -10000 0 -0.26 21 21
cell-cell adhesion 0.008 0.036 0.18 12 -10000 0 12
Ephrin B/EPHB2/RasGAP 0.018 0.045 -10000 0 -0.22 10 10
ITSN1 0.01 0 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
SHC1 0.01 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.063 0.12 -10000 0 -0.26 81 81
Ephrin B1/EPHB1 0.01 0.028 -10000 0 -0.26 3 3
HRAS/GDP 0.003 0.039 -10000 0 -0.22 6 6
Ephrin B/EPHB1/GRB7 0.015 0.05 -10000 0 -0.21 13 13
Endophilin/SYNJ1 0.01 0.044 -10000 0 -0.2 10 10
KRAS 0.01 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.015 0.05 -10000 0 -0.21 13 13
endothelial cell migration 0.021 0 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
GRB7 0.01 0 -10000 0 -10000 0 0
PAK1 0.012 0.045 -10000 0 -0.2 10 10
HRAS 0.01 0 -10000 0 -10000 0 0
RRAS 0.011 0.045 -10000 0 -0.2 10 10
DNM1 0.005 0.027 -10000 0 -0.44 1 1
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0.009 0.049 -10000 0 -0.2 13 13
lamellipodium assembly -0.008 0.036 -10000 0 -0.18 12 12
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.01 0.044 -10000 0 -0.19 12 12
PIK3R1 0.01 0 -10000 0 -10000 0 0
EPHB2 0.01 0.001 -10000 0 -10000 0 0
EPHB3 -0.12 0.2 -10000 0 -0.44 81 81
EPHB1 0.005 0.046 -10000 0 -0.44 3 3
EPHB4 0.01 0 -10000 0 -10000 0 0
mol:GDP 0.037 0.068 0.17 8 -0.23 6 14
Ephrin B/EPHB2 0.013 0.044 -10000 0 -0.22 10 10
Ephrin B/EPHB3 -0.052 0.11 -10000 0 -0.22 88 88
JNK cascade 0.013 0.026 -10000 0 -0.21 3 3
Ephrin B/EPHB1 0.01 0.049 -10000 0 -0.21 13 13
RAP1/GDP 0.044 0.061 0.16 1 -0.21 6 7
EFNB2 0.01 0 -10000 0 -10000 0 0
EFNB3 -0.007 0.082 -10000 0 -0.44 10 10
EFNB1 0.01 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.016 0.026 -10000 0 -0.23 3 3
RAP1B 0.01 0 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
CDC42/GTP 0.012 0.048 -10000 0 -0.22 9 9
Rap1/GTP 0.003 0.039 -10000 0 -0.18 12 12
axon guidance -0.007 0.071 -10000 0 -0.26 21 21
MAPK3 0.011 0.039 -10000 0 -0.19 3 3
MAPK1 0.011 0.039 -10000 0 -0.19 3 3
Rac1/GDP 0.042 0.064 0.17 8 -0.22 6 14
actin cytoskeleton reorganization -0.006 0.03 -10000 0 -10000 0 0
CDC42/GDP 0.042 0.064 0.17 8 -0.22 6 14
PI3K 0.023 0 -10000 0 -10000 0 0
EFNA5 -0.023 0.12 -10000 0 -0.44 21 21
Ephrin B2/EPHB4 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.008 0.042 -10000 0 -0.21 10 10
CDC42 0.01 0 -10000 0 -10000 0 0
RAS family/GTP -0.008 0.036 -10000 0 -10000 0 0
PTK2 0.004 0.005 -10000 0 -10000 0 0
MAP4K4 0.013 0.026 -10000 0 -0.22 3 3
SRC 0.01 0.001 -10000 0 -10000 0 0
KALRN 0.01 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0.015 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.018 0.045 -10000 0 -0.19 9 9
MAP2K1 0.01 0.041 -10000 0 -0.18 12 12
WASL 0.01 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.022 0.026 -10000 0 -0.23 3 3
cell migration 0.019 0.052 -10000 0 -0.21 13 13
NRAS 0.01 0 -10000 0 -10000 0 0
SYNJ1 0.011 0.045 -10000 0 -0.2 10 10
PXN 0.01 0 -10000 0 -10000 0 0
TF 0.007 0.048 -10000 0 -0.2 13 13
HRAS/GTP 0.011 0.043 -10000 0 -0.19 12 12
Ephrin B1/EPHB1-2 0.016 0.026 -10000 0 -0.23 3 3
cell adhesion mediated by integrin 0.026 0.065 0.25 10 -10000 0 10
RAC1 0.01 0 -10000 0 -10000 0 0
mol:GTP 0.013 0.046 -10000 0 -0.2 12 12
RAC1-CDC42/GTP -0.056 0.088 -10000 0 -0.19 79 79
RASA1 0.01 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.044 0.061 0.16 8 -0.21 6 14
ruffle organization 0.015 0.046 -10000 0 -0.18 12 12
NCK1 0.01 0 -10000 0 -10000 0 0
receptor internalization 0.003 0.041 -10000 0 -0.2 10 10
Ephrin B/EPHB2/KALRN 0.018 0.045 -10000 0 -0.22 10 10
ROCK1 -0.058 0.11 -10000 0 -0.23 81 81
RAS family/GDP -0.006 0.03 -10000 0 -0.18 6 6
Rac1/GTP -0.008 0.038 -10000 0 -0.19 12 12
Ephrin B/EPHB1/Src/Paxillin 0.005 0.047 -10000 0 -0.21 13 13
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.088 0.073 -10000 0 -0.37 2 2
epithelial cell differentiation -0.098 0.097 -10000 0 -0.23 86 86
ITCH 0.034 0.016 -10000 0 -10000 0 0
WWP1 -0.076 0.06 -10000 0 -10000 0 0
FYN 0.01 0 -10000 0 -10000 0 0
EGFR 0.01 0 -10000 0 -10000 0 0
PRL 0.001 0.003 -10000 0 -10000 0 0
neuron projection morphogenesis -0.046 0.048 -10000 0 -0.26 2 2
PTPRZ1 -0.003 0.058 -10000 0 -0.44 5 5
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.049 0.055 -10000 0 -0.28 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.067 0.058 -10000 0 -0.27 5 5
ADAM17 0.034 0.016 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.1 0.079 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.088 0.074 -10000 0 -0.37 3 3
NCOR1 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.059 0.056 -10000 0 -0.25 5 5
GRIN2B -0.055 0.053 -10000 0 -0.29 2 2
ErbB4/ErbB2/betacellulin -0.064 0.07 -10000 0 -0.3 12 12
STAT1 0.01 0.001 -10000 0 -10000 0 0
HBEGF 0.007 0.037 -10000 0 -0.44 2 2
PRLR -0.16 0.22 -10000 0 -0.44 111 111
E4ICDs/ETO2 -0.086 0.069 -10000 0 -10000 0 0
axon guidance -0.035 0.036 -10000 0 -10000 0 0
NEDD4 0.034 0.016 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.11 0.16 -10000 0 -0.31 111 111
CBFA2T3 0.01 0.001 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF -0.057 0.054 -10000 0 -0.31 2 2
MAPK3 -0.048 0.05 -10000 0 -0.27 2 2
STAT1 (dimer) -0.085 0.069 -10000 0 -10000 0 0
MAPK1 -0.048 0.05 -10000 0 -0.27 2 2
JAK2 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.06 0.054 -10000 0 -0.25 5 5
NRG1 0.019 0.045 -10000 0 -0.31 5 5
NRG3 0.004 0.046 -10000 0 -0.44 3 3
NRG2 0.005 0.046 -10000 0 -0.44 3 3
NRG4 0.007 0.026 -10000 0 -0.44 1 1
heart development -0.035 0.036 -10000 0 -10000 0 0
neural crest cell migration -0.06 0.054 -10000 0 -0.25 5 5
ERBB2 0.024 0.01 -10000 0 -10000 0 0
WWOX/E4ICDs -0.086 0.069 -10000 0 -10000 0 0
SHC1 0.01 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.077 0.067 -10000 0 -0.34 1 1
apoptosis 0.067 0.062 0.4 3 -10000 0 3
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.089 0.072 -10000 0 -0.28 3 3
ErbB4/ErbB2/epiregulin -0.031 0.042 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin -0.096 0.088 -10000 0 -0.36 12 12
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.15 0.12 -10000 0 -0.29 107 107
MDM2 -0.088 0.067 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.043 0.046 -10000 0 -0.25 5 5
STAT5A -0.03 0.036 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.059 0.056 -10000 0 -0.25 5 5
DLG4 0.01 0 -10000 0 -10000 0 0
GRB2/SHC 0.015 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.079 0.063 -10000 0 -10000 0 0
STAT5A (dimer) -0.1 0.1 -10000 0 -0.24 86 86
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.029 0.038 -10000 0 -10000 0 0
LRIG1 0.01 0.001 -10000 0 -10000 0 0
EREG 0.005 0.005 -10000 0 -10000 0 0
BTC -0.009 0.09 -10000 0 -0.44 12 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.036 0.036 -10000 0 -10000 0 0
ERBB4 -0.1 0.079 -10000 0 -10000 0 0
STAT5B 0.01 0 -10000 0 -10000 0 0
YAP1 -0.025 0.023 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.056 0.052 -10000 0 -0.31 1 1
glial cell differentiation 0.078 0.063 -10000 0 -10000 0 0
WWOX 0.01 0 -10000 0 -10000 0 0
cell proliferation -0.046 0.067 -10000 0 -0.29 13 13
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.009 0.058 -9999 0 -0.21 17 17
NF kappa B1 p50/RelA/I kappa B alpha 0.015 0.064 -9999 0 -0.22 2 2
alphaV/beta3 Integrin/Osteopontin/Src 0.013 0.034 -9999 0 -0.31 3 3
AP1 -0.014 0.11 -9999 0 -0.36 14 14
ILK 0.004 0.059 -9999 0 -0.22 17 17
bone resorption 0.007 0.062 -9999 0 -0.38 2 2
PTK2B 0.01 0 -9999 0 -10000 0 0
PYK2/p130Cas 0.016 0.057 -9999 0 -0.2 18 18
ITGAV 0.01 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.008 0.042 -9999 0 -0.31 5 5
alphaV/beta3 Integrin/Osteopontin 0.008 0.067 -9999 0 -0.25 17 17
MAP3K1 0.004 0.06 -9999 0 -0.23 17 17
JUN 0.01 0.001 -9999 0 -10000 0 0
MAPK3 0.004 0.063 -9999 0 -0.2 22 22
MAPK1 0.004 0.063 -9999 0 -0.2 22 22
Rac1/GDP 0.007 0 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
MAPK8 0.002 0.069 -9999 0 -0.23 20 20
ITGB3 -0.011 0.096 -9999 0 -0.44 14 14
NFKBIA 0.005 0.066 -9999 0 -0.24 5 5
FOS -0.058 0.16 -9999 0 -0.44 44 44
CD44 0.009 0.002 -9999 0 -10000 0 0
CHUK 0.01 0 -9999 0 -10000 0 0
PLAU -0.014 0.17 -9999 0 -1 7 7
NF kappa B1 p50/RelA 0.013 0.066 -9999 0 -0.28 5 5
BCAR1 0.01 0 -9999 0 -10000 0 0
RELA 0.01 0 -9999 0 -10000 0 0
alphaV beta3 Integrin 0.001 0.07 -9999 0 -0.31 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.003 0.061 -9999 0 -0.23 18 18
VAV3 0.003 0.06 -9999 0 -0.21 19 19
MAP3K14 0.004 0.061 -9999 0 -0.23 17 17
ROCK2 0.002 0.059 -9999 0 -0.44 5 5
SPP1 0.005 0.046 -9999 0 -0.44 3 3
RAC1 0.01 0 -9999 0 -10000 0 0
Rac1/GTP 0.007 0.054 -9999 0 -0.19 19 19
MMP2 -0.018 0.096 -9999 0 -0.31 14 14
Noncanonical Wnt signaling pathway

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
NFATC2 -0.025 0.12 -9999 0 -0.44 22 22
GNB1/GNG2 0.015 0.059 -9999 0 -0.19 20 20
mol:DAG 0.012 0.055 -9999 0 -0.18 1 1
PLCG1 0.012 0.056 -9999 0 -0.18 1 1
YES1 -0.003 0.056 -9999 0 -0.2 20 20
FZD3 0.01 0 -9999 0 -10000 0 0
FZD6 0.01 0 -9999 0 -10000 0 0
G protein 0.016 0.057 -9999 0 -10000 0 0
MAP3K7 -0.066 0.1 -9999 0 -0.33 6 6
mol:Ca2+ 0.011 0.054 -9999 0 -0.18 1 1
mol:IP3 0.012 0.055 -9999 0 -0.18 1 1
NLK 0.004 0.007 -9999 0 -10000 0 0
GNB1 0.01 0 -9999 0 -10000 0 0
CAMK2A -0.071 0.11 -9999 0 -0.2 94 94
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.003 0.06 -9999 0 -0.22 20 20
CSNK1A1 0.01 0 -9999 0 -10000 0 0
GNAS -0.003 0.056 -9999 0 -0.2 20 20
GO:0007205 0.01 0.053 -9999 0 -10000 0 0
WNT6 0.007 0.026 -9999 0 -0.44 1 1
WNT4 -0.004 0.078 -9999 0 -0.44 9 9
NFAT1/CK1 alpha 0 0.078 -9999 0 -0.37 1 1
GNG2 0.01 0 -9999 0 -10000 0 0
WNT5A 0.008 0.003 -9999 0 -10000 0 0
WNT11 -0.009 0.09 -9999 0 -0.44 12 12
CDC42 -0.002 0.053 -9999 0 -0.19 20 20
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.003 0.063 0.19 30 -10000 0 30
GNAI2 0.01 0 -10000 0 -10000 0 0
S1P/S1P5/G12 0.01 0.028 -10000 0 -0.26 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.029 0.13 -10000 0 -0.44 25 25
RhoA/GTP -0.003 0.064 -10000 0 -0.19 30 30
negative regulation of cAMP metabolic process -0.008 0.069 -10000 0 -0.21 30 30
GNAZ 0.01 0 -10000 0 -10000 0 0
GNAI3 0.01 0 -10000 0 -10000 0 0
GNA12 0.01 0 -10000 0 -10000 0 0
S1PR5 0.005 0.046 -10000 0 -0.44 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.009 0.069 -10000 0 -0.21 30 30
RhoA/GDP 0.007 0 -10000 0 -10000 0 0
RHOA 0.01 0 -10000 0 -10000 0 0
GNAI1 0.007 0.037 -10000 0 -0.44 2 2
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.029 0.13 -9999 0 -0.44 25 25
CDC42/GTP -0.001 0.061 -9999 0 -0.19 27 27
PLCG1 -0.005 0.062 -9999 0 -0.2 27 27
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.01 0 -9999 0 -10000 0 0
GNAI3 0.01 0 -9999 0 -10000 0 0
G12/G13 0.015 0.001 -9999 0 -10000 0 0
cell migration -0.001 0.06 -9999 0 -0.19 27 27
S1PR5 0.005 0.046 -9999 0 -0.44 3 3
S1PR4 0.01 0.001 -9999 0 -10000 0 0
MAPK3 -0.005 0.062 -9999 0 -0.2 27 27
MAPK1 -0.005 0.062 -9999 0 -0.2 27 27
S1P/S1P5/Gi -0.009 0.069 -9999 0 -0.21 30 30
GNAI1 0.007 0.037 -9999 0 -0.44 2 2
CDC42/GDP 0.007 0 -9999 0 -10000 0 0
S1P/S1P5/G12 0.01 0.028 -9999 0 -0.26 3 3
RHOA 0.013 0.01 -9999 0 -10000 0 0
S1P/S1P4/Gi -0.006 0.066 -9999 0 -0.21 27 27
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ 0.01 0 -9999 0 -10000 0 0
S1P/S1P4/G12/G13 0.019 0.003 -9999 0 -10000 0 0
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0.001 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.007 0.009 -10000 0 -10000 0 0
HSPA8 0.009 0.026 -10000 0 -0.43 1 1
SMAD3/SMAD4/ER alpha 0.004 0.073 -10000 0 -0.27 17 17
AKT1 0.012 0.003 -10000 0 -10000 0 0
GSC 0.017 0.028 -10000 0 -10000 0 0
NKX2-5 0.002 0.004 -10000 0 -10000 0 0
muscle cell differentiation -0.02 0.02 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.043 0.03 -10000 0 -10000 0 0
SMAD4 0.013 0.018 -10000 0 -10000 0 0
CBFB 0.01 0 -10000 0 -10000 0 0
SAP18 0.01 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.016 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.026 0.04 -10000 0 -0.22 5 5
MYC 0.008 0.006 -10000 0 -10000 0 0
CDKN2B 0.022 0.027 -10000 0 -10000 0 0
AP1 -0.001 0.085 -10000 0 -0.21 33 33
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.029 0.007 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.024 0.016 -10000 0 -10000 0 0
SP3 0.01 0 -10000 0 -10000 0 0
CREB1 0.01 0 -10000 0 -10000 0 0
FOXH1 0.01 0.004 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.024 0.027 -10000 0 -10000 0 0
GATA3 -0.33 0.19 -10000 0 -0.43 225 225
SKI/SIN3/HDAC complex/NCoR1 0.022 0.005 -10000 0 -10000 0 0
MEF2C/TIF2 0.014 0.061 -10000 0 -10000 0 0
endothelial cell migration 0.048 0.25 1.2 13 -10000 0 13
MAX 0.011 0.011 -10000 0 -10000 0 0
RBBP7 0.01 0.001 -10000 0 -10000 0 0
RBBP4 0.01 0.001 -10000 0 -10000 0 0
RUNX2 0.01 0.001 -10000 0 -10000 0 0
RUNX3 0.008 0.003 -10000 0 -10000 0 0
RUNX1 0.009 0.003 -10000 0 -10000 0 0
CTBP1 0.01 0 -10000 0 -10000 0 0
NR3C1 0.011 0.011 -10000 0 -10000 0 0
VDR 0.002 0.059 -10000 0 -0.44 5 5
CDKN1A 0.028 0.031 -10000 0 -10000 0 0
KAT2B 0.009 0.005 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.03 0.017 -10000 0 -10000 0 0
DCP1A 0.01 0 -10000 0 -10000 0 0
SKI 0.01 0.001 -10000 0 -10000 0 0
SERPINE1 -0.048 0.26 -10000 0 -1.2 13 13
SMAD3/SMAD4/ATF2 0.023 0.024 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.01 0.067 -10000 0 -0.28 13 13
SAP30 0.01 0.001 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.016 0.015 -10000 0 -10000 0 0
JUN -0.006 0.082 -10000 0 -0.2 33 33
SMAD3/SMAD4/IRF7 0.024 0.024 -10000 0 -10000 0 0
TFE3 0.01 0.015 -10000 0 -10000 0 0
COL1A2 0.015 0.025 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.022 0.024 -10000 0 -10000 0 0
DLX1 0.008 0.004 -10000 0 -10000 0 0
TCF3 0.01 0 -10000 0 -10000 0 0
FOS -0.056 0.16 -10000 0 -0.44 44 44
SMAD3/SMAD4/Max 0.024 0.027 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.018 0.009 -10000 0 -10000 0 0
ZBTB17 0.008 0.005 -10000 0 -10000 0 0
LAMC1 0.02 0.023 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.023 0.024 -10000 0 -10000 0 0
IRF7 0.011 0.004 -10000 0 -10000 0 0
ESR1 -0.018 0.11 -10000 0 -0.44 17 17
HNF4A -0.038 0.14 -10000 0 -0.44 31 31
MEF2C 0.03 0.026 -10000 0 -10000 0 0
SMAD2-3/SMAD4 0.027 0.024 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.017 0.011 -10000 0 -10000 0 0
IGHV3OR16-13 0.005 0.005 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.01 0 -10000 0 -10000 0 0
CREBBP 0.008 0.007 -10000 0 -10000 0 0
SKIL 0.01 0 -10000 0 -10000 0 0
HDAC1 0.01 0.001 -10000 0 -10000 0 0
HDAC2 0.01 0.001 -10000 0 -10000 0 0
SNIP1 0.01 0.001 -10000 0 -10000 0 0
GCN5L2 -0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.028 0.028 -10000 0 -10000 0 0
MSG1/HSC70 0.014 0.019 -10000 0 -0.3 1 1
SMAD2 0.013 0.004 -10000 0 -10000 0 0
SMAD3 0.012 0.019 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.022 0.016 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.005 0.011 -10000 0 -10000 0 0
NCOR1 0.01 0.001 -10000 0 -10000 0 0
NCOA2 -0.031 0.13 -10000 0 -0.44 26 26
NCOA1 0.01 0 -10000 0 -10000 0 0
MYOD/E2A 0.008 0.003 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.048 0.031 -10000 0 -10000 0 0
IFNB1 0.014 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.037 0.028 -10000 0 -10000 0 0
CITED1 0.009 0.002 -10000 0 -10000 0 0
SMAD2-3/SMAD4/ARC105 0.032 0.024 -10000 0 -10000 0 0
RBL1 0.01 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.029 0.018 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.016 0.008 -10000 0 -10000 0 0
SMAD7 0.008 0.085 -10000 0 -10000 0 0
MYC/MIZ-1 0.011 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.008 0.09 -10000 0 -0.41 13 13
IL10 -0.16 0.11 -10000 0 -0.24 198 198
PIASy/HDAC complex 0.011 0.006 -10000 0 -10000 0 0
PIAS3 0.009 0.005 -10000 0 -10000 0 0
CDK2 0.008 0.006 -10000 0 -10000 0 0
IL5 -0.17 0.11 -10000 0 -0.24 198 198
CDK4 0.008 0.007 -10000 0 -10000 0 0
PIAS4 0.011 0.006 -10000 0 -10000 0 0
ATF3 -0.01 0.093 -10000 0 -0.44 13 13
SMAD3/SMAD4/SP1 0.032 0.029 -10000 0 -10000 0 0
FOXG1 0.002 0.005 -10000 0 -10000 0 0
FOXO3 0.012 0.005 -10000 0 -10000 0 0
FOXO1 0.012 0.004 -10000 0 -10000 0 0
FOXO4 0.012 0.004 -10000 0 -10000 0 0
heart looping 0.03 0.026 -10000 0 -10000 0 0
CEBPB 0.01 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.021 0.023 -10000 0 -10000 0 0
MYOD1 0.001 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.007 0.092 -10000 0 -0.27 31 31
SMAD3/SMAD4/GATA3 -0.2 0.13 -10000 0 -0.27 209 209
SnoN/SIN3/HDAC complex/NCoR1 0.01 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.025 0.025 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.04 0.029 -10000 0 -10000 0 0
MED15 0.01 0 -10000 0 -10000 0 0
SP1 0.015 0.008 -10000 0 -10000 0 0
SIN3B 0.01 0.001 -10000 0 -10000 0 0
SIN3A 0.01 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.03 0.017 -10000 0 -10000 0 0
ITGB5 0.027 0.025 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.021 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/AR 0.011 0.063 -10000 0 -0.27 12 12
AR -0.009 0.09 -10000 0 -0.44 12 12
negative regulation of cell growth 0.018 0.038 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.016 0.021 -10000 0 -10000 0 0
E2F5 0.01 0 -10000 0 -10000 0 0
E2F4 0.01 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.035 0.017 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.026 0.016 -10000 0 -10000 0 0
TFDP1 0.01 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.005 0.087 -10000 0 -0.21 33 33
SMAD3/SMAD4/RUNX2 0.022 0.024 -10000 0 -10000 0 0
TGIF2 0.01 0 -10000 0 -10000 0 0
TGIF1 0.01 0 -10000 0 -10000 0 0
ATF2 0.01 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.001 0.06 -10000 0 -10000 0 0
HDAC1 0.008 0.003 -10000 0 -10000 0 0
AES 0.009 0.001 -10000 0 -10000 0 0
FBXW11 0.01 0 -10000 0 -10000 0 0
DTX1 0 0.064 -10000 0 -0.44 6 6
LRP6/FZD1 0.014 0.003 -10000 0 -10000 0 0
TLE1 0.009 0.001 -10000 0 -10000 0 0
AP1 -0.1 0.15 -10000 0 -0.27 113 113
NCSTN 0.01 0 -10000 0 -10000 0 0
ADAM10 0.01 0.001 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.028 0.031 -10000 0 -10000 0 0
NICD/RBPSUH 0.019 0.004 -10000 0 -10000 0 0
WIF1 0.006 0.005 -10000 0 -10000 0 0
NOTCH1 0.014 0.004 -10000 0 -10000 0 0
PSENEN 0.01 0 -10000 0 -10000 0 0
KREMEN2 0.008 0.004 -10000 0 -10000 0 0
DKK1 0.008 0.004 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.055 0.061 0.16 10 -10000 0 10
APH1B 0.008 0.026 -10000 0 -0.44 1 1
APH1A 0.01 0 -10000 0 -10000 0 0
AXIN1 -0.008 0.021 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.007 0.029 -10000 0 -0.22 4 4
PSEN1 0.01 0 -10000 0 -10000 0 0
FOS -0.058 0.16 -10000 0 -0.44 44 44
JUN 0.01 0 -10000 0 -10000 0 0
MAP3K7 0.009 0.001 -10000 0 -10000 0 0
CTNNB1 0.053 0.066 0.17 10 -10000 0 10
MAPK3 0.01 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.016 0.017 -10000 0 -0.26 1 1
HNF1A 0.003 0.052 -10000 0 -0.44 4 4
CTBP1 0.009 0.001 -10000 0 -10000 0 0
MYC 0.015 0.023 -10000 0 -10000 0 0
NKD1 -0.12 0.2 -10000 0 -0.44 82 82
FZD1 0.01 0.002 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.014 0.032 -10000 0 -10000 0 0
apoptosis -0.1 0.15 -10000 0 -0.27 113 113
Delta 1/NOTCHprecursor 0.001 0.06 -10000 0 -10000 0 0
DLL1 -0.026 0.12 -10000 0 -0.44 23 23
PPARD 0.013 0.007 -10000 0 -10000 0 0
Gamma Secretase 0.029 0.014 -10000 0 -0.22 1 1
APC -0.008 0.021 -10000 0 -10000 0 0
DVL1 0.013 0.005 -10000 0 -10000 0 0
CSNK2A1 0.01 0 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.015 0.007 -10000 0 -10000 0 0
LRP6 0.01 0 -10000 0 -10000 0 0
CSNK1A1 0.01 0 -10000 0 -10000 0 0
NLK 0.006 0.003 -10000 0 -10000 0 0
CCND1 0.009 0.074 -10000 0 -1.2 1 1
WNT1 0.008 0.004 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.043 0.035 -10000 0 -10000 0 0
DKK2 0.008 0.026 -10000 0 -0.44 1 1
NOTCH1 precursor/DVL1 0.026 0.007 -10000 0 -10000 0 0
GSK3B 0.01 0 -10000 0 -10000 0 0
FRAT1 0.009 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.015 0.032 -10000 0 -10000 0 0
PPP2R5D 0.074 0.1 0.24 82 -10000 0 82
MAPK1 0.01 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.019 0.009 -10000 0 -10000 0 0
RBPJ 0.01 0 -10000 0 -10000 0 0
CREBBP 0.011 0.001 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.009 0.002 -10000 0 -10000 0 0
MAP4K4 0.014 0.02 -10000 0 -10000 0 0
BAG4 0.01 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.061 0.024 -10000 0 -0.12 9 9
NFKBIA 0.01 0 -10000 0 -10000 0 0
BIRC3 0.009 0.002 -10000 0 -10000 0 0
BAX -0.026 0.011 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
AKT1 0.016 0.004 -10000 0 -10000 0 0
BAD -0.061 0.023 -10000 0 -0.12 9 9
SMPD1 0.012 0.019 -10000 0 -0.16 3 3
RB1 -0.061 0.023 -10000 0 -0.12 9 9
FADD/Caspase 8 0.023 0.021 -10000 0 -10000 0 0
MAP2K4 -0.057 0.021 -10000 0 -0.12 9 9
NSMAF 0.01 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.056 0.022 -10000 0 -0.12 9 9
EGF -0.4 0.14 -10000 0 -0.44 261 261
mol:ceramide -0.067 0.024 -10000 0 -0.13 9 9
MADD 0.01 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.002 -10000 0 -10000 0 0
ASAH1 0.01 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.061 0.022 -10000 0 -0.12 9 9
cell proliferation -0.047 0.033 -10000 0 -0.22 6 6
BID -0.002 0.017 -10000 0 -10000 0 0
MAP3K1 -0.061 0.023 -10000 0 -0.12 9 9
EIF2A -0.053 0.02 -10000 0 -10000 0 0
TRADD 0.01 0 -10000 0 -10000 0 0
CRADD 0.01 0 -10000 0 -10000 0 0
MAPK3 -0.05 0.02 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.05 0.02 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.06 0.024 -10000 0 -0.12 9 9
FADD 0.014 0.02 -10000 0 -10000 0 0
KSR1 -0.061 0.023 -10000 0 -0.12 9 9
MAPK8 -0.055 0.036 -10000 0 -0.28 5 5
PRKRA -0.061 0.023 -10000 0 -0.12 9 9
PDGFA 0.009 0.002 -10000 0 -10000 0 0
TRAF2 0.01 0 -10000 0 -10000 0 0
IGF1 0 0.064 -10000 0 -0.44 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.067 0.024 -10000 0 -0.13 9 9
CTSD 0.01 0.001 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.015 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.049 0.035 -10000 0 -0.23 6 6
PRKCD 0.01 0 -10000 0 -10000 0 0
PRKCZ 0.01 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.002 -10000 0 -10000 0 0
RelA/NF kappa B1 0.015 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.01 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.014 0.021 -10000 0 -0.18 3 3
TNFR1A/BAG4/TNF-alpha 0.016 0.028 -10000 0 -0.26 3 3
mol:Sphingosine-1-phosphate 0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.053 0.021 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
CYCS -0.04 0.015 -10000 0 -10000 0 0
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.015 0 -10000 0 -10000 0 0
EIF2AK2 -0.057 0.021 -10000 0 -0.12 9 9
TNF-alpha/TNFR1A/FAN 0.016 0.028 -10000 0 -0.26 3 3
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.018 0.014 -10000 0 -10000 0 0
MAP2K2 -0.053 0.021 -10000 0 -10000 0 0
SMPD3 0.015 0.02 -10000 0 -0.16 3 3
TNF 0.005 0.046 -10000 0 -0.44 3 3
PKC zeta/PAR4 0.015 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.18 0.061 0.2 261 -10000 0 261
NF kappa B1/RelA/I kappa B alpha 0.029 0 -10000 0 -10000 0 0
AIFM1 -0.04 0.015 -10000 0 -10000 0 0
BCL2 0.01 0 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.014 0.001 -9999 0 -10000 0 0
VLDLR 0.01 0 -9999 0 -10000 0 0
CRKL 0.01 0 -9999 0 -10000 0 0
LRPAP1 0.01 0 -9999 0 -10000 0 0
FYN 0.01 0 -9999 0 -10000 0 0
ITGA3 0.009 0.002 -9999 0 -10000 0 0
RELN/VLDLR/Fyn -0.001 0.061 -9999 0 -0.26 15 15
MAPK8IP1/MKK7/MAP3K11/JNK1 0.025 0.032 -9999 0 -0.22 5 5
AKT1 -0.003 0.047 -9999 0 -0.2 15 15
MAP2K7 0.01 0 -9999 0 -10000 0 0
RAPGEF1 0.01 0 -9999 0 -10000 0 0
DAB1 0.004 0.005 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.003 0.052 -9999 0 -0.22 15 15
LRPAP1/LRP8 0.014 0.002 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.001 0.049 -9999 0 -0.2 15 15
DAB1/alpha3/beta1 Integrin 0.001 0.045 -9999 0 -0.2 12 12
long-term memory -0.042 0.095 -9999 0 -0.22 49 49
DAB1/LIS1 0.004 0.048 -9999 0 -0.2 12 12
DAB1/CRLK/C3G 0.002 0.045 -9999 0 -0.2 12 12
PIK3CA 0.01 0 -9999 0 -10000 0 0
DAB1/NCK2 0.005 0.048 -9999 0 -0.21 12 12
ARHGEF2 0.01 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.095 0.19 -9999 0 -0.44 67 67
CDK5R1 0.01 0.001 -9999 0 -10000 0 0
RELN -0.017 0.099 -9999 0 -0.44 15 15
PIK3R1 0.01 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.001 0.059 -9999 0 -0.25 15 15
GRIN2A/RELN/LRP8/DAB1/Fyn -0.043 0.1 -9999 0 -0.2 79 79
MAPK8 0.002 0.059 -9999 0 -0.44 5 5
RELN/VLDLR/DAB1 -0.003 0.054 -9999 0 -0.23 15 15
ITGB1 0.01 0 -9999 0 -10000 0 0
MAP1B -0.003 0.05 -9999 0 -0.21 15 15
RELN/LRP8 -0.001 0.059 -9999 0 -0.25 15 15
GRIN2B/RELN/LRP8/DAB1/Fyn 0.002 0.05 -9999 0 -0.2 15 15
PI3K 0.015 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.014 0.003 -9999 0 -10000 0 0
RAP1A 0.029 0.057 -9999 0 -0.19 12 12
PAFAH1B1 0.01 0 -9999 0 -10000 0 0
MAPK8IP1 0.01 0 -9999 0 -10000 0 0
CRLK/C3G 0.015 0 -9999 0 -10000 0 0
GRIN2B 0.005 0.005 -9999 0 -10000 0 0
NCK2 0.01 0 -9999 0 -10000 0 0
neuron differentiation 0.015 0.046 -9999 0 -10000 0 0
neuron adhesion 0.034 0.057 -9999 0 -10000 0 0
LRP8 0.01 0.001 -9999 0 -10000 0 0
GSK3B -0.003 0.044 -9999 0 -0.19 14 14
RELN/VLDLR/DAB1/Fyn 0 0.051 -9999 0 -0.21 15 15
MAP3K11 0.01 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.004 0.05 -9999 0 -0.22 15 15
CDK5 0.01 0 -9999 0 -10000 0 0
MAPT -0.012 0.073 -9999 0 -0.4 10 10
neuron migration 0.019 0.067 -9999 0 -0.25 15 15
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.015 0.047 -9999 0 -10000 0 0
RELN/VLDLR 0.003 0.054 -9999 0 -0.22 15 15
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 0.01 0.003 -9999 0 -10000 0 0
VDR 0.002 0.059 -9999 0 -0.44 5 5
FAM120B 0.01 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.027 0.035 -9999 0 -0.25 3 3
RXRs/LXRs/DNA/Oxysterols 0.023 0.042 -9999 0 -0.39 3 3
MED1 0.01 0 -9999 0 -10000 0 0
mol:9cRA 0.003 0.007 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.008 0.044 -9999 0 -0.21 11 11
RXRs/NUR77 -0.079 0.13 -9999 0 -0.23 122 122
RXRs/PPAR 0.019 0.01 -9999 0 -10000 0 0
NCOR2 0.01 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 0.002 0.042 -9999 0 -0.31 5 5
RARs/VDR/DNA/Vit D3 0.019 0.031 -9999 0 -0.22 5 5
RARA 0.01 0 -9999 0 -10000 0 0
NCOA1 0.01 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.002 0.058 -9999 0 -0.44 5 5
RARs/RARs/DNA/9cRA 0.019 0.004 -9999 0 -10000 0 0
RARG 0.01 0.001 -9999 0 -10000 0 0
RPS6KB1 0.008 0.006 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.008 0.044 -9999 0 -0.21 11 11
THRA 0.01 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA 0.002 0.042 -9999 0 -0.31 5 5
RXRs/PPAR/9cRA/PGJ2/DNA 0.026 0.024 -9999 0 -10000 0 0
NR1H4 0.004 0.052 -9999 0 -0.44 4 4
RXRs/LXRs/DNA 0.04 0.029 -9999 0 -10000 0 0
NR1H2 0.013 0.007 -9999 0 -10000 0 0
NR1H3 0.013 0.007 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.022 0.036 -9999 0 -0.23 5 5
NR4A1 -0.18 0.22 -9999 0 -0.44 122 122
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.014 0.029 -9999 0 -0.2 4 4
RXRG 0.006 0.008 -9999 0 -10000 0 0
RXR alpha/CCPG 0.017 0.005 -9999 0 -10000 0 0
RXRA 0.013 0.007 -9999 0 -10000 0 0
RXRB 0.013 0.007 -9999 0 -10000 0 0
THRB -0.007 0.086 -9999 0 -0.44 11 11
PPARG 0.01 0.001 -9999 0 -10000 0 0
PPARD 0.01 0 -9999 0 -10000 0 0
TNF 0.017 0.1 -9999 0 -0.96 3 3
mol:Oxysterols 0.003 0.006 -9999 0 -10000 0 0
cholesterol transport 0.025 0.044 -9999 0 -0.38 3 3
PPARA 0.01 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.01 0 -9999 0 -10000 0 0
RXRs/NUR77/BCL2 -0.083 0.12 -9999 0 -0.22 122 122
SREBF1 0.03 0.046 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.026 0.024 -9999 0 -10000 0 0
ABCA1 0.031 0.046 -9999 0 -10000 0 0
RARs/THRs 0.02 0.047 -9999 0 -0.22 11 11
RXRs/FXR 0.025 0.033 -9999 0 -0.22 4 4
BCL2 0.01 0 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.088 0.1 -9999 0 -0.46 1 1
RAD9A 0.01 0.001 -9999 0 -10000 0 0
AP1 -0.032 0.12 -9999 0 -0.31 44 44
IFNAR2 0.012 0.004 -9999 0 -10000 0 0
AKT1 0.001 0.044 -9999 0 -0.17 17 17
ER alpha/Oestrogen -0.01 0.075 -9999 0 -0.31 17 17
NFX1/SIN3/HDAC complex 0.022 0.007 -9999 0 -10000 0 0
EGF -0.39 0.14 -9999 0 -0.44 261 261
SMG5 0.01 0 -9999 0 -10000 0 0
SMG6 0.01 0 -9999 0 -10000 0 0
SP3/HDAC2 0.018 0.007 -9999 0 -10000 0 0
TERT/c-Abl -0.086 0.084 -9999 0 -0.43 1 1
SAP18 0.01 0.001 -9999 0 -10000 0 0
MRN complex 0.019 0.016 -9999 0 -0.26 1 1
WT1 -0.24 0.22 -9999 0 -0.44 161 161
WRN 0.01 0 -9999 0 -10000 0 0
SP1 0.013 0.006 -9999 0 -10000 0 0
SP3 0.011 0.002 -9999 0 -10000 0 0
TERF2IP 0.01 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.081 0.075 -9999 0 -0.4 1 1
Mad/Max 0.017 0.005 -9999 0 -10000 0 0
TERT -0.09 0.1 -9999 0 -0.47 1 1
CCND1 -0.079 0.11 -9999 0 -1.1 1 1
MAX 0.011 0.002 -9999 0 -10000 0 0
RBBP7 0.01 0.001 -9999 0 -10000 0 0
RBBP4 0.01 0.001 -9999 0 -10000 0 0
TERF2 0.009 0 -9999 0 -10000 0 0
PTGES3 0.01 0 -9999 0 -10000 0 0
SIN3A 0.01 0.001 -9999 0 -10000 0 0
Telomerase/911 0.001 0.021 -9999 0 -10000 0 0
CDKN1B 0.014 0.005 -9999 0 -10000 0 0
RAD1 0.01 0 -9999 0 -10000 0 0
XRCC5 0.01 0 -9999 0 -10000 0 0
XRCC6 0.01 0 -9999 0 -10000 0 0
SAP30 0.01 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0.014 0 -9999 0 -10000 0 0
UBE3A 0.011 0.002 -9999 0 -10000 0 0
JUN 0.011 0.002 -9999 0 -10000 0 0
E6 0.001 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.004 -9999 0 -10000 0 0
FOS -0.058 0.16 -9999 0 -0.44 44 44
IFN-gamma/IRF1 0.018 0.007 -9999 0 -10000 0 0
PARP2 0.01 0 -9999 0 -10000 0 0
BLM 0.009 0.002 -9999 0 -10000 0 0
Telomerase -0.005 0.022 -9999 0 -10000 0 0
IRF1 0.013 0.002 -9999 0 -10000 0 0
ESR1 -0.016 0.11 -9999 0 -0.44 17 17
KU/TER 0.015 0 -9999 0 -10000 0 0
ATM/TRF2 0.015 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.025 0.007 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.026 0.007 -9999 0 -10000 0 0
HDAC1 0.01 0.001 -9999 0 -10000 0 0
HDAC2 0.012 0.005 -9999 0 -10000 0 0
ATM 0.003 0 -9999 0 -10000 0 0
SMAD3 0.007 0.004 -9999 0 -10000 0 0
ABL1 0.01 0 -9999 0 -10000 0 0
MXD1 0.011 0.002 -9999 0 -10000 0 0
MRE11A 0.01 0 -9999 0 -10000 0 0
HUS1 0.01 0 -9999 0 -10000 0 0
RPS6KB1 0.01 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.053 0.091 -9999 0 -0.4 1 1
NR2F2 0.007 0.006 -9999 0 -10000 0 0
MAPK3 0.008 0.004 -9999 0 -10000 0 0
MAPK1 0.008 0.004 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.009 0.001 -9999 0 -10000 0 0
NFKB1 0.01 0 -9999 0 -10000 0 0
HNRNPC 0.01 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.003 0 -9999 0 -10000 0 0
NBN 0.01 0 -9999 0 -10000 0 0
EGFR 0.01 0.001 -9999 0 -10000 0 0
mol:Oestrogen 0.001 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.28 0.098 -9999 0 -0.31 261 261
MYC 0.011 0.003 -9999 0 -10000 0 0
IL2 0.006 0.008 -9999 0 -10000 0 0
KU 0.015 0 -9999 0 -10000 0 0
RAD50 0.008 0.026 -9999 0 -0.44 1 1
HSP90AA1 0.01 0 -9999 0 -10000 0 0
TGFB1 0.009 0.001 -9999 0 -10000 0 0
TRF2/BLM 0.013 0.004 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.077 0.098 -9999 0 -0.43 1 1
SP1/HDAC2 0.02 0.012 -9999 0 -10000 0 0
PINX1 0.01 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.081 0.075 -9999 0 -0.4 1 1
Smad3/Myc 0.013 0.003 -9999 0 -10000 0 0
911 complex 0.02 0.001 -9999 0 -10000 0 0
IFNG 0.008 0.005 -9999 0 -10000 0 0
Telomerase/PinX1 -0.081 0.075 -9999 0 -0.4 1 1
Telomerase/AKT1/mTOR/p70S6K -0.006 0.036 -9999 0 -10000 0 0
SIN3B 0.01 0.001 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.081 0.075 -9999 0 -0.4 1 1
response to DNA damage stimulus 0.002 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.027 0.014 -9999 0 -0.21 1 1
TRF2/WRN 0.014 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.081 0.075 -9999 0 -0.4 1 1
E2F1 0.008 0.006 -9999 0 -10000 0 0
ZNFX1 0.01 0.001 -9999 0 -10000 0 0
PIF1 0.009 0.003 -9999 0 -10000 0 0
NCL 0.01 0 -9999 0 -10000 0 0
DKC1 0.01 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Visual signal transduction: Rods

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
mol:K + 0.01 0 -9999 0 -10000 0 0
GNAT1/GTP 0.002 0.003 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin 0.003 0.004 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP 0.002 0.038 -9999 0 -0.26 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.002 0.004 -9999 0 -10000 0 0
GRK1 0.002 0.004 -9999 0 -10000 0 0
CNG Channel -0.048 0.098 -9999 0 -0.2 79 79
mol:Na + -0.039 0.088 -9999 0 -0.2 62 62
mol:ADP 0.002 0.004 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.015 0.035 -9999 0 -0.24 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.038 0.091 -9999 0 -0.2 62 62
CNGB1 0.007 0.005 -9999 0 -10000 0 0
RDH5 0.006 0.037 -9999 0 -0.44 2 2
SAG 0 0.002 -9999 0 -10000 0 0
mol:Ca2+ -0.029 0.093 -9999 0 -0.19 62 62
Na + (4 Units) -0.038 0.083 -9999 0 -0.19 62 62
RGS9 0.003 0.052 -9999 0 -0.44 4 4
GNB1/GNGT1 0.01 0.005 -9999 0 -10000 0 0
GNAT1/GDP 0.014 0.029 -9999 0 -0.2 5 5
GUCY2D 0.007 0.004 -9999 0 -10000 0 0
GNGT1 0.006 0.005 -9999 0 -10000 0 0
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.01 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.005 0.038 -9999 0 -0.22 8 8
mol:11-cis-retinal 0.006 0.037 -9999 0 -0.44 2 2
mol:cGMP 0.012 0.007 -9999 0 -10000 0 0
GNB1 0.01 0 -9999 0 -10000 0 0
Rhodopsin 0.008 0.027 -9999 0 -0.31 2 2
SLC24A1 0.01 0 -9999 0 -10000 0 0
CNGA1 -0.11 0.2 -9999 0 -0.44 78 78
Metarhodopsin II 0.004 0.004 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family 0.014 0.008 -9999 0 -10000 0 0
RGS9BP 0.008 0.026 -9999 0 -0.44 1 1
Metarhodopsin II/Transducin 0.006 0.003 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0.012 0.005 -9999 0 -10000 0 0
PDE6A/B 0.01 0.027 -9999 0 -0.31 2 2
mol:Pi 0.014 0.034 -9999 0 -0.24 5 5
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin 0.01 0.006 -9999 0 -10000 0 0
PDE6B 0.007 0.037 -9999 0 -0.44 2 2
PDE6A 0.007 0.004 -9999 0 -10000 0 0
PDE6G 0 0.064 -9999 0 -0.44 6 6
RHO 0.005 0.005 -9999 0 -10000 0 0
PDE6 0.016 0.05 -9999 0 -0.23 10 10
GUCA1A 0.004 0.005 -9999 0 -10000 0 0
GC2/GCAP Family 0.012 0.005 -9999 0 -10000 0 0
GUCA1C 0.005 0.005 -9999 0 -10000 0 0
GUCA1B 0.01 0.001 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

Figure S58.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S58.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.01 0 -9999 0 -10000 0 0
SPHK1 0.005 0.005 -9999 0 -10000 0 0
GNAI2 0.01 0 -9999 0 -10000 0 0
mol:S1P 0.005 0.005 -9999 0 -10000 0 0
GNAO1 -0.029 0.13 -9999 0 -0.44 25 25
mol:Sphinganine-1-P 0.005 0.005 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.038 0.013 -9999 0 -10000 0 0
GNAI3 0.01 0 -9999 0 -10000 0 0
G12/G13 0.015 0.001 -9999 0 -10000 0 0
S1PR3 -0.026 0.12 -9999 0 -0.44 23 23
S1PR2 0.01 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.003 0.003 -9999 0 -10000 0 0
S1PR5 0.005 0.046 -9999 0 -0.44 3 3
S1PR4 0.01 0.001 -9999 0 -10000 0 0
GNAI1 0.007 0.037 -9999 0 -0.44 2 2
S1P/S1P5/G12 0.03 0.028 -9999 0 -0.2 3 3
S1P/S1P3/Gq -0.046 0.13 -9999 0 -0.26 66 66
S1P/S1P4/Gi 0.006 0.065 -9999 0 -0.2 27 27
GNAQ 0.01 0 -9999 0 -10000 0 0
GNAZ 0.01 0 -9999 0 -10000 0 0
GNA14 -0.085 0.18 -9999 0 -0.44 61 61
GNA15 0.009 0.002 -9999 0 -10000 0 0
GNA12 0.01 0 -9999 0 -10000 0 0
GNA13 0.01 0.001 -9999 0 -10000 0 0
GNA11 -0.001 0.069 -9999 0 -0.44 7 7
ABCC1 0.01 0 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.01 0 -10000 0 -10000 0 0
LAT2 0.002 0.034 -10000 0 -0.2 2 2
AP1 -0.006 0.088 -10000 0 -0.34 9 9
mol:PIP3 0.063 0.082 0.21 34 -0.24 8 42
IKBKB 0.048 0.057 0.16 32 -0.17 2 34
AKT1 0.046 0.059 0.15 21 -0.18 8 29
IKBKG 0.048 0.057 0.16 32 -0.17 2 34
MS4A2 0.005 0.026 -10000 0 -0.43 1 1
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.01 0.001 -10000 0 -10000 0 0
MAP3K1 0.048 0.056 0.17 1 -0.24 2 3
mol:Ca2+ 0.057 0.071 0.18 40 -0.19 8 48
LYN 0.013 0.003 -10000 0 -10000 0 0
CBLB 0.002 0.033 -10000 0 -0.22 1 1
SHC1 0.01 0 -10000 0 -10000 0 0
RasGAP/p62DOK 0.018 0.015 -10000 0 -0.23 1 1
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.009 0.002 -10000 0 -10000 0 0
PLD2 0.043 0.062 0.15 27 -0.21 9 36
PTPN13 0.033 0.042 -10000 0 -10000 0 0
PTPN11 0.011 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.046 0.051 0.16 3 -0.18 1 4
SYK 0.011 0.027 -10000 0 -0.45 1 1
GRB2 0.01 0 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.007 0.04 -10000 0 -0.24 8 8
LAT 0.002 0.031 -10000 0 -0.2 2 2
PAK2 0.049 0.06 0.18 1 -0.26 2 3
NFATC2 -0.031 0.11 -10000 0 -0.42 22 22
HRAS 0.049 0.062 0.17 3 -0.28 2 5
GAB2 0.01 0 -10000 0 -10000 0 0
PLA2G1B 0.006 0.009 -10000 0 -10000 0 0
Fc epsilon R1 0.002 0.049 -10000 0 -0.27 9 9
Antigen/IgE/Fc epsilon R1 0.002 0.045 -10000 0 -0.24 9 9
mol:GDP 0.033 0.058 -10000 0 -0.29 2 2
JUN 0.01 0 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.01 0.001 -10000 0 -10000 0 0
FOS -0.058 0.16 -10000 0 -0.44 44 44
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.002 0.035 -10000 0 -0.18 8 8
CHUK 0.048 0.057 0.15 38 -0.17 2 40
KLRG1 0.002 0.033 -10000 0 -0.17 8 8
VAV1 0.001 0.038 -10000 0 -0.3 2 2
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL 0.002 0.033 -10000 0 -0.2 2 2
negative regulation of mast cell degranulation 0.004 0.032 -10000 0 -0.17 2 2
BTK 0.004 0.034 -10000 0 -0.22 2 2
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK 0.002 0.05 -10000 0 -0.25 9 9
GAB2/PI3K/SHP2 -0.006 0.033 -10000 0 -0.2 8 8
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0.011 0.042 -10000 0 -0.19 9 9
RAF1 0.002 0.011 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP 0.006 0.048 -10000 0 -0.24 9 9
FCER1G 0.006 0.005 -10000 0 -10000 0 0
FCER1A 0 0.076 -10000 0 -0.45 8 8
Antigen/IgE/Fc epsilon R1/Fyn 0.005 0.042 -10000 0 -0.22 9 9
MAPK3 0.005 0.009 -10000 0 -10000 0 0
MAPK1 0.005 0.009 -10000 0 -10000 0 0
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 0.021 0.074 -10000 0 -0.52 5 5
DUSP1 0.008 0.026 -10000 0 -0.44 1 1
NF-kappa-B/RelA 0.008 0.02 -10000 0 -0.12 1 1
actin cytoskeleton reorganization 0.033 0.044 -10000 0 -10000 0 0
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.016 0.041 -10000 0 -0.28 2 2
FER 0.002 0.033 -10000 0 -0.2 2 2
RELA 0.01 0 -10000 0 -10000 0 0
ITK 0.003 0.01 -10000 0 -10000 0 0
SOS1 0.01 0 -10000 0 -10000 0 0
PLCG1 0.051 0.066 0.17 13 -0.3 2 15
cytokine secretion 0.002 0.013 -10000 0 -10000 0 0
SPHK1 0 0.029 -10000 0 -0.2 2 2
PTK2 0.033 0.044 -10000 0 -10000 0 0
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.008 0.042 -10000 0 -0.24 8 8
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.061 0.078 0.22 21 -0.23 8 29
MAP2K2 0.003 0.01 -10000 0 -10000 0 0
MAP2K1 0.003 0.01 -10000 0 -10000 0 0
MAP2K7 0.01 0 -10000 0 -10000 0 0
KLRG1/SHP2 0.003 0.033 -10000 0 -0.18 1 1
MAP2K4 0.018 0.005 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB 0.004 0.051 -10000 0 -0.26 9 9
mol:Choline 0.042 0.062 0.14 27 -0.2 9 36
SHC/Grb2/SOS1 0.018 0.037 -10000 0 -0.21 1 1
FYN 0.01 0 -10000 0 -10000 0 0
DOK1 0.01 0.001 -10000 0 -10000 0 0
PXN 0.033 0.042 -10000 0 -10000 0 0
HCLS1 0.002 0.033 -10000 0 -0.2 2 2
PRKCB 0.054 0.068 0.18 32 -0.19 8 40
FCGR2B 0.005 0.027 -10000 0 -0.44 1 1
IGHE 0.003 0.004 -10000 0 -10000 0 0
KLRG1/SHIP 0.004 0.033 -10000 0 -0.17 2 2
LCP2 0.01 0.002 -10000 0 -10000 0 0
PLA2G4A -0.003 0.051 -10000 0 -0.25 7 7
RASA1 0.01 0 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.042 0.062 0.14 27 -0.2 9 36
IKK complex 0.046 0.05 0.14 32 -0.15 1 33
WIPF1 0.01 0.001 -10000 0 -10000 0 0
IL23-mediated signaling events

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
CCL2 0.083 0.28 0.59 3 -0.98 7 10
IL23A 0.086 0.28 0.64 3 -0.85 10 13
NF kappa B1 p50/RelA/I kappa B alpha -0.011 0.19 -10000 0 -0.72 8 8
positive regulation of T cell mediated cytotoxicity 0.091 0.27 0.62 6 -0.8 8 14
ITGA3 0.09 0.26 0.64 3 -0.8 6 9
IL17F 0.077 0.2 0.46 5 -0.56 6 11
IL12B 0.029 0.04 0.17 1 -10000 0 1
STAT1 (dimer) 0.078 0.25 0.54 4 -0.77 8 12
CD4 0.092 0.26 0.59 5 -0.77 6 11
IL23 0.076 0.27 0.61 2 -0.83 10 12
IL23R 0.055 0.092 0.42 2 -10000 0 2
IL1B 0.081 0.3 0.63 3 -1.1 8 11
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 0.089 0.25 0.62 3 -0.77 6 9
TYK2 0.023 0.027 -10000 0 -10000 0 0
STAT4 0.009 0.003 -10000 0 -10000 0 0
STAT3 0.01 0.001 -10000 0 -10000 0 0
IL18RAP 0.009 0.004 -10000 0 -10000 0 0
IL12RB1 0.02 0.026 -10000 0 -10000 0 0
PIK3CA 0.01 0.001 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.025 0.031 -10000 0 -10000 0 0
IL23R/JAK2 0.073 0.11 0.42 1 -10000 0 1
positive regulation of chronic inflammatory response 0.091 0.27 0.62 6 -0.8 8 14
natural killer cell activation -0.004 0.008 -10000 0 -0.033 3 3
JAK2 0.033 0.04 0.15 7 -10000 0 7
PIK3R1 0.01 0.001 -10000 0 -10000 0 0
NFKB1 0.012 0.004 -10000 0 -10000 0 0
RELA 0.012 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation 0.077 0.26 0.6 2 -0.8 10 12
ALOX12B 0.091 0.25 0.59 3 -0.77 6 9
CXCL1 0.087 0.31 0.61 7 -0.93 12 19
T cell proliferation 0.091 0.27 0.62 6 -0.8 8 14
NFKBIA 0.012 0.004 -10000 0 -10000 0 0
IL17A 0.085 0.18 0.43 7 -0.44 6 13
PI3K 0.02 0.21 -10000 0 -0.75 8 8
IFNG 0.012 0.024 0.098 10 -10000 0 10
STAT3 (dimer) -0.013 0.19 -10000 0 -0.72 8 8
IL18R1 0.009 0.027 -10000 0 -0.44 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 0.086 0.19 0.47 8 -0.57 3 11
IL18/IL18R 0.017 0.023 -10000 0 -0.26 1 1
macrophage activation -0.003 0.012 -10000 0 -0.04 10 10
TNF 0.085 0.28 0.62 4 -0.94 8 12
STAT3/STAT4 0.017 0.21 -10000 0 -0.74 8 8
STAT4 (dimer) 0.066 0.25 0.55 3 -0.77 8 11
IL18 0.01 0.003 -10000 0 -10000 0 0
IL19 0.087 0.25 0.59 3 -0.77 6 9
STAT5A (dimer) 0.08 0.26 0.55 3 -0.77 8 11
STAT1 0.01 0.001 -10000 0 -10000 0 0
SOCS3 0.008 0.026 -10000 0 -0.44 1 1
CXCL9 0.089 0.26 0.6 4 -0.81 7 11
MPO 0.093 0.25 0.6 4 -0.76 6 10
positive regulation of humoral immune response 0.091 0.27 0.62 6 -0.8 8 14
IL23/IL23R/JAK2/TYK2 0.09 0.28 0.63 5 -0.82 8 13
IL6 0.016 0.41 0.62 4 -1 32 36
STAT5A 0.01 0 -10000 0 -10000 0 0
IL2 0.003 0.01 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.004 0.008 -10000 0 -0.033 3 3
CD3E 0.093 0.27 0.61 6 -0.85 6 12
keratinocyte proliferation 0.091 0.27 0.62 6 -0.8 8 14
NOS2 0.036 0.37 0.59 3 -0.98 26 29
Regulation of Androgen receptor activity

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
HDAC1 0.009 0.001 -9999 0 -10000 0 0
SMARCC1 0.003 0.009 -9999 0 -10000 0 0
REL 0.001 0.059 -9999 0 -0.44 5 5
HDAC7 -0.1 0.098 -9999 0 -0.4 5 5
JUN 0.01 0.001 -9999 0 -10000 0 0
EP300 0.01 0 -9999 0 -10000 0 0
KAT2B 0.01 0 -9999 0 -10000 0 0
KAT5 0.01 0 -9999 0 -10000 0 0
MAPK14 -0.011 0.017 -9999 0 -10000 0 0
FOXO1 0.01 0 -9999 0 -10000 0 0
T-DHT/AR -0.1 0.11 -9999 0 -0.38 6 6
MAP2K6 -0.005 0.012 -9999 0 -10000 0 0
BRM/BAF57 0.016 0.004 -9999 0 -10000 0 0
MAP2K4 -0.005 0.012 -9999 0 -10000 0 0
SMARCA2 0.01 0.002 -9999 0 -10000 0 0
PDE9A -0.13 0.12 -9999 0 -0.39 2 2
NCOA2 -0.03 0.13 -9999 0 -0.44 26 26
CEBPA 0.007 0.026 -9999 0 -0.44 1 1
EHMT2 0.01 0.001 -9999 0 -10000 0 0
cell proliferation -0.15 0.14 -9999 0 -0.4 46 46
NR0B1 0.004 0.005 -9999 0 -10000 0 0
EGR1 -0.025 0.12 -9999 0 -0.44 23 23
RXRs/9cRA 0.016 0.005 -9999 0 -10000 0 0
AR/RACK1/Src -0.03 0.06 -9999 0 -0.34 4 4
AR/GR -0.021 0.058 -9999 0 -0.24 14 14
GNB2L1 0.01 0.001 -9999 0 -10000 0 0
PKN1 0.01 0 -9999 0 -10000 0 0
RCHY1 0.01 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -9999 0 -10000 0 0
MAPK8 -0.016 0.045 -9999 0 -0.33 5 5
T-DHT/AR/TIF2/CARM1 -0.05 0.097 -9999 0 -0.31 24 24
SRC -0.03 0.043 -9999 0 -0.25 5 5
NR3C1 0.01 0 -9999 0 -10000 0 0
KLK3 -0.013 0.1 -9999 0 -10000 0 0
APPBP2 -0.006 0.012 -9999 0 -10000 0 0
TRIM24 0.011 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.041 0.057 -9999 0 -0.33 5 5
TMPRSS2 -0.66 0.48 -9999 0 -1 186 186
RXRG 0.003 0.005 -9999 0 -10000 0 0
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.01 0 -9999 0 -10000 0 0
RXRB 0.01 0 -9999 0 -10000 0 0
CARM1 0.01 0.001 -9999 0 -10000 0 0
NR2C2 0.005 0.046 -9999 0 -0.44 3 3
KLK2 -0.039 0.075 -9999 0 -0.44 4 4
AR -0.027 0.063 -9999 0 -0.27 14 14
SENP1 0.01 0 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
MDM2 0.008 0.005 -9999 0 -10000 0 0
SRY -0.001 0.004 -9999 0 -10000 0 0
GATA2 -0.083 0.18 -9999 0 -0.44 60 60
MYST2 0.01 0 -9999 0 -10000 0 0
HOXB13 0.006 0.006 -9999 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.035 0.057 -9999 0 -0.35 4 4
positive regulation of transcription -0.083 0.18 -9999 0 -0.44 60 60
DNAJA1 -0.006 0.012 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.012 0.001 -9999 0 -10000 0 0
NCOA1 0.016 0.003 -9999 0 -10000 0 0
SPDEF 0.009 0.005 -9999 0 -10000 0 0
T-DHT/AR/TIF2 -0.029 0.075 -9999 0 -0.26 19 19
T-DHT/AR/Hsp90 -0.041 0.057 -9999 0 -0.33 5 5
GSK3B 0.007 0.003 -9999 0 -10000 0 0
NR2C1 0.01 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.035 0.046 -9999 0 -0.28 5 5
SIRT1 0.01 0 -9999 0 -10000 0 0
ZMIZ2 0.008 0.005 -9999 0 -10000 0 0
POU2F1 -0.051 0.049 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.035 0.054 -9999 0 -0.3 5 5
CREBBP 0.01 0 -9999 0 -10000 0 0
SMARCE1 0.01 0.002 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.017 0.017 -10000 0 -10000 0 0
ACTA1 0.01 0.02 -10000 0 -10000 0 0
NUMA1 0.017 0.017 -10000 0 -10000 0 0
SPTAN1 0.01 0.02 -10000 0 -10000 0 0
LIMK1 0.011 0.022 -10000 0 -10000 0 0
BIRC3 0.009 0.002 -10000 0 -10000 0 0
BIRC2 0.01 0 -10000 0 -10000 0 0
BAX 0.01 0.001 -10000 0 -10000 0 0
CASP10 0.008 0.002 -10000 0 -10000 0 0
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.01 0 -10000 0 -10000 0 0
PTK2 0.017 0.017 -10000 0 -10000 0 0
DIABLO 0.01 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.01 0.02 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.01 0 -10000 0 -10000 0 0
GSN 0.01 0.02 -10000 0 -10000 0 0
MADD 0.01 0 -10000 0 -10000 0 0
TFAP2A -0.37 0.21 -10000 0 -0.48 229 229
BID 0.007 0.002 -10000 0 -10000 0 0
MAP3K1 0.009 0.01 -10000 0 -10000 0 0
TRADD 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.014 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.01 0.022 -10000 0 -10000 0 0
CASP9 0.01 0 -10000 0 -10000 0 0
DNA repair -0.004 0.012 -10000 0 -10000 0 0
neuron apoptosis 0.015 0.004 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.015 0.019 -10000 0 -10000 0 0
APAF1 0.01 0 -10000 0 -10000 0 0
CASP6 0.02 0.014 -10000 0 -10000 0 0
TRAF2 0.01 0 -10000 0 -10000 0 0
ICAD/CAD 0.011 0.019 -10000 0 -10000 0 0
CASP7 -0.01 0.021 -10000 0 -10000 0 0
KRT18 0.013 0.005 -10000 0 -10000 0 0
apoptosis 0.014 0.021 0.17 1 -10000 0 1
DFFA 0.01 0.02 -10000 0 -10000 0 0
DFFB 0.01 0.02 -10000 0 -10000 0 0
PARP1 0.004 0.012 -10000 0 -10000 0 0
actin filament polymerization -0.012 0.021 -10000 0 -10000 0 0
TNF 0.005 0.046 -10000 0 -0.44 3 3
CYCS 0.013 0.016 0.1 2 -10000 0 2
SATB1 0.02 0.018 -10000 0 -10000 0 0
SLK 0.01 0.02 -10000 0 -10000 0 0
p15 BID/BAX 0.017 0.013 -10000 0 -10000 0 0
CASP2 0.018 0.021 -10000 0 -10000 0 0
JNK cascade -0.009 0.01 -10000 0 -10000 0 0
CASP3 0.009 0.021 -10000 0 -10000 0 0
LMNB2 0.025 0.016 -10000 0 -10000 0 0
RIPK1 0.01 0 -10000 0 -10000 0 0
CASP4 0.01 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.024 0.006 -10000 0 -10000 0 0
negative regulation of DNA binding -0.37 0.21 -10000 0 -0.47 229 229
stress fiber formation 0.01 0.02 -10000 0 -10000 0 0
GZMB 0.008 0.002 -10000 0 -10000 0 0
CASP1 0.008 0.001 -10000 0 -10000 0 0
LMNB1 0.025 0.016 -10000 0 -10000 0 0
APP 0.015 0.004 -10000 0 -10000 0 0
TNFRSF1A 0.01 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.005 0 -10000 0 -10000 0 0
VIM 0.013 0.021 0.17 1 -10000 0 1
LMNA 0.025 0.016 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.018 0.022 -10000 0 -0.18 3 3
LRDD 0.01 0.001 -10000 0 -10000 0 0
SREBF1 0.01 0.02 -10000 0 -10000 0 0
APAF-1/Caspase 9 0.005 0.002 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.017 0.017 -10000 0 -10000 0 0
CFL2 0.012 0.021 -10000 0 -10000 0 0
GAS2 0.007 0.029 -10000 0 -0.23 2 2
positive regulation of apoptosis 0.027 0.017 -10000 0 -10000 0 0
PRF1 0.01 0.001 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.004 0.001 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.011 0.004 -10000 0 -10000 0 0
STXBP1 0.01 0 -10000 0 -10000 0 0
ACh/CHRNA1 0.004 0.008 -10000 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0.016 0.005 -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 0.005 0.005 -10000 0 -10000 0 0
mol:ACh 0.014 0.015 0.057 3 -0.11 1 4
RAB3GAP2 0.01 0 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.009 0.012 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.004 0.008 -10000 0 -10000 0 0
UNC13B 0.01 0 -10000 0 -10000 0 0
CHRNA1 0.002 0.004 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.07 0.13 -10000 0 -0.27 86 86
SNAP25 0.001 0.015 -10000 0 -0.26 1 1
VAMP2 0.003 0 -10000 0 -10000 0 0
SYT1 -0.12 0.2 -10000 0 -0.44 86 86
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.011 0.001 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.009 0.012 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.003 0.06 -9999 0 -0.22 20 20
FZD6 0.01 0 -9999 0 -10000 0 0
WNT6 0.007 0.026 -9999 0 -0.44 1 1
WNT4 -0.004 0.078 -9999 0 -0.44 9 9
FZD3 0.01 0 -9999 0 -10000 0 0
WNT5A 0.008 0.003 -9999 0 -10000 0 0
WNT11 -0.009 0.09 -9999 0 -0.44 12 12
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.001 0.026 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.088 0.12 -9999 0 -0.5 4 4
positive regulation of JNK cascade -0.1 0.13 -9999 0 -0.38 21 21
Syndecan-4/ADAM12 -0.088 0.12 -9999 0 -0.5 4 4
CCL5 0.009 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.007 0 -9999 0 -10000 0 0
DNM2 0.01 0 -9999 0 -10000 0 0
ITGA5 0.01 0 -9999 0 -10000 0 0
SDCBP 0.01 0 -9999 0 -10000 0 0
PLG -0.24 0.21 -9999 0 -0.43 164 164
ADAM12 0.009 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.006 0.007 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.092 0.13 -9999 0 -0.44 9 9
Syndecan-4/CXCL12/CXCR4 -0.11 0.13 -9999 0 -0.4 21 21
Syndecan-4/Laminin alpha3 -0.083 0.11 -9999 0 -0.47 4 4
MDK 0.007 0.004 -9999 0 -10000 0 0
Syndecan-4/FZD7 -0.093 0.13 -9999 0 -0.44 7 7
Syndecan-4/Midkine -0.085 0.11 -9999 0 -0.47 4 4
FZD7 -0.003 0.074 -9999 0 -0.44 8 8
Syndecan-4/FGFR1/FGF -0.088 0.11 -9999 0 -0.43 6 6
THBS1 -0.007 0.086 -9999 0 -0.44 11 11
integrin-mediated signaling pathway -0.087 0.12 -9999 0 -0.45 6 6
positive regulation of MAPKKK cascade -0.1 0.13 -9999 0 -0.38 21 21
Syndecan-4/TACI -0.093 0.12 -9999 0 -0.5 4 4
CXCR4 0.009 0.002 -9999 0 -10000 0 0
cell adhesion 0.018 0.009 -9999 0 -10000 0 0
Syndecan-4/Dynamin -0.088 0.12 -9999 0 -0.5 4 4
Syndecan-4/TSP1 -0.096 0.13 -9999 0 -0.43 10 10
Syndecan-4/GIPC -0.088 0.12 -9999 0 -0.5 4 4
Syndecan-4/RANTES -0.087 0.12 -9999 0 -0.5 4 4
ITGB1 0.01 0 -9999 0 -10000 0 0
LAMA1 -0.003 0.074 -9999 0 -0.44 8 8
LAMA3 0.007 0.004 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
PRKCA 0.035 0.034 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.088 0.12 -9999 0 -0.5 4 4
TFPI 0.008 0.026 -9999 0 -0.44 1 1
F2 0.01 0.007 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0.015 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.082 0.11 -9999 0 -0.41 9 9
ACTN1 0.01 0 -9999 0 -10000 0 0
TNC 0.003 0.052 -9999 0 -0.44 4 4
Syndecan-4/CXCL12 -0.11 0.14 -9999 0 -0.42 21 21
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
CXCL12 -0.046 0.15 -9999 0 -0.44 36 36
TNFRSF13B 0.006 0.005 -9999 0 -10000 0 0
FGF2 0.005 0.046 -9999 0 -0.44 3 3
FGFR1 0.01 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.1 0.11 -9999 0 -0.51 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 0.013 0.007 -9999 0 -10000 0 0
cell migration 0.002 0.004 -9999 0 -10000 0 0
PRKCD 0.013 0.007 -9999 0 -10000 0 0
vasculogenesis -0.093 0.13 -9999 0 -0.42 10 10
SDC4 -0.095 0.12 -9999 0 -0.53 4 4
Syndecan-4/Tenascin C -0.089 0.12 -9999 0 -0.47 6 6
Syndecan-4/PI-4-5-P2/PKC alpha -0.005 0.006 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.088 0.12 -9999 0 -0.5 4 4
MMP9 0.002 0.052 -9999 0 -0.43 4 4
Rac1/GTP 0.018 0.009 -9999 0 -10000 0 0
cytoskeleton organization -0.086 0.12 -9999 0 -0.49 4 4
GIPC1 0.01 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.088 0.12 -9999 0 -0.5 4 4
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0 0.064 0.44 6 -10000 0 6
PI3K Class IB/PDE3B 0 0.064 -10000 0 -0.44 6 6
PDE3B 0 0.064 -10000 0 -0.44 6 6
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.012 0.004 -9999 0 -10000 0 0
EPHB2 0.01 0.001 -9999 0 -10000 0 0
Syndecan-2/TACI 0.01 0.004 -9999 0 -10000 0 0
LAMA1 -0.003 0.074 -9999 0 -0.44 8 8
Syndecan-2/alpha2 ITGB1 0.015 0.026 -9999 0 -0.22 3 3
HRAS 0.01 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0.006 0.001 -9999 0 -10000 0 0
ITGA5 0.01 0 -9999 0 -10000 0 0
BAX 0.009 0.031 -9999 0 -10000 0 0
EPB41 0.01 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.012 0.001 -9999 0 -10000 0 0
LAMA3 0.007 0.004 -9999 0 -10000 0 0
EZR 0.01 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.01 0.001 -9999 0 -10000 0 0
Syndecan-2/MMP2 0.012 0.016 -9999 0 -0.26 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.011 0.033 -9999 0 -0.31 3 3
dendrite morphogenesis 0.013 0.002 -9999 0 -10000 0 0
Syndecan-2/GM-CSF 0.009 0.004 -9999 0 -10000 0 0
determination of left/right symmetry 0.009 0.005 -9999 0 -10000 0 0
Syndecan-2/PKC delta 0.013 0.001 -9999 0 -10000 0 0
GNB2L1 0.01 0 -9999 0 -10000 0 0
MAPK3 0.01 0.005 -9999 0 -10000 0 0
MAPK1 0.01 0.005 -9999 0 -10000 0 0
Syndecan-2/RACK1 0.018 0.003 -9999 0 -10000 0 0
NF1 0.01 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.009 0.005 -9999 0 -10000 0 0
ITGA2 0.005 0.046 -9999 0 -0.44 3 3
MAPK8 0.007 0.035 -9999 0 -0.26 5 5
Syndecan-2/alpha2/beta1 Integrin 0.014 0.046 -9999 0 -0.22 11 11
Syndecan-2/Kininogen -0.15 0.13 -9999 0 -0.26 169 169
ITGB1 0.01 0 -9999 0 -10000 0 0
SRC 0.013 0.004 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.012 0.001 -9999 0 -10000 0 0
extracellular matrix organization 0.013 0.002 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.012 0.004 -9999 0 -10000 0 0
Syndecan-2/Caveolin-2/Ras 0.019 0.004 -9999 0 -10000 0 0
Syndecan-2/Laminin alpha3 0.009 0.006 -9999 0 -10000 0 0
Syndecan-2/RasGAP 0.023 0.003 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0.015 0 -9999 0 -10000 0 0
PRKCD 0.01 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.013 0.002 -9999 0 -10000 0 0
GO:0007205 0.002 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.021 0.004 -9999 0 -10000 0 0
RHOA 0.01 0 -9999 0 -10000 0 0
SDCBP 0.01 0 -9999 0 -10000 0 0
TNFRSF13B 0.006 0.005 -9999 0 -10000 0 0
RASA1 0.01 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0.011 0.033 -9999 0 -0.31 3 3
Syndecan-2/Synbindin 0.013 0.001 -9999 0 -10000 0 0
TGFB1 0.01 0.001 -9999 0 -10000 0 0
CASP3 0.012 0.004 -9999 0 -10000 0 0
FN1 0.009 0.003 -9999 0 -10000 0 0
Syndecan-2/IL8 0.009 0.017 -9999 0 -0.26 1 1
SDC2 0.009 0.005 -9999 0 -10000 0 0
KNG1 -0.26 0.22 -9999 0 -0.44 169 169
Syndecan-2/Neurofibromin 0.013 0.001 -9999 0 -10000 0 0
TRAPPC4 0.01 0 -9999 0 -10000 0 0
CSF2 0.004 0.005 -9999 0 -10000 0 0
Syndecan-2/TGFB1 0.013 0.002 -9999 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.012 0.001 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0.019 0.004 -9999 0 -10000 0 0
PRKACA 0.012 0.004 -9999 0 -10000 0 0
angiogenesis 0.009 0.017 -9999 0 -0.26 1 1
MMP2 0.008 0.026 -9999 0 -0.44 1 1
IL8 0.006 0.027 -9999 0 -0.44 1 1
calcineurin-NFAT signaling pathway 0.01 0.004 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.013 0.005 -9999 0 -10000 0 0
CRKL 0.009 0.046 -9999 0 -10000 0 0
mol:PIP3 -0.005 0.003 -9999 0 -10000 0 0
AKT1 -0.001 0.002 -9999 0 -10000 0 0
PTK2B 0.01 0 -9999 0 -10000 0 0
RAPGEF1 0.01 0.044 -9999 0 -10000 0 0
RANBP10 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 0.003 0.06 -9999 0 -0.24 17 17
MAP3K5 0.017 0.043 -9999 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS 0.009 0.056 -9999 0 -0.21 17 17
AP1 -0.027 0.1 -9999 0 -0.27 44 44
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.01 0 -9999 0 -10000 0 0
apoptosis -0.091 0.26 -9999 0 -0.7 44 44
STAT3 (dimer) 0.008 0.054 -9999 0 -0.21 12 12
GAB1/CRKL/SHP2/PI3K 0.022 0.044 -9999 0 -10000 0 0
INPP5D 0.009 0.002 -9999 0 -10000 0 0
CBL/CRK 0.014 0.045 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.01 0 -9999 0 -10000 0 0
PTEN 0.01 0 -9999 0 -10000 0 0
ELK1 0.006 0.027 -9999 0 -10000 0 0
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.004 0.032 -9999 0 -10000 0 0
PAK1 0.001 0.002 -9999 0 -10000 0 0
HGF/MET/RANBP10 0.003 0.06 -9999 0 -0.24 17 17
HRAS 0.001 0.06 -9999 0 -10000 0 0
DOCK1 0.01 0.044 -9999 0 -10000 0 0
GAB1 0.008 0.048 -9999 0 -10000 0 0
CRK 0.009 0.046 -9999 0 -10000 0 0
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.01 0.1 -9999 0 -0.42 17 17
JUN 0.01 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.003 0.039 -9999 0 -0.16 17 17
PIK3R1 0.01 0 -9999 0 -10000 0 0
cell morphogenesis 0.013 0.057 -9999 0 -0.22 12 12
GRB2/SHC 0.013 0.039 -9999 0 -0.15 12 12
FOS -0.058 0.16 -9999 0 -0.44 44 44
GLMN 0.002 0 -9999 0 -10000 0 0
cell motility 0.006 0.027 -9999 0 -10000 0 0
HGF/MET/MUC20 -0.003 0.059 -9999 0 -0.24 17 17
cell migration 0.007 0.037 -9999 0 -0.15 12 12
GRB2 0.01 0 -9999 0 -10000 0 0
CBL 0.01 0 -9999 0 -10000 0 0
MET/RANBP10 0.013 0.005 -9999 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.002 0.052 -9999 0 -0.2 17 17
MET/MUC20 0.006 0.002 -9999 0 -10000 0 0
RAP1B 0.011 0.042 -9999 0 -10000 0 0
RAP1A 0.011 0.042 -9999 0 -10000 0 0
HGF/MET/RANBP9 0.003 0.06 -9999 0 -0.24 17 17
RAF1 0.007 0.058 -9999 0 -10000 0 0
STAT3 0.002 0.052 -9999 0 -0.22 12 12
cell proliferation 0.005 0.074 -9999 0 -0.29 17 17
RPS6KB1 0.006 0.017 -9999 0 -10000 0 0
MAPK3 0.002 0.025 -9999 0 -10000 0 0
MAPK1 0.002 0.025 -9999 0 -10000 0 0
RANBP9 0.01 0 -9999 0 -10000 0 0
MAPK8 0.015 0.068 -9999 0 -0.41 5 5
SRC 0.002 0.048 -9999 0 -0.2 12 12
PI3K 0.013 0.039 -9999 0 -0.15 12 12
MET/Glomulin 0.008 0.003 -9999 0 -10000 0 0
SOS1 0.01 0 -9999 0 -10000 0 0
MAP2K1 0.008 0.055 -9999 0 -10000 0 0
MET 0.009 0.003 -9999 0 -10000 0 0
MAP4K1 0.016 0.045 -9999 0 -10000 0 0
PTK2 0.01 0 -9999 0 -10000 0 0
MAP2K2 0.008 0.055 -9999 0 -10000 0 0
BAD 0.001 0.002 -9999 0 -10000 0 0
MAP2K4 0.017 0.04 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 0.01 0.041 -9999 0 -10000 0 0
INPPL1 0.01 0 -9999 0 -10000 0 0
PXN 0.01 0 -9999 0 -10000 0 0
SH3KBP1 0.01 0 -9999 0 -10000 0 0
HGS -0.002 0.036 -9999 0 -0.16 12 12
PLCgamma1/PKC 0.007 0 -9999 0 -10000 0 0
HGF -0.017 0.11 -9999 0 -0.44 17 17
RASA1 0.01 0 -9999 0 -10000 0 0
NCK1 0.01 0 -9999 0 -10000 0 0
PTPRJ 0.01 0 -9999 0 -10000 0 0
NCK/PLCgamma1 0.012 0.043 -9999 0 -0.17 12 12
PDPK1 -0.002 0.003 -9999 0 -10000 0 0
HGF/MET/SHIP 0.002 0.06 -9999 0 -0.24 17 17
IL1-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
UBC13/UEV1A 0.009 0.003 -9999 0 -10000 0 0
PRKCZ 0.01 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.01 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.012 0.02 -9999 0 -10000 0 0
IRAK/TOLLIP 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.01 0 -9999 0 -10000 0 0
IKBKG 0.01 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.071 0.14 -9999 0 -0.3 76 76
IL1A 0.008 0.004 -9999 0 -10000 0 0
IL1B 0.003 0.042 -9999 0 -0.31 5 5
IRAK/TRAF6/p62/Atypical PKCs 0.027 0.005 -9999 0 -10000 0 0
IL1R2 -0.11 0.2 -9999 0 -0.44 76 76
IL1R1 0.01 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.013 0.018 -9999 0 -10000 0 0
TOLLIP 0.01 0 -9999 0 -10000 0 0
TICAM2 0.008 0.026 -9999 0 -0.44 1 1
MAP3K3 0.01 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.007 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.025 0.004 -9999 0 -10000 0 0
JUN 0.007 0.025 -9999 0 -0.18 5 5
MAP3K7 0.01 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.024 0.031 -9999 0 -0.2 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88 0.021 0.009 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.025 0.01 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP 0.015 0.033 -9999 0 -0.23 5 5
NFKB1 0.01 0 -9999 0 -10000 0 0
MAPK8 0.007 0.027 -9999 0 -0.2 5 5
IRAK1 0.009 0.001 -9999 0 -10000 0 0
IL1RN/IL1R1 0.013 0.019 -9999 0 -0.31 1 1
IRAK4 0.01 0 -9999 0 -10000 0 0
PRKCI 0.01 0 -9999 0 -10000 0 0
TRAF6 0.01 0 -9999 0 -10000 0 0
PI3K 0.015 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.015 0.022 -9999 0 -10000 0 0
CHUK 0.01 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.015 0.033 -9999 0 -0.23 5 5
IL1 beta/IL1R2 -0.061 0.12 -9999 0 -0.26 80 80
IRAK/TRAF6/TAK1/TAB1/TAB2 0.017 0.001 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.017 0.027 -9999 0 -0.19 5 5
IRAK3 0.01 0.001 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.023 0.038 -9999 0 -0.25 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.014 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP 0.017 0.007 -9999 0 -10000 0 0
RELA 0.01 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.009 0.002 -9999 0 -10000 0 0
MYD88 0.01 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.02 0.001 -9999 0 -10000 0 0
IL1RAP 0.01 0.001 -9999 0 -10000 0 0
UBE2N 0.01 0 -9999 0 -10000 0 0
IRAK/TRAF6 0.012 0.031 -9999 0 -0.36 1 1
CASP1 0.01 0.001 -9999 0 -10000 0 0
IL1RN/IL1R2 -0.071 0.14 -9999 0 -0.31 77 77
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.02 0.031 -9999 0 -0.22 5 5
TMEM189-UBE2V1 0.002 0.004 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.016 0.006 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
IL1RN 0.008 0.026 -9999 0 -0.44 1 1
TRAF6/TAK1/TAB1/TAB2 0.015 0.002 -9999 0 -10000 0 0
MAP2K6 0.011 0.001 -9999 0 -10000 0 0
BCR signaling pathway

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
JUN 0.024 0.051 -10000 0 -0.29 4 4
IKBKB 0.027 0.042 -10000 0 -0.21 1 1
AKT1 0.023 0.043 0.15 7 -0.18 4 11
IKBKG 0.026 0.043 -10000 0 -0.19 3 3
CALM1 -0.002 0.075 0.17 8 -0.32 10 18
PIK3CA 0.01 0 -10000 0 -10000 0 0
MAP3K1 0.031 0.062 -10000 0 -0.42 3 3
MAP3K7 0.01 0 -10000 0 -10000 0 0
mol:Ca2+ -0.004 0.079 0.17 8 -0.34 10 18
DOK1 0.01 0.001 -10000 0 -10000 0 0
AP-1 0 0.059 0.13 1 -0.18 12 13
LYN 0.01 0 -10000 0 -10000 0 0
BLNK -0.006 0.082 -10000 0 -0.44 10 10
SHC1 0.01 0 -10000 0 -10000 0 0
BCR complex 0.007 0.042 -10000 0 -0.31 5 5
CD22 0 0.051 -10000 0 -0.33 6 6
CAMK2G -0.001 0.071 -10000 0 -0.31 9 9
CSNK2A1 0.01 0 -10000 0 -10000 0 0
INPP5D 0.009 0.002 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0 0.049 -10000 0 -0.2 15 15
GO:0007205 -0.004 0.08 0.17 8 -0.34 10 18
SYK 0.008 0.026 -10000 0 -0.44 1 1
ELK1 -0.003 0.076 0.17 8 -0.32 10 18
NFATC1 0.019 0.056 -10000 0 -0.3 5 5
B-cell antigen/BCR complex 0.007 0.042 -10000 0 -0.31 5 5
PAG1/CSK 0.015 0 -10000 0 -10000 0 0
NFKBIB 0.018 0.017 -10000 0 -10000 0 0
HRAS -0.002 0.069 -10000 0 -0.3 10 10
NFKBIA 0.018 0.017 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.02 0.015 -10000 0 -10000 0 0
RasGAP/Csk 0.013 0.036 -10000 0 -0.22 6 6
mol:GDP -0.007 0.078 0.17 8 -0.33 10 18
PTEN 0.01 0 -10000 0 -10000 0 0
CD79B 0.005 0.045 -10000 0 -0.44 3 3
NF-kappa-B/RelA/I kappa B alpha 0.02 0.015 -10000 0 -10000 0 0
GRB2 0.01 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.026 0.081 -10000 0 -0.48 4 4
PIK3R1 0.01 0 -10000 0 -10000 0 0
mol:IP3 -0.003 0.081 0.17 8 -0.34 10 18
CSK 0.01 0 -10000 0 -10000 0 0
FOS -0.031 0.11 0.16 6 -0.24 45 51
CHUK 0.026 0.043 -10000 0 -0.19 3 3
IBTK 0.01 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0 0.062 -10000 0 -0.33 7 7
PTPN6 0.009 0.051 -10000 0 -0.32 6 6
RELA 0.01 0 -10000 0 -10000 0 0
BCL2A1 0.017 0.018 -10000 0 -10000 0 0
VAV2 0.01 0.058 -10000 0 -0.38 5 5
ubiquitin-dependent protein catabolic process 0.019 0.016 -10000 0 -10000 0 0
BTK -0.003 0.03 -10000 0 -10000 0 0
CD19 0.001 0.052 -10000 0 -0.36 5 5
MAP4K1 0.008 0.003 -10000 0 -10000 0 0
CD72 0.009 0.002 -10000 0 -10000 0 0
PAG1 0.01 0 -10000 0 -10000 0 0
MAPK14 0.031 0.056 -10000 0 -0.36 3 3
SH3BP5 -0.009 0.09 -10000 0 -0.44 12 12
PIK3AP1 -0.001 0.083 0.19 8 -0.34 10 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.004 0.093 -10000 0 -0.43 10 10
RAF1 0 0.066 -10000 0 -0.28 10 10
RasGAP/p62DOK/SHIP 0.013 0.035 -10000 0 -0.2 6 6
CD79A 0.005 0.037 -10000 0 -0.44 2 2
re-entry into mitotic cell cycle 0 0.059 0.13 1 -0.18 12 13
RASA1 0.01 0 -10000 0 -10000 0 0
MAPK3 0.003 0.057 -10000 0 -0.27 7 7
MAPK1 0.003 0.057 -10000 0 -0.27 7 7
CD72/SHP1 0.025 0.055 -10000 0 -0.3 6 6
NFKB1 0.01 0 -10000 0 -10000 0 0
MAPK8 0.028 0.061 -10000 0 -0.36 3 3
actin cytoskeleton organization 0.025 0.061 -10000 0 -0.33 5 5
NF-kappa-B/RelA 0.041 0.03 -10000 0 -10000 0 0
Calcineurin 0.006 0.063 -10000 0 -0.32 7 7
PI3K -0.008 0.04 -10000 0 -0.3 4 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.006 0.085 0.2 8 -0.36 10 18
SOS1 0.01 0 -10000 0 -10000 0 0
Bam32/HPK1 0.016 0.076 -10000 0 -0.57 4 4
DAPP1 0.009 0.082 -10000 0 -0.63 4 4
cytokine secretion 0.019 0.053 -10000 0 -0.29 5 5
mol:DAG -0.003 0.081 0.17 8 -0.34 10 18
PLCG2 -0.015 0.1 -10000 0 -0.44 16 16
MAP2K1 0.002 0.062 -10000 0 -0.3 7 7
B-cell antigen/BCR complex/FcgammaRIIB 0.007 0.04 -10000 0 -0.26 6 6
mol:PI-3-4-5-P3 -0.001 0.032 -10000 0 -0.22 4 4
ETS1 0.001 0.066 -10000 0 -0.32 7 7
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.012 0.059 -10000 0 -0.23 15 15
B-cell antigen/BCR complex/LYN 0 0.056 -10000 0 -0.36 6 6
MALT1 0.01 0 -10000 0 -10000 0 0
TRAF6 0.01 0 -10000 0 -10000 0 0
RAC1 0.025 0.064 -10000 0 -0.38 4 4
B-cell antigen/BCR complex/LYN/SYK 0.011 0.052 -10000 0 -0.32 5 5
CARD11 0.015 0.084 0.17 8 -0.32 10 18
FCGR2B 0.005 0.027 -10000 0 -0.44 1 1
PPP3CA 0.01 0 -10000 0 -10000 0 0
BCL10 0.01 0 -10000 0 -10000 0 0
IKK complex 0.02 0.021 0.081 3 -10000 0 3
PTPRC 0.008 0.026 -10000 0 -0.44 1 1
PDPK1 0.021 0.038 0.14 7 -0.16 4 11
PPP3CB 0.01 0 -10000 0 -10000 0 0
PPP3CC 0.01 0 -10000 0 -10000 0 0
POU2F2 0.016 0.012 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.001 0.069 -9999 0 -0.36 10 10
PDGFB-D/PDGFRB/SLAP 0.004 0.058 -9999 0 -0.3 10 10
PDGFB-D/PDGFRB/APS/CBL 0.011 0.05 -9999 0 -0.26 10 10
AKT1 0.011 0.035 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.002 0.075 -9999 0 -0.39 10 10
PIK3CA 0.01 0 -9999 0 -10000 0 0
FGR -0.006 0.058 -9999 0 -0.29 11 11
mol:Ca2+ 0.012 0.084 -9999 0 -0.43 10 10
MYC 0.031 0.063 -9999 0 -10000 0 0
SHC1 0.01 0 -9999 0 -10000 0 0
HRAS/GDP 0.011 0.041 -9999 0 -0.2 10 10
LRP1/PDGFRB/PDGFB 0.01 0.053 -9999 0 -0.26 11 11
GRB10 0.01 0 -9999 0 -10000 0 0
PTPN11 0.01 0 -9999 0 -10000 0 0
GO:0007205 0.011 0.086 -9999 0 -0.44 10 10
PTEN 0.01 0 -9999 0 -10000 0 0
GRB2 0.01 0 -9999 0 -10000 0 0
GRB7 0.01 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.004 0.059 -9999 0 -0.31 10 10
PDGFB-D/PDGFRB/GRB10 0.004 0.059 -9999 0 -0.31 10 10
cell cycle arrest 0.004 0.057 -9999 0 -0.3 10 10
HRAS 0.01 0 -9999 0 -10000 0 0
HIF1A 0.011 0.032 -9999 0 -10000 0 0
GAB1 0.022 0.08 -9999 0 -0.39 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 0.025 0.075 -9999 0 -0.36 10 10
PDGFB-D/PDGFRB 0.013 0.052 -9999 0 -0.26 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.004 0.059 -9999 0 -0.31 10 10
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.002 0.063 -9999 0 -0.33 10 10
positive regulation of MAPKKK cascade 0.004 0.059 -9999 0 -0.31 10 10
PIK3R1 0.01 0 -9999 0 -10000 0 0
mol:IP3 0.012 0.086 -9999 0 -0.44 10 10
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.009 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.004 0.059 -9999 0 -0.31 10 10
SHB 0.01 0 -9999 0 -10000 0 0
BLK -0.005 0.051 -9999 0 -0.27 10 10
PTPN2 0.01 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.004 0.059 -9999 0 -0.31 10 10
BCAR1 0.01 0 -9999 0 -10000 0 0
VAV2 0.025 0.081 -9999 0 -0.38 10 10
CBL 0.01 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.004 0.059 -9999 0 -0.31 10 10
LCK -0.004 0.051 -9999 0 -0.27 10 10
PDGFRB -0.005 0.083 -9999 0 -0.44 10 10
ACP1 0.01 0 -9999 0 -10000 0 0
HCK -0.006 0.058 -9999 0 -0.29 11 11
ABL1 0.018 0.068 -9999 0 -0.33 10 10
PDGFB-D/PDGFRB/CBL 0.018 0.092 -9999 0 -0.46 10 10
PTPN1 0.01 0.002 -9999 0 -10000 0 0
SNX15 0.01 0 -9999 0 -10000 0 0
STAT3 0.01 0 -9999 0 -10000 0 0
STAT1 0.01 0.001 -9999 0 -10000 0 0
cell proliferation 0.031 0.06 -9999 0 -10000 0 0
SLA 0.009 0.002 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.014 0.04 -9999 0 -0.2 10 10
SRC -0.004 0.051 -9999 0 -0.27 10 10
PI3K -0.006 0.034 -9999 0 -0.19 10 10
PDGFB-D/PDGFRB/GRB7/SHC 0.011 0.05 -9999 0 -0.26 10 10
SH2B2 0.01 0.001 -9999 0 -10000 0 0
PLCgamma1/SPHK1 -0.002 0.077 -9999 0 -0.4 10 10
LYN -0.004 0.051 -9999 0 -0.27 10 10
LRP1 0.01 0 -9999 0 -10000 0 0
SOS1 0.01 0 -9999 0 -10000 0 0
STAT5B 0.01 0 -9999 0 -10000 0 0
STAT5A 0.01 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas 0.024 0.043 -9999 0 -0.2 10 10
SPHK1 0.005 0.005 -9999 0 -10000 0 0
EDG1 0.001 0.001 -9999 0 -10000 0 0
mol:DAG 0.012 0.086 -9999 0 -0.44 10 10
PLCG1 0.011 0.088 -9999 0 -0.45 10 10
NHERF/PDGFRB 0.011 0.05 -9999 0 -0.26 10 10
YES1 -0.004 0.051 -9999 0 -0.27 10 10
cell migration 0.011 0.05 -9999 0 -0.26 10 10
SHC/Grb2/SOS1 0.024 0.043 -9999 0 -0.2 10 10
SLC9A3R2 0.01 0 -9999 0 -10000 0 0
SLC9A3R1 0.01 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.017 0.047 -9999 0 -0.23 10 10
FYN -0.004 0.051 -9999 0 -0.27 10 10
DOK1 0.005 0.045 -9999 0 -0.23 10 10
HRAS/GTP 0.007 0 -9999 0 -10000 0 0
PDGFB 0.008 0.026 -9999 0 -0.44 1 1
RAC1 0.026 0.075 -9999 0 -0.35 10 10
PRKCD 0.006 0.045 -9999 0 -0.23 10 10
FER 0.006 0.045 -9999 0 -0.23 10 10
MAPKKK cascade -0.007 0.037 -9999 0 -0.2 10 10
RASA1 0.006 0.045 -9999 0 -0.23 10 10
NCK1 0.01 0 -9999 0 -10000 0 0
NCK2 0.01 0 -9999 0 -10000 0 0
p62DOK/Csk 0.009 0.042 -9999 0 -0.21 10 10
PDGFB-D/PDGFRB/SHB 0.004 0.059 -9999 0 -0.31 10 10
chemotaxis 0.018 0.067 -9999 0 -0.32 10 10
STAT1-3-5/STAT1-3-5 0.017 0.041 -9999 0 -0.2 10 10
Bovine Papilomavirus E5/PDGFRB -0.002 0.059 -9999 0 -0.31 10 10
PTPRJ 0.01 0 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.021 0.13 -9999 0 -0.32 44 44
MAP3K8 0.008 0.006 -9999 0 -10000 0 0
FOS -0.007 0.076 -9999 0 -0.59 1 1
PRKCA 0.007 0.008 -9999 0 -10000 0 0
PTPN7 0.004 0.029 -9999 0 -0.45 1 1
HRAS 0.009 0.001 -9999 0 -10000 0 0
PRKCB 0.007 0.008 -9999 0 -10000 0 0
NRAS 0.009 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.015 0.011 -9999 0 -10000 0 0
MAPK3 0.003 0.046 -9999 0 -0.5 1 1
MAP2K1 0.006 0.03 -9999 0 -10000 0 0
ELK1 0.005 0.012 -9999 0 -10000 0 0
BRAF 0.007 0.018 -9999 0 -10000 0 0
mol:GTP -0.001 0.002 -9999 0 -0.005 44 44
MAPK1 0.003 0.046 -9999 0 -0.5 1 1
RAF1 0.007 0.018 -9999 0 -10000 0 0
KRAS 0.009 0.001 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.01 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.025 0.091 -9999 0 -0.19 64 64
Syndecan-3/Neurocan 0.011 0.006 -9999 0 -10000 0 0
POMC 0.004 0.052 -9999 0 -0.44 4 4
EGFR 0.01 0 -9999 0 -10000 0 0
Syndecan-3/EGFR 0.014 0.004 -9999 0 -10000 0 0
AGRP 0.007 0.005 -9999 0 -10000 0 0
NCSTN 0.01 0 -9999 0 -10000 0 0
PSENEN 0.01 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.008 0.026 -9999 0 -0.44 1 1
APH1A 0.01 0 -9999 0 -10000 0 0
NCAN 0.007 0.005 -9999 0 -10000 0 0
long-term memory 0.019 0.004 -9999 0 -10000 0 0
Syndecan-3/IL8 0.01 0.015 -9999 0 -0.21 1 1
PSEN1 0.01 0 -9999 0 -10000 0 0
Src/Cortactin 0.015 0.001 -9999 0 -10000 0 0
FYN 0.01 0 -9999 0 -10000 0 0
limb bud formation 0.008 0.004 -9999 0 -10000 0 0
MC4R 0.002 0.004 -9999 0 -10000 0 0
SRC 0.01 0.001 -9999 0 -10000 0 0
PTN -0.091 0.19 -9999 0 -0.44 65 65
FGFR/FGF/Syndecan-3 0.008 0.004 -9999 0 -10000 0 0
neuron projection morphogenesis -0.03 0.082 -9999 0 -0.24 1 1
Syndecan-3/AgRP 0.012 0.005 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R 0.012 0.006 -9999 0 -10000 0 0
Fyn/Cortactin 0.015 0 -9999 0 -10000 0 0
SDC3 0.008 0.004 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration 0.01 0.014 -9999 0 -0.21 1 1
IL8 0.006 0.027 -9999 0 -0.44 1 1
Syndecan-3/Fyn/Cortactin 0.019 0.004 -9999 0 -10000 0 0
Syndecan-3/CASK 0.007 0.003 -9999 0 -10000 0 0
alpha-MSH/MC4R 0.005 0.038 -9999 0 -0.31 4 4
Gamma Secretase 0.028 0.014 -9999 0 -0.22 1 1
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.013 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.01 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.01 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.01 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.011 0.001 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.01 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.01 0 -9999 0 -10000 0 0
FYN 0.01 0 -9999 0 -10000 0 0
MAP3K12 0.01 0.001 -9999 0 -10000 0 0
FGR 0.008 0.026 -9999 0 -0.44 1 1
p38 alpha/TAB1 -0.001 0.011 -9999 0 -0.19 1 1
PRKG1 -0.1 0.2 -9999 0 -0.44 73 73
DUSP8 0.01 0 -9999 0 -10000 0 0
PGK/cGMP/p38 alpha -0.027 0.083 -9999 0 -0.17 64 64
apoptosis -0.001 0.011 -9999 0 -0.18 1 1
RAL/GTP 0.013 0 -9999 0 -10000 0 0
LYN 0.01 0 -9999 0 -10000 0 0
DUSP1 0.008 0.026 -9999 0 -0.44 1 1
PAK1 0.01 0 -9999 0 -10000 0 0
SRC 0.01 0.001 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.025 0 -9999 0 -10000 0 0
TRAF6 0.01 0 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.01 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.013 0 -9999 0 -10000 0 0
MAPK11 0.03 0.021 -9999 0 -0.27 1 1
BLK 0.008 0.004 -9999 0 -10000 0 0
HCK 0.007 0.026 -9999 0 -0.44 1 1
MAP2K3 0.01 0 -9999 0 -10000 0 0
DUSP16 0.01 0 -9999 0 -10000 0 0
DUSP10 0.009 0.003 -9999 0 -10000 0 0
TRAF6/MEKK3 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.028 0.016 -9999 0 -0.2 1 1
positive regulation of innate immune response 0.035 0.023 -9999 0 -0.3 1 1
LCK 0.01 0.001 -9999 0 -10000 0 0
p38alpha-beta/MKP7 0.039 0.022 -9999 0 -0.28 1 1
p38alpha-beta/MKP5 0.035 0.024 -9999 0 -0.28 1 1
PGK/cGMP -0.073 0.14 -9999 0 -0.31 73 73
PAK2 0.01 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.038 0.025 -9999 0 -0.28 1 1
CDC42 0.01 0 -9999 0 -10000 0 0
RALB 0.01 0 -9999 0 -10000 0 0
RALA 0.01 0 -9999 0 -10000 0 0
PAK3 0.008 0.004 -9999 0 -10000 0 0
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.022 0.014 -10000 0 -0.21 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.015 0.038 -10000 0 -10000 0 0
AP1 -0.009 0.084 -10000 0 -0.2 44 44
mol:PIP3 -0.001 0.01 -10000 0 -10000 0 0
AKT1 0.02 0.014 -10000 0 -10000 0 0
PTK2B 0.008 0.02 -10000 0 -0.17 1 1
RHOA 0.01 0.011 -10000 0 -10000 0 0
PIK3CB 0.01 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.006 0.045 0.14 1 -0.19 1 2
MAGI3 0.01 0 -10000 0 -10000 0 0
RELA 0.01 0 -10000 0 -10000 0 0
apoptosis 0.01 0.013 -10000 0 -0.21 1 1
HRAS/GDP 0.007 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.003 0.038 -10000 0 -0.18 9 9
NF kappa B1 p50/RelA 0.01 0.043 -10000 0 -10000 0 0
endothelial cell migration 0.01 0.032 -10000 0 -0.54 1 1
ADCY4 -0.01 0.077 -10000 0 -0.4 5 5
ADCY5 -0.01 0.071 -10000 0 -0.4 3 3
ADCY6 0.001 0.055 -10000 0 -0.39 1 1
ADCY7 0 0.055 -10000 0 -0.39 1 1
ADCY1 -0.085 0.12 -10000 0 -0.39 19 19
ADCY2 -0.006 0.05 -10000 0 -0.37 1 1
ADCY3 0.001 0.055 -10000 0 -0.39 1 1
ADCY8 0 0.055 -10000 0 -0.4 1 1
ADCY9 0.001 0.055 -10000 0 -0.39 1 1
GSK3B 0.009 0.019 -10000 0 -0.16 1 1
arachidonic acid secretion -0.001 0.063 -10000 0 -0.2 25 25
GNG2 0.01 0 -10000 0 -10000 0 0
TRIP6 0.012 0.005 -10000 0 -10000 0 0
GNAO1 -0.011 0.08 -10000 0 -0.27 25 25
HRAS 0.01 0 -10000 0 -10000 0 0
NFKBIA 0.004 0.037 -10000 0 -10000 0 0
GAB1 0.01 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly 0.018 0 -10000 0 -10000 0 0
JUN 0.01 0 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.015 0.006 -10000 0 -10000 0 0
TIAM1 0.014 0.002 -10000 0 -10000 0 0
PIK3R1 0.01 0 -10000 0 -10000 0 0
mol:IP3 -0.006 0.045 0.14 1 -0.2 1 2
PLCB3 0.012 0.007 -10000 0 -10000 0 0
FOS -0.058 0.16 -10000 0 -0.44 44 44
positive regulation of mitosis -0.001 0.063 -10000 0 -0.2 25 25
LPA/LPA1-2-3 0.019 0.015 -10000 0 -0.21 1 1
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.01 0 -10000 0 -10000 0 0
stress fiber formation 0.014 0.019 -10000 0 -0.17 1 1
GNAZ 0.012 0.019 -10000 0 -0.23 1 1
EGFR/PI3K-beta/Gab1 0.007 0.011 -10000 0 -10000 0 0
positive regulation of dendritic cell cytokine production 0.019 0.014 -10000 0 -0.21 1 1
LPA/LPA2/MAGI-3 0.014 0.006 -10000 0 -10000 0 0
ARHGEF1 0.015 0.017 -10000 0 -0.19 1 1
GNAI2 0.012 0.019 -10000 0 -0.23 1 1
GNAI3 0.012 0.019 -10000 0 -0.23 1 1
GNAI1 0.01 0.029 -10000 0 -0.25 3 3
LPA/LPA3 0.004 0.007 -10000 0 -0.11 1 1
LPA/LPA2 0.009 0.007 -10000 0 -0.1 1 1
LPA/LPA1 0.011 0.017 -10000 0 -0.28 1 1
HB-EGF/EGFR 0.004 0.039 -10000 0 -0.26 6 6
HBEGF -0.001 0.045 -10000 0 -0.31 6 6
mol:DAG -0.006 0.045 0.14 1 -0.2 1 2
cAMP biosynthetic process -0.017 0.073 -10000 0 -0.24 25 25
NFKB1 0.01 0 -10000 0 -10000 0 0
SRC 0.01 0.001 -10000 0 -10000 0 0
GNB1 0.01 0 -10000 0 -10000 0 0
LYN 0.004 0.037 -10000 0 -10000 0 0
GNAQ 0.01 0.007 -10000 0 -10000 0 0
LPAR2 0.01 0.001 -10000 0 -10000 0 0
LPAR3 0.004 0.005 -10000 0 -10000 0 0
LPAR1 0.011 0.01 -10000 0 -0.16 1 1
IL8 0.051 0.11 0.22 40 -0.32 6 46
PTK2 0.015 0.018 -10000 0 -0.19 1 1
Rac1/GDP 0.007 0 -10000 0 -10000 0 0
CASP3 0.01 0.013 -10000 0 -0.21 1 1
EGFR 0.01 0.001 -10000 0 -10000 0 0
PLCG1 -0.014 0.05 -10000 0 -0.23 1 1
PLD2 0.015 0.018 -10000 0 -0.19 1 1
G12/G13 0.022 0.014 -10000 0 -0.21 1 1
PI3K-beta -0.001 0.009 -10000 0 -10000 0 0
cell migration 0.021 0.009 -10000 0 -10000 0 0
SLC9A3R2 0.01 0 -10000 0 -10000 0 0
PXN 0.015 0.019 -10000 0 -0.17 1 1
HRAS/GTP -0.002 0.064 -10000 0 -0.2 25 25
RAC1 0.01 0 -10000 0 -10000 0 0
MMP9 0 0.052 -10000 0 -0.44 4 4
PRKCE 0.01 0 -10000 0 -10000 0 0
PRKCD -0.004 0.043 -10000 0 -0.19 1 1
Gi(beta/gamma) 0.002 0.056 -10000 0 -0.38 1 1
mol:LPA 0.002 0.01 -10000 0 -0.17 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.027 0.017 -10000 0 -10000 0 0
MAPKKK cascade -0.001 0.063 -10000 0 -0.2 25 25
contractile ring contraction involved in cytokinesis 0.01 0.011 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.043 0.1 -10000 0 -0.24 61 61
GNA15 0.009 0.007 -10000 0 -10000 0 0
GNA12 0.01 0 -10000 0 -10000 0 0
GNA13 0.01 0.001 -10000 0 -10000 0 0
MAPT 0.003 0.039 -10000 0 -0.19 9 9
GNA11 0.004 0.039 -10000 0 -0.24 7 7
Rac1/GTP 0.019 0 -10000 0 -10000 0 0
MMP2 0.01 0.032 -10000 0 -0.54 1 1
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.006 0.002 -9999 0 -10000 0 0
RAS family/GTP 0.049 0.052 -9999 0 -0.19 5 5
NFATC4 0.008 0.036 -9999 0 -0.17 10 10
ERBB2IP 0.009 0.001 -9999 0 -10000 0 0
HSP90 (dimer) 0.01 0 -9999 0 -10000 0 0
mammary gland morphogenesis 0.021 0.044 -9999 0 -0.21 8 8
JUN 0.047 0.067 -9999 0 -10000 0 0
HRAS 0.011 0.001 -9999 0 -10000 0 0
DOCK7 0.011 0.039 -9999 0 -0.2 8 8
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.016 0.041 -9999 0 -0.22 8 8
AKT1 0.005 0.002 -9999 0 -10000 0 0
BAD 0.006 0.001 -9999 0 -10000 0 0
MAPK10 0.01 0.023 -9999 0 -0.12 1 1
mol:GTP 0.001 0.001 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.024 0.048 -9999 0 -0.22 8 8
RAF1 0.059 0.061 -9999 0 -0.23 1 1
ErbB2/ErbB3/neuregulin 2 0.01 0.036 -9999 0 -0.24 6 6
STAT3 0.014 0.002 -9999 0 -10000 0 0
cell migration 0.012 0.028 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.001 -9999 0 -10000 0 0
cell proliferation 0.087 0.16 -9999 0 -0.44 1 1
FOS 0.04 0.22 -9999 0 -0.46 44 44
NRAS 0.011 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.021 0.044 -9999 0 -0.21 8 8
MAPK3 0.087 0.12 -9999 0 -0.34 1 1
MAPK1 0.087 0.12 -9999 0 -0.34 1 1
JAK2 0.011 0.039 -9999 0 -0.2 8 8
NF2 0.008 0.004 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.01 0.041 -9999 0 -0.23 8 8
NRG1 0.003 0.059 -9999 0 -0.44 5 5
GRB2/SOS1 0.015 0.001 -9999 0 -10000 0 0
MAPK8 0.012 0.058 -9999 0 -0.24 13 13
MAPK9 0.01 0.023 -9999 0 -0.12 1 1
ERBB2 0 0.003 -9999 0 -10000 0 0
ERBB3 0.006 0.046 -9999 0 -0.44 3 3
SHC1 0.011 0.001 -9999 0 -10000 0 0
RAC1 0.01 0 -9999 0 -10000 0 0
apoptosis -0.005 0.005 -9999 0 -10000 0 0
STAT3 (dimer) 0.014 0.002 -9999 0 -10000 0 0
RNF41 0.006 0.003 -9999 0 -10000 0 0
FRAP1 0.003 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.004 0.026 -9999 0 -0.15 8 8
ErbB2/ErbB2/HSP90 (dimer) 0.008 0.003 -9999 0 -10000 0 0
CHRNA1 0.11 0.12 -9999 0 -0.26 1 1
myelination 0.006 0.034 -9999 0 -0.17 10 10
PPP3CB 0.011 0.037 -9999 0 -0.19 8 8
KRAS 0.011 0.001 -9999 0 -10000 0 0
RAC1-CDC42/GDP 0.02 0.037 -9999 0 -0.2 8 8
NRG2 0.005 0.046 -9999 0 -0.44 3 3
mol:GDP 0.009 0.04 -9999 0 -0.23 8 8
SOS1 0.01 0.001 -9999 0 -10000 0 0
MAP2K2 0.064 0.068 -9999 0 -0.24 1 1
SRC 0.01 0.001 -9999 0 -10000 0 0
mol:cAMP 0 0.001 -9999 0 -10000 0 0
PTPN11 0.01 0.038 -9999 0 -0.2 8 8
MAP2K1 0.072 0.12 -9999 0 -0.41 1 1
heart morphogenesis 0.021 0.044 -9999 0 -0.21 8 8
RAS family/GDP 0.036 0.042 -9999 0 -0.19 5 5
GRB2 0.01 0.001 -9999 0 -10000 0 0
PRKACA 0.007 0.004 -9999 0 -10000 0 0
CHRNE 0.017 0.017 -9999 0 -10000 0 0
HSP90AA1 0.01 0 -9999 0 -10000 0 0
activation of caspase activity -0.005 0.002 -9999 0 -10000 0 0
nervous system development 0.021 0.044 -9999 0 -0.21 8 8
CDC42 0.01 0 -9999 0 -10000 0 0
Cellular roles of Anthrax toxin

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
ANTXR1 0.01 0 -10000 0 -10000 0 0
ANTXR2 0.01 0 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
monocyte activation 0.003 0.045 -10000 0 -0.38 4 4
MAP2K2 0.007 0 -10000 0 -10000 0 0
MAP2K1 0.003 0 -10000 0 -10000 0 0
MAP2K7 0.003 0 -10000 0 -10000 0 0
MAP2K6 0.003 0 -10000 0 -10000 0 0
CYAA 0.003 0 -10000 0 -10000 0 0
MAP2K4 0.003 0 -10000 0 -10000 0 0
IL1B 0.001 0.029 -10000 0 -0.21 5 5
Channel 0.013 0 -10000 0 -10000 0 0
NLRP1 0.003 0 -10000 0 -10000 0 0
CALM1 0.01 0 -10000 0 -10000 0 0
negative regulation of phagocytosis 0.007 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0 0 -10000 0 -10000 0 0
MAPK3 0.003 0 -10000 0 -10000 0 0
MAPK1 0.003 0 -10000 0 -10000 0 0
PGR -0.091 0.11 -10000 0 -0.22 121 121
PA/Cellular Receptors 0.013 0 -10000 0 -10000 0 0
apoptosis 0 0 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.012 0 -10000 0 -10000 0 0
macrophage activation 0.004 0 -10000 0 -10000 0 0
TNF 0.005 0.046 -10000 0 -0.44 3 3
VCAM1 0.003 0.045 -10000 0 -0.38 4 4
platelet activation 0.007 0 -10000 0 -10000 0 0
MAPKKK cascade -0.004 0 -10000 0 -10000 0 0
IL18 0.006 0.01 0.076 5 -10000 0 5
negative regulation of macrophage activation 0 0 -10000 0 -10000 0 0
LEF 0 0 -10000 0 -10000 0 0
CASP1 0.003 0 -10000 0 -10000 0 0
mol:cAMP 0.007 0 -10000 0 -10000 0 0
necrosis 0 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) 0.012 0 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.023 0.008 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.01 0 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.033 0.013 -10000 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.021 0.003 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.025 0.05 -10000 0 -0.17 1 1
CaM/Ca2+ 0.024 0.007 -10000 0 -10000 0 0
RAP1A 0.01 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.022 0.013 -10000 0 -10000 0 0
AKT1 0.019 0.013 -10000 0 -10000 0 0
MAP2K1 0.018 0.014 -10000 0 -10000 0 0
MAP3K11 0.018 0.014 -10000 0 -10000 0 0
IFNGR1 0.011 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.13 0.17 -10000 0 -0.33 119 119
Rap1/GTP 0 0 -10000 0 -10000 0 0
CRKL/C3G 0.015 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.026 0.008 -10000 0 -10000 0 0
CEBPB 0.031 0.016 -10000 0 -10000 0 0
STAT3 0.01 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.019 0.089 -10000 0 -1 2 2
STAT1 0.018 0.014 -10000 0 -10000 0 0
CALM1 0.01 0 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.006 0.005 -10000 0 -10000 0 0
PIK3CA 0.01 0 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.023 0.014 -10000 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 0.026 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0.022 0.007 -10000 0 -10000 0 0
MAPK3 0.023 0.014 -10000 0 -10000 0 0
STAT1 (dimer) -0.03 0.067 -10000 0 -0.23 1 1
MAPK1 0.023 0.014 -10000 0 -10000 0 0
JAK2 0.011 0.001 -10000 0 -10000 0 0
PIK3R1 0.01 0 -10000 0 -10000 0 0
JAK1 0.011 0.001 -10000 0 -10000 0 0
CAMK2D 0.01 0 -10000 0 -10000 0 0
DAPK1 0.029 0.013 -10000 0 -10000 0 0
SMAD7 -0.006 0.035 -10000 0 -10000 0 0
CBL/CRKL/C3G 0.027 0.012 -10000 0 -10000 0 0
PI3K 0.023 0.007 -10000 0 -10000 0 0
IFNG 0.006 0.005 -10000 0 -10000 0 0
apoptosis 0.019 0.015 -10000 0 -10000 0 0
CAMK2G 0.01 0 -10000 0 -10000 0 0
STAT3 (dimer) 0.01 0 -10000 0 -10000 0 0
CAMK2A -0.17 0.22 -10000 0 -0.44 116 116
CAMK2B 0.002 0.052 -10000 0 -0.44 4 4
FRAP1 0.016 0.013 -10000 0 -10000 0 0
PRKCD 0.02 0.014 -10000 0 -10000 0 0
RAP1B 0.01 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.025 0.05 -10000 0 -0.17 1 1
PTPN2 0.01 0 -10000 0 -10000 0 0
EP300 0.01 0 -10000 0 -10000 0 0
IRF1 0.022 0.03 -10000 0 -0.29 2 2
STAT1 (dimer)/PIASy 0.022 0.017 0.16 2 -10000 0 2
SOCS1 0 0.1 -10000 0 -1.2 2 2
mol:GDP 0.025 0.011 -10000 0 -10000 0 0
CASP1 -0.006 0.035 -10000 0 -10000 0 0
PTGES2 0.01 0 -10000 0 -10000 0 0
IRF9 0.021 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.017 0.005 -10000 0 -10000 0 0
RAP1/GDP 0.018 0.005 -10000 0 -10000 0 0
CBL 0.018 0.014 -10000 0 -10000 0 0
MAP3K1 0.018 0.014 -10000 0 -10000 0 0
PIAS1 0.01 0 -10000 0 -10000 0 0
PIAS4 0.01 0.001 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.025 0.05 -10000 0 -0.17 1 1
PTPN11 0.017 0.015 -10000 0 -10000 0 0
CREBBP 0.01 0 -10000 0 -10000 0 0
RAPGEF1 0.01 0 -10000 0 -10000 0 0
Nectin adhesion 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
PDGFRB -0.006 0.082 -9999 0 -0.44 10 10
alphaV beta3 Integrin -0.001 0.069 -9999 0 -0.31 14 14
PTK2 0.009 0.062 -9999 0 -0.44 4 4
positive regulation of JNK cascade -0.005 0.036 -9999 0 -0.31 4 4
CDC42/GDP 0.023 0.053 -9999 0 -0.41 4 4
Rac1/GDP 0.023 0.053 -9999 0 -0.41 4 4
RAP1B 0.01 0 -9999 0 -10000 0 0
RAP1A 0.01 0 -9999 0 -10000 0 0
CTNNB1 0.01 0 -9999 0 -10000 0 0
CDC42/GTP 0.018 0.048 -9999 0 -0.38 4 4
nectin-3/I-afadin 0.01 0.038 -9999 0 -0.31 4 4
RAPGEF1 0.015 0.057 -9999 0 -0.46 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0.065 -9999 0 -0.52 4 4
PDGFB-D/PDGFRB -0.006 0.082 -9999 0 -0.44 10 10
TLN1 0.007 0.018 -9999 0 -10000 0 0
Rap1/GTP -0.006 0.039 -9999 0 -0.33 4 4
IQGAP1 0.01 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.019 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.01 0.038 -9999 0 -0.31 4 4
PVR 0.01 0.001 -9999 0 -10000 0 0
Necl-5(dimer) 0.01 0.001 -9999 0 -10000 0 0
mol:GDP 0.02 0.063 -9999 0 -0.5 4 4
MLLT4 0.01 0 -9999 0 -10000 0 0
PIK3CA 0.01 0 -9999 0 -10000 0 0
PI3K 0.017 0.052 -9999 0 -0.22 14 14
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.015 0.001 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly 0.014 0.041 -9999 0 -0.32 4 4
PVRL1 0.01 0.001 -9999 0 -10000 0 0
PVRL3 0.004 0.052 -9999 0 -0.44 4 4
PVRL2 0.01 0 -9999 0 -10000 0 0
PIK3R1 0.01 0 -9999 0 -10000 0 0
CDH1 -0.027 0.12 -9999 0 -0.44 24 24
CLDN1 0.007 0.005 -9999 0 -10000 0 0
JAM-A/CLDN1 0.014 0.03 -9999 0 -0.21 4 4
SRC 0.012 0.071 -9999 0 -0.57 4 4
ITGB3 -0.012 0.096 -9999 0 -0.44 14 14
nectin-1(dimer)/I-afadin/I-afadin 0.015 0.001 -9999 0 -10000 0 0
FARP2 0.018 0.062 -9999 0 -0.49 4 4
RAC1 0.01 0 -9999 0 -10000 0 0
CTNNA1 0.01 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.016 0.033 -9999 0 -0.26 4 4
nectin-1/I-afadin 0.015 0.001 -9999 0 -10000 0 0
nectin-2/I-afadin 0.015 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.013 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.016 0.033 -9999 0 -0.26 4 4
CDC42/GTP/IQGAP1/filamentous actin 0.013 0 -9999 0 -10000 0 0
F11R 0.01 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.005 0.036 -9999 0 -0.31 4 4
alphaV/beta3 Integrin/Talin 0.008 0.053 -9999 0 -0.22 14 14
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.015 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.015 0 -9999 0 -10000 0 0
PIP5K1C 0.007 0.019 -9999 0 -0.16 4 4
VAV2 0.019 0.063 -9999 0 -0.5 4 4
RAP1/GDP 0.023 0.05 -9999 0 -0.38 4 4
ITGAV 0.01 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.016 0.032 -9999 0 -0.26 4 4
nectin-3(dimer)/I-afadin/I-afadin 0.01 0.038 -9999 0 -0.31 4 4
Rac1/GTP 0.019 0.05 -9999 0 -0.39 4 4
PTPRM 0.006 0.022 -9999 0 -0.18 4 4
E-cadherin/beta catenin/alpha catenin 0.009 0.065 -9999 0 -0.21 24 24
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.01 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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
MMP14 0.015 0.024 -10000 0 -10000 0 0
oxygen homeostasis 0.005 0.011 -10000 0 -10000 0 0
TCEB2 0.01 0.001 -10000 0 -10000 0 0
TCEB1 0.01 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A 0.042 0.05 -10000 0 -0.31 1 1
EPO 0.063 0.12 0.46 1 -0.49 1 2
FIH (dimer) 0.014 0.012 -10000 0 -10000 0 0
APEX1 0.012 0.012 -10000 0 -10000 0 0
SERPINE1 0.052 0.16 0.48 3 -0.54 11 14
FLT1 -0.015 0.11 -10000 0 -1.1 2 2
ADORA2A 0.059 0.12 0.49 3 -0.48 2 5
germ cell development 0.04 0.1 -10000 0 -0.47 2 2
SLC11A2 0.065 0.12 0.48 3 -0.49 2 5
BHLHE40 0.065 0.12 0.48 3 -0.49 2 5
HIF1AN 0.014 0.012 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.045 0.075 -10000 0 -0.4 1 1
ETS1 -0.004 0.042 -10000 0 -0.16 2 2
CITED2 0.014 0.02 -10000 0 -10000 0 0
KDR -0.16 0.39 -10000 0 -0.99 53 53
PGK1 0.065 0.12 0.48 3 -0.49 2 5
SIRT1 0.01 0.001 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.084 0.13 -10000 0 -0.51 3 3
EPAS1 0.037 0.065 0.35 3 -0.36 1 4
SP1 0.016 0.014 -10000 0 -10000 0 0
ABCG2 0.063 0.13 0.48 3 -0.51 4 7
EFNA1 0.065 0.12 0.48 3 -0.49 2 5
FXN 0.059 0.12 0.49 3 -0.48 2 5
POU5F1 0.04 0.11 -10000 0 -0.49 2 2
neuron apoptosis -0.082 0.13 0.5 3 -10000 0 3
EP300 0.01 0 -10000 0 -10000 0 0
EGLN3 0.012 0.01 -10000 0 -10000 0 0
EGLN2 0.014 0.012 -10000 0 -10000 0 0
EGLN1 0.014 0.012 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.02 0.002 -10000 0 -10000 0 0
VHL 0.01 0 -10000 0 -10000 0 0
ARNT 0.012 0.012 -10000 0 -10000 0 0
SLC2A1 0.05 0.11 0.37 1 -0.48 2 3
TWIST1 0.055 0.12 0.49 3 -0.59 2 5
ELK1 0.013 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.054 0.078 -10000 0 -0.4 1 1
VEGFA 0.06 0.12 -10000 0 -0.49 2 2
CREBBP 0.01 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S81.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S81.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.01 0 -9999 0 -10000 0 0
NFATC1 0.015 0.01 -9999 0 -10000 0 0
NFATC2 -0.023 0.053 -9999 0 -0.19 14 14
NFATC3 0.004 0.008 -9999 0 -10000 0 0
YWHAE 0.01 0 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.018 0.032 -9999 0 -10000 0 0
Exportin 1/Ran/NUP214 0.017 0.004 -9999 0 -10000 0 0
mol:DAG -0.002 0.003 -9999 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV