PARADIGM pathway analysis of mRNASeq expression and copy number 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 and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1W37VHW
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 26 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Nephrin/Neph1 signaling in the kidney podocyte 129
Angiopoietin receptor Tie2-mediated signaling 98
EGFR-dependent Endothelin signaling events 88
FOXA2 and FOXA3 transcription factor networks 81
PDGFR-alpha signaling pathway 63
Thromboxane A2 receptor signaling 48
Signaling mediated by p38-alpha and p38-beta 40
Glypican 1 network 38
BMP receptor signaling 33
Signaling events mediated by Stem cell factor receptor (c-Kit) 33
Results
Summary Table

The following list describes the columns found in Table 2.

  • Pathway.Name = Full pathway name of curated PARADIGM pathway

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 290 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 290 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Nephrin/Neph1 signaling in the kidney podocyte 0.4448 129 4394 34 -0.45 0.028 1000 -1000 -0.035 -1000
Angiopoietin receptor Tie2-mediated signaling 0.3379 98 8710 88 -0.9 0.094 1000 -1000 -0.065 -1000
EGFR-dependent Endothelin signaling events 0.3034 88 1866 21 -0.56 0.038 1000 -1000 -0.051 -1000
FOXA2 and FOXA3 transcription factor networks 0.2793 81 3741 46 -1.1 0.031 1000 -1000 -0.1 -1000
PDGFR-alpha signaling pathway 0.2172 63 2803 44 -0.25 0.038 1000 -1000 -0.057 -1000
Thromboxane A2 receptor signaling 0.1655 48 5102 105 -0.56 0.097 1000 -1000 -0.049 -1000
Signaling mediated by p38-alpha and p38-beta 0.1379 40 1775 44 -0.17 0.027 1000 -1000 -0.036 -1000
Glypican 1 network 0.1310 38 1854 48 -0.32 0.051 1000 -1000 -0.028 -1000
BMP receptor signaling 0.1138 33 2714 81 -0.37 0.055 1000 -1000 -0.048 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1138 33 2613 78 -0.27 0.064 1000 -1000 -0.052 -1000
Endothelins 0.1034 30 2974 96 -0.61 0.034 1000 -1000 -0.072 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1000 29 3683 125 -0.14 0.062 1000 -1000 -0.072 -1000
Arf6 signaling events 0.0931 27 1691 62 -0.56 0.059 1000 -1000 -0.045 -1000
IL4-mediated signaling events 0.0897 26 2410 91 -0.87 0.52 1000 -1000 -0.12 -1000
Integrins in angiogenesis 0.0793 23 1939 84 -0.41 0.058 1000 -1000 -0.053 -1000
Signaling events mediated by PTP1B 0.0759 22 1683 76 -0.56 0.084 1000 -1000 -0.044 -1000
S1P1 pathway 0.0759 22 820 36 -0.16 0.027 1000 -1000 -0.055 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0759 22 1541 68 -0.48 0.087 1000 -1000 -0.088 -1000
Ceramide signaling pathway 0.0724 21 1651 76 -0.56 0.2 1000 -1000 -0.043 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0724 21 2527 120 -0.23 0.11 1000 -1000 -0.057 -1000
amb2 Integrin signaling 0.0690 20 1715 82 -0.37 0.035 1000 -1000 -0.044 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0690 20 1503 74 -0.56 0.064 1000 -1000 -0.075 -1000
FoxO family signaling 0.0586 17 1134 64 -0.86 0.063 1000 -1000 -0.05 -1000
Ephrin A reverse signaling 0.0517 15 105 7 -0.032 0 1000 -1000 -0.018 -1000
Glucocorticoid receptor regulatory network 0.0517 15 1750 114 -0.57 0.15 1000 -1000 -0.056 -1000
Plasma membrane estrogen receptor signaling 0.0517 15 1340 86 -0.14 0.048 1000 -1000 -0.061 -1000
Signaling events regulated by Ret tyrosine kinase 0.0483 14 1175 82 -0.064 0.028 1000 -1000 -0.071 -1000
LPA4-mediated signaling events 0.0448 13 158 12 -0.14 0.007 1000 -1000 -0.024 -1000
Coregulation of Androgen receptor activity 0.0448 13 1002 76 -0.64 0.05 1000 -1000 -0.02 -1000
TCR signaling in naïve CD8+ T cells 0.0448 13 1225 93 -0.2 0.11 1000 -1000 -0.052 -1000
E-cadherin signaling events 0.0448 13 65 5 -0.025 0.027 1000 -1000 0 -1000
Signaling events mediated by the Hedgehog family 0.0414 12 625 52 -0.037 0.04 1000 -1000 -0.047 -1000
Nongenotropic Androgen signaling 0.0414 12 659 52 -0.11 0.045 1000 -1000 -0.041 -1000
Syndecan-3-mediated signaling events 0.0379 11 385 35 -0.096 0.075 1000 -1000 -0.036 -1000
TCGA08_rtk_signaling 0.0379 11 295 26 -0.22 0.062 1000 -1000 -0.011 -1000
E-cadherin signaling in keratinocytes 0.0379 11 492 43 -0.22 0.043 1000 -1000 -0.047 -1000
Caspase cascade in apoptosis 0.0345 10 800 74 -0.41 0.066 1000 -1000 -0.045 -1000
p75(NTR)-mediated signaling 0.0345 10 1350 125 -0.36 0.075 1000 -1000 -0.083 -1000
IL6-mediated signaling events 0.0345 10 755 75 -0.22 0.041 1000 -1000 -0.059 -1000
Regulation of nuclear SMAD2/3 signaling 0.0310 9 1234 136 -0.48 0.096 1000 -1000 -0.048 -1000
Calcium signaling in the CD4+ TCR pathway 0.0310 9 298 31 -0.11 0.028 1000 -1000 -0.051 -1000
IL27-mediated signaling events 0.0310 9 491 51 -1 0.25 1000 -1000 -0.057 -1000
IL23-mediated signaling events 0.0310 9 594 60 -0.062 0.04 1000 -1000 -0.084 -1000
S1P3 pathway 0.0310 9 416 42 -0.11 0.039 1000 -1000 -0.036 -1000
Osteopontin-mediated events 0.0276 8 330 38 -0.065 0.048 1000 -1000 -0.048 -1000
HIF-1-alpha transcription factor network 0.0276 8 656 76 -0.1 0.086 1000 -1000 -0.084 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0276 8 690 85 -0.1 0.11 1000 -1000 -0.059 -1000
Presenilin action in Notch and Wnt signaling 0.0276 8 525 61 -0.15 0.083 1000 -1000 -0.052 -1000
Reelin signaling pathway 0.0276 8 503 56 -0.12 0.071 1000 -1000 -0.056 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0276 8 453 52 -0.24 0.084 1000 -1000 -0.047 -1000
EPHB forward signaling 0.0276 8 751 85 -0.15 0.075 1000 -1000 -0.081 -1000
Effects of Botulinum toxin 0.0276 8 229 26 -0.17 0.045 1000 -1000 -0.01 -1000
E-cadherin signaling in the nascent adherens junction 0.0276 8 622 76 -0.033 0.048 1000 -1000 -0.068 -1000
Regulation of Telomerase 0.0276 8 894 102 -0.56 0.068 1000 -1000 -0.053 -1000
PDGFR-beta signaling pathway 0.0276 8 795 97 -0.032 0.059 1000 -1000 -0.062 -1000
Visual signal transduction: Rods 0.0276 8 429 52 -0.15 0.053 1000 -1000 -0.047 -1000
Regulation of Androgen receptor activity 0.0276 8 582 70 -0.75 0.044 1000 -1000 -0.049 -1000
Syndecan-1-mediated signaling events 0.0241 7 260 34 -0.037 0.028 1000 -1000 -0.046 -1000
ceramide signaling pathway 0.0241 7 368 49 0 0.041 1000 -1000 -0.049 -1000
Regulation of p38-alpha and p38-beta 0.0241 7 398 54 -0.14 0.065 1000 -1000 -0.053 -1000
ErbB4 signaling events 0.0207 6 476 69 -0.22 0.087 1000 -1000 -0.055 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0207 6 194 28 -0.11 0.044 1000 -1000 -0.031 -1000
Cellular roles of Anthrax toxin 0.0207 6 243 39 -0.15 0.036 1000 -1000 -0.026 -1000
IFN-gamma pathway 0.0207 6 420 68 -0.25 0.066 1000 -1000 -0.064 -1000
BCR signaling pathway 0.0207 6 603 99 -0.043 0.062 1000 -1000 -0.064 -1000
Syndecan-4-mediated signaling events 0.0207 6 445 67 -0.35 0.092 1000 -1000 -0.062 -1000
Class IB PI3K non-lipid kinase events 0.0207 6 18 3 -0.012 0.012 1000 -1000 -0.006 -1000
Ras signaling in the CD4+ TCR pathway 0.0207 6 107 17 -0.006 0.042 1000 -1000 -0.03 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0172 5 322 54 -0.059 0.047 1000 -1000 -0.057 -1000
Noncanonical Wnt signaling pathway 0.0172 5 141 26 -0.14 0.027 1000 -1000 -0.051 -1000
Syndecan-2-mediated signaling events 0.0172 5 365 69 -0.37 0.054 1000 -1000 -0.036 -1000
Fc-epsilon receptor I signaling in mast cells 0.0172 5 562 97 -0.065 0.05 1000 -1000 -0.065 -1000
PLK1 signaling events 0.0172 5 433 85 -0.008 0.054 1000 -1000 -0.025 -1000
Class I PI3K signaling events mediated by Akt 0.0172 5 398 68 -0.03 0.056 1000 -1000 -0.045 -1000
IL1-mediated signaling events 0.0172 5 336 62 -0.14 0.072 1000 -1000 -0.051 -1000
Ephrin B reverse signaling 0.0172 5 267 48 -0.019 0.039 1000 -1000 -0.039 -1000
TCGA08_p53 0.0172 5 39 7 -0.035 0.028 1000 -1000 -0.011 -1000
Canonical Wnt signaling pathway 0.0172 5 271 51 -0.15 0.078 1000 -1000 -0.058 -1000
Wnt signaling 0.0172 5 41 7 -0.003 0.027 1000 -1000 -0.027 -1000
ErbB2/ErbB3 signaling events 0.0138 4 267 65 -0.059 0.048 1000 -1000 -0.074 -1000
IL12-mediated signaling events 0.0138 4 378 87 -0.16 0.06 1000 -1000 -0.08 -1000
Nectin adhesion pathway 0.0138 4 265 63 -0.025 0.055 1000 -1000 -0.058 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0138 4 353 83 -0.23 0.048 1000 -1000 -0.045 -1000
LPA receptor mediated events 0.0138 4 480 102 -0.07 0.062 1000 -1000 -0.056 -1000
IGF1 pathway 0.0138 4 230 57 -0.023 0.065 1000 -1000 -0.05 -1000
BARD1 signaling events 0.0103 3 175 57 -0.049 0.06 1000 -1000 -0.058 -1000
mTOR signaling pathway 0.0103 3 200 53 -0.017 0.048 1000 -1000 -0.045 -1000
S1P5 pathway 0.0103 3 60 17 -0.012 0.027 1000 -1000 -0.024 -1000
HIF-2-alpha transcription factor network 0.0103 3 132 43 -0.18 0.096 1000 -1000 -0.062 -1000
FAS signaling pathway (CD95) 0.0103 3 150 47 -0.12 0.04 1000 -1000 -0.039 -1000
Class I PI3K signaling events 0.0103 3 247 73 -0.021 0.048 1000 -1000 -0.049 -1000
Signaling events mediated by PRL 0.0103 3 120 34 -0.037 0.04 1000 -1000 -0.054 -1000
FOXM1 transcription factor network 0.0103 3 156 51 -0.093 0.046 1000 -1000 -0.12 -1000
S1P4 pathway 0.0103 3 89 25 -0.012 0.053 1000 -1000 -0.035 -1000
Aurora B signaling 0.0103 3 226 67 -0.25 0.049 1000 -1000 -0.05 -1000
Signaling events mediated by HDAC Class II 0.0069 2 157 75 -0.1 0.071 1000 -1000 -0.031 -1000
Hedgehog signaling events mediated by Gli proteins 0.0069 2 187 65 -0.012 0.066 1000 -1000 -0.053 -1000
EPO signaling pathway 0.0069 2 160 55 -0.003 0.075 1000 -1000 -0.053 -1000
Insulin-mediated glucose transport 0.0069 2 73 32 -0.03 0.049 1000 -1000 -0.036 -1000
Signaling mediated by p38-gamma and p38-delta 0.0069 2 44 15 -0.01 0.028 1000 -1000 -0.036 -1000
Retinoic acid receptors-mediated signaling 0.0069 2 142 58 -0.033 0.058 1000 -1000 -0.029 -1000
IL2 signaling events mediated by PI3K 0.0069 2 156 58 -0.015 0.062 1000 -1000 -0.043 -1000
Arf6 trafficking events 0.0069 2 167 71 -0.25 0.047 1000 -1000 -0.037 -1000
Insulin Pathway 0.0069 2 188 74 -0.024 0.071 1000 -1000 -0.055 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0069 2 92 33 -0.054 0.068 1000 -1000 -0.037 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0034 1 26 23 -0.01 0.048 1000 -1000 -0.039 -1000
JNK signaling in the CD4+ TCR pathway 0.0034 1 24 17 0.014 0.045 1000 -1000 -0.046 -1000
Arf6 downstream pathway 0.0034 1 76 43 -0.044 0.045 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class I 0.0034 1 175 104 -0.1 0.067 1000 -1000 -0.039 -1000
Atypical NF-kappaB pathway 0.0034 1 33 31 0 0.04 1000 -1000 -0.024 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0034 1 64 45 0 0.077 1000 -1000 -0.052 -1000
TCGA08_retinoblastoma 0.0034 1 9 8 -0.053 0.032 1000 -1000 -0.003 -1000
VEGFR1 specific signals 0.0034 1 89 56 -0.012 0.064 1000 -1000 -0.05 -1000
Canonical NF-kappaB pathway 0.0000 0 18 39 0 0.061 1000 -1000 -0.042 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.009 0.026 1000 -1000 -0.016 -1000
Visual signal transduction: Cones 0.0000 0 29 38 -0.018 0.055 1000 -1000 -0.02 -1000
Circadian rhythm pathway 0.0000 0 6 22 -0.009 0.059 1000 -1000 -0.046 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0.027 0.04 1000 -1000 0.002 -1000
Aurora A signaling 0.0000 0 20 60 -0.009 0.062 1000 -1000 -0.025 -1000
Aurora C signaling 0.0000 0 0 7 -0.02 0.028 1000 -1000 -0.021 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0000 0 5 37 -0.01 0.063 1000 -1000 -0.046 -1000
Signaling events mediated by HDAC Class III 0.0000 0 22 40 -0.049 0.05 1000 -1000 -0.017 -1000
TRAIL signaling pathway 0.0000 0 8 48 0 0.07 1000 -1000 -0.05 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 1 36 -0.054 0.057 1000 -1000 -0.051 -1000
Glypican 2 network 0.0000 0 0 4 -0.005 -0.001 1000 -1000 -0.005 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 2 27 0 0.062 1000 -1000 -0.039 -1000
IL2 signaling events mediated by STAT5 0.0000 0 15 22 0.007 0.041 1000 -1000 -0.048 -1000
Rapid glucocorticoid signaling 0.0000 0 9 20 -0.004 0.034 1000 -1000 -0.006 -1000
p38 MAPK signaling pathway 0.0000 0 33 44 0 0.055 1000 -1000 -0.039 -1000
Arf1 pathway 0.0000 0 26 54 -0.001 0.048 1000 -1000 -0.025 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.075 1000 -1000 0 -1000
Total NA 1504 95807 7203 -24 8 131000 -131000 -6.1 -131000
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.37 0.28 0.55 195 -10000 0 195
KIRREL -0.11 0.19 -10000 0 -0.69 26 26
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.37 0.28 -10000 0 -0.55 195 195
PLCG1 0.027 0.007 -10000 0 -10000 0 0
ARRB2 0.025 0.01 -10000 0 -10000 0 0
WASL 0.022 0.012 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.38 0.3 -10000 0 -0.54 212 212
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.32 0.25 -10000 0 -0.47 188 188
FYN -0.38 0.27 0.26 1 -0.51 212 213
mol:Ca2+ -0.37 0.3 -10000 0 -0.53 206 206
mol:DAG -0.38 0.3 -10000 0 -0.54 206 206
NPHS2 -0.29 0.31 -10000 0 -0.69 107 107
mol:IP3 -0.38 0.3 -10000 0 -0.54 206 206
regulation of endocytosis -0.34 0.27 -10000 0 -0.48 207 207
Nephrin/NEPH1/podocin/Cholesterol -0.39 0.3 -10000 0 -0.54 212 212
establishment of cell polarity -0.37 0.28 -10000 0 -0.55 195 195
Nephrin/NEPH1/podocin/NCK1-2 -0.35 0.29 -10000 0 -0.5 210 210
Nephrin/NEPH1/beta Arrestin2 -0.35 0.28 -10000 0 -0.49 207 207
NPHS1 -0.45 0.31 -10000 0 -0.67 187 187
Nephrin/NEPH1/podocin -0.37 0.28 -10000 0 -0.51 212 212
TJP1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.027 0.006 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.38 0.3 -10000 0 -0.54 206 206
CD2AP 0.027 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.38 0.3 -10000 0 -0.54 206 206
GRB2 0.026 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.45 0.3 0.28 1 -0.57 229 230
cytoskeleton organization -0.39 0.3 -10000 0 -0.58 184 184
Nephrin/NEPH1 -0.27 0.22 -10000 0 -0.41 193 193
Nephrin/NEPH1/ZO-1 -0.3 0.24 -10000 0 -0.46 191 191
Angiopoietin receptor Tie2-mediated signaling

Figure S2.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S2.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.56 0.53 -10000 0 -1 164 164
NCK1/PAK1/Dok-R -0.25 0.21 -10000 0 -0.44 163 163
NCK1/Dok-R -0.7 0.7 -10000 0 -1.3 163 163
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
mol:beta2-estradiol 0.082 0.11 0.24 95 -10000 0 95
RELA 0.028 0.002 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
Rac/GDP 0.016 0.009 -10000 0 -10000 0 0
F2 0.094 0.12 0.26 95 -10000 0 95
TNIP2 0.027 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.63 0.63 -10000 0 -1.2 162 162
FN1 0.02 0.028 -10000 0 -10000 0 0
PLD2 -0.74 0.72 -10000 0 -1.3 164 164
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GRB14 -0.016 0.16 -10000 0 -0.61 20 20
ELK1 -0.63 0.6 -10000 0 -1.1 163 163
GRB7 0.026 0.007 -10000 0 -10000 0 0
PAK1 0.028 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.67 0.68 -10000 0 -1.2 163 163
CDKN1A -0.37 0.35 -10000 0 -0.67 164 164
ITGA5 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.7 0.7 -10000 0 -1.3 163 163
CRK 0.026 0.008 -10000 0 -10000 0 0
mol:NO -0.37 0.38 -10000 0 -0.69 164 164
PLG -0.9 0.69 -10000 0 -1.5 164 164
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.52 0.49 -10000 0 -0.94 164 164
GRB2 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.026 0.004 -10000 0 -10000 0 0
ANGPT2 -0.27 0.31 -10000 0 -0.72 72 72
BMX -0.75 0.72 -10000 0 -1.3 164 164
ANGPT1 -0.47 0.63 -10000 0 -1.4 95 95
tube development -0.43 0.4 -10000 0 -0.77 164 164
ANGPT4 0.013 0.023 -10000 0 -10000 0 0
response to hypoxia -0.039 0.034 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.79 0.77 -10000 0 -1.4 163 163
alpha5/beta1 Integrin 0.039 0.01 -10000 0 -10000 0 0
FGF2 0.022 0.059 -10000 0 -0.53 3 3
STAT5A (dimer) -0.49 0.47 -10000 0 -0.89 163 163
mol:L-citrulline -0.37 0.38 -10000 0 -0.69 164 164
AGTR1 -0.17 0.3 -10000 0 -0.64 87 87
MAPK14 -0.76 0.71 -10000 0 -1.3 164 164
Tie2/SHP2 -0.62 0.62 -10000 0 -1.2 148 148
TEK -0.69 0.7 -10000 0 -1.4 148 148
RPS6KB1 -0.52 0.5 -10000 0 -0.95 164 164
Angiotensin II/AT1 -0.13 0.23 -10000 0 -0.48 87 87
Tie2/Ang1/GRB2 -0.77 0.77 -10000 0 -1.4 163 163
MAPK3 -0.65 0.63 -10000 0 -1.2 162 162
MAPK1 -0.66 0.63 -10000 0 -1.2 163 163
Tie2/Ang1/GRB7 -0.77 0.77 -10000 0 -1.4 164 164
NFKB1 0.027 0.006 -10000 0 -10000 0 0
MAPK8 -0.75 0.73 -10000 0 -1.3 164 164
PI3K -0.67 0.64 -10000 0 -1.2 164 164
FES -0.75 0.71 -10000 0 -1.3 165 165
Crk/Dok-R -0.7 0.69 -10000 0 -1.3 162 162
Tie2/Ang1/ABIN2 -0.78 0.77 -10000 0 -1.4 163 163
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.48 0.46 -10000 0 -0.88 164 164
STAT5A 0.026 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.53 0.5 -10000 0 -0.96 164 164
Tie2/Ang2 -0.64 0.6 -10000 0 -1.1 164 164
Tie2/Ang1 -0.85 0.84 -10000 0 -1.5 164 164
FOXO1 -0.49 0.47 -10000 0 -0.89 164 164
ELF1 -0.044 0.074 -10000 0 -10000 0 0
ELF2 -0.76 0.73 -10000 0 -1.4 163 163
mol:Choline -0.69 0.66 -10000 0 -1.2 164 164
cell migration -0.14 0.12 -10000 0 -0.24 163 163
FYN -0.51 0.47 -10000 0 -0.9 164 164
DOK2 0.018 0.047 -10000 0 -0.64 1 1
negative regulation of cell cycle -0.33 0.32 -10000 0 -0.6 164 164
ETS1 -0.071 0.12 -10000 0 -0.25 83 83
PXN -0.42 0.4 -10000 0 -0.77 163 163
ITGB1 0.027 0.005 -10000 0 -10000 0 0
NOS3 -0.44 0.44 -10000 0 -0.8 164 164
RAC1 0.022 0.012 -10000 0 -10000 0 0
TNF -0.08 0.14 -10000 0 -0.27 88 88
MAPKKK cascade -0.69 0.66 -10000 0 -1.2 164 164
RASA1 0.027 0.004 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.78 0.77 -10000 0 -1.4 163 163
NCK1 0.027 0.006 -10000 0 -10000 0 0
vasculogenesis -0.33 0.34 -10000 0 -0.61 164 164
mol:Phosphatidic acid -0.69 0.66 -10000 0 -1.2 164 164
mol:Angiotensin II 0 0.001 -10000 0 -10000 0 0
mol:NADP -0.37 0.38 -10000 0 -0.69 164 164
Rac1/GTP -0.47 0.45 -10000 0 -0.86 164 164
MMP2 -0.74 0.72 -10000 0 -1.3 163 163
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.028 0.003 -9999 0 -10000 0 0
EGFR 0.022 0.012 -9999 0 -10000 0 0
EGF/EGFR -0.28 0.14 -9999 0 -0.36 191 191
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.26 0.15 -9999 0 -0.36 177 177
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.001 0.13 -9999 0 -0.64 12 12
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.56 0.21 -9999 0 -0.63 258 258
EGF/EGFR dimer/SHC -0.32 0.15 -9999 0 -0.37 248 248
mol:GDP -0.26 0.14 -9999 0 -0.36 177 177
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.024 0.041 -9999 0 -0.64 1 1
GRB2/SOS1 0.038 0.012 -9999 0 -10000 0 0
HRAS/GTP -0.24 0.13 -9999 0 -0.34 177 177
SHC1 0.027 0.005 -9999 0 -10000 0 0
HRAS/GDP -0.25 0.14 -9999 0 -0.34 177 177
FRAP1 -0.26 0.12 -9999 0 -0.35 177 177
EGF/EGFR dimer -0.37 0.17 -9999 0 -0.42 258 258
SOS1 0.027 0.005 -9999 0 -10000 0 0
GRB2 0.026 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.014 0.11 -9999 0 -0.48 13 13
FOXA2 and FOXA3 transcription factor networks

Figure S4.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S4.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.47 0.37 -10000 0 -0.9 101 101
PCK1 -1.1 0.67 -10000 0 -1.5 187 187
HNF4A -0.54 0.48 -10000 0 -1.2 82 82
KCNJ11 -0.5 0.37 -10000 0 -0.96 96 96
AKT1 -0.26 0.16 -10000 0 -0.45 68 68
response to starvation -0.004 0.014 -10000 0 -10000 0 0
DLK1 -0.51 0.39 -10000 0 -1 92 92
NKX2-1 -0.13 0.14 0.28 1 -0.39 17 18
ACADM -0.48 0.36 -10000 0 -0.9 101 101
TAT -0.44 0.23 -10000 0 -0.71 82 82
CEBPB -0.042 0.049 -10000 0 -10000 0 0
CEBPA -0.048 0.061 -10000 0 -0.44 2 2
TTR -0.74 0.4 -10000 0 -1 151 151
PKLR -0.59 0.52 -10000 0 -1.2 104 104
APOA1 -0.6 0.53 -10000 0 -1.3 82 82
CPT1C -0.49 0.38 -10000 0 -0.95 97 97
ALAS1 -0.21 0.15 -10000 0 -0.67 3 3
TFRC -0.58 0.29 -10000 0 -0.83 129 129
FOXF1 0.021 0.056 -10000 0 -0.64 2 2
NF1 0.031 0.008 -10000 0 -10000 0 0
HNF1A (dimer) -0.057 0.096 -10000 0 -0.68 4 4
CPT1A -0.48 0.36 -10000 0 -0.91 98 98
HMGCS1 -0.47 0.36 -10000 0 -0.91 97 97
NR3C1 0.018 0.048 -10000 0 -10000 0 0
CPT1B -0.47 0.37 -10000 0 -0.91 98 98
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.027 0.009 -10000 0 -10000 0 0
GCK -0.44 0.38 -10000 0 -0.93 88 88
CREB1 -0.094 0.079 -10000 0 -0.2 58 58
IGFBP1 -0.26 0.35 -10000 0 -1.4 22 22
PDX1 -0.26 0.19 -10000 0 -0.8 11 11
UCP2 -0.48 0.37 -10000 0 -0.9 103 103
ALDOB -1.1 0.37 -10000 0 -1.1 272 272
AFP -0.46 0.33 -10000 0 -0.92 69 69
BDH1 -0.47 0.37 -10000 0 -0.91 100 100
HADH -0.5 0.38 -10000 0 -0.95 96 96
F2 -0.56 0.46 -10000 0 -1.2 85 85
HNF1A -0.057 0.096 -10000 0 -0.68 4 4
G6PC -1 0.59 -10000 0 -1.4 198 198
SLC2A2 -0.46 0.55 -10000 0 -1.7 46 46
INS -0.01 0.049 -10000 0 -10000 0 0
FOXA1 -0.21 0.11 -10000 0 -0.26 209 209
FOXA3 -0.45 0.22 -10000 0 -0.51 232 232
FOXA2 -0.57 0.42 -10000 0 -1 103 103
ABCC8 -0.5 0.37 -10000 0 -0.95 98 98
ALB -1 0.37 -10000 0 -1.1 253 253
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.23 0.32 -9999 0 -0.64 109 109
PDGF/PDGFRA/CRKL -0.15 0.24 -9999 0 -0.47 108 108
positive regulation of JUN kinase activity -0.087 0.2 -9999 0 -0.37 91 91
CRKL 0.026 0.007 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.16 0.24 -9999 0 -0.46 109 109
AP1 -0.24 0.38 -9999 0 -1.1 43 43
mol:IP3 -0.17 0.24 -9999 0 -0.47 107 107
PLCG1 -0.17 0.24 -9999 0 -0.47 107 107
PDGF/PDGFRA/alphaV Integrin -0.15 0.24 -9999 0 -0.46 109 109
RAPGEF1 0.027 0.006 -9999 0 -10000 0 0
CRK 0.026 0.008 -9999 0 -10000 0 0
mol:Ca2+ -0.17 0.24 -9999 0 -0.47 107 107
CAV3 -0.009 0.018 -9999 0 -10000 0 0
CAV1 0.021 0.013 -9999 0 -10000 0 0
SHC/Grb2/SOS1 -0.087 0.2 -9999 0 -0.37 91 91
PDGF/PDGFRA/Shf -0.15 0.25 -9999 0 -0.47 108 108
FOS -0.25 0.37 -9999 0 -1.1 43 43
JUN -0.033 0.026 -9999 0 -10000 0 0
oligodendrocyte development -0.15 0.24 -9999 0 -0.46 109 109
GRB2 0.026 0.007 -9999 0 -10000 0 0
PIK3R1 0.028 0.004 -9999 0 -10000 0 0
mol:DAG -0.17 0.24 -9999 0 -0.47 107 107
PDGF/PDGFRA -0.23 0.32 -9999 0 -0.64 109 109
actin cytoskeleton reorganization -0.15 0.24 -9999 0 -0.47 108 108
SRF 0.018 0.011 -9999 0 -10000 0 0
SHC1 0.027 0.005 -9999 0 -10000 0 0
PI3K -0.11 0.22 -9999 0 -0.4 101 101
PDGF/PDGFRA/Crk/C3G -0.11 0.21 -9999 0 -0.41 93 93
JAK1 -0.16 0.23 -9999 0 -0.47 105 105
ELK1/SRF -0.13 0.18 -9999 0 -0.38 93 93
SHB 0.027 0.005 -9999 0 -10000 0 0
SHF 0.027 0.005 -9999 0 -10000 0 0
CSNK2A1 0.038 0.02 -9999 0 -10000 0 0
GO:0007205 -0.18 0.24 -9999 0 -0.49 109 109
SOS1 0.027 0.005 -9999 0 -10000 0 0
Ras protein signal transduction -0.087 0.2 -9999 0 -0.37 91 91
PDGF/PDGFRA/SHB -0.15 0.25 -9999 0 -0.47 108 108
PDGF/PDGFRA/Caveolin-1 -0.14 0.22 -9999 0 -0.4 109 109
ITGAV 0.028 0.003 -9999 0 -10000 0 0
ELK1 -0.17 0.21 -9999 0 -0.44 107 107
PIK3CA 0.027 0.005 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.15 0.24 -9999 0 -0.44 109 109
JAK-STAT cascade -0.16 0.23 -9999 0 -0.47 105 105
cell proliferation -0.15 0.24 -9999 0 -0.47 108 108
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.018 0.028 -10000 0 -10000 0 0
GNB1/GNG2 -0.097 0.09 -10000 0 -0.19 135 135
AKT1 -0.092 0.13 0.21 3 -0.33 19 22
EGF -0.56 0.21 -10000 0 -0.63 258 258
mol:TXA2 -0.001 0.001 -10000 0 -10000 0 0
FGR -0.019 0.08 -10000 0 -0.37 4 4
mol:Ca2+ -0.14 0.17 -10000 0 -0.3 128 128
LYN -0.018 0.074 -10000 0 -0.44 1 1
RhoA/GTP -0.057 0.068 -10000 0 -0.14 5 5
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.16 0.19 -10000 0 -0.34 145 145
GNG2 0.027 0.006 -10000 0 -10000 0 0
ARRB2 0.025 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.043 0.13 -10000 0 -0.49 12 12
G beta5/gamma2 -0.12 0.12 -10000 0 -0.25 122 122
PRKCH -0.17 0.2 -10000 0 -0.35 146 146
DNM1 -0.008 0.061 -10000 0 -0.64 1 1
TXA2/TP beta/beta Arrestin3 0.006 0.025 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.026 0.007 -10000 0 -10000 0 0
G12 family/GTP -0.14 0.15 -10000 0 -0.3 105 105
ADRBK1 0.028 0.002 -10000 0 -10000 0 0
ADRBK2 0.026 0.008 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.033 0.012 -10000 0 -10000 0 0
mol:GDP 0.097 0.14 0.41 29 -10000 0 29
mol:NADP 0.003 0.11 -10000 0 -0.64 8 8
RAB11A 0.028 0.004 -10000 0 -10000 0 0
PRKG1 -0.14 0.29 -10000 0 -0.63 73 73
mol:IP3 -0.18 0.21 -10000 0 -0.38 129 129
cell morphogenesis 0.033 0.012 -10000 0 -10000 0 0
PLCB2 -0.24 0.28 -10000 0 -0.52 129 129
mol:cGMP -0.001 0.001 -10000 0 -10000 0 0
BLK -0.02 0.072 -10000 0 -0.44 1 1
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.023 0.074 -10000 0 -0.68 1 1
RHOA 0.027 0.006 -10000 0 -10000 0 0
PTGIR 0.023 0.055 -10000 0 -0.64 2 2
PRKCB1 -0.18 0.21 -10000 0 -0.37 147 147
GNAQ 0.027 0.006 -10000 0 -10000 0 0
mol:L-citrulline 0.003 0.11 -10000 0 -0.64 8 8
TXA2/TXA2-R family -0.25 0.28 -10000 0 -0.52 146 146
LCK -0.018 0.075 -10000 0 -0.44 1 1
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.006 0.096 -10000 0 -0.33 20 20
TXA2-R family/G12 family/GDP/G beta/gamma -0.017 0.13 -10000 0 -0.42 26 26
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.01 0.09 -10000 0 -0.33 15 15
MAPK14 -0.11 0.13 0.18 1 -0.23 118 119
TGM2/GTP -0.2 0.23 -10000 0 -0.42 117 117
MAPK11 -0.1 0.13 0.18 1 -0.24 73 74
ARHGEF1 -0.081 0.091 -10000 0 -0.19 51 51
GNAI2 0.027 0.007 -10000 0 -10000 0 0
JNK cascade -0.18 0.21 -10000 0 -0.38 146 146
RAB11/GDP 0.029 0.004 -10000 0 -10000 0 0
ICAM1 -0.13 0.16 -10000 0 -0.28 145 145
cAMP biosynthetic process -0.16 0.19 -10000 0 -0.35 122 122
Gq family/GTP/EBP50 -0.039 0.1 -10000 0 -0.3 11 11
actin cytoskeleton reorganization 0.033 0.012 -10000 0 -10000 0 0
SRC -0.018 0.069 -10000 0 -0.44 1 1
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.025 0.008 -10000 0 -10000 0 0
EGF/EGFR -0.11 0.081 0.25 1 -0.3 24 25
VCAM1 -0.14 0.16 -10000 0 -0.29 145 145
TP beta/Gq family/GDP/G beta5/gamma2 -0.043 0.13 -10000 0 -0.49 12 12
platelet activation -0.14 0.17 0.25 1 -0.3 121 122
PGI2/IP 0.017 0.041 -10000 0 -0.48 2 2
PRKACA 0.016 0.027 -10000 0 -0.31 2 2
Gq family/GDP/G beta5/gamma2 -0.037 0.12 -10000 0 -0.41 15 15
TXA2/TP beta/beta Arrestin2 0.002 0.056 -10000 0 -0.44 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.017 0.098 -10000 0 -0.36 21 21
mol:DAG -0.2 0.23 -10000 0 -0.42 147 147
EGFR 0.022 0.012 -10000 0 -10000 0 0
TXA2/TP alpha -0.22 0.26 -10000 0 -0.48 122 122
Gq family/GTP -0.05 0.12 -10000 0 -0.26 66 66
YES1 -0.018 0.075 -10000 0 -0.44 1 1
GNAI2/GTP -0.003 0.086 -10000 0 -0.31 18 18
PGD2/DP 0.019 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
FYN -0.018 0.075 -10000 0 -0.44 1 1
mol:NO 0.003 0.11 -10000 0 -0.64 8 8
GNA15 0.02 0.027 -10000 0 -10000 0 0
PGK/cGMP -0.08 0.18 -10000 0 -0.37 79 79
RhoA/GDP 0.027 0.007 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.022 0.096 -10000 0 -0.34 16 16
NOS3 0.003 0.11 -10000 0 -0.64 8 8
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCA -0.16 0.19 0.28 2 -0.35 136 138
PRKCB -0.16 0.2 0.28 2 -0.36 132 134
PRKCE -0.17 0.2 0.27 1 -0.36 146 147
PRKCD -0.18 0.21 -10000 0 -0.38 142 142
PRKCG -0.19 0.21 -10000 0 -0.39 146 146
muscle contraction -0.23 0.26 -10000 0 -0.48 145 145
PRKCZ -0.16 0.19 -10000 0 -0.34 145 145
ARR3 -0.008 0.019 -10000 0 -10000 0 0
TXA2/TP beta 0.004 0.098 -10000 0 -0.33 20 20
PRKCQ -0.18 0.2 -10000 0 -0.36 145 145
MAPKKK cascade -0.21 0.24 -10000 0 -0.44 145 145
SELE -0.2 0.22 -10000 0 -0.41 146 146
TP beta/GNAI2/GDP/G beta/gamma 0.024 0.098 -10000 0 -0.33 18 18
ROCK1 0.026 0.007 -10000 0 -10000 0 0
GNA14 -0.11 0.27 -10000 0 -0.62 60 60
chemotaxis -0.29 0.32 -10000 0 -0.6 146 146
GNA12 0.022 0.011 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
GNA11 0.012 0.1 -10000 0 -0.64 7 7
Rac1/GTP 0.015 0.008 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.17 0.44 -10000 0 -1.1 47 47
MKNK1 0.026 0.007 -10000 0 -10000 0 0
MAPK14 -0.03 0.15 -10000 0 -0.34 52 52
ATF2/c-Jun -0.032 0.12 -10000 0 -0.44 9 9
MAPK11 -0.029 0.15 -10000 0 -0.35 47 47
MITF -0.043 0.17 -10000 0 -0.4 51 51
MAPKAPK5 -0.046 0.17 -10000 0 -0.4 51 51
KRT8 -0.047 0.17 -10000 0 -0.4 53 53
MAPKAPK3 0.027 0.007 -10000 0 -10000 0 0
MAPKAPK2 0.027 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.055 0.24 -10000 0 -0.54 48 48
CEBPB -0.046 0.17 -10000 0 -0.39 52 52
SLC9A1 -0.051 0.18 -10000 0 -0.41 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.043 0.17 -10000 0 -0.39 48 48
p38alpha-beta/MNK1 -0.03 0.2 -10000 0 -0.44 48 48
JUN -0.034 0.12 -10000 0 -0.44 9 9
PPARGC1A -0.057 0.19 -10000 0 -0.42 58 58
USF1 -0.051 0.18 -10000 0 -0.4 56 56
RAB5/GDP/GDI1 -0.033 0.13 -10000 0 -0.46 9 9
NOS2 -0.094 0.32 -10000 0 -1.2 21 21
DDIT3 -0.046 0.17 -10000 0 -0.39 53 53
RAB5A 0.027 0.006 -10000 0 -10000 0 0
HSPB1 0.005 0.17 0.28 44 -0.41 15 59
p38alpha-beta/HBP1 -0.033 0.19 -10000 0 -0.46 37 37
CREB1 -0.058 0.19 -10000 0 -0.43 57 57
RAB5/GDP 0.02 0.004 -10000 0 -10000 0 0
EIF4E -0.05 0.17 -10000 0 -0.41 43 43
RPS6KA4 -0.049 0.18 -10000 0 -0.4 54 54
PLA2G4A -0.062 0.19 -10000 0 -0.44 48 48
GDI1 -0.049 0.18 -10000 0 -0.4 54 54
TP53 -0.071 0.21 -10000 0 -0.52 44 44
RPS6KA5 -0.057 0.19 -10000 0 -0.42 57 57
ESR1 -0.071 0.22 -10000 0 -0.45 63 63
HBP1 0.022 0.012 -10000 0 -10000 0 0
MEF2C -0.05 0.17 -10000 0 -0.4 54 54
MEF2A -0.051 0.18 -10000 0 -0.4 56 56
EIF4EBP1 -0.059 0.19 -10000 0 -0.43 56 56
KRT19 -0.083 0.22 -10000 0 -0.45 66 66
ELK4 -0.051 0.18 -10000 0 -0.4 56 56
ATF6 -0.051 0.18 -10000 0 -0.4 56 56
ATF1 -0.057 0.19 -10000 0 -0.42 57 57
p38alpha-beta/MAPKAPK2 -0.03 0.2 -10000 0 -0.44 48 48
p38alpha-beta/MAPKAPK3 -0.027 0.2 -10000 0 -0.45 44 44
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0.047 0.045 -10000 0 -0.42 2 2
fibroblast growth factor receptor signaling pathway 0.047 0.044 -10000 0 -0.41 2 2
LAMA1 0.006 0.099 -10000 0 -0.59 7 7
PRNP 0.027 0.006 -10000 0 -10000 0 0
GPC1/SLIT2 -0.069 0.21 -10000 0 -0.46 62 62
SMAD2 0.017 0.02 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ 0.035 0.011 -10000 0 -10000 0 0
GPC1/Laminin alpha1 0.021 0.078 -10000 0 -0.44 7 7
TDGF1 -0.32 0.32 -10000 0 -0.63 148 148
CRIPTO/GPC1 -0.23 0.26 -10000 0 -0.48 148 148
APP/GPC1 0.037 0.014 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.21 0.2 -10000 0 -0.41 143 143
FLT1 0.022 0.056 -10000 0 -0.64 2 2
GPC1/TGFB/TGFBR1/TGFBR2 0.051 0.018 -10000 0 -10000 0 0
SERPINC1 -0.076 0.23 -10000 0 -0.62 43 43
FYN -0.21 0.2 -10000 0 -0.41 145 145
FGR -0.21 0.21 -10000 0 -0.42 145 145
positive regulation of MAPKKK cascade -0.22 0.24 0.4 4 -0.43 149 153
SLIT2 -0.11 0.27 -10000 0 -0.61 62 62
GPC1/NRG 0.03 0.064 -10000 0 -0.43 5 5
NRG1 0.015 0.081 -10000 0 -0.58 5 5
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.047 0.044 -10000 0 -0.42 2 2
LYN -0.21 0.2 -10000 0 -0.41 144 144
mol:Spermine 0.007 0.004 -10000 0 -10000 0 0
cell growth 0.047 0.044 -10000 0 -0.41 2 2
BMP signaling pathway -0.027 0.008 -10000 0 -10000 0 0
SRC -0.21 0.2 -10000 0 -0.41 139 139
TGFBR1 0.027 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.005 0.029 -10000 0 -10000 0 0
GPC1 0.027 0.008 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.027 0.006 -10000 0 -10000 0 0
VEGFA 0.025 0.013 -10000 0 -10000 0 0
BLK -0.21 0.2 -10000 0 -0.41 145 145
HCK -0.21 0.2 -10000 0 -0.41 145 145
FGF2 0.021 0.059 -10000 0 -0.54 3 3
FGFR1 0.027 0.006 -10000 0 -10000 0 0
VEGFR1 homodimer 0.022 0.055 -10000 0 -0.64 2 2
TGFBR2 0.027 0.006 -10000 0 -10000 0 0
cell death 0.037 0.014 -10000 0 -10000 0 0
ATIII/GPC1 -0.038 0.18 -10000 0 -0.47 43 43
PLA2G2A/GPC1 0.027 0.025 -10000 0 -10000 0 0
LCK -0.21 0.21 -10000 0 -0.42 145 145
neuron differentiation 0.03 0.064 -10000 0 -0.43 5 5
PrPc/Cu2+ 0.02 0.004 -10000 0 -10000 0 0
APP 0.026 0.007 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.027 0.006 -10000 0 -10000 0 0
BMP receptor signaling

Figure S9.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S9.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.37 0.3 -10000 0 -0.52 212 212
SMAD6-7/SMURF1 0.039 0.038 -10000 0 -0.42 1 1
NOG 0.016 0.058 -10000 0 -0.64 2 2
SMAD9 -0.087 0.18 -10000 0 -0.59 28 28
SMAD4 0.026 0.008 -10000 0 -10000 0 0
SMAD5 -0.18 0.18 -10000 0 -0.46 41 41
BMP7/USAG1 -0.21 0.28 -10000 0 -0.51 125 125
SMAD5/SKI -0.17 0.18 -10000 0 -0.45 39 39
SMAD1 -0.037 0.096 -10000 0 -0.49 7 7
BMP2 0.027 0.006 -10000 0 -10000 0 0
SMAD1/SMAD1/SMAD4 -0.032 0.091 -10000 0 -0.42 7 7
BMPR1A 0.028 0.004 -10000 0 -10000 0 0
BMPR1B -0.36 0.32 -10000 0 -0.63 169 169
BMPR1A-1B/BAMBI -0.22 0.23 -10000 0 -0.42 165 165
AHSG 0 0.026 -10000 0 -10000 0 0
CER1 -0.001 0.022 -10000 0 -10000 0 0
BMP2-4/CER1 0.045 0.019 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.15 -10000 0 -0.44 30 30
BMP2-4 (homodimer) 0.038 0.013 -10000 0 -10000 0 0
RGMB 0.028 0.004 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.2 0.22 -10000 0 -0.39 164 164
RGMA -0.055 0.22 -10000 0 -0.61 37 37
SMURF1 0.022 0.012 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.15 0.15 -10000 0 -0.4 37 37
BMP2-4/USAG1 -0.05 0.17 -10000 0 -0.41 51 51
SMAD6/SMURF1/SMAD5 -0.15 0.17 -10000 0 -0.46 34 34
SOSTDC1 -0.11 0.25 -10000 0 -0.64 51 51
BMP7/BMPR2/BMPR1A-1B -0.31 0.25 -10000 0 -0.46 201 201
SKI 0.025 0.008 -10000 0 -10000 0 0
BMP6 (homodimer) 0.02 0.068 -10000 0 -0.64 3 3
HFE2 0.013 0.022 -10000 0 -10000 0 0
ZFYVE16 0.027 0.004 -10000 0 -10000 0 0
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/CHRD 0.025 0.11 -10000 0 -0.39 17 17
SMAD5/SMAD5/SMAD4 -0.17 0.18 -10000 0 -0.45 39 39
MAPK1 0.026 0.008 -10000 0 -10000 0 0
TAK1/TAB family -0.11 0.14 -10000 0 -0.37 26 26
BMP7 (homodimer) -0.19 0.31 -10000 0 -0.64 91 91
NUP214 0.027 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.026 0.056 -10000 0 -0.49 3 3
SMAD1/SKI -0.03 0.11 0.28 1 -0.5 7 8
SMAD6 0.025 0.039 -10000 0 -0.64 1 1
CTDSP2 0.027 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.044 0.023 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.16 0.29 -10000 0 -0.63 80 80
BMPR2 (homodimer) 0.028 0.004 -10000 0 -10000 0 0
GADD34/PP1CA 0.055 0.01 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.26 0.25 -10000 0 -0.47 169 169
CHRDL1 -0.24 0.32 -10000 0 -0.64 114 114
ENDOFIN/SMAD1 -0.035 0.11 0.28 1 -0.49 8 9
SMAD6-7/SMURF1/SMAD1 -0.029 0.1 -10000 0 -0.46 8 8
SMAD6/SMURF1 0.022 0.012 -10000 0 -10000 0 0
BAMBI 0.024 0.04 -10000 0 -0.64 1 1
SMURF2 0.026 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.13 0.22 -10000 0 -0.4 114 114
BMP2-4/GREM1 -0.075 0.2 -10000 0 -0.4 77 77
SMAD7 0.026 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.083 0.19 -10000 0 -0.58 30 30
SMAD1/SMAD6 -0.035 0.1 -10000 0 -0.49 8 8
TAK1/SMAD6 0.031 0.018 -10000 0 -10000 0 0
BMP7 -0.19 0.31 -10000 0 -0.64 91 91
BMP6 0.02 0.068 -10000 0 -0.64 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.12 0.14 -10000 0 -0.36 44 44
PPM1A 0.027 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.037 0.1 -10000 0 -0.47 8 8
SMAD7/SMURF1 0.03 0.019 -10000 0 -10000 0 0
CTDSPL 0.027 0.006 -10000 0 -10000 0 0
PPP1CA 0.028 0.002 -10000 0 -10000 0 0
XIAP 0.028 0 -10000 0 -10000 0 0
CTDSP1 0.027 0.005 -10000 0 -10000 0 0
PPP1R15A 0.028 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.25 0.27 -10000 0 -0.61 79 79
CHRD -0.012 0.16 -10000 0 -0.64 17 17
BMPR2 0.028 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.16 0.16 -10000 0 -0.41 41 41
BMP4 0.027 0.006 -10000 0 -10000 0 0
FST -0.14 0.27 -10000 0 -0.64 64 64
BMP2-4/NOG 0.044 0.045 -10000 0 -0.42 2 2
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.27 0.24 -10000 0 -0.44 166 166
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.059 0.17 -10000 0 -0.42 48 48
CRKL -0.058 0.19 -10000 0 -0.44 50 50
HRAS -0.026 0.16 -10000 0 -0.42 18 18
mol:PIP3 -0.046 0.18 -10000 0 -0.41 47 47
SPRED1 0.027 0.005 -10000 0 -10000 0 0
SPRED2 0.027 0.004 -10000 0 -10000 0 0
GAB1 -0.059 0.2 -10000 0 -0.46 51 51
FOXO3 -0.036 0.21 0.27 4 -0.41 52 56
AKT1 -0.039 0.22 0.29 4 -0.43 60 64
BAD -0.036 0.21 0.27 4 -0.42 51 55
megakaryocyte differentiation -0.1 0.22 -10000 0 -0.44 78 78
GSK3B -0.031 0.21 0.4 6 -0.41 52 58
RAF1 -0.023 0.13 0.29 1 -0.35 12 13
SHC1 0.027 0.005 -10000 0 -10000 0 0
STAT3 -0.06 0.19 -10000 0 -0.46 48 48
STAT1 -0.14 0.4 -10000 0 -0.99 50 50
HRAS/SPRED1 -0.012 0.14 -10000 0 -0.36 13 13
cell proliferation -0.064 0.2 -10000 0 -0.46 54 54
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
TEC 0.027 0.006 -10000 0 -10000 0 0
RPS6KB1 -0.046 0.21 -10000 0 -0.46 50 50
HRAS/SPRED2 -0.011 0.14 -10000 0 -0.36 12 12
LYN/TEC/p62DOK -0.022 0.2 -10000 0 -0.44 50 50
MAPK3 -0.01 0.11 0.31 6 -0.28 5 11
STAP1 -0.26 0.25 -10000 0 -0.4 190 190
GRAP2 0.022 0.02 -10000 0 -10000 0 0
JAK2 -0.12 0.34 -10000 0 -0.86 50 50
STAT1 (dimer) -0.13 0.39 -10000 0 -0.97 50 50
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.028 0.19 -10000 0 -0.44 42 42
actin filament polymerization -0.066 0.18 -10000 0 -0.45 49 49
LYN 0.027 0.005 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.27 0.28 -10000 0 -0.7 61 61
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.031 0.17 -10000 0 -0.4 46 46
PI3K -0.023 0.2 -10000 0 -0.44 47 47
PTEN 0.028 0.004 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.16 0.47 -10000 0 -1.2 50 50
MAPK8 -0.066 0.2 -10000 0 -0.46 54 54
STAT3 (dimer) -0.058 0.18 -10000 0 -0.45 48 48
positive regulation of transcription -0.004 0.094 0.29 6 -0.23 4 10
mol:GDP -0.03 0.16 -10000 0 -0.39 39 39
PIK3C2B -0.059 0.2 -10000 0 -0.46 50 50
CBL/CRKL -0.043 0.18 -10000 0 -0.42 49 49
FER -0.06 0.2 -10000 0 -0.46 50 50
SH2B3 -0.059 0.19 -10000 0 -0.46 51 51
PDPK1 -0.031 0.16 0.31 6 -0.38 40 46
SNAI2 -0.091 0.23 -10000 0 -0.46 70 70
positive regulation of cell proliferation -0.095 0.3 -10000 0 -0.74 50 50
KITLG 0.013 0.074 -10000 0 -0.66 3 3
cell motility -0.095 0.3 -10000 0 -0.74 50 50
PTPN6 0.028 0.011 -10000 0 -10000 0 0
EPOR -0.007 0.14 -10000 0 -1.1 1 1
STAT5A (dimer) -0.079 0.26 -10000 0 -0.62 50 50
SOCS1 0.023 0.04 -10000 0 -0.64 1 1
cell migration 0.064 0.2 0.46 52 -10000 0 52
SOS1 0.027 0.005 -10000 0 -10000 0 0
EPO 0.012 0.023 -10000 0 -10000 0 0
VAV1 0 0.059 -10000 0 -0.64 1 1
GRB10 -0.068 0.19 -10000 0 -0.46 49 49
PTPN11 0.028 0.009 -10000 0 -10000 0 0
SCF/KIT -0.062 0.21 -10000 0 -0.49 51 51
GO:0007205 0.002 0.009 -10000 0 -10000 0 0
MAP2K1 -0.013 0.12 0.33 5 -0.31 5 10
CBL 0.027 0.005 -10000 0 -10000 0 0
KIT -0.2 0.51 -10000 0 -1.2 55 55
MAP2K2 -0.015 0.12 0.33 5 -0.31 5 10
SHC/Grb2/SOS1 -0.021 0.19 -10000 0 -0.44 45 45
STAT5A -0.082 0.26 -10000 0 -0.64 50 50
GRB2 0.026 0.007 -10000 0 -10000 0 0
response to radiation -0.089 0.22 -10000 0 -0.44 70 70
SHC/GRAP2 0.035 0.02 -10000 0 -10000 0 0
PTPRO -0.1 0.23 -10000 0 -0.45 78 78
SH2B2 -0.068 0.19 -10000 0 -0.46 49 49
DOK1 0.026 0.012 -10000 0 -10000 0 0
MATK -0.066 0.2 -10000 0 -0.47 52 52
CREBBP 0.023 0.051 -10000 0 -10000 0 0
BCL2 -0.049 0.23 -10000 0 -1.1 8 8
Endothelins

Figure S11.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.013 0.14 0.26 4 -0.44 14 18
PTK2B 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.3 0.45 -10000 0 -0.93 90 90
EDN1 0.021 0.082 -10000 0 -0.63 1 1
EDN3 0.011 0.024 -10000 0 -10000 0 0
EDN2 -0.001 0.13 -10000 0 -0.57 13 13
HRAS/GDP -0.12 0.21 0.28 2 -0.48 51 53
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.098 0.19 -10000 0 -0.41 56 56
ADCY4 -0.035 0.15 -10000 0 -0.46 22 22
ADCY5 -0.03 0.14 -10000 0 -0.4 24 24
ADCY6 -0.013 0.11 -10000 0 -0.38 13 13
ADCY7 -0.011 0.1 -10000 0 -0.38 10 10
ADCY1 -0.13 0.2 -10000 0 -0.39 93 93
ADCY2 -0.034 0.11 -10000 0 -0.39 14 14
ADCY3 -0.013 0.11 -10000 0 -0.38 13 13
ADCY8 -0.016 0.11 -10000 0 -0.38 13 13
ADCY9 -0.01 0.1 -10000 0 -0.38 10 10
arachidonic acid secretion -0.18 0.27 -10000 0 -0.59 64 64
ETB receptor/Endothelin-1/Gq/GTP -0.064 0.15 -10000 0 -0.34 54 54
GNAO1 -0.012 0.15 -10000 0 -0.64 16 16
HRAS 0.027 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.009 0.13 0.36 10 -0.41 11 21
ETA receptor/Endothelin-1/Gs/GTP 0.015 0.14 0.34 16 -0.39 14 30
mol:GTP -0.004 0.008 -10000 0 -10000 0 0
COL3A1 -0.023 0.17 -10000 0 -0.58 17 17
EDNRB 0.024 0.041 -10000 0 -0.64 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.039 0.19 -10000 0 -0.56 27 27
CYSLTR1 -0.013 0.14 -10000 0 -0.48 13 13
SLC9A1 -0.002 0.099 0.19 5 -0.34 13 18
mol:GDP -0.14 0.22 0.28 2 -0.49 56 58
SLC9A3 -0.61 0.37 -10000 0 -0.73 235 235
RAF1 -0.15 0.22 0.28 1 -0.52 55 56
JUN -0.17 0.28 -10000 0 -0.66 47 47
JAK2 -0.013 0.14 0.26 4 -0.44 14 18
mol:IP3 -0.12 0.2 -10000 0 -0.46 54 54
ETA receptor/Endothelin-1 0.012 0.18 0.43 16 -0.44 23 39
PLCB1 -0.062 0.22 -10000 0 -0.64 38 38
PLCB2 0.01 0.036 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 0.01 0.12 -10000 0 -0.47 12 12
FOS -0.2 0.35 -10000 0 -0.95 45 45
Gai/GDP -0.067 0.26 -10000 0 -0.76 33 33
CRK 0.025 0.008 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.21 -10000 0 -0.54 38 38
BCAR1 0.026 0.008 -10000 0 -10000 0 0
PRKCB1 -0.12 0.2 -10000 0 -0.45 56 56
GNAQ 0.014 0.023 -10000 0 -10000 0 0
GNAZ 0.026 0.008 -10000 0 -10000 0 0
GNAL 0.024 0.04 -10000 0 -0.64 1 1
Gs family/GDP -0.12 0.2 0.26 1 -0.46 52 53
ETA receptor/Endothelin-1/Gq/GTP -0.089 0.21 -10000 0 -0.47 48 48
MAPK14 -0.081 0.14 -10000 0 -0.4 26 26
TRPC6 -0.32 0.49 -10000 0 -1 89 89
GNAI2 0.027 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.018 0.056 -10000 0 -0.64 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.081 0.15 -10000 0 -0.35 47 47
ETB receptor/Endothelin-2 0.016 0.1 -10000 0 -0.42 14 14
ETB receptor/Endothelin-3 0.033 0.035 -10000 0 -0.48 1 1
ETB receptor/Endothelin-1 0.034 0.073 -10000 0 -0.52 2 2
MAPK3 -0.19 0.31 -10000 0 -0.77 51 51
MAPK1 -0.2 0.34 -10000 0 -0.84 51 51
Rac1/GDP -0.11 0.2 0.28 2 -0.48 41 43
cAMP biosynthetic process -0.078 0.16 0.28 6 -0.43 32 38
MAPK8 -0.2 0.34 -10000 0 -0.75 59 59
SRC 0.026 0.009 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.001 0.085 -10000 0 -0.38 7 7
p130Cas/CRK/Src/PYK2 -0.18 0.26 0.29 2 -0.57 66 68
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.2 0.28 2 -0.48 42 44
COL1A2 -0.005 0.11 -10000 0 -0.49 5 5
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.008 0.16 -10000 0 -0.49 23 23
mol:DAG -0.12 0.2 -10000 0 -0.46 54 54
MAP2K2 -0.16 0.25 -10000 0 -0.61 52 52
MAP2K1 -0.16 0.25 -10000 0 -0.61 52 52
EDNRA -0.007 0.16 0.23 5 -0.63 13 18
positive regulation of muscle contraction 0.025 0.15 0.38 6 -0.42 9 15
Gq family/GDP -0.14 0.25 -10000 0 -0.53 63 63
HRAS/GTP -0.14 0.21 -10000 0 -0.48 60 60
PRKCH -0.12 0.2 -10000 0 -0.47 49 49
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCA -0.11 0.19 0.26 3 -0.46 46 49
PRKCB -0.1 0.19 0.23 1 -0.45 44 45
PRKCE -0.12 0.2 0.23 1 -0.47 48 49
PRKCD -0.11 0.19 -10000 0 -0.47 46 46
PRKCG -0.13 0.2 -10000 0 -0.48 49 49
regulation of vascular smooth muscle contraction -0.24 0.4 -10000 0 -1.1 45 45
PRKCQ -0.12 0.2 -10000 0 -0.47 54 54
PLA2G4A -0.2 0.31 -10000 0 -0.66 64 64
GNA14 -0.12 0.26 -10000 0 -0.63 60 60
GNA15 0.011 0.032 -10000 0 -10000 0 0
GNA12 0.022 0.011 -10000 0 -10000 0 0
GNA11 0.002 0.1 -10000 0 -0.64 7 7
Rac1/GTP 0.009 0.13 0.36 10 -0.42 10 20
MMP1 -0.058 0.24 -10000 0 -0.98 18 18
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.013 0.11 -10000 0 -0.48 13 13
AKT1 -0.065 0.24 0.36 6 -0.59 45 51
PTK2B -0.1 0.27 0.34 1 -0.68 48 49
VEGFR2 homodimer/Frs2 -0.11 0.31 -10000 0 -0.78 50 50
CAV1 0.021 0.013 -10000 0 -10000 0 0
CALM1 0.027 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.087 0.3 -10000 0 -0.73 49 49
endothelial cell proliferation -0.036 0.25 0.52 12 -0.54 46 58
mol:Ca2+ -0.096 0.26 -10000 0 -0.66 49 49
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.074 0.27 -10000 0 -0.66 49 49
RP11-342D11.1 -0.11 0.26 -10000 0 -0.67 49 49
CDH5 0.026 0.007 -10000 0 -10000 0 0
VEGFA homodimer 0.062 0.026 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
SHC2 0.021 0.058 -10000 0 -0.64 2 2
HRAS/GDP -0.063 0.24 -10000 0 -0.59 49 49
SH2D2A 0.017 0.032 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.046 0.25 0.32 1 -0.58 48 49
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.09 0.3 -10000 0 -0.73 50 50
VEGFR1 homodimer 0.022 0.055 -10000 0 -0.64 2 2
SHC/GRB2/SOS1 -0.052 0.27 -10000 0 -0.65 49 49
GRB10 -0.093 0.25 -10000 0 -0.63 49 49
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
PAK1 0.028 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.058 0.28 -10000 0 -0.67 48 48
HRAS 0.028 0.003 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.059 0.16 -10000 0 -0.38 47 47
HIF1A 0.027 0.007 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.074 0.27 -10000 0 -0.65 49 49
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.011 0.1 -10000 0 -0.64 7 7
Nck/Pak 0.04 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.087 0.3 -10000 0 -0.74 49 49
mol:GDP -0.06 0.26 -10000 0 -0.62 49 49
mol:NADP -0.048 0.21 0.33 3 -0.49 48 51
eNOS/Hsp90 -0.032 0.21 0.33 2 -0.46 46 48
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 -0.098 0.26 -10000 0 -0.67 49 49
HIF1A/ARNT 0.039 0.011 -10000 0 -10000 0 0
SHB 0.027 0.005 -10000 0 -10000 0 0
VEGFA 0.027 0.013 -10000 0 -10000 0 0
VEGFC 0.026 0.011 -10000 0 -10000 0 0
FAK1/Vinculin -0.097 0.28 0.41 2 -0.68 49 51
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.088 0.3 -10000 0 -0.71 49 49
PTPN6 0.027 0.006 -10000 0 -10000 0 0
EPAS1 -0.04 0.17 -10000 0 -0.39 51 51
mol:L-citrulline -0.048 0.21 0.33 3 -0.49 48 51
ITGAV 0.028 0.003 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.07 0.28 -10000 0 -0.69 49 49
VEGFR2 homodimer/VEGFA homodimer -0.083 0.3 -10000 0 -0.73 49 49
VEGFR2/3 heterodimer -0.12 0.32 -10000 0 -0.77 55 55
VEGFB 0.028 0.002 -10000 0 -10000 0 0
MAPK11 -0.11 0.27 -10000 0 -0.7 50 50
VEGFR2 homodimer -0.14 0.34 -10000 0 -0.85 52 52
FLT1 0.022 0.056 -10000 0 -0.64 2 2
NEDD4 0.029 0.005 -10000 0 -10000 0 0
MAPK3 -0.091 0.23 0.34 1 -0.6 48 49
MAPK1 -0.092 0.24 0.33 2 -0.6 49 51
VEGFA145/NRP2 0.036 0.034 -10000 0 -0.46 1 1
VEGFR1/2 heterodimer -0.11 0.32 -10000 0 -0.8 50 50
KDR -0.14 0.34 -10000 0 -0.86 52 52
VEGFA165/NRP1/VEGFR2 homodimer -0.075 0.28 -10000 0 -0.68 49 49
SRC 0.026 0.009 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.083 0.25 0.36 6 -0.62 48 54
PI3K -0.087 0.28 -10000 0 -0.7 47 47
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.087 0.3 -10000 0 -0.73 49 49
FES -0.1 0.28 -10000 0 -0.7 49 49
GAB1 -0.091 0.28 -10000 0 -0.71 49 49
VEGFR2 homodimer/VEGFA homodimer/Src -0.085 0.29 -10000 0 -0.72 49 49
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
ARNT 0.027 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.042 0.19 0.33 3 -0.48 32 35
VEGFR2 homodimer/VEGFA homodimer/Yes -0.089 0.3 -10000 0 -0.73 49 49
PI3K/GAB1 -0.067 0.25 -10000 0 -0.6 48 48
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.06 0.28 -10000 0 -0.69 48 48
PRKACA 0.028 0.002 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.099 0.31 -10000 0 -0.74 53 53
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
CDC42 -0.1 0.27 -10000 0 -0.7 49 49
actin cytoskeleton reorganization -0.089 0.29 -10000 0 -0.72 50 50
PTK2 -0.11 0.29 -10000 0 -0.74 49 49
EDG1 -0.11 0.26 -10000 0 -0.67 49 49
mol:DAG -0.098 0.26 -10000 0 -0.67 49 49
CaM/Ca2+ -0.078 0.25 -10000 0 -0.62 49 49
MAP2K3 -0.1 0.26 -10000 0 -0.67 48 48
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.045 0.29 -10000 0 -0.66 49 49
PLCG1 -0.1 0.27 -10000 0 -0.68 49 49
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.069 0.28 -10000 0 -0.69 49 49
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
YES1 0.026 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.087 0.3 -10000 0 -0.73 49 49
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.088 0.3 -10000 0 -0.73 49 49
cell migration -0.068 0.24 0.32 1 -0.57 47 48
mol:PI-3-4-5-P3 -0.078 0.26 -10000 0 -0.64 47 47
FYN 0.027 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 -0.088 0.25 -10000 0 -0.64 49 49
mol:NO -0.048 0.21 0.33 3 -0.49 48 51
PXN 0.027 0.005 -10000 0 -10000 0 0
HRAS/GTP -0.079 0.23 -10000 0 -0.59 49 49
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.085 0.26 -10000 0 -0.66 49 49
VHL 0.027 0.006 -10000 0 -10000 0 0
ITGB3 -0.006 0.14 -10000 0 -0.64 13 13
NOS3 -0.059 0.24 0.34 3 -0.56 48 51
VEGFR2 homodimer/VEGFA homodimer/Sck -0.09 0.3 -10000 0 -0.73 50 50
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCA -0.095 0.24 -10000 0 -0.62 48 48
PRKCB -0.096 0.24 -10000 0 -0.64 45 45
VCL 0.028 0.004 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.091 0.27 -10000 0 -0.68 49 49
VEGFR1/2 heterodimer/VEGFA homodimer -0.09 0.3 -10000 0 -0.75 49 49
VEGFA165/NRP2 0.036 0.034 -10000 0 -0.46 1 1
MAPKKK cascade -0.07 0.22 -10000 0 -0.57 46 46
NRP2 0.024 0.041 -10000 0 -0.64 1 1
VEGFC homodimer 0.026 0.011 -10000 0 -10000 0 0
NCK1 0.027 0.006 -10000 0 -10000 0 0
ROCK1 0.026 0.007 -10000 0 -10000 0 0
FAK1/Paxillin -0.1 0.28 0.34 1 -0.68 49 50
MAP3K13 -0.1 0.28 -10000 0 -0.71 49 49
PDPK1 -0.076 0.22 -10000 0 -0.57 45 45
Arf6 signaling events

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
CENTA1/KIF3B 0.029 0.016 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 0.028 0.088 -10000 0 -0.8 3 3
EGFR 0.022 0.012 -10000 0 -10000 0 0
EPHA2 0.026 0.008 -10000 0 -10000 0 0
USP6 0.022 0.021 -10000 0 -10000 0 0
IQSEC1 0.027 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.37 0.17 -10000 0 -0.42 258 258
ARRB2 0.007 0.011 -10000 0 -10000 0 0
mol:GTP 0.027 0.052 0.19 18 -10000 0 18
ARRB1 0.026 0.039 -10000 0 -0.64 1 1
FBXO8 0.027 0.006 -10000 0 -10000 0 0
TSHR 0.017 0.021 -10000 0 -10000 0 0
EGF -0.56 0.21 -10000 0 -0.63 258 258
somatostatin receptor activity 0 0 0.001 5 -0.001 60 65
ARAP2 0.027 0.006 -10000 0 -10000 0 0
mol:GDP -0.073 0.14 0.25 1 -0.3 44 45
mol:PI-3-4-5-P3 0 0 0.001 5 -0.001 35 40
ITGA2B 0.019 0.026 -10000 0 -10000 0 0
ARF6 0.026 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.059 0.028 -10000 0 -10000 0 0
ADAP1 0.022 0.011 -10000 0 -10000 0 0
KIF13B 0.027 0.006 -10000 0 -10000 0 0
HGF/MET 0.01 0.094 -10000 0 -0.44 11 11
PXN 0.027 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.12 0.14 0.25 5 -0.31 66 71
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.31 0.16 -10000 0 -0.37 242 242
ADRB2 0.021 0.026 -10000 0 -10000 0 0
receptor agonist activity 0 0 0 7 0 59 66
actin filament binding 0 0 0.001 4 -0.001 66 70
SRC 0.026 0.009 -10000 0 -10000 0 0
ITGB3 -0.006 0.14 -10000 0 -0.64 13 13
GNAQ 0.026 0.006 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 27 -0.001 43 70
ARF6/GDP -0.04 0.13 0.27 2 -0.5 13 15
ARF6/GDP/GULP/ACAP1 -0.054 0.13 0.25 1 -0.39 11 12
alphaIIb/beta3 Integrin/paxillin/GIT1 0.043 0.095 -10000 0 -0.38 13 13
ACAP1 0.012 0.035 -10000 0 -10000 0 0
ACAP2 0.027 0.006 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.013 0.021 -10000 0 -10000 0 0
EFNA1 0.027 0.005 -10000 0 -10000 0 0
HGF -0.004 0.13 -10000 0 -0.64 11 11
CYTH3 0.006 0.003 -10000 0 -10000 0 0
CYTH2 0.008 0.1 -10000 0 -0.98 3 3
NCK1 0.027 0.006 -10000 0 -10000 0 0
fibronectin binding 0 0 0 30 0 51 81
endosomal lumen acidification 0 0 0.001 3 -0.001 86 89
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.028 0.004 -10000 0 -10000 0 0
GNAQ/ARNO 0.023 0.097 -10000 0 -0.91 3 3
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 10 10
MET 0.017 0.023 -10000 0 -10000 0 0
GNA14 -0.11 0.27 -10000 0 -0.62 60 60
GNA15 0.02 0.027 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 9 -0.001 44 53
GNA11 0.011 0.1 -10000 0 -0.64 7 7
LHCGR -0.006 0.033 -10000 0 -10000 0 0
AGTR1 -0.18 0.3 -10000 0 -0.64 87 87
desensitization of G-protein coupled receptor protein signaling pathway 0.013 0.021 -10000 0 -10000 0 0
IPCEF1/ARNO -0.24 0.13 -10000 0 -0.92 3 3
alphaIIb/beta3 Integrin 0.008 0.11 -10000 0 -0.48 13 13
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.47 0.44 -10000 0 -1.2 53 53
STAT6 (cleaved dimer) -0.47 0.45 -10000 0 -1.1 64 64
IGHG1 -0.16 0.14 -10000 0 -0.43 4 4
IGHG3 -0.46 0.43 -10000 0 -1.1 61 61
AKT1 -0.21 0.22 -10000 0 -0.77 14 14
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.14 0.15 -10000 0 -0.6 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.23 0.24 -10000 0 -0.85 17 17
THY1 -0.74 0.67 -10000 0 -1.5 117 117
MYB 0.002 0.045 -10000 0 -10000 0 0
HMGA1 0.024 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.26 0.23 -10000 0 -0.64 33 33
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.23 0.24 -10000 0 -0.85 16 16
SP1 0.031 0.011 -10000 0 -10000 0 0
INPP5D 0.024 0.02 -10000 0 -10000 0 0
SOCS5 0.038 0.02 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.46 0.46 -10000 0 -1.2 60 60
SOCS1 -0.31 0.28 -10000 0 -0.75 49 49
SOCS3 -0.22 0.21 -10000 0 -1.4 1 1
FCER2 -0.35 0.33 -10000 0 -0.9 40 40
PARP14 0.027 0.006 -10000 0 -10000 0 0
CCL17 -0.47 0.44 -10000 0 -1.2 52 52
GRB2 0.026 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.19 0.2 -10000 0 -0.74 13 13
T cell proliferation -0.46 0.45 -10000 0 -1.2 57 57
IL4R/JAK1 -0.46 0.45 -10000 0 -1.2 55 55
EGR2 -0.54 0.55 -10000 0 -1.4 63 63
JAK2 -0.031 0.04 -10000 0 -10000 0 0
JAK3 0.011 0.045 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
JAK1 0.001 0.023 -10000 0 -10000 0 0
COL1A2 -0.14 0.13 -10000 0 -10000 0 0
CCL26 -0.44 0.46 -10000 0 -1.2 53 53
IL4R -0.49 0.47 -10000 0 -1.3 55 55
PTPN6 0.038 0.015 -10000 0 -10000 0 0
IL13RA2 -0.87 0.65 -10000 0 -1.4 163 163
IL13RA1 -0.031 0.041 -10000 0 -10000 0 0
IRF4 -0.094 0.17 -10000 0 -0.8 11 11
ARG1 -0.13 0.14 -10000 0 -0.77 2 2
CBL -0.25 0.22 -10000 0 -0.63 27 27
GTF3A 0.028 0.015 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.037 0.055 -10000 0 -10000 0 0
IRF4/BCL6 -0.084 0.16 -10000 0 -0.76 11 11
CD40LG 0.027 0.025 -10000 0 -10000 0 0
MAPK14 -0.24 0.22 -10000 0 -0.66 20 20
mitosis -0.2 0.21 -10000 0 -0.72 14 14
STAT6 -0.54 0.53 -10000 0 -1.4 60 60
SPI1 0.01 0.041 -10000 0 -10000 0 0
RPS6KB1 -0.18 0.21 0.52 1 -0.69 14 15
STAT6 (dimer) -0.54 0.53 -10000 0 -1.4 60 60
STAT6 (dimer)/PARP14 -0.49 0.49 -10000 0 -1.3 59 59
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.2 0.19 -10000 0 -0.64 11 11
FRAP1 -0.2 0.22 -10000 0 -0.77 14 14
LTA -0.48 0.44 -10000 0 -1.2 54 54
FES 0.025 0.039 -10000 0 -0.64 1 1
T-helper 1 cell differentiation 0.52 0.51 1.3 61 -10000 0 61
CCL11 -0.55 0.54 -10000 0 -1.3 78 78
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.19 -10000 0 -0.66 10 10
IL2RG 0.029 0.021 -10000 0 -10000 0 0
IL10 -0.48 0.44 -10000 0 -1.2 56 56
IRS1 0.017 0.081 -10000 0 -0.58 5 5
IRS2 0.026 0.01 -10000 0 -10000 0 0
IL4 -0.11 0.13 -10000 0 -0.93 3 3
IL5 -0.48 0.44 -10000 0 -1.2 56 56
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.4 0.37 -10000 0 -0.94 59 59
COL1A1 -0.17 0.2 -10000 0 -1.1 7 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.47 0.46 -10000 0 -1.3 49 49
IL2R gamma/JAK3 0.024 0.043 -10000 0 -10000 0 0
TFF3 -0.59 0.59 -10000 0 -1.4 80 80
ALOX15 -0.47 0.44 -10000 0 -1.2 49 49
MYBL1 0.022 0.024 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.39 0.37 -10000 0 -0.92 64 64
SHC1 0.027 0.005 -10000 0 -10000 0 0
CEBPB 0.024 0.021 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.22 0.24 -10000 0 -0.97 13 13
mol:PI-3-4-5-P3 -0.2 0.22 -10000 0 -0.77 14 14
PI3K -0.21 0.24 -10000 0 -0.82 14 14
DOK2 0.018 0.047 -10000 0 -0.64 1 1
ETS1 0.037 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.17 0.19 -10000 0 -0.75 11 11
ITGB3 -0.5 0.48 -10000 0 -1.3 59 59
PIGR -0.51 0.49 -10000 0 -1.3 63 63
IGHE 0.043 0.051 0.18 21 -10000 0 21
MAPKKK cascade -0.17 0.19 0.46 1 -0.73 11 12
BCL6 0.026 0.008 -10000 0 -10000 0 0
OPRM1 -0.48 0.44 -10000 0 -1.2 56 56
RETNLB -0.47 0.44 -10000 0 -1.2 52 52
SELP -0.52 0.53 -10000 0 -1.4 60 60
AICDA -0.46 0.43 -10000 0 -1.2 54 54
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.053 0.2 -10000 0 -0.48 50 50
alphaV beta3 Integrin 0.023 0.11 -10000 0 -0.42 15 15
PTK2 -0.13 0.24 0.53 4 -0.57 37 41
IGF1R 0.028 0.004 -10000 0 -10000 0 0
PI4KB 0.027 0.005 -10000 0 -10000 0 0
MFGE8 0.028 0.004 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
CDKN1B -0.11 0.23 -10000 0 -0.52 67 67
VEGFA 0.025 0.013 -10000 0 -10000 0 0
ILK -0.12 0.23 -10000 0 -0.53 68 68
ROCK1 0.026 0.007 -10000 0 -10000 0 0
AKT1 -0.11 0.22 -10000 0 -0.5 67 67
PTK2B -0.055 0.16 -10000 0 -0.37 55 55
alphaV/beta3 Integrin/JAM-A -0.066 0.19 -10000 0 -0.38 77 77
CBL 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.26 0.22 -10000 0 -0.43 173 173
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.05 0.085 -10000 0 -0.38 10 10
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.11 0.19 -10000 0 -0.48 37 37
alphaV/beta3 Integrin/Syndecan-1 0.027 0.1 -10000 0 -0.42 14 14
PI4KA 0.026 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.021 0.12 -10000 0 -0.35 23 23
PI4 Kinase 0.038 0.012 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.021 0.11 -10000 0 -0.42 15 15
RPS6KB1 -0.037 0.095 -10000 0 -0.48 2 2
TLN1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.058 0.15 -10000 0 -0.54 18 18
GPR124 0.025 0.04 -10000 0 -0.64 1 1
MAPK1 -0.06 0.15 -10000 0 -0.54 18 18
PXN 0.027 0.005 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.007 0.15 -10000 0 -0.46 24 24
cell adhesion -0.21 0.19 -10000 0 -0.35 170 170
ANGPTL3 -0.41 0.3 -10000 0 -0.62 190 190
VEGFR2 homodimer/VEGFA homodimer/Src -0.028 0.17 -10000 0 -0.42 44 44
IGF-1R heterotetramer 0.028 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.009 -10000 0 -10000 0 0
TGFBR2 0.027 0.006 -10000 0 -10000 0 0
ITGB3 -0.006 0.14 -10000 0 -0.64 13 13
IGF1 0.013 0.095 -10000 0 -0.64 6 6
RAC1 0.022 0.012 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.026 0.099 -10000 0 -0.4 14 14
apoptosis 0.028 0.003 -10000 0 -10000 0 0
CD47 0.027 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.028 0.099 -10000 0 -0.42 13 13
VCL 0.028 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.034 0.19 -10000 0 -0.43 48 48
CSF1 0.021 0.056 -10000 0 -0.64 2 2
PIK3C2A -0.12 0.23 -10000 0 -0.53 68 68
PI4 Kinase/Pyk2 -0.12 0.21 -10000 0 -0.59 22 22
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.032 0.18 -10000 0 -0.39 56 56
FAK1/Vinculin -0.093 0.2 0.45 5 -0.46 32 37
alphaV beta3/Integrin/ppsTEM5 0.027 0.1 -10000 0 -0.4 14 14
RHOA 0.027 0.006 -10000 0 -10000 0 0
VTN -0.13 0.28 -10000 0 -0.63 67 67
BCAR1 0.026 0.008 -10000 0 -10000 0 0
FGF2 0.021 0.059 -10000 0 -0.54 3 3
F11R 0.009 0.043 -10000 0 -0.4 3 3
alphaV/beta3 Integrin/Lactadherin 0.028 0.099 -10000 0 -0.42 13 13
alphaV/beta3 Integrin/TGFBR2 0.027 0.099 -10000 0 -0.42 13 13
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.058 0.045 -10000 0 -0.38 2 2
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.026 0.091 -10000 0 -0.38 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.02 0.028 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.04 0.17 -10000 0 -0.37 55 55
SDC1 0.025 0.04 -10000 0 -0.64 1 1
VAV3 0.021 0.06 0.36 1 -0.36 3 4
PTPN11 0.027 0.005 -10000 0 -10000 0 0
IRS1 0.017 0.081 -10000 0 -0.58 5 5
FAK1/Paxillin -0.1 0.19 0.33 2 -0.46 32 34
cell migration -0.095 0.17 0.28 4 -0.41 32 36
ITGAV 0.028 0.003 -10000 0 -10000 0 0
PI3K -0.052 0.19 -10000 0 -0.35 76 76
SPP1 0.017 0.062 -10000 0 -0.54 3 3
KDR -0.09 0.25 -10000 0 -0.63 51 51
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.028 0.003 -10000 0 -10000 0 0
COL4A3 -0.006 0.14 -10000 0 -0.62 15 15
angiogenesis -0.08 0.18 -10000 0 -0.55 19 19
Rac1/GTP 0.024 0.046 -10000 0 -0.34 2 2
EDIL3 -0.068 0.23 -10000 0 -0.64 39 39
cell proliferation 0.027 0.098 -10000 0 -0.41 13 13
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.004 0.12 -10000 0 -0.64 10 10
Jak2/Leptin Receptor -0.15 0.18 -10000 0 -0.45 43 43
PTP1B/AKT1 -0.071 0.11 0.22 4 -0.33 27 31
FYN 0.027 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.084 0.12 0.21 6 -0.35 30 36
EGFR -0.014 0.017 -10000 0 -10000 0 0
EGF/EGFR -0.3 0.14 0.23 1 -0.38 203 204
CSF1 0.021 0.056 -10000 0 -0.64 2 2
AKT1 0.027 0.007 -10000 0 -10000 0 0
INSR 0.028 0.003 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.091 0.15 0.23 3 -0.41 36 39
Insulin Receptor/Insulin -0.045 0.1 0.25 1 -0.35 11 12
HCK 0.013 0.051 -10000 0 -0.64 1 1
CRK 0.026 0.008 -10000 0 -10000 0 0
TYK2 -0.082 0.11 0.23 3 -0.35 27 30
EGF -0.56 0.21 -10000 0 -0.63 258 258
YES1 0.026 0.008 -10000 0 -10000 0 0
CAV1 -0.14 0.13 0.22 6 -0.35 40 46
TXN 0.02 0.012 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.088 0.11 -10000 0 -0.38 27 27
cell migration 0.084 0.12 0.35 30 -0.21 6 36
STAT3 0.026 0.007 -10000 0 -10000 0 0
PRLR -0.22 0.32 -10000 0 -0.64 109 109
ITGA2B 0.017 0.026 -10000 0 -10000 0 0
CSF1R 0.021 0.044 -10000 0 -0.64 1 1
Prolactin Receptor/Prolactin -0.16 0.25 -10000 0 -0.48 109 109
FGR 0.02 0.044 -10000 0 -0.64 1 1
PTP1B/p130 Cas -0.082 0.11 0.26 1 -0.35 28 29
Crk/p130 Cas -0.081 0.1 0.27 1 -0.36 23 24
DOK1 -0.073 0.12 0.27 6 -0.34 31 37
JAK2 -0.16 0.2 0.24 1 -0.39 84 85
Jak2/Leptin Receptor/Leptin -0.089 0.11 -10000 0 -0.46 10 10
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
PTPN1 -0.084 0.12 0.21 6 -0.35 30 36
LYN 0.027 0.005 -10000 0 -10000 0 0
CDH2 -0.005 0.14 -10000 0 -0.64 13 13
SRC -0.017 0.1 -10000 0 -0.63 6 6
ITGB3 -0.008 0.14 -10000 0 -0.64 13 13
CAT1/PTP1B -0.19 0.2 0.32 6 -0.44 63 69
CAPN1 0.026 0.003 -10000 0 -10000 0 0
CSK 0.028 0.004 -10000 0 -10000 0 0
PI3K -0.045 0.096 -10000 0 -0.38 6 6
mol:H2O2 -0.005 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.081 0.098 -10000 0 -0.46 7 7
negative regulation of transcription -0.16 0.19 0.24 1 -0.38 84 85
FCGR2A 0.022 0.024 -10000 0 -10000 0 0
FER 0.021 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.005 0.11 -10000 0 -0.48 13 13
BLK 0.016 0.027 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.047 0.013 -10000 0 -10000 0 0
RHOA 0.025 0.006 -10000 0 -10000 0 0
LEPR 0.025 0.021 -10000 0 -0.32 1 1
BCAR1 0.026 0.008 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.026 0.007 -10000 0 -10000 0 0
mol:NADPH -0.006 0.003 -10000 0 -10000 0 0
TRPV6 -0.15 0.22 0.34 2 -0.51 39 41
PRL -0.01 0.018 -10000 0 -10000 0 0
SOCS3 0.028 0.1 -10000 0 -1.1 2 2
SPRY2 0.024 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.04 0.058 -10000 0 -0.42 4 4
CSF1/CSF1R -0.082 0.11 -10000 0 -0.36 27 27
Ras protein signal transduction 0.056 0.12 0.47 21 -10000 0 21
IRS1 0.017 0.081 -10000 0 -0.58 5 5
INS -0.007 0.019 -10000 0 -10000 0 0
LEP 0.001 0.033 -10000 0 -10000 0 0
STAT5B -0.11 0.13 0.24 2 -0.38 33 35
STAT5A -0.11 0.13 0.24 2 -0.36 37 39
GRB2 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.093 0.12 -10000 0 -0.36 37 37
CSN2 -0.061 0.11 -10000 0 -0.62 4 4
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
LAT -0.021 0.1 0.26 1 -0.55 8 9
YBX1 0.029 0.008 -10000 0 -10000 0 0
LCK 0.024 0.018 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
NOX4 -0.045 0.2 -10000 0 -0.64 30 30
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.058 0.2 -10000 0 -0.48 50 50
PDGFRB 0.004 0.12 -10000 0 -0.64 10 10
SPHK1 -0.011 0.049 -10000 0 -0.61 1 1
mol:S1P -0.011 0.053 -10000 0 -0.51 1 1
S1P1/S1P/Gi -0.077 0.19 -10000 0 -0.46 42 42
GNAO1 -0.017 0.15 -10000 0 -0.64 16 16
PDGFB-D/PDGFRB/PLCgamma1 -0.057 0.19 0.36 3 -0.46 33 36
PLCG1 -0.072 0.17 0.25 1 -0.44 40 41
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.12 -10000 0 -0.64 10 10
GNAI2 0.021 0.019 -10000 0 -10000 0 0
GNAI3 0.021 0.018 -10000 0 -10000 0 0
GNAI1 0.013 0.057 -10000 0 -0.64 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.072 0.16 -10000 0 -0.41 50 50
S1P1/S1P -0.063 0.14 -10000 0 -0.34 47 47
negative regulation of cAMP metabolic process -0.075 0.18 -10000 0 -0.45 42 42
MAPK3 -0.096 0.24 0.34 6 -0.57 48 54
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.009 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.005 -10000 0 -10000 0 0
KDR -0.094 0.25 -10000 0 -0.64 51 51
PLCB2 -0.052 0.14 0.27 5 -0.31 45 50
RAC1 0.022 0.012 -10000 0 -10000 0 0
RhoA/GTP -0.051 0.12 -10000 0 -0.3 44 44
receptor internalization -0.062 0.13 -10000 0 -0.32 47 47
PTGS2 -0.16 0.4 0.51 2 -1 49 51
Rac1/GTP -0.046 0.11 -10000 0 -0.3 33 33
RHOA 0.027 0.006 -10000 0 -10000 0 0
VEGFA 0.022 0.017 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.075 0.18 -10000 0 -0.45 42 42
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.018 -10000 0 -10000 0 0
MAPK1 -0.12 0.25 -10000 0 -0.6 55 55
S1P1/S1P/PDGFB-D/PDGFRB -0.058 0.17 0.28 3 -0.38 42 45
ABCC1 0.025 0.009 -10000 0 -10000 0 0
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 0.02 0.031 -10000 0 -10000 0 0
NFATC2 -0.003 0.19 -10000 0 -0.58 20 20
NFATC3 -0.01 0.11 -10000 0 -0.3 34 34
CD40LG -0.15 0.39 -10000 0 -1 40 40
ITCH 0.023 0.047 -10000 0 -10000 0 0
CBLB 0.024 0.047 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.075 0.24 -10000 0 -0.83 9 9
JUNB 0.028 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.031 0.056 -10000 0 -0.32 7 7
T cell anergy 0.015 0.078 -10000 0 -0.41 7 7
TLE4 -0.004 0.13 -10000 0 -0.42 17 17
Jun/NFAT1-c-4/p21SNFT -0.08 0.39 -10000 0 -0.95 41 41
AP-1/NFAT1-c-4 -0.14 0.48 -10000 0 -1.2 40 40
IKZF1 -0.003 0.11 -10000 0 -0.44 10 10
T-helper 2 cell differentiation -0.43 0.3 -10000 0 -0.8 73 73
AP-1/NFAT1 -0.031 0.2 -10000 0 -0.47 32 32
CALM1 0.031 0.036 -10000 0 -10000 0 0
EGR2 -0.17 0.52 -10000 0 -1.5 34 34
EGR3 -0.2 0.57 -10000 0 -1.5 45 45
NFAT1/FOXP3 0.015 0.14 -10000 0 -0.42 18 18
EGR1 -0.025 0.18 -10000 0 -0.64 23 23
JUN 0.022 0.022 -10000 0 -10000 0 0
EGR4 0.019 0.017 -10000 0 -10000 0 0
mol:Ca2+ 0.005 0.03 -10000 0 -10000 0 0
GBP3 -0.003 0.13 -10000 0 -0.46 9 9
FOSL1 0.022 0.057 -10000 0 -0.64 2 2
NFAT1-c-4/MAF/IRF4 -0.072 0.38 -10000 0 -0.94 40 40
DGKA -0.003 0.13 -10000 0 -0.46 9 9
CREM 0.027 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.085 0.39 -10000 0 -0.97 41 41
CTLA4 -0.01 0.11 -10000 0 -0.42 8 8
NFAT1-c-4 (dimer)/EGR1 -0.11 0.44 -10000 0 -1.1 41 41
NFAT1-c-4 (dimer)/EGR4 -0.088 0.39 -10000 0 -0.98 41 41
FOS -0.069 0.23 -10000 0 -0.6 43 43
IFNG -0.026 0.15 -10000 0 -0.63 5 5
T cell activation -0.075 0.23 -10000 0 -0.67 22 22
MAF 0.026 0.008 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.087 0.29 0.74 44 -10000 0 44
TNF -0.13 0.38 -10000 0 -0.96 42 42
FASLG -0.2 0.56 -10000 0 -1.4 48 48
TBX21 0.022 0.025 -10000 0 -10000 0 0
BATF3 0.027 0.009 -10000 0 -10000 0 0
PRKCQ 0.013 0.097 -10000 0 -0.59 7 7
PTPN1 -0.001 0.13 -10000 0 -0.42 17 17
NFAT1-c-4/ICER1 -0.089 0.39 -10000 0 -0.97 41 41
GATA3 -0.48 0.28 -10000 0 -0.63 222 222
T-helper 1 cell differentiation -0.025 0.15 -10000 0 -0.62 5 5
IL2RA -0.067 0.24 -10000 0 -0.78 11 11
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.003 0.13 -10000 0 -0.47 8 8
E2F1 0.003 0.047 -10000 0 -10000 0 0
PPARG 0.027 0.009 -10000 0 -10000 0 0
SLC3A2 -0.002 0.13 -10000 0 -0.42 17 17
IRF4 0.017 0.047 -10000 0 -0.64 1 1
PTGS2 -0.2 0.46 -10000 0 -1.1 45 45
CSF2 -0.15 0.39 -10000 0 -1 38 38
JunB/Fra1/NFAT1-c-4 -0.072 0.39 -10000 0 -0.95 41 41
IL4 -0.45 0.32 -10000 0 -0.88 66 66
IL5 -0.15 0.39 -10000 0 -1 38 38
IL2 -0.077 0.23 -10000 0 -0.7 20 20
IL3 -0.022 0.14 -10000 0 -0.88 5 5
RNF128 0.014 0.12 -10000 0 -0.72 7 7
NFATC1 -0.088 0.29 -10000 0 -0.74 44 44
CDK4 0.045 0.18 0.54 5 -10000 0 5
PTPRK -0.002 0.13 -10000 0 -0.42 17 17
IL8 -0.16 0.39 -10000 0 -1 41 41
POU2F1 0.027 0.006 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.01 0.01 -10000 0 -10000 0 0
MAP4K4 0.015 0.047 -10000 0 -0.33 1 1
BAG4 0.027 0.006 -10000 0 -10000 0 0
PKC zeta/ceramide -0.11 0.09 -10000 0 -0.27 60 60
NFKBIA 0.027 0.007 -10000 0 -10000 0 0
BIRC3 0.02 0.028 -10000 0 -10000 0 0
BAX -0.045 0.048 -10000 0 -0.37 3 3
RIPK1 0.027 0.006 -10000 0 -10000 0 0
AKT1 0.018 0.043 0.7 1 -10000 0 1
BAD -0.12 0.084 -10000 0 -0.27 60 60
SMPD1 0.01 0.054 0.2 5 -0.23 6 11
RB1 -0.12 0.085 -10000 0 -0.27 59 59
FADD/Caspase 8 0.014 0.062 -10000 0 -10000 0 0
MAP2K4 -0.1 0.082 0.21 1 -0.26 50 51
NSMAF 0.027 0.005 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.098 0.082 0.21 1 -0.26 46 47
EGF -0.56 0.21 -10000 0 -0.63 258 258
mol:ceramide -0.12 0.089 -10000 0 -0.29 60 60
MADD 0.028 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.01 0.01 -10000 0 -10000 0 0
ASAH1 0.027 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.11 0.084 -10000 0 -0.27 59 59
cell proliferation -0.088 0.083 -10000 0 -0.35 6 6
BID -0.054 0.19 -10000 0 -0.68 23 23
MAP3K1 -0.12 0.084 -10000 0 -0.27 59 59
EIF2A -0.099 0.081 0.24 1 -0.25 52 53
TRADD 0.026 0.007 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
MAPK3 -0.091 0.078 -10000 0 -0.24 46 46
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.099 0.08 0.2 1 -0.24 46 47
Cathepsin D/ceramide -0.11 0.088 -10000 0 -0.27 60 60
FADD 0.015 0.042 -10000 0 -10000 0 0
KSR1 -0.11 0.084 0.22 1 -0.27 49 50
MAPK8 -0.11 0.093 -10000 0 -0.26 66 66
PRKRA -0.12 0.085 0.19 1 -0.27 59 60
PDGFA 0.02 0.017 -10000 0 -10000 0 0
TRAF2 0.027 0.006 -10000 0 -10000 0 0
IGF1 0.013 0.095 -10000 0 -0.64 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.12 0.088 -10000 0 -0.28 60 60
CTSD 0.027 0.007 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.04 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.093 0.089 -10000 0 -0.37 6 6
PRKCD 0.027 0.007 -10000 0 -10000 0 0
PRKCZ 0.025 0.008 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.01 0.01 -10000 0 -10000 0 0
RelA/NF kappa B1 0.04 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.027 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.016 0.044 -10000 0 -0.35 1 1
TNFR1A/BAG4/TNF-alpha 0.041 0.054 -10000 0 -0.42 3 3
mol:Sphingosine-1-phosphate 0.01 0.01 -10000 0 -10000 0 0
MAP2K1 -0.095 0.08 0.2 1 -0.25 46 47
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.028 0.002 -10000 0 -10000 0 0
CYCS -0.05 0.042 -10000 0 -0.21 3 3
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
NFKB1 0.027 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.012 -10000 0 -10000 0 0
EIF2AK2 -0.11 0.085 -10000 0 -0.26 59 59
TNF-alpha/TNFR1A/FAN 0.042 0.054 -10000 0 -0.42 3 3
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.02 0.082 -10000 0 -0.4 7 7
MAP2K2 -0.095 0.08 0.2 1 -0.25 46 47
SMPD3 0.011 0.035 -10000 0 -0.21 2 2
TNF 0.014 0.071 -10000 0 -0.64 3 3
PKC zeta/PAR4 0.036 0.014 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.2 0.083 0.24 204 -10000 0 204
NF kappa B1/RelA/I kappa B alpha 0.071 0.031 -10000 0 -10000 0 0
AIFM1 -0.067 0.063 -10000 0 -0.17 60 60
BCL2 0.026 0.008 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.026 0.007 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.037 0.1 -10000 0 -0.29 13 13
NT3 (dimer)/TRKC -0.098 0.24 -10000 0 -0.5 73 73
NT3 (dimer)/TRKB -0.17 0.25 -10000 0 -0.44 129 129
SHC/Grb2/SOS1/GAB1/PI3K 0.028 0.013 -10000 0 -10000 0 0
RAPGEF1 0.027 0.006 -10000 0 -10000 0 0
BDNF 0.013 0.037 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
DYNLT1 0.027 0.006 -10000 0 -10000 0 0
NTRK1 -0.11 0.26 -10000 0 -0.63 56 56
NTRK2 -0.23 0.32 -10000 0 -0.63 113 113
NTRK3 -0.084 0.25 -10000 0 -0.64 48 48
NT-4/5 (dimer)/TRKB -0.14 0.22 -10000 0 -0.4 115 115
neuron apoptosis 0.11 0.17 0.45 34 -10000 0 34
SHC 2-3/Grb2 -0.12 0.18 -10000 0 -0.5 34 34
SHC1 0.027 0.005 -10000 0 -10000 0 0
SHC2 -0.11 0.16 -10000 0 -0.46 30 30
SHC3 -0.13 0.2 -10000 0 -0.52 41 41
STAT3 (dimer) 0.03 0.025 -10000 0 -0.37 1 1
NT3 (dimer)/TRKA -0.091 0.23 -10000 0 -0.45 80 80
RIN/GDP -0.023 0.11 0.31 8 -0.31 7 15
GIPC1 0.028 0.002 -10000 0 -10000 0 0
KRAS 0.027 0.006 -10000 0 -10000 0 0
DNAJA3 -0.053 0.12 -10000 0 -0.29 55 55
RIN/GTP 0.012 0.006 -10000 0 -10000 0 0
CCND1 0.016 0.053 -10000 0 -0.88 1 1
MAGED1 0.028 0.003 -10000 0 -10000 0 0
PTPN11 0.027 0.005 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.001 0.033 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.051 0.018 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.061 0.2 -10000 0 -0.42 64 64
TRKA/NEDD4-2 -0.063 0.2 -10000 0 -0.46 57 57
ELMO1 0.022 0.012 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.029 0.016 -10000 0 -10000 0 0
NGF 0.007 0.11 -10000 0 -0.64 8 8
HRAS 0.028 0.003 -10000 0 -10000 0 0
DOCK1 0.028 0.004 -10000 0 -10000 0 0
GAB2 0.028 0.003 -10000 0 -10000 0 0
RIT2 -0.013 0.014 -10000 0 -10000 0 0
RIT1 0.027 0.005 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
DNM1 -0.008 0.061 -10000 0 -0.64 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.044 0.13 -10000 0 -0.29 54 54
mol:GDP -0.043 0.16 0.38 8 -0.46 10 18
NGF (dimer) 0.007 0.11 -10000 0 -0.64 8 8
RhoG/GDP 0.016 0.009 -10000 0 -10000 0 0
RIT1/GDP -0.021 0.12 0.31 8 -0.3 8 16
TIAM1 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.14 0.22 -10000 0 -0.42 110 110
KIDINS220/CRKL/C3G 0.037 0.013 -10000 0 -10000 0 0
SHC/RasGAP 0.04 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2 0.052 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.063 0.025 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.004 -10000 0 -10000 0 0
NT3 (dimer) -0.047 0.2 -10000 0 -0.64 31 31
RAP1/GDP -0.026 0.085 -10000 0 -0.26 7 7
KIDINS220/CRKL 0.026 0.007 -10000 0 -10000 0 0
BDNF (dimer) 0.013 0.037 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.052 0.19 -10000 0 -0.42 60 60
Schwann cell development -0.034 0.033 -10000 0 -10000 0 0
EHD4 0.027 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.061 0.026 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.025 0.037 -10000 0 -10000 0 0
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP -0.19 0.24 -10000 0 -0.4 148 148
ABL1 0.027 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.038 0.012 -10000 0 -10000 0 0
Rap1/GTP -0.064 0.14 -10000 0 -0.48 13 13
STAT3 0.03 0.025 -10000 0 -0.37 1 1
axon guidance -0.19 0.22 -10000 0 -0.38 148 148
MAPK3 -0.074 0.16 -10000 0 -0.39 53 53
MAPK1 -0.08 0.16 -10000 0 -0.39 63 63
CDC42/GDP -0.018 0.12 0.3 9 -0.3 8 17
NTF3 -0.047 0.21 -10000 0 -0.64 31 31
NTF4 -0.001 0.033 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM -0.048 0.19 -10000 0 -0.4 61 61
PI3K 0.04 0.009 -10000 0 -10000 0 0
FRS3 0.027 0.006 -10000 0 -10000 0 0
FAIM 0.027 0.008 -10000 0 -10000 0 0
GAB1 0.027 0.006 -10000 0 -10000 0 0
RASGRF1 -0.058 0.13 -10000 0 -0.3 59 59
SOS1 0.027 0.005 -10000 0 -10000 0 0
MCF2L -0.099 0.2 -10000 0 -0.44 69 69
RGS19 0.025 0.013 -10000 0 -10000 0 0
CDC42 0.026 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.011 0.094 -10000 0 -0.47 3 3
Rac1/GDP -0.023 0.1 0.27 4 -0.32 6 10
NGF (dimer)/TRKA/GRIT -0.063 0.19 -10000 0 -0.42 61 61
neuron projection morphogenesis -0.033 0.14 -10000 0 -0.73 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.052 0.19 -10000 0 -0.42 60 60
MAP2K1 0.03 0.063 0.39 5 -10000 0 5
NGFR 0.012 0.095 -10000 0 -0.64 6 6
NGF (dimer)/TRKA/GIPC/GAIP -0.05 0.14 -10000 0 -0.31 57 57
RAS family/GTP/PI3K 0.024 0.01 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.071 0.031 -10000 0 -10000 0 0
NRAS 0.027 0.006 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.012 -10000 0 -10000 0 0
PRKCI 0.027 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCZ 0.025 0.008 -10000 0 -10000 0 0
MAPKKK cascade -0.14 0.27 -10000 0 -0.58 74 74
RASA1 0.027 0.004 -10000 0 -10000 0 0
TRKA/c-Abl -0.061 0.2 -10000 0 -0.48 54 54
SQSTM1 0.025 0.017 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.11 0.22 -10000 0 -0.38 109 109
NGF (dimer)/TRKA/p62/Atypical PKCs -0.021 0.18 -10000 0 -0.37 56 56
MATK 0.013 0.073 -10000 0 -0.64 3 3
NEDD4L 0.025 0.022 -10000 0 -0.33 1 1
RAS family/GDP -0.04 0.066 -10000 0 -0.23 7 7
NGF (dimer)/TRKA -0.055 0.14 -10000 0 -0.31 59 59
Rac1/GTP -0.053 0.098 -10000 0 -0.28 24 24
FRS2 family/SHP2/CRK family 0.067 0.034 -10000 0 -10000 0 0
amb2 Integrin signaling

Figure S21.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S21.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.016 0.057 -10000 0 -10000 0 0
alphaM/beta2 Integrin/GPIbA 0.013 0.062 -10000 0 -0.47 1 1
alphaM/beta2 Integrin/proMMP-9 -0.012 0.07 -10000 0 -0.41 2 2
PLAUR 0.02 0.027 -10000 0 -10000 0 0
HMGB1 0.018 0.031 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.015 0.056 -10000 0 -10000 0 0
AGER 0.011 0.04 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
SELPLG 0.016 0.033 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.014 0.1 -10000 0 -0.34 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 -0.019 0.073 -10000 0 -0.64 2 2
CYR61 0.009 0.1 -10000 0 -0.54 9 9
TLN1 0.027 0.005 -10000 0 -10000 0 0
Rap1/GTP -0.13 0.14 -10000 0 -0.43 31 31
RHOA 0.027 0.006 -10000 0 -10000 0 0
P-selectin oligomer -0.03 0.18 -10000 0 -0.6 26 26
MYH2 -0.2 0.19 -10000 0 -0.58 35 35
MST1R 0.014 0.053 -10000 0 -0.48 2 2
leukocyte activation during inflammatory response -0.018 0.12 -10000 0 -0.37 26 26
APOB -0.017 0.15 -10000 0 -0.64 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.024 0.016 -10000 0 -10000 0 0
JAM3 0.025 0.039 -10000 0 -0.64 1 1
GP1BA 0.023 0.04 -10000 0 -0.64 1 1
alphaM/beta2 Integrin/CTGF 0.006 0.082 -10000 0 -0.43 5 5
alphaM/beta2 Integrin -0.16 0.16 -10000 0 -0.44 43 43
JAM3 homodimer 0.025 0.039 -10000 0 -0.64 1 1
ICAM2 0.026 0.008 -10000 0 -10000 0 0
ICAM1 0.027 0.011 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.16 0.15 -10000 0 -0.44 42 42
cell adhesion 0.013 0.062 -10000 0 -0.47 1 1
NFKB1 -0.03 0.17 0.35 1 -0.5 27 28
THY1 -0.21 0.32 -10000 0 -0.63 105 105
RhoA/GDP 0.02 0.005 -10000 0 -10000 0 0
Lipoprotein(a) -0.018 0.13 -10000 0 -0.41 29 29
alphaM/beta2 Integrin/LRP/tPA -0.006 0.13 -10000 0 -0.39 22 22
IL6 -0.069 0.23 -10000 0 -0.73 29 29
ITGB2 0 0.046 -10000 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.016 0.088 -10000 0 -0.39 7 7
alphaM/beta2 Integrin/JAM2/JAM3 0.028 0.074 -10000 0 -0.39 3 3
JAM2 0.018 0.071 -10000 0 -0.56 4 4
alphaM/beta2 Integrin/ICAM1 0.035 0.072 -10000 0 -0.38 2 2
alphaM/beta2 Integrin/uPA/Plg -0.21 0.22 -10000 0 -0.4 153 153
RhoA/GTP -0.2 0.2 -10000 0 -0.57 40 40
positive regulation of phagocytosis -0.12 0.12 -10000 0 -0.37 28 28
Ron/MSP 0.027 0.053 -10000 0 -0.48 2 2
alphaM/beta2 Integrin/uPAR/uPA 0.018 0.09 -10000 0 -0.4 7 7
alphaM/beta2 Integrin/uPAR 0.012 0.06 -10000 0 -10000 0 0
PLAU 0.011 0.1 -10000 0 -0.64 7 7
PLAT -0.037 0.19 -10000 0 -0.61 29 29
actin filament polymerization -0.19 0.18 -10000 0 -0.55 35 35
MST1 0.024 0.04 -10000 0 -0.64 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.015 0.13 -10000 0 -0.38 26 26
TNF -0.035 0.17 0.34 1 -0.65 14 15
RAP1B 0.027 0.006 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.004 0.088 -10000 0 -0.43 7 7
fibrinolysis -0.21 0.21 -10000 0 -0.4 153 153
HCK 0.013 0.051 -10000 0 -0.64 1 1
dendritic cell antigen processing and presentation -0.16 0.15 -10000 0 -0.44 42 42
VTN -0.13 0.28 -10000 0 -0.63 67 67
alphaM/beta2 Integrin/CYR61 0.005 0.082 -10000 0 -0.37 6 6
LPA -0.034 0.14 -10000 0 -0.64 14 14
LRP1 0.027 0.005 -10000 0 -10000 0 0
cell migration -0.013 0.063 -10000 0 -0.38 2 2
FN1 0.02 0.028 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.14 0.21 -10000 0 -0.42 93 93
MPO 0.018 0.025 -10000 0 -10000 0 0
KNG1 -0.37 0.31 -10000 0 -0.64 164 164
RAP1/GDP 0.035 0.011 -10000 0 -10000 0 0
ROCK1 -0.19 0.19 -10000 0 -0.57 35 35
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.36 0.31 -10000 0 -0.63 162 162
CTGF 0.012 0.097 -10000 0 -0.59 7 7
alphaM/beta2 Integrin/Hck 0.01 0.068 -10000 0 -0.47 1 1
ITGAM 0.007 0.041 -10000 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.002 0.12 -10000 0 -0.39 16 16
HP 0.009 0.036 -10000 0 -10000 0 0
leukocyte adhesion -0.13 0.21 -10000 0 -0.4 94 94
SELP -0.03 0.18 -10000 0 -0.6 26 26
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.001 0.081 -10000 0 -0.28 22 22
epithelial cell differentiation 0.021 0.11 -10000 0 -0.36 22 22
CYFIP2 0.025 0.039 -10000 0 -0.64 1 1
ENAH 0 0.13 0.52 11 -10000 0 11
EGFR 0.022 0.012 -10000 0 -10000 0 0
EPHA2 0.026 0.008 -10000 0 -10000 0 0
MYO6 0.001 0.12 0.34 8 -0.35 22 30
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.052 0.031 -10000 0 -0.42 1 1
AQP5 -0.07 0.19 -10000 0 -0.56 31 31
CTNND1 0.028 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.003 0.12 0.34 9 -0.34 22 31
regulation of calcium-dependent cell-cell adhesion -0.024 0.15 0.35 6 -0.38 36 42
EGF -0.56 0.21 -10000 0 -0.63 258 258
NCKAP1 0.028 0.004 -10000 0 -10000 0 0
AQP3 -0.17 0.27 -10000 0 -0.56 88 88
cortical microtubule organization 0.021 0.11 -10000 0 -0.36 22 22
GO:0000145 -0.015 0.11 0.33 9 -0.33 22 31
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.026 0.11 -10000 0 -0.36 22 22
MLLT4 0.027 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.035 0.077 -10000 0 -10000 0 0
ARF6 0.027 0.006 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.06 0.028 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.012 0.096 0.34 2 -0.32 20 22
PVRL2 0.028 0.003 -10000 0 -10000 0 0
ZYX -0.007 0.1 0.35 3 -0.35 20 23
ARF6/GTP 0.064 0.032 -10000 0 -10000 0 0
CDH1 -0.025 0.18 -10000 0 -0.64 22 22
EGFR/EGFR/EGF/EGF -0.27 0.16 -10000 0 -0.37 185 185
RhoA/GDP 0.024 0.11 -10000 0 -0.34 22 22
actin cytoskeleton organization -0.016 0.11 0.33 8 -0.34 22 30
IGF-1R heterotetramer 0.028 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.007 -10000 0 -10000 0 0
IGF1R 0.028 0.004 -10000 0 -10000 0 0
IGF1 0.013 0.095 -10000 0 -0.64 6 6
DIAPH1 0.035 0.11 -10000 0 -0.55 1 1
Wnt receptor signaling pathway -0.021 0.11 0.36 22 -10000 0 22
RHOA 0.027 0.006 -10000 0 -10000 0 0
RhoA/GTP -0.035 0.078 -10000 0 -0.32 18 18
CTNNA1 0.027 0.005 -10000 0 -10000 0 0
VCL -0.017 0.11 0.33 8 -0.34 22 30
EFNA1 0.027 0.005 -10000 0 -10000 0 0
LPP -0.023 0.1 0.34 3 -0.33 22 25
Ephrin A1/EPHA2 0.016 0.1 -10000 0 -0.33 22 22
SEC6/SEC8 -0.013 0.086 -10000 0 -0.32 20 20
MGAT3 -0.025 0.15 0.35 6 -0.38 36 42
HGF/MET -0.002 0.12 -10000 0 -0.36 26 26
HGF -0.004 0.13 -10000 0 -0.64 11 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.001 0.081 -10000 0 -0.28 22 22
actin cable formation 0.03 0.15 0.56 14 -10000 0 14
KIAA1543 -0.015 0.12 0.33 9 -0.33 23 32
KIFC3 -0.015 0.096 -10000 0 -0.35 22 22
NCK1 0.027 0.006 -10000 0 -10000 0 0
EXOC3 0.027 0.005 -10000 0 -10000 0 0
ACTN1 0.003 0.12 0.34 9 -0.34 22 31
NCK1/GIT1 0.038 0.012 -10000 0 -10000 0 0
mol:GDP 0.021 0.11 -10000 0 -0.36 22 22
EXOC4 0.022 0.012 -10000 0 -10000 0 0
STX4 -0.014 0.097 -10000 0 -0.35 22 22
PIP5K1C 0.003 0.12 0.34 9 -0.35 22 31
LIMA1 0.027 0.005 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
ROCK1 0.001 0.15 0.54 12 -10000 0 12
adherens junction assembly 0.006 0.13 0.35 19 -0.35 1 20
IGF-1R heterotetramer/IGF1 0.01 0.11 -10000 0 -0.34 27 27
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.04 0.01 -10000 0 -10000 0 0
MET 0.018 0.023 -10000 0 -10000 0 0
PLEKHA7 0.002 0.12 0.34 9 -0.34 23 32
mol:GTP 0.057 0.027 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.003 0.11 0.32 3 -10000 0 3
cortical actin cytoskeleton stabilization 0.001 0.081 -10000 0 -0.28 22 22
regulation of cell-cell adhesion -0.016 0.11 0.33 8 -0.34 22 30
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.001 0.081 -10000 0 -0.28 22 22
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.86 0.61 -10000 0 -1.3 196 196
PLK1 0.044 0.098 0.42 1 -10000 0 1
CDKN1B -0.068 0.12 -10000 0 -0.35 9 9
FOXO3 0.046 0.05 -10000 0 -10000 0 0
KAT2B 0.035 0.009 -10000 0 -10000 0 0
FOXO1/SIRT1 -0.29 0.25 -10000 0 -0.44 195 195
CAT 0.034 0.074 -10000 0 -10000 0 0
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
AKT1 -0.029 0.049 -10000 0 -0.18 2 2
FOXO1 -0.31 0.27 -10000 0 -0.47 195 195
MAPK10 0.033 0.076 0.2 14 -10000 0 14
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.057 0.089 0.34 4 -10000 0 4
response to oxidative stress -0.034 0.035 -10000 0 -0.16 6 6
FOXO3A/SIRT1 0.063 0.082 -10000 0 -10000 0 0
XPO1 0.028 0.004 -10000 0 -10000 0 0
EP300 -0.037 0.051 -10000 0 -0.19 6 6
BCL2L11 0.028 0.061 -10000 0 -0.68 2 2
FOXO1/SKP2 -0.28 0.25 -10000 0 -0.43 193 193
mol:GDP -0.034 0.035 -10000 0 -0.16 6 6
RAN 0.028 0.005 -10000 0 -10000 0 0
GADD45A 0.047 0.17 -10000 0 -0.6 15 15
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.045 0.12 -10000 0 -0.44 17 17
MST1 0.032 0.041 -10000 0 -0.64 1 1
CSNK1D 0.026 0.007 -10000 0 -10000 0 0
CSNK1E 0.026 0.008 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.016 0.13 -10000 0 -0.55 11 11
YWHAB 0.026 0.007 -10000 0 -10000 0 0
MAPK8 0.028 0.081 0.2 14 -0.21 4 18
MAPK9 0.033 0.075 0.2 13 -10000 0 13
YWHAG 0.022 0.011 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
YWHAZ 0.027 0.004 -10000 0 -10000 0 0
SIRT1 0.03 0.006 -10000 0 -10000 0 0
SOD2 -0.075 0.14 -10000 0 -0.47 8 8
RBL2 0.056 0.084 -10000 0 -0.76 1 1
RAL/GDP -0.001 0.032 -10000 0 -10000 0 0
CHUK 0.036 0.006 -10000 0 -10000 0 0
Ran/GTP 0.023 0.004 -10000 0 -10000 0 0
CSNK1G2 0.028 0.003 -10000 0 -10000 0 0
RAL/GTP 0.012 0.029 -10000 0 -10000 0 0
CSNK1G1 0.028 0.004 -10000 0 -10000 0 0
FASLG 0.005 0.13 -10000 0 -0.75 8 8
SKP2 0.027 0.005 -10000 0 -10000 0 0
USP7 0.027 0.008 -10000 0 -10000 0 0
IKBKB 0.035 0.008 -10000 0 -10000 0 0
CCNB1 0.035 0.075 -10000 0 -10000 0 0
FOXO1-3a-4/beta catenin -0.053 0.13 0.36 1 -0.41 1 2
proteasomal ubiquitin-dependent protein catabolic process -0.28 0.25 -10000 0 -0.43 193 193
CSNK1A1 0.027 0.004 -10000 0 -10000 0 0
SGK1 0.035 0.008 -10000 0 -10000 0 0
CSNK1G3 0.027 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.01 -10000 0 -10000 0 0
ZFAND5 0.054 0.082 0.46 1 -10000 0 1
SFN -0.03 0.09 -10000 0 -0.58 5 5
CDK2 -0.055 0.062 -10000 0 -0.25 1 1
FOXO3A/14-3-3 -0.007 0.12 -10000 0 -0.57 8 8
CREBBP -0.051 0.06 -10000 0 -0.25 1 1
FBXO32 0.037 0.074 -10000 0 -10000 0 0
BCL6 0.056 0.093 -10000 0 -0.68 2 2
RALB 0.029 0.003 -10000 0 -10000 0 0
RALA 0.023 0.012 -10000 0 -10000 0 0
YWHAH 0.026 0.008 -10000 0 -10000 0 0
Ephrin A reverse signaling

Figure S24.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S24.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.004 0.12 -9999 0 -0.42 21 21
EFNA5 -0.022 0.17 -9999 0 -0.64 21 21
FYN -0.032 0.1 -9999 0 -0.38 21 21
neuron projection morphogenesis -0.004 0.12 -9999 0 -0.42 21 21
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.004 0.12 -9999 0 -0.42 21 21
EPHA5 -0.009 0.023 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.043 0.098 -10000 0 -0.95 2 2
SMARCC2 0.028 0.005 -10000 0 -10000 0 0
SMARCC1 0.028 0.007 -10000 0 -10000 0 0
TBX21 -0.045 0.077 0.35 2 -0.37 2 4
SUMO2 0.018 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.032 0.015 -10000 0 -10000 0 0
FKBP4 0.027 0.006 -10000 0 -10000 0 0
FKBP5 0.013 0.095 -10000 0 -0.64 6 6
GR alpha/HSP90/FKBP51/HSP90 0.076 0.088 0.32 3 -0.36 6 9
PRL -0.036 0.079 -10000 0 -0.57 1 1
cortisol/GR alpha (dimer)/TIF2 0.095 0.21 0.48 19 -0.44 10 29
RELA -0.085 0.12 -10000 0 -0.28 26 26
FGG 0.094 0.13 0.43 10 -10000 0 10
GR beta/TIF2 0.032 0.17 0.31 5 -0.45 26 31
IFNG -0.1 0.16 -10000 0 -0.57 10 10
apoptosis -0.051 0.22 -10000 0 -0.58 28 28
CREB1 0.019 0.058 -10000 0 -0.34 7 7
histone acetylation -0.032 0.068 -10000 0 -0.3 3 3
BGLAP -0.037 0.075 -10000 0 -0.47 1 1
GR/PKAc 0.097 0.062 0.33 2 -10000 0 2
NF kappa B1 p50/RelA -0.15 0.2 -10000 0 -0.36 98 98
SMARCD1 0.029 0.005 -10000 0 -10000 0 0
MDM2 0.047 0.055 0.21 9 -10000 0 9
GATA3 -0.48 0.28 -10000 0 -0.63 222 222
AKT1 0.023 0.015 0.21 1 -10000 0 1
CSF2 -0.034 0.056 -10000 0 -10000 0 0
GSK3B 0.019 0.019 -10000 0 -10000 0 0
NR1I3 -0.051 0.25 0.58 1 -0.76 18 19
CSN2 0.077 0.11 0.35 9 -10000 0 9
BRG1/BAF155/BAF170/BAF60A 0.071 0.022 -10000 0 -10000 0 0
NFATC1 0.027 0.009 -10000 0 -10000 0 0
POU2F1 0.028 0.006 -10000 0 -10000 0 0
CDKN1A 0.016 0.054 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.003 0.006 -10000 0 -10000 0 0
SFN -0.03 0.09 -10000 0 -0.58 5 5
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.06 0.11 0.33 1 -0.36 9 10
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.072 0.28 0.49 2 -0.82 27 29
JUN -0.083 0.15 -10000 0 -0.46 27 27
IL4 -0.044 0.074 -10000 0 -10000 0 0
CDK5R1 0.025 0.009 -10000 0 -10000 0 0
PRKACA 0.028 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.054 0.15 0.23 11 -0.39 33 44
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.089 0.086 0.32 3 -0.32 6 9
cortisol/GR alpha (monomer) 0.15 0.18 0.55 19 -10000 0 19
NCOA2 -0.033 0.19 -10000 0 -0.64 26 26
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.072 0.23 -10000 0 -0.61 41 41
AP-1/NFAT1-c-4 -0.13 0.24 -10000 0 -0.67 28 28
AFP -0.19 0.43 -10000 0 -1.4 32 32
SUV420H1 0.028 0.003 -10000 0 -10000 0 0
IRF1 0.086 0.086 0.43 2 -10000 0 2
TP53 0.038 0.016 -10000 0 -10000 0 0
PPP5C 0.028 0.003 -10000 0 -10000 0 0
KRT17 -0.16 0.32 -10000 0 -1.1 23 23
KRT14 -0.05 0.062 -10000 0 -10000 0 0
TBP 0.033 0.007 -10000 0 -10000 0 0
CREBBP 0.029 0.012 -10000 0 -10000 0 0
HDAC1 0.025 0.007 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
AP-1 -0.13 0.24 -10000 0 -0.67 28 28
MAPK14 0.019 0.019 -10000 0 -10000 0 0
MAPK10 0.019 0.018 -10000 0 -10000 0 0
MAPK11 0.017 0.019 -10000 0 -10000 0 0
KRT5 -0.12 0.22 -10000 0 -0.86 13 13
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 0.029 0.01 -10000 0 -10000 0 0
STAT1 0.032 0.015 -10000 0 -10000 0 0
CGA -0.073 0.19 -10000 0 -1.2 7 7
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.014 0.067 0.4 1 -10000 0 1
MAPK3 0.019 0.018 -10000 0 -10000 0 0
MAPK1 0.018 0.019 -10000 0 -10000 0 0
ICAM1 -0.15 0.18 -10000 0 -0.54 18 18
NFKB1 -0.08 0.11 -10000 0 -0.27 26 26
MAPK8 -0.079 0.13 -10000 0 -0.38 25 25
MAPK9 0.019 0.018 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.056 0.23 -10000 0 -0.61 28 28
BAX 0.02 0.046 -10000 0 -10000 0 0
POMC -0.2 0.27 -10000 0 -0.76 23 23
EP300 0.029 0.012 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.14 0.16 0.48 15 -10000 0 15
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.074 0.32 13 -10000 0 13
SGK1 0.04 0.072 -10000 0 -10000 0 0
IL13 -0.4 0.25 -10000 0 -0.73 73 73
IL6 -0.2 0.36 -10000 0 -1.1 33 33
PRKACG -0.009 0.019 -10000 0 -10000 0 0
IL5 -0.33 0.21 -10000 0 -0.6 59 59
IL2 -0.12 0.17 -10000 0 -0.61 14 14
CDK5 0.021 0.012 -10000 0 -10000 0 0
PRKACB 0.027 0.007 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
IL8 -0.16 0.19 -10000 0 -0.57 21 21
CDK5R1/CDK5 0.028 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.089 0.18 -10000 0 -0.42 24 24
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.13 0.15 0.48 14 -10000 0 14
SMARCA4 0.029 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.092 0.091 0.35 9 -10000 0 9
NF kappa B1 p50/RelA/Cbp -0.088 0.18 -10000 0 -0.43 24 24
JUN (dimer) -0.083 0.15 -10000 0 -0.46 27 27
YWHAH 0.026 0.008 -10000 0 -10000 0 0
VIPR1 -0.084 0.21 0.32 1 -0.96 14 15
NR3C1 0.084 0.11 0.4 9 -10000 0 9
NR4A1 -0.24 0.33 -10000 0 -0.64 116 116
TIF2/SUV420H1 -0.007 0.15 -10000 0 -0.48 26 26
MAPKKK cascade -0.051 0.22 -10000 0 -0.58 28 28
cortisol/GR alpha (dimer)/Src-1 0.14 0.16 0.49 16 -10000 0 16
PBX1 0.014 0.095 -10000 0 -0.64 6 6
POU1F1 0.005 0.023 -10000 0 -10000 0 0
SELE -0.57 0.58 -10000 0 -1.1 147 147
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.092 0.091 0.35 9 -10000 0 9
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.13 0.15 0.48 14 -10000 0 14
mol:cortisol 0.069 0.097 0.29 21 -10000 0 21
MMP1 -0.11 0.33 -10000 0 -1.1 26 26
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.037 0.092 -10000 0 -0.36 13 13
ER alpha/Gai/GDP/Gbeta gamma -0.052 0.22 -10000 0 -0.64 25 25
AKT1 -0.037 0.24 -10000 0 -0.8 25 25
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.035 0.25 -10000 0 -0.82 25 25
mol:Ca2+ -0.13 0.22 -10000 0 -0.49 63 63
IGF1R 0.028 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.005 0.11 -10000 0 -0.38 21 21
SHC1 0.027 0.005 -10000 0 -10000 0 0
apoptosis 0.034 0.23 0.76 25 -10000 0 25
RhoA/GTP 0.006 0.072 -10000 0 -0.33 11 11
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.017 0.19 -10000 0 -0.56 23 23
regulation of stress fiber formation 0.007 0.095 0.28 5 -0.35 6 11
E2/ERA-ERB (dimer) 0.011 0.097 -10000 0 -0.41 13 13
KRAS 0.027 0.006 -10000 0 -10000 0 0
G13/GTP 0.013 0.084 -10000 0 -0.35 13 13
pseudopodium formation -0.007 0.095 0.35 6 -0.28 5 11
E2/ER alpha (dimer)/PELP1 0.012 0.094 -10000 0 -0.36 16 16
GRB2 0.026 0.007 -10000 0 -10000 0 0
GNG2 0.027 0.006 -10000 0 -10000 0 0
GNAO1 -0.012 0.15 -10000 0 -0.64 16 16
HRAS 0.028 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.02 0.22 0.36 2 -0.59 27 29
E2/ER beta (dimer) 0.019 0.006 -10000 0 -10000 0 0
mol:GDP -0.008 0.11 -10000 0 -0.41 17 17
mol:NADP -0.02 0.22 0.36 2 -0.59 27 29
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 -0.14 0.23 -10000 0 -0.51 63 63
IGF-1R heterotetramer 0.028 0.004 -10000 0 -10000 0 0
PLCB1 -0.13 0.24 -10000 0 -0.47 82 82
PLCB2 -0.096 0.21 -10000 0 -0.49 59 59
IGF1 0.013 0.095 -10000 0 -0.64 6 6
mol:L-citrulline -0.02 0.22 0.36 2 -0.59 27 29
RHOA 0.027 0.006 -10000 0 -10000 0 0
Gai/GDP -0.038 0.22 -10000 0 -0.68 27 27
JNK cascade 0.019 0.006 -10000 0 -10000 0 0
BCAR1 0.026 0.008 -10000 0 -10000 0 0
ESR2 0.026 0.009 -10000 0 -10000 0 0
GNAQ 0.027 0.006 -10000 0 -10000 0 0
ESR1 -0.008 0.14 -10000 0 -0.56 17 17
Gq family/GDP/Gbeta gamma -0.057 0.18 -10000 0 -0.59 15 15
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.002 0.16 -10000 0 -0.83 7 7
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.015 0.19 0.28 1 -0.56 23 24
GNAZ 0.026 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.006 0.11 -10000 0 -0.42 17 17
STRN 0.016 0.087 -10000 0 -0.64 5 5
GNAL 0.024 0.04 -10000 0 -0.64 1 1
PELP1 0.026 0.008 -10000 0 -10000 0 0
MAPK11 0.013 0.006 -10000 0 -10000 0 0
GNAI2 0.027 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.018 0.056 -10000 0 -0.64 2 2
HBEGF -0.024 0.21 0.41 12 -0.58 24 36
cAMP biosynthetic process 0.008 0.082 -10000 0 -0.34 14 14
SRC -0.048 0.2 -10000 0 -0.61 24 24
PI3K 0.04 0.009 -10000 0 -10000 0 0
GNB1 0.025 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.021 0.1 -10000 0 -0.42 11 11
SOS1 0.027 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.041 0.15 -10000 0 -0.47 22 22
Gs family/GTP 0.014 0.085 -10000 0 -0.34 14 14
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.048 0.017 -10000 0 -10000 0 0
vasodilation -0.017 0.2 0.36 2 -0.56 27 29
mol:DAG -0.14 0.23 -10000 0 -0.51 63 63
Gs family/GDP/Gbeta gamma 0 0.096 -10000 0 -0.4 11 11
MSN -0.009 0.099 0.36 6 -0.3 5 11
Gq family/GTP -0.089 0.22 -10000 0 -0.52 58 58
mol:PI-3-4-5-P3 -0.032 0.24 -10000 0 -0.78 25 25
NRAS 0.027 0.006 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.017 0.2 0.56 27 -0.36 2 29
GRB2/SOS1 0.038 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.008 0.11 -10000 0 -0.39 17 17
NOS3 -0.024 0.23 0.36 2 -0.63 27 29
GNA11 0.012 0.1 -10000 0 -0.64 7 7
MAPKKK cascade -0.018 0.22 0.37 4 -0.65 25 29
E2/ER alpha (dimer)/PELP1/Src -0.02 0.2 0.3 1 -0.58 24 25
ruffle organization -0.007 0.095 0.35 6 -0.28 5 11
ROCK2 -0.007 0.11 0.38 6 -0.32 16 22
GNA14 -0.11 0.27 -10000 0 -0.62 60 60
GNA15 0.02 0.027 -10000 0 -10000 0 0
GNA13 0.026 0.007 -10000 0 -10000 0 0
MMP9 -0.044 0.2 0.38 4 -0.56 26 30
MMP2 -0.032 0.2 -10000 0 -0.58 23 23
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.003 0.09 -10000 0 -0.39 10 10
Crk/p130 Cas/Paxillin -0.03 0.11 -10000 0 -0.35 8 8
JUN -0.026 0.11 -10000 0 -0.42 9 9
HRAS 0.028 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.002 0.14 -10000 0 -0.39 29 29
RAP1A 0.027 0.006 -10000 0 -10000 0 0
FRS2 0.027 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.004 0.15 -10000 0 -0.4 34 34
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.026 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.01 0.12 -10000 0 -0.38 22 22
RHOA 0.027 0.006 -10000 0 -10000 0 0
RAP1A/GTP 0.007 0.13 -10000 0 -0.35 32 32
GRB7 0.026 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.006 0.15 -10000 0 -0.4 34 34
MAPKKK cascade -0.01 0.12 -10000 0 -0.35 30 30
BCAR1 0.026 0.008 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.004 0.13 -10000 0 -0.4 25 25
lamellipodium assembly -0.021 0.099 -10000 0 -0.31 20 20
RET51/GFRalpha1/GDNF/SHC 0.005 0.15 -10000 0 -0.4 34 34
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.011 0.12 -10000 0 -0.38 22 22
RET9/GFRalpha1/GDNF/Shank3 0.009 0.11 -10000 0 -0.38 22 22
MAPK3 -0.048 0.1 -10000 0 -0.33 32 32
DOK1 0.026 0.012 -10000 0 -10000 0 0
DOK6 -0.064 0.22 -10000 0 -0.62 40 40
PXN 0.027 0.005 -10000 0 -10000 0 0
neurite development -0.056 0.12 -10000 0 -0.35 31 31
DOK5 0.019 0.068 -10000 0 -0.64 3 3
GFRA1 -0.027 0.18 -10000 0 -0.62 23 23
MAPK8 -0.026 0.11 -10000 0 -0.43 10 10
HRAS/GTP 0.004 0.15 -10000 0 -0.39 32 32
tube development 0.017 0.11 -10000 0 -0.36 19 19
MAPK1 -0.039 0.12 0.34 3 -0.34 32 35
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.002 0.079 -10000 0 -0.29 19 19
Rac1/GDP 0.016 0.009 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
PDLIM7 0.027 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.037 0.2 -10000 0 -0.4 61 61
SHC1 0.027 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.005 0.14 -10000 0 -0.39 32 32
RET51/GFRalpha1/GDNF/Dok5 0.002 0.15 -10000 0 -0.39 33 33
PRKCA 0.026 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.002 -10000 0 -10000 0 0
CREB1 -0.011 0.1 -10000 0 -0.34 22 22
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.005 0.089 -10000 0 -0.31 21 21
RET51/GFRalpha1/GDNF/Grb7 0.006 0.14 -10000 0 -0.39 31 31
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.005 0.14 -10000 0 -0.62 14 14
DOK4 0.026 0.007 -10000 0 -10000 0 0
JNK cascade -0.025 0.11 -10000 0 -0.41 9 9
RET9/GFRalpha1/GDNF/FRS2 0.01 0.11 -10000 0 -0.38 21 21
SHANK3 0.026 0.008 -10000 0 -10000 0 0
RASA1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.004 0.083 -10000 0 -0.3 19 19
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.012 0.11 -10000 0 -0.3 31 31
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.016 0.11 -10000 0 -0.31 33 33
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.016 0.11 -10000 0 -0.32 32 32
PI3K -0.029 0.16 -10000 0 -0.46 22 22
SOS1 0.027 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.02 0.11 -10000 0 -0.36 19 19
GRB10 0.022 0.012 -10000 0 -10000 0 0
activation of MAPKK activity -0.01 0.093 -10000 0 -0.39 4 4
RET51/GFRalpha1/GDNF/FRS2 0.006 0.15 -10000 0 -0.4 32 32
GAB1 0.027 0.006 -10000 0 -10000 0 0
IRS1 0.017 0.081 -10000 0 -0.58 5 5
IRS2 0.026 0.01 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.019 0.12 -10000 0 -0.34 25 25
RET51/GFRalpha1/GDNF/PKC alpha 0.005 0.14 -10000 0 -0.39 31 31
GRB2 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.028 0.002 -10000 0 -10000 0 0
GDNF -0.007 0.019 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.002 0.16 -10000 0 -0.41 37 37
Rac1/GTP -0.021 0.12 -10000 0 -0.37 20 20
RET9/GFRalpha1/GDNF -0.006 0.12 -10000 0 -0.41 23 23
GFRalpha1/GDNF -0.008 0.14 -10000 0 -0.47 23 23
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.029 0.097 -10000 0 -0.41 17 17
ADCY5 -0.028 0.094 -10000 0 -0.41 16 16
ADCY6 -0.005 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.008 -10000 0 -10000 0 0
ADCY1 -0.14 0.19 -10000 0 -0.41 96 96
ADCY2 -0.027 0.029 -10000 0 -0.41 1 1
ADCY3 -0.005 0.001 -10000 0 -10000 0 0
ADCY8 -0.008 0.007 -10000 0 -10000 0 0
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.005 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.031 0.1 0.3 10 -0.24 18 28
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.026 0.007 -9999 0 -10000 0 0
SVIL 0.027 0.005 -9999 0 -10000 0 0
ZNF318 0.026 0.007 -9999 0 -10000 0 0
JMJD2C 0.001 0.005 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.061 0.1 -9999 0 -0.44 12 12
CARM1 0.028 0.003 -9999 0 -10000 0 0
PRDX1 0.026 0.007 -9999 0 -10000 0 0
PELP1 0.026 0.008 -9999 0 -10000 0 0
CTNNB1 0.027 0.007 -9999 0 -10000 0 0
AKT1 0.026 0.007 -9999 0 -10000 0 0
PTK2B 0.027 0.006 -9999 0 -10000 0 0
MED1 0.026 0.007 -9999 0 -10000 0 0
MAK 0.022 0.021 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
HIP1 0.018 0.056 -9999 0 -0.64 2 2
GSN 0.027 0.006 -9999 0 -10000 0 0
NCOA2 -0.033 0.19 -9999 0 -0.64 26 26
NCOA6 0.027 0.006 -9999 0 -10000 0 0
DNA-PK 0.05 0.018 -9999 0 -10000 0 0
NCOA4 0.027 0.005 -9999 0 -10000 0 0
PIAS3 0.027 0.007 -9999 0 -10000 0 0
cell proliferation -0.044 0.11 -9999 0 -0.49 14 14
XRCC5 0.027 0.005 -9999 0 -10000 0 0
UBE3A 0.028 0.005 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.083 0.13 -9999 0 -0.44 26 26
FHL2 -0.04 0.08 -9999 0 -0.37 10 10
RANBP9 0.027 0.006 -9999 0 -10000 0 0
JMJD1A -0.088 0.071 -9999 0 -0.14 185 185
CDK6 0.022 0.012 -9999 0 -10000 0 0
TGFB1I1 0.014 0.087 -9999 0 -0.64 5 5
T-DHT/AR/CyclinD1 -0.065 0.1 -9999 0 -0.44 13 13
XRCC6 0.026 0.008 -9999 0 -10000 0 0
T-DHT/AR -0.12 0.13 -9999 0 -0.32 26 26
CTDSP1 0.027 0.005 -9999 0 -10000 0 0
CTDSP2 0.027 0.005 -9999 0 -10000 0 0
BRCA1 0.025 0.013 -9999 0 -10000 0 0
TCF4 0.026 0.008 -9999 0 -10000 0 0
CDKN2A -0.054 0.044 -9999 0 -10000 0 0
SRF 0.032 0.008 -9999 0 -10000 0 0
NKX3-1 -0.16 0.12 -9999 0 -0.24 193 193
KLK3 0.014 0.038 -9999 0 -10000 0 0
TMF1 0.027 0.006 -9999 0 -10000 0 0
HNRNPA1 0.027 0.005 -9999 0 -10000 0 0
AOF2 0 0.001 -9999 0 -10000 0 0
APPL1 0.013 0.005 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.063 0.1 -9999 0 -0.44 12 12
AR -0.065 0.13 -9999 0 -0.66 12 12
UBA3 0.027 0.006 -9999 0 -10000 0 0
PATZ1 0.026 0.008 -9999 0 -10000 0 0
PAWR 0.027 0.005 -9999 0 -10000 0 0
PRKDC 0.027 0.005 -9999 0 -10000 0 0
PA2G4 0.027 0.005 -9999 0 -10000 0 0
UBE2I 0.026 0.008 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.054 0.093 -9999 0 -0.4 12 12
RPS6KA3 0.028 0.003 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.063 0.1 -9999 0 -0.44 12 12
LATS2 0.027 0.006 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.056 0.092 -9999 0 -0.4 12 12
Cyclin D3/CDK11 p58 0.02 0.005 -9999 0 -10000 0 0
VAV3 0.025 0.04 -9999 0 -0.64 1 1
KLK2 -0.056 0.06 -9999 0 -0.41 1 1
CASP8 0.028 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.083 0.16 -9999 0 -0.47 34 34
TMPRSS2 -0.64 0.49 -9999 0 -1 185 185
CCND1 0.026 0.039 -9999 0 -0.64 1 1
PIAS1 0.028 0.004 -9999 0 -10000 0 0
mol:T-DHT -0.043 0.034 -9999 0 -0.069 182 182
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.028 0.004 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.051 0.098 -9999 0 -0.42 12 12
CMTM2 0.018 0.027 -9999 0 -10000 0 0
SNURF -0.009 0.14 -9999 0 -0.62 14 14
ZMIZ1 -0.037 0.051 -9999 0 -10000 0 0
CCND3 0.027 0.006 -9999 0 -10000 0 0
TGIF1 0.026 0.008 -9999 0 -10000 0 0
FKBP4 0.027 0.006 -9999 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.019 0.085 -10000 0 -0.35 4 4
FYN 0.008 0.11 0.35 6 -0.43 5 11
LAT/GRAP2/SLP76 0.021 0.09 0.29 2 -0.35 5 7
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.017 0.12 0.36 18 -0.32 9 27
B2M 0.028 0.006 -10000 0 -10000 0 0
IKBKG 0.013 0.046 0.13 10 -10000 0 10
MAP3K8 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.057 0.048 -10000 0 -0.1 148 148
integrin-mediated signaling pathway 0.033 0.015 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.009 0.13 0.38 11 -0.42 7 18
TRPV6 -0.2 0.57 0.81 58 -0.64 160 218
CD28 0.02 0.046 -10000 0 -0.64 1 1
SHC1 0.003 0.097 0.31 3 -0.39 6 9
receptor internalization 0.004 0.098 0.21 1 -0.36 13 14
PRF1 0.01 0.12 -10000 0 -0.62 6 6
KRAS 0.027 0.006 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
COT/AKT1 0.027 0.11 0.34 18 -0.28 5 23
LAT 0.009 0.1 0.37 5 -0.4 6 11
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D 0.011 0.04 -10000 0 -10000 0 0
CD3E 0.017 0.05 -10000 0 -0.64 1 1
CD3G 0.022 0.024 -10000 0 -10000 0 0
RASGRP2 0.002 0.022 0.1 1 -0.16 3 4
RASGRP1 0.016 0.13 0.36 17 -0.33 10 27
HLA-A 0.001 0.002 -10000 0 -10000 0 0
RASSF5 0.024 0.017 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.034 0.015 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.037 0.087 0.24 23 -0.11 1 24
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.009 0.038 -10000 0 -0.19 2 2
PRKCA 0.007 0.057 0.2 6 -0.23 2 8
GRAP2 0.022 0.02 -10000 0 -10000 0 0
mol:IP3 0.11 0.14 0.25 127 -0.32 3 130
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.011 0.054 -10000 0 -0.4 2 2
ORAI1 0.047 0.38 0.66 5 -0.65 57 62
CSK 0.003 0.093 0.26 3 -0.39 6 9
B7 family/CD28 0.029 0.097 0.28 2 -0.36 2 4
CHUK 0.028 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.002 0.098 0.26 1 -0.39 9 10
PTPN6 -0.002 0.09 0.29 2 -0.38 6 8
VAV1 -0.003 0.1 0.28 4 -0.45 6 10
Monovalent TCR/CD3 0.012 0.036 -10000 0 -0.29 2 2
CBL 0.027 0.005 -10000 0 -10000 0 0
LCK 0.004 0.11 0.36 5 -0.38 10 15
PAG1 0.002 0.093 0.25 3 -0.39 6 9
RAP1A 0.027 0.006 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.001 0.098 0.27 3 -0.38 8 11
CD80 0.014 0.035 -10000 0 -10000 0 0
CD86 0.007 0.042 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.005 0.048 -10000 0 -0.22 2 2
HRAS 0.028 0.003 -10000 0 -10000 0 0
GO:0035030 -0.003 0.076 0.24 2 -0.32 2 4
CD8A 0.019 0.031 -10000 0 -10000 0 0
CD8B 0.021 0.028 -10000 0 -10000 0 0
PTPRC 0.022 0.043 -10000 0 -0.64 1 1
PDK1/PKC theta 0.021 0.15 0.46 19 -0.37 6 25
CSK/PAG1 0.003 0.09 0.27 4 -0.38 5 9
SOS1 0.027 0.005 -10000 0 -10000 0 0
peptide-MHC class I 0.022 0.006 -10000 0 -10000 0 0
GRAP2/SLP76 0.02 0.097 -10000 0 -0.39 5 5
STIM1 0.061 0.13 -10000 0 -0.82 3 3
RAS family/GTP 0.033 0.082 0.26 17 -0.18 3 20
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.003 0.1 0.21 1 -0.38 13 14
mol:DAG 0.026 0.082 0.14 5 -0.29 4 9
RAP1A/GDP 0.023 0.046 0.16 17 -10000 0 17
PLCG1 0.027 0.007 -10000 0 -10000 0 0
CD247 0.023 0.023 -10000 0 -10000 0 0
cytotoxic T cell degranulation 0.01 0.11 -10000 0 -0.6 6 6
RAP1A/GTP 0.001 0.008 -10000 0 -0.06 3 3
mol:PI-3-4-5-P3 0.011 0.12 0.37 11 -0.36 7 18
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.1 0.16 0.27 109 -0.39 4 113
NRAS 0.027 0.006 -10000 0 -10000 0 0
ZAP70 0.014 0.036 -10000 0 -10000 0 0
GRB2/SOS1 0.038 0.012 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.006 0.093 0.27 2 -0.39 5 7
MALT1 0.026 0.008 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
CD8 heterodimer 0.03 0.037 -10000 0 -10000 0 0
CARD11 -0.002 0.043 -10000 0 -10000 0 0
PRKCB 0.005 0.052 0.18 3 -0.23 2 5
PRKCE 0.008 0.056 0.21 5 -0.23 2 7
PRKCQ 0.009 0.13 0.4 12 -0.41 6 18
LCP2 0.024 0.018 -10000 0 -10000 0 0
BCL10 0.027 0.007 -10000 0 -10000 0 0
regulation of survival gene product expression 0.018 0.12 0.34 18 -0.27 9 27
IKK complex 0.044 0.12 0.35 27 -10000 0 27
RAS family/GDP 0.002 0.007 -10000 0 -10000 0 0
MAP3K14 0.009 0.065 0.22 8 -0.24 2 10
PDPK1 0.023 0.13 0.4 19 -0.3 6 25
TCR/CD3/MHC I/CD8/Fyn 0.003 0.11 -10000 0 -0.54 5 5
E-cadherin signaling events

Figure 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
E-cadherin/beta catenin-gamma catenin 0.013 0.12 -9999 0 -0.42 21 21
E-cadherin/beta catenin -0.003 0.14 -9999 0 -0.48 22 22
CTNNB1 0.027 0.006 -9999 0 -10000 0 0
JUP 0.026 0.007 -9999 0 -10000 0 0
CDH1 -0.025 0.18 -9999 0 -0.64 22 22
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.002 0.11 -10000 0 -10000 0 0
IHH -0.032 0.21 -10000 0 -0.66 28 28
SHH Np/Cholesterol/GAS1 -0.002 0.086 -10000 0 -0.32 18 18
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.002 0.085 0.32 18 -10000 0 18
SMO/beta Arrestin2 -0.007 0.13 -10000 0 -0.51 4 4
SMO -0.015 0.13 -10000 0 -0.43 20 20
AKT1 -0.01 0.13 -10000 0 -0.62 7 7
ARRB2 0.025 0.01 -10000 0 -10000 0 0
BOC 0.027 0.005 -10000 0 -10000 0 0
ADRBK1 0.028 0.002 -10000 0 -10000 0 0
heart looping -0.016 0.13 -10000 0 -0.42 21 21
STIL 0.021 0.12 -10000 0 -0.37 1 1
DHH N/PTCH2 0.004 0.12 -10000 0 -0.48 18 18
DHH N/PTCH1 -0.019 0.15 -10000 0 -0.36 42 42
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
DHH -0.018 0.16 -10000 0 -0.64 18 18
PTHLH -0.014 0.14 -10000 0 -10000 0 0
determination of left/right symmetry -0.016 0.13 -10000 0 -0.42 21 21
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
skeletal system development -0.013 0.14 -10000 0 -10000 0 0
IHH N/Hhip -0.026 0.17 -10000 0 -0.45 39 39
DHH N/Hhip -0.015 0.16 -10000 0 -0.52 26 26
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.016 0.13 -10000 0 -0.42 21 21
pancreas development -0.004 0.13 -10000 0 -0.64 11 11
HHAT 0.027 0.006 -10000 0 -10000 0 0
PI3K 0.04 0.009 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.008 0.15 -10000 0 -0.6 16 16
somite specification -0.016 0.13 -10000 0 -0.42 21 21
SHH Np/Cholesterol/PTCH1 -0.006 0.097 -10000 0 -0.34 6 6
SHH Np/Cholesterol/PTCH2 0.015 0.043 -10000 0 -0.37 3 3
SHH Np/Cholesterol/Megalin -0.021 0.12 -10000 0 -0.39 28 28
SHH 0.005 0.051 -10000 0 -0.48 3 3
catabolic process -0.007 0.12 -10000 0 -0.38 28 28
SMO/Vitamin D3 -0.009 0.11 -10000 0 -0.42 7 7
SHH Np/Cholesterol/Hhip 0 0.083 -10000 0 -0.38 12 12
LRP2 -0.034 0.19 -10000 0 -0.63 27 27
receptor-mediated endocytosis -0.037 0.16 -10000 0 -0.6 12 12
SHH Np/Cholesterol/BOC 0.016 0.043 -10000 0 -0.38 3 3
SHH Np/Cholesterol/CDO 0.015 0.044 -10000 0 -0.38 3 3
mesenchymal cell differentiation 0 0.082 0.38 12 -10000 0 12
mol:Vitamin D3 0.029 0.13 -10000 0 -0.34 6 6
IHH N/PTCH2 -0.005 0.14 -10000 0 -0.42 28 28
CDON 0.026 0.012 -10000 0 -10000 0 0
IHH N/PTCH1 0.001 0.13 -10000 0 -0.38 28 28
Megalin/LRPAP1 -0.007 0.15 -10000 0 -0.47 27 27
PTCH2 0.025 0.013 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.008 0.041 -10000 0 -0.38 3 3
PTCH1 -0.007 0.12 -10000 0 -0.38 28 28
HHIP -0.004 0.13 -10000 0 -0.64 11 11
Nongenotropic Androgen signaling

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
PTK2 0.007 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.087 -10000 0 -0.38 12 12
regulation of S phase of mitotic cell cycle 0.01 0.063 -10000 0 -0.3 11 11
GNAO1 -0.012 0.15 -10000 0 -0.64 16 16
HRAS 0.026 0.009 -10000 0 -10000 0 0
SHBG/T-DHT 0.008 0.057 -10000 0 -0.28 9 9
PELP1 0.025 0.008 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.022 0.081 -10000 0 -0.32 12 12
T-DHT/AR -0.003 0.1 -10000 0 -0.48 12 12
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.009 43 43
GNAI2 0.026 0.007 -10000 0 -10000 0 0
GNAI3 0.027 0.006 -10000 0 -10000 0 0
GNAI1 0.018 0.056 -10000 0 -0.64 2 2
mol:GDP -0.016 0.1 -10000 0 -0.49 12 12
cell proliferation -0.041 0.16 0.34 3 -0.44 32 35
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
FOS -0.11 0.3 0.32 1 -0.8 43 44
mol:Ca2+ -0.005 0.02 -10000 0 -0.069 17 17
MAPK3 -0.019 0.13 0.34 7 -0.4 4 11
MAPK1 -0.043 0.16 0.22 1 -0.49 24 25
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.005 43 43
cAMP biosynthetic process -0.001 0.064 0.24 7 -0.27 8 15
GNG2 0.027 0.006 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 43 43
HRAS/GTP 0.022 0.084 -10000 0 -0.34 12 12
actin cytoskeleton reorganization 0.03 0.021 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 43 43
PI3K 0.036 0.008 -10000 0 -10000 0 0
apoptosis 0.045 0.17 0.47 33 -0.34 1 34
T-DHT/AR/PELP1 0.015 0.088 -10000 0 -0.4 12 12
HRAS/GDP -0.002 0.099 -10000 0 -0.47 12 12
CREB1 -0.049 0.18 0.35 1 -0.5 33 34
RAC1-CDC42/GTP 0.038 0.026 -10000 0 -10000 0 0
AR -0.002 0.13 -10000 0 -0.64 12 12
GNB1 0.025 0.008 -10000 0 -10000 0 0
RAF1 -0.004 0.083 -10000 0 -0.33 12 12
RAC1-CDC42/GDP 0.012 0.099 -10000 0 -0.46 11 11
T-DHT/AR/PELP1/Src 0.029 0.086 -10000 0 -0.37 12 12
MAP2K2 -0.023 0.081 -10000 0 -0.32 12 12
T-DHT/AR/PELP1/Src/PI3K 0.01 0.064 -10000 0 -0.3 11 11
GNAZ 0.026 0.008 -10000 0 -10000 0 0
SHBG 0.011 0.09 -10000 0 -0.46 9 9
Gi family/GNB1/GNG2/GDP -0.027 0.15 -10000 0 -0.47 23 23
mol:T-DHT -0.001 0.003 -10000 0 -0.006 34 34
RAC1 0.022 0.012 -10000 0 -10000 0 0
GNRH1 -0.005 0.023 -10000 0 -10000 0 0
Gi family/GTP -0.017 0.075 -10000 0 -0.25 14 14
CDC42 0.026 0.008 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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
CTTN 0.028 0.004 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.047 0.17 -9999 0 -0.35 60 60
Syndecan-3/Neurocan -0.004 0.1 -9999 0 -0.36 22 22
POMC 0.019 0.071 -9999 0 -0.56 4 4
EGFR 0.022 0.012 -9999 0 -10000 0 0
Syndecan-3/EGFR -0.005 0.1 -9999 0 -0.36 22 22
AGRP 0.013 0.021 -9999 0 -10000 0 0
NCSTN 0.027 0.005 -9999 0 -10000 0 0
PSENEN 0.028 0.002 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.025 0.039 -9999 0 -0.64 1 1
APH1A 0.027 0.005 -9999 0 -10000 0 0
NCAN 0.007 0.035 -9999 0 -10000 0 0
long-term memory 0.018 0.1 -9999 0 -0.33 22 22
Syndecan-3/IL8 -0.011 0.1 -9999 0 -0.35 23 23
PSEN1 0.027 0.007 -9999 0 -10000 0 0
Src/Cortactin 0.039 0.012 -9999 0 -10000 0 0
FYN 0.027 0.005 -9999 0 -10000 0 0
limb bud formation -0.01 0.095 -9999 0 -0.38 18 18
MC4R -0.007 0.021 -9999 0 -10000 0 0
SRC 0.026 0.009 -9999 0 -10000 0 0
PTN -0.096 0.25 -9999 0 -0.64 50 50
FGFR/FGF/Syndecan-3 -0.01 0.095 -9999 0 -0.38 18 18
neuron projection morphogenesis -0.041 0.18 -9999 0 -0.41 18 18
Syndecan-3/AgRP -0.001 0.1 -9999 0 -0.36 20 20
Syndecan-3/AgRP/MC4R 0.008 0.1 -9999 0 -0.35 19 19
Fyn/Cortactin 0.04 0.009 -9999 0 -10000 0 0
SDC3 -0.011 0.096 -9999 0 -0.38 18 18
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.011 0.1 -9999 0 -0.35 23 23
IL8 0 0.059 -9999 0 -0.64 1 1
Syndecan-3/Fyn/Cortactin 0.019 0.1 -9999 0 -0.35 19 19
Syndecan-3/CASK -0.015 0.098 -9999 0 -0.35 22 22
alpha-MSH/MC4R 0.025 0.057 -9999 0 -0.42 4 4
Gamma Secretase 0.075 0.035 -9999 0 -0.36 1 1
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.22 0.32 -10000 0 -0.62 109 109
HRAS 0.028 0.003 -10000 0 -10000 0 0
EGFR 0.022 0.012 -10000 0 -10000 0 0
AKT 0.034 0.1 0.23 35 -10000 0 35
FOXO3 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.026 0.007 -10000 0 -10000 0 0
FOXO1 0.027 0.006 -10000 0 -10000 0 0
AKT3 0.027 0.006 -10000 0 -10000 0 0
FOXO4 0.028 0.002 -10000 0 -10000 0 0
MET 0.018 0.023 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
PIK3CB 0.027 0.006 -10000 0 -10000 0 0
NRAS 0.027 0.006 -10000 0 -10000 0 0
PIK3CG 0.018 0.042 -10000 0 -0.64 1 1
PIK3R3 0.026 0.007 -10000 0 -10000 0 0
PIK3R2 0.028 0.002 -10000 0 -10000 0 0
NF1 0.026 0.007 -10000 0 -10000 0 0
RAS -0.027 0.077 -10000 0 -0.16 66 66
ERBB2 0.026 0.007 -10000 0 -10000 0 0
proliferation/survival/translation -0.03 0.048 0.24 2 -0.2 3 5
PI3K 0.009 0.11 0.24 34 -0.21 8 42
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
KRAS 0.027 0.006 -10000 0 -10000 0 0
FOXO 0.062 0.085 0.23 37 -10000 0 37
AKT2 0.028 0.002 -10000 0 -10000 0 0
PTEN 0.028 0.004 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.009 0.053 -10000 0 -10000 0 0
adherens junction organization -0.004 0.098 0.25 5 -0.29 22 27
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.056 -10000 0 -10000 0 0
FMN1 -0.023 0.12 -10000 0 -0.36 16 16
mol:IP3 0.008 0.052 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0.088 -10000 0 -0.28 22 22
CTNNB1 0.027 0.008 -10000 0 -10000 0 0
AKT1 0.014 0.067 0.28 2 -10000 0 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.03 0.14 -10000 0 -0.48 22 22
CTNND1 0.03 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.003 0.082 -10000 0 -0.27 20 20
VASP -0.003 0.084 -10000 0 -0.27 22 22
ZYX -0.007 0.081 -10000 0 -10000 0 0
JUB -0.002 0.084 -10000 0 -0.27 22 22
EGFR(dimer) 0.008 0.088 -10000 0 -0.27 20 20
E-cadherin/beta catenin-gamma catenin 0.014 0.12 -10000 0 -0.4 21 21
mol:PI-3-4-5-P3 0.03 0.075 0.25 1 -10000 0 1
PIK3CA 0.028 0.007 -10000 0 -10000 0 0
PI3K 0.031 0.076 0.26 1 -10000 0 1
FYN -0.19 0.14 -10000 0 -0.4 22 22
mol:Ca2+ 0.008 0.052 -10000 0 -10000 0 0
JUP 0.027 0.008 -10000 0 -10000 0 0
PIK3R1 0.029 0.007 -10000 0 -10000 0 0
mol:DAG 0.008 0.052 -10000 0 -10000 0 0
CDH1 -0.025 0.18 -10000 0 -0.64 22 22
RhoA/GDP 0.043 0.078 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium -0.003 0.083 -10000 0 -0.27 22 22
SRC 0.026 0.009 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
EGFR 0.022 0.012 -10000 0 -10000 0 0
CASR -0.22 0.16 -10000 0 -0.33 179 179
RhoA/GTP 0.021 0.053 -10000 0 -10000 0 0
AKT2 0.015 0.069 0.28 2 -10000 0 2
actin cable formation -0.024 0.12 -10000 0 -0.36 16 16
apoptosis -0.025 0.096 -10000 0 -0.35 13 13
CTNNA1 0.029 0.008 -10000 0 -10000 0 0
mol:GDP 0.001 0.049 -10000 0 -10000 0 0
PIP5K1A -0.003 0.084 -10000 0 -0.27 20 20
PLCG1 0.008 0.053 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.085 -10000 0 -10000 0 0
homophilic cell adhesion 0.001 0.007 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 0.01 0.092 -10000 0 -0.44 9 9
ACTA1 -0.007 0.055 -10000 0 -0.49 1 1
NUMA1 0.009 0.095 -10000 0 -0.44 9 9
SPTAN1 -0.008 0.054 0.27 1 -0.48 1 2
LIMK1 0.03 0.094 0.27 2 -0.48 1 3
BIRC3 0.02 0.027 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
BAX 0.027 0.009 -10000 0 -10000 0 0
CASP10 -0.011 0.013 -10000 0 -10000 0 0
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.028 0 -10000 0 -10000 0 0
PTK2 0.004 0.14 -10000 0 -0.65 9 9
DIABLO 0.027 0.005 -10000 0 -10000 0 0
apoptotic nuclear changes -0.008 0.053 0.27 1 -0.48 1 2
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.027 0.005 -10000 0 -10000 0 0
GSN -0.008 0.054 0.27 1 -0.49 1 2
MADD 0.028 0.004 -10000 0 -10000 0 0
TFAP2A -0.41 0.28 -10000 0 -0.52 227 227
BID 0.005 0.007 -10000 0 -10000 0 0
MAP3K1 0.006 0.052 -10000 0 -0.45 3 3
TRADD 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.014 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.001 0.067 0.28 1 -0.48 1 2
CASP9 0.026 0.008 -10000 0 -10000 0 0
DNA repair 0.001 0.055 0.26 10 -10000 0 10
neuron apoptosis -0.014 0.17 -10000 0 -0.63 18 18
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0 0.078 -10000 0 -0.41 7 7
APAF1 0.027 0.005 -10000 0 -10000 0 0
CASP6 0.006 0.21 -10000 0 -0.96 12 12
TRAF2 0.027 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.008 0.049 -10000 0 -0.47 1 1
CASP7 -0.001 0.038 -10000 0 -0.27 3 3
KRT18 0.022 0.048 -10000 0 -0.48 1 1
apoptosis -0.007 0.1 -10000 0 -0.51 9 9
DFFA -0.007 0.049 -10000 0 -0.48 1 1
DFFB -0.006 0.051 -10000 0 -0.48 1 1
PARP1 -0.001 0.056 -10000 0 -0.26 10 10
actin filament polymerization -0.029 0.086 0.44 1 -0.26 2 3
TNF 0.014 0.071 -10000 0 -0.64 3 3
CYCS 0.014 0.025 0.17 1 -10000 0 1
SATB1 0.008 0.2 0.37 5 -0.9 12 17
SLK -0.008 0.052 -10000 0 -0.47 1 1
p15 BID/BAX 0.01 0.042 -10000 0 -10000 0 0
CASP2 0.037 0.094 0.21 48 -0.33 1 49
JNK cascade -0.006 0.051 0.44 3 -10000 0 3
CASP3 -0.007 0.056 -10000 0 -0.51 1 1
LMNB2 0.043 0.14 0.29 11 -0.5 9 20
RIPK1 0.027 0.006 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.066 0.019 -10000 0 -10000 0 0
negative regulation of DNA binding -0.41 0.27 -10000 0 -0.52 227 227
stress fiber formation -0.008 0.051 -10000 0 -0.46 1 1
GZMB 0.007 0.021 -10000 0 -10000 0 0
CASP1 0.015 0.005 -10000 0 -10000 0 0
LMNB1 0.043 0.14 0.29 11 -0.47 10 21
APP -0.015 0.17 -10000 0 -0.64 18 18
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.001 -10000 0 -10000 0 0
VIM -0.005 0.1 -10000 0 -0.5 11 11
LMNA 0.038 0.16 0.29 11 -0.64 9 20
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.009 0.058 -10000 0 -0.35 1 1
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0.002 0.069 0.28 1 -0.48 1 2
APAF-1/Caspase 9 -0.02 0.16 -10000 0 -0.6 20 20
nuclear fragmentation during apoptosis 0.009 0.093 -10000 0 -0.44 9 9
CFL2 0.029 0.087 0.26 2 -0.45 1 3
GAS2 -0.014 0.071 -10000 0 -0.43 5 5
positive regulation of apoptosis 0.045 0.15 0.3 11 -0.52 11 22
PRF1 0.025 0.017 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.039 0.01 -10000 0 -10000 0 0
Necdin/E2F1 -0.02 0.13 -10000 0 -0.42 23 23
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.053 0.096 -10000 0 -0.39 11 11
NGF (dimer)/p75(NTR)/BEX1 -0.001 0.15 -10000 0 -0.4 32 32
NT-4/5 (dimer)/p75(NTR) 0.017 0.078 -10000 0 -0.49 6 6
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.01 0.096 0.35 4 -0.39 10 14
IKBKG 0.028 0.002 -10000 0 -10000 0 0
BDNF 0.013 0.037 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.03 0.087 -10000 0 -0.38 11 11
FURIN 0.028 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.029 0.075 -10000 0 -0.43 6 6
LINGO1 0.016 0.087 -10000 0 -0.64 5 5
Sortilin/TRAF6/NRIF 0.034 0.025 -10000 0 -0.33 1 1
proBDNF (dimer) 0.013 0.037 -10000 0 -10000 0 0
NTRK1 -0.11 0.26 -10000 0 -0.63 56 56
RTN4R 0.024 0.016 -10000 0 -10000 0 0
neuron apoptosis 0.005 0.11 0.32 1 -0.45 7 8
IRAK1 0.028 0.002 -10000 0 -10000 0 0
SHC1 -0.004 0.092 -10000 0 -0.45 11 11
ARHGDIA 0.026 0.008 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.005 -10000 0 -10000 0 0
Gamma Secretase 0.075 0.035 -10000 0 -0.36 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.043 0.098 -10000 0 -0.41 11 11
MAGEH1 0.028 0.007 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.014 0.16 -10000 0 -0.45 25 25
Mammalian IAPs/DIABLO 0.066 0.019 -10000 0 -10000 0 0
proNGF (dimer) 0.007 0.11 -10000 0 -0.64 8 8
MAGED1 0.028 0.003 -10000 0 -10000 0 0
APP 0.026 0.007 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.001 0.033 -10000 0 -10000 0 0
ZNF274 0.028 0.002 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.018 0.085 -10000 0 -0.39 11 11
NGF 0.007 0.11 -10000 0 -0.64 8 8
cell cycle arrest -0.011 0.094 0.23 10 -0.37 11 21
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.015 0.067 -10000 0 -0.3 11 11
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.032 0.072 -10000 0 -0.42 6 6
NCSTN 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0.028 0.1 -10000 0 -0.41 13 13
PSENEN 0.028 0.002 -10000 0 -10000 0 0
mol:ceramide 0.005 0.094 -10000 0 -0.41 11 11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.01 0.062 -10000 0 -0.38 2 2
p75(NTR)/beta APP 0.025 0.075 -10000 0 -0.48 6 6
BEX1 -0.018 0.17 -10000 0 -0.64 19 19
mol:GDP -0.014 0.09 -10000 0 -0.41 13 13
NGF (dimer) -0.22 0.22 -10000 0 -0.41 162 162
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.046 0.082 -10000 0 -0.38 9 9
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
RAC1/GTP 0.018 0.084 -10000 0 -0.39 10 10
MYD88 0.027 0.006 -10000 0 -10000 0 0
CHUK 0.028 0.004 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.029 0.1 -10000 0 -0.41 13 13
RHOB 0.027 0.005 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.015 0.04 -10000 0 -10000 0 0
NT3 (dimer) -0.047 0.2 -10000 0 -0.64 31 31
TP53 -0.018 0.056 -10000 0 -0.36 6 6
PRDM4 0.003 0.091 -10000 0 -0.41 11 11
BDNF (dimer) -0.22 0.21 -10000 0 -0.4 160 160
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
SORT1 0.027 0.006 -10000 0 -10000 0 0
activation of caspase activity 0.047 0.093 -10000 0 -0.39 11 11
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.043 0.098 -10000 0 -0.41 11 11
RHOC 0.027 0.006 -10000 0 -10000 0 0
XIAP 0.028 0 -10000 0 -10000 0 0
MAPK10 0.018 0.099 0.25 5 -0.43 5 10
DIABLO 0.027 0.005 -10000 0 -10000 0 0
SMPD2 0.005 0.095 -10000 0 -0.41 11 11
APH1B 0.025 0.039 -10000 0 -0.64 1 1
APH1A 0.027 0.005 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.029 0.1 -10000 0 -0.41 13 13
PSEN1 0.027 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.037 0.014 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.028 0.17 -10000 0 -0.46 37 37
MAPK8 0.013 0.1 0.25 4 -0.42 6 10
MAPK9 0.017 0.099 0.25 5 -0.43 5 10
APAF1 0.027 0.005 -10000 0 -10000 0 0
NTF3 -0.047 0.21 -10000 0 -0.64 31 31
NTF4 -0.001 0.033 -10000 0 -10000 0 0
NDN -0.024 0.18 -10000 0 -0.61 23 23
RAC1/GDP 0.016 0.009 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.045 0.09 -10000 0 -0.37 11 11
p75 CTF/Sortilin/TRAF6/NRIF 0.066 0.021 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.028 0.1 -10000 0 -0.41 13 13
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.061 0.07 -10000 0 -0.38 6 6
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.051 0.07 -10000 0 -0.4 6 6
PRKACB 0.027 0.007 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.027 0.033 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.02 0.028 -10000 0 -10000 0 0
BIRC2 0.027 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis -0.023 0.12 0.27 2 -0.45 14 16
BAD 0.016 0.11 0.26 5 -0.43 5 10
RIPK2 0.027 0.004 -10000 0 -10000 0 0
NGFR 0.012 0.095 -10000 0 -0.64 6 6
CYCS 0 0.087 0.36 1 -0.39 11 12
ADAM17 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.043 0.098 -10000 0 -0.41 11 11
BCL2L11 0.017 0.11 0.28 6 -0.43 5 11
BDNF (dimer)/p75(NTR) 0.016 0.081 -10000 0 -0.5 6 6
PI3K 0.044 0.094 -10000 0 -0.42 10 10
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.043 0.098 -10000 0 -0.41 11 11
NDNL2 0.027 0.005 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
PRKCI 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.013 0.11 -10000 0 -0.48 13 13
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.043 0.098 -10000 0 -0.41 11 11
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCZ 0.025 0.008 -10000 0 -10000 0 0
PLG -0.36 0.31 -10000 0 -0.63 162 162
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.002 0.087 -10000 0 -0.41 11 11
SQSTM1 0.025 0.017 -10000 0 -10000 0 0
NGFRAP1 0.028 0 -10000 0 -10000 0 0
CASP3 0.016 0.1 0.26 7 -0.39 5 12
E2F1 -0.002 0.047 -10000 0 -10000 0 0
CASP9 0.026 0.008 -10000 0 -10000 0 0
IKK complex -0.028 0.17 -10000 0 -0.44 12 12
NGF (dimer)/TRKA -0.075 0.21 -10000 0 -0.47 63 63
MMP7 -0.013 0.096 -10000 0 -0.64 5 5
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.053 0.098 -10000 0 -0.39 11 11
MMP3 -0.012 0.026 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.003 0.068 -10000 0 -0.55 1 1
IL6-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
BCL2L1 -0.011 0.16 0.5 1 -10000 0 1
CRP -0.018 0.16 0.56 1 -10000 0 1
cell cycle arrest -0.022 0.16 -10000 0 -0.54 4 4
TIMP1 -0.013 0.15 -10000 0 -10000 0 0
IL6ST -0.073 0.24 -10000 0 -0.64 44 44
Rac1/GDP -0.048 0.14 -10000 0 -0.55 8 8
AP1 -0.029 0.16 -10000 0 -0.55 7 7
GAB2 0.028 0.004 -10000 0 -10000 0 0
TNFSF11 -0.019 0.15 -10000 0 -10000 0 0
HSP90B1 0.031 0.04 -10000 0 -10000 0 0
GAB1 0.027 0.006 -10000 0 -10000 0 0
MAPK14 -0.033 0.14 -10000 0 -0.55 8 8
AKT1 0.031 0.029 -10000 0 -10000 0 0
FOXO1 0.033 0.033 -10000 0 -10000 0 0
MAP2K6 -0.046 0.14 -10000 0 -0.51 10 10
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.043 0.13 0.34 1 -0.5 8 9
MITF -0.053 0.14 -10000 0 -0.41 24 24
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.028 0.002 -10000 0 -10000 0 0
A2M 0.009 0.15 -10000 0 -1.2 4 4
CEBPB 0.018 0.027 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.002 0.092 -10000 0 -0.45 4 4
STAT3 -0.028 0.16 -10000 0 -0.58 4 4
STAT1 0.01 0.04 -10000 0 -0.58 1 1
CEBPD -0.015 0.15 0.5 1 -10000 0 1
PIK3CA 0.028 0.005 -10000 0 -10000 0 0
PI3K 0.041 0.01 -10000 0 -10000 0 0
JUN 0.026 0.007 -10000 0 -10000 0 0
PIAS3/MITF -0.03 0.15 -10000 0 -0.49 12 12
MAPK11 -0.032 0.14 -10000 0 -0.55 8 8
STAT3 (dimer)/FOXO1 -0.027 0.14 -10000 0 -0.47 2 2
GRB2/SOS1/GAB family -0.007 0.15 -10000 0 -0.55 7 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.047 0.15 -10000 0 -0.34 51 51
GRB2 0.026 0.008 -10000 0 -10000 0 0
JAK2 0.027 0.007 -10000 0 -10000 0 0
LBP -0.22 0.44 -10000 0 -0.9 81 81
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
JAK1 0.027 0.009 -10000 0 -10000 0 0
MYC -0.016 0.15 0.5 1 -10000 0 1
FGG -0.021 0.15 -10000 0 -10000 0 0
macrophage differentiation -0.022 0.16 -10000 0 -0.54 4 4
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.027 0.18 -10000 0 -0.38 49 49
JUNB -0.016 0.15 -10000 0 -10000 0 0
FOS -0.066 0.22 -10000 0 -0.59 43 43
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.051 0.15 -10000 0 -0.39 30 30
STAT1/PIAS1 -0.029 0.15 -10000 0 -0.45 13 13
GRB2/SOS1/GAB family/SHP2/PI3K 0.033 0.03 -10000 0 -10000 0 0
STAT3 (dimer) -0.025 0.16 -10000 0 -0.56 4 4
PRKCD -0.008 0.16 0.33 3 -0.51 4 7
IL6R 0.026 0.04 -10000 0 -0.64 1 1
SOCS3 -0.024 0.15 -10000 0 -0.7 5 5
gp130 (dimer)/JAK1/JAK1/LMO4 -0.017 0.17 -10000 0 -0.41 44 44
Rac1/GTP -0.047 0.14 -10000 0 -0.52 9 9
HCK 0.013 0.05 -10000 0 -0.64 1 1
MAPKKK cascade 0.014 0.096 -10000 0 -0.5 5 5
bone resorption -0.017 0.15 -10000 0 -10000 0 0
IRF1 -0.015 0.16 0.56 1 -10000 0 1
mol:GDP -0.06 0.14 -10000 0 -0.4 25 25
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.061 0.14 -10000 0 -0.41 25 25
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.046 0.16 -10000 0 -0.55 13 13
PTPN11 0.013 0.02 -10000 0 -10000 0 0
IL6/IL6RA -0.007 0.13 -10000 0 -0.46 21 21
gp130 (dimer)/TYK2/TYK2/LMO4 -0.017 0.17 -10000 0 -0.41 44 44
gp130 (dimer)/JAK2/JAK2/LMO4 -0.019 0.17 -10000 0 -0.41 44 44
IL6 -0.028 0.17 -10000 0 -0.64 20 20
PIAS3 0.027 0.006 -10000 0 -10000 0 0
PTPRE 0.024 0.01 -10000 0 -10000 0 0
PIAS1 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.051 0.14 -10000 0 -0.33 51 51
LMO4 0.027 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.023 0.17 -10000 0 -0.6 4 4
MCL1 0.035 0.033 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 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
EP300 0.022 0.018 -10000 0 -10000 0 0
HSPA8 0.025 0.039 -10000 0 -0.62 1 1
SMAD3/SMAD4/ER alpha 0.026 0.11 -10000 0 -0.43 13 13
AKT1 0.028 0.008 -10000 0 -10000 0 0
GSC -0.002 0.087 -10000 0 -10000 0 0
NKX2-5 0.001 0 -10000 0 -10000 0 0
muscle cell differentiation -0.036 0.071 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.089 0.041 -10000 0 -10000 0 0
SMAD4 0.029 0.027 -10000 0 -10000 0 0
CBFB 0.026 0.007 -10000 0 -10000 0 0
SAP18 0.027 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.043 0.029 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.067 0.062 -10000 0 -0.34 2 2
MYC 0.024 0.015 -10000 0 -10000 0 0
CDKN2B -0.003 0.12 -10000 0 -0.53 7 7
AP1 0.004 0.12 -10000 0 -0.33 24 24
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.015 0.11 -10000 0 -0.42 11 11
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.017 0.046 -10000 0 -10000 0 0
SP3 0.029 0.004 -10000 0 -10000 0 0
CREB1 0.027 0.004 -10000 0 -10000 0 0
FOXH1 0.023 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.056 0.042 -10000 0 -10000 0 0
GATA3 -0.48 0.28 -10000 0 -0.63 222 222
SKI/SIN3/HDAC complex/NCoR1 0.023 0.074 -10000 0 -0.43 6 6
MEF2C/TIF2 0.008 0.11 -10000 0 -0.36 14 14
endothelial cell migration 0.042 0.28 1.3 13 -10000 0 13
MAX 0.028 0.013 -10000 0 -10000 0 0
RBBP7 0.028 0.003 -10000 0 -10000 0 0
RBBP4 0.026 0.007 -10000 0 -10000 0 0
RUNX2 0.024 0.018 -10000 0 -10000 0 0
RUNX3 0.012 0.035 -10000 0 -10000 0 0
RUNX1 0.018 0.028 -10000 0 -10000 0 0
CTBP1 0.027 0.005 -10000 0 -10000 0 0
NR3C1 0.029 0.012 -10000 0 -10000 0 0
VDR 0.018 0.078 -10000 0 -0.64 4 4
CDKN1A 0.024 0.08 -10000 0 -0.52 1 1
KAT2B 0.025 0.012 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.063 0.026 -10000 0 -10000 0 0
DCP1A 0.027 0.007 -10000 0 -10000 0 0
SKI 0.026 0.008 -10000 0 -10000 0 0
SERPINE1 -0.043 0.28 -10000 0 -1.3 13 13
SMAD3/SMAD4/ATF2 0.055 0.04 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.034 0.1 -10000 0 -0.42 12 12
SAP30 0.026 0.011 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.043 0.03 -10000 0 -10000 0 0
JUN -0.008 0.11 -10000 0 -0.32 20 20
SMAD3/SMAD4/IRF7 0.055 0.041 -10000 0 -10000 0 0
TFE3 0.028 0.022 -10000 0 -10000 0 0
COL1A2 0.027 0.042 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.052 0.039 -10000 0 -10000 0 0
DLX1 0.012 0.032 -10000 0 -10000 0 0
TCF3 0.028 0.003 -10000 0 -10000 0 0
FOS -0.052 0.22 -10000 0 -0.64 36 36
SMAD3/SMAD4/Max 0.055 0.044 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.043 0.027 -10000 0 -10000 0 0
ZBTB17 0.024 0.008 -10000 0 -10000 0 0
LAMC1 0.024 0.029 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.056 0.038 -10000 0 -10000 0 0
IRF7 0.028 0.007 -10000 0 -10000 0 0
ESR1 -0.009 0.14 -10000 0 -0.57 17 17
HNF4A -0.046 0.21 -10000 0 -0.64 31 31
MEF2C 0.026 0.033 0.3 2 -10000 0 2
SMAD2-3/SMAD4 0.061 0.042 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.043 0.027 -10000 0 -10000 0 0
IGHV3OR16-13 0.007 0.048 -10000 0 -0.35 5 5
TGIF2/HDAC complex 0.027 0.006 -10000 0 -10000 0 0
CREBBP 0.024 0.013 -10000 0 -10000 0 0
SKIL 0.027 0.005 -10000 0 -10000 0 0
HDAC1 0.026 0.007 -10000 0 -10000 0 0
HDAC2 0.027 0.006 -10000 0 -10000 0 0
SNIP1 0.027 0.007 -10000 0 -10000 0 0
GCN5L2 -0.001 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.059 0.047 -10000 0 -10000 0 0
MSG1/HSC70 0.038 0.032 -10000 0 -0.47 1 1
SMAD2 0.03 0.009 -10000 0 -10000 0 0
SMAD3 0.028 0.028 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.031 0.026 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.001 0.069 0.29 2 -0.41 4 6
NCOR1 0.026 0.008 -10000 0 -10000 0 0
NCOA2 -0.033 0.19 -10000 0 -0.64 26 26
NCOA1 0.027 0.005 -10000 0 -10000 0 0
MYOD/E2A 0.032 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.096 0.049 -10000 0 -10000 0 0
IFNB1 0.016 0.026 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.058 0.038 -10000 0 -10000 0 0
CITED1 0.025 0.015 -10000 0 -10000 0 0
SMAD2-3/SMAD4/ARC105 0.071 0.045 -10000 0 -10000 0 0
RBL1 0.027 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.025 0.05 -10000 0 -0.32 1 1
RUNX1-3/PEBPB2 0.027 0.041 -10000 0 -10000 0 0
SMAD7 0.021 0.11 -10000 0 -10000 0 0
MYC/MIZ-1 0.033 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.003 0.1 -10000 0 -0.45 12 12
IL10 -0.28 0.17 -10000 0 -0.38 210 210
PIASy/HDAC complex 0.029 0.008 -10000 0 -10000 0 0
PIAS3 0.024 0.013 -10000 0 -10000 0 0
CDK2 0.025 0.013 -10000 0 -10000 0 0
IL5 -0.28 0.17 -10000 0 -0.38 212 212
CDK4 0.025 0.013 -10000 0 -10000 0 0
PIAS4 0.029 0.008 -10000 0 -10000 0 0
ATF3 -0.003 0.14 -10000 0 -0.62 13 13
SMAD3/SMAD4/SP1 0.066 0.042 -10000 0 -10000 0 0
FOXG1 -0.006 0.026 -10000 0 -10000 0 0
FOXO3 0.015 0.007 -10000 0 -10000 0 0
FOXO1 0.016 0.006 -10000 0 -10000 0 0
FOXO4 0.016 0.006 -10000 0 -10000 0 0
heart looping 0.026 0.033 0.3 2 -10000 0 2
CEBPB 0.024 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.05 0.043 -10000 0 -10000 0 0
MYOD1 -0.013 0.018 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 0.004 0.16 -10000 0 -0.43 31 31
SMAD3/SMAD4/GATA3 -0.31 0.2 -10000 0 -0.43 215 215
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.063 0.049 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.085 0.039 -10000 0 -10000 0 0
MED15 0.026 0.007 -10000 0 -10000 0 0
SP1 0.033 0.008 -10000 0 -10000 0 0
SIN3B 0.028 0.002 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.064 0.026 -10000 0 -10000 0 0
ITGB5 0.032 0.033 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.02 0.074 -10000 0 -0.54 4 4
SMAD3/SMAD4/AR 0.034 0.11 -10000 0 -0.44 12 12
AR -0.001 0.13 -10000 0 -0.64 12 12
negative regulation of cell growth 0.019 0.06 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.048 0.041 -10000 0 -10000 0 0
E2F5 0.027 0.005 -10000 0 -10000 0 0
E2F4 0.026 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.078 0.039 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.032 0.02 -10000 0 -10000 0 0
TFDP1 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.023 0.13 -10000 0 -0.33 23 23
SMAD3/SMAD4/RUNX2 0.053 0.04 -10000 0 -10000 0 0
TGIF2 0.027 0.006 -10000 0 -10000 0 0
TGIF1 0.026 0.008 -10000 0 -10000 0 0
ATF2 0.028 0.004 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 0.007 0.023 -10000 0 -10000 0 0
NFATC2 -0.021 0.11 -10000 0 -0.41 20 20
NFATC3 0.009 0.021 -10000 0 -10000 0 0
CD40LG -0.057 0.18 0.35 3 -0.52 15 18
PTGS2 -0.11 0.26 0.35 3 -0.65 45 48
JUNB 0.028 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.014 0.019 -10000 0 -10000 0 0
CaM/Ca2+ 0.014 0.019 -10000 0 -10000 0 0
CALM1 0.022 0.017 -10000 0 -10000 0 0
JUN 0.022 0.017 -10000 0 -10000 0 0
mol:Ca2+ -0.002 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.018 0.006 -10000 0 -10000 0 0
FOSL1 0.022 0.057 -10000 0 -0.64 2 2
CREM 0.027 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.003 0.12 -10000 0 -0.42 6 6
FOS -0.069 0.23 -10000 0 -0.6 43 43
IFNG -0.057 0.17 0.35 3 -0.52 15 18
AP-1/NFAT1-c-4 -0.045 0.21 -10000 0 -0.59 16 16
FASLG -0.061 0.18 0.35 3 -0.53 14 17
NFAT1-c-4/ICER1 -0.006 0.1 -10000 0 -0.35 19 19
IL2RA -0.06 0.17 0.35 3 -0.52 14 17
FKBP12/FK506 0.02 0.004 -10000 0 -10000 0 0
CSF2 -0.059 0.18 0.35 3 -0.52 15 18
JunB/Fra1/NFAT1-c-4 0.004 0.11 -10000 0 -0.35 18 18
IL4 -0.06 0.17 0.35 3 -0.52 15 18
IL2 -0.023 0.18 -10000 0 -0.86 12 12
IL3 -0.008 0.13 -10000 0 -0.7 8 8
FKBP1A 0.027 0.006 -10000 0 -10000 0 0
BATF3 0.027 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.027 0.006 -10000 0 -10000 0 0
IL27-mediated signaling events

Figure S42.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S42.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.028 0.01 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.001 0.11 0.36 1 -10000 0 1
IL27/IL27R/JAK1 0.11 0.21 -10000 0 -10000 0 0
TBX21 0.061 0.15 0.47 3 -10000 0 3
IL12B 0.015 0.02 -10000 0 -10000 0 0
IL12A 0.005 0.006 -10000 0 -10000 0 0
IL6ST -0.069 0.24 -10000 0 -0.64 44 44
IL27RA/JAK1 0.041 0.034 -10000 0 -10000 0 0
IL27 0.021 0.025 -10000 0 -10000 0 0
TYK2 0.03 0.004 -10000 0 -10000 0 0
T-helper cell lineage commitment 0.001 0.11 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.001 0.11 0.36 1 -10000 0 1
T cell proliferation during immune response 0.001 0.11 0.36 1 -10000 0 1
MAPKKK cascade -0.001 0.11 -10000 0 -0.36 1 1
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT2 0.027 0.005 -10000 0 -10000 0 0
STAT1 0.031 0.015 -10000 0 -10000 0 0
IL12RB1 0.021 0.026 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.051 0.16 0.36 4 -0.46 3 7
IL27/IL27R/JAK2/TYK2 -0.001 0.11 -10000 0 -0.37 1 1
positive regulation of T cell mediated cytotoxicity -0.001 0.11 -10000 0 -0.36 1 1
STAT1 (dimer) 0.25 0.3 0.49 164 -10000 0 164
JAK2 0.028 0.007 -10000 0 -10000 0 0
JAK1 0.031 0.009 -10000 0 -10000 0 0
STAT2 (dimer) 0.014 0.12 -10000 0 -10000 0 0
T cell proliferation -0.027 0.13 0.36 1 -0.5 7 8
IL12/IL12R/TYK2/JAK2 0.035 0.085 -10000 0 -0.7 3 3
IL17A -0.012 0.1 -10000 0 -10000 0 0
mast cell activation 0.001 0.11 0.36 1 -10000 0 1
IFNG 0.009 0.024 -10000 0 -10000 0 0
T cell differentiation 0.001 0.005 0.013 1 -10000 0 1
STAT3 (dimer) 0.014 0.11 -10000 0 -10000 0 0
STAT5A (dimer) 0.014 0.11 -10000 0 -0.35 1 1
STAT4 (dimer) 0.012 0.12 -10000 0 -10000 0 0
STAT4 0.019 0.029 -10000 0 -10000 0 0
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.009 0.15 -10000 0 -10000 0 0
GATA3 -1 0.56 0.69 1 -1.3 222 223
IL18 0.006 0.008 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production 0.014 0.11 -10000 0 -10000 0 0
IL27/EBI3 0.033 0.051 -10000 0 -0.48 1 1
IL27RA 0.017 0.026 -10000 0 -10000 0 0
IL6 -0.03 0.17 -10000 0 -0.64 20 20
STAT5A 0.026 0.007 -10000 0 -10000 0 0
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.018 0.016 -10000 0 -10000 0 0
IL1B -0.001 0.064 -10000 0 -0.48 5 5
EBI3 0.018 0.055 -10000 0 -0.63 1 1
TNF -0.001 0.051 -10000 0 -0.48 3 3
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.019 0.3 -10000 0 -0.95 16 16
IL23A -0.026 0.3 -10000 0 -0.95 16 16
NF kappa B1 p50/RelA/I kappa B alpha 0.005 0.29 -10000 0 -0.89 17 17
positive regulation of T cell mediated cytotoxicity -0.024 0.31 -10000 0 -0.95 18 18
ITGA3 -0.012 0.28 -10000 0 -0.88 14 14
IL17F 0.001 0.22 0.49 3 -0.62 12 15
IL12B 0.022 0.04 -10000 0 -10000 0 0
STAT1 (dimer) -0.02 0.3 -10000 0 -0.92 18 18
CD4 -0.014 0.28 -10000 0 -0.89 14 14
IL23 -0.015 0.3 -10000 0 -0.93 16 16
IL23R -0.01 0.18 -10000 0 -0.75 11 11
IL1B -0.032 0.32 -10000 0 -1 17 17
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.021 0.28 -10000 0 -0.89 15 15
TYK2 0.024 0.031 -10000 0 -10000 0 0
STAT4 0.019 0.029 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
IL18RAP 0.014 0.036 -10000 0 -10000 0 0
IL12RB1 0.017 0.04 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.029 0.045 -10000 0 -10000 0 0
IL23R/JAK2 0.01 0.17 -10000 0 -0.65 11 11
positive regulation of chronic inflammatory response -0.024 0.31 -10000 0 -0.95 18 18
natural killer cell activation -0.001 0.006 -10000 0 -10000 0 0
JAK2 0.026 0.038 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
NFKB1 0.028 0.007 -10000 0 -10000 0 0
RELA 0.029 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.013 0.28 -10000 0 -0.89 16 16
ALOX12B -0.014 0.28 -10000 0 -0.87 13 13
CXCL1 -0.05 0.33 -10000 0 -1 23 23
T cell proliferation -0.024 0.31 -10000 0 -0.95 18 18
NFKBIA 0.027 0.007 -10000 0 -10000 0 0
IL17A 0.014 0.18 0.37 1 -0.5 6 7
PI3K -0.008 0.29 -10000 0 -0.9 16 16
IFNG 0.001 0.028 0.12 1 -0.11 7 8
STAT3 (dimer) -0.002 0.28 -10000 0 -0.86 14 14
IL18R1 0.026 0.039 -10000 0 -0.64 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 0.006 0.19 -10000 0 -0.63 3 3
IL18/IL18R 0.04 0.045 -10000 0 -0.42 1 1
macrophage activation -0.002 0.015 -10000 0 -0.042 14 14
TNF -0.029 0.3 -10000 0 -0.98 17 17
STAT3/STAT4 -0.013 0.28 -10000 0 -0.88 16 16
STAT4 (dimer) -0.021 0.3 -10000 0 -0.93 18 18
IL18 0.025 0.015 -10000 0 -10000 0 0
IL19 -0.024 0.28 -10000 0 -0.89 15 15
STAT5A (dimer) -0.022 0.29 -10000 0 -0.9 17 17
STAT1 0.026 0.014 -10000 0 -10000 0 0
SOCS3 0.023 0.041 -10000 0 -0.64 1 1
CXCL9 -0.024 0.28 -10000 0 -0.9 16 16
MPO -0.011 0.28 -10000 0 -0.88 12 12
positive regulation of humoral immune response -0.024 0.31 -10000 0 -0.95 18 18
IL23/IL23R/JAK2/TYK2 -0.025 0.31 -10000 0 -0.98 18 18
IL6 -0.048 0.42 -10000 0 -1.1 32 32
STAT5A 0.026 0.007 -10000 0 -10000 0 0
IL2 0.004 0.024 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.006 -10000 0 -10000 0 0
CD3E -0.025 0.29 -10000 0 -0.93 15 15
keratinocyte proliferation -0.024 0.31 -10000 0 -0.95 18 18
NOS2 -0.062 0.39 -10000 0 -1 31 31
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.004 0.12 -9999 0 -0.64 10 10
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.003 0.072 -9999 0 -0.28 14 14
GNAO1 -0.011 0.15 -9999 0 -0.64 16 16
S1P/S1P3/G12/G13 0.014 0.1 -9999 0 -0.34 19 19
AKT1 -0.027 0.17 -9999 0 -0.5 29 29
AKT3 -0.001 0.12 -9999 0 -0.52 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.004 0.12 -9999 0 -0.64 10 10
GNAI2 0.028 0.007 -9999 0 -10000 0 0
GNAI3 0.028 0.006 -9999 0 -10000 0 0
GNAI1 0.018 0.056 -9999 0 -0.64 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.024 0.18 -9999 0 -0.62 23 23
S1PR2 0.028 0.002 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.011 0.14 -9999 0 -0.34 31 31
MAPK3 -0.014 0.12 -9999 0 -0.48 9 9
MAPK1 -0.008 0.12 -9999 0 -0.5 9 9
JAK2 -0.014 0.14 -9999 0 -0.52 11 11
CXCR4 -0.02 0.13 -9999 0 -0.49 10 10
FLT1 0.024 0.056 -9999 0 -0.64 2 2
RhoA/GDP 0.02 0.005 -9999 0 -10000 0 0
Rac1/GDP 0.016 0.009 -9999 0 -10000 0 0
SRC -0.015 0.13 -9999 0 -0.54 8 8
S1P/S1P3/Gi -0.011 0.14 -9999 0 -0.35 30 30
RAC1 0.022 0.012 -9999 0 -10000 0 0
RhoA/GTP -0.006 0.13 -9999 0 -0.49 9 9
VEGFA 0.027 0.013 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.012 0.092 -9999 0 -0.32 12 12
VEGFR1 homodimer/VEGFA homodimer 0.039 0.046 -9999 0 -0.48 2 2
RHOA 0.027 0.006 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.071 0.18 -9999 0 -0.34 76 76
GNAQ 0.027 0.006 -9999 0 -10000 0 0
GNAZ 0.027 0.008 -9999 0 -10000 0 0
G12/G13 0.031 0.018 -9999 0 -10000 0 0
GNA14 -0.11 0.27 -9999 0 -0.62 60 60
GNA15 0.02 0.027 -9999 0 -10000 0 0
GNA12 0.022 0.011 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.012 0.1 -9999 0 -0.64 7 7
Rac1/GTP -0.015 0.12 -9999 0 -0.5 9 9
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.014 0.09 -10000 0 -0.34 15 15
NF kappa B1 p50/RelA/I kappa B alpha 0.039 0.12 0.36 16 -0.37 2 18
alphaV/beta3 Integrin/Osteopontin/Src 0.036 0.051 -10000 0 -0.47 2 2
AP1 -0.002 0.17 -10000 0 -0.53 11 11
ILK 0.011 0.097 -10000 0 -0.36 15 15
bone resorption 0.016 0.11 0.33 3 -0.62 2 5
PTK2B 0.027 0.006 -10000 0 -10000 0 0
PYK2/p130Cas 0.048 0.1 -10000 0 -0.34 11 11
ITGAV 0.029 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.025 0.071 -10000 0 -0.48 5 5
alphaV/beta3 Integrin/Osteopontin 0.032 0.11 -10000 0 -0.4 15 15
MAP3K1 0.009 0.098 -10000 0 -0.37 15 15
JUN 0.027 0.007 -10000 0 -10000 0 0
MAPK3 -0.008 0.085 -10000 0 -0.34 15 15
MAPK1 -0.009 0.084 -10000 0 -0.34 15 15
Rac1/GDP 0.016 0.009 -10000 0 -10000 0 0
NFKB1 0.027 0.006 -10000 0 -10000 0 0
MAPK8 0.001 0.11 0.38 2 -0.4 14 16
ITGB3 -0.005 0.14 -10000 0 -0.63 13 13
NFKBIA -0.011 0.086 -10000 0 -0.34 15 15
FOS -0.065 0.22 -10000 0 -0.59 43 43
CD44 0.021 0.026 -10000 0 -10000 0 0
CHUK 0.028 0.004 -10000 0 -10000 0 0
PLAU -0.002 0.21 0.45 8 -1.1 7 15
NF kappa B1 p50/RelA 0.038 0.1 -10000 0 -10000 0 0
BCAR1 0.026 0.008 -10000 0 -10000 0 0
RELA 0.028 0.002 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.017 0.11 -10000 0 -0.47 13 13
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.009 0.098 -10000 0 -0.37 15 15
VAV3 0.003 0.1 0.38 2 -0.34 16 18
MAP3K14 0 0.091 -10000 0 -0.37 15 15
ROCK2 0.016 0.087 -10000 0 -0.64 5 5
SPP1 0.019 0.063 -10000 0 -0.53 3 3
RAC1 0.022 0.012 -10000 0 -10000 0 0
Rac1/GTP 0.007 0.08 0.34 1 -0.32 7 8
MMP2 -0.026 0.12 0.31 1 -0.45 8 9
HIF-1-alpha transcription factor network

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
PKM2 0.015 0.26 -10000 0 -0.9 9 9
HDAC7 0.028 0.005 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.083 0.25 -10000 0 -0.71 5 5
SMAD4 0.027 0.008 -10000 0 -10000 0 0
ID2 0.028 0.27 -10000 0 -0.93 8 8
AP1 -0.03 0.17 -10000 0 -0.48 36 36
ABCG2 0.024 0.27 -10000 0 -0.92 9 9
HIF1A 0.025 0.066 -10000 0 -10000 0 0
TFF3 -0.037 0.34 -10000 0 -0.93 17 17
GATA2 -0.1 0.27 -10000 0 -0.64 57 57
AKT1 0.03 0.065 -10000 0 -10000 0 0
response to hypoxia 0.01 0.055 -10000 0 -10000 0 0
MCL1 0.027 0.26 -10000 0 -0.93 8 8
NDRG1 0.026 0.26 -10000 0 -0.93 8 8
SERPINE1 -0.018 0.27 -10000 0 -0.96 11 11
FECH 0.023 0.26 -10000 0 -0.92 8 8
FURIN 0.027 0.27 -10000 0 -0.93 8 8
NCOA2 -0.032 0.19 -10000 0 -0.64 26 26
EP300 0.035 0.079 -10000 0 -0.34 2 2
HMOX1 0.02 0.27 -10000 0 -0.97 8 8
BHLHE40 0.022 0.26 -10000 0 -0.92 8 8
BHLHE41 0.02 0.26 -10000 0 -0.93 8 8
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.079 0.1 -10000 0 -10000 0 0
ENG 0.037 0.082 0.34 1 -10000 0 1
JUN 0.027 0.008 -10000 0 -10000 0 0
RORA 0.026 0.27 -10000 0 -0.93 8 8
ABCB1 -0.052 0.26 -10000 0 -1.1 16 16
TFRC 0.025 0.26 -10000 0 -0.94 7 7
CXCR4 0.027 0.27 -10000 0 -0.93 8 8
TF 0.018 0.27 -10000 0 -0.94 7 7
CITED2 0.028 0.27 -10000 0 -0.93 8 8
HIF1A/ARNT 0.079 0.33 -10000 0 -1.1 8 8
LDHA 0.016 0.1 -10000 0 -0.62 5 5
ETS1 0.025 0.27 -10000 0 -0.93 8 8
PGK1 0.027 0.27 -10000 0 -0.93 8 8
NOS2 0.004 0.3 -10000 0 -0.91 15 15
ITGB2 0.015 0.26 -10000 0 -0.93 8 8
ALDOA 0.022 0.26 -10000 0 -0.92 7 7
Cbp/p300/CITED2 0.046 0.27 -10000 0 -0.96 6 6
FOS -0.064 0.22 -10000 0 -0.59 43 43
HK2 0.01 0.27 -10000 0 -0.95 8 8
SP1 0.025 0.036 -10000 0 -10000 0 0
GCK 0.032 0.15 -10000 0 -0.68 2 2
HK1 0.027 0.27 -10000 0 -0.93 8 8
NPM1 0.026 0.26 -10000 0 -0.93 8 8
EGLN1 0.026 0.26 -10000 0 -0.93 8 8
CREB1 0.033 0.005 -10000 0 -10000 0 0
PGM1 0.025 0.26 -10000 0 -0.93 8 8
SMAD3 0.029 0.004 -10000 0 -10000 0 0
EDN1 -0.064 0.25 -10000 0 -0.71 24 24
IGFBP1 -0.031 0.28 -10000 0 -0.87 13 13
VEGFA 0.059 0.21 0.49 2 -0.65 2 4
HIF1A/JAB1 0.039 0.052 -10000 0 -10000 0 0
CP -0.003 0.3 -10000 0 -0.87 13 13
CXCL12 -0.015 0.34 -10000 0 -0.87 24 24
COPS5 0.028 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.039 0.013 -10000 0 -10000 0 0
BNIP3 0.027 0.27 -10000 0 -0.93 8 8
EGLN3 0.026 0.27 -10000 0 -0.93 8 8
CA9 0.009 0.27 -10000 0 -0.92 9 9
TERT 0.018 0.26 -10000 0 -0.96 7 7
ENO1 0.026 0.26 -10000 0 -0.93 8 8
PFKL 0.02 0.26 -10000 0 -0.93 8 8
NCOA1 0.028 0.005 -10000 0 -10000 0 0
ADM 0.024 0.27 -10000 0 -0.97 8 8
ARNT 0.026 0.064 -10000 0 -10000 0 0
HNF4A -0.043 0.21 -10000 0 -0.64 31 31
ADFP 0.015 0.26 -10000 0 -0.9 9 9
SLC2A1 0.057 0.21 0.49 2 -0.65 2 4
LEP -0.01 0.24 -10000 0 -0.93 7 7
HIF1A/ARNT/Cbp/p300 0.075 0.25 -10000 0 -0.71 6 6
EPO -0.001 0.2 -10000 0 -0.74 5 5
CREBBP 0.037 0.068 -10000 0 -0.32 1 1
HIF1A/ARNT/Cbp/p300/HDAC7 0.086 0.25 -10000 0 -0.74 2 2
PFKFB3 0.027 0.26 -10000 0 -0.93 8 8
NT5E 0.027 0.27 -10000 0 -0.96 8 8
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.026 0.024 -10000 0 -10000 0 0
CRKL 0.026 0.13 0.3 3 -0.43 13 16
mol:PIP3 0.002 0.012 -10000 0 -10000 0 0
AKT1 0.012 0.053 -10000 0 -10000 0 0
PTK2B 0.027 0.006 -10000 0 -10000 0 0
RAPGEF1 0.027 0.12 0.33 2 -0.41 12 14
RANBP10 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.023 0.087 -10000 0 -0.42 9 9
MAP3K5 0.033 0.12 0.34 6 -0.42 8 14
HGF/MET/CIN85/CBL/ENDOPHILINS 0.037 0.084 -10000 0 -0.38 9 9
AP1 -0.007 0.15 -10000 0 -0.38 36 36
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
apoptosis -0.1 0.34 -10000 0 -0.78 51 51
STAT3 (dimer) 0.006 0.061 -10000 0 -0.36 1 1
GAB1/CRKL/SHP2/PI3K 0.053 0.12 -10000 0 -0.43 7 7
INPP5D 0.024 0.02 -10000 0 -10000 0 0
CBL/CRK 0.05 0.14 0.41 9 -0.41 13 22
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.027 0.007 -10000 0 -10000 0 0
PTEN 0.028 0.004 -10000 0 -10000 0 0
ELK1 0.088 0.16 0.34 76 -10000 0 76
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.003 0.049 -10000 0 -0.25 2 2
PAK1 0.011 0.05 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.022 0.084 -10000 0 -0.36 11 11
HRAS -0.008 0.1 -10000 0 -0.47 5 5
DOCK1 0.025 0.12 0.3 4 -0.41 13 17
GAB1 0.021 0.13 -10000 0 -0.45 13 13
CRK 0.034 0.14 0.42 7 -0.43 13 20
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.12 -10000 0 -0.5 11 11
JUN 0.026 0.007 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0 0.044 -10000 0 -0.23 9 9
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
cell morphogenesis 0.031 0.11 0.39 5 -10000 0 5
GRB2/SHC 0.049 0.069 -10000 0 -0.26 1 1
FOS -0.065 0.22 -10000 0 -0.59 43 43
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.087 0.16 0.34 76 -10000 0 76
HGF/MET/MUC20 0.01 0.082 -10000 0 -0.38 11 11
cell migration 0.023 0.049 -10000 0 -0.26 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
CBL 0.027 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.027 0.024 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.012 0.057 -10000 0 -0.29 7 7
MET/MUC20 0.013 0.015 -10000 0 -10000 0 0
RAP1B 0.031 0.13 0.38 9 -0.42 6 15
RAP1A 0.025 0.11 0.32 2 -0.4 6 8
HGF/MET/RANBP9 0.021 0.086 -10000 0 -0.41 9 9
RAF1 0.018 0.12 0.32 3 -0.54 2 5
STAT3 0.006 0.061 -10000 0 -0.36 1 1
cell proliferation 0.026 0.092 0.26 1 -0.38 6 7
RPS6KB1 0.007 0.026 -10000 0 -0.28 1 1
MAPK3 0.058 0.15 0.49 9 -10000 0 9
MAPK1 0.11 0.23 0.64 31 -10000 0 31
RANBP9 0.027 0.006 -10000 0 -10000 0 0
MAPK8 0.04 0.15 0.46 10 -0.52 6 16
SRC 0.003 0.054 -10000 0 -0.34 1 1
PI3K 0.05 0.068 -10000 0 -10000 0 0
MET/Glomulin 0.008 0.031 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K1 0.026 0.12 0.35 5 -0.5 2 7
MET 0.018 0.023 -10000 0 -10000 0 0
MAP4K1 0.036 0.13 0.36 6 -0.42 13 19
PTK2 0.027 0.004 -10000 0 -10000 0 0
MAP2K2 0.025 0.12 0.34 6 -0.5 2 8
BAD 0.011 0.05 -10000 0 -10000 0 0
MAP2K4 0.04 0.14 0.39 15 -0.4 6 21
SHP2/GRB2/SOS1/GAB1 0.014 0.097 -10000 0 -0.4 7 7
INPPL1 0.028 0.003 -10000 0 -10000 0 0
PXN 0.027 0.005 -10000 0 -10000 0 0
SH3KBP1 0.028 0.002 -10000 0 -10000 0 0
HGS -0.002 0.038 -10000 0 -0.21 8 8
PLCgamma1/PKC 0.02 0.005 -10000 0 -10000 0 0
HGF -0.004 0.13 -10000 0 -0.64 11 11
RASA1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.027 0.006 -10000 0 -10000 0 0
PTPRJ 0.028 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 0.026 0.053 -10000 0 -0.23 8 8
PDPK1 0.015 0.057 -10000 0 -10000 0 0
HGF/MET/SHIP 0.019 0.087 -10000 0 -0.38 11 11
Presenilin action in Notch and Wnt signaling

Figure 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
Delta 1/NOTCH/NOTCH(cleaved) 0.001 0.13 -10000 0 -0.5 4 4
HDAC1 0.024 0.007 -10000 0 -10000 0 0
AES 0.027 0.003 -10000 0 -10000 0 0
FBXW11 0.027 0.005 -10000 0 -10000 0 0
DTX1 0.013 0.095 -10000 0 -0.64 6 6
LRP6/FZD1 0.031 0.019 -10000 0 -10000 0 0
TLE1 0.026 0.006 -10000 0 -10000 0 0
AP1 -0.11 0.2 -10000 0 -0.37 96 96
NCSTN 0.027 0.005 -10000 0 -10000 0 0
ADAM10 0.027 0.007 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.035 0.067 -10000 0 -0.55 1 1
NICD/RBPSUH 0.025 0.093 -10000 0 -0.39 2 2
WIF1 0.009 0.025 -10000 0 -10000 0 0
NOTCH1 0.016 0.077 -10000 0 -0.39 9 9
PSENEN 0.028 0.002 -10000 0 -10000 0 0
KREMEN2 0.013 0.032 -10000 0 -10000 0 0
DKK1 0.014 0.028 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.064 0.11 0.32 3 -10000 0 3
APH1B 0.025 0.039 -10000 0 -0.64 1 1
APH1A 0.027 0.005 -10000 0 -10000 0 0
AXIN1 -0.005 0.052 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.011 0.053 -10000 0 -0.39 4 4
PSEN1 0.027 0.007 -10000 0 -10000 0 0
FOS -0.065 0.22 -10000 0 -0.59 43 43
JUN 0.026 0.007 -10000 0 -10000 0 0
MAP3K7 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.054 0.11 0.28 8 -0.29 2 10
MAPK3 0.026 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.038 0.042 -10000 0 -0.42 1 1
HNF1A 0.017 0.078 -10000 0 -0.64 4 4
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC 0.019 0.098 -10000 0 -0.79 4 4
NKD1 -0.15 0.29 -10000 0 -0.64 76 76
FZD1 0.022 0.014 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.016 0.11 -10000 0 -0.41 9 9
apoptosis -0.11 0.2 -10000 0 -0.37 96 96
Delta 1/NOTCHprecursor -0.001 0.13 -10000 0 -0.5 4 4
DLL1 -0.023 0.17 -10000 0 -0.58 23 23
PPARD -0.011 0.18 -10000 0 -0.78 15 15
Gamma Secretase 0.076 0.036 -10000 0 -0.36 1 1
APC -0.01 0.078 -10000 0 -0.57 3 3
DVL1 0.016 0.018 -10000 0 -10000 0 0
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.036 0.035 -10000 0 -10000 0 0
LRP6 0.027 0.006 -10000 0 -10000 0 0
CSNK1A1 0.028 0.004 -10000 0 -10000 0 0
NLK 0.011 0.005 -10000 0 -10000 0 0
CCND1 0.018 0.12 -10000 0 -0.96 4 4
WNT1 0.012 0.033 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.053 0.1 0.37 8 -0.49 2 10
DKK2 0.021 0.042 -10000 0 -0.64 1 1
NOTCH1 precursor/DVL1 0.016 0.12 -10000 0 -0.5 8 8
GSK3B 0.027 0.006 -10000 0 -10000 0 0
FRAT1 0.027 0.004 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.019 0.11 -10000 0 -0.5 3 3
PPP2R5D 0.083 0.16 0.32 72 -0.35 12 84
MAPK1 0.026 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.046 0.036 -10000 0 -10000 0 0
RBPJ 0.027 0.006 -10000 0 -10000 0 0
CREBBP 0.028 0.009 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.031 0.019 -10000 0 -10000 0 0
VLDLR 0.027 0.007 -10000 0 -10000 0 0
CRKL 0.026 0.007 -10000 0 -10000 0 0
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
ITGA3 0.021 0.024 -10000 0 -10000 0 0
RELN/VLDLR/Fyn -0.004 0.1 -10000 0 -0.41 15 15
MAPK8IP1/MKK7/MAP3K11/JNK1 0.071 0.058 -10000 0 -0.36 4 4
AKT1 -0.012 0.066 -10000 0 -0.29 15 15
MAP2K7 0.028 0.002 -10000 0 -10000 0 0
RAPGEF1 0.027 0.006 -10000 0 -10000 0 0
DAB1 -0.002 0.025 -10000 0 -10000 0 0
RELN/LRP8/DAB1 -0.008 0.094 -10000 0 -0.37 15 15
LRPAP1/LRP8 0.038 0.015 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.007 0.093 -10000 0 -0.37 14 14
DAB1/alpha3/beta1 Integrin 0.017 0.088 -10000 0 -0.35 14 14
long-term memory -0.054 0.17 -10000 0 -0.38 52 52
DAB1/LIS1 0.028 0.094 -10000 0 -0.35 14 14
DAB1/CRLK/C3G 0.019 0.087 -10000 0 -0.34 14 14
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
DAB1/NCK2 0.029 0.095 -10000 0 -0.36 14 14
ARHGEF2 0.027 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.12 0.27 -10000 0 -0.64 61 61
CDK5R1 0.026 0.009 -10000 0 -10000 0 0
RELN -0.036 0.15 -10000 0 -0.64 15 15
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
RELN/LRP8/Fyn -0.005 0.1 -10000 0 -0.42 14 14
GRIN2A/RELN/LRP8/DAB1/Fyn -0.05 0.18 -10000 0 -0.39 53 53
MAPK8 0.017 0.081 -10000 0 -0.58 5 5
RELN/VLDLR/DAB1 -0.008 0.095 -10000 0 -0.38 15 15
ITGB1 0.027 0.005 -10000 0 -10000 0 0
MAP1B 0.01 0.11 -10000 0 -0.37 14 14
RELN/LRP8 -0.004 0.1 -10000 0 -0.4 15 15
GRIN2B/RELN/LRP8/DAB1/Fyn 0.024 0.097 -10000 0 -0.37 14 14
PI3K 0.04 0.009 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.033 0.023 -10000 0 -10000 0 0
RAP1A 0.006 0.11 0.33 1 -0.35 1 2
PAFAH1B1 0.026 0.008 -10000 0 -10000 0 0
MAPK8IP1 0.028 0.004 -10000 0 -10000 0 0
CRLK/C3G 0.037 0.013 -10000 0 -10000 0 0
GRIN2B 0.004 0.025 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
neuron differentiation 0.014 0.083 -10000 0 -0.36 6 6
neuron adhesion 0.014 0.12 0.32 12 -10000 0 12
LRP8 0.025 0.014 -10000 0 -10000 0 0
GSK3B -0.015 0.063 -10000 0 -0.28 14 14
RELN/VLDLR/DAB1/Fyn 0.006 0.094 -10000 0 -0.36 15 15
MAP3K11 0.028 0.002 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.007 0.073 -10000 0 -0.3 15 15
CDK5 0.022 0.012 -10000 0 -10000 0 0
MAPT 0.016 0.2 0.69 16 -0.58 10 26
neuron migration 0.015 0.12 0.36 2 -0.37 14 16
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.014 0.083 -10000 0 -0.36 6 6
RELN/VLDLR 0.022 0.098 -10000 0 -0.38 14 14
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.023 0.077 -10000 0 -10000 0 0
VDR 0.018 0.078 -10000 0 -0.64 4 4
FAM120B 0.027 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.037 0.035 -10000 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.036 0.053 -10000 0 -0.38 3 3
MED1 0.026 0.007 -10000 0 -10000 0 0
mol:9cRA 0.004 0.006 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.018 0.058 -10000 0 -0.28 10 10
RXRs/NUR77 -0.11 0.22 -10000 0 -0.38 114 114
RXRs/PPAR 0.028 0.018 -10000 0 -10000 0 0
NCOR2 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.013 0.058 -10000 0 -0.48 4 4
RARs/VDR/DNA/Vit D3 0.054 0.05 -10000 0 -0.36 3 3
RARA 0.026 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.005 -10000 0 -10000 0 0
VDR/VDR/DNA 0.018 0.078 -10000 0 -0.64 4 4
RARs/RARs/DNA/9cRA 0.046 0.019 -10000 0 -10000 0 0
RARG 0.027 0.008 -10000 0 -10000 0 0
RPS6KB1 0.043 0.13 0.53 20 -10000 0 20
RARs/THRs/DNA/SMRT 0.018 0.06 -10000 0 -0.28 11 11
THRA 0.026 0.007 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.013 0.058 -10000 0 -0.48 4 4
RXRs/PPAR/9cRA/PGJ2/DNA 0.054 0.029 -10000 0 -10000 0 0
NR1H4 0.018 0.078 -10000 0 -0.64 4 4
RXRs/LXRs/DNA 0.084 0.044 -10000 0 -10000 0 0
NR1H2 0.031 0.009 -10000 0 -10000 0 0
NR1H3 0.031 0.01 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.055 0.058 -10000 0 -0.37 4 4
NR4A1 -0.24 0.33 -10000 0 -0.64 115 115
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.012 0.06 -10000 0 -0.32 8 8
RXRG 0.021 0.014 -10000 0 -10000 0 0
RXR alpha/CCPG 0.04 0.014 -10000 0 -10000 0 0
RXRA 0.029 0.011 -10000 0 -10000 0 0
RXRB 0.03 0.011 -10000 0 -10000 0 0
THRB 0.001 0.13 -10000 0 -0.64 11 11
PPARG 0.026 0.009 -10000 0 -10000 0 0
PPARD 0.027 0.006 -10000 0 -10000 0 0
TNF 0.021 0.12 -10000 0 -1.1 3 3
mol:Oxysterols 0.004 0.005 -10000 0 -10000 0 0
cholesterol transport 0.035 0.057 -10000 0 -0.38 3 3
PPARA 0.026 0.008 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.027 0.006 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 -0.11 0.17 -10000 0 -0.31 114 114
SREBF1 0.026 0.049 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.055 0.029 -10000 0 -10000 0 0
ABCA1 0.032 0.045 -10000 0 -10000 0 0
RARs/THRs 0.057 0.088 -10000 0 -0.36 11 11
RXRs/FXR 0.061 0.055 -10000 0 -0.36 3 3
BCL2 0.026 0.008 -10000 0 -10000 0 0
EPHB forward 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
Ephrin A5/EPHB2 0.001 0.12 -10000 0 -0.41 21 21
cell-cell adhesion 0.022 0.055 -10000 0 -10000 0 0
Ephrin B/EPHB2/RasGAP 0.053 0.08 -10000 0 -0.36 8 8
ITSN1 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.083 0.2 -10000 0 -0.41 77 77
Ephrin B1/EPHB1 0.029 0.048 -10000 0 -0.41 3 3
HRAS/GDP 0.008 0.074 -10000 0 -0.35 1 1
Ephrin B/EPHB1/GRB7 0.051 0.09 -10000 0 -0.36 11 11
Endophilin/SYNJ1 0.006 0.074 -10000 0 -0.34 9 9
KRAS 0.027 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.05 0.091 -10000 0 -0.36 11 11
endothelial cell migration 0.044 0.027 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.026 0.007 -10000 0 -10000 0 0
PAK1 -0.005 0.089 0.35 6 -0.35 8 14
HRAS 0.028 0.003 -10000 0 -10000 0 0
RRAS 0.008 0.078 -10000 0 -0.35 9 9
DNM1 -0.008 0.061 -10000 0 -0.64 1 1
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.004 0.077 0.35 1 -0.35 11 12
lamellipodium assembly -0.022 0.055 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.06 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
EPHB2 0.024 0.015 -10000 0 -10000 0 0
EPHB3 -0.15 0.3 -10000 0 -0.64 77 77
EPHB1 0.017 0.07 -10000 0 -0.64 3 3
EPHB4 0.022 0.012 -10000 0 -10000 0 0
mol:GDP 0.039 0.12 0.35 21 -0.36 5 26
Ephrin B/EPHB2 0.04 0.077 -10000 0 -0.36 9 9
Ephrin B/EPHB3 -0.065 0.2 -10000 0 -0.38 77 77
JNK cascade 0.016 0.069 0.35 8 -0.36 3 11
Ephrin B/EPHB1 0.037 0.086 -10000 0 -0.36 11 11
RAP1/GDP 0.075 0.13 0.34 19 -10000 0 19
EFNB2 0.027 0.006 -10000 0 -10000 0 0
EFNB3 -0.004 0.12 -10000 0 -0.61 10 10
EFNB1 0.028 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.04 0.049 -10000 0 -0.38 3 3
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.021 0.081 -10000 0 -10000 0 0
Rap1/GTP 0.007 0.066 -10000 0 -10000 0 0
axon guidance 0 0.12 -10000 0 -0.41 21 21
MAPK3 0.003 0.054 -10000 0 -10000 0 0
MAPK1 0.003 0.055 -10000 0 -10000 0 0
Rac1/GDP 0.024 0.097 0.32 3 -0.35 1 4
actin cytoskeleton reorganization -0.008 0.05 -10000 0 -10000 0 0
CDC42/GDP 0.072 0.13 0.35 21 -0.35 1 22
PI3K 0.049 0.03 -10000 0 -10000 0 0
EFNA5 -0.022 0.17 -10000 0 -0.64 21 21
Ephrin B2/EPHB4 0.028 0.017 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.007 0.062 -10000 0 -0.46 1 1
CDC42 0.026 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.066 -10000 0 -10000 0 0
PTK2 -0.002 0.045 0.52 2 -10000 0 2
MAP4K4 0.016 0.07 0.36 8 -0.36 3 11
SRC 0.026 0.009 -10000 0 -10000 0 0
KALRN 0.027 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.03 0.019 -10000 0 -10000 0 0
neuron projection morphogenesis 0.059 0.15 0.36 48 -10000 0 48
MAP2K1 0.007 0.057 -10000 0 -10000 0 0
WASL 0.022 0.012 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.057 0.052 -10000 0 -0.38 3 3
cell migration 0.035 0.12 0.43 11 -10000 0 11
NRAS 0.027 0.006 -10000 0 -10000 0 0
SYNJ1 0.006 0.075 -10000 0 -0.34 9 9
PXN 0.027 0.005 -10000 0 -10000 0 0
TF -0.018 0.074 -10000 0 -0.34 10 10
HRAS/GTP 0.031 0.076 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2 0.04 0.05 -10000 0 -0.38 3 3
cell adhesion mediated by integrin 0.051 0.1 0.4 9 -10000 0 9
RAC1 0.022 0.012 -10000 0 -10000 0 0
mol:GTP 0.033 0.079 -10000 0 -0.34 10 10
RAC1-CDC42/GTP -0.076 0.14 -10000 0 -0.56 5 5
RASA1 0.027 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.032 0.096 0.32 3 -10000 0 3
ruffle organization 0.04 0.15 0.33 50 -10000 0 50
NCK1 0.027 0.006 -10000 0 -10000 0 0
receptor internalization -0.02 0.073 -10000 0 -0.36 1 1
Ephrin B/EPHB2/KALRN 0.053 0.08 -10000 0 -0.36 8 8
ROCK1 -0.086 0.18 -10000 0 -0.38 76 76
RAS family/GDP -0.011 0.05 -10000 0 -10000 0 0
Rac1/GTP -0.002 0.064 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src/Paxillin 0.012 0.063 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.006 0.006 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.032 0.021 -10000 0 -10000 0 0
STXBP1 0.027 0.006 -10000 0 -10000 0 0
ACh/CHRNA1 -0.007 0.043 -10000 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0.045 0.024 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.003 0.029 -10000 0 -10000 0 0
mol:ACh 0.019 0.045 0.093 61 -0.14 1 62
RAB3GAP2 0.027 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.028 0.036 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.007 0.043 -10000 0 -10000 0 0
UNC13B 0.027 0.005 -10000 0 -10000 0 0
CHRNA1 -0.049 0.045 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.1 0.21 -10000 0 -0.42 83 83
SNAP25 -0.007 0.023 -10000 0 -0.32 1 1
VAMP2 0.005 0.001 -10000 0 -10000 0 0
SYT1 -0.17 0.3 -10000 0 -0.64 83 83
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.019 0.013 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.028 0.036 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.022 0.15 -10000 0 -0.51 22 22
KLHL20 0.018 0.085 0.2 2 -0.29 2 4
CYFIP2 0.025 0.039 -10000 0 -0.64 1 1
Rac1/GDP -0.003 0.11 0.32 5 -0.34 6 11
ENAH -0.024 0.15 -10000 0 -0.51 22 22
AP1M1 0.028 0.002 -10000 0 -10000 0 0
RAP1B 0.027 0.006 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
CTNNB1 0.027 0.006 -10000 0 -10000 0 0
CDC42/GTP 0.005 0.078 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.016 0.041 -10000 0 -0.19 2 2
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.026 0.12 -10000 0 -0.38 21 21
RAPGEF1 -0.019 0.13 -10000 0 -0.45 21 21
CTNND1 0.028 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.018 0.16 -10000 0 -0.53 22 22
CRK -0.024 0.14 -10000 0 -0.48 21 21
E-cadherin/gamma catenin/alpha catenin 0.014 0.12 -10000 0 -0.41 22 22
alphaE/beta7 Integrin 0.038 0.013 -10000 0 -10000 0 0
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
NCKAP1 0.028 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.048 0.018 -10000 0 -10000 0 0
DLG1 -0.024 0.15 -10000 0 -0.51 22 22
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.009 0.054 -10000 0 -10000 0 0
MLLT4 0.027 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.044 0.022 -10000 0 -10000 0 0
PI3K -0.007 0.07 -10000 0 -10000 0 0
ARF6 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.002 0.14 -10000 0 -0.47 22 22
TIAM1 0.026 0.007 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.026 0.11 -10000 0 -0.36 22 22
AKT1 0 0.046 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
CDH1 -0.025 0.18 -10000 0 -0.64 22 22
RhoA/GDP 0.01 0.12 0.4 5 -0.34 6 11
actin cytoskeleton organization 0.022 0.072 0.18 10 -0.21 2 12
CDC42/GDP 0.02 0.14 0.44 11 -0.34 3 14
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.004 0.081 -10000 0 -0.29 21 21
ITGB7 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.029 0.12 -10000 0 -0.38 22 22
E-cadherin/Ca2+/beta catenin/alpha catenin 0.013 0.11 -10000 0 -0.36 22 22
mol:GDP 0.002 0.15 0.48 10 -0.38 21 31
CDC42/GTP/IQGAP1 0.035 0.011 -10000 0 -10000 0 0
JUP 0.026 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.011 0.12 0.32 2 -0.35 5 7
RAC1/GTP/IQGAP1 0.029 0.016 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.041 0.004 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
CDC42 0.026 0.008 -10000 0 -10000 0 0
CTNNA1 0.027 0.005 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.028 0.074 0.25 14 -0.27 1 15
NME1 0.025 0.012 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.024 0.15 -10000 0 -0.51 22 22
regulation of cell-cell adhesion 0 0.066 -10000 0 -10000 0 0
WASF2 0.012 0.033 -10000 0 -10000 0 0
Rap1/GTP 0.008 0.091 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.037 0.12 -10000 0 -0.36 21 21
CCND1 0.027 0.071 0.22 11 -0.34 1 12
VAV2 -0.033 0.19 -10000 0 -0.56 18 18
RAP1/GDP 0.016 0.1 0.36 2 -10000 0 2
adherens junction assembly -0.022 0.14 -10000 0 -0.5 22 22
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.028 0.003 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.024 0.11 -10000 0 -0.35 21 21
E-cadherin/beta catenin -0.021 0.11 -10000 0 -0.42 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.024 0.15 -10000 0 -0.51 22 22
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
Rac1/GTP -0.023 0.1 -10000 0 -0.41 4 4
E-cadherin/beta catenin/alpha catenin 0.014 0.12 -10000 0 -0.42 22 22
ITGAE 0.026 0.008 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.019 0.16 -10000 0 -0.54 22 22
Regulation of Telomerase

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
Telomerase catalytic core complex -0.15 0.13 0.36 1 -0.57 8 9
RAD9A 0.028 0.007 -10000 0 -10000 0 0
AP1 -0.031 0.17 -10000 0 -0.48 36 36
IFNAR2 0.026 0.008 -10000 0 -10000 0 0
AKT1 0.004 0.055 -10000 0 -0.23 13 13
ER alpha/Oestrogen -0.005 0.11 -10000 0 -0.42 17 17
NFX1/SIN3/HDAC complex 0.014 0.086 -10000 0 -0.35 11 11
EGF -0.56 0.21 -10000 0 -0.63 258 258
SMG5 0.027 0.005 -10000 0 -10000 0 0
SMG6 0.026 0.008 -10000 0 -10000 0 0
SP3/HDAC2 0.04 0.01 -10000 0 -10000 0 0
TERT/c-Abl -0.14 0.12 -10000 0 -0.57 6 6
SAP18 0.027 0.006 -10000 0 -10000 0 0
MRN complex 0.051 0.031 -10000 0 -0.42 1 1
WT1 -0.34 0.33 -10000 0 -0.63 159 159
WRN 0.027 0.006 -10000 0 -10000 0 0
SP1 0.027 0.006 -10000 0 -10000 0 0
SP3 0.028 0.004 -10000 0 -10000 0 0
TERF2IP 0.026 0.008 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.13 0.12 -10000 0 -0.58 4 4
Mad/Max 0.039 0.012 -10000 0 -10000 0 0
TERT -0.15 0.13 0.37 1 -0.58 8 9
CCND1 -0.14 0.13 -10000 0 -0.88 3 3
MAX 0.027 0.007 -10000 0 -10000 0 0
RBBP7 0.028 0.002 -10000 0 -10000 0 0
RBBP4 0.026 0.007 -10000 0 -10000 0 0
TERF2 0.023 0.01 -10000 0 -10000 0 0
PTGES3 0.027 0.005 -10000 0 -10000 0 0
SIN3A 0.028 0.004 -10000 0 -10000 0 0
Telomerase/911 0.021 0.038 -10000 0 -10000 0 0
CDKN1B 0.017 0.016 -10000 0 -10000 0 0
RAD1 0.028 0.004 -10000 0 -10000 0 0
XRCC5 0.027 0.005 -10000 0 -10000 0 0
XRCC6 0.026 0.008 -10000 0 -10000 0 0
SAP30 0.026 0.011 -10000 0 -10000 0 0
TRF2/PARP2 0.035 0.015 -10000 0 -10000 0 0
UBE3A 0.027 0.005 -10000 0 -10000 0 0
JUN 0.027 0.007 -10000 0 -10000 0 0
E6 0 0.001 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.004 -10000 0 -10000 0 0
FOS -0.065 0.22 -10000 0 -0.59 43 43
IFN-gamma/IRF1 0.038 0.024 -10000 0 -10000 0 0
PARP2 0.026 0.007 -10000 0 -10000 0 0
BLM 0.02 0.027 -10000 0 -10000 0 0
Telomerase -0.027 0.12 -10000 0 -0.63 7 7
IRF1 0.031 0.005 -10000 0 -10000 0 0
ESR1 -0.008 0.14 -10000 0 -0.56 17 17
KU/TER 0.038 0.012 -10000 0 -10000 0 0
ATM/TRF2 0.038 0.013 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.018 0.081 -10000 0 -0.39 6 6
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.018 0.083 -10000 0 -0.4 6 6
HDAC1 0.026 0.007 -10000 0 -10000 0 0
HDAC2 0.027 0.006 -10000 0 -10000 0 0
ATM 0.01 0.003 -10000 0 -10000 0 0
SMAD3 0.013 0.006 -10000 0 -10000 0 0
ABL1 0.027 0.006 -10000 0 -10000 0 0
MXD1 0.028 0.004 -10000 0 -10000 0 0
MRE11A 0.027 0.005 -10000 0 -10000 0 0
HUS1 0.022 0.012 -10000 0 -10000 0 0
RPS6KB1 0.026 0.008 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.11 0.13 -10000 0 -0.56 8 8
NR2F2 0.027 0.004 -10000 0 -10000 0 0
MAPK3 -0.004 0.013 -10000 0 -10000 0 0
MAPK1 -0.004 0.014 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.027 0.009 -10000 0 -10000 0 0
NFKB1 0.027 0.006 -10000 0 -10000 0 0
HNRNPC 0.026 0.007 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.003 -10000 0 -10000 0 0
NBN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.022 0.012 -10000 0 -10000 0 0
mol:Oestrogen 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.37 0.17 -10000 0 -0.42 258 258
MYC 0.026 0.015 -10000 0 -10000 0 0
IL2 0.017 0.016 -10000 0 -10000 0 0
KU 0.038 0.012 -10000 0 -10000 0 0
RAD50 0.025 0.039 -10000 0 -0.64 1 1
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
TGFB1 0.027 0.009 -10000 0 -10000 0 0
TRF2/BLM 0.031 0.026 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.14 0.12 -10000 0 -0.63 4 4
SP1/HDAC2 0.039 0.012 -10000 0 -10000 0 0
PINX1 0.027 0.006 -10000 0 -10000 0 0
Telomerase/EST1A -0.13 0.12 -10000 0 -0.72 2 2
Smad3/Myc 0.029 0.012 -10000 0 -10000 0 0
911 complex 0.044 0.025 -10000 0 -10000 0 0
IFNG 0.02 0.026 -10000 0 -10000 0 0
Telomerase/PinX1 -0.13 0.12 -10000 0 -0.7 2 2
Telomerase/AKT1/mTOR/p70S6K -0.032 0.1 -10000 0 -0.52 7 7
SIN3B 0.028 0.002 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
Telomerase/EST1B -0.13 0.12 -10000 0 -0.62 3 3
response to DNA damage stimulus 0.001 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.068 0.038 -10000 0 -0.36 1 1
TRF2/WRN 0.036 0.014 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.13 0.12 -10000 0 -0.62 3 3
E2F1 -0.001 0.047 -10000 0 -10000 0 0
ZNFX1 0.027 0.007 -10000 0 -10000 0 0
PIF1 0.017 0.032 -10000 0 -10000 0 0
NCL 0.027 0.005 -10000 0 -10000 0 0
DKC1 0.028 0.002 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.002 0.1 -10000 0 -0.45 12 12
PDGFB-D/PDGFRB/SLAP 0.018 0.097 -10000 0 -0.48 10 10
PDGFB-D/PDGFRB/APS/CBL 0.028 0.081 -10000 0 -0.37 10 10
AKT1 0.023 0.14 0.51 17 -10000 0 17
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.004 0.12 -10000 0 -0.48 12 12
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
FGR -0.032 0.15 0.34 1 -0.41 33 34
mol:Ca2+ 0.008 0.13 0.3 6 -0.51 13 19
MYC 0.048 0.13 0.44 9 -0.41 2 11
SHC1 0.027 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.025 0.077 -10000 0 -0.34 10 10
LRP1/PDGFRB/PDGFB 0.033 0.09 -10000 0 -0.41 11 11
GRB10 0.022 0.012 -10000 0 -10000 0 0
PTPN11 0.027 0.005 -10000 0 -10000 0 0
GO:0007205 0.007 0.13 0.31 5 -0.52 13 18
PTEN 0.028 0.004 -10000 0 -10000 0 0
GRB2 0.026 0.007 -10000 0 -10000 0 0
GRB7 0.026 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.022 0.095 -10000 0 -0.48 10 10
PDGFB-D/PDGFRB/GRB10 0.017 0.085 -10000 0 -0.41 10 10
cell cycle arrest 0.018 0.097 -10000 0 -0.48 10 10
HRAS 0.028 0.003 -10000 0 -10000 0 0
HIF1A 0.021 0.14 0.49 17 -10000 0 17
GAB1 0.005 0.14 0.34 6 -0.48 13 19
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.006 0.12 0.33 9 -0.46 11 20
PDGFB-D/PDGFRB 0.035 0.088 -10000 0 -0.42 10 10
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.022 0.095 -10000 0 -0.48 10 10
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.003 0.093 -10000 0 -0.45 10 10
positive regulation of MAPKKK cascade 0.022 0.095 -10000 0 -0.48 10 10
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 0.007 0.14 0.32 5 -0.52 13 18
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.026 0.008 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.022 0.089 -10000 0 -0.43 10 10
SHB 0.027 0.005 -10000 0 -10000 0 0
BLK -0.013 0.11 -10000 0 -0.4 19 19
PTPN2 0.027 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.023 0.095 -10000 0 -0.48 10 10
BCAR1 0.026 0.008 -10000 0 -10000 0 0
VAV2 0.009 0.14 0.36 6 -0.48 12 18
CBL 0.027 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.023 0.095 -10000 0 -0.48 10 10
LCK -0.026 0.14 0.34 1 -0.41 29 30
PDGFRB 0.005 0.12 -10000 0 -0.64 10 10
ACP1 0.027 0.005 -10000 0 -10000 0 0
HCK -0.002 0.084 -10000 0 -0.4 11 11
ABL1 0.004 0.13 0.32 6 -0.44 14 20
PDGFB-D/PDGFRB/CBL 0.002 0.14 0.29 3 -0.54 14 17
PTPN1 0.027 0.007 -10000 0 -10000 0 0
SNX15 0.028 0.002 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
STAT1 0.026 0.014 -10000 0 -10000 0 0
cell proliferation 0.047 0.13 0.42 10 -0.38 2 12
SLA 0.023 0.023 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.03 0.086 0.34 7 -0.34 8 15
SRC 0.001 0.077 -10000 0 -0.39 10 10
PI3K 0.003 0.055 -10000 0 -0.33 7 7
PDGFB-D/PDGFRB/GRB7/SHC 0.037 0.081 -10000 0 -0.41 8 8
SH2B2 0.022 0.012 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.003 0.12 -10000 0 -0.5 12 12
LYN -0.004 0.09 -10000 0 -0.39 14 14
LRP1 0.027 0.005 -10000 0 -10000 0 0
SOS1 0.027 0.005 -10000 0 -10000 0 0
STAT5B 0.026 0.007 -10000 0 -10000 0 0
STAT5A 0.026 0.007 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.059 0.078 -10000 0 -0.35 8 8
SPHK1 -0.023 0.052 -10000 0 -10000 0 0
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.007 0.14 0.32 5 -0.52 13 18
PLCG1 0.006 0.14 0.32 5 -0.54 13 18
NHERF/PDGFRB 0.037 0.077 -10000 0 -0.41 7 7
YES1 -0.03 0.16 0.33 1 -0.51 27 28
cell migration 0.036 0.076 -10000 0 -0.41 7 7
SHC/Grb2/SOS1 0.057 0.079 -10000 0 -0.35 8 8
SLC9A3R2 0.026 0.008 -10000 0 -10000 0 0
SLC9A3R1 0.026 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.049 0.075 -10000 0 -0.38 7 7
FYN -0.011 0.11 -10000 0 -0.4 19 19
DOK1 0.008 0.081 -10000 0 -0.38 10 10
HRAS/GTP 0.021 0.002 -10000 0 -10000 0 0
PDGFB 0.024 0.04 -10000 0 -0.64 1 1
RAC1 0.046 0.15 0.42 11 -0.47 8 19
PRKCD 0.008 0.077 -10000 0 -0.38 9 9
FER 0.011 0.083 -10000 0 -0.38 10 10
MAPKKK cascade 0.003 0.1 0.41 9 -0.34 8 17
RASA1 0.011 0.083 -10000 0 -0.38 10 10
NCK1 0.027 0.006 -10000 0 -10000 0 0
NCK2 0.028 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.022 0.078 -10000 0 -0.36 10 10
PDGFB-D/PDGFRB/SHB 0.022 0.095 -10000 0 -0.48 10 10
chemotaxis 0.005 0.13 0.32 6 -0.43 14 20
STAT1-3-5/STAT1-3-5 0.047 0.071 -10000 0 -0.34 8 8
Bovine Papilomavirus E5/PDGFRB 0.003 0.091 -10000 0 -0.48 10 10
PTPRJ 0.028 0.004 -10000 0 -10000 0 0
Visual signal transduction: Rods

Figure S56.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S56.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.028 0.004 -10000 0 -10000 0 0
GNAT1/GTP 0.014 0.007 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.025 0.011 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.02 0.059 -10000 0 -0.41 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.007 0.02 -10000 0 -10000 0 0
GRK1 -0.008 0.02 -10000 0 -10000 0 0
CNG Channel -0.063 0.17 -10000 0 -0.35 68 68
mol:Na + -0.063 0.16 -10000 0 -0.35 60 60
mol:ADP -0.008 0.02 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.04 0.066 -10000 0 -0.42 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.056 0.17 -10000 0 -0.36 60 60
CNGB1 0.009 0.026 -10000 0 -10000 0 0
RDH5 0.015 0.061 -10000 0 -0.64 2 2
SAG -0.016 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.074 0.17 0.4 12 -0.35 34 46
Na + (4 Units) -0.063 0.15 -10000 0 -0.34 59 59
RGS9 0.013 0.08 -10000 0 -0.64 4 4
GNB1/GNGT1 0.02 0.027 -10000 0 -10000 0 0
GNAT1/GDP 0.043 0.061 -10000 0 -0.37 5 5
GUCY2D 0.005 0.036 -10000 0 -10000 0 0
GNGT1 0.001 0.031 -10000 0 -10000 0 0
GUCY2F -0.015 0.012 -10000 0 -10000 0 0
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) 0.01 0.058 -10000 0 -0.36 6 6
mol:11-cis-retinal 0.015 0.061 -10000 0 -0.64 2 2
mol:cGMP 0.027 0.037 -10000 0 -10000 0 0
GNB1 0.025 0.008 -10000 0 -10000 0 0
Rhodopsin 0.025 0.05 -10000 0 -0.48 2 2
SLC24A1 0.028 0.004 -10000 0 -10000 0 0
CNGA1 -0.15 0.29 -10000 0 -0.62 78 78
Metarhodopsin II 0.025 0.011 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.04 0.04 -10000 0 -10000 0 0
RGS9BP 0.024 0.04 -10000 0 -0.64 1 1
Metarhodopsin II/Transducin 0.005 0.024 -10000 0 -0.19 2 2
GCAP Family/Ca ++ 0.04 0.02 -10000 0 -10000 0 0
PDE6A/B 0.032 0.039 -10000 0 -0.36 2 2
mol:Pi 0.039 0.066 -10000 0 -0.42 5 5
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.025 0.029 -10000 0 -10000 0 0
PDE6B 0.023 0.046 -10000 0 -0.48 2 2
PDE6A 0.014 0.024 -10000 0 -10000 0 0
PDE6G 0.013 0.088 -10000 0 -0.64 5 5
RHO 0.003 0.024 -10000 0 -10000 0 0
PDE6 0.053 0.092 -10000 0 -0.39 10 10
GUCA1A -0.003 0.024 -10000 0 -10000 0 0
GC2/GCAP Family 0.05 0.024 -10000 0 -10000 0 0
GUCA1C 0.007 0.023 -10000 0 -10000 0 0
GUCA1B 0.026 0.009 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

Figure 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
HDAC1 0.013 0.005 -10000 0 -10000 0 0
SMARCC1 0.007 0.042 -10000 0 -0.65 1 1
REL 0.015 0.087 -10000 0 -0.64 5 5
HDAC7 -0.11 0.11 -10000 0 -0.46 3 3
JUN 0.026 0.007 -10000 0 -10000 0 0
EP300 0.026 0.008 -10000 0 -10000 0 0
KAT2B 0.027 0.006 -10000 0 -10000 0 0
KAT5 0.028 0.002 -10000 0 -10000 0 0
MAPK14 -0.015 0.025 -10000 0 -10000 0 0
FOXO1 0.027 0.006 -10000 0 -10000 0 0
T-DHT/AR -0.11 0.13 -10000 0 -0.48 3 3
MAP2K6 -0.005 0.025 -10000 0 -10000 0 0
BRM/BAF57 0.036 0.014 -10000 0 -10000 0 0
MAP2K4 -0.006 0.025 -10000 0 -10000 0 0
SMARCA2 0.026 0.007 -10000 0 -10000 0 0
PDE9A -0.18 0.21 -10000 0 -0.73 15 15
NCOA2 -0.033 0.19 -10000 0 -0.64 26 26
CEBPA 0.017 0.049 -10000 0 -0.64 1 1
EHMT2 0.027 0.006 -10000 0 -10000 0 0
cell proliferation -0.15 0.21 0.52 9 -0.49 36 45
NR0B1 -0.009 0.041 -10000 0 -10000 0 0
EGR1 -0.026 0.18 -10000 0 -0.64 23 23
RXRs/9cRA 0.044 0.016 -10000 0 -10000 0 0
AR/RACK1/Src -0.036 0.089 0.32 3 -0.39 3 6
AR/GR -0.014 0.091 0.24 8 -0.32 12 20
GNB2L1 0.027 0.005 -10000 0 -10000 0 0
PKN1 0.028 0.002 -10000 0 -10000 0 0
RCHY1 0.027 0.006 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.023 0.058 -10000 0 -0.4 5 5
T-DHT/AR/TIF2/CARM1 -0.058 0.16 0.33 6 -0.47 25 31
SRC -0.041 0.05 0.2 2 -0.39 2 4
NR3C1 0.027 0.004 -10000 0 -10000 0 0
KLK3 -0.064 0.16 -10000 0 -0.49 10 10
APPBP2 -0.005 0.026 -10000 0 -10000 0 0
TRIM24 0.022 0.012 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.04 0.095 0.34 4 -0.37 5 9
TMPRSS2 -0.75 0.53 -10000 0 -1.1 186 186
RXRG -0.003 0.022 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.027 0.006 -10000 0 -10000 0 0
RXRB 0.027 0.006 -10000 0 -10000 0 0
CARM1 0.028 0.003 -10000 0 -10000 0 0
NR2C2 0.021 0.059 -10000 0 -0.54 3 3
KLK2 -0.043 0.13 0.34 6 -0.52 5 11
AR -0.029 0.074 -10000 0 -0.33 14 14
SENP1 0.027 0.005 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
MDM2 0.027 0.006 -10000 0 -10000 0 0
SRY 0 0.001 -10000 0 -10000 0 0
GATA2 -0.1 0.26 -10000 0 -0.64 57 57
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.006 0.044 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.035 0.096 0.35 4 -0.4 3 7
positive regulation of transcription -0.1 0.26 -10000 0 -0.64 57 57
DNAJA1 -0.005 0.027 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.007 -10000 0 -10000 0 0
NCOA1 0.034 0.015 -10000 0 -10000 0 0
SPDEF 0.015 0.029 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.035 0.12 0.29 5 -0.45 8 13
T-DHT/AR/Hsp90 -0.036 0.094 0.29 8 -0.37 5 13
GSK3B 0.024 0.008 -10000 0 -10000 0 0
NR2C1 0.027 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.046 0.05 -10000 0 -0.42 2 2
SIRT1 0.028 0.004 -10000 0 -10000 0 0
ZMIZ2 0.022 0.012 -10000 0 -10000 0 0
POU2F1 -0.05 0.067 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.047 0.096 0.3 7 -0.38 5 12
CREBBP 0.026 0.008 -10000 0 -10000 0 0
SMARCE1 0.026 0.007 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.027 0.009 -10000 0 -10000 0 0
CCL5 0.015 0.032 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.03 0.12 0.25 2 -0.36 21 23
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.027 0.12 -10000 0 -0.59 5 5
Syndecan-1/Syntenin -0.023 0.12 -10000 0 -0.59 5 5
MAPK3 -0.023 0.11 0.22 1 -0.56 4 5
HGF/MET 0.01 0.094 -10000 0 -0.44 11 11
TGFB1/TGF beta receptor Type II 0.027 0.009 -10000 0 -10000 0 0
BSG 0.028 0.002 -10000 0 -10000 0 0
keratinocyte migration -0.026 0.11 -10000 0 -0.49 7 7
Syndecan-1/RANTES -0.027 0.12 -10000 0 -0.51 6 6
Syndecan-1/CD147 -0.006 0.12 -10000 0 -0.57 5 5
Syndecan-1/Syntenin/PIP2 -0.023 0.12 -10000 0 -0.57 5 5
LAMA5 0.026 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.023 0.11 -10000 0 -0.55 5 5
MMP7 -0.013 0.096 -10000 0 -0.64 5 5
HGF -0.004 0.13 -10000 0 -0.64 11 11
Syndecan-1/CASK -0.037 0.11 -10000 0 -0.34 22 22
Syndecan-1/HGF/MET -0.022 0.13 -10000 0 -0.48 11 11
regulation of cell adhesion -0.03 0.099 -10000 0 -0.55 4 4
HPSE -0.004 0.14 -10000 0 -0.64 13 13
positive regulation of cell migration -0.03 0.12 0.25 2 -0.36 21 23
SDC1 -0.031 0.12 -10000 0 -0.36 21 21
Syndecan-1/Collagen -0.03 0.12 0.25 2 -0.36 21 23
PPIB 0.028 0.004 -10000 0 -10000 0 0
MET 0.018 0.023 -10000 0 -10000 0 0
PRKACA 0.028 0.002 -10000 0 -10000 0 0
MMP9 -0.019 0.073 -10000 0 -0.64 2 2
MAPK1 -0.023 0.11 0.22 2 -0.54 5 7
homophilic cell adhesion -0.032 0.12 0.25 2 -0.35 21 23
MMP1 -0.023 0.16 -10000 0 -0.64 18 18
ceramide signaling pathway

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
MAP4K4 0.006 0.085 -10000 0 -0.41 6 6
BAG4 0.027 0.006 -10000 0 -10000 0 0
BAD 0.01 0.044 0.2 6 -0.18 1 7
NFKBIA 0.027 0.007 -10000 0 -10000 0 0
BIRC3 0.02 0.028 -10000 0 -10000 0 0
BAX 0.01 0.044 0.2 6 -0.18 1 7
EnzymeConsortium:3.1.4.12 0.009 0.032 0.13 8 -0.09 6 14
IKBKB 0.011 0.088 0.27 2 -0.38 6 8
MAP2K2 0.019 0.077 0.26 20 -10000 0 20
MAP2K1 0.02 0.076 0.26 19 -10000 0 19
SMPD1 0.01 0.036 0.15 6 -0.15 3 9
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.013 0.085 -10000 0 -0.38 5 5
MAP2K4 0.019 0.074 0.29 15 -10000 0 15
protein ubiquitination 0.015 0.098 0.34 5 -0.4 6 11
EnzymeConsortium:2.7.1.37 0.022 0.089 0.31 19 -10000 0 19
response to UV 0 0.001 0.004 20 -10000 0 20
RAF1 0.022 0.079 0.27 20 -10000 0 20
CRADD 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide 0.012 0.046 0.2 7 -0.16 2 9
I-kappa-B-alpha/RELA/p50/ubiquitin 0.036 0.009 -10000 0 -10000 0 0
MADD 0.028 0.004 -10000 0 -10000 0 0
MAP3K1 0.012 0.05 0.25 6 -10000 0 6
TRADD 0.026 0.008 -10000 0 -10000 0 0
RELA/p50 0.028 0.002 -10000 0 -10000 0 0
MAPK3 0.022 0.074 0.25 20 -10000 0 20
MAPK1 0.015 0.081 0.26 19 -10000 0 19
p50/RELA/I-kappa-B-alpha 0.039 0.01 -10000 0 -10000 0 0
FADD 0.006 0.081 -10000 0 -0.38 6 6
KSR1 0.02 0.069 0.26 17 -0.18 1 18
MAPK8 0.012 0.077 0.28 14 -0.28 3 17
TRAF2 0.027 0.006 -10000 0 -10000 0 0
response to radiation 0 0.001 0.005 7 -10000 0 7
CHUK 0.014 0.089 0.28 3 -0.39 6 9
TNF R/SODD 0.038 0.012 -10000 0 -10000 0 0
TNF 0.015 0.071 -10000 0 -0.64 3 3
CYCS 0.026 0.055 0.2 11 -10000 0 11
IKBKG 0.013 0.091 0.28 3 -0.39 6 9
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.009 0.086 -10000 0 -0.43 6 6
RELA 0.028 0.002 -10000 0 -10000 0 0
RIPK1 0.027 0.006 -10000 0 -10000 0 0
AIFM1 0.012 0.043 0.18 7 -10000 0 7
TNF/TNF R/SODD 0.041 0.054 -10000 0 -0.42 3 3
TNFRSF1A 0.027 0.006 -10000 0 -10000 0 0
response to heat 0 0.001 0.005 7 -10000 0 7
CASP8 0.021 0.082 -10000 0 -0.51 6 6
NSMAF 0.006 0.081 -10000 0 -0.4 5 5
response to hydrogen peroxide 0 0.001 0.004 20 -10000 0 20
BCL2 0.026 0.008 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

Figure 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
RIP1/MEKK3 0.033 0.013 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.027 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.026 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.026 0.008 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.013 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.026 0.008 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.026 0.008 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
MAP3K12 0.027 0.005 -10000 0 -10000 0 0
FGR 0.02 0.044 -10000 0 -0.64 1 1
p38 alpha/TAB1 -0.026 0.084 -10000 0 -0.38 12 12
PRKG1 -0.14 0.28 -10000 0 -0.63 73 73
DUSP8 0.028 0.004 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha -0.048 0.16 -10000 0 -0.32 58 58
apoptosis -0.025 0.08 -10000 0 -0.36 12 12
RAL/GTP 0.03 0.016 -10000 0 -10000 0 0
LYN 0.027 0.005 -10000 0 -10000 0 0
DUSP1 0.025 0.039 -10000 0 -0.64 1 1
PAK1 0.028 0.003 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.052 0.033 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.022 0.012 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.027 0.018 -10000 0 -10000 0 0
MAPK11 0.051 0.15 0.36 22 -0.43 10 32
BLK 0.016 0.027 -10000 0 -10000 0 0
HCK 0.013 0.051 -10000 0 -0.64 1 1
MAP2K3 0.026 0.008 -10000 0 -10000 0 0
DUSP16 0.027 0.006 -10000 0 -10000 0 0
DUSP10 0.018 0.03 -10000 0 -10000 0 0
TRAF6/MEKK3 0.033 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.045 0.14 0.35 18 -0.46 9 27
positive regulation of innate immune response 0.059 0.18 0.42 21 -0.48 11 32
LCK 0.024 0.018 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.054 0.15 0.35 14 -0.49 9 23
p38alpha-beta/MKP5 0.065 0.17 0.41 19 -0.48 9 28
PGK/cGMP -0.1 0.21 -10000 0 -0.47 73 73
PAK2 0.027 0.006 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.061 0.16 0.4 16 -0.49 9 25
CDC42 0.026 0.008 -10000 0 -10000 0 0
RALB 0.028 0.003 -10000 0 -10000 0 0
RALA 0.022 0.012 -10000 0 -10000 0 0
PAK3 0.018 0.02 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.1 0.1 -10000 0 -0.48 2 2
epithelial cell differentiation -0.15 0.17 -10000 0 -0.4 34 34
ITCH 0.055 0.023 -10000 0 -10000 0 0
WWP1 -0.086 0.078 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.022 0.012 -10000 0 -10000 0 0
PRL -0.011 0.016 -10000 0 -10000 0 0
neuron projection morphogenesis -0.054 0.082 0.33 1 -0.39 2 3
PTPRZ1 -0.006 0.078 -10000 0 -0.64 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.057 0.089 -10000 0 -0.42 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.081 0.081 -10000 0 -0.42 4 4
ADAM17 0.056 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.11 0.1 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.1 0.1 -10000 0 -0.53 3 3
NCOR1 0.026 0.008 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.072 0.083 -10000 0 -0.42 3 3
GRIN2B -0.076 0.074 -10000 0 -0.44 2 2
ErbB4/ErbB2/betacellulin -0.075 0.1 -10000 0 -0.45 9 9
STAT1 0.026 0.014 -10000 0 -10000 0 0
HBEGF 0.023 0.055 -10000 0 -0.64 2 2
PRLR -0.22 0.32 -10000 0 -0.64 109 109
E4ICDs/ETO2 -0.094 0.095 -10000 0 -10000 0 0
axon guidance -0.056 0.062 -10000 0 -10000 0 0
NEDD4 0.056 0.022 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.16 0.25 -10000 0 -0.48 109 109
CBFA2T3 0.025 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF -0.064 0.081 -10000 0 -0.52 1 1
MAPK3 -0.061 0.075 -10000 0 -0.4 2 2
STAT1 (dimer) -0.098 0.095 -10000 0 -10000 0 0
MAPK1 -0.06 0.075 -10000 0 -0.4 2 2
JAK2 0.027 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.069 0.084 -10000 0 -0.46 2 2
NRG1 0.022 0.063 -10000 0 -0.48 4 4
NRG3 0.015 0.071 -10000 0 -0.64 3 3
NRG2 0.021 0.059 -10000 0 -0.54 3 3
NRG4 0.022 0.026 -10000 0 -0.33 1 1
heart development -0.056 0.062 -10000 0 -10000 0 0
neural crest cell migration -0.068 0.083 -10000 0 -0.4 4 4
ERBB2 0.029 0.015 -10000 0 -10000 0 0
WWOX/E4ICDs -0.094 0.095 -10000 0 -10000 0 0
SHC1 0.027 0.005 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.066 0.095 -10000 0 -0.4 1 1
apoptosis 0.086 0.094 0.42 6 -10000 0 6
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.1 0.098 -10000 0 -0.4 2 2
ErbB4/ErbB2/epiregulin -0.079 0.076 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin -0.11 0.12 -10000 0 -0.51 11 11
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.21 0.2 -10000 0 -0.47 83 83
MDM2 -0.098 0.094 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.052 0.072 -10000 0 -0.4 4 4
STAT5A -0.049 0.064 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.055 0.084 -10000 0 -0.4 4 4
DLG4 0.026 0.008 -10000 0 -10000 0 0
GRB2/SHC 0.038 0.013 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.088 0.086 -10000 0 -10000 0 0
STAT5A (dimer) -0.16 0.18 -10000 0 -0.43 32 32
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.048 0.065 -10000 0 -10000 0 0
LRIG1 0.026 0.009 -10000 0 -10000 0 0
EREG -0.026 0.052 -10000 0 -10000 0 0
BTC 0 0.13 -10000 0 -0.61 12 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.056 0.062 -10000 0 -10000 0 0
ERBB4 -0.11 0.1 -10000 0 -10000 0 0
STAT5B 0.026 0.007 -10000 0 -10000 0 0
YAP1 -0.029 0.09 -10000 0 -0.53 8 8
GRB2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.066 0.077 -10000 0 -10000 0 0
glial cell differentiation 0.087 0.085 -10000 0 -10000 0 0
WWOX 0.026 0.008 -10000 0 -10000 0 0
cell proliferation -0.06 0.11 0.69 1 -0.48 4 5
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.028 0.003 -9999 0 -10000 0 0
SPHK1 -0.023 0.052 -9999 0 -10000 0 0
GNAI2 0.027 0.007 -9999 0 -10000 0 0
mol:S1P 0.002 0.013 -9999 0 -10000 0 0
GNAO1 -0.012 0.15 -9999 0 -0.64 16 16
mol:Sphinganine-1-P -0.017 0.032 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.044 0.032 -9999 0 -10000 0 0
GNAI3 0.027 0.006 -9999 0 -10000 0 0
G12/G13 0.031 0.018 -9999 0 -10000 0 0
S1PR3 -0.025 0.18 -9999 0 -0.62 23 23
S1PR2 0.028 0.002 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0 0.014 -9999 0 -10000 0 0
S1PR5 0.019 0.069 -9999 0 -0.64 3 3
S1PR4 0.026 0.016 -9999 0 -10000 0 0
GNAI1 0.018 0.056 -9999 0 -0.64 2 2
S1P/S1P5/G12 0.031 0.05 -9999 0 -0.35 3 3
S1P/S1P3/Gq -0.071 0.18 -9999 0 -0.34 74 74
S1P/S1P4/Gi 0.008 0.097 -9999 0 -0.38 6 6
GNAQ 0.027 0.006 -9999 0 -10000 0 0
GNAZ 0.026 0.008 -9999 0 -10000 0 0
GNA14 -0.11 0.27 -9999 0 -0.62 60 60
GNA15 0.02 0.027 -9999 0 -10000 0 0
GNA12 0.022 0.011 -9999 0 -10000 0 0
GNA13 0.026 0.007 -9999 0 -10000 0 0
GNA11 0.012 0.1 -9999 0 -0.64 7 7
ABCC1 0.026 0.008 -9999 0 -10000 0 0
Cellular roles of Anthrax 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
ANTXR1 0.027 0.004 -10000 0 -10000 0 0
ANTXR2 0.027 0.006 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0 -10000 0 -10000 0 0
monocyte activation -0.015 0.11 -10000 0 -0.35 27 27
MAP2K2 0.011 0.058 -10000 0 -0.56 3 3
MAP2K1 -0.003 0.001 -10000 0 -10000 0 0
MAP2K7 -0.003 0.001 -10000 0 -10000 0 0
MAP2K6 -0.002 0.001 -10000 0 -10000 0 0
CYAA -0.004 0.001 -10000 0 -10000 0 0
MAP2K4 -0.002 0.001 -10000 0 -10000 0 0
IL1B -0.001 0.051 0.24 1 -0.33 5 6
Channel 0.034 0.009 -10000 0 -10000 0 0
NLRP1 -0.003 0.003 -10000 0 -10000 0 0
CALM1 0.027 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.008 0.089 -10000 0 -0.38 16 16
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0 -10000 0 -10000 0 0
MAPK3 -0.002 0.001 -10000 0 -10000 0 0
MAPK1 -0.002 0.001 -10000 0 -10000 0 0
PGR -0.15 0.17 -10000 0 -0.35 119 119
PA/Cellular Receptors 0.036 0.009 -10000 0 -10000 0 0
apoptosis -0.001 0 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.033 0.009 -10000 0 -10000 0 0
macrophage activation -0.004 0.002 -10000 0 -10000 0 0
TNF 0.014 0.071 -10000 0 -0.64 3 3
VCAM1 -0.007 0.094 -10000 0 -0.33 21 21
platelet activation -0.008 0.089 -10000 0 -0.38 16 16
MAPKKK cascade -0.007 0.031 -10000 0 -0.13 16 16
IL18 0.004 0.023 -10000 0 -10000 0 0
negative regulation of macrophage activation -0.001 0 -10000 0 -10000 0 0
LEF -0.001 0 -10000 0 -10000 0 0
CASP1 0.001 0.002 -10000 0 -10000 0 0
mol:cAMP -0.008 0.09 -10000 0 -0.38 16 16
necrosis -0.001 0 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.033 0.009 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
IFN-gamma pathway

Figure 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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.059 0.029 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.026 0.007 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.049 0.037 0.3 3 -10000 0 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.054 0.026 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.042 0.081 -10000 0 -10000 0 0
CaM/Ca2+ 0.059 0.031 -10000 0 -10000 0 0
RAP1A 0.027 0.006 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.027 0.026 -10000 0 -10000 0 0
AKT1 0.017 0.068 0.35 8 -10000 0 8
MAP2K1 0.009 0.052 0.29 8 -10000 0 8
MAP3K11 0.022 0.053 0.29 9 -10000 0 9
IFNGR1 0.029 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.15 0.24 -10000 0 -0.44 113 113
Rap1/GTP 0.017 0.016 -10000 0 -10000 0 0
CRKL/C3G 0.037 0.013 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.066 0.035 -10000 0 -10000 0 0
CEBPB 0.024 0.11 0.4 6 -0.57 1 7
STAT3 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.062 0.1 -10000 0 -1.1 2 2
STAT1 0.02 0.051 0.29 8 -10000 0 8
CALM1 0.027 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.016 0.028 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.035 0.051 0.29 8 -10000 0 8
CEBPB/PTGES2/Cbp/p300 0.031 0.06 -10000 0 -0.35 1 1
mol:Ca2+ 0.056 0.028 -10000 0 -10000 0 0
MAPK3 0.021 0.052 -10000 0 -0.57 1 1
STAT1 (dimer) -0.044 0.12 -10000 0 -10000 0 0
MAPK1 -0.026 0.21 0.42 1 -0.69 24 25
JAK2 0.029 0.01 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
JAK1 0.028 0.01 -10000 0 -10000 0 0
CAMK2D 0.027 0.006 -10000 0 -10000 0 0
DAPK1 0.024 0.08 0.34 7 -0.32 1 8
SMAD7 -0.009 0.069 0.27 7 -10000 0 7
CBL/CRKL/C3G 0.046 0.052 0.29 9 -10000 0 9
PI3K 0.057 0.031 -10000 0 -10000 0 0
IFNG 0.016 0.028 -10000 0 -10000 0 0
apoptosis -0.008 0.1 0.27 1 -0.41 12 13
CAMK2G 0.028 0.004 -10000 0 -10000 0 0
STAT3 (dimer) 0.026 0.007 -10000 0 -10000 0 0
CAMK2A -0.25 0.31 -10000 0 -0.64 113 113
CAMK2B 0.002 0.083 -10000 0 -0.64 4 4
FRAP1 0.006 0.066 0.34 8 -10000 0 8
PRKCD 0.012 0.053 0.3 6 -10000 0 6
RAP1B 0.027 0.006 -10000 0 -10000 0 0
negative regulation of cell growth -0.042 0.081 -10000 0 -10000 0 0
PTPN2 0.026 0.008 -10000 0 -10000 0 0
EP300 0.026 0.008 -10000 0 -10000 0 0
IRF1 0.022 0.071 0.45 4 -0.38 1 5
STAT1 (dimer)/PIASy 0.033 0.05 0.29 8 -10000 0 8
SOCS1 0.018 0.11 -10000 0 -1.3 2 2
mol:GDP 0.042 0.049 0.27 9 -10000 0 9
CASP1 -0.008 0.071 0.26 9 -10000 0 9
PTGES2 0.027 0.006 -10000 0 -10000 0 0
IRF9 0.031 0.054 0.26 9 -10000 0 9
mol:PI-3-4-5-P3 0.042 0.023 -10000 0 -10000 0 0
RAP1/GDP 0.038 0.021 -10000 0 -10000 0 0
CBL 0.021 0.053 0.29 9 -10000 0 9
MAP3K1 0.021 0.051 0.29 8 -10000 0 8
PIAS1 0.028 0.004 -10000 0 -10000 0 0
PIAS4 0.028 0.003 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.042 0.081 -10000 0 -10000 0 0
PTPN11 0.013 0.02 -10000 0 -10000 0 0
CREBBP 0.026 0.008 -10000 0 -10000 0 0
RAPGEF1 0.027 0.006 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN 0.011 0.12 0.35 3 -0.46 9 12
IKBKB 0.029 0.091 0.29 7 -0.33 2 9
AKT1 0.013 0.094 0.29 21 -10000 0 21
IKBKG 0.034 0.08 0.29 7 -0.29 1 8
CALM1 0.002 0.088 0.36 1 -0.4 6 7
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.033 0.12 0.36 6 -0.46 7 13
MAP3K7 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0.092 -10000 0 -0.4 7 7
DOK1 0.026 0.012 -10000 0 -10000 0 0
AP-1 -0.01 0.094 0.24 4 -0.27 10 14
LYN 0.027 0.005 -10000 0 -10000 0 0
BLNK 0.004 0.12 -10000 0 -0.64 10 10
SHC1 0.027 0.005 -10000 0 -10000 0 0
BCR complex 0.02 0.063 -10000 0 -0.42 4 4
CD22 -0.002 0.065 -10000 0 -0.46 4 4
CAMK2G -0.001 0.085 0.34 1 -0.39 5 6
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
INPP5D 0.024 0.02 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.011 0.073 -10000 0 -0.38 7 7
GO:0007205 0 0.093 -10000 0 -0.4 7 7
SYK 0.024 0.04 -10000 0 -0.64 1 1
ELK1 -0.001 0.091 0.25 1 -0.4 6 7
NFATC1 0 0.082 0.34 4 -0.4 2 6
B-cell antigen/BCR complex 0.02 0.063 -10000 0 -0.42 4 4
PAG1/CSK 0.04 0.008 -10000 0 -10000 0 0
NFKBIB 0.027 0.051 0.14 11 -0.13 14 25
HRAS 0.004 0.083 0.25 2 -0.4 4 6
NFKBIA 0.027 0.05 0.14 11 -0.12 13 24
NF-kappa-B/RelA/I kappa B beta 0.031 0.045 0.16 9 -10000 0 9
RasGAP/Csk 0.051 0.063 -10000 0 -0.36 3 3
mol:GDP 0.001 0.092 -10000 0 -0.4 7 7
PTEN 0.028 0.004 -10000 0 -10000 0 0
CD79B 0.021 0.056 -10000 0 -0.64 2 2
NF-kappa-B/RelA/I kappa B alpha 0.032 0.044 0.16 9 -10000 0 9
GRB2 0.026 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.019 0.1 0.4 3 -0.51 2 5
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
mol:IP3 -0.001 0.092 -10000 0 -0.41 7 7
CSK 0.028 0.004 -10000 0 -10000 0 0
FOS -0.043 0.14 0.24 1 -0.46 16 17
CHUK 0.03 0.088 0.29 7 -0.28 6 13
IBTK 0.027 0.005 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.044 0.1 0.31 4 -0.39 3 7
PTPN6 -0.007 0.061 -10000 0 -0.44 4 4
RELA 0.028 0.002 -10000 0 -10000 0 0
BCL2A1 0.019 0.031 0.15 3 -10000 0 3
VAV2 -0.001 0.073 -10000 0 -0.49 3 3
ubiquitin-dependent protein catabolic process 0.029 0.05 0.15 11 -0.12 14 25
BTK 0.01 0.077 -10000 0 -0.89 2 2
CD19 -0.002 0.062 -10000 0 -0.46 4 4
MAP4K1 0.014 0.036 -10000 0 -10000 0 0
CD72 0.02 0.028 -10000 0 -10000 0 0
PAG1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.033 0.11 0.34 6 -0.39 7 13
SH3BP5 0.004 0.12 -10000 0 -0.64 10 10
PIK3AP1 0.001 0.097 -10000 0 -0.42 8 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.01 0.12 -10000 0 -0.49 14 14
RAF1 0.006 0.08 0.29 2 -0.42 3 5
RasGAP/p62DOK/SHIP 0.048 0.065 -10000 0 -0.35 3 3
CD79A 0.01 0.064 -10000 0 -0.64 2 2
re-entry into mitotic cell cycle -0.01 0.093 0.24 4 -0.27 9 13
RASA1 0.027 0.004 -10000 0 -10000 0 0
MAPK3 0.016 0.09 0.33 10 -0.33 2 12
MAPK1 0.005 0.07 0.26 2 -0.35 3 5
CD72/SHP1 0.014 0.077 0.34 2 -0.46 3 5
NFKB1 0.027 0.006 -10000 0 -10000 0 0
MAPK8 0.027 0.11 0.34 6 -0.4 8 14
actin cytoskeleton organization 0.034 0.1 0.33 5 -0.43 3 8
NF-kappa-B/RelA 0.062 0.085 0.28 9 -0.19 6 15
Calcineurin 0.031 0.087 0.32 1 -0.36 5 6
PI3K 0.002 0.059 -10000 0 -0.37 3 3
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.004 0.095 0.25 7 -0.43 8 15
SOS1 0.027 0.005 -10000 0 -10000 0 0
Bam32/HPK1 0.008 0.16 -10000 0 -0.65 14 14
DAPP1 -0.01 0.17 -10000 0 -0.7 15 15
cytokine secretion 0.001 0.079 0.34 4 -0.37 2 6
mol:DAG -0.001 0.092 -10000 0 -0.41 7 7
PLCG2 -0.003 0.13 -10000 0 -0.64 12 12
MAP2K1 0.006 0.076 0.28 2 -0.39 3 5
B-cell antigen/BCR complex/FcgammaRIIB 0.006 0.072 -10000 0 -0.42 4 4
mol:PI-3-4-5-P3 -0.016 0.048 0.24 1 -0.29 2 3
ETS1 -0.003 0.079 0.33 1 -0.36 5 6
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.05 0.094 -10000 0 -0.4 9 9
B-cell antigen/BCR complex/LYN 0.008 0.067 -10000 0 -0.44 5 5
MALT1 0.026 0.008 -10000 0 -10000 0 0
TRAF6 0.028 0.004 -10000 0 -10000 0 0
RAC1 0.034 0.1 0.3 4 -0.45 3 7
B-cell antigen/BCR complex/LYN/SYK 0.034 0.079 -10000 0 -0.55 2 2
CARD11 0.028 0.11 0.29 8 -0.45 3 11
FCGR2B -0.007 0.061 -10000 0 -0.64 1 1
PPP3CA 0.027 0.006 -10000 0 -10000 0 0
BCL10 0.026 0.007 -10000 0 -10000 0 0
IKK complex 0.023 0.052 0.18 14 -0.12 2 16
PTPRC 0.022 0.043 -10000 0 -0.64 1 1
PDPK1 -0.013 0.037 0.21 2 -0.21 1 3
PPP3CB 0.028 0.004 -10000 0 -10000 0 0
PPP3CC 0.027 0.006 -10000 0 -10000 0 0
POU2F2 0.024 0.031 0.15 3 -10000 0 3
Syndecan-4-mediated signaling 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
PTK2 -0.02 0.086 -10000 0 -0.69 3 3
Syndecan-4/Syndesmos -0.14 0.15 -10000 0 -0.56 3 3
positive regulation of JNK cascade -0.17 0.18 -10000 0 -0.56 17 17
Syndecan-4/ADAM12 -0.15 0.16 -10000 0 -0.56 3 3
CCL5 0.015 0.032 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.009 -10000 0 -10000 0 0
DNM2 0.028 0.002 -10000 0 -10000 0 0
ITGA5 0.027 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
PLG -0.35 0.31 -10000 0 -0.61 163 163
ADAM12 0.016 0.034 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.026 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.054 0.032 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.15 0.17 -10000 0 -0.6 7 7
Syndecan-4/CXCL12/CXCR4 -0.18 0.18 -10000 0 -0.6 17 17
Syndecan-4/Laminin alpha3 -0.15 0.16 -10000 0 -0.57 3 3
MDK 0 0.047 -10000 0 -10000 0 0
Syndecan-4/FZD7 -0.15 0.16 -10000 0 -0.59 6 6
Syndecan-4/Midkine -0.15 0.16 -10000 0 -0.56 3 3
FZD7 0.009 0.11 -10000 0 -0.64 8 8
Syndecan-4/FGFR1/FGF -0.14 0.16 -10000 0 -0.56 4 4
THBS1 0.004 0.12 -10000 0 -0.58 11 11
integrin-mediated signaling pathway -0.14 0.16 -10000 0 -0.52 6 6
positive regulation of MAPKKK cascade -0.17 0.18 -10000 0 -0.56 17 17
Syndecan-4/TACI -0.15 0.15 -10000 0 -0.57 3 3
CXCR4 0.02 0.027 -10000 0 -10000 0 0
cell adhesion 0.025 0.035 0.2 8 -10000 0 8
Syndecan-4/Dynamin -0.14 0.16 -10000 0 -0.56 3 3
Syndecan-4/TSP1 -0.16 0.17 -10000 0 -0.6 9 9
Syndecan-4/GIPC -0.14 0.16 -10000 0 -0.56 3 3
Syndecan-4/RANTES -0.15 0.15 -10000 0 -0.56 3 3
ITGB1 0.027 0.005 -10000 0 -10000 0 0
LAMA1 0.006 0.099 -10000 0 -0.59 7 7
LAMA3 -0.003 0.047 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
PRKCA 0.092 0.2 0.83 19 -10000 0 19
Syndecan-4/alpha-Actinin -0.14 0.16 -10000 0 -0.56 3 3
TFPI 0.025 0.04 -10000 0 -0.64 1 1
F2 0.015 0.037 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.01 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.16 -10000 0 -0.59 7 7
ACTN1 0.027 0.007 -10000 0 -10000 0 0
TNC 0.011 0.081 -10000 0 -0.64 4 4
Syndecan-4/CXCL12 -0.18 0.18 -10000 0 -0.6 18 18
FGF6 -0.016 0.009 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
CXCL12 -0.054 0.22 -10000 0 -0.62 36 36
TNFRSF13B 0.006 0.028 -10000 0 -10000 0 0
FGF2 0.021 0.059 -10000 0 -0.54 3 3
FGFR1 0.027 0.006 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.15 0.14 -10000 0 -0.49 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.021 0.035 -10000 0 -10000 0 0
cell migration -0.019 0.01 -10000 0 -10000 0 0
PRKCD 0.029 0.02 -10000 0 -10000 0 0
vasculogenesis -0.15 0.16 -10000 0 -0.56 10 10
SDC4 -0.15 0.15 -10000 0 -0.52 6 6
Syndecan-4/Tenascin C -0.15 0.16 -10000 0 -0.54 6 6
Syndecan-4/PI-4-5-P2/PKC alpha -0.043 0.025 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.14 0.16 -10000 0 -0.56 3 3
MMP9 -0.014 0.071 -10000 0 -0.63 2 2
Rac1/GTP 0.025 0.036 0.2 8 -10000 0 8
cytoskeleton organization -0.14 0.15 -10000 0 -0.54 3 3
GIPC1 0.028 0.002 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.14 0.16 -10000 0 -0.61 3 3
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process -0.012 0.096 0.64 6 -10000 0 6
PI3K Class IB/PDE3B 0.012 0.096 -10000 0 -0.64 6 6
PDE3B 0.012 0.096 -10000 0 -0.64 6 6
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.001 0.18 -10000 0 -0.56 14 14
MAP3K8 0.025 0.011 -10000 0 -10000 0 0
FOS 0.009 0.13 0.26 1 -0.46 13 14
PRKCA 0.02 0.018 -10000 0 -10000 0 0
PTPN7 0.017 0.046 -10000 0 -0.65 1 1
HRAS 0.027 0.007 -10000 0 -10000 0 0
PRKCB 0.019 0.022 -10000 0 -10000 0 0
NRAS 0.026 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.042 0.028 -10000 0 -10000 0 0
MAPK3 0.02 0.09 -10000 0 -0.44 9 9
MAP2K1 0.03 0.043 -10000 0 -10000 0 0
ELK1 0.019 0.024 -10000 0 -10000 0 0
BRAF 0.013 0.018 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 43 43
MAPK1 -0.006 0.14 -10000 0 -0.44 26 26
RAF1 0.016 0.023 -10000 0 -10000 0 0
KRAS 0.026 0.006 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.026 0.007 -10000 0 -10000 0 0
VLDLR 0.027 0.007 -10000 0 -10000 0 0
LRPAP1 0.027 0.005 -10000 0 -10000 0 0
NUDC 0.026 0.008 -10000 0 -10000 0 0
RELN/LRP8 -0.004 0.1 -10000 0 -0.4 15 15
CaM/Ca2+ 0.02 0.005 -10000 0 -10000 0 0
KATNA1 0.027 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.02 0.12 -10000 0 -0.38 14 14
IQGAP1/CaM 0.039 0.01 -10000 0 -10000 0 0
DAB1 -0.002 0.025 -10000 0 -10000 0 0
IQGAP1 0.028 0.004 -10000 0 -10000 0 0
PLA2G7 -0.059 0.04 -10000 0 -10000 0 0
CALM1 0.027 0.007 -10000 0 -10000 0 0
DYNLT1 0.027 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.038 0.015 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.027 0.005 -10000 0 -10000 0 0
CDK5R1 0.026 0.009 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.01 0.003 -10000 0 -10000 0 0
CDK5R2 -0.006 0.044 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.01 0.1 -10000 0 -0.42 15 15
YWHAE 0.026 0.008 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.039 0.15 0.31 49 -0.34 4 53
MAP1B 0.006 0.003 -10000 0 -10000 0 0
RAC1 0.011 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.012 0.081 -10000 0 -0.34 14 14
RELN -0.036 0.15 -10000 0 -0.64 15 15
PAFAH/LIS1 -0.029 0.027 -10000 0 -10000 0 0
LIS1/CLIP170 0.028 0.01 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.006 0.069 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.008 0.088 -10000 0 -0.3 15 15
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.012 0.09 0.3 6 -0.34 13 19
LIS1/IQGAP1 0.028 0.011 -10000 0 -10000 0 0
RHOA 0.013 0.006 -10000 0 -10000 0 0
PAFAH1B1 0.013 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.027 0.007 -10000 0 -10000 0 0
PAFAH1B2 0.025 0.04 -10000 0 -0.64 1 1
MAP1B/LIS1/Dynein heavy chain 0.026 0.019 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.047 0.14 0.31 49 -0.35 2 51
LRP8 0.025 0.014 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.038 0.15 0.31 49 -0.35 4 53
P39/CDK5 -0.026 0.081 -10000 0 -0.35 14 14
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.026 0.012 -10000 0 -10000 0 0
CDK5 -0.028 0.08 -10000 0 -0.36 14 14
PPP2R5D 0.027 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.024 0.009 -10000 0 -10000 0 0
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.004 0.093 -10000 0 -0.36 15 15
RELN/VLDLR 0.022 0.098 -10000 0 -0.38 14 14
CDC42 0.013 0.006 -10000 0 -10000 0 0
Noncanonical Wnt 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
NFATC2 -0.022 0.17 -9999 0 -0.64 20 20
GNB1/GNG2 0.019 0.099 -9999 0 -0.47 2 2
mol:DAG -0.004 0.079 -9999 0 -0.43 2 2
PLCG1 -0.005 0.081 -9999 0 -0.45 2 2
YES1 -0.01 0.083 -9999 0 -0.42 4 4
FZD3 0.027 0.006 -9999 0 -10000 0 0
FZD6 0.027 0.004 -9999 0 -10000 0 0
G protein 0.021 0.096 -9999 0 -0.45 2 2
MAP3K7 -0.13 0.16 -9999 0 -0.42 17 17
mol:Ca2+ -0.004 0.077 -9999 0 -0.42 2 2
mol:IP3 -0.004 0.079 -9999 0 -0.43 2 2
NLK 0 0.07 -9999 0 -0.82 2 2
GNB1 0.025 0.008 -9999 0 -10000 0 0
CAMK2A -0.14 0.17 -9999 0 -0.39 33 33
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD 0 0.09 -9999 0 -0.31 19 19
CSNK1A1 0.027 0.004 -9999 0 -10000 0 0
GNAS -0.007 0.079 -9999 0 -0.42 4 4
GO:0007205 -0.013 0.076 -9999 0 -0.43 2 2
WNT6 0.021 0.042 -9999 0 -0.64 1 1
WNT4 0.005 0.11 -9999 0 -0.6 9 9
NFAT1/CK1 alpha -0.009 0.12 -9999 0 -0.46 3 3
GNG2 0.027 0.006 -9999 0 -10000 0 0
WNT5A 0.012 0.037 -9999 0 -10000 0 0
WNT11 -0.003 0.13 -9999 0 -0.64 12 12
CDC42 -0.011 0.076 -9999 0 -0.41 3 3
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.024 0.019 -10000 0 -10000 0 0
EPHB2 0.024 0.015 -10000 0 -10000 0 0
Syndecan-2/TACI 0.022 0.016 -10000 0 -10000 0 0
LAMA1 0.006 0.099 -10000 0 -0.59 7 7
Syndecan-2/alpha2 ITGB1 0.045 0.046 -10000 0 -0.36 3 3
HRAS 0.028 0.003 -10000 0 -10000 0 0
Syndecan-2/CASK 0.009 0.003 -10000 0 -10000 0 0
ITGA5 0.027 0.005 -10000 0 -10000 0 0
BAX 0.001 0.044 -10000 0 -10000 0 0
EPB41 0.026 0.008 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.027 0.006 -10000 0 -10000 0 0
LAMA3 -0.003 0.047 -10000 0 -10000 0 0
EZR 0.027 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.02 0.016 -10000 0 -10000 0 0
Syndecan-2/MMP2 0.026 0.013 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.034 0.054 -10000 0 -0.48 3 3
dendrite morphogenesis 0.026 0.012 -10000 0 -10000 0 0
Syndecan-2/GM-CSF 0.024 0.01 -10000 0 -10000 0 0
determination of left/right symmetry 0.013 0.004 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.028 0.009 -10000 0 -10000 0 0
GNB2L1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.012 0.013 0.18 1 -10000 0 1
MAPK1 0.013 0.016 0.18 2 -10000 0 2
Syndecan-2/RACK1 0.042 0.011 -10000 0 -10000 0 0
NF1 0.026 0.007 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.013 0.004 -10000 0 -10000 0 0
ITGA2 0.021 0.068 -10000 0 -0.64 3 3
MAPK8 0.005 0.05 -10000 0 -0.4 4 4
Syndecan-2/alpha2/beta1 Integrin 0.04 0.073 -10000 0 -0.36 8 8
Syndecan-2/Kininogen -0.22 0.21 -10000 0 -0.41 163 163
ITGB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.019 0.022 -10000 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.025 0.009 -10000 0 -10000 0 0
extracellular matrix organization 0.029 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.024 0.019 -10000 0 -10000 0 0
Syndecan-2/Caveolin-2/Ras 0.034 0.022 -10000 0 -10000 0 0
Syndecan-2/Laminin alpha3 0.009 0.03 -10000 0 -10000 0 0
Syndecan-2/RasGAP 0.054 0.015 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.039 0.01 -10000 0 -10000 0 0
PRKCD 0.027 0.007 -10000 0 -10000 0 0
Syndecan-2 dimer 0.027 0.012 -10000 0 -10000 0 0
GO:0007205 0.002 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.038 0.019 -10000 0 -10000 0 0
RHOA 0.027 0.006 -10000 0 -10000 0 0
SDCBP 0.027 0.005 -10000 0 -10000 0 0
TNFRSF13B 0.006 0.028 -10000 0 -10000 0 0
RASA1 0.027 0.004 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.034 0.054 -10000 0 -0.48 3 3
Syndecan-2/Synbindin 0.029 0.008 -10000 0 -10000 0 0
TGFB1 0.027 0.009 -10000 0 -10000 0 0
CASP3 0.015 0.012 -10000 0 -10000 0 0
FN1 0.02 0.028 -10000 0 -10000 0 0
Syndecan-2/IL8 0.012 0.038 -10000 0 -0.41 1 1
SDC2 0.013 0.004 -10000 0 -10000 0 0
KNG1 -0.37 0.31 -10000 0 -0.64 164 164
Syndecan-2/Neurofibromin 0.028 0.01 -10000 0 -10000 0 0
TRAPPC4 0.027 0.005 -10000 0 -10000 0 0
CSF2 0.002 0.024 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.029 0.009 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.027 0.006 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.042 0.014 -10000 0 -10000 0 0
PRKACA 0.016 0.012 0.19 1 -10000 0 1
angiogenesis 0.012 0.038 -10000 0 -0.41 1 1
MMP2 0.024 0.016 -10000 0 -10000 0 0
IL8 0 0.059 -10000 0 -0.64 1 1
calcineurin-NFAT signaling pathway 0.022 0.016 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.028 0.004 -10000 0 -10000 0 0
LAT2 -0.011 0.058 -10000 0 -0.36 3 3
AP1 -0.008 0.15 -10000 0 -0.47 15 15
mol:PIP3 0.041 0.15 0.48 16 -0.45 2 18
IKBKB 0.038 0.12 0.42 16 -0.25 1 17
AKT1 -0.021 0.082 0.34 6 -10000 0 6
IKBKG 0.037 0.12 0.4 16 -0.25 1 17
MS4A2 -0.003 0.056 -10000 0 -0.5 1 1
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
MAP3K1 0.007 0.096 0.33 10 -0.39 4 14
mol:Ca2+ 0.039 0.13 0.43 17 -0.34 2 19
LYN 0.028 0.007 -10000 0 -10000 0 0
CBLB -0.008 0.06 -10000 0 -0.36 3 3
SHC1 0.027 0.005 -10000 0 -10000 0 0
RasGAP/p62DOK 0.05 0.021 -10000 0 -10000 0 0
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.024 0.02 -10000 0 -10000 0 0
PLD2 -0.027 0.066 0.34 2 -0.35 7 9
PTPN13 0.014 0.12 0.4 1 -0.85 4 5
PTPN11 0.025 0.013 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.014 0.11 0.4 13 -0.37 4 17
SYK 0.025 0.041 -10000 0 -0.65 1 1
GRB2 0.026 0.008 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.007 0.083 -10000 0 -0.47 2 2
LAT -0.009 0.06 -10000 0 -0.36 3 3
PAK2 0.006 0.099 0.33 10 -0.4 5 15
NFATC2 -0.042 0.15 -10000 0 -0.57 21 21
HRAS 0.002 0.092 0.29 7 -0.43 5 12
GAB2 0.028 0.003 -10000 0 -10000 0 0
PLA2G1B -0.001 0.14 -10000 0 -0.84 7 7
Fc epsilon R1 -0.009 0.09 -10000 0 -0.43 8 8
Antigen/IgE/Fc epsilon R1 0.001 0.084 -10000 0 -0.39 8 8
mol:GDP -0.004 0.088 -10000 0 -0.49 5 5
JUN 0.026 0.007 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
FOS -0.065 0.22 -10000 0 -0.59 43 43
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.002 0.066 -10000 0 -0.34 4 4
CHUK 0.037 0.12 0.4 16 -0.25 1 17
KLRG1 -0.009 0.056 -10000 0 -0.3 4 4
VAV1 -0.016 0.07 -10000 0 -0.41 4 4
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.008 0.061 -10000 0 -0.36 3 3
negative regulation of mast cell degranulation 0.008 0.064 0.22 1 -0.3 3 4
BTK 0 0.082 -10000 0 -0.51 4 4
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.004 0.071 -10000 0 -0.34 8 8
GAB2/PI3K/SHP2 -0.024 0.06 -10000 0 -0.34 7 7
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0.003 0.049 -10000 0 -0.24 8 8
RAF1 0.002 0.14 -10000 0 -0.89 7 7
Fc epsilon R1/FcgammaRIIB/SHIP 0.014 0.1 -10000 0 -0.41 8 8
FCER1G -0.003 0.049 -10000 0 -10000 0 0
FCER1A 0.007 0.11 -10000 0 -0.65 8 8
Antigen/IgE/Fc epsilon R1/Fyn 0.03 0.08 -10000 0 -0.37 8 8
MAPK3 0.002 0.13 -10000 0 -0.81 7 7
MAPK1 -0.007 0.14 -10000 0 -0.9 7 7
NFKB1 0.027 0.006 -10000 0 -10000 0 0
MAPK8 0.008 0.15 -10000 0 -0.65 11 11
DUSP1 0.025 0.039 -10000 0 -0.64 1 1
NF-kappa-B/RelA 0.02 0.046 0.15 4 -10000 0 4
actin cytoskeleton reorganization 0.016 0.13 -10000 0 -0.9 4 4
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.01 0.083 -10000 0 -0.43 4 4
FER -0.008 0.061 -10000 0 -0.36 3 3
RELA 0.028 0.002 -10000 0 -10000 0 0
ITK 0.005 0.026 -10000 0 -0.21 3 3
SOS1 0.027 0.005 -10000 0 -10000 0 0
PLCG1 0.011 0.1 0.34 8 -0.46 5 13
cytokine secretion 0.009 0.029 -10000 0 -10000 0 0
SPHK1 -0.022 0.06 -10000 0 -0.36 3 3
PTK2 0.015 0.14 -10000 0 -0.98 4 4
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.001 0.082 -10000 0 -0.46 2 2
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.034 0.14 0.44 15 -0.43 2 17
MAP2K2 -0.002 0.13 -10000 0 -0.83 7 7
MAP2K1 -0.002 0.13 -10000 0 -0.83 7 7
MAP2K7 0.028 0.002 -10000 0 -10000 0 0
KLRG1/SHP2 0.005 0.06 -10000 0 -0.28 3 3
MAP2K4 0.008 0.15 -10000 0 -0.79 10 10
Fc epsilon R1/FcgammaRIIB 0.008 0.1 -10000 0 -0.43 8 8
mol:Choline -0.027 0.065 0.34 2 -0.35 7 9
SHC/Grb2/SOS1 0.042 0.072 -10000 0 -0.33 2 2
FYN 0.027 0.005 -10000 0 -10000 0 0
DOK1 0.026 0.012 -10000 0 -10000 0 0
PXN 0.02 0.14 0.38 8 -0.86 4 12
HCLS1 -0.009 0.061 -10000 0 -0.36 3 3
PRKCB 0.041 0.13 0.45 16 -0.33 2 18
FCGR2B -0.007 0.061 -10000 0 -0.64 1 1
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP 0.008 0.065 0.22 1 -0.31 3 4
LCP2 0.025 0.018 -10000 0 -10000 0 0
PLA2G4A -0.011 0.077 -10000 0 -0.41 7 7
RASA1 0.027 0.004 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.027 0.065 0.34 2 -0.35 7 9
IKK complex 0.035 0.11 0.39 16 -10000 0 16
WIPF1 0.027 0.007 -10000 0 -10000 0 0
PLK1 signaling events

Figure 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
regulation of centriole-centriole cohesion -0.004 0.032 0.15 7 -0.13 7 14
BUB1B 0.008 0.036 0.14 6 -0.18 1 7
PLK1 0.009 0.03 0.12 12 -10000 0 12
PLK1S1 0.014 0.025 0.12 11 -10000 0 11
KIF2A 0.008 0.037 0.27 3 -10000 0 3
regulation of mitotic centrosome separation 0.009 0.03 0.12 12 -10000 0 12
GOLGA2 0.027 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.026 0.043 -10000 0 -10000 0 0
WEE1 0.015 0.056 -10000 0 -0.32 6 6
cytokinesis 0.004 0.058 0.22 5 -0.22 2 7
PP2A-alpha B56 0.054 0.058 -10000 0 -0.5 3 3
AURKA 0.012 0.02 0.12 2 -10000 0 2
PICH/PLK1 0.011 0.025 -10000 0 -10000 0 0
CENPE 0.006 0.032 0.2 3 -10000 0 3
RhoA/GTP 0.02 0.005 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.008 0.037 0.27 3 -10000 0 3
PPP2CA 0.027 0.004 -10000 0 -10000 0 0
FZR1 0.028 0.003 -10000 0 -10000 0 0
TPX2 0.01 0.027 0.12 11 -10000 0 11
PAK1 0.028 0.004 -10000 0 -10000 0 0
SPC24 0.006 0.042 -10000 0 -10000 0 0
FBXW11 0.027 0.005 -10000 0 -10000 0 0
CLSPN -0.006 0.067 -10000 0 -0.24 21 21
GORASP1 0.027 0.006 -10000 0 -10000 0 0
metaphase 0.001 0.005 0.019 23 -10000 0 23
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.004 0.017 0.066 12 -10000 0 12
G2 phase of mitotic cell cycle 0 0.003 0.011 11 -10000 0 11
STAG2 0.028 0.002 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.009 0.09 -10000 0 -0.52 8 8
spindle elongation 0.009 0.03 0.12 12 -10000 0 12
ODF2 0.027 0.006 -10000 0 -10000 0 0
BUB1 0.02 0.059 -10000 0 -0.53 3 3
TPT1 0.005 0.044 0.11 1 -0.2 11 12
CDC25C 0.007 0.038 -10000 0 -0.3 3 3
CDC25B 0.027 0.01 -10000 0 -10000 0 0
SGOL1 0.004 0.032 0.13 7 -0.15 7 14
RHOA 0.027 0.006 -10000 0 -10000 0 0
CCNB1/CDK1 0.039 0.027 -10000 0 -10000 0 0
CDC14B 0.006 0.003 -10000 0 -10000 0 0
CDC20 0.015 0.033 -10000 0 -10000 0 0
PLK1/PBIP1 0.007 0.026 0.12 3 -10000 0 3
mitosis -0.002 0.002 -10000 0 -10000 0 0
FBXO5 0.006 0.03 0.12 5 -0.12 1 6
CDC2 0.001 0.001 -10000 0 -0.01 1 1
NDC80 0.015 0.032 -10000 0 -10000 0 0
metaphase plate congression -0.005 0.073 -10000 0 -0.24 24 24
ERCC6L 0.016 0.029 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.009 0.025 0.1 11 -0.11 1 12
microtubule cytoskeleton organization 0.005 0.044 0.11 1 -0.2 11 12
G2/M transition DNA damage checkpoint 0 0.002 0.012 3 -10000 0 3
PPP1R12A 0.028 0.006 -10000 0 -10000 0 0
interphase 0 0.002 0.012 3 -10000 0 3
PLK1/PRC1-2 0.02 0.044 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.048 0.027 -10000 0 -10000 0 0
RAB1A 0.027 0.004 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.008 0.025 0.1 13 -10000 0 13
mitotic prometaphase 0.001 0.005 0.018 24 -10000 0 24
proteasomal ubiquitin-dependent protein catabolic process 0.019 0.037 -10000 0 -0.37 1 1
microtubule-based process 0.009 0.036 0.14 1 -10000 0 1
Golgi organization 0.009 0.03 0.12 12 -10000 0 12
Cohesin/SA2 0.026 0.023 0.13 1 -10000 0 1
PPP1CB/MYPT1 0.039 0.011 -10000 0 -10000 0 0
KIF20A -0.008 0.05 -10000 0 -10000 0 0
APC/C/CDC20 0.023 0.029 -10000 0 -10000 0 0
PPP2R1A 0.028 0.003 -10000 0 -10000 0 0
chromosome segregation 0.007 0.025 0.11 3 -10000 0 3
PRC1 0.024 0.02 -10000 0 -10000 0 0
ECT2 0.014 0.057 0.27 11 -10000 0 11
C13orf34 0.008 0.024 0.097 12 -10000 0 12
NUDC -0.005 0.073 -10000 0 -0.24 24 24
regulation of attachment of spindle microtubules to kinetochore 0.008 0.036 0.14 6 -0.18 1 7
spindle assembly 0.011 0.036 0.13 16 -10000 0 16
spindle stabilization 0.014 0.025 0.12 11 -10000 0 11
APC/C/HCDH1 0.025 0.006 -10000 0 -10000 0 0
MKLP2/PLK1 0.009 0.036 0.14 1 -10000 0 1
CCNB1 0.027 0.013 -10000 0 -10000 0 0
PPP1CB 0.028 0.005 -10000 0 -10000 0 0
BTRC 0.028 0.004 -10000 0 -10000 0 0
ROCK2 0.005 0.082 0.27 1 -0.36 11 12
TUBG1 0.012 0.027 0.13 6 -0.23 1 7
G2/M transition of mitotic cell cycle 0.007 0.02 -10000 0 -10000 0 0
MLF1IP 0.002 0.017 -10000 0 -10000 0 0
INCENP 0.028 0.002 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.014 0.003 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.045 0.012 -10000 0 -10000 0 0
CDKN1B 0.003 0.1 -10000 0 -0.37 16 16
CDKN1A 0.007 0.082 -10000 0 -0.31 14 14
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.027 0.005 -10000 0 -10000 0 0
FOXO3 0.007 0.081 -10000 0 -0.31 14 14
AKT1 -0.003 0.099 -10000 0 -0.39 15 15
BAD 0.028 0.002 -10000 0 -10000 0 0
AKT3 0.014 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.001 0.1 -10000 0 -0.36 17 17
AKT1/ASK1 0.019 0.11 -10000 0 -0.35 17 17
BAD/YWHAZ 0.056 0.01 -10000 0 -10000 0 0
RICTOR 0.027 0.005 -10000 0 -10000 0 0
RAF1 0.027 0.006 -10000 0 -10000 0 0
JNK cascade -0.017 0.1 0.34 17 -10000 0 17
TSC1 0.009 0.077 -10000 0 -0.31 12 12
YWHAZ 0.027 0.004 -10000 0 -10000 0 0
AKT1/RAF1 0.02 0.11 0.28 1 -0.37 16 17
EP300 0.026 0.008 -10000 0 -10000 0 0
mol:GDP 0 0.1 -10000 0 -0.37 17 17
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 -0.006 0.099 -10000 0 -0.36 17 17
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
TBC1D4 0.007 0.003 -10000 0 -10000 0 0
MAP3K5 0.027 0.006 -10000 0 -10000 0 0
MAPKAP1 0.027 0.006 -10000 0 -10000 0 0
negative regulation of cell cycle -0.018 0.1 0.42 8 -0.26 8 16
YWHAH 0.026 0.008 -10000 0 -10000 0 0
AKT1S1 0.003 0.1 -10000 0 -0.37 15 15
CASP9 0.015 0.056 -10000 0 -0.28 6 6
YWHAB 0.026 0.007 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.023 0.11 0.32 5 -0.58 4 9
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.048 0.022 -10000 0 -10000 0 0
YWHAE 0.026 0.008 -10000 0 -10000 0 0
SRC 0.026 0.009 -10000 0 -10000 0 0
AKT2/p21CIP1 -0.001 0.089 -10000 0 -0.55 4 4
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.008 0.028 -10000 0 -10000 0 0
CHUK 0.002 0.1 -10000 0 -0.37 16 16
BAD/BCL-XL 0.022 0.1 -10000 0 -0.58 4 4
mTORC2 0.034 0.009 -10000 0 -10000 0 0
AKT2 0.014 0.004 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.01 0.14 0.31 8 -0.64 7 15
PDPK1 0.026 0.008 -10000 0 -10000 0 0
MDM2 0.002 0.1 -10000 0 -0.37 16 16
MAPKKK cascade -0.02 0.11 0.36 16 -0.28 1 17
MDM2/Cbp/p300 0.024 0.1 0.27 1 -0.56 4 5
TSC1/TSC2 0.013 0.12 0.28 19 -0.59 4 23
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.097 0.26 1 -0.53 4 5
glucose import 0.007 0.04 0.21 8 -0.37 1 9
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.014 0.063 0.18 1 -0.34 4 5
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 0.001 0.022 -10000 0 -0.37 1 1
GSK3A 0.003 0.1 -10000 0 -0.37 15 15
FOXO1 0.012 0.066 -10000 0 -0.28 10 10
GSK3B 0 0.1 -10000 0 -0.36 17 17
SFN -0.03 0.09 -10000 0 -0.58 5 5
G1/S transition of mitotic cell cycle 0.007 0.11 0.31 7 -0.6 4 11
p27Kip1/14-3-3 family 0.032 0.063 -10000 0 -0.43 1 1
PRKACA 0.028 0.002 -10000 0 -10000 0 0
KPNA1 0.027 0.006 -10000 0 -10000 0 0
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
YWHAG 0.022 0.011 -10000 0 -10000 0 0
RHEB 0.022 0.012 -10000 0 -10000 0 0
CREBBP 0.026 0.008 -10000 0 -10000 0 0
IL1-mediated signaling 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
UBC13/UEV1A 0.02 0.004 -9999 0 -10000 0 0
PRKCZ 0.025 0.008 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.027 0.006 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 0.019 0.043 -9999 0 -10000 0 0
IRAK/TOLLIP 0.031 0.008 -9999 0 -10000 0 0
IKBKB 0.027 0.005 -9999 0 -10000 0 0
IKBKG 0.028 0.002 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.1 0.22 -9999 0 -0.48 74 74
IL1A 0.01 0.037 -9999 0 -10000 0 0
IL1B 0.004 0.065 -9999 0 -0.48 5 5
IRAK/TRAF6/p62/Atypical PKCs 0.062 0.032 -9999 0 -10000 0 0
IL1R2 -0.14 0.29 -9999 0 -0.63 74 74
IL1R1 0.028 0.003 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.014 0.037 -9999 0 -10000 0 0
TOLLIP 0.028 0.004 -9999 0 -10000 0 0
TICAM2 0.025 0.04 -9999 0 -0.64 1 1
MAP3K3 0.026 0.008 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0.018 0.003 -9999 0 -10000 0 0
IKK complex/ELKS 0.035 0.047 -9999 0 -10000 0 0
JUN -0.009 0.033 -9999 0 -0.31 2 2
MAP3K7 0.027 0.005 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.062 0.054 -9999 0 -0.35 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88 0.063 0.022 -9999 0 -10000 0 0
PIK3R1 0.028 0.004 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 0.072 0.027 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP 0.035 0.055 -9999 0 -0.38 4 4
NFKB1 0.027 0.006 -9999 0 -10000 0 0
MAPK8 -0.008 0.035 -9999 0 -0.33 2 2
IRAK1 0.015 0.003 -9999 0 -10000 0 0
IL1RN/IL1R1 0.035 0.026 -9999 0 -0.2 1 1
IRAK4 0.027 0.005 -9999 0 -10000 0 0
PRKCI 0.027 0.005 -9999 0 -10000 0 0
TRAF6 0.028 0.004 -9999 0 -10000 0 0
PI3K 0.04 0.009 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.02 0.041 -9999 0 -10000 0 0
CHUK 0.028 0.004 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.035 0.055 -9999 0 -0.38 4 4
IL1 beta/IL1R2 -0.088 0.2 -9999 0 -0.42 77 77
IRAK/TRAF6/TAK1/TAB1/TAB2 0.038 0.012 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.046 0.05 -9999 0 -0.33 4 4
IRAK3 0.026 0.01 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.06 0.056 -9999 0 -0.35 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.026 0.017 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP 0.04 0.036 -9999 0 -10000 0 0
RELA 0.028 0.002 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.025 0.017 -9999 0 -10000 0 0
MYD88 0.027 0.006 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.047 0.021 -9999 0 -10000 0 0
IL1RAP 0.026 0.012 -9999 0 -10000 0 0
UBE2N 0.027 0.005 -9999 0 -10000 0 0
IRAK/TRAF6 0.03 0.041 -9999 0 -10000 0 0
CASP1 0.026 0.012 -9999 0 -10000 0 0
IL1RN/IL1R2 -0.097 0.22 -9999 0 -0.47 75 75
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.05 0.054 -9999 0 -0.36 4 4
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.022 0.045 -9999 0 -10000 0 0
PIK3CA 0.027 0.005 -9999 0 -10000 0 0
IL1RN 0.02 0.032 -9999 0 -0.33 1 1
TRAF6/TAK1/TAB1/TAB2 0.038 0.011 -9999 0 -10000 0 0
MAP2K6 0.015 0.02 -9999 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.027 0.006 -10000 0 -10000 0 0
EPHB2 0.024 0.015 -10000 0 -10000 0 0
EFNB1 -0.008 0.041 -10000 0 -0.48 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.034 0.055 -10000 0 -0.35 3 3
Ephrin B2/EPHB1-2 0.039 0.049 -10000 0 -0.38 3 3
neuron projection morphogenesis 0.011 0.051 -10000 0 -0.33 3 3
Ephrin B1/EPHB1-2/Tiam1 0.017 0.065 -10000 0 -0.37 4 4
DNM1 -0.008 0.061 -10000 0 -0.64 1 1
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.001 0.087 -10000 0 -0.38 11 11
YES1 -0.01 0.13 -10000 0 -0.62 12 12
Ephrin B1/EPHB1-2/NCK2 0.02 0.066 -10000 0 -0.37 4 4
PI3K 0.026 0.088 -10000 0 -0.39 12 12
mol:GDP 0.016 0.064 -10000 0 -0.37 4 4
ITGA2B 0.019 0.026 -10000 0 -10000 0 0
endothelial cell proliferation 0.028 0.016 -10000 0 -10000 0 0
FYN -0.009 0.13 -10000 0 -0.62 12 12
MAP3K7 -0.005 0.07 -10000 0 -0.42 8 8
FGR -0.009 0.13 -10000 0 -0.62 12 12
TIAM1 0.026 0.007 -10000 0 -10000 0 0
PIK3R1 0.028 0.004 -10000 0 -10000 0 0
RGS3 0.027 0.006 -10000 0 -10000 0 0
cell adhesion -0.003 0.11 -10000 0 -0.4 10 10
LYN -0.007 0.13 -10000 0 -0.62 12 12
Ephrin B1/EPHB1-2/Src Family Kinases -0.011 0.11 -10000 0 -0.55 12 12
Ephrin B1/EPHB1-2 -0.007 0.084 -10000 0 -0.45 10 10
SRC -0.006 0.12 -10000 0 -0.6 12 12
ITGB3 -0.006 0.14 -10000 0 -0.64 13 13
EPHB1 0.017 0.07 -10000 0 -0.64 3 3
EPHB4 0.022 0.012 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.028 0.017 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.008 0.11 -10000 0 -0.48 13 13
BLK -0.006 0.13 -10000 0 -0.61 12 12
HCK -0.007 0.12 -10000 0 -0.59 12 12
regulation of stress fiber formation -0.019 0.064 0.36 4 -10000 0 4
MAPK8 -0.006 0.099 0.28 2 -0.38 14 16
Ephrin B1/EPHB1-2/RGS3 0.02 0.066 -10000 0 -0.37 4 4
endothelial cell migration 0.03 0.096 0.42 1 -0.32 8 9
NCK2 0.028 0.003 -10000 0 -10000 0 0
PTPN13 0.028 0.008 -10000 0 -10000 0 0
regulation of focal adhesion formation -0.019 0.064 0.36 4 -10000 0 4
chemotaxis -0.018 0.065 0.37 4 -10000 0 4
PIK3CA 0.027 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.051 -10000 0 -0.34 3 3
angiogenesis -0.009 0.091 -10000 0 -0.44 12 12
LCK -0.008 0.13 -10000 0 -0.62 12 12
TCGA08_p53

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

Figure 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
HDAC1 0.023 0.008 -10000 0 -10000 0 0
AES 0.025 0.005 -10000 0 -10000 0 0
FBXW11 0.027 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.032 0.019 -10000 0 -10000 0 0
SMAD4 0.026 0.008 -10000 0 -10000 0 0
DKK2 0.021 0.042 -10000 0 -0.64 1 1
TLE1 0.024 0.007 -10000 0 -10000 0 0
MACF1 0.027 0.008 -10000 0 -10000 0 0
CTNNB1 0.068 0.11 0.42 12 -0.35 1 13
WIF1 0.008 0.025 -10000 0 -10000 0 0
beta catenin/RanBP3 0.008 0.052 0.35 1 -10000 0 1
KREMEN2 0.013 0.032 -10000 0 -10000 0 0
DKK1 0.015 0.027 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.075 0.097 0.4 10 -10000 0 10
FZD1 0.022 0.014 -10000 0 -10000 0 0
AXIN2 0.047 0.15 0.61 15 -10000 0 15
AXIN1 0.026 0.008 -10000 0 -10000 0 0
RAN 0.027 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.028 0.055 -10000 0 -0.57 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.015 0.14 0.29 1 -0.55 8 9
Axin1/APC/GSK3 0.049 0.074 0.3 2 -0.42 1 3
Axin1/APC/GSK3/beta catenin/Macf1 0.054 0.078 0.38 3 -0.37 1 4
HNF1A 0.015 0.078 -10000 0 -0.64 4 4
CTBP1 0.024 0.006 -10000 0 -10000 0 0
MYC 0.012 0.055 0.6 1 -10000 0 1
RANBP3 0.028 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.039 0.042 -10000 0 -0.42 1 1
NKD1 -0.15 0.29 -10000 0 -0.64 76 76
TCF4 0.023 0.008 -10000 0 -10000 0 0
TCF3 0.025 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.05 0.033 -10000 0 -10000 0 0
Ran/GTP 0.02 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.027 0.096 0.42 1 -0.41 6 7
LEF1 -0.029 0.18 -10000 0 -0.64 23 23
DVL1 0.022 0.046 -10000 0 -0.56 1 1
CSNK2A1 0.027 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.041 0.1 0.33 2 -0.47 2 4
DKK1/LRP6/Kremen 2 0.036 0.036 -10000 0 -10000 0 0
LRP6 0.027 0.006 -10000 0 -10000 0 0
CSNK1A1 0.025 0.006 -10000 0 -10000 0 0
NLK 0.027 0.008 -10000 0 -10000 0 0
CCND1 0.006 0.1 0.9 1 -1.4 1 2
WNT1 0.014 0.032 -10000 0 -10000 0 0
GSK3A 0.029 0.004 -10000 0 -10000 0 0
GSK3B 0.027 0.006 -10000 0 -10000 0 0
FRAT1 0.027 0.004 -10000 0 -10000 0 0
PPP2R5D 0.078 0.16 0.31 73 -0.33 9 82
APC 0.064 0.12 0.5 12 -10000 0 12
WNT1/LRP6/FZD1 0.017 0.024 -10000 0 -10000 0 0
CREBBP 0.023 0.008 -10000 0 -10000 0 0
Wnt signaling

Figure 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
Noncanonical Wnts/FZD 0 0.09 -9999 0 -0.31 19 19
FZD6 0.027 0.004 -9999 0 -10000 0 0
WNT6 0.021 0.042 -9999 0 -0.64 1 1
WNT4 0.005 0.11 -9999 0 -0.6 9 9
FZD3 0.027 0.006 -9999 0 -10000 0 0
WNT5A 0.012 0.037 -9999 0 -10000 0 0
WNT11 -0.003 0.13 -9999 0 -0.64 12 12
ErbB2/ErbB3 signaling events

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
USP8 -0.004 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.034 0.069 -10000 0 -0.34 2 2
NFATC4 -0.008 0.075 0.31 8 -0.32 1 9
ERBB2IP 0.027 0.006 -10000 0 -10000 0 0
HSP90 (dimer) 0.026 0.007 -10000 0 -10000 0 0
mammary gland morphogenesis 0.011 0.059 -10000 0 -0.33 7 7
JUN 0.016 0.058 0.28 1 -10000 0 1
HRAS 0.027 0.003 -10000 0 -10000 0 0
DOCK7 -0.016 0.06 0.28 1 -0.32 6 7
ErbB2/ErbB3/neuregulin 1 beta/SHC 0.033 0.068 -10000 0 -0.37 7 7
AKT1 0.007 0.005 -10000 0 -10000 0 0
BAD -0.004 0.005 -10000 0 -10000 0 0
MAPK10 0.012 0.061 0.19 8 -10000 0 8
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta 0.013 0.064 -10000 0 -0.36 7 7
RAF1 0.008 0.071 0.32 3 -0.37 1 4
ErbB2/ErbB3/neuregulin 2 0.025 0.057 -10000 0 -0.39 5 5
STAT3 0.03 0.053 -10000 0 -0.83 1 1
cell migration 0.025 0.088 0.31 14 -10000 0 14
mol:PI-3-4-5-P3 0 0.002 -10000 0 -10000 0 0
cell proliferation -0.034 0.16 0.36 1 -0.58 8 9
FOS -0.059 0.19 0.3 2 -0.5 43 45
NRAS 0.026 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.011 0.059 -10000 0 -0.33 7 7
MAPK3 -0.007 0.1 0.33 2 -10000 0 2
MAPK1 -0.036 0.18 0.35 2 -0.67 13 15
JAK2 -0.016 0.061 0.28 1 -0.32 7 8
NF2 0.009 0.038 -10000 0 -0.62 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 0.013 0.067 -10000 0 -0.33 7 7
NRG1 0.015 0.081 -10000 0 -0.58 5 5
GRB2/SOS1 0.038 0.012 -10000 0 -10000 0 0
MAPK8 0.013 0.074 0.25 1 -0.3 7 8
MAPK9 0.011 0.059 0.19 7 -10000 0 7
ERBB2 -0.019 0.007 -10000 0 -10000 0 0
ERBB3 0.02 0.068 -10000 0 -0.64 3 3
SHC1 0.027 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.012 -10000 0 -10000 0 0
apoptosis 0 0.009 -10000 0 -10000 0 0
STAT3 (dimer) 0.03 0.052 -10000 0 -0.81 1 1
RNF41 -0.007 0.005 -10000 0 -10000 0 0
FRAP1 -0.002 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.001 0.041 -10000 0 -0.25 5 5
ErbB2/ErbB2/HSP90 (dimer) 0.013 0.014 -10000 0 -10000 0 0
CHRNA1 -0.022 0.1 0.32 2 -0.46 2 4
myelination -0.004 0.084 0.34 10 -0.28 1 11
PPP3CB -0.015 0.059 0.27 1 -0.3 7 8
KRAS 0.026 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.028 0.068 0.27 1 -0.42 1 2
NRG2 0.021 0.059 -10000 0 -0.54 3 3
mol:GDP 0.013 0.067 -10000 0 -0.33 7 7
SOS1 0.027 0.005 -10000 0 -10000 0 0
MAP2K2 -0.008 0.07 0.31 3 -0.35 1 4
SRC 0.026 0.009 -10000 0 -10000 0 0
mol:cAMP -0.001 0.001 -10000 0 -10000 0 0
PTPN11 -0.015 0.062 0.28 1 -0.32 7 8
MAP2K1 -0.015 0.14 0.36 1 -0.65 5 6
heart morphogenesis 0.011 0.059 -10000 0 -0.33 7 7
RAS family/GDP 0.048 0.071 0.27 1 -0.4 1 2
GRB2 0.026 0.007 -10000 0 -10000 0 0
PRKACA 0.013 0.04 -10000 0 -0.65 1 1
CHRNE 0.011 0.018 0.1 2 -10000 0 2
HSP90AA1 0.026 0.007 -10000 0 -10000 0 0
activation of caspase activity -0.007 0.005 -10000 0 -10000 0 0
nervous system development 0.011 0.059 -10000 0 -0.33 7 7
CDC42 0.026 0.008 -10000 0 -10000 0 0
IL12-mediated signaling events

Figure S81.  Get High-res Image This plot