PARADIGM pathway analysis of mRNASeq expression data
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1D50MBF
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 35 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Nephrin/Neph1 signaling in the kidney podocyte 134
EGFR-dependent Endothelin signaling events 113
Angiopoietin receptor Tie2-mediated signaling 97
Glypican 2 network 79
FOXA2 and FOXA3 transcription factor networks 69
PDGFR-alpha signaling pathway 66
Thromboxane A2 receptor signaling 51
Glypican 1 network 40
Arf6 signaling events 39
Signaling mediated by p38-alpha and p38-beta 39
Results
Summary Table

The following list describes the columns found in Table 2.

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

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

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

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

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

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

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

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

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

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

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

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

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
Nephrin/Neph1 signaling in the kidney podocyte 0.4621 134 4557 34 -0.6 0.013 1000 -1000 -0.058 -1000
EGFR-dependent Endothelin signaling events 0.3897 113 2382 21 -0.72 0.019 1000 -1000 -0.067 -1000
Angiopoietin receptor Tie2-mediated signaling 0.3345 97 8554 88 -0.98 0.084 1000 -1000 -0.11 -1000
Glypican 2 network 0.2724 79 317 4 -0.12 -1000 1000 -1000 -0.019 -1000
FOXA2 and FOXA3 transcription factor networks 0.2379 69 3185 46 -1.2 0.019 1000 -1000 -0.11 -1000
PDGFR-alpha signaling pathway 0.2276 66 2924 44 -0.32 0.028 1000 -1000 -0.059 -1000
Thromboxane A2 receptor signaling 0.1759 51 5458 105 -0.72 0.088 1000 -1000 -0.058 -1000
Glypican 1 network 0.1379 40 1933 48 -0.42 0.031 1000 -1000 -0.046 -1000
Arf6 signaling events 0.1345 39 2478 62 -0.72 0.032 1000 -1000 -0.065 -1000
Signaling mediated by p38-alpha and p38-beta 0.1345 39 1718 44 -0.2 0.013 1000 -1000 -0.051 -1000
BMP receptor signaling 0.1207 35 2861 81 -0.52 0.019 1000 -1000 -0.087 -1000
Endothelins 0.1207 35 3453 96 -0.62 0.013 1000 -1000 -0.082 -1000
amb2 Integrin signaling 0.1172 34 2821 82 -0.47 0.013 1000 -1000 -0.081 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1172 34 2707 78 -0.34 0.059 1000 -1000 -0.062 -1000
IL4-mediated signaling events 0.1103 32 2986 91 -0.92 0.57 1000 -1000 -0.14 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1103 32 4016 125 -0.16 0.032 1000 -1000 -0.09 -1000
TCGA08_retinoblastoma 0.1103 32 260 8 -0.23 0.061 1000 -1000 -0.014 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.1069 31 2115 68 -0.62 0.098 1000 -1000 -0.11 -1000
S1P1 pathway 0.0897 26 951 36 -0.2 0.013 1000 -1000 -0.055 -1000
FOXM1 transcription factor network 0.0897 26 1327 51 -0.22 0.023 1000 -1000 -0.16 -1000
Integrins in angiogenesis 0.0862 25 2178 84 -0.54 0.035 1000 -1000 -0.082 -1000
Signaling events mediated by PTP1B 0.0759 22 1727 76 -0.73 0.098 1000 -1000 -0.08 -1000
Effects of Botulinum toxin 0.0759 22 572 26 -0.23 0.015 1000 -1000 -0.065 -1000
Syndecan-4-mediated signaling events 0.0759 22 1528 67 -0.45 0.077 1000 -1000 -0.095 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0759 22 2653 120 -0.31 0.14 1000 -1000 -0.072 -1000
TCR signaling in naïve CD8+ T cells 0.0690 20 1927 93 -0.58 0.28 1000 -1000 -0.076 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0690 20 1536 74 -0.72 0.051 1000 -1000 -0.09 -1000
Aurora C signaling 0.0655 19 138 7 -0.13 0.012 1000 -1000 -0.031 -1000
FoxO family signaling 0.0586 17 1128 64 -0.9 0.09 1000 -1000 -0.074 -1000
LPA4-mediated signaling events 0.0552 16 196 12 -0.25 0.019 1000 -1000 -0.019 -1000
Ephrin A reverse signaling 0.0552 16 115 7 -0.048 0 1000 -1000 -0.032 -1000
Glucocorticoid receptor regulatory network 0.0552 16 1838 114 -0.66 0.17 1000 -1000 -0.065 -1000
Signaling events regulated by Ret tyrosine kinase 0.0552 16 1316 82 -0.13 0.013 1000 -1000 -0.073 -1000
Plasma membrane estrogen receptor signaling 0.0552 16 1423 86 -0.17 0.024 1000 -1000 -0.082 -1000
Syndecan-1-mediated signaling events 0.0517 15 541 34 -0.12 0.013 1000 -1000 -0.053 -1000
Signaling events mediated by the Hedgehog family 0.0483 14 772 52 -0.064 0.023 1000 -1000 -0.062 -1000
E-cadherin signaling events 0.0483 14 72 5 -0.055 0.013 1000 -1000 -0.04 -1000
Aurora B signaling 0.0483 14 986 67 -0.31 0.013 1000 -1000 -0.065 -1000
Coregulation of Androgen receptor activity 0.0448 13 1052 76 -0.72 0.022 1000 -1000 -0.044 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0448 13 389 28 -0.16 0.018 1000 -1000 -0.032 -1000
p75(NTR)-mediated signaling 0.0448 13 1702 125 -0.46 0.032 1000 -1000 -0.099 -1000
Calcium signaling in the CD4+ TCR pathway 0.0448 13 419 31 -0.16 0.014 1000 -1000 -0.082 -1000
Nongenotropic Androgen signaling 0.0448 13 685 52 -0.087 0.022 1000 -1000 -0.061 -1000
Wnt signaling 0.0448 13 97 7 -0.032 0.013 1000 -1000 -0.031 -1000
Reelin signaling pathway 0.0414 12 686 56 -0.18 0.019 1000 -1000 -0.071 -1000
IL27-mediated signaling events 0.0414 12 624 51 -1.1 0.18 1000 -1000 -0.084 -1000
IL6-mediated signaling events 0.0414 12 945 75 -0.27 0.053 1000 -1000 -0.091 -1000
IL12-mediated signaling events 0.0379 11 961 87 -0.18 0.025 1000 -1000 -0.14 -1000
ErbB4 signaling events 0.0379 11 786 69 -0.3 0.12 1000 -1000 -0.087 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0379 11 618 54 -0.24 0.025 1000 -1000 -0.083 -1000
HIF-1-alpha transcription factor network 0.0379 11 844 76 -0.16 0.05 1000 -1000 -0.15 -1000
E-cadherin signaling in keratinocytes 0.0379 11 479 43 -0.3 0.036 1000 -1000 -0.063 -1000
Regulation of nuclear SMAD2/3 signaling 0.0345 10 1455 136 -0.62 0.069 1000 -1000 -0.069 -1000
Osteopontin-mediated events 0.0345 10 394 38 -0.11 0.037 1000 -1000 -0.093 -1000
Noncanonical Wnt signaling pathway 0.0345 10 278 26 -0.16 0.013 1000 -1000 -0.056 -1000
Presenilin action in Notch and Wnt signaling 0.0345 10 627 61 -0.22 0.1 1000 -1000 -0.076 -1000
S1P3 pathway 0.0345 10 455 42 -0.16 0.02 1000 -1000 -0.032 -1000
Visual signal transduction: Rods 0.0345 10 564 52 -0.21 0.013 1000 -1000 -0.082 -1000
Class IB PI3K non-lipid kinase events 0.0345 10 30 3 -0.009 -1000 1000 -1000 -0.01 -1000
Regulation of Androgen receptor activity 0.0345 10 729 70 -0.83 0.028 1000 -1000 -0.064 -1000
EPHB forward signaling 0.0310 9 784 85 -0.22 0.071 1000 -1000 -0.099 -1000
Regulation of Telomerase 0.0310 9 1019 102 -0.73 0.043 1000 -1000 -0.1 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0310 9 307 33 -0.23 0.036 1000 -1000 -0.054 -1000
PLK2 and PLK4 events 0.0276 8 24 3 -0.011 0.01 1000 -1000 -0.013 -1000
S1P5 pathway 0.0276 8 151 17 -0.061 0.031 1000 -1000 -0.03 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0276 8 463 52 -0.33 0.057 1000 -1000 -0.056 -1000
E-cadherin signaling in the nascent adherens junction 0.0276 8 659 76 -0.055 0.03 1000 -1000 -0.076 -1000
Syndecan-2-mediated signaling events 0.0241 7 535 69 -0.47 0.04 1000 -1000 -0.047 -1000
Fc-epsilon receptor I signaling in mast cells 0.0241 7 692 97 -0.13 0.03 1000 -1000 -0.08 -1000
Insulin-mediated glucose transport 0.0241 7 249 32 -0.14 0.07 1000 -1000 -0.073 -1000
Ceramide signaling pathway 0.0241 7 597 76 -0.72 0.25 1000 -1000 -0.058 -1000
IL23-mediated signaling events 0.0241 7 463 60 -0.12 0.023 1000 -1000 -0.16 -1000
PDGFR-beta signaling pathway 0.0241 7 729 97 -0.14 0.046 1000 -1000 -0.08 -1000
Caspase cascade in apoptosis 0.0207 6 514 74 -0.41 0.041 1000 -1000 -0.037 -1000
JNK signaling in the CD4+ TCR pathway 0.0207 6 110 17 -0.032 0.029 1000 -1000 -0.056 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0207 6 555 85 -0.11 0.035 1000 -1000 -0.071 -1000
IL1-mediated signaling events 0.0207 6 423 62 -0.2 0.059 1000 -1000 -0.1 -1000
Syndecan-3-mediated signaling events 0.0207 6 222 35 -0.18 0.019 1000 -1000 -0.063 -1000
TCGA08_rtk_signaling 0.0207 6 178 26 -0.3 0.028 1000 -1000 -0.022 -1000
IL2 signaling events mediated by STAT5 0.0207 6 149 22 -0.048 0.046 1000 -1000 -0.045 -1000
BCR signaling pathway 0.0207 6 651 99 -0.08 0.032 1000 -1000 -0.084 -1000
BARD1 signaling events 0.0172 5 306 57 -0.12 0.027 1000 -1000 -0.072 -1000
Nectin adhesion pathway 0.0172 5 330 63 -0.085 0.047 1000 -1000 -0.067 -1000
IL2 signaling events mediated by PI3K 0.0172 5 306 58 -0.055 0.057 1000 -1000 -0.079 -1000
Canonical Wnt signaling pathway 0.0172 5 256 51 -0.22 0.11 1000 -1000 -0.057 -1000
Regulation of p38-alpha and p38-beta 0.0172 5 279 54 -0.19 0.062 1000 -1000 -0.06 -1000
S1P4 pathway 0.0172 5 149 25 -0.061 0.027 1000 -1000 -0.052 -1000
Ras signaling in the CD4+ TCR pathway 0.0172 5 101 17 -0.007 0.026 1000 -1000 -0.031 -1000
IFN-gamma pathway 0.0138 4 332 68 -0.32 0.068 1000 -1000 -0.09 -1000
Ephrin B reverse signaling 0.0138 4 223 48 -0.084 0.023 1000 -1000 -0.074 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0138 4 381 83 -0.27 0.049 1000 -1000 -0.069 -1000
LPA receptor mediated events 0.0138 4 442 102 -0.12 0.054 1000 -1000 -0.087 -1000
ErbB2/ErbB3 signaling events 0.0103 3 205 65 -0.12 0.034 1000 -1000 -0.069 -1000
Cellular roles of Anthrax toxin 0.0103 3 151 39 -0.2 0.018 1000 -1000 -0.028 -1000
FAS signaling pathway (CD95) 0.0103 3 164 47 -0.11 0.022 1000 -1000 -0.047 -1000
Arf6 trafficking events 0.0103 3 259 71 -0.34 0.041 1000 -1000 -0.076 -1000
IGF1 pathway 0.0103 3 198 57 -0.039 0.043 1000 -1000 -0.09 -1000
Signaling events mediated by PRL 0.0103 3 106 34 -0.03 0.022 1000 -1000 -0.043 -1000
Signaling events mediated by HDAC Class II 0.0069 2 170 75 -0.16 0.038 1000 -1000 -0.059 -1000
Aurora A signaling 0.0069 2 145 60 -0.095 0.04 1000 -1000 -0.052 -1000
PLK1 signaling events 0.0069 2 240 85 -0.091 0.024 1000 -1000 -0.042 -1000
Class I PI3K signaling events mediated by Akt 0.0069 2 141 68 -0.14 0.047 1000 -1000 -0.055 -1000
HIF-2-alpha transcription factor network 0.0069 2 104 43 -0.22 0.13 1000 -1000 -0.088 -1000
Signaling mediated by p38-gamma and p38-delta 0.0069 2 34 15 0 0.025 1000 -1000 -0.028 -1000
Retinoic acid receptors-mediated signaling 0.0069 2 156 58 -0.061 0.034 1000 -1000 -0.07 -1000
Class I PI3K signaling events 0.0069 2 216 73 -0.063 0.038 1000 -1000 -0.064 -1000
Insulin Pathway 0.0069 2 159 74 -0.044 0.034 1000 -1000 -0.087 -1000
Visual signal transduction: Cones 0.0034 1 72 38 -0.015 0.016 1000 -1000 -0.067 -1000
Hedgehog signaling events mediated by Gli proteins 0.0034 1 97 65 -0.061 0.062 1000 -1000 -0.063 -1000
EPO signaling pathway 0.0034 1 59 55 -0.035 0.075 1000 -1000 -0.085 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0034 1 47 37 -0.03 0.032 1000 -1000 -0.059 -1000
TRAIL signaling pathway 0.0034 1 54 48 -0.008 0.044 1000 -1000 -0.072 -1000
Signaling events mediated by HDAC Class I 0.0034 1 160 104 -0.16 0.053 1000 -1000 -0.067 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0034 1 66 45 -0.027 0.059 1000 -1000 -0.083 -1000
VEGFR1 specific signals 0.0034 1 91 56 -0.007 0.048 1000 -1000 -0.076 -1000
Rapid glucocorticoid signaling 0.0034 1 21 20 -0.002 0.013 1000 -1000 -0.043 -1000
p38 MAPK signaling pathway 0.0034 1 62 44 -0.042 0.041 1000 -1000 -0.064 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 10 23 -0.002 0.045 1000 -1000 -0.059 -1000
Canonical NF-kappaB pathway 0.0000 0 38 39 -0.011 0.078 1000 -1000 -0.087 -1000
Circadian rhythm pathway 0.0000 0 8 22 -0.012 0.044 1000 -1000 -0.05 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 1 5 0.011 0.018 1000 -1000 -0.02 -1000
Arf6 downstream pathway 0.0000 0 3 43 -0.025 0.026 1000 -1000 -0.042 -1000
mTOR signaling pathway 0.0000 0 51 53 -0.006 0.033 1000 -1000 -0.064 -1000
Signaling events mediated by HDAC Class III 0.0000 0 27 40 -0.02 0.022 1000 -1000 -0.046 -1000
ceramide signaling pathway 0.0000 0 45 49 -0.011 0.046 1000 -1000 -0.054 -1000
TCGA08_p53 0.0000 0 0 7 -0.15 0.096 1000 -1000 -0.016 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 3 36 -0.036 0.038 1000 -1000 -0.074 -1000
Atypical NF-kappaB pathway 0.0000 0 30 31 -0.003 0.046 1000 -1000 -0.044 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 3 27 -0.001 0.032 1000 -1000 -0.056 -1000
Arf1 pathway 0.0000 0 12 54 -0.006 0.03 1000 -1000 -0.043 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.019 1000 -1000 -0.065 -1000
Total NA 1865 108455 7203 -32 -2000 131000 -131000 -8.7 -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 0.48 0.35 0.72 195 -10000 0 195
KIRREL -0.12 0.24 -10000 0 -0.87 27 27
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.49 0.36 -10000 0 -0.72 195 195
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.011 0.018 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.52 0.38 -10000 0 -0.7 216 216
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.4 0.31 -10000 0 -0.54 216 216
FYN -0.49 0.36 -10000 0 -0.66 216 216
mol:Ca2+ -0.52 0.37 -10000 0 -0.69 216 216
mol:DAG -0.52 0.37 -10000 0 -0.7 216 216
NPHS2 -0.35 0.4 -10000 0 -0.87 109 109
mol:IP3 -0.52 0.37 -10000 0 -0.7 216 216
regulation of endocytosis -0.46 0.34 -10000 0 -0.62 216 216
Nephrin/NEPH1/podocin/Cholesterol -0.53 0.38 -10000 0 -0.71 216 216
establishment of cell polarity -0.48 0.35 -10000 0 -0.72 195 195
Nephrin/NEPH1/podocin/NCK1-2 -0.49 0.35 -10000 0 -0.65 216 216
Nephrin/NEPH1/beta Arrestin2 -0.47 0.35 -10000 0 -0.64 216 216
NPHS1 -0.55 0.4 -10000 0 -0.85 187 187
Nephrin/NEPH1/podocin -0.5 0.36 -10000 0 -0.67 216 216
TJP1 0.013 0 -10000 0 -10000 0 0
NCK1 0.013 0 -10000 0 -10000 0 0
NCK2 0.013 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.52 0.38 -10000 0 -0.7 216 216
CD2AP 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.52 0.38 -10000 0 -0.7 216 216
GRB2 0.013 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.6 0.4 -10000 0 -0.75 235 235
cytoskeleton organization -0.52 0.39 -10000 0 -0.7 216 216
Nephrin/NEPH1 -0.37 0.28 -10000 0 -0.55 195 195
Nephrin/NEPH1/ZO-1 -0.41 0.3 -10000 0 -0.6 195 195
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.013 0 -9999 0 -10000 0 0
EGFR 0.013 0 -9999 0 -10000 0 0
EGF/EGFR -0.42 0.16 -9999 0 -0.46 264 264
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.41 0.14 -9999 0 -0.46 261 261
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.024 0.17 -9999 0 -0.81 13 13
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.72 0.24 -9999 0 -0.81 261 261
EGF/EGFR dimer/SHC -0.48 0.16 -9999 0 -0.54 261 261
mol:GDP -0.4 0.14 -9999 0 -0.45 261 261
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.008 0.054 -9999 0 -0.46 3 3
GRB2/SOS1 0.019 0 -9999 0 -10000 0 0
HRAS/GTP -0.37 0.12 -9999 0 -0.42 261 261
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.38 0.13 -9999 0 -0.42 261 261
FRAP1 -0.39 0.14 -9999 0 -0.43 261 261
EGF/EGFR dimer -0.56 0.19 -9999 0 -0.62 261 261
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.014 0.14 -9999 0 -0.62 14 14
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.56 0.56 -10000 0 -1 166 166
NCK1/PAK1/Dok-R -0.26 0.22 -10000 0 -0.44 166 166
NCK1/Dok-R -0.74 0.72 -10000 0 -1.3 166 166
PIK3CA 0.014 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.084 0.12 0.25 96 -10000 0 96
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.011 0.002 -10000 0 -10000 0 0
Rac/GDP 0.009 0 -10000 0 -10000 0 0
F2 0.066 0.14 0.26 43 -0.31 13 56
TNIP2 0.013 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.68 0.61 -10000 0 -1.2 166 166
FN1 -0.009 0.079 -10000 0 -0.29 21 21
PLD2 -0.77 0.77 -10000 0 -1.4 166 166
PTPN11 0.013 0 -10000 0 -10000 0 0
GRB14 -0.044 0.21 -10000 0 -0.81 20 20
ELK1 -0.64 0.64 -10000 0 -1.2 166 166
GRB7 0.013 0 -10000 0 -10000 0 0
PAK1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.74 0.66 -10000 0 -1.3 166 166
CDKN1A -0.37 0.38 -10000 0 -0.7 155 155
ITGA5 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.74 0.72 -10000 0 -1.3 166 166
CRK 0.013 0 -10000 0 -10000 0 0
mol:NO -0.38 0.4 -10000 0 -0.72 166 166
PLG -0.98 0.72 -10000 0 -1.6 166 166
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.52 0.52 -10000 0 -0.96 166 166
GRB2 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.011 0.002 -10000 0 -10000 0 0
ANGPT2 -0.28 0.34 -10000 0 -0.77 74 74
BMX -0.77 0.77 -10000 0 -1.4 166 166
ANGPT1 -0.49 0.67 -10000 0 -1.4 96 96
tube development -0.43 0.42 -10000 0 -0.79 164 164
ANGPT4 0.003 0.036 -10000 0 -0.29 4 4
response to hypoxia -0.038 0.036 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.83 0.81 -10000 0 -1.5 166 166
alpha5/beta1 Integrin 0.019 0 -10000 0 -10000 0 0
FGF2 0.005 0.083 -10000 0 -0.8 3 3
STAT5A (dimer) -0.5 0.5 -10000 0 -0.92 164 164
mol:L-citrulline -0.38 0.4 -10000 0 -0.72 166 166
AGTR1 -0.24 0.38 -10000 0 -0.81 91 91
MAPK14 -0.76 0.74 -10000 0 -1.4 166 166
Tie2/SHP2 -0.67 0.64 -10000 0 -1.3 149 149
TEK -0.74 0.74 -10000 0 -1.4 149 149
RPS6KB1 -0.53 0.53 -10000 0 -0.98 166 166
Angiotensin II/AT1 -0.19 0.3 -10000 0 -0.63 91 91
Tie2/Ang1/GRB2 -0.81 0.81 -10000 0 -1.5 166 166
MAPK3 -0.67 0.67 -10000 0 -1.2 166 166
MAPK1 -0.67 0.67 -10000 0 -1.2 166 166
Tie2/Ang1/GRB7 -0.81 0.81 -10000 0 -1.5 166 166
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 -0.78 0.77 -10000 0 -1.4 166 166
PI3K -0.68 0.66 -10000 0 -1.2 166 166
FES -0.76 0.74 -10000 0 -1.4 166 166
Crk/Dok-R -0.74 0.72 -10000 0 -1.3 166 166
Tie2/Ang1/ABIN2 -0.81 0.81 -10000 0 -1.5 166 166
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.48 0.48 -10000 0 -0.89 166 166
STAT5A 0.013 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.53 0.53 -10000 0 -0.98 166 166
Tie2/Ang2 -0.65 0.63 -10000 0 -1.2 164 164
Tie2/Ang1 -0.9 0.9 -10000 0 -1.6 166 166
FOXO1 -0.48 0.49 -10000 0 -0.9 166 166
ELF1 -0.036 0.055 -10000 0 -10000 0 0
ELF2 -0.79 0.78 -10000 0 -1.4 166 166
mol:Choline -0.71 0.7 -10000 0 -1.3 166 166
cell migration -0.14 0.12 -10000 0 -0.26 84 84
FYN -0.5 0.5 -10000 0 -0.92 164 164
DOK2 -0.009 0.087 -10000 0 -0.81 1 1
negative regulation of cell cycle -0.33 0.34 -10000 0 -0.62 155 155
ETS1 -0.066 0.11 -10000 0 -10000 0 0
PXN -0.41 0.43 -10000 0 -0.78 166 166
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 -0.45 0.46 -10000 0 -0.85 166 166
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.09 0.15 -10000 0 -0.52 13 13
MAPKKK cascade -0.71 0.7 -10000 0 -1.3 166 166
RASA1 0.013 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.82 0.81 -10000 0 -1.5 166 166
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis -0.34 0.36 -10000 0 -0.64 166 166
mol:Phosphatidic acid -0.71 0.7 -10000 0 -1.3 166 166
mol:Angiotensin II 0 0.003 -10000 0 -10000 0 0
mol:NADP -0.38 0.4 -10000 0 -0.72 166 166
Rac1/GTP -0.52 0.44 -10000 0 -0.9 166 166
MMP2 -0.77 0.77 -10000 0 -1.4 166 166
Glypican 2 network

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
MDK -0.069 0.14 -9999 0 -0.29 78 78
GPC2 -0.12 0.15 -9999 0 -0.29 127 127
GPC2/Midkine -0.12 0.15 -9999 0 -0.37 56 56
neuron projection morphogenesis -0.12 0.15 -9999 0 -0.36 56 56
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.48 0.41 -9999 0 -1.1 76 76
PCK1 -1.1 0.71 -9999 0 -1.7 180 180
HNF4A -0.57 0.55 -9999 0 -1.3 80 80
KCNJ11 -0.5 0.43 -9999 0 -1.1 80 80
AKT1 -0.23 0.14 -9999 0 -0.45 9 9
response to starvation -0.005 0.017 -9999 0 -10000 0 0
DLK1 -0.52 0.44 -9999 0 -1.1 79 79
NKX2-1 -0.12 0.15 -9999 0 -10000 0 0
ACADM -0.48 0.42 -9999 0 -1.1 74 74
TAT -0.44 0.24 -9999 0 -0.75 71 71
CEBPB -0.035 0.064 -9999 0 -0.35 9 9
CEBPA -0.054 0.1 -9999 0 -0.38 20 20
TTR -0.74 0.41 -9999 0 -0.98 166 166
PKLR -0.63 0.62 -9999 0 -1.5 90 90
APOA1 -0.61 0.58 -9999 0 -1.4 77 77
CPT1C -0.5 0.44 -9999 0 -1.1 80 80
ALAS1 -0.2 0.15 -9999 0 -10000 0 0
TFRC -0.58 0.31 -9999 0 -0.88 117 117
FOXF1 0.006 0.068 -9999 0 -0.81 2 2
NF1 0.019 0 -9999 0 -10000 0 0
HNF1A (dimer) -0.041 0.11 -9999 0 -0.86 4 4
CPT1A -0.48 0.41 -9999 0 -1.1 76 76
HMGCS1 -0.48 0.41 -9999 0 -1.1 79 79
NR3C1 0.008 0.037 -9999 0 -10000 0 0
CPT1B -0.48 0.42 -9999 0 -1.1 76 76
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.007 -9999 0 -10000 0 0
GCK -0.48 0.41 -9999 0 -1.1 76 76
CREB1 -0.075 0.066 -9999 0 -10000 0 0
IGFBP1 -0.28 0.38 -9999 0 -1.4 25 25
PDX1 -0.25 0.2 -9999 0 -0.84 11 11
UCP2 -0.48 0.42 -9999 0 -1.1 78 78
ALDOB -1.2 0.42 -9999 0 -1.3 275 275
AFP -0.49 0.38 -9999 0 -0.97 77 77
BDH1 -0.48 0.42 -9999 0 -1 82 82
HADH -0.5 0.42 -9999 0 -1.1 76 76
F2 -0.57 0.5 -9999 0 -1.3 80 80
HNF1A -0.041 0.11 -9999 0 -0.86 4 4
G6PC -1.1 0.62 -9999 0 -1.5 197 197
SLC2A2 -0.47 0.58 -9999 0 -1.7 51 51
INS 0.001 0.043 -9999 0 -0.3 1 1
FOXA1 -0.23 0.13 -9999 0 -0.46 44 44
FOXA3 -0.46 0.28 -9999 0 -0.54 225 225
FOXA2 -0.58 0.48 -9999 0 -1.2 97 97
ABCC8 -0.51 0.43 -9999 0 -1.1 79 79
ALB -1.1 0.4 -9999 0 -1.2 262 262
PDGFR-alpha signaling pathway

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
PDGFRA -0.3 0.4 -9999 0 -0.82 109 109
PDGF/PDGFRA/CRKL -0.22 0.31 -9999 0 -0.61 109 109
positive regulation of JUN kinase activity -0.18 0.23 -9999 0 -0.47 109 109
CRKL 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.23 0.3 -9999 0 -0.62 109 109
AP1 -0.32 0.48 -9999 0 -1.4 44 44
mol:IP3 -0.23 0.32 -9999 0 -0.63 109 109
PLCG1 -0.23 0.32 -9999 0 -0.63 109 109
PDGF/PDGFRA/alphaV Integrin -0.22 0.31 -9999 0 -0.61 109 109
RAPGEF1 0.013 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.22 0.32 -9999 0 -0.63 109 109
CAV3 0.001 0.018 -9999 0 -0.29 1 1
CAV1 0.011 0.018 -9999 0 -0.29 1 1
SHC/Grb2/SOS1 -0.16 0.24 -9999 0 -0.47 109 109
PDGF/PDGFRA/Shf -0.22 0.31 -9999 0 -0.61 109 109
FOS -0.29 0.49 -9999 0 -1.3 44 44
JUN -0.021 0.026 -9999 0 -10000 0 0
oligodendrocyte development -0.22 0.3 -9999 0 -0.61 109 109
GRB2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:DAG -0.23 0.32 -9999 0 -0.63 109 109
PDGF/PDGFRA -0.3 0.4 -9999 0 -0.82 109 109
actin cytoskeleton reorganization -0.22 0.3 -9999 0 -0.61 109 109
SRF 0.028 0.011 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
PI3K -0.2 0.25 -9999 0 -0.52 109 109
PDGF/PDGFRA/Crk/C3G -0.2 0.26 -9999 0 -0.52 109 109
JAK1 -0.22 0.31 -9999 0 -0.61 109 109
ELK1/SRF -0.16 0.25 -9999 0 -0.47 109 109
SHB 0.013 0 -9999 0 -10000 0 0
SHF 0.013 0 -9999 0 -10000 0 0
CSNK2A1 0.021 0.025 -9999 0 -10000 0 0
GO:0007205 -0.23 0.32 -9999 0 -0.64 109 109
SOS1 0.013 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.18 0.23 -9999 0 -0.47 109 109
PDGF/PDGFRA/SHB -0.22 0.31 -9999 0 -0.61 109 109
PDGF/PDGFRA/Caveolin-1 -0.22 0.31 -9999 0 -0.61 109 109
ITGAV 0.013 0 -9999 0 -10000 0 0
ELK1 -0.2 0.29 -9999 0 -0.57 109 109
PIK3CA 0.013 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.22 0.31 -9999 0 -0.61 109 109
JAK-STAT cascade -0.22 0.31 -9999 0 -0.61 109 109
cell proliferation -0.22 0.3 -9999 0 -0.61 109 109
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.011 0.077 -10000 0 -0.29 20 20
GNB1/GNG2 -0.1 0.089 -10000 0 -0.2 86 86
AKT1 -0.09 0.12 -10000 0 -0.21 17 17
EGF -0.72 0.24 -10000 0 -0.81 261 261
mol:TXA2 -0.001 0.001 -10000 0 -10000 0 0
FGR 0.007 0.1 -10000 0 -0.34 20 20
mol:Ca2+ -0.15 0.17 -10000 0 -0.31 148 148
LYN 0.012 0.095 -10000 0 -0.33 20 20
RhoA/GTP -0.069 0.058 -10000 0 -0.14 7 7
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.17 0.19 -10000 0 -0.34 148 148
GNG2 0.012 0 -10000 0 -10000 0 0
ARRB2 0.011 0.018 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.028 0.12 -10000 0 -0.51 7 7
G beta5/gamma2 -0.13 0.12 -10000 0 -0.26 87 87
PRKCH -0.18 0.19 -10000 0 -0.36 148 148
DNM1 -0.085 0.15 -10000 0 -0.3 91 91
TXA2/TP beta/beta Arrestin3 -0.026 0.043 -10000 0 -0.3 1 1
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.012 0.001 -10000 0 -10000 0 0
G12 family/GTP -0.17 0.14 -10000 0 -0.3 148 148
ADRBK1 0.012 0 -10000 0 -10000 0 0
ADRBK2 0.012 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.004 0.008 -10000 0 -10000 0 0
mol:GDP 0.088 0.12 0.38 19 -10000 0 19
mol:NADP -0.016 0.15 -10000 0 -0.81 10 10
RAB11A 0.013 0 -10000 0 -10000 0 0
PRKG1 -0.19 0.36 -10000 0 -0.81 73 73
mol:IP3 -0.2 0.21 -10000 0 -0.38 148 148
cell morphogenesis 0.004 0.007 -10000 0 -10000 0 0
PLCB2 -0.27 0.28 -10000 0 -0.52 148 148
mol:cGMP -0.001 0.001 -10000 0 -10000 0 0
BLK 0.002 0.097 -10000 0 -0.34 15 15
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.002 0.1 -10000 0 -0.35 18 18
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.007 0.068 -10000 0 -0.81 2 2
PRKCB1 -0.19 0.21 -10000 0 -0.38 148 148
GNAQ 0.013 0 -10000 0 -10000 0 0
mol:L-citrulline -0.016 0.15 -10000 0 -0.81 10 10
TXA2/TXA2-R family -0.27 0.28 -10000 0 -0.53 148 148
LCK 0.009 0.096 -10000 0 -0.33 20 20
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.03 0.11 -10000 0 -0.42 20 20
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.034 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.03 0.11 -10000 0 -0.41 20 20
MAPK14 -0.1 0.13 -10000 0 -0.23 70 70
TGM2/GTP -0.22 0.23 -10000 0 -0.43 148 148
MAPK11 -0.1 0.13 -10000 0 -0.23 86 86
ARHGEF1 -0.082 0.1 -10000 0 -0.19 17 17
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.19 0.21 -10000 0 -0.39 148 148
RAB11/GDP 0.014 0.002 -10000 0 -10000 0 0
ICAM1 -0.14 0.16 -10000 0 -0.28 149 149
cAMP biosynthetic process -0.18 0.19 -10000 0 -0.36 148 148
Gq family/GTP/EBP50 -0.04 0.12 -10000 0 -0.36 8 8
actin cytoskeleton reorganization 0.004 0.007 -10000 0 -10000 0 0
SRC 0.011 0.096 -10000 0 -0.33 19 19
GNB5 0.012 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.1 0.083 -10000 0 -0.32 22 22
VCAM1 -0.15 0.17 -10000 0 -0.3 149 149
TP beta/Gq family/GDP/G beta5/gamma2 -0.028 0.12 -10000 0 -0.51 7 7
platelet activation -0.14 0.18 -10000 0 -0.3 148 148
PGI2/IP 0 0.052 -10000 0 -0.63 2 2
PRKACA 0.016 0.033 -10000 0 -0.38 2 2
Gq family/GDP/G beta5/gamma2 -0.022 0.11 -10000 0 -0.44 7 7
TXA2/TP beta/beta Arrestin2 -0.033 0.06 -10000 0 -0.64 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.011 0.13 -10000 0 -0.48 21 21
mol:DAG -0.22 0.23 -10000 0 -0.43 148 148
EGFR 0.013 0 -10000 0 -10000 0 0
TXA2/TP alpha -0.25 0.26 -10000 0 -0.49 148 148
Gq family/GTP -0.07 0.12 -10000 0 -0.29 67 67
YES1 0.012 0.095 -10000 0 -0.33 20 20
GNAI2/GTP -0.027 0.099 -10000 0 -0.38 20 20
PGD2/DP 0.004 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.013 0 -10000 0 -10000 0 0
FYN 0.012 0.095 -10000 0 -0.33 18 18
mol:NO -0.016 0.15 -10000 0 -0.81 10 10
GNA15 -0.008 0.077 -10000 0 -0.29 20 20
PGK/cGMP -0.15 0.26 -10000 0 -0.57 79 79
RhoA/GDP 0.014 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.003 0.12 -10000 0 -0.43 20 20
NOS3 -0.016 0.15 -10000 0 -0.81 10 10
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.18 0.19 -10000 0 -0.36 148 148
PRKCB -0.18 0.2 -10000 0 -0.36 148 148
PRKCE -0.18 0.2 -10000 0 -0.36 148 148
PRKCD -0.19 0.21 -10000 0 -0.39 148 148
PRKCG -0.21 0.22 -10000 0 -0.41 148 148
muscle contraction -0.25 0.26 -10000 0 -0.49 148 148
PRKCZ -0.17 0.19 -10000 0 -0.34 148 148
ARR3 0.003 0.005 -10000 0 -10000 0 0
TXA2/TP beta -0.021 0.12 -10000 0 -0.43 20 20
PRKCQ -0.19 0.2 -10000 0 -0.37 149 149
MAPKKK cascade -0.23 0.24 -10000 0 -0.46 148 148
SELE -0.21 0.23 -10000 0 -0.43 148 148
TP beta/GNAI2/GDP/G beta/gamma 0.011 0.12 -10000 0 -0.41 20 20
ROCK1 0.013 0 -10000 0 -10000 0 0
GNA14 -0.16 0.33 -10000 0 -0.81 61 61
chemotaxis -0.31 0.32 -10000 0 -0.62 148 148
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.011 0.018 -10000 0 -0.29 1 1
GNA11 -0.007 0.13 -10000 0 -0.81 7 7
Rac1/GTP 0.003 0.005 -10000 0 -10000 0 0
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 -0.006 0.055 -10000 0 -0.54 3 3
fibroblast growth factor receptor signaling pathway -0.006 0.054 -10000 0 -0.53 3 3
LAMA1 -0.025 0.15 -10000 0 -0.48 22 22
PRNP 0.013 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.12 0.26 -10000 0 -0.62 62 62
SMAD2 0.031 0.009 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ -0.001 0.009 -10000 0 -10000 0 0
GPC1/Laminin alpha1 -0.009 0.12 -10000 0 -0.64 8 8
TDGF1 -0.42 0.41 -10000 0 -0.81 150 150
CRIPTO/GPC1 -0.31 0.32 -10000 0 -0.62 150 150
APP/GPC1 0.018 0.012 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.27 0.28 -10000 0 -0.53 150 150
FLT1 0.007 0.068 -10000 0 -0.81 2 2
GPC1/TGFB/TGFBR1/TGFBR2 0 0.008 -10000 0 -10000 0 0
SERPINC1 -0.11 0.29 -10000 0 -0.81 44 44
FYN -0.27 0.28 -10000 0 -0.53 150 150
FGR -0.27 0.28 -10000 0 -0.54 150 150
positive regulation of MAPKKK cascade -0.26 0.29 -10000 0 -0.54 150 150
SLIT2 -0.16 0.34 -10000 0 -0.79 64 64
GPC1/NRG 0.005 0.089 -10000 0 -0.65 5 5
NRG1 -0.005 0.11 -10000 0 -0.61 8 8
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.006 0.047 -10000 0 -0.54 2 2
LYN -0.27 0.28 -10000 0 -0.53 150 150
mol:Spermine 0.01 0.012 -10000 0 -10000 0 0
cell growth -0.006 0.054 -10000 0 -0.53 3 3
BMP signaling pathway -0.011 0.018 0.29 1 -10000 0 1
SRC -0.27 0.28 -10000 0 -0.54 150 150
TGFBR1 0.013 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.014 0.073 -10000 0 -10000 0 0
GPC1 0.011 0.018 -10000 0 -0.29 1 1
TGFBR1 (dimer) 0.013 0 -10000 0 -10000 0 0
VEGFA 0.009 0.031 -10000 0 -10000 0 0
BLK -0.27 0.28 -10000 0 -0.54 150 150
HCK -0.28 0.28 -10000 0 -0.55 150 150
FGF2 0.004 0.083 -10000 0 -0.81 3 3
FGFR1 0.013 0 -10000 0 -10000 0 0
VEGFR1 homodimer 0.007 0.068 -10000 0 -0.81 2 2
TGFBR2 0.013 0 -10000 0 -10000 0 0
cell death 0.018 0.012 -10000 0 -10000 0 0
ATIII/GPC1 -0.08 0.23 -10000 0 -0.62 44 44
PLA2G2A/GPC1 -0.001 0.053 -10000 0 -0.37 1 1
LCK -0.27 0.28 -10000 0 -0.54 150 150
neuron differentiation 0.005 0.089 -10000 0 -0.65 5 5
PrPc/Cu2+ 0.009 0 -10000 0 -10000 0 0
APP 0.013 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.013 0 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.013 0.036 -9999 0 -0.41 1 1
EGFR 0.012 0 -9999 0 -10000 0 0
EPHA2 0.011 0.018 -9999 0 -10000 0 0
USP6 0 0.06 -9999 0 -0.29 12 12
IQSEC1 0.012 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.56 0.19 -9999 0 -0.62 261 261
ARRB2 -0.003 0.041 -9999 0 -10000 0 0
mol:GTP 0.015 0.012 -9999 0 -10000 0 0
ARRB1 0.01 0.048 -9999 0 -0.81 1 1
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR 0.007 0.031 -9999 0 -0.29 3 3
EGF -0.72 0.24 -9999 0 -0.81 261 261
somatostatin receptor activity 0 0 -9999 0 -0.001 118 118
ARAP2 0.012 0 -9999 0 -10000 0 0
mol:GDP -0.12 0.11 -9999 0 -0.27 89 89
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 52 52
ITGA2B -0.009 0.077 -9999 0 -0.29 20 20
ARF6 0.012 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.032 0.009 -9999 0 -10000 0 0
ADAP1 0.012 0 -9999 0 -10000 0 0
KIF13B 0.013 0 -9999 0 -10000 0 0
HGF/MET -0.044 0.17 -9999 0 -0.66 17 17
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.17 0.12 -9999 0 -0.31 116 116
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.48 0.16 -9999 0 -0.54 261 261
ADRB2 -0.006 0.071 -9999 0 -0.29 17 17
receptor agonist activity 0 0 -9999 0 0 117 117
actin filament binding 0 0 -9999 0 -0.001 118 118
SRC 0.011 0.018 -9999 0 -0.29 1 1
ITGB3 -0.033 0.18 -9999 0 -0.65 20 20
GNAQ 0.012 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 -0.001 0 -9999 0 -0.001 86 86
ARF6/GDP -0.029 0.057 -9999 0 -10000 0 0
ARF6/GDP/GULP/ACAP1 -0.11 0.11 -9999 0 -0.38 13 13
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.006 0.12 -9999 0 -0.49 14 14
ACAP1 -0.026 0.1 -9999 0 -0.29 37 37
ACAP2 0.012 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.012 0.053 -9999 0 -10000 0 0
EFNA1 0.013 0 -9999 0 -10000 0 0
HGF -0.037 0.19 -9999 0 -0.78 18 18
CYTH3 0.01 0 -9999 0 -10000 0 0
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 65 65
endosomal lumen acidification 0 0 -9999 0 -0.001 118 118
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.011 0.018 -9999 0 -0.29 1 1
GNAQ/ARNO 0.008 0.007 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 48 48
MET -0.025 0.1 -9999 0 -0.29 36 36
GNA14 -0.16 0.33 -9999 0 -0.81 61 61
GNA15 -0.009 0.077 -9999 0 -0.29 20 20
GIT1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 103 103
GNA11 -0.008 0.13 -9999 0 -0.81 7 7
LHCGR -0.026 0.09 -9999 0 -10000 0 0
AGTR1 -0.24 0.38 -9999 0 -0.81 91 91
desensitization of G-protein coupled receptor protein signaling pathway -0.012 0.053 -9999 0 -10000 0 0
IPCEF1/ARNO -0.38 0.13 -9999 0 -0.42 261 261
alphaIIb/beta3 Integrin -0.031 0.14 -9999 0 -0.62 14 14
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.2 0.5 -9999 0 -1.3 50 50
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.044 0.15 -9999 0 -0.47 8 8
ATF2/c-Jun -0.018 0.12 -9999 0 -0.43 8 8
MAPK11 -0.044 0.15 -9999 0 -0.32 63 63
MITF -0.046 0.18 -9999 0 -0.38 64 64
MAPKAPK5 -0.045 0.18 -9999 0 -0.38 63 63
KRT8 -0.048 0.18 -9999 0 -0.38 63 63
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.07 0.23 -9999 0 -0.49 63 63
CEBPB -0.049 0.18 -9999 0 -0.38 63 63
SLC9A1 -0.045 0.18 -9999 0 -0.38 63 63
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.038 0.18 -9999 0 -0.36 63 63
p38alpha-beta/MNK1 -0.046 0.19 -9999 0 -0.69 8 8
JUN -0.018 0.12 -9999 0 -0.42 8 8
PPARGC1A -0.057 0.2 -9999 0 -0.4 68 68
USF1 -0.045 0.18 -9999 0 -0.38 63 63
RAB5/GDP/GDI1 -0.059 0.12 -9999 0 -0.47 8 8
NOS2 -0.11 0.38 -9999 0 -1.3 21 21
DDIT3 -0.045 0.18 -9999 0 -0.38 63 63
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.032 0.15 -9999 0 -0.5 9 9
p38alpha-beta/HBP1 -0.046 0.19 -9999 0 -0.62 10 10
CREB1 -0.048 0.19 -9999 0 -0.4 63 63
RAB5/GDP 0.009 0 -9999 0 -10000 0 0
EIF4E -0.035 0.16 -9999 0 -0.62 8 8
RPS6KA4 -0.045 0.18 -9999 0 -0.38 63 63
PLA2G4A -0.049 0.2 -9999 0 -0.74 14 14
GDI1 -0.045 0.18 -9999 0 -0.38 63 63
TP53 -0.063 0.22 -9999 0 -0.47 63 63
RPS6KA5 -0.053 0.2 -9999 0 -0.4 65 65
ESR1 -0.076 0.24 -9999 0 -0.44 73 73
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.045 0.18 -9999 0 -0.38 63 63
MEF2A -0.045 0.18 -9999 0 -0.38 63 63
EIF4EBP1 -0.048 0.19 -9999 0 -0.4 63 63
KRT19 -0.1 0.24 -9999 0 -0.44 83 83
ELK4 -0.045 0.18 -9999 0 -0.38 63 63
ATF6 -0.045 0.18 -9999 0 -0.38 63 63
ATF1 -0.048 0.19 -9999 0 -0.4 63 63
p38alpha-beta/MAPKAPK2 -0.046 0.19 -9999 0 -0.69 8 8
p38alpha-beta/MAPKAPK3 -0.046 0.19 -9999 0 -0.69 8 8
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.52 0.36 -9999 0 -0.66 227 227
SMAD6-7/SMURF1 -0.002 0.031 -9999 0 -0.54 1 1
NOG 0 0.088 -9999 0 -0.55 6 6
SMAD9 -0.072 0.12 -9999 0 -0.5 13 13
SMAD4 0.013 0 -9999 0 -10000 0 0
SMAD5 -0.2 0.19 -9999 0 -0.35 172 172
BMP7/USAG1 -0.33 0.36 -9999 0 -0.7 127 127
SMAD5/SKI -0.18 0.18 -9999 0 -0.47 26 26
SMAD1 -0.011 0.046 -9999 0 -10000 0 0
BMP2 0.013 0 -9999 0 -10000 0 0
SMAD1/SMAD1/SMAD4 -0.008 0.024 -9999 0 -0.4 1 1
BMPR1A 0.013 0 -9999 0 -10000 0 0
BMPR1B -0.48 0.4 -9999 0 -0.8 173 173
BMPR1A-1B/BAMBI -0.32 0.26 -9999 0 -0.54 173 173
AHSG -0.005 0.054 -9999 0 -0.29 10 10
CER1 0.004 0.006 -9999 0 -10000 0 0
BMP2-4/CER1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.15 0.17 -9999 0 -0.54 22 22
BMP2-4 (homodimer) 0.019 0 -9999 0 -10000 0 0
RGMB 0.013 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.28 0.26 -9999 0 -0.49 173 173
RGMA -0.092 0.27 -9999 0 -0.81 37 37
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.17 0.17 -9999 0 -0.48 24 24
BMP2-4/USAG1 -0.12 0.2 -9999 0 -0.54 52 52
SMAD6/SMURF1/SMAD5 -0.18 0.18 -9999 0 -0.47 26 26
SOSTDC1 -0.19 0.31 -9999 0 -0.55 104 104
BMP7/BMPR2/BMPR1A-1B -0.44 0.31 -9999 0 -0.59 219 219
SKI 0.013 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.004 0.083 -9999 0 -0.81 3 3
HFE2 0.007 0.025 -9999 0 -0.29 2 2
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.037 0.14 -9999 0 -0.54 20 20
SMAD5/SMAD5/SMAD4 -0.18 0.18 -9999 0 -0.47 26 26
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.15 0.12 -9999 0 -0.41 22 22
BMP7 (homodimer) -0.25 0.38 -9999 0 -0.81 93 93
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA 0 0.077 -9999 0 -0.67 3 3
SMAD1/SKI -0.004 0.044 -9999 0 -10000 0 0
SMAD6 0.01 0.048 -9999 0 -0.81 1 1
CTDSP2 0.013 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.005 0.026 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.22 0.37 -9999 0 -0.79 84 84
BMPR2 (homodimer) 0.013 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.36 0.31 -9999 0 -0.62 172 172
CHRDL1 -0.31 0.4 -9999 0 -0.81 115 115
ENDOFIN/SMAD1 -0.004 0.044 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.016 0.029 -9999 0 -0.45 1 1
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI 0.008 0.054 -9999 0 -0.46 3 3
SMURF2 0.013 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.21 0.26 -9999 0 -0.54 115 115
BMP2-4/GREM1 -0.15 0.24 -9999 0 -0.54 81 81
SMAD7 0.013 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.06 0.11 -9999 0 -0.52 10 10
SMAD1/SMAD6 -0.004 0.044 -9999 0 -10000 0 0
TAK1/SMAD6 0.019 0 -9999 0 -10000 0 0
BMP7 -0.25 0.38 -9999 0 -0.81 93 93
BMP6 0.004 0.083 -9999 0 -0.81 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.14 0.15 -9999 0 -0.43 24 24
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.004 0.044 -9999 0 -10000 0 0
SMAD7/SMURF1 0.019 0 -9999 0 -10000 0 0
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.29 0.32 -9999 0 -0.78 67 67
CHRD -0.045 0.21 -9999 0 -0.78 21 21
BMPR2 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.18 0.17 -9999 0 -0.52 24 24
BMP4 0.013 0 -9999 0 -10000 0 0
FST -0.18 0.34 -9999 0 -0.77 70 70
BMP2-4/NOG -0.007 0.056 -9999 0 -0.54 3 3
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.42 0.29 -9999 0 -0.55 219 219
Endothelins

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
AKT1 -0.027 0.17 -10000 0 -0.57 17 17
PTK2B 0.012 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.28 0.48 -10000 0 -1 80 80
EDN1 -0.008 0.097 -10000 0 -0.48 3 3
EDN3 0.004 0.035 -10000 0 -0.29 4 4
EDN2 -0.027 0.17 -10000 0 -0.71 16 16
HRAS/GDP -0.12 0.23 -10000 0 -0.52 50 50
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.12 0.22 -10000 0 -0.44 71 71
ADCY4 -0.045 0.2 -10000 0 -0.55 29 29
ADCY5 -0.046 0.18 -10000 0 -0.51 31 31
ADCY6 -0.018 0.14 -10000 0 -0.48 17 17
ADCY7 -0.024 0.15 -10000 0 -0.48 17 17
ADCY1 -0.25 0.28 -10000 0 -0.5 142 142
ADCY2 -0.1 0.16 -10000 0 -0.48 27 27
ADCY3 -0.018 0.14 -10000 0 -0.48 17 17
ADCY8 -0.027 0.15 -10000 0 -0.47 19 19
ADCY9 -0.018 0.14 -10000 0 -0.49 16 16
arachidonic acid secretion -0.16 0.29 -10000 0 -0.59 70 70
ETB receptor/Endothelin-1/Gq/GTP -0.074 0.17 -10000 0 -0.37 66 66
GNAO1 -0.061 0.23 -10000 0 -0.81 25 25
HRAS 0.012 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.036 0.17 0.34 15 -0.53 17 32
ETA receptor/Endothelin-1/Gs/GTP -0.036 0.16 0.32 15 -0.51 17 32
mol:GTP -0.003 0.008 -10000 0 -10000 0 0
COL3A1 -0.043 0.22 -10000 0 -0.71 20 20
EDNRB 0.01 0.052 -10000 0 -0.55 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.094 0.26 -10000 0 -0.75 28 28
CYSLTR1 -0.029 0.18 -10000 0 -0.59 17 17
SLC9A1 -0.025 0.09 0.2 5 -0.31 14 19
mol:GDP -0.14 0.24 -10000 0 -0.54 55 55
SLC9A3 -0.62 0.36 -10000 0 -0.73 243 243
RAF1 -0.15 0.26 -10000 0 -0.55 64 64
JUN -0.15 0.28 -10000 0 -0.7 40 40
JAK2 -0.027 0.17 -10000 0 -0.57 17 17
mol:IP3 -0.13 0.24 -10000 0 -0.5 67 67
ETA receptor/Endothelin-1 -0.052 0.21 0.4 16 -0.66 17 33
PLCB1 -0.1 0.28 -10000 0 -0.81 40 40
PLCB2 -0.027 0.099 -10000 0 -0.29 36 36
ETA receptor/Endothelin-3 -0.037 0.15 -10000 0 -0.68 13 13
FOS -0.19 0.38 -10000 0 -0.95 50 50
Gai/GDP -0.059 0.24 -10000 0 -0.84 25 25
CRK 0.012 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.13 0.26 -10000 0 -0.59 47 47
BCAR1 0.013 0.001 -10000 0 -10000 0 0
PRKCB1 -0.13 0.23 -10000 0 -0.47 71 71
GNAQ 0.01 0.008 -10000 0 -10000 0 0
GNAZ 0.013 0 -10000 0 -10000 0 0
GNAL 0.01 0.048 -10000 0 -0.81 1 1
Gs family/GDP -0.15 0.19 -10000 0 -0.5 51 51
ETA receptor/Endothelin-1/Gq/GTP -0.11 0.24 -10000 0 -0.48 65 65
MAPK14 -0.086 0.17 -10000 0 -0.45 26 26
TRPC6 -0.31 0.52 -10000 0 -1.1 80 80
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.007 0.068 -10000 0 -0.81 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.098 0.18 -10000 0 -0.36 72 72
ETB receptor/Endothelin-2 -0.016 0.14 -10000 0 -0.62 14 14
ETB receptor/Endothelin-3 0.01 0.046 -10000 0 -0.62 1 1
ETB receptor/Endothelin-1 0.003 0.083 -10000 0 -0.65 2 2
MAPK3 -0.18 0.35 -10000 0 -0.82 54 54
MAPK1 -0.18 0.35 -10000 0 -0.82 54 54
Rac1/GDP -0.12 0.23 -10000 0 -0.52 49 49
cAMP biosynthetic process -0.15 0.19 -10000 0 -0.54 34 34
MAPK8 -0.19 0.35 -10000 0 -0.65 82 82
SRC 0.011 0.018 -10000 0 -0.29 1 1
ETB receptor/Endothelin-1/Gi/GTP -0.001 0.098 -10000 0 -0.3 21 21
p130Cas/CRK/Src/PYK2 -0.18 0.29 -10000 0 -0.6 76 76
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.12 0.23 -10000 0 -0.52 50 50
COL1A2 -0.016 0.16 -10000 0 -0.53 9 9
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.063 0.2 -10000 0 -0.68 25 25
mol:DAG -0.13 0.24 -10000 0 -0.5 66 66
MAP2K2 -0.16 0.29 -10000 0 -0.63 62 62
MAP2K1 -0.16 0.29 -10000 0 -0.62 64 64
EDNRA -0.041 0.2 -10000 0 -0.86 13 13
positive regulation of muscle contraction -0.017 0.15 -10000 0 -0.52 15 15
Gq family/GDP -0.19 0.26 -10000 0 -0.63 67 67
HRAS/GTP -0.14 0.24 -10000 0 -0.53 62 62
PRKCH -0.12 0.23 -10000 0 -0.5 58 58
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.12 0.23 -10000 0 -0.51 57 57
PRKCB -0.13 0.23 -10000 0 -0.5 59 59
PRKCE -0.12 0.23 -10000 0 -0.5 57 57
PRKCD -0.12 0.23 -10000 0 -0.53 51 51
PRKCG -0.16 0.24 -10000 0 -0.54 64 64
regulation of vascular smooth muscle contraction -0.22 0.44 -10000 0 -1.1 50 50
PRKCQ -0.14 0.24 -10000 0 -0.51 64 64
PLA2G4A -0.18 0.32 -10000 0 -0.65 70 70
GNA14 -0.16 0.34 -10000 0 -0.81 61 61
GNA15 -0.011 0.077 -10000 0 -0.29 20 20
GNA12 0.013 0 -10000 0 -10000 0 0
GNA11 -0.01 0.13 -10000 0 -0.81 7 7
Rac1/GTP -0.036 0.17 0.34 15 -0.54 16 31
MMP1 -0.046 0.29 -10000 0 -1.1 18 18
amb2 Integrin signaling

Figure S13.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S13.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.051 0.1 -9999 0 -0.4 8 8
alphaM/beta2 Integrin/GPIbA -0.049 0.1 -9999 0 -0.47 4 4
alphaM/beta2 Integrin/proMMP-9 -0.11 0.14 -9999 0 -0.38 51 51
PLAUR -0.008 0.077 -9999 0 -0.29 20 20
HMGB1 0.008 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.047 0.092 -9999 0 -0.35 3 3
AGER -0.014 0.081 -9999 0 -0.3 21 21
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG -0.02 0.094 -9999 0 -0.29 31 31
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.07 0.1 -9999 0 -0.4 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.12 0.17 -9999 0 -0.31 115 115
CYR61 -0.013 0.14 -9999 0 -0.81 9 9
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.19 0.15 -9999 0 -0.43 60 60
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.067 0.24 -9999 0 -0.81 28 28
MYH2 -0.27 0.22 -9999 0 -0.51 90 90
MST1R -0.019 0.11 -9999 0 -0.81 2 2
leukocyte activation during inflammatory response -0.091 0.16 -9999 0 -0.48 32 32
APOB -0.046 0.19 -9999 0 -0.56 29 29
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.004 0.062 -9999 0 -0.38 6 6
JAM3 0.01 0.048 -9999 0 -0.81 1 1
GP1BA 0.01 0.048 -9999 0 -0.81 1 1
alphaM/beta2 Integrin/CTGF -0.06 0.12 -9999 0 -0.5 10 10
alphaM/beta2 Integrin -0.23 0.19 -9999 0 -0.41 109 109
JAM3 homodimer 0.01 0.048 -9999 0 -0.81 1 1
ICAM2 0.013 0 -9999 0 -10000 0 0
ICAM1 0.009 0.031 -9999 0 -0.29 3 3
phagocytosis triggered by activation of immune response cell surface activating receptor -0.23 0.18 -9999 0 -0.41 109 109
cell adhesion -0.048 0.1 -9999 0 -0.46 4 4
NFKB1 -0.048 0.16 -9999 0 -0.53 7 7
THY1 -0.28 0.39 -9999 0 -0.81 105 105
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.063 0.16 -9999 0 -0.55 29 29
alphaM/beta2 Integrin/LRP/tPA -0.088 0.16 -9999 0 -0.51 30 30
IL6 -0.1 0.31 -9999 0 -0.94 30 30
ITGB2 -0.045 0.12 -9999 0 -0.32 6 6
elevation of cytosolic calcium ion concentration -0.06 0.12 -9999 0 -0.43 19 19
alphaM/beta2 Integrin/JAM2/JAM3 -0.047 0.1 -9999 0 -0.47 6 6
JAM2 0.001 0.096 -9999 0 -0.81 4 4
alphaM/beta2 Integrin/ICAM1 -0.05 0.092 -9999 0 -0.46 4 4
alphaM/beta2 Integrin/uPA/Plg -0.33 0.27 -9999 0 -0.54 168 168
RhoA/GTP -0.28 0.24 -9999 0 -0.48 118 118
positive regulation of phagocytosis -0.18 0.15 -9999 0 -0.43 51 51
Ron/MSP -0.007 0.086 -9999 0 -0.62 3 3
alphaM/beta2 Integrin/uPAR/uPA -0.06 0.12 -9999 0 -0.44 19 19
alphaM/beta2 Integrin/uPAR -0.057 0.12 -9999 0 -0.42 15 15
PLAU -0.007 0.13 -9999 0 -0.81 7 7
PLAT -0.07 0.25 -9999 0 -0.79 30 30
actin filament polymerization -0.26 0.21 -9999 0 -0.48 90 90
MST1 0.008 0.054 -9999 0 -0.46 3 3
alphaM/beta2 Integrin/lipoprotein(a) -0.092 0.16 -9999 0 -0.48 32 32
TNF -0.048 0.18 -9999 0 -0.71 8 8
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.06 0.12 -9999 0 -0.49 10 10
fibrinolysis -0.33 0.26 -9999 0 -0.54 168 168
HCK -0.022 0.1 -9999 0 -0.31 31 31
dendritic cell antigen processing and presentation -0.23 0.18 -9999 0 -0.41 109 109
VTN -0.2 0.36 -9999 0 -0.76 82 82
alphaM/beta2 Integrin/CYR61 -0.063 0.13 -9999 0 -0.53 12 12
LPA -0.036 0.18 -9999 0 -0.77 15 15
LRP1 0.013 0 -9999 0 -10000 0 0
cell migration -0.084 0.14 -9999 0 -0.41 31 31
FN1 -0.009 0.079 -9999 0 -0.29 21 21
alphaM/beta2 Integrin/Thy1 -0.24 0.26 -9999 0 -0.56 106 106
MPO -0.005 0.069 -9999 0 -10000 0 0
KNG1 -0.47 0.4 -9999 0 -0.81 169 169
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.26 0.22 -9999 0 -0.51 86 86
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.46 0.4 -9999 0 -0.81 164 164
CTGF -0.007 0.13 -9999 0 -0.81 7 7
alphaM/beta2 Integrin/Hck -0.064 0.13 -9999 0 -0.45 22 22
ITGAM -0.025 0.094 -9999 0 -0.29 31 31
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.1 0.17 -9999 0 -0.46 46 46
HP -0.033 0.11 -9999 0 -0.29 42 42
leukocyte adhesion -0.21 0.23 -9999 0 -0.48 106 106
SELP -0.067 0.24 -9999 0 -0.81 28 28
Signaling events mediated by Stem cell factor receptor (c-Kit)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K1 -0.044 0.17 -10000 0 -0.39 51 51
CRKL -0.037 0.18 -10000 0 -0.41 51 51
HRAS -0.028 0.16 -10000 0 -0.44 12 12
mol:PIP3 -0.047 0.16 -10000 0 -0.4 51 51
SPRED1 0.013 0 -10000 0 -10000 0 0
SPRED2 0.013 0 -10000 0 -10000 0 0
GAB1 -0.046 0.18 -10000 0 -0.44 51 51
FOXO3 -0.027 0.16 -10000 0 -0.37 50 50
AKT1 -0.038 0.17 -10000 0 -0.41 51 51
BAD -0.027 0.16 -10000 0 -0.37 50 50
megakaryocyte differentiation -0.11 0.26 -10000 0 -0.5 79 79
GSK3B -0.027 0.16 -10000 0 -0.37 50 50
RAF1 -0.014 0.13 -10000 0 -0.42 4 4
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.046 0.18 -10000 0 -0.44 51 51
STAT1 -0.13 0.41 -10000 0 -1 50 50
HRAS/SPRED1 -0.014 0.13 -10000 0 -0.42 4 4
cell proliferation -0.053 0.19 -10000 0 -0.45 54 54
PIK3CA 0.012 0 -10000 0 -10000 0 0
TEC 0.013 0 -10000 0 -10000 0 0
RPS6KB1 -0.045 0.18 -10000 0 -0.44 51 51
HRAS/SPRED2 -0.014 0.13 -10000 0 -0.42 4 4
LYN/TEC/p62DOK -0.073 0.16 -10000 0 -0.41 50 50
MAPK3 0.003 0.099 -10000 0 -0.28 4 4
STAP1 -0.34 0.28 -10000 0 -0.5 201 201
GRAP2 0.003 0.053 -10000 0 -0.29 9 9
JAK2 -0.14 0.33 -10000 0 -0.86 50 50
STAT1 (dimer) -0.12 0.4 -10000 0 -1 50 50
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.096 0.17 -10000 0 -0.44 52 52
actin filament polymerization -0.045 0.18 -10000 0 -0.43 51 51
LYN 0.013 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.34 0.31 -10000 0 -0.5 200 200
PIK3R1 0.012 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.02 0.16 -10000 0 -0.37 50 50
PI3K -0.032 0.18 -10000 0 -0.41 50 50
PTEN 0.013 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.16 0.5 -10000 0 -1.3 50 50
MAPK8 -0.054 0.2 -10000 0 -0.46 54 54
STAT3 (dimer) -0.045 0.18 -10000 0 -0.43 51 51
positive regulation of transcription 0.006 0.084 -10000 0 -0.23 4 4
mol:GDP -0.077 0.14 -10000 0 -0.48 12 12
PIK3C2B -0.046 0.18 -10000 0 -0.44 51 51
CBL/CRKL -0.027 0.17 -10000 0 -0.39 50 50
FER -0.046 0.18 -10000 0 -0.44 51 51
SH2B3 -0.046 0.18 -10000 0 -0.44 51 51
PDPK1 -0.037 0.15 -10000 0 -0.37 50 50
SNAI2 -0.089 0.24 -10000 0 -0.49 70 70
positive regulation of cell proliferation -0.083 0.3 -10000 0 -0.74 50 50
KITLG 0.004 0.089 -10000 0 -0.61 5 5
cell motility -0.083 0.3 -10000 0 -0.74 50 50
PTPN6 0.013 0.01 -10000 0 -10000 0 0
EPOR -0.001 0.12 -10000 0 -10000 0 0
STAT5A (dimer) -0.064 0.25 -10000 0 -0.61 51 51
SOCS1 0.006 0.07 -10000 0 -0.64 3 3
cell migration 0.059 0.19 0.45 53 -10000 0 53
SOS1 0.013 0 -10000 0 -10000 0 0
EPO 0.006 0.027 -10000 0 -0.29 2 2
VAV1 -0.063 0.14 -10000 0 -0.81 1 1
GRB10 -0.046 0.18 -10000 0 -0.44 51 51
PTPN11 0.013 0.007 -10000 0 -10000 0 0
SCF/KIT -0.056 0.19 -10000 0 -0.47 51 51
GO:0007205 0.001 0.01 -10000 0 -10000 0 0
MAP2K1 -0.001 0.11 -10000 0 -0.32 4 4
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.19 0.53 -10000 0 -1.3 50 50
MAP2K2 -0.001 0.11 -10000 0 -0.32 4 4
SHC/Grb2/SOS1 -0.072 0.16 -10000 0 -0.41 50 50
STAT5A -0.067 0.26 -10000 0 -0.63 51 51
GRB2 0.013 0 -10000 0 -10000 0 0
response to radiation -0.087 0.23 -10000 0 -0.48 70 70
SHC/GRAP2 0.012 0.036 -10000 0 -10000 0 0
PTPRO -0.11 0.26 -10000 0 -0.52 79 79
SH2B2 -0.047 0.18 -10000 0 -0.44 51 51
DOK1 0.009 0.031 -10000 0 -0.29 3 3
MATK -0.061 0.2 -10000 0 -0.46 53 53
CREBBP 0.031 0.014 -10000 0 -10000 0 0
BCL2 0 0.12 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.51 0.44 -10000 0 -1.2 65 65
STAT6 (cleaved dimer) -0.53 0.43 -10000 0 -1.1 92 92
IGHG1 -0.18 0.14 -10000 0 -0.37 29 29
IGHG3 -0.5 0.43 -10000 0 -1 84 84
AKT1 -0.23 0.2 -10000 0 -0.66 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.17 0.15 -10000 0 -0.6 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.24 0.2 -10000 0 -0.67 12 12
THY1 -0.79 0.68 -10000 0 -1.5 124 124
MYB -0.058 0.13 -10000 0 -0.29 67 67
HMGA1 0.006 0.043 -10000 0 -0.29 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.3 0.23 -10000 0 -0.66 35 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.24 0.19 -10000 0 -0.62 9 9
SP1 0.02 0.004 -10000 0 -10000 0 0
INPP5D 0.002 0.055 -10000 0 -0.29 10 10
SOCS5 0.026 0.012 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.5 0.43 -10000 0 -1.1 75 75
SOCS1 -0.33 0.28 -10000 0 -0.75 51 51
SOCS3 -0.25 0.21 -10000 0 -0.88 5 5
FCER2 -0.39 0.32 -10000 0 -0.86 48 48
PARP14 0.013 0.003 -10000 0 -10000 0 0
CCL17 -0.53 0.44 -10000 0 -1.2 66 66
GRB2 0.013 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.2 0.16 -10000 0 -0.58 5 5
T cell proliferation -0.5 0.45 -10000 0 -1.2 68 68
IL4R/JAK1 -0.5 0.44 -10000 0 -1.1 68 68
EGR2 -0.57 0.55 -10000 0 -1.4 74 74
JAK2 -0.014 0.025 -10000 0 -10000 0 0
JAK3 -0.043 0.12 -10000 0 -0.29 58 58
PIK3R1 0.013 0 -10000 0 -10000 0 0
JAK1 0.003 0.009 -10000 0 -10000 0 0
COL1A2 -0.16 0.14 -10000 0 -0.56 2 2
CCL26 -0.51 0.44 -10000 0 -1.2 67 67
IL4R -0.54 0.47 -10000 0 -1.2 68 68
PTPN6 0.026 0.01 -10000 0 -10000 0 0
IL13RA2 -0.92 0.67 -10000 0 -1.5 165 165
IL13RA1 -0.014 0.025 -10000 0 -10000 0 0
IRF4 -0.11 0.14 -10000 0 -0.81 4 4
ARG1 -0.15 0.13 -10000 0 -0.53 2 2
CBL -0.28 0.22 -10000 0 -0.66 22 22
GTF3A 0.018 0.006 -10000 0 -10000 0 0
PIK3CA 0.013 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.021 0.034 -10000 0 -10000 0 0
IRF4/BCL6 -0.095 0.13 -10000 0 -0.82 3 3
CD40LG 0.008 0.06 -10000 0 -0.3 10 10
MAPK14 -0.28 0.22 -10000 0 -0.68 20 20
mitosis -0.22 0.19 -10000 0 -0.62 8 8
STAT6 -0.58 0.52 -10000 0 -1.3 78 78
SPI1 -0.04 0.12 -10000 0 -0.29 52 52
RPS6KB1 -0.21 0.18 -10000 0 -0.62 6 6
STAT6 (dimer) -0.58 0.52 -10000 0 -1.3 78 78
STAT6 (dimer)/PARP14 -0.54 0.48 -10000 0 -1.2 69 69
mast cell activation 0.014 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.24 0.19 -10000 0 -0.64 12 12
FRAP1 -0.23 0.2 -10000 0 -0.66 8 8
LTA -0.52 0.44 -10000 0 -1.2 63 63
FES 0.01 0.048 -10000 0 -0.81 1 1
T-helper 1 cell differentiation 0.57 0.5 1.2 79 -10000 0 79
CCL11 -0.61 0.55 -10000 0 -1.3 93 93
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.23 0.19 -10000 0 -0.61 12 12
IL2RG 0.008 0.054 -10000 0 -0.29 9 9
IL10 -0.52 0.45 -10000 0 -1.2 68 68
IRS1 -0.002 0.11 -10000 0 -0.81 5 5
IRS2 0.01 0.025 -10000 0 -0.29 2 2
IL4 -0.12 0.098 -10000 0 -10000 0 0
IL5 -0.51 0.44 -10000 0 -1.2 68 68
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.42 0.33 -10000 0 -0.87 68 68
COL1A1 -0.18 0.16 -10000 0 -0.63 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.51 0.46 -10000 0 -1.2 61 61
IL2R gamma/JAK3 -0.025 0.1 -10000 0 -0.38 8 8
TFF3 -0.63 0.6 -10000 0 -1.4 87 87
ALOX15 -0.51 0.44 -10000 0 -1.2 63 63
MYBL1 -0.008 0.077 -10000 0 -0.29 20 20
T-helper 2 cell differentiation -0.42 0.34 -10000 0 -0.89 67 67
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.005 0.053 -10000 0 -0.29 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.23 0.19 -10000 0 -0.59 8 8
mol:PI-3-4-5-P3 -0.23 0.2 -10000 0 -0.66 8 8
PI3K -0.24 0.21 -10000 0 -0.7 8 8
DOK2 -0.009 0.087 -10000 0 -0.81 1 1
ETS1 0.027 0.01 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.18 0.16 -10000 0 -0.56 5 5
ITGB3 -0.55 0.49 -10000 0 -1.2 75 75
PIGR -0.55 0.49 -10000 0 -1.2 75 75
IGHE 0.041 0.044 -10000 0 -10000 0 0
MAPKKK cascade -0.18 0.15 -10000 0 -0.55 5 5
BCL6 0.011 0.018 -10000 0 -0.29 1 1
OPRM1 -0.52 0.44 -10000 0 -1.2 67 67
RETNLB -0.52 0.44 -10000 0 -1.2 67 67
SELP -0.56 0.54 -10000 0 -1.3 72 72
AICDA -0.52 0.43 -10000 0 -1.1 73 73
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.016 0.14 -9999 0 -0.62 14 14
AKT1 -0.044 0.27 -9999 0 -0.61 53 53
PTK2B -0.12 0.32 -9999 0 -0.77 53 53
VEGFR2 homodimer/Frs2 -0.14 0.36 -9999 0 -0.9 53 53
CAV1 0.011 0.018 -9999 0 -0.29 1 1
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.12 0.34 -9999 0 -0.84 53 53
endothelial cell proliferation -0.031 0.26 -9999 0 -0.57 53 53
mol:Ca2+ -0.096 0.31 -9999 0 -0.76 53 53
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.11 0.33 -9999 0 -0.8 53 53
RP11-342D11.1 -0.1 0.31 -9999 0 -0.76 53 53
CDH5 0.013 0 -9999 0 -10000 0 0
VEGFA homodimer 0.032 0.015 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 0 0.082 -9999 0 -0.41 9 9
HRAS/GDP -0.12 0.25 -9999 0 -0.65 53 53
SH2D2A -0.02 0.094 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.12 0.25 -9999 0 -0.63 53 53
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.14 0.34 -9999 0 -0.85 53 53
VEGFR1 homodimer 0.007 0.068 -9999 0 -0.81 2 2
SHC/GRB2/SOS1 -0.13 0.28 -9999 0 -0.73 53 53
GRB10 -0.095 0.31 -9999 0 -0.76 53 53
PTPN11 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
PAK1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.14 0.3 -9999 0 -0.77 53 53
HRAS 0.013 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.044 0.17 -9999 0 -0.38 53 53
HIF1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.14 0.3 -9999 0 -0.78 53 53
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.007 0.13 -9999 0 -0.81 7 7
Nck/Pak 0.019 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.12 0.34 -9999 0 -0.84 53 53
mol:GDP -0.13 0.27 -9999 0 -0.7 53 53
mol:NADP -0.042 0.24 -9999 0 -0.53 55 55
eNOS/Hsp90 -0.032 0.23 -9999 0 -0.5 53 53
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.098 0.32 -9999 0 -0.77 53 53
HIF1A/ARNT 0.019 0 -9999 0 -10000 0 0
SHB 0.013 0 -9999 0 -10000 0 0
VEGFA 0.011 0.03 -9999 0 -10000 0 0
VEGFC 0.01 0.025 -9999 0 -0.29 2 2
FAK1/Vinculin -0.097 0.32 -9999 0 -0.76 53 53
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.13 0.34 -9999 0 -0.75 65 65
PTPN6 0.013 0 -9999 0 -10000 0 0
EPAS1 -0.054 0.17 -9999 0 -0.4 53 53
mol:L-citrulline -0.042 0.24 -9999 0 -0.53 55 55
ITGAV 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.11 0.33 -9999 0 -0.8 53 53
VEGFR2 homodimer/VEGFA homodimer -0.11 0.34 -9999 0 -0.84 53 53
VEGFR2/3 heterodimer -0.15 0.38 -9999 0 -0.92 56 56
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 -0.098 0.33 -9999 0 -0.78 53 53
VEGFR2 homodimer -0.16 0.4 -9999 0 -1 53 53
FLT1 0.007 0.068 -9999 0 -0.81 2 2
NEDD4 0.014 0.001 -9999 0 -10000 0 0
MAPK3 -0.08 0.29 -9999 0 -0.69 53 53
MAPK1 -0.08 0.29 -9999 0 -0.69 53 53
VEGFA145/NRP2 0.014 0.047 -9999 0 -0.62 1 1
VEGFR1/2 heterodimer -0.14 0.37 -9999 0 -0.92 53 53
KDR -0.16 0.4 -9999 0 -1 53 53
VEGFA165/NRP1/VEGFR2 homodimer -0.1 0.32 -9999 0 -0.77 53 53
SRC 0.011 0.018 -9999 0 -0.29 1 1
platelet activating factor biosynthetic process -0.082 0.3 -9999 0 -0.71 53 53
PI3K -0.077 0.32 -9999 0 -0.75 53 53
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.12 0.34 -9999 0 -0.84 53 53
FES -0.1 0.33 -9999 0 -0.79 53 53
GAB1 -0.14 0.3 -9999 0 -0.77 53 53
VEGFR2 homodimer/VEGFA homodimer/Src -0.12 0.34 -9999 0 -0.84 53 53
CTNNB1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.033 0.23 -9999 0 -0.5 53 53
VEGFR2 homodimer/VEGFA homodimer/Yes -0.12 0.34 -9999 0 -0.84 53 53
PI3K/GAB1 -0.045 0.28 -9999 0 -0.62 53 53
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.14 0.3 -9999 0 -0.77 53 53
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.13 0.36 -9999 0 -0.86 56 56
HSP90AA1 0.013 0 -9999 0 -10000 0 0
CDC42 -0.1 0.32 -9999 0 -0.78 53 53
actin cytoskeleton reorganization -0.16 0.32 -9999 0 -0.84 53 53
PTK2 -0.12 0.35 -9999 0 -0.83 53 53
EDG1 -0.1 0.31 -9999 0 -0.76 53 53
mol:DAG -0.098 0.32 -9999 0 -0.77 53 53
CaM/Ca2+ -0.13 0.27 -9999 0 -0.7 53 53
MAP2K3 -0.09 0.32 -9999 0 -0.75 53 53
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.1 0.33 -9999 0 -0.8 53 53
PLCG1 -0.1 0.32 -9999 0 -0.78 53 53
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.11 0.33 -9999 0 -0.8 53 53
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.12 0.34 -9999 0 -0.84 53 53
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.12 0.34 -9999 0 -0.84 53 53
cell migration -0.056 0.28 -9999 0 -0.62 53 53
mol:PI-3-4-5-P3 -0.066 0.29 -9999 0 -0.68 53 53
FYN 0.013 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.091 0.3 -9999 0 -0.72 53 53
mol:NO -0.042 0.24 -9999 0 -0.53 55 55
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.12 0.25 -9999 0 -0.65 53 53
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.1 0.33 -9999 0 -0.8 53 53
VHL 0.013 0 -9999 0 -10000 0 0
ITGB3 -0.033 0.18 -9999 0 -0.65 20 20
NOS3 -0.056 0.28 -9999 0 -0.62 55 55
VEGFR2 homodimer/VEGFA homodimer/Sck -0.13 0.35 -9999 0 -0.84 55 55
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.083 0.3 -9999 0 -0.71 53 53
PRKCB -0.086 0.3 -9999 0 -0.71 53 53
VCL 0.013 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.1 0.31 -9999 0 -0.77 53 53
VEGFR1/2 heterodimer/VEGFA homodimer -0.12 0.35 -9999 0 -0.86 53 53
VEGFA165/NRP2 0.014 0.047 -9999 0 -0.62 1 1
MAPKKK cascade -0.06 0.28 -9999 0 -0.65 53 53
NRP2 0.007 0.057 -9999 0 -0.42 4 4
VEGFC homodimer 0.01 0.025 -9999 0 -0.29 2 2
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.013 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.097 0.32 -9999 0 -0.76 53 53
MAP3K13 -0.1 0.33 -9999 0 -0.8 53 53
PDPK1 -0.046 0.26 -9999 0 -0.59 53 53
TCGA08_retinoblastoma

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
CDKN2B -0.001 0.042 -10000 0 -0.29 6 6
CDKN2C 0.032 0.021 -10000 0 -0.26 1 1
CDKN2A -0.23 0.12 -10000 0 -0.29 228 228
CCND2 0.047 0.036 0.17 5 -10000 0 5
RB1 -0.052 0.04 -10000 0 -0.17 5 5
CDK4 0.061 0.037 0.18 5 -10000 0 5
CDK6 0.057 0.036 0.18 5 -10000 0 5
G1/S progression 0.052 0.04 0.17 5 -10000 0 5
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 -0.008 0.074 -10000 0 -0.4 7 7
NFATC2 -0.041 0.23 -10000 0 -0.72 23 23
NFATC3 -0.029 0.11 -10000 0 -0.31 22 22
CD40LG -0.21 0.45 -10000 0 -1.1 50 50
ITCH 0.038 0.05 -10000 0 -10000 0 0
CBLB 0.038 0.05 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.18 0.25 -10000 0 -0.83 17 17
JUNB 0.013 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.008 0.052 -10000 0 -0.34 7 7
T cell anergy 0.015 0.083 -10000 0 -0.44 7 7
TLE4 -0.007 0.17 -10000 0 -0.53 22 22
Jun/NFAT1-c-4/p21SNFT -0.16 0.4 -10000 0 -1 44 44
AP-1/NFAT1-c-4 -0.26 0.56 -10000 0 -1.3 56 56
IKZF1 -0.02 0.18 -10000 0 -0.53 23 23
T-helper 2 cell differentiation -0.51 0.32 -10000 0 -0.77 127 127
AP-1/NFAT1 -0.13 0.24 -10000 0 -0.58 57 57
CALM1 0.022 0.032 -10000 0 -10000 0 0
EGR2 -0.19 0.58 -10000 0 -1.6 35 35
EGR3 -0.23 0.63 -10000 0 -1.7 44 44
NFAT1/FOXP3 -0.035 0.18 -10000 0 -0.53 27 27
EGR1 -0.052 0.22 -10000 0 -0.81 23 23
JUN 0.008 0.017 -10000 0 -10000 0 0
EGR4 0.006 0.02 -10000 0 -0.29 1 1
mol:Ca2+ 0.009 0.034 -10000 0 -10000 0 0
GBP3 -0.007 0.17 -10000 0 -0.53 22 22
FOSL1 0.003 0.076 -10000 0 -0.46 6 6
NFAT1-c-4/MAF/IRF4 -0.16 0.39 -10000 0 -0.93 50 50
DGKA -0.013 0.17 -10000 0 -0.52 24 24
CREM 0.012 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.17 0.4 -10000 0 -0.97 51 51
CTLA4 -0.044 0.19 -10000 0 -0.55 18 18
NFAT1-c-4 (dimer)/EGR1 -0.18 0.48 -10000 0 -1.1 54 54
NFAT1-c-4 (dimer)/EGR4 -0.15 0.42 -10000 0 -0.98 51 51
FOS -0.12 0.3 -10000 0 -0.82 44 44
IFNG -0.095 0.18 -10000 0 -0.62 18 18
T cell activation -0.1 0.28 -10000 0 -0.76 33 33
MAF 0.013 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.098 0.31 0.74 50 -10000 0 50
TNF -0.16 0.42 -10000 0 -1 46 46
FASLG -0.23 0.59 -10000 0 -1.4 50 50
TBX21 0.002 0.061 -10000 0 -0.31 9 9
BATF3 0.012 0.018 -10000 0 -0.29 1 1
PRKCQ -0.01 0.13 -10000 0 -0.8 8 8
PTPN1 -0.007 0.17 -10000 0 -0.53 22 22
NFAT1-c-4/ICER1 -0.18 0.4 -10000 0 -0.97 51 51
GATA3 -0.62 0.34 -10000 0 -0.81 225 225
T-helper 1 cell differentiation -0.064 0.2 -10000 0 -0.61 18 18
IL2RA -0.17 0.24 -10000 0 -0.76 17 17
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.007 0.17 -10000 0 -0.53 22 22
E2F1 -0.065 0.14 -10000 0 -0.28 80 80
PPARG 0.012 0.018 -10000 0 -10000 0 0
SLC3A2 -0.007 0.17 -10000 0 -0.53 22 22
IRF4 -0.01 0.088 -10000 0 -0.32 20 20
PTGS2 -0.27 0.53 -10000 0 -1.1 66 66
CSF2 -0.21 0.45 -10000 0 -1.1 49 49
JunB/Fra1/NFAT1-c-4 -0.15 0.4 -10000 0 -0.94 51 51
IL4 -0.53 0.34 -10000 0 -0.84 115 115
IL5 -0.21 0.45 -10000 0 -1.1 49 49
IL2 -0.11 0.28 -10000 0 -0.77 33 33
IL3 -0.043 0.057 -10000 0 -10000 0 0
RNF128 0.023 0.14 -10000 0 -0.86 7 7
NFATC1 -0.098 0.31 -10000 0 -0.74 50 50
CDK4 0.04 0.2 0.52 17 -10000 0 17
PTPRK -0.007 0.17 -10000 0 -0.53 22 22
IL8 -0.24 0.45 -10000 0 -1.1 52 52
POU2F1 0.013 0 -10000 0 -10000 0 0
S1P1 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
VEGFR2 homodimer/VEGFA homodimer -0.1 0.25 -9999 0 -0.62 53 53
PDGFRB -0.017 0.15 -9999 0 -0.81 10 10
SPHK1 -0.067 0.061 -9999 0 -10000 0 0
mol:S1P -0.064 0.061 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.11 0.24 -9999 0 -0.56 49 49
GNAO1 -0.063 0.23 -9999 0 -0.82 25 25
PDGFB-D/PDGFRB/PLCgamma1 -0.097 0.23 -9999 0 -0.52 49 49
PLCG1 -0.1 0.22 -9999 0 -0.53 46 46
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.017 0.15 -9999 0 -0.81 10 10
GNAI2 0.011 0.005 -9999 0 -10000 0 0
GNAI3 0.01 0.005 -9999 0 -10000 0 0
GNAI1 0.005 0.068 -9999 0 -0.81 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.089 0.21 -9999 0 -0.54 53 53
S1P1/S1P -0.13 0.18 -9999 0 -0.49 53 53
negative regulation of cAMP metabolic process -0.11 0.23 -9999 0 -0.54 49 49
MAPK3 -0.13 0.29 -9999 0 -0.64 61 61
calcium-dependent phospholipase C activity -0.001 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
KDR -0.14 0.32 -9999 0 -0.81 53 53
PLCB2 -0.11 0.18 -9999 0 -0.44 54 54
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.11 0.15 -9999 0 -0.41 53 53
receptor internalization -0.12 0.17 -9999 0 -0.46 53 53
PTGS2 -0.2 0.43 -9999 0 -1 58 58
Rac1/GTP -0.11 0.15 -9999 0 -0.41 53 53
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.009 0.031 -9999 0 -10000 0 0
negative regulation of T cell proliferation -0.11 0.23 -9999 0 -0.54 49 49
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.01 0.005 -9999 0 -10000 0 0
MAPK1 -0.13 0.29 -9999 0 -0.66 58 58
S1P1/S1P/PDGFB-D/PDGFRB -0.12 0.22 -9999 0 -0.52 60 60
ABCC1 0.011 0.003 -9999 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.067 0.44 -9999 0 -0.94 28 28
PLK1 -0.019 0.16 -9999 0 -10000 0 0
BIRC5 -0.062 0.18 -9999 0 -10000 0 0
HSPA1B -0.067 0.44 -9999 0 -0.95 27 27
MAP2K1 0.023 0.038 -9999 0 -10000 0 0
BRCA2 -0.07 0.45 -9999 0 -0.97 30 30
FOXM1 -0.097 0.5 -9999 0 -1.1 37 37
XRCC1 -0.067 0.44 -9999 0 -0.94 28 28
FOXM1B/p19 -0.16 0.39 -9999 0 -0.92 35 35
Cyclin D1/CDK4 -0.058 0.42 -9999 0 -0.9 26 26
CDC2 -0.077 0.46 -9999 0 -0.94 36 36
TGFA -0.052 0.41 -9999 0 -0.9 25 25
SKP2 -0.067 0.44 -9999 0 -0.94 28 28
CCNE1 -0.005 0.078 -9999 0 -10000 0 0
CKS1B -0.067 0.44 -9999 0 -0.93 30 30
RB1 -0.1 0.16 -9999 0 -0.52 12 12
FOXM1C/SP1 -0.087 0.47 -9999 0 -1 35 35
AURKB -0.093 0.19 -9999 0 -10000 0 0
CENPF -0.086 0.47 -9999 0 -0.96 42 42
CDK4 0.016 0.015 -9999 0 -10000 0 0
MYC -0.05 0.4 -9999 0 -0.83 30 30
CHEK2 0.013 0.071 -9999 0 -0.31 10 10
ONECUT1 -0.067 0.43 -9999 0 -0.92 30 30
CDKN2A -0.22 0.12 -9999 0 -0.29 172 172
LAMA4 -0.075 0.44 -9999 0 -0.96 27 27
FOXM1B/HNF6 -0.086 0.47 -9999 0 -1.1 30 30
FOS -0.18 0.59 -9999 0 -1.2 56 56
SP1 0.013 0.002 -9999 0 -10000 0 0
CDC25B -0.067 0.44 -9999 0 -0.95 28 28
response to radiation 0.008 0.035 -9999 0 -10000 0 0
CENPB -0.067 0.44 -9999 0 -0.94 28 28
CENPA -0.11 0.48 -9999 0 -0.99 37 37
NEK2 -0.095 0.48 -9999 0 -0.98 38 38
HIST1H2BA -0.072 0.44 -9999 0 -0.92 32 32
CCNA2 -0.03 0.11 -9999 0 -0.3 38 38
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.089 0.48 -9999 0 -1 32 32
CCNB2 -0.096 0.48 -9999 0 -0.94 46 46
CCNB1 -0.075 0.46 -9999 0 -0.97 32 32
ETV5 -0.067 0.44 -9999 0 -0.93 30 30
ESR1 -0.11 0.51 -9999 0 -1.1 42 42
CCND1 -0.057 0.42 -9999 0 -0.91 27 27
GSK3A 0.023 0.031 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0 0.11 -9999 0 -10000 0 0
CDK2 0.014 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.008 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.22 0.34 -9999 0 -0.93 40 40
GAS1 -0.11 0.51 -9999 0 -1.1 41 41
MMP2 -0.071 0.44 -9999 0 -0.93 33 33
RB1/FOXM1C -0.062 0.44 -9999 0 -0.96 29 29
CREBBP 0.013 0 -9999 0 -10000 0 0
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.1 0.25 -9999 0 -0.62 53 53
alphaV beta3 Integrin -0.034 0.13 -9999 0 -0.54 17 17
PTK2 -0.16 0.27 -9999 0 -0.65 41 41
IGF1R 0.013 0 -9999 0 -10000 0 0
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 0.013 0 -9999 0 -10000 0 0
SRC 0.011 0.018 -9999 0 -0.29 1 1
CDKN1B -0.17 0.27 -9999 0 -0.6 76 76
VEGFA 0.009 0.031 -9999 0 -10000 0 0
ILK -0.17 0.27 -9999 0 -0.61 74 74
ROCK1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.13 0.26 -9999 0 -0.57 74 74
PTK2B -0.08 0.21 -9999 0 -0.47 65 65
alphaV/beta3 Integrin/JAM-A -0.12 0.24 -9999 0 -0.48 88 88
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.38 0.27 -9999 0 -0.55 200 200
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.013 0.099 -9999 0 -0.49 11 11
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.12 0.22 -9999 0 -0.66 26 26
alphaV/beta3 Integrin/Syndecan-1 -0.031 0.12 -9999 0 -0.54 15 15
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.048 0.13 -9999 0 -0.43 27 27
PI4 Kinase 0.019 0 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.039 0.13 -9999 0 -0.51 19 19
RPS6KB1 0 0.14 -9999 0 -0.64 2 2
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.058 0.17 -9999 0 -0.61 17 17
GPR124 0.01 0.048 -9999 0 -0.81 1 1
MAPK1 -0.058 0.17 -9999 0 -0.61 17 17
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.056 0.18 -9999 0 -0.59 26 26
cell adhesion -0.3 0.22 -9999 0 -0.43 200 200
ANGPTL3 -0.54 0.38 -9999 0 -0.81 193 193
VEGFR2 homodimer/VEGFA homodimer/Src -0.1 0.21 -9999 0 -0.54 53 53
IGF-1R heterotetramer 0.013 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
TGFBR2 0.013 0 -9999 0 -10000 0 0
ITGB3 -0.033 0.18 -9999 0 -0.65 20 20
IGF1 -0.004 0.12 -9999 0 -0.81 6 6
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.031 0.12 -9999 0 -0.53 15 15
apoptosis 0.012 0 -9999 0 -10000 0 0
CD47 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.029 0.12 -9999 0 -0.54 14 14
VCL 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.11 0.22 -9999 0 -0.58 50 50
CSF1 0.005 0.072 -9999 0 -0.55 4 4
PIK3C2A -0.17 0.27 -9999 0 -0.6 76 76
PI4 Kinase/Pyk2 -0.19 0.25 -9999 0 -0.73 27 27
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.092 0.23 -9999 0 -0.5 65 65
FAK1/Vinculin -0.12 0.21 -9999 0 -0.51 35 35
alphaV beta3/Integrin/ppsTEM5 -0.031 0.12 -9999 0 -0.54 15 15
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.2 0.36 -9999 0 -0.76 82 82
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 0.004 0.083 -9999 0 -0.81 3 3
F11R 0.015 0.065 -9999 0 -0.62 3 3
alphaV/beta3 Integrin/Lactadherin -0.029 0.12 -9999 0 -0.54 14 14
alphaV/beta3 Integrin/TGFBR2 -0.029 0.12 -9999 0 -0.54 14 14
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.028 0.045 -9999 0 -0.49 2 2
HSP90AA1 0.013 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.004 0.11 -9999 0 -0.49 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.009 0.079 -9999 0 -0.29 21 21
alphaV/beta3 Integrin/Pyk2 -0.079 0.21 -9999 0 -0.47 65 65
SDC1 0.009 0.051 -9999 0 -0.55 2 2
VAV3 0.031 0.051 -9999 0 -0.45 3 3
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 -0.002 0.11 -9999 0 -0.81 5 5
FAK1/Paxillin -0.12 0.21 -9999 0 -0.51 35 35
cell migration -0.097 0.19 -9999 0 -0.45 35 35
ITGAV 0.013 0 -9999 0 -10000 0 0
PI3K -0.13 0.2 -9999 0 -0.43 88 88
SPP1 -0.006 0.099 -9999 0 -0.41 13 13
KDR -0.14 0.32 -9999 0 -0.81 53 53
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.013 0 -9999 0 -10000 0 0
COL4A3 -0.03 0.18 -9999 0 -0.81 15 15
angiogenesis -0.086 0.21 -9999 0 -0.59 21 21
Rac1/GTP 0.035 0.047 -9999 0 -0.41 3 3
EDIL3 -0.11 0.28 -9999 0 -0.7 50 50
cell proliferation -0.029 0.12 -9999 0 -0.53 14 14
Signaling events mediated by PTP1B

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
PDGFRB -0.016 0.15 -10000 0 -0.81 10 10
Jak2/Leptin Receptor -0.15 0.15 -10000 0 -0.42 30 30
PTP1B/AKT1 -0.08 0.075 -10000 0 -0.3 23 23
FYN 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.098 0.084 -10000 0 -0.34 24 24
EGFR 0.001 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.44 0.14 -10000 0 -0.48 261 261
CSF1 0.005 0.072 -10000 0 -0.55 4 4
AKT1 0.012 0.001 -10000 0 -10000 0 0
INSR 0.012 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.11 0.14 -10000 0 -0.46 31 31
Insulin Receptor/Insulin -0.054 0.057 -10000 0 -0.35 1 1
HCK -0.022 0.1 -10000 0 -0.31 31 31
CRK 0.013 0 -10000 0 -10000 0 0
TYK2 -0.086 0.081 -10000 0 -0.32 23 23
EGF -0.73 0.25 -10000 0 -0.81 261 261
YES1 0.013 0 -10000 0 -10000 0 0
CAV1 -0.18 0.084 -10000 0 -0.35 33 33
TXN -0.002 0.03 -10000 0 -0.3 3 3
PTP1B/IRS1/GRB2 -0.084 0.1 -10000 0 -0.36 27 27
cell migration 0.098 0.084 0.34 24 -10000 0 24
STAT3 0.012 0.001 -10000 0 -10000 0 0
PRLR -0.3 0.4 -10000 0 -0.81 111 111
ITGA2B -0.01 0.077 -10000 0 -0.29 20 20
CSF1R -0.001 0.073 -10000 0 -0.34 11 11
Prolactin Receptor/Prolactin -0.24 0.3 -10000 0 -0.63 111 111
FGR -0.001 0.073 -10000 0 -0.34 11 11
PTP1B/p130 Cas -0.086 0.081 -10000 0 -0.32 23 23
Crk/p130 Cas -0.076 0.078 -10000 0 -0.3 23 23
DOK1 -0.078 0.088 -10000 0 -0.31 28 28
JAK2 -0.16 0.16 -10000 0 -0.36 110 110
Jak2/Leptin Receptor/Leptin -0.1 0.098 -10000 0 -0.57 3 3
PIK3R1 0.013 0 -10000 0 -10000 0 0
PTPN1 -0.099 0.085 -10000 0 -0.34 24 24
LYN 0.013 0 -10000 0 -10000 0 0
CDH2 -0.026 0.17 -10000 0 -0.81 13 13
SRC -0.026 0.032 -10000 0 -10000 0 0
ITGB3 -0.035 0.18 -10000 0 -0.65 20 20
CAT1/PTP1B -0.25 0.14 -10000 0 -0.41 63 63
CAPN1 0.011 0.001 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.038 0.053 -10000 0 -10000 0 0
mol:H2O2 -0.007 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.09 0.092 -10000 0 -0.66 2 2
negative regulation of transcription -0.16 0.16 -10000 0 -0.35 110 110
FCGR2A -0.002 0.065 -10000 0 -0.29 14 14
FER 0.001 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.046 0.14 -10000 0 -0.62 14 14
BLK -0.004 0.065 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.001 0.01 -10000 0 -10000 0 0
RHOA 0.011 0.001 -10000 0 -10000 0 0
LEPR 0.01 0.048 -10000 0 -0.8 1 1
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0 -10000 0 -10000 0 0
mol:NADPH -0.007 0.002 -10000 0 -10000 0 0
TRPV6 -0.19 0.14 -10000 0 -0.4 31 31
PRL 0 0.018 -10000 0 -0.29 1 1
SOCS3 0.023 0.09 -10000 0 -1.4 1 1
SPRY2 0.007 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.008 0.072 -10000 0 -0.55 5 5
CSF1/CSF1R -0.086 0.1 -10000 0 -0.37 22 22
Ras protein signal transduction 0.046 0.022 -10000 0 -10000 0 0
IRS1 -0.002 0.11 -10000 0 -0.81 5 5
INS 0 0.017 -10000 0 -0.29 1 1
LEP -0.024 0.093 -10000 0 -0.29 31 31
STAT5B -0.12 0.098 -10000 0 -0.33 31 31
STAT5A -0.12 0.098 -10000 0 -0.33 31 31
GRB2 0.013 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.1 0.12 -10000 0 -0.39 32 32
CSN2 -0.058 0.1 -10000 0 -10000 0 0
PIK3CA 0.013 0 -10000 0 -10000 0 0
LAT -0.04 0.048 -10000 0 -0.27 1 1
YBX1 0.015 0.002 -10000 0 -10000 0 0
LCK 0.005 0.047 -10000 0 -0.29 7 7
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.079 0.25 -10000 0 -0.82 30 30
Effects of Botulinum toxin

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
STX1A 0.008 0.024 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.005 0.043 -9999 0 -10000 0 0
STXBP1 0.013 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.13 0.085 -9999 0 -0.2 96 96
RAB3GAP2/RIMS1/UNC13B -0.007 0.031 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.007 0.064 -9999 0 -10000 0 0
mol:ACh -0.016 0.028 -9999 0 -0.1 4 4
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.019 0.031 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.13 0.085 -9999 0 -0.2 96 96
UNC13B 0.013 0 -9999 0 -10000 0 0
CHRNA1 -0.2 0.14 -9999 0 -0.29 203 203
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.18 0.26 -9999 0 -0.58 86 86
SNAP25 -0.045 0.06 -9999 0 -0.38 1 1
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.23 0.37 -9999 0 -0.81 86 86
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.015 0.02 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.019 0.031 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.022 0.047 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.23 0.19 -9999 0 -0.59 19 19
positive regulation of JNK cascade -0.26 0.21 -9999 0 -0.59 49 49
Syndecan-4/ADAM12 -0.24 0.2 -9999 0 -0.58 28 28
CCL5 -0.018 0.091 -9999 0 -0.29 29 29
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
PLG -0.45 0.39 -9999 0 -0.79 164 164
ADAM12 -0.021 0.095 -9999 0 -0.29 32 32
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.06 0.041 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.24 0.21 -9999 0 -0.59 33 33
Syndecan-4/CXCL12/CXCR4 -0.28 0.23 -9999 0 -0.63 49 49
Syndecan-4/Laminin alpha3 -0.26 0.2 -9999 0 -0.57 35 35
MDK -0.069 0.14 -9999 0 -0.29 78 78
Syndecan-4/FZD7 -0.24 0.2 -9999 0 -0.63 22 22
Syndecan-4/Midkine -0.26 0.2 -9999 0 -0.6 31 31
FZD7 -0.01 0.13 -9999 0 -0.81 8 8
Syndecan-4/FGFR1/FGF -0.22 0.17 -9999 0 -0.56 22 22
THBS1 -0.019 0.16 -9999 0 -0.81 11 11
integrin-mediated signaling pathway -0.23 0.19 -9999 0 -0.57 24 24
positive regulation of MAPKKK cascade -0.26 0.21 -9999 0 -0.59 49 49
Syndecan-4/TACI -0.24 0.2 -9999 0 -0.6 23 23
CXCR4 -0.008 0.077 -9999 0 -0.29 20 20
cell adhesion 0.033 0.031 -9999 0 -10000 0 0
Syndecan-4/Dynamin -0.23 0.19 -9999 0 -0.59 19 19
Syndecan-4/TSP1 -0.24 0.21 -9999 0 -0.63 26 26
Syndecan-4/GIPC -0.23 0.19 -9999 0 -0.59 19 19
Syndecan-4/RANTES -0.24 0.2 -9999 0 -0.59 24 24
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.025 0.15 -9999 0 -0.48 22 22
LAMA3 -0.079 0.14 -9999 0 -0.29 87 87
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.077 0.051 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.23 0.19 -9999 0 -0.59 19 19
TFPI 0.006 0.059 -9999 0 -0.39 5 5
F2 -0.027 0.096 -9999 0 -0.29 18 18
alpha5/beta1 Integrin 0.019 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.27 0.2 -9999 0 -0.57 46 46
ACTN1 0.013 0 -9999 0 -10000 0 0
TNC -0.018 0.12 -9999 0 -0.38 22 22
Syndecan-4/CXCL12 -0.28 0.23 -9999 0 -0.65 45 45
FGF6 0 0.002 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.089 0.27 -9999 0 -0.81 36 36
TNFRSF13B -0.007 0.064 -9999 0 -0.29 14 14
FGF2 0.004 0.083 -9999 0 -0.81 3 3
FGFR1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.23 0.19 -9999 0 -0.46 76 76
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.008 0.076 -9999 0 -0.28 21 21
cell migration -0.017 0.012 -9999 0 -10000 0 0
PRKCD 0.014 0.012 -9999 0 -10000 0 0
vasculogenesis -0.24 0.2 -9999 0 -0.6 26 26
SDC4 -0.25 0.2 -9999 0 -0.49 76 76
Syndecan-4/Tenascin C -0.24 0.2 -9999 0 -0.59 24 24
Syndecan-4/PI-4-5-P2/PKC alpha -0.048 0.033 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.23 0.19 -9999 0 -0.59 19 19
MMP9 -0.11 0.17 -9999 0 -0.3 115 115
Rac1/GTP 0.033 0.032 -9999 0 -10000 0 0
cytoskeleton organization -0.22 0.19 -9999 0 -0.56 19 19
GIPC1 0.013 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.23 0.2 -9999 0 -0.59 21 21
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.013 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.035 0.12 -10000 0 -0.34 6 6
NT3 (dimer)/TRKC -0.15 0.3 -10000 0 -0.66 73 73
NT3 (dimer)/TRKB -0.28 0.31 -10000 0 -0.59 137 137
SHC/Grb2/SOS1/GAB1/PI3K 0.036 0 -10000 0 -10000 0 0
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.028 0.1 -10000 0 -0.29 39 39
PIK3CA 0.013 0 -10000 0 -10000 0 0
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 -0.15 0.32 -10000 0 -0.81 56 56
NTRK2 -0.31 0.4 -10000 0 -0.81 113 113
NTRK3 -0.12 0.3 -10000 0 -0.81 48 48
NT-4/5 (dimer)/TRKB -0.24 0.27 -10000 0 -0.56 119 119
neuron apoptosis 0.14 0.18 0.52 33 -10000 0 33
SHC 2-3/Grb2 -0.15 0.2 -10000 0 -0.58 33 33
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.14 0.17 -10000 0 -0.51 33 33
SHC3 -0.15 0.2 -10000 0 -0.61 32 32
STAT3 (dimer) 0.019 0.024 -10000 0 -0.38 1 1
NT3 (dimer)/TRKA -0.17 0.3 -10000 0 -0.61 82 82
RIN/GDP -0.019 0.092 -10000 0 -0.27 4 4
GIPC1 0.013 0 -10000 0 -10000 0 0
KRAS 0.013 0 -10000 0 -10000 0 0
DNAJA3 -0.08 0.15 -10000 0 -0.55 10 10
RIN/GTP 0 0.012 -10000 0 -10000 0 0
CCND1 0.026 0.061 -10000 0 -1 1 1
MAGED1 0.013 0 -10000 0 -10000 0 0
PTPN11 0.013 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.019 0.084 -10000 0 -0.29 25 25
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.14 0.23 -10000 0 -0.55 66 66
TRKA/NEDD4-2 -0.11 0.25 -10000 0 -0.62 57 57
ELMO1 0.013 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.012 0.14 -10000 0 -0.81 8 8
HRAS 0.013 0 -10000 0 -10000 0 0
DOCK1 0.013 0 -10000 0 -10000 0 0
GAB2 0.013 0 -10000 0 -10000 0 0
RIT2 0 0.018 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.013 0 -10000 0 -10000 0 0
DNM1 -0.085 0.15 -10000 0 -0.3 91 91
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.013 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.078 0.15 -10000 0 -0.54 10 10
mol:GDP -0.03 0.13 -10000 0 -0.34 17 17
NGF (dimer) -0.012 0.14 -10000 0 -0.81 8 8
RhoG/GDP 0.009 0 -10000 0 -10000 0 0
RIT1/GDP -0.013 0.093 -10000 0 -0.26 5 5
TIAM1 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.013 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.23 0.26 -10000 0 -0.55 113 113
KIDINS220/CRKL/C3G 0.019 0 -10000 0 -10000 0 0
SHC/RasGAP 0.019 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.001 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.032 0 -10000 0 -10000 0 0
RIT1/GTP 0.009 0 -10000 0 -10000 0 0
NT3 (dimer) -0.076 0.25 -10000 0 -0.81 31 31
RAP1/GDP -0.035 0.062 -10000 0 -0.25 1 1
KIDINS220/CRKL 0.013 0 -10000 0 -10000 0 0
BDNF (dimer) -0.028 0.1 -10000 0 -0.29 39 39
ubiquitin-dependent protein catabolic process -0.12 0.23 -10000 0 -0.54 64 64
Schwann cell development -0.044 0.037 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.031 0.016 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.038 0.01 -10000 0 -10000 0 0
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.28 0.28 -10000 0 -0.5 158 158
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
Rap1/GTP -0.074 0.09 -10000 0 -10000 0 0
STAT3 0.019 0.024 -10000 0 -0.38 1 1
axon guidance -0.26 0.26 -10000 0 -0.48 158 158
MAPK3 -0.1 0.22 -10000 0 -0.5 66 66
MAPK1 -0.1 0.22 -10000 0 -0.5 66 66
CDC42/GDP -0.013 0.093 -10000 0 -0.26 5 5
NTF3 -0.076 0.25 -10000 0 -0.81 31 31
NTF4 -0.019 0.084 -10000 0 -0.29 25 25
NGF (dimer)/TRKA/FAIM -0.12 0.23 -10000 0 -0.54 63 63
PI3K 0.019 0 -10000 0 -10000 0 0
FRS3 0.009 0.031 -10000 0 -0.29 3 3
FAIM 0.01 0.025 -10000 0 -0.29 2 2
GAB1 0.013 0 -10000 0 -10000 0 0
RASGRF1 -0.082 0.16 -10000 0 -0.56 12 12
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.12 0.27 -10000 0 -0.57 73 73
RGS19 0.009 0.031 -10000 0 -0.29 3 3
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.024 0.063 -10000 0 -10000 0 0
Rac1/GDP -0.013 0.093 -10000 0 -0.26 5 5
NGF (dimer)/TRKA/GRIT -0.12 0.23 -10000 0 -0.55 63 63
neuron projection morphogenesis -0.044 0.15 -10000 0 -0.68 4 4
NGF (dimer)/TRKA/NEDD4-2 -0.12 0.23 -10000 0 -0.54 64 64
MAP2K1 0.037 0 -10000 0 -10000 0 0
NGFR -0.01 0.13 -10000 0 -0.81 8 8
NGF (dimer)/TRKA/GIPC/GAIP -0.081 0.17 -10000 0 -0.38 63 63
RAS family/GTP/PI3K 0.03 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.001 0.011 -10000 0 -10000 0 0
NRAS 0.013 0 -10000 0 -10000 0 0
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
PRKCI 0.013 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
MAPKKK cascade -0.14 0.26 -10000 0 -0.63 63 63
RASA1 0.013 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.11 0.25 -10000 0 -0.62 56 56
SQSTM1 0.003 0.053 -10000 0 -0.29 9 9
BDNF (dimer)/TRKB/GIPC -0.19 0.25 -10000 0 -0.5 113 113
NGF (dimer)/TRKA/p62/Atypical PKCs -0.1 0.19 -10000 0 -0.47 63 63
MATK -0.018 0.11 -10000 0 -0.36 24 24
NEDD4L 0.01 0.048 -10000 0 -0.81 1 1
RAS family/GDP -0.034 0.06 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.085 0.16 -10000 0 -0.36 68 68
Rac1/GTP -0.07 0.1 -10000 0 -0.31 28 28
FRS2 family/SHP2/CRK family -0.001 0.011 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.028 0.092 -10000 0 -0.42 9 9
FYN 0.017 0.13 -10000 0 -0.47 13 13
LAT/GRAP2/SLP76 0.004 0.14 -10000 0 -0.47 15 15
IKBKB 0.013 0 -10000 0 -10000 0 0
AKT1 0.006 0.12 -10000 0 -0.38 15 15
B2M 0.014 0.003 -10000 0 -10000 0 0
IKBKG -0.015 0.034 -10000 0 -0.15 1 1
MAP3K8 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ -0.087 0.056 -10000 0 -0.12 206 206
integrin-mediated signaling pathway -0.004 0.023 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.006 0.16 -10000 0 -0.52 17 17
TRPV6 -0.58 0.37 -10000 0 -0.81 208 208
CD28 -0.006 0.083 -10000 0 -0.33 16 16
SHC1 0.013 0.13 -10000 0 -0.48 12 12
receptor internalization 0.009 0.13 -10000 0 -0.47 12 12
PRF1 0.014 0.12 -10000 0 -0.59 6 6
KRAS 0.013 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
COT/AKT1 0.013 0.098 -10000 0 -0.31 13 13
LAT 0.001 0.14 -10000 0 -0.53 12 12
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D -0.034 0.11 -10000 0 -0.29 46 46
CD3E -0.016 0.1 -10000 0 -0.32 27 27
CD3G -0.002 0.067 -10000 0 -0.3 14 14
RASGRP2 -0.002 0.022 -10000 0 -0.18 2 2
RASGRP1 0.012 0.12 -10000 0 -0.37 16 16
HLA-A 0.012 0.026 -10000 0 -0.3 2 2
RASSF5 0.005 0.047 -10000 0 -0.29 7 7
RAP1A/GTP/RAPL -0.004 0.023 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.026 0.044 -10000 0 -0.1 4 4
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.03 0.057 -10000 0 -0.23 11 11
PRKCA 0.009 0.083 -10000 0 -0.25 12 12
GRAP2 0.003 0.053 -10000 0 -0.29 9 9
mol:IP3 0.14 0.19 0.26 187 -0.38 14 201
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.006 0.1 -10000 0 -0.36 15 15
ORAI1 0.28 0.17 0.38 206 -10000 0 206
CSK 0.01 0.13 -10000 0 -0.49 12 12
B7 family/CD28 -0.061 0.15 -10000 0 -0.56 17 17
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.004 0.14 -10000 0 -0.5 15 15
PTPN6 0.011 0.13 -10000 0 -0.48 12 12
VAV1 -0.017 0.17 -10000 0 -0.51 22 22
Monovalent TCR/CD3 -0.008 0.094 -10000 0 -0.33 16 16
CBL 0.013 0 -10000 0 -10000 0 0
LCK 0.012 0.14 -10000 0 -0.49 13 13
PAG1 0.01 0.13 -10000 0 -0.49 12 12
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.006 0.14 -10000 0 -0.49 15 15
CD80 -0.023 0.099 -10000 0 -0.29 34 34
CD86 -0.046 0.12 -10000 0 -0.29 56 56
PDK1/CARD11/BCL10/MALT1 -0.037 0.069 -10000 0 -0.27 13 13
HRAS 0.013 0 -10000 0 -10000 0 0
GO:0035030 -0.006 0.15 -10000 0 -0.48 16 16
CD8A -0.013 0.087 -10000 0 -0.3 23 23
CD8B -0.007 0.079 -10000 0 -0.3 20 20
PTPRC 0.002 0.067 -10000 0 -0.36 8 8
PDK1/PKC theta 0.004 0.14 -10000 0 -0.46 15 15
CSK/PAG1 0.014 0.13 -10000 0 -0.5 10 10
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.018 0.019 -10000 0 -10000 0 0
GRAP2/SLP76 0.006 0.14 -10000 0 -0.53 14 14
STIM1 0.14 0.087 -10000 0 -10000 0 0
RAS family/GTP 0.03 0.055 -10000 0 -0.16 4 4
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.008 0.13 -10000 0 -0.5 12 12
mol:DAG 0.034 0.13 -10000 0 -0.36 14 14
RAP1A/GDP 0.013 0.019 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 0 0.064 -10000 0 -0.3 13 13
cytotoxic T cell degranulation 0.015 0.11 -10000 0 -0.57 6 6
RAP1A/GTP -0.001 0.007 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0.14 -10000 0 -0.43 17 17
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.13 0.22 0.28 168 -0.51 14 182
NRAS 0.013 0 -10000 0 -10000 0 0
ZAP70 -0.025 0.1 -10000 0 -10000 0 0
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.017 0.15 -10000 0 -0.52 15 15
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.013 0 -10000 0 -10000 0 0
CD8 heterodimer -0.01 0.097 -10000 0 -0.37 15 15
CARD11 -0.072 0.14 -10000 0 -0.29 81 81
PRKCB 0.007 0.085 -10000 0 -0.26 13 13
PRKCE 0.009 0.083 -10000 0 -0.25 12 12
PRKCQ -0.005 0.16 -10000 0 -0.53 15 15
LCP2 0.004 0.05 -10000 0 -0.29 8 8
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.009 0.1 -10000 0 -0.32 15 15
IKK complex 0.03 0.045 -10000 0 -0.11 2 2
RAS family/GDP -0.002 0.005 -10000 0 -10000 0 0
MAP3K14 0.019 0.079 -10000 0 -0.26 7 7
PDPK1 0.009 0.12 -10000 0 -0.36 15 15
TCR/CD3/MHC I/CD8/Fyn 0.006 0.13 -10000 0 -0.52 11 11
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0 0.099 -10000 0 -0.33 24 24
epithelial cell differentiation -0.038 0.13 -10000 0 -0.46 24 24
CYFIP2 0.01 0.048 -10000 0 -0.81 1 1
ENAH 0.034 0.09 -10000 0 -10000 0 0
EGFR 0.013 0 -10000 0 -10000 0 0
EPHA2 0.011 0.018 -10000 0 -10000 0 0
MYO6 -0.003 0.13 -10000 0 -0.43 24 24
CTNNB1 0.013 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.002 0.031 -10000 0 -0.54 1 1
AQP5 -0.097 0.21 -10000 0 -0.61 33 33
CTNND1 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.003 0.13 -10000 0 -0.43 24 24
regulation of calcium-dependent cell-cell adhesion -0.042 0.19 -10000 0 -0.48 44 44
EGF -0.72 0.24 -10000 0 -0.81 261 261
NCKAP1 0.013 0 -10000 0 -10000 0 0
AQP3 -0.24 0.31 -10000 0 -0.63 107 107
cortical microtubule organization -0.038 0.13 -10000 0 -0.46 24 24
GO:0000145 -0.003 0.12 -10000 0 -0.41 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.038 0.13 -10000 0 -0.46 24 24
MLLT4 0.013 0 -10000 0 -10000 0 0
ARF6/GDP -0.03 0.098 -10000 0 -10000 0 0
ARF6 0.013 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.032 0.009 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.009 0.12 -10000 0 -0.4 24 24
PVRL2 0.013 0 -10000 0 -10000 0 0
ZYX -0.003 0.13 -10000 0 -0.43 24 24
ARF6/GTP 0 0.006 -10000 0 -10000 0 0
CDH1 -0.055 0.23 -10000 0 -0.81 24 24
EGFR/EGFR/EGF/EGF -0.41 0.16 -10000 0 -0.45 266 266
RhoA/GDP -0.035 0.12 -10000 0 -0.43 24 24
actin cytoskeleton organization 0.004 0.12 -10000 0 -0.41 24 24
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
GIT1 0.013 0 -10000 0 -10000 0 0
IGF1R 0.013 0 -10000 0 -10000 0 0
IGF1 -0.004 0.12 -10000 0 -0.81 6 6
DIAPH1 -0.004 0.039 -10000 0 -0.65 1 1
Wnt receptor signaling pathway 0.038 0.13 0.46 24 -10000 0 24
RHOA 0.013 0 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.1 -10000 0 -10000 0 0
CTNNA1 0.013 0 -10000 0 -10000 0 0
VCL 0.003 0.13 -10000 0 -0.42 24 24
EFNA1 0.013 0 -10000 0 -10000 0 0
LPP 0.005 0.12 -10000 0 -0.41 24 24
Ephrin A1/EPHA2 -0.035 0.11 -10000 0 -0.41 24 24
SEC6/SEC8 -0.031 0.1 -10000 0 -10000 0 0
MGAT3 -0.043 0.2 -10000 0 -0.49 44 44
HGF/MET -0.071 0.16 -10000 0 -0.47 38 38
HGF -0.037 0.19 -10000 0 -0.78 18 18
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0 0.099 -10000 0 -0.33 24 24
actin cable formation 0.051 0.087 -10000 0 -10000 0 0
KIAA1543 0.003 0.13 -10000 0 -0.41 25 25
KIFC3 -0.003 0.13 -10000 0 -0.43 24 24
NCK1 0.013 0 -10000 0 -10000 0 0
EXOC3 0.013 0 -10000 0 -10000 0 0
ACTN1 -0.003 0.13 -10000 0 -0.43 24 24
NCK1/GIT1 0.019 0 -10000 0 -10000 0 0
mol:GDP -0.038 0.13 -10000 0 -0.46 24 24
EXOC4 0.013 0 -10000 0 -10000 0 0
STX4 -0.003 0.13 -10000 0 -0.43 24 24
PIP5K1C -0.003 0.13 -10000 0 -0.43 24 24
LIMA1 0.013 0 -10000 0 -10000 0 0
ABI1 0.013 0 -10000 0 -10000 0 0
ROCK1 0.028 0.1 -10000 0 -10000 0 0
adherens junction assembly 0.02 0.12 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.043 0.13 -10000 0 -0.42 30 30
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.019 0 -10000 0 -10000 0 0
MET -0.025 0.1 -10000 0 -0.29 36 36
PLEKHA7 -0.005 0.13 -10000 0 -0.43 25 25
mol:GTP 0 0.007 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.024 0.12 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0 0.099 -10000 0 -0.33 24 24
regulation of cell-cell adhesion 0.004 0.12 -10000 0 -0.41 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0 0.099 -10000 0 -0.33 24 24
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.013 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.049 0.076 -9999 0 -10000 0 0
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.017 0.018 -9999 0 -10000 0 0
AURKB -0.13 0.15 -9999 0 -0.29 138 138
AURKC 0.012 0.001 -9999 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.9 0.65 -9999 0 -1.4 197 197
PLK1 0.037 0.13 -9999 0 -10000 0 0
CDKN1B -0.032 0.1 -9999 0 -10000 0 0
FOXO3 0.059 0.094 -9999 0 -10000 0 0
KAT2B 0.02 0.012 -9999 0 -10000 0 0
FOXO1/SIRT1 -0.25 0.18 -9999 0 -0.38 197 197
CAT 0.063 0.087 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
AKT1 -0.015 0.027 -9999 0 -10000 0 0
FOXO1 -0.27 0.21 -9999 0 -0.42 197 197
MAPK10 0.021 0.012 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.067 0.044 -9999 0 -10000 0 0
response to oxidative stress -0.031 0.03 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.055 0.09 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
EP300 -0.024 0.026 -9999 0 -10000 0 0
BCL2L11 0.028 0.018 -9999 0 -10000 0 0
FOXO1/SKP2 -0.24 0.2 -9999 0 -0.38 197 197
mol:GDP -0.031 0.03 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
GADD45A 0.09 0.05 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family -0.03 0.063 -9999 0 -10000 0 0
MST1 0.015 0.056 -9999 0 -0.56 2 2
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.009 0.06 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.013 0.067 -9999 0 -0.48 5 5
MAPK9 0.021 0.012 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
SIRT1 0.014 0.01 -9999 0 -10000 0 0
SOD2 -0.038 0.13 -9999 0 -10000 0 0
RBL2 0.073 0.071 -9999 0 -10000 0 0
RAL/GDP 0.006 0.016 -9999 0 -10000 0 0
CHUK 0.02 0.012 -9999 0 -10000 0 0
Ran/GTP 0.013 0.003 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.012 0.017 -9999 0 -10000 0 0
CSNK1G1 0.013 0 -9999 0 -10000 0 0
FASLG -0.002 0.095 -9999 0 -10000 0 0
SKP2 0.013 0 -9999 0 -10000 0 0
USP7 0.014 0 -9999 0 -10000 0 0
IKBKB 0.02 0.012 -9999 0 -10000 0 0
CCNB1 0.061 0.094 -9999 0 -10000 0 0
FOXO1-3a-4/beta catenin -0.026 0.12 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.24 0.19 -9999 0 -0.38 197 197
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.02 0.012 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.023 0.005 -9999 0 -10000 0 0
ZFAND5 0.07 0.039 -9999 0 -10000 0 0
SFN -0.14 0.17 -9999 0 -0.31 136 136
CDK2 -0.045 0.041 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.02 0.055 -9999 0 -10000 0 0
CREBBP -0.045 0.041 -9999 0 -10000 0 0
FBXO32 0.06 0.095 -9999 0 -10000 0 0
BCL6 0.072 0.073 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.014 0.13 -9999 0 -0.54 17 17
ADCY5 -0.015 0.13 -9999 0 -0.54 17 17
ADCY6 0.019 0 -9999 0 -10000 0 0
ADCY7 0.011 0.036 -9999 0 -10000 0 0
ADCY1 -0.25 0.28 -9999 0 -0.54 140 140
ADCY2 -0.085 0.088 -9999 0 -0.54 1 1
ADCY3 0.019 0 -9999 0 -10000 0 0
ADCY8 0.01 0.031 -9999 0 -10000 0 0
PRKCE 0.011 0 -9999 0 -10000 0 0
ADCY9 0.019 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.083 0.092 -9999 0 -0.32 21 21
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.045 0.14 -9999 0 -0.55 21 21
EFNA5 -0.048 0.21 -9999 0 -0.81 21 21
FYN -0.024 0.14 -9999 0 -0.5 21 21
neuron projection morphogenesis -0.045 0.14 -9999 0 -0.55 21 21
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.045 0.14 -9999 0 -0.55 21 21
EPHA5 -0.007 0.054 -9999 0 -0.29 10 10
Glucocorticoid receptor regulatory network

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
PCK2 -0.005 0.12 -10000 0 -1.1 3 3
SMARCC2 0.014 0 -10000 0 -10000 0 0
SMARCC1 0.014 0 -10000 0 -10000 0 0
TBX21 -0.028 0.094 -10000 0 -0.49 2 2
SUMO2 0.01 0.006 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.039 -10000 0 -0.28 5 5
FKBP4 0.013 0 -10000 0 -10000 0 0
FKBP5 -0.004 0.12 -10000 0 -0.81 6 6
GR alpha/HSP90/FKBP51/HSP90 0.06 0.1 0.34 2 -0.47 6 8
PRL -0.026 0.084 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.11 0.24 0.52 17 -0.5 19 36
RELA -0.094 0.098 -10000 0 -10000 0 0
FGG 0.1 0.16 0.48 6 -10000 0 6
GR beta/TIF2 0.016 0.2 0.37 2 -0.58 26 28
IFNG -0.14 0.19 -10000 0 -0.56 20 20
apoptosis -0.071 0.21 -10000 0 -0.68 13 13
CREB1 0.005 0.053 -10000 0 -0.34 6 6
histone acetylation -0.01 0.072 -10000 0 -0.4 2 2
BGLAP -0.014 0.072 -10000 0 -10000 0 0
GR/PKAc 0.071 0.063 0.32 2 -10000 0 2
NF kappa B1 p50/RelA -0.17 0.18 -10000 0 -0.43 47 47
SMARCD1 0.014 0 -10000 0 -10000 0 0
MDM2 0.058 0.059 0.26 4 -10000 0 4
GATA3 -0.62 0.34 -10000 0 -0.8 225 225
AKT1 0.002 0.018 -10000 0 -10000 0 0
CSF2 -0.029 0.068 -10000 0 -10000 0 0
GSK3B 0.01 0.006 -10000 0 -10000 0 0
NR1I3 -0.036 0.25 -10000 0 -0.91 13 13
CSN2 0.1 0.11 0.41 3 -10000 0 3
BRG1/BAF155/BAF170/BAF60A 0.041 0 -10000 0 -10000 0 0
NFATC1 0.015 0.004 -10000 0 -10000 0 0
POU2F1 0.013 0.006 -10000 0 -10000 0 0
CDKN1A 0.024 0.051 -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 -0.14 0.17 -10000 0 -0.31 136 136
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.011 0.14 -10000 0 -0.51 8 8
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.059 0.29 -10000 0 -0.89 25 25
JUN -0.096 0.17 -10000 0 -0.52 26 26
IL4 -0.028 0.077 -10000 0 -10000 0 0
CDK5R1 0.007 0.031 -10000 0 -0.29 3 3
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.099 0.21 0.27 2 -0.54 41 43
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.065 0.096 0.32 2 -0.44 5 7
cortisol/GR alpha (monomer) 0.17 0.19 0.56 25 -10000 0 25
NCOA2 -0.061 0.23 -10000 0 -0.81 26 26
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.13 0.3 -10000 0 -0.83 44 44
AP-1/NFAT1-c-4 -0.19 0.3 -10000 0 -0.73 50 50
AFP -0.2 0.46 -10000 0 -1.5 32 32
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.1 0.094 0.47 2 -10000 0 2
TP53 0.029 0.024 -10000 0 -10000 0 0
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.23 0.36 -10000 0 -1.1 33 33
KRT14 -0.07 0.11 -10000 0 -0.49 1 1
TBP 0.022 0 -10000 0 -10000 0 0
CREBBP 0.023 0.028 -10000 0 -10000 0 0
HDAC1 0.011 0.003 -10000 0 -10000 0 0
HDAC2 0.012 0.003 -10000 0 -10000 0 0
AP-1 -0.19 0.3 -10000 0 -0.74 50 50
MAPK14 0.01 0.005 -10000 0 -10000 0 0
MAPK10 0.01 0.006 -10000 0 -10000 0 0
MAPK11 0.01 0.006 -10000 0 -10000 0 0
KRT5 -0.17 0.27 -10000 0 -0.88 19 19
interleukin-1 receptor activity -0.001 0.003 -10000 0 -10000 0 0
NCOA1 0.014 0.009 -10000 0 -10000 0 0
STAT1 0.015 0.039 -10000 0 -0.28 5 5
CGA -0.059 0.21 -10000 0 -1.2 8 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.034 0.076 0.34 4 -10000 0 4
MAPK3 0.01 0.006 -10000 0 -10000 0 0
MAPK1 0.01 0.005 -10000 0 -10000 0 0
ICAM1 -0.17 0.18 -10000 0 -0.57 10 10
NFKB1 -0.094 0.098 -10000 0 -0.26 16 16
MAPK8 -0.084 0.15 -10000 0 -0.49 17 17
MAPK9 0.01 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.079 0.22 -10000 0 -0.72 13 13
BAX 0.027 0.037 -10000 0 -10000 0 0
POMC -0.23 0.29 -10000 0 -0.65 46 46
EP300 0.023 0.028 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.17 0.17 0.53 17 -10000 0 17
proteasomal ubiquitin-dependent protein catabolic process 0.04 0.046 0.22 1 -10000 0 1
SGK1 0.068 0.041 -10000 0 -10000 0 0
IL13 -0.48 0.28 -10000 0 -0.79 98 98
IL6 -0.27 0.42 -10000 0 -1.3 33 33
PRKACG 0.001 0.018 -10000 0 -0.29 1 1
IL5 -0.4 0.22 -10000 0 -0.62 105 105
IL2 -0.14 0.18 -10000 0 -0.6 10 10
CDK5 0.01 0.005 -10000 0 -10000 0 0
PRKACB 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0 -10000 0 -10000 0 0
IL8 -0.22 0.21 -10000 0 -0.62 21 21
CDK5R1/CDK5 0.01 0.022 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.1 0.13 -10000 0 -0.4 1 1
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.16 0.15 0.51 15 -10000 0 15
SMARCA4 0.014 0 -10000 0 -10000 0 0
chromatin remodeling 0.12 0.094 0.4 5 -10000 0 5
NF kappa B1 p50/RelA/Cbp -0.099 0.15 -10000 0 -0.4 5 5
JUN (dimer) -0.096 0.17 -10000 0 -0.52 26 26
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.065 0.24 -10000 0 -1 16 16
NR3C1 0.095 0.1 0.4 10 -10000 0 10
NR4A1 -0.33 0.41 -10000 0 -0.81 123 123
TIF2/SUV420H1 -0.038 0.18 -10000 0 -0.62 26 26
MAPKKK cascade -0.071 0.21 -10000 0 -0.68 13 13
cortisol/GR alpha (dimer)/Src-1 0.16 0.16 0.52 18 -10000 0 18
PBX1 -0.004 0.12 -10000 0 -0.81 6 6
POU1F1 0.006 0.009 -10000 0 -10000 0 0
SELE -0.66 0.63 -10000 0 -1.3 148 148
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.12 0.095 0.4 5 -10000 0 5
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.16 0.15 0.51 15 -10000 0 15
mol:cortisol 0.083 0.11 0.31 24 -10000 0 24
MMP1 -0.13 0.34 -10000 0 -1.4 18 18
Signaling events regulated by Ret tyrosine kinase

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 -0.016 0.042 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.045 0.11 -9999 0 -0.36 23 23
JUN -0.01 0.13 -9999 0 -0.54 7 7
HRAS 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.044 0.18 -9999 0 -0.5 36 36
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.013 0 -9999 0 -10000 0 0
RAP1A/GDP 0.009 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.046 0.18 -9999 0 -0.51 36 36
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.027 0.14 -9999 0 -0.5 23 23
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.059 0.15 -9999 0 -0.45 36 36
GRB7 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.044 0.18 -9999 0 -0.5 36 36
MAPKKK cascade -0.054 0.14 -9999 0 -0.41 36 36
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.035 0.16 -9999 0 -0.53 26 26
lamellipodium assembly -0.042 0.1 -9999 0 -0.34 23 23
RET51/GFRalpha1/GDNF/SHC -0.044 0.18 -9999 0 -0.5 36 36
PIK3CA 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.027 0.14 -9999 0 -0.5 23 23
RET9/GFRalpha1/GDNF/Shank3 -0.027 0.14 -9999 0 -0.5 23 23
MAPK3 -0.025 0.15 -9999 0 -0.42 36 36
DOK1 0.009 0.031 -9999 0 -0.29 3 3
DOK6 -0.11 0.29 -9999 0 -0.81 43 43
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.038 0.16 -9999 0 -0.58 8 8
DOK5 0.002 0.086 -9999 0 -0.6 5 5
GFRA1 -0.06 0.22 -9999 0 -0.69 30 30
MAPK8 -0.018 0.14 -9999 0 -0.54 8 8
HRAS/GTP -0.062 0.16 -9999 0 -0.47 36 36
tube development -0.034 0.13 -9999 0 -0.47 23 23
MAPK1 -0.025 0.15 -9999 0 -0.42 36 36
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.006 0.098 -9999 0 -0.33 23 23
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC 0.011 0.018 -9999 0 -0.29 1 1
PDLIM7 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.13 0.23 -9999 0 -0.52 72 72
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.044 0.18 -9999 0 -0.5 36 36
RET51/GFRalpha1/GDNF/Dok5 -0.05 0.18 -9999 0 -0.51 39 39
PRKCA 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
CREB1 -0.01 0.12 -9999 0 -0.37 23 23
PIK3R1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.006 0.098 -9999 0 -0.33 23 23
RET51/GFRalpha1/GDNF/Grb7 -0.044 0.18 -9999 0 -0.5 36 36
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.028 0.18 -9999 0 -0.77 15 15
DOK4 0.013 0 -9999 0 -10000 0 0
JNK cascade -0.01 0.13 -9999 0 -0.53 7 7
RET9/GFRalpha1/GDNF/FRS2 -0.027 0.14 -9999 0 -0.5 23 23
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.006 0.098 -9999 0 -0.34 23 23
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.018 0.12 -9999 0 -0.34 36 36
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.019 0.13 -9999 0 -0.35 36 36
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.019 0.13 -9999 0 -0.35 36 36
PI3K -0.016 0.18 -9999 0 -0.51 26 26
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.04 0.13 -9999 0 -0.47 23 23
GRB10 0.013 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.012 0.11 -9999 0 -0.32 23 23
RET51/GFRalpha1/GDNF/FRS2 -0.044 0.18 -9999 0 -0.5 36 36
GAB1 0.013 0 -9999 0 -10000 0 0
IRS1 -0.002 0.11 -9999 0 -0.81 5 5
IRS2 0.01 0.025 -9999 0 -0.29 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.019 0.13 -9999 0 -0.35 36 36
RET51/GFRalpha1/GDNF/PKC alpha -0.044 0.18 -9999 0 -0.5 36 36
GRB2 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF 0.003 0.005 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.053 0.19 -9999 0 -0.53 39 39
Rac1/GTP -0.049 0.12 -9999 0 -0.41 23 23
RET9/GFRalpha1/GDNF -0.047 0.15 -9999 0 -0.55 23 23
GFRalpha1/GDNF -0.044 0.17 -9999 0 -0.62 23 23
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.027 0.11 -10000 0 -0.46 17 17
ER alpha/Gai/GDP/Gbeta gamma -0.02 0.18 -10000 0 -0.45 37 37
AKT1 -0.019 0.21 -10000 0 -0.84 17 17
PIK3CA 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.021 0.21 -10000 0 -0.86 17 17
mol:Ca2+ -0.16 0.28 -10000 0 -0.54 92 92
IGF1R 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.041 0.14 -10000 0 -0.54 22 22
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.016 0.2 0.8 17 -10000 0 17
RhoA/GTP -0.024 0.095 -10000 0 -0.4 17 17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.052 0.15 -10000 0 -0.6 17 17
regulation of stress fiber formation -0.021 0.097 0.32 22 -10000 0 22
E2/ERA-ERB (dimer) -0.032 0.13 -10000 0 -0.54 17 17
KRAS 0.013 0 -10000 0 -10000 0 0
G13/GTP -0.015 0.12 -10000 0 -0.5 17 17
pseudopodium formation 0.021 0.097 -10000 0 -0.32 22 22
E2/ER alpha (dimer)/PELP1 -0.032 0.13 -10000 0 -0.54 17 17
GRB2 0.013 0 -10000 0 -10000 0 0
GNG2 0.013 0 -10000 0 -10000 0 0
GNAO1 -0.061 0.23 -10000 0 -0.81 25 25
HRAS 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.011 0.18 -10000 0 -0.62 19 19
E2/ER beta (dimer) 0.009 0.012 -10000 0 -10000 0 0
mol:GDP -0.032 0.13 -10000 0 -0.54 17 17
mol:NADP -0.011 0.18 -10000 0 -0.62 19 19
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.17 0.3 -10000 0 -0.56 92 92
IGF-1R heterotetramer 0.013 0 -10000 0 -10000 0 0
PLCB1 -0.17 0.3 -10000 0 -0.58 92 92
PLCB2 -0.12 0.26 -10000 0 -0.57 63 63
IGF1 -0.004 0.12 -10000 0 -0.81 6 6
mol:L-citrulline -0.011 0.18 -10000 0 -0.62 19 19
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.067 0.21 -10000 0 -0.73 25 25
JNK cascade 0.009 0.012 -10000 0 -10000 0 0
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 0.011 0.018 -10000 0 -0.29 1 1
GNAQ 0.013 0 -10000 0 -10000 0 0
ESR1 -0.036 0.19 -10000 0 -0.81 17 17
Gq family/GDP/Gbeta gamma -0.051 0.16 -10000 0 -0.56 8 8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.014 0.087 -10000 0 -0.33 17 17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.052 0.15 -10000 0 -0.6 17 17
GNAZ 0.013 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.028 0.15 -10000 0 -0.63 17 17
STRN -0.002 0.11 -10000 0 -0.81 5 5
GNAL 0.01 0.048 -10000 0 -0.81 1 1
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.017 0.01 -10000 0 -10000 0 0
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.007 0.068 -10000 0 -0.81 2 2
HBEGF -0.035 0.17 -10000 0 -0.5 23 23
cAMP biosynthetic process -0.028 0.11 -10000 0 -0.44 18 18
SRC -0.012 0.17 -10000 0 -0.55 17 17
PI3K 0.019 0 -10000 0 -10000 0 0
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.028 0.11 -10000 0 -0.48 17 17
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.046 0.13 -10000 0 -0.49 19 19
Gs family/GTP -0.028 0.11 -10000 0 -0.45 18 18
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.024 0 -10000 0 -10000 0 0
vasodilation -0.009 0.17 -10000 0 -0.59 19 19
mol:DAG -0.17 0.3 -10000 0 -0.56 92 92
Gs family/GDP/Gbeta gamma -0.027 0.1 -10000 0 -0.43 18 18
MSN 0.02 0.1 -10000 0 -0.34 22 22
Gq family/GTP -0.12 0.27 -10000 0 -0.6 63 63
mol:PI-3-4-5-P3 -0.019 0.2 -10000 0 -0.82 17 17
NRAS 0.013 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.009 0.17 0.59 19 -10000 0 19
GRB2/SOS1 0.019 0 -10000 0 -10000 0 0
RhoA/GDP -0.03 0.12 -10000 0 -0.51 17 17
NOS3 -0.014 0.19 -10000 0 -0.67 19 19
GNA11 -0.007 0.13 -10000 0 -0.81 7 7
MAPKKK cascade -0.004 0.18 -10000 0 -0.62 22 22
E2/ER alpha (dimer)/PELP1/Src -0.056 0.16 -10000 0 -0.64 17 17
ruffle organization 0.021 0.097 -10000 0 -0.32 22 22
ROCK2 0.013 0.11 -10000 0 -0.38 22 22
GNA14 -0.16 0.33 -10000 0 -0.81 61 61
GNA15 -0.008 0.077 -10000 0 -0.29 20 20
GNA13 0.011 0.018 -10000 0 -0.29 1 1
MMP9 -0.059 0.18 -10000 0 -0.52 25 25
MMP2 -0.007 0.17 -10000 0 -0.52 18 18
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0.025 -9999 0 -0.29 2 2
CCL5 -0.018 0.091 -9999 0 -0.29 29 29
SDCBP 0.013 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.075 0.14 -9999 0 -0.43 25 25
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.065 0.14 -9999 0 -0.52 12 12
Syndecan-1/Syntenin -0.065 0.14 -9999 0 -0.52 12 12
MAPK3 -0.046 0.13 -9999 0 -0.51 9 9
HGF/MET -0.044 0.17 -9999 0 -0.66 17 17
TGFB1/TGF beta receptor Type II 0.01 0.025 -9999 0 -0.29 2 2
BSG 0.013 0 -9999 0 -10000 0 0
keratinocyte migration -0.064 0.14 -9999 0 -0.51 12 12
Syndecan-1/RANTES -0.078 0.15 -9999 0 -0.49 16 16
Syndecan-1/CD147 -0.055 0.13 -9999 0 -0.53 10 10
Syndecan-1/Syntenin/PIP2 -0.063 0.13 -9999 0 -0.5 12 12
LAMA5 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.075 0.12 -9999 0 -0.48 12 12
MMP7 -0.083 0.16 -9999 0 -0.81 5 5
HGF -0.037 0.19 -9999 0 -0.78 18 18
Syndecan-1/CASK -0.072 0.14 -9999 0 -0.41 25 25
Syndecan-1/HGF/MET -0.099 0.19 -9999 0 -0.55 30 30
regulation of cell adhesion -0.038 0.12 -9999 0 -0.66 4 4
HPSE -0.025 0.17 -9999 0 -0.77 14 14
positive regulation of cell migration -0.075 0.14 -9999 0 -0.43 25 25
SDC1 -0.076 0.15 -9999 0 -0.43 25 25
Syndecan-1/Collagen -0.075 0.14 -9999 0 -0.43 25 25
PPIB 0.013 0 -9999 0 -10000 0 0
MET -0.025 0.1 -9999 0 -0.29 36 36
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.12 0.17 -9999 0 -0.31 115 115
MAPK1 -0.046 0.13 -9999 0 -0.58 6 6
homophilic cell adhesion -0.075 0.14 -9999 0 -0.42 25 25
MMP1 -0.052 0.2 -9999 0 -0.81 18 18
Signaling events mediated by the Hedgehog family

Figure S36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 0.005 0.15 -10000 0 -0.6 3 3
IHH -0.061 0.25 -10000 0 -0.83 28 28
SHH Np/Cholesterol/GAS1 -0.015 0.13 -10000 0 -0.5 20 20
LRPAP1 0.013 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.015 0.13 0.5 20 -10000 0 20
SMO/beta Arrestin2 0.003 0.16 -10000 0 -0.57 7 7
SMO -0.003 0.17 -10000 0 -0.5 29 29
AKT1 0.023 0.078 -10000 0 -10000 0 0
ARRB2 0.011 0.018 -10000 0 -10000 0 0
BOC 0.013 0 -10000 0 -10000 0 0
ADRBK1 0.013 0 -10000 0 -10000 0 0
heart looping -0.002 0.17 -10000 0 -0.49 29 29
STIL 0.005 0.14 -10000 0 -0.44 11 11
DHH N/PTCH2 -0.026 0.16 -10000 0 -0.62 19 19
DHH N/PTCH1 -0.036 0.19 -10000 0 -0.46 46 46
PIK3CA 0.013 0 -10000 0 -10000 0 0
DHH -0.042 0.2 -10000 0 -0.81 19 19
PTHLH -0.002 0.17 -10000 0 -0.77 3 3
determination of left/right symmetry -0.002 0.17 -10000 0 -0.49 29 29
PIK3R1 0.013 0 -10000 0 -10000 0 0
skeletal system development -0.002 0.17 -10000 0 -0.76 3 3
IHH N/Hhip -0.063 0.21 -10000 0 -0.58 39 39
DHH N/Hhip -0.051 0.21 -10000 0 -0.68 27 27
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.002 0.17 -10000 0 -0.49 29 29
pancreas development -0.026 0.16 -10000 0 -0.62 17 17
HHAT 0.013 0 -10000 0 -10000 0 0
PI3K 0.019 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.036 0.19 -10000 0 -0.81 17 17
somite specification -0.002 0.17 -10000 0 -0.49 29 29
SHH Np/Cholesterol/PTCH1 0 0.14 -10000 0 -0.39 31 31
SHH Np/Cholesterol/PTCH2 0.014 0.057 -10000 0 -0.49 3 3
SHH Np/Cholesterol/Megalin -0.033 0.16 -10000 0 -0.51 29 29
SHH 0.011 0.07 -10000 0 -0.62 3 3
catabolic process -0.008 0.16 -10000 0 -0.48 28 28
SMO/Vitamin D3 0.001 0.15 -10000 0 -0.5 9 9
SHH Np/Cholesterol/Hhip -0.009 0.11 -10000 0 -0.49 14 14
LRP2 -0.064 0.24 -10000 0 -0.81 27 27
receptor-mediated endocytosis -0.023 0.2 -10000 0 -0.66 15 15
SHH Np/Cholesterol/BOC 0.015 0.056 -10000 0 -0.49 3 3
SHH Np/Cholesterol/CDO 0.013 0.058 -10000 0 -0.49 3 3
mesenchymal cell differentiation 0.009 0.11 0.49 14 -10000 0 14
mol:Vitamin D3 0.003 0.14 -10000 0 -0.39 31 31
IHH N/PTCH2 -0.033 0.17 -10000 0 -0.54 28 28
CDON 0.008 0.035 -10000 0 -0.29 4 4
IHH N/PTCH1 -0.008 0.16 -10000 0 -0.49 28 28
Megalin/LRPAP1 -0.041 0.18 -10000 0 -0.62 27 27
PTCH2 0.009 0.031 -10000 0 -0.29 3 3
SHH Np/Cholesterol -0.008 0.053 -10000 0 -0.5 3 3
PTCH1 -0.008 0.16 -10000 0 -0.48 28 28
HHIP -0.026 0.16 -10000 0 -0.62 17 17
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.044 0.15 -9999 0 -0.54 24 24
E-cadherin/beta catenin -0.034 0.18 -9999 0 -0.62 24 24
CTNNB1 0.013 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
CDH1 -0.055 0.23 -9999 0 -0.81 24 24
Aurora B 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
Condensin I complex -0.048 0.1 -9999 0 -10000 0 0
STMN1 -0.073 0.1 -9999 0 -10000 0 0
Aurora B/RasGAP/Survivin -0.11 0.14 -9999 0 -10000 0 0
Chromosomal passenger complex/Cul3 protein complex -0.059 0.12 -9999 0 -0.35 21 21
BIRC5 -0.099 0.15 -9999 0 -0.3 103 103
DES -0.31 0.3 -9999 0 -0.65 122 122
Aurora C/Aurora B/INCENP -0.049 0.076 -9999 0 -10000 0 0
Aurora B/TACC1 -0.063 0.082 -9999 0 -10000 0 0
Aurora B/PP2A -0.079 0.1 -9999 0 -0.36 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.014 0.032 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.002 0.003 -9999 0 -10000 0 0
NDC80 -0.095 0.14 -9999 0 -0.37 34 34
Cul3 protein complex -0.039 0.14 -9999 0 -0.54 21 21
KIF2C -0.047 0.086 -9999 0 -0.24 32 32
PEBP1 0.008 0.006 -9999 0 -10000 0 0
KIF20A -0.091 0.14 -9999 0 -0.29 37 37
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.078 0.099 -9999 0 -10000 0 0
SEPT1 0.007 0.04 -9999 0 -0.29 5 5
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.042 0.075 -9999 0 -10000 0 0
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.002 -9999 0 -10000 0 0
H3F3B -0.045 0.068 -9999 0 -10000 0 0
AURKB -0.13 0.16 -9999 0 -0.29 138 138
AURKC 0.012 0.001 -9999 0 -10000 0 0
CDCA8 -0.025 0.098 -9999 0 -0.3 32 32
cytokinesis -0.12 0.12 -9999 0 -0.4 11 11
Aurora B/Septin1 -0.097 0.13 -9999 0 -0.38 13 13
AURKA 0.008 0.04 -9999 0 -0.29 5 5
INCENP 0.008 0.006 -9999 0 -10000 0 0
KLHL13 -0.044 0.21 -9999 0 -0.81 20 20
BUB1 -0.098 0.15 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin -0.11 0.15 -9999 0 -0.42 28 28
EVI5 0.012 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.08 0.1 -9999 0 -0.42 1 1
SGOL1 -0.017 0.09 -9999 0 -0.29 28 28
CENPA -0.078 0.12 -9999 0 -0.24 78 78
NCAPG -0.074 0.14 -9999 0 -0.29 83 83
Aurora B/HC8 Proteasome -0.078 0.099 -9999 0 -10000 0 0
NCAPD2 0.013 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.078 0.099 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.046 0.12 -9999 0 -0.29 56 56
NPM1 -0.055 0.069 -9999 0 -10000 0 0
RASA1 0.013 0 -9999 0 -10000 0 0
KLHL9 0.01 0.048 -9999 0 -0.81 1 1
mitotic prometaphase -0.004 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.078 0.099 -9999 0 -10000 0 0
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.09 0.11 -9999 0 -0.36 4 4
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
NSUN2 -0.055 0.069 -9999 0 -10000 0 0
MYLK -0.061 0.11 -9999 0 -0.52 10 10
KIF23 0.008 0.025 -9999 0 -0.3 2 2
VIM -0.075 0.1 -9999 0 -0.37 1 1
RACGAP1 0.01 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.055 0.069 -9999 0 -10000 0 0
Chromosomal passenger complex -0.088 0.14 -9999 0 -0.3 67 67
Chromosomal passenger complex/EVI5 -0.087 0.16 -9999 0 -0.38 32 32
TACC1 0.013 0 -9999 0 -10000 0 0
PPP2R5D 0.011 0.018 -9999 0 -10000 0 0
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NRIP1 0.012 0.003 -9999 0 -10000 0 0
SVIL 0.012 0.003 -9999 0 -10000 0 0
ZNF318 0.014 0.011 -9999 0 -10000 0 0
JMJD2C -0.002 0.017 -9999 0 -0.062 21 21
T-DHT/AR/Ubc9 -0.064 0.12 -9999 0 -0.57 12 12
CARM1 0.012 0 -9999 0 -10000 0 0
PRDX1 0.013 0.001 -9999 0 -10000 0 0
PELP1 0.013 0.002 -9999 0 -10000 0 0
CTNNB1 0.012 0.003 -9999 0 -10000 0 0
AKT1 0.013 0.003 -9999 0 -10000 0 0
PTK2B 0.012 0.003 -9999 0 -10000 0 0
MED1 0.013 0.003 -9999 0 -10000 0 0
MAK 0.003 0.057 -9999 0 -0.29 10 10
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.007 0.068 -9999 0 -0.81 2 2
GSN 0.012 0.003 -9999 0 -10000 0 0
NCOA2 -0.061 0.23 -9999 0 -0.81 26 26
NCOA6 0.012 0.003 -9999 0 -10000 0 0
DNA-PK 0.004 0.017 -9999 0 -10000 0 0
NCOA4 0.012 0 -9999 0 -10000 0 0
PIAS3 0.012 0.003 -9999 0 -10000 0 0
cell proliferation -0.034 0.035 -9999 0 -10000 0 0
XRCC5 0.013 0.002 -9999 0 -10000 0 0
UBE3A 0.012 0.006 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.094 0.16 -9999 0 -0.58 27 27
FHL2 -0.032 0.081 -9999 0 -1.1 1 1
RANBP9 0.012 0.003 -9999 0 -10000 0 0
JMJD1A -0.089 0.078 -9999 0 -0.15 186 186
CDK6 0.013 0 -9999 0 -10000 0 0
TGFB1I1 -0.002 0.11 -9999 0 -0.81 5 5
T-DHT/AR/CyclinD1 -0.066 0.12 -9999 0 -0.57 13 13
XRCC6 0.013 0.002 -9999 0 -10000 0 0
T-DHT/AR -0.12 0.14 -9999 0 -0.59 12 12
CTDSP1 0.012 0.002 -9999 0 -10000 0 0
CTDSP2 0.013 0.007 -9999 0 -10000 0 0
BRCA1 0.009 0.032 -9999 0 -0.31 1 1
TCF4 0.013 0.005 -9999 0 -10000 0 0
CDKN2A -0.23 0.12 -9999 0 -0.29 216 216
SRF 0.02 0.01 -9999 0 -10000 0 0
NKX3-1 -0.15 0.13 -9999 0 -0.38 1 1
KLK3 0.005 0.068 -9999 0 -10000 0 0
TMF1 0.012 0.002 -9999 0 -10000 0 0
HNRNPA1 0.013 0.004 -9999 0 -10000 0 0
AOF2 0 0.005 -9999 0 -10000 0 0
APPL1 0.022 0.006 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.064 0.12 -9999 0 -0.57 12 12
AR -0.065 0.16 -9999 0 -0.75 14 14
UBA3 0.012 0.002 -9999 0 -10000 0 0
PATZ1 0.013 0.004 -9999 0 -10000 0 0
PAWR 0.012 0.002 -9999 0 -10000 0 0
PRKDC 0.013 0.002 -9999 0 -10000 0 0
PA2G4 0.013 0.005 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.058 0.11 -9999 0 -0.5 13 13
RPS6KA3 0.012 0.003 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.064 0.12 -9999 0 -0.57 12 12
LATS2 0.013 0.004 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.056 0.11 -9999 0 -0.52 12 12
Cyclin D3/CDK11 p58 0.007 0.021 -9999 0 -0.2 3 3
VAV3 0.009 0.048 -9999 0 -0.81 1 1
KLK2 -0.072 0.084 -9999 0 -0.51 1 1
CASP8 0.013 0.001 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.094 0.2 -9999 0 -0.6 34 34
TMPRSS2 -0.72 0.55 -9999 0 -1.1 186 186
CCND1 0.01 0.048 -9999 0 -0.81 1 1
PIAS1 0.012 0.006 -9999 0 -10000 0 0
mol:T-DHT -0.047 0.039 -9999 0 -0.076 183 183
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.011 0.009 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.064 0.12 -9999 0 -0.57 12 12
CMTM2 -0.006 0.071 -9999 0 -0.29 17 17
SNURF -0.032 0.18 -9999 0 -0.81 15 15
ZMIZ1 -0.029 0.035 -9999 0 -10000 0 0
CCND3 0.009 0.031 -9999 0 -0.29 3 3
TGIF1 0.013 0.004 -9999 0 -10000 0 0
FKBP4 0.012 0.003 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 -0.14 0.15 -9999 0 -0.29 145 145
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P -0.036 0.057 -9999 0 -10000 0 0
GNAO1 -0.061 0.23 -9999 0 -0.81 25 25
mol:Sphinganine-1-P -0.082 0.1 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.003 0.041 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.018 0.012 -9999 0 -10000 0 0
S1PR3 -0.052 0.22 -9999 0 -0.81 23 23
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.039 0.039 -9999 0 -10000 0 0
S1PR5 -0.002 0.093 -9999 0 -0.46 9 9
S1PR4 0.006 0.043 -9999 0 -0.29 6 6
GNAI1 0.007 0.068 -9999 0 -0.81 2 2
S1P/S1P5/G12 -0.02 0.068 -9999 0 -0.53 3 3
S1P/S1P3/Gq -0.1 0.2 -9999 0 -0.42 62 62
S1P/S1P4/Gi -0.016 0.1 -9999 0 -0.33 25 25
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
GNA14 -0.16 0.33 -9999 0 -0.81 61 61
GNA15 -0.008 0.077 -9999 0 -0.29 20 20
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.011 0.018 -9999 0 -0.29 1 1
GNA11 -0.007 0.13 -9999 0 -0.81 7 7
ABCC1 0.013 0 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

Figure S41.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S41.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.019 0 -9999 0 -10000 0 0
Necdin/E2F1 -0.088 0.19 -9999 0 -0.64 23 23
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.026 0.11 -9999 0 -0.48 15 15
NGF (dimer)/p75(NTR)/BEX1 -0.067 0.18 -9999 0 -0.56 34 34
NT-4/5 (dimer)/p75(NTR) -0.02 0.12 -9999 0 -0.64 8 8
IKBKB 0.013 0 -9999 0 -10000 0 0
AKT1 0.009 0.12 -9999 0 -0.48 15 15
IKBKG 0.013 0 -9999 0 -10000 0 0
BDNF -0.028 0.1 -9999 0 -0.29 39 39
MGDIs/NGR/p75(NTR)/LINGO1 -0.026 0.12 -9999 0 -0.57 12 12
FURIN 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.034 0.1 -9999 0 -0.59 8 8
LINGO1 -0.002 0.11 -9999 0 -0.81 5 5
Sortilin/TRAF6/NRIF -0.001 0.023 -9999 0 -10000 0 0
proBDNF (dimer) -0.028 0.1 -9999 0 -0.29 39 39
NTRK1 -0.15 0.32 -9999 0 -0.81 56 56
RTN4R 0.007 0.04 -9999 0 -0.29 5 5
neuron apoptosis -0.005 0.12 -9999 0 -0.54 8 8
IRAK1 0.013 0 -9999 0 -10000 0 0
SHC1 -0.005 0.13 -9999 0 -0.56 15 15
ARHGDIA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0.009 0 -9999 0 -10000 0 0
Gamma Secretase -0.002 0.027 -9999 0 -0.46 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.002 0.12 -9999 0 -0.52 15 15
MAGEH1 0.011 0.018 -9999 0 -0.29 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.037 0.2 -9999 0 -0.57 33 33
Mammalian IAPs/DIABLO 0.022 0.039 -9999 0 -10000 0 0
proNGF (dimer) -0.012 0.14 -9999 0 -0.81 8 8
MAGED1 0.013 0 -9999 0 -10000 0 0
APP 0.013 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.019 0.084 -9999 0 -0.29 25 25
ZNF274 0.013 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI 0.003 0.12 -9999 0 -0.49 15 15
NGF -0.012 0.14 -9999 0 -0.81 8 8
cell cycle arrest -0.012 0.12 -9999 0 -0.47 15 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.015 0.087 -9999 0 -0.35 15 15
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.027 0.098 -9999 0 -0.56 8 8
NCSTN 0.013 0 -9999 0 -10000 0 0
mol:GTP -0.03 0.13 -9999 0 -0.56 15 15
PSENEN 0.013 0 -9999 0 -10000 0 0
mol:ceramide 0.002 0.12 -9999 0 -0.51 15 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.022 0.073 -9999 0 -0.53 1 1
p75(NTR)/beta APP 0.001 0.1 -9999 0 -0.62 8 8
BEX1 -0.045 0.2 -9999 0 -0.72 23 23
mol:GDP -0.015 0.13 -9999 0 -0.57 15 15
NGF (dimer) -0.32 0.28 -9999 0 -0.55 167 167
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.007 0.12 -9999 0 -0.52 12 12
PIK3R1 0.013 0 -9999 0 -10000 0 0
RAC1/GTP -0.027 0.11 -9999 0 -0.5 15 15
MYD88 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.03 0.13 -9999 0 -0.57 15 15
RHOB 0.013 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.038 0.092 -9999 0 -10000 0 0
NT3 (dimer) -0.076 0.25 -9999 0 -0.81 31 31
TP53 0.012 0.094 -9999 0 -0.47 8 8
PRDM4 0.002 0.12 -9999 0 -0.52 15 15
BDNF (dimer) -0.34 0.26 -9999 0 -0.56 167 167
PIK3CA 0.013 0 -9999 0 -10000 0 0
SORT1 0.013 0 -9999 0 -10000 0 0
activation of caspase activity -0.026 0.11 -9999 0 -0.48 15 15
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.003 0.12 -9999 0 -0.52 15 15
RHOC 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
MAPK10 0.024 0.11 -9999 0 -0.52 5 5
DIABLO 0.013 0 -9999 0 -10000 0 0
SMPD2 0.002 0.12 -9999 0 -0.52 15 15
APH1B 0.01 0.048 -9999 0 -0.81 1 1
APH1A 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.03 0.13 -9999 0 -0.57 15 15
PSEN1 0.013 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.019 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.067 0.22 -9999 0 -0.65 37 37
MAPK8 0.018 0.12 -9999 0 -0.52 5 5
MAPK9 0.024 0.11 -9999 0 -0.52 5 5
APAF1 0.013 0 -9999 0 -10000 0 0
NTF3 -0.076 0.25 -9999 0 -0.81 31 31
NTF4 -0.019 0.084 -9999 0 -0.29 25 25
NDN -0.052 0.22 -9999 0 -0.81 23 23
RAC1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.024 0.1 -9999 0 -0.45 15 15
p75 CTF/Sortilin/TRAF6/NRIF 0.032 0 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.03 0.13 -9999 0 -0.56 15 15
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.027 0.088 -9999 0 -0.5 8 8
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.002 0.1 -9999 0 -0.54 8 8
PRKACB 0.013 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.009 0.07 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.008 0.077 -9999 0 -0.29 20 20
BIRC2 0.013 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.03 0.16 -9999 0 -0.59 15 15
BAD 0.028 0.11 -9999 0 -0.5 5 5
RIPK2 0.013 0 -9999 0 -10000 0 0
NGFR -0.01 0.13 -9999 0 -0.81 8 8
CYCS 0.009 0.12 -9999 0 -0.48 15 15
ADAM17 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.003 0.12 -9999 0 -0.52 15 15
BCL2L11 0.028 0.11 -9999 0 -0.5 5 5
BDNF (dimer)/p75(NTR) -0.026 0.13 -9999 0 -0.67 8 8
PI3K 0.003 0.12 -9999 0 -0.52 15 15
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.003 0.12 -9999 0 -0.52 15 15
NDNL2 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.018 0.15 -9999 0 -0.65 15 15
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.003 0.12 -9999 0 -0.52 15 15
TRAF6 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
PLG -0.46 0.4 -9999 0 -0.81 164 164
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.009 0.13 -9999 0 -0.52 15 15
SQSTM1 0.003 0.053 -9999 0 -0.29 9 9
NGFRAP1 0.013 0 -9999 0 -10000 0 0
CASP3 0.029 0.1 -9999 0 -0.46 5 5
E2F1 -0.071 0.14 -9999 0 -0.29 80 80
CASP9 0.013 0 -9999 0 -10000 0 0
IKK complex -0.092 0.17 -9999 0 -0.64 5 5
NGF (dimer)/TRKA -0.12 0.27 -9999 0 -0.63 63 63
MMP7 -0.083 0.16 -9999 0 -0.81 5 5
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.026 0.11 -9999 0 -0.48 15 15
MMP3 -0.015 0.071 -9999 0 -0.29 18 18
APAF-1/Caspase 9 -0.022 0.082 -9999 0 -0.65 1 1
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.014 0.023 -9999 0 -10000 0 0
NFATC2 -0.029 0.15 -9999 0 -0.54 22 22
NFATC3 0.014 0.023 -9999 0 -10000 0 0
CD40LG -0.093 0.26 -9999 0 -0.64 33 33
PTGS2 -0.16 0.37 -9999 0 -0.85 52 52
JUNB 0.013 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.008 -9999 0 -10000 0 0
CaM/Ca2+ -0.003 0.008 -9999 0 -10000 0 0
CALM1 0.012 0.006 -9999 0 -10000 0 0
JUN 0.012 0.007 -9999 0 -10000 0 0
mol:Ca2+ -0.004 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.003 -9999 0 -10000 0 0
FOSL1 0.003 0.076 -9999 0 -0.46 6 6
CREM 0.012 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.058 0.12 -9999 0 -0.52 8 8
FOS -0.11 0.3 -9999 0 -0.82 44 44
IFNG -0.1 0.26 -9999 0 -0.63 38 38
AP-1/NFAT1-c-4 -0.12 0.3 -9999 0 -0.75 35 35
FASLG -0.1 0.27 -9999 0 -0.64 36 36
NFAT1-c-4/ICER1 -0.03 0.13 -9999 0 -0.44 22 22
IL2RA -0.1 0.26 -9999 0 -0.63 34 34
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSF2 -0.095 0.26 -9999 0 -0.63 32 32
JunB/Fra1/NFAT1-c-4 -0.045 0.12 -9999 0 -0.42 24 24
IL4 -0.095 0.25 -9999 0 -0.63 32 32
IL2 -0.006 0.025 -9999 0 -10000 0 0
IL3 -0.015 0.021 -9999 0 -10000 0 0
FKBP1A 0.013 0 -9999 0 -10000 0 0
BATF3 0.011 0.018 -9999 0 -0.29 1 1
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0 -9999 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0 -10000 0 -10000 0 0
GNB1/GNG2 0.001 0.1 -10000 0 -0.49 12 12
regulation of S phase of mitotic cell cycle 0.012 0.074 -10000 0 -0.34 12 12
GNAO1 -0.061 0.23 -10000 0 -0.81 25 25
HRAS 0.012 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.016 0.096 -10000 0 -0.55 9 9
PELP1 0.012 0.001 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
MAP2K1 0.008 0.1 -10000 0 -0.41 12 12
T-DHT/AR -0.019 0.13 -10000 0 -0.57 14 14
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.008 44 44
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.007 0.068 -10000 0 -0.81 2 2
mol:GDP -0.026 0.12 -10000 0 -0.6 12 12
cell proliferation -0.016 0.17 -10000 0 -0.44 14 14
PIK3CA 0.013 0 -10000 0 -10000 0 0
FOS -0.087 0.32 -10000 0 -0.85 44 44
mol:Ca2+ -0.011 0.024 -10000 0 -0.074 29 29
MAPK3 -0.003 0.13 -10000 0 -0.41 12 12
MAPK1 -0.003 0.087 -10000 0 -0.3 2 2
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.005 44 44
cAMP biosynthetic process -0.008 0.094 -10000 0 -0.52 9 9
GNG2 0.013 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.005 44 44
HRAS/GTP -0.024 0.092 -10000 0 -0.46 12 12
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.011 0.018 -10000 0 -0.29 1 1
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.005 44 44
PI3K 0.002 0.006 -10000 0 -10000 0 0
apoptosis 0.022 0.17 0.4 44 -10000 0 44
T-DHT/AR/PELP1 -0.023 0.11 -10000 0 -0.54 12 12
HRAS/GDP -0.023 0.11 -10000 0 -0.57 12 12
CREB1 -0.026 0.18 -10000 0 -0.43 44 44
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.024 0.16 -10000 0 -0.74 14 14
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 0.006 0.099 -10000 0 -0.44 12 12
RAC1-CDC42/GDP -0.02 0.11 -10000 0 -0.55 12 12
T-DHT/AR/PELP1/Src -0.001 0.11 -10000 0 -0.51 12 12
MAP2K2 0.008 0.1 -10000 0 -0.41 12 12
T-DHT/AR/PELP1/Src/PI3K 0.012 0.074 -10000 0 -0.34 12 12
GNAZ 0.012 0 -10000 0 -10000 0 0
SHBG -0.013 0.14 -10000 0 -0.81 9 9
Gi family/GNB1/GNG2/GDP -0.001 0.12 -10000 0 -0.39 25 25
mol:T-DHT 0 0.001 -10000 0 -0.003 41 41
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 -0.034 0.085 -10000 0 -10000 0 0
Gi family/GTP -0.011 0.093 -10000 0 -0.26 27 27
CDC42 0.013 0 -10000 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.011 0.1 -9999 0 -0.34 22 22
FZD6 0.013 0 -9999 0 -10000 0 0
WNT6 0.008 0.051 -9999 0 -0.55 2 2
WNT4 -0.015 0.14 -9999 0 -0.71 11 11
FZD3 0.013 0 -9999 0 -10000 0 0
WNT5A -0.032 0.11 -9999 0 -0.29 43 43
WNT11 -0.029 0.17 -9999 0 -0.62 19 19
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.017 0.021 -9999 0 -10000 0 0
VLDLR 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
ITGA3 -0.003 0.067 -9999 0 -0.29 15 15
RELN/VLDLR/Fyn -0.078 0.13 -9999 0 -0.54 15 15
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.008 0.059 -9999 0 -0.46 5 5
AKT1 -0.021 0.083 -9999 0 -0.32 15 15
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 -0.004 0.052 -9999 0 -0.29 9 9
RELN/LRP8/DAB1 -0.068 0.13 -9999 0 -0.52 15 15
LRPAP1/LRP8 0.014 0.029 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.071 0.11 -9999 0 -0.49 15 15
DAB1/alpha3/beta1 Integrin -0.062 0.1 -9999 0 -0.44 15 15
long-term memory -0.16 0.22 -9999 0 -0.5 79 79
DAB1/LIS1 -0.062 0.1 -9999 0 -0.46 15 15
DAB1/CRLK/C3G -0.057 0.1 -9999 0 -0.44 15 15
PIK3CA 0.013 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.062 0.1 -9999 0 -0.46 15 15
ARHGEF2 0.013 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.18 0.34 -9999 0 -0.79 69 69
CDK5R1 0.009 0.031 -9999 0 -0.29 3 3
RELN -0.14 0.21 -9999 0 -0.36 116 116
PIK3R1 0.013 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.081 0.13 -9999 0 -0.55 15 15
GRIN2A/RELN/LRP8/DAB1/Fyn -0.18 0.22 -9999 0 -0.53 79 79
MAPK8 -0.002 0.11 -9999 0 -0.81 5 5
RELN/VLDLR/DAB1 -0.065 0.13 -9999 0 -0.51 15 15
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.049 0.12 -9999 0 -0.48 15 15
RELN/LRP8 -0.081 0.13 -9999 0 -0.55 15 15
GRIN2B/RELN/LRP8/DAB1/Fyn -0.071 0.11 -9999 0 -0.49 15 15
PI3K 0.019 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.008 0.045 -9999 0 -10000 0 0
RAP1A -0.024 0.11 -9999 0 -0.41 15 15
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 0.013 0 -9999 0 -10000 0 0
CRLK/C3G 0.019 0 -9999 0 -10000 0 0
GRIN2B 0.002 0.035 -9999 0 -0.29 4 4
NCK2 0.013 0 -9999 0 -10000 0 0
neuron differentiation -0.006 0.071 -9999 0 -0.29 6 6
neuron adhesion -0.016 0.11 -9999 0 -0.47 3 3
LRP8 0.006 0.043 -9999 0 -0.29 6 6
GSK3B -0.013 0.079 -9999 0 -0.37 1 1
RELN/VLDLR/DAB1/Fyn -0.069 0.11 -9999 0 -0.48 15 15
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.031 0.087 -9999 0 -0.34 15 15
CDK5 0.013 0 -9999 0 -10000 0 0
MAPT -0.013 0.14 -9999 0 -0.75 10 10
neuron migration -0.006 0.11 -9999 0 -0.41 15 15
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.006 0.072 -9999 0 -0.29 6 6
RELN/VLDLR -0.051 0.13 -9999 0 -0.5 15 15
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.012 0.025 -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 0.028 0.14 0.44 8 -10000 0 8
IL27/IL27R/JAK1 0.036 0.25 -10000 0 -0.62 9 9
TBX21 -0.006 0.19 -10000 0 -0.59 4 4
IL12B 0.003 0.031 -10000 0 -10000 0 0
IL12A 0.009 0.004 -10000 0 -10000 0 0
IL6ST -0.11 0.3 -10000 0 -0.81 44 44
IL27RA/JAK1 0.025 0.027 -10000 0 -10000 0 0
IL27 -0.001 0.057 -10000 0 -0.3 10 10
TYK2 0.013 0.004 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.028 0.12 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.028 0.14 0.44 8 -10000 0 8
T cell proliferation during immune response 0.028 0.14 0.44 8 -10000 0 8
MAPKKK cascade -0.028 0.14 -10000 0 -0.44 8 8
STAT3 0.013 0 -10000 0 -10000 0 0
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.01 0.04 -10000 0 -0.29 5 5
IL12RB1 -0.007 0.074 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.065 0.21 -10000 0 -0.51 25 25
IL27/IL27R/JAK2/TYK2 -0.028 0.14 -10000 0 -0.44 8 8
positive regulation of T cell mediated cytotoxicity -0.028 0.14 -10000 0 -0.44 8 8
STAT1 (dimer) 0.18 0.35 0.5 85 -0.69 5 90
JAK2 0.013 0.004 -10000 0 -10000 0 0
JAK1 0.015 0.004 -10000 0 -10000 0 0
STAT2 (dimer) -0.02 0.13 -10000 0 -0.44 5 5
T cell proliferation -0.072 0.2 -10000 0 -0.52 28 28
IL12/IL12R/TYK2/JAK2 0.014 0.048 -10000 0 -10000 0 0
IL17A -0.029 0.12 -10000 0 -10000 0 0
mast cell activation 0.028 0.14 0.44 8 -10000 0 8
IFNG -0.002 0.027 -10000 0 -0.087 3 3
T cell differentiation -0.003 0.005 -10000 0 -0.02 1 1
STAT3 (dimer) -0.02 0.13 -10000 0 -0.44 5 5
STAT5A (dimer) -0.02 0.13 -10000 0 -0.44 5 5
STAT4 (dimer) -0.031 0.14 -10000 0 -0.51 7 7
STAT4 -0.013 0.084 -10000 0 -0.29 24 24
T cell activation -0.01 0.006 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.053 0.17 -10000 0 -0.53 1 1
GATA3 -1.1 0.59 -10000 0 -1.4 225 225
IL18 0.007 0.027 -10000 0 -0.2 5 5
positive regulation of mast cell cytokine production -0.02 0.13 -10000 0 -0.44 5 5
IL27/EBI3 -0.016 0.097 -10000 0 -0.41 8 8
IL27RA 0.011 0.023 -10000 0 -10000 0 0
IL6 -0.081 0.25 -10000 0 -0.81 29 29
STAT5A 0.013 0 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.001 0.016 -10000 0 -10000 0 0
IL1B -0.001 0.084 -10000 0 -0.63 5 5
EBI3 -0.03 0.12 -10000 0 -0.32 22 22
TNF -0.006 0.078 -10000 0 -0.63 3 3
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.05 0.19 -9999 0 -0.66 3 3
CRP -0.061 0.2 -9999 0 -0.69 5 5
cell cycle arrest -0.067 0.2 -9999 0 -0.69 8 8
TIMP1 -0.083 0.2 -9999 0 -0.57 12 12
IL6ST -0.11 0.3 -9999 0 -0.81 44 44
Rac1/GDP -0.077 0.19 -9999 0 -0.55 19 19
AP1 -0.064 0.17 -9999 0 -0.48 24 24
GAB2 0.013 0.003 -9999 0 -10000 0 0
TNFSF11 -0.064 0.2 -9999 0 -0.69 5 5
HSP90B1 0.012 0.049 -9999 0 -10000 0 0
GAB1 0.013 0.001 -9999 0 -10000 0 0
MAPK14 -0.041 0.18 -9999 0 -0.66 9 9
AKT1 0.048 0.013 -9999 0 -10000 0 0
FOXO1 0.053 0.013 -9999 0 -10000 0 0
MAP2K6 -0.053 0.18 -9999 0 -0.66 10 10
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.065 0.19 -9999 0 -0.56 14 14
MITF -0.061 0.19 -9999 0 -0.53 20 20
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.013 0 -9999 0 -10000 0 0
A2M 0.012 0.12 -9999 0 -1.4 2 2
CEBPB 0.006 0.053 -9999 0 -0.29 9 9
GRB2/SOS1/GAB family/SHP2 -0.009 0.075 -9999 0 -10000 0 0
STAT3 -0.072 0.21 -9999 0 -0.74 8 8
STAT1 -0.011 0.025 -9999 0 -10000 0 0
CEBPD -0.05 0.19 -9999 0 -0.64 4 4
PIK3CA 0.014 0 -9999 0 -10000 0 0
PI3K 0.021 0.001 -9999 0 -10000 0 0
JUN 0.012 0.001 -9999 0 -10000 0 0
PIAS3/MITF -0.048 0.18 -9999 0 -0.69 9 9
MAPK11 -0.041 0.18 -9999 0 -0.66 9 9
STAT3 (dimer)/FOXO1 -0.02 0.18 -9999 0 -0.54 7 7
GRB2/SOS1/GAB family -0.076 0.15 -9999 0 -0.69 7 7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.072 0.2 -9999 0 -0.47 32 32
GRB2 0.013 0.001 -9999 0 -10000 0 0
JAK2 0.013 0 -9999 0 -10000 0 0
LBP -0.27 0.45 -9999 0 -0.95 82 82
PIK3R1 0.014 0 -9999 0 -10000 0 0
JAK1 0.014 0.003 -9999 0 -10000 0 0
MYC -0.052 0.19 -9999 0 -0.63 5 5
FGG -0.067 0.2 -9999 0 -0.7 4 4
macrophage differentiation -0.067 0.2 -9999 0 -0.69 8 8
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.11 0.22 -9999 0 -0.49 68 68
JUNB -0.049 0.18 -9999 0 -0.62 4 4
FOS -0.11 0.29 -9999 0 -0.81 44 44
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.07 0.19 -9999 0 -0.45 38 38
STAT1/PIAS1 -0.06 0.18 -9999 0 -0.58 13 13
GRB2/SOS1/GAB family/SHP2/PI3K 0.032 0.021 -9999 0 -10000 0 0
STAT3 (dimer) -0.07 0.21 -9999 0 -0.72 8 8
PRKCD -0.053 0.19 -9999 0 -0.62 7 7
IL6R 0.011 0.048 -9999 0 -0.81 1 1
SOCS3 -0.035 0.18 -9999 0 -0.81 6 6
gp130 (dimer)/JAK1/JAK1/LMO4 -0.06 0.2 -9999 0 -0.54 44 44
Rac1/GTP -0.079 0.19 -9999 0 -0.58 16 16
HCK -0.022 0.1 -9999 0 -0.31 31 31
MAPKKK cascade 0.007 0.058 -9999 0 -10000 0 0
bone resorption -0.062 0.19 -9999 0 -0.66 5 5
IRF1 -0.05 0.19 -9999 0 -0.64 4 4
mol:GDP -0.09 0.2 -9999 0 -0.52 28 28
SOS1 0.012 0.003 -9999 0 -10000 0 0
VAV1 -0.092 0.2 -9999 0 -0.52 28 28
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.05 0.18 -9999 0 -0.71 9 9
PTPN11 -0.008 0.016 -9999 0 -10000 0 0
IL6/IL6RA -0.055 0.2 -9999 0 -0.61 30 30
gp130 (dimer)/TYK2/TYK2/LMO4 -0.065 0.2 -9999 0 -0.54 44 44
gp130 (dimer)/JAK2/JAK2/LMO4 -0.065 0.2 -9999 0 -0.54 44 44
IL6 -0.081 0.25 -9999 0 -0.68 38 38
PIAS3 0.013 0 -9999 0 -10000 0 0
PTPRE 0.01 0.009 -9999 0 -10000 0 0
PIAS1 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.078 0.19 -9999 0 -0.39 68 68
LMO4 0.013 0.019 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.11 0.18 -9999 0 -0.75 8 8
MCL1 0.053 0.013 -9999 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.018 0.093 -10000 0 -0.4 3 3
TBX21 -0.027 0.27 -10000 0 -0.87 12 12
B2M 0.013 0.004 -10000 0 -10000 0 0
TYK2 0.016 0.017 -10000 0 -10000 0 0
IL12RB1 -0.003 0.082 -10000 0 -0.33 14 14
GADD45B -0.004 0.23 -10000 0 -0.79 4 4
IL12RB2 -0.13 0.17 -10000 0 -0.3 138 138
GADD45G -0.008 0.24 -10000 0 -1 4 4
natural killer cell activation 0.006 0.02 -10000 0 -10000 0 0
RELB 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL18 0.01 0.041 -10000 0 -0.3 5 5
IL2RA -0.018 0.091 -10000 0 -0.29 29 29
IFNG -0.013 0.076 -10000 0 -0.29 20 20
STAT3 (dimer) -0.009 0.24 -10000 0 -0.63 18 18
HLA-DRB5 -0.01 0.095 -10000 0 -0.35 17 17
FASLG -0.037 0.28 -10000 0 -0.86 15 15
NF kappa B2 p52/RelB -0.1 0.21 -10000 0 -0.68 23 23
CD4 -0.001 0.06 -10000 0 -0.29 12 12
SOCS1 0.006 0.07 -10000 0 -0.64 3 3
EntrezGene:6955 -0.003 0.011 -10000 0 -10000 0 0
CD3D -0.037 0.11 -10000 0 -0.3 46 46
CD3E -0.018 0.1 -10000 0 -0.32 27 27
CD3G -0.003 0.068 -10000 0 -0.3 14 14
IL12Rbeta2/JAK2 -0.077 0.12 -10000 0 -0.64 3 3
CCL3 -0.039 0.29 -10000 0 -0.81 18 18
CCL4 -0.034 0.28 -10000 0 -0.86 15 15
HLA-A 0.011 0.026 -10000 0 -0.3 2 2
IL18/IL18R 0.025 0.085 -10000 0 -0.52 1 1
NOS2 -0.069 0.4 -10000 0 -1.1 29 29
IL12/IL12R/TYK2/JAK2/SPHK2 -0.015 0.09 -10000 0 -0.41 2 2
IL1R1 -0.023 0.26 -10000 0 -0.8 12 12
IL4 -0.002 0.021 -10000 0 -10000 0 0
JAK2 0.016 0.017 -10000 0 -10000 0 0
EntrezGene:6957 -0.002 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.011 0.14 -10000 0 -0.5 15 15
RAB7A 0.017 0.21 -10000 0 -0.8 1 1
lysosomal transport 0.019 0.2 -10000 0 -0.76 1 1
FOS -0.18 0.5 -10000 0 -1.3 46 46
STAT4 (dimer) -0.007 0.24 -10000 0 -0.72 12 12
STAT5A (dimer) -0.11 0.22 -10000 0 -0.69 25 25
GZMA -0.031 0.27 -10000 0 -0.83 16 16
GZMB -0.028 0.27 -10000 0 -0.85 13 13
HLX 0.011 0.018 -10000 0 -0.29 1 1
LCK -0.03 0.28 -10000 0 -0.76 23 23
TCR/CD3/MHC II/CD4 -0.03 0.13 -10000 0 -0.41 15 15
IL2/IL2R -0.01 0.088 -10000 0 -0.44 4 4
MAPK14 0.004 0.24 -10000 0 -0.66 9 9
CCR5 -0.021 0.25 -10000 0 -0.69 16 16
IL1B 0.001 0.11 -10000 0 -0.82 5 5
STAT6 0.01 0.093 -10000 0 -10000 0 0
STAT4 -0.013 0.084 -10000 0 -0.29 24 24
STAT3 0.013 0 -10000 0 -10000 0 0
STAT1 0.007 0.04 -10000 0 -0.29 5 5
NFKB1 0.013 0 -10000 0 -10000 0 0
NFKB2 0.013 0 -10000 0 -10000 0 0
IL12B 0.011 0.036 -10000 0 -0.33 1 1
CD8A -0.013 0.088 -10000 0 -0.3 17 17
CD8B -0.008 0.079 -10000 0 -0.3 20 20
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.018 0.093 0.39 3 -10000 0 3
IL2RB -0.021 0.095 -10000 0 -0.29 32 32
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.23 -10000 0 -0.67 12 12
IL2RG 0.003 0.053 -10000 0 -0.29 9 9
IL12 0.022 0.037 -10000 0 -10000 0 0
STAT5A 0.013 0 -10000 0 -10000 0 0
CD247 -0.002 0.065 -10000 0 -0.3 13 13
IL2 0.003 0.018 -10000 0 -0.29 1 1
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.015 0.018 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.034 0.29 -10000 0 -0.75 25 25
MAP2K3 0 0.23 -10000 0 -0.64 10 10
RIPK2 0.013 0 -10000 0 -10000 0 0
MAP2K6 0 0.23 -10000 0 -0.64 10 10
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.062 -10000 0 -0.38 6 6
IL18RAP -0.024 0.1 -10000 0 -0.29 38 38
IL12Rbeta1/TYK2 0.009 0.064 -10000 0 -10000 0 0
EOMES -0.01 0.078 -10000 0 -10000 0 0
STAT1 (dimer) -0.013 0.24 -10000 0 -0.65 18 18
T cell proliferation 0.012 0.21 -10000 0 -0.53 12 12
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.013 0.049 -10000 0 -0.8 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.083 0.17 -10000 0 -0.58 11 11
ATF2 0.012 0.22 -10000 0 -0.66 5 5
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.11 0.1 -10000 0 -0.67 2 2
epithelial cell differentiation -0.18 0.19 -10000 0 -0.43 85 85
ITCH 0.046 0.022 -10000 0 -10000 0 0
WWP1 -0.094 0.085 -10000 0 -10000 0 0
FYN 0.013 0 -10000 0 -10000 0 0
EGFR 0.013 0 -10000 0 -10000 0 0
PRL 0.001 0.018 -10000 0 -0.29 1 1
neuron projection morphogenesis -0.033 0.077 -10000 0 -0.48 2 2
PTPRZ1 -0.013 0.11 -10000 0 -0.55 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.065 0.065 -10000 0 -0.53 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.082 0.094 -10000 0 -0.54 5 5
ADAM17 0.046 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.13 0.11 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.11 -10000 0 -0.47 7 7
NCOR1 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.069 0.088 -10000 0 -0.5 5 5
GRIN2B -0.063 0.085 -10000 0 -0.48 5 5
ErbB4/ErbB2/betacellulin -0.079 0.12 -10000 0 -0.57 12 12
STAT1 0.007 0.04 -10000 0 -0.29 5 5
HBEGF 0.007 0.068 -10000 0 -0.81 2 2
PRLR -0.3 0.4 -10000 0 -0.81 111 111
E4ICDs/ETO2 -0.1 0.092 -10000 0 -0.31 1 1
axon guidance -0.036 0.053 -10000 0 -10000 0 0
NEDD4 0.046 0.022 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.23 0.31 -10000 0 -0.63 111 111
CBFA2T3 0.011 0.018 -10000 0 -0.29 1 1
ErbB4/ErbB2/HBEGF -0.062 0.079 -10000 0 -0.58 2 2
MAPK3 -0.04 0.078 -10000 0 -0.5 2 2
STAT1 (dimer) -0.11 0.095 -10000 0 -0.31 5 5
MAPK1 -0.04 0.078 -10000 0 -0.5 2 2
JAK2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.069 0.088 -10000 0 -0.5 5 5
NRG1 0.028 0.09 -10000 0 -0.62 5 5
NRG3 -0.009 0.1 -10000 0 -0.39 15 15
NRG2 0.003 0.085 -10000 0 -0.68 4 4
NRG4 0.006 0.057 -10000 0 -0.81 1 1
heart development -0.036 0.053 -10000 0 -10000 0 0
neural crest cell migration -0.068 0.087 -10000 0 -0.5 5 5
ERBB2 0.042 0.013 -10000 0 -10000 0 0
WWOX/E4ICDs -0.1 0.091 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.092 0.088 -10000 0 -0.63 1 1
apoptosis 0.12 0.087 0.55 3 -10000 0 3
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.11 0.1 -10000 0 -0.56 3 3
ErbB4/ErbB2/epiregulin -0.13 0.1 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin -0.12 0.14 -10000 0 -0.66 12 12
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.26 0.23 -10000 0 -0.55 106 106
MDM2 -0.1 0.093 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.056 0.073 -10000 0 -0.51 5 5
STAT5A -0.027 0.049 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.069 0.088 -10000 0 -0.5 5 5
DLG4 0.013 0 -10000 0 -10000 0 0
GRB2/SHC 0.019 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.1 0.069 -10000 0 -10000 0 0
STAT5A (dimer) -0.19 0.2 -10000 0 -0.46 84 84
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.027 0.049 -10000 0 -10000 0 0
LRIG1 0.011 0.018 -10000 0 -10000 0 0
EREG -0.13 0.15 -10000 0 -0.29 138 138
BTC -0.022 0.16 -10000 0 -0.81 12 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.037 0.053 -10000 0 -10000 0 0
ERBB4 -0.13 0.11 -10000 0 -10000 0 0
STAT5B 0.013 0 -10000 0 -10000 0 0
YAP1 -0.035 0.023 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.064 0.071 -10000 0 -0.58 1 1
glial cell differentiation 0.1 0.068 -10000 0 -10000 0 0
WWOX 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.045 0.11 -10000 0 -0.47 3 3
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR 0.013 0 -9999 0 -10000 0 0
LRPAP1 0.013 0 -9999 0 -10000 0 0
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.081 0.13 -9999 0 -0.55 15 15
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
KATNA1 0.013 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.051 0.13 -9999 0 -0.5 15 15
IQGAP1/CaM 0.019 0 -9999 0 -10000 0 0
DAB1 -0.004 0.052 -9999 0 -0.29 9 9
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.24 0.12 -9999 0 -0.29 237 237
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.014 0.029 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.013 0 -9999 0 -10000 0 0
CDK5R1 0.009 0.031 -9999 0 -0.29 3 3
LIS1/Poliovirus Protein 3A 0.016 0 -9999 0 -10000 0 0
CDK5R2 -0.063 0.13 -9999 0 -0.29 70 70
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.085 0.13 -9999 0 -0.55 15 15
YWHAE 0.013 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.035 0.11 -9999 0 -0.46 4 4
MAP1B 0 0.009 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.032 0.12 -9999 0 -0.44 15 15
RELN -0.14 0.21 -9999 0 -0.36 116 116
PAFAH/LIS1 -0.11 0.066 -9999 0 -10000 0 0
LIS1/CLIP170 0.025 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.036 0.07 -9999 0 -0.37 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.021 0.089 -9999 0 -0.33 16 16
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.044 0.11 -9999 0 -0.42 15 15
LIS1/IQGAP1 0.025 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.022 0 -9999 0 -10000 0 0
PAFAH1B3 0.011 0.018 -9999 0 -0.29 1 1
PAFAH1B2 0.01 0.048 -9999 0 -0.81 1 1
MAP1B/LIS1/Dynein heavy chain 0.024 0.006 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.028 0.1 -9999 0 -0.44 4 4
LRP8 0.006 0.043 -9999 0 -0.29 6 6
NDEL1/Katanin 60 -0.035 0.11 -9999 0 -0.39 15 15
P39/CDK5 -0.065 0.12 -9999 0 -0.45 15 15
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0 -9999 0 -10000 0 0
CDK5 -0.04 0.12 -9999 0 -0.47 15 15
PPP2R5D 0.011 0.018 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.046 0.12 -9999 0 -0.47 15 15
RELN/VLDLR -0.051 0.13 -9999 0 -0.5 15 15
CDC42 0 0 -9999 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.058 0.37 -9999 0 -1.1 11 11
HDAC7 0.014 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.073 0.24 -9999 0 -0.84 4 4
SMAD4 0.014 0 -9999 0 -10000 0 0
ID2 -0.058 0.37 -9999 0 -1.1 12 12
AP1 -0.076 0.23 -9999 0 -0.62 44 44
ABCG2 -0.061 0.37 -9999 0 -1.1 12 12
HIF1A 0.003 0.069 -9999 0 -10000 0 0
TFF3 -0.14 0.45 -9999 0 -1.1 22 22
GATA2 -0.16 0.33 -9999 0 -0.81 60 60
AKT1 0.007 0.072 -9999 0 -10000 0 0
response to hypoxia -0.009 0.077 -9999 0 -10000 0 0
MCL1 -0.058 0.37 -9999 0 -1 13 13
NDRG1 -0.058 0.37 -9999 0 -1.1 11 11
SERPINE1 -0.078 0.4 -9999 0 -1.2 16 16
FECH -0.058 0.37 -9999 0 -1.1 11 11
FURIN -0.058 0.37 -9999 0 -1 13 13
NCOA2 -0.06 0.23 -9999 0 -0.81 26 26
EP300 0.029 0.097 -9999 0 -10000 0 0
HMOX1 -0.069 0.38 -9999 0 -1.1 12 12
BHLHE40 -0.058 0.37 -9999 0 -1 13 13
BHLHE41 -0.08 0.38 -9999 0 -1.1 12 12
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.009 0.048 -9999 0 -10000 0 0
ENG 0.05 0.088 -9999 0 -10000 0 0
JUN 0.013 0.001 -9999 0 -10000 0 0
RORA -0.059 0.37 -9999 0 -1 13 13
ABCB1 -0.098 0.3 -9999 0 -1.3 16 16
TFRC -0.058 0.37 -9999 0 -1.1 12 12
CXCR4 -0.067 0.37 -9999 0 -1.1 13 13
TF -0.068 0.38 -9999 0 -1.1 14 14
CITED2 -0.058 0.37 -9999 0 -1.1 12 12
HIF1A/ARNT -0.1 0.38 -9999 0 -1.2 14 14
LDHA -0.016 0.032 -9999 0 -10000 0 0
ETS1 -0.058 0.37 -9999 0 -1.1 12 12
PGK1 -0.058 0.37 -9999 0 -1.1 10 10
NOS2 -0.089 0.42 -9999 0 -1.2 21 21
ITGB2 -0.081 0.38 -9999 0 -1.1 13 13
ALDOA -0.058 0.37 -9999 0 -1 13 13
Cbp/p300/CITED2 -0.044 0.36 -9999 0 -1.1 9 9
FOS -0.11 0.29 -9999 0 -0.81 44 44
HK2 -0.14 0.39 -9999 0 -1.1 15 15
SP1 0.017 0.022 -9999 0 -10000 0 0
GCK 0.015 0.17 -9999 0 -10000 0 0
HK1 -0.058 0.37 -9999 0 -1.1 10 10
NPM1 -0.058 0.37 -9999 0 -1.1 11 11
EGLN1 -0.058 0.37 -9999 0 -1.1 11 11
CREB1 0.02 0 -9999 0 -10000 0 0
PGM1 -0.058 0.37 -9999 0 -1.1 10 10
SMAD3 0.014 0 -9999 0 -10000 0 0
EDN1 -0.078 0.28 -9999 0 -0.84 21 21
IGFBP1 -0.099 0.41 -9999 0 -1.1 17 17
VEGFA 0.014 0.28 -9999 0 -0.85 3 3
HIF1A/JAB1 -0.007 0.026 -9999 0 -10000 0 0
CP -0.1 0.41 -9999 0 -1.1 18 18
CXCL12 -0.11 0.45 -9999 0 -1.1 26 26
COPS5 0.014 0.001 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.058 0.37 -9999 0 -1.1 10 10
EGLN3 -0.063 0.37 -9999 0 -1.1 12 12
CA9 -0.14 0.39 -9999 0 -1.1 14 14
TERT -0.083 0.38 -9999 0 -1.1 13 13
ENO1 -0.058 0.37 -9999 0 -1.1 12 12
PFKL -0.058 0.37 -9999 0 -1 13 13
NCOA1 0.013 0.001 -9999 0 -10000 0 0
ADM -0.061 0.37 -9999 0 -1.1 13 13
ARNT 0.002 0.069 -9999 0 -10000 0 0
HNF4A -0.072 0.25 -9999 0 -0.81 31 31
ADFP -0.068 0.36 -9999 0 -1 14 14
SLC2A1 0.011 0.28 -9999 0 -0.82 5 5
LEP -0.075 0.38 -9999 0 -1.1 14 14
HIF1A/ARNT/Cbp/p300 -0.048 0.28 -9999 0 -0.82 7 7
EPO -0.02 0.26 -9999 0 -0.83 5 5
CREBBP 0.029 0.097 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 -0.076 0.24 -9999 0 -0.8 9 9
PFKFB3 -0.058 0.37 -9999 0 -1.1 11 11
NT5E -0.059 0.37 -9999 0 -1.1 11 11
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.031 0.056 -9999 0 -10000 0 0
adherens junction organization 0.007 0.1 -9999 0 -0.31 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.036 0.055 -9999 0 -10000 0 0
FMN1 -0.015 0.15 -9999 0 -0.37 40 40
mol:IP3 0.023 0.057 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.007 0.097 -9999 0 -0.32 24 24
CTNNB1 0.013 0.004 -9999 0 -10000 0 0
AKT1 0.027 0.065 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.037 0.16 -9999 0 -0.56 24 24
CTNND1 0.013 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.091 -9999 0 -0.29 24 24
VASP 0.014 0.093 -9999 0 -10000 0 0
ZYX 0.014 0.093 -9999 0 -0.3 24 24
JUB 0.014 0.093 -9999 0 -10000 0 0
EGFR(dimer) 0.014 0.093 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin -0.043 0.14 -9999 0 -0.52 24 24
mol:PI-3-4-5-P3 -0.017 0.057 -9999 0 -10000 0 0
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
PI3K 0.02 0.069 -9999 0 -10000 0 0
FYN -0.24 0.17 -9999 0 -0.49 15 15
mol:Ca2+ 0.023 0.056 -9999 0 -10000 0 0
JUP 0.013 0.004 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
mol:DAG 0.023 0.057 -9999 0 -10000 0 0
CDH1 -0.056 0.22 -9999 0 -0.81 24 24
RhoA/GDP 0.036 0.055 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.014 0.091 -9999 0 -10000 0 0
SRC 0.011 0.018 -9999 0 -0.29 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
EGFR 0.013 0 -9999 0 -10000 0 0
CASR -0.3 0.2 -9999 0 -0.42 213 213
RhoA/GTP -0.012 0.04 -9999 0 -10000 0 0
AKT2 0.027 0.065 -9999 0 -10000 0 0
actin cable formation -0.008 0.14 -9999 0 -0.44 18 18
apoptosis -0.025 0.063 -9999 0 -10000 0 0
CTNNA1 0.013 0.001 -9999 0 -10000 0 0
mol:GDP 0.03 0.058 -9999 0 -10000 0 0
PIP5K1A 0.014 0.093 -9999 0 -0.3 24 24
PLCG1 0.023 0.058 -9999 0 -10000 0 0
Rac1/GTP -0.022 0.074 -9999 0 -10000 0 0
homophilic cell adhesion 0.001 0.001 -9999 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.011 0.007 -10000 0 -10000 0 0
HSPA8 0.01 0.048 -10000 0 -0.8 1 1
SMAD3/SMAD4/ER alpha -0.032 0.13 -10000 0 -0.56 17 17
AKT1 0.015 0.004 -10000 0 -10000 0 0
GSC 0.016 0.048 -10000 0 -10000 0 0
NKX2-5 -0.014 0.07 -10000 0 -0.29 18 18
muscle cell differentiation 0.003 0.026 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.064 0.042 -10000 0 -10000 0 0
SMAD4 0.019 0.026 -10000 0 -10000 0 0
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.013 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.006 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR -0.006 0.061 -10000 0 -0.45 5 5
MYC 0.005 0.04 -10000 0 -0.3 5 5
CDKN2B 0.033 0.046 -10000 0 -10000 0 0
AP1 -0.013 0.17 -10000 0 -0.41 35 35
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.062 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.046 0.028 -10000 0 -10000 0 0
SP3 0.015 0 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.007 0.08 -10000 0 -0.29 22 22
SMAD3/SMAD4/GR -0.002 0.02 -10000 0 -10000 0 0
GATA3 -0.62 0.34 -10000 0 -0.8 225 225
SKI/SIN3/HDAC complex/NCoR1 0.046 0.008 -10000 0 -10000 0 0
MEF2C/TIF2 -0.006 0.16 -10000 0 -0.52 17 17
endothelial cell migration 0.058 0.29 1.4 13 -10000 0 13
MAX 0.013 0.011 -10000 0 -10000 0 0
RBBP7 0.013 0.001 -10000 0 -10000 0 0
RBBP4 0.013 0.001 -10000 0 -10000 0 0
RUNX2 0.005 0.047 -10000 0 -0.29 7 7
RUNX3 -0.027 0.1 -10000 0 -0.29 38 38
RUNX1 -0.011 0.08 -10000 0 -0.29 22 22
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.013 0.011 -10000 0 -10000 0 0
VDR -0.002 0.11 -10000 0 -0.81 5 5
CDKN1A 0.051 0.054 -10000 0 -10000 0 0
KAT2B 0.012 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.021 0.052 -10000 0 -10000 0 0
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.013 0.001 -10000 0 -10000 0 0
SERPINE1 -0.061 0.3 -10000 0 -1.4 13 13
SMAD3/SMAD4/ATF2 0 0.02 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.027 0.12 -10000 0 -0.57 13 13
SAP30 0.011 0.025 -10000 0 -0.29 2 2
Cbp/p300/PIAS3 0.007 0.017 -10000 0 -10000 0 0
JUN -0.012 0.16 -10000 0 -0.4 31 31
SMAD3/SMAD4/IRF7 -0.001 0.025 -10000 0 -10000 0 0
TFE3 0.016 0.013 -10000 0 -10000 0 0
COL1A2 0.005 0.07 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.004 0.028 -10000 0 -10000 0 0
DLX1 -0.014 0.083 -10000 0 -0.29 24 24
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.1 0.29 -10000 0 -0.8 44 44
SMAD3/SMAD4/Max -0.002 0.02 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.001 0.007 -10000 0 -10000 0 0
ZBTB17 0.011 0.004 -10000 0 -10000 0 0
LAMC1 0.045 0.038 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0 0.02 -10000 0 -10000 0 0
IRF7 0.013 0.008 -10000 0 -10000 0 0
ESR1 -0.037 0.19 -10000 0 -0.81 17 17
HNF4A -0.075 0.25 -10000 0 -0.81 31 31
MEF2C 0.031 0.055 -10000 0 -10000 0 0
SMAD2-3/SMAD4 0.022 0.035 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.008 0.014 -10000 0 -10000 0 0
IGHV3OR16-13 -0.004 0.013 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.013 0 -10000 0 -10000 0 0
CREBBP 0.012 0.005 -10000 0 -10000 0 0
SKIL 0.013 0 -10000 0 -10000 0 0
HDAC1 0.013 0.001 -10000 0 -10000 0 0
HDAC2 0.013 0.001 -10000 0 -10000 0 0
SNIP1 0.013 0.002 -10000 0 -10000 0 0
GCN5L2 -0.001 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.043 0.038 -10000 0 -10000 0 0
MSG1/HSC70 0.014 0.042 -10000 0 -0.61 1 1
SMAD2 0.019 0.006 -10000 0 -10000 0 0
SMAD3 0.016 0.025 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.04 0.023 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.014 0.013 -10000 0 -10000 0 0
NCOR1 0.013 0.001 -10000 0 -10000 0 0
NCOA2 -0.061 0.23 -10000 0 -0.81 26 26
NCOA1 0.013 0 -10000 0 -10000 0 0
MYOD/E2A 0.007 0.026 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.069 0.041 -10000 0 -10000 0 0
IFNB1 0.031 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.039 0.061 -10000 0 -10000 0 0
CITED1 0.009 0.031 -10000 0 -0.29 3 3
SMAD2-3/SMAD4/ARC105 0.046 0.033 -10000 0 -10000 0 0
RBL1 0.013 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.053 0.033 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.03 0.067 -10000 0 -0.3 6 6
SMAD7 0.033 0.13 -10000 0 -10000 0 0
MYC/MIZ-1 -0.002 0.028 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.016 0.092 -10000 0 -0.42 13 13
IL10 -0.38 0.23 -10000 0 -0.49 225 225
PIASy/HDAC complex 0.014 0.007 -10000 0 -10000 0 0
PIAS3 0.012 0.003 -10000 0 -10000 0 0
CDK2 0.012 0.003 -10000 0 -10000 0 0
IL5 -0.37 0.22 -10000 0 -0.49 225 225
CDK4 0.012 0.004 -10000 0 -10000 0 0
PIAS4 0.014 0.007 -10000 0 -10000 0 0
ATF3 -0.026 0.17 -10000 0 -0.81 13 13
SMAD3/SMAD4/SP1 0.048 0.042 -10000 0 -10000 0 0
FOXG1 -0.009 0.059 -10000 0 -0.29 12 12
FOXO3 0.025 0.006 -10000 0 -10000 0 0
FOXO1 0.025 0.006 -10000 0 -10000 0 0
FOXO4 0.025 0.006 -10000 0 -10000 0 0
heart looping 0.031 0.055 -10000 0 -10000 0 0
CEBPB 0.004 0.053 -10000 0 -0.29 9 9
SMAD3/SMAD4/DLX1 -0.013 0.052 -10000 0 -10000 0 0
MYOD1 -0.004 0.038 -10000 0 -0.29 5 5
SMAD3/SMAD4/HNF4 -0.06 0.18 -10000 0 -0.56 31 31
SMAD3/SMAD4/GATA3 -0.43 0.23 -10000 0 -0.55 225 225
SnoN/SIN3/HDAC complex/NCoR1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.012 0.071 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.057 0.04 -10000 0 -10000 0 0
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.02 0.013 -10000 0 -10000 0 0
SIN3B 0.013 0.001 -10000 0 -10000 0 0
SIN3A 0.013 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.017 0.062 -10000 0 -10000 0 0
ITGB5 0.059 0.031 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.045 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.024 0.11 -10000 0 -0.56 12 12
AR -0.024 0.16 -10000 0 -0.73 14 14
negative regulation of cell growth 0.034 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.004 0.031 -10000 0 -10000 0 0
E2F5 0.013 0 -10000 0 -10000 0 0
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.03 0.045 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.052 0.027 -10000 0 -10000 0 0
TFDP1 0.013 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.01 0.17 -10000 0 -0.42 30 30
SMAD3/SMAD4/RUNX2 -0.003 0.029 -10000 0 -10000 0 0
TGIF2 0.013 0 -10000 0 -10000 0 0
TGIF1 0.013 0 -10000 0 -10000 0 0
ATF2 0.013 0 -10000 0 -10000 0 0
Osteopontin-mediated events

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
IKK alpha homodimer 0.016 0.12 -9999 0 -0.43 17 17
NF kappa B1 p50/RelA/I kappa B alpha 0.037 0.11 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin/Src -0.012 0.069 -9999 0 -0.6 3 3
AP1 -0.032 0.22 -9999 0 -0.66 17 17
ILK 0.008 0.12 -9999 0 -0.46 17 17
bone resorption 0.015 0.14 -9999 0 -0.69 3 3
PTK2B 0.013 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.03 0.1 -9999 0 -0.41 18 18
ITGAV 0.016 0.004 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.006 0.096 -9999 0 -0.62 5 5
alphaV/beta3 Integrin/Osteopontin -0.038 0.12 -9999 0 -0.52 17 17
MAP3K1 0.008 0.12 -9999 0 -0.46 17 17
JUN 0.013 0.001 -9999 0 -10000 0 0
MAPK3 0.018 0.12 -9999 0 -0.43 17 17
MAPK1 0.018 0.12 -9999 0 -0.43 17 17
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.009 0.14 -9999 0 -0.48 20 20
ITGB3 -0.029 0.18 -9999 0 -0.64 20 20
NFKBIA 0.027 0.12 -9999 0 -0.41 17 17
FOS -0.11 0.29 -9999 0 -0.81 44 44
CD44 -0.007 0.075 -9999 0 -0.29 19 19
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU 0.01 0.22 -9999 0 -1.2 7 7
NF kappa B1 p50/RelA -0.03 0.091 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.033 0.13 -9999 0 -0.61 14 14
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.005 0.13 -9999 0 -0.47 18 18
VAV3 0.011 0.12 -9999 0 -0.43 19 19
MAP3K14 0.009 0.13 -9999 0 -0.46 17 17
ROCK2 -0.002 0.11 -9999 0 -0.81 5 5
SPP1 -0.003 0.098 -9999 0 -0.4 13 13
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP 0.016 0.11 -9999 0 -0.39 19 19
MMP2 -0.018 0.19 -9999 0 -0.57 14 14
Noncanonical Wnt 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
NFATC2 -0.05 0.22 -9999 0 -0.81 22 22
GNB1/GNG2 0.004 0.092 -9999 0 -0.4 2 2
mol:DAG 0.012 0.086 -9999 0 -0.36 1 1
PLCG1 0.012 0.089 -9999 0 -10000 0 0
YES1 -0.002 0.096 -9999 0 -0.42 2 2
FZD3 0.013 0 -9999 0 -10000 0 0
FZD6 0.013 0 -9999 0 -10000 0 0
G protein 0.012 0.089 -9999 0 -10000 0 0
MAP3K7 -0.14 0.21 -9999 0 -0.46 28 28
mol:Ca2+ 0.012 0.085 -9999 0 -0.35 1 1
mol:IP3 0.012 0.086 -9999 0 -0.36 1 1
NLK -0.009 0.012 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.16 0.23 -9999 0 -0.42 116 116
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.011 0.1 -9999 0 -0.34 22 22
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.002 0.096 -9999 0 -0.42 2 2
GO:0007205 0.012 0.085 -9999 0 -10000 0 0
WNT6 0.008 0.051 -9999 0 -0.55 2 2
WNT4 -0.015 0.14 -9999 0 -0.71 11 11
NFAT1/CK1 alpha -0.018 0.14 -9999 0 -0.5 4 4
GNG2 0.013 0 -9999 0 -10000 0 0
WNT5A -0.032 0.11 -9999 0 -0.29 43 43
WNT11 -0.029 0.17 -9999 0 -0.62 19 19
CDC42 0.005 0.091 -9999 0 -0.39 2 2
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.038 0.12 -10000 0 -0.45 23 23
HDAC1 0.009 0.003 -10000 0 -10000 0 0
AES 0.012 0.001 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 -0.004 0.12 -10000 0 -0.81 6 6
LRP6/FZD1 0.012 0.036 -10000 0 -10000 0 0
TLE1 0.012 0.001 -10000 0 -10000 0 0
AP1 -0.15 0.25 -10000 0 -0.43 113 113
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 0.011 0.018 -10000 0 -0.29 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.05 0.044 -10000 0 -10000 0 0
NICD/RBPSUH 0 0.01 -10000 0 -10000 0 0
WIF1 0.002 0.043 -10000 0 -0.29 6 6
NOTCH1 -0.001 0.01 -10000 0 -10000 0 0
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.024 0.097 -10000 0 -0.29 34 34
DKK1 -0.004 0.065 -10000 0 -0.29 14 14
beta catenin/beta TrCP1 0.083 0.089 -10000 0 -10000 0 0
APH1B 0.01 0.048 -10000 0 -0.81 1 1
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 -0.016 0.037 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.016 0.044 -10000 0 -0.34 4 4
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.11 0.29 -10000 0 -0.81 44 44
JUN 0.013 0 -10000 0 -10000 0 0
MAP3K7 0.011 0.001 -10000 0 -10000 0 0
CTNNB1 0.08 0.096 0.25 1 -10000 0 1
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.02 0.059 -10000 0 -0.38 3 3
HNF1A 0 0.096 -10000 0 -0.81 4 4
CTBP1 0.012 0.001 -10000 0 -10000 0 0
MYC 0.022 0.039 -10000 0 -10000 0 0
NKD1 -0.22 0.37 -10000 0 -0.81 82 82
FZD1 0.003 0.053 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.009 0.064 -10000 0 -0.45 6 6
apoptosis -0.15 0.25 -10000 0 -0.43 113 113
Delta 1/NOTCHprecursor -0.037 0.12 -10000 0 -0.45 23 23
DLL1 -0.058 0.22 -10000 0 -0.72 28 28
PPARD 0.026 0.009 -10000 0 -10000 0 0
Gamma Secretase 0.025 0.033 -10000 0 -0.46 1 1
APC -0.016 0.037 -10000 0 -10000 0 0
DVL1 0.001 0.008 -10000 0 -10000 0 0
CSNK2A1 0.013 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.024 0.057 -10000 0 -10000 0 0
LRP6 0.013 0 -10000 0 -10000 0 0
CSNK1A1 0.013 0.001 -10000 0 -10000 0 0
NLK 0.012 0.004 -10000 0 -10000 0 0
CCND1 0.021 0.086 -10000 0 -1.4 1 1
WNT1 -0.018 0.089 -10000 0 -0.29 28 28
Axin1/APC/beta catenin 0.069 0.047 -10000 0 -10000 0 0
DKK2 0.007 0.054 -10000 0 -0.46 3 3
NOTCH1 precursor/DVL1 0.002 0.01 -10000 0 -10000 0 0
GSK3B 0.012 0 -10000 0 -10000 0 0
FRAT1 0.012 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.01 0.064 -10000 0 -0.45 6 6
PPP2R5D 0.1 0.16 0.36 82 -10000 0 82
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.006 0.057 -10000 0 -10000 0 0
RBPJ 0.013 0 -10000 0 -10000 0 0
CREBBP 0.016 0.002 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB -0.016 0.15 -9999 0 -0.81 10 10
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.004 0.09 -9999 0 -0.27 27 27
GNAO1 -0.06 0.23 -9999 0 -0.81 25 25
S1P/S1P3/G12/G13 -0.015 0.14 -9999 0 -0.49 23 23
AKT1 -0.011 0.15 -9999 0 -0.7 10 10
AKT3 0.014 0.089 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.016 0.15 -9999 0 -0.81 10 10
GNAI2 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0 -9999 0 -10000 0 0
GNAI1 0.008 0.068 -9999 0 -0.81 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.051 0.22 -9999 0 -0.81 23 23
S1PR2 0.013 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.023 0.18 -9999 0 -0.4 42 42
MAPK3 -0.015 0.17 -9999 0 -0.78 7 7
MAPK1 -0.015 0.17 -9999 0 -0.86 6 6
JAK2 -0.017 0.17 -9999 0 -0.8 7 7
CXCR4 -0.025 0.17 -9999 0 -0.8 7 7
FLT1 0.01 0.068 -9999 0 -0.81 2 2
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC -0.016 0.17 -9999 0 -0.86 6 6
S1P/S1P3/Gi -0.024 0.18 -9999 0 -0.4 42 42
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.016 0.16 -9999 0 -0.76 7 7
VEGFA 0.012 0.031 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.006 0.1 -9999 0 -0.32 25 25
VEGFR1 homodimer/VEGFA homodimer 0.02 0.057 -9999 0 -0.62 2 2
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.089 0.2 -9999 0 -0.4 77 77
GNAQ 0.013 0 -9999 0 -10000 0 0
GNAZ 0.014 0 -9999 0 -10000 0 0
G12/G13 0.018 0.012 -9999 0 -10000 0 0
GNA14 -0.16 0.33 -9999 0 -0.81 61 61
GNA15 -0.008 0.077 -9999 0 -0.29 20 20
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.011 0.018 -9999 0 -0.29 1 1
GNA11 -0.007 0.13 -9999 0 -0.81 7 7
Rac1/GTP -0.016 0.16 -9999 0 -0.84 6 6
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0.02 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.002 0.019 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.015 0.08 -9999 0 -0.54 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0 0.03 -9999 0 -0.29 3 3
GRK1 0.002 0.018 -9999 0 -0.29 1 1
CNG Channel -0.14 0.2 -9999 0 -0.44 85 85
mol:Na + -0.14 0.2 -9999 0 -0.45 78 78
mol:ADP 0.002 0.018 -9999 0 -0.29 1 1
RGS9-1/Gbeta5/R9AP -0.015 0.078 -9999 0 -0.56 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.14 0.2 -9999 0 -0.46 78 78
CNGB1 -0.001 0.052 -9999 0 -0.29 9 9
RDH5 -0.016 0.1 -9999 0 -0.81 2 2
SAG 0.001 0.003 -9999 0 -10000 0 0
mol:Ca2+ -0.11 0.2 -9999 0 -0.52 20 20
Na + (4 Units) -0.13 0.18 -9999 0 -0.5 20 20
RGS9 -0.01 0.11 -9999 0 -0.43 15 15
GNB1/GNGT1 -0.014 0.072 -9999 0 -10000 0 0
GNAT1/GDP -0.014 0.069 -9999 0 -0.49 5 5
GUCY2D -0.032 0.1 -9999 0 -0.29 41 41
GNGT1 -0.036 0.11 -9999 0 -0.29 43 43
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.013 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.001 0.088 -9999 0 -0.47 8 8
mol:11-cis-retinal -0.016 0.1 -9999 0 -0.81 2 2
mol:cGMP -0.005 0.059 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.009 0.079 -9999 0 -0.54 3 3
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 -0.21 0.36 -9999 0 -0.81 78 78
Metarhodopsin II 0.003 0.023 -9999 0 -0.28 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.006 0.064 -9999 0 -10000 0 0
RGS9BP 0.008 0.051 -9999 0 -0.55 2 2
Metarhodopsin II/Transducin -0.003 0.04 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0.009 0.033 -9999 0 -10000 0 0
PDE6A/B 0.004 0.065 -9999 0 -0.63 2 2
mol:Pi -0.015 0.078 -9999 0 -0.56 5 5
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.008 0.058 -9999 0 -10000 0 0
PDE6B 0.004 0.074 -9999 0 -0.5 5 5
PDE6A 0.001 0.05 -9999 0 -0.29 8 8
PDE6G -0.008 0.12 -9999 0 -0.64 9 9
RHO 0.002 0.035 -9999 0 -0.29 4 4
PDE6 -0.029 0.1 -9999 0 -0.49 12 12
GUCA1A -0.004 0.052 -9999 0 -0.29 9 9
GC2/GCAP Family 0.01 0.033 -9999 0 -10000 0 0
GUCA1C 0.006 0.019 -9999 0 -0.29 1 1
GUCA1B 0.009 0.031 -9999 0 -0.29 3 3
Class IB PI3K non-lipid kinase events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.009 0.12 0.6 10 -10000 0 10
PI3K Class IB/PDE3B -0.009 0.12 -10000 0 -0.6 10 10
PDE3B -0.009 0.12 -10000 0 -0.6 10 10
Regulation of Androgen receptor activity

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
HDAC1 0.022 0.001 -9999 0 -10000 0 0
SMARCC1 0.011 0.008 -9999 0 -10000 0 0
REL -0.003 0.11 -9999 0 -0.72 6 6
HDAC7 -0.084 0.13 -9999 0 -0.68 4 4
JUN 0.012 0.003 -9999 0 -10000 0 0
EP300 0.013 0 -9999 0 -10000 0 0
KAT2B 0.013 0 -9999 0 -10000 0 0
KAT5 0.013 0 -9999 0 -10000 0 0
MAPK14 0.003 0.017 -9999 0 -10000 0 0
FOXO1 0.013 0 -9999 0 -10000 0 0
T-DHT/AR -0.094 0.14 -9999 0 -0.67 5 5
MAP2K6 0.004 0.008 -9999 0 -10000 0 0
BRM/BAF57 0.018 0.005 -9999 0 -10000 0 0
MAP2K4 0.004 0.008 -9999 0 -10000 0 0
SMARCA2 0.012 0.002 -9999 0 -10000 0 0
PDE9A -0.18 0.2 -9999 0 -0.6 36 36
NCOA2 -0.061 0.23 -9999 0 -0.81 26 26
CEBPA -0.017 0.098 -9999 0 -0.81 1 1
EHMT2 0.012 0.003 -9999 0 -10000 0 0
cell proliferation -0.15 0.18 -9999 0 -0.5 39 39
NR0B1 -0.054 0.12 -9999 0 -0.29 59 59
EGR1 -0.053 0.22 -9999 0 -0.81 23 23
RXRs/9cRA 0.018 0.011 -9999 0 -10000 0 0
AR/RACK1/Src -0.03 0.081 -9999 0 -0.56 5 5
AR/GR -0.007 0.088 -9999 0 -0.36 12 12
GNB2L1 0.012 0.001 -9999 0 -10000 0 0
PKN1 0.013 0 -9999 0 -10000 0 0
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -9999 0 -10000 0 0
MAPK8 -0.008 0.086 -9999 0 -0.64 5 5
T-DHT/AR/TIF2/CARM1 -0.06 0.19 -9999 0 -0.6 26 26
SRC -0.012 0.074 -9999 0 -0.5 5 5
NR3C1 0.013 0 -9999 0 -10000 0 0
KLK3 -0.1 0.2 -9999 0 -0.52 26 26
APPBP2 0.004 0.008 -9999 0 -10000 0 0
TRIM24 0.012 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.026 0.09 -9999 0 -0.59 5 5
TMPRSS2 -0.83 0.57 -9999 0 -1.2 186 186
RXRG 0.003 0.018 -9999 0 -0.29 1 1
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.012 0 -9999 0 -10000 0 0
RXRB 0.012 0 -9999 0 -10000 0 0
CARM1 0.012 0.001 -9999 0 -10000 0 0
NR2C2 0.004 0.083 -9999 0 -0.81 3 3
KLK2 -0.044 0.15 -9999 0 -0.61 10 10
AR -0.016 0.097 -9999 0 -0.38 15 15
SENP1 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
MDM2 0.013 0.004 -9999 0 -10000 0 0
SRY 0.001 0.004 -9999 0 -10000 0 0
GATA2 -0.16 0.33 -9999 0 -0.81 60 60
MYST2 0.013 0 -9999 0 -10000 0 0
HOXB13 -0.074 0.14 -9999 0 -0.29 80 80
T-DHT/AR/RACK1/Src -0.019 0.089 -9999 0 -0.57 5 5
positive regulation of transcription -0.16 0.33 -9999 0 -0.81 60 60
DNAJA1 0.004 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.028 0.001 -9999 0 -10000 0 0
NCOA1 0.019 0.005 -9999 0 -10000 0 0
SPDEF -0.011 0.079 -9999 0 -0.3 4 4
T-DHT/AR/TIF2 -0.015 0.12 -9999 0 -0.56 7 7
T-DHT/AR/Hsp90 -0.026 0.09 -9999 0 -0.59 5 5
GSK3B 0.009 0.004 -9999 0 -10000 0 0
NR2C1 0.013 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.02 0.079 -9999 0 -0.54 5 5
SIRT1 0.013 0 -9999 0 -10000 0 0
ZMIZ2 0.013 0.004 -9999 0 -10000 0 0
POU2F1 -0.036 0.049 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.061 0.1 -9999 0 -0.64 5 5
CREBBP 0.013 0 -9999 0 -10000 0 0
SMARCE1 0.012 0.002 -9999 0 -10000 0 0
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.042 0.14 -10000 0 -0.54 21 21
cell-cell adhesion 0.025 0.079 0.47 1 -10000 0 1
Ephrin B/EPHB2/RasGAP -0.025 0.087 -10000 0 -0.46 10 10
ITSN1 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.013 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.15 0.24 -10000 0 -0.54 81 81
Ephrin B1/EPHB1 -0.01 0.06 -10000 0 -0.54 3 3
HRAS/GDP -0.021 0.077 -10000 0 -0.42 7 7
Ephrin B/EPHB1/GRB7 -0.032 0.099 -10000 0 -0.46 13 13
Endophilin/SYNJ1 0.008 0.09 -10000 0 -0.43 10 10
KRAS 0.013 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.032 0.1 -10000 0 -0.46 13 13
endothelial cell migration 0 0 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
GRB7 0.013 0 -10000 0 -10000 0 0
PAK1 0.014 0.092 -10000 0 -0.43 10 10
HRAS 0.013 0 -10000 0 -10000 0 0
RRAS 0.007 0.092 -10000 0 -0.43 10 10
DNM1 -0.085 0.15 -10000 0 -0.3 91 91
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0 0.1 -10000 0 -0.44 13 13
lamellipodium assembly -0.025 0.079 -10000 0 -0.47 1 1
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.015 0.07 -10000 0 -0.33 4 4
PIK3R1 0.013 0 -10000 0 -10000 0 0
EPHB2 0.008 0.035 -10000 0 -0.29 4 4
EPHB3 -0.22 0.37 -10000 0 -0.81 81 81
EPHB1 -0.005 0.097 -10000 0 -0.42 12 12
EPHB4 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.055 0.12 -10000 0 -0.44 7 7
Ephrin B/EPHB2 -0.026 0.088 -10000 0 -0.46 10 10
Ephrin B/EPHB3 -0.15 0.23 -10000 0 -0.49 88 88
JNK cascade 0.026 0.058 -10000 0 -0.45 3 3
Ephrin B/EPHB1 -0.033 0.1 -10000 0 -0.47 13 13
RAP1/GDP 0.03 0.11 -10000 0 -0.45 1 1
EFNB2 0.013 0 -10000 0 -10000 0 0
EFNB3 -0.039 0.17 -10000 0 -0.45 32 32
EFNB1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.012 0.062 -10000 0 -0.49 3 3
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.027 0.087 -10000 0 -0.52 1 1
Rap1/GTP -0.025 0.079 -10000 0 -0.48 1 1
axon guidance -0.042 0.14 -10000 0 -0.54 21 21
MAPK3 0.028 0.063 -10000 0 -10000 0 0
MAPK1 0.028 0.063 -10000 0 -10000 0 0
Rac1/GDP 0.059 0.11 -10000 0 -0.4 7 7
actin cytoskeleton reorganization -0.016 0.058 -10000 0 -0.38 1 1
CDC42/GDP 0.059 0.11 -10000 0 -0.4 7 7
PI3K 0 0 -10000 0 -10000 0 0
EFNA5 -0.048 0.21 -10000 0 -0.81 21 21
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.014 0.07 -10000 0 -0.32 10 10
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.024 0.077 -10000 0 -0.46 1 1
PTK2 0.003 0.014 -10000 0 -10000 0 0
MAP4K4 0.026 0.058 -10000 0 -0.45 3 3
SRC 0.011 0.018 -10000 0 -0.29 1 1
KALRN 0.013 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0.019 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.04 0.084 -10000 0 -10000 0 0
MAP2K1 0.022 0.066 -10000 0 -0.33 1 1
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.02 0.062 -10000 0 -0.49 3 3
cell migration 0.038 0.08 -10000 0 -0.39 1 1
NRAS 0.013 0 -10000 0 -10000 0 0
SYNJ1 0.007 0.092 -10000 0 -0.43 10 10
PXN 0.013 0 -10000 0 -10000 0 0
TF 0.004 0.1 -10000 0 -0.41 13 13
HRAS/GTP -0.027 0.085 -10000 0 -0.5 1 1
Ephrin B1/EPHB1-2 0.012 0.062 -10000 0 -0.49 3 3
cell adhesion mediated by integrin 0.071 0.12 0.51 10 -10000 0 10
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.03 0.092 -10000 0 -0.43 13 13
RAC1-CDC42/GTP -0.13 0.19 -10000 0 -0.56 15 15
RASA1 0.013 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.03 0.11 -10000 0 -0.45 1 1
ruffle organization 0.025 0.096 -10000 0 -0.48 1 1
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization -0.028 0.11 -10000 0 -0.48 2 2
Ephrin B/EPHB2/KALRN -0.025 0.087 -10000 0 -0.46 10 10
ROCK1 -0.12 0.23 -10000 0 -0.49 81 81
RAS family/GDP -0.016 0.059 -10000 0 -0.39 1 1
Rac1/GTP -0.026 0.084 -10000 0 -0.5 1 1
Ephrin B/EPHB1/Src/Paxillin 0.008 0.08 -10000 0 -0.42 1 1
Regulation of Telomerase

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
Telomerase catalytic core complex -0.19 0.14 -9999 0 -0.53 10 10
RAD9A 0.011 0.018 -9999 0 -0.29 1 1
AP1 -0.079 0.23 -9999 0 -0.62 44 44
IFNAR2 0.012 0.005 -9999 0 -10000 0 0
AKT1 -0.002 0.072 -9999 0 -0.29 17 17
ER alpha/Oestrogen -0.029 0.15 -9999 0 -0.63 17 17
NFX1/SIN3/HDAC complex 0.038 0.017 -9999 0 -10000 0 0
EGF -0.73 0.24 -9999 0 -0.81 261 261
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.018 0.007 -9999 0 -10000 0 0
TERT/c-Abl -0.18 0.13 -9999 0 -0.5 7 7
SAP18 0.012 0.001 -9999 0 -10000 0 0
MRN complex -0.002 0.031 -9999 0 -0.54 1 1
WT1 -0.45 0.4 -9999 0 -0.8 162 162
WRN 0.013 0 -9999 0 -10000 0 0
SP1 0.012 0.005 -9999 0 -10000 0 0
SP3 0.012 0.002 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.15 0.12 -9999 0 -10000 0 0
Mad/Max 0.017 0.007 -9999 0 -10000 0 0
TERT -0.2 0.14 -9999 0 -0.54 9 9
CCND1 -0.17 0.14 -9999 0 -1.2 1 1
MAX 0.012 0.002 -9999 0 -10000 0 0
RBBP7 0.012 0.001 -9999 0 -10000 0 0
RBBP4 0.012 0.001 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.012 0.001 -9999 0 -10000 0 0
Telomerase/911 0.004 0.021 -9999 0 -10000 0 0
CDKN1B 0.021 0.042 -9999 0 -10000 0 0
RAD1 0.013 0 -9999 0 -10000 0 0
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.01 0.025 -9999 0 -0.29 2 2
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.012 0.002 -9999 0 -10000 0 0
JUN 0.012 0.002 -9999 0 -10000 0 0
E6 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.004 -9999 0 -10000 0 0
FOS -0.11 0.29 -9999 0 -0.81 44 44
IFN-gamma/IRF1 -0.006 0.047 -9999 0 -10000 0 0
PARP2 0.013 0 -9999 0 -10000 0 0
BLM -0.008 0.077 -9999 0 -0.29 20 20
Telomerase -0.025 0.038 -9999 0 -10000 0 0
IRF1 0.017 0.002 -9999 0 -10000 0 0
ESR1 -0.036 0.19 -9999 0 -0.81 17 17
KU/TER 0.019 0 -9999 0 -10000 0 0
ATM/TRF2 0.02 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.043 0.018 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.043 0.018 -9999 0 -10000 0 0
HDAC1 0.012 0.001 -9999 0 -10000 0 0
HDAC2 0.012 0.005 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.021 0.017 -9999 0 -10000 0 0
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.012 0.002 -9999 0 -10000 0 0
MRE11A 0.013 0 -9999 0 -10000 0 0
HUS1 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.013 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.13 0.12 -9999 0 -0.55 2 2
NR2F2 0.013 0.004 -9999 0 -10000 0 0
MAPK3 0.013 0.014 -9999 0 -10000 0 0
MAPK1 0.013 0.014 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.011 0.025 -9999 0 -0.29 2 2
NFKB1 0.013 0 -9999 0 -10000 0 0
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.013 0 -9999 0 -10000 0 0
EGFR 0.012 0.001 -9999 0 -10000 0 0
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.56 0.19 -9999 0 -0.62 261 261
MYC 0.006 0.04 -9999 0 -0.29 5 5
IL2 0.003 0.019 -9999 0 -0.29 1 1
KU 0.019 0 -9999 0 -10000 0 0
RAD50 0.01 0.048 -9999 0 -0.81 1 1
HSP90AA1 0.013 0 -9999 0 -10000 0 0
TGFB1 0.011 0.025 -9999 0 -0.29 2 2
TRF2/BLM -0.012 0.043 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.17 0.13 -9999 0 -0.5 2 2
SP1/HDAC2 0.019 0.008 -9999 0 -10000 0 0
PINX1 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.15 0.12 -9999 0 -10000 0 0
Smad3/Myc 0.022 0.026 -9999 0 -10000 0 0
911 complex 0 0.008 -9999 0 -10000 0 0
IFNG -0.008 0.075 -9999 0 -0.28 20 20
Telomerase/PinX1 -0.15 0.12 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K -0.021 0.043 -9999 0 -10000 0 0
SIN3B 0.012 0.001 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.15 0.12 -9999 0 -10000 0 0
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.002 0.026 -9999 0 -0.45 1 1
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.15 0.12 -9999 0 -10000 0 0
E2F1 -0.072 0.14 -9999 0 -0.29 80 80
ZNFX1 0.012 0.001 -9999 0 -10000 0 0
PIF1 -0.018 0.091 -9999 0 -0.29 29 29
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.013 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.078 0.25 -9999 0 -0.76 34 34
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.01 0.025 -9999 0 -0.29 2 2
TCEB1 0.013 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.009 -9999 0 -10000 0 0
HIF1A 0.022 0.009 -9999 0 -10000 0 0
COPS5 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.001 0.009 -9999 0 -10000 0 0
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.23 0.12 -9999 0 -0.29 229 229
ARNT/IPAS -0.052 0.2 -9999 0 -0.62 31 31
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.009 -9999 0 -10000 0 0
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.013 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.012 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.009 -9999 0 -10000 0 0
PHD1-3/OS9 0.027 0.029 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0 0.007 -9999 0 -10000 0 0
VHL 0.013 0 -9999 0 -10000 0 0
HSP90AA1 0.013 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.029 0.009 -9999 0 -10000 0 0
EGLN3 0.001 0.058 -9999 0 -0.29 11 11
EGLN2 0.013 0 -9999 0 -10000 0 0
EGLN1 0.013 0 -9999 0 -10000 0 0
TP53 0.013 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.036 0.008 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.074 0.055 -9999 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.011 0.08 -9999 0 -0.29 22 22
PLK4 0.01 0.025 -9999 0 -0.29 2 2
regulation of centriole replication 0.004 0.057 -9999 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.031 0.086 0.28 28 -10000 0 28
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.009 0.059 -10000 0 -0.54 3 3
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.061 0.23 -10000 0 -0.81 25 25
RhoA/GTP 0 0.099 -10000 0 -0.29 28 28
negative regulation of cAMP metabolic process -0.006 0.11 -10000 0 -0.32 28 28
GNAZ 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 -0.002 0.093 -10000 0 -0.46 9 9
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.006 0.11 -10000 0 -0.33 28 28
RhoA/GDP 0.009 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.007 0.068 -10000 0 -0.81 2 2
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.001 0.024 -9999 0 -10000 0 0
VDR -0.002 0.11 -9999 0 -0.81 5 5
FAM120B 0.013 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.047 0.042 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.052 0.06 -9999 0 -0.38 3 3
MED1 0.013 0 -9999 0 -10000 0 0
mol:9cRA 0.005 0.009 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.022 0.069 -9999 0 -0.32 11 11
RXRs/NUR77 -0.18 0.26 -9999 0 -0.49 122 122
RXRs/PPAR 0.037 0.014 -9999 0 -10000 0 0
NCOR2 0.013 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.083 -9999 0 -0.63 5 5
RARs/VDR/DNA/Vit D3 -0.008 0.06 -9999 0 -0.46 5 5
RARA 0.013 0 -9999 0 -10000 0 0
NCOA1 0.013 0 -9999 0 -10000 0 0
VDR/VDR/DNA -0.002 0.11 -9999 0 -0.81 5 5
RARs/RARs/DNA/9cRA 0.024 0.011 -9999 0 -10000 0 0
RARG 0.011 0.018 -9999 0 -0.29 1 1
RPS6KB1 0.002 0.016 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.022 0.069 -9999 0 -0.32 11 11
THRA 0.013 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.083 -9999 0 -0.63 5 5
RXRs/PPAR/9cRA/PGJ2/DNA 0.034 0.026 -9999 0 -10000 0 0
NR1H4 0 0.097 -9999 0 -0.81 4 4
RXRs/LXRs/DNA 0.055 0.031 -9999 0 -10000 0 0
NR1H2 0.018 0.006 -9999 0 -10000 0 0
NR1H3 0.018 0.007 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.027 0.068 -9999 0 -0.47 5 5
NR4A1 -0.33 0.4 -9999 0 -0.81 122 122
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.027 0.046 -9999 0 -0.34 4 4
RXRG 0.008 0.02 -9999 0 -0.29 1 1
RXR alpha/CCPG 0.022 0.006 -9999 0 -10000 0 0
RXRA 0.017 0.006 -9999 0 -10000 0 0
RXRB 0.018 0.007 -9999 0 -10000 0 0
THRB -0.019 0.16 -9999 0 -0.81 11 11
PPARG 0.011 0.018 -9999 0 -10000 0 0
PPARD 0.013 0 -9999 0 -10000 0 0
TNF 0.042 0.14 -9999 0 -1.2 3 3
mol:Oxysterols 0.005 0.008 -9999 0 -10000 0 0
cholesterol transport 0.052 0.059 -9999 0 -0.38 3 3
PPARA 0.013 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.013 0 -9999 0 -10000 0 0
RXRs/NUR77/BCL2 -0.12 0.18 -9999 0 -0.34 122 122
SREBF1 0.056 0.057 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.035 0.026 -9999 0 -10000 0 0
ABCA1 0.057 0.055 -9999 0 -10000 0 0
RARs/THRs -0.018 0.087 -9999 0 -0.46 11 11
RXRs/FXR 0.031 0.064 -9999 0 -0.49 4 4
BCL2 0.013 0 -9999 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.01 0.17 -9999 0 -0.57 24 24
KLHL20 -0.014 0.048 -9999 0 -0.35 1 1
CYFIP2 0.01 0.048 -9999 0 -0.81 1 1
Rac1/GDP 0.025 0.11 -9999 0 -0.34 24 24
ENAH -0.01 0.17 -9999 0 -0.57 24 24
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.024 0.078 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.01 0.033 -9999 0 -0.22 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.01 0.14 -9999 0 -0.49 24 24
RAPGEF1 0.007 0.14 -9999 0 -0.48 24 24
CTNND1 0.013 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.049 0.16 -9999 0 -0.59 24 24
CRK -0.001 0.16 -9999 0 -0.52 24 24
E-cadherin/gamma catenin/alpha catenin -0.044 0.15 -9999 0 -0.54 24 24
alphaE/beta7 Integrin 0.019 0 -9999 0 -10000 0 0
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.024 0.001 -9999 0 -10000 0 0
DLG1 -0.01 0.17 -9999 0 -0.57 24 24
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.056 -9999 0 -10000 0 0
MLLT4 0.013 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.023 0.015 -9999 0 -10000 0 0
PI3K -0.022 0.073 -9999 0 -10000 0 0
ARF6 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.034 0.18 -9999 0 -0.62 24 24
TIAM1 0.013 0 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ -0.01 0.14 -9999 0 -0.46 24 24
AKT1 -0.012 0.041 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 -0.055 0.23 -9999 0 -0.81 24 24
RhoA/GDP 0.025 0.11 -9999 0 -0.34 24 24
actin cytoskeleton organization 0.03 0.048 -9999 0 -0.24 1 1
CDC42/GDP 0.025 0.11 -9999 0 -0.36 1 1
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.006 0.1 -9999 0 -0.34 24 24
ITGB7 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.01 0.14 -9999 0 -0.49 24 24
E-cadherin/Ca2+/beta catenin/alpha catenin -0.018 0.14 -9999 0 -0.47 24 24
mol:GDP 0.017 0.13 -9999 0 -0.41 24 24
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.013 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP -0.029 0.096 -9999 0 -0.35 24 24
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.019 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.025 0.036 -9999 0 -0.29 1 1
NME1 0.009 0.031 -9999 0 -0.29 3 3
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.01 0.17 -9999 0 -0.57 24 24
regulation of cell-cell adhesion -0.021 0.069 -9999 0 -10000 0 0
WASF2 -0.005 0.017 -9999 0 -10000 0 0
Rap1/GTP -0.027 0.09 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.038 0.12 -9999 0 -0.46 24 24
CCND1 0.028 0.043 -9999 0 -0.38 1 1
VAV2 0.005 0.15 -9999 0 -0.5 24 24
RAP1/GDP 0.022 0.11 -9999 0 -10000 0 0
adherens junction assembly -0.008 0.16 -9999 0 -0.55 24 24
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.004 0.13 -9999 0 -0.43 24 24
E-cadherin/beta catenin -0.041 0.14 -9999 0 -0.49 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.01 0.17 -9999 0 -0.57 24 24
PIK3CA 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.023 0.079 -9999 0 -0.65 1 1
E-cadherin/beta catenin/alpha catenin -0.044 0.15 -9999 0 -0.54 24 24
ITGAE 0.013 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.05 0.17 -9999 0 -0.6 24 24
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.011 0.044 -9999 0 -10000 0 0
EPHB2 0.008 0.035 -9999 0 -0.29 4 4
Syndecan-2/TACI 0.006 0.037 -9999 0 -10000 0 0
LAMA1 -0.025 0.15 -9999 0 -0.48 22 22
Syndecan-2/alpha2 ITGB1 -0.012 0.08 -9999 0 -0.46 3 3
HRAS 0.013 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0 0.006 -9999 0 -10000 0 0
ITGA5 0.013 0 -9999 0 -10000 0 0
BAX 0.027 0.07 -9999 0 -10000 0 0
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0.005 -9999 0 -10000 0 0
LAMA3 -0.079 0.14 -9999 0 -0.29 87 87
EZR 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.007 0.04 -9999 0 -0.29 5 5
Syndecan-2/MMP2 0.018 0.04 -9999 0 -0.54 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.012 0.064 -9999 0 -0.62 3 3
dendrite morphogenesis 0.02 0.021 -9999 0 -10000 0 0
Syndecan-2/GM-CSF 0.008 0.023 -9999 0 -10000 0 0
determination of left/right symmetry 0.018 0.009 -9999 0 -10000 0 0
Syndecan-2/PKC delta 0.023 0.007 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 0.024 0.019 -9999 0 -10000 0 0
MAPK1 0.024 0.019 -9999 0 -10000 0 0
Syndecan-2/RACK1 0.028 0.006 -9999 0 -10000 0 0
NF1 0.013 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.018 0.009 -9999 0 -10000 0 0
ITGA2 0.004 0.083 -9999 0 -0.81 3 3
MAPK8 0.022 0.074 -9999 0 -0.53 5 5
Syndecan-2/alpha2/beta1 Integrin 0.01 0.098 -9999 0 -0.46 11 11
Syndecan-2/Kininogen -0.31 0.26 -9999 0 -0.54 169 169
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.034 0.01 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.021 0.006 -9999 0 -10000 0 0
extracellular matrix organization 0.022 0.016 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.011 0.044 -9999 0 -10000 0 0
Syndecan-2/Caveolin-2/Ras 0.027 0.021 -9999 0 -10000 0 0
Syndecan-2/Laminin alpha3 -0.028 0.078 -9999 0 -10000 0 0
Syndecan-2/RasGAP 0 0.005 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0.019 0 -9999 0 -10000 0 0
PRKCD 0.013 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.021 0.021 -9999 0 -10000 0 0
GO:0007205 0.003 0.006 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.01 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0 -9999 0 -10000 0 0
TNFRSF13B -0.007 0.064 -9999 0 -0.29 14 14
RASA1 0.013 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0.012 0.064 -9999 0 -0.62 3 3
Syndecan-2/Synbindin 0.023 0.007 -9999 0 -10000 0 0
TGFB1 0.01 0.025 -9999 0 -0.29 2 2
CASP3 0.03 0.011 -9999 0 -10000 0 0
FN1 -0.009 0.079 -9999 0 -0.29 21 21
Syndecan-2/IL8 -0.019 0.079 -9999 0 -0.54 1 1
SDC2 0.018 0.009 -9999 0 -10000 0 0
KNG1 -0.47 0.4 -9999 0 -0.81 169 169
Syndecan-2/Neurofibromin 0.023 0.007 -9999 0 -10000 0 0
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 0.002 0.035 -9999 0 -0.29 4 4
Syndecan-2/TGFB1 0.022 0.016 -9999 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.021 0.006 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0.029 0.007 -9999 0 -10000 0 0
PRKACA 0.03 0.007 -9999 0 -10000 0 0
angiogenesis -0.019 0.078 -9999 0 -0.53 1 1
MMP2 0.004 0.062 -9999 0 -0.38 6 6
IL8 -0.061 0.14 -9999 0 -0.81 1 1
calcineurin-NFAT signaling pathway 0.006 0.037 -9999 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.013 0 -9999 0 -10000 0 0
LAT2 -0.038 0.1 -9999 0 -0.3 13 13
AP1 -0.11 0.15 -9999 0 -0.48 22 22
mol:PIP3 -0.059 0.14 -9999 0 -0.4 17 17
IKBKB -0.022 0.086 -9999 0 -0.27 3 3
AKT1 -0.022 0.099 -9999 0 -10000 0 0
IKBKG -0.022 0.086 -9999 0 -0.27 3 3
MS4A2 -0.074 0.14 -9999 0 -0.3 81 81
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
MAP3K1 -0.028 0.11 -9999 0 -0.45 1 1
mol:Ca2+ -0.044 0.12 -9999 0 -0.29 28 28
LYN 0.01 0.004 -9999 0 -10000 0 0
CBLB -0.023 0.076 -9999 0 -0.32 1 1
SHC1 0.012 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.021 0.034 -9999 0 -0.49 1 1
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.002 0.055 -9999 0 -0.29 10 10
PLD2 -0.052 0.11 -9999 0 -0.42 11 11
PTPN13 -0.012 0.071 -9999 0 -10000 0 0
PTPN11 0.012 0.003 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.003 0.081 -9999 0 -10000 0 0
SYK 0.008 0.048 -9999 0 -0.81 1 1
GRB2 0.012 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.089 0.12 -9999 0 -0.41 16 16
LAT -0.036 0.086 -9999 0 -0.34 3 3
PAK2 -0.038 0.12 -9999 0 -0.51 1 1
NFATC2 -0.081 0.19 -9999 0 -0.72 22 22
HRAS -0.048 0.12 -9999 0 -0.46 2 2
GAB2 0.013 0 -9999 0 -10000 0 0
PLA2G1B 0.03 0.012 -9999 0 -10000 0 0
Fc epsilon R1 -0.1 0.13 -9999 0 -0.37 36 36
Antigen/IgE/Fc epsilon R1 -0.09 0.12 -9999 0 -0.34 36 36
mol:GDP -0.061 0.13 -9999 0 -0.41 4 4
JUN 0.013 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.001 -9999 0 -10000 0 0
FOS -0.11 0.29 -9999 0 -0.81 44 44
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.032 0.08 -9999 0 -0.31 2 2
CHUK -0.022 0.086 -9999 0 -0.27 3 3
KLRG1 -0.027 0.077 -9999 0 -10000 0 0
VAV1 -0.055 0.12 -9999 0 -0.43 4 4
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.023 0.076 -9999 0 -0.32 1 1
negative regulation of mast cell degranulation -0.023 0.078 -9999 0 -0.34 1 1
BTK -0.049 0.11 -9999 0 -0.32 2 2
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.059 0.12 -9999 0 -0.38 13 13
GAB2/PI3K/SHP2 -0.058 0.085 -9999 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.03 0.08 -9999 0 -0.28 10 10
RAF1 0.019 0.015 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.15 -9999 0 -0.42 35 35
FCER1G -0.071 0.14 -9999 0 -0.29 80 80
FCER1A -0.018 0.14 -9999 0 -0.62 13 13
Antigen/IgE/Fc epsilon R1/Fyn -0.079 0.1 -9999 0 -0.44 11 11
MAPK3 0.028 0.012 -9999 0 -10000 0 0
MAPK1 0.028 0.012 -9999 0 -10000 0 0
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 -0.006 0.094 -9999 0 -0.65 5 5
DUSP1 0.01 0.048 -9999 0 -0.81 1 1
NF-kappa-B/RelA -0.025 0.04 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.019 0.073 -9999 0 -10000 0 0
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.071 0.1 -9999 0 -0.6 1 1
FER -0.023 0.076 -9999 0 -0.32 1 1
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.014 0.028 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG1 -0.056 0.14 -9999 0 -0.35 14 14
cytokine secretion -0.019 0.029 -9999 0 -10000 0 0
SPHK1 -0.09 0.1 -9999 0 -0.32 14 14
PTK2 -0.02 0.074 -9999 0 -10000 0 0
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.09 0.13 -9999 0 -0.4 27 27
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.049 0.14 -9999 0 -0.42 8 8
MAP2K2 0.025 0.013 -9999 0 -10000 0 0
MAP2K1 0.025 0.013 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.043 0.059 -9999 0 -10000 0 0
MAP2K4 0.016 0.008 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.13 0.15 -9999 0 -0.45 31 31
mol:Choline -0.051 0.11 -9999 0 -0.41 11 11
SHC/Grb2/SOS1 -0.034 0.055 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
DOK1 0.009 0.031 -9999 0 -0.29 3 3
PXN -0.012 0.071 -9999 0 -10000 0 0
HCLS1 -0.026 0.08 -9999 0 -0.32 1 1
PRKCB -0.039 0.11 -9999 0 -0.3 13 13
FCGR2B -0.08 0.14 -9999 0 -0.81 1 1
IGHE -0.002 0.005 -9999 0 -10000 0 0
KLRG1/SHIP -0.023 0.079 -9999 0 -0.34 1 1
LCP2 0.004 0.05 -9999 0 -0.29 8 8
PLA2G4A -0.036 0.11 -9999 0 -0.5 9 9
RASA1 0.013 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.051 0.11 -9999 0 -0.41 11 11
IKK complex -0.005 0.069 -9999 0 -10000 0 0
WIPF1 0.011 0.018 -9999 0 -0.29 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.006 0.022 -9999 0 -10000 0 0
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
AKT1 0.013 0 -9999 0 -10000 0 0
AKT2 0.013 0 -9999 0 -10000 0 0
STXBP4 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.068 0.066 -9999 0 -10000 0 0
YWHAZ 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
TBC1D4 0.022 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
SNARE/Synip 0 0 -9999 0 -10000 0 0
YWHAG 0.013 0 -9999 0 -10000 0 0
ASIP -0.11 0.15 -9999 0 -0.29 113 113
PRKCI 0.013 0 -9999 0 -10000 0 0
AS160/CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
GYS1 0.03 0 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
TRIP10 0.013 0 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
AS160/14-3-3 0.003 0.052 -9999 0 -10000 0 0
VAMP2 0.013 0 -9999 0 -10000 0 0
SLC2A4 0.07 0.069 -9999 0 -10000 0 0
STX4 0.013 0 -9999 0 -10000 0 0
GSK3B 0.025 0 -9999 0 -10000 0 0
SFN -0.14 0.17 -9999 0 -0.31 136 136
LNPEP 0.013 0 -9999 0 -10000 0 0
YWHAE 0.013 0 -9999 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.015 0.036 -10000 0 -10000 0 0
MAP4K4 0.034 0.039 -10000 0 -10000 0 0
BAG4 0.013 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.099 0.036 -10000 0 -10000 0 0
NFKBIA 0.013 0 -10000 0 -10000 0 0
BIRC3 -0.008 0.077 -10000 0 -0.29 20 20
BAX -0.045 0.019 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.037 0.007 -10000 0 -10000 0 0
BAD -0.099 0.036 -10000 0 -10000 0 0
SMPD1 0.021 0.033 -10000 0 -0.24 3 3
RB1 -0.099 0.036 -10000 0 -10000 0 0
FADD/Caspase 8 0.044 0.037 -10000 0 -10000 0 0
MAP2K4 -0.087 0.034 -10000 0 -10000 0 0
NSMAF 0.013 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.088 0.035 -10000 0 -0.23 1 1
EGF -0.72 0.24 -10000 0 -0.81 261 261
mol:ceramide -0.11 0.038 -10000 0 -10000 0 0
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.015 0.036 -10000 0 -10000 0 0
ASAH1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.098 0.036 -10000 0 -10000 0 0
cell proliferation -0.063 0.062 -10000 0 -0.44 6 6
BID -0.006 0.03 -10000 0 -10000 0 0
MAP3K1 -0.099 0.036 -10000 0 -10000 0 0
EIF2A -0.077 0.033 -10000 0 -10000 0 0
TRADD 0.013 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 -0.072 0.033 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.072 0.033 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.099 0.037 -10000 0 -0.25 1 1
FADD 0.034 0.039 -10000 0 -10000 0 0
KSR1 -0.1 0.037 -10000 0 -0.25 1 1
MAPK8 -0.086 0.051 -10000 0 -0.37 5 5
PRKRA -0.099 0.036 -10000 0 -10000 0 0
PDGFA 0.003 0.053 -10000 0 -10000 0 0
TRAF2 0.013 0 -10000 0 -10000 0 0
IGF1 -0.004 0.12 -10000 0 -0.81 6 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.038 -10000 0 -10000 0 0
CTSD 0.011 0.018 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.019 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.067 0.068 -10000 0 -0.47 6 6
PRKCD 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.013 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.015 0.036 -10000 0 -10000 0 0
RelA/NF kappa B1 0.019 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.013 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.028 0.042 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.013 0.062 -10000 0 -0.54 3 3
mol:Sphingosine-1-phosphate 0.015 0.036 -10000 0 -10000 0 0
MAP2K1 -0.077 0.034 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS -0.065 0.025 -10000 0 -10000 0 0
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.019 0 -10000 0 -10000 0 0
EIF2AK2 -0.087 0.034 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.013 0.062 -10000 0 -0.54 3 3
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.035 0.025 -10000 0 -10000 0 0
MAP2K2 -0.077 0.034 -10000 0 -10000 0 0
SMPD3 0.023 0.035 -10000 0 -0.24 3 3
TNF -0.011 0.1 -10000 0 -0.38 17 17
PKC zeta/PAR4 0.019 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.25 0.089 0.28 261 -10000 0 261
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 -0.065 0.025 -10000 0 -10000 0 0
BCL2 0.013 0 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.033 0.3 -10000 0 -0.98 12 12
IL23A -0.032 0.3 -10000 0 -1 8 8
NF kappa B1 p50/RelA/I kappa B alpha -0.11 0.21 -10000 0 -0.85 11 11
positive regulation of T cell mediated cytotoxicity -0.035 0.3 -10000 0 -0.94 11 11
ITGA3 -0.031 0.28 -10000 0 -0.91 8 8
IL17F -0.003 0.22 -10000 0 -0.64 6 6
IL12B 0.012 0.042 -10000 0 -0.34 1 1
STAT1 (dimer) -0.035 0.28 -10000 0 -0.9 11 11
CD4 -0.028 0.28 -10000 0 -0.9 8 8
IL23 -0.044 0.29 -10000 0 -1 7 7
IL23R 0.011 0.092 -10000 0 -10000 0 0
IL1B -0.039 0.32 -10000 0 -1.2 9 9
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.027 0.28 -10000 0 -0.93 7 7
TYK2 0.017 0.018 -10000 0 -10000 0 0
STAT4 -0.013 0.084 -10000 0 -0.29 24 24
STAT3 0.013 0.001 -10000 0 -10000 0 0
IL18RAP -0.028 0.1 -10000 0 -0.29 38 38
IL12RB1 -0.003 0.08 -10000 0 -0.32 10 10
PIK3CA 0.013 0.001 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.008 0.059 -10000 0 -10000 0 0
IL23R/JAK2 0.02 0.1 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.035 0.3 -10000 0 -0.94 11 11
natural killer cell activation 0 0.009 0.037 5 -10000 0 5
JAK2 0.023 0.023 -10000 0 -10000 0 0
PIK3R1 0.013 0.001 -10000 0 -10000 0 0
NFKB1 0.013 0.003 -10000 0 -10000 0 0
RELA 0.013 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.041 0.28 -10000 0 -0.95 8 8
ALOX12B -0.028 0.28 -10000 0 -0.86 11 11
CXCL1 -0.085 0.34 -10000 0 -1.1 16 16
T cell proliferation -0.035 0.3 -10000 0 -0.94 11 11
NFKBIA 0.013 0.003 -10000 0 -10000 0 0
IL17A 0.018 0.19 -10000 0 -0.52 2 2
PI3K -0.099 0.22 -10000 0 -0.87 11 11
IFNG 0.001 0.027 0.086 2 -0.087 2 4
STAT3 (dimer) -0.11 0.2 -10000 0 -0.83 11 11
IL18R1 0.009 0.048 -10000 0 -0.81 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 0 0.2 -10000 0 -0.72 2 2
IL18/IL18R -0.005 0.069 -10000 0 -0.54 1 1
macrophage activation -0.009 0.013 -10000 0 -0.043 7 7
TNF -0.039 0.31 -10000 0 -1 11 11
STAT3/STAT4 -0.11 0.23 -10000 0 -0.91 11 11
STAT4 (dimer) -0.044 0.29 -10000 0 -0.94 11 11
IL18 0.007 0.04 -10000 0 -0.29 5 5
IL19 -0.031 0.28 -10000 0 -0.88 9 9
STAT5A (dimer) -0.033 0.28 -10000 0 -0.9 11 11
STAT1 0.007 0.04 -10000 0 -0.29 5 5
SOCS3 0.007 0.057 -10000 0 -0.81 1 1
CXCL9 -0.031 0.29 -10000 0 -0.92 10 10
MPO -0.031 0.28 -10000 0 -0.92 7 7
positive regulation of humoral immune response -0.035 0.3 -10000 0 -0.94 11 11
IL23/IL23R/JAK2/TYK2 -0.037 0.3 -10000 0 -0.97 11 11
IL6 -0.12 0.45 -10000 0 -1.2 34 34
STAT5A 0.013 0 -10000 0 -10000 0 0
IL2 0.003 0.02 -10000 0 -0.29 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0.009 0.037 5 -10000 0 5
CD3E -0.036 0.3 -10000 0 -0.97 10 10
keratinocyte proliferation -0.035 0.3 -10000 0 -0.94 11 11
NOS2 -0.085 0.41 -10000 0 -1.2 27 27
PDGFR-beta signaling pathway

Figure S73.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S73.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.055 0.11 -9999 0 -0.58 10 10
PDGFB-D/PDGFRB/SLAP -0.021 0.12 -9999 0 -0.63 10 10
PDGFB-D/PDGFRB/APS/CBL -0.017 0.098 -9999 0 -0.53 10 10
AKT1 0.041 0.074 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.044 0.13 -9999 0 -0.62 10 10
PIK3CA 0.013 0 -9999 0 -10000 0 0
FGR -0.019 0.1 -9999 0 -0.52 11 11
mol:Ca2+ -0.003 0.12 -9999 0 -0.63 10 10
MYC 0.013 0.089 -9999 0 -0.38 10 10
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.017 0.085 -9999 0 -0.43 10 10
LRP1/PDGFRB/PDGFB -0.018 0.1 -9999 0 -0.53 11 11
GRB10 0.013 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
GO:0007205 -0.004 0.12 -9999 0 -0.64 10 10
PTEN 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0 -9999 0 -10000 0 0
GRB7 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 -0.012 0.11 -9999 0 -0.62 10 10
PDGFB-D/PDGFRB/GRB10 -0.012 0.11 -9999 0 -0.62 10 10
cell cycle arrest -0.021 0.12 -9999 0 -0.63 10 10
HRAS 0.013 0 -9999 0 -10000 0 0
HIF1A 0.046 0.067 -9999 0 -10000 0 0
GAB1 -0.01 0.12 -9999 0 -0.61 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.011 0.11 -9999 0 -0.56 10 10
PDGFB-D/PDGFRB -0.015 0.1 -9999 0 -0.54 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.012 0.11 -9999 0 -0.62 10 10
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.053 0.11 -9999 0 -0.57 10 10
positive regulation of MAPKKK cascade -0.012 0.11 -9999 0 -0.61 10 10
PIK3R1 0.013 0 -9999 0 -10000 0 0
mol:IP3 -0.004 0.12 -9999 0 -0.65 10 10
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.012 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.012 0.11 -9999 0 -0.62 10 10
SHB 0.013 0 -9999 0 -10000 0 0
BLK -0.018 0.096 -9999 0 -0.51 10 10
PTPN2 0.012 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.012 0.11 -9999 0 -0.62 10 10
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 -0.007 0.12 -9999 0 -0.57 11 11
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.012 0.11 -9999 0 -0.62 10 10
LCK -0.016 0.095 -9999 0 -0.51 10 10
PDGFRB -0.016 0.15 -9999 0 -0.81 10 10
ACP1 0.013 0 -9999 0 -10000 0 0
HCK -0.025 0.11 -9999 0 -0.53 11 11
ABL1 -0.005 0.11 -9999 0 -0.56 10 10
PDGFB-D/PDGFRB/CBL -0.01 0.13 -9999 0 -0.66 10 10
PTPN1 0.012 0.002 -9999 0 -10000 0 0
SNX15 0.013 0 -9999 0 -10000 0 0
STAT3 0.013 0 -9999 0 -10000 0 0
STAT1 0.007 0.04 -9999 0 -0.29 5 5
cell proliferation 0.013 0.083 -9999 0 -0.36 10 10
SLA -0.001 0.063 -9999 0 -0.29 13 13
actin cytoskeleton reorganization 0.03 0.084 -9999 0 -0.41 10 10
SRC -0.013 0.095 -9999 0 -0.51 10 10
PI3K -0.013 0.07 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.016 0.097 -9999 0 -0.53 10 10
SH2B2 0.011 0.018 -9999 0 -0.29 1 1
PLCgamma1/SPHK1 -0.045 0.13 -9999 0 -0.65 10 10
LYN -0.012 0.095 -9999 0 -0.51 10 10
LRP1 0.013 0 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.013 0 -9999 0 -10000 0 0
STAT5A 0.013 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.013 0.079 -9999 0 -0.43 10 10
SPHK1 -0.14 0.15 -9999 0 -0.29 145 145
EDG1 -0.001 0.002 -9999 0 -10000 0 0
mol:DAG -0.004 0.12 -9999 0 -0.65 10 10
PLCG1 -0.004 0.13 -9999 0 -0.67 10 10
NHERF/PDGFRB -0.016 0.097 -9999 0 -0.53 10 10
YES1 -0.013 0.095 -9999 0 -0.51 10 10
cell migration -0.018 0.096 -9999 0 -0.53 10 10
SHC/Grb2/SOS1 -0.013 0.079 -9999 0 -0.43 10 10
SLC9A3R2 0.013 0 -9999 0 -10000 0 0
SLC9A3R1 0.013 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.001 0.093 -9999 0 -0.48 10 10
FYN -0.013 0.095 -9999 0 -0.51 10 10
DOK1 0.011 0.095 -9999 0 -0.48 10 10
HRAS/GTP 0.009 0 -9999 0 -10000 0 0
PDGFB 0.01 0.048 -9999 0 -0.81 1 1
RAC1 0.001 0.11 -9999 0 -0.53 10 10
PRKCD 0.012 0.094 -9999 0 -0.49 10 10
FER 0.012 0.094 -9999 0 -0.49 10 10
MAPKKK cascade -0.014 0.077 -9999 0 -0.42 10 10
RASA1 0.012 0.094 -9999 0 -0.49 10 10
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.013 0 -9999 0 -10000 0 0
p62DOK/Csk 0.019 0.089 -9999 0 -0.45 10 10
PDGFB-D/PDGFRB/SHB -0.012 0.11 -9999 0 -0.62 10 10
chemotaxis -0.004 0.11 -9999 0 -0.54 10 10
STAT1-3-5/STAT1-3-5 -0.016 0.075 -9999 0 -0.41 10 10
Bovine Papilomavirus E5/PDGFRB -0.017 0.12 -9999 0 -0.63 10 10
PTPRJ 0.013 0 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.023 0.038 -9999 0 -10000 0 0
ACTA1 0.017 0.045 -9999 0 -10000 0 0
NUMA1 0.023 0.038 -9999 0 -10000 0 0
SPTAN1 0.018 0.045 -9999 0 -10000 0 0
LIMK1 0.016 0.048 -9999 0 -10000 0 0
BIRC3 -0.008 0.077 -9999 0 -0.29 20 20
BIRC2 0.013 0 -9999 0 -10000 0 0
BAX 0.01 0.025 -9999 0 -10000 0 0
CASP10 0.011 0.059 -9999 0 -10000 0 0
CRMA 0 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
PTK2 0.023 0.038 -9999 0 -10000 0 0
DIABLO 0.013 0 -9999 0 -10000 0 0
apoptotic nuclear changes 0.018 0.044 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
CRADD 0.013 0 -9999 0 -10000 0 0
GSN 0.018 0.045 -9999 0 -10000 0 0
MADD 0.013 0 -9999 0 -10000 0 0
TFAP2A -0.41 0.24 -9999 0 -0.53 229 229
BID 0.015 0.031 -9999 0 -10000 0 0
MAP3K1 0.013 0.02 -9999 0 -10000 0 0
TRADD 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.019 0 -9999 0 -10000 0 0
mol:Activated DNA 0 0 -9999 0 -10000 0 0
ARHGDIB 0.017 0.049 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
DNA repair -0.01 0.022 -9999 0 -10000 0 0
neuron apoptosis 0.024 0.007 -9999 0 -10000 0 0
mol:NAD 0 0 -9999 0 -10000 0 0
DNA fragmentation during apoptosis 0.025 0.043 -9999 0 -10000 0 0
APAF1 0.012 0 -9999 0 -10000 0 0
CASP6 0.031 0.027 -9999 0 -10000 0 0
TRAF2 0.013 0 -9999 0 -10000 0 0
ICAD/CAD 0.024 0.043 -9999 0 -10000 0 0
CASP7 -0.002 0.036 -9999 0 -10000 0 0
KRT18 0.015 0.02 -9999 0 -10000 0 0
apoptosis 0.029 0.044 -9999 0 -10000 0 0
DFFA 0.018 0.045 -9999 0 -10000 0 0
DFFB 0.018 0.045 -9999 0 -10000 0 0
PARP1 0.01 0.022 -9999 0 -10000 0 0
actin filament polymerization -0.022 0.046 -9999 0 -10000 0 0
TNF -0.011 0.1 -9999 0 -0.38 17 17
CYCS 0.014 0.026 -9999 0 -10000 0 0
SATB1 0.035 0.037 -9999 0 -0.42 1 1
SLK 0.018 0.045 -9999 0 -10000 0 0
p15 BID/BAX 0.019 0.03 -9999 0 -10000 0 0
CASP2 0.037 0.038 -9999 0 -10000 0 0
JNK cascade -0.013 0.02 -9999 0 -10000 0 0
CASP3 0.011 0.047 -9999 0 -10000 0 0
LMNB2 0.04 0.027 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
CASP4 0.013 0 -9999 0 -10000 0 0
Mammalian IAPs/DIABLO 0.022 0.039 -9999 0 -10000 0 0
negative regulation of DNA binding -0.41 0.23 -9999 0 -0.52 229 229
stress fiber formation 0.018 0.044 -9999 0 -10000 0 0
GZMB 0.002 0.07 -9999 0 -0.37 5 5
CASP1 0.015 0.014 -9999 0 -10000 0 0
LMNB1 0.037 0.031 -9999 0 -10000 0 0
APP 0.024 0.007 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
CASP8 0.011 0 -9999 0 -10000 0 0
VIM 0.023 0.044 -9999 0 -0.3 1 1
LMNA 0.04 0.027 -9999 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.031 0.04 -9999 0 -10000 0 0
LRDD 0.011 0.018 -9999 0 -0.29 1 1
SREBF1 0.018 0.045 -9999 0 -10000 0 0
APAF-1/Caspase 9 0.002 0.015 -9999 0 -10000 0 0
nuclear fragmentation during apoptosis 0.023 0.037 -9999 0 -10000 0 0
CFL2 0.022 0.046 -9999 0 -10000 0 0
GAS2 0.011 0.077 -9999 0 -0.53 4 4
positive regulation of apoptosis 0.041 0.029 -9999 0 -10000 0 0
PRF1 0.005 0.047 -9999 0 -0.29 7 7
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 -0.011 0.095 -9999 0 -0.46 5 5
MAP4K1 -0.027 0.1 -9999 0 -0.29 38 38
MAP3K8 0.013 0 -9999 0 -10000 0 0
PRKCB 0.007 0.04 -9999 0 -0.29 5 5
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.013 0 -9999 0 -10000 0 0
MAP3K1 0.021 0.054 -9999 0 -10000 0 0
JUN 0.019 0.082 -9999 0 -0.57 5 5
MAP3K7 0.021 0.054 -9999 0 -10000 0 0
GRAP2 0.003 0.053 -9999 0 -0.29 9 9
CRK 0.013 0 -9999 0 -10000 0 0
MAP2K4 0.029 0.052 -9999 0 -10000 0 0
LAT -0.017 0.09 -9999 0 -0.29 28 28
LCP2 0.004 0.05 -9999 0 -0.29 8 8
MAPK8 0.013 0.086 -9999 0 -0.61 5 5
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.014 0.057 -9999 0 -0.32 2 2
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.032 0.077 -9999 0 -0.43 5 5
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.007 0.068 -9999 0 -10000 0 0
CRKL 0.01 0.077 -9999 0 -0.33 5 5
mol:PIP3 -0.019 0.004 -9999 0 -10000 0 0
AKT1 0.001 0.003 -9999 0 -10000 0 0
PTK2B 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.017 0.074 -9999 0 -0.31 5 5
RANBP10 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.05 0.14 -9999 0 -0.57 17 17
MAP3K5 0.017 0.071 -9999 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS -0.017 0.14 -9999 0 -0.53 17 17
AP1 -0.076 0.2 -9999 0 -0.56 44 44
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.013 0 -9999 0 -10000 0 0
apoptosis -0.098 0.26 -9999 0 -0.72 44 44
STAT3 (dimer) 0.009 0.09 -9999 0 -0.33 17 17
GAB1/CRKL/SHP2/PI3K -0.017 0.056 -9999 0 -10000 0 0
INPP5D 0.002 0.055 -9999 0 -0.29 10 10
CBL/CRK 0.017 0.074 -9999 0 -0.31 5 5
PTPN11 0.013 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.013 0 -9999 0 -10000 0 0
PTEN 0.013 0 -9999 0 -10000 0 0
ELK1 -0.014 0.04 -9999 0 -10000 0 0
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.015 0.048 -9999 0 -0.25 5 5
PAK1 0.008 0.003 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.05 0.14 -9999 0 -0.57 17 17
HRAS -0.002 0.11 -9999 0 -0.42 17 17
DOCK1 0.017 0.074 -9999 0 -0.31 5 5
GAB1 0.003 0.081 -9999 0 -0.3 17 17
CRK 0.01 0.077 -9999 0 -0.33 5 5
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.044 0.14 -9999 0 -0.59 17 17
JUN 0.013 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.014 0.075 -9999 0 -0.28 17 17
PIK3R1 0.013 0 -9999 0 -10000 0 0
cell morphogenesis 0.035 0.091 -9999 0 -10000 0 0
GRB2/SHC 0.003 0.067 -9999 0 -0.3 5 5
FOS -0.11 0.29 -9999 0 -0.81 44 44
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.014 0.04 -9999 0 -10000 0 0
HGF/MET/MUC20 -0.051 0.14 -9999 0 -0.58 17 17
cell migration 0.003 0.066 -9999 0 -0.3 5 5
GRB2 0.013 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
MET/RANBP10 -0.007 0.068 -9999 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.002 0.094 -9999 0 -0.35 17 17
MET/MUC20 -0.016 0.068 -9999 0 -0.2 36 36
RAP1B 0.023 0.07 -9999 0 -10000 0 0
RAP1A 0.023 0.07 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.05 0.14 -9999 0 -0.57 17 17
RAF1 0.005 0.11 -9999 0 -0.47 5 5
STAT3 0.008 0.091 -9999 0 -0.33 17 17
cell proliferation 0.012 0.12 -9999 0 -0.44 17 17
RPS6KB1 0.003 0.028 -9999 0 -10000 0 0
MAPK3 -0.018 0.036 -9999 0 -10000 0 0
MAPK1 -0.018 0.036 -9999 0 -10000 0 0
RANBP9 0.013 0 -9999 0 -10000 0 0
MAPK8 0.025 0.095 -9999 0 -0.52 5 5
SRC 0.009 0.089 -9999 0 -0.39 5 5
PI3K 0.003 0.067 -9999 0 -0.3 5 5
MET/Glomulin -0.01 0.059 -9999 0 -10000 0 0
SOS1 0.013 0 -9999 0 -10000 0 0
MAP2K1 0.012 0.1 -9999 0 -0.43 5 5
MET -0.025 0.1 -9999 0 -0.29 36 36
MAP4K1 0.01 0.074 -9999 0 -0.31 5 5
PTK2 0.013 0 -9999 0 -10000 0 0
MAP2K2 0.012 0.1 -9999 0 -0.43 5 5
BAD 0.008 0.003 -9999 0 -10000 0 0
MAP2K4 0.023 0.066 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.022 0.062 -9999 0 -10000 0 0
INPPL1 0.013 0 -9999 0 -10000 0 0
PXN 0.013 0 -9999 0 -10000 0 0
SH3KBP1 0.013 0 -9999 0 -10000 0 0
HGS -0.005 0.07 -9999 0 -0.32 5 5
PLCgamma1/PKC 0.009 0 -9999 0 -10000 0 0
HGF -0.037 0.19 -9999 0 -0.78 18 18
RASA1 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
PTPRJ 0.013 0 -9999 0 -10000 0 0
NCK/PLCgamma1 0.003 0.074 -9999 0 -0.33 5 5
PDPK1 -0.008 0.004 -9999 0 -10000 0 0
HGF/MET/SHIP -0.055 0.14 -9999 0 -0.57 17 17
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.011 0.004 -9999 0 -10000 0 0
PRKCZ 0.013 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.005 0.031 -9999 0 -10000 0 0
IRAK/TOLLIP 0.026 0.003 -9999 0 -10000 0 0
IKBKB 0.013 0 -9999 0 -10000 0 0
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.18 0.28 -9999 0 -0.63 76 76
IL1A -0.028 0.1 -9999 0 -0.29 38 38
IL1B 0.008 0.087 -9999 0 -0.62 5 5
IRAK/TRAF6/p62/Atypical PKCs -0.003 0.015 -9999 0 -10000 0 0
IL1R2 -0.2 0.36 -9999 0 -0.8 77 77
IL1R1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.032 0.032 -9999 0 -10000 0 0
TOLLIP 0.013 0 -9999 0 -10000 0 0
TICAM2 0.01 0.048 -9999 0 -0.81 1 1
MAP3K3 0.013 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.059 0.007 -9999 0 -10000 0 0
JUN 0.033 0.055 -9999 0 -0.38 5 5
MAP3K7 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.031 0.065 -9999 0 -0.43 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88 0.01 0.055 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.015 0.038 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP 0.019 0.071 -9999 0 -0.49 5 5
NFKB1 0.013 0 -9999 0 -10000 0 0
MAPK8 0.028 0.059 -9999 0 -0.42 5 5
IRAK1 0.02 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 0.005 0.059 -9999 0 -0.62 1 1
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0 -9999 0 -10000 0 0
TRAF6 0.013 0 -9999 0 -10000 0 0
PI3K 0.019 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.032 0.04 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.019 0.071 -9999 0 -0.49 5 5
IL1 beta/IL1R2 -0.13 0.26 -9999 0 -0.54 80 80
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.008 0.052 -9999 0 -10000 0 0
IRAK3 0.01 0.025 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.03 0.079 -9999 0 -0.52 5 5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.021 0.036 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP -0.02 0.052 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.003 0.053 -9999 0 -0.29 9 9
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.033 0.003 -9999 0 -10000 0 0
IL1RAP 0.009 0.031 -9999 0 -0.29 3 3
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.009 0.059 -9999 0 -0.71 1 1
CASP1 0.009 0.031 -9999 0 -0.29 3 3
IL1RN/IL1R2 -0.16 0.28 -9999 0 -0.62 77 77
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.026 0.067 -9999 0 -0.46 5 5
TMEM189-UBE2V1 0.003 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.029 0.028 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
IL1RN -0.007 0.084 -9999 0 -0.32 17 17
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.03 0.003 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.013 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.098 0.17 -9999 0 -0.42 65 65
Syndecan-3/Neurocan -0.014 0.037 -9999 0 -10000 0 0
POMC 0 0.097 -9999 0 -0.7 5 5
EGFR 0.013 0 -9999 0 -10000 0 0
Syndecan-3/EGFR -0.002 0.012 -9999 0 -10000 0 0
AGRP 0.008 0.018 -9999 0 -0.29 1 1
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.013 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.01 0.048 -9999 0 -0.81 1 1
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN -0.024 0.094 -9999 0 -10000 0 0
long-term memory -0.001 0.011 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.03 0.055 -9999 0 -0.46 1 1
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0.018 0.012 -9999 0 -10000 0 0
FYN 0.013 0 -9999 0 -10000 0 0
limb bud formation -0.002 0.014 -9999 0 -10000 0 0
MC4R 0 0.03 -9999 0 -0.29 3 3
SRC 0.011 0.018 -9999 0 -0.29 1 1
PTN -0.18 0.34 -9999 0 -0.75 73 73
FGFR/FGF/Syndecan-3 -0.002 0.014 -9999 0 -10000 0 0
neuron projection morphogenesis -0.1 0.17 -9999 0 -0.41 65 65
Syndecan-3/AgRP -0.002 0.014 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.003 0.017 -9999 0 -10000 0 0
Fyn/Cortactin 0.019 0 -9999 0 -10000 0 0
SDC3 -0.002 0.014 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.029 0.055 -9999 0 -0.45 1 1
IL8 -0.061 0.14 -9999 0 -0.81 1 1
Syndecan-3/Fyn/Cortactin -0.001 0.011 -9999 0 -10000 0 0
Syndecan-3/CASK -0.002 0.013 -9999 0 -10000 0 0
alpha-MSH/MC4R 0 0.078 -9999 0 -0.63 4 4
Gamma Secretase -0.002 0.027 -9999 0 -0.46 1 1
TCGA08_rtk_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
PDGFRA -0.3 0.4 -9999 0 -0.81 109 109
HRAS 0.013 0 -9999 0 -10000 0 0
EGFR 0.013 0 -9999 0 -10000 0 0
AKT 0.023 0.022 -9999 0 -10000 0 0
FOXO3 0.013 0 -9999 0 -10000 0 0
AKT1 0.013 0 -9999 0 -10000 0 0
FOXO1 0.013 0 -9999 0 -10000 0 0
AKT3 0.013 0 -9999 0 -10000 0 0
FOXO4 0.013 0 -9999 0 -10000 0 0
MET -0.025 0.1 -9999 0 -0.29 36 36
PIK3CA 0.013 0 -9999 0 -10000 0 0
PIK3CB 0.011 0.018 -9999 0 -0.29 1 1
NRAS 0.013 0 -9999 0 -10000 0 0
PIK3CG 0.004 0.074 -9999 0 -0.5 5 5
PIK3R3 0.013 0 -9999 0 -10000 0 0
PIK3R2 0.013 0 -9999 0 -10000 0 0
NF1 0.013 0 -9999 0 -10000 0 0
RAS -0.056 0.098 -9999 0 -0.25 12 12
ERBB2 0.013 0 -9999 0 -10000 0 0
proliferation/survival/translation -0.027 0.013 -9999 0 -10000 0 0
PI3K -0.04 0.093 -9999 0 -0.22 15 15
PIK3R1 0.013 0 -9999 0 -10000 0 0
KRAS 0.013 0 -9999 0 -10000 0 0
FOXO 0.028 0.025 -9999 0 -10000 0 0
AKT2 0.013 0 -9999 0 -10000 0 0
PTEN 0.013 0 -9999 0 -10000 0 0
IL2 signaling events mediated by STAT5

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
GAB2 0.013 0.001 -9999 0 -10000 0 0
ELF1 0.004 0.05 -9999 0 -10000 0 0
CCNA2 -0.031 0.11 -9999 0 -0.29 42 42
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
JAK3 -0.048 0.12 -9999 0 -0.29 58 58
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
JAK1 0.013 0.001 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.042 0.065 -9999 0 -10000 0 0
SHC1 0.013 0.001 -9999 0 -10000 0 0
SP1 -0.005 0.06 -9999 0 -10000 0 0
IL2RA 0 0.09 -9999 0 -10000 0 0
IL2RB -0.02 0.095 -9999 0 -0.29 32 32
SOS1 0.013 0.001 -9999 0 -10000 0 0
IL2RG 0.004 0.053 -9999 0 -0.29 9 9
G1/S transition of mitotic cell cycle -0.004 0.077 -9999 0 -10000 0 0
PTPN11 0.013 0.001 -9999 0 -10000 0 0
CCND2 -0.016 0.11 -9999 0 -10000 0 0
LCK 0.006 0.047 -9999 0 -0.29 7 7
GRB2 0.013 0.001 -9999 0 -10000 0 0
IL2 0.004 0.018 -9999 0 -0.29 1 1
CDK6 0.013 0 -9999 0 -10000 0 0
CCND3 0.046 0.064 -9999 0 -10000 0 0
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.012 0.076 -10000 0 -0.36 5 5
IKBKB 0.002 0.057 -10000 0 -0.26 1 1
AKT1 0.007 0.059 -10000 0 -0.24 2 2
IKBKG 0.003 0.059 -10000 0 -0.28 1 1
CALM1 -0.015 0.11 -10000 0 -0.48 9 9
PIK3CA 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.005 0.093 -10000 0 -0.5 4 4
MAP3K7 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ -0.023 0.12 0.24 8 -0.52 9 17
DOK1 0.009 0.031 -10000 0 -0.29 3 3
AP-1 -0.013 0.092 0.19 5 -0.25 12 17
LYN 0.013 0 -10000 0 -10000 0 0
BLNK -0.016 0.15 -10000 0 -0.81 10 10
SHC1 0.013 0 -10000 0 -10000 0 0
BCR complex -0.018 0.1 -10000 0 -0.58 6 6
CD22 -0.041 0.095 -10000 0 -0.48 9 9
CAMK2G -0.007 0.1 -10000 0 -0.49 7 7
CSNK2A1 0.013 0 -10000 0 -10000 0 0
INPP5D 0.002 0.055 -10000 0 -0.29 10 10
SHC/GRB2/SOS1 -0.031 0.097 -10000 0 -0.79 1 1
GO:0007205 -0.024 0.12 0.24 8 -0.53 9 17
SYK 0.01 0.048 -10000 0 -0.81 1 1
ELK1 -0.016 0.11 -10000 0 -0.49 9 9
NFATC1 0 0.085 -10000 0 -0.45 5 5
B-cell antigen/BCR complex -0.018 0.1 -10000 0 -0.58 6 6
PAG1/CSK 0.019 0 -10000 0 -10000 0 0
NFKBIB 0.009 0.024 0.085 7 -10000 0 7
HRAS -0.007 0.11 -10000 0 -0.48 9 9
NFKBIA 0.01 0.023 0.085 7 -10000 0 7
NF-kappa-B/RelA/I kappa B beta 0.014 0.021 -10000 0 -10000 0 0
RasGAP/Csk -0.055 0.089 -10000 0 -0.45 6 6
mol:GDP -0.022 0.11 -10000 0 -0.51 9 9
PTEN 0.013 0 -10000 0 -10000 0 0
CD79B 0.003 0.085 -10000 0 -0.68 4 4
NF-kappa-B/RelA/I kappa B alpha 0.014 0.021 -10000 0 -10000 0 0
GRB2 0.013 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.006 0.11 -10000 0 -0.55 5 5
PIK3R1 0.013 0 -10000 0 -10000 0 0
mol:IP3 -0.024 0.12 0.24 8 -0.54 9 17
CSK 0.013 0 -10000 0 -10000 0 0
FOS -0.074 0.19 -10000 0 -0.47 47 47
CHUK 0.003 0.059 -10000 0 -0.28 1 1
IBTK 0.013 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.05 0.089 -10000 0 -0.47 6 6
PTPN6 -0.03 0.093 -10000 0 -0.48 7 7
RELA 0.013 0 -10000 0 -10000 0 0
BCL2A1 -0.004 0.031 -10000 0 -10000 0 0
VAV2 -0.036 0.097 -10000 0 -0.58 5 5
ubiquitin-dependent protein catabolic process 0.014 0.023 0.088 7 -10000 0 7
BTK -0.033 0.064 -10000 0 -10000 0 0
CD19 -0.04 0.1 -10000 0 -0.49 8 8
MAP4K1 -0.027 0.1 -10000 0 -0.29 38 38
CD72 -0.008 0.077 -10000 0 -0.29 20 20
PAG1 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0.083 -10000 0 -0.42 4 4
SH3BP5 -0.021 0.16 -10000 0 -0.81 12 12
PIK3AP1 -0.014 0.12 0.27 8 -0.52 10 18
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.025 0.14 -10000 0 -0.67 10 10
RAF1 0.001 0.1 -10000 0 -0.44 9 9
RasGAP/p62DOK/SHIP -0.055 0.088 -10000 0 -0.43 6 6
CD79A -0.03 0.12 -10000 0 -0.32 37 37
re-entry into mitotic cell cycle -0.013 0.091 0.19 5 -0.24 14 19
RASA1 0.013 0 -10000 0 -10000 0 0
MAPK3 0.015 0.086 -10000 0 -0.41 6 6
MAPK1 0.015 0.086 -10000 0 -0.41 6 6
CD72/SHP1 -0.015 0.11 -10000 0 -0.5 6 6
NFKB1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.006 0.099 -10000 0 -0.41 9 9
actin cytoskeleton organization -0.002 0.095 -10000 0 -0.49 5 5
NF-kappa-B/RelA 0.032 0.04 0.17 7 -10000 0 7
Calcineurin -0.022 0.078 -10000 0 -0.46 6 6
PI3K -0.035 0.082 -10000 0 -0.44 5 5
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.026 0.12 0.27 8 -0.57 9 17
SOS1 0.013 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.018 0.11 -10000 0 -0.63 5 5
DAPP1 -0.028 0.1 -10000 0 -0.76 4 4
cytokine secretion 0.001 0.081 -10000 0 -0.42 5 5
mol:DAG -0.024 0.12 0.24 8 -0.54 9 17
PLCG2 -0.035 0.19 -10000 0 -0.75 18 18
MAP2K1 0.008 0.093 -10000 0 -0.46 6 6
B-cell antigen/BCR complex/FcgammaRIIB -0.073 0.11 -10000 0 -0.54 6 6
mol:PI-3-4-5-P3 -0.027 0.061 -10000 0 -0.32 5 5
ETS1 0.001 0.094 -10000 0 -0.46 6 6
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.036 0.12 -10000 0 -0.49 15 15
B-cell antigen/BCR complex/LYN -0.033 0.088 -10000 0 -0.55 6 6
MALT1 0.013 0 -10000 0 -10000 0 0
TRAF6 0.013 0 -10000 0 -10000 0 0
RAC1 -0.004 0.1 -10000 0 -0.53 5 5
B-cell antigen/BCR complex/LYN/SYK -0.033 0.094 -10000 0 -0.52 6 6
CARD11 -0.052 0.12 -10000 0 -0.45 12 12
FCGR2B -0.08 0.14 -10000 0 -0.81 1 1
PPP3CA 0.013 0 -10000 0 -10000 0 0
BCL10 0.013 0 -10000 0 -10000 0 0
IKK complex 0.011 0.027 -10000 0 -10000 0 0
PTPRC 0.002 0.067 -10000 0 -0.36 8 8
PDPK1 0.003 0.055 -10000 0 -0.23 1 1
PPP3CB 0.013 0 -10000 0 -10000 0 0
PPP3CC 0.013 0 -10000 0 -10000 0 0
POU2F2 0.014 0.018 -10000 0 -10000 0 0
BARD1 signaling events

Figure S82.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S82.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.003 0.098 -10000 0 -0.62 7 7
ATM 0.013 0 -10000 0 -10000 0 0
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.013 0 -10000 0 -10000 0 0
ATR 0.013 0 -10000 0 -10000 0 0
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.024 0.011 -10000 0 -10000 0 0
protein ubiquitination -0.019 0.075 -10000 0 -0.45 7 7
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex -0.002 0.031 -10000 0 -0.54 1 1
MRE11A 0.013 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.016 0.042 -10000 0 -10000 0 0
FANCF 0.013 0 -10000 0 -10000 0 0
BRCA1 0.009 0.031 -10000 0 -10000 0 0
CCNE1 -0.006 0.073 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.006 0.049 -10000 0 -10000 0 0
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.001 0.1 -10000 0 -0.62 7 7
FANCE 0.013 0 -10000 0 -10000 0 0
FANCC 0.013 0 -10000 0 -10000 0 0
NBN 0.013 0 -10000 0 -10000 0 0
FANCA -0.12 0.15 -10000 0 -0.29 124 124
DNA repair 0.014 0.094 -10000 0 -10000 0 0
BRCA1/BARD1/ubiquitin 0.001 0.1 -10000 0 -0.62 7 7
BARD1/DNA-PK 0.02 0.08 -10000 0 -0.49 7 7
FANCL 0.013 0 -10000 0 -10000 0 0
mRNA polyadenylation -0.003 0.097 0.62 7 -10000 0 7
BRCA1/BARD1/CTIP/M/R/N Complex 0.027 0.06 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.014 0.083 -10000 0 -0.54 7 7
BRCA1/BARD1/P53 0.018 0.081 -10000 0 -0.49 7 7
BARD1/CSTF1/BRCA1 -0.014 0.083 -10000 0 -0.54 7 7
BRCA1/BACH1 0.009 0.031 -10000 0 -10000 0 0
BARD1 -0.008 0.13 -10000 0 -0.81 7 7
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.014 0.083 -10000 0 -0.54 7 7
BRCA1/BARD1/UbcH7 -0.014 0.083 -10000 0 -0.54 7 7
BRCA1/BARD1/RAD51/PCNA 0.002 0.094 -10000 0 -0.49 7 7
BARD1/DNA-PK/P53 -0.011 0.07 -10000 0 -0.46 7 7
BRCA1/BARD1/Ubiquitin 0.001 0.1 -10000 0 -0.62 7 7
BRCA1/BARD1/CTIP 0.016 0.086 -10000 0 -0.49 8 8
FA complex -0.004 0.049 -10000 0 -10000 0 0
BARD1/EWS 0.003 0.098 -10000 0 -0.62 7 7
RBBP8 0.019 0.038 -10000 0 -0.62 1 1
TP53 0.013 0 -10000 0 -10000 0 0
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.013 0.075 0.48 7 -10000 0 7
BRCA1/BARD1 -0.019 0.076 -10000 0 -0.46 7 7
CSTF1 0.013 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.006 0.098 -10000 0 -0.63 7 7
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.02 0.094 -10000 0 -0.29 31 31
RAD50 0.01 0.048 -10000 0 -0.81 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.001 0.1 -10000 0 -0.62 7 7
EWSR1 0.013 0 -10000 0 -10000 0 0
Nectin adhesion pathway

Figure S83.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S83.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.016 0.15 -9999 0 -0.81 10 10
alphaV beta3 Integrin -0.016 0.14 -9999 0 -0.62 14 14
PTK2 -0.018 0.088 -9999 0 -0.66 4 4
positive regulation of JNK cascade -0.007 0.042 -9999 0 -0.35 4 4
CDC42/GDP 0.046 0.067 -9999 0 -0.48 4 4
Rac1/GDP 0.047 0.066 -9999 0 -0.48 4 4
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.013 0 -9999 0 -10000 0 0
CDC42/GTP -0.008 0.052 -9999 0 -0.44 4 4
nectin-3/I-afadin 0.01 0.074 -9999 0 -0.62 4 4
RAPGEF1 0.04 0.075 -9999 0 -0.55 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.035 0.086 -9999 0 -0.65 4 4
PDGFB-D/PDGFRB -0.016 0.15 -9999 0 -0.81 10 10
TLN1 0.028 0.03 -9999 0 -10000 0 0
Rap1/GTP -0.007 0.045 -9999 0 -0.38 4 4
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.024 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.01 0.074 -9999 0 -0.62 4 4
PVR 0.011 0.018 -9999 0 -0.29 1 1
Necl-5(dimer) 0.011 0.018 -9999 0 -0.29 1 1
mol:GDP 0.044 0.081 -9999 0 -0.61 4 4
MLLT4 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.013 0 -9999 0 -10000 0 0
PI3K -0.022 0.097 -9999 0 -0.45 14 14
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.018 0.012 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.007 0.044 -9999 0 -0.37 4 4
PVRL1 0.011 0.018 -9999 0 -0.29 1 1
PVRL3 0.001 0.096 -9999 0 -0.81 4 4
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.013 0 -9999 0 -10000 0 0
CDH1 -0.055 0.23 -9999 0 -0.81 24 24
CLDN1 -0.085 0.14 -9999 0 -0.29 93 93
JAM-A/CLDN1 -0.024 0.092 -9999 0 -0.52 4 4
SRC -0.014 0.089 -9999 0 -0.74 4 4
ITGB3 -0.033 0.18 -9999 0 -0.65 20 20
nectin-1(dimer)/I-afadin/I-afadin 0.018 0.012 -9999 0 -10000 0 0
FARP2 0.038 0.079 -9999 0 -0.6 4 4
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.008 0.063 -9999 0 -0.54 4 4
nectin-1/I-afadin 0.018 0.012 -9999 0 -10000 0 0
nectin-2/I-afadin 0.019 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.008 0.063 -9999 0 -0.54 4 4
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.013 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.007 0.042 -9999 0 -0.35 4 4
alphaV/beta3 Integrin/Talin 0.015 0.11 -9999 0 -0.45 14 14
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.019 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.019 0 -9999 0 -10000 0 0
PIP5K1C 0.022 0.032 -9999 0 -0.25 4 4
VAV2 0.038 0.08 -9999 0 -0.61 4 4
RAP1/GDP -0.008 0.053 -9999 0 -0.44 4 4
ITGAV 0.013 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.007 0.062 -9999 0 -0.54 4 4
nectin-3(dimer)/I-afadin/I-afadin 0.01 0.074 -9999 0 -0.62 4 4
Rac1/GTP -0.008 0.054 -9999 0 -0.46 4 4
PTPRM 0.015 0.036 -9999 0 -0.29 4 4
E-cadherin/beta catenin/alpha catenin -0.036 0.12 -9999 0 -0.43 24 24
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.031 0.059 -10000 0 -10000 0 0
UGCG 0.014 0.057 -10000 0 -0.64 2 2
AKT1/mTOR/p70S6K/Hsp90/TERT 0.038 0.063 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.017 0.056 -10000 0 -0.63 2 2
mol:DAG 0.001 0.002 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.009 0.034 -10000 0 -10000 0 0
FRAP1 0.053 0.066 -10000 0 -10000 0 0
FOXO3 0.057 0.062 -10000 0 -10000 0 0
AKT1 0.052 0.065 -10000 0 -10000 0 0
GAB2 0.013 0.001 -10000 0 -10000 0 0
SMPD1 0.019 0.017 -10000 0 -10000 0 0
SGMS1 0.019 0.017 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.021 0.003 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation 0.034 0.044 -10000 0 -0.31 2 2
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.024 0.003 -10000 0 -10000 0 0
RPS6KB1 0.005 0.041 -10000 0 -10000 0 0
mol:sphingomyelin 0.001 0.002 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.001 -10000 0 -10000 0 0
JAK3 -0.045 0.12 -10000 0 -0.29 58 58
PIK3R1 0.015 0.001 -10000 0 -10000 0 0
JAK1 0.015 0.001 -10000 0 -10000 0 0
NFKB1 0.013 0 -10000 0 -10000 0 0
MYC 0.055 0.066 -10000 0 -10000 0 0
MYB -0.055 0.13 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.044 0.065 -10000 0 -0.36 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.019 0.038 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.044 0.064 -10000 0 -0.35 1 1
Rac1/GDP 0.027 0.004 -10000 0 -10000 0 0
T cell proliferation 0.049 0.061 -10000 0 -10000 0 0
SHC1 0.013 0.001 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.003 0.014 -10000 0 -0.028 67 67
PRKCZ 0.05 0.062 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.006 0.043 -10000 0 -10000 0 0
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.024 0.064 -10000 0 -0.36 1 1
HSP90AA1 0.013 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.017 0.091 -10000 0 -0.29 29 29
IL2RB -0.018 0.095 -10000 0 -0.29 32 32
TERT -0.037 0.1 -10000 0 -10000 0 0
E2F1 -0.039 0.094 -10000 0 -0.25 27 27
SOS1 0.013 0.001 -10000 0 -10000 0 0
RPS6 0.013 0 -10000 0 -10000 0 0
mol:cAMP 0.001 0.007 0.014 67 -10000 0 67
PTPN11 0.013 0.002 -10000 0 -10000 0 0
IL2RG 0.006 0.053 -10000 0 -0.29 9 9
actin cytoskeleton organization 0.049 0.061 -10000 0 -10000 0 0
GRB2 0.013 0.001 -10000 0 -10000 0 0
IL2 0.006 0.018 -10000 0 -0.29 1 1
PIK3CA 0.015 0.001 -10000 0 -10000 0 0
Rac1/GTP 0.029 0.013 -10000 0 -10000 0 0
LCK 0.008 0.047 -10000 0 -0.29 7 7
BCL2 0.057 0.058 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

Figure S85.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of p