PARADIGM pathway analysis of mRNASeq expression and copy number data
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1JM288W
Overview
Introduction

PAthway Representation and Analysis by Direct Inference on Graphical Models (PARADIGM) predicts the activity of a diverse set of molecular concepts such as genes, complexes, and processes. The predicted activities are called Inferred Pathway Levels (IPLs) and are derived from a probabilistic belief propagation strategy that incorporates multimodal data such as copy number and gene expression estimates with a concept's pathway context.

Summary

There were 25 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
Nephrin/Neph1 signaling in the kidney podocyte 90
FOXA2 and FOXA3 transcription factor networks 66
Angiopoietin receptor Tie2-mediated signaling 63
EGFR-dependent Endothelin signaling events 61
PDGFR-alpha signaling pathway 37
Thromboxane A2 receptor signaling 32
Glypican 1 network 27
Signaling mediated by p38-alpha and p38-beta 25
BMP receptor signaling 21
Endothelins 21
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 198 . 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 ( 198 ).

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 0.4545 90 3079 34 -0.48 0.027 1000 -1000 -0.034 -1000
FOXA2 and FOXA3 transcription factor networks 0.3333 66 3062 46 -1.1 0.03 1000 -1000 -0.076 -1000
Angiopoietin receptor Tie2-mediated signaling 0.3182 63 5567 88 -0.85 0.089 1000 -1000 -0.062 -1000
EGFR-dependent Endothelin signaling events 0.3081 61 1294 21 -0.58 0.037 1000 -1000 -0.046 -1000
PDGFR-alpha signaling pathway 0.1869 37 1657 44 -0.24 0.036 1000 -1000 -0.04 -1000
Thromboxane A2 receptor signaling 0.1616 32 3447 105 -0.58 0.093 1000 -1000 -0.044 -1000
Glypican 1 network 0.1364 27 1325 48 -0.35 0.05 1000 -1000 -0.037 -1000
Signaling mediated by p38-alpha and p38-beta 0.1263 25 1130 44 -0.14 0.026 1000 -1000 -0.031 -1000
BMP receptor signaling 0.1061 21 1781 81 -0.38 0.053 1000 -1000 -0.057 -1000
Endothelins 0.1061 21 2055 96 -0.6 0.038 1000 -1000 -0.055 -1000
Arf6 signaling events 0.1010 20 1274 62 -0.58 0.058 1000 -1000 -0.04 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0960 19 2440 125 -0.13 0.06 1000 -1000 -0.06 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0960 19 1550 78 -0.24 0.052 1000 -1000 -0.046 -1000
Integrins in angiogenesis 0.0808 16 1423 84 -0.43 0.059 1000 -1000 -0.059 -1000
Signaling events mediated by PTP1B 0.0758 15 1183 76 -0.58 0.082 1000 -1000 -0.039 -1000
IL4-mediated signaling events 0.0758 15 1373 91 -0.82 0.43 1000 -1000 -0.12 -1000
amb2 Integrin signaling 0.0758 15 1243 82 -0.4 0.036 1000 -1000 -0.042 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0758 15 1065 68 -0.47 0.078 1000 -1000 -0.085 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0758 15 1816 120 -0.25 0.13 1000 -1000 -0.056 -1000
Ceramide signaling pathway 0.0707 14 1091 76 -0.58 0.2 1000 -1000 -0.045 -1000
S1P1 pathway 0.0707 14 514 36 -0.13 0.026 1000 -1000 -0.053 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0657 13 1015 74 -0.58 0.063 1000 -1000 -0.067 -1000
FoxO family signaling 0.0606 12 776 64 -0.89 0.062 1000 -1000 -0.061 -1000
Ephrin A reverse signaling 0.0505 10 70 7 -0.031 0 1000 -1000 -0.018 -1000
Glucocorticoid receptor regulatory network 0.0505 10 1173 114 -0.54 0.13 1000 -1000 -0.052 -1000
Signaling events mediated by the Hedgehog family 0.0455 9 517 52 -0.055 0.039 1000 -1000 -0.042 -1000
Plasma membrane estrogen receptor signaling 0.0455 9 844 86 -0.12 0.047 1000 -1000 -0.061 -1000
E-cadherin signaling events 0.0455 9 45 5 -0.027 0.026 1000 -1000 0 -1000
LPA4-mediated signaling events 0.0404 8 105 12 -0.15 0.007 1000 -1000 -0.027 -1000
TCR signaling in naïve CD8+ T cells 0.0404 8 793 93 -0.23 0.11 1000 -1000 -0.054 -1000
Nongenotropic Androgen signaling 0.0404 8 456 52 -0.11 0.049 1000 -1000 -0.047 -1000
IL6-mediated signaling events 0.0404 8 610 75 -0.21 0.04 1000 -1000 -0.047 -1000
E-cadherin signaling in keratinocytes 0.0404 8 356 43 -0.21 0.041 1000 -1000 -0.042 -1000
Caspase cascade in apoptosis 0.0354 7 573 74 -0.42 0.065 1000 -1000 -0.044 -1000
Coregulation of Androgen receptor activity 0.0354 7 544 76 -0.66 0.049 1000 -1000 -0.031 -1000
p75(NTR)-mediated signaling 0.0354 7 988 125 -0.38 0.071 1000 -1000 -0.077 -1000
Signaling events regulated by Ret tyrosine kinase 0.0354 7 631 82 -0.062 0.028 1000 -1000 -0.064 -1000
S1P3 pathway 0.0354 7 312 42 -0.11 0.037 1000 -1000 -0.037 -1000
Regulation of nuclear SMAD2/3 signaling 0.0303 6 861 136 -0.47 0.092 1000 -1000 -0.043 -1000
ErbB4 signaling events 0.0303 6 477 69 -0.28 0.089 1000 -1000 -0.056 -1000
Noncanonical Wnt signaling pathway 0.0303 6 171 26 -0.17 0.027 1000 -1000 -0.057 -1000
Presenilin action in Notch and Wnt signaling 0.0303 6 385 61 -0.14 0.079 1000 -1000 -0.048 -1000
Syndecan-3-mediated signaling events 0.0303 6 225 35 -0.1 0.071 1000 -1000 -0.039 -1000
EPHB forward signaling 0.0303 6 516 85 -0.12 0.073 1000 -1000 -0.074 -1000
Calcium signaling in the CD4+ TCR pathway 0.0303 6 202 31 -0.094 0.027 1000 -1000 -0.045 -1000
IL27-mediated signaling events 0.0303 6 334 51 -0.97 0.24 1000 -1000 -0.054 -1000
E-cadherin signaling in the nascent adherens junction 0.0303 6 506 76 -0.03 0.047 1000 -1000 -0.06 -1000
IL23-mediated signaling events 0.0303 6 417 60 -0.066 0.046 1000 -1000 -0.076 -1000
PDGFR-beta signaling pathway 0.0303 6 601 97 -0.037 0.056 1000 -1000 -0.063 -1000
Syndecan-1-mediated signaling events 0.0253 5 173 34 -0.035 0.027 1000 -1000 -0.047 -1000
HIF-1-alpha transcription factor network 0.0253 5 417 76 -0.09 0.1 1000 -1000 -0.068 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0253 5 492 85 -0.11 0.1 1000 -1000 -0.054 -1000
IFN-gamma pathway 0.0253 5 347 68 -0.31 0.064 1000 -1000 -0.061 -1000
Reelin signaling pathway 0.0253 5 334 56 -0.11 0.067 1000 -1000 -0.043 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0253 5 305 52 -0.24 0.08 1000 -1000 -0.042 -1000
TCGA08_p53 0.0253 5 38 7 -0.032 0.028 1000 -1000 -0.011 -1000
Effects of Botulinum toxin 0.0253 5 140 26 -0.15 0.048 1000 -1000 -0.015 -1000
TCGA08_rtk_signaling 0.0253 5 146 26 -0.19 0.063 1000 -1000 -0.013 -1000
Regulation of Telomerase 0.0253 5 581 102 -0.58 0.069 1000 -1000 -0.054 -1000
Syndecan-4-mediated signaling events 0.0253 5 362 67 -0.37 0.099 1000 -1000 -0.046 -1000
Regulation of Androgen receptor activity 0.0253 5 383 70 -0.77 0.042 1000 -1000 -0.053 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0202 4 139 28 -0.11 0.044 1000 -1000 -0.025 -1000
Osteopontin-mediated events 0.0202 4 175 38 -0.07 0.055 1000 -1000 -0.049 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0202 4 231 54 -0.048 0.042 1000 -1000 -0.054 -1000
Cellular roles of Anthrax toxin 0.0202 4 167 39 -0.14 0.035 1000 -1000 -0.027 -1000
ceramide signaling pathway 0.0202 4 234 49 0 0.043 1000 -1000 -0.049 -1000
Signaling mediated by p38-gamma and p38-delta 0.0202 4 61 15 -0.009 0.027 1000 -1000 -0.037 -1000
Regulation of p38-alpha and p38-beta 0.0202 4 235 54 -0.13 0.064 1000 -1000 -0.051 -1000
BCR signaling pathway 0.0202 4 416 99 -0.05 0.058 1000 -1000 -0.058 -1000
Visual signal transduction: Rods 0.0202 4 237 52 -0.14 0.051 1000 -1000 -0.052 -1000
Signaling events mediated by PRL 0.0202 4 157 34 -0.041 0.039 1000 -1000 -0.044 -1000
Ras signaling in the CD4+ TCR pathway 0.0202 4 72 17 -0.01 0.041 1000 -1000 -0.035 -1000
Syndecan-2-mediated signaling events 0.0152 3 249 69 -0.4 0.053 1000 -1000 -0.043 -1000
Fc-epsilon receptor I signaling in mast cells 0.0152 3 358 97 -0.07 0.049 1000 -1000 -0.064 -1000
PLK1 signaling events 0.0152 3 301 85 -0.005 0.053 1000 -1000 -0.032 -1000
S1P5 pathway 0.0152 3 58 17 -0.014 0.026 1000 -1000 -0.023 -1000
Ephrin B reverse signaling 0.0152 3 178 48 -0.038 0.039 1000 -1000 -0.04 -1000
Canonical Wnt signaling pathway 0.0152 3 178 51 -0.14 0.07 1000 -1000 -0.049 -1000
Wnt signaling 0.0152 3 27 7 -0.007 0.027 1000 -1000 -0.024 -1000
LPA receptor mediated events 0.0152 3 360 102 -0.079 0.056 1000 -1000 -0.055 -1000
Arf6 trafficking events 0.0152 3 270 71 -0.26 0.045 1000 -1000 -0.036 -1000
IGF1 pathway 0.0152 3 173 57 -0.021 0.062 1000 -1000 -0.058 -1000
Class IB PI3K non-lipid kinase events 0.0152 3 9 3 -0.015 0.015 1000 -1000 -0.003 -1000
S1P4 pathway 0.0152 3 82 25 -0.007 0.052 1000 -1000 -0.036 -1000
ErbB2/ErbB3 signaling events 0.0101 2 176 65 -0.056 0.049 1000 -1000 -0.063 -1000
BARD1 signaling events 0.0101 2 144 57 -0.045 0.056 1000 -1000 -0.05 -1000
EPO signaling pathway 0.0101 2 111 55 -0.01 0.073 1000 -1000 -0.052 -1000
mTOR signaling pathway 0.0101 2 116 53 -0.016 0.045 1000 -1000 -0.042 -1000
Nectin adhesion pathway 0.0101 2 150 63 -0.027 0.053 1000 -1000 -0.051 -1000
IL1-mediated signaling events 0.0101 2 177 62 -0.099 0.071 1000 -1000 -0.06 -1000
HIF-2-alpha transcription factor network 0.0101 2 107 43 -0.17 0.091 1000 -1000 -0.051 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0101 2 233 83 -0.24 0.047 1000 -1000 -0.045 -1000
Class I PI3K signaling events 0.0101 2 146 73 -0.018 0.045 1000 -1000 -0.055 -1000
Aurora B signaling 0.0101 2 164 67 -0.24 0.053 1000 -1000 -0.047 -1000
Signaling events mediated by HDAC Class II 0.0051 1 97 75 -0.092 0.066 1000 -1000 -0.036 -1000
IL12-mediated signaling events 0.0051 1 150 87 -0.18 0.061 1000 -1000 -0.09 -1000
Hedgehog signaling events mediated by Gli proteins 0.0051 1 110 65 -0.007 0.065 1000 -1000 -0.052 -1000
Arf6 downstream pathway 0.0051 1 78 43 -0.042 0.043 1000 -1000 -0.031 -1000
Insulin-mediated glucose transport 0.0051 1 34 32 -0.017 0.047 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 0.0051 1 70 68 -0.019 0.054 1000 -1000 -0.043 -1000
FAS signaling pathway (CD95) 0.0051 1 91 47 -0.1 0.039 1000 -1000 -0.036 -1000
Retinoic acid receptors-mediated signaling 0.0051 1 95 58 -0.029 0.057 1000 -1000 -0.048 -1000
IL2 signaling events mediated by PI3K 0.0051 1 89 58 -0.015 0.06 1000 -1000 -0.052 -1000
TCGA08_retinoblastoma 0.0051 1 8 8 -0.048 0.031 1000 -1000 -0.004 -1000
Insulin Pathway 0.0051 1 120 74 -0.017 0.07 1000 -1000 -0.055 -1000
VEGFR1 specific signals 0.0051 1 88 56 -0.014 0.059 1000 -1000 -0.058 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0051 1 50 33 -0.048 0.064 1000 -1000 -0.025 -1000
FOXM1 transcription factor network 0.0051 1 91 51 -0.078 0.055 1000 -1000 -0.1 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 16 23 -0.013 0.046 1000 -1000 -0.043 -1000
Canonical NF-kappaB pathway 0.0000 0 7 39 0 0.064 1000 -1000 -0.041 -1000
PLK2 and PLK4 events 0.0000 0 0 3 0.01 0.025 1000 -1000 -0.015 -1000
Visual signal transduction: Cones 0.0000 0 24 38 -0.015 0.053 1000 -1000 -0.021 -1000
Circadian rhythm pathway 0.0000 0 5 22 -0.009 0.056 1000 -1000 -0.04 -1000
JNK signaling in the CD4+ TCR pathway 0.0000 0 16 17 0.011 0.043 1000 -1000 -0.037 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0.026 0.038 1000 -1000 0.002 -1000
Aurora A signaling 0.0000 0 16 60 -0.011 0.06 1000 -1000 -0.028 -1000
Aurora C signaling 0.0000 0 0 7 -0.015 0.042 1000 -1000 -0.018 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0000 0 4 37 -0.007 0.062 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class III 0.0000 0 11 40 -0.047 0.048 1000 -1000 -0.023 -1000
TRAIL signaling pathway 0.0000 0 11 48 0 0.069 1000 -1000 -0.047 -1000
Signaling events mediated by HDAC Class I 0.0000 0 90 104 -0.092 0.065 1000 -1000 -0.039 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 0 36 -0.053 0.055 1000 -1000 -0.047 -1000
Atypical NF-kappaB pathway 0.0000 0 8 31 0 0.039 1000 -1000 -0.031 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0000 0 36 45 0.001 0.074 1000 -1000 -0.056 -1000
Glypican 2 network 0.0000 0 0 4 -0.002 0.003 1000 -1000 -0.002 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 1 27 0 0.06 1000 -1000 -0.043 -1000
IL2 signaling events mediated by STAT5 0.0000 0 8 22 0.008 0.04 1000 -1000 -0.046 -1000
Rapid glucocorticoid signaling 0.0000 0 4 20 -0.003 0.033 1000 -1000 -0.008 -1000
p38 MAPK signaling pathway 0.0000 0 29 44 0 0.05 1000 -1000 -0.036 -1000
Arf1 pathway 0.0000 0 16 54 -0.001 0.05 1000 -1000 -0.023 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.073 1000 -1000 0 -1000
Total NA 1007 64954 7203 -24 7.8 131000 -131000 -5.8 -131000
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.39 0.29 0.57 135 -10000 0 135
KIRREL -0.11 0.2 -10000 0 -0.7 19 19
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.39 0.29 -10000 0 -0.57 135 135
PLCG1 0.026 0.006 -10000 0 -10000 0 0
ARRB2 0.025 0.01 -10000 0 -10000 0 0
WASL 0.022 0.011 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.41 0.31 -10000 0 -0.56 148 148
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.34 0.26 -10000 0 -0.49 134 134
FYN -0.4 0.28 0.26 1 -0.53 148 149
mol:Ca2+ -0.41 0.31 -10000 0 -0.56 144 144
mol:DAG -0.41 0.31 -10000 0 -0.57 144 144
NPHS2 -0.32 0.33 -10000 0 -0.71 80 80
mol:IP3 -0.41 0.31 -10000 0 -0.57 144 144
regulation of endocytosis -0.37 0.28 -10000 0 -0.51 146 146
Nephrin/NEPH1/podocin/Cholesterol -0.42 0.31 -10000 0 -0.56 148 148
establishment of cell polarity -0.39 0.29 -10000 0 -0.57 135 135
Nephrin/NEPH1/podocin/NCK1-2 -0.38 0.3 -10000 0 -0.53 147 147
Nephrin/NEPH1/beta Arrestin2 -0.38 0.28 -10000 0 -0.52 146 146
NPHS1 -0.47 0.32 -10000 0 -0.69 130 130
Nephrin/NEPH1/podocin -0.4 0.29 -10000 0 -0.54 148 148
TJP1 0.027 0.004 -10000 0 -10000 0 0
NCK1 0.026 0.005 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.41 0.31 -10000 0 -0.57 144 144
CD2AP 0.026 0.007 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.41 0.31 -10000 0 -0.57 144 144
GRB2 0.025 0.007 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.48 0.31 0.28 1 -0.6 157 158
cytoskeleton organization -0.42 0.31 -10000 0 -0.6 135 135
Nephrin/NEPH1 -0.29 0.22 -10000 0 -0.43 135 135
Nephrin/NEPH1/ZO-1 -0.32 0.25 -10000 0 -0.48 131 131
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.51 0.38 -10000 0 -0.91 80 80
PCK1 -1.1 0.66 -10000 0 -1.5 140 140
HNF4A -0.6 0.51 -10000 0 -1.2 76 76
KCNJ11 -0.54 0.38 -10000 0 -0.97 74 74
AKT1 -0.28 0.16 -10000 0 -0.46 51 51
response to starvation -0.004 0.013 -10000 0 -10000 0 0
DLK1 -0.55 0.4 -10000 0 -1 75 75
NKX2-1 -0.15 0.15 -10000 0 -0.55 3 3
ACADM -0.52 0.38 -10000 0 -0.91 80 80
TAT -0.46 0.22 -10000 0 -0.65 87 87
CEBPB -0.043 0.047 -10000 0 -10000 0 0
CEBPA -0.05 0.066 -10000 0 -0.45 2 2
TTR -0.78 0.42 -10000 0 -1 119 119
PKLR -0.65 0.54 -10000 0 -1.2 84 84
APOA1 -0.68 0.57 -10000 0 -1.3 77 77
CPT1C -0.53 0.38 -10000 0 -0.94 77 77
ALAS1 -0.23 0.14 -10000 0 -0.64 2 2
TFRC -0.61 0.28 -10000 0 -0.76 132 132
FOXF1 0.018 0.069 -10000 0 -0.66 2 2
NF1 0.03 0.007 -10000 0 -10000 0 0
HNF1A (dimer) -0.063 0.1 -10000 0 -0.29 14 14
CPT1A -0.52 0.37 -10000 0 -0.91 79 79
HMGCS1 -0.52 0.38 -10000 0 -0.91 80 80
NR3C1 0.016 0.052 -10000 0 -10000 0 0
CPT1B -0.51 0.38 -10000 0 -0.92 79 79
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.027 0.007 -10000 0 -10000 0 0
GCK -0.49 0.38 -10000 0 -0.92 73 73
CREB1 -0.098 0.077 -10000 0 -0.2 38 38
IGFBP1 -0.29 0.37 -10000 0 -1.3 20 20
PDX1 -0.27 0.2 -10000 0 -0.58 36 36
UCP2 -0.52 0.38 -10000 0 -0.92 79 79
ALDOB -1.1 0.36 -10000 0 -1.2 188 188
AFP -0.45 0.32 -10000 0 -0.55 132 132
BDH1 -0.52 0.38 -10000 0 -0.91 80 80
HADH -0.54 0.38 -10000 0 -0.95 77 77
F2 -0.61 0.48 -10000 0 -1.1 78 78
HNF1A -0.062 0.1 -10000 0 -0.29 14 14
G6PC -1.1 0.57 -10000 0 -1.4 139 139
SLC2A2 -0.5 0.57 -10000 0 -1.6 38 38
INS -0.007 0.053 0.21 2 -10000 0 2
FOXA1 -0.21 0.1 -10000 0 -0.26 145 145
FOXA3 -0.45 0.22 -10000 0 -0.48 178 178
FOXA2 -0.62 0.42 -10000 0 -1.1 78 78
ABCC8 -0.55 0.38 -10000 0 -0.97 75 75
ALB -1 0.34 -10000 0 -1.1 179 179
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 -0.52 0.52 -10000 0 -1 105 105
NCK1/PAK1/Dok-R -0.24 0.21 -10000 0 -0.43 105 105
NCK1/Dok-R -0.64 0.68 -10000 0 -1.2 105 105
PIK3CA 0.028 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.075 0.11 0.24 60 -10000 0 60
RELA 0.027 0.002 -10000 0 -10000 0 0
SHC1 0.025 0.005 -10000 0 -10000 0 0
Rac/GDP 0.016 0.008 -10000 0 -10000 0 0
F2 0.089 0.12 0.26 60 -10000 0 60
TNIP2 0.026 0.005 -10000 0 -10000 0 0
NF kappa B/RelA -0.58 0.63 -10000 0 -1.1 104 104
FN1 0.02 0.025 -10000 0 -10000 0 0
PLD2 -0.68 0.71 -10000 0 -1.3 105 105
PTPN11 0.026 0.006 -10000 0 -10000 0 0
GRB14 -0.011 0.15 -10000 0 -0.61 12 12
ELK1 -0.58 0.6 -10000 0 -1.1 105 105
GRB7 0.025 0.007 -10000 0 -10000 0 0
PAK1 0.027 0.003 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.62 0.67 -10000 0 -1.2 105 105
CDKN1A -0.34 0.35 -10000 0 -0.66 103 103
ITGA5 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.64 0.69 -10000 0 -1.2 105 105
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:NO -0.34 0.37 -10000 0 -0.68 105 105
PLG -0.85 0.68 -10000 0 -1.4 105 105
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.48 0.49 -10000 0 -0.92 105 105
GRB2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.025 0.004 -10000 0 -10000 0 0
ANGPT2 -0.26 0.3 -10000 0 -0.72 44 44
BMX -0.69 0.71 -10000 0 -1.3 105 105
ANGPT1 -0.43 0.62 -10000 0 -1.4 60 60
tube development -0.4 0.4 -10000 0 -0.76 105 105
ANGPT4 0.012 0.023 -10000 0 -10000 0 0
response to hypoxia -0.036 0.034 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.73 0.75 -10000 0 -1.4 105 105
alpha5/beta1 Integrin 0.038 0.01 -10000 0 -10000 0 0
FGF2 0.027 0.006 -10000 0 -10000 0 0
STAT5A (dimer) -0.45 0.47 -10000 0 -0.88 104 104
mol:L-citrulline -0.34 0.37 -10000 0 -0.68 105 105
AGTR1 -0.19 0.31 -10000 0 -0.65 62 62
MAPK14 -0.7 0.7 -10000 0 -1.3 105 105
Tie2/SHP2 -0.56 0.62 -10000 0 -1.2 90 90
TEK -0.62 0.69 -10000 0 -1.4 90 90
RPS6KB1 -0.48 0.5 -10000 0 -0.94 105 105
Angiotensin II/AT1 -0.14 0.24 -10000 0 -0.49 62 62
Tie2/Ang1/GRB2 -0.7 0.75 -10000 0 -1.4 105 105
MAPK3 -0.6 0.62 -10000 0 -1.2 104 104
MAPK1 -0.61 0.62 -10000 0 -1.2 105 105
Tie2/Ang1/GRB7 -0.7 0.75 -10000 0 -1.4 105 105
NFKB1 0.026 0.006 -10000 0 -10000 0 0
MAPK8 -0.69 0.72 -10000 0 -1.3 105 105
PI3K -0.61 0.63 -10000 0 -1.2 105 105
FES -0.68 0.7 -10000 0 -1.3 106 106
Crk/Dok-R -0.64 0.68 -10000 0 -1.2 104 104
Tie2/Ang1/ABIN2 -0.71 0.76 -10000 0 -1.4 105 105
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.45 0.46 -10000 0 -0.87 105 105
STAT5A 0.026 0.007 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.49 0.5 -10000 0 -0.95 105 105
Tie2/Ang2 -0.58 0.59 -10000 0 -1.1 105 105
Tie2/Ang1 -0.78 0.83 -10000 0 -1.5 105 105
FOXO1 -0.45 0.46 -10000 0 -0.88 105 105
ELF1 -0.038 0.072 -10000 0 -10000 0 0
ELF2 -0.69 0.72 -10000 0 -1.3 105 105
mol:Choline -0.63 0.65 -10000 0 -1.2 105 105
cell migration -0.13 0.12 -10000 0 -0.24 104 104
FYN -0.47 0.46 -10000 0 -0.89 105 105
DOK2 0.017 0.054 -10000 0 -0.66 1 1
negative regulation of cell cycle -0.31 0.32 -10000 0 -0.6 105 105
ETS1 -0.063 0.12 -10000 0 -0.25 41 41
PXN -0.39 0.4 -10000 0 -0.76 104 104
ITGB1 0.027 0.005 -10000 0 -10000 0 0
NOS3 -0.4 0.43 -10000 0 -0.79 105 105
RAC1 0.022 0.011 -10000 0 -10000 0 0
TNF -0.073 0.14 -10000 0 -0.27 57 57
MAPKKK cascade -0.63 0.65 -10000 0 -1.2 105 105
RASA1 0.027 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.71 0.76 -10000 0 -1.4 105 105
NCK1 0.026 0.005 -10000 0 -10000 0 0
vasculogenesis -0.3 0.33 -10000 0 -0.61 105 105
mol:Phosphatidic acid -0.63 0.65 -10000 0 -1.2 105 105
mol:Angiotensin II 0 0.001 -10000 0 -10000 0 0
mol:NADP -0.34 0.37 -10000 0 -0.68 105 105
Rac1/GTP -0.44 0.45 -10000 0 -0.85 105 105
MMP2 -0.68 0.71 -10000 0 -1.3 105 105
EGFR-dependent Endothelin signaling events

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
HRAS 0.027 0.003 -9999 0 -10000 0 0
EGFR 0.022 0.011 -9999 0 -10000 0 0
EGF/EGFR -0.29 0.15 -9999 0 -0.38 135 135
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.28 0.15 -9999 0 -0.38 124 124
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.005 0.14 -9999 0 -0.66 9 9
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.58 0.21 -9999 0 -0.65 176 176
EGF/EGFR dimer/SHC -0.33 0.16 -9999 0 -0.39 169 169
mol:GDP -0.28 0.15 -9999 0 -0.37 124 124
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.025 0.009 -9999 0 -10000 0 0
GRB2/SOS1 0.037 0.012 -9999 0 -10000 0 0
HRAS/GTP -0.26 0.14 -9999 0 -0.35 124 124
SHC1 0.026 0.005 -9999 0 -10000 0 0
HRAS/GDP -0.26 0.14 -9999 0 -0.36 124 124
FRAP1 -0.27 0.13 -9999 0 -0.36 124 124
EGF/EGFR dimer -0.39 0.17 -9999 0 -0.44 176 176
SOS1 0.027 0.004 -9999 0 -10000 0 0
GRB2 0.025 0.007 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 0.012 0.11 -9999 0 -0.5 9 9
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.2 0.32 -10000 0 -0.66 63 63
PDGF/PDGFRA/CRKL -0.13 0.24 -10000 0 -0.49 63 63
positive regulation of JUN kinase activity -0.071 0.2 -10000 0 -0.39 54 54
CRKL 0.025 0.008 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.13 0.24 -10000 0 -0.48 63 63
AP1 -0.24 0.4 -10000 0 -1.1 30 30
mol:IP3 -0.15 0.23 -10000 0 -0.48 63 63
PLCG1 -0.15 0.24 -10000 0 -0.48 63 63
PDGF/PDGFRA/alphaV Integrin -0.13 0.24 -10000 0 -0.48 63 63
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.15 0.23 -10000 0 -0.48 63 63
CAV3 -0.009 0.018 -10000 0 -10000 0 0
CAV1 0.021 0.013 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.07 0.2 -10000 0 -0.39 54 54
PDGF/PDGFRA/Shf -0.13 0.25 -10000 0 -0.49 63 63
FOS -0.24 0.39 0.32 1 -1.1 30 31
JUN -0.03 0.025 -10000 0 -10000 0 0
oligodendrocyte development -0.13 0.24 -10000 0 -0.48 63 63
GRB2 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
mol:DAG -0.15 0.23 -10000 0 -0.48 63 63
PDGF/PDGFRA -0.2 0.32 -10000 0 -0.66 63 63
actin cytoskeleton reorganization -0.13 0.24 -10000 0 -0.49 63 63
SRF 0.017 0.01 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
PI3K -0.094 0.22 -10000 0 -0.41 62 62
PDGF/PDGFRA/Crk/C3G -0.097 0.21 -10000 0 -0.41 62 62
JAK1 -0.15 0.23 -10000 0 -0.49 62 62
ELK1/SRF -0.11 0.18 -10000 0 -0.4 52 52
SHB 0.026 0.006 -10000 0 -10000 0 0
SHF 0.027 0.005 -10000 0 -10000 0 0
CSNK2A1 0.036 0.02 -10000 0 -10000 0 0
GO:0007205 -0.16 0.24 -10000 0 -0.5 63 63
SOS1 0.027 0.004 -10000 0 -10000 0 0
Ras protein signal transduction -0.071 0.2 -10000 0 -0.39 54 54
PDGF/PDGFRA/SHB -0.13 0.24 -10000 0 -0.49 63 63
PDGF/PDGFRA/Caveolin-1 -0.12 0.22 -10000 0 -0.43 63 63
ITGAV 0.027 0.003 -10000 0 -10000 0 0
ELK1 -0.15 0.21 -10000 0 -0.46 63 63
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk -0.13 0.24 -10000 0 -0.47 63 63
JAK-STAT cascade -0.15 0.23 -10000 0 -0.49 62 62
cell proliferation -0.13 0.24 -10000 0 -0.49 63 63
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.017 0.026 -10000 0 -10000 0 0
GNB1/GNG2 -0.092 0.089 -10000 0 -0.18 92 92
AKT1 -0.089 0.13 0.22 2 -0.31 16 18
EGF -0.58 0.21 -10000 0 -0.65 176 176
mol:TXA2 -0.001 0.001 -10000 0 -10000 0 0
FGR -0.019 0.085 -10000 0 -0.7 1 1
mol:Ca2+ -0.13 0.17 0.22 1 -0.3 94 95
LYN -0.019 0.077 -10000 0 -0.46 1 1
RhoA/GTP -0.054 0.068 -10000 0 -0.14 6 6
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.15 0.19 0.23 1 -0.34 94 95
GNG2 0.026 0.007 -10000 0 -10000 0 0
ARRB2 0.025 0.01 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.046 0.13 -10000 0 -0.54 7 7
G beta5/gamma2 -0.12 0.12 -10000 0 -0.24 91 91
PRKCH -0.15 0.19 -10000 0 -0.35 94 94
DNM1 0 0.043 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin3 0.008 0.021 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.025 0.007 -10000 0 -10000 0 0
G12 family/GTP -0.13 0.15 -10000 0 -0.3 66 66
ADRBK1 0.027 0.002 -10000 0 -10000 0 0
ADRBK2 0.025 0.008 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.032 0.011 -10000 0 -10000 0 0
mol:GDP 0.093 0.14 0.44 17 -10000 0 17
mol:NADP 0.008 0.096 -10000 0 -0.66 4 4
RAB11A 0.027 0.003 -10000 0 -10000 0 0
PRKG1 -0.13 0.28 -10000 0 -0.65 45 45
mol:IP3 -0.16 0.21 -10000 0 -0.37 94 94
cell morphogenesis 0.032 0.011 -10000 0 -10000 0 0
PLCB2 -0.22 0.27 -10000 0 -0.5 94 94
mol:cGMP -0.001 0.001 -10000 0 -10000 0 0
BLK -0.02 0.075 -10000 0 -0.46 1 1
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.024 0.077 -10000 0 -0.7 1 1
RHOA 0.026 0.005 -10000 0 -10000 0 0
PTGIR 0.02 0.069 -10000 0 -0.66 2 2
PRKCB1 -0.16 0.2 -10000 0 -0.37 94 94
GNAQ 0.026 0.007 -10000 0 -10000 0 0
mol:L-citrulline 0.008 0.096 -10000 0 -0.66 4 4
TXA2/TXA2-R family -0.23 0.28 -10000 0 -0.51 94 94
LCK -0.018 0.077 -10000 0 -0.46 1 1
TXA2/TP beta/beta Arrestin3/RAB11/GDP 0.005 0.097 -10000 0 -0.35 12 12
TXA2-R family/G12 family/GDP/G beta/gamma -0.017 0.13 -10000 0 -0.42 17 17
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.007 0.097 -10000 0 -0.34 13 13
MAPK14 -0.098 0.13 0.19 1 -0.23 75 76
TGM2/GTP -0.18 0.22 -10000 0 -0.42 79 79
MAPK11 -0.098 0.13 0.19 1 -0.22 92 93
ARHGEF1 -0.075 0.092 -10000 0 -0.18 60 60
GNAI2 0.026 0.006 -10000 0 -10000 0 0
JNK cascade -0.17 0.21 0.25 1 -0.38 94 95
RAB11/GDP 0.028 0.004 -10000 0 -10000 0 0
ICAM1 -0.12 0.16 0.21 1 -0.28 94 95
cAMP biosynthetic process -0.15 0.19 -10000 0 -0.35 80 80
Gq family/GTP/EBP50 -0.042 0.1 -10000 0 -0.3 7 7
actin cytoskeleton reorganization 0.032 0.011 -10000 0 -10000 0 0
SRC -0.019 0.069 -10000 0 -0.46 1 1
GNB5 0.027 0.004 -10000 0 -10000 0 0
GNB1 0.025 0.008 -10000 0 -10000 0 0
EGF/EGFR -0.11 0.082 0.25 1 -0.31 14 15
VCAM1 -0.12 0.16 0.21 1 -0.29 94 95
TP beta/Gq family/GDP/G beta5/gamma2 -0.046 0.13 -10000 0 -0.54 7 7
platelet activation -0.13 0.17 0.26 1 -0.3 92 93
PGI2/IP 0.014 0.052 -10000 0 -0.5 2 2
PRKACA 0.014 0.034 -10000 0 -0.32 2 2
Gq family/GDP/G beta5/gamma2 -0.041 0.12 -10000 0 -0.46 8 8
TXA2/TP beta/beta Arrestin2 0.007 0.039 -10000 0 -0.34 1 1
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.016 0.099 -10000 0 -0.38 13 13
mol:DAG -0.18 0.23 -10000 0 -0.42 95 95
EGFR 0.022 0.011 -10000 0 -10000 0 0
TXA2/TP alpha -0.21 0.25 -10000 0 -0.47 80 80
Gq family/GTP -0.051 0.12 -10000 0 -0.26 45 45
YES1 -0.017 0.078 -10000 0 -0.46 1 1
GNAI2/GTP -0.004 0.088 -10000 0 -0.32 12 12
PGD2/DP 0.018 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.025 0.007 -10000 0 -10000 0 0
FYN -0.018 0.078 -10000 0 -0.46 1 1
mol:NO 0.008 0.096 -10000 0 -0.66 4 4
GNA15 0.021 0.023 -10000 0 -10000 0 0
PGK/cGMP -0.072 0.19 -10000 0 -0.38 48 48
RhoA/GDP 0.027 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.021 0.095 -10000 0 -0.36 9 9
NOS3 0.008 0.097 -10000 0 -0.66 4 4
RAC1 0.022 0.011 -10000 0 -10000 0 0
PRKCA -0.15 0.19 0.3 1 -0.35 88 89
PRKCB -0.15 0.19 0.3 1 -0.35 84 85
PRKCE -0.16 0.2 -10000 0 -0.35 94 94
PRKCD -0.17 0.21 -10000 0 -0.38 94 94
PRKCG -0.17 0.21 -10000 0 -0.38 94 94
muscle contraction -0.21 0.26 -10000 0 -0.47 94 94
PRKCZ -0.15 0.19 0.23 1 -0.34 94 95
ARR3 -0.011 0.017 -10000 0 -10000 0 0
TXA2/TP beta 0.003 0.099 -10000 0 -0.35 12 12
PRKCQ -0.16 0.2 -10000 0 -0.36 95 95
MAPKKK cascade -0.19 0.24 -10000 0 -0.44 93 93
SELE -0.18 0.22 0.21 1 -0.41 94 95
TP beta/GNAI2/GDP/G beta/gamma 0.022 0.1 -10000 0 -0.35 12 12
ROCK1 0.025 0.007 -10000 0 -10000 0 0
GNA14 -0.11 0.27 -10000 0 -0.64 41 41
chemotaxis -0.27 0.32 -10000 0 -0.6 94 94
GNA12 0.022 0.011 -10000 0 -10000 0 0
GNA13 0.025 0.007 -10000 0 -10000 0 0
GNA11 0.015 0.088 -10000 0 -0.58 4 4
Rac1/GTP 0.016 0.008 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.05 0.017 -10000 0 -10000 0 0
fibroblast growth factor receptor signaling pathway 0.05 0.017 -10000 0 -10000 0 0
LAMA1 0.004 0.099 -10000 0 -0.66 4 4
PRNP 0.026 0.006 -10000 0 -10000 0 0
GPC1/SLIT2 -0.075 0.22 -10000 0 -0.48 43 43
SMAD2 0.016 0.021 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ 0.034 0.01 -10000 0 -10000 0 0
GPC1/Laminin alpha1 0.019 0.077 -10000 0 -0.49 4 4
TDGF1 -0.35 0.33 -10000 0 -0.65 105 105
CRIPTO/GPC1 -0.24 0.26 -10000 0 -0.49 105 105
APP/GPC1 0.036 0.013 -10000 0 -10000 0 0
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.22 0.21 -10000 0 -0.43 99 99
FLT1 0.02 0.069 -10000 0 -0.66 2 2
GPC1/TGFB/TGFBR1/TGFBR2 0.05 0.017 -10000 0 -10000 0 0
SERPINC1 -0.16 0.29 -10000 0 -0.65 51 51
FYN -0.22 0.21 -10000 0 -0.43 102 102
FGR -0.23 0.22 -10000 0 -0.43 102 102
positive regulation of MAPKKK cascade -0.23 0.24 0.5 2 -0.45 102 104
SLIT2 -0.12 0.28 -10000 0 -0.64 43 43
GPC1/NRG 0.029 0.066 -10000 0 -0.49 3 3
NRG1 0.015 0.085 -10000 0 -0.66 3 3
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.045 0.051 -10000 0 -0.43 2 2
LYN -0.22 0.21 -10000 0 -0.43 101 101
mol:Spermine 0.007 0.001 -10000 0 -10000 0 0
cell growth 0.05 0.017 -10000 0 -10000 0 0
BMP signaling pathway -0.026 0.005 -10000 0 -10000 0 0
SRC -0.22 0.21 -10000 0 -0.43 97 97
TGFBR1 0.026 0.006 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.004 0.029 -10000 0 -10000 0 0
GPC1 0.026 0.005 -10000 0 -10000 0 0
TGFBR1 (dimer) 0.026 0.006 -10000 0 -10000 0 0
VEGFA 0.025 0.009 -10000 0 -10000 0 0
BLK -0.23 0.21 -10000 0 -0.43 100 100
HCK -0.23 0.21 -10000 0 -0.44 97 97
FGF2 0.026 0.006 -10000 0 -10000 0 0
FGFR1 0.027 0.005 -10000 0 -10000 0 0
VEGFR1 homodimer 0.019 0.069 -10000 0 -0.66 2 2
TGFBR2 0.026 0.006 -10000 0 -10000 0 0
cell death 0.036 0.013 -10000 0 -10000 0 0
ATIII/GPC1 -0.1 0.23 -10000 0 -0.49 51 51
PLA2G2A/GPC1 0.026 0.025 -10000 0 -10000 0 0
LCK -0.22 0.21 -10000 0 -0.43 102 102
neuron differentiation 0.029 0.066 -10000 0 -0.49 3 3
PrPc/Cu2+ 0.019 0.005 -10000 0 -10000 0 0
APP 0.025 0.007 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.026 0.006 -10000 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.14 0.41 -10000 0 -1.1 27 27
MKNK1 0.026 0.007 -10000 0 -10000 0 0
MAPK14 -0.022 0.14 -10000 0 -0.34 29 29
ATF2/c-Jun -0.03 0.12 -10000 0 -0.42 5 5
MAPK11 -0.024 0.14 -10000 0 -0.33 32 32
MITF -0.035 0.16 -10000 0 -0.39 31 31
MAPKAPK5 -0.038 0.16 -10000 0 -0.39 32 32
KRT8 -0.038 0.16 -10000 0 -0.39 32 32
MAPKAPK3 0.026 0.006 -10000 0 -10000 0 0
MAPKAPK2 0.026 0.005 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.045 0.22 -10000 0 -0.49 34 34
CEBPB -0.038 0.16 -10000 0 -0.39 32 32
SLC9A1 -0.046 0.17 -10000 0 -0.4 35 35
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.035 0.16 -10000 0 -0.39 30 30
p38alpha-beta/MNK1 -0.022 0.18 -10000 0 -0.43 29 29
JUN -0.032 0.11 -10000 0 -0.41 5 5
PPARGC1A -0.051 0.19 -10000 0 -0.42 36 36
USF1 -0.046 0.17 -10000 0 -0.4 35 35
RAB5/GDP/GDI1 -0.029 0.13 -10000 0 -0.36 10 10
NOS2 -0.093 0.33 -10000 0 -1.2 15 15
DDIT3 -0.037 0.16 -10000 0 -0.39 32 32
RAB5A 0.026 0.006 -10000 0 -10000 0 0
HSPB1 0.005 0.16 0.28 26 -0.33 23 49
p38alpha-beta/HBP1 -0.023 0.17 -10000 0 -0.44 23 23
CREB1 -0.049 0.18 -10000 0 -0.42 35 35
RAB5/GDP 0.019 0.004 -10000 0 -10000 0 0
EIF4E -0.041 0.15 -10000 0 -0.39 26 26
RPS6KA4 -0.042 0.16 -10000 0 -0.38 35 35
PLA2G4A -0.052 0.17 -10000 0 -0.41 30 30
GDI1 -0.042 0.16 -10000 0 -0.38 35 35
TP53 -0.061 0.19 -10000 0 -0.49 30 30
RPS6KA5 -0.05 0.18 -10000 0 -0.42 35 35
ESR1 -0.063 0.21 -10000 0 -0.45 39 39
HBP1 0.022 0.011 -10000 0 -10000 0 0
MEF2C -0.043 0.16 -10000 0 -0.38 35 35
MEF2A -0.044 0.17 -10000 0 -0.4 35 35
EIF4EBP1 -0.052 0.18 -10000 0 -0.42 36 36
KRT19 -0.071 0.19 -10000 0 -0.41 44 44
ELK4 -0.046 0.17 -10000 0 -0.4 35 35
ATF6 -0.046 0.17 -10000 0 -0.4 35 35
ATF1 -0.052 0.18 -10000 0 -0.42 36 36
p38alpha-beta/MAPKAPK2 -0.022 0.18 -10000 0 -0.43 29 29
p38alpha-beta/MAPKAPK3 -0.02 0.18 -10000 0 -0.43 27 27
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.37 0.3 -10000 0 -0.52 144 144
SMAD6-7/SMURF1 0.038 0.042 -10000 0 -0.43 1 1
NOG 0.015 0.07 -10000 0 -0.66 2 2
SMAD9 -0.081 0.16 -10000 0 -0.52 19 19
SMAD4 0.025 0.008 -10000 0 -10000 0 0
SMAD5 -0.18 0.18 -10000 0 -0.47 26 26
BMP7/USAG1 -0.2 0.28 -10000 0 -0.52 80 80
SMAD5/SKI -0.18 0.19 -10000 0 -0.46 27 27
SMAD1 -0.038 0.089 -10000 0 -0.53 3 3
BMP2 0.026 0.006 -10000 0 -10000 0 0
SMAD1/SMAD1/SMAD4 -0.037 0.091 -10000 0 -0.42 4 4
BMPR1A 0.027 0.003 -10000 0 -10000 0 0
BMPR1B -0.38 0.33 -10000 0 -0.65 116 116
BMPR1A-1B/BAMBI -0.23 0.24 -10000 0 -0.43 115 115
AHSG -0.002 0.025 -10000 0 -10000 0 0
CER1 -0.003 0.021 -10000 0 -10000 0 0
BMP2-4/CER1 0.043 0.019 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.16 -10000 0 -0.44 23 23
BMP2-4 (homodimer) 0.036 0.013 -10000 0 -10000 0 0
RGMB 0.027 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.21 0.22 -10000 0 -0.4 114 114
RGMA -0.036 0.2 -10000 0 -0.62 19 19
SMURF1 0.022 0.011 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.15 0.16 -10000 0 -0.41 24 24
BMP2-4/USAG1 -0.041 0.18 -10000 0 -0.43 33 33
SMAD6/SMURF1/SMAD5 -0.16 0.18 -10000 0 -0.47 22 22
SOSTDC1 -0.1 0.25 -10000 0 -0.66 33 33
BMP7/BMPR2/BMPR1A-1B -0.32 0.26 -10000 0 -0.46 143 143
SKI 0.025 0.008 -10000 0 -10000 0 0
BMP6 (homodimer) 0.026 0.006 -10000 0 -10000 0 0
HFE2 0.012 0.022 -10000 0 -10000 0 0
ZFYVE16 0.027 0.005 -10000 0 -10000 0 0
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/CHRD 0.029 0.094 -10000 0 -0.39 9 9
SMAD5/SMAD5/SMAD4 -0.18 0.19 0.26 1 -0.46 28 29
MAPK1 0.025 0.008 -10000 0 -10000 0 0
TAK1/TAB family -0.11 0.14 -10000 0 -0.38 16 16
BMP7 (homodimer) -0.17 0.31 -10000 0 -0.66 57 57
NUP214 0.026 0.006 -10000 0 -10000 0 0
BMP6/FETUA 0.031 0.017 -10000 0 -10000 0 0
SMAD1/SKI -0.035 0.1 -10000 0 -0.48 5 5
SMAD6 0.024 0.049 -10000 0 -0.66 1 1
CTDSP2 0.026 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.045 0.018 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.12 0.27 -10000 0 -0.64 40 40
BMPR2 (homodimer) 0.027 0.004 -10000 0 -10000 0 0
GADD34/PP1CA 0.053 0.012 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.28 0.26 -10000 0 -0.49 116 116
CHRDL1 -0.24 0.33 -10000 0 -0.66 77 77
ENDOFIN/SMAD1 -0.04 0.1 -10000 0 -0.49 5 5
SMAD6-7/SMURF1/SMAD1 -0.034 0.1 -10000 0 -0.46 5 5
SMAD6/SMURF1 0.022 0.011 -10000 0 -10000 0 0
BAMBI 0.023 0.049 -10000 0 -0.66 1 1
SMURF2 0.025 0.007 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.13 0.23 -10000 0 -0.41 77 77
BMP2-4/GREM1 -0.045 0.19 -10000 0 -0.41 39 39
SMAD7 0.025 0.008 -10000 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.08 0.18 -10000 0 -0.54 21 21
SMAD1/SMAD6 -0.039 0.1 -10000 0 -0.49 5 5
TAK1/SMAD6 0.032 0.017 -10000 0 -10000 0 0
BMP7 -0.17 0.31 -10000 0 -0.66 57 57
BMP6 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.12 0.14 -10000 0 -0.36 27 27
PPM1A 0.026 0.007 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.042 0.098 -10000 0 -0.5 4 4
SMAD7/SMURF1 0.03 0.018 -10000 0 -10000 0 0
CTDSPL 0.026 0.006 -10000 0 -10000 0 0
PPP1CA 0.027 0.002 -10000 0 -10000 0 0
XIAP 0.027 0 -10000 0 -10000 0 0
CTDSP1 0.026 0.005 -10000 0 -10000 0 0
PPP1R15A 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.24 0.28 -10000 0 -0.62 52 52
CHRD -0.005 0.14 -10000 0 -0.66 9 9
BMPR2 0.027 0.004 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.16 0.16 -10000 0 -0.44 25 25
BMP4 0.026 0.007 -10000 0 -10000 0 0
FST -0.13 0.27 -10000 0 -0.66 40 40
BMP2-4/NOG 0.041 0.052 -10000 0 -0.43 2 2
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.28 0.24 -10000 0 -0.45 114 114
Endothelins

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
AKT1 -0.004 0.13 -10000 0 -0.47 10 10
PTK2B 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.28 0.45 -10000 0 -0.92 60 60
EDN1 0.031 0.063 -10000 0 -0.32 1 1
EDN3 0.012 0.022 -10000 0 -10000 0 0
EDN2 0 0.12 -10000 0 -0.58 8 8
HRAS/GDP -0.11 0.21 0.27 1 -0.48 32 33
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.082 0.18 -10000 0 -0.42 34 34
ADCY4 -0.027 0.15 -10000 0 -0.45 17 17
ADCY5 -0.02 0.14 -10000 0 -0.4 17 17
ADCY6 -0.004 0.11 -10000 0 -0.39 10 10
ADCY7 -0.002 0.1 -10000 0 -0.41 7 7
ADCY1 -0.14 0.2 -10000 0 -0.39 65 65
ADCY2 -0.016 0.11 -10000 0 -0.41 10 10
ADCY3 -0.003 0.11 -10000 0 -0.39 10 10
ADCY8 -0.006 0.11 -10000 0 -0.4 10 10
ADCY9 -0.002 0.1 -10000 0 -0.41 7 7
arachidonic acid secretion -0.17 0.27 -10000 0 -0.53 53 53
ETB receptor/Endothelin-1/Gq/GTP -0.065 0.16 -10000 0 -0.35 40 40
GNAO1 -0.007 0.14 -10000 0 -0.66 9 9
HRAS 0.027 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.018 0.13 0.38 8 -0.43 8 16
ETA receptor/Endothelin-1/Gs/GTP 0.022 0.14 0.35 11 -0.41 10 21
mol:GTP -0.003 0.008 -10000 0 -10000 0 0
COL3A1 -0.01 0.16 -10000 0 -0.55 11 11
EDNRB 0.02 0.069 -10000 0 -0.66 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.019 0.16 -10000 0 -0.54 14 14
CYSLTR1 -0.005 0.14 -10000 0 -0.51 10 10
SLC9A1 0.006 0.085 -10000 0 -0.28 10 10
mol:GDP -0.12 0.22 0.27 1 -0.49 37 38
SLC9A3 -0.6 0.37 -10000 0 -0.72 158 158
RAF1 -0.14 0.22 -10000 0 -0.51 37 37
JUN -0.16 0.29 -10000 0 -0.67 33 33
JAK2 -0.005 0.13 0.25 4 -0.47 10 14
mol:IP3 -0.1 0.2 -10000 0 -0.44 40 40
ETA receptor/Endothelin-1 0.023 0.18 0.44 11 -0.49 13 24
PLCB1 -0.024 0.18 -10000 0 -0.66 14 14
PLCB2 0.009 0.033 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 0.013 0.12 -10000 0 -0.49 9 9
FOS -0.2 0.35 -10000 0 -0.89 35 35
Gai/GDP -0.054 0.24 -10000 0 -0.76 19 19
CRK 0.025 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.093 0.21 -10000 0 -0.56 23 23
BCAR1 0.026 0.007 -10000 0 -10000 0 0
PRKCB1 -0.1 0.19 -10000 0 -0.43 42 42
GNAQ 0.014 0.023 -10000 0 -10000 0 0
GNAZ 0.025 0.008 -10000 0 -10000 0 0
GNAL 0.025 0.008 -10000 0 -10000 0 0
Gs family/GDP -0.11 0.2 0.25 1 -0.46 34 35
ETA receptor/Endothelin-1/Gq/GTP -0.086 0.22 -10000 0 -0.48 35 35
MAPK14 -0.069 0.14 -10000 0 -0.4 15 15
TRPC6 -0.3 0.49 -10000 0 -1 60 60
GNAI2 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.05 -10000 0 -0.66 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.067 0.15 -10000 0 -0.34 33 33
ETB receptor/Endothelin-2 0.013 0.11 -10000 0 -0.44 10 10
ETB receptor/Endothelin-3 0.03 0.056 -10000 0 -0.5 2 2
ETB receptor/Endothelin-1 0.038 0.075 -10000 0 -0.54 2 2
MAPK3 -0.18 0.3 -10000 0 -0.74 37 37
MAPK1 -0.2 0.34 -10000 0 -0.81 37 37
Rac1/GDP -0.098 0.2 0.27 1 -0.5 26 27
cAMP biosynthetic process -0.07 0.17 0.28 6 -0.46 17 23
MAPK8 -0.19 0.34 -10000 0 -0.7 47 47
SRC 0.026 0.006 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0 0.084 -10000 0 -0.35 7 7
p130Cas/CRK/Src/PYK2 -0.16 0.26 0.3 1 -0.51 55 56
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.098 0.2 0.27 1 -0.49 27 28
COL1A2 0.003 0.12 -10000 0 -0.5 4 4
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.004 0.16 -10000 0 -0.51 15 15
mol:DAG -0.1 0.2 -10000 0 -0.44 40 40
MAP2K2 -0.15 0.25 -10000 0 -0.58 39 39
MAP2K1 -0.15 0.25 -10000 0 -0.58 38 38
EDNRA -0.003 0.16 -10000 0 -0.64 10 10
positive regulation of muscle contraction 0.028 0.14 0.4 3 -0.43 7 10
Gq family/GDP -0.13 0.25 -10000 0 -0.54 42 42
HRAS/GTP -0.13 0.21 -10000 0 -0.48 39 39
PRKCH -0.11 0.19 -10000 0 -0.46 35 35
RAC1 0.022 0.011 -10000 0 -10000 0 0
PRKCA -0.094 0.2 0.32 1 -0.46 32 33
PRKCB -0.091 0.19 0.23 1 -0.45 31 32
PRKCE -0.1 0.19 -10000 0 -0.46 32 32
PRKCD -0.1 0.19 -10000 0 -0.47 31 31
PRKCG -0.11 0.2 -10000 0 -0.46 36 36
regulation of vascular smooth muscle contraction -0.23 0.41 -10000 0 -1 35 35
PRKCQ -0.11 0.2 -10000 0 -0.47 34 34
PLA2G4A -0.19 0.31 -10000 0 -0.59 53 53
GNA14 -0.12 0.27 -10000 0 -0.65 41 41
GNA15 0.012 0.029 -10000 0 -10000 0 0
GNA12 0.022 0.011 -10000 0 -10000 0 0
GNA11 0.006 0.089 -10000 0 -0.58 4 4
Rac1/GTP 0.018 0.13 0.38 8 -0.45 7 15
MMP1 -0.056 0.23 -10000 0 -0.99 11 11
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.029 0.015 -10000 0 -10000 0 0
ARNO/beta Arrestin1-2 0.02 0.12 -10000 0 -0.79 4 4
EGFR 0.022 0.011 -10000 0 -10000 0 0
EPHA2 0.025 0.008 -10000 0 -10000 0 0
USP6 0.021 0.02 -10000 0 -10000 0 0
IQSEC1 0.026 0.006 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.39 0.17 -10000 0 -0.44 176 176
ARRB2 0.008 0.009 -10000 0 -10000 0 0
mol:GTP 0.025 0.043 0.17 10 -10000 0 10
ARRB1 0.027 0.003 -10000 0 -10000 0 0
FBXO8 0.026 0.006 -10000 0 -10000 0 0
TSHR 0.018 0.018 -10000 0 -10000 0 0
EGF -0.58 0.21 -10000 0 -0.65 176 176
somatostatin receptor activity 0 0 0.001 4 -0.001 61 65
ARAP2 0.026 0.005 -10000 0 -10000 0 0
mol:GDP -0.083 0.14 -10000 0 -0.3 37 37
mol:PI-3-4-5-P3 0 0 0.001 3 -0.001 33 36
ITGA2B 0.019 0.024 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.058 0.027 -10000 0 -10000 0 0
ADAP1 0.022 0.011 -10000 0 -10000 0 0
KIF13B 0.026 0.005 -10000 0 -10000 0 0
HGF/MET 0.013 0.088 -10000 0 -0.46 6 6
PXN 0.026 0.006 -10000 0 -10000 0 0
ARF6/GTP -0.13 0.14 0.22 4 -0.3 61 65
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.33 0.16 -10000 0 -0.38 173 173
ADRB2 0.02 0.024 -10000 0 -10000 0 0
receptor agonist activity 0 0 0 6 0 57 63
actin filament binding 0 0 0 4 -0.001 61 65
SRC 0.026 0.006 -10000 0 -10000 0 0
ITGB3 0.006 0.11 -10000 0 -0.66 5 5
GNAQ 0.025 0.007 -10000 0 -10000 0 0
EFA6/PI-4-5-P2 0 0.001 0.001 17 -0.001 40 57
ARF6/GDP -0.044 0.13 0.24 1 -0.48 10 11
ARF6/GDP/GULP/ACAP1 -0.062 0.14 -10000 0 -0.4 9 9
alphaIIb/beta3 Integrin/paxillin/GIT1 0.051 0.075 -10000 0 -0.4 5 5
ACAP1 0.013 0.032 -10000 0 -10000 0 0
ACAP2 0.027 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.014 0.019 -10000 0 -10000 0 0
EFNA1 0.026 0.005 -10000 0 -10000 0 0
HGF 0.001 0.12 -10000 0 -0.66 6 6
CYTH3 0.006 0.003 -10000 0 -10000 0 0
CYTH2 -0.003 0.14 -10000 0 -0.98 4 4
NCK1 0.026 0.005 -10000 0 -10000 0 0
fibronectin binding 0 0 0 21 0 38 59
endosomal lumen acidification 0 0 0.001 2 -0.001 64 66
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 0.027 0.004 -10000 0 -10000 0 0
GNAQ/ARNO 0.012 0.13 -10000 0 -0.91 4 4
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 8 8
MET 0.017 0.023 -10000 0 -10000 0 0
GNA14 -0.11 0.27 -10000 0 -0.64 41 41
GNA15 0.021 0.023 -10000 0 -10000 0 0
GIT1 0.026 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 4 -0.001 44 48
GNA11 0.014 0.088 -10000 0 -0.58 4 4
LHCGR -0.004 0.029 -10000 0 -10000 0 0
AGTR1 -0.19 0.31 -10000 0 -0.65 62 62
desensitization of G-protein coupled receptor protein signaling pathway 0.014 0.019 -10000 0 -10000 0 0
IPCEF1/ARNO -0.26 0.15 -10000 0 -0.9 4 4
alphaIIb/beta3 Integrin 0.017 0.087 -10000 0 -0.5 5 5
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin 0.022 0.085 -10000 0 -0.5 5 5
AKT1 -0.063 0.24 0.34 4 -0.58 32 36
PTK2B -0.093 0.27 -10000 0 -0.69 31 31
VEGFR2 homodimer/Frs2 -0.11 0.31 -10000 0 -0.79 33 33
CAV1 0.021 0.013 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.085 0.3 -10000 0 -0.74 33 33
endothelial cell proliferation -0.031 0.25 0.5 8 -0.55 30 38
mol:Ca2+ -0.094 0.26 -10000 0 -0.67 32 32
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.073 0.28 -10000 0 -0.68 32 32
RP11-342D11.1 -0.1 0.26 -10000 0 -0.69 32 32
CDH5 0.026 0.007 -10000 0 -10000 0 0
VEGFA homodimer 0.06 0.026 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
SHC2 0.017 0.071 -10000 0 -0.66 2 2
HRAS/GDP -0.062 0.24 -10000 0 -0.6 32 32
SH2D2A 0.016 0.03 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.042 0.25 0.32 1 -0.58 32 33
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.088 0.3 -10000 0 -0.73 34 34
VEGFR1 homodimer 0.019 0.069 -10000 0 -0.66 2 2
SHC/GRB2/SOS1 -0.052 0.27 -10000 0 -0.66 32 32
GRB10 -0.092 0.25 -10000 0 -0.65 32 32
PTPN11 0.026 0.006 -10000 0 -10000 0 0
GRB2 0.025 0.007 -10000 0 -10000 0 0
PAK1 0.027 0.003 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.057 0.28 -10000 0 -0.69 32 32
HRAS 0.027 0.003 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.056 0.17 -10000 0 -0.4 32 32
HIF1A 0.026 0.007 -10000 0 -10000 0 0
FRS2 0.026 0.006 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.072 0.27 -10000 0 -0.67 32 32
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.009 0.11 -10000 0 -0.66 5 5
Nck/Pak 0.039 0.009 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.085 0.3 -10000 0 -0.73 34 34
mol:GDP -0.059 0.26 -10000 0 -0.64 32 32
mol:NADP -0.044 0.21 0.33 3 -0.49 32 35
eNOS/Hsp90 -0.029 0.2 0.33 2 -0.47 30 32
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
mol:IP3 -0.095 0.26 -10000 0 -0.68 32 32
HIF1A/ARNT 0.037 0.011 -10000 0 -10000 0 0
SHB 0.026 0.006 -10000 0 -10000 0 0
VEGFA 0.027 0.01 -10000 0 -10000 0 0
VEGFC 0.025 0.009 -10000 0 -10000 0 0
FAK1/Vinculin -0.085 0.28 0.48 1 -0.7 31 32
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.079 0.29 -10000 0 -0.69 36 36
PTPN6 0.026 0.006 -10000 0 -10000 0 0
EPAS1 -0.037 0.16 -10000 0 -0.39 33 33
mol:L-citrulline -0.044 0.21 0.33 3 -0.49 32 35
ITGAV 0.027 0.003 -10000 0 -10000 0 0
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.068 0.29 -10000 0 -0.71 32 32
VEGFR2 homodimer/VEGFA homodimer -0.082 0.3 -10000 0 -0.74 33 33
VEGFR2/3 heterodimer -0.12 0.33 -10000 0 -0.79 36 36
VEGFB 0.027 0.002 -10000 0 -10000 0 0
MAPK11 -0.11 0.28 -10000 0 -0.72 33 33
VEGFR2 homodimer -0.13 0.34 -10000 0 -0.87 34 34
FLT1 0.02 0.069 -10000 0 -0.66 2 2
NEDD4 0.028 0.004 -10000 0 -10000 0 0
MAPK3 -0.089 0.23 0.34 1 -0.62 31 32
MAPK1 -0.087 0.24 0.34 1 -0.61 32 33
VEGFA145/NRP2 0.035 0.039 -10000 0 -0.48 1 1
VEGFR1/2 heterodimer -0.11 0.32 -10000 0 -0.81 34 34
KDR -0.13 0.34 -10000 0 -0.88 34 34
VEGFA165/NRP1/VEGFR2 homodimer -0.074 0.28 -10000 0 -0.69 33 33
SRC 0.026 0.006 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.081 0.25 0.4 3 -0.63 32 35
PI3K -0.084 0.28 -10000 0 -0.7 32 32
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.084 0.3 -10000 0 -0.74 33 33
FES -0.099 0.27 -10000 0 -0.71 32 32
GAB1 -0.09 0.29 -10000 0 -0.73 32 32
VEGFR2 homodimer/VEGFA homodimer/Src -0.082 0.29 -10000 0 -0.72 33 33
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
SOS1 0.027 0.004 -10000 0 -10000 0 0
ARNT 0.026 0.005 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.039 0.19 0.33 3 -0.49 21 24
VEGFR2 homodimer/VEGFA homodimer/Yes -0.087 0.3 -10000 0 -0.75 32 32
PI3K/GAB1 -0.063 0.24 -10000 0 -0.61 31 31
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.057 0.28 -10000 0 -0.69 32 32
PRKACA 0.027 0.002 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.097 0.31 -10000 0 -0.74 36 36
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
CDC42 -0.099 0.27 -10000 0 -0.71 32 32
actin cytoskeleton reorganization -0.087 0.3 -10000 0 -0.72 34 34
PTK2 -0.1 0.29 -10000 0 -0.75 32 32
EDG1 -0.1 0.26 -10000 0 -0.69 32 32
mol:DAG -0.095 0.26 -10000 0 -0.68 32 32
CaM/Ca2+ -0.075 0.25 -10000 0 -0.63 32 32
MAP2K3 -0.1 0.26 -10000 0 -0.68 32 32
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.047 0.29 -10000 0 -0.68 32 32
PLCG1 -0.097 0.27 -10000 0 -0.69 32 32
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.067 0.28 -10000 0 -0.7 32 32
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
YES1 0.025 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.085 0.3 -10000 0 -0.74 33 33
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.085 0.3 -10000 0 -0.74 33 33
cell migration -0.057 0.24 -10000 0 -0.58 31 31
mol:PI-3-4-5-P3 -0.075 0.25 -10000 0 -0.64 32 32
FYN 0.027 0.005 -10000 0 -10000 0 0
VEGFB/NRP1 -0.086 0.26 -10000 0 -0.66 32 32
mol:NO -0.044 0.21 0.33 3 -0.49 32 35
PXN 0.026 0.006 -10000 0 -10000 0 0
HRAS/GTP -0.077 0.23 -10000 0 -0.6 32 32
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.084 0.27 -10000 0 -0.68 32 32
VHL 0.026 0.006 -10000 0 -10000 0 0
ITGB3 0.006 0.11 -10000 0 -0.66 5 5
NOS3 -0.055 0.24 0.34 3 -0.57 31 34
VEGFR2 homodimer/VEGFA homodimer/Sck -0.09 0.3 -10000 0 -0.74 34 34
RAC1 0.022 0.011 -10000 0 -10000 0 0
PRKCA -0.092 0.24 -10000 0 -0.64 31 31
PRKCB -0.093 0.24 -10000 0 -0.65 30 30
VCL 0.027 0.003 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.089 0.27 -10000 0 -0.69 32 32
VEGFR1/2 heterodimer/VEGFA homodimer -0.089 0.31 -10000 0 -0.76 33 33
VEGFA165/NRP2 0.035 0.039 -10000 0 -0.48 1 1
MAPKKK cascade -0.065 0.23 0.34 1 -0.59 30 31
NRP2 0.022 0.05 -10000 0 -0.66 1 1
VEGFC homodimer 0.025 0.009 -10000 0 -10000 0 0
NCK1 0.026 0.005 -10000 0 -10000 0 0
ROCK1 0.025 0.007 -10000 0 -10000 0 0
FAK1/Paxillin -0.089 0.28 -10000 0 -0.69 33 33
MAP3K13 -0.1 0.28 -10000 0 -0.73 32 32
PDPK1 -0.072 0.22 0.26 1 -0.57 30 31
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.047 0.16 -10000 0 -0.42 28 28
CRKL -0.047 0.17 -10000 0 -0.44 29 29
HRAS -0.015 0.15 -10000 0 -0.43 11 11
mol:PIP3 -0.036 0.17 -10000 0 -0.41 28 28
SPRED1 0.027 0.004 -10000 0 -10000 0 0
SPRED2 0.027 0.003 -10000 0 -10000 0 0
GAB1 -0.046 0.18 -10000 0 -0.47 29 29
FOXO3 -0.032 0.2 0.28 1 -0.42 30 31
AKT1 -0.035 0.22 0.29 1 -0.43 39 40
BAD -0.032 0.2 0.28 1 -0.42 32 33
megakaryocyte differentiation -0.09 0.22 -10000 0 -0.44 50 50
GSK3B -0.028 0.21 0.34 4 -0.42 32 36
RAF1 -0.013 0.12 -10000 0 -0.38 7 7
SHC1 0.026 0.005 -10000 0 -10000 0 0
STAT3 -0.047 0.18 -10000 0 -0.45 29 29
STAT1 -0.11 0.37 -10000 0 -0.99 29 29
HRAS/SPRED1 -0.002 0.13 -10000 0 -0.37 8 8
cell proliferation -0.052 0.19 -10000 0 -0.47 31 31
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
TEC 0.026 0.005 -10000 0 -10000 0 0
RPS6KB1 -0.036 0.2 -10000 0 -0.46 30 30
HRAS/SPRED2 -0.002 0.13 -10000 0 -0.38 7 7
LYN/TEC/p62DOK -0.008 0.19 -10000 0 -0.44 29 29
MAPK3 -0.004 0.1 0.28 4 -0.29 4 8
STAP1 -0.24 0.24 -10000 0 -0.4 123 123
GRAP2 0.022 0.017 -10000 0 -10000 0 0
JAK2 -0.1 0.33 -10000 0 -0.87 29 29
STAT1 (dimer) -0.11 0.36 -10000 0 -0.97 29 29
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.015 0.18 -10000 0 -0.45 24 24
actin filament polymerization -0.053 0.17 -10000 0 -0.46 28 28
LYN 0.027 0.004 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.24 0.28 -10000 0 -0.69 36 36
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.019 0.16 -10000 0 -0.39 28 28
PI3K -0.012 0.19 -10000 0 -0.44 27 27
PTEN 0.027 0.003 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.12 0.43 -10000 0 -1.2 29 29
MAPK8 -0.054 0.2 -10000 0 -0.48 31 31
STAT3 (dimer) -0.046 0.17 -10000 0 -0.44 29 29
positive regulation of transcription 0.001 0.088 0.26 4 -0.24 3 7
mol:GDP -0.019 0.15 -10000 0 -0.4 21 21
PIK3C2B -0.046 0.18 -10000 0 -0.46 29 29
CBL/CRKL -0.032 0.17 -10000 0 -0.42 29 29
FER -0.046 0.18 -10000 0 -0.46 29 29
SH2B3 -0.045 0.18 -10000 0 -0.46 29 29
PDPK1 -0.02 0.15 0.29 4 -0.38 23 27
SNAI2 -0.074 0.21 -10000 0 -0.46 40 40
positive regulation of cell proliferation -0.076 0.28 -10000 0 -0.74 29 29
KITLG 0.02 0.026 -10000 0 -10000 0 0
cell motility -0.076 0.28 -10000 0 -0.74 29 29
PTPN6 0.027 0.01 -10000 0 -10000 0 0
EPOR -0.007 0.14 -10000 0 -0.83 2 2
STAT5A (dimer) -0.061 0.24 -10000 0 -0.62 29 29
SOCS1 0.017 0.069 -10000 0 -0.66 2 2
cell migration 0.052 0.19 0.47 30 -10000 0 30
SOS1 0.027 0.004 -10000 0 -10000 0 0
EPO 0.014 0.021 -10000 0 -10000 0 0
VAV1 0.006 0.06 -10000 0 -0.66 1 1
GRB10 -0.055 0.18 -10000 0 -0.46 28 28
PTPN11 0.027 0.008 -10000 0 -10000 0 0
SCF/KIT -0.048 0.2 -10000 0 -0.5 29 29
GO:0007205 0.001 0.009 -10000 0 -10000 0 0
MAP2K1 -0.006 0.11 0.31 3 -0.32 4 7
CBL 0.026 0.005 -10000 0 -10000 0 0
KIT -0.16 0.48 -10000 0 -1.3 30 30
MAP2K2 -0.007 0.11 0.31 3 -0.32 4 7
SHC/Grb2/SOS1 -0.007 0.18 -10000 0 -0.43 26 26
STAT5A -0.064 0.25 -10000 0 -0.64 29 29
GRB2 0.025 0.007 -10000 0 -10000 0 0
response to radiation -0.072 0.21 -10000 0 -0.45 40 40
SHC/GRAP2 0.034 0.019 -10000 0 -10000 0 0
PTPRO -0.092 0.22 -10000 0 -0.45 50 50
SH2B2 -0.055 0.18 -10000 0 -0.46 28 28
DOK1 0.027 0.008 -10000 0 -10000 0 0
MATK -0.053 0.2 -10000 0 -0.48 30 30
CREBBP 0.025 0.045 -10000 0 -10000 0 0
BCL2 -0.048 0.23 -10000 0 -1 7 7
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.052 0.2 -10000 0 -0.5 33 33
alphaV beta3 Integrin 0.037 0.077 -10000 0 -0.43 5 5
PTK2 -0.14 0.25 0.6 3 -0.6 26 29
IGF1R 0.027 0.004 -10000 0 -10000 0 0
PI4KB 0.027 0.005 -10000 0 -10000 0 0
MFGE8 0.027 0.004 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
CDKN1B -0.17 0.26 -10000 0 -0.53 66 66
VEGFA 0.025 0.009 -10000 0 -10000 0 0
ILK -0.17 0.26 -10000 0 -0.53 66 66
ROCK1 0.025 0.007 -10000 0 -10000 0 0
AKT1 -0.16 0.24 -10000 0 -0.5 65 65
PTK2B -0.046 0.16 -10000 0 -0.38 33 33
alphaV/beta3 Integrin/JAM-A -0.1 0.21 -10000 0 -0.39 68 68
CBL 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.27 0.23 -10000 0 -0.43 127 127
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.046 0.089 -10000 0 -0.4 7 7
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.13 0.2 -10000 0 -0.51 31 31
alphaV/beta3 Integrin/Syndecan-1 0.035 0.085 -10000 0 -0.44 6 6
PI4KA 0.025 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.028 0.1 -10000 0 -0.35 12 12
PI4 Kinase 0.036 0.013 -10000 0 -10000 0 0
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.03 0.092 -10000 0 -0.43 7 7
RPS6KB1 -0.029 0.084 -10000 0 -0.36 1 1
TLN1 0.026 0.006 -10000 0 -10000 0 0
MAPK3 -0.065 0.13 -10000 0 -0.56 7 7
GPR124 0.023 0.049 -10000 0 -0.66 1 1
MAPK1 -0.068 0.14 -10000 0 -0.56 7 7
PXN 0.026 0.006 -10000 0 -10000 0 0
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin 0.016 0.13 -10000 0 -0.46 13 13
cell adhesion -0.22 0.19 -10000 0 -0.36 117 117
ANGPTL3 -0.43 0.31 -10000 0 -0.64 131 131
VEGFR2 homodimer/VEGFA homodimer/Src -0.026 0.17 -10000 0 -0.41 32 32
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.008 -10000 0 -10000 0 0
TGFBR2 0.026 0.006 -10000 0 -10000 0 0
ITGB3 0.006 0.11 -10000 0 -0.66 5 5
IGF1 0.009 0.11 -10000 0 -0.66 5 5
RAC1 0.022 0.011 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.034 0.084 -10000 0 -0.43 6 6
apoptosis 0.027 0.003 -10000 0 -10000 0 0
CD47 0.026 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/CD47 0.037 0.077 -10000 0 -0.43 5 5
VCL 0.027 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.007 0.16 -10000 0 -0.43 23 23
CSF1 0.022 0.05 -10000 0 -0.66 1 1
PIK3C2A -0.17 0.26 -10000 0 -0.53 66 66
PI4 Kinase/Pyk2 -0.15 0.23 -10000 0 -0.43 62 62
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.024 0.18 -10000 0 -0.41 34 34
FAK1/Vinculin -0.1 0.21 0.56 3 -0.48 24 27
alphaV beta3/Integrin/ppsTEM5 0.035 0.084 -10000 0 -0.43 6 6
RHOA 0.026 0.005 -10000 0 -10000 0 0
VTN -0.21 0.32 -10000 0 -0.66 66 66
BCAR1 0.026 0.007 -10000 0 -10000 0 0
FGF2 0.026 0.006 -10000 0 -10000 0 0
F11R 0.013 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin 0.038 0.077 -10000 0 -0.43 5 5
alphaV/beta3 Integrin/TGFBR2 0.037 0.078 -10000 0 -0.43 5 5
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.059 0.041 -10000 0 -0.4 1 1
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.035 0.072 -10000 0 -0.4 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.02 0.025 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.032 0.16 -10000 0 -0.38 33 33
SDC1 0.023 0.049 -10000 0 -0.66 1 1
VAV3 0.022 0.055 0.36 1 -0.38 1 2
PTPN11 0.026 0.006 -10000 0 -10000 0 0
IRS1 0.017 0.074 -10000 0 -0.55 3 3
FAK1/Paxillin -0.11 0.19 0.34 1 -0.47 25 26
cell migration -0.1 0.17 0.27 3 -0.43 24 27
ITGAV 0.027 0.003 -10000 0 -10000 0 0
PI3K -0.087 0.2 -10000 0 -0.36 66 66
SPP1 0.015 0.075 -10000 0 -0.55 3 3
KDR -0.09 0.26 -10000 0 -0.65 34 34
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.027 0.003 -10000 0 -10000 0 0
COL4A3 -0.007 0.14 -10000 0 -0.63 10 10
angiogenesis -0.097 0.17 -10000 0 -0.59 7 7
Rac1/GTP 0.026 0.044 -10000 0 -0.35 1 1
EDIL3 -0.044 0.2 -10000 0 -0.66 19 19
cell proliferation 0.036 0.077 -10000 0 -0.43 5 5
Signaling events mediated by PTP1B

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
PDGFRB -0.001 0.14 -10000 0 -0.66 8 8
Jak2/Leptin Receptor -0.18 0.17 -10000 0 -0.44 32 32
PTP1B/AKT1 -0.069 0.1 0.23 3 -0.33 14 17
FYN 0.027 0.005 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.082 0.11 0.22 5 -0.35 17 22
EGFR -0.015 0.017 -10000 0 -10000 0 0
EGF/EGFR -0.32 0.14 0.23 1 -0.38 144 145
CSF1 0.022 0.05 -10000 0 -0.66 1 1
AKT1 0.025 0.008 -10000 0 -10000 0 0
INSR 0.027 0.004 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.088 0.14 0.23 3 -0.42 21 24
Insulin Receptor/Insulin -0.052 0.094 -10000 0 -0.38 5 5
HCK 0.011 0.057 -10000 0 -0.66 1 1
CRK 0.025 0.007 -10000 0 -10000 0 0
TYK2 -0.08 0.1 0.23 3 -0.34 16 19
EGF -0.58 0.21 -10000 0 -0.65 176 176
YES1 0.025 0.008 -10000 0 -10000 0 0
CAV1 -0.14 0.12 0.23 5 -0.36 22 27
TXN 0.02 0.009 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.085 0.098 -10000 0 -0.37 15 15
cell migration 0.082 0.11 0.35 17 -0.22 5 22
STAT3 0.025 0.007 -10000 0 -10000 0 0
PRLR -0.28 0.34 -10000 0 -0.66 89 89
ITGA2B 0.018 0.023 -10000 0 -10000 0 0
CSF1R 0.02 0.051 -10000 0 -0.66 1 1
Prolactin Receptor/Prolactin -0.21 0.26 -10000 0 -0.5 89 89
FGR 0.019 0.052 -10000 0 -0.66 1 1
PTP1B/p130 Cas -0.08 0.099 0.26 1 -0.33 17 18
Crk/p130 Cas -0.079 0.096 0.27 1 -0.34 15 16
DOK1 -0.074 0.12 0.28 5 -0.36 17 22
JAK2 -0.18 0.19 0.24 1 -0.37 73 74
Jak2/Leptin Receptor/Leptin -0.094 0.11 -10000 0 -0.41 12 12
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
PTPN1 -0.083 0.11 0.22 5 -0.35 17 22
LYN 0.027 0.004 -10000 0 -10000 0 0
CDH2 -0.004 0.14 -10000 0 -0.66 8 8
SRC -0.017 0.096 -10000 0 -0.62 4 4
ITGB3 0.004 0.11 -10000 0 -0.66 5 5
CAT1/PTP1B -0.19 0.19 0.31 5 -0.47 30 35
CAPN1 0.025 0.003 -10000 0 -10000 0 0
CSK 0.027 0.004 -10000 0 -10000 0 0
PI3K -0.044 0.09 -10000 0 -0.4 3 3
mol:H2O2 -0.006 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.086 0.1 -10000 0 -0.4 9 9
negative regulation of transcription -0.18 0.19 0.24 1 -0.35 91 92
FCGR2A 0.022 0.02 -10000 0 -10000 0 0
FER 0.02 0.005 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.014 0.087 -10000 0 -0.5 5 5
BLK 0.016 0.025 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.046 0.012 -10000 0 -10000 0 0
RHOA 0.024 0.005 -10000 0 -10000 0 0
LEPR 0.024 0.027 -10000 0 -0.34 1 1
BCAR1 0.026 0.007 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.025 0.007 -10000 0 -10000 0 0
mol:NADPH -0.006 0.003 -10000 0 -10000 0 0
TRPV6 -0.14 0.19 0.33 2 -0.48 23 25
PRL -0.01 0.017 -10000 0 -10000 0 0
SOCS3 0.031 0.098 -10000 0 -1.3 1 1
SPRY2 0.023 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.04 0.053 -10000 0 -0.44 2 2
CSF1/CSF1R -0.081 0.11 -10000 0 -0.37 15 15
Ras protein signal transduction 0.059 0.13 0.48 15 -10000 0 15
IRS1 0.017 0.074 -10000 0 -0.55 3 3
INS -0.007 0.018 -10000 0 -10000 0 0
LEP 0.003 0.03 -10000 0 -10000 0 0
STAT5B -0.12 0.13 0.24 2 -0.36 24 26
STAT5A -0.12 0.13 0.24 2 -0.36 23 25
GRB2 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.094 0.12 -10000 0 -0.38 23 23
CSN2 -0.073 0.1 -10000 0 -0.62 1 1
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
LAT -0.022 0.11 0.27 1 -0.55 6 7
YBX1 0.028 0.008 -10000 0 -10000 0 0
LCK 0.023 0.017 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
NOX4 -0.045 0.2 -10000 0 -0.65 20 20
IL4-mediated signaling events

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
BCL2L1 -0.39 0.41 -10000 0 -1.1 28 28
STAT6 (cleaved dimer) -0.39 0.42 -10000 0 -1.1 36 36
IGHG1 -0.14 0.15 -10000 0 -0.42 3 3
IGHG3 -0.38 0.4 -10000 0 -1 35 35
AKT1 -0.17 0.23 -10000 0 -0.78 9 9
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.11 0.16 -10000 0 -0.6 4 4
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.25 -10000 0 -0.83 11 11
THY1 -0.61 0.64 -10000 0 -1.4 66 66
MYB 0.003 0.041 -10000 0 -10000 0 0
HMGA1 0.023 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.22 0.24 -10000 0 -0.65 18 18
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.19 0.24 -10000 0 -0.85 10 10
SP1 0.03 0.01 -10000 0 -10000 0 0
INPP5D 0.023 0.017 -10000 0 -10000 0 0
SOCS5 0.034 0.022 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.38 0.42 -10000 0 -1.1 33 33
SOCS1 -0.26 0.28 -10000 0 -0.75 25 25
SOCS3 -0.18 0.22 -10000 0 -0.72 6 6
FCER2 -0.3 0.34 -10000 0 -0.92 22 22
PARP14 0.027 0.006 -10000 0 -10000 0 0
CCL17 -0.39 0.41 -10000 0 -1.1 26 26
GRB2 0.025 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.16 0.2 -10000 0 -0.71 10 10
T cell proliferation -0.38 0.42 -10000 0 -1.1 31 31
IL4R/JAK1 -0.38 0.42 -10000 0 -1.1 28 28
EGR2 -0.46 0.53 -10000 0 -1.4 35 35
JAK2 -0.025 0.042 -10000 0 -10000 0 0
JAK3 0.012 0.041 -10000 0 -10000 0 0
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
JAK1 0.004 0.023 -10000 0 -10000 0 0
COL1A2 -0.11 0.14 -10000 0 -10000 0 0
CCL26 -0.36 0.43 -10000 0 -1.1 29 29
IL4R -0.41 0.44 -10000 0 -1.2 28 28
PTPN6 0.035 0.015 -10000 0 -10000 0 0
IL13RA2 -0.82 0.66 -10000 0 -1.3 113 113
IL13RA1 -0.024 0.044 -10000 0 -10000 0 0
IRF4 -0.079 0.17 -10000 0 -0.74 8 8
ARG1 -0.11 0.14 -10000 0 -0.97 1 1
CBL -0.21 0.23 -10000 0 -0.63 17 17
GTF3A 0.028 0.014 -10000 0 -10000 0 0
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.029 0.058 -10000 0 -10000 0 0
IRF4/BCL6 -0.072 0.16 -10000 0 -0.7 8 8
CD40LG 0.027 0.021 -10000 0 -10000 0 0
MAPK14 -0.21 0.23 -10000 0 -0.64 16 16
mitosis -0.16 0.22 -10000 0 -0.73 9 9
STAT6 -0.44 0.48 -10000 0 -1.2 34 34
SPI1 0.011 0.038 -10000 0 -10000 0 0
RPS6KB1 -0.15 0.21 0.53 1 -0.69 9 10
STAT6 (dimer) -0.44 0.48 -10000 0 -1.2 34 34
STAT6 (dimer)/PARP14 -0.4 0.45 -10000 0 -1.2 32 32
mast cell activation 0.011 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.17 0.2 -10000 0 -0.63 9 9
FRAP1 -0.17 0.23 -10000 0 -0.78 9 9
LTA -0.4 0.41 -10000 0 -1.1 30 30
FES 0.027 0.004 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.43 0.46 1.2 34 -10000 0 34
CCL11 -0.44 0.5 -10000 0 -1.3 39 39
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.17 0.2 -10000 0 -0.66 7 7
IL2RG 0.029 0.019 -10000 0 -10000 0 0
IL10 -0.4 0.41 -10000 0 -1.1 29 29
IRS1 0.017 0.074 -10000 0 -0.55 3 3
IRS2 0.026 0.008 -10000 0 -10000 0 0
IL4 -0.1 0.15 -10000 0 -0.93 3 3
IL5 -0.4 0.41 -10000 0 -1.1 29 29
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.34 0.36 -10000 0 -0.93 32 32
COL1A1 -0.14 0.19 -10000 0 -1.1 3 3
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.39 0.42 -10000 0 -1.2 25 25
IL2R gamma/JAK3 0.026 0.039 -10000 0 -10000 0 0
TFF3 -0.5 0.56 -10000 0 -1.4 48 48
ALOX15 -0.39 0.41 -10000 0 -1.1 27 27
MYBL1 0.022 0.022 -10000 0 -10000 0 0
T-helper 2 cell differentiation -0.33 0.35 -10000 0 -0.89 35 35
SHC1 0.026 0.005 -10000 0 -10000 0 0
CEBPB 0.026 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.19 0.24 -10000 0 -0.95 8 8
mol:PI-3-4-5-P3 -0.17 0.23 -10000 0 -0.78 9 9
PI3K -0.18 0.24 -10000 0 -0.84 9 9
DOK2 0.017 0.054 -10000 0 -0.66 1 1
ETS1 0.034 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.14 0.2 0.47 1 -0.75 7 8
ITGB3 -0.41 0.44 -10000 0 -1.2 32 32
PIGR -0.43 0.46 -10000 0 -1.2 36 36
IGHE 0.037 0.05 0.19 11 -10000 0 11
MAPKKK cascade -0.14 0.19 0.47 1 -0.73 7 8
BCL6 0.026 0.008 -10000 0 -10000 0 0
OPRM1 -0.4 0.42 -10000 0 -1.1 29 29
RETNLB -0.4 0.41 -10000 0 -1.2 27 27
SELP -0.44 0.5 -10000 0 -1.4 30 30
AICDA -0.38 0.4 -10000 0 -1.1 28 28
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 0.023 0.051 -9999 0 -10000 0 0
alphaM/beta2 Integrin/GPIbA 0.02 0.061 -9999 0 -0.48 1 1
alphaM/beta2 Integrin/proMMP-9 0.004 0.073 -9999 0 -0.43 2 2
PLAUR 0.019 0.027 -9999 0 -10000 0 0
HMGB1 0.018 0.031 -9999 0 -0.18 1 1
alphaM/beta2 Integrin/Talin 0.022 0.051 -9999 0 -10000 0 0
AGER 0.008 0.041 -9999 0 -10000 0 0
RAP1A 0.026 0.005 -9999 0 -10000 0 0
SELPLG 0.017 0.028 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 0.022 0.098 -9999 0 -0.34 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.015 0.079 -9999 0 -0.66 2 2
CYR61 0.003 0.12 -9999 0 -0.54 8 8
TLN1 0.026 0.006 -9999 0 -10000 0 0
Rap1/GTP -0.16 0.14 -9999 0 -0.42 30 30
RHOA 0.026 0.005 -9999 0 -10000 0 0
P-selectin oligomer -0.016 0.16 -9999 0 -0.61 13 13
MYH2 -0.23 0.19 -9999 0 -0.58 32 32
MST1R 0.013 0.041 -9999 0 -0.35 1 1
leukocyte activation during inflammatory response -0.037 0.15 -9999 0 -0.39 27 27
APOB -0.016 0.15 -9999 0 -0.66 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.025 0.012 -9999 0 -10000 0 0
JAM3 0.027 0.004 -9999 0 -10000 0 0
GP1BA 0.022 0.049 -9999 0 -0.66 1 1
alphaM/beta2 Integrin/CTGF 0.015 0.076 -9999 0 -0.45 3 3
alphaM/beta2 Integrin -0.19 0.16 -9999 0 -0.43 41 41
JAM3 homodimer 0.027 0.004 -9999 0 -10000 0 0
ICAM2 0.025 0.007 -9999 0 -10000 0 0
ICAM1 0.027 0.007 -9999 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.19 0.16 -9999 0 -0.43 39 39
cell adhesion 0.02 0.061 -9999 0 -0.48 1 1
NFKB1 -0.025 0.16 -9999 0 -0.48 17 17
THY1 -0.17 0.31 -9999 0 -0.65 56 56
RhoA/GDP 0.02 0.004 -9999 0 -10000 0 0
Lipoprotein(a) -0.043 0.16 -9999 0 -0.43 30 30
alphaM/beta2 Integrin/LRP/tPA 0.004 0.12 -9999 0 -0.37 14 14
IL6 -0.059 0.23 -9999 0 -0.77 17 17
ITGB2 0.002 0.042 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.024 0.066 -9999 0 -0.44 1 1
alphaM/beta2 Integrin/JAM2/JAM3 0.03 0.072 -9999 0 -0.41 2 2
JAM2 0.015 0.084 -9999 0 -0.66 3 3
alphaM/beta2 Integrin/ICAM1 0.036 0.067 -9999 0 -0.37 1 1
alphaM/beta2 Integrin/uPA/Plg -0.21 0.22 -9999 0 -0.41 103 103
RhoA/GTP -0.24 0.2 -9999 0 -0.6 34 34
positive regulation of phagocytosis -0.14 0.12 -9999 0 -0.37 27 27
Ron/MSP 0.025 0.05 -9999 0 -0.36 2 2
alphaM/beta2 Integrin/uPAR/uPA 0.025 0.068 -9999 0 -0.45 1 1
alphaM/beta2 Integrin/uPAR 0.018 0.055 -9999 0 -10000 0 0
PLAU 0.024 0.049 -9999 0 -0.66 1 1
PLAT -0.026 0.18 -9999 0 -0.62 16 16
actin filament polymerization -0.22 0.18 -9999 0 -0.56 31 31
MST1 0.023 0.049 -9999 0 -0.66 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.034 0.15 -9999 0 -0.39 27 27
TNF -0.03 0.17 -9999 0 -0.63 9 9
RAP1B 0.026 0.005 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.021 0.062 -9999 0 -0.48 1 1
fibrinolysis -0.21 0.21 -9999 0 -0.4 103 103
HCK 0.011 0.057 -9999 0 -0.66 1 1
dendritic cell antigen processing and presentation -0.19 0.16 -9999 0 -0.43 39 39
VTN -0.21 0.32 -9999 0 -0.66 66 66
alphaM/beta2 Integrin/CYR61 0.01 0.087 -9999 0 -0.36 6 6
LPA -0.071 0.2 -9999 0 -0.66 20 20
LRP1 0.026 0.005 -9999 0 -10000 0 0
cell migration -0.008 0.065 -9999 0 -0.4 2 2
FN1 0.02 0.025 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 -0.097 0.21 -9999 0 -0.41 55 55
MPO 0.017 0.025 -9999 0 -10000 0 0
KNG1 -0.4 0.31 -9999 0 -0.66 118 118
RAP1/GDP 0.034 0.01 -9999 0 -10000 0 0
ROCK1 -0.23 0.19 -9999 0 -0.57 32 32
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.38 0.32 -9999 0 -0.65 113 113
CTGF 0.016 0.084 -9999 0 -0.66 3 3
alphaM/beta2 Integrin/Hck 0.015 0.067 -9999 0 -0.48 1 1
ITGAM 0.007 0.037 -9999 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 0.01 0.1 -9999 0 -0.39 8 8
HP 0.012 0.03 -9999 0 -10000 0 0
leukocyte adhesion -0.098 0.2 -9999 0 -0.41 51 51
SELP -0.016 0.16 -9999 0 -0.61 13 13
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 0.02 0.028 -10000 0 -10000 0 0
NFATC2 0.001 0.19 -10000 0 -0.61 13 13
NFATC3 -0.008 0.11 -10000 0 -0.3 23 23
CD40LG -0.13 0.38 -10000 0 -0.93 30 30
ITCH 0.023 0.044 -10000 0 -10000 0 0
CBLB 0.023 0.044 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.064 0.23 -10000 0 -0.78 6 6
JUNB 0.027 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.03 0.052 -10000 0 -0.32 4 4
T cell anergy 0.017 0.075 -10000 0 -0.41 4 4
TLE4 -0.003 0.13 -10000 0 -0.45 10 10
Jun/NFAT1-c-4/p21SNFT -0.062 0.37 -10000 0 -0.9 27 27
AP-1/NFAT1-c-4 -0.12 0.47 -10000 0 -1.1 30 30
IKZF1 0.003 0.11 -10000 0 -0.49 4 4
T-helper 2 cell differentiation -0.41 0.31 -10000 0 -0.78 52 52
AP-1/NFAT1 -0.031 0.21 -10000 0 -0.45 29 29
CALM1 0.03 0.033 -10000 0 -10000 0 0
EGR2 -0.15 0.49 -10000 0 -1.4 22 22
EGR3 -0.18 0.54 -10000 0 -1.4 30 30
NFAT1/FOXP3 0.018 0.14 -10000 0 -0.44 12 12
EGR1 -0.029 0.19 -10000 0 -0.66 16 16
JUN 0.023 0.021 -10000 0 -10000 0 0
EGR4 0.018 0.018 -10000 0 -10000 0 0
mol:Ca2+ 0.006 0.027 -10000 0 -0.18 4 4
GBP3 0.001 0.13 -10000 0 -0.49 6 6
FOSL1 0.025 0.014 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.056 0.36 -10000 0 -0.9 26 26
DGKA -0.001 0.13 -10000 0 -0.49 6 6
CREM 0.026 0.005 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.071 0.37 -10000 0 -0.92 27 27
CTLA4 -0.006 0.11 -10000 0 -0.43 6 6
NFAT1-c-4 (dimer)/EGR1 -0.097 0.42 -10000 0 -1.1 27 27
NFAT1-c-4 (dimer)/EGR4 -0.072 0.37 -10000 0 -0.93 27 27
FOS -0.074 0.24 -10000 0 -0.62 30 30
IFNG -0.019 0.15 -10000 0 -0.62 4 4
T cell activation -0.071 0.23 -10000 0 -0.65 18 18
MAF 0.025 0.007 -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 0.078 0.28 0.72 29 -10000 0 29
TNF -0.11 0.36 -10000 0 -0.93 28 28
FASLG -0.18 0.53 -10000 0 -1.3 31 31
TBX21 0.021 0.023 -10000 0 -10000 0 0
BATF3 0.026 0.009 -10000 0 -10000 0 0
PRKCQ 0.021 0.069 -10000 0 -0.66 2 2
PTPN1 0.001 0.13 -10000 0 -0.45 10 10
NFAT1-c-4/ICER1 -0.074 0.37 -10000 0 -0.93 27 27
GATA3 -0.47 0.3 -10000 0 -0.65 146 146
T-helper 1 cell differentiation -0.019 0.15 -10000 0 -0.61 4 4
IL2RA -0.056 0.23 -10000 0 -0.74 7 7
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.001 0.13 -10000 0 -0.44 11 11
E2F1 0.001 0.044 -10000 0 -10000 0 0
PPARG 0.026 0.006 -10000 0 -10000 0 0
SLC3A2 0.001 0.13 -10000 0 -0.5 5 5
IRF4 0.019 0.025 -10000 0 -10000 0 0
PTGS2 -0.17 0.44 -10000 0 -1 33 33
CSF2 -0.14 0.38 -10000 0 -0.96 27 27
JunB/Fra1/NFAT1-c-4 -0.056 0.36 -10000 0 -0.89 27 27
IL4 -0.43 0.33 -10000 0 -0.82 52 52
IL5 -0.14 0.38 -10000 0 -0.94 29 29
IL2 -0.072 0.23 -10000 0 -0.68 16 16
IL3 -0.024 0.15 -10000 0 -0.76 5 5
RNF128 0.015 0.11 -10000 0 -0.74 4 4
NFATC1 -0.078 0.28 -10000 0 -0.72 29 29
CDK4 0.042 0.18 0.5 15 -10000 0 15
PTPRK 0 0.13 -10000 0 -0.5 5 5
IL8 -0.14 0.38 -10000 0 -0.94 30 30
POU2F1 0.026 0.006 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.025 0.008 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.04 0.1 -10000 0 -0.3 10 10
NT3 (dimer)/TRKC -0.11 0.25 -10000 0 -0.52 51 51
NT3 (dimer)/TRKB -0.21 0.28 -10000 0 -0.47 96 96
SHC/Grb2/SOS1/GAB1/PI3K 0.027 0.012 -10000 0 -10000 0 0
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
BDNF 0.014 0.032 -10000 0 -10000 0 0
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
DYNLT1 0.026 0.005 -10000 0 -10000 0 0
NTRK1 -0.11 0.26 -10000 0 -0.65 37 37
NTRK2 -0.25 0.33 -10000 0 -0.65 82 82
NTRK3 -0.067 0.24 -10000 0 -0.66 27 27
NT-4/5 (dimer)/TRKB -0.16 0.24 -10000 0 -0.42 84 84
neuron apoptosis 0.13 0.19 0.48 30 -10000 0 30
SHC 2-3/Grb2 -0.14 0.21 -10000 0 -0.53 30 30
SHC1 0.026 0.005 -10000 0 -10000 0 0
SHC2 -0.12 0.18 -10000 0 -0.5 26 26
SHC3 -0.14 0.22 -10000 0 -0.54 36 36
STAT3 (dimer) 0.031 0.009 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.11 0.27 -10000 0 -0.5 58 58
RIN/GDP -0.025 0.12 0.32 5 -0.28 6 11
GIPC1 0.027 0.002 -10000 0 -10000 0 0
KRAS 0.026 0.006 -10000 0 -10000 0 0
DNAJA3 -0.055 0.13 -10000 0 -0.31 36 36
RIN/GTP 0.012 0.006 -10000 0 -10000 0 0
CCND1 0.018 0.006 -10000 0 -10000 0 0
MAGED1 0.027 0.003 -10000 0 -10000 0 0
PTPN11 0.026 0.006 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.003 0.032 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.05 0.018 -10000 0 -10000 0 0
GRB2 0.025 0.007 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.06 0.2 -10000 0 -0.44 44 44
TRKA/NEDD4-2 -0.065 0.2 -10000 0 -0.48 38 38
ELMO1 0.022 0.011 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0.029 0.015 -10000 0 -10000 0 0
NGF 0.004 0.12 -10000 0 -0.66 6 6
HRAS 0.027 0.003 -10000 0 -10000 0 0
DOCK1 0.027 0.004 -10000 0 -10000 0 0
GAB2 0.027 0.003 -10000 0 -10000 0 0
RIT2 -0.013 0.013 -10000 0 -10000 0 0
RIT1 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.006 -10000 0 -10000 0 0
DNM1 0 0.043 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.047 0.14 -10000 0 -0.31 37 37
mol:GDP -0.046 0.16 0.39 5 -0.39 11 16
NGF (dimer) 0.004 0.12 -10000 0 -0.66 6 6
RhoG/GDP 0.016 0.008 -10000 0 -10000 0 0
RIT1/GDP -0.024 0.12 0.31 6 -0.28 6 12
TIAM1 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.15 0.24 -10000 0 -0.43 80 80
KIDINS220/CRKL/C3G 0.036 0.014 -10000 0 -10000 0 0
SHC/RasGAP 0.038 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2 0.049 0.018 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.061 0.025 -10000 0 -10000 0 0
RIT1/GTP 0.02 0.004 -10000 0 -10000 0 0
NT3 (dimer) -0.077 0.24 -10000 0 -0.66 29 29
RAP1/GDP -0.029 0.084 -10000 0 -0.24 6 6
KIDINS220/CRKL 0.025 0.008 -10000 0 -10000 0 0
BDNF (dimer) 0.014 0.032 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.055 0.2 -10000 0 -0.43 42 42
Schwann cell development -0.037 0.034 -10000 0 -10000 0 0
EHD4 0.027 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.059 0.026 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.023 0.032 -10000 0 -0.25 1 1
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP -0.21 0.24 -10000 0 -0.41 106 106
ABL1 0.026 0.006 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.037 0.012 -10000 0 -10000 0 0
Rap1/GTP -0.072 0.14 -10000 0 -0.46 11 11
STAT3 0.031 0.009 -10000 0 -10000 0 0
axon guidance -0.21 0.22 -10000 0 -0.39 106 106
MAPK3 -0.075 0.16 -10000 0 -0.4 36 36
MAPK1 -0.082 0.17 -10000 0 -0.4 43 43
CDC42/GDP -0.021 0.12 0.29 7 -0.28 6 13
NTF3 -0.077 0.24 -10000 0 -0.66 29 29
NTF4 -0.003 0.032 -10000 0 -10000 0 0
NGF (dimer)/TRKA/FAIM -0.05 0.2 -10000 0 -0.42 41 41
PI3K 0.039 0.009 -10000 0 -10000 0 0
FRS3 0.026 0.007 -10000 0 -10000 0 0
FAIM 0.026 0.009 -10000 0 -10000 0 0
GAB1 0.026 0.006 -10000 0 -10000 0 0
RASGRF1 -0.062 0.15 -10000 0 -0.33 38 38
SOS1 0.027 0.004 -10000 0 -10000 0 0
MCF2L -0.11 0.21 -10000 0 -0.47 47 47
RGS19 0.025 0.009 -10000 0 -10000 0 0
CDC42 0.025 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.013 0.09 -10000 0 -0.49 2 2
Rac1/GDP -0.026 0.1 0.26 3 -0.29 5 8
NGF (dimer)/TRKA/GRIT -0.065 0.19 -10000 0 -0.43 42 42
neuron projection morphogenesis -0.03 0.14 -10000 0 -0.52 5 5
NGF (dimer)/TRKA/NEDD4-2 -0.055 0.2 -10000 0 -0.43 42 42
MAP2K1 0.03 0.065 0.36 5 -10000 0 5
NGFR 0.008 0.11 -10000 0 -0.66 5 5
NGF (dimer)/TRKA/GIPC/GAIP -0.049 0.14 -10000 0 -0.31 40 40
RAS family/GTP/PI3K 0.023 0.009 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 0.068 0.031 -10000 0 -10000 0 0
NRAS 0.026 0.006 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.012 -10000 0 -10000 0 0
PRKCI 0.027 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.022 0.011 -10000 0 -10000 0 0
PRKCZ 0.025 0.008 -10000 0 -10000 0 0
MAPKKK cascade -0.14 0.27 -10000 0 -0.6 49 49
RASA1 0.027 0.005 -10000 0 -10000 0 0
TRKA/c-Abl -0.062 0.21 -10000 0 -0.49 37 37
SQSTM1 0.024 0.015 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.13 0.22 -10000 0 -0.4 79 79
NGF (dimer)/TRKA/p62/Atypical PKCs -0.024 0.18 -10000 0 -0.38 38 38
MATK 0.011 0.086 -10000 0 -0.66 3 3
NEDD4L 0.023 0.027 -10000 0 -0.35 1 1
RAS family/GDP -0.042 0.066 -10000 0 -0.23 4 4
NGF (dimer)/TRKA -0.059 0.15 -10000 0 -0.34 38 38
Rac1/GTP -0.057 0.1 -10000 0 -0.31 17 17
FRS2 family/SHP2/CRK family 0.064 0.034 -10000 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.009 0.011 -10000 0 -10000 0 0
MAP4K4 0.011 0.053 -10000 0 -0.33 1 1
BAG4 0.027 0.005 -10000 0 -10000 0 0
PKC zeta/ceramide -0.11 0.089 -10000 0 -0.27 37 37
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.02 0.024 -10000 0 -10000 0 0
BAX -0.048 0.056 -10000 0 -0.36 4 4
RIPK1 0.026 0.006 -10000 0 -10000 0 0
AKT1 0.019 0.051 0.71 1 -10000 0 1
BAD -0.12 0.081 -10000 0 -0.27 37 37
SMPD1 0.009 0.055 0.22 4 -0.22 4 8
RB1 -0.11 0.083 -10000 0 -0.27 37 37
FADD/Caspase 8 0.012 0.064 -10000 0 -10000 0 0
MAP2K4 -0.1 0.082 0.21 1 -0.26 33 34
NSMAF 0.027 0.004 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.099 0.082 0.21 1 -0.26 31 32
EGF -0.58 0.21 -10000 0 -0.65 176 176
mol:ceramide -0.12 0.086 -10000 0 -0.29 37 37
MADD 0.027 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.009 0.011 -10000 0 -10000 0 0
ASAH1 0.026 0.005 -10000 0 -10000 0 0
negative regulation of cell cycle -0.11 0.083 -10000 0 -0.27 37 37
cell proliferation -0.092 0.086 -10000 0 -0.35 5 5
BID -0.06 0.2 -10000 0 -0.69 17 17
MAP3K1 -0.11 0.083 -10000 0 -0.27 36 36
EIF2A -0.099 0.082 0.24 1 -0.25 34 35
TRADD 0.026 0.007 -10000 0 -10000 0 0
CRADD 0.026 0.005 -10000 0 -10000 0 0
MAPK3 -0.092 0.08 -10000 0 -0.24 31 31
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.1 0.083 -10000 0 -0.24 30 30
Cathepsin D/ceramide -0.11 0.086 -10000 0 -0.27 37 37
FADD 0.012 0.045 -10000 0 -10000 0 0
KSR1 -0.11 0.083 0.22 1 -0.27 32 33
MAPK8 -0.11 0.1 -10000 0 -0.26 47 47
PRKRA -0.11 0.084 0.19 1 -0.27 36 37
PDGFA 0.02 0.018 -10000 0 -10000 0 0
TRAF2 0.026 0.006 -10000 0 -10000 0 0
IGF1 0.009 0.11 -10000 0 -0.66 5 5
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.12 0.086 -10000 0 -0.29 37 37
CTSD 0.027 0.003 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.039 0.009 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.097 0.092 -10000 0 -0.38 5 5
PRKCD 0.026 0.005 -10000 0 -10000 0 0
PRKCZ 0.025 0.008 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.009 0.011 -10000 0 -10000 0 0
RelA/NF kappa B1 0.039 0.009 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.026 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.012 0.05 -10000 0 -0.35 1 1
TNFR1A/BAG4/TNF-alpha 0.043 0.051 -10000 0 -0.43 2 2
mol:Sphingosine-1-phosphate 0.009 0.011 -10000 0 -10000 0 0
MAP2K1 -0.095 0.081 -10000 0 -0.25 30 30
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.027 0.002 -10000 0 -10000 0 0
CYCS -0.052 0.041 -10000 0 -0.19 3 3
TNFRSF1A 0.026 0.006 -10000 0 -10000 0 0
NFKB1 0.026 0.006 -10000 0 -10000 0 0
TNFR1A/BAG4 0.038 0.01 -10000 0 -10000 0 0
EIF2AK2 -0.11 0.081 0.18 1 -0.26 36 37
TNF-alpha/TNFR1A/FAN 0.044 0.051 -10000 0 -0.43 2 2
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.019 0.082 -10000 0 -0.44 4 4
MAP2K2 -0.096 0.08 0.2 1 -0.25 31 32
SMPD3 0.01 0.036 -10000 0 -10000 0 0
TNF 0.013 0.072 -10000 0 -0.66 2 2
PKC zeta/PAR4 0.035 0.014 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.2 0.084 0.25 145 -10000 0 145
NF kappa B1/RelA/I kappa B alpha 0.068 0.031 -10000 0 -10000 0 0
AIFM1 -0.068 0.06 -10000 0 -0.17 37 37
BCL2 0.025 0.008 -10000 0 -10000 0 0
S1P1 pathway

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 -0.057 0.2 -10000 0 -0.5 33 33
PDGFRB -0.001 0.14 -10000 0 -0.66 8 8
SPHK1 -0.004 0.032 -10000 0 -10000 0 0
mol:S1P -0.003 0.042 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.062 0.18 0.32 1 -0.45 25 26
GNAO1 -0.011 0.14 -10000 0 -0.66 9 9
PDGFB-D/PDGFRB/PLCgamma1 -0.048 0.18 0.43 1 -0.46 20 21
PLCG1 -0.056 0.17 0.33 2 -0.43 24 26
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.001 0.14 -10000 0 -0.66 8 8
GNAI2 0.022 0.018 -10000 0 -10000 0 0
GNAI3 0.021 0.017 -10000 0 -10000 0 0
GNAI1 0.015 0.051 -10000 0 -0.66 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.071 0.16 -10000 0 -0.43 33 33
S1P1/S1P -0.055 0.14 -10000 0 -0.34 29 29
negative regulation of cAMP metabolic process -0.06 0.17 0.31 1 -0.44 25 26
MAPK3 -0.07 0.22 0.36 7 -0.57 26 33
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
KDR -0.093 0.26 -10000 0 -0.65 34 34
PLCB2 -0.042 0.14 0.28 4 -0.32 24 28
RAC1 0.022 0.011 -10000 0 -10000 0 0
RhoA/GTP -0.047 0.12 -10000 0 -0.3 27 27
receptor internalization -0.055 0.12 -10000 0 -0.32 29 29
PTGS2 -0.13 0.38 0.48 2 -1 28 30
Rac1/GTP -0.043 0.1 -10000 0 -0.3 21 21
RHOA 0.026 0.005 -10000 0 -10000 0 0
VEGFA 0.022 0.015 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.06 0.17 0.31 1 -0.44 25 26
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.02 0.017 -10000 0 -10000 0 0
MAPK1 -0.092 0.24 0.3 1 -0.6 31 32
S1P1/S1P/PDGFB-D/PDGFRB -0.054 0.17 0.27 2 -0.37 32 34
ABCC1 0.024 0.009 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0 0.082 -10000 0 -0.28 15 15
epithelial cell differentiation 0.02 0.11 -10000 0 -0.37 15 15
CYFIP2 0.026 0.005 -10000 0 -10000 0 0
ENAH -0.006 0.12 0.5 6 -10000 0 6
EGFR 0.022 0.011 -10000 0 -10000 0 0
EPHA2 0.025 0.008 -10000 0 -10000 0 0
MYO6 -0.001 0.12 0.35 5 -0.36 15 20
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.051 0.016 -10000 0 -10000 0 0
AQP5 -0.069 0.19 -10000 0 -0.58 20 20
CTNND1 0.027 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0.12 0.35 5 -0.35 15 20
regulation of calcium-dependent cell-cell adhesion -0.025 0.15 0.35 4 -0.38 23 27
EGF -0.58 0.21 -10000 0 -0.65 176 176
NCKAP1 0.027 0.004 -10000 0 -10000 0 0
AQP3 -0.16 0.26 -10000 0 -0.57 52 52
cortical microtubule organization 0.02 0.11 -10000 0 -0.37 15 15
GO:0000145 -0.018 0.11 0.34 5 -0.34 15 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.024 0.12 -10000 0 -0.38 15 15
MLLT4 0.026 0.005 -10000 0 -10000 0 0
ARF6/GDP -0.035 0.079 -10000 0 -0.32 12 12
ARF6 0.026 0.007 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.059 0.027 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.013 0.099 0.34 1 -0.33 15 16
PVRL2 0.027 0.004 -10000 0 -10000 0 0
ZYX -0.008 0.11 0.35 2 -0.36 14 16
ARF6/GTP 0.063 0.031 -10000 0 -10000 0 0
CDH1 -0.027 0.18 -10000 0 -0.66 15 15
EGFR/EGFR/EGF/EGF -0.29 0.16 -10000 0 -0.39 128 128
RhoA/GDP 0.022 0.11 -10000 0 -0.36 15 15
actin cytoskeleton organization -0.018 0.11 0.33 5 -0.35 15 20
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
GIT1 0.026 0.006 -10000 0 -10000 0 0
IGF1R 0.027 0.004 -10000 0 -10000 0 0
IGF1 0.009 0.11 -10000 0 -0.66 5 5
DIAPH1 0.031 0.1 -10000 0 -0.53 3 3
Wnt receptor signaling pathway -0.02 0.11 0.37 15 -10000 0 15
RHOA 0.026 0.005 -10000 0 -10000 0 0
RhoA/GTP -0.036 0.08 -10000 0 -0.33 12 12
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
VCL -0.019 0.12 0.34 5 -0.36 15 20
EFNA1 0.026 0.005 -10000 0 -10000 0 0
LPP -0.024 0.1 0.34 2 -0.34 15 17
Ephrin A1/EPHA2 0.014 0.11 -10000 0 -0.35 15 15
SEC6/SEC8 -0.015 0.09 -10000 0 -0.34 14 14
MGAT3 -0.026 0.15 0.35 4 -0.39 23 27
HGF/MET -0.001 0.12 -10000 0 -0.37 17 17
HGF 0.001 0.12 -10000 0 -0.66 6 6
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0 0.083 -10000 0 -0.29 15 15
actin cable formation 0.024 0.14 0.56 8 -0.29 1 9
KIAA1543 -0.019 0.12 0.34 5 -0.34 16 21
KIFC3 -0.015 0.1 -10000 0 -0.36 15 15
NCK1 0.026 0.005 -10000 0 -10000 0 0
EXOC3 0.026 0.005 -10000 0 -10000 0 0
ACTN1 0 0.12 0.35 5 -0.36 15 20
NCK1/GIT1 0.037 0.011 -10000 0 -10000 0 0
mol:GDP 0.02 0.11 -10000 0 -0.37 15 15
EXOC4 0.022 0.011 -10000 0 -10000 0 0
STX4 -0.017 0.099 -10000 0 -0.36 15 15
PIP5K1C -0.001 0.12 0.35 5 -0.36 15 20
LIMA1 0.026 0.005 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
ROCK1 -0.004 0.14 0.52 7 -10000 0 7
adherens junction assembly 0.001 0.13 0.35 11 -0.44 1 12
IGF-1R heterotetramer/IGF1 0.005 0.12 -10000 0 -0.35 20 20
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.038 0.01 -10000 0 -10000 0 0
MET 0.017 0.023 -10000 0 -10000 0 0
PLEKHA7 -0.002 0.12 0.35 5 -0.36 16 21
mol:GTP 0.057 0.026 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity -0.003 0.11 0.33 1 -10000 0 1
cortical actin cytoskeleton stabilization 0 0.082 -10000 0 -0.28 15 15
regulation of cell-cell adhesion -0.018 0.11 0.33 5 -0.35 15 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0 0.083 -10000 0 -0.29 15 15
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.89 0.59 -10000 0 -1.3 139 139
PLK1 0.047 0.097 -10000 0 -10000 0 0
CDKN1B -0.072 0.12 -10000 0 -0.35 6 6
FOXO3 0.047 0.046 -10000 0 -10000 0 0
KAT2B 0.034 0.008 -10000 0 -10000 0 0
FOXO1/SIRT1 -0.3 0.26 -10000 0 -0.44 138 138
CAT 0.033 0.07 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
AKT1 -0.031 0.048 -10000 0 -10000 0 0
FOXO1 -0.33 0.27 -10000 0 -0.47 139 139
MAPK10 0.029 0.074 0.21 7 -10000 0 7
mol:GTP 0.001 0 -10000 0 -10000 0 0
FOXO4 0.052 0.09 0.36 3 -10000 0 3
response to oxidative stress -0.037 0.036 -10000 0 -0.17 5 5
FOXO3A/SIRT1 0.062 0.079 -10000 0 -10000 0 0
XPO1 0.028 0.003 -10000 0 -10000 0 0
EP300 -0.04 0.051 -10000 0 -0.19 5 5
BCL2L11 0.029 0.052 -10000 0 -0.68 1 1
FOXO1/SKP2 -0.3 0.25 -10000 0 -0.44 138 138
mol:GDP -0.037 0.036 -10000 0 -0.17 5 5
RAN 0.027 0.006 -10000 0 -10000 0 0
GADD45A 0.048 0.16 -10000 0 -0.6 8 8
YWHAQ 0.027 0.005 -10000 0 -10000 0 0
FOXO1/14-3-3 family -0.048 0.12 -10000 0 -0.46 9 9
MST1 0.031 0.049 -10000 0 -0.65 1 1
CSNK1D 0.025 0.007 -10000 0 -10000 0 0
CSNK1E 0.025 0.008 -10000 0 -10000 0 0
FOXO4/14-3-3 family -0.01 0.12 -10000 0 -0.5 6 6
YWHAB 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.023 0.08 0.21 5 -0.23 3 8
MAPK9 0.029 0.074 0.3 1 -10000 0 1
YWHAG 0.022 0.011 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
YWHAZ 0.027 0.004 -10000 0 -10000 0 0
SIRT1 0.029 0.005 -10000 0 -10000 0 0
SOD2 -0.081 0.14 -10000 0 -0.56 3 3
RBL2 0.057 0.066 -10000 0 -10000 0 0
RAL/GDP -0.003 0.032 -10000 0 -10000 0 0
CHUK 0.035 0.005 -10000 0 -10000 0 0
Ran/GTP 0.022 0.005 -10000 0 -10000 0 0
CSNK1G2 0.027 0.004 -10000 0 -10000 0 0
RAL/GTP 0.001 0.031 -10000 0 -10000 0 0
CSNK1G1 0.027 0.003 -10000 0 -10000 0 0
FASLG 0.009 0.12 -10000 0 -0.72 5 5
SKP2 0.027 0.004 -10000 0 -10000 0 0
USP7 0.026 0.009 -10000 0 -10000 0 0
IKBKB 0.035 0.007 -10000 0 -10000 0 0
CCNB1 0.035 0.07 -10000 0 -10000 0 0
FOXO1-3a-4/beta catenin -0.062 0.13 0.35 1 -0.41 1 2
proteasomal ubiquitin-dependent protein catabolic process -0.3 0.25 -10000 0 -0.43 138 138
CSNK1A1 0.026 0.005 -10000 0 -10000 0 0
SGK1 0.035 0.007 -10000 0 -10000 0 0
CSNK1G3 0.026 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.04 0.009 -10000 0 -10000 0 0
ZFAND5 0.049 0.084 0.46 1 -10000 0 1
SFN -0.017 0.047 -10000 0 -10000 0 0
CDK2 -0.058 0.061 -10000 0 -0.23 2 2
FOXO3A/14-3-3 -0.001 0.11 -10000 0 -0.52 4 4
CREBBP -0.053 0.058 -10000 0 -0.25 1 1
FBXO32 0.037 0.072 -10000 0 -10000 0 0
BCL6 0.056 0.081 -10000 0 -0.6 1 1
RALB 0.028 0.003 -10000 0 -10000 0 0
RALA 0.023 0.011 -10000 0 -10000 0 0
YWHAH 0.025 0.008 -10000 0 -10000 0 0
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.005 0.12 -9999 0 -0.43 14 14
EFNA5 -0.023 0.18 -9999 0 -0.66 14 14
FYN -0.031 0.1 -9999 0 -0.4 14 14
neuron projection morphogenesis -0.005 0.12 -9999 0 -0.43 14 14
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.005 0.12 -9999 0 -0.43 14 14
EPHA5 -0.007 0.023 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.033 0.1 -10000 0 -0.9 2 2
SMARCC2 0.028 0.005 -10000 0 -10000 0 0
SMARCC1 0.028 0.006 -10000 0 -10000 0 0
TBX21 -0.042 0.071 0.32 1 -0.32 1 2
SUMO2 0.017 0.018 -10000 0 -10000 0 0
STAT1 (dimer) 0.031 0.013 -10000 0 -10000 0 0
FKBP4 0.026 0.006 -10000 0 -10000 0 0
FKBP5 0.015 0.084 -10000 0 -0.66 3 3
GR alpha/HSP90/FKBP51/HSP90 0.07 0.08 -10000 0 -0.38 3 3
PRL -0.029 0.065 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/TIF2 0.088 0.2 0.46 11 -0.44 8 19
RELA -0.08 0.12 -10000 0 -0.28 19 19
FGG 0.086 0.12 0.4 6 -10000 0 6
GR beta/TIF2 0.03 0.16 0.27 3 -0.47 16 19
IFNG -0.092 0.15 -10000 0 -0.57 5 5
apoptosis -0.056 0.23 -10000 0 -0.58 23 23
CREB1 0.015 0.067 -10000 0 -0.36 6 6
histone acetylation -0.026 0.061 -10000 0 -0.28 1 1
BGLAP -0.03 0.066 -10000 0 -10000 0 0
GR/PKAc 0.091 0.056 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.14 0.2 -10000 0 -0.34 88 88
SMARCD1 0.028 0.005 -10000 0 -10000 0 0
MDM2 0.042 0.051 0.19 5 -10000 0 5
GATA3 -0.47 0.3 -10000 0 -0.65 146 146
AKT1 0.023 0.02 -10000 0 -10000 0 0
CSF2 -0.03 0.049 -10000 0 -10000 0 0
GSK3B 0.018 0.019 -10000 0 -10000 0 0
NR1I3 -0.065 0.27 -10000 0 -0.81 15 15
CSN2 0.069 0.1 0.33 5 -10000 0 5
BRG1/BAF155/BAF170/BAF60A 0.071 0.02 -10000 0 -10000 0 0
NFATC1 0.026 0.008 -10000 0 -10000 0 0
POU2F1 0.027 0.006 -10000 0 -10000 0 0
CDKN1A 0.016 0.057 -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 -0.017 0.047 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.064 0.086 -10000 0 -0.34 3 3
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.073 0.29 0.41 1 -0.82 20 21
JUN -0.07 0.14 -10000 0 -0.44 17 17
IL4 -0.039 0.066 -10000 0 -10000 0 0
CDK5R1 0.025 0.007 -10000 0 -10000 0 0
PRKACA 0.027 0.002 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.05 0.15 0.22 7 -0.39 25 32
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.083 0.078 -10000 0 -0.34 3 3
cortisol/GR alpha (monomer) 0.13 0.17 0.51 11 -10000 0 11
NCOA2 -0.029 0.19 -10000 0 -0.66 16 16
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.075 0.23 -10000 0 -0.61 30 30
AP-1/NFAT1-c-4 -0.12 0.23 -10000 0 -0.61 25 25
AFP -0.16 0.41 -10000 0 -1.3 20 20
SUV420H1 0.027 0.004 -10000 0 -10000 0 0
IRF1 0.078 0.077 -10000 0 -10000 0 0
TP53 0.037 0.015 -10000 0 -10000 0 0
PPP5C 0.027 0.004 -10000 0 -10000 0 0
KRT17 -0.12 0.26 -10000 0 -1.1 10 10
KRT14 -0.042 0.057 -10000 0 -10000 0 0
TBP 0.033 0.007 -10000 0 -10000 0 0
CREBBP 0.027 0.011 -10000 0 -10000 0 0
HDAC1 0.025 0.007 -10000 0 -10000 0 0
HDAC2 0.026 0.005 -10000 0 -10000 0 0
AP-1 -0.12 0.23 -10000 0 -0.61 25 25
MAPK14 0.018 0.018 -10000 0 -10000 0 0
MAPK10 0.019 0.018 -10000 0 -10000 0 0
MAPK11 0.017 0.019 -10000 0 -10000 0 0
KRT5 -0.1 0.21 -10000 0 -0.97 6 6
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 0.027 0.015 -10000 0 -10000 0 0
STAT1 0.031 0.013 -10000 0 -10000 0 0
CGA -0.075 0.21 -10000 0 -1.2 6 6
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.008 0.062 -10000 0 -10000 0 0
MAPK3 0.018 0.017 -10000 0 -10000 0 0
MAPK1 0.017 0.018 -10000 0 -10000 0 0
ICAM1 -0.14 0.18 -10000 0 -0.48 20 20
NFKB1 -0.076 0.11 -10000 0 -0.28 14 14
MAPK8 -0.069 0.12 -10000 0 -0.42 11 11
MAPK9 0.019 0.017 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.062 0.24 -10000 0 -0.62 23 23
BAX 0.02 0.048 -10000 0 -10000 0 0
POMC -0.19 0.27 -10000 0 -0.97 9 9
EP300 0.028 0.011 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.13 0.15 0.47 11 -10000 0 11
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.08 0.34 10 -10000 0 10
SGK1 0.037 0.073 -10000 0 -10000 0 0
IL13 -0.38 0.26 -10000 0 -0.67 60 60
IL6 -0.19 0.35 -10000 0 -1.1 20 20
PRKACG -0.009 0.018 -10000 0 -10000 0 0
IL5 -0.31 0.21 -10000 0 -0.59 40 40
IL2 -0.1 0.16 -10000 0 -0.67 6 6
CDK5 0.021 0.011 -10000 0 -10000 0 0
PRKACB 0.026 0.006 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
IL8 -0.15 0.18 -10000 0 -0.52 18 18
CDK5R1/CDK5 0.028 0.019 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.081 0.17 -10000 0 -0.42 15 15
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.11 0.14 0.46 6 -10000 0 6
SMARCA4 0.028 0.003 -10000 0 -10000 0 0
chromatin remodeling 0.086 0.083 0.31 5 -10000 0 5
NF kappa B1 p50/RelA/Cbp -0.08 0.17 -10000 0 -0.42 17 17
JUN (dimer) -0.071 0.14 -10000 0 -0.44 17 17
YWHAH 0.025 0.008 -10000 0 -10000 0 0
VIPR1 -0.084 0.21 0.32 1 -0.96 10 11
NR3C1 0.076 0.097 0.35 5 -10000 0 5
NR4A1 -0.25 0.34 -10000 0 -0.66 79 79
TIF2/SUV420H1 -0.004 0.15 -10000 0 -0.5 16 16
MAPKKK cascade -0.056 0.23 -10000 0 -0.58 23 23
cortisol/GR alpha (dimer)/Src-1 0.12 0.15 0.45 9 -10000 0 9
PBX1 0.02 0.069 -10000 0 -0.66 2 2
POU1F1 0.005 0.023 -10000 0 -10000 0 0
SELE -0.54 0.58 -10000 0 -1.1 95 95
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.086 0.083 0.31 5 -10000 0 5
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.11 0.14 0.46 6 -10000 0 6
mol:cortisol 0.062 0.089 0.27 13 -10000 0 13
MMP1 -0.098 0.31 -10000 0 -1.1 15 15
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.011 0.12 -10000 0 -0.38 2 2
IHH -0.049 0.23 -10000 0 -0.68 23 23
SHH Np/Cholesterol/GAS1 -0.001 0.085 -10000 0 -0.34 11 11
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.001 0.085 0.34 11 -10000 0 11
SMO/beta Arrestin2 -0.02 0.15 -10000 0 -0.49 5 5
SMO -0.028 0.15 -10000 0 -0.44 18 18
AKT1 -0.024 0.15 -10000 0 -0.63 7 7
ARRB2 0.025 0.01 -10000 0 -10000 0 0
BOC 0.026 0.005 -10000 0 -10000 0 0
ADRBK1 0.027 0.002 -10000 0 -10000 0 0
heart looping -0.028 0.15 -10000 0 -0.44 18 18
STIL 0.009 0.13 -10000 0 -0.38 1 1
DHH N/PTCH2 0.011 0.11 -10000 0 -0.49 9 9
DHH N/PTCH1 -0.022 0.15 -10000 0 -0.37 31 31
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
DHH -0.008 0.14 -10000 0 -0.66 9 9
PTHLH -0.025 0.15 -10000 0 -0.48 2 2
determination of left/right symmetry -0.028 0.15 -10000 0 -0.44 18 18
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
skeletal system development -0.025 0.15 -10000 0 -0.48 2 2
IHH N/Hhip -0.041 0.19 -10000 0 -0.46 32 32
DHH N/Hhip -0.012 0.16 -10000 0 -0.54 16 16
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.028 0.15 -10000 0 -0.44 18 18
pancreas development -0.009 0.14 -10000 0 -0.66 9 9
HHAT 0.026 0.006 -10000 0 -10000 0 0
PI3K 0.039 0.009 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0 0.13 -10000 0 -0.62 8 8
somite specification -0.028 0.15 -10000 0 -0.44 18 18
SHH Np/Cholesterol/PTCH1 -0.016 0.11 -10000 0 -0.32 18 18
SHH Np/Cholesterol/PTCH2 0.012 0.052 -10000 0 -0.39 3 3
SHH Np/Cholesterol/Megalin -0.033 0.14 -10000 0 -0.41 24 24
SHH 0.002 0.063 -10000 0 -0.5 3 3
catabolic process -0.018 0.14 -10000 0 -0.39 23 23
SMO/Vitamin D3 -0.02 0.13 -10000 0 -0.44 6 6
SHH Np/Cholesterol/Hhip -0.006 0.097 -10000 0 -0.38 12 12
LRP2 -0.05 0.22 -10000 0 -0.66 22 22
receptor-mediated endocytosis -0.055 0.18 -10000 0 -0.62 12 12
SHH Np/Cholesterol/BOC 0.014 0.053 -10000 0 -0.4 3 3
SHH Np/Cholesterol/CDO 0.012 0.053 -10000 0 -0.4 3 3
mesenchymal cell differentiation 0.006 0.097 0.38 12 -10000 0 12
mol:Vitamin D3 0.016 0.14 -10000 0 -0.35 5 5
IHH N/PTCH2 -0.015 0.15 -10000 0 -0.43 23 23
CDON 0.025 0.013 -10000 0 -10000 0 0
IHH N/PTCH1 -0.01 0.14 -10000 0 -0.39 23 23
Megalin/LRPAP1 -0.02 0.17 -10000 0 -0.49 22 22
PTCH2 0.024 0.012 -10000 0 -10000 0 0
SHH Np/Cholesterol 0.005 0.05 -10000 0 -0.39 3 3
PTCH1 -0.018 0.14 -10000 0 -0.39 23 23
HHIP -0.009 0.14 -10000 0 -0.66 9 9
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.037 0.087 -10000 0 -0.38 7 7
ER alpha/Gai/GDP/Gbeta gamma -0.041 0.19 -10000 0 -0.58 16 16
AKT1 -0.029 0.22 -10000 0 -0.79 14 14
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.026 0.23 -10000 0 -0.78 15 15
mol:Ca2+ -0.11 0.21 -10000 0 -0.45 47 47
IGF1R 0.027 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin 0.009 0.1 -10000 0 -0.38 13 13
SHC1 0.026 0.005 -10000 0 -10000 0 0
apoptosis 0.027 0.21 0.73 15 -10000 0 15
RhoA/GTP 0.007 0.071 -10000 0 -0.34 7 7
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.013 0.17 -10000 0 -0.53 13 13
regulation of stress fiber formation 0.008 0.092 -10000 0 -0.34 4 4
E2/ERA-ERB (dimer) 0.013 0.09 -10000 0 -0.36 10 10
KRAS 0.026 0.006 -10000 0 -10000 0 0
G13/GTP 0.013 0.083 -10000 0 -0.33 10 10
pseudopodium formation -0.008 0.092 0.34 4 -10000 0 4
E2/ER alpha (dimer)/PELP1 0.013 0.09 -10000 0 -0.36 10 10
GRB2 0.025 0.007 -10000 0 -10000 0 0
GNG2 0.026 0.007 -10000 0 -10000 0 0
GNAO1 -0.007 0.14 -10000 0 -0.66 9 9
HRAS 0.027 0.003 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.012 0.19 0.36 2 -0.55 16 18
E2/ER beta (dimer) 0.019 0.007 -10000 0 -10000 0 0
mol:GDP -0.008 0.1 -10000 0 -0.44 10 10
mol:NADP -0.012 0.19 0.36 2 -0.55 16 18
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
mol:IP3 -0.12 0.22 -10000 0 -0.47 47 47
IGF-1R heterotetramer 0.027 0.004 -10000 0 -10000 0 0
PLCB1 -0.12 0.23 -10000 0 -0.48 49 49
PLCB2 -0.097 0.21 -10000 0 -0.49 42 42
IGF1 0.009 0.11 -10000 0 -0.66 5 5
mol:L-citrulline -0.012 0.19 0.36 2 -0.55 16 18
RHOA 0.026 0.005 -10000 0 -10000 0 0
Gai/GDP -0.032 0.21 -10000 0 -0.69 16 16
JNK cascade 0.019 0.007 -10000 0 -10000 0 0
BCAR1 0.026 0.007 -10000 0 -10000 0 0
ESR2 0.025 0.01 -10000 0 -10000 0 0
GNAQ 0.026 0.007 -10000 0 -10000 0 0
ESR1 -0.003 0.13 -10000 0 -0.56 10 10
Gq family/GDP/Gbeta gamma -0.065 0.2 -10000 0 -0.64 13 13
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.007 0.13 -10000 0 -0.74 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.012 0.17 -10000 0 -0.55 12 12
GNAZ 0.025 0.008 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.002 0.1 -10000 0 -0.42 10 10
STRN 0.017 0.084 -10000 0 -0.66 3 3
GNAL 0.025 0.008 -10000 0 -10000 0 0
PELP1 0.025 0.007 -10000 0 -10000 0 0
MAPK11 0.012 0.006 -10000 0 -10000 0 0
GNAI2 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.05 -10000 0 -0.66 1 1
HBEGF -0.019 0.19 0.43 6 -0.53 15 21
cAMP biosynthetic process 0.01 0.074 -10000 0 -0.35 7 7
SRC -0.037 0.18 0.32 1 -0.56 14 15
PI3K 0.039 0.009 -10000 0 -10000 0 0
GNB1 0.025 0.008 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.021 0.1 -10000 0 -0.4 9 9
SOS1 0.027 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.04 0.14 -10000 0 -0.46 13 13
Gs family/GTP 0.016 0.077 -10000 0 -0.36 7 7
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.047 0.016 -10000 0 -10000 0 0
vasodilation -0.01 0.18 0.36 2 -0.52 16 18
mol:DAG -0.12 0.22 -10000 0 -0.47 47 47
Gs family/GDP/Gbeta gamma 0.002 0.091 -10000 0 -0.38 9 9
MSN -0.009 0.096 0.35 4 -10000 0 4
Gq family/GTP -0.092 0.23 -10000 0 -0.5 43 43
mol:PI-3-4-5-P3 -0.023 0.22 -10000 0 -0.75 15 15
NRAS 0.026 0.006 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.01 0.18 0.52 16 -0.36 2 18
GRB2/SOS1 0.037 0.012 -10000 0 -10000 0 0
RhoA/GDP 0.01 0.11 -10000 0 -0.41 10 10
NOS3 -0.015 0.21 0.37 2 -0.58 16 18
GNA11 0.015 0.088 -10000 0 -0.58 4 4
MAPKKK cascade -0.012 0.2 0.38 3 -0.59 17 20
E2/ER alpha (dimer)/PELP1/Src -0.017 0.18 -10000 0 -0.56 13 13
ruffle organization -0.008 0.092 0.34 4 -10000 0 4
ROCK2 -0.007 0.1 0.36 4 -0.34 3 7
GNA14 -0.11 0.27 -10000 0 -0.64 41 41
GNA15 0.021 0.023 -10000 0 -10000 0 0
GNA13 0.025 0.007 -10000 0 -10000 0 0
MMP9 -0.034 0.18 0.41 3 -0.54 14 17
MMP2 -0.021 0.18 0.49 1 -0.55 13 14
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.012 0.13 -9999 0 -0.42 15 15
E-cadherin/beta catenin -0.004 0.14 -9999 0 -0.5 15 15
CTNNB1 0.026 0.005 -9999 0 -10000 0 0
JUP 0.025 0.007 -9999 0 -10000 0 0
CDH1 -0.027 0.18 -9999 0 -0.66 15 15
LPA4-mediated signaling events

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
ADCY4 -0.031 0.1 -10000 0 -0.43 12 12
ADCY5 -0.027 0.093 -10000 0 -0.43 10 10
ADCY6 -0.005 0.001 -10000 0 -10000 0 0
ADCY7 -0.006 0.007 -10000 0 -10000 0 0
ADCY1 -0.15 0.2 -10000 0 -0.43 70 70
ADCY2 -0.023 0.016 -10000 0 -10000 0 0
ADCY3 -0.005 0.001 -10000 0 -10000 0 0
ADCY8 -0.008 0.006 -10000 0 -10000 0 0
PRKCE 0.007 0.001 -10000 0 -10000 0 0
ADCY9 -0.005 0.002 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.028 0.11 0.35 6 -0.26 7 13
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC 0.017 0.084 -10000 0 -0.32 1 1
FYN 0.008 0.11 0.36 5 -0.46 2 7
LAT/GRAP2/SLP76 0.022 0.088 0.29 2 -0.32 2 4
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.019 0.13 0.36 14 -0.33 4 18
B2M 0.028 0.005 -10000 0 -10000 0 0
IKBKG 0.013 0.048 0.15 7 -10000 0 7
MAP3K8 0.027 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.059 0.05 -10000 0 -0.11 103 103
integrin-mediated signaling pathway 0.033 0.013 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.01 0.13 0.4 8 -0.39 6 14
TRPV6 -0.23 0.57 0.81 35 -0.66 110 145
CD28 0.019 0.053 -10000 0 -0.66 1 1
SHC1 0.003 0.098 0.32 3 -0.35 3 6
receptor internalization 0.005 0.094 -10000 0 -0.35 8 8
PRF1 0.016 0.092 -10000 0 -0.57 2 2
KRAS 0.026 0.006 -10000 0 -10000 0 0
GRB2 0.025 0.007 -10000 0 -10000 0 0
COT/AKT1 0.028 0.12 0.34 14 -0.27 3 17
LAT 0.01 0.1 0.36 4 -0.36 3 7
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D 0.01 0.038 -10000 0 -10000 0 0
CD3E 0.017 0.055 -10000 0 -0.66 1 1
CD3G 0.021 0.024 -10000 0 -10000 0 0
RASGRP2 0.001 0.026 0.084 2 -0.16 3 5
RASGRP1 0.021 0.13 0.4 11 -0.34 4 15
HLA-A 0.026 0.012 -10000 0 -10000 0 0
RASSF5 0.025 0.013 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0.034 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.039 0.094 0.31 13 -10000 0 13
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.009 0.038 -10000 0 -0.18 1 1
PRKCA 0.01 0.054 0.2 3 -0.25 1 4
GRAP2 0.022 0.017 -10000 0 -10000 0 0
mol:IP3 0.11 0.13 0.25 86 -0.37 1 87
EntrezGene:6957 0.001 0.002 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.014 0.047 -10000 0 -0.3 1 1
ORAI1 0.068 0.37 0.67 4 -0.66 34 38
CSK 0.004 0.094 0.29 3 -0.36 2 5
B7 family/CD28 0.031 0.096 0.28 1 -0.38 1 2
CHUK 0.027 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0.003 0.099 0.28 2 -0.37 4 6
PTPN6 0.004 0.097 0.29 3 -0.35 3 6
VAV1 -0.002 0.11 0.3 3 -0.42 4 7
Monovalent TCR/CD3 0.014 0.032 -10000 0 -0.3 1 1
CBL 0.026 0.005 -10000 0 -10000 0 0
LCK 0.004 0.12 0.38 4 -0.4 5 9
PAG1 0.004 0.097 0.3 4 -0.36 2 6
RAP1A 0.026 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.003 0.097 0.28 2 -0.37 4 6
CD80 0.013 0.033 -10000 0 -10000 0 0
CD86 0.008 0.038 -10000 0 -10000 0 0
PDK1/CARD11/BCL10/MALT1 -0.004 0.049 -10000 0 -0.22 1 1
HRAS 0.027 0.003 -10000 0 -10000 0 0
GO:0035030 -0.002 0.076 0.24 2 -0.33 1 3
CD8A 0.018 0.029 -10000 0 -10000 0 0
CD8B 0.02 0.027 -10000 0 -10000 0 0
PTPRC 0.022 0.051 -10000 0 -0.66 1 1
PDK1/PKC theta 0.027 0.16 0.48 14 -0.37 3 17
CSK/PAG1 0.003 0.09 0.29 3 -0.37 1 4
SOS1 0.027 0.004 -10000 0 -10000 0 0
peptide-MHC class I 0.038 0.015 -10000 0 -10000 0 0
GRAP2/SLP76 0.019 0.094 -10000 0 -0.35 2 2
STIM1 0.059 0.15 -10000 0 -0.82 3 3
RAS family/GTP 0.036 0.087 0.29 12 -10000 0 12
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.004 0.097 -10000 0 -0.36 8 8
mol:DAG 0.03 0.08 0.16 2 -0.35 1 3
RAP1A/GDP 0.024 0.052 0.18 11 -10000 0 11
PLCG1 0.026 0.006 -10000 0 -10000 0 0
CD247 0.023 0.02 -10000 0 -10000 0 0
cytotoxic T cell degranulation 0.017 0.09 -10000 0 -0.55 2 2
RAP1A/GTP 0.001 0.009 -10000 0 -0.062 2 2
mol:PI-3-4-5-P3 0.012 0.12 0.39 8 -0.33 6 14
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.11 0.15 0.27 71 -0.5 1 72
NRAS 0.026 0.006 -10000 0 -10000 0 0
ZAP70 0.015 0.032 -10000 0 -10000 0 0
GRB2/SOS1 0.037 0.012 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 0.008 0.089 0.28 1 -0.52 1 2
MALT1 0.025 0.008 -10000 0 -10000 0 0
TRAF6 0.027 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.029 0.036 -10000 0 -10000 0 0
CARD11 -0.001 0.04 -10000 0 -10000 0 0
PRKCB 0.007 0.05 0.16 1 -0.25 1 2
PRKCE 0.01 0.054 0.22 2 -0.25 1 3
PRKCQ 0.012 0.14 0.44 8 -0.39 4 12
LCP2 0.024 0.015 -10000 0 -10000 0 0
BCL10 0.026 0.006 -10000 0 -10000 0 0
regulation of survival gene product expression 0.019 0.12 0.35 14 -0.28 4 18
IKK complex 0.048 0.13 0.37 18 -10000 0 18
RAS family/GDP 0 0.007 -10000 0 -10000 0 0
MAP3K14 0.009 0.068 0.21 8 -0.22 2 10
PDPK1 0.026 0.14 0.42 14 -0.3 3 17
TCR/CD3/MHC I/CD8/Fyn 0.004 0.099 -10000 0 -0.42 3 3
Nongenotropic Androgen 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
PTK2 0.006 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.088 -10000 0 -0.39 8 8
regulation of S phase of mitotic cell cycle 0.01 0.062 -10000 0 -0.3 7 7
GNAO1 -0.007 0.14 -10000 0 -0.66 9 9
HRAS 0.026 0.008 -10000 0 -10000 0 0
SHBG/T-DHT 0.003 0.074 -10000 0 -0.34 8 8
PELP1 0.025 0.008 -10000 0 -10000 0 0
AKT1 0.007 0.002 -10000 0 -10000 0 0
MAP2K1 -0.024 0.083 -10000 0 -0.35 6 6
T-DHT/AR -0.003 0.1 -10000 0 -0.5 8 8
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.004 -10000 0 -0.009 30 30
GNAI2 0.026 0.006 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.049 -10000 0 -0.66 1 1
mol:GDP -0.016 0.1 -10000 0 -0.5 8 8
cell proliferation -0.044 0.17 0.41 1 -0.44 23 24
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
FOS -0.11 0.3 0.3 1 -0.81 30 31
mol:Ca2+ -0.005 0.02 -10000 0 -0.071 11 11
MAPK3 -0.02 0.13 0.34 4 -0.49 2 6
MAPK1 -0.049 0.16 -10000 0 -0.48 18 18
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
mol:IP3 -0.001 0.002 -10000 0 -0.005 30 30
cAMP biosynthetic process -0.007 0.078 0.23 5 -0.32 8 13
GNG2 0.026 0.007 -10000 0 -10000 0 0
potassium channel inhibitor activity -0.001 0.002 -10000 0 -0.005 30 30
HRAS/GTP 0.021 0.085 -10000 0 -0.35 8 8
actin cytoskeleton reorganization 0.03 0.02 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
voltage-gated calcium channel activity -0.001 0.002 -10000 0 -0.005 30 30
PI3K 0.035 0.008 -10000 0 -10000 0 0
apoptosis 0.049 0.18 0.47 24 -0.33 1 25
T-DHT/AR/PELP1 0.014 0.088 -10000 0 -0.4 8 8
HRAS/GDP -0.003 0.1 -10000 0 -0.48 8 8
CREB1 -0.054 0.19 0.33 1 -0.51 24 25
RAC1-CDC42/GTP 0.038 0.025 -10000 0 -10000 0 0
AR -0.003 0.14 -10000 0 -0.66 8 8
GNB1 0.025 0.008 -10000 0 -10000 0 0
RAF1 -0.005 0.084 -10000 0 -0.35 7 7
RAC1-CDC42/GDP 0.013 0.099 -10000 0 -0.48 7 7
T-DHT/AR/PELP1/Src 0.028 0.086 -10000 0 -0.38 8 8
MAP2K2 -0.025 0.083 -10000 0 -0.34 7 7
T-DHT/AR/PELP1/Src/PI3K 0.01 0.062 -10000 0 -0.3 7 7
GNAZ 0.025 0.008 -10000 0 -10000 0 0
SHBG 0.002 0.12 -10000 0 -0.54 8 8
Gi family/GNB1/GNG2/GDP -0.024 0.15 -10000 0 -0.46 16 16
mol:T-DHT -0.001 0.003 0.001 1 -0.005 26 27
RAC1 0.022 0.011 -10000 0 -10000 0 0
GNRH1 -0.004 0.02 -10000 0 -10000 0 0
Gi family/GTP -0.016 0.072 -10000 0 -0.26 9 9
CDC42 0.025 0.007 -10000 0 -10000 0 0
IL6-mediated signaling events

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
BCL2L1 -0.005 0.15 0.5 1 -10000 0 1
CRP -0.013 0.16 0.57 1 -10000 0 1
cell cycle arrest -0.018 0.16 0.41 1 -0.56 2 3
TIMP1 -0.009 0.15 -10000 0 -0.46 2 2
IL6ST -0.069 0.24 -10000 0 -0.66 28 28
Rac1/GDP -0.04 0.14 -10000 0 -0.42 12 12
AP1 -0.027 0.15 -10000 0 -0.44 8 8
GAB2 0.027 0.004 -10000 0 -10000 0 0
TNFSF11 -0.015 0.15 -10000 0 -0.51 1 1
HSP90B1 0.032 0.039 -10000 0 -10000 0 0
GAB1 0.026 0.006 -10000 0 -10000 0 0
MAPK14 -0.027 0.14 -10000 0 -0.51 7 7
AKT1 0.029 0.034 -10000 0 -10000 0 0
FOXO1 0.031 0.036 -10000 0 -10000 0 0
MAP2K6 -0.043 0.13 -10000 0 -0.32 29 29
mol:GTP 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.034 0.13 0.34 1 -0.48 6 7
MITF -0.048 0.14 -10000 0 -0.33 30 30
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.027 0.003 -10000 0 -10000 0 0
A2M 0.006 0.16 -10000 0 -1.3 3 3
CEBPB 0.019 0.024 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.006 0.089 -10000 0 -0.41 3 3
STAT3 -0.021 0.16 -10000 0 -0.6 2 2
STAT1 0.013 0.019 -10000 0 -10000 0 0
CEBPD -0.01 0.15 0.5 1 -10000 0 1
PIK3CA 0.028 0.004 -10000 0 -10000 0 0
PI3K 0.04 0.009 -10000 0 -10000 0 0
JUN 0.025 0.007 -10000 0 -10000 0 0
PIAS3/MITF -0.025 0.15 -10000 0 -0.41 13 13
MAPK11 -0.027 0.14 -10000 0 -0.48 8 8
STAT3 (dimer)/FOXO1 -0.022 0.13 -10000 0 -0.48 3 3
GRB2/SOS1/GAB family -0.003 0.15 -10000 0 -0.51 6 6
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.044 0.15 -10000 0 -0.35 32 32
GRB2 0.025 0.007 -10000 0 -10000 0 0
JAK2 0.026 0.007 -10000 0 -10000 0 0
LBP -0.21 0.43 0.41 2 -0.9 53 55
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
JAK1 0.026 0.01 -10000 0 -10000 0 0
MYC -0.01 0.15 0.5 1 -10000 0 1
FGG -0.015 0.15 -10000 0 -0.51 1 1
macrophage differentiation -0.018 0.16 0.41 1 -0.56 2 3
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.022 0.17 -10000 0 -0.38 31 31
JUNB -0.012 0.14 -10000 0 -0.48 2 2
FOS -0.071 0.23 -10000 0 -0.61 30 30
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.047 0.15 -10000 0 -0.34 33 33
STAT1/PIAS1 -0.025 0.15 -10000 0 -0.38 16 16
GRB2/SOS1/GAB family/SHP2/PI3K 0.032 0.035 -10000 0 -0.31 1 1
STAT3 (dimer) -0.019 0.16 -10000 0 -0.58 2 2
PRKCD -0.001 0.16 0.35 3 -0.44 5 8
IL6R 0.027 0.008 -10000 0 -10000 0 0
SOCS3 -0.021 0.16 -10000 0 -0.69 5 5
gp130 (dimer)/JAK1/JAK1/LMO4 -0.014 0.17 -10000 0 -0.42 28 28
Rac1/GTP -0.039 0.14 -10000 0 -0.46 9 9
HCK 0.011 0.057 -10000 0 -0.65 1 1
MAPKKK cascade 0.019 0.089 -10000 0 -0.48 3 3
bone resorption -0.013 0.14 -10000 0 -0.48 2 2
IRF1 -0.01 0.15 0.57 1 -0.51 1 2
mol:GDP -0.054 0.14 -10000 0 -0.36 24 24
SOS1 0.027 0.005 -10000 0 -10000 0 0
VAV1 -0.054 0.14 -10000 0 -0.37 24 24
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.039 0.16 -10000 0 -0.5 11 11
PTPN11 0.01 0.066 -10000 0 -0.87 1 1
IL6/IL6RA -0.006 0.13 -10000 0 -0.49 13 13
gp130 (dimer)/TYK2/TYK2/LMO4 -0.016 0.17 -10000 0 -0.43 28 28
gp130 (dimer)/JAK2/JAK2/LMO4 -0.019 0.17 -10000 0 -0.43 28 28
IL6 -0.027 0.17 -10000 0 -0.66 13 13
PIAS3 0.026 0.006 -10000 0 -10000 0 0
PTPRE 0.024 0.01 -10000 0 -10000 0 0
PIAS1 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.022 0.011 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.047 0.14 -10000 0 -0.33 33 33
LMO4 0.027 0.011 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.016 0.16 -10000 0 -0.63 2 2
MCL1 0.034 0.042 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.009 0.055 -10000 0 -10000 0 0
adherens junction organization 0 0.091 0.25 2 -0.28 14 16
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.055 -10000 0 -10000 0 0
FMN1 -0.012 0.097 -10000 0 -0.29 19 19
mol:IP3 0.009 0.053 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.002 0.087 -10000 0 -0.29 15 15
CTNNB1 0.027 0.007 -10000 0 -10000 0 0
AKT1 0.014 0.068 0.32 1 -10000 0 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.029 0.13 -10000 0 -0.47 15 15
CTNND1 0.029 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.081 -10000 0 -0.27 14 14
VASP -0.002 0.083 -10000 0 -0.28 14 14
ZYX -0.005 0.08 -10000 0 -0.28 13 13
JUB -0.001 0.083 -10000 0 -0.27 15 15
EGFR(dimer) 0.01 0.087 -10000 0 -0.28 13 13
E-cadherin/beta catenin-gamma catenin 0.013 0.12 -10000 0 -0.4 15 15
mol:PI-3-4-5-P3 0.03 0.073 -10000 0 -10000 0 0
PIK3CA 0.028 0.006 -10000 0 -10000 0 0
PI3K 0.031 0.075 -10000 0 -10000 0 0
FYN -0.18 0.15 -10000 0 -0.38 16 16
mol:Ca2+ 0.009 0.052 -10000 0 -10000 0 0
JUP 0.026 0.008 -10000 0 -10000 0 0
PIK3R1 0.028 0.007 -10000 0 -10000 0 0
mol:DAG 0.009 0.053 -10000 0 -10000 0 0
CDH1 -0.027 0.18 -10000 0 -0.66 15 15
RhoA/GDP 0.041 0.078 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium -0.002 0.081 -10000 0 -0.28 14 14
SRC 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.022 0.011 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
EGFR 0.022 0.011 -10000 0 -10000 0 0
CASR -0.21 0.17 -10000 0 -0.34 121 121
RhoA/GTP 0.022 0.054 -10000 0 -10000 0 0
AKT2 0.015 0.07 0.32 1 -10000 0 1
actin cable formation -0.013 0.096 -10000 0 -0.32 5 5
apoptosis -0.023 0.094 -10000 0 -0.37 7 7
CTNNA1 0.028 0.008 -10000 0 -10000 0 0
mol:GDP 0.001 0.049 -10000 0 -10000 0 0
PIP5K1A -0.002 0.082 -10000 0 -0.28 14 14
PLCG1 0.009 0.054 -10000 0 -10000 0 0
Rac1/GTP 0.018 0.085 -10000 0 -0.26 13 13
homophilic cell adhesion 0.001 0.006 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.007 0.098 -10000 0 -0.43 8 8
ACTA1 -0.009 0.064 -10000 0 -0.45 2 2
NUMA1 0.005 0.1 -10000 0 -0.43 8 8
SPTAN1 -0.011 0.062 -10000 0 -0.45 2 2
LIMK1 0.023 0.098 0.28 1 -0.45 2 3
BIRC3 0.02 0.024 -10000 0 -10000 0 0
BIRC2 0.027 0.004 -10000 0 -10000 0 0
BAX 0.026 0.008 -10000 0 -10000 0 0
CASP10 -0.013 0.032 -10000 0 -0.43 1 1
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.027 0 -10000 0 -10000 0 0
PTK2 0.005 0.12 -10000 0 -0.5 8 8
DIABLO 0.026 0.006 -10000 0 -10000 0 0
apoptotic nuclear changes -0.011 0.062 -10000 0 -0.44 2 2
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.026 0.005 -10000 0 -10000 0 0
GSN -0.011 0.063 -10000 0 -0.45 2 2
MADD 0.027 0.004 -10000 0 -10000 0 0
TFAP2A -0.42 0.28 -10000 0 -0.53 156 156
BID 0.003 0.018 -10000 0 -0.23 1 1
MAP3K1 0.003 0.061 -10000 0 -0.44 3 3
TRADD 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.035 0.014 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.002 0.077 0.28 1 -0.45 2 3
CASP9 0.025 0.008 -10000 0 -10000 0 0
DNA repair 0 0.049 0.24 6 -10000 0 6
neuron apoptosis -0.018 0.17 -10000 0 -0.62 13 13
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.003 0.086 -10000 0 -0.41 6 6
APAF1 0.026 0.006 -10000 0 -10000 0 0
CASP6 0.002 0.21 -10000 0 -0.97 8 8
TRAF2 0.026 0.006 -10000 0 -10000 0 0
ICAD/CAD -0.01 0.06 -10000 0 -0.44 2 2
CASP7 0.001 0.03 -10000 0 -10000 0 0
KRT18 0.022 0.038 -10000 0 -10000 0 0
apoptosis -0.01 0.1 -10000 0 -0.49 8 8
DFFA -0.01 0.06 -10000 0 -0.45 2 2
DFFB -0.008 0.062 -10000 0 -0.45 2 2
PARP1 0 0.049 -10000 0 -0.24 6 6
actin filament polymerization -0.023 0.09 0.41 2 -0.26 1 3
TNF 0.013 0.072 -10000 0 -0.66 2 2
CYCS 0.012 0.029 0.18 1 -10000 0 1
SATB1 0.004 0.2 0.42 2 -0.92 8 10
SLK -0.011 0.062 -10000 0 -0.44 2 2
p15 BID/BAX 0.009 0.045 -10000 0 -10000 0 0
CASP2 0.032 0.095 0.21 31 -0.33 1 32
JNK cascade -0.003 0.06 0.44 3 -10000 0 3
CASP3 -0.01 0.067 -10000 0 -0.47 2 2
LMNB2 0.033 0.16 0.32 6 -0.57 7 13
RIPK1 0.026 0.006 -10000 0 -10000 0 0
CASP4 0.027 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.065 0.018 -10000 0 -10000 0 0
negative regulation of DNA binding -0.42 0.28 -10000 0 -0.53 156 156
stress fiber formation -0.011 0.061 -10000 0 -0.43 2 2
GZMB 0.004 0.041 -10000 0 -0.5 1 1
CASP1 0.014 0.003 -10000 0 -10000 0 0
LMNB1 0.037 0.14 0.31 6 -0.52 6 12
APP -0.019 0.18 -10000 0 -0.63 13 13
TNFRSF1A 0.026 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.007 0.001 -10000 0 -10000 0 0
VIM -0.007 0.11 -10000 0 -0.51 8 8
LMNA 0.036 0.14 0.31 6 -0.53 6 12
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.006 0.062 -10000 0 -0.34 1 1
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.003 0.077 0.28 1 -0.45 2 3
APAF-1/Caspase 9 -0.022 0.16 -10000 0 -0.6 14 14
nuclear fragmentation during apoptosis 0.005 0.099 -10000 0 -0.42 8 8
CFL2 0.023 0.091 0.26 1 -0.42 2 3
GAS2 -0.021 0.086 -10000 0 -0.44 6 6
positive regulation of apoptosis 0.038 0.15 0.32 6 -0.51 8 14
PRF1 0.024 0.017 -10000 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.025 0.012 -9999 0 -10000 0 0
SVIL 0.026 0.01 -9999 0 -10000 0 0
ZNF318 0.026 0.013 -9999 0 -10000 0 0
JMJD2C 0.001 0.005 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.06 0.1 -9999 0 -0.47 8 8
CARM1 0.027 0.004 -9999 0 -10000 0 0
PRDX1 0.026 0.007 -9999 0 -10000 0 0
PELP1 0.025 0.008 -9999 0 -10000 0 0
CTNNB1 0.026 0.009 -9999 0 -10000 0 0
AKT1 0.025 0.009 -9999 0 -10000 0 0
PTK2B 0.027 0.005 -9999 0 -10000 0 0
MED1 0.026 0.009 -9999 0 -10000 0 0
MAK 0.021 0.024 -9999 0 -10000 0 0
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.019 0.05 -9999 0 -0.66 1 1
GSN 0.026 0.011 -9999 0 -10000 0 0
NCOA2 -0.029 0.19 -9999 0 -0.66 16 16
NCOA6 0.026 0.01 -9999 0 -10000 0 0
DNA-PK 0.049 0.022 -9999 0 -10000 0 0
NCOA4 0.027 0.005 -9999 0 -10000 0 0
PIAS3 0.026 0.009 -9999 0 -10000 0 0
cell proliferation -0.045 0.11 -9999 0 -0.49 10 10
XRCC5 0.027 0.005 -9999 0 -10000 0 0
UBE3A 0.027 0.01 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.089 0.14 -9999 0 -0.46 20 20
FHL2 -0.039 0.079 -9999 0 -10000 0 0
RANBP9 0.026 0.009 -9999 0 -10000 0 0
JMJD1A -0.087 0.071 -9999 0 -0.14 130 130
CDK6 0.022 0.011 -9999 0 -10000 0 0
TGFB1I1 0.018 0.069 -9999 0 -0.66 2 2
T-DHT/AR/CyclinD1 -0.064 0.1 -9999 0 -0.47 8 8
XRCC6 0.025 0.008 -9999 0 -10000 0 0
T-DHT/AR -0.12 0.14 -9999 0 -0.5 8 8
CTDSP1 0.026 0.007 -9999 0 -10000 0 0
CTDSP2 0.026 0.009 -9999 0 -10000 0 0
BRCA1 0.024 0.015 -9999 0 -10000 0 0
TCF4 0.025 0.008 -9999 0 -10000 0 0
CDKN2A -0.049 0.038 -9999 0 -10000 0 0
SRF 0.031 0.01 -9999 0 -10000 0 0
NKX3-1 -0.15 0.13 -9999 0 -0.51 3 3
KLK3 0.01 0.1 -9999 0 -1.3 1 1
TMF1 0.026 0.007 -9999 0 -10000 0 0
HNRNPA1 0.027 0.007 -9999 0 -10000 0 0
AOF2 0 0.005 -9999 0 -0.068 1 1
APPL1 0.012 0.009 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.062 0.11 -9999 0 -0.47 8 8
AR -0.066 0.14 -9999 0 -0.68 8 8
UBA3 0.026 0.007 -9999 0 -10000 0 0
PATZ1 0.025 0.01 -9999 0 -10000 0 0
PAWR 0.026 0.007 -9999 0 -10000 0 0
PRKDC 0.027 0.005 -9999 0 -10000 0 0
PA2G4 0.027 0.008 -9999 0 -10000 0 0
UBE2I 0.025 0.008 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.054 0.097 -9999 0 -0.43 8 8
RPS6KA3 0.027 0.009 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.063 0.1 -9999 0 -0.47 8 8
LATS2 0.027 0.007 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.056 0.097 -9999 0 -0.43 8 8
Cyclin D3/CDK11 p58 0.019 0.005 -9999 0 -10000 0 0
VAV3 0.026 0.009 -9999 0 -10000 0 0
KLK2 -0.056 0.067 -9999 0 -0.4 1 1
CASP8 0.027 0.004 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.082 0.17 -9999 0 -0.54 19 19
TMPRSS2 -0.66 0.49 -9999 0 -1 130 130
CCND1 0.027 0.006 -9999 0 -10000 0 0
PIAS1 0.027 0.01 -9999 0 -10000 0 0
mol:T-DHT -0.043 0.035 -9999 0 -0.069 126 126
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.027 0.014 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.053 0.1 -9999 0 -0.44 8 8
CMTM2 0.018 0.024 -9999 0 -10000 0 0
SNURF -0.019 0.16 -9999 0 -0.63 12 12
ZMIZ1 -0.038 0.05 -9999 0 -10000 0 0
CCND3 0.026 0.007 -9999 0 -10000 0 0
TGIF1 0.025 0.009 -9999 0 -10000 0 0
FKBP4 0.026 0.01 -9999 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.038 0.009 -10000 0 -10000 0 0
Necdin/E2F1 -0.015 0.12 -10000 0 -0.44 12 12
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.048 0.11 -10000 0 -0.41 9 9
NGF (dimer)/p75(NTR)/BEX1 -0.006 0.16 -10000 0 -0.43 23 23
NT-4/5 (dimer)/p75(NTR) 0.012 0.087 -10000 0 -0.5 5 5
IKBKB 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.007 0.1 0.35 2 -0.41 8 10
IKBKG 0.027 0.002 -10000 0 -10000 0 0
BDNF 0.014 0.032 -10000 0 -10000 0 0
MGDIs/NGR/p75(NTR)/LINGO1 0.03 0.089 -10000 0 -0.42 7 7
FURIN 0.027 0.004 -10000 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin 0.035 0.078 -10000 0 -0.44 5 5
LINGO1 0.02 0.069 -10000 0 -0.66 2 2
Sortilin/TRAF6/NRIF 0.032 0.03 -10000 0 -0.34 1 1
proBDNF (dimer) 0.014 0.032 -10000 0 -10000 0 0
NTRK1 -0.11 0.26 -10000 0 -0.65 37 37
RTN4R 0.023 0.015 -10000 0 -10000 0 0
neuron apoptosis 0.002 0.12 0.33 1 -0.54 4 5
IRAK1 0.027 0.002 -10000 0 -10000 0 0
SHC1 -0.007 0.1 -10000 0 -0.47 9 9
ARHGDIA 0.025 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.02 0.004 -10000 0 -10000 0 0
Gamma Secretase 0.071 0.041 -10000 0 -0.38 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.038 0.11 -10000 0 -0.43 9 9
MAGEH1 0.027 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.015 0.16 -10000 0 -0.48 16 16
Mammalian IAPs/DIABLO 0.065 0.018 -10000 0 -10000 0 0
proNGF (dimer) 0.004 0.12 -10000 0 -0.66 6 6
MAGED1 0.027 0.003 -10000 0 -10000 0 0
APP 0.025 0.007 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.003 0.032 -10000 0 -10000 0 0
ZNF274 0.027 0.003 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.014 0.096 -10000 0 -0.41 9 9
NGF 0.004 0.12 -10000 0 -0.66 6 6
cell cycle arrest -0.013 0.1 0.34 1 -0.39 9 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.011 0.078 -10000 0 -0.33 8 8
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.034 0.077 -10000 0 -0.43 5 5
NCSTN 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0.024 0.11 -10000 0 -0.44 10 10
PSENEN 0.027 0.003 -10000 0 -10000 0 0
mol:ceramide 0.003 0.11 -10000 0 -0.42 9 9
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.004 0.078 -10000 0 -0.44 3 3
p75(NTR)/beta APP 0.022 0.084 -10000 0 -0.49 5 5
BEX1 -0.019 0.17 -10000 0 -0.66 13 13
mol:GDP -0.027 0.1 -10000 0 -0.44 10 10
NGF (dimer) -0.22 0.24 -10000 0 -0.42 114 114
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.043 0.087 -10000 0 -0.39 7 7
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
RAC1/GTP 0.017 0.092 -10000 0 -0.37 9 9
MYD88 0.026 0.006 -10000 0 -10000 0 0
CHUK 0.027 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.025 0.11 -10000 0 -0.44 10 10
RHOB 0.027 0.005 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.013 0.039 -10000 0 -10000 0 0
NT3 (dimer) -0.077 0.24 -10000 0 -0.66 29 29
TP53 -0.018 0.062 -10000 0 -0.37 5 5
PRDM4 0.001 0.1 -10000 0 -0.43 9 9
BDNF (dimer) -0.23 0.22 -10000 0 -0.41 112 112
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
SORT1 0.026 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.043 0.1 -10000 0 -0.41 9 9
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.038 0.11 -10000 0 -0.43 9 9
RHOC 0.026 0.005 -10000 0 -10000 0 0
XIAP 0.027 0 -10000 0 -10000 0 0
MAPK10 0.012 0.1 0.25 3 -0.46 4 7
DIABLO 0.026 0.006 -10000 0 -10000 0 0
SMPD2 0.003 0.11 -10000 0 -0.43 9 9
APH1B 0.024 0.049 -10000 0 -0.66 1 1
APH1A 0.027 0.005 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.025 0.11 -10000 0 -0.44 10 10
PSEN1 0.026 0.007 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.035 0.014 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.053 0.21 -10000 0 -0.51 32 32
MAPK8 0.007 0.11 0.25 2 -0.46 4 6
MAPK9 0.012 0.1 0.25 3 -0.46 4 7
APAF1 0.026 0.006 -10000 0 -10000 0 0
NTF3 -0.077 0.24 -10000 0 -0.66 29 29
NTF4 -0.003 0.032 -10000 0 -10000 0 0
NDN -0.015 0.16 -10000 0 -0.61 13 13
RAC1/GDP 0.016 0.008 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.04 0.1 -10000 0 -0.38 9 9
p75 CTF/Sortilin/TRAF6/NRIF 0.064 0.021 -10000 0 -10000 0 0
RhoA-B-C/GTP 0.024 0.11 -10000 0 -0.44 10 10
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.058 0.076 -10000 0 -0.38 5 5
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 0.049 0.077 -10000 0 -0.4 5 5
PRKACB 0.026 0.006 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.028 0.03 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.02 0.024 -10000 0 -10000 0 0
BIRC2 0.027 0.004 -10000 0 -10000 0 0
neuron projection morphogenesis -0.023 0.13 0.34 1 -0.48 10 11
BAD 0.012 0.11 0.28 3 -0.46 4 7
RIPK2 0.027 0.004 -10000 0 -10000 0 0
NGFR 0.008 0.11 -10000 0 -0.66 5 5
CYCS 0 0.095 0.36 1 -0.42 7 8
ADAM17 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.038 0.11 -10000 0 -0.43 9 9
BCL2L11 0.013 0.11 0.3 4 -0.46 4 8
BDNF (dimer)/p75(NTR) 0.015 0.089 -10000 0 -0.51 5 5
PI3K 0.039 0.11 -10000 0 -0.44 8 8
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.038 0.11 -10000 0 -0.43 9 9
NDNL2 0.027 0.004 -10000 0 -10000 0 0
YWHAE 0.025 0.007 -10000 0 -10000 0 0
PRKCI 0.027 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.008 0.12 -10000 0 -0.51 10 10
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.038 0.11 -10000 0 -0.43 9 9
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.022 0.011 -10000 0 -10000 0 0
PRKCZ 0.025 0.008 -10000 0 -10000 0 0
PLG -0.38 0.32 -10000 0 -0.65 113 113
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.006 0.097 -10000 0 -0.42 9 9
SQSTM1 0.024 0.015 -10000 0 -10000 0 0
NGFRAP1 0.027 0 -10000 0 -10000 0 0
CASP3 0.012 0.11 0.27 5 -0.45 4 9
E2F1 -0.003 0.044 -10000 0 -10000 0 0
CASP9 0.025 0.008 -10000 0 -10000 0 0
IKK complex -0.031 0.18 -10000 0 -0.48 11 11
NGF (dimer)/TRKA -0.077 0.22 -10000 0 -0.49 42 42
MMP7 -0.009 0.094 -10000 0 -0.58 4 4
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.047 0.11 -10000 0 -0.41 9 9
MMP3 -0.011 0.026 -10000 0 -10000 0 0
APAF-1/Caspase 9 -0.004 0.071 -10000 0 -0.57 1 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 0.006 0.072 -10000 0 -0.6 1 1
Crk/p130 Cas/Paxillin -0.022 0.1 -10000 0 -0.35 11 11
JUN -0.022 0.11 -10000 0 -0.46 6 6
HRAS 0.027 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.011 0.13 -10000 0 -0.41 15 15
RAP1A 0.026 0.005 -10000 0 -10000 0 0
FRS2 0.026 0.006 -10000 0 -10000 0 0
RAP1A/GDP 0.02 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.018 0.14 -10000 0 -0.42 18 18
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.025 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma 0.019 0.1 -10000 0 -0.4 11 11
RHOA 0.026 0.005 -10000 0 -10000 0 0
RAP1A/GTP 0.015 0.12 -10000 0 -0.37 18 18
GRB7 0.025 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF 0.019 0.14 -10000 0 -0.42 18 18
MAPKKK cascade -0.002 0.12 -10000 0 -0.37 16 16
BCAR1 0.026 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 0.014 0.12 -10000 0 -0.44 12 12
lamellipodium assembly -0.013 0.092 -10000 0 -0.33 10 10
RET51/GFRalpha1/GDNF/SHC 0.017 0.14 -10000 0 -0.42 18 18
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC 0.019 0.1 -10000 0 -0.4 11 11
RET9/GFRalpha1/GDNF/Shank3 0.017 0.1 -10000 0 -0.39 11 11
MAPK3 -0.041 0.099 -10000 0 -0.35 18 18
DOK1 0.027 0.008 -10000 0 -10000 0 0
DOK6 -0.062 0.22 -10000 0 -0.63 26 26
PXN 0.026 0.006 -10000 0 -10000 0 0
neurite development -0.05 0.12 -10000 0 -0.46 7 7
DOK5 0.015 0.084 -10000 0 -0.66 3 3
GFRA1 -0.013 0.16 -10000 0 -0.66 11 11
MAPK8 -0.022 0.11 -10000 0 -0.46 7 7
HRAS/GTP 0.014 0.14 -10000 0 -0.41 18 18
tube development 0.026 0.1 -10000 0 -0.38 9 9
MAPK1 -0.032 0.12 0.34 2 -0.35 18 20
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.004 0.068 -10000 0 -0.29 9 9
Rac1/GDP 0.016 0.008 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
PDLIM7 0.026 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.027 0.19 -10000 0 -0.42 36 36
SHC1 0.026 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.017 0.14 -10000 0 -0.41 18 18
RET51/GFRalpha1/GDNF/Dok5 0.011 0.14 -10000 0 -0.41 20 20
PRKCA 0.025 0.007 -10000 0 -10000 0 0
HRAS/GDP 0.02 0.002 -10000 0 -10000 0 0
CREB1 -0.004 0.096 -10000 0 -0.38 10 10
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.002 0.077 -10000 0 -0.32 10 10
RET51/GFRalpha1/GDNF/Grb7 0.017 0.14 -10000 0 -0.42 16 16
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.002 0.14 -10000 0 -0.66 8 8
DOK4 0.026 0.007 -10000 0 -10000 0 0
JNK cascade -0.021 0.11 -10000 0 -0.45 6 6
RET9/GFRalpha1/GDNF/FRS2 0.018 0.1 -10000 0 -0.4 11 11
SHANK3 0.025 0.008 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.004 0.068 -10000 0 -0.29 8 8
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.005 0.1 -10000 0 -0.32 16 16
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.007 0.11 -10000 0 -0.32 18 18
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.006 0.11 -10000 0 -0.34 15 15
PI3K -0.015 0.15 -10000 0 -0.5 11 11
SOS1 0.027 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 0.028 0.094 -10000 0 -0.38 9 9
GRB10 0.022 0.011 -10000 0 -10000 0 0
activation of MAPKK activity -0.004 0.087 -10000 0 -0.32 10 10
RET51/GFRalpha1/GDNF/FRS2 0.016 0.14 -10000 0 -0.42 18 18
GAB1 0.026 0.006 -10000 0 -10000 0 0
IRS1 0.017 0.074 -10000 0 -0.55 3 3
IRS2 0.026 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.009 0.11 -10000 0 -0.35 17 17
RET51/GFRalpha1/GDNF/PKC alpha 0.017 0.14 -10000 0 -0.42 16 16
GRB2 0.025 0.007 -10000 0 -10000 0 0
PRKACA 0.027 0.002 -10000 0 -10000 0 0
GDNF -0.007 0.019 -10000 0 -10000 0 0
RAC1 0.022 0.011 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.012 0.15 -10000 0 -0.44 19 19
Rac1/GTP -0.011 0.11 -10000 0 -0.39 10 10
RET9/GFRalpha1/GDNF 0.004 0.11 -10000 0 -0.43 11 11
GFRalpha1/GDNF 0.002 0.12 -10000 0 -0.5 11 11
S1P3 pathway

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
PDGFRB -0.001 0.14 -9999 0 -0.66 8 8
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.005 0.068 -9999 0 -0.28 9 9
GNAO1 -0.006 0.14 -9999 0 -0.66 9 9
S1P/S1P3/G12/G13 0.008 0.11 -9999 0 -0.34 16 16
AKT1 -0.036 0.18 -9999 0 -0.48 24 24
AKT3 -0.005 0.13 -9999 0 -0.57 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.001 0.14 -9999 0 -0.66 8 8
GNAI2 0.027 0.006 -9999 0 -10000 0 0
GNAI3 0.027 0.006 -9999 0 -10000 0 0
GNAI1 0.02 0.05 -9999 0 -0.66 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.032 0.19 -9999 0 -0.66 17 17
S1PR2 0.027 0.003 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.015 0.15 -9999 0 -0.41 19 19
MAPK3 -0.019 0.14 -9999 0 -0.52 9 9
MAPK1 -0.014 0.14 -9999 0 -0.51 10 10
JAK2 -0.018 0.15 -9999 0 -0.54 10 10
CXCR4 -0.024 0.15 -9999 0 -0.5 11 11
FLT1 0.021 0.069 -9999 0 -0.66 2 2
RhoA/GDP 0.02 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.016 0.008 -9999 0 -10000 0 0
SRC -0.017 0.14 -9999 0 -0.56 8 8
S1P/S1P3/Gi -0.015 0.16 -9999 0 -0.42 19 19
RAC1 0.022 0.011 -9999 0 -10000 0 0
RhoA/GTP -0.01 0.15 -9999 0 -0.5 10 10
VEGFA 0.027 0.01 -9999 0 -10000 0 0
S1P/S1P2/Gi 0.014 0.088 -9999 0 -0.31 9 9
VEGFR1 homodimer/VEGFA homodimer 0.037 0.056 -9999 0 -0.5 2 2
RHOA 0.026 0.005 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.074 0.18 -9999 0 -0.36 51 51
GNAQ 0.026 0.007 -9999 0 -10000 0 0
GNAZ 0.026 0.008 -9999 0 -10000 0 0
G12/G13 0.031 0.017 -9999 0 -10000 0 0
GNA14 -0.11 0.27 -9999 0 -0.64 41 41
GNA15 0.021 0.023 -9999 0 -10000 0 0
GNA12 0.022 0.011 -9999 0 -10000 0 0
GNA13 0.025 0.007 -9999 0 -10000 0 0
GNA11 0.015 0.088 -9999 0 -0.58 4 4
Rac1/GTP -0.02 0.14 -9999 0 -0.5 10 10
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.02 0.02 -10000 0 -10000 0 0
HSPA8 0.027 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.027 0.1 -10000 0 -0.42 8 8
AKT1 0.027 0.008 -10000 0 -10000 0 0
GSC -0.005 0.095 -10000 0 -10000 0 0
NKX2-5 0.015 0.02 -10000 0 -10000 0 0
muscle cell differentiation -0.031 0.074 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.086 0.042 -10000 0 -10000 0 0
SMAD4 0.028 0.028 -10000 0 -10000 0 0
CBFB 0.026 0.007 -10000 0 -10000 0 0
SAP18 0.027 0.005 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.039 0.031 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR 0.059 0.068 -10000 0 -0.36 2 2
MYC 0.024 0.011 -10000 0 -10000 0 0
CDKN2B -0.005 0.12 -10000 0 -0.48 7 7
AP1 -0.001 0.13 -10000 0 -0.33 24 24
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.017 0.096 -10000 0 -0.45 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.015 0.048 -10000 0 -10000 0 0
SP3 0.029 0.004 -10000 0 -10000 0 0
CREB1 0.027 0.004 -10000 0 -10000 0 0
FOXH1 0.024 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/GR 0.056 0.044 -10000 0 -10000 0 0
GATA3 -0.47 0.3 -10000 0 -0.64 146 146
SKI/SIN3/HDAC complex/NCoR1 0.02 0.073 -10000 0 -0.42 4 4
MEF2C/TIF2 0.003 0.11 -10000 0 -0.37 14 14
endothelial cell migration 0.063 0.32 1.3 12 -10000 0 12
MAX 0.027 0.014 -10000 0 -10000 0 0
RBBP7 0.027 0.003 -10000 0 -10000 0 0
RBBP4 0.026 0.007 -10000 0 -10000 0 0
RUNX2 0.023 0.016 -10000 0 -10000 0 0
RUNX3 0.012 0.033 -10000 0 -10000 0 0
RUNX1 0.017 0.027 -10000 0 -10000 0 0
CTBP1 0.026 0.005 -10000 0 -10000 0 0
NR3C1 0.028 0.014 -10000 0 -10000 0 0
VDR 0.016 0.084 -10000 0 -0.66 3 3
CDKN1A 0.021 0.076 -10000 0 -10000 0 0
KAT2B 0.023 0.013 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.062 0.026 -10000 0 -10000 0 0
DCP1A 0.026 0.005 -10000 0 -10000 0 0
SKI 0.025 0.008 -10000 0 -10000 0 0
SERPINE1 -0.064 0.32 -10000 0 -1.3 12 12
SMAD3/SMAD4/ATF2 0.052 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.032 0.1 -10000 0 -0.45 7 7
SAP30 0.026 0.009 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.039 0.032 -10000 0 -10000 0 0
JUN -0.011 0.12 -10000 0 -0.32 24 24
SMAD3/SMAD4/IRF7 0.053 0.042 -10000 0 -10000 0 0
TFE3 0.025 0.024 -10000 0 -10000 0 0
COL1A2 0.026 0.039 -10000 0 -10000 0 0
mesenchymal cell differentiation -0.05 0.04 -10000 0 -10000 0 0
DLX1 0.015 0.026 -10000 0 -10000 0 0
TCF3 0.027 0.004 -10000 0 -10000 0 0
FOS -0.066 0.23 -10000 0 -0.6 30 30
SMAD3/SMAD4/Max 0.054 0.046 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.04 0.028 -10000 0 -10000 0 0
ZBTB17 0.024 0.008 -10000 0 -10000 0 0
LAMC1 0.021 0.031 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.052 0.039 -10000 0 -10000 0 0
IRF7 0.027 0.006 -10000 0 -10000 0 0
ESR1 -0.005 0.13 -10000 0 -0.57 10 10
HNF4A -0.058 0.22 -10000 0 -0.66 24 24
MEF2C 0.022 0.04 0.35 1 -10000 0 1
SMAD2-3/SMAD4 0.057 0.043 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.04 0.029 -10000 0 -10000 0 0
IGHV3OR16-13 0.008 0.045 -10000 0 -0.35 3 3
TGIF2/HDAC complex 0.026 0.006 -10000 0 -10000 0 0
CREBBP 0.022 0.015 -10000 0 -10000 0 0
SKIL 0.027 0.005 -10000 0 -10000 0 0
HDAC1 0.026 0.007 -10000 0 -10000 0 0
HDAC2 0.027 0.005 -10000 0 -10000 0 0
SNIP1 0.026 0.007 -10000 0 -10000 0 0
GCN5L2 -0.002 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.054 0.049 -10000 0 -10000 0 0
MSG1/HSC70 0.039 0.011 -10000 0 -10000 0 0
SMAD2 0.029 0.009 -10000 0 -10000 0 0
SMAD3 0.027 0.029 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.03 0.026 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 -0.001 0.067 -10000 0 -0.41 3 3
NCOR1 0.025 0.008 -10000 0 -10000 0 0
NCOA2 -0.029 0.19 -10000 0 -0.66 16 16
NCOA1 0.027 0.004 -10000 0 -10000 0 0
MYOD/E2A 0.031 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.092 0.048 -10000 0 -10000 0 0
IFNB1 0.015 0.027 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.053 0.04 -10000 0 -10000 0 0
CITED1 0.025 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/ARC105 0.067 0.046 -10000 0 -10000 0 0
RBL1 0.026 0.006 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.024 0.047 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 0.039 0.028 -10000 0 -10000 0 0
SMAD7 0.016 0.11 -10000 0 -10000 0 0
MYC/MIZ-1 0.033 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.014 0.11 -10000 0 -0.41 12 12
IL10 -0.28 0.18 -10000 0 -0.39 139 139
PIASy/HDAC complex 0.029 0.009 -10000 0 -10000 0 0
PIAS3 0.023 0.013 -10000 0 -10000 0 0
CDK2 0.023 0.014 -10000 0 -10000 0 0
IL5 -0.28 0.18 -10000 0 -0.39 138 138
CDK4 0.023 0.015 -10000 0 -10000 0 0
PIAS4 0.029 0.009 -10000 0 -10000 0 0
ATF3 -0.002 0.13 -10000 0 -0.59 9 9
SMAD3/SMAD4/SP1 0.063 0.043 -10000 0 -10000 0 0
FOXG1 -0.005 0.025 -10000 0 -10000 0 0
FOXO3 0.015 0.007 -10000 0 -10000 0 0
FOXO1 0.015 0.006 -10000 0 -10000 0 0
FOXO4 0.015 0.007 -10000 0 -10000 0 0
heart looping 0.022 0.04 0.35 1 -10000 0 1
CEBPB 0.025 0.015 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.049 0.043 -10000 0 -10000 0 0
MYOD1 -0.013 0.018 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.008 0.17 -10000 0 -0.45 24 24
SMAD3/SMAD4/GATA3 -0.31 0.22 -10000 0 -0.44 142 142
SnoN/SIN3/HDAC complex/NCoR1 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.059 0.051 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.082 0.04 -10000 0 -10000 0 0
MED15 0.025 0.008 -10000 0 -10000 0 0
SP1 0.033 0.007 -10000 0 -10000 0 0
SIN3B 0.028 0.002 -10000 0 -10000 0 0
SIN3A 0.027 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.072 0.03 -10000 0 -10000 0 0
ITGB5 0.034 0.037 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.021 0.063 -10000 0 -0.51 2 2
SMAD3/SMAD4/AR 0.031 0.11 -10000 0 -0.46 8 8
AR -0.001 0.14 -10000 0 -0.66 8 8
negative regulation of cell growth 0.016 0.064 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD 0.046 0.041 -10000 0 -10000 0 0
E2F5 0.027 0.004 -10000 0 -10000 0 0
E2F4 0.026 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.075 0.039 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.03 0.02 -10000 0 -10000 0 0
TFDP1 0.026 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.017 0.14 -10000 0 -0.33 24 24
SMAD3/SMAD4/RUNX2 0.05 0.04 -10000 0 -10000 0 0
TGIF2 0.026 0.006 -10000 0 -10000 0 0
TGIF1 0.025 0.008 -10000 0 -10000 0 0
ATF2 0.027 0.004 -10000 0 -10000 0 0
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.1 0.11 -10000 0 -0.46 3 3
epithelial cell differentiation -0.18 0.18 -10000 0 -0.4 57 57
ITCH 0.055 0.024 -10000 0 -10000 0 0
WWP1 -0.088 0.08 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
EGFR 0.022 0.011 -10000 0 -10000 0 0
PRL -0.012 0.015 -10000 0 -10000 0 0
neuron projection morphogenesis -0.052 0.088 0.33 1 -0.4 2 3
PTPRZ1 -0.008 0.096 -10000 0 -0.66 4 4
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.058 0.093 -10000 0 -0.44 2 2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.083 0.087 -10000 0 -0.46 3 3
ADAM17 0.056 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.12 0.1 -10000 0 -0.31 5 5
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.11 0.11 -10000 0 -0.45 4 4
NCOR1 0.025 0.007 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.072 0.089 -10000 0 -0.43 3 3
GRIN2B -0.077 0.079 -10000 0 -0.42 3 3
ErbB4/ErbB2/betacellulin -0.071 0.094 -10000 0 -0.44 4 4
STAT1 0.025 0.012 -10000 0 -10000 0 0
HBEGF 0.016 0.084 -10000 0 -0.66 3 3
PRLR -0.28 0.34 -10000 0 -0.65 89 89
E4ICDs/ETO2 -0.094 0.097 -10000 0 -10000 0 0
axon guidance -0.056 0.063 -10000 0 -10000 0 0
NEDD4 0.056 0.022 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.21 0.26 -10000 0 -0.5 89 89
CBFA2T3 0.025 0.01 -10000 0 -10000 0 0
ErbB4/ErbB2/HBEGF -0.068 0.087 -10000 0 -0.45 2 2
MAPK3 -0.061 0.079 -10000 0 -0.41 2 2
STAT1 (dimer) -0.098 0.097 -10000 0 -10000 0 0
MAPK1 -0.06 0.079 -10000 0 -0.42 2 2
JAK2 0.026 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.071 0.088 -10000 0 -0.44 3 3
NRG1 0.021 0.066 -10000 0 -0.5 3 3
NRG3 0.012 0.085 -10000 0 -0.66 3 3
NRG2 0.021 0.055 -10000 0 -0.5 2 2
NRG4 0.02 0.031 -10000 0 -0.35 1 1
heart development -0.056 0.063 -10000 0 -10000 0 0
neural crest cell migration -0.071 0.087 -10000 0 -0.43 3 3
ERBB2 0.029 0.015 -10000 0 -10000 0 0
WWOX/E4ICDs -0.095 0.097 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.07 0.098 -10000 0 -0.41 1 1
apoptosis 0.087 0.094 0.43 4 -10000 0 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.1 0.1 -10000 0 -0.36 2 2
ErbB4/ErbB2/epiregulin -0.074 0.081 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin -0.11 0.12 -10000 0 -0.5 5 5
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.24 0.21 -10000 0 -0.45 89 89
MDM2 -0.1 0.097 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.053 0.077 -10000 0 -0.43 3 3
STAT5A -0.048 0.068 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.058 0.089 -10000 0 -0.44 3 3
DLG4 0.025 0.007 -10000 0 -10000 0 0
GRB2/SHC 0.037 0.012 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.09 0.088 -10000 0 -10000 0 0
STAT5A (dimer) -0.19 0.2 -10000 0 -0.42 54 54
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.047 0.066 -10000 0 -10000 0 0
LRIG1 0.026 0.009 -10000 0 -10000 0 0
EREG -0.023 0.046 -10000 0 -10000 0 0
BTC 0.01 0.1 -10000 0 -0.6 5 5
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.055 0.063 -10000 0 -10000 0 0
ERBB4 -0.12 0.1 -10000 0 -0.31 5 5
STAT5B 0.025 0.007 -10000 0 -10000 0 0
YAP1 -0.028 0.078 -10000 0 -0.48 5 5
GRB2 0.025 0.007 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.066 0.079 -10000 0 -0.35 1 1
glial cell differentiation 0.089 0.087 -10000 0 -10000 0 0
WWOX 0.025 0.007 -10000 0 -10000 0 0
cell proliferation -0.055 0.12 0.7 1 -0.43 6 7
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.021 0.17 -9999 0 -0.66 13 13
GNB1/GNG2 0.02 0.094 -9999 0 -0.43 1 1
mol:DAG -0.003 0.074 -9999 0 -0.4 1 1
PLCG1 -0.003 0.075 -9999 0 -0.42 1 1
YES1 -0.008 0.078 -9999 0 -0.34 3 3
FZD3 0.026 0.005 -9999 0 -10000 0 0
FZD6 0.027 0.004 -9999 0 -10000 0 0
G protein 0.021 0.088 -9999 0 -0.42 1 1
MAP3K7 -0.16 0.16 -9999 0 -0.37 27 27
mol:Ca2+ -0.003 0.072 -9999 0 -0.39 1 1
mol:IP3 -0.003 0.074 -9999 0 -0.4 1 1
NLK 0.003 0.013 -9999 0 -10000 0 0
GNB1 0.025 0.008 -9999 0 -10000 0 0
CAMK2A -0.17 0.18 -9999 0 -0.35 88 88
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD 0 0.085 -9999 0 -0.3 13 13
CSNK1A1 0.026 0.005 -9999 0 -10000 0 0
GNAS -0.006 0.074 -9999 0 -0.34 3 3
GO:0007205 -0.012 0.07 -9999 0 -0.4 1 1
WNT6 0.018 0.051 -9999 0 -0.66 1 1
WNT4 0.01 0.097 -9999 0 -0.66 4 4
NFAT1/CK1 alpha -0.007 0.12 -9999 0 -0.45 2 2
GNG2 0.026 0.007 -9999 0 -10000 0 0
WNT5A 0.012 0.034 -9999 0 -10000 0 0
WNT11 -0.007 0.14 -9999 0 -0.66 9 9
CDC42 -0.009 0.077 -9999 0 -0.43 1 1
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) 0.002 0.13 -10000 0 -0.42 11 11
HDAC1 0.023 0.006 -10000 0 -10000 0 0
AES 0.026 0.004 -10000 0 -10000 0 0
FBXW11 0.026 0.005 -10000 0 -10000 0 0
DTX1 0.019 0.069 -10000 0 -0.66 2 2
LRP6/FZD1 0.032 0.018 -10000 0 -10000 0 0
TLE1 0.025 0.006 -10000 0 -10000 0 0
AP1 -0.11 0.2 0.19 1 -0.37 63 64
NCSTN 0.026 0.005 -10000 0 -10000 0 0
ADAM10 0.026 0.008 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.029 0.092 -10000 0 -0.74 2 2
NICD/RBPSUH 0.021 0.099 -10000 0 -0.38 8 8
WIF1 0.01 0.024 -10000 0 -10000 0 0
NOTCH1 0.01 0.088 -10000 0 -0.39 9 9
PSENEN 0.027 0.003 -10000 0 -10000 0 0
KREMEN2 0.013 0.029 -10000 0 -10000 0 0
DKK1 0.012 0.028 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.057 0.11 0.33 2 -10000 0 2
APH1B 0.024 0.049 -10000 0 -0.66 1 1
APH1A 0.027 0.005 -10000 0 -10000 0 0
AXIN1 -0.006 0.071 -10000 0 -0.65 1 1
CtBP/CBP/TCF1/TLE1/AES 0.009 0.059 -10000 0 -0.44 3 3
PSEN1 0.026 0.007 -10000 0 -10000 0 0
FOS -0.07 0.23 -10000 0 -0.61 30 30
JUN 0.026 0.007 -10000 0 -10000 0 0
MAP3K7 0.025 0.004 -10000 0 -10000 0 0
CTNNB1 0.049 0.11 0.3 5 -10000 0 5
MAPK3 0.025 0.008 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.041 0.041 -10000 0 -0.43 1 1
HNF1A 0.015 0.084 -10000 0 -0.66 3 3
CTBP1 0.026 0.005 -10000 0 -10000 0 0
MYC 0.025 0.062 -10000 0 -0.82 1 1
NKD1 -0.14 0.29 -10000 0 -0.66 47 47
FZD1 0.022 0.013 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.016 0.11 -10000 0 -0.41 10 10
apoptosis -0.11 0.2 0.19 1 -0.37 63 64
Delta 1/NOTCHprecursor -0.001 0.13 -10000 0 -0.42 11 11
DLL1 -0.014 0.15 -10000 0 -0.61 12 12
PPARD -0.02 0.2 -10000 0 -0.79 12 12
Gamma Secretase 0.072 0.041 -10000 0 -0.38 1 1
APC -0.011 0.09 -10000 0 -0.57 3 3
DVL1 0.015 0.011 -10000 0 -10000 0 0
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
MAP3K7IP1 -0.001 0 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.042 0.026 -10000 0 -10000 0 0
LRP6 0.026 0.006 -10000 0 -10000 0 0
CSNK1A1 0.027 0.005 -10000 0 -10000 0 0
NLK 0.011 0.003 -10000 0 -10000 0 0
CCND1 0.017 0.11 -10000 0 -0.84 3 3
WNT1 0.01 0.033 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.048 0.11 0.35 8 -0.49 2 10
DKK2 0.02 0.05 -10000 0 -0.66 1 1
NOTCH1 precursor/DVL1 0.01 0.12 -10000 0 -0.52 5 5
GSK3B 0.026 0.005 -10000 0 -10000 0 0
FRAT1 0.027 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.019 0.11 -10000 0 -0.42 9 9
PPP2R5D 0.079 0.16 0.33 45 -0.3 9 54
MAPK1 0.025 0.008 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.051 0.028 -10000 0 -10000 0 0
RBPJ 0.026 0.005 -10000 0 -10000 0 0
CREBBP 0.027 0.009 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.027 0.004 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.052 0.18 -9999 0 -0.48 10 10
Syndecan-3/Neurocan -0.006 0.1 -9999 0 -0.36 15 15
POMC 0.018 0.073 -9999 0 -0.55 3 3
EGFR 0.022 0.011 -9999 0 -10000 0 0
Syndecan-3/EGFR -0.004 0.1 -9999 0 -0.36 15 15
AGRP 0.013 0.021 -9999 0 -10000 0 0
NCSTN 0.026 0.005 -9999 0 -10000 0 0
PSENEN 0.027 0.003 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.024 0.049 -9999 0 -0.66 1 1
APH1A 0.027 0.005 -9999 0 -10000 0 0
NCAN 0.004 0.034 -9999 0 -10000 0 0
long-term memory 0.017 0.1 -9999 0 -0.34 13 13
Syndecan-3/IL8 -0.012 0.1 -9999 0 -0.36 15 15
PSEN1 0.026 0.007 -9999 0 -10000 0 0
Src/Cortactin 0.038 0.011 -9999 0 -10000 0 0
FYN 0.027 0.005 -9999 0 -10000 0 0
limb bud formation -0.012 0.097 -9999 0 -0.37 13 13
MC4R -0.006 0.021 -9999 0 -10000 0 0
SRC 0.026 0.006 -9999 0 -10000 0 0
PTN -0.1 0.26 -9999 0 -0.66 36 36
FGFR/FGF/Syndecan-3 -0.012 0.097 -9999 0 -0.38 13 13
neuron projection morphogenesis -0.045 0.19 -9999 0 -0.59 5 5
Syndecan-3/AgRP -0.001 0.1 -9999 0 -0.36 14 14
Syndecan-3/AgRP/MC4R 0.008 0.1 -9999 0 -0.35 12 12
Fyn/Cortactin 0.039 0.009 -9999 0 -10000 0 0
SDC3 -0.012 0.098 -9999 0 -0.38 13 13
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.011 0.1 -9999 0 -0.35 15 15
IL8 0 0.062 -9999 0 -0.66 1 1
Syndecan-3/Fyn/Cortactin 0.018 0.1 -9999 0 -0.35 12 12
Syndecan-3/CASK -0.015 0.098 -9999 0 -0.36 15 15
alpha-MSH/MC4R 0.024 0.059 -9999 0 -0.42 3 3
Gamma Secretase 0.071 0.041 -9999 0 -0.38 1 1
EPHB forward 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
Ephrin A5/EPHB2 -0.001 0.12 -10000 0 -0.43 14 14
cell-cell adhesion 0.02 0.051 0.32 5 -10000 0 5
Ephrin B/EPHB2/RasGAP 0.056 0.07 -10000 0 -0.38 4 4
ITSN1 0.025 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.062 0.19 -10000 0 -0.42 42 42
Ephrin B1/EPHB1 0.026 0.058 -10000 0 -0.43 3 3
HRAS/GDP 0.012 0.066 -10000 0 -0.34 3 3
Ephrin B/EPHB1/GRB7 0.053 0.084 -10000 0 -0.38 6 6
Endophilin/SYNJ1 0.006 0.063 -10000 0 -0.35 4 4
KRAS 0.026 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.051 0.084 -10000 0 -0.38 6 6
endothelial cell migration 0.045 0.025 -10000 0 -10000 0 0
GRB2 0.025 0.007 -10000 0 -10000 0 0
GRB7 0.025 0.007 -10000 0 -10000 0 0
PAK1 -0.004 0.073 0.34 2 -0.36 3 5
HRAS 0.027 0.003 -10000 0 -10000 0 0
RRAS 0.009 0.067 -10000 0 -0.36 4 4
DNM1 0 0.043 -10000 0 -10000 0 0
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.004 0.071 -10000 0 -0.36 6 6
lamellipodium assembly -0.02 0.051 -10000 0 -0.32 5 5
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.017 0.055 -10000 0 -0.28 3 3
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
EPHB2 0.023 0.015 -10000 0 -10000 0 0
EPHB3 -0.12 0.28 -10000 0 -0.66 42 42
EPHB1 0.013 0.085 -10000 0 -0.66 3 3
EPHB4 0.022 0.011 -10000 0 -10000 0 0
mol:GDP 0.033 0.11 0.35 12 -0.37 3 15
Ephrin B/EPHB2 0.043 0.066 -10000 0 -0.38 4 4
Ephrin B/EPHB3 -0.04 0.18 -10000 0 -0.36 45 45
JNK cascade 0.011 0.069 0.35 4 -0.37 3 7
Ephrin B/EPHB1 0.04 0.079 -10000 0 -0.38 6 6
RAP1/GDP 0.073 0.12 0.34 11 -0.33 3 14
EFNB2 0.027 0.005 -10000 0 -10000 0 0
EFNB3 0.001 0.099 -10000 0 -0.66 4 4
EFNB1 0.027 0.002 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.038 0.057 -10000 0 -0.4 3 3
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.024 0.075 -10000 0 -0.36 3 3
Rap1/GTP 0.006 0.066 -10000 0 -10000 0 0
axon guidance -0.001 0.12 -10000 0 -0.42 14 14
MAPK3 0.009 0.054 -10000 0 -10000 0 0
MAPK1 0.008 0.055 -10000 0 -10000 0 0
Rac1/GDP 0.023 0.09 0.33 3 -0.34 3 6
actin cytoskeleton reorganization -0.006 0.047 -10000 0 -10000 0 0
CDC42/GDP 0.068 0.13 0.34 13 -0.34 3 16
PI3K 0.049 0.028 -10000 0 -10000 0 0
EFNA5 -0.023 0.18 -10000 0 -0.66 14 14
Ephrin B2/EPHB4 0.029 0.015 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.009 0.056 -10000 0 -0.33 4 4
CDC42 0.025 0.007 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.063 -10000 0 -10000 0 0
PTK2 0 0.054 0.53 2 -10000 0 2
MAP4K4 0.011 0.069 0.36 4 -0.38 3 7
SRC 0.026 0.006 -10000 0 -10000 0 0
KALRN 0.026 0.005 -10000 0 -10000 0 0
Intersectin/N-WASP 0.03 0.018 -10000 0 -10000 0 0
neuron projection morphogenesis 0.059 0.15 0.36 33 -10000 0 33
MAP2K1 0.009 0.053 -10000 0 -10000 0 0
WASL 0.022 0.011 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.054 0.061 -10000 0 -0.4 3 3
cell migration 0.036 0.11 0.43 7 -10000 0 7
NRAS 0.026 0.006 -10000 0 -10000 0 0
SYNJ1 0.006 0.063 -10000 0 -0.36 4 4
PXN 0.026 0.006 -10000 0 -10000 0 0
TF -0.017 0.07 -10000 0 -0.35 6 6
HRAS/GTP 0.032 0.072 -10000 0 -0.34 6 6
Ephrin B1/EPHB1-2 0.039 0.057 -10000 0 -0.4 3 3
cell adhesion mediated by integrin 0.041 0.088 0.4 4 -10000 0 4
RAC1 0.022 0.011 -10000 0 -10000 0 0
mol:GTP 0.034 0.075 -10000 0 -0.35 6 6
RAC1-CDC42/GTP -0.062 0.14 -10000 0 -0.35 28 28
RASA1 0.027 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.034 0.089 0.32 3 -0.34 2 5
ruffle organization 0.037 0.14 0.32 33 -10000 0 33
NCK1 0.026 0.005 -10000 0 -10000 0 0
receptor internalization -0.016 0.06 -10000 0 -0.34 4 4
Ephrin B/EPHB2/KALRN 0.057 0.066 -10000 0 -0.38 3 3
ROCK1 -0.068 0.17 -10000 0 -0.39 41 41
RAS family/GDP -0.017 0.044 -10000 0 -10000 0 0
Rac1/GTP -0.001 0.059 -10000 0 -0.34 5 5
Ephrin B/EPHB1/Src/Paxillin 0.013 0.058 -10000 0 -0.28 6 6
Calcium signaling in the CD4+ TCR 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
NFATC1 0.008 0.022 -10000 0 -10000 0 0
NFATC2 -0.019 0.11 -10000 0 -0.43 13 13
NFATC3 0.01 0.019 -10000 0 -10000 0 0
CD40LG -0.052 0.17 0.36 2 -0.53 10 12
PTGS2 -0.094 0.26 0.36 2 -0.65 28 30
JUNB 0.027 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.015 0.017 -10000 0 -10000 0 0
CaM/Ca2+ 0.015 0.017 -10000 0 -10000 0 0
CALM1 0.022 0.016 -10000 0 -10000 0 0
JUN 0.023 0.016 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.017 0.006 -10000 0 -10000 0 0
FOSL1 0.025 0.014 -10000 0 -10000 0 0
CREM 0.026 0.005 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.008 0.12 -10000 0 -0.39 7 7
FOS -0.074 0.23 -10000 0 -0.62 30 30
IFNG -0.052 0.17 0.35 2 -0.53 10 12
AP-1/NFAT1-c-4 -0.038 0.2 -10000 0 -0.61 10 10
FASLG -0.056 0.17 0.36 2 -0.53 10 12
NFAT1-c-4/ICER1 -0.002 0.1 -10000 0 -0.37 12 12
IL2RA -0.057 0.17 0.36 2 -0.53 10 12
FKBP12/FK506 0.019 0.005 -10000 0 -10000 0 0
CSF2 -0.054 0.17 0.35 2 -0.53 10 12
JunB/Fra1/NFAT1-c-4 0.009 0.11 -10000 0 -0.36 12 12
IL4 -0.054 0.17 0.35 2 -0.53 10 12
IL2 -0.022 0.17 -10000 0 -0.85 8 8
IL3 -0.01 0.14 -10000 0 -0.68 8 8
FKBP1A 0.026 0.006 -10000 0 -10000 0 0
BATF3 0.026 0.009 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.026 0.006 -10000 0 -10000 0 0
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 0.027 0.011 -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 0.008 0.11 0.38 1 -10000 0 1
IL27/IL27R/JAK1 0.097 0.22 -10000 0 -10000 0 0
TBX21 0.058 0.15 0.35 1 -10000 0 1
IL12B 0.015 0.018 -10000 0 -10000 0 0
IL12A 0.005 0.006 -10000 0 -10000 0 0
IL6ST -0.066 0.24 -10000 0 -0.66 28 28
IL27RA/JAK1 0.038 0.033 -10000 0 -10000 0 0
IL27 0.019 0.025 -10000 0 -10000 0 0
TYK2 0.029 0.004 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.002 0.11 -10000 0 -0.48 1 1
T-helper 2 cell differentiation 0.008 0.11 0.38 1 -10000 0 1
T cell proliferation during immune response 0.008 0.11 0.38 1 -10000 0 1
MAPKKK cascade -0.008 0.11 -10000 0 -0.38 1 1
STAT3 0.025 0.007 -10000 0 -10000 0 0
STAT2 0.026 0.005 -10000 0 -10000 0 0
STAT1 0.03 0.013 -10000 0 -10000 0 0
IL12RB1 0.021 0.024 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 0.051 0.16 0.35 3 -0.5 2 5
IL27/IL27R/JAK2/TYK2 -0.009 0.12 -10000 0 -0.39 1 1
positive regulation of T cell mediated cytotoxicity -0.008 0.11 -10000 0 -0.38 1 1
STAT1 (dimer) 0.24 0.3 0.49 111 -10000 0 111
JAK2 0.027 0.008 -10000 0 -10000 0 0
JAK1 0.03 0.009 -10000 0 -10000 0 0
STAT2 (dimer) 0.009 0.12 -10000 0 -0.37 1 1
T cell proliferation -0.03 0.13 -10000 0 -0.45 8 8
IL12/IL12R/TYK2/JAK2 0.03 0.1 -10000 0 -0.69 3 3
IL17A -0.01 0.099 -10000 0 -0.48 1 1
mast cell activation 0.008 0.11 0.38 1 -10000 0 1
IFNG 0.008 0.024 -10000 0 -10000 0 0
T cell differentiation 0.001 0.005 -10000 0 -10000 0 0
STAT3 (dimer) 0.01 0.11 -10000 0 -10000 0 0
STAT5A (dimer) 0.01 0.11 -10000 0 -10000 0 0
STAT4 (dimer) 0.008 0.12 -10000 0 -10000 0 0
STAT4 0.02 0.025 -10000 0 -10000 0 0
T cell activation -0.008 0.005 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 0.006 0.15 -10000 0 -10000 0 0
GATA3 -0.97 0.58 0.69 1 -1.3 146 147
IL18 0.007 0.005 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production 0.01 0.11 -10000 0 -10000 0 0
IL27/EBI3 0.032 0.053 -10000 0 -0.49 1 1
IL27RA 0.015 0.021 -10000 0 -10000 0 0
IL6 -0.029 0.17 -10000 0 -0.66 13 13
STAT5A 0.025 0.007 -10000 0 -10000 0 0
monocyte differentiation 0 0 -10000 0 -10000 0 0
IL2 -0.017 0.016 -10000 0 -10000 0 0
IL1B -0.003 0.071 -10000 0 -0.5 4 4
EBI3 0.016 0.06 -10000 0 -0.65 1 1
TNF -0.001 0.051 -10000 0 -0.5 2 2
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.022 0.15 -10000 0 -0.52 15 15
KLHL20 0.019 0.084 0.22 2 -0.25 1 3
CYFIP2 0.026 0.005 -10000 0 -10000 0 0
Rac1/GDP 0 0.11 0.34 4 -0.33 13 17
ENAH -0.023 0.15 -10000 0 -0.52 15 15
AP1M1 0.027 0.002 -10000 0 -10000 0 0
RAP1B 0.026 0.005 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
CDC42/GTP 0.004 0.078 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.039 -10000 0 -0.17 1 1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.025 0.12 -10000 0 -0.4 14 14
RAPGEF1 -0.017 0.13 0.25 1 -0.45 14 15
CTNND1 0.027 0.002 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.018 0.16 -10000 0 -0.53 15 15
CRK -0.024 0.14 -10000 0 -0.48 15 15
E-cadherin/gamma catenin/alpha catenin 0.012 0.13 -10000 0 -0.42 15 15
alphaE/beta7 Integrin 0.037 0.012 -10000 0 -10000 0 0
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
NCKAP1 0.027 0.004 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.047 0.017 -10000 0 -10000 0 0
DLG1 -0.023 0.15 -10000 0 -0.52 15 15
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.009 0.054 -10000 0 -10000 0 0
MLLT4 0.026 0.005 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.043 0.021 -10000 0 -10000 0 0
PI3K -0.008 0.071 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.004 0.14 -10000 0 -0.48 15 15
TIAM1 0.025 0.008 -10000 0 -10000 0 0
E-cadherin(dimer)/Ca2+ 0.024 0.12 -10000 0 -0.38 15 15
AKT1 -0.001 0.046 -10000 0 -10000 0 0
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
CDH1 -0.027 0.18 -10000 0 -0.66 15 15
RhoA/GDP 0.01 0.12 0.36 5 -0.33 14 19
actin cytoskeleton organization 0.021 0.068 0.18 5 -0.18 1 6
CDC42/GDP 0.018 0.14 0.42 8 -0.33 14 22
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.005 0.082 -10000 0 -0.29 15 15
ITGB7 0.026 0.005 -10000 0 -10000 0 0
RAC1 0.022 0.011 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.027 0.12 -10000 0 -0.4 15 15
E-cadherin/Ca2+/beta catenin/alpha catenin 0.011 0.11 -10000 0 -0.37 15 15
mol:GDP 0.001 0.15 0.44 8 -0.38 14 22
CDC42/GTP/IQGAP1 0.034 0.011 -10000 0 -10000 0 0
JUP 0.025 0.007 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP 0.009 0.11 0.25 2 -0.34 14 16
RAC1/GTP/IQGAP1 0.029 0.015 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.04 0.006 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
CDC42 0.025 0.007 -10000 0 -10000 0 0
CTNNA1 0.026 0.005 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.026 0.068 0.25 8 -10000 0 8
NME1 0.024 0.012 -10000 0 -10000 0 0
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.023 0.15 -10000 0 -0.52 15 15
regulation of cell-cell adhesion -0.001 0.067 -10000 0 -10000 0 0
WASF2 0.011 0.032 -10000 0 -10000 0 0
Rap1/GTP 0.007 0.092 -10000 0 -0.3 13 13
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.035 0.12 -10000 0 -0.38 14 14
CCND1 0.023 0.058 0.17 5 -10000 0 5
VAV2 -0.03 0.19 -10000 0 -0.52 24 24
RAP1/GDP 0.012 0.1 0.26 2 -0.31 14 16
adherens junction assembly -0.022 0.14 -10000 0 -0.5 15 15
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.027 0.005 -10000 0 -10000 0 0
PIP5K1C 0.027 0.004 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.023 0.11 -10000 0 -0.36 14 14
E-cadherin/beta catenin -0.022 0.12 -10000 0 -0.43 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.023 0.15 -10000 0 -0.52 15 15
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.021 0.097 -10000 0 -0.32 7 7
E-cadherin/beta catenin/alpha catenin 0.012 0.13 -10000 0 -0.43 15 15
ITGAE 0.025 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.019 0.16 -10000 0 -0.55 15 15
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.015 0.3 -10000 0 -0.91 12 12
IL23A -0.021 0.3 -10000 0 -0.98 10 10
NF kappa B1 p50/RelA/I kappa B alpha 0.007 0.28 -10000 0 -0.87 11 11
positive regulation of T cell mediated cytotoxicity -0.017 0.3 -10000 0 -0.91 13 13
ITGA3 -0.006 0.28 -10000 0 -0.85 11 11
IL17F 0.004 0.21 0.51 2 -0.61 10 12
IL12B 0.023 0.038 -10000 0 -10000 0 0
STAT1 (dimer) -0.014 0.29 -10000 0 -0.9 12 12
CD4 -0.01 0.27 -10000 0 -0.87 10 10
IL23 -0.01 0.29 -10000 0 -0.96 10 10
IL23R -0.005 0.16 -10000 0 -0.72 6 6
IL1B -0.027 0.32 -10000 0 -1.1 11 11
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.016 0.27 -10000 0 -0.87 10 10
TYK2 0.023 0.031 -10000 0 -10000 0 0
STAT4 0.02 0.025 -10000 0 -10000 0 0
STAT3 0.026 0.007 -10000 0 -10000 0 0
IL18RAP 0.015 0.032 -10000 0 -10000 0 0
IL12RB1 0.017 0.038 -10000 0 -10000 0 0
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.029 0.044 -10000 0 -10000 0 0
IL23R/JAK2 0.014 0.15 -10000 0 -0.71 3 3
positive regulation of chronic inflammatory response -0.017 0.3 -10000 0 -0.91 13 13
natural killer cell activation -0.001 0.006 -10000 0 -10000 0 0
JAK2 0.026 0.038 -10000 0 -10000 0 0
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
NFKB1 0.027 0.006 -10000 0 -10000 0 0
RELA 0.028 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.008 0.28 -10000 0 -0.92 10 10
ALOX12B -0.01 0.27 -10000 0 -0.84 10 10
CXCL1 -0.042 0.32 -10000 0 -0.98 15 15
T cell proliferation -0.017 0.3 -10000 0 -0.91 13 13
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
IL17A 0.016 0.18 0.37 1 -0.48 10 11
PI3K -0.005 0.28 -10000 0 -0.87 12 12
IFNG 0.002 0.029 0.12 1 -0.12 3 4
STAT3 (dimer) 0 0.27 -10000 0 -0.84 11 11
IL18R1 0.024 0.049 -10000 0 -0.66 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 0.009 0.19 -10000 0 -0.77 1 1
IL18/IL18R 0.046 0.042 -10000 0 -0.43 1 1
macrophage activation -0.002 0.015 -10000 0 -0.042 10 10
TNF -0.023 0.3 -10000 0 -0.99 11 11
STAT3/STAT4 -0.008 0.28 -10000 0 -0.85 12 12
STAT4 (dimer) -0.015 0.29 -10000 0 -0.9 12 12
IL18 0.025 0.011 -10000 0 -10000 0 0
IL19 -0.019 0.27 -10000 0 -0.87 10 10
STAT5A (dimer) -0.019 0.28 -10000 0 -0.88 12 12
STAT1 0.025 0.012 -10000 0 -10000 0 0
SOCS3 0.021 0.05 -10000 0 -0.66 1 1
CXCL9 -0.025 0.29 -10000 0 -0.91 12 12
MPO -0.006 0.28 -10000 0 -0.85 10 10
positive regulation of humoral immune response -0.017 0.3 -10000 0 -0.91 13 13
IL23/IL23R/JAK2/TYK2 -0.02 0.3 -10000 0 -0.94 13 13
IL6 -0.042 0.41 -10000 0 -1.1 22 22
STAT5A 0.025 0.007 -10000 0 -10000 0 0
IL2 0.004 0.024 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.006 -10000 0 -10000 0 0
CD3E -0.021 0.28 -10000 0 -0.93 10 10
keratinocyte proliferation -0.017 0.3 -10000 0 -0.91 13 13
NOS2 -0.066 0.4 -10000 0 -1.1 23 23
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.003 0.12 -10000 0 -0.48 9 9
PDGFB-D/PDGFRB/SLAP 0.015 0.11 -10000 0 -0.5 8 8
PDGFB-D/PDGFRB/APS/CBL 0.025 0.088 -10000 0 -0.42 6 6
AKT1 0.024 0.15 0.5 12 -10000 0 12
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.001 0.13 0.26 1 -0.5 10 11
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
FGR -0.037 0.16 0.34 1 -0.46 17 18
mol:Ca2+ 0.005 0.15 0.32 5 -0.51 11 16
MYC 0.043 0.14 0.48 6 -0.45 1 7
SHC1 0.026 0.005 -10000 0 -10000 0 0
HRAS/GDP 0.021 0.084 -10000 0 -0.36 8 8
LRP1/PDGFRB/PDGFB 0.027 0.1 -10000 0 -0.42 9 9
GRB10 0.022 0.011 -10000 0 -10000 0 0
PTPN11 0.026 0.006 -10000 0 -10000 0 0
GO:0007205 0.004 0.15 0.32 5 -0.52 11 16
PTEN 0.027 0.003 -10000 0 -10000 0 0
GRB2 0.025 0.007 -10000 0 -10000 0 0
GRB7 0.025 0.007 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 0.017 0.11 -10000 0 -0.49 8 8
PDGFB-D/PDGFRB/GRB10 0.014 0.092 -10000 0 -0.41 8 8
cell cycle arrest 0.015 0.11 -10000 0 -0.5 8 8
HRAS 0.027 0.003 -10000 0 -10000 0 0
HIF1A 0.022 0.14 0.49 12 -10000 0 12
GAB1 0.003 0.15 0.36 5 -0.51 10 15
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.005 0.14 0.35 7 -0.48 9 16
PDGFB-D/PDGFRB 0.03 0.098 -10000 0 -0.44 8 8
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.017 0.11 -10000 0 -0.49 8 8
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.001 0.1 -10000 0 -0.47 8 8
positive regulation of MAPKKK cascade 0.017 0.1 -10000 0 -0.49 8 8
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
mol:IP3 0.004 0.15 0.32 5 -0.53 11 16
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.025 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.017 0.1 -10000 0 -0.47 8 8
SHB 0.026 0.006 -10000 0 -10000 0 0
BLK -0.012 0.098 -10000 0 -0.42 9 9
PTPN2 0.026 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.018 0.1 -10000 0 -0.49 8 8
BCAR1 0.026 0.007 -10000 0 -10000 0 0
VAV2 0.007 0.15 0.38 5 -0.52 9 14
CBL 0.026 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.017 0.11 -10000 0 -0.49 8 8
LCK -0.03 0.14 0.34 1 -0.46 14 15
PDGFRB -0.001 0.14 -10000 0 -0.66 8 8
ACP1 0.027 0.005 -10000 0 -10000 0 0
HCK -0.008 0.094 -10000 0 -0.42 9 9
ABL1 0.004 0.14 0.35 5 -0.47 10 15
PDGFB-D/PDGFRB/CBL -0.002 0.16 0.3 3 -0.56 11 14
PTPN1 0.026 0.007 -10000 0 -10000 0 0
SNX15 0.027 0.002 -10000 0 -10000 0 0
STAT3 0.025 0.007 -10000 0 -10000 0 0
STAT1 0.025 0.012 -10000 0 -10000 0 0
cell proliferation 0.044 0.13 0.47 6 -0.38 2 8
SLA 0.024 0.017 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.025 0.086 0.34 3 -0.36 6 9
SRC -0.003 0.084 -10000 0 -0.4 8 8
PI3K 0 0.059 -10000 0 -0.34 5 5
PDGFB-D/PDGFRB/GRB7/SHC 0.031 0.092 -10000 0 -0.43 7 7
SH2B2 0.022 0.011 -10000 0 -10000 0 0
PLCgamma1/SPHK1 0.001 0.13 -10000 0 -0.54 9 9
LYN -0.005 0.087 -10000 0 -0.4 8 8
LRP1 0.026 0.005 -10000 0 -10000 0 0
SOS1 0.027 0.004 -10000 0 -10000 0 0
STAT5B 0.025 0.007 -10000 0 -10000 0 0
STAT5A 0.025 0.007 -10000 0 -10000 0 0
NCK1-2/p130 Cas 0.056 0.083 -10000 0 -0.36 6 6
SPHK1 -0.017 0.047 -10000 0 -10000 0 0
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG 0.004 0.15 0.32 5 -0.53 11 16
PLCG1 0.003 0.15 0.34 4 -0.54 11 15
NHERF/PDGFRB 0.031 0.084 -10000 0 -0.35 8 8
YES1 -0.037 0.17 0.34 1 -0.52 20 21
cell migration 0.03 0.083 -10000 0 -0.35 8 8
SHC/Grb2/SOS1 0.052 0.088 -10000 0 -0.36 7 7
SLC9A3R2 0.025 0.008 -10000 0 -10000 0 0
SLC9A3R1 0.025 0.007 -10000 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN 0.043 0.082 -10000 0 -0.39 5 5
FYN -0.012 0.11 -10000 0 -0.42 12 12
DOK1 0.005 0.088 -10000 0 -0.39 8 8
HRAS/GTP 0.02 0.002 -10000 0 -10000 0 0
PDGFB 0.021 0.049 -10000 0 -0.66 1 1
RAC1 0.041 0.16 0.43 7 -0.48 6 13
PRKCD 0.005 0.088 -10000 0 -0.4 8 8
FER 0.008 0.091 -10000 0 -0.4 8 8
MAPKKK cascade 0.002 0.12 0.43 7 -0.36 7 14
RASA1 0.007 0.091 -10000 0 -0.4 8 8
NCK1 0.026 0.005 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
p62DOK/Csk 0.019 0.085 -10000 0 -0.37 8 8
PDGFB-D/PDGFRB/SHB 0.017 0.11 -10000 0 -0.49 8 8
chemotaxis 0.004 0.14 0.35 5 -0.46 10 15
STAT1-3-5/STAT1-3-5 0.042 0.081 -10000 0 -0.35 7 7
Bovine Papilomavirus E5/PDGFRB -0.001 0.1 -10000 0 -0.5 8 8
PTPRJ 0.027 0.004 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.026 0.01 -10000 0 -10000 0 0
CCL5 0.015 0.03 -10000 0 -10000 0 0
SDCBP 0.027 0.004 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.028 0.13 0.26 2 -0.38 13 15
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.024 0.12 -10000 0 -0.53 5 5
Syndecan-1/Syntenin -0.019 0.13 -10000 0 -0.49 6 6
MAPK3 -0.019 0.11 -10000 0 -0.63 3 3
HGF/MET 0.013 0.088 -10000 0 -0.46 6 6
TGFB1/TGF beta receptor Type II 0.026 0.01 -10000 0 -10000 0 0
BSG 0.027 0.003 -10000 0 -10000 0 0
keratinocyte migration -0.023 0.12 -10000 0 -0.52 5 5
Syndecan-1/RANTES -0.024 0.12 -10000 0 -0.59 4 4
Syndecan-1/CD147 -0.003 0.13 -10000 0 -0.67 3 3
Syndecan-1/Syntenin/PIP2 -0.019 0.12 -10000 0 -0.47 6 6
LAMA5 0.026 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion -0.019 0.12 -10000 0 -0.46 6 6
MMP7 -0.009 0.094 -10000 0 -0.58 4 4
HGF 0.001 0.12 -10000 0 -0.66 6 6
Syndecan-1/CASK -0.035 0.12 -10000 0 -0.36 13 13
Syndecan-1/HGF/MET -0.018 0.14 -10000 0 -0.59 6 6
regulation of cell adhesion -0.025 0.11 -10000 0 -0.61 3 3
HPSE -0.002 0.14 -10000 0 -0.66 8 8
positive regulation of cell migration -0.028 0.13 0.26 2 -0.38 13 15
SDC1 -0.028 0.12 -10000 0 -0.39 13 13
Syndecan-1/Collagen -0.028 0.13 0.26 2 -0.38 13 15
PPIB 0.027 0.003 -10000 0 -10000 0 0
MET 0.017 0.023 -10000 0 -10000 0 0
PRKACA 0.027 0.002 -10000 0 -10000 0 0
MMP9 -0.015 0.079 -10000 0 -0.66 2 2
MAPK1 -0.019 0.12 -10000 0 -0.63 3 3
homophilic cell adhesion -0.03 0.13 0.25 2 -0.38 13 15
MMP1 -0.02 0.16 -10000 0 -0.66 11 11
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 0.044 0.26 -10000 0 -0.88 4 4
HDAC7 0.028 0.006 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.096 0.25 -10000 0 -0.7 2 2
SMAD4 0.026 0.008 -10000 0 -10000 0 0
ID2 0.044 0.26 -10000 0 -0.83 5 5
AP1 -0.035 0.18 -10000 0 -0.45 30 30
ABCG2 0.04 0.26 -10000 0 -0.83 6 6
HIF1A 0.029 0.067 -10000 0 -10000 0 0
TFF3 -0.015 0.33 -10000 0 -0.82 14 14
GATA2 -0.09 0.26 -10000 0 -0.66 34 34
AKT1 0.034 0.065 -10000 0 -10000 0 0
response to hypoxia 0.014 0.056 -10000 0 -0.19 1 1
MCL1 0.042 0.26 -10000 0 -0.88 4 4
NDRG1 0.045 0.26 -10000 0 -0.83 5 5
SERPINE1 -0.006 0.28 -10000 0 -0.84 10 10
FECH 0.035 0.26 -10000 0 -0.83 5 5
FURIN 0.044 0.26 -10000 0 -0.88 4 4
NCOA2 -0.028 0.19 -10000 0 -0.66 16 16
EP300 0.038 0.085 -10000 0 -0.28 4 4
HMOX1 0.037 0.27 -10000 0 -0.97 4 4
BHLHE40 0.04 0.26 -10000 0 -0.88 4 4
BHLHE41 0.04 0.26 -10000 0 -0.84 5 5
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.079 0.11 -10000 0 -10000 0 0
ENG 0.043 0.084 0.34 1 -10000 0 1
JUN 0.026 0.007 -10000 0 -10000 0 0
RORA 0.043 0.26 -10000 0 -0.88 4 4
ABCB1 -0.047 0.25 -10000 0 -1.1 10 10
TFRC 0.043 0.26 -10000 0 -0.88 4 4
CXCR4 0.044 0.26 -10000 0 -0.88 4 4
TF 0.036 0.27 -10000 0 -0.88 4 4
CITED2 0.045 0.26 -10000 0 -0.88 4 4
HIF1A/ARNT 0.1 0.32 -10000 0 -0.98 4 4
LDHA 0.004 0.11 -10000 0 -0.71 3 3
ETS1 0.042 0.26 -10000 0 -0.88 4 4
PGK1 0.045 0.26 -10000 0 -0.83 5 5
NOS2 0.018 0.3 -10000 0 -0.87 10 10
ITGB2 0.031 0.26 -10000 0 -0.83 5 5
ALDOA 0.038 0.25 -10000 0 -0.85 4 4
Cbp/p300/CITED2 0.062 0.26 -10000 0 -0.91 3 3
FOS -0.069 0.23 -10000 0 -0.6 30 30
HK2 0.037 0.26 -10000 0 -0.85 5 5
SP1 0.025 0.035 -10000 0 -10000 0 0
GCK 0.032 0.16 -10000 0 -0.62 2 2
HK1 0.044 0.26 -10000 0 -0.88 4 4
NPM1 0.042 0.26 -10000 0 -0.88 4 4
EGLN1 0.041 0.26 -10000 0 -0.88 4 4
CREB1 0.032 0.005 -10000 0 -10000 0 0
PGM1 0.04 0.26 -10000 0 -0.88 4 4
SMAD3 0.028 0.003 -10000 0 -10000 0 0
EDN1 -0.052 0.24 -10000 0 -0.68 16 16
IGFBP1 -0.015 0.28 -10000 0 -0.86 8 8
VEGFA 0.071 0.22 0.51 1 -0.61 2 3
HIF1A/JAB1 0.042 0.053 -10000 0 -10000 0 0
CP 0.018 0.29 -10000 0 -0.83 8 8
CXCL12 0.011 0.33 -10000 0 -0.85 16 16
COPS5 0.027 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4 0.038 0.013 -10000 0 -10000 0 0
BNIP3 0.043 0.26 -10000 0 -0.88 4 4
EGLN3 0.046 0.26 -10000 0 -0.88 4 4
CA9 0.033 0.26 -10000 0 -0.85 5 5
TERT 0.036 0.26 -10000 0 -0.89 4 4
ENO1 0.04 0.26 -10000 0 -0.88 4 4
PFKL 0.036 0.26 -10000 0 -0.88 4 4
NCOA1 0.027 0.004 -10000 0 -10000 0 0
ADM 0.04 0.27 -10000 0 -0.97 4 4
ARNT 0.029 0.066 -10000 0 -10000 0 0
HNF4A -0.056 0.22 -10000 0 -0.66 24 24
ADFP 0.032 0.25 -10000 0 -0.83 5 5
SLC2A1 0.067 0.22 0.51 1 -0.59 3 4
LEP 0.008 0.24 -10000 0 -0.86 4 4
HIF1A/ARNT/Cbp/p300 0.089 0.26 -10000 0 -0.65 5 5
EPO 0.017 0.21 -10000 0 -0.72 3 3
CREBBP 0.04 0.073 -10000 0 -0.28 2 2
HIF1A/ARNT/Cbp/p300/HDAC7 0.098 0.25 -10000 0 -0.7 2 2
PFKFB3 0.044 0.26 -10000 0 -0.88 4 4
NT5E 0.045 0.26 -10000 0 -0.83 5 5
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.026 0.024 -10000 0 -10000 0 0
CRKL 0.026 0.12 0.32 2 -0.4 9 11
mol:PIP3 0.002 0.011 -10000 0 -10000 0 0
AKT1 0.015 0.057 -10000 0 -10000 0 0
PTK2B 0.026 0.005 -10000 0 -10000 0 0
RAPGEF1 0.027 0.12 0.31 3 -0.38 9 12
RANBP10 0.026 0.007 -10000 0 -10000 0 0
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.029 0.08 -10000 0 -0.4 6 6
MAP3K5 0.032 0.12 0.37 4 -0.37 9 13
HGF/MET/CIN85/CBL/ENDOPHILINS 0.04 0.079 -10000 0 -0.4 5 5
AP1 -0.013 0.16 -10000 0 -0.38 27 27
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.026 0.005 -10000 0 -10000 0 0
apoptosis -0.11 0.33 -10000 0 -0.76 37 37
STAT3 (dimer) 0.01 0.05 -10000 0 -0.27 3 3
GAB1/CRKL/SHP2/PI3K 0.052 0.12 -10000 0 -0.38 9 9
INPP5D 0.023 0.017 -10000 0 -10000 0 0
CBL/CRK 0.049 0.13 0.47 4 -0.39 9 13
PTPN11 0.026 0.006 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.026 0.006 -10000 0 -10000 0 0
PTEN 0.027 0.003 -10000 0 -10000 0 0
ELK1 0.079 0.16 0.31 56 -10000 0 56
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 0.004 0.045 -10000 0 -0.23 1 1
PAK1 0.014 0.053 -10000 0 -10000 0 0
HGF/MET/RANBP10 0.028 0.08 -10000 0 -0.4 6 6
HRAS -0.006 0.1 -10000 0 -0.57 2 2
DOCK1 0.026 0.12 0.31 3 -0.38 9 12
GAB1 0.023 0.12 0.24 1 -0.43 9 10
CRK 0.032 0.13 0.42 3 -0.41 9 12
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.005 0.11 -10000 0 -0.54 6 6
JUN 0.026 0.007 -10000 0 -10000 0 0
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET 0.001 0.041 -10000 0 -0.24 5 5
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
cell morphogenesis 0.033 0.097 0.33 4 -10000 0 4
GRB2/SHC 0.032 0.057 -10000 0 -0.27 1 1
FOS -0.07 0.23 -10000 0 -0.61 30 30
GLMN 0.003 0.001 -10000 0 -10000 0 0
cell motility 0.079 0.16 0.31 56 -10000 0 56
HGF/MET/MUC20 0.013 0.076 -10000 0 -0.4 6 6
cell migration 0.023 0.048 -10000 0 -0.26 1 1
GRB2 0.025 0.007 -10000 0 -10000 0 0
CBL 0.026 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.026 0.024 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.015 0.048 -10000 0 -0.28 3 3
MET/MUC20 0.013 0.015 -10000 0 -10000 0 0
RAP1B 0.032 0.13 0.41 6 -0.36 9 15
RAP1A 0.024 0.11 0.3 3 -0.36 7 10
HGF/MET/RANBP9 0.028 0.079 -10000 0 -0.39 6 6
RAF1 0.02 0.12 0.33 1 -0.54 2 3
STAT3 0.01 0.051 -10000 0 -0.27 3 3
cell proliferation 0.029 0.087 0.26 1 -0.38 3 4
RPS6KB1 0.008 0.018 -10000 0 -10000 0 0
MAPK3 0.05 0.14 0.47 6 -10000 0 6
MAPK1 0.1 0.23 0.65 21 -10000 0 21
RANBP9 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.038 0.15 0.55 4 -0.54 5 9
SRC 0.007 0.043 -10000 0 -0.27 3 3
PI3K 0.033 0.054 -10000 0 -10000 0 0
MET/Glomulin 0.008 0.029 -10000 0 -10000 0 0
SOS1 0.027 0.004 -10000 0 -10000 0 0
MAP2K1 0.027 0.12 0.36 3 -0.5 2 5
MET 0.017 0.023 -10000 0 -10000 0 0
MAP4K1 0.034 0.13 0.38 4 -0.4 9 13
PTK2 0.027 0.004 -10000 0 -10000 0 0
MAP2K2 0.027 0.12 0.36 3 -0.5 2 5
BAD 0.014 0.053 -10000 0 -10000 0 0
MAP2K4 0.037 0.13 0.38 9 -0.37 4 13
SHP2/GRB2/SOS1/GAB1 0.016 0.092 -10000 0 -0.36 8 8
INPPL1 0.027 0.003 -10000 0 -10000 0 0
PXN 0.026 0.006 -10000 0 -10000 0 0
SH3KBP1 0.027 0.003 -10000 0 -10000 0 0
HGS -0.002 0.038 -10000 0 -0.22 5 5
PLCgamma1/PKC 0.019 0.005 -10000 0 -10000 0 0
HGF 0.001 0.12 -10000 0 -0.66 6 6
RASA1 0.027 0.005 -10000 0 -10000 0 0
NCK1 0.026 0.005 -10000 0 -10000 0 0
PTPRJ 0.027 0.004 -10000 0 -10000 0 0
NCK/PLCgamma1 0.027 0.048 -10000 0 -0.23 4 4
PDPK1 0.017 0.06 -10000 0 -10000 0 0
HGF/MET/SHIP 0.028 0.08 -10000 0 -0.4 6 6
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.057 0.029 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0.025 0.008 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.045 0.038 0.3 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.053 0.028 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.058 0.085 -10000 0 -0.24 1 1
CaM/Ca2+ 0.057 0.031 -10000 0 -10000 0 0
RAP1A 0.026 0.005 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.025 0.025 -10000 0 -10000 0 0
AKT1 0.017 0.069 0.35 6 -10000 0 6
MAP2K1 0.009 0.054 0.29 6 -10000 0 6
MAP3K11 0.022 0.056 0.29 7 -10000 0 7
IFNGR1 0.029 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.2 0.24 -10000 0 -0.45 94 94
Rap1/GTP 0.016 0.016 -10000 0 -10000 0 0
CRKL/C3G 0.036 0.014 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.064 0.036 -10000 0 -10000 0 0
CEBPB 0.018 0.12 0.43 4 -0.57 1 5
STAT3 0.025 0.007 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.053 0.13 -10000 0 -0.97 3 3
STAT1 0.021 0.053 0.29 6 -10000 0 6
CALM1 0.026 0.007 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.015 0.027 -10000 0 -10000 0 0
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.034 0.053 0.29 6 -10000 0 6
CEBPB/PTGES2/Cbp/p300 0.025 0.064 -10000 0 -0.35 1 1
mol:Ca2+ 0.054 0.028 -10000 0 -10000 0 0
MAPK3 0.013 0.074 -10000 0 -0.63 2 2
STAT1 (dimer) -0.069 0.12 -10000 0 -10000 0 0
MAPK1 -0.034 0.22 0.42 1 -0.69 18 19
JAK2 0.028 0.01 -10000 0 -10000 0 0
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
JAK1 0.028 0.01 -10000 0 -10000 0 0
CAMK2D 0.026 0.006 -10000 0 -10000 0 0
DAPK1 0.02 0.086 0.32 7 -0.32 1 8
SMAD7 -0.016 0.076 0.27 7 -10000 0 7
CBL/CRKL/C3G 0.048 0.052 0.29 7 -10000 0 7
PI3K 0.056 0.031 -10000 0 -10000 0 0
IFNG 0.015 0.027 -10000 0 -10000 0 0
apoptosis -0.013 0.1 -10000 0 -0.43 8 8
CAMK2G 0.027 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.007 -10000 0 -10000 0 0
CAMK2A -0.31 0.33 -10000 0 -0.65 93 93
CAMK2B 0.001 0.098 -10000 0 -0.66 4 4
FRAP1 0.007 0.067 0.34 6 -10000 0 6
PRKCD 0.013 0.058 0.31 5 -10000 0 5
RAP1B 0.026 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.058 0.085 -10000 0 -0.24 1 1
PTPN2 0.025 0.008 -10000 0 -10000 0 0
EP300 0.025 0.008 -10000 0 -10000 0 0
IRF1 0.024 0.076 0.38 5 -0.38 1 6
STAT1 (dimer)/PIASy 0.032 0.053 0.29 6 -10000 0 6
SOCS1 0.008 0.15 -10000 0 -1.2 3 3
mol:GDP 0.041 0.052 0.27 7 -10000 0 7
CASP1 -0.017 0.077 0.27 7 -10000 0 7
PTGES2 0.026 0.006 -10000 0 -10000 0 0
IRF9 0.03 0.058 0.27 7 -10000 0 7
mol:PI-3-4-5-P3 0.041 0.023 -10000 0 -10000 0 0
RAP1/GDP 0.037 0.02 -10000 0 -10000 0 0
CBL 0.022 0.056 0.29 7 -10000 0 7
MAP3K1 0.021 0.053 0.29 6 -10000 0 6
PIAS1 0.027 0.003 -10000 0 -10000 0 0
PIAS4 0.027 0.004 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.058 0.085 -10000 0 -0.24 1 1
PTPN11 0.012 0.019 -10000 0 -10000 0 0
CREBBP 0.025 0.009 -10000 0 -10000 0 0
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.031 0.017 -10000 0 -10000 0 0
VLDLR 0.026 0.007 -10000 0 -10000 0 0
CRKL 0.025 0.008 -10000 0 -10000 0 0
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
ITGA3 0.021 0.021 -10000 0 -10000 0 0
RELN/VLDLR/Fyn 0.014 0.1 -10000 0 -0.42 10 10
MAPK8IP1/MKK7/MAP3K11/JNK1 0.067 0.061 -10000 0 -0.37 3 3
AKT1 -0.013 0.069 -10000 0 -0.3 10 10
MAP2K7 0.027 0.003 -10000 0 -10000 0 0
RAPGEF1 0.026 0.006 -10000 0 -10000 0 0
DAB1 -0.001 0.025 -10000 0 -10000 0 0
RELN/LRP8/DAB1 0 0.096 -10000 0 -0.39 10 10
LRPAP1/LRP8 0.036 0.016 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn 0.019 0.094 -10000 0 -0.38 9 9
DAB1/alpha3/beta1 Integrin 0.018 0.088 -10000 0 -0.36 9 9
long-term memory -0.044 0.18 -10000 0 -0.4 33 33
DAB1/LIS1 0.028 0.095 -10000 0 -0.37 9 9
DAB1/CRLK/C3G 0.018 0.088 -10000 0 -0.36 9 9
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
DAB1/NCK2 0.03 0.096 -10000 0 -0.37 9 9
ARHGEF2 0.026 0.005 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A -0.11 0.27 -10000 0 -0.66 39 39
CDK5R1 0.026 0.007 -10000 0 -10000 0 0
RELN -0.037 0.15 -10000 0 -0.66 10 10
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.013 0.1 -10000 0 -0.41 10 10
GRIN2A/RELN/LRP8/DAB1/Fyn -0.047 0.18 -10000 0 -0.41 34 34
MAPK8 0.015 0.088 -10000 0 -0.58 4 4
RELN/VLDLR/DAB1 -0.002 0.097 -10000 0 -0.4 10 10
ITGB1 0.027 0.005 -10000 0 -10000 0 0
MAP1B 0.005 0.11 -10000 0 -0.38 9 9
RELN/LRP8 0.013 0.1 -10000 0 -0.41 10 10
GRIN2B/RELN/LRP8/DAB1/Fyn 0.026 0.098 -10000 0 -0.39 9 9
PI3K 0.039 0.009 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.033 0.02 -10000 0 -10000 0 0
RAP1A 0.003 0.11 0.33 1 -0.34 8 9
PAFAH1B1 0.025 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.027 0.004 -10000 0 -10000 0 0
CRLK/C3G 0.036 0.014 -10000 0 -10000 0 0
GRIN2B 0.005 0.024 -10000 0 -10000 0 0
NCK2 0.027 0.003 -10000 0 -10000 0 0
neuron differentiation 0.013 0.081 -10000 0 -0.36 4 4
neuron adhesion 0.011 0.12 0.33 7 -0.35 1 8
LRP8 0.024 0.015 -10000 0 -10000 0 0
GSK3B -0.012 0.069 -10000 0 -0.34 3 3
RELN/VLDLR/DAB1/Fyn 0.017 0.095 -10000 0 -0.38 10 10
MAP3K11 0.027 0.002 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.006 0.076 -10000 0 -0.32 10 10
CDK5 0.022 0.011 -10000 0 -10000 0 0
MAPT 0.012 0.21 0.69 12 -0.6 9 21
neuron migration 0.017 0.13 0.37 1 -0.38 9 10
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 0.013 0.082 -10000 0 -0.36 4 4
RELN/VLDLR 0.023 0.098 -10000 0 -0.4 9 9
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.021 0.074 -10000 0 -10000 0 0
VDR 0.016 0.084 -10000 0 -0.66 3 3
FAM120B 0.026 0.005 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.035 0.034 -10000 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.034 0.054 -10000 0 -0.39 2 2
MED1 0.025 0.007 -10000 0 -10000 0 0
mol:9cRA 0.003 0.006 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.018 0.057 -10000 0 -0.28 6 6
RXRs/NUR77 -0.12 0.22 -10000 0 -0.39 77 77
RXRs/PPAR 0.027 0.017 -10000 0 -10000 0 0
NCOR2 0.026 0.006 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.012 0.063 -10000 0 -0.49 3 3
RARs/VDR/DNA/Vit D3 0.051 0.057 -10000 0 -0.38 3 3
RARA 0.025 0.007 -10000 0 -10000 0 0
NCOA1 0.027 0.004 -10000 0 -10000 0 0
VDR/VDR/DNA 0.016 0.084 -10000 0 -0.66 3 3
RARs/RARs/DNA/9cRA 0.045 0.018 -10000 0 -10000 0 0
RARG 0.026 0.009 -10000 0 -10000 0 0
RPS6KB1 0.041 0.13 0.52 13 -10000 0 13
RARs/THRs/DNA/SMRT 0.017 0.059 -10000 0 -0.28 7 7
THRA 0.025 0.007 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.012 0.063 -10000 0 -0.49 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.052 0.029 -10000 0 -10000 0 0
NR1H4 0.015 0.084 -10000 0 -0.66 3 3
RXRs/LXRs/DNA 0.08 0.044 -10000 0 -10000 0 0
NR1H2 0.03 0.009 -10000 0 -10000 0 0
NR1H3 0.03 0.01 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.051 0.06 -10000 0 -0.37 3 3
NR4A1 -0.24 0.33 -10000 0 -0.66 78 78
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.011 0.059 -10000 0 -0.36 4 4
RXRG 0.021 0.015 -10000 0 -10000 0 0
RXR alpha/CCPG 0.039 0.014 -10000 0 -10000 0 0
RXRA 0.029 0.011 -10000 0 -10000 0 0
RXRB 0.029 0.011 -10000 0 -10000 0 0
THRB 0.002 0.13 -10000 0 -0.66 7 7
PPARG 0.026 0.006 -10000 0 -10000 0 0
PPARD 0.026 0.007 -10000 0 -10000 0 0
TNF 0.019 0.12 -10000 0 -1.1 2 2
mol:Oxysterols 0.003 0.005 -10000 0 -10000 0 0
cholesterol transport 0.034 0.053 -10000 0 -0.38 2 2
PPARA 0.025 0.008 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.026 0.006 -10000 0 -10000 0 0
RXRs/NUR77/BCL2 -0.11 0.17 -10000 0 -0.32 77 77
SREBF1 0.024 0.05 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.052 0.029 -10000 0 -10000 0 0
ABCA1 0.03 0.045 -10000 0 -10000 0 0
RARs/THRs 0.056 0.087 -10000 0 -0.38 7 7
RXRs/FXR 0.057 0.057 -10000 0 -0.38 2 2
BCL2 0.025 0.008 -10000 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.032 0.021 -10000 0 -10000 0 0
TP53 -0.011 0.04 -10000 0 -0.19 9 9
Senescence -0.012 0.041 -10000 0 -0.19 10 10
Apoptosis -0.012 0.041 -10000 0 -0.19 10 10
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.028 0.065 0.32 9 -10000 0 9
MDM4 0.026 0.006 -10000 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A 0.005 0.006 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.031 0.021 -10000 0 -10000 0 0
STXBP1 0.026 0.006 -10000 0 -10000 0 0
ACh/CHRNA1 -0.004 0.041 -10000 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0.048 0.015 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.005 0.028 -10000 0 -10000 0 0
mol:ACh 0.018 0.043 0.091 38 -0.14 1 39
RAB3GAP2 0.026 0.005 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.029 0.038 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction -0.004 0.041 -10000 0 -10000 0 0
UNC13B 0.026 0.005 -10000 0 -10000 0 0
CHRNA1 -0.044 0.04 -10000 0 -10000 0 0
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.093 0.2 -10000 0 -0.44 50 50
SNAP25 -0.004 0.025 -10000 0 -0.33 1 1
VAMP2 0.005 0.001 -10000 0 -10000 0 0
SYT1 -0.15 0.3 -10000 0 -0.66 50 50
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.019 0.012 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 0.029 0.038 -10000 0 -10000 0 0
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.19 0.32 -10000 0 -0.65 63 63
HRAS 0.027 0.003 -10000 0 -10000 0 0
EGFR 0.022 0.011 -10000 0 -10000 0 0
AKT 0.036 0.1 0.24 20 -10000 0 20
FOXO3 0.027 0.005 -10000 0 -10000 0 0
AKT1 0.025 0.008 -10000 0 -10000 0 0
FOXO1 0.026 0.005 -10000 0 -10000 0 0
AKT3 0.026 0.006 -10000 0 -10000 0 0
FOXO4 0.027 0.002 -10000 0 -10000 0 0
MET 0.017 0.023 -10000 0 -10000 0 0
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
PIK3CB 0.026 0.005 -10000 0 -10000 0 0
NRAS 0.026 0.006 -10000 0 -10000 0 0
PIK3CG 0.017 0.051 -10000 0 -0.66 1 1
PIK3R3 0.026 0.007 -10000 0 -10000 0 0
PIK3R2 0.027 0.003 -10000 0 -10000 0 0
NF1 0.026 0.006 -10000 0 -10000 0 0
RAS -0.025 0.079 -10000 0 -0.22 8 8
ERBB2 0.025 0.007 -10000 0 -10000 0 0
proliferation/survival/translation -0.026 0.054 0.24 2 -10000 0 2
PI3K 0.012 0.11 0.24 22 -0.21 7 29
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
KRAS 0.026 0.006 -10000 0 -10000 0 0
FOXO 0.063 0.082 0.24 23 -10000 0 23
AKT2 0.027 0.003 -10000 0 -10000 0 0
PTEN 0.027 0.003 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.15 0.12 -9999 0 -0.86 1 1
RAD9A 0.027 0.002 -9999 0 -10000 0 0
AP1 -0.036 0.18 -9999 0 -0.45 30 30
IFNAR2 0.026 0.008 -9999 0 -10000 0 0
AKT1 0.005 0.051 -9999 0 -0.24 7 7
ER alpha/Oestrogen -0.002 0.1 -9999 0 -0.42 10 10
NFX1/SIN3/HDAC complex 0.014 0.077 -9999 0 -0.43 3 3
EGF -0.58 0.21 -9999 0 -0.65 176 176
SMG5 0.026 0.005 -9999 0 -10000 0 0
SMG6 0.025 0.007 -9999 0 -10000 0 0
SP3/HDAC2 0.04 0.009 -9999 0 -10000 0 0
TERT/c-Abl -0.15 0.11 -9999 0 -0.8 1 1
SAP18 0.027 0.005 -9999 0 -10000 0 0
MRN complex 0.052 0.015 -9999 0 -10000 0 0
WT1 -0.38 0.33 -9999 0 -0.66 116 116
WRN 0.026 0.005 -9999 0 -10000 0 0
SP1 0.027 0.005 -9999 0 -10000 0 0
SP3 0.027 0.003 -9999 0 -10000 0 0
TERF2IP 0.026 0.007 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.14 0.11 -9999 0 -0.73 1 1
Mad/Max 0.038 0.011 -9999 0 -10000 0 0
TERT -0.16 0.12 -9999 0 -0.89 1 1
CCND1 -0.14 0.11 -9999 0 -0.76 1 1
MAX 0.026 0.007 -9999 0 -10000 0 0
RBBP7 0.027 0.003 -9999 0 -10000 0 0
RBBP4 0.026 0.007 -9999 0 -10000 0 0
TERF2 0.023 0.009 -9999 0 -10000 0 0
PTGES3 0.026 0.005 -9999 0 -10000 0 0
SIN3A 0.027 0.003 -9999 0 -10000 0 0
Telomerase/911 0.016 0.038 -9999 0 -10000 0 0
CDKN1B 0.016 0.015 -9999 0 -10000 0 0
RAD1 0.027 0.004 -9999 0 -10000 0 0
XRCC5 0.027 0.005 -9999 0 -10000 0 0
XRCC6 0.025 0.008 -9999 0 -10000 0 0
SAP30 0.025 0.009 -9999 0 -10000 0 0
TRF2/PARP2 0.034 0.015 -9999 0 -10000 0 0
UBE3A 0.027 0.004 -9999 0 -10000 0 0
JUN 0.026 0.007 -9999 0 -10000 0 0
E6 0 0 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.02 0.003 -9999 0 -10000 0 0
FOS -0.07 0.23 -9999 0 -0.61 30 30
IFN-gamma/IRF1 0.036 0.024 -9999 0 -10000 0 0
PARP2 0.025 0.007 -9999 0 -10000 0 0
BLM 0.019 0.027 -9999 0 -10000 0 0
Telomerase -0.028 0.11 -9999 0 -0.87 2 2
IRF1 0.03 0.006 -9999 0 -10000 0 0
ESR1 -0.003 0.13 -9999 0 -0.56 10 10
KU/TER 0.036 0.013 -9999 0 -10000 0 0
ATM/TRF2 0.038 0.012 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.018 0.073 -9999 0 -0.36 3 3
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.018 0.075 -9999 0 -0.37 3 3
HDAC1 0.026 0.007 -9999 0 -10000 0 0
HDAC2 0.027 0.005 -9999 0 -10000 0 0
ATM 0.01 0.003 -9999 0 -10000 0 0
SMAD3 0.013 0.007 -9999 0 -10000 0 0
ABL1 0.026 0.006 -9999 0 -10000 0 0
MXD1 0.027 0.003 -9999 0 -10000 0 0
MRE11A 0.027 0.004 -9999 0 -10000 0 0
HUS1 0.022 0.011 -9999 0 -10000 0 0
RPS6KB1 0.025 0.007 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.12 0.12 -9999 0 -0.8 1 1
NR2F2 0.026 0.004 -9999 0 -10000 0 0
MAPK3 -0.003 0.013 -9999 0 -10000 0 0
MAPK1 -0.004 0.013 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.026 0.01 -9999 0 -10000 0 0
NFKB1 0.026 0.006 -9999 0 -10000 0 0
HNRNPC 0.025 0.007 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.01 0.003 -9999 0 -10000 0 0
NBN 0.027 0.004 -9999 0 -10000 0 0
EGFR 0.022 0.011 -9999 0 -10000 0 0
mol:Oestrogen 0 0 -9999 0 -10000 0 0
EGF/EGFR -0.39 0.17 -9999 0 -0.44 176 176
MYC 0.026 0.01 -9999 0 -10000 0 0
IL2 0.016 0.015 -9999 0 -10000 0 0
KU 0.036 0.013 -9999 0 -10000 0 0
RAD50 0.026 0.005 -9999 0 -10000 0 0
HSP90AA1 0.025 0.007 -9999 0 -10000 0 0
TGFB1 0.026 0.01 -9999 0 -10000 0 0
TRF2/BLM 0.03 0.025 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.14 0.12 -9999 0 -0.8 1 1
SP1/HDAC2 0.039 0.011 -9999 0 -10000 0 0
PINX1 0.026 0.005 -9999 0 -10000 0 0
Telomerase/EST1A -0.14 0.11 -9999 0 -0.73 1 1
Smad3/Myc 0.028 0.011 -9999 0 -10000 0 0
911 complex 0.044 0.023 -9999 0 -10000 0 0
IFNG 0.019 0.026 -9999 0 -10000 0 0
Telomerase/PinX1 -0.14 0.11 -9999 0 -0.72 1 1
Telomerase/AKT1/mTOR/p70S6K -0.036 0.1 -9999 0 -0.52 4 4
SIN3B 0.027 0.002 -9999 0 -10000 0 0
YWHAE 0.025 0.007 -9999 0 -10000 0 0
Telomerase/EST1B -0.14 0.11 -9999 0 -0.72 1 1
response to DNA damage stimulus 0.001 0.019 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0.069 0.026 -9999 0 -10000 0 0
TRF2/WRN 0.036 0.012 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.14 0.11 -9999 0 -0.72 1 1
E2F1 -0.002 0.044 -9999 0 -10000 0 0
ZNFX1 0.026 0.006 -9999 0 -10000 0 0
PIF1 0.017 0.029 -9999 0 -10000 0 0
NCL 0.026 0.005 -9999 0 -10000 0 0
DKC1 0.027 0.002 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Syndecan-4-mediated signaling events

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.017 0.085 -10000 0 -0.72 2 2
Syndecan-4/Syndesmos -0.15 0.16 -10000 0 -0.5 6 6
positive regulation of JNK cascade -0.16 0.17 -10000 0 -0.58 10 10
Syndecan-4/ADAM12 -0.15 0.16 -10000 0 -0.5 6 6
CCL5 0.015 0.03 -10000 0 -10000 0 0
Rac1/GDP 0.016 0.008 -10000 0 -10000 0 0
DNM2 0.027 0.003 -10000 0 -10000 0 0
ITGA5 0.026 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.004 -10000 0 -10000 0 0
PLG -0.37 0.32 -10000 0 -0.63 114 114
ADAM12 0.013 0.034 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.025 0.008 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.056 0.032 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.16 0.17 -10000 0 -0.57 9 9
Syndecan-4/CXCL12/CXCR4 -0.17 0.18 -10000 0 -0.62 10 10
Syndecan-4/Laminin alpha3 -0.16 0.16 -10000 0 -0.51 6 6
MDK 0.006 0.04 -10000 0 -10000 0 0
Syndecan-4/FZD7 -0.16 0.17 -10000 0 -0.53 9 9
Syndecan-4/Midkine -0.15 0.16 -10000 0 -0.51 6 6
FZD7 0.006 0.12 -10000 0 -0.66 6 6
Syndecan-4/FGFR1/FGF -0.14 0.16 -10000 0 -0.5 5 5
THBS1 0.015 0.088 -10000 0 -0.58 4 4
integrin-mediated signaling pathway -0.15 0.16 -10000 0 -0.5 6 6
positive regulation of MAPKKK cascade -0.16 0.17 -10000 0 -0.58 10 10
Syndecan-4/TACI -0.15 0.16 -10000 0 -0.53 5 5
CXCR4 0.02 0.025 -10000 0 -10000 0 0
cell adhesion 0.027 0.038 0.2 7 -10000 0 7
Syndecan-4/Dynamin -0.15 0.16 -10000 0 -0.5 6 6
Syndecan-4/TSP1 -0.16 0.17 -10000 0 -0.53 8 8
Syndecan-4/GIPC -0.15 0.16 -10000 0 -0.5 6 6
Syndecan-4/RANTES -0.15 0.16 -10000 0 -0.53 5 5
ITGB1 0.027 0.005 -10000 0 -10000 0 0
LAMA1 0.004 0.099 -10000 0 -0.66 4 4
LAMA3 -0.001 0.042 -10000 0 -10000 0 0
RAC1 0.022 0.011 -10000 0 -10000 0 0
PRKCA 0.099 0.22 0.87 14 -10000 0 14
Syndecan-4/alpha-Actinin -0.15 0.16 -10000 0 -0.5 6 6
TFPI 0.026 0.01 -10000 0 -10000 0 0
F2 0.018 0.031 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.038 0.01 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.16 0.17 -10000 0 -0.56 9 9
ACTN1 0.026 0.007 -10000 0 -10000 0 0
TNC 0.012 0.073 -10000 0 -0.66 2 2
Syndecan-4/CXCL12 -0.18 0.18 -10000 0 -0.61 11 11
FGF6 -0.015 0.01 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
CXCL12 -0.036 0.2 -10000 0 -0.66 18 18
TNFRSF13B 0.006 0.027 -10000 0 -10000 0 0
FGF2 0.026 0.006 -10000 0 -10000 0 0
FGFR1 0.027 0.005 -10000 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.16 0.15 -10000 0 -0.5 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.022 0.029 -10000 0 -10000 0 0
cell migration -0.02 0.01 -10000 0 -10000 0 0
PRKCD 0.029 0.018 -10000 0 -10000 0 0
vasculogenesis -0.15 0.16 -10000 0 -0.51 8 8
SDC4 -0.16 0.16 -10000 0 -0.53 6 6
Syndecan-4/Tenascin C -0.15 0.16 -10000 0 -0.52 6 6
Syndecan-4/PI-4-5-P2/PKC alpha -0.044 0.026 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.15 0.16 -10000 0 -0.5 6 6
MMP9 -0.01 0.078 -10000 0 -0.65 2 2
Rac1/GTP 0.028 0.039 0.2 7 -10000 0 7
cytoskeleton organization -0.14 0.15 -10000 0 -0.48 6 6
GIPC1 0.027 0.002 -10000 0 -10000 0 0
Syndecan-4/TFPI -0.15 0.16 -10000 0 -0.52 5 5
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.012 0.005 -10000 0 -10000 0 0
SMARCC1 0.004 0.05 -10000 0 -0.65 1 1
REL 0.023 0.049 -10000 0 -0.66 1 1
HDAC7 -0.12 0.11 -10000 0 -0.5 1 1
JUN 0.026 0.007 -10000 0 -10000 0 0
EP300 0.025 0.008 -10000 0 -10000 0 0
KAT2B 0.026 0.006 -10000 0 -10000 0 0
KAT5 0.027 0.002 -10000 0 -10000 0 0
MAPK14 -0.016 0.024 -10000 0 -10000 0 0
FOXO1 0.026 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.12 0.13 -10000 0 -0.44 2 2
MAP2K6 -0.006 0.025 -10000 0 -10000 0 0
BRM/BAF57 0.035 0.014 -10000 0 -10000 0 0
MAP2K4 -0.007 0.025 -10000 0 -10000 0 0
SMARCA2 0.026 0.007 -10000 0 -10000 0 0
PDE9A -0.18 0.21 -10000 0 -0.79 10 10
NCOA2 -0.029 0.19 -10000 0 -0.66 16 16
CEBPA 0.017 0.054 -10000 0 -0.66 1 1
EHMT2 0.026 0.006 -10000 0 -10000 0 0
cell proliferation -0.15 0.21 0.51 7 -0.5 23 30
NR0B1 -0.006 0.037 -10000 0 -10000 0 0
EGR1 -0.029 0.19 -10000 0 -0.66 16 16
RXRs/9cRA 0.042 0.017 -10000 0 -10000 0 0
AR/RACK1/Src -0.037 0.091 0.32 2 -0.37 3 5
AR/GR -0.018 0.091 0.24 4 -0.34 8 12
GNB2L1 0.027 0.005 -10000 0 -10000 0 0
PKN1 0.027 0.002 -10000 0 -10000 0 0
RCHY1 0.026 0.005 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
MAPK8 -0.025 0.061 -10000 0 -0.39 4 4
T-DHT/AR/TIF2/CARM1 -0.062 0.16 0.34 3 -0.5 16 19
SRC -0.041 0.05 0.19 2 -0.38 1 3
NR3C1 0.026 0.005 -10000 0 -10000 0 0
KLK3 -0.064 0.19 -10000 0 -0.65 7 7
APPBP2 -0.006 0.025 -10000 0 -10000 0 0
TRIM24 0.022 0.012 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.042 0.097 0.34 3 -0.37 4 7
TMPRSS2 -0.77 0.53 -10000 0 -1.1 130 130
RXRG -0.002 0.022 -10000 0 -10000 0 0
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0.026 0.006 -10000 0 -10000 0 0
RXRB 0.026 0.006 -10000 0 -10000 0 0
CARM1 0.027 0.003 -10000 0 -10000 0 0
NR2C2 0.024 0.027 -10000 0 -0.35 1 1
KLK2 -0.045 0.13 0.35 3 -0.5 5 8
AR -0.031 0.078 -10000 0 -0.36 9 9
SENP1 0.026 0.005 -10000 0 -10000 0 0
HSP90AA1 0.025 0.007 -10000 0 -10000 0 0
MDM2 0.026 0.006 -10000 0 -10000 0 0
SRY 0 0.003 0.033 1 -10000 0 1
GATA2 -0.092 0.26 -10000 0 -0.66 34 34
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 -0.005 0.042 -10000 0 -10000 0 0
T-DHT/AR/RACK1/Src -0.038 0.094 0.33 2 -0.38 3 5
positive regulation of transcription -0.092 0.26 -10000 0 -0.66 34 34
DNAJA1 -0.007 0.027 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.007 -10000 0 -10000 0 0
NCOA1 0.033 0.015 -10000 0 -10000 0 0
SPDEF 0.015 0.027 -10000 0 -10000 0 0
T-DHT/AR/TIF2 -0.036 0.13 0.3 4 -0.48 7 11
T-DHT/AR/Hsp90 -0.038 0.096 0.34 3 -0.37 4 7
GSK3B 0.022 0.009 -10000 0 -10000 0 0
NR2C1 0.026 0.005 -10000 0 -10000 0 0
mol:T-DHT -0.046 0.047 -10000 0 -0.4 1 1
SIRT1 0.027 0.003 -10000 0 -10000 0 0
ZMIZ2 0.022 0.011 -10000 0 -10000 0 0
POU2F1 -0.052 0.066 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.05 0.096 0.34 3 -0.39 4 7
CREBBP 0.025 0.008 -10000 0 -10000 0 0
SMARCE1 0.025 0.008 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.027 0.004 -9999 0 -10000 0 0
SPHK1 -0.017 0.047 -9999 0 -10000 0 0
GNAI2 0.026 0.006 -9999 0 -10000 0 0
mol:S1P 0.004 0.011 -9999 0 -10000 0 0
GNAO1 -0.007 0.14 -9999 0 -0.66 9 9
mol:Sphinganine-1-P -0.013 0.029 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.044 0.035 -9999 0 -10000 0 0
GNAI3 0.026 0.005 -9999 0 -10000 0 0
G12/G13 0.031 0.017 -9999 0 -10000 0 0
S1PR3 -0.033 0.19 -9999 0 -0.66 17 17
S1PR2 0.027 0.003 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P 0.001 0.016 -9999 0 -10000 0 0
S1PR5 0.018 0.07 -9999 0 -0.66 2 2
S1PR4 0.025 0.012 -9999 0 -10000 0 0
GNAI1 0.019 0.05 -9999 0 -0.66 1 1
S1P/S1P5/G12 0.033 0.055 -9999 0 -0.38 2 2
S1P/S1P3/Gq -0.073 0.18 -9999 0 -0.34 53 53
S1P/S1P4/Gi 0.012 0.094 -9999 0 -0.31 10 10
GNAQ 0.026 0.007 -9999 0 -10000 0 0
GNAZ 0.025 0.008 -9999 0 -10000 0 0
GNA14 -0.11 0.27 -9999 0 -0.64 41 41
GNA15 0.021 0.023 -9999 0 -10000 0 0
GNA12 0.022 0.011 -9999 0 -10000 0 0
GNA13 0.025 0.007 -9999 0 -10000 0 0
GNA11 0.015 0.088 -9999 0 -0.58 4 4
ABCC1 0.025 0.008 -9999 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.023 0.079 -10000 0 -0.36 7 7
NF kappa B1 p50/RelA/I kappa B alpha 0.05 0.12 0.36 12 -0.39 1 13
alphaV/beta3 Integrin/Osteopontin/Src 0.035 0.059 -10000 0 -0.49 2 2
AP1 0.002 0.16 -10000 0 -0.58 5 5
ILK 0.019 0.087 -10000 0 -0.37 7 7
bone resorption 0.022 0.1 0.32 1 -0.65 1 2
PTK2B 0.026 0.005 -10000 0 -10000 0 0
PYK2/p130Cas 0.055 0.09 -10000 0 -0.35 7 7
ITGAV 0.03 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.025 0.069 -10000 0 -0.5 3 3
alphaV/beta3 Integrin/Osteopontin 0.039 0.093 -10000 0 -0.42 7 7
MAP3K1 0.017 0.088 -10000 0 -0.38 7 7
JUN 0.026 0.007 -10000 0 -10000 0 0
MAPK3 0 0.074 -10000 0 -0.36 7 7
MAPK1 -0.001 0.073 -10000 0 -0.36 7 7
Rac1/GDP 0.016 0.008 -10000 0 -10000 0 0
NFKB1 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.007 0.1 0.38 2 -0.41 7 9
ITGB3 0.008 0.11 -10000 0 -0.65 5 5
NFKBIA -0.003 0.074 -10000 0 -0.36 7 7
FOS -0.07 0.23 -10000 0 -0.61 30 30
CD44 0.02 0.025 -10000 0 -10000 0 0
CHUK 0.027 0.003 -10000 0 -10000 0 0
PLAU 0.026 0.15 0.51 4 -1.1 1 5
NF kappa B1 p50/RelA 0.05 0.088 -10000 0 -10000 0 0
BCAR1 0.026 0.007 -10000 0 -10000 0 0
RELA 0.027 0.002 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.026 0.085 -10000 0 -0.49 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.016 0.088 -10000 0 -0.38 7 7
VAV3 0.012 0.093 0.38 2 -0.36 7 9
MAP3K14 0.009 0.08 -10000 0 -0.38 7 7
ROCK2 0.016 0.084 -10000 0 -0.66 3 3
SPP1 0.018 0.075 -10000 0 -0.55 3 3
RAC1 0.022 0.011 -10000 0 -10000 0 0
Rac1/GTP 0.016 0.073 0.34 1 -0.33 4 5
MMP2 -0.022 0.12 0.31 1 -0.46 5 6
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.025 0.007 -10000 0 -10000 0 0
VLDLR 0.026 0.007 -10000 0 -10000 0 0
LRPAP1 0.026 0.005 -10000 0 -10000 0 0
NUDC 0.025 0.007 -10000 0 -10000 0 0
RELN/LRP8 0.013 0.1 -10000 0 -0.41 10 10
CaM/Ca2+ 0.019 0.005 -10000 0 -10000 0 0
KATNA1 0.026 0.005 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 0.015 0.12 -10000 0 -0.39 9 9
IQGAP1/CaM 0.038 0.011 -10000 0 -10000 0 0
DAB1 -0.001 0.025 -10000 0 -10000 0 0
IQGAP1 0.027 0.004 -10000 0 -10000 0 0
PLA2G7 -0.048 0.039 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
DYNLT1 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.036 0.016 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.026 0.006 -10000 0 -10000 0 0
CDK5R1 0.026 0.007 -10000 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0.009 0.003 -10000 0 -10000 0 0
CDK5R2 -0.005 0.041 -10000 0 -10000 0 0
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.003 0.1 -10000 0 -0.43 10 10
YWHAE 0.025 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.036 0.14 0.31 32 -0.35 3 35
MAP1B 0.006 0.003 -10000 0 -10000 0 0
RAC1 0.011 0.007 -10000 0 -10000 0 0
p35/CDK5 -0.014 0.081 -10000 0 -0.36 9 9
RELN -0.037 0.15 -10000 0 -0.66 10 10
PAFAH/LIS1 -0.024 0.026 -10000 0 -10000 0 0
LIS1/CLIP170 0.027 0.011 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.007 0.068 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.009 0.093 -10000 0 -0.32 10 10
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.007 0.12 0.31 16 -0.35 9 25
LIS1/IQGAP1 0.027 0.01 -10000 0 -10000 0 0
RHOA 0.013 0.005 -10000 0 -10000 0 0
PAFAH1B1 0.012 0.004 -10000 0 -10000 0 0
PAFAH1B3 0.026 0.008 -10000 0 -10000 0 0
PAFAH1B2 0.023 0.049 -10000 0 -0.66 1 1
MAP1B/LIS1/Dynein heavy chain 0.025 0.02 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain 0.042 0.14 0.31 32 -0.35 2 34
LRP8 0.024 0.015 -10000 0 -10000 0 0
NDEL1/Katanin 60 0.035 0.14 0.31 32 -0.33 9 41
P39/CDK5 -0.026 0.081 -10000 0 -0.36 9 9
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0.012 -10000 0 -10000 0 0
CDK5 -0.029 0.081 -10000 0 -0.37 9 9
PPP2R5D 0.026 0.006 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.023 0.009 -10000 0 -10000 0 0
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.005 0.095 -10000 0 -0.38 10 10
RELN/VLDLR 0.023 0.098 -10000 0 -0.4 9 9
CDC42 0.012 0.006 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.027 0.003 -10000 0 -10000 0 0
ANTXR2 0.026 0.006 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.001 0 -10000 0 -10000 0 0
monocyte activation -0.014 0.11 -10000 0 -0.33 19 19
MAP2K2 0.005 0.081 -10000 0 -0.56 4 4
MAP2K1 -0.003 0.001 -10000 0 -10000 0 0
MAP2K7 -0.003 0.001 -10000 0 -10000 0 0
MAP2K6 -0.002 0.001 -10000 0 -10000 0 0
CYAA -0.004 0.001 -10000 0 -10000 0 0
MAP2K4 -0.002 0.001 -10000 0 -10000 0 0
IL1B -0.004 0.054 0.18 1 -0.34 4 5
Channel 0.033 0.008 -10000 0 -10000 0 0
NLRP1 -0.003 0.003 -10000 0 -10000 0 0
CALM1 0.026 0.007 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.011 0.093 -10000 0 -0.38 12 12
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.001 0 -10000 0 -10000 0 0
MAPK3 -0.002 0.001 -10000 0 -10000 0 0
MAPK1 -0.002 0.001 -10000 0 -10000 0 0
PGR -0.14 0.18 -10000 0 -0.37 77 77
PA/Cellular Receptors 0.035 0.009 -10000 0 -10000 0 0
apoptosis -0.001 0 -10000 0 -10000 0 0
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.032 0.008 -10000 0 -10000 0 0
macrophage activation -0.004 0.002 -10000 0 -10000 0 0
TNF 0.013 0.072 -10000 0 -0.66 2 2
VCAM1 -0.006 0.09 -10000 0 -0.32 15 15
platelet activation -0.011 0.093 -10000 0 -0.38 12 12
MAPKKK cascade -0.006 0.031 -10000 0 -0.13 9 9
IL18 0.003 0.021 -10000 0 -10000 0 0
negative regulation of macrophage activation -0.001 0 -10000 0 -10000 0 0
LEF -0.001 0 -10000 0 -10000 0 0
CASP1 0.001 0.001 -10000 0 -10000 0 0
mol:cAMP -0.011 0.094 -10000 0 -0.38 12 12
necrosis -0.001 0 -10000 0 -10000 0 0
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.033 0.008 -10000 0 -10000 0 0
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.002 0.087 -10000 0 -0.42 4 4
BAG4 0.027 0.005 -10000 0 -10000 0 0
BAD 0.009 0.045 0.22 4 -0.18 1 5
NFKBIA 0.026 0.007 -10000 0 -10000 0 0
BIRC3 0.02 0.024 -10000 0 -10000 0 0
BAX 0.009 0.045 0.22 4 -0.18 1 5
EnzymeConsortium:3.1.4.12 0.008 0.032 0.14 5 -0.092 4 9
IKBKB 0.007 0.089 0.26 1 -0.4 4 5
MAP2K2 0.015 0.076 0.27 12 -10000 0 12
MAP2K1 0.016 0.076 0.27 12 -10000 0 12
SMPD1 0.009 0.036 0.16 4 -0.18 1 5
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.01 0.086 -10000 0 -0.37 4 4
MAP2K4 0.017 0.074 0.31 9 -10000 0 9
protein ubiquitination 0.013 0.1 0.36 4 -0.41 4 8
EnzymeConsortium:2.7.1.37 0.018 0.088 0.32 12 -10000 0 12
response to UV 0 0.001 0.005 12 -10000 0 12
RAF1 0.018 0.078 0.28 12 -10000 0 12
CRADD 0.027 0.005 -10000 0 -10000 0 0
mol:ceramide 0.011 0.047 0.2 5 -0.19 1 6
I-kappa-B-alpha/RELA/p50/ubiquitin 0.035 0.01 -10000 0 -10000 0 0
MADD 0.027 0.004 -10000 0 -10000 0 0
MAP3K1 0.011 0.052 0.28 4 -10000 0 4
TRADD 0.026 0.007 -10000 0 -10000 0 0
RELA/p50 0.027 0.002 -10000 0 -10000 0 0
MAPK3 0.018 0.074 0.26 12 -10000 0 12
MAPK1 0.011 0.081 0.27 11 -10000 0 11
p50/RELA/I-kappa-B-alpha 0.038 0.01 -10000 0 -10000 0 0
FADD 0.003 0.081 -10000 0 -0.38 4 4
KSR1 0.017 0.069 0.27 10 -0.18 1 11
MAPK8 0.008 0.079 0.3 8 -0.32 2 10
TRAF2 0.026 0.006 -10000 0 -10000 0 0
response to radiation 0 0.001 0.005 5 -10000 0 5
CHUK 0.009 0.093 0.27 3 -0.4 4 7
TNF R/SODD 0.038 0.01 -10000 0 -10000 0 0
TNF 0.013 0.072 -10000 0 -0.66 2 2
CYCS 0.024 0.056 0.21 7 -10000 0 7
IKBKG 0.01 0.094 0.27 3 -0.4 4 7
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.005 0.09 -10000 0 -0.44 4 4
RELA 0.027 0.002 -10000 0 -10000 0 0
RIPK1 0.026 0.006 -10000 0 -10000 0 0
AIFM1 0.012 0.045 0.21 4 -10000 0 4
TNF/TNF R/SODD 0.043 0.051 -10000 0 -0.43 2 2
TNFRSF1A 0.026 0.006 -10000 0 -10000 0 0
response to heat 0 0.001 0.005 5 -10000 0 5
CASP8 0.02 0.085 -10000 0 -0.55 4 4
NSMAF 0.003 0.083 -10000 0 -0.42 3 3
response to hydrogen peroxide 0 0.001 0.005 12 -10000 0 12
BCL2 0.025 0.008 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.007 0.005 -10000 0 -10000 0 0
SNTA1 0.015 0.084 -10000 0 -0.66 3 3
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.009 0.029 -10000 0 -0.41 1 1
MAPK12 0.014 0.058 0.21 13 -0.38 1 14
CCND1 0.016 0.039 -10000 0 -0.34 1 1
p38 gamma/SNTA1 0.022 0.068 -10000 0 -0.36 4 4
MAP2K3 0.025 0.007 -10000 0 -10000 0 0
PKN1 0.027 0.002 -10000 0 -10000 0 0
G2/M transition checkpoint 0.014 0.058 0.21 13 -0.38 1 14
MAP2K6 0.007 0.002 -10000 0 -10000 0 0
MAPT 0.005 0.11 0.28 13 -0.36 10 23
MAPK13 0.01 0.035 -10000 0 -0.48 1 1
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.015 0.002 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.032 0.012 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.026 0.006 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.025 0.007 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.025 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.013 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.025 0.008 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.025 0.007 -10000 0 -10000 0 0
FYN 0.027 0.005 -10000 0 -10000 0 0
MAP3K12 0.026 0.005 -10000 0 -10000 0 0
FGR 0.019 0.052 -10000 0 -0.66 1 1
p38 alpha/TAB1 -0.023 0.068 -10000 0 -0.31 7 7
PRKG1 -0.13 0.28 -10000 0 -0.65 45 45
DUSP8 0.027 0.003 -10000 0 -10000 0 0
PGK/cGMP/p38 alpha -0.041 0.16 -10000 0 -0.32 36 36
apoptosis -0.022 0.065 -10000 0 -0.3 7 7
RAL/GTP 0.03 0.015 -10000 0 -10000 0 0
LYN 0.027 0.004 -10000 0 -10000 0 0
DUSP1 0.023 0.049 -10000 0 -0.66 1 1
PAK1 0.027 0.003 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.052 0.031 -10000 0 -10000 0 0
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.022 0.011 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.022 0.011 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.027 0.017 -10000 0 -10000 0 0
MAPK11 0.051 0.14 0.36 14 -0.39 5 19
BLK 0.016 0.025 -10000 0 -10000 0 0
HCK 0.011 0.057 -10000 0 -0.66 1 1
MAP2K3 0.025 0.007 -10000 0 -10000 0 0
DUSP16 0.026 0.006 -10000 0 -10000 0 0
DUSP10 0.02 0.024 -10000 0 -10000 0 0
TRAF6/MEKK3 0.032 0.01 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.046 0.13 0.35 11 -0.37 5 16
positive regulation of innate immune response 0.059 0.16 0.42 13 -0.39 6 19
LCK 0.023 0.017 -10000 0 -10000 0 0
p38alpha-beta/MKP7 0.051 0.13 0.31 7 -0.41 4 11
p38alpha-beta/MKP5 0.064 0.15 0.41 11 -0.41 4 15
PGK/cGMP -0.097 0.21 -10000 0 -0.49 45 45
PAK2 0.027 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 0.058 0.14 0.39 8 -0.41 4 12
CDC42 0.025 0.007 -10000 0 -10000 0 0
RALB 0.027 0.003 -10000 0 -10000 0 0
RALA 0.022 0.011 -10000 0 -10000 0 0
PAK3 0.018 0.019 -10000 0 -10000 0 0
BCR signaling pathway

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
JUN 0.008 0.12 0.39 2 -0.47 5 7
IKBKB 0.03 0.088 0.29 5 -0.32 1 6
AKT1 0.014 0.099 0.29 15 -0.22 1 16
IKBKG 0.031 0.078 0.31 3 -0.29 1 4
CALM1 -0.004 0.1 0.36 1 -0.43 5 6
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
MAP3K1 0.031 0.12 0.44 3 -0.48 3 6
MAP3K7 0.027 0.004 -10000 0 -10000 0 0
mol:Ca2+ -0.005 0.1 -10000 0 -0.42 6 6
DOK1 0.027 0.008 -10000 0 -10000 0 0
AP-1 -0.013 0.097 0.25 3 -0.27 8 11
LYN 0.027 0.004 -10000 0 -10000 0 0
BLNK -0.004 0.14 -10000 0 -0.66 9 9
SHC1 0.026 0.005 -10000 0 -10000 0 0
BCR complex 0.016 0.071 -10000 0 -0.5 3 3
CD22 -0.002 0.061 -10000 0 -0.42 3 3
CAMK2G -0.006 0.095 0.35 1 -0.43 4 5
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
INPP5D 0.024 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.002 0.088 -10000 0 -0.38 8 8
GO:0007205 -0.005 0.11 -10000 0 -0.43 6 6
SYK 0.022 0.049 -10000 0 -0.66 1 1
ELK1 -0.006 0.1 0.25 1 -0.43 5 6
NFATC1 0 0.089 0.37 3 -0.36 3 6
B-cell antigen/BCR complex 0.016 0.071 -10000 0 -0.5 3 3
PAG1/CSK 0.039 0.008 -10000 0 -10000 0 0
NFKBIB 0.024 0.05 0.16 5 -0.13 9 14
HRAS 0 0.096 0.28 1 -0.44 4 5
NFKBIA 0.025 0.048 0.16 5 -0.12 7 12
NF-kappa-B/RelA/I kappa B beta 0.029 0.043 0.16 5 -10000 0 5
RasGAP/Csk 0.05 0.068 -10000 0 -0.38 3 3
mol:GDP -0.004 0.1 -10000 0 -0.42 6 6
PTEN 0.027 0.003 -10000 0 -10000 0 0
CD79B 0.021 0.05 -10000 0 -0.66 1 1
NF-kappa-B/RelA/I kappa B alpha 0.03 0.043 0.16 5 -10000 0 5
GRB2 0.025 0.007 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.017 0.11 0.46 2 -0.47 3 5
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
mol:IP3 -0.006 0.1 -10000 0 -0.43 6 6
CSK 0.027 0.004 -10000 0 -10000 0 0
FOS -0.05 0.16 0.24 1 -0.42 22 23
CHUK 0.029 0.082 0.31 3 -0.27 2 5
IBTK 0.027 0.004 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.036 0.11 0.31 2 -0.49 2 4
PTPN6 -0.007 0.058 -10000 0 -0.45 2 2
RELA 0.027 0.002 -10000 0 -10000 0 0
BCL2A1 0.019 0.031 0.15 2 -10000 0 2
VAV2 0.007 0.08 -10000 0 -0.5 2 2
ubiquitin-dependent protein catabolic process 0.027 0.049 0.16 5 -0.12 8 13
BTK 0.01 0.092 -10000 0 -0.9 2 2
CD19 -0.003 0.062 -10000 0 -0.43 3 3
MAP4K1 0.015 0.032 -10000 0 -10000 0 0
CD72 0.018 0.028 -10000 0 -10000 0 0
PAG1 0.027 0.004 -10000 0 -10000 0 0
MAPK14 0.031 0.11 0.42 3 -0.41 3 6
SH3BP5 0.005 0.12 -10000 0 -0.66 6 6
PIK3AP1 -0.002 0.1 -10000 0 -0.44 6 6
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.019 0.14 -10000 0 -0.5 11 11
RAF1 0.001 0.091 0.27 1 -0.53 2 3
RasGAP/p62DOK/SHIP 0.047 0.069 -10000 0 -0.36 3 3
CD79A 0.005 0.075 -10000 0 -0.66 2 2
re-entry into mitotic cell cycle -0.013 0.095 0.29 2 -0.26 8 10
RASA1 0.027 0.005 -10000 0 -10000 0 0
MAPK3 0.014 0.098 0.32 6 -0.44 2 8
MAPK1 0.002 0.077 0.24 1 -0.43 2 3
CD72/SHP1 0.015 0.076 0.34 2 -0.52 1 3
NFKB1 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.024 0.12 0.42 3 -0.42 4 7
actin cytoskeleton organization 0.032 0.11 0.4 2 -0.43 2 4
NF-kappa-B/RelA 0.058 0.083 0.29 5 -10000 0 5
Calcineurin 0.025 0.096 0.33 1 -0.4 4 5
PI3K 0.001 0.063 -10000 0 -0.38 2 2
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.002 0.11 0.25 4 -0.43 7 11
SOS1 0.027 0.004 -10000 0 -10000 0 0
Bam32/HPK1 0.01 0.16 -10000 0 -0.65 9 9
DAPP1 -0.009 0.16 -10000 0 -0.72 9 9
cytokine secretion 0.001 0.086 0.36 3 -0.34 3 6
mol:DAG -0.006 0.1 -10000 0 -0.43 6 6
PLCG2 -0.01 0.15 -10000 0 -0.66 10 10
MAP2K1 0.001 0.086 0.25 1 -0.49 2 3
B-cell antigen/BCR complex/FcgammaRIIB 0.027 0.073 -10000 0 -0.43 4 4
mol:PI-3-4-5-P3 -0.016 0.049 -10000 0 -0.31 1 1
ETS1 -0.007 0.088 0.33 1 -0.43 3 4
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.041 0.11 -10000 0 -0.42 9 9
B-cell antigen/BCR complex/LYN 0.009 0.065 -10000 0 -0.44 3 3
MALT1 0.025 0.008 -10000 0 -10000 0 0
TRAF6 0.027 0.003 -10000 0 -10000 0 0
RAC1 0.032 0.1 0.33 1 -0.46 2 3
B-cell antigen/BCR complex/LYN/SYK 0.037 0.076 -10000 0 -0.46 2 2
CARD11 0.02 0.12 0.35 2 -0.48 3 5
FCGR2B -0.005 0.064 -10000 0 -0.66 1 1
PPP3CA 0.026 0.006 -10000 0 -10000 0 0
BCL10 0.026 0.006 -10000 0 -10000 0 0
IKK complex 0.024 0.052 0.18 10 -0.12 1 11
PTPRC 0.021 0.05 -10000 0 -0.66 1 1
PDPK1 -0.014 0.037 0.21 1 -0.21 1 2
PPP3CB 0.027 0.003 -10000 0 -10000 0 0
PPP3CC 0.026 0.005 -10000 0 -10000 0 0
POU2F2 0.022 0.03 0.15 2 -10000 0 2
Visual signal transduction: Rods

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
mol:K + 0.027 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.013 0.008 -10000 0 -10000 0 0
Metarhodopsin II/Arrestin 0.024 0.011 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP 0.016 0.073 -10000 0 -0.43 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 -0.007 0.021 -10000 0 -10000 0 0
GRK1 -0.008 0.019 -10000 0 -10000 0 0
CNG Channel -0.065 0.17 -10000 0 -0.37 44 44
mol:Na + -0.054 0.16 -10000 0 -0.36 36 36
mol:ADP -0.008 0.019 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0.04 0.071 -10000 0 -0.44 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.046 0.17 -10000 0 -0.37 36 36
CNGB1 0.011 0.025 -10000 0 -10000 0 0
RDH5 0.013 0.072 -10000 0 -0.66 2 2
SAG -0.015 0.01 -10000 0 -10000 0 0
mol:Ca2+ -0.074 0.17 0.38 8 -0.4 2 10
Na + (4 Units) -0.056 0.15 -10000 0 -0.36 9 9
RGS9 0.012 0.085 -10000 0 -0.66 3 3
GNB1/GNGT1 0.02 0.026 -10000 0 -10000 0 0
GNAT1/GDP 0.043 0.065 -10000 0 -0.38 4 4
GUCY2D 0.009 0.03 -10000 0 -10000 0 0
GNGT1 0.001 0.03 -10000 0 -10000 0 0
GUCY2F -0.014 0.012 -10000 0 -10000 0 0
GNB5 0.027 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.001 0.071 -10000 0 -0.38 6 6
mol:11-cis-retinal 0.013 0.072 -10000 0 -0.66 2 2
mol:cGMP 0.033 0.031 -10000 0 -10000 0 0
GNB1 0.025 0.008 -10000 0 -10000 0 0
Rhodopsin 0.022 0.058 -10000 0 -0.5 2 2
SLC24A1 0.027 0.003 -10000 0 -10000 0 0
CNGA1 -0.14 0.29 -10000 0 -0.64 50 50
Metarhodopsin II 0.024 0.011 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.051 0.026 -10000 0 -10000 0 0
RGS9BP 0.022 0.05 -10000 0 -0.66 1 1
Metarhodopsin II/Transducin 0.006 0.018 -10000 0 -10000 0 0
GCAP Family/Ca ++ 0.041 0.016 -10000 0 -10000 0 0
PDE6A/B 0.029 0.047 -10000 0 -0.37 2 2
mol:Pi 0.039 0.07 -10000 0 -0.44 4 4
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.027 0.027 -10000 0 -10000 0 0
PDE6B 0.02 0.056 -10000 0 -0.5 2 2
PDE6A 0.013 0.024 -10000 0 -10000 0 0
PDE6G 0.007 0.11 -10000 0 -0.66 5 5
RHO 0.002 0.024 -10000 0 -10000 0 0
PDE6 0.045 0.1 -10000 0 -0.37 10 10
GUCA1A -0.002 0.024 -10000 0 -10000 0 0
GC2/GCAP Family 0.051 0.021 -10000 0 -10000 0 0
GUCA1C 0.008 0.023 -10000 0 -10000 0 0
GUCA1B 0.026 0.007 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.02 0.025 -10000 0 -10000 0 0
mol:Halofuginone 0.003 0.001 -10000 0 -10000 0 0
ITGA1 0.02 0.069 -10000 0 -0.66 2 2
CDKN1A -0.017 0.12 -10000 0 -0.41 14 14
PRL-3/alpha Tubulin 0.039 0.009 -10000 0 -10000 0 0
mol:Ca2+ -0.041 0.1 -10000 0 -0.51 9 9
AGT -0.005 0.14 -10000 0 -0.66 9 9
CCNA2 -0.032 0.093 -10000 0 -0.36 14 14
TUBA1B 0.026 0.005 -10000 0 -10000 0 0
EGR1 -0.026 0.14 -10000 0 -0.49 16 16
CDK2/Cyclin E1 0.005 0.14 -10000 0 -0.53 6 6
MAPK3 0.012 0.004 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0.038 0.011 -10000 0 -10000 0 0
MAPK1 0.012 0.004 -10000 0 -10000 0 0
PTP4A1 -0.023 0.099 -10000 0 -0.38 14 14
PTP4A3 0.027 0.004 -10000 0 -10000 0 0
PTP4A2 0.025 0.007 -10000 0 -10000 0 0
ITGB1 0.013 0.003 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
RAC1 0.007 0.041 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0.037 0.012 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.001 0.11 -10000 0 -0.36 14 14
RABGGTA 0.025 0.007 -10000 0 -10000 0 0
BCAR1 -0.019 0.005 -10000 0 -10000 0 0
RHOC -0.001 0.085 -10000 0 -0.41 6 6
RHOA 0.002 0.074 -10000 0 -0.36 5 5
cell motility 0.002 0.1 0.29 3 -0.35 8 11
PRL-1/alpha Tubulin -0.001 0.1 -10000 0 -0.36 14 14
PRL-3/alpha1 Integrin 0.034 0.054 -10000 0 -0.5 2 2
ROCK1 0.001 0.09 0.28 1 -0.37 6 7
RABGGTB 0.026 0.006 -10000 0 -10000 0 0
CDK2 0.026 0.005 -10000 0 -10000 0 0
mitosis -0.025 0.1 -10000 0 -0.38 14 14
ATF5 0.027 0.004 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.007 0.18 -10000 0 -0.56 11 11
MAP3K8 0.024 0.011 -10000 0 -10000 0 0
FOS 0.005 0.13 0.27 2 -0.45 9 11
PRKCA 0.02 0.018 -10000 0 -10000 0 0
PTPN7 0.015 0.054 -10000 0 -0.67 1 1
HRAS 0.026 0.007 -10000 0 -10000 0 0
PRKCB 0.018 0.021 -10000 0 -10000 0 0
NRAS 0.025 0.009 -10000 0 -10000 0 0
RAS family/GTP 0.041 0.027 -10000 0 -10000 0 0
MAPK3 0.017 0.096 -10000 0 -0.44 7 7
MAP2K1 0.029 0.046 -10000 0 -10000 0 0
ELK1 0.018 0.024 -10000 0 -10000 0 0
BRAF 0.012 0.018 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 30 30
MAPK1 -0.01 0.15 -10000 0 -0.48 12 12
RAF1 0.015 0.018 -10000 0 -10000 0 0
KRAS 0.026 0.006 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0.024 0.017 -10000 0 -10000 0 0
EPHB2 0.023 0.015 -10000 0 -10000 0 0
Syndecan-2/TACI 0.022 0.016 -10000 0 -10000 0 0
LAMA1 0.004 0.099 -10000 0 -0.66 4 4
Syndecan-2/alpha2 ITGB1 0.049 0.02 -10000 0 -10000 0 0
HRAS 0.027 0.003 -10000 0 -10000 0 0
Syndecan-2/CASK 0.009 0.002 -10000 0 -10000 0 0
ITGA5 0.026 0.005 -10000 0 -10000 0 0
BAX 0 0.048 -10000 0 -10000 0 0
EPB41 0.025 0.007 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.026 0.005 -10000 0 -10000 0 0
LAMA3 -0.001 0.042 -10000 0 -10000 0 0
EZR 0.026 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 0.021 0.013 -10000 0 -10000 0 0
Syndecan-2/MMP2 0.027 0.01 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.038 0.009 -10000 0 -10000 0 0
dendrite morphogenesis 0.025 0.013 -10000 0 -10000 0 0
Syndecan-2/GM-CSF 0.023 0.01 -10000 0 -10000 0 0
determination of left/right symmetry 0.012 0.003 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0.028 0.008 -10000 0 -10000 0 0
GNB2L1 0.026 0.005 -10000 0 -10000 0 0
MAPK3 0.011 0.015 -10000 0 -10000 0 0
MAPK1 0.012 0.019 -10000 0 -10000 0 0
Syndecan-2/RACK1 0.041 0.01 -10000 0 -10000 0 0
NF1 0.026 0.006 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.012 0.003 -10000 0 -10000 0 0
ITGA2 0.027 0.004 -10000 0 -10000 0 0
MAPK8 0.004 0.055 -10000 0 -0.42 3 3
Syndecan-2/alpha2/beta1 Integrin 0.044 0.059 -10000 0 -0.37 3 3
Syndecan-2/Kininogen -0.24 0.22 -10000 0 -0.42 117 117
ITGB1 0.027 0.005 -10000 0 -10000 0 0
SRC 0.018 0.02 -10000 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0.025 0.008 -10000 0 -10000 0 0
extracellular matrix organization 0.028 0.009 -10000 0 -10000 0 0
actin cytoskeleton reorganization 0.024 0.017 -10000 0 -10000 0 0
Syndecan-2/Caveolin-2/Ras 0.035 0.019 -10000 0 -10000 0 0
Syndecan-2/Laminin alpha3 0.01 0.027 -10000 0 -10000 0 0
Syndecan-2/RasGAP 0.053 0.014 -10000 0 -10000 0 0
alpha5/beta1 Integrin 0.038 0.01 -10000 0 -10000 0 0
PRKCD 0.026 0.005 -10000 0 -10000 0 0
Syndecan-2 dimer 0.025 0.013 -10000 0 -10000 0 0
GO:0007205 0.002 0.001 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.037 0.015 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
SDCBP 0.027 0.004 -10000 0 -10000 0 0
TNFRSF13B 0.006 0.027 -10000 0 -10000 0 0
RASA1 0.027 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.038 0.009 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0.028 0.008 -10000 0 -10000 0 0
TGFB1 0.026 0.01 -10000 0 -10000 0 0
CASP3 0.015 0.014 0.19 1 -10000 0 1
FN1 0.02 0.025 -10000 0 -10000 0 0
Syndecan-2/IL8 0.012 0.041 -10000 0 -0.42 1 1
SDC2 0.012 0.003 -10000 0 -10000 0 0
KNG1 -0.4 0.31 -10000 0 -0.66 118 118
Syndecan-2/Neurofibromin 0.028 0.008 -10000 0 -10000 0 0
TRAPPC4 0.026 0.005 -10000 0 -10000 0 0
CSF2 0.001 0.024 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.028 0.009 -10000 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0.026 0.005 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0.042 0.013 -10000 0 -10000 0 0
PRKACA 0.016 0.013 -10000 0 -10000 0 0
angiogenesis 0.012 0.041 -10000 0 -0.42 1 1
MMP2 0.025 0.012 -10000 0 -10000 0 0
IL8 0 0.062 -10000 0 -0.66 1 1
calcineurin-NFAT signaling pathway 0.021 0.015 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.027 0.004 -10000 0 -10000 0 0
LAT2 -0.008 0.053 -10000 0 -0.34 1 1
AP1 -0.007 0.15 -10000 0 -0.49 9 9
mol:PIP3 0.048 0.15 0.52 10 -0.45 2 12
IKBKB 0.044 0.13 0.42 12 -0.26 1 13
AKT1 -0.016 0.083 0.33 5 -0.34 1 6
IKBKG 0.043 0.12 0.39 12 -0.26 1 13
MS4A2 -0.005 0.058 -10000 0 -0.52 1 1
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
MAP3K1 0.013 0.093 0.34 6 -0.38 2 8
mol:Ca2+ 0.046 0.13 0.48 10 -0.34 2 12
LYN 0.027 0.008 -10000 0 -10000 0 0
CBLB -0.004 0.054 -10000 0 -0.34 1 1
SHC1 0.026 0.005 -10000 0 -10000 0 0
RasGAP/p62DOK 0.049 0.022 -10000 0 -10000 0 0
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.023 0.017 -10000 0 -10000 0 0
PLD2 -0.022 0.066 0.34 2 -0.37 4 6
PTPN13 0.023 0.097 0.41 1 -0.91 1 2
PTPN11 0.025 0.012 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.022 0.11 0.41 10 -0.39 1 11
SYK 0.023 0.05 -10000 0 -0.67 1 1
GRB2 0.026 0.007 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs 0.011 0.079 -10000 0 -0.47 2 2
LAT -0.006 0.053 -10000 0 -0.34 1 1
PAK2 0.011 0.095 0.33 6 -0.42 2 8
NFATC2 -0.038 0.15 -10000 0 -0.57 14 14
HRAS 0.008 0.089 0.28 6 -0.41 3 9
GAB2 0.027 0.003 -10000 0 -10000 0 0
PLA2G1B -0.004 0.14 -10000 0 -0.84 5 5
Fc epsilon R1 0.004 0.082 -10000 0 -0.45 4 4
Antigen/IgE/Fc epsilon R1 0.014 0.075 -10000 0 -0.41 4 4
mol:GDP 0.001 0.082 -10000 0 -0.46 3 3
JUN 0.026 0.007 -10000 0 -10000 0 0
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
FOS -0.07 0.23 -10000 0 -0.61 30 30
Antigen/IgE/Fc epsilon R1/LYN/SYK 0.002 0.059 -10000 0 -0.3 2 2
CHUK 0.042 0.12 0.39 12 -0.26 1 13
KLRG1 -0.005 0.05 -10000 0 -0.27 2 2
VAV1 -0.011 0.067 -10000 0 -0.45 2 2
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.004 0.054 -10000 0 -0.34 1 1
negative regulation of mast cell degranulation 0.012 0.06 0.22 1 -0.29 1 2
BTK 0.006 0.077 -10000 0 -0.5 2 2
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK 0 0.073 -10000 0 -0.41 4 4
GAB2/PI3K/SHP2 -0.02 0.057 -10000 0 -0.35 4 4
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP 0.007 0.045 -10000 0 -0.25 3 3
RAF1 0 0.15 -10000 0 -0.9 5 5
Fc epsilon R1/FcgammaRIIB/SHIP 0.026 0.098 -10000 0 -0.47 4 4
FCER1G 0.003 0.042 -10000 0 -10000 0 0
FCER1A 0.012 0.099 -10000 0 -0.67 4 4
Antigen/IgE/Fc epsilon R1/Fyn 0.036 0.072 -10000 0 -0.38 4 4
MAPK3 -0.001 0.13 -10000 0 -0.82 5 5
MAPK1 -0.011 0.15 -10000 0 -0.89 5 5
NFKB1 0.026 0.006 -10000 0 -10000 0 0
MAPK8 0.009 0.15 -10000 0 -0.68 7 7
DUSP1 0.023 0.049 -10000 0 -0.66 1 1
NF-kappa-B/RelA 0.024 0.046 0.14 4 -10000 0 4
actin cytoskeleton reorganization 0.025 0.099 -10000 0 -0.96 1 1
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K 0.016 0.08 -10000 0 -0.44 2 2
FER -0.004 0.054 -10000 0 -0.34 1 1
RELA 0.027 0.002 -10000 0 -10000 0 0
ITK 0.004 0.03 -10000 0 -0.21 3 3
SOS1 0.027 0.004 -10000 0 -10000 0 0
PLCG1 0.017 0.1 0.34 6 -0.45 3 9
cytokine secretion 0.01 0.028 -10000 0 -10000 0 0
SPHK1 -0.017 0.055 -10000 0 -0.34 1 1
PTK2 0.024 0.1 -10000 0 -1 1 1
NTAL/PLCgamma1/GRB2/SLP76/GADs 0.007 0.077 -10000 0 -0.47 2 2
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG 0.041 0.14 0.47 10 -0.43 2 12
MAP2K2 -0.004 0.14 -10000 0 -0.83 5 5
MAP2K1 -0.004 0.14 -10000 0 -0.84 5 5
MAP2K7 0.027 0.003 -10000 0 -10000 0 0
KLRG1/SHP2 0.008 0.053 -10000 0 -0.26 1 1
MAP2K4 0.002 0.17 -10000 0 -0.82 8 8
Fc epsilon R1/FcgammaRIIB 0.017 0.098 -10000 0 -0.5 4 4
mol:Choline -0.022 0.066 0.34 2 -0.36 4 6
SHC/Grb2/SOS1 0.043 0.067 -10000 0 -0.31 1 1
FYN 0.027 0.005 -10000 0 -10000 0 0
DOK1 0.027 0.008 -10000 0 -10000 0 0
PXN 0.03 0.11 0.38 6 -0.92 1 7
HCLS1 -0.005 0.055 -10000 0 -0.34 1 1
PRKCB 0.048 0.14 0.44 12 -0.33 2 14
FCGR2B -0.005 0.064 -10000 0 -0.66 1 1
IGHE 0 0.006 -10000 0 -10000 0 0
KLRG1/SHIP 0.012 0.061 0.22 1 -0.29 1 2
LCP2 0.025 0.015 -10000 0 -10000 0 0
PLA2G4A -0.007 0.064 -10000 0 -0.34 4 4
RASA1 0.027 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.022 0.066 0.34 2 -0.36 4 6
IKK complex 0.04 0.12 0.41 11 -10000 0 11
WIPF1 0.027 0.004 -10000 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.004 0.032 0.14 5 -0.13 4 9
BUB1B 0.009 0.036 0.15 3 -0.18 1 4
PLK1 0.01 0.03 0.12 9 -10000 0 9
PLK1S1 0.015 0.027 0.13 8 -10000 0 8
KIF2A 0.009 0.04 0.33 2 -10000 0 2
regulation of mitotic centrosome separation 0.01 0.03 0.12 9 -10000 0 9
GOLGA2 0.026 0.006 -10000 0 -10000 0 0
Hec1/SPC24 0.03 0.039 -10000 0 -10000 0 0
WEE1 0.016 0.058 0.18 1 -0.33 4 5
cytokinesis 0.006 0.06 0.23 4 -0.22 1 5
PP2A-alpha B56 0.053 0.057 -10000 0 -0.49 2 2
AURKA 0.013 0.021 0.12 2 -10000 0 2
PICH/PLK1 0.01 0.025 -10000 0 -10000 0 0
CENPE 0.007 0.035 0.23 2 -10000 0 2
RhoA/GTP 0.02 0.004 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.009 0.04 0.33 2 -10000 0 2
PPP2CA 0.026 0.005 -10000 0 -10000 0 0
FZR1 0.027 0.004 -10000 0 -10000 0 0
TPX2 0.012 0.028 0.12 9 -10000 0 9
PAK1 0.027 0.003 -10000 0 -10000 0 0
SPC24 0.009 0.036 -10000 0 -10000 0 0
FBXW11 0.026 0.005 -10000 0 -10000 0 0
CLSPN -0.004 0.065 -10000 0 -0.24 13 13
GORASP1 0.026 0.006 -10000 0 -10000 0 0
metaphase 0.002 0.005 0.018 19 -10000 0 19
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.005 0.017 0.067 9 -10000 0 9
G2 phase of mitotic cell cycle 0 0.003 0.012 6 -10000 0 6
STAG2 0.027 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.01 0.086 -10000 0 -0.52 5 5
spindle elongation 0.01 0.03 0.12 9 -10000 0 9
ODF2 0.026 0.006 -10000 0 -10000 0 0
BUB1 0.022 0.057 -10000 0 -0.53 2 2
TPT1 0.006 0.041 -10000 0 -0.21 6 6
CDC25C 0.008 0.044 0.14 1 -0.3 3 4
CDC25B 0.026 0.011 -10000 0 -10000 0 0
SGOL1 0.004 0.032 0.14 4 -0.14 5 9
RHOA 0.026 0.005 -10000 0 -10000 0 0
CCNB1/CDK1 0.037 0.028 -10000 0 -10000 0 0
CDC14B 0.006 0.003 -10000 0 -10000 0 0
CDC20 0.015 0.03 -10000 0 -10000 0 0
PLK1/PBIP1 0.008 0.026 0.12 2 -10000 0 2
mitosis -0.002 0.002 -10000 0 -10000 0 0
FBXO5 0.007 0.029 0.13 4 -10000 0 4
CDC2 0.001 0.002 -10000 0 -10000 0 0
NDC80 0.015 0.029 -10000 0 -10000 0 0
metaphase plate congression -0.004 0.073 -10000 0 -0.24 16 16
ERCC6L 0.014 0.03 -10000 0 -10000 0 0
NLP/gamma Tubulin 0.01 0.024 0.094 10 -10000 0 10
microtubule cytoskeleton organization 0.006 0.041 -10000 0 -0.2 6 6
G2/M transition DNA damage checkpoint 0 0.002 0.013 2 -10000 0 2
PPP1R12A 0.027 0.006 -10000 0 -10000 0 0
interphase 0 0.002 0.013 2 -10000 0 2
PLK1/PRC1-2 0.026 0.039 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 0.048 0.026 -10000 0 -10000 0 0
RAB1A 0.027 0.003 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.008 0.026 0.1 11 -10000 0 11
mitotic prometaphase 0.001 0.005 0.017 16 -10000 0 16
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.024 -10000 0 -10000 0 0
microtubule-based process 0.01 0.035 0.15 1 -10000 0 1
Golgi organization 0.01 0.03 0.12 9 -10000 0 9
Cohesin/SA2 0.026 0.023 0.13 2 -10000 0 2
PPP1CB/MYPT1 0.039 0.01 -10000 0 -10000 0 0
KIF20A -0.005 0.045 -10000 0 -10000 0 0
APC/C/CDC20 0.023 0.029 0.15 1 -10000 0 1
PPP2R1A 0.027 0.004 -10000 0 -10000 0 0
chromosome segregation 0.007 0.025 0.12 2 -10000 0 2
PRC1 0.023 0.019 -10000 0 -10000 0 0
ECT2 0.013 0.054 0.28 6 -10000 0 6
C13orf34 0.008 0.025 0.098 9 -10000 0 9
NUDC -0.004 0.073 -10000 0 -0.24 16 16
regulation of attachment of spindle microtubules to kinetochore 0.009 0.036 0.15 3 -0.17 1 4
spindle assembly 0.012 0.036 0.13 11 -10000 0 11
spindle stabilization 0.015 0.027 0.12 8 -10000 0 8
APC/C/HCDH1 0.024 0.006 -10000 0 -10000 0 0
MKLP2/PLK1 0.01 0.035 0.15 1 -10000 0 1
CCNB1 0.026 0.014 -10000 0 -10000 0 0
PPP1CB 0.027 0.005 -10000 0 -10000 0 0
BTRC 0.027 0.003 -10000 0 -10000 0 0
ROCK2 0.007 0.078 0.28 1 -0.34 7 8
TUBG1 0.013 0.023 0.14 4 -10000 0 4
G2/M transition of mitotic cell cycle 0.006 0.022 -10000 0 -10000 0 0
MLF1IP 0.002 0.016 -10000 0 -10000 0 0
INCENP 0.027 0.002 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration -0.014 0.09 0.28 11 -10000 0 11
GNAI2 0.026 0.006 -10000 0 -10000 0 0
S1P/S1P5/G12 0.024 0.049 -10000 0 -0.43 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.007 0.14 -10000 0 -0.66 9 9
RhoA/GTP 0.014 0.092 -10000 0 -0.29 11 11
negative regulation of cAMP metabolic process 0.007 0.093 -10000 0 -0.32 11 11
GNAZ 0.025 0.008 -10000 0 -10000 0 0
GNAI3 0.026 0.005 -10000 0 -10000 0 0
GNA12 0.022 0.011 -10000 0 -10000 0 0
S1PR5 0.018 0.07 -10000 0 -0.66 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.007 0.094 -10000 0 -0.32 11 11
RhoA/GDP 0.02 0.004 -10000 0 -10000 0 0
RHOA 0.026 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.05 -10000 0 -0.66 1 1
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.027 0.005 -10000 0 -10000 0 0
EPHB2 0.023 0.016 -10000 0 -10000 0 0
EFNB1 -0.003 0.027 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.035 0.057 -10000 0 -0.37 2 2
Ephrin B2/EPHB1-2 0.038 0.057 -10000 0 -0.39 3 3
neuron projection morphogenesis 0.016 0.051 -10000 0 -0.35 2 2
Ephrin B1/EPHB1-2/Tiam1 0.035 0.06 -10000 0 -0.39 3 3
DNM1 0 0.043 -10000 0 -10000 0 0
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.002 0.082 -10000 0 -0.38 7 7
YES1 -0.011 0.13 -10000 0 -0.62 8 8
Ephrin B1/EPHB1-2/NCK2 0.039 0.06 -10000 0 -0.39 3 3
PI3K 0.026 0.087 -10000 0 -0.39 8 8
mol:GDP 0.034 0.059 -10000 0 -0.39 3 3
ITGA2B 0.019 0.024 -10000 0 -10000 0 0
endothelial cell proliferation 0.029 0.015 -10000 0 -10000 0 0
FYN -0.008 0.13 -10000 0 -0.62 8 8
MAP3K7 -0.007 0.072 -10000 0 -0.41 6 6
FGR -0.008 0.13 -10000 0 -0.62 8 8
TIAM1 0.025 0.007 -10000 0 -10000 0 0
PIK3R1 0.027 0.004 -10000 0 -10000 0 0
RGS3 0.026 0.006 -10000 0 -10000 0 0
cell adhesion 0.003 0.099 -10000 0 -0.38 11 11
LYN -0.007 0.12 -10000 0 -0.61 8 8
Ephrin B1/EPHB1-2/Src Family Kinases -0.011 0.11 -10000 0 -0.56 8 8
Ephrin B1/EPHB1-2 -0.007 0.084 -10000 0 -0.45 7 7
SRC -0.006 0.12 -10000 0 -0.6 8 8
ITGB3 0.006 0.11 -10000 0 -0.66 5 5
EPHB1 0.013 0.085 -10000 0 -0.66 3 3
EPHB4 0.022 0.011 -10000 0 -10000 0 0
RAC1 0.022 0.011 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.029 0.016 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.017 0.087 -10000 0 -0.5 5 5
BLK -0.006 0.12 -10000 0 -0.6 8 8
HCK -0.007 0.12 -10000 0 -0.6 8 8
regulation of stress fiber formation -0.038 0.059 0.39 3 -10000 0 3
MAPK8 -0.008 0.099 0.3 1 -0.4 8 9
Ephrin B1/EPHB1-2/RGS3 0.039 0.06 -10000 0 -0.39 3 3
endothelial cell migration 0.022 0.096 -10000 0 -0.32 7 7
NCK2 0.027 0.003 -10000 0 -10000 0 0
PTPN13 0.027 0.008 -10000 0 -10000 0 0
regulation of focal adhesion formation -0.038 0.059 0.39 3 -10000 0 3
chemotaxis -0.038 0.059 0.39 3 -10000 0 3
PIK3CA 0.027 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.028 0.053 -10000 0 -0.36 2 2
angiogenesis -0.009 0.089 -10000 0 -0.44 8 8
LCK -0.007 0.13 -10000 0 -0.62 8 8
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.022 0.006 -10000 0 -10000 0 0
AES 0.024 0.003 -10000 0 -10000 0 0
FBXW11 0.026 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.032 0.018 -10000 0 -10000 0 0
SMAD4 0.025 0.008 -10000 0 -10000 0 0
DKK2 0.02 0.05 -10000 0 -0.66 1 1
TLE1 0.023 0.006 -10000 0 -10000 0 0
MACF1 0.026 0.007 -10000 0 -10000 0 0
CTNNB1 0.064 0.11 0.47 6 -0.35 1 7
WIF1 0.01 0.024 -10000 0 -10000 0 0
beta catenin/RanBP3 0.002 0.049 -10000 0 -10000 0 0
KREMEN2 0.013 0.029 -10000 0 -10000 0 0
DKK1 0.013 0.028 -10000 0 -10000 0 0
beta catenin/beta TrCP1 0.07 0.098 0.45 4 -10000 0 4
FZD1 0.022 0.013 -10000 0 -10000 0 0
AXIN2 0.049 0.15 0.62 9 -10000 0 9
AXIN1 0.025 0.009 -10000 0 -10000 0 0
RAN 0.026 0.005 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.023 0.071 -10000 0 -0.57 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.002 0.16 0.3 1 -0.59 8 9
Axin1/APC/GSK3 0.044 0.079 0.3 2 -0.42 1 3
Axin1/APC/GSK3/beta catenin/Macf1 0.048 0.083 0.41 2 -10000 0 2
HNF1A 0.013 0.084 -10000 0 -0.66 3 3
CTBP1 0.023 0.005 -10000 0 -10000 0 0
MYC 0.015 0.062 0.6 1 -10000 0 1
RANBP3 0.027 0.004 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.04 0.042 -10000 0 -0.43 1 1
NKD1 -0.14 0.29 -10000 0 -0.66 47 47
TCF4 0.022 0.007 -10000 0 -10000 0 0
TCF3 0.024 0.003 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.049 0.032 -10000 0 -10000 0 0
Ran/GTP 0.019 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES -0.033 0.097 -10000 0 -0.41 6 6
LEF1 -0.029 0.18 -10000 0 -0.66 15 15
DVL1 0.019 0.053 -10000 0 -0.56 1 1
CSNK2A1 0.026 0.006 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.035 0.11 0.37 1 -0.45 4 5
DKK1/LRP6/Kremen 2 0.041 0.027 -10000 0 -10000 0 0
LRP6 0.027 0.006 -10000 0 -10000 0 0
CSNK1A1 0.024 0.005 -10000 0 -10000 0 0
NLK 0.027 0.006 -10000 0 -10000 0 0
CCND1 0.013 0.071 0.9 1 -10000 0 1
WNT1 0.012 0.033 -10000 0 -10000 0 0
GSK3A 0.028 0.005 -10000 0 -10000 0 0
GSK3B 0.027 0.006 -10000 0 -10000 0 0
FRAT1 0.027 0.003 -10000 0 -10000 0 0
PPP2R5D 0.069 0.15 0.32 45 -0.27 9 54
APC 0.062 0.12 0.55 7 -10000 0 7
WNT1/LRP6/FZD1 0.016 0.027 -10000 0 -10000 0 0
CREBBP 0.022 0.008 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD 0 0.085 -9999 0 -0.3 13 13
FZD6 0.027 0.004 -9999 0 -10000 0 0
WNT6 0.018 0.051 -9999 0 -0.66 1 1
WNT4 0.01 0.097 -9999 0 -0.66 4 4
FZD3 0.026 0.005 -9999 0 -10000 0 0
WNT5A 0.012 0.034 -9999 0 -10000 0 0
WNT11 -0.007 0.14 -9999 0 -0.66 9 9
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.046 0.044 -10000 0 -0.49 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.011 0.091 0.3 2 -10000 0 2
AP1 -0.015 0.14 -10000 0 -0.36 25 25
mol:PIP3 0.011 0.014 -10000 0 -10000 0 0
AKT1 0.037 0.063 0.33 3 -10000 0 3
PTK2B 0.005 0.053 -10000 0 -0.39 1 1
RHOA 0.023 0.054 0.19 2 -0.25 3 5
PIK3CB 0.026 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.011 0.081 0.32 1 -0.34 1 2
MAGI3 0.026 0.005 -10000 0 -10000 0 0
RELA 0.027 0.002 -10000 0 -10000 0 0
apoptosis 0.014 0.035 -10000 0 -0.45 1 1
HRAS/GDP 0.02 0.002 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.003 0.11 0.28 7 -0.38 9 16
NF kappa B1 p50/RelA 0.004 0.068 -10000 0 -10000 0 0
endothelial cell migration 0.016 0.03 -10000 0 -0.38 1 1
ADCY4 0.003 0.089 -10000 0 -0.33 4 4
ADCY5 0.003 0.097 -10000 0 -0.45 4 4
ADCY6 0.014 0.069 -10000 0 -0.29 1 1
ADCY7 0.013 0.069 -10000 0 -0.29 1 1
ADCY1 -0.079 0.14 -10000 0 -0.51 10 10
ADCY2 0.01 0.07 -10000 0 -0.28 2 2
ADCY3 0.014 0.074 -10000 0 -0.44 1 1
ADCY8 0.015 0.069 -10000 0 -0.27 2 2
ADCY9 0.013 0.068 -10000 0 -0.27 2 2
GSK3B 0.007 0.06 0.23 5 -0.37 1 6
arachidonic acid secretion 0.007 0.081 -10000 0 -0.28 10 10
GNG2 0.026 0.007 -10000 0 -10000 0 0
TRIP6 0.018 0.01 -10000 0 -10000 0 0
GNAO1 -0.005 0.096 -10000 0 -0.42 10 10
HRAS 0.027 0.003 -10000 0 -10000 0 0
NFKBIA -0.01 0.09 0.31 2 -0.35 1 3
GAB1 0.026 0.006 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.018 0.21 -10000 0 -0.75 14 14
JUN 0.026 0.007 -10000 0 -10000 0 0
LPA/LPA2/NHERF2 0.035 0.013 -10000 0 -10000 0 0
TIAM1 -0.037 0.24 -10000 0 -0.91 14 14
PIK3R1 0.026 0.004 -10000 0 -10000 0 0
mol:IP3 -0.008 0.078 0.32 1 -0.35 1 2
PLCB3 0.032 0.048 -10000 0 -10000 0 0
FOS -0.07 0.23 -10000 0 -0.61 30 30
positive regulation of mitosis 0.007 0.081 -10000 0 -0.28 10 10
LPA/LPA1-2-3 0.047 0.041 -10000 0 -0.48 1 1
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.026 0.007 -10000 0 -10000 0 0
stress fiber formation 0.015 0.048 -10000 0 -0.45 1 1
GNAZ 0.015 0.039 -10000 0 -0.52 1 1
EGFR/PI3K-beta/Gab1 0.021 0.019 -10000 0 -10000 0 0
positive regulation of dendritic cell cytokine production 0.045 0.041 -10000 0 -0.48 1 1
LPA/LPA2/MAGI-3 0.037 0.017 -10000 0 -10000 0 0
ARHGEF1 0.056 0.079 0.36 3 -10000 0 3
GNAI2 0.017 0.026 -10000 0 -0.33 1 1
GNAI3 0.016 0.039 -10000 0 -0.52 1 1
GNAI1 0.012 0.041 -10000 0 -0.38 2 2
LPA/LPA3 0.015 0.018 -10000 0 -0.21 1 1
LPA/LPA2 0.021 0.016 -10000 0 -0.2 1 1
LPA/LPA1 0.022 0.045 -10000 0 -0.59 1 1
HB-EGF/EGFR -0.008 0.069 -10000 0 -0.44 4 4
HBEGF -0.02 0.078 -10000 0 -0.46 5 5
mol:DAG -0.008 0.078 0.32 1 -0.35 1 2
cAMP biosynthetic process -0.002 0.12 0.37 4 -0.37 9 13
NFKB1 0.026 0.006 -10000 0 -10000 0 0
SRC 0.026 0.006 -10000 0 -10000 0 0
GNB1 0.024 0.008 -10000 0 -10000 0 0
LYN -0.002 0.083 0.3 3 -0.35 1 4
GNAQ 0.014 0.014 -10000 0 -10000 0 0
LPAR2 0.027 0.003 -10000 0 -10000 0 0
LPAR3 -0.003 0.023 -10000 0 -10000 0 0
LPAR1 0.027 0.025 -10000 0 -0.3 1 1
IL8 -0.021 0.11 0.43 1 -0.41 7 8
PTK2 0.013 0.026 -10000 0 -0.28 1 1
Rac1/GDP 0.016 0.008 -10000 0 -10000 0 0
CASP3 0.014 0.035 -10000 0 -0.45 1 1
EGFR 0.022 0.011 -10000 0 -10000 0 0
PLCG1 -0.017 0.062 -10000 0 -0.23 3 3
PLD2 0.013 0.026 -10000 0 -0.28 1 1
G12/G13 0.042 0.028 -10000 0 -10000 0 0
PI3K-beta 0.014 0.033 -10000 0 -10000 0 0
cell migration 0.011 0.067 -10000 0 -0.24 10 10
SLC9A3R2 0.025 0.008 -10000 0 -10000 0 0
PXN 0.015 0.049 -10000 0 -0.46 1 1
HRAS/GTP 0.008 0.079 -10000 0 -0.29 9 9
RAC1 0.022 0.011 -10000 0 -10000 0 0
MMP9 -0.015 0.08 -10000 0 -0.66 2 2
PRKCE 0.027 0.004 -10000 0 -10000 0 0
PRKCD -0.011 0.085 0.31 3 -0.32 1 4
Gi(beta/gamma) 0.014 0.078 -10000 0 -0.4 3 3
mol:LPA 0.001 0.021 -10000 0 -0.29 1 1
TRIP6/p130 Cas/FAK1/Paxillin 0.038 0.049 -10000 0 -0.39 1 1
MAPKKK cascade 0.007 0.081 -10000 0 -0.28 10 10
contractile ring contraction involved in cytokinesis 0.022 0.061 -10000 0 -0.28 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.063 0.15 -10000 0 -0.35 41 41
GNA15 0.012 0.017 -10000 0 -10000 0 0
GNA12 0.022 0.011 -10000 0 -10000 0 0
GNA13 0.025 0.007 -10000 0 -10000 0 0
MAPT 0.002 0.11 0.28 7 -0.39 9 16
GNA11 0.008 0.047 -10000 0 -0.35 3 3
Rac1/GTP -0.019 0.22 -10000 0 -0.79 14 14
MMP2 0.016 0.03 -10000 0 -0.38 1 1
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.021 0.05 -10000 0 -0.66 1 1
CLTC 0.01 0.098 -10000 0 -0.37 11 11
calcium ion-dependent exocytosis 0.02 0.05 -10000 0 -0.26 2 2
Dynamin 2/GTP 0.024 0.011 -10000 0 -10000 0 0
EXOC4 0.022 0.011 -10000 0 -10000 0 0
CD59 0.007 0.079 -10000 0 -0.3 11 11
CPE 0.013 0.007 -10000 0 -10000 0 0
CTNNB1 0.026 0.005 -10000 0 -10000 0 0
membrane fusion 0.025 0.038 -10000 0 -10000 0 0
CTNND1 0.023 0.044 -10000 0 -10000 0 0
DNM2 0.027 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.062 -10000 0 -0.31 3 3
TSHR 0.009 0.01 -10000 0 -10000 0 0
INS 0.009 0.058 -10000 0 -0.42 3 3
BIN1 0.02 0.069 -10000 0 -0.66 2 2
mol:Choline 0.025 0.038 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.007 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.026 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.023 0.011 -10000 0 -10000 0 0
JUP 0.006 0.079 -10000 0 -0.3 11 11
ASAP2/amphiphysin II 0.042 0.056 -10000 0 -0.39 3 3
ARF6/GTP 0.019 0.005 -10000 0 -10000 0 0
CDH1 -0.01 0.12 -10000 0 -0.41 11 11
clathrin-independent pinocytosis 0.019 0.005 -10000 0 -10000 0 0
MAPK8IP3 0.023 0.016 -10000 0 -10000 0 0
positive regulation of endocytosis 0.019 0.005 -10000 0 -10000 0 0
EXOC2 0.026 0.006 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.012 0.046 -10000 0 -0.31 2 2
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.025 0.007 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.017 0.12 0.53 4 -10000 0 4
positive regulation of phagocytosis 0.013 0.005 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.03 0.016 -10000 0 -10000 0 0
ACAP1 0.026 0.045 -10000 0 -0.22 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.006 0.075 -10000 0 -0.31 11 11
clathrin heavy chain/ACAP1 0.018 0.086 0.26 1 -0.38 3 4
JIP4/KLC1