PARADIGM pathway analysis of mRNASeq expression 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 data. Broad Institute of MIT and Harvard. doi:10.7908/C1PC310M
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 32 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 94
EGFR-dependent Endothelin signaling events 77
Angiopoietin receptor Tie2-mediated signaling 63
FOXA2 and FOXA3 transcription factor networks 53
Glypican 2 network 48
PDGFR-alpha signaling pathway 38
Thromboxane A2 receptor signaling 33
Glypican 1 network 29
Arf6 signaling events 27
Signaling mediated by p38-alpha and p38-beta 24
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 0.4747 94 3196 34 -0.62 0.012 1000 -1000 -0.061 -1000
EGFR-dependent Endothelin signaling events 0.3889 77 1622 21 -0.73 0.018 1000 -1000 -0.072 -1000
Angiopoietin receptor Tie2-mediated signaling 0.3182 63 5558 88 -0.92 0.077 1000 -1000 -0.098 -1000
FOXA2 and FOXA3 transcription factor networks 0.2677 53 2463 46 -1.2 0.018 1000 -1000 -0.095 -1000
Glypican 2 network 0.2424 48 192 4 -0.11 -0.11 1000 -1000 -0.015 -1000
PDGFR-alpha signaling pathway 0.1919 38 1701 44 -0.3 0.026 1000 -1000 -0.067 -1000
Thromboxane A2 receptor signaling 0.1667 33 3471 105 -0.73 0.079 1000 -1000 -0.065 -1000
Glypican 1 network 0.1465 29 1398 48 -0.43 0.031 1000 -1000 -0.043 -1000
Arf6 signaling events 0.1364 27 1732 62 -0.73 0.019 1000 -1000 -0.059 -1000
Signaling mediated by p38-alpha and p38-beta 0.1212 24 1077 44 -0.17 0.012 1000 -1000 -0.053 -1000
BMP receptor signaling 0.1162 23 1870 81 -0.51 0.018 1000 -1000 -0.094 -1000
TCGA08_retinoblastoma 0.1162 23 187 8 -0.23 0.06 1000 -1000 -0.02 -1000
amb2 Integrin signaling 0.1111 22 1820 82 -0.49 0.012 1000 -1000 -0.095 -1000
TCGA08_p53 0.1111 22 159 7 -0.15 0.094 1000 -1000 -0.013 -1000
Endothelins 0.1061 21 2083 96 -0.61 0.012 1000 -1000 -0.086 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.1010 20 2573 125 -0.16 0.018 1000 -1000 -0.089 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.1010 20 1617 78 -0.3 0.044 1000 -1000 -0.065 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0960 19 1333 68 -0.6 0.085 1000 -1000 -0.12 -1000
Integrins in angiogenesis 0.0909 18 1577 84 -0.54 0.032 1000 -1000 -0.082 -1000
FOXM1 transcription factor network 0.0909 18 943 51 -0.22 0.023 1000 -1000 -0.16 -1000
IL4-mediated signaling events 0.0859 17 1633 91 -0.88 0.48 1000 -1000 -0.14 -1000
Signaling events mediated by PTP1B 0.0808 16 1246 76 -0.73 0.096 1000 -1000 -0.076 -1000
S1P1 pathway 0.0758 15 561 36 -0.16 0.012 1000 -1000 -0.058 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0657 13 1034 74 -0.73 0.049 1000 -1000 -0.081 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0657 13 1679 120 -0.33 0.16 1000 -1000 -0.075 -1000
FoxO family signaling 0.0606 12 796 64 -0.94 0.086 1000 -1000 -0.076 -1000
TCR signaling in naïve CD8+ T cells 0.0606 12 1189 93 -0.56 0.27 1000 -1000 -0.08 -1000
LPA4-mediated signaling events 0.0505 10 130 12 -0.25 0.018 1000 -1000 -0.024 -1000
Signaling events mediated by the Hedgehog family 0.0505 10 570 52 -0.09 0.018 1000 -1000 -0.068 -1000
Ephrin A reverse signaling 0.0505 10 71 7 -0.048 0 1000 -1000 -0.029 -1000
Glucocorticoid receptor regulatory network 0.0505 10 1152 114 -0.62 0.16 1000 -1000 -0.073 -1000
Syndecan-4-mediated signaling events 0.0505 10 721 67 -0.46 0.076 1000 -1000 -0.09 -1000
Coregulation of Androgen receptor activity 0.0455 9 733 76 -0.75 0.022 1000 -1000 -0.047 -1000
Syndecan-1-mediated signaling events 0.0455 9 325 34 -0.1 0.012 1000 -1000 -0.061 -1000
p75(NTR)-mediated signaling 0.0455 9 1227 125 -0.47 0.031 1000 -1000 -0.1 -1000
Nongenotropic Androgen signaling 0.0455 9 473 52 -0.091 0.025 1000 -1000 -0.048 -1000
E-cadherin signaling events 0.0455 9 48 5 -0.054 0.012 1000 -1000 -0.035 -1000
Aurora B signaling 0.0455 9 624 67 -0.29 0.012 1000 -1000 -0.071 -1000
HIF-1-alpha transcription factor network 0.0404 8 636 76 -0.14 0.049 1000 -1000 -0.13 -1000
Calcium signaling in the CD4+ TCR pathway 0.0404 8 252 31 -0.14 0.014 1000 -1000 -0.086 -1000
IL27-mediated signaling events 0.0404 8 440 51 -1 0.17 1000 -1000 -0.079 -1000
IL6-mediated signaling events 0.0404 8 668 75 -0.26 0.052 1000 -1000 -0.096 -1000
Plasma membrane estrogen receptor signaling 0.0404 8 766 86 -0.16 0.023 1000 -1000 -0.078 -1000
E-cadherin signaling in keratinocytes 0.0404 8 362 43 -0.28 0.035 1000 -1000 -0.057 -1000
IL12-mediated signaling events 0.0354 7 609 87 -0.18 0.025 1000 -1000 -0.12 -1000
ErbB4 signaling events 0.0354 7 532 69 -0.36 0.12 1000 -1000 -0.092 -1000
Presenilin action in Notch and Wnt signaling 0.0354 7 441 61 -0.2 0.092 1000 -1000 -0.072 -1000
Reelin signaling pathway 0.0354 7 439 56 -0.17 0.018 1000 -1000 -0.079 -1000
Signaling events regulated by Ret tyrosine kinase 0.0354 7 649 82 -0.11 0.012 1000 -1000 -0.083 -1000
S1P3 pathway 0.0354 7 294 42 -0.16 0.018 1000 -1000 -0.038 -1000
Visual signal transduction: Rods 0.0354 7 402 52 -0.2 0.012 1000 -1000 -0.082 -1000
Regulation of Androgen receptor activity 0.0354 7 503 70 -0.85 0.027 1000 -1000 -0.061 -1000
Regulation of nuclear SMAD2/3 signaling 0.0303 6 886 136 -0.6 0.08 1000 -1000 -0.062 -1000
Noncanonical Wnt signaling pathway 0.0303 6 173 26 -0.2 0.012 1000 -1000 -0.06 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0303 6 312 52 -0.33 0.054 1000 -1000 -0.065 -1000
Regulation of Telomerase 0.0303 6 707 102 -0.73 0.042 1000 -1000 -0.1 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0303 6 200 33 -0.23 0.035 1000 -1000 -0.057 -1000
Caspase cascade in apoptosis 0.0253 5 378 74 -0.42 0.039 1000 -1000 -0.043 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0253 5 140 28 -0.16 0.017 1000 -1000 -0.046 -1000
Syndecan-2-mediated signaling events 0.0253 5 352 69 -0.49 0.04 1000 -1000 -0.049 -1000
Ceramide signaling pathway 0.0253 5 419 76 -0.73 0.25 1000 -1000 -0.057 -1000
EPHB forward signaling 0.0253 5 493 85 -0.17 0.059 1000 -1000 -0.079 -1000
E-cadherin signaling in the nascent adherens junction 0.0253 5 452 76 -0.054 0.028 1000 -1000 -0.068 -1000
BCR signaling pathway 0.0253 5 527 99 -0.083 0.028 1000 -1000 -0.088 -1000
IL23-mediated signaling events 0.0253 5 324 60 -0.12 0.023 1000 -1000 -0.15 -1000
BARD1 signaling events 0.0202 4 246 57 -0.11 0.024 1000 -1000 -0.062 -1000
Osteopontin-mediated events 0.0202 4 176 38 -0.12 0.048 1000 -1000 -0.1 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0202 4 254 54 -0.22 0.025 1000 -1000 -0.092 -1000
JNK signaling in the CD4+ TCR pathway 0.0202 4 73 17 -0.031 0.029 1000 -1000 -0.052 -1000
Fc-epsilon receptor I signaling in mast cells 0.0202 4 391 97 -0.12 0.029 1000 -1000 -0.081 -1000
Syndecan-3-mediated signaling events 0.0202 4 157 35 -0.17 0.018 1000 -1000 -0.062 -1000
Effects of Botulinum toxin 0.0202 4 124 26 -0.21 0.014 1000 -1000 -0.054 -1000
Wnt signaling 0.0202 4 31 7 -0.034 0.012 1000 -1000 -0.035 -1000
PDGFR-beta signaling pathway 0.0202 4 433 97 -0.13 0.043 1000 -1000 -0.083 -1000
Ras signaling in the CD4+ TCR pathway 0.0202 4 71 17 -0.011 0.025 1000 -1000 -0.039 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0152 3 286 85 -0.12 0.039 1000 -1000 -0.074 -1000
IFN-gamma pathway 0.0152 3 256 68 -0.39 0.065 1000 -1000 -0.083 -1000
Nectin adhesion pathway 0.0152 3 201 63 -0.091 0.049 1000 -1000 -0.067 -1000
IL1-mediated signaling events 0.0152 3 237 62 -0.14 0.057 1000 -1000 -0.095 -1000
S1P5 pathway 0.0152 3 54 17 -0.051 0.026 1000 -1000 -0.044 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0152 3 258 83 -0.27 0.047 1000 -1000 -0.067 -1000
Canonical Wnt signaling pathway 0.0152 3 176 51 -0.2 0.098 1000 -1000 -0.066 -1000
Regulation of p38-alpha and p38-beta 0.0152 3 201 54 -0.18 0.059 1000 -1000 -0.059 -1000
TCGA08_rtk_signaling 0.0152 3 102 26 -0.25 0.03 1000 -1000 -0.025 -1000
Signaling events mediated by PRL 0.0152 3 119 34 -0.03 0.021 1000 -1000 -0.038 -1000
Class IB PI3K non-lipid kinase events 0.0152 3 9 3 -0.005 -1000 1000 -1000 -0.022 -1000
Cellular roles of Anthrax toxin 0.0101 2 98 39 -0.19 0.018 1000 -1000 -0.022 -1000
Insulin-mediated glucose transport 0.0101 2 91 32 -0.12 0.065 1000 -1000 -0.061 -1000
Ephrin B reverse signaling 0.0101 2 136 48 -0.069 0.034 1000 -1000 -0.062 -1000
FAS signaling pathway (CD95) 0.0101 2 112 47 -0.099 0.022 1000 -1000 -0.041 -1000
IL2 signaling events mediated by PI3K 0.0101 2 173 58 -0.056 0.056 1000 -1000 -0.089 -1000
LPA receptor mediated events 0.0101 2 226 102 -0.12 0.053 1000 -1000 -0.084 -1000
IL2 signaling events mediated by STAT5 0.0101 2 63 22 -0.047 0.043 1000 -1000 -0.059 -1000
Class I PI3K signaling events 0.0101 2 182 73 -0.046 0.039 1000 -1000 -0.064 -1000
Arf6 trafficking events 0.0101 2 195 71 -0.35 0.04 1000 -1000 -0.068 -1000
IGF1 pathway 0.0101 2 156 57 -0.036 0.04 1000 -1000 -0.089 -1000
S1P4 pathway 0.0101 2 52 25 -0.051 0.026 1000 -1000 -0.052 -1000
ErbB2/ErbB3 signaling events 0.0051 1 118 65 -0.12 0.032 1000 -1000 -0.062 -1000
Signaling events mediated by HDAC Class II 0.0051 1 119 75 -0.14 0.036 1000 -1000 -0.056 -1000
Visual signal transduction: Cones 0.0051 1 45 38 -0.015 0.013 1000 -1000 -0.063 -1000
Hedgehog signaling events mediated by Gli proteins 0.0051 1 76 65 -0.05 0.062 1000 -1000 -0.055 -1000
Aurora A signaling 0.0051 1 117 60 -0.11 0.038 1000 -1000 -0.046 -1000
PLK1 signaling events 0.0051 1 164 85 -0.091 0.023 1000 -1000 -0.043 -1000
Class I PI3K signaling events mediated by Akt 0.0051 1 93 68 -0.12 0.046 1000 -1000 -0.056 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0051 1 50 37 -0.033 0.035 1000 -1000 -0.048 -1000
HIF-2-alpha transcription factor network 0.0051 1 81 43 -0.21 0.12 1000 -1000 -0.082 -1000
Signaling events mediated by HDAC Class I 0.0051 1 110 104 -0.14 0.052 1000 -1000 -0.066 -1000
Signaling mediated by p38-gamma and p38-delta 0.0051 1 23 15 0 0.024 1000 -1000 -0.03 -1000
Retinoic acid receptors-mediated signaling 0.0051 1 112 58 -0.06 0.032 1000 -1000 -0.07 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0051 1 45 45 -0.023 0.058 1000 -1000 -0.082 -1000
Insulin Pathway 0.0051 1 121 74 -0.038 0.033 1000 -1000 -0.086 -1000
VEGFR1 specific signals 0.0051 1 90 56 -0.01 0.044 1000 -1000 -0.065 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 6 23 0 0.043 1000 -1000 -0.06 -1000
Canonical NF-kappaB pathway 0.0000 0 27 39 -0.013 0.075 1000 -1000 -0.081 -1000
PLK2 and PLK4 events 0.0000 0 2 3 -0.006 0.009 1000 -1000 -0.023 -1000
Circadian rhythm pathway 0.0000 0 6 22 -0.012 0.042 1000 -1000 -0.049 -1000
a4b1 and a4b7 Integrin signaling 0.0000 0 0 5 0.012 0.018 1000 -1000 -0.02 -1000
Arf6 downstream pathway 0.0000 0 3 43 -0.022 0.023 1000 -1000 -0.039 -1000
Aurora C signaling 0.0000 0 0 7 -0.13 0.012 1000 -1000 -0.029 -1000
EPO signaling pathway 0.0000 0 46 55 -0.039 0.073 1000 -1000 -0.091 -1000
mTOR signaling pathway 0.0000 0 30 53 -0.006 0.028 1000 -1000 -0.052 -1000
Signaling events mediated by HDAC Class III 0.0000 0 13 40 -0.019 0.021 1000 -1000 -0.042 -1000
TRAIL signaling pathway 0.0000 0 41 48 -0.013 0.043 1000 -1000 -0.066 -1000
ceramide signaling pathway 0.0000 0 32 49 -0.013 0.045 1000 -1000 -0.042 -1000
Paxillin-dependent events mediated by a4b1 0.0000 0 19 36 -0.016 0.037 1000 -1000 -0.063 -1000
Atypical NF-kappaB pathway 0.0000 0 14 31 0 0.044 1000 -1000 -0.039 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 3 27 -0.002 0.031 1000 -1000 -0.052 -1000
Rapid glucocorticoid signaling 0.0000 0 6 20 -0.001 0.012 1000 -1000 -0.044 -1000
p38 MAPK signaling pathway 0.0000 0 42 44 -0.036 0.039 1000 -1000 -0.064 -1000
Arf1 pathway 0.0000 0 8 54 -0.006 0.03 1000 -1000 -0.046 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.018 1000 -1000 -0.065 -1000
Total NA 1178 70141 7203 -31 -990 131000 -131000 -8.7 -131000
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.5 0.35 0.73 135 -10000 0 135
KIRREL -0.13 0.25 -10000 0 -0.88 19 19
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.5 0.35 -10000 0 -0.73 135 135
PLCG1 0.012 0 -10000 0 -10000 0 0
ARRB2 0.011 0.021 -10000 0 -0.28 1 1
WASL 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.55 0.38 -10000 0 -0.72 152 152
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.42 0.31 -10000 0 -0.55 152 152
FYN -0.52 0.36 -10000 0 -0.68 152 152
mol:Ca2+ -0.54 0.37 -10000 0 -0.71 152 152
mol:DAG -0.55 0.37 -10000 0 -0.71 152 152
NPHS2 -0.39 0.41 -10000 0 -0.87 82 82
mol:IP3 -0.55 0.37 -10000 0 -0.71 152 152
regulation of endocytosis -0.48 0.34 -10000 0 -0.64 152 152
Nephrin/NEPH1/podocin/Cholesterol -0.56 0.38 -10000 0 -0.73 152 152
establishment of cell polarity -0.5 0.35 -10000 0 -0.73 135 135
Nephrin/NEPH1/podocin/NCK1-2 -0.51 0.36 -10000 0 -0.67 152 152
Nephrin/NEPH1/beta Arrestin2 -0.5 0.35 -10000 0 -0.65 152 152
NPHS1 -0.57 0.4 -10000 0 -0.86 130 130
Nephrin/NEPH1/podocin -0.53 0.36 -10000 0 -0.69 152 152
TJP1 0.012 0 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
NCK2 0.012 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.55 0.38 -10000 0 -0.72 152 152
CD2AP 0.012 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.55 0.38 -10000 0 -0.72 152 152
GRB2 0.012 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.62 0.41 -10000 0 -0.76 161 161
cytoskeleton organization -0.54 0.39 -10000 0 -0.72 152 152
Nephrin/NEPH1 -0.39 0.28 -10000 0 -0.56 135 135
Nephrin/NEPH1/ZO-1 -0.42 0.3 -10000 0 -0.61 135 135
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.012 0 -9999 0 -10000 0 0
EGFR 0.012 0 -9999 0 -10000 0 0
EGF/EGFR -0.42 0.16 -9999 0 -0.47 179 179
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.41 0.14 -9999 0 -0.46 178 178
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.025 0.17 -9999 0 -0.81 9 9
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.73 0.25 -9999 0 -0.81 178 178
EGF/EGFR dimer/SHC -0.48 0.16 -9999 0 -0.54 178 178
mol:GDP -0.41 0.14 -9999 0 -0.45 178 178
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.011 0.021 -9999 0 -0.28 1 1
GRB2/SOS1 0.018 0 -9999 0 -10000 0 0
HRAS/GTP -0.38 0.13 -9999 0 -0.42 178 178
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP -0.38 0.13 -9999 0 -0.43 178 178
FRAP1 -0.39 0.14 -9999 0 -0.44 178 178
EGF/EGFR dimer -0.56 0.19 -9999 0 -0.62 178 178
SOS1 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.012 0.13 -9999 0 -0.62 9 9
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 0.55 -10000 0 -1 106 106
NCK1/PAK1/Dok-R -0.24 0.22 -10000 0 -0.44 106 106
NCK1/Dok-R -0.67 0.71 -10000 0 -1.3 106 106
PIK3CA 0.013 0.001 -10000 0 -10000 0 0
mol:beta2-estradiol 0.077 0.11 0.25 61 -10000 0 61
RELA 0.012 0 -10000 0 -10000 0 0
SHC1 0.011 0.002 -10000 0 -10000 0 0
Rac/GDP 0.009 0 -10000 0 -10000 0 0
F2 0.065 0.13 0.25 48 -0.3 6 54
TNIP2 0.012 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.63 0.61 -10000 0 -1.2 106 106
FN1 -0.009 0.076 -10000 0 -0.28 14 14
PLD2 -0.71 0.76 -10000 0 -1.4 106 106
PTPN11 0.012 0 -10000 0 -10000 0 0
GRB14 -0.038 0.2 -10000 0 -0.81 12 12
ELK1 -0.59 0.64 -10000 0 -1.2 106 106
GRB7 0.012 0 -10000 0 -10000 0 0
PAK1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.68 0.66 -10000 0 -1.3 106 106
CDKN1A -0.34 0.37 -10000 0 -0.7 96 96
ITGA5 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.67 0.71 -10000 0 -1.3 106 106
CRK 0.012 0 -10000 0 -10000 0 0
mol:NO -0.35 0.4 -10000 0 -0.72 106 106
PLG -0.92 0.71 -10000 0 -1.5 106 106
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.48 0.52 -10000 0 -0.96 106 106
GRB2 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.011 0.002 -10000 0 -10000 0 0
ANGPT2 -0.28 0.33 -10000 0 -0.69 64 64
BMX -0.71 0.76 -10000 0 -1.4 106 106
ANGPT1 -0.45 0.66 -10000 0 -1.4 62 62
tube development -0.4 0.42 -10000 0 -0.78 104 104
ANGPT4 0.002 0.042 -10000 0 -0.29 4 4
response to hypoxia -0.035 0.037 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.76 0.79 -10000 0 -1.5 106 106
alpha5/beta1 Integrin 0.018 0 -10000 0 -10000 0 0
FGF2 0.013 0.002 -10000 0 -10000 0 0
STAT5A (dimer) -0.46 0.49 -10000 0 -0.91 104 104
mol:L-citrulline -0.35 0.4 -10000 0 -0.72 106 106
AGTR1 -0.25 0.38 -10000 0 -0.81 64 64
MAPK14 -0.7 0.73 -10000 0 -1.4 106 106
Tie2/SHP2 -0.6 0.63 -10000 0 -1.3 91 91
TEK -0.66 0.73 -10000 0 -1.4 91 91
RPS6KB1 -0.49 0.52 -10000 0 -0.97 106 106
Angiotensin II/AT1 -0.2 0.3 -10000 0 -0.63 64 64
Tie2/Ang1/GRB2 -0.74 0.8 -10000 0 -1.4 106 106
MAPK3 -0.62 0.66 -10000 0 -1.2 106 106
MAPK1 -0.62 0.66 -10000 0 -1.2 106 106
Tie2/Ang1/GRB7 -0.74 0.8 -10000 0 -1.4 106 106
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 -0.71 0.76 -10000 0 -1.4 106 106
PI3K -0.62 0.66 -10000 0 -1.2 106 106
FES -0.69 0.73 -10000 0 -1.3 106 106
Crk/Dok-R -0.67 0.71 -10000 0 -1.3 106 106
Tie2/Ang1/ABIN2 -0.74 0.8 -10000 0 -1.4 106 106
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.44 0.48 -10000 0 -0.88 106 106
STAT5A 0.012 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.49 0.52 -10000 0 -0.97 106 106
Tie2/Ang2 -0.6 0.62 -10000 0 -1.2 104 104
Tie2/Ang1 -0.82 0.88 -10000 0 -1.6 106 106
FOXO1 -0.45 0.49 -10000 0 -0.89 106 106
ELF1 -0.031 0.054 -10000 0 -10000 0 0
ELF2 -0.72 0.77 -10000 0 -1.4 106 106
mol:Choline -0.65 0.69 -10000 0 -1.3 106 106
cell migration -0.13 0.12 -10000 0 -0.24 106 106
FYN -0.47 0.49 -10000 0 -0.91 104 104
DOK2 -0.01 0.091 -10000 0 -0.32 13 13
negative regulation of cell cycle -0.3 0.33 -10000 0 -0.62 98 98
ETS1 -0.061 0.11 -10000 0 -10000 0 0
PXN -0.38 0.42 -10000 0 -0.77 106 106
ITGB1 0.012 0 -10000 0 -10000 0 0
NOS3 -0.42 0.46 -10000 0 -0.84 106 106
RAC1 0.012 0 -10000 0 -10000 0 0
TNF -0.087 0.15 -10000 0 -0.55 8 8
MAPKKK cascade -0.65 0.69 -10000 0 -1.3 106 106
RASA1 0.012 0 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.74 0.8 -10000 0 -1.4 106 106
NCK1 0.012 0 -10000 0 -10000 0 0
vasculogenesis -0.31 0.35 -10000 0 -0.63 106 106
mol:Phosphatidic acid -0.65 0.69 -10000 0 -1.3 106 106
mol:Angiotensin II 0 0.002 -10000 0 -10000 0 0
mol:NADP -0.35 0.4 -10000 0 -0.72 106 106
Rac1/GTP -0.48 0.44 -10000 0 -0.89 106 106
MMP2 -0.71 0.76 -10000 0 -1.4 106 106
FOXA2 and FOXA3 transcription factor networks

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.53 0.43 -9999 0 -1 67 67
PCK1 -1.2 0.7 -9999 0 -1.6 134 134
HNF4A -0.63 0.58 -9999 0 -1.3 70 70
KCNJ11 -0.55 0.44 -9999 0 -1.1 63 63
AKT1 -0.24 0.14 -9999 0 -0.45 6 6
response to starvation -0.004 0.015 -9999 0 -10000 0 0
DLK1 -0.57 0.45 -9999 0 -1.1 69 69
NKX2-1 -0.13 0.15 -9999 0 -10000 0 0
ACADM -0.53 0.43 -9999 0 -1.1 65 65
TAT -0.46 0.23 -9999 0 -0.74 52 52
CEBPB -0.034 0.054 -9999 0 -0.35 4 4
CEBPA -0.052 0.1 -9999 0 -0.39 13 13
TTR -0.78 0.43 -9999 0 -1 119 119
PKLR -0.7 0.64 -9999 0 -1.4 75 75
APOA1 -0.68 0.61 -9999 0 -1.4 71 71
CPT1C -0.54 0.44 -9999 0 -1.1 69 69
ALAS1 -0.22 0.15 -9999 0 -10000 0 0
TFRC -0.6 0.3 -9999 0 -0.87 91 91
FOXF1 0.002 0.083 -9999 0 -0.81 2 2
NF1 0.018 0 -9999 0 -10000 0 0
HNF1A (dimer) -0.048 0.11 -9999 0 -0.86 3 3
CPT1A -0.53 0.43 -9999 0 -1.1 64 64
HMGCS1 -0.53 0.43 -9999 0 -1.1 63 63
NR3C1 0.007 0.04 -9999 0 -10000 0 0
CPT1B -0.53 0.43 -9999 0 -1.1 64 64
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.013 0.007 -9999 0 -10000 0 0
GCK -0.53 0.43 -9999 0 -1.1 64 64
CREB1 -0.08 0.063 -9999 0 -10000 0 0
IGFBP1 -0.31 0.4 -9999 0 -1.4 19 19
PDX1 -0.27 0.21 -9999 0 -0.9 6 6
UCP2 -0.53 0.43 -9999 0 -1 68 68
ALDOB -1.2 0.41 -9999 0 -1.3 190 190
AFP -0.48 0.36 -9999 0 -0.87 58 58
BDH1 -0.53 0.43 -9999 0 -1.1 64 64
HADH -0.55 0.44 -9999 0 -1.1 65 65
F2 -0.62 0.51 -9999 0 -1.2 67 67
HNF1A -0.048 0.11 -9999 0 -0.86 3 3
G6PC -1.1 0.61 -9999 0 -1.5 140 140
SLC2A2 -0.52 0.61 -9999 0 -1.7 37 37
INS 0.004 0.042 -9999 0 -10000 0 0
FOXA1 -0.24 0.12 -9999 0 -0.46 28 28
FOXA3 -0.46 0.27 -9999 0 -0.52 164 164
FOXA2 -0.64 0.49 -9999 0 -1.1 79 79
ABCC8 -0.56 0.44 -9999 0 -1.1 67 67
ALB -1.2 0.37 -9999 0 -1.3 180 180
Glypican 2 network

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
MDK -0.055 0.12 -9999 0 -0.28 45 45
GPC2 -0.11 0.15 -9999 0 -0.28 83 83
GPC2/Midkine -0.11 0.14 -9999 0 -0.36 32 32
neuron projection morphogenesis -0.11 0.14 -9999 0 -0.36 32 32
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.26 0.39 -9999 0 -0.83 63 63
PDGF/PDGFRA/CRKL -0.19 0.3 -9999 0 -0.62 63 63
positive regulation of JUN kinase activity -0.15 0.22 -9999 0 -0.48 63 63
CRKL 0.012 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.19 0.3 -9999 0 -0.63 63 63
AP1 -0.3 0.5 -9999 0 -1.4 31 31
mol:IP3 -0.19 0.31 -9999 0 -0.64 63 63
PLCG1 -0.19 0.31 -9999 0 -0.64 63 63
PDGF/PDGFRA/alphaV Integrin -0.19 0.3 -9999 0 -0.62 63 63
RAPGEF1 0.012 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ -0.19 0.31 -9999 0 -0.64 63 63
CAV3 0.002 0.005 -9999 0 -10000 0 0
CAV1 0.011 0.021 -9999 0 -0.28 1 1
SHC/Grb2/SOS1 -0.15 0.22 -9999 0 -0.48 63 63
PDGF/PDGFRA/Shf -0.19 0.3 -9999 0 -0.62 63 63
FOS -0.27 0.5 -9999 0 -1.3 31 31
JUN -0.019 0.026 -9999 0 -10000 0 0
oligodendrocyte development -0.18 0.3 -9999 0 -0.62 63 63
GRB2 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:DAG -0.19 0.31 -9999 0 -0.64 63 63
PDGF/PDGFRA -0.26 0.39 -9999 0 -0.82 63 63
actin cytoskeleton reorganization -0.18 0.3 -9999 0 -0.62 63 63
SRF 0.026 0.011 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
PI3K -0.17 0.25 -9999 0 -0.53 63 63
PDGF/PDGFRA/Crk/C3G -0.17 0.25 -9999 0 -0.53 63 63
JAK1 -0.18 0.3 -9999 0 -0.62 63 63
ELK1/SRF -0.13 0.24 -9999 0 -0.48 63 63
SHB 0.012 0 -9999 0 -10000 0 0
SHF 0.012 0 -9999 0 -10000 0 0
CSNK2A1 0.018 0.025 -9999 0 -10000 0 0
GO:0007205 -0.19 0.32 -9999 0 -0.65 63 63
SOS1 0.012 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.15 0.22 -9999 0 -0.48 63 63
PDGF/PDGFRA/SHB -0.19 0.3 -9999 0 -0.62 63 63
PDGF/PDGFRA/Caveolin-1 -0.19 0.3 -9999 0 -0.62 63 63
ITGAV 0.012 0 -9999 0 -10000 0 0
ELK1 -0.17 0.29 -9999 0 -0.59 63 63
PIK3CA 0.012 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.19 0.3 -9999 0 -0.62 63 63
JAK-STAT cascade -0.18 0.3 -9999 0 -0.62 63 63
cell proliferation -0.18 0.3 -9999 0 -0.62 63 63
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.014 0.078 -10000 0 -0.28 15 15
GNB1/GNG2 -0.095 0.089 -10000 0 -0.19 68 68
AKT1 -0.081 0.12 -10000 0 -0.21 6 6
EGF -0.73 0.25 -10000 0 -0.81 178 178
mol:TXA2 -0.001 0.001 -10000 0 -10000 0 0
FGR 0.008 0.1 -10000 0 -0.81 1 1
mol:Ca2+ -0.14 0.17 -10000 0 -0.3 95 95
LYN 0.013 0.093 -10000 0 -0.35 8 8
RhoA/GTP -0.064 0.058 -10000 0 -0.14 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.15 0.19 -10000 0 -0.34 95 95
GNG2 0.012 0 -10000 0 -10000 0 0
ARRB2 0.011 0.021 -10000 0 -0.28 1 1
TP alpha/Gq family/GDP/G beta5/gamma2 -0.025 0.11 -10000 0 -0.45 4 4
G beta5/gamma2 -0.12 0.12 -10000 0 -0.26 51 51
PRKCH -0.16 0.19 -10000 0 -0.35 95 95
DNM1 -0.069 0.13 -10000 0 -0.28 54 54
TXA2/TP beta/beta Arrestin3 -0.021 0.036 -10000 0 -10000 0 0
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR 0.012 0.001 -10000 0 -10000 0 0
G12 family/GTP -0.16 0.14 -10000 0 -0.3 95 95
ADRBK1 0.012 0 -10000 0 -10000 0 0
ADRBK2 0.012 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.004 0.007 -10000 0 -10000 0 0
mol:GDP 0.079 0.12 0.37 11 -10000 0 11
mol:NADP -0.009 0.13 -10000 0 -0.81 5 5
RAB11A 0.012 0 -10000 0 -10000 0 0
PRKG1 -0.18 0.34 -10000 0 -0.81 45 45
mol:IP3 -0.18 0.21 -10000 0 -0.38 95 95
cell morphogenesis 0.002 0.006 -10000 0 -10000 0 0
PLCB2 -0.25 0.28 -10000 0 -0.52 95 95
mol:cGMP -0.001 0.001 -10000 0 -10000 0 0
BLK 0.004 0.096 -10000 0 -0.36 9 9
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.002 0.11 -10000 0 -0.81 1 1
RHOA 0.012 0 -10000 0 -10000 0 0
PTGIR 0.004 0.082 -10000 0 -0.81 2 2
PRKCB1 -0.18 0.21 -10000 0 -0.38 95 95
GNAQ 0.012 0 -10000 0 -10000 0 0
mol:L-citrulline -0.009 0.13 -10000 0 -0.81 5 5
TXA2/TXA2-R family -0.25 0.28 -10000 0 -0.53 95 95
LCK 0.01 0.094 -10000 0 -0.52 1 1
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.028 0.11 -10000 0 -0.43 12 12
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.033 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.028 0.11 -10000 0 -0.43 12 12
MAPK14 -0.095 0.13 -10000 0 -0.23 68 68
TGM2/GTP -0.2 0.23 -10000 0 -0.43 95 95
MAPK11 -0.095 0.13 -10000 0 -0.23 70 70
ARHGEF1 -0.075 0.1 -10000 0 -0.18 24 24
GNAI2 0.012 0 -10000 0 -10000 0 0
JNK cascade -0.18 0.21 -10000 0 -0.39 95 95
RAB11/GDP 0.013 0.002 -10000 0 -10000 0 0
ICAM1 -0.12 0.16 -10000 0 -0.28 95 95
cAMP biosynthetic process -0.17 0.19 -10000 0 -0.35 95 95
Gq family/GTP/EBP50 -0.039 0.11 -10000 0 -0.33 5 5
actin cytoskeleton reorganization 0.002 0.006 -10000 0 -10000 0 0
SRC 0.013 0.093 -10000 0 -0.34 10 10
GNB5 0.012 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
EGF/EGFR -0.1 0.082 -10000 0 -0.34 12 12
VCAM1 -0.14 0.17 -10000 0 -0.3 95 95
TP beta/Gq family/GDP/G beta5/gamma2 -0.025 0.11 -10000 0 -0.45 4 4
platelet activation -0.13 0.18 -10000 0 -0.3 95 95
PGI2/IP -0.003 0.064 -10000 0 -0.63 2 2
PRKACA 0.014 0.04 -10000 0 -0.38 2 2
Gq family/GDP/G beta5/gamma2 -0.021 0.1 -10000 0 -0.41 4 4
TXA2/TP beta/beta Arrestin2 -0.026 0.043 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.009 0.13 -10000 0 -0.49 13 13
mol:DAG -0.2 0.23 -10000 0 -0.43 95 95
EGFR 0.012 0 -10000 0 -10000 0 0
TXA2/TP alpha -0.23 0.26 -10000 0 -0.48 95 95
Gq family/GTP -0.069 0.12 -10000 0 -0.29 46 46
YES1 0.013 0.093 -10000 0 -0.52 1 1
GNAI2/GTP -0.025 0.097 -10000 0 -0.39 12 12
PGD2/DP 0.004 0.005 -10000 0 -10000 0 0
SLC9A3R1 0.012 0 -10000 0 -10000 0 0
FYN 0.013 0.093 -10000 0 -0.52 1 1
mol:NO -0.009 0.13 -10000 0 -0.81 5 5
GNA15 -0.006 0.071 -10000 0 -10000 0 0
PGK/cGMP -0.13 0.25 -10000 0 -0.57 48 48
RhoA/GDP 0.013 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.033 0.11 -10000 0 -0.43 12 12
NOS3 -0.009 0.13 -10000 0 -0.81 5 5
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.16 0.19 -10000 0 -0.35 95 95
PRKCB -0.17 0.2 -10000 0 -0.36 95 95
PRKCE -0.16 0.2 -10000 0 -0.36 95 95
PRKCD -0.18 0.21 -10000 0 -0.38 95 95
PRKCG -0.19 0.22 -10000 0 -0.41 95 95
muscle contraction -0.22 0.26 -10000 0 -0.49 95 95
PRKCZ -0.15 0.19 -10000 0 -0.34 95 95
ARR3 0.002 0.004 -10000 0 -10000 0 0
TXA2/TP beta -0.028 0.11 -10000 0 -0.44 12 12
PRKCQ -0.17 0.2 -10000 0 -0.36 97 97
MAPKKK cascade -0.21 0.24 -10000 0 -0.45 95 95
SELE -0.2 0.23 -10000 0 -0.43 95 95
TP beta/GNAI2/GDP/G beta/gamma -0.027 0.1 -10000 0 -0.42 12 12
ROCK1 0.012 0 -10000 0 -10000 0 0
GNA14 -0.16 0.34 -10000 0 -0.81 42 42
chemotaxis -0.29 0.32 -10000 0 -0.61 95 95
GNA12 0.012 0 -10000 0 -10000 0 0
GNA13 0.011 0.021 -10000 0 -10000 0 0
GNA11 -0.005 0.12 -10000 0 -0.81 4 4
Rac1/GTP 0.003 0.005 -10000 0 -10000 0 0
Glypican 1 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer 0 0 -9999 0 -10000 0 0
fibroblast growth factor receptor signaling pathway 0 0 -9999 0 -10000 0 0
LAMA1 -0.03 0.15 -9999 0 -0.42 19 19
PRNP 0.012 0 -9999 0 -10000 0 0
GPC1/SLIT2 -0.12 0.26 -9999 0 -0.62 43 43
SMAD2 0.031 0 -9999 0 -10000 0 0
GPC1/PrPc/Cu2+ 0 0 -9999 0 -10000 0 0
GPC1/Laminin alpha1 -0.012 0.11 -9999 0 -0.62 5 5
TDGF1 -0.43 0.41 -9999 0 -0.81 106 106
CRIPTO/GPC1 -0.33 0.32 -9999 0 -0.62 106 106
APP/GPC1 0.018 0 -9999 0 -10000 0 0
mol:NO 0 0 -9999 0 -10000 0 0
YES1 -0.28 0.28 -9999 0 -0.54 106 106
FLT1 0.004 0.082 -9999 0 -0.81 2 2
GPC1/TGFB/TGFBR1/TGFBR2 0 0 -9999 0 -10000 0 0
SERPINC1 -0.21 0.36 -9999 0 -0.81 52 52
FYN -0.28 0.28 -9999 0 -0.54 106 106
FGR -0.28 0.28 -9999 0 -0.55 106 106
positive regulation of MAPKKK cascade -0.28 0.29 -9999 0 -0.54 106 106
SLIT2 -0.17 0.34 -9999 0 -0.79 45 45
GPC1/NRG 0.005 0.082 -9999 0 -0.62 3 3
NRG1 -0.005 0.11 -9999 0 -0.81 3 3
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.006 0.055 -9999 0 -0.54 2 2
LYN -0.28 0.28 -9999 0 -0.54 106 106
mol:Spermine 0.01 0 -9999 0 -10000 0 0
cell growth 0 0 -9999 0 -10000 0 0
BMP signaling pathway -0.012 0 -9999 0 -10000 0 0
SRC -0.28 0.28 -9999 0 -0.54 106 106
TGFBR1 0.012 0 -9999 0 -10000 0 0
mol:Cu2+ 0 0 -9999 0 -10000 0 0
PLA2G2A -0.018 0.079 -9999 0 -10000 0 0
GPC1 0.012 0 -9999 0 -10000 0 0
TGFBR1 (dimer) 0.012 0 -9999 0 -10000 0 0
VEGFA 0.011 0.021 -9999 0 -0.28 1 1
BLK -0.29 0.28 -9999 0 -0.55 106 106
HCK -0.3 0.28 -9999 0 -0.55 106 106
FGF2 0.012 0 -9999 0 -10000 0 0
FGFR1 0.012 0 -9999 0 -10000 0 0
VEGFR1 homodimer 0.004 0.082 -9999 0 -0.81 2 2
TGFBR2 0.012 0 -9999 0 -10000 0 0
cell death 0.018 0 -9999 0 -10000 0 0
ATIII/GPC1 -0.15 0.28 -9999 0 -0.62 52 52
PLA2G2A/GPC1 -0.003 0.053 -9999 0 -10000 0 0
LCK -0.28 0.28 -9999 0 -0.54 106 106
neuron differentiation 0.005 0.081 -9999 0 -0.62 3 3
PrPc/Cu2+ 0.009 0 -9999 0 -10000 0 0
APP 0.012 0 -9999 0 -10000 0 0
TGFBR2 (dimer) 0.012 0 -9999 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0 0 -9999 0 -10000 0 0
ARNO/beta Arrestin1-2 -0.01 0.027 -9999 0 -10000 0 0
EGFR 0.012 0 -9999 0 -10000 0 0
EPHA2 0.011 0.021 -9999 0 -0.28 1 1
USP6 -0.001 0.062 -9999 0 -0.28 9 9
IQSEC1 0.012 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.56 0.19 -9999 0 -0.62 178 178
ARRB2 0 0.036 -9999 0 -10000 0 0
mol:GTP 0.014 0.011 -9999 0 -10000 0 0
ARRB1 0.012 0 -9999 0 -10000 0 0
FBXO8 0.012 0 -9999 0 -10000 0 0
TSHR 0.008 0.021 -9999 0 -0.28 1 1
EGF -0.73 0.25 -9999 0 -0.81 178 178
somatostatin receptor activity 0 0 -9999 0 -0.001 77 77
ARAP2 0.012 0 -9999 0 -10000 0 0
mol:GDP -0.12 0.11 -9999 0 -0.27 61 61
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 52 52
ITGA2B -0.008 0.073 -9999 0 -0.28 13 13
ARF6 0.012 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.019 0.018 -9999 0 -10000 0 0
ADAP1 0.012 0 -9999 0 -10000 0 0
KIF13B 0.012 0 -9999 0 -10000 0 0
HGF/MET -0.041 0.14 -9999 0 -0.64 9 9
PXN 0.012 0 -9999 0 -10000 0 0
ARF6/GTP -0.17 0.12 -9999 0 -0.31 77 77
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.48 0.16 -9999 0 -0.54 178 178
ADRB2 -0.006 0.071 -9999 0 -0.28 12 12
receptor agonist activity 0 0 -9999 0 0 77 77
actin filament binding 0 0 -9999 0 -0.001 77 77
SRC 0.012 0 -9999 0 -10000 0 0
ITGB3 -0.016 0.14 -9999 0 -0.55 10 10
GNAQ 0.012 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 -0.001 0 -9999 0 -0.001 76 76
ARF6/GDP -0.029 0.055 -9999 0 -10000 0 0
ARF6/GDP/GULP/ACAP1 -0.11 0.11 -9999 0 -0.35 13 13
alphaIIb/beta3 Integrin/paxillin/GIT1 0.004 0.09 -9999 0 -0.49 5 5
ACAP1 -0.027 0.1 -9999 0 -0.28 26 26
ACAP2 0.012 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 -0.008 0.046 -9999 0 -10000 0 0
EFNA1 0.012 0 -9999 0 -10000 0 0
HGF -0.026 0.17 -9999 0 -0.81 9 9
CYTH3 0.01 0 -9999 0 -10000 0 0
CYTH2 0.006 0.002 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 46 46
endosomal lumen acidification 0 0 -9999 0 -0.001 77 77
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 0.011 0.021 -9999 0 -0.28 1 1
GNAQ/ARNO 0.008 0.007 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 62 62
MET -0.021 0.093 -9999 0 -0.28 22 22
GNA14 -0.16 0.34 -9999 0 -0.81 42 42
GNA15 -0.006 0.071 -9999 0 -10000 0 0
GIT1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 76 76
GNA11 -0.005 0.12 -9999 0 -0.81 4 4
LHCGR -0.018 0.079 -9999 0 -0.28 16 16
AGTR1 -0.26 0.38 -9999 0 -0.81 64 64
desensitization of G-protein coupled receptor protein signaling pathway -0.008 0.046 -9999 0 -10000 0 0
IPCEF1/ARNO -0.38 0.13 -9999 0 -0.43 178 178
alphaIIb/beta3 Integrin -0.017 0.11 -9999 0 -0.62 5 5
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.17 0.47 -9999 0 -1.3 29 29
MKNK1 0.012 0 -9999 0 -10000 0 0
MAPK14 -0.039 0.14 -9999 0 -0.48 4 4
ATF2/c-Jun -0.014 0.12 -9999 0 -0.43 4 4
MAPK11 -0.039 0.14 -9999 0 -0.31 40 40
MITF -0.038 0.17 -9999 0 -0.37 40 40
MAPKAPK5 -0.038 0.17 -9999 0 -0.37 40 40
KRT8 -0.041 0.17 -9999 0 -0.38 40 40
MAPKAPK3 0.012 0 -9999 0 -10000 0 0
MAPKAPK2 0.012 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.061 0.22 -9999 0 -0.48 40 40
CEBPB -0.041 0.18 -9999 0 -0.38 40 40
SLC9A1 -0.038 0.17 -9999 0 -0.37 40 40
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.031 0.17 -9999 0 -0.36 40 40
p38alpha-beta/MNK1 -0.039 0.18 -9999 0 -0.69 4 4
JUN -0.014 0.11 -9999 0 -0.42 4 4
PPARGC1A -0.052 0.2 -9999 0 -0.4 43 43
USF1 -0.038 0.17 -9999 0 -0.37 40 40
RAB5/GDP/GDI1 -0.054 0.11 -9999 0 -0.47 4 4
NOS2 -0.1 0.37 -9999 0 -1.3 15 15
DDIT3 -0.039 0.17 -9999 0 -0.37 40 40
RAB5A 0.012 0 -9999 0 -10000 0 0
HSPB1 -0.026 0.15 -9999 0 -0.48 6 6
p38alpha-beta/HBP1 -0.039 0.18 -9999 0 -0.58 6 6
CREB1 -0.042 0.19 -9999 0 -0.4 40 40
RAB5/GDP 0.009 0 -9999 0 -10000 0 0
EIF4E -0.029 0.16 -9999 0 -0.62 4 4
RPS6KA4 -0.038 0.17 -9999 0 -0.37 40 40
PLA2G4A -0.039 0.19 -9999 0 -0.72 7 7
GDI1 -0.038 0.17 -9999 0 -0.37 40 40
TP53 -0.054 0.21 -9999 0 -0.47 40 40
RPS6KA5 -0.047 0.2 -9999 0 -0.41 41 41
ESR1 -0.066 0.24 -9999 0 -0.45 45 45
HBP1 0.012 0 -9999 0 -10000 0 0
MEF2C -0.038 0.17 -9999 0 -0.37 40 40
MEF2A -0.038 0.17 -9999 0 -0.37 40 40
EIF4EBP1 -0.042 0.19 -9999 0 -0.4 40 40
KRT19 -0.087 0.21 -9999 0 -0.41 53 53
ELK4 -0.038 0.17 -9999 0 -0.37 40 40
ATF6 -0.038 0.17 -9999 0 -0.37 40 40
ATF1 -0.042 0.19 -9999 0 -0.4 40 40
p38alpha-beta/MAPKAPK2 -0.039 0.18 -9999 0 -0.69 4 4
p38alpha-beta/MAPKAPK3 -0.039 0.18 -9999 0 -0.69 4 4
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.51 0.35 -9999 0 -0.65 154 154
SMAD6-7/SMURF1 -0.003 0.038 -9999 0 -0.54 1 1
NOG 0.001 0.085 -9999 0 -0.64 3 3
SMAD9 -0.066 0.1 -9999 0 -0.43 9 9
SMAD4 0.012 0 -9999 0 -10000 0 0
SMAD5 -0.2 0.2 -9999 0 -0.35 118 118
BMP7/USAG1 -0.3 0.35 -9999 0 -0.7 81 81
SMAD5/SKI -0.18 0.19 -9999 0 -0.47 17 17
SMAD1 -0.012 0.046 -9999 0 -10000 0 0
BMP2 0.012 0 -9999 0 -10000 0 0
SMAD1/SMAD1/SMAD4 -0.009 0.029 -9999 0 -10000 0 0
BMPR1A 0.012 0 -9999 0 -10000 0 0
BMPR1B -0.48 0.4 -9999 0 -0.81 118 118
BMPR1A-1B/BAMBI -0.32 0.26 -9999 0 -0.54 119 119
AHSG -0.005 0.054 -9999 0 -0.28 7 7
CER1 0.004 0.006 -9999 0 -10000 0 0
BMP2-4/CER1 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.14 0.17 -9999 0 -0.54 15 15
BMP2-4 (homodimer) 0.018 0 -9999 0 -10000 0 0
RGMB 0.012 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.28 0.26 -9999 0 -0.49 118 118
RGMA -0.067 0.24 -9999 0 -0.81 19 19
SMURF1 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.16 0.17 -9999 0 -0.48 17 17
BMP2-4/USAG1 -0.11 0.2 -9999 0 -0.54 33 33
SMAD6/SMURF1/SMAD5 -0.18 0.19 -9999 0 -0.47 17 17
SOSTDC1 -0.18 0.3 -9999 0 -0.54 67 67
BMP7/BMPR2/BMPR1A-1B -0.43 0.31 -9999 0 -0.58 147 147
SKI 0.012 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.012 0 -9999 0 -10000 0 0
HFE2 0.005 0.03 -9999 0 -10000 0 0
ZFYVE16 0.012 0 -9999 0 -10000 0 0
MAP3K7 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.024 0.11 -9999 0 -0.54 9 9
SMAD5/SMAD5/SMAD4 -0.18 0.19 -9999 0 -0.47 17 17
MAPK1 0.012 0 -9999 0 -10000 0 0
TAK1/TAB family -0.15 0.13 -9999 0 -0.42 15 15
BMP7 (homodimer) -0.23 0.37 -9999 0 -0.8 59 59
NUP214 0.012 0 -9999 0 -10000 0 0
BMP6/FETUA 0.006 0.036 -9999 0 -10000 0 0
SMAD1/SKI -0.005 0.044 -9999 0 -10000 0 0
SMAD6 0.008 0.058 -9999 0 -0.81 1 1
CTDSP2 0.012 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.005 0.026 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.16 0.33 -9999 0 -0.73 47 47
BMPR2 (homodimer) 0.012 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.36 0.31 -9999 0 -0.62 118 118
CHRDL1 -0.31 0.4 -9999 0 -0.81 77 77
ENDOFIN/SMAD1 -0.005 0.044 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.018 0.034 -9999 0 -0.46 1 1
SMAD6/SMURF1 0.012 0 -9999 0 -10000 0 0
BAMBI 0.008 0.058 -9999 0 -0.81 1 1
SMURF2 0.012 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.21 0.26 -9999 0 -0.54 77 77
BMP2-4/GREM1 -0.11 0.22 -9999 0 -0.54 40 40
SMAD7 0.012 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.055 0.098 -9999 0 -0.47 6 6
SMAD1/SMAD6 -0.005 0.044 -9999 0 -10000 0 0
TAK1/SMAD6 0.018 0 -9999 0 -10000 0 0
BMP7 -0.23 0.37 -9999 0 -0.8 59 59
BMP6 0.012 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.13 0.15 -9999 0 -0.43 17 17
PPM1A 0.012 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.005 0.044 -9999 0 -10000 0 0
SMAD7/SMURF1 0.018 0 -9999 0 -10000 0 0
CTDSPL 0.012 0 -9999 0 -10000 0 0
PPP1CA 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
CTDSP1 0.012 0 -9999 0 -10000 0 0
PPP1R15A 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.28 0.32 -9999 0 -0.77 45 45
CHRD -0.025 0.17 -9999 0 -0.81 9 9
BMPR2 0.012 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.17 0.18 -9999 0 -0.52 17 17
BMP4 0.012 0 -9999 0 -10000 0 0
FST -0.17 0.33 -9999 0 -0.75 46 46
BMP2-4/NOG -0.006 0.055 -9999 0 -0.54 2 2
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.41 0.29 -9999 0 -0.55 147 147
TCGA08_retinoblastoma

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
CDKN2B -0.002 0.045 -10000 0 -0.28 5 5
CDKN2C 0.031 0.023 -10000 0 -10000 0 0
CDKN2A -0.23 0.12 -10000 0 -0.29 159 159
CCND2 0.046 0.036 0.17 4 -10000 0 4
RB1 -0.051 0.039 -10000 0 -0.16 5 5
CDK4 0.06 0.036 0.17 5 -10000 0 5
CDK6 0.056 0.035 0.18 4 -10000 0 4
G1/S progression 0.051 0.039 0.16 5 -10000 0 5
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.05 0.099 -9999 0 -0.48 2 2
alphaM/beta2 Integrin/GPIbA -0.048 0.1 -9999 0 -0.8 1 1
alphaM/beta2 Integrin/proMMP-9 -0.1 0.14 -9999 0 -0.45 17 17
PLAUR -0.012 0.081 -9999 0 -0.28 16 16
HMGB1 0.008 0.016 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.046 0.09 -9999 0 -10000 0 0
AGER -0.024 0.094 -9999 0 -0.29 21 21
RAP1A 0.012 0 -9999 0 -10000 0 0
SELPLG -0.015 0.085 -9999 0 -0.28 18 18
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.072 0.098 -9999 0 -0.38 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.1 0.17 -9999 0 -0.81 3 3
CYR61 -0.021 0.16 -9999 0 -0.81 8 8
TLN1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP -0.22 0.15 -9999 0 -0.43 51 51
RHOA 0.012 0 -9999 0 -10000 0 0
P-selectin oligomer -0.05 0.22 -9999 0 -0.81 15 15
MYH2 -0.31 0.22 -9999 0 -0.51 77 77
MST1R -0.028 0.11 -9999 0 -0.81 1 1
leukocyte activation during inflammatory response -0.11 0.18 -9999 0 -0.5 30 30
APOB -0.041 0.19 -9999 0 -0.59 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.005 0.065 -9999 0 -0.46 3 3
JAM3 0.012 0 -9999 0 -10000 0 0
GP1BA 0.008 0.058 -9999 0 -0.81 1 1
alphaM/beta2 Integrin/CTGF -0.054 0.11 -9999 0 -0.56 3 3
alphaM/beta2 Integrin -0.26 0.18 -9999 0 -0.43 82 82
JAM3 homodimer 0.012 0 -9999 0 -10000 0 0
ICAM2 0.012 0 -9999 0 -10000 0 0
ICAM1 0.011 0.021 -9999 0 -0.28 1 1
phagocytosis triggered by activation of immune response cell surface activating receptor -0.26 0.18 -9999 0 -0.42 82 82
cell adhesion -0.048 0.1 -9999 0 -0.79 1 1
NFKB1 -0.052 0.16 -9999 0 -0.5 4 4
THY1 -0.22 0.37 -9999 0 -0.81 56 56
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.089 0.2 -9999 0 -0.55 30 30
alphaM/beta2 Integrin/LRP/tPA -0.078 0.16 -9999 0 -0.54 16 16
IL6 -0.1 0.29 -9999 0 -0.96 18 18
ITGB2 -0.046 0.11 -9999 0 -0.32 4 4
elevation of cytosolic calcium ion concentration -0.052 0.11 -9999 0 -0.41 8 8
alphaM/beta2 Integrin/JAM2/JAM3 -0.046 0.098 -9999 0 -0.5 3 3
JAM2 0 0.1 -9999 0 -0.81 3 3
alphaM/beta2 Integrin/ICAM1 -0.051 0.088 -9999 0 -0.45 2 2
alphaM/beta2 Integrin/uPA/Plg -0.33 0.26 -9999 0 -0.54 115 115
RhoA/GTP -0.32 0.24 -9999 0 -0.5 91 91
positive regulation of phagocytosis -0.2 0.14 -9999 0 -0.43 42 42
Ron/MSP -0.013 0.09 -9999 0 -0.62 2 2
alphaM/beta2 Integrin/uPAR/uPA -0.052 0.11 -9999 0 -0.41 8 8
alphaM/beta2 Integrin/uPAR -0.058 0.11 -9999 0 -0.44 7 7
PLAU 0.008 0.058 -9999 0 -0.81 1 1
PLAT -0.056 0.22 -9999 0 -0.78 17 17
actin filament polymerization -0.29 0.21 -9999 0 -0.48 77 77
MST1 0.008 0.058 -9999 0 -0.81 1 1
alphaM/beta2 Integrin/lipoprotein(a) -0.11 0.18 -9999 0 -0.5 30 30
TNF -0.052 0.18 -9999 0 -0.82 3 3
RAP1B 0.012 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.049 0.098 -9999 0 -0.59 1 1
fibrinolysis -0.32 0.26 -9999 0 -0.53 115 115
HCK -0.026 0.11 -9999 0 -0.31 24 24
dendritic cell antigen processing and presentation -0.26 0.18 -9999 0 -0.42 82 82
VTN -0.28 0.39 -9999 0 -0.78 74 74
alphaM/beta2 Integrin/CYR61 -0.067 0.14 -9999 0 -0.6 8 8
LPA -0.079 0.25 -9999 0 -0.81 20 20
LRP1 0.012 0 -9999 0 -10000 0 0
cell migration -0.079 0.14 -9999 0 -0.42 18 18
FN1 -0.009 0.076 -9999 0 -0.28 14 14
alphaM/beta2 Integrin/Thy1 -0.2 0.25 -9999 0 -0.56 56 56
MPO -0.008 0.073 -9999 0 -0.28 13 13
KNG1 -0.49 0.4 -9999 0 -0.81 120 120
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.3 0.22 -9999 0 -0.53 66 66
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.47 0.4 -9999 0 -0.81 114 114
CTGF 0 0.1 -9999 0 -0.81 3 3
alphaM/beta2 Integrin/Hck -0.066 0.13 -9999 0 -0.44 16 16
ITGAM -0.024 0.091 -9999 0 -10000 0 0
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.088 0.16 -9999 0 -0.45 27 27
HP -0.022 0.093 -9999 0 -0.28 22 22
leukocyte adhesion -0.18 0.22 -9999 0 -0.61 23 23
SELP -0.05 0.22 -9999 0 -0.81 15 15
TCGA08_p53

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
CDKN2A -0.15 0.08 -9999 0 -0.19 159 159
TP53 -0.051 0.025 -9999 0 -10000 0 0
Senescence -0.051 0.025 -9999 0 -10000 0 0
Apoptosis -0.051 0.025 -9999 0 -10000 0 0
Activated_Oncogenes 0 0 -9999 0 -10000 0 0
MDM2 0.094 0.047 -9999 0 -10000 0 0
MDM4 0.012 0 -9999 0 -10000 0 0
Endothelins

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
AKT1 -0.017 0.17 -10000 0 -0.6 10 10
PTK2B 0.012 0.001 -10000 0 -10000 0 0
mol:Ca2+ -0.26 0.47 -10000 0 -1 52 52
EDN1 0.002 0.081 -10000 0 -0.35 2 2
EDN3 0.007 0.021 -10000 0 -0.28 1 1
EDN2 -0.024 0.16 -10000 0 -0.71 10 10
HRAS/GDP -0.11 0.23 -10000 0 -0.53 31 31
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.1 0.22 -10000 0 -0.49 34 34
ADCY4 -0.036 0.19 -10000 0 -0.55 19 19
ADCY5 -0.032 0.17 -10000 0 -0.51 18 18
ADCY6 -0.008 0.14 -10000 0 -0.5 10 10
ADCY7 -0.013 0.14 -10000 0 -0.5 10 10
ADCY1 -0.23 0.28 -10000 0 -0.5 95 95
ADCY2 -0.082 0.16 -10000 0 -0.54 13 13
ADCY3 -0.008 0.14 -10000 0 -0.5 10 10
ADCY8 -0.016 0.14 -10000 0 -0.49 11 11
ADCY9 -0.008 0.14 -10000 0 -0.5 10 10
arachidonic acid secretion -0.15 0.29 -10000 0 -0.6 43 43
ETB receptor/Endothelin-1/Gq/GTP -0.072 0.18 -10000 0 -0.38 42 42
GNAO1 -0.051 0.21 -10000 0 -0.72 17 17
HRAS 0.011 0.003 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.026 0.17 0.35 11 -0.56 10 21
ETA receptor/Endothelin-1/Gs/GTP -0.025 0.16 0.32 11 -0.53 10 21
mol:GTP -0.003 0.007 -10000 0 -10000 0 0
COL3A1 -0.028 0.2 -10000 0 -0.71 11 11
EDNRB 0.005 0.083 -10000 0 -0.81 2 2
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.068 0.22 -10000 0 -0.68 15 15
CYSLTR1 -0.019 0.18 -10000 0 -0.65 10 10
SLC9A1 -0.02 0.087 0.2 4 -0.31 10 14
mol:GDP -0.12 0.24 -10000 0 -0.56 34 34
SLC9A3 -0.61 0.36 -10000 0 -0.72 165 165
RAF1 -0.14 0.26 -10000 0 -0.58 38 38
JUN -0.14 0.29 -10000 0 -0.74 23 23
JAK2 -0.017 0.17 -10000 0 -0.6 10 10
mol:IP3 -0.12 0.24 -10000 0 -0.53 37 37
ETA receptor/Endothelin-1 -0.039 0.21 0.41 11 -0.69 10 21
PLCB1 -0.056 0.22 -10000 0 -0.81 16 16
PLCB2 -0.029 0.099 -10000 0 -0.28 26 26
ETA receptor/Endothelin-3 -0.033 0.15 -10000 0 -0.66 9 9
FOS -0.18 0.38 -10000 0 -0.93 36 36
Gai/GDP -0.044 0.22 -10000 0 -0.83 14 14
CRK 0.012 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.26 -10000 0 -0.64 27 27
BCAR1 0.012 0.001 -10000 0 -10000 0 0
PRKCB1 -0.12 0.23 -10000 0 -0.52 37 37
GNAQ 0.009 0.007 -10000 0 -10000 0 0
GNAZ 0.012 0 -10000 0 -10000 0 0
GNAL 0.012 0 -10000 0 -10000 0 0
Gs family/GDP -0.13 0.19 -10000 0 -0.51 31 31
ETA receptor/Endothelin-1/Gq/GTP -0.1 0.26 -10000 0 -0.57 33 33
MAPK14 -0.071 0.16 -10000 0 -0.48 11 11
TRPC6 -0.28 0.51 -10000 0 -1.1 51 51
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.008 0.058 -10000 0 -0.81 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.083 0.17 -10000 0 -0.4 28 28
ETB receptor/Endothelin-2 -0.017 0.14 -10000 0 -0.62 10 10
ETB receptor/Endothelin-3 0.007 0.066 -10000 0 -0.63 2 2
ETB receptor/Endothelin-1 0.001 0.089 -10000 0 -0.66 2 2
MAPK3 -0.17 0.35 -10000 0 -0.82 38 38
MAPK1 -0.17 0.35 -10000 0 -0.82 38 38
Rac1/GDP -0.11 0.23 -10000 0 -0.53 31 31
cAMP biosynthetic process -0.13 0.19 -10000 0 -0.57 18 18
MAPK8 -0.18 0.36 -10000 0 -0.75 41 41
SRC 0.012 0.001 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP 0.004 0.091 -10000 0 -0.3 8 8
p130Cas/CRK/Src/PYK2 -0.16 0.29 -10000 0 -0.61 44 44
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.11 0.23 -10000 0 -0.54 30 30
COL1A2 -0.01 0.15 -10000 0 -0.53 6 6
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.057 0.2 -10000 0 -0.69 16 16
mol:DAG -0.12 0.24 -10000 0 -0.54 37 37
MAP2K2 -0.15 0.29 -10000 0 -0.63 42 42
MAP2K1 -0.15 0.29 -10000 0 -0.63 43 43
EDNRA -0.036 0.19 -10000 0 -0.8 10 10
positive regulation of muscle contraction -0.008 0.15 -10000 0 -0.52 10 10
Gq family/GDP -0.18 0.27 -10000 0 -0.64 44 44
HRAS/GTP -0.13 0.24 -10000 0 -0.56 36 36
PRKCH -0.11 0.23 -10000 0 -0.53 33 33
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCA -0.11 0.23 -10000 0 -0.53 33 33
PRKCB -0.11 0.23 -10000 0 -0.53 33 33
PRKCE -0.11 0.23 -10000 0 -0.53 33 33
PRKCD -0.11 0.23 -10000 0 -0.54 33 33
PRKCG -0.14 0.24 -10000 0 -0.57 37 37
regulation of vascular smooth muscle contraction -0.21 0.44 -10000 0 -1.1 36 36
PRKCQ -0.12 0.23 -10000 0 -0.53 36 36
PLA2G4A -0.17 0.32 -10000 0 -0.67 43 43
GNA14 -0.16 0.34 -10000 0 -0.82 42 42
GNA15 -0.008 0.071 -10000 0 -0.3 2 2
GNA12 0.012 0 -10000 0 -10000 0 0
GNA11 -0.007 0.12 -10000 0 -0.81 4 4
Rac1/GTP -0.026 0.17 0.35 11 -0.56 10 21
MMP1 -0.042 0.27 -10000 0 -1.1 11 11
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.003 0.1 -9999 0 -0.62 5 5
AKT1 -0.038 0.26 -9999 0 -0.61 34 34
PTK2B -0.1 0.32 -9999 0 -0.74 38 38
VEGFR2 homodimer/Frs2 -0.13 0.36 -9999 0 -0.91 34 34
CAV1 0.011 0.021 -9999 0 -0.28 1 1
CALM1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.15 0.32 -9999 0 -0.85 34 34
endothelial cell proliferation -0.024 0.25 -9999 0 -0.58 34 34
mol:Ca2+ -0.088 0.31 -9999 0 -0.76 34 34
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.14 0.31 -9999 0 -0.81 34 34
RP11-342D11.1 -0.096 0.31 -9999 0 -0.77 34 34
CDH5 0.012 0 -9999 0 -10000 0 0
VEGFA homodimer 0 0.008 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
SHC2 -0.007 0.098 -9999 0 -0.4 9 9
HRAS/GDP -0.11 0.25 -9999 0 -0.65 34 34
SH2D2A -0.024 0.097 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.11 0.24 -9999 0 -0.64 34 34
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.16 0.32 -9999 0 -0.86 34 34
VEGFR1 homodimer 0.004 0.082 -9999 0 -0.81 2 2
SHC/GRB2/SOS1 -0.13 0.28 -9999 0 -0.73 34 34
GRB10 -0.088 0.31 -9999 0 -0.76 34 34
PTPN11 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
PAK1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.13 0.29 -9999 0 -0.78 34 34
HRAS 0.012 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.034 0.17 -9999 0 -0.39 34 34
HIF1A 0.012 0 -9999 0 -10000 0 0
FRS2 0.012 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.14 0.3 -9999 0 -0.79 34 34
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 -0.009 0.13 -9999 0 -0.81 5 5
Nck/Pak 0.018 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.15 0.32 -9999 0 -0.85 34 34
mol:GDP -0.12 0.27 -9999 0 -0.7 34 34
mol:NADP -0.033 0.23 -9999 0 -0.54 34 34
eNOS/Hsp90 -0.024 0.22 -9999 0 -0.5 34 34
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 -0.091 0.31 -9999 0 -0.78 34 34
HIF1A/ARNT 0.018 0 -9999 0 -10000 0 0
SHB 0.012 0 -9999 0 -10000 0 0
VEGFA 0.012 0.021 -9999 0 -0.28 1 1
VEGFC 0.011 0.021 -9999 0 -0.28 1 1
FAK1/Vinculin -0.083 0.31 -9999 0 -0.76 34 34
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.15 0.32 -9999 0 -0.78 38 38
PTPN6 0.012 0 -9999 0 -10000 0 0
EPAS1 -0.052 0.17 -9999 0 -0.41 34 34
mol:L-citrulline -0.033 0.23 -9999 0 -0.54 34 34
ITGAV 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.14 0.31 -9999 0 -0.81 34 34
VEGFR2 homodimer/VEGFA homodimer -0.11 0.34 -9999 0 -0.84 34 34
VEGFR2/3 heterodimer -0.14 0.38 -9999 0 -0.93 36 36
VEGFB 0.012 0 -9999 0 -10000 0 0
MAPK11 -0.091 0.32 -9999 0 -0.8 34 34
VEGFR2 homodimer -0.15 0.4 -9999 0 -1 34 34
FLT1 0.004 0.082 -9999 0 -0.81 2 2
NEDD4 0.014 0.001 -9999 0 -10000 0 0
MAPK3 -0.073 0.28 -9999 0 -0.7 34 34
MAPK1 -0.073 0.28 -9999 0 -0.7 34 34
VEGFA145/NRP2 -0.003 0.05 -9999 0 -0.62 1 1
VEGFR1/2 heterodimer -0.13 0.37 -9999 0 -0.94 34 34
KDR -0.15 0.4 -9999 0 -1 34 34
VEGFA165/NRP1/VEGFR2 homodimer -0.096 0.31 -9999 0 -0.77 35 35
SRC 0.012 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.075 0.29 -9999 0 -0.71 34 34
PI3K -0.07 0.32 -9999 0 -0.76 34 34
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.15 0.32 -9999 0 -0.85 34 34
FES -0.093 0.32 -9999 0 -0.79 34 34
GAB1 -0.14 0.3 -9999 0 -0.78 34 34
VEGFR2 homodimer/VEGFA homodimer/Src -0.15 0.32 -9999 0 -0.85 34 34
CTNNB1 0.012 0 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
ARNT 0.012 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.025 0.22 -9999 0 -0.5 34 34
VEGFR2 homodimer/VEGFA homodimer/Yes -0.15 0.32 -9999 0 -0.85 34 34
PI3K/GAB1 -0.04 0.27 -9999 0 -0.63 34 34
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.13 0.29 -9999 0 -0.78 34 34
PRKACA 0.012 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.13 0.36 -9999 0 -0.87 36 36
HSP90AA1 0.012 0 -9999 0 -10000 0 0
CDC42 -0.093 0.32 -9999 0 -0.79 34 34
actin cytoskeleton reorganization -0.16 0.32 -9999 0 -0.85 34 34
PTK2 -0.099 0.34 -9999 0 -0.84 34 34
EDG1 -0.096 0.31 -9999 0 -0.77 34 34
mol:DAG -0.091 0.31 -9999 0 -0.78 34 34
CaM/Ca2+ -0.12 0.27 -9999 0 -0.71 34 34
MAP2K3 -0.085 0.32 -9999 0 -0.77 34 34
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.094 0.32 -9999 0 -0.8 34 34
PLCG1 -0.093 0.32 -9999 0 -0.79 34 34
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.14 0.31 -9999 0 -0.81 34 34
IQGAP1 0.012 0 -9999 0 -10000 0 0
YES1 0.012 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.15 0.32 -9999 0 -0.85 34 34
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.15 0.32 -9999 0 -0.85 34 34
cell migration -0.044 0.27 -9999 0 -0.63 34 34
mol:PI-3-4-5-P3 -0.059 0.29 -9999 0 -0.68 34 34
FYN 0.012 0 -9999 0 -10000 0 0
VEGFB/NRP1 -0.085 0.29 -9999 0 -0.73 34 34
mol:NO -0.033 0.23 -9999 0 -0.54 34 34
PXN 0.012 0 -9999 0 -10000 0 0
HRAS/GTP -0.11 0.25 -9999 0 -0.65 34 34
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.095 0.32 -9999 0 -0.8 34 34
VHL 0.012 0 -9999 0 -10000 0 0
ITGB3 -0.016 0.14 -9999 0 -0.55 10 10
NOS3 -0.046 0.27 -9999 0 -0.62 34 34
VEGFR2 homodimer/VEGFA homodimer/Sck -0.16 0.33 -9999 0 -0.85 36 36
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA -0.077 0.29 -9999 0 -0.72 34 34
PRKCB -0.079 0.29 -9999 0 -0.72 34 34
VCL 0.012 0 -9999 0 -10000 0 0
VEGFA165/NRP1 -0.096 0.31 -9999 0 -0.77 34 34
VEGFR1/2 heterodimer/VEGFA homodimer -0.15 0.33 -9999 0 -0.88 34 34
VEGFA165/NRP2 -0.003 0.05 -9999 0 -0.62 1 1
MAPKKK cascade -0.054 0.27 -9999 0 -0.65 34 34
NRP2 0.005 0.065 -9999 0 -0.46 3 3
VEGFC homodimer 0.011 0.021 -9999 0 -0.28 1 1
NCK1 0.012 0 -9999 0 -10000 0 0
ROCK1 0.012 0 -9999 0 -10000 0 0
FAK1/Paxillin -0.083 0.31 -9999 0 -0.76 34 34
MAP3K13 -0.097 0.33 -9999 0 -0.82 34 34
PDPK1 -0.041 0.25 -9999 0 -0.6 34 34
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.031 0.15 -10000 0 -0.38 29 29
CRKL -0.023 0.16 -10000 0 -0.4 29 29
HRAS -0.013 0.14 -10000 0 -0.43 6 6
mol:PIP3 -0.034 0.15 -10000 0 -0.39 29 29
SPRED1 0.012 0 -10000 0 -10000 0 0
SPRED2 0.012 0 -10000 0 -10000 0 0
GAB1 -0.032 0.17 -10000 0 -0.43 29 29
FOXO3 -0.015 0.14 -10000 0 -0.36 29 29
AKT1 -0.024 0.16 -10000 0 -0.4 29 29
BAD -0.015 0.14 -10000 0 -0.36 29 29
megakaryocyte differentiation -0.093 0.24 -10000 0 -0.48 50 50
GSK3B -0.015 0.14 -10000 0 -0.36 29 29
RAF1 -0.001 0.12 -10000 0 -0.41 2 2
SHC1 0.012 0 -10000 0 -10000 0 0
STAT3 -0.032 0.17 -10000 0 -0.43 29 29
STAT1 -0.095 0.38 -10000 0 -1 29 29
HRAS/SPRED1 -0.002 0.12 -10000 0 -0.41 2 2
cell proliferation -0.04 0.18 -10000 0 -0.45 31 31
PIK3CA 0.012 0 -10000 0 -10000 0 0
TEC 0.012 0 -10000 0 -10000 0 0
RPS6KB1 -0.031 0.16 -10000 0 -0.43 29 29
HRAS/SPRED2 -0.002 0.12 -10000 0 -0.41 2 2
LYN/TEC/p62DOK -0.059 0.14 -10000 0 -0.4 29 29
MAPK3 0.012 0.092 -10000 0 -0.28 2 2
STAP1 -0.3 0.28 -10000 0 -0.49 125 125
GRAP2 0.005 0.046 -10000 0 -0.28 5 5
JAK2 -0.12 0.3 -10000 0 -0.84 29 29
STAT1 (dimer) -0.092 0.37 -10000 0 -0.98 29 29
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.08 0.16 -10000 0 -0.44 30 30
actin filament polymerization -0.031 0.16 -10000 0 -0.42 29 29
LYN 0.012 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.29 0.31 -10000 0 -0.5 125 125
PIK3R1 0.012 0 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.008 0.15 -10000 0 -0.36 29 29
PI3K -0.018 0.16 -10000 0 -0.4 29 29
PTEN 0.012 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.12 0.46 -10000 0 -1.2 29 29
MAPK8 -0.041 0.19 -10000 0 -0.46 31 31
STAT3 (dimer) -0.031 0.16 -10000 0 -0.42 29 29
positive regulation of transcription 0.014 0.079 -10000 0 -0.23 2 2
mol:GDP -0.064 0.13 -10000 0 -0.49 6 6
PIK3C2B -0.032 0.17 -10000 0 -0.43 29 29
CBL/CRKL -0.015 0.15 -10000 0 -0.38 29 29
FER -0.032 0.17 -10000 0 -0.43 29 29
SH2B3 -0.032 0.17 -10000 0 -0.43 29 29
PDPK1 -0.025 0.14 -10000 0 -0.36 29 29
SNAI2 -0.067 0.22 -10000 0 -0.48 40 40
positive regulation of cell proliferation -0.06 0.28 -10000 0 -0.73 29 29
KITLG 0.01 0.031 -10000 0 -0.28 2 2
cell motility -0.06 0.28 -10000 0 -0.73 29 29
PTPN6 0.012 0.009 -10000 0 -10000 0 0
EPOR 0.006 0.11 -10000 0 -10000 0 0
STAT5A (dimer) -0.045 0.23 -10000 0 -0.6 29 29
SOCS1 0.002 0.085 -10000 0 -0.64 3 3
cell migration 0.044 0.18 0.46 31 -10000 0 31
SOS1 0.012 0 -10000 0 -10000 0 0
EPO 0.006 0.03 -10000 0 -0.28 2 2
VAV1 -0.046 0.13 -10000 0 -0.3 37 37
GRB10 -0.032 0.17 -10000 0 -0.43 29 29
PTPN11 0.012 0.006 -10000 0 -10000 0 0
SCF/KIT -0.041 0.17 -10000 0 -0.46 29 29
GO:0007205 0.001 0.009 -10000 0 -10000 0 0
MAP2K1 0.009 0.1 -10000 0 -0.31 2 2
CBL 0.012 0 -10000 0 -10000 0 0
KIT -0.15 0.49 -10000 0 -1.3 29 29
MAP2K2 0.009 0.1 -10000 0 -0.31 2 2
SHC/Grb2/SOS1 -0.058 0.14 -10000 0 -0.4 29 29
STAT5A -0.047 0.24 -10000 0 -0.62 29 29
GRB2 0.012 0 -10000 0 -10000 0 0
response to radiation -0.065 0.21 -10000 0 -0.47 40 40
SHC/GRAP2 0.013 0.031 -10000 0 -10000 0 0
PTPRO -0.095 0.24 -10000 0 -0.49 50 50
SH2B2 -0.032 0.17 -10000 0 -0.43 29 29
DOK1 0.011 0.021 -10000 0 -0.28 1 1
MATK -0.046 0.19 -10000 0 -0.46 31 31
CREBBP 0.031 0.013 -10000 0 -10000 0 0
BCL2 0.007 0.11 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.009 0.075 -10000 0 -0.4 5 5
NFATC2 -0.033 0.22 -10000 0 -0.74 14 14
NFATC3 -0.027 0.11 -10000 0 -0.31 12 12
CD40LG -0.2 0.44 -10000 0 -1 32 32
ITCH 0.038 0.046 -10000 0 -10000 0 0
CBLB 0.038 0.046 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.18 0.24 -10000 0 -0.82 9 9
JUNB 0.012 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.048 -10000 0 -0.34 4 4
T cell anergy 0.015 0.078 -10000 0 -0.44 4 4
TLE4 -0.001 0.16 -10000 0 -0.55 13 13
Jun/NFAT1-c-4/p21SNFT -0.15 0.37 -10000 0 -1 24 24
AP-1/NFAT1-c-4 -0.24 0.54 -10000 0 -1.3 33 33
IKZF1 -0.012 0.17 -10000 0 -0.55 14 14
T-helper 2 cell differentiation -0.48 0.32 -10000 0 -0.74 91 91
AP-1/NFAT1 -0.13 0.24 -10000 0 -0.58 41 41
CALM1 0.022 0.029 -10000 0 -10000 0 0
EGR2 -0.17 0.54 -10000 0 -1.6 22 22
EGR3 -0.2 0.59 -10000 0 -1.6 27 27
NFAT1/FOXP3 -0.031 0.18 -10000 0 -0.55 16 16
EGR1 -0.054 0.22 -10000 0 -0.81 16 16
JUN 0.008 0.016 -10000 0 -10000 0 0
EGR4 0.006 0.022 -10000 0 -0.28 1 1
mol:Ca2+ 0.01 0.031 -10000 0 -10000 0 0
GBP3 -0.001 0.16 -10000 0 -0.55 13 13
FOSL1 0.006 0.042 -10000 0 -10000 0 0
NFAT1-c-4/MAF/IRF4 -0.14 0.37 -10000 0 -0.91 30 30
DGKA -0.008 0.17 -10000 0 -0.54 14 14
CREM 0.012 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.16 0.38 -10000 0 -0.93 33 33
CTLA4 -0.042 0.19 -10000 0 -0.56 12 12
NFAT1-c-4 (dimer)/EGR1 -0.17 0.46 -10000 0 -1.1 34 34
NFAT1-c-4 (dimer)/EGR4 -0.14 0.39 -10000 0 -0.94 32 32
FOS -0.12 0.3 -10000 0 -0.83 31 31
IFNG -0.09 0.18 -10000 0 -0.62 12 12
T cell activation -0.098 0.28 -10000 0 -0.76 21 21
MAF 0.012 0 -10000 0 -10000 0 0
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.085 0.3 0.76 25 -10000 0 25
TNF -0.14 0.41 -10000 0 -1 28 28
FASLG -0.2 0.56 -10000 0 -1.4 32 32
TBX21 0.001 0.06 -10000 0 -0.3 7 7
BATF3 0.011 0.021 -10000 0 -10000 0 0
PRKCQ 0 0.1 -10000 0 -0.81 3 3
PTPN1 -0.001 0.16 -10000 0 -0.55 13 13
NFAT1-c-4/ICER1 -0.16 0.38 -10000 0 -0.93 33 33
GATA3 -0.6 0.36 -10000 0 -0.81 147 147
T-helper 1 cell differentiation -0.06 0.19 -10000 0 -0.6 13 13
IL2RA -0.16 0.23 -10000 0 -0.79 8 8
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.003 0.16 -10000 0 -0.55 13 13
E2F1 -0.075 0.14 -10000 0 -0.28 62 62
PPARG 0.012 0 -10000 0 -10000 0 0
SLC3A2 -0.001 0.16 -10000 0 -0.55 13 13
IRF4 -0.007 0.073 -10000 0 -0.28 13 13
PTGS2 -0.24 0.51 -10000 0 -1.2 38 38
CSF2 -0.2 0.44 -10000 0 -1 32 32
JunB/Fra1/NFAT1-c-4 -0.14 0.37 -10000 0 -0.92 29 29
IL4 -0.51 0.34 -10000 0 -0.8 86 86
IL5 -0.2 0.44 -10000 0 -1 32 32
IL2 -0.1 0.28 -10000 0 -0.79 19 19
IL3 -0.042 0.057 -10000 0 -10000 0 0
RNF128 0.025 0.13 -10000 0 -0.87 4 4
NFATC1 -0.085 0.3 -10000 0 -0.77 24 24
CDK4 0.028 0.19 0.55 1 -10000 0 1
PTPRK -0.001 0.16 -10000 0 -0.55 13 13
IL8 -0.22 0.44 -10000 0 -1 35 35
POU2F1 0.012 0 -10000 0 -10000 0 0
Integrins in angiogenesis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.093 0.24 -9999 0 -0.62 34 34
alphaV beta3 Integrin -0.017 0.087 -9999 0 -0.54 5 5
PTK2 -0.16 0.27 -9999 0 -0.57 48 48
IGF1R 0.012 0 -9999 0 -10000 0 0
PI4KB 0.012 0 -9999 0 -10000 0 0
MFGE8 0.012 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
CDKN1B -0.22 0.29 -9999 0 -0.6 70 70
VEGFA 0.011 0.021 -9999 0 -0.28 1 1
ILK -0.22 0.29 -9999 0 -0.6 70 70
ROCK1 0.012 0 -9999 0 -10000 0 0
AKT1 -0.18 0.28 -9999 0 -0.56 69 69
PTK2B -0.065 0.2 -9999 0 -0.47 38 38
alphaV/beta3 Integrin/JAM-A -0.16 0.25 -9999 0 -0.48 72 72
CBL 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.38 0.26 -9999 0 -0.55 135 135
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.009 0.1 -9999 0 -0.49 8 8
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.14 0.23 -9999 0 -0.36 88 88
alphaV/beta3 Integrin/Syndecan-1 -0.021 0.098 -9999 0 -0.56 6 6
PI4KA 0.012 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.036 0.11 -9999 0 -0.43 13 13
PI4 Kinase 0.018 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.029 0.11 -9999 0 -0.54 8 8
RPS6KB1 0.011 0.12 -9999 0 -0.4 13 13
TLN1 0.012 0 -9999 0 -10000 0 0
MAPK3 -0.061 0.14 -9999 0 -0.64 5 5
GPR124 0.008 0.058 -9999 0 -0.81 1 1
MAPK1 -0.061 0.14 -9999 0 -0.64 5 5
PXN 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.044 0.15 -9999 0 -0.57 14 14
cell adhesion -0.29 0.21 -9999 0 -0.43 135 135
ANGPTL3 -0.54 0.38 -9999 0 -0.81 133 133
VEGFR2 homodimer/VEGFA homodimer/Src -0.093 0.2 -9999 0 -0.54 34 34
IGF-1R heterotetramer 0.012 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
TGFBR2 0.012 0 -9999 0 -10000 0 0
ITGB3 -0.016 0.14 -9999 0 -0.55 10 10
IGF1 -0.009 0.13 -9999 0 -0.81 5 5
RAC1 0.012 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.02 0.094 -9999 0 -0.54 6 6
apoptosis 0.012 0 -9999 0 -10000 0 0
CD47 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.017 0.087 -9999 0 -0.54 5 5
VCL 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.074 0.18 -9999 0 -0.57 23 23
CSF1 0.005 0.065 -9999 0 -0.81 1 1
PIK3C2A -0.22 0.29 -9999 0 -0.6 70 70
PI4 Kinase/Pyk2 -0.21 0.26 -9999 0 -0.75 22 22
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.076 0.21 -9999 0 -0.51 38 38
FAK1/Vinculin -0.12 0.21 -9999 0 -0.51 27 27
alphaV beta3/Integrin/ppsTEM5 -0.02 0.094 -9999 0 -0.54 6 6
RHOA 0.012 0 -9999 0 -10000 0 0
VTN -0.28 0.39 -9999 0 -0.78 74 74
BCAR1 0.012 0 -9999 0 -10000 0 0
FGF2 0.012 0 -9999 0 -10000 0 0
F11R 0.021 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Lactadherin -0.017 0.087 -9999 0 -0.54 5 5
alphaV/beta3 Integrin/TGFBR2 -0.017 0.087 -9999 0 -0.54 5 5
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.027 0.04 -9999 0 -0.49 1 1
HSP90AA1 0.012 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.007 0.084 -9999 0 -0.5 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.009 0.076 -9999 0 -0.28 14 14
alphaV/beta3 Integrin/Pyk2 -0.064 0.2 -9999 0 -0.47 38 38
SDC1 0.006 0.062 -9999 0 -0.55 2 2
VAV3 0.032 0.037 -9999 0 -0.46 1 1
PTPN11 0.012 0 -9999 0 -10000 0 0
IRS1 -0.002 0.1 -9999 0 -0.68 4 4
FAK1/Paxillin -0.12 0.21 -9999 0 -0.52 26 26
cell migration -0.1 0.2 -9999 0 -0.47 25 25
ITGAV 0.012 0 -9999 0 -10000 0 0
PI3K -0.16 0.21 -9999 0 -0.43 72 72
SPP1 -0.008 0.11 -9999 0 -0.81 3 3
KDR -0.13 0.31 -9999 0 -0.81 34 34
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.012 0 -9999 0 -10000 0 0
COL4A3 -0.03 0.18 -9999 0 -0.81 10 10
angiogenesis -0.1 0.19 -9999 0 -0.6 7 7
Rac1/GTP -0.003 0.031 -9999 0 -0.42 1 1
EDIL3 -0.079 0.25 -9999 0 -0.66 27 27
cell proliferation -0.017 0.086 -9999 0 -0.54 5 5
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 -0.069 0.44 -9999 0 -0.94 19 19
PLK1 -0.019 0.16 -9999 0 -10000 0 0
BIRC5 -0.076 0.18 -9999 0 -10000 0 0
HSPA1B -0.069 0.44 -9999 0 -0.94 19 19
MAP2K1 0.022 0.037 -9999 0 -10000 0 0
BRCA2 -0.074 0.44 -9999 0 -0.96 22 22
FOXM1 -0.1 0.5 -9999 0 -1.1 26 26
XRCC1 -0.069 0.44 -9999 0 -0.94 19 19
FOXM1B/p19 -0.15 0.39 -9999 0 -0.9 25 25
Cyclin D1/CDK4 -0.058 0.41 -9999 0 -0.9 16 16
CDC2 -0.079 0.45 -9999 0 -0.94 25 25
TGFA -0.054 0.41 -9999 0 -0.9 18 18
SKP2 -0.069 0.44 -9999 0 -0.95 18 18
CCNE1 -0.008 0.08 -9999 0 -10000 0 0
CKS1B -0.069 0.44 -9999 0 -0.92 21 21
RB1 -0.1 0.16 -9999 0 -0.52 7 7
FOXM1C/SP1 -0.089 0.46 -9999 0 -1 24 24
AURKB -0.086 0.18 -9999 0 -10000 0 0
CENPF -0.089 0.47 -9999 0 -0.97 27 27
CDK4 0.016 0.014 -9999 0 -10000 0 0
MYC -0.051 0.4 -9999 0 -0.84 18 18
CHEK2 0.001 0.087 -9999 0 -0.32 8 8
ONECUT1 -0.068 0.43 -9999 0 -0.92 20 20
CDKN2A -0.22 0.12 -9999 0 -0.28 159 159
LAMA4 -0.076 0.44 -9999 0 -0.94 20 20
FOXM1B/HNF6 -0.088 0.47 -9999 0 -1.1 21 21
FOS -0.19 0.59 -9999 0 -1.1 42 42
SP1 0.013 0.002 -9999 0 -10000 0 0
CDC25B -0.07 0.44 -9999 0 -0.95 19 19
response to radiation 0.008 0.034 -9999 0 -10000 0 0
CENPB -0.069 0.44 -9999 0 -0.96 17 17
CENPA -0.1 0.47 -9999 0 -0.96 29 29
NEK2 -0.097 0.47 -9999 0 -1 24 24
HIST1H2BA -0.075 0.44 -9999 0 -0.97 17 17
CCNA2 -0.038 0.12 -9999 0 -0.3 34 34
EP300 0.012 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.091 0.47 -9999 0 -1 21 21
CCNB2 -0.099 0.47 -9999 0 -0.99 26 26
CCNB1 -0.078 0.45 -9999 0 -0.97 22 22
ETV5 -0.069 0.44 -9999 0 -0.94 19 19
ESR1 -0.11 0.5 -9999 0 -1 29 29
CCND1 -0.058 0.42 -9999 0 -0.9 18 18
GSK3A 0.023 0.03 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.006 0.11 -9999 0 -10000 0 0
CDK2 0.013 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.008 0.04 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.22 0.34 -9999 0 -0.94 26 26
GAS1 -0.1 0.48 -9999 0 -0.99 29 29
MMP2 -0.074 0.44 -9999 0 -0.95 21 21
RB1/FOXM1C -0.064 0.44 -9999 0 -0.98 18 18
CREBBP 0.012 0 -9999 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.43 0.42 -10000 0 -1.1 32 32
STAT6 (cleaved dimer) -0.46 0.39 -10000 0 -0.99 54 54
IGHG1 -0.16 0.15 -10000 0 -0.46 2 2
IGHG3 -0.42 0.4 -10000 0 -0.97 52 52
AKT1 -0.2 0.2 -10000 0 -0.65 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.15 0.15 -10000 0 -0.57 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.21 0.2 -10000 0 -0.72 5 5
THY1 -0.66 0.65 -10000 0 -1.5 66 66
MYB -0.057 0.12 -10000 0 -0.28 46 46
HMGA1 0.003 0.051 -10000 0 -0.28 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.26 0.24 -10000 0 -0.63 24 24
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.21 0.2 -10000 0 -0.61 4 4
SP1 0.019 0.003 -10000 0 -10000 0 0
INPP5D 0.003 0.051 -10000 0 -0.28 6 6
SOCS5 0.024 0.012 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.43 0.4 -10000 0 -1.1 42 42
SOCS1 -0.28 0.28 -10000 0 -0.74 30 30
SOCS3 -0.22 0.22 -10000 0 -0.98 3 3
FCER2 -0.34 0.32 -10000 0 -0.82 33 33
PARP14 0.012 0.003 -10000 0 -10000 0 0
CCL17 -0.46 0.42 -10000 0 -1.1 40 40
GRB2 0.012 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.17 0.17 -10000 0 -0.58 2 2
T cell proliferation -0.42 0.42 -10000 0 -1.1 36 36
IL4R/JAK1 -0.43 0.42 -10000 0 -1.1 35 35
EGR2 -0.5 0.54 -10000 0 -1.4 42 42
JAK2 -0.01 0.026 -10000 0 -10000 0 0
JAK3 -0.043 0.12 -10000 0 -0.3 3 3
PIK3R1 0.012 0 -10000 0 -10000 0 0
JAK1 0.004 0.01 -10000 0 -10000 0 0
COL1A2 -0.14 0.14 -10000 0 -10000 0 0
CCL26 -0.44 0.42 -10000 0 -1.1 35 35
IL4R -0.46 0.44 -10000 0 -1.2 36 36
PTPN6 0.024 0.011 -10000 0 -10000 0 0
IL13RA2 -0.88 0.68 -10000 0 -1.4 113 113
IL13RA1 -0.01 0.026 -10000 0 -10000 0 0
IRF4 -0.091 0.12 -10000 0 -0.61 1 1
ARG1 -0.13 0.13 -10000 0 -10000 0 0
CBL -0.24 0.22 -10000 0 -0.62 16 16
GTF3A 0.018 0.007 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.015 0.037 -10000 0 -10000 0 0
IRF4/BCL6 -0.079 0.11 -10000 0 -0.55 1 1
CD40LG 0.008 0.058 -10000 0 -0.29 7 7
MAPK14 -0.24 0.23 -10000 0 -0.73 8 8
mitosis -0.19 0.19 -10000 0 -0.62 5 5
STAT6 -0.49 0.48 -10000 0 -1.2 46 46
SPI1 -0.041 0.12 -10000 0 -10000 0 0
RPS6KB1 -0.18 0.19 -10000 0 -0.61 4 4
STAT6 (dimer) -0.49 0.48 -10000 0 -1.2 46 46
STAT6 (dimer)/PARP14 -0.45 0.44 -10000 0 -1.1 41 41
mast cell activation 0.012 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.21 0.2 -10000 0 -0.65 6 6
FRAP1 -0.2 0.2 -10000 0 -0.65 5 5
LTA -0.44 0.42 -10000 0 -1.1 35 35
FES 0.012 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0.48 0.47 1.1 47 -10000 0 47
CCL11 -0.5 0.52 -10000 0 -1.3 47 47
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.2 0.19 -10000 0 -0.61 6 6
IL2RG 0.008 0.052 -10000 0 -0.3 1 1
IL10 -0.44 0.42 -10000 0 -1.1 36 36
IRS1 -0.002 0.1 -10000 0 -0.68 4 4
IRS2 0.011 0.021 -10000 0 -0.28 1 1
IL4 -0.11 0.1 -10000 0 -10000 0 0
IL5 -0.44 0.42 -10000 0 -1.1 35 35
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.36 0.33 -10000 0 -0.85 36 36
COL1A1 -0.16 0.16 -10000 0 -0.56 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.43 0.43 -10000 0 -1.2 30 30
IL2R gamma/JAK3 -0.024 0.097 -10000 0 -0.37 5 5
TFF3 -0.55 0.57 -10000 0 -1.4 51 51
ALOX15 -0.44 0.42 -10000 0 -1.1 35 35
MYBL1 -0.007 0.073 -10000 0 -0.28 13 13
T-helper 2 cell differentiation -0.36 0.33 -10000 0 -0.86 37 37
SHC1 0.012 0 -10000 0 -10000 0 0
CEBPB 0.009 0.042 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.2 0.19 -10000 0 -0.56 6 6
mol:PI-3-4-5-P3 -0.2 0.2 -10000 0 -0.65 5 5
PI3K -0.2 0.21 -10000 0 -0.69 5 5
DOK2 -0.01 0.091 -10000 0 -0.32 13 13
ETS1 0.025 0.011 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.16 0.16 -10000 0 -0.56 2 2
ITGB3 -0.46 0.45 -10000 0 -1.1 43 43
PIGR -0.48 0.47 -10000 0 -1.2 39 39
IGHE 0.036 0.043 -10000 0 -10000 0 0
MAPKKK cascade -0.16 0.16 -10000 0 -0.55 2 2
BCL6 0.01 0.021 -10000 0 -0.28 1 1
OPRM1 -0.44 0.42 -10000 0 -1.1 36 36
RETNLB -0.44 0.42 -10000 0 -1.1 36 36
SELP -0.48 0.52 -10000 0 -1.3 37 37
AICDA -0.44 0.41 -10000 0 -1.1 44 44
Signaling events mediated by PTP1B

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.021 0.16 -10000 0 -0.81 8 8
Jak2/Leptin Receptor -0.17 0.16 -10000 0 -0.34 89 89
PTP1B/AKT1 -0.078 0.071 -10000 0 -0.31 3 3
FYN 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B -0.096 0.079 -10000 0 -0.33 15 15
EGFR 0.001 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.44 0.14 -10000 0 -0.48 178 178
CSF1 0.005 0.065 -10000 0 -0.81 1 1
AKT1 0.012 0.001 -10000 0 -10000 0 0
INSR 0.012 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.1 0.14 -10000 0 -0.45 21 21
Insulin Receptor/Insulin -0.051 0.052 -10000 0 -10000 0 0
HCK -0.026 0.11 -10000 0 -0.31 24 24
CRK 0.012 0 -10000 0 -10000 0 0
TYK2 -0.084 0.076 -10000 0 -0.31 15 15
EGF -0.73 0.25 -10000 0 -0.82 178 178
YES1 0.012 0 -10000 0 -10000 0 0
CAV1 -0.18 0.082 -10000 0 -0.37 16 16
TXN 0 0.021 -10000 0 -0.29 1 1
PTP1B/IRS1/GRB2 -0.082 0.092 -10000 0 -0.34 17 17
cell migration 0.096 0.079 0.33 15 -10000 0 15
STAT3 0.011 0.001 -10000 0 -10000 0 0
PRLR -0.36 0.41 -10000 0 -0.81 90 90
ITGA2B -0.009 0.073 -10000 0 -0.28 13 13
CSF1R -0.001 0.077 -10000 0 -0.36 7 7
Prolactin Receptor/Prolactin -0.29 0.31 -10000 0 -0.63 90 90
FGR -0.001 0.077 -10000 0 -0.36 7 7
PTP1B/p130 Cas -0.084 0.076 -10000 0 -0.31 15 15
Crk/p130 Cas -0.074 0.074 -10000 0 -0.3 14 14
DOK1 -0.077 0.088 -10000 0 -0.34 10 10
JAK2 -0.18 0.17 -10000 0 -0.36 88 88
Jak2/Leptin Receptor/Leptin -0.11 0.1 -10000 0 -0.57 3 3
PIK3R1 0.012 0 -10000 0 -10000 0 0
PTPN1 -0.096 0.08 -10000 0 -0.34 15 15
LYN 0.012 0 -10000 0 -10000 0 0
CDH2 -0.024 0.16 -10000 0 -0.71 10 10
SRC -0.025 0.029 -10000 0 -10000 0 0
ITGB3 -0.018 0.14 -10000 0 -0.55 10 10
CAT1/PTP1B -0.24 0.13 -10000 0 -0.42 37 37
CAPN1 0.01 0.002 -10000 0 -10000 0 0
CSK 0.012 0 -10000 0 -10000 0 0
PI3K -0.037 0.048 -10000 0 -10000 0 0
mol:H2O2 -0.007 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.096 0.095 -10000 0 -0.56 3 3
negative regulation of transcription -0.18 0.16 -10000 0 -0.35 88 88
FCGR2A 0 0.058 -10000 0 -0.28 8 8
FER 0.001 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.032 0.11 -10000 0 -0.63 5 5
BLK -0.004 0.065 -10000 0 -0.28 10 10
Insulin Receptor/Insulin/Shc 0 0 -10000 0 -10000 0 0
RHOA 0.01 0.002 -10000 0 -10000 0 0
LEPR 0.008 0.058 -10000 0 -0.81 1 1
BCAR1 0.012 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.012 0 -10000 0 -10000 0 0
mol:NADPH -0.007 0.003 -10000 0 -10000 0 0
TRPV6 -0.19 0.14 -10000 0 -0.38 24 24
PRL -0.001 0.021 -10000 0 -0.28 1 1
SOCS3 0.022 0.11 -10000 0 -1.4 1 1
SPRY2 0.004 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.009 0.068 -10000 0 -0.55 3 3
CSF1/CSF1R -0.084 0.097 -10000 0 -0.51 4 4
Ras protein signal transduction 0.045 0.021 -10000 0 -10000 0 0
IRS1 -0.002 0.1 -10000 0 -0.68 4 4
INS 0.001 0.002 -10000 0 -10000 0 0
LEP -0.02 0.086 -10000 0 -0.28 19 19
STAT5B -0.13 0.098 -10000 0 -0.34 19 19
STAT5A -0.13 0.098 -10000 0 -0.34 19 19
GRB2 0.012 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.1 0.12 -10000 0 -0.4 22 22
CSN2 -0.075 0.11 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
LAT -0.039 0.045 -10000 0 -10000 0 0
YBX1 0.015 0.002 -10000 0 -10000 0 0
LCK 0.005 0.046 -10000 0 -0.28 5 5
SHC1 0.012 0 -10000 0 -10000 0 0
NOX4 -0.08 0.25 -10000 0 -0.82 20 20
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer -0.095 0.24 -9999 0 -0.62 34 34
PDGFRB -0.023 0.16 -9999 0 -0.82 8 8
SPHK1 -0.059 0.056 -9999 0 -10000 0 0
mol:S1P -0.056 0.057 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.094 0.23 -9999 0 -0.57 26 26
GNAO1 -0.052 0.22 -9999 0 -0.72 17 17
PDGFB-D/PDGFRB/PLCgamma1 -0.082 0.22 -9999 0 -0.58 23 23
PLCG1 -0.083 0.21 -9999 0 -0.61 18 18
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.023 0.16 -9999 0 -0.82 8 8
GNAI2 0.011 0.005 -9999 0 -10000 0 0
GNAI3 0.01 0.005 -9999 0 -10000 0 0
GNAI1 0.006 0.058 -9999 0 -0.81 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.082 0.21 -9999 0 -0.54 34 34
S1P1/S1P -0.12 0.18 -9999 0 -0.48 34 34
negative regulation of cAMP metabolic process -0.091 0.22 -9999 0 -0.55 26 26
MAPK3 -0.11 0.27 -9999 0 -0.66 33 33
calcium-dependent phospholipase C activity -0.001 0.004 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
KDR -0.13 0.31 -9999 0 -0.81 34 34
PLCB2 -0.1 0.17 -9999 0 -0.44 34 34
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.098 0.15 -9999 0 -0.4 34 34
receptor internalization -0.11 0.16 -9999 0 -0.45 34 34
PTGS2 -0.16 0.41 -9999 0 -1 33 33
Rac1/GTP -0.098 0.15 -9999 0 -0.4 34 34
RHOA 0.012 0 -9999 0 -10000 0 0
VEGFA 0.01 0.021 -9999 0 -0.28 1 1
negative regulation of T cell proliferation -0.091 0.22 -9999 0 -0.55 26 26
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.01 0.005 -9999 0 -10000 0 0
MAPK1 -0.11 0.27 -9999 0 -0.66 33 33
S1P1/S1P/PDGFB-D/PDGFRB -0.11 0.22 -9999 0 -0.52 36 36
ABCC1 0.011 0.003 -9999 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0 0.098 -10000 0 -0.33 16 16
epithelial cell differentiation -0.037 0.12 -10000 0 -0.46 16 16
CYFIP2 0.012 0 -10000 0 -10000 0 0
ENAH 0.033 0.089 -10000 0 -10000 0 0
EGFR 0.012 0 -10000 0 -10000 0 0
EPHA2 0.011 0.021 -10000 0 -0.28 1 1
MYO6 -0.003 0.13 -10000 0 -0.44 16 16
CTNNB1 0.012 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0 0 -10000 0 -10000 0 0
AQP5 -0.092 0.21 -10000 0 -0.63 21 21
CTNND1 0.012 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.003 0.13 -10000 0 -0.43 16 16
regulation of calcium-dependent cell-cell adhesion -0.04 0.19 -10000 0 -0.48 29 29
EGF -0.73 0.25 -10000 0 -0.81 178 178
NCKAP1 0.012 0 -10000 0 -10000 0 0
AQP3 -0.22 0.3 -10000 0 -0.63 65 65
cortical microtubule organization -0.037 0.12 -10000 0 -0.46 16 16
GO:0000145 -0.003 0.12 -10000 0 -0.41 16 16
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.038 0.13 -10000 0 -0.47 16 16
MLLT4 0.012 0 -10000 0 -10000 0 0
ARF6/GDP -0.029 0.098 -10000 0 -10000 0 0
ARF6 0.012 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.03 0.011 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.009 0.12 -10000 0 -0.4 16 16
PVRL2 0.012 0 -10000 0 -10000 0 0
ZYX -0.003 0.13 -10000 0 -0.44 16 16
ARF6/GTP -0.001 0.007 -10000 0 -10000 0 0
CDH1 -0.054 0.22 -10000 0 -0.81 16 16
EGFR/EGFR/EGF/EGF -0.42 0.17 -10000 0 -0.46 180 180
RhoA/GDP -0.035 0.12 -10000 0 -0.43 16 16
actin cytoskeleton organization 0.003 0.12 -10000 0 -0.41 16 16
IGF-1R heterotetramer 0.012 0 -10000 0 -10000 0 0
GIT1 0.012 0 -10000 0 -10000 0 0
IGF1R 0.012 0 -10000 0 -10000 0 0
IGF1 -0.009 0.13 -10000 0 -0.81 5 5
DIAPH1 -0.002 0.007 -10000 0 -10000 0 0
Wnt receptor signaling pathway 0.037 0.12 0.46 16 -10000 0 16
RHOA 0.012 0 -10000 0 -10000 0 0
RhoA/GTP -0.03 0.1 -10000 0 -10000 0 0
CTNNA1 0.012 0 -10000 0 -10000 0 0
VCL 0.003 0.13 -10000 0 -0.42 16 16
EFNA1 0.012 0 -10000 0 -10000 0 0
LPP 0.004 0.12 -10000 0 -0.41 16 16
Ephrin A1/EPHA2 -0.034 0.11 -10000 0 -0.42 16 16
SEC6/SEC8 -0.031 0.1 -10000 0 -0.38 16 16
MGAT3 -0.041 0.19 -10000 0 -0.49 29 29
HGF/MET -0.063 0.15 -10000 0 -0.45 24 24
HGF -0.025 0.17 -10000 0 -0.81 9 9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0 0.098 -10000 0 -0.33 16 16
actin cable formation 0.049 0.086 -10000 0 -10000 0 0
KIAA1543 0.002 0.13 -10000 0 -0.41 17 17
KIFC3 -0.003 0.13 -10000 0 -0.44 16 16
NCK1 0.012 0 -10000 0 -10000 0 0
EXOC3 0.012 0 -10000 0 -10000 0 0
ACTN1 -0.003 0.13 -10000 0 -0.44 16 16
NCK1/GIT1 0.018 0 -10000 0 -10000 0 0
mol:GDP -0.037 0.12 -10000 0 -0.46 16 16
EXOC4 0.012 0 -10000 0 -10000 0 0
STX4 -0.003 0.13 -10000 0 -0.44 16 16
PIP5K1C -0.003 0.13 -10000 0 -0.44 16 16
LIMA1 0.012 0 -10000 0 -10000 0 0
ABI1 0.012 0 -10000 0 -10000 0 0
ROCK1 0.026 0.1 -10000 0 -10000 0 0
adherens junction assembly 0.019 0.12 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.045 0.13 -10000 0 -0.42 21 21
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.018 0 -10000 0 -10000 0 0
MET -0.021 0.093 -10000 0 -0.28 22 22
PLEKHA7 -0.006 0.13 -10000 0 -0.44 17 17
mol:GTP -0.001 0.008 -10000 0 -10000 0 0
establishment of epithelial cell apical/basal polarity 0.023 0.12 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization 0 0.098 -10000 0 -0.33 16 16
regulation of cell-cell adhesion 0.003 0.12 -10000 0 -0.41 16 16
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0 0.098 -10000 0 -0.33 16 16
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.012 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.038 0.12 -10000 0 -0.34 5 5
NT3 (dimer)/TRKC -0.16 0.31 -10000 0 -0.67 51 51
NT3 (dimer)/TRKB -0.31 0.32 -10000 0 -0.6 103 103
SHC/Grb2/SOS1/GAB1/PI3K 0.035 0 -10000 0 -10000 0 0
RAPGEF1 0.012 0 -10000 0 -10000 0 0
BDNF -0.025 0.098 -10000 0 -0.28 25 25
PIK3CA 0.012 0 -10000 0 -10000 0 0
DYNLT1 0.012 0 -10000 0 -10000 0 0
NTRK1 -0.14 0.32 -10000 0 -0.81 37 37
NTRK2 -0.33 0.41 -10000 0 -0.81 82 82
NTRK3 -0.1 0.28 -10000 0 -0.81 27 27
NT-4/5 (dimer)/TRKB -0.25 0.28 -10000 0 -0.56 85 85
neuron apoptosis 0.16 0.19 0.54 26 -10000 0 26
SHC 2-3/Grb2 -0.16 0.22 -10000 0 -0.61 26 26
SHC1 0.012 0 -10000 0 -10000 0 0
SHC2 -0.15 0.19 -10000 0 -0.55 24 24
SHC3 -0.16 0.22 -10000 0 -0.61 27 27
STAT3 (dimer) 0.02 0 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.19 0.32 -10000 0 -0.64 59 59
RIN/GDP -0.022 0.091 -10000 0 -0.28 3 3
GIPC1 0.012 0 -10000 0 -10000 0 0
KRAS 0.012 0 -10000 0 -10000 0 0
DNAJA3 -0.078 0.16 -10000 0 -0.64 6 6
RIN/GTP 0 0.014 -10000 0 -10000 0 0
CCND1 0.028 0 -10000 0 -10000 0 0
MAGED1 0.012 0 -10000 0 -10000 0 0
PTPN11 0.012 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.026 0.091 -10000 0 -0.28 22 22
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.13 0.23 -10000 0 -0.55 45 45
TRKA/NEDD4-2 -0.11 0.25 -10000 0 -0.62 38 38
ELMO1 0.012 0 -10000 0 -10000 0 0
RhoG/GTP/ELMO1/DOCK1 0 0 -10000 0 -10000 0 0
NGF -0.015 0.14 -10000 0 -0.81 6 6
HRAS 0.012 0 -10000 0 -10000 0 0
DOCK1 0.012 0 -10000 0 -10000 0 0
GAB2 0.012 0 -10000 0 -10000 0 0
RIT2 0 0.02 -10000 0 -0.28 1 1
RIT1 0.012 0 -10000 0 -10000 0 0
FRS2 0.012 0 -10000 0 -10000 0 0
DNM1 -0.069 0.13 -10000 0 -0.28 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.076 0.15 -10000 0 -0.63 6 6
mol:GDP -0.034 0.13 -10000 0 -0.42 4 4
NGF (dimer) -0.015 0.14 -10000 0 -0.81 6 6
RhoG/GDP 0.009 0 -10000 0 -10000 0 0
RIT1/GDP -0.017 0.092 -10000 0 -0.29 2 2
TIAM1 0.012 0 -10000 0 -10000 0 0
PIK3R1 0.012 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.24 0.26 -10000 0 -0.55 82 82
KIDINS220/CRKL/C3G 0.018 0 -10000 0 -10000 0 0
SHC/RasGAP 0.018 0 -10000 0 -10000 0 0
FRS2 family/SHP2 -0.002 0.017 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.031 0 -10000 0 -10000 0 0
RIT1/GTP 0.009 0 -10000 0 -10000 0 0
NT3 (dimer) -0.11 0.29 -10000 0 -0.81 29 29
RAP1/GDP -0.037 0.062 -10000 0 -10000 0 0
KIDINS220/CRKL 0.012 0 -10000 0 -10000 0 0
BDNF (dimer) -0.025 0.098 -10000 0 -0.28 25 25
ubiquitin-dependent protein catabolic process -0.12 0.23 -10000 0 -0.55 43 43
Schwann cell development -0.046 0.036 -10000 0 -10000 0 0
EHD4 0.012 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.029 0.018 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.036 0.012 -10000 0 -10000 0 0
RAP1B 0.012 0 -10000 0 -10000 0 0
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.29 0.28 -10000 0 -0.72 34 34
ABL1 0.012 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
Rap1/GTP -0.08 0.091 -10000 0 -10000 0 0
STAT3 0.02 0 -10000 0 -10000 0 0
axon guidance -0.28 0.26 -10000 0 -0.67 34 34
MAPK3 -0.099 0.22 -10000 0 -0.5 45 45
MAPK1 -0.099 0.22 -10000 0 -0.5 45 45
CDC42/GDP -0.017 0.092 -10000 0 -0.27 3 3
NTF3 -0.11 0.29 -10000 0 -0.81 29 29
NTF4 -0.026 0.091 -10000 0 -0.28 22 22
NGF (dimer)/TRKA/FAIM -0.12 0.23 -10000 0 -0.55 42 42
PI3K 0.018 0 -10000 0 -10000 0 0
FRS3 0.008 0.036 -10000 0 -0.28 3 3
FAIM 0.009 0.03 -10000 0 -10000 0 0
GAB1 0.012 0 -10000 0 -10000 0 0
RASGRF1 -0.081 0.16 -10000 0 -0.66 7 7
SOS1 0.012 0 -10000 0 -10000 0 0
MCF2L -0.13 0.28 -10000 0 -0.58 51 51
RGS19 0.011 0.021 -10000 0 -0.28 1 1
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP 0.023 0.063 -10000 0 -10000 0 0
Rac1/GDP -0.017 0.092 -10000 0 -0.27 3 3
NGF (dimer)/TRKA/GRIT -0.12 0.23 -10000 0 -0.56 42 42
neuron projection morphogenesis -0.042 0.16 -10000 0 -0.68 4 4
NGF (dimer)/TRKA/NEDD4-2 -0.12 0.23 -10000 0 -0.55 43 43
MAP2K1 0.036 0 -10000 0 -10000 0 0
NGFR -0.009 0.13 -10000 0 -0.81 5 5
NGF (dimer)/TRKA/GIPC/GAIP -0.073 0.16 -10000 0 -0.36 42 42
RAS family/GTP/PI3K 0.029 0 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.002 0.013 -10000 0 -10000 0 0
NRAS 0.012 0 -10000 0 -10000 0 0
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
PRKCI 0.012 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
MAPKKK cascade -0.15 0.26 -10000 0 -0.64 42 42
RASA1 0.012 0 -10000 0 -10000 0 0
TRKA/c-Abl -0.1 0.25 -10000 0 -0.62 37 37
SQSTM1 0.003 0.051 -10000 0 -0.28 6 6
BDNF (dimer)/TRKB/GIPC -0.2 0.25 -10000 0 -0.5 82 82
NGF (dimer)/TRKA/p62/Atypical PKCs -0.1 0.2 -10000 0 -0.47 42 42
MATK -0.017 0.12 -10000 0 -0.4 14 14
NEDD4L 0.008 0.058 -10000 0 -0.81 1 1
RAS family/GDP -0.035 0.06 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.084 0.17 -10000 0 -0.38 44 44
Rac1/GTP -0.07 0.1 -10000 0 -0.39 7 7
FRS2 family/SHP2/CRK family -0.002 0.013 -10000 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC -0.94 0.63 -9999 0 -1.4 140 140
PLK1 0.035 0.13 -9999 0 -10000 0 0
CDKN1B -0.041 0.1 -9999 0 -10000 0 0
FOXO3 0.056 0.096 -9999 0 -10000 0 0
KAT2B 0.019 0.012 -9999 0 -10000 0 0
FOXO1/SIRT1 -0.26 0.18 -9999 0 -0.38 140 140
CAT 0.06 0.089 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
AKT1 -0.017 0.026 -9999 0 -10000 0 0
FOXO1 -0.28 0.21 -9999 0 -0.42 140 140
MAPK10 0.019 0.012 -9999 0 -10000 0 0
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.062 0.047 -9999 0 -10000 0 0
response to oxidative stress -0.033 0.029 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.053 0.091 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
EP300 -0.026 0.026 -9999 0 -10000 0 0
BCL2L11 0.027 0.018 -9999 0 -10000 0 0
FOXO1/SKP2 -0.26 0.19 -9999 0 -0.38 140 140
mol:GDP -0.033 0.029 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
GADD45A 0.086 0.051 -9999 0 -10000 0 0
YWHAQ 0.012 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family -0.031 0.058 -9999 0 -10000 0 0
MST1 0.015 0.06 -9999 0 -0.82 1 1
CSNK1D 0.012 0 -9999 0 -10000 0 0
CSNK1E 0.012 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.015 0.042 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
MAPK8 0.01 0.072 -9999 0 -0.49 4 4
MAPK9 0.019 0.012 -9999 0 -10000 0 0
YWHAG 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
YWHAZ 0.012 0 -9999 0 -10000 0 0
SIRT1 0.014 0.009 -9999 0 -10000 0 0
SOD2 -0.048 0.12 -9999 0 -10000 0 0
RBL2 0.069 0.072 -9999 0 -10000 0 0
RAL/GDP 0.004 0.015 -9999 0 -10000 0 0
CHUK 0.019 0.012 -9999 0 -10000 0 0
Ran/GTP 0.013 0.003 -9999 0 -10000 0 0
CSNK1G2 0.012 0 -9999 0 -10000 0 0
RAL/GTP 0.008 0.018 -9999 0 -10000 0 0
CSNK1G1 0.012 0 -9999 0 -10000 0 0
FASLG 0.001 0.087 -9999 0 -10000 0 0
SKP2 0.012 0 -9999 0 -10000 0 0
USP7 0.013 0 -9999 0 -10000 0 0
IKBKB 0.019 0.012 -9999 0 -10000 0 0
CCNB1 0.057 0.098 -9999 0 -10000 0 0
FOXO1-3a-4/beta catenin -0.036 0.12 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.25 0.19 -9999 0 -0.38 140 140
CSNK1A1 0.012 0 -9999 0 -10000 0 0
SGK1 0.019 0.012 -9999 0 -10000 0 0
CSNK1G3 0.012 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.022 0.005 -9999 0 -10000 0 0
ZFAND5 0.065 0.041 -9999 0 -10000 0 0
SFN -0.12 0.15 -9999 0 -0.28 91 91
CDK2 -0.048 0.04 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.025 0.042 -9999 0 -10000 0 0
CREBBP -0.048 0.04 -9999 0 -10000 0 0
FBXO32 0.057 0.097 -9999 0 -10000 0 0
BCL6 0.068 0.075 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
YWHAH 0.012 0 -9999 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.028 0.09 -10000 0 -0.45 4 4
FYN 0.013 0.13 -10000 0 -0.49 7 7
LAT/GRAP2/SLP76 -0.002 0.13 -10000 0 -0.45 9 9
IKBKB 0.012 0 -10000 0 -10000 0 0
AKT1 0.005 0.11 -10000 0 -0.36 11 11
B2M 0.013 0.003 -10000 0 -10000 0 0
IKBKG -0.014 0.032 -10000 0 -10000 0 0
MAP3K8 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ -0.085 0.058 -10000 0 -0.12 136 136
integrin-mediated signaling pathway -0.002 0.018 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.006 0.15 -10000 0 -0.51 11 11
TRPV6 -0.56 0.38 -10000 0 -0.82 137 137
CD28 -0.006 0.085 -10000 0 -0.34 10 10
SHC1 0.008 0.13 -10000 0 -0.48 8 8
receptor internalization 0.005 0.12 -10000 0 -0.46 8 8
PRF1 0.01 0.12 -10000 0 -0.59 4 4
KRAS 0.012 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
COT/AKT1 0.012 0.094 -10000 0 -0.31 7 7
LAT -0.005 0.14 -10000 0 -0.48 10 10
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D -0.041 0.12 -10000 0 -0.29 36 36
CD3E -0.015 0.1 -10000 0 -0.38 6 6
CD3G -0.005 0.072 -10000 0 -0.29 12 12
RASGRP2 -0.003 0.023 -10000 0 -0.18 2 2
RASGRP1 0.012 0.12 -10000 0 -0.36 10 10
HLA-A 0.01 0.03 -10000 0 -0.29 2 2
RASSF5 0.008 0.036 -10000 0 -0.28 3 3
RAP1A/GTP/RAPL -0.002 0.018 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.025 0.042 -10000 0 -0.1 2 2
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.029 0.055 -10000 0 -0.23 4 4
PRKCA 0.008 0.079 -10000 0 -0.25 8 8
GRAP2 0.005 0.046 -10000 0 -0.28 5 5
mol:IP3 0.14 0.18 0.26 123 -0.38 9 132
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.002 0.1 -10000 0 -0.41 7 7
ORAI1 0.27 0.17 0.38 136 -10000 0 136
CSK 0.006 0.13 -10000 0 -0.48 8 8
B7 family/CD28 -0.062 0.14 -10000 0 -0.53 12 12
CHUK 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 0 0.14 -10000 0 -0.51 9 9
PTPN6 0.006 0.13 -10000 0 -0.47 8 8
VAV1 -0.015 0.16 -10000 0 -0.54 11 11
Monovalent TCR/CD3 -0.01 0.092 -10000 0 -0.33 11 11
CBL 0.012 0 -10000 0 -10000 0 0
LCK 0.008 0.13 -10000 0 -0.5 8 8
PAG1 0.006 0.13 -10000 0 -0.48 8 8
RAP1A 0.012 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK 0.001 0.14 -10000 0 -0.52 8 8
CD80 -0.027 0.1 -10000 0 -0.29 26 26
CD86 -0.046 0.12 -10000 0 -0.29 39 39
PDK1/CARD11/BCL10/MALT1 -0.036 0.066 -10000 0 -0.27 6 6
HRAS 0.012 0 -10000 0 -10000 0 0
GO:0035030 -0.011 0.14 -10000 0 -0.45 12 12
CD8A -0.015 0.089 -10000 0 -0.29 19 19
CD8B -0.009 0.08 -10000 0 -0.29 7 7
PTPRC 0.003 0.069 -10000 0 -0.42 4 4
PDK1/PKC theta 0.005 0.14 -10000 0 -0.46 9 9
CSK/PAG1 0.01 0.13 -10000 0 -0.48 7 7
SOS1 0.012 0 -10000 0 -10000 0 0
peptide-MHC class I 0.017 0.022 -10000 0 -10000 0 0
GRAP2/SLP76 0.002 0.14 -10000 0 -0.47 11 11
STIM1 0.14 0.09 -10000 0 -10000 0 0
RAS family/GTP 0.029 0.053 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin 0.004 0.13 -10000 0 -0.48 8 8
mol:DAG 0.033 0.12 -10000 0 -0.34 10 10
RAP1A/GDP 0.012 0.018 -10000 0 -10000 0 0
PLCG1 0.012 0 -10000 0 -10000 0 0
CD247 0.001 0.06 -10000 0 -0.29 8 8
cytotoxic T cell degranulation 0.01 0.11 -10000 0 -0.57 4 4
RAP1A/GTP -0.001 0.008 -10000 0 -0.066 1 1
mol:PI-3-4-5-P3 -0.001 0.13 -10000 0 -0.43 11 11
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.13 0.21 0.28 107 -0.5 9 116
NRAS 0.012 0 -10000 0 -10000 0 0
ZAP70 -0.025 0.099 -10000 0 -10000 0 0
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.016 0.14 -10000 0 -0.5 10 10
MALT1 0.012 0 -10000 0 -10000 0 0
TRAF6 0.012 0 -10000 0 -10000 0 0
CD8 heterodimer -0.013 0.1 -10000 0 -0.36 12 12
CARD11 -0.078 0.14 -10000 0 -10000 0 0
PRKCB 0.006 0.08 -10000 0 -0.26 7 7
PRKCE 0.008 0.079 -10000 0 -0.25 7 7
PRKCQ -0.004 0.15 -10000 0 -0.49 11 11
LCP2 0.006 0.042 -10000 0 -0.28 4 4
BCL10 0.012 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.007 0.1 -10000 0 -0.31 11 11
IKK complex 0.029 0.043 -10000 0 -0.11 1 1
RAS family/GDP -0.002 0.005 -10000 0 -10000 0 0
MAP3K14 0.018 0.075 -10000 0 -0.26 3 3
PDPK1 0.008 0.11 -10000 0 -0.37 8 8
TCR/CD3/MHC I/CD8/Fyn 0.001 0.13 -10000 0 -0.52 7 7
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.016 0.14 -9999 0 -0.55 12 12
ADCY5 -0.011 0.12 -9999 0 -0.55 10 10
ADCY6 0.018 0 -9999 0 -10000 0 0
ADCY7 0.011 0.033 -9999 0 -10000 0 0
ADCY1 -0.25 0.28 -9999 0 -0.55 94 94
ADCY2 -0.077 0.083 -9999 0 -10000 0 0
ADCY3 0.018 0 -9999 0 -10000 0 0
ADCY8 0.01 0.028 -9999 0 -10000 0 0
PRKCE 0.01 0 -9999 0 -10000 0 0
ADCY9 0.018 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.078 0.093 -9999 0 -0.31 14 14
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.007 0.16 -10000 0 -0.6 2 2
IHH -0.08 0.27 -10000 0 -0.83 23 23
SHH Np/Cholesterol/GAS1 -0.009 0.12 -10000 0 -0.5 11 11
LRPAP1 0.012 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.009 0.12 0.49 11 -10000 0 11
SMO/beta Arrestin2 -0.012 0.18 -10000 0 -0.48 24 24
SMO -0.018 0.19 -10000 0 -0.51 24 24
AKT1 0.015 0.085 -10000 0 -10000 0 0
ARRB2 0.011 0.021 -10000 0 -0.28 1 1
BOC 0.012 0 -10000 0 -10000 0 0
ADRBK1 0.012 0 -10000 0 -10000 0 0
heart looping -0.018 0.18 -10000 0 -0.5 24 24
STIL -0.008 0.15 -10000 0 -0.44 9 9
DHH N/PTCH2 -0.014 0.13 -10000 0 -0.62 9 9
DHH N/PTCH1 -0.038 0.19 -10000 0 -0.46 31 31
PIK3CA 0.012 0 -10000 0 -10000 0 0
DHH -0.026 0.17 -10000 0 -0.81 9 9
PTHLH -0.016 0.19 -10000 0 -0.76 2 2
determination of left/right symmetry -0.018 0.18 -10000 0 -0.5 24 24
PIK3R1 0.012 0 -10000 0 -10000 0 0
skeletal system development -0.016 0.18 -10000 0 -0.76 2 2
IHH N/Hhip -0.079 0.23 -10000 0 -0.59 32 32
DHH N/Hhip -0.043 0.2 -10000 0 -0.69 16 16
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.018 0.18 -10000 0 -0.5 24 24
pancreas development -0.031 0.17 -10000 0 -0.68 12 12
HHAT 0.012 0 -10000 0 -10000 0 0
PI3K 0.018 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.021 0.16 -10000 0 -0.81 8 8
somite specification -0.018 0.18 -10000 0 -0.5 24 24
SHH Np/Cholesterol/PTCH1 -0.013 0.15 -10000 0 -0.46 7 7
SHH Np/Cholesterol/PTCH2 0.01 0.068 -10000 0 -0.5 3 3
SHH Np/Cholesterol/Megalin -0.046 0.18 -10000 0 -0.52 24 24
SHH 0.007 0.083 -10000 0 -0.62 3 3
catabolic process -0.021 0.17 -10000 0 -0.48 23 23
SMO/Vitamin D3 -0.015 0.17 -10000 0 -0.56 5 5
SHH Np/Cholesterol/Hhip -0.016 0.13 -10000 0 -0.5 12 12
LRP2 -0.079 0.26 -10000 0 -0.81 22 22
receptor-mediated endocytosis -0.09 0.2 -10000 0 -0.67 14 14
SHH Np/Cholesterol/BOC 0.012 0.066 -10000 0 -0.5 3 3
SHH Np/Cholesterol/CDO 0.009 0.069 -10000 0 -0.5 3 3
mesenchymal cell differentiation 0.016 0.12 0.49 12 -10000 0 12
mol:Vitamin D3 -0.011 0.15 -10000 0 -0.46 7 7
IHH N/PTCH2 -0.046 0.18 -10000 0 -0.55 23 23
CDON 0.006 0.042 -10000 0 -0.28 4 4
IHH N/PTCH1 -0.021 0.17 -10000 0 -0.49 23 23
Megalin/LRPAP1 -0.053 0.2 -10000 0 -0.62 22 22
PTCH2 0.009 0.03 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.01 0.064 -10000 0 -0.5 3 3
PTCH1 -0.021 0.17 -10000 0 -0.49 23 23
HHIP -0.031 0.17 -10000 0 -0.68 12 12
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.045 0.14 -9999 0 -0.56 14 14
EFNA5 -0.048 0.21 -9999 0 -0.78 15 15
FYN -0.025 0.14 -9999 0 -0.51 14 14
neuron projection morphogenesis -0.045 0.14 -9999 0 -0.56 14 14
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.046 0.14 -9999 0 -0.56 14 14
EPHA5 -0.008 0.057 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.006 0.11 -10000 0 -1.1 2 2
SMARCC2 0.014 0 -10000 0 -10000 0 0
SMARCC1 0.014 0 -10000 0 -10000 0 0
TBX21 -0.025 0.084 -10000 0 -0.34 2 2
SUMO2 0.01 0.005 -10000 0 -10000 0 0
STAT1 (dimer) 0.015 0.036 -10000 0 -0.28 3 3
FKBP4 0.012 0 -10000 0 -10000 0 0
FKBP5 0 0.1 -10000 0 -0.81 3 3
GR alpha/HSP90/FKBP51/HSP90 0.058 0.09 -10000 0 -0.49 3 3
PRL -0.019 0.069 -10000 0 -0.48 1 1
cortisol/GR alpha (dimer)/TIF2 0.1 0.23 0.48 11 -0.51 12 23
RELA -0.089 0.097 -10000 0 -0.26 5 5
FGG 0.097 0.15 0.45 2 -10000 0 2
GR beta/TIF2 0.016 0.19 -10000 0 -0.59 16 16
IFNG -0.13 0.18 -10000 0 -0.52 14 14
apoptosis -0.073 0.22 -10000 0 -0.69 11 11
CREB1 0.001 0.062 -10000 0 -0.34 6 6
histone acetylation -0.007 0.064 -10000 0 -10000 0 0
BGLAP -0.011 0.062 -10000 0 -10000 0 0
GR/PKAc 0.066 0.059 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.16 0.18 -10000 0 -0.43 28 28
SMARCD1 0.014 0 -10000 0 -10000 0 0
MDM2 0.053 0.053 0.22 2 -10000 0 2
GATA3 -0.6 0.36 -10000 0 -0.81 147 147
AKT1 0.002 0.018 -10000 0 -10000 0 0
CSF2 -0.025 0.062 -10000 0 -10000 0 0
GSK3B 0.01 0.005 -10000 0 -10000 0 0
NR1I3 -0.047 0.28 -10000 0 -0.93 12 12
CSN2 0.095 0.1 -10000 0 -10000 0 0
BRG1/BAF155/BAF170/BAF60A 0.039 0 -10000 0 -10000 0 0
NFATC1 0.014 0.004 -10000 0 -10000 0 0
POU2F1 0.013 0.006 -10000 0 -10000 0 0
CDKN1A 0.023 0.05 -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 -0.12 0.15 -10000 0 -0.28 91 91
GR alpha/HSP90/FKBP51/HSP90/14-3-3 -0.004 0.11 -10000 0 -0.44 3 3
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.061 0.3 -10000 0 -0.89 18 18
JUN -0.081 0.16 -10000 0 -0.54 13 13
IL4 -0.022 0.067 -10000 0 -10000 0 0
CDK5R1 0.007 0.03 -10000 0 -0.28 2 2
PRKACA 0.012 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.099 0.22 -10000 0 -0.56 27 27
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.063 0.085 -10000 0 -0.44 3 3
cortisol/GR alpha (monomer) 0.16 0.18 0.51 17 -10000 0 17
NCOA2 -0.054 0.22 -10000 0 -0.81 16 16
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.13 0.3 -10000 0 -0.83 31 31
AP-1/NFAT1-c-4 -0.18 0.3 -10000 0 -0.76 32 32
AFP -0.17 0.42 -10000 0 -1.4 19 19
SUV420H1 0.012 0 -10000 0 -10000 0 0
IRF1 0.097 0.085 -10000 0 -10000 0 0
TP53 0.029 0.023 -10000 0 -10000 0 0
PPP5C 0.012 0 -10000 0 -10000 0 0
KRT17 -0.19 0.31 -10000 0 -0.77 26 26
KRT14 -0.065 0.1 -10000 0 -10000 0 0
TBP 0.021 0 -10000 0 -10000 0 0
CREBBP 0.023 0.029 -10000 0 -10000 0 0
HDAC1 0.011 0.003 -10000 0 -10000 0 0
HDAC2 0.012 0.004 -10000 0 -10000 0 0
AP-1 -0.18 0.3 -10000 0 -0.76 32 32
MAPK14 0.01 0.005 -10000 0 -10000 0 0
MAPK10 0.01 0.005 -10000 0 -10000 0 0
MAPK11 0.01 0.005 -10000 0 -10000 0 0
KRT5 -0.15 0.26 -10000 0 -1.1 8 8
interleukin-1 receptor activity 0 0.004 -10000 0 -10000 0 0
NCOA1 0.014 0.009 -10000 0 -10000 0 0
STAT1 0.015 0.036 -10000 0 -0.28 3 3
CGA -0.061 0.23 -10000 0 -1.3 6 6
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.032 0.074 0.32 2 -10000 0 2
MAPK3 0.01 0.005 -10000 0 -10000 0 0
MAPK1 0.01 0.005 -10000 0 -10000 0 0
ICAM1 -0.16 0.17 -10000 0 -0.47 19 19
NFKB1 -0.089 0.097 -10000 0 -10000 0 0
MAPK8 -0.073 0.15 -10000 0 -0.6 7 7
MAPK9 0.01 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.08 0.23 -10000 0 -0.74 11 11
BAX 0.027 0.034 -10000 0 -10000 0 0
POMC -0.22 0.28 -10000 0 -0.85 13 13
EP300 0.023 0.029 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.16 0.16 0.48 13 -10000 0 13
proteasomal ubiquitin-dependent protein catabolic process 0.037 0.042 -10000 0 -10000 0 0
SGK1 0.065 0.039 -10000 0 -10000 0 0
IL13 -0.45 0.28 -10000 0 -0.78 57 57
IL6 -0.25 0.4 -10000 0 -1.3 21 21
PRKACG 0.001 0.021 -10000 0 -0.28 1 1
IL5 -0.37 0.22 -10000 0 -0.67 39 39
IL2 -0.12 0.17 -10000 0 -0.65 3 3
CDK5 0.01 0.005 -10000 0 -10000 0 0
PRKACB 0.012 0 -10000 0 -10000 0 0
HSP90AA1 0.012 0 -10000 0 -10000 0 0
IL8 -0.2 0.2 -10000 0 -0.52 31 31
CDK5R1/CDK5 0.008 0.021 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.095 0.13 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.15 0.14 0.46 11 -10000 0 11
SMARCA4 0.014 0 -10000 0 -10000 0 0
chromatin remodeling 0.11 0.087 0.35 2 -10000 0 2
NF kappa B1 p50/RelA/Cbp -0.092 0.15 -10000 0 -0.39 5 5
JUN (dimer) -0.08 0.16 -10000 0 -0.54 13 13
YWHAH 0.012 0 -10000 0 -10000 0 0
VIPR1 -0.066 0.25 -10000 0 -1.1 10 10
NR3C1 0.087 0.093 0.38 2 -10000 0 2
NR4A1 -0.33 0.41 -10000 0 -0.81 84 84
TIF2/SUV420H1 -0.034 0.18 -10000 0 -0.62 16 16
MAPKKK cascade -0.073 0.22 -10000 0 -0.69 11 11
cortisol/GR alpha (dimer)/Src-1 0.16 0.15 0.47 13 -10000 0 13
PBX1 0.004 0.083 -10000 0 -0.81 2 2
POU1F1 0.006 0.01 -10000 0 -10000 0 0
SELE -0.62 0.62 -10000 0 -1.3 95 95
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.11 0.087 0.35 2 -10000 0 2
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.15 0.14 0.46 11 -10000 0 11
mol:cortisol 0.077 0.096 0.26 20 -10000 0 20
MMP1 -0.12 0.32 -10000 0 -1.4 11 11
Syndecan-4-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
PTK2 -0.022 0.046 -9999 0 -10000 0 0
Syndecan-4/Syndesmos -0.22 0.2 -9999 0 -0.61 11 11
positive regulation of JNK cascade -0.25 0.2 -9999 0 -0.59 23 23
Syndecan-4/ADAM12 -0.24 0.2 -9999 0 -0.61 17 17
CCL5 -0.019 0.091 -9999 0 -0.28 21 21
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
DNM2 0.012 0 -9999 0 -10000 0 0
ITGA5 0.012 0 -9999 0 -10000 0 0
SDCBP 0.012 0 -9999 0 -10000 0 0
PLG -0.46 0.39 -9999 0 -0.8 114 114
ADAM12 -0.03 0.1 -9999 0 -0.28 28 28
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.06 0.042 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.24 0.22 -9999 0 -0.63 19 19
Syndecan-4/CXCL12/CXCR4 -0.26 0.21 -9999 0 -0.63 23 23
Syndecan-4/Laminin alpha3 -0.26 0.2 -9999 0 -0.58 23 23
MDK -0.055 0.12 -9999 0 -0.28 45 45
Syndecan-4/FZD7 -0.24 0.21 -9999 0 -0.66 14 14
Syndecan-4/Midkine -0.25 0.2 -9999 0 -0.6 19 19
FZD7 -0.013 0.14 -9999 0 -0.81 6 6
Syndecan-4/FGFR1/FGF -0.22 0.17 -9999 0 -0.57 10 10
THBS1 -0.005 0.12 -9999 0 -0.81 4 4
integrin-mediated signaling pathway -0.23 0.19 -9999 0 -0.58 14 14
positive regulation of MAPKKK cascade -0.25 0.2 -9999 0 -0.59 23 23
Syndecan-4/TACI -0.23 0.2 -9999 0 -0.62 14 14
CXCR4 -0.009 0.076 -9999 0 -0.28 14 14
cell adhesion 0.032 0.029 -9999 0 -10000 0 0
Syndecan-4/Dynamin -0.22 0.2 -9999 0 -0.61 11 11
Syndecan-4/TSP1 -0.23 0.2 -9999 0 -0.63 13 13
Syndecan-4/GIPC -0.22 0.2 -9999 0 -0.61 11 11
Syndecan-4/RANTES -0.24 0.2 -9999 0 -0.61 14 14
ITGB1 0.012 0 -9999 0 -10000 0 0
LAMA1 -0.03 0.15 -9999 0 -0.42 19 19
LAMA3 -0.076 0.14 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCA 0.076 0.052 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.22 0.2 -9999 0 -0.61 11 11
TFPI 0.008 0.036 -9999 0 -10000 0 0
F2 -0.019 0.085 -9999 0 -0.28 19 19
alpha5/beta1 Integrin 0.018 0 -9999 0 -10000 0 0
positive regulation of cell adhesion -0.26 0.21 -9999 0 -0.58 32 32
ACTN1 0.012 0 -9999 0 -10000 0 0
TNC -0.019 0.11 -9999 0 -0.81 2 2
Syndecan-4/CXCL12 -0.26 0.22 -9999 0 -0.66 21 21
FGF6 0.001 0.003 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
CXCL12 -0.063 0.24 -9999 0 -0.81 18 18
TNFRSF13B -0.009 0.067 -9999 0 -10000 0 0
FGF2 0.012 0 -9999 0 -10000 0 0
FGFR1 0.012 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 -0.23 0.2 -9999 0 -0.53 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.008 0.072 -9999 0 -0.27 14 14
cell migration -0.017 0.012 -9999 0 -10000 0 0
PRKCD 0.013 0.012 -9999 0 -10000 0 0
vasculogenesis -0.23 0.2 -9999 0 -0.61 13 13
SDC4 -0.24 0.21 -9999 0 -0.65 11 11
Syndecan-4/Tenascin C -0.24 0.2 -9999 0 -0.6 14 14
Syndecan-4/PI-4-5-P2/PKC alpha -0.048 0.033 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.22 0.2 -9999 0 -0.61 11 11
MMP9 -0.099 0.16 -9999 0 -0.8 3 3
Rac1/GTP 0.033 0.03 -9999 0 -10000 0 0
cytoskeleton organization -0.22 0.19 -9999 0 -0.58 11 11
GIPC1 0.012 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.23 0.2 -9999 0 -0.61 12 12
Coregulation of Androgen receptor activity

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
NRIP1 0.012 0.006 -9999 0 -10000 0 0
SVIL 0.012 0.005 -9999 0 -10000 0 0
ZNF318 0.013 0.014 -9999 0 -10000 0 0
JMJD2C -0.001 0.016 -9999 0 -0.059 13 13
T-DHT/AR/Ubc9 -0.065 0.12 -9999 0 -0.59 8 8
CARM1 0.012 0.001 -9999 0 -10000 0 0
PRDX1 0.012 0.001 -9999 0 -10000 0 0
PELP1 0.012 0.002 -9999 0 -10000 0 0
CTNNB1 0.012 0.005 -9999 0 -10000 0 0
AKT1 0.012 0.004 -9999 0 -10000 0 0
PTK2B 0.012 0.004 -9999 0 -10000 0 0
MED1 0.012 0.005 -9999 0 -10000 0 0
MAK 0 0.064 -9999 0 -0.28 9 9
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.008 0.059 -9999 0 -0.81 1 1
GSN 0.012 0.006 -9999 0 -10000 0 0
NCOA2 -0.055 0.22 -9999 0 -0.81 16 16
NCOA6 0.012 0.005 -9999 0 -10000 0 0
DNA-PK 0.004 0.018 -9999 0 -10000 0 0
NCOA4 0.012 0.001 -9999 0 -10000 0 0
PIAS3 0.012 0.005 -9999 0 -10000 0 0
cell proliferation -0.036 0.038 -9999 0 -10000 0 0
XRCC5 0.012 0.003 -9999 0 -10000 0 0
UBE3A 0.012 0.009 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.1 0.17 -9999 0 -0.59 20 20
FHL2 -0.032 0.061 -9999 0 -0.5 1 1
RANBP9 0.012 0.005 -9999 0 -10000 0 0
JMJD1A -0.092 0.077 -9999 0 -0.15 131 131
CDK6 0.012 0.001 -9999 0 -10000 0 0
TGFB1I1 0.004 0.082 -9999 0 -0.81 2 2
T-DHT/AR/CyclinD1 -0.066 0.12 -9999 0 -0.59 8 8
XRCC6 0.012 0.003 -9999 0 -10000 0 0
T-DHT/AR -0.12 0.15 -9999 0 -0.62 8 8
CTDSP1 0.012 0.002 -9999 0 -10000 0 0
CTDSP2 0.013 0.01 -9999 0 -10000 0 0
BRCA1 0.009 0.031 -9999 0 -0.29 2 2
TCF4 0.013 0.007 -9999 0 -10000 0 0
CDKN2A -0.22 0.12 -9999 0 -0.28 158 158
SRF 0.02 0.005 -9999 0 -10000 0 0
NKX3-1 -0.15 0.12 -9999 0 -10000 0 0
KLK3 0.004 0.12 -9999 0 -1.5 1 1
TMF1 0.012 0.002 -9999 0 -10000 0 0
HNRNPA1 0.013 0.006 -9999 0 -10000 0 0
AOF2 0 0.006 -9999 0 -0.071 1 1
APPL1 0.022 0.009 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.065 0.12 -9999 0 -0.59 8 8
AR -0.065 0.16 -9999 0 -0.78 9 9
UBA3 0.012 0.002 -9999 0 -10000 0 0
PATZ1 0.013 0.006 -9999 0 -10000 0 0
PAWR 0.012 0.002 -9999 0 -10000 0 0
PRKDC 0.012 0.003 -9999 0 -10000 0 0
PA2G4 0.013 0.007 -9999 0 -10000 0 0
UBE2I 0.012 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.06 0.11 -9999 0 -0.51 9 9
RPS6KA3 0.012 0.006 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.066 0.12 -9999 0 -0.59 8 8
LATS2 0.013 0.005 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.058 0.11 -9999 0 -0.55 8 8
Cyclin D3/CDK11 p58 0.006 0.025 -9999 0 -10000 0 0
VAV3 0.012 0.005 -9999 0 -10000 0 0
KLK2 -0.069 0.079 -9999 0 -0.34 4 4
CASP8 0.012 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.091 0.21 -9999 0 -0.68 19 19
TMPRSS2 -0.75 0.54 -9999 0 -1.1 131 131
CCND1 0.012 0.002 -9999 0 -10000 0 0
PIAS1 0.012 0.009 -9999 0 -10000 0 0
mol:T-DHT -0.048 0.039 -9999 0 -0.076 127 127
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.011 0.013 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.065 0.12 -9999 0 -0.59 8 8
CMTM2 -0.005 0.068 -9999 0 -0.28 11 11
SNURF -0.039 0.2 -9999 0 -0.81 12 12
ZMIZ1 -0.03 0.035 -9999 0 -10000 0 0
CCND3 0.008 0.036 -9999 0 -10000 0 0
TGIF1 0.013 0.006 -9999 0 -10000 0 0
FKBP4 0.012 0.005 -9999 0 -10000 0 0
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.009 0.03 -9999 0 -0.28 2 2
CCL5 -0.019 0.091 -9999 0 -0.28 21 21
SDCBP 0.012 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.069 0.15 -9999 0 -0.44 17 17
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.059 0.14 -9999 0 -0.54 8 8
Syndecan-1/Syntenin -0.059 0.14 -9999 0 -0.57 7 7
MAPK3 -0.041 0.13 -9999 0 -0.88 2 2
HGF/MET -0.033 0.15 -9999 0 -0.64 9 9
TGFB1/TGF beta receptor Type II 0.009 0.03 -9999 0 -0.28 2 2
BSG 0.012 0 -9999 0 -10000 0 0
keratinocyte migration -0.059 0.14 -9999 0 -0.53 8 8
Syndecan-1/RANTES -0.073 0.15 -9999 0 -0.56 8 8
Syndecan-1/CD147 -0.05 0.14 -9999 0 -0.58 6 6
Syndecan-1/Syntenin/PIP2 -0.058 0.14 -9999 0 -0.55 7 7
LAMA5 0.012 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.071 0.12 -9999 0 -0.53 7 7
MMP7 -0.078 0.16 -9999 0 -0.32 53 53
HGF -0.025 0.17 -9999 0 -0.81 9 9
Syndecan-1/CASK -0.067 0.14 -9999 0 -0.42 17 17
Syndecan-1/HGF/MET -0.085 0.18 -9999 0 -0.54 18 18
regulation of cell adhesion -0.033 0.13 -9999 0 -0.84 2 2
HPSE -0.023 0.16 -9999 0 -0.81 8 8
positive regulation of cell migration -0.069 0.15 -9999 0 -0.44 17 17
SDC1 -0.07 0.15 -9999 0 -0.45 17 17
Syndecan-1/Collagen -0.069 0.15 -9999 0 -0.44 17 17
PPIB 0.012 0 -9999 0 -10000 0 0
MET -0.021 0.093 -9999 0 -0.28 22 22
PRKACA 0.012 0 -9999 0 -10000 0 0
MMP9 -0.1 0.17 -9999 0 -0.81 3 3
MAPK1 -0.041 0.13 -9999 0 -0.88 2 2
homophilic cell adhesion -0.069 0.15 -9999 0 -0.44 17 17
MMP1 -0.047 0.19 -9999 0 -0.59 19 19
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.018 0 -9999 0 -10000 0 0
Necdin/E2F1 -0.086 0.18 -9999 0 -0.66 13 13
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.026 0.12 -9999 0 -0.5 10 10
NGF (dimer)/p75(NTR)/BEX1 -0.067 0.19 -9999 0 -0.57 23 23
NT-4/5 (dimer)/p75(NTR) -0.024 0.12 -9999 0 -0.63 5 5
IKBKB 0.012 0 -9999 0 -10000 0 0
AKT1 0.008 0.12 -9999 0 -0.5 10 10
IKBKG 0.012 0 -9999 0 -10000 0 0
BDNF -0.025 0.098 -9999 0 -0.28 25 25
MGDIs/NGR/p75(NTR)/LINGO1 -0.022 0.1 -9999 0 -0.54 7 7
FURIN 0.012 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.031 0.1 -9999 0 -0.59 5 5
LINGO1 0.004 0.082 -9999 0 -0.81 2 2
Sortilin/TRAF6/NRIF -0.002 0.028 -9999 0 -10000 0 0
proBDNF (dimer) -0.025 0.098 -9999 0 -0.28 25 25
NTRK1 -0.14 0.32 -9999 0 -0.81 37 37
RTN4R 0.006 0.042 -9999 0 -0.28 4 4
neuron apoptosis -0.006 0.11 -9999 0 -0.55 5 5
IRAK1 0.012 0 -9999 0 -10000 0 0
SHC1 -0.006 0.14 -9999 0 -0.58 10 10
ARHGDIA 0.012 0 -9999 0 -10000 0 0
RhoA/GTP 0.009 0 -9999 0 -10000 0 0
Gamma Secretase -0.002 0.033 -9999 0 -0.46 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.001 0.13 -9999 0 -0.54 10 10
MAGEH1 0.011 0.021 -9999 0 -0.28 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.031 0.2 -9999 0 -0.61 19 19
Mammalian IAPs/DIABLO 0.021 0.037 -9999 0 -10000 0 0
proNGF (dimer) -0.015 0.14 -9999 0 -0.81 6 6
MAGED1 0.012 0 -9999 0 -10000 0 0
APP 0.012 0 -9999 0 -10000 0 0
NT-4/5 (dimer) -0.026 0.091 -9999 0 -0.28 22 22
ZNF274 0.012 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI 0.002 0.12 -9999 0 -0.51 10 10
NGF -0.015 0.14 -9999 0 -0.81 6 6
cell cycle arrest -0.013 0.12 -9999 0 -0.49 10 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.014 0.09 -9999 0 -0.66 1 1
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.029 0.094 -9999 0 -0.54 5 5
NCSTN 0.012 0 -9999 0 -10000 0 0
mol:GTP -0.03 0.13 -9999 0 -0.58 10 10
PSENEN 0.012 0 -9999 0 -10000 0 0
mol:ceramide 0.002 0.13 -9999 0 -0.53 10 10
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.021 0.075 -9999 0 -0.54 1 1
p75(NTR)/beta APP 0.002 0.1 -9999 0 -0.62 5 5
BEX1 -0.045 0.2 -9999 0 -0.74 15 15
mol:GDP -0.015 0.14 -9999 0 -0.59 10 10
NGF (dimer) -0.33 0.28 -9999 0 -0.54 117 117
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.01 0.098 -9999 0 -0.49 7 7
PIK3R1 0.012 0 -9999 0 -10000 0 0
RAC1/GTP -0.027 0.12 -9999 0 -0.52 10 10
MYD88 0.012 0 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.03 0.13 -9999 0 -0.59 10 10
RHOB 0.012 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.044 0.092 -9999 0 -10000 0 0
NT3 (dimer) -0.11 0.29 -9999 0 -0.81 29 29
TP53 0.013 0.09 -9999 0 -0.48 5 5
PRDM4 0.001 0.13 -9999 0 -0.53 10 10
BDNF (dimer) -0.35 0.26 -9999 0 -0.55 116 116
PIK3CA 0.012 0 -9999 0 -10000 0 0
SORT1 0.012 0 -9999 0 -10000 0 0
activation of caspase activity -0.026 0.11 -9999 0 -0.5 10 10
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.002 0.13 -9999 0 -0.54 10 10
RHOC 0.012 0 -9999 0 -10000 0 0
XIAP 0.012 0 -9999 0 -10000 0 0
MAPK10 0.024 0.11 -9999 0 -0.56 3 3
DIABLO 0.012 0 -9999 0 -10000 0 0
SMPD2 0.001 0.13 -9999 0 -0.53 10 10
APH1B 0.008 0.058 -9999 0 -0.81 1 1
APH1A 0.012 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.03 0.13 -9999 0 -0.59 10 10
PSEN1 0.012 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.018 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.091 0.25 -9999 0 -0.65 32 32
MAPK8 0.017 0.12 -9999 0 -0.56 3 3
MAPK9 0.024 0.11 -9999 0 -0.56 3 3
APAF1 0.012 0 -9999 0 -10000 0 0
NTF3 -0.11 0.29 -9999 0 -0.81 29 29
NTF4 -0.026 0.091 -9999 0 -0.28 22 22
NDN -0.042 0.2 -9999 0 -0.81 13 13
RAC1/GDP 0.009 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.024 0.11 -9999 0 -0.47 10 10
p75 CTF/Sortilin/TRAF6/NRIF 0.031 0 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.03 0.13 -9999 0 -0.58 10 10
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.025 0.085 -9999 0 -0.51 5 5
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.001 0.1 -9999 0 -0.54 5 5
PRKACB 0.012 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.007 0.066 -9999 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.007 0.073 -9999 0 -0.28 13 13
BIRC2 0.012 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.028 0.17 -9999 0 -0.62 10 10
BAD 0.028 0.11 -9999 0 -0.54 3 3
RIPK2 0.012 0 -9999 0 -10000 0 0
NGFR -0.009 0.13 -9999 0 -0.81 5 5
CYCS 0.008 0.12 -9999 0 -0.5 10 10
ADAM17 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.002 0.13 -9999 0 -0.54 10 10
BCL2L11 0.028 0.11 -9999 0 -0.54 3 3
BDNF (dimer)/p75(NTR) -0.023 0.12 -9999 0 -0.68 5 5
PI3K 0.002 0.13 -9999 0 -0.54 10 10
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.002 0.13 -9999 0 -0.54 10 10
NDNL2 0.012 0 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
PRKCI 0.012 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.018 0.16 -9999 0 -0.67 10 10
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.002 0.13 -9999 0 -0.54 10 10
TRAF6 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
PRKCZ 0.012 0 -9999 0 -10000 0 0
PLG -0.47 0.4 -9999 0 -0.81 114 114
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.008 0.13 -9999 0 -0.52 10 10
SQSTM1 0.003 0.051 -9999 0 -0.28 6 6
NGFRAP1 0.012 0 -9999 0 -10000 0 0
CASP3 0.029 0.1 -9999 0 -0.49 3 3
E2F1 -0.081 0.14 -9999 0 -0.28 62 62
CASP9 0.012 0 -9999 0 -10000 0 0
IKK complex -0.091 0.18 -9999 0 -0.56 9 9
NGF (dimer)/TRKA -0.12 0.27 -9999 0 -0.64 42 42
MMP7 -0.078 0.16 -9999 0 -0.32 53 53
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.026 0.12 -9999 0 -0.5 10 10
MMP3 -0.019 0.076 -9999 0 -0.28 15 15
APAF-1/Caspase 9 -0.022 0.084 -9999 0 -0.66 1 1
Nongenotropic Androgen 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
PTK2 0.01 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.017 0.099 -10000 0 -0.5 8 8
regulation of S phase of mitotic cell cycle 0.012 0.071 -10000 0 -0.33 8 8
GNAO1 -0.051 0.21 -10000 0 -0.72 17 17
HRAS 0.012 0.001 -10000 0 -10000 0 0
SHBG/T-DHT -0.021 0.11 -10000 0 -0.55 8 8
PELP1 0.012 0.001 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
MAP2K1 0.007 0.1 -10000 0 -0.42 8 8
T-DHT/AR -0.026 0.12 -10000 0 -0.58 9 9
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.003 -10000 0 -0.007 31 31
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.008 0.058 -10000 0 -0.81 1 1
mol:GDP -0.025 0.12 -10000 0 -0.6 8 8
cell proliferation -0.018 0.18 -10000 0 -0.44 13 13
PIK3CA 0.012 0 -10000 0 -10000 0 0
FOS -0.091 0.33 -10000 0 -0.85 31 31
mol:Ca2+ -0.01 0.023 -10000 0 -0.077 17 17
MAPK3 -0.005 0.14 -10000 0 -0.42 8 8
MAPK1 -0.004 0.089 -10000 0 -0.28 3 3
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 0 0.002 -10000 0 -0.005 31 31
cAMP biosynthetic process -0.014 0.11 -10000 0 -0.53 8 8
GNG2 0.012 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.005 31 31
HRAS/GTP -0.023 0.091 -10000 0 -0.46 8 8
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.012 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.005 31 31
PI3K 0.002 0.006 -10000 0 -10000 0 0
apoptosis 0.025 0.17 0.4 31 -10000 0 31
T-DHT/AR/PELP1 -0.022 0.11 -10000 0 -0.55 8 8
HRAS/GDP -0.022 0.11 -10000 0 -0.57 8 8
CREB1 -0.029 0.18 -10000 0 -0.43 31 31
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
AR -0.023 0.16 -10000 0 -0.76 9 9
GNB1 0.012 0 -10000 0 -10000 0 0
RAF1 0.005 0.098 -10000 0 -0.44 8 8
RAC1-CDC42/GDP -0.019 0.11 -10000 0 -0.54 8 8
T-DHT/AR/PELP1/Src -0.021 0.1 -10000 0 -0.5 8 8
MAP2K2 0.007 0.1 -10000 0 -0.42 8 8
T-DHT/AR/PELP1/Src/PI3K 0.012 0.072 -10000 0 -0.33 8 8
GNAZ 0.012 0 -10000 0 -10000 0 0
SHBG -0.021 0.16 -10000 0 -0.81 8 8
Gi family/GNB1/GNG2/GDP 0.005 0.12 -10000 0 -0.4 14 14
mol:T-DHT 0 0.001 0.001 2 -0.003 28 30
RAC1 0.012 0 -10000 0 -10000 0 0
GNRH1 -0.032 0.082 -10000 0 -10000 0 0
Gi family/GTP -0.007 0.088 -10000 0 -0.27 15 15
CDC42 0.012 0 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.044 0.15 -9999 0 -0.54 16 16
E-cadherin/beta catenin -0.034 0.18 -9999 0 -0.62 16 16
CTNNB1 0.012 0 -9999 0 -10000 0 0
JUP 0.012 0 -9999 0 -10000 0 0
CDH1 -0.054 0.22 -9999 0 -0.81 16 16
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex -0.045 0.099 -9999 0 -10000 0 0
STMN1 -0.07 0.1 -9999 0 -10000 0 0
Aurora B/RasGAP/Survivin -0.12 0.14 -9999 0 -0.29 19 19
Chromosomal passenger complex/Cul3 protein complex -0.059 0.11 -9999 0 -0.35 13 13
BIRC5 -0.12 0.15 -9999 0 -0.29 83 83
DES -0.29 0.29 -9999 0 -0.64 78 78
Aurora C/Aurora B/INCENP -0.047 0.074 -9999 0 -10000 0 0
Aurora B/TACC1 -0.059 0.08 -9999 0 -10000 0 0
Aurora B/PP2A -0.075 0.099 -9999 0 -0.36 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 -0.013 0.031 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0.001 0.003 -9999 0 -10000 0 0
NDC80 -0.09 0.13 -9999 0 -0.36 23 23
Cul3 protein complex -0.035 0.13 -9999 0 -0.54 13 13
KIF2C -0.049 0.084 -9999 0 -0.22 25 25
PEBP1 0.008 0.005 -9999 0 -10000 0 0
KIF20A -0.091 0.14 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.074 0.097 -9999 0 -10000 0 0
SEPT1 0.006 0.042 -9999 0 -0.28 4 4
SMC2 0.012 0 -9999 0 -10000 0 0
SMC4 0.012 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.04 0.072 -9999 0 -10000 0 0
PSMA3 0.012 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.002 -9999 0 -10000 0 0
H3F3B -0.042 0.065 -9999 0 -10000 0 0
AURKB -0.12 0.15 -9999 0 -10000 0 0
AURKC 0.012 0 -9999 0 -10000 0 0
CDCA8 -0.027 0.098 -9999 0 -0.3 23 23
cytokinesis -0.12 0.12 -9999 0 -0.39 5 5
Aurora B/Septin1 -0.099 0.13 -9999 0 -0.4 2 2
AURKA 0.005 0.047 -9999 0 -0.29 5 5
INCENP 0.008 0.006 -9999 0 -10000 0 0
KLHL13 -0.038 0.2 -9999 0 -0.81 12 12
BUB1 -0.1 0.14 -9999 0 -0.28 75 75
hSgo1/Aurora B/Survivin -0.12 0.15 -9999 0 -0.4 18 18
EVI5 0.011 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.079 0.099 -9999 0 -0.4 1 1
SGOL1 -0.015 0.085 -9999 0 -10000 0 0
CENPA -0.075 0.11 -9999 0 -0.24 48 48
NCAPG -0.07 0.13 -9999 0 -0.28 55 55
Aurora B/HC8 Proteasome -0.074 0.097 -9999 0 -10000 0 0
NCAPD2 0.012 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma -0.074 0.097 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
NCAPH -0.048 0.12 -9999 0 -0.28 40 40
NPM1 -0.052 0.066 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
KLHL9 0.008 0.058 -9999 0 -0.81 1 1
mitotic prometaphase -0.004 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.074 0.097 -9999 0 -10000 0 0
PPP1CC 0.012 0 -9999 0 -10000 0 0
Centraspindlin -0.09 0.11 -9999 0 -0.35 4 4
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
NSUN2 -0.052 0.066 -9999 0 -10000 0 0
MYLK -0.056 0.11 -9999 0 -0.53 6 6
KIF23 0.008 0.022 -9999 0 -0.29 1 1
VIM -0.071 0.1 -9999 0 -0.36 1 1
RACGAP1 0.01 0.003 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.052 0.066 -9999 0 -10000 0 0
Chromosomal passenger complex -0.089 0.13 -9999 0 -0.29 48 48
Chromosomal passenger complex/EVI5 -0.093 0.16 -9999 0 -0.37 19 19
TACC1 0.012 0 -9999 0 -10000 0 0
PPP2R5D 0.011 0.021 -9999 0 -0.28 1 1
CUL3 0.012 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.052 0.35 -9999 0 -0.97 9 9
HDAC7 0.014 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.064 0.24 -9999 0 -0.78 5 5
SMAD4 0.013 0 -9999 0 -10000 0 0
ID2 -0.052 0.35 -9999 0 -0.97 9 9
AP1 -0.08 0.23 -9999 0 -0.62 31 31
ABCG2 -0.054 0.35 -9999 0 -0.96 10 10
HIF1A 0.003 0.067 -9999 0 -10000 0 0
TFF3 -0.12 0.43 -9999 0 -1 20 20
GATA2 -0.14 0.32 -9999 0 -0.81 36 36
AKT1 0.006 0.069 -9999 0 -10000 0 0
response to hypoxia -0.009 0.074 -9999 0 -10000 0 0
MCL1 -0.052 0.35 -9999 0 -0.97 9 9
NDRG1 -0.052 0.35 -9999 0 -0.97 9 9
SERPINE1 -0.08 0.39 -9999 0 -0.99 16 16
FECH -0.052 0.35 -9999 0 -0.97 9 9
FURIN -0.052 0.35 -9999 0 -0.97 9 9
NCOA2 -0.053 0.22 -9999 0 -0.81 16 16
EP300 0.028 0.092 -9999 0 -10000 0 0
HMOX1 -0.063 0.37 -9999 0 -1 9 9
BHLHE40 -0.052 0.35 -9999 0 -0.97 9 9
BHLHE41 -0.073 0.36 -9999 0 -0.98 11 11
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.008 0.048 -9999 0 -10000 0 0
ENG 0.049 0.086 -9999 0 -10000 0 0
JUN 0.013 0.001 -9999 0 -10000 0 0
RORA -0.054 0.35 -9999 0 -0.96 10 10
ABCB1 -0.091 0.29 -9999 0 -1.3 10 10
TFRC -0.052 0.35 -9999 0 -0.98 9 9
CXCR4 -0.061 0.36 -9999 0 -1 9 9
TF -0.065 0.36 -9999 0 -1 11 11
CITED2 -0.052 0.35 -9999 0 -0.97 9 9
HIF1A/ARNT -0.078 0.38 -9999 0 -1.1 10 10
LDHA -0.016 0.032 -9999 0 -10000 0 0
ETS1 -0.052 0.35 -9999 0 -0.97 9 9
PGK1 -0.052 0.35 -9999 0 -0.97 9 9
NOS2 -0.086 0.41 -9999 0 -1.1 15 15
ITGB2 -0.075 0.36 -9999 0 -1 9 9
ALDOA -0.052 0.35 -9999 0 -0.97 9 9
Cbp/p300/CITED2 -0.035 0.34 -9999 0 -1.1 5 5
FOS -0.12 0.3 -9999 0 -0.81 31 31
HK2 -0.14 0.37 -9999 0 -1 12 12
SP1 0.017 0.02 -9999 0 -10000 0 0
GCK 0.01 0.17 -9999 0 -10000 0 0
HK1 -0.052 0.35 -9999 0 -0.97 9 9
NPM1 -0.052 0.35 -9999 0 -0.97 9 9
EGLN1 -0.052 0.35 -9999 0 -0.97 9 9
CREB1 0.019 0 -9999 0 -10000 0 0
PGM1 -0.052 0.35 -9999 0 -0.97 9 9
SMAD3 0.013 0 -9999 0 -10000 0 0
EDN1 -0.066 0.26 -9999 0 -0.82 12 12
IGFBP1 -0.098 0.41 -9999 0 -1 16 16
VEGFA 0.016 0.27 -9999 0 -0.87 2 2
HIF1A/JAB1 -0.006 0.026 -9999 0 -10000 0 0
CP -0.092 0.39 -9999 0 -0.97 15 15
CXCL12 -0.092 0.43 -9999 0 -1 24 24
COPS5 0.013 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 0 0 -9999 0 -10000 0 0
BNIP3 -0.052 0.35 -9999 0 -0.97 9 9
EGLN3 -0.055 0.36 -9999 0 -0.99 9 9
CA9 -0.13 0.38 -9999 0 -0.98 13 13
TERT -0.077 0.36 -9999 0 -1 9 9
ENO1 -0.052 0.35 -9999 0 -0.97 9 9
PFKL -0.052 0.35 -9999 0 -0.97 9 9
NCOA1 0.012 0.001 -9999 0 -10000 0 0
ADM -0.056 0.36 -9999 0 -1 9 9
ARNT 0.002 0.067 -9999 0 -10000 0 0
HNF4A -0.085 0.27 -9999 0 -0.81 24 24
ADFP -0.063 0.35 -9999 0 -0.98 9 9
SLC2A1 0.011 0.27 -9999 0 -0.82 4 4
LEP -0.067 0.36 -9999 0 -1 9 9
HIF1A/ARNT/Cbp/p300 -0.035 0.28 -9999 0 -0.78 6 6
EPO -0.016 0.25 -9999 0 -0.7 4 4
CREBBP 0.028 0.092 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 -0.065 0.24 -9999 0 -0.8 6 6
PFKFB3 -0.052 0.35 -9999 0 -0.97 9 9
NT5E -0.052 0.35 -9999 0 -0.97 9 9
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 0.014 0.022 -9999 0 -10000 0 0
NFATC2 -0.023 0.14 -9999 0 -0.55 13 13
NFATC3 0.014 0.022 -9999 0 -10000 0 0
CD40LG -0.089 0.25 -9999 0 -0.64 20 20
PTGS2 -0.14 0.35 -9999 0 -0.87 30 30
JUNB 0.012 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.003 0.008 -9999 0 -10000 0 0
CaM/Ca2+ -0.003 0.008 -9999 0 -10000 0 0
CALM1 0.011 0.006 -9999 0 -10000 0 0
JUN 0.011 0.006 -9999 0 -10000 0 0
mol:Ca2+ -0.003 0.009 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.001 0.003 -9999 0 -10000 0 0
FOSL1 0.006 0.042 -9999 0 -10000 0 0
CREM 0.012 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.052 0.12 -9999 0 -0.53 5 5
FOS -0.12 0.3 -9999 0 -0.82 31 31
IFNG -0.096 0.26 -9999 0 -0.63 23 23
AP-1/NFAT1-c-4 -0.11 0.29 -9999 0 -0.75 22 22
FASLG -0.096 0.26 -9999 0 -0.63 23 23
NFAT1-c-4/ICER1 -0.031 0.12 -9999 0 -0.45 13 13
IL2RA -0.098 0.25 -9999 0 -0.64 20 20
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSF2 -0.091 0.25 -9999 0 -0.64 20 20
JunB/Fra1/NFAT1-c-4 -0.038 0.11 -9999 0 -0.43 12 12
IL4 -0.09 0.25 -9999 0 -0.64 20 20
IL2 -0.006 0.027 -9999 0 -10000 0 0
IL3 -0.014 0.021 -9999 0 -10000 0 0
FKBP1A 0.012 0 -9999 0 -10000 0 0
BATF3 0.011 0.021 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.012 0 -9999 0 -10000 0 0
IL27-mediated signaling events

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
TGFB1 0.011 0.03 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.028 0.14 0.45 6 -10000 0 6
IL27/IL27R/JAK1 0.033 0.25 -10000 0 -0.62 8 8
TBX21 -0.007 0.19 -10000 0 -0.56 5 5
IL12B 0.005 0.021 -10000 0 -0.28 1 1
IL12A 0.009 0.004 -10000 0 -10000 0 0
IL6ST -0.1 0.29 -10000 0 -0.82 28 28
IL27RA/JAK1 0.024 0.027 -10000 0 -10000 0 0
IL27 -0.004 0.063 -10000 0 -0.3 4 4
TYK2 0.012 0.004 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.026 0.11 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.028 0.14 0.45 6 -10000 0 6
T cell proliferation during immune response 0.028 0.14 0.45 6 -10000 0 6
MAPKKK cascade -0.028 0.14 -10000 0 -0.45 6 6
STAT3 0.012 0 -10000 0 -10000 0 0
STAT2 0.012 0 -10000 0 -10000 0 0
STAT1 0.01 0.037 -10000 0 -0.28 3 3
IL12RB1 -0.008 0.074 -10000 0 -0.29 13 13
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.062 0.22 -10000 0 -0.51 19 19
IL27/IL27R/JAK2/TYK2 -0.028 0.14 -10000 0 -0.47 5 5
positive regulation of T cell mediated cytotoxicity -0.028 0.14 -10000 0 -0.45 6 6
STAT1 (dimer) 0.17 0.35 0.5 62 -0.66 6 68
JAK2 0.012 0.005 -10000 0 -10000 0 0
JAK1 0.014 0.004 -10000 0 -10000 0 0
STAT2 (dimer) -0.021 0.14 -10000 0 -0.45 4 4
T cell proliferation -0.068 0.21 -10000 0 -0.58 17 17
IL12/IL12R/TYK2/JAK2 0.013 0.047 -10000 0 -10000 0 0
IL17A -0.027 0.11 -10000 0 -10000 0 0
mast cell activation 0.028 0.14 0.45 6 -10000 0 6
IFNG -0.002 0.028 -10000 0 -0.09 2 2
T cell differentiation -0.003 0.005 -10000 0 -0.02 1 1
STAT3 (dimer) -0.021 0.14 -10000 0 -0.45 4 4
STAT5A (dimer) -0.021 0.14 -10000 0 -0.46 3 3
STAT4 (dimer) -0.03 0.15 -10000 0 -0.53 5 5
STAT4 -0.01 0.078 -10000 0 -10000 0 0
T cell activation -0.01 0.006 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.051 0.17 -10000 0 -0.53 1 1
GATA3 -1 0.62 -10000 0 -1.4 147 147
IL18 0.008 0.02 -10000 0 -10000 0 0
positive regulation of mast cell cytokine production -0.02 0.13 -10000 0 -0.44 4 4
IL27/EBI3 -0.022 0.1 -10000 0 -0.4 7 7
IL27RA 0.01 0.024 -10000 0 -10000 0 0
IL6 -0.075 0.24 -10000 0 -0.81 18 18
STAT5A 0.012 0 -10000 0 -10000 0 0
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 -0.001 0.017 -10000 0 -10000 0 0
IL1B -0.004 0.091 -10000 0 -0.63 4 4
EBI3 -0.035 0.12 -10000 0 -0.3 31 31
TNF -0.007 0.078 -10000 0 -0.63 2 2
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.043 0.18 -9999 0 -0.65 4 4
CRP -0.054 0.19 -9999 0 -0.66 6 6
cell cycle arrest -0.06 0.2 -9999 0 -0.71 7 7
TIMP1 -0.073 0.2 -9999 0 -0.58 10 10
IL6ST -0.1 0.29 -9999 0 -0.81 28 28
Rac1/GDP -0.065 0.2 -9999 0 -0.6 13 13
AP1 -0.064 0.17 -9999 0 -0.49 16 16
GAB2 0.012 0.003 -9999 0 -10000 0 0
TNFSF11 -0.058 0.19 -9999 0 -0.68 5 5
HSP90B1 0.014 0.044 -9999 0 -10000 0 0
GAB1 0.012 0.002 -9999 0 -10000 0 0
MAPK14 -0.038 0.18 -9999 0 -0.68 8 8
AKT1 0.047 0.013 -9999 0 -10000 0 0
FOXO1 0.052 0.012 -9999 0 -10000 0 0
MAP2K6 -0.049 0.19 -9999 0 -0.63 10 10
mol:GTP 0 0.001 -9999 0 -10000 0 0
MAP2K4 -0.054 0.19 -9999 0 -0.6 11 11
MITF -0.054 0.19 -9999 0 -0.57 13 13
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.012 0 -9999 0 -10000 0 0
A2M 0.006 0.14 -9999 0 -1.4 2 2
CEBPB 0.009 0.042 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.006 0.074 -9999 0 -10000 0 0
STAT3 -0.064 0.21 -9999 0 -0.77 7 7
STAT1 -0.009 0.022 -9999 0 -10000 0 0
CEBPD -0.043 0.18 -9999 0 -0.64 5 5
PIK3CA 0.013 0 -9999 0 -10000 0 0
PI3K 0.02 0.002 -9999 0 -10000 0 0
JUN 0.011 0.001 -9999 0 -10000 0 0
PIAS3/MITF -0.042 0.18 -9999 0 -0.76 6 6
MAPK11 -0.038 0.18 -9999 0 -0.68 8 8
STAT3 (dimer)/FOXO1 -0.015 0.18 -9999 0 -0.57 5 5
GRB2/SOS1/GAB family -0.073 0.16 -9999 0 -0.72 6 6
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.069 0.2 -9999 0 -0.49 25 25
GRB2 0.012 0.002 -9999 0 -10000 0 0
JAK2 0.012 0 -9999 0 -10000 0 0
LBP -0.26 0.44 -9999 0 -0.95 54 54
PIK3R1 0.013 0 -9999 0 -10000 0 0
JAK1 0.013 0.003 -9999 0 -10000 0 0
MYC -0.045 0.18 -9999 0 -0.65 4 4
FGG -0.06 0.2 -9999 0 -0.68 4 4
macrophage differentiation -0.06 0.2 -9999 0 -0.71 7 7
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.1 0.22 -9999 0 -0.51 41 41
JUNB -0.043 0.18 -9999 0 -0.63 4 4
FOS -0.12 0.3 -9999 0 -0.81 31 31
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.065 0.2 -9999 0 -0.5 22 22
STAT1/PIAS1 -0.056 0.18 -9999 0 -0.54 14 14
GRB2/SOS1/GAB family/SHP2/PI3K 0.031 0.02 -9999 0 -10000 0 0
STAT3 (dimer) -0.062 0.21 -9999 0 -0.74 7 7
PRKCD -0.042 0.18 -9999 0 -0.63 7 7
IL6R 0.013 0.003 -9999 0 -10000 0 0
SOCS3 -0.033 0.19 -9999 0 -0.77 7 7
gp130 (dimer)/JAK1/JAK1/LMO4 -0.055 0.2 -9999 0 -0.54 28 28
Rac1/GTP -0.068 0.19 -9999 0 -0.6 13 13
HCK -0.027 0.11 -9999 0 -0.31 24 24
MAPKKK cascade 0.009 0.058 -9999 0 -10000 0 0
bone resorption -0.055 0.19 -9999 0 -0.64 5 5
IRF1 -0.043 0.18 -9999 0 -0.65 4 4
mol:GDP -0.078 0.2 -9999 0 -0.54 20 20
SOS1 0.011 0.004 -9999 0 -10000 0 0
VAV1 -0.08 0.21 -9999 0 -0.55 20 20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.046 0.19 -9999 0 -0.71 8 8
PTPN11 -0.007 0.016 -9999 0 -10000 0 0
IL6/IL6RA -0.049 0.18 -9999 0 -0.62 18 18
gp130 (dimer)/TYK2/TYK2/LMO4 -0.06 0.2 -9999 0 -0.54 28 28
gp130 (dimer)/JAK2/JAK2/LMO4 -0.06 0.2 -9999 0 -0.54 28 28
IL6 -0.076 0.24 -9999 0 -0.64 27 27
PIAS3 0.012 0 -9999 0 -10000 0 0
PTPRE 0.009 0.009 -9999 0 -10000 0 0
PIAS1 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.073 0.2 -9999 0 -0.41 41 41
LMO4 0.013 0.008 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.1 0.18 -9999 0 -0.77 7 7
MCL1 0.052 0.012 -9999 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.024 0.1 -10000 0 -0.47 10 10
ER alpha/Gai/GDP/Gbeta gamma -0.012 0.17 -10000 0 -0.6 10 10
AKT1 -0.012 0.19 -10000 0 -0.85 10 10
PIK3CA 0.012 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.014 0.2 -10000 0 -0.86 10 10
mol:Ca2+ -0.14 0.26 -10000 0 -0.54 54 54
IGF1R 0.012 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.036 0.14 -10000 0 -0.55 13 13
SHC1 0.012 0 -10000 0 -10000 0 0
apoptosis 0.009 0.18 0.8 10 -10000 0 10
RhoA/GTP -0.021 0.09 -10000 0 -0.41 10 10
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.044 0.14 -10000 0 -0.61 10 10
regulation of stress fiber formation -0.023 0.091 -10000 0 -10000 0 0
E2/ERA-ERB (dimer) -0.028 0.12 -10000 0 -0.55 10 10
KRAS 0.012 0 -10000 0 -10000 0 0
G13/GTP -0.011 0.11 -10000 0 -0.5 10 10
pseudopodium formation 0.023 0.091 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1 -0.028 0.12 -10000 0 -0.55 10 10
GRB2 0.012 0 -10000 0 -10000 0 0
GNG2 0.012 0 -10000 0 -10000 0 0
GNAO1 -0.051 0.21 -10000 0 -0.72 17 17
HRAS 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.002 0.17 -10000 0 -0.64 11 11
E2/ER beta (dimer) 0.008 0.014 -10000 0 -10000 0 0
mol:GDP -0.028 0.12 -10000 0 -0.55 10 10
mol:NADP -0.002 0.17 -10000 0 -0.64 11 11
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 -0.15 0.28 -10000 0 -0.56 54 54
IGF-1R heterotetramer 0.012 0 -10000 0 -10000 0 0
PLCB1 -0.14 0.28 -10000 0 -0.57 54 54
PLCB2 -0.12 0.25 -10000 0 -0.57 43 43
IGF1 -0.009 0.13 -10000 0 -0.81 5 5
mol:L-citrulline -0.002 0.17 -10000 0 -0.64 11 11
RHOA 0.012 0 -10000 0 -10000 0 0
Gai/GDP -0.056 0.19 -10000 0 -0.74 14 14
JNK cascade 0.008 0.014 -10000 0 -10000 0 0
BCAR1 0.012 0 -10000 0 -10000 0 0
ESR2 0.011 0.021 -10000 0 -0.28 1 1
GNAQ 0.012 0 -10000 0 -10000 0 0
ESR1 -0.03 0.18 -10000 0 -0.81 10 10
Gq family/GDP/Gbeta gamma -0.05 0.16 -10000 0 -0.54 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.016 0.082 -10000 0 -0.36 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.044 0.14 -10000 0 -0.61 10 10
GNAZ 0.012 0 -10000 0 -10000 0 0
E2/ER alpha (dimer) -0.023 0.14 -10000 0 -0.63 10 10
STRN 0 0.1 -10000 0 -0.81 3 3
GNAL 0.012 0 -10000 0 -10000 0 0
PELP1 0.012 0 -10000 0 -10000 0 0
MAPK11 0.017 0.012 -10000 0 -10000 0 0
GNAI2 0.012 0 -10000 0 -10000 0 0
GNAI3 0.012 0 -10000 0 -10000 0 0
GNAI1 0.008 0.058 -10000 0 -0.81 1 1
HBEGF -0.026 0.16 -10000 0 -0.54 11 11
cAMP biosynthetic process -0.023 0.098 -10000 0 -0.44 10 10
SRC -0.004 0.16 -10000 0 -0.56 10 10
PI3K 0.018 0 -10000 0 -10000 0 0
GNB1 0.012 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.025 0.1 -10000 0 -0.48 10 10
SOS1 0.012 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.041 0.13 -10000 0 -0.51 11 11
Gs family/GTP -0.023 0.099 -10000 0 -0.45 10 10
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.023 0 -10000 0 -10000 0 0
vasodilation 0 0.16 -10000 0 -0.6 11 11
mol:DAG -0.15 0.28 -10000 0 -0.56 54 54
Gs family/GDP/Gbeta gamma -0.023 0.097 -10000 0 -0.44 10 10
MSN 0.023 0.097 -10000 0 -10000 0 0
Gq family/GTP -0.12 0.27 -10000 0 -0.6 43 43
mol:PI-3-4-5-P3 -0.012 0.19 -10000 0 -0.82 10 10
NRAS 0.012 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0 0.16 0.6 11 -10000 0 11
GRB2/SOS1 0.018 0 -10000 0 -10000 0 0
RhoA/GDP -0.026 0.11 -10000 0 -0.51 10 10
NOS3 -0.004 0.18 -10000 0 -0.69 11 11
GNA11 -0.005 0.12 -10000 0 -0.81 4 4
MAPKKK cascade 0.003 0.17 -10000 0 -0.61 13 13
E2/ER alpha (dimer)/PELP1/Src -0.047 0.15 -10000 0 -0.65 10 10
ruffle organization 0.023 0.091 -10000 0 -10000 0 0
ROCK2 0.016 0.11 -10000 0 -0.38 13 13
GNA14 -0.16 0.34 -10000 0 -0.81 42 42
GNA15 -0.006 0.071 -10000 0 -10000 0 0
GNA13 0.011 0.021 -10000 0 -10000 0 0
MMP9 -0.047 0.16 -10000 0 -0.53 12 12
MMP2 0.001 0.16 -10000 0 -0.53 11 11
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.03 0.055 -9999 0 -10000 0 0
adherens junction organization 0.011 0.095 -9999 0 -0.3 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0.035 0.055 -9999 0 -10000 0 0
FMN1 -0.001 0.12 -9999 0 -0.33 22 22
mol:IP3 0.022 0.056 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.007 0.097 -9999 0 -0.32 16 16
CTNNB1 0.013 0.004 -9999 0 -10000 0 0
AKT1 0.026 0.065 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.033 0.16 -9999 0 -0.56 16 16
CTNND1 0.013 0.001 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.091 -9999 0 -0.29 16 16
VASP 0.013 0.092 -9999 0 -0.3 16 16
ZYX 0.013 0.092 -9999 0 -0.3 16 16
JUB 0.013 0.092 -9999 0 -0.3 16 16
EGFR(dimer) 0.013 0.092 -9999 0 -0.3 16 16
E-cadherin/beta catenin-gamma catenin -0.042 0.14 -9999 0 -0.52 16 16
mol:PI-3-4-5-P3 -0.017 0.057 -9999 0 -10000 0 0
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
PI3K 0.019 0.068 -9999 0 -10000 0 0
FYN -0.22 0.18 -9999 0 -0.49 9 9
mol:Ca2+ 0.022 0.055 -9999 0 -10000 0 0
JUP 0.013 0.004 -9999 0 -10000 0 0
PIK3R1 0.013 0.001 -9999 0 -10000 0 0
mol:DAG 0.022 0.056 -9999 0 -10000 0 0
CDH1 -0.055 0.22 -9999 0 -0.81 16 16
RhoA/GDP 0.035 0.055 -9999 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.014 0.091 -9999 0 -0.29 16 16
SRC 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
EGFR 0.012 0 -9999 0 -10000 0 0
CASR -0.28 0.22 -9999 0 -0.42 133 133
RhoA/GTP -0.012 0.04 -9999 0 -10000 0 0
AKT2 0.026 0.065 -9999 0 -10000 0 0
actin cable formation 0.006 0.12 -9999 0 -0.41 6 6
apoptosis 0.015 0.051 -9999 0 -10000 0 0
CTNNA1 0.013 0.001 -9999 0 -10000 0 0
mol:GDP 0.029 0.057 -9999 0 -10000 0 0
PIP5K1A 0.013 0.092 -9999 0 -0.3 16 16
PLCG1 0.022 0.057 -9999 0 -10000 0 0
Rac1/GTP -0.022 0.074 -9999 0 -10000 0 0
homophilic cell adhesion 0.001 0.001 -9999 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.019 0.093 -10000 0 -0.39 2 2
TBX21 -0.029 0.26 -10000 0 -0.77 9 9
B2M 0.012 0.004 -10000 0 -10000 0 0
TYK2 0.015 0.016 -10000 0 -10000 0 0
IL12RB1 -0.005 0.082 -10000 0 -0.31 13 13
GADD45B -0.008 0.22 -10000 0 -0.93 2 2
IL12RB2 -0.13 0.16 -10000 0 -0.29 92 92
GADD45G -0.013 0.24 -10000 0 -0.82 6 6
natural killer cell activation 0.005 0.019 -10000 0 -10000 0 0
RELB 0.012 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
IL18 0.012 0.03 -10000 0 -0.28 1 1
IL2RA -0.021 0.093 -10000 0 -10000 0 0
IFNG -0.016 0.08 -10000 0 -0.28 16 16
STAT3 (dimer) -0.013 0.23 -10000 0 -0.61 10 10
HLA-DRB5 -0.011 0.1 -10000 0 -0.38 11 11
FASLG -0.037 0.27 -10000 0 -0.77 11 11
NF kappa B2 p52/RelB -0.1 0.19 -10000 0 -0.64 14 14
CD4 -0.001 0.058 -10000 0 -0.28 8 8
SOCS1 0.002 0.085 -10000 0 -0.64 3 3
EntrezGene:6955 -0.003 0.011 -10000 0 -10000 0 0
CD3D -0.043 0.12 -10000 0 -0.29 36 36
CD3E -0.017 0.1 -10000 0 -0.34 11 11
CD3G -0.007 0.074 -10000 0 -0.3 12 12
IL12Rbeta2/JAK2 -0.074 0.12 -10000 0 -0.63 2 2
CCL3 -0.045 0.29 -10000 0 -0.94 8 8
CCL4 -0.038 0.27 -10000 0 -0.79 10 10
HLA-A 0.009 0.03 -10000 0 -0.29 2 2
IL18/IL18R 0.025 0.084 -10000 0 -0.53 1 1
NOS2 -0.076 0.39 -10000 0 -1.1 20 20
IL12/IL12R/TYK2/JAK2/SPHK2 -0.014 0.088 -10000 0 -0.41 1 1
IL1R1 -0.025 0.25 -10000 0 -0.7 10 10
IL4 -0.002 0.02 -10000 0 -10000 0 0
JAK2 0.015 0.016 -10000 0 -10000 0 0
EntrezGene:6957 -0.003 0.01 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.016 0.14 -10000 0 -0.49 10 10
RAB7A 0.013 0.2 -10000 0 -0.67 2 2
lysosomal transport 0.014 0.2 -10000 0 -0.64 2 2
FOS -0.18 0.5 -10000 0 -1.2 33 33
STAT4 (dimer) -0.009 0.23 -10000 0 -0.72 6 6
STAT5A (dimer) -0.11 0.2 -10000 0 -0.68 14 14
GZMA -0.029 0.26 -10000 0 -0.8 9 9
GZMB -0.035 0.27 -10000 0 -0.86 9 9
HLX 0.011 0.021 -10000 0 -10000 0 0
LCK -0.032 0.27 -10000 0 -0.72 14 14
TCR/CD3/MHC II/CD4 -0.034 0.13 -10000 0 -0.38 12 12
IL2/IL2R -0.012 0.087 -10000 0 -0.44 3 3
MAPK14 -0.001 0.23 -10000 0 -0.64 7 7
CCR5 -0.02 0.24 -10000 0 -0.67 9 9
IL1B -0.003 0.12 -10000 0 -0.73 5 5
STAT6 0.008 0.091 -10000 0 -10000 0 0
STAT4 -0.01 0.078 -10000 0 -10000 0 0
STAT3 0.012 0 -10000 0 -10000 0 0
STAT1 0.008 0.036 -10000 0 -0.28 3 3
NFKB1 0.012 0 -10000 0 -10000 0 0
NFKB2 0.012 0 -10000 0 -10000 0 0
IL12B 0.011 0.026 -10000 0 -0.25 1 1
CD8A -0.016 0.09 -10000 0 -0.29 19 19
CD8B -0.01 0.081 -10000 0 -0.3 9 9
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.018 0.093 0.39 2 -10000 0 2
IL2RB -0.022 0.095 -10000 0 -0.28 23 23
proteasomal ubiquitin-dependent protein catabolic process -0.005 0.22 -10000 0 -0.66 6 6
IL2RG 0.003 0.051 -10000 0 -10000 0 0
IL12 0.021 0.031 -10000 0 -10000 0 0
STAT5A 0.012 0 -10000 0 -10000 0 0
CD247 -0.001 0.06 -10000 0 -0.29 8 8
IL2 0.003 0.021 -10000 0 -0.28 1 1
SPHK2 0.012 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.014 0.017 -10000 0 -10000 0 0
IL12/IL12R/TYK2/JAK2 -0.036 0.27 -10000 0 -0.7 16 16
MAP2K3 -0.004 0.23 -10000 0 -0.62 8 8
RIPK2 0.012 0 -10000 0 -10000 0 0
MAP2K6 -0.004 0.23 -10000 0 -0.62 8 8
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.066 -10000 0 -0.46 3 3
IL18RAP -0.022 0.1 -10000 0 -0.28 25 25
IL12Rbeta1/TYK2 0.007 0.063 -10000 0 -10000 0 0
EOMES -0.012 0.08 -10000 0 -10000 0 0
STAT1 (dimer) -0.017 0.23 -10000 0 -0.64 10 10
T cell proliferation 0.008 0.2 -10000 0 -0.52 7 7
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.011 0.059 -10000 0 -0.8 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.081 0.17 -10000 0 -0.57 7 7
ATF2 0.008 0.22 -10000 0 -0.61 6 6
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.11 0.11 -10000 0 -0.62 3 3
epithelial cell differentiation -0.21 0.2 -10000 0 -0.44 67 67
ITCH 0.046 0.022 -10000 0 -10000 0 0
WWP1 -0.094 0.085 -10000 0 -10000 0 0
FYN 0.012 0 -10000 0 -10000 0 0
EGFR 0.012 0 -10000 0 -10000 0 0
PRL 0 0.021 -10000 0 -0.28 1 1
neuron projection morphogenesis -0.034 0.078 -10000 0 -0.48 2 2
PTPRZ1 -0.019 0.13 -10000 0 -0.61 8 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.065 0.067 -10000 0 -0.5 3 3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.082 0.095 -10000 0 -0.58 3 3
ADAM17 0.046 0.022 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.13 0.11 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.12 0.11 -10000 0 -0.62 3 3
NCOR1 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.069 0.089 -10000 0 -0.54 3 3
GRIN2B -0.063 0.087 -10000 0 -0.52 3 3
ErbB4/ErbB2/betacellulin -0.072 0.11 -10000 0 -0.59 5 5
STAT1 0.008 0.036 -10000 0 -0.28 3 3
HBEGF 0 0.1 -10000 0 -0.81 3 3
PRLR -0.36 0.41 -10000 0 -0.81 90 90
E4ICDs/ETO2 -0.1 0.093 -10000 0 -0.31 1 1
axon guidance -0.036 0.055 -10000 0 -10000 0 0
NEDD4 0.046 0.022 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.28 0.32 -10000 0 -0.63 90 90
CBFA2T3 0.011 0.021 -10000 0 -0.28 1 1
ErbB4/ErbB2/HBEGF -0.067 0.089 -10000 0 -0.54 3 3
MAPK3 -0.041 0.08 -10000 0 -0.5 2 2
STAT1 (dimer) -0.11 0.095 -10000 0 -10000 0 0
MAPK1 -0.041 0.08 -10000 0 -0.5 2 2
JAK2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 1 beta -0.069 0.089 -10000 0 -0.54 3 3
NRG1 0.028 0.086 -10000 0 -0.62 3 3
NRG3 -0.011 0.11 -10000 0 -0.81 3 3
NRG2 0.004 0.082 -10000 0 -0.81 2 2
NRG4 0.004 0.065 -10000 0 -0.46 3 3
heart development -0.036 0.055 -10000 0 -10000 0 0
neural crest cell migration -0.069 0.088 -10000 0 -0.54 3 3
ERBB2 0.041 0.013 -10000 0 -10000 0 0
WWOX/E4ICDs -0.1 0.092 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.093 0.091 -10000 0 -0.63 1 1
apoptosis 0.12 0.091 0.51 3 -10000 0 3
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.11 0.1 -10000 0 -0.59 2 2
ErbB4/ErbB2/epiregulin -0.13 0.099 -10000 0 -10000 0 0
ErbB4/ErbB4/betacellulin/betacellulin -0.12 0.13 -10000 0 -0.68 5 5
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.3 0.24 -10000 0 -0.55 92 92
MDM2 -0.1 0.094 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.061 0.069 -10000 0 -0.54 3 3
STAT5A -0.027 0.052 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.069 0.089 -10000 0 -0.54 3 3
DLG4 0.012 0 -10000 0 -10000 0 0
GRB2/SHC 0.018 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.1 0.07 -10000 0 -10000 0 0
STAT5A (dimer) -0.22 0.21 -10000 0 -0.61 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.027 0.051 -10000 0 -10000 0 0
LRIG1 0.011 0.021 -10000 0 -0.28 1 1
EREG -0.13 0.15 -10000 0 -0.28 96 96
BTC -0.009 0.13 -10000 0 -0.81 5 5
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.036 0.055 -10000 0 -10000 0 0
ERBB4 -0.13 0.11 -10000 0 -10000 0 0
STAT5B 0.012 0 -10000 0 -10000 0 0
YAP1 -0.035 0.023 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.065 0.075 -10000 0 -0.59 1 1
glial cell differentiation 0.1 0.07 -10000 0 -10000 0 0
WWOX 0.012 0 -10000 0 -10000 0 0
cell proliferation -0.042 0.097 -10000 0 -0.45 4 4
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.031 0.11 -10000 0 -0.45 12 12
HDAC1 0.008 0.002 -10000 0 -10000 0 0
AES 0.011 0 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
DTX1 0.004 0.082 -10000 0 -0.81 2 2
LRP6/FZD1 0.013 0.031 -10000 0 -10000 0 0
TLE1 0.011 0 -10000 0 -10000 0 0
AP1 -0.14 0.25 -10000 0 -0.43 73 73
NCSTN 0.012 0 -10000 0 -10000 0 0
ADAM10 0.01 0.021 -10000 0 -0.28 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.049 0.041 -10000 0 -10000 0 0
NICD/RBPSUH -0.001 0.01 -10000 0 -10000 0 0
WIF1 0.002 0.041 -10000 0 -0.28 4 4
NOTCH1 -0.001 0.011 -10000 0 -10000 0 0
PSENEN 0.012 0 -10000 0 -10000 0 0
KREMEN2 -0.025 0.096 -10000 0 -0.28 24 24
DKK1 -0.01 0.073 -10000 0 -0.28 13 13
beta catenin/beta TrCP1 0.076 0.086 -10000 0 -10000 0 0
APH1B 0.008 0.058 -10000 0 -0.81 1 1
APH1A 0.012 0 -10000 0 -10000 0 0
AXIN1 -0.014 0.036 -10000 0 -10000 0 0
CtBP/CBP/TCF1/TLE1/AES 0.014 0.045 -10000 0 -0.34 3 3
PSEN1 0.012 0 -10000 0 -10000 0 0
FOS -0.12 0.3 -10000 0 -0.81 31 31
JUN 0.012 0 -10000 0 -10000 0 0
MAP3K7 0.01 0.001 -10000 0 -10000 0 0
CTNNB1 0.074 0.093 0.23 50 -10000 0 50
MAPK3 0.012 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.024 0.074 -10000 0 -0.42 4 4
HNF1A -0.001 0.1 -10000 0 -0.81 3 3
CTBP1 0.011 0 -10000 0 -10000 0 0
MYC 0.023 0.029 -10000 0 -10000 0 0
NKD1 -0.2 0.36 -10000 0 -0.81 50 50
FZD1 0.005 0.046 -10000 0 -0.28 5 5
NOTCH1 precursor/Deltex homolog 1 -0.006 0.046 -10000 0 -0.45 2 2
apoptosis -0.14 0.25 -10000 0 -0.43 73 73
Delta 1/NOTCHprecursor -0.031 0.11 -10000 0 -0.45 12 12
DLL1 -0.045 0.2 -10000 0 -0.66 17 17
PPARD 0.026 0.006 -10000 0 -10000 0 0
Gamma Secretase -0.002 0.033 -10000 0 -0.46 1 1
APC -0.014 0.036 -10000 0 -10000 0 0
DVL1 0 0.006 -10000 0 -10000 0 0
CSNK2A1 0.013 0 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.001 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.027 0.063 -10000 0 -0.29 4 4
LRP6 0.012 0 -10000 0 -10000 0 0
CSNK1A1 0.013 0 -10000 0 -10000 0 0
NLK 0.012 0.002 -10000 0 -10000 0 0
CCND1 0.026 0.006 -10000 0 -10000 0 0
WNT1 -0.027 0.098 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.064 0.045 -10000 0 -10000 0 0
DKK2 0 0.087 -10000 0 -0.55 4 4
NOTCH1 precursor/DVL1 0.003 0.011 -10000 0 -10000 0 0
GSK3B 0.012 0 -10000 0 -10000 0 0
FRAT1 0.011 0 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.006 0.046 -10000 0 -0.45 2 2
PPP2R5D 0.092 0.16 0.36 50 -10000 0 50
MAPK1 0.012 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.003 0.056 -10000 0 -10000 0 0
RBPJ 0.012 0 -10000 0 -10000 0 0
CREBBP 0.015 0.002 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.016 0.02 -9999 0 -10000 0 0
VLDLR 0.012 0 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
LRPAP1 0.012 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
ITGA3 -0.001 0.062 -9999 0 -10000 0 0
RELN/VLDLR/Fyn -0.079 0.12 -9999 0 -0.54 10 10
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.009 0.065 -9999 0 -0.46 4 4
AKT1 -0.022 0.082 -9999 0 -0.32 10 10
MAP2K7 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
DAB1 -0.005 0.054 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.072 0.13 -9999 0 -0.54 10 10
LRPAP1/LRP8 0.012 0.034 -9999 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.073 0.12 -9999 0 -0.51 10 10
DAB1/alpha3/beta1 Integrin -0.063 0.1 -9999 0 -0.46 10 10
long-term memory -0.16 0.22 -9999 0 -0.52 50 50
DAB1/LIS1 -0.063 0.11 -9999 0 -0.47 10 10
DAB1/CRLK/C3G -0.059 0.1 -9999 0 -0.46 10 10
PIK3CA 0.012 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.064 0.11 -9999 0 -0.48 10 10
ARHGEF2 0.012 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.16 0.34 -9999 0 -0.8 43 43
CDK5R1 0.009 0.03 -9999 0 -0.28 2 2
RELN -0.14 0.21 -9999 0 -0.35 83 83
PIK3R1 0.012 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.083 0.13 -9999 0 -0.56 10 10
GRIN2A/RELN/LRP8/DAB1/Fyn -0.17 0.22 -9999 0 -0.54 50 50
MAPK8 -0.005 0.12 -9999 0 -0.81 4 4
RELN/VLDLR/DAB1 -0.067 0.13 -9999 0 -0.52 10 10
ITGB1 0.012 0 -9999 0 -10000 0 0
MAP1B -0.052 0.12 -9999 0 -0.5 10 10
RELN/LRP8 -0.083 0.13 -9999 0 -0.57 10 10
GRIN2B/RELN/LRP8/DAB1/Fyn -0.073 0.11 -9999 0 -0.5 10 10
PI3K 0.018 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.009 0.042 -9999 0 -10000 0 0
RAP1A -0.027 0.11 -9999 0 -0.5 3 3
PAFAH1B1 0.012 0 -9999 0 -10000 0 0
MAPK8IP1 0.012 0 -9999 0 -10000 0 0
CRLK/C3G 0.018 0 -9999 0 -10000 0 0
GRIN2B 0.002 0.036 -9999 0 -0.28 3 3
NCK2 0.012 0 -9999 0 -10000 0 0
neuron differentiation -0.009 0.072 -9999 0 -0.29 5 5
neuron adhesion -0.019 0.11 -9999 0 -0.47 3 3
LRP8 0.003 0.051 -9999 0 -0.28 6 6
GSK3B -0.014 0.078 -9999 0 -0.37 1 1
RELN/VLDLR/DAB1/Fyn -0.07 0.11 -9999 0 -0.48 10 10
MAP3K11 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.032 0.087 -9999 0 -0.35 10 10
CDK5 0.012 0 -9999 0 -10000 0 0
MAPT -0.022 0.16 -9999 0 -0.76 9 9
neuron migration -0.009 0.11 -9999 0 -0.42 10 10
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.009 0.073 -9999 0 -0.29 3 3
RELN/VLDLR -0.054 0.13 -9999 0 -0.52 10 10
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.012 0.038 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.034 0.1 -9999 0 -0.52 3 3
JUN -0.001 0.13 -9999 0 -0.55 6 6
HRAS 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 -0.028 0.16 -9999 0 -0.52 18 18
RAP1A 0.012 0 -9999 0 -10000 0 0
FRS2 0.012 0 -9999 0 -10000 0 0
RAP1A/GDP 0.009 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.028 0.16 -9999 0 -0.53 18 18
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.014 0.12 -9999 0 -0.5 11 11
RHOA 0.012 0 -9999 0 -10000 0 0
RAP1A/GTP -0.045 0.14 -9999 0 -0.47 18 18
GRB7 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF -0.028 0.16 -9999 0 -0.52 18 18
MAPKKK cascade -0.04 0.12 -9999 0 -0.46 8 8
BCAR1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.023 0.15 -9999 0 -0.58 12 12
lamellipodium assembly -0.031 0.095 -9999 0 -0.36 11 11
RET51/GFRalpha1/GDNF/SHC -0.028 0.16 -9999 0 -0.52 18 18
PIK3CA 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.014 0.12 -9999 0 -0.5 11 11
RET9/GFRalpha1/GDNF/Shank3 -0.014 0.12 -9999 0 -0.5 11 11
MAPK3 -0.01 0.14 -9999 0 -0.44 18 18
DOK1 0.011 0.021 -9999 0 -0.28 1 1
DOK6 -0.1 0.29 -9999 0 -0.81 28 28
PXN 0.012 0 -9999 0 -10000 0 0
neurite development -0.024 0.15 -9999 0 -0.6 5 5
DOK5 -0.002 0.1 -9999 0 -0.68 4 4
GFRA1 -0.04 0.19 -9999 0 -0.67 15 15
MAPK8 -0.009 0.14 -9999 0 -0.58 6 6
HRAS/GTP -0.046 0.14 -9999 0 -0.49 18 18
tube development -0.028 0.11 -9999 0 -0.47 11 11
MAPK1 -0.01 0.14 -9999 0 -0.44 18 18
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 0.002 0.083 -9999 0 -0.34 11 11
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC 0.012 0 -9999 0 -10000 0 0
PDLIM7 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.11 0.22 -9999 0 -0.52 42 42
SHC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.028 0.16 -9999 0 -0.52 18 18
RET51/GFRalpha1/GDNF/Dok5 -0.036 0.17 -9999 0 -0.52 21 21
PRKCA 0.012 0 -9999 0 -10000 0 0
HRAS/GDP 0.009 0 -9999 0 -10000 0 0
CREB1 0.001 0.1 -9999 0 -0.39 11 11
PIK3R1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 0.002 0.083 -9999 0 -0.34 11 11
RET51/GFRalpha1/GDNF/Grb7 -0.028 0.16 -9999 0 -0.52 18 18
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.021 0.16 -9999 0 -0.81 8 8
DOK4 0.012 0 -9999 0 -10000 0 0
JNK cascade -0.001 0.13 -9999 0 -0.53 6 6
RET9/GFRalpha1/GDNF/FRS2 -0.014 0.12 -9999 0 -0.5 11 11
SHANK3 0.012 0 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 0.002 0.084 -9999 0 -0.34 11 11
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.006 0.11 -9999 0 -0.35 18 18
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.007 0.11 -9999 0 -0.36 18 18
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.008 0.12 -9999 0 -0.36 18 18
PI3K 0 0.17 -9999 0 -0.57 11 11
SOS1 0.012 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.028 0.11 -9999 0 -0.47 11 11
GRB10 0.012 0 -9999 0 -10000 0 0
activation of MAPKK activity -0.002 0.097 -9999 0 -0.35 7 7
RET51/GFRalpha1/GDNF/FRS2 -0.028 0.16 -9999 0 -0.52 18 18
GAB1 0.012 0 -9999 0 -10000 0 0
IRS1 -0.002 0.1 -9999 0 -0.68 4 4
IRS2 0.011 0.021 -9999 0 -0.28 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.008 0.12 -9999 0 -0.36 18 18
RET51/GFRalpha1/GDNF/PKC alpha -0.028 0.16 -9999 0 -0.52 18 18
GRB2 0.012 0 -9999 0 -10000 0 0
PRKACA 0.012 0 -9999 0 -10000 0 0
GDNF 0.003 0.005 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.036 0.18 -9999 0 -0.57 19 19
Rac1/GTP -0.037 0.11 -9999 0 -0.44 11 11
RET9/GFRalpha1/GDNF -0.034 0.13 -9999 0 -0.55 11 11
GFRalpha1/GDNF -0.028 0.15 -9999 0 -0.63 11 11
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.021 0.16 -9999 0 -0.81 8 8
mol:S1P 0.001 0 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.008 0.082 -9999 0 -0.28 7 7
GNAO1 -0.049 0.21 -9999 0 -0.72 17 17
S1P/S1P3/G12/G13 -0.019 0.15 -9999 0 -0.5 17 17
AKT1 -0.014 0.16 -9999 0 -0.69 8 8
AKT3 0.014 0.094 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.021 0.16 -9999 0 -0.81 8 8
GNAI2 0.014 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
GNAI1 0.009 0.058 -9999 0 -0.81 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 -0.057 0.23 -9999 0 -0.81 17 17
S1PR2 0.012 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.024 0.19 -9999 0 -0.46 25 25
MAPK3 -0.016 0.18 -9999 0 -0.87 6 6
MAPK1 -0.016 0.18 -9999 0 -0.87 6 6
JAK2 -0.018 0.18 -9999 0 -0.8 7 7
CXCR4 -0.026 0.18 -9999 0 -0.8 7 7
FLT1 0.007 0.083 -9999 0 -0.81 2 2
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
SRC -0.016 0.18 -9999 0 -0.87 6 6
S1P/S1P3/Gi -0.024 0.19 -9999 0 -0.46 25 25
RAC1 0.012 0 -9999 0 -10000 0 0
RhoA/GTP -0.017 0.18 -9999 0 -0.84 6 6
VEGFA 0.013 0.021 -9999 0 -0.28 1 1
S1P/S1P2/Gi 0.01 0.095 -9999 0 -0.32 14 14
VEGFR1 homodimer/VEGFA homodimer 0.018 0.066 -9999 0 -0.62 2 2
RHOA 0.012 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.09 0.2 -9999 0 -0.41 52 52
GNAQ 0.012 0 -9999 0 -10000 0 0
GNAZ 0.013 0 -9999 0 -10000 0 0
G12/G13 0.017 0.014 -9999 0 -10000 0 0
GNA14 -0.16 0.34 -9999 0 -0.81 42 42
GNA15 -0.006 0.071 -9999 0 -10000 0 0
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.011 0.021 -9999 0 -10000 0 0
GNA11 -0.005 0.12 -9999 0 -0.81 4 4
Rac1/GTP -0.017 0.18 -9999 0 -0.84 6 6
Visual signal transduction: Rods

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
mol:K + 0.012 0 -9999 0 -10000 0 0
GNAT1/GTP -0.001 0.024 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.003 0.022 -9999 0 -10000 0 0
PDE6G/GNAT1/GTP -0.017 0.088 -9999 0 -0.55 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.001 0.035 -9999 0 -0.28 3 3
GRK1 0.001 0.021 -9999 0 -0.28 1 1
CNG Channel -0.14 0.2 -9999 0 -0.45 56 56
mol:Na + -0.13 0.2 -9999 0 -0.46 50 50
mol:ADP 0.001 0.021 -9999 0 -0.28 1 1
RGS9-1/Gbeta5/R9AP -0.015 0.083 -9999 0 -0.57 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.13 0.2 -9999 0 -0.47 50 50
CNGB1 -0.003 0.058 -9999 0 -0.28 8 8
RDH5 -0.016 0.11 -9999 0 -0.35 15 15
SAG 0.001 0.003 -9999 0 -10000 0 0
mol:Ca2+ -0.098 0.21 -9999 0 -0.56 11 11
Na + (4 Units) -0.12 0.18 -9999 0 -0.52 13 13
RGS9 -0.008 0.11 -9999 0 -0.48 8 8
GNB1/GNGT1 -0.014 0.069 -9999 0 -10000 0 0
GNAT1/GDP -0.015 0.075 -9999 0 -0.5 4 4
GUCY2D -0.021 0.091 -9999 0 -0.28 21 21
GNGT1 -0.035 0.1 -9999 0 -0.28 29 29
GUCY2F 0.001 0.003 -9999 0 -10000 0 0
GNB5 0.012 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.004 0.098 -9999 0 -0.47 7 7
mol:11-cis-retinal -0.016 0.11 -9999 0 -0.35 15 15
mol:cGMP -0.001 0.055 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
Rhodopsin -0.01 0.084 -9999 0 -0.63 2 2
SLC24A1 0.012 0 -9999 0 -10000 0 0
CNGA1 -0.2 0.36 -9999 0 -0.81 50 50
Metarhodopsin II 0.002 0.026 -9999 0 -0.27 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.002 0.059 -9999 0 -10000 0 0
RGS9BP 0.006 0.062 -9999 0 -0.55 2 2
Metarhodopsin II/Transducin -0.004 0.04 -9999 0 -10000 0 0
GCAP Family/Ca ++ 0.008 0.036 -9999 0 -10000 0 0
PDE6A/B 0 0.076 -9999 0 -0.63 2 2
mol:Pi -0.015 0.083 -9999 0 -0.57 4 4
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.009 0.057 -9999 0 -10000 0 0
PDE6B 0.001 0.087 -9999 0 -0.55 4 4
PDE6A -0.001 0.054 -9999 0 -0.28 7 7
PDE6G -0.01 0.13 -9999 0 -0.72 6 6
RHO 0 0.041 -9999 0 -0.28 4 4
PDE6 -0.032 0.11 -9999 0 -0.46 11 11
GUCA1A -0.007 0.057 -9999 0 -0.28 8 8
GC2/GCAP Family 0.008 0.036 -9999 0 -10000 0 0
GUCA1C 0.006 0.021 -9999 0 -10000 0 0
GUCA1B 0.009 0.03 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.021 0.001 -9999 0 -10000 0 0
SMARCC1 0.01 0.008 -9999 0 -10000 0 0
REL 0.006 0.062 -9999 0 -0.55 2 2
HDAC7 -0.092 0.13 -9999 0 -0.7 3 3
JUN 0.012 0.003 -9999 0 -10000 0 0
EP300 0.012 0 -9999 0 -10000 0 0
KAT2B 0.012 0 -9999 0 -10000 0 0
KAT5 0.012 0 -9999 0 -10000 0 0
MAPK14 0.002 0.017 -9999 0 -10000 0 0
FOXO1 0.012 0 -9999 0 -10000 0 0
T-DHT/AR -0.1 0.14 -9999 0 -0.68 4 4
MAP2K6 0.003 0.008 -9999 0 -10000 0 0
BRM/BAF57 0.018 0.004 -9999 0 -10000 0 0
MAP2K4 0.003 0.008 -9999 0 -10000 0 0
SMARCA2 0.012 0.002 -9999 0 -10000 0 0
PDE9A -0.17 0.19 -9999 0 -0.61 22 22
NCOA2 -0.055 0.22 -9999 0 -0.81 16 16
CEBPA -0.015 0.097 -9999 0 -0.81 1 1
EHMT2 0.012 0.003 -9999 0 -10000 0 0
cell proliferation -0.14 0.18 -9999 0 -0.51 24 24
NR0B1 -0.05 0.12 -9999 0 -0.28 39 39
EGR1 -0.055 0.22 -9999 0 -0.81 16 16
RXRs/9cRA 0.018 0.012 -9999 0 -10000 0 0
AR/RACK1/Src -0.032 0.088 -9999 0 -0.57 4 4
AR/GR -0.01 0.095 -9999 0 -0.54 4 4
GNB2L1 0.012 0.001 -9999 0 -10000 0 0
PKN1 0.012 0 -9999 0 -10000 0 0
RCHY1 0.012 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.001 -9999 0 -10000 0 0
MAPK8 -0.011 0.093 -9999 0 -0.65 4 4
T-DHT/AR/TIF2/CARM1 -0.059 0.19 -9999 0 -0.65 16 16
SRC -0.015 0.079 -9999 0 -0.5 4 4
NR3C1 0.012 0 -9999 0 -10000 0 0
KLK3 -0.092 0.22 -9999 0 -0.5 33 33
APPBP2 0.003 0.008 -9999 0 -10000 0 0
TRIM24 0.012 0.003 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.03 0.097 -9999 0 -0.6 4 4
TMPRSS2 -0.85 0.57 -9999 0 -1.2 131 131
RXRG 0.003 0.021 -9999 0 -0.28 1 1
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.012 0.001 -9999 0 -10000 0 0
RXRB 0.012 0.001 -9999 0 -10000 0 0
CARM1 0.012 0.001 -9999 0 -10000 0 0
NR2C2 0.008 0.058 -9999 0 -0.81 1 1
KLK2 -0.04 0.15 -9999 0 -0.59 9 9
AR -0.018 0.1 -9999 0 -0.42 10 10
SENP1 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
MDM2 0.012 0.004 -9999 0 -10000 0 0
SRY 0 0.004 -9999 0 -10000 0 0
GATA2 -0.14 0.32 -9999 0 -0.81 36 36
MYST2 0.012 0 -9999 0 -10000 0 0
HOXB13 -0.08 0.14 -9999 0 -0.28 60 60
T-DHT/AR/RACK1/Src -0.022 0.095 -9999 0 -0.58 4 4
positive regulation of transcription -0.14 0.32 -9999 0 -0.81 36 36
DNAJA1 0.003 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.001 -9999 0 -10000 0 0
NCOA1 0.019 0.004 -9999 0 -10000 0 0
SPDEF -0.012 0.079 -9999 0 -10000 0 0
T-DHT/AR/TIF2 -0.015 0.12 -9999 0 -0.54 7 7
T-DHT/AR/Hsp90 -0.03 0.097 -9999 0 -0.61 4 4
GSK3B 0.008 0.004 -9999 0 -10000 0 0
NR2C1 0.012 0.001 -9999 0 -10000 0 0
mol:T-DHT -0.024 0.083 -9999 0 -0.54 4 4
SIRT1 0.012 0 -9999 0 -10000 0 0
ZMIZ2 0.012 0.004 -9999 0 -10000 0 0
POU2F1 -0.039 0.048 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.063 0.11 -9999 0 -0.67 4 4
CREBBP 0.012 0 -9999 0 -10000 0 0
SMARCE1 0.012 0.002 -9999 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.01 0.008 -10000 0 -10000 0 0
HSPA8 0.013 0.002 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha -0.03 0.12 -10000 0 -0.56 10 10
AKT1 0.014 0.004 -10000 0 -10000 0 0
GSC 0.016 0.05 -10000 0 -10000 0 0
NKX2-5 -0.013 0.068 -10000 0 -10000 0 0
muscle cell differentiation 0.003 0.024 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1 0.06 0.043 -10000 0 -10000 0 0
SMAD4 0.017 0.025 -10000 0 -10000 0 0
CBFB 0.012 0 -10000 0 -10000 0 0
SAP18 0.012 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.005 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR -0.005 0.058 -10000 0 -0.46 3 3
MYC 0.007 0.03 -10000 0 -0.29 2 2
CDKN2B 0.032 0.048 -10000 0 -10000 0 0
AP1 -0.018 0.17 -10000 0 -0.42 23 23
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.06 0.013 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.043 0.03 -10000 0 -10000 0 0
SP3 0.015 0 -10000 0 -10000 0 0
CREB1 0.012 0 -10000 0 -10000 0 0
FOXH1 -0.003 0.071 -10000 0 -0.28 12 12
SMAD3/SMAD4/GR -0.003 0.017 -10000 0 -10000 0 0
GATA3 -0.6 0.36 -10000 0 -0.81 147 147
SKI/SIN3/HDAC complex/NCoR1 0.045 0.008 -10000 0 -10000 0 0
MEF2C/TIF2 -0.002 0.15 -10000 0 -0.49 15 15
endothelial cell migration 0.08 0.34 1.4 12 -10000 0 12
MAX 0.013 0.012 -10000 0 -10000 0 0
RBBP7 0.012 0.001 -10000 0 -10000 0 0
RBBP4 0.012 0.001 -10000 0 -10000 0 0
RUNX2 0.005 0.046 -10000 0 -10000 0 0
RUNX3 -0.03 0.1 -10000 0 -0.28 28 28
RUNX1 -0.013 0.083 -10000 0 -10000 0 0
CTBP1 0.012 0 -10000 0 -10000 0 0
NR3C1 0.013 0.012 -10000 0 -10000 0 0
VDR 0 0.1 -10000 0 -0.81 3 3
CDKN1A 0.049 0.053 -10000 0 -10000 0 0
KAT2B 0.011 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.022 0.049 -10000 0 -10000 0 0
DCP1A 0.012 0 -10000 0 -10000 0 0
SKI 0.012 0.001 -10000 0 -10000 0 0
SERPINE1 -0.082 0.34 -10000 0 -1.4 12 12
SMAD3/SMAD4/ATF2 -0.002 0.018 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 -0.028 0.12 -10000 0 -0.57 9 9
SAP30 0.011 0.021 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.007 0.018 -10000 0 -10000 0 0
JUN -0.016 0.17 -10000 0 -0.43 4 4
SMAD3/SMAD4/IRF7 -0.002 0.022 -10000 0 -10000 0 0
TFE3 0.015 0.015 -10000 0 -10000 0 0
COL1A2 0.005 0.064 -10000 0 -10000 0 0
mesenchymal cell differentiation 0.005 0.026 -10000 0 -10000 0 0
DLX1 -0.005 0.065 -10000 0 -0.28 10 10
TCF3 0.012 0 -10000 0 -10000 0 0
FOS -0.11 0.3 -10000 0 -0.8 31 31
SMAD3/SMAD4/Max -0.003 0.017 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.002 0.008 -10000 0 -10000 0 0
ZBTB17 0.011 0.004 -10000 0 -10000 0 0
LAMC1 0.042 0.041 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.002 0.018 -10000 0 -10000 0 0
IRF7 0.012 0.008 -10000 0 -10000 0 0
ESR1 -0.031 0.18 -10000 0 -0.81 10 10
HNF4A -0.088 0.27 -10000 0 -0.81 24 24
MEF2C 0.032 0.052 -10000 0 -10000 0 0
SMAD2-3/SMAD4 0.012 0.031 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.001 0.01 -10000 0 -10000 0 0
IGHV3OR16-13 -0.004 0.013 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.012 0 -10000 0 -10000 0 0
CREBBP 0.011 0.005 -10000 0 -10000 0 0
SKIL 0.012 0 -10000 0 -10000 0 0
HDAC1 0.012 0.001 -10000 0 -10000 0 0
HDAC2 0.012 0.001 -10000 0 -10000 0 0
SNIP1 0.012 0.002 -10000 0 -10000 0 0
GCN5L2 -0.002 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.04 0.038 -10000 0 -10000 0 0
MSG1/HSC70 0.014 0.021 -10000 0 -10000 0 0
SMAD2 0.018 0.006 -10000 0 -10000 0 0
SMAD3 0.015 0.025 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.038 0.023 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.013 0.014 -10000 0 -10000 0 0
NCOR1 0.012 0.001 -10000 0 -10000 0 0
NCOA2 -0.054 0.22 -10000 0 -0.81 16 16
NCOA1 0.012 0 -10000 0 -10000 0 0
MYOD/E2A 0.006 0.027 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.065 0.042 -10000 0 -10000 0 0
IFNB1 0.029 0.04 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C 0.038 0.058 -10000 0 -10000 0 0
CITED1 0.009 0.03 -10000 0 -0.28 2 2
SMAD2-3/SMAD4/ARC105 0.043 0.033 -10000 0 -10000 0 0
RBL1 0.012 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.051 0.034 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.032 0.07 -10000 0 -10000 0 0
SMAD7 0.027 0.14 -10000 0 -10000 0 0
MYC/MIZ-1 0 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.022 0.11 -10000 0 -0.43 12 12
IL10 -0.36 0.24 -10000 0 -0.49 147 147
PIASy/HDAC complex 0.013 0.007 -10000 0 -10000 0 0
PIAS3 0.011 0.003 -10000 0 -10000 0 0
CDK2 0.011 0.003 -10000 0 -10000 0 0
IL5 -0.36 0.23 -10000 0 -0.49 147 147
CDK4 0.012 0.004 -10000 0 -10000 0 0
PIAS4 0.013 0.007 -10000 0 -10000 0 0
ATF3 -0.027 0.17 -10000 0 -0.76 10 10
SMAD3/SMAD4/SP1 0.044 0.042 -10000 0 -10000 0 0
FOXG1 -0.009 0.06 -10000 0 -10000 0 0
FOXO3 0.024 0.006 -10000 0 -10000 0 0
FOXO1 0.024 0.006 -10000 0 -10000 0 0
FOXO4 0.024 0.006 -10000 0 -10000 0 0
heart looping 0.032 0.051 -10000 0 -10000 0 0
CEBPB 0.007 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.01 0.042 -10000 0 -10000 0 0
MYOD1 -0.004 0.04 -10000 0 -0.28 4 4
SMAD3/SMAD4/HNF4 -0.07 0.19 -10000 0 -0.57 24 24
SMAD3/SMAD4/GATA3 -0.42 0.24 -10000 0 -0.56 147 147
SnoN/SIN3/HDAC complex/NCoR1 0.012 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.003 0.067 -10000 0 -10000 0 0
SMAD3/SMAD4/SP1-3 0.054 0.04 -10000 0 -10000 0 0
MED15 0.012 0 -10000 0 -10000 0 0
SP1 0.02 0.012 -10000 0 -10000 0 0
SIN3B 0.012 0.001 -10000 0 -10000 0 0
SIN3A 0.012 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.018 0.058 -10000 0 -10000 0 0
ITGB5 0.057 0.032 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.044 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.025 0.12 -10000 0 -0.58 8 8
AR -0.023 0.16 -10000 0 -0.75 9 9
negative regulation of cell growth 0.032 0.059 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.006 0.028 -10000 0 -10000 0 0
E2F5 0.012 0 -10000 0 -10000 0 0
E2F4 0.012 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.031 0.042 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 0.049 0.028 -10000 0 -10000 0 0
TFDP1 0.012 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.016 0.17 -10000 0 -0.44 5 5
SMAD3/SMAD4/RUNX2 -0.005 0.026 -10000 0 -10000 0 0
TGIF2 0.012 0 -10000 0 -10000 0 0
TGIF1 0.012 0 -10000 0 -10000 0 0
ATF2 0.012 0 -10000 0 -10000 0 0
Noncanonical Wnt 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
NFATC2 -0.043 0.2 -9999 0 -0.81 13 13
GNB1/GNG2 0.004 0.091 -9999 0 -0.39 2 2
mol:DAG 0.011 0.085 -9999 0 -10000 0 0
PLCG1 0.011 0.087 -9999 0 -10000 0 0
YES1 -0.002 0.094 -9999 0 -0.41 2 2
FZD3 0.012 0 -9999 0 -10000 0 0
FZD6 0.012 0 -9999 0 -10000 0 0
G protein 0.011 0.088 -9999 0 -10000 0 0
MAP3K7 -0.18 0.22 -9999 0 -0.46 24 24
mol:Ca2+ 0.011 0.083 -9999 0 -10000 0 0
mol:IP3 0.011 0.085 -9999 0 -10000 0 0
NLK -0.011 0.012 -9999 0 -10000 0 0
GNB1 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.2 0.23 -9999 0 -0.43 95 95
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.01 0.1 -9999 0 -0.34 14 14
CSNK1A1 0.012 0 -9999 0 -10000 0 0
GNAS -0.002 0.094 -9999 0 -0.41 2 2
GO:0007205 0.012 0.084 -9999 0 -10000 0 0
WNT6 0.005 0.062 -9999 0 -0.55 2 2
WNT4 -0.008 0.12 -9999 0 -0.64 6 6
NFAT1/CK1 alpha -0.014 0.14 -9999 0 -0.57 2 2
GNG2 0.012 0 -9999 0 -10000 0 0
WNT5A -0.034 0.11 -9999 0 -10000 0 0
WNT11 -0.032 0.18 -9999 0 -0.81 9 9
CDC42 0.005 0.09 -9999 0 -0.39 2 2
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 0.027 -9999 0 -10000 0 0
VDR 0 0.1 -9999 0 -0.81 3 3
FAM120B 0.012 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.045 0.042 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.049 0.06 -9999 0 -0.39 2 2
MED1 0.012 0 -9999 0 -10000 0 0
mol:9cRA 0.004 0.009 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.021 0.067 -9999 0 -0.33 7 7
RXRs/NUR77 -0.18 0.26 -9999 0 -0.49 83 83
RXRs/PPAR 0.036 0.014 -9999 0 -10000 0 0
NCOR2 0.012 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.001 0.078 -9999 0 -0.63 3 3
RARs/VDR/DNA/Vit D3 -0.008 0.057 -9999 0 -0.47 3 3
RARA 0.012 0 -9999 0 -10000 0 0
NCOA1 0.012 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0 0.1 -9999 0 -0.81 3 3
RARs/RARs/DNA/9cRA 0.023 0.012 -9999 0 -10000 0 0
RARG 0.011 0.021 -9999 0 -0.28 1 1
RPS6KB1 0.002 0.018 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT 0.021 0.067 -9999 0 -0.33 7 7
THRA 0.012 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.001 0.078 -9999 0 -0.63 3 3
RXRs/PPAR/9cRA/PGJ2/DNA 0.033 0.027 -9999 0 -10000 0 0
NR1H4 -0.002 0.1 -9999 0 -0.68 4 4
RXRs/LXRs/DNA 0.052 0.032 -9999 0 -10000 0 0
NR1H2 0.017 0.006 -9999 0 -10000 0 0
NR1H3 0.017 0.007 -9999 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.027 0.063 -9999 0 -0.46 3 3
NR4A1 -0.33 0.41 -9999 0 -0.81 83 83
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.025 0.049 -9999 0 -0.34 3 3
RXRG 0.007 0.022 -9999 0 -10000 0 0
RXR alpha/CCPG 0.021 0.006 -9999 0 -10000 0 0
RXRA 0.017 0.006 -9999 0 -10000 0 0
RXRB 0.017 0.007 -9999 0 -10000 0 0
THRB -0.017 0.15 -9999 0 -0.81 7 7
PPARG 0.012 0 -9999 0 -10000 0 0
PPARD 0.012 0 -9999 0 -10000 0 0
TNF 0.039 0.14 -9999 0 -1.2 2 2
mol:Oxysterols 0.004 0.008 -9999 0 -10000 0 0
cholesterol transport 0.049 0.06 -9999 0 -0.38 2 2
PPARA 0.012 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.012 0 -9999 0 -10000 0 0
RXRs/NUR77/BCL2 -0.12 0.18 -9999 0 -0.34 83 83
SREBF1 0.053 0.058 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.033 0.027 -9999 0 -10000 0 0
ABCA1 0.054 0.056 -9999 0 -10000 0 0
RARs/THRs -0.017 0.085 -9999 0 -0.46 7 7
RXRs/FXR 0.028 0.068 -9999 0 -0.5 3 3
BCL2 0.012 0 -9999 0 -10000 0 0
Regulation of Telomerase

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Telomerase catalytic core complex -0.2 0.13 -9999 0 -0.49 13 13
RAD9A 0.012 0 -9999 0 -10000 0 0
AP1 -0.084 0.23 -9999 0 -0.62 31 31
IFNAR2 0.011 0.004 -9999 0 -10000 0 0
AKT1 0 0.068 -9999 0 -0.29 10 10
ER alpha/Oestrogen -0.024 0.14 -9999 0 -0.63 10 10
NFX1/SIN3/HDAC complex 0.037 0.016 -9999 0 -10000 0 0
EGF -0.73 0.25 -9999 0 -0.81 178 178
SMG5 0.012 0 -9999 0 -10000 0 0
SMG6 0.012 0 -9999 0 -10000 0 0
SP3/HDAC2 0.017 0.007 -9999 0 -10000 0 0
TERT/c-Abl -0.18 0.13 -9999 0 -0.48 7 7
SAP18 0.012 0.001 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.48 0.4 -9999 0 -0.81 117 117
WRN 0.012 0 -9999 0 -10000 0 0
SP1 0.012 0.005 -9999 0 -10000 0 0
SP3 0.012 0.002 -9999 0 -10000 0 0
TERF2IP 0.012 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.16 0.12 -9999 0 -10000 0 0
Mad/Max 0.017 0.007 -9999 0 -10000 0 0
TERT -0.2 0.14 -9999 0 -0.5 13 13
CCND1 -0.18 0.12 -9999 0 -0.48 1 1
MAX 0.012 0.002 -9999 0 -10000 0 0
RBBP7 0.012 0.001 -9999 0 -10000 0 0
RBBP4 0.012 0.001 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.012 0 -9999 0 -10000 0 0
SIN3A 0.012 0.001 -9999 0 -10000 0 0
Telomerase/911 0.002 0.02 -9999 0 -10000 0 0
CDKN1B 0.019 0.044 -9999 0 -10000 0 0
RAD1 0.012 0 -9999 0 -10000 0 0
XRCC5 0.012 0 -9999 0 -10000 0 0
XRCC6 0.012 0 -9999 0 -10000 0 0
SAP30 0.01 0.021 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.012 0.001 -9999 0 -10000 0 0
JUN 0.012 0.002 -9999 0 -10000 0 0
E6 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.003 -9999 0 -10000 0 0
FOS -0.12 0.3 -9999 0 -0.81 31 31
IFN-gamma/IRF1 -0.009 0.049 -9999 0 -10000 0 0
PARP2 0.012 0 -9999 0 -10000 0 0
BLM -0.012 0.081 -9999 0 -0.28 16 16
Telomerase -0.026 0.037 -9999 0 -10000 0 0
IRF1 0.016 0.002 -9999 0 -10000 0 0
ESR1 -0.03 0.18 -9999 0 -0.81 10 10
KU/TER 0.018 0 -9999 0 -10000 0 0
ATM/TRF2 0.019 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.042 0.017 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.042 0.017 -9999 0 -10000 0 0
HDAC1 0.012 0.001 -9999 0 -10000 0 0
HDAC2 0.011 0.005 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.019 0.02 -9999 0 -10000 0 0
ABL1 0.012 0 -9999 0 -10000 0 0
MXD1 0.012 0.002 -9999 0 -10000 0 0
MRE11A 0.012 0 -9999 0 -10000 0 0
HUS1 0.012 0 -9999 0 -10000 0 0
RPS6KB1 0.012 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.14 0.12 -9999 0 -0.54 1 1
NR2F2 0.012 0.004 -9999 0 -10000 0 0
MAPK3 0.012 0.015 -9999 0 -10000 0 0
MAPK1 0.012 0.015 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.009 0.03 -9999 0 -0.28 2 2
NFKB1 0.012 0 -9999 0 -10000 0 0
HNRNPC 0.012 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.012 0 -9999 0 -10000 0 0
EGFR 0.012 0.001 -9999 0 -10000 0 0
mol:Oestrogen 0 0.001 -9999 0 -10000 0 0
EGF/EGFR -0.56 0.19 -9999 0 -0.62 178 178
MYC 0.008 0.03 -9999 0 -0.29 2 2
IL2 0.002 0.022 -9999 0 -0.28 1 1
KU 0.018 0 -9999 0 -10000 0 0
RAD50 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
TGFB1 0.009 0.03 -9999 0 -0.28 2 2
TRF2/BLM -0.013 0.045 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.18 0.13 -9999 0 -0.48 6 6
SP1/HDAC2 0.018 0.007 -9999 0 -10000 0 0
PINX1 0.012 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.16 0.12 -9999 0 -10000 0 0
Smad3/Myc 0.022 0.023 -9999 0 -10000 0 0
911 complex 0 0 -9999 0 -10000 0 0
IFNG -0.011 0.079 -9999 0 -0.28 16 16
Telomerase/PinX1 -0.16 0.12 -9999 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K -0.022 0.041 -9999 0 -10000 0 0
SIN3B 0.012 0.001 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.16 0.12 -9999 0 -10000 0 0
response to DNA damage stimulus 0.003 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.16 0.12 -9999 0 -10000 0 0
E2F1 -0.081 0.14 -9999 0 -0.29 62 62
ZNFX1 0.012 0.001 -9999 0 -10000 0 0
PIF1 -0.018 0.089 -9999 0 -10000 0 0
NCL 0.012 0 -9999 0 -10000 0 0
DKC1 0.012 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure 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
HIF3A -0.059 0.23 -9999 0 -0.73 19 19
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.011 0.021 -9999 0 -0.28 1 1
TCEB1 0.012 0 -9999 0 -10000 0 0
HIF1A/p53 0.029 0.007 -9999 0 -10000 0 0
HIF1A 0.022 0.007 -9999 0 -10000 0 0
COPS5 0.012 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.001 0.007 -9999 0 -10000 0 0
FIH (dimer) 0.012 0 -9999 0 -10000 0 0
CDKN2A -0.23 0.12 -9999 0 -0.28 159 159
ARNT/IPAS -0.037 0.18 -9999 0 -0.62 16 16
HIF1AN 0.012 0 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.029 0.007 -9999 0 -10000 0 0
CUL2 0.012 0 -9999 0 -10000 0 0
OS9 0.012 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.001 0.01 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.029 0.007 -9999 0 -10000 0 0
PHD1-3/OS9 0.027 0.023 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C 0 0.006 -9999 0 -10000 0 0
VHL 0.012 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.029 0.007 -9999 0 -10000 0 0
EGLN3 0.005 0.046 -9999 0 -0.28 5 5
EGLN2 0.012 0 -9999 0 -10000 0 0
EGLN1 0.012 0 -9999 0 -10000 0 0
TP53 0.012 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.006 -9999 0 -10000 0 0
ARNT 0.012 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.012 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.073 0.051 -9999 0 -10000 0 0
Caspase cascade in apoptosis

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
TOP1 0.018 0.049 -10000 0 -0.39 1 1
ACTA1 0.011 0.06 -10000 0 -0.51 1 1
NUMA1 0.018 0.049 -10000 0 -0.39 1 1
SPTAN1 0.012 0.059 -10000 0 -0.5 1 1
LIMK1 0.01 0.063 -10000 0 -0.5 1 1
BIRC3 -0.007 0.073 -10000 0 -0.28 13 13
BIRC2 0.012 0 -10000 0 -10000 0 0
BAX 0.011 0.021 -10000 0 -0.28 1 1
CASP10 0.006 0.072 -10000 0 -0.54 1 1
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.012 0 -10000 0 -10000 0 0
PTK2 0.018 0.049 -10000 0 -0.39 1 1
DIABLO 0.012 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.012 0.059 -10000 0 -0.5 1 1
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
GSN 0.012 0.06 -10000 0 -0.51 1 1
MADD 0.012 0 -10000 0 -10000 0 0
TFAP2A -0.42 0.24 -10000 0 -0.53 157 157
BID 0.012 0.038 -10000 0 -0.27 1 1
MAP3K1 0.011 0.024 -10000 0 -10000 0 0
TRADD 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.017 0.004 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0.012 0.059 -10000 0 -0.5 1 1
CASP9 0.012 0 -10000 0 -10000 0 0
DNA repair -0.008 0.024 -10000 0 -10000 0 0
neuron apoptosis 0.023 0.008 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.019 0.057 -10000 0 -0.48 1 1
APAF1 0.012 0 -10000 0 -10000 0 0
CASP6 0.028 0.032 -10000 0 -10000 0 0
TRAF2 0.012 0 -10000 0 -10000 0 0
ICAD/CAD 0.019 0.058 -10000 0 -0.48 1 1
CASP7 -0.002 0.035 -10000 0 -10000 0 0
KRT18 0.014 0.019 -10000 0 -10000 0 0
apoptosis 0.023 0.057 -10000 0 -0.43 1 1
DFFA 0.012 0.059 -10000 0 -0.5 1 1
DFFB 0.012 0.059 -10000 0 -0.5 1 1
PARP1 0.008 0.024 -10000 0 -10000 0 0
actin filament polymerization -0.017 0.059 0.46 1 -10000 0 1
TNF -0.013 0.1 -10000 0 -0.36 13 13
CYCS 0.012 0.031 -10000 0 -0.19 1 1
SATB1 0.031 0.044 -10000 0 -0.42 1 1
SLK 0.012 0.059 -10000 0 -0.5 1 1
p15 BID/BAX 0.016 0.035 -10000 0 -10000 0 0
CASP2 0.036 0.038 -10000 0 -10000 0 0
JNK cascade -0.011 0.024 -10000 0 -10000 0 0
CASP3 0.006 0.063 -10000 0 -0.54 1 1
LMNB2 0.038 0.028 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
CASP4 0.012 0 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.019 0.037 -10000 0 -10000 0 0
negative regulation of DNA binding -0.42 0.23 -10000 0 -0.53 157 157
stress fiber formation 0.012 0.059 -10000 0 -0.5 1 1
GZMB -0.004 0.085 -10000 0 -0.41 5 5
CASP1 0.015 0.009 -10000 0 -10000 0 0
LMNB1 0.034 0.031 -10000 0 -10000 0 0
APP 0.023 0.008 -10000 0 -10000 0 0
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM 0.018 0.056 -10000 0 -0.42 1 1
LMNA 0.038 0.028 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.03 0.04 -10000 0 -10000 0 0
LRDD 0.012 0 -10000 0 -10000 0 0
SREBF1 0.012 0.06 -10000 0 -0.5 1 1
APAF-1/Caspase 9 0.001 0.015 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.018 0.049 -10000 0 -0.38 1 1
CFL2 0.017 0.06 -10000 0 -0.48 1 1
GAS2 0 0.1 -10000 0 -0.53 6 6
positive regulation of apoptosis 0.039 0.029 -10000 0 -10000 0 0
PRF1 0.003 0.051 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0 -9999 0 -10000 0 0
SPHK1 -0.13 0.15 -9999 0 -10000 0 0
GNAI2 0.012 0 -9999 0 -10000 0 0
mol:S1P -0.031 0.055 -9999 0 -10000 0 0
GNAO1 -0.051 0.21 -9999 0 -0.72 17 17
mol:Sphinganine-1-P -0.074 0.1 -9999 0 -10000 0 0
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.001 0.039 -9999 0 -10000 0 0
GNAI3 0.012 0 -9999 0 -10000 0 0
G12/G13 0.017 0.014 -9999 0 -10000 0 0
S1PR3 -0.059 0.23 -9999 0 -0.81 17 17
S1PR2 0.012 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.035 0.037 -9999 0 -10000 0 0
S1PR5 -0.002 0.092 -9999 0 -0.81 2 2
S1PR4 0.008 0.036 -9999 0 -10000 0 0
GNAI1 0.008 0.058 -9999 0 -0.81 1 1
S1P/S1P5/G12 -0.016 0.066 -9999 0 -0.52 2 2
S1P/S1P3/Gq -0.098 0.19 -9999 0 -0.43 41 41
S1P/S1P4/Gi -0.009 0.094 -9999 0 -0.33 14 14
GNAQ 0.012 0 -9999 0 -10000 0 0
GNAZ 0.012 0 -9999 0 -10000 0 0
GNA14 -0.16 0.34 -9999 0 -0.81 42 42
GNA15 -0.006 0.071 -9999 0 -10000 0 0
GNA12 0.012 0 -9999 0 -10000 0 0
GNA13 0.011 0.021 -9999 0 -10000 0 0
GNA11 -0.005 0.12 -9999 0 -0.81 4 4
ABCC1 0.012 0 -9999 0 -10000 0 0
Syndecan-2-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
Syndecan-2/Fibronectin 0.011 0.043 -9999 0 -10000 0 0
EPHB2 0.006 0.042 -9999 0 -0.28 4 4
Syndecan-2/TACI 0.005 0.038 -9999 0 -10000 0 0
LAMA1 -0.03 0.15 -9999 0 -0.42 19 19
Syndecan-2/alpha2 ITGB1 -0.006 0.064 -9999 0 -10000 0 0
HRAS 0.012 0 -9999 0 -10000 0 0
Syndecan-2/CASK 0 0.005 -9999 0 -10000 0 0
ITGA5 0.012 0 -9999 0 -10000 0 0
BAX 0.025 0.075 -9999 0 -0.48 4 4
EPB41 0.012 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0.005 -9999 0 -10000 0 0
LAMA3 -0.076 0.14 -9999 0 -10000 0 0
EZR 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.009 0.03 -9999 0 -0.28 2 2
Syndecan-2/MMP2 0.018 0.043 -9999 0 -0.54 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 0.018 0 -9999 0 -10000 0 0
dendrite morphogenesis 0.019 0.024 -9999 0 -10000 0 0
Syndecan-2/GM-CSF 0.007 0.025 -9999 0 -10000 0 0
determination of left/right symmetry 0.018 0.008 -9999 0 -10000 0 0
Syndecan-2/PKC delta 0.022 0.006 -9999 0 -10000 0 0
GNB2L1 0.012 0 -9999 0 -10000 0 0
MAPK3 0.022 0.021 -9999 0 -10000 0 0
MAPK1 0.022 0.021 -9999 0 -10000 0 0
Syndecan-2/RACK1 0.027 0.005 -9999 0 -10000 0 0
NF1 0.012 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.018 0.008 -9999 0 -10000 0 0
ITGA2 0.012 0 -9999 0 -10000 0 0
MAPK8 0.019 0.08 -9999 0 -0.53 4 4
Syndecan-2/alpha2/beta1 Integrin 0.013 0.084 -9999 0 -0.46 5 5
Syndecan-2/Kininogen -0.33 0.26 -9999 0 -0.54 120 120
ITGB1 0.012 0 -9999 0 -10000 0 0
SRC 0.033 0.005 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0 0.005 -9999 0 -10000 0 0
extracellular matrix organization 0.021 0.017 -9999 0 -10000 0 0
actin cytoskeleton reorganization 0.011 0.043 -9999 0 -10000 0 0
Syndecan-2/Caveolin-2/Ras 0.027 0.016 -9999 0 -10000 0 0
Syndecan-2/Laminin alpha3 -0.027 0.075 -9999 0 -10000 0 0
Syndecan-2/RasGAP 0 0.002 -9999 0 -10000 0 0
alpha5/beta1 Integrin 0.018 0 -9999 0 -10000 0 0
PRKCD 0.012 0 -9999 0 -10000 0 0
Syndecan-2 dimer 0.019 0.024 -9999 0 -10000 0 0
GO:0007205 0.003 0.005 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.04 0.005 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
SDCBP 0.012 0 -9999 0 -10000 0 0
TNFRSF13B -0.009 0.067 -9999 0 -10000 0 0
RASA1 0.012 0 -9999 0 -10000 0 0
alpha2/beta1 Integrin 0.018 0 -9999 0 -10000 0 0
Syndecan-2/Synbindin 0.022 0.006 -9999 0 -10000 0 0
TGFB1 0.009 0.03 -9999 0 -0.28 2 2
CASP3 0.028 0.016 -9999 0 -10000 0 0
FN1 -0.009 0.076 -9999 0 -0.28 14 14
Syndecan-2/IL8 -0.02 0.08 -9999 0 -0.54 1 1
SDC2 0.018 0.008 -9999 0 -10000 0 0
KNG1 -0.49 0.4 -9999 0 -0.81 120 120
Syndecan-2/Neurofibromin 0.022 0.006 -9999 0 -10000 0 0
TRAPPC4 0.012 0 -9999 0 -10000 0 0
CSF2 0 0.041 -9999 0 -0.28 4 4
Syndecan-2/TGFB1 0.021 0.018 -9999 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 0 0.005 -9999 0 -10000 0 0
Syndecan-2/Ezrin 0.029 0.005 -9999 0 -10000 0 0
PRKACA 0.029 0.005 -9999 0 -10000 0 0
angiogenesis -0.02 0.08 -9999 0 -0.54 1 1
MMP2 0.005 0.065 -9999 0 -0.46 3 3
IL8 -0.062 0.14 -9999 0 -0.3 48 48
calcineurin-NFAT signaling pathway 0.005 0.038 -9999 0 -10000 0 0
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0.04 -10000 0 -10000 0 0
MAP4K4 0.033 0.039 -10000 0 -10000 0 0
BAG4 0.012 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.099 0.037 -10000 0 -10000 0 0
NFKBIA 0.012 0 -10000 0 -10000 0 0
BIRC3 -0.007 0.073 -10000 0 -0.28 13 13
BAX -0.045 0.019 -10000 0 -10000 0 0
RIPK1 0.012 0 -10000 0 -10000 0 0
AKT1 0.036 0.007 -10000 0 -10000 0 0
BAD -0.099 0.037 -10000 0 -10000 0 0
SMPD1 0.02 0.033 -10000 0 -0.24 2 2
RB1 -0.099 0.037 -10000 0 -10000 0 0
FADD/Caspase 8 0.042 0.037 -10000 0 -10000 0 0
MAP2K4 -0.087 0.035 -10000 0 -10000 0 0
NSMAF 0.012 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.088 0.036 -10000 0 -0.23 1 1
EGF -0.73 0.25 -10000 0 -0.81 178 178
mol:ceramide -0.11 0.039 -10000 0 -10000 0 0
MADD 0.012 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.013 0.04 -10000 0 -10000 0 0
ASAH1 0.012 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.098 0.036 -10000 0 -10000 0 0
cell proliferation -0.066 0.067 -10000 0 -0.44 5 5
BID -0.007 0.029 -10000 0 -10000 0 0
MAP3K1 -0.099 0.037 -10000 0 -10000 0 0
EIF2A -0.077 0.033 -10000 0 -10000 0 0
TRADD 0.012 0 -10000 0 -10000 0 0
CRADD 0.012 0 -10000 0 -10000 0 0
MAPK3 -0.072 0.034 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.072 0.034 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.099 0.037 -10000 0 -10000 0 0
FADD 0.033 0.039 -10000 0 -10000 0 0
KSR1 -0.099 0.038 -10000 0 -0.25 1 1
MAPK8 -0.087 0.053 -10000 0 -0.37 4 4
PRKRA -0.099 0.037 -10000 0 -10000 0 0
PDGFA 0 0.058 -10000 0 -0.28 8 8
TRAF2 0.012 0 -10000 0 -10000 0 0
IGF1 -0.009 0.13 -10000 0 -0.81 5 5
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.11 0.039 -10000 0 -10000 0 0
CTSD 0.012 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.018 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.069 0.073 -10000 0 -0.47 5 5
PRKCD 0.012 0 -10000 0 -10000 0 0
PRKCZ 0.012 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.013 0.04 -10000 0 -10000 0 0
RelA/NF kappa B1 0.018 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.012 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.027 0.042 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.013 0.062 -10000 0 -0.54 2 2
mol:Sphingosine-1-phosphate 0.013 0.04 -10000 0 -10000 0 0
MAP2K1 -0.077 0.035 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.012 0 -10000 0 -10000 0 0
CYCS -0.065 0.025 -10000 0 -10000 0 0
TNFRSF1A 0.012 0 -10000 0 -10000 0 0
NFKB1 0.012 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0.018 0 -10000 0 -10000 0 0
EIF2AK2 -0.087 0.035 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.013 0.062 -10000 0 -0.54 2 2
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.034 0.025 -10000 0 -10000 0 0
MAP2K2 -0.077 0.035 -10000 0 -10000 0 0
SMPD3 0.022 0.035 -10000 0 -0.24 2 2
TNF -0.013 0.1 -10000 0 -0.36 13 13
PKC zeta/PAR4 0.018 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.25 0.09 0.28 178 -10000 0 178
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 -0.065 0.025 -10000 0 -10000 0 0
BCL2 0.012 0 -10000 0 -10000 0 0
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.042 0.14 -10000 0 -0.55 14 14
cell-cell adhesion 0.024 0.073 0.37 7 -10000 0 7
Ephrin B/EPHB2/RasGAP -0.023 0.073 -10000 0 -0.46 4 4
ITSN1 0.012 0 -10000 0 -10000 0 0
PIK3CA 0.012 0 -10000 0 -10000 0 0
SHC1 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.12 0.23 -10000 0 -0.55 44 44
Ephrin B1/EPHB1 -0.012 0.07 -10000 0 -0.55 3 3
HRAS/GDP -0.02 0.068 -10000 0 -0.4 4 4
Ephrin B/EPHB1/GRB7 -0.031 0.09 -10000 0 -0.46 7 7
Endophilin/SYNJ1 0.007 0.078 -10000 0 -0.43 4 4
KRAS 0.012 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.031 0.09 -10000 0 -0.46 7 7
endothelial cell migration 0 0 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
GRB7 0.012 0 -10000 0 -10000 0 0
PAK1 0.014 0.079 -10000 0 -0.43 4 4
HRAS 0.012 0 -10000 0 -10000 0 0
RRAS 0.007 0.079 -10000 0 -0.44 4 4
DNM1 -0.069 0.13 -10000 0 -0.28 54 54
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK 0 0.096 -10000 0 -0.44 7 7
lamellipodium assembly -0.024 0.073 -10000 0 -0.37 7 7
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.014 0.066 -10000 0 -0.32 3 3
PIK3R1 0.012 0 -10000 0 -10000 0 0
EPHB2 0.006 0.042 -10000 0 -0.28 4 4
EPHB3 -0.17 0.34 -10000 0 -0.81 44 44
EPHB1 -0.008 0.11 -10000 0 -0.48 8 8
EPHB4 0.012 0 -10000 0 -10000 0 0
mol:GDP 0.02 0.11 -10000 0 -0.43 3 3
Ephrin B/EPHB2 -0.024 0.075 -10000 0 -0.47 4 4
Ephrin B/EPHB3 -0.13 0.21 -10000 0 -0.49 47 47
JNK cascade 0.022 0.067 -10000 0 -0.45 3 3
Ephrin B/EPHB1 -0.032 0.092 -10000 0 -0.47 7 7
RAP1/GDP 0.021 0.1 -10000 0 -0.37 3 3
EFNB2 0.012 0 -10000 0 -10000 0 0
EFNB3 -0.039 0.15 -10000 0 -0.36 27 27
EFNB1 0.012 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 0.009 0.071 -10000 0 -0.44 4 4
RAP1B 0.012 0 -10000 0 -10000 0 0
RAP1A 0.012 0 -10000 0 -10000 0 0
CDC42/GTP -0.025 0.078 -10000 0 -0.42 4 4
Rap1/GTP -0.024 0.072 -10000 0 -10000 0 0
axon guidance -0.042 0.14 -10000 0 -0.54 14 14
MAPK3 0.027 0.059 -10000 0 -10000 0 0
MAPK1 0.027 0.059 -10000 0 -10000 0 0
Rac1/GDP 0.05 0.1 -10000 0 -0.39 3 3
actin cytoskeleton reorganization -0.015 0.052 -10000 0 -10000 0 0
CDC42/GDP 0.05 0.1 -10000 0 -0.39 3 3
PI3K 0 0 -10000 0 -10000 0 0
EFNA5 -0.048 0.21 -10000 0 -0.78 15 15
Ephrin B2/EPHB4 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP 0.014 0.06 -10000 0 -0.33 4 4
CDC42 0.012 0 -10000 0 -10000 0 0
RAS family/GTP -0.023 0.071 -10000 0 -10000 0 0
PTK2 0.003 0.015 -10000 0 -10000 0 0
MAP4K4 0.022 0.067 -10000 0 -0.46 3 3
SRC 0.012 0 -10000 0 -10000 0 0
KALRN 0.012 0 -10000 0 -10000 0 0
Intersectin/N-WASP 0.018 0 -10000 0 -10000 0 0
neuron projection morphogenesis 0.038 0.077 -10000 0 -10000 0 0
MAP2K1 0.021 0.062 -10000 0 -0.3 3 3
WASL 0.012 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.017 0.072 -10000 0 -0.49 3 3
cell migration 0.035 0.073 -10000 0 -0.33 1 1
NRAS 0.012 0 -10000 0 -10000 0 0
SYNJ1 0.007 0.079 -10000 0 -0.44 4 4
PXN 0.012 0 -10000 0 -10000 0 0
TF 0.001 0.096 -10000 0 -0.42 7 7
HRAS/GTP -0.027 0.078 -10000 0 -0.4 7 7
Ephrin B1/EPHB1-2 0.009 0.071 -10000 0 -0.5 3 3
cell adhesion mediated by integrin 0.059 0.1 0.4 8 -10000 0 8
RAC1 0.012 0 -10000 0 -10000 0 0
mol:GTP -0.029 0.085 -10000 0 -0.42 7 7
RAC1-CDC42/GTP -0.11 0.18 -10000 0 -0.57 8 8
RASA1 0.012 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.021 0.1 -10000 0 -0.37 3 3
ruffle organization 0.023 0.089 -10000 0 -10000 0 0
NCK1 0.012 0 -10000 0 -10000 0 0
receptor internalization -0.021 0.095 -10000 0 -0.41 4 4
Ephrin B/EPHB2/KALRN -0.023 0.073 -10000 0 -0.46 4 4
ROCK1 -0.092 0.22 -10000 0 -0.5 44 44
RAS family/GDP -0.014 0.05 -10000 0 -10000 0 0
Rac1/GTP -0.026 0.077 -10000 0 -0.39 7 7
Ephrin B/EPHB1/Src/Paxillin 0.008 0.073 -10000 0 -0.33 7 7
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.01 0.17 -9999 0 -0.57 16 16
KLHL20 -0.014 0.045 -9999 0 -10000 0 0
CYFIP2 0.012 0 -9999 0 -10000 0 0
Rac1/GDP 0.025 0.11 -9999 0 -0.34 16 16
ENAH -0.01 0.17 -9999 0 -0.57 16 16
AP1M1 0.012 0 -9999 0 -10000 0 0
RAP1B 0.012 0 -9999 0 -10000 0 0
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
CDC42/GTP -0.023 0.078 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.009 0.03 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.011 0.14 -9999 0 -0.49 16 16
RAPGEF1 0.007 0.14 -9999 0 -0.48 16 16
CTNND1 0.012 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.048 0.16 -9999 0 -0.59 16 16
CRK -0.001 0.16 -9999 0 -0.53 16 16
E-cadherin/gamma catenin/alpha catenin -0.044 0.15 -9999 0 -0.54 16 16
alphaE/beta7 Integrin 0.018 0 -9999 0 -10000 0 0
IQGAP1 0.012 0 -9999 0 -10000 0 0
NCKAP1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.024 0 -9999 0 -10000 0 0
DLG1 -0.01 0.17 -9999 0 -0.57 16 16
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.017 0.056 -9999 0 -10000 0 0
MLLT4 0.012 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.021 0.018 -9999 0 -10000 0 0
PI3K -0.021 0.072 -9999 0 -10000 0 0
ARF6 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.034 0.18 -9999 0 -0.62 16 16
TIAM1 0.012 0 -9999 0 -10000 0 0
E-cadherin(dimer)/Ca2+ -0.038 0.13 -9999 0 -0.47 16 16
AKT1 -0.012 0.041 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
CDH1 -0.054 0.22 -9999 0 -0.81 16 16
RhoA/GDP 0.024 0.11 -9999 0 -0.34 16 16
actin cytoskeleton organization -0.01 0.034 -9999 0 -10000 0 0
CDC42/GDP 0.024 0.11 -9999 0 -0.34 16 16
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.006 0.099 -9999 0 -0.34 16 16
ITGB7 0.012 0 -9999 0 -10000 0 0
RAC1 0.012 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.011 0.14 -9999 0 -0.49 16 16
E-cadherin/Ca2+/beta catenin/alpha catenin -0.038 0.13 -9999 0 -0.47 16 16
mol:GDP 0.017 0.13 -9999 0 -0.41 16 16
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.012 0 -9999 0 -10000 0 0
p120 catenin/RhoA/GDP -0.028 0.095 -9999 0 -0.35 16 16
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.018 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.012 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.025 0.031 -9999 0 -10000 0 0
NME1 0.008 0.036 -9999 0 -0.28 3 3
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.01 0.17 -9999 0 -0.57 16 16
regulation of cell-cell adhesion -0.02 0.068 -9999 0 -10000 0 0
WASF2 -0.005 0.016 -9999 0 -10000 0 0
Rap1/GTP -0.027 0.089 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.037 0.12 -9999 0 -0.46 16 16
CCND1 0.028 0.036 -9999 0 -10000 0 0
VAV2 0.005 0.15 -9999 0 -0.5 16 16
RAP1/GDP 0.021 0.1 -9999 0 -10000 0 0
adherens junction assembly -0.009 0.16 -9999 0 -0.55 16 16
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.012 0 -9999 0 -10000 0 0
PIP5K1C 0.012 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.004 0.13 -9999 0 -0.44 16 16
E-cadherin/beta catenin -0.04 0.14 -9999 0 -0.5 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.01 0.17 -9999 0 -0.57 16 16
PIK3CA 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.021 0.072 -9999 0 -0.32 1 1
E-cadherin/beta catenin/alpha catenin -0.044 0.15 -9999 0 -0.54 16 16
ITGAE 0.012 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.049 0.16 -9999 0 -0.61 16 16
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.007 0.079 -10000 0 -0.37 3 3
IKBKB -0.003 0.057 -10000 0 -0.26 1 1
AKT1 0.004 0.059 -10000 0 -0.24 1 1
IKBKG -0.002 0.06 -10000 0 -0.28 1 1
CALM1 -0.023 0.12 -10000 0 -0.5 7 7
PIK3CA 0.012 0 -10000 0 -10000 0 0
MAP3K1 0.001 0.093 -10000 0 -0.5 3 3
MAP3K7 0.012 0 -10000 0 -10000 0 0
mol:Ca2+ -0.032 0.12 0.24 4 -0.54 7 11
DOK1 0.011 0.021 -10000 0 -0.28 1 1
AP-1 -0.018 0.094 0.18 3 -0.27 8 11
LYN 0.012 0 -10000 0 -10000 0 0
BLNK -0.025 0.17 -10000 0 -0.81 9 9
SHC1 0.012 0 -10000 0 -10000 0 0
BCR complex -0.026 0.11 -10000 0 -0.57 5 5
CD22 -0.041 0.092 -10000 0 -0.48 6 6
CAMK2G -0.015 0.11 -10000 0 -0.49 6 6
CSNK2A1 0.012 0 -10000 0 -10000 0 0
INPP5D 0.003 0.051 -10000 0 -0.28 6 6
SHC/GRB2/SOS1 -0.039 0.11 -10000 0 -0.8 1 1
GO:0007205 -0.032 0.12 0.24 4 -0.55 7 11
SYK 0.008 0.058 -10000 0 -0.81 1 1
ELK1 -0.024 0.12 -10000 0 -0.51 7 7
NFATC1 -0.005 0.088 -10000 0 -0.44 4 4
B-cell antigen/BCR complex -0.026 0.11 -10000 0 -0.57 5 5
PAG1/CSK 0.018 0 -10000 0 -10000 0 0
NFKBIB 0.007 0.023 0.084 3 -10000 0 3
HRAS -0.016 0.12 -10000 0 -0.5 7 7
NFKBIA 0.007 0.023 0.084 3 -10000 0 3
NF-kappa-B/RelA/I kappa B beta 0.012 0.02 -10000 0 -10000 0 0
RasGAP/Csk -0.058 0.091 -10000 0 -0.46 5 5
mol:GDP -0.03 0.12 0.22 4 -0.53 7 11
PTEN 0.012 0 -10000 0 -10000 0 0
CD79B 0.002 0.085 -10000 0 -0.64 3 3
NF-kappa-B/RelA/I kappa B alpha 0.012 0.02 -10000 0 -10000 0 0
GRB2 0.012 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.012 0.11 -10000 0 -0.51 5 5
PIK3R1 0.012 0 -10000 0 -10000 0 0
mol:IP3 -0.033 0.13 0.24 4 -0.56 7 11
CSK 0.012 0 -10000 0 -10000 0 0
FOS -0.083 0.2 -10000 0 -0.49 33 33
CHUK -0.002 0.06 -10000 0 -0.28 1 1
IBTK 0.012 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.057 0.095 -10000 0 -0.48 5 5
PTPN6 -0.035 0.087 -10000 0 -0.49 4 4
RELA 0.012 0 -10000 0 -10000 0 0
BCL2A1 -0.005 0.029 -10000 0 -10000 0 0
VAV2 -0.038 0.099 -10000 0 -0.57 4 4
ubiquitin-dependent protein catabolic process 0.011 0.022 0.084 4 -10000 0 4
BTK -0.028 0.058 -10000 0 -10000 0 0
CD19 -0.041 0.1 -10000 0 -0.5 6 6
MAP4K1 -0.025 0.098 -10000 0 -0.28 25 25
CD72 -0.013 0.083 -10000 0 -0.28 17 17
PAG1 0.012 0 -10000 0 -10000 0 0
MAPK14 0.009 0.082 -10000 0 -0.42 3 3
SH3BP5 -0.013 0.14 -10000 0 -0.81 6 6
PIK3AP1 -0.021 0.13 0.27 4 -0.6 6 10
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.035 0.16 -10000 0 -0.68 8 8
RAF1 -0.008 0.11 -10000 0 -0.49 6 6
RasGAP/p62DOK/SHIP -0.057 0.089 -10000 0 -0.44 5 5
CD79A -0.04 0.13 -10000 0 -0.32 31 31
re-entry into mitotic cell cycle -0.018 0.094 0.18 3 -0.27 8 11
RASA1 0.012 0 -10000 0 -10000 0 0
MAPK3 0.007 0.092 -10000 0 -0.42 5 5
MAPK1 0.007 0.092 -10000 0 -0.42 5 5
CD72/SHP1 -0.019 0.1 -10000 0 -0.49 4 4
NFKB1 0.012 0 -10000 0 -10000 0 0
MAPK8 0.001 0.1 -10000 0 -0.41 7 7
actin cytoskeleton organization -0.007 0.097 -10000 0 -0.49 4 4
NF-kappa-B/RelA 0.028 0.038 0.17 3 -10000 0 3
Calcineurin -0.026 0.086 -10000 0 -0.47 5 5
PI3K -0.036 0.082 -10000 0 -0.43 4 4
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.037 0.13 0.27 4 -0.6 7 11
SOS1 0.012 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.022 0.12 -10000 0 -0.62 4 4
DAPP1 -0.031 0.11 -10000 0 -0.78 3 3
cytokine secretion -0.004 0.083 -10000 0 -0.41 4 4
mol:DAG -0.033 0.13 0.24 4 -0.56 7 11
PLCG2 -0.039 0.2 -10000 0 -0.77 13 13
MAP2K1 0 0.1 -10000 0 -0.47 5 5
B-cell antigen/BCR complex/FcgammaRIIB -0.077 0.11 -10000 0 -0.54 5 5
mol:PI-3-4-5-P3 -0.028 0.061 -10000 0 -0.31 4 4
ETS1 -0.007 0.099 -10000 0 -0.47 5 5
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.048 0.13 -10000 0 -0.5 13 13
B-cell antigen/BCR complex/LYN -0.035 0.091 -10000 0 -0.52 5 5
MALT1 0.012 0 -10000 0 -10000 0 0
TRAF6 0.012 0 -10000 0 -10000 0 0
RAC1 -0.008 0.1 -10000 0 -0.52 4 4
B-cell antigen/BCR complex/LYN/SYK -0.035 0.093 -10000 0 -0.51 4 4
CARD11 -0.062 0.13 -10000 0 -0.47 9 9
FCGR2B -0.079 0.14 -10000 0 -0.29 59 59
PPP3CA 0.012 0 -10000 0 -10000 0 0
BCL10 0.012 0 -10000 0 -10000 0 0
IKK complex 0.008 0.027 -10000 0 -10000 0 0
PTPRC 0.003 0.068 -10000 0 -0.42 4 4
PDPK1 0.001 0.054 -10000 0 -10000 0 0
PPP3CB 0.012 0 -10000 0 -10000 0 0
PPP3CC 0.012 0 -10000 0 -10000 0 0
POU2F2 0.012 0.018 -10000 0 -10000 0 0
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.034 0.31 -10000 0 -0.98 8 8
IL23A -0.034 0.31 -10000 0 -1.1 5 5
NF kappa B1 p50/RelA/I kappa B alpha -0.12 0.21 -10000 0 -0.84 8 8
positive regulation of T cell mediated cytotoxicity -0.037 0.31 -10000 0 -0.94 8 8
ITGA3 -0.031 0.29 -10000 0 -0.91 6 6
IL17F -0.004 0.22 -10000 0 -0.62 6 6
IL12B 0.013 0.035 -10000 0 -0.28 1 1
STAT1 (dimer) -0.037 0.29 -10000 0 -0.9 8 8
CD4 -0.029 0.29 -10000 0 -0.86 7 7
IL23 -0.044 0.3 -10000 0 -1.1 5 5
IL23R 0.011 0.093 -10000 0 -10000 0 0
IL1B -0.042 0.33 -10000 0 -1.1 8 8
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.029 0.28 -10000 0 -0.88 7 7
TYK2 0.016 0.018 -10000 0 -10000 0 0
STAT4 -0.01 0.078 -10000 0 -10000 0 0
STAT3 0.012 0.001 -10000 0 -10000 0 0
IL18RAP -0.026 0.099 -10000 0 -0.28 25 25
IL12RB1 -0.004 0.081 -10000 0 -0.3 12 12
PIK3CA 0.012 0.001 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.007 0.06 -10000 0 -10000 0 0
IL23R/JAK2 0.02 0.11 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.037 0.31 -10000 0 -0.94 8 8
natural killer cell activation 0 0.009 0.036 3 -10000 0 3
JAK2 0.023 0.023 -10000 0 -10000 0 0
PIK3R1 0.012 0.001 -10000 0 -10000 0 0
NFKB1 0.013 0.003 -10000 0 -10000 0 0
RELA 0.013 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.041 0.29 -10000 0 -1 5 5
ALOX12B -0.028 0.28 -10000 0 -0.86 8 8
CXCL1 -0.079 0.35 -10000 0 -1.1 11 11
T cell proliferation -0.037 0.31 -10000 0 -0.94 8 8
NFKBIA 0.013 0.003 -10000 0 -10000 0 0
IL17A 0.017 0.19 -10000 0 -0.51 2 2
PI3K -0.11 0.23 -10000 0 -0.87 8 8
IFNG 0 0.028 0.084 1 -0.086 1 2
STAT3 (dimer) -0.11 0.21 -10000 0 -0.83 8 8
IL18R1 0.007 0.059 -10000 0 -0.81 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 0 0.2 -10000 0 -0.61 3 3
IL18/IL18R -0.005 0.069 -10000 0 -0.54 1 1
macrophage activation -0.009 0.013 -10000 0 -0.043 5 5
TNF -0.04 0.32 -10000 0 -1.1 7 7
STAT3/STAT4 -0.11 0.23 -10000 0 -0.9 8 8
STAT4 (dimer) -0.044 0.3 -10000 0 -0.93 8 8
IL18 0.009 0.03 -10000 0 -0.28 2 2
IL19 -0.032 0.28 -10000 0 -0.87 7 7
STAT5A (dimer) -0.035 0.29 -10000 0 -0.9 8 8
STAT1 0.008 0.036 -10000 0 -0.28 3 3
SOCS3 0.005 0.065 -10000 0 -0.46 3 3
CXCL9 -0.039 0.31 -10000 0 -0.94 9 9
MPO -0.033 0.29 -10000 0 -0.88 7 7
positive regulation of humoral immune response -0.037 0.31 -10000 0 -0.94 8 8
IL23/IL23R/JAK2/TYK2 -0.038 0.31 -10000 0 -0.97 8 8
IL6 -0.11 0.44 -10000 0 -1.2 22 22
STAT5A 0.012 0 -10000 0 -10000 0 0
IL2 0.002 0.023 -10000 0 -0.29 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0 0.009 0.036 3 -10000 0 3
CD3E -0.037 0.31 -10000 0 -1 6 6
keratinocyte proliferation -0.037 0.31 -10000 0 -0.94 8 8
NOS2 -0.088 0.42 -10000 0 -1.2 19 19
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.002 0.11 -10000 0 -0.62 6 6
ATM 0.012 0 -10000 0 -10000 0 0
UBE2D3 0.012 0 -10000 0 -10000 0 0
PRKDC 0.012 0 -10000 0 -10000 0 0
ATR 0.012 0 -10000 0 -10000 0 0
UBE2L3 0.012 0 -10000 0 -10000 0 0
FANCD2 0.023 0.009 -10000 0 -10000 0 0
protein ubiquitination -0.022 0.082 -10000 0 -0.45 6 6
XRCC5 0.012 0 -10000 0 -10000 0 0
XRCC6 0.012 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.012 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.011 0.023 -10000 0 -10000 0 0
FANCF 0.012 0 -10000 0 -10000 0 0
BRCA1 0.009 0.03 -10000 0 -0.28 2 2
CCNE1 -0.009 0.076 -10000 0 -10000 0 0
CDK2/Cyclin E1 0.004 0.051 -10000 0 -10000 0 0
FANCG 0.012 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.004 0.11 -10000 0 -0.62 6 6
FANCE 0.012 0 -10000 0 -10000 0 0
FANCC 0.012 0 -10000 0 -10000 0 0
NBN 0.012 0 -10000 0 -10000 0 0
FANCA -0.11 0.15 -10000 0 -0.28 81 81
DNA repair 0.008 0.1 -10000 0 -10000 0 0
BRCA1/BARD1/ubiquitin -0.004 0.11 -10000 0 -0.62 6 6
BARD1/DNA-PK 0.015 0.089 -10000 0 -0.49 6 6
FANCL 0.012 0 -10000 0 -10000 0 0
mRNA polyadenylation 0.002 0.11 0.62 6 -10000 0 6
BRCA1/BARD1/CTIP/M/R/N Complex 0.024 0.064 -10000 0 -0.32 6 6
BRCA1/BACH1/BARD1/TopBP1 -0.018 0.093 -10000 0 -0.54 6 6
BRCA1/BARD1/P53 0.014 0.09 -10000 0 -0.49 6 6
BARD1/CSTF1/BRCA1 -0.018 0.093 -10000 0 -0.54 6 6
BRCA1/BACH1 0.009 0.03 -10000 0 -0.28 2 2
BARD1 -0.013 0.14 -10000 0 -0.81 6 6
PCNA 0.012 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.018 0.093 -10000 0 -0.54 6 6
BRCA1/BARD1/UbcH7 -0.018 0.093 -10000 0 -0.54 6 6
BRCA1/BARD1/RAD51/PCNA -0.007 0.1 -10000 0 -0.49 6 6
BARD1/DNA-PK/P53 -0.014 0.079 -10000 0 -0.46 6 6
BRCA1/BARD1/Ubiquitin -0.004 0.11 -10000 0 -0.62 6 6
BRCA1/BARD1/CTIP 0.011 0.097 -10000 0 -0.49 7 7
FA complex -0.002 0.047 -10000 0 -10000 0 0
BARD1/EWS -0.002 0.11 -10000 0 -0.62 6 6
RBBP8 0.018 0.046 -10000 0 -0.62 1 1
TP53 0.012 0 -10000 0 -10000 0 0
TOPBP1 0.012 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.016 0.084 0.49 6 -10000 0 6
BRCA1/BARD1 -0.022 0.083 -10000 0 -0.46 6 6
CSTF1 0.012 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.011 0.11 -10000 0 -0.63 6 6
CDK2 0.012 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.028 0.1 -10000 0 -0.28 27 27
RAD50 0.012 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.004 0.11 -10000 0 -0.62 6 6
EWSR1 0.012 0 -10000 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.026 0.1 -9999 0 -0.43 8 8
NF kappa B1 p50/RelA/I kappa B alpha 0.048 0.094 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin/Src -0.013 0.079 -9999 0 -0.61 3 3
AP1 -0.025 0.22 -9999 0 -0.78 6 6
ILK 0.018 0.11 -9999 0 -0.46 8 8
bone resorption 0.022 0.12 -9999 0 -0.64 2 2
PTK2B 0.012 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.023 0.09 -9999 0 -0.42 9 9
ITGAV 0.016 0.002 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.007 0.093 -9999 0 -0.62 3 3
alphaV/beta3 Integrin/Osteopontin -0.027 0.11 -9999 0 -0.52 8 8
MAP3K1 0.018 0.11 -9999 0 -0.47 8 8
JUN 0.013 0.001 -9999 0 -10000 0 0
MAPK3 0.03 0.1 -9999 0 -0.43 8 8
MAPK1 0.03 0.1 -9999 0 -0.43 8 8
Rac1/GDP 0.009 0 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 0.017 0.13 -9999 0 -0.48 11 11
ITGB3 -0.012 0.14 -9999 0 -0.54 10 10
NFKBIA 0.039 0.1 -9999 0 -10000 0 0
FOS -0.12 0.3 -9999 0 -0.81 31 31
CD44 -0.01 0.078 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
PLAU 0.039 0.13 -9999 0 -1.1 1 1
NF kappa B1 p50/RelA -0.018 0.073 -9999 0 -10000 0 0
BCAR1 0.012 0 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.02 0.099 -9999 0 -0.61 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
SYK 0.014 0.11 -9999 0 -0.47 9 9
VAV3 0.022 0.11 -9999 0 -0.44 9 9
MAP3K14 0.02 0.11 -9999 0 -0.47 8 8
ROCK2 0 0.1 -9999 0 -0.81 3 3
SPP1 -0.004 0.11 -9999 0 -0.8 3 3
RAC1 0.012 0 -9999 0 -10000 0 0
Rac1/GTP -0.022 0.085 -9999 0 -0.4 9 9
MMP2 -0.012 0.19 -9999 0 -0.65 6 6
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.012 0 -9999 0 -10000 0 0
VLDLR 0.012 0 -9999 0 -10000 0 0
LRPAP1 0.012 0 -9999 0 -10000 0 0
NUDC 0.012 0 -9999 0 -10000 0 0
RELN/LRP8 -0.083 0.13 -9999 0 -0.57 10 10
CaM/Ca2+ 0.009 0 -9999 0 -10000 0 0
KATNA1 0.012 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.054 0.13 -9999 0 -0.51 10 10
IQGAP1/CaM 0.018 0 -9999 0 -10000 0 0
DAB1 -0.005 0.054 -9999 0 -10000 0 0
IQGAP1 0.012 0 -9999 0 -10000 0 0
PLA2G7 -0.22 0.12 -9999 0 -10000 0 0
CALM1 0.012 0 -9999 0 -10000 0 0
DYNLT1 0.012 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.012 0.034 -9999 0 -10000 0 0
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0 -9999 0 -10000 0 0
CDK5R1 0.009 0.03 -9999 0 -0.28 2 2
LIS1/Poliovirus Protein 3A 0.016 0 -9999 0 -10000 0 0
CDK5R2 -0.065 0.13 -9999 0 -0.28 50 50
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.086 0.13 -9999 0 -0.56 10 10
YWHAE 0.012 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.038 0.11 -9999 0 -0.47 3 3
MAP1B 0 0.011 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.035 0.12 -9999 0 -0.45 10 10
RELN -0.14 0.21 -9999 0 -0.35 83 83
PAFAH/LIS1 -0.1 0.069 -9999 0 -10000 0 0
LIS1/CLIP170 0.025 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.037 0.071 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.024 0.09 -9999 0 -0.34 11 11
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.047 0.11 -9999 0 -0.43 10 10
LIS1/IQGAP1 0.025 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.021 0 -9999 0 -10000 0 0
PAFAH1B3 0.011 0.021 -9999 0 -0.28 1 1
PAFAH1B2 0.008 0.058 -9999 0 -0.81 1 1
MAP1B/LIS1/Dynein heavy chain 0.023 0.006 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.05 0.09 -9999 0 -0.45 3 3
LRP8 0.003 0.051 -9999 0 -0.28 6 6
NDEL1/Katanin 60 -0.038 0.11 -9999 0 -0.47 3 3
P39/CDK5 -0.068 0.12 -9999 0 -0.46 10 10
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0 -9999 0 -10000 0 0
CDK5 -0.043 0.12 -9999 0 -0.48 10 10
PPP2R5D 0.011 0.021 -9999 0 -0.28 1 1
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.012 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.049 0.12 -9999 0 -0.48 10 10
RELN/VLDLR -0.054 0.13 -9999 0 -0.52 10 10
CDC42 0 0 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.01 0.087 -9999 0 -0.4 3 3
MAP4K1 -0.025 0.098 -9999 0 -0.28 25 25
MAP3K8 0.012 0 -9999 0 -10000 0 0
PRKCB 0.008 0.036 -9999 0 -0.28 3 3
DBNL 0.012 0 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
MAP3K1 0.021 0.047 -9999 0 -10000 0 0
JUN 0.017 0.088 -9999 0 -0.58 4 4
MAP3K7 0.021 0.047 -9999 0 -10000 0 0
GRAP2 0.005 0.046 -9999 0 -0.28 5 5
CRK 0.012 0 -9999 0 -10000 0 0
MAP2K4 0.029 0.046 -9999 0 -10000 0 0
LAT -0.021 0.093 -9999 0 -0.28 22 22
LCP2 0.006 0.042 -9999 0 -0.28 4 4
MAPK8 0.011 0.093 -9999 0 -0.62 4 4
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.014 0.05 -9999 0 -10000 0 0
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.031 0.068 -9999 0 -0.37 3 3
Fc-epsilon receptor I signaling in mast cells

Figure S70.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S70.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.012 0 -9999 0 -10000 0 0
LAT2 -0.034 0.097 -9999 0 -0.33 2 2
AP1 -0.1 0.16 -9999 0 -0.49 17 17
mol:PIP3 -0.049 0.14 -9999 0 -0.44 5 5
IKBKB -0.016 0.081 -9999 0 -0.28 1 1
AKT1 -0.017 0.094 -9999 0 -10000 0 0
IKBKG -0.016 0.081 -9999 0 -0.26 2 2
MS4A2 -0.082 0.15 -9999 0 -0.29 61 61
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.001 -9999 0 -10000 0 0
MAP3K1 -0.018 0.1 -9999 0 -0.45 1 1
mol:Ca2+ -0.036 0.11 -9999 0 -0.33 5 5
LYN 0.01 0.004 -9999 0 -10000 0 0
CBLB -0.019 0.073 -9999 0 -0.32 1 1
SHC1 0.012 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.02 0.038 -9999 0 -0.5 1 1
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.003 0.051 -9999 0 -0.28 6 6
PLD2 -0.046 0.11 -9999 0 -0.42 6 6
PTPN13 -0.008 0.068 -9999 0 -10000 0 0
PTPN11 0.012 0.003 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation 0.007 0.076 -9999 0 -10000 0 0
SYK 0.006 0.059 -9999 0 -0.82 1 1
GRB2 0.012 0 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.078 0.11 -9999 0 -0.45 5 5
LAT -0.033 0.084 -9999 0 -0.34 3 3
PAK2 -0.027 0.11 -9999 0 -0.51 1 1
NFATC2 -0.072 0.18 -9999 0 -0.72 13 13
HRAS -0.036 0.12 -9999 0 -0.56 1 1
GAB2 0.012 0 -9999 0 -10000 0 0
PLA2G1B 0.029 0.012 -9999 0 -10000 0 0
Fc epsilon R1 -0.092 0.12 -9999 0 -0.52 6 6
Antigen/IgE/Fc epsilon R1 -0.082 0.11 -9999 0 -0.48 6 6
mol:GDP -0.047 0.12 -9999 0 -0.62 1 1
JUN 0.012 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.001 -9999 0 -10000 0 0
FOS -0.12 0.3 -9999 0 -0.81 31 31
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.028 0.077 -9999 0 -0.31 2 2
CHUK -0.016 0.081 -9999 0 -0.28 1 1
KLRG1 -0.023 0.074 -9999 0 -10000 0 0
VAV1 -0.044 0.11 -9999 0 -0.51 2 2
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.019 0.073 -9999 0 -0.32 1 1
negative regulation of mast cell degranulation -0.019 0.074 -9999 0 -10000 0 0
BTK -0.04 0.1 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.053 0.12 -9999 0 -0.4 8 8
GAB2/PI3K/SHP2 -0.053 0.08 -9999 0 -10000 0 0
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.026 0.076 -9999 0 -0.31 2 2
RAF1 0.018 0.014 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.11 0.14 -9999 0 -0.42 21 21
FCER1G -0.058 0.13 -9999 0 -0.29 47 47
FCER1A -0.01 0.12 -9999 0 -0.82 4 4
Antigen/IgE/Fc epsilon R1/Fyn -0.072 0.099 -9999 0 -0.45 6 6
MAPK3 0.028 0.012 -9999 0 -10000 0 0
MAPK1 0.028 0.012 -9999 0 -10000 0 0
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.005 0.1 -9999 0 -0.66 4 4
DUSP1 0.008 0.058 -9999 0 -0.81 1 1
NF-kappa-B/RelA -0.022 0.037 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.015 0.07 -9999 0 -10000 0 0
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.059 0.099 -9999 0 -0.6 1 1
FER -0.019 0.073 -9999 0 -0.32 1 1
RELA 0.012 0 -9999 0 -10000 0 0
ITK -0.014 0.029 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
PLCG1 -0.043 0.13 -9999 0 -0.62 1 1
cytokine secretion -0.016 0.028 -9999 0 -10000 0 0
SPHK1 -0.08 0.099 -9999 0 -0.34 2 2
PTK2 -0.016 0.071 -9999 0 -10000 0 0
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.078 0.12 -9999 0 -0.52 2 2
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.038 0.13 -9999 0 -0.44 3 3
MAP2K2 0.024 0.012 -9999 0 -10000 0 0
MAP2K1 0.024 0.012 -9999 0 -10000 0 0
MAP2K7 0.012 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.039 0.056 -9999 0 -10000 0 0
MAP2K4 0.016 0.008 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.12 0.15 -9999 0 -0.45 19 19
mol:Choline -0.045 0.1 -9999 0 -0.41 6 6
SHC/Grb2/SOS1 -0.031 0.052 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
DOK1 0.011 0.021 -9999 0 -0.28 1 1
PXN -0.008 0.068 -9999 0 -10000 0 0
HCLS1 -0.02 0.076 -9999 0 -0.32 1 1
PRKCB -0.031 0.1 -9999 0 -0.33 5 5
FCGR2B -0.079 0.14 -9999 0 -0.29 59 59
IGHE -0.002 0.005 -9999 0 -10000 0 0
KLRG1/SHIP -0.019 0.075 -9999 0 -10000 0 0
LCP2 0.006 0.042 -9999 0 -0.29 4 4
PLA2G4A -0.028 0.096 -9999 0 -0.43 5 5
RASA1 0.012 0 -9999 0 -10000 0 0
mol:Phosphatidic acid -0.045 0.1 -9999 0 -0.41 6 6
IKK complex 0 0.066 -9999 0 -10000 0 0
WIPF1 0.012 0 -9999 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.012 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.093 0.18 -9999 0 -0.42 43 43
Syndecan-3/Neurocan -0.016 0.039 -9999 0 -10000 0 0
POMC 0 0.1 -9999 0 -0.81 3 3
EGFR 0.012 0 -9999 0 -10000 0 0
Syndecan-3/EGFR -0.001 0.009 -9999 0 -10000 0 0
AGRP 0.008 0.006 -9999 0 -10000 0 0
NCSTN 0.012 0 -9999 0 -10000 0 0
PSENEN 0.012 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.008 0.058 -9999 0 -0.81 1 1
APH1A 0.012 0 -9999 0 -10000 0 0
NCAN -0.033 0.1 -9999 0 -10000 0 0
long-term memory -0.001 0.008 -9999 0 -10000 0 0
Syndecan-3/IL8 -0.029 0.056 -9999 0 -0.46 1 1
PSEN1 0.012 0 -9999 0 -10000 0 0
Src/Cortactin 0.018 0 -9999 0 -10000 0 0
FYN 0.012 0 -9999 0 -10000 0 0
limb bud formation -0.001 0.01 -9999 0 -10000 0 0
MC4R -0.001 0.036 -9999 0 -0.28 3 3
SRC 0.012 0 -9999 0 -10000 0 0
PTN -0.17 0.34 -9999 0 -0.79 45 45
FGFR/FGF/Syndecan-3 -0.001 0.01 -9999 0 -10000 0 0
neuron projection morphogenesis -0.1 0.17 -9999 0 -0.51 8 8
Syndecan-3/AgRP -0.001 0.009 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.002 0.015 -9999 0 -10000 0 0
Fyn/Cortactin 0.018 0 -9999 0 -10000 0 0
SDC3 -0.001 0.01 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.029 0.055 -9999 0 -0.45 1 1
IL8 -0.062 0.14 -9999 0 -0.3 48 48
Syndecan-3/Fyn/Cortactin -0.001 0.008 -9999 0 -10000 0 0
Syndecan-3/CASK -0.001 0.009 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.001 0.082 -9999 0 -0.63 3 3
Gamma Secretase -0.002 0.033 -9999 0 -0.46 1 1
Effects of Botulinum toxin

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
STX1A 0.007 0.025 -9999 0 -10000 0 0
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0.004 0.045 -9999 0 -10000 0 0
STXBP1 0.012 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.12 0.084 -9999 0 -0.25 2 2
RAB3GAP2/RIMS1/UNC13B -0.008 0.032 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.009 0.067 -9999 0 -0.28 11 11
mol:ACh -0.012 0.027 -9999 0 -0.12 2 2
RAB3GAP2 0.012 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.018 0.033 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.12 0.084 -9999 0 -0.25 2 2
UNC13B 0.012 0 -9999 0 -10000 0 0
CHRNA1 -0.2 0.13 -9999 0 -10000 0 0
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.16 0.26 -9999 0 -0.58 53 53
SNAP25 -0.037 0.059 -9999 0 -0.38 1 1
VAMP2 0.006 0 -9999 0 -10000 0 0
SYT1 -0.21 0.36 -9999 0 -0.81 53 53
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.014 0.02 -9999 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.018 0.033 -9999 0 -10000 0 0
Wnt signaling

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
Noncanonical Wnts/FZD -0.01 0.1 -9999 0 -0.34 14 14
FZD6 0.012 0 -9999 0 -10000 0 0
WNT6 0.005 0.062 -9999 0 -0.55 2 2
WNT4 -0.008 0.12 -9999 0 -0.64 6 6
FZD3 0.012 0 -9999 0 -10000 0 0
WNT5A -0.034 0.11 -9999 0 -10000 0 0
WNT11 -0.032 0.18 -9999 0 -0.81 9 9
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.054 0.12 -9999 0 -0.58 8 8
PDGFB-D/PDGFRB/SLAP -0.021 0.13 -9999 0 -0.64 8 8
PDGFB-D/PDGFRB/APS/CBL -0.021 0.1 -9999 0 -0.53 8 8
AKT1 0.037 0.08 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.043 0.13 -9999 0 -0.62 8 8
PIK3CA 0.012 0 -9999 0 -10000 0 0
FGR -0.023 0.11 -9999 0 -0.53 9 9
mol:Ca2+ -0.007 0.13 -9999 0 -0.63 8 8
MYC 0.012 0.092 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
HRAS/GDP 0.014 0.093 -9999 0 -0.44 8 8
LRP1/PDGFRB/PDGFB -0.024 0.11 -9999 0 -0.53 9 9
GRB10 0.012 0 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
GO:0007205 -0.008 0.13 -9999 0 -0.64 8 8
PTEN 0.012 0 -9999 0 -10000 0 0
GRB2 0.012 0 -9999 0 -10000 0 0
GRB7 0.012 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SHP2 -0.015 0.12 -9999 0 -0.62 8 8
PDGFB-D/PDGFRB/GRB10 -0.015 0.12 -9999 0 -0.62 8 8
cell cycle arrest -0.021 0.13 -9999 0 -0.64 8 8
HRAS 0.012 0 -9999 0 -10000 0 0
HIF1A 0.043 0.072 -9999 0 -10000 0 0
GAB1 -0.013 0.13 -9999 0 -0.61 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.012 0.12 -9999 0 -0.57 8 8
PDGFB-D/PDGFRB -0.018 0.11 -9999 0 -0.55 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.015 0.12 -9999 0 -0.62 8 8
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.052 0.11 -9999 0 -0.57 8 8
positive regulation of MAPKKK cascade -0.015 0.12 -9999 0 -0.62 8 8
PIK3R1 0.012 0 -9999 0 -10000 0 0
mol:IP3 -0.008 0.13 -9999 0 -0.65 8 8
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.012 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.015 0.12 -9999 0 -0.62 8 8
SHB 0.012 0 -9999 0 -10000 0 0
BLK -0.021 0.1 -9999 0 -0.51 8 8
PTPN2 0.012 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 -0.015 0.12 -9999 0 -0.62 8 8
BCAR1 0.012 0 -9999 0 -10000 0 0
VAV2 -0.01 0.13 -9999 0 -0.59 8 8
CBL 0.012 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.015 0.12 -9999 0 -0.62 8 8
LCK -0.019 0.1 -9999 0 -0.51 8 8
PDGFRB -0.022 0.16 -9999 0 -0.82 8 8
ACP1 0.012 0 -9999 0 -10000 0 0
HCK -0.03 0.12 -9999 0 -0.54 9 9
ABL1 -0.008 0.12 -9999 0 -0.56 8 8
PDGFB-D/PDGFRB/CBL -0.013 0.14 -9999 0 -0.66 8 8
PTPN1 0.012 0.002 -9999 0 -10000 0 0
SNX15 0.012 0 -9999 0 -10000 0 0
STAT3 0.012 0 -9999 0 -10000 0 0
STAT1 0.008 0.036 -9999 0 -0.28 3 3
cell proliferation 0.012 0.086 -9999 0 -0.37 4 4
SLA 0.003 0.051 -9999 0 -0.28 6 6
actin cytoskeleton reorganization 0.027 0.091 -9999 0 -10000 0 0
SRC -0.016 0.1 -9999 0 -0.51 8 8
PI3K -0.016 0.077 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7/SHC -0.021 0.1 -9999 0 -0.53 8 8
SH2B2 0.012 0 -9999 0 -10000 0 0
PLCgamma1/SPHK1 -0.044 0.14 -9999 0 -0.65 8 8
LYN -0.016 0.1 -9999 0 -0.51 8 8
LRP1 0.012 0 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
STAT5B 0.012 0 -9999 0 -10000 0 0
STAT5A 0.012 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.016 0.086 -9999 0 -0.43 8 8
SPHK1 -0.13 0.15 -9999 0 -10000 0 0
EDG1 -0.001 0.002 -9999 0 -10000 0 0
mol:DAG -0.008 0.13 -9999 0 -0.65 8 8
PLCG1 -0.008 0.14 -9999 0 -0.67 8 8
NHERF/PDGFRB -0.021 0.1 -9999 0 -0.53 8 8
YES1 -0.016 0.1 -9999 0 -0.51 8 8
cell migration -0.021 0.1 -9999 0 -0.53 8 8
SHC/Grb2/SOS1 -0.016 0.086 -9999 0 -0.43 8 8
SLC9A3R2 0.012 0 -9999 0 -10000 0 0
SLC9A3R1 0.012 0 -9999 0 -10000 0 0
NHERF1-2/PDGFRB/PTEN -0.003 0.1 -9999 0 -0.48 8 8
FYN -0.016 0.1 -9999 0 -0.51 8 8
DOK1 0.008 0.1 -9999 0 -0.49 8 8
HRAS/GTP 0.009 0 -9999 0 -10000 0 0
PDGFB 0.008 0.058 -9999 0 -0.81 1 1
RAC1 -0.002 0.12 -9999 0 -0.53 8 8
PRKCD 0.009 0.1 -9999 0 -0.49 8 8
FER 0.009 0.1 -9999 0 -0.49 8 8
MAPKKK cascade -0.017 0.083 -9999 0 -0.42 8 8
RASA1 0.009 0.1 -9999 0 -0.49 8 8
NCK1 0.012 0 -9999 0 -10000 0 0
NCK2 0.012 0 -9999 0 -10000 0 0
p62DOK/Csk 0.015 0.096 -9999 0 -0.45 8 8
PDGFB-D/PDGFRB/SHB -0.015 0.12 -9999 0 -0.62 8 8
chemotaxis -0.007 0.11 -9999 0 -0.54 8 8
STAT1-3-5/STAT1-3-5 -0.018 0.082 -9999 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB -0.02 0.12 -9999 0 -0.63 8 8
PTPRJ 0.012 0 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.011 0.16 -9999 0 -0.38 31 31
MAP3K8 0.011 0.005 -9999 0 -10000 0 0
FOS 0.008 0.1 -9999 0 -0.72 1 1
PRKCA 0.011 0.005 -9999 0 -10000 0 0
PTPN7 0.005 0.066 -9999 0 -0.46 3 3
HRAS 0.012 0.001 -9999 0 -10000 0 0
PRKCB 0.007 0.037 -9999 0 -0.29 3 3
NRAS 0.012 0.001 -9999 0 -10000 0 0
RAS family/GTP 0.021 0.009 -9999 0 -10000 0 0
MAPK3 0.014 0.061 -9999 0 -0.55 1 1
MAP2K1 0.025 0.041 -9999 0 -10000 0 0
ELK1 0.009 0.01 -9999 0 -10000 0 0
BRAF -0.006 0.017 -9999 0 -10000 0 0
mol:GTP -0.001 0.002 -9999 0 -0.006 31 31
MAPK1 0.014 0.061 -9999 0 -0.55 1 1
RAF1 -0.006 0.017 -9999 0 -10000 0 0
KRAS 0.012 0.001 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.004 0.063 -9999 0 -10000 0 0
CRKL 0.015 0.066 -9999 0 -0.33 1 1
mol:PIP3 -0.019 0.004 -9999 0 -10000 0 0
AKT1 0.001 0.003 -9999 0 -10000 0 0
PTK2B 0.012 0 -9999 0 -10000 0 0
RAPGEF1 0.021 0.063 -9999 0 -10000 0 0
RANBP10 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.04 0.12 -9999 0 -0.55 9 9
MAP3K5 0.021 0.061 -9999 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS -0.009 0.12 -9999 0 -0.5 9 9
AP1 -0.079 0.21 -9999 0 -0.56 31 31
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.012 0 -9999 0 -10000 0 0
apoptosis -0.1 0.27 -9999 0 -0.73 31 31
STAT3 (dimer) 0.014 0.077 -9999 0 -0.32 9 9
GAB1/CRKL/SHP2/PI3K -0.013 0.047 -9999 0 -10000 0 0
INPP5D 0.003 0.051 -9999 0 -0.28 6 6
CBL/CRK 0.021 0.063 -9999 0 -10000 0 0
PTPN11 0.012 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.012 0 -9999 0 -10000 0 0
PTEN 0.012 0 -9999 0 -10000 0 0
ELK1 -0.012 0.037 -9999 0 -10000 0 0
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.012 0.04 -9999 0 -0.25 1 1
PAK1 0.007 0.003 -9999 0 -10000 0 0
HGF/MET/RANBP10 -0.04 0.12 -9999 0 -0.55 9 9
HRAS 0.005 0.095 -9999 0 -0.4 9 9
DOCK1 0.021 0.063 -9999 0 -10000 0 0
GAB1 0.008 0.069 -9999 0 -0.35 1 1
CRK 0.015 0.066 -9999 0 -0.33 1 1
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.035 0.12 -9999 0 -0.57 9 9
JUN 0.012 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.009 0.064 -9999 0 -0.26 9 9
PIK3R1 0.012 0 -9999 0 -10000 0 0
cell morphogenesis 0.039 0.078 -9999 0 -10000 0 0
GRB2/SHC 0.007 0.057 -9999 0 -0.3 1 1
FOS -0.12 0.3 -9999 0 -0.81 31 31
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.012 0.037 -9999 0 -10000 0 0
HGF/MET/MUC20 -0.041 0.12 -9999 0 -0.56 9 9
cell migration 0.007 0.057 -9999 0 -0.29 1 1
GRB2 0.012 0 -9999 0 -10000 0 0
CBL 0.012 0 -9999 0 -10000 0 0
MET/RANBP10 -0.004 0.063 -9999 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.007 0.081 -9999 0 -0.34 9 9
MET/MUC20 -0.013 0.063 -9999 0 -0.19 22 22
RAP1B 0.027 0.06 -9999 0 -10000 0 0
RAP1A 0.027 0.06 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.04 0.12 -9999 0 -0.55 9 9
RAF1 0.012 0.091 -9999 0 -0.46 1 1
STAT3 0.014 0.078 -9999 0 -0.32 9 9
cell proliferation 0.019 0.1 -9999 0 -0.43 9 9
RPS6KB1 0.004 0.024 -9999 0 -10000 0 0
MAPK3 -0.016 0.033 -9999 0 -10000 0 0
MAPK1 -0.016 0.033 -9999 0 -10000 0 0
RANBP9 0.012 0 -9999 0 -10000 0 0
MAPK8 0.026 0.097 -9999 0 -0.54 4 4
SRC 0.015 0.077 -9999 0 -0.39 1 1
PI3K 0.007 0.057 -9999 0 -0.3 1 1
MET/Glomulin -0.008 0.054 -9999 0 -10000 0 0
SOS1 0.012 0 -9999 0 -10000 0 0
MAP2K1 0.018 0.086 -9999 0 -0.43 1 1
MET -0.021 0.093 -9999 0 -0.28 22 22
MAP4K1 0.015 0.064 -9999 0 -10000 0 0
PTK2 0.012 0 -9999 0 -10000 0 0
MAP2K2 0.018 0.086 -9999 0 -0.43 1 1
BAD 0.007 0.003 -9999 0 -10000 0 0
MAP2K4 0.027 0.058 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.017 0.051 -9999 0 -10000 0 0
INPPL1 0.012 0 -9999 0 -10000 0 0
PXN 0.012 0 -9999 0 -10000 0 0
SH3KBP1 0.012 0 -9999 0 -10000 0 0
HGS -0.001 0.06 -9999 0 -0.32 1 1
PLCgamma1/PKC 0.009 0 -9999 0 -10000 0 0
HGF -0.025 0.17 -9999 0 -0.81 9 9
RASA1 0.012 0 -9999 0 -10000 0 0
NCK1 0.012 0 -9999 0 -10000 0 0
PTPRJ 0.012 0 -9999 0 -10000 0 0
NCK/PLCgamma1 0.008 0.063 -9999 0 -0.33 1 1
PDPK1 -0.008 0.003 -9999 0 -10000 0 0
HGF/MET/SHIP -0.044 0.12 -9999 0 -0.55 9 9
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.027 0.033 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.001 -9999 0 -10000 0 0
CRKL 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 0.052 0.034 -9999 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.073 0.079 -9999 0 -0.3 1 1
CaM/Ca2+ -0.006 0.02 -9999 0 -10000 0 0
RAP1A 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 0.032 0.037 -9999 0 -10000 0 0
AKT1 0.042 0.029 -9999 0 -10000 0 0
MAP2K1 0.04 0.03 -9999 0 -10000 0 0
MAP3K11 0.032 0.031 -9999 0 -10000 0 0
IFNGR1 0.013 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.25 0.25 -9999 0 -0.51 95 95
Rap1/GTP -0.003 0.01 -9999 0 -10000 0 0
CRKL/C3G 0.018 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.001 0.03 -9999 0 -10000 0 0
CEBPB 0.065 0.029 -9999 0 -10000 0 0
STAT3 0.012 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.019 0.13 -9999 0 -1.2 2 2
STAT1 0.031 0.037 -9999 0 -10000 0 0
CALM1 0.012 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.014 0.079 -9999 0 -0.28 16 16
PIK3CA 0.012 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 0.037 0.036 -9999 0 -10000 0 0
CEBPB/PTGES2/Cbp/p300 0.001 0.005 -9999 0 -10000 0 0
mol:Ca2+ 0.024 0.032 -9999 0 -10000 0 0
MAPK3 0.048 0.027 -9999 0 -10000 0 0
STAT1 (dimer) -0.093 0.11 -9999 0 -0.42 1 1
MAPK1 0.048 0.027 -9999 0 -10000 0 0
JAK2 0.013 0.003 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
JAK1 0.013 0.003 -9999 0 -10000 0 0
CAMK2D 0.012 0 -9999 0 -10000 0 0
DAPK1 0.061 0.024 -9999 0 -10000 0 0
SMAD7 -0.013 0.065 -9999 0 -10000 0 0
CBL/CRKL/C3G 0.012 0.029 -9999 0 -10000 0 0
PI3K -0.005 0.017 -9999 0 -10000 0 0
IFNG -0.014 0.079 -9999 0 -0.28 16 16
apoptosis 0.036 0.025 -9999 0 -10000 0 0
CAMK2G 0.012 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.012 0 -9999 0 -10000 0 0
CAMK2A -0.39 0.41 -9999 0 -0.81 95 95
CAMK2B -0.036 0.14 -9999 0 -0.37 25 25
FRAP1 0.04 0.027 -9999 0 -10000 0 0
PRKCD 0.043 0.029 -9999 0 -10000 0 0
RAP1B 0.012 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.073 0.079 -9999 0 -0.3 1 1
PTPN2 0.012 0 -9999 0 -10000 0 0
EP300 0.013 0.001 -9999 0 -10000 0 0
IRF1 0.057 0.045 -9999 0 -10000 0 0
STAT1 (dimer)/PIASy 0.034 0.038 -9999 0 -10000 0 0
SOCS1 -0.014 0.14 -9999 0 -1.4 2 2
mol:GDP -0.004 0.015 -9999 0 -10000 0 0
CASP1 -0.013 0.066 -9999 0 -0.24 1 1
PTGES2 0.012 0 -9999 0 -10000 0 0
IRF9 0.051 0.013 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.017 -9999 0 -10000 0 0
RAP1/GDP -0.003 0.01 -9999 0 -10000 0 0
CBL 0.031 0.031 -9999 0 -10000 0 0
MAP3K1 0.033 0.032 -9999 0 -10000 0 0
PIAS1 0.012 0 -9999 0 -10000 0 0
PIAS4 0.012 0.001 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.073 0.079 -9999 0 -0.3 1 1
PTPN11 0.025 0.033 -9999 0 -10000 0 0
CREBBP 0.013 0.001 -9999 0 -10000 0 0
RAPGEF1 0.012 0 -9999 0 -10000 0 0
Nectin adhesion 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
PDGFRB -0.021 0.16 -9999 0 -0.81 8 8
alphaV beta3 Integrin -0.003 0.1 -9999 0 -0.62 5 5
PTK2 -0.011 0.057 -9999 0 -0.48 2 2
positive regulation of JNK cascade -0.004 0.032 -9999 0 -0.32 2 2
CDC42/GDP 0.048 0.051 -9999 0 -0.43 2 2
Rac1/GDP 0.049 0.051 -9999 0 -0.42 2 2
RAP1B 0.012 0 -9999 0 -10000 0 0
RAP1A 0.012 0 -9999 0 -10000 0 0
CTNNB1 0.012 0 -9999 0 -10000 0 0
CDC42/GTP -0.005 0.04 -9999 0 -0.39 2 2
nectin-3/I-afadin 0.012 0.064 -9999 0 -0.62 2 2
RAPGEF1 0.043 0.057 -9999 0 -0.48 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.038 0.064 -9999 0 -0.56 2 2
PDGFB-D/PDGFRB -0.021 0.16 -9999 0 -0.81 8 8
TLN1 0.028 0.026 -9999 0 -10000 0 0
Rap1/GTP -0.004 0.034 -9999 0 -0.34 2 2
IQGAP1 0.012 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.023 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.012 0.064 -9999 0 -0.62 2 2
PVR 0.011 0.021 -9999 0 -0.28 1 1
Necl-5(dimer) 0.011 0.021 -9999 0 -0.28 1 1
mol:GDP 0.047 0.061 -9999 0 -0.53 2 2
MLLT4 0.012 0 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
PI3K -0.023 0.1 -9999 0 -0.46 10 10
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.017 0.014 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.004 0.034 -9999 0 -0.33 2 2
PVRL1 0.011 0.021 -9999 0 -10000 0 0
PVRL3 0.004 0.082 -9999 0 -0.81 2 2
PVRL2 0.012 0 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
CDH1 -0.054 0.22 -9999 0 -0.81 16 16
CLDN1 -0.091 0.14 -9999 0 -0.28 69 69
JAM-A/CLDN1 -0.026 0.089 -9999 0 -0.55 2 2
SRC -0.009 0.064 -9999 0 -0.62 2 2
ITGB3 -0.016 0.14 -9999 0 -0.55 10 10
nectin-1(dimer)/I-afadin/I-afadin 0.017 0.014 -9999 0 -10000 0 0
FARP2 0.042 0.06 -9999 0 -0.52 2 2
RAC1 0.012 0 -9999 0 -10000 0 0
CTNNA1 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.006 0.055 -9999 0 -0.54 2 2
nectin-1/I-afadin 0.017 0.014 -9999 0 -10000 0 0
nectin-2/I-afadin 0.018 0 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.006 0.055 -9999 0 -0.54 2 2
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.012 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.004 0.032 -9999 0 -0.32 2 2
alphaV/beta3 Integrin/Talin 0.025 0.078 -9999 0 -0.42 5 5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.018 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.018 0 -9999 0 -10000 0 0
PIP5K1C 0.022 0.028 -9999 0 -0.25 2 2
VAV2 0.041 0.061 -9999 0 -0.53 2 2
RAP1/GDP -0.005 0.04 -9999 0 -0.4 2 2
ITGAV 0.012 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.005 0.054 -9999 0 -0.54 2 2
nectin-3(dimer)/I-afadin/I-afadin 0.012 0.064 -9999 0 -0.62 2 2
Rac1/GTP -0.005 0.041 -9999 0 -0.41 2 2
PTPRM 0.015 0.031 -9999 0 -0.29 2 2
E-cadherin/beta catenin/alpha catenin -0.036 0.12 -9999 0 -0.44 16 16
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.012 0 -9999 0 -10000 0 0
IL1-mediated signaling events

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
UBC13/UEV1A 0.011 0.004 -9999 0 -10000 0 0
PRKCZ 0.012 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.006 0.033 -9999 0 -10000 0 0
IRAK/TOLLIP 0.025 0.003 -9999 0 -10000 0 0
IKBKB 0.012 0 -9999 0 -10000 0 0
IKBKG 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.13 0.25 -9999 0 -0.63 36 36
IL1A -0.035 0.11 -9999 0 -0.28 31 31
IL1B 0.006 0.093 -9999 0 -0.62 4 4
IRAK/TRAF6/p62/Atypical PKCs -0.003 0.015 -9999 0 -10000 0 0
IL1R2 -0.14 0.32 -9999 0 -0.8 37 37
IL1R1 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.031 0.034 -9999 0 -10000 0 0
TOLLIP 0.012 0 -9999 0 -10000 0 0
TICAM2 0.008 0.058 -9999 0 -0.81 1 1
MAP3K3 0.012 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.057 0.007 -9999 0 -10000 0 0
JUN 0.031 0.06 -9999 0 -0.39 4 4
MAP3K7 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.01 0.062 -9999 0 -0.44 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88 0.006 0.057 -9999 0 -10000 0 0
PIK3R1 0.012 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.017 0.04 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP 0.017 0.076 -9999 0 -0.49 4 4
NFKB1 0.012 0 -9999 0 -10000 0 0
MAPK8 0.025 0.064 -9999 0 -0.42 4 4
IRAK1 0.019 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 0.002 0.066 -9999 0 -0.62 1 1
IRAK4 0.012 0 -9999 0 -10000 0 0
PRKCI 0.012 0 -9999 0 -10000 0 0
TRAF6 0.012 0 -9999 0 -10000 0 0
PI3K 0.018 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.03 0.043 -9999 0 -10000 0 0
CHUK 0.012 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.017 0.076 -9999 0 -0.49 4 4
IL1 beta/IL1R2 -0.092 0.23 -9999 0 -0.54 40 40
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.009 0.056 -9999 0 -10000 0 0
IRAK3 0.011 0.021 -9999 0 -0.28 1 1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.013 0.082 -9999 0 -0.55 4 4
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.018 0.037 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP -0.023 0.055 -9999 0 -10000 0 0
RELA 0.012 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.003 0.051 -9999 0 -0.28 6 6
MYD88 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.032 0.003 -9999 0 -10000 0 0
IL1RAP 0.009 0.03 -9999 0 -10000 0 0
UBE2N 0.012 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.01 0.067 -9999 0 -0.72 1 1
CASP1 0.011 0.021 -9999 0 -10000 0 0
IL1RN/IL1R2 -0.12 0.25 -9999 0 -0.63 37 37
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.024 0.072 -9999 0 -0.46 4 4
TMEM189-UBE2V1 0.003 0.005 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.027 0.029 -9999 0 -10000 0 0
PIK3CA 0.012 0 -9999 0 -10000 0 0
IL1RN -0.012 0.093 -9999 0 -0.32 14 14
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.029 0.003 -9999 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.026 0.08 -9999 0 -10000 0 0
GNAI2 0.012 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.009 0.058 -9999 0 -0.55 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
GNAO1 -0.051 0.21 -9999 0 -0.72 17 17
RhoA/GTP -0.027 0.081 -9999 0 -10000 0 0
negative regulation of cAMP metabolic process -0.001 0.1 -9999 0 -0.32 16 16
GNAZ 0.012 0 -9999 0 -10000 0 0
GNAI3 0.012 0 -9999 0 -10000 0 0
GNA12 0.012 0 -9999 0 -10000 0 0
S1PR5 -0.002 0.092 -9999 0 -0.81 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
S1P/S1P5/Gi -0.002 0.1 -9999 0 -0.33 16 16
RhoA/GDP 0.009 0 -9999 0 -10000 0 0
RHOA 0.012 0 -9999 0 -10000 0 0
GNAI1 0.008 0.058 -9999 0 -0.81 1 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.012 0 -9999 0 -10000 0 0
NFATC1 0.041 0.016 -9999 0 -10000 0 0
NFATC2 -0.014 0.073 -9999 0 -0.26 8 8
NFATC3 0.013 0.011 -9999 0 -10000 0 0
YWHAE 0.012 0 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.015 0.041 -9999 0 -10000 0 0
Exportin 1/Ran/NUP214 0 0 -9999 0 -10000 0 0
mol:DAG -0.003 0.004 -9999 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.009 0.026 -9999 0 -10000 0 0
BCL2/BAX 0.017 0.014 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 0.001 0.011 -9999 0 -10000 0 0
CaM/Ca2+ 0.001 0.011 -9999 0 -10000 0 0
BAX 0.011 0.021 -9999 0 -0.28 1 1
MAPK14 0.007 0.006 -9999 0 -10000 0 0
BAD 0.012 0 -9999 0 -10000 0 0
CABIN1/MEF2D 0.017 0.039 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/BCL2 0.012 0 -9999 0 -10000 0 0
FKBP8 0.012 0 -9999 0 -10000 0 0
activation-induced cell death of T cells -0.017 0.039 -9999 0 -10000 0 0
KPNB1 0.012 0 -9999 0 -10000 0 0
KPNA2 0.012 0 -9999 0 -10000 0 0
XPO1 0.011 0.001 -9999 0 -10000 0 0
SFN -0.12 0.15 -9999 0 -0.28 91 91
MAP3K8 0.007 0.006 -9999 0 -10000 0 0
NFAT4/CK1 alpha 0 0 -9999 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.11 0.2 -9999 0 -0.49 9 9
CABIN1 0.015 0.041 -9999 0 -10000 0 0
CALM1 0.007 0.006 -9999 0 -10000 0 0
RAN 0.011 0.001 -9999 0 -10000 0 0
MAP3K1 0.012 0 -9999 0 -10000 0 0
CAMK4 0.012 0.002 -9999 0 -10000 0 0
mol:Ca2+ -0.007 0.01 -9999 0 -10000 0 0
MAPK3 0.012 0 -9999 0 -10000 0 0
YWHAH 0.012 0 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.01 0.016 -9999 0 -10000 0 0
YWHAB 0.012 0 -9999 0 -10000 0 0
MAPK8 -0.009 0.12 -9999 0 -0.82 4 4
MAPK9 0.012 0 -9999 0 -10000 0 0
YWHAG 0.012 0 -9999 0 -10000 0 0
FKBP1A 0.012 0 -9999 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.035 0.043 -9999 0 -10000 0 0
PRKCH 0.012 0 -9999 0 -10000 0 0
CABIN1/Cbp/p300 -0.005 0.007 -9999 0 -10000 0 0
CASP3 0.004 0.03 -9999 0 -0.29 2 2
PIM1 0.008 0.036 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.005 0.004 -9999 0 -10000 0 0
apoptosis 0 0.006 -9999 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.005 0.034 -9999 0 -10000 0 0
PRKCB 0.008 0.036 -9999 0 -0.28 3 3
PRKCE 0.012 0 -9999 0 -10000 0 0
JNK2/NFAT4 0.02 0.008 -9999 0 -10000 0 0
BAD/BCL-XL 0.018 0 -9999 0 -10000 0 0
PRKCD 0.012 0 -9999 0 -10000 0 0
NUP214 0.011 0.001 -9999 0 -10000 0 0
PRKCZ 0.007 0.006 -9999 0 -10000 0 0
PRKCA 0.012 0 -9999 0 -10000 0 0
PRKCG -0.063 0.12 -9999 0 -0.28 48 48
PRKCQ 0 0.1 -9999 0 -0.81 3 3
FKBP38/BCL2 0.018 0 -9999 0 -10000 0 0
EP300 0.006 0.009 -9999 0 -10000 0 0
PRKCB1 0 0 -9999 0 -10000 0 0
CSNK2A1 0.012 0 -9999 0 -10000 0 0
NFATc/JNK1 0.024 0.07 -9999 0 -0.42 4 4
CaM/Ca2+/FKBP38 0.01 0.009 -9999 0 -10000 0 0
FKBP12/FK506 0.009 0 -9999 0 -10000 0 0
CSNK1A1 0.008 0.014 -9999 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.01 0.009 -9999 0 -10000 0 0
NFATc/ERK1 0.047 0.015 -9999 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.006 0.023 -9999 0 -10000 0 0
NR4A1 -0.27 0.39 -9999 0 -0.73 83 83
GSK3B 0.007 0.006 -9999 0 -10000 0 0
positive T cell selection 0.013 0.011 -9999 0 -10000 0 0
NFAT1/CK1 alpha -0.029 0.047 -9999 0 -0.34 1 1
RCH1/ KPNB1 0.018 0 -9999 0 -10000 0 0
YWHAQ 0.012 0 -9999 0 -10000 0 0
PRKACA 0.007 0.006 -9999 0 -10000 0 0
AKAP5 0.011 0.021 -9999 0 -0.28 1 1
MEF2D 0.006 0.009 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
YWHAZ 0.012 0 -9999 0 -10000 0 0
NFATc/p38 alpha 0.033 0.03 -9999 0 -10000 0 0
CREBBP 0.006 0.009 -9999 0 -10000 0 0
BCL2 0.012 0 -9999 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0 0.003 -10000 0 -10000 0 0
AES 0.007 0.003 -10000 0 -10000 0 0
FBXW11 0.012 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 0.012 0.031 -10000 0 -10000 0 0
SMAD4 0.012 0 -10000 0 -10000 0 0
DKK2 0 0.087 -10000 0 -0.55 4 4
TLE1 0.008 0.002 -10000 0 -10000 0 0
MACF1 0.012 0 -10000 0 -10000 0 0
CTNNB1 0.043 0.054 -10000 0 -10000 0 0
WIF1 0.002 0.041 -10000 0 -0.28 4 4
beta catenin/RanBP3 -0.006 0.021 -10000 0 -10000 0 0
KREMEN2 -0.025 0.096 -10000 0 -0.28 24 24
DKK1 -0.01 0.073 -10000 0 -0.28 13 13
beta catenin/beta TrCP1 0.047 0.051 -10000 0 -10000 0 0
FZD1 0.005 0.046 -10000 0 -0.28 5 5
AXIN2 0.022 0.02 -10000 0 -10000 0 0
AXIN1 0.012 0.001 -10000 0 -10000 0 0
RAN 0.012 0 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.004 0.01 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.029 0.089 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.036 0.068 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.041 0.045 -10000 0 -10000 0 0
HNF1A -0.011 0.1 -10000 0 -0.82 3 3
CTBP1 0.001 0.004 -10000 0 -10000 0 0
MYC 0.02 0.035 -10000 0 -10000 0 0
RANBP3 0.012 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.024 0.074 -10000 0 -0.42 4 4
NKD1 -0.2 0.36 -10000 0 -0.81 50 50
TCF4 0 0.003 -10000 0 -10000 0 0
TCF3 0.001 0.004 -10000 0 -1000