PARADIGM pathway analysis of mRNASeq expression data
Liver Hepatocellular Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C18P5Z4Q
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/C18P5Z4Q
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 65 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
FOXM1 transcription factor network 55
Plasma membrane estrogen receptor signaling 52
PDGFR-alpha signaling pathway 48
Signaling events regulated by Ret tyrosine kinase 46
Nongenotropic Androgen signaling 42
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 41
Glypican 2 network 39
p75(NTR)-mediated signaling 38
IL4-mediated signaling events 38
EPO signaling pathway 38
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 191 . 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 ( 191 ).

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
FOXM1 transcription factor network 0.2880 55 2827 51 -0.14 0.56 1000 -1000 -0.11 -1000
Plasma membrane estrogen receptor signaling 0.2723 52 4508 86 -0.51 0.46 1000 -1000 -0.071 -1000
PDGFR-alpha signaling pathway 0.2513 48 2135 44 -0.72 0.032 1000 -1000 -0.046 -1000
Signaling events regulated by Ret tyrosine kinase 0.2408 46 3834 82 -0.46 0.014 1000 -1000 -0.072 -1000
Nongenotropic Androgen signaling 0.2199 42 2198 52 -0.42 0.24 1000 -1000 -0.048 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.2147 41 2816 68 -0.75 0.26 1000 -1000 -0.065 -1000
Glypican 2 network 0.2042 39 159 4 0.05 0.16 1000 -1000 -0.017 -1000
p75(NTR)-mediated signaling 0.1990 38 4753 125 -0.58 0.21 1000 -1000 -0.077 -1000
IL4-mediated signaling events 0.1990 38 3489 91 -0.98 0.47 1000 -1000 -0.097 -1000
EPO signaling pathway 0.1990 38 2096 55 -0.29 0 1000 -1000 -0.078 -1000
FOXA2 and FOXA3 transcription factor networks 0.1937 37 1713 46 -0.71 0.036 1000 -1000 -0.02 -1000
Aurora B signaling 0.1885 36 2463 67 -0.021 0.31 1000 -1000 -0.049 -1000
HIF-1-alpha transcription factor network 0.1832 35 2706 76 -0.57 0.013 1000 -1000 -0.044 -1000
Signaling mediated by p38-alpha and p38-beta 0.1832 35 1567 44 -0.37 0 1000 -1000 -0.034 -1000
Ephrin A reverse signaling 0.1780 34 240 7 -0.16 0.012 1000 -1000 -0.023 -1000
TCGA08_retinoblastoma 0.1780 34 279 8 -0.086 0.22 1000 -1000 -0.014 -1000
Reelin signaling pathway 0.1728 33 1855 56 -0.29 0.064 1000 -1000 -0.081 -1000
IL6-mediated signaling events 0.1728 33 2548 75 -0.47 0.036 1000 -1000 -0.058 -1000
IGF1 pathway 0.1728 33 1901 57 -0.34 0.13 1000 -1000 -0.078 -1000
Ephrin B reverse signaling 0.1623 31 1502 48 -0.29 0.083 1000 -1000 -0.053 -1000
EPHB forward signaling 0.1571 30 2560 85 -0.24 0.19 1000 -1000 -0.078 -1000
PLK1 signaling events 0.1518 29 2478 85 -0.059 0.28 1000 -1000 -0.046 -1000
Wnt signaling 0.1518 29 207 7 -0.24 0.014 1000 -1000 -0.029 -1000
ErbB2/ErbB3 signaling events 0.1361 26 1744 65 -0.34 0.075 1000 -1000 -0.046 -1000
Endothelins 0.1361 26 2535 96 -0.53 0.16 1000 -1000 -0.062 -1000
Calcium signaling in the CD4+ TCR pathway 0.1361 26 808 31 -0.44 0.002 1000 -1000 -0.035 -1000
Glypican 1 network 0.1309 25 1211 48 -0.34 0.048 1000 -1000 -0.038 -1000
LPA receptor mediated events 0.1309 25 2629 102 -0.4 0.039 1000 -1000 -0.066 -1000
IL23-mediated signaling events 0.1309 25 1511 60 -0.31 0.039 1000 -1000 -0.11 -1000
Signaling events mediated by the Hedgehog family 0.1204 23 1212 52 -0.4 0.28 1000 -1000 -0.054 -1000
Thromboxane A2 receptor signaling 0.1204 23 2503 105 -0.14 0.08 1000 -1000 -0.047 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.1204 23 1987 85 -0.41 0.017 1000 -1000 -0.057 -1000
Noncanonical Wnt signaling pathway 0.1152 22 572 26 -0.24 0.014 1000 -1000 -0.054 -1000
S1P5 pathway 0.1099 21 358 17 -0.4 0.16 1000 -1000 -0.039 -1000
BCR signaling pathway 0.1047 20 2066 99 -0.44 0.009 1000 -1000 -0.076 -1000
IL12-mediated signaling events 0.0995 19 1705 87 -0.64 0.016 1000 -1000 -0.086 -1000
amb2 Integrin signaling 0.0995 19 1573 82 -0.42 0.089 1000 -1000 -0.052 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0995 19 1758 88 -0.25 0.014 1000 -1000 -0.082 -1000
ErbB4 signaling events 0.0942 18 1264 69 -0.26 0.075 1000 -1000 -0.061 -1000
Syndecan-1-mediated signaling events 0.0942 18 628 34 -0.41 0.093 1000 -1000 -0.059 -1000
Osteopontin-mediated events 0.0942 18 713 38 -0.4 0.061 1000 -1000 -0.06 -1000
S1P1 pathway 0.0942 18 670 36 -0.4 0.16 1000 -1000 -0.051 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0890 17 938 54 -0.3 0.036 1000 -1000 -0.072 -1000
Glucocorticoid receptor regulatory network 0.0890 17 1980 114 -0.78 0.21 1000 -1000 -0.058 -1000
Syndecan-4-mediated signaling events 0.0890 17 1166 67 -0.38 0.18 1000 -1000 -0.074 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0890 17 2066 120 -0.62 0.18 1000 -1000 -0.061 -1000
Ras signaling in the CD4+ TCR pathway 0.0890 17 295 17 -0.2 0.004 1000 -1000 -0.044 -1000
Signaling events mediated by PRL 0.0838 16 573 34 -0.32 0.052 1000 -1000 -0.046 -1000
Arf6 signaling events 0.0733 14 916 62 -0.41 0.08 1000 -1000 -0.039 -1000
Aurora C signaling 0.0733 14 101 7 0 0.18 1000 -1000 -0.018 -1000
Integrins in angiogenesis 0.0733 14 1220 84 -0.34 0.089 1000 -1000 -0.062 -1000
S1P4 pathway 0.0733 14 356 25 -0.4 0.16 1000 -1000 -0.042 -1000
Fc-epsilon receptor I signaling in mast cells 0.0681 13 1282 97 -0.43 0.049 1000 -1000 -0.08 -1000
TCR signaling in naïve CD8+ T cells 0.0681 13 1244 93 -0.25 0.11 1000 -1000 -0.069 -1000
Coregulation of Androgen receptor activity 0.0628 12 917 76 -0.25 0.22 1000 -1000 -0.034 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0628 12 340 28 -0.4 0.16 1000 -1000 -0.038 -1000
Presenilin action in Notch and Wnt signaling 0.0628 12 736 61 -0.4 0.11 1000 -1000 -0.066 -1000
PLK2 and PLK4 events 0.0576 11 35 3 0 0.062 1000 -1000 -0.021 -1000
BMP receptor signaling 0.0576 11 926 81 -0.19 0.062 1000 -1000 -0.067 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0576 11 849 74 -0.41 0.08 1000 -1000 -0.081 -1000
S1P3 pathway 0.0576 11 494 42 -0.4 0.16 1000 -1000 -0.04 -1000
p38 MAPK signaling pathway 0.0576 11 489 44 -0.42 0.009 1000 -1000 -0.046 -1000
LPA4-mediated signaling events 0.0524 10 123 12 -0.2 0.02 1000 -1000 -0.008 -1000
IL27-mediated signaling events 0.0524 10 541 51 -0.22 0.15 1000 -1000 -0.052 -1000
Visual signal transduction: Rods 0.0524 10 539 52 -0.21 0.037 1000 -1000 -0.061 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0471 9 334 37 -0.29 0.002 1000 -1000 -0.05 -1000
IL1-mediated signaling events 0.0471 9 610 62 -0.14 0.004 1000 -1000 -0.065 -1000
FAS signaling pathway (CD95) 0.0471 9 439 47 -0.41 0.035 1000 -1000 -0.031 -1000
Regulation of nuclear SMAD2/3 signaling 0.0419 8 1206 136 -0.45 0.39 1000 -1000 -0.049 -1000
JNK signaling in the CD4+ TCR pathway 0.0419 8 144 17 -0.077 0.017 1000 -1000 -0.035 -1000
Nectin adhesion pathway 0.0419 8 557 63 -0.081 0.005 1000 -1000 -0.052 -1000
FoxO family signaling 0.0419 8 574 64 -0.17 0.28 1000 -1000 -0.059 -1000
IL2 signaling events mediated by PI3K 0.0419 8 485 58 -0.077 0.14 1000 -1000 -0.063 -1000
IL2 signaling events mediated by STAT5 0.0419 8 189 22 -0.077 0.18 1000 -1000 -0.038 -1000
Regulation of Telomerase 0.0419 8 857 102 -0.44 0.22 1000 -1000 -0.085 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0366 7 269 34 -0.051 0.02 1000 -1000 -0.047 -1000
Syndecan-2-mediated signaling events 0.0366 7 532 69 -0.19 0.07 1000 -1000 -0.035 -1000
Syndecan-3-mediated signaling events 0.0366 7 260 35 -0.19 0.012 1000 -1000 -0.033 -1000
Canonical Wnt signaling pathway 0.0366 7 387 51 -0.16 0.14 1000 -1000 -0.054 -1000
Regulation of Androgen receptor activity 0.0366 7 558 70 -0.27 0.077 1000 -1000 -0.058 -1000
Signaling events mediated by PTP1B 0.0314 6 513 76 -0.19 0.16 1000 -1000 -0.058 -1000
Aurora A signaling 0.0314 6 380 60 -0.021 0.23 1000 -1000 -0.042 -1000
Signaling events mediated by HDAC Class III 0.0314 6 264 40 -0.33 0.01 1000 -1000 -0.022 -1000
HIF-2-alpha transcription factor network 0.0314 6 272 43 -0.23 0.07 1000 -1000 -0.051 -1000
Effects of Botulinum toxin 0.0314 6 165 26 -0.12 0.012 1000 -1000 -0.031 -1000
Class IB PI3K non-lipid kinase events 0.0314 6 18 3 -0.027 -1000 1000 -1000 -0.01 -1000
E-cadherin signaling events 0.0314 6 30 5 -0.045 0 1000 -1000 -0.033 -1000
Ceramide signaling pathway 0.0262 5 436 76 -0.34 0.08 1000 -1000 -0.04 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0262 5 289 52 -0.12 0.032 1000 -1000 -0.038 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0262 5 187 33 -0.022 0.22 1000 -1000 -0.039 -1000
E-cadherin signaling in keratinocytes 0.0262 5 215 43 -0.1 0.021 1000 -1000 -0.062 -1000
Cellular roles of Anthrax toxin 0.0209 4 159 39 -0.073 0.003 1000 -1000 -0.019 -1000
Hedgehog signaling events mediated by Gli proteins 0.0209 4 320 65 -0.4 0.16 1000 -1000 -0.065 -1000
Insulin-mediated glucose transport 0.0209 4 143 32 -0.036 0.19 1000 -1000 -0.047 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0209 4 387 83 -0.13 0.19 1000 -1000 -0.067 -1000
Retinoic acid receptors-mediated signaling 0.0209 4 283 58 -0.18 0.047 1000 -1000 -0.051 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0209 4 215 45 -0.059 0.038 1000 -1000 -0.064 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0209 4 619 125 -0.07 0.041 1000 -1000 -0.083 -1000
TCGA08_rtk_signaling 0.0209 4 117 26 -0.34 0.022 1000 -1000 -0.02 -1000
E-cadherin signaling in the nascent adherens junction 0.0209 4 376 76 -0.054 0.022 1000 -1000 -0.074 -1000
EGFR-dependent Endothelin signaling events 0.0209 4 88 21 -0.018 0.08 1000 -1000 -0.052 -1000
Rapid glucocorticoid signaling 0.0209 4 84 20 -0.022 0.059 1000 -1000 -0.027 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0209 4 363 78 -0.29 0.025 1000 -1000 -0.079 -1000
Caspase cascade in apoptosis 0.0157 3 267 74 -0.045 0.025 1000 -1000 -0.035 -1000
Signaling events mediated by HDAC Class II 0.0157 3 272 75 -0.44 0.007 1000 -1000 -0.035 -1000
BARD1 signaling events 0.0157 3 184 57 -0.016 0.12 1000 -1000 -0.045 -1000
Regulation of p38-alpha and p38-beta 0.0157 3 215 54 -0.18 0.039 1000 -1000 -0.056 -1000
Visual signal transduction: Cones 0.0105 2 111 38 -0.016 0.034 1000 -1000 -0.038 -1000
a4b1 and a4b7 Integrin signaling 0.0105 2 14 5 -0.016 -0.009 1000 -1000 -0.011 -1000
Arf6 downstream pathway 0.0105 2 86 43 -0.031 0.021 1000 -1000 -0.035 -1000
IFN-gamma pathway 0.0105 2 172 68 -0.42 0.061 1000 -1000 -0.073 -1000
Class I PI3K signaling events mediated by Akt 0.0105 2 172 68 -0.06 0.19 1000 -1000 -0.052 -1000
TRAIL signaling pathway 0.0105 2 132 48 -0.025 0.007 1000 -1000 -0.054 -1000
Signaling mediated by p38-gamma and p38-delta 0.0105 2 40 15 -0.023 0.058 1000 -1000 -0.038 -1000
Paxillin-dependent events mediated by a4b1 0.0105 2 89 36 -0.062 0.007 1000 -1000 -0.057 -1000
Class I PI3K signaling events 0.0105 2 182 73 -0.18 0.024 1000 -1000 -0.057 -1000
PDGFR-beta signaling pathway 0.0105 2 233 97 -0.14 0.043 1000 -1000 -0.078 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0052 1 31 23 -0.054 0.032 1000 -1000 -0.047 -1000
Canonical NF-kappaB pathway 0.0052 1 40 39 -0.045 0.059 1000 -1000 -0.066 -1000
mTOR signaling pathway 0.0052 1 82 53 -0.04 0.027 1000 -1000 -0.048 -1000
ceramide signaling pathway 0.0052 1 73 49 -0.049 0.033 1000 -1000 -0.032 -1000
Signaling events mediated by HDAC Class I 0.0052 1 141 104 -0.045 0.009 1000 -1000 -0.051 -1000
Atypical NF-kappaB pathway 0.0052 1 55 31 -0.032 0.012 1000 -1000 -0.047 -1000
Arf6 trafficking events 0.0052 1 77 71 -0.037 0.029 1000 -1000 -0.057 -1000
Insulin Pathway 0.0052 1 111 74 -0.08 0.01 1000 -1000 -0.07 -1000
VEGFR1 specific signals 0.0052 1 67 56 -0.044 0.048 1000 -1000 -0.074 -1000
Circadian rhythm pathway 0.0000 0 11 22 -0.01 0.032 1000 -1000 -0.052 -1000
TCGA08_p53 0.0000 0 0 7 -0.059 0.028 1000 -1000 -0.012 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 1 27 0 0.002 1000 -1000 -0.047 -1000
Arf1 pathway 0.0000 0 42 54 -0.063 0.015 1000 -1000 -0.023 -1000
Alternative NF-kappaB pathway 0.0000 0 1 13 0 0.002 1000 -1000 -0.026 -1000
Total NA 1853 112632 7203 -32 -990 131000 -131000 -6.7 -131000
FOXM1 transcription factor network

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
NFATC3 0.48 0.52 1.1 56 -0.83 5 61
PLK1 0.33 0.26 0.64 55 -10000 0 55
BIRC5 0.34 0.25 0.63 62 -10000 0 62
HSPA1B 0.48 0.53 1.1 56 -0.83 5 61
MAP2K1 0.14 0.13 0.37 22 -10000 0 22
BRCA2 0.47 0.57 1.1 57 -1 8 65
FOXM1 0.56 0.65 1.3 63 -0.94 6 69
XRCC1 0.48 0.53 1.1 56 -0.83 5 61
FOXM1B/p19 0.28 0.48 0.72 90 -0.8 10 100
Cyclin D1/CDK4 0.29 0.52 0.92 49 -0.9 10 59
CDC2 0.51 0.58 1.2 63 -0.84 6 69
TGFA 0.25 0.64 0.98 49 -1 22 71
SKP2 0.48 0.52 1.1 56 -0.83 5 61
CCNE1 0.15 0.18 0.38 68 -10000 0 68
CKS1B 0.48 0.53 1.1 55 -0.83 5 60
RB1 0.19 0.35 0.68 57 -10000 0 57
FOXM1C/SP1 0.26 0.5 0.83 73 -0.9 6 79
AURKB 0.3 0.26 0.66 47 -10000 0 47
CENPF 0.55 0.58 1.2 71 -0.83 5 76
CDK4 0.05 0.05 -10000 0 -10000 0 0
MYC 0.35 0.53 0.94 53 -0.85 13 66
CHEK2 0.15 0.15 0.4 28 -10000 0 28
ONECUT1 0.34 0.54 0.99 52 -0.87 10 62
CDKN2A 0.074 0.19 0.32 41 -10000 0 41
LAMA4 0.48 0.53 1.1 56 -0.83 5 61
FOXM1B/HNF6 0.34 0.56 1 51 -1 10 61
FOS -0.037 0.86 1.1 47 -1.1 55 102
SP1 -0.008 0.037 -10000 0 -10000 0 0
CDC25B 0.48 0.53 1.1 56 -0.83 5 61
response to radiation 0.09 0.095 0.27 12 -10000 0 12
CENPB 0.48 0.52 1.1 61 -0.8 6 67
CENPA 0.55 0.58 1.2 62 -0.83 5 67
NEK2 0.56 0.57 1.2 67 -0.8 5 72
HIST1H2BA 0.47 0.52 1.1 56 -0.84 5 61
CCNA2 0.21 0.19 0.38 103 -10000 0 103
EP300 0 0 -10000 0 -10000 0 0
CCNB1/CDK1 0.5 0.57 1.2 55 -0.9 6 61
CCNB2 0.56 0.58 1.1 77 -0.83 5 82
CCNB1 0.54 0.6 1.2 62 -0.88 5 67
ETV5 0.48 0.52 1.1 57 -0.83 5 62
ESR1 -0.14 0.7 1.1 24 -1 41 65
CCND1 0.35 0.56 1 53 -0.94 10 63
GSK3A 0.098 0.092 0.29 4 -10000 0 4
Cyclin A-E1/CDK1-2 0.28 0.23 0.52 80 -10000 0 80
CDK2 0.036 0.034 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.13 0.14 0.32 51 -10000 0 51
FOXM1B/Cbp/p300 -0.062 0.18 -10000 0 -0.75 9 9
GAS1 0.31 0.74 1.1 57 -1.1 28 85
MMP2 0.45 0.59 1.1 57 -1.1 10 67
RB1/FOXM1C 0.39 0.5 0.96 56 -0.84 8 64
CREBBP 0 0 -10000 0 -10000 0 0
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.26 0.26 -10000 0 -0.51 99 99
ER alpha/Gai/GDP/Gbeta gamma -0.46 0.45 -10000 0 -0.83 98 98
AKT1 -0.5 0.48 -10000 0 -0.96 99 99
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.51 0.49 -10000 0 -0.98 99 99
mol:Ca2+ -0.18 0.29 -10000 0 -0.74 35 35
IGF1R -0.005 0.095 0.34 2 -0.86 2 4
E2/ER alpha (dimer)/Striatin -0.32 0.31 -10000 0 -0.61 101 101
SHC1 0 0 -10000 0 -10000 0 0
apoptosis 0.46 0.46 0.9 99 -10000 0 99
RhoA/GTP -0.23 0.22 -10000 0 -0.45 98 98
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.41 0.36 -10000 0 -0.74 98 98
regulation of stress fiber formation 0.17 0.2 0.36 100 -10000 0 100
E2/ERA-ERB (dimer) -0.3 0.3 -10000 0 -0.59 98 98
KRAS 0 0 -10000 0 -10000 0 0
G13/GTP -0.28 0.27 -10000 0 -0.55 98 98
pseudopodium formation -0.17 0.2 -10000 0 -0.36 100 100
E2/ER alpha (dimer)/PELP1 -0.3 0.3 -10000 0 -0.59 98 98
GRB2 0 0 -10000 0 -10000 0 0
GNG2 -0.005 0.062 -10000 0 -0.86 1 1
GNAO1 -0.4 0.43 -10000 0 -0.86 88 88
HRAS 0.004 0.035 0.34 2 -10000 0 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.39 0.4 -10000 0 -0.75 99 99
E2/ER beta (dimer) 0.001 0.016 0.23 1 -10000 0 1
mol:GDP -0.3 0.3 -10000 0 -0.59 98 98
mol:NADP -0.39 0.4 -10000 0 -0.75 99 99
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
mol:IP3 -0.2 0.3 -10000 0 -0.8 35 35
IGF-1R heterotetramer -0.005 0.095 0.34 2 -0.86 2 4
PLCB1 -0.2 0.3 -10000 0 -0.83 32 32
PLCB2 -0.22 0.31 -10000 0 -0.83 35 35
IGF1 -0.34 0.42 -10000 0 -0.86 74 74
mol:L-citrulline -0.39 0.4 -10000 0 -0.75 99 99
RHOA 0 0 -10000 0 -10000 0 0
Gai/GDP -0.41 0.48 -10000 0 -0.92 88 88
JNK cascade 0.001 0.016 0.23 1 -10000 0 1
BCAR1 0 0 -10000 0 -10000 0 0
ESR2 0.002 0.025 0.34 1 -10000 0 1
GNAQ -0.005 0.062 -10000 0 -0.86 1 1
ESR1 -0.44 0.43 -10000 0 -0.86 98 98
Gq family/GDP/Gbeta gamma -0.084 0.18 -10000 0 -0.74 6 6
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.19 0.18 -10000 0 -0.38 62 62
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.41 0.36 -10000 0 -0.74 98 98
GNAZ 0.16 0.17 0.34 91 -10000 0 91
E2/ER alpha (dimer) -0.35 0.34 -10000 0 -0.68 98 98
STRN -0.027 0.15 -10000 0 -0.86 6 6
GNAL 0.059 0.13 0.34 33 -10000 0 33
PELP1 0 0 -10000 0 -10000 0 0
MAPK11 0.005 0.031 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.009 0.088 -10000 0 -0.86 2 2
HBEGF -0.38 0.38 -10000 0 -0.77 79 79
cAMP biosynthetic process -0.23 0.25 -10000 0 -0.48 98 98
SRC -0.42 0.43 -10000 0 -0.76 98 98
PI3K -0.006 0.087 -10000 0 -1.2 1 1
GNB1 0 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.27 0.26 -10000 0 -0.52 99 99
SOS1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.41 0.32 -10000 0 -0.66 106 106
Gs family/GTP -0.24 0.26 -10000 0 -0.49 98 98
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.021 -10000 0 -10000 0 0
vasodilation -0.36 0.37 -10000 0 -0.7 99 99
mol:DAG -0.2 0.3 -10000 0 -0.8 35 35
Gs family/GDP/Gbeta gamma -0.24 0.25 -10000 0 -0.47 99 99
MSN -0.2 0.2 -10000 0 -0.38 100 100
Gq family/GTP -0.22 0.33 -10000 0 -0.88 33 33
mol:PI-3-4-5-P3 -0.48 0.47 -10000 0 -0.93 99 99
NRAS 0 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.36 0.37 0.7 99 -10000 0 99
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.28 0.28 -10000 0 -0.55 98 98
NOS3 -0.42 0.43 -10000 0 -0.81 99 99
GNA11 -0.023 0.14 -10000 0 -0.86 5 5
MAPKKK cascade -0.4 0.4 -10000 0 -0.76 101 101
E2/ER alpha (dimer)/PELP1/Src -0.44 0.39 -10000 0 -0.79 98 98
ruffle organization -0.17 0.2 -10000 0 -0.36 100 100
ROCK2 -0.22 0.22 -10000 0 -0.43 100 100
GNA14 -0.14 0.31 -10000 0 -0.86 30 30
GNA15 0.002 0.025 0.34 1 -10000 0 1
GNA13 0 0 -10000 0 -10000 0 0
MMP9 -0.39 0.39 -10000 0 -0.82 76 76
MMP2 -0.39 0.39 -10000 0 -0.8 79 79
PDGFR-alpha signaling pathway

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
PDGFRA -0.35 0.43 -9999 0 -0.89 74 74
PDGF/PDGFRA/CRKL -0.26 0.33 -9999 0 -0.68 74 74
positive regulation of JUN kinase activity -0.21 0.26 -9999 0 -0.53 74 74
CRKL 0 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.27 0.33 -9999 0 -0.69 74 74
AP1 -0.72 0.67 -9999 0 -1.4 89 89
mol:IP3 -0.28 0.34 -9999 0 -0.71 74 74
PLCG1 -0.28 0.35 -9999 0 -0.71 74 74
PDGF/PDGFRA/alphaV Integrin -0.26 0.33 -9999 0 -0.68 74 74
RAPGEF1 0 0 -9999 0 -10000 0 0
CRK 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.28 0.34 -9999 0 -0.71 74 74
CAV3 0 0 -9999 0 -10000 0 0
CAV1 0 0 -9999 0 -10000 0 0
SHC/Grb2/SOS1 -0.21 0.26 -9999 0 -0.54 74 74
PDGF/PDGFRA/Shf -0.31 0.37 -9999 0 -0.72 81 81
FOS -0.69 0.67 -9999 0 -1.4 89 89
JUN -0.05 0.11 -9999 0 -0.75 4 4
oligodendrocyte development -0.26 0.33 -9999 0 -0.68 74 74
GRB2 0 0 -9999 0 -10000 0 0
PIK3R1 -0.005 0.062 -9999 0 -0.86 1 1
mol:DAG -0.28 0.34 -9999 0 -0.71 74 74
PDGF/PDGFRA -0.35 0.43 -9999 0 -0.89 74 74
actin cytoskeleton reorganization -0.26 0.33 -9999 0 -0.68 74 74
SRF 0.024 0.019 -9999 0 -10000 0 0
SHC1 0 0 -9999 0 -10000 0 0
PI3K -0.23 0.3 -9999 0 -0.6 74 74
PDGF/PDGFRA/Crk/C3G -0.23 0.29 -9999 0 -0.59 74 74
JAK1 -0.26 0.34 -9999 0 -0.68 74 74
ELK1/SRF -0.22 0.26 -9999 0 -0.55 74 74
SHB 0 0 -9999 0 -10000 0 0
SHF -0.059 0.22 -9999 0 -0.86 13 13
CSNK2A1 0.032 0.026 -9999 0 -10000 0 0
GO:0007205 -0.28 0.35 -9999 0 -0.72 74 74
SOS1 0 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.21 0.26 -9999 0 -0.53 74 74
PDGF/PDGFRA/SHB -0.26 0.33 -9999 0 -0.68 74 74
PDGF/PDGFRA/Caveolin-1 -0.26 0.33 -9999 0 -0.68 74 74
ITGAV 0 0 -9999 0 -10000 0 0
ELK1 -0.26 0.32 -9999 0 -0.66 74 74
PIK3CA -0.005 0.062 -9999 0 -0.86 1 1
PDGF/PDGFRA/Crk -0.26 0.33 -9999 0 -0.68 74 74
JAK-STAT cascade -0.26 0.34 -9999 0 -0.68 74 74
cell proliferation -0.31 0.37 -9999 0 -0.72 81 81
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.098 0.08 -10000 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.25 0.21 -10000 0 -0.49 55 55
JUN -0.28 0.28 -10000 0 -0.69 44 44
HRAS 0.004 0.035 0.34 2 -10000 0 2
RET51/GFRalpha1/GDNF/GRB10 -0.42 0.39 -10000 0 -0.68 118 118
RAP1A 0 0 -10000 0 -10000 0 0
FRS2 0 0 -10000 0 -10000 0 0
RAP1A/GDP 0 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.42 0.39 -10000 0 -0.68 118 118
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.16 0.26 -10000 0 -0.54 57 57
RHOA 0 0 -10000 0 -10000 0 0
RAP1A/GTP -0.38 0.35 -10000 0 -0.62 118 118
GRB7 -0.002 0.1 0.34 4 -0.86 2 6
RET51/GFRalpha1/GDNF -0.42 0.39 -10000 0 -0.68 118 118
MAPKKK cascade -0.34 0.31 -10000 0 -0.55 114 114
BCAR1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.16 0.25 -10000 0 -0.54 57 57
lamellipodium assembly -0.22 0.19 -10000 0 -0.44 57 57
RET51/GFRalpha1/GDNF/SHC -0.42 0.39 -10000 0 -0.68 118 118
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
RET9/GFRalpha1/GDNF/SHC -0.16 0.25 -10000 0 -0.54 57 57
RET9/GFRalpha1/GDNF/Shank3 -0.16 0.26 -10000 0 -0.54 57 57
MAPK3 -0.35 0.32 -10000 0 -0.58 118 118
DOK1 0 0 -10000 0 -10000 0 0
DOK6 -0.11 0.3 0.34 2 -0.86 26 28
PXN 0 0 -10000 0 -10000 0 0
neurite development -0.35 0.31 -10000 0 -0.56 115 115
DOK5 -0.003 0.12 0.34 6 -0.86 3 9
GFRA1 -0.26 0.4 -10000 0 -0.86 57 57
MAPK8 -0.29 0.28 -10000 0 -0.72 42 42
HRAS/GTP -0.39 0.36 -10000 0 -0.64 118 118
tube development -0.15 0.24 -10000 0 -0.51 57 57
MAPK1 -0.35 0.32 -10000 0 -0.58 118 118
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.1 0.17 -10000 0 -0.36 57 57
Rac1/GDP 0 0 -10000 0 -10000 0 0
SRC 0.002 0.025 0.34 1 -10000 0 1
PDLIM7 0.004 0.035 0.34 2 -10000 0 2
RET51/GFRalpha1/GDNF/Dok6 -0.46 0.42 -10000 0 -0.71 125 125
SHC1 0 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.42 0.39 -10000 0 -0.68 118 118
RET51/GFRalpha1/GDNF/Dok5 -0.42 0.39 -10000 0 -0.68 120 120
PRKCA 0 0 -10000 0 -10000 0 0
HRAS/GDP 0.002 0.023 0.23 2 -10000 0 2
CREB1 -0.21 0.24 -10000 0 -0.55 57 57
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.1 0.17 -10000 0 -0.36 54 54
RET51/GFRalpha1/GDNF/Grb7 -0.42 0.38 -10000 0 -0.68 120 120
mol:GDP 0 0 -10000 0 -10000 0 0
RET -0.43 0.44 0.34 2 -0.86 95 97
DOK4 0 0 -10000 0 -10000 0 0
JNK cascade -0.26 0.28 -10000 0 -0.67 44 44
RET9/GFRalpha1/GDNF/FRS2 -0.16 0.25 -10000 0 -0.54 57 57
SHANK3 0.002 0.025 0.34 1 -10000 0 1
RASA1 -0.009 0.088 -10000 0 -0.86 2 2
NCK1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.1 0.17 -10000 0 -0.36 57 57
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.28 0.26 -10000 0 -0.46 115 115
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.28 0.27 -10000 0 -0.47 115 115
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.33 0.36 -10000 0 -0.55 115 115
PI3K -0.35 0.33 -10000 0 -0.75 57 57
SOS1 0 0 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.15 0.24 -10000 0 -0.51 57 57
GRB10 0 0 -10000 0 -10000 0 0
activation of MAPKK activity -0.22 0.22 -10000 0 -0.52 48 48
RET51/GFRalpha1/GDNF/FRS2 -0.42 0.39 -10000 0 -0.68 118 118
GAB1 0 0 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
IRS2 -0.023 0.14 -10000 0 -0.86 5 5
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.33 0.36 -10000 0 -0.55 115 115
RET51/GFRalpha1/GDNF/PKC alpha -0.42 0.39 -10000 0 -0.68 118 118
GRB2 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
GDNF 0.014 0.068 0.34 8 -10000 0 8
RAC1 0 0 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.42 0.39 -10000 0 -0.68 118 118
Rac1/GTP -0.26 0.23 -10000 0 -0.54 57 57
RET9/GFRalpha1/GDNF -0.17 0.28 -10000 0 -0.59 57 57
GFRalpha1/GDNF -0.2 0.31 -10000 0 -0.67 57 57
Nongenotropic Androgen signaling

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
PTK2 0.004 0.004 -10000 0 -10000 0 0
GNB1/GNG2 -0.15 0.24 -10000 0 -0.54 54 54
regulation of S phase of mitotic cell cycle -0.1 0.17 -10000 0 -0.37 54 54
GNAO1 -0.4 0.43 -10000 0 -0.86 88 88
HRAS 0.004 0.034 0.34 2 -10000 0 2
SHBG/T-DHT -0.24 0.29 -10000 0 -0.6 76 76
PELP1 0 0 -10000 0 -10000 0 0
AKT1 0.003 0.004 -10000 0 -10000 0 0
MAP2K1 -0.14 0.22 -10000 0 -0.49 53 53
T-DHT/AR -0.19 0.31 -10000 0 -0.68 53 53
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.003 0.004 -10000 0 -0.008 60 60
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.009 0.088 -10000 0 -0.86 2 2
mol:GDP -0.18 0.29 -10000 0 -0.65 54 54
cell proliferation -0.26 0.28 -10000 0 -0.54 71 71
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
FOS -0.42 0.44 -10000 0 -0.88 89 89
mol:Ca2+ -0.049 0.057 -10000 0 -0.1 84 84
MAPK3 -0.21 0.25 -10000 0 -0.55 53 53
MAPK1 -0.12 0.13 -10000 0 -0.32 29 29
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
mol:IP3 -0.002 0.002 -10000 0 -0.004 89 89
cAMP biosynthetic process -0.19 0.29 -10000 0 -0.55 76 76
GNG2 -0.005 0.062 -10000 0 -0.86 1 1
potassium channel inhibitor activity -0.002 0.002 -10000 0 -0.004 89 89
HRAS/GTP -0.15 0.23 -10000 0 -0.52 53 53
actin cytoskeleton reorganization -0.005 0.067 -10000 0 -0.93 1 1
SRC 0.002 0.024 0.34 1 -10000 0 1
voltage-gated calcium channel activity -0.002 0.002 -10000 0 -0.004 89 89
PI3K -0.006 0.08 -10000 0 -1.1 1 1
apoptosis 0.24 0.26 0.48 89 -10000 0 89
T-DHT/AR/PELP1 -0.17 0.27 -10000 0 -0.6 53 53
HRAS/GDP -0.18 0.28 -10000 0 -0.62 54 54
CREB1 -0.26 0.28 -10000 0 -0.52 89 89
RAC1-CDC42/GTP -0.005 0.069 -10000 0 -0.96 1 1
AR -0.24 0.39 -10000 0 -0.87 53 53
GNB1 0 0 -10000 0 -10000 0 0
RAF1 -0.16 0.22 -10000 0 -0.5 53 53
RAC1-CDC42/GDP -0.17 0.27 -10000 0 -0.59 54 54
T-DHT/AR/PELP1/Src -0.15 0.25 -10000 0 -0.55 53 53
MAP2K2 -0.14 0.22 -10000 0 -0.49 53 53
T-DHT/AR/PELP1/Src/PI3K -0.1 0.17 -10000 0 -0.37 54 54
GNAZ 0.16 0.17 0.34 91 -10000 0 91
SHBG -0.34 0.42 -10000 0 -0.86 76 76
Gi family/GNB1/GNG2/GDP -0.23 0.29 -10000 0 -0.54 79 79
mol:T-DHT -0.001 0.002 -10000 0 -0.003 59 59
RAC1 0 0 -10000 0 -10000 0 0
GNRH1 0.005 0.012 -10000 0 -10000 0 0
Gi family/GTP -0.2 0.27 -10000 0 -0.52 63 63
CDC42 0 0 -10000 0 -10000 0 0
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.007 0.17 0.35 10 -0.86 5 15
NFATC2 -0.18 0.37 0.6 1 -0.78 47 48
NFATC3 -0.055 0.12 -10000 0 -10000 0 0
CD40LG -0.57 0.59 0.68 1 -1.2 85 86
ITCH -0.006 0.042 -10000 0 -10000 0 0
CBLB -0.006 0.042 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.32 0.49 0.67 5 -1.1 39 44
JUNB -0.045 0.19 -10000 0 -0.86 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.007 0.051 -10000 0 -0.36 4 4
T cell anergy -0.004 0.096 -10000 0 -0.51 4 4
TLE4 -0.11 0.31 -10000 0 -0.63 42 42
Jun/NFAT1-c-4/p21SNFT -0.4 0.56 0.59 1 -1.1 67 68
AP-1/NFAT1-c-4 -0.75 0.84 0.72 4 -1.6 85 89
IKZF1 -0.12 0.35 0.58 1 -0.71 39 40
T-helper 2 cell differentiation -0.26 0.4 0.5 1 -0.84 51 52
AP-1/NFAT1 -0.4 0.42 0.42 4 -0.74 106 110
CALM1 -0.004 0.027 -10000 0 -10000 0 0
EGR2 -0.53 0.85 -10000 0 -1.6 64 64
EGR3 -0.43 0.76 -10000 0 -1.4 61 61
NFAT1/FOXP3 -0.13 0.33 0.46 7 -0.66 42 49
EGR1 -0.27 0.4 -10000 0 -0.86 59 59
JUN -0.019 0.12 -10000 0 -0.87 4 4
EGR4 0.005 0.042 0.34 3 -10000 0 3
mol:Ca2+ -0.004 0.03 -10000 0 -10000 0 0
GBP3 -0.16 0.39 -10000 0 -0.79 46 46
FOSL1 -0.031 0.18 0.34 3 -0.86 8 11
NFAT1-c-4/MAF/IRF4 -0.46 0.61 0.61 2 -1.1 73 75
DGKA -0.1 0.29 0.58 1 -0.6 41 42
CREM 0 0 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.4 0.55 -10000 0 -1.1 66 66
CTLA4 -0.072 0.32 0.49 6 -0.7 25 31
NFAT1-c-4 (dimer)/EGR1 -0.54 0.66 -10000 0 -1.3 73 73
NFAT1-c-4 (dimer)/EGR4 -0.4 0.56 -10000 0 -1.1 68 68
FOS -0.41 0.44 -10000 0 -0.87 89 89
IFNG -0.21 0.35 0.47 4 -0.77 39 43
T cell activation -0.33 0.44 -10000 0 -0.87 67 67
MAF -0.005 0.062 -10000 0 -0.86 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.26 0.41 0.78 64 -10000 0 64
TNF -0.46 0.56 -10000 0 -1.1 72 72
FASLG -0.52 0.8 -10000 0 -1.5 66 66
TBX21 -0.019 0.17 -10000 0 -0.86 7 7
BATF3 -0.007 0.091 0.34 1 -0.86 2 3
PRKCQ -0.028 0.17 0.34 2 -0.86 7 9
PTPN1 -0.1 0.29 -10000 0 -0.64 35 35
NFAT1-c-4/ICER1 -0.4 0.55 -10000 0 -1.1 67 67
GATA3 -0.066 0.23 0.34 1 -0.86 15 16
T-helper 1 cell differentiation -0.2 0.34 0.47 4 -0.76 39 43
IL2RA -0.32 0.46 0.65 5 -0.93 50 55
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.11 0.3 -10000 0 -0.66 35 35
E2F1 0.22 0.17 0.35 118 -10000 0 118
PPARG 0.002 0.025 0.34 1 -10000 0 1
SLC3A2 -0.1 0.29 -10000 0 -0.61 40 40
IRF4 -0.17 0.36 0.34 6 -0.86 40 46
PTGS2 -0.65 0.67 -10000 0 -1.3 86 86
CSF2 -0.55 0.6 -10000 0 -1.2 84 84
JunB/Fra1/NFAT1-c-4 -0.41 0.57 0.59 1 -1.1 68 69
IL4 -0.28 0.43 0.51 1 -0.89 51 52
IL5 -0.54 0.61 -10000 0 -1.2 84 84
IL2 -0.34 0.45 -10000 0 -0.9 65 65
IL3 -0.084 0.066 -10000 0 -10000 0 0
RNF128 -0.019 0.13 -10000 0 -0.92 4 4
NFATC1 -0.26 0.42 -10000 0 -0.78 64 64
CDK4 0.22 0.28 0.65 38 -10000 0 38
PTPRK -0.1 0.29 -10000 0 -0.64 35 35
IL8 -0.64 0.64 0.62 1 -1.2 93 94
POU2F1 0.002 0.004 -10000 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.18 0.17 0.34 101 -9999 0 101
GPC2 0.05 0.12 0.34 28 -9999 0 28
GPC2/Midkine 0.16 0.14 0.48 15 -9999 0 15
neuron projection morphogenesis 0.16 0.14 0.48 15 -9999 0 15
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 0.007 0.07 0.23 9 -0.67 1 10
Necdin/E2F1 0.13 0.16 0.48 3 -0.64 4 7
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.24 0.33 -10000 0 -0.59 79 79
NGF (dimer)/p75(NTR)/BEX1 -0.44 0.42 -10000 0 -0.74 115 115
NT-4/5 (dimer)/p75(NTR) -0.27 0.33 -10000 0 -0.68 76 76
IKBKB 0 0 -10000 0 -10000 0 0
AKT1 -0.22 0.29 -10000 0 -0.55 78 78
IKBKG 0 0 -10000 0 -10000 0 0
BDNF 0.011 0.059 0.34 6 -10000 0 6
MGDIs/NGR/p75(NTR)/LINGO1 -0.21 0.32 -10000 0 -0.59 76 76
FURIN -0.009 0.088 -10000 0 -0.86 2 2
proBDNF (dimer)/p75(NTR)/Sortilin -0.22 0.3 0.42 1 -0.58 76 77
LINGO1 0.052 0.12 0.34 29 -10000 0 29
Sortilin/TRAF6/NRIF -0.002 0.032 -10000 0 -0.44 1 1
proBDNF (dimer) 0.011 0.059 0.34 6 -10000 0 6
NTRK1 0.002 0.025 0.34 1 -10000 0 1
RTN4R -0.005 0.062 -10000 0 -0.86 1 1
neuron apoptosis -0.12 0.27 -10000 0 -0.54 26 26
IRAK1 0.002 0.025 0.34 1 -10000 0 1
SHC1 -0.26 0.32 -10000 0 -0.63 78 78
ARHGDIA 0 0 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.23 0.31 -10000 0 -0.58 78 78
MAGEH1 -0.005 0.062 -10000 0 -0.86 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.24 0.33 0.4 1 -0.6 78 79
Mammalian IAPs/DIABLO 0.004 0.053 -10000 0 -0.54 1 1
proNGF (dimer) -0.041 0.18 -10000 0 -0.86 9 9
MAGED1 0 0 -10000 0 -10000 0 0
APP -0.009 0.088 -10000 0 -0.86 2 2
NT-4/5 (dimer) 0.002 0.025 0.34 1 -10000 0 1
ZNF274 0 0 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI -0.22 0.28 -10000 0 -0.55 78 78
NGF -0.041 0.18 -10000 0 -0.86 9 9
cell cycle arrest -0.18 0.32 0.25 1 -0.53 78 79
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.16 0.2 -10000 0 -0.39 78 78
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.24 0.29 -10000 0 -0.59 77 77
NCSTN 0 0 -10000 0 -10000 0 0
mol:GTP -0.26 0.32 -10000 0 -0.63 78 78
PSENEN 0 0 -10000 0 -10000 0 0
mol:ceramide -0.23 0.3 -10000 0 -0.57 78 78
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.14 0.18 -10000 0 -0.33 81 81
p75(NTR)/beta APP -0.27 0.34 -10000 0 -0.68 77 77
BEX1 -0.27 0.44 0.34 15 -0.86 65 80
mol:GDP -0.26 0.33 -10000 0 -0.64 78 78
NGF (dimer) -0.23 0.31 -10000 0 -0.58 80 80
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.19 0.29 -10000 0 -0.54 76 76
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
RAC1/GTP -0.23 0.29 -10000 0 -0.56 78 78
MYD88 0 0 -10000 0 -10000 0 0
CHUK 0 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.26 0.32 -10000 0 -0.63 78 78
RHOB -0.041 0.18 -10000 0 -0.86 9 9
RHOA 0 0 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.14 0.11 -10000 0 -10000 0 0
NT3 (dimer) -0.46 0.43 -10000 0 -0.86 102 102
TP53 -0.19 0.23 -10000 0 -0.47 77 77
PRDM4 -0.23 0.3 -10000 0 -0.57 78 78
BDNF (dimer) -0.2 0.3 0.4 1 -0.55 74 75
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
SORT1 0.016 0.072 0.34 9 -10000 0 9
activation of caspase activity -0.23 0.32 -10000 0 -0.58 79 79
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.23 0.31 -10000 0 -0.58 78 78
RHOC 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
MAPK10 -0.17 0.28 -10000 0 -0.49 78 78
DIABLO 0 0 -10000 0 -10000 0 0
SMPD2 -0.23 0.3 -10000 0 -0.57 78 78
APH1B 0 0 -10000 0 -10000 0 0
APH1A 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.25 0.33 -10000 0 -0.63 78 78
PSEN1 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.58 0.51 -10000 0 -0.95 117 117
MAPK8 -0.17 0.27 -10000 0 -0.48 78 78
MAPK9 -0.16 0.26 -10000 0 -0.47 78 78
APAF1 0 0 -10000 0 -10000 0 0
NTF3 -0.46 0.43 -10000 0 -0.86 102 102
NTF4 0.002 0.025 0.34 1 -10000 0 1
NDN -0.011 0.13 0.34 4 -0.86 4 8
RAC1/GDP 0 0 -10000 0 -10000 0 0
RhoA-B-C/GDP -0.23 0.3 -10000 0 -0.55 79 79
p75 CTF/Sortilin/TRAF6/NRIF 0.007 0.059 -10000 0 -0.54 1 1
RhoA-B-C/GTP -0.26 0.32 -10000 0 -0.62 78 78
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.19 0.26 0.38 1 -0.5 77 78
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.2 0.27 0.4 1 -0.53 77 78
PRKACB 0 0 -10000 0 -10000 0 0
proBDNF (dimer)/p75 ECD 0.007 0.041 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.006 0.087 0.34 6 -0.86 1 7
BIRC2 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.17 0.33 0.29 1 -0.53 78 79
BAD -0.16 0.27 -10000 0 -0.47 78 78
RIPK2 0 0 -10000 0 -10000 0 0
NGFR -0.34 0.42 -10000 0 -0.86 76 76
CYCS -0.22 0.28 -10000 0 -0.54 78 78
ADAM17 0 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.24 0.3 -10000 0 -0.59 78 78
BCL2L11 -0.16 0.27 -10000 0 -0.47 78 78
BDNF (dimer)/p75(NTR) -0.26 0.33 -10000 0 -0.67 76 76
PI3K -0.24 0.31 -10000 0 -0.59 78 78
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.23 0.31 -10000 0 -0.58 78 78
NDNL2 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.29 0.37 -10000 0 -0.72 78 78
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.23 0.31 -10000 0 -0.58 78 78
TRAF6 -0.005 0.062 -10000 0 -0.86 1 1
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.036 0.17 -10000 0 -0.86 8 8
PLG -0.15 0.33 -10000 0 -0.86 34 34
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.23 0.3 -10000 0 -0.57 78 78
SQSTM1 0.004 0.035 0.34 2 -10000 0 2
NGFRAP1 -0.034 0.18 0.34 1 -0.86 8 9
CASP3 -0.15 0.25 -10000 0 -0.43 78 78
E2F1 0.21 0.17 0.34 118 -10000 0 118
CASP9 0 0 -10000 0 -10000 0 0
IKK complex -0.12 0.18 -10000 0 -0.7 12 12
NGF (dimer)/TRKA -0.031 0.14 -10000 0 -0.68 9 9
MMP7 -0.16 0.39 0.34 19 -0.86 43 62
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.22 0.29 -10000 0 -0.55 78 78
MMP3 0.016 0.072 0.34 9 -10000 0 9
APAF-1/Caspase 9 -0.16 0.21 -10000 0 -0.71 7 7
IL4-mediated 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
BCL2L1 -0.41 0.58 -10000 0 -1.1 65 65
STAT6 (cleaved dimer) -0.53 0.55 -10000 0 -1.1 84 84
IGHG1 -0.14 0.24 0.5 2 -0.41 41 43
IGHG3 -0.41 0.56 -10000 0 -0.98 80 80
AKT1 -0.21 0.36 0.65 1 -0.7 45 46
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.17 0.33 0.63 1 -0.62 39 40
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.2 0.34 0.64 1 -0.63 42 43
THY1 -0.39 0.61 0.88 1 -1.1 59 60
MYB 0.032 0.1 0.34 18 -10000 0 18
HMGA1 0.018 0.076 0.34 10 -10000 0 10
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.3 0.48 0.7 2 -0.81 70 72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.2 0.34 0.64 1 -0.63 43 44
SP1 0.018 0.025 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.019 0.026 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.51 0.54 -10000 0 -1.1 81 81
SOCS1 -0.28 0.39 -10000 0 -0.73 61 61
SOCS3 -0.32 0.55 -10000 0 -1.2 42 42
FCER2 -0.4 0.58 0.81 2 -1 76 78
PARP14 0.001 0.009 -10000 0 -10000 0 0
CCL17 -0.41 0.59 0.88 1 -1.1 65 66
GRB2 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.15 0.28 0.58 1 -0.54 29 30
T cell proliferation -0.43 0.61 -10000 0 -1.1 69 69
IL4R/JAK1 -0.42 0.58 -10000 0 -1.1 66 66
EGR2 -0.62 0.81 -10000 0 -1.5 79 79
JAK2 -0.006 0.079 -10000 0 -0.9 1 1
JAK3 0.007 0.077 0.37 3 -0.84 1 4
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
JAK1 0.01 0.021 -10000 0 -10000 0 0
COL1A2 -0.099 0.24 -10000 0 -1.7 1 1
CCL26 -0.4 0.6 0.88 1 -1.1 63 64
IL4R -0.44 0.63 -10000 0 -1.2 66 66
PTPN6 0.014 0.015 -10000 0 -10000 0 0
IL13RA2 -0.98 0.74 -10000 0 -1.4 134 134
IL13RA1 -0.002 0.045 -10000 0 -10000 0 0
IRF4 -0.36 0.69 0.8 1 -1.6 43 44
ARG1 -0.35 0.63 -10000 0 -1.6 38 38
CBL -0.28 0.45 0.66 1 -0.78 65 66
GTF3A 0.026 0.037 -10000 0 -10000 0 0
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
IL13RA1/JAK2 -0.003 0.084 -10000 0 -0.7 1 1
IRF4/BCL6 -0.37 0.6 -10000 0 -1.5 43 43
CD40LG -0.029 0.19 0.49 1 -0.88 9 10
MAPK14 -0.3 0.5 0.67 1 -0.87 64 65
mitosis -0.2 0.34 0.64 1 -0.66 44 45
STAT6 -0.48 0.72 0.94 1 -1.2 79 80
SPI1 -0.02 0.088 -10000 0 -0.51 3 3
RPS6KB1 -0.19 0.33 0.63 1 -0.64 41 42
STAT6 (dimer) -0.48 0.72 0.94 1 -1.2 79 80
STAT6 (dimer)/PARP14 -0.45 0.62 0.68 1 -1.1 75 76
mast cell activation 0.007 0.019 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.21 0.37 0.66 1 -0.68 44 45
FRAP1 -0.21 0.36 0.65 1 -0.7 45 46
LTA -0.41 0.59 -10000 0 -1.1 65 65
FES -0.009 0.088 -10000 0 -0.86 2 2
T-helper 1 cell differentiation 0.47 0.68 1.2 79 -0.94 1 80
CCL11 -0.4 0.57 -10000 0 -1.1 66 66
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.21 0.37 0.66 1 -0.68 44 45
IL2RG -0.005 0.13 0.34 4 -0.86 4 8
IL10 -0.47 0.66 -10000 0 -1.2 66 66
IRS1 0 0 -10000 0 -10000 0 0
IRS2 -0.023 0.14 -10000 0 -0.86 5 5
IL4 -0.076 0.18 -10000 0 -10000 0 0
IL5 -0.42 0.58 -10000 0 -1.1 65 65
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.32 0.47 0.81 1 -0.83 67 68
COL1A1 -0.1 0.32 0.67 4 -1.8 3 7
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.43 0.59 -10000 0 -1.2 60 60
IL2R gamma/JAK3 -0.007 0.13 0.43 2 -0.8 4 6
TFF3 -0.42 0.61 -10000 0 -1.2 61 61
ALOX15 -0.41 0.59 -10000 0 -1.1 64 64
MYBL1 0.005 0.042 0.34 3 -10000 0 3
T-helper 2 cell differentiation -0.35 0.5 -10000 0 -0.89 72 72
SHC1 0 0 -10000 0 -10000 0 0
CEBPB -0.015 0.059 -10000 0 -0.3 2 2
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.2 0.34 0.61 1 -0.62 45 46
mol:PI-3-4-5-P3 -0.21 0.36 0.65 1 -0.7 45 46
PI3K -0.23 0.39 0.66 1 -0.75 44 45
DOK2 -0.009 0.088 -10000 0 -0.86 2 2
ETS1 0.01 0.022 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.14 0.27 0.56 1 -0.54 23 24
ITGB3 -0.47 0.66 -10000 0 -1.2 67 67
PIGR -0.57 0.72 -10000 0 -1.3 79 79
IGHE 0.019 0.061 -10000 0 -10000 0 0
MAPKKK cascade -0.13 0.27 0.55 1 -0.52 23 24
BCL6 0 0.003 -10000 0 -10000 0 0
OPRM1 -0.42 0.58 -10000 0 -1.1 61 61
RETNLB -0.42 0.58 -10000 0 -1.1 65 65
SELP -0.66 0.8 -10000 0 -1.4 87 87
AICDA -0.41 0.56 -10000 0 -1.1 65 65
EPO signaling pathway

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
BCL2L1 -0.11 0.24 -10000 0 -10000 0 0
CRKL -0.15 0.21 -10000 0 -0.44 69 69
mol:DAG -0.17 0.24 -10000 0 -0.48 68 68
HRAS -0.13 0.17 -10000 0 -10000 0 0
MAPK8 -0.2 0.26 -10000 0 -0.51 76 76
RAP1A -0.15 0.21 -10000 0 -0.44 69 69
GAB1 -0.15 0.21 -10000 0 -0.44 69 69
MAPK14 -0.18 0.24 -10000 0 -0.5 68 68
EPO -0.29 0.43 0.35 8 -0.86 68 76
PLCG1 -0.17 0.24 -10000 0 -0.5 68 68
EPOR/TRPC2/IP3 Receptors -0.011 0.017 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.27 0.34 -10000 0 -0.63 84 84
GAB1/SHC/GRB2/SOS1 -0.14 0.18 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.23 0.33 -10000 0 -0.67 68 68
IRS2 -0.17 0.23 -10000 0 -0.46 71 71
STAT1 -0.17 0.24 -10000 0 -0.49 68 68
STAT5B -0.17 0.24 -10000 0 -0.49 68 68
cell proliferation -0.17 0.25 -10000 0 -0.48 76 76
GAB1/SHIP/PIK3R1/SHP2/SHC -0.13 0.18 -10000 0 -0.75 1 1
TEC -0.16 0.22 -10000 0 -0.44 73 73
SOCS3 -0.11 0.29 -10000 0 -0.86 25 25
STAT1 (dimer) -0.16 0.24 -10000 0 -0.48 68 68
JAK2 -0.016 0.063 -10000 0 -0.86 1 1
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
EPO/EPOR (dimer)/JAK2 -0.16 0.24 -10000 0 -0.46 69 69
EPO/EPOR -0.23 0.33 -10000 0 -0.67 68 68
LYN 0 0 -10000 0 -10000 0 0
TEC/VAV2 -0.16 0.21 -10000 0 -0.42 73 73
elevation of cytosolic calcium ion concentration -0.011 0.017 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.19 0.28 -10000 0 -0.56 68 68
mol:IP3 -0.17 0.24 -10000 0 -0.48 68 68
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.16 0.21 -10000 0 -0.73 5 5
SH2B3 -0.011 0.017 -10000 0 -10000 0 0
NFKB1 -0.18 0.24 -10000 0 -0.5 68 68
EPO/EPOR (dimer)/JAK2/SOCS3 -0.17 0.22 -10000 0 -0.4 84 84
PTPN6 -0.16 0.22 -10000 0 -0.46 69 69
TEC/VAV2/GRB2 -0.15 0.2 -10000 0 -0.44 4 4
EPOR -0.011 0.017 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP -0.14 0.18 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
PLCG2 -0.018 0.12 -10000 0 -0.86 4 4
CRKL/CBL/C3G -0.14 0.2 -10000 0 -10000 0 0
VAV2 -0.15 0.21 -10000 0 -0.44 69 69
CBL -0.15 0.21 -10000 0 -0.44 69 69
SHC/Grb2/SOS1 -0.14 0.2 -10000 0 -10000 0 0
STAT5A -0.17 0.24 -10000 0 -0.49 68 68
GRB2 0 0 -10000 0 -10000 0 0
STAT5 (dimer) -0.15 0.22 -10000 0 -0.44 68 68
LYN/PLCgamma2 -0.014 0.096 -10000 0 -0.67 4 4
PTPN11 0 0 -10000 0 -10000 0 0
BTK -0.16 0.22 -10000 0 -0.44 71 71
BCL2 -0.11 0.24 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.38 0.62 -10000 0 -1.2 57 57
PCK1 -0.71 0.86 -10000 0 -1.7 82 82
HNF4A -0.45 0.74 -10000 0 -1.5 56 56
KCNJ11 -0.37 0.64 -10000 0 -1.2 55 55
AKT1 -0.14 0.22 -10000 0 -0.41 55 55
response to starvation -0.007 0.022 -10000 0 -10000 0 0
DLK1 -0.37 0.65 -10000 0 -1.2 55 55
NKX2-1 -0.1 0.24 -10000 0 -0.54 1 1
ACADM -0.39 0.64 -10000 0 -1.2 58 58
TAT -0.69 0.86 -10000 0 -1.7 76 76
CEBPB -0.008 0.02 -10000 0 -10000 0 0
CEBPA -0.009 0.094 -10000 0 -0.9 2 2
TTR -0.48 0.69 -10000 0 -1.4 62 62
PKLR -0.42 0.69 -10000 0 -1.3 60 60
APOA1 -0.53 0.84 -10000 0 -1.6 62 62
CPT1C -0.37 0.62 -10000 0 -1.2 57 57
ALAS1 -0.15 0.3 -10000 0 -1.9 2 2
TFRC -0.3 0.51 -10000 0 -0.91 55 55
FOXF1 -0.077 0.25 -10000 0 -0.86 17 17
NF1 0.007 0.064 -10000 0 -0.86 1 1
HNF1A (dimer) -0.009 0.13 -10000 0 -0.91 3 3
CPT1A -0.38 0.62 -10000 0 -1.2 55 55
HMGCS1 -0.38 0.62 -10000 0 -1.2 57 57
NR3C1 -0.061 0.095 -10000 0 -0.29 3 3
CPT1B -0.38 0.62 -10000 0 -1.2 57 57
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.014 0.054 -10000 0 -10000 0 0
GCK -0.65 0.8 -10000 0 -1.4 94 94
CREB1 -0.044 0.082 -10000 0 -0.29 2 2
IGFBP1 -0.46 0.7 -10000 0 -1.6 47 47
PDX1 -0.17 0.46 -10000 0 -1.6 13 13
UCP2 -0.38 0.62 -10000 0 -1.2 59 59
ALDOB -0.53 0.81 -10000 0 -1.5 68 68
AFP -0.1 0.36 -10000 0 -1.1 16 16
BDH1 -0.4 0.67 -10000 0 -1.2 60 60
HADH -0.37 0.63 -10000 0 -1.2 59 59
F2 -0.45 0.74 -10000 0 -1.5 53 53
HNF1A -0.009 0.13 -10000 0 -0.92 3 3
G6PC -0.28 0.58 -10000 0 -1.6 29 29
SLC2A2 -0.35 0.68 -10000 0 -1.7 32 32
INS 0.036 0.085 0.31 7 -10000 0 7
FOXA1 -0.016 0.18 -10000 0 -0.79 6 6
FOXA3 -0.16 0.29 -10000 0 -0.73 27 27
FOXA2 -0.44 0.77 -10000 0 -1.3 65 65
ABCC8 -0.36 0.64 -10000 0 -1.2 55 55
ALB -0.23 0.53 -10000 0 -1.4 30 30
Aurora B signaling

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
Condensin I complex 0.15 0.12 0.27 76 -10000 0 76
STMN1 0.097 0.095 0.29 14 -10000 0 14
Aurora B/RasGAP/Survivin 0.23 0.19 0.4 96 -0.52 2 98
Chromosomal passenger complex/Cul3 protein complex 0.13 0.12 0.23 81 -0.28 4 85
BIRC5 0.24 0.16 0.35 130 -10000 0 130
DES 0.054 0.25 0.45 2 -0.55 15 17
Aurora C/Aurora B/INCENP 0.11 0.099 0.38 1 -10000 0 1
Aurora B/TACC1 0.1 0.099 -10000 0 -10000 0 0
Aurora B/PP2A 0.12 0.11 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.036 0.034 -10000 0 -10000 0 0
mitotic metaphase/anaphase transition -0.008 0.005 -10000 0 -10000 0 0
NDC80 0.18 0.13 0.29 96 -10000 0 96
Cul3 protein complex -0.017 0.1 -10000 0 -0.58 6 6
KIF2C 0.19 0.14 0.29 124 -10000 0 124
PEBP1 -0.021 0.14 -10000 0 -0.87 5 5
KIF20A 0.23 0.15 0.34 133 -10000 0 133
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.11 0.14 -10000 0 -0.64 2 2
SEPT1 0.002 0.025 0.34 1 -10000 0 1
SMC2 0.002 0.025 0.34 1 -10000 0 1
SMC4 0.004 0.035 0.34 2 -10000 0 2
NSUN2/NPM1/Nucleolin 0.16 0.13 0.33 28 -10000 0 28
PSMA3 0 0 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.005 -10000 0 -10000 0 0
H3F3B 0.076 0.071 -10000 0 -10000 0 0
AURKB 0.18 0.17 0.34 98 -10000 0 98
AURKC 0.002 0.025 0.34 1 -10000 0 1
CDCA8 0.18 0.17 0.35 97 -10000 0 97
cytokinesis 0.22 0.2 0.4 97 -10000 0 97
Aurora B/Septin1 0.23 0.22 0.44 98 -10000 0 98
AURKA 0.095 0.15 0.34 54 -10000 0 54
INCENP 0.011 0.026 0.35 1 -10000 0 1
KLHL13 -0.021 0.14 0.34 1 -0.86 5 6
BUB1 0.23 0.16 0.34 129 -10000 0 129
hSgo1/Aurora B/Survivin 0.31 0.24 0.52 107 -10000 0 107
EVI5 0.005 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.22 0.24 0.46 90 -10000 0 90
SGOL1 0.15 0.17 0.34 84 -10000 0 84
CENPA 0.21 0.14 0.33 107 -10000 0 107
NCAPG 0.22 0.16 0.34 126 -10000 0 126
Aurora B/HC8 Proteasome 0.12 0.11 -10000 0 -10000 0 0
NCAPD2 0.007 0.049 0.34 4 -10000 0 4
Aurora B/PP1-gamma 0.12 0.11 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
NCAPH 0.16 0.17 0.34 91 -10000 0 91
NPM1 0.11 0.1 -10000 0 -10000 0 0
RASA1 -0.009 0.088 -10000 0 -0.86 2 2
KLHL9 -0.005 0.062 -10000 0 -0.86 1 1
mitotic prometaphase 0.002 0.002 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.12 0.11 -10000 0 -10000 0 0
PPP1CC 0 0 -10000 0 -10000 0 0
Centraspindlin 0.25 0.27 0.52 91 -10000 0 91
RhoA/GDP 0 0 -10000 0 -10000 0 0
NSUN2 0.11 0.1 -10000 0 -10000 0 0
MYLK 0.066 0.091 -10000 0 -0.33 4 4
KIF23 0.17 0.18 0.35 92 -10000 0 92
VIM 0.088 0.082 0.28 1 -10000 0 1
RACGAP1 0.066 0.13 0.36 30 -10000 0 30
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.11 0.1 -10000 0 -10000 0 0
Chromosomal passenger complex 0.22 0.15 0.33 120 -10000 0 120
Chromosomal passenger complex/EVI5 0.3 0.22 0.47 113 -10000 0 113
TACC1 0 0 -10000 0 -10000 0 0
PPP2R5D 0 0 -10000 0 -10000 0 0
CUL3 0 0 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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
PKM2 -0.25 0.47 0.83 1 -1 37 38
HDAC7 0.002 0.025 0.34 1 -10000 0 1
HIF1A/ARNT/Cbp/p300/Src-1 -0.36 0.42 0.9 2 -0.9 55 57
SMAD4 -0.005 0.062 -10000 0 -0.86 1 1
ID2 -0.26 0.47 0.83 1 -1 37 38
AP1 -0.32 0.36 -10000 0 -0.7 89 89
ABCG2 -0.32 0.53 0.83 1 -1.1 47 48
HIF1A -0.027 0.068 0.42 1 -10000 0 1
TFF3 -0.25 0.49 1.1 1 -1 38 39
GATA2 -0.003 0.068 0.34 1 -0.87 1 2
AKT1 -0.044 0.12 0.47 1 -0.22 19 20
response to hypoxia -0.057 0.12 0.47 1 -0.23 35 36
MCL1 -0.25 0.47 0.83 1 -1 37 38
NDRG1 -0.25 0.47 0.83 1 -1 37 38
SERPINE1 -0.37 0.56 0.83 1 -1.1 60 61
FECH -0.25 0.47 -10000 0 -1 37 37
FURIN -0.26 0.47 0.83 1 -1 38 39
NCOA2 -0.095 0.27 -10000 0 -0.86 21 21
EP300 -0.087 0.21 0.53 2 -0.32 67 69
HMOX1 -0.27 0.49 0.83 1 -1 39 40
BHLHE40 -0.26 0.48 0.83 1 -1 38 39
BHLHE41 -0.26 0.49 0.83 2 -1 39 41
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.027 0.074 0.52 1 -0.43 1 2
ENG -0.024 0.058 -10000 0 -10000 0 0
JUN -0.018 0.12 -10000 0 -0.86 4 4
RORA -0.26 0.47 0.83 1 -1 39 40
ABCB1 -0.21 0.43 0.5 1 -1.4 22 23
TFRC -0.25 0.47 0.83 1 -1 37 38
CXCR4 -0.26 0.47 0.83 1 -1 37 38
TF -0.29 0.51 0.83 1 -1 45 46
CITED2 -0.26 0.47 0.83 1 -1 37 38
HIF1A/ARNT -0.32 0.52 1.4 1 -1.2 37 38
LDHA -0.056 0.068 0.51 1 -10000 0 1
ETS1 -0.25 0.47 0.83 1 -1 37 38
PGK1 -0.25 0.47 0.83 1 -1 37 38
NOS2 -0.24 0.48 0.83 2 -1 37 39
ITGB2 -0.26 0.47 0.83 1 -1 37 38
ALDOA -0.25 0.47 0.83 1 -1 37 38
Cbp/p300/CITED2 -0.41 0.52 0.99 1 -1.1 55 56
FOS -0.4 0.43 -10000 0 -0.86 89 89
HK2 -0.25 0.49 1.1 1 -1 38 39
SP1 0.005 0.029 -10000 0 -10000 0 0
GCK -0.57 0.81 0.87 1 -1.5 82 83
HK1 -0.25 0.47 0.83 1 -1 37 38
NPM1 -0.25 0.47 0.83 1 -1 37 38
EGLN1 -0.25 0.47 0.83 1 -1 37 38
CREB1 0.013 0 -10000 0 -10000 0 0
PGM1 -0.26 0.47 0.83 1 -1 37 38
SMAD3 0 0 -10000 0 -10000 0 0
EDN1 -0.26 0.34 -10000 0 -0.68 52 52
IGFBP1 -0.36 0.57 0.83 1 -1.1 54 55
VEGFA -0.28 0.36 0.87 1 -0.76 46 47
HIF1A/JAB1 -0.015 0.048 0.35 1 -10000 0 1
CP -0.31 0.55 0.83 1 -1.2 45 46
CXCL12 -0.46 0.55 -10000 0 -1 75 75
COPS5 -0.001 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.003 0.048 -10000 0 -0.67 1 1
BNIP3 -0.25 0.47 0.83 1 -1 37 38
EGLN3 -0.24 0.49 1.1 1 -1 37 38
CA9 -0.35 0.56 1.1 1 -1 60 61
TERT -0.2 0.5 1.1 1 -0.99 37 38
ENO1 -0.25 0.47 0.83 1 -1 37 38
PFKL -0.25 0.47 0.83 1 -1 37 38
NCOA1 0 0.007 -10000 0 -10000 0 0
ADM -0.25 0.47 0.83 1 -1 37 38
ARNT -0.026 0.065 0.4 1 -10000 0 1
HNF4A -0.042 0.14 -10000 0 -0.9 4 4
ADFP -0.26 0.47 0.82 1 -0.93 46 47
SLC2A1 -0.28 0.37 1.1 1 -0.77 45 46
LEP -0.25 0.48 0.94 2 -1 37 39
HIF1A/ARNT/Cbp/p300 -0.36 0.43 1.2 1 -0.91 54 55
EPO -0.53 0.62 1 1 -1.2 81 82
CREBBP -0.087 0.21 0.53 2 -0.33 65 67
HIF1A/ARNT/Cbp/p300/HDAC7 -0.34 0.41 1.2 1 -0.9 49 50
PFKFB3 -0.26 0.48 0.83 1 -1 38 39
NT5E -0.27 0.49 0.83 1 -1.1 38 39
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.37 0.64 -10000 0 -1.3 59 59
MKNK1 0 0 -10000 0 -10000 0 0
MAPK14 -0.068 0.16 -10000 0 -0.31 53 53
ATF2/c-Jun -0.083 0.22 -10000 0 -1.4 4 4
MAPK11 -0.061 0.17 0.4 4 -0.39 4 8
MITF -0.07 0.2 -10000 0 -0.37 52 52
MAPKAPK5 -0.072 0.2 0.3 1 -0.37 52 53
KRT8 -0.074 0.2 0.3 1 -0.37 53 54
MAPKAPK3 0 0 -10000 0 -10000 0 0
MAPKAPK2 0 0 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.12 0.23 0.39 1 -0.46 53 54
CEBPB -0.072 0.2 -10000 0 -0.37 52 52
SLC9A1 -0.071 0.2 -10000 0 -0.37 52 52
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.073 0.22 0.31 1 -0.38 53 54
p38alpha-beta/MNK1 -0.091 0.18 0.33 1 -0.5 4 5
JUN -0.082 0.22 -10000 0 -1.3 4 4
PPARGC1A -0.15 0.31 -10000 0 -0.5 68 68
USF1 -0.072 0.2 0.3 1 -0.37 52 53
RAB5/GDP/GDI1 -0.076 0.12 -10000 0 -0.36 4 4
NOS2 -0.053 0.21 0.46 1 -0.48 4 5
DDIT3 -0.07 0.2 0.3 1 -0.37 52 53
RAB5A 0 0 -10000 0 -10000 0 0
HSPB1 -0.051 0.16 -10000 0 -0.38 4 4
p38alpha-beta/HBP1 -0.091 0.18 0.33 1 -0.36 52 53
CREB1 -0.1 0.19 0.29 1 -0.39 52 53
RAB5/GDP 0 0 -10000 0 -10000 0 0
EIF4E -0.083 0.15 -10000 0 -0.44 4 4
RPS6KA4 -0.072 0.2 0.3 1 -0.37 52 53
PLA2G4A -0.12 0.25 -10000 0 -0.72 19 19
GDI1 -0.072 0.2 -10000 0 -0.37 52 52
TP53 -0.094 0.24 -10000 0 -0.45 53 53
RPS6KA5 -0.081 0.21 0.3 1 -0.38 55 56
ESR1 -0.35 0.37 0.3 1 -0.56 122 123
HBP1 0 0 -10000 0 -10000 0 0
MEF2C -0.072 0.2 0.3 1 -0.37 52 53
MEF2A -0.072 0.2 -10000 0 -0.37 52 52
EIF4EBP1 -0.1 0.19 0.29 1 -0.39 52 53
KRT19 -0.26 0.4 -10000 0 -0.63 85 85
ELK4 -0.072 0.2 -10000 0 -0.37 52 52
ATF6 -0.072 0.2 -10000 0 -0.37 52 52
ATF1 -0.1 0.19 0.29 1 -0.39 52 53
p38alpha-beta/MAPKAPK2 -0.091 0.18 0.33 1 -0.5 4 5
p38alpha-beta/MAPKAPK3 -0.091 0.18 0.33 1 -0.5 4 5
Ephrin A reverse signaling

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
MAPKKK cascade -0.11 0.27 0.41 3 -0.59 42 45
EFNA5 -0.16 0.38 0.34 14 -0.86 42 56
FYN -0.11 0.23 -10000 0 -0.54 42 42
neuron projection morphogenesis -0.11 0.27 0.41 3 -0.59 42 45
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 -0.11 0.27 0.41 3 -0.6 42 45
EPHA5 0.012 0.064 0.34 7 -10000 0 7
TCGA08_retinoblastoma

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
CDKN2B 0.026 0.075 0.34 10 -10000 0 10
CDKN2C 0.03 0.09 0.34 15 -10000 0 15
CDKN2A 0.22 0.16 0.34 123 -10000 0 123
CCND2 -0.072 0.065 -10000 0 -0.19 26 26
RB1 0.08 0.072 0.21 28 -10000 0 28
CDK4 -0.078 0.066 -10000 0 -0.21 21 21
CDK6 -0.086 0.085 -10000 0 -0.24 28 28
G1/S progression -0.08 0.072 -10000 0 -0.21 28 28
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.001 0.017 -10000 0 -10000 0 0
VLDLR -0.006 0.25 0.34 27 -0.86 12 39
CRKL 0 0 -10000 0 -10000 0 0
LRPAP1 0 0 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
ITGA3 0.029 0.094 0.34 16 -10000 0 16
RELN/VLDLR/Fyn -0.21 0.34 -10000 0 -0.63 69 69
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.025 0.11 -10000 0 -0.5 10 10
AKT1 -0.18 0.23 -10000 0 -0.4 83 83
MAP2K7 0 0 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
DAB1 -0.14 0.32 -10000 0 -0.86 31 31
RELN/LRP8/DAB1 -0.26 0.32 -10000 0 -0.59 86 86
LRPAP1/LRP8 0.024 0.071 -10000 0 -10000 0 0
RELN/LRP8/DAB1/Fyn -0.24 0.31 -10000 0 -0.56 86 86
DAB1/alpha3/beta1 Integrin -0.23 0.32 0.39 2 -0.56 72 74
long-term memory -0.22 0.3 -10000 0 -0.53 81 81
DAB1/LIS1 -0.24 0.33 0.33 3 -0.55 90 93
DAB1/CRLK/C3G -0.24 0.31 -10000 0 -0.55 77 77
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
DAB1/NCK2 -0.24 0.33 0.33 4 -0.56 88 92
ARHGEF2 0.002 0.025 0.34 1 -10000 0 1
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.055 0.13 0.34 31 -10000 0 31
CDK5R1 0.002 0.025 0.34 1 -10000 0 1
RELN -0.29 0.41 -10000 0 -0.86 64 64
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
RELN/LRP8/Fyn -0.18 0.29 -10000 0 -0.58 64 64
GRIN2A/RELN/LRP8/DAB1/Fyn -0.22 0.32 0.38 3 -0.54 86 89
MAPK8 -0.041 0.18 -10000 0 -0.86 9 9
RELN/VLDLR/DAB1 -0.28 0.36 -10000 0 -0.63 91 91
ITGB1 0 0 -10000 0 -10000 0 0
MAP1B -0.26 0.32 -10000 0 -0.57 91 91
RELN/LRP8 -0.18 0.29 -10000 0 -0.58 64 64
GRIN2B/RELN/LRP8/DAB1/Fyn -0.24 0.3 -10000 0 -0.55 86 86
PI3K -0.006 0.087 -10000 0 -1.2 1 1
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.019 0.064 -10000 0 -10000 0 0
RAP1A -0.23 0.27 -10000 0 -0.85 15 15
PAFAH1B1 0 0 -10000 0 -10000 0 0
MAPK8IP1 -0.005 0.062 -10000 0 -0.86 1 1
CRLK/C3G 0 0 -10000 0 -10000 0 0
GRIN2B 0 0 -10000 0 -10000 0 0
NCK2 0.002 0.025 0.34 1 -10000 0 1
neuron differentiation -0.12 0.17 -10000 0 -0.54 14 14
neuron adhesion -0.21 0.27 -10000 0 -0.8 15 15
LRP8 0.036 0.1 0.34 20 -10000 0 20
GSK3B -0.17 0.22 -10000 0 -0.66 16 16
RELN/VLDLR/DAB1/Fyn -0.26 0.34 -10000 0 -0.59 91 91
MAP3K11 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.19 0.25 -10000 0 -0.43 83 83
CDK5 0 0 -10000 0 -10000 0 0
MAPT 0.064 0.066 -10000 0 -10000 0 0
neuron migration -0.18 0.27 -10000 0 -0.47 80 80
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.13 0.17 -10000 0 -0.54 14 14
RELN/VLDLR -0.17 0.33 0.4 5 -0.58 69 74
IL6-mediated signaling events

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
BCL2L1 -0.3 0.37 -10000 0 -0.74 62 62
CRP -0.47 0.55 -10000 0 -1 82 82
cell cycle arrest -0.36 0.45 -10000 0 -0.89 66 66
TIMP1 -0.27 0.34 -10000 0 -0.7 54 54
IL6ST -0.21 0.38 -10000 0 -0.87 46 46
Rac1/GDP -0.22 0.26 -10000 0 -0.57 56 56
AP1 -0.22 0.26 -10000 0 -0.5 84 84
GAB2 0.004 0.01 -10000 0 -10000 0 0
TNFSF11 -0.46 0.53 -10000 0 -1 80 80
HSP90B1 -0.023 0.059 -10000 0 -10000 0 0
GAB1 0.003 0.007 -10000 0 -10000 0 0
MAPK14 -0.22 0.33 -10000 0 -0.86 31 31
AKT1 0.019 0.048 -10000 0 -0.53 1 1
FOXO1 0.032 0.067 -10000 0 -0.48 3 3
MAP2K6 -0.22 0.3 -10000 0 -0.58 60 60
mol:GTP -0.002 0.003 -10000 0 -10000 0 0
MAP2K4 -0.22 0.31 -10000 0 -0.63 53 53
MITF -0.18 0.27 -10000 0 -0.54 54 54
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0 0 -10000 0 -10000 0 0
A2M -0.18 0.51 -10000 0 -1.5 24 24
CEBPB 0.012 0.003 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 -0.049 0.083 -10000 0 -10000 0 0
STAT3 -0.39 0.5 -10000 0 -0.97 66 66
STAT1 -0.019 0.028 -10000 0 -10000 0 0
CEBPD -0.3 0.38 -10000 0 -0.76 62 62
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
PI3K -0.006 0.087 -10000 0 -1.2 1 1
JUN -0.018 0.12 -10000 0 -0.86 4 4
PIAS3/MITF -0.19 0.24 -10000 0 -0.51 53 53
MAPK11 -0.22 0.33 -10000 0 -0.85 31 31
STAT3 (dimer)/FOXO1 -0.27 0.37 -10000 0 -0.75 51 51
GRB2/SOS1/GAB family -0.14 0.21 -10000 0 -0.67 12 12
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.18 0.25 -10000 0 -0.48 69 69
GRB2 0.003 0.007 -10000 0 -10000 0 0
JAK2 -0.005 0.062 -10000 0 -0.86 1 1
LBP -0.28 0.36 -10000 0 -0.74 56 56
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
JAK1 -0.001 0.006 -10000 0 -10000 0 0
MYC -0.34 0.44 -10000 0 -0.86 65 65
FGG -0.33 0.42 -10000 0 -0.82 66 66
macrophage differentiation -0.36 0.45 -10000 0 -0.89 66 66
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.22 0.3 -10000 0 -0.59 72 72
JUNB -0.3 0.39 -10000 0 -0.77 62 62
FOS -0.4 0.43 -10000 0 -0.86 89 89
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.2 0.28 -10000 0 -0.52 70 70
STAT1/PIAS1 -0.21 0.24 -10000 0 -0.54 54 54
GRB2/SOS1/GAB family/SHP2/PI3K 0.005 0.046 -10000 0 -0.57 1 1
STAT3 (dimer) -0.39 0.5 -10000 0 -0.96 66 66
PRKCD -0.25 0.34 -10000 0 -0.69 53 53
IL6R -0.024 0.14 -10000 0 -0.87 5 5
SOCS3 -0.24 0.46 -10000 0 -1.2 29 29
gp130 (dimer)/JAK1/JAK1/LMO4 -0.15 0.26 -10000 0 -0.6 46 46
Rac1/GTP -0.24 0.28 -10000 0 -0.6 57 57
HCK -0.026 0.15 -10000 0 -0.86 6 6
MAPKKK cascade -0.006 0.077 -10000 0 -10000 0 0
bone resorption -0.42 0.48 -10000 0 -0.93 80 80
IRF1 -0.3 0.37 -10000 0 -0.74 62 62
mol:GDP -0.21 0.29 -10000 0 -0.58 57 57
SOS1 0.004 0.01 -10000 0 -10000 0 0
VAV1 -0.21 0.3 -10000 0 -0.6 57 57
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.2 0.28 -10000 0 -0.71 31 31
PTPN11 -0.017 0.027 -10000 0 -10000 0 0
IL6/IL6RA -0.11 0.26 -10000 0 -0.7 31 31
gp130 (dimer)/TYK2/TYK2/LMO4 -0.14 0.26 -10000 0 -0.6 46 46
gp130 (dimer)/JAK2/JAK2/LMO4 -0.15 0.26 -10000 0 -0.61 46 46
IL6 -0.11 0.31 0.34 5 -0.88 26 31
PIAS3 0 0 -10000 0 -10000 0 0
PTPRE 0.007 0.091 -10000 0 -0.86 2 2
PIAS1 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.17 0.23 -10000 0 -0.45 69 69
LMO4 0.005 0.01 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.39 0.4 -10000 0 -0.88 64 64
MCL1 0.036 0.04 -10000 0 -0.47 1 1
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.002 0.025 0.34 1 -10000 0 1
PTK2 0 0 -10000 0 -10000 0 0
CRKL -0.19 0.24 -10000 0 -0.49 74 74
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.004 0.035 0.34 2 -10000 0 2
IRS1/Crk -0.19 0.24 -10000 0 -0.49 74 74
IGF-1R heterotetramer/IGF1/PTP1B -0.22 0.28 -10000 0 -0.56 74 74
AKT1 -0.16 0.21 -10000 0 -0.42 73 73
BAD -0.12 0.22 -10000 0 -0.81 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.19 0.24 -10000 0 -0.49 74 74
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.19 0.24 -10000 0 -0.49 74 74
RAF1 -0.12 0.21 -10000 0 -0.74 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.18 0.23 -10000 0 -0.46 74 74
YWHAZ 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.2 0.26 -10000 0 -0.53 74 74
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
RPS6KB1 -0.16 0.21 -10000 0 -0.9 3 3
GNB2L1 0 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.098 0.18 -10000 0 -0.59 3 3
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.16 0.21 -10000 0 -0.41 72 72
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.18 0.23 -10000 0 -0.46 74 74
IGF-1R heterotetramer -0.043 0.11 0.35 1 -0.98 2 3
IGF-1R heterotetramer/IGF1/IRS/Nck -0.19 0.25 -10000 0 -0.49 74 74
Crk/p130 Cas/Paxillin -0.17 0.22 -10000 0 -0.44 74 74
IGF1R -0.043 0.11 0.35 1 -0.98 2 3
IGF1 -0.34 0.43 -10000 0 -0.88 74 74
IRS2/Crk -0.19 0.24 -10000 0 -0.47 77 77
PI3K -0.18 0.24 -10000 0 -0.47 74 74
apoptosis 0.13 0.17 0.65 3 -10000 0 3
HRAS/GDP 0.002 0.023 0.23 2 -10000 0 2
PRKCD -0.21 0.27 -10000 0 -0.55 74 74
RAF1/14-3-3 E -0.12 0.16 -10000 0 -0.6 3 3
BAD/14-3-3 -0.14 0.18 -10000 0 -0.71 3 3
PRKCZ -0.18 0.24 -10000 0 -0.73 11 11
Crk/p130 Cas/Paxillin/FAK1 -0.14 0.18 -10000 0 -0.73 3 3
PTPN1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.23 0.29 -10000 0 -0.58 74 74
BCAR1 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.19 0.25 -10000 0 -0.5 74 74
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.19 0.24 -10000 0 -0.48 74 74
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 -0.19 0.24 -10000 0 -0.49 74 74
IRS1 -0.2 0.26 -10000 0 -0.53 74 74
IRS2 -0.2 0.26 -10000 0 -0.5 77 77
IGF-1R heterotetramer/IGF1 -0.27 0.35 -10000 0 -0.7 74 74
GRB2 0 0 -10000 0 -10000 0 0
PDPK1 -0.17 0.23 -10000 0 -0.44 73 73
YWHAE 0 0 -10000 0 -10000 0 0
PRKD1 -0.21 0.27 -10000 0 -0.55 75 75
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0 0 -10000 0 -10000 0 0
EPHB2 0.07 0.14 0.34 39 -10000 0 39
EFNB1 -0.004 0.12 -10000 0 -0.67 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.096 0.25 -10000 0 -0.5 43 43
Ephrin B2/EPHB1-2 -0.087 0.24 -10000 0 -0.53 42 42
neuron projection morphogenesis -0.099 0.23 -10000 0 -0.47 46 46
Ephrin B1/EPHB1-2/Tiam1 -0.1 0.27 -10000 0 -0.52 51 51
DNM1 0.002 0.17 0.34 14 -0.87 5 19
cell-cell signaling -0.001 0.002 -10000 0 -10000 0 0
MAP2K4 -0.18 0.36 -10000 0 -0.82 46 46
YES1 -0.25 0.45 -10000 0 -1 46 46
Ephrin B1/EPHB1-2/NCK2 -0.082 0.25 0.5 1 -0.5 46 47
PI3K -0.2 0.37 -10000 0 -0.85 46 46
mol:GDP -0.1 0.27 -10000 0 -0.52 51 51
ITGA2B 0.005 0.042 0.34 3 -10000 0 3
endothelial cell proliferation 0.001 0.015 -10000 0 -10000 0 0
FYN -0.25 0.45 -10000 0 -1 46 46
MAP3K7 -0.21 0.38 -10000 0 -0.87 46 46
FGR -0.25 0.45 -10000 0 -1 46 46
TIAM1 -0.032 0.16 -10000 0 -0.86 7 7
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
RGS3 0 0 -10000 0 -10000 0 0
cell adhesion -0.22 0.38 -10000 0 -0.8 52 52
LYN -0.25 0.45 -10000 0 -1 46 46
Ephrin B1/EPHB1-2/Src Family Kinases -0.24 0.42 -10000 0 -0.98 46 46
Ephrin B1/EPHB1-2 -0.23 0.4 -10000 0 -0.93 46 46
SRC -0.25 0.45 -10000 0 -1 46 46
ITGB3 -0.068 0.23 -10000 0 -0.86 15 15
EPHB1 -0.19 0.36 -10000 0 -0.86 42 42
EPHB4 0.002 0.025 0.34 1 -10000 0 1
RAC1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.001 0.015 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.049 0.18 -10000 0 -0.67 15 15
BLK -0.29 0.46 -10000 0 -1.1 46 46
HCK -0.25 0.45 -10000 0 -1.1 46 46
regulation of stress fiber formation 0.082 0.25 0.5 46 -0.49 1 47
MAPK8 -0.19 0.35 -10000 0 -0.74 54 54
Ephrin B1/EPHB1-2/RGS3 -0.083 0.25 -10000 0 -0.5 46 46
endothelial cell migration -0.18 0.33 -10000 0 -0.76 46 46
NCK2 0.002 0.025 0.34 1 -10000 0 1
PTPN13 -0.23 0.42 0.34 1 -0.98 46 47
regulation of focal adhesion formation 0.082 0.25 0.5 46 -0.49 1 47
chemotaxis 0.083 0.25 0.5 46 -10000 0 46
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
Rac1/GTP -0.097 0.24 -10000 0 -0.49 44 44
angiogenesis -0.22 0.4 -10000 0 -0.92 46 46
LCK -0.26 0.46 -10000 0 -1.1 46 46
EPHB forward signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Ephrin A5/EPHB2 -0.08 0.28 0.41 1 -0.58 42 43
cell-cell adhesion 0.19 0.26 0.52 62 -10000 0 62
Ephrin B/EPHB2/RasGAP -0.1 0.26 0.38 1 -0.5 51 52
ITSN1 0 0 -10000 0 -10000 0 0
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
SHC1 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.056 0.19 -10000 0 -0.59 21 21
Ephrin B1/EPHB1 -0.13 0.24 -10000 0 -0.59 42 42
HRAS/GDP -0.19 0.27 -10000 0 -0.55 59 59
Ephrin B/EPHB1/GRB7 -0.24 0.34 -10000 0 -0.64 74 74
Endophilin/SYNJ1 -0.11 0.21 -10000 0 -0.46 50 50
KRAS 0 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.24 0.34 -10000 0 -0.64 72 72
endothelial cell migration -0.004 0.072 -10000 0 -0.98 1 1
GRB2 0 0 -10000 0 -10000 0 0
GRB7 -0.002 0.1 0.34 4 -0.86 2 6
PAK1 -0.11 0.22 -10000 0 -0.48 50 50
HRAS 0.004 0.035 0.34 2 -10000 0 2
RRAS -0.11 0.22 -10000 0 -0.47 50 50
DNM1 0.002 0.17 0.34 14 -0.86 5 19
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.23 0.32 -10000 0 -0.61 72 72
lamellipodium assembly -0.19 0.26 -10000 0 -0.52 62 62
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.15 0.22 -10000 0 -0.49 42 42
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
EPHB2 0.07 0.14 0.34 39 -10000 0 39
EPHB3 -0.081 0.28 0.34 8 -0.86 21 29
EPHB1 -0.19 0.36 -10000 0 -0.86 42 42
EPHB4 0.002 0.025 0.34 1 -10000 0 1
mol:GDP -0.17 0.27 -10000 0 -0.58 45 45
Ephrin B/EPHB2 -0.1 0.25 0.37 1 -0.5 50 51
Ephrin B/EPHB3 -0.18 0.31 0.37 1 -0.61 59 60
JNK cascade -0.094 0.21 -10000 0 -0.48 42 42
Ephrin B/EPHB1 -0.24 0.34 -10000 0 -0.64 72 72
RAP1/GDP -0.15 0.22 -10000 0 -0.49 45 45
EFNB2 0 0 -10000 0 -10000 0 0
EFNB3 -0.22 0.38 0.34 1 -0.86 50 51
EFNB1 0 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.087 0.25 -10000 0 -0.53 42 42
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.19 0.3 -10000 0 -0.63 45 45
Rap1/GTP -0.2 0.27 -10000 0 -0.79 21 21
axon guidance -0.08 0.28 0.41 1 -0.58 42 43
MAPK3 -0.13 0.19 -10000 0 -0.56 20 20
MAPK1 -0.13 0.19 -10000 0 -0.56 20 20
Rac1/GDP -0.15 0.24 -10000 0 -0.52 45 45
actin cytoskeleton reorganization -0.14 0.2 -10000 0 -0.56 21 21
CDC42/GDP -0.15 0.24 -10000 0 -0.52 45 45
PI3K -0.004 0.074 -10000 0 -1 1 1
EFNA5 -0.16 0.38 0.34 14 -0.86 42 56
Ephrin B2/EPHB4 0.001 0.015 -10000 0 -10000 0 0
Ephrin B/EPHB2/Intersectin/N-WASP -0.07 0.17 -10000 0 -0.35 40 40
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.19 0.26 -10000 0 -0.75 21 21
PTK2 0.023 0.043 -10000 0 -10000 0 0
MAP4K4 -0.096 0.21 -10000 0 -0.49 42 42
SRC 0.002 0.025 0.34 1 -10000 0 1
KALRN -0.005 0.062 -10000 0 -0.86 1 1
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.14 0.22 -10000 0 -0.57 21 21
MAP2K1 -0.14 0.2 -10000 0 -0.6 20 20
WASL 0 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.085 0.24 -10000 0 -0.52 42 42
cell migration -0.13 0.24 -10000 0 -0.5 42 42
NRAS 0 0 -10000 0 -10000 0 0
SYNJ1 -0.11 0.22 -10000 0 -0.47 50 50
PXN 0 0 -10000 0 -10000 0 0
TF -0.14 0.23 -10000 0 -0.47 62 62
HRAS/GTP -0.2 0.3 -10000 0 -0.57 61 61
Ephrin B1/EPHB1-2 -0.087 0.25 -10000 0 -0.53 42 42
cell adhesion mediated by integrin 0.14 0.24 0.52 50 -10000 0 50
RAC1 0 0 -10000 0 -10000 0 0
mol:GTP -0.21 0.33 -10000 0 -0.59 73 73
RAC1-CDC42/GTP -0.23 0.31 -10000 0 -0.84 27 27
RASA1 -0.009 0.088 -10000 0 -0.86 2 2
RAC1-CDC42/GDP -0.15 0.22 -10000 0 -0.49 45 45
ruffle organization -0.2 0.27 -10000 0 -0.79 21 21
NCK1 0 0 -10000 0 -10000 0 0
receptor internalization -0.11 0.23 -10000 0 -0.46 53 53
Ephrin B/EPHB2/KALRN -0.1 0.25 0.38 1 -0.5 50 51
ROCK1 -0.056 0.17 -10000 0 -0.54 21 21
RAS family/GDP -0.14 0.19 -10000 0 -0.54 21 21
Rac1/GTP -0.21 0.29 -10000 0 -0.57 62 62
Ephrin B/EPHB1/Src/Paxillin -0.17 0.24 -10000 0 -0.45 72 72
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.059 0.054 -10000 0 -0.12 83 83
BUB1B 0.11 0.068 0.17 82 -10000 0 82
PLK1 0.058 0.031 0.099 45 -10000 0 45
PLK1S1 0.033 0.014 -10000 0 -10000 0 0
KIF2A 0.059 0.027 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.058 0.031 0.099 45 -10000 0 45
GOLGA2 0 0 -10000 0 -10000 0 0
Hec1/SPC24 0.26 0.19 0.38 128 -10000 0 128
WEE1 0.063 0.034 -10000 0 -10000 0 0
cytokinesis 0.15 0.099 0.24 92 -0.23 1 93
PP2A-alpha B56 0 0 -10000 0 -10000 0 0
AURKA 0.063 0.053 0.14 54 -10000 0 54
PICH/PLK1 0.12 0.12 0.28 55 -10000 0 55
CENPE 0.079 0.047 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.058 0.027 -10000 0 -10000 0 0
PPP2CA 0 0 -10000 0 -10000 0 0
FZR1 0 0 -10000 0 -10000 0 0
TPX2 0.047 0.043 0.15 25 -10000 0 25
PAK1 0 0 -10000 0 -10000 0 0
SPC24 0.15 0.17 0.34 83 -10000 0 83
FBXW11 0 0 -10000 0 -10000 0 0
CLSPN 0.079 0.068 0.17 69 -10000 0 69
GORASP1 0 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.029 0.014 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0.001 0.002 -10000 0 -10000 0 0
STAG2 0 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0 0 -10000 0 -10000 0 0
spindle elongation 0.058 0.031 0.099 45 -10000 0 45
ODF2 0.003 0.005 -10000 0 -10000 0 0
BUB1 0.15 0.1 -10000 0 -10000 0 0
TPT1 0.033 0.014 -10000 0 -10000 0 0
CDC25C 0.14 0.074 0.18 141 -10000 0 141
CDC25B 0.011 0.026 0.35 1 -10000 0 1
SGOL1 0.059 0.054 0.12 83 -10000 0 83
RHOA 0 0 -10000 0 -10000 0 0
CCNB1/CDK1 0.1 0.11 0.41 1 -10000 0 1
CDC14B -0.022 0.13 -10000 0 -0.69 7 7
CDC20 0.24 0.16 0.34 134 -10000 0 134
PLK1/PBIP1 0.019 0.052 0.17 16 -10000 0 16
mitosis -0.004 0.007 -10000 0 -10000 0 0
FBXO5 0.051 0.023 -10000 0 -10000 0 0
CDC2 0.006 0.005 0.012 94 -10000 0 94
NDC80 0.22 0.16 0.34 126 -10000 0 126
metaphase plate congression 0.04 0.02 -10000 0 -10000 0 0
ERCC6L 0.11 0.12 0.27 55 -10000 0 55
NLP/gamma Tubulin 0.034 0.015 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.033 0.014 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.001 0.001 -10000 0 -10000 0 0
PPP1R12A 0 0 -10000 0 -10000 0 0
interphase -0.001 0.001 -10000 0 -10000 0 0
PLK1/PRC1-2 0.28 0.2 0.4 134 -10000 0 134
GRASP65/GM130/RAB1/GTP/PLK1 0 0 -10000 0 -10000 0 0
RAB1A 0 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.05 0.027 -10000 0 -10000 0 0
mitotic prometaphase 0.001 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.069 0.065 -10000 0 -10000 0 0
microtubule-based process 0.19 0.13 0.28 133 -10000 0 133
Golgi organization 0.058 0.031 0.099 45 -10000 0 45
Cohesin/SA2 0 0 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0 -10000 0 -10000 0 0
KIF20A 0.24 0.16 0.34 133 -10000 0 133
APC/C/CDC20 0.2 0.13 0.28 134 -10000 0 134
PPP2R1A 0 0 -10000 0 -10000 0 0
chromosome segregation 0.019 0.052 0.16 16 -10000 0 16
PRC1 0.17 0.17 0.34 94 -10000 0 94
ECT2 0.071 0.041 -10000 0 -10000 0 0
C13orf34 0.051 0.025 -10000 0 -10000 0 0
NUDC 0.04 0.02 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.11 0.068 0.17 82 -10000 0 82
spindle assembly 0.047 0.022 -10000 0 -10000 0 0
spindle stabilization 0.033 0.014 -10000 0 -10000 0 0
APC/C/HCDH1 -0.022 0.11 -10000 0 -0.59 7 7
MKLP2/PLK1 0.2 0.13 0.28 133 -10000 0 133
CCNB1 0.17 0.17 0.34 94 -10000 0 94
PPP1CB 0 0 -10000 0 -10000 0 0
BTRC 0 0 -10000 0 -10000 0 0
ROCK2 0.03 0.095 -10000 0 -0.48 6 6
TUBG1 0.033 0.014 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.063 0.065 0.22 1 -10000 0 1
MLF1IP 0.022 0.052 -10000 0 -10000 0 0
INCENP 0.003 0.025 0.34 1 -10000 0 1
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.18 0.3 -10000 0 -0.49 71 71
FZD6 0 0 -10000 0 -10000 0 0
WNT6 0.014 0.068 0.34 8 -10000 0 8
WNT4 -0.07 0.33 0.34 24 -0.86 25 49
FZD3 -0.014 0.11 -10000 0 -0.86 3 3
WNT5A -0.074 0.26 0.34 4 -0.86 18 22
WNT11 -0.24 0.39 -10000 0 -0.86 54 54
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.005 0.008 -10000 0 -10000 0 0
RAS family/GTP -0.13 0.16 0.3 1 -0.41 4 5
NFATC4 -0.12 0.17 -10000 0 -0.32 77 77
ERBB2IP 0.006 0.007 -10000 0 -10000 0 0
HSP90 (dimer) 0 0 -10000 0 -10000 0 0
mammary gland morphogenesis -0.18 0.22 -10000 0 -0.44 78 78
JUN -0.051 0.08 -10000 0 -0.46 2 2
HRAS 0.004 0.035 0.34 2 -10000 0 2
DOCK7 -0.17 0.2 -10000 0 -0.41 78 78
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.22 0.26 -10000 0 -0.53 78 78
AKT1 0.003 0.004 -10000 0 -10000 0 0
BAD 0.01 0.008 -10000 0 -10000 0 0
MAPK10 -0.091 0.12 0.17 1 -0.39 9 10
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.19 0.24 -10000 0 -0.47 78 78
RAF1 -0.1 0.16 -10000 0 -0.4 4 4
ErbB2/ErbB3/neuregulin 2 0.031 0.12 -10000 0 -0.53 4 4
STAT3 -0.002 0.017 -10000 0 -10000 0 0
cell migration -0.072 0.12 -10000 0 -0.31 10 10
mol:PI-3-4-5-P3 -0.003 0.004 -10000 0 -10000 0 0
cell proliferation -0.2 0.23 -10000 0 -0.53 36 36
FOS -0.26 0.28 0.33 1 -0.54 89 90
NRAS 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.18 0.22 -10000 0 -0.44 78 78
MAPK3 -0.15 0.19 -10000 0 -0.44 36 36
MAPK1 -0.15 0.19 -10000 0 -0.44 36 36
JAK2 -0.17 0.21 -10000 0 -0.42 78 78
NF2 -0.01 0.012 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.16 0.19 -10000 0 -0.38 78 78
NRG1 -0.34 0.42 -10000 0 -0.86 76 76
GRB2/SOS1 0 0 -10000 0 -10000 0 0
MAPK8 -0.16 0.18 -10000 0 -0.36 84 84
MAPK9 -0.083 0.1 -10000 0 -0.3 2 2
ERBB2 -0.007 0.07 -10000 0 -0.69 2 2
ERBB3 -0.009 0.088 -10000 0 -0.86 2 2
SHC1 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
apoptosis -0.003 0.011 -10000 0 -10000 0 0
STAT3 (dimer) -0.002 0.017 -10000 0 -10000 0 0
RNF41 0.007 0.011 -10000 0 -10000 0 0
FRAP1 0.005 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.12 0.14 -10000 0 -0.29 73 73
ErbB2/ErbB2/HSP90 (dimer) -0.006 0.061 -10000 0 -0.6 2 2
CHRNA1 -0.11 0.15 0.37 1 -0.34 14 15
myelination -0.11 0.18 -10000 0 -0.32 78 78
PPP3CB -0.16 0.19 -10000 0 -0.38 78 78
KRAS 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.13 0.16 -10000 0 -0.33 73 73
NRG2 0.075 0.14 0.34 42 -10000 0 42
mol:GDP -0.16 0.19 -10000 0 -0.38 78 78
SOS1 0 0 -10000 0 -10000 0 0
MAP2K2 -0.092 0.16 -10000 0 -0.4 4 4
SRC 0.002 0.025 0.34 1 -10000 0 1
mol:cAMP -0.002 0.003 -10000 0 -10000 0 0
PTPN11 -0.17 0.2 -10000 0 -0.41 78 78
MAP2K1 -0.18 0.2 -10000 0 -0.49 37 37
heart morphogenesis -0.18 0.22 -10000 0 -0.44 78 78
RAS family/GDP -0.13 0.16 -10000 0 -0.42 3 3
GRB2 0 0 -10000 0 -10000 0 0
PRKACA -0.014 0.016 -10000 0 -10000 0 0
CHRNE -0.005 0.03 -10000 0 -0.25 2 2
HSP90AA1 0 0 -10000 0 -10000 0 0
activation of caspase activity -0.003 0.004 -10000 0 -10000 0 0
nervous system development -0.18 0.22 -10000 0 -0.44 78 78
CDC42 0 0 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.041 0.14 0.36 1 -0.52 11 12
PTK2B 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.046 0.25 0.53 1 -0.69 14 15
EDN1 -0.038 0.14 -10000 0 -0.64 7 7
EDN3 0.009 0.054 0.34 5 -10000 0 5
EDN2 -0.065 0.25 0.34 4 -0.86 16 20
HRAS/GDP -0.15 0.26 0.35 1 -0.66 31 32
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.081 0.21 0.32 1 -0.48 30 31
ADCY4 -0.024 0.12 -10000 0 -0.49 7 7
ADCY5 -0.11 0.24 -10000 0 -0.55 37 37
ADCY6 -0.024 0.12 -10000 0 -0.49 7 7
ADCY7 -0.024 0.12 -10000 0 -0.49 7 7
ADCY1 -0.19 0.28 -10000 0 -0.54 70 70
ADCY2 -0.021 0.13 0.35 2 -0.49 7 9
ADCY3 -0.023 0.12 -10000 0 -0.49 7 7
ADCY8 0 0.15 0.3 4 -0.5 7 11
ADCY9 -0.024 0.12 -10000 0 -0.49 7 7
arachidonic acid secretion -0.22 0.33 0.47 1 -0.52 85 86
ETB receptor/Endothelin-1/Gq/GTP -0.11 0.29 -10000 0 -0.6 38 38
GNAO1 -0.4 0.43 -10000 0 -0.86 88 88
HRAS 0.004 0.035 0.34 2 -10000 0 2
ETA receptor/Endothelin-1/G12/GTP -0.036 0.14 0.51 1 -0.51 9 10
ETA receptor/Endothelin-1/Gs/GTP -0.008 0.15 0.48 1 -0.52 7 8
mol:GTP -0.001 0.007 -10000 0 -10000 0 0
COL3A1 -0.06 0.24 0.47 3 -0.88 12 15
EDNRB -0.065 0.23 -10000 0 -0.86 15 15
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.056 0.21 -10000 0 -0.81 10 10
CYSLTR1 -0.053 0.19 -10000 0 -0.72 11 11
SLC9A1 -0.024 0.079 0.27 1 -0.31 6 7
mol:GDP -0.14 0.31 0.37 1 -0.67 37 38
SLC9A3 -0.04 0.27 0.4 2 -0.79 17 19
RAF1 -0.21 0.34 -10000 0 -0.73 40 40
JUN -0.065 0.28 0.46 1 -0.79 17 18
JAK2 -0.044 0.15 0.36 1 -0.54 11 12
mol:IP3 -0.12 0.28 0.3 1 -0.62 37 38
ETA receptor/Endothelin-1 -0.053 0.17 0.45 3 -0.61 11 14
PLCB1 0.014 0.068 0.34 8 -10000 0 8
PLCB2 -0.022 0.14 -10000 0 -0.87 5 5
ETA receptor/Endothelin-3 -0.006 0.063 0.33 1 -10000 0 1
FOS -0.46 0.54 -10000 0 -1 92 92
Gai/GDP -0.33 0.42 -10000 0 -0.77 88 88
CRK 0 0 -10000 0 -10000 0 0
mol:Ca ++ -0.11 0.31 0.4 1 -0.82 24 25
BCAR1 0 0.001 -10000 0 -10000 0 0
PRKCB1 -0.11 0.27 0.29 1 -0.6 37 38
GNAQ -0.003 0.063 -10000 0 -0.87 1 1
GNAZ 0.16 0.17 0.34 91 -10000 0 91
GNAL 0.059 0.13 0.34 33 -10000 0 33
Gs family/GDP -0.13 0.26 0.26 10 -0.62 31 41
ETA receptor/Endothelin-1/Gq/GTP -0.084 0.22 0.38 1 -0.5 34 35
MAPK14 -0.081 0.24 -10000 0 -0.59 27 27
TRPC6 -0.05 0.26 0.53 1 -0.73 14 15
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.009 0.088 -10000 0 -0.86 2 2
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.11 0.25 -10000 0 -0.52 39 39
ETB receptor/Endothelin-2 -0.1 0.26 -10000 0 -0.69 30 30
ETB receptor/Endothelin-3 -0.044 0.19 -10000 0 -0.67 15 15
ETB receptor/Endothelin-1 -0.07 0.23 -10000 0 -0.75 17 17
MAPK3 -0.38 0.47 -10000 0 -0.84 92 92
MAPK1 -0.38 0.47 -10000 0 -0.84 92 92
Rac1/GDP -0.16 0.26 0.35 1 -0.66 31 32
cAMP biosynthetic process -0.079 0.2 -10000 0 -0.5 25 25
MAPK8 -0.083 0.31 0.48 1 -0.75 24 25
SRC 0.002 0.025 0.34 1 -10000 0 1
ETB receptor/Endothelin-1/Gi/GTP -0.14 0.23 0.22 1 -0.48 34 35
p130Cas/CRK/Src/PYK2 -0.1 0.3 0.43 1 -0.68 30 31
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.16 0.26 0.35 1 -0.66 31 32
COL1A2 -0.066 0.23 0.47 3 -0.71 14 17
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.062 0.19 0.33 1 -0.67 16 17
mol:DAG -0.13 0.28 0.3 1 -0.62 37 38
MAP2K2 -0.28 0.38 -10000 0 -0.63 92 92
MAP2K1 -0.28 0.38 -10000 0 -0.63 92 92
EDNRA -0.02 0.081 0.54 1 -0.34 2 3
positive regulation of muscle contraction -0.033 0.12 0.32 1 -0.52 7 8
Gq family/GDP -0.19 0.3 -10000 0 -0.71 41 41
HRAS/GTP -0.16 0.32 0.31 1 -0.64 43 44
PRKCH -0.11 0.27 0.3 1 -0.61 35 36
RAC1 0 0 -10000 0 -10000 0 0
PRKCA -0.11 0.27 -10000 0 -0.65 30 30
PRKCB -0.15 0.33 -10000 0 -0.66 46 46
PRKCE -0.11 0.28 -10000 0 -0.67 30 30
PRKCD -0.11 0.27 -10000 0 -0.66 30 30
PRKCG -0.11 0.27 -10000 0 -0.66 30 30
regulation of vascular smooth muscle contraction -0.53 0.62 -10000 0 -1.2 92 92
PRKCQ -0.12 0.3 -10000 0 -0.68 34 34
PLA2G4A -0.24 0.37 0.48 1 -0.58 84 85
GNA14 -0.13 0.32 -10000 0 -0.87 30 30
GNA15 0.004 0.025 0.34 1 -10000 0 1
GNA12 0 0 -10000 0 -10000 0 0
GNA11 -0.021 0.14 -10000 0 -0.87 5 5
Rac1/GTP -0.036 0.14 0.51 1 -0.55 7 8
MMP1 0.09 0.14 0.46 5 -10000 0 5
Calcium signaling in the CD4+ TCR pathway

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
NFATC1 -0.006 0.064 -10000 0 -0.6 2 2
NFATC2 -0.1 0.23 -10000 0 -0.6 32 32
NFATC3 0 0.021 -10000 0 -10000 0 0
CD40LG -0.34 0.36 0.48 3 -0.78 64 67
PTGS2 -0.44 0.46 0.42 3 -1 69 72
JUNB -0.045 0.19 -10000 0 -0.86 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.013 -10000 0 -10000 0 0
CaM/Ca2+ -0.001 0.013 -10000 0 -10000 0 0
CALM1 0 0.006 -10000 0 -10000 0 0
JUN -0.018 0.12 -10000 0 -0.87 4 4
mol:Ca2+ -0.003 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.001 -10000 0 -10000 0 0
FOSL1 -0.031 0.18 0.34 3 -0.86 8 11
CREM 0 0 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.11 0.24 0.4 3 -0.56 36 39
FOS -0.4 0.44 -10000 0 -0.87 89 89
IFNG -0.32 0.35 0.56 4 -0.74 63 67
AP-1/NFAT1-c-4 -0.41 0.46 0.64 4 -0.96 63 67
FASLG -0.34 0.36 0.53 3 -0.77 64 67
NFAT1-c-4/ICER1 -0.093 0.21 -10000 0 -0.54 32 32
IL2RA -0.33 0.36 0.56 4 -0.74 64 68
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSF2 -0.33 0.34 0.42 3 -0.74 63 66
JunB/Fra1/NFAT1-c-4 -0.13 0.26 0.43 1 -0.55 45 46
IL4 -0.33 0.34 0.42 3 -0.74 63 66
IL2 -0.017 0.023 -10000 0 -10000 0 0
IL3 -0.033 0.028 -10000 0 -10000 0 0
FKBP1A 0 0 -10000 0 -10000 0 0
BATF3 -0.007 0.091 0.34 1 -0.86 2 3
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.002 0.004 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.08 0.21 0.42 1 -0.58 28 29
fibroblast growth factor receptor signaling pathway -0.08 0.21 0.41 1 -0.58 28 29
LAMA1 -0.093 0.31 0.34 11 -0.86 25 36
PRNP -0.059 0.22 -10000 0 -0.86 13 13
GPC1/SLIT2 -0.065 0.23 0.48 1 -0.67 22 23
SMAD2 -0.03 0.12 -10000 0 -0.53 11 11
GPC1/PrPc/Cu2+ -0.072 0.22 -10000 0 -0.7 20 20
GPC1/Laminin alpha1 -0.11 0.29 0.48 1 -0.7 34 35
TDGF1 -0.01 0.29 0.34 35 -0.86 16 51
CRIPTO/GPC1 -0.054 0.27 -10000 0 -0.68 26 26
APP/GPC1 -0.044 0.17 -10000 0 -0.67 13 13
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.062 0.22 -10000 0 -0.6 26 26
FLT1 0 0 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 -0.033 0.14 -10000 0 -0.58 11 11
SERPINC1 -0.14 0.31 -10000 0 -0.86 30 30
FYN -0.062 0.22 -10000 0 -0.6 26 26
FGR -0.066 0.22 -10000 0 -0.6 27 27
positive regulation of MAPKKK cascade -0.1 0.27 -10000 0 -0.65 30 30
SLIT2 -0.034 0.22 0.34 9 -0.86 11 20
GPC1/NRG -0.3 0.36 -10000 0 -0.71 81 81
NRG1 -0.34 0.42 -10000 0 -0.86 76 76
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.033 0.14 -10000 0 -0.58 11 11
LYN -0.062 0.22 -10000 0 -0.6 26 26
mol:Spermine -0.038 0.16 -10000 0 -0.68 11 11
cell growth -0.08 0.21 0.41 1 -0.58 28 29
BMP signaling pathway 0.048 0.2 0.86 11 -0.34 1 12
SRC -0.062 0.22 -10000 0 -0.6 26 26
TGFBR1 0 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.33 0.45 0.34 14 -0.86 78 92
GPC1 -0.048 0.2 0.34 1 -0.86 11 12
TGFBR1 (dimer) 0 0 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
BLK -0.19 0.33 -10000 0 -0.64 60 60
HCK -0.081 0.24 -10000 0 -0.61 31 31
FGF2 -0.064 0.24 0.34 2 -0.86 15 17
FGFR1 -0.005 0.095 0.34 2 -0.86 2 4
VEGFR1 homodimer 0 0 -10000 0 -10000 0 0
TGFBR2 0 0 -10000 0 -10000 0 0
cell death -0.044 0.17 -10000 0 -0.67 13 13
ATIII/GPC1 -0.14 0.28 -10000 0 -0.67 41 41
PLA2G2A/GPC1 -0.29 0.37 -10000 0 -0.7 85 85
LCK -0.083 0.25 -10000 0 -0.61 32 32
neuron differentiation -0.3 0.36 -10000 0 -0.71 81 81
PrPc/Cu2+ -0.046 0.17 -10000 0 -0.68 13 13
APP -0.009 0.088 -10000 0 -0.86 2 2
TGFBR2 (dimer) 0 0 -10000 0 -10000 0 0
LPA receptor mediated 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
GNB1/GNG2 -0.12 0.24 0.34 1 -0.57 41 42
NF kappa B1 p50/RelA/I kappa B alpha -0.046 0.089 -10000 0 -0.47 3 3
AP1 -0.32 0.37 -10000 0 -0.61 105 105
mol:PIP3 -0.11 0.19 -10000 0 -0.45 42 42
AKT1 -0.084 0.16 -10000 0 -0.39 36 36
PTK2B -0.047 0.15 -10000 0 -0.31 42 42
RHOA -0.022 0.068 -10000 0 -0.53 1 1
PIK3CB 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.008 0.093 -10000 0 -0.49 3 3
MAGI3 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
apoptosis -0.091 0.2 0.28 1 -0.44 44 45
HRAS/GDP 0.002 0.023 0.23 2 -10000 0 2
positive regulation of microtubule depolymerization -0.018 0.14 -10000 0 -0.47 4 4
NF kappa B1 p50/RelA -0.093 0.22 -10000 0 -0.55 21 21
endothelial cell migration -0.14 0.3 0.34 3 -0.65 44 47
ADCY4 -0.23 0.32 -10000 0 -0.73 44 44
ADCY5 -0.3 0.4 -10000 0 -0.85 55 55
ADCY6 -0.23 0.32 -10000 0 -0.73 44 44
ADCY7 -0.23 0.32 -10000 0 -0.73 44 44
ADCY1 -0.37 0.43 -10000 0 -0.86 70 70
ADCY2 -0.23 0.32 -10000 0 -0.74 44 44
ADCY3 -0.23 0.32 -10000 0 -0.73 44 44
ADCY8 -0.22 0.32 -10000 0 -0.73 44 44
ADCY9 -0.23 0.32 -10000 0 -0.73 44 44
GSK3B -0.038 0.14 -10000 0 -0.37 15 15
arachidonic acid secretion -0.25 0.3 -10000 0 -0.56 71 71
GNG2 -0.005 0.062 -10000 0 -0.86 1 1
TRIP6 -0.006 0.071 -10000 0 -0.46 4 4
GNAO1 -0.4 0.38 -10000 0 -0.68 111 111
HRAS 0.004 0.035 0.34 2 -10000 0 2
NFKBIA -0.015 0.13 -10000 0 -0.55 3 3
GAB1 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.039 0.2 -10000 0 -0.98 8 8
JUN -0.018 0.12 -10000 0 -0.86 4 4
LPA/LPA2/NHERF2 0 0.088 -10000 0 -0.59 3 3
TIAM1 -0.047 0.24 -10000 0 -1.2 8 8
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
mol:IP3 0.008 0.095 -10000 0 -0.5 3 3
PLCB3 -0.005 0.071 -10000 0 -0.54 3 3
FOS -0.4 0.43 -10000 0 -0.86 89 89
positive regulation of mitosis -0.25 0.3 -10000 0 -0.56 71 71
LPA/LPA1-2-3 -0.096 0.27 0.42 4 -0.56 43 47
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0.001 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
stress fiber formation -0.059 0.18 -10000 0 -0.39 42 42
GNAZ -0.055 0.3 0.32 3 -0.57 44 47
EGFR/PI3K-beta/Gab1 -0.11 0.2 -10000 0 -0.47 42 42
positive regulation of dendritic cell cytokine production -0.095 0.27 0.41 4 -0.55 43 47
LPA/LPA2/MAGI-3 0.006 0.064 -10000 0 -0.59 1 1
ARHGEF1 -0.11 0.22 -10000 0 -0.52 41 41
GNAI2 -0.13 0.26 -10000 0 -0.59 44 44
GNAI3 -0.13 0.26 -10000 0 -0.59 44 44
GNAI1 -0.14 0.26 -10000 0 -0.6 45 45
LPA/LPA3 0.025 0.076 0.24 21 -10000 0 21
LPA/LPA2 0.006 0.072 0.23 9 -0.67 1 10
LPA/LPA1 -0.15 0.3 0.32 2 -0.67 44 46
HB-EGF/EGFR -0.014 0.15 -10000 0 -0.58 12 12
HBEGF 0.004 0.16 -10000 0 -0.67 9 9
mol:DAG 0.008 0.095 -10000 0 -0.5 3 3
cAMP biosynthetic process -0.32 0.37 -10000 0 -0.59 110 110
NFKB1 0 0 -10000 0 -10000 0 0
SRC 0.002 0.025 0.34 1 -10000 0 1
GNB1 0 0 -10000 0 -10000 0 0
LYN -0.015 0.13 -10000 0 -0.46 5 5
GNAQ 0.01 0.064 -10000 0 -0.46 2 2
LPAR2 0.012 0.096 0.34 9 -0.86 1 10
LPAR3 0.039 0.11 0.34 22 -10000 0 22
LPAR1 -0.19 0.36 0.38 2 -0.87 41 43
IL8 -0.2 0.28 0.34 3 -0.54 66 69
PTK2 -0.11 0.23 -10000 0 -0.53 41 41
Rac1/GDP 0 0 -10000 0 -10000 0 0
CASP3 -0.092 0.2 0.29 1 -0.45 44 45
EGFR -0.013 0.11 -10000 0 -0.86 3 3
PLCG1 -0.015 0.084 -10000 0 -0.36 4 4
PLD2 -0.11 0.23 -10000 0 -0.53 41 41
G12/G13 -0.12 0.24 0.34 1 -0.56 41 42
PI3K-beta -0.097 0.18 -10000 0 -0.45 37 37
cell migration -0.04 0.098 -10000 0 -0.28 12 12
SLC9A3R2 -0.009 0.088 -10000 0 -0.86 2 2
PXN -0.06 0.19 -10000 0 -0.4 42 42
HRAS/GTP -0.26 0.32 -10000 0 -0.58 71 71
RAC1 0 0 -10000 0 -10000 0 0
MMP9 0.024 0.23 0.34 34 -0.86 8 42
PRKCE -0.003 0.067 0.34 1 -0.86 1 2
PRKCD 0.014 0.09 -10000 0 -0.47 3 3
Gi(beta/gamma) -0.24 0.3 -10000 0 -0.71 44 44
mol:LPA -0.002 0.03 -10000 0 -0.22 3 3
TRIP6/p130 Cas/FAK1/Paxillin -0.095 0.22 -10000 0 -0.5 40 40
MAPKKK cascade -0.25 0.3 -10000 0 -0.56 71 71
contractile ring contraction involved in cytokinesis -0.005 0.074 -10000 0 -0.53 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.059 0.17 -10000 0 -0.44 30 30
GNA15 0.013 0.056 0.2 1 -0.46 1 2
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
MAPT -0.019 0.14 -10000 0 -0.48 4 4
GNA11 0.001 0.093 -10000 0 -0.46 6 6
Rac1/GTP -0.042 0.21 -10000 0 -1 8 8
MMP2 -0.14 0.3 0.34 3 -0.66 44 47
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.17 0.64 0.83 3 -1.3 36 39
IL23A -0.14 0.61 0.81 3 -1.3 33 36
NF kappa B1 p50/RelA/I kappa B alpha -0.28 0.46 -10000 0 -1.1 39 39
positive regulation of T cell mediated cytotoxicity -0.16 0.67 0.86 6 -1.3 39 45
ITGA3 -0.12 0.57 0.86 2 -1.2 29 31
IL17F -0.046 0.38 0.65 2 -0.74 29 31
IL12B 0.029 0.076 0.52 2 -10000 0 2
STAT1 (dimer) -0.3 0.53 0.7 3 -1.2 39 42
CD4 -0.14 0.6 0.82 2 -1.2 35 37
IL23 -0.18 0.56 0.78 3 -1.2 33 36
IL23R 0.035 0.14 0.54 1 -10000 0 1
IL1B -0.19 0.69 0.82 3 -1.4 37 40
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.12 0.55 0.89 2 -1.1 32 34
TYK2 0.02 0.037 -10000 0 -10000 0 0
STAT4 -0.032 0.16 -10000 0 -0.86 7 7
STAT3 0 0 -10000 0 -10000 0 0
IL18RAP -0.062 0.22 -10000 0 -0.86 14 14
IL12RB1 -0.017 0.19 -10000 0 -0.9 8 8
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
IL12Rbeta1/TYK2 -0.017 0.15 -10000 0 -0.71 8 8
IL23R/JAK2 0.039 0.17 0.57 1 -0.69 1 2
positive regulation of chronic inflammatory response -0.16 0.67 0.86 6 -1.3 39 45
natural killer cell activation -0.003 0.013 -10000 0 -0.05 3 3
JAK2 0.032 0.084 -10000 0 -0.9 1 1
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
NFKB1 0.001 0.005 -10000 0 -10000 0 0
RELA 0.001 0.005 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.16 0.53 0.77 3 -1.1 33 36
ALOX12B -0.12 0.55 0.82 3 -1.1 33 36
CXCL1 -0.31 0.75 0.85 4 -1.3 64 68
T cell proliferation -0.16 0.67 0.86 6 -1.3 39 45
NFKBIA 0.001 0.005 -10000 0 -10000 0 0
IL17A -0.008 0.32 0.61 3 -0.58 24 27
PI3K -0.29 0.49 -10000 0 -1.2 39 39
IFNG -0.002 0.056 0.19 6 -0.1 19 25
STAT3 (dimer) -0.27 0.45 -10000 0 -1.1 39 39
IL18R1 -0.13 0.31 -10000 0 -0.86 29 29
IL23/IL23R/JAK2/TYK2/SOCS3 -0.076 0.45 0.66 6 -0.96 26 32
IL18/IL18R -0.13 0.3 -10000 0 -0.7 38 38
macrophage activation -0.01 0.024 0.062 9 -0.045 30 39
TNF -0.16 0.63 0.82 3 -1.3 33 36
STAT3/STAT4 -0.29 0.49 -10000 0 -1.2 39 39
STAT4 (dimer) -0.3 0.54 0.7 3 -1.2 39 42
IL18 -0.015 0.13 0.34 1 -0.86 4 5
IL19 -0.12 0.55 0.82 2 -1.2 30 32
STAT5A (dimer) -0.29 0.53 0.66 4 -1.2 39 43
STAT1 0 0 -10000 0 -10000 0 0
SOCS3 -0.11 0.29 -10000 0 -0.86 25 25
CXCL9 -0.11 0.56 0.89 4 -1.2 29 33
MPO -0.14 0.58 0.82 2 -1.2 37 39
positive regulation of humoral immune response -0.16 0.67 0.86 6 -1.3 39 45
IL23/IL23R/JAK2/TYK2 -0.19 0.75 0.86 6 -1.4 39 45
IL6 -0.21 0.67 0.8 1 -1.3 45 46
STAT5A 0.002 0.025 0.34 1 -10000 0 1
IL2 0.005 0.014 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.003 0.013 -10000 0 -0.05 3 3
CD3E -0.13 0.58 0.89 2 -1.1 37 39
keratinocyte proliferation -0.16 0.67 0.86 6 -1.3 39 45
NOS2 -0.11 0.55 0.82 3 -1.1 34 37
Signaling events mediated by the Hedgehog family

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
TGFB2 0.072 0.25 0.58 9 -0.65 13 22
IHH 0.014 0.21 0.4 9 -0.86 8 17
SHH Np/Cholesterol/GAS1 -0.12 0.24 -10000 0 -0.58 38 38
LRPAP1 0 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.11 0.24 0.57 38 -10000 0 38
SMO/beta Arrestin2 -0.005 0.23 0.36 1 -0.72 14 15
SMO -0.005 0.24 0.41 1 -0.77 14 15
AKT1 0.008 0.15 0.27 1 -0.47 8 9
ARRB2 0 0 -10000 0 -10000 0 0
BOC 0.011 0.059 0.34 6 -10000 0 6
ADRBK1 0 0 -10000 0 -10000 0 0
heart looping -0.003 0.24 0.41 1 -0.75 14 15
STIL 0.009 0.22 0.38 4 -0.62 14 18
DHH N/PTCH2 -0.001 0.054 -10000 0 -0.67 1 1
DHH N/PTCH1 0.006 0.21 0.38 2 -0.66 13 15
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
DHH 0.002 0.025 0.34 1 -10000 0 1
PTHLH 0.078 0.26 0.56 9 -0.71 13 22
determination of left/right symmetry -0.003 0.24 0.41 1 -0.75 14 15
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
skeletal system development 0.078 0.26 0.56 9 -0.7 13 22
IHH N/Hhip -0.34 0.39 0.29 1 -0.73 94 95
DHH N/Hhip -0.31 0.34 -10000 0 -0.67 90 90
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.003 0.24 0.41 1 -0.75 14 15
pancreas development -0.4 0.43 0.34 1 -0.86 90 91
HHAT -0.001 0.072 0.34 2 -0.86 1 3
PI3K -0.006 0.087 -10000 0 -1.2 1 1
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.14 0.32 -10000 0 -0.86 31 31
somite specification -0.003 0.24 0.41 1 -0.75 14 15
SHH Np/Cholesterol/PTCH1 -0.017 0.22 0.35 1 -0.6 19 20
SHH Np/Cholesterol/PTCH2 -0.029 0.14 -10000 0 -0.59 10 10
SHH Np/Cholesterol/Megalin -0.087 0.23 -10000 0 -0.56 35 35
SHH -0.033 0.16 -10000 0 -0.73 9 9
catabolic process 0.035 0.24 0.39 9 -0.7 14 23
SMO/Vitamin D3 -0.012 0.25 0.35 6 -0.64 20 26
SHH Np/Cholesterol/Hhip -0.28 0.29 -10000 0 -0.56 96 96
LRP2 -0.096 0.32 0.34 12 -0.86 26 38
receptor-mediated endocytosis -0.059 0.26 0.34 1 -0.71 17 18
SHH Np/Cholesterol/BOC -0.021 0.14 -10000 0 -0.59 9 9
SHH Np/Cholesterol/CDO -0.027 0.13 -10000 0 -0.6 9 9
mesenchymal cell differentiation 0.28 0.29 0.56 96 -10000 0 96
mol:Vitamin D3 -0.007 0.23 0.35 6 -0.6 19 25
IHH N/PTCH2 0 0.14 0.29 1 -0.59 9 10
CDON 0 0 -10000 0 -10000 0 0
IHH N/PTCH1 0.024 0.25 0.44 11 -0.71 14 25
Megalin/LRPAP1 -0.077 0.24 -10000 0 -0.67 26 26
PTCH2 -0.003 0.067 0.34 1 -0.86 1 2
SHH Np/Cholesterol -0.026 0.14 -10000 0 -0.6 9 9
PTCH1 0.035 0.24 0.39 9 -0.7 14 23
HHIP -0.4 0.43 0.34 1 -0.86 90 91
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 -0.018 0.12 -10000 0 -0.87 4 4
GNB1/GNG2 -0.067 0.089 -10000 0 -0.19 58 58
AKT1 -0.032 0.12 0.23 1 -0.21 57 58
EGF 0.08 0.14 0.34 45 -10000 0 45
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR -0.053 0.14 -10000 0 -0.46 13 13
mol:Ca2+ -0.059 0.17 -10000 0 -0.31 59 59
LYN -0.05 0.14 -10000 0 -0.47 12 12
RhoA/GTP -0.04 0.058 -10000 0 -0.14 6 6
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.066 0.19 -10000 0 -0.35 58 58
GNG2 -0.005 0.062 -10000 0 -0.86 1 1
ARRB2 0 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.032 0.13 -10000 0 -0.5 8 8
G beta5/gamma2 -0.088 0.12 -10000 0 -0.26 58 58
PRKCH -0.071 0.2 -10000 0 -0.36 58 58
DNM1 0.002 0.17 0.34 14 -0.86 5 19
TXA2/TP beta/beta Arrestin3 -0.01 0.065 -10000 0 -0.33 5 5
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.05 0.2 -10000 0 -0.86 11 11
G12 family/GTP -0.099 0.14 -10000 0 -0.31 58 58
ADRBK1 0 0 -10000 0 -10000 0 0
ADRBK2 0.006 0.087 0.34 6 -0.86 1 7
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.051 0.16 0.39 21 -10000 0 21
mol:NADP -0.005 0.062 -10000 0 -0.86 1 1
RAB11A 0 0 -10000 0 -10000 0 0
PRKG1 -0.032 0.16 -10000 0 -0.86 7 7
mol:IP3 -0.081 0.21 -10000 0 -0.39 59 59
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.12 0.28 -10000 0 -0.53 59 59
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.13 0.22 -10000 0 -0.48 48 48
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.062 0.16 -10000 0 -0.5 16 16
RHOA 0 0 -10000 0 -10000 0 0
PTGIR -0.063 0.22 -10000 0 -0.86 14 14
PRKCB1 -0.081 0.21 -10000 0 -0.38 59 59
GNAQ -0.005 0.062 -10000 0 -0.86 1 1
mol:L-citrulline -0.005 0.062 -10000 0 -0.86 1 1
TXA2/TXA2-R family -0.12 0.29 -10000 0 -0.55 58 58
LCK -0.063 0.16 -10000 0 -0.5 17 17
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.069 0.18 -10000 0 -0.45 29 29
TXA2-R family/G12 family/GDP/G beta/gamma -0.017 0.047 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.068 0.18 -10000 0 -0.45 29 29
MAPK14 -0.033 0.13 -10000 0 -0.23 57 57
TGM2/GTP -0.096 0.24 -10000 0 -0.44 59 59
MAPK11 -0.032 0.13 -10000 0 -0.24 28 28
ARHGEF1 -0.056 0.083 0.18 1 -0.2 10 11
GNAI2 0 0 -10000 0 -10000 0 0
JNK cascade -0.081 0.22 -10000 0 -0.4 58 58
RAB11/GDP 0 0 -10000 0 -10000 0 0
ICAM1 -0.051 0.16 -10000 0 -0.28 58 58
cAMP biosynthetic process -0.076 0.2 -10000 0 -0.36 59 59
Gq family/GTP/EBP50 -0.053 0.14 -10000 0 -0.3 34 34
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.049 0.14 -10000 0 -0.47 12 12
GNB5 0.002 0.025 0.34 1 -10000 0 1
GNB1 0 0 -10000 0 -10000 0 0
EGF/EGFR -0.022 0.14 -10000 0 -0.35 17 17
VCAM1 -0.064 0.18 -10000 0 -0.33 57 57
TP beta/Gq family/GDP/G beta5/gamma2 -0.032 0.13 -10000 0 -0.5 8 8
platelet activation -0.046 0.18 -10000 0 -0.31 58 58
PGI2/IP -0.05 0.18 -10000 0 -0.68 14 14
PRKACA -0.057 0.17 -10000 0 -0.49 22 22
Gq family/GDP/G beta5/gamma2 -0.031 0.13 -10000 0 -0.49 8 8
TXA2/TP beta/beta Arrestin2 -0.009 0.13 0.24 6 -0.69 5 11
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.079 0.21 -10000 0 -0.52 29 29
mol:DAG -0.093 0.23 -10000 0 -0.44 58 58
EGFR -0.014 0.11 -10000 0 -0.86 3 3
TXA2/TP alpha -0.11 0.27 -10000 0 -0.5 59 59
Gq family/GTP -0.055 0.14 -10000 0 -0.33 34 34
YES1 -0.05 0.14 -10000 0 -0.47 12 12
GNAI2/GTP -0.059 0.16 -10000 0 -0.56 12 12
PGD2/DP -0.039 0.16 -10000 0 -0.68 11 11
SLC9A3R1 -0.005 0.062 -10000 0 -0.86 1 1
FYN -0.05 0.14 -10000 0 -0.47 12 12
mol:NO -0.005 0.062 -10000 0 -0.86 1 1
GNA15 0.002 0.025 0.34 1 -10000 0 1
PGK/cGMP -0.025 0.12 -10000 0 -0.59 8 8
RhoA/GDP 0 0 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.078 0.21 -10000 0 -0.68 14 14
NOS3 -0.005 0.062 -10000 0 -0.86 1 1
RAC1 0 0 -10000 0 -10000 0 0
PRKCA -0.071 0.2 -10000 0 -0.36 58 58
PRKCB -0.094 0.23 -10000 0 -0.4 63 63
PRKCE -0.071 0.2 -10000 0 -0.36 58 58
PRKCD -0.08 0.21 -10000 0 -0.39 58 58
PRKCG -0.083 0.21 -10000 0 -0.39 58 58
muscle contraction -0.11 0.27 -10000 0 -0.5 58 58
PRKCZ -0.076 0.2 -10000 0 -0.36 61 61
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta -0.066 0.2 -10000 0 -0.52 21 21
PRKCQ -0.08 0.21 -10000 0 -0.38 60 60
MAPKKK cascade -0.11 0.26 -10000 0 -0.47 58 58
SELE -0.09 0.22 0.29 1 -0.41 58 59
TP beta/GNAI2/GDP/G beta/gamma -0.069 0.19 -10000 0 -0.65 12 12
ROCK1 0 0 -10000 0 -10000 0 0
GNA14 -0.14 0.31 -10000 0 -0.86 30 30
chemotaxis -0.14 0.32 -10000 0 -0.62 58 58
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.023 0.14 -10000 0 -0.86 5 5
Rac1/GTP 0 0 -10000 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.001 0.017 -10000 0 -10000 0 0
CRKL -0.11 0.15 -10000 0 -0.36 1 1
mol:PIP3 -0.002 0.079 0.76 2 -10000 0 2
AKT1 0.011 0.048 0.48 2 -10000 0 2
PTK2B 0 0 -10000 0 -10000 0 0
RAPGEF1 -0.1 0.15 -10000 0 -0.34 1 1
RANBP10 0 0 -10000 0 -10000 0 0
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
HGF/MET/SHIP2 -0.27 0.29 -10000 0 -0.58 90 90
MAP3K5 -0.13 0.21 -10000 0 -0.64 17 17
HGF/MET/CIN85/CBL/ENDOPHILINS -0.25 0.27 -10000 0 -0.54 90 90
AP1 -0.29 0.32 -10000 0 -0.63 89 89
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
apoptosis -0.4 0.44 -10000 0 -0.86 89 89
STAT3 (dimer) -0.16 0.17 -10000 0 -0.34 91 91
GAB1/CRKL/SHP2/PI3K -0.12 0.13 -10000 0 -0.9 1 1
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.12 0.13 -10000 0 -0.34 1 1
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0 0 -10000 0 -10000 0 0
PTEN -0.009 0.088 -10000 0 -0.86 2 2
ELK1 -0.011 0.017 -10000 0 -10000 0 0
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.093 0.099 -10000 0 -0.23 1 1
PAK1 0.017 0.044 0.44 2 -10000 0 2
HGF/MET/RANBP10 -0.27 0.29 -10000 0 -0.58 90 90
HRAS -0.2 0.21 -10000 0 -0.42 89 89
DOCK1 -0.11 0.17 -10000 0 -0.62 5 5
GAB1 -0.13 0.16 -10000 0 -0.29 90 90
CRK -0.11 0.15 -10000 0 -0.36 1 1
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.28 0.3 -10000 0 -0.6 90 90
JUN -0.018 0.12 -10000 0 -0.86 4 4
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.13 0.14 -10000 0 -0.27 90 90
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
cell morphogenesis -0.13 0.2 -10000 0 -0.72 2 2
GRB2/SHC -0.11 0.11 -10000 0 -10000 0 0
FOS -0.4 0.43 -10000 0 -0.86 89 89
GLMN 0 0 -10000 0 -10000 0 0
cell motility -0.011 0.017 -10000 0 -10000 0 0
HGF/MET/MUC20 -0.28 0.3 -10000 0 -0.59 90 90
cell migration -0.1 0.11 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
CBL 0 0 -10000 0 -10000 0 0
MET/RANBP10 0.001 0.017 -10000 0 -10000 0 0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.17 0.18 -10000 0 -0.36 91 91
MET/MUC20 0.001 0.016 0.23 1 -10000 0 1
RAP1B -0.091 0.14 -10000 0 -10000 0 0
RAP1A -0.091 0.14 -10000 0 -10000 0 0
HGF/MET/RANBP9 -0.27 0.29 -10000 0 -0.58 90 90
RAF1 -0.17 0.22 -10000 0 -0.4 89 89
STAT3 -0.16 0.17 -10000 0 -0.34 91 91
cell proliferation -0.19 0.25 -10000 0 -0.45 90 90
RPS6KB1 -0.044 0.047 -10000 0 -10000 0 0
MAPK3 -0.011 0.013 -10000 0 -10000 0 0
MAPK1 -0.011 0.013 -10000 0 -10000 0 0
RANBP9 0 0 -10000 0 -10000 0 0
MAPK8 -0.11 0.2 -10000 0 -0.54 23 23
SRC -0.16 0.17 -10000 0 -0.33 90 90
PI3K -0.11 0.13 -10000 0 -0.97 1 1
MET/Glomulin 0.001 0.018 0.25 1 -10000 0 1
SOS1 0 0 -10000 0 -10000 0 0
MAP2K1 -0.15 0.2 -10000 0 -10000 0 0
MET 0.002 0.025 0.34 1 -10000 0 1
MAP4K1 -0.11 0.16 -10000 0 -0.52 5 5
PTK2 0 0 -10000 0 -10000 0 0
MAP2K2 -0.15 0.2 -10000 0 -10000 0 0
BAD 0.017 0.044 0.44 2 -10000 0 2
MAP2K4 -0.11 0.19 -10000 0 -0.57 17 17
SHP2/GRB2/SOS1/GAB1 -0.11 0.12 -10000 0 -10000 0 0
INPPL1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
SH3KBP1 0 0 -10000 0 -10000 0 0
HGS -0.12 0.12 -10000 0 -0.24 90 90
PLCgamma1/PKC 0 0 -10000 0 -10000 0 0
HGF -0.41 0.43 -10000 0 -0.86 90 90
RASA1 -0.009 0.088 -10000 0 -0.86 2 2
NCK1 0 0 -10000 0 -10000 0 0
PTPRJ 0 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.12 0.13 -10000 0 -10000 0 0
PDPK1 0.005 0.057 0.55 2 -10000 0 2
HGF/MET/SHIP -0.27 0.29 -10000 0 -0.58 90 90
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 -0.14 0.32 -10000 0 -0.86 32 32
GNB1/GNG2 -0.16 0.27 -10000 0 -0.76 20 20
mol:DAG -0.14 0.23 -10000 0 -0.66 20 20
PLCG1 -0.15 0.25 -10000 0 -0.7 20 20
YES1 -0.16 0.28 -10000 0 -0.46 71 71
FZD3 -0.014 0.11 -10000 0 -0.86 3 3
FZD6 0 0 -10000 0 -10000 0 0
G protein -0.15 0.25 -10000 0 -0.71 20 20
MAP3K7 -0.086 0.2 -10000 0 -0.52 20 20
mol:Ca2+ -0.14 0.22 -10000 0 -0.63 20 20
mol:IP3 -0.14 0.23 -10000 0 -0.66 20 20
NLK -0.008 0.012 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
CAMK2A -0.12 0.21 -10000 0 -0.58 20 20
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.18 0.3 -10000 0 -0.49 71 71
CSNK1A1 0 0 -10000 0 -10000 0 0
GNAS -0.16 0.28 -10000 0 -0.8 19 19
GO:0007205 -0.14 0.23 -10000 0 -0.65 20 20
WNT6 0.014 0.068 0.34 8 -10000 0 8
WNT4 -0.07 0.33 0.34 24 -0.86 25 49
NFAT1/CK1 alpha -0.22 0.3 -10000 0 -0.66 43 43
GNG2 -0.005 0.062 -10000 0 -0.86 1 1
WNT5A -0.074 0.26 0.34 4 -0.86 18 22
WNT11 -0.24 0.39 -10000 0 -0.86 54 54
CDC42 -0.15 0.26 -10000 0 -0.75 19 19
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.14 0.15 0.33 42 -10000 0 42
GNAI2 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.011 0.086 -10000 0 -0.59 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.4 0.43 -10000 0 -0.86 88 88
RhoA/GTP -0.14 0.16 -10000 0 -0.34 42 42
negative regulation of cAMP metabolic process -0.14 0.2 -10000 0 -0.37 42 42
GNAZ 0.16 0.17 0.34 91 -10000 0 91
GNAI3 0 0 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
S1PR5 -0.016 0.13 0.34 1 -0.86 4 5
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.14 0.2 -10000 0 -0.38 42 42
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
GNAI1 -0.009 0.088 -10000 0 -0.86 2 2
BCR signaling pathway

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
JUN -0.095 0.17 0.39 1 -0.42 20 21
IKBKB -0.029 0.085 -10000 0 -0.26 7 7
AKT1 -0.067 0.12 0.24 2 -0.25 41 43
IKBKG -0.029 0.089 -10000 0 -0.28 8 8
CALM1 -0.061 0.13 -10000 0 -0.48 7 7
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
MAP3K1 -0.14 0.22 0.47 1 -0.49 38 39
MAP3K7 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.075 0.14 0.24 1 -0.52 7 8
DOK1 0 0 -10000 0 -10000 0 0
AP-1 -0.12 0.13 0.28 1 -0.27 52 53
LYN 0 0 -10000 0 -10000 0 0
BLNK -0.027 0.15 -10000 0 -0.86 6 6
SHC1 0 0 -10000 0 -10000 0 0
BCR complex -0.18 0.31 0.48 1 -0.67 53 54
CD22 -0.25 0.32 0.38 1 -0.63 66 67
CAMK2G -0.051 0.12 -10000 0 -0.44 7 7
CSNK2A1 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.13 0.22 -10000 0 -0.86 3 3
GO:0007205 -0.072 0.14 0.24 1 -0.52 7 8
SYK 0 0 -10000 0 -10000 0 0
ELK1 -0.062 0.13 -10000 0 -0.49 7 7
NFATC1 -0.12 0.19 -10000 0 -0.44 33 33
B-cell antigen/BCR complex -0.18 0.31 0.48 1 -0.67 53 54
PAG1/CSK -0.005 0.072 -10000 0 -0.67 2 2
NFKBIB -0.003 0.029 -10000 0 -10000 0 0
HRAS -0.055 0.15 -10000 0 -0.49 7 7
NFKBIA -0.003 0.029 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.003 0.023 -10000 0 -10000 0 0
RasGAP/Csk -0.38 0.37 0.38 1 -0.64 116 117
mol:GDP -0.058 0.13 0.26 1 -0.49 7 8
PTEN -0.009 0.088 -10000 0 -0.86 2 2
CD79B 0.002 0.025 0.34 1 -10000 0 1
NF-kappa-B/RelA/I kappa B alpha 0.003 0.023 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.15 0.23 0.37 1 -0.49 53 54
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
mol:IP3 -0.077 0.14 0.24 1 -0.53 7 8
CSK 0 0 -10000 0 -10000 0 0
FOS -0.27 0.28 -10000 0 -0.55 91 91
CHUK -0.029 0.089 -10000 0 -0.26 10 10
IBTK 0 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.072 0.13 -10000 0 -0.52 11 11
PTPN6 -0.23 0.3 0.34 1 -0.65 52 53
RELA 0 0 -10000 0 -10000 0 0
BCL2A1 -0.001 0.037 -10000 0 -0.14 10 10
VAV2 -0.19 0.25 0.34 1 -0.55 51 52
ubiquitin-dependent protein catabolic process 0 0.028 -10000 0 -10000 0 0
BTK -0.026 0.15 -10000 0 -1.2 3 3
CD19 -0.2 0.26 0.38 1 -0.54 60 61
MAP4K1 -0.019 0.14 0.34 2 -0.86 5 7
CD72 -0.015 0.13 0.34 2 -0.86 4 6
PAG1 -0.005 0.095 0.34 2 -0.86 2 4
MAPK14 -0.11 0.19 0.46 1 -0.43 29 30
SH3BP5 -0.009 0.088 -10000 0 -0.86 2 2
PIK3AP1 -0.064 0.14 -10000 0 -0.5 8 8
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.14 0.24 0.26 1 -0.5 53 54
RAF1 -0.046 0.14 -10000 0 -0.46 7 7
RasGAP/p62DOK/SHIP -0.37 0.35 -10000 0 -0.61 116 116
CD79A -0.23 0.39 0.34 4 -0.86 53 57
re-entry into mitotic cell cycle -0.11 0.13 0.27 1 -0.27 52 53
RASA1 -0.009 0.088 -10000 0 -0.86 2 2
MAPK3 -0.026 0.12 -10000 0 -0.41 5 5
MAPK1 -0.026 0.12 -10000 0 -0.41 5 5
CD72/SHP1 -0.22 0.29 0.52 1 -0.61 54 55
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.13 0.21 0.46 1 -0.54 23 24
actin cytoskeleton organization -0.15 0.22 0.32 1 -0.5 36 37
NF-kappa-B/RelA 0.009 0.046 -10000 0 -10000 0 0
Calcineurin -0.059 0.1 -10000 0 -0.44 5 5
PI3K -0.18 0.22 -10000 0 -0.53 45 45
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.078 0.14 0.27 1 -0.54 7 8
SOS1 0 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.18 0.28 0.7 1 -0.97 14 15
DAPP1 -0.2 0.31 0.53 1 -1.1 13 14
cytokine secretion -0.11 0.18 -10000 0 -0.41 33 33
mol:DAG -0.077 0.14 0.24 1 -0.53 7 8
PLCG2 -0.018 0.12 -10000 0 -0.86 4 4
MAP2K1 -0.036 0.13 -10000 0 -0.46 5 5
B-cell antigen/BCR complex/FcgammaRIIB -0.44 0.41 0.42 1 -0.73 115 116
mol:PI-3-4-5-P3 -0.13 0.15 0.35 1 -0.36 44 45
ETS1 -0.041 0.11 -10000 0 -0.44 5 5
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.15 0.25 0.38 1 -0.53 56 57
B-cell antigen/BCR complex/LYN -0.22 0.27 0.38 1 -0.56 61 62
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 -0.005 0.062 -10000 0 -0.86 1 1
RAC1 -0.16 0.24 -10000 0 -0.54 36 36
B-cell antigen/BCR complex/LYN/SYK -0.25 0.33 0.42 1 -0.69 59 60
CARD11 -0.077 0.17 -10000 0 -0.6 12 12
FCGR2B -0.43 0.43 0.34 1 -0.86 95 96
PPP3CA 0 0 -10000 0 -10000 0 0
BCL10 0 0 -10000 0 -10000 0 0
IKK complex -0.008 0.039 0.13 1 -0.14 1 2
PTPRC -0.071 0.24 0.34 1 -0.86 16 17
PDPK1 -0.08 0.11 0.22 2 -0.27 22 24
PPP3CB 0 0 -10000 0 -10000 0 0
PPP3CC 0 0 -10000 0 -10000 0 0
POU2F2 0.002 0.032 0.12 1 -0.15 6 7
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.016 0.14 0.33 1 -0.41 16 17
TBX21 -0.17 0.44 0.67 1 -1.1 26 27
B2M -0.002 0.009 -10000 0 -10000 0 0
TYK2 0.009 0.02 -10000 0 -10000 0 0
IL12RB1 -0.029 0.18 -10000 0 -0.9 8 8
GADD45B -0.3 0.58 0.6 1 -1.2 50 51
IL12RB2 -0.012 0.18 0.34 7 -0.86 7 14
GADD45G -0.29 0.56 -10000 0 -1.2 48 48
natural killer cell activation -0.004 0.024 -10000 0 -10000 0 0
RELB 0.002 0.025 0.34 1 -10000 0 1
RELA 0 0 -10000 0 -10000 0 0
IL18 -0.01 0.13 0.34 1 -0.87 4 5
IL2RA -0.001 0.13 0.34 7 -0.86 3 10
IFNG 0.016 0.072 0.34 9 -10000 0 9
STAT3 (dimer) -0.16 0.35 0.57 1 -0.74 36 37
HLA-DRB5 -0.008 0.12 0.33 3 -0.87 3 6
FASLG -0.17 0.44 0.78 1 -0.98 32 33
NF kappa B2 p52/RelB -0.21 0.35 -10000 0 -0.86 33 33
CD4 -0.064 0.23 -10000 0 -0.87 14 14
SOCS1 -0.007 0.091 0.34 1 -0.86 2 3
EntrezGene:6955 -0.013 0.018 -10000 0 -10000 0 0
CD3D -0.032 0.2 0.34 7 -0.88 9 16
CD3E -0.047 0.2 0.34 1 -0.88 10 11
CD3G -0.039 0.21 0.33 6 -0.88 10 16
IL12Rbeta2/JAK2 -0.009 0.15 -10000 0 -0.68 8 8
CCL3 -0.21 0.5 0.67 1 -1.1 35 36
CCL4 -0.18 0.48 0.67 1 -1.3 22 23
HLA-A -0.002 0.009 -10000 0 -10000 0 0
IL18/IL18R -0.11 0.33 -10000 0 -0.72 38 38
NOS2 -0.14 0.39 0.66 1 -0.88 29 30
IL12/IL12R/TYK2/JAK2/SPHK2 -0.012 0.13 0.33 1 -0.38 15 16
IL1R1 -0.16 0.42 0.67 1 -1.1 22 23
IL4 0.004 0.024 -10000 0 -10000 0 0
JAK2 0.004 0.068 -10000 0 -0.9 1 1
EntrezGene:6957 -0.012 0.018 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.19 0.56 0.34 3 -1.4 29 32
RAB7A -0.2 0.4 -10000 0 -0.78 48 48
lysosomal transport -0.19 0.38 -10000 0 -0.73 48 48
FOS -0.64 0.75 -10000 0 -1.4 90 90
STAT4 (dimer) -0.19 0.42 0.59 1 -0.79 49 50
STAT5A (dimer) -0.2 0.36 0.4 5 -0.86 33 38
GZMA -0.17 0.45 0.74 1 -1 29 30
GZMB -0.17 0.42 0.74 1 -0.95 32 33
HLX 0 0 -10000 0 -10000 0 0
LCK -0.17 0.48 0.67 1 -1 33 34
TCR/CD3/MHC II/CD4 -0.15 0.31 0.32 1 -0.69 31 32
IL2/IL2R -0.056 0.22 0.4 2 -0.64 20 22
MAPK14 -0.27 0.51 0.59 1 -0.93 61 62
CCR5 -0.16 0.41 -10000 0 -0.98 26 26
IL1B -0.12 0.31 -10000 0 -0.89 27 27
STAT6 -0.031 0.14 0.42 1 -0.33 15 16
STAT4 -0.032 0.16 -10000 0 -0.86 7 7
STAT3 0 0 -10000 0 -10000 0 0
STAT1 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
NFKB2 0 0 -10000 0 -10000 0 0
IL12B 0.007 0.042 0.35 2 -10000 0 2
CD8A -0.066 0.24 0.34 3 -0.87 15 18
CD8B -0.035 0.2 0.34 5 -0.88 9 14
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.016 0.14 0.41 16 -0.33 1 17
IL2RB -0.077 0.25 -10000 0 -0.86 17 17
proteasomal ubiquitin-dependent protein catabolic process -0.17 0.38 0.58 1 -0.71 49 50
IL2RG -0.011 0.13 0.34 4 -0.86 4 8
IL12 0.014 0.05 -10000 0 -10000 0 0
STAT5A 0.002 0.025 0.34 1 -10000 0 1
CD247 -0.01 0.093 0.34 1 -0.88 2 3
IL2 0 0 -10000 0 -10000 0 0
SPHK2 0 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.012 0.047 0.34 3 -10000 0 3
IL12/IL12R/TYK2/JAK2 -0.19 0.54 0.76 1 -1.1 33 34
MAP2K3 -0.27 0.51 0.59 1 -0.92 62 63
RIPK2 0 0 -10000 0 -10000 0 0
MAP2K6 -0.28 0.52 0.59 1 -0.92 62 63
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA -0.007 0.092 0.34 1 -0.87 2 3
IL18RAP -0.058 0.23 -10000 0 -0.87 14 14
IL12Rbeta1/TYK2 -0.021 0.15 -10000 0 -0.72 8 8
EOMES -0.19 0.52 -10000 0 -1.5 26 26
STAT1 (dimer) -0.14 0.35 0.72 1 -0.73 34 35
T cell proliferation -0.15 0.32 0.52 1 -0.61 51 52
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.13 0.32 -10000 0 -0.87 29 29
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.26 0.33 -10000 0 -0.72 54 54
ATF2 -0.24 0.46 0.57 1 -0.84 61 62
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.03 0.16 -10000 0 -0.86 6 6
alphaM/beta2 Integrin/GPIbA -0.027 0.12 -10000 0 -0.6 7 7
alphaM/beta2 Integrin/proMMP-9 -0.002 0.18 -10000 0 -0.65 10 10
PLAUR 0.001 0.076 0.34 3 -0.86 1 4
HMGB1 -0.007 0.017 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.016 0.079 -10000 0 -0.61 3 3
AGER -0.002 0.047 0.34 3 -10000 0 3
RAP1A 0 0 -10000 0 -10000 0 0
SELPLG 0 0 -10000 0 -10000 0 0
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.036 0.12 -10000 0 -0.6 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.024 0.23 0.34 34 -0.86 8 42
CYR61 -0.086 0.26 -10000 0 -0.86 19 19
TLN1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.1 0.18 -10000 0 -0.53 20 20
RHOA 0 0 -10000 0 -10000 0 0
P-selectin oligomer -0.27 0.4 -10000 0 -0.86 60 60
MYH2 -0.15 0.31 -10000 0 -0.54 58 58
MST1R 0.043 0.17 0.34 32 -0.86 3 35
leukocyte activation during inflammatory response -0.29 0.28 -10000 0 -0.54 101 101
APOB -0.05 0.2 -10000 0 -0.86 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 -0.022 0.16 0.34 3 -0.86 6 9
JAM3 0.002 0.025 0.34 1 -10000 0 1
GP1BA -0.015 0.13 0.34 2 -0.86 4 6
alphaM/beta2 Integrin/CTGF -0.028 0.13 -10000 0 -0.69 6 6
alphaM/beta2 Integrin -0.12 0.21 -10000 0 -0.52 29 29
JAM3 homodimer 0.002 0.025 0.34 1 -10000 0 1
ICAM2 0.002 0.025 0.34 1 -10000 0 1
ICAM1 0 0 -10000 0 -10000 0 0
phagocytosis triggered by activation of immune response cell surface activating receptor -0.12 0.2 -10000 0 -0.51 29 29
cell adhesion -0.027 0.12 -10000 0 -0.59 7 7
NFKB1 -0.07 0.19 -10000 0 -0.73 8 8
THY1 0.089 0.15 0.34 50 -10000 0 50
RhoA/GDP 0 0 -10000 0 -10000 0 0
Lipoprotein(a) -0.32 0.32 -10000 0 -0.62 98 98
alphaM/beta2 Integrin/LRP/tPA -0.019 0.11 -10000 0 -0.65 5 5
IL6 -0.14 0.37 -10000 0 -1 26 26
ITGB2 -0.011 0.064 -10000 0 -0.86 1 1
elevation of cytosolic calcium ion concentration -0.008 0.096 0.39 2 -0.55 4 6
alphaM/beta2 Integrin/JAM2/JAM3 -0.031 0.13 0.4 1 -0.55 10 11
JAM2 -0.03 0.16 0.34 1 -0.86 7 8
alphaM/beta2 Integrin/ICAM1 -0.04 0.18 -10000 0 -0.49 23 23
alphaM/beta2 Integrin/uPA/Plg -0.11 0.21 -10000 0 -0.53 37 37
RhoA/GTP -0.17 0.32 -10000 0 -0.56 58 58
positive regulation of phagocytosis -0.094 0.18 -10000 0 -0.59 17 17
Ron/MSP -0.04 0.22 -10000 0 -0.65 20 20
alphaM/beta2 Integrin/uPAR/uPA -0.008 0.098 0.4 2 -0.55 4 6
alphaM/beta2 Integrin/uPAR -0.016 0.094 -10000 0 -0.6 4 4
PLAU 0.009 0.054 0.34 5 -10000 0 5
PLAT -0.004 0.098 0.34 3 -0.86 2 5
actin filament polymerization -0.14 0.29 -10000 0 -0.5 58 58
MST1 -0.077 0.25 -10000 0 -0.86 17 17
alphaM/beta2 Integrin/lipoprotein(a) -0.29 0.28 -10000 0 -0.55 101 101
TNF -0.093 0.28 -10000 0 -1.1 11 11
RAP1B 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.011 0.087 -10000 0 -0.61 3 3
fibrinolysis -0.11 0.21 -10000 0 -0.53 37 37
HCK -0.027 0.15 -10000 0 -0.86 6 6
dendritic cell antigen processing and presentation -0.12 0.2 -10000 0 -0.51 29 29
VTN -0.032 0.16 -10000 0 -0.86 7 7
alphaM/beta2 Integrin/CYR61 -0.074 0.2 -10000 0 -0.62 21 21
LPA -0.42 0.43 -10000 0 -0.86 93 93
LRP1 -0.005 0.062 -10000 0 -0.86 1 1
cell migration -0.029 0.2 -10000 0 -0.7 13 13
FN1 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Thy1 0.04 0.13 0.42 1 -0.61 3 4
MPO -0.025 0.15 0.34 1 -0.86 6 7
KNG1 -0.086 0.26 -10000 0 -0.86 19 19
RAP1/GDP 0 0 -10000 0 -10000 0 0
ROCK1 -0.13 0.3 -10000 0 -0.51 57 57
ELA2 0 0 -10000 0 -10000 0 0
PLG -0.15 0.33 -10000 0 -0.86 34 34
CTGF -0.018 0.12 -10000 0 -0.86 4 4
alphaM/beta2 Integrin/Hck -0.034 0.15 -10000 0 -0.78 7 7
ITGAM -0.015 0.095 0.34 1 -0.89 2 3
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.18 0.28 -10000 0 -0.58 60 60
HP -0.25 0.39 -10000 0 -0.86 56 56
leukocyte adhesion -0.004 0.16 0.36 1 -0.57 5 6
SELP -0.27 0.4 -10000 0 -0.86 60 60
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.1 0.42 -10000 0 -0.99 34 34
NCK1/PAK1/Dok-R -0.084 0.17 -10000 0 -0.44 35 35
NCK1/Dok-R -0.22 0.45 -10000 0 -1.2 34 34
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
mol:beta2-estradiol -0.001 0.031 0.25 2 -10000 0 2
RELA 0 0 -10000 0 -10000 0 0
SHC1 0 0.002 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.066 0.24 -10000 0 -0.86 16 16
TNIP2 0 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.2 0.41 -10000 0 -1.1 34 34
FN1 0 0 -10000 0 -10000 0 0
PLD2 -0.16 0.5 -10000 0 -1.2 34 34
PTPN11 0 0 -10000 0 -10000 0 0
GRB14 -0.009 0.088 -10000 0 -0.86 2 2
ELK1 -0.14 0.45 -10000 0 -1.1 34 34
GRB7 -0.002 0.1 0.34 4 -0.86 2 6
PAK1 0 0 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.21 0.44 -10000 0 -1.1 34 34
CDKN1A -0.052 0.31 -10000 0 -0.69 35 35
ITGA5 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.22 0.46 -10000 0 -1.2 34 34
CRK 0 0 -10000 0 -10000 0 0
mol:NO -0.051 0.31 -10000 0 -0.71 34 34
PLG -0.25 0.52 -10000 0 -1.3 36 36
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.16 0.36 -10000 0 -0.93 34 34
GRB2 0 0 -10000 0 -10000 0 0
PIK3R1 -0.004 0.063 -10000 0 -0.87 1 1
ANGPT2 0.007 0.16 -10000 0 -0.59 6 6
BMX -0.21 0.55 -10000 0 -1.4 34 34
ANGPT1 -0.004 0.2 -10000 0 -1.6 2 2
tube development -0.064 0.34 -10000 0 -0.77 34 34
ANGPT4 0.014 0.064 0.34 7 -10000 0 7
response to hypoxia -0.01 0.028 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.24 0.48 -10000 0 -1.3 34 34
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
FGF2 -0.064 0.24 0.34 2 -0.86 15 17
STAT5A (dimer) -0.086 0.39 -10000 0 -0.89 35 35
mol:L-citrulline -0.051 0.31 -10000 0 -0.71 34 34
AGTR1 -0.08 0.25 -10000 0 -0.86 18 18
MAPK14 -0.17 0.52 -10000 0 -1.3 34 34
Tie2/SHP2 -0.22 0.48 -10000 0 -1.2 34 34
TEK -0.25 0.53 -10000 0 -1.4 34 34
RPS6KB1 -0.096 0.4 -10000 0 -0.94 34 34
Angiotensin II/AT1 -0.06 0.2 -10000 0 -0.68 18 18
Tie2/Ang1/GRB2 -0.23 0.48 -10000 0 -1.3 34 34
MAPK3 -0.14 0.46 -10000 0 -1.1 34 34
MAPK1 -0.14 0.46 -10000 0 -1.1 34 34
Tie2/Ang1/GRB7 -0.23 0.49 -10000 0 -1.3 34 34
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.19 0.52 -10000 0 -1.3 34 34
PI3K -0.14 0.49 -10000 0 -1.2 34 34
FES -0.17 0.52 -10000 0 -1.3 34 34
Crk/Dok-R -0.22 0.45 -10000 0 -1.2 34 34
Tie2/Ang1/ABIN2 -0.23 0.48 -10000 0 -1.3 34 34
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.081 0.37 -10000 0 -0.87 34 34
STAT5A 0.002 0.025 0.34 1 -10000 0 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.096 0.4 -10000 0 -0.94 34 34
Tie2/Ang2 -0.13 0.47 -10000 0 -1.1 34 34
Tie2/Ang1 -0.22 0.53 -10000 0 -1.3 34 34
FOXO1 -0.08 0.38 -10000 0 -0.88 34 34
ELF1 -0.009 0.076 -10000 0 -0.91 1 1
ELF2 -0.17 0.51 -10000 0 -1.2 34 34
mol:Choline -0.15 0.47 -10000 0 -1.2 34 34
cell migration -0.046 0.092 -10000 0 -0.25 8 8
FYN -0.085 0.39 -10000 0 -0.89 34 34
DOK2 -0.009 0.088 -10000 0 -0.86 2 2
negative regulation of cell cycle -0.04 0.28 -10000 0 -0.62 35 35
ETS1 0.01 0.027 -10000 0 -10000 0 0
PXN -0.061 0.33 -10000 0 -0.76 34 34
ITGB1 0 0 -10000 0 -10000 0 0
NOS3 -0.069 0.36 -10000 0 -0.82 34 34
RAC1 0 0 -10000 0 -10000 0 0
TNF -0.035 0.2 -10000 0 -0.87 10 10
MAPKKK cascade -0.15 0.47 -10000 0 -1.2 34 34
RASA1 -0.009 0.088 -10000 0 -0.86 2 2
Tie2/Ang1/Shc -0.21 0.5 -10000 0 -1.3 34 34
NCK1 0 0 -10000 0 -10000 0 0
vasculogenesis -0.038 0.28 -10000 0 -0.63 34 34
mol:Phosphatidic acid -0.15 0.47 -10000 0 -1.2 34 34
mol:Angiotensin II 0.002 0.005 -10000 0 -10000 0 0
mol:NADP -0.051 0.31 -10000 0 -0.71 34 34
Rac1/GTP -0.16 0.33 -10000 0 -0.87 34 34
MMP2 -0.18 0.52 -10000 0 -1.3 34 34
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.004 0.043 -10000 0 -0.56 1 1
epithelial cell differentiation -0.056 0.092 -10000 0 -0.46 6 6
ITCH 0.001 0.005 -10000 0 -10000 0 0
WWP1 0.001 0.02 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
EGFR -0.014 0.11 -10000 0 -0.86 3 3
PRL 0.002 0.025 0.34 1 -10000 0 1
neuron projection morphogenesis -0.16 0.2 -10000 0 -0.53 1 1
PTPRZ1 0.014 0.068 0.34 8 -10000 0 8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.18 0.22 -10000 0 -0.46 76 76
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.21 0.26 -10000 0 -0.54 76 76
ADAM17 0.001 0.005 -10000 0 -10000 0 0
ErbB4/ErbB4 0.001 0.026 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.083 0.21 0.31 1 -0.56 30 31
NCOR1 -0.009 0.088 -10000 0 -0.86 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.2 0.25 -10000 0 -0.5 76 76
GRIN2B -0.19 0.23 -10000 0 -0.48 76 76
ErbB4/ErbB2/betacellulin -0.005 0.055 -10000 0 -0.5 2 2
STAT1 0 0 -10000 0 -10000 0 0
HBEGF -0.005 0.062 -10000 0 -0.86 1 1
PRLR -0.023 0.14 -10000 0 -0.86 5 5
E4ICDs/ETO2 -0.077 0.19 -10000 0 -0.56 26 26
axon guidance -0.054 0.094 -10000 0 -10000 0 0
NEDD4 -0.009 0.088 -10000 0 -0.87 2 2
Prolactin receptor/Prolactin receptor/Prolactin -0.016 0.11 -10000 0 -0.68 5 5
CBFA2T3 -0.12 0.3 -10000 0 -0.86 26 26
ErbB4/ErbB2/HBEGF -0.009 0.063 -10000 0 -0.5 3 3
MAPK3 -0.17 0.21 -10000 0 -0.43 73 73
STAT1 (dimer) 0.001 0.02 -10000 0 -10000 0 0
MAPK1 -0.17 0.21 -10000 0 -0.43 73 73
JAK2 -0.005 0.062 -10000 0 -0.86 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.21 0.26 -10000 0 -0.52 76 76
NRG1 -0.26 0.34 -10000 0 -0.68 76 76
NRG3 -0.13 0.32 0.34 4 -0.86 30 34
NRG2 0.075 0.14 0.34 42 -10000 0 42
NRG4 -0.12 0.3 -10000 0 -0.86 27 27
heart development -0.054 0.094 -10000 0 -10000 0 0
neural crest cell migration -0.2 0.25 -10000 0 -0.51 76 76
ERBB2 0.003 0.071 -10000 0 -0.68 2 2
WWOX/E4ICDs -0.002 0.015 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.082 0.19 -10000 0 -0.53 29 29
apoptosis 0.051 0.16 0.41 26 -0.25 1 27
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.055 0.11 0.31 3 -10000 0 3
ErbB4/ErbB2/epiregulin 0.018 0.091 -10000 0 -0.5 2 2
ErbB4/ErbB4/betacellulin/betacellulin 0 0.024 0.25 1 -10000 0 1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.017 0.093 -10000 0 -0.48 7 7
MDM2 0.017 0.026 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.21 0.25 -10000 0 -0.52 76 76
STAT5A -0.044 0.089 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.21 0.25 -10000 0 -0.5 79 79
DLG4 0 0 -10000 0 -10000 0 0
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.007 0.055 -10000 0 -0.52 2 2
STAT5A (dimer) -0.059 0.099 -10000 0 -0.57 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.061 0.074 -10000 0 -10000 0 0
LRIG1 0 0 -10000 0 -10000 0 0
EREG 0.036 0.1 0.34 20 -10000 0 20
BTC 0.002 0.025 0.34 1 -10000 0 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.064 0.087 -10000 0 -10000 0 0
ERBB4 0.001 0.026 -10000 0 -10000 0 0
STAT5B 0 0 -10000 0 -10000 0 0
YAP1 0.001 0.008 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.077 0.18 -10000 0 -0.5 29 29
glial cell differentiation 0.007 0.054 0.52 2 -10000 0 2
WWOX 0 0 -10000 0 -10000 0 0
cell proliferation -0.18 0.26 -10000 0 -0.49 76 76
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.005 0.042 0.34 3 -10000 0 3
CCL5 -0.034 0.18 0.34 1 -0.86 8 9
SDCBP 0 0 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.043 0.23 -10000 0 -0.62 13 13
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 -0.091 0.18 0.43 1 -0.75 8 9
Syndecan-1/Syntenin -0.094 0.18 -10000 0 -0.64 11 11
MAPK3 -0.074 0.17 -10000 0 -0.67 8 8
HGF/MET -0.32 0.34 -10000 0 -0.67 90 90
TGFB1/TGF beta receptor Type II 0.005 0.042 0.34 3 -10000 0 3
BSG 0.004 0.035 0.34 2 -10000 0 2
keratinocyte migration -0.089 0.18 0.43 1 -0.69 9 10
Syndecan-1/RANTES -0.11 0.23 0.43 1 -0.83 13 14
Syndecan-1/CD147 -0.088 0.17 -10000 0 -0.72 8 8
Syndecan-1/Syntenin/PIP2 -0.091 0.17 -10000 0 -0.62 11 11
LAMA5 0.004 0.035 0.34 2 -10000 0 2
positive regulation of cell-cell adhesion -0.089 0.17 -10000 0 -0.6 11 11
MMP7 -0.16 0.39 0.34 19 -0.86 43 62
HGF -0.41 0.43 -10000 0 -0.86 90 90
Syndecan-1/CASK -0.056 0.21 -10000 0 -0.59 13 13
Syndecan-1/HGF/MET -0.3 0.33 0.29 1 -0.62 83 84
regulation of cell adhesion -0.033 0.19 -10000 0 -0.64 8 8
HPSE -0.048 0.2 0.34 1 -0.86 11 12
positive regulation of cell migration -0.043 0.23 -10000 0 -0.62 13 13
SDC1 -0.044 0.23 -10000 0 -0.63 13 13
Syndecan-1/Collagen -0.043 0.23 -10000 0 -0.62 13 13
PPIB 0 0 -10000 0 -10000 0 0
MET 0.002 0.025 0.34 1 -10000 0 1
PRKACA 0 0 -10000 0 -10000 0 0
MMP9 0.024 0.23 0.34 34 -0.86 8 42
MAPK1 -0.074 0.17 -10000 0 -0.67 8 8
homophilic cell adhesion -0.042 0.22 -10000 0 -0.61 13 13
MMP1 0.093 0.15 0.34 52 -10000 0 52
Osteopontin-mediated 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
IKK alpha homodimer -0.035 0.19 -10000 0 -0.49 27 27
NF kappa B1 p50/RelA/I kappa B alpha -0.06 0.15 -10000 0 -0.43 26 26
alphaV/beta3 Integrin/Osteopontin/Src 0.038 0.22 0.28 3 -0.66 13 16
AP1 -0.26 0.36 0.42 2 -0.93 29 31
ILK -0.039 0.2 -10000 0 -0.52 27 27
bone resorption -0.037 0.21 0.32 1 -0.49 24 25
PTK2B 0 0 -10000 0 -10000 0 0
PYK2/p130Cas 0 0.22 -10000 0 -0.47 27 27
ITGAV 0.001 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.018 0.13 -10000 0 -0.67 7 7
alphaV/beta3 Integrin/Osteopontin -0.011 0.25 0.29 3 -0.58 27 30
MAP3K1 -0.04 0.21 -10000 0 -0.52 27 27
JUN -0.018 0.12 -10000 0 -0.86 4 4
MAPK3 -0.006 0.2 -10000 0 -0.49 27 27
MAPK1 -0.006 0.2 -10000 0 -0.49 27 27
Rac1/GDP 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.061 0.24 -10000 0 -0.55 32 32
ITGB3 -0.067 0.23 -10000 0 -0.86 15 15
NFKBIA 0.002 0.2 -10000 0 -0.47 27 27
FOS -0.4 0.43 -10000 0 -0.86 89 89
CD44 0.004 0.083 0.34 5 -0.86 1 6
CHUK 0 0 -10000 0 -10000 0 0
PLAU -0.004 0.19 -10000 0 -0.82 1 1
NF kappa B1 p50/RelA -0.054 0.15 -10000 0 -0.8 1 1
BCAR1 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin -0.052 0.18 -10000 0 -0.66 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
SYK -0.041 0.21 -10000 0 -0.52 27 27
VAV3 -0.036 0.19 -10000 0 -0.49 27 27
MAP3K14 -0.038 0.21 -10000 0 -0.52 27 27
ROCK2 -0.027 0.15 -10000 0 -0.86 6 6
SPP1 0.061 0.3 0.34 66 -0.86 13 79
RAC1 0 0 -10000 0 -10000 0 0
Rac1/GTP -0.037 0.17 -10000 0 -0.45 27 27
MMP2 -0.21 0.3 0.43 3 -0.72 30 33
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.021 0.12 -10000 0 -0.68 6 6
PDGFRB 0.005 0.042 0.34 3 -10000 0 3
SPHK1 -0.009 0.12 -10000 0 -0.94 2 2
mol:S1P -0.017 0.12 0.24 1 -0.84 2 3
S1P1/S1P/Gi -0.24 0.29 -10000 0 -0.61 52 52
GNAO1 -0.4 0.43 -10000 0 -0.87 88 88
PDGFB-D/PDGFRB/PLCgamma1 -0.2 0.25 0.31 1 -0.6 36 37
PLCG1 -0.21 0.28 -10000 0 -0.65 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.005 0.042 0.34 3 -10000 0 3
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GNAI1 -0.009 0.089 -10000 0 -0.87 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.007 0.11 -10000 0 -0.6 6 6
S1P1/S1P -0.036 0.14 -10000 0 -0.63 7 7
negative regulation of cAMP metabolic process -0.22 0.29 -10000 0 -0.59 52 52
MAPK3 -0.28 0.36 -10000 0 -0.72 61 61
calcium-dependent phospholipase C activity -0.004 0.004 -10000 0 -10000 0 0
Rac1/GDP 0 0 -10000 0 -10000 0 0
RhoA/GDP 0 0 -10000 0 -10000 0 0
KDR -0.027 0.15 -10000 0 -0.87 6 6
PLCB2 -0.028 0.16 -10000 0 -0.56 11 11
RAC1 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.041 0.1 -10000 0 -0.51 7 7
receptor internalization -0.034 0.13 -10000 0 -0.57 7 7
PTGS2 -0.4 0.53 -10000 0 -1.2 59 59
Rac1/GTP -0.041 0.1 -10000 0 -0.51 7 7
RHOA 0 0 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.22 0.29 -10000 0 -0.59 52 52
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ 0.16 0.17 0.34 91 -10000 0 91
MAPK1 -0.28 0.36 -10000 0 -0.72 61 61
S1P1/S1P/PDGFB-D/PDGFRB -0.034 0.15 -10000 0 -0.64 7 7
ABCC1 0.005 0.042 0.34 3 -10000 0 3
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0 0 -10000 0 -10000 0 0
VLDLR -0.006 0.25 0.34 27 -0.86 12 39
LRPAP1 0 0 -10000 0 -10000 0 0
NUDC 0 0 -10000 0 -10000 0 0
RELN/LRP8 -0.18 0.29 -10000 0 -0.58 64 64
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
KATNA1 0 0 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.17 0.25 -10000 0 -0.53 64 64
IQGAP1/CaM 0 0 -10000 0 -10000 0 0
DAB1 -0.14 0.32 -10000 0 -0.86 31 31
IQGAP1 0 0 -10000 0 -10000 0 0
PLA2G7 0.008 0.09 0.34 7 -0.86 1 8
CALM1 0 0 -10000 0 -10000 0 0
DYNLT1 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.024 0.071 -10000 0 -10000 0 0
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0 0 -10000 0 -10000 0 0
CDK5R1 0.002 0.025 0.34 1 -10000 0 1
LIS1/Poliovirus Protein 3A 0 0 -10000 0 -10000 0 0
CDK5R2 0.009 0.054 0.34 5 -10000 0 5
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 -0.3 0.39 -10000 0 -0.67 91 91
YWHAE 0 0 -10000 0 -10000 0 0
NDEL1/14-3-3 E -0.13 0.2 -10000 0 -0.41 57 57
MAP1B 0.002 0.016 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
p35/CDK5 -0.15 0.22 -10000 0 -0.46 64 64
RELN -0.29 0.41 -10000 0 -0.86 64 64
PAFAH/LIS1 0.006 0.062 -10000 0 -0.58 1 1
LIS1/CLIP170 0 0 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.11 0.15 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.18 0.27 -10000 0 -0.86 15 15
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 -0.14 0.21 -10000 0 -0.44 62 62
LIS1/IQGAP1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PAFAH1B1 0 0 -10000 0 -10000 0 0
PAFAH1B3 0.034 0.1 0.34 19 -10000 0 19
PAFAH1B2 0 0 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0 0 -10000 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.13 0.19 -10000 0 -10000 0 0
LRP8 0.036 0.1 0.34 20 -10000 0 20
NDEL1/Katanin 60 -0.13 0.2 -10000 0 -0.41 40 40
P39/CDK5 -0.15 0.23 -10000 0 -0.46 64 64
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -10000 0 -10000 0 0
CDK5 -0.16 0.24 -10000 0 -0.49 64 64
PPP2R5D 0 0 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.26 0.34 -10000 0 -0.58 91 91
RELN/VLDLR -0.17 0.33 0.4 5 -0.58 69 74
CDC42 0 0 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 -0.081 0.4 -10000 0 -1.2 19 19
SMARCC2 -0.002 0.011 -10000 0 -10000 0 0
SMARCC1 -0.002 0.011 -10000 0 -10000 0 0
TBX21 -0.11 0.27 -10000 0 -0.91 12 12
SUMO2 0.003 0.008 -10000 0 -10000 0 0
STAT1 (dimer) 0.012 0.002 -10000 0 -10000 0 0
FKBP4 0 0 -10000 0 -10000 0 0
FKBP5 0 0 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.073 0.11 0.33 3 -10000 0 3
PRL -0.062 0.14 -10000 0 -0.57 4 4
cortisol/GR alpha (dimer)/TIF2 0.11 0.37 0.51 53 -0.59 22 75
RELA -0.068 0.11 -10000 0 -0.28 6 6
FGG 0.051 0.35 0.49 17 -0.95 15 32
GR beta/TIF2 -0.003 0.26 0.32 11 -0.66 21 32
IFNG -0.13 0.27 0.53 4 -0.6 18 22
apoptosis -0.16 0.3 0.57 2 -0.76 18 20
CREB1 0.019 0.039 -10000 0 -10000 0 0
histone acetylation -0.077 0.14 -10000 0 -0.38 16 16
BGLAP -0.044 0.13 -10000 0 -0.49 1 1
GR/PKAc 0.073 0.1 0.35 1 -10000 0 1
NF kappa B1 p50/RelA -0.12 0.2 -10000 0 -0.46 24 24
SMARCD1 -0.002 0.011 -10000 0 -10000 0 0
MDM2 0.057 0.095 0.25 15 -10000 0 15
GATA3 -0.055 0.24 0.35 1 -0.86 15 16
AKT1 0.015 0.047 0.22 1 -10000 0 1
CSF2 -0.06 0.11 -10000 0 -0.47 1 1
GSK3B 0.003 0.008 -10000 0 -10000 0 0
NR1I3 -0.25 0.44 0.6 1 -1 41 42
CSN2 0.068 0.19 0.4 9 -0.45 3 12
BRG1/BAF155/BAF170/BAF60A -0.007 0.037 -10000 0 -10000 0 0
NFATC1 -0.009 0.088 -10000 0 -0.86 2 2
POU2F1 0.002 0.008 -10000 0 -10000 0 0
CDKN1A 0.01 0.2 -10000 0 -1.6 3 3
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.004 0.01 -10000 0 -10000 0 0
SFN 0.19 0.17 0.34 108 -10000 0 108
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.18 0.15 0.4 34 -10000 0 34
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.3 0.46 0.58 1 -0.93 61 62
JUN -0.024 0.24 0.46 7 -0.55 18 25
IL4 -0.065 0.15 -10000 0 -0.74 3 3
CDK5R1 0.002 0.024 0.33 1 -10000 0 1
PRKACA 0 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.27 0.28 -10000 0 -0.54 90 90
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.075 0.1 0.36 1 -10000 0 1
cortisol/GR alpha (monomer) 0.21 0.35 0.61 57 -0.52 6 63
NCOA2 -0.095 0.27 -10000 0 -0.86 21 21
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.36 0.45 -10000 0 -0.84 89 89
AP-1/NFAT1-c-4 -0.24 0.42 0.5 6 -0.68 74 80
AFP -0.026 0.35 0.52 2 -1.1 12 14
SUV420H1 0 0 -10000 0 -10000 0 0
IRF1 0.099 0.15 0.49 2 -10000 0 2
TP53 0.015 0.064 -10000 0 -0.49 3 3
PPP5C 0 0 -10000 0 -10000 0 0
KRT17 -0.14 0.38 0.56 3 -0.98 16 19
KRT14 -0.035 0.16 -10000 0 -10000 0 0
TBP 0.014 0.014 -10000 0 -10000 0 0
CREBBP -0.011 0.054 -10000 0 -10000 0 0
HDAC1 0 0 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
AP-1 -0.24 0.42 0.51 6 -0.67 74 80
MAPK14 0.002 0.007 -10000 0 -10000 0 0
MAPK10 -0.024 0.17 0.33 3 -0.86 7 10
MAPK11 0.011 0.053 0.33 5 -10000 0 5
KRT5 -0.12 0.29 0.56 2 -0.72 13 15
interleukin-1 receptor activity -0.001 0.001 -10000 0 -10000 0 0
NCOA1 -0.006 0.021 -10000 0 -10000 0 0
STAT1 0.012 0.003 -10000 0 -10000 0 0
CGA -0.032 0.15 0.44 1 -0.37 8 9
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.03 0.14 0.33 5 -0.42 1 6
MAPK3 0.003 0.007 -10000 0 -10000 0 0
MAPK1 0.002 0.007 -10000 0 -10000 0 0
ICAM1 -0.15 0.24 -10000 0 -0.64 22 22
NFKB1 -0.068 0.11 -10000 0 -10000 0 0
MAPK8 -0.072 0.24 0.42 4 -0.51 26 30
MAPK9 0.002 0.007 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.17 0.32 0.57 2 -0.8 19 21
BAX 0.029 0.054 -10000 0 -10000 0 0
POMC -0.11 0.23 -10000 0 -0.78 7 7
EP300 -0.011 0.054 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.19 0.29 0.54 51 -0.58 3 54
proteasomal ubiquitin-dependent protein catabolic process 0.039 0.073 0.23 2 -10000 0 2
SGK1 -0.009 0.3 -10000 0 -1.5 7 7
IL13 -0.15 0.31 -10000 0 -0.91 17 17
IL6 -0.29 0.54 -10000 0 -1.3 33 33
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.14 0.26 -10000 0 -0.82 14 14
IL2 -0.15 0.26 -10000 0 -0.55 29 29
CDK5 0 0.003 -10000 0 -10000 0 0
PRKACB 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
IL8 -0.39 0.63 0.46 1 -1.4 50 51
CDK5R1/CDK5 0.002 0.017 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/PKAc -0.091 0.13 -10000 0 -0.46 2 2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.19 0.26 0.51 49 -0.45 2 51
SMARCA4 -0.002 0.011 -10000 0 -10000 0 0
chromatin remodeling 0.093 0.18 0.38 18 -0.4 3 21
NF kappa B1 p50/RelA/Cbp -0.12 0.15 -10000 0 -0.56 6 6
JUN (dimer) -0.024 0.24 0.46 7 -0.55 18 25
YWHAH 0 0 -10000 0 -10000 0 0
VIPR1 -0.78 0.58 -10000 0 -1.2 128 128
NR3C1 0.11 0.19 0.41 31 -10000 0 31
NR4A1 -0.11 0.3 -10000 0 -0.84 27 27
TIF2/SUV420H1 -0.074 0.21 -10000 0 -0.67 21 21
MAPKKK cascade -0.16 0.3 0.57 2 -0.76 18 20
cortisol/GR alpha (dimer)/Src-1 0.18 0.3 0.54 49 -0.56 4 53
PBX1 -0.057 0.22 -10000 0 -0.86 13 13
POU1F1 0.003 0.026 0.34 1 -10000 0 1
SELE -0.42 0.63 -10000 0 -1.4 53 53
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.092 0.18 0.39 18 -0.4 3 21
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.19 0.26 0.51 49 -0.45 2 51
mol:cortisol 0.098 0.2 0.34 56 -0.27 8 64
MMP1 0.032 0.18 0.46 6 -10000 0 6
Syndecan-4-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
PTK2 0.009 0.039 -10000 0 -10000 0 0
Syndecan-4/Syndesmos -0.12 0.3 -10000 0 -0.81 25 25
positive regulation of JNK cascade -0.3 0.29 -10000 0 -0.77 35 35
Syndecan-4/ADAM12 -0.11 0.3 -10000 0 -0.8 25 25
CCL5 -0.034 0.18 0.34 1 -0.86 8 9
Rac1/GDP 0 0 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
ITGA5 0 0 -10000 0 -10000 0 0
SDCBP 0 0 -10000 0 -10000 0 0
PLG -0.15 0.32 -10000 0 -0.85 34 34
ADAM12 0.038 0.13 0.34 24 -0.86 1 25
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.025 0.045 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.17 0.33 -10000 0 -0.82 27 27
Syndecan-4/CXCL12/CXCR4 -0.32 0.32 -10000 0 -0.85 35 35
Syndecan-4/Laminin alpha3 -0.095 0.32 -10000 0 -0.82 25 25
MDK 0.18 0.17 0.34 101 -10000 0 101
Syndecan-4/FZD7 -0.12 0.3 -10000 0 -0.81 25 25
Syndecan-4/Midkine -0.022 0.35 -10000 0 -0.8 25 25
FZD7 -0.004 0.098 0.34 3 -0.86 2 5
Syndecan-4/FGFR1/FGF -0.16 0.29 -10000 0 -0.76 29 29
THBS1 -0.14 0.31 -10000 0 -0.86 30 30
integrin-mediated signaling pathway -0.14 0.3 -10000 0 -0.79 25 25
positive regulation of MAPKKK cascade -0.3 0.29 -10000 0 -0.77 35 35
Syndecan-4/TACI -0.11 0.3 -10000 0 -0.82 25 25
CXCR4 -0.005 0.062 -10000 0 -0.86 1 1
cell adhesion 0.001 0.007 -10000 0 -10000 0 0
Syndecan-4/Dynamin -0.12 0.3 -10000 0 -0.81 25 25
Syndecan-4/TSP1 -0.19 0.34 -10000 0 -0.87 28 28
Syndecan-4/GIPC -0.12 0.3 -10000 0 -0.81 25 25
Syndecan-4/RANTES -0.14 0.32 -10000 0 -0.85 25 25
ITGB1 0 0 -10000 0 -10000 0 0
LAMA1 -0.093 0.31 0.34 11 -0.86 25 36
LAMA3 0.043 0.15 0.34 29 -0.86 2 31
RAC1 0 0 -10000 0 -10000 0 0
PRKCA 0.025 0.055 -10000 0 -10000 0 0
Syndecan-4/alpha-Actinin -0.12 0.3 -10000 0 -0.81 25 25
TFPI -0.036 0.17 -10000 0 -0.86 8 8
F2 -0.068 0.24 -10000 0 -0.85 16 16
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
positive regulation of cell adhesion -0.15 0.32 -10000 0 -0.79 27 27
ACTN1 0 0 -10000 0 -10000 0 0
TNC -0.049 0.22 0.34 3 -0.86 12 15
Syndecan-4/CXCL12 -0.32 0.35 -10000 0 -0.88 35 35
FGF6 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
CXCL12 -0.38 0.43 -10000 0 -0.86 84 84
TNFRSF13B -0.001 0.072 0.34 2 -0.86 1 3
FGF2 -0.064 0.24 0.34 2 -0.86 15 17
FGFR1 -0.005 0.095 0.34 2 -0.86 2 4
Syndecan-4/PI-4-5-P2 -0.099 0.31 -10000 0 -0.82 25 25
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.003 0.009 -10000 0 -10000 0 0
cell migration -0.007 0.014 -10000 0 -10000 0 0
PRKCD 0.003 0.009 -10000 0 -10000 0 0
vasculogenesis -0.18 0.32 -10000 0 -0.82 28 28
SDC4 -0.11 0.34 -10000 0 -0.89 25 25
Syndecan-4/Tenascin C -0.14 0.32 -10000 0 -0.84 25 25
Syndecan-4/PI-4-5-P2/PKC alpha -0.02 0.035 -10000 0 -10000 0 0
Syndecan-4/Syntenin -0.12 0.3 -10000 0 -0.81 25 25
MMP9 0.024 0.23 0.34 34 -0.86 8 42
Rac1/GTP 0.001 0.007 -10000 0 -10000 0 0
cytoskeleton organization -0.11 0.28 -10000 0 -0.76 25 25
GIPC1 0.002 0.025 0.34 1 -10000 0 1
Syndecan-4/TFPI -0.14 0.32 -10000 0 -0.87 25 25
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0 0 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.15 0.15 -10000 0 -0.48 11 11
NT3 (dimer)/TRKC -0.38 0.36 -10000 0 -0.69 106 106
NT3 (dimer)/TRKB -0.62 0.56 -10000 0 -1 120 120
SHC/Grb2/SOS1/GAB1/PI3K -0.004 0.051 -10000 0 -0.71 1 1
RAPGEF1 0 0 -10000 0 -10000 0 0
BDNF 0.011 0.059 0.34 6 -10000 0 6
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
DYNLT1 0 0 -10000 0 -10000 0 0
NTRK1 0.002 0.025 0.34 1 -10000 0 1
NTRK2 -0.17 0.36 0.34 5 -0.86 40 45
NTRK3 -0.029 0.18 0.34 4 -0.86 8 12
NT-4/5 (dimer)/TRKB -0.34 0.42 -10000 0 -0.76 88 88
neuron apoptosis 0.18 0.23 0.57 37 -10000 0 37
SHC 2-3/Grb2 -0.2 0.26 -10000 0 -0.64 37 37
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.21 0.27 -10000 0 -0.49 76 76
SHC3 -0.17 0.25 -10000 0 -0.64 32 32
STAT3 (dimer) -0.021 0.088 -10000 0 -0.39 10 10
NT3 (dimer)/TRKA -0.52 0.46 -10000 0 -0.86 117 117
RIN/GDP -0.097 0.12 -10000 0 -0.26 12 12
GIPC1 0.002 0.025 0.34 1 -10000 0 1
KRAS 0 0 -10000 0 -10000 0 0
DNAJA3 -0.2 0.24 -10000 0 -0.48 78 78
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 -0.035 0.24 -10000 0 -1.1 10 10
MAGED1 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.025 0.34 1 -10000 0 1
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.024 0.13 -10000 0 -0.59 9 9
TRKA/NEDD4-2 0.001 0.017 -10000 0 -10000 0 0
ELMO1 -0.005 0.062 -10000 0 -0.86 1 1
RhoG/GTP/ELMO1/DOCK1 -0.015 0.11 -10000 0 -0.72 4 4
NGF -0.041 0.18 -10000 0 -0.86 9 9
HRAS 0.004 0.035 0.34 2 -10000 0 2
DOCK1 -0.018 0.12 -10000 0 -0.86 4 4
GAB2 0 0 -10000 0 -10000 0 0
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0 0 -10000 0 -10000 0 0
FRS2 0 0 -10000 0 -10000 0 0
DNM1 0.002 0.17 0.34 14 -0.86 5 19
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.19 0.24 -10000 0 -0.47 78 78
mol:GDP -0.15 0.18 -10000 0 -0.38 34 34
NGF (dimer) -0.041 0.18 -10000 0 -0.86 9 9
RhoG/GDP -0.004 0.049 -10000 0 -0.68 1 1
RIT1/GDP -0.094 0.12 -10000 0 -0.28 4 4
TIAM1 -0.032 0.16 -10000 0 -0.86 7 7
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
BDNF (dimer)/TRKB -0.11 0.25 0.42 1 -0.58 40 41
KIDINS220/CRKL/C3G 0 0 -10000 0 -10000 0 0
SHC/RasGAP -0.007 0.068 -10000 0 -0.67 2 2
FRS2 family/SHP2 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.46 0.43 -10000 0 -0.86 102 102
RAP1/GDP -0.095 0.086 -10000 0 -10000 0 0
KIDINS220/CRKL 0 0 -10000 0 -10000 0 0
BDNF (dimer) 0.011 0.059 0.34 6 -10000 0 6
ubiquitin-dependent protein catabolic process -0.026 0.12 -10000 0 -0.58 9 9
Schwann cell development -0.057 0.045 -10000 0 -10000 0 0
EHD4 0 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0 0 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.34 0.33 -10000 0 -0.58 112 112
ABL1 0 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.04 0.089 -10000 0 -10000 0 0
STAT3 -0.021 0.087 -10000 0 -0.39 10 10
axon guidance -0.32 0.31 -10000 0 -0.55 115 115
MAPK3 -0.024 0.11 -10000 0 -0.54 9 9
MAPK1 -0.024 0.11 -10000 0 -0.54 9 9
CDC42/GDP -0.094 0.12 -10000 0 -0.26 12 12
NTF3 -0.46 0.43 -10000 0 -0.86 102 102
NTF4 0.002 0.025 0.34 1 -10000 0 1
NGF (dimer)/TRKA/FAIM -0.027 0.13 -10000 0 -0.59 9 9
PI3K -0.006 0.087 -10000 0 -1.2 1 1
FRS3 0 0 -10000 0 -10000 0 0
FAIM 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
RASGRF1 -0.18 0.25 -10000 0 -0.48 77 77
SOS1 0 0 -10000 0 -10000 0 0
MCF2L -0.33 0.31 -10000 0 -0.6 106 106
RGS19 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.024 0.092 -10000 0 -10000 0 0
Rac1/GDP -0.094 0.12 -10000 0 -0.27 6 6
NGF (dimer)/TRKA/GRIT -0.027 0.13 -10000 0 -0.6 9 9
neuron projection morphogenesis -0.18 0.25 -10000 0 -0.68 15 15
NGF (dimer)/TRKA/NEDD4-2 -0.027 0.13 -10000 0 -0.59 9 9
MAP2K1 0 0 -10000 0 -10000 0 0
NGFR -0.34 0.42 -10000 0 -0.86 76 76
NGF (dimer)/TRKA/GIPC/GAIP -0.017 0.098 -10000 0 -0.35 14 14
RAS family/GTP/PI3K -0.003 0.044 -10000 0 -0.59 1 1
FRS2 family/SHP2/GRB2/SOS1 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
PRKCZ -0.036 0.17 -10000 0 -0.86 8 8
MAPKKK cascade -0.073 0.16 -10000 0 -0.77 9 9
RASA1 -0.009 0.088 -10000 0 -0.86 2 2
TRKA/c-Abl 0.001 0.017 -10000 0 -10000 0 0
SQSTM1 0.004 0.035 0.34 2 -10000 0 2
BDNF (dimer)/TRKB/GIPC -0.099 0.23 0.4 1 -0.54 40 41
NGF (dimer)/TRKA/p62/Atypical PKCs -0.043 0.14 -10000 0 -0.5 17 17
MATK 0.004 0.035 0.34 2 -10000 0 2
NEDD4L 0 0 -10000 0 -10000 0 0
RAS family/GDP -0.091 0.081 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.21 0.26 -10000 0 -0.51 78 78
Rac1/GTP -0.17 0.16 -10000 0 -0.37 70 70
FRS2 family/SHP2/CRK family 0 0 -10000 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.2 0.24 -10000 0 -0.43 89 89
MAP3K8 -0.009 0.088 -10000 0 -0.86 2 2
FOS -0.1 0.18 -10000 0 -0.56 14 14
PRKCA 0 0 -10000 0 -10000 0 0
PTPN7 0.001 0.076 0.34 3 -0.87 1 4
HRAS 0.004 0.034 0.34 2 -10000 0 2
PRKCB -0.078 0.25 -10000 0 -0.87 17 17
NRAS 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.019 -10000 0 -10000 0 0
MAPK3 -0.047 0.11 -10000 0 -0.32 14 14
MAP2K1 -0.067 0.19 -10000 0 -0.64 17 17
ELK1 -0.006 0.007 -10000 0 -10000 0 0
BRAF -0.067 0.17 -10000 0 -0.59 17 17
mol:GTP -0.003 0.003 -10000 0 -0.006 88 88
MAPK1 -0.047 0.11 -10000 0 -0.32 14 14
RAF1 -0.067 0.17 -10000 0 -0.59 17 17
KRAS 0 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.12 0.16 0.34 68 -10000 0 68
mol:Halofuginone 0 0.004 -10000 0 -10000 0 0
ITGA1 0 0 -10000 0 -10000 0 0
CDKN1A -0.07 0.12 -10000 0 -0.54 4 4
PRL-3/alpha Tubulin 0.035 0.083 -10000 0 -10000 0 0
mol:Ca2+ -0.041 0.1 -10000 0 -0.68 2 2
AGT -0.009 0.088 -10000 0 -0.86 2 2
CCNA2 -0.11 0.26 -10000 0 -0.48 59 59
TUBA1B 0 0 -10000 0 -10000 0 0
EGR1 -0.2 0.32 -10000 0 -0.68 59 59
CDK2/Cyclin E1 0.001 0.16 -10000 0 -0.59 2 2
MAPK3 0.026 0.061 -10000 0 -10000 0 0
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.026 0.061 -10000 0 -10000 0 0
PTP4A1 -0.15 0.27 -10000 0 -0.54 59 59
PTP4A3 0.052 0.12 0.34 29 -10000 0 29
PTP4A2 0 0 -10000 0 -10000 0 0
ITGB1 0.026 0.061 -10000 0 -10000 0 0
SRC 0.002 0.025 0.34 1 -10000 0 1
RAC1 -0.035 0.11 -10000 0 -0.32 1 1
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.32 0.32 -10000 0 -0.58 103 103
RABGGTA 0 0 -10000 0 -10000 0 0
BCAR1 -0.034 0.081 -10000 0 -10000 0 0
RHOC -0.035 0.11 -10000 0 -0.32 1 1
RHOA -0.035 0.11 -10000 0 -0.32 1 1
cell motility -0.024 0.12 -10000 0 -0.35 1 1
PRL-1/alpha Tubulin -0.16 0.24 -10000 0 -0.5 59 59
PRL-3/alpha1 Integrin 0.035 0.083 -10000 0 -10000 0 0
ROCK1 -0.024 0.12 -10000 0 -0.36 1 1
RABGGTB 0 0 -10000 0 -10000 0 0
CDK2 0 0 -10000 0 -10000 0 0
mitosis -0.14 0.27 -10000 0 -0.54 59 59
ATF5 -0.28 0.4 -10000 0 -0.86 62 62
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B -0.014 0.11 -10000 0 -0.59 6 6
ARNO/beta Arrestin1-2 -0.063 0.16 -10000 0 -0.45 27 27
EGFR -0.014 0.11 -10000 0 -0.86 3 3
EPHA2 -0.036 0.17 -10000 0 -0.86 8 8
USP6 0 0 -10000 0 -10000 0 0
IQSEC1 0 0 -10000 0 -10000 0 0
EGFR/EGFR/EGF/EGF 0.043 0.13 -10000 0 -0.66 3 3
ARRB2 0 0 -10000 0 -10000 0 0
mol:GTP 0.002 0.054 -10000 0 -0.23 7 7
ARRB1 -0.014 0.11 -10000 0 -0.86 3 3
FBXO8 0 0 -10000 0 -10000 0 0
TSHR 0 0 -10000 0 -10000 0 0
EGF 0.08 0.14 0.34 45 -10000 0 45
somatostatin receptor activity 0 0 -10000 0 -0.001 41 41
ARAP2 -0.023 0.14 -10000 0 -0.86 5 5
mol:GDP -0.068 0.13 -10000 0 -0.34 25 25
mol:PI-3-4-5-P3 0 0 -10000 0 -0.001 28 28
ITGA2B 0.005 0.042 0.34 3 -10000 0 3
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.028 0.12 -10000 0 -0.54 10 10
ADAP1 -0.02 0.16 0.34 4 -0.86 6 10
KIF13B 0 0 -10000 0 -10000 0 0
HGF/MET -0.32 0.34 -10000 0 -0.67 90 90
PXN 0 0 -10000 0 -10000 0 0
ARF6/GTP -0.07 0.13 -10000 0 -0.29 40 40
EGFR/EGFR/EGF/EGF/ARFGEP100 0.04 0.12 -10000 0 -0.57 3 3
ADRB2 -0.11 0.29 -10000 0 -0.86 24 24
receptor agonist activity 0 0 -10000 0 0 43 43
actin filament binding 0 0 -10000 0 -0.001 42 42
SRC 0.002 0.025 0.34 1 -10000 0 1
ITGB3 -0.068 0.23 -10000 0 -0.86 15 15
GNAQ -0.005 0.062 -10000 0 -0.86 1 1
EFA6/PI-4-5-P2 0 0 -10000 0 -0.001 35 35
ARF6/GDP -0.021 0.11 -10000 0 -0.4 10 10
ARF6/GDP/GULP/ACAP1 -0.09 0.21 -10000 0 -0.55 26 26
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.039 0.15 -10000 0 -0.54 15 15
ACAP1 -0.024 0.16 0.34 2 -0.86 6 8
ACAP2 0 0 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0 0 -10000 0 -10000 0 0
EFNA1 -0.009 0.088 -10000 0 -0.86 2 2
HGF -0.41 0.43 -10000 0 -0.86 90 90
CYTH3 0.002 0.012 -10000 0 -10000 0 0
CYTH2 0.004 0.002 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
fibronectin binding 0 0 -10000 0 0 41 41
endosomal lumen acidification 0 0 -10000 0 0 33 33
microtubule-based process 0 0 -10000 0 -10000 0 0
GULP1 -0.009 0.28 0.34 33 -0.86 15 48
GNAQ/ARNO -0.003 0.037 -10000 0 -0.51 1 1
mol:Phosphatidic acid 0 0 -10000 0 -10000 0 0
PIP3-E 0 0 -10000 0 0 11 11
MET 0.002 0.025 0.34 1 -10000 0 1
GNA14 -0.14 0.31 -10000 0 -0.86 30 30
GNA15 0.002 0.025 0.34 1 -10000 0 1
GIT1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -0.001 40 40
GNA11 -0.023 0.14 -10000 0 -0.86 5 5
LHCGR 0 0 -10000 0 -10000 0 0
AGTR1 -0.081 0.25 -10000 0 -0.86 18 18
desensitization of G-protein coupled receptor protein signaling pathway 0 0 -10000 0 -10000 0 0
IPCEF1/ARNO 0.036 0.1 -10000 0 -0.46 3 3
alphaIIb/beta3 Integrin -0.049 0.18 -10000 0 -0.67 15 15
Aurora C signaling

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
INCENP 0.002 0.025 0.34 1 -9999 0 1
Aurora C/Aurora B/INCENP 0.1 0.1 0.39 1 -9999 0 1
metaphase 0 0 -10000 0 -9999 0 0
mitosis 0 0 -10000 0 -9999 0 0
H3F3B 0 0 -10000 0 -9999 0 0
AURKB 0.18 0.17 0.34 98 -9999 0 98
AURKC 0.002 0.025 0.34 1 -9999 0 1
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.021 0.12 -10000 0 -0.67 6 6
alphaV beta3 Integrin -0.088 0.24 -10000 0 -0.66 26 26
PTK2 -0.028 0.21 -10000 0 -0.58 19 19
IGF1R -0.005 0.095 0.34 2 -0.86 2 4
PI4KB 0 0 -10000 0 -10000 0 0
MFGE8 0.004 0.035 0.34 2 -10000 0 2
SRC 0.002 0.025 0.34 1 -10000 0 1
CDKN1B -0.052 0.14 -10000 0 -0.64 7 7
VEGFA 0 0 -10000 0 -10000 0 0
ILK -0.052 0.14 -10000 0 -0.51 11 11
ROCK1 0 0 -10000 0 -10000 0 0
AKT1 -0.048 0.13 -10000 0 -0.59 7 7
PTK2B -0.055 0.17 -10000 0 -0.55 19 19
alphaV/beta3 Integrin/JAM-A -0.096 0.22 -10000 0 -0.56 33 33
CBL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.11 0.25 -10000 0 -0.63 34 34
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.21 0.27 -10000 0 -0.55 74 74
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.041 0.11 -10000 0 -0.57 2 2
alphaV/beta3 Integrin/Syndecan-1 -0.055 0.17 -10000 0 -0.58 18 18
PI4KA 0 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.25 0.32 -10000 0 -0.57 84 84
PI4 Kinase 0 0 -10000 0 -10000 0 0
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
alphaV/beta3 Integrin/Osteopontin -0.018 0.26 -10000 0 -0.59 27 27
RPS6KB1 -0.23 0.29 -10000 0 -0.53 82 82
TLN1 0 0 -10000 0 -10000 0 0
MAPK3 -0.17 0.3 -10000 0 -0.86 26 26
GPR124 -0.009 0.088 -10000 0 -0.86 2 2
MAPK1 -0.17 0.3 -10000 0 -0.86 26 26
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
alphaV/beta3 Integrin/Tumstatin -0.067 0.25 -10000 0 -0.7 22 22
cell adhesion -0.096 0.22 -10000 0 -0.53 35 35
ANGPTL3 -0.099 0.28 -10000 0 -0.86 22 22
VEGFR2 homodimer/VEGFA homodimer/Src -0.017 0.1 -10000 0 -0.58 6 6
IGF-1R heterotetramer -0.005 0.095 0.34 2 -0.86 2 4
Rac1/GDP 0 0 -10000 0 -10000 0 0
TGFBR2 0 0 -10000 0 -10000 0 0
ITGB3 -0.068 0.23 -10000 0 -0.86 15 15
IGF1 -0.34 0.42 -10000 0 -0.86 74 74
RAC1 0 0 -10000 0 -10000 0 0
regulation of cell-matrix adhesion -0.052 0.17 -10000 0 -0.58 17 17
apoptosis 0 0 -10000 0 -10000 0 0
CD47 -0.005 0.062 -10000 0 -0.86 1 1
alphaV/beta3 Integrin/CD47 -0.049 0.16 -10000 0 -0.58 16 16
VCL 0.002 0.025 0.34 1 -10000 0 1
alphaV/beta3 Integrin/Del1 0.009 0.2 -10000 0 -0.59 15 15
CSF1 -0.005 0.062 -10000 0 -0.86 1 1
PIK3C2A -0.052 0.14 -10000 0 -0.51 11 11
PI4 Kinase/Pyk2 -0.093 0.21 -10000 0 -0.49 37 37
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.058 0.18 -10000 0 -0.59 19 19
FAK1/Vinculin -0.013 0.17 -10000 0 -0.46 15 15
alphaV beta3/Integrin/ppsTEM5 -0.052 0.17 -10000 0 -0.58 17 17
RHOA 0 0 -10000 0 -10000 0 0
VTN -0.032 0.16 -10000 0 -0.86 7 7
BCAR1 0 0 -10000 0 -10000 0 0
FGF2 -0.064 0.24 0.34 2 -0.86 15 17
F11R -0.051 0.18 -10000 0 -0.67 15 15
alphaV/beta3 Integrin/Lactadherin -0.044 0.16 -10000 0 -0.58 15 15
alphaV/beta3 Integrin/TGFBR2 -0.046 0.16 -10000 0 -0.58 15 15
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.039 -10000 0 -0.54 1 1
HSP90AA1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.043 0.15 -10000 0 -0.54 15 15
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Pyk2 -0.055 0.17 -10000 0 -0.55 19 19
SDC1 -0.014 0.11 -10000 0 -0.86 3 3
VAV3 0.002 0.048 -10000 0 -0.5 1 1
PTPN11 0 0 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
FAK1/Paxillin -0.013 0.17 -10000 0 -0.44 19 19
cell migration -0.001 0.15 -10000 0 -0.41 15 15
ITGAV 0 0 -10000 0 -10000 0 0
PI3K -0.091 0.22 -10000 0 -0.53 33 33
SPP1 0.059 0.3 0.34 66 -0.86 13 79
KDR -0.027 0.15 -10000 0 -0.86 6 6
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0 0 -10000 0 -10000 0 0
COL4A3 -0.031 0.23 0.34 13 -0.86 12 25
angiogenesis -0.14 0.3 -10000 0 -0.8 29 29
Rac1/GTP 0.002 0.044 -10000 0 -0.46 1 1
EDIL3 0.089 0.15 0.34 50 -10000 0 50
cell proliferation -0.046 0.16 -10000 0 -0.58 15 15
S1P4 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 -0.4 0.43 -10000 0 -0.86 88 88
CDC42/GTP -0.13 0.15 -10000 0 -0.5 2 2
PLCG1 -0.12 0.18 -10000 0 -0.34 39 39
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
G12/G13 0 0 -10000 0 -10000 0 0
cell migration -0.13 0.14 -10000 0 -0.32 39 39
S1PR5 -0.016 0.13 0.34 1 -0.86 4 5
S1PR4 0.002 0.025 0.34 1 -10000 0 1
MAPK3 -0.12 0.18 -10000 0 -0.52 2 2
MAPK1 -0.12 0.18 -10000 0 -0.52 2 2
S1P/S1P5/Gi -0.14 0.2 -10000 0 -0.38 42 42
GNAI1 -0.009 0.088 -10000 0 -0.86 2 2
CDC42/GDP 0 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.011 0.086 -10000 0 -0.59 4 4
RHOA 0 0.005 -10000 0 -10000 0 0
S1P/S1P4/Gi -0.13 0.19 -10000 0 -0.36 39 39
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ 0.16 0.17 0.34 91 -10000 0 91
S1P/S1P4/G12/G13 0.001 0.015 -10000 0 -10000 0 0
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0 0 -10000 0 -10000 0 0
LAT2 -0.038 0.097 -10000 0 -0.38 3 3
AP1 -0.23 0.25 -10000 0 -0.47 89 89
mol:PIP3 -0.026 0.19 -10000 0 -0.45 29 29
IKBKB -0.008 0.12 -10000 0 -0.34 13 13
AKT1 -0.06 0.15 -10000 0 -0.77 1 1
IKBKG -0.008 0.12 -10000 0 -0.34 13 13
MS4A2 0.005 0.043 0.34 3 -10000 0 3
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA -0.004 0.063 -10000 0 -0.87 1 1
MAP3K1 0.001 0.12 -10000 0 -0.62 3 3
mol:Ca2+ -0.013 0.14 -10000 0 -0.33 29 29
LYN 0 0 -10000 0 -10000 0 0
CBLB -0.037 0.095 -10000 0 -0.37 3 3
SHC1 0 0 -10000 0 -10000 0 0
RasGAP/p62DOK -0.042 0.16 -10000 0 -0.58 14 14
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
PLD2 -0.067 0.17 -10000 0 -0.48 27 27
PTPN13 -0.12 0.24 -10000 0 -0.52 45 45
PTPN11 0 0.002 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation 0.01 0.12 -10000 0 -0.35 3 3
SYK 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.076 0.17 -10000 0 -0.46 29 29
LAT -0.037 0.096 -10000 0 -0.37 3 3
PAK2 -0.007 0.14 -10000 0 -0.63 4 4
NFATC2 -0.15 0.3 -10000 0 -0.79 32 32
HRAS -0.016 0.15 -10000 0 -0.56 7 7
GAB2 0 0 -10000 0 -10000 0 0
PLA2G1B 0.049 0.034 -10000 0 -10000 0 0
Fc epsilon R1 -0.08 0.21 -10000 0 -0.59 27 27
Antigen/IgE/Fc epsilon R1 -0.074 0.19 -10000 0 -0.55 27 27
mol:GDP -0.025 0.16 -10000 0 -0.57 9 9
JUN -0.018 0.12 -10000 0 -0.86 4 4
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 -0.004 0.063 -10000 0 -0.87 1 1
FOS -0.4 0.43 -10000 0 -0.86 89 89
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.04 0.1 -10000 0 -0.4 3 3
CHUK -0.008 0.12 -10000 0 -0.34 13 13
KLRG1 -0.041 0.1 -10000 0 -0.39 5 5
VAV1 -0.055 0.14 -10000 0 -0.57 8 8
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.037 0.095 -10000 0 -0.37 3 3
negative regulation of mast cell degranulation -0.037 0.096 -10000 0 -0.38 4 4
BTK -0.049 0.14 -10000 0 -0.68 5 5
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.25 0.31 -10000 0 -0.49 98 98
GAB2/PI3K/SHP2 -0.066 0.16 -10000 0 -0.49 9 9
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.042 0.11 -10000 0 -0.3 27 27
RAF1 0.04 0.037 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.32 0.34 -10000 0 -0.62 100 100
FCER1G -0.013 0.11 -10000 0 -0.86 3 3
FCER1A -0.11 0.29 -10000 0 -0.87 24 24
Antigen/IgE/Fc epsilon R1/Fyn -0.069 0.18 -10000 0 -0.51 27 27
MAPK3 0.044 0.032 -10000 0 -10000 0 0
MAPK1 0.044 0.032 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.019 0.13 -10000 0 -0.58 9 9
DUSP1 -0.059 0.22 -10000 0 -0.86 13 13
NF-kappa-B/RelA -0.028 0.061 -10000 0 -0.24 1 1
actin cytoskeleton reorganization -0.012 0.1 -10000 0 -0.39 2 2
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.054 0.14 -10000 0 -0.6 8 8
FER -0.037 0.095 -10000 0 -0.37 3 3
RELA 0 0 -10000 0 -10000 0 0
ITK -0.041 0.14 -10000 0 -0.6 11 11
SOS1 0 0 -10000 0 -10000 0 0
PLCG1 -0.022 0.17 -10000 0 -0.59 8 8
cytokine secretion -0.02 0.044 -10000 0 -10000 0 0
SPHK1 -0.03 0.11 -10000 0 -0.45 4 4
PTK2 -0.013 0.11 -10000 0 -0.41 2 2
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.079 0.18 -10000 0 -0.48 29 29
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.023 0.18 -10000 0 -0.44 29 29
MAP2K2 0.043 0.033 -10000 0 -10000 0 0
MAP2K1 0.042 0.032 -10000 0 -10000 0 0
MAP2K7 0 0 -10000 0 -10000 0 0
KLRG1/SHP2 -0.04 0.1 -10000 0 -0.45 2 2
MAP2K4 0.011 0.008 -10000 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.34 0.36 -10000 0 -0.66 100 100
mol:Choline -0.066 0.16 -10000 0 -0.47 27 27
SHC/Grb2/SOS1 -0.034 0.088 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
DOK1 0 0 -10000 0 -10000 0 0
PXN -0.006 0.1 -10000 0 -0.38 2 2
HCLS1 -0.037 0.095 -10000 0 -0.37 3 3
PRKCB -0.028 0.17 -10000 0 -0.39 32 32
FCGR2B -0.43 0.43 0.34 1 -0.86 95 96
IGHE 0 0.005 -10000 0 -10000 0 0
KLRG1/SHIP -0.038 0.097 -10000 0 -0.38 4 4
LCP2 -0.018 0.12 -10000 0 -0.87 4 4
PLA2G4A -0.075 0.18 -10000 0 -0.58 17 17
RASA1 -0.009 0.088 -10000 0 -0.86 2 2
mol:Phosphatidic acid -0.066 0.16 -10000 0 -0.47 27 27
IKK complex 0.009 0.096 -10000 0 -0.26 10 10
WIPF1 0 0 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.063 0.18 -10000 0 -0.66 14 14
FYN -0.04 0.29 0.37 3 -0.91 16 19
LAT/GRAP2/SLP76 -0.051 0.21 0.69 1 -0.64 18 19
IKBKB 0 0 -10000 0 -10000 0 0
AKT1 0.002 0.17 0.38 3 -0.5 16 19
B2M 0 0.001 -10000 0 -10000 0 0
IKBKG -0.015 0.042 -10000 0 -0.19 5 5
MAP3K8 -0.009 0.088 -10000 0 -0.86 2 2
mol:Ca2+ -0.038 0.06 -10000 0 -0.13 54 54
integrin-mediated signaling pathway -0.009 0.073 -10000 0 -0.59 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.02 0.25 0.43 3 -0.78 16 19
TRPV6 -0.25 0.4 -10000 0 -0.87 55 55
CD28 -0.003 0.067 0.35 1 -0.86 1 2
SHC1 -0.031 0.27 0.4 3 -0.85 16 19
receptor internalization -0.041 0.28 0.4 3 -0.76 21 24
PRF1 -0.031 0.26 -10000 0 -0.89 13 13
KRAS 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
COT/AKT1 0.007 0.14 0.35 3 -0.42 15 18
LAT -0.03 0.27 0.41 3 -0.85 16 19
EntrezGene:6955 0.001 0.002 -10000 0 -10000 0 0
CD3D -0.028 0.2 0.34 7 -0.87 9 16
CD3E -0.044 0.2 0.35 1 -0.88 10 11
CD3G -0.035 0.2 0.34 6 -0.87 10 16
RASGRP2 -0.004 0.031 0.17 3 -0.2 1 4
RASGRP1 0.011 0.18 0.47 3 -0.51 16 19
HLA-A 0 0.002 -10000 0 -10000 0 0
RASSF5 -0.014 0.11 -10000 0 -0.86 3 3
RAP1A/GTP/RAPL -0.009 0.073 -10000 0 -0.59 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.027 0.064 0.27 4 -0.12 13 17
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.029 0.077 -10000 0 -0.27 15 15
PRKCA -0.016 0.096 0.42 1 -0.3 13 14
GRAP2 -0.013 0.13 0.34 3 -0.86 4 7
mol:IP3 0.021 0.2 0.28 46 -0.49 14 60
EntrezGene:6957 0.001 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.047 0.28 0.34 3 -0.91 15 18
ORAI1 0.11 0.18 0.39 55 -10000 0 55
CSK -0.034 0.28 0.39 3 -0.88 16 19
B7 family/CD28 -0.094 0.26 0.53 1 -0.73 22 23
CHUK 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.082 0.32 0.41 3 -1 17 20
PTPN6 -0.039 0.28 0.37 3 -0.89 16 19
VAV1 -0.039 0.29 0.4 3 -0.89 17 20
Monovalent TCR/CD3 -0.056 0.22 0.24 5 -0.59 21 26
CBL 0 0 -10000 0 -10000 0 0
LCK -0.05 0.32 0.41 2 -0.96 17 19
PAG1 -0.035 0.28 0.39 3 -0.86 17 20
RAP1A 0 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.094 0.31 0.4 3 -1 17 20
CD80 -0.023 0.14 -10000 0 -0.86 5 5
CD86 -0.018 0.12 -10000 0 -0.87 4 4
PDK1/CARD11/BCL10/MALT1 -0.033 0.093 -10000 0 -0.34 14 14
HRAS 0.004 0.035 0.34 2 -10000 0 2
GO:0035030 -0.074 0.2 0.45 1 -0.58 22 23
CD8A -0.063 0.24 0.35 3 -0.87 15 18
CD8B -0.032 0.2 0.35 5 -0.87 9 14
PTPRC -0.071 0.24 0.35 1 -0.87 16 17
PDK1/PKC theta 0 0.22 0.43 3 -0.64 16 19
CSK/PAG1 -0.029 0.27 0.42 2 -0.86 16 18
SOS1 0 0 -10000 0 -10000 0 0
peptide-MHC class I 0 0 -10000 0 -10000 0 0
GRAP2/SLP76 -0.066 0.25 0.68 1 -0.77 18 19
STIM1 0.06 0.093 -10000 0 -10000 0 0
RAS family/GTP 0.029 0.078 0.32 3 -0.18 13 16
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.052 0.31 0.4 3 -0.83 21 24
mol:DAG -0.02 0.14 -10000 0 -0.44 14 14
RAP1A/GDP 0.012 0.03 0.16 3 -10000 0 3
PLCG1 0 0 -10000 0 -10000 0 0
CD247 -0.007 0.092 0.34 1 -0.87 2 3
cytotoxic T cell degranulation -0.028 0.24 -10000 0 -0.84 13 13
RAP1A/GTP -0.002 0.007 -10000 0 -0.071 1 1
mol:PI-3-4-5-P3 -0.006 0.2 0.41 3 -0.61 16 19
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.008 0.25 0.31 39 -0.68 14 53
NRAS 0 0 -10000 0 -10000 0 0
ZAP70 -0.004 0.098 0.34 3 -0.87 2 5
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.049 0.21 0.67 1 -0.67 15 16
MALT1 0 0 -10000 0 -10000 0 0
TRAF6 -0.005 0.062 -10000 0 -0.86 1 1
CD8 heterodimer -0.07 0.28 0.48 3 -0.9 17 20
CARD11 -0.024 0.16 0.34 2 -0.86 6 8
PRKCB -0.037 0.15 0.42 1 -0.44 19 20
PRKCE -0.017 0.1 0.31 2 -0.31 14 16
PRKCQ -0.014 0.25 0.44 3 -0.76 16 19
LCP2 -0.018 0.12 -10000 0 -0.86 4 4
BCL10 0 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.008 0.15 0.37 3 -0.41 16 19
IKK complex 0.029 0.062 0.25 3 -0.13 11 14
RAS family/GDP -0.003 0.008 -10000 0 -10000 0 0
MAP3K14 0.016 0.11 0.31 3 -0.31 15 18
PDPK1 0.007 0.16 0.38 3 -0.49 14 17
TCR/CD3/MHC I/CD8/Fyn -0.099 0.35 0.43 3 -1.1 17 20
Coregulation of Androgen receptor activity

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
NRIP1 0.001 0.009 -10000 0 -10000 0 0
SVIL -0.004 0.062 -10000 0 -0.85 1 1
ZNF318 0.002 0.025 -10000 0 -10000 0 0
JMJD2C 0.014 0.037 0.13 18 -10000 0 18
T-DHT/AR/Ubc9 -0.18 0.27 -10000 0 -0.61 53 53
CARM1 0 0 -10000 0 -10000 0 0
PRDX1 0 0 -10000 0 -10000 0 0
PELP1 0 0.004 -10000 0 -10000 0 0
CTNNB1 0.001 0.007 -10000 0 -10000 0 0
AKT1 0.001 0.006 -10000 0 -10000 0 0
PTK2B 0.001 0.005 -10000 0 -10000 0 0
MED1 0.001 0.006 -10000 0 -10000 0 0
MAK 0.002 0.025 -10000 0 -10000 0 0
response to oxidative stress 0 0.002 -10000 0 -10000 0 0
HIP1 -0.017 0.12 -10000 0 -0.86 4 4
GSN 0.001 0.009 -10000 0 -10000 0 0
NCOA2 -0.095 0.27 -10000 0 -0.86 21 21
NCOA6 0.001 0.009 -10000 0 -10000 0 0
DNA-PK 0.002 0.022 -10000 0 -10000 0 0
NCOA4 0 0 -10000 0 -10000 0 0
PIAS3 0.001 0.007 -10000 0 -10000 0 0
cell proliferation -0.031 0.048 -10000 0 -10000 0 0
XRCC5 0.001 0.006 -10000 0 -10000 0 0
UBE3A 0.001 0.014 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.18 0.28 -10000 0 -0.62 55 55
FHL2 -0.15 0.34 -10000 0 -1.3 15 15
RANBP9 0.001 0.009 -10000 0 -10000 0 0
JMJD1A -0.009 0.051 -10000 0 -0.13 29 29
CDK6 -0.054 0.21 -10000 0 -0.86 12 12
TGFB1I1 0.001 0.01 -10000 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.2 0.31 -10000 0 -0.65 59 59
XRCC6 0.001 0.006 -10000 0 -10000 0 0
T-DHT/AR -0.18 0.3 -10000 0 -0.61 57 57
CTDSP1 0.001 0.003 -10000 0 -10000 0 0
CTDSP2 0.002 0.014 -10000 0 -10000 0 0
BRCA1 0.001 0.01 -10000 0 -10000 0 0
TCF4 0.001 0.01 -10000 0 -10000 0 0
CDKN2A 0.22 0.16 0.34 123 -10000 0 123
SRF 0.002 0.037 -10000 0 -10000 0 0
NKX3-1 -0.21 0.43 -10000 0 -1.4 22 22
KLK3 -0.014 0.21 -10000 0 -1.6 3 3
TMF1 0.001 0.003 -10000 0 -10000 0 0
HNRNPA1 0.001 0.008 -10000 0 -10000 0 0
AOF2 0 0.01 -10000 0 -0.073 3 3
APPL1 0.002 0.013 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.18 0.27 -10000 0 -0.61 53 53
AR -0.25 0.39 -10000 0 -0.88 53 53
UBA3 0.001 0.003 -10000 0 -10000 0 0
PATZ1 0.001 0.008 -10000 0 -10000 0 0
PAWR 0.001 0.003 -10000 0 -10000 0 0
PRKDC 0.001 0.006 -10000 0 -10000 0 0
PA2G4 0.001 0.011 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.16 0.25 -10000 0 -0.57 53 53
RPS6KA3 -0.004 0.063 -10000 0 -0.86 1 1
T-DHT/AR/ARA70 -0.18 0.28 -10000 0 -0.61 53 53
LATS2 0.001 0.008 -10000 0 -10000 0 0
T-DHT/AR/PRX1 -0.16 0.25 -10000 0 -0.56 53 53
Cyclin D3/CDK11 p58 0 0 -10000 0 -10000 0 0
VAV3 0.008 0.049 0.34 4 -10000 0 4
KLK2 -0.042 0.14 -10000 0 -10000 0 0
CASP8 0 0.002 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.22 0.33 -10000 0 -0.67 61 61
TMPRSS2 -0.13 0.28 -10000 0 -1.4 8 8
CCND1 -0.045 0.19 -10000 0 -0.87 10 10
PIAS1 0.001 0.014 -10000 0 -10000 0 0
mol:T-DHT -0.006 0.033 -10000 0 -0.084 24 24
CDC2L1 0 0.001 -10000 0 -10000 0 0
PIAS4 0 0.024 -10000 0 -10000 0 0
T-DHT/AR/CDK6 -0.21 0.31 -10000 0 -0.64 61 61
CMTM2 0.004 0.035 0.34 2 -10000 0 2
SNURF -0.01 0.11 0.34 2 -0.86 3 5
ZMIZ1 -0.004 0.035 0.33 1 -10000 0 1
CCND3 0 0 -10000 0 -10000 0 0
TGIF1 0.001 0.008 -10000 0 -10000 0 0
FKBP4 0.001 0.009 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0 0 -10000 0 -10000 0 0
SPHK1 0.043 0.15 0.34 29 -0.86 2 31
GNAI2 0 0 -10000 0 -10000 0 0
mol:S1P 0.017 0.064 0.23 2 -0.38 2 4
GNAO1 -0.4 0.43 -10000 0 -0.86 88 88
mol:Sphinganine-1-P 0.019 0.093 -10000 0 -0.67 2 2
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 -0.005 0.045 -10000 0 -0.5 1 1
GNAI3 0 0 -10000 0 -10000 0 0
G12/G13 0 0 -10000 0 -10000 0 0
S1PR3 -0.007 0.091 0.34 1 -0.86 2 3
S1PR2 -0.005 0.062 -10000 0 -0.86 1 1
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P 0.011 0.048 -10000 0 -0.33 2 2
S1PR5 -0.016 0.13 0.34 1 -0.86 4 5
S1PR4 0.002 0.025 0.34 1 -10000 0 1
GNAI1 -0.009 0.088 -10000 0 -0.86 2 2
S1P/S1P5/G12 -0.013 0.091 -10000 0 -0.6 4 4
S1P/S1P3/Gq -0.053 0.15 -10000 0 -0.34 31 31
S1P/S1P4/Gi -0.11 0.18 -10000 0 -0.35 34 34
GNAQ -0.005 0.062 -10000 0 -0.86 1 1
GNAZ 0.16 0.17 0.34 91 -10000 0 91
GNA14 -0.14 0.31 -10000 0 -0.86 30 30
GNA15 0.002 0.025 0.34 1 -10000 0 1
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.023 0.14 -10000 0 -0.86 5 5
ABCC1 0.005 0.042 0.34 3 -10000 0 3
Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved) -0.012 0.11 -10000 0 -0.68 4 4
HDAC1 0.006 0.017 -10000 0 -10000 0 0
AES 0.003 0.008 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
DTX1 -0.28 0.4 -10000 0 -0.86 62 62
LRP6/FZD1 -0.009 0.085 -10000 0 -0.67 3 3
TLE1 0.001 0.007 -10000 0 -10000 0 0
AP1 -0.18 0.24 -10000 0 -0.39 94 94
NCSTN 0 0 -10000 0 -10000 0 0
ADAM10 -0.005 0.062 -10000 0 -0.86 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.034 0.096 -10000 0 -0.61 1 1
NICD/RBPSUH -0.004 0.054 -10000 0 -0.75 1 1
WIF1 0.032 0.1 0.34 18 -10000 0 18
NOTCH1 -0.004 0.058 -10000 0 -0.8 1 1
PSENEN 0 0 -10000 0 -10000 0 0
KREMEN2 0.036 0.1 0.34 20 -10000 0 20
DKK1 0.11 0.16 0.34 63 -10000 0 63
beta catenin/beta TrCP1 -0.013 0.023 -10000 0 -10000 0 0
APH1B 0 0 -10000 0 -10000 0 0
APH1A 0 0 -10000 0 -10000 0 0
AXIN1 0.002 0.025 -10000 0 -0.22 1 1
CtBP/CBP/TCF1/TLE1/AES 0.016 0.074 0.28 5 -0.37 2 7
PSEN1 0 0 -10000 0 -10000 0 0
FOS -0.4 0.43 -10000 0 -0.86 89 89
JUN -0.018 0.12 -10000 0 -0.86 4 4
MAP3K7 0.003 0.008 -10000 0 -10000 0 0
CTNNB1 0.006 0.055 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.052 0.098 0.42 3 -10000 0 3
HNF1A -0.011 0.11 -10000 0 -0.86 3 3
CTBP1 0.003 0.008 -10000 0 -10000 0 0
MYC -0.15 0.45 -10000 0 -1.6 18 18
NKD1 0.029 0.24 0.34 39 -0.86 9 48
FZD1 -0.012 0.11 0.34 1 -0.86 3 4
NOTCH1 precursor/Deltex homolog 1 -0.16 0.24 -10000 0 -0.5 63 63
apoptosis -0.18 0.24 -10000 0 -0.39 94 94
Delta 1/NOTCHprecursor -0.012 0.11 -10000 0 -0.68 4 4
DLL1 -0.015 0.13 0.34 2 -0.86 4 6
PPARD -0.01 0.03 -10000 0 -10000 0 0
Gamma Secretase 0 0 -10000 0 -10000 0 0
APC 0.002 0.025 -10000 0 -0.22 1 1
DVL1 -0.001 0.011 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0.001 0.007 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.092 0.12 0.42 7 -10000 0 7
LRP6 0 0 -10000 0 -10000 0 0
CSNK1A1 0 0 -10000 0 -10000 0 0
NLK 0.007 0.019 -10000 0 -10000 0 0
CCND1 -0.087 0.35 -10000 0 -1.6 10 10
WNT1 0.005 0.042 0.34 3 -10000 0 3
Axin1/APC/beta catenin 0.022 0.036 -10000 0 -10000 0 0
DKK2 0.048 0.12 0.34 27 -10000 0 27
NOTCH1 precursor/DVL1 -0.004 0.049 -10000 0 -0.68 1 1
GSK3B 0.001 0.004 -10000 0 -10000 0 0
FRAT1 0.002 0.005 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.16 0.24 -10000 0 -0.5 63 63
PPP2R5D 0.001 0.086 0.36 9 -10000 0 9
MAPK1 0 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.015 0.096 -10000 0 -0.54 3 3
RBPJ 0 0 -10000 0 -10000 0 0
CREBBP 0.009 0.003 -10000 0 -10000 0 0
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0 0 -10000 0 -9999 0 0
PLK4 0.062 0.13 0.34 35 -9999 0 35
regulation of centriole replication 0.031 0.065 -10000 0 -9999 0 0
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.14 0.26 0.38 1 -0.52 58 59
SMAD6-7/SMURF1 -0.024 0.12 -10000 0 -0.58 8 8
NOG 0.005 0.042 0.34 3 -10000 0 3
SMAD9 -0.053 0.13 -10000 0 -0.56 9 9
SMAD4 -0.005 0.062 -10000 0 -0.86 1 1
SMAD5 -0.073 0.18 -10000 0 -0.38 40 40
BMP7/USAG1 0.062 0.12 0.48 6 -10000 0 6
SMAD5/SKI -0.096 0.15 -10000 0 -0.55 4 4
SMAD1 0.01 0.065 -10000 0 -0.69 1 1
BMP2 -0.014 0.11 -10000 0 -0.86 3 3
SMAD1/SMAD1/SMAD4 -0.026 0.096 -10000 0 -0.64 2 2
BMPR1A 0 0 -10000 0 -10000 0 0
BMPR1B -0.19 0.37 0.34 3 -0.86 43 46
BMPR1A-1B/BAMBI -0.17 0.31 -10000 0 -0.66 51 51
AHSG -0.15 0.33 -10000 0 -0.86 33 33
CER1 0.005 0.042 0.34 3 -10000 0 3
BMP2-4/CER1 0.008 0.094 -10000 0 -0.58 3 3
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.086 0.16 -10000 0 -0.62 4 4
BMP2-4 (homodimer) 0.005 0.1 -10000 0 -0.66 3 3
RGMB -0.007 0.091 0.34 1 -0.86 2 3
BMP6/BMPR2/BMPR1A-1B -0.12 0.23 -10000 0 -0.54 44 44
RGMA 0.023 0.086 0.34 13 -10000 0 13
SMURF1 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.091 0.16 -10000 0 -0.6 4 4
BMP2-4/USAG1 0.038 0.12 0.42 1 -0.57 3 4
SMAD6/SMURF1/SMAD5 -0.096 0.15 -10000 0 -0.55 4 4
SOSTDC1 0.052 0.12 0.34 29 -10000 0 29
BMP7/BMPR2/BMPR1A-1B -0.095 0.25 0.4 1 -0.54 43 44
SKI 0 0 -10000 0 -10000 0 0
BMP6 (homodimer) -0.003 0.067 0.34 1 -0.86 1 2
HFE2 -0.11 0.29 -10000 0 -0.86 24 24
ZFYVE16 0 0 -10000 0 -10000 0 0
MAP3K7 0 0 -10000 0 -10000 0 0
BMP2-4/CHRD -0.014 0.14 -10000 0 -0.57 9 9
SMAD5/SMAD5/SMAD4 -0.098 0.15 -10000 0 -0.53 5 5
MAPK1 0 0 -10000 0 -10000 0 0
TAK1/TAB family -0.084 0.12 -10000 0 -0.51 4 4
BMP7 (homodimer) 0.039 0.11 0.34 22 -10000 0 22
NUP214 0 0 -10000 0 -10000 0 0
BMP6/FETUA -0.12 0.26 -10000 0 -0.67 34 34
SMAD1/SKI -0.015 0.051 -10000 0 -0.65 1 1
SMAD6 -0.027 0.15 -10000 0 -0.86 6 6
CTDSP2 0 0 -10000 0 -10000 0 0
BMP2-4/FETUA -0.097 0.24 -10000 0 -0.58 36 36
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 -0.064 0.29 0.34 15 -0.86 20 35
BMPR2 (homodimer) 0 0 -10000 0 -10000 0 0
GADD34/PP1CA 0.001 0.015 -10000 0 -10000 0 0
BMPR1A-1B (homodimer) -0.15 0.28 -10000 0 -0.67 43 43
CHRDL1 -0.17 0.36 0.34 6 -0.86 39 45
ENDOFIN/SMAD1 -0.015 0.051 -10000 0 -0.65 1 1
SMAD6-7/SMURF1/SMAD1 -0.03 0.11 -10000 0 -0.5 8 8
SMAD6/SMURF1 0 0 -10000 0 -10000 0 0
BAMBI -0.066 0.23 0.34 1 -0.86 15 16
SMURF2 0 0 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.11 0.26 -10000 0 -0.59 41 41
BMP2-4/GREM1 -0.041 0.21 -10000 0 -0.58 23 23
SMAD7 -0.009 0.088 -10000 0 -0.86 2 2
SMAD8A/SMAD8A/SMAD4 -0.055 0.12 -10000 0 -0.52 10 10
SMAD1/SMAD6 -0.015 0.051 -10000 0 -0.65 1 1
TAK1/SMAD6 0 0 -10000 0 -10000 0 0
BMP7 0.039 0.11 0.34 22 -10000 0 22
BMP6 -0.003 0.067 0.34 1 -0.86 1 2
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.074 0.13 -10000 0 -0.49 5 5
PPM1A 0 0 -10000 0 -10000 0 0
SMAD1/SMURF2 -0.015 0.051 -10000 0 -0.65 1 1
SMAD7/SMURF1 -0.007 0.068 -10000 0 -0.67 2 2
CTDSPL 0 0 -10000 0 -10000 0 0
PPP1CA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
CTDSP1 0 0 -10000 0 -10000 0 0
PPP1R15A 0.002 0.025 0.34 1 -10000 0 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.11 0.18 -10000 0 -0.57 12 12
CHRD -0.027 0.15 -10000 0 -0.86 6 6
BMPR2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.092 0.16 -10000 0 -0.62 4 4
BMP4 0.025 0.089 0.34 14 -10000 0 14
FST -0.075 0.25 0.34 1 -0.86 17 18
BMP2-4/NOG 0.008 0.094 -10000 0 -0.58 3 3
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.089 0.23 0.38 1 -0.5 43 44
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization -0.019 0.079 -10000 0 -0.36 10 10
epithelial cell differentiation -0.026 0.11 -10000 0 -0.5 10 10
CYFIP2 -0.054 0.21 -10000 0 -0.86 12 12
ENAH 0.022 0.12 -10000 0 -0.51 4 4
EGFR -0.014 0.11 -10000 0 -0.86 3 3
EPHA2 -0.036 0.17 -10000 0 -0.86 8 8
MYO6 -0.025 0.11 -10000 0 -0.48 10 10
CTNNB1 0 0 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.037 0.14 -10000 0 -0.58 12 12
AQP5 -0.018 0.093 -10000 0 -0.42 8 8
CTNND1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.025 0.1 -10000 0 -0.47 10 10
regulation of calcium-dependent cell-cell adhesion -0.013 0.12 -10000 0 -0.47 11 11
EGF 0.08 0.14 0.34 45 -10000 0 45
NCKAP1 0 0 -10000 0 -10000 0 0
AQP3 -0.074 0.2 -10000 0 -0.67 16 16
cortical microtubule organization -0.026 0.11 -10000 0 -0.5 10 10
GO:0000145 -0.023 0.1 -10000 0 -0.45 10 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.027 0.11 -10000 0 -0.51 10 10
MLLT4 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.042 0.15 -10000 0 -0.78 4 4
ARF6 0 0 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.028 0.12 -10000 0 -0.54 10 10
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.023 0.099 -10000 0 -0.44 10 10
PVRL2 0 0 -10000 0 -10000 0 0
ZYX -0.025 0.11 -10000 0 -0.48 10 10
ARF6/GTP -0.026 0.11 -10000 0 -0.49 10 10
CDH1 -0.045 0.19 -10000 0 -0.86 10 10
EGFR/EGFR/EGF/EGF -0.004 0.15 -10000 0 -0.54 11 11
RhoA/GDP -0.025 0.1 -10000 0 -0.47 10 10
actin cytoskeleton organization -0.023 0.1 -10000 0 -0.45 10 10
IGF-1R heterotetramer -0.005 0.095 0.34 2 -0.86 2 4
GIT1 0 0 -10000 0 -10000 0 0
IGF1R -0.005 0.095 0.34 2 -0.86 2 4
IGF1 -0.34 0.42 -10000 0 -0.86 74 74
DIAPH1 -0.052 0.18 -10000 0 -0.72 13 13
Wnt receptor signaling pathway 0.026 0.11 0.5 10 -10000 0 10
RHOA 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.042 0.15 -10000 0 -0.79 4 4
CTNNA1 0 0 -10000 0 -10000 0 0
VCL -0.024 0.1 -10000 0 -0.46 10 10
EFNA1 -0.009 0.088 -10000 0 -0.86 2 2
LPP -0.024 0.1 -10000 0 -0.45 10 10
Ephrin A1/EPHA2 -0.048 0.17 -10000 0 -0.58 16 16
SEC6/SEC8 -0.022 0.094 -10000 0 -0.42 10 10
MGAT3 -0.014 0.13 -10000 0 -0.48 11 11
HGF/MET -0.24 0.26 -10000 0 -0.5 93 93
HGF -0.41 0.43 -10000 0 -0.86 90 90
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN -0.019 0.08 -10000 0 -0.36 10 10
actin cable formation 0.029 0.11 -10000 0 -0.4 6 6
KIAA1543 -0.036 0.15 -10000 0 -0.57 12 12
KIFC3 -0.025 0.11 -10000 0 -0.48 10 10
NCK1 0 0 -10000 0 -10000 0 0
EXOC3 0 0 -10000 0 -10000 0 0
ACTN1 -0.025 0.11 -10000 0 -0.48 10 10
NCK1/GIT1 0 0 -10000 0 -10000 0 0
mol:GDP -0.026 0.11 -10000 0 -0.5 10 10
EXOC4 0 0 -10000 0 -10000 0 0
STX4 -0.025 0.11 -10000 0 -0.48 10 10
PIP5K1C -0.025 0.11 -10000 0 -0.48 10 10
LIMA1 0 0 -10000 0 -10000 0 0
ABI1 0 0 -10000 0 -10000 0 0
ROCK1 -0.035 0.12 -10000 0 -0.64 4 4
adherens junction assembly 0.01 0.15 -10000 0 -0.65 6 6
IGF-1R heterotetramer/IGF1 -0.21 0.24 -10000 0 -0.48 83 83
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
MET 0.002 0.025 0.34 1 -10000 0 1
PLEKHA7 -0.03 0.12 -10000 0 -0.48 12 12
mol:GTP -0.028 0.12 -10000 0 -0.53 10 10
establishment of epithelial cell apical/basal polarity -0.021 0.09 -10000 0 -10000 0 0
cortical actin cytoskeleton stabilization -0.019 0.079 -10000 0 -0.36 10 10
regulation of cell-cell adhesion -0.023 0.1 -10000 0 -0.45 10 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton -0.019 0.08 -10000 0 -0.36 10 10
S1P3 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
PDGFRB 0.005 0.042 0.34 3 -10000 0 3
mol:S1P 0.001 0.001 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.095 0.16 -10000 0 -0.3 40 40
GNAO1 -0.4 0.43 -10000 0 -0.86 88 88
S1P/S1P3/G12/G13 -0.004 0.057 -10000 0 -0.54 2 2
AKT1 -0.037 0.076 0.21 1 -0.24 2 3
AKT3 -0.054 0.11 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.005 0.042 0.34 3 -10000 0 3
GNAI2 0 0.003 -10000 0 -10000 0 0
GNAI3 0 0.001 -10000 0 -10000 0 0
GNAI1 -0.009 0.088 -10000 0 -0.86 2 2
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 -0.007 0.092 0.34 1 -0.86 2 3
S1PR2 -0.005 0.062 -10000 0 -0.86 1 1
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.2 -10000 0 -0.38 40 40
MAPK3 -0.12 0.19 -10000 0 -0.73 4 4
MAPK1 -0.12 0.19 -10000 0 -0.73 4 4
JAK2 -0.1 0.2 -10000 0 -0.36 40 40
CXCR4 -0.12 0.19 -10000 0 -0.68 5 5
FLT1 0 0.004 -10000 0 -10000 0 0
RhoA/GDP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0 0 -10000 0 -10000 0 0
SRC -0.12 0.19 -10000 0 -0.73 4 4
S1P/S1P3/Gi -0.13 0.2 -10000 0 -0.39 40 40
RAC1 0 0 -10000 0 -10000 0 0
RhoA/GTP -0.14 0.16 -10000 0 -0.7 4 4
VEGFA 0 0.004 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.13 0.2 -10000 0 -0.38 40 40
VEGFR1 homodimer/VEGFA homodimer 0.001 0.01 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
S1P/S1P3/Gq -0.071 0.16 -10000 0 -0.39 36 36
GNAQ -0.005 0.062 -10000 0 -0.86 1 1
GNAZ 0.16 0.17 0.34 91 -10000 0 91
G12/G13 0 0 -10000 0 -10000 0 0
GNA14 -0.14 0.31 -10000 0 -0.86 30 30
GNA15 0.002 0.025 0.34 1 -10000 0 1
GNA12 0 0 -10000 0 -10000 0 0
GNA13 0 0 -10000 0 -10000 0 0
GNA11 -0.023 0.14 -10000 0 -0.86 5 5
Rac1/GTP -0.14 0.16 -10000 0 -0.7 4 4
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.037 0.13 -10000 0 -0.51 14 14
TRAF2/ASK1 -0.04 0.15 -10000 0 -0.59 13 13
ATM 0 0 -10000 0 -10000 0 0
MAP2K3 -0.045 0.084 -10000 0 -0.3 4 4
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.062 0.15 -10000 0 -0.52 15 15
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.13 0.31 -10000 0 -0.86 28 28
TXN 0 0 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
GADD45A -0.014 0.11 -10000 0 -0.86 3 3
GADD45B -0.14 0.31 -10000 0 -0.86 30 30
MAP3K1 0 0 -10000 0 -10000 0 0
MAP3K6 0.002 0.025 0.34 1 -10000 0 1
MAP3K7 0 0 -10000 0 -10000 0 0
MAP3K4 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 -0.044 0.17 -10000 0 -0.67 13 13
TAK1/TAB family -0.003 0.02 -10000 0 -0.22 1 1
RAC1/OSM/MEKK3 0 0 -10000 0 -10000 0 0
TRAF2 0 0 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.041 0.053 -10000 0 -10000 0 0
TRAF6 -0.002 0.034 -10000 0 -0.47 1 1
RAC1 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.42 0.43 -10000 0 -0.86 92 92
CCM2 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.28 0.3 -10000 0 -0.59 92 92
MAPK11 0.009 0.054 0.34 5 -10000 0 5
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.3 0.29 -10000 0 -0.56 101 101
OSM/MEKK3 0 0 -10000 0 -10000 0 0
TAOK1 -0.002 0.034 -10000 0 -0.47 1 1
TAOK2 0 0 -10000 0 -10000 0 0
TAOK3 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 -0.059 0.22 -10000 0 -0.86 13 13
MAP3K10 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
TRX/ASK1 -0.04 0.15 -10000 0 -0.58 13 13
GADD45/MTK1/MTK1 -0.16 0.3 -10000 0 -0.63 49 49
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.013 0.044 -9999 0 -0.59 1 1
ADCY5 -0.092 0.23 -9999 0 -0.59 34 34
ADCY6 0.013 0.044 -9999 0 -0.59 1 1
ADCY7 0.013 0.044 -9999 0 -0.59 1 1
ADCY1 -0.2 0.3 -9999 0 -0.6 66 66
ADCY2 0.011 0.047 -9999 0 -0.6 1 1
ADCY3 0.014 0.045 -9999 0 -0.59 1 1
ADCY8 0.02 0.054 -9999 0 -0.6 1 1
PRKCE -0.003 0.05 -9999 0 -0.68 1 1
ADCY9 0.013 0.044 -9999 0 -0.59 1 1
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.032 0.095 -9999 0 -0.28 15 15
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.008 0.043 0.34 3 -10000 0 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.15 0.25 0.8 13 -10000 0 13
IL27/IL27R/JAK1 -0.22 0.3 -10000 0 -0.85 15 15
TBX21 -0.15 0.26 -10000 0 -0.66 19 19
IL12B 0.005 0.037 0.36 2 -10000 0 2
IL12A 0.01 0.02 -10000 0 -10000 0 0
IL6ST -0.21 0.37 -10000 0 -0.87 46 46
IL27RA/JAK1 -0.008 0.017 -10000 0 -10000 0 0
IL27 -0.17 0.35 -10000 0 -0.87 38 38
TYK2 0.003 0.01 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.032 0.14 -10000 0 -10000 0 0
T-helper 2 cell differentiation 0.15 0.25 0.8 13 -10000 0 13
T cell proliferation during immune response 0.15 0.25 0.8 13 -10000 0 13
MAPKKK cascade -0.15 0.25 -10000 0 -0.8 13 13
STAT3 0 0 -10000 0 -10000 0 0
STAT2 0 0 -10000 0 -10000 0 0
STAT1 0 0.003 -10000 0 -10000 0 0
IL12RB1 -0.035 0.17 -10000 0 -0.86 8 8
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.14 0.26 -10000 0 -0.68 18 18
IL27/IL27R/JAK2/TYK2 -0.15 0.26 -10000 0 -0.82 13 13
positive regulation of T cell mediated cytotoxicity -0.15 0.25 -10000 0 -0.8 13 13
STAT1 (dimer) -0.22 0.31 0.5 6 -0.91 15 21
JAK2 -0.002 0.064 -10000 0 -0.87 1 1
JAK1 0 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.16 0.23 -10000 0 -0.89 10 10
T cell proliferation -0.21 0.28 -10000 0 -0.66 34 34
IL12/IL12R/TYK2/JAK2 0.002 0.087 -10000 0 -10000 0 0
IL17A -0.032 0.14 -10000 0 -10000 0 0
mast cell activation 0.15 0.25 0.8 13 -10000 0 13
IFNG -0.012 0.037 0.12 3 -0.09 10 13
T cell differentiation -0.006 0.007 -10000 0 -0.021 13 13
STAT3 (dimer) -0.16 0.23 -10000 0 -0.89 10 10
STAT5A (dimer) -0.16 0.23 -10000 0 -0.89 10 10
STAT4 (dimer) -0.18 0.26 -10000 0 -0.87 16 16
STAT4 -0.032 0.16 -10000 0 -0.86 7 7
T cell activation -0.012 0.008 -10000 0 -10000 0 0
IL27R/JAK2/TYK2 -0.12 0.24 -10000 0 -0.62 12 12
GATA3 -0.075 0.41 -10000 0 -1.5 15 15
IL18 -0.009 0.099 -10000 0 -0.68 4 4
positive regulation of mast cell cytokine production -0.15 0.22 -10000 0 -0.86 10 10
IL27/EBI3 -0.16 0.29 -10000 0 -0.67 47 47
IL27RA -0.012 0.021 -10000 0 -10000 0 0
IL6 -0.11 0.3 0.34 5 -0.86 26 31
STAT5A 0.002 0.025 0.34 1 -10000 0 1
monocyte differentiation 0 0.001 -10000 0 -10000 0 0
IL2 0.01 0.016 -10000 0 -10000 0 0
IL1B -0.092 0.24 -10000 0 -0.68 27 27
EBI3 -0.039 0.18 -10000 0 -0.86 9 9
TNF -0.032 0.15 -10000 0 -0.68 10 10
Visual signal transduction: Rods

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:K + 0 0 -10000 0 -10000 0 0
GNAT1/GTP 0.002 0.023 0.23 2 -10000 0 2
Metarhodopsin II/Arrestin 0.002 0.021 -10000 0 -10000 0 0
PDE6G/GNAT1/GTP -0.016 0.11 -10000 0 -0.59 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.004 0.035 0.34 2 -10000 0 2
GRK1 0 0 -10000 0 -10000 0 0
CNG Channel -0.12 0.22 -10000 0 -0.48 49 49
mol:Na + -0.12 0.21 -10000 0 -0.47 50 50
mol:ADP 0 0 -10000 0 -10000 0 0
RGS9-1/Gbeta5/R9AP 0 0.13 0.42 2 -0.58 7 9
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel -0.12 0.22 -10000 0 -0.48 50 50
CNGB1 0.009 0.054 0.34 5 -10000 0 5
RDH5 -0.11 0.29 -10000 0 -0.86 25 25
SAG 0.002 0.025 0.34 1 -10000 0 1
mol:Ca2+ -0.12 0.2 -10000 0 -0.46 45 45
Na + (4 Units) -0.11 0.2 -10000 0 -0.44 45 45
RGS9 -0.016 0.18 0.34 9 -0.86 7 16
GNB1/GNGT1 0.026 0.073 -10000 0 -10000 0 0
GNAT1/GDP 0.002 0.12 0.37 2 -0.51 7 9
GUCY2D 0.027 0.092 0.34 15 -10000 0 15
GNGT1 0.037 0.11 0.34 21 -10000 0 21
GUCY2F 0 0 -10000 0 -10000 0 0
GNB5 0.002 0.025 0.34 1 -10000 0 1
mol:GMP (4 units) -0.002 0.12 -10000 0 -0.59 6 6
mol:11-cis-retinal -0.11 0.29 -10000 0 -0.86 25 25
mol:cGMP -0.004 0.09 -10000 0 -0.52 5 5
GNB1 0 0 -10000 0 -10000 0 0
Rhodopsin -0.087 0.23 -10000 0 -0.67 25 25
SLC24A1 0 0 -10000 0 -10000 0 0
CNGA1 -0.21 0.37 -10000 0 -0.86 46 46
Metarhodopsin II 0.001 0.014 -10000 0 -10000 0 0
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.002 0.1 -10000 0 -0.55 5 5
RGS9BP 0.016 0.072 0.34 9 -10000 0 9
Metarhodopsin II/Transducin 0.014 0.036 -10000 0 -10000 0 0
GCAP Family/Ca ++ -0.013 0.09 -10000 0 -0.55 5 5
PDE6A/B 0.017 0.083 -10000 0 -0.68 1 1
mol:Pi 0 0.13 0.41 2 -0.58 7 9
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.024 0.065 -10000 0 -10000 0 0
PDE6B 0.01 0.093 0.34 8 -0.86 1 9
PDE6A 0.016 0.072 0.34 9 -10000 0 9
PDE6G -0.027 0.15 -10000 0 -0.86 6 6
RHO 0.002 0.025 0.34 1 -10000 0 1
PDE6 -0.004 0.16 0.33 3 -0.52 13 16
GUCA1A 0.002 0.025 0.34 1 -10000 0 1
GC2/GCAP Family -0.013 0.089 -10000 0 -0.55 5 5
GUCA1C 0 0 -10000 0 -10000 0 0
GUCA1B -0.023 0.14 -10000 0 -0.86 5 5
Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.013 0.089 -10000 0 -0.55 5 5
CRKL 0 0 -10000 0 -10000 0 0
Rac1/GDP 0 0 -10000 0 -10000 0 0
DOCK1 -0.018 0.12 -10000 0 -0.86 4 4
ITGA4 -0.012 0.11 0.34 1 -0.86 3 4
alpha4/beta7 Integrin/MAdCAM1 -0.012 0.091 0.4 1 -0.54 5 6
EPO -0.29 0.43 0.34 8 -0.86 68 76
alpha4/beta7 Integrin -0.016 0.11 -10000 0 -0.67 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.009 0.085 -10000 0 -0.67 3 3
EPO/EPOR (dimer) -0.23 0.33 -10000 0 -0.67 68 68
lamellipodium assembly -0.005 0.063 -10000 0 -0.87 1 1
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
PI3K -0.006 0.087 -10000 0 -1.2 1 1
ARF6 0 0 -10000 0 -10000 0 0
JAK2 -0.14 0.2 -10000 0 -0.4 70 70
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
MADCAM1 0.002 0.025 0.34 1 -10000 0 1
cell adhesion -0.012 0.09 0.39 1 -0.53 5 6
CRKL/CBL 0 0 -10000 0 -10000 0 0
ITGB1 0 0 -10000 0 -10000 0 0
SRC -0.045 0.17 -10000 0 -0.6 15 15
ITGB7 -0.009 0.088 -10000 0 -0.86 2 2
RAC1 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.049 0.18 -10000 0 -0.65 15 15
p130Cas/Crk/Dock1 -0.049 0.17 -10000 0 -0.59 16 16
VCAM1 -0.062 0.23 0.34 1 -0.86 14 15
RHOA 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.007 0.068 -10000 0 -0.54 3 3
BCAR1 -0.042 0.16 -10000 0 -0.56 15 15
EPOR 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0 0 -10000 0 -10000 0 0
GIT1 0 0 -10000 0 -10000 0 0
Rac1/GTP -0.005 0.067 -10000 0 -0.92 1 1
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -10000 0 -10000 0 0
PRKCZ -0.036 0.17 -10000 0 -0.86 8 8
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.074 0.16 -10000 0 -0.4 20 20
IRAK/TOLLIP 0.001 0.012 -10000 0 -10000 0 0
IKBKB 0 0 -10000 0 -10000 0 0
IKBKG 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.001 0.054 -10000 0 -0.67 1 1
IL1A 0.002 0.025 0.34 1 -10000 0 1
IL1B -0.095 0.23 -10000 0 -0.67 27 27
IRAK/TRAF6/p62/Atypical PKCs -0.019 0.1 -10000 0 -0.46 9 9
IL1R2 -0.003 0.067 0.34 1 -0.86 1 2
IL1R1 -0.014 0.11 -10000 0 -0.86 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.06 0.15 -10000 0 -0.78 4 4
TOLLIP 0 0 -10000 0 -10000 0 0
TICAM2 -0.005 0.062 -10000 0 -0.86 1 1
MAP3K3 0 0 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -10000 0 -10000 0 0
IKK complex/ELKS -0.006 0.035 -10000 0 -10000 0 0
JUN -0.004 0.15 -10000 0 -0.5 15 15
MAP3K7 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.13 0.26 -10000 0 -0.55 44 44
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.063 0.2 -10000 0 -0.61 20 20
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.06 0.19 -10000 0 -0.58 20 20
IL1 beta fragment/IL1R1/IL1RAP -0.14 0.28 -10000 0 -0.6 44 44
NFKB1 0 0 -10000 0 -10000 0 0
MAPK8 -0.03 0.13 -10000 0 -0.49 13 13
IRAK1 0.001 0.014 -10000 0 -10000 0 0
IL1RN/IL1R1 -0.088 0.23 -10000 0 -0.67 25 25
IRAK4 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
TRAF6 -0.005 0.062 -10000 0 -0.86 1 1
PI3K -0.006 0.087 -10000 0 -1.2 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.083 0.18 -10000 0 -0.46 20 20
CHUK 0 0 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.14 0.28 -10000 0 -0.6 44 44
IL1 beta/IL1R2 -0.084 0.22 -10000 0 -0.6 27 27
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.036 -10000 0 -0.48 1 1
NF kappa B1 p50/RelA -0.11 0.23 -10000 0 -0.49 44 44
IRAK3 -0.023 0.14 -10000 0 -0.86 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.13 0.25 -10000 0 -0.54 45 45
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.042 0.13 -10000 0 -0.41 20 20
IL1 alpha/IL1R1/IL1RAP -0.069 0.21 -10000 0 -0.67 20 20
RELA 0 0 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.004 0.035 0.34 2 -10000 0 2
MYD88 0 0 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 -0.002 0.039 -10000 0 -0.51 1 1
IL1RAP -0.09 0.26 -10000 0 -0.86 20 20
UBE2N 0 0 -10000 0 -10000 0 0
IRAK/TRAF6 -0.1 0.2 -10000 0 -0.93 4 4
CASP1 0 0 -10000 0 -10000 0 0
IL1RN/IL1R2 -0.079 0.23 -10000 0 -0.7 22 22
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.13 0.26 -10000 0 -0.57 44 44
TMEM189-UBE2V1 0 0 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.033 0.11 -10000 0 -0.68 3 3
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
IL1RN -0.099 0.28 -10000 0 -0.86 22 22
TRAF6/TAK1/TAB1/TAB2 -0.003 0.036 -10000 0 -0.5 1 1
MAP2K6 -0.007 0.096 -10000 0 -0.59 4 4
FAS signaling pathway (CD95)

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
SPTAN1 0 0.036 -10000 0 -0.39 1 1
RFC1 0 0.036 -10000 0 -0.39 1 1
PRKDC 0 0.036 -10000 0 -0.39 1 1
RIPK1 0 0 -10000 0 -10000 0 0
CASP7 -0.01 0.046 0.27 1 -10000 0 1
FASLG/FAS/FADD/FAF1 0.035 0.15 0.28 32 -0.39 8 40
MAP2K4 -0.012 0.14 -10000 0 -0.44 8 8
mol:ceramide -0.041 0.13 -10000 0 -0.47 12 12
GSN 0 0.036 0.21 1 -0.39 1 2
FASLG/FAS/FADD/FAF1/Caspase 8 0.013 0.14 0.31 2 -0.51 5 7
FAS -0.022 0.14 -10000 0 -0.86 5 5
BID 0.002 0.035 0.32 2 -10000 0 2
MAP3K1 0.002 0.086 -10000 0 -0.32 3 3
MAP3K7 0 0.002 -10000 0 -10000 0 0
RB1 0 0.036 -10000 0 -0.39 1 1
CFLAR 0 0 -10000 0 -10000 0 0
HGF/MET -0.4 0.43 -10000 0 -0.77 100 100
ARHGDIB 0 0.036 -10000 0 -0.39 1 1
FADD 0.002 0.025 0.34 1 -10000 0 1
actin filament polymerization 0 0.035 0.38 1 -0.21 1 2
NFKB1 -0.03 0.082 -10000 0 -10000 0 0
MAPK8 -0.049 0.21 -10000 0 -0.46 34 34
DFFA 0 0.036 -10000 0 -0.39 1 1
DNA fragmentation during apoptosis -0.003 0.054 -10000 0 -0.47 2 2
FAS/FADD/MET -0.014 0.094 -10000 0 -0.58 5 5
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 -0.006 0.092 0.34 1 -0.86 2 3
FAF1 0.001 0.005 -10000 0 -10000 0 0
PARP1 0 0.036 -10000 0 -0.39 1 1
DFFB -0.003 0.054 -10000 0 -0.48 2 2
CHUK -0.026 0.073 -10000 0 -10000 0 0
FASLG -0.032 0.18 0.34 2 -0.87 8 10
FAS/FADD -0.016 0.11 -10000 0 -0.67 5 5
HGF -0.41 0.43 -10000 0 -0.86 90 90
LMNA 0 0.033 -10000 0 -0.35 1 1
CASP6 0 0.036 -10000 0 -0.39 1 1
CASP10 0.001 0.004 -10000 0 -10000 0 0
CASP3 0 0.041 0.24 2 -0.44 1 3
PTPN13 -0.21 0.37 0.34 1 -0.86 46 47
CASP8 0.004 0.05 0.46 2 -10000 0 2
IL6 -0.16 0.49 -10000 0 -1.4 26 26
MET 0.002 0.025 0.34 1 -10000 0 1
ICAD/CAD -0.003 0.05 -10000 0 -0.44 2 2
FASLG/FAS/FADD/FAF1/Caspase 10 -0.041 0.13 -10000 0 -0.48 12 12
activation of caspase activity by cytochrome c 0.002 0.035 0.32 2 -10000 0 2
PAK2 0 0.035 -10000 0 -0.39 1 1
BCL2 0 0 -10000 0 -10000 0 0
Regulation of nuclear SMAD2/3 signaling

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
EP300 -0.005 0.009 -10000 0 -10000 0 0
HSPA8 0 0.063 -10000 0 -0.86 1 1
SMAD3/SMAD4/ER alpha -0.34 0.31 -10000 0 -0.63 98 98
AKT1 0.002 0.011 -10000 0 -10000 0 0
GSC 0.039 0.069 -10000 0 -10000 0 0
NKX2-5 0.014 0.069 0.34 8 -10000 0 8
muscle cell differentiation 0.012 0.059 0.65 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.002 0.076 -10000 0 -0.55 1 1
SMAD4 -0.014 0.081 -10000 0 -0.92 1 1
CBFB 0 0 -10000 0 -10000 0 0
SAP18 0 0 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.006 0.045 -10000 0 -10000 0 0
SMAD3/SMAD4/VDR -0.02 0.11 -10000 0 -0.55 6 6
MYC -0.084 0.25 -10000 0 -0.87 18 18
CDKN2B 0.068 0.088 0.53 1 -10000 0 1
AP1 -0.23 0.28 -10000 0 -0.5 89 89
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.002 0.028 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.006 0.053 -10000 0 -10000 0 0
SP3 0 0 -10000 0 -10000 0 0
CREB1 0 0 -10000 0 -10000 0 0
FOXH1 0.033 0.1 0.35 17 -10000 0 17
SMAD3/SMAD4/GR -0.017 0.064 -10000 0 -0.63 1 1
GATA3 -0.079 0.24 0.35 1 -0.89 15 16
SKI/SIN3/HDAC complex/NCoR1 0.014 0.035 -10000 0 -10000 0 0
MEF2C/TIF2 -0.046 0.15 -10000 0 -0.47 16 16
endothelial cell migration 0.39 0.66 1.5 51 -10000 0 51
MAX 0.015 0.024 -10000 0 -10000 0 0
RBBP7 0 0 -10000 0 -10000 0 0
RBBP4 0 0 -10000 0 -10000 0 0
RUNX2 -0.015 0.13 0.34 2 -0.86 4 6
RUNX3 -0.023 0.14 -10000 0 -0.86 5 5
RUNX1 -0.005 0.062 -10000 0 -0.86 1 1
CTBP1 0 0 -10000 0 -10000 0 0
NR3C1 0.015 0.024 -10000 0 -10000 0 0
VDR -0.012 0.15 0.34 6 -0.86 5 11
CDKN1A 0.006 0.19 -10000 0 -1.4 3 3
KAT2B -0.009 0.088 -10000 0 -0.86 2 2
SMAD2/SMAD2/SMAD4/FOXH1 0.021 0.088 0.36 3 -0.58 1 4
DCP1A 0 0 -10000 0 -10000 0 0
SKI 0 0 -10000 0 -10000 0 0
SERPINE1 -0.4 0.68 -10000 0 -1.5 51 51
SMAD3/SMAD4/ATF2 -0.024 0.089 -10000 0 -0.61 3 3
SMAD3/SMAD4/ATF3 -0.044 0.15 -10000 0 -0.66 9 9
SAP30 0 0 -10000 0 -10000 0 0
Cbp/p300/PIAS3 -0.008 0.014 -10000 0 -10000 0 0
JUN -0.22 0.28 -10000 0 -0.49 89 89
SMAD3/SMAD4/IRF7 -0.028 0.1 -10000 0 -0.65 4 4
TFE3 -0.009 0.018 -10000 0 -10000 0 0
COL1A2 0.11 0.15 0.49 5 -1.2 1 6
mesenchymal cell differentiation 0.029 0.12 0.68 5 -0.35 1 6
DLX1 0.03 0.097 0.34 17 -10000 0 17
TCF3 0 0 -10000 0 -10000 0 0
FOS -0.4 0.43 -10000 0 -0.86 89 89
SMAD3/SMAD4/Max -0.017 0.064 -10000 0 -0.63 1 1
Cbp/p300/SNIP1 -0.001 0.002 -10000 0 -10000 0 0
ZBTB17 -0.001 0.006 -10000 0 -10000 0 0
LAMC1 0.001 0.071 0.35 1 -0.55 1 2
TGIF2/HDAC complex/SMAD3/SMAD4 -0.018 0.066 -10000 0 -0.63 1 1
IRF7 -0.014 0.11 -10000 0 -0.86 3 3
ESR1 -0.45 0.43 -10000 0 -0.87 98 98
HNF4A -0.018 0.12 -10000 0 -0.86 4 4
MEF2C 0.012 0.055 -10000 0 -0.48 1 1
SMAD2-3/SMAD4 -0.014 0.067 -10000 0 -0.62 1 1
Cbp/p300/Src-1 -0.003 0.006 -10000 0 -10000 0 0
IGHV3OR16-13 -0.006 0.024 -10000 0 -10000 0 0
TGIF2/HDAC complex 0 0 -10000 0 -10000 0 0
CREBBP -0.002 0.004 -10000 0 -10000 0 0
SKIL 0 0 -10000 0 -10000 0 0
HDAC1 0 0 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
SNIP1 0.004 0.006 -10000 0 -10000 0 0
GCN5L2 -0.008 0.012 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.019 0.07 -10000 0 -0.62 1 1
MSG1/HSC70 0.015 0.068 -10000 0 -0.62 1 1
SMAD2 0.004 0.014 -10000 0 -10000 0 0
SMAD3 -0.013 0.047 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.003 0.058 -10000 0 -0.39 2 2
SMAD2/SMAD2/SMAD4 -0.009 0.065 -10000 0 -0.48 3 3
NCOR1 -0.009 0.088 -10000 0 -0.86 2 2
NCOA2 -0.095 0.27 -10000 0 -0.86 21 21
NCOA1 0 0 -10000 0 -10000 0 0
MYOD/E2A 0 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.006 0.074 -10000 0 -0.51 1 1
IFNB1 -0.01 0.097 -10000 0 -0.58 4 4
SMAD3/SMAD4/MEF2C 0.007 0.065 -10000 0 -0.5 1 1
CITED1 0.018 0.076 0.34 10 -10000 0 10
SMAD2-3/SMAD4/ARC105 -0.008 0.061 -10000 0 -0.56 1 1
RBL1 0.016 0.072 0.34 9 -10000 0 9
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.008 0.058 -10000 0 -10000 0 0
RUNX1-3/PEBPB2 -0.018 0.12 -10000 0 -0.69 5 5
SMAD7 -0.16 0.22 -10000 0 -0.85 7 7
MYC/MIZ-1 -0.067 0.2 -10000 0 -0.68 18 18
SMAD3/SMAD4 -0.14 0.2 -10000 0 -0.47 51 51
IL10 -0.12 0.31 0.37 1 -0.79 30 31
PIASy/HDAC complex 0.01 0.015 -10000 0 -10000 0 0
PIAS3 0 0 -10000 0 -10000 0 0
CDK2 0 0.002 -10000 0 -10000 0 0
IL5 -0.06 0.2 -10000 0 -0.62 16 16
CDK4 0 0.002 -10000 0 -10000 0 0
PIAS4 0.01 0.015 -10000 0 -10000 0 0
ATF3 -0.036 0.17 -10000 0 -0.86 8 8
SMAD3/SMAD4/SP1 -0.011 0.077 -10000 0 -0.62 1 1
FOXG1 0.012 0.065 0.34 7 -10000 0 7
FOXO3 0.023 0.012 -10000 0 -10000 0 0
FOXO1 0.016 0.072 -10000 0 -0.67 2 2
FOXO4 0.023 0.012 -10000 0 -10000 0 0
heart looping 0.012 0.054 -10000 0 -0.47 1 1
CEBPB 0.002 0.007 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.001 0.094 0.36 1 -0.64 1 2
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.032 0.1 -10000 0 -0.58 5 5
SMAD3/SMAD4/GATA3 -0.084 0.22 -10000 0 -0.6 24 24
SnoN/SIN3/HDAC complex/NCoR1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.027 0.12 -10000 0 -0.65 6 6
SMAD3/SMAD4/SP1-3 -0.006 0.068 -10000 0 -0.55 1 1
MED15 0 0 -10000 0 -10000 0 0
SP1 0.001 0.018 -10000 0 -10000 0 0
SIN3B 0 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.03 0.098 0.38 5 -0.52 1 6
ITGB5 -0.003 0.058 -10000 0 -0.5 1 1
TGIF/SIN3/HDAC complex/CtBP 0 0.003 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.19 0.28 -10000 0 -0.62 54 54
AR -0.24 0.39 -10000 0 -0.86 53 53
negative regulation of cell growth -0.008 0.075 -10000 0 -0.5 1 1
SMAD3/SMAD4/MYOD -0.021 0.068 -10000 0 -0.64 1 1
E2F5 0.006 0.087 0.34 6 -0.86 1 7
E2F4 0 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.017 0.074 0.32 2 -0.49 1 3
SMAD2-3/SMAD4/FOXO1-3a-4 0.004 0.054 -10000 0 -10000 0 0
TFDP1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 -0.23 0.29 -10000 0 -0.5 89 89
SMAD3/SMAD4/RUNX2 -0.029 0.12 0.36 1 -0.68 5 6
TGIF2 0 0 -10000 0 -10000 0 0
TGIF1 0 0 -10000 0 -10000 0 0
ATF2 -0.009 0.088 -10000 0 -0.86 2 2
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.029 0.18 0.59 1 -0.76 9 10
MAP4K1 -0.019 0.14 0.34 2 -0.86 5 7
MAP3K8 -0.009 0.088 -10000 0 -0.86 2 2
PRKCB -0.077 0.25 -10000 0 -0.86 17 17
DBNL 0 0 -10000 0 -10000 0 0
CRKL 0 0 -10000 0 -10000 0 0
MAP3K1 -0.021 0.13 0.24 1 -0.62 6 7
JUN -0.076 0.26 -10000 0 -0.66 29 29
MAP3K7 -0.021 0.13 0.24 1 -0.62 6 7
GRAP2 -0.013 0.13 0.34 3 -0.86 4 7
CRK 0 0 -10000 0 -10000 0 0
MAP2K4 0.017 0.14 -10000 0 -0.58 7 7
LAT 0.002 0.025 0.34 1 -10000 0 1
LCP2 -0.018 0.12 -10000 0 -0.86 4 4
MAPK8 -0.076 0.26 -10000 0 -0.7 26 26
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.022 0.14 0.27 1 -0.54 9 10
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.028 0.18 0.56 1 -0.72 9 10
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.005 0.042 0.34 3 -10000 0 3
alphaV beta3 Integrin -0.053 0.18 -10000 0 -0.67 15 15
PTK2 -0.073 0.21 -10000 0 -0.68 18 18
positive regulation of JNK cascade -0.038 0.11 -10000 0 -0.36 19 19
CDC42/GDP -0.05 0.15 -10000 0 -0.5 18 18
Rac1/GDP -0.049 0.14 -10000 0 -0.49 18 18
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CTNNB1 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.047 0.13 -10000 0 -0.45 19 19
nectin-3/I-afadin -0.063 0.2 -10000 0 -0.67 18 18
RAPGEF1 -0.02 0.18 -10000 0 -0.57 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.034 0.21 -10000 0 -0.67 18 18
PDGFB-D/PDGFRB 0.005 0.042 0.34 3 -10000 0 3
TLN1 -0.026 0.079 -10000 0 -0.47 1 1
Rap1/GTP -0.039 0.11 -10000 0 -0.39 18 18
IQGAP1 0 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.063 0.2 -10000 0 -0.67 18 18
PVR 0 0 -10000 0 -10000 0 0
Necl-5(dimer) 0 0 -10000 0 -10000 0 0
mol:GDP -0.026 0.2 -10000 0 -0.63 18 18
MLLT4 0 0 -10000 0 -10000 0 0
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
PI3K -0.049 0.16 -10000 0 -0.53 19 19
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.001 0.017 -10000 0 -10000 0 0
positive regulation of lamellipodium assembly -0.038 0.11 -10000 0 -0.38 18 18
PVRL1 0.002 0.025 0.34 1 -10000 0 1
PVRL3 -0.081 0.25 -10000 0 -0.86 18 18
PVRL2 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
CDH1 -0.045 0.19 -10000 0 -0.86 10 10
CLDN1 -0.018 0.12 -10000 0 -0.86 4 4
JAM-A/CLDN1 -0.061 0.18 -10000 0 -0.56 21 21
SRC -0.076 0.23 -10000 0 -0.76 18 18
ITGB3 -0.068 0.23 -10000 0 -0.86 15 15
nectin-1(dimer)/I-afadin/I-afadin 0.001 0.017 -10000 0 -10000 0 0
FARP2 -0.031 0.2 -10000 0 -0.61 19 19
RAC1 0 0 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.055 0.17 -10000 0 -0.58 18 18
nectin-1/I-afadin 0.001 0.017 -10000 0 -10000 0 0
nectin-2/I-afadin 0 0 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0 0 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.054 0.17 -10000 0 -0.58 18 18
CDC42/GTP/IQGAP1/filamentous actin 0 0 -10000 0 -10000 0 0
F11R 0 0 -10000 0 -10000 0 0
positive regulation of filopodium formation -0.038 0.11 -10000 0 -0.36 19 19
alphaV/beta3 Integrin/Talin -0.06 0.17 -10000 0 -0.6 15 15
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -10000 0 -10000 0 0
PIP5K1C -0.028 0.087 -10000 0 -0.51 1 1
VAV2 -0.03 0.2 -10000 0 -0.62 18 18
RAP1/GDP -0.046 0.13 -10000 0 -0.46 18 18
ITGAV 0 0 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.055 0.17 -10000 0 -0.58 18 18
nectin-3(dimer)/I-afadin/I-afadin -0.063 0.2 -10000 0 -0.67 18 18
Rac1/GTP -0.047 0.14 -10000 0 -0.47 18 18
PTPRM -0.032 0.097 -10000 0 -0.32 19 19
E-cadherin/beta catenin/alpha catenin -0.024 0.11 -10000 0 -0.48 10 10
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC -0.17 0.54 -10000 0 -1.4 29 29
PLK1 0.29 0.27 0.57 57 -0.64 2 59
CDKN1B 0.18 0.17 0.52 3 -0.37 1 4
FOXO3 0.25 0.26 0.52 70 -0.58 5 75
KAT2B 0.045 0.1 -10000 0 -0.85 2 2
FOXO1/SIRT1 -0.059 0.16 -10000 0 -0.42 29 29
CAT 0.17 0.41 0.63 2 -1.3 11 13
CTNNB1 0 0 -10000 0 -10000 0 0
AKT1 0.05 0.042 -10000 0 -10000 0 0
FOXO1 -0.021 0.18 -10000 0 -0.44 29 29
MAPK10 0.024 0.11 0.26 1 -0.5 7 8
mol:GTP 0.001 0.002 -10000 0 -10000 0 0
FOXO4 0.075 0.13 -10000 0 -0.52 5 5
response to oxidative stress 0.044 0.044 -10000 0 -10000 0 0
FOXO3A/SIRT1 0.016 0.18 0.44 14 -0.64 5 19
XPO1 0 0 -10000 0 -10000 0 0
EP300 -0.002 0.017 -10000 0 -10000 0 0
BCL2L11 0.077 0.063 -10000 0 -10000 0 0
FOXO1/SKP2 -0.06 0.15 -10000 0 -0.4 29 29
mol:GDP 0.044 0.044 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
GADD45A 0.16 0.21 0.5 1 -0.8 5 6
YWHAQ 0 0 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.076 0.049 -10000 0 -10000 0 0
MST1 -0.023 0.25 -10000 0 -0.83 17 17
CSNK1D 0 0 -10000 0 -10000 0 0
CSNK1E 0 0 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.077 0.068 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 0.016 0.12 -10000 0 -0.52 9 9
MAPK9 0.041 0.021 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
YWHAZ 0 0 -10000 0 -10000 0 0
SIRT1 0 0.065 -10000 0 -0.86 1 1
SOD2 0.18 0.23 0.51 2 -0.79 4 6
RBL2 0.18 0.28 0.54 2 -1.2 5 7
RAL/GDP 0.035 0.035 -10000 0 -10000 0 0
CHUK 0.055 0.039 -10000 0 -10000 0 0
Ran/GTP 0 0 -10000 0 -10000 0 0
CSNK1G2 0 0 -10000 0 -10000 0 0
RAL/GTP 0.047 0.029 -10000 0 -10000 0 0
CSNK1G1 0 0 -10000 0 -10000 0 0
FASLG 0.018 0.32 -10000 0 -1.5 8 8
SKP2 0 0 -10000 0 -10000 0 0
USP7 0 0 -10000 0 -10000 0 0
IKBKB 0.055 0.039 -10000 0 -10000 0 0
CCNB1 0.28 0.27 0.57 54 -0.64 2 56
FOXO1-3a-4/beta catenin -0.025 0.09 -10000 0 -0.41 6 6
proteasomal ubiquitin-dependent protein catabolic process -0.06 0.15 -10000 0 -0.39 29 29
CSNK1A1 0 0 -10000 0 -10000 0 0
SGK1 0.022 0.17 -10000 0 -0.84 7 7
CSNK1G3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
ZFAND5 0.077 0.12 -10000 0 -1 1 1
SFN 0.19 0.17 0.34 108 -10000 0 108
CDK2 -0.012 0.028 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.13 0.094 -10000 0 -10000 0 0
CREBBP -0.012 0.028 -10000 0 -10000 0 0
FBXO32 0.23 0.26 0.64 5 -0.87 3 8
BCL6 0.21 0.2 0.54 2 -0.59 2 4
RALB 0 0 -10000 0 -10000 0 0
RALA 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.005 0.18 -10000 0 -0.78 8 8
UGCG -0.067 0.21 -10000 0 -0.73 16 16
AKT1/mTOR/p70S6K/Hsp90/TERT 0.052 0.13 0.34 1 -0.37 7 8
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.05 0.21 -10000 0 -0.72 16 16
mol:DAG -0.001 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.057 0.14 -10000 0 -0.41 21 21
FRAP1 0.002 0.2 0.36 1 -0.49 21 22
FOXO3 0.001 0.2 0.34 1 -0.48 22 23
AKT1 -0.009 0.22 0.35 1 -0.5 25 26
GAB2 0 0 -10000 0 -10000 0 0
SMPD1 -0.007 0.031 -10000 0 -10000 0 0
SGMS1 -0.007 0.031 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.081 -10000 0 -1.1 1 1
CALM1 0 0 -10000 0 -10000 0 0
cell proliferation -0.033 0.18 -10000 0 -0.35 33 33
EIF3A 0 0 -10000 0 -10000 0 0
PI3K -0.006 0.087 -10000 0 -1.2 1 1
RPS6KB1 0.026 0.041 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.005 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -10000 0 0
JAK3 0.001 0.076 0.34 3 -0.86 1 4
PIK3R1 -0.004 0.062 -10000 0 -0.86 1 1
JAK1 0 0.001 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
MYC -0.057 0.34 -10000 0 -1 21 21
MYB 0.13 0.11 0.42 13 -10000 0 13
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.002 0.2 0.35 1 -0.66 11 12
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.002 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.19 0.35 1 -0.63 11 12
Rac1/GDP -0.005 0.074 -10000 0 -1 1 1
T cell proliferation -0.013 0.2 0.33 1 -0.53 18 19
SHC1 0 0 -10000 0 -10000 0 0
RAC1 0 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.015 0.032 0.12 18 -10000 0 18
PRKCZ -0.015 0.21 -10000 0 -0.55 18 18
NF kappa B1 p50/RelA -0.056 0.14 -10000 0 -0.59 7 7
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.047 0.2 0.28 1 -0.89 8 9
HSP90AA1 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
IL2RA -0.001 0.13 0.34 7 -0.87 3 10
IL2RB -0.077 0.25 -10000 0 -0.86 17 17
TERT 0.12 0.16 0.34 68 -10000 0 68
E2F1 0.14 0.11 0.38 18 -10000 0 18
SOS1 0 0 -10000 0 -10000 0 0
RPS6 0 0 -10000 0 -10000 0 0
mol:cAMP -0.006 0.013 -10000 0 -0.047 18 18
PTPN11 0 0 -10000 0 -10000 0 0
IL2RG -0.01 0.13 0.34 4 -0.86 4 8
actin cytoskeleton organization -0.013 0.2 0.33 1 -0.53 18 19
GRB2 0 0 -10000 0 -10000 0 0
IL2 0.002 0.004 -10000 0 -10000 0 0
PIK3CA -0.004 0.062 -10000 0 -0.86 1 1
Rac1/GTP -0.002 0.073 -10000 0 -0.99 1 1
LCK -0.029 0.16 0.35 1 -0.86 7 8
BCL2 0.017 0.16 -10000 0 -0.52 7 7
IL2 signaling events mediated by STAT5

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
GAB2 0 0 -10000 0 -10000 0 0
ELF1 -0.004 0.085 -10000 0 -0.51 4 4
CCNA2 0.18 0.17 0.34 103 -10000 0 103
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
JAK3 0.001 0.076 0.34 3 -0.86 1 4
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
JAK1 0 0 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.035 0.17 0.32 1 -0.69 9 10
SHC1 0 0 -10000 0 -10000 0 0
SP1 0.004 0.024 -10000 0 -10000 0 0
IL2RA 0.012 0.16 -10000 0 -0.97 4 4
IL2RB -0.077 0.25 -10000 0 -0.86 17 17
SOS1 0 0 -10000 0 -10000 0 0
IL2RG -0.011 0.13 0.34 4 -0.86 4 8
G1/S transition of mitotic cell cycle 0.061 0.15 -10000 0 -0.45 12 12
PTPN11 0 0 -10000 0 -10000 0 0
CCND2 0.028 0.042 -10000 0 -10000 0 0
LCK -0.03 0.16 0.34 1 -0.86 7 8
GRB2 0 0 -10000 0 -10000 0 0
IL2 0 0 -10000 0 -10000 0 0
CDK6 -0.054 0.21 -10000 0 -0.86 12 12
CCND3 0.023 0.15 -10000 0 -0.7 5 5
Regulation of Telomerase

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
Telomerase catalytic core complex 0.087 0.18 -10000 0 -0.57 3 3
RAD9A 0 0 -10000 0 -10000 0 0
AP1 -0.31 0.36 -10000 0 -0.69 89 89
IFNAR2 0.01 0.015 -10000 0 -10000 0 0
AKT1 -0.14 0.15 -10000 0 -0.29 98 98
ER alpha/Oestrogen -0.34 0.34 -10000 0 -0.67 98 98
NFX1/SIN3/HDAC complex 0.023 0.034 -10000 0 -10000 0 0
EGF 0.084 0.14 0.34 45 -10000 0 45
SMG5 0 0 -10000 0 -10000 0 0
SMG6 0 0 -10000 0 -10000 0 0
SP3/HDAC2 0.017 0.024 -10000 0 -10000 0 0
TERT/c-Abl -0.027 0.077 -10000 0 -0.53 3 3
SAP18 0.002 0.004 -10000 0 -10000 0 0
MRN complex 0 0 -10000 0 -10000 0 0
WT1 0.033 0.087 0.35 13 -10000 0 13
WRN 0 0 -10000 0 -10000 0 0
SP1 0.014 0.021 -10000 0 -10000 0 0
SP3 0.006 0.009 -10000 0 -10000 0 0
TERF2IP 0 0 -10000 0 -10000 0 0
Telomerase/Nucleolin -0.021 0.068 -10000 0 -0.54 1 1
Mad/Max 0.015 0.027 0.27 1 -10000 0 1
TERT 0.087 0.18 -10000 0 -0.58 3 3
CCND1 0.042 0.31 -10000 0 -1.2 10 10
MAX 0.006 0.009 -10000 0 -10000 0 0
RBBP7 0.002 0.005 -10000 0 -10000 0 0
RBBP4 0.002 0.004 -10000 0 -10000 0 0
TERF2 0 0 -10000 0 -10000 0 0
PTGES3 0 0 -10000 0 -10000 0 0
SIN3A 0.002 0.004 -10000 0 -10000 0 0
Telomerase/911 0.029 0.05 -10000 0 -10000 0 0
CDKN1B 0.02 0.032 -10000 0 -10000 0 0
RAD1 0 0 -10000 0 -10000 0 0
XRCC5 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
SAP30 0.002 0.005 -10000 0 -10000 0 0
TRF2/PARP2 0 0 -10000 0 -10000 0 0
UBE3A 0.006 0.008 -10000 0 -10000 0 0
JUN -0.015 0.12 -10000 0 -0.86 4 4
E6 0.004 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.011 0.016 -10000 0 -10000 0 0
FOS -0.4 0.43 -10000 0 -0.86 89 89
IFN-gamma/IRF1 0.026 0.056 -10000 0 -10000 0 0
PARP2 0 0 -10000 0 -10000 0 0
BLM 0.12 0.16 0.34 67 -10000 0 67
Telomerase 0.045 0.067 -10000 0 -10000 0 0
IRF1 0.008 0.011 -10000 0 -10000 0 0
ESR1 -0.44 0.43 -10000 0 -0.86 98 98
KU/TER 0 0 -10000 0 -10000 0 0
ATM/TRF2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.024 0.035 -10000 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.024 0.035 -10000 0 -10000 0 0
HDAC1 0.002 0.004 -10000 0 -10000 0 0
HDAC2 0.012 0.017 -10000 0 -10000 0 0
ATM 0 0 -10000 0 -10000 0 0
SMAD3 0.004 0.021 -10000 0 -10000 0 0
ABL1 0 0 -10000 0 -10000 0 0
MXD1 0.008 0.027 0.36 1 -10000 0 1
MRE11A 0 0 -10000 0 -10000 0 0
HUS1 0 0 -10000 0 -10000 0 0
RPS6KB1 0 0 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.039 0.12 -10000 0 -0.62 2 2
NR2F2 0.001 0.004 -10000 0 -10000 0 0
MAPK3 0.018 0.012 -10000 0 -10000 0 0
MAPK1 0.018 0.012 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.005 0.042 0.34 3 -10000 0 3
NFKB1 0 0 -10000 0 -10000 0 0
HNRNPC 0 0 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -10000 0 -10000 0 0
NBN 0 0 -10000 0 -10000 0 0
EGFR -0.008 0.11 -10000 0 -0.86 3 3
mol:Oestrogen 0.001 0.002 -10000 0 -10000 0 0
EGF/EGFR 0.051 0.13 -10000 0 -0.65 3 3
MYC -0.075 0.25 -10000 0 -0.86 18 18
IL2 0.013 0.018 -10000 0 -10000 0 0
KU 0 0 -10000 0 -10000 0 0
RAD50 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
TGFB1 0.005 0.042 0.34 3 -10000 0 3
TRF2/BLM 0.078 0.11 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT -0.026 0.076 -10000 0 -0.59 1 1
SP1/HDAC2 0.026 0.038 -10000 0 -10000 0 0
PINX1 0 0 -10000 0 -10000 0 0
Telomerase/EST1A -0.021 0.068 -10000 0 -0.54 1 1
Smad3/Myc -0.053 0.17 -10000 0 -0.58 18 18
911 complex 0 0 -10000 0 -10000 0 0
IFNG 0.024 0.074 0.35 9 -10000 0 9
Telomerase/PinX1 -0.021 0.068 -10000 0 -0.54 1 1
Telomerase/AKT1/mTOR/p70S6K 0.011 0.083 -10000 0 -10000 0 0
SIN3B 0.002 0.005 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
Telomerase/EST1B -0.021 0.068 -10000 0 -0.54 1 1
response to DNA damage stimulus 0.002 0 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -10000 0 -10000 0 0
TRF2/WRN 0 0 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.021 0.068 -10000 0 -0.54 1 1
E2F1 0.22 0.17 0.35 118 -10000 0 118
ZNFX1 0.002 0.004 -10000 0 -10000 0 0
PIF1 0.093 0.15 0.34 52 -10000 0 52
NCL 0 0 -10000 0 -10000 0 0
DKC1 0 0 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.026 0.18 0.67 12 -10000 0 12
KIRREL -0.051 0.21 0.35 1 -0.86 12 13
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.026 0.18 -10000 0 -0.68 12 12
PLCG1 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
WASL 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.017 0.14 -10000 0 -0.52 12 12
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.013 0.099 -10000 0 -0.38 11 11
FYN -0.025 0.12 -10000 0 -0.49 12 12
mol:Ca2+ -0.017 0.14 -10000 0 -0.51 12 12
mol:DAG -0.017 0.14 -10000 0 -0.52 12 12
NPHS2 0.003 0.045 0.33 3 -10000 0 3
mol:IP3 -0.017 0.14 -10000 0 -0.52 12 12
regulation of endocytosis -0.015 0.12 -10000 0 -0.46 12 12
Nephrin/NEPH1/podocin/Cholesterol -0.018 0.14 -10000 0 -0.52 12 12
establishment of cell polarity -0.026 0.18 -10000 0 -0.67 12 12
Nephrin/NEPH1/podocin/NCK1-2 -0.014 0.13 -10000 0 -0.48 12 12
Nephrin/NEPH1/beta Arrestin2 -0.015 0.13 -10000 0 -0.46 12 12
NPHS1 0.02 0.089 0.34 13 -10000 0 13
Nephrin/NEPH1/podocin -0.015 0.13 -10000 0 -0.49 12 12
TJP1 0 0 -10000 0 -10000 0 0
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0.002 0.025 0.34 1 -10000 0 1
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.017 0.14 -10000 0 -0.52 12 12
CD2AP 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.017 0.14 -10000 0 -0.52 12 12
GRB2 0 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.007 0.14 -10000 0 -0.48 12 12
cytoskeleton organization -0.02 0.13 -10000 0 -0.48 12 12
Nephrin/NEPH1 -0.019 0.14 -10000 0 -0.51 12 12
Nephrin/NEPH1/ZO-1 -0.021 0.15 -10000 0 -0.56 12 12
Syndecan-2-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Syndecan-2/Fibronectin 0 0 -10000 0 -10000 0 0
EPHB2 0.07 0.14 0.34 39 -10000 0 39
Syndecan-2/TACI -0.001 0.049 0.24 2 -0.59 1 3
LAMA1 -0.093 0.31 0.34 11 -0.86 25 36
Syndecan-2/alpha2 ITGB1 0.063 0.14 0.4 13 -0.5 2 15
HRAS 0.004 0.035 0.34 2 -10000 0 2
Syndecan-2/CASK 0 0 -10000 0 -10000 0 0
ITGA5 0 0 -10000 0 -10000 0 0
BAX 0.005 0.12 -10000 0 -0.52 9 9
EPB41 0 0 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0 0 -10000 0 -10000 0 0
LAMA3 0.043 0.15 0.34 29 -0.86 2 31
EZR 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.023 0.14 -10000 0 -0.86 5 5
Syndecan-2/MMP2 -0.015 0.11 0.24 3 -0.59 6 9
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.041 0.089 -10000 0 -10000 0 0
dendrite morphogenesis 0.049 0.096 0.24 39 -10000 0 39
Syndecan-2/GM-CSF 0 0 -10000 0 -10000 0 0
determination of left/right symmetry 0.015 0.001 -10000 0 -10000 0 0
Syndecan-2/PKC delta 0 0 -10000 0 -10000 0 0
GNB2L1 0 0 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
Syndecan-2/RACK1 0.002 0.021 -10000 0 -10000 0 0
NF1 -0.005 0.062 -10000 0 -0.86 1 1
FGFR/FGF/Syndecan-2 0.015 0.001 -10000 0 -10000 0 0
ITGA2 0.061 0.13 0.34 34 -10000 0 34
MAPK8 -0.002 0.13 -10000 0 -0.58 9 9
Syndecan-2/alpha2/beta1 Integrin -0.021 0.21 0.4 5 -0.5 25 30
Syndecan-2/Kininogen -0.058 0.18 -10000 0 -0.59 19 19
ITGB1 0 0 -10000 0 -10000 0 0
SRC 0.002 0.017 -10000 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 0 0 -10000 0 -10000 0 0
extracellular matrix organization 0.004 0.03 0.24 3 -10000 0 3
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
Syndecan-2/Caveolin-2/Ras -0.012 0.089 -10000 0 -0.54 5 5
Syndecan-2/Laminin alpha3 0.03 0.11 -10000 0 -0.59 2 2
Syndecan-2/RasGAP -0.004 0.05 -10000 0 -0.47 2 2
alpha5/beta1 Integrin 0 0 -10000 0 -10000 0 0
PRKCD 0 0 -10000 0 -10000 0 0
Syndecan-2 dimer 0.049 0.096 0.24 39 -10000 0 39
GO:0007205 0 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.003 0.048 -10000 0 -0.45 2 2
RHOA 0 0 -10000 0 -10000 0 0
SDCBP 0 0 -10000 0 -10000 0 0
TNFRSF13B -0.001 0.072 0.34 2 -0.86 1 3
RASA1 -0.009 0.088 -10000 0 -0.86 2 2
alpha2/beta1 Integrin 0.041 0.089 -10000 0 -10000 0 0
Syndecan-2/Synbindin 0 0 -10000 0 -10000 0 0
TGFB1 0.005 0.042 0.34 3 -10000 0 3
CASP3 -0.003 0.039 -10000 0 -0.54 1 1
FN1 0 0 -10000 0 -10000 0 0
Syndecan-2/IL8 -0.13 0.26 0.24 6 -0.59 45 51
SDC2 0.015 0.001 -10000 0 -10000 0 0
KNG1 -0.086 0.26 -10000 0 -0.86 19 19
Syndecan-2/Neurofibromin -0.003 0.042 -10000 0 -0.59 1 1
TRAPPC4 0 0 -10000 0 -10000 0 0
CSF2 0 0 -10000 0 -10000 0 0
Syndecan-2/TGFB1 0.004 0.03 0.24 3 -10000 0 3
Syndecan-2/Syntenin/PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-2/Ezrin 0 0 -10000 0 -10000 0 0
PRKACA -0.003 0.039 -10000 0 -0.53 1 1
angiogenesis -0.13 0.26 0.24 6 -0.58 45 51
MMP2 -0.022 0.16 0.34 3 -0.86 6 9
IL8 -0.19 0.38 0.34 6 -0.86 45 51
calcineurin-NFAT signaling pathway -0.001 0.049 0.24 2 -0.58 1 3
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0 0 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.052 0.16 -10000 0 -0.49 21 21
Syndecan-3/Neurocan 0.001 0.064 0.22 4 -0.77 1 5
POMC -0.003 0.067 0.34 1 -0.86 1 2
EGFR -0.014 0.11 -10000 0 -0.86 3 3
Syndecan-3/EGFR -0.012 0.083 -10000 0 -0.57 4 4
AGRP 0.012 0.064 0.34 7 -10000 0 7
NCSTN 0 0 -10000 0 -10000 0 0
PSENEN 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0 0 -10000 0 -10000 0 0
APH1A 0 0 -10000 0 -10000 0 0
NCAN 0.007 0.049 0.34 4 -10000 0 4
long-term memory -0.004 0.051 -10000 0 -0.71 1 1
Syndecan-3/IL8 -0.12 0.23 0.22 6 -0.52 45 51
PSEN1 0 0 -10000 0 -10000 0 0
Src/Cortactin 0.001 0.017 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
limb bud formation -0.004 0.057 -10000 0 -0.78 1 1
MC4R 0 0 -10000 0 -10000 0 0
SRC 0.002 0.025 0.34 1 -10000 0 1
PTN -0.091 0.27 0.34 2 -0.86 21 23
FGFR/FGF/Syndecan-3 -0.004 0.057 -10000 0 -0.8 1 1
neuron projection morphogenesis -0.047 0.16 -10000 0 -0.47 21 21
Syndecan-3/AgRP 0.004 0.069 0.22 7 -0.77 1 8
Syndecan-3/AgRP/MC4R 0.004 0.067 -10000 0 -0.74 1 1
Fyn/Cortactin 0 0 -10000 0 -10000 0 0
SDC3 -0.004 0.058 -10000 0 -0.81 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration -0.11 0.23 0.22 6 -0.51 45 51
IL8 -0.19 0.38 0.34 6 -0.86 45 51
Syndecan-3/Fyn/Cortactin -0.004 0.053 -10000 0 -0.73 1 1
Syndecan-3/CASK -0.004 0.055 -10000 0 -0.77 1 1
alpha-MSH/MC4R -0.002 0.052 -10000 0 -0.68 1 1
Gamma Secretase 0 0 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.016 0.042 -10000 0 -10000 0 0
AES 0.013 0.035 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -10000 0 0
LRP6/FZD1 -0.009 0.085 -10000 0 -0.67 3 3
SMAD4 -0.005 0.062 -10000 0 -0.86 1 1
DKK2 0.048 0.12 0.34 27 -10000 0 27
TLE1 0.014 0.036 -10000 0 -10000 0 0
MACF1 0 0 -10000 0 -10000 0 0
CTNNB1 0.038 0.067 -10000 0 -10000 0 0
WIF1 0.032 0.099 0.34 18 -10000 0 18
beta catenin/RanBP3 0.044 0.17 0.42 27 -10000 0 27
KREMEN2 0.036 0.1 0.34 20 -10000 0 20
DKK1 0.11 0.16 0.34 63 -10000 0 63
beta catenin/beta TrCP1 -0.002 0.05 -10000 0 -10000 0 0
FZD1 -0.012 0.11 0.34 1 -0.86 3 4
AXIN2 -0.051 0.34 -10000 0 -1.5 8 8
AXIN1 0 0 -10000 0 -10000 0 0
RAN 0 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.01 0.029 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.058 0.073 0.32 1 -0.4 1 2
Axin1/APC/GSK3 -0.001 0.045 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.032 0.068 -10000 0 -0.49 2 2
HNF1A 0.001 0.11 -10000 0 -0.85 3 3
CTBP1 0.015 0.039 -10000 0 -10000 0 0
MYC -0.16 0.49 -10000 0 -1.7 18 18
RANBP3 0 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.052 0.098 0.42 3 -10000 0 3
NKD1 0.029 0.24 0.34 39 -0.86 9 48
TCF4 0.014 0.038 -10000 0 -10000 0 0
TCF3 0.014 0.038 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.004 0.074 -10000 0 -0.54 3 3
Ran/GTP 0.001 0.004 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.08 0.22 0.56 27 -10000 0 27
LEF1 0.14 0.16 0.34 72 -10000 0 72
DVL1 0.008 0.033 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.051 0.11 -10000 0 -0.46 1 1
DKK1/LRP6/Kremen 2 0.092 0.12 0.42 7 -10000 0 7
LRP6 0 0 -10000 0 -10000 0 0
CSNK1A1 0.016 0.041 -10000 0 -10000 0 0
NLK 0.002 0.004 -10000 0 -10000 0 0
CCND1 -0.099 0.38 -10000 0 -1.5 12 12
WNT1 0.005 0.042 0.34 3 -10000 0 3
GSK3A 0 0 -10000 0 -10000 0 0
GSK3B 0 0 -10000 0 -10000 0 0
FRAT1 0 0 -10000 0 -10000 0 0
PPP2R5D 0.004 0.092 0.38 9 -10000 0 9
APC -0.006 0.064 -10000 0 -0.5 3 3
WNT1/LRP6/FZD1 -0.009 0.055 -10000 0 -0.36 3 3
CREBBP 0.014 0.038 -10000 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.002 0.006 -10000 0 -10000 0 0
SMARCC1 0.005 0.009 -10000 0 -10000 0 0
REL -0.031 0.16 -10000 0 -0.86 7 7
HDAC7 -0.072 0.15 -10000 0 -0.59 8 8
JUN -0.017 0.12 -10000 0 -0.86 4 4
EP300 0 0 -10000 0 -10000 0 0
KAT2B -0.009 0.088 -10000 0 -0.86 2 2
KAT5 0 0 -10000 0 -10000 0 0
MAPK14 0.006 0.1 -10000 0 -0.67 4 4
FOXO1 -0.009 0.088 -10000 0 -0.86 2 2
T-DHT/AR -0.078 0.16 -10000 0 -0.56 13 13
MAP2K6 -0.009 0.14 0.34 5 -0.86 4 9
BRM/BAF57 -0.019 0.12 -10000 0 -0.68 6 6
MAP2K4 0 0.004 -10000 0 -10000 0 0
SMARCA2 -0.026 0.15 -10000 0 -0.87 6 6
PDE9A -0.16 0.41 -10000 0 -1.3 23 23
NCOA2 -0.093 0.27 -10000 0 -0.86 21 21
CEBPA -0.009 0.088 -10000 0 -0.86 2 2
EHMT2 0.001 0.004 -10000 0 -10000 0 0
cell proliferation -0.02 0.17 -10000 0 -0.51 11 11
NR0B1 0.059 0.13 0.34 33 -10000 0 33
EGR1 -0.27 0.4 -10000 0 -0.86 59 59
RXRs/9cRA 0.014 0.095 -10000 0 -0.54 3 3
AR/RACK1/Src -0.044 0.15 -10000 0 -0.54 12 12
AR/GR -0.11 0.17 -10000 0 -0.5 13 13
GNB2L1 0.001 0.004 -10000 0 -10000 0 0
PKN1 0.002 0.025 0.34 1 -10000 0 1
RCHY1 0 0 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0.002 -10000 0 -10000 0 0
MAPK8 -0.016 0.15 -10000 0 -0.68 9 9
T-DHT/AR/TIF2/CARM1 -0.1 0.26 -10000 0 -0.7 26 26
SRC -0.001 0.14 -10000 0 -0.5 13 13
NR3C1 0 0 -10000 0 -10000 0 0
KLK3 -0.002 0.2 -10000 0 -1.3 3 3
APPBP2 0 0.001 -10000 0 -10000 0 0
TRIM24 0.002 0.007 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.067 0.15 -10000 0 -0.57 13 13
TMPRSS2 -0.074 0.27 -10000 0 -1.3 8 8
RXRG 0.024 0.16 0.34 21 -0.86 3 24
mol:9cRA 0 0.001 -10000 0 -10000 0 0
RXRA 0 0 -10000 0 -10000 0 0
RXRB 0 0 -10000 0 -10000 0 0
CARM1 0.001 0.005 -10000 0 -10000 0 0
NR2C2 -0.005 0.062 -10000 0 -0.86 1 1
KLK2 -0.022 0.2 -10000 0 -0.55 13 13
AR -0.12 0.19 -10000 0 -0.38 55 55
SENP1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
MDM2 0.001 0.005 -10000 0 -10000 0 0
SRY 0.001 0.026 0.34 1 -10000 0 1
GATA2 -0.003 0.067 0.34 1 -0.86 1 2
MYST2 0 0 -10000 0 -10000 0 0
HOXB13 0.077 0.14 0.34 42 -10000 0 42
T-DHT/AR/RACK1/Src -0.053 0.15 -10000 0 -0.55 13 13
positive regulation of transcription -0.003 0.067 0.34 1 -0.86 1 2
DNAJA1 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.003 -10000 0 -10000 0 0
NCOA1 0.008 0.01 -10000 0 -10000 0 0
SPDEF 0.063 0.13 0.34 34 -10000 0 34
T-DHT/AR/TIF2 -0.046 0.19 -10000 0 -0.53 20 20
T-DHT/AR/Hsp90 -0.067 0.15 -10000 0 -0.57 13 13
GSK3B 0.001 0.003 -10000 0 -10000 0 0
NR2C1 0 0 -10000 0 -10000 0 0
mol:T-DHT -0.01 0.15 -10000 0 -0.54 13 13
SIRT1 -0.005 0.062 -10000 0 -0.86 1 1
ZMIZ2 0.001 0.005 -10000 0 -10000 0 0
POU2F1 0.005 0.034 -10000 0 -10000 0 0
T-DHT/AR/DAX-1 -0.03 0.18 -10000 0 -0.57 13 13
CREBBP 0 0 -10000 0 -10000 0 0
SMARCE1 0.001 0.005 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.005 0.042 0.34 3 -10000 0 3
Jak2/Leptin Receptor -0.071 0.2 0.22 1 -0.46 36 37
PTP1B/AKT1 -0.004 0.029 -10000 0 -0.26 1 1
FYN 0 0 -10000 0 -10000 0 0
p210 bcr-abl/PTP1B 0.057 0.056 -10000 0 -0.28 1 1
EGFR -0.01 0.11 -10000 0 -0.87 3 3
EGF/EGFR 0.043 0.12 0.25 23 -0.46 3 26
CSF1 -0.005 0.062 -10000 0 -0.86 1 1
AKT1 0 0.002 -10000 0 -10000 0 0
INSR 0 0.002 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.017 0.083 -10000 0 -0.49 5 5
Insulin Receptor/Insulin 0 0.041 0.25 2 -10000 0 2
HCK -0.027 0.15 -10000 0 -0.86 6 6
CRK 0 0 -10000 0 -10000 0 0
TYK2 0.06 0.053 -10000 0 -10000 0 0
EGF 0.081 0.14 0.34 45 -10000 0 45
YES1 0 0 -10000 0 -10000 0 0
CAV1 0.065 0.057 -10000 0 -10000 0 0
TXN 0.001 0.004 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.005 0.025 -10000 0 -10000 0 0
cell migration -0.057 0.056 0.28 1 -10000 0 1
STAT3 0 0 -10000 0 -10000 0 0
PRLR -0.02 0.14 -10000 0 -0.86 5 5
ITGA2B 0.005 0.042 0.34 3 -10000 0 3
CSF1R -0.014 0.11 -10000 0 -0.86 3 3
Prolactin Receptor/Prolactin -0.011 0.11 -10000 0 -0.68 5 5
FGR -0.005 0.062 -10000 0 -0.86 1 1
PTP1B/p130 Cas -0.006 0.027 -10000 0 -10000 0 0
Crk/p130 Cas -0.005 0.025 -10000 0 -10000 0 0
DOK1 0.062 0.051 -10000 0 -10000 0 0
JAK2 0.041 0.074 -10000 0 -0.43 2 2
Jak2/Leptin Receptor/Leptin -0.11 0.23 -10000 0 -0.66 25 25
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
PTPN1 0.057 0.056 -10000 0 -0.28 1 1
LYN 0 0 -10000 0 -10000 0 0
CDH2 -0.023 0.14 -10000 0 -0.86 5 5
SRC 0.037 0.028 -10000 0 -10000 0 0
ITGB3 -0.068 0.23 -10000 0 -0.86 15 15
CAT1/PTP1B -0.059 0.19 -10000 0 -0.47 19 19
CAPN1 0.002 0.004 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PI3K -0.005 0.073 -10000 0 -0.9 1 1
mol:H2O2 -0.001 0.003 -10000 0 -10000 0 0
STAT3 (dimer) -0.11 0.24 -10000 0 -0.7 25 25
negative regulation of transcription 0.041 0.074 -10000 0 -0.43 2 2
FCGR2A 0.002 0.025 0.34 1 -10000 0 1
FER 0.001 0.004 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin -0.049 0.18 -10000 0 -0.67 15 15
BLK -0.18 0.36 0.34 2 -0.86 41 43
Insulin Receptor/Insulin/Shc 0.004 0.03 -10000 0 -10000 0 0
RHOA 0.002 0.004 -10000 0 -10000 0 0
LEPR -0.16 0.34 -10000 0 -0.86 36 36
BCAR1 0 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0 0 -10000 0 -10000 0 0
mol:NADPH 0.002 0.002 -10000 0 -10000 0 0
TRPV6 -0.14 0.23 -10000 0 -0.5 31 31
PRL 0.004 0.025 0.34 1 -10000 0 1
SOCS3 -0.19 0.51 -10000 0 -1.5 25 25
SPRY2 -0.008 0.089 -10000 0 -0.87 2 2
Insulin Receptor/Insulin/IRS1 0.004 0.03 -10000 0 -10000 0 0
CSF1/CSF1R -0.014 0.066 -10000 0 -0.43 4 4
Ras protein signal transduction -0.007 0.02 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
INS 0.008 0.049 0.34 4 -10000 0 4
LEP 0.01 0.06 0.34 6 -10000 0 6
STAT5B 0.053 0.056 -10000 0 -0.23 2 2
STAT5A 0.054 0.056 -10000 0 -0.24 1 1
GRB2 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.001 0.046 0.3 3 -10000 0 3
CSN2 -0.016 0.039 -10000 0 -10000 0 0
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
LAT 0.038 0.028 -10000 0 -10000 0 0
YBX1 0 0 -10000 0 -10000 0 0
LCK -0.03 0.16 0.34 1 -0.86 7 8
SHC1 0 0 -10000 0 -10000 0 0
NOX4 0.16 0.17 0.34 86 -10000 0 86
Aurora A signaling

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
Aurora A/GADD45A 0 0.084 -10000 0 -0.58 3 3
BIRC5 0.23 0.16 0.34 130 -10000 0 130
NFKBIA 0.014 0.04 -10000 0 -10000 0 0
CPEB1 0.014 0.068 0.34 8 -10000 0 8
AKT1 0.014 0.04 -10000 0 -10000 0 0
NDEL1 0 0 -10000 0 -10000 0 0
Aurora A/BRCA1 0.009 0.035 -10000 0 -10000 0 0
NDEL1/TACC3 0.035 0.077 -10000 0 -10000 0 0
GADD45A -0.014 0.11 -10000 0 -0.86 3 3
GSK3B -0.003 0.005 -10000 0 -10000 0 0
PAK1/Aurora A 0.01 0.039 -10000 0 -10000 0 0
MDM2 0 0 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.022 0.057 -10000 0 -10000 0 0
TP53 0.017 0.028 -10000 0 -10000 0 0
DLG7 0.005 0.041 -10000 0 -10000 0 0
AURKAIP1 0 0 -10000 0 -10000 0 0
ARHGEF7 0 0 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.037 0.081 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.009 0.035 -10000 0 -10000 0 0
AURKA 0.011 0.057 -10000 0 -10000 0 0
AURKB 0.11 0.091 0.2 90 -10000 0 90
CDC25B 0.021 0.035 -10000 0 -10000 0 0
G2/M transition checkpoint 0.009 0.035 -10000 0 -10000 0 0
mRNA polyadenylation 0.015 0.054 0.26 3 -10000 0 3
Aurora A/CPEB 0.015 0.055 0.26 3 -10000 0 3
Aurora A/TACC1/TRAP/chTOG 0.016 0.033 -10000 0 -10000 0 0
BRCA1 0 0 -10000 0 -10000 0 0
centrosome duplication 0.01 0.039 -10000 0 -10000 0 0
regulation of centrosome cycle 0.034 0.075 -10000 0 -10000 0 0
spindle assembly 0.015 0.032 -10000 0 -10000 0 0
TDRD7 0 0 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.13 0.11 -10000 0 -0.46 2 2
CENPA 0.12 0.099 0.2 111 -10000 0 111
Aurora A/PP2A 0.01 0.039 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process 0.022 0.034 -10000 0 -10000 0 0
negative regulation of DNA binding 0.017 0.028 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0 0 -10000 0 -10000 0 0
RASA1 -0.009 0.088 -10000 0 -0.86 2 2
Ajuba/Aurora A 0.009 0.035 -10000 0 -10000 0 0
mitotic prometaphase -0.021 0.021 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.057 -10000 0 -10000 0 0
TACC1 0 0 -10000 0 -10000 0 0
TACC3 0.041 0.11 0.34 23 -10000 0 23
Aurora A/Antizyme1 0.013 0.035 -10000 0 -10000 0 0
Aurora A/RasGAP 0.003 0.073 -10000 0 -0.6 2 2
OAZ1 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.003 0.005 -10000 0 -10000 0 0
GIT1 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.022 0.057 -10000 0 -10000 0 0
PPP2R5D 0 0 -10000 0 -10000 0 0
Aurora A/TPX2 0.03 0.061 -10000 0 -10000 0 0
PAK1 0 0 -10000 0 -10000 0 0
CKAP5 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0 0 -10000 0 -10000 0 0
HDAC4 0.002 0.025 0.34 1 -10000 0 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.01 0.064 0.63 1 -10000 0 1
CDKN1A -0.015 0.12 -10000 0 -1 3 3
KAT2B -0.009 0.088 -10000 0 -0.86 2 2
BAX 0 0 -10000 0 -10000 0 0
FOXO3 0.001 0.012 -10000 0 -10000 0 0
FOXO1 -0.009 0.088 -10000 0 -0.86 2 2
FOXO4 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0 0 -10000 0 -10000 0 0
TAT -0.33 0.42 -10000 0 -0.86 73 73
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.007 0.069 -10000 0 -0.68 2 2
PPARGC1A -0.12 0.3 -10000 0 -0.86 27 27
FHL2 -0.068 0.23 -10000 0 -0.86 15 15
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 -0.001 0.052 -10000 0 -0.67 1 1
HIST2H4A 0.01 0.064 -10000 0 -0.63 1 1
SIRT1/FOXO3a -0.001 0.046 -10000 0 -0.59 1 1
SIRT1 -0.001 0.068 -10000 0 -0.86 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0 0.048 -10000 0 -0.58 1 1
SIRT1/Histone H1b 0.003 0.045 -10000 0 -0.51 1 1
apoptosis 0.001 0.045 0.58 1 -10000 0 1
SIRT1/PGC1A -0.086 0.21 -10000 0 -0.59 28 28
p53/SIRT1 0.003 0.073 0.43 3 -0.67 1 4
SIRT1/FOXO4 0 0.046 -10000 0 -0.57 1 1
FOXO1/FHL2/SIRT1 -0.049 0.16 -10000 0 -0.54 18 18
HIST1H1E 0.005 0.025 -10000 0 -10000 0 0
SIRT1/p300 -0.001 0.052 -10000 0 -0.67 1 1
muscle cell differentiation 0.007 0.092 0.84 2 -10000 0 2
TP53 0.003 0.026 -10000 0 -10000 0 0
KU70/SIRT1/BAX -0.001 0.046 -10000 0 -0.58 1 1
CREBBP 0 0 -10000 0 -10000 0 0
MEF2D 0 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.26 0.33 -10000 0 -0.68 73 73
ACSS2 -0.001 0.051 -10000 0 -0.67 1 1
SIRT1/PCAF/MYOD -0.007 0.092 -10000 0 -0.85 2 2
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.003 0.048 -10000 0 -10000 0 0
oxygen homeostasis 0.001 0.018 -10000 0 -10000 0 0
TCEB2 0.002 0.025 0.34 1 -10000 0 1
TCEB1 0 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.026 0.057 -10000 0 -0.38 1 1
EPO -0.23 0.47 0.64 3 -0.8 69 72
FIH (dimer) 0.01 0.014 -10000 0 -10000 0 0
APEX1 0.001 0.016 -10000 0 -10000 0 0
SERPINE1 -0.14 0.43 -10000 0 -0.79 51 51
FLT1 -0.012 0.027 -10000 0 -10000 0 0
ADORA2A -0.02 0.25 -10000 0 -0.73 4 4
germ cell development 0.015 0.25 0.64 2 -0.67 4 6
SLC11A2 -0.004 0.24 -10000 0 -0.7 4 4
BHLHE40 -0.011 0.26 -10000 0 -0.85 5 5
HIF1AN 0.01 0.014 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.069 0.17 0.44 6 -0.46 4 10
ETS1 0.015 0.018 -10000 0 -10000 0 0
CITED2 -0.018 0.1 -10000 0 -1.4 1 1
KDR -0.046 0.21 -10000 0 -1.2 6 6
PGK1 -0.004 0.24 -10000 0 -0.7 4 4
SIRT1 -0.004 0.062 -10000 0 -0.86 1 1
response to hypoxia -0.005 0.008 -10000 0 -10000 0 0
HIF2A/ARNT -0.072 0.24 0.61 4 -0.85 4 8
EPAS1 0.02 0.12 -10000 0 -0.39 3 3
SP1 0.016 0.019 -10000 0 -10000 0 0
ABCG2 -0.078 0.35 -10000 0 -0.77 27 27
EFNA1 -0.01 0.26 -10000 0 -0.77 6 6
FXN -0.02 0.25 -10000 0 -0.73 4 4
POU5F1 0.014 0.26 0.65 2 -0.7 4 6
neuron apoptosis 0.07 0.24 0.82 4 -0.6 4 8
EP300 0 0 -10000 0 -10000 0 0
EGLN3 0.03 0.17 0.35 22 -0.86 4 26
EGLN2 0.01 0.014 -10000 0 -10000 0 0
EGLN1 0.01 0.014 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.001 0.015 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
ARNT 0.001 0.016 -10000 0 -10000 0 0
SLC2A1 -0.017 0.26 0.58 2 -0.75 5 7
TWIST1 -0.018 0.25 -10000 0 -0.73 4 4
ELK1 0.013 0.001 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.032 0.12 0.39 3 -10000 0 3
VEGFA -0.004 0.24 -10000 0 -0.7 4 4
CREBBP 0 0 -10000 0 -10000 0 0
Effects of Botulinum toxin

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

Table S85.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A 0.006 0.03 -10000 0 -10000 0 0
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.004 0.029 -10000 0 -10000 0 0
STXBP1 0 0 -10000 0 -10000 0 0
ACh/CHRNA1 0.001 0.063 0.27 7 -10000 0 7
RAB3GAP2/RIMS1/UNC13B 0.003 0.026 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.004 0.035 0.34 2 -10000 0 2
mol:ACh -0.001 0.052 0.074 4 -0.16 17 21
RAB3GAP2 0 0 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.014 0.061 -10000 0 -10000 0 0
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.001 0.063 0.27 7 -10000 0 7
UNC13B 0.002 0.025 0.34 1 -10000 0 1
CHRNA1 0.012 0.064 0.34 7 -10000 0 7
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 -0.091 0.24 0.26 9 -0.64 30 39
SNAP25 -0.021 0.12 0.12 23 -0.39 17 40
VAMP2 0 0 -10000 0 -10000 0 0
SYT1 -0.12 0.33 0.34 11 -0.86 30 41
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.004 0.022 -10000 0 -10000 0 0
STX1A/SNAP25 fragment 1/VAMP2 -0.014 0.061 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
cAMP biosynthetic process 0.027 0.15 0.86 6 -10000 0 6
PI3K Class IB/PDE3B -0.027 0.15 -10000 0 -0.86 6 6
PDE3B -0.027 0.15 -10000 0 -0.86 6 6
E-cadherin signaling events

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.031 0.13 -9999 0 -0.58 10 10
E-cadherin/beta catenin -0.035 0.15 -9999 0 -0.67 10 10
CTNNB1 0 0 -9999 0 -10000 0 0
JUP 0 0 -9999 0 -10000 0 0
CDH1 -0.045 0.19 -9999 0 -0.86 10 10
Ceramide signaling pathway

Figure S88.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S88.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.006 0.032 -10000 0 -10000 0 0
MAP4K4 -0.014 0.068 -10000 0 -10000 0 0
BAG4 -0.027 0.15 -10000 0 -0.86 6 6
PKC zeta/ceramide -0.024 0.1 -10000 0 -0.52 8 8
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 0.006 0.087 0.34 6 -0.86 1 7
BAX 0.003 0.008 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AKT1 0.015 0.019 -10000 0 -10000 0 0
BAD 0.005 0.014 -10000 0 -10000 0 0
SMPD1 0.008 0.065 -10000 0 -0.26 10 10
RB1 0.005 0.014 -10000 0 -10000 0 0
FADD/Caspase 8 -0.012 0.064 -10000 0 -10000 0 0
MAP2K4 0.011 0.014 -10000 0 -10000 0 0
NSMAF 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.011 0.014 -10000 0 -10000 0 0
EGF 0.08 0.14 0.34 45 -10000 0 45
mol:ceramide -0.002 0.016 -10000 0 -10000 0 0
MADD 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.006 0.032 -10000 0 -10000 0 0
ASAH1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle 0.005 0.014 -10000 0 -10000 0 0
cell proliferation -0.16 0.2 -10000 0 -0.4 74 74
BID 0.016 0.053 -10000 0 -10000 0 0
MAP3K1 0.005 0.014 -10000 0 -10000 0 0
EIF2A 0.017 0.013 -10000 0 -10000 0 0
TRADD -0.005 0.062 -10000 0 -0.86 1 1
CRADD -0.005 0.062 -10000 0 -0.86 1 1
MAPK3 0.02 0.013 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.02 0.013 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.002 0.006 -10000 0 -10000 0 0
FADD -0.014 0.069 -10000 0 -10000 0 0
KSR1 0.005 0.014 -10000 0 -10000 0 0
MAPK8 -0.017 0.12 -10000 0 -0.37 15 15
PRKRA 0.005 0.014 -10000 0 -10000 0 0
PDGFA 0.012 0.064 0.34 7 -10000 0 7
TRAF2 0 0 -10000 0 -10000 0 0
IGF1 -0.34 0.42 -10000 0 -0.86 74 74
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.002 0.016 -10000 0 -10000 0 0
CTSD 0 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.17 0.21 -10000 0 -0.44 74 74
PRKCD 0 0 -10000 0 -10000 0 0
PRKCZ -0.036 0.17 -10000 0 -0.86 8 8
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.006 0.032 -10000 0 -10000 0 0
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.016 0.074 -10000 0 -0.28 13 13
TNFR1A/BAG4/TNF-alpha -0.049 0.16 -10000 0 -0.58 16 16
mol:Sphingosine-1-phosphate 0.006 0.032 -10000 0 -10000 0 0
MAP2K1 0.017 0.013 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
CYCS 0.005 0.01 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.021 0.12 -10000 0 -0.67 6 6
EIF2AK2 0.011 0.014 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/FAN -0.031 0.13 -10000 0 -0.58 10 10
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.008 0.041 -10000 0 -10000 0 0
MAP2K2 0.017 0.014 -10000 0 -10000 0 0
SMPD3 -0.04 0.16 -10000 0 -0.4 29 29
TNF -0.045 0.19 -10000 0 -0.86 10 10
PKC zeta/PAR4 -0.028 0.13 -10000 0 -0.67 8 8
mol:PHOSPHOCHOLINE -0.041 0.049 -10000 0 -0.18 6 6
NF kappa B1/RelA/I kappa B alpha -0.021 0.1 -10000 0 -0.5 8 8
AIFM1 0.005 0.01 -10000 0 -10000 0 0
BCL2 0 0 -10000 0 -10000 0 0
RXR and RAR heterodimerization with other nuclear receptor

Figure S89.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S89.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.008 0.04 -10000 0 -10000 0 0
VDR -0.012 0.15 0.34 6 -0.86 5 11
FAM120B 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.006 0.09 -10000 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols -0.015 0.11 -10000 0 -0.4 12 12
MED1 0 0 -10000 0 -10000 0 0
mol:9cRA 0.001 0.015 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.015 0.071 -10000 0 -0.35 8 8
RXRs/NUR77 -0.064 0.21 -10000 0 -0.55 28 28
RXRs/PPAR 0.007 0.062 -10000 0 -0.35 3 3
NCOR2 0 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.011 0.12 0.23 6 -0.68 5 11
RARs/VDR/DNA/Vit D3 -0.023 0.12 -10000 0 -0.51 11 11
RARA 0 0 -10000 0 -10000 0 0
NCOA1 0 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.012 0.15 0.34 6 -0.86 5 11
RARs/RARs/DNA/9cRA -0.016 0.089 -10000 0 -0.51 6 6
RARG 0 0 -10000 0 -10000 0 0
RPS6KB1 0.008 0.033 -10000 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.015 0.071 -10000 0 -0.35 8 8
THRA 0 0 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.011 0.12 0.23 6 -0.68 5 11
RXRs/PPAR/9cRA/PGJ2/DNA 0.008 0.1 -10000 0 -0.53 3 3
NR1H4 -0.036 0.17 -10000 0 -0.86 8 8
RXRs/LXRs/DNA 0.007 0.1 -10000 0 -0.48 3 3
NR1H2 0.009 0.01 -10000 0 -10000 0 0
NR1H3 -0.001 0.01 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.003 0.13 0.38 3 -0.51 8 11
NR4A1 -0.12 0.3 -10000 0 -0.86 26 26
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.013 0.09 -10000 0 -0.34 11 11
RXRG 0.023 0.16 0.35 21 -0.86 3 24
RXR alpha/CCPG 0 0.002 -10000 0 -10000 0 0
RXRA -0.002 0.007 -10000 0 -10000 0 0
RXRB -0.002 0.009 -10000 0 -10000 0 0
THRB -0.009 0.088 -10000 0 -0.86 2 2
PPARG 0.002 0.025 0.34 1 -10000 0 1
PPARD 0 0 -10000 0 -10000 0 0
TNF -0.014 0.29 -10000 0 -1.2 10 10
mol:Oxysterols 0.002 0.012 -10000 0 -10000 0 0
cholesterol transport -0.015 0.11 -10000 0 -0.4 12 12
PPARA 0 0 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.027 0.15 -10000 0 -0.86 6 6
RXRs/NUR77/BCL2 -0.043 0.14 -10000 0 -0.36 28 28
SREBF1 0.032 0.11 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.008 0.1 -10000 0 -0.53 3 3
ABCA1 0.023 0.17 -10000 0 -1.2 2 2
RARs/THRs -0.021 0.1 -10000 0 -0.5 8 8
RXRs/FXR -0.01 0.15 -10000 0 -0.53 11 11
BCL2 0 0 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S90.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S90.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.022 0.16 0.34 3 -0.86 6 9
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.002 0.025 0.34 1 -10000 0 1
TCEB1 0 0 -10000 0 -10000 0 0
HIF1A/p53 -0.002 0.016 -10000 0 -10000 0 0
HIF1A -0.003 0.018 -10000 0 -10000 0 0
COPS5 0 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.001 0.014 -10000 0 -10000 0 0
FIH (dimer) 0 0 -10000 0 -10000 0 0
CDKN2A 0.22 0.16 0.34 123 -10000 0 123
ARNT/IPAS -0.017 0.12 -10000 0 -0.67 6 6
HIF1AN 0 0 -10000 0 -10000 0 0
GNB2L1 0 0 -10000 0 -10000 0 0
HIF1A/ARNT -0.002 0.016 -10000 0 -10000 0 0
CUL2 0 0 -10000 0 -10000 0 0
OS9 0 0 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.001 0.015 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 -0.002 0.016 -10000 0 -10000 0 0
PHD1-3/OS9 0.013 0.1 -10000 0 -0.54 4 4
HIF1A/RACK1/Elongin B/Elongin C -0.001 0.02 -10000 0 -10000 0 0
VHL 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
HIF1A/JAB1 -0.002 0.016 -10000 0 -10000 0 0
EGLN3 0.021 0.17 0.34 22 -0.86 4 26
EGLN2 0 0 -10000 0 -10000 0 0
EGLN1 0 0 -10000 0 -10000 0 0
TP53 0 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0 0.008 -10000 0 -10000 0 0
ARNT 0 0 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0 0 -10000 0 -10000 0 0
HIF1A/p19ARF 0.14 0.11 0.24 18 -10000 0 18
E-cadherin signaling in keratinocytes

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.014 0.073 -10000 0 -0.87 1 1
adherens junction organization 0.016 0.081 -10000 0 -0.32 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.019 0.092 -10000 0 -0.6 4 4
FMN1 -0.014 0.075 -10000 0 -0.33 2 2
mol:IP3 -0.014 0.072 -10000 0 -0.84 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.019 0.077 -10000 0 -0.34 10 10
CTNNB1 0.001 0.005 -10000 0 -10000 0 0
AKT1 -0.015 0.076 -10000 0 -0.84 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin -0.031 0.13 -10000 0 -0.57 10 10
CTNND1 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.014 0.079 -10000 0 -0.32 10 10
VASP -0.018 0.072 -10000 0 -0.32 10 10
ZYX -0.018 0.072 -10000 0 -0.32 10 10
JUB -0.018 0.072 -10000 0 -10000 0 0
EGFR(dimer) -0.025 0.11 -10000 0 -0.69 3 3
E-cadherin/beta catenin-gamma catenin -0.03 0.13 -10000 0 -0.57 10 10
mol:PI-3-4-5-P3 -0.017 0.082 -10000 0 -0.9 1 1
PIK3CA -0.005 0.064 -10000 0 -0.88 1 1
PI3K -0.017 0.085 -10000 0 -0.95 1 1
FYN -0.053 0.18 -10000 0 -0.39 39 39
mol:Ca2+ -0.014 0.07 -10000 0 -0.8 1 1
JUP 0.001 0.005 -10000 0 -10000 0 0
PIK3R1 -0.005 0.064 -10000 0 -0.88 1 1
mol:DAG -0.014 0.072 -10000 0 -0.84 1 1
CDH1 -0.045 0.19 -10000 0 -0.86 10 10
RhoA/GDP -0.019 0.092 -10000 0 -0.6 4 4
establishment of polarity of embryonic epithelium 0.014 0.079 -10000 0 -0.32 10 10
SRC 0.002 0.025 0.34 1 -10000 0 1
RAC1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
EGFR -0.014 0.11 -10000 0 -0.86 3 3
CASR -0.1 0.2 -10000 0 -0.47 39 39
RhoA/GTP -0.012 0.063 -10000 0 -0.72 1 1
AKT2 -0.015 0.076 -10000 0 -0.84 1 1
actin cable formation 0.021 0.079 -10000 0 -10000 0 0
apoptosis 0.015 0.074 0.82 1 -10000 0 1
CTNNA1 0 0 -10000 0 -10000 0 0
mol:GDP -0.021 0.1 -10000 0 -0.65 4 4
PIP5K1A -0.018 0.072 -10000 0 -0.32 10 10
PLCG1 -0.014 0.075 -10000 0 -0.88 1 1
Rac1/GTP -0.023 0.098 -10000 0 -0.62 3 3
homophilic cell adhesion 0.001 0.002 -10000 0 -10000 0 0
Cellular roles of Anthrax toxin

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 -0.005 0.062 -10000 0 -0.86 1 1
ANTXR2 -0.009 0.088 -10000 0 -0.86 2 2
negative regulation of myeloid dendritic cell antigen processing and presentation -0.002 0.013 -10000 0 -0.11 3 3
monocyte activation -0.063 0.2 -10000 0 -0.58 21 21
MAP2K2 0 0.017 -10000 0 -10000 0 0
MAP2K1 -0.001 0.011 -10000 0 -10000 0 0
MAP2K7 -0.001 0.011 -10000 0 -10000 0 0
MAP2K6 -0.011 0.077 -10000 0 -0.53 4 4
CYAA -0.008 0.064 -10000 0 -0.52 3 3
MAP2K4 -0.001 0.011 -10000 0 -10000 0 0
IL1B -0.061 0.18 -10000 0 -0.52 27 27
Channel -0.009 0.068 -10000 0 -0.55 3 3
NLRP1 -0.001 0.013 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.002 0.016 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.002 0.013 0.11 3 -10000 0 3
MAPK3 -0.001 0.011 -10000 0 -10000 0 0
MAPK1 -0.001 0.011 -10000 0 -10000 0 0
PGR -0.073 0.18 -10000 0 -0.53 26 26
PA/Cellular Receptors -0.009 0.073 -10000 0 -0.59 3 3
apoptosis -0.002 0.013 -10000 0 -0.11 3 3
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.008 0.064 -10000 0 -0.51 3 3
macrophage activation -0.001 0.01 -10000 0 -10000 0 0
TNF -0.045 0.19 -10000 0 -0.86 10 10
VCAM1 -0.064 0.2 -10000 0 -0.58 21 21
platelet activation -0.002 0.016 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.022 0.1 7 -10000 0 7
IL18 0.003 0.079 -10000 0 -0.53 4 4
negative regulation of macrophage activation -0.002 0.013 -10000 0 -0.11 3 3
LEF -0.002 0.013 -10000 0 -0.11 3 3
CASP1 -0.001 0.012 -10000 0 -0.092 3 3
mol:cAMP -0.002 0.016 -10000 0 -10000 0 0
necrosis -0.002 0.013 -10000 0 -0.11 3 3
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.008 0.065 -10000 0 -0.52 3 3
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

Figure S93.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S93.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -10000 0 -10000 0 0
HDAC2 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.009 0.073 -10000 0 -0.59 3 3
forebrain development -0.019 0.13 -10000 0 -0.52 8 8
GNAO1 -0.4 0.43 -10000 0 -0.86 88 88
SMO/beta Arrestin2 -0.007 0.069 -10000 0 -0.67 2 2
SMO -0.009 0.088 -10000 0 -0.87 2 2
ARRB2 0 0 -10000 0 -10000 0 0
GLI3/SPOP -0.002 0.025 -10000 0 -0.31 1 1
mol:GTP 0 0.001 -10000 0 -10000 0 0
GSK3B 0 0 -10000 0 -10000 0 0
GNAI2 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0 0 -10000 0 -10000 0 0
GNAI1 -0.009 0.088 -10000 0 -0.86 2 2
XPO1 0 0.002 -10000 0 -10000 0 0
GLI1/Su(fu) -0.04 0.11 -10000 0 -0.54 6 6
SAP30 0 0 -10000 0 -10000 0 0
mol:GDP -0.009 0.088 -10000 0 -0.86 2 2
MIM/GLI2A 0.012 0.01 -10000 0 -10000 0 0
IFT88 0 0 -10000 0 -10000 0 0
GNAI3 0 0 -10000 0 -10000 0 0
GLI2 0.015 0.071 -10000 0 -10000 0 0
GLI3 0.031 0.037 0.3 1 -0.33 1 2
CSNK1D 0 0 -10000 0 -10000 0 0
CSNK1E 0 0 -10000 0 -10000 0 0
SAP18 0 0 -10000 0 -10000 0 0
embryonic digit morphogenesis 0 0 -10000 0 -10000 0 0
GNG2 -0.005 0.062 -10000 0 -0.86 1 1
Gi family/GTP -0.13 0.2 -10000 0 -0.38 46 46
SIN3B 0 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
GLI3/Su(fu) -0.002 0.025 -10000 0 -10000 0 0
GLI2/Su(fu) -0.016 0.06 -10000 0 -0.44 1 1
FOXA2 -0.014 0.13 -10000 0 -1.3 2 2
neural tube patterning -0.019 0.13 -10000 0 -0.52 8 8
SPOP 0 0 -10000 0 -10000 0 0
Su(fu)/PIAS1 -0.003 0.028 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
CSNK1G2 0 0 -10000 0 -10000 0 0
CSNK1G3 0 0 -10000 0 -10000 0 0
MTSS1 0.012 0.01 -10000 0 -10000 0 0
embryonic limb morphogenesis -0.019 0.13 -10000 0 -0.52 8 8
SUFU -0.003 0.031 -10000 0 -0.32 1 1
LGALS3 0.029 0.094 0.34 16 -10000 0 16
catabolic process -0.013 0.046 -10000 0 -10000 0 0
GLI3A/CBP 0.007 0.048 -10000 0 -0.39 1 1
KIF3A 0 0 -10000 0 -10000 0 0
GLI1 -0.02 0.13 -10000 0 -0.54 8 8
RAB23 0 0 -10000 0 -10000 0 0
CSNK1A1 0 0 -10000 0 -10000 0 0
IFT172 0 0 -10000 0 -10000 0 0
RBBP7 0 0 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.017 0.072 -10000 0 -10000 0 0
GNAZ 0.16 0.17 0.34 91 -10000 0 91
RBBP4 0 0 -10000 0 -10000 0 0
CSNK1G1 0 0 -10000 0 -10000 0 0
PIAS1 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
GLI2/SPOP -0.016 0.056 -10000 0 -10000 0 0
STK36 0 0.002 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.098 0.16 -10000 0 -0.47 5 5
PTCH1 -0.039 0.25 -10000 0 -1.3 7 7
MIM/GLI1 -0.013 0.14 -10000 0 -0.54 8 8
CREBBP 0.007 0.048 -10000 0 -0.39 1 1
Su(fu)/SIN3/HDAC complex 0.002 0.012 -10000 0 -10000 0 0
Insulin-mediated glucose transport

Figure S94.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S94.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.019 0.079 -10000 0 -0.37 8 8
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0 0 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
STXBP4 0.002 0.025 0.34 1 -10000 0 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose 0.029 0.1 -10000 0 -0.41 8 8
YWHAZ 0 0 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 -0.007 0.068 -10000 0 -0.67 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
SNARE/Synip 0.001 0.015 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
ASIP 0 0 -10000 0 -10000 0 0
PRKCI 0 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0 0 -10000 0 -10000 0 0
GYS1 0 0 -10000 0 -10000 0 0
PRKCZ -0.036 0.17 -10000 0 -0.86 8 8
TRIP10 0 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.059 0.059 -10000 0 -10000 0 0
VAMP2 0 0 -10000 0 -10000 0 0
SLC2A4 0.028 0.11 -10000 0 -0.46 8 8
STX4 0 0 -10000 0 -10000 0 0
GSK3B 0 0 -10000 0 -10000 0 0
SFN 0.19 0.17 0.34 108 -10000 0 108
LNPEP 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S95.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -10000 0 -10000 0 0
NFATC1 0.02 0.086 -10000 0 -0.4 2 2
NFATC2 -0.032 0.11 -10000 0 -0.31 12 12
NFATC3 -0.023 0.11 -10000 0 -0.55 8 8
YWHAE 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.008 0.12 -10000 0 -0.56 6 6
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.081 0.18 0.24 1 -0.5 27 28
BCL2/BAX 0 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.002 0.004 -10000 0 -10000 0 0
CaM/Ca2+ -0.002 0.004 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.033 0.11 -10000 0 -0.58 5 5
Calcineurin A alpha-beta B1/BCL2 0 0 -10000 0 -10000 0 0
FKBP8 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.032 0.11 0.57 5 -10000 0 5
KPNB1 0 0 -10000 0 -10000 0 0
KPNA2 0.002 0.025 0.34 1 -10000 0 1
XPO1 0 0 -10000 0 -10000 0 0
SFN 0.19 0.17 0.34 108 -10000 0 108
MAP3K8 -0.009 0.088 -10000 0 -0.86 2 2
NFAT4/CK1 alpha -0.016 0.074 -10000 0 -0.37 8 8
MEF2D/NFAT1/Cbp/p300 -0.08 0.14 -10000 0 -0.5 8 8
CABIN1 -0.009 0.12 -10000 0 -0.57 6 6
CALM1 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
MAP3K1 0 0 -10000 0 -10000 0 0
CAMK4 -0.1 0.28 0.34 1 -0.86 23 24
mol:Ca2+ -0.002 0.007 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.001 0.017 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
MAPK8 -0.041 0.18 -10000 0 -0.86 9 9
MAPK9 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
FKBP1A 0 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.031 0.1 -10000 0 -0.46 9 9
PRKCH 0 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.004 -10000 0 -10000 0 0
CASP3 -0.005 0.063 -10000 0 -0.87 1 1
PIM1 0 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis 0 0 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.055 0.048 -10000 0 -10000 0 0
PRKCB -0.077 0.25 -10000 0 -0.86 17 17
PRKCE -0.003 0.067 0.34 1 -0.86 1 2
JNK2/NFAT4 -0.021 0.1 -10000 0 -0.5 8 8
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0 0 -10000 0 -10000 0 0
NUP214 0 0 -10000 0 -10000 0 0
PRKCZ -0.036 0.17 -10000 0 -0.86 8 8
PRKCA 0 0 -10000 0 -10000 0 0
PRKCG 0.002 0.025 0.34 1 -10000 0 1
PRKCQ -0.028 0.17 0.34 2 -0.86 7 9
FKBP38/BCL2 0 0 -10000 0 -10000 0 0
EP300 -0.001 0.002 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0 0 -10000 0 -10000 0 0
NFATc/JNK1 -0.037 0.13 -10000 0 -0.5 10 10
CaM/Ca2+/FKBP38 0 0.001 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.071 0.19 -10000 0 -0.59 23 23
NFATc/ERK1 -0.017 0.071 -10000 0 -0.38 1 1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.081 0.18 0.24 1 -0.5 27 28
NR4A1 -0.13 0.27 -10000 0 -0.79 26 26
GSK3B 0 0 -10000 0 -10000 0 0
positive T cell selection -0.023 0.11 -10000 0 -0.55 8 8
NFAT1/CK1 alpha -0.042 0.075 -10000 0 -0.42 2 2
RCH1/ KPNB1 0.001 0.017 -10000 0 -10000 0 0
YWHAQ 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
AKAP5 0.002 0.025 0.34 1 -10000 0 1
MEF2D -0.001 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0 0 -10000 0 -10000 0 0
NFATc/p38 alpha -0.017 0.071 -10000 0 -0.38 1 1
CREBBP -0.001 0.002 -10000 0 -10000 0 0
BCL2 0 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

Figure S96.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S96.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -10000 0 -10000 0 0
HDAC3 0 0 -10000 0 -10000 0 0
VDR -0.012 0.15 0.34 6 -0.86 5 11
Cbp/p300/PCAF -0.006 0.059 -10000 0 -0.58 2 2
EP300 0 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.017 0.058 -10000 0 -10000 0 0
KAT2B -0.009 0.088 -10000 0 -0.86 2 2
MAPK14 0 0 -10000 0 -10000 0 0
AKT1 0.047 0.11 0.24 37 -0.36 3 40
RAR alpha/9cRA/Cyclin H -0.013 0.059 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA -0.016 0.058 -10000 0 -0.28 8 8
CDC2 0.001 0 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.033 0.15 -10000 0 -0.7 9 9
NCOR2 0 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.011 0.12 0.23 6 -0.68 5 11
RXRs/RARs/NRIP1/9cRA 0.038 0.074 -10000 0 -10000 0 0
NCOA2 -0.095 0.27 -10000 0 -0.86 21 21
NCOA3 0 0 -10000 0 -10000 0 0
NCOA1 0 0 -10000 0 -10000 0 0
VDR/VDR/DNA -0.012 0.15 0.34 6 -0.86 5 11
RARG 0 0 -10000 0 -10000 0 0
RAR gamma1/9cRA 0 0 -10000 0 -10000 0 0
MAPK3 0 0 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
MAPK8 -0.041 0.18 -10000 0 -0.86 9 9
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.014 0.094 -10000 0 -0.45 5 5
RARA -0.014 0.068 -10000 0 -0.32 9 9
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.049 0.13 -10000 0 -0.36 26 26
PRKCA 0 0 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC1 0.024 0.065 -10000 0 -10000 0 0
RXRG 0.021 0.076 -10000 0 -0.46 3 3
RXRA 0.012 0.068 -10000 0 -0.29 9 9
RXRB 0.011 0.013 -10000 0 -10000 0 0
VDR/Vit D3/DNA -0.011 0.12 0.23 6 -0.68 5 11
RBP1 -0.18 0.36 0.34 3 -0.86 41 44
CRBP1/9-cic-RA -0.14 0.28 0.23 3 -0.68 41 44
RARB -0.027 0.15 -10000 0 -0.86 6 6
PRKCG 0.004 0.025 0.34 1 -10000 0 1
MNAT1 0 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.031 0.11 0.36 1 -10000 0 1
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.039 0.074 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.071 -10000 0 -10000 0 0
RXRs/RARs/NRIP1/9cRA/HDAC3 0.024 0.065 -10000 0 -10000 0 0
positive regulation of DNA binding -0.013 0.056 -10000 0 -10000 0 0
NRIP1 0.025 0.056 -10000 0 -10000 0 0
RXRs/RARs 0.02 0.06 -10000 0 -10000 0 0
RXRs/RXRs/DNA/9cRA -0.005 0.052 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
CDK7 0 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.009 0.042 -10000 0 -10000 0 0
CCNH 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure S97.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S97.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 -0.027 0.15 -10000 0 -0.86 6 6
Caspase 8 (4 units) -0.042 0.13 -10000 0 -0.76 3 3
NEF -0.008 0.043 -10000 0 -10000 0 0
NFKBIA 0.001 0.012 -10000 0 -10000 0 0
BIRC3 0.006 0.085 0.32 6 -0.87 1 7
CYCS -0.002 0.14 -10000 0 -0.75 3 3
RIPK1 0 0 -10000 0 -10000 0 0
CD247 -0.015 0.11 0.34 1 -0.97 2 3
MAP2K7 -0.004 0.14 -10000 0 -0.58 6 6
protein ubiquitination 0.024 0.11 -10000 0 -0.5 5 5
CRADD -0.005 0.062 -10000 0 -0.86 1 1
DAXX 0 0 -10000 0 -10000 0 0
FAS -0.023 0.14 -10000 0 -0.86 5 5
BID -0.042 0.14 -10000 0 -0.81 3 3
NF-kappa-B/RelA/I kappa B alpha 0.004 0.043 -10000 0 -0.35 1 1
TRADD -0.005 0.062 -10000 0 -0.86 1 1
MAP3K5 -0.059 0.22 -10000 0 -0.86 13 13
CFLAR 0 0 -10000 0 -10000 0 0
FADD 0.002 0.025 0.34 1 -10000 0 1
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.004 0.044 -10000 0 -0.36 1 1
MAPK8 -0.019 0.17 -10000 0 -0.54 15 15
APAF1 0 0 -10000 0 -10000 0 0
TRAF1 0.002 0.025 0.34 1 -10000 0 1
TRAF2 0 0 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.046 0.15 -10000 0 -0.4 22 22
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.033 0.13 -10000 0 -0.64 6 6
CHUK 0.023 0.12 -10000 0 -0.55 5 5
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.046 0.16 -10000 0 -0.53 17 17
TCRz/NEF -0.02 0.12 0.23 1 -0.49 9 10
TNF -0.045 0.19 -10000 0 -0.86 10 10
FASLG -0.041 0.21 0.31 2 -0.95 9 11
NFKB1 0.001 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.049 0.16 -10000 0 -0.58 16 16
CASP6 -0.03 0.091 -10000 0 -0.5 3 3
CASP7 0.038 0.12 -10000 0 -0.5 4 4
RELA 0.001 0.012 -10000 0 -10000 0 0
CASP2 0 0 -10000 0 -10000 0 0
CASP3 0.036 0.12 -10000 0 -0.5 4 4
TNFRSF1A 0 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.021 0.12 -10000 0 -0.67 6 6
CASP8 0 0 -10000 0 -10000 0 0
CASP9 0 0 -10000 0 -10000 0 0
MAP3K14 0.016 0.13 -10000 0 -0.58 6 6
APAF-1/Caspase 9 -0.022 0.093 0.28 1 -0.46 4 5
BCL2 -0.01 0.16 -10000 0 -0.48 15 15
Signaling events mediated by VEGFR1 and VEGFR2

Figure S98.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S98.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.053 0.18 -10000 0 -0.67 15 15
AKT1 0.041 0.14 -10000 0 -0.67 6 6
PTK2B -0.061 0.2 -10000 0 -0.61 19 19
VEGFR2 homodimer/Frs2 -0.03 0.17 -10000 0 -0.96 6 6
CAV1 0 0 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.028 0.16 -10000 0 -0.9 6 6
endothelial cell proliferation 0.028 0.15 -10000 0 -0.64 6 6
mol:Ca2+ -0.03 0.16 -10000 0 -0.81 7 7
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.027 0.15 -10000 0 -0.85 6 6
RP11-342D11.1 -0.03 0.16 -10000 0 -0.82 7 7
CDH5 -0.005 0.062 -10000 0 -0.86 1 1
VEGFA homodimer 0 0 -10000 0 -10000 0 0
SHC1 0 0 -10000 0 -10000 0 0
SHC2 -0.023 0.14 -10000 0 -0.86 5 5
HRAS/GDP -0.024 0.13 -10000 0 -0.73 6 6
SH2D2A -0.028 0.17 0.34 2 -0.86 7 9
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.025 0.12 -10000 0 -0.64 7 7
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.045 0.2 -10000 0 -0.75 12 12
VEGFR1 homodimer 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.029 0.15 -10000 0 -0.84 6 6
GRB10 -0.03 0.16 -10000 0 -0.81 7 7
PTPN11 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
PAK1 0 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.028 0.16 -10000 0 -0.89 6 6
HRAS 0.004 0.035 0.34 2 -10000 0 2
VEGF/Rho/ROCK1/Integrin Complex -0.034 0.11 -10000 0 -0.49 6 6
HIF1A 0 0 -10000 0 -10000 0 0
FRS2 0 0 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.026 0.15 -10000 0 -0.84 6 6
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 -0.005 0.062 -10000 0 -0.86 1 1
Nck/Pak 0 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.028 0.16 -10000 0 -0.9 6 6
mol:GDP -0.027 0.14 -10000 0 -0.8 6 6
mol:NADP 0.037 0.12 -10000 0 -0.53 7 7
eNOS/Hsp90 0.038 0.11 -10000 0 -0.5 7 7
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
mol:IP3 -0.03 0.16 -10000 0 -0.83 7 7
HIF1A/ARNT 0 0 -10000 0 -10000 0 0
SHB 0 0 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
VEGFC 0.002 0.025 0.34 1 -10000 0 1
FAK1/Vinculin -0.047 0.17 -10000 0 -0.88 6 6
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.065 0.21 -10000 0 -0.66 19 19
PTPN6 0 0 -10000 0 -10000 0 0
EPAS1 -0.012 0.069 -10000 0 -0.39 6 6
mol:L-citrulline 0.037 0.12 -10000 0 -0.53 7 7
ITGAV 0 0 -10000 0 -10000 0 0
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.027 0.15 -10000 0 -0.85 6 6
VEGFR2 homodimer/VEGFA homodimer -0.033 0.18 -10000 0 -0.9 7 7
VEGFR2/3 heterodimer -0.033 0.18 -10000 0 -1 6 6
VEGFB -0.03 0.16 0.34 1 -0.86 7 8
MAPK11 0.017 0.17 -10000 0 -0.84 7 7
VEGFR2 homodimer -0.008 0.19 -10000 0 -1.1 6 6
FLT1 0 0 -10000 0 -10000 0 0
NEDD4 -0.009 0.088 -10000 0 -0.86 2 2
MAPK3 0.009 0.16 -10000 0 -0.75 7 7
MAPK1 0.009 0.16 -10000 0 -0.75 7 7
VEGFA145/NRP2 -0.006 0.07 -10000 0 -0.67 2 2
VEGFR1/2 heterodimer -0.03 0.17 -10000 0 -0.96 6 6
KDR -0.008 0.19 -10000 0 -1.1 6 6
VEGFA165/NRP1/VEGFR2 homodimer -0.034 0.18 -10000 0 -0.84 8 8
SRC 0.002 0.025 0.34 1 -10000 0 1
platelet activating factor biosynthetic process 0.01 0.16 -10000 0 -0.78 7 7
PI3K -0.033 0.16 -10000 0 -0.88 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.028 0.16 -10000 0 -0.9 6 6
FES -0.036 0.17 -10000 0 -0.77 9 9
GAB1 -0.028 0.15 -10000 0 -0.85 6 6
VEGFR2 homodimer/VEGFA homodimer/Src -0.027 0.16 -10000 0 -0.9 6 6
CTNNB1 0 0 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
ARNT 0 0 -10000 0 -10000 0 0
eNOS/Caveolin-1 0.038 0.11 -10000 0 -0.5 7 7
VEGFR2 homodimer/VEGFA homodimer/Yes -0.028 0.16 -10000 0 -0.9 6 6
PI3K/GAB1 -0.025 0.13 -10000 0 -0.69 6 6
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.026 0.14 -10000 0 -0.82 6 6
PRKACA 0 0 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.03 0.17 -10000 0 -0.98 6 6
HSP90AA1 0 0 -10000 0 -10000 0 0
CDC42 -0.031 0.16 -10000 0 -0.85 7 7
actin cytoskeleton reorganization -0.044 0.19 -10000 0 -0.74 12 12
PTK2 -0.003 0.2 -10000 0 -0.98 6 6
EDG1 -0.03 0.16 -10000 0 -0.82 7 7
mol:DAG -0.03 0.16 -10000 0 -0.83 7 7
CaM/Ca2+ -0.028 0.15 -10000 0 -0.76 7 7
MAP2K3 -0.034 0.16 -10000 0 -0.72 9 9
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.032 0.17 -10000 0 -0.86 7 7
PLCG1 -0.031 0.16 -10000 0 -0.85 7 7
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.026 0.15 -10000 0 -0.85 6 6
IQGAP1 0 0 -10000 0 -10000 0 0
YES1 0 0 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.028 0.16 -10000 0 -0.9 6 6
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.028 0.16 -10000 0 -0.9 6 6
cell migration 0.028 0.16 -10000 0 -0.71 6 6
mol:PI-3-4-5-P3 -0.029 0.14 -10000 0 -0.77 6 6
FYN 0 0 -10000 0 -10000 0 0
VEGFB/NRP1 -0.045 0.17 -10000 0 -0.62 14 14
mol:NO 0.037 0.12 -10000 0 -0.53 7 7
PXN 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.025 0.13 -10000 0 -0.74 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.032 0.17 -10000 0 -0.86 7 7
VHL 0 0 -10000 0 -10000 0 0
ITGB3 -0.068 0.23 -10000 0 -0.86 15 15
NOS3 0.035 0.13 -10000 0 -0.62 7 7
VEGFR2 homodimer/VEGFA homodimer/Sck -0.042 0.18 -10000 0 -0.73 11 11
RAC1 0 0 -10000 0 -10000 0 0
PRKCA -0.028 0.15 -10000 0 -0.76 7 7
PRKCB -0.07 0.2 -10000 0 -0.58 23 23
VCL 0.002 0.025 0.34 1 -10000 0 1
VEGFA165/NRP1 -0.03 0.16 -10000 0 -0.82 7 7
VEGFR1/2 heterodimer/VEGFA homodimer -0.028 0.16 -10000 0 -0.9 6 6
VEGFA165/NRP2 -0.006 0.07 -10000 0 -0.67 2 2
MAPKKK cascade -0.025 0.13 -10000 0 -0.74 6 6
NRP2 -0.007 0.091 0.34 1 -0.86 2 3
VEGFC homodimer 0.002 0.025 0.34 1 -10000 0 1
NCK1 0 0 -10000 0 -10000 0 0
ROCK1 0 0 -10000 0 -10000 0 0
FAK1/Paxillin -0.048 0.17 -10000 0 -0.88 6 6
MAP3K13 -0.036 0.17 -10000 0 -0.77 9 9
PDPK1 -0.025 0.12 -10000 0 -0.66 6 6
TCGA08_rtk_signaling

Figure S99.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S99.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.34 0.42 -10000 0 -0.86 74 74
HRAS 0.004 0.035 0.34 2 -10000 0 2
EGFR -0.014 0.11 -10000 0 -0.86 3 3
AKT 0.021 0.022 -10000 0 -10000 0 0
FOXO3 0 0 -10000 0 -10000 0 0
AKT1 0 0 -10000 0 -10000 0 0
FOXO1 -0.009 0.088 -10000 0 -0.86 2 2
AKT3 0.002 0.025 0.34 1 -10000 0 1
FOXO4 0 0 -10000 0 -10000 0 0
MET 0.002 0.025 0.34 1 -10000 0 1
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
PIK3CB 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
PIK3CG -0.022 0.16 0.34 3 -0.86 6 9
PIK3R3 0.002 0.025 0.34 1 -10000 0 1
PIK3R2 0 0 -10000 0 -10000 0 0
NF1 -0.005 0.062 -10000 0 -0.86 1 1
RAS -0.073 0.095 -10000 0 -0.3 5 5
ERBB2 -0.009 0.088 -10000 0 -0.86 2 2
proliferation/survival/translation -0.012 0.035 0.22 1 -10000 0 1
PI3K -0.051 0.11 -10000 0 -0.28 11 11
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
KRAS 0 0 -10000 0 -10000 0 0
FOXO 0.022 0.025 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
PTEN -0.009 0.088 -10000 0 -0.86 2 2
E-cadherin signaling in the nascent adherens junction

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -0.032 0.14 -10000 0 -0.61 10 10
KLHL20 -0.026 0.071 -10000 0 -0.35 3 3
CYFIP2 -0.054 0.21 -10000 0 -0.86 12 12
Rac1/GDP -0.016 0.085 -10000 0 -0.37 10 10
ENAH -0.032 0.14 -10000 0 -0.61 10 10
AP1M1 0 0 -10000 0 -10000 0 0
RAP1B 0 0 -10000 0 -10000 0 0
RAP1A 0 0 -10000 0 -10000 0 0
CTNNB1 0 0 -10000 0 -10000 0 0
CDC42/GTP -0.016 0.07 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.027 0.061 -10000 0 -0.19 14 14
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.031 0.13 -10000 0 -0.54 12 12
RAPGEF1 0.013 0.12 -10000 0 -0.51 10 10
CTNND1 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.033 0.14 -10000 0 -0.64 10 10
CRK 0.004 0.13 -10000 0 -0.56 10 10
E-cadherin/gamma catenin/alpha catenin -0.031 0.13 -10000 0 -0.58 10 10
alphaE/beta7 Integrin -0.005 0.072 -10000 0 -0.67 2 2
IQGAP1 0 0 -10000 0 -10000 0 0
NCKAP1 0 0 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -10000 0 -10000 0 0
DLG1 -0.032 0.14 -10000 0 -0.61 10 10
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.014 0.056 -10000 0 -0.37 1 1
MLLT4 0 0 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.018 0.1 -10000 0 -0.54 7 7
PI3K -0.018 0.074 -10000 0 -0.51 1 1
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin -0.035 0.15 -10000 0 -0.67 10 10
TIAM1 -0.032 0.16 -10000 0 -0.86 7 7
E-cadherin(dimer)/Ca2+ -0.027 0.11 -10000 0 -0.51 10 10
AKT1 -0.01 0.04 -10000 0 -0.26 1 1
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
CDH1 -0.045 0.19 -10000 0 -0.86 10 10
RhoA/GDP -0.016 0.085 -10000 0 -0.37 10 10
actin cytoskeleton organization -0.018 0.052 -10000 0 -0.25 3 3
CDC42/GDP -0.016 0.085 -10000 0 -0.37 10 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.019 0.081 -10000 0 -0.36 10 10
ITGB7 -0.009 0.088 -10000 0 -0.86 2 2
RAC1 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.028 0.12 -10000 0 -0.54 10 10
E-cadherin/Ca2+/beta catenin/alpha catenin -0.027 0.12 -10000 0 -0.52 10 10
mol:GDP 0.022 0.11 -10000 0 -0.44 10 10
CDC42/GTP/IQGAP1 0 0 -10000 0 -10000 0 0
JUP 0 0 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP -0.02 0.084 -10000 0 -0.38 10 10
RAC1/GTP/IQGAP1 0 0 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
CDC42 0 0 -10000 0 -10000 0 0
CTNNA1 0 0 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle -0.02 0.065 -10000 0 -0.28 10 10
NME1 0.004 0.035 0.34 2 -10000 0 2
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.032 0.14 -10000 0 -0.61 10 10
regulation of cell-cell adhesion -0.014 0.061 -10000 0 -10000 0 0
WASF2 -0.014 0.031 -10000 0 -0.14 1 1
Rap1/GTP -0.019 0.08 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.03 0.12 -10000 0 -0.5 12 12
CCND1 -0.026 0.083 -10000 0 -0.36 10 10
VAV2 0.007 0.13 -10000 0 -0.54 10 10
RAP1/GDP -0.019 0.081 -10000 0 -10000 0 0
adherens junction assembly -0.031 0.13 -10000 0 -0.59 10 10
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0 0 -10000 0 -10000 0 0
PIP5K1C 0 0 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.028 0.12 -10000 0 -0.48 12 12
E-cadherin/beta catenin -0.028 0.12 -10000 0 -0.53 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.032 0.14 -10000 0 -0.61 10 10
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
Rac1/GTP -0.043 0.12 -10000 0 -0.43 10 10
E-cadherin/beta catenin/alpha catenin -0.031 0.13 -10000 0 -0.58 10 10
ITGAE 0.004 0.035 0.34 2 -10000 0 2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.034 0.14 -10000 0 -0.65 10 10
EGFR-dependent Endothelin signaling events

Figure S101.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S101.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.004 0.035 0.34 2 -10000 0 2
EGFR -0.014 0.11 -10000 0 -0.86 3 3
EGF/EGFR 0.02 0.12 0.32 1 -0.48 7 8
EGF/EGFR dimer/SHC/GRB2/SOS1 0.038 0.11 -10000 0 -0.49 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.002 0.025 0.34 1 -10000 0 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.08 0.14 0.34 45 -10000 0 45
EGF/EGFR dimer/SHC 0.04 0.12 -10000 0 -0.57 3 3
mol:GDP 0.034 0.1 -10000 0 -0.48 3 3
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.018 0.12 -10000 0 -0.86 4 4
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP 0.02 0.076 -10000 0 -0.45 3 3
SHC1 0 0 -10000 0 -10000 0 0
HRAS/GDP 0.029 0.089 -10000 0 -0.46 3 3
FRAP1 0.01 0.068 -10000 0 -0.47 3 3
EGF/EGFR dimer 0.043 0.13 -10000 0 -0.66 3 3
SOS1 0 0 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.013 0.098 -10000 0 -0.67 4 4
Rapid glucocorticoid signaling

Figure S102.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S102.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.03 0.081 -10000 0 -0.52 1 1
MAPK9 0 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.001 0.011 -10000 0 -10000 0 0
GNB1/GNG2 -0.003 0.043 -10000 0 -0.59 1 1
GNB1 0 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0 0 -10000 0 -10000 0 0
Gs family/GTP 0.033 0.073 0.19 33 -10000 0 33
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0 0 -10000 0 -10000 0 0
GNAL 0.059 0.13 0.34 33 -10000 0 33
GNG2 -0.005 0.062 -10000 0 -0.86 1 1
CRH 0.002 0.025 0.34 1 -10000 0 1
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 -0.022 0.1 -10000 0 -0.47 9 9
MAPK11 0.004 0.023 0.14 5 -10000 0 5
Signaling events mediated by Stem cell factor receptor (c-Kit)

Figure S103.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S103.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.002 0.11 -10000 0 -0.48 8 8
CRKL 0.008 0.071 -10000 0 -0.41 4 4
HRAS -0.021 0.11 -10000 0 -0.63 3 3
mol:PIP3 -0.003 0.072 -10000 0 -0.4 4 4
SPRED1 0 0 -10000 0 -10000 0 0
SPRED2 0 0 -10000 0 -10000 0 0
GAB1 -0.018 0.068 -10000 0 -0.44 4 4
FOXO3 0.012 0.066 -10000 0 -0.38 4 4
AKT1 0.005 0.07 -10000 0 -0.41 4 4
BAD 0.012 0.066 -10000 0 -0.38 4 4
megakaryocyte differentiation -0.022 0.13 -10000 0 -0.48 13 13
GSK3B 0.012 0.066 -10000 0 -0.38 4 4
RAF1 0.016 0.095 -10000 0 -0.48 3 3
SHC1 0 0 -10000 0 -10000 0 0
STAT3 -0.018 0.068 -10000 0 -0.44 4 4
STAT1 -0.034 0.18 -10000 0 -1.1 4 4
HRAS/SPRED1 -0.017 0.084 0.25 1 -0.48 3 4
cell proliferation -0.022 0.12 -10000 0 -0.46 13 13
PIK3CA -0.005 0.062 -10000 0 -0.87 1 1
TEC -0.018 0.12 -10000 0 -0.86 4 4
RPS6KB1 0.001 0.073 -10000 0 -0.44 4 4
HRAS/SPRED2 -0.017 0.084 0.25 1 -0.48 3 4
LYN/TEC/p62DOK -0.025 0.084 -10000 0 -0.42 8 8
MAPK3 0.025 0.071 -10000 0 -0.32 3 3
STAP1 -0.018 0.068 -10000 0 -0.44 4 4
GRAP2 -0.013 0.13 0.34 3 -0.86 4 7
JAK2 -0.06 0.14 -10000 0 -0.89 4 4
STAT1 (dimer) -0.033 0.18 -10000 0 -1 4 4
mol:Gleevec -0.001 0.003 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.036 0.12 -10000 0 -0.48 12 12
actin filament polymerization 0.002 0.073 -10000 0 -0.43 4 4
LYN 0 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.028 0.096 -10000 0 -0.62 4 4
PIK3R1 -0.005 0.062 -10000 0 -0.87 1 1
CBL/CRKL/GRB2 -0.012 0.053 -10000 0 -10000 0 0
PI3K -0.02 0.089 -10000 0 -0.52 5 5
PTEN -0.009 0.088 -10000 0 -0.86 2 2
SCF/KIT/EPO/EPOR -0.2 0.31 -10000 0 -1.5 4 4
MAPK8 -0.041 0.12 -10000 0 -0.47 13 13
STAT3 (dimer) 0.001 0.073 -10000 0 -0.43 4 4
positive regulation of transcription 0.024 0.06 -10000 0 -0.26 3 3
mol:GDP -0.029 0.12 0.31 1 -0.65 4 5
PIK3C2B -0.018 0.068 -10000 0 -0.44 4 4
CBL/CRKL -0.013 0.058 -10000 0 -0.39 4 4
FER -0.018 0.068 -10000 0 -0.44 4 4
SH2B3 -0.018 0.068 -10000 0 -0.44 4 4
PDPK1 0.003 0.068 -10000 0 -0.36 4 4
SNAI2 -0.018 0.081 -10000 0 -0.47 5 5
positive regulation of cell proliferation -0.014 0.13 -10000 0 -0.76 4 4
KITLG 0.008 0.006 -10000 0 -10000 0 0
cell motility -0.014 0.13 -10000 0 -0.76 4 4
PTPN6 0.004 0.006 -10000 0 -10000 0 0
EPOR 0.013 0.056 -10000 0 -10000 0 0
STAT5A (dimer) -0.01 0.11 -10000 0 -0.63 4 4
SOCS1 -0.007 0.091 0.34 1 -0.86 2 3
cell migration -0.002 0.074 0.43 4 -10000 0 4
SOS1 0 0 -10000 0 -10000 0 0
EPO -0.29 0.43 0.34 8 -0.87 68 76
VAV1 -0.032 0.16 -10000 0 -0.86 7 7
GRB10 -0.018 0.068 -10000 0 -0.44 4 4
PTPN11 0.001 0.003 -10000 0 -10000 0 0
SCF/KIT -0.023 0.071 -10000 0 -0.47 4 4
GO:0007205 0 0.005 -10000 0 -10000 0 0
MAP2K1 0.023 0.077 -10000 0 -0.36 3 3
CBL 0 0 -10000 0 -10000 0 0
KIT -0.01 0.22 -10000 0 -1.5 4 4
MAP2K2 0.023 0.077 -10000 0 -0.36 3 3
SHC/Grb2/SOS1 -0.016 0.058 -10000 0 -0.4 4 4
STAT5A -0.01 0.11 -10000 0 -0.65 4 4
GRB2 0 0 -10000 0 -10000 0 0
response to radiation 0 0.085 -10000 0 -0.46 5 5
SHC/GRAP2 -0.01 0.1 -10000 0 -0.67 4 4
PTPRO -0.041 0.12 -10000 0 -0.49 13 13
SH2B2 -0.017 0.068 -10000 0 -0.44 4 4
DOK1 0 0 -10000 0 -10000 0 0
MATK -0.017 0.069 -10000 0 -0.44 4 4
CREBBP 0.023 0.014 -10000 0 -10000 0 0
BCL2 0.015 0.053 -10000 0 -10000 0 0
Caspase cascade in apoptosis

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.005 0.093 -10000 0 -0.48 6 6
ACTA1 0.001 0.12 -10000 0 -0.64 6 6
NUMA1 0.005 0.093 -10000 0 -0.48 6 6
SPTAN1 0 0.12 -10000 0 -0.63 6 6
LIMK1 0.001 0.12 -10000 0 -0.63 6 6
BIRC3 0.006 0.087 0.34 6 -0.86 1 7
BIRC2 0 0 -10000 0 -10000 0 0
BAX 0 0 -10000 0 -10000 0 0
CASP10 0.002 0.13 -10000 0 -0.67 6 6
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0 0 -10000 0 -10000 0 0
PTK2 0.005 0.093 -10000 0 -0.48 6 6
DIABLO 0 0 -10000 0 -10000 0 0
apoptotic nuclear changes 0.001 0.12 -10000 0 -0.62 6 6
response to UV 0 0 -10000 0 -10000 0 0
CRADD -0.005 0.062 -10000 0 -0.86 1 1
GSN 0 0.12 -10000 0 -0.63 6 6
MADD 0 0 -10000 0 -10000 0 0
TFAP2A 0.012 0.17 -10000 0 -0.64 10 10
BID -0.009 0.054 -10000 0 -0.3 6 6
MAP3K1 0.005 0.038 -10000 0 -0.25 1 1
TRADD -0.005 0.062 -10000 0 -0.86 1 1
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB 0 0.12 -10000 0 -0.63 6 6
CASP9 0 0 -10000 0 -10000 0 0
DNA repair -0.001 0.033 0.18 1 -0.22 1 2
neuron apoptosis 0.007 0.079 -10000 0 -0.75 2 2
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis 0.002 0.12 -10000 0 -0.59 7 7
APAF1 0 0 -10000 0 -10000 0 0
CASP6 0.014 0.059 -10000 0 -0.37 2 2
TRAF2 0 0 -10000 0 -10000 0 0
ICAD/CAD 0.004 0.12 -10000 0 -0.59 7 7
CASP7 -0.011 0.036 0.33 1 -10000 0 1
KRT18 0.01 0.017 -10000 0 -10000 0 0
apoptosis 0.01 0.11 -10000 0 -0.54 6 6
DFFA 0 0.12 -10000 0 -0.63 6 6
DFFB -0.003 0.13 -10000 0 -0.61 7 7
PARP1 0.001 0.033 0.22 1 -0.18 1 2
actin filament polymerization -0.006 0.12 0.56 7 -10000 0 7
TNF -0.045 0.19 -10000 0 -0.86 10 10
CYCS 0.012 0.043 -10000 0 -0.22 6 6
SATB1 -0.019 0.15 -10000 0 -0.48 16 16
SLK 0 0.12 -10000 0 -0.63 6 6
p15 BID/BAX -0.008 0.047 -10000 0 -0.36 1 1
CASP2 -0.014 0.067 -10000 0 -10000 0 0
JNK cascade -0.005 0.038 0.25 1 -10000 0 1
CASP3 -0.007 0.13 -10000 0 -0.67 6 6
LMNB2 0.025 0.058 -10000 0 -0.31 1 1
RIPK1 0 0 -10000 0 -10000 0 0
CASP4 -0.005 0.062 -10000 0 -0.86 1 1
Mammalian IAPs/DIABLO 0.004 0.053 -10000 0 -0.54 1 1
negative regulation of DNA binding 0.013 0.17 -10000 0 -0.64 10 10
stress fiber formation 0.001 0.12 -10000 0 -0.62 6 6
GZMB -0.022 0.14 -10000 0 -0.76 6 6
CASP1 -0.002 0.034 -10000 0 -0.47 1 1
LMNB1 0.022 0.057 -10000 0 -0.31 1 1
APP 0.007 0.081 -10000 0 -0.76 2 2
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0 0.001 -10000 0 -10000 0 0
VIM 0.005 0.1 -10000 0 -0.53 6 6
LMNA 0.022 0.058 -10000 0 -0.31 1 1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.016 0.073 -10000 0 -0.28 12 12
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 0 0.12 -10000 0 -0.63 6 6
APAF-1/Caspase 9 -0.004 0.022 -10000 0 -10000 0 0
nuclear fragmentation during apoptosis 0.005 0.091 -10000 0 -0.48 6 6
CFL2 0.005 0.12 -10000 0 -0.58 7 7
GAS2 -0.027 0.17 -10000 0 -0.55 16 16
positive regulation of apoptosis 0.025 0.058 -10000 0 -0.3 1 1
PRF1 -0.009 0.088 -10000 0 -0.86 2 2
Signaling events mediated by HDAC Class II

Figure S105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 -0.003 0.039 -10000 0 -0.54 1 1
HDAC3 0 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -10000 0 0
GATA1/HDAC4 0.004 0.029 -10000 0 -10000 0 0
GATA1/HDAC5 0.002 0.024 -10000 0 -10000 0 0
GATA2/HDAC5 -0.002 0.051 -10000 0 -0.67 1 1
HDAC5/BCL6/BCoR 0 0 -10000 0 -10000 0 0
HDAC9 -0.041 0.18 -10000 0 -0.86 9 9
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -10000 0 -10000 0 0
HDAC4/ANKRA2 -0.002 0.051 -10000 0 -0.67 1 1
HDAC5/YWHAB 0 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
GATA2 -0.003 0.067 0.34 1 -0.86 1 2
HDAC4/RFXANK 0.004 0.029 -10000 0 -10000 0 0
BCOR 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0 0 -10000 0 -10000 0 0
HDAC5 0 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.004 0.048 -10000 0 -0.67 1 1
Histones -0.01 0.064 -10000 0 -10000 0 0
ADRBK1 0 0 -10000 0 -10000 0 0
HDAC4 0.002 0.025 0.34 1 -10000 0 1
XPO1 0 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 -0.004 0.048 -10000 0 -0.67 1 1
HDAC4/Ubc9 0.001 0.017 -10000 0 -10000 0 0
HDAC7 0.002 0.025 0.34 1 -10000 0 1
HDAC5/14-3-3 E 0 0 -10000 0 -10000 0 0
TUBA1B 0 0 -10000 0 -10000 0 0
HDAC6 0 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.002 0.024 -10000 0 -10000 0 0
CAMK4 -0.1 0.28 0.34 1 -0.86 23 24
Tubulin/HDAC6 0 0 -10000 0 -10000 0 0
SUMO1 0 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
GATA1 0.004 0.035 0.34 2 -10000 0 2
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
NR3C1 0 0 -10000 0 -10000 0 0
SUMO1/HDAC4 0.001 0.015 -10000 0 -10000 0 0
SRF 0 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0.001 0.017 -10000 0 -10000 0 0
Tubulin 0 0 -10000 0 -10000 0 0
HDAC4/14-3-3 E 0.001 0.017 -10000 0 -10000 0 0
GNB1 0 0 -10000 0 -10000 0 0
RANGAP1 0 0 -10000 0 -10000 0 0
BCL6/BCoR 0 0 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.001 0.015 -10000 0 -10000 0 0
HDAC4/SRF -0.068 0.19 -10000 0 -0.58 23 23
HDAC4/ER alpha -0.34 0.34 -10000 0 -0.67 98 98
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.009 0.064 -10000 0 -10000 0 0
cell motility 0 0 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.001 0.017 -10000 0 -10000 0 0
BCL6 0 0 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.002 0.025 0.34 1 -10000 0 1
Hsp90/HDAC6 0 0 -10000 0 -10000 0 0
ESR1 -0.44 0.43 -10000 0 -0.86 98 98
HDAC6/HDAC11 0.005 0.033 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
MEF2C 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0.001 0.014 -10000 0 -10000 0 0
GNG2 -0.005 0.062 -10000 0 -0.86 1 1
NCOR2 0 0 -10000 0 -10000 0 0
TUBB2A 0 0 -10000 0 -10000 0 0
HDAC11 0.007 0.049 0.34 4 -10000 0 4
HSP90AA1 0 0 -10000 0 -10000 0 0
RANBP2 0 0 -10000 0 -10000 0 0
ANKRA2 -0.005 0.062 -10000 0 -0.86 1 1
RFXANK 0.004 0.035 0.34 2 -10000 0 2
nuclear import -0.001 0.011 -10000 0 -10000 0 0
BARD1 signaling events

Figure S106.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S106.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.016 0.058 -10000 0 -9999 0 0
ATM 0 0 -10000 0 -9999 0 0
UBE2D3 0 0 -10000 0 -9999 0 0
PRKDC 0 0 -10000 0 -9999 0 0
ATR 0 0 -10000 0 -9999 0 0
UBE2L3 0 0 -10000 0 -9999 0 0
FANCD2 0.04 0.067 -10000 0 -9999 0 0
protein ubiquitination 0.076 0.1 0.35 8 -9999 0 8
XRCC5 0 0 -10000 0 -9999 0 0
XRCC6 0 0 -10000 0 -9999 0 0
M/R/N Complex 0 0 -10000 0 -9999 0 0
MRE11A 0 0 -10000 0 -9999 0 0
DNA-PK 0 0 -10000 0 -9999 0 0
FA complex/FANCD2/Ubiquitin 0.026 0.051 -10000 0 -9999 0 0
FANCF 0 0 -10000 0 -9999 0 0
BRCA1 0 0 -10000 0 -9999 0 0
CCNE1 0.12 0.16 0.34 68 -9999 0 68
CDK2/Cyclin E1 0.083 0.11 -10000 0 -9999 0 0
FANCG 0.004 0.035 0.34 2 -9999 0 2
BRCA1/BACH1/BARD1 0.016 0.058 -10000 0 -9999 0 0
FANCE 0.012 0.064 0.34 7 -9999 0 7
FANCC 0 0 -10000 0 -9999 0 0
NBN 0 0 -10000 0 -9999 0 0
FANCA 0 0 -10000 0 -9999 0 0
DNA repair 0.092 0.049 -10000 0 -9999 0 0
BRCA1/BARD1/ubiquitin 0.016 0.058 -10000 0 -9999 0 0
BARD1/DNA-PK 0.014 0.052 -10000 0 -9999 0 0
FANCL 0 0 -10000 0 -9999 0 0
mRNA polyadenylation -0.016 0.058 -10000 0 -9999 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.008 0.031 -10000 0 -9999 0 0
BRCA1/BACH1/BARD1/TopBP1 0.014 0.054 -10000 0 -9999 0 0
BRCA1/BARD1/P53 0.014 0.052 -10000 0 -9999 0 0
BARD1/CSTF1/BRCA1 0.014 0.054 -10000 0 -9999 0 0
BRCA1/BACH1 0 0 -10000 0 -9999 0 0
BARD1 0.023 0.086 0.34 13 -9999 0 13
PCNA 0 0 -10000 0 -9999 0 0
BRCA1/BARD1/UbcH5C 0.014 0.054 -10000 0 -9999 0 0
BRCA1/BARD1/UbcH7 0.014 0.054 -10000 0 -9999 0 0
BRCA1/BARD1/RAD51/PCNA 0.074 0.12 0.4 9 -9999 0 9
BARD1/DNA-PK/P53 0.013 0.049 -10000 0 -9999 0 0
BRCA1/BARD1/Ubiquitin 0.016 0.058 -10000 0 -9999 0 0
BRCA1/BARD1/CTIP 0.015 0.055 -10000 0 -9999 0 0
FA complex 0.006 0.026 -10000 0 -9999 0 0
BARD1/EWS 0.016 0.058 -10000 0 -9999 0 0
RBBP8 0 0 -10000 0 -9999 0 0
TP53 0 0 -10000 0 -9999 0 0
TOPBP1 0 0 -10000 0 -9999 0 0
G1/S transition of mitotic cell cycle -0.014 0.05 -10000 0 -9999 0 0
BRCA1/BARD1 0.082 0.11 0.38 8 -9999 0 8
CSTF1 0 0 -10000 0 -9999 0 0
BARD1/EWS-Fli1 0.015 0.057 0.23 13 -9999 0 13
CDK2 0 0 -10000 0 -9999 0 0
UniProt:Q9BZD1 0 0 -10000 0 -9999 0 0
RAD51 0.1 0.16 0.34 56 -9999 0 56
RAD50 0 0 -10000 0 -9999 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.016 0.058 -10000 0 -9999 0 0
EWSR1 0 0 -10000 0 -9999 0 0
Regulation of p38-alpha and p38-beta

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0 0 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.009 0.14 0.34 5 -0.86 4 9
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.011 0.031 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
YES1 0 0 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0 0 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
MAP3K12 0 0 -10000 0 -10000 0 0
FGR -0.005 0.062 -10000 0 -0.86 1 1
p38 alpha/TAB1 -0.041 0.082 -10000 0 -0.36 7 7
PRKG1 -0.032 0.16 -10000 0 -0.86 7 7
DUSP8 -0.005 0.062 -10000 0 -0.86 1 1
PGK/cGMP/p38 alpha -0.054 0.11 -10000 0 -0.4 14 14
apoptosis -0.04 0.079 -10000 0 -0.34 7 7
RAL/GTP 0 0 -10000 0 -10000 0 0
LYN 0 0 -10000 0 -10000 0 0
DUSP1 -0.059 0.22 -10000 0 -0.86 13 13
PAK1 0 0 -10000 0 -10000 0 0
SRC 0.002 0.025 0.34 1 -10000 0 1
RAC1/OSM/MEKK3/MKK3 0 0 -10000 0 -10000 0 0
TRAF6 -0.005 0.062 -10000 0 -0.86 1 1
RAC1 0 0 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0 0 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0 0 -10000 0 -10000 0 0
MAPK11 -0.02 0.14 -10000 0 -0.46 8 8
BLK -0.18 0.36 0.34 2 -0.86 41 43
HCK -0.027 0.15 -10000 0 -0.86 6 6
MAP2K3 0 0 -10000 0 -10000 0 0
DUSP16 -0.005 0.062 -10000 0 -0.86 1 1
DUSP10 -0.014 0.11 -10000 0 -0.86 3 3
TRAF6/MEKK3 -0.003 0.04 -10000 0 -0.55 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.008 0.11 -10000 0 -0.39 7 7
positive regulation of innate immune response -0.018 0.15 -10000 0 -0.49 8 8
LCK -0.03 0.16 0.34 1 -0.86 7 8
p38alpha-beta/MKP7 -0.063 0.12 -10000 0 -0.46 9 9
p38alpha-beta/MKP5 -0.067 0.13 -10000 0 -0.48 11 11
PGK/cGMP -0.025 0.13 -10000 0 -0.68 7 7
PAK2 0 0 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.088 0.16 -10000 0 -0.49 20 20
CDC42 0 0 -10000 0 -10000 0 0
RALB 0 0 -10000 0 -10000 0 0
RALA 0 0 -10000 0 -10000 0 0
PAK3 0.039 0.11 0.34 22 -10000 0 22
Visual signal transduction: Cones

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin -0.003 0.071 -10000 0 -0.52 3 3
RGS9BP 0.016 0.072 0.34 9 -10000 0 9
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0 0 -10000 0 -10000 0 0
mol:Na + 0.021 0.065 0.41 1 -10000 0 1
mol:ADP 0 0 -10000 0 -10000 0 0
GNAT2 0.002 0.025 0.34 1 -10000 0 1
RGS9-1/Gbeta5/R9AP 0 0.13 0.42 2 -0.58 7 9
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.001 0.015 -10000 0 -10000 0 0
GRK7 0 0 -10000 0 -10000 0 0
CNGB3 0.034 0.1 0.34 19 -10000 0 19
Cone Metarhodopsin II/X-Arrestin 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.008 0.023 -10000 0 -10000 0 0
Cone PDE6 0.006 0.12 0.37 3 -0.5 7 10
Cone Metarhodopsin II 0 0 -10000 0 -10000 0 0
Na + (4 Units) 0.02 0.061 0.38 1 -10000 0 1
GNAT2/GDP 0.001 0.12 0.37 2 -0.51 7 9
GNB5 0.002 0.025 0.34 1 -10000 0 1
mol:GMP (4 units) 0.006 0.034 -10000 0 -10000 0 0
Cone Transducin -0.003 0.075 -10000 0 -0.54 3 3
SLC24A2 0 0 -10000 0 -10000 0 0
GNB3/GNGT2 -0.006 0.09 -10000 0 -0.67 3 3
GNB3 0.007 0.049 0.34 4 -10000 0 4
GNAT2/GTP 0.001 0.016 0.23 1 -10000 0 1
CNGA3 0.002 0.025 0.34 1 -10000 0 1
ARR3 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.021 0.066 0.41 1 -10000 0 1
mol:Pi 0 0.13 0.41 2 -0.58 7 9
Cone CNG Channel 0.022 0.057 0.32 1 -10000 0 1
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0 0 -10000 0 -10000 0 0
RGS9 -0.016 0.18 0.34 9 -0.86 7 16
PDE6C 0.011 0.059 0.34 6 -10000 0 6
GNGT2 -0.014 0.11 -10000 0 -0.86 3 3
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0 0 -10000 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0 0 -10000 0 -10000 0 0
ITGB7 -0.009 0.088 -10000 0 -0.86 2 2
ITGA4 -0.012 0.11 0.34 1 -0.86 3 4
alpha4/beta7 Integrin -0.016 0.11 -10000 0 -0.67 5 5
alpha4/beta1 Integrin -0.009 0.085 -10000 0 -0.67 3 3
Arf6 downstream pathway

Figure S110.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S110.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR -0.003 0.1 -10000 0 -1.3 1 1
regulation of axonogenesis 0.012 0.066 0.34 7 -10000 0 7
myoblast fusion 0.001 0.039 0.43 1 -10000 0 1
mol:GTP 0 0.022 -10000 0 -0.24 1 1
regulation of calcium-dependent cell-cell adhesion 0.017 0.11 0.56 7 -10000 0 7
ARF1/GTP 0 0.018 -10000 0 -10000 0 0
mol:GM1 0 0.018 -10000 0 -10000 0 0
mol:Choline -0.02 0.11 -10000 0 -0.56 7 7
lamellipodium assembly 0.004 0.048 -10000 0 -0.46 1 1
MAPK3 0.021 0.036 -10000 0 -0.35 1 1
ARF6/GTP/NME1/Tiam1 -0.017 0.11 -10000 0 -0.56 7 7
ARF1 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.001 0.039 -10000 0 -0.43 1 1
ARF1/GDP 0.001 0.035 -10000 0 -0.39 1 1
ARF6 0 0.012 -10000 0 -10000 0 0
RAB11A 0 0 -10000 0 -10000 0 0
TIAM1 -0.031 0.16 -10000 0 -0.86 7 7
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.021 0.036 -10000 0 -0.35 1 1
actin filament bundle formation 0.003 0.03 0.39 1 -10000 0 1
KALRN -0.001 0.049 -10000 0 -0.43 2 2
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.003 0.03 -10000 0 -0.39 1 1
NME1 0.004 0.035 0.34 2 -10000 0 2
Rac1/GDP -0.003 0.03 -10000 0 -0.39 1 1
substrate adhesion-dependent cell spreading 0 0.022 -10000 0 -0.24 1 1
cortical actin cytoskeleton organization 0.004 0.048 -10000 0 -0.47 1 1
RAC1 0 0 -10000 0 -10000 0 0
liver development 0 0.022 -10000 0 -0.24 1 1
ARF6/GTP 0 0.023 -10000 0 -0.24 1 1
RhoA/GTP 0 0.017 -10000 0 -10000 0 0
mol:GDP 0.004 0.046 -10000 0 -0.43 1 1
ARF6/GTP/RAB11FIP3/RAB11A 0.001 0.016 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
PLD1 -0.023 0.12 -10000 0 -0.63 7 7
RAB11FIP3 0 0 -10000 0 -10000 0 0
tube morphogenesis 0.004 0.048 -10000 0 -0.46 1 1
ruffle organization -0.012 0.066 -10000 0 -0.34 7 7
regulation of epithelial cell migration 0 0.022 -10000 0 -0.24 1 1
PLD2 0.001 0.018 -10000 0 -10000 0 0
PIP5K1A -0.012 0.066 -10000 0 -0.34 7 7
mol:Phosphatidic acid -0.02 0.11 -10000 0 -0.56 7 7
Rac1/GTP 0.004 0.048 -10000 0 -0.47 1 1
IFN-gamma pathway

Figure S111.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S111.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.007 0.055 -10000 0 -0.47 1 1
positive regulation of NF-kappaB transcription factor activity 0 0.001 -10000 0 -10000 0 0
CRKL 0 0 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.002 0.028 -10000 0 -10000 0 0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.001 0.043 -10000 0 -0.58 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.053 0.068 -10000 0 -0.46 2 2
CaM/Ca2+ 0.006 0.049 -10000 0 -0.44 1 1
RAP1A 0 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 0.003 0.038 -10000 0 -0.44 1 1
AKT1 -0.002 0.079 -10000 0 -1.1 1 1
MAP2K1 0.044 0.035 -10000 0 -0.41 1 1
MAP3K11 0.002 0.037 -10000 0 -0.44 1 1
IFNGR1 0 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.17 0.2 -10000 0 -0.46 5 5
Rap1/GTP -0.002 0.024 -10000 0 -10000 0 0
CRKL/C3G 0 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.007 0.056 -10000 0 -0.49 1 1
CEBPB 0.059 0.058 -10000 0 -10000 0 0
STAT3 0 0 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.006 0.14 -10000 0 -1.3 2 2
STAT1 0.003 0.038 -10000 0 -0.44 1 1
CALM1 0 0 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.017 0.074 0.35 9 -10000 0 9
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
STAT1 (dimer)/PIAS1 0.002 0.035 -10000 0 -0.41 1 1
CEBPB/PTGES2/Cbp/p300 -0.004 0.03 -10000 0 -10000 0 0
mol:Ca2+ 0.007 0.053 -10000 0 -0.46 1 1
MAPK3 0.047 0.038 -10000 0 -10000 0 0
STAT1 (dimer) -0.07 0.1 -10000 0 -0.77 2 2
MAPK1 0.047 0.038 -10000 0 -10000 0 0
JAK2 -0.005 0.062 -10000 0 -0.86 1 1
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
JAK1 0 0.002 -10000 0 -10000 0 0
CAMK2D 0 0 -10000 0 -10000 0 0
DAPK1 0.052 0.077 -10000 0 -0.66 2 2
SMAD7 -0.001 0.068 -10000 0 -0.4 2 2
CBL/CRKL/C3G -0.002 0.029 -10000 0 -10000 0 0
PI3K 0 0.098 -10000 0 -1.3 1 1
IFNG 0.017 0.074 0.35 9 -10000 0 9
apoptosis 0.032 0.056 -10000 0 -0.46 2 2
CAMK2G 0 0 -10000 0 -10000 0 0
STAT3 (dimer) 0 0 -10000 0 -10000 0 0
CAMK2A 0.027 0.092 0.34 15 -10000 0 15
CAMK2B -0.42 0.43 -10000 0 -0.86 92 92
FRAP1 0 0.069 -10000 0 -0.92 1 1
PRKCD -0.002 0.082 -10000 0 -1.1 1 1
RAP1B 0 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.053 0.068 -10000 0 -0.46 2 2
PTPN2 0 0 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
IRF1 0.061 0.045 -10000 0 -10000 0 0
STAT1 (dimer)/PIASy 0.003 0.039 -10000 0 -0.42 1 1
SOCS1 -0.014 0.16 -10000 0 -1.5 2 2
mol:GDP -0.002 0.027 -10000 0 -10000 0 0
CASP1 0.001 0.057 -10000 0 -0.24 1 1
PTGES2 0.002 0.025 0.34 1 -10000 0 1
IRF9 0.027 0.029 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.001 0.087 -10000 0 -1.2 1 1
RAP1/GDP -0.002 0.024 -10000 0 -10000 0 0
CBL 0.002 0.037 -10000 0 -0.44 1 1
MAP3K1 0.002 0.037 -10000 0 -0.44 1 1
PIAS1 0 0 -10000 0 -10000 0 0
PIAS4 0 0 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.053 0.068 -10000 0 -0.46 2 2
PTPN11 0.001 0.037 -10000 0 -0.46 1 1
CREBBP 0 0 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

Figure S112.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S112.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -10000 0 -10000 0 0
CDKN1B 0.029 0.002 -10000 0 -10000 0 0
CDKN1A 0.021 0.064 -10000 0 -0.48 3 3
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0 0 -10000 0 -10000 0 0
FOXO3 0.029 0.002 -10000 0 -10000 0 0
AKT1 0 0.004 -10000 0 -10000 0 0
BAD 0 0 -10000 0 -10000 0 0
AKT3 0.001 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.029 0.002 -10000 0 -10000 0 0
AKT1/ASK1 -0.032 0.12 -10000 0 -0.47 13 13
BAD/YWHAZ 0 0 -10000 0 -10000 0 0
RICTOR 0 0 -10000 0 -10000 0 0
RAF1 0 0 -10000 0 -10000 0 0
JNK cascade 0.031 0.11 0.45 13 -10000 0 13
TSC1 0.029 0.002 -10000 0 -10000 0 0
YWHAZ 0 0 -10000 0 -10000 0 0
AKT1/RAF1 0 0 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
mol:GDP 0 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.023 0.052 -10000 0 -0.48 2 2
YWHAQ 0 0 -10000 0 -10000 0 0
TBC1D4 -0.006 0.059 -10000 0 -0.58 2 2
MAP3K5 -0.059 0.22 -10000 0 -0.86 13 13
MAPKAP1 0 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.06 0.027 -10000 0 -10000 0 0
YWHAH 0 0 -10000 0 -10000 0 0
AKT1S1 0.029 0.002 -10000 0 -10000 0 0
CASP9 0.029 0.002 -10000 0 -10000 0 0
YWHAB 0 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0 0 -10000 0 -10000 0 0
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.001 0.015 -10000 0 -10000 0 0
YWHAE 0 0 -10000 0 -10000 0 0
SRC 0.002 0.025 0.34 1 -10000 0 1
AKT2/p21CIP1 -0.007 0.058 -10000 0 -0.47 3 3
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.013 0.001 -10000 0 -10000 0 0
CHUK 0.029 0.002 -10000 0 -10000 0 0
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
mTORC2 0 0 -10000 0 -10000 0 0
AKT2 0 0 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.075 0.032 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
MDM2 0.029 0.002 -10000 0 -10000 0 0
MAPKKK cascade 0 0 -10000 0 -10000 0 0
MDM2/Cbp/p300 0 0 -10000 0 -10000 0 0
TSC1/TSC2 0.029 0.051 -10000 0 -0.46 2 2
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -10000 0 0
glucose import 0.012 0.089 -10000 0 -0.53 5 5
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.024 0.002 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.012 0.086 -10000 0 -0.53 5 5
GSK3A 0.029 0.002 -10000 0 -10000 0 0
FOXO1 0.023 0.052 -10000 0 -0.48 2 2
GSK3B 0.029 0.002 -10000 0 -10000 0 0
SFN 0.19 0.17 0.34 108 -10000 0 108
G1/S transition of mitotic cell cycle 0.034 0.002 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.059 0.051 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
KPNA1 0 0 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
YWHAG 0 0 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
CREBBP 0 0 -10000 0 -10000 0 0
TRAIL signaling pathway

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.014 0.11 -10000 0 -0.86 3 3
positive regulation of NF-kappaB transcription factor activity -0.014 0.096 -10000 0 -0.67 4 4
MAP2K4 -0.009 0.053 -10000 0 -0.36 1 1
IKBKB 0 0 -10000 0 -10000 0 0
TNFRSF10B 0 0 -10000 0 -10000 0 0
TNFRSF10A -0.018 0.12 -10000 0 -0.86 4 4
SMPD1 -0.005 0.038 -10000 0 -0.31 3 3
IKBKG 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.005 0.062 -10000 0 -0.86 1 1
TRAIL/TRAILR2 -0.011 0.083 -10000 0 -0.67 3 3
TRAIL/TRAILR3 -0.006 0.09 -10000 0 -0.67 3 3
TRAIL/TRAILR1 -0.025 0.13 -10000 0 -0.67 7 7
TRAIL/TRAILR4 -0.014 0.096 -10000 0 -0.67 4 4
TRAIL/TRAILR1/DAP3/GTP -0.02 0.1 -10000 0 -0.54 7 7
IKK complex -0.007 0.036 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 -0.011 0.083 -10000 0 -0.67 3 3
MAP3K1 -0.01 0.056 -10000 0 -0.36 4 4
TRAILR4 (trimer) -0.005 0.062 -10000 0 -0.86 1 1
TRADD -0.005 0.062 -10000 0 -0.86 1 1
TRAILR1 (trimer) -0.018 0.12 -10000 0 -0.86 4 4
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.014 0.071 -10000 0 -0.35 8 8
CFLAR 0 0 -10000 0 -10000 0 0
MAPK1 -0.011 0.083 -10000 0 -0.67 3 3
TRAIL/TRAILR1/FADD/TRADD/RIP -0.02 0.1 -10000 0 -0.5 8 8
mol:ceramide -0.005 0.038 -10000 0 -0.31 3 3
FADD 0.002 0.025 0.34 1 -10000 0 1
MAPK8 0.007 0.13 -10000 0 -0.54 9 9
TRAF2 0 0 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.007 0.049 0.34 4 -10000 0 4
CHUK 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.02 0.11 -10000 0 -0.58 7 7
DAP3 0 0 -10000 0 -10000 0 0
CASP10 -0.013 0.083 0.31 1 -0.56 3 4
JNK cascade -0.014 0.096 -10000 0 -0.67 4 4
TRAIL (trimer) -0.014 0.11 -10000 0 -0.86 3 3
TNFRSF10C 0.007 0.049 0.34 4 -10000 0 4
TRAIL/TRAILR1/DAP3/GTP/FADD -0.018 0.097 -10000 0 -0.51 7 7
TRAIL/TRAILR2/FADD -0.008 0.074 -10000 0 -0.58 3 3
cell death -0.005 0.038 -10000 0 -0.3 3 3
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.007 0.051 -10000 0 -0.35 4 4
TRAILR2 (trimer) 0 0 -10000 0 -10000 0 0
CASP8 0.001 0.021 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.009 0.073 -10000 0 -0.5 4 4
Signaling mediated by p38-gamma and p38-delta

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.028 0.083 -10000 0 -0.58 3 3
SNTA1 0.002 0.025 0.34 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 0.034 0.087 -10000 0 -0.58 3 3
MAPK12 0.001 0.08 -10000 0 -0.51 4 4
CCND1 -0.023 0.12 -10000 0 -0.5 10 10
p38 gamma/SNTA1 0.002 0.076 -10000 0 -0.48 4 4
MAP2K3 0 0 -10000 0 -10000 0 0
PKN1 0.002 0.025 0.34 1 -10000 0 1
G2/M transition checkpoint 0.022 0.08 -10000 0 -0.51 4 4
MAP2K6 -0.009 0.085 -10000 0 -0.58 4 4
MAPT 0.058 0.07 -10000 0 -0.3 3 3
MAPK13 0.015 0.11 -10000 0 -0.67 3 3
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.001 0.011 -10000 0 -10000 0 0
Paxillin-dependent events mediated by a4b1

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -10000 0 -10000 0 0
Rac1/GDP 0.001 0.008 -10000 0 -10000 0 0
DOCK1 -0.018 0.12 -10000 0 -0.86 4 4
ITGA4 -0.012 0.11 0.34 1 -0.86 3 4
RAC1 0 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.016 0.11 -10000 0 -0.67 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.008 0.074 -10000 0 -0.58 3 3
alpha4/beta7 Integrin/Paxillin -0.013 0.087 -10000 0 -0.54 5 5
lamellipodium assembly -0.01 0.078 -10000 0 -0.51 4 4
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
PI3K -0.006 0.087 -10000 0 -1.2 1 1
ARF6 0 0 -10000 0 -10000 0 0
TLN1 0 0 -10000 0 -10000 0 0
PXN 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
ARF6/GTP -0.006 0.058 -10000 0 -0.46 3 3
cell adhesion -0.007 0.064 -10000 0 -0.5 3 3
CRKL/CBL 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin -0.007 0.069 -10000 0 -0.54 3 3
ITGB1 0 0 -10000 0 -10000 0 0
ITGB7 -0.009 0.088 -10000 0 -0.86 2 2
ARF6/GDP 0.001 0.008 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.042 0.16 -10000 0 -0.57 15 15
p130Cas/Crk/Dock1 -0.012 0.084 -10000 0 -0.58 4 4
VCAM1 -0.062 0.23 0.34 1 -0.86 14 15
alpha4/beta1 Integrin/Paxillin/Talin -0.007 0.064 -10000 0 -0.5 3 3
alpha4/beta1 Integrin/Paxillin/GIT1 -0.007 0.064 -10000 0 -0.5 3 3
BCAR1 0 0 -10000 0 -10000 0 0
mol:GDP 0.007 0.064 0.5 3 -10000 0 3
CBL 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
GIT1 0 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.007 0.064 -10000 0 -0.5 3 3
Rac1/GTP -0.012 0.093 -10000 0 -0.6 4 4
Class I PI3K signaling events

Figure S116.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S116.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP 0.004 0.031 -10000 0 -10000 0 0
DAPP1 -0.047 0.17 -10000 0 -0.63 8 8
Src family/SYK family/BLNK-LAT/BTK-ITK -0.056 0.21 0.34 1 -0.69 11 12
mol:DAG 0.001 0.094 0.27 1 -0.31 5 6
HRAS 0.004 0.035 0.34 2 -10000 0 2
RAP1A 0 0 -10000 0 -10000 0 0
ARF5/GDP -0.014 0.05 -10000 0 -10000 0 0
PLCG2 -0.018 0.12 -10000 0 -0.86 4 4
PLCG1 0 0 -10000 0 -10000 0 0
ARF5 0 0 -10000 0 -10000 0 0
mol:GTP 0.003 0.027 -10000 0 -10000 0 0
ARF1/GTP 0.004 0.03 -10000 0 -10000 0 0
RHOA 0 0 -10000 0 -10000 0 0
YES1 0 0 -10000 0 -10000 0 0
RAP1A/GTP 0.003 0.025 -10000 0 -10000 0 0
ADAP1 -0.009 0.089 -10000 0 -0.47 6 6
ARAP3 0.003 0.027 -10000 0 -10000 0 0
INPPL1 0 0 -10000 0 -10000 0 0
PREX1 0 0 -10000 0 -10000 0 0
ARHGEF6 0 0 -10000 0 -10000 0 0
ARHGEF7 0 0 -10000 0 -10000 0 0
ARF1 0 0 -10000 0 -10000 0 0
NRAS 0 0 -10000 0 -10000 0 0
FYN 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
FGR -0.005 0.062 -10000 0 -0.86 1 1
mol:Ca2+ 0.008 0.053 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 -0.032 0.16 -10000 0 -0.86 7 7
ZAP70 -0.004 0.098 0.34 3 -0.86 2 5
mol:IP3 0.006 0.072 0.23 1 -0.3 1 2
LYN 0 0 -10000 0 -10000 0 0
ARF1/GDP -0.014 0.05 -10000 0 -10000 0 0
RhoA/GDP -0.002 0.033 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.001 0.015 -10000 0 -10000 0 0
BLNK -0.027 0.15 -10000 0 -0.86 6 6
actin cytoskeleton reorganization 0.04 0.058 -10000 0 -10000 0 0
SRC 0.002 0.025 0.34 1 -10000 0 1
PLEKHA2 0.021 0.044 -10000 0 -0.59 1 1
RAC1 0 0 -10000 0 -10000 0 0
PTEN -0.009 0.086 -10000 0 -0.84 2 2
HSP90AA1 0 0 -10000 0 -10000 0 0
ARF6/GTP 0.003 0.03 -10000 0 -10000 0 0
RhoA/GTP 0.003 0.025 -10000 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.079 0.15 0.3 1 -0.57 8 9
BLK -0.18 0.36 0.34 2 -0.86 41 43
PDPK1 0 0 -10000 0 -10000 0 0
CYTH1 0.003 0.027 -10000 0 -10000 0 0
HCK -0.027 0.15 -10000 0 -0.86 6 6
CYTH3 0.004 0.028 -10000 0 -10000 0 0
CYTH2 0.003 0.027 -10000 0 -10000 0 0
KRAS 0 0 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.018 0.11 -10000 0 -0.57 7 7
SGK1 -0.02 0.12 -10000 0 -0.63 7 7
INPP5D 0 0 -10000 0 -10000 0 0
mol:GDP 0.014 0.063 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
SYK 0 0 -10000 0 -10000 0 0
ARF6/GDP -0.002 0.034 0.28 2 -10000 0 2
mol:PI-3-4-5-P3 0.005 0.038 0.37 2 -10000 0 2
ARAP3/RAP1A/GTP 0.003 0.025 -10000 0 -10000 0 0
VAV1 -0.032 0.16 -10000 0 -0.86 7 7
mol:PI-3-4-P2 0 0 -10000 0 -10000 0 0
RAS family/GTP/PI3K Class I 0.002 0.021 -10000 0 -10000 0 0
PLEKHA1 0.024 0 -10000 0 -10000 0 0
Rac1/GDP -0.014 0.05 -10000 0 -10000 0 0
LAT 0.002 0.025 0.34 1 -10000 0 1
Rac1/GTP -0.022 0.082 -10000 0 -0.36 7 7
ITK -0.023 0.11 -10000 0 -0.47 11 11
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.007 0.13 0.3 1 -0.46 5 6
LCK -0.03 0.16 0.34 1 -0.86 7 8
BTK -0.004 0.065 -10000 0 -0.47 3 3
PDGFR-beta signaling pathway

Figure S117.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S117.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.013 0.11 0.33 2 -0.54 2 4
PDGFB-D/PDGFRB/SLAP -0.014 0.11 -10000 0 -0.68 5 5
PDGFB-D/PDGFRB/APS/CBL 0.006 0.04 0.42 1 -10000 0 1
AKT1 -0.014 0.082 -10000 0 -0.73 1 1
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.015 0.11 0.33 2 -0.55 2 4
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
FGR -0.007 0.053 -10000 0 -0.66 1 1
mol:Ca2+ 0.01 0.05 -10000 0 -10000 0 0
MYC -0.05 0.27 -10000 0 -0.88 18 18
SHC1 0 0 -10000 0 -10000 0 0
HRAS/GDP -0.002 0.051 -10000 0 -0.46 2 2
LRP1/PDGFRB/PDGFB 0.001 0.052 -10000 0 -0.58 1 1
GRB10 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
GO:0007205 0.01 0.051 -10000 0 -10000 0 0
PTEN -0.009 0.088 -10000 0 -0.86 2 2
GRB2 0 0 -10000 0 -10000 0 0
GRB7 -0.002 0.1 0.34 4 -0.86 2 6
PDGFB-D/PDGFRB/SHP2 0.004 0.029 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.004 0.029 -10000 0 -10000 0 0
cell cycle arrest -0.014 0.11 -10000 0 -0.68 5 5
HRAS 0.004 0.035 0.34 2 -10000 0 2
HIF1A 0.035 0.081 -10000 0 -0.61 1 1
GAB1 -0.001 0.086 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 0.005 0.085 -10000 0 -0.33 2 2
PDGFB-D/PDGFRB 0.008 0.028 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.004 0.029 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.005 0.12 0.38 2 -0.61 2 4
positive regulation of MAPKKK cascade 0.004 0.029 -10000 0 -10000 0 0
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
mol:IP3 0.01 0.051 -10000 0 -10000 0 0
E5 0 0.001 -10000 0 -10000 0 0
CSK 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0 0.079 -10000 0 -0.66 2 2
SHB 0 0 -10000 0 -10000 0 0
BLK -0.14 0.27 -10000 0 -0.65 41 41
PTPN2 0 0.001 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.004 0.029 -10000 0 -10000 0 0
BCAR1 0 0 -10000 0 -10000 0 0
VAV2 -0.005 0.11 -10000 0 -0.42 1 1
CBL 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.004 0.029 -10000 0 -10000 0 0
LCK -0.027 0.14 -10000 0 -0.72 7 7
PDGFRB 0.007 0.043 0.34 3 -10000 0 3
ACP1 0 0 -10000 0 -10000 0 0
HCK -0.018 0.11 -10000 0 -0.62 6 6
ABL1 -0.003 0.075 -10000 0 -0.32 1 1
PDGFB-D/PDGFRB/CBL -0.004 0.086 -10000 0 -10000 0 0
PTPN1 0 0.001 -10000 0 -10000 0 0
SNX15 0 0 -10000 0 -10000 0 0
STAT3 0 0 -10000 0 -10000 0 0
STAT1 0 0 -10000 0 -10000 0 0
cell proliferation -0.04 0.24 -10000 0 -0.76 18 18
SLA -0.023 0.14 -10000 0 -0.86 5 5
actin cytoskeleton reorganization 0.004 0.03 -10000 0 -10000 0 0
SRC -0.001 0.026 -10000 0 -10000 0 0
PI3K -0.016 0.093 -10000 0 -0.55 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.001 0.069 -10000 0 -0.57 2 2
SH2B2 0.004 0.035 0.34 2 -10000 0 2
PLCgamma1/SPHK1 0.015 0.11 0.34 2 -0.56 2 4
LYN -0.002 0.023 -10000 0 -10000 0 0
LRP1 -0.005 0.062 -10000 0 -0.86 1 1
SOS1 0 0 -10000 0 -10000 0 0
STAT5B 0 0 -10000 0 -10000 0 0
STAT5A 0.002 0.025 0.34 1 -10000 0 1
NCK1-2/p130 Cas 0.004 0.03 0.34 1 -10000 0 1
SPHK1 0.043 0.15 0.34 29 -0.87 2 31
EDG1 0.001 0.003 -10000 0 -10000 0 0
mol:DAG 0.01 0.051 -10000 0 -10000 0 0
PLCG1 0.01 0.052 -10000 0 -10000 0 0
NHERF/PDGFRB -0.006 0.078 -10000 0 -0.59 3 3
YES1 -0.002 0.023 -10000 0 -10000 0 0
cell migration -0.006 0.078 -10000 0 -0.58 3 3
SHC/Grb2/SOS1 0.003 0.022 -10000 0 -10000 0 0
SLC9A3R2 -0.009 0.088 -10000 0 -0.86 2 2
SLC9A3R1 -0.005 0.062 -10000 0 -0.86 1 1
NHERF1-2/PDGFRB/PTEN -0.011 0.09 -10000 0 -0.54 5 5
FYN -0.001 0.023 -10000 0 -10000 0 0
DOK1 0.002 0.012 -10000 0 -10000 0 0
HRAS/GTP 0.002 0.023 0.23 2 -10000 0 2
PDGFB 0.002 0.025 0.34 1 -10000 0 1
RAC1 -0.015 0.16 -10000 0 -0.47 18 18
PRKCD 0.003 0.013 -10000 0 -10000 0 0
FER 0.003 0.013 -10000 0 -10000 0 0
MAPKKK cascade 0.002 0.016 -10000 0 -10000 0 0
RASA1 -0.003 0.057 -10000 0 -0.54 2 2
NCK1 0 0 -10000 0 -10000 0 0
NCK2 0.002 0.025 0.34 1 -10000 0 1
p62DOK/Csk 0.004 0.013 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SHB 0.004 0.029 -10000 0 -10000 0 0
chemotaxis -0.002 0.074 -10000 0 -0.31 1 1
STAT1-3-5/STAT1-3-5 0.002 0.017 -10000 0 -10000 0 0
Bovine Papilomavirus E5/PDGFRB 0.005 0.028 0.23 3 -10000 0 3
PTPRJ 0 0 -10000 0 -10000 0 0
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

Figure S118.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S118.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 -0.005 0.062 -10000 0 -0.86 1 1
SMAD2 0.011 0 -10000 0 -10000 0 0
SMAD3 0.032 0 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.001 0.026 -10000 0 -0.32 1 1
SMAD4/Ubc9/PIASy -0.003 0.042 -10000 0 -0.58 1 1
SMAD2/SMAD2/SMAD4 -0.001 0.036 -10000 0 -0.46 1 1
PPM1A 0 0 -10000 0 -10000 0 0
CALM1 0 0 -10000 0 -10000 0 0
SMAD2/SMAD4 -0.003 0.038 -10000 0 -0.53 1 1
MAP3K1 0 0 -10000 0 -10000 0 0
TRAP-1/SMAD4 -0.046 0.17 -10000 0 -0.67 13 13
MAPK3 0 0 -10000 0 -10000 0 0
MAPK1 0 0 -10000 0 -10000 0 0
NUP214 0 0 -10000 0 -10000 0 0
CTDSP1 0 0 -10000 0 -10000 0 0
CTDSP2 0 0 -10000 0 -10000 0 0
CTDSPL 0 0 -10000 0 -10000 0 0
KPNB1 0 0 -10000 0 -10000 0 0
TGFBRAP1 -0.054 0.21 -10000 0 -0.86 12 12
UBE2I 0 0 -10000 0 -10000 0 0
NUP153 0 0 -10000 0 -10000 0 0
KPNA2 0.002 0.025 0.34 1 -10000 0 1
PIAS4 0 0 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

Figure S119.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S119.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.059 0.029 -9999 0 -10000 0 0
ERC1 0 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.014 0.096 -9999 0 -0.67 4 4
NFKBIA 0 0 -9999 0 -10000 0 0
BIRC2 0 0 -9999 0 -10000 0 0
IKBKB 0 0 -9999 0 -10000 0 0
RIPK2 0 0 -9999 0 -10000 0 0
IKBKG -0.007 0.042 -9999 0 -10000 0 0
IKK complex/A20 -0.028 0.11 -9999 0 -0.46 10 10
NEMO/A20/RIP2 0 0 -9999 0 -10000 0 0
XPO1 0 0 -9999 0 -10000 0 0
NEMO/ATM -0.006 0.039 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.005 0.034 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.003 0.042 -9999 0 -0.58 1 1
NOD2 -0.018 0.12 -9999 0 -0.86 4 4
NFKB1 0 0 -9999 0 -10000 0 0
RELA 0 0 -9999 0 -10000 0 0
MALT1 0 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
TNF/TNFR1A -0.035 0.15 -9999 0 -0.67 10 10
TRAF6 -0.005 0.062 -9999 0 -0.86 1 1
PRKCA 0 0 -9999 0 -10000 0 0
CHUK 0 0 -9999 0 -10000 0 0
UBE2D3 0 0 -9999 0 -10000 0 0
TNF -0.045 0.19 -9999 0 -0.86 10 10
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.037 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -9999 0 -10000 0 0
TNFRSF1A 0 0 -9999 0 -10000 0 0
IKK complex -0.006 0.037 -9999 0 -10000 0 0
CYLD 0 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.006 0.035 -9999 0 -10000 0 0
mTOR signaling pathway

Figure S120.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S120.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0 0 -10000 0 -10000 0 0
mol:PIP3 -0.001 0.075 0.33 2 -0.92 1 3
FRAP1 0.013 0.031 0.23 2 -10000 0 2
AKT1 -0.003 0.067 -10000 0 -0.83 1 1
INSR 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.004 0.03 -10000 0 -10000 0 0
mol:GTP -0.008 0.06 -10000 0 -0.46 3 3
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.002 0.016 -10000 0 -10000 0 0
TSC2 -0.009 0.088 -10000 0 -0.86 2 2
RHEB/GDP -0.007 0.055 -10000 0 -0.41 3 3
TSC1 0 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0 0 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.002 0.019 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0 0 -10000 0 -10000 0 0
RPS6KB1 0.022 0.042 -10000 0 -0.43 1 1
MAP3K5 -0.024 0.12 -10000 0 -0.46 13 13
PIK3R1 -0.005 0.063 -10000 0 -0.87 1 1
apoptosis -0.024 0.12 -10000 0 -0.46 13 13
mol:LY294002 0 0 0.001 1 -10000 0 1
EIF4B 0.027 0.038 -10000 0 -0.37 1 1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.002 0.026 -10000 0 -0.34 1 1
eIF4E/eIF4G1/eIF4A1 -0.001 0.01 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.005 0.07 -10000 0 -0.98 1 1
mTOR/RHEB/GTP/Raptor/GBL 0.023 0.033 -10000 0 -0.31 1 1
FKBP1A 0 0 -10000 0 -10000 0 0
RHEB/GTP -0.007 0.054 -10000 0 -0.4 3 3
mol:Amino Acids 0 0 0.001 1 -10000 0 1
FKBP12/Rapamycin 0 0.002 -10000 0 -10000 0 0
PDPK1 -0.002 0.067 -10000 0 -0.85 1 1
EIF4E 0 0 -10000 0 -10000 0 0
ASK1/PP5C -0.04 0.16 -10000 0 -0.63 13 13
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0 0.002 -10000 0 -10000 0 0
TSC1/TSC2 -0.009 0.067 -10000 0 -0.5 3 3
tumor necrosis factor receptor activity 0 0 -10000 0 -0.001 1 1
RPS6 0 0 -10000 0 -10000 0 0
PPP5C 0 0 -10000 0 -10000 0 0
EIF4G1 0 0 -10000 0 -10000 0 0
IRS1 0.006 0.002 -10000 0 -10000 0 0
INS 0.007 0.049 0.34 4 -10000 0 4
PTEN -0.009 0.088 -10000 0 -0.86 2 2
PDK2 -0.004 0.075 -10000 0 -0.66 2 2
EIF4EBP1 0.008 0.024 0.33 1 -10000 0 1
PIK3CA -0.005 0.063 -10000 0 -0.87 1 1
PPP2R5D 0.019 0.03 -10000 0 -10000 0 0
peptide biosynthetic process 0.002 0.012 -10000 0 -10000 0 0
RHEB 0 0 -10000 0 -10000 0 0
EIF4A1 0 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 2 -0.004 1 3
EEF2 0.002 0.012 -10000 0 -10000 0 0
eIF4E/4E-BP1 0 0 -10000 0 -10000 0 0
ceramide signaling pathway

Figure S121.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S121.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.024 0.075 -10000 0 -0.33 1 1
BAG4 -0.027 0.15 -10000 0 -0.86 6 6
BAD 0.021 0.03 -10000 0 -10000 0 0
NFKBIA 0 0 -10000 0 -10000 0 0
BIRC3 0.006 0.087 0.34 6 -0.86 1 7
BAX 0.021 0.03 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.008 0.022 -10000 0 -0.071 13 13
IKBKB 0.029 0.071 -10000 0 -10000 0 0
MAP2K2 0.03 0.035 -10000 0 -10000 0 0
MAP2K1 0.03 0.034 -10000 0 -10000 0 0
SMPD1 0.013 0.022 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.029 0.073 -10000 0 -10000 0 0
MAP2K4 0.026 0.031 -10000 0 -10000 0 0
protein ubiquitination 0.031 0.072 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.033 0.039 -10000 0 -10000 0 0
response to UV 0 0.001 -10000 0 -10000 0 0
RAF1 0.026 0.034 -10000 0 -10000 0 0
CRADD -0.005 0.062 -10000 0 -0.86 1 1
mol:ceramide 0.015 0.031 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0 0 -10000 0 -10000 0 0
MAP3K1 0.021 0.031 -10000 0 -10000 0 0
TRADD -0.005 0.062 -10000 0 -0.86 1 1
RELA/p50 0 0 -10000 0 -10000 0 0
MAPK3 0.031 0.034 -10000 0 -10000 0 0
MAPK1 0.031 0.034 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.024 0.075 -10000 0 -0.33 1 1
KSR1 0.021 0.032 -10000 0 -10000 0 0
MAPK8 0.009 0.11 -10000 0 -0.45 9 9
TRAF2 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.029 0.071 -10000 0 -10000 0 0
TNF R/SODD -0.021 0.12 -10000 0 -0.67 6 6
TNF -0.045 0.19 -10000 0 -0.86 10 10
CYCS 0.022 0.029 -10000 0 -10000 0 0
IKBKG 0.029 0.071 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.014 0.071 -10000 0 -0.36 1 1
RELA 0 0 -10000 0 -10000 0 0
RIPK1 0 0 -10000 0 -10000 0 0
AIFM1 0.022 0.029 -10000 0 -10000 0 0
TNF/TNF R/SODD -0.049 0.16 -10000 0 -0.58 16 16
TNFRSF1A 0 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 -0.004 0.015 -10000 0 -10000 0 0
NSMAF 0.024 0.074 -10000 0 -0.32 1 1
response to hydrogen peroxide 0 0.001 -10000 0 -10000 0 0
BCL2 0 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.028 0.12 -10000 0 -0.54 10 10
Ran/GTP/Exportin 1/HDAC1 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha -0.023 0.1 -10000 0 -0.45 10 10
SUMO1 0 0 -10000 0 -10000 0 0
ZFPM1 -0.005 0.062 -10000 0 -0.86 1 1
NPC/RanGAP1/SUMO1/Ubc9 0 0 -10000 0 -10000 0 0
FKBP3 0 0 -10000 0 -10000 0 0
Histones -0.012 0.051 -10000 0 -10000 0 0
YY1/LSF -0.003 0.033 -10000 0 -0.32 2 2
SMG5 0 0 -10000 0 -10000 0 0
RAN 0 0 -10000 0 -10000 0 0
I kappa B alpha/HDAC3 -0.021 0.088 -10000 0 -0.39 10 10
I kappa B alpha/HDAC1 -0.014 0.059 -10000 0 -10000 0 0
SAP18 0 0 -10000 0 -10000 0 0
RELA -0.018 0.076 -10000 0 -0.34 10 10
HDAC1/Smad7 -0.006 0.059 -10000 0 -0.58 2 2
RANGAP1 0 0 -10000 0 -10000 0 0
HDAC3/TR2 -0.014 0.059 -10000 0 -10000 0 0
NuRD/MBD3 Complex 0.003 0.016 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.016 0.069 -10000 0 -10000 0 0
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.003 0.067 0.34 1 -0.86 1 2
GATA1 0.004 0.035 0.34 2 -10000 0 2
Mad/Max 0.001 0.017 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 0.003 0.027 -10000 0 -10000 0 0
RBBP7 0 0 -10000 0 -10000 0 0
NPC 0 0 -10000 0 -10000 0 0
RBBP4 0 0 -10000 0 -10000 0 0
MAX 0 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
NFKBIA -0.016 0.067 -10000 0 -0.3 10 10
KAT2B -0.009 0.088 -10000 0 -0.86 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex 0 0 -10000 0 -10000 0 0
SIN3 complex 0 0 -10000 0 -10000 0 0
SMURF1 0 0 -10000 0 -10000 0 0
CHD3 0.009 0.054 0.34 5 -10000 0 5
SAP30 0 0 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 -0.009 0.088 -10000 0 -0.86 2 2
YY1/HDAC3 -0.015 0.065 -10000 0 -0.52 1 1
YY1/HDAC2 -0.003 0.033 -10000 0 -0.32 2 2
YY1/HDAC1 -0.003 0.033 -10000 0 -10000 0 0
NuRD/MBD2 Complex (MeCP1) 0.003 0.016 -10000 0 -10000 0 0
PPARG -0.029 0.13 -10000 0 -0.52 11 11
HDAC8/hEST1B 0 0 -10000 0 -10000 0 0
UBE2I 0 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -10000 0 -10000 0 0
TNFRSF1A 0 0 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) -0.014 0.059 -10000 0 -10000 0 0
MBD3L2 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.006 0.059 -10000 0 -0.58 2 2
CREBBP 0 0 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.003 0.017 -10000 0 -10000 0 0
HDAC1 0 0 -10000 0 -10000 0 0
HDAC3 -0.016 0.067 -10000 0 -0.3 10 10
HDAC2 0 0 -10000 0 -10000 0 0
YY1 -0.004 0.038 -10000 0 -0.38 2 2
HDAC8 0 0 -10000 0 -10000 0 0
SMAD7 -0.009 0.088 -10000 0 -0.86 2 2
NCOR2 0 0 -10000 0 -10000 0 0
MXD1 0.002 0.025 0.34 1 -10000 0 1
STAT3 0 0 -10000 0 -10000 0 0
NFKB1 0 0 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0 0 -10000 0 -10000 0 0
YY1/LSF/HDAC1 -0.003 0.029 -10000 0 -10000 0 0
YY1/SAP30/HDAC1 -0.003 0.029 -10000 0 -10000 0 0
EP300 0 0 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0 0 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.016 0.067 -10000 0 -0.3 10 10
histone deacetylation 0.003 0.016 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 -0.013 0.054 -10000 0 -10000 0 0
nuclear export 0 0 -10000 0 -10000 0 0
PRKACA 0 0 -10000 0 -10000 0 0
GATAD2B 0 0 -10000 0 -10000 0 0
GATAD2A 0 0 -10000 0 -10000 0 0
GATA2/HDAC3 -0.016 0.072 -10000 0 -0.53 1 1
GATA1/HDAC1 0.002 0.024 -10000 0 -10000 0 0
GATA1/HDAC3 -0.012 0.065 -10000 0 -10000 0 0
CHD4 0 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A -0.035 0.15 -10000 0 -0.67 10 10
SIN3/HDAC complex/Mad/Max 0.001 0.007 -10000 0 -10000 0 0
NuRD Complex 0.003 0.017 -10000 0 -10000 0 0
positive regulation of chromatin silencing -0.012 0.05 -10000 0 -10000 0 0
SIN3B 0 0 -10000 0 -10000 0 0
MTA2 0 0 -10000 0 -10000 0 0
SIN3A 0 0 -10000 0 -10000 0 0
XPO1 0 0 -10000 0 -10000 0 0
SUMO1/HDAC1 0 0 -10000 0 -10000 0 0
HDAC complex 0 0 -10000 0 -10000 0 0
GATA1/Fog1 -0.001 0.054 -10000 0 -0.68 1 1
FKBP25/HDAC1/HDAC2 0 0 -10000 0 -10000 0 0
TNF -0.045 0.19 -10000 0 -0.86 10 10
negative regulation of cell growth 0.001 0.007 -10000 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.003 0.016 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.025 0.1 -10000 0 -0.47 10 10
SIN3/HDAC complex/NCoR1 -0.002 0.023 -10000 0 -10000 0 0
TFCP2 0 0 -10000 0 -10000 0 0
NR2C1 0 0 -10000 0 -10000 0 0
MBD3 0 0 -10000 0 -10000 0 0
MBD2 0 0 -10000 0 -10000 0 0
Atypical NF-kappaB pathway

Figure S123.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S123.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0 0 -10000 0 -10000 0 0
FBXW11 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.021 0.11 -10000 0 -0.58 7 7
NF kappa B1 p50/RelA/I kappa B alpha -0.009 0.045 -10000 0 -10000 0 0
NFKBIA 0.012 0.06 -10000 0 -0.29 7 7
MAPK14 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/p50 0 0 -10000 0 -10000 0 0
ARRB2 0 0 -10000 0 -10000 0 0
REL -0.032 0.16 -10000 0 -0.86 7 7
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA 0 0 -10000 0 -10000 0 0
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
NF kappa B1 p50 dimer 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
NFKB1 0 0 -10000 0 -10000 0 0
RELA 0 0 -10000 0 -10000 0 0
positive regulation of anti-apoptosis -0.009 0.055 -10000 0 -0.29 7 7
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 -0.009 0.044 -10000 0 -10000 0 0
SRC 0.002 0.025 0.34 1 -10000 0 1
PI3K -0.006 0.087 -10000 0 -1.2 1 1
NF kappa B1 p50/RelA -0.01 0.056 -10000 0 -0.29 7 7
IKBKB 0 0 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -10000 0 -10000 0 0
SYK 0 0 -10000 0 -10000 0 0
I kappa B alpha/PIK3R1 -0.013 0.062 -10000 0 -0.5 1 1
cell death -0.008 0.042 -10000 0 -10000 0 0
NF kappa B1 p105/c-Rel -0.021 0.11 -10000 0 -0.58 7 7
LCK -0.03 0.16 0.34 1 -0.86 7 8
BCL3 0 0 -10000 0 -10000 0 0
Arf6 trafficking events

Figure S124.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S124.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.003 0.12 0.34 6 -0.86 3 9
CLTC 0.022 0.015 -10000 0 -10000 0 0
calcium ion-dependent exocytosis -0.007 0.038 -10000 0 -0.2 7 7
Dynamin 2/GTP 0.001 0.012 -10000 0 -10000 0 0
EXOC4 0 0 -10000 0 -10000 0 0
CD59 -0.002 0.016 -10000 0 -10000 0 0
CPE 0.005 0.03 -10000 0 -10000 0 0
CTNNB1 0 0 -10000 0 -10000 0 0
membrane fusion -0.008 0.041 -10000 0 -0.22 7 7
CTNND1 0.001 0.008 -10000 0 -10000 0 0
DNM2 0 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.021 0.023 -10000 0 -10000 0 0
TSHR 0 0 -10000 0 -10000 0 0
INS 0.012 0.025 0.19 3 -10000 0 3
BIN1 0 0 -10000 0 -10000 0 0
mol:Choline -0.008 0.041 -10000 0 -0.22 7 7
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.002 0.019 -10000 0 -10000 0 0
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.011 -10000 0 -10000 0 0
JUP -0.002 0.016 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.001 0.015 -10000 0 -10000 0 0
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 -0.018 0.069 -10000 0 -0.4 1 1
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.013 0.048 -10000 0 -10000 0 0
positive regulation of phagocytosis 0 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 -0.009 0.042 -10000 0 -0.34 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.004 0.027 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.023 0.029 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0 0 -10000 0 -10000 0 0
exocyst 0 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.001 0.008 -10000 0 -10000 0 0
NME1 0.002 0.019 -10000 0 -10000 0 0
clathrin coat assembly 0.021 0.015 -10000 0 -10000 0 0
IL2RA -0.004 0.043 -10000 0 -10000 0 0
VAMP3 0 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.005 0.068 -10000 0 -0.45 3 3
EXOC6 0 0 -10000 0 -10000 0 0
PLD1 -0.013 0.068 -10000 0 -0.36 7 7
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0 0 -10000 0 -10000 0 0
PIP5K1C 0.021 0.024 -10000 0 -10000 0 0
SDC1 -0.007 0.04 -10000 0 -10000 0 0
ARF6/GDP 0.001 0.012 -10000 0 -10000 0 0
EXOC7 0 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.013 0.05 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.008 0.041 -10000 0 -0.22 7 7
endocytosis -0.001 0.014 -10000 0 -10000 0 0
SCAMP2 0 0 -10000 0 -10000 0 0
ADRB2 -0.037 0.17 -10000 0 -0.48 24 24
EXOC3 0 0 -10000 0 -10000 0 0
ASAP2 0.002 0.025 0.34 1 -10000 0 1
Dynamin 2/GDP 0.002 0.016 -10000 0 -10000 0 0
KLC1 0 0 -10000 0 -10000 0 0
AVPR2 0.029 0.018 -10000 0 -10000 0 0
RALA 0 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.011 0.044 -10000 0 -10000 0 0
Insulin Pathway

Figure S125.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S125.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP 0.001 0.041 -10000 0 -0.47 1 1
TC10/GTP -0.001 0.035 -10000 0 -0.46 1 1
Insulin Receptor/Insulin/IRS1/Shp2 0.004 0.029 -10000 0 -10000 0 0
HRAS 0.004 0.035 0.34 2 -10000 0 2
APS homodimer 0.004 0.035 0.34 2 -10000 0 2
GRB14 -0.009 0.088 -10000 0 -0.86 2 2
FOXO3 -0.027 0.14 -10000 0 -0.73 7 7
AKT1 -0.009 0.071 -10000 0 -0.54 3 3
INSR 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.004 0.03 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0 0 -10000 0 -10000 0 0
SORBS1 -0.005 0.062 -10000 0 -0.86 1 1
CRK 0 0 -10000 0 -10000 0 0
PTPN1 0.004 0.014 -10000 0 -10000 0 0
CAV1 0.002 0.01 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II/C3G -0.001 0.042 -10000 0 -0.5 1 1
Insulin Receptor/Insulin/IRS1/NCK2 0.005 0.033 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.002 0.071 -10000 0 -0.94 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.003 0.018 -10000 0 -10000 0 0
RPS6KB1 -0.006 0.064 -10000 0 -0.69 1 1
PARD6A 0.002 0.025 0.34 1 -10000 0 1
CBL 0 0 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0 0 -10000 0 -10000 0 0
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.004 0.066 -10000 0 -0.68 1 1
HRAS/GTP 0 0 -10000 0 -10000 0 0
Insulin Receptor 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.004 0.028 -10000 0 -10000 0 0
PRKCI -0.002 0.016 -10000 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.009 0.078 -10000 0 -0.6 3 3
SHC1 0 0 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade -0.005 0.052 -10000 0 -0.52 2 2
PI3K -0.002 0.075 -10000 0 -0.98 1 1
NCK2 0.002 0.025 0.34 1 -10000 0 1
RHOQ 0 0 -10000 0 -10000 0 0
mol:H2O2 0 0 -10000 0 -10000 0 0
HRAS/GDP 0.002 0.023 0.23 2 -10000 0 2
AKT2 -0.009 0.071 -10000 0 -0.54 3 3
PRKCZ -0.029 0.13 -10000 0 -0.65 8 8
SH2B2 0.004 0.035 0.34 2 -10000 0 2
SHC/SHIP 0.002 0.01 -10000 0 -10000 0 0
F2RL2 -0.08 0.28 0.34 6 -0.86 20 26
TRIP10 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.004 0.028 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.004 0.028 -10000 0 -10000 0 0
RAPGEF1 0 0 -10000 0 -10000 0 0
RASA1 -0.009 0.088 -10000 0 -0.86 2 2
NCK1 0 0 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.001 0.044 -10000 0 -0.54 1 1
TC10/GDP 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.004 0.029 -10000 0 -10000 0 0
INPP5D 0.002 0.01 -10000 0 -10000 0 0
SOS1 0 0 -10000 0 -10000 0 0
SGK1 -0.039 0.2 -10000 0 -1.1 7 7
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
IRS1 0 0 -10000 0 -10000 0 0
p62DOK/RasGAP -0.005 0.053 -10000 0 -0.52 2 2
INS 0.01 0.049 0.35 4 -10000 0 4
mol:PI-3-4-P2 0.002 0.01 -10000 0 -10000 0 0
GRB2 0 0 -10000 0 -10000 0 0
EIF4EBP1 -0.005 0.065 -10000 0 -0.69 1 1
PTPRA 0 0 -10000 0 -10000 0 0
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
TC10/GTP/CIP4 0 0 -10000 0 -10000 0 0
PDPK1 0 0 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.003 0.017 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 0.004 0.028 -10000 0 -10000 0 0
Insulin Receptor/Insulin/IRS3 0.005 0.034 -10000 0 -10000 0 0
Par3/Par6 -0.046 0.16 -10000 0 -0.51 20 20
VEGFR1 specific signals

Figure S126.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S126.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer -0.02 0.11 -10000 0 -0.58 7 7
VEGFR1 homodimer/NRP1 0 0 -10000 0 -10000 0 0
mol:DAG 0.001 0.013 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1/VEGFR 121 0 0 -10000 0 -10000 0 0
CaM/Ca2+ 0.001 0.012 -10000 0 -10000 0 0
HIF1A 0 0 -10000 0 -10000 0 0
GAB1 0 0 -10000 0 -10000 0 0
AKT1 -0.004 0.066 -10000 0 -0.9 1 1
PLCG1 0.001 0.013 -10000 0 -10000 0 0
NOS3 0.047 0.037 -10000 0 -10000 0 0
CBL 0 0 -10000 0 -10000 0 0
mol:NO 0.047 0.036 -10000 0 -10000 0 0
FLT1 0.022 0 -10000 0 -10000 0 0
PGF 0.004 0.035 0.34 2 -10000 0 2
VEGFR1 homodimer/NRP2/VEGFR121 -0.004 0.057 -10000 0 -0.53 2 2
CALM1 0 0 -10000 0 -10000 0 0
PIK3CA -0.005 0.062 -10000 0 -0.86 1 1
eNOS/Hsp90 -0.003 0.029 -10000 0 -10000 0 0
endothelial cell proliferation 0.01 0.11 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.013 -10000 0 -10000 0 0
MAPK3 0.043 0.005 -10000 0 -10000 0 0
MAPK1 0.043 0.005 -10000 0 -10000 0 0
PIK3R1 -0.005 0.062 -10000 0 -0.86 1 1
PLGF homodimer 0.004 0.035 0.34 2 -10000 0 2
PRKACA 0 0 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 0 0 -10000 0 -10000 0 0
VEGFA homodimer 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0 0 -10000 0 -10000 0 0
platelet activating factor biosynthetic process 0.048 0.004 -10000 0 -10000 0 0
PI3K -0.003 0.075 -10000 0 -0.99 1 1
PRKCA 0.001 0.01 -10000 0 -10000 0 0
PRKCB -0.044 0.14 -10000 0 -0.5 17 17
VEGFR1 homodimer/PLGF homodimer 0.003 0.025 -10000 0 -10000 0 0
VEGFA 0 0 -10000 0 -10000 0 0
VEGFB -0.03 0.16 0.34 1 -0.86 7 8
mol:IP3 0.001 0.013 -10000 0 -10000 0 0
RASA1 -0.024 0.11 -10000 0 -0.53 9 9
NRP2 -0.007 0.091 0.34 1 -0.86 2 3
VEGFR1 homodimer 0.022 0 -10000 0 -10000 0 0
VEGFB homodimer -0.03 0.16 0.34 1 -0.86 7 8
NCK1 0 0 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.003 0.029 -10000 0 -10000 0 0
PTPN11 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.073 -10000 0 -0.97 1 1
mol:L-citrulline 0.047 0.036 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0 0 -10000 0 -10000 0 0
CD2AP 0 0 -10000 0 -10000 0 0
PI3K/GAB1 -0.003 0.072 -10000 0 -0.95 1 1
PDPK1 -0.004 0.066 -10000 0 -0.91 1 1
VEGFR1 homodimer/VEGFA homodimer/SHP2 0 0 -10000 0 -10000 0 0
mol:NADP 0.047 0.036 -10000 0 -10000 0 0
HSP90AA1 0 0 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0 0 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 -0.005 0.062 -10000 0 -0.58 2 2
Circadian rhythm pathway

Figure S127.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S127.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.003 0.038 -10000 0 -10000 0 0
CLOCK 0 0.003 -10000 0 -10000 0 0
TIMELESS/CRY2 -0.002 0.026 -10000 0 -10000 0 0
DEC1/BMAL1 0 0.002 -10000 0 -10000 0 0
ATR 0 0 -10000 0 -10000 0 0
NR1D1 0.024 0.11 -10000 0 -1.5 1 1
ARNTL 0 0.003 -10000 0 -10000 0 0
TIMELESS 0.03 0.031 -10000 0 -10000 0 0
NPAS2 -0.005 0.062 -10000 0 -0.86 1 1
CRY2 0 0 -10000 0 -10000 0 0
mol:CO -0.01 0.011 0.14 1 -10000 0 1
CHEK1 0.007 0.049 0.34 4 -10000 0 4
mol:HEME 0.01 0.011 -10000 0 -0.14 1 1
PER1 0 0 -10000 0 -10000 0 0
BMAL/CLOCK/NPAS2 -0.004 0.042 -10000 0 -0.58 1 1
BMAL1/CLOCK 0.032 0.069 -10000 0 -0.91 1 1
S phase of mitotic cell cycle 0.003 0.038 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.003 0.038 -10000 0 -10000 0 0
mol:NADPH 0.01 0.011 -10000 0 -0.14 1 1
PER1/TIMELESS -0.002 0.026 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0 0 -10000 0 -10000 0 0
TCGA08_p53

Figure S128.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0.1 0.076 -9999 0 -9999 0 0
TP53 0.028 0.021 -9999 0 -9999 0 0
Senescence 0.028 0.021 -9999 0 -9999 0 0
Apoptosis 0.028 0.021 -9999 0 -9999 0 0
Activated_Oncogenes 0 0 -9999 0 -9999 0 0
MDM2 -0.059 0.044 -9999 0 -9999 0 0
MDM4 0 0 -9999 0 -9999 0 0
Sumoylation by RanBP2 regulates transcriptional repression

Figure S129.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S129.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 -10000 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -10000 0 -9999 0 0
MDM2/SUMO1 0 0 -10000 0 -9999 0 0
HDAC4 0.002 0.025 0.34 1 -9999 0 1
Ran/GTP/Exportin 1/HDAC1 0 0 -10000 0 -9999 0 0
SUMO1 0 0 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1 0 0 -10000 0 -9999 0 0
mol:GTP 0 0 -10000 0 -9999 0 0
XPO1 0 0 -10000 0 -9999 0 0
EntrezGene:23636 0 0 -10000 0 -9999 0 0
RAN 0 0 -10000 0 -9999 0 0
EntrezGene:8021 0 0 -10000 0 -9999 0 0
RANBP2 0 0 -10000 0 -9999 0 0
SUMO1/HDAC4 0.001 0.015 -10000 0 -9999 0 0
SUMO1/HDAC1 0 0 -10000 0 -9999 0 0
RANGAP1 0 0 -10000 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -10000 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0 0 -10000 0 -9999 0 0
Ran/GTP 0 0 -10000 0 -9999 0 0
EntrezGene:23225 0 0 -10000 0 -9999 0 0
MDM2 0 0 -10000 0 -9999 0 0
UBE2I 0 0 -10000 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -10000 0 -9999 0 0
NPC 0 0 -10000 0 -9999 0 0
PIAS2 0 0 -10000 0 -9999 0 0
PIAS1 0 0 -10000 0 -9999 0 0
EntrezGene:9972 0 0 -10000 0 -9999 0 0
Arf1 pathway

Figure S130.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S130.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0 -9999 0 -10000 0 0
AP2 0 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0 0 -9999 0 -10000 0 0
CD4 -0.063 0.22 -9999 0 -0.86 14 14
CLTA 0 0 -9999 0 -10000 0 0
mol:GTP 0.001 0 -9999 0 -10000 0 0
ARFGAP1 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP -0.021 0.076 -9999 0 -0.29 14 14
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.043 0.15 -9999 0 -0.58 14 14
Alternative NF-kappaB pathway

Figure S131.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S131.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

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 0 -10000 0 -9999 0 0
FBXW11 0 0 -10000 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -10000 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0 0 -10000 0 -9999 0 0
CHUK 0 0 -10000 0 -9999 0 0
NF kappa B2 p100/RelB 0.001 0.014 -10000 0 -9999 0 0
NFKB1 0 0 -10000 0 -9999 0 0
MAP3K14 0 0 -10000 0 -9999 0 0
NF kappa B1 p50/RelB 0.001 0.017 -10000 0 -9999 0 0
RELB 0.002 0.025 0.34 1 -9999 0 1
NFKB2 0 0 -10000 0 -9999 0 0
NF kappa B2 p52/RelB 0.001 0.015 -10000 0 -9999 0 0
regulation of B cell activation 0.001 0.015 -10000 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 191 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.UB.A7MF TCGA.UB.A7ME TCGA.UB.A7MC TCGA.UB.A7MB
109_MAP3K5 -0.23 0.041 -0.23 -0.23
47_PPARGC1A 0 -0.86 0 0
105_BMP4 0 0 0 0
105_BMP6 0 0 0 0
105_BMP7 0 0 0 0
105_BMP2 -0.86 0 0 0
131_RELN/VLDLR -0.53 -0.53 0.21 -0.53
30_TGFB1/TGF beta receptor Type II 0 0 0 0
84_STAT5B 0.032 0.031 0.055 0.1
84_STAT5A 0.032 0.031 0.055 0.1
Methods & Data
Input

  • Expression Data Normalization = Normal controls were used to median center the expression data used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LIHC-TP/8100493/LIHC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = Copy number data was not used in this analysis.

Data Sets and Pathway Interactions

Both copy number and expression data are incorporated into PARADIGM's inference. Whenever normal tissue controls are available for analysis in the expression data, each patient's gene-value is normalized by subtracting the gene's median level observed in the normal control. Copy number data is also normalized to reflect the difference in copy number between a gene's levels detected in tumor versus control (e.g. blood normal). The collection of pathways used by PARADIGM includes those from NCI-PID on September 15, 2009 containing 131 pathways, 11,563 interactions, and 7,204 entities. All gene identifiers were translated into HUGO standard identifiers wherever possible. We refer to molecular entities as "concepts," which include gene products such as proteins and miRNAs, small molecules, protein complexes, and abstract concepts. Each concept is represented as "node" in PARADIGM's graphical model. The abstract concepts correspond to general cellular processes (such as "apoptosis" or "DNA damage response") and families of genes that share functional activity such as the RAS family of signal transducers. Various types of concept-concept interactions are included in the pathways including protein-protein interactions, transcriptional regulatory interactions, and protein modifications such as phosphorylation and ubiquitinylation interactions.

Pathway Inference Method

The PARADIGM algorithm (described in PMID: 20529912) assigns an integrated pathway level (IPL) reflecting the activity of a concept determined through a belief propagation strategy. The belief propagation is given the copy number and gene expression measurements of all of the genes and iteratively updates hidden states reflecting the activities of all of the genes in a pathway so as to maximize the likelihood of the observed data given the interactions in the pathway. In the end, the inferred level of a concept reflects both the data observed for the concept and the neighborhood of activity surrounding the concept.

Determining significantly altered levels

The significance of the IPL obtained for each concept in each patient sample is assessed using a permutation analysis. Importantly, the permutation analysis preserves data tuples so as to preserve any implicit correlations between the different data modalities. For example, genes that are deleted have concomitantly lower expression levels. Preserving the copy number and expression pairs therefore retains this data property. The simulation therefore makes "null samples" by permuting data tuples across all of the genes in the genome so that each gene in a null sample is associated with a random tuple of another gene with equal probability. This approach has the added benefit of preserving the pathway structure so that every observed IPL can be compared to a distribution of random IPLs derived from exactly the same interaction context. PARADIGM inferences are then obtained for 1000 "null" patients and serve as a background distribution to contrast the observed IPLs against. Pathway concepts are excluded from further analysis if they did not obtain a minimum IPL of 0.5 in any patient sample both observed or simulated.

An IPL I(i,j) for concept i in sample j, is considered to be deviated if its absolute level is two standard deviations from the average level observed for concept i in the 1000 null samples. The degree to which a concept has significantly altered levels across a patient cohort is summarized in the proportion of deviated samples (PDS) score. For example, a protein with a PDS of 0.10 reflects that the protein's level of activity was inferred to be significantly higher or lower in tumors compared to normal in 10% of the patient samples. An average PDS for a pathway is also reported by computing the mean PDS over all concepts in the pathway.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
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