PARADIGM pathway analysis of mRNASeq expression and copy number data
Lung Adenocarcinoma (Primary solid tumor)
21 April 2013  |  analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1QJ7F95
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Lung Adenocarcinoma (Primary solid tumor cohort) - 21 April 2013: PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C1QJ7F95
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 45 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 185
Glypican 2 network 132
Angiopoietin receptor Tie2-mediated signaling 107
Aurora B signaling 101
HIF-1-alpha transcription factor network 95
Signaling events mediated by the Hedgehog family 83
PLK1 signaling events 63
Endothelins 63
Aurora C signaling 54
Visual signal transduction: Cones 48
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • 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.

Pathway.Name 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 185 9439 51 -0.04 0.81 1000 -1000 -0.097 -1000
Glypican 2 network 132 530 4 0.085 0.14 1000 -1000 0.018 -1000
Angiopoietin receptor Tie2-mediated signaling 107 9471 88 -0.53 0.11 1000 -1000 -0.056 -1000
Aurora B signaling 101 6781 67 -0.16 0.29 1000 -1000 -0.029 -1000
HIF-1-alpha transcription factor network 95 7246 76 -0.053 0.44 1000 -1000 -0.03 -1000
Signaling events mediated by the Hedgehog family 83 4326 52 -0.22 0.1 1000 -1000 -0.026 -1000
PLK1 signaling events 63 5357 85 -0.053 0.2 1000 -1000 -0.025 -1000
Endothelins 63 6068 96 -0.3 0.2 1000 -1000 -0.031 -1000
Aurora C signaling 54 384 7 0 0.17 1000 -1000 -0.01 -1000
Visual signal transduction: Cones 48 1839 38 -0.087 0.12 1000 -1000 -0.017 -1000
Signaling mediated by p38-alpha and p38-beta 48 2113 44 -0.098 0.021 1000 -1000 -0.016 -1000
Osteopontin-mediated events 44 1675 38 -0.004 0.25 1000 -1000 -0.018 -1000
Fc-epsilon receptor I signaling in mast cells 44 4272 97 -0.1 0.022 1000 -1000 -0.055 -1000
FOXA2 and FOXA3 transcription factor networks 43 1997 46 -0.2 0.15 1000 -1000 -0.08 -1000
Signaling events regulated by Ret tyrosine kinase 43 3549 82 -0.081 0.063 1000 -1000 -0.042 -1000
IL4-mediated signaling events 42 3865 91 -0.65 0.36 1000 -1000 -0.1 -1000
BMP receptor signaling 40 3308 81 -0.18 0.23 1000 -1000 -0.022 -1000
RXR and RAR heterodimerization with other nuclear receptor 40 2088 52 -0.14 0.045 1000 -1000 -0.031 -1000
amb2 Integrin signaling 39 3228 82 -0.3 0.077 1000 -1000 -0.03 -1000
Visual signal transduction: Rods 37 1942 52 -0.087 0.1 1000 -1000 -0.033 -1000
Ephrin B reverse signaling 36 1751 48 -0.079 0.08 1000 -1000 -0.03 -1000
IL23-mediated signaling events 33 2011 60 -0.19 0.028 1000 -1000 -0.083 -1000
p75(NTR)-mediated signaling 31 3959 125 -0.14 0.14 1000 -1000 -0.043 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 31 2167 68 -0.15 0.064 1000 -1000 -0.049 -1000
Syndecan-1-mediated signaling events 29 993 34 0 0.22 1000 -1000 -0.023 -1000
Integrins in angiogenesis 28 2422 84 -0.084 0.25 1000 -1000 -0.033 -1000
TCGA08_retinoblastoma 28 226 8 -0.022 0.1 1000 -1000 -0.002 -1000
LPA4-mediated signaling events 27 325 12 -0.073 0 1000 -1000 -0.015 -1000
HIF-2-alpha transcription factor network 27 1169 43 -0.14 0.15 1000 -1000 -0.031 -1000
Neurotrophic factor-mediated Trk receptor signaling 27 3274 120 -0.16 0.14 1000 -1000 -0.04 -1000
Arf6 signaling events 26 1631 62 -0.11 0.075 1000 -1000 -0.017 -1000
TCGA08_p53 26 185 7 -0.021 0.02 1000 -1000 -0.01 -1000
Glucocorticoid receptor regulatory network 25 2857 114 -0.27 0.18 1000 -1000 -0.038 -1000
Thromboxane A2 receptor signaling 24 2559 105 -0.1 0.075 1000 -1000 -0.038 -1000
Aurora A signaling 24 1468 60 -0.029 0.19 1000 -1000 -0.02 -1000
Reelin signaling pathway 24 1380 56 -0.039 0.048 1000 -1000 -0.023 -1000
Canonical Wnt signaling pathway 24 1265 51 -0.21 0.095 1000 -1000 -0.036 -1000
EGFR-dependent Endothelin signaling events 24 513 21 -0.024 0.075 1000 -1000 -0.03 -1000
Presenilin action in Notch and Wnt signaling 23 1454 61 -0.21 0.095 1000 -1000 -0.034 -1000
IL6-mediated signaling events 23 1726 75 -0.15 0.053 1000 -1000 -0.047 -1000
FoxO family signaling 22 1469 64 0 0.21 1000 -1000 -0.041 -1000
Glypican 1 network 21 1030 48 -0.052 0.038 1000 -1000 -0.021 -1000
Effects of Botulinum toxin 21 560 26 0 0.043 1000 -1000 -0.01 -1000
Nongenotropic Androgen signaling 20 1076 52 -0.069 0.049 1000 -1000 -0.019 -1000
S1P4 pathway 20 501 25 -0.028 0.028 1000 -1000 -0.014 -1000
ErbB4 signaling events 19 1315 69 -0.11 0.14 1000 -1000 -0.028 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 19 649 33 -0.077 0.098 1000 -1000 -0.017 -1000
Syndecan-4-mediated signaling events 18 1207 67 -0.045 0.14 1000 -1000 -0.026 -1000
ErbB2/ErbB3 signaling events 17 1139 65 -0.051 0.03 1000 -1000 -0.065 -1000
PDGFR-alpha signaling pathway 17 781 44 -0.18 0.038 1000 -1000 -0.023 -1000
IL1-mediated signaling events 17 1091 62 -0.076 0.043 1000 -1000 -0.038 -1000
Wnt signaling 17 125 7 -0.026 0.039 1000 -1000 -0.012 -1000
LPA receptor mediated events 17 1812 102 -0.055 0.072 1000 -1000 -0.048 -1000
Noncanonical Wnt signaling pathway 16 424 26 -0.048 0.039 1000 -1000 -0.025 -1000
Syndecan-2-mediated signaling events 16 1146 69 -0.045 0.057 1000 -1000 -0.027 -1000
Calcium signaling in the CD4+ TCR pathway 16 496 31 -0.037 0.034 1000 -1000 -0.03 -1000
Signaling events mediated by VEGFR1 and VEGFR2 16 2060 125 -0.18 0.042 1000 -1000 -0.039 -1000
Regulation of Androgen receptor activity 16 1183 70 -0.14 0.12 1000 -1000 -0.031 -1000
Nephrin/Neph1 signaling in the kidney podocyte 15 518 34 -0.036 0.06 1000 -1000 -0.027 -1000
Ceramide signaling pathway 15 1184 76 -0.02 0.075 1000 -1000 -0.021 -1000
S1P5 pathway 15 270 17 -0.019 0.021 1000 -1000 -0.003 -1000
FAS signaling pathway (CD95) 15 731 47 -0.23 0.035 1000 -1000 -0.047 -1000
EPHB forward signaling 15 1302 85 -0.033 0.089 1000 -1000 -0.044 -1000
Class IB PI3K non-lipid kinase events 15 45 3 -0.008 0.008 1000 -1000 -0.025 -1000
PLK2 and PLK4 events 14 42 3 -0.007 0.038 1000 -1000 -0.017 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 14 781 54 -0.033 0.11 1000 -1000 -0.032 -1000
Signaling events mediated by PTP1B 14 1073 76 -0.052 0.075 1000 -1000 -0.039 -1000
Coregulation of Androgen receptor activity 13 1028 76 -0.06 0.097 1000 -1000 -0.022 -1000
IL12-mediated signaling events 13 1194 87 -0.13 0.06 1000 -1000 -0.061 -1000
Nectin adhesion pathway 13 834 63 -0.04 0.051 1000 -1000 -0.052 -1000
TCR signaling in naïve CD8+ T cells 13 1241 93 -0.031 0.033 1000 -1000 -0.037 -1000
BCR signaling pathway 13 1351 99 -0.045 0.082 1000 -1000 -0.058 -1000
Plasma membrane estrogen receptor signaling 13 1199 86 -0.063 0.06 1000 -1000 -0.033 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 12 1064 85 -0.065 0.036 1000 -1000 -0.027 -1000
S1P1 pathway 12 455 36 -0.086 0.021 1000 -1000 -0.026 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 12 974 78 -0.042 0.023 1000 -1000 -0.039 -1000
Caspase cascade in apoptosis 11 846 74 -0.03 0.077 1000 -1000 -0.026 -1000
BARD1 signaling events 11 682 57 -0.047 0.12 1000 -1000 -0.035 -1000
Syndecan-3-mediated signaling events 11 385 35 -0.11 0.047 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class III 10 433 40 -0.06 0.066 1000 -1000 -0.031 -1000
Regulation of p38-alpha and p38-beta 10 571 54 -0.039 0.058 1000 -1000 -0.04 -1000
IL2 signaling events mediated by STAT5 10 223 22 -0.028 0.1 1000 -1000 -0.025 -1000
IL27-mediated signaling events 9 509 51 -0.043 0.036 1000 -1000 -0.04 -1000
PDGFR-beta signaling pathway 9 887 97 -0.038 0.053 1000 -1000 -0.038 -1000
Signaling events mediated by PRL 9 308 34 -0.023 0.088 1000 -1000 -0.028 -1000
Class I PI3K signaling events 8 632 73 -0.04 0.053 1000 -1000 -0.025 -1000
VEGFR1 specific signals 8 467 56 -0.18 0.05 1000 -1000 -0.024 -1000
Sphingosine 1-phosphate (S1P) pathway 7 197 28 -0.018 0.033 1000 -1000 -0.018 -1000
Ephrin A reverse signaling 7 55 7 -0.014 0.03 1000 -1000 -0.009 -1000
Stabilization and expansion of the E-cadherin adherens junction 7 580 74 -0.094 0.075 1000 -1000 -0.046 -1000
Insulin Pathway 7 566 74 -0.1 0.052 1000 -1000 -0.037 -1000
Regulation of nuclear SMAD2/3 signaling 6 934 136 -0.17 0.075 1000 -1000 -0.025 -1000
JNK signaling in the CD4+ TCR pathway 6 116 17 -0.008 0.047 1000 -1000 -0.018 -1000
Cellular roles of Anthrax toxin 6 260 39 -0.031 0.029 1000 -1000 -0.016 -1000
Hedgehog signaling events mediated by Gli proteins 6 453 65 -0.13 0.048 1000 -1000 -0.035 -1000
EPO signaling pathway 6 347 55 -0.026 0.045 1000 -1000 -0.026 -1000
mTOR signaling pathway 6 355 53 -0.062 0.025 1000 -1000 -0.029 -1000
IFN-gamma pathway 6 421 68 -0.03 0.061 1000 -1000 -0.039 -1000
ceramide signaling pathway 6 308 49 -0.01 0.027 1000 -1000 -0.026 -1000
Retinoic acid receptors-mediated signaling 6 384 58 -0.091 0.041 1000 -1000 -0.041 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 6 278 45 -0.024 0.05 1000 -1000 -0.03 -1000
Arf6 trafficking events 6 483 71 -0.038 0.039 1000 -1000 -0.031 -1000
Ras signaling in the CD4+ TCR pathway 6 103 17 -0.005 0.031 1000 -1000 -0.02 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 5 470 83 -0.057 0.041 1000 -1000 -0.017 -1000
Signaling events mediated by HDAC Class I 5 556 104 -0.035 0.048 1000 -1000 -0.033 -1000
Signaling mediated by p38-gamma and p38-delta 5 76 15 -0.018 0.022 1000 -1000 -0.02 -1000
E-cadherin signaling in the nascent adherens junction 5 417 76 -0.033 0.055 1000 -1000 -0.044 -1000
Regulation of Telomerase 5 555 102 -0.021 0.096 1000 -1000 -0.044 -1000
S1P3 pathway 5 220 42 -0.025 0.035 1000 -1000 -0.018 -1000
Arf6 downstream pathway 4 196 43 -0.05 0.054 1000 -1000 -0.026 -1000
IL2 signaling events mediated by PI3K 4 267 58 -0.014 0.07 1000 -1000 -0.028 -1000
TCGA08_rtk_signaling 4 129 26 -0.01 0.048 1000 -1000 -0.009 -1000
IGF1 pathway 4 229 57 -0.032 0.048 1000 -1000 -0.028 -1000
E-cadherin signaling in keratinocytes 4 189 43 -0.015 0.04 1000 -1000 -0.02 -1000
p38 MAPK signaling pathway 4 213 44 -0.009 0.061 1000 -1000 -0.018 -1000
Signaling events mediated by HDAC Class II 3 286 75 -0.02 0.057 1000 -1000 -0.023 -1000
Circadian rhythm pathway 3 74 22 -0.004 0.048 1000 -1000 -0.033 -1000
Class I PI3K signaling events mediated by Akt 3 262 68 -0.028 0.046 1000 -1000 -0.025 -1000
Canonical NF-kappaB pathway 2 99 39 -0.017 0.043 1000 -1000 -0.019 -1000
Paxillin-independent events mediated by a4b1 and a4b7 2 76 37 -0.026 0.051 1000 -1000 -0.021 -1000
a4b1 and a4b7 Integrin signaling 1 7 5 0.02 0.03 1000 -1000 0.016 -1000
Insulin-mediated glucose transport 1 61 32 -0.016 0.038 1000 -1000 -0.021 -1000
TRAIL signaling pathway 1 84 48 -0.018 0.046 1000 -1000 -0.021 -1000
Paxillin-dependent events mediated by a4b1 1 58 36 -0.036 0.039 1000 -1000 -0.026 -1000
Atypical NF-kappaB pathway 1 38 31 -0.018 0.03 1000 -1000 -0.018 -1000
Rapid glucocorticoid signaling 1 35 20 -0.008 0.027 1000 -1000 -0.01 -1000
E-cadherin signaling events 1 6 5 0.019 0.039 1000 -1000 0.018 -1000
Arf1 pathway 1 100 54 -0.008 0.034 1000 -1000 -0.013 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0 22 23 0 0.036 1000 -1000 -0.013 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 21 27 -0.019 0.046 1000 -1000 -0.028 -1000
Alternative NF-kappaB pathway 0 0 13 0 0.056 1000 -1000 0 -1000
Total 2743 162692 7203 -9.6 11 131000 -131000 -3.8 -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 0.65 0.5 1 217 -10000 0 217
PLK1 0.38 0.33 0.7 182 -0.68 2 184
BIRC5 0.42 0.33 0.7 200 -0.71 1 201
HSPA1B 0.66 0.5 1.1 223 -10000 0 223
MAP2K1 0.2 0.15 0.33 204 -10000 0 204
BRCA2 0.65 0.5 1 218 -10000 0 218
FOXM1 0.81 0.66 1.3 228 -10000 0 228
XRCC1 0.66 0.5 1.1 219 -10000 0 219
FOXM1B/p19 0.22 0.36 0.83 91 -0.84 1 92
Cyclin D1/CDK4 0.54 0.44 0.92 204 -10000 0 204
CDC2 0.73 0.57 1.2 229 -10000 0 229
TGFA 0.57 0.46 0.94 218 -10000 0 218
SKP2 0.71 0.55 1.1 226 -10000 0 226
CCNE1 0.16 0.16 0.38 136 -10000 0 136
CKS1B 0.71 0.55 1.1 219 -10000 0 219
RB1 0.38 0.36 0.73 186 -0.61 3 189
FOXM1C/SP1 0.57 0.43 0.93 212 -10000 0 212
AURKB 0.36 0.38 0.7 185 -0.71 15 200
CENPF 0.74 0.57 1.2 228 -10000 0 228
CDK4 0.088 0.068 0.17 128 -10000 0 128
MYC 0.42 0.43 0.87 173 -10000 0 173
CHEK2 0.2 0.16 0.34 203 -10000 0 203
ONECUT1 0.62 0.49 1 215 -10000 0 215
CDKN2A -0.04 0.15 0.25 38 -0.23 116 154
LAMA4 0.64 0.51 1 217 -1.2 3 220
FOXM1B/HNF6 0.62 0.5 1 208 -10000 0 208
FOS 0.59 0.54 1.1 197 -0.93 2 199
SP1 0.022 0.006 -10000 0 -10000 0 0
CDC25B 0.65 0.5 1 219 -10000 0 219
response to radiation 0.14 0.11 0.23 212 -10000 0 212
CENPB 0.65 0.5 1 218 -10000 0 218
CENPA 0.74 0.57 1.2 228 -10000 0 228
NEK2 0.76 0.58 1.2 236 -10000 0 236
HIST1H2BA 0.66 0.5 1.1 220 -10000 0 220
CCNA2 0.14 0.16 0.4 101 -10000 0 101
EP300 0.021 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.71 0.55 1.1 219 -10000 0 219
CCNB2 0.73 0.57 1.2 224 -10000 0 224
CCNB1 0.76 0.6 1.2 226 -10000 0 226
ETV5 0.64 0.52 1.1 213 -1.1 2 215
ESR1 0.63 0.52 1.1 211 -1 4 215
CCND1 0.61 0.48 1 221 -10000 0 221
GSK3A 0.15 0.12 0.26 193 -10000 0 193
Cyclin A-E1/CDK1-2 0.27 0.22 0.44 211 -10000 0 211
CDK2 0.062 0.041 0.14 15 -10000 0 15
G2/M transition of mitotic cell cycle 0.18 0.15 0.29 228 -10000 0 228
FOXM1B/Cbp/p300 0.16 0.27 0.7 53 -0.77 1 54
GAS1 0.62 0.52 1 212 -1.1 4 216
MMP2 0.65 0.5 1 219 -10000 0 219
RB1/FOXM1C 0.52 0.45 0.91 202 -10000 0 202
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Glypican 2 network

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
MDK 0.12 0.14 0.33 122 -9999 0 122
GPC2 0.085 0.13 0.33 82 -9999 0 82
GPC2/Midkine 0.14 0.14 0.29 163 -9999 0 163
neuron projection morphogenesis 0.14 0.14 0.29 163 -9999 0 163
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.42 0.47 -10000 0 -0.93 171 171
NCK1/PAK1/Dok-R -0.2 0.2 -10000 0 -0.42 172 172
NCK1/Dok-R -0.46 0.56 -10000 0 -1.1 170 170
PIK3CA 0.022 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.056 0.093 0.23 85 -10000 0 85
RELA 0.021 0.003 -10000 0 -10000 0 0
SHC1 0.012 0.014 -10000 0 -10000 0 0
Rac/GDP 0.014 0.006 -10000 0 -10000 0 0
F2 0.11 0.16 0.32 119 -10000 0 119
TNIP2 0.021 0.004 -10000 0 -10000 0 0
NF kappa B/RelA -0.41 0.52 -10000 0 -0.97 170 170
FN1 0.018 0.035 -10000 0 -0.33 4 4
PLD2 -0.48 0.58 -10000 0 -1.1 169 169
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB14 0.034 0.081 0.33 21 -0.33 5 26
ELK1 -0.44 0.51 -10000 0 -0.98 170 170
GRB7 0.019 0.025 -10000 0 -0.33 2 2
PAK1 0.021 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.43 0.55 -10000 0 -1 170 170
CDKN1A -0.3 0.31 -10000 0 -0.65 170 170
ITGA5 0.021 0.024 0.33 1 -0.33 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.46 0.57 -10000 0 -1.1 170 170
CRK 0.02 0.007 -10000 0 -10000 0 0
mol:NO -0.3 0.33 -10000 0 -0.67 171 171
PLG -0.48 0.58 -10000 0 -1.1 170 170
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.39 0.43 -10000 0 -0.86 171 171
GRB2 0.021 0.005 -10000 0 -10000 0 0
PIK3R1 0.011 0.017 -10000 0 -10000 0 0
ANGPT2 -0.28 0.31 0.35 1 -0.68 115 116
BMX -0.52 0.6 -10000 0 -1.2 169 169
ANGPT1 -0.28 0.46 -10000 0 -1.1 88 88
tube development -0.34 0.35 -10000 0 -0.73 171 171
ANGPT4 -0.16 0.17 -10000 0 -0.33 189 189
response to hypoxia -0.029 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.48 0.61 -10000 0 -1.1 170 170
alpha5/beta1 Integrin 0.031 0.018 0.24 1 -0.23 1 2
FGF2 -0.021 0.11 -10000 0 -0.33 47 47
STAT5A (dimer) -0.39 0.41 -10000 0 -0.84 170 170
mol:L-citrulline -0.3 0.33 -10000 0 -0.67 171 171
AGTR1 -0.077 0.16 -10000 0 -0.33 110 110
MAPK14 -0.53 0.62 -10000 0 -1.2 172 172
Tie2/SHP2 -0.42 0.51 -10000 0 -1 156 156
TEK -0.46 0.56 -10000 0 -1.1 155 155
RPS6KB1 -0.4 0.45 -10000 0 -0.89 172 172
Angiotensin II/AT1 -0.051 0.11 -10000 0 -0.22 110 110
Tie2/Ang1/GRB2 -0.48 0.61 -10000 0 -1.1 170 170
MAPK3 -0.44 0.52 -10000 0 -1 169 169
MAPK1 -0.44 0.52 -10000 0 -0.99 168 168
Tie2/Ang1/GRB7 -0.48 0.61 -10000 0 -1.1 170 170
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.48 0.58 -10000 0 -1.1 170 170
PI3K -0.49 0.56 -10000 0 -1.1 172 172
FES -0.53 0.62 -10000 0 -1.2 172 172
Crk/Dok-R -0.46 0.57 -10000 0 -1.1 170 170
Tie2/Ang1/ABIN2 -0.49 0.61 -10000 0 -1.1 170 170
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.37 0.41 -10000 0 -0.82 171 171
STAT5A 0.02 0.018 -10000 0 -0.33 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.39 0.45 -10000 0 -0.87 172 172
Tie2/Ang2 -0.48 0.52 -10000 0 -1 172 172
Tie2/Ang1 -0.52 0.65 -10000 0 -1.2 170 170
FOXO1 -0.38 0.41 -10000 0 -0.83 171 171
ELF1 -0.029 0.067 -10000 0 -0.13 52 52
ELF2 -0.47 0.58 -10000 0 -1.1 168 168
mol:Choline -0.45 0.54 -10000 0 -1 169 169
cell migration -0.11 0.11 -10000 0 -0.23 173 173
FYN -0.4 0.41 -10000 0 -0.84 171 171
DOK2 -0.005 0.087 -10000 0 -0.33 26 26
negative regulation of cell cycle -0.28 0.28 -10000 0 -0.58 170 170
ETS1 -0.046 0.1 -10000 0 -0.25 76 76
PXN -0.32 0.36 -10000 0 -0.72 172 172
ITGB1 0.021 0.004 -10000 0 -10000 0 0
NOS3 -0.35 0.38 -10000 0 -0.77 171 171
RAC1 0.019 0.007 -10000 0 -10000 0 0
TNF -0.061 0.12 -10000 0 -0.27 94 94
MAPKKK cascade -0.45 0.54 -10000 0 -1 169 169
RASA1 0.021 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.48 0.6 -10000 0 -1.1 170 170
NCK1 0.021 0.003 -10000 0 -10000 0 0
vasculogenesis -0.27 0.3 -10000 0 -0.6 171 171
mol:Phosphatidic acid -0.45 0.54 -10000 0 -1 169 169
mol:Angiotensin II 0 0.003 -10000 0 -10000 0 0
mol:NADP -0.3 0.33 -10000 0 -0.67 171 171
Rac1/GTP -0.36 0.41 -10000 0 -0.81 171 171
MMP2 -0.48 0.58 -10000 0 -1.1 170 170
Aurora B signaling

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
Condensin I complex 0.11 0.12 0.24 165 -0.18 6 171
STMN1 0.072 0.089 0.16 191 -10000 0 191
Aurora B/RasGAP/Survivin 0.22 0.18 0.37 216 -10000 0 216
Chromosomal passenger complex/Cul3 protein complex 0.091 0.11 0.2 170 -0.2 7 177
BIRC5 0.2 0.16 0.34 216 -10000 0 216
DES -0.16 0.28 -10000 0 -0.56 82 82
Aurora C/Aurora B/INCENP 0.12 0.098 0.22 184 -0.16 3 187
Aurora B/TACC1 0.092 0.1 0.21 156 -0.15 11 167
Aurora B/PP2A 0.12 0.11 0.24 179 -10000 0 179
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.036 0.037 0.14 15 -10000 0 15
mitotic metaphase/anaphase transition -0.005 0.006 -10000 0 -10000 0 0
NDC80 0.15 0.16 0.28 213 -10000 0 213
Cul3 protein complex 0.031 0.047 0.23 3 -0.2 12 15
KIF2C 0.16 0.13 0.26 242 -0.32 1 243
PEBP1 0.023 0.005 -10000 0 -10000 0 0
KIF20A 0.19 0.15 0.33 215 -10000 0 215
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.13 0.11 0.24 186 -10000 0 186
SEPT1 0.02 0.018 -10000 0 -0.33 1 1
SMC2 0.021 0.004 -10000 0 -10000 0 0
SMC4 0.021 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.1 0.2 0.29 115 -0.43 29 144
PSMA3 0.021 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.006 0.006 -10000 0 -10000 0 0
H3F3B 0.077 0.073 0.15 193 -10000 0 193
AURKB 0.17 0.16 0.34 193 -10000 0 193
AURKC 0.019 0.035 0.33 1 -0.33 3 4
CDCA8 0.14 0.15 0.34 140 -10000 0 140
cytokinesis 0.15 0.16 0.3 180 -0.32 3 183
Aurora B/Septin1 0.19 0.19 0.38 179 -0.26 7 186
AURKA 0.058 0.13 0.32 71 -10000 0 71
INCENP 0.028 0.01 -10000 0 -10000 0 0
KLHL13 0.013 0.067 0.33 3 -0.33 12 15
BUB1 0.094 0.14 0.33 108 -10000 0 108
hSgo1/Aurora B/Survivin 0.29 0.24 0.48 223 -10000 0 223
EVI5 0.027 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.17 0.16 0.35 149 -0.32 1 150
SGOL1 0.17 0.16 0.33 185 -10000 0 185
CENPA 0.17 0.16 0.3 208 -0.21 9 217
NCAPG 0.15 0.15 0.33 167 -10000 0 167
Aurora B/HC8 Proteasome 0.13 0.11 0.24 186 -10000 0 186
NCAPD2 0.02 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.13 0.11 0.24 188 -10000 0 188
RHOA 0.021 0.004 -10000 0 -10000 0 0
NCAPH 0.16 0.15 0.33 173 -10000 0 173
NPM1 0.073 0.14 0.2 121 -0.34 23 144
RASA1 0.021 0.005 -10000 0 -10000 0 0
KLHL9 0.018 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.13 0.11 0.24 186 -10000 0 186
PPP1CC 0.021 0.004 -10000 0 -10000 0 0
Centraspindlin 0.19 0.18 0.36 178 -0.26 2 180
RhoA/GDP 0.016 0.003 -10000 0 -10000 0 0
NSUN2 0.093 0.13 0.24 99 -0.3 16 115
MYLK 0.071 0.076 0.15 188 -0.15 7 195
KIF23 0.1 0.14 0.34 93 -10000 0 93
VIM 0.07 0.09 0.16 186 -10000 0 186
RACGAP1 0.032 0.033 0.33 4 -10000 0 4
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.076 0.13 0.22 23 -0.3 23 46
Chromosomal passenger complex 0.17 0.16 0.3 211 -0.22 4 215
Chromosomal passenger complex/EVI5 0.29 0.22 0.48 206 -10000 0 206
TACC1 0.009 0.058 -10000 0 -0.33 11 11
PPP2R5D 0.021 0.004 -10000 0 -10000 0 0
CUL3 0.022 0.002 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.28 0.24 0.54 116 -0.68 4 120
HDAC7 0.032 0.016 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.32 0.32 0.66 135 -0.84 3 138
SMAD4 0.019 0.009 -10000 0 -10000 0 0
ID2 0.29 0.24 0.54 120 -0.68 4 124
AP1 -0.002 0.078 -10000 0 -0.24 30 30
ABCG2 0.26 0.25 0.55 111 -0.66 5 116
HIF1A 0.1 0.094 0.26 61 -0.22 2 63
TFF3 0.32 0.28 0.6 144 -0.71 4 148
GATA2 -0.02 0.1 -10000 0 -0.34 35 35
AKT1 0.1 0.1 0.27 59 -0.24 4 63
response to hypoxia 0.081 0.1 0.2 105 -0.22 8 113
MCL1 0.23 0.24 0.54 96 -0.75 2 98
NDRG1 0.24 0.24 0.55 97 -0.64 4 101
SERPINE1 0.27 0.24 0.55 112 -0.68 4 116
FECH 0.26 0.25 0.55 110 -0.68 4 114
FURIN 0.29 0.25 0.56 117 -0.68 4 121
NCOA2 0.018 0.026 -10000 0 -0.33 2 2
EP300 0.12 0.14 0.29 98 -0.3 11 109
HMOX1 0.28 0.24 0.54 122 -0.64 4 126
BHLHE40 0.28 0.24 0.55 119 -0.68 4 123
BHLHE41 0.26 0.25 0.55 103 -0.66 6 109
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.14 0.14 0.37 61 -10000 0 61
ENG 0.11 0.099 0.29 35 -0.26 2 37
JUN 0.01 0.036 -10000 0 -0.34 2 2
RORA 0.28 0.24 0.54 117 -0.71 4 121
ABCB1 0.014 0.18 0.37 22 -0.73 14 36
TFRC 0.27 0.24 0.54 109 -0.68 4 113
CXCR4 0.29 0.24 0.54 118 -0.68 4 122
TF 0.33 0.29 0.63 138 -0.64 5 143
CITED2 0.27 0.25 0.55 114 -0.68 4 118
HIF1A/ARNT 0.44 0.41 0.85 153 -0.82 3 156
LDHA 0.053 0.11 0.42 13 -0.51 2 15
ETS1 0.28 0.24 0.55 112 -0.61 4 116
PGK1 0.28 0.24 0.55 117 -0.68 4 121
NOS2 0.27 0.26 0.55 118 -0.74 4 122
ITGB2 0.28 0.24 0.54 121 -0.78 4 125
ALDOA 0.29 0.24 0.55 118 -0.68 4 122
Cbp/p300/CITED2 0.28 0.29 0.61 111 -0.88 4 115
FOS -0.013 0.094 -10000 0 -0.34 28 28
HK2 0.28 0.24 0.55 118 -0.7 5 123
SP1 0.015 0.037 -10000 0 -0.18 8 8
GCK 0.16 0.27 0.52 49 -1 11 60
HK1 0.28 0.24 0.54 119 -0.68 4 123
NPM1 0.27 0.24 0.55 113 -0.68 4 117
EGLN1 0.27 0.24 0.54 113 -0.82 2 115
CREB1 0.024 0.01 -10000 0 -10000 0 0
PGM1 0.28 0.24 0.55 114 -0.68 4 118
SMAD3 0.021 0.009 -10000 0 -10000 0 0
EDN1 -0.053 0.4 0.51 2 -0.99 56 58
IGFBP1 0.29 0.27 0.59 126 -0.68 4 130
VEGFA 0.26 0.24 0.52 121 -0.69 3 124
HIF1A/JAB1 0.082 0.069 0.23 26 -0.18 1 27
CP 0.39 0.3 0.62 193 -0.67 4 197
CXCL12 0.28 0.25 0.55 118 -0.78 4 122
COPS5 0.02 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4 0.028 0.014 -10000 0 -10000 0 0
BNIP3 0.28 0.24 0.54 116 -0.68 4 120
EGLN3 0.32 0.29 0.63 136 -0.6 4 140
CA9 0.42 0.3 0.63 216 -0.68 4 220
TERT 0.29 0.3 0.63 130 -0.68 3 133
ENO1 0.28 0.24 0.55 116 -0.68 4 120
PFKL 0.28 0.24 0.54 118 -0.68 4 122
NCOA1 0.022 0.003 -10000 0 -10000 0 0
ADM 0.28 0.25 0.55 115 -0.72 4 119
ARNT 0.092 0.09 0.24 68 -10000 0 68
HNF4A 0.067 0.14 0.33 72 -0.26 16 88
ADFP 0.26 0.25 0.5 142 -0.68 4 146
SLC2A1 0.34 0.28 0.6 169 -0.66 3 172
LEP 0.3 0.26 0.58 126 -0.68 4 130
HIF1A/ARNT/Cbp/p300 0.33 0.33 0.7 130 -0.86 3 133
EPO 0.23 0.23 0.54 80 -0.79 2 82
CREBBP 0.12 0.14 0.3 97 -0.28 9 106
HIF1A/ARNT/Cbp/p300/HDAC7 0.35 0.34 0.71 145 -0.8 3 148
PFKFB3 0.28 0.24 0.55 112 -0.68 4 116
NT5E 0.28 0.25 0.57 115 -0.68 4 119
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.09 0.19 0.32 6 -0.5 36 42
IHH -0.013 0.13 0.29 6 -0.37 35 41
SHH Np/Cholesterol/GAS1 -0.036 0.057 0.12 1 -0.18 49 50
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.036 0.057 0.18 49 -0.11 1 50
SMO/beta Arrestin2 -0.14 0.18 0.32 1 -0.33 156 157
SMO -0.14 0.19 0.34 1 -0.34 154 155
AKT1 -0.078 0.14 0.27 1 -0.49 26 27
ARRB2 0.02 0.006 -10000 0 -10000 0 0
BOC 0.02 0.018 -10000 0 -0.33 1 1
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
heart looping -0.14 0.19 0.34 1 -0.33 154 155
STIL -0.083 0.14 0.26 9 -0.31 52 61
DHH N/PTCH2 0.013 0.067 -10000 0 -0.23 27 27
DHH N/PTCH1 -0.1 0.16 -10000 0 -0.34 55 55
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
DHH -0.002 0.087 -10000 0 -0.33 26 26
PTHLH -0.12 0.23 0.39 6 -0.55 35 41
determination of left/right symmetry -0.14 0.19 0.34 1 -0.33 154 155
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
skeletal system development -0.12 0.23 0.39 6 -0.55 35 41
IHH N/Hhip -0.22 0.18 0.21 3 -0.32 288 291
DHH N/Hhip -0.12 0.14 -10000 0 -0.25 213 213
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.14 0.19 0.34 1 -0.33 154 155
pancreas development -0.17 0.17 -10000 0 -0.33 209 209
HHAT 0.018 0.026 -10000 0 -0.33 2 2
PI3K 0.03 0.009 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.012 0.055 -10000 0 -0.33 10 10
somite specification -0.14 0.19 0.34 1 -0.33 154 155
SHH Np/Cholesterol/PTCH1 -0.1 0.14 0.18 2 -0.33 55 57
SHH Np/Cholesterol/PTCH2 -0.034 0.052 0.12 1 -0.18 44 45
SHH Np/Cholesterol/Megalin -0.068 0.087 0.12 1 -0.2 115 116
SHH -0.039 0.069 0.16 1 -0.23 44 45
catabolic process -0.11 0.16 0.23 3 -0.26 184 187
SMO/Vitamin D3 -0.12 0.18 0.37 2 -0.4 53 55
SHH Np/Cholesterol/Hhip -0.11 0.1 0.12 1 -0.2 195 196
LRP2 -0.072 0.16 0.33 1 -0.33 105 106
receptor-mediated endocytosis -0.16 0.19 0.3 2 -0.41 102 104
SHH Np/Cholesterol/BOC -0.033 0.052 0.12 1 -0.18 43 44
SHH Np/Cholesterol/CDO -0.034 0.056 0.12 1 -0.18 45 46
mesenchymal cell differentiation 0.1 0.1 0.2 195 -0.11 1 196
mol:Vitamin D3 -0.091 0.15 0.36 5 -0.34 53 58
IHH N/PTCH2 -0.095 0.13 0.21 4 -0.21 210 214
CDON 0.014 0.047 -10000 0 -0.33 7 7
IHH N/PTCH1 -0.097 0.18 0.27 3 -0.26 184 187
Megalin/LRPAP1 -0.037 0.12 0.24 1 -0.23 102 103
PTCH2 0.021 0.018 -10000 0 -0.33 1 1
SHH Np/Cholesterol -0.029 0.052 -10000 0 -0.17 44 44
PTCH1 -0.11 0.16 0.23 3 -0.26 184 187
HHIP -0.17 0.17 -10000 0 -0.33 209 209
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.053 0.065 0.12 12 -0.12 185 197
BUB1B 0.077 0.078 0.15 182 -0.11 7 189
PLK1 0.032 0.041 0.095 88 -0.08 1 89
PLK1S1 0.015 0.038 0.12 2 -0.16 11 13
KIF2A 0.025 0.045 0.16 19 -10000 0 19
regulation of mitotic centrosome separation 0.033 0.041 0.094 88 -0.08 1 89
GOLGA2 0.021 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.19 0.18 0.35 195 -10000 0 195
WEE1 0.031 0.062 0.18 2 -0.26 9 11
cytokinesis 0.094 0.099 0.21 113 -0.2 2 115
PP2A-alpha B56 0.085 0.089 -10000 0 -0.48 3 3
AURKA 0.04 0.06 0.14 85 -0.19 4 89
PICH/PLK1 0.086 0.12 0.23 148 -10000 0 148
CENPE 0.037 0.056 0.13 74 -10000 0 74
RhoA/GTP 0.016 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.026 0.045 0.16 19 -10000 0 19
PPP2CA 0.021 0.005 -10000 0 -10000 0 0
FZR1 0.02 0.006 -10000 0 -10000 0 0
TPX2 0.078 0.07 0.14 218 -0.17 4 222
PAK1 0.02 0.005 -10000 0 -10000 0 0
SPC24 0.11 0.14 0.33 116 -10000 0 116
FBXW11 0.02 0.005 -10000 0 -10000 0 0
CLSPN 0.065 0.076 0.15 149 -0.19 5 154
GORASP1 0.021 0.004 -10000 0 -10000 0 0
metaphase 0 0.003 0.016 8 -0.011 1 9
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.015 0.02 0.054 37 -10000 0 37
G2 phase of mitotic cell cycle 0 0.003 0.017 6 -10000 0 6
STAG2 0.021 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.004 0.093 -10000 0 -0.51 12 12
spindle elongation 0.033 0.041 0.094 88 -0.08 1 89
ODF2 0.022 0.007 -10000 0 -10000 0 0
BUB1 0.077 0.1 -10000 0 -0.52 3 3
TPT1 0.009 0.047 0.12 1 -0.16 22 23
CDC25C 0.1 0.098 0.17 248 -0.23 13 261
CDC25B 0.023 0.012 -10000 0 -10000 0 0
SGOL1 0.053 0.065 0.12 185 -0.12 12 197
RHOA 0.021 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.081 0.092 0.22 112 -10000 0 112
CDC14B -0.009 0.003 -10000 0 -10000 0 0
CDC20 0.2 0.15 0.33 231 -10000 0 231
PLK1/PBIP1 0.012 0.045 0.15 33 -10000 0 33
mitosis -0.004 0.006 0.021 5 -0.016 57 62
FBXO5 0.015 0.042 0.12 11 -0.11 2 13
CDC2 0.004 0.005 0.012 115 -0.01 2 117
NDC80 0.16 0.16 0.33 183 -10000 0 183
metaphase plate congression 0.022 0.047 -10000 0 -0.22 10 10
ERCC6L 0.087 0.11 0.22 139 -10000 0 139
NLP/gamma Tubulin 0.017 0.024 0.075 20 -0.086 3 23
microtubule cytoskeleton organization 0.009 0.047 0.12 1 -0.16 22 23
G2/M transition DNA damage checkpoint -0.001 0.002 0.014 1 -10000 0 1
PPP1R12A 0.022 0.005 -10000 0 -10000 0 0
interphase -0.001 0.002 0.014 1 -10000 0 1
PLK1/PRC1-2 0.18 0.16 0.31 211 -10000 0 211
GRASP65/GM130/RAB1/GTP/PLK1 0.054 0.032 -10000 0 -10000 0 0
RAB1A 0.022 0.001 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.026 0.037 0.085 85 -0.066 1 86
mitotic prometaphase 0.001 0.003 0.019 10 -10000 0 10
proteasomal ubiquitin-dependent protein catabolic process 0.047 0.059 0.18 1 -0.25 3 4
microtubule-based process 0.15 0.12 0.26 215 -10000 0 215
Golgi organization 0.033 0.041 0.094 88 -0.08 1 89
Cohesin/SA2 0.039 0.032 0.12 12 -10000 0 12
PPP1CB/MYPT1 0.032 0.007 -10000 0 -10000 0 0
KIF20A 0.19 0.16 0.33 215 -10000 0 215
APC/C/CDC20 0.16 0.12 0.26 232 -10000 0 232
PPP2R1A 0.021 0.004 -10000 0 -10000 0 0
chromosome segregation 0.012 0.044 0.15 33 -10000 0 33
PRC1 0.075 0.12 0.33 68 -10000 0 68
ECT2 0.035 0.063 0.19 40 -10000 0 40
C13orf34 0.026 0.034 0.079 87 -0.067 1 88
NUDC 0.022 0.047 -10000 0 -0.22 10 10
regulation of attachment of spindle microtubules to kinetochore 0.077 0.077 0.15 182 -0.11 7 189
spindle assembly 0.024 0.033 0.094 33 -0.071 1 34
spindle stabilization 0.015 0.038 0.12 2 -0.16 11 13
APC/C/HCDH1 0.016 0.007 -10000 0 -10000 0 0
MKLP2/PLK1 0.15 0.12 0.26 215 -10000 0 215
CCNB1 0.12 0.14 0.33 121 -10000 0 121
PPP1CB 0.022 0.005 -10000 0 -10000 0 0
BTRC 0.021 0.003 -10000 0 -10000 0 0
ROCK2 0.028 0.036 0.17 2 -10000 0 2
TUBG1 0.019 0.029 0.12 4 -0.2 3 7
G2/M transition of mitotic cell cycle 0.033 0.061 0.12 104 -10000 0 104
MLF1IP 0.007 0.046 0.16 32 -10000 0 32
INCENP 0.021 0.003 -10000 0 -10000 0 0
Endothelins

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
AKT1 -0.082 0.11 0.23 1 -0.34 36 37
PTK2B 0.018 0.008 -10000 0 -10000 0 0
mol:Ca2+ -0.13 0.27 -10000 0 -0.78 47 47
EDN1 -0.074 0.13 -10000 0 -0.35 56 56
EDN3 -0.072 0.15 0.33 1 -0.33 102 103
EDN2 0.1 0.14 0.33 103 -0.33 2 105
HRAS/GDP -0.15 0.19 -10000 0 -0.42 100 100
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.072 0.13 -10000 0 -0.35 50 50
ADCY4 -0.068 0.11 0.2 3 -0.28 45 48
ADCY5 -0.08 0.13 0.22 7 -0.31 60 67
ADCY6 -0.063 0.1 0.25 4 -0.28 36 40
ADCY7 -0.064 0.1 0.24 3 -0.28 36 39
ADCY1 -0.06 0.1 0.22 3 -0.28 37 40
ADCY2 -0.06 0.11 0.25 8 -0.3 40 48
ADCY3 -0.064 0.11 0.24 5 -0.28 38 43
ADCY8 -0.098 0.12 0.38 2 -0.26 94 96
ADCY9 -0.066 0.11 0.29 3 -0.28 44 47
arachidonic acid secretion -0.13 0.2 -10000 0 -0.48 72 72
ETB receptor/Endothelin-1/Gq/GTP -0.14 0.16 -10000 0 -0.27 200 200
GNAO1 0.021 0.034 0.33 2 -0.33 2 4
HRAS 0.021 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.051 0.12 0.31 1 -0.3 34 35
ETA receptor/Endothelin-1/Gs/GTP -0.052 0.12 0.29 1 -0.29 38 39
mol:GTP -0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.049 0.16 0.29 24 -0.33 36 60
EDNRB -0.16 0.18 -10000 0 -0.33 201 201
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.087 0.13 0.23 1 -0.38 38 39
CYSLTR1 -0.09 0.13 0.23 1 -0.39 36 37
SLC9A1 -0.05 0.081 0.16 1 -0.22 40 41
mol:GDP -0.16 0.2 0.21 1 -0.44 103 104
SLC9A3 -0.3 0.34 -10000 0 -0.64 148 148
RAF1 -0.16 0.2 -10000 0 -0.48 86 86
JUN -0.11 0.21 -10000 0 -0.63 41 41
JAK2 -0.078 0.11 0.23 1 -0.33 36 37
mol:IP3 -0.12 0.17 -10000 0 -0.39 82 82
ETA receptor/Endothelin-1 -0.082 0.15 0.36 1 -0.36 44 45
PLCB1 0.018 0.02 0.33 1 -10000 0 1
PLCB2 0.009 0.051 -10000 0 -0.33 8 8
ETA receptor/Endothelin-3 -0.078 0.12 0.19 1 -0.24 108 109
FOS -0.16 0.25 -10000 0 -0.68 56 56
Gai/GDP -0.05 0.2 -10000 0 -0.8 22 22
CRK 0.019 0.007 -10000 0 -10000 0 0
mol:Ca ++ -0.16 0.19 -10000 0 -0.44 92 92
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
PRKCB1 -0.13 0.17 -10000 0 -0.36 96 96
GNAQ 0.014 0.024 -10000 0 -0.33 1 1
GNAZ -0.01 0.099 -10000 0 -0.33 34 34
GNAL 0.019 0.045 0.33 3 -0.33 4 7
Gs family/GDP -0.15 0.18 -10000 0 -0.4 100 100
ETA receptor/Endothelin-1/Gq/GTP -0.069 0.13 -10000 0 -0.32 55 55
MAPK14 -0.13 0.15 0.2 1 -0.33 104 105
TRPC6 -0.13 0.29 -10000 0 -0.83 47 47
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.018 -10000 0 -0.33 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.14 0.16 -10000 0 -0.34 111 111
ETB receptor/Endothelin-2 -0.073 0.15 0.24 36 -0.21 195 231
ETB receptor/Endothelin-3 -0.15 0.16 0.24 1 -0.28 231 232
ETB receptor/Endothelin-1 -0.15 0.16 0.21 7 -0.3 194 201
MAPK3 -0.17 0.25 -10000 0 -0.65 64 64
MAPK1 -0.18 0.25 -10000 0 -0.64 68 68
Rac1/GDP -0.14 0.18 -10000 0 -0.41 91 91
cAMP biosynthetic process -0.078 0.14 0.3 6 -0.34 49 55
MAPK8 -0.12 0.24 -10000 0 -0.66 51 51
SRC 0.021 0.005 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.13 0.14 -10000 0 -0.28 140 140
p130Cas/CRK/Src/PYK2 -0.17 0.23 0.31 1 -0.55 75 76
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.14 0.19 -10000 0 -0.41 91 91
COL1A2 -0.16 0.18 0.32 7 -0.37 121 128
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.042 0.12 0.22 95 -0.19 13 108
mol:DAG -0.12 0.17 -10000 0 -0.39 82 82
MAP2K2 -0.16 0.22 -10000 0 -0.53 78 78
MAP2K1 -0.16 0.22 -10000 0 -0.53 79 79
EDNRA -0.038 0.078 0.23 1 -0.25 13 14
positive regulation of muscle contraction -0.056 0.11 0.2 18 -0.29 34 52
Gq family/GDP -0.12 0.18 0.35 1 -0.41 75 76
HRAS/GTP -0.15 0.2 -10000 0 -0.42 98 98
PRKCH -0.12 0.16 -10000 0 -0.39 79 79
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.13 0.17 0.19 1 -0.38 83 84
PRKCB -0.13 0.17 0.19 1 -0.4 84 85
PRKCE -0.13 0.17 -10000 0 -0.38 85 85
PRKCD -0.13 0.16 -10000 0 -0.36 91 91
PRKCG -0.12 0.16 -10000 0 -0.36 88 88
regulation of vascular smooth muscle contraction -0.19 0.3 -10000 0 -0.81 56 56
PRKCQ -0.14 0.18 -10000 0 -0.41 89 89
PLA2G4A -0.14 0.22 -10000 0 -0.52 72 72
GNA14 0.007 0.058 -10000 0 -0.34 10 10
GNA15 0.015 0.016 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA11 0.015 0.016 -10000 0 -10000 0 0
Rac1/GTP -0.051 0.12 0.31 1 -0.3 34 35
MMP1 0.2 0.17 0.34 194 -0.68 2 196
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.021 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.12 0.096 0.22 184 -0.16 3 187
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.016 0.014 -10000 0 -10000 0 0
AURKB 0.17 0.16 0.33 193 -10000 0 193
AURKC 0.019 0.035 0.33 1 -0.33 3 4
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.037 0.047 0.2 18 -0.17 7 25
RGS9BP -0.028 0.12 -10000 0 -0.33 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.036 0.072 0.33 22 -10000 0 22
mol:Na + 0.1 0.11 0.24 146 -10000 0 146
mol:ADP -0.006 0.046 0.16 25 -10000 0 25
GNAT2 0.021 0.016 0.33 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.06 0.13 -10000 0 -0.22 148 148
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.016 0.21 2 -10000 0 2
GRK7 0.021 0.016 0.33 1 -10000 0 1
CNGB3 0.062 0.11 0.33 56 -10000 0 56
Cone Metarhodopsin II/X-Arrestin 0.015 0.011 0.22 1 -10000 0 1
mol:Ca2+ 0.056 0.093 0.21 82 -10000 0 82
Cone PDE6 -0.043 0.12 -10000 0 -0.2 144 144
Cone Metarhodopsin II 0.034 0.042 0.2 23 -10000 0 23
Na + (4 Units) 0.11 0.12 0.25 149 -10000 0 149
GNAT2/GDP -0.046 0.12 -10000 0 -0.19 147 147
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.014 0.027 0.17 7 -10000 0 7
Cone Transducin 0.04 0.05 0.22 18 -0.18 7 25
SLC24A2 0.044 0.086 0.33 32 -10000 0 32
GNB3/GNGT2 0.034 0.057 0.24 18 -0.23 7 25
GNB3 0.034 0.068 0.33 18 -0.33 1 19
GNAT2/GTP 0.016 0.011 0.22 1 -10000 0 1
CNGA3 0.12 0.14 0.33 125 -10000 0 125
ARR3 0.02 0.016 0.33 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.1 0.11 0.24 146 -10000 0 146
mol:Pi -0.06 0.13 -10000 0 -0.22 148 148
Cone CNG Channel 0.094 0.092 0.21 125 -10000 0 125
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.044 0.086 0.33 32 -10000 0 32
RGS9 -0.087 0.16 -10000 0 -0.33 120 120
PDE6C 0.019 0.003 -10000 0 -10000 0 0
GNGT2 0.016 0.043 -10000 0 -0.33 6 6
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.019 0.017 0.33 1 -10000 0 1
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.082 0.26 -10000 0 -0.66 57 57
MKNK1 0.021 0.003 -10000 0 -10000 0 0
MAPK14 -0.02 0.12 -10000 0 -0.29 57 57
ATF2/c-Jun -0.032 0.1 -10000 0 -0.33 17 17
MAPK11 -0.018 0.12 -10000 0 -0.31 52 52
MITF -0.042 0.14 -10000 0 -0.35 60 60
MAPKAPK5 -0.037 0.13 -10000 0 -0.35 56 56
KRT8 -0.036 0.13 0.28 2 -0.34 57 59
MAPKAPK3 0.021 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.02 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.032 0.17 -10000 0 -0.41 59 59
CEBPB -0.035 0.13 -10000 0 -0.36 51 51
SLC9A1 -0.038 0.13 -10000 0 -0.36 56 56
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.038 0.13 0.25 1 -0.34 58 59
p38alpha-beta/MNK1 -0.012 0.14 -10000 0 -0.34 56 56
JUN -0.031 0.1 -10000 0 -0.33 17 17
PPARGC1A -0.098 0.18 -10000 0 -0.33 127 127
USF1 -0.03 0.12 0.3 2 -0.35 49 51
RAB5/GDP/GDI1 -0.025 0.1 -10000 0 -0.26 57 57
NOS2 -0.078 0.25 0.33 4 -0.64 55 59
DDIT3 -0.035 0.13 0.23 1 -0.35 55 56
RAB5A 0.021 0.004 -10000 0 -10000 0 0
HSPB1 -0.036 0.11 0.26 9 -0.3 51 60
p38alpha-beta/HBP1 -0.013 0.14 -10000 0 -0.34 54 54
CREB1 -0.043 0.14 0.24 1 -0.37 59 60
RAB5/GDP 0.016 0.003 -10000 0 -10000 0 0
EIF4E -0.056 0.11 -10000 0 -0.32 49 49
RPS6KA4 -0.038 0.13 -10000 0 -0.35 58 58
PLA2G4A -0.027 0.13 0.19 50 -0.32 46 96
GDI1 -0.036 0.13 -10000 0 -0.35 55 55
TP53 -0.062 0.15 0.26 1 -0.43 53 54
RPS6KA5 -0.036 0.13 0.3 2 -0.35 56 58
ESR1 -0.042 0.15 0.28 1 -0.38 58 59
HBP1 0.021 0.005 -10000 0 -10000 0 0
MEF2C -0.037 0.13 -10000 0 -0.35 55 55
MEF2A -0.038 0.13 -10000 0 -0.35 56 56
EIF4EBP1 -0.047 0.15 0.25 1 -0.39 59 60
KRT19 -0.038 0.14 -10000 0 -0.36 56 56
ELK4 -0.034 0.13 -10000 0 -0.34 53 53
ATF6 -0.032 0.12 0.32 1 -0.35 50 51
ATF1 -0.043 0.14 0.24 2 -0.37 60 62
p38alpha-beta/MAPKAPK2 -0.013 0.14 -10000 0 -0.34 54 54
p38alpha-beta/MAPKAPK3 -0.014 0.14 -10000 0 -0.34 57 57
Osteopontin-mediated events

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
IKK alpha homodimer 0.078 0.077 0.2 64 -10000 0 64
NF kappa B1 p50/RelA/I kappa B alpha 0.087 0.095 0.3 26 -0.28 1 27
alphaV/beta3 Integrin/Osteopontin/Src 0.19 0.097 0.25 282 -10000 0 282
AP1 0.078 0.11 0.33 15 -10000 0 15
ILK 0.071 0.07 0.24 21 -10000 0 21
bone resorption 0.047 0.073 0.23 16 -10000 0 16
PTK2B 0.018 0.008 -10000 0 -10000 0 0
PYK2/p130Cas 0.14 0.12 0.29 62 -0.17 2 64
ITGAV 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.029 0.024 -10000 0 -0.23 3 3
alphaV/beta3 Integrin/Osteopontin 0.19 0.12 0.26 275 -0.2 3 278
MAP3K1 0.07 0.069 0.21 30 -0.18 3 33
JUN 0.02 0.025 -10000 0 -0.33 2 2
MAPK3 0.063 0.084 0.22 66 -10000 0 66
MAPK1 0.062 0.081 0.22 62 -10000 0 62
Rac1/GDP 0.014 0.006 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.048 0.062 0.21 21 -10000 0 21
ITGB3 0.038 0.081 0.34 21 -0.33 4 25
NFKBIA 0.058 0.086 0.23 62 -0.2 1 63
FOS -0.004 0.09 -10000 0 -0.33 28 28
CD44 0.018 0.035 -10000 0 -0.33 4 4
CHUK 0.021 0.003 -10000 0 -10000 0 0
PLAU 0.089 0.14 0.35 63 -10000 0 63
NF kappa B1 p50/RelA 0.09 0.1 0.27 66 -10000 0 66
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
RELA 0.021 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.048 0.06 0.26 21 -0.23 4 25
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.069 0.07 0.21 31 -0.18 4 35
VAV3 0.045 0.064 0.21 22 -0.29 2 24
MAP3K14 0.078 0.078 0.2 74 -0.18 3 77
ROCK2 0.022 0.002 -10000 0 -10000 0 0
SPP1 0.25 0.14 0.34 285 -10000 0 285
RAC1 0.019 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.038 0.06 0.19 17 -0.27 2 19
MMP2 0.032 0.076 0.3 6 -10000 0 6
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.021 0.017 0.33 1 -10000 0 1
LAT2 -0.073 0.13 -10000 0 -0.31 68 68
AP1 -0.082 0.2 -10000 0 -0.46 62 62
mol:PIP3 -0.077 0.18 0.28 21 -0.35 78 99
IKBKB -0.029 0.12 0.25 28 -0.23 47 75
AKT1 -0.037 0.15 0.32 39 -0.27 33 72
IKBKG -0.039 0.12 0.23 21 -0.22 54 75
MS4A2 -0.063 0.14 -10000 0 -0.32 89 89
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.02 0.007 -10000 0 -10000 0 0
MAP3K1 -0.066 0.15 0.23 9 -0.35 55 64
mol:Ca2+ -0.057 0.14 0.26 21 -0.27 77 98
LYN 0.014 0.018 -10000 0 -10000 0 0
CBLB -0.074 0.13 -10000 0 -0.3 70 70
SHC1 0.018 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK 0.02 0.06 -10000 0 -0.18 31 31
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.019 0.031 -10000 0 -0.33 3 3
PLD2 -0.044 0.15 0.3 40 -0.24 81 121
PTPN13 -0.089 0.17 -10000 0 -0.52 24 24
PTPN11 0.011 0.025 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.047 0.12 0.3 10 -0.28 33 43
SYK 0.014 0.03 -10000 0 -0.33 2 2
GRB2 0.021 0.005 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.086 0.16 -10000 0 -0.35 82 82
LAT -0.075 0.13 -10000 0 -0.31 70 70
PAK2 -0.072 0.16 0.24 8 -0.38 58 66
NFATC2 -0.032 0.086 -10000 0 -0.48 10 10
HRAS -0.074 0.17 0.25 7 -0.37 72 79
GAB2 0.017 0.035 -10000 0 -0.33 4 4
PLA2G1B -0.047 0.16 -10000 0 -0.92 12 12
Fc epsilon R1 -0.055 0.14 0.22 1 -0.26 121 122
Antigen/IgE/Fc epsilon R1 -0.047 0.13 0.21 1 -0.23 121 122
mol:GDP -0.089 0.18 -10000 0 -0.45 58 58
JUN 0.019 0.025 -10000 0 -0.33 2 2
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.02 0.007 -10000 0 -10000 0 0
FOS -0.004 0.09 -10000 0 -0.33 28 28
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.07 0.14 -10000 0 -0.31 72 72
CHUK -0.044 0.11 0.22 21 -0.22 60 81
KLRG1 -0.065 0.11 0.14 1 -0.27 66 67
VAV1 -0.069 0.13 -10000 0 -0.31 63 63
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.072 0.12 -10000 0 -0.3 67 67
negative regulation of mast cell degranulation -0.056 0.12 -10000 0 -0.32 44 44
BTK -0.097 0.2 -10000 0 -0.49 61 61
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.08 0.15 -10000 0 -0.29 112 112
GAB2/PI3K/SHP2 -0.08 0.086 -10000 0 -0.23 80 80
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.065 0.13 -10000 0 -0.27 86 86
RAF1 -0.011 0.17 -10000 0 -0.97 12 12
Fc epsilon R1/FcgammaRIIB/SHIP -0.034 0.14 0.22 1 -0.23 117 118
FCER1G 0.011 0.047 -10000 0 -0.33 6 6
FCER1A -0.066 0.15 0.33 1 -0.34 89 90
Antigen/IgE/Fc epsilon R1/Fyn -0.041 0.13 0.21 1 -0.22 119 120
MAPK3 -0.014 0.16 -10000 0 -0.89 12 12
MAPK1 -0.017 0.16 -10000 0 -0.9 12 12
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.07 0.22 -10000 0 -0.65 40 40
DUSP1 -0.007 0.094 -10000 0 -0.33 31 31
NF-kappa-B/RelA -0.032 0.064 0.14 8 -0.15 38 46
actin cytoskeleton reorganization -0.073 0.16 -10000 0 -0.53 15 15
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.063 0.15 -10000 0 -0.34 70 70
FER -0.073 0.13 -10000 0 -0.31 68 68
RELA 0.021 0.003 -10000 0 -10000 0 0
ITK -0.024 0.065 -10000 0 -0.3 15 15
SOS1 0.022 0.003 -10000 0 -10000 0 0
PLCG1 -0.088 0.18 0.26 3 -0.43 61 64
cytokine secretion -0.028 0.041 -10000 0 -0.15 3 3
SPHK1 -0.073 0.12 -10000 0 -0.3 68 68
PTK2 -0.076 0.17 -10000 0 -0.56 15 15
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.087 0.16 0.22 1 -0.36 82 83
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.075 0.18 0.27 22 -0.34 81 103
MAP2K2 -0.018 0.16 -10000 0 -0.9 12 12
MAP2K1 -0.018 0.16 -10000 0 -0.91 12 12
MAP2K7 0.02 0.006 -10000 0 -10000 0 0
KLRG1/SHP2 -0.05 0.11 0.17 1 -0.28 46 47
MAP2K4 -0.1 0.33 -10000 0 -0.91 55 55
Fc epsilon R1/FcgammaRIIB -0.041 0.14 0.22 1 -0.23 121 122
mol:Choline -0.043 0.15 0.3 40 -0.24 81 121
SHC/Grb2/SOS1 -0.043 0.13 -10000 0 -0.29 61 61
FYN 0.019 0.019 -10000 0 -0.33 1 1
DOK1 0.022 0.002 -10000 0 -10000 0 0
PXN -0.074 0.16 0.34 1 -0.52 15 16
HCLS1 -0.073 0.13 -10000 0 -0.31 68 68
PRKCB -0.058 0.15 0.24 24 -0.29 65 89
FCGR2B 0.019 0.007 -10000 0 -10000 0 0
IGHE -0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.057 0.12 -10000 0 -0.32 44 44
LCP2 0.019 0.026 -10000 0 -0.33 2 2
PLA2G4A -0.067 0.13 0.19 1 -0.3 64 65
RASA1 0.021 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.043 0.15 0.3 40 -0.24 81 121
IKK complex -0.021 0.1 0.24 25 -0.18 35 60
WIPF1 0.021 0.003 -10000 0 -10000 0 0
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.027 0.29 0.55 26 -0.63 22 48
PCK1 0.06 0.24 0.58 37 -0.67 1 38
HNF4A -0.1 0.47 0.69 44 -0.78 84 128
KCNJ11 0.012 0.3 0.59 26 -0.77 13 39
AKT1 0.037 0.19 0.41 36 -0.53 2 38
response to starvation -0.026 0.075 0.15 3 -0.21 30 33
DLK1 0.033 0.3 0.62 29 -0.66 8 37
NKX2-1 -0.052 0.34 0.58 4 -1.1 29 33
ACADM -0.03 0.29 0.54 24 -0.63 22 46
TAT 0.048 0.23 0.56 33 -10000 0 33
CEBPB 0.027 0.02 0.16 1 -10000 0 1
CEBPA 0.014 0.082 0.22 3 -0.33 19 22
TTR 0.067 0.28 0.65 40 -0.72 8 48
PKLR -0.001 0.3 0.62 28 -0.64 19 47
APOA1 -0.2 0.61 0.78 28 -1.1 103 131
CPT1C -0.027 0.3 0.55 26 -0.63 21 47
ALAS1 0.03 0.19 0.49 13 -0.56 1 14
TFRC 0.077 0.3 0.66 41 -0.88 7 48
FOXF1 -0.007 0.12 0.27 12 -0.33 42 54
NF1 0.022 0.004 -10000 0 -10000 0 0
HNF1A (dimer) 0.1 0.15 0.4 74 -0.33 1 75
CPT1A -0.025 0.29 0.55 25 -0.63 21 46
HMGCS1 0 0.3 0.61 29 -0.62 20 49
NR3C1 0.044 0.045 0.21 8 -10000 0 8
CPT1B -0.027 0.29 0.54 28 -0.63 23 51
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.04 -10000 0 -10000 0 0
GCK -0.022 0.31 0.56 31 -0.66 26 57
CREB1 0.037 0.039 0.19 6 -10000 0 6
IGFBP1 0.029 0.21 0.5 35 -0.52 1 36
PDX1 0.094 0.27 0.68 44 -0.55 1 45
UCP2 -0.026 0.3 0.55 28 -0.63 22 50
ALDOB 0.03 0.31 0.65 35 -0.72 10 45
AFP 0.083 0.11 0.34 35 -10000 0 35
BDH1 -0.028 0.29 0.56 24 -0.64 19 43
HADH 0.016 0.28 0.58 28 -0.66 8 36
F2 -0.023 0.43 0.8 38 -0.83 25 63
HNF1A 0.1 0.16 0.4 74 -0.33 1 75
G6PC 0.078 0.13 0.48 19 -10000 0 19
SLC2A2 0.078 0.29 0.66 48 -0.74 2 50
INS -0.033 0.035 -10000 0 -0.14 1 1
FOXA1 0.071 0.1 0.31 43 -0.33 1 44
FOXA3 0.15 0.19 0.42 108 -0.29 3 111
FOXA2 0.053 0.38 0.82 43 -0.74 9 52
ABCC8 -0.01 0.36 0.63 32 -0.79 37 69
ALB 0.093 0.12 0.35 46 -10000 0 46
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.006 0.051 -10000 0 -0.33 7 7
Crk/p130 Cas/Paxillin -0.06 0.089 -10000 0 -0.23 69 69
JUN -0.034 0.092 0.24 2 -0.28 7 9
HRAS 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.01 0.11 0.24 35 -0.18 68 103
RAP1A 0.021 0.004 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.015 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.009 0.12 0.24 37 -0.18 77 114
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.007 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.016 0.091 0.22 5 -0.18 89 94
RHOA 0.021 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.006 0.1 0.34 2 -0.17 74 76
GRB7 0.019 0.025 -10000 0 -0.33 2 2
RET51/GFRalpha1/GDNF 0.006 0.12 0.24 36 -0.18 77 113
MAPKKK cascade -0.048 0.091 0.18 6 -0.21 62 68
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.015 0.093 0.22 6 -0.18 90 96
lamellipodium assembly -0.037 0.09 -10000 0 -0.21 61 61
RET51/GFRalpha1/GDNF/SHC 0.01 0.11 0.24 33 -0.18 65 98
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.011 0.084 0.22 4 -0.18 73 77
RET9/GFRalpha1/GDNF/Shank3 -0.016 0.094 0.22 6 -0.18 90 96
MAPK3 -0.02 0.1 0.22 14 -0.3 1 15
DOK1 0.022 0.002 -10000 0 -10000 0 0
DOK6 -0.006 0.09 -10000 0 -0.33 28 28
PXN 0.021 0.004 -10000 0 -10000 0 0
neurite development -0.029 0.092 0.2 5 -0.24 12 17
DOK5 0.063 0.11 0.33 55 -10000 0 55
GFRA1 -0.081 0.16 0.33 1 -0.33 115 116
MAPK8 -0.04 0.089 0.16 5 -0.28 7 12
HRAS/GTP -0.006 0.12 0.35 2 -0.21 76 78
tube development -0.013 0.091 0.2 12 -0.17 83 95
MAPK1 -0.02 0.098 0.22 12 -0.3 1 13
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.032 0.084 -10000 0 -0.19 78 78
Rac1/GDP 0.014 0.006 -10000 0 -10000 0 0
SRC 0.021 0.005 -10000 0 -10000 0 0
PDLIM7 0.021 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.001 0.13 0.24 32 -0.2 83 115
SHC1 0.018 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.009 0.12 0.24 36 -0.18 86 122
RET51/GFRalpha1/GDNF/Dok5 0.024 0.13 0.25 58 -0.17 79 137
PRKCA 0.019 0.025 -10000 0 -0.33 2 2
HRAS/GDP 0.016 0.003 -10000 0 -10000 0 0
CREB1 -0.023 0.096 0.2 2 -0.23 58 60
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.027 0.083 0.18 2 -0.2 67 69
RET51/GFRalpha1/GDNF/Grb7 0.007 0.12 0.24 36 -0.18 90 126
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.062 0.11 0.33 54 -0.33 3 57
DOK4 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.034 0.092 0.23 2 -0.28 7 9
RET9/GFRalpha1/GDNF/FRS2 -0.014 0.09 0.22 6 -0.18 84 90
SHANK3 0.017 0.031 -10000 0 -0.33 3 3
RASA1 0.021 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.025 0.079 0.16 4 -0.19 65 69
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.021 0.096 0.18 9 -0.19 72 81
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.026 0.1 0.18 6 -0.2 79 85
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.012 0.091 0.19 10 -0.2 58 68
PI3K -0.05 0.14 0.27 2 -0.3 72 74
SOS1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.007 0.093 0.22 6 -0.17 83 89
GRB10 0.019 0.007 -10000 0 -10000 0 0
activation of MAPKK activity -0.022 0.087 0.17 2 -0.19 34 36
RET51/GFRalpha1/GDNF/FRS2 0.008 0.12 0.24 36 -0.18 75 111
GAB1 0.021 0.018 -10000 0 -0.33 1 1
IRS1 0.021 0.018 -10000 0 -0.33 1 1
IRS2 0.02 0.018 -10000 0 -0.33 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.015 0.095 0.19 10 -0.2 62 72
RET51/GFRalpha1/GDNF/PKC alpha 0.008 0.12 0.24 36 -0.18 74 110
GRB2 0.021 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GDNF 0.022 0.043 0.33 7 -10000 0 7
RAC1 0.019 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.008 0.12 0.24 37 -0.19 78 115
Rac1/GTP -0.034 0.11 0.22 1 -0.25 57 58
RET9/GFRalpha1/GDNF -0.025 0.094 0.21 6 -0.19 89 95
GFRalpha1/GDNF -0.032 0.11 0.24 6 -0.23 89 95
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.32 0.56 0.77 3 -1.2 74 77
STAT6 (cleaved dimer) -0.34 0.55 -10000 0 -1.2 87 87
IGHG1 -0.089 0.24 0.42 13 -0.61 13 26
IGHG3 -0.31 0.54 0.62 3 -1.1 90 93
AKT1 -0.15 0.32 0.52 2 -0.91 28 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.12 0.3 0.5 2 -0.92 27 29
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.15 0.32 0.5 4 -0.9 26 30
THY1 -0.32 0.56 0.7 3 -1.2 79 82
MYB 0.022 0.028 0.33 3 -10000 0 3
HMGA1 0.05 0.091 0.33 37 -10000 0 37
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.17 0.36 0.52 9 -0.73 61 70
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.15 0.33 0.5 4 -0.92 26 30
SP1 0.027 0.026 -10000 0 -10000 0 0
INPP5D 0.019 0.031 -10000 0 -0.33 3 3
SOCS5 0.011 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.32 0.55 0.61 2 -1.2 77 79
SOCS1 -0.2 0.36 0.52 3 -0.74 75 78
SOCS3 -0.14 0.3 0.52 2 -0.81 24 26
FCER2 -0.25 0.49 0.71 7 -1.1 62 69
PARP14 0.023 0.011 -10000 0 -10000 0 0
CCL17 -0.38 0.63 0.73 4 -1.3 94 98
GRB2 0.021 0.005 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.27 0.5 4 -0.73 27 31
T cell proliferation -0.33 0.56 0.63 2 -1.3 74 76
IL4R/JAK1 -0.33 0.56 0.64 1 -1.2 74 75
EGR2 -0.34 0.6 0.82 2 -1.3 76 78
JAK2 -0.008 0.064 0.2 1 -0.37 1 2
JAK3 0.02 0.016 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
JAK1 0.002 0.035 -10000 0 -10000 0 0
COL1A2 -0.068 0.22 0.47 2 -1.3 3 5
CCL26 -0.31 0.57 0.71 7 -1.2 73 80
IL4R -0.34 0.6 0.8 4 -1.3 74 78
PTPN6 0.016 0.031 -10000 0 -10000 0 0
IL13RA2 -0.36 0.62 0.71 3 -1.3 87 90
IL13RA1 -0.008 0.065 0.2 2 -10000 0 2
IRF4 -0.059 0.25 0.55 2 -0.93 20 22
ARG1 -0.098 0.25 0.51 4 -0.67 31 35
CBL -0.16 0.33 0.54 3 -0.7 57 60
GTF3A 0.063 0.06 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.003 0.088 0.24 9 -0.28 1 10
IRF4/BCL6 -0.062 0.22 -10000 0 -0.86 20 20
CD40LG 0.011 0.076 0.17 1 -0.33 17 18
MAPK14 -0.16 0.33 0.54 3 -0.76 43 46
mitosis -0.14 0.3 0.51 2 -0.84 28 30
STAT6 -0.37 0.69 0.84 5 -1.4 83 88
SPI1 0.004 0.08 -10000 0 -0.33 21 21
RPS6KB1 -0.14 0.29 0.49 2 -0.82 26 28
STAT6 (dimer) -0.37 0.68 0.84 5 -1.4 83 88
STAT6 (dimer)/PARP14 -0.35 0.61 0.7 2 -1.3 82 84
mast cell activation 0.005 0.017 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.18 0.36 0.49 4 -0.89 47 51
FRAP1 -0.15 0.32 0.52 2 -0.91 28 30
LTA -0.32 0.56 0.79 4 -1.2 74 78
FES 0.02 0.018 -10000 0 -0.33 1 1
T-helper 1 cell differentiation 0.36 0.65 1.4 83 -0.84 5 88
CCL11 -0.33 0.56 0.65 1 -1.2 80 81
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.33 0.5 3 -1 25 28
IL2RG 0.017 0.037 -10000 0 -0.31 4 4
IL10 -0.32 0.57 0.76 5 -1.3 74 79
IRS1 0.021 0.018 -10000 0 -0.33 1 1
IRS2 0.02 0.018 -10000 0 -0.33 1 1
IL4 -0.072 0.26 0.55 3 -1 16 19
IL5 -0.33 0.56 0.7 3 -1.2 77 80
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.27 0.5 0.71 5 -1 77 82
COL1A1 -0.023 0.29 0.59 10 -0.9 12 22
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.34 0.57 -10000 0 -1.3 73 73
IL2R gamma/JAK3 0.028 0.03 -10000 0 -0.19 4 4
TFF3 -0.32 0.6 0.75 5 -1.3 83 88
ALOX15 -0.65 0.72 0.72 2 -1.3 191 193
MYBL1 0.023 0.036 0.33 5 -10000 0 5
T-helper 2 cell differentiation -0.26 0.47 0.66 3 -0.99 76 79
SHC1 0.018 0.008 -10000 0 -10000 0 0
CEBPB 0.022 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.31 0.5 3 -0.85 25 28
mol:PI-3-4-5-P3 -0.15 0.32 0.52 2 -0.9 28 30
PI3K -0.16 0.34 0.52 2 -0.99 28 30
DOK2 -0.005 0.087 -10000 0 -0.33 26 26
ETS1 0.012 0.037 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.099 0.25 0.46 5 -0.67 25 30
ITGB3 -0.32 0.57 0.7 4 -1.3 73 77
PIGR -0.45 0.7 0.78 4 -1.4 121 125
IGHE 0.01 0.077 0.2 19 -0.2 7 26
MAPKKK cascade -0.097 0.25 0.46 5 -0.65 25 30
BCL6 0.018 0.014 -10000 0 -10000 0 0
OPRM1 -0.33 0.56 0.7 3 -1.2 79 82
RETNLB -0.32 0.56 0.72 2 -1.2 74 76
SELP -0.42 0.68 0.74 4 -1.4 108 112
AICDA -0.35 0.57 0.75 2 -1.2 90 92
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.023 0.11 0.24 26 -0.19 65 91
SMAD6-7/SMURF1 0.01 0.076 -10000 0 -0.2 43 43
NOG 0.009 0.09 0.33 8 -0.33 20 28
SMAD9 -0.11 0.22 -10000 0 -0.46 102 102
SMAD4 0.019 0.007 -10000 0 -10000 0 0
SMAD5 -0.046 0.1 -10000 0 -0.31 31 31
BMP7/USAG1 -0.12 0.14 0.24 7 -0.25 212 219
SMAD5/SKI -0.035 0.12 0.24 2 -0.31 34 36
SMAD1 -0.001 0.056 -10000 0 -0.29 6 6
BMP2 -0.022 0.12 -10000 0 -0.33 48 48
SMAD1/SMAD1/SMAD4 -0.009 0.073 -10000 0 -0.34 4 4
BMPR1A 0.021 0.003 -10000 0 -10000 0 0
BMPR1B -0.011 0.11 0.33 3 -0.33 39 42
BMPR1A-1B/BAMBI 0.023 0.083 0.23 13 -0.2 40 53
AHSG 0.041 0.079 0.33 27 -10000 0 27
CER1 0.02 0.032 0.33 4 -10000 0 4
BMP2-4/CER1 0.005 0.083 0.23 2 -0.2 51 53
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.034 0.1 -10000 0 -0.32 28 28
BMP2-4 (homodimer) -0.007 0.092 -10000 0 -0.24 52 52
RGMB 0.021 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.001 0.11 0.23 4 -0.2 82 86
RGMA 0.024 0.046 0.33 6 -0.33 2 8
SMURF1 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.029 0.086 -10000 0 -0.29 18 18
BMP2-4/USAG1 -0.12 0.14 -10000 0 -0.23 219 219
SMAD6/SMURF1/SMAD5 -0.033 0.11 0.24 2 -0.32 29 31
SOSTDC1 -0.18 0.17 -10000 0 -0.33 219 219
BMP7/BMPR2/BMPR1A-1B 0.015 0.1 0.23 14 -0.19 64 78
SKI 0.021 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) -0.028 0.13 0.33 2 -0.33 57 59
HFE2 0.025 0.041 0.33 7 -10000 0 7
ZFYVE16 0.021 0.005 -10000 0 -10000 0 0
MAP3K7 0.02 0.007 -10000 0 -10000 0 0
BMP2-4/CHRD 0.014 0.085 0.23 9 -0.19 48 57
SMAD5/SMAD5/SMAD4 -0.033 0.11 0.24 2 -0.36 21 23
MAPK1 0.021 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.015 0.089 -10000 0 -0.27 18 18
BMP7 (homodimer) 0.001 0.12 0.33 15 -0.33 35 50
NUP214 0.021 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.008 0.11 0.24 27 -0.23 52 79
SMAD1/SKI 0.009 0.06 -10000 0 -0.3 4 4
SMAD6 -0.023 0.12 -10000 0 -0.33 49 49
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.02 0.095 0.23 24 -0.2 48 72
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.23 0.14 0.33 268 -10000 0 268
BMPR2 (homodimer) 0.021 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.038 0.022 -10000 0 -0.2 2 2
BMPR1A-1B (homodimer) 0.006 0.082 0.24 3 -0.23 39 42
CHRDL1 -0.097 0.17 -10000 0 -0.33 132 132
ENDOFIN/SMAD1 0.009 0.059 -10000 0 -0.3 3 3
SMAD6-7/SMURF1/SMAD1 -0.001 0.084 -10000 0 -0.37 4 4
SMAD6/SMURF1 0.02 0.005 -10000 0 -10000 0 0
BAMBI 0.028 0.062 0.33 12 -0.33 3 15
SMURF2 0.021 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.064 0.14 -10000 0 -0.23 147 147
BMP2-4/GREM1 0.11 0.14 0.23 216 -0.16 50 266
SMAD7 0.019 0.019 -10000 0 -0.33 1 1
SMAD8A/SMAD8A/SMAD4 -0.1 0.21 -10000 0 -0.44 103 103
SMAD1/SMAD6 0.007 0.062 -10000 0 -0.28 6 6
TAK1/SMAD6 0.027 0.012 -10000 0 -10000 0 0
BMP7 0.001 0.12 0.33 15 -0.33 35 50
BMP6 -0.028 0.13 0.33 2 -0.33 57 59
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.031 0.1 -10000 0 -0.32 28 28
PPM1A 0.021 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.008 0.061 -10000 0 -0.28 5 5
SMAD7/SMURF1 0.027 0.018 -10000 0 -0.23 1 1
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
PPP1CA 0.021 0.004 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
CTDSP1 0.022 0.002 -10000 0 -10000 0 0
PPP1R15A 0.019 0.025 -10000 0 -0.33 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.032 0.1 -10000 0 -0.31 26 26
CHRD 0.03 0.059 0.33 13 -0.33 1 14
BMPR2 0.021 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.035 0.092 -10000 0 -0.32 17 17
BMP4 0.015 0.055 0.33 2 -0.33 8 10
FST 0.029 0.089 0.33 21 -0.33 9 30
BMP2-4/NOG 0.001 0.1 0.23 6 -0.22 59 65
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.023 0.097 0.23 12 -0.19 56 68
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.009 0.1 0.51 11 -10000 0 11
VDR 0.021 0.024 0.33 1 -0.33 1 2
FAM120B 0.02 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.086 0.12 -10000 0 -0.34 27 27
RXRs/LXRs/DNA/Oxysterols -0.091 0.14 -10000 0 -0.51 22 22
MED1 0.021 0.004 -10000 0 -10000 0 0
mol:9cRA -0.001 0.012 -10000 0 -0.1 2 2
RARs/THRs/DNA/Src-1 -0.009 0.067 -10000 0 -0.2 34 34
RXRs/NUR77 -0.092 0.13 -10000 0 -0.21 201 201
RXRs/PPAR -0.11 0.13 -10000 0 -0.23 187 187
NCOR2 0.021 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.016 0.22 1 -0.22 1 2
RARs/VDR/DNA/Vit D3 0.045 0.026 0.22 1 -0.17 3 4
RARA 0.021 0.004 -10000 0 -10000 0 0
NCOA1 0.022 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.024 0.33 1 -0.33 1 2
RARs/RARs/DNA/9cRA 0.032 0.024 -10000 0 -0.17 2 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RPS6KB1 0.032 0.12 0.62 14 -10000 0 14
RARs/THRs/DNA/SMRT -0.009 0.067 -10000 0 -0.19 44 44
THRA 0.021 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.016 0.016 0.22 1 -0.22 1 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.064 0.11 -10000 0 -0.18 172 172
NR1H4 0.042 0.08 0.33 28 -10000 0 28
RXRs/LXRs/DNA -0.055 0.12 -10000 0 -0.27 15 15
NR1H2 0.018 0.018 -10000 0 -10000 0 0
NR1H3 0.018 0.02 -10000 0 -0.13 1 1
RXRs/VDR/DNA/Vit D3 -0.055 0.11 -10000 0 -0.17 168 168
NR4A1 -0.047 0.14 -10000 0 -0.33 76 76
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.068 0.097 -10000 0 -0.18 158 158
RXRG -0.14 0.17 -10000 0 -0.33 174 174
RXR alpha/CCPG 0.026 0.018 -10000 0 -10000 0 0
RXRA 0.018 0.019 -10000 0 -10000 0 0
RXRB 0.018 0.017 -10000 0 -10000 0 0
THRB -0.01 0.1 -10000 0 -0.33 35 35
PPARG -0.023 0.12 -10000 0 -0.33 49 49
PPARD 0.021 0.005 -10000 0 -10000 0 0
TNF -0.11 0.21 -10000 0 -0.9 21 21
mol:Oxysterols -0.001 0.011 -10000 0 -0.087 1 1
cholesterol transport -0.09 0.14 -10000 0 -0.5 22 22
PPARA 0.02 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.025 -10000 0 -0.33 2 2
RXRs/NUR77/BCL2 -0.12 0.13 -10000 0 -0.23 199 199
SREBF1 -0.081 0.13 -10000 0 -0.51 15 15
RXRs/RXRs/DNA/9cRA -0.064 0.11 -10000 0 -0.18 172 172
ABCA1 -0.084 0.13 -10000 0 -0.5 17 17
RARs/THRs 0.038 0.071 -10000 0 -0.18 34 34
RXRs/FXR -0.053 0.12 0.23 13 -0.19 159 172
BCL2 0.02 0.017 0.33 1 -10000 0 1
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.007 0.08 0.23 1 -0.3 15 16
alphaM/beta2 Integrin/GPIbA 0.003 0.085 0.23 1 -0.29 20 21
alphaM/beta2 Integrin/proMMP-9 0.04 0.11 0.22 63 -0.27 13 76
PLAUR 0.021 0.005 -10000 0 -10000 0 0
HMGB1 0.005 0.03 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.007 0.081 -10000 0 -0.31 15 15
AGER -0.3 0.12 -10000 0 -0.34 342 342
RAP1A 0.021 0.004 -10000 0 -10000 0 0
SELPLG 0.01 0.06 -10000 0 -0.33 12 12
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.2 0.12 -10000 0 -0.24 326 326
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.072 0.12 0.33 65 -10000 0 65
CYR61 0.005 0.073 -10000 0 -0.33 18 18
TLN1 0.02 0.018 -10000 0 -0.33 1 1
Rap1/GTP -0.049 0.14 -10000 0 -0.36 39 39
RHOA 0.021 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.047 0.14 -10000 0 -0.33 74 74
MYH2 -0.1 0.16 0.22 2 -0.38 64 66
MST1R 0.021 0.024 0.33 1 -0.33 1 2
leukocyte activation during inflammatory response 0.011 0.088 0.2 18 -0.22 29 47
APOB 0.024 0.1 0.33 22 -0.33 16 38
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.022 0.016 0.33 1 -10000 0 1
JAM3 0.019 0.025 -10000 0 -0.33 2 2
GP1BA 0.015 0.046 0.33 1 -0.33 6 7
alphaM/beta2 Integrin/CTGF 0 0.087 -10000 0 -0.27 26 26
alphaM/beta2 Integrin -0.066 0.15 0.21 2 -0.38 44 46
JAM3 homodimer 0.019 0.025 -10000 0 -0.33 2 2
ICAM2 0.018 0.031 -10000 0 -0.33 3 3
ICAM1 0.016 0.04 -10000 0 -0.33 5 5
phagocytosis triggered by activation of immune response cell surface activating receptor -0.065 0.15 0.21 2 -0.38 44 46
cell adhesion 0.003 0.084 0.23 1 -0.29 20 21
NFKB1 -0.23 0.17 -10000 0 -0.48 100 100
THY1 0.03 0.054 0.33 12 -10000 0 12
RhoA/GDP 0.016 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.027 0.064 0.21 24 -0.19 16 40
alphaM/beta2 Integrin/LRP/tPA 0.035 0.1 0.23 26 -0.32 13 39
IL6 -0.24 0.25 -10000 0 -0.66 92 92
ITGB2 -0.002 0.059 -10000 0 -0.36 8 8
elevation of cytosolic calcium ion concentration 0.043 0.11 0.22 55 -0.3 13 68
alphaM/beta2 Integrin/JAM2/JAM3 -0.001 0.1 -10000 0 -0.25 39 39
JAM2 -0.009 0.097 -10000 0 -0.33 33 33
alphaM/beta2 Integrin/ICAM1 0.023 0.09 0.23 9 -0.28 17 26
alphaM/beta2 Integrin/uPA/Plg 0.047 0.11 0.23 65 -0.27 15 80
RhoA/GTP -0.078 0.16 0.23 2 -0.4 45 47
positive regulation of phagocytosis -0.051 0.13 -10000 0 -0.38 35 35
Ron/MSP 0.037 0.042 0.24 13 -0.23 2 15
alphaM/beta2 Integrin/uPAR/uPA 0.045 0.11 0.23 55 -0.3 13 68
alphaM/beta2 Integrin/uPAR 0.008 0.078 -10000 0 -0.33 13 13
PLAU 0.077 0.12 0.33 70 -10000 0 70
PLAT 0.05 0.098 0.33 41 -0.33 1 42
actin filament polymerization -0.1 0.15 0.22 2 -0.36 64 66
MST1 0.03 0.057 0.33 12 -0.33 1 13
alphaM/beta2 Integrin/lipoprotein(a) 0.014 0.092 0.21 19 -0.22 29 48
TNF -0.23 0.19 -10000 0 -0.51 93 93
RAP1B 0.02 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.04 0.11 0.22 66 -0.3 15 81
fibrinolysis 0.045 0.11 0.23 65 -0.27 15 80
HCK 0.008 0.065 -10000 0 -0.33 14 14
dendritic cell antigen processing and presentation -0.065 0.15 0.21 2 -0.38 44 46
VTN -0.031 0.14 0.33 6 -0.33 64 70
alphaM/beta2 Integrin/CYR61 -0.002 0.093 -10000 0 -0.27 30 30
LPA 0.019 0.023 0.33 2 -10000 0 2
LRP1 0.017 0.035 -10000 0 -0.33 4 4
cell migration 0.018 0.076 0.21 1 -0.25 13 14
FN1 0.018 0.035 -10000 0 -0.33 4 4
alphaM/beta2 Integrin/Thy1 0.012 0.085 0.22 11 -0.29 15 26
MPO 0.016 0.046 0.33 1 -0.33 6 7
KNG1 0.041 0.081 0.33 28 -10000 0 28
RAP1/GDP 0.027 0.009 -10000 0 -10000 0 0
ROCK1 -0.075 0.15 0.24 4 -0.38 44 48
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.024 0.047 0.33 9 -10000 0 9
CTGF 0.006 0.067 -10000 0 -0.33 15 15
alphaM/beta2 Integrin/Hck 0.002 0.093 -10000 0 -0.33 19 19
ITGAM -0.009 0.076 -10000 0 -0.35 15 15
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.026 0.12 -10000 0 -0.23 78 78
HP -0.039 0.16 0.33 16 -0.33 81 97
leukocyte adhesion -0.19 0.13 -10000 0 -0.36 103 103
SELP -0.047 0.14 -10000 0 -0.33 74 74
Visual signal transduction: Rods

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
mol:K + 0.021 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.018 0.029 0.22 8 -10000 0 8
Metarhodopsin II/Arrestin 0.026 0.011 0.21 1 -10000 0 1
PDE6G/GNAT1/GTP 0.028 0.035 0.24 7 -0.17 3 10
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.025 0.044 0.33 8 -10000 0 8
GRK1 0.036 0.072 0.33 22 -10000 0 22
CNG Channel 0.045 0.088 0.27 13 -0.18 24 37
mol:Na + 0.083 0.086 0.28 27 -0.17 3 30
mol:ADP 0.036 0.072 0.33 22 -10000 0 22
RGS9-1/Gbeta5/R9AP -0.06 0.13 -10000 0 -0.22 148 148
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.1 0.1 0.33 27 -0.18 3 30
CNGB1 0.074 0.12 0.33 68 -0.33 1 69
RDH5 0.027 0.041 0.33 7 -10000 0 7
SAG 0.02 0.016 0.33 1 -10000 0 1
mol:Ca2+ 0.017 0.094 0.29 28 -10000 0 28
Na + (4 Units) 0.025 0.084 0.13 135 -0.17 3 138
RGS9 -0.087 0.16 -10000 0 -0.33 120 120
GNB1/GNGT1 0.063 0.079 0.24 66 -10000 0 66
GNAT1/GDP -0.044 0.12 0.21 4 -0.19 145 149
GUCY2D 0.019 0.041 0.33 3 -0.33 3 6
GNGT1 0.078 0.12 0.33 74 -10000 0 74
GUCY2F 0.02 0.016 0.33 1 -10000 0 1
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.03 0.052 0.14 8 -0.18 30 38
mol:11-cis-retinal 0.027 0.041 0.33 7 -10000 0 7
mol:cGMP 0.061 0.077 0.22 63 -0.18 4 67
GNB1 0.021 0.004 -10000 0 -10000 0 0
Rhodopsin 0.033 0.028 0.24 7 -10000 0 7
SLC24A1 0.021 0.003 -10000 0 -10000 0 0
CNGA1 0.063 0.11 0.33 53 -10000 0 53
Metarhodopsin II 0.033 0.041 0.2 22 -10000 0 22
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.072 0.08 0.23 65 -0.18 4 69
RGS9BP -0.028 0.12 -10000 0 -0.33 54 54
Metarhodopsin II/Transducin 0.025 0.044 0.16 7 -0.17 3 10
GCAP Family/Ca ++ 0.066 0.072 0.22 66 -0.15 2 68
PDE6A/B 0.01 0.072 0.24 1 -0.23 31 32
mol:Pi -0.06 0.13 -10000 0 -0.22 148 148
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.067 0.073 0.22 69 -10000 0 69
PDE6B 0.017 0.035 -10000 0 -0.33 4 4
PDE6A -0.004 0.093 0.33 1 -0.33 29 30
PDE6G 0.02 0.038 0.33 2 -0.33 3 5
RHO 0.019 0.003 -10000 0 -10000 0 0
PDE6 -0.05 0.14 -10000 0 -0.21 145 145
GUCA1A 0.074 0.12 0.33 68 -10000 0 68
GC2/GCAP Family 0.078 0.074 0.23 66 -0.19 1 67
GUCA1C 0.018 0.003 -10000 0 -10000 0 0
GUCA1B 0.021 0.034 0.33 2 -0.33 2 4
Ephrin B reverse 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
EFNB2 0.018 0.031 -10000 0 -0.33 3 3
EPHB2 0.058 0.1 0.33 46 -10000 0 46
EFNB1 -0.013 0.03 0.19 5 -0.23 2 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.066 0.083 0.3 16 -0.21 4 20
Ephrin B2/EPHB1-2 0.073 0.086 0.23 77 -0.17 4 81
neuron projection morphogenesis 0.045 0.065 0.23 15 -0.2 4 19
Ephrin B1/EPHB1-2/Tiam1 0.075 0.091 0.24 73 -0.19 6 79
DNM1 0.025 0.032 0.34 4 -10000 0 4
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.062 0.16 -10000 0 -0.5 45 45
YES1 -0.073 0.24 -10000 0 -0.72 45 45
Ephrin B1/EPHB1-2/NCK2 0.08 0.087 0.24 76 -0.18 3 79
PI3K -0.029 0.17 -10000 0 -0.49 47 47
mol:GDP 0.072 0.089 0.24 73 -0.19 6 79
ITGA2B -0.011 0.11 0.33 3 -0.33 39 42
endothelial cell proliferation 0.024 0.021 -10000 0 -0.19 3 3
FYN -0.078 0.24 -10000 0 -0.73 45 45
MAP3K7 -0.061 0.17 -10000 0 -0.53 45 45
FGR -0.079 0.24 -10000 0 -0.73 45 45
TIAM1 0.016 0.04 -10000 0 -0.33 5 5
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
RGS3 0.021 0.004 -10000 0 -10000 0 0
cell adhesion -0.061 0.17 0.24 1 -0.49 45 46
LYN -0.071 0.23 -10000 0 -0.72 45 45
Ephrin B1/EPHB1-2/Src Family Kinases -0.068 0.21 -10000 0 -0.66 45 45
Ephrin B1/EPHB1-2 -0.06 0.18 -10000 0 -0.57 44 44
SRC -0.07 0.23 -10000 0 -0.72 45 45
ITGB3 0.034 0.079 0.33 21 -0.33 4 25
EPHB1 0.055 0.099 0.33 43 -0.33 1 44
EPHB4 0.021 0.005 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.024 0.021 -10000 0 -0.19 3 3
alphaIIb/beta3 Integrin 0.015 0.1 0.24 24 -0.24 42 66
BLK -0.07 0.24 -10000 0 -0.72 45 45
HCK -0.076 0.24 -10000 0 -0.73 45 45
regulation of stress fiber formation -0.077 0.085 0.18 3 -0.23 76 79
MAPK8 -0.061 0.16 0.25 1 -0.48 46 47
Ephrin B1/EPHB1-2/RGS3 0.076 0.084 0.24 72 -0.18 3 75
endothelial cell migration -0.044 0.14 0.2 12 -0.43 41 53
NCK2 0.022 0.002 -10000 0 -10000 0 0
PTPN13 -0.027 0.14 -10000 0 -0.44 42 42
regulation of focal adhesion formation -0.077 0.085 0.18 3 -0.23 76 79
chemotaxis -0.074 0.082 0.18 3 -0.23 72 75
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.057 0.075 0.27 15 -0.19 5 20
angiogenesis -0.059 0.18 -10000 0 -0.57 44 44
LCK -0.069 0.23 -10000 0 -0.72 45 45
IL23-mediated 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
CCL2 -0.1 0.45 0.72 4 -1.1 44 48
IL23A -0.088 0.48 0.71 10 -1.1 46 56
NF kappa B1 p50/RelA/I kappa B alpha -0.092 0.45 0.64 3 -1 49 52
positive regulation of T cell mediated cytotoxicity -0.12 0.52 0.78 4 -1.2 52 56
ITGA3 -0.099 0.45 0.74 4 -1.1 42 46
IL17F -0.066 0.31 0.53 7 -0.68 50 57
IL12B 0.02 0.063 0.26 5 -0.34 1 6
STAT1 (dimer) -0.12 0.49 0.67 3 -1.1 52 55
CD4 -0.1 0.46 0.71 5 -1.1 40 45
IL23 -0.08 0.46 0.7 6 -1.1 45 51
IL23R 0.006 0.18 0.5 2 -1 8 10
IL1B -0.11 0.5 0.75 5 -1.2 45 50
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.085 0.44 0.73 5 -1.1 41 46
TYK2 0.017 0.045 0.19 1 -10000 0 1
STAT4 0.022 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
IL18RAP 0.008 0.07 -10000 0 -0.33 16 16
IL12RB1 0.009 0.072 0.18 2 -0.36 9 11
PIK3CA 0.021 0.005 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.02 0.067 0.21 2 -0.26 8 10
IL23R/JAK2 0.017 0.19 0.52 1 -0.93 8 9
positive regulation of chronic inflammatory response -0.12 0.52 0.78 4 -1.2 52 56
natural killer cell activation -0.001 0.01 -10000 0 -0.045 3 3
JAK2 0.018 0.056 0.2 2 -0.33 1 3
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.014 0.022 -10000 0 -10000 0 0
RELA 0.013 0.022 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.072 0.44 0.7 6 -1 45 51
ALOX12B -0.087 0.45 0.66 8 -1.1 44 52
CXCL1 -0.11 0.47 0.8 3 -1.1 48 51
T cell proliferation -0.12 0.52 0.78 4 -1.2 52 56
NFKBIA 0.011 0.021 -10000 0 -10000 0 0
IL17A -0.018 0.27 0.45 25 -0.54 41 66
PI3K -0.11 0.47 0.64 3 -1.1 52 55
IFNG 0.01 0.048 0.14 26 -0.1 8 34
STAT3 (dimer) -0.1 0.45 0.62 2 -1 52 54
IL18R1 0.009 0.068 -10000 0 -0.33 15 15
IL23/IL23R/JAK2/TYK2/SOCS3 -0.059 0.35 0.5 13 -0.85 36 49
IL18/IL18R 0.028 0.085 -10000 0 -0.23 29 29
macrophage activation -0.003 0.025 0.052 29 -0.045 27 56
TNF -0.11 0.5 0.76 5 -1.2 45 50
STAT3/STAT4 -0.11 0.47 0.67 2 -1.1 52 54
STAT4 (dimer) -0.12 0.49 0.67 3 -1.1 52 55
IL18 0.014 0.051 -10000 0 -0.33 8 8
IL19 -0.083 0.44 0.69 6 -1.1 42 48
STAT5A (dimer) -0.12 0.49 0.67 3 -1.2 52 55
STAT1 0.022 0.002 -10000 0 -10000 0 0
SOCS3 0.019 0.025 -10000 0 -0.33 2 2
CXCL9 -0.099 0.46 0.68 8 -1.1 45 53
MPO -0.1 0.46 0.72 4 -1.1 45 49
positive regulation of humoral immune response -0.12 0.52 0.78 4 -1.2 52 56
IL23/IL23R/JAK2/TYK2 -0.13 0.56 0.78 4 -1.3 52 56
IL6 -0.19 0.58 0.73 3 -1.1 91 94
STAT5A 0.02 0.018 -10000 0 -0.33 1 1
IL2 0.014 0.029 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.01 -10000 0 -0.045 3 3
CD3E -0.1 0.45 0.72 3 -1.1 46 49
keratinocyte proliferation -0.12 0.52 0.78 4 -1.2 52 56
NOS2 -0.14 0.5 0.72 4 -1.1 63 67
p75(NTR)-mediated 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
Sortilin/TRAF6 0.029 0.02 -10000 0 -0.23 2 2
Necdin/E2F1 0.029 0.035 0.24 4 -0.23 4 8
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.048 0.072 0.23 20 -0.18 22 42
NGF (dimer)/p75(NTR)/BEX1 -0.013 0.13 0.23 28 -0.2 106 134
NT-4/5 (dimer)/p75(NTR) 0.018 0.073 0.26 7 -0.23 25 32
IKBKB 0.019 0.008 -10000 0 -10000 0 0
AKT1 -0.018 0.057 0.19 16 -0.18 14 30
IKBKG 0.021 0.004 -10000 0 -10000 0 0
BDNF -0.14 0.17 -10000 0 -0.33 179 179
MGDIs/NGR/p75(NTR)/LINGO1 0.062 0.075 0.23 52 -0.19 7 59
FURIN 0.03 0.051 0.33 11 -10000 0 11
proBDNF (dimer)/p75(NTR)/Sortilin -0.067 0.12 0.23 5 -0.2 177 182
LINGO1 0.064 0.11 0.33 54 -10000 0 54
Sortilin/TRAF6/NRIF -0.03 0.019 -10000 0 -0.18 1 1
proBDNF (dimer) -0.14 0.17 -10000 0 -0.33 179 179
NTRK1 0.009 0.063 0.33 1 -0.33 12 13
RTN4R 0.02 0.018 -10000 0 -0.33 1 1
neuron apoptosis -0.094 0.14 0.32 4 -0.38 36 40
IRAK1 0.021 0.005 -10000 0 -10000 0 0
SHC1 -0.015 0.045 0.11 21 -0.2 12 33
ARHGDIA 0.021 0.005 -10000 0 -10000 0 0
RhoA/GTP 0.016 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.047 0.031 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.049 0.068 0.23 21 -0.18 19 40
MAGEH1 0.021 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.044 0.073 0.23 20 -0.18 23 43
Mammalian IAPs/DIABLO 0.052 0.03 0.23 4 -0.18 2 6
proNGF (dimer) 0.024 0.087 0.33 17 -0.33 11 28
MAGED1 0.022 0.016 0.33 1 -10000 0 1
APP 0.02 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.003 0.077 -10000 0 -0.33 20 20
ZNF274 0.021 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.02 0.047 0.21 2 -0.17 17 19
NGF 0.024 0.087 0.33 17 -0.33 11 28
cell cycle arrest 0.002 0.072 0.23 15 -10000 0 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.007 0.058 0.18 7 -0.2 16 23
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.029 0.066 0.25 7 -0.2 25 32
NCSTN 0.019 0.007 -10000 0 -10000 0 0
mol:GTP 0.04 0.067 0.23 22 -0.2 17 39
PSENEN 0.02 0.005 -10000 0 -10000 0 0
mol:ceramide -0.016 0.054 0.2 10 -0.18 14 24
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.004 0.053 0.16 9 -0.28 3 12
p75(NTR)/beta APP 0.029 0.043 0.24 7 -0.23 6 13
BEX1 -0.056 0.17 0.33 14 -0.33 99 113
mol:GDP -0.014 0.047 0.21 1 -0.19 17 18
NGF (dimer) 0.073 0.096 0.24 79 -0.18 15 94
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.07 0.073 0.23 51 -0.17 7 58
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.03 0.055 0.2 17 -0.16 16 33
MYD88 0.021 0.004 -10000 0 -10000 0 0
CHUK 0.021 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.04 0.068 0.23 22 -0.2 17 39
RHOB 0.022 0.002 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.031 0.021 0.24 3 -10000 0 3
NT3 (dimer) 0.003 0.082 0.33 2 -0.33 21 23
TP53 -0.082 0.095 0.23 12 -0.3 4 16
PRDM4 -0.019 0.056 0.2 11 -0.18 16 27
BDNF (dimer) 0.006 0.17 0.27 88 -0.16 159 247
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
SORT1 0.019 0.025 -10000 0 -0.33 2 2
activation of caspase activity 0.043 0.069 -10000 0 -0.18 22 22
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.049 0.068 0.23 21 -0.18 19 40
RHOC 0.021 0.004 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
MAPK10 -0.072 0.13 0.3 11 -0.33 39 50
DIABLO 0.021 0.004 -10000 0 -10000 0 0
SMPD2 -0.016 0.054 0.2 10 -0.18 14 24
APH1B 0.02 0.018 -10000 0 -0.33 1 1
APH1A 0.018 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.039 0.069 0.23 21 -0.2 19 40
PSEN1 0.021 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.008 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.016 0.078 0.3 7 -0.24 26 33
MAPK8 -0.056 0.11 0.3 10 -0.28 24 34
MAPK9 -0.054 0.11 0.3 10 -0.28 21 31
APAF1 0.021 0.004 -10000 0 -10000 0 0
NTF3 0.003 0.082 0.33 2 -0.33 21 23
NTF4 0.003 0.077 -10000 0 -0.33 20 20
NDN 0.016 0.04 -10000 0 -0.33 5 5
RAC1/GDP 0.014 0.006 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.048 0.059 -10000 0 -0.17 16 16
p75 CTF/Sortilin/TRAF6/NRIF 0.049 0.024 -10000 0 -0.18 2 2
RhoA-B-C/GTP 0.039 0.067 0.22 22 -0.2 17 39
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.049 0.12 -10000 0 -0.18 173 173
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.054 0.12 0.23 5 -0.19 174 179
PRKACB 0.022 0.016 0.33 1 -10000 0 1
proBDNF (dimer)/p75 ECD -0.089 0.13 -10000 0 -0.23 178 178
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.022 0.04 0.33 4 -0.33 2 6
BIRC2 0.021 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.008 0.074 0.23 11 -0.2 13 24
BAD -0.067 0.12 0.3 13 -0.32 25 38
RIPK2 0.019 0.007 -10000 0 -10000 0 0
NGFR 0.021 0.06 0.33 7 -0.33 6 13
CYCS -0.021 0.055 0.21 10 -0.18 15 25
ADAM17 0.022 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.044 0.066 0.23 18 -0.18 17 35
BCL2L11 -0.066 0.12 0.31 11 -0.32 25 36
BDNF (dimer)/p75(NTR) -0.087 0.14 0.24 5 -0.23 178 183
PI3K 0.048 0.066 0.23 20 -0.18 17 37
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.047 0.068 0.23 21 -0.18 18 39
NDNL2 0.021 0.005 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
PRKCI 0.021 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.03 0.074 0.24 22 -0.23 17 39
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.049 0.068 0.23 21 -0.18 19 40
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.018 0.031 -10000 0 -0.33 3 3
PLG 0.024 0.047 0.33 9 -10000 0 9
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.093 0.098 0.14 2 -0.19 172 174
SQSTM1 0.021 0.005 -10000 0 -10000 0 0
NGFRAP1 0.018 0.035 -10000 0 -0.33 4 4
CASP3 -0.063 0.12 0.29 12 -0.3 26 38
E2F1 0.024 0.032 0.33 4 -10000 0 4
CASP9 0.021 0.004 -10000 0 -10000 0 0
IKK complex 0.028 0.073 0.23 3 -0.27 9 12
NGF (dimer)/TRKA 0.022 0.072 0.24 15 -0.23 20 35
MMP7 0.063 0.12 0.33 61 -0.33 6 67
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.054 0.067 -10000 0 -0.18 18 18
MMP3 0.14 0.15 0.33 152 -10000 0 152
APAF-1/Caspase 9 -0.041 0.036 -10000 0 -0.17 1 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.072 0.12 0.34 59 -0.22 2 61
NFATC2 0.009 0.14 -10000 0 -0.5 11 11
NFATC3 -0.006 0.086 -10000 0 -0.26 31 31
CD40LG -0.086 0.29 0.41 1 -0.76 50 51
ITCH -0.025 0.077 -10000 0 -0.2 63 63
CBLB -0.029 0.081 -10000 0 -0.2 71 71
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.025 0.25 0.41 19 -0.7 27 46
JUNB 0.018 0.026 -10000 0 -0.33 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.028 0.1 -10000 0 -0.24 74 74
T cell anergy -0.058 0.14 0.3 2 -0.34 69 71
TLE4 -0.007 0.1 -10000 0 -0.46 10 10
Jun/NFAT1-c-4/p21SNFT -0.031 0.29 0.52 1 -0.76 47 48
AP-1/NFAT1-c-4 -0.043 0.34 0.65 2 -0.84 48 50
IKZF1 -0.002 0.085 -10000 0 -0.39 8 8
T-helper 2 cell differentiation -0.026 0.19 -10000 0 -0.7 16 16
AP-1/NFAT1 0.018 0.13 0.34 2 -0.32 16 18
CALM1 -0.01 0.069 -10000 0 -0.15 74 74
EGR2 -0.086 0.32 -10000 0 -0.89 42 42
EGR3 -0.13 0.4 -10000 0 -1.1 49 49
NFAT1/FOXP3 0.059 0.14 0.39 17 -0.34 10 27
EGR1 -0.003 0.086 -10000 0 -0.33 25 25
JUN 0.014 0.036 -10000 0 -0.33 2 2
EGR4 0.048 0.092 0.33 37 -10000 0 37
mol:Ca2+ -0.025 0.055 -10000 0 -0.14 76 76
GBP3 -0.013 0.12 -10000 0 -0.53 16 16
FOSL1 0.034 0.075 0.33 20 -0.33 3 23
NFAT1-c-4/MAF/IRF4 -0.029 0.28 -10000 0 -0.74 46 46
DGKA -0.004 0.09 0.5 1 -0.36 10 11
CREM 0.021 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.067 0.3 -10000 0 -0.8 48 48
CTLA4 0.015 0.092 0.34 4 -0.29 7 11
NFAT1-c-4 (dimer)/EGR1 -0.059 0.3 0.46 1 -0.81 48 49
NFAT1-c-4 (dimer)/EGR4 -0.032 0.3 0.46 2 -0.77 48 50
FOS -0.009 0.094 -10000 0 -0.34 28 28
IFNG -0.025 0.21 0.36 2 -0.73 18 20
T cell activation -0.033 0.16 -10000 0 -0.62 10 10
MAF 0.02 0.018 -10000 0 -0.33 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.064 0.23 0.65 47 -10000 0 47
TNF -0.085 0.28 0.48 1 -0.76 49 50
FASLG -0.15 0.43 -10000 0 -1.2 51 51
TBX21 0.016 0.079 0.33 1 -0.32 17 18
BATF3 0.021 0.017 0.33 1 -10000 0 1
PRKCQ -0.022 0.12 -10000 0 -0.33 47 47
PTPN1 -0.004 0.089 0.34 1 -0.36 10 11
NFAT1-c-4/ICER1 -0.045 0.28 -10000 0 -0.75 48 48
GATA3 0.021 0.024 0.33 1 -0.33 1 2
T-helper 1 cell differentiation -0.023 0.2 0.35 3 -0.71 18 21
IL2RA -0.012 0.26 0.46 22 -0.66 31 53
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.005 0.087 -10000 0 -0.36 10 10
E2F1 0.026 0.032 0.33 4 -10000 0 4
PPARG -0.023 0.12 -10000 0 -0.33 49 49
SLC3A2 -0.003 0.085 -10000 0 -0.37 8 8
IRF4 0.028 0.057 0.33 11 -0.33 2 13
PTGS2 -0.089 0.29 0.46 2 -0.78 47 49
CSF2 -0.089 0.29 0.45 5 -0.77 49 54
JunB/Fra1/NFAT1-c-4 -0.03 0.29 0.5 2 -0.74 48 50
IL4 -0.027 0.19 -10000 0 -0.73 16 16
IL5 -0.083 0.28 0.41 1 -0.73 50 51
IL2 -0.034 0.16 -10000 0 -0.64 9 9
IL3 -0.026 0.13 -10000 0 -0.57 16 16
RNF128 -0.077 0.17 -10000 0 -0.43 74 74
NFATC1 -0.064 0.23 -10000 0 -0.66 47 47
CDK4 0.044 0.16 0.52 25 -10000 0 25
PTPRK -0.003 0.084 -10000 0 -0.36 9 9
IL8 -0.074 0.29 0.44 9 -0.74 49 58
POU2F1 0.02 0.007 -10000 0 -10000 0 0
Syndecan-1-mediated signaling events

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
TGFB1 0.021 0.004 -10000 0 -10000 0 0
CCL5 0.018 0.035 -10000 0 -0.33 4 4
SDCBP 0.02 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.079 0.081 0.24 29 -0.35 1 30
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 0.069 0.091 0.23 26 -0.31 4 30
Syndecan-1/Syntenin 0.069 0.091 0.23 26 -0.32 4 30
MAPK3 0.054 0.089 0.21 30 -0.29 4 34
HGF/MET 0.015 0.076 0.24 8 -0.24 27 35
TGFB1/TGF beta receptor Type II 0.021 0.004 -10000 0 -10000 0 0
BSG 0.02 0.006 -10000 0 -10000 0 0
keratinocyte migration 0.069 0.09 0.22 26 -0.31 4 30
Syndecan-1/RANTES 0.073 0.095 0.24 29 -0.29 6 35
Syndecan-1/CD147 0.081 0.093 0.24 29 -0.29 4 33
Syndecan-1/Syntenin/PIP2 0.063 0.086 0.21 25 -0.3 4 29
LAMA5 0.017 0.031 -10000 0 -0.33 3 3
positive regulation of cell-cell adhesion 0.062 0.084 0.21 25 -0.3 4 29
MMP7 0.063 0.12 0.33 61 -0.33 6 67
HGF 0.009 0.075 0.33 3 -0.33 16 19
Syndecan-1/CASK 0.057 0.086 0.19 31 -0.31 4 35
Syndecan-1/HGF/MET 0.067 0.11 0.26 13 -0.34 6 19
regulation of cell adhesion 0.045 0.082 0.19 31 -0.28 4 35
HPSE 0.023 0.022 0.33 2 -10000 0 2
positive regulation of cell migration 0.079 0.081 0.24 29 -0.35 1 30
SDC1 0.078 0.08 0.24 28 -0.35 1 29
Syndecan-1/Collagen 0.079 0.081 0.24 29 -0.35 1 30
PPIB 0.022 0.016 0.33 1 -10000 0 1
MET 0.013 0.072 0.33 5 -0.33 13 18
PRKACA 0.02 0.005 -10000 0 -10000 0 0
MMP9 0.072 0.12 0.33 65 -10000 0 65
MAPK1 0.054 0.085 0.2 30 -0.28 4 34
homophilic cell adhesion 0.074 0.093 0.24 32 -0.34 1 33
MMP1 0.22 0.15 0.33 252 -0.33 2 254
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.026 0.036 -10000 0 -0.23 7 7
alphaV beta3 Integrin 0.021 0.094 0.23 19 -0.2 48 67
PTK2 -0.039 0.13 0.34 10 -0.36 21 31
IGF1R 0.02 0.018 -10000 0 -0.33 1 1
PI4KB 0.018 0.008 -10000 0 -10000 0 0
MFGE8 0.021 0.003 -10000 0 -10000 0 0
SRC 0.021 0.005 -10000 0 -10000 0 0
CDKN1B -0.054 0.16 0.18 5 -0.41 59 64
VEGFA 0.021 0.004 -10000 0 -10000 0 0
ILK -0.056 0.16 0.18 5 -0.41 62 67
ROCK1 0.021 0.005 -10000 0 -10000 0 0
AKT1 -0.064 0.14 -10000 0 -0.38 61 61
PTK2B -0.011 0.058 0.18 22 -0.19 8 30
alphaV/beta3 Integrin/JAM-A -0.001 0.11 0.23 22 -0.19 79 101
CBL 0.021 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.056 0.063 0.23 39 -0.19 4 43
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.049 0.037 0.23 1 -0.21 6 7
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.02 0.081 0.16 1 -0.31 10 11
alphaV/beta3 Integrin/Syndecan-1 0.049 0.05 0.23 21 -0.2 4 25
PI4KA 0.021 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.019 0.092 -10000 0 -0.2 44 44
PI4 Kinase 0.026 0.013 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.18 0.11 0.24 275 -0.18 4 279
RPS6KB1 -0.046 0.071 0.31 2 -0.35 7 9
TLN1 0.02 0.018 -10000 0 -0.33 1 1
MAPK3 -0.053 0.14 0.28 1 -0.43 40 41
GPR124 0.017 0.026 -10000 0 -0.33 2 2
MAPK1 -0.052 0.14 0.28 2 -0.42 43 45
PXN 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.023 0.12 0.23 17 -0.2 118 135
cell adhesion 0.042 0.056 0.22 21 -0.21 5 26
ANGPTL3 0.036 0.07 0.33 21 -10000 0 21
VEGFR2 homodimer/VEGFA homodimer/Src 0.036 0.032 -10000 0 -0.2 6 6
IGF-1R heterotetramer 0.02 0.018 -10000 0 -0.33 1 1
Rac1/GDP 0.014 0.006 -10000 0 -10000 0 0
TGFBR2 0.016 0.043 -10000 0 -0.33 6 6
ITGB3 0.034 0.079 0.33 21 -0.33 4 25
IGF1 0.018 0.043 0.33 1 -0.33 5 6
RAC1 0.019 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.042 0.054 0.23 19 -0.23 5 24
apoptosis 0.022 0.002 -10000 0 -10000 0 0
CD47 0.02 0.018 -10000 0 -0.33 1 1
alphaV/beta3 Integrin/CD47 0.048 0.052 0.23 21 -0.2 5 26
VCL 0.021 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.033 0.079 0.24 18 -0.21 26 44
CSF1 0.02 0.018 -10000 0 -0.33 1 1
PIK3C2A -0.056 0.16 0.18 5 -0.41 62 67
PI4 Kinase/Pyk2 -0.052 0.073 0.11 17 -0.2 49 66
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.053 0.06 0.23 21 -0.2 10 31
FAK1/Vinculin -0.03 0.12 0.31 11 -0.3 18 29
alphaV beta3/Integrin/ppsTEM5 0.042 0.055 0.23 19 -0.23 5 24
RHOA 0.021 0.004 -10000 0 -10000 0 0
VTN -0.031 0.14 0.33 6 -0.33 64 70
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
FGF2 -0.021 0.11 -10000 0 -0.33 47 47
F11R -0.034 0.061 -10000 0 -0.23 33 33
alphaV/beta3 Integrin/Lactadherin 0.049 0.05 0.23 21 -0.2 4 25
alphaV/beta3 Integrin/TGFBR2 0.045 0.059 0.23 21 -0.2 10 31
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.048 0.025 -10000 0 -0.18 2 2
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.045 0.049 0.22 20 -0.21 4 24
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.018 0.035 -10000 0 -0.33 4 4
alphaV/beta3 Integrin/Pyk2 0.033 0.059 0.19 30 -0.19 10 40
SDC1 0.022 0.002 -10000 0 -10000 0 0
VAV3 -0.02 0.046 0.16 18 -0.21 4 22
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.021 0.018 -10000 0 -0.33 1 1
FAK1/Paxillin -0.031 0.11 0.3 9 -0.3 19 28
cell migration -0.032 0.1 0.26 12 -0.28 18 30
ITGAV 0.022 0.002 -10000 0 -10000 0 0
PI3K 0.006 0.1 0.28 2 -0.19 64 66
SPP1 0.25 0.14 0.33 285 -10000 0 285
KDR 0.015 0.047 -10000 0 -0.33 7 7
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.022 0.002 -10000 0 -10000 0 0
COL4A3 -0.084 0.16 -10000 0 -0.33 118 118
angiogenesis -0.049 0.16 0.28 2 -0.45 38 40
Rac1/GTP -0.019 0.043 0.16 16 -0.28 1 17
EDIL3 0 0.086 0.33 1 -0.33 24 25
cell proliferation 0.044 0.058 0.23 21 -0.2 10 31
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.04 -10000 0 -0.3 5 5
CDKN2C 0 0.033 0.34 1 -10000 0 1
CDKN2A 0.1 0.14 0.33 103 -10000 0 103
CCND2 -0.02 0.041 0.14 4 -0.14 8 12
RB1 0.02 0.048 0.19 6 -0.16 3 9
CDK4 -0.022 0.045 0.17 4 -0.12 8 12
CDK6 -0.022 0.044 0.17 3 -0.14 9 12
G1/S progression 0.008 0.091 0.18 66 -0.23 6 72
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 -0.022 0.04 -10000 0 -0.2 18 18
ADCY5 -0.036 0.065 0.091 6 -0.2 51 57
ADCY6 -0.015 0.016 -10000 0 -0.19 3 3
ADCY7 -0.015 0.016 -10000 0 -0.19 3 3
ADCY1 -0.014 0.025 0.14 3 -0.19 5 8
ADCY2 -0.019 0.05 0.12 9 -0.19 24 33
ADCY3 -0.015 0.016 -10000 0 -0.19 3 3
ADCY8 -0.073 0.087 0.091 1 -0.19 132 133
PRKCE -0.011 0.019 -10000 0 -0.22 3 3
ADCY9 -0.019 0.031 -10000 0 -0.19 12 12
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.003 0.11 0.21 43 -0.27 9 52
HIF-2-alpha transcription factor network

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
MMP14 0.018 0.074 0.43 1 -0.54 5 6
oxygen homeostasis 0.01 0.014 -10000 0 -10000 0 0
TCEB2 0.021 0.004 -10000 0 -10000 0 0
TCEB1 0.02 0.017 0.33 1 -10000 0 1
VHL/Elongin B/Elongin C/HIF2A 0.072 0.1 0.27 13 -0.26 5 18
EPO 0.1 0.16 0.4 44 -0.38 1 45
FIH (dimer) 0.026 0.022 -10000 0 -10000 0 0
APEX1 0.029 0.026 -10000 0 -10000 0 0
SERPINE1 0.11 0.17 0.41 52 -0.41 1 53
FLT1 -0.007 0.13 -10000 0 -0.56 17 17
ADORA2A 0.1 0.15 0.38 55 -0.4 1 56
germ cell development 0.11 0.17 0.41 58 -0.39 5 63
SLC11A2 0.11 0.16 0.41 42 -0.41 1 43
BHLHE40 0.12 0.16 0.4 56 -0.41 1 57
HIF1AN 0.026 0.022 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.084 0.12 0.34 28 -0.28 3 31
ETS1 0.021 0.018 -10000 0 -10000 0 0
CITED2 -0.021 0.15 -10000 0 -0.53 26 26
KDR -0.003 0.15 -10000 0 -0.68 15 15
PGK1 0.12 0.16 0.4 56 -0.41 1 57
SIRT1 0.021 0.004 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.14 0.2 0.54 37 -0.45 1 38
EPAS1 0.054 0.099 0.24 46 -0.23 7 53
SP1 0.023 0.01 -10000 0 -10000 0 0
ABCG2 0.1 0.19 0.4 51 -0.44 8 59
EFNA1 0.094 0.15 0.4 41 -0.41 1 42
FXN 0.1 0.15 0.38 46 -0.38 1 47
POU5F1 0.11 0.18 0.41 58 -0.4 5 63
neuron apoptosis -0.14 0.19 0.44 1 -0.53 37 38
EP300 0.021 0.004 -10000 0 -10000 0 0
EGLN3 0.098 0.14 0.35 93 -0.32 1 94
EGLN2 0.027 0.023 -10000 0 -10000 0 0
EGLN1 0.025 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.038 0.019 0.23 1 -10000 0 1
VHL 0.021 0.004 -10000 0 -10000 0 0
ARNT 0.025 0.027 -10000 0 -10000 0 0
SLC2A1 0.15 0.19 0.42 95 -0.4 1 96
TWIST1 0.12 0.18 0.44 66 -10000 0 66
ELK1 0.022 0.008 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.09 0.13 0.35 27 -0.29 2 29
VEGFA 0.11 0.16 0.4 54 -0.41 1 55
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.026 0.073 -10000 0 -0.24 23 23
NT3 (dimer)/TRKC -0.029 0.12 0.24 2 -0.25 82 84
NT3 (dimer)/TRKB -0.039 0.13 0.3 7 -0.21 128 135
SHC/Grb2/SOS1/GAB1/PI3K 0.007 0.027 -10000 0 -0.18 4 4
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
BDNF -0.14 0.17 -10000 0 -0.33 179 179
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
DYNLT1 0.02 0.006 -10000 0 -10000 0 0
NTRK1 0.009 0.063 0.33 1 -0.33 12 13
NTRK2 -0.084 0.16 0.33 3 -0.33 120 123
NTRK3 -0.046 0.14 -10000 0 -0.33 75 75
NT-4/5 (dimer)/TRKB -0.041 0.13 0.28 6 -0.21 132 138
neuron apoptosis 0.14 0.17 0.4 93 -10000 0 93
SHC 2-3/Grb2 -0.15 0.19 -10000 0 -0.43 93 93
SHC1 0.018 0.008 -10000 0 -10000 0 0
SHC2 -0.11 0.15 -10000 0 -0.42 53 53
SHC3 -0.16 0.22 -10000 0 -0.52 91 91
STAT3 (dimer) 0.019 0.037 -10000 0 -0.3 5 5
NT3 (dimer)/TRKA 0.022 0.075 0.28 7 -0.21 26 33
RIN/GDP -0.018 0.076 0.34 2 -0.23 9 11
GIPC1 0.02 0.005 -10000 0 -10000 0 0
KRAS 0.02 0.006 -10000 0 -10000 0 0
DNAJA3 -0.015 0.057 0.17 3 -0.21 20 23
RIN/GTP 0.013 0.011 0.22 1 -10000 0 1
CCND1 -0.023 0.065 -10000 0 -0.59 5 5
MAGED1 0.022 0.016 0.33 1 -10000 0 1
PTPN11 0.021 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.003 0.077 -10000 0 -0.33 20 20
SHC/GRB2/SOS1 0.035 0.018 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.021 0.078 0.23 12 -0.2 32 44
TRKA/NEDD4-2 0.017 0.048 0.24 1 -0.23 12 13
ELMO1 0.018 0.026 -10000 0 -0.33 2 2
RhoG/GTP/ELMO1/DOCK1 0.025 0.018 -10000 0 -0.19 2 2
NGF 0.024 0.087 0.33 17 -0.33 11 28
HRAS 0.021 0.004 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
GAB2 0.017 0.035 -10000 0 -0.33 4 4
RIT2 0.018 0.017 0.33 1 -10000 0 1
RIT1 0.018 0.008 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
DNM1 0.024 0.031 0.33 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.007 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.011 0.067 0.18 2 -0.21 21 23
mol:GDP -0.032 0.1 0.4 2 -0.31 14 16
NGF (dimer) 0.024 0.087 0.33 17 -0.33 11 28
RhoG/GDP 0.013 0.018 -10000 0 -0.22 2 2
RIT1/GDP -0.025 0.062 -10000 0 -0.23 7 7
TIAM1 0.016 0.04 -10000 0 -0.33 5 5
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.13 0.15 0.23 1 -0.24 239 240
KIDINS220/CRKL/C3G 0.03 0.008 -10000 0 -10000 0 0
SHC/RasGAP 0.026 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.039 0.015 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.044 0.026 -10000 0 -0.18 1 1
RIT1/GTP 0.014 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.003 0.082 0.33 2 -0.33 21 23
RAP1/GDP -0.022 0.061 -10000 0 -0.2 10 10
KIDINS220/CRKL 0.021 0.004 -10000 0 -10000 0 0
BDNF (dimer) -0.14 0.17 -10000 0 -0.33 179 179
ubiquitin-dependent protein catabolic process 0.026 0.065 0.23 13 -0.19 20 33
Schwann cell development -0.036 0.025 -10000 0 -10000 0 0
EHD4 0.021 0.005 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.049 0.023 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.005 0.046 -10000 0 -0.19 4 4
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.15 -10000 0 -0.25 222 222
ABL1 0.021 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.065 0.095 -10000 0 -0.42 13 13
STAT3 0.019 0.037 -10000 0 -0.3 5 5
axon guidance -0.15 0.12 -10000 0 -0.24 222 222
MAPK3 -0.016 0.077 0.18 30 -0.2 26 56
MAPK1 -0.014 0.077 0.18 32 -0.2 24 56
CDC42/GDP -0.019 0.077 0.34 2 -0.22 9 11
NTF3 0.003 0.082 0.33 2 -0.33 21 23
NTF4 0.003 0.077 -10000 0 -0.33 20 20
NGF (dimer)/TRKA/FAIM 0.032 0.065 0.23 15 -0.19 19 34
PI3K 0.03 0.009 -10000 0 -10000 0 0
FRS3 0.021 0.005 -10000 0 -10000 0 0
FAIM 0.021 0.003 -10000 0 -10000 0 0
GAB1 0.021 0.018 -10000 0 -0.33 1 1
RASGRF1 -0.06 0.088 0.15 1 -0.27 27 28
SOS1 0.021 0.003 -10000 0 -10000 0 0
MCF2L -0.056 0.086 0.17 3 -0.22 76 79
RGS19 0.02 0.006 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.083 0.27 1 -0.36 6 7
Rac1/GDP -0.022 0.069 -10000 0 -0.23 10 10
NGF (dimer)/TRKA/GRIT 0.021 0.061 0.21 15 -0.19 20 35
neuron projection morphogenesis 0.004 0.11 -10000 0 -0.88 3 3
NGF (dimer)/TRKA/NEDD4-2 0.027 0.065 0.23 13 -0.19 20 33
MAP2K1 0.014 0.092 0.19 74 -0.18 1 75
NGFR 0.021 0.06 0.33 7 -0.33 6 13
NGF (dimer)/TRKA/GIPC/GAIP -0.003 0.063 0.18 4 -0.22 17 21
RAS family/GTP/PI3K 0.005 0.03 -10000 0 -0.17 5 5
FRS2 family/SHP2/GRB2/SOS1 0.054 0.026 -10000 0 -10000 0 0
NRAS 0.021 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
PRKCI 0.021 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.018 0.031 -10000 0 -0.33 3 3
MAPKKK cascade -0.066 0.19 -10000 0 -0.56 44 44
RASA1 0.021 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.02 0.048 0.24 1 -0.23 12 13
SQSTM1 0.021 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.12 0.14 0.23 2 -0.22 239 241
NGF (dimer)/TRKA/p62/Atypical PKCs 0.04 0.068 0.23 12 -0.18 19 31
MATK 0.007 0.067 -10000 0 -0.33 15 15
NEDD4L 0.019 0.007 -10000 0 -10000 0 0
RAS family/GDP -0.03 0.045 -10000 0 -0.18 12 12
NGF (dimer)/TRKA 0 0.063 0.19 4 -0.21 20 24
Rac1/GTP -0.063 0.071 -10000 0 -0.21 47 47
FRS2 family/SHP2/CRK family 0.05 0.03 -10000 0 -10000 0 0
Arf6 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CENTA1/KIF3B 0.021 0.016 -10000 0 -0.17 1 1
ARNO/beta Arrestin1-2 -0.056 0.18 -10000 0 -0.82 16 16
EGFR 0.015 0.043 0.33 1 -0.33 5 6
EPHA2 0.015 0.047 -10000 0 -0.33 7 7
USP6 0.02 0.006 -10000 0 -10000 0 0
IQSEC1 0.02 0.018 -10000 0 -0.33 1 1
EGFR/EGFR/EGF/EGF 0.053 0.089 0.24 58 -0.24 8 66
ARRB2 0.016 0.035 0.14 27 -10000 0 27
mol:GTP 0.003 0.042 0.18 4 -0.14 9 13
ARRB1 0.018 0.031 -10000 0 -0.33 3 3
FBXO8 0.021 0.004 -10000 0 -10000 0 0
TSHR 0.053 0.095 0.33 41 -10000 0 41
EGF 0.075 0.13 0.33 72 -0.33 4 76
somatostatin receptor activity 0 0 0.001 13 -0.001 44 57
ARAP2 0.009 0.063 -10000 0 -0.33 13 13
mol:GDP -0.06 0.14 0.17 7 -0.29 72 79
mol:PI-3-4-5-P3 0 0 0.001 13 -0.001 26 39
ITGA2B -0.012 0.11 0.33 3 -0.33 39 42
ARF6 0.02 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.04 0.037 -10000 0 -0.18 6 6
ADAP1 0.018 0.019 -10000 0 -0.33 1 1
KIF13B 0.018 0.008 -10000 0 -10000 0 0
HGF/MET 0.015 0.076 0.24 8 -0.24 27 35
PXN 0.021 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.044 0.12 0.25 11 -0.28 44 55
EGFR/EGFR/EGF/EGF/ARFGEP100 0.056 0.079 0.23 52 -0.2 9 61
ADRB2 -0.11 0.17 -10000 0 -0.33 142 142
receptor agonist activity 0 0 0.001 3 0 41 44
actin filament binding 0 0 0.001 10 -0.001 45 55
SRC 0.021 0.005 -10000 0 -10000 0 0
ITGB3 0.034 0.079 0.33 21 -0.33 4 25
GNAQ 0.02 0.018 -10000 0 -0.33 1 1
EFA6/PI-4-5-P2 0 0.001 0.001 16 -0.001 27 43
ARF6/GDP -0.041 0.15 0.44 1 -0.41 40 41
ARF6/GDP/GULP/ACAP1 -0.043 0.14 -10000 0 -0.32 47 47
alphaIIb/beta3 Integrin/paxillin/GIT1 0.036 0.089 0.23 22 -0.19 42 64
ACAP1 0.019 0.019 -10000 0 -0.33 1 1
ACAP2 0.021 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.03 0.069 0.25 30 -10000 0 30
EFNA1 0.017 0.019 -10000 0 -0.33 1 1
HGF 0.009 0.075 0.33 3 -0.33 16 19
CYTH3 -0.007 0.017 0.22 2 -10000 0 2
CYTH2 -0.026 0.2 -10000 0 -0.99 16 16
NCK1 0.021 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 10 0 32 42
endosomal lumen acidification 0 0 0 34 0 23 57
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.021 0.018 -10000 0 -0.33 1 1
GNAQ/ARNO -0.012 0.19 -10000 0 -0.92 16 16
mol:Phosphatidic acid 0 0 0 3 -10000 0 3
PIP3-E 0 0 0 6 0 5 11
MET 0.012 0.072 0.33 5 -0.33 13 18
GNA14 0.012 0.055 -10000 0 -0.33 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 12 -0.001 33 45
GNA11 0.02 0.006 -10000 0 -10000 0 0
LHCGR 0.041 0.083 0.33 29 -10000 0 29
AGTR1 -0.078 0.16 -10000 0 -0.33 110 110
desensitization of G-protein coupled receptor protein signaling pathway 0.03 0.068 0.25 30 -10000 0 30
IPCEF1/ARNO 0.014 0.19 -10000 0 -0.84 16 16
alphaIIb/beta3 Integrin 0.015 0.1 0.24 24 -0.24 42 66
TCGA08_p53

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
CDKN2A 0.039 0.075 0.16 105 -10000 0 105
TP53 0.01 0.037 -10000 0 -0.12 20 20
Senescence 0.01 0.037 -10000 0 -0.12 20 20
Apoptosis 0.01 0.037 -10000 0 -0.12 20 20
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.021 0.078 0.26 18 -0.19 2 20
MDM4 0.02 0.007 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.023 0.083 0.28 1 -0.33 1 2
SMARCC2 0.021 0.01 -10000 0 -0.16 1 1
SMARCC1 0.021 0.008 -10000 0 -10000 0 0
TBX21 -0.042 0.17 0.36 3 -0.52 29 32
SUMO2 0.019 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0.023 0.002 -10000 0 -10000 0 0
FKBP4 0.02 0.005 -10000 0 -10000 0 0
FKBP5 0.021 0.005 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.039 0.11 0.27 25 -10000 0 25
PRL -0.015 0.11 0.45 2 -10000 0 2
cortisol/GR alpha (dimer)/TIF2 0.057 0.22 0.49 44 -0.36 7 51
RELA -0.032 0.1 -10000 0 -0.2 74 74
FGG 0.011 0.29 0.48 63 -0.4 62 125
GR beta/TIF2 0.032 0.11 0.28 28 -0.23 1 29
IFNG -0.033 0.25 0.44 15 -0.57 36 51
apoptosis 0.001 0.14 0.44 10 -0.48 11 21
CREB1 0.041 0.047 0.2 1 -10000 0 1
histone acetylation -0.067 0.12 -10000 0 -0.32 35 35
BGLAP -0.013 0.1 -10000 0 -0.38 4 4
GR/PKAc 0.045 0.11 0.29 20 -10000 0 20
NF kappa B1 p50/RelA -0.057 0.18 0.29 1 -0.33 93 94
SMARCD1 0.021 0.007 -10000 0 -10000 0 0
MDM2 0.031 0.086 0.21 45 -10000 0 45
GATA3 0.022 0.024 0.33 1 -0.33 1 2
AKT1 0.02 0.005 -10000 0 -10000 0 0
CSF2 -0.12 0.27 -10000 0 -0.92 33 33
GSK3B 0.019 0.014 -10000 0 -10000 0 0
NR1I3 0.017 0.14 0.45 8 -0.47 5 13
CSN2 0.043 0.18 0.38 44 -0.31 11 55
BRG1/BAF155/BAF170/BAF60A 0.049 0.03 -10000 0 -0.26 2 2
NFATC1 0.018 0.026 -10000 0 -0.33 2 2
POU2F1 0.023 0.017 -10000 0 -10000 0 0
CDKN1A -0.007 0.075 -10000 0 -1 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.006 -10000 0 -10000 0 0
SFN 0.026 0.045 0.33 7 -0.33 1 8
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.051 0.1 0.28 20 -10000 0 20
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.026 0.21 0.44 7 -0.69 27 34
JUN 0 0.18 0.32 36 -0.37 33 69
IL4 -0.029 0.12 -10000 0 -0.5 8 8
CDK5R1 0.026 0.048 0.33 9 -10000 0 9
PRKACA 0.02 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.041 0.064 0.17 3 -0.23 19 22
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.044 0.1 0.29 13 -10000 0 13
cortisol/GR alpha (monomer) 0.078 0.27 0.6 50 -0.4 12 62
NCOA2 0.018 0.026 -10000 0 -0.33 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.011 0.12 0.23 11 -0.33 22 33
AP-1/NFAT1-c-4 0.006 0.26 0.42 32 -0.45 56 88
AFP -0.003 0.17 0.44 9 -0.48 3 12
SUV420H1 0.021 0.004 -10000 0 -10000 0 0
IRF1 0.044 0.14 0.39 20 -0.33 1 21
TP53 0.021 0.048 -10000 0 -0.92 1 1
PPP5C 0.021 0.005 -10000 0 -10000 0 0
KRT17 -0.038 0.29 0.45 21 -0.66 40 61
KRT14 0.038 0.18 0.41 13 -0.42 4 17
TBP 0.021 0.007 -10000 0 -10000 0 0
CREBBP -0.016 0.071 -10000 0 -0.27 1 1
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.024 0.023 -10000 0 -10000 0 0
AP-1 0.006 0.26 0.42 32 -0.45 56 88
MAPK14 0.019 0.014 -10000 0 -10000 0 0
MAPK10 -0.02 0.11 -10000 0 -0.33 45 45
MAPK11 0.016 0.028 -10000 0 -0.33 2 2
KRT5 -0.18 0.45 0.45 14 -0.92 96 110
interleukin-1 receptor activity 0.005 0.02 -10000 0 -10000 0 0
NCOA1 0.022 0.002 -10000 0 -10000 0 0
STAT1 0.023 0.002 -10000 0 -10000 0 0
CGA 0.005 0.13 0.36 10 -0.4 4 14
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.002 0.18 0.47 28 -0.34 8 36
MAPK3 0.019 0.014 -10000 0 -10000 0 0
MAPK1 0.019 0.013 -10000 0 -10000 0 0
ICAM1 -0.098 0.22 -10000 0 -0.61 38 38
NFKB1 -0.032 0.1 -10000 0 -0.26 28 28
MAPK8 -0.009 0.16 0.3 16 -0.36 35 51
MAPK9 0.019 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0 0.15 0.44 10 -0.5 11 21
BAX -0.012 0.067 -10000 0 -0.43 1 1
POMC -0.12 0.28 0.38 1 -0.83 34 35
EP300 -0.018 0.073 -10000 0 -0.27 1 1
cortisol/GR alpha (dimer)/p53 0.062 0.22 0.52 41 -0.36 6 47
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.072 0.2 23 -10000 0 23
SGK1 -0.027 0.11 -10000 0 -1.1 1 1
IL13 -0.04 0.19 -10000 0 -0.54 23 23
IL6 -0.19 0.37 -10000 0 -0.81 92 92
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.039 0.17 -10000 0 -0.54 12 12
IL2 -0.046 0.23 0.38 6 -0.56 33 39
CDK5 0.019 0.011 -10000 0 -10000 0 0
PRKACB 0.022 0.016 0.33 1 -10000 0 1
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
IL8 -0.08 0.2 0.33 4 -0.52 37 41
CDK5R1/CDK5 0.033 0.036 0.24 9 -10000 0 9
NF kappa B1 p50/RelA/PKAc -0.02 0.15 -10000 0 -0.29 54 54
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.064 0.21 0.49 43 -0.34 6 49
SMARCA4 0.02 0.019 -10000 0 -0.33 1 1
chromatin remodeling 0.034 0.13 0.34 29 -0.34 1 30
NF kappa B1 p50/RelA/Cbp -0.062 0.17 0.37 1 -0.36 46 47
JUN (dimer) 0 0.18 0.33 33 -0.37 32 65
YWHAH 0.021 0.004 -10000 0 -10000 0 0
VIPR1 -0.27 0.35 -10000 0 -0.68 159 159
NR3C1 0.05 0.17 0.38 47 -0.26 1 48
NR4A1 -0.06 0.16 -10000 0 -0.36 85 85
TIF2/SUV420H1 0.027 0.022 -10000 0 -0.23 2 2
MAPKKK cascade 0.001 0.14 0.44 10 -0.48 11 21
cortisol/GR alpha (dimer)/Src-1 0.074 0.23 0.52 49 -0.36 7 56
PBX1 0.014 0.055 -10000 0 -0.33 9 9
POU1F1 0.022 0.026 0.43 1 -10000 0 1
SELE -0.15 0.32 0.38 1 -0.8 67 68
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.034 0.13 0.34 29 -0.34 1 30
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.064 0.21 0.49 43 -0.34 6 49
mol:cortisol 0.044 0.16 0.35 51 -0.21 12 63
MMP1 0.18 0.2 0.39 55 -0.69 6 61
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.017 0.031 -10000 0 -0.33 3 3
GNB1/GNG2 -0.045 0.066 -10000 0 -0.19 63 63
AKT1 -0.033 0.096 -10000 0 -0.27 13 13
EGF 0.075 0.13 0.33 72 -0.33 4 76
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.032 0.061 -10000 0 -0.23 15 15
mol:Ca2+ -0.053 0.13 -10000 0 -0.31 60 60
LYN -0.022 0.041 -10000 0 -0.21 3 3
RhoA/GTP -0.029 0.051 -10000 0 -0.13 51 51
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.062 0.14 -10000 0 -0.34 62 62
GNG2 0.02 0.018 -10000 0 -0.33 1 1
ARRB2 0.02 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.039 0.16 -10000 0 -0.62 26 26
G beta5/gamma2 -0.057 0.086 -10000 0 -0.25 60 60
PRKCH -0.062 0.15 -10000 0 -0.36 59 59
DNM1 0.024 0.031 0.33 4 -10000 0 4
TXA2/TP beta/beta Arrestin3 0.007 0.05 -10000 0 -0.53 3 3
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.014 0.047 -10000 0 -0.33 7 7
G12 family/GTP -0.052 0.12 -10000 0 -0.3 61 61
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
ADRBK2 0.021 0.004 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.027 0.008 -10000 0 -10000 0 0
mol:GDP 0.036 0.11 0.35 20 -10000 0 20
mol:NADP 0.024 0.052 0.33 7 -0.33 3 10
RAB11A 0.021 0.003 -10000 0 -10000 0 0
PRKG1 -0.012 0.1 -10000 0 -0.33 37 37
mol:IP3 -0.068 0.16 -10000 0 -0.39 63 63
cell morphogenesis 0.027 0.008 -10000 0 -10000 0 0
PLCB2 -0.095 0.22 -10000 0 -0.53 64 64
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.001 0.068 0.24 2 -0.2 3 5
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.026 0.051 -10000 0 -0.22 8 8
RHOA 0.021 0.004 -10000 0 -10000 0 0
PTGIR 0.016 0.04 -10000 0 -0.33 5 5
PRKCB1 -0.065 0.16 -10000 0 -0.38 63 63
GNAQ 0.02 0.018 -10000 0 -0.33 1 1
mol:L-citrulline 0.024 0.052 0.33 7 -0.33 3 10
TXA2/TXA2-R family -0.093 0.21 -10000 0 -0.52 63 63
LCK -0.023 0.048 -10000 0 -0.22 4 4
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.009 0.049 0.18 1 -0.2 9 10
TXA2-R family/G12 family/GDP/G beta/gamma 0.007 0.072 -10000 0 -0.43 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.01 0.047 -10000 0 -0.2 9 9
MAPK14 -0.039 0.1 0.26 5 -0.23 52 57
TGM2/GTP -0.077 0.17 -10000 0 -0.43 60 60
MAPK11 -0.044 0.094 -10000 0 -0.24 53 53
ARHGEF1 -0.038 0.069 -10000 0 -0.18 52 52
GNAI2 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.067 0.16 -10000 0 -0.38 62 62
RAB11/GDP 0.021 0.006 -10000 0 -10000 0 0
ICAM1 -0.048 0.12 -10000 0 -0.29 58 58
cAMP biosynthetic process -0.065 0.15 -10000 0 -0.36 59 59
Gq family/GTP/EBP50 -0.002 0.046 -10000 0 -0.2 17 17
actin cytoskeleton reorganization 0.027 0.008 -10000 0 -10000 0 0
SRC -0.023 0.043 -10000 0 -0.21 3 3
GNB5 0.021 0.004 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.01 0.077 0.2 8 -0.23 14 22
VCAM1 -0.049 0.12 -10000 0 -0.29 61 61
TP beta/Gq family/GDP/G beta5/gamma2 -0.039 0.16 -10000 0 -0.62 26 26
platelet activation -0.052 0.13 0.31 3 -0.3 55 58
PGI2/IP 0.012 0.027 -10000 0 -0.23 5 5
PRKACA 0.003 0.038 -10000 0 -0.22 10 10
Gq family/GDP/G beta5/gamma2 -0.021 0.12 -10000 0 -0.54 17 17
TXA2/TP beta/beta Arrestin2 -0.005 0.061 0.17 3 -0.36 6 9
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.014 0.035 -10000 0 -0.21 10 10
mol:DAG -0.074 0.18 -10000 0 -0.43 62 62
EGFR 0.015 0.043 0.33 1 -0.33 5 6
TXA2/TP alpha -0.089 0.2 -10000 0 -0.49 61 61
Gq family/GTP -0.017 0.073 0.22 1 -0.23 34 35
YES1 -0.021 0.045 -10000 0 -0.2 3 3
GNAI2/GTP -0.025 0.036 -10000 0 -0.19 9 9
PGD2/DP 0.011 0.032 -10000 0 -0.22 7 7
SLC9A3R1 0.022 0.016 0.33 1 -10000 0 1
FYN -0.021 0.043 -10000 0 -0.2 3 3
mol:NO 0.024 0.052 0.33 7 -0.33 3 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
PGK/cGMP 0.01 0.071 0.21 7 -0.2 36 43
RhoA/GDP 0.021 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.019 0.053 -10000 0 -0.21 11 11
NOS3 0.024 0.052 0.33 7 -0.33 3 10
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.061 0.15 0.28 1 -0.36 58 59
PRKCB -0.063 0.15 -10000 0 -0.37 61 61
PRKCE -0.062 0.15 0.29 1 -0.36 60 61
PRKCD -0.067 0.15 -10000 0 -0.38 61 61
PRKCG -0.066 0.16 -10000 0 -0.39 63 63
muscle contraction -0.089 0.2 -10000 0 -0.49 63 63
PRKCZ -0.062 0.14 -10000 0 -0.34 62 62
ARR3 0.02 0.016 0.33 1 -10000 0 1
TXA2/TP beta 0.008 0.05 -10000 0 -0.2 9 9
PRKCQ -0.073 0.15 -10000 0 -0.38 66 66
MAPKKK cascade -0.084 0.19 -10000 0 -0.46 63 63
SELE -0.06 0.14 -10000 0 -0.36 61 61
TP beta/GNAI2/GDP/G beta/gamma 0.021 0.051 -10000 0 -0.2 10 10
ROCK1 0.021 0.005 -10000 0 -10000 0 0
GNA14 0.012 0.055 -10000 0 -0.33 10 10
chemotaxis -0.1 0.23 -10000 0 -0.59 61 61
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.014 0.005 -10000 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.006 0.058 -10000 0 -10000 0 0
BIRC5 0.19 0.16 0.33 216 -10000 0 216
NFKBIA 0.001 0.077 0.28 21 -10000 0 21
CPEB1 -0.026 0.12 0.33 2 -0.33 54 56
AKT1 -0.014 0.046 0.27 2 -10000 0 2
NDEL1 0.02 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.005 0.052 -10000 0 -10000 0 0
NDEL1/TACC3 0 0.056 -10000 0 -10000 0 0
GADD45A 0.021 0.004 -10000 0 -10000 0 0
GSK3B -0.017 0.032 -10000 0 -10000 0 0
PAK1/Aurora A -0.007 0.057 -10000 0 -0.16 2 2
MDM2 0.02 0.006 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.087 0.097 0.17 220 -10000 0 220
TP53 -0.003 0.058 0.22 1 -0.22 17 18
DLG7 -0.01 0.037 0.16 1 -10000 0 1
AURKAIP1 0.021 0.004 -10000 0 -10000 0 0
ARHGEF7 0.02 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.001 0.059 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.052 -10000 0 -10000 0 0
AURKA -0.003 0.057 0.2 1 -10000 0 1
AURKB 0.1 0.09 0.19 192 -10000 0 192
CDC25B -0.002 0.042 -10000 0 -0.23 2 2
G2/M transition checkpoint -0.013 0.04 -10000 0 -0.13 5 5
mRNA polyadenylation -0.029 0.082 0.36 1 -0.2 42 43
Aurora A/CPEB -0.029 0.082 0.36 1 -0.2 42 43
Aurora A/TACC1/TRAP/chTOG 0.002 0.068 -10000 0 -0.22 5 5
BRCA1 0.021 0.003 -10000 0 -10000 0 0
centrosome duplication -0.006 0.057 -10000 0 -0.16 2 2
regulation of centrosome cycle 0 0.055 -10000 0 -10000 0 0
spindle assembly 0.001 0.067 -10000 0 -0.22 5 5
TDRD7 0.021 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.11 0.1 0.25 83 -10000 0 83
CENPA 0.11 0.093 0.2 203 -10000 0 203
Aurora A/PP2A -0.006 0.057 -10000 0 -10000 0 0
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.006 0.05 0.17 5 -0.18 2 7
negative regulation of DNA binding -0.003 0.058 0.22 1 -0.22 17 18
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.03 0.009 -10000 0 -10000 0 0
RASA1 0.021 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A -0.013 0.04 -10000 0 -0.13 5 5
mitotic prometaphase -0.014 0.032 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.057 0.2 1 -10000 0 1
TACC1 0.009 0.058 -10000 0 -0.33 11 11
TACC3 0.021 0.004 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.003 0.059 -10000 0 -10000 0 0
Aurora A/RasGAP -0.005 0.056 -10000 0 -10000 0 0
OAZ1 0.02 0.006 -10000 0 -10000 0 0
RAN 0.023 0.022 0.33 2 -10000 0 2
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.017 0.031 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.039 0.015 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.087 0.096 0.17 220 -10000 0 220
PPP2R5D 0.021 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.054 0.084 0.18 84 -10000 0 84
PAK1 0.021 0.005 -10000 0 -10000 0 0
CKAP5 0.021 0.003 -10000 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 0.035 0.032 0.24 9 -10000 0 9
VLDLR 0.013 0.047 -10000 0 -0.33 7 7
CRKL 0.021 0.004 -10000 0 -10000 0 0
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
FYN 0.019 0.019 -10000 0 -0.33 1 1
ITGA3 0.018 0.031 -10000 0 -0.33 3 3
RELN/VLDLR/Fyn 0.007 0.085 0.23 5 -0.2 49 54
MAPK8IP1/MKK7/MAP3K11/JNK1 0.048 0.031 -10000 0 -0.18 1 1
AKT1 -0.033 0.073 0.2 3 -0.21 47 50
MAP2K7 0.02 0.006 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
DAB1 0.024 0.035 0.33 5 -10000 0 5
RELN/LRP8/DAB1 0.021 0.081 0.23 16 -0.18 44 60
LRPAP1/LRP8 0.035 0.028 0.24 7 -10000 0 7
RELN/LRP8/DAB1/Fyn 0.025 0.081 0.23 15 -0.17 45 60
DAB1/alpha3/beta1 Integrin 0.016 0.078 0.27 1 -0.18 43 44
long-term memory 0.012 0.1 0.26 13 -0.18 65 78
DAB1/LIS1 0.024 0.086 0.36 1 -0.18 44 45
DAB1/CRLK/C3G 0.016 0.078 0.27 1 -0.18 41 42
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
DAB1/NCK2 0.029 0.086 0.36 1 -0.18 44 45
ARHGEF2 0.018 0.008 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.01 0.14 0.33 32 -0.33 40 72
CDK5R1 0.028 0.047 0.33 9 -10000 0 9
RELN -0.015 0.12 0.33 5 -0.33 44 49
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.015 0.085 0.23 12 -0.2 45 57
GRIN2A/RELN/LRP8/DAB1/Fyn 0.023 0.12 0.24 34 -0.19 67 101
MAPK8 0.021 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.013 0.081 0.24 9 -0.18 47 56
ITGB1 0.021 0.004 -10000 0 -10000 0 0
MAP1B -0.028 0.076 0.17 20 -0.2 43 63
RELN/LRP8 0.018 0.084 0.23 11 -0.2 44 55
GRIN2B/RELN/LRP8/DAB1/Fyn 0.033 0.092 0.26 19 -0.18 43 62
PI3K 0.03 0.009 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.024 -10000 0 -0.23 3 3
RAP1A -0.033 0.075 0.25 4 -0.3 2 6
PAFAH1B1 0.02 0.007 -10000 0 -10000 0 0
MAPK8IP1 0.021 0.003 -10000 0 -10000 0 0
CRLK/C3G 0.03 0.008 -10000 0 -10000 0 0
GRIN2B 0.025 0.047 0.33 9 -10000 0 9
NCK2 0.022 0.002 -10000 0 -10000 0 0
neuron differentiation -0.008 0.077 0.24 2 -0.32 8 10
neuron adhesion -0.034 0.085 0.29 9 -0.3 2 11
LRP8 0.028 0.044 0.33 8 -10000 0 8
GSK3B -0.036 0.07 0.18 3 -0.2 44 47
RELN/VLDLR/DAB1/Fyn 0.017 0.081 0.24 8 -0.17 48 56
MAP3K11 0.02 0.018 -10000 0 -0.33 1 1
RELN/VLDLR/DAB1/P13K -0.021 0.082 0.19 3 -0.21 48 51
CDK5 0.021 0.005 -10000 0 -10000 0 0
MAPT -0.005 0.12 0.77 7 -0.29 19 26
neuron migration -0.039 0.098 0.24 8 -0.27 40 48
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.008 0.078 0.24 2 -0.32 8 10
RELN/VLDLR 0.022 0.088 0.23 11 -0.19 48 59
Canonical Wnt signaling pathway

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
HDAC1 0.024 0.017 0.19 1 -10000 0 1
AES 0.022 0.014 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.029 0.011 -10000 0 -10000 0 0
SMAD4 0.019 0.007 -10000 0 -10000 0 0
DKK2 -0.039 0.13 -10000 0 -0.33 67 67
TLE1 0.023 0.014 0.17 1 -10000 0 1
MACF1 0.018 0.035 -10000 0 -0.33 4 4
CTNNB1 0.08 0.1 0.28 22 -0.31 4 26
WIF1 -0.21 0.16 -10000 0 -0.33 253 253
beta catenin/RanBP3 0.052 0.1 0.44 15 -0.36 1 16
KREMEN2 0.095 0.13 0.33 93 -10000 0 93
DKK1 0.038 0.16 0.33 61 -0.33 35 96
beta catenin/beta TrCP1 0.081 0.097 0.3 15 -0.34 2 17
FZD1 0.021 0.005 -10000 0 -10000 0 0
AXIN2 -0.029 0.25 0.57 14 -1.2 14 28
AXIN1 0.022 0.004 -10000 0 -10000 0 0
RAN 0.023 0.022 0.33 2 -10000 0 2
Axin1/APC/GSK3/beta catenin 0.029 0.087 -10000 0 -0.65 5 5
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.014 0.18 0.28 1 -0.59 22 23
Axin1/APC/GSK3 0.051 0.073 0.23 18 -0.37 2 20
Axin1/APC/GSK3/beta catenin/Macf1 0.034 0.079 0.26 9 -0.36 4 13
HNF1A 0.076 0.12 0.33 69 -0.33 1 70
CTBP1 0.023 0.015 0.18 1 -10000 0 1
MYC 0.081 0.25 0.56 67 -1.3 2 69
RANBP3 0.02 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.034 0.11 0.23 59 -0.2 37 96
NKD1 -0.016 0.12 0.33 4 -0.33 44 48
TCF4 0.019 0.029 -10000 0 -0.33 2 2
TCF3 0.022 0.016 0.18 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.051 0.03 0.23 4 -10000 0 4
Ran/GTP 0.017 0.015 0.22 2 -10000 0 2
CtBP/CBP/TCF/TLE1/AES 0.006 0.12 0.42 14 -0.46 6 20
LEF1 0.025 0.027 0.28 3 -10000 0 3
DVL1 0.035 0.054 -10000 0 -0.41 2 2
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.019 0.18 -10000 0 -0.62 19 19
DKK1/LRP6/Kremen 2 0.082 0.13 0.26 111 -0.2 23 134
LRP6 0.021 0.006 -10000 0 -10000 0 0
CSNK1A1 0.024 0.016 -10000 0 -10000 0 0
NLK 0.019 0.011 -10000 0 -10000 0 0
CCND1 -0.002 0.19 0.58 16 -1.3 5 21
WNT1 0.026 0.038 0.33 6 -10000 0 6
GSK3A 0.021 0.005 -10000 0 -10000 0 0
GSK3B 0.022 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.004 -10000 0 -10000 0 0
PPP2R5D 0.046 0.079 0.24 34 -0.26 2 36
APC -0.004 0.061 0.18 37 -10000 0 37
WNT1/LRP6/FZD1 0.092 0.088 0.22 26 -0.19 2 28
CREBBP 0.023 0.016 0.18 1 -10000 0 1
EGFR-dependent Endothelin signaling events

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
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.043 0.33 1 -0.33 5 6
EGF/EGFR 0.027 0.089 0.18 46 -0.17 41 87
EGF/EGFR dimer/SHC/GRB2/SOS1 0.061 0.076 0.23 44 -0.2 6 50
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.021 0.018 -10000 0 -0.33 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.075 0.13 0.33 72 -0.33 4 76
EGF/EGFR dimer/SHC 0.05 0.077 0.23 46 -0.21 7 53
mol:GDP 0.056 0.071 0.21 44 -0.2 6 50
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.024 0.12 -10000 0 -0.33 50 50
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.035 0.05 0.23 1 -0.18 6 7
SHC1 0.018 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.05 0.063 0.29 1 -0.2 5 6
FRAP1 -0.014 0.036 0.17 4 -0.19 6 10
EGF/EGFR dimer 0.053 0.089 0.24 58 -0.24 8 66
SOS1 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.003 0.088 -10000 0 -0.23 51 51
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.005 0.1 -10000 0 -0.42 18 18
HDAC1 0.021 0.006 -10000 0 -10000 0 0
AES 0.02 0.006 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
DTX1 0.023 0.022 0.33 2 -10000 0 2
LRP6/FZD1 0.029 0.011 -10000 0 -10000 0 0
TLE1 0.021 0.005 -10000 0 -10000 0 0
AP1 -0.026 0.09 -10000 0 -0.23 53 53
NCSTN 0.019 0.007 -10000 0 -10000 0 0
ADAM10 0.021 0.004 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.021 0.096 -10000 0 -0.69 5 5
NICD/RBPSUH 0.015 0.11 -10000 0 -0.42 18 18
WIF1 -0.21 0.17 -10000 0 -0.33 253 253
NOTCH1 -0.004 0.091 -10000 0 -0.44 16 16
PSENEN 0.02 0.005 -10000 0 -10000 0 0
KREMEN2 0.095 0.13 0.33 93 -10000 0 93
DKK1 0.038 0.16 0.33 61 -0.33 35 96
beta catenin/beta TrCP1 0.014 0.073 0.3 1 -0.31 1 2
APH1B 0.02 0.018 -10000 0 -0.33 1 1
APH1A 0.018 0.008 -10000 0 -10000 0 0
AXIN1 0.002 0.07 -10000 0 -0.42 5 5
CtBP/CBP/TCF1/TLE1/AES 0.02 0.056 0.2 6 -10000 0 6
PSEN1 0.021 0.004 -10000 0 -10000 0 0
FOS -0.004 0.09 -10000 0 -0.33 28 28
JUN 0.019 0.025 -10000 0 -0.33 2 2
MAP3K7 0.019 0.007 -10000 0 -10000 0 0
CTNNB1 0.01 0.073 0.27 2 -0.29 2 4
MAPK3 0.021 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.033 0.11 0.23 59 -0.2 37 96
HNF1A 0.074 0.12 0.33 68 -0.33 1 69
CTBP1 0.021 0.005 -10000 0 -10000 0 0
MYC 0.007 0.087 -10000 0 -1.2 2 2
NKD1 -0.016 0.12 0.33 4 -0.33 44 48
FZD1 0.021 0.005 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.017 0.11 -10000 0 -0.42 18 18
apoptosis -0.026 0.089 -10000 0 -0.23 53 53
Delta 1/NOTCHprecursor 0.012 0.11 -10000 0 -0.42 18 18
DLL1 0.014 0.043 -10000 0 -0.33 6 6
PPARD 0.013 0.061 -10000 0 -0.8 2 2
Gamma Secretase 0.047 0.031 -10000 0 -10000 0 0
APC -0.009 0.096 -10000 0 -0.44 11 11
DVL1 -0.031 0.063 -10000 0 -0.26 24 24
CSNK2A1 0.02 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.082 0.13 0.26 111 -0.2 23 134
LRP6 0.02 0.006 -10000 0 -10000 0 0
CSNK1A1 0.021 0.006 -10000 0 -10000 0 0
NLK 0.006 0.005 -10000 0 -10000 0 0
CCND1 -0.001 0.15 -10000 0 -1.1 7 7
WNT1 0.026 0.038 0.33 6 -10000 0 6
Axin1/APC/beta catenin 0.006 0.1 0.32 5 -0.43 7 12
DKK2 -0.039 0.13 -10000 0 -0.33 67 67
NOTCH1 precursor/DVL1 -0.031 0.11 -10000 0 -0.43 19 19
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.009 0.1 -10000 0 -0.42 18 18
PPP2R5D 0.01 0.076 0.24 2 -0.32 7 9
MAPK1 0.021 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.091 0.11 0.23 2 -0.18 231 233
RBPJ 0.021 0.004 -10000 0 -10000 0 0
CREBBP 0.021 0.005 -10000 0 -10000 0 0
IL6-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
BCL2L1 0.014 0.28 0.57 19 -0.68 6 25
CRP 0.032 0.3 0.58 30 -0.73 6 36
cell cycle arrest 0.003 0.31 0.55 25 -0.63 23 48
TIMP1 0.018 0.27 0.54 21 -0.64 11 32
IL6ST 0.008 0.062 0.14 1 -0.32 10 11
Rac1/GDP 0 0.14 0.32 15 -0.31 24 39
AP1 0.053 0.13 0.38 7 -0.45 7 14
GAB2 0.019 0.036 -10000 0 -0.33 4 4
TNFSF11 0.038 0.3 0.59 28 -0.71 6 34
HSP90B1 0.018 0.16 0.46 1 -0.7 12 13
GAB1 0.022 0.018 -10000 0 -0.33 1 1
MAPK14 -0.022 0.1 0.28 3 -0.48 5 8
AKT1 0.011 0.091 0.26 5 -0.57 5 10
FOXO1 0.01 0.089 0.32 2 -0.54 5 7
MAP2K6 -0.015 0.11 0.29 9 -0.36 8 17
mol:GTP 0 0.004 -10000 0 -10000 0 0
MAP2K4 0.002 0.17 0.36 22 -0.37 24 46
MITF -0.002 0.13 0.26 23 -0.29 28 51
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.02 0.005 -10000 0 -10000 0 0
A2M -0.12 0.38 -10000 0 -1.2 45 45
CEBPB 0.025 0.01 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.017 0.094 0.28 4 -0.38 7 11
STAT3 -0.002 0.31 0.55 25 -0.67 23 48
STAT1 0.023 0.037 -10000 0 -10000 0 0
CEBPD 0.02 0.3 0.58 22 -0.84 6 28
PIK3CA 0.021 0.005 -10000 0 -10000 0 0
PI3K 0.03 0.01 -10000 0 -10000 0 0
JUN 0.02 0.025 -10000 0 -0.33 2 2
PIAS3/MITF 0.002 0.13 0.28 15 -0.28 27 42
MAPK11 -0.021 0.098 0.29 2 -0.48 5 7
STAT3 (dimer)/FOXO1 -0.017 0.26 0.48 23 -0.69 10 33
GRB2/SOS1/GAB family 0.008 0.12 0.27 3 -0.31 11 14
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.017 0.11 0.24 4 -0.28 34 38
GRB2 0.022 0.006 -10000 0 -10000 0 0
JAK2 0.018 0.019 -10000 0 -0.33 1 1
LBP 0.053 0.28 0.54 42 -0.6 10 52
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
JAK1 0.013 0.026 -10000 0 -10000 0 0
MYC 0.035 0.29 0.59 24 -0.82 5 29
FGG -0.15 0.51 0.57 27 -0.89 116 143
macrophage differentiation 0.003 0.31 0.55 25 -0.63 23 48
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.003 0.096 0.26 1 -0.22 27 28
JUNB 0.004 0.27 0.54 16 -0.71 7 23
FOS -0.004 0.09 -10000 0 -0.33 28 28
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.003 0.13 0.29 21 -0.3 29 50
STAT1/PIAS1 0.014 0.16 0.33 24 -0.31 22 46
GRB2/SOS1/GAB family/SHP2/PI3K 0.014 0.09 -10000 0 -0.51 7 7
STAT3 (dimer) 0 0.31 0.55 25 -0.66 23 48
PRKCD 0.023 0.23 0.42 42 -0.44 23 65
IL6R 0.003 0.053 -10000 0 -0.32 8 8
SOCS3 -0.018 0.12 -10000 0 -1.1 2 2
gp130 (dimer)/JAK1/JAK1/LMO4 0.032 0.069 0.25 2 -0.19 7 9
Rac1/GTP -0.001 0.15 0.32 20 -0.33 26 46
HCK 0.009 0.064 -10000 0 -0.32 14 14
MAPKKK cascade 0.032 0.12 0.34 1 -0.51 8 9
bone resorption 0.041 0.3 0.57 30 -0.67 6 36
IRF1 0.007 0.28 0.56 17 -0.72 6 23
mol:GDP 0.002 0.13 0.28 23 -0.3 21 44
SOS1 0.024 0.007 -10000 0 -10000 0 0
VAV1 0.002 0.13 0.28 23 -0.3 21 44
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.019 0.1 0.38 1 -0.45 9 10
PTPN11 0.009 0.11 -10000 0 -0.71 8 8
IL6/IL6RA -0.017 0.099 0.18 1 -0.24 60 61
gp130 (dimer)/TYK2/TYK2/LMO4 0.03 0.057 0.21 1 -0.18 9 10
gp130 (dimer)/JAK2/JAK2/LMO4 0.029 0.055 0.21 1 -0.18 8 9
IL6 -0.045 0.14 -10000 0 -0.33 72 72
PIAS3 0.021 0.004 -10000 0 -10000 0 0
PTPRE -0.002 0.046 -10000 0 -0.24 4 4
PIAS1 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.017 0.014 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.019 0.1 0.25 3 -0.28 33 36
LMO4 0.017 0.033 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.022 0.28 0.51 19 -0.63 24 43
MCL1 0.039 0.11 0.41 3 -0.58 3 6
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.015 0.068 0.35 1 -10000 0 1
PLK1 0.22 0.27 0.57 118 -10000 0 118
CDKN1B 0.14 0.18 0.4 72 -0.34 5 77
FOXO3 0.2 0.24 0.52 117 -10000 0 117
KAT2B 0.057 0.046 0.18 11 -10000 0 11
FOXO1/SIRT1 0.009 0.043 -10000 0 -0.24 1 1
CAT 0.16 0.25 0.48 104 -0.71 5 109
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.058 0.046 0.17 10 -10000 0 10
FOXO1 0.018 0.059 0.24 12 -0.25 1 13
MAPK10 0.018 0.068 0.2 35 -0.16 11 46
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.035 0.078 0.3 6 -10000 0 6
response to oxidative stress 0.039 0.045 0.12 54 -10000 0 54
FOXO3A/SIRT1 0.17 0.21 0.44 112 -0.43 2 114
XPO1 0.022 0.002 -10000 0 -10000 0 0
EP300 0.023 0.007 -10000 0 -10000 0 0
BCL2L11 0.067 0.064 -10000 0 -10000 0 0
FOXO1/SKP2 0.023 0.044 0.2 4 -10000 0 4
mol:GDP 0.039 0.045 0.12 53 -10000 0 53
RAN 0.023 0.022 0.33 2 -10000 0 2
GADD45A 0.12 0.18 0.43 30 -0.65 6 36
YWHAQ 0.022 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.001 0.12 -10000 0 -0.44 16 16
MST1 0.066 0.07 0.23 38 -10000 0 38
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.021 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.004 0.089 -10000 0 -0.39 10 10
YWHAB 0.021 0.005 -10000 0 -10000 0 0
MAPK8 0.029 0.063 0.2 41 -10000 0 41
MAPK9 0.028 0.065 0.2 40 -10000 0 40
YWHAG 0.021 0.005 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
YWHAZ 0.019 0.008 -10000 0 -10000 0 0
SIRT1 0.001 0.025 -10000 0 -10000 0 0
SOD2 0.13 0.19 0.42 56 -0.44 2 58
RBL2 0.14 0.22 0.49 44 -0.65 6 50
RAL/GDP 0.049 0.033 0.17 1 -10000 0 1
CHUK 0.058 0.045 0.16 27 -10000 0 27
Ran/GTP 0.017 0.015 0.22 2 -10000 0 2
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
RAL/GTP 0.047 0.032 0.19 1 -10000 0 1
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
FASLG 0.051 0.15 -10000 0 -1.1 5 5
SKP2 0.018 0.018 0.33 1 -10000 0 1
USP7 0.021 0.003 -10000 0 -10000 0 0
IKBKB 0.049 0.044 0.17 5 -10000 0 5
CCNB1 0.2 0.27 0.56 116 -10000 0 116
FOXO1-3a-4/beta catenin 0.13 0.16 0.39 60 -10000 0 60
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.044 0.2 4 -10000 0 4
CSNK1A1 0.021 0.005 -10000 0 -10000 0 0
SGK1 0.055 0.047 0.16 28 -10000 0 28
CSNK1G3 0.021 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.015 0.21 2 -10000 0 2
ZFAND5 0.029 0.071 0.44 1 -10000 0 1
SFN 0.026 0.045 0.33 7 -0.33 1 8
CDK2 0.011 0.022 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.048 0.11 0.26 17 -0.39 6 23
CREBBP 0.01 0.022 -10000 0 -10000 0 0
FBXO32 0.21 0.27 0.54 117 -0.52 1 118
BCL6 0.14 0.23 0.51 35 -0.79 7 42
RALB 0.022 0.003 -10000 0 -10000 0 0
RALA 0.02 0.007 -10000 0 -10000 0 0
YWHAH 0.021 0.004 -10000 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.01 0.077 -10000 0 -0.2 45 45
fibroblast growth factor receptor signaling pathway 0.01 0.077 -10000 0 -0.2 45 45
LAMA1 0.026 0.069 0.33 13 -0.33 5 18
PRNP 0.02 0.018 -10000 0 -0.33 1 1
GPC1/SLIT2 -0.025 0.11 -10000 0 -0.23 83 83
SMAD2 -0.023 0.026 0.17 2 -0.18 6 8
GPC1/PrPc/Cu2+ 0.026 0.02 -10000 0 -0.18 3 3
GPC1/Laminin alpha1 0.032 0.051 0.24 12 -0.22 7 19
TDGF1 0.022 0.076 0.33 12 -0.33 9 21
CRIPTO/GPC1 0.03 0.058 0.24 12 -0.23 11 23
APP/GPC1 0.028 0.021 -10000 0 -0.23 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.02 0.034 0.1 10 -0.2 9 19
FLT1 0.02 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.037 0.037 0.23 1 -0.2 8 9
SERPINC1 0.022 0.032 0.33 4 -10000 0 4
FYN -0.02 0.038 0.1 11 -0.22 9 20
FGR -0.034 0.06 0.1 10 -0.21 35 45
positive regulation of MAPKKK cascade -0.022 0.096 0.26 2 -0.32 24 26
SLIT2 -0.052 0.14 -10000 0 -0.33 82 82
GPC1/NRG -0.013 0.094 -10000 0 -0.23 60 60
NRG1 -0.034 0.12 -10000 0 -0.33 58 58
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.038 0.022 -10000 0 -0.2 2 2
LYN -0.018 0.034 0.1 12 -0.2 8 20
mol:Spermine -0.01 0.015 -10000 0 -0.22 2 2
cell growth 0.01 0.077 -10000 0 -0.2 45 45
BMP signaling pathway -0.02 0.025 0.33 2 -10000 0 2
SRC -0.021 0.036 -10000 0 -0.2 10 10
TGFBR1 0.022 0.016 0.33 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.012 0.12 0.33 8 -0.33 44 52
GPC1 0.02 0.025 -10000 0 -0.33 2 2
TGFBR1 (dimer) 0.022 0.016 0.33 1 -10000 0 1
VEGFA 0.021 0.004 -10000 0 -10000 0 0
BLK 0.003 0.07 0.16 53 -0.2 9 62
HCK -0.026 0.047 0.1 11 -0.2 22 33
FGF2 -0.021 0.11 -10000 0 -0.33 47 47
FGFR1 0.018 0.019 -10000 0 -0.33 1 1
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 0.016 0.043 -10000 0 -0.33 6 6
cell death 0.028 0.021 -10000 0 -0.23 2 2
ATIII/GPC1 0.029 0.03 0.24 4 -0.23 2 6
PLA2G2A/GPC1 0.005 0.09 0.24 8 -0.23 45 53
LCK -0.022 0.039 0.11 13 -0.2 12 25
neuron differentiation -0.013 0.093 -10000 0 -0.23 60 60
PrPc/Cu2+ 0.015 0.013 -10000 0 -0.22 1 1
APP 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.016 0.043 -10000 0 -0.33 6 6
Effects of Botulinum toxin

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
STX1A 0.033 0.077 0.17 91 -10000 0 91
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.015 0.075 0.24 9 -0.23 27 36
STXBP1 0.018 0.031 -10000 0 -0.33 3 3
ACh/CHRNA1 0.027 0.073 0.25 28 -0.16 12 40
RAB3GAP2/RIMS1/UNC13B 0.024 0.065 0.23 7 -0.2 24 31
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.003 0.1 0.33 10 -0.33 27 37
mol:ACh 0.004 0.032 0.088 18 -0.11 8 26
RAB3GAP2 0.02 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.025 0.068 0.23 1 -0.16 23 24
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.027 0.073 0.25 28 -0.16 12 40
UNC13B 0.021 0.005 -10000 0 -10000 0 0
CHRNA1 0.036 0.093 0.33 27 -0.33 7 34
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.028 0.069 0.26 25 -0.16 6 31
SNAP25 0.004 0.032 0.12 15 -0.22 4 19
VAMP2 0.002 0.001 -10000 0 -10000 0 0
SYT1 0.036 0.088 0.33 25 -0.33 6 31
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.043 0.056 0.14 90 -0.19 3 93
STX1A/SNAP25 fragment 1/VAMP2 0.025 0.068 0.23 1 -0.16 23 24
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.012 0.072 0.21 1 -0.18 47 48
regulation of S phase of mitotic cell cycle -0.017 0.073 0.16 1 -0.2 48 49
GNAO1 0.021 0.034 0.33 2 -0.33 2 4
HRAS 0.018 0.012 -10000 0 -10000 0 0
SHBG/T-DHT 0.014 0.01 0.2 1 -10000 0 1
PELP1 0.017 0.012 -10000 0 -10000 0 0
AKT1 -0.009 0.002 -10000 0 -10000 0 0
MAP2K1 -0.042 0.067 0.16 12 -0.26 10 22
T-DHT/AR -0.015 0.081 0.22 1 -0.23 49 50
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.006 30 30
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.018 -10000 0 -0.33 1 1
mol:GDP -0.049 0.1 0.2 1 -0.31 52 53
cell proliferation -0.065 0.13 0.27 2 -0.43 35 37
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
FOS -0.069 0.2 -10000 0 -0.71 32 32
mol:Ca2+ -0.009 0.02 -10000 0 -0.057 43 43
MAPK3 -0.055 0.1 0.26 3 -0.33 32 35
MAPK1 -0.032 0.091 0.2 1 -0.32 22 23
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 29 29
cAMP biosynthetic process 0.002 0.02 0.23 1 -10000 0 1
GNG2 0.02 0.018 -10000 0 -0.33 1 1
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 29 29
HRAS/GTP 0.006 0.07 -10000 0 -0.17 46 46
actin cytoskeleton reorganization 0.027 0.015 -10000 0 -10000 0 0
SRC 0.018 0.012 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 29 29
PI3K 0.027 0.008 -10000 0 -10000 0 0
apoptosis 0.049 0.13 0.45 32 -0.26 1 33
T-DHT/AR/PELP1 -0.003 0.074 0.2 1 -0.19 49 50
HRAS/GDP -0.05 0.099 0.19 1 -0.3 51 52
CREB1 -0.053 0.14 0.27 1 -0.49 32 33
RAC1-CDC42/GTP 0.033 0.018 -10000 0 -10000 0 0
AR -0.024 0.12 0.33 1 -0.33 49 50
GNB1 0.021 0.004 -10000 0 -10000 0 0
RAF1 -0.036 0.065 0.18 13 -0.24 8 21
RAC1-CDC42/GDP -0.017 0.1 0.2 1 -0.29 45 46
T-DHT/AR/PELP1/Src 0.007 0.072 0.2 1 -0.18 47 48
MAP2K2 -0.042 0.066 0.16 11 -0.25 10 21
T-DHT/AR/PELP1/Src/PI3K -0.016 0.073 0.16 1 -0.2 48 49
GNAZ -0.01 0.099 -10000 0 -0.33 34 34
SHBG 0.02 0.017 0.33 1 -10000 0 1
Gi family/GNB1/GNG2/GDP -0.024 0.1 -10000 0 -0.34 24 24
mol:T-DHT 0 0.001 -10000 0 -0.003 5 5
RAC1 0.019 0.007 -10000 0 -10000 0 0
GNRH1 -0.009 0.016 -10000 0 -0.22 2 2
Gi family/GTP -0.029 0.072 -10000 0 -0.21 44 44
CDC42 0.021 0.004 -10000 0 -10000 0 0
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.034 0.33 2 -0.33 2 4
CDC42/GTP -0.015 0.081 -10000 0 -0.21 29 29
PLCG1 -0.027 0.069 0.27 1 -0.19 51 52
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.004 -10000 0 -10000 0 0
G12/G13 0.028 0.012 -10000 0 -10000 0 0
cell migration -0.015 0.079 -10000 0 -0.2 29 29
S1PR5 0.001 0.084 0.33 1 -0.33 23 24
S1PR4 0.005 0.071 -10000 0 -0.33 17 17
MAPK3 -0.028 0.069 -10000 0 -0.19 54 54
MAPK1 -0.024 0.061 -10000 0 -0.18 49 49
S1P/S1P5/Gi -0.019 0.081 -10000 0 -0.2 58 58
GNAI1 0.02 0.018 -10000 0 -0.33 1 1
CDC42/GDP 0.016 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.012 0.052 0.21 1 -0.19 22 23
RHOA -0.002 0.079 0.19 44 -0.17 14 58
S1P/S1P4/Gi -0.017 0.076 -10000 0 -0.19 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.01 0.099 -10000 0 -0.33 34 34
S1P/S1P4/G12/G13 0.025 0.044 -10000 0 -0.18 15 15
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
ErbB4 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.047 0.1 -10000 0 -0.3 22 22
epithelial cell differentiation -0.028 0.092 -10000 0 -0.31 5 5
ITCH 0.031 0.017 -10000 0 -10000 0 0
WWP1 -0.016 0.076 -10000 0 -10000 0 0
FYN 0.019 0.019 -10000 0 -0.33 1 1
EGFR 0.015 0.043 0.33 1 -0.33 5 6
PRL 0.025 0.044 0.33 8 -10000 0 8
neuron projection morphogenesis -0.027 0.097 0.25 11 -10000 0 11
PTPRZ1 0.029 0.16 0.33 52 -0.33 36 88
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.019 0.083 -10000 0 -0.24 19 19
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.041 0.084 -10000 0 -0.26 27 27
ADAM17 0.033 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.035 0.068 -10000 0 -0.32 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.087 0.12 -10000 0 -0.29 64 64
NCOR1 0.02 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.037 0.086 -10000 0 -0.25 27 27
GRIN2B -0.047 0.081 0.26 3 -0.25 21 24
ErbB4/ErbB2/betacellulin -0.013 0.067 -10000 0 -0.26 6 6
STAT1 0.022 0.002 -10000 0 -10000 0 0
HBEGF -0.033 0.13 -10000 0 -0.33 60 60
PRLR 0.024 0.095 0.33 21 -0.33 12 33
E4ICDs/ETO2 -0.031 0.09 -10000 0 -0.29 12 12
axon guidance -0.027 0.073 -10000 0 -0.34 5 5
NEDD4 0.03 0.024 -10000 0 -0.31 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.03 0.074 0.25 25 -0.23 12 37
CBFA2T3 -0.003 0.087 -10000 0 -0.33 26 26
ErbB4/ErbB2/HBEGF -0.032 0.085 -10000 0 -0.25 17 17
MAPK3 -0.035 0.083 0.2 6 -10000 0 6
STAT1 (dimer) -0.023 0.078 -10000 0 -0.31 2 2
MAPK1 -0.032 0.083 0.21 7 -10000 0 7
JAK2 0.018 0.019 -10000 0 -0.33 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.051 0.076 -10000 0 -0.25 25 25
NRG1 -0.037 0.08 -10000 0 -0.23 57 57
NRG3 -0.11 0.17 0.33 1 -0.33 150 151
NRG2 -0.02 0.11 -10000 0 -0.33 46 46
NRG4 0.036 0.093 0.33 27 -0.33 7 34
heart development -0.027 0.073 -10000 0 -0.34 5 5
neural crest cell migration -0.051 0.075 -10000 0 -0.25 25 25
ERBB2 -0.001 0.03 0.29 2 -10000 0 2
WWOX/E4ICDs -0.021 0.077 -10000 0 -0.3 2 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.002 0.093 0.3 1 -0.28 7 8
apoptosis 0.14 0.2 0.38 131 -10000 0 131
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.041 0.1 -10000 0 -0.29 25 25
ErbB4/ErbB2/epiregulin 0.001 0.12 0.32 4 -0.26 15 19
ErbB4/ErbB4/betacellulin/betacellulin -0.025 0.085 -10000 0 -0.31 8 8
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.013 0.11 0.33 1 -0.28 19 20
MDM2 -0.02 0.08 0.24 14 -0.29 1 15
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.031 0.077 -10000 0 -0.23 28 28
STAT5A -0.027 0.074 -10000 0 -0.39 2 2
ErbB4/EGFR/neuregulin 1 beta -0.032 0.082 -10000 0 -0.26 22 22
DLG4 0.02 0.006 -10000 0 -10000 0 0
GRB2/SHC 0.026 0.013 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.02 0.071 -10000 0 -0.28 2 2
STAT5A (dimer) -0.023 0.1 -10000 0 -0.36 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.019 0.084 -10000 0 -0.36 3 3
LRIG1 0.019 0.025 -10000 0 -0.33 2 2
EREG 0.018 0.18 0.33 60 -0.33 57 117
BTC 0.012 0.055 -10000 0 -0.33 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.026 0.07 -10000 0 -0.34 4 4
ERBB4 -0.035 0.068 -10000 0 -0.32 1 1
STAT5B 0.021 0.003 -10000 0 -10000 0 0
YAP1 -0.009 0.076 -10000 0 -0.47 9 9
GRB2 0.021 0.005 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.002 0.08 -10000 0 -0.25 5 5
glial cell differentiation 0.02 0.07 0.28 2 -10000 0 2
WWOX 0.021 0.005 -10000 0 -10000 0 0
cell proliferation -0.059 0.11 0.33 3 -0.38 13 16
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.077 0.16 -10000 0 -0.33 109 109
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.021 0.004 -10000 0 -10000 0 0
TCEB1 0.02 0.017 0.33 1 -10000 0 1
HIF1A/p53 0.027 0.055 0.21 2 -0.24 8 10
HIF1A 0.009 0.046 -10000 0 -0.25 8 8
COPS5 0.019 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.053 0.028 -10000 0 -10000 0 0
FIH (dimer) 0.021 0.003 -10000 0 -10000 0 0
CDKN2A 0.098 0.14 0.33 103 -10000 0 103
ARNT/IPAS -0.036 0.11 -10000 0 -0.23 91 91
HIF1AN 0.021 0.003 -10000 0 -10000 0 0
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.046 0.21 2 -0.23 5 7
CUL2 0.021 0.004 -10000 0 -10000 0 0
OS9 0.02 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.038 0.019 0.23 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.027 0.052 -10000 0 -0.25 8 8
PHD1-3/OS9 0.082 0.083 0.23 80 -10000 0 80
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.053 0.24 2 -0.24 6 8
VHL 0.021 0.004 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
HIF1A/JAB1 0.024 0.053 0.24 1 -0.25 8 9
EGLN3 0.092 0.14 0.33 93 -0.33 1 94
EGLN2 0.021 0.004 -10000 0 -10000 0 0
EGLN1 0.02 0.006 -10000 0 -10000 0 0
TP53 0.02 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.01 0.1 -10000 0 -0.49 15 15
ARNT 0.018 0.008 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.021 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.068 0.099 0.22 99 -0.22 6 105
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.014 0.1 -10000 0 -0.58 8 8
Syndecan-4/Syndesmos 0.032 0.16 0.32 4 -0.73 11 15
positive regulation of JNK cascade 0.03 0.15 0.3 4 -0.65 12 16
Syndecan-4/ADAM12 0.096 0.2 0.33 65 -0.74 11 76
CCL5 0.018 0.035 -10000 0 -0.33 4 4
Rac1/GDP 0.014 0.006 -10000 0 -10000 0 0
DNM2 0.02 0.006 -10000 0 -10000 0 0
ITGA5 0.021 0.024 0.33 1 -0.33 1 2
SDCBP 0.02 0.007 -10000 0 -10000 0 0
PLG 0.014 0.052 0.32 9 -10000 0 9
ADAM12 0.14 0.15 0.33 144 -10000 0 144
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.021 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.036 0.019 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.034 0.16 0.32 7 -0.72 11 18
Syndecan-4/CXCL12/CXCR4 0.032 0.16 0.32 4 -0.7 12 16
Syndecan-4/Laminin alpha3 0.013 0.16 0.33 1 -0.7 13 14
MDK 0.12 0.14 0.33 122 -10000 0 122
Syndecan-4/FZD7 0.031 0.16 0.32 4 -0.74 11 15
Syndecan-4/Midkine 0.088 0.19 0.35 41 -0.74 11 52
FZD7 0.021 0.018 -10000 0 -0.33 1 1
Syndecan-4/FGFR1/FGF 0.017 0.16 0.31 1 -0.67 14 15
THBS1 0.021 0.005 -10000 0 -10000 0 0
integrin-mediated signaling pathway 0.042 0.16 0.32 12 -0.72 11 23
positive regulation of MAPKKK cascade 0.03 0.15 0.3 4 -0.65 12 16
Syndecan-4/TACI 0.04 0.17 0.33 18 -0.74 11 29
CXCR4 0.022 0.002 -10000 0 -10000 0 0
cell adhesion 0.006 0.041 0.19 8 -0.27 4 12
Syndecan-4/Dynamin 0.031 0.15 0.31 3 -0.74 11 14
Syndecan-4/TSP1 0.029 0.16 0.32 4 -0.74 11 15
Syndecan-4/GIPC 0.031 0.16 0.32 3 -0.74 11 14
Syndecan-4/RANTES 0.03 0.16 0.31 3 -0.74 11 14
ITGB1 0.021 0.004 -10000 0 -10000 0 0
LAMA1 0.026 0.069 0.33 13 -0.33 5 18
LAMA3 -0.045 0.14 -10000 0 -0.33 72 72
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA 0.004 0.14 0.74 13 -0.33 1 14
Syndecan-4/alpha-Actinin 0.03 0.16 0.32 3 -0.74 11 14
TFPI 0.008 0.067 -10000 0 -0.33 15 15
F2 0.061 0.11 0.33 52 -10000 0 52
alpha5/beta1 Integrin 0.031 0.018 0.24 1 -0.23 1 2
positive regulation of cell adhesion -0.005 0.16 0.32 1 -0.64 14 15
ACTN1 0.021 0.004 -10000 0 -10000 0 0
TNC 0.036 0.09 0.33 26 -0.33 6 32
Syndecan-4/CXCL12 0.027 0.16 0.32 4 -0.72 12 16
FGF6 0.017 0.005 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CXCL12 0 0.084 -10000 0 -0.33 24 24
TNFRSF13B 0.036 0.088 0.33 26 -0.33 5 31
FGF2 -0.021 0.11 -10000 0 -0.33 47 47
FGFR1 0.018 0.019 -10000 0 -0.33 1 1
Syndecan-4/PI-4-5-P2 0.015 0.15 0.29 3 -0.74 11 14
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.013 0.039 -10000 0 -0.32 4 4
cell migration -0.021 0.013 -10000 0 -10000 0 0
PRKCD 0.016 0.019 -10000 0 -10000 0 0
vasculogenesis 0.029 0.15 0.31 4 -0.7 11 15
SDC4 0.022 0.15 0.31 4 -0.84 9 13
Syndecan-4/Tenascin C 0.041 0.16 0.32 12 -0.76 11 23
Syndecan-4/PI-4-5-P2/PKC alpha -0.029 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.027 0.16 0.32 4 -0.74 11 15
MMP9 0.072 0.12 0.33 65 -10000 0 65
Rac1/GTP 0.006 0.042 0.19 8 -0.28 4 12
cytoskeleton organization 0.032 0.15 0.31 4 -0.69 11 15
GIPC1 0.02 0.005 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.028 0.16 0.32 3 -0.76 11 14
ErbB2/ErbB3 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
USP8 -0.014 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.003 0.085 0.22 1 -0.23 5 6
NFATC4 -0.04 0.065 0.22 8 -10000 0 8
ERBB2IP 0.02 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.021 0.005 -10000 0 -10000 0 0
mammary gland morphogenesis -0.049 0.063 -10000 0 -0.2 47 47
JUN -0.007 0.063 0.25 3 -10000 0 3
HRAS 0.021 0.006 -10000 0 -10000 0 0
DOCK7 -0.05 0.064 -10000 0 -0.2 44 44
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.001 0.07 0.2 1 -0.18 44 45
AKT1 -0.009 0.006 -10000 0 -10000 0 0
BAD -0.014 0.005 -10000 0 -10000 0 0
MAPK10 -0.03 0.069 0.17 12 -0.2 13 25
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.051 0.068 -10000 0 -0.21 45 45
RAF1 -0.012 0.096 0.25 12 -0.24 5 17
ErbB2/ErbB3/neuregulin 2 -0.014 0.067 0.19 1 -0.19 42 43
STAT3 0.004 0.13 -10000 0 -0.9 8 8
cell migration -0.023 0.077 0.21 15 -0.2 11 26
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.032 0.18 0.38 4 -0.51 28 32
FOS -0.03 0.16 0.34 5 -0.41 41 46
NRAS 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.049 0.063 -10000 0 -0.2 47 47
MAPK3 -0.019 0.15 0.36 5 -0.47 16 21
MAPK1 -0.026 0.16 0.37 4 -0.52 18 22
JAK2 -0.048 0.064 -10000 0 -0.2 44 44
NF2 -0.032 0.14 -10000 0 -0.61 22 22
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.016 0.069 0.2 3 -0.21 41 44
NRG1 -0.034 0.12 -10000 0 -0.33 58 58
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
MAPK8 -0.045 0.084 -10000 0 -0.24 39 39
MAPK9 -0.02 0.06 0.17 14 -10000 0 14
ERBB2 -0.02 0.017 0.27 1 -10000 0 1
ERBB3 0.014 0.028 -10000 0 -0.33 2 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
apoptosis 0.011 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.004 0.13 -10000 0 -0.88 8 8
RNF41 -0.019 0.009 -10000 0 -10000 0 0
FRAP1 -0.007 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.043 0.043 -10000 0 -0.16 35 35
ErbB2/ErbB2/HSP90 (dimer) -0.021 0.016 0.2 1 -10000 0 1
CHRNA1 -0.007 0.14 0.3 18 -0.46 15 33
myelination -0.031 0.085 0.26 16 -10000 0 16
PPP3CB -0.048 0.059 -10000 0 -0.19 4 4
KRAS 0.02 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0.001 0.077 -10000 0 -0.19 31 31
NRG2 -0.02 0.11 -10000 0 -0.33 46 46
mol:GDP -0.016 0.069 0.2 3 -0.2 41 44
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K2 -0.015 0.097 0.26 12 -0.27 5 17
SRC 0.021 0.005 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.05 0.065 -10000 0 -0.2 44 44
MAP2K1 -0.037 0.17 0.39 2 -0.52 23 25
heart morphogenesis -0.049 0.063 -10000 0 -0.2 47 47
RAS family/GDP 0.004 0.086 0.23 1 -0.22 5 6
GRB2 0.021 0.005 -10000 0 -10000 0 0
PRKACA -0.03 0.15 -10000 0 -0.65 22 22
CHRNE 0.002 0.021 0.16 4 -10000 0 4
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
activation of caspase activity 0.009 0.006 -10000 0 -10000 0 0
nervous system development -0.049 0.063 -10000 0 -0.2 47 47
CDC42 0.021 0.004 -10000 0 -10000 0 0
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.013 0.04 -10000 0 -0.32 4 4
PDGF/PDGFRA/CRKL 0.024 0.031 -10000 0 -0.21 4 4
positive regulation of JUN kinase activity 0.036 0.031 -10000 0 -0.18 1 1
CRKL 0.021 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.033 0.11 -10000 0 -0.24 85 85
AP1 -0.072 0.19 0.27 2 -0.72 30 32
mol:IP3 -0.022 0.027 -10000 0 -0.24 3 3
PLCG1 -0.022 0.027 -10000 0 -0.24 3 3
PDGF/PDGFRA/alphaV Integrin 0.024 0.031 -10000 0 -0.22 4 4
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
CRK 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.022 0.027 -10000 0 -0.24 3 3
CAV3 -0.055 0.14 -10000 0 -0.33 83 83
CAV1 -0.18 0.17 -10000 0 -0.33 228 228
SHC/Grb2/SOS1 0.038 0.032 -10000 0 -0.18 1 1
PDGF/PDGFRA/Shf 0.024 0.034 0.24 2 -0.21 4 6
FOS -0.071 0.19 0.3 2 -0.71 29 31
JUN -0.025 0.025 -10000 0 -0.24 2 2
oligodendrocyte development 0.024 0.031 -10000 0 -0.22 4 4
GRB2 0.021 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:DAG -0.022 0.027 -10000 0 -0.24 3 3
PDGF/PDGFRA 0.013 0.04 -10000 0 -0.32 4 4
actin cytoskeleton reorganization 0.023 0.031 -10000 0 -0.21 4 4
SRF -0.014 0.013 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
PI3K 0.033 0.031 -10000 0 -0.18 4 4
PDGF/PDGFRA/Crk/C3G 0.031 0.032 -10000 0 -0.18 4 4
JAK1 -0.019 0.021 -10000 0 -0.22 3 3
ELK1/SRF -0.023 0.041 0.16 14 -0.2 3 17
SHB 0.02 0.006 -10000 0 -10000 0 0
SHF 0.022 0.023 0.33 2 -10000 0 2
CSNK2A1 0.023 0.017 -10000 0 -10000 0 0
GO:0007205 -0.017 0.028 -10000 0 -0.26 3 3
SOS1 0.021 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.036 0.031 -10000 0 -0.18 1 1
PDGF/PDGFRA/SHB 0.023 0.031 -10000 0 -0.21 4 4
PDGF/PDGFRA/Caveolin-1 -0.13 0.13 -10000 0 -0.24 222 222
ITGAV 0.022 0.002 -10000 0 -10000 0 0
ELK1 -0.022 0.031 -10000 0 -0.23 3 3
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.021 0.031 -10000 0 -0.21 4 4
JAK-STAT cascade -0.019 0.021 -10000 0 -0.22 3 3
cell proliferation 0.024 0.034 0.24 2 -0.21 4 6
IL1-mediated signaling events

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
UBC13/UEV1A 0.029 0.014 0.24 1 -10000 0 1
PRKCZ 0.018 0.031 -10000 0 -0.33 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.02 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.001 0.059 -10000 0 -0.27 11 11
IRAK/TOLLIP -0.021 0.015 0.14 2 -10000 0 2
IKBKB 0.019 0.008 -10000 0 -10000 0 0
IKBKG 0.021 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.035 0.13 0.24 17 -0.24 111 128
IL1A -0.076 0.16 0.33 2 -0.33 111 113
IL1B -0.03 0.054 0.16 1 -0.23 25 26
IRAK/TRAF6/p62/Atypical PKCs 0.043 0.038 -10000 0 -0.18 2 2
IL1R2 0.032 0.069 0.33 16 -0.33 3 19
IL1R1 0.02 0.025 -10000 0 -0.33 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.051 -10000 0 -0.25 7 7
TOLLIP 0.021 0.004 -10000 0 -10000 0 0
TICAM2 0.019 0.025 -10000 0 -0.33 2 2
MAP3K3 0.021 0.005 -10000 0 -10000 0 0
TAK1/TAB1/TAB2 0.013 0.005 -10000 0 -10000 0 0
IKK complex/ELKS -0.001 0.064 -10000 0 -0.33 1 1
JUN -0.02 0.044 0.15 19 -10000 0 19
MAP3K7 0.02 0.007 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.034 0.059 -10000 0 -0.18 24 24
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.014 0.11 0.23 1 -0.18 110 111
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.007 0.11 0.23 1 -0.18 109 110
IL1 beta fragment/IL1R1/IL1RAP 0.016 0.055 -10000 0 -0.19 25 25
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.015 0.049 0.17 21 -10000 0 21
IRAK1 -0.018 0.015 0.15 2 -10000 0 2
IL1RN/IL1R1 0.027 0.041 0.24 1 -0.23 9 10
IRAK4 0.021 0.004 -10000 0 -10000 0 0
PRKCI 0.021 0.005 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.03 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.06 -10000 0 -0.29 9 9
CHUK 0.021 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.016 0.055 -10000 0 -0.19 25 25
IL1 beta/IL1R2 0.016 0.071 0.22 14 -0.21 25 39
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.003 0.026 0.16 1 -10000 0 1
NF kappa B1 p50/RelA 0.023 0.055 -10000 0 -0.18 19 19
IRAK3 0.012 0.055 -10000 0 -0.33 10 10
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.033 0.061 -10000 0 -0.18 24 24
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.046 0.099 -10000 0 -0.2 104 104
IL1 alpha/IL1R1/IL1RAP -0.025 0.11 0.23 2 -0.2 110 112
RELA 0.021 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.021 0.005 -10000 0 -10000 0 0
MYD88 0.021 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.034 0.031 -10000 0 -10000 0 0
IL1RAP 0.021 0.005 -10000 0 -10000 0 0
UBE2N 0.021 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.046 0.034 -10000 0 -10000 0 0
CASP1 0.018 0.031 -10000 0 -0.33 3 3
IL1RN/IL1R2 0.035 0.062 0.24 17 -0.25 9 26
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.026 0.056 -10000 0 -0.18 25 25
TMEM189-UBE2V1 0.019 0.017 0.33 1 -10000 0 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.038 0.094 -10000 0 -0.33 17 17
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
IL1RN 0.016 0.049 0.33 1 -0.33 7 8
TRAF6/TAK1/TAB1/TAB2 0.034 0.019 0.18 1 -10000 0 1
MAP2K6 -0.009 0.057 0.18 28 -10000 0 28
Wnt signaling

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
Noncanonical Wnts/FZD -0.026 0.098 0.18 2 -0.33 19 21
FZD6 0.018 0.019 -10000 0 -0.33 1 1
WNT6 0.039 0.071 0.33 22 -10000 0 22
WNT4 0.007 0.085 0.33 5 -0.33 20 25
FZD3 0.019 0.018 0.33 1 -10000 0 1
WNT5A 0.017 0.039 -10000 0 -0.33 5 5
WNT11 -0.022 0.12 0.33 1 -0.33 49 50
LPA receptor mediated events

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
GNB1/GNG2 0.038 0.021 -10000 0 -0.18 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.012 0.11 0.25 1 -0.29 36 37
AP1 0.003 0.076 -10000 0 -0.17 59 59
mol:PIP3 -0.037 0.044 -10000 0 -0.17 30 30
AKT1 -0.01 0.067 0.23 3 -0.31 5 8
PTK2B -0.044 0.12 0.25 1 -0.25 67 68
RHOA -0.005 0.073 0.18 6 -0.37 10 16
PIK3CB 0.021 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.03 0.087 0.22 7 -0.24 34 41
MAGI3 0.017 0.035 -10000 0 -0.33 4 4
RELA 0.021 0.003 -10000 0 -10000 0 0
apoptosis -0.012 0.06 -10000 0 -0.2 36 36
HRAS/GDP 0.016 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.049 0.11 0.21 8 -0.32 31 39
NF kappa B1 p50/RelA -0.053 0.087 -10000 0 -0.26 40 40
endothelial cell migration -0.01 0.017 0.3 1 -10000 0 1
ADCY4 -0.014 0.055 0.24 1 -0.26 4 5
ADCY5 -0.025 0.075 0.22 2 -0.26 19 21
ADCY6 -0.01 0.049 0.24 1 -0.25 4 5
ADCY7 -0.01 0.044 -10000 0 -0.2 4 4
ADCY1 -0.009 0.05 0.24 1 -0.23 7 8
ADCY2 -0.014 0.057 0.24 1 -0.24 8 9
ADCY3 -0.008 0.046 0.24 1 -0.2 4 5
ADCY8 -0.055 0.081 -10000 0 -0.24 14 14
ADCY9 -0.013 0.056 0.24 1 -0.24 8 9
GSK3B -0.045 0.12 0.19 5 -0.33 31 36
arachidonic acid secretion -0.016 0.05 -10000 0 -0.28 6 6
GNG2 0.019 0.019 -10000 0 -0.33 1 1
TRIP6 0.01 0.023 -10000 0 -0.29 2 2
GNAO1 -0.011 0.02 0.16 3 -0.19 2 5
HRAS 0.021 0.004 -10000 0 -10000 0 0
NFKBIA -0.03 0.12 0.24 5 -0.29 47 52
GAB1 0.021 0.018 -10000 0 -0.33 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.013 0.2 -10000 0 -0.83 21 21
JUN 0.019 0.025 -10000 0 -0.33 2 2
LPA/LPA2/NHERF2 0.026 0.024 -10000 0 -0.19 4 4
TIAM1 -0.028 0.23 -10000 0 -0.97 21 21
PIK3R1 0.02 0.007 -10000 0 -10000 0 0
mol:IP3 -0.023 0.076 0.21 8 -0.22 29 37
PLCB3 -0.013 0.035 0.18 10 -0.18 4 14
FOS -0.004 0.09 -10000 0 -0.33 28 28
positive regulation of mitosis -0.016 0.05 -10000 0 -0.28 6 6
LPA/LPA1-2-3 0.023 0.066 0.22 4 -0.17 36 40
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
stress fiber formation -0.026 0.096 0.23 1 -0.33 19 20
GNAZ -0.026 0.051 0.12 1 -0.19 34 35
EGFR/PI3K-beta/Gab1 -0.035 0.048 -10000 0 -0.18 28 28
positive regulation of dendritic cell cytokine production 0.022 0.065 0.21 4 -0.17 36 40
LPA/LPA2/MAGI-3 0.026 0.024 -10000 0 -0.19 4 4
ARHGEF1 0.007 0.075 0.19 49 -10000 0 49
GNAI2 -0.011 0.008 0.12 1 -10000 0 1
GNAI3 -0.011 0.008 0.12 1 -10000 0 1
GNAI1 -0.011 0.012 0.12 1 -0.19 1 2
LPA/LPA3 -0.004 0.073 0.22 4 -0.22 36 40
LPA/LPA2 0.016 0.006 -10000 0 -10000 0 0
LPA/LPA1 0.018 0.01 0.19 1 -10000 0 1
HB-EGF/EGFR -0.018 0.086 0.13 52 -0.21 45 97
HBEGF -0.019 0.1 0.16 59 -0.23 54 113
mol:DAG -0.023 0.076 0.21 8 -0.22 29 37
cAMP biosynthetic process -0.021 0.065 0.3 2 -0.24 7 9
NFKB1 0.022 0.003 -10000 0 -10000 0 0
SRC 0.021 0.005 -10000 0 -10000 0 0
GNB1 0.02 0.007 -10000 0 -10000 0 0
LYN -0.033 0.11 0.28 3 -0.3 40 43
GNAQ -0.013 0.062 -10000 0 -0.21 34 34
LPAR2 0.021 0.005 -10000 0 -10000 0 0
LPAR3 -0.008 0.11 0.33 4 -0.33 36 40
LPAR1 0.022 0.007 -10000 0 -10000 0 0
IL8 -0.02 0.13 0.3 16 -0.37 17 33
PTK2 -0.025 0.051 0.17 7 -10000 0 7
Rac1/GDP 0.014 0.006 -10000 0 -10000 0 0
CASP3 -0.012 0.061 -10000 0 -0.2 36 36
EGFR 0.016 0.043 0.33 1 -0.33 5 6
PLCG1 -0.016 0.073 0.14 6 -0.23 33 39
PLD2 -0.024 0.057 0.19 11 -0.17 6 17
G12/G13 0.037 0.019 -10000 0 -10000 0 0
PI3K-beta -0.025 0.048 -10000 0 -0.33 6 6
cell migration -0.01 0.066 -10000 0 -0.25 20 20
SLC9A3R2 0.018 0.035 -10000 0 -0.33 4 4
PXN -0.026 0.097 0.23 1 -0.34 18 19
HRAS/GTP -0.017 0.05 -10000 0 -0.27 7 7
RAC1 0.019 0.007 -10000 0 -10000 0 0
MMP9 0.072 0.12 0.33 65 -10000 0 65
PRKCE 0.018 0.031 -10000 0 -0.33 3 3
PRKCD -0.037 0.087 0.27 3 -0.34 14 17
Gi(beta/gamma) -0.01 0.046 -10000 0 -0.23 3 3
mol:LPA 0.001 0.004 -10000 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.009 0.087 -10000 0 -0.35 10 10
MAPKKK cascade -0.016 0.05 -10000 0 -0.28 6 6
contractile ring contraction involved in cytokinesis -0.004 0.074 0.18 6 -0.36 11 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.017 0.069 -10000 0 -0.21 41 41
GNA15 -0.011 0.057 -10000 0 -0.2 32 32
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
MAPT -0.051 0.12 0.21 8 -0.33 31 39
GNA11 -0.011 0.057 -10000 0 -0.2 32 32
Rac1/GTP -0.015 0.21 -10000 0 -0.88 21 21
MMP2 -0.01 0.017 0.31 1 -10000 0 1
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.011 0.058 -10000 0 -0.33 11 11
GNB1/GNG2 -0.008 0.1 0.23 1 -0.3 19 20
mol:DAG -0.038 0.085 0.19 2 -0.28 17 19
PLCG1 -0.039 0.087 0.2 2 -0.29 17 19
YES1 -0.036 0.089 0.21 4 -0.32 18 22
FZD3 0.019 0.018 0.33 1 -10000 0 1
FZD6 0.018 0.019 -10000 0 -0.33 1 1
G protein -0.007 0.1 0.25 3 -0.3 17 20
MAP3K7 -0.044 0.09 0.19 2 -0.28 28 30
mol:Ca2+ -0.037 0.083 0.19 2 -0.28 17 19
mol:IP3 -0.038 0.085 0.19 2 -0.28 17 19
NLK -0.002 0.092 -10000 0 -0.8 5 5
GNB1 0.021 0.004 -10000 0 -10000 0 0
CAMK2A -0.048 0.097 0.2 1 -0.28 32 33
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.026 0.098 0.18 2 -0.33 19 21
CSNK1A1 0.021 0.005 -10000 0 -10000 0 0
GNAS -0.037 0.086 0.16 2 -0.32 17 19
GO:0007205 -0.036 0.083 0.19 2 -0.28 18 20
WNT6 0.039 0.071 0.33 22 -10000 0 22
WNT4 0.007 0.085 0.33 5 -0.33 20 25
NFAT1/CK1 alpha -0.016 0.1 0.3 3 -0.31 17 20
GNG2 0.02 0.018 -10000 0 -0.33 1 1
WNT5A 0.017 0.039 -10000 0 -0.33 5 5
WNT11 -0.022 0.12 0.33 1 -0.33 49 50
CDC42 -0.033 0.089 0.22 4 -0.31 18 22
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin 0.013 0.03 -10000 0 -0.22 6 6
EPHB2 0.057 0.1 0.33 46 -10000 0 46
Syndecan-2/TACI 0.026 0.061 0.23 26 -0.19 7 33
LAMA1 0.026 0.069 0.33 13 -0.33 5 18
Syndecan-2/alpha2 ITGB1 0.007 0.082 0.23 8 -0.18 53 61
HRAS 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK -0.007 0.016 -10000 0 -0.18 3 3
ITGA5 0.021 0.024 0.33 1 -0.33 1 2
BAX -0.014 0.013 -10000 0 -10000 0 0
EPB41 0.021 0.003 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.013 0.017 -10000 0 -0.17 3 3
LAMA3 -0.045 0.14 -10000 0 -0.33 72 72
EZR 0.02 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.042 0.13 -10000 0 -0.33 70 70
Syndecan-2/MMP2 0.015 0.022 0.22 1 -0.19 3 4
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.034 0.041 0.24 11 -0.23 2 13
dendrite morphogenesis 0.04 0.074 0.23 46 -0.19 3 49
Syndecan-2/GM-CSF 0.009 0.053 0.25 5 -0.19 19 24
determination of left/right symmetry -0.008 0.019 -10000 0 -0.22 3 3
Syndecan-2/PKC delta 0.014 0.019 -10000 0 -0.19 3 3
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
MAPK3 -0.002 0.072 0.18 39 -0.18 18 57
MAPK1 0 0.07 0.18 39 -0.18 14 53
Syndecan-2/RACK1 0.023 0.02 -10000 0 -0.16 3 3
NF1 0.021 0.004 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.008 0.019 -10000 0 -0.22 3 3
ITGA2 0.027 0.058 0.33 11 -0.33 2 13
MAPK8 -0.012 0.016 -10000 0 -0.19 3 3
Syndecan-2/alpha2/beta1 Integrin 0.043 0.062 0.25 20 -0.2 5 25
Syndecan-2/Kininogen 0.028 0.059 0.23 28 -0.18 3 31
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC 0.002 0.063 0.17 45 -0.16 2 47
Syndecan-2/CASK/Protein 4.1 0.013 0.017 -10000 0 -0.17 3 3
extracellular matrix organization 0.014 0.019 -10000 0 -0.19 3 3
actin cytoskeleton reorganization 0.013 0.03 -10000 0 -0.22 6 6
Syndecan-2/Caveolin-2/Ras -0.004 0.072 -10000 0 -0.18 56 56
Syndecan-2/Laminin alpha3 -0.018 0.075 -10000 0 -0.19 61 61
Syndecan-2/RasGAP 0.031 0.024 -10000 0 -0.16 3 3
alpha5/beta1 Integrin 0.031 0.018 0.24 1 -0.23 1 2
PRKCD 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.04 0.075 0.24 46 -0.19 3 49
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.018 0.025 0.16 5 -10000 0 5
RHOA 0.021 0.004 -10000 0 -10000 0 0
SDCBP 0.02 0.007 -10000 0 -10000 0 0
TNFRSF13B 0.036 0.088 0.33 26 -0.33 5 31
RASA1 0.021 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.034 0.041 0.24 11 -0.23 2 13
Syndecan-2/Synbindin 0.015 0.016 -10000 0 -0.19 2 2
TGFB1 0.021 0.004 -10000 0 -10000 0 0
CASP3 0.004 0.064 0.18 43 -0.18 3 46
FN1 0.018 0.035 -10000 0 -0.33 4 4
Syndecan-2/IL8 0.024 0.053 0.24 18 -0.19 4 22
SDC2 -0.008 0.019 -10000 0 -0.22 3 3
KNG1 0.041 0.081 0.33 28 -10000 0 28
Syndecan-2/Neurofibromin 0.015 0.019 -10000 0 -0.18 3 3
TRAPPC4 0.021 0.005 -10000 0 -10000 0 0
CSF2 0.003 0.092 0.33 5 -0.33 24 29
Syndecan-2/TGFB1 0.014 0.019 -10000 0 -0.19 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.017 -10000 0 -0.17 3 3
Syndecan-2/Ezrin 0.023 0.022 -10000 0 -0.17 3 3
PRKACA 0.006 0.064 0.18 45 -0.18 2 47
angiogenesis 0.024 0.052 0.24 18 -0.19 4 22
MMP2 0.022 0.016 0.33 1 -10000 0 1
IL8 0.034 0.07 0.33 18 -0.33 2 20
calcineurin-NFAT signaling pathway 0.025 0.061 0.23 26 -0.19 7 33
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.009 0.029 0.11 1 -0.22 2 3
NFATC2 -0.013 0.041 0.11 1 -0.21 11 12
NFATC3 -0.009 0.025 0.11 1 -10000 0 1
CD40LG -0.033 0.14 0.28 18 -0.37 23 41
PTGS2 -0.037 0.15 0.29 21 -0.35 39 60
JUNB 0.018 0.026 -10000 0 -0.33 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.021 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.021 -10000 0 -10000 0 0
CALM1 0.014 0.02 -10000 0 -10000 0 0
JUN 0.013 0.033 -10000 0 -0.34 2 2
mol:Ca2+ -0.001 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.011 0.012 -10000 0 -10000 0 0
FOSL1 0.034 0.075 0.33 20 -0.33 3 23
CREM 0.021 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.022 0.093 0.28 15 -0.24 8 23
FOS -0.01 0.092 -10000 0 -0.33 28 28
IFNG -0.016 0.15 0.34 30 -0.34 17 47
AP-1/NFAT1-c-4 0.02 0.17 0.47 15 -0.37 18 33
FASLG -0.028 0.12 0.28 18 -0.33 18 36
NFAT1-c-4/ICER1 0.009 0.062 0.26 1 -0.2 8 9
IL2RA -0.015 0.15 0.35 34 -0.34 16 50
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSF2 -0.036 0.15 0.32 19 -0.38 31 50
JunB/Fra1/NFAT1-c-4 0.025 0.086 0.31 9 -0.23 8 17
IL4 -0.03 0.12 0.28 18 -0.33 17 35
IL2 0.001 0.1 -10000 0 -0.82 6 6
IL3 -0.013 0.13 -10000 0 -0.63 17 17
FKBP1A 0.021 0.005 -10000 0 -10000 0 0
BATF3 0.021 0.017 0.33 1 -10000 0 1
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.02 0.007 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.04 0.055 0.24 21 -0.23 4 25
AKT1 -0.023 0.1 0.34 6 -0.39 12 18
PTK2B -0.03 0.089 0.33 2 -0.44 8 10
VEGFR2 homodimer/Frs2 -0.008 0.086 -10000 0 -0.24 40 40
CAV1 -0.18 0.17 -10000 0 -0.33 228 228
CALM1 0.021 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.005 0.083 -10000 0 -0.23 37 37
endothelial cell proliferation -0.021 0.12 0.38 9 -0.35 19 28
mol:Ca2+ -0.037 0.075 0.17 6 -0.42 7 13
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.011 0.087 -10000 0 -0.23 35 35
RP11-342D11.1 -0.034 0.075 0.16 11 -0.44 7 18
CDH5 -0.016 0.11 -10000 0 -0.33 41 41
VEGFA homodimer 0.042 0.024 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
SHC2 0.014 0.047 -10000 0 -0.33 7 7
HRAS/GDP 0.007 0.072 -10000 0 -0.38 7 7
SH2D2A 0.02 0.017 0.33 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.02 0.13 -10000 0 -0.42 27 27
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.003 0.086 0.22 1 -0.24 35 36
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.023 0.083 -10000 0 -0.41 7 7
GRB10 -0.035 0.075 -10000 0 -0.44 7 7
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
PAK1 0.021 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.006 0.12 -10000 0 -0.41 18 18
HRAS 0.021 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.009 0.074 -10000 0 -0.32 12 12
HIF1A 0.021 0.004 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.01 0.086 -10000 0 -0.23 35 35
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.012 0.055 -10000 0 -0.33 10 10
Nck/Pak 0.03 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.002 0.086 -10000 0 -0.23 39 39
mol:GDP 0.013 0.077 -10000 0 -0.4 7 7
mol:NADP -0.025 0.13 0.36 6 -0.39 29 35
eNOS/Hsp90 -0.016 0.13 0.4 4 -0.38 27 31
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:IP3 -0.038 0.075 0.17 5 -0.42 7 12
HIF1A/ARNT 0.026 0.013 -10000 0 -10000 0 0
SHB 0.02 0.006 -10000 0 -10000 0 0
VEGFA 0.021 0.004 -10000 0 -10000 0 0
VEGFC 0.02 0.03 0.33 1 -0.33 2 3
FAK1/Vinculin -0.009 0.12 0.3 8 -0.41 16 24
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.022 0.1 0.22 21 -0.23 39 60
PTPN6 0.02 0.005 -10000 0 -10000 0 0
EPAS1 -0.019 0.12 -10000 0 -0.34 46 46
mol:L-citrulline -0.025 0.13 0.36 6 -0.39 29 35
ITGAV 0.022 0.002 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.015 0.081 -10000 0 -0.22 34 34
VEGFR2 homodimer/VEGFA homodimer 0.004 0.088 -10000 0 -0.24 37 37
VEGFR2/3 heterodimer -0.013 0.099 -10000 0 -0.26 42 42
VEGFB 0.021 0.003 -10000 0 -10000 0 0
MAPK11 -0.026 0.09 0.34 4 -0.38 10 14
VEGFR2 homodimer -0.044 0.095 -10000 0 -0.29 42 42
FLT1 0.02 0.005 -10000 0 -10000 0 0
NEDD4 0.02 0.018 -10000 0 -0.33 1 1
MAPK3 -0.027 0.091 0.35 6 -0.39 8 14
MAPK1 -0.026 0.087 0.31 6 -0.39 7 13
VEGFA145/NRP2 0.03 0.019 -10000 0 -0.22 2 2
VEGFR1/2 heterodimer -0.01 0.091 -10000 0 -0.25 41 41
KDR -0.044 0.095 -10000 0 -0.29 42 42
VEGFA165/NRP1/VEGFR2 homodimer 0.005 0.084 -10000 0 -0.46 7 7
SRC 0.021 0.005 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.023 0.1 0.34 10 -0.39 8 18
PI3K -0.039 0.078 -10000 0 -0.41 9 9
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.004 0.088 -10000 0 -0.24 38 38
FES -0.039 0.077 0.17 10 -0.45 7 17
GAB1 -0.024 0.095 -10000 0 -0.41 12 12
VEGFR2 homodimer/VEGFA homodimer/Src 0.003 0.087 -10000 0 -0.23 40 40
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
ARNT 0.018 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.094 0.13 -10000 0 -0.44 30 30
VEGFR2 homodimer/VEGFA homodimer/Yes 0.004 0.086 -10000 0 -0.24 37 37
PI3K/GAB1 -0.012 0.096 -10000 0 -0.41 10 10
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.026 0.085 -10000 0 -0.4 7 7
PRKACA 0.02 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.096 -10000 0 -0.24 42 42
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
CDC42 -0.037 0.078 0.17 11 -0.45 7 18
actin cytoskeleton reorganization 0.003 0.086 0.22 1 -0.24 35 36
PTK2 -0.022 0.11 0.35 3 -0.44 16 19
EDG1 -0.034 0.075 0.16 11 -0.44 7 18
mol:DAG -0.038 0.075 0.17 5 -0.42 7 12
CaM/Ca2+ -0.033 0.074 -10000 0 -0.39 7 7
MAP2K3 -0.032 0.075 0.34 1 -0.36 7 8
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.016 0.099 -10000 0 -0.46 7 7
PLCG1 -0.038 0.076 0.17 5 -0.43 7 12
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.013 0.086 -10000 0 -0.22 36 36
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
YES1 0.02 0.006 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.003 0.088 -10000 0 -0.23 40 40
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.004 0.085 -10000 0 -0.24 35 35
cell migration -0.019 0.12 0.29 5 -0.43 15 20
mol:PI-3-4-5-P3 -0.037 0.074 -10000 0 -0.38 9 9
FYN 0.019 0.019 -10000 0 -0.33 1 1
VEGFB/NRP1 -0.036 0.072 -10000 0 -0.42 7 7
mol:NO -0.025 0.13 0.36 6 -0.39 29 35
PXN 0.021 0.004 -10000 0 -10000 0 0
HRAS/GTP -0.041 0.059 -10000 0 -0.38 7 7
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.041 0.07 -10000 0 -0.46 7 7
VHL 0.021 0.004 -10000 0 -10000 0 0
ITGB3 0.034 0.079 0.33 21 -0.33 4 25
NOS3 -0.029 0.14 0.39 5 -0.44 29 34
VEGFR2 homodimer/VEGFA homodimer/Sck -0.001 0.094 -10000 0 -0.25 39 39
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.034 0.076 -10000 0 -0.43 6 6
PRKCB -0.038 0.082 0.33 1 -0.41 8 9
VCL 0.021 0.003 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.033 0.076 -10000 0 -0.44 7 7
VEGFR1/2 heterodimer/VEGFA homodimer 0.003 0.087 -10000 0 -0.23 39 39
VEGFA165/NRP2 0.03 0.019 -10000 0 -0.22 2 2
MAPKKK cascade -0.026 0.085 0.31 1 -0.41 6 7
NRP2 0.02 0.025 -10000 0 -0.33 2 2
VEGFC homodimer 0.02 0.03 0.33 1 -0.33 2 3
NCK1 0.021 0.003 -10000 0 -10000 0 0
ROCK1 0.021 0.005 -10000 0 -10000 0 0
FAK1/Paxillin -0.01 0.12 0.27 7 -0.42 16 23
MAP3K13 -0.035 0.073 0.17 11 -0.4 7 18
PDPK1 -0.036 0.072 0.24 2 -0.35 9 11
Regulation of Androgen receptor activity

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
HDAC1 -0.017 0.005 -10000 0 -10000 0 0
SMARCC1 0.002 0.012 -10000 0 -10000 0 0
REL 0.021 0.007 -10000 0 -10000 0 0
HDAC7 -0.037 0.079 0.31 3 -0.28 16 19
JUN 0.019 0.025 -10000 0 -0.33 2 2
EP300 0.021 0.004 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
KAT5 0.021 0.003 -10000 0 -10000 0 0
MAPK14 -0.013 0.037 0.16 11 -0.25 2 13
FOXO1 0.02 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.036 0.079 -10000 0 -0.29 16 16
MAP2K6 0.023 0.058 0.33 10 -0.34 2 12
BRM/BAF57 0.027 0.022 -10000 0 -0.23 2 2
MAP2K4 0.016 0.016 -10000 0 -10000 0 0
SMARCA2 0.018 0.026 -10000 0 -0.33 2 2
PDE9A -0.034 0.16 -10000 0 -0.89 11 11
NCOA2 0.018 0.026 -10000 0 -0.33 2 2
CEBPA 0.002 0.077 -10000 0 -0.33 20 20
EHMT2 0.021 0.005 -10000 0 -10000 0 0
cell proliferation -0.029 0.14 0.36 14 -0.38 21 35
NR0B1 0.082 0.12 0.33 79 -10000 0 79
EGR1 -0.001 0.086 -10000 0 -0.33 25 25
RXRs/9cRA -0.06 0.1 -10000 0 -0.18 172 172
AR/RACK1/Src -0.013 0.085 0.32 8 -0.29 2 10
AR/GR -0.02 0.087 0.22 4 -0.23 42 46
GNB2L1 0.021 0.005 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
RCHY1 0.021 0.004 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 0.016 1 -10000 0 1
MAPK8 -0.016 0.014 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.019 0.069 0.22 2 -0.28 3 5
SRC -0.023 0.034 0.19 4 -0.2 2 6
NR3C1 0.021 0.004 -10000 0 -10000 0 0
KLK3 0.01 0.096 -10000 0 -0.42 1 1
APPBP2 0.016 0.016 -10000 0 -10000 0 0
TRIM24 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.023 0.063 0.21 3 -0.31 2 5
TMPRSS2 -0.085 0.28 -10000 0 -0.9 38 38
RXRG -0.14 0.17 -10000 0 -0.33 174 174
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.021 0.004 -10000 0 -10000 0 0
RXRB 0.021 0.005 -10000 0 -10000 0 0
CARM1 0.021 0.006 -10000 0 -10000 0 0
NR2C2 0.021 0.004 -10000 0 -10000 0 0
KLK2 -0.004 0.086 0.3 18 -10000 0 18
AR -0.029 0.078 0.19 2 -0.24 43 45
SENP1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
MDM2 0.019 0.009 -10000 0 -10000 0 0
SRY 0 0.003 -10000 0 -0.028 5 5
GATA2 -0.01 0.1 -10000 0 -0.33 35 35
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.12 0.15 0.33 130 -10000 0 130
T-DHT/AR/RACK1/Src -0.018 0.079 0.35 6 -0.3 2 8
positive regulation of transcription -0.01 0.1 -10000 0 -0.33 35 35
DNAJA1 0.016 0.017 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.012 0.17 2 -10000 0 2
NCOA1 0.024 0.014 -10000 0 -10000 0 0
SPDEF 0.12 0.15 0.33 123 -0.33 3 126
T-DHT/AR/TIF2 -0.008 0.071 0.25 5 -0.3 5 10
T-DHT/AR/Hsp90 -0.022 0.062 0.22 2 -0.31 2 4
GSK3B 0.018 0.013 -10000 0 -10000 0 0
NR2C1 0.021 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.022 0.029 0.21 1 -0.21 2 3
SIRT1 0.021 0.003 -10000 0 -10000 0 0
ZMIZ2 0.019 0.01 -10000 0 -10000 0 0
POU2F1 0.009 0.04 -10000 0 -0.18 3 3
T-DHT/AR/DAX-1 0.017 0.11 0.22 61 -0.31 2 63
CREBBP 0.021 0.004 -10000 0 -10000 0 0
SMARCE1 0.021 0.005 -10000 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.036 0.056 0.24 4 -0.24 19 23
KIRREL 0.017 0.038 -10000 0 -0.34 4 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.036 0.056 0.24 19 -0.24 4 23
PLCG1 0.021 0.005 -10000 0 -10000 0 0
ARRB2 0.02 0.006 -10000 0 -10000 0 0
WASL 0.021 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.052 0.054 0.22 19 -0.18 4 23
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.013 0.038 0.16 2 -0.2 4 6
FYN 0.017 0.085 0.21 53 -0.18 4 57
mol:Ca2+ 0.049 0.052 0.22 19 -0.18 4 23
mol:DAG 0.05 0.053 0.22 19 -0.18 4 23
NPHS2 -0.004 0.024 -10000 0 -10000 0 0
mol:IP3 0.05 0.053 0.22 19 -0.18 4 23
regulation of endocytosis 0.035 0.046 0.2 16 -0.17 4 20
Nephrin/NEPH1/podocin/Cholesterol 0.042 0.05 0.21 19 -0.18 4 23
establishment of cell polarity 0.036 0.056 0.24 19 -0.24 4 23
Nephrin/NEPH1/podocin/NCK1-2 0.06 0.055 0.28 1 -0.17 4 5
Nephrin/NEPH1/beta Arrestin2 0.037 0.047 0.21 16 -0.17 4 20
NPHS1 0.038 0.078 0.34 23 -10000 0 23
Nephrin/NEPH1/podocin 0.039 0.048 0.21 19 -0.17 5 24
TJP1 0.021 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.022 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.052 0.054 0.22 19 -0.18 4 23
CD2AP 0.021 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.051 0.053 0.22 18 -0.18 4 22
GRB2 0.021 0.005 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.007 0.096 0.22 49 -0.18 22 71
cytoskeleton organization -0.004 0.052 0.22 11 -0.21 4 15
Nephrin/NEPH1 0.03 0.044 0.19 19 -0.16 4 23
Nephrin/NEPH1/ZO-1 0.041 0.049 0.22 17 -0.19 4 21
Ceramide signaling pathway

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
SPHK2 -0.02 0.033 -10000 0 -0.23 9 9
MAP4K4 -0.007 0.053 -10000 0 -0.27 4 4
BAG4 0.019 0.008 -10000 0 -10000 0 0
PKC zeta/ceramide 0.002 0.066 -10000 0 -0.18 44 44
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.022 0.04 0.33 4 -0.33 2 6
BAX -0.01 0.076 -10000 0 -0.34 17 17
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.006 0.12 0.71 10 -10000 0 10
BAD -0.013 0.062 0.2 2 -0.18 44 46
SMPD1 0.005 0.059 0.2 10 -0.22 4 14
RB1 -0.015 0.06 -10000 0 -0.18 44 44
FADD/Caspase 8 0 0.06 0.2 8 -0.27 4 12
MAP2K4 -0.017 0.059 0.18 3 -0.17 40 43
NSMAF 0.02 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.016 0.065 0.22 7 -0.17 43 50
EGF 0.075 0.13 0.33 72 -0.33 4 76
mol:ceramide -0.009 0.065 0.12 5 -0.18 44 49
MADD 0.021 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.017 0.03 -10000 0 -0.23 7 7
ASAH1 0.018 0.008 -10000 0 -10000 0 0
negative regulation of cell cycle -0.014 0.06 -10000 0 -0.17 44 44
cell proliferation 0.001 0.068 0.21 5 -0.21 3 8
BID -0.003 0.11 -10000 0 -0.59 10 10
MAP3K1 -0.012 0.063 0.19 4 -0.18 42 46
EIF2A -0.015 0.071 0.21 14 -0.18 32 46
TRADD 0.021 0.004 -10000 0 -10000 0 0
CRADD 0.022 0.016 0.33 1 -10000 0 1
MAPK3 -0.015 0.063 0.2 7 -0.17 21 28
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.018 0.065 0.2 7 -0.18 23 30
Cathepsin D/ceramide 0.003 0.066 -10000 0 -0.18 44 44
FADD -0.005 0.051 -10000 0 -0.27 4 4
KSR1 -0.011 0.069 0.24 7 -0.18 43 50
MAPK8 -0.012 0.067 -10000 0 -0.27 5 5
PRKRA -0.011 0.066 0.23 5 -0.18 42 47
PDGFA 0.012 0.05 -10000 0 -0.33 8 8
TRAF2 0.021 0.004 -10000 0 -10000 0 0
IGF1 0.018 0.043 0.33 1 -0.33 5 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.009 0.064 0.12 5 -0.18 44 49
CTSD 0.021 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.031 0.006 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.002 0.072 0.23 5 -0.22 3 8
PRKCD 0.021 0.004 -10000 0 -10000 0 0
PRKCZ 0.018 0.031 -10000 0 -0.33 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.017 0.03 -10000 0 -0.23 7 7
RelA/NF kappa B1 0.031 0.006 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.021 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.004 0.05 0.16 2 -0.28 3 5
TNFR1A/BAG4/TNF-alpha 0.025 0.052 0.23 1 -0.2 18 19
mol:Sphingosine-1-phosphate -0.02 0.033 -10000 0 -0.23 9 9
MAP2K1 -0.018 0.064 0.19 10 -0.17 34 44
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
CYCS 0.004 0.052 0.18 3 -0.17 12 15
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.013 -10000 0 -10000 0 0
EIF2AK2 -0.014 0.065 0.2 9 -0.17 40 49
TNF-alpha/TNFR1A/FAN 0.026 0.051 0.23 1 -0.2 16 17
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.05 -10000 0 -0.32 4 4
MAP2K2 -0.019 0.062 0.21 7 -0.18 31 38
SMPD3 0.005 0.058 0.18 4 -0.26 6 10
TNF 0.005 0.077 0.33 1 -0.33 19 20
PKC zeta/PAR4 0.028 0.024 -10000 0 -0.23 3 3
mol:PHOSPHOCHOLINE -0.02 0.066 0.17 8 -0.14 49 57
NF kappa B1/RelA/I kappa B alpha 0.049 0.032 -10000 0 -0.18 2 2
AIFM1 -0.003 0.061 0.17 4 -0.18 12 16
BCL2 0.02 0.017 0.33 1 -10000 0 1
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.016 0.083 0.21 34 -10000 0 34
GNAI2 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.012 0.052 0.21 1 -0.19 22 23
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.021 0.034 0.33 2 -0.33 2 4
RhoA/GTP -0.016 0.084 -10000 0 -0.21 34 34
negative regulation of cAMP metabolic process -0.019 0.08 -10000 0 -0.2 58 58
GNAZ -0.01 0.099 -10000 0 -0.33 34 34
GNAI3 0.021 0.004 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
S1PR5 0.001 0.084 0.33 1 -0.33 23 24
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.019 0.081 -10000 0 -0.2 58 58
RhoA/GDP 0.016 0.003 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.018 -10000 0 -0.33 1 1
FAS signaling pathway (CD95)

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
SPTAN1 -0.014 0.034 -10000 0 -0.2 10 10
RFC1 -0.009 0.044 0.22 7 -0.21 8 15
PRKDC -0.001 0.057 0.22 20 -0.19 7 27
RIPK1 0.023 0.007 -10000 0 -10000 0 0
CASP7 -0.016 0.1 -10000 0 -0.67 8 8
FASLG/FAS/FADD/FAF1 0.004 0.057 0.16 22 -0.27 3 25
MAP2K4 -0.062 0.14 0.23 3 -0.32 73 76
mol:ceramide -0.02 0.078 -10000 0 -0.26 12 12
GSN -0.014 0.034 -10000 0 -0.2 10 10
FASLG/FAS/FADD/FAF1/Caspase 8 -0.004 0.061 0.2 1 -0.29 3 4
FAS 0.006 0.042 -10000 0 -0.34 4 4
BID -0.023 0.016 -10000 0 -0.2 2 2
MAP3K1 -0.032 0.1 0.24 2 -0.44 11 13
MAP3K7 0.011 0.018 -10000 0 -10000 0 0
RB1 -0.012 0.027 -10000 0 -0.19 8 8
CFLAR 0.024 0.005 -10000 0 -10000 0 0
HGF/MET 0.008 0.1 0.23 8 -0.23 52 60
ARHGDIB -0.011 0.038 0.22 4 -0.2 8 12
FADD 0.009 0.023 -10000 0 -10000 0 0
actin filament polymerization 0.015 0.036 0.2 12 -10000 0 12
NFKB1 -0.023 0.1 -10000 0 -0.68 4 4
MAPK8 -0.1 0.21 0.24 1 -0.47 85 86
DFFA -0.012 0.033 0.21 2 -0.19 9 11
DNA fragmentation during apoptosis -0.012 0.04 0.21 4 -0.18 12 16
FAS/FADD/MET 0.017 0.06 0.23 5 -0.2 15 20
CFLAR/RIP1 0.035 0.01 -10000 0 -10000 0 0
FAIM3 0.022 0.023 0.33 2 -10000 0 2
FAF1 0.009 0.025 -10000 0 -10000 0 0
PARP1 -0.013 0.037 0.22 2 -0.2 10 12
DFFB -0.011 0.037 0.21 4 -0.19 9 13
CHUK -0.029 0.096 -10000 0 -0.64 4 4
FASLG 0.007 0.034 -10000 0 -0.34 2 2
FAS/FADD 0.013 0.04 -10000 0 -0.25 4 4
HGF 0.009 0.075 0.33 3 -0.33 16 19
LMNA -0.008 0.055 0.19 19 -0.19 12 31
CASP6 -0.013 0.036 0.21 2 -0.21 9 11
CASP10 0.008 0.029 -10000 0 -0.34 1 1
CASP3 -0.006 0.026 -10000 0 -0.27 3 3
PTPN13 -0.016 0.11 -10000 0 -0.33 42 42
CASP8 -0.023 0.02 -10000 0 -0.23 3 3
IL6 -0.23 0.47 -10000 0 -1.1 87 87
MET 0.013 0.072 0.33 5 -0.33 13 18
ICAD/CAD -0.014 0.044 0.3 4 -0.18 9 13
FASLG/FAS/FADD/FAF1/Caspase 10 -0.02 0.078 -10000 0 -0.26 12 12
activation of caspase activity by cytochrome c -0.023 0.016 -10000 0 -0.2 2 2
PAK2 -0.009 0.044 0.21 8 -0.2 8 16
BCL2 0.021 0.017 0.33 1 -10000 0 1
EPHB forward signaling

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
Ephrin A5/EPHB2 0.048 0.066 0.22 44 -0.17 3 47
cell-cell adhesion 0.02 0.033 0.16 5 -10000 0 5
Ephrin B/EPHB2/RasGAP 0.066 0.068 0.23 41 -0.17 6 47
ITSN1 0.021 0.004 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.03 0.032 0.21 8 -0.19 2 10
Ephrin B1/EPHB1 0.046 0.061 0.21 42 -0.19 3 45
HRAS/GDP 0.013 0.072 -10000 0 -0.23 12 12
Ephrin B/EPHB1/GRB7 0.063 0.066 0.23 32 -0.17 8 40
Endophilin/SYNJ1 -0.009 0.048 0.18 14 -10000 0 14
KRAS 0.02 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.064 0.064 0.23 34 -0.17 6 40
endothelial cell migration 0.037 0.025 -10000 0 -0.17 3 3
GRB2 0.021 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.025 -10000 0 -0.33 2 2
PAK1 -0.013 0.055 0.21 8 -0.29 1 9
HRAS 0.021 0.004 -10000 0 -10000 0 0
RRAS -0.012 0.049 0.18 12 -0.31 1 13
DNM1 0.024 0.031 0.33 4 -10000 0 4
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.011 0.049 0.2 13 -10000 0 13
lamellipodium assembly -0.02 0.033 -10000 0 -0.16 5 5
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.014 0.057 0.2 7 -0.2 11 18
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
EPHB2 0.057 0.1 0.33 46 -10000 0 46
EPHB3 0.027 0.044 0.33 8 -10000 0 8
EPHB1 0.054 0.099 0.33 43 -0.33 1 44
EPHB4 0.021 0.005 -10000 0 -10000 0 0
mol:GDP -0.006 0.051 0.22 7 -0.27 4 11
Ephrin B/EPHB2 0.059 0.064 0.22 43 -0.17 6 49
Ephrin B/EPHB3 0.043 0.039 0.22 6 -0.17 6 12
JNK cascade -0.002 0.063 0.26 10 -0.18 3 13
Ephrin B/EPHB1 0.056 0.061 0.22 35 -0.17 7 42
RAP1/GDP -0.012 0.08 0.23 14 -0.25 10 24
EFNB2 0.018 0.031 -10000 0 -0.33 3 3
EFNB3 0.02 0.024 0.33 1 -0.33 1 2
EFNB1 0.02 0.025 -10000 0 -0.33 2 2
Ephrin B2/EPHB1-2 0.073 0.086 0.23 77 -0.18 4 81
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.042 0.065 0.21 5 -0.21 6 11
Rap1/GTP -0.019 0.044 0.099 5 -10000 0 5
axon guidance 0.047 0.066 0.22 44 -0.17 3 47
MAPK3 -0.003 0.054 0.24 6 -0.26 2 8
MAPK1 -0.003 0.05 0.22 4 -0.26 2 6
Rac1/GDP -0.017 0.069 0.22 6 -0.25 10 16
actin cytoskeleton reorganization -0.027 0.044 0.093 4 -0.19 5 9
CDC42/GDP -0.012 0.081 0.23 15 -0.25 11 26
PI3K 0.041 0.027 -10000 0 -0.17 3 3
EFNA5 0.02 0.038 0.33 2 -0.33 3 5
Ephrin B2/EPHB4 0.024 0.021 -10000 0 -0.19 3 3
Ephrin B/EPHB2/Intersectin/N-WASP 0.008 0.061 0.18 3 -0.22 6 9
CDC42 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.022 0.038 -10000 0 -10000 0 0
PTK2 0.056 0.19 0.53 52 -10000 0 52
MAP4K4 -0.002 0.063 0.26 10 -0.18 3 13
SRC 0.021 0.005 -10000 0 -10000 0 0
KALRN 0.019 0.031 -10000 0 -0.33 3 3
Intersectin/N-WASP 0.03 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis 0.002 0.088 0.27 20 -0.31 1 21
MAP2K1 0.006 0.052 0.19 9 -0.21 7 16
WASL 0.021 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.089 0.086 0.25 79 -0.18 3 82
cell migration 0.013 0.087 0.28 13 -0.28 5 18
NRAS 0.021 0.005 -10000 0 -10000 0 0
SYNJ1 -0.009 0.048 0.18 14 -10000 0 14
PXN 0.021 0.004 -10000 0 -10000 0 0
TF 0.007 0.07 0.22 16 -10000 0 16
HRAS/GTP 0.043 0.05 0.18 6 -0.16 7 13
Ephrin B1/EPHB1-2 0.076 0.085 0.23 79 -0.18 3 82
cell adhesion mediated by integrin 0.015 0.037 0.17 6 -0.2 7 13
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:GTP 0.05 0.058 0.22 7 -0.16 7 14
RAC1-CDC42/GTP -0.022 0.036 -10000 0 -0.17 5 5
RASA1 0.021 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.018 0.07 0.22 6 -0.25 9 15
ruffle organization 0.01 0.097 0.34 16 -10000 0 16
NCK1 0.021 0.003 -10000 0 -10000 0 0
receptor internalization -0.014 0.045 0.17 13 -10000 0 13
Ephrin B/EPHB2/KALRN 0.067 0.072 0.23 43 -0.19 8 51
ROCK1 -0.012 0.034 0.18 9 -0.18 2 11
RAS family/GDP -0.033 0.038 -10000 0 -0.2 5 5
Rac1/GTP -0.017 0.042 0.12 5 -0.17 5 10
Ephrin B/EPHB1/Src/Paxillin 0.008 0.059 0.18 1 -0.22 6 7
Class IB PI3K non-lipid kinase 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
cAMP biosynthetic process -0.008 0.067 0.33 15 -10000 0 15
PI3K Class IB/PDE3B 0.008 0.067 -10000 0 -0.33 15 15
PDE3B 0.008 0.067 -10000 0 -0.33 15 15
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.021 0.005 -10000 0 -9999 0 0
PLK4 0.038 0.07 0.33 21 -9999 0 21
regulation of centriole replication -0.007 0.041 0.16 21 -9999 0 21
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.021 0.005 -10000 0 -10000 0 0
VLDLR 0.013 0.047 -10000 0 -0.33 7 7
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
NUDC 0.021 0.004 -10000 0 -10000 0 0
RELN/LRP8 0.018 0.084 0.23 11 -0.2 44 55
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
KATNA1 0.02 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.029 0.068 0.17 17 -0.18 42 59
IQGAP1/CaM 0.03 0.008 -10000 0 -10000 0 0
DAB1 0.024 0.035 0.33 5 -10000 0 5
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
PLA2G7 0.024 0.046 0.33 6 -0.33 2 8
CALM1 0.021 0.005 -10000 0 -10000 0 0
DYNLT1 0.02 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.035 0.028 0.24 7 -10000 0 7
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.021 0.004 -10000 0 -10000 0 0
CDK5R1 0.028 0.047 0.33 9 -10000 0 9
LIS1/Poliovirus Protein 3A -0.012 0.005 -10000 0 -10000 0 0
CDK5R2 0.11 0.14 0.33 112 -10000 0 112
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.012 0.088 0.25 9 -0.2 47 56
YWHAE 0.02 0.007 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.005 0.094 0.29 17 -0.23 1 18
MAP1B 0.003 0.015 -10000 0 -0.22 1 1
RAC1 0.004 0.002 -10000 0 -10000 0 0
p35/CDK5 -0.03 0.072 0.18 20 -10000 0 20
RELN -0.015 0.12 0.33 5 -0.33 44 49
PAFAH/LIS1 -0.015 0.033 0.22 6 -0.2 2 8
LIS1/CLIP170 -0.018 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.019 0.064 0.16 2 -10000 0 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.022 0.091 0.26 2 -0.29 18 20
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.001 0.081 0.28 10 -0.23 1 11
LIS1/IQGAP1 -0.018 0.008 -10000 0 -10000 0 0
RHOA 0.005 0.002 -10000 0 -10000 0 0
PAFAH1B1 -0.016 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.033 0.062 0.33 16 -10000 0 16
PAFAH1B2 0.021 0.005 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.009 0.032 -10000 0 -0.17 4 4
NDEL1/Katanin 60/Dynein heavy chain 0.001 0.096 0.29 15 -10000 0 15
LRP8 0.028 0.044 0.33 8 -10000 0 8
NDEL1/Katanin 60 0.004 0.096 0.29 18 -0.23 2 20
P39/CDK5 0.022 0.12 0.2 106 -10000 0 106
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.018 0.008 -10000 0 -10000 0 0
CDK5 -0.033 0.061 0.17 12 -0.18 39 51
PPP2R5D 0.021 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.015 0.006 -10000 0 -10000 0 0
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.012 0.081 0.25 8 -0.18 47 55
RELN/VLDLR 0.022 0.088 0.23 11 -0.19 48 59
CDC42 0.005 0.002 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.021 0.004 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.007 0.13 -10000 0 -0.35 33 33
PTP1B/AKT1 0.012 0.076 0.21 3 -0.33 8 11
FYN 0.019 0.019 -10000 0 -0.33 1 1
p210 bcr-abl/PTP1B 0.005 0.08 0.24 4 -0.35 8 12
EGFR 0.016 0.045 0.33 1 -0.34 5 6
EGF/EGFR 0.035 0.1 0.22 35 -0.34 7 42
CSF1 0.02 0.018 -10000 0 -0.33 1 1
AKT1 0.019 0.01 -10000 0 -10000 0 0
INSR 0.02 0.008 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.032 0.098 0.24 33 -0.32 8 41
Insulin Receptor/Insulin 0.022 0.074 -10000 0 -0.36 5 5
HCK 0.008 0.065 -10000 0 -0.33 14 14
CRK 0.02 0.007 -10000 0 -10000 0 0
TYK2 0.002 0.077 0.28 4 -0.38 6 10
EGF 0.075 0.13 0.33 72 -0.34 4 76
YES1 0.02 0.006 -10000 0 -10000 0 0
CAV1 -0.052 0.11 0.23 6 -0.32 23 29
TXN 0.022 0.017 0.33 1 -10000 0 1
PTP1B/IRS1/GRB2 0.022 0.077 0.24 2 -0.32 7 9
cell migration -0.005 0.08 0.35 8 -0.24 4 12
STAT3 0.022 0.003 -10000 0 -10000 0 0
PRLR 0.024 0.095 0.33 21 -0.33 12 33
ITGA2B -0.012 0.11 0.33 3 -0.33 39 42
CSF1R 0.016 0.043 -10000 0 -0.33 6 6
Prolactin Receptor/Prolactin 0.03 0.074 0.25 25 -0.23 12 37
FGR -0.006 0.093 -10000 0 -0.33 30 30
PTP1B/p130 Cas 0.013 0.078 0.22 4 -0.34 8 12
Crk/p130 Cas 0.02 0.079 0.24 3 -0.34 7 10
DOK1 0.001 0.085 0.26 3 -0.34 11 14
JAK2 -0.007 0.13 0.24 3 -0.35 32 35
Jak2/Leptin Receptor/Leptin 0.028 0.1 0.24 8 -0.33 8 16
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
PTPN1 0.005 0.081 0.24 4 -0.35 8 12
LYN 0.02 0.007 -10000 0 -10000 0 0
CDH2 0.046 0.1 0.33 38 -0.33 5 43
SRC 0.01 0.086 -10000 0 -0.45 10 10
ITGB3 0.031 0.081 0.33 21 -0.33 4 25
CAT1/PTP1B -0.028 0.14 0.3 4 -0.37 35 39
CAPN1 0.021 0.005 -10000 0 -10000 0 0
CSK 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.026 0.07 -10000 0 -0.3 5 5
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.092 0.23 4 -0.31 7 11
negative regulation of transcription -0.007 0.13 0.24 3 -0.35 32 35
FCGR2A 0.017 0.026 -10000 0 -0.33 2 2
FER 0.021 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.015 0.1 0.24 24 -0.24 42 66
BLK 0.053 0.1 0.33 45 -0.33 1 46
Insulin Receptor/Insulin/Shc 0.033 0.018 -10000 0 -10000 0 0
RHOA 0.021 0.005 -10000 0 -10000 0 0
LEPR -0.003 0.088 -10000 0 -0.32 27 27
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
p210 bcr-abl/Grb2 0.021 0.005 -10000 0 -10000 0 0
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.045 0.16 0.2 2 -0.35 54 56
PRL 0.024 0.045 0.33 8 -10000 0 8
SOCS3 0.001 0.13 -10000 0 -1.1 6 6
SPRY2 0.019 0.02 -10000 0 -0.33 1 1
Insulin Receptor/Insulin/IRS1 0.038 0.017 -10000 0 -0.19 1 1
CSF1/CSF1R 0.02 0.084 0.23 2 -0.35 9 11
Ras protein signal transduction 0.008 0.12 0.55 16 -10000 0 16
IRS1 0.021 0.018 -10000 0 -0.33 1 1
INS 0.011 0.016 -10000 0 -10000 0 0
LEP 0.051 0.095 0.33 40 -10000 0 40
STAT5B 0.006 0.092 0.23 6 -0.31 16 22
STAT5A 0.006 0.093 0.24 5 -0.33 13 18
GRB2 0.021 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.079 0.24 3 -0.33 8 11
CSN2 0.022 0.067 0.49 1 -10000 0 1
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
LAT 0.016 0.062 -10000 0 -0.38 6 6
YBX1 0.024 0.005 -10000 0 -10000 0 0
LCK 0.021 0.024 0.33 1 -0.33 1 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
NOX4 0.032 0.056 0.33 13 -10000 0 13
Coregulation of Androgen receptor activity

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
NRIP1 0.021 0.006 -10000 0 -10000 0 0
SVIL 0.021 0.004 -10000 0 -10000 0 0
ZNF318 0.02 0.009 -10000 0 -10000 0 0
JMJD2C 0.007 0.028 0.13 19 -10000 0 19
T-DHT/AR/Ubc9 0.005 0.088 0.18 5 -0.2 50 55
CARM1 0.02 0.006 -10000 0 -10000 0 0
PRDX1 0.021 0.005 -10000 0 -10000 0 0
PELP1 0.019 0.008 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.02 0.008 -10000 0 -10000 0 0
PTK2B 0.018 0.008 -10000 0 -10000 0 0
MED1 0.02 0.007 -10000 0 -10000 0 0
MAK 0.009 0.065 0.33 1 -0.33 13 14
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.018 0.031 -10000 0 -0.33 3 3
GSN 0.021 0.005 -10000 0 -10000 0 0
NCOA2 0.018 0.026 -10000 0 -0.33 2 2
NCOA6 0.021 0.005 -10000 0 -10000 0 0
DNA-PK 0.037 0.018 -10000 0 -10000 0 0
NCOA4 0.022 0.002 -10000 0 -10000 0 0
PIAS3 0.021 0.005 -10000 0 -10000 0 0
cell proliferation -0.012 0.12 0.26 1 -0.62 13 14
XRCC5 0.021 0.006 -10000 0 -10000 0 0
UBE3A 0.021 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF 0 0.094 0.18 5 -0.2 58 63
FHL2 0.044 0.11 0.32 46 -10000 0 46
RANBP9 0.021 0.005 -10000 0 -10000 0 0
JMJD1A -0.009 0.037 -10000 0 -0.13 35 35
CDK6 0.02 0.018 -10000 0 -0.33 1 1
TGFB1I1 0.02 0.025 -10000 0 -0.33 2 2
T-DHT/AR/CyclinD1 0.005 0.089 0.18 5 -0.21 48 53
XRCC6 0.021 0.007 -10000 0 -10000 0 0
T-DHT/AR 0.018 0.11 0.27 8 -0.21 54 62
CTDSP1 0.022 0.002 -10000 0 -10000 0 0
CTDSP2 0.02 0.008 -10000 0 -10000 0 0
BRCA1 0.022 0.004 -10000 0 -10000 0 0
TCF4 0.017 0.026 -10000 0 -0.33 2 2
CDKN2A 0.097 0.14 0.33 103 -10000 0 103
SRF 0.04 0.047 0.17 1 -10000 0 1
NKX3-1 -0.028 0.12 -10000 0 -0.38 29 29
KLK3 -0.01 0.059 -10000 0 -10000 0 0
TMF1 0.021 0.004 -10000 0 -10000 0 0
HNRNPA1 0.021 0.007 -10000 0 -10000 0 0
AOF2 0 0.002 -10000 0 -10000 0 0
APPL1 -0.017 0.006 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.006 0.089 0.18 4 -0.2 50 54
AR -0.021 0.12 0.33 1 -0.34 49 50
UBA3 0.021 0.004 -10000 0 -10000 0 0
PATZ1 0.02 0.007 -10000 0 -10000 0 0
PAWR 0.021 0.004 -10000 0 -10000 0 0
PRKDC 0.019 0.008 -10000 0 -10000 0 0
PA2G4 0.02 0.007 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.006 0.08 0.17 4 -0.18 49 53
RPS6KA3 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.007 0.088 0.18 5 -0.2 49 54
LATS2 0.019 0.008 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.007 0.079 0.17 4 -0.18 49 53
Cyclin D3/CDK11 p58 0.015 0.004 -10000 0 -10000 0 0
VAV3 0.019 0.035 0.33 1 -0.33 3 4
KLK2 0.007 0.081 0.32 15 -0.34 3 18
CASP8 0.02 0.019 -10000 0 -0.33 1 1
T-DHT/AR/TIF2/CARM1 0.016 0.082 0.2 2 -0.19 42 44
TMPRSS2 -0.06 0.22 -10000 0 -0.77 34 34
CCND1 0.016 0.04 -10000 0 -0.33 5 5
PIAS1 0.022 0.005 -10000 0 -10000 0 0
mol:T-DHT 0.002 0.019 0.06 6 -0.058 17 23
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.021 0.007 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.006 0.086 0.18 4 -0.2 47 51
CMTM2 -0.042 0.13 -10000 0 -0.33 70 70
SNURF 0.011 0.055 -10000 0 -0.33 10 10
ZMIZ1 0.02 0.028 -10000 0 -10000 0 0
CCND3 0.021 0.005 -10000 0 -10000 0 0
TGIF1 0.019 0.008 -10000 0 -10000 0 0
FKBP4 0.021 0.006 -10000 0 -10000 0 0
IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.015 0.096 -10000 0 -0.31 22 22
TBX21 -0.11 0.32 -10000 0 -1.1 26 26
B2M 0.021 0.007 -10000 0 -10000 0 0
TYK2 0.01 0.028 -10000 0 -10000 0 0
IL12RB1 0.002 0.061 -10000 0 -0.35 9 9
GADD45B -0.096 0.28 -10000 0 -1 20 20
IL12RB2 0.035 0.096 0.33 33 -0.34 2 35
GADD45G -0.087 0.27 -10000 0 -0.97 21 21
natural killer cell activation -0.004 0.012 -10000 0 -10000 0 0
RELB 0.021 0.005 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
IL18 0.007 0.053 -10000 0 -0.33 8 8
IL2RA 0.043 0.085 0.33 30 -0.33 1 31
IFNG 0.041 0.086 0.33 29 -0.33 2 31
STAT3 (dimer) -0.077 0.23 -10000 0 -0.74 27 27
HLA-DRB5 -0.014 0.1 -10000 0 -0.33 35 35
FASLG -0.077 0.27 -10000 0 -0.96 20 20
NF kappa B2 p52/RelB -0.076 0.27 -10000 0 -0.84 27 27
CD4 0.009 0.051 -10000 0 -0.33 8 8
SOCS1 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:6955 -0.002 0.008 -10000 0 -10000 0 0
CD3D 0.014 0.032 -10000 0 -0.35 2 2
CD3E 0.014 0.035 -10000 0 -0.33 3 3
CD3G 0.009 0.053 -10000 0 -0.34 8 8
IL12Rbeta2/JAK2 0.032 0.073 0.24 28 -0.24 3 31
CCL3 -0.09 0.27 -10000 0 -1 19 19
CCL4 -0.09 0.27 -10000 0 -0.98 20 20
HLA-A 0.021 0.008 -10000 0 -10000 0 0
IL18/IL18R 0.015 0.087 -10000 0 -0.25 29 29
NOS2 -0.13 0.37 -10000 0 -1.1 42 42
IL12/IL12R/TYK2/JAK2/SPHK2 -0.017 0.1 -10000 0 -0.32 26 26
IL1R1 -0.09 0.26 -10000 0 -0.99 19 19
IL4 0.004 0.027 -10000 0 -10000 0 0
JAK2 0.009 0.032 -10000 0 -0.32 1 1
EntrezGene:6957 -0.001 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.017 0.13 -10000 0 -1 5 5
RAB7A -0.078 0.22 -10000 0 -0.84 16 16
lysosomal transport -0.074 0.21 -10000 0 -0.79 16 16
FOS -0.12 0.34 -10000 0 -0.97 46 46
STAT4 (dimer) -0.075 0.26 -10000 0 -0.83 24 24
STAT5A (dimer) -0.065 0.27 -10000 0 -0.85 26 26
GZMA -0.087 0.26 -10000 0 -1 18 18
GZMB -0.098 0.3 -10000 0 -1.1 21 21
HLX 0.016 0.036 -10000 0 -0.33 4 4
LCK -0.09 0.28 -10000 0 -0.94 25 25
TCR/CD3/MHC II/CD4 -0.029 0.11 -10000 0 -0.3 39 39
IL2/IL2R 0.06 0.061 0.23 30 -0.28 3 33
MAPK14 -0.094 0.28 -10000 0 -0.94 24 24
CCR5 -0.082 0.25 -10000 0 -0.95 19 19
IL1B -0.009 0.089 0.34 1 -0.34 23 24
STAT6 -0.01 0.073 -10000 0 -0.3 1 1
STAT4 0.022 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.022 0.002 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
NFKB2 0.021 0.003 -10000 0 -10000 0 0
IL12B 0.012 0.041 0.31 3 -0.34 1 4
CD8A 0.02 0.036 0.33 1 -0.34 3 4
CD8B 0.02 0.046 0.33 3 -0.33 4 7
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.014 0.096 0.31 22 -10000 0 22
IL2RB 0.019 0.025 -10000 0 -0.33 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.068 0.23 -10000 0 -0.76 23 23
IL2RG 0.018 0.035 -10000 0 -0.33 4 4
IL12 0.017 0.05 0.22 3 -0.25 4 7
STAT5A 0.02 0.018 -10000 0 -0.33 1 1
CD247 0.014 0.029 -10000 0 -0.33 2 2
IL2 0.02 0.003 -10000 0 -10000 0 0
SPHK2 0.02 0.018 -10000 0 -0.33 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.007 0.052 0.34 1 -0.34 5 6
IL12/IL12R/TYK2/JAK2 -0.089 0.31 -10000 0 -1 24 24
MAP2K3 -0.1 0.29 -10000 0 -0.98 24 24
RIPK2 0.019 0.007 -10000 0 -10000 0 0
MAP2K6 -0.089 0.28 -10000 0 -0.9 27 27
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.066 -10000 0 -0.33 14 14
IL18RAP 0.001 0.072 -10000 0 -0.34 16 16
IL12Rbeta1/TYK2 0.012 0.053 -10000 0 -0.25 8 8
EOMES -0.007 0.15 -10000 0 -0.6 18 18
STAT1 (dimer) -0.058 0.23 -10000 0 -0.75 23 23
T cell proliferation -0.062 0.19 -10000 0 -0.6 25 25
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.002 0.07 -10000 0 -0.33 15 15
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.066 0.22 -10000 0 -0.62 32 32
ATF2 -0.088 0.26 -10000 0 -0.85 24 24
Nectin adhesion 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
PDGFRB 0.021 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.04 0.055 0.24 21 -0.23 4 25
PTK2 -0.02 0.1 -10000 0 -0.36 20 20
positive regulation of JNK cascade -0.018 0.11 -10000 0 -0.3 26 26
CDC42/GDP -0.016 0.15 -10000 0 -0.4 26 26
Rac1/GDP -0.019 0.14 -10000 0 -0.4 24 24
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.021 0.004 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.017 0.13 -10000 0 -0.36 26 26
nectin-3/I-afadin 0.014 0.061 -10000 0 -0.23 23 23
RAPGEF1 -0.034 0.14 0.28 1 -0.38 35 36
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.039 0.15 -10000 0 -0.42 38 38
PDGFB-D/PDGFRB 0.021 0.004 -10000 0 -10000 0 0
TLN1 -0.025 0.057 -10000 0 -0.35 9 9
Rap1/GTP -0.024 0.1 -10000 0 -0.29 34 34
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.016 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.014 0.061 -10000 0 -0.23 23 23
PVR 0.021 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.021 0.005 -10000 0 -10000 0 0
mol:GDP -0.033 0.17 -10000 0 -0.48 26 26
MLLT4 0.02 0.007 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PI3K 0.041 0.055 -10000 0 -0.17 19 19
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.033 0.035 0.24 10 -10000 0 10
positive regulation of lamellipodium assembly -0.02 0.11 -10000 0 -0.32 23 23
PVRL1 0.028 0.049 0.33 10 -10000 0 10
PVRL3 0.002 0.084 0.33 1 -0.33 23 24
PVRL2 0.021 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
CDH1 0.019 0.025 -10000 0 -0.33 2 2
CLDN1 0.026 0.058 0.33 10 -0.33 3 13
JAM-A/CLDN1 0.036 0.066 0.23 10 -0.2 19 29
SRC -0.04 0.16 -10000 0 -0.44 46 46
ITGB3 0.034 0.079 0.33 21 -0.33 4 25
nectin-1(dimer)/I-afadin/I-afadin 0.033 0.035 0.24 10 -10000 0 10
FARP2 -0.029 0.17 -10000 0 -0.52 15 15
RAC1 0.019 0.007 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.025 0.055 -10000 0 -0.2 21 21
nectin-1/I-afadin 0.033 0.035 0.24 10 -10000 0 10
nectin-2/I-afadin 0.028 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.025 0.011 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.029 0.06 0.23 8 -0.19 20 28
CDC42/GTP/IQGAP1/filamentous actin 0.028 0.007 -10000 0 -10000 0 0
F11R 0.018 0.019 -10000 0 -0.33 1 1
positive regulation of filopodium formation -0.018 0.11 -10000 0 -0.3 26 26
alphaV/beta3 Integrin/Talin -0.024 0.083 0.2 22 -0.32 11 33
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
PIP5K1C -0.02 0.061 -10000 0 -0.38 9 9
VAV2 -0.034 0.18 -10000 0 -0.51 24 24
RAP1/GDP -0.015 0.14 -10000 0 -0.36 24 24
ITGAV 0.022 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.025 0.056 -10000 0 -0.2 22 22
nectin-3(dimer)/I-afadin/I-afadin 0.014 0.061 -10000 0 -0.23 23 23
Rac1/GTP -0.022 0.14 -10000 0 -0.39 23 23
PTPRM -0.012 0.073 -10000 0 -0.24 27 27
E-cadherin/beta catenin/alpha catenin 0.051 0.04 -10000 0 -0.18 1 1
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC 0.035 0.1 0.26 27 -0.33 10 37
FYN 0.002 0.12 0.26 11 -0.36 18 29
LAT/GRAP2/SLP76 0.015 0.1 0.26 5 -0.35 16 21
IKBKB 0.019 0.008 -10000 0 -10000 0 0
AKT1 -0.002 0.096 0.24 10 -0.31 18 28
B2M 0.019 0.012 -10000 0 -10000 0 0
IKBKG -0.001 0.035 0.12 7 -0.1 2 9
MAP3K8 0.02 0.018 -10000 0 -0.33 1 1
mol:Ca2+ -0.017 0.014 0.084 2 -0.059 9 11
integrin-mediated signaling pathway 0.024 0.018 -10000 0 -0.19 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.007 0.12 0.24 8 -0.4 20 28
TRPV6 0.001 0.25 1.2 15 -10000 0 15
CD28 0.02 0.009 -10000 0 -10000 0 0
SHC1 0.02 0.12 0.26 35 -0.37 14 49
receptor internalization -0.008 0.12 0.2 1 -0.42 20 21
PRF1 -0.031 0.22 -10000 0 -0.91 21 21
KRAS 0.02 0.006 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
COT/AKT1 0.007 0.084 0.25 7 -0.27 14 21
LAT -0.002 0.11 0.27 8 -0.37 19 27
EntrezGene:6955 -0.001 0.005 -10000 0 -10000 0 0
CD3D 0.018 0.028 -10000 0 -0.34 2 2
CD3E 0.017 0.034 -10000 0 -0.34 3 3
CD3G 0.012 0.051 -10000 0 -0.33 8 8
RASGRP2 -0.009 0.039 -10000 0 -0.15 25 25
RASGRP1 -0.012 0.1 0.26 5 -0.36 13 18
HLA-A 0.019 0.012 -10000 0 -10000 0 0
RASSF5 0.018 0.026 -10000 0 -0.33 2 2
RAP1A/GTP/RAPL 0.025 0.018 -10000 0 -0.19 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.051 0.14 19 -0.13 6 25
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.034 -10000 0 -0.15 9 9
PRKCA -0.009 0.052 0.16 3 -0.21 6 9
GRAP2 0.011 0.058 -10000 0 -0.33 11 11
mol:IP3 0.015 0.087 0.17 32 -0.28 15 47
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.01 0.081 0.15 1 -0.34 14 15
ORAI1 -0.021 0.2 0.4 1 -0.98 15 16
CSK -0.001 0.11 0.27 3 -0.36 19 22
B7 family/CD28 0.018 0.12 -10000 0 -0.43 15 15
CHUK 0.021 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.005 0.12 -10000 0 -0.39 21 21
PTPN6 -0.007 0.1 0.22 4 -0.38 15 19
VAV1 -0.006 0.11 0.23 2 -0.37 20 22
Monovalent TCR/CD3 0.002 0.046 -10000 0 -0.26 9 9
CBL 0.021 0.005 -10000 0 -10000 0 0
LCK 0.005 0.11 0.26 8 -0.38 14 22
PAG1 0.005 0.11 0.24 9 -0.35 19 28
RAP1A 0.021 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.005 0.11 0.2 1 -0.38 19 20
CD80 0.012 0.053 -10000 0 -0.33 9 9
CD86 0.014 0.047 -10000 0 -0.33 7 7
PDK1/CARD11/BCL10/MALT1 0.003 0.049 0.15 2 -0.18 10 12
HRAS 0.021 0.004 -10000 0 -10000 0 0
GO:0035030 -0.016 0.095 0.19 5 -0.36 16 21
CD8A 0.018 0.037 0.33 1 -0.34 3 4
CD8B 0.019 0.047 0.33 3 -0.34 4 7
PTPRC 0.014 0.044 -10000 0 -0.33 6 6
PDK1/PKC theta -0.012 0.12 0.3 9 -0.34 22 31
CSK/PAG1 0.003 0.11 0.24 13 -0.37 15 28
SOS1 0.021 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.028 0.017 -10000 0 -10000 0 0
GRAP2/SLP76 0.017 0.12 0.23 2 -0.37 20 22
STIM1 -0.001 0.075 1.2 1 -10000 0 1
RAS family/GTP 0.012 0.061 0.18 11 -0.17 12 23
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.009 0.12 -10000 0 -0.44 20 20
mol:DAG -0.02 0.063 0.092 5 -0.24 19 24
RAP1A/GDP 0.009 0.024 0.08 9 -0.062 4 13
PLCG1 0.021 0.005 -10000 0 -10000 0 0
CD247 0.017 0.027 -10000 0 -0.32 2 2
cytotoxic T cell degranulation -0.029 0.21 -10000 0 -0.87 21 21
RAP1A/GTP -0.005 0.015 -10000 0 -0.06 24 24
mol:PI-3-4-5-P3 -0.003 0.1 0.22 9 -0.34 19 28
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.019 0.1 0.22 13 -0.35 15 28
NRAS 0.021 0.005 -10000 0 -10000 0 0
ZAP70 0.016 0.043 -10000 0 -0.33 6 6
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.011 0.098 0.28 3 -0.34 17 20
MALT1 0.019 0.007 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.028 0.051 0.31 3 -0.32 5 8
CARD11 0.033 0.066 0.33 18 -10000 0 18
PRKCB -0.013 0.059 0.17 1 -0.24 11 12
PRKCE -0.011 0.056 0.16 4 -0.21 9 13
PRKCQ -0.015 0.12 0.24 7 -0.37 24 31
LCP2 0.019 0.025 -10000 0 -0.33 2 2
BCL10 0.021 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression 0 0.086 0.23 10 -0.27 17 27
IKK complex 0.008 0.053 0.19 15 -0.11 3 18
RAS family/GDP -0.004 0.008 -10000 0 -10000 0 0
MAP3K14 -0.005 0.064 0.2 8 -0.21 12 20
PDPK1 -0.003 0.095 0.26 12 -0.3 16 28
TCR/CD3/MHC I/CD8/Fyn -0.013 0.12 -10000 0 -0.46 17 17
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN 0.034 0.11 0.27 17 -0.44 7 24
IKBKB 0.026 0.091 0.24 9 -0.28 11 20
AKT1 0.033 0.079 0.22 32 -0.23 1 33
IKBKG 0.032 0.068 0.25 4 -0.25 5 9
CALM1 0.018 0.085 0.26 5 -0.41 6 11
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
MAP3K1 0.041 0.13 0.28 20 -0.49 5 25
MAP3K7 0.019 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0.019 0.091 0.22 1 -0.46 6 7
DOK1 0.022 0.002 -10000 0 -10000 0 0
AP-1 0.019 0.079 0.22 12 -0.25 6 18
LYN 0.02 0.007 -10000 0 -10000 0 0
BLNK 0.02 0.018 -10000 0 -0.33 1 1
SHC1 0.018 0.008 -10000 0 -10000 0 0
BCR complex 0.071 0.1 0.26 75 -0.32 2 77
CD22 0.011 0.072 0.24 11 -0.41 3 14
CAMK2G 0.014 0.08 0.26 4 -0.38 6 10
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
INPP5D 0.019 0.031 -10000 0 -0.33 3 3
SHC/GRB2/SOS1 -0.006 0.05 0.16 7 -10000 0 7
GO:0007205 0.018 0.092 0.22 1 -0.47 6 7
SYK 0.019 0.025 -10000 0 -0.33 2 2
ELK1 0.014 0.088 0.23 2 -0.44 6 8
NFATC1 0.036 0.097 0.25 20 -0.35 6 26
B-cell antigen/BCR complex 0.071 0.1 0.26 75 -0.32 2 77
PAG1/CSK 0.028 0.012 -10000 0 -10000 0 0
NFKBIB 0.023 0.04 0.14 5 -0.13 3 8
HRAS 0.023 0.081 0.25 9 -0.37 4 13
NFKBIA 0.023 0.04 0.14 5 -0.13 3 8
NF-kappa-B/RelA/I kappa B beta 0.025 0.036 0.14 5 -10000 0 5
RasGAP/Csk 0.08 0.085 0.24 70 -0.15 2 72
mol:GDP 0.019 0.093 0.22 1 -0.46 6 7
PTEN 0.021 0.003 -10000 0 -10000 0 0
CD79B 0.026 0.048 0.33 8 -0.33 1 9
NF-kappa-B/RelA/I kappa B alpha 0.026 0.036 0.14 5 -10000 0 5
GRB2 0.021 0.005 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.048 0.12 0.31 12 -0.48 6 18
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:IP3 0.02 0.091 0.22 2 -0.51 5 7
CSK 0.021 0.003 -10000 0 -10000 0 0
FOS 0.003 0.093 0.26 5 -0.36 10 15
CHUK 0.028 0.077 0.25 4 -0.27 10 14
IBTK 0.02 0.007 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.035 0.079 -10000 0 -0.33 5 5
PTPN6 0.006 0.069 0.22 11 -0.38 4 15
RELA 0.021 0.003 -10000 0 -10000 0 0
BCL2A1 0.017 0.027 0.12 1 -10000 0 1
VAV2 0.049 0.093 0.27 16 -0.45 3 19
ubiquitin-dependent protein catabolic process 0.024 0.04 0.14 5 -0.13 4 9
BTK -0.045 0.25 -10000 0 -0.95 28 28
CD19 0.046 0.09 0.27 21 -0.39 2 23
MAP4K1 0.017 0.036 -10000 0 -0.33 4 4
CD72 0.021 0.016 0.33 1 -10000 0 1
PAG1 0.019 0.007 -10000 0 -10000 0 0
MAPK14 0.042 0.12 0.28 30 -0.42 5 35
SH3BP5 0.019 0.025 -10000 0 -0.33 2 2
PIK3AP1 0.02 0.092 0.24 1 -0.5 6 7
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.015 0.13 0.21 1 -0.58 11 12
RAF1 0.017 0.077 0.24 8 -0.36 4 12
RasGAP/p62DOK/SHIP 0.076 0.079 0.36 7 -0.24 2 9
CD79A 0.077 0.12 0.33 74 -0.33 2 76
re-entry into mitotic cell cycle 0.018 0.078 0.21 13 -0.25 6 19
RASA1 0.021 0.005 -10000 0 -10000 0 0
MAPK3 0.012 0.073 0.23 8 -0.31 4 12
MAPK1 0.013 0.068 0.22 9 -0.33 3 12
CD72/SHP1 0.023 0.091 0.26 13 -0.36 4 17
NFKB1 0.022 0.003 -10000 0 -10000 0 0
MAPK8 0.037 0.12 0.27 23 -0.42 5 28
actin cytoskeleton organization 0.063 0.1 0.28 34 -0.43 2 36
NF-kappa-B/RelA 0.051 0.071 0.26 5 -0.23 1 6
Calcineurin 0.032 0.079 0.32 1 -0.39 4 5
PI3K 0.003 0.068 0.19 7 -0.28 5 12
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.021 0.086 0.25 1 -0.52 5 6
SOS1 0.021 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.037 0.13 -10000 0 -0.58 10 10
DAPP1 0.024 0.13 -10000 0 -0.64 10 10
cytokine secretion 0.035 0.094 0.24 20 -0.33 6 26
mol:DAG 0.02 0.091 0.22 2 -0.51 5 7
PLCG2 0.018 0.031 -10000 0 -0.33 3 3
MAP2K1 0.013 0.074 0.24 8 -0.33 4 12
B-cell antigen/BCR complex/FcgammaRIIB 0.072 0.09 0.25 72 -0.18 2 74
mol:PI-3-4-5-P3 0.016 0.07 0.19 17 -0.25 2 19
ETS1 0.012 0.075 0.24 7 -0.39 3 10
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.082 0.087 0.24 71 -0.25 2 73
B-cell antigen/BCR complex/LYN 0.03 0.068 0.29 7 -0.4 3 10
MALT1 0.019 0.007 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.06 0.1 0.28 32 -0.45 2 34
B-cell antigen/BCR complex/LYN/SYK 0.056 0.1 0.36 12 -0.35 3 15
CARD11 0.035 0.1 0.28 11 -0.42 6 17
FCGR2B 0.019 0.007 -10000 0 -10000 0 0
PPP3CA 0.021 0.003 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
IKK complex 0.023 0.048 0.14 21 -0.12 3 24
PTPRC 0.014 0.043 -10000 0 -0.33 6 6
PDPK1 0.02 0.071 0.21 24 -0.21 1 25
PPP3CB 0.021 0.003 -10000 0 -10000 0 0
PPP3CC 0.018 0.008 -10000 0 -10000 0 0
POU2F2 0.019 0.027 0.12 5 -10000 0 5
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.042 0.044 0.22 8 -0.17 8 16
ER alpha/Gai/GDP/Gbeta gamma -0.036 0.14 -10000 0 -0.48 21 21
AKT1 -0.063 0.24 -10000 0 -0.68 47 47
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.06 0.24 -10000 0 -0.69 47 47
mol:Ca2+ -0.023 0.072 -10000 0 -0.34 17 17
IGF1R 0.02 0.018 -10000 0 -0.33 1 1
E2/ER alpha (dimer)/Striatin 0.027 0.043 0.21 10 -0.19 7 17
SHC1 0.018 0.008 -10000 0 -10000 0 0
apoptosis 0.06 0.23 0.65 47 -10000 0 47
RhoA/GTP -0.025 0.026 -10000 0 -0.16 7 7
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.02 0.12 0.24 2 -0.39 22 24
regulation of stress fiber formation 0.017 0.055 0.25 1 -0.25 3 4
E2/ERA-ERB (dimer) 0.026 0.044 0.21 10 -0.19 8 18
KRAS 0.02 0.006 -10000 0 -10000 0 0
G13/GTP 0.025 0.039 0.2 10 -0.17 7 17
pseudopodium formation -0.017 0.055 0.25 3 -0.25 1 4
E2/ER alpha (dimer)/PELP1 0.024 0.042 0.21 8 -0.19 8 16
GRB2 0.021 0.005 -10000 0 -10000 0 0
GNG2 0.02 0.018 -10000 0 -0.33 1 1
GNAO1 0.021 0.034 0.33 2 -0.33 2 4
HRAS 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.04 0.16 0.26 1 -0.42 46 47
E2/ER beta (dimer) 0.016 0.003 -10000 0 -10000 0 0
mol:GDP -0.005 0.071 0.18 11 -0.27 10 21
mol:NADP -0.04 0.16 0.26 1 -0.42 46 47
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:IP3 -0.024 0.075 -10000 0 -0.35 17 17
IGF-1R heterotetramer 0.02 0.018 -10000 0 -0.33 1 1
PLCB1 -0.009 0.07 -10000 0 -0.36 13 13
PLCB2 -0.011 0.074 -10000 0 -0.36 14 14
IGF1 0.018 0.043 0.33 1 -0.33 5 6
mol:L-citrulline -0.04 0.16 0.26 1 -0.42 46 47
RHOA 0.021 0.004 -10000 0 -10000 0 0
Gai/GDP -0.022 0.15 -10000 0 -0.6 21 21
JNK cascade 0.015 0.003 -10000 0 -10000 0 0
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
ESR2 0.021 0.004 -10000 0 -10000 0 0
GNAQ 0.02 0.018 -10000 0 -0.33 1 1
ESR1 0.02 0.071 0.33 10 -0.33 8 18
Gq family/GDP/Gbeta gamma -0.051 0.21 -10000 0 -0.73 33 33
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.012 0.065 -10000 0 -0.52 3 3
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.018 0.12 -10000 0 -0.39 21 21
GNAZ -0.01 0.099 -10000 0 -0.33 34 34
E2/ER alpha (dimer) 0.015 0.048 0.22 10 -0.22 8 18
STRN 0.021 0.003 -10000 0 -10000 0 0
GNAL 0.019 0.045 0.33 3 -0.33 4 7
PELP1 0.02 0.006 -10000 0 -10000 0 0
MAPK11 -0.013 0.018 0.22 1 -0.19 2 3
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.02 0.018 -10000 0 -0.33 1 1
HBEGF -0.043 0.15 0.35 9 -0.45 26 35
cAMP biosynthetic process 0.019 0.041 0.14 12 -0.18 10 22
SRC -0.035 0.13 0.28 1 -0.45 21 22
PI3K 0.03 0.009 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.018 0.068 -10000 0 -0.27 6 6
SOS1 0.021 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.028 0.093 -10000 0 -0.34 19 19
Gs family/GTP 0.025 0.045 0.17 12 -0.18 10 22
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.036 0.015 -10000 0 -10000 0 0
vasodilation -0.038 0.15 0.26 1 -0.4 46 47
mol:DAG -0.024 0.075 -10000 0 -0.35 17 17
Gs family/GDP/Gbeta gamma 0 0.065 -10000 0 -0.27 9 9
MSN -0.018 0.057 0.26 3 -0.26 1 4
Gq family/GTP -0.001 0.078 -10000 0 -0.37 15 15
mol:PI-3-4-5-P3 -0.057 0.23 -10000 0 -0.66 48 48
NRAS 0.021 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.038 0.15 0.4 46 -0.26 1 47
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.006 0.074 0.19 9 -0.26 10 19
NOS3 -0.043 0.17 0.26 1 -0.44 46 47
GNA11 0.02 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.034 0.17 0.32 3 -0.47 42 45
E2/ER alpha (dimer)/PELP1/Src -0.021 0.13 0.25 6 -0.41 21 27
ruffle organization -0.017 0.055 0.25 3 -0.25 1 4
ROCK2 -0.012 0.06 0.27 3 -10000 0 3
GNA14 0.012 0.055 -10000 0 -0.33 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
MMP9 -0.027 0.13 0.37 4 -0.44 19 23
MMP2 -0.033 0.13 0.27 8 -0.46 18 26
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.024 0.052 0.24 5 -0.23 12 17
CRKL -0.001 0.09 0.29 4 -0.4 8 12
mol:PIP3 0.01 0.009 -10000 0 -10000 0 0
AKT1 0.005 0.042 -10000 0 -10000 0 0
PTK2B 0.018 0.008 -10000 0 -10000 0 0
RAPGEF1 -0.005 0.084 0.27 4 -0.37 8 12
RANBP10 0.021 0.004 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.029 0.065 0.23 8 -0.2 24 32
MAP3K5 -0.004 0.093 0.27 5 -0.38 9 14
HGF/MET/CIN85/CBL/ENDOPHILINS 0.036 0.068 0.23 7 -0.19 25 32
AP1 -0.024 0.062 -10000 0 -0.21 25 25
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
apoptosis -0.065 0.24 -10000 0 -0.7 48 48
STAT3 (dimer) -0.012 0.078 0.23 1 -0.24 24 25
GAB1/CRKL/SHP2/PI3K 0.022 0.09 0.29 1 -0.38 8 9
INPP5D 0.019 0.031 -10000 0 -0.33 3 3
CBL/CRK 0.009 0.088 0.35 2 -0.36 8 10
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.021 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.003 -10000 0 -10000 0 0
ELK1 0.006 0.096 0.3 30 -10000 0 30
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.003 0.047 0.14 1 -0.25 6 7
PAK1 0.008 0.057 0.39 2 -10000 0 2
HGF/MET/RANBP10 0.027 0.068 0.23 8 -0.2 25 33
HRAS -0.009 0.12 0.29 1 -0.49 18 19
DOCK1 -0.006 0.088 0.27 5 -0.39 8 13
GAB1 0 0.086 0.23 1 -0.41 7 8
CRK -0.003 0.09 0.37 2 -0.4 8 10
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.011 0.12 -10000 0 -0.42 30 30
JUN 0.019 0.025 -10000 0 -0.33 2 2
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.003 0.053 0.15 4 -0.18 25 29
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.013 0.099 0.32 10 -0.32 10 20
GRB2/SHC 0.019 0.054 0.21 1 -0.2 11 12
FOS -0.004 0.09 -10000 0 -0.33 28 28
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.006 0.096 0.3 30 -10000 0 30
HGF/MET/MUC20 0.015 0.065 0.21 8 -0.2 27 35
cell migration 0.018 0.053 0.21 1 -0.2 11 12
GRB2 0.021 0.005 -10000 0 -10000 0 0
CBL 0.021 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.023 0.052 0.24 5 -0.23 12 17
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.01 0.067 0.18 1 -0.22 23 24
MET/MUC20 0.01 0.049 0.22 5 -0.22 13 18
RAP1B 0.001 0.088 0.26 7 -0.35 8 15
RAP1A -0.009 0.08 0.25 5 -0.35 8 13
HGF/MET/RANBP9 0.028 0.068 0.23 8 -0.2 25 33
RAF1 -0.008 0.12 0.27 1 -0.47 18 19
STAT3 -0.012 0.078 0.23 1 -0.24 24 25
cell proliferation 0 0.11 0.29 16 -0.31 20 36
RPS6KB1 0.004 0.031 -10000 0 -0.21 3 3
MAPK3 -0.003 0.083 0.42 4 -10000 0 4
MAPK1 0.013 0.13 0.5 19 -10000 0 19
RANBP9 0.021 0.004 -10000 0 -10000 0 0
MAPK8 -0.001 0.088 0.27 3 -0.34 9 12
SRC -0.022 0.058 0.14 5 -0.22 18 23
PI3K 0.019 0.059 0.21 1 -0.18 23 24
MET/Glomulin 0.01 0.05 0.24 5 -0.2 13 18
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K1 -0.011 0.11 -10000 0 -0.44 18 18
MET 0.013 0.072 0.33 5 -0.33 13 18
MAP4K1 -0.001 0.098 0.28 5 -0.41 9 14
PTK2 0.019 0.008 -10000 0 -10000 0 0
MAP2K2 -0.011 0.11 -10000 0 -0.44 18 18
BAD 0.001 0.044 0.4 1 -10000 0 1
MAP2K4 -0.007 0.085 0.26 4 -0.35 9 13
SHP2/GRB2/SOS1/GAB1 0.01 0.085 -10000 0 -0.32 14 14
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PXN 0.021 0.004 -10000 0 -10000 0 0
SH3KBP1 0.021 0.004 -10000 0 -10000 0 0
HGS -0.012 0.046 0.14 4 -0.17 23 27
PLCgamma1/PKC 0.015 0.004 -10000 0 -10000 0 0
HGF 0.009 0.075 0.33 3 -0.33 16 19
RASA1 0.021 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.019 0.061 0.21 1 -0.18 25 26
PDPK1 0.007 0.033 -10000 0 -10000 0 0
HGF/MET/SHIP 0.025 0.075 0.23 7 -0.22 27 34
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer 0.021 0.04 -10000 0 -0.24 7 7
PDGFRB 0.015 0.016 -10000 0 -10000 0 0
SPHK1 -0.001 0.061 -10000 0 -0.62 3 3
mol:S1P -0.008 0.058 -10000 0 -0.53 3 3
S1P1/S1P/Gi -0.038 0.13 0.21 6 -0.38 39 45
GNAO1 0.017 0.036 0.32 2 -0.33 2 4
PDGFB-D/PDGFRB/PLCgamma1 -0.032 0.13 0.24 5 -0.36 37 42
PLCG1 -0.045 0.12 0.2 7 -0.37 37 44
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.014 0.016 -10000 0 -10000 0 0
GNAI2 0.017 0.015 -10000 0 -10000 0 0
GNAI3 0.017 0.015 -10000 0 -10000 0 0
GNAI1 0.016 0.023 -10000 0 -0.33 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.018 0.026 -10000 0 -0.2 7 7
S1P1/S1P -0.021 0.061 0.21 1 -0.33 5 6
negative regulation of cAMP metabolic process -0.037 0.13 0.21 6 -0.37 39 45
MAPK3 -0.06 0.17 0.27 8 -0.55 37 45
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.006 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.003 -10000 0 -10000 0 0
KDR 0.011 0.048 -10000 0 -0.33 7 7
PLCB2 -0.016 0.071 0.27 4 -0.31 6 10
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.026 0.048 -10000 0 -0.29 5 5
receptor internalization -0.021 0.055 -10000 0 -0.31 5 5
PTGS2 -0.086 0.28 0.37 1 -0.89 38 39
Rac1/GTP -0.024 0.047 -10000 0 -0.29 5 5
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFA 0.017 0.014 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.037 0.13 0.21 6 -0.37 39 45
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.014 0.099 -10000 0 -0.33 34 34
MAPK1 -0.059 0.17 0.24 6 -0.54 36 42
S1P1/S1P/PDGFB-D/PDGFRB -0.024 0.07 0.22 4 -0.27 7 11
ABCC1 0.017 0.015 -10000 0 -10000 0 0
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.014 0.091 0.42 2 -0.38 14 16
CRKL -0.018 0.086 0.49 1 -0.39 16 17
HRAS -0.005 0.08 -10000 0 -0.35 13 13
mol:PIP3 0.006 0.11 0.37 2 -0.42 15 17
SPRED1 0.021 0.005 -10000 0 -10000 0 0
SPRED2 0.022 0.001 -10000 0 -10000 0 0
GAB1 -0.013 0.092 0.32 1 -0.41 17 18
FOXO3 -0.001 0.11 0.32 1 -0.4 20 21
AKT1 0.003 0.12 -10000 0 -0.42 20 20
BAD 0 0.11 -10000 0 -0.4 20 20
megakaryocyte differentiation -0.025 0.099 -10000 0 -0.4 20 20
GSK3B 0 0.11 0.25 1 -0.4 20 21
RAF1 -0.006 0.076 0.22 3 -0.31 10 13
SHC1 0.018 0.008 -10000 0 -10000 0 0
STAT3 -0.014 0.094 0.32 1 -0.41 18 19
STAT1 -0.041 0.2 0.45 1 -0.94 17 18
HRAS/SPRED1 0.008 0.076 -10000 0 -0.31 10 10
cell proliferation -0.014 0.09 -10000 0 -0.4 17 17
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
TEC 0.021 0.004 -10000 0 -10000 0 0
RPS6KB1 0 0.11 0.24 1 -0.43 18 19
HRAS/SPRED2 0.008 0.077 -10000 0 -0.31 10 10
LYN/TEC/p62DOK 0.02 0.098 0.32 1 -0.4 15 16
MAPK3 0 0.068 0.2 8 -0.22 9 17
STAP1 -0.016 0.094 0.32 1 -0.4 18 19
GRAP2 0.011 0.058 -10000 0 -0.33 11 11
JAK2 -0.036 0.18 0.42 1 -0.79 18 19
STAT1 (dimer) -0.038 0.2 0.45 1 -0.92 17 18
mol:Gleevec 0 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.019 0.094 -10000 0 -0.38 15 15
actin filament polymerization -0.012 0.084 0.32 1 -0.38 16 17
LYN 0.02 0.007 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.032 0.13 0.36 1 -0.55 19 20
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.008 0.084 0.41 2 -0.37 11 13
PI3K 0.018 0.11 -10000 0 -0.43 15 15
PTEN 0.021 0.003 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.022 0.23 -10000 0 -1.1 17 17
MAPK8 -0.014 0.091 -10000 0 -0.41 17 17
STAT3 (dimer) -0.014 0.092 0.32 1 -0.4 18 19
positive regulation of transcription 0.002 0.06 0.19 8 -0.19 8 16
mol:GDP 0 0.081 -10000 0 -0.38 11 11
PIK3C2B -0.014 0.097 0.44 2 -0.42 16 18
CBL/CRKL -0.002 0.089 0.42 2 -0.39 13 15
FER -0.014 0.092 0.32 1 -0.41 17 18
SH2B3 -0.014 0.093 0.32 1 -0.42 17 18
PDPK1 0.005 0.1 0.33 5 -0.38 15 20
SNAI2 -0.012 0.09 0.32 1 -0.41 16 17
positive regulation of cell proliferation -0.032 0.16 0.41 1 -0.69 18 19
KITLG 0.013 0.041 -10000 0 -0.35 4 4
cell motility -0.032 0.16 0.41 1 -0.69 18 19
PTPN6 0.019 0.012 -10000 0 -10000 0 0
EPOR -0.022 0.16 -10000 0 -0.62 20 20
STAT5A (dimer) -0.024 0.14 0.38 1 -0.56 19 20
SOCS1 0.021 0.004 -10000 0 -10000 0 0
cell migration 0.019 0.093 0.41 18 -10000 0 18
SOS1 0.021 0.003 -10000 0 -10000 0 0
EPO 0.02 0.03 0.33 3 -10000 0 3
VAV1 0.018 0.031 -10000 0 -0.33 3 3
GRB10 -0.014 0.09 0.33 1 -0.4 16 17
PTPN11 0.019 0.011 -10000 0 -10000 0 0
SCF/KIT -0.009 0.1 0.35 1 -0.42 18 19
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.005 0.067 0.19 8 -0.24 9 17
CBL 0.021 0.005 -10000 0 -10000 0 0
KIT -0.032 0.24 0.47 1 -1 21 22
MAP2K2 -0.003 0.065 0.19 8 -0.25 10 18
SHC/Grb2/SOS1 0.016 0.09 -10000 0 -0.4 12 12
STAT5A -0.023 0.14 0.38 1 -0.58 19 20
GRB2 0.021 0.005 -10000 0 -10000 0 0
response to radiation -0.012 0.089 0.32 1 -0.4 16 17
SHC/GRAP2 0.023 0.032 -10000 0 -0.23 5 5
PTPRO -0.024 0.1 -10000 0 -0.42 19 19
SH2B2 -0.012 0.086 0.32 1 -0.38 16 17
DOK1 0.022 0.002 -10000 0 -10000 0 0
MATK -0.02 0.095 -10000 0 -0.42 18 18
CREBBP 0.021 0.034 0.3 1 -10000 0 1
BCL2 -0.042 0.2 0.47 1 -0.85 10 11
Caspase cascade in apoptosis

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
TOP1 -0.013 0.086 -10000 0 -0.33 16 16
ACTA1 -0.021 0.084 -10000 0 -0.29 20 20
NUMA1 -0.009 0.078 -10000 0 -0.38 8 8
SPTAN1 -0.026 0.084 -10000 0 -0.29 23 23
LIMK1 -0.02 0.092 0.23 7 -0.3 21 28
BIRC3 0.022 0.04 0.33 4 -0.33 2 6
BIRC2 0.021 0.005 -10000 0 -10000 0 0
BAX 0.021 0.005 -10000 0 -10000 0 0
CASP10 -0.03 0.048 -10000 0 -0.22 21 21
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
PTK2 -0.011 0.078 -10000 0 -0.36 10 10
DIABLO 0.021 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.026 0.083 -10000 0 -0.29 23 23
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.022 0.016 0.33 1 -10000 0 1
GSN -0.026 0.083 -10000 0 -0.29 23 23
MADD 0.021 0.003 -10000 0 -10000 0 0
TFAP2A 0.077 0.16 0.38 1 -0.47 21 22
BID -0.012 0.036 -10000 0 -0.16 21 21
MAP3K1 -0.015 0.09 -10000 0 -0.42 16 16
TRADD 0.021 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.008 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.024 0.087 0.26 2 -0.29 23 25
CASP9 0.021 0.004 -10000 0 -10000 0 0
DNA repair 0 0.038 0.18 3 -0.16 1 4
neuron apoptosis -0.011 0.13 -10000 0 -0.61 16 16
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.017 0.087 0.23 1 -0.4 9 10
APAF1 0.021 0.004 -10000 0 -10000 0 0
CASP6 -0.006 0.11 -10000 0 -0.83 5 5
TRAF2 0.021 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.027 0.087 0.38 3 -0.29 21 24
CASP7 -0.004 0.067 0.28 1 -0.46 2 3
KRT18 0.012 0.037 -10000 0 -0.49 1 1
apoptosis -0.022 0.085 -10000 0 -0.41 10 10
DFFA -0.025 0.085 0.2 3 -0.29 23 26
DFFB -0.024 0.085 0.2 4 -0.29 22 26
PARP1 0 0.039 0.16 1 -0.18 3 4
actin filament polymerization 0.002 0.11 0.26 20 -0.3 17 37
TNF 0.005 0.077 0.33 1 -0.33 19 20
CYCS 0.002 0.044 0.15 8 -0.19 4 12
SATB1 -0.012 0.1 -10000 0 -0.73 6 6
SLK -0.026 0.083 -10000 0 -0.29 23 23
p15 BID/BAX 0.006 0.047 0.18 1 -0.25 3 4
CASP2 -0.003 0.055 0.19 9 -0.25 3 12
JNK cascade 0.015 0.09 0.41 16 -10000 0 16
CASP3 -0.023 0.088 -10000 0 -0.3 23 23
LMNB2 -0.014 0.13 0.21 2 -0.4 28 30
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CASP4 0.021 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.052 0.03 0.23 4 -0.19 2 6
negative regulation of DNA binding 0.077 0.16 0.38 1 -0.47 21 22
stress fiber formation -0.026 0.082 -10000 0 -0.29 23 23
GZMB -0.03 0.057 -10000 0 -0.26 21 21
CASP1 0.005 0.022 -10000 0 -0.25 3 3
LMNB1 -0.001 0.11 0.21 3 -0.4 17 20
APP -0.012 0.13 -10000 0 -0.62 16 16
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.01 0.011 -10000 0 -0.22 1 1
VIM -0.017 0.086 -10000 0 -0.41 10 10
LMNA 0.004 0.066 -10000 0 -0.33 5 5
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.003 0.055 -10000 0 -0.25 6 6
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.024 0.085 0.18 3 -0.29 23 26
APAF-1/Caspase 9 0.001 0.1 -10000 0 -0.64 9 9
nuclear fragmentation during apoptosis -0.009 0.077 -10000 0 -0.37 8 8
CFL2 -0.002 0.11 0.3 17 -0.26 20 37
GAS2 -0.027 0.09 0.23 3 -0.3 24 27
positive regulation of apoptosis -0.003 0.11 0.21 2 -0.41 14 16
PRF1 0.008 0.067 -10000 0 -0.33 15 15
BARD1 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
BARD1/CSTF1 0.03 0.019 0.24 1 -0.23 1 2
ATM 0.021 0.005 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
PRKDC 0.02 0.007 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
UBE2L3 0.021 0.004 -10000 0 -10000 0 0
FANCD2 0.011 0.01 -10000 0 -10000 0 0
protein ubiquitination 0.1 0.078 0.21 111 -10000 0 111
XRCC5 0.022 0.002 -10000 0 -10000 0 0
XRCC6 0.021 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.036 0.018 -10000 0 -10000 0 0
MRE11A 0.021 0.005 -10000 0 -10000 0 0
DNA-PK 0.038 0.015 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.001 0.091 -10000 0 -0.54 8 8
FANCF 0.021 0.003 -10000 0 -10000 0 0
BRCA1 0.021 0.003 -10000 0 -10000 0 0
CCNE1 0.12 0.14 0.33 123 -10000 0 123
CDK2/Cyclin E1 0.091 0.097 0.24 118 -10000 0 118
FANCG 0.021 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.031 0.018 0.24 1 -0.23 1 2
FANCE 0.021 0.005 -10000 0 -10000 0 0
FANCC 0.021 0.004 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
FANCA 0.03 0.054 0.33 12 -10000 0 12
DNA repair 0.004 0.071 0.21 5 -0.36 5 10
BRCA1/BARD1/ubiquitin 0.031 0.018 0.24 1 -0.23 1 2
BARD1/DNA-PK 0.048 0.022 -10000 0 -0.17 1 1
FANCL 0.022 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.029 0.019 0.23 1 -0.24 1 2
BRCA1/BARD1/CTIP/M/R/N Complex 0.012 0.04 -10000 0 -0.22 5 5
BRCA1/BACH1/BARD1/TopBP1 0.042 0.018 0.23 1 -0.2 1 2
BRCA1/BARD1/P53 0.049 0.024 0.23 1 -0.18 1 2
BARD1/CSTF1/BRCA1 0.04 0.02 0.23 1 -0.2 1 2
BRCA1/BACH1 0.021 0.003 -10000 0 -10000 0 0
BARD1 0.021 0.024 0.33 1 -0.33 1 2
PCNA 0.021 0.016 0.33 1 -10000 0 1
BRCA1/BARD1/UbcH5C 0.042 0.018 0.23 1 -0.2 1 2
BRCA1/BARD1/UbcH7 0.041 0.017 -10000 0 -0.2 1 1
BRCA1/BARD1/RAD51/PCNA 0.081 0.076 0.24 70 -0.15 1 71
BARD1/DNA-PK/P53 0.051 0.03 -10000 0 -0.16 1 1
BRCA1/BARD1/Ubiquitin 0.031 0.018 0.24 1 -0.23 1 2
BRCA1/BARD1/CTIP 0.028 0.018 0.22 1 -0.17 1 2
FA complex 0.009 0.044 -10000 0 -0.28 4 4
BARD1/EWS 0.031 0.018 0.24 1 -0.23 1 2
RBBP8 -0.016 0.006 -10000 0 -10000 0 0
TP53 0.02 0.006 -10000 0 -10000 0 0
TOPBP1 0.021 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.047 0.023 0.18 1 -0.22 1 2
BRCA1/BARD1 0.11 0.084 0.23 111 -10000 0 111
CSTF1 0.02 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.016 0.016 0.22 1 -0.22 1 2
CDK2 0.021 0.004 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.08 0.12 0.33 75 -10000 0 75
RAD50 0.021 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.031 0.018 0.24 1 -0.23 1 2
EWSR1 0.021 0.004 -10000 0 -10000 0 0
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.021 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.029 0.074 -10000 0 -0.3 2 2
Syndecan-3/Neurocan 0.024 0.047 0.31 2 -0.28 3 5
POMC 0.014 0.076 0.33 6 -0.33 14 20
EGFR 0.015 0.043 0.33 1 -0.33 5 6
Syndecan-3/EGFR 0.016 0.039 0.3 1 -0.3 3 4
AGRP -0.11 0.17 -10000 0 -0.33 150 150
NCSTN 0.019 0.007 -10000 0 -10000 0 0
PSENEN 0.02 0.005 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.02 0.018 -10000 0 -0.33 1 1
APH1A 0.018 0.008 -10000 0 -10000 0 0
NCAN 0.028 0.052 0.33 11 -10000 0 11
long-term memory 0.037 0.039 -10000 0 -0.29 2 2
Syndecan-3/IL8 0.027 0.056 0.26 6 -0.3 3 9
PSEN1 0.021 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.03 0.009 -10000 0 -10000 0 0
FYN 0.019 0.019 -10000 0 -0.33 1 1
limb bud formation 0.004 0.021 -10000 0 -0.4 1 1
MC4R 0.04 0.08 0.33 27 -10000 0 27
SRC 0.021 0.005 -10000 0 -10000 0 0
PTN -0.022 0.12 0.33 4 -0.33 51 55
FGFR/FGF/Syndecan-3 0.004 0.021 -10000 0 -0.41 1 1
neuron projection morphogenesis -0.015 0.064 0.25 2 -0.38 1 3
Syndecan-3/AgRP -0.036 0.083 -10000 0 -0.32 4 4
Syndecan-3/AgRP/MC4R -0.02 0.1 0.26 3 -0.34 3 6
Fyn/Cortactin 0.028 0.011 -10000 0 -10000 0 0
SDC3 0.004 0.021 -10000 0 -0.41 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.027 0.056 0.26 6 -0.29 3 9
IL8 0.034 0.07 0.33 18 -0.33 2 20
Syndecan-3/Fyn/Cortactin 0.038 0.04 -10000 0 -0.3 2 2
Syndecan-3/CASK 0.002 0.027 -10000 0 -0.29 3 3
alpha-MSH/MC4R 0.034 0.073 0.24 28 -0.21 14 42
Gamma Secretase 0.047 0.031 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.021 0.004 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.049 -10000 0 -0.17 26 26
CDKN1A -0.012 0.005 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
BAX 0.021 0.005 -10000 0 -10000 0 0
FOXO3 -0.002 0.002 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
FOXO4 0.006 0.002 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.021 0.004 -10000 0 -10000 0 0
TAT 0.042 0.079 0.33 27 -10000 0 27
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.017 0.016 0.16 3 -10000 0 3
PPARGC1A -0.06 0.15 0.33 1 -0.33 92 93
FHL2 0.066 0.11 0.33 56 -10000 0 56
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.031 0.013 0.25 1 -10000 0 1
HIST2H4A -0.005 0.049 0.17 26 -10000 0 26
SIRT1/FOXO3a 0.014 0.025 0.24 1 -0.2 1 2
SIRT1 0.021 0.017 0.35 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.036 0.02 0.24 1 -10000 0 1
SIRT1/Histone H1b 0.027 0.041 0.24 2 -0.22 3 5
apoptosis -0.04 0.016 -10000 0 -0.24 1 1
SIRT1/PGC1A -0.022 0.094 0.22 2 -0.19 90 92
p53/SIRT1 0.028 0.028 0.55 1 -10000 0 1
SIRT1/FOXO4 0.017 0.032 0.24 1 -0.22 3 4
FOXO1/FHL2/SIRT1 0.062 0.063 0.22 54 -10000 0 54
HIST1H1E 0.015 0.033 0.24 1 -10000 0 1
SIRT1/p300 0.031 0.013 0.25 1 -10000 0 1
muscle cell differentiation -0.025 0.02 -10000 0 -0.21 4 4
TP53 0.02 0.018 0.35 1 -10000 0 1
KU70/SIRT1/BAX 0.041 0.016 0.24 1 -10000 0 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
MEF2D 0.018 0.008 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.043 0.052 0.24 26 -10000 0 26
ACSS2 -0.017 0.019 0.27 1 -0.23 1 2
SIRT1/PCAF/MYOD 0.025 0.02 0.21 4 -10000 0 4
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.027 0.008 -10000 0 -10000 0 0
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.027 0.055 0.33 10 -0.33 2 12
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.02 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.016 0.032 0.16 7 -0.17 1 8
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.02 0.006 -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 0.021 0.005 -10000 0 -10000 0 0
FYN 0.019 0.019 -10000 0 -0.33 1 1
MAP3K12 0.021 0.003 -10000 0 -10000 0 0
FGR -0.006 0.093 -10000 0 -0.33 30 30
p38 alpha/TAB1 -0.039 0.085 -10000 0 -0.28 32 32
PRKG1 -0.012 0.1 -10000 0 -0.33 37 37
DUSP8 0.014 0.05 -10000 0 -0.33 8 8
PGK/cGMP/p38 alpha -0.018 0.12 -10000 0 -0.31 36 36
apoptosis -0.038 0.082 -10000 0 -0.27 32 32
RAL/GTP 0.026 0.009 -10000 0 -10000 0 0
LYN 0.02 0.007 -10000 0 -10000 0 0
DUSP1 -0.007 0.094 -10000 0 -0.33 31 31
PAK1 0.021 0.005 -10000 0 -10000 0 0
SRC 0.021 0.005 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.043 0.024 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -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 0.02 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.025 0.011 -10000 0 -10000 0 0
MAPK11 -0.006 0.12 0.27 8 -0.31 25 33
BLK 0.053 0.1 0.33 45 -0.33 1 46
HCK 0.008 0.065 -10000 0 -0.33 14 14
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
DUSP16 0.02 0.005 -10000 0 -10000 0 0
DUSP10 0.019 0.019 -10000 0 -0.33 1 1
TRAF6/MEKK3 0.026 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.006 0.12 0.24 9 -0.33 24 33
positive regulation of innate immune response -0.009 0.14 0.32 7 -0.37 26 33
LCK 0.021 0.024 0.33 1 -0.33 1 2
p38alpha-beta/MKP7 0 0.14 0.33 6 -0.37 22 28
p38alpha-beta/MKP5 -0.001 0.13 0.31 6 -0.36 23 29
PGK/cGMP -0.007 0.07 -10000 0 -0.22 37 37
PAK2 0.021 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.007 0.14 0.33 6 -0.36 27 33
CDC42 0.021 0.004 -10000 0 -10000 0 0
RALB 0.021 0.003 -10000 0 -10000 0 0
RALA 0.02 0.007 -10000 0 -10000 0 0
PAK3 0.058 0.11 0.33 51 -0.33 4 55
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0.035 -10000 0 -0.33 4 4
ELF1 0.034 0.042 0.18 30 -10000 0 30
CCNA2 0.1 0.14 0.33 100 -10000 0 100
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
JAK3 0.02 0.006 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
JAK1 0.021 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.015 0.074 -10000 0 -0.44 3 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
SP1 0.016 0.049 -10000 0 -0.3 9 9
IL2RA 0.01 0.085 0.3 30 -10000 0 30
IL2RB 0.019 0.025 -10000 0 -0.33 2 2
SOS1 0.022 0.003 -10000 0 -10000 0 0
IL2RG 0.018 0.035 -10000 0 -0.33 4 4
G1/S transition of mitotic cell cycle 0.028 0.11 0.32 12 -0.43 11 23
PTPN11 0.021 0.004 -10000 0 -10000 0 0
CCND2 -0.028 0.087 -10000 0 -0.59 9 9
LCK 0.022 0.024 0.33 1 -0.33 1 2
GRB2 0.021 0.005 -10000 0 -10000 0 0
IL2 0.02 0.003 -10000 0 -10000 0 0
CDK6 0.02 0.018 -10000 0 -0.33 1 1
CCND3 0.018 0.081 0.36 3 -0.39 3 6
IL27-mediated signaling events

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
TGFB1 0.024 0.016 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.017 0.11 0.38 15 -10000 0 15
IL27/IL27R/JAK1 0.036 0.092 -10000 0 -0.88 1 1
TBX21 -0.021 0.11 0.89 1 -0.46 7 8
IL12B 0.024 0.033 0.32 3 -0.33 1 4
IL12A -0.009 0.027 0.16 1 -0.22 5 6
IL6ST 0.011 0.058 -10000 0 -0.33 10 10
IL27RA/JAK1 0.01 0.063 0.38 1 -1.1 1 2
IL27 0.009 0.058 -10000 0 -0.34 10 10
TYK2 0.022 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.015 0.13 0.43 2 -10000 0 2
T-helper 2 cell differentiation 0.017 0.11 0.38 15 -10000 0 15
T cell proliferation during immune response 0.017 0.11 0.38 15 -10000 0 15
MAPKKK cascade -0.017 0.11 -10000 0 -0.38 15 15
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT2 0.021 0.004 -10000 0 -10000 0 0
STAT1 0.021 0.01 -10000 0 -10000 0 0
IL12RB1 0.013 0.053 -10000 0 -0.33 9 9
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.008 0.12 0.39 9 -0.49 4 13
IL27/IL27R/JAK2/TYK2 -0.017 0.11 -10000 0 -0.39 14 14
positive regulation of T cell mediated cytotoxicity -0.017 0.11 -10000 0 -0.38 15 15
STAT1 (dimer) 0.033 0.13 -10000 0 -0.61 4 4
JAK2 0.021 0.022 -10000 0 -0.33 1 1
JAK1 0.02 0.01 -10000 0 -10000 0 0
STAT2 (dimer) -0.008 0.12 0.45 1 -0.41 10 11
T cell proliferation -0.039 0.12 0.34 3 -0.39 23 26
IL12/IL12R/TYK2/JAK2 -0.034 0.25 -10000 0 -0.8 33 33
IL17A -0.02 0.12 0.48 1 -10000 0 1
mast cell activation 0.017 0.11 0.38 15 -10000 0 15
IFNG 0.004 0.042 0.11 31 -0.1 13 44
T cell differentiation -0.001 0.005 0.013 8 -0.02 9 17
STAT3 (dimer) -0.009 0.12 0.45 1 -0.39 14 15
STAT5A (dimer) -0.01 0.12 0.45 1 -0.43 10 11
STAT4 (dimer) -0.01 0.12 0.45 1 -0.38 16 17
STAT4 0.022 0.002 -10000 0 -10000 0 0
T cell activation -0.003 0.007 0.11 1 -10000 0 1
IL27R/JAK2/TYK2 0.033 0.075 -10000 0 -0.86 1 1
GATA3 -0.007 0.088 0.62 4 -1.1 1 5
IL18 -0.012 0.031 -10000 0 -0.22 8 8
positive regulation of mast cell cytokine production -0.009 0.12 0.44 1 -0.38 14 15
IL27/EBI3 0.025 0.047 -10000 0 -0.23 10 10
IL27RA 0.001 0.062 -10000 0 -1.1 1 1
IL6 -0.043 0.14 -10000 0 -0.33 73 73
STAT5A 0.02 0.018 -10000 0 -0.33 1 1
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.01 0.031 0.42 1 -10000 0 1
IL1B -0.02 0.052 0.16 1 -0.22 23 24
EBI3 0.021 0.015 -10000 0 -10000 0 0
TNF -0.018 0.048 0.16 1 -0.22 19 20
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.002 0.077 0.2 1 -0.29 17 18
PDGFB-D/PDGFRB/SLAP 0.022 0.034 -10000 0 -0.23 6 6
PDGFB-D/PDGFRB/APS/CBL 0.038 0.02 -10000 0 -0.2 1 1
AKT1 -0.013 0.083 0.36 10 -10000 0 10
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.004 0.094 0.3 4 -0.33 18 22
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
FGR -0.035 0.15 0.33 2 -0.47 37 39
mol:Ca2+ -0.005 0.1 0.28 6 -0.36 20 26
MYC 0.035 0.13 0.38 13 -0.56 4 17
SHC1 0.018 0.008 -10000 0 -10000 0 0
HRAS/GDP -0.015 0.04 0.16 19 -10000 0 19
LRP1/PDGFRB/PDGFB 0.036 0.034 -10000 0 -0.2 7 7
GRB10 0.019 0.007 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 -0.005 0.1 0.3 5 -0.37 20 25
PTEN 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.021 0.005 -10000 0 -10000 0 0
GRB7 0.019 0.025 -10000 0 -0.33 2 2
PDGFB-D/PDGFRB/SHP2 0.03 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.028 0.012 -10000 0 -10000 0 0
cell cycle arrest 0.022 0.034 -10000 0 -0.23 6 6
HRAS 0.021 0.004 -10000 0 -10000 0 0
HIF1A -0.016 0.078 0.34 10 -10000 0 10
GAB1 -0.003 0.1 0.33 4 -0.32 22 26
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.002 0.09 0.3 7 -0.29 15 22
PDGFB-D/PDGFRB 0.039 0.017 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.031 0.008 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.005 0.059 0.2 1 -0.25 8 9
positive regulation of MAPKKK cascade 0.03 0.009 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
mol:IP3 -0.005 0.1 0.3 5 -0.37 20 25
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.019 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.029 0.021 -10000 0 -0.23 2 2
SHB 0.02 0.006 -10000 0 -10000 0 0
BLK -0.038 0.17 0.31 1 -0.39 61 62
PTPN2 0.02 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.031 0.009 -10000 0 -10000 0 0
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
VAV2 -0.006 0.11 0.34 4 -0.38 18 22
CBL 0.021 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.031 0.008 -10000 0 -10000 0 0
LCK 0.006 0.06 0.33 2 -0.41 3 5
PDGFRB 0.02 0.009 -10000 0 -10000 0 0
ACP1 0.022 0.002 -10000 0 -10000 0 0
HCK -0.015 0.12 0.32 1 -0.53 18 19
ABL1 -0.008 0.099 0.25 8 -0.32 22 30
PDGFB-D/PDGFRB/CBL -0.009 0.11 0.29 1 -0.39 22 23
PTPN1 0.019 0.009 -10000 0 -10000 0 0
SNX15 0.021 0.003 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.022 0.002 -10000 0 -10000 0 0
cell proliferation 0.036 0.13 0.36 15 -0.46 5 20
SLA 0.012 0.047 -10000 0 -0.33 7 7
actin cytoskeleton reorganization -0.016 0.061 0.3 6 -10000 0 6
SRC -0.001 0.086 0.31 1 -0.6 6 7
PI3K -0.034 0.02 -10000 0 -0.17 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.025 -10000 0 -0.2 2 2
SH2B2 0.02 0.018 -10000 0 -0.33 1 1
PLCgamma1/SPHK1 0.004 0.096 0.31 4 -0.34 18 22
LYN 0.004 0.06 0.31 1 -0.45 3 4
LRP1 0.017 0.035 -10000 0 -0.33 4 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
STAT5B 0.021 0.003 -10000 0 -10000 0 0
STAT5A 0.02 0.018 -10000 0 -0.33 1 1
NCK1-2/p130 Cas 0.053 0.032 -10000 0 -0.18 1 1
SPHK1 0.022 0.028 0.33 3 -10000 0 3
EDG1 0 0.003 -10000 0 -10000 0 0
mol:DAG -0.005 0.1 0.3 5 -0.37 20 25
PLCG1 -0.005 0.11 0.3 5 -0.38 20 25
NHERF/PDGFRB 0.038 0.03 0.23 1 -0.2 4 5
YES1 -0.011 0.12 0.34 1 -0.58 14 15
cell migration 0.037 0.029 0.23 1 -0.2 4 5
SHC/Grb2/SOS1 0.046 0.033 -10000 0 -10000 0 0
SLC9A3R2 0.018 0.035 -10000 0 -0.33 4 4
SLC9A3R1 0.022 0.016 0.33 1 -10000 0 1
NHERF1-2/PDGFRB/PTEN 0.048 0.032 0.23 1 -0.18 4 5
FYN -0.03 0.13 0.31 1 -0.39 37 38
DOK1 -0.013 0.042 0.16 20 -10000 0 20
HRAS/GTP 0.016 0.003 -10000 0 -10000 0 0
PDGFB 0.017 0.035 -10000 0 -0.33 4 4
RAC1 0.01 0.12 0.4 6 -0.42 12 18
PRKCD -0.012 0.043 0.16 21 -10000 0 21
FER -0.012 0.042 0.17 20 -10000 0 20
MAPKKK cascade 0.014 0.099 0.19 75 -10000 0 75
RASA1 -0.013 0.041 0.17 19 -10000 0 19
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.022 0.002 -10000 0 -10000 0 0
p62DOK/Csk -0.017 0.041 0.16 20 -10000 0 20
PDGFB-D/PDGFRB/SHB 0.029 0.01 -10000 0 -10000 0 0
chemotaxis -0.008 0.098 0.25 8 -0.31 22 30
STAT1-3-5/STAT1-3-5 0.043 0.027 -10000 0 -0.19 1 1
Bovine Papilomavirus E5/PDGFRB 0.015 0.006 -10000 0 -10000 0 0
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.12 0.14 0.33 123 -10000 0 123
mol:Halofuginone 0.001 0 -10000 0 -10000 0 0
ITGA1 0.02 0.018 -10000 0 -0.33 1 1
CDKN1A 0.002 0.033 -10000 0 -0.32 3 3
PRL-3/alpha Tubulin 0.027 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.067 0.17 44 -0.24 4 48
AGT 0.058 0.11 0.33 53 -0.33 4 57
CCNA2 -0.006 0.059 0.31 6 -10000 0 6
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
EGR1 -0.02 0.053 -10000 0 -0.22 25 25
CDK2/Cyclin E1 0.088 0.1 0.34 9 -0.3 3 12
MAPK3 -0.015 0.016 0.28 1 -10000 0 1
PRL-2 /Rab GGTase beta 0.031 0.007 -10000 0 -10000 0 0
MAPK1 -0.015 0.007 -10000 0 -10000 0 0
PTP4A1 -0.023 0.037 -10000 0 -10000 0 0
PTP4A3 0.019 0.008 -10000 0 -10000 0 0
PTP4A2 0.021 0.003 -10000 0 -10000 0 0
ITGB1 -0.015 0.016 0.28 1 -10000 0 1
SRC 0.021 0.005 -10000 0 -10000 0 0
RAC1 0 0.04 -10000 0 -0.41 3 3
Rab GGTase beta/Rab GGTase alpha 0.03 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.021 0.05 -10000 0 -10000 0 0
RABGGTA 0.021 0.005 -10000 0 -10000 0 0
BCAR1 -0.019 0.016 -10000 0 -0.21 2 2
RHOC -0.001 0.049 -10000 0 -0.37 6 6
RHOA -0.001 0.047 -10000 0 -0.34 6 6
cell motility 0.003 0.066 0.26 2 -0.34 6 8
PRL-1/alpha Tubulin -0.022 0.049 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.026 0.018 -10000 0 -0.23 1 1
ROCK1 0.001 0.053 0.27 1 -0.39 3 4
RABGGTB 0.021 0.004 -10000 0 -10000 0 0
CDK2 0.021 0.004 -10000 0 -10000 0 0
mitosis -0.023 0.036 -10000 0 -10000 0 0
ATF5 0.022 0.016 0.33 1 -10000 0 1
Class I PI3K signaling 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
ARF5/GTP -0.011 0.064 0.24 3 -10000 0 3
DAPP1 -0.022 0.11 0.22 3 -0.31 33 36
Src family/SYK family/BLNK-LAT/BTK-ITK -0.04 0.16 -10000 0 -0.46 38 38
mol:DAG -0.017 0.072 0.2 8 -0.21 16 24
HRAS 0.021 0.007 -10000 0 -10000 0 0
RAP1A 0.021 0.007 -10000 0 -10000 0 0
ARF5/GDP -0.004 0.094 0.22 1 -0.3 22 23
PLCG2 0.018 0.031 -10000 0 -0.33 3 3
PLCG1 0.021 0.005 -10000 0 -10000 0 0
ARF5 0.021 0.004 -10000 0 -10000 0 0
mol:GTP -0.019 0.046 0.15 23 -10000 0 23
ARF1/GTP -0.005 0.049 0.26 2 -0.18 2 4
RHOA 0.021 0.004 -10000 0 -10000 0 0
YES1 0.02 0.006 -10000 0 -10000 0 0
RAP1A/GTP -0.019 0.045 0.16 21 -10000 0 21
ADAP1 -0.018 0.05 0.2 7 -0.28 1 8
ARAP3 -0.019 0.045 0.15 23 -10000 0 23
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PREX1 0.017 0.036 -10000 0 -0.33 4 4
ARHGEF6 0.009 0.065 -10000 0 -0.33 14 14
ARHGEF7 0.02 0.005 -10000 0 -10000 0 0
ARF1 0.02 0.006 -10000 0 -10000 0 0
NRAS 0.021 0.008 -10000 0 -10000 0 0
FYN 0.019 0.019 -10000 0 -0.33 1 1
ARF6 0.021 0.005 -10000 0 -10000 0 0
FGR -0.006 0.093 -10000 0 -0.33 30 30
mol:Ca2+ -0.012 0.04 0.14 6 -0.13 6 12
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.016 0.04 -10000 0 -0.33 5 5
ZAP70 0.016 0.043 -10000 0 -0.33 6 6
mol:IP3 -0.019 0.054 0.16 8 -0.17 9 17
LYN 0.02 0.007 -10000 0 -10000 0 0
ARF1/GDP -0.001 0.088 0.22 1 -0.3 18 19
RhoA/GDP -0.012 0.067 0.26 3 -0.25 4 7
PDK1/Src/Hsp90 0.04 0.014 -10000 0 -10000 0 0
BLNK 0.02 0.018 -10000 0 -0.33 1 1
actin cytoskeleton reorganization -0.008 0.088 0.3 6 -0.3 12 18
SRC 0.021 0.005 -10000 0 -10000 0 0
PLEKHA2 -0.018 0.008 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PTEN 0.02 0.014 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
ARF6/GTP -0.025 0.044 0.28 1 -10000 0 1
RhoA/GTP -0.022 0.047 0.22 4 -10000 0 4
Src family/SYK family/BLNK-LAT -0.018 0.1 -10000 0 -0.32 22 22
BLK 0.053 0.1 0.33 45 -0.33 1 46
PDPK1 0.021 0.004 -10000 0 -10000 0 0
CYTH1 -0.021 0.047 0.21 6 -10000 0 6
HCK 0.008 0.065 -10000 0 -0.33 14 14
CYTH3 -0.018 0.048 0.19 8 -10000 0 8
CYTH2 -0.021 0.047 0.28 3 -10000 0 3
KRAS 0.02 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.004 0.046 -10000 0 -0.34 4 4
SGK1 -0.018 0.1 -10000 0 -0.34 33 33
INPP5D 0.019 0.031 -10000 0 -0.33 3 3
mol:GDP -0.014 0.095 0.2 2 -0.3 25 27
SOS1 0.021 0.003 -10000 0 -10000 0 0
SYK 0.019 0.025 -10000 0 -0.33 2 2
ARF6/GDP -0.014 0.06 0.27 2 -0.27 2 4
mol:PI-3-4-5-P3 -0.021 0.041 0.19 3 -10000 0 3
ARAP3/RAP1A/GTP -0.019 0.045 0.16 21 -10000 0 21
VAV1 0.018 0.031 -10000 0 -0.33 3 3
mol:PI-3-4-P2 -0.019 0.016 -10000 0 -0.23 2 2
RAS family/GTP/PI3K Class I -0.023 0.035 0.18 9 -10000 0 9
PLEKHA1 -0.021 0.014 -10000 0 -0.2 2 2
Rac1/GDP -0.006 0.09 -10000 0 -0.31 21 21
LAT 0.022 0.016 0.33 1 -10000 0 1
Rac1/GTP -0.004 0.091 -10000 0 -0.35 19 19
ITK -0.026 0.046 0.2 2 -10000 0 2
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.027 0.091 0.24 6 -0.28 19 25
LCK 0.021 0.024 0.33 1 -0.33 1 2
BTK -0.03 0.058 0.23 3 -0.29 2 5
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.018 0.006 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.012 0.004 -10000 0 -10000 0 0
mol:DAG -0.014 0.036 0.24 4 -10000 0 4
VEGFR1 homodimer/NRP1/VEGFR 121 0.016 0.006 -10000 0 -10000 0 0
CaM/Ca2+ -0.018 0.031 0.19 3 -10000 0 3
HIF1A 0.023 0.005 -10000 0 -10000 0 0
GAB1 0.021 0.018 -10000 0 -0.33 1 1
AKT1 -0.015 0.043 0.38 2 -10000 0 2
PLCG1 -0.014 0.036 0.24 4 -10000 0 4
NOS3 -0.011 0.083 0.4 4 -0.35 9 13
CBL 0.021 0.005 -10000 0 -10000 0 0
mol:NO -0.007 0.091 0.43 6 -0.34 9 15
FLT1 -0.015 0.005 -10000 0 -10000 0 0
PGF 0.032 0.058 0.33 14 -10000 0 14
VEGFR1 homodimer/NRP2/VEGFR121 0.028 0.018 -10000 0 -0.17 2 2
CALM1 0.021 0.005 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 -0.015 0.085 0.37 3 -0.34 11 14
endothelial cell proliferation -0.007 0.055 0.34 5 -10000 0 5
mol:Ca2+ -0.014 0.036 0.24 4 -10000 0 4
MAPK3 -0.02 0.042 0.22 9 -10000 0 9
MAPK1 -0.021 0.038 0.24 6 -10000 0 6
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.032 0.058 0.33 14 -10000 0 14
PRKACA 0.02 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.18 0.17 -10000 0 -0.33 228 228
VEGFA homodimer 0.021 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.018 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.022 0.047 0.33 5 -10000 0 5
PI3K 0.043 0.037 0.22 13 -10000 0 13
PRKCA -0.02 0.028 0.27 2 -10000 0 2
PRKCB -0.02 0.038 0.23 5 -10000 0 5
VEGFR1 homodimer/PLGF homodimer 0.026 0.039 0.23 14 -10000 0 14
VEGFA 0.021 0.004 -10000 0 -10000 0 0
VEGFB 0.021 0.003 -10000 0 -10000 0 0
mol:IP3 -0.014 0.036 0.24 4 -10000 0 4
RASA1 -0.017 0.027 0.18 7 -10000 0 7
NRP2 0.02 0.025 -10000 0 -0.33 2 2
VEGFR1 homodimer -0.015 0.005 -10000 0 -10000 0 0
VEGFB homodimer 0.021 0.003 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.089 0.11 0.44 2 -0.37 24 26
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.036 0.21 13 -10000 0 13
mol:L-citrulline -0.007 0.091 0.43 6 -0.34 9 15
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.038 0.019 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.029 0.012 -10000 0 -10000 0 0
CD2AP 0.021 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.05 0.041 -10000 0 -0.17 1 1
PDPK1 -0.014 0.057 0.36 5 -10000 0 5
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.029 0.012 -10000 0 -10000 0 0
mol:NADP -0.007 0.091 0.43 6 -0.34 9 15
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.036 0.018 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.017 0.017 -10000 0 -0.2 2 2
Sphingosine 1-phosphate (S1P) 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 0.02 0.018 -10000 0 -0.33 1 1
SPHK1 0.023 0.027 0.33 3 -10000 0 3
GNAI2 0.021 0.004 -10000 0 -10000 0 0
mol:S1P 0.006 0.015 -10000 0 -0.22 1 1
GNAO1 0.021 0.034 0.33 2 -0.33 2 4
mol:Sphinganine-1-P -0.016 0.019 0.16 3 -0.23 1 4
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.033 0.037 -10000 0 -0.21 2 2
GNAI3 0.021 0.004 -10000 0 -10000 0 0
G12/G13 0.028 0.012 -10000 0 -10000 0 0
S1PR3 0.022 0.016 0.33 1 -10000 0 1
S1PR2 0.02 0.006 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.001 0.029 -10000 0 -0.24 2 2
S1PR5 0.001 0.084 0.33 1 -0.33 23 24
S1PR4 0.005 0.071 -10000 0 -0.33 17 17
GNAI1 0.02 0.018 -10000 0 -0.33 1 1
S1P/S1P5/G12 0.015 0.057 0.22 1 -0.18 21 22
S1P/S1P3/Gq 0.002 0.073 -10000 0 -0.3 18 18
S1P/S1P4/Gi -0.018 0.091 -10000 0 -0.22 52 52
GNAQ 0.02 0.018 -10000 0 -0.33 1 1
GNAZ -0.01 0.099 -10000 0 -0.33 34 34
GNA14 0.012 0.055 -10000 0 -0.33 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.006 -10000 0 -10000 0 0
ABCC1 0.021 0.003 -10000 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.029 0.034 0.21 9 -0.17 3 12
EFNA5 0.02 0.038 0.33 2 -0.33 3 5
FYN -0.014 0.026 0.18 4 -0.18 2 6
neuron projection morphogenesis 0.029 0.034 0.21 9 -0.17 3 12
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.03 0.034 0.21 9 -0.17 3 12
EPHA5 0.026 0.044 0.33 8 -10000 0 8
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.007 0.03 -10000 0 -0.18 7 7
epithelial cell differentiation 0.042 0.021 -10000 0 -0.17 2 2
CYFIP2 0.016 0.043 -10000 0 -0.33 6 6
ENAH -0.019 0.06 0.4 2 -0.23 1 3
EGFR 0.015 0.043 0.33 1 -0.33 5 6
EPHA2 0.015 0.047 -10000 0 -0.33 7 7
MYO6 -0.018 0.044 0.22 9 -10000 0 9
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.039 0.024 -10000 0 -0.2 3 3
AQP5 -0.057 0.16 0.38 4 -0.37 72 76
CTNND1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.019 0.044 0.22 10 -10000 0 10
regulation of calcium-dependent cell-cell adhesion -0.092 0.076 0.16 3 -0.3 1 4
EGF 0.075 0.13 0.33 72 -0.33 4 76
NCKAP1 0.022 0.002 -10000 0 -10000 0 0
AQP3 -0.023 0.076 0.24 1 -0.32 20 21
cortical microtubule organization 0.042 0.021 -10000 0 -0.17 2 2
GO:0000145 -0.018 0.042 0.2 10 -10000 0 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.046 0.022 -10000 0 -0.17 2 2
MLLT4 0.02 0.007 -10000 0 -10000 0 0
ARF6/GDP -0.034 0.026 -10000 0 -0.17 5 5
ARF6 0.021 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.04 0.037 -10000 0 -0.18 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.011 0.043 0.42 2 -10000 0 2
PVRL2 0.021 0.005 -10000 0 -10000 0 0
ZYX -0.019 0.045 0.22 10 -10000 0 10
ARF6/GTP 0.042 0.037 -10000 0 -0.18 5 5
CDH1 0.019 0.025 -10000 0 -0.33 2 2
EGFR/EGFR/EGF/EGF 0.041 0.057 0.25 1 -0.19 8 9
RhoA/GDP 0.042 0.022 -10000 0 -0.17 2 2
actin cytoskeleton organization -0.02 0.042 0.21 9 -0.17 2 11
IGF-1R heterotetramer 0.02 0.018 -10000 0 -0.33 1 1
GIT1 0.021 0.004 -10000 0 -10000 0 0
IGF1R 0.02 0.018 -10000 0 -0.33 1 1
IGF1 0.018 0.043 0.33 1 -0.33 5 6
DIAPH1 0.013 0.13 -10000 0 -0.51 20 20
Wnt receptor signaling pathway -0.042 0.021 0.17 2 -10000 0 2
RHOA 0.021 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.035 0.028 -10000 0 -0.19 6 6
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
VCL -0.02 0.042 0.21 9 -0.18 2 11
EFNA1 0.017 0.019 -10000 0 -0.33 1 1
LPP -0.022 0.043 0.21 10 -10000 0 10
Ephrin A1/EPHA2 0.026 0.037 -10000 0 -0.18 8 8
SEC6/SEC8 -0.026 0.02 -10000 0 -0.17 1 1
MGAT3 -0.094 0.077 0.16 3 -0.31 1 4
HGF/MET 0.022 0.056 -10000 0 -0.17 24 24
HGF 0.009 0.075 0.33 3 -0.33 16 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.007 0.03 -10000 0 -0.18 7 7
actin cable formation 0.01 0.091 0.31 15 -0.25 3 18
KIAA1543 -0.021 0.032 0.17 8 -10000 0 8
KIFC3 -0.024 0.024 0.16 4 -10000 0 4
NCK1 0.021 0.003 -10000 0 -10000 0 0
EXOC3 0.016 0.01 -10000 0 -10000 0 0
ACTN1 -0.019 0.044 0.22 10 -10000 0 10
NCK1/GIT1 0.031 0.007 -10000 0 -10000 0 0
mol:GDP 0.042 0.021 -10000 0 -0.17 2 2
EXOC4 0.021 0.005 -10000 0 -10000 0 0
STX4 -0.022 0.032 0.19 7 -10000 0 7
PIP5K1C -0.019 0.045 0.22 10 -10000 0 10
LIMA1 0.021 0.003 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
ROCK1 -0.006 0.083 0.34 8 -0.26 1 9
adherens junction assembly -0.026 0.097 0.34 7 -0.46 8 15
IGF-1R heterotetramer/IGF1 0.032 0.034 -10000 0 -0.16 8 8
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.028 0.011 -10000 0 -10000 0 0
MET 0.013 0.072 0.33 5 -0.33 13 18
PLEKHA7 -0.022 0.034 0.18 8 -10000 0 8
mol:GTP 0.038 0.036 -10000 0 -0.18 6 6
establishment of epithelial cell apical/basal polarity 0.021 0.098 0.3 15 -10000 0 15
cortical actin cytoskeleton stabilization 0.007 0.03 -10000 0 -0.18 7 7
regulation of cell-cell adhesion -0.02 0.042 0.21 9 -0.17 2 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.007 0.03 -10000 0 -0.18 7 7
Insulin Pathway

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
CBL/APS/CAP 0.027 0.046 -10000 0 -0.16 16 16
TC10/GTP 0.023 0.042 -10000 0 -0.16 14 14
Insulin Receptor/Insulin/IRS1/Shp2 0.05 0.022 -10000 0 -0.15 1 1
HRAS 0.021 0.004 -10000 0 -10000 0 0
APS homodimer 0.02 0.018 -10000 0 -0.33 1 1
GRB14 0.034 0.081 0.33 21 -0.33 5 26
FOXO3 -0.054 0.2 -10000 0 -0.63 43 43
AKT1 -0.021 0.056 0.28 5 -10000 0 5
INSR 0.022 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.041 0.032 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.019 0.007 -10000 0 -10000 0 0
SORBS1 0.004 0.075 -10000 0 -0.33 19 19
CRK 0.02 0.007 -10000 0 -10000 0 0
PTPN1 -0.013 0.022 -10000 0 -10000 0 0
CAV1 -0.1 0.08 -10000 0 -0.18 206 206
CBL/APS/CAP/Crk-II/C3G 0.041 0.053 -10000 0 -0.17 16 16
Insulin Receptor/Insulin/IRS1/NCK2 0.05 0.021 -10000 0 -0.15 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.038 0.02 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.004 0.078 -10000 0 -0.32 18 18
RPS6KB1 -0.025 0.05 0.26 4 -10000 0 4
PARD6A 0.02 0.018 -10000 0 -0.33 1 1
CBL 0.021 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.011 0.043 -10000 0 -0.57 2 2
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.029 0.042 -10000 0 -10000 0 0
HRAS/GTP -0.029 0.02 -10000 0 -0.15 1 1
Insulin Receptor 0.022 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.048 0.03 -10000 0 -10000 0 0
PRKCI -0.001 0.082 -10000 0 -0.3 21 21
Insulin Receptor/Insulin/GRB14/PDK1 -0.025 0.033 -10000 0 -0.17 3 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.029 0.044 -10000 0 -0.49 2 2
PI3K 0.046 0.024 -10000 0 -10000 0 0
NCK2 0.022 0.002 -10000 0 -10000 0 0
RHOQ 0.021 0.003 -10000 0 -10000 0 0
mol:H2O2 -0.002 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.016 0.003 -10000 0 -10000 0 0
AKT2 -0.021 0.056 0.31 4 -10000 0 4
PRKCZ -0.007 0.094 -10000 0 -0.33 26 26
SH2B2 0.02 0.018 -10000 0 -0.33 1 1
SHC/SHIP -0.02 0.023 -10000 0 -0.17 2 2
F2RL2 0.039 0.088 0.33 28 -0.33 4 32
TRIP10 0.02 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.032 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.027 0.009 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.048 0.03 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
RASA1 0.021 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.035 0.05 -10000 0 -0.18 16 16
TC10/GDP 0.016 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.039 0.026 -10000 0 -10000 0 0
INPP5D -0.02 0.021 0.15 2 -0.18 2 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
SGK1 -0.053 0.2 -10000 0 -0.66 37 37
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.021 0.018 -10000 0 -0.33 1 1
p62DOK/RasGAP 0.029 0.044 -10000 0 -0.49 2 2
INS -0.015 0.015 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.02 0.021 0.15 2 -0.18 2 4
GRB2 0.021 0.005 -10000 0 -10000 0 0
EIF4EBP1 -0.019 0.053 0.22 7 -10000 0 7
PTPRA 0.022 0.007 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.027 0.009 -10000 0 -10000 0 0
PDPK1 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.007 0.025 -10000 0 -0.19 1 1
Insulin Receptor/Insulin/IRS1 0.038 0.017 -10000 0 -0.14 1 1
Insulin Receptor/Insulin/IRS3 0.03 0.013 -10000 0 -10000 0 0
Par3/Par6 0.052 0.05 0.22 24 -0.16 4 28
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.016 0.018 -10000 0 -10000 0 0
HSPA8 0.02 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.023 0.065 0.24 7 -0.23 7 14
AKT1 0.015 0.026 -10000 0 -10000 0 0
GSC 0.044 0.12 0.46 10 -0.42 6 16
NKX2-5 0.041 0.081 0.33 28 -10000 0 28
muscle cell differentiation -0.011 0.073 0.3 1 -10000 0 1
SMAD2-3/SMAD4/SP1 0.048 0.062 -10000 0 -10000 0 0
SMAD4 0.016 0.032 -10000 0 -10000 0 0
CBFB 0.021 0.004 -10000 0 -10000 0 0
SAP18 0.02 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.026 0.062 0.22 6 -0.2 19 25
SMAD3/SMAD4/VDR 0.04 0.053 -10000 0 -0.24 1 1
MYC 0.018 0.028 -10000 0 -0.33 2 2
CDKN2B -0.17 0.38 -10000 0 -1.1 44 44
AP1 0.004 0.06 -10000 0 -0.24 7 7
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.021 0.093 -10000 0 -0.32 21 21
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.021 0.096 0.18 1 -0.32 27 28
SP3 0.022 0.003 -10000 0 -10000 0 0
CREB1 0.021 0.003 -10000 0 -10000 0 0
FOXH1 0.045 0.083 0.34 29 -10000 0 29
SMAD3/SMAD4/GR 0.029 0.043 -10000 0 -10000 0 0
GATA3 0.02 0.028 0.33 1 -0.33 1 2
SKI/SIN3/HDAC complex/NCoR1 -0.016 0.073 -10000 0 -0.33 11 11
MEF2C/TIF2 0.01 0.068 0.24 7 -10000 0 7
endothelial cell migration -0.014 0.079 0.71 3 -10000 0 3
MAX 0.02 0.01 -10000 0 -10000 0 0
RBBP7 0.021 0.005 -10000 0 -10000 0 0
RBBP4 0.022 0.003 -10000 0 -10000 0 0
RUNX2 0.026 0.041 0.33 7 -10000 0 7
RUNX3 0.019 0.025 -10000 0 -0.33 2 2
RUNX1 0.021 0.004 -10000 0 -10000 0 0
CTBP1 0.021 0.004 -10000 0 -10000 0 0
NR3C1 0.02 0.011 -10000 0 -10000 0 0
VDR 0.021 0.024 0.33 1 -0.33 1 2
CDKN1A -0.002 0.058 -10000 0 -0.85 1 1
KAT2B 0.017 0.014 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.058 0.075 0.26 25 -10000 0 25
DCP1A 0.021 0.004 -10000 0 -10000 0 0
SKI 0.021 0.004 -10000 0 -10000 0 0
SERPINE1 0.013 0.08 -10000 0 -0.72 3 3
SMAD3/SMAD4/ATF2 0.031 0.042 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.019 0.061 -10000 0 -0.21 14 14
SAP30 0.021 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.034 0.031 -10000 0 -10000 0 0
JUN -0.02 0.054 0.22 1 -0.24 6 7
SMAD3/SMAD4/IRF7 0.032 0.046 0.41 1 -10000 0 1
TFE3 0.022 0.008 -10000 0 -10000 0 0
COL1A2 0.021 0.08 0.31 15 -0.58 3 18
mesenchymal cell differentiation -0.033 0.047 -10000 0 -0.24 5 5
DLX1 0.037 0.07 0.33 21 -10000 0 21
TCF3 0.02 0.006 -10000 0 -10000 0 0
FOS -0.008 0.091 -10000 0 -0.34 27 27
SMAD3/SMAD4/Max 0.029 0.043 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.035 0.025 -10000 0 -10000 0 0
ZBTB17 0.022 0.009 -10000 0 -10000 0 0
LAMC1 -0.013 0.032 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.03 0.041 -10000 0 -10000 0 0
IRF7 0.023 0.025 0.36 2 -10000 0 2
ESR1 0.017 0.073 0.33 10 -0.33 8 18
HNF4A 0.068 0.14 0.33 72 -0.33 10 82
MEF2C 0.022 0.083 0.26 17 -10000 0 17
SMAD2-3/SMAD4 0.035 0.052 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.034 0.028 -10000 0 -10000 0 0
IGHV3OR16-13 0.003 0.018 -10000 0 -0.32 1 1
TGIF2/HDAC complex 0.021 0.005 -10000 0 -10000 0 0
CREBBP 0.016 0.016 -10000 0 -10000 0 0
SKIL 0.021 0.005 -10000 0 -10000 0 0
HDAC1 0.022 0.003 -10000 0 -10000 0 0
HDAC2 0.02 0.007 -10000 0 -10000 0 0
SNIP1 0.021 0.007 -10000 0 -10000 0 0
GCN5L2 -0.001 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.034 0.043 -10000 0 -10000 0 0
MSG1/HSC70 0.021 0.064 0.24 7 -0.23 19 26
SMAD2 0.02 0.026 -10000 0 -10000 0 0
SMAD3 0.007 0.033 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.001 0.045 0.17 1 -0.22 2 3
SMAD2/SMAD2/SMAD4 -0.013 0.074 0.19 2 -0.35 9 11
NCOR1 0.02 0.006 -10000 0 -10000 0 0
NCOA2 0.018 0.026 -10000 0 -0.33 2 2
NCOA1 0.022 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.028 0.014 0.24 1 -10000 0 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.054 0.066 -10000 0 -10000 0 0
IFNB1 -0.013 0.036 0.34 2 -10000 0 2
SMAD3/SMAD4/MEF2C 0.051 0.072 0.27 2 -10000 0 2
CITED1 0.01 0.087 0.33 7 -0.33 19 26
SMAD2-3/SMAD4/ARC105 0.044 0.052 -10000 0 -10000 0 0
RBL1 0.021 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.039 0.14 -10000 0 -0.51 28 28
RUNX1-3/PEBPB2 0.039 0.021 -10000 0 -0.19 2 2
SMAD7 -0.002 0.079 -10000 0 -0.46 4 4
MYC/MIZ-1 0.027 0.025 0.2 1 -0.23 1 2
SMAD3/SMAD4 -0.01 0.068 -10000 0 -0.31 3 3
IL10 -0.016 0.048 0.3 2 -0.32 4 6
PIASy/HDAC complex 0.018 0.014 -10000 0 -10000 0 0
PIAS3 0.017 0.014 -10000 0 -10000 0 0
CDK2 0.017 0.016 -10000 0 -10000 0 0
IL5 -0.017 0.035 -10000 0 -10000 0 0
CDK4 0.016 0.016 -10000 0 -10000 0 0
PIAS4 0.019 0.014 -10000 0 -10000 0 0
ATF3 0.006 0.067 -10000 0 -0.33 15 15
SMAD3/SMAD4/SP1 0.035 0.051 -10000 0 -10000 0 0
FOXG1 0.044 0.087 0.33 33 -10000 0 33
FOXO3 -0.02 0.022 -10000 0 -0.14 2 2
FOXO1 -0.021 0.022 -10000 0 -0.14 2 2
FOXO4 -0.021 0.021 -10000 0 -0.14 1 1
heart looping 0.022 0.082 0.26 17 -10000 0 17
CEBPB 0.015 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.04 0.055 0.24 12 -10000 0 12
MYOD1 0.021 0.027 0.33 3 -10000 0 3
SMAD3/SMAD4/HNF4 0.056 0.094 0.24 55 -0.21 10 65
SMAD3/SMAD4/GATA3 0.03 0.048 -10000 0 -0.21 2 2
SnoN/SIN3/HDAC complex/NCoR1 0.021 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.044 0.05 -10000 0 -0.21 1 1
SMAD3/SMAD4/SP1-3 0.044 0.054 -10000 0 -10000 0 0
MED15 0.021 0.004 -10000 0 -10000 0 0
SP1 0.019 0.022 -10000 0 -10000 0 0
SIN3B 0.021 0.005 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.075 0.09 0.36 13 -10000 0 13
ITGB5 -0.015 0.042 0.2 1 -10000 0 1
TGIF/SIN3/HDAC complex/CtBP -0.011 0.063 -10000 0 -0.32 7 7
SMAD3/SMAD4/AR 0.002 0.089 -10000 0 -0.22 46 46
AR -0.022 0.12 0.33 1 -0.33 49 50
negative regulation of cell growth -0.006 0.067 -10000 0 -0.26 12 12
SMAD3/SMAD4/MYOD 0.03 0.043 0.26 1 -10000 0 1
E2F5 0.019 0.007 -10000 0 -10000 0 0
E2F4 0.021 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.072 0.074 0.3 6 -10000 0 6
SMAD2-3/SMAD4/FOXO1-3a-4 -0.018 0.094 -10000 0 -0.37 23 23
TFDP1 0.02 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.022 0.067 -10000 0 -0.24 7 7
SMAD3/SMAD4/RUNX2 0.033 0.048 0.24 5 -10000 0 5
TGIF2 0.021 0.005 -10000 0 -10000 0 0
TGIF1 0.02 0.006 -10000 0 -10000 0 0
ATF2 0.021 0.003 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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
LAT/GRAP2/SLP76/HPK1 0.041 0.05 0.23 1 -0.2 12 13
MAP4K1 0.017 0.036 -10000 0 -0.33 4 4
MAP3K8 0.02 0.018 -10000 0 -0.33 1 1
PRKCB 0.013 0.053 -10000 0 -0.33 9 9
DBNL 0.02 0.007 -10000 0 -10000 0 0
CRKL 0.021 0.004 -10000 0 -10000 0 0
MAP3K1 -0.001 0.053 -10000 0 -0.35 4 4
JUN -0.008 0.12 -10000 0 -0.54 16 16
MAP3K7 0 0.049 -10000 0 -0.23 10 10
GRAP2 0.011 0.058 -10000 0 -0.33 11 11
CRK 0.02 0.007 -10000 0 -10000 0 0
MAP2K4 -0.006 0.073 0.2 1 -0.39 7 8
LAT 0.022 0.016 0.33 1 -10000 0 1
LCP2 0.019 0.025 -10000 0 -0.33 2 2
MAPK8 -0.004 0.12 -10000 0 -0.55 17 17
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.063 -10000 0 -0.26 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55 0.047 0.045 0.23 1 -0.22 6 7
Cellular roles of Anthrax toxin

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
ANTXR1 0.021 0.018 -10000 0 -0.33 1 1
ANTXR2 0.021 0.003 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.002 -10000 0 -0.047 1 1
monocyte activation -0.019 0.12 -10000 0 -0.38 34 34
MAP2K2 -0.031 0.15 -10000 0 -0.57 29 29
MAP2K1 -0.008 0.003 -10000 0 -10000 0 0
MAP2K7 -0.008 0.002 -10000 0 -10000 0 0
MAP2K6 -0.006 0.02 0.078 11 -0.16 2 13
CYAA -0.012 0.008 -10000 0 -0.16 1 1
MAP2K4 -0.007 0.003 -10000 0 -10000 0 0
IL1B -0.016 0.038 0.16 3 -0.16 20 23
Channel 0.027 0.011 -10000 0 -0.17 1 1
NLRP1 -0.008 0.008 -10000 0 -0.16 1 1
CALM1 0.021 0.005 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.056 -10000 0 -0.39 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.002 0.047 1 -10000 0 1
MAPK3 -0.008 0.002 -10000 0 -10000 0 0
MAPK1 -0.008 0.002 -10000 0 -10000 0 0
PGR -0.031 0.055 -10000 0 -0.16 61 61
PA/Cellular Receptors 0.029 0.012 -10000 0 -0.19 1 1
apoptosis -0.003 0.002 -10000 0 -0.047 1 1
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.01 -10000 0 -0.17 1 1
macrophage activation -0.013 0.003 -10000 0 -10000 0 0
TNF 0.005 0.077 0.33 1 -0.33 19 20
VCAM1 -0.016 0.12 -10000 0 -0.4 30 30
platelet activation -0.001 0.056 -10000 0 -0.39 8 8
MAPKKK cascade 0.006 0.019 -10000 0 -0.14 1 1
IL18 -0.01 0.029 0.14 2 -0.19 7 9
negative regulation of macrophage activation -0.003 0.002 -10000 0 -0.047 1 1
LEF -0.003 0.002 -10000 0 -0.047 1 1
CASP1 -0.004 0.012 -10000 0 -0.13 3 3
mol:cAMP -0.001 0.057 -10000 0 -0.39 8 8
necrosis -0.003 0.002 -10000 0 -0.047 1 1
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.027 0.01 -10000 0 -0.16 1 1
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.022 0.003 -10000 0 -10000 0 0
HDAC2 0.02 0.007 -10000 0 -10000 0 0
GNB1/GNG2 0.037 0.025 0.23 1 -0.2 2 3
forebrain development -0.034 0.14 -10000 0 -0.56 14 14
GNAO1 0.014 0.037 0.33 2 -0.33 2 4
SMO/beta Arrestin2 0.021 0.031 0.23 3 -0.21 1 4
SMO 0.016 0.037 0.33 3 -0.33 1 4
ARRB2 0.014 0.016 -10000 0 -10000 0 0
GLI3/SPOP 0.002 0.083 -10000 0 -0.34 11 11
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
GNAI2 0.015 0.015 -10000 0 -10000 0 0
SIN3/HDAC complex 0.048 0.021 -10000 0 -10000 0 0
GNAI1 0.014 0.023 -10000 0 -0.33 1 1
XPO1 0.014 0.02 -10000 0 -10000 0 0
GLI1/Su(fu) -0.033 0.14 -10000 0 -0.52 16 16
SAP30 0.021 0.004 -10000 0 -10000 0 0
mol:GDP 0.016 0.036 0.33 3 -0.33 1 4
MIM/GLI2A 0.002 0.048 -10000 0 -0.23 2 2
IFT88 0.02 0.006 -10000 0 -10000 0 0
GNAI3 0.014 0.016 -10000 0 -10000 0 0
GLI2 -0.01 0.081 0.19 1 -0.38 11 12
GLI3 -0.009 0.084 -10000 0 -0.35 12 12
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.021 0.004 -10000 0 -10000 0 0
SAP18 0.02 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.02 0.006 -10000 0 -10000 0 0
GNG2 0.02 0.018 -10000 0 -0.33 1 1
Gi family/GTP -0.014 0.07 -10000 0 -0.2 38 38
SIN3B 0.021 0.005 -10000 0 -10000 0 0
SIN3A 0.022 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) -0.01 0.088 -10000 0 -0.34 15 15
GLI2/Su(fu) -0.008 0.086 -10000 0 -0.38 13 13
FOXA2 -0.13 0.34 -10000 0 -0.84 70 70
neural tube patterning -0.034 0.14 -10000 0 -0.56 14 14
SPOP 0.021 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.013 0.04 -10000 0 -0.17 3 3
GNB1 0.021 0.004 -10000 0 -10000 0 0
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
CSNK1G3 0.021 0.005 -10000 0 -10000 0 0
MTSS1 0.002 0.048 -10000 0 -0.23 2 2
embryonic limb morphogenesis -0.034 0.14 -10000 0 -0.56 14 14
SUFU 0.007 0.015 -10000 0 -0.14 1 1
LGALS3 0.021 0.005 -10000 0 -10000 0 0
catabolic process -0.005 0.12 -10000 0 -0.44 19 19
GLI3A/CBP 0.006 0.062 -10000 0 -0.33 11 11
KIF3A 0.021 0.005 -10000 0 -10000 0 0
GLI1 -0.035 0.14 -10000 0 -0.57 14 14
RAB23 0.021 0.005 -10000 0 -10000 0 0
CSNK1A1 0.021 0.005 -10000 0 -10000 0 0
IFT172 0.022 0.002 -10000 0 -10000 0 0
RBBP7 0.021 0.005 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.012 0.039 -10000 0 -0.16 5 5
GNAZ -0.015 0.099 -10000 0 -0.33 34 34
RBBP4 0.022 0.003 -10000 0 -10000 0 0
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
PIAS1 0.021 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GLI2/SPOP -0.001 0.084 -10000 0 -0.39 11 11
STK36 0.014 0.02 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.014 0.066 -10000 0 -0.22 20 20
PTCH1 -0.041 0.17 -10000 0 -0.84 10 10
MIM/GLI1 -0.047 0.18 -10000 0 -0.46 53 53
CREBBP 0.006 0.062 -10000 0 -0.33 11 11
Su(fu)/SIN3/HDAC complex -0.003 0.068 -10000 0 -0.36 7 7
EPO signaling pathway

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
BCL2L1 0.017 0.062 0.34 2 -10000 0 2
CRKL -0.01 0.049 0.26 5 -10000 0 5
mol:DAG 0.008 0.034 0.24 1 -0.23 1 2
HRAS 0.001 0.078 0.25 13 -10000 0 13
MAPK8 0 0.061 0.17 43 -10000 0 43
RAP1A -0.01 0.05 0.22 9 -10000 0 9
GAB1 -0.011 0.05 0.22 8 -10000 0 8
MAPK14 -0.001 0.059 0.17 41 -10000 0 41
EPO 0.009 0.035 0.33 3 -10000 0 3
PLCG1 0.008 0.035 0.24 1 -0.23 1 2
EPOR/TRPC2/IP3 Receptors 0.022 0.009 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.038 0.028 0.22 2 -0.2 2 4
GAB1/SHC/GRB2/SOS1 -0.018 0.046 0.24 3 -10000 0 3
EPO/EPOR (dimer) 0.03 0.024 0.23 3 -10000 0 3
IRS2 -0.01 0.05 0.22 9 -10000 0 9
STAT1 0.009 0.038 0.32 1 -0.23 1 2
STAT5B 0.009 0.036 0.28 1 -0.23 1 2
cell proliferation -0.003 0.065 0.17 43 -10000 0 43
GAB1/SHIP/PIK3R1/SHP2/SHC -0.026 0.037 -10000 0 -0.29 1 1
TEC -0.011 0.051 0.22 9 -10000 0 9
SOCS3 0.019 0.025 -10000 0 -0.33 2 2
STAT1 (dimer) 0.009 0.038 0.32 1 -0.23 1 2
JAK2 0.02 0.02 -10000 0 -0.33 1 1
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.045 0.04 0.36 1 -0.16 3 4
EPO/EPOR 0.03 0.024 0.23 3 -10000 0 3
LYN 0.02 0.007 -10000 0 -10000 0 0
TEC/VAV2 -0.014 0.049 0.21 8 -10000 0 8
elevation of cytosolic calcium ion concentration 0.022 0.009 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.038 0.026 0.22 3 -10000 0 3
mol:IP3 0.008 0.034 0.24 1 -0.23 1 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.015 0.056 0.26 4 -0.29 1 5
SH2B3 0.021 0.026 -10000 0 -0.33 2 2
NFKB1 0 0.062 0.17 44 -10000 0 44
EPO/EPOR (dimer)/JAK2/SOCS3 0.003 0.043 0.19 1 -0.23 9 10
PTPN6 -0.009 0.045 0.29 1 -10000 0 1
TEC/VAV2/GRB2 -0.017 0.049 0.26 4 -10000 0 4
EPOR 0.022 0.009 -10000 0 -10000 0 0
INPP5D 0.019 0.031 -10000 0 -0.33 3 3
mol:GDP -0.018 0.046 0.24 3 -10000 0 3
SOS1 0.021 0.003 -10000 0 -10000 0 0
PLCG2 0.018 0.031 -10000 0 -0.33 3 3
CRKL/CBL/C3G -0.017 0.05 0.26 4 -10000 0 4
VAV2 -0.011 0.051 0.22 9 -10000 0 9
CBL -0.01 0.05 0.22 9 -10000 0 9
SHC/Grb2/SOS1 0.024 0.026 0.19 1 -10000 0 1
STAT5A 0.008 0.04 0.28 1 -0.3 2 3
GRB2 0.021 0.005 -10000 0 -10000 0 0
STAT5 (dimer) 0.02 0.043 0.38 1 -0.34 1 2
LYN/PLCgamma2 0.026 0.025 -10000 0 -0.23 3 3
PTPN11 0.021 0.004 -10000 0 -10000 0 0
BTK -0.017 0.061 0.22 8 -0.3 2 10
BCL2 0.007 0.076 0.39 2 -10000 0 2
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.021 0.003 -10000 0 -10000 0 0
mol:PIP3 -0.014 0.025 -10000 0 -0.2 5 5
FRAP1 -0.007 0.087 -10000 0 -0.43 14 14
AKT1 -0.01 0.036 0.15 6 -0.24 4 10
INSR 0.02 0.006 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.025 0.008 -10000 0 -10000 0 0
mol:GTP -0.012 0.047 0.24 2 -0.22 2 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.016 0.028 -10000 0 -0.21 4 4
TSC2 0.021 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.023 0.026 -10000 0 -0.19 2 2
TSC1 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.015 0.028 -10000 0 -0.22 5 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.012 0.039 -10000 0 -0.23 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.022 0.002 -10000 0 -10000 0 0
RPS6KB1 0.006 0.062 0.24 3 -0.37 4 7
MAP3K5 -0.011 0.055 0.18 4 -0.18 34 38
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
apoptosis -0.011 0.055 0.18 4 -0.18 34 38
mol:LY294002 0 0 -10000 0 -0.001 2 2
EIF4B 0.004 0.062 0.28 3 -0.33 4 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.021 0.053 0.23 2 -0.31 3 5
eIF4E/eIF4G1/eIF4A1 0.003 0.055 -10000 0 -0.28 13 13
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.025 0.03 -10000 0 -0.21 5 5
mTOR/RHEB/GTP/Raptor/GBL -0.004 0.036 0.16 5 -0.15 3 8
FKBP1A 0.021 0.005 -10000 0 -10000 0 0
RHEB/GTP -0.016 0.041 0.2 1 -0.19 2 3
mol:Amino Acids 0 0 -10000 0 -0.001 2 2
FKBP12/Rapamycin 0.015 0.004 -10000 0 -10000 0 0
PDPK1 -0.016 0.032 0.15 7 -0.21 4 11
EIF4E 0.021 0.003 -10000 0 -10000 0 0
ASK1/PP5C -0.032 0.18 -10000 0 -0.52 43 43
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.005 0.041 -10000 0 -0.23 10 10
TSC1/TSC2 -0.012 0.051 0.26 2 -0.23 2 4
tumor necrosis factor receptor activity 0 0 0.001 2 -10000 0 2
RPS6 0.02 0.006 -10000 0 -10000 0 0
PPP5C 0.021 0.005 -10000 0 -10000 0 0
EIF4G1 0.021 0.005 -10000 0 -10000 0 0
IRS1 0.001 0.028 -10000 0 -0.24 5 5
INS 0.018 0.003 -10000 0 -10000 0 0
PTEN 0.021 0.005 -10000 0 -10000 0 0
PDK2 -0.016 0.032 0.15 7 -0.21 4 11
EIF4EBP1 -0.062 0.3 -10000 0 -1 33 33
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PPP2R5D -0.004 0.086 0.29 1 -0.4 13 14
peptide biosynthetic process -0.017 0.015 0.17 2 -10000 0 2
RHEB 0.021 0.005 -10000 0 -10000 0 0
EIF4A1 0.02 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 8 -0.003 1 9
EEF2 -0.017 0.015 0.17 2 -10000 0 2
eIF4E/4E-BP1 -0.05 0.28 -10000 0 -0.96 33 33
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.048 0.059 0.22 28 -0.17 3 31
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.021 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.009 0.058 0.27 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.038 0.026 -10000 0 -0.2 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.018 0.037 -10000 0 -0.16 1 1
CaM/Ca2+ 0.045 0.054 -10000 0 -0.16 3 3
RAP1A 0.021 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.009 0.047 0.16 1 -10000 0 1
AKT1 -0.009 0.058 0.29 5 -10000 0 5
MAP2K1 -0.013 0.05 0.24 4 -10000 0 4
MAP3K11 -0.01 0.05 0.27 3 -10000 0 3
IFNGR1 0.02 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.001 0.12 0.23 4 -0.32 36 40
Rap1/GTP -0.03 0.024 -10000 0 -10000 0 0
CRKL/C3G 0.03 0.008 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.058 0.061 0.23 28 -0.18 2 30
CEBPB -0.003 0.094 0.37 1 -0.4 11 12
STAT3 0.021 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.055 0.079 -10000 0 -0.69 2 2
STAT1 -0.009 0.051 0.27 3 -10000 0 3
CALM1 0.021 0.005 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.039 0.088 0.33 29 -0.33 2 31
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.009 0.056 0.27 3 -10000 0 3
CEBPB/PTGES2/Cbp/p300 0.008 0.062 -10000 0 -0.29 7 7
mol:Ca2+ 0.045 0.056 0.21 28 -0.17 3 31
MAPK3 0.003 0.065 -10000 0 -0.45 2 2
STAT1 (dimer) -0.02 0.051 -10000 0 -10000 0 0
MAPK1 -0.013 0.12 -10000 0 -0.66 11 11
JAK2 0.019 0.021 -10000 0 -0.33 1 1
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
JAK1 0.022 0.01 -10000 0 -10000 0 0
CAMK2D 0.021 0.003 -10000 0 -10000 0 0
DAPK1 -0.006 0.093 0.29 2 -0.52 8 10
SMAD7 -0.003 0.038 0.2 4 -0.17 1 5
CBL/CRKL/C3G -0.011 0.056 0.27 3 -10000 0 3
PI3K 0.041 0.05 -10000 0 -0.17 2 2
IFNG 0.039 0.088 0.33 29 -0.33 2 31
apoptosis -0.004 0.089 -10000 0 -0.42 12 12
CAMK2G 0.021 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.003 -10000 0 -10000 0 0
CAMK2A -0.012 0.1 0.33 1 -0.33 37 38
CAMK2B 0.061 0.11 0.33 53 -10000 0 53
FRAP1 -0.01 0.054 0.28 5 -10000 0 5
PRKCD -0.011 0.06 0.28 6 -10000 0 6
RAP1B 0.02 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.018 0.037 -10000 0 -0.16 1 1
PTPN2 0.021 0.005 -10000 0 -10000 0 0
EP300 0.021 0.004 -10000 0 -10000 0 0
IRF1 -0.012 0.047 0.22 2 -10000 0 2
STAT1 (dimer)/PIASy -0.009 0.055 0.27 3 -10000 0 3
SOCS1 0.014 0.074 -10000 0 -1 2 2
mol:GDP -0.011 0.053 0.25 3 -10000 0 3
CASP1 -0.004 0.04 0.2 4 -0.19 2 6
PTGES2 0.021 0.004 -10000 0 -10000 0 0
IRF9 -0.003 0.032 0.14 1 -10000 0 1
mol:PI-3-4-5-P3 0.029 0.04 -10000 0 -0.16 2 2
RAP1/GDP -0.026 0.033 -10000 0 -10000 0 0
CBL -0.008 0.049 0.27 3 -10000 0 3
MAP3K1 -0.009 0.05 0.27 3 -10000 0 3
PIAS1 0.021 0.003 -10000 0 -10000 0 0
PIAS4 0.02 0.006 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.018 0.037 -10000 0 -0.16 1 1
PTPN11 -0.005 0.049 0.22 2 -0.17 3 5
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 -0.01 0.077 -10000 0 -0.39 7 7
BAG4 0.019 0.008 -10000 0 -10000 0 0
BAD -0.003 0.038 0.3 2 -0.14 4 6
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.022 0.04 0.33 4 -0.33 2 6
BAX -0.003 0.035 0.16 3 -0.13 3 6
EnzymeConsortium:3.1.4.12 0 0.023 0.075 5 -0.085 7 12
IKBKB 0.003 0.091 0.28 8 -0.36 7 15
MAP2K2 -0.007 0.037 0.17 7 -10000 0 7
MAP2K1 -0.008 0.042 0.16 10 -0.16 1 11
SMPD1 -0.002 0.027 0.11 2 -0.12 5 7
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0 0.08 0.24 2 -0.38 7 9
MAP2K4 -0.004 0.038 0.19 6 -0.15 1 7
protein ubiquitination -0.001 0.087 0.3 4 -0.37 7 11
EnzymeConsortium:2.7.1.37 -0.01 0.044 0.17 8 -0.17 1 9
response to UV 0 0.001 0.002 8 -0.002 1 9
RAF1 -0.005 0.04 0.17 7 -0.15 1 8
CRADD 0.022 0.016 0.33 1 -10000 0 1
mol:ceramide 0.001 0.035 0.11 6 -0.13 7 13
I-kappa-B-alpha/RELA/p50/ubiquitin 0.024 0.011 -10000 0 -10000 0 0
MADD 0.021 0.003 -10000 0 -10000 0 0
MAP3K1 -0.001 0.04 0.2 6 -0.14 3 9
TRADD 0.021 0.004 -10000 0 -10000 0 0
RELA/p50 0.021 0.003 -10000 0 -10000 0 0
MAPK3 -0.006 0.04 0.17 7 -10000 0 7
MAPK1 -0.008 0.044 0.17 7 -0.2 2 9
p50/RELA/I-kappa-B-alpha 0.027 0.012 -10000 0 -10000 0 0
FADD -0.006 0.077 -10000 0 -0.38 7 7
KSR1 -0.002 0.041 0.16 9 -0.13 4 13
MAPK8 -0.008 0.042 0.19 10 -10000 0 10
TRAF2 0.021 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.01 0.079 0.36 1 -0.37 7 8
TNF R/SODD 0.026 0.013 -10000 0 -10000 0 0
TNF 0.004 0.077 0.33 1 -0.33 19 20
CYCS 0.007 0.045 0.16 8 -0.14 1 9
IKBKG -0.005 0.082 0.28 3 -0.36 6 9
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.005 0.078 -10000 0 -0.4 7 7
RELA 0.021 0.003 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AIFM1 0.001 0.04 0.19 3 -0.13 2 5
TNF/TNF R/SODD 0.025 0.052 0.23 1 -0.2 18 19
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.01 0.08 -10000 0 -0.56 7 7
NSMAF 0.003 0.088 0.24 4 -0.38 7 11
response to hydrogen peroxide 0 0.001 0.002 8 -0.002 1 9
BCL2 0.02 0.017 0.33 1 -10000 0 1
Retinoic acid receptors-mediated signaling

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
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC3 0.021 0.004 -10000 0 -10000 0 0
VDR 0.021 0.024 0.33 1 -0.33 1 2
Cbp/p300/PCAF 0.041 0.012 -10000 0 -10000 0 0
EP300 0.021 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.011 0.043 -10000 0 -0.34 2 2
KAT2B 0.021 0.004 -10000 0 -10000 0 0
MAPK14 0.021 0.005 -10000 0 -10000 0 0
AKT1 0.005 0.045 0.26 1 -0.23 2 3
RAR alpha/9cRA/Cyclin H 0.032 0.052 -10000 0 -0.24 3 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.008 0.051 0.2 1 -0.26 5 6
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.019 0.038 -10000 0 -0.19 6 6
NCOR2 0.021 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.016 0.016 0.22 1 -0.22 1 2
RXRs/RARs/NRIP1/9cRA -0.017 0.1 0.43 2 -0.44 10 12
NCOA2 0.018 0.026 -10000 0 -0.33 2 2
NCOA3 0.02 0.005 -10000 0 -10000 0 0
NCOA1 0.022 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.024 0.33 1 -0.33 1 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.027 0.008 -10000 0 -10000 0 0
MAPK3 0.022 0.003 -10000 0 -10000 0 0
MAPK1 0.021 0.005 -10000 0 -10000 0 0
MAPK8 0.022 0.003 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.013 0.089 0.28 1 -0.38 11 12
RARA 0.013 0.03 0.17 1 -0.2 2 3
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.006 0.048 0.2 1 -0.27 4 5
PRKCA 0.02 0.025 -10000 0 -0.33 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.021 0.11 0.35 2 -0.48 10 12
RXRG -0.091 0.13 0.16 12 -0.25 148 160
RXRA 0.007 0.026 0.18 2 -0.19 2 4
RXRB 0.019 0.046 0.16 26 -0.25 2 28
VDR/Vit D3/DNA 0.016 0.016 0.22 1 -0.22 1 2
RBP1 0.024 0.039 0.33 5 -0.33 1 6
CRBP1/9-cic-RA 0.018 0.026 0.22 5 -0.22 1 6
RARB 0.02 0.025 -10000 0 -0.33 2 2
PRKCG 0.04 0.076 0.33 25 -10000 0 25
MNAT1 0.021 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.019 0.09 0.27 1 -0.42 10 11
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.011 0.085 0.41 1 -0.38 9 10
proteasomal ubiquitin-dependent protein catabolic process 0.009 0.074 0.28 3 -0.31 8 11
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.022 0.11 0.35 2 -0.49 10 12
positive regulation of DNA binding 0.022 0.044 -10000 0 -0.22 3 3
NRIP1 -0.02 0.11 0.46 1 -0.57 4 5
RXRs/RARs -0.024 0.11 0.28 1 -0.49 11 12
RXRs/RXRs/DNA/9cRA -0.023 0.082 0.28 1 -0.38 11 12
PRKACA 0.02 0.005 -10000 0 -10000 0 0
CDK7 0.021 0.005 -10000 0 -10000 0 0
TFIIH 0.04 0.013 -10000 0 -10000 0 0
RAR alpha/9cRA 0.041 0.044 -10000 0 -0.22 1 1
CCNH 0.021 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.034 0.019 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.019 0.008 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.02 0.051 -10000 0 -0.28 3 3
NEF -0.001 0.02 -10000 0 -0.17 5 5
NFKBIA 0.019 0.009 -10000 0 -10000 0 0
BIRC3 0.005 0.069 0.3 4 -10000 0 4
CYCS -0.004 0.05 0.15 20 -0.3 2 22
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CD247 0.018 0.029 -10000 0 -0.24 4 4
MAP2K7 -0.024 0.18 -10000 0 -0.65 27 27
protein ubiquitination -0.002 0.071 0.31 3 -0.31 4 7
CRADD 0.022 0.016 0.33 1 -10000 0 1
DAXX 0.021 0.005 -10000 0 -10000 0 0
FAS 0.018 0.035 -10000 0 -0.33 4 4
BID 0.006 0.05 0.16 22 -0.28 3 25
NF-kappa-B/RelA/I kappa B alpha 0.04 0.026 0.23 4 -10000 0 4
TRADD 0.021 0.004 -10000 0 -10000 0 0
MAP3K5 0.02 0.006 -10000 0 -10000 0 0
CFLAR 0.022 0.002 -10000 0 -10000 0 0
FADD 0.021 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.04 0.026 0.23 4 -10000 0 4
MAPK8 -0.024 0.17 0.35 2 -0.6 27 29
APAF1 0.021 0.004 -10000 0 -10000 0 0
TRAF1 0.021 0.004 -10000 0 -10000 0 0
TRAF2 0.021 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.035 -10000 0 -0.27 4 4
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.001 0.07 -10000 0 -0.31 9 9
CHUK -0.004 0.074 0.31 3 -0.33 4 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.05 0.032 -10000 0 -0.18 1 1
TCRz/NEF 0.014 0.025 -10000 0 -0.23 4 4
TNF 0.005 0.077 0.33 1 -0.33 19 20
FASLG -0.014 0.033 -10000 0 -0.31 4 4
NFKB1 0.022 0.012 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0.025 0.052 0.23 1 -0.2 18 19
CASP6 0.028 0.07 -10000 0 -0.48 3 3
CASP7 0.025 0.097 0.32 13 -0.3 2 15
RELA 0.021 0.012 -10000 0 -0.13 2 2
CASP2 0.021 0.005 -10000 0 -10000 0 0
CASP3 0.023 0.093 0.32 11 -10000 0 11
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.013 -10000 0 -10000 0 0
CASP8 0.021 0.018 -10000 0 -0.33 1 1
CASP9 0.021 0.004 -10000 0 -10000 0 0
MAP3K14 -0.001 0.07 -10000 0 -0.34 5 5
APAF-1/Caspase 9 -0.011 0.054 0.18 4 -0.28 1 5
BCL2 -0.022 0.16 0.33 2 -0.55 27 29
Arf6 trafficking events

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
SLC2A4 0.018 0.035 0.33 1 -0.33 3 4
CLTC 0.017 0.065 0.23 2 -0.44 5 7
calcium ion-dependent exocytosis 0.011 0.03 0.19 3 -0.16 1 4
Dynamin 2/GTP 0 0.048 0.13 42 -10000 0 42
EXOC4 0.021 0.005 -10000 0 -10000 0 0
CD59 0.012 0.042 -10000 0 -0.31 4 4
CPE -0.004 0.045 0.2 16 -10000 0 16
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.027 -10000 0 -10000 0 0
CTNND1 0 0.057 0.2 24 -10000 0 24
DNM2 0.02 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.05 0.18 5 -0.33 2 7
TSHR 0.006 0.057 0.17 41 -10000 0 41
INS 0.003 0.069 -10000 0 -0.48 7 7
BIN1 0.022 0.001 -10000 0 -10000 0 0
mol:Choline 0.011 0.027 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.07 0.19 46 -10000 0 46
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.021 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.046 0.13 40 -10000 0 40
JUP 0.012 0.037 -10000 0 -0.3 3 3
ASAP2/amphiphysin II 0.039 0.011 -10000 0 -10000 0 0
ARF6/GTP 0.015 0.004 -10000 0 -10000 0 0
CDH1 0.012 0.043 -10000 0 -0.31 4 4
clathrin-independent pinocytosis 0.015 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.021 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.015 0.004 -10000 0 -10000 0 0
EXOC2 0.021 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.006 0.02 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.021 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.032 0.05 0.3 4 -10000 0 4
positive regulation of phagocytosis -0.013 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.027 0.008 -10000 0 -10000 0 0
ACAP1 0.015 0.027 -10000 0 -0.15 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.011 0.064 -10000 0 -0.31 4 4
clathrin heavy chain/ACAP1 0.015 0.06 0.23 6 -0.33 5 11
JIP4/KLC1 0.038 0.013 -10000 0 -10000 0 0
EXOC1 0.021 0.004 -10000 0 -10000 0 0
exocyst 0.006 0.02 -10000 0 -10000 0 0
RALA/GTP 0.015 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.027 0.008 -10000 0 -10000 0 0
receptor recycling 0.015 0.004 -10000 0 -10000 0 0
CTNNA1 0 0.057 0.2 23 -10000 0 23
NME1 0.011 0.07 0.19 46 -10000 0 46
clathrin coat assembly 0.016 0.068 0.23 3 -0.4 6 9
IL2RA 0.015 0.046 -10000 0 -0.33 4 4
VAMP3 -0.013 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.017 0.052 0.22 1 -0.31 5 6
EXOC6 0.021 0.003 -10000 0 -10000 0 0
PLD1 0.004 0.006 -10000 0 -10000 0 0
PLD2 0.005 0.005 -10000 0 -10000 0 0
EXOC5 0.021 0.004 -10000 0 -10000 0 0
PIP5K1C 0.007 0.049 0.18 5 -0.26 4 9
SDC1 0.012 0.042 -10000 0 -0.31 4 4
ARF6/GDP 0.029 0.038 0.14 42 -10000 0 42
EXOC7 0.021 0.005 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.034 0.052 -10000 0 -0.3 4 4
mol:Phosphatidic acid 0.011 0.027 -10000 0 -10000 0 0
endocytosis -0.038 0.011 -10000 0 -10000 0 0
SCAMP2 0.021 0.003 -10000 0 -10000 0 0
ADRB2 -0.037 0.093 -10000 0 -0.45 6 6
EXOC3 0.016 0.01 -10000 0 -10000 0 0
ASAP2 0.022 0.002 -10000 0 -10000 0 0
Dynamin 2/GDP 0.035 0.052 0.18 42 -10000 0 42
KLC1 0.021 0.005 -10000 0 -10000 0 0
AVPR2 -0.014 0.095 0.27 7 -0.41 6 13
RALA 0.02 0.007 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.024 0.055 0.33 2 -0.29 4 6
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 0.006 0.11 -9999 0 -0.43 11 11
MAP3K8 0.017 0.021 -9999 0 -0.33 1 1
FOS 0.005 0.083 -9999 0 -0.39 7 7
PRKCA 0.016 0.029 -9999 0 -0.33 2 2
PTPN7 0.015 0.016 -9999 0 -10000 0 0
HRAS 0.018 0.011 -9999 0 -10000 0 0
PRKCB 0.01 0.054 -9999 0 -0.33 9 9
NRAS 0.018 0.011 -9999 0 -10000 0 0
RAS family/GTP 0.031 0.023 -9999 0 -10000 0 0
MAPK3 0.011 0.043 -9999 0 -0.34 1 1
MAP2K1 -0.004 0.081 -9999 0 -0.39 11 11
ELK1 0.017 0.017 -9999 0 -10000 0 0
BRAF -0.003 0.059 -9999 0 -0.34 10 10
mol:GTP 0 0.001 -9999 0 -0.004 30 30
MAPK1 0.002 0.08 -9999 0 -0.43 9 9
RAF1 -0.005 0.062 -9999 0 -0.33 12 12
KRAS 0.018 0.011 -9999 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.02 0.005 -10000 0 -10000 0 0
NFATC1 -0.018 0.1 0.4 1 -0.4 14 15
NFATC2 -0.013 0.06 0.18 2 -0.25 11 13
NFATC3 0.006 0.024 -10000 0 -0.3 2 2
YWHAE 0.02 0.007 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.019 0.089 0.22 2 -0.29 21 23
Exportin 1/Ran/NUP214 0.041 0.017 0.23 2 -10000 0 2
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0 0.081 -10000 0 -0.29 14 14
BCL2/BAX 0.028 0.016 0.24 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.016 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.016 -10000 0 -10000 0 0
BAX 0.021 0.005 -10000 0 -10000 0 0
MAPK14 0.013 0.016 -10000 0 -10000 0 0
BAD 0.021 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.006 0.08 -10000 0 -0.31 14 14
Calcineurin A alpha-beta B1/BCL2 0.02 0.017 0.33 1 -10000 0 1
FKBP8 0.02 0.018 -10000 0 -0.33 1 1
activation-induced cell death of T cells 0.006 0.079 0.3 14 -10000 0 14
KPNB1 0.021 0.004 -10000 0 -10000 0 0
KPNA2 0.024 0.032 0.33 4 -10000 0 4
XPO1 0.021 0.002 -10000 0 -10000 0 0
SFN 0.026 0.045 0.33 7 -0.33 1 8
MAP3K8 0.012 0.024 -10000 0 -0.33 1 1
NFAT4/CK1 alpha 0.007 0.027 -10000 0 -0.17 2 2
MEF2D/NFAT1/Cbp/p300 -0.017 0.1 -10000 0 -0.23 58 58
CABIN1 -0.019 0.085 0.18 1 -0.29 20 21
CALM1 0.012 0.018 -10000 0 -10000 0 0
RAN 0.022 0.022 0.33 2 -10000 0 2
MAP3K1 0.021 0.005 -10000 0 -10000 0 0
CAMK4 0.019 0.035 0.33 1 -0.33 3 4
mol:Ca2+ -0.002 0.005 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
YWHAH 0.021 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.027 0.021 -10000 0 -0.23 2 2
YWHAB 0.021 0.005 -10000 0 -10000 0 0
MAPK8 0.013 0.017 -10000 0 -10000 0 0
MAPK9 0.021 0.005 -10000 0 -10000 0 0
YWHAG 0.021 0.005 -10000 0 -10000 0 0
FKBP1A 0.021 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.017 0.11 0.3 3 -0.39 17 20
PRKCH 0.021 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.018 0.028 -10000 0 -10000 0 0
CASP3 0.013 0.016 -10000 0 -10000 0 0
PIM1 0.021 0.005 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.011 -10000 0 -10000 0 0
apoptosis 0.011 0.019 0.15 1 -10000 0 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0 0.036 -10000 0 -0.26 1 1
PRKCB 0.013 0.053 -10000 0 -0.33 9 9
PRKCE 0.019 0.031 -10000 0 -0.33 3 3
JNK2/NFAT4 0.015 0.039 -10000 0 -0.28 2 2
BAD/BCL-XL 0.03 0.009 -10000 0 -10000 0 0
PRKCD 0.021 0.004 -10000 0 -10000 0 0
NUP214 0.021 0.004 -10000 0 -10000 0 0
PRKCZ 0.011 0.034 -10000 0 -0.33 3 3
PRKCA 0.019 0.025 -10000 0 -0.33 2 2
PRKCG 0.04 0.076 0.33 25 -10000 0 25
PRKCQ -0.022 0.11 -10000 0 -0.33 47 47
FKBP38/BCL2 0.027 0.021 0.24 1 -0.23 1 2
EP300 0.012 0.02 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
NFATc/JNK1 -0.011 0.1 0.38 1 -0.38 14 15
CaM/Ca2+/FKBP38 0.017 0.024 -10000 0 -0.2 1 1
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSNK1A1 -0.016 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.016 0.03 0.21 1 -0.19 3 4
NFATc/ERK1 -0.008 0.1 0.38 1 -0.38 14 15
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.002 0.09 -10000 0 -0.3 16 16
NR4A1 -0.057 0.15 0.25 3 -0.36 67 70
GSK3B 0.013 0.017 -10000 0 -10000 0 0
positive T cell selection 0.006 0.023 -10000 0 -0.3 2 2
NFAT1/CK1 alpha -0.011 0.044 0.14 1 -0.2 8 9
RCH1/ KPNB1 0.033 0.022 0.24 4 -10000 0 4
YWHAQ 0.022 0.002 -10000 0 -10000 0 0
PRKACA 0.013 0.016 -10000 0 -10000 0 0
AKAP5 0.019 0.025 -10000 0 -0.33 2 2
MEF2D 0.01 0.019 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.019 0.008 -10000 0 -10000 0 0
NFATc/p38 alpha -0.014 0.1 -10000 0 -0.38 14 14
CREBBP 0.012 0.02 -10000 0 -10000 0 0
BCL2 0.02 0.017 0.33 1 -10000 0 1
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA 0.025 0.074 0.23 1 -0.25 19 20
Ran/GTP/Exportin 1/HDAC1 -0.019 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.004 0.073 -10000 0 -0.28 16 16
SUMO1 0.021 0.003 -10000 0 -10000 0 0
ZFPM1 0.021 0.017 0.33 1 -10000 0 1
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
FKBP3 0.021 0.005 -10000 0 -10000 0 0
Histones 0.031 0.061 -10000 0 -0.3 3 3
YY1/LSF 0.015 0.043 -10000 0 -0.24 4 4
SMG5 0.018 0.008 -10000 0 -10000 0 0
RAN 0.023 0.022 0.33 2 -10000 0 2
I kappa B alpha/HDAC3 0 0.044 -10000 0 -0.2 14 14
I kappa B alpha/HDAC1 0.011 0.046 -10000 0 -0.32 1 1
SAP18 0.02 0.006 -10000 0 -10000 0 0
RELA 0.004 0.055 -10000 0 -0.21 16 16
HDAC1/Smad7 0.036 0.021 -10000 0 -0.2 1 1
RANGAP1 0.021 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.012 0.056 -10000 0 -0.23 8 8
NuRD/MBD3 Complex 0 0.066 -10000 0 -0.3 9 9
NF kappa B1 p50/RelA 0.01 0.075 -10000 0 -0.32 9 9
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.01 0.1 -10000 0 -0.33 35 35
GATA1 -0.015 0.11 -10000 0 -0.33 40 40
Mad/Max 0.031 0.007 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.023 0.095 -10000 0 -0.31 20 20
RBBP7 0.021 0.004 -10000 0 -10000 0 0
NPC 0.013 0.001 -10000 0 -10000 0 0
RBBP4 0.021 0.003 -10000 0 -10000 0 0
MAX 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NFKBIA 0.004 0.029 -10000 0 -0.14 14 14
KAT2B 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.013 0.056 -10000 0 -0.37 3 3
SIN3 complex 0.047 0.021 -10000 0 -10000 0 0
SMURF1 0.02 0.005 -10000 0 -10000 0 0
CHD3 0.02 0.006 -10000 0 -10000 0 0
SAP30 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.02 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.003 0.051 -10000 0 -0.26 9 9
YY1/HDAC2 0.015 0.04 -10000 0 -0.24 4 4
YY1/HDAC1 0.015 0.043 -10000 0 -0.24 4 4
NuRD/MBD2 Complex (MeCP1) -0.004 0.068 -10000 0 -0.33 8 8
PPARG -0.028 0.12 -10000 0 -0.3 51 51
HDAC8/hEST1B 0.035 0.018 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.012 0.056 -10000 0 -0.32 3 3
MBD3L2 0.017 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.036 0.02 -10000 0 -0.2 1 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.005 0.085 -10000 0 -0.34 14 14
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC3 0.003 0.038 -10000 0 -0.34 2 2
HDAC2 0.02 0.007 -10000 0 -10000 0 0
YY1 0.007 0.003 -10000 0 -10000 0 0
HDAC8 0.021 0.003 -10000 0 -10000 0 0
SMAD7 0.019 0.019 -10000 0 -0.33 1 1
NCOR2 0.021 0.004 -10000 0 -10000 0 0
MXD1 0.022 0.002 -10000 0 -10000 0 0
STAT3 0.011 0.003 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.022 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.026 0.044 -10000 0 -0.22 4 4
YY1/SAP30/HDAC1 0.025 0.044 -10000 0 -0.22 4 4
EP300 0.021 0.004 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.011 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.004 0.029 -10000 0 -0.14 14 14
histone deacetylation -0.004 0.068 -10000 0 -0.33 8 8
STAT3 (dimer non-phopshorylated)/HDAC3 0.003 0.044 -10000 0 -0.23 7 7
nuclear export -0.035 0.018 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GATAD2B 0.018 0.008 -10000 0 -10000 0 0
GATAD2A 0.021 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 -0.002 0.075 -10000 0 -0.28 8 8
GATA1/HDAC1 0.004 0.08 -10000 0 -0.23 40 40
GATA1/HDAC3 -0.006 0.077 -10000 0 -0.31 7 7
CHD4 0.02 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.017 0.057 0.24 1 -0.23 18 19
SIN3/HDAC complex/Mad/Max -0.011 0.062 -10000 0 -0.3 8 8
NuRD Complex -0.008 0.08 -10000 0 -0.33 11 11
positive regulation of chromatin silencing 0.029 0.06 -10000 0 -0.3 3 3
SIN3B 0.02 0.005 -10000 0 -10000 0 0
MTA2 0.021 0.003 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.022 0.002 -10000 0 -10000 0 0
SUMO1/HDAC1 0.03 0.026 -10000 0 -0.18 2 2
HDAC complex 0.048 0.02 -10000 0 -10000 0 0
GATA1/Fog1 0.003 0.078 -10000 0 -0.23 40 40
FKBP25/HDAC1/HDAC2 0.038 0.016 -10000 0 -10000 0 0
TNF 0.005 0.077 0.33 1 -0.33 19 20
negative regulation of cell growth -0.01 0.061 -10000 0 -0.3 8 8
NuRD/MBD2/PRMT5 Complex -0.004 0.068 -10000 0 -0.33 8 8
Ran/GTP/Exportin 1 0.03 0.028 0.2 1 -0.18 2 3
NF kappa B/RelA/I kappa B alpha -0.006 0.065 -10000 0 -0.28 16 16
SIN3/HDAC complex/NCoR1 -0.014 0.072 -10000 0 -0.34 11 11
TFCP2 0.021 0.003 -10000 0 -10000 0 0
NR2C1 0.021 0.003 -10000 0 -10000 0 0
MBD3 0.018 0.026 -10000 0 -0.33 2 2
MBD2 0.019 0.007 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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
EEF2K -0.018 0.008 -10000 0 -10000 0 0
SNTA1 0.022 0.023 0.33 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.016 0.032 0.3 3 -10000 0 3
MAPK12 -0.009 0.021 0.18 2 -0.17 2 4
CCND1 -0.001 0.054 -10000 0 -0.38 7 7
p38 gamma/SNTA1 -0.009 0.048 0.18 13 -0.28 1 14
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.004 0.037 0.19 11 -0.17 2 13
MAP2K6 -0.004 0.024 0.22 2 -0.18 2 4
MAPT -0.008 0.073 0.21 10 -0.25 19 29
MAPK13 -0.016 0.006 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.002 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.005 0.067 -10000 0 -0.31 16 16
KLHL20 0 0.052 0.17 2 -0.22 7 9
CYFIP2 0.016 0.043 -10000 0 -0.33 6 6
Rac1/GDP -0.01 0.062 0.32 3 -0.26 7 10
ENAH -0.004 0.067 -10000 0 -0.32 16 16
AP1M1 0.021 0.005 -10000 0 -10000 0 0
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.021 0.004 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.026 0.028 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.025 -10000 0 -0.15 8 8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.029 -10000 0 -0.18 3 3
RAPGEF1 -0.009 0.058 0.2 2 -0.29 10 12
CTNND1 0.021 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.006 0.072 -10000 0 -0.32 17 17
CRK -0.012 0.057 -10000 0 -0.31 12 12
E-cadherin/gamma catenin/alpha catenin 0.039 0.021 -10000 0 -0.2 2 2
alphaE/beta7 Integrin 0.028 0.017 -10000 0 -0.23 1 1
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
NCKAP1 0.022 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.016 -10000 0 -10000 0 0
DLG1 -0.003 0.063 -10000 0 -0.32 14 14
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.027 0.016 -10000 0 -0.13 2 2
MLLT4 0.02 0.007 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.052 0.059 0.22 38 -0.17 4 42
PI3K -0.033 0.02 -10000 0 -0.17 2 2
ARF6 0.021 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.029 0.02 -10000 0 -0.23 2 2
TIAM1 0.016 0.04 -10000 0 -0.33 5 5
E-cadherin(dimer)/Ca2+ 0.046 0.022 -10000 0 -0.17 2 2
AKT1 -0.018 0.026 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
CDH1 0.019 0.025 -10000 0 -0.33 2 2
RhoA/GDP -0.011 0.066 0.29 4 -0.25 7 11
actin cytoskeleton organization 0.004 0.045 0.15 8 -0.16 7 15
CDC42/GDP -0.011 0.065 0.29 4 -0.26 7 11
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.008 0.019 -10000 0 -0.18 4 4
ITGB7 0.02 0.018 -10000 0 -0.33 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.05 0.024 -10000 0 -0.18 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.035 0.018 -10000 0 -0.17 2 2
mol:GDP -0.011 0.07 0.3 4 -0.29 7 11
CDC42/GTP/IQGAP1 0.028 0.007 -10000 0 -10000 0 0
JUP 0.021 0.004 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP -0.012 0.059 0.2 2 -0.26 4 6
RAC1/GTP/IQGAP1 0.025 0.011 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.03 0.009 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.006 0.043 0.16 12 -0.15 5 17
NME1 0.055 0.097 0.33 43 -10000 0 43
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 -0.001 0.058 -10000 0 -0.32 11 11
regulation of cell-cell adhesion -0.027 0.019 -10000 0 -10000 0 0
WASF2 -0.003 0.024 -10000 0 -10000 0 0
Rap1/GTP -0.025 0.032 0.14 5 -10000 0 5
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.034 -10000 0 -0.18 3 3
CCND1 0.005 0.044 0.15 10 -0.18 5 15
VAV2 -0.006 0.12 -10000 0 -0.6 11 11
RAP1/GDP -0.02 0.046 0.19 1 -0.23 2 3
adherens junction assembly -0.002 0.061 -10000 0 -0.31 13 13
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
PIP5K1C 0.02 0.006 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.036 0.03 -10000 0 -0.18 3 3
E-cadherin/beta catenin 0.004 0.022 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.006 0.07 -10000 0 -0.32 17 17
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.005 0.062 -10000 0 -0.34 9 9
E-cadherin/beta catenin/alpha catenin 0.039 0.021 -10000 0 -0.2 2 2
ITGAE 0.02 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.005 0.073 -10000 0 -0.32 17 17
Regulation of Telomerase

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
Telomerase catalytic core complex 0.092 0.16 0.45 10 -10000 0 10
RAD9A 0.021 0.004 -10000 0 -10000 0 0
AP1 0.018 0.071 -10000 0 -0.22 29 29
IFNAR2 0.028 0.014 -10000 0 -10000 0 0
AKT1 0.02 0.036 -10000 0 -0.35 1 1
ER alpha/Oestrogen 0.019 0.048 0.23 10 -0.22 8 18
NFX1/SIN3/HDAC complex 0.007 0.055 -10000 0 -0.3 6 6
EGF 0.077 0.13 0.33 72 -0.32 4 76
SMG5 0.018 0.008 -10000 0 -10000 0 0
SMG6 0.02 0.007 -10000 0 -10000 0 0
SP3/HDAC2 0.039 0.024 -10000 0 -10000 0 0
TERT/c-Abl 0.085 0.14 0.41 9 -10000 0 9
SAP18 0.021 0.007 -10000 0 -10000 0 0
MRN complex 0.036 0.018 -10000 0 -10000 0 0
WT1 0.015 0.094 0.35 8 -0.32 21 29
WRN 0.018 0.008 -10000 0 -10000 0 0
SP1 0.031 0.018 -10000 0 -10000 0 0
SP3 0.024 0.008 -10000 0 -10000 0 0
TERF2IP 0.021 0.005 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.058 0.11 -10000 0 -10000 0 0
Mad/Max 0.039 0.016 -10000 0 -10000 0 0
TERT 0.092 0.16 0.46 8 -10000 0 8
CCND1 0.082 0.18 0.5 7 -0.9 5 12
MAX 0.024 0.008 -10000 0 -10000 0 0
RBBP7 0.022 0.006 -10000 0 -10000 0 0
RBBP4 0.023 0.004 -10000 0 -10000 0 0
TERF2 -0.018 0.015 -10000 0 -10000 0 0
PTGES3 0.021 0.004 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
Telomerase/911 0.053 0.063 0.26 1 -0.31 1 2
CDKN1B 0.002 0.04 0.22 2 -10000 0 2
RAD1 0.018 0.009 -10000 0 -10000 0 0
XRCC5 0.022 0.002 -10000 0 -10000 0 0
XRCC6 0.021 0.004 -10000 0 -10000 0 0
SAP30 0.022 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.028 0.011 -10000 0 -10000 0 0
UBE3A 0.023 0.008 -10000 0 -10000 0 0
JUN 0.022 0.026 -10000 0 -0.32 2 2
E6 0.003 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.013 -10000 0 -10000 0 0
FOS -0.001 0.09 -10000 0 -0.32 28 28
IFN-gamma/IRF1 0.052 0.062 0.25 29 -0.23 2 31
PARP2 0.02 0.005 -10000 0 -10000 0 0
BLM 0.053 0.094 0.33 40 -10000 0 40
Telomerase 0.031 0.079 0.25 5 -0.49 2 7
IRF1 0.025 0.009 -10000 0 -10000 0 0
ESR1 0.022 0.071 0.33 10 -0.32 8 18
KU/TER 0.031 0.006 -10000 0 -10000 0 0
ATM/TRF2 0.028 0.015 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.009 0.053 -10000 0 -0.27 5 5
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.009 0.053 -10000 0 -0.28 5 5
HDAC1 0.023 0.003 -10000 0 -10000 0 0
HDAC2 0.027 0.017 -10000 0 -10000 0 0
ATM 0.01 0.008 -10000 0 -10000 0 0
SMAD3 -0.021 0.009 -10000 0 -10000 0 0
ABL1 0.021 0.004 -10000 0 -10000 0 0
MXD1 0.025 0.007 -10000 0 -10000 0 0
MRE11A 0.021 0.005 -10000 0 -10000 0 0
HUS1 0.02 0.007 -10000 0 -10000 0 0
RPS6KB1 0.021 0.005 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.089 0.14 0.42 6 -10000 0 6
NR2F2 0.006 0.026 -10000 0 -10000 0 0
MAPK3 -0.007 0.02 -10000 0 -10000 0 0
MAPK1 -0.007 0.019 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.009 0.02 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
HNRNPC 0.021 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.008 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
EGFR 0.018 0.043 0.34 1 -0.32 5 6
mol:Oestrogen 0.002 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.058 0.089 0.25 58 -0.23 8 66
MYC 0.019 0.028 -10000 0 -0.32 2 2
IL2 0.029 0.018 -10000 0 -10000 0 0
KU 0.031 0.006 -10000 0 -10000 0 0
RAD50 0.021 0.005 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
TGFB1 0.009 0.02 -10000 0 -10000 0 0
TRF2/BLM 0.048 0.059 0.23 37 -10000 0 37
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.096 0.14 0.43 7 -10000 0 7
SP1/HDAC2 0.045 0.035 -10000 0 -10000 0 0
PINX1 0.018 0.008 -10000 0 -10000 0 0
Telomerase/EST1A 0.054 0.11 -10000 0 -10000 0 0
Smad3/Myc -0.02 0.016 -10000 0 -0.18 2 2
911 complex 0.032 0.02 -10000 0 -10000 0 0
IFNG 0.045 0.086 0.34 29 -0.33 2 31
Telomerase/PinX1 0.046 0.1 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.047 0.088 0.31 5 -0.41 3 8
SIN3B 0.022 0.007 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
Telomerase/EST1B 0.049 0.1 -10000 0 -10000 0 0
response to DNA damage stimulus 0.002 0.019 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.048 0.028 -10000 0 -10000 0 0
TRF2/WRN 0.025 0.012 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.057 0.11 -10000 0 -10000 0 0
E2F1 0.032 0.038 0.32 6 -10000 0 6
ZNFX1 0.021 0.006 -10000 0 -10000 0 0
PIF1 0.057 0.1 0.33 46 -10000 0 46
NCL 0.021 0.003 -10000 0 -10000 0 0
DKC1 0.021 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
S1P3 pathway

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
PDGFRB 0.021 0.004 -10000 0 -10000 0 0
mol:S1P 0 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.01 0.064 -10000 0 -0.19 39 39
GNAO1 0.021 0.034 0.33 2 -0.34 2 4
S1P/S1P3/G12/G13 0.035 0.017 -10000 0 -10000 0 0
AKT1 0.005 0.065 -10000 0 -0.41 8 8
AKT3 -0.008 0.1 -10000 0 -0.98 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.021 0.004 -10000 0 -10000 0 0
GNAI2 0.021 0.007 -10000 0 -10000 0 0
GNAI3 0.021 0.005 -10000 0 -10000 0 0
GNAI1 0.02 0.019 -10000 0 -0.33 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.022 0.017 0.33 1 -10000 0 1
S1PR2 0.02 0.006 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.068 -10000 0 -0.23 10 10
MAPK3 -0.015 0.062 -10000 0 -0.26 5 5
MAPK1 -0.012 0.058 -10000 0 -0.38 2 2
JAK2 -0.025 0.082 0.2 2 -0.3 14 16
CXCR4 -0.015 0.063 -10000 0 -0.28 5 5
FLT1 0.02 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.016 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.006 -10000 0 -10000 0 0
SRC -0.014 0.066 0.27 2 -0.28 5 7
S1P/S1P3/Gi -0.007 0.068 -10000 0 -0.23 10 10
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.002 0.073 -10000 0 -0.26 7 7
VEGFA 0.021 0.007 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.009 0.069 -10000 0 -0.18 42 42
VEGFR1 homodimer/VEGFA homodimer 0.03 0.013 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.006 0.04 -10000 0 -0.22 10 10
GNAQ 0.02 0.018 -10000 0 -0.33 1 1
GNAZ -0.009 0.099 -10000 0 -0.33 34 34
G12/G13 0.028 0.012 -10000 0 -10000 0 0
GNA14 0.012 0.055 -10000 0 -0.33 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.021 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.07 -10000 0 -0.31 5 5
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 0.01 0.017 -10000 0 -10000 0 0
regulation of axonogenesis 0.003 0.018 0.25 2 -10000 0 2
myoblast fusion -0.01 0.027 0.32 1 -10000 0 1
mol:GTP 0.015 0.021 -10000 0 -0.16 5 5
regulation of calcium-dependent cell-cell adhesion -0.05 0.063 0.2 4 -0.22 37 41
ARF1/GTP 0.025 0.02 -10000 0 -10000 0 0
mol:GM1 0.004 0.014 -10000 0 -10000 0 0
mol:Choline -0.011 0.01 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.043 -10000 0 -0.38 4 4
MAPK3 0.011 0.014 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.051 0.064 0.22 37 -0.2 4 41
ARF1 0.02 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.01 0.027 -10000 0 -0.32 1 1
ARF1/GDP 0.012 0.033 -10000 0 -0.3 1 1
ARF6 0.026 0.01 -10000 0 -10000 0 0
RAB11A 0.021 0.003 -10000 0 -10000 0 0
TIAM1 0.016 0.04 -10000 0 -0.32 5 5
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.011 0.012 -10000 0 -10000 0 0
actin filament bundle formation -0.015 0.036 0.24 4 -10000 0 4
KALRN 0.002 0.022 -10000 0 -0.21 3 3
RAB11FIP3/RAB11A 0.031 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.037 -10000 0 -0.24 4 4
NME1 0.054 0.098 0.33 43 -10000 0 43
Rac1/GDP 0.013 0.036 -10000 0 -0.29 2 2
substrate adhesion-dependent cell spreading 0.015 0.021 -10000 0 -0.16 5 5
cortical actin cytoskeleton organization 0.002 0.043 -10000 0 -0.38 4 4
RAC1 0.019 0.007 -10000 0 -10000 0 0
liver development 0.015 0.021 -10000 0 -0.16 5 5
ARF6/GTP 0.015 0.021 -10000 0 -0.16 5 5
RhoA/GTP 0.025 0.021 -10000 0 -10000 0 0
mol:GDP 0.002 0.025 -10000 0 -0.24 3 3
ARF6/GTP/RAB11FIP3/RAB11A 0.037 0.022 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
PLD1 0.009 0.016 -10000 0 -10000 0 0
RAB11FIP3 0.021 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.002 0.043 -10000 0 -0.38 4 4
ruffle organization -0.003 0.018 -10000 0 -0.25 2 2
regulation of epithelial cell migration 0.015 0.021 -10000 0 -0.16 5 5
PLD2 0.009 0.013 -10000 0 -10000 0 0
PIP5K1A -0.003 0.018 -10000 0 -0.25 2 2
mol:Phosphatidic acid -0.011 0.01 -10000 0 -10000 0 0
Rac1/GTP 0.002 0.043 -10000 0 -0.38 4 4
IL2 signaling events mediated by PI3K

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
BCL2L1 0.001 0.064 -10000 0 -0.5 1 1
UGCG 0 0.1 -10000 0 -0.62 10 10
AKT1/mTOR/p70S6K/Hsp90/TERT 0.051 0.087 0.28 7 -0.4 3 10
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.001 0.1 -10000 0 -0.62 10 10
mol:DAG 0.003 0.083 -10000 0 -0.78 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.024 0.081 0.29 2 -0.41 5 7
FRAP1 0.018 0.09 0.31 2 -0.46 5 7
FOXO3 0.013 0.086 0.31 1 -0.46 5 6
AKT1 0.016 0.091 0.32 1 -0.47 6 7
GAB2 0.017 0.036 -10000 0 -0.33 4 4
SMPD1 0.005 0.084 -10000 0 -0.6 7 7
SGMS1 0.01 0.061 -10000 0 -0.56 4 4
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 -0.012 0.004 -10000 0 -10000 0 0
CALM1 0.021 0.005 -10000 0 -10000 0 0
cell proliferation 0.026 0.086 0.31 1 -0.38 9 10
EIF3A 0.022 0.002 -10000 0 -10000 0 0
PI3K 0.03 0.01 -10000 0 -10000 0 0
RPS6KB1 0.014 0.065 -10000 0 -0.84 2 2
mol:sphingomyelin 0.003 0.083 -10000 0 -0.78 4 4
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.021 0.006 -10000 0 -10000 0 0
PIK3R1 0.021 0.006 -10000 0 -10000 0 0
JAK1 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MYC 0.04 0.12 0.4 3 -0.78 3 6
MYB 0.005 0.1 -10000 0 -0.97 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.015 0.073 -10000 0 -0.38 5 5
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.034 0.064 -10000 0 -0.77 2 2
mol:PI-3-4-5-P3 0.014 0.072 -10000 0 -0.37 5 5
Rac1/GDP -0.014 0.008 -10000 0 -10000 0 0
T cell proliferation 0.01 0.07 -10000 0 -0.33 4 4
SHC1 0.018 0.009 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.009 0.088 3 -0.066 2 5
PRKCZ 0.011 0.069 -10000 0 -0.31 4 4
NF kappa B1 p50/RelA 0.034 0.087 0.3 2 -0.42 5 7
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.001 0.054 -10000 0 -0.35 5 5
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
IL2RA 0.043 0.085 0.33 30 -0.33 1 31
IL2RB 0.019 0.026 -10000 0 -0.33 2 2
TERT 0.07 0.12 0.33 69 -10000 0 69
E2F1 0.012 0.078 -10000 0 -0.46 8 8
SOS1 0.021 0.004 -10000 0 -10000 0 0
RPS6 0.02 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.032 2 -0.047 3 5
PTPN11 0.021 0.005 -10000 0 -10000 0 0
IL2RG 0.018 0.035 -10000 0 -0.33 4 4
actin cytoskeleton organization 0.01 0.07 -10000 0 -0.33 4 4
GRB2 0.021 0.006 -10000 0 -10000 0 0
IL2 0.02 0.005 -10000 0 -10000 0 0
PIK3CA 0.021 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.032 0.018 -10000 0 -10000 0 0
LCK 0.022 0.024 0.33 1 -0.33 1 2
BCL2 0.017 0.08 0.47 1 -0.42 2 3
TCGA08_rtk_signaling

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
PDGFRA 0.017 0.035 -10000 0 -0.33 4 4
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.043 0.33 1 -0.33 5 6
AKT 0.031 0.067 0.23 11 -0.21 3 14
FOXO3 0.02 0.007 -10000 0 -10000 0 0
AKT1 0.021 0.005 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
AKT3 0.018 0.026 -10000 0 -0.33 2 2
FOXO4 0.022 0.002 -10000 0 -10000 0 0
MET 0.013 0.072 0.33 5 -0.33 13 18
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PIK3CB 0.021 0.003 -10000 0 -10000 0 0
NRAS 0.021 0.005 -10000 0 -10000 0 0
PIK3CG 0.013 0.053 -10000 0 -0.33 9 9
PIK3R3 0.021 0.018 -10000 0 -0.33 1 1
PIK3R2 0.02 0.005 -10000 0 -10000 0 0
NF1 0.021 0.004 -10000 0 -10000 0 0
RAS 0.018 0.042 0.19 4 -0.12 12 16
ERBB2 0.021 0.004 -10000 0 -10000 0 0
proliferation/survival/translation -0.01 0.073 0.27 14 -10000 0 14
PI3K 0.022 0.062 0.22 20 -0.14 12 32
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
KRAS 0.02 0.006 -10000 0 -10000 0 0
FOXO 0.048 0.051 0.22 13 -10000 0 13
AKT2 0.021 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.003 -10000 0 -10000 0 0
IGF1 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
NCK2 0.022 0.002 -10000 0 -10000 0 0
PTK2 0.019 0.008 -10000 0 -10000 0 0
CRKL -0.019 0.025 0.15 1 -0.2 5 6
GRB2/SOS1/SHC 0.035 0.018 -10000 0 -10000 0 0
HRAS 0.021 0.004 -10000 0 -10000 0 0
IRS1/Crk -0.019 0.025 0.11 1 -0.19 6 7
IGF-1R heterotetramer/IGF1/PTP1B 0.036 0.029 0.21 1 -0.19 4 5
AKT1 -0.024 0.037 0.15 9 -0.24 1 10
BAD -0.028 0.036 0.14 9 -0.24 1 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.018 0.025 0.15 1 -0.2 5 6
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.019 0.032 0.19 2 -0.2 6 8
RAF1 -0.018 0.071 0.26 1 -0.39 11 12
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.042 0.037 -10000 0 -0.21 4 4
YWHAZ 0.019 0.008 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.023 0.032 0.2 1 -0.21 6 7
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.023 0.038 0.15 10 -0.24 1 11
GNB2L1 0.021 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.005 0.069 0.25 4 -0.29 7 11
PXN 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
HRAS/GTP -0.025 0.017 -10000 0 -0.17 1 1
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.048 0.034 -10000 0 -0.16 1 1
IGF-1R heterotetramer 0.02 0.023 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck 0.033 0.037 0.2 1 -0.2 6 7
Crk/p130 Cas/Paxillin 0.037 0.038 0.2 1 -0.18 7 8
IGF1R 0.02 0.023 -10000 0 -0.35 1 1
IGF1 0.018 0.046 0.34 1 -0.35 5 6
IRS2/Crk -0.022 0.026 0.14 1 -0.19 6 7
PI3K 0.04 0.039 -10000 0 -0.19 6 6
apoptosis 0.023 0.042 0.22 1 -0.27 1 2
HRAS/GDP 0.016 0.003 -10000 0 -10000 0 0
PRKCD -0.004 0.041 -10000 0 -0.25 6 6
RAF1/14-3-3 E -0.01 0.077 0.27 4 -0.34 11 15
BAD/14-3-3 -0.024 0.043 0.28 1 -0.23 1 2
PRKCZ -0.025 0.041 -10000 0 -0.24 1 1
Crk/p130 Cas/Paxillin/FAK1 -0.032 0.031 -10000 0 -0.22 1 1
PTPN1 0.02 0.006 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.001 0.044 -10000 0 -0.27 5 5
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.038 0.033 0.22 1 -0.17 3 4
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.017 0.033 -10000 0 -0.2 6 6
GRB10 0.019 0.007 -10000 0 -10000 0 0
PTPN11 -0.019 0.026 0.15 1 -0.2 6 7
IRS1 -0.015 0.031 0.12 6 -0.21 6 12
IRS2 -0.019 0.026 0.15 1 -0.2 6 7
IGF-1R heterotetramer/IGF1 0.026 0.038 0.23 1 -0.26 6 7
GRB2 0.021 0.005 -10000 0 -10000 0 0
PDPK1 -0.021 0.04 0.16 10 -0.19 5 15
YWHAE 0.02 0.007 -10000 0 -10000 0 0
PRKD1 -0.008 0.046 -10000 0 -0.32 3 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation -0.004 0.043 0.29 2 -0.25 4 6
adherens junction organization -0.005 0.049 -10000 0 -0.28 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.014 0.049 0.19 5 -0.21 2 7
FMN1 -0.01 0.05 -10000 0 -0.25 9 9
mol:IP3 -0.013 0.026 -10000 0 -0.2 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.002 0.051 -10000 0 -0.24 11 11
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 -0.013 0.035 0.23 1 -0.22 3 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0.092 -10000 0 -0.46 10 10
CTNND1 0.021 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.008 0.041 -10000 0 -0.24 8 8
VASP -0.005 0.04 -10000 0 -0.28 5 5
ZYX -0.008 0.045 -10000 0 -0.24 9 9
JUB -0.001 0.048 -10000 0 -0.23 11 11
EGFR(dimer) 0.008 0.057 0.2 2 -0.24 11 13
E-cadherin/beta catenin-gamma catenin 0.04 0.021 -10000 0 -0.18 2 2
mol:PI-3-4-5-P3 0.022 0.047 0.25 1 -0.22 3 4
PIK3CA 0.02 0.009 -10000 0 -10000 0 0
PI3K 0.023 0.048 0.25 1 -0.23 3 4
FYN -0.015 0.062 0.28 2 -0.25 7 9
mol:Ca2+ -0.012 0.026 -10000 0 -0.2 1 1
JUP 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.008 -10000 0 -10000 0 0
mol:DAG -0.013 0.026 -10000 0 -0.2 1 1
CDH1 0.019 0.025 -10000 0 -0.33 2 2
RhoA/GDP -0.005 0.063 0.19 5 -0.2 1 6
establishment of polarity of embryonic epithelium -0.005 0.039 -10000 0 -0.27 5 5
SRC 0.021 0.005 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.043 0.33 1 -0.33 5 6
CASR -0.007 0.045 0.27 3 -0.19 1 4
RhoA/GTP 0.011 0.035 -10000 0 -0.18 2 2
AKT2 -0.012 0.035 0.23 1 -0.22 3 4
actin cable formation -0.012 0.043 -10000 0 -0.28 5 5
apoptosis -0.005 0.048 0.22 4 -0.27 5 9
CTNNA1 0.021 0.005 -10000 0 -10000 0 0
mol:GDP -0.014 0.039 0.18 4 -0.2 2 6
PIP5K1A -0.008 0.041 -10000 0 -0.25 8 8
PLCG1 -0.013 0.027 -10000 0 -0.2 1 1
Rac1/GTP 0.015 0.055 -10000 0 -0.24 9 9
homophilic cell adhesion -0.001 0.002 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.014 0.011 -10000 0 -10000 0 0
TRAF2/ASK1 0.026 0.01 -10000 0 -10000 0 0
ATM 0.021 0.005 -10000 0 -10000 0 0
MAP2K3 -0.009 0.096 0.29 2 -0.34 15 17
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.005 0.084 0.37 1 -0.33 11 12
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.019 0.035 0.33 1 -0.33 3 4
TXN 0.004 0.012 0.17 2 -10000 0 2
CALM1 0.021 0.005 -10000 0 -10000 0 0
GADD45A 0.021 0.004 -10000 0 -10000 0 0
GADD45B 0.018 0.026 -10000 0 -0.33 2 2
MAP3K1 0.021 0.005 -10000 0 -10000 0 0
MAP3K6 0.021 0.004 -10000 0 -10000 0 0
MAP3K7 0.02 0.007 -10000 0 -10000 0 0
MAP3K4 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.029 0.01 -10000 0 -10000 0 0
TAK1/TAB family 0.001 0.019 0.13 2 -0.13 1 3
RAC1/OSM/MEKK3 0.035 0.016 -10000 0 -10000 0 0
TRAF2 0.021 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0 0.078 -10000 0 -0.3 12 12
TRAF6 0.004 0.001 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.061 0.11 0.33 53 -10000 0 53
CCM2 0.02 0.007 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.05 0.064 0.21 51 -10000 0 51
MAPK11 0.018 0.026 -10000 0 -0.33 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.054 0.062 0.22 46 -10000 0 46
OSM/MEKK3 0.028 0.011 -10000 0 -10000 0 0
TAOK1 0.007 0.002 -10000 0 -10000 0 0
TAOK2 0.007 0.002 -10000 0 -10000 0 0
TAOK3 0.007 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.021 0.005 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.02 0.006 -10000 0 -10000 0 0
MAP3K10 0.018 0.031 -10000 0 -0.33 3 3
MAP3K3 0.021 0.005 -10000 0 -10000 0 0
TRX/ASK1 0.016 0.019 0.16 1 -10000 0 1
GADD45/MTK1/MTK1 0.041 0.035 0.22 1 -0.21 4 5
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.048 0.022 -10000 0 -0.18 1 1
HDAC3 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.019 0.006 -10000 0 -10000 0 0
GATA1/HDAC4 0.004 0.079 -10000 0 -0.23 39 39
GATA1/HDAC5 0.004 0.079 -10000 0 -0.23 39 39
GATA2/HDAC5 0.008 0.074 -10000 0 -0.23 34 34
HDAC5/BCL6/BCoR 0.04 0.014 -10000 0 -10000 0 0
HDAC9 0.02 0.05 0.33 5 -0.33 4 9
Glucocorticoid receptor/Hsp90/HDAC6 0.04 0.013 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.03 0.008 -10000 0 -10000 0 0
HDAC5/YWHAB 0.03 0.009 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
GATA2 -0.01 0.1 -10000 0 -0.33 35 35
HDAC4/RFXANK 0.03 0.009 -10000 0 -10000 0 0
BCOR 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.019 0.019 -10000 0 -0.33 1 1
HDAC5 0.021 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.029 0.016 -10000 0 -0.23 1 1
Histones 0.01 0.051 -10000 0 -0.26 4 4
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.022 0.002 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.03 0.008 -10000 0 -10000 0 0
HDAC4/Ubc9 0.031 0.007 -10000 0 -10000 0 0
HDAC7 0.021 0.004 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.028 0.011 -10000 0 -10000 0 0
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
HDAC6 0.021 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.03 0.009 -10000 0 -10000 0 0
CAMK4 0.019 0.035 0.33 1 -0.33 3 4
Tubulin/HDAC6 0.044 0.028 0.23 7 -10000 0 7
SUMO1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.021 0.005 -10000 0 -10000 0 0
GATA1 -0.015 0.11 -10000 0 -0.33 40 40
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
NR3C1 0.021 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.03 0.025 -10000 0 -0.18 2 2
SRF 0.021 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.03 0.009 -10000 0 -10000 0 0
Tubulin 0.034 0.028 0.24 7 -10000 0 7
HDAC4/14-3-3 E 0.029 0.01 -10000 0 -10000 0 0
GNB1 0.021 0.004 -10000 0 -10000 0 0
RANGAP1 0.021 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.03 0.009 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.041 0.013 -10000 0 -10000 0 0
HDAC4/SRF 0.038 0.027 0.23 1 -0.2 3 4
HDAC4/ER alpha 0.028 0.05 0.24 9 -0.23 8 17
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.01 0.051 -10000 0 -0.26 4 4
cell motility 0.044 0.028 0.23 7 -10000 0 7
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.03 0.008 -10000 0 -10000 0 0
BCL6 0.021 0.005 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.021 0.003 -10000 0 -10000 0 0
Hsp90/HDAC6 0.03 0.009 -10000 0 -10000 0 0
ESR1 0.02 0.071 0.33 10 -0.33 8 18
HDAC6/HDAC11 0.031 0.008 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.028 0.2 1 -0.18 2 3
NPC 0.013 0.001 -10000 0 -10000 0 0
MEF2C 0.021 0.005 -10000 0 -10000 0 0
RAN 0.023 0.022 0.33 2 -10000 0 2
HDAC4/MEF2C 0.057 0.024 -10000 0 -10000 0 0
GNG2 0.02 0.018 -10000 0 -0.33 1 1
NCOR2 0.021 0.004 -10000 0 -10000 0 0
TUBB2A 0.027 0.041 0.33 7 -10000 0 7
HDAC11 0.021 0.004 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
RANBP2 0.022 0.002 -10000 0 -10000 0 0
ANKRA2 0.021 0.004 -10000 0 -10000 0 0
RFXANK 0.021 0.005 -10000 0 -10000 0 0
nuclear import -0.02 0.009 -10000 0 -10000 0 0
Circadian rhythm 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
chromatin modification 0.046 0.057 0.42 4 -10000 0 4
CLOCK 0.022 0.005 -10000 0 -10000 0 0
TIMELESS/CRY2 0.026 0.033 -10000 0 -10000 0 0
DEC1/BMAL1 0.029 0.008 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
NR1D1 0.008 0.025 -10000 0 -10000 0 0
ARNTL 0.022 0.005 -10000 0 -10000 0 0
TIMELESS 0.01 0.039 0.38 2 -10000 0 2
NPAS2 0.024 0.022 0.33 2 -10000 0 2
CRY2 0.021 0.003 -10000 0 -10000 0 0
mol:CO -0.004 0.013 -10000 0 -0.11 6 6
CHEK1 0.04 0.076 0.33 25 -10000 0 25
mol:HEME 0.004 0.013 0.11 6 -10000 0 6
PER1 0.008 0.063 -10000 0 -0.33 13 13
BMAL/CLOCK/NPAS2 0.046 0.023 0.23 2 -10000 0 2
BMAL1/CLOCK 0.01 0.045 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.046 0.057 0.42 4 -10000 0 4
TIMELESS/CHEK1/ATR 0.048 0.059 0.42 4 -10000 0 4
mol:NADPH 0.004 0.013 0.11 6 -10000 0 6
PER1/TIMELESS 0.019 0.045 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.004 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 -0.016 0.006 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.024 0.014 -10000 0 -10000 0 0
CDKN1B 0.006 0.048 -10000 0 -0.29 7 7
CDKN1A 0.007 0.053 -10000 0 -0.29 8 8
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.02 0.007 -10000 0 -10000 0 0
FOXO3 0.007 0.038 -10000 0 -0.29 4 4
AKT1 -0.001 0.043 -10000 0 -0.3 8 8
BAD 0.021 0.003 -10000 0 -10000 0 0
AKT3 0.006 0.013 -10000 0 -0.25 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.005 0.049 -10000 0 -0.29 8 8
AKT1/ASK1 0.024 0.06 -10000 0 -0.28 7 7
BAD/YWHAZ 0.035 0.018 -10000 0 -10000 0 0
RICTOR 0.017 0.009 -10000 0 -10000 0 0
RAF1 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.022 0.057 0.27 7 -10000 0 7
TSC1 0.007 0.04 -10000 0 -0.29 5 5
YWHAZ 0.019 0.008 -10000 0 -10000 0 0
AKT1/RAF1 0.028 0.064 -10000 0 -0.29 8 8
EP300 0.021 0.004 -10000 0 -10000 0 0
mol:GDP 0.01 0.049 -10000 0 -0.29 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.004 0.047 -10000 0 -0.29 8 8
YWHAQ 0.022 0.002 -10000 0 -10000 0 0
TBC1D4 -0.006 0.002 -10000 0 -10000 0 0
MAP3K5 0.02 0.006 -10000 0 -10000 0 0
MAPKAP1 0.021 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.018 0.069 0.29 5 -0.24 7 12
YWHAH 0.021 0.004 -10000 0 -10000 0 0
AKT1S1 0.006 0.044 -10000 0 -0.3 6 6
CASP9 0.007 0.046 -10000 0 -0.3 6 6
YWHAB 0.021 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.029 0.069 0.3 4 -0.28 8 12
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.04 0.014 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
SRC 0.021 0.005 -10000 0 -10000 0 0
AKT2/p21CIP1 0.009 0.056 0.23 4 -0.26 6 10
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.007 0.041 0.18 1 -0.32 4 5
CHUK 0.005 0.048 -10000 0 -0.29 8 8
BAD/BCL-XL 0.025 0.059 -10000 0 -0.28 8 8
mTORC2 0.022 0.012 -10000 0 -10000 0 0
AKT2 0.007 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.019 0.087 0.3 6 -0.37 6 12
PDPK1 0.021 0.004 -10000 0 -10000 0 0
MDM2 0.015 0.061 -10000 0 -0.29 7 7
MAPKKK cascade -0.028 0.063 0.28 8 -10000 0 8
MDM2/Cbp/p300 0.046 0.076 0.32 4 -0.28 7 11
TSC1/TSC2 0.002 0.053 0.26 5 -0.29 6 11
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.073 0.3 4 -0.27 7 11
glucose import -0.009 0.026 0.2 4 -0.17 3 7
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.042 0.22 1 -0.28 2 3
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.015 -10000 0 -0.17 3 3
GSK3A 0.007 0.049 -10000 0 -0.29 7 7
FOXO1 0.005 0.042 -10000 0 -0.29 6 6
GSK3B 0.005 0.046 -10000 0 -0.29 7 7
SFN 0.026 0.045 0.33 7 -0.33 1 8
G1/S transition of mitotic cell cycle 0.006 0.059 0.24 5 -0.29 6 11
p27Kip1/14-3-3 family 0.013 0.044 -10000 0 -0.26 4 4
PRKACA 0.02 0.005 -10000 0 -10000 0 0
KPNA1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.021 0.005 -10000 0 -10000 0 0
YWHAG 0.021 0.005 -10000 0 -10000 0 0
RHEB 0.021 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -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 0.021 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.016 0.061 0.22 2 -0.31 4 6
ERC1 0.02 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.027 0.012 -10000 0 -10000 0 0
NFKBIA -0.017 0.018 0.2 2 -10000 0 2
BIRC2 0.021 0.005 -10000 0 -10000 0 0
IKBKB 0.019 0.008 -10000 0 -10000 0 0
RIPK2 0.019 0.007 -10000 0 -10000 0 0
IKBKG -0.001 0.06 -10000 0 -0.38 8 8
IKK complex/A20 0.024 0.08 -10000 0 -0.38 6 6
NEMO/A20/RIP2 0.019 0.007 -10000 0 -10000 0 0
XPO1 0.022 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.023 0.075 -10000 0 -0.36 9 9
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.023 0.022 0.33 2 -10000 0 2
Exportin 1/RanGTP 0.029 0.014 0.21 2 -10000 0 2
IKK complex/ELKS 0.021 0.068 -10000 0 -0.36 7 7
BCL10/MALT1/TRAF6 0.037 0.016 -10000 0 -10000 0 0
NOD2 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.022 0.003 -10000 0 -10000 0 0
RELA 0.022 0.004 -10000 0 -10000 0 0
MALT1 0.019 0.007 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.03 0.008 -10000 0 -10000 0 0
ATM 0.021 0.005 -10000 0 -10000 0 0
TNF/TNFR1A 0.017 0.057 0.24 1 -0.23 18 19
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PRKCA 0.019 0.025 -10000 0 -0.33 2 2
CHUK 0.021 0.003 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
TNF 0.005 0.077 0.33 1 -0.33 19 20
NF kappa B1 p50/RelA 0.043 0.013 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.017 0.018 0.19 2 -10000 0 2
beta TrCP1/SCF ubiquitin ligase complex 0.021 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
IKK complex 0.026 0.074 -10000 0 -0.38 7 7
CYLD 0.021 0.005 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.03 0.075 -10000 0 -0.37 7 7
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.008 0.019 -10000 0 -0.23 2 2
CRKL 0.021 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.006 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.025 -10000 0 -0.33 2 2
alpha4/beta7 Integrin/MAdCAM1 0.049 0.032 0.23 3 -0.18 3 6
EPO 0.022 0.028 0.33 3 -10000 0 3
alpha4/beta7 Integrin 0.029 0.024 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.03 0.015 -10000 0 -0.23 1 1
EPO/EPOR (dimer) 0.029 0.021 0.24 3 -10000 0 3
lamellipodium assembly 0 0.058 -10000 0 -0.46 4 4
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PI3K 0.03 0.009 -10000 0 -10000 0 0
ARF6 0.021 0.005 -10000 0 -10000 0 0
JAK2 0.01 0.021 0.18 1 -0.3 1 2
PXN 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
MADCAM1 0.023 0.032 0.33 4 -10000 0 4
cell adhesion 0.047 0.031 0.22 3 -0.18 3 6
CRKL/CBL 0.03 0.009 -10000 0 -10000 0 0
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC -0.018 0.035 0.17 11 -0.18 2 13
ITGB7 0.02 0.018 -10000 0 -0.33 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.04 0.026 0.23 1 -0.2 3 4
p130Cas/Crk/Dock1 -0.026 0.037 0.18 2 -10000 0 2
VCAM1 0.02 0.03 0.33 1 -0.33 2 3
RHOA 0.021 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.051 0.02 -10000 0 -0.18 1 1
BCAR1 -0.022 0.033 0.17 9 -0.18 3 12
EPOR 0.02 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.021 0.005 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
Rac1/GTP 0 0.06 -10000 0 -0.48 4 4
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.021 0.004 -9999 0 -10000 0 0
ITGB7 0.02 0.018 -9999 0 -0.33 1 1
ITGA4 0.02 0.025 -9999 0 -0.33 2 2
alpha4/beta7 Integrin 0.029 0.024 -9999 0 -0.23 3 3
alpha4/beta1 Integrin 0.03 0.015 -9999 0 -0.23 1 1
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.006 0.11 -10000 0 -0.38 13 13
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
AKT1 0.021 0.005 -10000 0 -10000 0 0
AKT2 0.021 0.005 -10000 0 -10000 0 0
STXBP4 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.011 0.11 0.24 1 -0.41 14 15
YWHAZ 0.019 0.008 -10000 0 -10000 0 0
CALM1 0.021 0.005 -10000 0 -10000 0 0
YWHAQ 0.022 0.002 -10000 0 -10000 0 0
TBC1D4 -0.016 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.021 0.004 -10000 0 -10000 0 0
YWHAB 0.021 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.038 0.016 -10000 0 -10000 0 0
YWHAG 0.021 0.005 -10000 0 -10000 0 0
ASIP 0.02 0.016 0.33 1 -10000 0 1
PRKCI 0.021 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
RHOQ 0.021 0.003 -10000 0 -10000 0 0
GYS1 -0.005 0.012 0.23 1 -10000 0 1
PRKCZ 0.018 0.031 -10000 0 -0.33 3 3
TRIP10 0.02 0.006 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.027 0.009 -10000 0 -10000 0 0
AS160/14-3-3 0.003 0.052 -10000 0 -0.25 5 5
VAMP2 0.02 0.006 -10000 0 -10000 0 0
SLC2A4 -0.013 0.12 0.24 1 -0.46 14 15
STX4 0.021 0.003 -10000 0 -10000 0 0
GSK3B 0.01 0.004 -10000 0 -10000 0 0
SFN 0.026 0.045 0.33 7 -0.33 1 8
LNPEP 0.021 0.005 -10000 0 -10000 0 0
YWHAE 0.02 0.007 -10000 0 -10000 0 0
TRAIL signaling 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
TNFSF10 0.018 0.031 -10000 0 -0.33 3 3
positive regulation of NF-kappaB transcription factor activity 0.023 0.025 -10000 0 -0.22 3 3
MAP2K4 0.004 0.025 -10000 0 -0.24 1 1
IKBKB 0.019 0.008 -10000 0 -10000 0 0
TNFRSF10B 0.018 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.008 -10000 0 -10000 0 0
SMPD1 0.004 0.015 0.14 1 -0.14 3 4
IKBKG 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.017 0.019 -10000 0 -0.33 1 1
TRAIL/TRAILR2 0.024 0.026 -10000 0 -0.22 3 3
TRAIL/TRAILR3 0.021 0.037 -10000 0 -0.23 7 7
TRAIL/TRAILR1 0.024 0.026 -10000 0 -0.22 3 3
TRAIL/TRAILR4 0.024 0.026 -10000 0 -0.22 3 3
TRAIL/TRAILR1/DAP3/GTP 0.028 0.025 -10000 0 -0.18 2 2
IKK complex -0.001 0.049 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.014 0.006 -10000 0 -10000 0 0
MAPK3 -0.018 0.024 0.28 1 -0.23 3 4
MAP3K1 0.012 0.02 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.017 0.019 -10000 0 -0.33 1 1
TRADD 0.021 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.04 -10000 0 -0.19 2 2
CFLAR 0.022 0.002 -10000 0 -10000 0 0
MAPK1 -0.017 0.022 0.28 1 -0.23 2 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.046 0.036 -10000 0 -0.18 2 2
mol:ceramide 0.004 0.015 0.14 1 -0.14 3 4
FADD 0.021 0.004 -10000 0 -10000 0 0
MAPK8 -0.008 0.042 -10000 0 -0.25 2 2
TRAF2 0.021 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.013 0.04 -10000 0 -0.33 5 5
CHUK 0.021 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.032 0.027 -10000 0 -0.19 3 3
DAP3 0.018 0.008 -10000 0 -10000 0 0
CASP10 -0.004 0.042 0.26 2 -0.23 2 4
JNK cascade 0.023 0.025 -10000 0 -0.22 3 3
TRAIL (trimer) 0.018 0.031 -10000 0 -0.33 3 3
TNFRSF10C 0.013 0.04 -10000 0 -0.33 5 5
TRAIL/TRAILR1/DAP3/GTP/FADD 0.034 0.03 -10000 0 -0.17 2 2
TRAIL/TRAILR2/FADD 0.032 0.027 -10000 0 -0.19 3 3
cell death 0.004 0.015 0.14 1 -0.14 3 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.002 0.04 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.018 0.008 -10000 0 -10000 0 0
CASP8 0.008 0.06 -10000 0 -0.73 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.045 0.036 -10000 0 -0.18 2 2
Paxillin-dependent events mediated by a4b1

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
CRKL 0.021 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.021 0.011 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.02 0.025 -10000 0 -0.33 2 2
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.024 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.02 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.039 0.018 -10000 0 -0.2 1 1
alpha4/beta7 Integrin/Paxillin 0.027 0.021 -10000 0 -0.18 3 3
lamellipodium assembly -0.009 0.083 -10000 0 -0.38 14 14
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
PI3K 0.03 0.009 -10000 0 -10000 0 0
ARF6 0.021 0.005 -10000 0 -10000 0 0
TLN1 0.02 0.018 -10000 0 -0.33 1 1
PXN -0.017 0.005 -10000 0 -10000 0 0
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.036 0.021 -10000 0 -0.17 1 1
cell adhesion 0.036 0.022 -10000 0 -0.17 2 2
CRKL/CBL 0.03 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.028 0.015 -10000 0 -0.18 1 1
ITGB1 0.021 0.004 -10000 0 -10000 0 0
ITGB7 0.02 0.018 -10000 0 -0.33 1 1
ARF6/GDP 0.023 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.037 0.027 0.22 1 -0.18 3 4
p130Cas/Crk/Dock1 0.037 0.02 -10000 0 -0.2 1 1
VCAM1 0.02 0.03 0.33 1 -0.33 2 3
alpha4/beta1 Integrin/Paxillin/Talin 0.037 0.022 -10000 0 -0.17 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.038 0.02 -10000 0 -0.18 1 1
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
mol:GDP -0.036 0.02 0.18 1 -10000 0 1
CBL 0.021 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.037 0.022 -10000 0 -0.17 2 2
Rac1/GTP -0.011 0.092 -10000 0 -0.42 14 14
Atypical NF-kappaB 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
BCL3/RelA 0.029 0.016 -10000 0 -0.23 1 1
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.018 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.018 0.043 -10000 0 -0.18 2 2
NFKBIA 0.001 0.009 -10000 0 -0.17 1 1
MAPK14 0.021 0.005 -10000 0 -10000 0 0
NF kappa B1 p105/p50 -0.017 0.009 -10000 0 -10000 0 0
ARRB2 0.007 0.003 -10000 0 -10000 0 0
REL 0.022 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.017 0.009 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.018 0.008 -10000 0 -10000 0 0
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
NF kappa B1 p50 dimer -0.014 0.015 0.24 1 -10000 0 1
PIK3R1 0.021 0.005 -10000 0 -10000 0 0
NFKB1 -0.015 0.007 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.007 0.035 -10000 0 -0.18 4 4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.016 0.042 -10000 0 -0.19 3 3
SRC 0.021 0.005 -10000 0 -10000 0 0
PI3K 0.03 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.007 0.036 -10000 0 -0.19 4 4
IKBKB 0.019 0.008 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
SYK 0.019 0.025 -10000 0 -0.33 2 2
I kappa B alpha/PIK3R1 0.027 0.054 0.26 8 -0.17 6 14
cell death 0.016 0.041 -10000 0 -0.18 3 3
NF kappa B1 p105/c-Rel -0.018 0.008 -10000 0 -10000 0 0
LCK 0.021 0.024 0.33 1 -0.33 1 2
BCL3 0.02 0.018 -10000 0 -0.33 1 1
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma 0.033 0.028 0.2 3 -0.17 4 7
MAPK9 0.004 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.015 0.16 3 -10000 0 3
GNB1/GNG2 0.027 0.014 -10000 0 -0.19 1 1
GNB1 0.021 0.004 -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 0.004 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.013 0.024 0.19 3 -0.17 4 7
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 0.002 0.005 0.048 4 -10000 0 4
GNAL 0.019 0.045 0.33 3 -0.33 4 7
GNG2 0.02 0.018 -10000 0 -0.33 1 1
CRH 0.02 0.028 0.33 3 -10000 0 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.001 -10000 0 -10000 0 0
MAPK11 0.002 0.018 -10000 0 -0.25 2 2
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin 0.039 0.021 -9999 0 -0.2 2 2
E-cadherin/beta catenin 0.029 0.02 -9999 0 -0.23 2 2
CTNNB1 0.021 0.004 -9999 0 -10000 0 0
JUP 0.021 0.004 -9999 0 -10000 0 0
CDH1 0.019 0.025 -9999 0 -0.33 2 2
Arf1 pathway

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
coatomer protein complex 0.008 0.043 0.15 30 -0.17 2 32
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.039 -10000 0 -0.16 3 3
AP2 0.03 0.009 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.021 0.017 -10000 0 -10000 0 0
CLTB 0.02 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.006 -10000 0 -10000 0 0
CD4 0.013 0.05 -10000 0 -0.33 8 8
CLTA 0.02 0.006 -10000 0 -10000 0 0
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.008 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.01 -10000 0 -10000 0 0
ARF1/GTP 0.022 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.005 0.015 -10000 0 -10000 0 0
mol:Choline -0.002 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.021 0.01 -10000 0 -10000 0 0
DDEF1 -0.001 0.01 -10000 0 -10000 0 0
ARF1/GDP 0 0.018 -10000 0 -0.096 7 7
AP2M1 0.021 0.005 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.008 0.011 -10000 0 -10000 0 0
Rac/GTP 0.015 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.014 -10000 0 -10000 0 0
ARFIP2 0.009 0.021 -10000 0 -10000 0 0
COPA 0.019 0.007 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex -0.001 0.035 -10000 0 -0.18 8 8
ARF1/GTP/ARHGAP10 0.012 0.008 -10000 0 -10000 0 0
GGA3 0.021 0.005 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.012 0.026 -10000 0 -0.29 2 2
AP2A1 0.021 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.001 0.029 -10000 0 -0.16 9 9
ARF1/GDP/Membrin 0.017 0.03 -10000 0 -0.32 2 2
Arfaptin 2/Rac/GDP 0.019 0.019 -10000 0 -10000 0 0
CYTH2 0.024 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.013 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.014 0.006 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.003 0.041 -10000 0 -0.21 10 10
PLD2 -0.002 0.01 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.008 0.003 -10000 0 -10000 0 0
PIP5K1A -0.002 0.01 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.007 0.023 -10000 0 -0.13 3 3
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.01 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.008 0.003 -10000 0 -10000 0 0
GOSR2 0.006 0.006 -10000 0 -10000 0 0
USO1 0.003 0.033 -10000 0 -0.32 4 4
GBF1 0.003 0.033 -10000 0 -0.32 4 4
ARF1/GTP/Arfaptin 2 0.024 0.017 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.034 0.036 -10000 0 -0.19 8 8
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4 0.019 0.007 -10000 0 -10000 0 0
SMAD2 0 0.043 0.22 1 -0.22 4 5
SMAD3 0.009 0.037 -10000 0 -10000 0 0
SMAD3/SMAD4 0.022 0.037 -10000 0 -0.48 1 1
SMAD4/Ubc9/PIASy 0.036 0.017 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.029 0.049 -10000 0 -0.22 2 2
PPM1A 0.021 0.004 -10000 0 -10000 0 0
CALM1 0.021 0.005 -10000 0 -10000 0 0
SMAD2/SMAD4 0.006 0.041 -10000 0 -0.21 6 6
MAP3K1 0.021 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.027 0.021 -10000 0 -0.22 2 2
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.021 0.005 -10000 0 -10000 0 0
NUP214 0.021 0.004 -10000 0 -10000 0 0
CTDSP1 0.022 0.002 -10000 0 -10000 0 0
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
KPNB1 0.021 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.02 0.025 -10000 0 -0.33 2 2
UBE2I 0.021 0.004 -10000 0 -10000 0 0
NUP153 0.021 0.004 -10000 0 -10000 0 0
KPNA2 0.024 0.032 0.33 4 -10000 0 4
PIAS4 0.02 0.006 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1 0.021 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.019 0.009 -10000 0 -10000 0 0
MDM2/SUMO1 0.029 0.029 0.18 2 -0.18 2 4
HDAC4 0.021 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.019 0.009 -10000 0 -10000 0 0
SUMO1 0.021 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.005 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.005 0.012 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.023 0.022 0.33 2 -10000 0 2
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.022 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.03 0.025 -10000 0 -0.18 2 2
SUMO1/HDAC1 0.03 0.026 -10000 0 -0.18 2 2
RANGAP1 0.021 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.046 0.025 0.2 2 -10000 0 2
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.006 0.002 -10000 0 -10000 0 0
Ran/GTP 0.02 0.026 0.2 1 -0.18 2 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.02 0.006 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.016 0.031 0.21 4 -0.18 2 6
NPC 0.013 0.001 -10000 0 -10000 0 0
PIAS2 0.02 0.007 -10000 0 -10000 0 0
PIAS1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
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 0.031 0.007 -9999 0 -9999 0 0
FBXW11 0.02 0.005 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -9999 0 -9999 0 0
CHUK 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.056 0.023 -9999 0 -9999 0 0
NFKB1 0.021 0.003 -9999 0 -9999 0 0
MAP3K14 0.021 0.004 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.03 0.008 -9999 0 -9999 0 0
RELB 0.021 0.005 -9999 0 -9999 0 0
NFKB2 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.028 0.008 -9999 0 -9999 0 0
regulation of B cell activation 0.027 0.007 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 391 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.J2.8194 TCGA.J2.8192 TCGA.99.8033 TCGA.99.8032
109_MAP3K5 -0.025 0.0079 0.0079 0.0079
47_PPARGC1A 0 0.022 0.022 0.022
105_BMP4 0.022 0.022 0.022 0.022
105_BMP6 0.022 0.022 0.022 0.022
105_BMP7 0.022 0.022 -0.33 0.022
105_BMP2 0.022 0.022 0.022 0.022
131_RELN/VLDLR 0.056 0.056 0.056 0.056
30_TGFB1/TGF beta receptor Type II 0.022 0.022 0.022 -0.025
84_STAT5B -0.038 0.11 0.039 0.02
84_STAT5A -0.038 0.11 0.039 0.02
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/LUAD-TP/3026100/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUAD-TP/3140812/all_data_by_genes.txt

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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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