Breast Invasive Carcinoma: PARADIGM pathway analysis of mRNASeq expression data
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 48 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
IL4-mediated signaling events 145
Signaling events regulated by Ret tyrosine kinase 131
Wnt signaling 118
Ephrin A reverse signaling 114
Glucocorticoid receptor regulatory network 110
IL23-mediated signaling events 110
Syndecan-1-mediated signaling events 103
Class IB PI3K non-lipid kinase events 97
IL12-mediated signaling events 96
TCR signaling in naïve CD8+ T cells 95
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
IL4-mediated signaling events 145 13265 91 -0.7 0.59 1000 -1000 -0.14 -1000
Signaling events regulated by Ret tyrosine kinase 131 10755 82 -0.24 0.013 1000 -1000 -0.091 -1000
Wnt signaling 118 826 7 -0.14 -0.041 1000 -1000 -0.026 -1000
Ephrin A reverse signaling 114 800 7 -0.094 0 1000 -1000 -0.025 -1000
Glucocorticoid receptor regulatory network 110 12638 114 -0.63 0.37 1000 -1000 -0.067 -1000
IL23-mediated signaling events 110 6636 60 -0.44 0.012 1000 -1000 -0.18 -1000
Syndecan-1-mediated signaling events 103 3507 34 -0.23 0.013 1000 -1000 -0.059 -1000
Class IB PI3K non-lipid kinase events 97 291 3 -0.057 -1000 1000 -1000 -0.015 -1000
IL12-mediated signaling events 96 8380 87 -0.32 0.13 1000 -1000 -0.14 -1000
TCR signaling in naïve CD8+ T cells 95 8888 93 -0.21 0.11 1000 -1000 -0.091 -1000
Plasma membrane estrogen receptor signaling 93 8042 86 -0.18 0.16 1000 -1000 -0.089 -1000
HIF-1-alpha transcription factor network 92 6992 76 -0.43 0.021 1000 -1000 -0.15 -1000
EGFR-dependent Endothelin signaling events 92 1947 21 -0.16 0.019 1000 -1000 -0.072 -1000
Noncanonical Wnt signaling pathway 90 2360 26 -0.14 0.013 1000 -1000 -0.058 -1000
LPA4-mediated signaling events 82 995 12 -0.13 0.013 1000 -1000 -0.027 -1000
BMP receptor signaling 82 6717 81 -0.29 0.027 1000 -1000 -0.091 -1000
Effects of Botulinum toxin 79 2059 26 -0.21 0.013 1000 -1000 -0.064 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 79 5381 68 -0.35 0.094 1000 -1000 -0.13 -1000
FOXA2 and FOXA3 transcription factor networks 78 3631 46 -0.43 0.017 1000 -1000 -0.089 -1000
Calcium signaling in the CD4+ TCR pathway 72 2258 31 -0.22 0.013 1000 -1000 -0.091 -1000
p75(NTR)-mediated signaling 71 8932 125 -0.19 0.034 1000 -1000 -0.11 -1000
Endothelins 70 6747 96 -0.29 0.035 1000 -1000 -0.087 -1000
BCR signaling pathway 68 6813 99 -0.23 0.021 1000 -1000 -0.099 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 68 5352 78 -0.17 0.098 1000 -1000 -0.087 -1000
Visual signal transduction: Cones 65 2488 38 -0.12 0.01 1000 -1000 -0.061 -1000
IGF1 pathway 64 3663 57 -0.11 0.027 1000 -1000 -0.1 -1000
Glypican 2 network 62 250 4 -0.065 -0.052 1000 -1000 -0.029 -1000
Nongenotropic Androgen signaling 62 3227 52 -0.13 0.033 1000 -1000 -0.068 -1000
IL27-mediated signaling events 62 3173 51 -0.2 0.074 1000 -1000 -0.096 -1000
FAS signaling pathway (CD95) 61 2870 47 -0.19 0.045 1000 -1000 -0.052 -1000
Visual signal transduction: Rods 61 3206 52 -0.15 0.013 1000 -1000 -0.07 -1000
Caspase cascade in apoptosis 60 4461 74 -0.13 0.074 1000 -1000 -0.041 -1000
Signaling events mediated by the Hedgehog family 59 3090 52 -0.24 0.018 1000 -1000 -0.048 -1000
Syndecan-4-mediated signaling events 59 3990 67 -0.13 0.018 1000 -1000 -0.074 -1000
FOXM1 transcription factor network 59 3032 51 -0.2 0.033 1000 -1000 -0.18 -1000
Reelin signaling pathway 58 3250 56 -0.15 0.025 1000 -1000 -0.083 -1000
LPA receptor mediated events 58 5929 102 -0.17 0.038 1000 -1000 -0.091 -1000
Arf6 signaling events 57 3595 62 -0.16 0.026 1000 -1000 -0.071 -1000
amb2 Integrin signaling 56 4630 82 -0.19 0.018 1000 -1000 -0.09 -1000
Glypican 1 network 55 2661 48 -0.2 0.023 1000 -1000 -0.048 -1000
IL6-mediated signaling events 50 3757 75 -0.27 0.05 1000 -1000 -0.1 -1000
Nephrin/Neph1 signaling in the kidney podocyte 49 1678 34 -0.054 0.013 1000 -1000 -0.048 -1000
Neurotrophic factor-mediated Trk receptor signaling 49 5947 120 -0.19 0.11 1000 -1000 -0.087 -1000
ErbB4 signaling events 48 3357 69 -0.22 0.096 1000 -1000 -0.093 -1000
Fc-epsilon receptor I signaling in mast cells 48 4748 97 -0.14 0.031 1000 -1000 -0.093 -1000
TCGA08_retinoblastoma 48 387 8 -0.06 0.025 1000 -1000 -0.018 -1000
Coregulation of Androgen receptor activity 46 3520 76 -0.18 0.024 1000 -1000 -0.043 -1000
Signaling mediated by p38-alpha and p38-beta 44 1947 44 -0.11 0.013 1000 -1000 -0.055 -1000
JNK signaling in the CD4+ TCR pathway 42 728 17 -0.065 0.013 1000 -1000 -0.044 -1000
E-cadherin signaling events 41 209 5 -0.04 0.011 1000 -1000 -0.028 -1000
Signaling events mediated by PTP1B 40 3060 76 -0.23 0.023 1000 -1000 -0.088 -1000
Stabilization and expansion of the E-cadherin adherens junction 40 2980 74 -0.15 0.046 1000 -1000 -0.1 -1000
Ras signaling in the CD4+ TCR pathway 40 694 17 -0.066 0.018 1000 -1000 -0.043 -1000
Thromboxane A2 receptor signaling 38 4062 105 -0.14 0.03 1000 -1000 -0.074 -1000
Syndecan-2-mediated signaling events 38 2650 69 -0.11 0.028 1000 -1000 -0.03 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 38 3305 85 -0.092 0.013 1000 -1000 -0.077 -1000
IL2 signaling events mediated by PI3K 38 2245 58 -0.13 0.029 1000 -1000 -0.099 -1000
Canonical Wnt signaling pathway 37 1891 51 -0.18 0.07 1000 -1000 -0.055 -1000
IL2 signaling events mediated by STAT5 37 824 22 -0.091 0.021 1000 -1000 -0.061 -1000
Ephrin B reverse signaling 36 1764 48 -0.083 0.013 1000 -1000 -0.072 -1000
Integrins in angiogenesis 34 2934 84 -0.14 0.026 1000 -1000 -0.097 -1000
Presenilin action in Notch and Wnt signaling 33 2051 61 -0.18 0.031 1000 -1000 -0.091 -1000
Osteopontin-mediated events 32 1231 38 -0.071 0.014 1000 -1000 -0.11 -1000
Cellular roles of Anthrax toxin 32 1252 39 -0.18 0.016 1000 -1000 -0.03 -1000
Regulation of Telomerase 32 3283 102 -0.17 0.039 1000 -1000 -0.1 -1000
ErbB2/ErbB3 signaling events 31 2018 65 -0.11 0.021 1000 -1000 -0.069 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 31 1685 54 -0.15 0.025 1000 -1000 -0.099 -1000
Signaling events mediated by HDAC Class III 31 1248 40 -0.2 0.021 1000 -1000 -0.045 -1000
Aurora B signaling 31 2091 67 -0.12 0.013 1000 -1000 -0.078 -1000
PDGFR-alpha signaling pathway 30 1355 44 -0.11 0.022 1000 -1000 -0.076 -1000
Angiopoietin receptor Tie2-mediated signaling 30 2677 88 -0.22 0.044 1000 -1000 -0.12 -1000
a4b1 and a4b7 Integrin signaling 29 146 5 -0.016 0.008 1000 -1000 -0.021 -1000
Signaling mediated by p38-gamma and p38-delta 29 445 15 -0.069 0.021 1000 -1000 -0.032 -1000
Syndecan-3-mediated signaling events 29 1033 35 -0.11 0.034 1000 -1000 -0.054 -1000
S1P4 pathway 29 725 25 -0.076 0.02 1000 -1000 -0.056 -1000
Nectin adhesion pathway 28 1764 63 -0.073 0.029 1000 -1000 -0.077 -1000
Regulation of Androgen receptor activity 28 2024 70 -0.2 0.027 1000 -1000 -0.088 -1000
Regulation of nuclear SMAD2/3 signaling 27 3769 136 -0.16 0.05 1000 -1000 -0.072 -1000
IL1-mediated signaling events 27 1682 62 -0.092 0.06 1000 -1000 -0.096 -1000
EPHB forward signaling 27 2366 85 -0.11 0.049 1000 -1000 -0.095 -1000
TRAIL signaling pathway 26 1289 48 -0.034 0.029 1000 -1000 -0.077 -1000
TCGA08_p53 25 176 7 -0.041 0.026 1000 -1000 -0.014 -1000
Sphingosine 1-phosphate (S1P) pathway 24 674 28 -0.076 0.03 1000 -1000 -0.039 -1000
TCGA08_rtk_signaling 24 640 26 -0.076 0.033 1000 -1000 -0.021 -1000
Paxillin-independent events mediated by a4b1 and a4b7 23 869 37 -0.079 0.028 1000 -1000 -0.057 -1000
S1P1 pathway 23 829 36 -0.078 0.013 1000 -1000 -0.055 -1000
Regulation of p38-alpha and p38-beta 23 1247 54 -0.14 0.033 1000 -1000 -0.059 -1000
E-cadherin signaling in the nascent adherens junction 23 1792 76 -0.046 0.027 1000 -1000 -0.091 -1000
RXR and RAR heterodimerization with other nuclear receptor 22 1146 52 -0.057 0.021 1000 -1000 -0.051 -1000
S1P5 pathway 21 368 17 -0.076 0.044 1000 -1000 -0.044 -1000
Insulin Pathway 21 1625 74 -0.22 0.033 1000 -1000 -0.092 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 20 931 45 -0.11 0.04 1000 -1000 -0.098 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 20 682 33 -0.11 0.038 1000 -1000 -0.051 -1000
Aurora C signaling 19 137 7 -0.024 0 1000 -1000 -0.031 -1000
Ceramide signaling pathway 19 1446 76 -0.14 0.036 1000 -1000 -0.054 -1000
Signaling events mediated by PRL 19 669 34 -0.13 0.024 1000 -1000 -0.041 -1000
Hedgehog signaling events mediated by Gli proteins 18 1204 65 -0.076 0.055 1000 -1000 -0.066 -1000
EPO signaling pathway 18 1018 55 -0.077 0.018 1000 -1000 -0.1 -1000
Class I PI3K signaling events 18 1338 73 -0.14 0.035 1000 -1000 -0.079 -1000
IFN-gamma pathway 17 1202 68 -0.14 0.035 1000 -1000 -0.1 -1000
p38 MAPK signaling pathway 17 750 44 -0.14 0.025 1000 -1000 -0.069 -1000
BARD1 signaling events 16 947 57 -0.042 0.038 1000 -1000 -0.066 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 16 1334 83 -0.084 0.057 1000 -1000 -0.081 -1000
S1P3 pathway 16 672 42 -0.075 0.022 1000 -1000 -0.044 -1000
Aurora A signaling 15 927 60 -0.073 0.028 1000 -1000 -0.043 -1000
PLK1 signaling events 15 1310 85 -0.034 0.021 1000 -1000 -0.046 -1000
PDGFR-beta signaling pathway 15 1547 97 -0.098 0.037 1000 -1000 -0.089 -1000
Signaling events mediated by HDAC Class II 14 1063 75 -0.16 0.038 1000 -1000 -0.052 -1000
PLK2 and PLK4 events 14 42 3 0.002 0.011 1000 -1000 -0.014 -1000
Retinoic acid receptors-mediated signaling 14 862 58 -0.075 0.032 1000 -1000 -0.071 -1000
E-cadherin signaling in keratinocytes 13 561 43 -0.076 0.03 1000 -1000 -0.075 -1000
ceramide signaling pathway 11 575 49 -0.057 0.032 1000 -1000 -0.059 -1000
Canonical NF-kappaB pathway 9 351 39 -0.049 0.067 1000 -1000 -0.094 -1000
mTOR signaling pathway 9 522 53 -0.021 0.024 1000 -1000 -0.067 -1000
HIF-2-alpha transcription factor network 9 411 43 -0.094 0.1 1000 -1000 -0.099 -1000
Paxillin-dependent events mediated by a4b1 9 340 36 -0.028 0.031 1000 -1000 -0.076 -1000
Atypical NF-kappaB pathway 9 307 31 -0.07 0.024 1000 -1000 -0.053 -1000
Rapid glucocorticoid signaling 9 194 20 -0.022 0.017 1000 -1000 -0.021 -1000
Signaling events mediated by HDAC Class I 7 811 104 -0.089 0.053 1000 -1000 -0.079 -1000
Signaling events mediated by VEGFR1 and VEGFR2 7 904 125 -0.055 0.075 1000 -1000 -0.099 -1000
Circadian rhythm pathway 6 145 22 -0.02 0.04 1000 -1000 -0.05 -1000
FoxO family signaling 6 388 64 -0.11 0.11 1000 -1000 -0.091 -1000
Arf6 trafficking events 6 431 71 -0.051 0.038 1000 -1000 -0.077 -1000
Arf6 downstream pathway 4 205 43 -0.023 0.025 1000 -1000 -0.039 -1000
Insulin-mediated glucose transport 3 112 32 -0.021 0.036 1000 -1000 -0.065 -1000
VEGFR1 specific signals 3 210 56 -0.008 0.057 1000 -1000 -0.066 -1000
Class I PI3K signaling events mediated by Akt 2 198 68 -0.036 0.049 1000 -1000 -0.06 -1000
Alternative NF-kappaB pathway 2 29 13 0 0.037 1000 -1000 -0.037 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 1 43 23 0.003 0.044 1000 -1000 -0.054 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0 13 27 0 0.033 1000 -1000 -0.064 -1000
Arf1 pathway 0 25 54 -0.001 0.033 1000 -1000 -0.044 -1000
Total 5340 308770 7203 -18 -990 131000 -131000 -9.3 -131000
IL4-mediated signaling events

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
BCL2L1 -0.51 0.56 -10000 0 -1.3 234 234
STAT6 (cleaved dimer) -0.58 0.55 -10000 0 -1.2 317 317
IGHG1 -0.16 0.18 -10000 0 -0.39 113 113
IGHG3 -0.5 0.53 -10000 0 -1.1 303 303
AKT1 -0.26 0.33 -10000 0 -0.78 143 143
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.22 0.35 -10000 0 -0.88 108 108
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.28 0.36 -10000 0 -0.79 171 171
THY1 -0.52 0.56 -10000 0 -1.3 237 237
MYB -0.066 0.22 -10000 0 -0.67 97 97
HMGA1 0.01 0.036 -10000 0 -0.46 5 5
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.35 0.43 -10000 0 -0.86 234 234
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.27 0.35 -10000 0 -0.79 148 148
SP1 0.02 0.009 -10000 0 -10000 0 0
INPP5D 0.005 0.067 -10000 0 -0.52 13 13
SOCS5 0.026 0.023 -10000 0 -0.43 1 1
STAT6 (dimer)/ETS1 -0.54 0.6 -10000 0 -1.2 288 288
SOCS1 -0.33 0.37 -10000 0 -0.79 240 240
SOCS3 -0.28 0.34 -10000 0 -0.93 100 100
FCER2 -0.51 0.55 -10000 0 -1.2 261 261
PARP14 0.005 0.064 -10000 0 -0.6 9 9
CCL17 -0.6 0.64 -10000 0 -1.4 278 278
GRB2 0.013 0.016 -10000 0 -0.46 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.21 0.28 -10000 0 -0.79 84 84
T cell proliferation -0.53 0.59 -10000 0 -1.3 258 258
IL4R/JAK1 -0.52 0.56 -10000 0 -1.3 238 238
EGR2 -0.55 0.58 -10000 0 -1.3 250 250
JAK2 -0.011 0.043 -10000 0 -0.6 2 2
JAK3 -0.011 0.12 -10000 0 -0.56 39 39
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
JAK1 0.006 0.027 -10000 0 -0.67 1 1
COL1A2 -0.21 0.38 -10000 0 -1.6 50 50
CCL26 -0.56 0.6 -10000 0 -1.3 289 289
IL4R -0.56 0.6 -10000 0 -1.3 245 245
PTPN6 0.024 0.02 -10000 0 -0.44 1 1
IL13RA2 -0.56 0.6 -10000 0 -1.3 262 262
IL13RA1 -0.011 0.043 -10000 0 -0.6 2 2
IRF4 -0.3 0.54 -10000 0 -1.3 166 166
ARG1 -0.12 0.16 -10000 0 -0.72 16 16
CBL -0.32 0.39 -10000 0 -0.8 223 223
GTF3A 0.017 0.034 -10000 0 -0.45 4 4
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
IL13RA1/JAK2 -0.015 0.055 -10000 0 -0.45 4 4
IRF4/BCL6 -0.27 0.49 -10000 0 -1.2 153 153
CD40LG -0.084 0.23 -10000 0 -0.61 134 134
MAPK14 -0.32 0.4 -10000 0 -0.85 194 194
mitosis -0.24 0.31 -10000 0 -0.73 143 143
STAT6 -0.63 0.74 -10000 0 -1.4 293 293
SPI1 0.01 0.059 -10000 0 -0.62 7 7
RPS6KB1 -0.23 0.3 -10000 0 -0.72 127 127
STAT6 (dimer) -0.63 0.74 -10000 0 -1.4 293 293
STAT6 (dimer)/PARP14 -0.58 0.63 -10000 0 -1.3 299 299
mast cell activation 0.012 0.013 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.27 0.38 -10000 0 -0.88 143 143
FRAP1 -0.26 0.33 -10000 0 -0.78 143 143
LTA -0.57 0.62 -10000 0 -1.3 264 264
FES 0.004 0.078 -10000 0 -0.64 12 12
T-helper 1 cell differentiation 0.59 0.66 1.3 294 -10000 0 294
CCL11 -0.55 0.59 -10000 0 -1.3 260 260
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.27 0.38 -10000 0 -0.88 133 133
IL2RG -0.036 0.17 -10000 0 -0.56 75 75
IL10 -0.53 0.58 -10000 0 -1.3 239 239
IRS1 -0.033 0.17 -10000 0 -0.66 58 58
IRS2 -0.017 0.13 -10000 0 -0.52 48 48
IL4 -0.11 0.13 -10000 0 -0.24 162 162
IL5 -0.52 0.55 -10000 0 -1.1 303 303
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.4 0.41 -10000 0 -0.89 255 255
COL1A1 -0.24 0.43 -10000 0 -1.6 64 64
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.53 0.58 -10000 0 -1.3 235 235
IL2R gamma/JAK3 -0.035 0.18 -10000 0 -0.55 81 81
TFF3 -0.68 0.7 -10000 0 -1.5 316 316
ALOX15 -0.66 0.66 -10000 0 -1.4 325 325
MYBL1 -0.041 0.16 -10000 0 -0.53 84 84
T-helper 2 cell differentiation -0.44 0.48 -10000 0 -0.97 295 295
SHC1 0.013 0 -10000 0 -10000 0 0
CEBPB 0.008 0.059 -10000 0 -0.48 12 12
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.26 0.35 -10000 0 -0.8 141 141
mol:PI-3-4-5-P3 -0.26 0.33 -10000 0 -0.78 143 143
PI3K -0.28 0.37 -10000 0 -0.86 143 143
DOK2 -0.014 0.13 -10000 0 -0.58 39 39
ETS1 0.021 0.052 -10000 0 -0.56 6 6
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.19 0.27 -10000 0 -0.8 73 73
ITGB3 -0.53 0.57 -10000 0 -1.2 261 261
PIGR -0.7 0.68 -10000 0 -1.4 337 337
IGHE 0.044 0.069 0.29 19 -0.26 1 20
MAPKKK cascade -0.19 0.26 -10000 0 -0.78 73 73
BCL6 0.012 0.045 -10000 0 -0.62 4 4
OPRM1 -0.52 0.55 -10000 0 -1.1 303 303
RETNLB -0.52 0.55 -10000 0 -1.1 303 303
SELP -0.62 0.66 -10000 0 -1.4 291 291
AICDA -0.51 0.54 -10000 0 -1.2 245 245
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.056 0.063 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.16 0.18 -9999 0 -0.46 170 170
JUN -0.13 0.21 -9999 0 -0.5 142 142
HRAS 0.009 0.05 -9999 0 -0.63 5 5
RET51/GFRalpha1/GDNF/GRB10 -0.22 0.29 -9999 0 -0.54 318 318
RAP1A 0.013 0 -9999 0 -10000 0 0
FRS2 0.005 0.062 -9999 0 -0.46 15 15
RAP1A/GDP 0.01 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.22 0.29 -9999 0 -0.55 317 317
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0.024 -9999 0 -0.67 1 1
RET9/GFRalpha1/GDNF/Enigma -0.12 0.2 -9999 0 -0.4 247 247
RHOA 0.013 0 -9999 0 -10000 0 0
RAP1A/GTP -0.21 0.25 -9999 0 -0.49 319 319
GRB7 -0.028 0.14 -9999 0 -0.47 73 73
RET51/GFRalpha1/GDNF -0.22 0.29 -9999 0 -0.54 317 317
MAPKKK cascade -0.19 0.23 -9999 0 -0.62 141 141
BCAR1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.14 0.24 -9999 0 -0.47 258 258
lamellipodium assembly -0.14 0.17 -9999 0 -0.42 176 176
RET51/GFRalpha1/GDNF/SHC -0.22 0.29 -9999 0 -0.54 317 317
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
RET9/GFRalpha1/GDNF/SHC -0.12 0.19 -9999 0 -0.4 246 246
RET9/GFRalpha1/GDNF/Shank3 -0.12 0.19 -9999 0 -0.4 246 246
MAPK3 -0.18 0.25 -9999 0 -0.62 147 147
DOK1 0.009 0.055 -9999 0 -0.64 6 6
DOK6 -0.02 0.14 -9999 0 -0.61 45 45
PXN 0.013 0 -9999 0 -10000 0 0
neurite development -0.16 0.24 -9999 0 -0.59 148 148
DOK5 -0.031 0.15 -9999 0 -0.55 65 65
GFRA1 -0.2 0.31 -9999 0 -0.65 277 277
MAPK8 -0.14 0.22 -9999 0 -0.54 139 139
HRAS/GTP -0.22 0.27 -9999 0 -0.7 146 146
tube development -0.11 0.18 -9999 0 -0.37 246 246
MAPK1 -0.18 0.25 -9999 0 -0.62 147 147
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.08 0.15 -9999 0 -0.3 246 246
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
SRC 0.011 0.037 -9999 0 -0.6 3 3
PDLIM7 0.012 0.033 -9999 0 -0.67 2 2
RET51/GFRalpha1/GDNF/Dok6 -0.22 0.29 -9999 0 -0.53 331 331
SHC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.22 0.29 -9999 0 -0.54 319 319
RET51/GFRalpha1/GDNF/Dok5 -0.24 0.31 -9999 0 -0.57 337 337
PRKCA -0.011 0.11 -9999 0 -0.53 37 37
HRAS/GDP 0.007 0.037 -9999 0 -0.47 5 5
CREB1 -0.13 0.22 -9999 0 -0.44 245 245
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.078 0.15 -9999 0 -0.3 246 246
RET51/GFRalpha1/GDNF/Grb7 -0.24 0.3 -9999 0 -0.57 320 320
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.18 0.29 -9999 0 -0.6 257 257
DOK4 0.01 0.044 -9999 0 -0.62 4 4
JNK cascade -0.12 0.2 -9999 0 -0.49 142 142
RET9/GFRalpha1/GDNF/FRS2 -0.12 0.2 -9999 0 -0.4 246 246
SHANK3 0.013 0 -9999 0 -10000 0 0
RASA1 0.011 0.037 -9999 0 -0.51 4 4
NCK1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.078 0.15 -9999 0 -0.3 246 246
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.15 0.22 -9999 0 -0.5 170 170
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.15 0.23 -9999 0 -0.57 139 139
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.18 0.28 -9999 0 -0.73 138 138
PI3K -0.2 0.31 -9999 0 -0.65 215 215
SOS1 0.013 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.11 0.18 -9999 0 -0.37 246 246
GRB10 0.012 0.029 -9999 0 -0.56 2 2
activation of MAPKK activity -0.13 0.19 -9999 0 -0.47 138 138
RET51/GFRalpha1/GDNF/FRS2 -0.22 0.29 -9999 0 -0.54 320 320
GAB1 0.012 0.024 -9999 0 -0.67 1 1
IRS1 -0.033 0.17 -9999 0 -0.66 58 58
IRS2 -0.017 0.13 -9999 0 -0.52 48 48
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.18 0.28 -9999 0 -0.73 138 138
RET51/GFRalpha1/GDNF/PKC alpha -0.23 0.3 -9999 0 -0.56 328 328
GRB2 0.013 0.016 -9999 0 -0.46 1 1
PRKACA 0.013 0 -9999 0 -10000 0 0
GDNF -0.014 0.095 -9999 0 -0.46 37 37
RAC1 0.013 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.24 0.32 -9999 0 -0.59 328 328
Rac1/GTP -0.18 0.21 -9999 0 -0.52 176 176
RET9/GFRalpha1/GDNF -0.14 0.21 -9999 0 -0.41 302 302
GFRalpha1/GDNF -0.16 0.24 -9999 0 -0.48 302 302
Wnt 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
Noncanonical Wnts/FZD -0.14 0.25 -9999 0 -0.46 233 233
FZD6 -0.018 0.14 -9999 0 -0.66 39 39
WNT6 -0.11 0.23 -9999 0 -0.52 195 195
WNT4 -0.075 0.22 -9999 0 -0.61 119 119
FZD3 -0.009 0.12 -9999 0 -0.66 28 28
WNT5A -0.041 0.18 -9999 0 -0.61 73 73
WNT11 -0.079 0.21 -9999 0 -0.54 139 139
Ephrin A reverse 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
MAPKKK cascade -0.063 0.16 -9999 0 -0.36 175 175
EFNA5 -0.094 0.24 -9999 0 -0.6 146 146
FYN -0.051 0.15 -9999 0 -0.4 99 99
neuron projection morphogenesis -0.063 0.16 -9999 0 -0.36 175 175
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.063 0.16 -9999 0 -0.36 175 175
EPHA5 -0.007 0.086 -9999 0 -0.46 30 30
Glucocorticoid receptor regulatory 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
PCK2 0.047 0.13 0.36 7 -1 3 10
SMARCC2 0.015 0.009 -10000 0 -10000 0 0
SMARCC1 0.013 0.035 -10000 0 -0.67 2 2
TBX21 -0.2 0.32 -10000 0 -0.73 177 177
SUMO2 0.01 0.019 -10000 0 -0.46 1 1
STAT1 (dimer) 0.017 0.041 -10000 0 -0.41 7 7
FKBP4 0.012 0.024 -10000 0 -0.67 1 1
FKBP5 -0.019 0.14 -10000 0 -0.57 46 46
GR alpha/HSP90/FKBP51/HSP90 0.12 0.15 0.33 126 -0.38 11 137
PRL -0.11 0.15 -10000 0 -0.62 12 12
cortisol/GR alpha (dimer)/TIF2 0.29 0.3 0.58 341 -0.49 7 348
RELA -0.038 0.083 -10000 0 -10000 0 0
FGG 0.18 0.31 0.53 206 -0.57 55 261
GR beta/TIF2 0.13 0.18 0.35 164 -0.44 34 198
IFNG -0.48 0.47 -10000 0 -0.95 333 333
apoptosis -0.06 0.22 0.5 20 -0.63 31 51
CREB1 -0.062 0.12 -10000 0 -0.34 82 82
histone acetylation -0.052 0.16 0.35 9 -0.41 64 73
BGLAP -0.12 0.18 -10000 0 -0.62 32 32
GR/PKAc 0.11 0.14 0.31 134 -0.39 4 138
NF kappa B1 p50/RelA -0.064 0.15 -10000 0 -0.47 26 26
SMARCD1 0.015 0.009 -10000 0 -10000 0 0
MDM2 0.12 0.11 0.28 194 -0.21 1 195
GATA3 -0.095 0.25 -10000 0 -0.67 134 134
AKT1 0.002 0.014 -10000 0 -10000 0 0
CSF2 -0.093 0.15 -10000 0 -0.53 39 39
GSK3B 0.01 0.01 -10000 0 -10000 0 0
NR1I3 -0.034 0.21 0.5 15 -0.69 20 35
CSN2 0.2 0.18 0.38 307 -0.31 9 316
BRG1/BAF155/BAF170/BAF60A 0.038 0.036 -10000 0 -0.39 5 5
NFATC1 0.003 0.081 -10000 0 -0.64 13 13
POU2F1 0.013 0.024 -10000 0 -0.46 1 1
CDKN1A 0.018 0.15 -10000 0 -1.5 7 7
response to stress 0 0 -10000 0 -10000 0 0
response to UV -0.002 0.008 -10000 0 -10000 0 0
SFN -0.013 0.13 -10000 0 -0.62 35 35
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.1 0.16 0.33 107 -0.48 13 120
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.052 0.24 0.49 13 -0.82 31 44
JUN -0.31 0.26 -10000 0 -0.59 306 306
IL4 -0.14 0.18 -10000 0 -0.35 274 274
CDK5R1 0.005 0.059 -10000 0 -0.5 11 11
PRKACA 0.013 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.26 0.32 0.28 30 -0.61 316 346
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.12 0.14 0.33 119 -0.38 5 124
cortisol/GR alpha (monomer) 0.37 0.35 0.71 351 -0.42 6 357
NCOA2 -0.015 0.14 -10000 0 -0.67 34 34
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.12 0.21 -10000 0 -0.62 112 112
AP-1/NFAT1-c-4 -0.51 0.42 -10000 0 -0.9 385 385
AFP -0.37 0.46 -10000 0 -1.2 143 143
SUV420H1 0.013 0 -10000 0 -10000 0 0
IRF1 0.2 0.18 0.51 89 -0.88 3 92
TP53 0.022 0.086 -10000 0 -0.58 16 16
PPP5C 0.013 0 -10000 0 -10000 0 0
KRT17 -0.61 0.64 -10000 0 -1.2 367 367
KRT14 -0.48 0.62 -10000 0 -1.3 255 255
TBP 0.022 0.013 -10000 0 -10000 0 0
CREBBP 0.086 0.11 0.29 71 -0.68 2 73
HDAC1 0.012 0.024 -10000 0 -0.67 1 1
HDAC2 0.012 0.03 -10000 0 -0.57 2 2
AP-1 -0.52 0.43 -10000 0 -0.91 387 387
MAPK14 0.01 0.008 -10000 0 -10000 0 0
MAPK10 -0.09 0.23 -10000 0 -0.62 134 134
MAPK11 0.003 0.067 -10000 0 -0.62 9 9
KRT5 -0.63 0.64 -10000 0 -1.3 354 354
interleukin-1 receptor activity 0 0.007 -10000 0 -10000 0 0
NCOA1 0.015 0.025 -10000 0 -0.67 1 1
STAT1 0.017 0.041 -10000 0 -0.41 7 7
CGA -0.36 0.45 -10000 0 -0.97 240 240
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.18 0.18 0.41 250 -10000 0 250
MAPK3 0.01 0.009 -10000 0 -10000 0 0
MAPK1 0.01 0.008 -10000 0 -10000 0 0
ICAM1 -0.21 0.3 -10000 0 -0.8 107 107
NFKB1 -0.039 0.086 -10000 0 -0.65 1 1
MAPK8 -0.24 0.22 -10000 0 -0.5 271 271
MAPK9 0.01 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) -0.068 0.23 0.51 20 -0.66 33 53
BAX 0.029 0.059 -10000 0 -10000 0 0
POMC -0.22 0.35 -10000 0 -1.2 60 60
EP300 0.088 0.11 0.3 56 -10000 0 56
cortisol/GR alpha (dimer)/p53 0.32 0.28 0.6 330 -0.59 2 332
proteasomal ubiquitin-dependent protein catabolic process 0.086 0.086 0.24 86 -10000 0 86
SGK1 0.16 0.17 -10000 0 -1.2 4 4
IL13 -0.36 0.34 -10000 0 -0.85 203 203
IL6 -0.33 0.45 -10000 0 -1.1 180 180
PRKACG 0 0 -10000 0 -10000 0 0
IL5 -0.31 0.28 -10000 0 -0.55 399 399
IL2 -0.37 0.34 -10000 0 -0.76 289 289
CDK5 0.011 0.024 -10000 0 -0.67 1 1
PRKACB -0.028 0.14 -10000 0 -0.49 70 70
HSP90AA1 0.013 0.016 -10000 0 -0.46 1 1
IL8 -0.3 0.41 -10000 0 -0.95 190 190
CDK5R1/CDK5 0.009 0.047 -10000 0 -0.36 12 12
NF kappa B1 p50/RelA/PKAc -0.048 0.14 -10000 0 -0.48 19 19
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.31 0.25 0.56 335 -10000 0 335
SMARCA4 0.015 0.009 -10000 0 -10000 0 0
chromatin remodeling 0.21 0.16 0.41 228 -10000 0 228
NF kappa B1 p50/RelA/Cbp 0.028 0.16 0.36 8 -0.57 2 10
JUN (dimer) -0.31 0.26 -10000 0 -0.59 306 306
YWHAH 0.013 0 -10000 0 -10000 0 0
VIPR1 -0.16 0.28 -10000 0 -0.71 126 126
NR3C1 0.22 0.22 0.51 239 -0.36 1 240
NR4A1 -0.034 0.15 -10000 0 -0.46 77 77
TIF2/SUV420H1 -0.001 0.1 -10000 0 -0.5 34 34
MAPKKK cascade -0.06 0.22 0.5 20 -0.63 31 51
cortisol/GR alpha (dimer)/Src-1 0.32 0.28 0.59 350 -10000 0 350
PBX1 0.002 0.089 -10000 0 -0.64 15 15
POU1F1 0 0.019 -10000 0 -10000 0 0
SELE -0.28 0.41 -10000 0 -0.97 166 166
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.21 0.16 0.42 226 -10000 0 226
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.31 0.25 0.56 335 -10000 0 335
mol:cortisol 0.21 0.23 0.42 370 -0.23 10 380
MMP1 -0.45 0.56 -10000 0 -1.2 266 266
IL23-mediated signaling events

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
CCL2 -0.35 0.51 -10000 0 -1.2 159 159
IL23A -0.36 0.52 -10000 0 -1.2 160 160
NF kappa B1 p50/RelA/I kappa B alpha -0.39 0.47 -10000 0 -1.2 177 177
positive regulation of T cell mediated cytotoxicity -0.4 0.59 -10000 0 -1.3 186 186
ITGA3 -0.36 0.52 -10000 0 -1.2 150 150
IL17F -0.22 0.33 -10000 0 -0.74 151 151
IL12B -0.08 0.22 -10000 0 -0.6 121 121
STAT1 (dimer) -0.39 0.56 -10000 0 -1.3 184 184
CD4 -0.34 0.49 -10000 0 -1.2 143 143
IL23 -0.38 0.52 -10000 0 -1.2 173 173
IL23R -0.04 0.099 -10000 0 -10000 0 0
IL1B -0.37 0.55 -10000 0 -1.3 170 170
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.4 0.55 -10000 0 -1.3 185 185
TYK2 0.005 0.021 -10000 0 -10000 0 0
STAT4 -0.044 0.18 -10000 0 -0.6 78 78
STAT3 0.012 0.024 -10000 0 -0.67 1 1
IL18RAP -0.067 0.2 -10000 0 -0.56 114 114
IL12RB1 -0.041 0.17 -10000 0 -0.62 63 63
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
IL12Rbeta1/TYK2 -0.028 0.13 -10000 0 -0.46 63 63
IL23R/JAK2 -0.045 0.12 -10000 0 -10000 0 0
positive regulation of chronic inflammatory response -0.4 0.59 -10000 0 -1.3 186 186
natural killer cell activation 0.004 0.009 0.044 11 -10000 0 11
JAK2 0.011 0.039 -10000 0 -0.6 2 2
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
NFKB1 0.011 0.024 -10000 0 -0.68 1 1
RELA 0.011 0.004 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.35 0.48 -10000 0 -1.1 173 173
ALOX12B -0.35 0.5 -10000 0 -1.2 154 154
CXCL1 -0.44 0.58 -10000 0 -1.3 218 218
T cell proliferation -0.4 0.59 -10000 0 -1.3 186 186
NFKBIA 0.011 0.017 -10000 0 -0.46 1 1
IL17A -0.16 0.27 -10000 0 -0.58 125 125
PI3K -0.41 0.48 -10000 0 -1.2 190 190
IFNG -0.029 0.05 0.097 2 -0.12 128 130
STAT3 (dimer) -0.38 0.45 -10000 0 -1.1 184 184
IL18R1 -0.018 0.13 -10000 0 -0.62 38 38
IL23/IL23R/JAK2/TYK2/SOCS3 -0.21 0.32 -10000 0 -0.82 92 92
IL18/IL18R -0.056 0.19 -10000 0 -0.45 130 130
macrophage activation -0.019 0.018 -10000 0 -0.045 116 116
TNF -0.38 0.56 -10000 0 -1.3 167 167
STAT3/STAT4 -0.42 0.5 -10000 0 -1.2 200 200
STAT4 (dimer) -0.4 0.58 -10000 0 -1.3 191 191
IL18 -0.009 0.11 -10000 0 -0.56 30 30
IL19 -0.38 0.5 -10000 0 -1.2 163 163
STAT5A (dimer) -0.39 0.56 -10000 0 -1.3 182 182
STAT1 0.01 0.036 -10000 0 -0.46 5 5
SOCS3 0.003 0.077 -10000 0 -0.54 16 16
CXCL9 -0.42 0.57 -10000 0 -1.3 184 184
MPO -0.38 0.53 -10000 0 -1.2 174 174
positive regulation of humoral immune response -0.4 0.59 -10000 0 -1.3 186 186
IL23/IL23R/JAK2/TYK2 -0.44 0.68 -10000 0 -1.5 184 184
IL6 -0.43 0.58 -10000 0 -1.3 200 200
STAT5A 0.007 0.064 -10000 0 -0.65 8 8
IL2 -0.003 0.067 -10000 0 -0.46 17 17
positive regulation of tyrosine phosphorylation of STAT protein 0.004 0.009 0.044 11 -10000 0 11
CD3E -0.38 0.55 -10000 0 -1.3 159 159
keratinocyte proliferation -0.4 0.59 -10000 0 -1.3 186 186
NOS2 -0.36 0.51 -10000 0 -1.2 154 154
Syndecan-1-mediated 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
TGFB1 0.011 0.041 -9999 0 -0.67 3 3
CCL5 -0.049 0.18 -9999 0 -0.56 91 91
SDCBP 0.013 0.016 -9999 0 -0.46 1 1
FGFR/FGF2/Syndecan-1 -0.19 0.28 -9999 0 -0.71 138 138
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.18 0.27 -9999 0 -0.67 142 142
Syndecan-1/Syntenin -0.17 0.27 -9999 0 -0.68 138 138
MAPK3 -0.14 0.24 -9999 0 -0.65 117 117
HGF/MET -0.072 0.21 -9999 0 -0.5 148 148
TGFB1/TGF beta receptor Type II 0.011 0.041 -9999 0 -0.67 3 3
BSG 0.013 0 -9999 0 -10000 0 0
keratinocyte migration -0.17 0.26 -9999 0 -0.66 142 142
Syndecan-1/RANTES -0.2 0.3 -9999 0 -0.69 167 167
Syndecan-1/CD147 -0.16 0.26 -9999 0 -0.68 125 125
Syndecan-1/Syntenin/PIP2 -0.17 0.26 -9999 0 -0.65 138 138
LAMA5 0.007 0.059 -9999 0 -0.55 9 9
positive regulation of cell-cell adhesion -0.18 0.24 -9999 0 -0.63 138 138
MMP7 -0.13 0.26 -9999 0 -0.57 205 205
HGF -0.033 0.17 -9999 0 -0.66 58 58
Syndecan-1/CASK -0.18 0.27 -9999 0 -0.68 138 138
Syndecan-1/HGF/MET -0.22 0.31 -9999 0 -0.7 191 191
regulation of cell adhesion -0.13 0.24 -9999 0 -0.63 113 113
HPSE -0.02 0.14 -9999 0 -0.63 43 43
positive regulation of cell migration -0.19 0.28 -9999 0 -0.71 138 138
SDC1 -0.19 0.29 -9999 0 -0.72 138 138
Syndecan-1/Collagen -0.19 0.28 -9999 0 -0.71 138 138
PPIB 0.013 0.016 -9999 0 -0.46 1 1
MET -0.066 0.21 -9999 0 -0.6 108 108
PRKACA 0.013 0 -9999 0 -10000 0 0
MMP9 -0.088 0.23 -9999 0 -0.59 140 140
MAPK1 -0.14 0.24 -9999 0 -0.65 117 117
homophilic cell adhesion -0.18 0.28 -9999 0 -0.7 138 138
MMP1 -0.23 0.3 -9999 0 -0.58 341 341
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.057 0.2 0.59 97 -10000 0 97
PI3K Class IB/PDE3B -0.057 0.2 -10000 0 -0.59 97 97
PDE3B -0.057 0.2 -10000 0 -0.59 97 97
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.13 0.25 -10000 0 -0.52 174 174
TBX21 -0.24 0.54 -10000 0 -1.2 164 164
B2M 0.011 0.025 -10000 0 -0.68 1 1
TYK2 0.013 0.021 -10000 0 -10000 0 0
IL12RB1 -0.032 0.17 -10000 0 -0.62 63 63
GADD45B -0.14 0.39 -10000 0 -0.93 118 118
IL12RB2 -0.14 0.25 -10000 0 -0.53 239 239
GADD45G -0.16 0.43 -10000 0 -0.94 151 151
natural killer cell activation 0.002 0.023 -10000 0 -10000 0 0
RELB 0.009 0.049 -10000 0 -0.52 7 7
RELA 0.013 0 -10000 0 -10000 0 0
IL18 -0.005 0.11 -10000 0 -0.56 30 30
IL2RA -0.086 0.23 -10000 0 -0.6 136 136
IFNG -0.11 0.23 -10000 0 -0.54 180 180
STAT3 (dimer) -0.16 0.39 -10000 0 -0.84 161 161
HLA-DRB5 -0.049 0.18 -10000 0 -0.56 90 90
FASLG -0.25 0.55 -10000 0 -1.2 172 172
NF kappa B2 p52/RelB -0.27 0.43 -10000 0 -1 173 173
CD4 0.007 0.06 -10000 0 -0.59 8 8
SOCS1 -0.02 0.14 -10000 0 -0.56 48 48
EntrezGene:6955 -0.003 0.012 -10000 0 -10000 0 0
CD3D -0.077 0.22 -10000 0 -0.6 122 122
CD3E -0.077 0.22 -10000 0 -0.59 124 124
CD3G -0.097 0.24 -10000 0 -0.61 147 147
IL12Rbeta2/JAK2 -0.09 0.2 -10000 0 -0.4 210 210
CCL3 -0.22 0.5 -10000 0 -1.1 160 160
CCL4 -0.21 0.5 -10000 0 -1.1 154 154
HLA-A 0.005 0.064 -10000 0 -0.57 10 10
IL18/IL18R -0.027 0.21 -10000 0 -0.5 106 106
NOS2 -0.18 0.46 -10000 0 -1.1 131 131
IL12/IL12R/TYK2/JAK2/SPHK2 -0.11 0.22 -10000 0 -0.5 145 145
IL1R1 -0.22 0.49 -10000 0 -1.1 156 156
IL4 -0.002 0.023 -10000 0 -10000 0 0
JAK2 0.012 0.035 -10000 0 -0.55 2 2
EntrezGene:6957 -0.003 0.012 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.24 0.6 -10000 0 -1.2 175 175
RAB7A -0.1 0.33 -10000 0 -0.79 94 94
lysosomal transport -0.096 0.32 -10000 0 -0.74 97 97
FOS -0.21 0.46 -10000 0 -1.1 151 151
STAT4 (dimer) -0.18 0.45 -10000 0 -0.97 170 170
STAT5A (dimer) -0.32 0.44 -10000 0 -0.99 210 210
GZMA -0.24 0.55 -10000 0 -1.2 163 163
GZMB -0.29 0.58 -10000 0 -1.2 191 191
HLX 0.012 0.029 -10000 0 -0.56 2 2
LCK -0.26 0.57 -10000 0 -1.2 179 179
TCR/CD3/MHC II/CD4 -0.14 0.35 -10000 0 -0.77 158 158
IL2/IL2R -0.087 0.25 -10000 0 -0.58 138 138
MAPK14 -0.15 0.41 -10000 0 -0.88 155 155
CCR5 -0.17 0.45 -10000 0 -1.1 109 109
IL1B -0.028 0.16 -10000 0 -0.61 56 56
STAT6 -0.038 0.14 -10000 0 -0.31 59 59
STAT4 -0.044 0.18 -10000 0 -0.6 78 78
STAT3 0.012 0.024 -10000 0 -0.67 1 1
STAT1 0.01 0.036 -10000 0 -0.46 5 5
NFKB1 0.012 0.024 -10000 0 -0.67 1 1
NFKB2 0.013 0.016 -10000 0 -0.46 1 1
IL12B -0.072 0.22 -10000 0 -0.59 121 121
CD8A -0.054 0.19 -10000 0 -0.58 95 95
CD8B -0.078 0.22 -10000 0 -0.59 125 125
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.13 0.25 0.52 174 -10000 0 174
IL2RB -0.035 0.16 -10000 0 -0.55 72 72
proteasomal ubiquitin-dependent protein catabolic process -0.16 0.4 -10000 0 -0.86 169 169
IL2RG -0.039 0.17 -10000 0 -0.57 75 75
IL12 -0.11 0.22 -10000 0 -0.44 244 244
STAT5A 0.007 0.064 -10000 0 -0.65 8 8
CD247 -0.064 0.2 -10000 0 -0.59 105 105
IL2 -0.003 0.065 -10000 0 -0.46 17 17
SPHK2 0.013 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.084 0.22 -10000 0 -0.54 148 148
IL12/IL12R/TYK2/JAK2 -0.27 0.62 -10000 0 -1.3 180 180
MAP2K3 -0.15 0.41 -10000 0 -0.88 158 158
RIPK2 0.012 0.028 -10000 0 -0.46 3 3
MAP2K6 -0.16 0.42 -10000 0 -0.88 163 163
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0 0.089 -10000 0 -0.61 17 17
IL18RAP -0.062 0.2 -10000 0 -0.56 114 114
IL12Rbeta1/TYK2 -0.015 0.13 -10000 0 -0.47 63 63
EOMES -0.15 0.43 -10000 0 -1.4 79 79
STAT1 (dimer) -0.2 0.4 -10000 0 -0.82 196 196
T cell proliferation -0.097 0.32 -10000 0 -0.67 146 146
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 -0.013 0.14 -10000 0 -0.63 38 38
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.2 0.3 -10000 0 -0.76 151 151
ATF2 -0.13 0.38 -10000 0 -0.82 144 144
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.13 0.24 -10000 0 -0.63 144 144
FYN -0.12 0.36 -10000 0 -0.83 148 148
LAT/GRAP2/SLP76 -0.12 0.28 -10000 0 -0.68 152 152
IKBKB 0.01 0.04 -10000 0 -0.5 5 5
AKT1 -0.054 0.22 -10000 0 -0.5 146 146
B2M 0.011 0.025 -10000 0 -0.68 1 1
IKBKG -0.028 0.054 -10000 0 -0.17 42 42
MAP3K8 0.002 0.079 -10000 0 -0.55 16 16
mol:Ca2+ -0.04 0.047 -10000 0 -0.12 117 117
integrin-mediated signaling pathway 0.011 0.053 -10000 0 -0.38 15 15
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.11 0.34 -10000 0 -0.78 153 153
TRPV6 -0.21 0.29 -10000 0 -0.58 302 302
CD28 -0.027 0.15 -10000 0 -0.59 56 56
SHC1 -0.12 0.36 -10000 0 -0.83 151 151
receptor internalization -0.15 0.4 -10000 0 -0.89 165 165
PRF1 -0.14 0.41 -10000 0 -1 131 131
KRAS 0.013 0.016 -10000 0 -0.46 1 1
GRB2 0.013 0.016 -10000 0 -0.46 1 1
COT/AKT1 -0.035 0.18 -10000 0 -0.4 137 137
LAT -0.13 0.37 -10000 0 -0.86 150 150
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.076 0.22 -10000 0 -0.61 122 122
CD3E -0.075 0.22 -10000 0 -0.59 124 124
CD3G -0.096 0.24 -10000 0 -0.61 147 147
RASGRP2 -0.007 0.042 -10000 0 -0.19 26 26
RASGRP1 -0.07 0.23 -10000 0 -0.51 157 157
HLA-A 0.005 0.065 -10000 0 -0.57 10 10
RASSF5 0.002 0.082 -10000 0 -0.6 15 15
RAP1A/GTP/RAPL 0.011 0.053 -10000 0 -0.38 15 15
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.003 0.07 -10000 0 -0.13 105 105
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.051 0.097 -10000 0 -0.27 103 103
PRKCA -0.052 0.13 -10000 0 -0.31 138 138
GRAP2 -0.037 0.17 -10000 0 -0.6 69 69
mol:IP3 -0.038 0.24 0.23 207 -0.49 139 346
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.15 0.44 -10000 0 -0.98 148 148
ORAI1 0.11 0.15 0.35 165 -0.33 1 166
CSK -0.13 0.36 -10000 0 -0.85 150 150
B7 family/CD28 -0.18 0.35 -10000 0 -0.87 158 158
CHUK 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.16 0.44 -10000 0 -1 158 158
PTPN6 -0.12 0.37 -10000 0 -0.87 147 147
VAV1 -0.13 0.36 -10000 0 -0.84 156 156
Monovalent TCR/CD3 -0.14 0.38 -10000 0 -0.75 186 186
CBL 0.013 0 -10000 0 -10000 0 0
LCK -0.14 0.4 -10000 0 -0.93 150 150
PAG1 -0.13 0.37 -10000 0 -0.86 149 149
RAP1A 0.013 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.16 0.43 -10000 0 -1 154 154
CD80 -0.022 0.15 -10000 0 -0.63 45 45
CD86 0.005 0.073 -10000 0 -0.66 10 10
PDK1/CARD11/BCL10/MALT1 -0.063 0.12 -10000 0 -0.32 121 121
HRAS 0.009 0.05 -10000 0 -0.63 5 5
GO:0035030 -0.099 0.3 -10000 0 -0.68 154 154
CD8A -0.054 0.19 -10000 0 -0.58 95 95
CD8B -0.077 0.22 -10000 0 -0.6 125 125
PTPRC -0.032 0.16 -10000 0 -0.59 62 62
PDK1/PKC theta -0.077 0.28 -10000 0 -0.65 148 148
CSK/PAG1 -0.12 0.35 -10000 0 -0.84 146 146
SOS1 0.013 0 -10000 0 -10000 0 0
peptide-MHC class I 0.012 0.056 -10000 0 -0.46 10 10
GRAP2/SLP76 -0.15 0.33 -10000 0 -0.81 155 155
STIM1 0.058 0.075 -10000 0 -10000 0 0
RAS family/GTP 0 0.094 -10000 0 -0.19 87 87
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.17 0.45 -10000 0 -1 165 165
mol:DAG -0.065 0.18 -10000 0 -0.44 142 142
RAP1A/GDP 0.003 0.031 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
CD247 -0.062 0.2 -10000 0 -0.59 105 105
cytotoxic T cell degranulation -0.13 0.38 -10000 0 -0.94 133 133
RAP1A/GTP -0.005 0.013 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.075 0.27 -10000 0 -0.61 153 153
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.068 0.3 0.25 190 -0.66 141 331
NRAS 0.007 0.062 -10000 0 -0.62 8 8
ZAP70 -0.079 0.22 -10000 0 -0.57 134 134
GRB2/SOS1 0.019 0.012 -10000 0 -0.32 1 1
LAT/GRAP2/SLP76/VAV1 -0.12 0.27 -10000 0 -0.66 148 148
MALT1 0.012 0.024 -10000 0 -0.67 1 1
TRAF6 0.013 0.016 -10000 0 -0.46 1 1
CD8 heterodimer -0.09 0.25 -10000 0 -0.61 148 148
CARD11 -0.024 0.15 -10000 0 -0.6 51 51
PRKCB -0.065 0.16 -10000 0 -0.39 142 142
PRKCE -0.048 0.13 -10000 0 -0.3 133 133
PRKCQ -0.1 0.33 -10000 0 -0.76 153 153
LCP2 0.01 0.047 -10000 0 -0.59 5 5
BCL10 0.013 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.04 0.19 -10000 0 -0.42 145 145
IKK complex 0.013 0.069 -10000 0 -0.13 78 78
RAS family/GDP -0.007 0.014 -10000 0 -0.094 4 4
MAP3K14 -0.016 0.14 -10000 0 -0.3 120 120
PDPK1 -0.047 0.21 -10000 0 -0.48 142 142
TCR/CD3/MHC I/CD8/Fyn -0.16 0.45 -10000 0 -1 150 150
Plasma membrane estrogen receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.077 0.18 -10000 0 -0.37 224 224
ER alpha/Gai/GDP/Gbeta gamma -0.1 0.22 -10000 0 -0.43 214 214
AKT1 -0.18 0.36 -10000 0 -0.8 207 207
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.18 0.36 -10000 0 -0.81 207 207
mol:Ca2+ -0.076 0.19 -10000 0 -0.58 72 72
IGF1R -0.061 0.21 -10000 0 -0.64 96 96
E2/ER alpha (dimer)/Striatin -0.1 0.2 -10000 0 -0.43 224 224
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis 0.16 0.34 0.76 207 -10000 0 207
RhoA/GTP -0.083 0.14 -10000 0 -0.62 6 6
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.14 0.21 -10000 0 -0.48 212 212
regulation of stress fiber formation 0.029 0.13 0.45 8 -10000 0 8
E2/ERA-ERB (dimer) -0.1 0.2 -10000 0 -0.43 231 231
KRAS 0.013 0.016 -10000 0 -0.46 1 1
G13/GTP -0.086 0.18 -10000 0 -0.39 213 213
pseudopodium formation -0.029 0.13 -10000 0 -0.45 8 8
E2/ER alpha (dimer)/PELP1 -0.095 0.19 -10000 0 -0.43 213 213
GRB2 0.013 0.016 -10000 0 -0.46 1 1
GNG2 0.011 0.033 -10000 0 -0.53 3 3
GNAO1 -0.076 0.21 -10000 0 -0.53 139 139
HRAS 0.009 0.05 -10000 0 -0.63 5 5
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.11 0.24 -10000 0 -0.51 210 210
E2/ER beta (dimer) -0.002 0.076 -10000 0 -0.46 22 22
mol:GDP -0.13 0.21 -10000 0 -0.46 222 222
mol:NADP -0.11 0.24 -10000 0 -0.51 210 210
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
mol:IP3 -0.08 0.2 -10000 0 -0.62 72 72
IGF-1R heterotetramer -0.061 0.21 -10000 0 -0.63 96 96
PLCB1 -0.086 0.21 -10000 0 -0.63 74 74
PLCB2 -0.059 0.18 -10000 0 -0.63 59 59
IGF1 -0.07 0.21 -10000 0 -0.59 115 115
mol:L-citrulline -0.11 0.24 -10000 0 -0.51 210 210
RHOA 0.013 0 -10000 0 -10000 0 0
Gai/GDP -0.047 0.19 -10000 0 -0.74 48 48
JNK cascade -0.002 0.076 -10000 0 -0.46 22 22
BCAR1 0.013 0 -10000 0 -10000 0 0
ESR2 -0.003 0.1 -10000 0 -0.61 22 22
GNAQ 0.007 0.062 -10000 0 -0.67 7 7
ESR1 -0.16 0.3 -10000 0 -0.67 213 213
Gq family/GDP/Gbeta gamma -0.01 0.12 -10000 0 -0.55 21 21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 -0.046 0.14 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.14 0.21 -10000 0 -0.48 212 212
GNAZ -0.002 0.099 -10000 0 -0.65 19 19
E2/ER alpha (dimer) -0.12 0.22 -10000 0 -0.5 213 213
STRN 0.003 0.085 -10000 0 -0.67 13 13
GNAL -0.022 0.14 -10000 0 -0.56 51 51
PELP1 0.013 0 -10000 0 -10000 0 0
MAPK11 0.004 0.08 -10000 0 -0.4 30 30
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.003 0.077 -10000 0 -0.54 16 16
HBEGF -0.11 0.21 -10000 0 -0.51 94 94
cAMP biosynthetic process -0.11 0.18 -10000 0 -0.38 239 239
SRC -0.093 0.21 -10000 0 -0.4 213 213
PI3K 0.018 0.023 -10000 0 -0.32 4 4
GNB1 0.013 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.11 0.18 -10000 0 -0.41 208 208
SOS1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.16 0.22 -10000 0 -0.5 221 221
Gs family/GTP -0.11 0.18 -10000 0 -0.38 239 239
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.019 0.048 -10000 0 -0.39 10 10
vasodilation -0.1 0.23 -10000 0 -0.49 210 210
mol:DAG -0.08 0.2 -10000 0 -0.62 72 72
Gs family/GDP/Gbeta gamma -0.12 0.18 -10000 0 -0.4 210 210
MSN -0.033 0.14 -10000 0 -0.49 8 8
Gq family/GTP -0.067 0.19 -10000 0 -0.65 60 60
mol:PI-3-4-5-P3 -0.17 0.35 -10000 0 -0.78 207 207
NRAS 0.007 0.062 -10000 0 -0.62 8 8
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.1 0.23 0.49 210 -10000 0 210
GRB2/SOS1 0.019 0.012 -10000 0 -0.32 1 1
RhoA/GDP -0.12 0.19 -10000 0 -0.43 222 222
NOS3 -0.12 0.26 -10000 0 -0.54 210 210
GNA11 0.01 0.047 -10000 0 -0.67 4 4
MAPKKK cascade -0.13 0.28 -10000 0 -0.6 213 213
E2/ER alpha (dimer)/PELP1/Src -0.14 0.22 -10000 0 -0.5 213 213
ruffle organization -0.029 0.13 -10000 0 -0.45 8 8
ROCK2 -0.043 0.15 -10000 0 -0.56 7 7
GNA14 -0.054 0.19 -10000 0 -0.57 97 97
GNA15 -0.002 0.096 -10000 0 -0.61 20 20
GNA13 0.013 0 -10000 0 -10000 0 0
MMP9 -0.13 0.22 -10000 0 -0.56 95 95
MMP2 -0.098 0.21 -10000 0 -0.56 67 67
HIF-1-alpha transcription factor network

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
PKM2 -0.29 0.5 -9999 0 -1.2 123 123
HDAC7 0.015 0.002 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.24 0.36 -9999 0 -0.91 100 100
SMAD4 0.014 0.024 -9999 0 -0.67 1 1
ID2 -0.29 0.5 -9999 0 -1.2 125 125
AP1 -0.039 0.15 -9999 0 -0.41 114 114
ABCG2 -0.3 0.52 -9999 0 -1.2 132 132
HIF1A -0.041 0.12 -9999 0 -0.72 15 15
TFF3 -0.38 0.57 -9999 0 -1.3 185 185
GATA2 -0.089 0.23 -9999 0 -0.61 139 139
AKT1 -0.031 0.083 -9999 0 -10000 0 0
response to hypoxia -0.05 0.087 -9999 0 -0.26 7 7
MCL1 -0.29 0.5 -9999 0 -1.2 122 122
NDRG1 -0.3 0.51 -9999 0 -1.2 130 130
SERPINE1 -0.3 0.51 -9999 0 -1.2 128 128
FECH -0.29 0.5 -9999 0 -1.2 125 125
FURIN -0.29 0.5 -9999 0 -1.2 129 129
NCOA2 -0.016 0.14 -9999 0 -0.68 34 34
EP300 -0.026 0.12 -9999 0 -0.35 31 31
HMOX1 -0.29 0.5 -9999 0 -1.2 131 131
BHLHE40 -0.29 0.51 -9999 0 -1.2 126 126
BHLHE41 -0.3 0.51 -9999 0 -1.2 129 129
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.038 0.091 -9999 0 -0.52 16 16
ENG 0.005 0.12 -9999 0 -0.52 10 10
JUN 0.009 0.049 -9999 0 -0.52 7 7
RORA -0.29 0.5 -9999 0 -1.2 125 125
ABCB1 -0.16 0.34 -9999 0 -1.3 58 58
TFRC -0.29 0.5 -9999 0 -1.2 126 126
CXCR4 -0.29 0.5 -9999 0 -1.2 127 127
TF -0.4 0.56 -9999 0 -1.2 186 186
CITED2 -0.29 0.5 -9999 0 -1.2 122 122
HIF1A/ARNT -0.38 0.59 -9999 0 -1.4 142 142
LDHA -0.037 0.047 -9999 0 -10000 0 0
ETS1 -0.29 0.5 -9999 0 -1.2 130 130
PGK1 -0.29 0.5 -9999 0 -1.2 122 122
NOS2 -0.3 0.51 -9999 0 -1.2 128 128
ITGB2 -0.29 0.5 -9999 0 -1.2 134 134
ALDOA -0.29 0.5 -9999 0 -1.2 128 128
Cbp/p300/CITED2 -0.3 0.49 -9999 0 -1.2 118 118
FOS -0.062 0.2 -9999 0 -0.55 112 112
HK2 -0.29 0.5 -9999 0 -1.2 127 127
SP1 0.016 0.022 -9999 0 -10000 0 0
GCK -0.092 0.34 -9999 0 -1.4 43 43
HK1 -0.29 0.5 -9999 0 -1.2 125 125
NPM1 -0.29 0.5 -9999 0 -1.2 125 125
EGLN1 -0.29 0.5 -9999 0 -1.2 125 125
CREB1 0.021 0 -9999 0 -10000 0 0
PGM1 -0.29 0.5 -9999 0 -1.2 126 126
SMAD3 0.011 0.05 -9999 0 -0.63 5 5
EDN1 -0.14 0.36 -9999 0 -1.1 72 72
IGFBP1 -0.31 0.5 -9999 0 -1.2 132 132
VEGFA -0.16 0.35 -9999 0 -0.88 52 52
HIF1A/JAB1 -0.029 0.079 -9999 0 -0.55 15 15
CP -0.42 0.56 -9999 0 -1.2 190 190
CXCL12 -0.3 0.51 -9999 0 -1.2 128 128
COPS5 0.011 0.017 -9999 0 -0.46 1 1
SMAD3/SMAD4 0.019 0.042 -9999 0 -0.47 6 6
BNIP3 -0.29 0.5 -9999 0 -1.2 122 122
EGLN3 -0.3 0.52 -9999 0 -1.2 131 131
CA9 -0.43 0.55 -9999 0 -1.2 182 182
TERT -0.32 0.52 -9999 0 -1.2 144 144
ENO1 -0.29 0.5 -9999 0 -1.2 125 125
PFKL -0.29 0.5 -9999 0 -1.2 125 125
NCOA1 0.012 0.024 -9999 0 -0.67 1 1
ADM -0.31 0.52 -9999 0 -1.2 135 135
ARNT -0.027 0.072 -9999 0 -10000 0 0
HNF4A -0.005 0.065 -9999 0 -0.46 15 15
ADFP -0.31 0.48 -9999 0 -1.2 139 139
SLC2A1 -0.16 0.35 -9999 0 -0.91 51 51
LEP -0.4 0.54 -9999 0 -1.2 173 173
HIF1A/ARNT/Cbp/p300 -0.25 0.36 -9999 0 -0.94 104 104
EPO -0.2 0.36 -9999 0 -0.95 71 71
CREBBP -0.027 0.12 -9999 0 -0.35 37 37
HIF1A/ARNT/Cbp/p300/HDAC7 -0.23 0.36 -9999 0 -0.94 90 90
PFKFB3 -0.29 0.5 -9999 0 -1.2 132 132
NT5E -0.29 0.51 -9999 0 -1.2 126 126
EGFR-dependent Endothelin signaling events

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
HRAS 0.009 0.05 -9999 0 -0.63 5 5
EGFR -0.076 0.22 -9999 0 -0.57 129 129
EGF/EGFR -0.15 0.21 -9999 0 -0.43 247 247
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.093 0.19 -9999 0 -0.39 209 209
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.002 0.1 -9999 0 -0.66 19 19
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.14 0.27 -9999 0 -0.61 201 201
EGF/EGFR dimer/SHC -0.12 0.22 -9999 0 -0.46 209 209
mol:GDP -0.12 0.17 -9999 0 -0.38 209 209
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.035 0.17 -9999 0 -0.6 66 66
GRB2/SOS1 0.019 0.012 -9999 0 -0.32 1 1
HRAS/GTP -0.11 0.16 -9999 0 -0.53 32 32
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP -0.11 0.16 -9999 0 -0.54 32 32
FRAP1 -0.09 0.18 -9999 0 -0.37 209 209
EGF/EGFR dimer -0.16 0.25 -9999 0 -0.47 298 298
SOS1 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0.016 -9999 0 -0.46 1 1
ETA receptor/Endothelin-1 -0.027 0.15 -9999 0 -0.47 80 80
Noncanonical Wnt signaling pathway

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
NFATC2 -0.044 0.19 -9999 0 -0.65 72 72
GNB1/GNG2 -0.11 0.23 -9999 0 -0.58 115 115
mol:DAG -0.096 0.21 -9999 0 -0.52 113 113
PLCG1 -0.1 0.22 -9999 0 -0.55 113 113
YES1 -0.13 0.24 -9999 0 -0.61 118 118
FZD3 -0.009 0.12 -9999 0 -0.66 28 28
FZD6 -0.018 0.14 -9999 0 -0.66 39 39
G protein -0.1 0.22 -9999 0 -0.56 114 114
MAP3K7 -0.084 0.19 -9999 0 -0.51 92 92
mol:Ca2+ -0.093 0.2 -9999 0 -0.5 113 113
mol:IP3 -0.096 0.21 -9999 0 -0.52 113 113
NLK -0.005 0.011 -9999 0 -10000 0 0
GNB1 0.013 0 -9999 0 -10000 0 0
CAMK2A -0.098 0.21 -9999 0 -0.53 112 112
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.14 0.25 -9999 0 -0.46 233 233
CSNK1A1 0.013 0 -9999 0 -10000 0 0
GNAS -0.13 0.24 -9999 0 -0.6 119 119
GO:0007205 -0.094 0.2 -9999 0 -0.54 96 96
WNT6 -0.11 0.23 -9999 0 -0.52 195 195
WNT4 -0.075 0.22 -9999 0 -0.61 119 119
NFAT1/CK1 alpha -0.12 0.24 -9999 0 -0.6 124 124
GNG2 0.011 0.033 -9999 0 -0.53 3 3
WNT5A -0.041 0.18 -9999 0 -0.61 73 73
WNT11 -0.079 0.21 -9999 0 -0.54 139 139
CDC42 -0.11 0.23 -9999 0 -0.58 117 117
LPA4-mediated signaling events

Figure S15.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S15.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.008 0.07 -9999 0 -0.42 22 22
ADCY5 -0.13 0.2 -9999 0 -0.37 320 320
ADCY6 0.013 0.051 -9999 0 -0.43 11 11
ADCY7 0.012 0.058 -9999 0 -0.43 14 14
ADCY1 -0.081 0.17 -9999 0 -0.35 228 228
ADCY2 -0.086 0.18 -9999 0 -0.37 226 226
ADCY3 0.013 0.052 -9999 0 -0.39 13 13
ADCY8 -0.008 0.079 -9999 0 -0.3 56 56
PRKCE 0.005 0.056 -9999 0 -0.51 10 10
ADCY9 0.004 0.087 -9999 0 -0.48 25 25
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.075 0.13 -9999 0 -0.39 70 70
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.24 0.25 -9999 0 -0.51 315 315
SMAD6-7/SMURF1 0.022 0.045 -9999 0 -0.36 11 11
NOG -0.058 0.19 -9999 0 -0.55 105 105
SMAD9 -0.063 0.16 -9999 0 -0.74 36 36
SMAD4 0.012 0.024 -9999 0 -0.67 1 1
SMAD5 -0.12 0.17 -9999 0 -0.49 76 76
BMP7/USAG1 -0.24 0.29 -9999 0 -0.5 419 419
SMAD5/SKI -0.11 0.16 -9999 0 -0.52 52 52
SMAD1 0.009 0.036 -9999 0 -10000 0 0
BMP2 -0.028 0.15 -9999 0 -0.54 63 63
SMAD1/SMAD1/SMAD4 -0.003 0.031 -9999 0 -10000 0 0
BMPR1A 0.012 0.033 -9999 0 -0.67 2 2
BMPR1B -0.29 0.29 -9999 0 -0.54 459 459
BMPR1A-1B/BAMBI -0.22 0.24 -9999 0 -0.52 270 270
AHSG 0 0 -9999 0 -10000 0 0
CER1 0 0 -9999 0 -10000 0 0
BMP2-4/CER1 -0.058 0.17 -9999 0 -0.51 85 85
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.11 0.17 -9999 0 -0.52 68 68
BMP2-4 (homodimer) -0.068 0.2 -9999 0 -0.58 85 85
RGMB 0.012 0.033 -9999 0 -0.67 2 2
BMP6/BMPR2/BMPR1A-1B -0.15 0.18 -9999 0 -0.4 193 193
RGMA -0.063 0.19 -9999 0 -0.52 119 119
SMURF1 0.013 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.13 0.18 -9999 0 -0.47 120 120
BMP2-4/USAG1 -0.19 0.26 -9999 0 -0.52 257 257
SMAD6/SMURF1/SMAD5 -0.11 0.16 -9999 0 -0.48 65 65
SOSTDC1 -0.21 0.29 -9999 0 -0.57 319 319
BMP7/BMPR2/BMPR1A-1B -0.22 0.23 -9999 0 -0.49 272 272
SKI 0.013 0.016 -9999 0 -0.46 1 1
BMP6 (homodimer) -0.008 0.11 -9999 0 -0.53 33 33
HFE2 -0.001 0.053 -9999 0 -0.46 11 11
ZFYVE16 0.013 0 -9999 0 -10000 0 0
MAP3K7 0.013 0.016 -9999 0 -0.46 1 1
BMP2-4/CHRD -0.11 0.25 -9999 0 -0.62 130 130
SMAD5/SMAD5/SMAD4 -0.11 0.16 -9999 0 -0.51 53 53
MAPK1 0.013 0 -9999 0 -10000 0 0
TAK1/TAB family -0.11 0.14 -9999 0 -0.48 74 74
BMP7 (homodimer) -0.13 0.26 -9999 0 -0.56 213 213
NUP214 0.013 0 -9999 0 -10000 0 0
BMP6/FETUA -0.006 0.079 -9999 0 -0.38 33 33
SMAD1/SKI 0.017 0.035 -9999 0 -10000 0 0
SMAD6 0.007 0.064 -9999 0 -0.6 9 9
CTDSP2 0.013 0.016 -9999 0 -0.46 1 1
BMP2-4/FETUA -0.058 0.17 -9999 0 -0.51 85 85
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.051 0.2 -9999 0 -0.63 84 84
BMPR2 (homodimer) 0.012 0.024 -9999 0 -0.67 1 1
GADD34/PP1CA 0.027 0.01 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.2 0.21 -9999 0 -0.39 460 460
CHRDL1 -0.16 0.28 -9999 0 -0.59 243 243
ENDOFIN/SMAD1 0.017 0.034 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 0 0.036 -9999 0 -10000 0 0
SMAD6/SMURF1 0.013 0 -9999 0 -10000 0 0
BAMBI -0.081 0.23 -9999 0 -0.62 125 125
SMURF2 0.012 0.029 -9999 0 -0.56 2 2
BMP2-4/CHRDL1 -0.16 0.24 -9999 0 -0.5 222 222
BMP2-4/GREM1 -0.088 0.23 -9999 0 -0.55 130 130
SMAD7 0.012 0.029 -9999 0 -0.56 2 2
SMAD8A/SMAD8A/SMAD4 -0.052 0.16 -9999 0 -0.68 37 37
SMAD1/SMAD6 0.017 0.034 -9999 0 -10000 0 0
TAK1/SMAD6 0.019 0.012 -9999 0 -0.32 1 1
BMP7 -0.13 0.26 -9999 0 -0.56 213 213
BMP6 -0.008 0.11 -9999 0 -0.53 33 33
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.1 0.16 -9999 0 -0.48 76 76
PPM1A 0.013 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.016 0.038 -9999 0 -0.42 1 1
SMAD7/SMURF1 0.019 0.021 -9999 0 -0.41 2 2
CTDSPL 0.013 0 -9999 0 -10000 0 0
PPP1CA 0.013 0 -9999 0 -10000 0 0
XIAP 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
PPP1R15A 0.013 0.016 -9999 0 -0.46 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.17 0.25 -9999 0 -0.58 158 158
CHRD -0.086 0.23 -9999 0 -0.59 139 139
BMPR2 0.012 0.024 -9999 0 -0.67 1 1
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.13 0.19 -9999 0 -0.49 127 127
BMP4 -0.067 0.21 -9999 0 -0.59 112 112
FST -0.061 0.2 -9999 0 -0.59 104 104
BMP2-4/NOG -0.093 0.21 -9999 0 -0.51 133 133
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.2 0.22 -9999 0 -0.46 272 272
Effects of Botulinum toxin

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
STX1A 0.003 0.054 -9999 0 -0.33 21 21
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.11 0.2 -9999 0 -0.41 256 256
STXBP1 0.007 0.064 -9999 0 -0.65 8 8
ACh/CHRNA1 -0.063 0.16 -9999 0 -0.44 126 126
RAB3GAP2/RIMS1/UNC13B -0.085 0.18 -9999 0 -0.43 127 127
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.16 0.27 -9999 0 -0.56 248 248
mol:ACh -0.01 0.044 -9999 0 -0.14 70 70
RAB3GAP2 0.013 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.096 0.14 -9999 0 -0.43 45 45
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.062 0.16 -9999 0 -0.43 126 126
UNC13B 0.007 0.059 -9999 0 -0.5 11 11
CHRNA1 -0.082 0.23 -9999 0 -0.62 126 126
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.15 0.19 -9999 0 -0.37 337 337
SNAP25 -0.034 0.096 -9999 0 -0.23 148 148
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.21 0.28 -9999 0 -0.55 337 337
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 0.007 0.063 -9999 0 -0.32 28 28
STX1A/SNAP25 fragment 1/VAMP2 -0.096 0.14 -9999 0 -0.43 45 45
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.047 0.18 -10000 0 -0.68 55 55
NFATC2 -0.1 0.3 -10000 0 -0.83 81 81
NFATC3 -0.014 0.077 0.28 1 -0.31 2 3
CD40LG -0.3 0.46 -10000 0 -1 179 179
ITCH 0.01 0.087 -10000 0 -10000 0 0
CBLB 0.01 0.087 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.35 0.51 -10000 0 -1.2 189 189
JUNB 0.007 0.056 -10000 0 -0.5 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.038 0.089 -10000 0 -10000 0 0
T cell anergy -0.029 0.15 -10000 0 -0.49 42 42
TLE4 -0.063 0.26 -10000 0 -0.88 49 49
Jun/NFAT1-c-4/p21SNFT -0.18 0.38 -10000 0 -1.1 86 86
AP-1/NFAT1-c-4 -0.31 0.51 -10000 0 -1.2 153 153
IKZF1 -0.073 0.28 -10000 0 -0.9 56 56
T-helper 2 cell differentiation -0.19 0.33 -10000 0 -0.75 177 177
AP-1/NFAT1 -0.12 0.25 -10000 0 -0.66 99 99
CALM1 0.003 0.058 -10000 0 -10000 0 0
EGR2 -0.12 0.35 -10000 0 -1.1 52 52
EGR3 -0.16 0.44 -10000 0 -1.4 76 76
NFAT1/FOXP3 -0.12 0.31 -10000 0 -0.8 101 101
EGR1 -0.032 0.15 -10000 0 -0.53 68 68
JUN -0.004 0.054 -10000 0 -0.52 7 7
EGR4 -0.035 0.14 -10000 0 -0.48 76 76
mol:Ca2+ -0.012 0.062 -10000 0 -10000 0 0
GBP3 -0.1 0.32 -10000 0 -0.87 99 99
FOSL1 -0.042 0.16 -10000 0 -0.48 94 94
NFAT1-c-4/MAF/IRF4 -0.19 0.4 -10000 0 -1.1 103 103
DGKA -0.058 0.24 -10000 0 -0.76 54 54
CREM 0.013 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.16 0.37 -10000 0 -1.1 85 85
CTLA4 -0.15 0.37 -10000 0 -0.9 128 128
NFAT1-c-4 (dimer)/EGR1 -0.17 0.39 -10000 0 -1.1 93 93
NFAT1-c-4 (dimer)/EGR4 -0.18 0.38 -10000 0 -1.1 82 82
FOS -0.077 0.2 -10000 0 -0.57 112 112
IFNG -0.29 0.44 -10000 0 -1 182 182
T cell activation -0.1 0.24 -10000 0 -0.75 54 54
MAF 0.011 0.037 -10000 0 -0.6 3 3
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.094 0.27 0.83 59 -10000 0 59
TNF -0.2 0.39 -10000 0 -1 108 108
FASLG -0.27 0.58 -10000 0 -1.5 121 121
TBX21 -0.084 0.22 -10000 0 -0.6 121 121
BATF3 0.002 0.084 -10000 0 -0.59 16 16
PRKCQ -0.087 0.23 -10000 0 -0.59 140 140
PTPN1 -0.059 0.23 -10000 0 -0.74 54 54
NFAT1-c-4/ICER1 -0.17 0.35 -10000 0 -1.1 83 83
GATA3 -0.096 0.25 -10000 0 -0.67 134 134
T-helper 1 cell differentiation -0.26 0.44 -10000 0 -0.98 185 185
IL2RA -0.31 0.45 -10000 0 -1.1 173 173
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.055 0.22 -10000 0 -0.81 39 39
E2F1 -0.001 0.11 -10000 0 -0.65 25 25
PPARG -0.008 0.1 -10000 0 -0.5 36 36
SLC3A2 -0.055 0.23 -10000 0 -0.78 44 44
IRF4 -0.097 0.23 -10000 0 -0.57 159 159
PTGS2 -0.3 0.45 -10000 0 -1.1 163 163
CSF2 -0.27 0.42 -10000 0 -0.98 153 153
JunB/Fra1/NFAT1-c-4 -0.16 0.37 -10000 0 -1.1 83 83
IL4 -0.2 0.35 -10000 0 -0.79 176 176
IL5 -0.27 0.41 -10000 0 -0.96 155 155
IL2 -0.11 0.24 -10000 0 -0.77 53 53
IL3 -0.054 0.055 -10000 0 -10000 0 0
RNF128 -0.044 0.22 -10000 0 -0.51 136 136
NFATC1 -0.095 0.28 -10000 0 -0.84 58 58
CDK4 0.069 0.19 0.68 16 -10000 0 16
PTPRK -0.082 0.28 -10000 0 -0.89 68 68
IL8 -0.32 0.45 -10000 0 -1 174 174
POU2F1 0.013 0.016 -10000 0 -0.46 1 1
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.18 0.32 -10000 0 -0.93 70 70
PCK1 -0.43 0.53 -10000 0 -1.4 175 175
HNF4A -0.2 0.34 -10000 0 -1 61 61
KCNJ11 -0.26 0.48 -10000 0 -1.2 130 130
AKT1 -0.1 0.15 -10000 0 -0.42 22 22
response to starvation -0.005 0.022 -10000 0 -10000 0 0
DLK1 -0.29 0.46 -10000 0 -1.1 150 150
NKX2-1 -0.018 0.16 0.41 15 -0.39 26 41
ACADM -0.18 0.32 -10000 0 -0.92 77 77
TAT -0.41 0.47 -10000 0 -1.2 175 175
CEBPB 0.006 0.058 -10000 0 -0.47 12 12
CEBPA 0.006 0.068 -10000 0 -0.61 10 10
TTR -0.3 0.31 -10000 0 -0.9 118 118
PKLR -0.18 0.32 -10000 0 -0.93 74 74
APOA1 -0.23 0.39 -10000 0 -1.2 62 62
CPT1C -0.19 0.34 -10000 0 -0.97 86 86
ALAS1 -0.069 0.16 -10000 0 -0.89 1 1
TFRC -0.27 0.28 -10000 0 -0.8 88 88
FOXF1 -0.009 0.11 -10000 0 -0.57 32 32
NF1 0.017 0.044 -10000 0 -0.61 4 4
HNF1A (dimer) 0.007 0.056 -10000 0 -0.47 11 11
CPT1A -0.18 0.33 -10000 0 -0.93 80 80
HMGCS1 -0.18 0.32 -10000 0 -0.92 74 74
NR3C1 -0.025 0.074 -10000 0 -0.72 3 3
CPT1B -0.18 0.32 -10000 0 -0.93 76 76
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.013 0 -10000 0 -10000 0 0
GCK -0.21 0.38 -10000 0 -1 105 105
CREB1 -0.02 0.06 -10000 0 -10000 0 0
IGFBP1 -0.1 0.18 -10000 0 -0.62 17 17
PDX1 -0.08 0.15 -10000 0 -0.4 41 41
UCP2 -0.19 0.35 -10000 0 -0.99 83 83
ALDOB -0.2 0.37 -10000 0 -1 92 92
AFP -0.36 0.4 -10000 0 -0.82 269 269
BDH1 -0.18 0.33 -10000 0 -0.99 69 69
HADH -0.18 0.34 -10000 0 -0.98 68 68
F2 -0.21 0.36 -10000 0 -1 74 74
HNF1A 0.007 0.056 -10000 0 -0.48 11 11
G6PC -0.12 0.13 -10000 0 -0.38 87 87
SLC2A2 -0.11 0.19 -10000 0 -0.48 71 71
INS -0.006 0.023 -10000 0 -10000 0 0
FOXA1 -0.17 0.27 -10000 0 -0.7 145 145
FOXA3 -0.29 0.28 -10000 0 -0.63 278 278
FOXA2 -0.22 0.38 -10000 0 -1 102 102
ABCC8 -0.34 0.52 -10000 0 -1.2 193 193
ALB -0.38 0.41 -10000 0 -0.83 294 294
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.006 0.063 -9999 0 -0.42 13 13
NFATC2 -0.038 0.13 -9999 0 -0.45 69 69
NFATC3 0.001 0.035 -9999 0 -10000 0 0
CD40LG -0.21 0.36 -9999 0 -0.75 213 213
PTGS2 -0.21 0.35 -9999 0 -0.7 229 229
JUNB 0.007 0.056 -9999 0 -0.5 10 10
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.01 0.015 -9999 0 -10000 0 0
CaM/Ca2+ -0.01 0.015 -9999 0 -10000 0 0
CALM1 0.008 0.011 -9999 0 -10000 0 0
JUN 0.004 0.05 -9999 0 -0.52 7 7
mol:Ca2+ -0.01 0.014 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.011 -9999 0 -0.28 1 1
FOSL1 -0.042 0.16 -9999 0 -0.48 94 94
CREM 0.013 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.12 0.17 -9999 0 -0.53 74 74
FOS -0.068 0.2 -9999 0 -0.56 112 112
IFNG -0.22 0.36 -9999 0 -0.69 262 262
AP-1/NFAT1-c-4 -0.22 0.39 -9999 0 -0.8 206 206
FASLG -0.21 0.36 -9999 0 -0.74 211 211
NFAT1-c-4/ICER1 -0.061 0.14 -9999 0 -0.49 50 50
IL2RA -0.22 0.37 -9999 0 -0.76 215 215
FKBP12/FK506 0.009 0.012 -9999 0 -0.32 1 1
CSF2 -0.18 0.32 -9999 0 -0.67 190 190
JunB/Fra1/NFAT1-c-4 -0.095 0.15 -9999 0 -0.5 64 64
IL4 -0.18 0.31 -9999 0 -0.64 206 206
IL2 -0.012 0.058 -9999 0 -0.41 13 13
IL3 -0.021 0.024 -9999 0 -10000 0 0
FKBP1A 0.013 0.016 -9999 0 -0.46 1 1
BATF3 0.002 0.084 -9999 0 -0.59 16 16
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.013 0.016 -9999 0 -0.46 1 1
p75(NTR)-mediated 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
Sortilin/TRAF6 0.017 0.035 -9999 0 -0.43 5 5
Necdin/E2F1 -0.007 0.11 -9999 0 -0.48 45 45
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.059 0.18 -9999 0 -0.4 151 151
NGF (dimer)/p75(NTR)/BEX1 -0.19 0.24 -9999 0 -0.52 217 217
NT-4/5 (dimer)/p75(NTR) -0.14 0.25 -9999 0 -0.49 256 256
IKBKB 0.01 0.04 -9999 0 -0.5 5 5
AKT1 -0.042 0.16 -9999 0 -0.38 125 125
IKBKG 0.013 0 -9999 0 -10000 0 0
BDNF -0.067 0.19 -9999 0 -0.51 130 130
MGDIs/NGR/p75(NTR)/LINGO1 -0.088 0.2 -9999 0 -0.47 129 129
FURIN 0.01 0.039 -9999 0 -0.46 6 6
proBDNF (dimer)/p75(NTR)/Sortilin -0.094 0.2 -9999 0 -0.47 125 125
LINGO1 -0.05 0.17 -9999 0 -0.5 104 104
Sortilin/TRAF6/NRIF -0.007 0.045 -9999 0 -0.63 1 1
proBDNF (dimer) -0.067 0.19 -9999 0 -0.51 130 130
NTRK1 -0.048 0.18 -9999 0 -0.56 90 90
RTN4R 0.002 0.08 -9999 0 -0.56 16 16
neuron apoptosis -0.067 0.18 -9999 0 -0.58 40 40
IRAK1 0.012 0.028 -9999 0 -0.46 3 3
SHC1 -0.065 0.18 -9999 0 -0.45 124 124
ARHGDIA 0.013 0 -9999 0 -10000 0 0
RhoA/GTP 0.01 0 -9999 0 -10000 0 0
Gamma Secretase 0.034 0.046 -9999 0 -0.35 11 11
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.056 0.17 -9999 0 -0.41 130 130
MAGEH1 0.008 0.058 -9999 0 -0.67 6 6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.062 0.18 -9999 0 -0.43 138 138
Mammalian IAPs/DIABLO 0.013 0.083 -9999 0 -0.38 25 25
proNGF (dimer) -0.023 0.14 -9999 0 -0.57 52 52
MAGED1 0.008 0.06 -9999 0 -0.64 7 7
APP 0.009 0.055 -9999 0 -0.64 6 6
NT-4/5 (dimer) -0.093 0.23 -9999 0 -0.6 145 145
ZNF274 0.011 0.033 -9999 0 -0.53 3 3
RhoA/GDP/RHOGDI -0.048 0.16 -9999 0 -0.38 124 124
NGF -0.023 0.14 -9999 0 -0.57 52 52
cell cycle arrest -0.029 0.17 -9999 0 -0.36 126 126
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.026 0.12 -9999 0 -0.54 10 10
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.11 0.22 -9999 0 -0.48 189 189
NCSTN 0.013 0 -9999 0 -10000 0 0
mol:GTP -0.09 0.2 -9999 0 -0.48 133 133
PSENEN 0.013 0 -9999 0 -10000 0 0
mol:ceramide -0.054 0.16 -9999 0 -0.4 126 126
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.011 0.11 -9999 0 -0.44 10 10
p75(NTR)/beta APP -0.065 0.18 -9999 0 -0.44 154 154
BEX1 -0.19 0.27 -9999 0 -0.53 319 319
mol:GDP -0.074 0.18 -9999 0 -0.39 191 191
NGF (dimer) -0.078 0.18 -9999 0 -0.43 138 138
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.072 0.18 -9999 0 -0.43 129 129
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
RAC1/GTP -0.056 0.16 -9999 0 -0.39 124 124
MYD88 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.09 0.2 -9999 0 -0.48 133 133
RHOB -0.01 0.12 -9999 0 -0.67 29 29
RHOA 0.013 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 0.005 0.086 -9999 0 -0.47 26 26
NT3 (dimer) -0.082 0.21 -9999 0 -0.54 145 145
TP53 -0.061 0.17 -9999 0 -0.61 22 22
PRDM4 -0.053 0.17 -9999 0 -0.4 126 126
BDNF (dimer) -0.16 0.25 -9999 0 -0.54 202 202
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
SORT1 0.01 0.044 -9999 0 -0.62 4 4
activation of caspase activity -0.088 0.16 -9999 0 -0.4 151 151
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.053 0.17 -9999 0 -0.41 126 126
RHOC 0.012 0.024 -9999 0 -0.67 1 1
XIAP 0.013 0 -9999 0 -10000 0 0
MAPK10 -0.082 0.19 -9999 0 -0.55 65 65
DIABLO 0.013 0 -9999 0 -10000 0 0
SMPD2 -0.055 0.17 -9999 0 -0.4 126 126
APH1B 0.003 0.081 -9999 0 -0.64 13 13
APH1A 0.013 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.067 0.18 -9999 0 -0.45 126 126
PSEN1 0.013 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.019 0.018 -9999 0 -0.5 1 1
NT3 (dimer)/p75(NTR) -0.13 0.24 -9999 0 -0.46 262 262
MAPK8 -0.044 0.17 -9999 0 -0.52 35 35
MAPK9 -0.044 0.17 -9999 0 -0.52 35 35
APAF1 0.012 0.024 -9999 0 -0.67 1 1
NTF3 -0.082 0.21 -9999 0 -0.54 145 145
NTF4 -0.093 0.23 -9999 0 -0.6 145 145
NDN -0.003 0.1 -9999 0 -0.66 20 20
RAC1/GDP 0.01 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.094 0.17 -9999 0 -0.62 37 37
p75 CTF/Sortilin/TRAF6/NRIF 0.031 0.034 -9999 0 -0.38 4 4
RhoA-B-C/GTP -0.09 0.2 -9999 0 -0.48 133 133
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.067 0.17 -9999 0 -0.61 23 23
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.077 0.18 -9999 0 -0.43 125 125
PRKACB -0.028 0.14 -9999 0 -0.49 70 70
proBDNF (dimer)/p75 ECD -0.039 0.14 -9999 0 -0.36 130 130
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.023 0.14 -9999 0 -0.56 54 54
BIRC2 0.013 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.034 0.19 -9999 0 -0.44 91 91
BAD -0.053 0.17 -9999 0 -0.5 51 51
RIPK2 0.012 0.028 -9999 0 -0.46 3 3
NGFR -0.096 0.24 -9999 0 -0.6 150 150
CYCS -0.046 0.16 -9999 0 -0.37 132 132
ADAM17 0.013 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.052 0.17 -9999 0 -0.41 124 124
BCL2L11 -0.053 0.17 -9999 0 -0.5 51 51
BDNF (dimer)/p75(NTR) -0.12 0.22 -9999 0 -0.42 261 261
PI3K -0.052 0.17 -9999 0 -0.41 125 125
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.053 0.17 -9999 0 -0.41 126 126
NDNL2 0.013 0.016 -9999 0 -0.46 1 1
YWHAE 0.012 0.024 -9999 0 -0.67 1 1
PRKCI 0.013 0.016 -9999 0 -0.46 1 1
NGF (dimer)/p75(NTR) -0.087 0.21 -9999 0 -0.45 191 191
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.056 0.17 -9999 0 -0.4 132 132
TRAF6 0.013 0.016 -9999 0 -0.46 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCZ 0.011 0.041 -9999 0 -0.67 3 3
PLG 0 0 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.085 0.19 -9999 0 -0.44 150 150
SQSTM1 0.012 0.023 -9999 0 -0.46 2 2
NGFRAP1 -0.016 0.14 -9999 0 -0.67 36 36
CASP3 -0.047 0.16 -9999 0 -0.46 51 51
E2F1 -0.006 0.11 -9999 0 -0.65 25 25
CASP9 0.013 0 -9999 0 -10000 0 0
IKK complex -0.064 0.12 -9999 0 -0.55 19 19
NGF (dimer)/TRKA -0.052 0.17 -9999 0 -0.42 138 138
MMP7 -0.13 0.26 -9999 0 -0.57 205 205
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.044 0.16 -9999 0 -0.38 127 127
MMP3 -0.091 0.24 -9999 0 -0.61 141 141
APAF-1/Caspase 9 -0.066 0.12 -9999 0 -0.49 25 25
Endothelins

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
AKT1 0.018 0.25 -10000 0 -0.76 51 51
PTK2B 0.01 0.047 -10000 0 -0.59 5 5
mol:Ca2+ 0.026 0.2 -10000 0 -0.83 25 25
EDN1 0.003 0.22 -10000 0 -0.61 70 70
EDN3 -0.17 0.27 -10000 0 -0.56 259 259
EDN2 -0.1 0.24 -10000 0 -0.6 162 162
HRAS/GDP -0.022 0.22 -10000 0 -0.58 71 71
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.004 0.19 -10000 0 -0.55 57 57
ADCY4 -0.015 0.23 -10000 0 -0.73 57 57
ADCY5 -0.13 0.29 -10000 0 -0.71 116 116
ADCY6 -0.011 0.22 -10000 0 -0.71 54 54
ADCY7 -0.012 0.23 -10000 0 -0.71 58 58
ADCY1 -0.088 0.27 -10000 0 -0.68 99 99
ADCY2 -0.092 0.28 -10000 0 -0.69 106 106
ADCY3 -0.011 0.23 -10000 0 -0.7 57 57
ADCY8 -0.03 0.23 -10000 0 -0.66 68 68
ADCY9 -0.018 0.24 -10000 0 -0.72 60 60
arachidonic acid secretion -0.019 0.22 -10000 0 -0.59 61 61
ETB receptor/Endothelin-1/Gq/GTP -0.012 0.16 -10000 0 -0.47 51 51
GNAO1 -0.076 0.21 -10000 0 -0.53 139 139
HRAS 0.009 0.05 -10000 0 -0.63 5 5
ETA receptor/Endothelin-1/G12/GTP 0.033 0.27 0.33 221 -0.73 49 270
ETA receptor/Endothelin-1/Gs/GTP 0.01 0.28 0.35 134 -0.73 59 193
mol:GTP 0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.008 0.32 -10000 0 -0.98 63 63
EDNRB -0.003 0.099 -10000 0 -0.56 23 23
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.002 0.3 -10000 0 -0.86 65 65
CYSLTR1 -0.003 0.3 -10000 0 -0.88 60 60
SLC9A1 0.011 0.13 0.2 127 -0.37 40 167
mol:GDP -0.029 0.24 -10000 0 -0.6 83 83
SLC9A3 0.003 0.23 -10000 0 -0.66 66 66
RAF1 -0.037 0.22 -10000 0 -0.6 70 70
JUN 0.03 0.19 -10000 0 -0.77 22 22
JAK2 0.017 0.26 -10000 0 -0.77 51 51
mol:IP3 -0.014 0.2 -10000 0 -0.59 54 54
ETA receptor/Endothelin-1 0.032 0.33 0.45 143 -0.75 71 214
PLCB1 -0.048 0.18 -10000 0 -0.57 88 88
PLCB2 0.007 0.06 -10000 0 -0.59 8 8
ETA receptor/Endothelin-3 -0.11 0.23 -10000 0 -0.51 157 157
FOS -0.055 0.29 -10000 0 -0.92 60 60
Gai/GDP -0.03 0.19 -10000 0 -0.7 50 50
CRK 0.013 0.024 -10000 0 -0.68 1 1
mol:Ca ++ -0.024 0.3 -10000 0 -0.83 69 69
BCAR1 0.013 0.001 -10000 0 -10000 0 0
PRKCB1 -0.014 0.19 -10000 0 -0.56 56 56
GNAQ 0.009 0.063 -10000 0 -0.68 7 7
GNAZ -0.002 0.099 -10000 0 -0.65 19 19
GNAL -0.022 0.14 -10000 0 -0.56 51 51
Gs family/GDP -0.092 0.19 -10000 0 -0.57 88 88
ETA receptor/Endothelin-1/Gq/GTP 0.008 0.21 -10000 0 -0.6 53 53
MAPK14 -0.011 0.15 -10000 0 -0.5 39 39
TRPC6 0.024 0.21 -10000 0 -0.92 24 24
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.003 0.077 -10000 0 -0.54 16 16
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.019 0.16 -10000 0 -0.49 47 47
ETB receptor/Endothelin-2 -0.079 0.2 -10000 0 -0.44 181 181
ETB receptor/Endothelin-3 -0.12 0.21 -10000 0 -0.42 272 272
ETB receptor/Endothelin-1 0 0.19 -10000 0 -0.57 60 60
MAPK3 -0.05 0.27 -10000 0 -0.81 66 66
MAPK1 -0.05 0.27 -10000 0 -0.81 67 67
Rac1/GDP -0.018 0.22 -10000 0 -0.58 70 70
cAMP biosynthetic process -0.11 0.28 -10000 0 -0.66 122 122
MAPK8 0.02 0.22 -10000 0 -0.8 32 32
SRC 0.011 0.037 -10000 0 -0.6 3 3
ETB receptor/Endothelin-1/Gi/GTP -0.011 0.14 -10000 0 -0.45 39 39
p130Cas/CRK/Src/PYK2 -0.014 0.22 -10000 0 -0.63 59 59
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.018 0.22 -10000 0 -0.59 68 68
COL1A2 -0.015 0.36 -10000 0 -1.1 65 65
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.067 0.23 -10000 0 -0.53 123 123
mol:DAG -0.014 0.2 -10000 0 -0.59 54 54
MAP2K2 -0.04 0.24 -10000 0 -0.65 71 71
MAP2K1 -0.04 0.24 -10000 0 -0.65 71 71
EDNRA 0.035 0.17 -10000 0 -0.65 30 30
positive regulation of muscle contraction 0.022 0.22 -10000 0 -0.7 48 48
Gq family/GDP -0.09 0.19 -10000 0 -0.6 78 78
HRAS/GTP -0.037 0.22 -10000 0 -0.56 78 78
PRKCH -0.008 0.19 -10000 0 -0.57 53 53
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.019 0.21 -10000 0 -0.57 67 67
PRKCB -0.048 0.23 -10000 0 -0.58 89 89
PRKCE -0.011 0.2 -10000 0 -0.56 61 61
PRKCD -0.008 0.19 -10000 0 -0.57 52 52
PRKCG -0.02 0.2 -10000 0 -0.56 62 62
regulation of vascular smooth muscle contraction -0.067 0.33 -10000 0 -1.1 61 61
PRKCQ -0.057 0.24 -10000 0 -0.59 98 98
PLA2G4A -0.025 0.24 -10000 0 -0.66 61 61
GNA14 -0.052 0.19 -10000 0 -0.57 97 97
GNA15 -0.001 0.096 -10000 0 -0.61 20 20
GNA12 0.013 0 -10000 0 -10000 0 0
GNA11 0.011 0.048 -10000 0 -0.67 4 4
Rac1/GTP 0.033 0.27 0.38 143 -0.73 49 192
MMP1 -0.29 0.44 -10000 0 -0.8 308 308
BCR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
JUN -0.077 0.17 0.25 1 -0.46 82 83
IKBKB -0.024 0.084 -10000 0 -0.29 12 12
AKT1 -0.063 0.12 0.23 1 -0.27 83 84
IKBKG -0.022 0.088 -10000 0 -0.29 19 19
CALM1 -0.065 0.15 -10000 0 -0.5 60 60
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
MAP3K1 -0.13 0.24 -10000 0 -0.58 143 143
MAP3K7 0.013 0.016 -10000 0 -0.46 1 1
mol:Ca2+ -0.075 0.16 -10000 0 -0.52 64 64
DOK1 0.009 0.055 -10000 0 -0.64 6 6
AP-1 -0.043 0.1 0.23 1 -0.26 69 70
LYN 0.006 0.061 -10000 0 -0.49 12 12
BLNK 0 0.094 -10000 0 -0.67 16 16
SHC1 0.013 0 -10000 0 -10000 0 0
BCR complex -0.16 0.28 -10000 0 -0.53 268 268
CD22 -0.17 0.28 -10000 0 -0.57 202 202
CAMK2G -0.054 0.14 -10000 0 -0.49 50 50
CSNK2A1 0.012 0.033 -10000 0 -0.67 2 2
INPP5D 0.005 0.067 -10000 0 -0.52 13 13
SHC/GRB2/SOS1 -0.12 0.19 -10000 0 -0.65 52 52
GO:0007205 -0.076 0.16 -10000 0 -0.53 64 64
SYK 0 0.094 -10000 0 -0.65 17 17
ELK1 -0.066 0.15 -10000 0 -0.5 60 60
NFATC1 -0.12 0.22 -10000 0 -0.49 156 156
B-cell antigen/BCR complex -0.16 0.28 -10000 0 -0.53 268 268
PAG1/CSK 0.015 0.045 -10000 0 -0.36 11 11
NFKBIB 0.001 0.031 -10000 0 -0.14 1 1
HRAS -0.069 0.16 -10000 0 -0.51 65 65
NFKBIA 0.001 0.03 -10000 0 -0.14 1 1
NF-kappa-B/RelA/I kappa B beta 0.008 0.025 -10000 0 -0.18 1 1
RasGAP/Csk -0.11 0.23 -10000 0 -0.46 212 212
mol:GDP -0.072 0.15 -10000 0 -0.5 64 64
PTEN 0.008 0.058 -10000 0 -0.67 6 6
CD79B -0.055 0.19 -10000 0 -0.56 101 101
NF-kappa-B/RelA/I kappa B alpha 0.008 0.025 -10000 0 -0.18 1 1
GRB2 0.013 0.016 -10000 0 -0.46 1 1
PI3K/BCAP/CD19 -0.15 0.24 -10000 0 -0.57 137 137
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
mol:IP3 -0.077 0.16 -10000 0 -0.54 64 64
CSK 0.013 0 -10000 0 -10000 0 0
FOS -0.09 0.17 -10000 0 -0.47 101 101
CHUK -0.022 0.088 -10000 0 -0.29 20 20
IBTK 0.012 0.024 -10000 0 -0.67 1 1
CARD11/BCL10/MALT1/TAK1 -0.077 0.15 -10000 0 -0.49 67 67
PTPN6 -0.14 0.27 -10000 0 -0.7 117 117
RELA 0.013 0 -10000 0 -10000 0 0
BCL2A1 0.003 0.034 -10000 0 -0.12 24 24
VAV2 -0.19 0.31 -10000 0 -0.72 158 158
ubiquitin-dependent protein catabolic process 0.006 0.03 -10000 0 -0.13 1 1
BTK -0.018 0.14 0.39 1 -1.1 13 14
CD19 -0.23 0.31 -10000 0 -0.56 310 310
MAP4K1 -0.033 0.16 -10000 0 -0.59 64 64
CD72 -0.001 0.091 -10000 0 -0.55 22 22
PAG1 0.006 0.061 -10000 0 -0.52 11 11
MAPK14 -0.1 0.2 -10000 0 -0.49 127 127
SH3BP5 0.012 0.029 -10000 0 -0.56 2 2
PIK3AP1 -0.074 0.18 -10000 0 -0.58 66 66
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.099 0.23 -10000 0 -0.49 165 165
RAF1 -0.058 0.15 -10000 0 -0.5 56 56
RasGAP/p62DOK/SHIP -0.13 0.21 -10000 0 -0.59 99 99
CD79A -0.17 0.28 -10000 0 -0.58 256 256
re-entry into mitotic cell cycle -0.044 0.1 0.22 1 -0.26 69 70
RASA1 0.011 0.037 -10000 0 -0.51 4 4
MAPK3 -0.035 0.13 -10000 0 -0.42 51 51
MAPK1 -0.035 0.13 -10000 0 -0.42 51 51
CD72/SHP1 -0.12 0.26 -10000 0 -0.68 114 114
NFKB1 0.012 0.024 -10000 0 -0.67 1 1
MAPK8 -0.1 0.2 -10000 0 -0.49 127 127
actin cytoskeleton organization -0.15 0.25 -10000 0 -0.59 152 152
NF-kappa-B/RelA 0.021 0.048 -10000 0 -0.2 1 1
Calcineurin -0.065 0.12 -10000 0 -0.46 51 51
PI3K -0.18 0.21 -10000 0 -0.56 144 144
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.08 0.18 -10000 0 -0.58 65 65
SOS1 0.013 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.15 0.32 -10000 0 -0.82 127 127
DAPP1 -0.18 0.34 -10000 0 -1 97 97
cytokine secretion -0.11 0.2 -10000 0 -0.46 156 156
mol:DAG -0.077 0.16 -10000 0 -0.54 64 64
PLCG2 0.003 0.07 -10000 0 -0.48 17 17
MAP2K1 -0.047 0.14 -10000 0 -0.47 52 52
B-cell antigen/BCR complex/FcgammaRIIB -0.14 0.26 -10000 0 -0.54 211 211
mol:PI-3-4-5-P3 -0.12 0.14 0.26 2 -0.38 140 142
ETS1 -0.045 0.13 -10000 0 -0.45 53 53
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.11 0.24 -10000 0 -0.46 222 222
B-cell antigen/BCR complex/LYN -0.15 0.27 -10000 0 -0.53 212 212
MALT1 0.012 0.024 -10000 0 -0.67 1 1
TRAF6 0.013 0.016 -10000 0 -0.46 1 1
RAC1 -0.17 0.28 -10000 0 -0.65 152 152
B-cell antigen/BCR complex/LYN/SYK -0.17 0.27 -10000 0 -0.72 119 119
CARD11 -0.084 0.18 -10000 0 -0.54 90 90
FCGR2B -0.006 0.11 -10000 0 -0.62 25 25
PPP3CA 0.007 0.057 -10000 0 -0.53 9 9
BCL10 0.013 0 -10000 0 -10000 0 0
IKK complex -0.003 0.039 -10000 0 -0.11 1 1
PTPRC -0.031 0.16 -10000 0 -0.59 62 62
PDPK1 -0.064 0.11 0.21 1 -0.27 83 84
PPP3CB 0.013 0 -10000 0 -10000 0 0
PPP3CC 0.008 0.058 -10000 0 -0.67 6 6
POU2F2 0.009 0.025 -10000 0 -0.12 7 7
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.061 0.18 -10000 0 -0.48 87 87
CRKL -0.049 0.17 -10000 0 -0.45 91 91
HRAS -0.05 0.18 -10000 0 -0.54 59 59
mol:PIP3 -0.057 0.15 -10000 0 -0.42 88 88
SPRED1 0.011 0.041 -10000 0 -0.67 3 3
SPRED2 0.009 0.053 -10000 0 -0.67 5 5
GAB1 -0.058 0.17 -10000 0 -0.46 97 97
FOXO3 -0.039 0.15 -10000 0 -0.42 80 80
AKT1 -0.048 0.16 -10000 0 -0.44 81 81
BAD -0.038 0.15 -10000 0 -0.41 78 78
megakaryocyte differentiation -0.064 0.18 -10000 0 -0.48 106 106
GSK3B -0.038 0.15 -10000 0 -0.41 78 78
RAF1 -0.03 0.15 -10000 0 -0.45 45 45
SHC1 0.013 0 -10000 0 -10000 0 0
STAT3 -0.058 0.18 -10000 0 -0.47 92 92
STAT1 -0.14 0.36 -10000 0 -0.95 113 113
HRAS/SPRED1 -0.033 0.15 -10000 0 -0.45 47 47
cell proliferation -0.056 0.17 -10000 0 -0.45 97 97
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
TEC 0.007 0.062 -10000 0 -0.62 8 8
RPS6KB1 -0.057 0.17 -10000 0 -0.46 98 98
HRAS/SPRED2 -0.034 0.15 -10000 0 -0.46 48 48
LYN/TEC/p62DOK -0.076 0.16 -10000 0 -0.47 88 88
MAPK3 -0.009 0.11 -10000 0 -0.32 34 34
STAP1 -0.11 0.22 -10000 0 -0.47 176 176
GRAP2 -0.037 0.17 -10000 0 -0.6 69 69
JAK2 -0.15 0.29 -10000 0 -0.85 98 98
STAT1 (dimer) -0.13 0.36 -10000 0 -0.92 114 114
mol:Gleevec 0.001 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.092 0.18 -10000 0 -0.5 95 95
actin filament polymerization -0.064 0.18 -10000 0 -0.46 107 107
LYN 0.006 0.061 -10000 0 -0.49 12 12
STAP1/STAT5A (dimer) -0.12 0.27 -10000 0 -0.65 127 127
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
CBL/CRKL/GRB2 -0.031 0.15 -10000 0 -0.41 79 79
PI3K -0.043 0.17 -10000 0 -0.46 81 81
PTEN 0.008 0.058 -10000 0 -0.67 6 6
SCF/KIT/EPO/EPOR -0.17 0.42 -10000 0 -1.2 96 96
MAPK8 -0.058 0.17 -10000 0 -0.46 97 97
STAT3 (dimer) -0.057 0.17 -10000 0 -0.46 92 92
positive regulation of transcription -0.003 0.094 -10000 0 -0.27 21 21
mol:GDP -0.059 0.2 -10000 0 -0.56 66 66
PIK3C2B -0.058 0.17 -10000 0 -0.47 92 92
CBL/CRKL -0.038 0.16 -10000 0 -0.43 79 79
FER -0.062 0.18 -10000 0 -0.47 102 102
SH2B3 -0.058 0.17 -10000 0 -0.47 92 92
PDPK1 -0.046 0.14 -10000 0 -0.4 76 76
SNAI2 -0.063 0.19 -10000 0 -0.48 107 107
positive regulation of cell proliferation -0.098 0.28 -10000 0 -0.74 102 102
KITLG -0.031 0.17 -10000 0 -0.63 59 59
cell motility -0.098 0.28 -10000 0 -0.74 102 102
PTPN6 0.015 0.019 -10000 0 -0.46 1 1
EPOR -0.028 0.18 -10000 0 -1.2 10 10
STAT5A (dimer) -0.082 0.24 -10000 0 -0.63 102 102
SOCS1 -0.02 0.14 -10000 0 -0.56 48 48
cell migration 0.098 0.21 0.47 155 -10000 0 155
SOS1 0.013 0 -10000 0 -10000 0 0
EPO -0.08 0.19 -10000 0 -0.47 158 158
VAV1 -0.006 0.11 -10000 0 -0.62 26 26
GRB10 -0.058 0.17 -10000 0 -0.47 92 92
PTPN11 0.015 0.007 -10000 0 -10000 0 0
SCF/KIT -0.068 0.18 -10000 0 -0.47 111 111
GO:0007205 0.002 0.009 -10000 0 -10000 0 0
MAP2K1 -0.014 0.12 -10000 0 -0.35 40 40
CBL 0.013 0 -10000 0 -10000 0 0
KIT -0.12 0.38 -10000 0 -1.3 73 73
MAP2K2 -0.014 0.12 -10000 0 -0.35 40 40
SHC/Grb2/SOS1 -0.068 0.15 -10000 0 -0.45 79 79
STAT5A -0.085 0.24 -10000 0 -0.65 102 102
GRB2 0.013 0.016 -10000 0 -0.46 1 1
response to radiation -0.062 0.18 -10000 0 -0.47 107 107
SHC/GRAP2 -0.017 0.13 -10000 0 -0.43 69 69
PTPRO -0.065 0.19 -10000 0 -0.48 106 106
SH2B2 -0.065 0.18 -10000 0 -0.47 107 107
DOK1 0.009 0.055 -10000 0 -0.64 6 6
MATK -0.1 0.21 -10000 0 -0.48 156 156
CREBBP 0.027 0.038 -10000 0 -0.69 2 2
BCL2 -0.13 0.43 -10000 0 -1.4 87 87
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.002 0.091 -9999 0 -0.37 40 40
RGS9BP -0.058 0.2 -9999 0 -0.61 96 96
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 -0.002 0.053 -9999 0 -0.46 11 11
mol:Na + -0.073 0.16 -9999 0 -0.33 209 209
mol:ADP 0 0.062 -9999 0 -0.33 28 28
GNAT2 0.009 0.037 -9999 0 -0.51 4 4
RGS9-1/Gbeta5/R9AP -0.092 0.2 -9999 0 -0.46 143 143
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0.007 0.023 -9999 0 -0.31 4 4
GRK7 -0.001 0.067 -9999 0 -0.46 18 18
CNGB3 -0.019 0.1 -9999 0 -0.46 45 45
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.12 0.21 -9999 0 -0.47 175 175
Cone PDE6 -0.077 0.17 -9999 0 -0.4 143 143
Cone Metarhodopsin II 0 0.048 -9999 0 -0.25 28 28
Na + (4 Units) -0.12 0.21 -9999 0 -0.47 175 175
GNAT2/GDP -0.074 0.17 -9999 0 -0.4 144 144
GNB5 0.01 0.047 -9999 0 -0.67 4 4
mol:GMP (4 units) 0.009 0.023 -9999 0 -0.4 1 1
Cone Transducin -0.001 0.097 -9999 0 -0.4 40 40
SLC24A2 -0.1 0.25 -9999 0 -0.64 147 147
GNB3/GNGT2 -0.012 0.12 -9999 0 -0.44 57 57
GNB3 -0.024 0.15 -9999 0 -0.6 51 51
GNAT2/GTP 0.007 0.027 -9999 0 -0.37 4 4
CNGA3 -0.1 0.23 -9999 0 -0.54 173 173
ARR3 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.073 0.16 -9999 0 -0.33 209 209
mol:Pi -0.092 0.19 -9999 0 -0.46 143 143
Cone CNG Channel -0.067 0.12 -9999 0 -0.38 71 71
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.1 0.25 -9999 0 -0.64 147 147
RGS9 -0.1 0.23 -9999 0 -0.55 171 171
PDE6C 0.004 0.017 -9999 0 -0.46 1 1
GNGT2 0.008 0.058 -9999 0 -0.67 6 6
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0 0 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.011 0.033 -10000 0 -0.53 3 3
PTK2 0.013 0 -10000 0 -10000 0 0
CRKL -0.075 0.2 -10000 0 -0.44 156 156
GRB2/SOS1/SHC 0.027 0.01 -10000 0 -10000 0 0
HRAS 0.009 0.05 -10000 0 -0.63 5 5
IRS1/Crk -0.075 0.2 -10000 0 -0.47 138 138
IGF-1R heterotetramer/IGF1/PTP1B -0.097 0.18 -10000 0 -0.45 148 148
AKT1 -0.044 0.18 -10000 0 -0.6 47 47
BAD -0.034 0.16 -10000 0 -0.56 47 47
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.075 0.2 -10000 0 -0.47 138 138
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.075 0.2 -10000 0 -0.47 137 137
RAF1 -0.027 0.16 -10000 0 -0.52 46 46
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.063 0.2 -10000 0 -0.44 137 137
YWHAZ 0.013 0.016 -10000 0 -0.46 1 1
IGF-1R heterotetramer/IGF1/IRS1 -0.088 0.22 -10000 0 -0.48 155 155
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
RPS6KB1 -0.046 0.18 -10000 0 -0.6 48 48
GNB2L1 0.013 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.024 0.13 -10000 0 -0.44 46 46
PXN 0.013 0 -10000 0 -10000 0 0
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.019 0.012 -10000 0 -0.32 1 1
HRAS/GTP -0.079 0.16 -10000 0 -0.62 45 45
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.043 0.16 -10000 0 -0.49 45 45
IGF-1R heterotetramer -0.076 0.22 -10000 0 -0.68 96 96
IGF-1R heterotetramer/IGF1/IRS/Nck -0.075 0.2 -10000 0 -0.47 138 138
Crk/p130 Cas/Paxillin -0.055 0.19 -10000 0 -0.66 46 46
IGF1R -0.076 0.22 -10000 0 -0.68 96 96
IGF1 -0.083 0.22 -10000 0 -0.62 115 115
IRS2/Crk -0.079 0.21 -10000 0 -0.46 143 143
PI3K -0.064 0.19 -10000 0 -0.44 137 137
apoptosis 0.022 0.14 0.47 47 -10000 0 47
HRAS/GDP 0.007 0.037 -10000 0 -0.47 5 5
PRKCD -0.051 0.19 -10000 0 -0.51 94 94
RAF1/14-3-3 E -0.015 0.14 -10000 0 -0.44 44 44
BAD/14-3-3 -0.024 0.15 -10000 0 -0.5 47 47
PRKCZ -0.046 0.18 -10000 0 -0.61 48 48
Crk/p130 Cas/Paxillin/FAK1 -0.064 0.13 -10000 0 -0.51 44 44
PTPN1 0.007 0.056 -10000 0 -0.46 12 12
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.062 0.2 -10000 0 -0.47 137 137
BCAR1 0.013 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.056 0.17 -10000 0 -0.41 138 138
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.013 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.075 0.2 -10000 0 -0.47 138 138
GRB10 0.012 0.029 -10000 0 -0.56 2 2
PTPN11 -0.074 0.2 -10000 0 -0.47 137 137
IRS1 -0.088 0.21 -10000 0 -0.48 155 155
IRS2 -0.091 0.22 -10000 0 -0.49 142 142
IGF-1R heterotetramer/IGF1 -0.11 0.24 -10000 0 -0.5 196 196
GRB2 0.013 0.016 -10000 0 -0.46 1 1
PDPK1 -0.054 0.18 -10000 0 -0.64 47 47
YWHAE 0.012 0.024 -10000 0 -0.67 1 1
PRKD1 -0.063 0.21 -10000 0 -0.52 110 110
SHC1 0.013 0 -10000 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.007 0.11 -9999 0 -0.55 31 31
GPC2 -0.065 0.19 -9999 0 -0.51 127 127
GPC2/Midkine -0.052 0.16 -9999 0 -0.54 46 46
neuron projection morphogenesis -0.052 0.16 -9999 0 -0.54 46 46
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.011 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.062 0.17 -10000 0 -0.39 172 172
regulation of S phase of mitotic cell cycle -0.037 0.13 -10000 0 -0.28 173 173
GNAO1 -0.077 0.21 -10000 0 -0.53 139 139
HRAS 0.009 0.05 -10000 0 -0.63 5 5
SHBG/T-DHT 0.004 0.039 -10000 0 -0.3 13 13
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.011 0 -10000 0 -10000 0 0
MAP2K1 -0.039 0.14 -10000 0 -0.41 20 20
T-DHT/AR -0.098 0.21 -10000 0 -0.5 177 177
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.006 103 103
GNAI2 0.013 0 -10000 0 -10000 0 0
GNAI3 0.013 0 -10000 0 -10000 0 0
GNAI1 0.003 0.077 -10000 0 -0.54 16 16
mol:GDP -0.11 0.2 -10000 0 -0.51 171 171
cell proliferation -0.045 0.17 -10000 0 -0.54 22 22
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
FOS -0.059 0.23 -10000 0 -0.79 59 59
mol:Ca2+ -0.018 0.026 -10000 0 -0.09 43 43
MAPK3 -0.042 0.15 -10000 0 -0.5 20 20
MAPK1 -0.015 0.082 -10000 0 -0.28 12 12
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
mol:IP3 0 0.001 -10000 0 -0.004 112 112
cAMP biosynthetic process 0.013 0.045 -10000 0 -0.28 13 13
GNG2 0.011 0.033 -10000 0 -0.53 3 3
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 112 112
HRAS/GTP -0.077 0.14 -10000 0 -0.35 177 177
actin cytoskeleton reorganization -0.001 0.014 -10000 0 -10000 0 0
SRC 0.011 0.037 -10000 0 -0.6 3 3
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 112 112
PI3K 0.017 0.019 -10000 0 -0.26 4 4
apoptosis 0.033 0.14 0.42 59 -10000 0 59
T-DHT/AR/PELP1 -0.076 0.18 -10000 0 -0.43 177 177
HRAS/GDP -0.099 0.19 -10000 0 -0.48 175 175
CREB1 -0.037 0.15 -10000 0 -0.45 59 59
RAC1-CDC42/GTP -0.001 0.014 -10000 0 -10000 0 0
AR -0.13 0.28 -10000 0 -0.67 177 177
GNB1 0.013 0 -10000 0 -10000 0 0
RAF1 -0.046 0.15 -10000 0 -0.33 177 177
RAC1-CDC42/GDP -0.091 0.18 -10000 0 -0.46 171 171
T-DHT/AR/PELP1/Src -0.063 0.17 -10000 0 -0.39 173 173
MAP2K2 -0.039 0.14 -10000 0 -0.41 20 20
T-DHT/AR/PELP1/Src/PI3K -0.037 0.13 -10000 0 -0.29 173 173
GNAZ -0.002 0.099 -10000 0 -0.65 19 19
SHBG 0.005 0.063 -10000 0 -0.49 13 13
Gi family/GNB1/GNG2/GDP -0.025 0.12 -10000 0 -0.4 54 54
mol:T-DHT 0 0.001 -10000 0 -0.003 39 39
RAC1 0.013 0 -10000 0 -10000 0 0
GNRH1 0.003 0.063 -10000 0 -0.44 16 16
Gi family/GTP -0.05 0.12 -10000 0 -0.39 40 40
CDC42 0.013 0 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.011 0.041 -10000 0 -0.67 3 3
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.074 0.19 0.57 60 -10000 0 60
IL27/IL27R/JAK1 -0.11 0.25 -10000 0 -0.92 40 40
TBX21 -0.13 0.27 -10000 0 -0.64 134 134
IL12B -0.075 0.21 -10000 0 -0.58 121 121
IL12A -0.061 0.16 -10000 0 -0.39 148 148
IL6ST -0.072 0.22 -10000 0 -0.65 105 105
IL27RA/JAK1 -0.027 0.18 -10000 0 -1.3 14 14
IL27 -0.013 0.11 -10000 0 -0.55 33 33
TYK2 0.011 0.007 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.052 0.12 -10000 0 -0.33 104 104
T-helper 2 cell differentiation 0.074 0.19 0.57 60 -10000 0 60
T cell proliferation during immune response 0.074 0.19 0.57 60 -10000 0 60
MAPKKK cascade -0.074 0.19 -10000 0 -0.57 60 60
STAT3 0.012 0.024 -10000 0 -0.67 1 1
STAT2 0.013 0 -10000 0 -10000 0 0
STAT1 0.01 0.037 -10000 0 -0.46 5 5
IL12RB1 -0.033 0.16 -10000 0 -0.58 63 63
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.16 0.29 -10000 0 -0.62 191 191
IL27/IL27R/JAK2/TYK2 -0.076 0.19 -10000 0 -0.58 60 60
positive regulation of T cell mediated cytotoxicity -0.074 0.19 -10000 0 -0.57 60 60
STAT1 (dimer) -0.16 0.32 0.51 21 -0.86 87 108
JAK2 0.01 0.03 -10000 0 -0.57 2 2
JAK1 0.012 0.024 -10000 0 -0.69 1 1
STAT2 (dimer) -0.064 0.18 -10000 0 -0.58 49 49
T cell proliferation -0.14 0.23 -10000 0 -0.58 100 100
IL12/IL12R/TYK2/JAK2 -0.14 0.29 -10000 0 -0.88 82 82
IL17A -0.053 0.12 -10000 0 -0.33 104 104
mast cell activation 0.074 0.19 0.57 60 -10000 0 60
IFNG -0.024 0.048 0.072 2 -0.11 149 151
T cell differentiation -0.007 0.009 0.016 3 -0.023 145 148
STAT3 (dimer) -0.065 0.18 -10000 0 -0.6 46 46
STAT5A (dimer) -0.068 0.19 -10000 0 -0.59 52 52
STAT4 (dimer) -0.094 0.22 -10000 0 -0.61 71 71
STAT4 -0.044 0.18 -10000 0 -0.6 78 78
T cell activation -0.004 0.022 0.082 43 -10000 0 43
IL27R/JAK2/TYK2 -0.072 0.22 -10000 0 -0.97 28 28
GATA3 -0.2 0.52 -10000 0 -1.4 134 134
IL18 -0.004 0.08 -10000 0 -0.41 30 30
positive regulation of mast cell cytokine production -0.064 0.18 -10000 0 -0.58 47 47
IL27/EBI3 -0.03 0.14 -10000 0 -0.45 79 79
IL27RA -0.037 0.19 -10000 0 -1.4 14 14
IL6 -0.13 0.25 -10000 0 -0.56 207 207
STAT5A 0.007 0.064 -10000 0 -0.65 8 8
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.017 0.087 0.48 14 -10000 0 14
IL1B -0.02 0.12 -10000 0 -0.44 56 56
EBI3 -0.027 0.15 -10000 0 -0.63 49 49
TNF -0.035 0.14 -10000 0 -0.42 90 90
FAS signaling pathway (CD95)

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
SPTAN1 0.037 0.094 0.29 84 -10000 0 84
RFC1 0.037 0.094 0.29 84 -10000 0 84
PRKDC 0.036 0.095 0.29 84 -10000 0 84
RIPK1 0.015 0.004 -10000 0 -10000 0 0
CASP7 -0.007 0.061 0.26 19 -10000 0 19
FASLG/FAS/FADD/FAF1 -0.023 0.12 0.26 49 -0.34 57 106
MAP2K4 -0.03 0.15 -10000 0 -0.49 39 39
mol:ceramide -0.04 0.16 -10000 0 -0.46 73 73
GSN 0.036 0.095 0.29 83 -0.41 1 84
FASLG/FAS/FADD/FAF1/Caspase 8 -0.02 0.13 0.32 5 -0.41 58 63
FAS -0.002 0.091 -10000 0 -0.65 16 16
BID 0.015 0.065 0.31 36 -10000 0 36
MAP3K1 0.004 0.099 0.3 9 -0.36 7 16
MAP3K7 0.011 0.017 -10000 0 -0.46 1 1
RB1 0.028 0.1 0.29 78 -0.38 11 89
CFLAR 0.013 0.033 -10000 0 -0.66 2 2
HGF/MET -0.079 0.22 -10000 0 -0.5 152 152
ARHGDIB 0.031 0.1 0.29 82 -0.38 9 91
FADD 0.004 0.058 -10000 0 -0.46 13 13
actin filament polymerization -0.036 0.095 0.41 1 -0.29 83 84
NFKB1 -0.049 0.088 -10000 0 -1.2 1 1
MAPK8 -0.048 0.19 -10000 0 -0.48 97 97
DFFA 0.037 0.094 0.29 84 -10000 0 84
DNA fragmentation during apoptosis 0.037 0.094 0.29 84 -10000 0 84
FAS/FADD/MET -0.041 0.16 -10000 0 -0.47 81 81
CFLAR/RIP1 0.013 0.025 -10000 0 -0.48 2 2
FAIM3 -0.025 0.15 -10000 0 -0.61 52 52
FAF1 0.011 0.006 -10000 0 -10000 0 0
PARP1 0.037 0.094 0.29 84 -10000 0 84
DFFB 0.037 0.094 0.29 84 -10000 0 84
CHUK -0.042 0.078 -10000 0 -1.2 1 1
FASLG -0.076 0.21 -10000 0 -0.57 125 125
FAS/FADD 0.001 0.082 -10000 0 -0.42 28 28
HGF -0.033 0.17 -10000 0 -0.66 58 58
LMNA 0.032 0.087 0.26 84 -0.38 2 86
CASP6 0.037 0.094 0.29 84 -10000 0 84
CASP10 0.001 0.073 -10000 0 -0.53 15 15
CASP3 0.045 0.12 0.33 104 -10000 0 104
PTPN13 -0.028 0.16 -10000 0 -0.67 51 51
CASP8 0.022 0.09 0.42 37 -10000 0 37
IL6 -0.19 0.45 -10000 0 -1.3 104 104
MET -0.066 0.21 -10000 0 -0.6 108 108
ICAD/CAD 0.034 0.086 0.27 84 -10000 0 84
FASLG/FAS/FADD/FAF1/Caspase 10 -0.041 0.16 -10000 0 -0.47 73 73
activation of caspase activity by cytochrome c 0.015 0.065 0.31 36 -10000 0 36
PAK2 0.037 0.093 0.29 84 -10000 0 84
BCL2 -0.057 0.21 -10000 0 -0.66 87 87
Visual signal transduction: Rods

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
mol:K + 0.013 0 -9999 0 -10000 0 0
GNAT1/GTP -0.003 0.052 -9999 0 -0.32 21 21
Metarhodopsin II/Arrestin -0.011 0.074 -9999 0 -0.28 59 59
PDE6G/GNAT1/GTP -0.007 0.082 -9999 0 -0.31 55 55
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 -0.005 0.072 -9999 0 -0.46 21 21
GRK1 -0.002 0.053 -9999 0 -0.46 11 11
CNG Channel -0.14 0.19 -9999 0 -0.52 97 97
mol:Na + -0.11 0.16 -9999 0 -0.39 172 172
mol:ADP -0.002 0.052 -9999 0 -0.46 11 11
RGS9-1/Gbeta5/R9AP -0.092 0.2 -9999 0 -0.46 143 143
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.11 0.17 -9999 0 -0.4 172 172
CNGB1 -0.034 0.13 -9999 0 -0.46 74 74
RDH5 -0.031 0.15 -9999 0 -0.49 74 74
SAG -0.018 0.1 -9999 0 -0.46 43 43
mol:Ca2+ -0.083 0.17 -9999 0 -0.46 75 75
Na + (4 Units) -0.1 0.15 -9999 0 -0.45 75 75
RGS9 -0.1 0.23 -9999 0 -0.55 171 171
GNB1/GNGT1 -0.022 0.13 -9999 0 -0.47 61 61
GNAT1/GDP -0.081 0.17 -9999 0 -0.4 146 146
GUCY2D -0.039 0.17 -9999 0 -0.56 75 75
GNGT1 -0.042 0.17 -9999 0 -0.64 61 61
GUCY2F 0 0 -9999 0 -10000 0 0
GNB5 0.01 0.047 -9999 0 -0.67 4 4
mol:GMP (4 units) -0.053 0.15 -9999 0 -0.38 127 127
mol:11-cis-retinal -0.031 0.14 -9999 0 -0.49 74 74
mol:cGMP -0.027 0.12 -9999 0 -0.37 63 63
GNB1 0.013 0 -9999 0 -10000 0 0
Rhodopsin -0.024 0.12 -9999 0 -0.35 90 90
SLC24A1 0.013 0 -9999 0 -10000 0 0
CNGA1 -0.11 0.24 -9999 0 -0.55 183 183
Metarhodopsin II -0.001 0.046 -9999 0 -0.24 29 29
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.029 0.13 -9999 0 -0.39 63 63
RGS9BP -0.058 0.2 -9999 0 -0.61 96 96
Metarhodopsin II/Transducin -0.013 0.083 -9999 0 -0.3 57 57
GCAP Family/Ca ++ -0.007 0.084 -9999 0 -0.3 61 61
PDE6A/B -0.064 0.19 -9999 0 -0.46 145 145
mol:Pi -0.092 0.19 -9999 0 -0.46 143 143
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.018 0.11 -9999 0 -0.39 51 51
PDE6B -0.076 0.23 -9999 0 -0.67 110 110
PDE6A -0.01 0.1 -9999 0 -0.46 39 39
PDE6G -0.009 0.11 -9999 0 -0.55 34 34
RHO -0.002 0.067 -9999 0 -0.46 18 18
PDE6 -0.15 0.21 -9999 0 -0.62 80 80
GUCA1A -0.007 0.089 -9999 0 -0.46 32 32
GC2/GCAP Family -0.007 0.084 -9999 0 -0.3 61 61
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B -0.009 0.12 -9999 0 -0.63 29 29
Caspase cascade in apoptosis

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
TOP1 -0.062 0.17 0.21 1 -0.39 140 141
ACTA1 -0.12 0.22 0.25 1 -0.52 157 158
NUMA1 -0.062 0.17 0.21 1 -0.39 140 141
SPTAN1 -0.087 0.22 -10000 0 -0.52 134 134
LIMK1 -0.087 0.22 -10000 0 -0.51 135 135
BIRC3 -0.023 0.14 -10000 0 -0.56 54 54
BIRC2 0.013 0 -10000 0 -10000 0 0
BAX 0.013 0 -10000 0 -10000 0 0
CASP10 -0.11 0.24 -10000 0 -0.54 160 160
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.013 0 -10000 0 -10000 0 0
PTK2 -0.062 0.17 0.21 1 -0.4 132 133
DIABLO 0.013 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.085 0.21 -10000 0 -0.5 134 134
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.013 0 -10000 0 -10000 0 0
GSN -0.088 0.22 0.25 1 -0.52 136 137
MADD 0.013 0 -10000 0 -10000 0 0
TFAP2A -0.04 0.18 -10000 0 -0.7 54 54
BID -0.043 0.11 -10000 0 -0.26 156 156
MAP3K1 -0.026 0.081 -10000 0 -0.26 36 36
TRADD 0.012 0.033 -10000 0 -0.67 2 2
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.02 0.018 -10000 0 -0.5 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.092 0.22 0.25 1 -0.52 140 141
CASP9 0.013 0 -10000 0 -10000 0 0
DNA repair 0.012 0.056 0.18 1 -0.21 9 10
neuron apoptosis 0.007 0.063 -10000 0 -0.74 5 5
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.076 0.21 -10000 0 -0.49 132 132
APAF1 0.013 0.024 -10000 0 -0.67 1 1
CASP6 -0.024 0.11 -10000 0 -0.4 17 17
TRAF2 0.012 0.024 -10000 0 -0.67 1 1
ICAD/CAD -0.077 0.21 -10000 0 -0.5 130 130
CASP7 0.015 0.072 0.29 42 -10000 0 42
KRT18 -0.012 0.1 -10000 0 -0.66 19 19
apoptosis -0.063 0.19 0.27 1 -0.44 128 129
DFFA -0.087 0.22 -10000 0 -0.52 134 134
DFFB -0.087 0.22 -10000 0 -0.52 134 134
PARP1 -0.012 0.056 0.21 9 -0.18 1 10
actin filament polymerization 0.074 0.2 0.48 131 -10000 0 131
TNF -0.049 0.18 -10000 0 -0.57 90 90
CYCS -0.03 0.087 -10000 0 -0.23 62 62
SATB1 -0.026 0.12 -10000 0 -0.47 25 25
SLK -0.087 0.22 -10000 0 -0.51 136 136
p15 BID/BAX -0.032 0.1 -10000 0 -0.32 33 33
CASP2 0.018 0.08 -10000 0 -0.44 6 6
JNK cascade 0.026 0.08 0.26 36 -10000 0 36
CASP3 -0.099 0.23 0.26 1 -0.52 151 152
LMNB2 0.009 0.073 -10000 0 -0.42 5 5
RIPK1 0.013 0 -10000 0 -10000 0 0
CASP4 0.01 0.047 -10000 0 -0.67 4 4
Mammalian IAPs/DIABLO 0.013 0.083 -10000 0 -0.38 25 25
negative regulation of DNA binding -0.039 0.18 -10000 0 -0.68 54 54
stress fiber formation -0.085 0.21 -10000 0 -0.5 136 136
GZMB -0.13 0.26 -10000 0 -0.5 245 245
CASP1 0.009 0.066 -10000 0 -0.48 12 12
LMNB1 0.008 0.075 -10000 0 -0.4 6 6
APP 0.007 0.064 -10000 0 -0.75 5 5
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.011 0 -10000 0 -10000 0 0
VIM -0.066 0.18 0.28 1 -0.42 132 133
LMNA 0.008 0.076 -10000 0 -0.43 7 7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.012 0.085 -10000 0 -0.47 6 6
LRDD 0.01 0.04 -10000 0 -0.56 4 4
SREBF1 -0.09 0.22 -10000 0 -0.52 139 139
APAF-1/Caspase 9 -0.01 0.038 -10000 0 -0.31 1 1
nuclear fragmentation during apoptosis -0.061 0.17 0.21 1 -0.38 140 141
CFL2 -0.076 0.21 -10000 0 -0.49 131 131
GAS2 -0.11 0.23 -10000 0 -0.51 157 157
positive regulation of apoptosis 0.012 0.074 -10000 0 -0.37 7 7
PRF1 -0.049 0.18 -10000 0 -0.56 91 91
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.1 0.3 -10000 0 -0.8 103 103
IHH -0.028 0.1 -10000 0 -0.45 30 30
SHH Np/Cholesterol/GAS1 -0.016 0.12 -10000 0 -0.41 57 57
LRPAP1 0.012 0.033 -10000 0 -0.67 2 2
dorsoventral neural tube patterning 0.016 0.11 0.41 57 -10000 0 57
SMO/beta Arrestin2 -0.049 0.22 -10000 0 -0.77 48 48
SMO -0.06 0.23 -10000 0 -0.82 50 50
AKT1 -0.003 0.091 -10000 0 -0.34 11 11
ARRB2 0.013 0 -10000 0 -10000 0 0
BOC -0.014 0.12 -10000 0 -0.52 43 43
ADRBK1 0.013 0.016 -10000 0 -0.46 1 1
heart looping -0.058 0.22 -10000 0 -0.79 50 50
STIL -0.043 0.17 -10000 0 -0.65 40 40
DHH N/PTCH2 -0.038 0.17 -10000 0 -0.48 98 98
DHH N/PTCH1 -0.077 0.22 -10000 0 -0.59 95 95
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
DHH -0.038 0.17 -10000 0 -0.63 66 66
PTHLH -0.12 0.35 -10000 0 -0.93 100 100
determination of left/right symmetry -0.058 0.22 -10000 0 -0.79 50 50
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
skeletal system development -0.12 0.34 -10000 0 -0.92 100 100
IHH N/Hhip -0.023 0.11 -10000 0 -0.41 48 48
DHH N/Hhip -0.038 0.15 -10000 0 -0.42 108 108
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.058 0.22 -10000 0 -0.79 50 50
pancreas development -0.015 0.11 -10000 0 -0.46 46 46
HHAT 0 0.094 -10000 0 -0.67 16 16
PI3K 0.018 0.023 -10000 0 -0.32 4 4
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.024 0.15 -10000 0 -0.65 47 47
somite specification -0.058 0.22 -10000 0 -0.79 50 50
SHH Np/Cholesterol/PTCH1 -0.051 0.18 -10000 0 -0.66 44 44
SHH Np/Cholesterol/PTCH2 -0.011 0.1 -10000 0 -0.41 35 35
SHH Np/Cholesterol/Megalin -0.14 0.2 -10000 0 -0.41 232 232
SHH -0.003 0.088 -10000 0 -0.41 35 35
catabolic process -0.06 0.21 -10000 0 -0.67 57 57
SMO/Vitamin D3 -0.055 0.21 -10000 0 -0.71 52 52
SHH Np/Cholesterol/Hhip -0.011 0.096 -10000 0 -0.43 28 28
LRP2 -0.24 0.31 -10000 0 -0.59 355 355
receptor-mediated endocytosis -0.15 0.23 -10000 0 -0.68 85 85
SHH Np/Cholesterol/BOC -0.01 0.096 -10000 0 -0.41 29 29
SHH Np/Cholesterol/CDO -0.008 0.1 -10000 0 -0.42 39 39
mesenchymal cell differentiation 0.011 0.095 0.43 28 -10000 0 28
mol:Vitamin D3 -0.049 0.18 -10000 0 -0.66 44 44
IHH N/PTCH2 -0.024 0.12 -10000 0 -0.44 48 48
CDON -0.009 0.12 -10000 0 -0.62 30 30
IHH N/PTCH1 -0.061 0.21 -10000 0 -0.67 57 57
Megalin/LRPAP1 -0.17 0.23 -10000 0 -0.43 355 355
PTCH2 -0.016 0.13 -10000 0 -0.54 44 44
SHH Np/Cholesterol -0.008 0.068 -10000 0 -0.42 16 16
PTCH1 -0.061 0.21 -10000 0 -0.67 57 57
HHIP -0.015 0.11 -10000 0 -0.46 46 46
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.013 0.14 -9999 0 -0.61 42 42
Syndecan-4/Syndesmos -0.052 0.2 -9999 0 -0.58 92 92
positive regulation of JNK cascade -0.057 0.2 -9999 0 -0.55 102 102
Syndecan-4/ADAM12 -0.07 0.24 -9999 0 -0.64 106 106
CCL5 -0.049 0.18 -9999 0 -0.56 91 91
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
DNM2 0.013 0 -9999 0 -10000 0 0
ITGA5 0.011 0.037 -9999 0 -0.6 3 3
SDCBP 0.013 0.016 -9999 0 -0.46 1 1
PLG 0 0.009 -9999 0 -10000 0 0
ADAM12 -0.023 0.15 -9999 0 -0.64 47 47
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.013 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.016 0.032 -9999 0 -0.11 55 55
Syndecan-4/Laminin alpha1 -0.092 0.25 -9999 0 -0.65 117 117
Syndecan-4/CXCL12/CXCR4 -0.06 0.22 -9999 0 -0.59 102 102
Syndecan-4/Laminin alpha3 -0.1 0.23 -9999 0 -0.62 101 101
MDK -0.007 0.11 -9999 0 -0.55 31 31
Syndecan-4/FZD7 -0.061 0.22 -9999 0 -0.6 97 97
Syndecan-4/Midkine -0.062 0.21 -9999 0 -0.6 93 93
FZD7 -0.006 0.1 -9999 0 -0.56 28 28
Syndecan-4/FGFR1/FGF -0.11 0.21 -9999 0 -0.58 112 112
THBS1 -0.003 0.1 -9999 0 -0.64 21 21
integrin-mediated signaling pathway -0.081 0.23 -9999 0 -0.62 102 102
positive regulation of MAPKKK cascade -0.057 0.2 -9999 0 -0.55 102 102
Syndecan-4/TACI -0.1 0.22 -9999 0 -0.6 99 99
CXCR4 0.003 0.073 -9999 0 -0.51 16 16
cell adhesion -0.002 0.11 -9999 0 -0.39 49 49
Syndecan-4/Dynamin -0.052 0.2 -9999 0 -0.58 92 92
Syndecan-4/TSP1 -0.06 0.21 -9999 0 -0.6 99 99
Syndecan-4/GIPC -0.053 0.2 -9999 0 -0.58 92 92
Syndecan-4/RANTES -0.083 0.23 -9999 0 -0.61 103 103
ITGB1 0.013 0 -9999 0 -10000 0 0
LAMA1 -0.068 0.21 -9999 0 -0.62 108 108
LAMA3 -0.082 0.23 -9999 0 -0.61 128 128
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA -0.004 0.11 -9999 0 -0.48 37 37
Syndecan-4/alpha-Actinin -0.053 0.2 -9999 0 -0.58 92 92
TFPI -0.002 0.088 -9999 0 -0.5 25 25
F2 -0.004 0.061 -9999 0 -0.46 14 14
alpha5/beta1 Integrin 0.018 0.028 -9999 0 -0.44 3 3
positive regulation of cell adhesion -0.13 0.27 -9999 0 -0.64 136 136
ACTN1 0.012 0.024 -9999 0 -0.67 1 1
TNC -0.053 0.19 -9999 0 -0.59 92 92
Syndecan-4/CXCL12 -0.065 0.22 -9999 0 -0.61 99 99
FGF6 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CXCL12 -0.012 0.13 -9999 0 -0.66 31 31
TNFRSF13B -0.089 0.22 -9999 0 -0.56 149 149
FGF2 -0.044 0.17 -9999 0 -0.52 89 89
FGFR1 -0.013 0.12 -9999 0 -0.51 42 42
Syndecan-4/PI-4-5-P2 -0.061 0.2 -9999 0 -0.59 92 92
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.023 0.15 -9999 0 -0.62 49 49
cell migration -0.002 0.011 -9999 0 -0.072 1 1
PRKCD 0.015 0.018 -9999 0 -0.45 1 1
vasculogenesis -0.058 0.2 -9999 0 -0.57 99 99
SDC4 -0.064 0.22 -9999 0 -0.63 92 92
Syndecan-4/Tenascin C -0.085 0.24 -9999 0 -0.65 102 102
Syndecan-4/PI-4-5-P2/PKC alpha -0.013 0.026 -9999 0 -0.093 42 42
Syndecan-4/Syntenin -0.053 0.2 -9999 0 -0.58 92 92
MMP9 -0.086 0.23 -9999 0 -0.59 140 140
Rac1/GTP -0.003 0.11 -9999 0 -0.4 49 49
cytoskeleton organization -0.05 0.2 -9999 0 -0.56 92 92
GIPC1 0.012 0.024 -9999 0 -0.67 1 1
Syndecan-4/TFPI -0.059 0.21 -9999 0 -0.59 97 97
FOXM1 transcription factor network

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
NFATC3 0.014 0.44 -9999 0 -1.1 63 63
PLK1 -0.02 0.32 -9999 0 -1.5 36 36
BIRC5 -0.03 0.33 -9999 0 -1.5 38 38
HSPA1B 0.013 0.44 -9999 0 -1.2 52 52
MAP2K1 0.033 0.038 -9999 0 -10000 0 0
BRCA2 0.005 0.46 -9999 0 -1.1 67 67
FOXM1 -0.031 0.59 -9999 0 -1.6 68 68
XRCC1 0.014 0.44 -9999 0 -1.1 60 60
FOXM1B/p19 -0.2 0.37 -9999 0 -1.1 92 92
Cyclin D1/CDK4 -0.028 0.47 -9999 0 -1.1 99 99
CDC2 0.006 0.46 -9999 0 -1.2 68 68
TGFA -0.031 0.46 -9999 0 -1 87 87
SKP2 0.01 0.45 -9999 0 -1.1 63 63
CCNE1 -0.038 0.16 -9999 0 -0.49 94 94
CKS1B 0.014 0.44 -9999 0 -1.2 51 51
RB1 -0.12 0.26 -9999 0 -0.91 61 61
FOXM1C/SP1 -0.016 0.5 -9999 0 -1.3 69 69
AURKB -0.027 0.33 -9999 0 -1.5 37 37
CENPF 0.007 0.46 -9999 0 -1.2 62 62
CDK4 0.018 0.032 -9999 0 -0.44 3 3
MYC 0.011 0.42 -9999 0 -0.98 69 69
CHEK2 0.031 0.053 -9999 0 -0.57 3 3
ONECUT1 -0.017 0.46 -9999 0 -1.1 86 86
CDKN2A -0.065 0.18 -9999 0 -0.5 119 119
LAMA4 0.012 0.45 -9999 0 -1.1 61 61
FOXM1B/HNF6 -0.046 0.54 -9999 0 -1.3 88 88
FOS -0.041 0.52 -9999 0 -1.2 94 94
SP1 0.014 0.006 -9999 0 -10000 0 0
CDC25B 0.011 0.45 -9999 0 -1.1 66 66
response to radiation 0.016 0.035 -9999 0 -10000 0 0
CENPB 0.014 0.44 -9999 0 -1.1 63 63
CENPA -0.007 0.49 -9999 0 -1.3 71 71
NEK2 0.001 0.47 -9999 0 -1.2 68 68
HIST1H2BA 0.006 0.44 -9999 0 -1.1 68 68
CCNA2 -0.008 0.13 -9999 0 -0.64 32 32
EP300 0.013 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.01 0.5 -9999 0 -1.3 63 63
CCNB2 0.006 0.46 -9999 0 -1.2 64 64
CCNB1 0.007 0.46 -9999 0 -1.2 63 63
ETV5 0.01 0.45 -9999 0 -1.1 61 61
ESR1 -0.19 0.67 -9999 0 -1.2 247 247
CCND1 -0.029 0.48 -9999 0 -1.1 100 100
GSK3A 0.031 0.032 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.005 0.15 -9999 0 -0.52 34 34
CDK2 0.017 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.019 0.041 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.18 0.36 -9999 0 -1.2 73 73
GAS1 -0.019 0.5 -9999 0 -1.2 86 86
MMP2 -0.015 0.5 -9999 0 -1.3 81 81
RB1/FOXM1C -0.028 0.49 -9999 0 -1.1 100 100
CREBBP 0.012 0.033 -9999 0 -0.67 2 2
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 0.014 0.046 -9999 0 -0.36 12 12
VLDLR -0.011 0.12 -9999 0 -0.59 34 34
CRKL 0.012 0.024 -9999 0 -0.67 1 1
LRPAP1 0.012 0.033 -9999 0 -0.67 2 2
FYN 0.009 0.046 -9999 0 -0.53 6 6
ITGA3 -0.008 0.12 -9999 0 -0.63 28 28
RELN/VLDLR/Fyn -0.096 0.19 -9999 0 -0.45 133 133
MAPK8IP1/MKK7/MAP3K11/JNK1 0.025 0.071 -9999 0 -0.36 21 21
AKT1 -0.052 0.13 -9999 0 -0.44 23 23
MAP2K7 0.013 0 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
DAB1 -0.036 0.14 -9999 0 -0.46 82 82
RELN/LRP8/DAB1 -0.11 0.18 -9999 0 -0.45 136 136
LRPAP1/LRP8 0.002 0.081 -9999 0 -0.36 39 39
RELN/LRP8/DAB1/Fyn -0.097 0.18 -9999 0 -0.42 137 137
DAB1/alpha3/beta1 Integrin -0.12 0.16 -9999 0 -0.52 59 59
long-term memory -0.14 0.22 -9999 0 -0.56 112 112
DAB1/LIS1 -0.12 0.16 -9999 0 -0.53 49 49
DAB1/CRLK/C3G -0.11 0.16 -9999 0 -0.52 50 50
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
DAB1/NCK2 -0.12 0.16 -9999 0 -0.54 51 51
ARHGEF2 0.012 0.033 -9999 0 -0.67 2 2
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.074 0.21 -9999 0 -0.57 125 125
CDK5R1 0.007 0.059 -9999 0 -0.5 11 11
RELN -0.15 0.26 -9999 0 -0.56 244 244
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
RELN/LRP8/Fyn -0.094 0.18 -9999 0 -0.45 122 122
GRIN2A/RELN/LRP8/DAB1/Fyn -0.14 0.22 -9999 0 -0.46 198 198
MAPK8 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.11 0.19 -9999 0 -0.44 148 148
ITGB1 0.013 0 -9999 0 -10000 0 0
MAP1B -0.11 0.19 -9999 0 -0.45 143 143
RELN/LRP8 -0.093 0.18 -9999 0 -0.45 121 121
GRIN2B/RELN/LRP8/DAB1/Fyn -0.1 0.19 -9999 0 -0.43 149 149
PI3K 0.018 0.023 -9999 0 -0.32 4 4
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin 0.004 0.087 -9999 0 -0.46 28 28
RAP1A -0.071 0.17 -9999 0 -0.54 33 33
PAFAH1B1 0.013 0 -9999 0 -10000 0 0
MAPK8IP1 -0.012 0.12 -9999 0 -0.57 37 37
CRLK/C3G 0.019 0.018 -9999 0 -0.5 1 1
GRIN2B -0.017 0.1 -9999 0 -0.46 44 44
NCK2 0.011 0.033 -9999 0 -0.53 3 3
neuron differentiation -0.033 0.11 -9999 0 -0.36 40 40
neuron adhesion -0.065 0.17 -9999 0 -0.51 40 40
LRP8 -0.009 0.11 -9999 0 -0.5 37 37
GSK3B -0.043 0.12 -9999 0 -0.41 23 23
RELN/VLDLR/DAB1/Fyn -0.099 0.18 -9999 0 -0.42 148 148
MAP3K11 0.013 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.064 0.14 -9999 0 -0.32 149 149
CDK5 0.012 0.024 -9999 0 -0.67 1 1
MAPT -0.13 0.27 -9999 0 -0.62 199 199
neuron migration -0.054 0.17 -9999 0 -0.49 41 41
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.033 0.11 -9999 0 -0.36 40 40
RELN/VLDLR -0.09 0.18 -9999 0 -0.41 140 140
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.005 0.1 -9999 0 -0.48 25 25
NF kappa B1 p50/RelA/I kappa B alpha -0.046 0.14 -9999 0 -0.45 20 20
AP1 -0.14 0.18 -9999 0 -0.48 104 104
mol:PIP3 -0.13 0.17 -9999 0 -0.5 90 90
AKT1 0.038 0.075 -9999 0 -0.43 9 9
PTK2B -0.011 0.083 -9999 0 -0.32 36 36
RHOA 0.021 0.042 -9999 0 -0.38 1 1
PIK3CB 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ -0.058 0.14 -9999 0 -0.41 39 39
MAGI3 0.009 0.05 -9999 0 -0.63 5 5
RELA 0.013 0 -9999 0 -10000 0 0
apoptosis -0.085 0.17 -9999 0 -0.39 155 155
HRAS/GDP 0.007 0.037 -9999 0 -0.47 5 5
positive regulation of microtubule depolymerization -0.078 0.17 -9999 0 -0.36 199 199
NF kappa B1 p50/RelA -0.094 0.15 -9999 0 -0.53 38 38
endothelial cell migration -0.023 0.19 -9999 0 -0.68 60 60
ADCY4 -0.024 0.16 -9999 0 -0.59 44 44
ADCY5 -0.087 0.21 -9999 0 -0.58 91 91
ADCY6 -0.021 0.15 -9999 0 -0.56 43 43
ADCY7 -0.022 0.16 -9999 0 -0.57 45 45
ADCY1 -0.061 0.18 -9999 0 -0.56 67 67
ADCY2 -0.067 0.2 -9999 0 -0.6 75 75
ADCY3 -0.021 0.15 -9999 0 -0.56 45 45
ADCY8 -0.028 0.16 -9999 0 -0.56 46 46
ADCY9 -0.026 0.16 -9999 0 -0.58 45 45
GSK3B -0.004 0.079 -9999 0 -0.33 23 23
arachidonic acid secretion -0.019 0.15 -9999 0 -0.55 41 41
GNG2 0.011 0.033 -9999 0 -0.53 3 3
TRIP6 0.001 0.1 -9999 0 -0.46 37 37
GNAO1 -0.056 0.18 -9999 0 -0.38 169 169
HRAS 0.009 0.05 -9999 0 -0.63 5 5
NFKBIA -0.057 0.16 -9999 0 -0.46 36 36
GAB1 0.012 0.024 -9999 0 -0.67 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.022 0.15 -9999 0 -0.93 21 21
JUN 0.009 0.049 -9999 0 -0.52 7 7
LPA/LPA2/NHERF2 -0.006 0.038 -9999 0 -0.4 6 6
TIAM1 -0.027 0.17 -9999 0 -1.1 21 21
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
mol:IP3 -0.059 0.15 -9999 0 -0.42 39 39
PLCB3 0.02 0.04 -9999 0 -0.38 6 6
FOS -0.062 0.2 -9999 0 -0.55 112 112
positive regulation of mitosis -0.019 0.15 -9999 0 -0.55 41 41
LPA/LPA1-2-3 -0.1 0.19 -9999 0 -0.43 155 155
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.013 0 -9999 0 -10000 0 0
stress fiber formation -0.034 0.12 -9999 0 -0.4 36 36
GNAZ -0.011 0.13 -9999 0 -0.41 71 71
EGFR/PI3K-beta/Gab1 -0.13 0.18 -9999 0 -0.52 90 90
positive regulation of dendritic cell cytokine production -0.12 0.18 -9999 0 -0.43 155 155
LPA/LPA2/MAGI-3 -0.005 0.038 -9999 0 -0.39 6 6
ARHGEF1 0.013 0.097 -9999 0 -0.44 24 24
GNAI2 -0.001 0.11 -9999 0 -0.39 55 55
GNAI3 -0.001 0.11 -9999 0 -0.39 55 55
GNAI1 -0.007 0.12 -9999 0 -0.41 58 58
LPA/LPA3 -0.13 0.2 -9999 0 -0.42 265 265
LPA/LPA2 -0.001 0.028 -9999 0 -0.32 1 1
LPA/LPA1 -0.032 0.12 -9999 0 -0.44 61 61
HB-EGF/EGFR -0.099 0.21 -9999 0 -0.48 152 152
HBEGF -0.057 0.18 -9999 0 -0.44 145 145
mol:DAG -0.059 0.15 -9999 0 -0.42 39 39
cAMP biosynthetic process -0.055 0.18 -9999 0 -0.54 73 73
NFKB1 0.012 0.024 -9999 0 -0.67 1 1
SRC 0.011 0.037 -9999 0 -0.6 3 3
GNB1 0.013 0 -9999 0 -10000 0 0
LYN -0.06 0.16 -9999 0 -0.47 37 37
GNAQ -0.074 0.15 -9999 0 -0.35 143 143
LPAR2 0.012 0.016 -9999 0 -0.46 1 1
LPAR3 -0.17 0.27 -9999 0 -0.56 265 265
LPAR1 -0.012 0.13 -9999 0 -0.72 25 25
IL8 -0.16 0.22 -9999 0 -0.5 175 175
PTK2 -0.085 0.18 -9999 0 -0.4 155 155
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
CASP3 -0.085 0.17 -9999 0 -0.39 155 155
EGFR -0.077 0.22 -9999 0 -0.57 129 129
PLCG1 -0.081 0.16 -9999 0 -0.38 151 151
PLD2 -0.085 0.18 -9999 0 -0.4 155 155
G12/G13 0.007 0.1 -9999 0 -0.48 24 24
PI3K-beta -0.018 0.07 -9999 0 -0.5 9 9
cell migration -0.04 0.071 -9999 0 -0.27 29 29
SLC9A3R2 0.009 0.053 -9999 0 -0.67 5 5
PXN -0.034 0.12 -9999 0 -0.4 36 36
HRAS/GTP -0.02 0.16 -9999 0 -0.57 41 41
RAC1 0.013 0 -9999 0 -10000 0 0
MMP9 -0.088 0.23 -9999 0 -0.59 140 140
PRKCE 0.005 0.075 -9999 0 -0.68 10 10
PRKCD -0.05 0.14 -9999 0 -0.43 27 27
Gi(beta/gamma) -0.017 0.15 -9999 0 -0.54 43 43
mol:LPA -0.005 0.041 -9999 0 -0.2 31 31
TRIP6/p130 Cas/FAK1/Paxillin -0.096 0.16 -9999 0 -0.54 45 45
MAPKKK cascade -0.019 0.15 -9999 0 -0.55 41 41
contractile ring contraction involved in cytokinesis 0.021 0.041 -9999 0 -0.38 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.1 0.19 -9999 0 -0.41 180 180
GNA15 -0.078 0.15 -9999 0 -0.36 153 153
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
MAPT -0.08 0.18 -9999 0 -0.37 199 199
GNA11 -0.072 0.14 -9999 0 -0.35 141 141
Rac1/GTP 0 0.16 -9999 0 -1 21 21
MMP2 -0.024 0.19 -9999 0 -0.69 60 60
Arf6 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
CENTA1/KIF3B -0.018 0.13 -9999 0 -0.45 65 65
ARNO/beta Arrestin1-2 -0.022 0.074 -9999 0 -0.53 2 2
EGFR -0.076 0.22 -9999 0 -0.57 129 129
EPHA2 0.003 0.075 -9999 0 -0.54 15 15
USP6 0.009 0.046 -9999 0 -0.49 7 7
IQSEC1 0.013 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.16 0.25 -9999 0 -0.47 298 298
ARRB2 0.007 0.029 -9999 0 -10000 0 0
mol:GTP -0.004 0.058 -9999 0 -0.19 47 47
ARRB1 0.005 0.067 -9999 0 -0.5 14 14
FBXO8 0.013 0 -9999 0 -10000 0 0
TSHR -0.041 0.17 -9999 0 -0.55 81 81
EGF -0.14 0.27 -9999 0 -0.61 201 201
somatostatin receptor activity 0 0 -9999 0 -0.001 93 93
ARAP2 -0.004 0.11 -9999 0 -0.64 22 22
mol:GDP -0.059 0.12 -9999 0 -0.34 87 87
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 56 56
ITGA2B -0.059 0.19 -9999 0 -0.54 110 110
ARF6 0.013 0.016 -9999 0 -0.46 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.026 0.052 -9999 0 -0.38 8 8
ADAP1 -0.025 0.16 -9999 0 -0.66 47 47
KIF13B -0.005 0.11 -9999 0 -0.65 23 23
HGF/MET -0.072 0.21 -9999 0 -0.5 148 148
PXN 0.013 0 -9999 0 -10000 0 0
ARF6/GTP -0.067 0.12 -9999 0 -0.32 96 96
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.12 0.22 -9999 0 -0.46 209 209
ADRB2 -0.024 0.15 -9999 0 -0.59 52 52
receptor agonist activity 0 0 -9999 0 0 88 88
actin filament binding 0 0 -9999 0 -0.001 94 94
SRC 0.011 0.037 -9999 0 -0.6 3 3
ITGB3 -0.009 0.12 -9999 0 -0.59 31 31
GNAQ 0.007 0.063 -9999 0 -0.68 7 7
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 76 76
ARF6/GDP -0.029 0.13 -9999 0 -0.42 58 58
ARF6/GDP/GULP/ACAP1 -0.096 0.19 -9999 0 -0.5 106 106
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.023 0.13 -9999 0 -0.4 63 63
ACAP1 -0.07 0.21 -9999 0 -0.59 116 116
ACAP2 0.013 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0 0.039 -9999 0 -0.27 17 17
EFNA1 0.012 0.024 -9999 0 -0.67 1 1
HGF -0.033 0.17 -9999 0 -0.66 58 58
CYTH3 0.008 0.036 -9999 0 -0.51 4 4
CYTH2 0.009 0.002 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 78 78
endosomal lumen acidification 0 0 -9999 0 -0.001 90 90
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.022 0.15 -9999 0 -0.62 47 47
GNAQ/ARNO 0.011 0.035 -9999 0 -0.36 7 7
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 54 54
MET -0.066 0.21 -9999 0 -0.6 108 108
GNA14 -0.054 0.19 -9999 0 -0.57 97 97
GNA15 -0.002 0.096 -9999 0 -0.61 20 20
GIT1 0.01 0.043 -9999 0 -0.49 6 6
mol:PI-4-5-P2 0 0 -9999 0 -0.001 79 79
GNA11 0.01 0.047 -9999 0 -0.67 4 4
LHCGR -0.005 0.065 -9999 0 -0.46 17 17
AGTR1 -0.16 0.26 -9999 0 -0.52 268 268
desensitization of G-protein coupled receptor protein signaling pathway 0 0.039 -9999 0 -0.27 17 17
IPCEF1/ARNO -0.096 0.17 -9999 0 -0.54 32 32
alphaIIb/beta3 Integrin -0.05 0.16 -9999 0 -0.4 138 138
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.048 0.14 -9999 0 -0.48 66 66
alphaM/beta2 Integrin/GPIbA -0.055 0.14 -9999 0 -0.46 71 71
alphaM/beta2 Integrin/proMMP-9 -0.087 0.18 -9999 0 -0.48 122 122
PLAUR 0.008 0.057 -9999 0 -0.61 7 7
HMGB1 0.003 0.021 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.027 0.098 -9999 0 -0.51 27 27
AGER -0.014 0.11 -9999 0 -0.62 23 23
RAP1A 0.013 0 -9999 0 -10000 0 0
SELPLG 0.007 0.064 -9999 0 -0.65 8 8
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.074 0.14 -9999 0 -0.52 46 46
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.088 0.23 -9999 0 -0.59 140 140
CYR61 -0.012 0.12 -9999 0 -0.58 36 36
TLN1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP -0.087 0.14 -9999 0 -0.49 52 52
RHOA 0.013 0 -9999 0 -10000 0 0
P-selectin oligomer -0.12 0.26 -9999 0 -0.61 188 188
MYH2 -0.11 0.19 -9999 0 -0.5 102 102
MST1R -0.032 0.17 -9999 0 -0.67 55 55
leukocyte activation during inflammatory response -0.071 0.14 -9999 0 -0.41 92 92
APOB -0.084 0.21 -9999 0 -0.55 143 143
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.021 0.15 -9999 0 -0.65 44 44
JAM3 0.007 0.06 -9999 0 -0.59 8 8
GP1BA -0.035 0.16 -9999 0 -0.55 71 71
alphaM/beta2 Integrin/CTGF -0.043 0.13 -9999 0 -0.5 50 50
alphaM/beta2 Integrin -0.093 0.18 -9999 0 -0.44 105 105
JAM3 homodimer 0.007 0.06 -9999 0 -0.59 8 8
ICAM2 0.009 0.052 -9999 0 -0.6 6 6
ICAM1 -0.003 0.096 -9999 0 -0.56 24 24
phagocytosis triggered by activation of immune response cell surface activating receptor -0.092 0.17 -9999 0 -0.44 105 105
cell adhesion -0.055 0.14 -9999 0 -0.46 71 71
NFKB1 -0.072 0.22 -9999 0 -0.71 41 41
THY1 0.006 0.069 -9999 0 -0.65 9 9
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.052 0.14 -9999 0 -0.34 143 143
alphaM/beta2 Integrin/LRP/tPA -0.043 0.16 -9999 0 -0.47 70 70
IL6 -0.14 0.34 -9999 0 -0.85 131 131
ITGB2 -0.009 0.086 -9999 0 -0.6 16 16
elevation of cytosolic calcium ion concentration -0.037 0.13 -9999 0 -0.52 42 42
alphaM/beta2 Integrin/JAM2/JAM3 -0.008 0.12 -9999 0 -0.51 37 37
JAM2 -0.001 0.096 -9999 0 -0.63 19 19
alphaM/beta2 Integrin/ICAM1 -0.036 0.17 -9999 0 -0.44 104 104
alphaM/beta2 Integrin/uPA/Plg -0.017 0.13 -9999 0 -0.48 47 47
RhoA/GTP -0.11 0.2 -9999 0 -0.52 101 101
positive regulation of phagocytosis -0.079 0.14 -9999 0 -0.55 45 45
Ron/MSP -0.034 0.16 -9999 0 -0.5 87 87
alphaM/beta2 Integrin/uPAR/uPA -0.012 0.14 -9999 0 -0.53 42 42
alphaM/beta2 Integrin/uPAR -0.03 0.11 -9999 0 -0.53 30 30
PLAU -0.009 0.12 -9999 0 -0.62 30 30
PLAT -0.061 0.19 -9999 0 -0.53 114 114
actin filament polymerization -0.1 0.18 -9999 0 -0.47 102 102
MST1 -0.014 0.13 -9999 0 -0.61 36 36
alphaM/beta2 Integrin/lipoprotein(a) -0.071 0.14 -9999 0 -0.41 92 92
TNF -0.095 0.28 -9999 0 -0.82 77 77
RAP1B 0.013 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.04 0.13 -9999 0 -0.52 47 47
fibrinolysis -0.037 0.12 -9999 0 -0.48 46 46
HCK 0.002 0.078 -9999 0 -0.52 18 18
dendritic cell antigen processing and presentation -0.092 0.17 -9999 0 -0.44 105 105
VTN -0.063 0.18 -9999 0 -0.5 124 124
alphaM/beta2 Integrin/CYR61 -0.042 0.13 -9999 0 -0.49 48 48
LPA 0 0 -9999 0 -10000 0 0
LRP1 0.003 0.082 -9999 0 -0.67 12 12
cell migration -0.074 0.2 -9999 0 -0.48 136 136
FN1 -0.025 0.16 -9999 0 -0.64 49 49
alphaM/beta2 Integrin/Thy1 -0.031 0.11 -9999 0 -0.5 35 35
MPO -0.044 0.18 -9999 0 -0.58 79 79
KNG1 0 0 -9999 0 -10000 0 0
RAP1/GDP 0.018 0 -9999 0 -10000 0 0
ROCK1 -0.099 0.19 -9999 0 -0.5 91 91
ELA2 0 0 -9999 0 -10000 0 0
PLG 0 0 -9999 0 -10000 0 0
CTGF -0.014 0.13 -9999 0 -0.6 37 37
alphaM/beta2 Integrin/Hck -0.033 0.12 -9999 0 -0.58 31 31
ITGAM -0.014 0.11 -9999 0 -0.65 22 22
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.08 0.2 -9999 0 -0.45 148 148
HP -0.19 0.28 -9999 0 -0.57 288 288
leukocyte adhesion -0.068 0.14 -9999 0 -0.58 41 41
SELP -0.13 0.26 -9999 0 -0.61 188 188
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.03 0.14 -10000 0 -0.44 49 49
fibroblast growth factor receptor signaling pathway -0.03 0.13 -10000 0 -0.44 49 49
LAMA1 -0.068 0.21 -10000 0 -0.62 108 108
PRNP 0.003 0.081 -10000 0 -0.64 13 13
GPC1/SLIT2 -0.022 0.14 -10000 0 -0.49 69 69
SMAD2 0.023 0.059 -10000 0 -0.38 16 16
GPC1/PrPc/Cu2+ 0.007 0.072 -10000 0 -0.42 22 22
GPC1/Laminin alpha1 -0.046 0.17 -10000 0 -0.46 115 115
TDGF1 -0.024 0.13 -10000 0 -0.5 58 58
CRIPTO/GPC1 -0.013 0.11 -10000 0 -0.37 68 68
APP/GPC1 0.011 0.07 -10000 0 -0.49 15 15
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.005 0.1 -10000 0 -0.42 27 27
FLT1 0.012 0.024 -10000 0 -0.67 1 1
GPC1/TGFB/TGFBR1/TGFBR2 0.017 0.065 -10000 0 -0.42 16 16
SERPINC1 -0.027 0.14 -10000 0 -0.54 59 59
FYN -0.003 0.097 -10000 0 -0.43 23 23
FGR -0.006 0.11 -10000 0 -0.46 28 28
positive regulation of MAPKKK cascade -0.051 0.16 -10000 0 -0.53 52 52
SLIT2 -0.034 0.17 -10000 0 -0.66 59 59
GPC1/NRG -0.078 0.19 -10000 0 -0.44 179 179
NRG1 -0.11 0.25 -10000 0 -0.6 171 171
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.018 0.057 -10000 0 -0.42 9 9
LYN -0.005 0.1 -10000 0 -0.44 22 22
mol:Spermine 0.005 0.053 -10000 0 -0.47 10 10
cell growth -0.03 0.13 -10000 0 -0.44 49 49
BMP signaling pathway -0.006 0.07 0.63 10 -10000 0 10
SRC -0.002 0.096 -10000 0 -0.42 22 22
TGFBR1 0.01 0.04 -10000 0 -0.56 4 4
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.2 0.29 -10000 0 -0.57 312 312
GPC1 0.006 0.07 -10000 0 -0.63 10 10
TGFBR1 (dimer) 0.01 0.04 -10000 0 -0.56 4 4
VEGFA 0.008 0.051 -10000 0 -0.46 10 10
BLK -0.095 0.19 -10000 0 -0.46 132 132
HCK -0.008 0.1 -10000 0 -0.42 25 25
FGF2 -0.044 0.17 -10000 0 -0.52 89 89
FGFR1 -0.013 0.12 -10000 0 -0.51 42 42
VEGFR1 homodimer 0.012 0.024 -10000 0 -0.67 1 1
TGFBR2 0.008 0.06 -10000 0 -0.64 7 7
cell death 0.011 0.07 -10000 0 -0.49 15 15
ATIII/GPC1 -0.015 0.12 -10000 0 -0.4 69 69
PLA2G2A/GPC1 -0.15 0.22 -10000 0 -0.42 319 319
LCK -0.054 0.17 -10000 0 -0.46 98 98
neuron differentiation -0.078 0.19 -10000 0 -0.44 179 179
PrPc/Cu2+ 0.002 0.061 -10000 0 -0.48 13 13
APP 0.009 0.055 -10000 0 -0.64 6 6
TGFBR2 (dimer) 0.008 0.06 -10000 0 -0.64 7 7
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.1 0.25 -9999 0 -0.75 39 39
CRP -0.11 0.25 -9999 0 -0.75 43 43
cell cycle arrest -0.13 0.28 -9999 0 -0.82 58 58
TIMP1 -0.082 0.22 -9999 0 -0.7 24 24
IL6ST -0.069 0.22 -9999 0 -0.64 105 105
Rac1/GDP -0.088 0.2 -9999 0 -0.55 81 81
AP1 -0.038 0.13 -9999 0 -0.5 15 15
GAB2 0 0.082 -9999 0 -0.47 24 24
TNFSF11 -0.15 0.35 -9999 0 -1 76 76
HSP90B1 0.005 0.061 -9999 0 -0.85 1 1
GAB1 0.013 0.024 -9999 0 -0.67 1 1
MAPK14 -0.082 0.2 -9999 0 -0.58 65 65
AKT1 0.044 0.028 -9999 0 -10000 0 0
FOXO1 0.048 0.036 -9999 0 -10000 0 0
MAP2K6 -0.098 0.21 -9999 0 -0.56 84 84
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
MAP2K4 -0.087 0.22 -9999 0 -0.6 67 67
MITF -0.094 0.2 -9999 0 -0.54 86 86
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.013 0 -9999 0 -10000 0 0
A2M 0.008 0.11 -9999 0 -1.4 4 4
CEBPB 0.01 0.059 -9999 0 -0.47 12 12
GRB2/SOS1/GAB family/SHP2 -0.02 0.085 -9999 0 -0.47 3 3
STAT3 -0.14 0.3 -9999 0 -0.89 58 58
STAT1 -0.009 0.023 -9999 0 -10000 0 0
CEBPD -0.11 0.27 -9999 0 -0.91 34 34
PIK3CA 0.014 0.023 -9999 0 -0.45 2 2
PI3K 0.021 0.023 -9999 0 -0.31 4 4
JUN 0.008 0.049 -9999 0 -0.52 7 7
PIAS3/MITF -0.08 0.19 -9999 0 -0.55 67 67
MAPK11 -0.086 0.2 -9999 0 -0.59 69 69
STAT3 (dimer)/FOXO1 -0.065 0.23 -9999 0 -0.69 26 26
GRB2/SOS1/GAB family -0.094 0.16 -9999 0 -0.56 46 46
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.092 0.2 -9999 0 -0.49 102 102
GRB2 0.013 0.016 -9999 0 -0.46 1 1
JAK2 0.012 0.029 -9999 0 -0.56 2 2
LBP -0.27 0.42 -9999 0 -0.94 199 199
PIK3R1 0.013 0.023 -9999 0 -0.46 2 2
JAK1 0.013 0.024 -9999 0 -0.68 1 1
MYC -0.12 0.29 -9999 0 -1 43 43
FGG -0.16 0.33 -9999 0 -0.9 86 86
macrophage differentiation -0.13 0.28 -9999 0 -0.82 58 58
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.13 0.21 -9999 0 -0.51 134 134
JUNB -0.1 0.24 -9999 0 -0.77 32 32
FOS -0.063 0.2 -9999 0 -0.55 112 112
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.1 0.2 -9999 0 -0.52 102 102
STAT1/PIAS1 -0.09 0.19 -9999 0 -0.5 92 92
GRB2/SOS1/GAB family/SHP2/PI3K 0.03 0.032 -9999 0 -10000 0 0
STAT3 (dimer) -0.13 0.3 -9999 0 -0.88 58 58
PRKCD -0.084 0.23 -9999 0 -0.67 51 51
IL6R -0.013 0.13 -9999 0 -0.62 35 35
SOCS3 -0.076 0.21 -9999 0 -0.8 29 29
gp130 (dimer)/JAK1/JAK1/LMO4 -0.048 0.18 -9999 0 -0.47 110 110
Rac1/GTP -0.092 0.21 -9999 0 -0.56 84 84
HCK 0.002 0.078 -9999 0 -0.52 18 18
MAPKKK cascade -0.001 0.074 -9999 0 -0.62 2 2
bone resorption -0.14 0.32 -9999 0 -0.94 78 78
IRF1 -0.1 0.25 -9999 0 -0.87 24 24
mol:GDP -0.099 0.21 -9999 0 -0.54 100 100
SOS1 0.013 0.003 -9999 0 -10000 0 0
VAV1 -0.1 0.21 -9999 0 -0.55 100 100
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.085 0.2 -9999 0 -0.56 79 79
PTPN11 -0.008 0.02 -9999 0 -10000 0 0
IL6/IL6RA -0.1 0.21 -9999 0 -0.44 223 223
gp130 (dimer)/TYK2/TYK2/LMO4 -0.053 0.17 -9999 0 -0.47 109 109
gp130 (dimer)/JAK2/JAK2/LMO4 -0.054 0.17 -9999 0 -0.47 108 108
IL6 -0.13 0.26 -9999 0 -0.57 207 207
PIAS3 0.013 0 -9999 0 -10000 0 0
PTPRE 0.011 0.035 -9999 0 -0.67 2 2
PIAS1 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.099 0.18 -9999 0 -0.41 158 158
LMO4 -0.023 0.14 -9999 0 -0.53 56 56
STAT3 (dimer)/PIAS3 -0.17 0.25 -9999 0 -0.82 59 59
MCL1 0.05 0.027 -9999 0 -10000 0 0
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.053 0.16 0.41 138 -10000 0 138
KIRREL -0.036 0.17 -10000 0 -0.67 56 56
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.053 0.16 -10000 0 -0.41 138 138
PLCG1 0.013 0 -10000 0 -10000 0 0
ARRB2 0.013 0 -10000 0 -10000 0 0
WASL 0.013 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.049 0.12 -10000 0 -0.4 58 58
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.01 0.098 -10000 0 -0.45 8 8
FYN -0.03 0.12 -10000 0 -0.39 59 59
mol:Ca2+ -0.048 0.12 -10000 0 -0.4 58 58
mol:DAG -0.048 0.12 -10000 0 -0.4 58 58
NPHS2 -0.007 0.021 -10000 0 -10000 0 0
mol:IP3 -0.048 0.12 -10000 0 -0.4 58 58
regulation of endocytosis -0.021 0.11 -10000 0 -0.36 59 59
Nephrin/NEPH1/podocin/Cholesterol -0.039 0.12 -10000 0 -0.3 138 138
establishment of cell polarity -0.053 0.16 -10000 0 -0.41 138 138
Nephrin/NEPH1/podocin/NCK1-2 -0.019 0.12 -10000 0 -0.37 59 59
Nephrin/NEPH1/beta Arrestin2 -0.02 0.12 -10000 0 -0.37 59 59
NPHS1 -0.044 0.15 -10000 0 -0.47 88 88
Nephrin/NEPH1/podocin -0.031 0.12 -10000 0 -0.4 59 59
TJP1 0.011 0.041 -10000 0 -0.67 3 3
NCK1 0.013 0 -10000 0 -10000 0 0
NCK2 0.011 0.033 -10000 0 -0.53 3 3
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.048 0.12 -10000 0 -0.4 58 58
CD2AP 0.013 0.016 -10000 0 -0.46 1 1
Nephrin/NEPH1/podocin/GRB2 -0.049 0.12 -10000 0 -0.4 60 60
GRB2 0.013 0.016 -10000 0 -0.46 1 1
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.032 0.13 -10000 0 -0.4 65 65
cytoskeleton organization -0.011 0.12 -10000 0 -0.39 59 59
Nephrin/NEPH1 -0.036 0.12 -10000 0 -0.29 138 138
Nephrin/NEPH1/ZO-1 -0.054 0.13 -10000 0 -0.45 59 59
Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.012 0.024 -10000 0 -0.67 1 1
RAS family/GTP/Tiam1 -0.051 0.11 -10000 0 -0.37 24 24
NT3 (dimer)/TRKC -0.17 0.25 -10000 0 -0.44 346 346
NT3 (dimer)/TRKB -0.16 0.27 -10000 0 -0.56 214 214
SHC/Grb2/SOS1/GAB1/PI3K 0.036 0.016 -10000 0 -10000 0 0
RAPGEF1 0.013 0 -10000 0 -10000 0 0
BDNF -0.067 0.19 -10000 0 -0.51 130 130
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
DYNLT1 0.013 0 -10000 0 -10000 0 0
NTRK1 -0.048 0.18 -10000 0 -0.56 90 90
NTRK2 -0.092 0.23 -10000 0 -0.56 154 154
NTRK3 -0.16 0.27 -10000 0 -0.56 251 251
NT-4/5 (dimer)/TRKB -0.17 0.28 -10000 0 -0.55 240 240
neuron apoptosis 0.11 0.21 0.57 101 -10000 0 101
SHC 2-3/Grb2 -0.12 0.24 -10000 0 -0.64 101 101
SHC1 0.013 0 -10000 0 -10000 0 0
SHC2 -0.14 0.24 0.22 3 -0.65 123 126
SHC3 -0.12 0.19 0.22 4 -0.55 104 108
STAT3 (dimer) -0.009 0.1 -10000 0 -0.37 53 53
NT3 (dimer)/TRKA -0.14 0.23 -10000 0 -0.5 188 188
RIN/GDP -0.026 0.088 -10000 0 -0.27 16 16
GIPC1 0.012 0.024 -10000 0 -0.67 1 1
KRAS 0.013 0.016 -10000 0 -0.46 1 1
DNAJA3 -0.082 0.15 0.26 5 -0.41 101 106
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 -0.038 0.23 -10000 0 -0.75 74 74
MAGED1 0.008 0.06 -10000 0 -0.64 7 7
PTPN11 0.013 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) -0.093 0.23 -10000 0 -0.6 145 145
SHC/GRB2/SOS1 0.027 0.01 -10000 0 -10000 0 0
GRB2 0.013 0.016 -10000 0 -0.46 1 1
NGF (dimer)/TRKA/MATK -0.087 0.2 -10000 0 -0.48 132 132
TRKA/NEDD4-2 -0.029 0.14 -10000 0 -0.41 94 94
ELMO1 0.009 0.049 -10000 0 -0.52 7 7
RhoG/GTP/ELMO1/DOCK1 0.015 0.034 -10000 0 -0.33 8 8
NGF -0.023 0.14 -10000 0 -0.57 52 52
HRAS 0.009 0.05 -10000 0 -0.63 5 5
DOCK1 0.012 0.024 -10000 0 -0.67 1 1
GAB2 -0.001 0.082 -10000 0 -0.47 24 24
RIT2 0 0 -10000 0 -10000 0 0
RIT1 0.013 0 -10000 0 -10000 0 0
FRS2 0.005 0.062 -10000 0 -0.46 15 15
DNM1 -0.002 0.096 -10000 0 -0.61 20 20
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0.024 -10000 0 -0.67 1 1
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.081 0.15 0.25 5 -0.41 105 110
mol:GDP -0.039 0.13 -10000 0 -0.39 23 23
NGF (dimer) -0.023 0.14 -10000 0 -0.57 52 52
RhoG/GDP 0.007 0.036 -10000 0 -0.38 7 7
RIT1/GDP -0.02 0.089 -10000 0 -0.28 10 10
TIAM1 0.002 0.084 -10000 0 -0.62 15 15
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
BDNF (dimer)/TRKB -0.088 0.19 -10000 0 -0.47 109 109
KIDINS220/CRKL/C3G 0.019 0.018 -10000 0 -0.5 1 1
SHC/RasGAP 0.018 0.027 -10000 0 -0.36 4 4
FRS2 family/SHP2 0.021 0.04 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.033 0.017 -10000 0 -0.38 1 1
RIT1/GTP 0.01 0 -10000 0 -10000 0 0
NT3 (dimer) -0.082 0.21 -10000 0 -0.54 145 145
RAP1/GDP -0.038 0.058 -10000 0 -10000 0 0
KIDINS220/CRKL 0.012 0.024 -10000 0 -0.67 1 1
BDNF (dimer) -0.067 0.19 -10000 0 -0.51 130 130
ubiquitin-dependent protein catabolic process -0.037 0.15 -10000 0 -0.44 73 73
Schwann cell development -0.038 0.035 -10000 0 -10000 0 0
EHD4 0.013 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.029 0.037 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.033 0.036 -10000 0 -0.39 1 1
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.19 0.23 -10000 0 -0.65 112 112
ABL1 0.013 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.019 0.012 -10000 0 -0.32 1 1
Rap1/GTP -0.034 0.064 -10000 0 -0.73 1 1
STAT3 -0.009 0.1 -10000 0 -0.37 53 53
axon guidance -0.18 0.22 -10000 0 -0.61 112 112
MAPK3 -0.071 0.18 -10000 0 -0.44 132 132
MAPK1 -0.071 0.18 -10000 0 -0.44 132 132
CDC42/GDP -0.02 0.089 -10000 0 -0.27 11 11
NTF3 -0.082 0.21 -10000 0 -0.54 145 145
NTF4 -0.093 0.23 -10000 0 -0.6 145 145
NGF (dimer)/TRKA/FAIM -0.035 0.14 -10000 0 -0.44 69 69
PI3K 0.018 0.023 -10000 0 -0.32 4 4
FRS3 0.012 0.023 -10000 0 -0.46 2 2
FAIM 0.013 0 -10000 0 -10000 0 0
GAB1 0.012 0.024 -10000 0 -0.67 1 1
RASGRF1 -0.13 0.19 0.26 3 -0.46 142 145
SOS1 0.013 0 -10000 0 -10000 0 0
MCF2L -0.14 0.22 -10000 0 -0.48 185 185
RGS19 0.013 0 -10000 0 -10000 0 0
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP 0.004 0.076 -10000 0 -10000 0 0
Rac1/GDP -0.02 0.089 -10000 0 -0.27 11 11
NGF (dimer)/TRKA/GRIT -0.044 0.14 -10000 0 -0.36 138 138
neuron projection morphogenesis -0.064 0.17 -10000 0 -0.58 33 33
NGF (dimer)/TRKA/NEDD4-2 -0.037 0.15 -10000 0 -0.45 73 73
MAP2K1 0.038 0.016 -10000 0 -10000 0 0
NGFR -0.096 0.24 -10000 0 -0.6 150 150
NGF (dimer)/TRKA/GIPC/GAIP -0.01 0.11 -10000 0 -0.47 12 12
RAS family/GTP/PI3K 0.026 0.037 -10000 0 -0.29 10 10
FRS2 family/SHP2/GRB2/SOS1 0.034 0.035 -10000 0 -10000 0 0
NRAS 0.007 0.062 -10000 0 -0.62 8 8
GRB2/SOS1 0.019 0.012 -10000 0 -0.32 1 1
PRKCI 0.013 0.016 -10000 0 -0.46 1 1
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.011 0.041 -10000 0 -0.67 3 3
MAPKKK cascade -0.083 0.18 -10000 0 -0.67 67 67
RASA1 0.011 0.037 -10000 0 -0.51 4 4
TRKA/c-Abl -0.026 0.13 -10000 0 -0.4 90 90
SQSTM1 0.012 0.023 -10000 0 -0.46 2 2
BDNF (dimer)/TRKB/GIPC -0.072 0.17 -10000 0 -0.43 110 110
NGF (dimer)/TRKA/p62/Atypical PKCs -0.016 0.13 -10000 0 -0.37 71 71
MATK -0.071 0.21 -10000 0 -0.58 120 120
NEDD4L 0.009 0.052 -10000 0 -0.6 6 6
RAS family/GDP -0.037 0.056 -10000 0 -0.28 3 3
NGF (dimer)/TRKA -0.088 0.16 0.28 5 -0.38 159 164
Rac1/GTP -0.095 0.12 -10000 0 -0.34 95 95
FRS2 family/SHP2/CRK family 0.034 0.041 -10000 0 -0.46 2 2
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.021 0.14 -10000 0 -0.86 12 12
epithelial cell differentiation -0.041 0.11 -10000 0 -0.72 13 13
ITCH 0.022 0.02 -10000 0 -10000 0 0
WWP1 -0.02 0.17 -10000 0 -1.6 7 7
FYN 0.009 0.046 -10000 0 -0.53 6 6
EGFR -0.076 0.22 -10000 0 -0.57 129 129
PRL -0.007 0.075 -10000 0 -0.46 23 23
neuron projection morphogenesis -0.03 0.16 -10000 0 -0.7 13 13
PTPRZ1 -0.22 0.29 -10000 0 -0.56 338 338
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.049 0.17 -10000 0 -0.56 36 36
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.078 0.19 -10000 0 -0.45 128 128
ADAM17 0.022 0.02 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.026 0.15 -10000 0 -0.93 12 12
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.071 0.19 -10000 0 -0.5 86 86
NCOR1 0.012 0.033 -10000 0 -0.67 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.069 0.19 -10000 0 -0.6 43 43
GRIN2B -0.072 0.19 -10000 0 -0.57 47 47
ErbB4/ErbB2/betacellulin -0.062 0.18 -10000 0 -0.65 36 36
STAT1 0.01 0.036 -10000 0 -0.46 5 5
HBEGF 0.008 0.052 -10000 0 -0.51 8 8
PRLR -0.019 0.14 -10000 0 -0.66 40 40
E4ICDs/ETO2 -0.075 0.21 -10000 0 -0.53 111 111
axon guidance 0.025 0.14 -10000 0 -0.87 9 9
NEDD4 0.013 0.081 -10000 0 -0.67 11 11
Prolactin receptor/Prolactin receptor/Prolactin -0.019 0.12 -10000 0 -0.44 60 60
CBFA2T3 -0.081 0.23 -10000 0 -0.64 121 121
ErbB4/ErbB2/HBEGF -0.027 0.14 -10000 0 -0.81 12 12
MAPK3 -0.038 0.16 -10000 0 -0.69 15 15
STAT1 (dimer) -0.019 0.14 -10000 0 -0.78 14 14
MAPK1 -0.038 0.16 -10000 0 -0.53 34 34
JAK2 0.012 0.029 -10000 0 -0.56 2 2
ErbB4/ErbB2/neuregulin 1 beta -0.093 0.2 -10000 0 -0.58 56 56
NRG1 -0.067 0.19 -10000 0 -0.44 171 171
NRG3 -0.075 0.2 -10000 0 -0.53 135 135
NRG2 -0.11 0.23 -10000 0 -0.52 188 188
NRG4 -0.009 0.099 -10000 0 -0.47 36 36
heart development 0.025 0.14 -10000 0 -0.87 9 9
neural crest cell migration -0.092 0.19 -10000 0 -0.57 56 56
ERBB2 -0.01 0.11 -10000 0 -0.34 86 86
WWOX/E4ICDs -0.026 0.14 -10000 0 -0.77 15 15
SHC1 0.013 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.072 0.19 -10000 0 -0.42 135 135
apoptosis 0.096 0.17 0.55 70 -10000 0 70
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.088 0.2 -10000 0 -0.46 128 128
ErbB4/ErbB2/epiregulin -0.099 0.18 -10000 0 -0.56 49 49
ErbB4/ErbB4/betacellulin/betacellulin -0.059 0.18 -10000 0 -0.48 91 91
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.058 0.15 -10000 0 -0.62 37 37
MDM2 -0.017 0.14 -10000 0 -0.85 12 12
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.088 0.17 -10000 0 -0.44 116 116
STAT5A 0.027 0.13 -10000 0 -0.76 11 11
ErbB4/EGFR/neuregulin 1 beta -0.11 0.23 -10000 0 -0.62 94 94
DLG4 0.012 0.033 -10000 0 -0.67 2 2
GRB2/SHC 0.019 0.012 -10000 0 -0.32 1 1
E4ICDs/TAB2/NCoR1 -0.043 0.12 -10000 0 -0.75 14 14
STAT5A (dimer) -0.044 0.13 -10000 0 -0.82 13 13
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) 0.025 0.13 -10000 0 -0.76 11 11
LRIG1 0.009 0.055 -10000 0 -0.64 6 6
EREG -0.12 0.24 -10000 0 -0.52 210 210
BTC -0.053 0.2 -10000 0 -0.63 86 86
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.025 0.14 -10000 0 -0.89 9 9
ERBB4 -0.026 0.15 -10000 0 -0.94 12 12
STAT5B 0.009 0.053 -10000 0 -0.67 5 5
YAP1 -0.015 0.067 -10000 0 -0.62 8 8
GRB2 0.013 0.016 -10000 0 -0.46 1 1
ErbB4/ErbB2/neuregulin 4 -0.038 0.16 -10000 0 -0.66 23 23
glial cell differentiation 0.043 0.12 0.73 14 -10000 0 14
WWOX -0.001 0.082 -10000 0 -0.47 24 24
cell proliferation -0.077 0.2 -10000 0 -0.61 50 50
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.012 0.029 -9999 0 -0.56 2 2
LAT2 -0.065 0.19 -9999 0 -0.56 66 66
AP1 -0.11 0.18 -9999 0 -0.55 80 80
mol:PIP3 -0.071 0.22 -9999 0 -0.59 74 74
IKBKB -0.034 0.13 -9999 0 -0.32 83 83
AKT1 -0.055 0.18 -9999 0 -0.57 50 50
IKBKG -0.033 0.13 -9999 0 -0.32 83 83
MS4A2 -0.11 0.26 -9999 0 -0.62 166 166
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
MAP3K1 -0.035 0.17 -9999 0 -0.49 66 66
mol:Ca2+ -0.048 0.16 -9999 0 -0.42 74 74
LYN 0.004 0.062 -9999 0 -0.5 12 12
CBLB -0.062 0.18 -9999 0 -0.55 63 63
SHC1 0.013 0 -9999 0 -10000 0 0
RasGAP/p62DOK 0.003 0.093 -9999 0 -0.41 33 33
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.005 0.067 -9999 0 -0.52 13 13
PLD2 -0.086 0.2 -9999 0 -0.57 70 70
PTPN13 -0.072 0.2 -9999 0 -0.6 66 66
PTPN11 0.01 0.009 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.023 0.14 -9999 0 -0.39 46 46
SYK -0.003 0.096 -9999 0 -0.66 17 17
GRB2 0.012 0.016 -9999 0 -0.46 1 1
LAT/PLCgamma1/GRB2/SLP76/GADs -0.12 0.2 -9999 0 -0.6 81 81
LAT -0.076 0.2 -9999 0 -0.56 80 80
PAK2 -0.046 0.18 -9999 0 -0.55 63 63
NFATC2 -0.093 0.21 -9999 0 -0.76 64 64
HRAS -0.059 0.2 -9999 0 -0.6 68 68
GAB2 -0.001 0.082 -9999 0 -0.47 24 24
PLA2G1B 0.031 0.019 -9999 0 -10000 0 0
Fc epsilon R1 -0.14 0.23 -9999 0 -0.51 190 190
Antigen/IgE/Fc epsilon R1 -0.13 0.21 -9999 0 -0.47 190 190
mol:GDP -0.066 0.21 -9999 0 -0.62 69 69
JUN 0.009 0.049 -9999 0 -0.52 7 7
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
FOS -0.062 0.2 -9999 0 -0.55 112 112
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.074 0.19 -9999 0 -0.44 134 134
CHUK -0.033 0.13 -9999 0 -0.31 86 86
KLRG1 -0.067 0.18 -9999 0 -0.53 71 71
VAV1 -0.072 0.2 -9999 0 -0.56 78 78
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.062 0.18 -9999 0 -0.55 63 63
negative regulation of mast cell degranulation -0.058 0.18 -9999 0 -0.53 61 61
BTK -0.069 0.21 -9999 0 -0.63 67 67
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.085 0.23 -9999 0 -0.78 57 57
GAB2/PI3K/SHP2 -0.1 0.17 -9999 0 -0.62 51 51
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.072 0.2 -9999 0 -0.66 60 60
RAF1 0.02 0.023 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.13 0.22 -9999 0 -0.67 69 69
FCER1G 0.011 0.052 -9999 0 -0.65 5 5
FCER1A -0.1 0.24 -9999 0 -0.6 157 157
Antigen/IgE/Fc epsilon R1/Fyn -0.12 0.2 -9999 0 -0.44 190 190
MAPK3 0.03 0.019 -9999 0 -10000 0 0
MAPK1 0.03 0.019 -9999 0 -10000 0 0
NFKB1 0.012 0.024 -9999 0 -0.67 1 1
MAPK8 0.003 0.063 -9999 0 -0.41 6 6
DUSP1 -0.019 0.14 -9999 0 -0.59 45 45
NF-kappa-B/RelA -0.039 0.062 -9999 0 -0.3 2 2
actin cytoskeleton reorganization -0.06 0.18 -9999 0 -0.59 50 50
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.087 0.17 -9999 0 -0.57 62 62
FER -0.067 0.19 -9999 0 -0.55 70 70
RELA 0.013 0 -9999 0 -10000 0 0
ITK -0.076 0.16 -9999 0 -0.51 87 87
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG1 -0.063 0.21 -9999 0 -0.62 69 69
cytokine secretion -0.029 0.045 -9999 0 -10000 0 0
SPHK1 -0.075 0.2 -9999 0 -0.53 89 89
PTK2 -0.063 0.19 -9999 0 -0.62 50 50
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.12 0.2 -9999 0 -0.62 73 73
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.061 0.21 -9999 0 -0.57 69 69
MAP2K2 0.026 0.02 -9999 0 -10000 0 0
MAP2K1 0.026 0.02 -9999 0 -10000 0 0
MAP2K7 0.013 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.084 0.16 -9999 0 -0.53 59 59
MAP2K4 0.011 0.079 -9999 0 -0.91 6 6
Fc epsilon R1/FcgammaRIIB -0.13 0.22 -9999 0 -0.48 198 198
mol:Choline -0.085 0.2 -9999 0 -0.56 71 71
SHC/Grb2/SOS1 -0.08 0.16 -9999 0 -0.56 50 50
FYN 0.009 0.046 -9999 0 -0.53 6 6
DOK1 0.009 0.055 -9999 0 -0.64 6 6
PXN -0.051 0.17 -9999 0 -0.56 49 49
HCLS1 -0.065 0.19 -9999 0 -0.55 68 68
PRKCB -0.06 0.18 -9999 0 -0.45 95 95
FCGR2B -0.006 0.11 -9999 0 -0.62 25 25
IGHE -0.002 0.007 -9999 0 -10000 0 0
KLRG1/SHIP -0.06 0.18 -9999 0 -0.55 61 61
LCP2 0.009 0.047 -9999 0 -0.59 5 5
PLA2G4A -0.087 0.22 -9999 0 -0.59 91 91
RASA1 0.011 0.037 -9999 0 -0.51 4 4
mol:Phosphatidic acid -0.085 0.2 -9999 0 -0.56 71 71
IKK complex -0.012 0.1 -9999 0 -0.26 33 33
WIPF1 0.004 0.076 -9999 0 -0.65 11 11
TCGA08_retinoblastoma

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
CDKN2B 0.001 0.084 -10000 0 -0.56 18 18
CDKN2C 0.012 0.054 -10000 0 -0.47 9 9
CDKN2A -0.06 0.18 -10000 0 -0.5 119 119
CCND2 0.018 0.065 0.25 40 -0.17 4 44
RB1 -0.008 0.076 0.17 2 -0.26 48 50
CDK4 0.025 0.073 0.28 41 -10000 0 41
CDK6 0.017 0.073 0.27 39 -0.18 17 56
G1/S progression 0.008 0.076 0.26 48 -0.17 2 50
Coregulation of Androgen receptor activity

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
NRIP1 -0.003 0.099 -9999 0 -0.65 19 19
SVIL 0.009 0.053 -9999 0 -0.67 5 5
ZNF318 0.016 0.029 -9999 0 -0.46 2 2
JMJD2C -0.001 0.029 -9999 0 -0.097 63 63
T-DHT/AR/Ubc9 -0.094 0.19 -9999 0 -0.45 175 175
CARM1 0.013 0.001 -9999 0 -10000 0 0
PRDX1 0.013 0.001 -9999 0 -10000 0 0
PELP1 0.014 0.003 -9999 0 -10000 0 0
CTNNB1 0.011 0.033 -9999 0 -0.53 3 3
AKT1 0.014 0.005 -9999 0 -10000 0 0
PTK2B 0.009 0.047 -9999 0 -0.59 5 5
MED1 -0.006 0.095 -9999 0 -0.46 36 36
MAK -0.058 0.19 -9999 0 -0.53 115 115
response to oxidative stress 0 0.001 -9999 0 -10000 0 0
HIP1 0.01 0.041 -9999 0 -0.67 3 3
GSN 0.011 0.035 -9999 0 -0.69 2 2
NCOA2 -0.015 0.14 -9999 0 -0.67 34 34
NCOA6 0.012 0.017 -9999 0 -0.46 1 1
DNA-PK 0.019 0.029 -9999 0 -10000 0 0
NCOA4 0.013 0.016 -9999 0 -0.46 1 1
PIAS3 0.013 0.004 -9999 0 -10000 0 0
cell proliferation -0.079 0.19 -9999 0 -0.84 41 41
XRCC5 0.014 0.004 -9999 0 -10000 0 0
UBE3A 0.011 0.01 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.13 0.24 -9999 0 -0.52 210 210
FHL2 -0.061 0.24 -9999 0 -1.1 35 35
RANBP9 0.013 0.004 -9999 0 -10000 0 0
JMJD1A -0.022 0.062 -9999 0 -0.12 224 224
CDK6 -0.024 0.14 -9999 0 -0.52 59 59
TGFB1I1 0.002 0.085 -9999 0 -0.68 13 13
T-DHT/AR/CyclinD1 -0.13 0.24 -9999 0 -0.51 205 205
XRCC6 0.014 0.004 -9999 0 -10000 0 0
T-DHT/AR -0.11 0.22 -9999 0 -0.47 189 189
CTDSP1 0.012 0.004 -9999 0 -10000 0 0
CTDSP2 0.015 0.02 -9999 0 -0.46 1 1
BRCA1 -0.003 0.1 -9999 0 -0.68 19 19
TCF4 0.008 0.071 -9999 0 -0.67 9 9
CDKN2A -0.058 0.18 -9999 0 -0.5 119 119
SRF 0.016 0.027 -9999 0 -10000 0 0
NKX3-1 -0.14 0.3 -9999 0 -0.67 134 134
KLK3 -0.009 0.11 -9999 0 -10000 0 0
TMF1 0.012 0.003 -9999 0 -10000 0 0
HNRNPA1 0.014 0.006 -9999 0 -10000 0 0
AOF2 -0.001 0.008 -9999 0 -10000 0 0
APPL1 0.024 0.021 -9999 0 -0.5 1 1
T-DHT/AR/Caspase 8 -0.093 0.19 -9999 0 -0.45 175 175
AR -0.14 0.28 -9999 0 -0.68 177 177
UBA3 0.012 0.004 -9999 0 -10000 0 0
PATZ1 0.014 0.006 -9999 0 -10000 0 0
PAWR 0.009 0.044 -9999 0 -0.62 4 4
PRKDC 0.012 0.028 -9999 0 -0.46 3 3
PA2G4 0.014 0.017 -9999 0 -0.42 1 1
UBE2I 0.013 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.085 0.18 -9999 0 -0.42 175 175
RPS6KA3 0.008 0.05 -9999 0 -0.63 5 5
T-DHT/AR/ARA70 -0.096 0.19 -9999 0 -0.45 175 175
LATS2 0.014 0.024 -9999 0 -0.67 1 1
T-DHT/AR/PRX1 -0.084 0.18 -9999 0 -0.42 175 175
Cyclin D3/CDK11 p58 0.01 0.012 -9999 0 -0.32 1 1
VAV3 -0.055 0.2 -9999 0 -0.67 83 83
KLK2 -0.094 0.21 -9999 0 -0.94 36 36
CASP8 0.014 0.002 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.095 0.2 -9999 0 -0.46 185 185
TMPRSS2 -0.18 0.38 -9999 0 -1.1 115 115
CCND1 -0.041 0.18 -9999 0 -0.61 73 73
PIAS1 0.011 0.01 -9999 0 -10000 0 0
mol:T-DHT -0.015 0.035 -9999 0 -0.083 125 125
CDC2L1 0 0.001 -9999 0 -10000 0 0
PIAS4 0.01 0.016 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.12 0.22 -9999 0 -0.49 200 200
CMTM2 0.006 0.061 -9999 0 -0.51 11 11
SNURF -0.044 0.19 -9999 0 -0.67 70 70
ZMIZ1 -0.001 0.043 -9999 0 -0.49 3 3
CCND3 0.013 0.016 -9999 0 -0.46 1 1
TGIF1 0.013 0.034 -9999 0 -0.67 2 2
FKBP4 0.012 0.024 -9999 0 -0.67 1 1
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.079 0.31 -9999 0 -1.2 48 48
MKNK1 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.014 0.1 -9999 0 -0.45 10 10
ATF2/c-Jun 0.002 0.11 -9999 0 -0.53 16 16
MAPK11 -0.021 0.12 -9999 0 -0.56 19 19
MITF -0.014 0.14 -9999 0 -0.42 69 69
MAPKAPK5 -0.009 0.13 -9999 0 -0.39 64 64
KRT8 -0.017 0.15 -9999 0 -0.59 22 22
MAPKAPK3 0.013 0 -9999 0 -10000 0 0
MAPKAPK2 0.011 0.041 -9999 0 -0.67 3 3
p38alpha-beta/CK2 -0.026 0.16 -9999 0 -0.49 66 66
CEBPB -0.012 0.13 -9999 0 -0.48 22 22
SLC9A1 -0.009 0.13 -9999 0 -0.39 64 64
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.005 0.13 -9999 0 -0.55 17 17
p38alpha-beta/MNK1 -0.008 0.13 -9999 0 -0.57 17 17
JUN 0.002 0.1 -9999 0 -0.52 16 16
PPARGC1A -0.065 0.21 -9999 0 -0.45 140 140
USF1 -0.009 0.13 -9999 0 -0.39 64 64
RAB5/GDP/GDI1 -0.032 0.08 -9999 0 -0.45 12 12
NOS2 -0.033 0.24 -9999 0 -1.2 27 27
DDIT3 -0.011 0.13 -9999 0 -0.4 64 64
RAB5A 0.013 0 -9999 0 -10000 0 0
HSPB1 -0.014 0.14 -9999 0 -0.49 36 36
p38alpha-beta/HBP1 -0.008 0.13 -9999 0 -0.57 17 17
CREB1 -0.009 0.14 -9999 0 -0.4 70 70
RAB5/GDP 0.01 0 -9999 0 -10000 0 0
EIF4E -0.001 0.12 -9999 0 -0.59 12 12
RPS6KA4 -0.009 0.13 -9999 0 -0.39 65 65
PLA2G4A -0.03 0.16 -9999 0 -0.56 34 34
GDI1 -0.009 0.13 -9999 0 -0.39 64 64
TP53 -0.02 0.16 -9999 0 -0.49 66 66
RPS6KA5 -0.016 0.14 -9999 0 -0.39 78 78
ESR1 -0.11 0.23 -9999 0 -0.44 221 221
HBP1 0.013 0 -9999 0 -10000 0 0
MEF2C -0.011 0.14 -9999 0 -0.4 64 64
MEF2A -0.009 0.13 -9999 0 -0.39 64 64
EIF4EBP1 -0.012 0.14 -9999 0 -0.4 70 70
KRT19 -0.024 0.16 -9999 0 -0.42 92 92
ELK4 -0.009 0.13 -9999 0 -0.39 64 64
ATF6 -0.009 0.13 -9999 0 -0.39 64 64
ATF1 -0.009 0.14 -9999 0 -0.4 70 70
p38alpha-beta/MAPKAPK2 -0.009 0.14 -9999 0 -0.6 19 19
p38alpha-beta/MAPKAPK3 -0.008 0.13 -9999 0 -0.57 17 17
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.037 0.2 -9999 0 -0.55 98 98
MAP4K1 -0.033 0.16 -9999 0 -0.59 64 64
MAP3K8 0.002 0.079 -9999 0 -0.55 16 16
PRKCB -0.065 0.21 -9999 0 -0.59 110 110
DBNL 0.013 0 -9999 0 -10000 0 0
CRKL 0.012 0.024 -9999 0 -0.67 1 1
MAP3K1 -0.005 0.15 -9999 0 -0.52 43 43
JUN -0.035 0.2 -9999 0 -0.68 67 67
MAP3K7 -0.003 0.14 -9999 0 -0.53 39 39
GRAP2 -0.037 0.17 -9999 0 -0.6 69 69
CRK 0.012 0.024 -9999 0 -0.67 1 1
MAP2K4 0 0.14 -9999 0 -0.62 28 28
LAT -0.014 0.12 -9999 0 -0.57 39 39
LCP2 0.01 0.047 -9999 0 -0.59 5 5
MAPK8 -0.042 0.21 -9999 0 -0.73 66 66
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family -0.011 0.15 -9999 0 -0.56 39 39
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.029 0.19 -9999 0 -0.72 43 43
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.011 0.13 -9999 0 -0.43 67 67
E-cadherin/beta catenin -0.022 0.14 -9999 0 -0.49 69 69
CTNNB1 0.011 0.033 -9999 0 -0.53 3 3
JUP 0.01 0.04 -9999 0 -0.56 4 4
CDH1 -0.04 0.18 -9999 0 -0.67 66 66
Signaling events mediated by PTP1B

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
PDGFRB 0.002 0.088 -10000 0 -0.67 14 14
Jak2/Leptin Receptor -0.033 0.1 -10000 0 -0.46 25 25
PTP1B/AKT1 -0.014 0.087 -10000 0 -0.37 23 23
FYN 0.009 0.046 -10000 0 -0.53 6 6
p210 bcr-abl/PTP1B -0.023 0.096 -10000 0 -0.36 37 37
EGFR -0.079 0.22 -10000 0 -0.58 129 129
EGF/EGFR -0.14 0.2 -10000 0 -0.44 214 214
CSF1 0.002 0.08 -10000 0 -0.55 17 17
AKT1 0.013 0.001 -10000 0 -10000 0 0
INSR 0.012 0.023 -10000 0 -0.46 2 2
PTP1B/N-cadherin -0.05 0.15 -10000 0 -0.42 85 85
Insulin Receptor/Insulin -0.025 0.059 -10000 0 -0.37 9 9
HCK 0.002 0.078 -10000 0 -0.52 18 18
CRK 0.012 0.024 -10000 0 -0.67 1 1
TYK2 -0.015 0.092 -10000 0 -0.36 30 30
EGF -0.14 0.27 -10000 0 -0.62 201 201
YES1 0.007 0.064 -10000 0 -0.65 8 8
CAV1 -0.041 0.13 -10000 0 -0.39 46 46
TXN 0.01 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.031 0.14 -10000 0 -0.43 67 67
cell migration 0.023 0.096 0.36 37 -10000 0 37
STAT3 0.012 0.024 -10000 0 -0.68 1 1
PRLR -0.019 0.14 -10000 0 -0.66 40 40
ITGA2B -0.06 0.19 -10000 0 -0.54 110 110
CSF1R 0.004 0.074 -10000 0 -0.6 12 12
Prolactin Receptor/Prolactin -0.031 0.12 -10000 0 -0.45 60 60
FGR 0.005 0.069 -10000 0 -0.54 13 13
PTP1B/p130 Cas -0.015 0.092 -10000 0 -0.39 24 24
Crk/p130 Cas -0.007 0.09 -10000 0 -0.44 14 14
DOK1 -0.011 0.1 -10000 0 -0.46 24 24
JAK2 -0.02 0.097 -10000 0 -0.41 26 26
Jak2/Leptin Receptor/Leptin -0.13 0.15 -10000 0 -0.49 54 54
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
PTPN1 -0.023 0.097 -10000 0 -0.36 37 37
LYN 0.006 0.061 -10000 0 -0.49 12 12
CDH2 -0.054 0.19 -10000 0 -0.56 98 98
SRC 0.006 0.047 -10000 0 -0.61 2 2
ITGB3 -0.01 0.12 -10000 0 -0.59 31 31
CAT1/PTP1B -0.1 0.18 -10000 0 -0.49 81 81
CAPN1 0.013 0.002 -10000 0 -10000 0 0
CSK 0.013 0 -10000 0 -10000 0 0
PI3K -0.017 0.055 -10000 0 -0.46 3 3
mol:H2O2 -0.003 0.004 -10000 0 -10000 0 0
STAT3 (dimer) -0.11 0.14 -10000 0 -0.48 41 41
negative regulation of transcription -0.02 0.095 -10000 0 -0.41 26 26
FCGR2A 0.009 0.052 -10000 0 -0.6 6 6
FER 0.001 0.075 -10000 0 -0.68 10 10
alphaIIb/beta3 Integrin -0.058 0.16 -10000 0 -0.4 138 138
BLK -0.14 0.26 -10000 0 -0.56 218 218
Insulin Receptor/Insulin/Shc 0.017 0.014 -10000 0 -10000 0 0
RHOA 0.013 0.002 -10000 0 -10000 0 0
LEPR -0.005 0.097 -10000 0 -0.51 29 29
BCAR1 0.013 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.013 0.016 -10000 0 -0.46 1 1
mol:NADPH -0.002 0.004 -10000 0 -10000 0 0
TRPV6 -0.12 0.2 -10000 0 -0.54 95 95
PRL -0.008 0.075 -10000 0 -0.46 23 23
SOCS3 0.001 0.13 -10000 0 -1.4 6 6
SPRY2 0 0.078 -10000 0 -0.52 18 18
Insulin Receptor/Insulin/IRS1 -0.014 0.12 -10000 0 -0.43 59 59
CSF1/CSF1R -0.017 0.12 -10000 0 -0.44 36 36
Ras protein signal transduction 0.021 0.03 -10000 0 -0.34 1 1
IRS1 -0.033 0.17 -10000 0 -0.66 58 58
INS 0 0.001 -10000 0 -10000 0 0
LEP -0.23 0.3 -10000 0 -0.57 354 354
STAT5B -0.019 0.09 -10000 0 -0.33 34 34
STAT5A -0.02 0.092 -10000 0 -0.34 34 34
GRB2 0.013 0.016 -10000 0 -0.46 1 1
PDGFB-D/PDGFRB -0.021 0.12 -10000 0 -0.48 31 31
CSN2 -0.001 0.045 0.1 1 -0.16 51 52
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
LAT -0.012 0.11 -10000 0 -0.62 22 22
YBX1 0.015 0.039 -10000 0 -0.44 3 3
LCK -0.07 0.21 -10000 0 -0.6 114 114
SHC1 0.013 0 -10000 0 -10000 0 0
NOX4 -0.017 0.14 -10000 0 -0.67 35 35
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.001 0.091 -10000 0 -0.28 76 76
epithelial cell differentiation -0.03 0.098 -10000 0 -0.36 68 68
CYFIP2 -0.025 0.15 -10000 0 -0.63 50 50
ENAH 0.035 0.081 -10000 0 -10000 0 0
EGFR -0.076 0.22 -10000 0 -0.57 129 129
EPHA2 0.003 0.075 -10000 0 -0.54 15 15
MYO6 0.005 0.1 -10000 0 -0.34 70 70
CTNNB1 0.011 0.033 -10000 0 -0.53 3 3
ABI1/Sra1/Nap1 0.002 0.099 -10000 0 -0.42 39 39
AQP5 -0.15 0.21 -10000 0 -0.54 173 173
CTNND1 0.012 0.023 -10000 0 -0.46 2 2
mol:PI-4-5-P2 0.006 0.1 -10000 0 -0.33 68 68
regulation of calcium-dependent cell-cell adhesion -0.014 0.12 -10000 0 -0.34 80 80
EGF -0.14 0.27 -10000 0 -0.61 201 201
NCKAP1 0.013 0 -10000 0 -10000 0 0
AQP3 -0.1 0.19 -10000 0 -0.54 111 111
cortical microtubule organization -0.03 0.098 -10000 0 -0.36 68 68
GO:0000145 0.005 0.097 -10000 0 -0.32 68 68
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.002 0.11 -10000 0 -0.36 68 68
MLLT4 0.006 0.07 -10000 0 -0.63 10 10
ARF6/GDP -0.028 0.082 -10000 0 -10000 0 0
ARF6 0.013 0.016 -10000 0 -0.46 1 1
Ephrin A1/EPHA2/NCK1/GIT1 0.026 0.052 -10000 0 -0.38 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP 0.016 0.099 -10000 0 -10000 0 0
PVRL2 0.013 0 -10000 0 -10000 0 0
ZYX 0.005 0.1 -10000 0 -0.34 68 68
ARF6/GTP -0.007 0.043 -10000 0 -10000 0 0
CDH1 -0.04 0.18 -10000 0 -0.67 66 66
EGFR/EGFR/EGF/EGF -0.14 0.18 -10000 0 -0.56 51 51
RhoA/GDP -0.028 0.091 -10000 0 -0.33 68 68
actin cytoskeleton organization 0.01 0.1 -10000 0 -0.49 1 1
IGF-1R heterotetramer -0.061 0.21 -10000 0 -0.63 96 96
GIT1 0.01 0.043 -10000 0 -0.49 6 6
IGF1R -0.061 0.21 -10000 0 -0.64 96 96
IGF1 -0.07 0.21 -10000 0 -0.59 115 115
DIAPH1 -0.032 0.14 -10000 0 -0.64 39 39
Wnt receptor signaling pathway 0.03 0.098 0.36 68 -10000 0 68
RHOA 0.013 0 -10000 0 -10000 0 0
RhoA/GTP -0.028 0.082 -10000 0 -10000 0 0
CTNNA1 0.012 0.033 -10000 0 -0.67 2 2
VCL 0.01 0.1 -10000 0 -0.5 1 1
EFNA1 0.012 0.024 -10000 0 -0.67 1 1
LPP 0.01 0.1 -10000 0 -10000 0 0
Ephrin A1/EPHA2 -0.032 0.094 -10000 0 -0.39 2 2
SEC6/SEC8 -0.028 0.086 -10000 0 -0.55 2 2
MGAT3 -0.014 0.12 -10000 0 -0.35 80 80
HGF/MET -0.085 0.16 -10000 0 -0.64 26 26
HGF -0.033 0.17 -10000 0 -0.66 58 58
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.001 0.091 -10000 0 -0.29 76 76
actin cable formation 0.046 0.082 -10000 0 -10000 0 0
KIAA1543 0.01 0.11 -10000 0 -0.75 2 2
KIFC3 0.002 0.11 -10000 0 -0.34 76 76
NCK1 0.013 0 -10000 0 -10000 0 0
EXOC3 0.013 0 -10000 0 -10000 0 0
ACTN1 0.005 0.1 -10000 0 -0.34 69 69
NCK1/GIT1 0.017 0.031 -10000 0 -0.5 1 1
mol:GDP -0.03 0.098 -10000 0 -0.36 68 68
EXOC4 0.013 0 -10000 0 -10000 0 0
STX4 0.005 0.1 -10000 0 -0.34 70 70
PIP5K1C 0.005 0.1 -10000 0 -0.34 68 68
LIMA1 0.007 0.067 -10000 0 -0.67 8 8
ABI1 0.013 0 -10000 0 -10000 0 0
ROCK1 0.029 0.091 -10000 0 -10000 0 0
adherens junction assembly 0.021 0.11 -10000 0 -0.59 3 3
IGF-1R heterotetramer/IGF1 -0.099 0.17 -10000 0 -0.65 33 33
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.014 0.053 -10000 0 -0.46 10 10
MET -0.066 0.21 -10000 0 -0.6 108 108
PLEKHA7 0.004 0.11 -10000 0 -0.34 71 71
mol:GTP 0.025 0.051 -10000 0 -0.38 8 8
establishment of epithelial cell apical/basal polarity 0.027 0.1 -10000 0 -0.52 2 2
cortical actin cytoskeleton stabilization 0.001 0.091 -10000 0 -0.28 76 76
regulation of cell-cell adhesion 0.01 0.1 -10000 0 -0.49 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.001 0.091 -10000 0 -0.29 76 76
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.033 0.19 -9999 0 -0.69 36 36
MAP3K8 0.002 0.079 -9999 0 -0.55 16 16
FOS -0.028 0.17 -9999 0 -0.67 35 35
PRKCA -0.011 0.11 -9999 0 -0.53 37 37
PTPN7 -0.02 0.13 -9999 0 -0.55 49 49
HRAS 0.009 0.05 -9999 0 -0.63 5 5
PRKCB -0.066 0.21 -9999 0 -0.59 110 110
NRAS 0.007 0.062 -9999 0 -0.62 8 8
RAS family/GTP 0.018 0.049 -9999 0 -0.39 10 10
MAPK3 -0.018 0.14 -9999 0 -0.74 23 23
MAP2K1 -0.031 0.17 -9999 0 -0.51 76 76
ELK1 0.012 0.006 -9999 0 -10000 0 0
BRAF -0.035 0.16 -9999 0 -0.5 78 78
mol:GTP 0 0.002 -9999 0 -0.005 108 108
MAPK1 -0.018 0.14 -9999 0 -0.72 24 24
RAF1 -0.035 0.16 -9999 0 -0.5 78 78
KRAS 0.012 0.016 -9999 0 -0.46 1 1
Thromboxane A2 receptor signaling

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
TGM2 0 0.081 -10000 0 -0.5 21 21
GNB1/GNG2 -0.034 0.064 -10000 0 -0.2 62 62
AKT1 0.013 0.096 -10000 0 -0.22 24 24
EGF -0.14 0.27 -10000 0 -0.61 201 201
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.027 0.067 -10000 0 -0.45 3 3
mol:Ca2+ -0.003 0.13 -10000 0 -0.3 96 96
LYN 0.028 0.063 -10000 0 -0.51 1 1
RhoA/GTP -0.021 0.042 -10000 0 -0.16 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.008 0.15 -10000 0 -0.36 96 96
GNG2 0.011 0.033 -10000 0 -0.53 3 3
ARRB2 0.013 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.006 0.09 -10000 0 -0.42 25 25
G beta5/gamma2 -0.044 0.085 -10000 0 -0.27 61 61
PRKCH -0.005 0.15 -10000 0 -0.34 96 96
DNM1 -0.002 0.096 -10000 0 -0.61 20 20
TXA2/TP beta/beta Arrestin3 -0.007 0.037 -10000 0 -0.24 17 17
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR -0.022 0.14 -10000 0 -0.55 52 52
G12 family/GTP -0.053 0.1 -10000 0 -0.31 93 93
ADRBK1 0.013 0.016 -10000 0 -0.46 1 1
ADRBK2 0.01 0.047 -10000 0 -0.67 4 4
RhoA/GTP/ROCK1 0.013 0.017 -10000 0 -0.43 1 1
mol:GDP -0.005 0.096 0.36 19 -10000 0 19
mol:NADP 0.011 0.037 -10000 0 -0.51 4 4
RAB11A 0.012 0.023 -10000 0 -0.46 2 2
PRKG1 -0.041 0.18 -10000 0 -0.67 67 67
mol:IP3 -0.011 0.16 -10000 0 -0.38 96 96
cell morphogenesis 0.013 0.017 -10000 0 -0.43 1 1
PLCB2 -0.026 0.2 -10000 0 -0.51 96 96
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.04 0.13 -10000 0 -0.45 11 11
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.026 0.066 -10000 0 -0.33 1 1
RHOA 0.013 0 -10000 0 -10000 0 0
PTGIR 0.007 0.067 -10000 0 -0.68 8 8
PRKCB1 -0.011 0.15 -10000 0 -0.37 96 96
GNAQ 0.007 0.062 -10000 0 -0.67 7 7
mol:L-citrulline 0.011 0.037 -10000 0 -0.51 4 4
TXA2/TXA2-R family -0.029 0.21 -10000 0 -0.54 96 96
LCK -0.007 0.13 -10000 0 -0.5 19 19
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.014 0.054 -10000 0 -0.42 1 1
TXA2-R family/G12 family/GDP/G beta/gamma 0.027 0.023 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.013 0.052 -10000 0 -0.41 1 1
MAPK14 0.007 0.11 -10000 0 -0.25 41 41
TGM2/GTP -0.018 0.18 -10000 0 -0.43 97 97
MAPK11 0.005 0.11 -10000 0 -0.26 47 47
ARHGEF1 0.007 0.082 -10000 0 -0.2 25 25
GNAI2 0.013 0 -10000 0 -10000 0 0
JNK cascade -0.012 0.16 -10000 0 -0.39 97 97
RAB11/GDP 0.012 0.023 -10000 0 -0.45 2 2
ICAM1 -0.004 0.13 -10000 0 -0.3 97 97
cAMP biosynthetic process -0.014 0.15 -10000 0 -0.36 96 96
Gq family/GTP/EBP50 -0.009 0.095 -10000 0 -0.32 36 36
actin cytoskeleton reorganization 0.013 0.017 -10000 0 -0.43 1 1
SRC 0.03 0.059 -10000 0 -0.33 1 1
GNB5 0.01 0.047 -10000 0 -0.67 4 4
GNB1 0.013 0 -10000 0 -10000 0 0
EGF/EGFR -0.036 0.12 -10000 0 -0.37 37 37
VCAM1 -0.008 0.14 -10000 0 -0.33 99 99
TP beta/Gq family/GDP/G beta5/gamma2 0.006 0.09 -10000 0 -0.42 25 25
platelet activation 0.009 0.14 -10000 0 -0.31 92 92
PGI2/IP 0.005 0.05 -10000 0 -0.51 8 8
PRKACA 0.003 0.072 -10000 0 -0.32 31 31
Gq family/GDP/G beta5/gamma2 0.005 0.087 -10000 0 -0.39 25 25
TXA2/TP beta/beta Arrestin2 -0.012 0.076 -10000 0 -0.58 14 14
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R 0.01 0.068 -10000 0 -0.3 31 31
mol:DAG -0.014 0.17 -10000 0 -0.42 96 96
EGFR -0.076 0.22 -10000 0 -0.57 129 129
TXA2/TP alpha -0.025 0.2 -10000 0 -0.49 96 96
Gq family/GTP -0.029 0.087 -10000 0 -0.28 71 71
YES1 0.028 0.063 -10000 0 -0.33 1 1
GNAI2/GTP -0.013 0.051 -10000 0 -0.39 1 1
PGD2/DP -0.016 0.1 -10000 0 -0.41 52 52
SLC9A3R1 -0.005 0.1 -10000 0 -0.58 26 26
FYN 0.029 0.063 -10000 0 -0.56 2 2
mol:NO 0.011 0.037 -10000 0 -0.51 4 4
GNA15 -0.002 0.096 -10000 0 -0.61 20 20
PGK/cGMP -0.019 0.12 -10000 0 -0.43 69 69
RhoA/GDP 0.013 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.022 0.075 -10000 0 -0.52 3 3
NOS3 0.011 0.037 -10000 0 -0.51 4 4
RAC1 0.013 0 -10000 0 -10000 0 0
PRKCA -0.012 0.15 -10000 0 -0.36 98 98
PRKCB -0.024 0.18 -10000 0 -0.41 102 102
PRKCE -0.004 0.15 -10000 0 -0.35 84 84
PRKCD -0.008 0.16 -10000 0 -0.37 94 94
PRKCG -0.015 0.16 -10000 0 -0.39 96 96
muscle contraction -0.025 0.2 -10000 0 -0.5 96 96
PRKCZ -0.005 0.15 -10000 0 -0.35 94 94
ARR3 0 0 -10000 0 -10000 0 0
TXA2/TP beta 0.014 0.067 -10000 0 -0.43 1 1
PRKCQ -0.031 0.18 -10000 0 -0.4 111 111
MAPKKK cascade -0.025 0.19 -10000 0 -0.47 99 99
SELE -0.019 0.16 -10000 0 -0.39 100 100
TP beta/GNAI2/GDP/G beta/gamma 0.028 0.065 -10000 0 -0.5 2 2
ROCK1 0.012 0.024 -10000 0 -0.67 1 1
GNA14 -0.054 0.19 -10000 0 -0.57 97 97
chemotaxis -0.038 0.24 -10000 0 -0.62 96 96
GNA12 0.013 0 -10000 0 -10000 0 0
GNA13 0.013 0 -10000 0 -10000 0 0
GNA11 0.01 0.047 -10000 0 -0.67 4 4
Rac1/GTP 0.008 0.005 -10000 0 -10000 0 0
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 0.13 -9999 0 -0.48 47 47
EPHB2 0.003 0.077 -9999 0 -0.56 15 15
Syndecan-2/TACI -0.054 0.15 -9999 0 -0.43 81 81
LAMA1 -0.068 0.21 -9999 0 -0.62 108 108
Syndecan-2/alpha2 ITGB1 -0.042 0.17 -9999 0 -0.41 120 120
HRAS 0.009 0.05 -9999 0 -0.63 5 5
Syndecan-2/CASK 0.001 0.067 -9999 0 -0.32 34 34
ITGA5 0.011 0.037 -9999 0 -0.6 3 3
BAX 0.027 0.061 -9999 0 -10000 0 0
EPB41 0.013 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion 0.01 0.062 -9999 0 -0.28 35 35
LAMA3 -0.082 0.23 -9999 0 -0.61 128 128
EZR 0.012 0.024 -9999 0 -0.67 1 1
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.006 0.064 -9999 0 -0.56 10 10
Syndecan-2/MMP2 -0.011 0.13 -9999 0 -0.41 68 68
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.002 0.1 -9999 0 -0.48 36 36
dendrite morphogenesis 0.005 0.086 -9999 0 -0.34 46 46
Syndecan-2/GM-CSF -0.002 0.08 -9999 0 -0.29 58 58
determination of left/right symmetry 0.004 0.079 -9999 0 -0.37 34 34
Syndecan-2/PKC delta 0.011 0.068 -9999 0 -0.42 11 11
GNB2L1 0.013 0 -9999 0 -10000 0 0
MAPK3 0.008 0.073 -9999 0 -0.38 11 11
MAPK1 0.008 0.073 -9999 0 -0.38 11 11
Syndecan-2/RACK1 0.016 0.066 -9999 0 -0.37 15 15
NF1 0.01 0.044 -9999 0 -0.62 4 4
FGFR/FGF/Syndecan-2 0.004 0.079 -9999 0 -0.37 34 34
ITGA2 -0.015 0.14 -9999 0 -0.65 36 36
MAPK8 0.02 0.068 -9999 0 -0.42 11 11
Syndecan-2/alpha2/beta1 Integrin -0.034 0.17 -9999 0 -0.44 102 102
Syndecan-2/Kininogen 0.001 0.067 -9999 0 -0.32 34 34
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.022 0.066 -9999 0 -0.35 17 17
Syndecan-2/CASK/Protein 4.1 0.01 0.062 -9999 0 -0.28 34 34
extracellular matrix organization 0.009 0.075 -9999 0 -0.32 36 36
actin cytoskeleton reorganization -0.013 0.13 -9999 0 -0.48 47 47
Syndecan-2/Caveolin-2/Ras 0.013 0.085 -9999 0 -0.46 18 18
Syndecan-2/Laminin alpha3 -0.049 0.16 -9999 0 -0.45 99 99
Syndecan-2/RasGAP 0.021 0.066 -9999 0 -0.35 16 16
alpha5/beta1 Integrin 0.018 0.028 -9999 0 -0.44 3 3
PRKCD 0.013 0.016 -9999 0 -0.46 1 1
Syndecan-2 dimer 0.005 0.087 -9999 0 -0.34 46 46
GO:0007205 0.004 0 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.028 0.067 -9999 0 -0.33 18 18
RHOA 0.013 0 -9999 0 -10000 0 0
SDCBP 0.013 0.016 -9999 0 -0.46 1 1
TNFRSF13B -0.089 0.22 -9999 0 -0.56 149 149
RASA1 0.011 0.037 -9999 0 -0.51 4 4
alpha2/beta1 Integrin -0.002 0.1 -9999 0 -0.48 36 36
Syndecan-2/Synbindin 0.011 0.068 -9999 0 -0.31 34 34
TGFB1 0.011 0.041 -9999 0 -0.67 3 3
CASP3 0.019 0.062 -9999 0 -0.38 11 11
FN1 -0.025 0.16 -9999 0 -0.64 49 49
Syndecan-2/IL8 -0.066 0.16 -9999 0 -0.34 212 212
SDC2 0.004 0.08 -9999 0 -0.37 34 34
KNG1 0 0 -9999 0 -10000 0 0
Syndecan-2/Neurofibromin 0.009 0.073 -9999 0 -0.32 38 38
TRAPPC4 0.013 0 -9999 0 -10000 0 0
CSF2 -0.007 0.077 -9999 0 -0.46 24 24
Syndecan-2/TGFB1 0.01 0.075 -9999 0 -0.33 36 36
Syndecan-2/Syntenin/PI-4-5-P2 0.01 0.062 -9999 0 -0.28 35 35
Syndecan-2/Ezrin 0.019 0.063 -9999 0 -0.38 12 12
PRKACA 0.018 0.067 -9999 0 -0.38 14 14
angiogenesis -0.066 0.16 -9999 0 -0.33 212 212
MMP2 -0.021 0.15 -9999 0 -0.65 44 44
IL8 -0.11 0.24 -9999 0 -0.54 188 188
calcineurin-NFAT signaling pathway -0.054 0.15 -9999 0 -0.43 81 81
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.04 0.16 -10000 0 -0.44 108 108
CRKL -0.014 0.12 -10000 0 -0.34 79 79
mol:PIP3 -0.014 0.055 0.63 6 -10000 0 6
AKT1 0.005 0.036 0.42 6 -10000 0 6
PTK2B 0.01 0.047 -10000 0 -0.59 5 5
RAPGEF1 -0.006 0.12 -10000 0 -0.46 20 20
RANBP10 0.013 0 -10000 0 -10000 0 0
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
HGF/MET/SHIP2 -0.053 0.18 -10000 0 -0.48 114 114
MAP3K5 -0.012 0.14 -10000 0 -0.48 32 32
HGF/MET/CIN85/CBL/ENDOPHILINS -0.04 0.17 -10000 0 -0.43 114 114
AP1 -0.049 0.14 -10000 0 -0.37 114 114
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.013 0 -10000 0 -10000 0 0
apoptosis -0.05 0.19 -10000 0 -0.77 51 51
STAT3 (dimer) -0.014 0.13 -10000 0 -0.54 19 19
GAB1/CRKL/SHP2/PI3K -0.039 0.095 -10000 0 -0.48 15 15
INPP5D 0.005 0.067 -10000 0 -0.52 13 13
CBL/CRK -0.005 0.12 -10000 0 -0.46 20 20
PTPN11 0.013 0 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.013 0 -10000 0 -10000 0 0
PTEN 0.008 0.058 -10000 0 -0.67 6 6
ELK1 -0.027 0.074 -10000 0 -0.22 108 108
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.03 0.077 -10000 0 -0.37 19 19
PAK1 0.005 0.05 0.39 6 -0.37 2 8
HGF/MET/RANBP10 -0.053 0.18 -10000 0 -0.48 114 114
HRAS -0.055 0.23 -10000 0 -0.72 77 77
DOCK1 -0.006 0.12 -10000 0 -0.47 21 21
GAB1 -0.021 0.13 -10000 0 -0.36 79 79
CRK -0.014 0.12 -10000 0 -0.34 79 79
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.092 0.23 -10000 0 -0.64 113 113
JUN 0.009 0.049 -10000 0 -0.52 7 7
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.037 0.12 -10000 0 -0.32 116 116
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
cell morphogenesis 0.009 0.13 -10000 0 -0.55 15 15
GRB2/SHC -0.017 0.11 -10000 0 -0.46 18 18
FOS -0.062 0.2 -10000 0 -0.55 112 112
GLMN 0 0.005 -10000 0 -10000 0 0
cell motility -0.027 0.074 -10000 0 -0.22 108 108
HGF/MET/MUC20 -0.062 0.18 -10000 0 -0.44 148 148
cell migration -0.017 0.11 -10000 0 -0.46 18 18
GRB2 0.013 0.016 -10000 0 -0.46 1 1
CBL 0.013 0 -10000 0 -10000 0 0
MET/RANBP10 -0.04 0.16 -10000 0 -0.44 108 108
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.02 0.13 -10000 0 -0.57 18 18
MET/MUC20 -0.049 0.16 -10000 0 -0.45 108 108
RAP1B 0.002 0.11 -10000 0 -0.47 15 15
RAP1A 0.002 0.11 -10000 0 -0.47 15 15
HGF/MET/RANBP9 -0.053 0.18 -10000 0 -0.48 114 114
RAF1 -0.044 0.21 -10000 0 -0.66 77 77
STAT3 -0.014 0.13 -10000 0 -0.54 19 19
cell proliferation -0.022 0.18 -10000 0 -0.48 77 77
RPS6KB1 -0.006 0.046 -10000 0 -0.25 1 1
MAPK3 -0.03 0.067 -10000 0 -10000 0 0
MAPK1 -0.03 0.067 -10000 0 -10000 0 0
RANBP9 0.013 0 -10000 0 -10000 0 0
MAPK8 0.009 0.11 -10000 0 -0.4 23 23
SRC -0.013 0.13 -10000 0 -0.52 20 20
PI3K -0.018 0.11 -10000 0 -0.46 18 18
MET/Glomulin -0.04 0.14 -10000 0 -0.4 108 108
SOS1 0.013 0 -10000 0 -10000 0 0
MAP2K1 -0.032 0.2 -10000 0 -0.6 77 77
MET -0.066 0.21 -10000 0 -0.6 108 108
MAP4K1 -0.019 0.14 -10000 0 -0.48 36 36
PTK2 0.013 0 -10000 0 -10000 0 0
MAP2K2 -0.032 0.2 -10000 0 -0.6 77 77
BAD 0.011 0.033 0.39 6 -10000 0 6
MAP2K4 -0.006 0.13 -10000 0 -0.45 29 29
SHP2/GRB2/SOS1/GAB1 -0.055 0.14 -10000 0 -0.45 77 77
INPPL1 0.013 0 -10000 0 -10000 0 0
PXN 0.013 0 -10000 0 -10000 0 0
SH3KBP1 0.013 0.016 -10000 0 -0.46 1 1
HGS -0.027 0.12 -10000 0 -0.33 79 79
PLCgamma1/PKC 0.01 0 -10000 0 -10000 0 0
HGF -0.033 0.17 -10000 0 -0.66 58 58
RASA1 0.011 0.037 -10000 0 -0.51 4 4
NCK1 0.013 0 -10000 0 -10000 0 0
PTPRJ 0.011 0.041 -10000 0 -0.67 3 3
NCK/PLCgamma1 -0.016 0.12 -10000 0 -0.48 18 18
PDPK1 -0.004 0.042 0.48 6 -10000 0 6
HGF/MET/SHIP -0.058 0.19 -10000 0 -0.49 118 118
IL2 signaling events mediated by PI3K

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
BCL2L1 -0.016 0.2 -10000 0 -0.76 38 38
UGCG -0.02 0.14 -10000 0 -0.69 28 28
AKT1/mTOR/p70S6K/Hsp90/TERT -0.047 0.18 -10000 0 -0.43 92 92
mol:GTP 0 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.02 0.14 -10000 0 -0.68 28 28
mol:DAG -0.002 0.005 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.1 0.18 -10000 0 -0.5 106 106
FRAP1 -0.061 0.25 -10000 0 -0.59 106 106
FOXO3 -0.034 0.21 -10000 0 -0.6 67 67
AKT1 -0.044 0.23 -10000 0 -0.65 69 69
GAB2 -0.002 0.082 -10000 0 -0.47 24 24
SMPD1 0.005 0.04 -10000 0 -10000 0 0
SGMS1 0.005 0.04 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.021 -10000 0 -0.27 4 4
CALM1 0.013 0 -10000 0 -10000 0 0
cell proliferation -0.017 0.13 -10000 0 -0.4 43 43
EIF3A 0.013 0 -10000 0 -10000 0 0
PI3K 0.021 0.025 -10000 0 -0.32 4 4
RPS6KB1 -0.011 0.08 -10000 0 -10000 0 0
mol:sphingomyelin -0.002 0.005 -10000 0 -10000 0 0
natural killer cell activation 0 0.003 -10000 0 -0.015 3 3
JAK3 -0.012 0.12 -10000 0 -0.57 39 39
PIK3R1 0.013 0.023 -10000 0 -0.46 2 2
JAK1 0.014 0.024 -10000 0 -0.67 1 1
NFKB1 0.012 0.024 -10000 0 -0.67 1 1
MYC -0.044 0.25 -10000 0 -0.8 59 59
MYB -0.13 0.42 -10000 0 -1.3 97 97
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.045 0.23 -10000 0 -0.7 68 68
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.005 0.075 -10000 0 -0.39 1 1
mol:PI-3-4-5-P3 -0.043 0.22 -10000 0 -0.67 68 68
Rac1/GDP 0.023 0.02 -10000 0 -10000 0 0
T cell proliferation -0.031 0.21 -10000 0 -0.62 66 66
SHC1 0.012 0.005 -10000 0 -10000 0 0
RAC1 0.013 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.003 0.023 -10000 0 -0.066 97 97
PRKCZ -0.035 0.22 -10000 0 -0.65 66 66
NF kappa B1 p50/RelA -0.097 0.18 -10000 0 -0.53 85 85
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.03 0.22 -10000 0 -0.68 67 67
HSP90AA1 0.013 0.016 -10000 0 -0.46 1 1
RELA 0.013 0 -10000 0 -10000 0 0
IL2RA -0.087 0.23 -10000 0 -0.6 136 136
IL2RB -0.033 0.16 -10000 0 -0.55 72 72
TERT -0.06 0.19 -10000 0 -0.55 108 108
E2F1 -0.042 0.17 -10000 0 -0.46 119 119
SOS1 0.012 0.004 -10000 0 -10000 0 0
RPS6 0.013 0.016 -10000 0 -0.46 1 1
mol:cAMP 0.001 0.011 0.031 97 -10000 0 97
PTPN11 0.012 0.005 -10000 0 -10000 0 0
IL2RG -0.037 0.17 -10000 0 -0.57 75 75
actin cytoskeleton organization -0.031 0.21 -10000 0 -0.62 66 66
GRB2 0.012 0.017 -10000 0 -0.46 1 1
IL2 -0.001 0.065 -10000 0 -0.45 17 17
PIK3CA 0.013 0.024 -10000 0 -0.46 2 2
Rac1/GTP 0.029 0.023 -10000 0 -10000 0 0
LCK -0.069 0.21 -10000 0 -0.6 114 114
BCL2 -0.087 0.32 -10000 0 -0.84 107 107
Canonical Wnt signaling pathway

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 0.012 0.042 -10000 0 -0.68 1 1
AES 0.018 0.027 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.012 0.053 -10000 0 -0.38 14 14
SMAD4 0.012 0.024 -10000 0 -0.67 1 1
DKK2 -0.024 0.15 -10000 0 -0.62 49 49
TLE1 -0.005 0.13 -10000 0 -0.67 29 29
MACF1 0.014 0 -10000 0 -10000 0 0
CTNNB1 0.041 0.089 0.3 6 -0.35 2 8
WIF1 -0.17 0.26 -10000 0 -0.54 282 282
beta catenin/RanBP3 0.033 0.14 0.41 81 -10000 0 81
KREMEN2 -0.12 0.24 -10000 0 -0.54 204 204
DKK1 -0.18 0.27 -10000 0 -0.55 293 293
beta catenin/beta TrCP1 0.047 0.084 0.29 6 -10000 0 6
FZD1 0.008 0.057 -10000 0 -0.56 8 8
AXIN2 -0.052 0.3 -10000 0 -1.5 31 31
AXIN1 0.014 0.001 -10000 0 -10000 0 0
RAN 0.013 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.021 0.034 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.055 0.11 0.3 2 -0.53 14 16
Axin1/APC/GSK3 0.019 0.053 0.26 12 -10000 0 12
Axin1/APC/GSK3/beta catenin/Macf1 0.05 0.053 -10000 0 -10000 0 0
HNF1A 0.012 0.06 -10000 0 -0.45 10 10
CTBP1 0.018 0.029 -10000 0 -10000 0 0
MYC -0.052 0.28 -10000 0 -1.5 27 27
RANBP3 0.013 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.088 0.18 -10000 0 -0.45 117 117
NKD1 -0.03 0.16 -10000 0 -0.64 56 56
TCF4 0.011 0.076 -10000 0 -0.66 9 9
TCF3 0.018 0.029 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.02 0.054 -10000 0 -0.38 5 5
Ran/GTP 0.01 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.045 0.18 0.51 88 -0.57 4 92
LEF1 -0.004 0.11 -10000 0 -0.52 35 35
DVL1 0.052 0.05 -10000 0 -0.32 5 5
CSNK2A1 0.012 0.033 -10000 0 -0.67 2 2
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.037 0.13 -10000 0 -0.54 15 15
DKK1/LRP6/Kremen 2 -0.18 0.23 -10000 0 -0.49 233 233
LRP6 0.01 0.043 -10000 0 -0.49 6 6
CSNK1A1 0.017 0.033 -10000 0 -10000 0 0
NLK 0.012 0.017 -10000 0 -0.45 1 1
CCND1 -0.095 0.38 -10000 0 -1.6 52 52
WNT1 0.002 0.064 -10000 0 -0.46 16 16
GSK3A 0.013 0.001 -10000 0 -10000 0 0
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.008 0.058 -10000 0 -0.67 6 6
PPP2R5D 0.047 0.076 0.31 55 -10000 0 55
APC 0.029 0.05 -10000 0 -0.35 5 5
WNT1/LRP6/FZD1 0.07 0.096 0.25 103 -0.29 4 107
CREBBP 0.017 0.044 -10000 0 -0.68 2 2
IL2 signaling events mediated by STAT5

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
GAB2 0 0.082 -9999 0 -0.47 24 24
ELF1 -0.032 0.12 -9999 0 -0.36 89 89
CCNA2 -0.011 0.12 -9999 0 -0.63 32 32
PIK3CA 0.013 0.023 -9999 0 -0.45 2 2
JAK3 -0.013 0.12 -9999 0 -0.57 39 39
PIK3R1 0.013 0.023 -9999 0 -0.46 2 2
JAK1 0.013 0.024 -9999 0 -0.67 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.025 0.23 -9999 0 -0.67 70 70
SHC1 0.014 0.001 -9999 0 -10000 0 0
SP1 0.017 0.037 -9999 0 -0.36 7 7
IL2RA -0.091 0.3 -9999 0 -0.73 136 136
IL2RB -0.034 0.16 -9999 0 -0.55 72 72
SOS1 0.014 0.001 -9999 0 -10000 0 0
IL2RG -0.038 0.17 -9999 0 -0.57 75 75
G1/S transition of mitotic cell cycle -0.006 0.16 -9999 0 -0.6 45 45
PTPN11 0.014 0.001 -9999 0 -10000 0 0
CCND2 0.021 0.088 -9999 0 -0.75 10 10
LCK -0.07 0.21 -9999 0 -0.6 114 114
GRB2 0.013 0.016 -9999 0 -0.46 1 1
IL2 -0.002 0.065 -9999 0 -0.46 17 17
CDK6 -0.024 0.14 -9999 0 -0.52 59 59
CCND3 -0.008 0.19 -9999 0 -0.73 29 29
Ephrin B reverse signaling

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
EFNB2 0.006 0.07 -10000 0 -0.63 10 10
EPHB2 0.003 0.077 -10000 0 -0.56 15 15
EFNB1 0.009 0.079 -10000 0 -0.45 22 22
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.028 0.11 -10000 0 -0.53 16 16
Ephrin B2/EPHB1-2 -0.014 0.11 -10000 0 -0.46 24 24
neuron projection morphogenesis -0.037 0.1 -10000 0 -0.5 16 16
Ephrin B1/EPHB1-2/Tiam1 -0.009 0.13 -10000 0 -0.43 43 43
DNM1 -0.002 0.096 -10000 0 -0.61 20 20
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 -0.027 0.17 -10000 0 -0.67 55 55
YES1 -0.055 0.22 -10000 0 -0.94 50 50
Ephrin B1/EPHB1-2/NCK2 -0.004 0.12 -10000 0 -0.41 37 37
PI3K -0.023 0.17 -10000 0 -0.7 50 50
mol:GDP -0.009 0.12 -10000 0 -0.43 43 43
ITGA2B -0.059 0.19 -10000 0 -0.54 110 110
endothelial cell proliferation 0.009 0.058 -10000 0 -0.4 16 16
FYN -0.054 0.22 -10000 0 -0.93 50 50
MAP3K7 -0.043 0.18 -10000 0 -0.74 50 50
FGR -0.055 0.22 -10000 0 -0.92 50 50
TIAM1 0.002 0.084 -10000 0 -0.62 15 15
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
RGS3 0.013 0 -10000 0 -10000 0 0
cell adhesion -0.054 0.2 -10000 0 -0.68 58 58
LYN -0.055 0.22 -10000 0 -0.93 50 50
Ephrin B1/EPHB1-2/Src Family Kinases -0.053 0.21 -10000 0 -0.87 50 50
Ephrin B1/EPHB1-2 -0.051 0.19 -10000 0 -0.79 50 50
SRC -0.054 0.22 -10000 0 -0.92 50 50
ITGB3 -0.009 0.12 -10000 0 -0.59 31 31
EPHB1 -0.04 0.15 -10000 0 -0.48 91 91
EPHB4 0.009 0.055 -10000 0 -0.64 6 6
RAC1 0.013 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.01 0.058 -10000 0 -0.4 16 16
alphaIIb/beta3 Integrin -0.05 0.16 -10000 0 -0.4 138 138
BLK -0.083 0.23 -10000 0 -0.95 50 50
HCK -0.055 0.22 -10000 0 -0.92 50 50
regulation of stress fiber formation 0.004 0.11 0.41 37 -10000 0 37
MAPK8 -0.018 0.16 -10000 0 -0.63 55 55
Ephrin B1/EPHB1-2/RGS3 -0.002 0.11 -10000 0 -0.41 34 34
endothelial cell migration -0.042 0.16 -10000 0 -0.59 61 61
NCK2 0.011 0.033 -10000 0 -0.53 3 3
PTPN13 -0.038 0.19 -10000 0 -0.78 51 51
regulation of focal adhesion formation 0.004 0.11 0.41 37 -10000 0 37
chemotaxis 0.003 0.11 0.41 34 -10000 0 34
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
Rac1/GTP -0.038 0.1 -10000 0 -0.52 16 16
angiogenesis -0.051 0.19 -10000 0 -0.79 50 50
LCK -0.072 0.23 -10000 0 -0.94 50 50
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.012 0.055 -9999 0 -0.37 16 16
alphaV beta3 Integrin -0.024 0.14 -9999 0 -0.49 45 45
PTK2 -0.028 0.15 -9999 0 -0.59 28 28
IGF1R -0.061 0.21 -9999 0 -0.64 96 96
PI4KB 0.013 0 -9999 0 -10000 0 0
MFGE8 -0.02 0.13 -9999 0 -0.5 55 55
SRC 0.011 0.037 -9999 0 -0.6 3 3
CDKN1B -0.042 0.16 -9999 0 -0.59 46 46
VEGFA 0.008 0.051 -9999 0 -0.46 10 10
ILK -0.033 0.13 -9999 0 -0.53 33 33
ROCK1 0.012 0.024 -9999 0 -0.67 1 1
AKT1 -0.022 0.12 -9999 0 -0.54 26 26
PTK2B 0.018 0.094 -9999 0 -0.44 25 25
alphaV/beta3 Integrin/JAM-A -0.044 0.16 -9999 0 -0.45 75 75
CBL 0.013 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.003 0.093 -9999 0 -0.43 27 27
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.084 0.23 -9999 0 -0.5 155 155
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.007 0.091 -9999 0 -0.55 9 9
alphaV/beta3 Integrin/Syndecan-1 -0.004 0.12 -9999 0 -0.47 44 44
PI4KA 0.013 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.14 0.26 -9999 0 -0.72 101 101
PI4 Kinase 0.02 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
alphaV/beta3 Integrin/Osteopontin -0.044 0.17 -9999 0 -0.46 92 92
RPS6KB1 -0.1 0.25 -9999 0 -0.69 89 89
TLN1 0.013 0 -9999 0 -10000 0 0
MAPK3 -0.064 0.22 -9999 0 -0.85 45 45
GPR124 0.008 0.058 -9999 0 -0.67 6 6
MAPK1 -0.064 0.22 -9999 0 -0.85 45 45
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
alphaV/beta3 Integrin/Tumstatin -0.055 0.16 -9999 0 -0.46 85 85
cell adhesion -0.017 0.11 -9999 0 -0.44 33 33
ANGPTL3 0.001 0.053 -9999 0 -0.46 11 11
VEGFR2 homodimer/VEGFA homodimer/Src 0.019 0.053 -9999 0 -0.42 7 7
IGF-1R heterotetramer -0.061 0.21 -9999 0 -0.63 96 96
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
TGFBR2 0.008 0.06 -9999 0 -0.64 7 7
ITGB3 -0.009 0.12 -9999 0 -0.59 31 31
IGF1 -0.07 0.21 -9999 0 -0.59 115 115
RAC1 0.013 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion 0.008 0.098 -9999 0 -0.5 23 23
apoptosis 0.011 0.041 -9999 0 -0.67 3 3
CD47 0.011 0.037 -9999 0 -0.6 3 3
alphaV/beta3 Integrin/CD47 0.01 0.088 -9999 0 -0.48 21 21
VCL 0.011 0.033 -9999 0 -0.53 3 3
alphaV/beta3 Integrin/Del1 -0.046 0.18 -9999 0 -0.5 99 99
CSF1 0.002 0.08 -9999 0 -0.55 17 17
PIK3C2A -0.033 0.13 -9999 0 -0.58 26 26
PI4 Kinase/Pyk2 -0.063 0.13 -9999 0 -0.61 21 21
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.014 0.097 -9999 0 -0.49 22 22
FAK1/Vinculin -0.015 0.12 -9999 0 -0.46 26 26
alphaV beta3/Integrin/ppsTEM5 0.008 0.098 -9999 0 -0.51 23 23
RHOA 0.013 0 -9999 0 -10000 0 0
VTN -0.063 0.18 -9999 0 -0.5 124 124
BCAR1 0.013 0 -9999 0 -10000 0 0
FGF2 -0.044 0.17 -9999 0 -0.52 89 89
F11R -0.02 0.13 -9999 0 -0.37 90 90
alphaV/beta3 Integrin/Lactadherin -0.009 0.12 -9999 0 -0.5 29 29
alphaV/beta3 Integrin/TGFBR2 0.008 0.099 -9999 0 -0.51 24 24
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.026 0.053 -9999 0 -0.38 10 10
HSP90AA1 0.013 0.016 -9999 0 -0.46 1 1
alphaV/beta3 Integrin/Talin 0.011 0.079 -9999 0 -0.45 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.025 0.16 -9999 0 -0.64 49 49
alphaV/beta3 Integrin/Pyk2 0.019 0.095 -9999 0 -0.44 25 25
SDC1 -0.011 0.12 -9999 0 -0.65 30 30
VAV3 -0.007 0.13 -9999 0 -0.37 81 81
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 -0.033 0.17 -9999 0 -0.66 58 58
FAK1/Paxillin -0.014 0.12 -9999 0 -0.46 24 24
cell migration -0.005 0.12 -9999 0 -0.46 16 16
ITGAV 0.011 0.041 -9999 0 -0.67 3 3
PI3K -0.065 0.13 -9999 0 -0.53 31 31
SPP1 -0.075 0.22 -9999 0 -0.59 123 123
KDR 0.009 0.055 -9999 0 -0.64 6 6
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.011 0.041 -9999 0 -0.67 3 3
COL4A3 -0.093 0.22 -9999 0 -0.55 159 159
angiogenesis -0.061 0.21 -9999 0 -0.82 46 46
Rac1/GTP 0 0.12 -9999 0 -0.66 3 3
EDIL3 -0.078 0.23 -9999 0 -0.63 119 119
cell proliferation 0.008 0.099 -9999 0 -0.5 24 24
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.012 0.08 -10000 0 -0.92 5 5
HDAC1 0.012 0.027 -10000 0 -0.68 1 1
AES 0.013 0.004 -10000 0 -10000 0 0
FBXW11 0.013 0 -10000 0 -10000 0 0
DTX1 -0.018 0.14 -10000 0 -0.65 40 40
LRP6/FZD1 0.013 0.052 -10000 0 -0.38 14 14
TLE1 -0.01 0.12 -10000 0 -0.67 29 29
AP1 -0.029 0.12 -10000 0 -0.34 91 91
NCSTN 0.013 0 -10000 0 -10000 0 0
ADAM10 0.01 0.047 -10000 0 -0.67 4 4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.006 0.1 -10000 0 -0.45 8 8
NICD/RBPSUH 0.026 0.07 -10000 0 -0.83 5 5
WIF1 -0.17 0.26 -10000 0 -0.54 282 282
NOTCH1 -0.007 0.07 -10000 0 -0.89 5 5
PSENEN 0.013 0 -10000 0 -10000 0 0
KREMEN2 -0.12 0.24 -10000 0 -0.54 204 204
DKK1 -0.18 0.27 -10000 0 -0.55 293 293
beta catenin/beta TrCP1 0.021 0.059 0.3 4 -10000 0 4
APH1B 0.003 0.081 -10000 0 -0.64 13 13
APH1A 0.013 0 -10000 0 -10000 0 0
AXIN1 0.002 0.033 0.28 5 -0.26 4 9
CtBP/CBP/TCF1/TLE1/AES 0.022 0.076 0.29 2 -0.36 2 4
PSEN1 0.013 0 -10000 0 -10000 0 0
FOS -0.062 0.2 -10000 0 -0.55 112 112
JUN 0.009 0.049 -10000 0 -0.52 7 7
MAP3K7 0.013 0.016 -10000 0 -0.44 1 1
CTNNB1 0.014 0.062 0.29 6 -0.27 2 8
MAPK3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.083 0.18 -10000 0 -0.45 117 117
HNF1A 0.007 0.056 -10000 0 -0.47 11 11
CTBP1 0.013 0.004 -10000 0 -10000 0 0
MYC -0.03 0.26 -10000 0 -1.5 27 27
NKD1 -0.03 0.16 -10000 0 -0.64 56 56
FZD1 0.008 0.057 -10000 0 -0.56 8 8
NOTCH1 precursor/Deltex homolog 1 0.009 0.11 -10000 0 -0.9 5 5
apoptosis -0.029 0.12 -10000 0 -0.34 91 91
Delta 1/NOTCHprecursor 0.021 0.084 -10000 0 -0.9 5 5
DLL1 0.003 0.077 -10000 0 -0.58 14 14
PPARD 0.015 0.029 -10000 0 -10000 0 0
Gamma Secretase 0.031 0.047 -10000 0 -0.36 11 11
APC 0.002 0.033 0.28 5 -0.28 2 7
DVL1 -0.009 0.05 -10000 0 -0.47 6 6
CSNK2A1 0.012 0.034 -10000 0 -0.67 2 2
MAP3K7IP1 0 0.006 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.18 0.23 -10000 0 -0.49 233 233
LRP6 0.01 0.043 -10000 0 -0.49 6 6
CSNK1A1 0.013 0.002 -10000 0 -10000 0 0
NLK 0.017 0.016 -10000 0 -10000 0 0
CCND1 -0.078 0.36 -10000 0 -1.4 52 52
WNT1 0.002 0.064 -10000 0 -0.46 16 16
Axin1/APC/beta catenin 0.025 0.054 0.29 4 -0.39 2 6
DKK2 -0.024 0.15 -10000 0 -0.62 49 49
NOTCH1 precursor/DVL1 -0.009 0.069 -10000 0 -0.76 5 5
GSK3B 0.013 0.001 -10000 0 -10000 0 0
FRAT1 0.008 0.058 -10000 0 -0.67 6 6
NOTCH/Deltex homolog 1 -0.023 0.1 -10000 0 -0.92 5 5
PPP2R5D 0.011 0.079 0.3 53 -10000 0 53
MAPK1 0.013 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.086 0.16 -10000 0 -0.39 119 119
RBPJ 0.013 0 -10000 0 -10000 0 0
CREBBP 0.013 0.034 -10000 0 -0.68 2 2
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.009 0.15 -9999 0 -0.51 28 28
NF kappa B1 p50/RelA/I kappa B alpha 0.014 0.15 -9999 0 -0.58 19 19
alphaV/beta3 Integrin/Osteopontin/Src -0.063 0.16 -9999 0 -0.5 79 79
AP1 -0.032 0.21 -9999 0 -0.74 37 37
ILK -0.019 0.16 -9999 0 -0.53 27 27
bone resorption -0.005 0.15 -9999 0 -0.68 13 13
PTK2B 0.01 0.047 -9999 0 -0.59 5 5
PYK2/p130Cas -0.013 0.16 -9999 0 -0.59 21 21
ITGAV 0.014 0.042 -9999 0 -0.68 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.009 0.071 -9999 0 -0.45 19 19
alphaV/beta3 Integrin/Osteopontin -0.065 0.16 -9999 0 -0.46 92 92
MAP3K1 -0.022 0.16 -9999 0 -0.41 97 97
JUN 0.009 0.049 -9999 0 -0.52 7 7
MAPK3 -0.007 0.16 -9999 0 -0.59 22 22
MAPK1 -0.007 0.16 -9999 0 -0.55 27 27
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
NFKB1 0.012 0.024 -9999 0 -0.67 1 1
MAPK8 -0.012 0.15 -9999 0 -0.52 29 29
ITGB3 -0.005 0.12 -9999 0 -0.59 31 31
NFKBIA 0.001 0.16 -9999 0 -0.64 19 19
FOS -0.062 0.2 -9999 0 -0.55 112 112
CD44 0.003 0.081 -9999 0 -0.61 14 14
CHUK 0.013 0 -9999 0 -10000 0 0
PLAU -0.013 0.24 -9999 0 -1.1 30 30
NF kappa B1 p50/RelA -0.049 0.12 -9999 0 -0.59 19 19
BCAR1 0.013 0 -9999 0 -10000 0 0
RELA 0.013 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.014 0.095 -9999 0 -0.47 31 31
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.027 0.17 -9999 0 -0.42 104 104
VAV3 -0.055 0.2 -9999 0 -0.6 40 40
MAP3K14 -0.018 0.16 -9999 0 -0.42 92 92
ROCK2 0.009 0.05 -9999 0 -0.63 5 5
SPP1 -0.071 0.22 -9999 0 -0.58 123 123
RAC1 0.013 0 -9999 0 -10000 0 0
Rac1/GTP -0.045 0.18 -9999 0 -0.6 30 30
MMP2 -0.031 0.22 -9999 0 -0.68 55 55
Cellular roles of Anthrax toxin

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
ANTXR1 -0.006 0.11 -10000 0 -0.62 26 26
ANTXR2 0.006 0.071 -10000 0 -0.67 9 9
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.017 -10000 0 -0.084 32 32
monocyte activation -0.031 0.14 -10000 0 -0.46 69 69
MAP2K2 -0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.003 0.014 -10000 0 -10000 0 0
MAP2K7 -0.003 0.014 -10000 0 -10000 0 0
MAP2K6 -0.018 0.073 -10000 0 -0.33 40 40
CYAA 0 0.079 -10000 0 -0.38 32 32
MAP2K4 -0.006 0.035 -10000 0 -0.36 7 7
IL1B -0.011 0.092 -10000 0 -0.31 65 65
Channel 0.001 0.084 -10000 0 -0.4 32 32
NLRP1 -0.008 0.047 -10000 0 -0.35 13 13
CALM1 0.013 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.004 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.017 0.084 32 -10000 0 32
MAPK3 -0.003 0.014 -10000 0 -10000 0 0
MAPK1 -0.003 0.014 -10000 0 -10000 0 0
PGR -0.18 0.17 -10000 0 -0.32 452 452
PA/Cellular Receptors 0.001 0.091 -10000 0 -0.44 32 32
apoptosis -0.003 0.017 -10000 0 -0.084 32 32
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.002 0.079 -10000 0 -0.37 32 32
macrophage activation 0.016 0.015 -10000 0 -10000 0 0
TNF -0.049 0.18 -10000 0 -0.57 90 90
VCAM1 -0.031 0.14 -10000 0 -0.47 69 69
platelet activation -0.004 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.008 0.028 0.16 6 -10000 0 6
IL18 0 0.073 -10000 0 -0.3 38 38
negative regulation of macrophage activation -0.003 0.017 -10000 0 -0.084 32 32
LEF -0.003 0.017 -10000 0 -0.085 32 32
CASP1 -0.006 0.032 -10000 0 -0.19 16 16
mol:cAMP -0.004 0.019 -10000 0 -10000 0 0
necrosis -0.003 0.017 -10000 0 -0.084 32 32
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.002 0.08 -10000 0 -0.38 32 32
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.15 0.32 -9999 0 -0.94 91 91
RAD9A 0.013 0.016 -9999 0 -0.46 1 1
AP1 -0.04 0.15 -9999 0 -0.41 114 114
IFNAR2 0.011 0.025 -9999 0 -0.68 1 1
AKT1 -0.055 0.12 -9999 0 -0.27 135 135
ER alpha/Oestrogen -0.12 0.22 -9999 0 -0.5 213 213
NFX1/SIN3/HDAC complex 0.034 0.039 -9999 0 -10000 0 0
EGF -0.14 0.27 -9999 0 -0.61 201 201
SMG5 0.013 0 -9999 0 -10000 0 0
SMG6 0.013 0 -9999 0 -10000 0 0
SP3/HDAC2 0.017 0.025 -9999 0 -0.43 2 2
TERT/c-Abl -0.14 0.29 -9999 0 -0.91 81 81
SAP18 0.013 0.002 -9999 0 -10000 0 0
MRN complex 0.026 0.018 -9999 0 -0.42 1 1
WT1 -0.17 0.27 -9999 0 -0.55 269 269
WRN 0.013 0 -9999 0 -10000 0 0
SP1 0.012 0.008 -9999 0 -10000 0 0
SP3 0.012 0.005 -9999 0 -10000 0 0
TERF2IP 0.013 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.13 0.25 -9999 0 -0.87 67 67
Mad/Max 0.017 0.018 -9999 0 -0.31 2 2
TERT -0.15 0.34 -9999 0 -1 88 88
CCND1 -0.17 0.38 -9999 0 -1.1 101 101
MAX 0.012 0.005 -9999 0 -10000 0 0
RBBP7 0.008 0.051 -9999 0 -0.48 9 9
RBBP4 0.013 0.002 -9999 0 -10000 0 0
TERF2 0.012 0.001 -9999 0 -10000 0 0
PTGES3 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0.002 -9999 0 -10000 0 0
Telomerase/911 0.02 0.036 -9999 0 -10000 0 0
CDKN1B -0.053 0.18 -9999 0 -0.48 81 81
RAD1 0.013 0 -9999 0 -10000 0 0
XRCC5 0.013 0 -9999 0 -10000 0 0
XRCC6 0.013 0 -9999 0 -10000 0 0
SAP30 0.004 0.074 -9999 0 -0.63 11 11
TRF2/PARP2 0 0.002 -9999 0 -10000 0 0
UBE3A 0.012 0.004 -9999 0 -10000 0 0
JUN 0.008 0.049 -9999 0 -0.52 7 7
E6 -0.001 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.009 0.006 -9999 0 -10000 0 0
FOS -0.063 0.2 -9999 0 -0.55 112 112
IFN-gamma/IRF1 -0.068 0.18 -9999 0 -0.44 115 115
PARP2 0.013 0 -9999 0 -10000 0 0
BLM -0.001 0.093 -9999 0 -0.6 19 19
Telomerase -0.01 0.11 -9999 0 -0.48 29 29
IRF1 0.01 0.055 -9999 0 -0.56 6 6
ESR1 -0.16 0.3 -9999 0 -0.67 213 213
KU/TER 0.02 0 -9999 0 -10000 0 0
ATM/TRF2 0.02 0.009 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.039 0.037 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.038 0.038 -9999 0 -10000 0 0
HDAC1 0.012 0.024 -9999 0 -0.67 1 1
HDAC2 0.011 0.031 -9999 0 -0.58 2 2
ATM 0 0.009 -9999 0 -0.27 1 1
SMAD3 0.019 0.049 -9999 0 -0.48 8 8
ABL1 0.013 0 -9999 0 -10000 0 0
MXD1 0.011 0.023 -9999 0 -0.45 2 2
MRE11A 0.013 0.016 -9999 0 -0.46 1 1
HUS1 0.013 0 -9999 0 -10000 0 0
RPS6KB1 0.009 0.045 -9999 0 -0.46 8 8
TERT/NF kappa B1/14-3-3 -0.15 0.29 -9999 0 -0.86 91 91
NR2F2 0 0.1 -9999 0 -0.67 18 18
MAPK3 0.008 0.048 -9999 0 -0.32 17 17
MAPK1 0.008 0.048 -9999 0 -0.32 17 17
TGFB1/TGF beta receptor Type II 0.011 0.041 -9999 0 -0.67 3 3
NFKB1 0.012 0.024 -9999 0 -0.67 1 1
HNRNPC 0.013 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0.009 -9999 0 -0.27 1 1
NBN 0.013 0 -9999 0 -10000 0 0
EGFR -0.077 0.22 -9999 0 -0.57 129 129
mol:Oestrogen -0.001 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.16 0.25 -9999 0 -0.47 298 298
MYC -0.013 0.12 -9999 0 -0.65 31 31
IL2 -0.004 0.066 -9999 0 -0.46 17 17
KU 0.02 0 -9999 0 -10000 0 0
RAD50 0.012 0.024 -9999 0 -0.67 1 1
HSP90AA1 0.013 0.016 -9999 0 -0.46 1 1
TGFB1 0.011 0.041 -9999 0 -0.68 3 3
TRF2/BLM -0.009 0.062 -9999 0 -0.41 19 19
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.12 0.3 -9999 0 -0.95 74 74
SP1/HDAC2 0.018 0.027 -9999 0 -0.44 2 2
PINX1 0.012 0.029 -9999 0 -0.56 2 2
Telomerase/EST1A -0.13 0.25 -9999 0 -0.88 66 66
Smad3/Myc 0.008 0.092 -9999 0 -0.43 34 34
911 complex 0.027 0.01 -9999 0 -10000 0 0
IFNG -0.1 0.23 -9999 0 -0.53 180 180
Telomerase/PinX1 -0.13 0.25 -9999 0 -0.87 67 67
Telomerase/AKT1/mTOR/p70S6K -0.021 0.085 -9999 0 -0.34 2 2
SIN3B 0.013 0.002 -9999 0 -10000 0 0
YWHAE 0.012 0.024 -9999 0 -0.67 1 1
Telomerase/EST1B -0.13 0.25 -9999 0 -0.88 66 66
response to DNA damage stimulus 0.003 0.002 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 -0.001 0.014 -9999 0 -10000 0 0
TRF2/WRN 0 0.002 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.13 0.25 -9999 0 -0.88 66 66
E2F1 -0.007 0.11 -9999 0 -0.65 25 25
ZNFX1 0.012 0.016 -9999 0 -0.46 1 1
PIF1 -0.026 0.15 -9999 0 -0.57 56 56
NCL 0.013 0 -9999 0 -10000 0 0
DKC1 0.012 0.023 -9999 0 -0.46 2 2
telomeric DNA binding 0 0 -9999 0 -10000 0 0
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.016 0.015 -9999 0 -0.26 2 2
RAS family/GTP -0.024 0.12 -9999 0 -0.53 10 10
NFATC4 -0.033 0.12 -9999 0 -0.39 17 17
ERBB2IP 0.013 0.024 -9999 0 -0.67 1 1
HSP90 (dimer) 0.013 0.016 -9999 0 -0.46 1 1
mammary gland morphogenesis -0.05 0.14 -9999 0 -0.36 50 50
JUN 0.009 0.087 -9999 0 -0.34 17 17
HRAS 0.009 0.05 -9999 0 -0.63 5 5
DOCK7 -0.043 0.14 -9999 0 -0.48 12 12
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.075 0.16 -9999 0 -0.39 130 130
AKT1 0.01 0.003 -9999 0 -10000 0 0
BAD 0.018 0.003 -9999 0 -10000 0 0
MAPK10 -0.041 0.12 -9999 0 -0.34 47 47
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.053 0.15 -9999 0 -0.4 48 48
RAF1 -0.015 0.13 -9999 0 -0.54 8 8
ErbB2/ErbB3/neuregulin 2 -0.085 0.16 -9999 0 -0.44 78 78
STAT3 -0.001 0.065 -9999 0 -1.1 3 3
cell migration -0.019 0.095 -9999 0 -0.28 29 29
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.06 0.25 -9999 0 -0.64 99 99
FOS -0.042 0.2 -9999 0 -0.45 102 102
NRAS 0.007 0.062 -9999 0 -0.62 8 8
mol:Ca2+ -0.05 0.14 -9999 0 -0.36 50 50
MAPK3 -0.042 0.21 -9999 0 -0.57 55 55
MAPK1 -0.042 0.21 -9999 0 -0.56 61 61
JAK2 -0.043 0.13 -9999 0 -0.47 12 12
NF2 -0.002 0.006 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.04 0.13 -9999 0 -0.32 121 121
NRG1 -0.11 0.25 -9999 0 -0.6 171 171
GRB2/SOS1 0.019 0.012 -9999 0 -0.32 1 1
MAPK8 -0.03 0.12 -9999 0 -0.33 28 28
MAPK9 -0.006 0.077 -9999 0 -0.26 4 4
ERBB2 -0.036 0.11 -9999 0 -0.35 85 85
ERBB3 0.004 0.075 -9999 0 -0.68 10 10
SHC1 0.013 0.001 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
apoptosis 0.003 0.011 -9999 0 -10000 0 0
STAT3 (dimer) 0.014 0.064 -9999 0 -1 3 3
RNF41 0.021 0.015 -9999 0 -10000 0 0
FRAP1 0.008 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.049 0.084 -9999 0 -0.33 12 12
ErbB2/ErbB2/HSP90 (dimer) -0.029 0.089 -9999 0 -0.29 86 86
CHRNA1 -0.058 0.25 -9999 0 -0.66 102 102
myelination -0.029 0.12 -9999 0 -0.37 17 17
PPP3CB -0.039 0.13 -9999 0 -0.43 12 12
KRAS 0.013 0.016 -9999 0 -0.46 1 1
RAC1-CDC42/GDP -0.021 0.11 -9999 0 -0.41 10 10
NRG2 -0.11 0.23 -9999 0 -0.52 188 188
mol:GDP -0.04 0.13 -9999 0 -0.32 121 121
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.011 0.13 -9999 0 -0.52 7 7
SRC 0.011 0.037 -9999 0 -0.6 3 3
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.043 0.13 -9999 0 -0.47 12 12
MAP2K1 -0.048 0.19 -9999 0 -0.57 43 43
heart morphogenesis -0.05 0.14 -9999 0 -0.36 50 50
RAS family/GDP -0.023 0.12 -9999 0 -0.56 9 9
GRB2 0.013 0.016 -9999 0 -0.46 1 1
PRKACA -0.005 0.008 -9999 0 -10000 0 0
CHRNE 0.009 0.037 -9999 0 -0.18 25 25
HSP90AA1 0.013 0.016 -9999 0 -0.46 1 1
activation of caspase activity -0.01 0.003 -9999 0 -10000 0 0
nervous system development -0.05 0.14 -9999 0 -0.36 50 50
CDC42 0.013 0 -9999 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.013 0 -9999 0 -10000 0 0
VLDLR -0.011 0.12 -9999 0 -0.59 34 34
LRPAP1 0.012 0.033 -9999 0 -0.67 2 2
NUDC 0.013 0 -9999 0 -10000 0 0
RELN/LRP8 -0.093 0.18 -9999 0 -0.45 121 121
CaM/Ca2+ 0.01 0 -9999 0 -10000 0 0
KATNA1 0.013 0.016 -9999 0 -0.46 1 1
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.076 0.17 -9999 0 -0.4 121 121
IQGAP1/CaM 0.02 0 -9999 0 -10000 0 0
DAB1 -0.036 0.14 -9999 0 -0.46 82 82
IQGAP1 0.013 0 -9999 0 -10000 0 0
PLA2G7 -0.044 0.18 -9999 0 -0.59 79 79
CALM1 0.013 0 -9999 0 -10000 0 0
DYNLT1 0.013 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 0.002 0.081 -9999 0 -0.36 39 39
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.012 0.024 -9999 0 -0.67 1 1
CDK5R1 0.007 0.059 -9999 0 -0.5 11 11
LIS1/Poliovirus Protein 3A 0.016 0.022 -9999 0 -0.43 2 2
CDK5R2 -0.042 0.14 -9999 0 -0.46 89 89
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.12 0.2 -9999 0 -0.48 148 148
YWHAE 0.012 0.024 -9999 0 -0.67 1 1
NDEL1/14-3-3 E -0.051 0.14 -9999 0 -0.47 25 25
MAP1B -0.007 0.049 -9999 0 -0.34 15 15
RAC1 0 0.009 -9999 0 -10000 0 0
p35/CDK5 -0.056 0.15 -9999 0 -0.54 13 13
RELN -0.15 0.26 -9999 0 -0.56 244 244
PAFAH/LIS1 -0.011 0.12 -9999 0 -0.42 51 51
LIS1/CLIP170 0.025 0.027 -9999 0 -0.42 3 3
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.062 0.093 -9999 0 -0.44 6 6
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.054 0.14 -9999 0 -0.49 24 24
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.061 0.15 -9999 0 -0.5 24 24
LIS1/IQGAP1 0.025 0.022 -9999 0 -0.42 2 2
RHOA 0 0.009 -9999 0 -10000 0 0
PAFAH1B1 0.021 0.025 -9999 0 -0.5 2 2
PAFAH1B3 0.012 0.023 -9999 0 -0.46 2 2
PAFAH1B2 0.009 0.053 -9999 0 -0.67 5 5
MAP1B/LIS1/Dynein heavy chain 0.019 0.04 -9999 0 -0.46 2 2
NDEL1/Katanin 60/Dynein heavy chain -0.043 0.14 -9999 0 -0.44 23 23
LRP8 -0.009 0.11 -9999 0 -0.5 37 37
NDEL1/Katanin 60 -0.051 0.14 -9999 0 -0.46 24 24
P39/CDK5 -0.081 0.16 -9999 0 -0.53 30 30
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.025 0.022 -9999 0 -0.42 2 2
CDK5 -0.064 0.16 -9999 0 -0.37 122 122
PPP2R5D 0.012 0.028 -9999 0 -0.46 3 3
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0.022 0.023 -9999 0 -0.37 3 3
CSNK2A1 0.012 0.033 -9999 0 -0.67 2 2
RELN/VLDLR/DAB1/LIS1 -0.09 0.18 -9999 0 -0.4 150 150
RELN/VLDLR -0.09 0.18 -9999 0 -0.41 140 140
CDC42 0 0.009 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.013 0 -10000 0 -10000 0 0
HDAC4 0.012 0.024 -10000 0 -0.67 1 1
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.004 0.099 0.38 50 -10000 0 50
CDKN1A -0.008 0.081 -10000 0 -0.84 7 7
KAT2B 0.01 0.044 -10000 0 -0.62 4 4
BAX 0.013 0 -10000 0 -10000 0 0
FOXO3 -0.001 0.018 -10000 0 -0.3 2 2
FOXO1 0.01 0.044 -10000 0 -0.62 4 4
FOXO4 0.021 0.021 -10000 0 -0.32 3 3
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
TAT -0.2 0.27 -10000 0 -0.52 344 344
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.009 0.033 -10000 0 -0.46 4 4
PPARGC1A -0.086 0.22 -10000 0 -0.55 147 147
FHL2 -0.021 0.14 -10000 0 -0.59 48 48
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.002 0.015 -10000 0 -10000 0 0
HIST2H4A -0.004 0.099 -10000 0 -0.39 50 50
SIRT1/FOXO3a 0.001 0.019 -10000 0 -10000 0 0
SIRT1 0.002 0.02 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.002 0.021 -10000 0 -0.42 1 1
SIRT1/Histone H1b -0.01 0.057 -10000 0 -0.7 1 1
apoptosis -0.002 0.015 -10000 0 -10000 0 0
SIRT1/PGC1A -0.058 0.14 -10000 0 -0.34 145 145
p53/SIRT1 0 0.067 0.42 7 -0.5 9 16
SIRT1/FOXO4 0.001 0.023 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.019 0.083 -10000 0 -0.39 32 32
HIST1H1E 0.007 0.069 -10000 0 -0.34 25 25
SIRT1/p300 0.002 0.015 -10000 0 -10000 0 0
muscle cell differentiation 0 0.03 0.38 4 -10000 0 4
TP53 -0.005 0.073 -10000 0 -0.68 9 9
KU70/SIRT1/BAX 0.002 0.015 -10000 0 -10000 0 0
CREBBP 0.012 0.033 -10000 0 -0.67 2 2
MEF2D 0.013 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.15 0.19 -10000 0 -0.37 342 342
ACSS2 0.02 0.023 -10000 0 -0.32 3 3
SIRT1/PCAF/MYOD 0 0.03 -10000 0 -0.38 4 4
Aurora B signaling

Figure S69.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S69.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.003 0.14 -9999 0 -0.78 23 23
STMN1 -0.01 0.13 -9999 0 -0.48 55 55
Aurora B/RasGAP/Survivin -0.038 0.17 -9999 0 -0.67 50 50
Chromosomal passenger complex/Cul3 protein complex -0.03 0.15 -9999 0 -0.51 48 48
BIRC5 -0.028 0.16 -9999 0 -0.62 55 55
DES -0.12 0.28 -9999 0 -0.76 116 116
Aurora C/Aurora B/INCENP -0.01 0.11 -9999 0 -0.41 48 48
Aurora B/TACC1 -0.025 0.11 -9999 0 -0.39 65 65
Aurora B/PP2A -0.008 0.12 -9999 0 -0.45 53 53
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.006 0.043 -9999 0 -0.18 37 37
mitotic metaphase/anaphase transition 0 0.003 -9999 0 -10000 0 0
NDC80 -0.022 0.17 -9999 0 -0.59 62 62
Cul3 protein complex -0.034 0.15 -9999 0 -0.43 83 83
KIF2C -0.026 0.22 -9999 0 -0.83 45 45
PEBP1 0.013 0.004 -9999 0 -10000 0 0
KIF20A -0.012 0.13 -9999 0 -0.68 30 30
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP -0.009 0.12 -9999 0 -0.46 52 52
SEPT1 -0.005 0.096 -9999 0 -0.5 30 30
SMC2 0.013 0 -9999 0 -10000 0 0
SMC4 0.013 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin -0.011 0.19 -9999 0 -0.88 37 37
PSMA3 0.013 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.003 -9999 0 -10000 0 0
H3F3B -0.003 0.088 -9999 0 -0.4 37 37
AURKB -0.023 0.16 -9999 0 -0.63 50 50
AURKC -0.012 0.12 -9999 0 -0.52 39 39
CDCA8 0 0.087 -9999 0 -0.55 20 20
cytokinesis -0.061 0.23 -9999 0 -0.97 42 42
Aurora B/Septin1 -0.049 0.22 -9999 0 -0.92 42 42
AURKA -0.004 0.1 -9999 0 -0.61 23 23
INCENP 0.013 0.006 -9999 0 -10000 0 0
KLHL13 -0.076 0.22 -9999 0 -0.59 124 124
BUB1 -0.011 0.12 -9999 0 -0.65 30 30
hSgo1/Aurora B/Survivin -0.052 0.22 -9999 0 -0.74 60 60
EVI5 0.013 0.024 -9999 0 -0.67 1 1
RhoA/GTP -0.047 0.2 -9999 0 -0.95 35 35
SGOL1 -0.019 0.14 -9999 0 -0.65 41 41
CENPA -0.033 0.26 -9999 0 -0.81 57 57
NCAPG -0.001 0.099 -9999 0 -0.67 18 18
Aurora B/HC8 Proteasome -0.007 0.12 -9999 0 -0.46 50 50
NCAPD2 0.009 0.045 -9999 0 -0.46 8 8
Aurora B/PP1-gamma -0.007 0.12 -9999 0 -0.46 50 50
RHOA 0.013 0 -9999 0 -10000 0 0
NCAPH -0.007 0.11 -9999 0 -0.66 25 25
NPM1 -0.013 0.14 -9999 0 -0.67 37 37
RASA1 0.011 0.037 -9999 0 -0.51 4 4
KLHL9 0.008 0.06 -9999 0 -0.64 7 7
mitotic prometaphase 0 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.007 0.11 -9999 0 -0.45 50 50
PPP1CC 0.013 0 -9999 0 -10000 0 0
Centraspindlin -0.055 0.24 -9999 0 -1.1 36 36
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
NSUN2 -0.013 0.14 -9999 0 -0.67 37 37
MYLK -0.013 0.11 -9999 0 -0.41 50 50
KIF23 0 0.096 -9999 0 -0.69 16 16
VIM -0.008 0.12 -9999 0 -0.46 55 55
RACGAP1 0.012 0.024 -9999 0 -0.69 1 1
mitosis 0 0 -9999 0 -10000 0 0
NCL -0.013 0.14 -9999 0 -0.67 37 37
Chromosomal passenger complex -0.024 0.25 -9999 0 -0.87 48 48
Chromosomal passenger complex/EVI5 -0.03 0.18 -9999 0 -0.66 49 49
TACC1 -0.001 0.091 -9999 0 -0.58 20 20
PPP2R5D 0.012 0.028 -9999 0 -0.46 3 3
CUL3 0.013 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
PDGFR-alpha signaling 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
PDGFRA -0.024 0.15 -10000 0 -0.67 43 43
PDGF/PDGFRA/CRKL -0.008 0.11 -10000 0 -0.48 44 44
positive regulation of JUN kinase activity 0.012 0.087 -10000 0 -0.36 42 42
CRKL 0.012 0.024 -10000 0 -0.67 1 1
PDGF/PDGFRA/Caveolin-3 -0.023 0.12 -10000 0 -0.43 67 67
AP1 -0.11 0.27 -10000 0 -1 55 55
mol:IP3 -0.007 0.12 -10000 0 -0.5 43 43
PLCG1 -0.008 0.12 -10000 0 -0.5 43 43
PDGF/PDGFRA/alphaV Integrin -0.009 0.12 -10000 0 -0.5 45 45
RAPGEF1 0.013 0 -10000 0 -10000 0 0
CRK 0.012 0.024 -10000 0 -0.67 1 1
mol:Ca2+ -0.007 0.12 -10000 0 -0.5 43 43
CAV3 -0.009 0.077 -10000 0 -0.46 24 24
CAV1 0.006 0.066 -10000 0 -0.59 10 10
SHC/Grb2/SOS1 0.013 0.088 -10000 0 -0.37 42 42
PDGF/PDGFRA/Shf -0.014 0.13 -10000 0 -0.48 54 54
FOS -0.069 0.28 -10000 0 -1 55 55
JUN -0.01 0.042 0.42 1 -0.38 7 8
oligodendrocyte development -0.009 0.12 -10000 0 -0.49 45 45
GRB2 0.013 0.016 -10000 0 -0.46 1 1
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
mol:DAG -0.007 0.12 -10000 0 -0.5 43 43
PDGF/PDGFRA -0.024 0.15 -10000 0 -0.67 43 43
actin cytoskeleton reorganization -0.008 0.11 -10000 0 -0.48 44 44
SRF 0.022 0.026 -10000 0 -0.48 2 2
SHC1 0.013 0 -10000 0 -10000 0 0
PI3K 0.003 0.097 -10000 0 -0.41 42 42
PDGF/PDGFRA/Crk/C3G 0.003 0.099 -10000 0 -0.42 42 42
JAK1 -0.005 0.11 -10000 0 -0.48 44 44
ELK1/SRF 0.015 0.09 -10000 0 -0.37 43 43
SHB 0.012 0.024 -10000 0 -0.67 1 1
SHF 0.004 0.069 -10000 0 -0.5 15 15
CSNK2A1 0.007 0.037 -10000 0 -0.65 2 2
GO:0007205 -0.008 0.12 -10000 0 -0.52 42 42
SOS1 0.013 0 -10000 0 -10000 0 0
Ras protein signal transduction 0.012 0.087 -10000 0 -0.36 42 42
PDGF/PDGFRA/SHB -0.008 0.11 -10000 0 -0.48 44 44
PDGF/PDGFRA/Caveolin-1 -0.012 0.13 -10000 0 -0.5 50 50
ITGAV 0.011 0.041 -10000 0 -0.67 3 3
ELK1 -0.002 0.11 -10000 0 -0.45 42 42
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
PDGF/PDGFRA/Crk -0.008 0.11 -10000 0 -0.5 43 43
JAK-STAT cascade -0.005 0.11 -10000 0 -0.48 44 44
cell proliferation -0.013 0.12 -10000 0 -0.48 54 54
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.032 0.2 -10000 0 -0.94 27 27
NCK1/PAK1/Dok-R -0.031 0.089 -10000 0 -0.43 28 28
NCK1/Dok-R 0.001 0.23 -10000 0 -1.1 27 27
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
mol:beta2-estradiol -0.002 0.04 0.24 13 -10000 0 13
RELA 0.013 0 -10000 0 -10000 0 0
SHC1 0.014 0.001 -10000 0 -10000 0 0
Rac/GDP 0.01 0 -10000 0 -10000 0 0
F2 -0.007 0.069 0.25 11 -0.46 13 24
TNIP2 0.012 0.024 -10000 0 -0.67 1 1
NF kappa B/RelA -0.046 0.19 -10000 0 -1 27 27
FN1 -0.025 0.16 -10000 0 -0.64 49 49
PLD2 0.011 0.23 -10000 0 -1.2 27 27
PTPN11 0.013 0 -10000 0 -10000 0 0
GRB14 -0.22 0.29 -10000 0 -0.56 338 338
ELK1 0.024 0.21 -10000 0 -1 27 27
GRB7 -0.028 0.14 -10000 0 -0.47 73 73
PAK1 0.002 0.075 -10000 0 -0.48 20 20
Tie2/Ang1/alpha5/beta1 Integrin -0.063 0.22 -10000 0 -1.2 28 28
CDKN1A 0.027 0.17 -10000 0 -0.73 26 26
ITGA5 0.011 0.037 -10000 0 -0.6 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R 0 0.23 -10000 0 -1.1 27 27
CRK 0.012 0.024 -10000 0 -0.67 1 1
mol:NO 0.043 0.15 -10000 0 -0.67 27 27
PLG 0.003 0.23 -10000 0 -1.2 27 27
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.031 0.19 -10000 0 -0.9 27 27
GRB2 0.013 0.016 -10000 0 -0.46 1 1
PIK3R1 0.013 0.023 -10000 0 -0.45 2 2
ANGPT2 -0.022 0.16 -10000 0 -0.74 20 20
BMX -0.04 0.27 -10000 0 -1.2 31 31
ANGPT1 -0.015 0.22 -10000 0 -1.2 19 19
tube development 0.025 0.17 -10000 0 -0.73 27 27
ANGPT4 -0.008 0.092 -10000 0 -0.45 34 34
response to hypoxia 0.001 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.11 0.28 -10000 0 -1.3 28 28
alpha5/beta1 Integrin 0.018 0.028 -10000 0 -0.44 3 3
FGF2 -0.045 0.17 -10000 0 -0.52 89 89
STAT5A (dimer) 0.024 0.2 -10000 0 -0.87 26 26
mol:L-citrulline 0.043 0.15 -10000 0 -0.67 27 27
AGTR1 -0.16 0.26 -10000 0 -0.52 268 268
MAPK14 0.01 0.24 -10000 0 -1.2 27 27
Tie2/SHP2 -0.028 0.16 -10000 0 -1.2 15 15
TEK 0.013 0.19 -10000 0 -1.3 15 15
RPS6KB1 0.031 0.19 -10000 0 -0.9 27 27
Angiotensin II/AT1 -0.11 0.19 -10000 0 -0.38 268 268
Tie2/Ang1/GRB2 0.008 0.24 -10000 0 -1.2 27 27
MAPK3 0.019 0.21 -10000 0 -1.1 27 27
MAPK1 0.019 0.21 -10000 0 -1.1 27 27
Tie2/Ang1/GRB7 -0.012 0.25 -10000 0 -1.2 29 29
NFKB1 0.012 0.024 -10000 0 -0.67 1 1
MAPK8 0.011 0.23 -10000 0 -1.2 27 27
PI3K 0.022 0.22 -10000 0 -1.1 27 27
FES 0.005 0.24 -10000 0 -1.2 28 28
Crk/Dok-R 0.001 0.23 -10000 0 -1.1 27 27
Tie2/Ang1/ABIN2 0.008 0.24 -10000 0 -1.2 27 27
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.035 0.18 -10000 0 -0.83 27 27
STAT5A 0.007 0.064 -10000 0 -0.65 8 8
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.033 0.19 -10000 0 -0.9 27 27
Tie2/Ang2 0.011 0.22 -10000 0 -1.1 26 26
Tie2/Ang1 0.002 0.26 -10000 0 -1.3 27 27
FOXO1 0.039 0.18 -10000 0 -0.83 28 28
ELF1 0.02 0.015 -10000 0 -10000 0 0
ELF2 0.007 0.23 -10000 0 -1.2 27 27
mol:Choline 0.013 0.22 -10000 0 -1.1 27 27
cell migration -0.02 0.052 -10000 0 -0.25 19 19
FYN 0.021 0.19 -10000 0 -0.86 26 26
DOK2 -0.014 0.13 -10000 0 -0.58 39 39
negative regulation of cell cycle 0.029 0.15 -10000 0 -0.64 27 27
ETS1 0.011 0.069 -10000 0 -0.6 7 7
PXN 0.042 0.16 -10000 0 -0.73 27 27
ITGB1 0.013 0 -10000 0 -10000 0 0
NOS3 0.041 0.17 -10000 0 -0.78 27 27
RAC1 0.013 0 -10000 0 -10000 0 0
TNF -0.047 0.19 -10000 0 -0.58 90 90
MAPKKK cascade 0.013 0.22 -10000 0 -1.1 27 27
RASA1 0.011 0.037 -10000 0 -0.51 4 4
Tie2/Ang1/Shc 0.009 0.24 -10000 0 -1.2 27 27
NCK1 0.013 0 -10000 0 -10000 0 0
vasculogenesis 0.044 0.14 -10000 0 -0.6 27 27
mol:Phosphatidic acid 0.013 0.22 -10000 0 -1.1 27 27
mol:Angiotensin II 0.001 0.002 -10000 0 -10000 0 0
mol:NADP 0.043 0.15 -10000 0 -0.67 27 27
Rac1/GTP -0.039 0.15 -10000 0 -0.83 27 27
MMP2 -0.006 0.26 -10000 0 -1.3 29 29
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.013 0 -9999 0 -10000 0 0
ITGB7 -0.016 0.13 -9999 0 -0.59 40 40
ITGA4 -0.003 0.098 -9999 0 -0.56 24 24
alpha4/beta7 Integrin -0.013 0.12 -9999 0 -0.46 58 58
alpha4/beta1 Integrin 0.008 0.073 -9999 0 -0.41 24 24
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.025 0.04 -9999 0 -0.47 5 5
SNTA1 0.012 0.024 -9999 0 -0.67 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.021 0.055 -9999 0 -0.46 7 7
MAPK12 0.003 0.097 -9999 0 -0.38 39 39
CCND1 -0.021 0.12 -9999 0 -0.43 60 60
p38 gamma/SNTA1 0.009 0.092 -9999 0 -0.37 33 33
MAP2K3 0.012 0.023 -9999 0 -0.46 2 2
PKN1 0.012 0.033 -9999 0 -0.67 2 2
G2/M transition checkpoint 0.003 0.096 -9999 0 -0.38 39 39
MAP2K6 0.002 0.09 -9999 0 -0.36 47 47
MAPT -0.069 0.17 -9999 0 -0.37 197 197
MAPK13 0.019 0.046 -9999 0 -0.51 6 6
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.013 0.038 -9999 0 -0.39 7 7
Syndecan-3-mediated signaling events

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
CTTN 0.008 0.051 -9999 0 -0.46 10 10
Syndecan-3/Src/Cortactin -0.006 0.11 -9999 0 -0.54 5 5
Syndecan-3/Neurocan -0.017 0.06 -9999 0 -0.65 1 1
POMC -0.04 0.17 -9999 0 -0.54 82 82
EGFR -0.076 0.22 -9999 0 -0.57 129 129
Syndecan-3/EGFR -0.045 0.11 -9999 0 -0.37 68 68
AGRP 0.002 0.051 -9999 0 -0.46 10 10
NCSTN 0.013 0 -9999 0 -10000 0 0
PSENEN 0.013 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.003 0.081 -9999 0 -0.64 13 13
APH1A 0.013 0 -9999 0 -10000 0 0
NCAN -0.026 0.12 -9999 0 -0.46 64 64
long-term memory 0.025 0.041 -9999 0 -0.6 1 1
Syndecan-3/IL8 -0.061 0.12 -9999 0 -0.36 73 73
PSEN1 0.013 0 -9999 0 -10000 0 0
Src/Cortactin 0.014 0.046 -9999 0 -0.34 13 13
FYN 0.009 0.046 -9999 0 -0.53 6 6
limb bud formation -0.002 0.025 -9999 0 -0.67 1 1
MC4R -0.006 0.079 -9999 0 -0.46 25 25
SRC 0.011 0.037 -9999 0 -0.6 3 3
PTN -0.067 0.2 -9999 0 -0.53 124 124
FGFR/FGF/Syndecan-3 -0.002 0.025 -9999 0 -0.68 1 1
neuron projection morphogenesis -0.026 0.12 -9999 0 -0.54 12 12
Syndecan-3/AgRP -0.004 0.033 -9999 0 -0.66 1 1
Syndecan-3/AgRP/MC4R 0.001 0.05 -9999 0 -0.63 1 1
Fyn/Cortactin 0.013 0.05 -9999 0 -0.34 16 16
SDC3 -0.002 0.025 -9999 0 -0.69 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.06 0.12 -9999 0 -0.35 73 73
IL8 -0.11 0.24 -9999 0 -0.54 188 188
Syndecan-3/Fyn/Cortactin 0.026 0.042 -9999 0 -0.62 1 1
Syndecan-3/CASK -0.002 0.024 -9999 0 -0.66 1 1
alpha-MSH/MC4R -0.033 0.14 -9999 0 -0.4 99 99
Gamma Secretase 0.034 0.046 -9999 0 -0.35 11 11
S1P4 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
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 -0.076 0.21 -9999 0 -0.53 139 139
CDC42/GTP -0.028 0.14 -9999 0 -0.56 26 26
PLCG1 -0.028 0.14 -9999 0 -0.57 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.02 0 -9999 0 -10000 0 0
cell migration -0.054 0.12 -9999 0 -0.54 26 26
S1PR5 -0.025 0.14 -9999 0 -0.55 57 57
S1PR4 -0.051 0.19 -9999 0 -0.58 92 92
MAPK3 -0.028 0.14 -9999 0 -0.57 26 26
MAPK1 -0.028 0.14 -9999 0 -0.57 26 26
S1P/S1P5/Gi -0.025 0.13 -9999 0 -0.55 20 20
GNAI1 0.003 0.077 -9999 0 -0.54 16 16
CDC42/GDP 0.01 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.006 0.091 -9999 0 -0.34 57 57
RHOA -0.004 0.1 -9999 0 -0.36 51 51
S1P/S1P4/Gi -0.038 0.15 -9999 0 -0.37 93 93
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.002 0.099 -9999 0 -0.65 19 19
S1P/S1P4/G12/G13 -0.012 0.11 -9999 0 -0.39 51 51
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.002 0.088 -9999 0 -0.67 14 14
alphaV beta3 Integrin 0.002 0.097 -9999 0 -0.47 31 31
PTK2 -0.035 0.13 -9999 0 -0.52 47 47
positive regulation of JNK cascade -0.02 0.076 -9999 0 -0.32 47 47
CDC42/GDP 0.028 0.12 -9999 0 -0.44 47 47
Rac1/GDP 0.029 0.12 -9999 0 -0.44 47 47
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.011 0.033 -9999 0 -0.53 3 3
CDC42/GTP -0.024 0.094 -9999 0 -0.4 47 47
nectin-3/I-afadin -0.013 0.13 -9999 0 -0.5 54 54
RAPGEF1 0.02 0.13 -9999 0 -0.5 47 47
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.011 0.15 -9999 0 -0.58 47 47
PDGFB-D/PDGFRB 0.002 0.088 -9999 0 -0.67 14 14
TLN1 0.015 0.072 -9999 0 -0.45 9 9
Rap1/GTP -0.021 0.081 -9999 0 -0.35 47 47
IQGAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.021 0.042 -9999 0 -0.39 8 8
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.013 0.13 -9999 0 -0.5 54 54
PVR 0.01 0.04 -9999 0 -0.5 5 5
Necl-5(dimer) 0.01 0.04 -9999 0 -0.5 5 5
mol:GDP 0.021 0.14 -9999 0 -0.55 47 47
MLLT4 0.006 0.07 -9999 0 -0.63 10 10
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
PI3K 0.007 0.12 -9999 0 -0.42 54 54
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.011 0.063 -9999 0 -0.43 16 16
positive regulation of lamellipodium assembly -0.021 0.08 -9999 0 -0.34 47 47
PVRL1 0.009 0.046 -9999 0 -0.53 6 6
PVRL3 -0.024 0.15 -9999 0 -0.65 47 47
PVRL2 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
CDH1 -0.04 0.18 -9999 0 -0.67 66 66
CLDN1 -0.073 0.21 -9999 0 -0.57 124 124
JAM-A/CLDN1 -0.042 0.17 -9999 0 -0.43 106 106
SRC -0.04 0.15 -9999 0 -0.65 47 47
ITGB3 -0.009 0.12 -9999 0 -0.59 31 31
nectin-1(dimer)/I-afadin/I-afadin 0.011 0.063 -9999 0 -0.43 16 16
FARP2 0.016 0.14 -9999 0 -0.54 47 47
RAC1 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.012 0.033 -9999 0 -0.67 2 2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.004 0.12 -9999 0 -0.45 48 48
nectin-1/I-afadin 0.011 0.063 -9999 0 -0.43 16 16
nectin-2/I-afadin 0.014 0.053 -9999 0 -0.46 10 10
RAC1/GTP/IQGAP1/filamentous actin 0.018 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.004 0.12 -9999 0 -0.46 48 48
CDC42/GTP/IQGAP1/filamentous actin 0.018 0 -9999 0 -10000 0 0
F11R 0.012 0.024 -9999 0 -0.67 1 1
positive regulation of filopodium formation -0.02 0.076 -9999 0 -0.32 47 47
alphaV/beta3 Integrin/Talin 0.016 0.11 -9999 0 -0.51 23 23
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.014 0.053 -9999 0 -0.46 10 10
nectin-2(dimer)/I-afadin/I-afadin 0.014 0.053 -9999 0 -0.46 10 10
PIP5K1C 0.008 0.077 -9999 0 -0.46 10 10
VAV2 0.015 0.14 -9999 0 -0.55 47 47
RAP1/GDP -0.024 0.095 -9999 0 -0.41 47 47
ITGAV 0.011 0.041 -9999 0 -0.67 3 3
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.002 0.11 -9999 0 -0.45 47 47
nectin-3(dimer)/I-afadin/I-afadin -0.013 0.13 -9999 0 -0.5 54 54
Rac1/GTP -0.025 0.098 -9999 0 -0.42 47 47
PTPRM -0.001 0.084 -9999 0 -0.3 51 51
E-cadherin/beta catenin/alpha catenin -0.033 0.1 -9999 0 -0.62 2 2
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

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
HDAC1 0.022 0.018 -9999 0 -0.5 1 1
SMARCC1 0.003 0.072 -9999 0 -1.4 2 2
REL -0.011 0.13 -9999 0 -0.67 30 30
HDAC7 -0.011 0.14 -9999 0 -0.53 16 16
JUN 0.008 0.049 -9999 0 -0.52 7 7
EP300 0.013 0 -9999 0 -10000 0 0
KAT2B 0.01 0.044 -9999 0 -0.62 4 4
KAT5 0.013 0 -9999 0 -10000 0 0
MAPK14 -0.002 0.1 -9999 0 -0.45 40 40
FOXO1 0.01 0.044 -9999 0 -0.62 4 4
T-DHT/AR -0.016 0.14 -9999 0 -0.53 20 20
MAP2K6 -0.018 0.13 -9999 0 -0.61 40 40
BRM/BAF57 0.017 0.026 -9999 0 -0.31 5 5
MAP2K4 0.006 0.061 -9999 0 -0.65 7 7
SMARCA2 0.013 0.003 -9999 0 -10000 0 0
PDE9A -0.12 0.28 -9999 0 -1.1 49 49
NCOA2 -0.015 0.14 -9999 0 -0.67 34 34
CEBPA 0.006 0.068 -9999 0 -0.61 10 10
EHMT2 0.012 0.004 -9999 0 -10000 0 0
cell proliferation -0.03 0.18 -9999 0 -0.48 59 59
NR0B1 -0.04 0.14 -9999 0 -0.46 80 80
EGR1 -0.031 0.15 -9999 0 -0.53 68 68
RXRs/9cRA -0.009 0.096 -9999 0 -0.39 28 28
AR/RACK1/Src -0.01 0.11 -9999 0 -0.49 15 15
AR/GR -0.041 0.14 -9999 0 -0.34 83 83
GNB2L1 0.013 0.002 -9999 0 -10000 0 0
PKN1 0.012 0.033 -9999 0 -0.67 2 2
RCHY1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.015 0.048 -9999 0 -0.48 7 7
T-DHT/AR/TIF2/CARM1 -0.017 0.14 -9999 0 -0.47 38 38
SRC 0.011 0.094 -9999 0 -0.38 33 33
NR3C1 0.011 0.041 -9999 0 -0.67 3 3
KLK3 -0.14 0.2 -9999 0 -0.57 94 94
APPBP2 0.009 0.04 -9999 0 -0.45 6 6
TRIM24 0.012 0.017 -9999 0 -0.46 1 1
T-DHT/AR/TIP60 -0.011 0.11 -9999 0 -0.42 35 35
TMPRSS2 -0.2 0.41 -9999 0 -1.2 105 105
RXRG -0.044 0.17 -9999 0 -0.53 87 87
mol:9cRA 0 0.001 -9999 0 -10000 0 0
RXRA 0.013 0.001 -9999 0 -10000 0 0
RXRB 0.013 0.001 -9999 0 -10000 0 0
CARM1 0.013 0.002 -9999 0 -10000 0 0
NR2C2 0.013 0.001 -9999 0 -10000 0 0
KLK2 -0.026 0.18 -9999 0 -0.68 35 35
AR -0.05 0.15 -9999 0 -0.32 176 176
SENP1 0.013 0.001 -9999 0 -10000 0 0
HSP90AA1 0.013 0.016 -9999 0 -0.46 1 1
MDM2 0.01 0.043 -9999 0 -0.46 7 7
SRY 0.001 0.005 -9999 0 -10000 0 0
GATA2 -0.089 0.23 -9999 0 -0.6 139 139
MYST2 0.011 0.036 -9999 0 -0.46 5 5
HOXB13 -0.19 0.29 -9999 0 -0.6 264 264
T-DHT/AR/RACK1/Src -0.005 0.11 -9999 0 -0.49 15 15
positive regulation of transcription -0.089 0.23 -9999 0 -0.6 139 139
DNAJA1 0.012 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.018 -9999 0 -0.28 1 1
NCOA1 0.016 0.027 -9999 0 -0.7 1 1
SPDEF -0.085 0.24 -9999 0 -0.67 120 120
T-DHT/AR/TIF2 0.004 0.096 -9999 0 -0.39 11 11
T-DHT/AR/Hsp90 -0.011 0.11 -9999 0 -0.48 18 18
GSK3B 0.013 0.003 -9999 0 -10000 0 0
NR2C1 0.012 0.034 -9999 0 -0.67 2 2
mol:T-DHT 0.006 0.098 -9999 0 -0.42 32 32
SIRT1 0.013 0 -9999 0 -10000 0 0
ZMIZ2 0.014 0.005 -9999 0 -10000 0 0
POU2F1 0.013 0.04 -9999 0 -0.56 1 1
T-DHT/AR/DAX-1 -0.056 0.12 -9999 0 -0.43 37 37
CREBBP 0.012 0.033 -9999 0 -0.67 2 2
SMARCE1 0.01 0.036 -9999 0 -0.46 5 5
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.016 0.012 -10000 0 -10000 0 0
HSPA8 0.011 0.034 -10000 0 -0.68 2 2
SMAD3/SMAD4/ER alpha -0.11 0.2 0.23 1 -0.45 209 210
AKT1 0.015 0.009 -10000 0 -10000 0 0
GSC -0.13 0.42 -10000 0 -1.5 73 73
NKX2-5 -0.079 0.19 -10000 0 -0.48 151 151
muscle cell differentiation 0.037 0.083 0.48 13 -10000 0 13
SMAD2-3/SMAD4/SP1 0.043 0.1 -10000 0 -0.44 11 11
SMAD4 0.008 0.055 -10000 0 -0.42 3 3
CBFB 0.013 0 -10000 0 -10000 0 0
SAP18 0.013 0.001 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.06 0.16 -10000 0 -0.42 94 94
SMAD3/SMAD4/VDR 0.004 0.065 -10000 0 -0.42 6 6
MYC -0.013 0.12 -10000 0 -0.65 31 31
CDKN2B 0.013 0.17 -10000 0 -1.4 10 10
AP1 0.008 0.13 -10000 0 -0.52 19 19
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.046 0.053 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 0.033 0.066 -10000 0 -0.4 4 4
SP3 0.015 0.01 -10000 0 -10000 0 0
CREB1 0.013 0 -10000 0 -10000 0 0
FOXH1 -0.033 0.16 -10000 0 -0.61 53 53
SMAD3/SMAD4/GR -0.005 0.061 -10000 0 -0.43 8 8
GATA3 -0.098 0.25 -10000 0 -0.67 134 134
SKI/SIN3/HDAC complex/NCoR1 0.038 0.035 -10000 0 -10000 0 0
MEF2C/TIF2 -0.043 0.17 -10000 0 -0.63 31 31
endothelial cell migration 0.019 0.21 1.4 18 -10000 0 18
MAX 0.013 0.008 -10000 0 -10000 0 0
RBBP7 0.008 0.051 -10000 0 -0.48 9 9
RBBP4 0.013 0.001 -10000 0 -10000 0 0
RUNX2 -0.009 0.12 -10000 0 -0.66 28 28
RUNX3 -0.018 0.13 -10000 0 -0.55 47 47
RUNX1 0.008 0.058 -10000 0 -0.67 6 6
CTBP1 0.013 0 -10000 0 -10000 0 0
NR3C1 0.01 0.04 -10000 0 -0.65 3 3
VDR 0.007 0.067 -10000 0 -0.67 8 8
CDKN1A 0.034 0.15 -10000 0 -1.4 7 7
KAT2B 0.011 0.044 -10000 0 -0.62 4 4
SMAD2/SMAD2/SMAD4/FOXH1 -0.009 0.14 -10000 0 -0.45 42 42
DCP1A 0.013 0 -10000 0 -10000 0 0
SKI 0.012 0.016 -10000 0 -0.46 1 1
SERPINE1 -0.02 0.21 -10000 0 -1.4 18 18
SMAD3/SMAD4/ATF2 0 0.06 -10000 0 -0.42 7 7
SMAD3/SMAD4/ATF3 -0.022 0.11 -10000 0 -0.45 34 34
SAP30 0.004 0.074 -10000 0 -0.64 11 11
Cbp/p300/PIAS3 0.018 0.042 -10000 0 -0.4 2 2
JUN 0.007 0.13 -10000 0 -0.52 19 19
SMAD3/SMAD4/IRF7 -0.021 0.1 -10000 0 -0.45 29 29
TFE3 0.017 0.018 -10000 0 -10000 0 0
COL1A2 -0.026 0.28 -10000 0 -1.1 49 49
mesenchymal cell differentiation 0.016 0.1 0.5 31 -10000 0 31
DLX1 -0.15 0.25 -10000 0 -0.51 256 256
TCF3 0.013 0 -10000 0 -10000 0 0
FOS -0.057 0.2 -10000 0 -0.55 112 112
SMAD3/SMAD4/Max -0.003 0.053 -10000 0 -0.39 5 5
Cbp/p300/SNIP1 0.028 0.024 -10000 0 -0.41 2 2
ZBTB17 0.011 0.025 -10000 0 -0.68 1 1
LAMC1 0.035 0.089 -10000 0 -0.71 8 8
TGIF2/HDAC complex/SMAD3/SMAD4 -0.001 0.061 -10000 0 -0.4 9 9
IRF7 -0.008 0.11 -10000 0 -0.65 23 23
ESR1 -0.16 0.3 -10000 0 -0.66 213 213
HNF4A -0.003 0.061 -10000 0 -0.46 15 15
MEF2C -0.038 0.16 -10000 0 -0.61 22 22
SMAD2-3/SMAD4 0.012 0.071 -10000 0 -0.4 8 8
Cbp/p300/Src-1 0.03 0.031 -10000 0 -0.4 3 3
IGHV3OR16-13 -0.006 0.021 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.011 0.041 -10000 0 -0.67 3 3
CREBBP 0.014 0.034 -10000 0 -0.66 2 2
SKIL 0.005 0.067 -10000 0 -0.5 14 14
HDAC1 0.012 0.024 -10000 0 -0.67 1 1
HDAC2 0.012 0.029 -10000 0 -0.57 2 2
SNIP1 0.012 0.003 -10000 0 -10000 0 0
GCN5L2 0.002 0.01 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.038 0.073 -10000 0 -0.4 9 9
MSG1/HSC70 -0.089 0.19 -10000 0 -0.4 216 216
SMAD2 0.008 0.032 -10000 0 -10000 0 0
SMAD3 0.012 0.064 -10000 0 -0.63 5 5
SMAD3/E2F4-5/DP1/p107/SMAD4 0.035 0.05 -10000 0 -0.38 2 2
SMAD2/SMAD2/SMAD4 0.015 0.046 -10000 0 -0.57 3 3
NCOR1 0.011 0.034 -10000 0 -0.68 2 2
NCOA2 -0.015 0.14 -10000 0 -0.67 34 34
NCOA1 0.012 0.024 -10000 0 -0.67 1 1
MYOD/E2A 0.01 0 -10000 0 -10000 0 0
SMAD2-3/SMAD4/SP1/MIZ-1 0.05 0.096 -10000 0 -0.47 5 5
IFNB1 0.004 0.13 -10000 0 -0.43 57 57
SMAD3/SMAD4/MEF2C -0.026 0.16 -10000 0 -0.6 23 23
CITED1 -0.13 0.25 -10000 0 -0.55 214 214
SMAD2-3/SMAD4/ARC105 0.033 0.067 -10000 0 -0.41 3 3
RBL1 0.01 0.04 -10000 0 -0.56 4 4
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB 0.044 0.081 -10000 0 -0.49 12 12
RUNX1-3/PEBPB2 0.004 0.093 -10000 0 -0.44 25 25
SMAD7 0.041 0.13 -10000 0 -0.74 6 6
MYC/MIZ-1 -0.012 0.095 -10000 0 -0.5 28 28
SMAD3/SMAD4 0.024 0.11 0.3 34 -0.46 13 47
IL10 -0.05 0.22 -10000 0 -0.6 66 66
PIASy/HDAC complex 0.012 0.008 -10000 0 -10000 0 0
PIAS3 0.014 0.004 -10000 0 -10000 0 0
CDK2 0.015 0.008 -10000 0 -10000 0 0
IL5 -0.044 0.18 -10000 0 -0.42 137 137
CDK4 0.014 0.03 -10000 0 -0.46 3 3
PIAS4 0.012 0.008 -10000 0 -10000 0 0
ATF3 -0.023 0.14 -10000 0 -0.56 52 52
SMAD3/SMAD4/SP1 0.031 0.099 -10000 0 -0.42 15 15
FOXG1 -0.028 0.12 -10000 0 -0.46 59 59
FOXO3 0.023 0.035 -10000 0 -0.38 5 5
FOXO1 0.023 0.035 -10000 0 -0.45 4 4
FOXO4 0.025 0.022 -10000 0 -0.5 1 1
heart looping -0.037 0.16 -10000 0 -0.6 22 22
CEBPB 0.007 0.059 -10000 0 -0.48 12 12
SMAD3/SMAD4/DLX1 -0.097 0.16 -10000 0 -0.44 90 90
MYOD1 0 0 -10000 0 -10000 0 0
SMAD3/SMAD4/HNF4 -0.007 0.066 -10000 0 -0.38 7 7
SMAD3/SMAD4/GATA3 -0.081 0.19 -10000 0 -0.47 138 138
SnoN/SIN3/HDAC complex/NCoR1 0.005 0.067 -10000 0 -0.5 14 14
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.021 0.11 -10000 0 -0.48 18 18
SMAD3/SMAD4/SP1-3 0.044 0.098 -10000 0 -0.5 8 8
MED15 0.013 0 -10000 0 -10000 0 0
SP1 0.012 0.041 -10000 0 -10000 0 0
SIN3B 0.013 0.001 -10000 0 -10000 0 0
SIN3A 0.013 0.001 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.046 0.17 -10000 0 -0.52 43 43
ITGB5 0.037 0.12 -10000 0 -0.75 12 12
TGIF/SIN3/HDAC complex/CtBP 0.041 0.032 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.096 0.2 -10000 0 -0.47 174 174
AR -0.13 0.28 -10000 0 -0.67 177 177
negative regulation of cell growth 0.031 0.076 -10000 0 -0.49 5 5
SMAD3/SMAD4/MYOD -0.003 0.056 -10000 0 -0.36 8 8
E2F5 0.011 0.037 -10000 0 -0.51 4 4
E2F4 0.013 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.012 0.11 -10000 0 -0.49 11 11
SMAD2-3/SMAD4/FOXO1-3a-4 0.043 0.063 -10000 0 -0.38 1 1
TFDP1 0.01 0.036 -10000 0 -0.46 5 5
SMAD3/SMAD4/AP1 0.012 0.13 -10000 0 -0.53 19 19
SMAD3/SMAD4/RUNX2 -0.014 0.11 -10000 0 -0.5 31 31
TGIF2 0.011 0.041 -10000 0 -0.67 3 3
TGIF1 0.012 0.033 -10000 0 -0.67 2 2
ATF2 0.012 0.029 -10000 0 -0.56 2 2
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0.012 0.028 -9999 0 -0.32 6 6
PRKCZ 0.011 0.041 -9999 0 -0.67 3 3
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.019 0.059 -9999 0 -0.34 10 10
IRAK/TOLLIP 0.026 0.028 -9999 0 -10000 0 0
IKBKB 0.01 0.04 -9999 0 -0.5 5 5
IKBKG 0.013 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.091 0.21 -9999 0 -0.45 196 196
IL1A -0.033 0.16 -9999 0 -0.57 66 66
IL1B -0.015 0.14 -9999 0 -0.46 66 66
IRAK/TRAF6/p62/Atypical PKCs -0.004 0.028 -9999 0 -10000 0 0
IL1R2 -0.092 0.23 -9999 0 -0.56 153 153
IL1R1 -0.008 0.12 -9999 0 -0.61 29 29
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.022 0.082 -9999 0 -0.44 5 5
TOLLIP 0.013 0.016 -9999 0 -0.46 1 1
TICAM2 0.01 0.047 -9999 0 -0.67 4 4
MAP3K3 0.013 0.016 -9999 0 -0.46 1 1
TAK1/TAB1/TAB2 0.009 0.01 -9999 0 -0.27 1 1
IKK complex/ELKS 0.06 0.027 -9999 0 -10000 0 0
JUN 0.026 0.071 -9999 0 -0.48 2 2
MAP3K7 0.013 0.016 -9999 0 -0.46 1 1
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.001 0.13 -9999 0 -0.63 12 12
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.011 0.13 -9999 0 -0.41 61 61
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.003 0.12 -9999 0 -0.38 61 61
IL1 beta fragment/IL1R1/IL1RAP -0.014 0.14 -9999 0 -0.44 65 65
NFKB1 0.012 0.024 -9999 0 -0.67 1 1
MAPK8 0.022 0.07 -9999 0 -0.38 1 1
IRAK1 0.02 0.029 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.03 0.15 -9999 0 -0.46 87 87
IRAK4 0.013 0 -9999 0 -10000 0 0
PRKCI 0.013 0.016 -9999 0 -0.46 1 1
TRAF6 0.013 0.016 -9999 0 -0.46 1 1
PI3K 0.018 0.023 -9999 0 -0.32 4 4
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.01 0.088 -9999 0 -0.42 11 11
CHUK 0.013 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.014 0.14 -9999 0 -0.44 65 65
IL1 beta/IL1R2 -0.072 0.19 -9999 0 -0.47 123 123
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.002 0.021 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.035 0.1 -9999 0 -0.59 11 11
IRAK3 -0.025 0.13 -9999 0 -0.48 66 66
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0 0.13 -9999 0 -0.4 66 66
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.004 0.098 -9999 0 -0.76 3 3
IL1 alpha/IL1R1/IL1RAP -0.022 0.14 -9999 0 -0.45 61 61
RELA 0.013 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.012 0.023 -9999 0 -0.46 2 2
MYD88 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.033 0.027 -9999 0 -10000 0 0
IL1RAP 0.004 0.073 -9999 0 -0.55 14 14
UBE2N 0.013 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.034 0.099 -9999 0 -0.55 14 14
CASP1 0.003 0.081 -9999 0 -0.61 14 14
IL1RN/IL1R2 -0.091 0.21 -9999 0 -0.44 201 201
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.005 0.13 -9999 0 -0.41 65 65
TMEM189-UBE2V1 0.003 0.039 -9999 0 -0.46 6 6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.013 0.09 -9999 0 -0.38 22 22
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
IL1RN -0.033 0.17 -9999 0 -0.61 63 63
TRAF6/TAK1/TAB1/TAB2 -0.002 0.02 -9999 0 -10000 0 0
MAP2K6 0.015 0.073 -9999 0 -0.34 28 28
EPHB forward signaling

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
Ephrin A5/EPHB2 -0.057 0.16 -10000 0 -0.38 156 156
cell-cell adhesion 0.049 0.12 0.55 21 -10000 0 21
Ephrin B/EPHB2/RasGAP -0.002 0.12 -10000 0 -0.42 54 54
ITSN1 0.012 0.033 -10000 0 -0.67 2 2
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
SHC1 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.004 0.064 -10000 0 -0.28 39 39
Ephrin B1/EPHB1 -0.015 0.096 -10000 0 -0.28 93 93
HRAS/GDP -0.048 0.12 -10000 0 -0.58 17 17
Ephrin B/EPHB1/GRB7 -0.044 0.16 -10000 0 -0.45 68 68
Endophilin/SYNJ1 -0.001 0.12 -10000 0 -0.38 54 54
KRAS 0.013 0.016 -10000 0 -0.46 1 1
Ephrin B/EPHB1/Src -0.024 0.14 -10000 0 -0.43 63 63
endothelial cell migration -0.007 0.047 -10000 0 -0.36 13 13
GRB2 0.013 0.016 -10000 0 -0.46 1 1
GRB7 -0.028 0.14 -10000 0 -0.47 73 73
PAK1 -0.009 0.14 -10000 0 -0.67 17 17
HRAS 0.009 0.05 -10000 0 -0.63 5 5
RRAS -0.003 0.12 -10000 0 -0.39 56 56
DNM1 -0.002 0.096 -10000 0 -0.61 20 20
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.023 0.14 -10000 0 -0.41 63 63
lamellipodium assembly -0.049 0.12 -10000 0 -0.55 21 21
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.003 0.1 -10000 0 -0.55 12 12
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
EPHB2 0.003 0.077 -10000 0 -0.56 15 15
EPHB3 -0.008 0.098 -10000 0 -0.46 37 37
EPHB1 -0.04 0.15 -10000 0 -0.48 91 91
EPHB4 0.009 0.055 -10000 0 -0.64 6 6
mol:GDP -0.011 0.14 -10000 0 -0.58 20 20
Ephrin B/EPHB2 -0.009 0.12 -10000 0 -0.42 54 54
Ephrin B/EPHB3 -0.014 0.12 -10000 0 -0.41 54 54
JNK cascade 0.003 0.1 -10000 0 -0.53 11 11
Ephrin B/EPHB1 -0.031 0.14 -10000 0 -0.44 62 62
RAP1/GDP 0.004 0.12 -10000 0 -0.54 15 15
EFNB2 0.006 0.07 -10000 0 -0.63 10 10
EFNB3 -0.041 0.17 -10000 0 -0.57 78 78
EFNB1 0.011 0.033 -10000 0 -0.53 3 3
Ephrin B2/EPHB1-2 -0.014 0.11 -10000 0 -0.46 24 24
RAP1B 0.013 0 -10000 0 -10000 0 0
RAP1A 0.013 0 -10000 0 -10000 0 0
CDC42/GTP -0.051 0.12 -10000 0 -0.63 18 18
Rap1/GTP -0.047 0.11 -10000 0 -0.56 18 18
axon guidance -0.057 0.16 -10000 0 -0.38 156 156
MAPK3 0.012 0.094 -10000 0 -0.57 8 8
MAPK1 0.012 0.094 -10000 0 -0.57 8 8
Rac1/GDP -0.001 0.12 -10000 0 -0.52 20 20
actin cytoskeleton reorganization -0.041 0.095 -10000 0 -0.43 23 23
CDC42/GDP -0.001 0.12 -10000 0 -0.52 20 20
PI3K 0.023 0.053 -10000 0 -0.36 13 13
EFNA5 -0.094 0.24 -10000 0 -0.6 146 146
Ephrin B2/EPHB4 0.01 0.058 -10000 0 -0.4 16 16
Ephrin B/EPHB2/Intersectin/N-WASP 0.005 0.1 -10000 0 -0.61 9 9
CDC42 0.013 0 -10000 0 -10000 0 0
RAS family/GTP -0.05 0.12 -10000 0 -0.53 23 23
PTK2 0.008 0.023 -10000 0 -10000 0 0
MAP4K4 0.003 0.1 -10000 0 -0.54 11 11
SRC 0.011 0.037 -10000 0 -0.6 3 3
KALRN -0.003 0.1 -10000 0 -0.65 20 20
Intersectin/N-WASP 0.018 0.025 -10000 0 -0.5 2 2
neuron projection morphogenesis 0.009 0.13 -10000 0 -0.48 24 24
MAP2K1 0.005 0.099 -10000 0 -0.52 12 12
WASL 0.013 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.002 0.1 -10000 0 -0.43 21 21
cell migration 0.007 0.11 -10000 0 -0.57 12 12
NRAS 0.007 0.062 -10000 0 -0.62 8 8
SYNJ1 -0.002 0.12 -10000 0 -0.39 54 54
PXN 0.013 0 -10000 0 -10000 0 0
TF -0.11 0.2 -10000 0 -0.6 52 52
HRAS/GTP -0.053 0.12 -10000 0 -0.5 32 32
Ephrin B1/EPHB1-2 -0.01 0.1 -10000 0 -0.44 21 21
cell adhesion mediated by integrin 0.031 0.1 0.4 47 -10000 0 47
RAC1 0.013 0 -10000 0 -10000 0 0
mol:GTP -0.021 0.14 -10000 0 -0.53 32 32
RAC1-CDC42/GTP -0.055 0.12 -10000 0 -0.56 24 24
RASA1 0.011 0.037 -10000 0 -0.51 4 4
RAC1-CDC42/GDP 0.004 0.12 -10000 0 -0.54 15 15
ruffle organization -0.001 0.14 -10000 0 -0.56 21 21
NCK1 0.013 0 -10000 0 -10000 0 0
receptor internalization -0.001 0.14 -10000 0 -0.66 18 18
Ephrin B/EPHB2/KALRN -0.01 0.15 -10000 0 -0.44 64 64
ROCK1 0.012 0.059 -10000 0 -0.41 4 4
RAS family/GDP -0.04 0.096 -10000 0 -0.46 21 21
Rac1/GTP -0.052 0.12 -10000 0 -0.59 21 21
Ephrin B/EPHB1/Src/Paxillin -0.009 0.11 -10000 0 -0.6 12 12
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.02 0.14 -10000 0 -0.61 45 45
positive regulation of NF-kappaB transcription factor activity -0.028 0.14 -10000 0 -0.42 91 91
MAP2K4 0.023 0.084 -10000 0 -0.44 11 11
IKBKB 0.01 0.04 -10000 0 -0.5 5 5
TNFRSF10B 0.009 0.053 -10000 0 -0.67 5 5
TNFRSF10A 0.003 0.082 -10000 0 -0.67 12 12
SMPD1 0.006 0.058 -10000 0 -0.26 35 35
IKBKG 0.013 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.019 0.13 -10000 0 -0.52 51 51
TRAIL/TRAILR2 -0.008 0.12 -10000 0 -0.48 47 47
TRAIL/TRAILR3 -0.034 0.16 -10000 0 -0.44 99 99
TRAIL/TRAILR1 -0.012 0.12 -10000 0 -0.47 55 55
TRAIL/TRAILR4 -0.028 0.14 -10000 0 -0.42 91 91
TRAIL/TRAILR1/DAP3/GTP 0 0.1 -10000 0 -0.41 42 42
IKK complex -0.011 0.041 -10000 0 -0.44 1 1
RIPK1 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.01 0 -10000 0 -10000 0 0
MAPK3 -0.003 0.11 -10000 0 -0.45 45 45
MAP3K1 0.019 0.079 -10000 0 -0.52 5 5
TRAILR4 (trimer) -0.019 0.13 -10000 0 -0.52 51 51
TRADD 0.012 0.033 -10000 0 -0.67 2 2
TRAILR1 (trimer) 0.003 0.081 -10000 0 -0.67 12 12
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 0.014 0.085 -10000 0 -0.65 4 4
CFLAR 0.012 0.033 -10000 0 -0.67 2 2
MAPK1 -0.003 0.11 -10000 0 -0.45 45 45
TRAIL/TRAILR1/FADD/TRADD/RIP 0.011 0.1 -10000 0 -0.74 4 4
mol:ceramide 0.006 0.058 -10000 0 -0.26 35 35
FADD 0.006 0.058 -10000 0 -0.46 13 13
MAPK8 0.029 0.08 -10000 0 -0.47 7 7
TRAF2 0.012 0.024 -10000 0 -0.67 1 1
TRAILR3 (trimer) -0.028 0.15 -10000 0 -0.54 62 62
CHUK 0.013 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.005 0.12 -10000 0 -0.45 42 42
DAP3 0.013 0 -10000 0 -10000 0 0
CASP10 -0.018 0.12 0.28 13 -0.46 33 46
JNK cascade -0.028 0.14 -10000 0 -0.42 91 91
TRAIL (trimer) -0.02 0.14 -10000 0 -0.61 45 45
TNFRSF10C -0.028 0.15 -10000 0 -0.54 62 62
TRAIL/TRAILR1/DAP3/GTP/FADD 0.004 0.1 -10000 0 -0.39 42 42
TRAIL/TRAILR2/FADD -0.001 0.11 -10000 0 -0.46 35 35
cell death 0.006 0.057 -10000 0 -0.25 35 35
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 0.017 0.076 -10000 0 -0.5 4 4
TRAILR2 (trimer) 0.009 0.053 -10000 0 -0.67 5 5
CASP8 0.006 0.031 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.014 0.097 -10000 0 -0.65 4 4
TCGA08_p53

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
CDKN2A -0.041 0.13 -10000 0 -0.36 119 119
TP53 -0.018 0.058 -10000 0 -0.39 9 9
Senescence -0.018 0.058 -10000 0 -0.39 9 9
Apoptosis -0.018 0.058 -10000 0 -0.39 9 9
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.026 0.078 0.29 23 -0.32 7 30
MDM4 0.013 0 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.013 0 -9999 0 -10000 0 0
SPHK1 -0.011 0.12 -9999 0 -0.6 33 33
GNAI2 0.013 0 -9999 0 -10000 0 0
mol:S1P 0.01 0.06 -9999 0 -0.32 24 24
GNAO1 -0.076 0.21 -9999 0 -0.53 139 139
mol:Sphinganine-1-P 0.004 0.091 -9999 0 -0.44 33 33
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 0.03 0.046 -9999 0 -10000 0 0
GNAI3 0.013 0 -9999 0 -10000 0 0
G12/G13 0.02 0 -9999 0 -10000 0 0
S1PR3 0 0.088 -9999 0 -0.55 20 20
S1PR2 0.012 0.023 -9999 0 -0.46 2 2
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.01 0.048 -9999 0 -0.28 24 24
S1PR5 -0.025 0.14 -9999 0 -0.55 57 57
S1PR4 -0.051 0.19 -9999 0 -0.58 92 92
GNAI1 0.003 0.077 -9999 0 -0.54 16 16
S1P/S1P5/G12 0.002 0.098 -9999 0 -0.39 29 29
S1P/S1P3/Gq -0.007 0.12 -9999 0 -0.49 24 24
S1P/S1P4/Gi -0.033 0.15 -9999 0 -0.57 32 32
GNAQ 0.007 0.062 -9999 0 -0.67 7 7
GNAZ -0.002 0.099 -9999 0 -0.65 19 19
GNA14 -0.054 0.19 -9999 0 -0.57 97 97
GNA15 -0.002 0.096 -9999 0 -0.61 20 20
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.01 0.047 -9999 0 -0.67 4 4
ABCC1 0.012 0.033 -9999 0 -0.67 2 2
TCGA08_rtk_signaling

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
PDGFRA -0.022 0.15 -10000 0 -0.67 43 43
HRAS 0.009 0.05 -10000 0 -0.63 5 5
EGFR -0.076 0.22 -10000 0 -0.57 129 129
AKT 0.016 0.081 0.22 1 -0.42 21 22
FOXO3 0.01 0.044 -10000 0 -0.54 5 5
AKT1 0.013 0 -10000 0 -10000 0 0
FOXO1 0.01 0.044 -10000 0 -0.62 4 4
AKT3 -0.009 0.11 -10000 0 -0.54 33 33
FOXO4 0.012 0.024 -10000 0 -0.67 1 1
MET -0.066 0.21 -10000 0 -0.6 108 108
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
PIK3CB 0.013 0 -10000 0 -10000 0 0
NRAS 0.007 0.062 -10000 0 -0.62 8 8
PIK3CG -0.016 0.13 -10000 0 -0.62 38 38
PIK3R3 0.009 0.05 -10000 0 -0.63 5 5
PIK3R2 0.013 0 -10000 0 -10000 0 0
NF1 0.01 0.044 -10000 0 -0.62 4 4
RAS -0.037 0.12 0.24 1 -0.37 61 62
ERBB2 -0.037 0.15 -10000 0 -0.48 86 86
proliferation/survival/translation -0.021 0.045 0.28 4 -0.21 1 5
PI3K -0.027 0.11 0.22 3 -0.34 66 69
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
KRAS 0.013 0.016 -10000 0 -0.46 1 1
FOXO 0.033 0.031 0.21 1 -10000 0 1
AKT2 0.013 0.016 -10000 0 -0.46 1 1
PTEN 0.008 0.058 -10000 0 -0.67 6 6
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.006 0.098 -9999 0 -0.4 40 40
CRKL 0.012 0.024 -9999 0 -0.67 1 1
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
DOCK1 0.012 0.024 -9999 0 -0.67 1 1
ITGA4 -0.003 0.098 -9999 0 -0.56 24 24
alpha4/beta7 Integrin/MAdCAM1 -0.009 0.12 -9999 0 -0.43 43 43
EPO -0.079 0.19 -9999 0 -0.47 158 158
alpha4/beta7 Integrin -0.013 0.12 -9999 0 -0.46 58 58
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.012 0.024 -9999 0 -0.67 1 1
alpha4/beta1 Integrin 0.008 0.073 -9999 0 -0.41 24 24
EPO/EPOR (dimer) -0.052 0.14 -9999 0 -0.34 168 168
lamellipodium assembly 0.001 0.016 -9999 0 -10000 0 0
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
PI3K 0.018 0.023 -9999 0 -0.32 4 4
ARF6 0.013 0.016 -9999 0 -0.46 1 1
JAK2 -0.014 0.097 -9999 0 -0.35 30 30
PXN 0.013 0 -9999 0 -10000 0 0
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
MADCAM1 -0.018 0.11 -9999 0 -0.46 52 52
cell adhesion -0.01 0.12 -9999 0 -0.43 43 43
CRKL/CBL 0.019 0.018 -9999 0 -0.5 1 1
ITGB1 0.013 0 -9999 0 -10000 0 0
SRC 0.007 0.096 -9999 0 -0.39 37 37
ITGB7 -0.016 0.13 -9999 0 -0.59 40 40
RAC1 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0 0.1 -9999 0 -0.44 35 35
p130Cas/Crk/Dock1 0.028 0.085 -9999 0 -0.51 2 2
VCAM1 -0.012 0.12 -9999 0 -0.6 35 35
RHOA 0.013 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.023 0.062 -9999 0 -0.38 13 13
BCAR1 0.015 0.09 -9999 0 -0.36 37 37
EPOR 0.005 0.07 -9999 0 -0.6 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.013 0 -9999 0 -10000 0 0
GIT1 0.01 0.043 -9999 0 -0.49 6 6
Rac1/GTP 0.001 0.016 -9999 0 -10000 0 0
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.01 0.056 -9999 0 -0.38 16 16
PDGFRB 0.001 0.089 -9999 0 -0.68 14 14
SPHK1 -0.034 0.15 -9999 0 -0.9 22 22
mol:S1P -0.034 0.14 -9999 0 -0.77 24 24
S1P1/S1P/Gi -0.036 0.17 -9999 0 -0.58 40 40
GNAO1 -0.078 0.21 -9999 0 -0.53 139 139
PDGFB-D/PDGFRB/PLCgamma1 -0.027 0.16 -9999 0 -0.58 38 38
PLCG1 -0.029 0.16 -9999 0 -0.56 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.001 0.089 -9999 0 -0.68 14 14
GNAI2 0.012 0.006 -9999 0 -10000 0 0
GNAI3 0.012 0.006 -9999 0 -10000 0 0
GNAI1 0.001 0.077 -9999 0 -0.54 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.01 0.048 -9999 0 -0.32 16 16
S1P1/S1P -0.031 0.11 -9999 0 -0.55 29 29
negative regulation of cAMP metabolic process -0.035 0.16 -9999 0 -0.56 40 40
MAPK3 -0.044 0.2 -9999 0 -0.63 57 57
calcium-dependent phospholipase C activity -0.001 0.003 -9999 0 -10000 0 0
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
KDR 0.008 0.055 -9999 0 -0.64 6 6
PLCB2 0.003 0.11 -9999 0 -0.48 30 30
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.028 0.09 -9999 0 -0.47 26 26
receptor internalization -0.029 0.1 -9999 0 -0.5 29 29
PTGS2 -0.073 0.28 -9999 0 -1 49 49
Rac1/GTP -0.028 0.09 -9999 0 -0.47 26 26
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFA 0.007 0.051 -9999 0 -0.46 10 10
negative regulation of T cell proliferation -0.035 0.16 -9999 0 -0.56 40 40
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.003 0.1 -9999 0 -0.66 19 19
MAPK1 -0.044 0.2 -9999 0 -0.63 57 57
S1P1/S1P/PDGFB-D/PDGFRB 0 0.14 -9999 0 -0.54 33 33
ABCC1 0.011 0.034 -9999 0 -0.68 2 2
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.018 0.01 -9999 0 -0.26 1 1
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.013 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.016 0.13 -9999 0 -0.6 40 40
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.008 0.06 -9999 0 -0.64 7 7
RAC1-CDC42/GTP/PAK family -0.008 0.084 -9999 0 -0.26 65 65
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.007 0.064 -9999 0 -0.65 8 8
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.013 0.016 -9999 0 -0.46 1 1
FYN 0.009 0.046 -9999 0 -0.53 6 6
MAP3K12 0.004 0.078 -9999 0 -0.67 11 11
FGR 0.005 0.069 -9999 0 -0.54 13 13
p38 alpha/TAB1 -0.041 0.08 -9999 0 -0.34 30 30
PRKG1 -0.041 0.18 -9999 0 -0.67 67 67
DUSP8 0.004 0.08 -9999 0 -0.66 12 12
PGK/cGMP/p38 alpha -0.062 0.12 -9999 0 -0.36 90 90
apoptosis -0.04 0.077 -9999 0 -0.32 30 30
RAL/GTP 0.018 0 -9999 0 -10000 0 0
LYN 0.006 0.061 -9999 0 -0.49 12 12
DUSP1 -0.019 0.14 -9999 0 -0.59 45 45
PAK1 0.002 0.075 -9999 0 -0.48 20 20
SRC 0.011 0.037 -9999 0 -0.6 3 3
RAC1/OSM/MEKK3/MKK3 0.033 0.015 -9999 0 -10000 0 0
TRAF6 0.013 0.016 -9999 0 -0.46 1 1
RAC1 0.013 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 0.013 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP 0.018 0 -9999 0 -10000 0 0
MAPK11 -0.027 0.14 -9999 0 -0.42 45 45
BLK -0.14 0.26 -9999 0 -0.56 218 218
HCK 0.002 0.078 -9999 0 -0.52 18 18
MAP2K3 0.012 0.023 -9999 0 -0.46 2 2
DUSP16 0.012 0.033 -9999 0 -0.67 2 2
DUSP10 0.001 0.089 -9999 0 -0.61 17 17
TRAF6/MEKK3 0.016 0.012 -9999 0 -0.24 2 2
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 -0.011 0.11 -9999 0 -0.37 29 29
positive regulation of innate immune response -0.024 0.14 -9999 0 -0.45 43 43
LCK -0.07 0.21 -9999 0 -0.6 114 114
p38alpha-beta/MKP7 -0.017 0.14 -9999 0 -0.49 26 26
p38alpha-beta/MKP5 -0.022 0.14 -9999 0 -0.48 31 31
PGK/cGMP -0.031 0.14 -9999 0 -0.5 67 67
PAK2 0.013 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 -0.031 0.15 -9999 0 -0.51 37 37
CDC42 0.013 0 -9999 0 -10000 0 0
RALB 0.013 0 -9999 0 -10000 0 0
RALA 0.013 0 -9999 0 -10000 0 0
PAK3 -0.079 0.21 -9999 0 -0.56 134 134
E-cadherin signaling in the nascent adherens junction

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
CTTN -0.007 0.15 -9999 0 -0.51 66 66
KLHL20 -0.029 0.063 -9999 0 -0.28 11 11
CYFIP2 -0.025 0.15 -9999 0 -0.63 50 50
Rac1/GDP 0.027 0.1 -9999 0 -0.49 2 2
ENAH -0.005 0.15 -9999 0 -0.51 66 66
AP1M1 0.013 0 -9999 0 -10000 0 0
RAP1B 0.013 0 -9999 0 -10000 0 0
RAP1A 0.013 0 -9999 0 -10000 0 0
CTNNB1 0.011 0.033 -9999 0 -0.53 3 3
CDC42/GTP -0.021 0.066 -9999 0 -0.44 2 2
ABI1/Sra1/Nap1 -0.025 0.048 -9999 0 -0.21 11 11
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.016 0.14 -9999 0 -0.4 88 88
RAPGEF1 0.01 0.13 -9999 0 -0.43 66 66
CTNND1 0.012 0.023 -9999 0 -0.46 2 2
regulation of calcium-dependent cell-cell adhesion -0.015 0.15 -9999 0 -0.53 66 66
CRK 0.002 0.14 -9999 0 -0.48 66 66
E-cadherin/gamma catenin/alpha catenin -0.013 0.13 -9999 0 -0.43 68 68
alphaE/beta7 Integrin -0.002 0.098 -9999 0 -0.43 41 41
IQGAP1 0.013 0 -9999 0 -10000 0 0
NCKAP1 0.013 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0.021 0.042 -9999 0 -0.39 8 8
DLG1 -0.005 0.15 -9999 0 -0.51 66 66
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.016 0.048 -9999 0 -0.3 2 2
MLLT4 0.006 0.07 -9999 0 -0.63 10 10
ARF6/GTP/NME1/Tiam1 0.016 0.056 -9999 0 -0.39 11 11
PI3K -0.02 0.062 -9999 0 -0.4 2 2
ARF6 0.013 0.016 -9999 0 -0.46 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.023 0.14 -9999 0 -0.5 69 69
TIAM1 0.002 0.084 -9999 0 -0.62 15 15
E-cadherin(dimer)/Ca2+ -0.004 0.11 -9999 0 -0.36 68 68
AKT1 -0.011 0.035 -9999 0 -0.21 2 2
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
CDH1 -0.04 0.18 -9999 0 -0.67 66 66
RhoA/GDP 0.027 0.1 -9999 0 -0.49 2 2
actin cytoskeleton organization 0.016 0.064 -9999 0 -0.21 9 9
CDC42/GDP 0.027 0.1 -9999 0 -0.49 2 2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin -0.002 0.089 -9999 0 -0.3 68 68
ITGB7 -0.016 0.13 -9999 0 -0.59 40 40
RAC1 0.013 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.003 0.11 -9999 0 -0.38 68 68
E-cadherin/Ca2+/beta catenin/alpha catenin -0.01 0.11 -9999 0 -0.37 68 68
mol:GDP 0.02 0.12 -9999 0 -0.44 7 7
CDC42/GTP/IQGAP1 0.018 0 -9999 0 -10000 0 0
JUP 0.01 0.04 -9999 0 -0.56 4 4
p120 catenin/RhoA/GDP -0.024 0.086 -9999 0 -0.5 2 2
RAC1/GTP/IQGAP1 0.018 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0.02 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
CDC42 0.013 0 -9999 0 -10000 0 0
CTNNA1 0.012 0.033 -9999 0 -0.67 2 2
positive regulation of S phase of mitotic cell cycle 0.003 0.077 -9999 0 -0.23 73 73
NME1 0.009 0.045 -9999 0 -0.46 8 8
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 -0.006 0.15 -9999 0 -0.52 66 66
regulation of cell-cell adhesion -0.019 0.059 -9999 0 -0.37 2 2
WASF2 -0.013 0.026 -9999 0 -10000 0 0
Rap1/GTP -0.024 0.076 -9999 0 -0.51 2 2
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.01 0.13 -9999 0 -0.68 4 4
CCND1 0.002 0.096 -9999 0 -0.28 73 73
VAV2 0.006 0.14 -9999 0 -0.56 7 7
RAP1/GDP 0.023 0.094 -9999 0 -0.51 2 2
adherens junction assembly -0.005 0.15 -9999 0 -0.5 66 66
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.013 0 -9999 0 -10000 0 0
PIP5K1C 0.013 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.003 0.13 -9999 0 -0.66 5 5
E-cadherin/beta catenin -0.034 0.12 -9999 0 -0.43 65 65
mol:GTP 0 0 -9999 0 -10000 0 0
SRC -0.008 0.15 -9999 0 -0.52 66 66
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
Rac1/GTP -0.046 0.1 -9999 0 -0.46 14 14
E-cadherin/beta catenin/alpha catenin -0.012 0.12 -9999 0 -0.42 68 68
ITGAE 0.013 0.016 -9999 0 -0.46 1 1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.045 0.15 -9999 0 -0.54 66 66
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.002 0.085 -10000 0 -1.3 3 3
VDR 0.007 0.067 -10000 0 -0.67 8 8
FAM120B 0.013 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.011 0.11 -10000 0 -0.4 18 18
RXRs/LXRs/DNA/Oxysterols 0.009 0.14 -10000 0 -0.5 29 29
MED1 -0.007 0.095 -10000 0 -0.46 36 36
mol:9cRA 0.001 0.017 -10000 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.008 0.1 -10000 0 -0.36 48 48
RXRs/NUR77 -0.01 0.12 -10000 0 -0.37 39 39
RXRs/PPAR 0.007 0.086 -10000 0 -0.37 10 10
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.005 0.05 -10000 0 -0.51 8 8
RARs/VDR/DNA/Vit D3 0.012 0.087 -10000 0 -0.41 26 26
RARA -0.003 0.098 -10000 0 -0.6 22 22
NCOA1 0.012 0.024 -10000 0 -0.67 1 1
VDR/VDR/DNA 0.007 0.067 -10000 0 -0.67 8 8
RARs/RARs/DNA/9cRA 0.008 0.075 -10000 0 -0.4 20 20
RARG 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.009 0.058 -10000 0 -0.43 11 11
RARs/THRs/DNA/SMRT 0.009 0.1 -10000 0 -0.35 48 48
THRA 0.005 0.063 -10000 0 -0.49 13 13
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.005 0.05 -10000 0 -0.51 8 8
RXRs/PPAR/9cRA/PGJ2/DNA -0.001 0.11 0.3 3 -0.38 39 42
NR1H4 0 0 -10000 0 -10000 0 0
RXRs/LXRs/DNA 0.018 0.11 -10000 0 -0.42 13 13
NR1H2 0.016 0.012 -10000 0 -10000 0 0
NR1H3 0.015 0.014 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 0.002 0.11 -10000 0 -0.39 37 37
NR4A1 -0.017 0.12 -10000 0 -0.47 53 53
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0 0.073 -10000 0 -0.26 35 35
RXRG -0.042 0.17 -10000 0 -0.53 87 87
RXR alpha/CCPG 0.021 0.009 -10000 0 -10000 0 0
RXRA 0.016 0.012 -10000 0 -10000 0 0
RXRB 0.015 0.014 -10000 0 -10000 0 0
THRB -0.015 0.14 -10000 0 -0.66 35 35
PPARG -0.009 0.1 -10000 0 -0.5 36 36
PPARD 0.013 0 -10000 0 -10000 0 0
TNF -0.035 0.3 -10000 0 -1.1 50 50
mol:Oxysterols 0.002 0.015 -10000 0 -10000 0 0
cholesterol transport 0.009 0.14 -10000 0 -0.49 29 29
PPARA 0.01 0.047 -10000 0 -0.59 5 5
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB -0.001 0.086 -10000 0 -0.52 22 22
RXRs/NUR77/BCL2 -0.034 0.13 -10000 0 -0.33 106 106
SREBF1 0.012 0.16 -10000 0 -0.91 11 11
RXRs/RXRs/DNA/9cRA -0.001 0.11 0.29 3 -0.38 39 42
ABCA1 0.01 0.17 -10000 0 -1.1 11 11
RARs/THRs 0.004 0.12 -10000 0 -0.42 50 50
RXRs/FXR -0.001 0.1 -10000 0 -0.37 39 39
BCL2 -0.057 0.21 -10000 0 -0.66 87 87
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.044 0.099 0.48 20 -10000 0 20
GNAI2 0.013 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.006 0.091 -10000 0 -0.34 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 -0.076 0.21 -10000 0 -0.53 139 139
RhoA/GTP -0.016 0.12 -10000 0 -0.5 20 20
negative regulation of cAMP metabolic process -0.025 0.12 -10000 0 -0.54 20 20
GNAZ -0.002 0.099 -10000 0 -0.65 19 19
GNAI3 0.013 0 -10000 0 -10000 0 0
GNA12 0.013 0 -10000 0 -10000 0 0
S1PR5 -0.025 0.14 -10000 0 -0.55 57 57
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.025 0.13 -10000 0 -0.55 20 20
RhoA/GDP 0.01 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
GNAI1 0.003 0.077 -10000 0 -0.54 16 16
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 -0.037 0.11 -9999 0 -0.6 10 10
TC10/GTP -0.014 0.06 -9999 0 -0.53 1 1
Insulin Receptor/Insulin/IRS1/Shp2 -0.001 0.11 -9999 0 -0.4 55 55
HRAS 0.009 0.05 -9999 0 -0.63 5 5
APS homodimer -0.002 0.092 -9999 0 -0.53 24 24
GRB14 -0.22 0.29 -9999 0 -0.56 338 338
FOXO3 -0.023 0.069 -9999 0 -0.77 6 6
AKT1 -0.083 0.17 -9999 0 -0.52 35 35
INSR 0.013 0.023 -9999 0 -0.45 2 2
Insulin Receptor/Insulin 0.029 0.056 -9999 0 -0.43 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.012 0.029 -9999 0 -0.56 2 2
SORBS1 -0.002 0.097 -9999 0 -0.6 21 21
CRK 0.012 0.024 -9999 0 -0.67 1 1
PTPN1 0.027 0.056 -9999 0 -0.43 12 12
CAV1 -0.005 0.11 -9999 0 -0.37 61 61
CBL/APS/CAP/Crk-II/C3G 0.022 0.076 -9999 0 -0.58 1 1
Insulin Receptor/Insulin/IRS1/NCK2 -0.002 0.11 -9999 0 -0.4 56 56
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.025 0.087 -9999 0 -0.35 55 55
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.017 0.072 -9999 0 -0.39 1 1
RPS6KB1 -0.072 0.16 -9999 0 -0.47 36 36
PARD6A 0.007 0.064 -9999 0 -0.65 8 8
CBL 0.013 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 -0.005 0.07 -9999 0 -0.9 5 5
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.1 0.13 -9999 0 -0.49 36 36
HRAS/GTP -0.025 0.079 -9999 0 -0.46 1 1
Insulin Receptor 0.013 0.023 -9999 0 -0.45 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.006 0.1 -9999 0 -0.37 55 55
PRKCI -0.028 0.043 -9999 0 -0.53 2 2
Insulin Receptor/Insulin/GRB14/PDK1 -0.12 0.16 -9999 0 -0.56 37 37
SHC1 0.013 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade -0.005 0.066 -9999 0 -0.83 5 5
PI3K -0.025 0.088 -9999 0 -0.35 55 55
NCK2 0.011 0.033 -9999 0 -0.53 3 3
RHOQ 0.013 0 -9999 0 -10000 0 0
mol:H2O2 -0.001 0.006 -9999 0 -10000 0 0
HRAS/GDP 0.007 0.037 -9999 0 -0.47 5 5
AKT2 -0.084 0.17 -9999 0 -0.52 36 36
PRKCZ -0.03 0.056 -9999 0 -0.58 5 5
SH2B2 -0.002 0.092 -9999 0 -0.53 24 24
SHC/SHIP 0.003 0.1 -9999 0 -0.35 59 59
F2RL2 -0.078 0.23 -9999 0 -0.66 115 115
TRIP10 0.012 0.033 -9999 0 -0.67 2 2
Insulin Receptor/Insulin/Shc 0.019 0.013 -9999 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.017 0.022 -9999 0 -0.43 2 2
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.033 0.015 -9999 0 -10000 0 0
RAPGEF1 0.013 0 -9999 0 -10000 0 0
RASA1 0.011 0.037 -9999 0 -0.51 4 4
NCK1 0.013 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.016 0.08 -9999 0 -0.39 23 23
TC10/GDP 0.01 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.027 0.021 -9999 0 -0.4 1 1
INPP5D -0.006 0.1 -9999 0 -0.37 59 59
SOS1 0.013 0 -9999 0 -10000 0 0
SGK1 -0.013 0.07 -9999 0 -1 4 4
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.013 0 -9999 0 -10000 0 0
IRS1 -0.033 0.17 -9999 0 -0.66 58 58
p62DOK/RasGAP -0.005 0.068 -9999 0 -0.85 5 5
INS 0.002 0.006 -9999 0 -10000 0 0
mol:PI-3-4-P2 -0.006 0.1 -9999 0 -0.37 59 59
GRB2 0.013 0.016 -9999 0 -0.46 1 1
EIF4EBP1 -0.078 0.16 -9999 0 -0.48 41 41
PTPRA 0.014 0.005 -9999 0 -10000 0 0
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
TC10/GTP/CIP4 0.017 0.022 -9999 0 -0.43 2 2
PDPK1 0.013 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.011 0.079 -9999 0 -0.42 1 1
Insulin Receptor/Insulin/IRS1 -0.01 0.11 -9999 0 -0.4 58 58
Insulin Receptor/Insulin/IRS3 0.012 0.018 -9999 0 -0.32 2 2
Par3/Par6 -0.025 0.14 -9999 0 -0.37 112 112
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 -0.003 0.087 -9999 0 -0.47 28 28
Caspase 8 (4 units) -0.036 0.093 -9999 0 -0.54 12 12
NEF -0.015 0.051 -9999 0 -10000 0 0
NFKBIA 0.009 0.032 -9999 0 -0.55 1 1
BIRC3 0.005 0.15 -9999 0 -0.55 54 54
CYCS 0 0.11 -9999 0 -0.52 13 13
RIPK1 0.013 0 -9999 0 -10000 0 0
CD247 -0.082 0.24 -9999 0 -0.68 105 105
MAP2K7 0.008 0.095 -9999 0 -0.54 6 6
protein ubiquitination 0.039 0.072 -9999 0 -0.44 3 3
CRADD 0.013 0 -9999 0 -10000 0 0
DAXX 0.013 0 -9999 0 -10000 0 0
FAS 0.001 0.091 -9999 0 -0.65 16 16
BID -0.007 0.12 -9999 0 -0.56 12 12
NF-kappa-B/RelA/I kappa B alpha -0.017 0.067 -9999 0 -0.45 2 2
TRADD 0.012 0.033 -9999 0 -0.67 2 2
MAP3K5 0.01 0.047 -9999 0 -0.59 5 5
CFLAR 0.012 0.033 -9999 0 -0.67 2 2
FADD 0.006 0.058 -9999 0 -0.46 13 13
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.017 0.067 -9999 0 -0.45 2 2
MAPK8 0.015 0.09 -9999 0 -0.65 3 3
APAF1 0.012 0.024 -9999 0 -0.67 1 1
TRAF1 0.005 0.068 -9999 0 -0.55 12 12
TRAF2 0.012 0.024 -9999 0 -0.67 1 1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.015 0.12 -9999 0 -0.37 40 40
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.027 0.088 -9999 0 -0.62 3 3
CHUK 0.04 0.077 -9999 0 -0.49 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.027 0.072 -9999 0 -0.42 15 15
TCRz/NEF -0.096 0.21 -9999 0 -0.54 136 136
TNF -0.049 0.18 -9999 0 -0.57 90 90
FASLG -0.11 0.3 -9999 0 -0.7 152 152
NFKB1 0.009 0.035 -9999 0 -0.67 1 1
TNFR1A/BAG4/TNF-alpha -0.022 0.13 -9999 0 -0.45 49 49
CASP6 -0.021 0.063 -9999 0 -0.71 3 3
CASP7 0.023 0.15 -9999 0 -0.6 26 26
RELA 0.01 0.026 -9999 0 -10000 0 0
CASP2 0.013 0 -9999 0 -10000 0 0
CASP3 0.023 0.15 -9999 0 -0.6 26 26
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0.008 0.063 -9999 0 -0.33 28 28
CASP8 0.013 0 -9999 0 -10000 0 0
CASP9 0.013 0 -9999 0 -10000 0 0
MAP3K14 0.034 0.083 -9999 0 -0.56 3 3
APAF-1/Caspase 9 -0.043 0.11 -9999 0 -0.45 40 40
BCL2 -0.013 0.14 -9999 0 -0.47 23 23
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.11 0.24 -9999 0 -0.54 188 188
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.012 0.028 -9999 0 -0.46 3 3
TCEB1 0.013 0.016 -9999 0 -0.46 1 1
HIF1A/p53 0.017 0.059 -9999 0 -0.35 13 13
HIF1A 0.013 0.046 -9999 0 -0.3 12 12
COPS5 0.013 0.016 -9999 0 -0.46 1 1
VHL/Elongin B/Elongin C/RBX1/CUL2 0.038 0.019 -9999 0 -10000 0 0
FIH (dimer) 0.013 0 -9999 0 -10000 0 0
CDKN2A -0.059 0.18 -9999 0 -0.5 119 119
ARNT/IPAS -0.072 0.17 -9999 0 -0.39 188 188
HIF1AN 0.013 0 -9999 0 -10000 0 0
GNB2L1 0.013 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.021 0.045 -9999 0 -0.35 4 4
CUL2 0.013 0 -9999 0 -10000 0 0
OS9 0.012 0.028 -9999 0 -0.46 3 3
RACK1/Elongin B/Elongin C 0.026 0.019 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.02 0.045 -9999 0 -0.35 4 4
PHD1-3/OS9 0.01 0.088 -9999 0 -0.38 26 26
HIF1A/RACK1/Elongin B/Elongin C -0.008 0.037 -9999 0 -0.35 4 4
VHL 0.013 0.016 -9999 0 -0.46 1 1
HSP90AA1 0.013 0.016 -9999 0 -0.46 1 1
HIF1A/JAB1 0.02 0.045 -9999 0 -0.35 4 4
EGLN3 -0.022 0.14 -9999 0 -0.55 53 53
EGLN2 0.01 0.04 -9999 0 -0.5 5 5
EGLN1 0.012 0.033 -9999 0 -0.67 2 2
TP53 0.006 0.071 -9999 0 -0.67 9 9
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.035 0.015 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.013 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.014 0.1 -9999 0 -0.32 41 41
Aurora C signaling

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
INCENP 0.013 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.011 0.11 -9999 0 -0.4 48 48
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.01 0.029 -9999 0 -10000 0 0
AURKB -0.024 0.15 -9999 0 -0.62 50 50
AURKC -0.012 0.12 -9999 0 -0.52 39 39
Ceramide signaling pathway

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
SPHK2 0.02 0.03 -10000 0 -0.41 4 4
MAP4K4 0.013 0.094 -10000 0 -0.62 6 6
BAG4 -0.003 0.087 -10000 0 -0.47 28 28
PKC zeta/ceramide -0.019 0.046 0.18 2 -0.43 3 5
NFKBIA 0.013 0.016 -10000 0 -0.46 1 1
BIRC3 -0.023 0.14 -10000 0 -0.56 54 54
BAX -0.005 0.019 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AKT1 0.021 0.009 -10000 0 -10000 0 0
BAD -0.018 0.039 0.19 2 -10000 0 2
SMPD1 0.006 0.064 -10000 0 -0.22 46 46
RB1 -0.026 0.065 0.18 1 -0.39 17 18
FADD/Caspase 8 0.022 0.092 -10000 0 -0.55 8 8
MAP2K4 -0.016 0.057 0.2 1 -0.36 13 14
NSMAF 0.011 0.041 -10000 0 -0.67 3 3
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.013 0.047 0.2 1 -0.31 6 7
EGF -0.14 0.27 -10000 0 -0.61 201 201
mol:ceramide -0.028 0.041 0.2 2 -10000 0 2
MADD 0.013 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.012 0.066 -10000 0 -0.37 23 23
ASAH1 0.001 0.08 -10000 0 -0.51 19 19
negative regulation of cell cycle -0.026 0.064 0.18 1 -0.38 17 18
cell proliferation -0.028 0.1 -10000 0 -0.36 30 30
BID 0.007 0.069 -10000 0 -0.42 7 7
MAP3K1 -0.021 0.049 0.19 2 -0.38 6 8
EIF2A -0.003 0.035 -10000 0 -10000 0 0
TRADD 0.012 0.033 -10000 0 -0.67 2 2
CRADD 0.013 0 -10000 0 -10000 0 0
MAPK3 -0.002 0.044 -10000 0 -0.3 4 4
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.002 0.044 -10000 0 -0.3 4 4
Cathepsin D/ceramide -0.022 0.052 0.18 2 -0.27 15 17
FADD 0.011 0.096 -10000 0 -0.58 8 8
KSR1 -0.021 0.049 0.19 2 -0.3 10 12
MAPK8 -0.009 0.048 0.2 1 -0.26 12 13
PRKRA -0.018 0.039 0.19 2 -10000 0 2
PDGFA 0.01 0.04 -10000 0 -0.56 4 4
TRAF2 0.012 0.024 -10000 0 -0.67 1 1
IGF1 -0.07 0.21 -10000 0 -0.59 115 115
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.028 0.041 0.2 2 -10000 0 2
CTSD 0.004 0.069 -10000 0 -0.5 15 15
regulation of nitric oxide biosynthetic process 0.019 0.018 -10000 0 -0.5 1 1
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.028 0.11 -10000 0 -0.4 28 28
PRKCD 0.013 0.016 -10000 0 -0.46 1 1
PRKCZ 0.011 0.041 -10000 0 -0.67 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.012 0.066 -10000 0 -0.37 23 23
RelA/NF kappa B1 0.019 0.018 -10000 0 -0.5 1 1
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.01 0.044 -10000 0 -0.62 4 4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.007 0.095 -10000 0 -0.63 6 6
TNFR1A/BAG4/TNF-alpha -0.022 0.13 -10000 0 -0.45 49 49
mol:Sphingosine-1-phosphate 0.02 0.03 -10000 0 -0.41 4 4
MAP2K1 -0.006 0.045 -10000 0 -0.31 4 4
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.013 0 -10000 0 -10000 0 0
CYCS 0.007 0.055 0.17 51 -10000 0 51
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
NFKB1 0.012 0.024 -10000 0 -0.67 1 1
TNFR1A/BAG4 0.008 0.063 -10000 0 -0.33 28 28
EIF2AK2 -0.011 0.037 0.2 1 -10000 0 1
TNF-alpha/TNFR1A/FAN -0.014 0.12 -10000 0 -0.43 48 48
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.024 0.054 -10000 0 -10000 0 0
MAP2K2 -0.006 0.045 -10000 0 -0.31 4 4
SMPD3 -0.018 0.12 -10000 0 -0.39 49 49
TNF -0.049 0.18 -10000 0 -0.57 90 90
PKC zeta/PAR4 0.016 0.045 -10000 0 -0.47 7 7
mol:PHOSPHOCHOLINE 0.036 0.1 0.21 195 -10000 0 195
NF kappa B1/RelA/I kappa B alpha 0.036 0.037 -10000 0 -0.35 7 7
AIFM1 0.007 0.055 0.17 51 -10000 0 51
BCL2 -0.057 0.21 -10000 0 -0.66 87 87
Signaling events mediated by PRL

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
CCNE1 -0.042 0.16 -9999 0 -0.48 94 94
mol:Halofuginone 0.005 0.008 -9999 0 -10000 0 0
ITGA1 0.008 0.058 -9999 0 -0.67 6 6
CDKN1A 0.016 0.063 -9999 0 -0.49 7 7
PRL-3/alpha Tubulin 0.018 0.02 -9999 0 -0.32 3 3
mol:Ca2+ -0.11 0.19 -9999 0 -0.42 215 215
AGT -0.13 0.26 -9999 0 -0.56 215 215
CCNA2 0.002 0.11 -9999 0 -0.57 6 6
TUBA1B 0.013 0 -9999 0 -10000 0 0
EGR1 -0.009 0.11 -9999 0 -0.37 68 68
CDK2/Cyclin E1 0.001 0.099 -9999 0 -0.4 19 19
MAPK3 0.021 0.02 -9999 0 -0.32 3 3
PRL-2 /Rab GGTase beta 0.019 0.016 -9999 0 -0.32 2 2
MAPK1 0.021 0.02 -9999 0 -0.32 3 3
PTP4A1 0.009 0.091 -9999 0 -10000 0 0
PTP4A3 0.012 0.028 -9999 0 -0.46 3 3
PTP4A2 0.012 0.023 -9999 0 -0.46 2 2
ITGB1 0.021 0.02 -9999 0 -0.32 3 3
SRC 0.011 0.037 -9999 0 -0.6 3 3
RAC1 0.021 0.042 -9999 0 -0.29 1 1
Rab GGTase beta/Rab GGTase alpha 0.02 0 -9999 0 -10000 0 0
PRL-1/ATF-5 0.014 0.086 -9999 0 -10000 0 0
RABGGTA 0.013 0 -9999 0 -10000 0 0
BCAR1 0.001 0.013 -9999 0 -10000 0 0
RHOC 0.02 0.044 -9999 0 -0.35 2 2
RHOA 0.021 0.042 -9999 0 -10000 0 0
cell motility 0.024 0.045 -9999 0 -0.29 1 1
PRL-1/alpha Tubulin 0.015 0.085 -9999 0 -10000 0 0
PRL-3/alpha1 Integrin 0.015 0.048 -9999 0 -0.44 9 9
ROCK1 0.024 0.045 -9999 0 -0.29 1 1
RABGGTB 0.013 0 -9999 0 -10000 0 0
CDK2 0.013 0 -9999 0 -10000 0 0
mitosis 0.009 0.09 -9999 0 -10000 0 0
ATF5 0.012 0.028 -9999 0 -0.46 3 3
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.012 0.024 -9999 0 -0.67 1 1
HDAC2 0.012 0.029 -9999 0 -0.56 2 2
GNB1/GNG2 0.003 0.095 -9999 0 -0.42 32 32
forebrain development -0.034 0.2 -9999 0 -0.56 82 82
GNAO1 -0.076 0.21 -9999 0 -0.53 139 139
SMO/beta Arrestin2 -0.004 0.11 -9999 0 -0.44 47 47
SMO -0.021 0.14 -9999 0 -0.6 47 47
ARRB2 0.013 0.003 -9999 0 -10000 0 0
GLI3/SPOP 0.038 0.071 -9999 0 -10000 0 0
mol:GTP 0 0.002 -9999 0 -10000 0 0
GSK3B 0.013 0 -9999 0 -10000 0 0
GNAI2 0.013 0.003 -9999 0 -10000 0 0
SIN3/HDAC complex 0.029 0.045 -9999 0 -0.38 9 9
GNAI1 0.003 0.077 -9999 0 -0.54 16 16
XPO1 0.015 0.003 -9999 0 -10000 0 0
GLI1/Su(fu) -0.059 0.17 -9999 0 -0.71 36 36
SAP30 0.005 0.074 -9999 0 -0.63 11 11
mol:GDP -0.021 0.14 -9999 0 -0.6 47 47
MIM/GLI2A -0.001 0.091 -9999 0 -0.54 22 22
IFT88 0.013 0 -9999 0 -10000 0 0
GNAI3 0.013 0.002 -9999 0 -10000 0 0
GLI2 0.035 0.046 -9999 0 -10000 0 0
GLI3 0.032 0.075 -9999 0 -0.34 1 1
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
SAP18 0.013 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.013 0 -9999 0 -10000 0 0
GNG2 0.011 0.033 -9999 0 -0.53 3 3
Gi family/GTP -0.023 0.13 -9999 0 -0.35 81 81
SIN3B 0.013 0.001 -9999 0 -10000 0 0
SIN3A 0.013 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.044 0.067 -9999 0 -0.43 5 5
GLI2/Su(fu) 0.039 0.071 -9999 0 -0.35 2 2
FOXA2 -0.021 0.093 -9999 0 -0.85 9 9
neural tube patterning -0.034 0.2 -9999 0 -0.56 82 82
SPOP 0.013 0.016 -9999 0 -0.46 1 1
Su(fu)/PIAS1 0.019 0.059 -9999 0 -0.4 5 5
GNB1 0.013 0 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
CSNK1G3 0.013 0 -9999 0 -10000 0 0
MTSS1 -0.001 0.091 -9999 0 -0.55 22 22
embryonic limb morphogenesis -0.034 0.2 -9999 0 -0.56 82 82
SUFU 0.013 0.065 -9999 0 -0.44 5 5
LGALS3 -0.006 0.11 -9999 0 -0.64 25 25
catabolic process 0.055 0.073 -9999 0 -0.41 1 1
GLI3A/CBP -0.017 0.11 -9999 0 -0.37 62 62
KIF3A 0.013 0 -9999 0 -10000 0 0
GLI1 -0.036 0.21 -9999 0 -0.58 82 82
RAB23 0.012 0.033 -9999 0 -0.67 2 2
CSNK1A1 0.013 0 -9999 0 -10000 0 0
IFT172 0.012 0.024 -9999 0 -0.67 1 1
RBBP7 0.008 0.051 -9999 0 -0.48 9 9
Su(fu)/Galectin3 0.007 0.093 -9999 0 -0.43 26 26
GNAZ -0.002 0.099 -9999 0 -0.65 19 19
RBBP4 0.013 0.001 -9999 0 -10000 0 0
CSNK1G1 0.013 0.016 -9999 0 -0.46 1 1
PIAS1 0.013 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GLI2/SPOP 0.039 0.044 -9999 0 -10000 0 0
STK36 0.01 0.053 -9999 0 -0.68 5 5
Gi family/GNB1/GNG2/GDP -0.008 0.11 -9999 0 -0.44 22 22
PTCH1 -0.047 0.27 -9999 0 -1.1 41 41
MIM/GLI1 -0.034 0.2 -9999 0 -0.63 57 57
CREBBP -0.017 0.11 -9999 0 -0.37 62 62
Su(fu)/SIN3/HDAC complex 0.04 0.038 -9999 0 -10000 0 0
EPO signaling 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
BCL2L1 0.001 0.14 -9999 0 -0.61 2 2
CRKL -0.007 0.1 -9999 0 -0.48 4 4
mol:DAG -0.005 0.11 -9999 0 -0.52 5 5
HRAS 0.018 0.091 -9999 0 -0.46 3 3
MAPK8 -0.021 0.11 -9999 0 -0.39 19 19
RAP1A -0.006 0.099 -9999 0 -0.43 3 3
GAB1 -0.007 0.1 -9999 0 -0.49 4 4
MAPK14 -0.021 0.11 -9999 0 -0.39 19 19
EPO -0.077 0.19 -9999 0 -0.47 158 158
PLCG1 -0.006 0.11 -9999 0 -0.53 5 5
EPOR/TRPC2/IP3 Receptors 0.003 0.071 -9999 0 -0.59 11 11
RAPGEF1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.036 0.13 -9999 0 -0.47 24 24
GAB1/SHC/GRB2/SOS1 -0.033 0.067 -9999 0 -0.5 2 2
EPO/EPOR (dimer) -0.049 0.14 -9999 0 -0.33 168 168
IRS2 -0.022 0.12 -9999 0 -0.48 14 14
STAT1 -0.008 0.13 -9999 0 -0.53 6 6
STAT5B -0.009 0.12 -9999 0 -0.54 6 6
cell proliferation -0.012 0.1 -9999 0 -0.45 6 6
GAB1/SHIP/PIK3R1/SHP2/SHC -0.033 0.068 -9999 0 -0.46 3 3
TEC -0.009 0.1 -9999 0 -0.46 6 6
SOCS3 0.003 0.077 -9999 0 -0.54 16 16
STAT1 (dimer) -0.007 0.13 -9999 0 -0.52 6 6
JAK2 0.009 0.03 -9999 0 -0.56 2 2
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
EPO/EPOR (dimer)/JAK2 -0.004 0.11 -9999 0 -0.34 18 18
EPO/EPOR -0.049 0.14 -9999 0 -0.33 168 168
LYN 0.006 0.061 -9999 0 -0.49 12 12
TEC/VAV2 0 0.1 -9999 0 -0.44 6 6
elevation of cytosolic calcium ion concentration 0.003 0.071 -9999 0 -0.59 11 11
SHC1 0.013 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.029 0.13 -9999 0 -0.44 20 20
mol:IP3 -0.005 0.11 -9999 0 -0.52 5 5
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.011 0.12 -9999 0 -0.52 9 9
SH2B3 0.01 0.01 -9999 0 -10000 0 0
NFKB1 -0.022 0.11 -9999 0 -0.4 20 20
EPO/EPOR (dimer)/JAK2/SOCS3 -0.034 0.072 -9999 0 -0.34 16 16
PTPN6 -0.014 0.1 -9999 0 -0.34 18 18
TEC/VAV2/GRB2 0.005 0.1 -9999 0 -0.45 4 4
EPOR 0.003 0.071 -9999 0 -0.6 11 11
INPP5D 0.005 0.067 -9999 0 -0.52 13 13
mol:GDP -0.033 0.068 -9999 0 -0.51 2 2
SOS1 0.013 0 -9999 0 -10000 0 0
PLCG2 0.003 0.07 -9999 0 -0.48 17 17
CRKL/CBL/C3G 0.008 0.096 -9999 0 -0.52 2 2
VAV2 -0.006 0.099 -9999 0 -0.43 3 3
CBL -0.006 0.099 -9999 0 -0.43 3 3
SHC/Grb2/SOS1 -0.036 0.07 -9999 0 -0.46 1 1
STAT5A -0.01 0.13 -9999 0 -0.58 8 8
GRB2 0.013 0.016 -9999 0 -0.46 1 1
STAT5 (dimer) -0.006 0.15 -9999 0 -0.5 34 34
LYN/PLCgamma2 0.007 0.068 -9999 0 -0.35 28 28
PTPN11 0.013 0 -9999 0 -10000 0 0
BTK -0.013 0.11 -9999 0 -0.49 11 11
BCL2 -0.059 0.31 -9999 0 -0.95 83 83
Class I PI3K signaling events

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
ARF5/GTP -0.005 0.047 0.28 5 -10000 0 5
DAPP1 -0.046 0.16 -10000 0 -0.53 47 47
Src family/SYK family/BLNK-LAT/BTK-ITK -0.079 0.24 -10000 0 -0.64 95 95
mol:DAG -0.012 0.11 0.2 2 -0.3 48 50
HRAS 0.01 0.05 -10000 0 -0.63 5 5
RAP1A 0.014 0.003 -10000 0 -10000 0 0
ARF5/GDP 0.018 0.076 -10000 0 -0.35 14 14
PLCG2 0.003 0.07 -10000 0 -0.48 17 17
PLCG1 0.013 0 -10000 0 -10000 0 0
ARF5 0.013 0.016 -10000 0 -0.46 1 1
mol:GTP -0.004 0.044 0.25 5 -10000 0 5
ARF1/GTP -0.004 0.043 0.26 5 -10000 0 5
RHOA 0.013 0 -10000 0 -10000 0 0
YES1 0.007 0.064 -10000 0 -0.65 8 8
RAP1A/GTP -0.004 0.043 0.24 5 -10000 0 5
ADAP1 -0.022 0.087 0.24 4 -0.61 3 7
ARAP3 -0.004 0.043 0.25 5 -10000 0 5
INPPL1 0.013 0 -10000 0 -10000 0 0
PREX1 -0.04 0.18 -10000 0 -0.63 69 69
ARHGEF6 0.005 0.068 -10000 0 -0.55 12 12
ARHGEF7 0.013 0 -10000 0 -10000 0 0
ARF1 0.013 0 -10000 0 -10000 0 0
NRAS 0.008 0.062 -10000 0 -0.62 8 8
FYN 0.009 0.046 -10000 0 -0.53 6 6
ARF6 0.013 0.016 -10000 0 -0.46 1 1
FGR 0.005 0.069 -10000 0 -0.54 13 13
mol:Ca2+ 0.003 0.06 -10000 0 -10000 0 0
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.002 0.084 -10000 0 -0.62 15 15
ZAP70 -0.079 0.22 -10000 0 -0.57 134 134
mol:IP3 -0.001 0.081 -10000 0 -0.26 2 2
LYN 0.006 0.061 -10000 0 -0.49 12 12
ARF1/GDP 0.018 0.075 -10000 0 -0.35 14 14
RhoA/GDP -0.009 0.046 0.26 2 -10000 0 2
PDK1/Src/Hsp90 0.025 0.026 -10000 0 -0.42 2 2
BLNK 0 0.094 -10000 0 -0.67 16 16
actin cytoskeleton reorganization 0.035 0.082 -10000 0 -0.42 8 8
SRC 0.011 0.037 -10000 0 -0.6 3 3
PLEKHA2 0.02 0.057 -10000 0 -0.42 8 8
RAC1 0.013 0 -10000 0 -10000 0 0
PTEN -0.004 0.055 -10000 0 -0.65 6 6
HSP90AA1 0.013 0.016 -10000 0 -0.46 1 1
ARF6/GTP -0.003 0.042 0.28 5 -10000 0 5
RhoA/GTP -0.003 0.041 0.24 5 -10000 0 5
Src family/SYK family/BLNK-LAT -0.079 0.23 -10000 0 -0.6 98 98
BLK -0.14 0.26 -10000 0 -0.56 218 218
PDPK1 0.013 0 -10000 0 -10000 0 0
CYTH1 -0.003 0.041 0.24 5 -10000 0 5
HCK 0.002 0.078 -10000 0 -0.52 18 18
CYTH3 -0.005 0.047 0.24 5 -10000 0 5
CYTH2 -0.003 0.041 0.24 5 -10000 0 5
KRAS 0.013 0.016 -10000 0 -0.45 1 1
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 0.035 0.055 -10000 0 -0.55 4 4
SGK1 -0.005 0.051 -10000 0 -0.6 4 4
INPP5D 0.005 0.067 -10000 0 -0.52 13 13
mol:GDP 0.011 0.078 -10000 0 -0.36 15 15
SOS1 0.013 0 -10000 0 -10000 0 0
SYK 0 0.094 -10000 0 -0.65 17 17
ARF6/GDP -0.009 0.047 0.27 2 -10000 0 2
mol:PI-3-4-5-P3 -0.003 0.046 0.32 5 -10000 0 5
ARAP3/RAP1A/GTP -0.004 0.043 0.24 5 -10000 0 5
VAV1 -0.006 0.11 -10000 0 -0.62 26 26
mol:PI-3-4-P2 0.016 0.05 -10000 0 -0.37 13 13
RAS family/GTP/PI3K Class I 0.025 0.044 -10000 0 -10000 0 0
PLEKHA1 0.021 0.057 -10000 0 -0.48 7 7
Rac1/GDP 0.018 0.075 -10000 0 -0.35 14 14
LAT -0.014 0.12 -10000 0 -0.57 39 39
Rac1/GTP 0.007 0.1 -10000 0 -0.58 12 12
ITK -0.047 0.11 0.24 4 -0.59 5 9
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.026 0.15 0.23 2 -0.4 70 72
LCK -0.07 0.21 -10000 0 -0.6 114 114
BTK -0.009 0.061 0.24 4 -0.58 2 6
IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.018 0.12 -10000 0 -0.33 65 65
positive regulation of NF-kappaB transcription factor activity 0 0.002 -10000 0 -10000 0 0
CRKL 0.012 0.024 -10000 0 -0.67 1 1
STAT1 (dimer)/Cbp/p300 0.01 0.12 -10000 0 -0.62 3 3
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.009 0.027 -10000 0 -0.44 2 2
antigen processing and presentation of peptide antigen via MHC class I -0.037 0.067 -10000 0 -0.33 7 7
CaM/Ca2+ -0.046 0.093 -10000 0 -0.39 3 3
RAP1A 0.013 0 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.01 0.12 -10000 0 -0.4 8 8
AKT1 0.002 0.1 -10000 0 -10000 0 0
MAP2K1 -0.004 0.11 -10000 0 -0.44 5 5
MAP3K11 -0.011 0.11 -10000 0 -0.38 4 4
IFNGR1 0.009 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII -0.099 0.16 -10000 0 -0.49 81 81
Rap1/GTP -0.033 0.068 -10000 0 -10000 0 0
CRKL/C3G 0.019 0.018 -10000 0 -0.5 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.022 0.12 -10000 0 -0.34 65 65
CEBPB 0.024 0.12 -10000 0 -0.49 7 7
STAT3 0.012 0.024 -10000 0 -0.67 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.055 0.24 -10000 0 -1.2 24 24
STAT1 -0.01 0.12 -10000 0 -0.4 8 8
CALM1 0.013 0 -10000 0 -10000 0 0
IFN-gamma (dimer) -0.1 0.23 -10000 0 -0.53 180 180
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
STAT1 (dimer)/PIAS1 -0.002 0.11 -10000 0 -0.38 7 7
CEBPB/PTGES2/Cbp/p300 -0.025 0.061 -10000 0 -0.46 5 5
mol:Ca2+ -0.021 0.12 -10000 0 -0.33 65 65
MAPK3 0.011 0.1 -10000 0 -0.54 2 2
STAT1 (dimer) -0.047 0.09 -10000 0 -0.46 7 7
MAPK1 0.011 0.1 -10000 0 -0.54 2 2
JAK2 0.008 0.03 -10000 0 -0.56 2 2
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
JAK1 0.009 0.027 -10000 0 -0.69 1 1
CAMK2D 0.002 0.082 -10000 0 -0.6 15 15
DAPK1 0.028 0.11 -10000 0 -0.53 13 13
SMAD7 0.016 0.059 -10000 0 -0.28 2 2
CBL/CRKL/C3G 0 0.1 -10000 0 -10000 0 0
PI3K -0.044 0.09 -10000 0 -0.38 3 3
IFNG -0.1 0.23 -10000 0 -0.53 180 180
apoptosis 0.017 0.087 0.33 1 -0.42 10 11
CAMK2G 0.013 0.016 -10000 0 -0.46 1 1
STAT3 (dimer) 0.012 0.024 -10000 0 -0.67 1 1
CAMK2A -0.022 0.15 -10000 0 -0.64 45 45
CAMK2B -0.14 0.26 -10000 0 -0.57 218 218
FRAP1 0.003 0.098 -10000 0 -10000 0 0
PRKCD 0.003 0.1 -10000 0 -10000 0 0
RAP1B 0.013 0 -10000 0 -10000 0 0
negative regulation of cell growth -0.037 0.067 -10000 0 -0.33 7 7
PTPN2 0.012 0.023 -10000 0 -0.46 2 2
EP300 0.014 0.001 -10000 0 -10000 0 0
IRF1 0.012 0.12 -10000 0 -0.64 9 9
STAT1 (dimer)/PIASy -0.002 0.11 -10000 0 -0.42 3 3
SOCS1 -0.046 0.25 -10000 0 -1.4 24 24
mol:GDP -0.039 0.08 -10000 0 -0.34 1 1
CASP1 0.013 0.069 -10000 0 -0.31 13 13
PTGES2 0.013 0 -10000 0 -10000 0 0
IRF9 0.035 0.052 -10000 0 -0.33 5 5
mol:PI-3-4-5-P3 -0.043 0.088 -10000 0 -0.36 3 3
RAP1/GDP -0.033 0.068 -10000 0 -10000 0 0
CBL -0.011 0.11 -10000 0 -0.39 3 3
MAP3K1 -0.013 0.12 -10000 0 -0.41 9 9
PIAS1 0.013 0 -10000 0 -10000 0 0
PIAS4 0.013 0.002 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.037 0.067 -10000 0 -0.33 7 7
PTPN11 -0.02 0.12 -10000 0 -0.33 65 65
CREBBP 0.012 0.033 -10000 0 -0.67 2 2
RAPGEF1 0.013 0 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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
TRAF6/ASK1 0.012 0.026 -10000 0 -0.31 5 5
TRAF2/ASK1 0.015 0.034 -10000 0 -0.43 4 4
ATM 0.013 0.016 -10000 0 -0.46 1 1
MAP2K3 0.012 0.059 -10000 0 -0.45 5 5
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.011 0.072 -10000 0 -0.36 9 9
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G -0.015 0.13 -10000 0 -0.6 39 39
TXN 0.009 0 -10000 0 -10000 0 0
CALM1 0.013 0 -10000 0 -10000 0 0
GADD45A 0.011 0.033 -10000 0 -0.53 3 3
GADD45B 0.008 0.057 -10000 0 -0.61 7 7
MAP3K1 0.009 0.055 -10000 0 -0.64 6 6
MAP3K6 0.011 0.041 -10000 0 -0.67 3 3
MAP3K7 0.013 0.016 -10000 0 -0.46 1 1
MAP3K4 0.013 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.015 0.047 -10000 0 -0.45 8 8
TAK1/TAB family 0.002 0.02 0.2 7 -10000 0 7
RAC1/OSM/MEKK3 0.025 0.009 -10000 0 -10000 0 0
TRAF2 0.012 0.024 -10000 0 -0.67 1 1
RAC1/OSM/MEKK3/MKK3 -0.009 0.033 -10000 0 -0.38 3 3
TRAF6 0.008 0.007 -10000 0 -0.2 1 1
RAC1 0.013 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B -0.14 0.26 -10000 0 -0.57 218 218
CCM2 0.013 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB -0.079 0.17 -10000 0 -0.35 218 218
MAPK11 0.006 0.066 -10000 0 -0.62 9 9
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.065 0.16 -10000 0 -0.39 120 120
OSM/MEKK3 0.019 0.012 -10000 0 -0.32 1 1
TAOK1 -0.001 0.083 -10000 0 -0.39 36 36
TAOK2 0.017 0.007 -10000 0 -10000 0 0
TAOK3 0.017 0.007 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.013 0 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.01 0.047 -10000 0 -0.59 5 5
MAP3K10 0.011 0.033 -10000 0 -0.53 3 3
MAP3K3 0.013 0.016 -10000 0 -0.46 1 1
TRX/ASK1 0.014 0.029 -10000 0 -0.36 5 5
GADD45/MTK1/MTK1 0.012 0.081 -10000 0 -0.36 31 31
BARD1 signaling 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
BARD1/CSTF1 0.011 0.067 -10000 0 -0.49 15 15
ATM 0.013 0.016 -10000 0 -0.46 1 1
UBE2D3 0.013 0 -10000 0 -10000 0 0
PRKDC 0.012 0.028 -10000 0 -0.46 3 3
ATR 0.013 0 -10000 0 -10000 0 0
UBE2L3 0.013 0 -10000 0 -10000 0 0
FANCD2 0.025 0.014 -10000 0 -10000 0 0
protein ubiquitination -0.038 0.1 -10000 0 -0.4 42 42
XRCC5 0.013 0 -10000 0 -10000 0 0
XRCC6 0.013 0 -10000 0 -10000 0 0
M/R/N Complex 0.026 0.018 -10000 0 -0.42 1 1
MRE11A 0.013 0.016 -10000 0 -0.46 1 1
DNA-PK 0.026 0.017 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin 0.038 0.044 -10000 0 -10000 0 0
FANCF 0.012 0.024 -10000 0 -0.67 1 1
BRCA1 -0.002 0.1 -10000 0 -0.67 19 19
CCNE1 -0.042 0.16 -10000 0 -0.48 94 94
CDK2/Cyclin E1 -0.02 0.11 -10000 0 -0.33 94 94
FANCG 0.013 0 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 -0.001 0.1 -10000 0 -0.5 33 33
FANCE 0.01 0.036 -10000 0 -0.46 5 5
FANCC 0.013 0 -10000 0 -10000 0 0
NBN 0.013 0 -10000 0 -10000 0 0
FANCA -0.005 0.1 -10000 0 -0.56 26 26
DNA repair 0.037 0.1 -10000 0 -0.46 9 9
BRCA1/BARD1/ubiquitin -0.001 0.1 -10000 0 -0.5 33 33
BARD1/DNA-PK 0.026 0.055 -10000 0 -0.38 14 14
FANCL 0.012 0.023 -10000 0 -0.46 2 2
mRNA polyadenylation -0.011 0.067 0.49 15 -10000 0 15
BRCA1/BARD1/CTIP/M/R/N Complex 0.027 0.058 -10000 0 -0.78 1 1
BRCA1/BACH1/BARD1/TopBP1 0.009 0.088 -10000 0 -0.42 33 33
BRCA1/BARD1/P53 0.014 0.096 -10000 0 -0.41 39 39
BARD1/CSTF1/BRCA1 0.009 0.088 -10000 0 -0.42 33 33
BRCA1/BACH1 -0.002 0.1 -10000 0 -0.67 19 19
BARD1 0.002 0.088 -10000 0 -0.67 14 14
PCNA 0.013 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C 0.009 0.088 -10000 0 -0.42 33 33
BRCA1/BARD1/UbcH7 0.009 0.088 -10000 0 -0.42 33 33
BRCA1/BARD1/RAD51/PCNA 0.007 0.1 -10000 0 -0.38 55 55
BARD1/DNA-PK/P53 0.028 0.068 -10000 0 -0.37 22 22
BRCA1/BARD1/Ubiquitin -0.001 0.1 -10000 0 -0.5 33 33
BRCA1/BARD1/CTIP 0.012 0.086 -10000 0 -0.38 33 33
FA complex 0.031 0.046 -10000 0 -10000 0 0
BARD1/EWS 0.011 0.066 -10000 0 -0.5 14 14
RBBP8 0.016 0.045 -10000 0 -0.32 15 15
TP53 0.006 0.071 -10000 0 -0.67 9 9
TOPBP1 0.013 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.013 0.095 0.41 39 -10000 0 39
BRCA1/BARD1 -0.005 0.12 -10000 0 -0.41 42 42
CSTF1 0.013 0.016 -10000 0 -0.46 1 1
BARD1/EWS-Fli1 0.001 0.066 -10000 0 -0.51 14 14
CDK2 0.013 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 -0.005 0.11 -10000 0 -0.66 23 23
RAD50 0.012 0.024 -10000 0 -0.67 1 1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.001 0.1 -10000 0 -0.5 33 33
EWSR1 0.013 0 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.013 0 -10000 0 -10000 0 0
NFATC1 0.044 0.059 -10000 0 -10000 0 0
NFATC2 0.022 0.053 -10000 0 -0.3 3 3
NFATC3 0.021 0.029 -10000 0 -0.45 3 3
YWHAE 0.012 0.024 -10000 0 -0.67 1 1
Calcineurin A alpha-beta B1/CABIN1 -0.034 0.14 -10000 0 -0.47 54 54
Exportin 1/Ran/NUP214 0.026 0.007 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.068 0.15 -10000 0 -0.54 59 59
BCL2/BAX -0.033 0.16 -10000 0 -0.49 87 87
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.004 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.004 -10000 0 -10000 0 0
BAX 0.013 0 -10000 0 -10000 0 0
MAPK14 0.013 0.003 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.025 0.14 -10000 0 -0.5 41 41
Calcineurin A alpha-beta B1/BCL2 -0.057 0.21 -10000 0 -0.66 87 87
FKBP8 0.013 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.025 0.13 0.49 41 -10000 0 41
KPNB1 0.013 0 -10000 0 -10000 0 0
KPNA2 0.01 0.04 -10000 0 -0.5 5 5
XPO1 0.013 0 -10000 0 -10000 0 0
SFN -0.013 0.13 -10000 0 -0.62 35 35
MAP3K8 0.002 0.079 -10000 0 -0.55 16 16
NFAT4/CK1 alpha -0.003 0.032 -10000 0 -0.35 5 5
MEF2D/NFAT1/Cbp/p300 0.037 0.081 -10000 0 -0.43 3 3
CABIN1 -0.034 0.14 -10000 0 -0.48 54 54
CALM1 0.013 0.002 -10000 0 -10000 0 0
RAN 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.009 0.055 -10000 0 -0.64 6 6
CAMK4 -0.033 0.16 -10000 0 -0.6 63 63
mol:Ca2+ 0 0.004 -10000 0 -10000 0 0
MAPK3 0.013 0 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.004 0.092 -10000 0 -0.36 50 50
YWHAB 0.013 0 -10000 0 -10000 0 0
MAPK8 0.013 0.003 -10000 0 -10000 0 0
MAPK9 0.013 0 -10000 0 -10000 0 0
YWHAG 0.013 0.016 -10000 0 -0.46 1 1
FKBP1A 0.013 0.016 -10000 0 -0.46 1 1
NFAT1-c-4/YWHAQ 0.057 0.055 -10000 0 -0.37 1 1
PRKCH 0.012 0.033 -10000 0 -0.67 2 2
CABIN1/Cbp/p300 0.019 0.026 -10000 0 -0.5 2 2
CASP3 0.013 0.003 -10000 0 -10000 0 0
PIM1 0.003 0.077 -10000 0 -0.54 16 16
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.01 -10000 0 -0.27 1 1
apoptosis -0.016 0.046 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.034 0.042 -10000 0 -10000 0 0
PRKCB -0.065 0.21 -10000 0 -0.59 110 110
PRKCE 0.005 0.074 -10000 0 -0.67 10 10
JNK2/NFAT4 0.027 0.026 -10000 0 -0.41 3 3
BAD/BCL-XL 0.02 0 -10000 0 -10000 0 0
PRKCD 0.013 0.016 -10000 0 -0.46 1 1
NUP214 0.013 0 -10000 0 -10000 0 0
PRKCZ 0.01 0.041 -10000 0 -0.68 3 3
PRKCA -0.011 0.11 -10000 0 -0.53 37 37
PRKCG -0.014 0.099 -10000 0 -0.46 40 40
PRKCQ -0.084 0.22 -10000 0 -0.57 140 140
FKBP38/BCL2 -0.033 0.16 -10000 0 -0.49 87 87
EP300 0.013 0.002 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.012 0.033 -10000 0 -0.67 2 2
NFATc/JNK1 0.048 0.057 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0.018 0.005 -10000 0 -10000 0 0
FKBP12/FK506 0.009 0.012 -10000 0 -0.32 1 1
CSNK1A1 0.019 0.005 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.011 0.11 -10000 0 -0.43 43 43
NFATc/ERK1 0.05 0.056 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.068 0.15 -10000 0 -0.54 59 59
NR4A1 0.028 0.12 -10000 0 -0.52 11 11
GSK3B 0.013 0.003 -10000 0 -10000 0 0
positive T cell selection 0.021 0.029 -10000 0 -0.45 3 3
NFAT1/CK1 alpha -0.011 0.032 -10000 0 -0.29 2 2
RCH1/ KPNB1 0.017 0.029 -10000 0 -0.35 5 5
YWHAQ 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0.003 -10000 0 -10000 0 0
AKAP5 -0.018 0.13 -10000 0 -0.51 50 50
MEF2D 0.013 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.013 0.016 -10000 0 -0.46 1 1
NFATc/p38 alpha 0.048 0.057 -10000 0 -10000 0 0
CREBBP 0.012 0.034 -10000 0 -0.67 2 2
BCL2 -0.057 0.21 -10000 0 -0.66 87 87
S1P3 pathway

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
PDGFRB 0.002 0.088 -9999 0 -0.67 14 14
mol:S1P 0.001 0.005 -9999 0 -10000 0 0
S1P1/S1P/Gi -0.009 0.097 -9999 0 -0.37 24 24
GNAO1 -0.075 0.21 -9999 0 -0.53 139 139
S1P/S1P3/G12/G13 0.02 0.052 -9999 0 -0.39 9 9
AKT1 0.003 0.1 -9999 0 -0.71 14 14
AKT3 -0.004 0.19 -9999 0 -1.3 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.002 0.088 -9999 0 -0.67 14 14
GNAI2 0.014 0.004 -9999 0 -10000 0 0
GNAI3 0.014 0.003 -9999 0 -10000 0 0
GNAI1 0.004 0.077 -9999 0 -0.54 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.001 0.088 -9999 0 -0.55 20 20
S1PR2 0.012 0.023 -9999 0 -0.46 2 2
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.011 0.12 -9999 0 -0.52 15 15
MAPK3 -0.003 0.11 -9999 0 -0.49 15 15
MAPK1 -0.003 0.11 -9999 0 -0.49 15 15
JAK2 -0.003 0.12 -9999 0 -0.49 20 20
CXCR4 -0.008 0.12 -9999 0 -0.52 20 20
FLT1 0.015 0.025 -9999 0 -0.69 1 1
RhoA/GDP 0.01 0 -9999 0 -10000 0 0
Rac1/GDP 0.01 0 -9999 0 -10000 0 0
SRC -0.005 0.12 -9999 0 -0.5 17 17
S1P/S1P3/Gi -0.011 0.12 -9999 0 -0.53 15 15
RAC1 0.013 0 -9999 0 -10000 0 0
RhoA/GTP -0.004 0.11 -9999 0 -0.48 15 15
VEGFA 0.01 0.051 -9999 0 -0.45 10 10
S1P/S1P2/Gi -0.007 0.1 -9999 0 -0.46 12 12
VEGFR1 homodimer/VEGFA homodimer 0.022 0.042 -9999 0 -0.33 11 11
RHOA 0.013 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.013 0.11 -9999 0 -0.33 79 79
GNAQ 0.007 0.062 -9999 0 -0.67 7 7
GNAZ -0.001 0.099 -9999 0 -0.65 19 19
G12/G13 0.02 0 -9999 0 -10000 0 0
GNA14 -0.054 0.19 -9999 0 -0.57 97 97
GNA15 -0.002 0.096 -9999 0 -0.61 20 20
GNA12 0.013 0 -9999 0 -10000 0 0
GNA13 0.013 0 -9999 0 -10000 0 0
GNA11 0.01 0.047 -9999 0 -0.67 4 4
Rac1/GTP -0.004 0.11 -9999 0 -0.48 15 15
Aurora A signaling

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
Aurora A/GADD45A 0.02 0.048 -9999 0 -0.34 4 4
BIRC5 -0.027 0.16 -9999 0 -0.61 55 55
NFKBIA 0.024 0.046 -9999 0 -0.32 3 3
CPEB1 -0.073 0.22 -9999 0 -0.6 118 118
AKT1 0.024 0.045 -9999 0 -0.32 3 3
NDEL1 0.013 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.011 0.069 -9999 0 -0.37 22 22
NDEL1/TACC3 0.023 0.057 -9999 0 -0.43 8 8
GADD45A 0.011 0.033 -9999 0 -0.53 3 3
GSK3B 0.014 0.009 -9999 0 -10000 0 0
PAK1/Aurora A 0.014 0.063 -9999 0 -0.36 5 5
MDM2 0.009 0.043 -9999 0 -0.46 7 7
JUB -0.006 0.11 -9999 0 -0.67 23 23
TPX2 0.006 0.091 -9999 0 -0.48 28 28
TP53 0.021 0.05 -9999 0 -0.33 9 9
DLG7 0.015 0.045 -9999 0 -0.27 16 16
AURKAIP1 0.008 0.06 -9999 0 -0.64 7 7
ARHGEF7 0.013 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.024 0.061 -9999 0 -0.45 8 8
G2/M transition of mitotic cell cycle -0.011 0.068 -9999 0 -0.37 22 22
AURKA 0.018 0.054 -9999 0 -0.32 16 16
AURKB -0.012 0.11 -9999 0 -0.38 55 55
CDC25B 0.017 0.055 -9999 0 -0.32 5 5
G2/M transition checkpoint -0.013 0.074 -9999 0 -0.38 26 26
mRNA polyadenylation -0.049 0.12 -9999 0 -0.39 80 80
Aurora A/CPEB -0.049 0.12 -9999 0 -0.39 80 80
Aurora A/TACC1/TRAP/chTOG 0.028 0.063 -9999 0 -0.35 11 11
BRCA1 -0.002 0.1 -9999 0 -0.67 19 19
centrosome duplication 0.014 0.063 -9999 0 -0.36 5 5
regulation of centrosome cycle -0.005 0.054 -9999 0 -0.42 8 8
spindle assembly 0.027 0.062 -9999 0 -0.35 11 11
TDRD7 0.013 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.002 0.12 -9999 0 -0.42 41 41
CENPA -0.009 0.11 -9999 0 -0.48 38 38
Aurora A/PP2A 0.02 0.047 -9999 0 -0.32 3 3
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.027 0.047 -9999 0 -0.29 4 4
negative regulation of DNA binding 0.021 0.05 -9999 0 -0.33 9 9
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0.017 0.031 -9999 0 -0.35 6 6
RASA1 0.011 0.037 -9999 0 -0.51 4 4
Ajuba/Aurora A -0.013 0.074 -9999 0 -0.38 26 26
mitotic prometaphase 0.004 0.018 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.054 -9999 0 -0.32 16 16
TACC1 -0.001 0.091 -9999 0 -0.58 20 20
TACC3 0.007 0.067 -9999 0 -0.67 8 8
Aurora A/Antizyme1 0.025 0.053 -9999 0 -0.38 6 6
Aurora A/RasGAP 0.02 0.051 -9999 0 -0.38 5 5
OAZ1 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.014 0.009 -9999 0 -10000 0 0
GIT1 0.01 0.043 -9999 0 -0.49 6 6
GIT1/beta-PIX/PAK1 0.018 0.056 -9999 0 -0.62 2 2
Importin alpha/Importin beta/TPX2 0.006 0.091 -9999 0 -0.48 28 28
PPP2R5D 0.012 0.028 -9999 0 -0.46 3 3
Aurora A/TPX2 0.016 0.095 -9999 0 -0.48 25 25
PAK1 0.002 0.075 -9999 0 -0.48 20 20
CKAP5 0.013 0 -9999 0 -10000 0 0
PLK1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion 0.004 0.066 0.29 41 -10000 0 41
BUB1B 0.005 0.094 -10000 0 -0.49 27 27
PLK1 0.009 0.04 -10000 0 -0.19 27 27
PLK1S1 0.011 0.019 -10000 0 -10000 0 0
KIF2A 0.015 0.044 -10000 0 -0.24 16 16
regulation of mitotic centrosome separation 0.009 0.04 -10000 0 -0.19 27 27
GOLGA2 0.013 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.016 0.16 -10000 0 -0.55 58 58
WEE1 0.017 0.034 -10000 0 -0.25 3 3
cytokinesis 0.002 0.14 -10000 0 -0.71 30 30
PP2A-alpha B56 0.012 0.14 -10000 0 -0.74 26 26
AURKA 0.006 0.054 -10000 0 -0.36 16 16
PICH/PLK1 0.018 0.089 -10000 0 -0.48 21 21
CENPE 0.002 0.1 -10000 0 -0.48 33 33
RhoA/GTP 0.01 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.015 0.043 -10000 0 -0.24 16 16
PPP2CA 0.013 0 -10000 0 -10000 0 0
FZR1 0.013 0 -10000 0 -10000 0 0
TPX2 0.002 0.065 -10000 0 -0.36 25 25
PAK1 0.001 0.075 -10000 0 -0.48 20 20
SPC24 -0.034 0.17 -10000 0 -0.64 61 61
FBXW11 0.013 0 -10000 0 -10000 0 0
CLSPN -0.007 0.091 -10000 0 -0.39 41 41
GORASP1 0.013 0 -10000 0 -10000 0 0
metaphase -0.001 0.005 -10000 0 -0.022 36 36
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.006 0.019 -10000 0 -0.085 27 27
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.012 16 16
STAG2 0.012 0.024 -10000 0 -0.67 1 1
GRASP65/GM130/RAB1/GTP 0.001 0.007 -10000 0 -10000 0 0
spindle elongation 0.009 0.04 -10000 0 -0.19 27 27
ODF2 0.013 0.002 -10000 0 -10000 0 0
BUB1 -0.025 0.14 -10000 0 -0.81 26 26
TPT1 0.011 0.019 -10000 0 -10000 0 0
CDC25C -0.012 0.12 -10000 0 -0.48 47 47
CDC25B 0.006 0.06 -10000 0 -0.47 13 13
SGOL1 -0.004 0.066 -10000 0 -0.29 41 41
RHOA 0.013 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.008 0.045 -10000 0 -0.53 4 4
CDC14B 0.003 0.063 -10000 0 -0.52 12 12
CDC20 -0.018 0.14 -10000 0 -0.59 44 44
PLK1/PBIP1 -0.01 0.055 -10000 0 -0.32 19 19
mitosis 0.001 0.006 0.034 23 -10000 0 23
FBXO5 0.015 0.033 -10000 0 -0.21 6 6
CDC2 0.001 0.002 -10000 0 -0.021 4 4
NDC80 -0.013 0.12 -10000 0 -0.6 36 36
metaphase plate congression 0.011 0.026 -10000 0 -0.16 1 1
ERCC6L 0.017 0.087 -10000 0 -0.48 21 21
NLP/gamma Tubulin 0.009 0.021 -10000 0 -0.098 16 16
microtubule cytoskeleton organization 0.011 0.019 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 0.01 2 -10000 0 2
PPP1R12A 0.013 0.001 -10000 0 -10000 0 0
interphase 0 0.001 0.01 2 -10000 0 2
PLK1/PRC1-2 0.004 0.13 -10000 0 -0.6 32 32
GRASP65/GM130/RAB1/GTP/PLK1 -0.005 0.025 -10000 0 -10000 0 0
RAB1A 0.013 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.013 0.036 -10000 0 -0.2 16 16
mitotic prometaphase -0.001 0.003 -10000 0 -0.014 26 26
proteasomal ubiquitin-dependent protein catabolic process 0.021 0.05 -10000 0 -10000 0 0
microtubule-based process 0.002 0.1 -10000 0 -0.51 30 30
Golgi organization 0.009 0.04 -10000 0 -0.19 27 27
Cohesin/SA2 -0.008 0.035 -10000 0 -0.23 14 14
PPP1CB/MYPT1 0.019 0.003 -10000 0 -10000 0 0
KIF20A -0.011 0.13 -10000 0 -0.67 30 30
APC/C/CDC20 -0.002 0.1 -10000 0 -0.41 45 45
PPP2R1A 0.013 0 -10000 0 -10000 0 0
chromosome segregation -0.01 0.054 -10000 0 -0.32 19 19
PRC1 0.001 0.089 -10000 0 -0.61 17 17
ECT2 0.015 0.043 -10000 0 -0.24 15 15
C13orf34 0.013 0.037 -10000 0 -0.2 16 16
NUDC 0.011 0.026 -10000 0 -0.16 1 1
regulation of attachment of spindle microtubules to kinetochore 0.005 0.092 -10000 0 -0.48 27 27
spindle assembly 0.011 0.031 -10000 0 -0.15 18 18
spindle stabilization 0.011 0.019 -10000 0 -10000 0 0
APC/C/HCDH1 0.012 0.054 -10000 0 -0.44 12 12
MKLP2/PLK1 0.002 0.1 -10000 0 -0.51 30 30
CCNB1 0.011 0.042 -10000 0 -0.69 3 3
PPP1CB 0.013 0.001 -10000 0 -10000 0 0
BTRC 0.01 0.036 -10000 0 -0.46 5 5
ROCK2 0.016 0.043 -10000 0 -0.46 4 4
TUBG1 0.011 0.019 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.008 0.044 -10000 0 -0.51 4 4
MLF1IP 0.007 0.049 -10000 0 -0.52 7 7
INCENP 0.013 0.002 -10000 0 -10000 0 0
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate 0.001 0.12 -9999 0 -0.52 30 30
PDGFB-D/PDGFRB/SLAP 0.001 0.095 -9999 0 -0.47 31 31
PDGFB-D/PDGFRB/APS/CBL 0.009 0.083 -9999 0 -0.44 22 22
AKT1 0.035 0.082 -9999 0 -0.55 3 3
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate 0 0.12 -9999 0 -0.55 30 30
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
FGR -0.013 0.095 -9999 0 -0.59 16 16
mol:Ca2+ 0.004 0.1 -9999 0 -0.68 14 14
MYC -0.002 0.17 -9999 0 -0.76 35 35
SHC1 0.013 0 -9999 0 -10000 0 0
HRAS/GDP 0.022 0.067 -9999 0 -0.36 19 19
LRP1/PDGFRB/PDGFB 0.01 0.095 -9999 0 -0.53 22 22
GRB10 0.012 0.029 -9999 0 -0.56 2 2
PTPN11 0.013 0 -9999 0 -10000 0 0
GO:0007205 0.003 0.1 -9999 0 -0.7 14 14
PTEN 0.008 0.058 -9999 0 -0.67 6 6
GRB2 0.013 0.016 -9999 0 -0.46 1 1
GRB7 -0.028 0.14 -9999 0 -0.47 73 73
PDGFB-D/PDGFRB/SHP2 0.01 0.067 -9999 0 -0.5 14 14
PDGFB-D/PDGFRB/GRB10 0.009 0.07 -9999 0 -0.49 16 16
cell cycle arrest 0.001 0.094 -9999 0 -0.47 31 31
HRAS 0.009 0.05 -9999 0 -0.63 5 5
HIF1A 0.035 0.088 -9999 0 -0.5 7 7
GAB1 -0.007 0.12 -9999 0 -0.66 17 17
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.002 0.11 -9999 0 -0.63 16 16
PDGFB-D/PDGFRB 0.016 0.07 -9999 0 -0.43 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.01 0.069 -9999 0 -0.5 15 15
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.03 0.12 -9999 0 -0.54 30 30
positive regulation of MAPKKK cascade 0.01 0.067 -9999 0 -0.5 14 14
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
mol:IP3 0.003 0.1 -9999 0 -0.71 14 14
E5 0 0.001 -9999 0 -10000 0 0
CSK 0.013 0.001 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.02 0.12 -9999 0 -0.36 87 87
SHB 0.012 0.024 -9999 0 -0.67 1 1
BLK -0.098 0.2 -9999 0 -0.59 111 111
PTPN2 0.012 0.023 -9999 0 -0.46 2 2
PDGFB-D/PDGFRB/SNX15 0.01 0.068 -9999 0 -0.49 15 15
BCAR1 0.013 0 -9999 0 -10000 0 0
VAV2 -0.004 0.12 -9999 0 -0.61 21 21
CBL 0.013 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.009 0.074 -9999 0 -0.5 17 17
LCK -0.068 0.2 -9999 0 -0.62 85 85
PDGFRB 0.002 0.089 -9999 0 -0.68 14 14
ACP1 0.012 0.024 -9999 0 -0.67 1 1
HCK -0.01 0.083 -9999 0 -0.5 18 18
ABL1 -0.007 0.11 -9999 0 -0.58 18 18
PDGFB-D/PDGFRB/CBL -0.009 0.13 -9999 0 -0.74 16 16
PTPN1 0.007 0.056 -9999 0 -0.46 12 12
SNX15 0.013 0.016 -9999 0 -0.46 1 1
STAT3 0.012 0.024 -9999 0 -0.67 1 1
STAT1 0.01 0.036 -9999 0 -0.46 5 5
cell proliferation 0.002 0.15 -9999 0 -0.67 35 35
SLA 0.001 0.087 -9999 0 -0.58 18 18
actin cytoskeleton reorganization 0.037 0.061 -9999 0 -0.53 1 1
SRC -0.008 0.072 -9999 0 -0.48 15 15
PI3K -0.02 0.075 -9999 0 -0.62 3 3
PDGFB-D/PDGFRB/GRB7/SHC -0.007 0.099 -9999 0 -0.42 18 18
SH2B2 -0.002 0.092 -9999 0 -0.53 24 24
PLCgamma1/SPHK1 -0.001 0.13 -9999 0 -0.57 30 30
LYN -0.009 0.082 -9999 0 -0.53 14 14
LRP1 0.003 0.082 -9999 0 -0.67 12 12
SOS1 0.013 0 -9999 0 -10000 0 0
STAT5B 0.009 0.053 -9999 0 -0.67 5 5
STAT5A 0.007 0.064 -9999 0 -0.65 8 8
NCK1-2/p130 Cas 0.005 0.06 -9999 0 -0.55 1 1
SPHK1 -0.011 0.12 -9999 0 -0.6 33 33
EDG1 0 0.002 -9999 0 -10000 0 0
mol:DAG 0.003 0.1 -9999 0 -0.71 14 14
PLCG1 0.003 0.11 -9999 0 -0.73 14 14
NHERF/PDGFRB 0.004 0.098 -9999 0 -0.45 32 32
YES1 -0.011 0.084 -9999 0 -0.5 20 20
cell migration 0.004 0.097 -9999 0 -0.45 32 32
SHC/Grb2/SOS1 0.006 0.056 -9999 0 -10000 0 0
SLC9A3R2 0.009 0.053 -9999 0 -0.67 5 5
SLC9A3R1 -0.005 0.1 -9999 0 -0.58 26 26
NHERF1-2/PDGFRB/PTEN 0.01 0.098 -9999 0 -0.41 37 37
FYN -0.008 0.087 -9999 0 -0.57 13 13
DOK1 0.018 0.073 -9999 0 -0.41 18 18
HRAS/GTP 0.007 0.037 -9999 0 -0.47 5 5
PDGFB 0.01 0.044 -9999 0 -0.54 5 5
RAC1 0.003 0.14 -9999 0 -0.52 40 40
PRKCD 0.02 0.064 -9999 0 -0.39 14 14
FER 0.016 0.079 -9999 0 -0.41 23 23
MAPKKK cascade -0.008 0.05 -9999 0 -10000 0 0
RASA1 0.019 0.066 -9999 0 -0.39 15 15
NCK1 0.013 0 -9999 0 -10000 0 0
NCK2 0.011 0.033 -9999 0 -0.53 3 3
p62DOK/Csk 0.025 0.067 -9999 0 -0.37 18 18
PDGFB-D/PDGFRB/SHB 0.01 0.069 -9999 0 -0.5 15 15
chemotaxis -0.006 0.1 -9999 0 -0.56 18 18
STAT1-3-5/STAT1-3-5 -0.015 0.07 -9999 0 -0.58 5 5
Bovine Papilomavirus E5/PDGFRB 0.001 0.067 -9999 0 -0.51 14 14
PTPRJ 0.011 0.041 -9999 0 -0.67 3 3
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 0.033 0.021 -10000 0 -0.38 1 1
HDAC3 0.013 0 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0.011 -10000 0 -0.32 1 1
GATA1/HDAC4 0.01 0.05 -10000 0 -0.32 18 18
GATA1/HDAC5 0.01 0.047 -10000 0 -0.32 17 17
GATA2/HDAC5 -0.056 0.18 -10000 0 -0.44 139 139
HDAC5/BCL6/BCoR 0.021 0.05 -10000 0 -0.42 10 10
HDAC9 -0.024 0.14 -10000 0 -0.49 62 62
Glucocorticoid receptor/Hsp90/HDAC6 0.025 0.029 -10000 0 -0.42 3 3
HDAC4/ANKRA2 0.018 0.025 -10000 0 -0.5 2 2
HDAC5/YWHAB 0.02 0 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.021 0 -10000 0 -10000 0 0
GATA2 -0.089 0.23 -10000 0 -0.6 139 139
HDAC4/RFXANK 0.019 0.021 -10000 0 -0.41 2 2
BCOR 0.007 0.062 -10000 0 -0.67 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.012 0.033 -10000 0 -0.67 2 2
HDAC5 0.013 0 -10000 0 -10000 0 0
GNB1/GNG2 0.018 0.024 -10000 0 -0.38 3 3
Histones 0.024 0.057 -10000 0 -0.39 2 2
ADRBK1 0.013 0.016 -10000 0 -0.46 1 1
HDAC4 0.012 0.024 -10000 0 -0.67 1 1
XPO1 0.013 0 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.019 0.018 -10000 0 -0.5 1 1
HDAC4/Ubc9 0.019 0.018 -10000 0 -0.5 1 1
HDAC7 0.013 0 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.019 0.018 -10000 0 -0.5 1 1
TUBA1B 0.013 0 -10000 0 -10000 0 0
HDAC6 0.013 0 -10000 0 -10000 0 0
HDAC5/RFXANK 0.019 0.012 -10000 0 -0.32 1 1
CAMK4 -0.033 0.16 -10000 0 -0.6 63 63
Tubulin/HDAC6 0.022 0.045 -10000 0 -0.42 6 6
SUMO1 0.013 0 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
GATA1 0 0.066 -10000 0 -0.46 17 17
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.012 0.024 -10000 0 -0.67 1 1
NR3C1 0.011 0.041 -10000 0 -0.67 3 3
SUMO1/HDAC4 0.03 0.013 -10000 0 -0.35 1 1
SRF 0.013 0 -10000 0 -10000 0 0
HDAC4/YWHAB 0.019 0.018 -10000 0 -0.5 1 1
Tubulin 0.014 0.052 -10000 0 -0.41 12 12
HDAC4/14-3-3 E 0.018 0.025 -10000 0 -0.5 2 2
GNB1 0.013 0 -10000 0 -10000 0 0
RANGAP1 0.013 0 -10000 0 -10000 0 0
BCL6/BCoR 0.013 0.057 -10000 0 -0.5 10 10
HDAC4/HDAC3/SMRT (N-CoR2) 0.026 0.016 -10000 0 -0.42 1 1
HDAC4/SRF -0.003 0.11 -10000 0 -0.43 43 43
HDAC4/ER alpha -0.11 0.22 -10000 0 -0.5 214 214
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.024 0.057 -10000 0 -0.39 2 2
cell motility 0.021 0.044 -10000 0 -0.42 6 6
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.013 0 -10000 0 -10000 0 0
HDAC7/HDAC3 0.02 0 -10000 0 -10000 0 0
BCL6 0.01 0.044 -10000 0 -0.62 4 4
HDAC4/CaMK II delta B 0.012 0.024 -10000 0 -0.67 1 1
Hsp90/HDAC6 0.019 0.012 -10000 0 -0.32 1 1
ESR1 -0.16 0.3 -10000 0 -0.67 213 213
HDAC6/HDAC11 0.013 0.057 -10000 0 -0.48 11 11
Ran/GTP/Exportin 1 0.033 0 -10000 0 -10000 0 0
NPC 0.008 0 -10000 0 -10000 0 0
MEF2C 0.011 0.037 -10000 0 -0.6 3 3
RAN 0.013 0 -10000 0 -10000 0 0
HDAC4/MEF2C 0.038 0.025 -10000 0 -0.35 3 3
GNG2 0.011 0.033 -10000 0 -0.53 3 3
NCOR2 0.013 0 -10000 0 -10000 0 0
TUBB2A 0.005 0.07 -10000 0 -0.56 12 12
HDAC11 0.004 0.076 -10000 0 -0.65 11 11
HSP90AA1 0.013 0.016 -10000 0 -0.46 1 1
RANBP2 0.013 0 -10000 0 -10000 0 0
ANKRA2 0.012 0.024 -10000 0 -0.67 1 1
RFXANK 0.013 0.016 -10000 0 -0.46 1 1
nuclear import -0.028 0.019 0.37 2 -10000 0 2
PLK2 and PLK4 events

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
PLK2 0.002 0.084 -9999 0 -0.59 16 16
PLK4 0.009 0.05 -9999 0 -0.63 5 5
regulation of centriole replication 0.011 0.073 -9999 0 -0.44 21 21
Retinoic acid receptors-mediated signaling

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
HDAC1 0.012 0.024 -10000 0 -0.67 1 1
HDAC3 0.013 0 -10000 0 -10000 0 0
VDR 0.007 0.067 -10000 0 -0.67 8 8
Cbp/p300/PCAF 0.024 0.036 -10000 0 -0.42 5 5
EP300 0.013 0 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.031 0.043 -10000 0 -0.29 2 2
KAT2B 0.01 0.044 -10000 0 -0.62 4 4
MAPK14 0.013 0 -10000 0 -10000 0 0
AKT1 0.032 0.069 0.23 45 -0.27 4 49
RAR alpha/9cRA/Cyclin H -0.015 0.052 -10000 0 -0.44 1 1
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.028 0.051 -10000 0 -0.38 4 4
CDC2 0 0.002 -10000 0 -10000 0 0
response to UV 0.001 0.004 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.005 0.055 -10000 0 -0.34 2 2
NCOR2 0.013 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.005 0.05 -10000 0 -0.51 8 8
RXRs/RARs/NRIP1/9cRA 0.02 0.12 -10000 0 -0.53 29 29
NCOA2 -0.015 0.14 -10000 0 -0.67 34 34
NCOA3 0.012 0.029 -10000 0 -0.56 2 2
NCOA1 0.012 0.024 -10000 0 -0.67 1 1
VDR/VDR/DNA 0.007 0.067 -10000 0 -0.67 8 8
RARG 0.014 0.002 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.018 0.003 -10000 0 -10000 0 0
MAPK3 0.014 0.002 -10000 0 -10000 0 0
MAPK1 0.013 0 -10000 0 -10000 0 0
MAPK8 0.014 0.003 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.027 0.1 -10000 0 -0.54 20 20
RARA 0.005 0.068 -10000 0 -0.28 28 28
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.018 0.072 -10000 0 -0.31 14 14
PRKCA -0.008 0.12 -10000 0 -0.53 37 37
RXRs/RARs/NRIP1/9cRA/HDAC1 0.007 0.13 -10000 0 -0.57 31 31
RXRG -0.025 0.12 -10000 0 -0.38 55 55
RXRA 0.016 0.061 -10000 0 -0.29 17 17
RXRB 0.003 0.077 -10000 0 -0.37 17 17
VDR/Vit D3/DNA 0.005 0.05 -10000 0 -0.51 8 8
RBP1 -0.075 0.21 -10000 0 -0.54 133 133
CRBP1/9-cic-RA -0.055 0.15 -10000 0 -0.4 133 133
RARB 0.001 0.086 -10000 0 -0.52 22 22
PRKCG -0.012 0.1 -10000 0 -0.46 40 40
MNAT1 0.013 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.029 0.12 -10000 0 -0.52 16 16
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.028 0.092 -10000 0 -0.41 16 16
proteasomal ubiquitin-dependent protein catabolic process 0.027 0.061 -10000 0 -0.33 5 5
RXRs/RARs/NRIP1/9cRA/HDAC3 0.007 0.13 -10000 0 -0.57 31 31
positive regulation of DNA binding -0.014 0.05 -10000 0 -0.32 8 8
NRIP1 -0.005 0.2 -10000 0 -1.1 22 22
RXRs/RARs 0.005 0.11 -10000 0 -0.47 33 33
RXRs/RXRs/DNA/9cRA -0.028 0.091 -10000 0 -0.53 16 16
PRKACA 0.013 0 -10000 0 -10000 0 0
CDK7 0.013 0 -10000 0 -10000 0 0
TFIIH 0.027 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.01 0.033 -10000 0 -10000 0 0
CCNH 0.013 0 -10000 0 -10000 0 0
CREBBP 0.012 0.033 -10000 0 -0.67 2 2
RAR gamma2/9cRA 0 0 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.032 0.055 -10000 0 -0.44 1 1
adherens junction organization 0.005 0.096 -10000 0 -0.39 8 8
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.005 0.11 -10000 0 -0.48 4 4
FMN1 -0.011 0.13 -10000 0 -0.36 62 62
mol:IP3 0.024 0.055 -10000 0 -0.45 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.009 0.091 -10000 0 -0.69 1 1
CTNNB1 0.012 0.033 -10000 0 -0.53 3 3
AKT1 0.028 0.063 -10000 0 -0.49 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0.14 -10000 0 -0.46 67 67
CTNND1 0.013 0.023 -10000 0 -0.45 2 2
mol:PI-4-5-P2 0.017 0.085 -10000 0 -0.63 1 1
VASP 0.016 0.087 -10000 0 -0.65 1 1
ZYX 0.016 0.087 -10000 0 -0.65 1 1
JUB 0.006 0.1 -10000 0 -0.34 24 24
EGFR(dimer) -0.03 0.14 -10000 0 -0.35 72 72
E-cadherin/beta catenin-gamma catenin -0.034 0.11 -10000 0 -0.41 67 67
mol:PI-3-4-5-P3 0.021 0.065 -10000 0 -0.52 1 1
PIK3CA 0.013 0.023 -10000 0 -0.45 2 2
PI3K 0.021 0.066 -10000 0 -0.53 1 1
FYN 0.03 0.057 -10000 0 -0.37 1 1
mol:Ca2+ 0.024 0.054 -10000 0 -0.44 1 1
JUP 0.011 0.041 -10000 0 -0.56 4 4
PIK3R1 0.013 0.023 -10000 0 -0.45 2 2
mol:DAG 0.024 0.055 -10000 0 -0.45 1 1
CDH1 -0.041 0.18 -10000 0 -0.67 66 66
RhoA/GDP -0.005 0.11 -10000 0 -0.48 4 4
establishment of polarity of embryonic epithelium 0.017 0.085 -10000 0 -0.63 1 1
SRC 0.011 0.037 -10000 0 -0.6 3 3
RAC1 0.013 0 -10000 0 -10000 0 0
RHOA 0.013 0 -10000 0 -10000 0 0
EGFR -0.076 0.22 -10000 0 -0.57 129 129
CASR 0.022 0.06 -10000 0 -0.38 2 2
RhoA/GTP -0.012 0.038 -10000 0 -0.4 1 1
AKT2 0.028 0.063 -10000 0 -0.49 1 1
actin cable formation -0.004 0.13 -10000 0 -0.53 9 9
apoptosis -0.026 0.061 0.47 1 -10000 0 1
CTNNA1 0.012 0.034 -10000 0 -0.68 2 2
mol:GDP -0.013 0.12 -10000 0 -0.5 5 5
PIP5K1A 0.016 0.087 -10000 0 -0.65 1 1
PLCG1 0.024 0.056 -10000 0 -0.46 1 1
Rac1/GTP -0.057 0.11 -10000 0 -0.55 6 6
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
ceramide signaling pathway

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
MAP4K4 0.017 0.093 -10000 0 -0.54 6 6
BAG4 -0.003 0.087 -10000 0 -0.47 28 28
BAD 0.02 0.034 -10000 0 -10000 0 0
NFKBIA 0.013 0.016 -10000 0 -0.46 1 1
BIRC3 -0.023 0.14 -10000 0 -0.56 54 54
BAX 0.02 0.034 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.007 0.025 -10000 0 -0.12 6 6
IKBKB 0.022 0.091 -10000 0 -0.5 6 6
MAP2K2 0.028 0.043 -10000 0 -0.38 1 1
MAP2K1 0.028 0.043 -10000 0 -0.38 1 1
SMPD1 0.012 0.025 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.023 0.093 -10000 0 -0.49 8 8
MAP2K4 0.021 0.053 -10000 0 -0.32 11 11
protein ubiquitination 0.025 0.09 -10000 0 -0.51 6 6
EnzymeConsortium:2.7.1.37 0.031 0.048 -10000 0 -0.41 1 1
response to UV 0 0.001 -10000 0 -0.003 2 2
RAF1 0.023 0.044 -10000 0 -0.41 1 1
CRADD 0.013 0 -10000 0 -10000 0 0
mol:ceramide 0.014 0.035 -10000 0 -0.16 6 6
I-kappa-B-alpha/RELA/p50/ubiquitin 0.018 0.01 -10000 0 -0.26 1 1
MADD 0.013 0 -10000 0 -10000 0 0
MAP3K1 0.018 0.045 -10000 0 -0.35 5 5
TRADD 0.012 0.034 -10000 0 -0.68 2 2
RELA/p50 0.013 0 -10000 0 -10000 0 0
MAPK3 0.031 0.043 -10000 0 -0.38 1 1
MAPK1 0.031 0.043 -10000 0 -0.38 1 1
p50/RELA/I-kappa-B-alpha 0.019 0.012 -10000 0 -0.32 1 1
FADD 0.015 0.095 -10000 0 -0.52 8 8
KSR1 0.018 0.044 -10000 0 -0.33 2 2
MAPK8 0.027 0.05 -10000 0 -0.29 11 11
TRAF2 0.012 0.024 -10000 0 -0.67 1 1
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.024 0.089 -10000 0 -0.5 6 6
TNF R/SODD 0.008 0.063 -10000 0 -0.33 28 28
TNF -0.049 0.18 -10000 0 -0.57 90 90
CYCS 0.032 0.045 0.14 61 -10000 0 61
IKBKG 0.024 0.089 -10000 0 -0.5 6 6
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.012 0.093 -10000 0 -0.54 6 6
RELA 0.013 0 -10000 0 -10000 0 0
RIPK1 0.013 0 -10000 0 -10000 0 0
AIFM1 0.032 0.045 0.14 61 -0.17 1 62
TNF/TNF R/SODD -0.022 0.13 -10000 0 -0.45 49 49
TNFRSF1A 0.013 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.022 0.025 -10000 0 -10000 0 0
NSMAF 0.018 0.092 -10000 0 -0.51 7 7
response to hydrogen peroxide 0 0.001 -10000 0 -0.003 2 2
BCL2 -0.057 0.21 -10000 0 -0.66 87 87
Canonical NF-kappaB 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
FBXW11 0.016 0.003 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.067 0.054 -9999 0 -0.34 1 1
ERC1 0.013 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.01 0.12 -9999 0 -0.45 53 53
NFKBIA 0.044 0.021 -9999 0 -0.42 1 1
BIRC2 0.013 0 -9999 0 -10000 0 0
IKBKB 0.01 0.04 -9999 0 -0.5 5 5
RIPK2 0.012 0.028 -9999 0 -0.46 3 3
IKBKG -0.012 0.049 -9999 0 -10000 0 0
IKK complex/A20 -0.035 0.089 -9999 0 -0.52 6 6
NEMO/A20/RIP2 0.012 0.028 -9999 0 -0.46 3 3
XPO1 0.013 0 -9999 0 -10000 0 0
NEMO/ATM 0.036 0.057 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0.018 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.011 0.042 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0.026 0.018 -9999 0 -0.42 1 1
NOD2 -0.025 0.15 -9999 0 -0.63 50 50
NFKB1 0.016 0.024 -9999 0 -0.67 1 1
RELA 0.016 0.003 -9999 0 -10000 0 0
MALT1 0.012 0.024 -9999 0 -0.67 1 1
cIAP1/UbcH5C 0.02 0 -9999 0 -10000 0 0
ATM 0.013 0.016 -9999 0 -0.46 1 1
TNF/TNFR1A -0.026 0.14 -9999 0 -0.41 90 90
TRAF6 0.013 0.016 -9999 0 -0.46 1 1
PRKCA -0.011 0.11 -9999 0 -0.53 37 37
CHUK 0.013 0 -9999 0 -10000 0 0
UBE2D3 0.013 0 -9999 0 -10000 0 0
TNF -0.049 0.18 -9999 0 -0.57 90 90
NF kappa B1 p50/RelA -0.001 0.016 -9999 0 -0.41 1 1
BCL10 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.044 0.021 -9999 0 -0.41 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.016 0.003 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
IKK complex 0.041 0.059 -9999 0 -0.4 1 1
CYLD 0.013 0.016 -9999 0 -0.46 1 1
IKK complex/PKC alpha -0.02 0.066 -9999 0 -0.52 3 3
mTOR signaling pathway

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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.013 0 -10000 0 -10000 0 0
mol:PIP3 -0.02 0.079 0.3 3 -0.31 52 55
FRAP1 0.01 0.019 -10000 0 -10000 0 0
AKT1 0.008 0.073 0.23 3 -0.45 1 4
INSR 0.012 0.023 -10000 0 -0.46 2 2
Insulin Receptor/Insulin 0.008 0.014 -10000 0 -0.27 2 2
mol:GTP -0.014 0.049 -10000 0 -0.35 1 1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.005 0.016 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.012 0.042 -10000 0 -0.31 1 1
TSC1 0.013 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 -0.01 0.1 -10000 0 -0.38 56 56
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.006 0.02 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.013 0 -10000 0 -10000 0 0
RPS6KB1 0.016 0.043 -10000 0 -10000 0 0
MAP3K5 0.009 0.027 -10000 0 -0.33 5 5
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
apoptosis 0.009 0.027 -10000 0 -0.33 5 5
mol:LY294002 0 0 -10000 0 -0.002 58 58
EIF4B 0.022 0.04 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.024 0.037 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 -0.001 0.011 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K -0.001 0.091 -10000 0 -0.34 55 55
mTOR/RHEB/GTP/Raptor/GBL 0.024 0.028 0.17 3 -10000 0 3
FKBP1A 0.013 0.016 -10000 0 -0.46 1 1
RHEB/GTP -0.012 0.041 -10000 0 -0.31 1 1
mol:Amino Acids 0 0 -10000 0 -0.002 58 58
FKBP12/Rapamycin 0.009 0.012 -10000 0 -0.32 1 1
PDPK1 -0.018 0.071 0.24 3 -0.32 1 4
EIF4E 0.013 0 -10000 0 -10000 0 0
ASK1/PP5C 0.017 0.04 -10000 0 -0.61 3 3
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.017 0.002 -10000 0 -10000 0 0
TSC1/TSC2 0.021 0.063 -10000 0 -0.38 1 1
tumor necrosis factor receptor activity 0 0 0.002 58 -10000 0 58
RPS6 0.013 0.016 -10000 0 -0.46 1 1
PPP5C 0.013 0 -10000 0 -10000 0 0
EIF4G1 0.013 0 -10000 0 -10000 0 0
IRS1 -0.019 0.1 -10000 0 -0.4 58 58
INS 0 0 -10000 0 -10000 0 0
PTEN 0.008 0.058 -10000 0 -0.67 6 6
PDK2 -0.021 0.079 0.24 3 -0.29 59 62
EIF4EBP1 0.003 0.076 -10000 0 -1.1 3 3
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
PPP2R5D 0.016 0.022 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.012 -10000 0 -0.24 2 2
RHEB 0.013 0 -10000 0 -10000 0 0
EIF4A1 0.012 0.024 -10000 0 -0.67 1 1
mol:Rapamycin 0 0 0.003 6 -10000 0 6
EEF2 0.016 0.012 -10000 0 -0.24 2 2
eIF4E/4E-BP1 0.01 0.07 -10000 0 -1.1 3 3
HIF-2-alpha transcription factor network

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
MMP14 -0.023 0.18 -10000 0 -1.3 17 17
oxygen homeostasis 0.008 0.014 -10000 0 -10000 0 0
TCEB2 0.012 0.028 -10000 0 -0.46 3 3
TCEB1 0.013 0.016 -10000 0 -0.46 1 1
VHL/Elongin B/Elongin C/HIF2A -0.013 0.061 -10000 0 -0.39 5 5
EPO 0.048 0.25 -10000 0 -0.75 14 14
FIH (dimer) 0.022 0.013 -10000 0 -10000 0 0
APEX1 0.021 0.014 -10000 0 -10000 0 0
SERPINE1 0.088 0.24 -10000 0 -0.88 20 20
FLT1 -0.002 0.09 -10000 0 -1.2 4 4
ADORA2A 0.074 0.23 -10000 0 -0.81 14 14
germ cell development 0.073 0.24 -10000 0 -0.74 19 19
SLC11A2 0.1 0.21 -10000 0 -0.74 12 12
BHLHE40 0.092 0.23 -10000 0 -0.83 18 18
HIF1AN 0.022 0.013 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.052 0.14 -10000 0 -0.48 8 8
ETS1 0.024 0.055 -10000 0 -0.61 6 6
CITED2 -0.003 0.07 -10000 0 -1.3 2 2
KDR -0.007 0.12 -10000 0 -1.4 6 6
PGK1 0.1 0.21 -10000 0 -0.74 12 12
SIRT1 0.012 0.003 -10000 0 -10000 0 0
response to hypoxia -0.002 0.005 -10000 0 -10000 0 0
HIF2A/ARNT 0.095 0.24 -10000 0 -0.86 15 15
EPAS1 0.059 0.11 -10000 0 -0.4 14 14
SP1 0.02 0.009 -10000 0 -10000 0 0
ABCG2 0.081 0.25 -10000 0 -0.82 30 30
EFNA1 0.1 0.21 -10000 0 -0.76 13 13
FXN 0.089 0.21 -10000 0 -0.76 9 9
POU5F1 0.072 0.25 -10000 0 -0.78 19 19
neuron apoptosis -0.094 0.23 0.82 15 -10000 0 15
EP300 0.013 0 -10000 0 -10000 0 0
EGLN3 -0.014 0.14 -10000 0 -0.55 53 53
EGLN2 0.019 0.042 -10000 0 -0.49 5 5
EGLN1 0.02 0.036 -10000 0 -0.67 2 2
VHL/Elongin B/Elongin C 0.025 0.022 -10000 0 -10000 0 0
VHL 0.013 0.016 -10000 0 -0.46 1 1
ARNT 0.021 0.014 -10000 0 -10000 0 0
SLC2A1 0.086 0.21 -10000 0 -0.72 16 16
TWIST1 0.074 0.24 -10000 0 -0.8 31 31
ELK1 0.021 0.003 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.023 0.082 -10000 0 -0.48 8 8
VEGFA 0.098 0.21 -10000 0 -0.72 17 17
CREBBP 0.012 0.033 -10000 0 -0.67 2 2
Paxillin-dependent events mediated by a4b1

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
CRKL 0.012 0.024 -10000 0 -0.67 1 1
Rac1/GDP 0.002 0.01 -10000 0 -10000 0 0
DOCK1 0.012 0.024 -10000 0 -0.67 1 1
ITGA4 -0.003 0.098 -10000 0 -0.56 24 24
RAC1 0.013 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.013 0.12 -10000 0 -0.46 58 58
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.012 0.024 -10000 0 -0.67 1 1
alpha4/beta1 Integrin 0.017 0.063 -10000 0 -0.42 12 12
alpha4/beta7 Integrin/Paxillin 0.007 0.1 -10000 0 -0.4 40 40
lamellipodium assembly 0.001 0.02 -10000 0 -10000 0 0
PIK3CA 0.012 0.023 -10000 0 -0.46 2 2
PI3K 0.018 0.023 -10000 0 -0.32 4 4
ARF6 0.013 0.016 -10000 0 -0.46 1 1
TLN1 0.013 0 -10000 0 -10000 0 0
PXN 0.022 0 -10000 0 -10000 0 0
PIK3R1 0.012 0.023 -10000 0 -0.46 2 2
ARF6/GTP -0.009 0.047 -10000 0 -10000 0 0
cell adhesion 0.03 0.054 -10000 0 -0.35 12 12
CRKL/CBL 0.019 0.018 -10000 0 -0.5 1 1
alpha4/beta1 Integrin/Paxillin 0.024 0.057 -10000 0 -0.38 12 12
ITGB1 0.013 0 -10000 0 -10000 0 0
ITGB7 -0.016 0.13 -10000 0 -0.59 40 40
ARF6/GDP 0.001 0.018 -10000 0 -0.45 1 1
alpha4/beta1 Integrin/Paxillin/VCAM1 0.017 0.09 -10000 0 -0.37 35 35
p130Cas/Crk/Dock1 0.026 0.022 -10000 0 -0.42 2 2
VCAM1 -0.012 0.12 -10000 0 -0.6 35 35
alpha4/beta1 Integrin/Paxillin/Talin 0.031 0.054 -10000 0 -0.35 12 12
alpha4/beta1 Integrin/Paxillin/GIT1 0.029 0.059 -10000 0 -0.35 13 13
BCAR1 0.013 0 -10000 0 -10000 0 0
mol:GDP -0.028 0.058 0.35 13 -10000 0 13
CBL 0.013 0 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
GIT1 0.01 0.043 -10000 0 -0.49 6 6
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.031 0.054 -10000 0 -0.35 12 12
Rac1/GTP 0.001 0.022 -10000 0 -10000 0 0
Atypical NF-kappaB 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
BCL3/RelA 0.019 0.018 -9999 0 -0.5 1 1
FBXW11 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.008 0.09 -9999 0 -0.44 31 31
NF kappa B1 p50/RelA/I kappa B alpha 0.012 0.093 -9999 0 -0.56 7 7
NFKBIA -0.009 0.1 -9999 0 -0.55 10 10
MAPK14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.024 0.029 -9999 0 -0.42 2 2
ARRB2 0.017 0 -9999 0 -10000 0 0
REL -0.011 0.13 -9999 0 -0.67 30 30
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.024 0.033 -9999 0 -0.42 3 3
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.024 0.029 -9999 0 -0.42 2 2
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
NF kappa B1 p50 dimer 0.017 0.034 -9999 0 -0.5 2 2
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
NFKB1 0.02 0.034 -9999 0 -0.5 2 2
RELA 0.013 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis -0.002 0.094 -9999 0 -0.46 8 8
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.016 0.09 -9999 0 -0.54 7 7
SRC 0.011 0.037 -9999 0 -0.6 3 3
PI3K 0.018 0.023 -9999 0 -0.32 4 4
NF kappa B1 p50/RelA -0.002 0.094 -9999 0 -0.47 8 8
IKBKB 0.01 0.04 -9999 0 -0.5 5 5
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
SYK 0 0.094 -9999 0 -0.65 17 17
I kappa B alpha/PIK3R1 -0.001 0.096 -9999 0 -0.58 8 8
cell death 0.016 0.087 -9999 0 -0.52 7 7
NF kappa B1 p105/c-Rel 0.008 0.09 -9999 0 -0.44 31 31
LCK -0.07 0.21 -9999 0 -0.6 114 114
BCL3 0.012 0.024 -9999 0 -0.67 1 1
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.004 0.079 -10000 0 -0.37 26 26
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0 0 -10000 0 -10000 0 0
GNB1/GNG2 0.017 0.021 -10000 0 -0.32 3 3
GNB1 0.013 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.012 0.082 -10000 0 -0.32 51 51
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 0.005 0.02 0.083 51 -10000 0 51
GNAL -0.022 0.14 -10000 0 -0.56 51 51
GNG2 0.011 0.033 -10000 0 -0.53 3 3
CRH 0 0 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.009 0 -10000 0 -10000 0 0
MAPK11 0.005 0.038 -10000 0 -0.35 9 9
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.032 0.098 -9999 0 -0.4 46 46
Ran/GTP/Exportin 1/HDAC1 0 0.011 -9999 0 -0.32 1 1
NF kappa B1 p50/RelA/I kappa B alpha 0.016 0.098 -9999 0 -10000 0 0
SUMO1 0.013 0 -9999 0 -10000 0 0
ZFPM1 0.005 0.072 -9999 0 -0.65 10 10
NPC/RanGAP1/SUMO1/Ubc9 0.021 0 -9999 0 -10000 0 0
FKBP3 0.013 0 -9999 0 -10000 0 0
Histones 0.026 0.059 -9999 0 -10000 0 0
YY1/LSF 0.024 0.053 -9999 0 -0.41 10 10
SMG5 0.013 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.006 0.085 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.012 0.063 -9999 0 -0.38 1 1
SAP18 0.013 0 -9999 0 -10000 0 0
RELA 0.012 0.078 -9999 0 -0.27 47 47
HDAC1/Smad7 0.026 0.024 -9999 0 -0.42 2 2
RANGAP1 0.013 0 -9999 0 -10000 0 0
HDAC3/TR2 0.012 0.063 -9999 0 -0.38 2 2
NuRD/MBD3 Complex 0.045 0.017 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.017 0.073 -9999 0 -0.36 2 2
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 -0.089 0.23 -9999 0 -0.6 139 139
GATA1 0 0.066 -9999 0 -0.46 17 17
Mad/Max 0.019 0.016 -9999 0 -0.32 2 2
NuRD/MBD3 Complex/GATA1/Fog1 0.049 0.036 -9999 0 -10000 0 0
RBBP7 0.008 0.051 -9999 0 -0.48 9 9
NPC 0.008 0 -9999 0 -10000 0 0
RBBP4 0.013 0 -9999 0 -10000 0 0
MAX 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
NFKBIA 0.006 0.068 -9999 0 -0.31 1 1
KAT2B 0.01 0.044 -9999 0 -0.62 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.037 0.035 -9999 0 -10000 0 0
SIN3 complex 0.029 0.044 -9999 0 -0.38 9 9
SMURF1 0.013 0 -9999 0 -10000 0 0
CHD3 0.013 0 -9999 0 -10000 0 0
SAP30 0.005 0.074 -9999 0 -0.63 11 11
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.012 0.033 -9999 0 -0.67 2 2
YY1/HDAC3 0.023 0.061 -9999 0 -0.38 2 2
YY1/HDAC2 0.028 0.029 -9999 0 -0.41 1 1
YY1/HDAC1 0.029 0.028 -9999 0 -0.41 1 1
NuRD/MBD2 Complex (MeCP1) 0.045 0.017 -9999 0 -10000 0 0
PPARG -0.003 0.11 -9999 0 -0.38 54 54
HDAC8/hEST1B 0.027 0 -9999 0 -10000 0 0
UBE2I 0.013 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
TNFRSF1A 0.013 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.013 0.06 -9999 0 -10000 0 0
MBD3L2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.025 0.024 -9999 0 -0.42 2 2
CREBBP 0.012 0.033 -9999 0 -0.67 2 2
NuRD/MBD3/MBD3L2 Complex 0.048 0.02 -9999 0 -10000 0 0
HDAC1 0.012 0.024 -9999 0 -0.67 1 1
HDAC3 0.006 0.067 -9999 0 -10000 0 0
HDAC2 0.012 0.029 -9999 0 -0.56 2 2
YY1 0.028 0.027 -9999 0 -0.31 5 5
HDAC8 0.013 0 -9999 0 -10000 0 0
SMAD7 0.012 0.029 -9999 0 -0.56 2 2
NCOR2 0.013 0 -9999 0 -10000 0 0
MXD1 0.012 0.023 -9999 0 -0.46 2 2
STAT3 0.024 0.024 -9999 0 -0.38 3 3
NFKB1 0.012 0.024 -9999 0 -0.67 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 0.03 0.051 -9999 0 -0.37 11 11
YY1/SAP30/HDAC1 0.03 0.051 -9999 0 -0.38 11 11
EP300 0.013 0 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.024 0.024 -9999 0 -0.38 3 3
proteasomal ubiquitin-dependent protein catabolic process 0.006 0.068 -9999 0 -0.31 1 1
histone deacetylation 0.045 0.017 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.021 0.061 -9999 0 -0.43 2 2
nuclear export -0.027 0 -9999 0 -10000 0 0
PRKACA 0.013 0 -9999 0 -10000 0 0
GATAD2B 0.013 0 -9999 0 -10000 0 0
GATAD2A 0.013 0 -9999 0 -10000 0 0
GATA2/HDAC3 -0.047 0.15 -9999 0 -0.41 99 99
GATA1/HDAC1 0.01 0.05 -9999 0 -0.32 18 18
GATA1/HDAC3 0 0.068 -9999 0 -10000 0 0
CHD4 0.013 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.026 0.14 -9999 0 -0.41 90 90
SIN3/HDAC complex/Mad/Max 0.042 0.031 -9999 0 -0.31 1 1
NuRD Complex 0.053 0.019 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.014 0.045 -9999 0 -10000 0 0
SIN3B 0.013 0 -9999 0 -10000 0 0
MTA2 0.013 0 -9999 0 -10000 0 0
SIN3A 0.013 0 -9999 0 -10000 0 0
XPO1 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.03 0.013 -9999 0 -0.35 1 1
HDAC complex 0.03 0.036 -9999 0 -0.38 3 3
GATA1/Fog1 0.004 0.072 -9999 0 -0.38 27 27
FKBP25/HDAC1/HDAC2 0.026 0.024 -9999 0 -0.42 2 2
TNF -0.049 0.18 -9999 0 -0.57 90 90
negative regulation of cell growth 0.042 0.031 -9999 0 -0.31 1 1
NuRD/MBD2/PRMT5 Complex 0.045 0.017 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.033 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.01 0.1 -9999 0 -0.37 46 46
SIN3/HDAC complex/NCoR1 0.04 0.032 -9999 0 -10000 0 0
TFCP2 0.005 0.074 -9999 0 -0.67 10 10
NR2C1 0.012 0.033 -9999 0 -0.67 2 2
MBD3 0.013 0 -9999 0 -10000 0 0
MBD2 0.013 0 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.002 0.097 -9999 0 -0.47 31 31
AKT1 0.07 0.077 -9999 0 -0.59 5 5
PTK2B 0.034 0.1 -9999 0 -0.84 7 7
VEGFR2 homodimer/Frs2 0.026 0.075 -9999 0 -0.79 5 5
CAV1 0.006 0.066 -9999 0 -0.59 10 10
CALM1 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.033 0.075 -9999 0 -0.73 5 5
endothelial cell proliferation 0.053 0.1 -9999 0 -0.63 5 5
mol:Ca2+ 0.043 0.077 -9999 0 -0.64 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.044 0.064 -9999 0 -0.69 5 5
RP11-342D11.1 0.034 0.077 -9999 0 -0.65 6 6
CDH5 0.01 0.047 -9999 0 -0.67 4 4
VEGFA homodimer 0.025 0.059 -9999 0 -0.38 12 12
SHC1 0.013 0 -9999 0 -10000 0 0
SHC2 -0.041 0.18 -9999 0 -0.67 67 67
HRAS/GDP -0.011 0.061 -9999 0 -0.55 6 6
SH2D2A -0.055 0.19 -9999 0 -0.59 96 96
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.009 0.057 -9999 0 -0.6 5 5
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.003 0.13 -9999 0 -0.74 7 7
VEGFR1 homodimer 0.012 0.024 -9999 0 -0.67 1 1
SHC/GRB2/SOS1 -0.01 0.063 -9999 0 -0.61 6 6
GRB10 0.042 0.081 -9999 0 -0.65 7 7
PTPN11 0.013 0 -9999 0 -10000 0 0
GRB2 0.013 0.016 -9999 0 -0.46 1 1
PAK1 0.002 0.075 -9999 0 -0.48 20 20
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.008 0.073 -9999 0 -0.87 5 5
HRAS 0.009 0.05 -9999 0 -0.63 5 5
VEGF/Rho/ROCK1/Integrin Complex 0.037 0.077 -9999 0 -0.58 8 8
HIF1A 0.002 0.086 -9999 0 -0.63 15 15
FRS2 0.005 0.062 -9999 0 -0.46 15 15
oxygen and reactive oxygen species metabolic process -0.006 0.057 -9999 0 -0.68 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.01 0.047 -9999 0 -0.59 5 5
Nck/Pak 0.011 0.054 -9999 0 -0.33 20 20
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.035 0.076 -9999 0 -0.8 5 5
mol:GDP -0.01 0.062 -9999 0 -0.59 6 6
mol:NADP 0.065 0.063 -9999 0 -0.51 5 5
eNOS/Hsp90 0.068 0.06 -9999 0 -0.48 5 5
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
mol:IP3 0.043 0.078 -9999 0 -0.65 6 6
HIF1A/ARNT 0.011 0.065 -9999 0 -0.46 15 15
SHB 0.012 0.024 -9999 0 -0.67 1 1
VEGFA 0.01 0.051 -9999 0 -0.45 10 10
VEGFC 0.009 0.055 -9999 0 -0.64 6 6
FAK1/Vinculin 0.054 0.092 -9999 0 -0.74 7 7
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.013 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.03 0.11 -9999 0 -0.83 8 8
PTPN6 0.013 0.016 -9999 0 -0.46 1 1
EPAS1 0.021 0.031 -9999 0 -0.36 5 5
mol:L-citrulline 0.065 0.063 -9999 0 -0.51 5 5
ITGAV 0.011 0.041 -9999 0 -0.67 3 3
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.039 0.072 -9999 0 -0.69 5 5
VEGFR2 homodimer/VEGFA homodimer 0.037 0.084 -9999 0 -0.7 6 6
VEGFR2/3 heterodimer 0.029 0.08 -9999 0 -0.85 6 6
VEGFB 0.013 0 -9999 0 -10000 0 0
MAPK11 0.042 0.083 -9999 0 -0.64 7 7
VEGFR2 homodimer 0.029 0.073 -9999 0 -0.81 6 6
FLT1 0.012 0.024 -9999 0 -0.67 1 1
NEDD4 0.006 0.078 -9999 0 -0.67 11 11
MAPK3 0.027 0.093 -9999 0 -0.64 7 7
MAPK1 0.027 0.093 -9999 0 -0.64 7 7
VEGFA145/NRP2 0.012 0.063 -9999 0 -0.38 19 19
VEGFR1/2 heterodimer 0.03 0.071 -9999 0 -0.86 5 5
KDR 0.029 0.073 -9999 0 -0.81 6 6
VEGFA165/NRP1/VEGFR2 homodimer 0.039 0.088 -9999 0 -0.68 7 7
SRC 0.011 0.037 -9999 0 -0.6 3 3
platelet activating factor biosynthetic process 0.03 0.093 -9999 0 -0.66 7 7
PI3K 0.059 0.087 -9999 0 -0.67 6 6
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.037 0.067 -9999 0 -0.73 5 5
FES 0.038 0.09 -9999 0 -0.66 6 6
GAB1 -0.009 0.063 -9999 0 -0.74 5 5
VEGFR2 homodimer/VEGFA homodimer/Src 0.036 0.07 -9999 0 -0.73 5 5
CTNNB1 0.011 0.033 -9999 0 -0.53 3 3
SOS1 0.013 0 -9999 0 -10000 0 0
ARNT 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.065 0.071 -9999 0 -0.57 5 5
VEGFR2 homodimer/VEGFA homodimer/Yes 0.033 0.077 -9999 0 -0.73 5 5
PI3K/GAB1 0.072 0.077 -9999 0 -0.6 5 5
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.014 0.068 -9999 0 -0.64 6 6
PRKACA 0.013 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer 0.032 0.082 -9999 0 -0.88 5 5
HSP90AA1 0.013 0.016 -9999 0 -0.46 1 1
CDC42 0.043 0.079 -9999 0 -0.66 6 6
actin cytoskeleton reorganization -0.003 0.13 -9999 0 -0.74 7 7
PTK2 0.049 0.099 -9999 0 -0.82 7 7
EDG1 0.034 0.077 -9999 0 -0.65 6 6
mol:DAG 0.043 0.078 -9999 0 -0.65 6 6
CaM/Ca2+ 0.045 0.072 -9999 0 -0.6 6 6
MAP2K3 0.042 0.089 -9999 0 -0.63 7 7
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.043 0.084 -9999 0 -0.67 7 7
PLCG1 0.043 0.079 -9999 0 -0.66 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.042 0.069 -9999 0 -0.69 5 5
IQGAP1 0.013 0 -9999 0 -10000 0 0
YES1 0.007 0.064 -9999 0 -0.65 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.037 0.067 -9999 0 -0.73 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.037 0.068 -9999 0 -0.73 5 5
cell migration 0.075 0.082 -9999 0 -0.72 5 5
mol:PI-3-4-5-P3 0.058 0.082 -9999 0 -0.62 6 6
FYN 0.009 0.046 -9999 0 -0.53 6 6
VEGFB/NRP1 0.04 0.073 -9999 0 -0.61 6 6
mol:NO 0.065 0.063 -9999 0 -0.51 5 5
PXN 0.013 0 -9999 0 -10000 0 0
HRAS/GTP -0.011 0.06 -9999 0 -0.55 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.043 0.084 -9999 0 -0.67 7 7
VHL 0.013 0.016 -9999 0 -0.46 1 1
ITGB3 -0.009 0.12 -9999 0 -0.59 31 31
NOS3 0.066 0.07 -9999 0 -0.59 5 5
VEGFR2 homodimer/VEGFA homodimer/Sck 0.005 0.13 -9999 0 -0.67 8 8
RAC1 0.013 0 -9999 0 -10000 0 0
PRKCA 0.036 0.097 -9999 0 -0.66 6 6
PRKCB 0.007 0.14 -9999 0 -0.69 9 9
VCL 0.011 0.033 -9999 0 -0.53 3 3
VEGFA165/NRP1 0.035 0.077 -9999 0 -0.65 6 6
VEGFR1/2 heterodimer/VEGFA homodimer 0.037 0.073 -9999 0 -0.8 5 5
VEGFA165/NRP2 0.012 0.063 -9999 0 -0.38 19 19
MAPKKK cascade 0.061 0.076 -9999 0 -0.56 6 6
NRP2 0.006 0.066 -9999 0 -0.59 10 10
VEGFC homodimer 0.009 0.055 -9999 0 -0.64 6 6
NCK1 0.013 0 -9999 0 -10000 0 0
ROCK1 0.012 0.024 -9999 0 -0.67 1 1
FAK1/Paxillin 0.055 0.091 -9999 0 -0.74 7 7
MAP3K13 0.037 0.092 -9999 0 -0.66 7 7
PDPK1 0.063 0.075 -9999 0 -0.56 5 5
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.04 0.036 -10000 0 -10000 0 0
CLOCK 0.01 0.067 -10000 0 -0.67 8 8
TIMELESS/CRY2 0.036 0.032 -10000 0 -10000 0 0
DEC1/BMAL1 0.011 0.018 -10000 0 -0.5 1 1
ATR 0.013 0 -10000 0 -10000 0 0
NR1D1 0.031 0.066 -10000 0 -1.4 1 1
ARNTL 0.015 0.024 -10000 0 -0.67 1 1
TIMELESS 0.033 0.035 -10000 0 -10000 0 0
NPAS2 -0.02 0.14 -10000 0 -0.54 54 54
CRY2 0.013 0 -10000 0 -10000 0 0
mol:CO -0.013 0.01 0.08 10 -10000 0 10
CHEK1 0.01 0.039 -10000 0 -0.46 6 6
mol:HEME 0.013 0.01 -10000 0 -0.08 10 10
PER1 0.007 0.056 -10000 0 -0.46 12 12
BMAL/CLOCK/NPAS2 0.015 0.1 -10000 0 -0.41 31 31
BMAL1/CLOCK 0.034 0.067 -10000 0 -0.87 1 1
S phase of mitotic cell cycle 0.04 0.036 -10000 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.04 0.037 -10000 0 -10000 0 0
mol:NADPH 0.013 0.01 -10000 0 -0.08 10 10
PER1/TIMELESS 0.032 0.043 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0 0 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.028 0.026 -9999 0 -0.28 5 5
PLK1 0.02 0.29 -9999 0 -1.2 37 37
CDKN1B 0.11 0.11 -9999 0 -0.51 13 13
FOXO3 0.055 0.16 -9999 0 -0.72 7 7
KAT2B 0.017 0.047 -9999 0 -0.62 4 4
FOXO1/SIRT1 0.013 0.035 -9999 0 -0.3 1 1
CAT 0.057 0.16 -9999 0 -0.92 5 5
CTNNB1 0.011 0.033 -9999 0 -0.53 3 3
AKT1 0.022 0.014 -9999 0 -10000 0 0
FOXO1 0.031 0.028 -9999 0 -0.31 5 5
MAPK10 -0.019 0.13 -9999 0 -0.36 99 99
mol:GTP 0.002 0.001 -9999 0 -10000 0 0
FOXO4 0.072 0.075 -9999 0 -10000 0 0
response to oxidative stress 0.009 0.017 -9999 0 -10000 0 0
FOXO3A/SIRT1 -0.007 0.11 -9999 0 -0.72 5 5
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.014 0.001 -9999 0 -10000 0 0
BCL2L11 0.029 0.032 -9999 0 -10000 0 0
FOXO1/SKP2 0.03 0.046 -9999 0 -0.33 6 6
mol:GDP 0.009 0.017 -9999 0 -10000 0 0
RAN 0.015 0.001 -9999 0 -10000 0 0
GADD45A 0.093 0.082 -9999 0 -1 1 1
YWHAQ 0.013 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.065 0.037 -9999 0 -10000 0 0
MST1 -0.006 0.13 -9999 0 -0.61 36 36
CSNK1D 0.013 0 -9999 0 -10000 0 0
CSNK1E 0.013 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.044 0.062 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
MAPK8 0.038 0.009 -9999 0 -10000 0 0
MAPK9 0.038 0.009 -9999 0 -10000 0 0
YWHAG 0.013 0.016 -9999 0 -0.46 1 1
YWHAE 0.012 0.024 -9999 0 -0.67 1 1
YWHAZ 0.013 0.016 -9999 0 -0.46 1 1
SIRT1 0.016 0.019 -9999 0 -10000 0 0
SOD2 0.11 0.1 -9999 0 -10000 0 0
RBL2 0.073 0.11 -9999 0 -10000 0 0
RAL/GDP 0.028 0.014 -9999 0 -10000 0 0
CHUK 0.021 0.014 -9999 0 -10000 0 0
Ran/GTP 0.014 0.002 -9999 0 -10000 0 0
CSNK1G2 0.013 0 -9999 0 -10000 0 0
RAL/GTP 0.036 0.014 -9999 0 -10000 0 0
CSNK1G1 0.013 0.016 -9999 0 -0.46 1 1
FASLG -0.11 0.41 -9999 0 -1.5 66 66
SKP2 0.003 0.068 -9999 0 -0.47 17 17
USP7 0.015 0.001 -9999 0 -10000 0 0
IKBKB 0.018 0.042 -9999 0 -0.48 5 5
CCNB1 0.057 0.16 -9999 0 -1.3 4 4
FOXO1-3a-4/beta catenin 0.11 0.11 -9999 0 -0.4 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.029 0.046 -9999 0 -0.33 6 6
CSNK1A1 0.013 0 -9999 0 -10000 0 0
SGK1 0.014 0.062 -9999 0 -0.56 9 9
CSNK1G3 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.024 0.004 -9999 0 -10000 0 0
ZFAND5 0.075 0.067 -9999 0 -10000 0 0
SFN -0.013 0.13 -9999 0 -0.62 35 35
CDK2 0.013 0.001 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.051 0.063 -9999 0 -10000 0 0
CREBBP 0.011 0.033 -9999 0 -0.67 2 2
FBXO32 0.05 0.18 -9999 0 -1 9 9
BCL6 0.069 0.13 -9999 0 -1.2 3 3
RALB 0.015 0.001 -9999 0 -10000 0 0
RALA 0.015 0.001 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
Arf6 trafficking events

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
SLC2A4 -0.051 0.18 -10000 0 -0.54 98 98
CLTC 0.028 0.021 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.024 0.019 -10000 0 -10000 0 0
Dynamin 2/GTP 0.021 0.026 -10000 0 -10000 0 0
EXOC4 0.013 0 -10000 0 -10000 0 0
CD59 0.025 0.021 -10000 0 -10000 0 0
CPE 0 0.083 -10000 0 -0.36 41 41
CTNNB1 0.011 0.033 -10000 0 -0.53 3 3
membrane fusion 0.023 0.02 -10000 0 -10000 0 0
CTNND1 0.028 0.027 -10000 0 -10000 0 0
DNM2 0.013 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.03 0.014 -10000 0 -10000 0 0
TSHR -0.016 0.11 -10000 0 -0.34 82 82
INS 0.011 0.005 -10000 0 -10000 0 0
BIN1 0.001 0.085 -10000 0 -0.56 18 18
mol:Choline 0.023 0.02 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.015 0.029 -10000 0 -0.26 9 9
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.013 0.016 -10000 0 -0.46 1 1
mol:Ca2+ 0.021 0.026 -10000 0 -10000 0 0
JUP 0.025 0.02 -10000 0 -10000 0 0
ASAP2/amphiphysin II 0.017 0.058 -10000 0 -0.41 12 12
ARF6/GTP 0.009 0.012 -10000 0 -0.32 1 1
CDH1 0.006 0.07 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0.009 0.011 -10000 0 -0.32 1 1
MAPK8IP3 0.01 0.044 -10000 0 -0.62 4 4
positive regulation of endocytosis 0.009 0.011 -10000 0 -0.32 1 1
EXOC2 0.004 0.066 -10000 0 -0.46 17 17
substrate adhesion-dependent cell spreading 0.038 0.028 -10000 0 -0.29 3 3
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.011 0.032 -10000 0 -0.46 4 4
regulation of calcium-dependent cell-cell adhesion 0.014 0.046 -10000 0 -10000 0 0
positive regulation of phagocytosis 0.018 0.01 -10000 0 -0.26 1 1
ARF6/GTP/JIP3 0.016 0.03 -10000 0 -0.36 5 5
ACAP1 0.01 0.043 -10000 0 -0.28 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.021 0.015 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.03 0.024 -10000 0 -10000 0 0
JIP4/KLC1 0.024 0.02 -10000 0 -10000 0 0
EXOC1 0.013 0 -10000 0 -10000 0 0
exocyst 0.038 0.029 -10000 0 -0.29 3 3
RALA/GTP 0.01 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.016 0.022 -10000 0 -0.26 5 5
receptor recycling 0.009 0.011 -10000 0 -0.32 1 1
CTNNA1 0.028 0.031 -10000 0 -0.36 2 2
NME1 0.016 0.029 -10000 0 -0.26 9 9
clathrin coat assembly 0.028 0.021 -10000 0 -10000 0 0
IL2RA -0.009 0.085 -10000 0 -0.32 4 4
VAMP3 0.018 0.01 -10000 0 -0.26 1 1
GLUT4/clathrin heavy chain/ACAP1 -0.029 0.078 -10000 0 -0.34 9 9
EXOC6 0.011 0.041 -10000 0 -0.67 3 3
PLD1 0.018 0.031 -10000 0 -0.31 6 6
PLD2 0.022 0.004 -10000 0 -10000 0 0
EXOC5 0.013 0 -10000 0 -10000 0 0
PIP5K1C 0.03 0.014 -10000 0 -10000 0 0
SDC1 0.017 0.049 -10000 0 -0.32 1 1
ARF6/GDP 0.015 0.029 -10000 0 -0.26 9 9
EXOC7 0.013 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.015 0.047 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.023 0.02 -10000 0 -10000 0 0
endocytosis -0.016 0.057 0.4 12 -10000 0 12
SCAMP2 0.013 0 -10000 0 -10000 0 0
ADRB2 0.015 0.08 -10000 0 -0.38 3 3
EXOC3 0.013 0 -10000 0 -10000 0 0
ASAP2 0.011 0.041 -10000 0 -0.67 3 3
Dynamin 2/GDP 0.022 0.026 -10000 0 -10000 0 0
KLC1 0.013 0 -10000 0 -10000 0 0
AVPR2 -0.003 0.1 -10000 0 -0.34 56 56
RALA 0.013 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.013 0.044 -10000 0 -10000 0 0
Arf6 downstream pathway

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
PLAUR 0.033 0.097 -10000 0 -1.2 5 5
regulation of axonogenesis -0.023 0.035 0.35 2 -10000 0 2
myoblast fusion -0.013 0.046 0.47 5 -10000 0 5
mol:GTP -0.003 0.022 -10000 0 -0.26 4 4
regulation of calcium-dependent cell-cell adhesion -0.023 0.064 0.42 11 -10000 0 11
ARF1/GTP -0.002 0.015 -10000 0 -10000 0 0
mol:GM1 0.009 0.018 -10000 0 -0.24 1 1
mol:Choline 0.021 0.049 -10000 0 -0.42 7 7
lamellipodium assembly -0.004 0.045 -10000 0 -0.46 5 5
MAPK3 0.025 0.031 -10000 0 -0.35 5 5
ARF6/GTP/NME1/Tiam1 0.024 0.064 -10000 0 -0.43 11 11
ARF1 0.013 0 -10000 0 -10000 0 0
ARF6/GDP 0.013 0.046 -10000 0 -0.47 5 5
ARF1/GDP 0.023 0.044 -10000 0 -0.47 4 4
ARF6 0.011 0.019 -10000 0 -0.43 1 1
RAB11A 0.012 0.023 -10000 0 -0.46 2 2
TIAM1 0.004 0.085 -10000 0 -0.62 15 15
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.025 0.031 -10000 0 -0.35 5 5
actin filament bundle formation -0.02 0.043 0.47 4 -10000 0 4
KALRN -0.009 0.065 -10000 0 -0.39 21 21
RAB11FIP3/RAB11A 0.016 0.039 -10000 0 -0.44 6 6
RhoA/GDP 0.02 0.043 -10000 0 -0.48 4 4
NME1 0.01 0.045 -10000 0 -0.45 8 8
Rac1/GDP 0.02 0.043 -10000 0 -0.44 5 5
substrate adhesion-dependent cell spreading -0.003 0.022 -10000 0 -0.26 4 4
cortical actin cytoskeleton organization -0.004 0.045 -10000 0 -0.46 5 5
RAC1 0.013 0 -10000 0 -10000 0 0
liver development -0.003 0.022 -10000 0 -0.26 4 4
ARF6/GTP -0.003 0.022 -10000 0 -0.26 4 4
RhoA/GTP -0.002 0.015 -10000 0 -10000 0 0
mol:GDP -0.004 0.046 -10000 0 -0.48 5 5
ARF6/GTP/RAB11FIP3/RAB11A -0.004 0.032 -10000 0 -0.4 4 4
RHOA 0.013 0 -10000 0 -10000 0 0
PLD1 0.013 0.056 -10000 0 -0.38 14 14
RAB11FIP3 0.01 0.047 -10000 0 -0.67 4 4
tube morphogenesis -0.004 0.045 -10000 0 -0.46 5 5
ruffle organization 0.023 0.035 -10000 0 -0.35 2 2
regulation of epithelial cell migration -0.003 0.022 -10000 0 -0.26 4 4
PLD2 0.019 0.018 -10000 0 -10000 0 0
PIP5K1A 0.023 0.036 -10000 0 -0.35 2 2
mol:Phosphatidic acid 0.021 0.049 -10000 0 -0.42 7 7
Rac1/GTP -0.004 0.045 -10000 0 -0.46 5 5
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.021 0.064 -9999 0 -0.42 7 7
CaM/Ca2+ 0.01 0 -9999 0 -10000 0 0
AKT1 0.013 0 -9999 0 -10000 0 0
AKT2 0.013 0.016 -9999 0 -0.46 1 1
STXBP4 0.01 0.04 -9999 0 -0.5 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
mol:glucose 0.023 0.074 -9999 0 -0.38 6 6
YWHAZ 0.013 0.016 -9999 0 -0.46 1 1
CALM1 0.013 0 -9999 0 -10000 0 0
YWHAQ 0.013 0 -9999 0 -10000 0 0
TBC1D4 0.021 0.025 -9999 0 -0.5 2 2
mol:Ca2+ 0 0 -9999 0 -10000 0 0
YWHAH 0.013 0 -9999 0 -10000 0 0
YWHAB 0.013 0 -9999 0 -10000 0 0
SNARE/Synip 0.024 0.033 -9999 0 -0.42 3 3
YWHAG 0.013 0.016 -9999 0 -0.46 1 1
ASIP -0.001 0.064 -9999 0 -0.46 16 16
PRKCI 0.013 0.016 -9999 0 -0.46 1 1
AS160/CaM/Ca2+ 0.01 0 -9999 0 -10000 0 0
RHOQ 0.013 0 -9999 0 -10000 0 0
GYS1 0.031 0.006 -9999 0 -10000 0 0
PRKCZ 0.011 0.041 -9999 0 -0.67 3 3
TRIP10 0.012 0.033 -9999 0 -0.67 2 2
TC10/GTP/CIP4/Exocyst 0.017 0.022 -9999 0 -0.43 2 2
AS160/14-3-3 0.036 0.049 -9999 0 -10000 0 0
VAMP2 0.013 0 -9999 0 -10000 0 0
SLC2A4 0.023 0.079 -9999 0 -0.42 6 6
STX4 0.012 0.033 -9999 0 -0.67 2 2
GSK3B 0.025 0.007 -9999 0 -10000 0 0
SFN -0.013 0.13 -9999 0 -0.62 35 35
LNPEP -0.001 0.096 -9999 0 -0.65 18 18
YWHAE 0.012 0.024 -9999 0 -0.67 1 1
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.024 0.062 -9999 0 -0.8 1 1
VEGFR1 homodimer/NRP1 0.014 0.061 -9999 0 -0.45 13 13
mol:DAG 0.029 0.066 -9999 0 -0.63 3 3
VEGFR1 homodimer/NRP1/VEGFR 121 0.019 0.063 -9999 0 -0.75 1 1
CaM/Ca2+ 0.035 0.063 -9999 0 -0.69 2 2
HIF1A 0.009 0.086 -9999 0 -0.6 16 16
GAB1 0.012 0.024 -9999 0 -0.67 1 1
AKT1 0.048 0.061 -9999 0 -0.64 2 2
PLCG1 0.029 0.067 -9999 0 -0.64 3 3
NOS3 0.052 0.061 -9999 0 -0.63 2 2
CBL 0.013 0 -9999 0 -10000 0 0
mol:NO 0.052 0.059 -9999 0 -0.6 2 2
FLT1 0.021 0.072 -9999 0 -0.52 13 13
PGF 0.009 0.05 -9999 0 -0.56 6 6
VEGFR1 homodimer/NRP2/VEGFR121 0.024 0.085 -9999 0 -0.79 5 5
CALM1 0.013 0 -9999 0 -10000 0 0
PIK3CA 0.012 0.023 -9999 0 -0.46 2 2
eNOS/Hsp90 0.057 0.058 -9999 0 -0.58 2 2
endothelial cell proliferation 0.002 0.13 -9999 0 -0.7 11 11
mol:Ca2+ 0.029 0.066 -9999 0 -0.63 3 3
MAPK3 0.028 0.089 -9999 0 -0.73 4 4
MAPK1 0.028 0.089 -9999 0 -0.73 4 4
PIK3R1 0.012 0.023 -9999 0 -0.46 2 2
PLGF homodimer 0.009 0.049 -9999 0 -0.56 6 6
PRKACA 0.013 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.006 0.066 -9999 0 -0.59 10 10
VEGFA homodimer 0.008 0.051 -9999 0 -0.46 10 10
VEGFR1 homodimer/VEGFA homodimer 0.021 0.068 -9999 0 -0.8 1 1
platelet activating factor biosynthetic process 0.034 0.086 -9999 0 -0.7 4 4
PI3K 0.035 0.065 -9999 0 -0.7 2 2
PRKCA 0.022 0.093 -9999 0 -0.77 4 4
PRKCB -0.008 0.14 -9999 0 -0.73 9 9
VEGFR1 homodimer/PLGF homodimer 0.022 0.073 -9999 0 -0.7 3 3
VEGFA 0.008 0.051 -9999 0 -0.46 10 10
VEGFB 0.013 0 -9999 0 -10000 0 0
mol:IP3 0.029 0.066 -9999 0 -0.63 3 3
RASA1 0.03 0.06 -9999 0 -0.74 1 1
NRP2 0.006 0.066 -9999 0 -0.59 10 10
VEGFR1 homodimer 0.021 0.071 -9999 0 -0.52 13 13
VEGFB homodimer 0.013 0 -9999 0 -10000 0 0
NCK1 0.013 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.054 0.079 -9999 0 -0.68 6 6
PTPN11 0.013 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0.033 0.065 -9999 0 -0.69 2 2
mol:L-citrulline 0.052 0.059 -9999 0 -0.6 2 2
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.035 0.061 -9999 0 -0.7 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.028 0.063 -9999 0 -0.74 1 1
CD2AP 0.013 0.016 -9999 0 -0.46 1 1
PI3K/GAB1 0.039 0.064 -9999 0 -0.66 2 2
PDPK1 0.039 0.061 -9999 0 -0.65 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.063 -9999 0 -0.74 1 1
mol:NADP 0.052 0.059 -9999 0 -0.6 2 2
HSP90AA1 0.013 0.016 -9999 0 -0.46 1 1
ubiquitin-dependent protein catabolic process 0.033 0.06 -9999 0 -0.69 1 1
VEGFR1 homodimer/NRP2 0.02 0.085 -9999 0 -0.89 4 4
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.022 0 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.033 0.009 -10000 0 -10000 0 0
CDKN1B 0.029 0.048 -10000 0 -0.34 13 13
CDKN1A 0.031 0.04 -10000 0 -0.34 7 7
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.012 0.028 -10000 0 -0.46 3 3
FOXO3 0.033 0.026 -10000 0 -0.34 2 2
AKT1 -0.001 0.011 -10000 0 -10000 0 0
BAD 0.013 0 -10000 0 -10000 0 0
AKT3 0.006 0.059 -10000 0 -0.39 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.035 0.018 -10000 0 -0.34 1 1
AKT1/ASK1 0.032 0.027 -10000 0 -0.33 3 3
BAD/YWHAZ 0.027 0.01 -10000 0 -10000 0 0
RICTOR 0.012 0.033 -10000 0 -0.67 2 2
RAF1 0.013 0 -10000 0 -10000 0 0
JNK cascade 0.002 0.023 0.32 3 -10000 0 3
TSC1 0.035 0.013 -10000 0 -10000 0 0
YWHAZ 0.013 0.016 -10000 0 -0.46 1 1
AKT1/RAF1 0.035 0.013 -10000 0 -10000 0 0
EP300 0.013 0 -10000 0 -10000 0 0
mol:GDP 0.029 0.014 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.035 0.013 -10000 0 -10000 0 0
YWHAQ 0.013 0 -10000 0 -10000 0 0
TBC1D4 0.022 0.022 -10000 0 -0.42 2 2
MAP3K5 0.01 0.047 -10000 0 -0.59 5 5
MAPKAP1 0.013 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.036 0.032 -10000 0 -10000 0 0
YWHAH 0.013 0 -10000 0 -10000 0 0
AKT1S1 0.035 0.013 -10000 0 -10000 0 0
CASP9 0.035 0.013 -10000 0 -10000 0 0
YWHAB 0.013 0 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.036 0.046 -10000 0 -0.31 13 13
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.025 0.026 -10000 0 -0.42 2 2
YWHAE 0.012 0.024 -10000 0 -0.67 1 1
SRC 0.011 0.037 -10000 0 -0.6 3 3
AKT2/p21CIP1 -0.005 0.033 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.018 0.005 -10000 0 -10000 0 0
CHUK 0.035 0.013 -10000 0 -10000 0 0
BAD/BCL-XL 0.048 0.013 -10000 0 -10000 0 0
mTORC2 0.016 0.02 -10000 0 -0.4 2 2
AKT2 0.017 0.007 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.049 0.039 -10000 0 -10000 0 0
PDPK1 0.013 0 -10000 0 -10000 0 0
MDM2 0.033 0.024 -10000 0 -10000 0 0
MAPKKK cascade -0.035 0.013 -10000 0 -10000 0 0
MDM2/Cbp/p300 0.045 0.029 -10000 0 -10000 0 0
TSC1/TSC2 0.041 0.013 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.028 -10000 0 -10000 0 0
glucose import -0.008 0.1 -10000 0 -0.38 40 40
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.03 0.01 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.008 0.11 -10000 0 -0.38 40 40
GSK3A 0.035 0.013 -10000 0 -10000 0 0
FOXO1 0.034 0.027 -10000 0 -0.34 3 3
GSK3B 0.035 0.013 -10000 0 -10000 0 0
SFN -0.013 0.13 -10000 0 -0.62 35 35
G1/S transition of mitotic cell cycle 0.041 0.013 -10000 0 -10000 0 0
p27Kip1/14-3-3 family 0.037 0.045 -10000 0 -10000 0 0
PRKACA 0.013 0 -10000 0 -10000 0 0
KPNA1 0.013 0 -10000 0 -10000 0 0
HSP90AA1 0.013 0.016 -10000 0 -0.46 1 1
YWHAG 0.013 0.016 -10000 0 -0.46 1 1
RHEB 0.013 0 -10000 0 -10000 0 0
CREBBP 0.012 0.033 -10000 0 -0.67 2 2
Alternative NF-kappaB 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
IKK alpha homodimer 0.02 0 -9999 0 -10000 0 0
FBXW11 0.013 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.013 0 -9999 0 -10000 0 0
CHUK 0.013 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB 0.037 0.03 -9999 0 -0.38 3 3
NFKB1 0.012 0.024 -9999 0 -0.67 1 1
MAP3K14 0.013 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB 0.016 0.04 -9999 0 -0.5 3 3
RELB 0.009 0.049 -9999 0 -0.52 7 7
NFKB2 0.013 0.016 -9999 0 -0.46 1 1
NF kappa B2 p52/RelB 0.015 0.034 -9999 0 -0.35 7 7
regulation of B cell activation 0.015 0.034 -9999 0 -0.35 7 7
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 0.012 0.024 -9999 0 -0.67 1 1
SMAD2 0.015 0.011 -9999 0 -10000 0 0
SMAD3 0.039 0.02 -9999 0 -10000 0 0
SMAD3/SMAD4 0.044 0.021 -9999 0 -0.37 1 1
SMAD4/Ubc9/PIASy 0.026 0.016 -9999 0 -0.42 1 1
SMAD2/SMAD2/SMAD4 0.037 0.023 -9999 0 -10000 0 0
PPM1A 0.013 0 -9999 0 -10000 0 0
CALM1 0.013 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.021 0.013 -9999 0 -10000 0 0
MAP3K1 0.009 0.055 -9999 0 -0.64 6 6
TRAP-1/SMAD4 0.011 0.066 -9999 0 -0.5 14 14
MAPK3 0.013 0 -9999 0 -10000 0 0
MAPK1 0.013 0 -9999 0 -10000 0 0
NUP214 0.013 0 -9999 0 -10000 0 0
CTDSP1 0.013 0 -9999 0 -10000 0 0
CTDSP2 0.013 0.016 -9999 0 -0.46 1 1
CTDSPL 0.013 0 -9999 0 -10000 0 0
KPNB1 0.013 0 -9999 0 -10000 0 0
TGFBRAP1 0.003 0.085 -9999 0 -0.67 13 13
UBE2I 0.013 0 -9999 0 -10000 0 0
NUP153 0.013 0.016 -9999 0 -0.46 1 1
KPNA2 0.01 0.04 -9999 0 -0.5 5 5
PIAS4 0.013 0 -9999 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 0.012 0.024 -9999 0 -0.67 1 1
Ran/GTP/Exportin 1/HDAC4 0 0.01 -9999 0 -10000 0 0
MDM2/SUMO1 0.028 0.021 -9999 0 -10000 0 0
HDAC4 0.012 0.024 -9999 0 -0.67 1 1
Ran/GTP/Exportin 1/HDAC1 0 0.01 -9999 0 -10000 0 0
SUMO1 0.013 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
XPO1 0.028 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
RAN 0.013 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.013 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.03 0.013 -9999 0 -0.35 1 1
SUMO1/HDAC1 0.03 0.013 -9999 0 -0.35 1 1
RANGAP1 0.013 0 -9999 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.032 0.027 -9999 0 -0.38 1 1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.021 0 -9999 0 -10000 0 0
Ran/GTP 0.027 0 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
MDM2 0.009 0.043 -9999 0 -0.46 7 7
UBE2I 0.013 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.033 0 -9999 0 -10000 0 0
NPC 0.008 0 -9999 0 -10000 0 0
PIAS2 0.012 0.024 -9999 0 -0.67 1 1
PIAS1 0.013 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
Arf1 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
coatomer protein complex -0.001 0.014 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.02 0.002 -9999 0 -10000 0 0
AP2 0.02 0 -9999 0 -10000 0 0
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.012 0.029 -9999 0 -0.56 2 2
coatomer protein complex/ARF1/GTP/ER cargo protein 0.025 0.012 -9999 0 -0.29 1 1
CD4 0.007 0.06 -9999 0 -0.59 8 8
CLTA 0.013 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.01 0.016 -9999 0 -0.32 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.026 0.012 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.013 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP -0.001 0.011 -9999 0 -0.22 2 2
AP2M1 0.013 0 -9999 0 -10000 0 0
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.017 0 -9999 0 -10000 0 0
Rac/GTP 0.011 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.012 -9999 0 -10000 0 0
ARFIP2 0.012 0 -9999 0 -10000 0 0
COPA 0.013 0 -9999 0 -10000 0 0
RAC1 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.025 0.007 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0.018 0.004 -9999 0 -10000 0 0
AP2A1 0.013 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.026 0.014 -9999 0 -0.29 1 1
ARF1/GDP/Membrin 0.018 0.004 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.013 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0.01 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.033 0.024 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.01 0.016 -9999 0 -0.32 2 2
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0.001 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.01 0.016 -9999 0 -0.32 2 2
GOSR2 0 0.004 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.023 0.038 -9999 0 -0.42 5 5
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 841 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.HN.A2NL TCGA.GM.A3NY TCGA.GM.A2DO TCGA.GM.A2DN
109_MAP3K5 0.053 0.053 -0.043 0.053
47_PPARGC1A -0.46 0.013 0.013 0.013
105_BMP4 -0.67 0.013 -0.67 0.013
105_BMP6 0.013 0.013 0.013 0.013
105_BMP7 -0.46 0.013 0.013 0.013
105_BMP2 -0.46 0.013 0.013 0.013
131_RELN/VLDLR -0.22 -0.38 0.034 -0.38
30_TGFB1/TGF beta receptor Type II 0.019 0.013 0.013 0.013
84_STAT5B -0.32 0.046 -0.037 0.044
84_STAT5A -0.32 0.046 -0.037 0.044
Methods & Data
Input

  • Expression Data Normalization = Expression data was not used in this analysis.

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/BRCA-TP/2282001/0.mRNAseq_preprocessor.Finished/BRCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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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