PARADIGM pathway analysis of mRNASeq expression and copy number data
Lung Adenocarcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C12Z13J4
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNASeq expression and copy number data. Broad Institute of MIT and Harvard. doi:10.7908/C12Z13J4
Overview
Introduction

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

Summary

There were 45 significant pathways identified in this analysis.

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

Pathway.Name Avg.Num.Perturbations
FOXM1 transcription factor network 185
Glypican 2 network 132
Angiopoietin receptor Tie2-mediated signaling 107
Aurora B signaling 100
HIF-1-alpha transcription factor network 95
Signaling events mediated by the Hedgehog family 85
Endothelins 64
PLK1 signaling events 63
Aurora C signaling 55
Signaling mediated by p38-alpha and p38-beta 50
Results
Summary Table

The following list describes the columns found in Table 2.

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

  • Significance.Ratio = (Ave.Num.Perturbations)/ (Cohort Size) where Cohort Size is 393 . Pathway is significant if Significance.Ratio > 0.05 .

  • Avg.Num.Perturbations = Average number of samples with perturbations across the pathway concepts determined by a background permutation model (>2 standard deviations away from the permuted distribution)

  • Total.Perturbations = Total number of perturbed concepts across all samples (>2 standard deviations away from the permuted distribution)

  • Num.Entities = Number of concepts that belong to the pathway

  • Min.Mean.Truth = Minimum IPL for concepts in the pathway among real samples

  • Max.Mean.Truth = Maximum IPL for concepts in the pathway among real samples

  • Min.Mean.Within = Minimum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Max.Mean.Within = Maximum IPL for concepts in the pathway among null samples using "within permutation" (values are permuted across genes)

  • Min.Mean.Any = Minimum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes)

  • Max.Mean.Any = Maximum IPL for concepts in the pathway among null samples using "any permutation" (values are permuted across samples and genes).

Table 2.  Get Full Table This summary table provides a report of cancer type specific pathway perturbations. Click on the links in the first column to display more detailed results for each pathway. A pathway is defined as significant (red number in Significance.Ratio column) if the Ave.Num.Perturbationsis > 5% of the cohort size ( 393 ).

Pathway.Name Significance.Ratio Avg.Num.Perturbations Total.Perturbations Num.Entities Min.Mean.Truth Max.Mean.Truth Min.Mean.Within Max.Mean.Within Min.Mean.Any Max.Mean.Within.1
FOXM1 transcription factor network 0.4707 185 9471 51 -0.04 0.82 1000 -1000 -0.089 -1000
Glypican 2 network 0.3359 132 530 4 0.085 0.14 1000 -1000 0.017 -1000
Angiopoietin receptor Tie2-mediated signaling 0.2723 107 9439 88 -0.53 0.1 1000 -1000 -0.049 -1000
Aurora B signaling 0.2545 100 6738 67 -0.15 0.29 1000 -1000 -0.028 -1000
HIF-1-alpha transcription factor network 0.2417 95 7280 76 -0.052 0.44 1000 -1000 -0.029 -1000
Signaling events mediated by the Hedgehog family 0.2163 85 4465 52 -0.22 0.1 1000 -1000 -0.03 -1000
Endothelins 0.1628 64 6219 96 -0.3 0.2 1000 -1000 -0.029 -1000
PLK1 signaling events 0.1603 63 5373 85 -0.053 0.2 1000 -1000 -0.03 -1000
Aurora C signaling 0.1399 55 387 7 0 0.17 1000 -1000 -0.005 -1000
Signaling mediated by p38-alpha and p38-beta 0.1272 50 2203 44 -0.098 0.021 1000 -1000 -0.016 -1000
Visual signal transduction: Cones 0.1221 48 1844 38 -0.088 0.12 1000 -1000 -0.015 -1000
Signaling events regulated by Ret tyrosine kinase 0.1221 48 3939 82 -0.081 0.063 1000 -1000 -0.043 -1000
FOXA2 and FOXA3 transcription factor networks 0.1196 47 2206 46 -0.2 0.15 1000 -1000 -0.063 -1000
IL4-mediated signaling events 0.1120 44 4092 91 -0.65 0.36 1000 -1000 -0.088 -1000
Osteopontin-mediated events 0.1094 43 1647 38 -0.004 0.25 1000 -1000 -0.033 -1000
Fc-epsilon receptor I signaling in mast cells 0.1069 42 4166 97 -0.1 0.021 1000 -1000 -0.041 -1000
BMP receptor signaling 0.1018 40 3278 81 -0.18 0.23 1000 -1000 -0.022 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.1018 40 2127 52 -0.14 0.045 1000 -1000 -0.024 -1000
Syndecan-1-mediated signaling events 0.0992 39 1331 34 0 0.22 1000 -1000 -0.019 -1000
amb2 Integrin signaling 0.0992 39 3277 82 -0.3 0.076 1000 -1000 -0.024 -1000
Ephrin B reverse signaling 0.0992 39 1887 48 -0.079 0.079 1000 -1000 -0.025 -1000
Visual signal transduction: Rods 0.0941 37 1946 52 -0.088 0.1 1000 -1000 -0.03 -1000
p75(NTR)-mediated signaling 0.0814 32 4005 125 -0.14 0.14 1000 -1000 -0.043 -1000
IL23-mediated signaling events 0.0763 30 1835 60 -0.19 0.027 1000 -1000 -0.09 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0738 29 2017 68 -0.15 0.065 1000 -1000 -0.048 -1000
Glucocorticoid receptor regulatory network 0.0712 28 3198 114 -0.27 0.18 1000 -1000 -0.037 -1000
LPA4-mediated signaling events 0.0687 27 325 12 -0.072 0 1000 -1000 -0.016 -1000
Integrins in angiogenesis 0.0687 27 2278 84 -0.084 0.25 1000 -1000 -0.041 -1000
Arf6 signaling events 0.0662 26 1666 62 -0.11 0.074 1000 -1000 -0.029 -1000
HIF-2-alpha transcription factor network 0.0662 26 1138 43 -0.14 0.15 1000 -1000 -0.038 -1000
Canonical Wnt signaling pathway 0.0662 26 1359 51 -0.2 0.094 1000 -1000 -0.026 -1000
TCGA08_retinoblastoma 0.0662 26 215 8 -0.022 0.1 1000 -1000 -0.005 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0662 26 3130 120 -0.16 0.14 1000 -1000 -0.04 -1000
EGFR-dependent Endothelin signaling events 0.0636 25 525 21 -0.024 0.074 1000 -1000 -0.028 -1000
Thromboxane A2 receptor signaling 0.0611 24 2617 105 -0.1 0.074 1000 -1000 -0.036 -1000
Presenilin action in Notch and Wnt signaling 0.0611 24 1479 61 -0.21 0.094 1000 -1000 -0.029 -1000
Aurora A signaling 0.0611 24 1469 60 -0.029 0.19 1000 -1000 -0.018 -1000
Reelin signaling pathway 0.0611 24 1376 56 -0.038 0.047 1000 -1000 -0.023 -1000
TCGA08_p53 0.0611 24 172 7 -0.021 0.019 1000 -1000 -0.008 -1000
IL6-mediated signaling events 0.0611 24 1802 75 -0.15 0.053 1000 -1000 -0.039 -1000
Wnt signaling 0.0585 23 161 7 -0.026 0.038 1000 -1000 -0.006 -1000
Noncanonical Wnt signaling pathway 0.0534 21 564 26 -0.047 0.038 1000 -1000 -0.023 -1000
Glypican 1 network 0.0534 21 1018 48 -0.053 0.037 1000 -1000 -0.021 -1000
Effects of Botulinum toxin 0.0534 21 563 26 0 0.042 1000 -1000 -0.01 -1000
Nongenotropic Androgen signaling 0.0509 20 1063 52 -0.069 0.049 1000 -1000 -0.026 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0483 19 647 33 -0.077 0.098 1000 -1000 -0.022 -1000
S1P4 pathway 0.0483 19 492 25 -0.028 0.027 1000 -1000 -0.014 -1000
FoxO family signaling 0.0458 18 1200 64 0 0.21 1000 -1000 -0.035 -1000
Syndecan-4-mediated signaling events 0.0458 18 1257 67 -0.046 0.14 1000 -1000 -0.026 -1000
ErbB4 signaling events 0.0433 17 1209 69 -0.11 0.14 1000 -1000 -0.026 -1000
PDGFR-alpha signaling pathway 0.0433 17 778 44 -0.18 0.037 1000 -1000 -0.03 -1000
IL1-mediated signaling events 0.0433 17 1095 62 -0.076 0.042 1000 -1000 -0.04 -1000
LPA receptor mediated events 0.0433 17 1776 102 -0.056 0.072 1000 -1000 -0.061 -1000
Regulation of Androgen receptor activity 0.0433 17 1205 70 -0.14 0.12 1000 -1000 -0.027 -1000
Syndecan-2-mediated signaling events 0.0407 16 1147 69 -0.046 0.057 1000 -1000 -0.032 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0382 15 513 34 -0.035 0.059 1000 -1000 -0.022 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0382 15 816 54 -0.033 0.11 1000 -1000 -0.031 -1000
S1P5 pathway 0.0382 15 262 17 -0.02 0.021 1000 -1000 -0.002 -1000
FAS signaling pathway (CD95) 0.0382 15 736 47 -0.23 0.034 1000 -1000 -0.026 -1000
EPHB forward signaling 0.0382 15 1295 85 -0.032 0.088 1000 -1000 -0.044 -1000
Calcium signaling in the CD4+ TCR pathway 0.0382 15 493 31 -0.037 0.034 1000 -1000 -0.028 -1000
Class IB PI3K non-lipid kinase events 0.0382 15 45 3 -0.007 0.007 1000 -1000 -0.019 -1000
IL12-mediated signaling events 0.0356 14 1291 87 -0.13 0.059 1000 -1000 -0.054 -1000
PLK2 and PLK4 events 0.0356 14 42 3 -0.007 0.038 1000 -1000 -0.015 -1000
Signaling events mediated by PTP1B 0.0356 14 1083 76 -0.053 0.075 1000 -1000 -0.029 -1000
Ceramide signaling pathway 0.0356 14 1126 76 -0.02 0.074 1000 -1000 -0.025 -1000
BCR signaling pathway 0.0356 14 1418 99 -0.046 0.081 1000 -1000 -0.039 -1000
Plasma membrane estrogen receptor signaling 0.0356 14 1268 86 -0.063 0.06 1000 -1000 -0.038 -1000
Coregulation of Androgen receptor activity 0.0331 13 1020 76 -0.06 0.097 1000 -1000 -0.014 -1000
Nectin adhesion pathway 0.0331 13 873 63 -0.041 0.05 1000 -1000 -0.045 -1000
TCR signaling in naïve CD8+ T cells 0.0331 13 1218 93 -0.031 0.033 1000 -1000 -0.037 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0305 12 1070 85 -0.066 0.036 1000 -1000 -0.035 -1000
S1P1 pathway 0.0305 12 434 36 -0.086 0.021 1000 -1000 -0.026 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0305 12 928 74 -0.093 0.074 1000 -1000 -0.048 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0305 12 948 78 -0.041 0.022 1000 -1000 -0.036 -1000
ErbB2/ErbB3 signaling events 0.0280 11 772 65 -0.05 0.03 1000 -1000 -0.049 -1000
Caspase cascade in apoptosis 0.0280 11 845 74 -0.03 0.078 1000 -1000 -0.028 -1000
BARD1 signaling events 0.0280 11 683 57 -0.046 0.12 1000 -1000 -0.04 -1000
Regulation of p38-alpha and p38-beta 0.0280 11 596 54 -0.038 0.058 1000 -1000 -0.04 -1000
Signaling events mediated by HDAC Class III 0.0254 10 432 40 -0.061 0.065 1000 -1000 -0.029 -1000
Syndecan-3-mediated signaling events 0.0254 10 384 35 -0.11 0.046 1000 -1000 -0.017 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0229 9 1167 125 -0.18 0.041 1000 -1000 -0.047 -1000
Signaling events mediated by PRL 0.0229 9 307 34 -0.023 0.089 1000 -1000 -0.03 -1000
IL27-mediated signaling events 0.0204 8 444 51 -0.044 0.036 1000 -1000 -0.036 -1000
IL2 signaling events mediated by STAT5 0.0204 8 192 22 -0.028 0.1 1000 -1000 -0.029 -1000
Regulation of nuclear SMAD2/3 signaling 0.0178 7 957 136 -0.17 0.074 1000 -1000 -0.029 -1000
Ephrin A reverse signaling 0.0178 7 55 7 -0.014 0.029 1000 -1000 -0.011 -1000
Class I PI3K signaling events 0.0178 7 537 73 -0.038 0.053 1000 -1000 -0.026 -1000
Insulin Pathway 0.0178 7 539 74 -0.099 0.051 1000 -1000 -0.038 -1000
VEGFR1 specific signals 0.0178 7 418 56 -0.18 0.049 1000 -1000 -0.028 -1000
PDGFR-beta signaling pathway 0.0178 7 753 97 -0.035 0.052 1000 -1000 -0.04 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0153 6 169 28 -0.019 0.032 1000 -1000 -0.018 -1000
JNK signaling in the CD4+ TCR pathway 0.0153 6 118 17 -0.008 0.046 1000 -1000 -0.026 -1000
Cellular roles of Anthrax toxin 0.0153 6 261 39 -0.031 0.028 1000 -1000 -0.015 -1000
Hedgehog signaling events mediated by Gli proteins 0.0153 6 449 65 -0.13 0.047 1000 -1000 -0.038 -1000
EPO signaling pathway 0.0153 6 380 55 -0.026 0.045 1000 -1000 -0.025 -1000
mTOR signaling pathway 0.0153 6 335 53 -0.057 0.025 1000 -1000 -0.028 -1000
IFN-gamma pathway 0.0153 6 428 68 -0.029 0.061 1000 -1000 -0.039 -1000
Retinoic acid receptors-mediated signaling 0.0153 6 363 58 -0.091 0.04 1000 -1000 -0.025 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0153 6 273 45 -0.023 0.049 1000 -1000 -0.034 -1000
Arf6 trafficking events 0.0153 6 496 71 -0.037 0.038 1000 -1000 -0.032 -1000
S1P3 pathway 0.0153 6 267 42 -0.025 0.034 1000 -1000 -0.02 -1000
Ras signaling in the CD4+ TCR pathway 0.0153 6 104 17 -0.005 0.031 1000 -1000 -0.019 -1000
ceramide signaling pathway 0.0127 5 286 49 -0.01 0.026 1000 -1000 -0.024 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0127 5 455 83 -0.058 0.041 1000 -1000 -0.02 -1000
Signaling events mediated by HDAC Class I 0.0127 5 537 104 -0.034 0.047 1000 -1000 -0.033 -1000
Signaling mediated by p38-gamma and p38-delta 0.0127 5 78 15 -0.018 0.022 1000 -1000 -0.026 -1000
E-cadherin signaling in the nascent adherens junction 0.0127 5 420 76 -0.032 0.055 1000 -1000 -0.041 -1000
Regulation of Telomerase 0.0127 5 555 102 -0.021 0.096 1000 -1000 -0.044 -1000
p38 MAPK signaling pathway 0.0127 5 223 44 -0.008 0.061 1000 -1000 -0.023 -1000
Arf6 downstream pathway 0.0102 4 194 43 -0.05 0.054 1000 -1000 -0.02 -1000
IL2 signaling events mediated by PI3K 0.0102 4 267 58 -0.014 0.07 1000 -1000 -0.026 -1000
TCGA08_rtk_signaling 0.0102 4 110 26 -0.009 0.047 1000 -1000 -0.009 -1000
IGF1 pathway 0.0102 4 242 57 -0.032 0.047 1000 -1000 -0.029 -1000
E-cadherin signaling in keratinocytes 0.0102 4 182 43 -0.014 0.039 1000 -1000 -0.019 -1000
Signaling events mediated by HDAC Class II 0.0076 3 286 75 -0.02 0.056 1000 -1000 -0.024 -1000
Circadian rhythm pathway 0.0076 3 75 22 -0.004 0.046 1000 -1000 -0.031 -1000
Class I PI3K signaling events mediated by Akt 0.0076 3 268 68 -0.027 0.045 1000 -1000 -0.022 -1000
Canonical NF-kappaB pathway 0.0051 2 96 39 -0.017 0.042 1000 -1000 -0.02 -1000
Insulin-mediated glucose transport 0.0051 2 65 32 -0.016 0.038 1000 -1000 -0.024 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0051 2 82 37 -0.026 0.05 1000 -1000 -0.019 -1000
a4b1 and a4b7 Integrin signaling 0.0025 1 7 5 0.019 0.03 1000 -1000 0.019 -1000
TRAIL signaling pathway 0.0025 1 89 48 -0.018 0.045 1000 -1000 -0.024 -1000
Paxillin-dependent events mediated by a4b1 0.0025 1 56 36 -0.036 0.039 1000 -1000 -0.03 -1000
Atypical NF-kappaB pathway 0.0025 1 37 31 -0.018 0.029 1000 -1000 -0.021 -1000
Rapid glucocorticoid signaling 0.0025 1 35 20 -0.008 0.026 1000 -1000 -0.009 -1000
E-cadherin signaling events 0.0025 1 6 5 0.019 0.039 1000 -1000 0.018 -1000
Arf1 pathway 0.0025 1 83 54 -0.008 0.033 1000 -1000 -0.014 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0000 0 22 23 0 0.036 1000 -1000 -0.012 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 17 27 -0.019 0.045 1000 -1000 -0.028 -1000
Alternative NF-kappaB pathway 0.0000 0 0 13 0 0.055 1000 -1000 0 -1000
Total NA 2760 163002 7203 -9.6 11 131000 -131000 -3.7 -131000
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.65 0.5 1 223 -10000 0 223
PLK1 0.38 0.33 0.7 189 -0.68 2 191
BIRC5 0.42 0.33 0.7 205 -0.71 1 206
HSPA1B 0.66 0.5 1.1 223 -10000 0 223
MAP2K1 0.2 0.15 0.33 204 -10000 0 204
BRCA2 0.65 0.5 1 222 -10000 0 222
FOXM1 0.82 0.66 1.3 230 -0.83 1 231
XRCC1 0.66 0.5 1 223 -10000 0 223
FOXM1B/p19 0.22 0.37 0.83 91 -0.84 1 92
Cyclin D1/CDK4 0.54 0.44 0.92 204 -10000 0 204
CDC2 0.73 0.57 1.2 233 -10000 0 233
TGFA 0.57 0.46 0.94 218 -10000 0 218
SKP2 0.72 0.55 1.1 226 -10000 0 226
CCNE1 0.16 0.17 0.38 136 -10000 0 136
CKS1B 0.71 0.55 1.1 228 -10000 0 228
RB1 0.38 0.37 0.74 187 -0.61 3 190
FOXM1C/SP1 0.57 0.43 0.92 214 -0.78 1 215
AURKB 0.36 0.38 0.7 182 -0.73 14 196
CENPF 0.74 0.57 1.2 234 -10000 0 234
CDK4 0.088 0.068 0.2 49 -10000 0 49
MYC 0.43 0.43 0.87 173 -10000 0 173
CHEK2 0.2 0.16 0.33 210 -10000 0 210
ONECUT1 0.62 0.49 1 215 -10000 0 215
CDKN2A -0.04 0.15 0.25 38 -0.22 117 155
LAMA4 0.64 0.51 1 222 -1.2 3 225
FOXM1B/HNF6 0.62 0.5 1 207 -10000 0 207
FOS 0.59 0.54 1.1 201 -0.92 2 203
SP1 0.021 0.005 -10000 0 -10000 0 0
CDC25B 0.65 0.5 1 220 -10000 0 220
response to radiation 0.14 0.11 0.23 215 -10000 0 215
CENPB 0.65 0.5 1 222 -10000 0 222
CENPA 0.74 0.57 1.2 235 -10000 0 235
NEK2 0.77 0.58 1.2 238 -10000 0 238
HIST1H2BA 0.66 0.5 1 223 -10000 0 223
CCNA2 0.14 0.16 0.4 101 -10000 0 101
EP300 0.021 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.71 0.55 1.1 222 -10000 0 222
CCNB2 0.73 0.57 1.2 227 -10000 0 227
CCNB1 0.76 0.6 1.2 229 -10000 0 229
ETV5 0.64 0.52 1.1 218 -1.1 2 220
ESR1 0.63 0.52 1 220 -1 4 224
CCND1 0.61 0.48 1 221 -10000 0 221
GSK3A 0.15 0.12 0.26 188 -10000 0 188
Cyclin A-E1/CDK1-2 0.27 0.22 0.44 211 -10000 0 211
CDK2 0.061 0.041 0.16 3 -10000 0 3
G2/M transition of mitotic cell cycle 0.18 0.15 0.29 229 -10000 0 229
FOXM1B/Cbp/p300 0.15 0.26 0.68 51 -0.77 1 52
GAS1 0.62 0.52 1 223 -1.1 4 227
MMP2 0.65 0.5 1 229 -10000 0 229
RB1/FOXM1C 0.52 0.45 0.92 202 -0.74 1 203
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK 0.12 0.14 0.33 122 -9999 0 122
GPC2 0.085 0.13 0.33 82 -9999 0 82
GPC2/Midkine 0.14 0.14 0.29 163 -9999 0 163
neuron projection morphogenesis 0.14 0.14 0.29 163 -9999 0 163
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.42 0.47 -10000 0 -0.93 171 171
NCK1/PAK1/Dok-R -0.2 0.2 -10000 0 -0.42 176 176
NCK1/Dok-R -0.46 0.56 -10000 0 -1 172 172
PIK3CA 0.021 0.005 -10000 0 -10000 0 0
mol:beta2-estradiol 0.056 0.093 0.23 85 -10000 0 85
RELA 0.021 0.003 -10000 0 -10000 0 0
SHC1 0.011 0.015 -10000 0 -10000 0 0
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
F2 0.1 0.16 0.32 119 -10000 0 119
TNIP2 0.021 0.004 -10000 0 -10000 0 0
NF kappa B/RelA -0.41 0.52 -10000 0 -0.97 170 170
FN1 0.017 0.035 -10000 0 -0.33 4 4
PLD2 -0.48 0.58 -10000 0 -1.1 169 169
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB14 0.033 0.081 0.33 21 -0.33 5 26
ELK1 -0.44 0.51 -10000 0 -0.98 170 170
GRB7 0.019 0.025 -10000 0 -0.33 2 2
PAK1 0.02 0.005 -10000 0 -10000 0 0
Tie2/Ang1/alpha5/beta1 Integrin -0.43 0.55 -10000 0 -1 170 170
CDKN1A -0.3 0.31 -10000 0 -0.64 170 170
ITGA5 0.021 0.024 0.33 1 -0.33 1 2
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.46 0.56 -10000 0 -1 172 172
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:NO -0.3 0.33 -10000 0 -0.67 172 172
PLG -0.48 0.58 -10000 0 -1.1 170 170
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis -0.39 0.43 -10000 0 -0.86 172 172
GRB2 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.008 0.018 -10000 0 -10000 0 0
ANGPT2 -0.27 0.3 -10000 0 -0.69 109 109
BMX -0.52 0.6 -10000 0 -1.1 171 171
ANGPT1 -0.28 0.46 -10000 0 -1.1 86 86
tube development -0.34 0.35 -10000 0 -0.73 171 171
ANGPT4 -0.16 0.17 -10000 0 -0.33 189 189
response to hypoxia -0.029 0.032 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.48 0.61 -10000 0 -1.1 170 170
alpha5/beta1 Integrin 0.03 0.018 0.24 1 -0.23 1 2
FGF2 -0.021 0.11 -10000 0 -0.33 47 47
STAT5A (dimer) -0.39 0.41 -10000 0 -0.84 170 170
mol:L-citrulline -0.3 0.33 -10000 0 -0.67 172 172
AGTR1 -0.077 0.16 -10000 0 -0.33 110 110
MAPK14 -0.53 0.62 -10000 0 -1.2 172 172
Tie2/SHP2 -0.42 0.51 -10000 0 -1 159 159
TEK -0.46 0.56 -10000 0 -1.1 157 157
RPS6KB1 -0.4 0.45 -10000 0 -0.89 173 173
Angiotensin II/AT1 -0.051 0.11 -10000 0 -0.22 110 110
Tie2/Ang1/GRB2 -0.48 0.61 -10000 0 -1.1 170 170
MAPK3 -0.44 0.52 -10000 0 -1 169 169
MAPK1 -0.44 0.52 -10000 0 -0.99 168 168
Tie2/Ang1/GRB7 -0.49 0.61 -10000 0 -1.1 170 170
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.48 0.58 -10000 0 -1.1 170 170
PI3K -0.49 0.56 -10000 0 -1.1 173 173
FES -0.53 0.62 -10000 0 -1.2 172 172
Crk/Dok-R -0.46 0.56 -10000 0 -1 172 172
Tie2/Ang1/ABIN2 -0.49 0.61 -10000 0 -1.1 170 170
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity -0.37 0.41 -10000 0 -0.82 171 171
STAT5A 0.02 0.018 -10000 0 -0.33 1 1
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 -0.39 0.45 -10000 0 -0.87 173 173
Tie2/Ang2 -0.48 0.52 -10000 0 -1 171 171
Tie2/Ang1 -0.52 0.65 -10000 0 -1.2 170 170
FOXO1 -0.38 0.41 -10000 0 -0.83 171 171
ELF1 -0.029 0.066 -10000 0 -10000 0 0
ELF2 -0.47 0.58 -10000 0 -1.1 167 167
mol:Choline -0.45 0.54 -10000 0 -1 169 169
cell migration -0.11 0.11 -10000 0 -0.23 175 175
FYN -0.39 0.41 -10000 0 -0.84 171 171
DOK2 -0.006 0.088 -10000 0 -0.33 27 27
negative regulation of cell cycle -0.28 0.28 -10000 0 -0.58 170 170
ETS1 -0.047 0.1 -10000 0 -0.25 77 77
PXN -0.32 0.36 -10000 0 -0.71 172 172
ITGB1 0.021 0.004 -10000 0 -10000 0 0
NOS3 -0.35 0.38 -10000 0 -0.77 171 171
RAC1 0.019 0.007 -10000 0 -10000 0 0
TNF -0.062 0.12 -10000 0 -0.27 95 95
MAPKKK cascade -0.45 0.54 -10000 0 -1 169 169
RASA1 0.02 0.005 -10000 0 -10000 0 0
Tie2/Ang1/Shc -0.48 0.6 -10000 0 -1.1 170 170
NCK1 0.021 0.003 -10000 0 -10000 0 0
vasculogenesis -0.27 0.3 -10000 0 -0.59 172 172
mol:Phosphatidic acid -0.45 0.54 -10000 0 -1 169 169
mol:Angiotensin II 0 0.003 -10000 0 -10000 0 0
mol:NADP -0.3 0.33 -10000 0 -0.67 172 172
Rac1/GTP -0.36 0.41 -10000 0 -0.81 172 172
MMP2 -0.48 0.58 -10000 0 -1.1 170 170
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.11 0.12 0.24 170 -0.18 6 176
STMN1 0.072 0.089 0.16 192 -10000 0 192
Aurora B/RasGAP/Survivin 0.22 0.18 0.37 218 -10000 0 218
Chromosomal passenger complex/Cul3 protein complex 0.092 0.11 0.2 172 -0.22 4 176
BIRC5 0.2 0.16 0.34 217 -10000 0 217
DES -0.15 0.28 -10000 0 -0.56 81 81
Aurora C/Aurora B/INCENP 0.12 0.098 0.22 186 -0.16 3 189
Aurora B/TACC1 0.092 0.1 0.21 157 -0.15 12 169
Aurora B/PP2A 0.12 0.11 0.24 180 -10000 0 180
mol:GTP 0 0 -10000 0 -10000 0 0
CBX5 0.036 0.037 0.14 15 -10000 0 15
mitotic metaphase/anaphase transition -0.005 0.006 -10000 0 -10000 0 0
NDC80 0.15 0.16 0.28 215 -10000 0 215
Cul3 protein complex 0.03 0.047 0.23 3 -0.2 12 15
KIF2C 0.17 0.13 0.26 237 -0.32 1 238
PEBP1 0.023 0.005 -10000 0 -10000 0 0
KIF20A 0.19 0.15 0.33 215 -10000 0 215
mol:GDP 0 0 -10000 0 -10000 0 0
Aurora B/RasGAP 0.13 0.11 0.24 187 -10000 0 187
SEPT1 0.02 0.018 -10000 0 -0.33 1 1
SMC2 0.021 0.004 -10000 0 -10000 0 0
SMC4 0.021 0.004 -10000 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.11 0.2 0.3 107 -0.43 28 135
PSMA3 0.02 0.004 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.006 0.006 -10000 0 -10000 0 0
H3F3B 0.078 0.073 0.15 195 -10000 0 195
AURKB 0.18 0.16 0.34 194 -10000 0 194
AURKC 0.018 0.035 0.33 1 -0.33 3 4
CDCA8 0.14 0.15 0.34 140 -10000 0 140
cytokinesis 0.15 0.16 0.31 179 -0.42 1 180
Aurora B/Septin1 0.19 0.19 0.38 180 -0.25 7 187
AURKA 0.058 0.13 0.32 71 -10000 0 71
INCENP 0.028 0.01 -10000 0 -10000 0 0
KLHL13 0.013 0.066 0.33 3 -0.33 12 15
BUB1 0.094 0.14 0.33 108 -10000 0 108
hSgo1/Aurora B/Survivin 0.29 0.24 0.48 225 -10000 0 225
EVI5 0.026 0.007 -10000 0 -10000 0 0
RhoA/GTP 0.17 0.16 0.35 147 -0.32 1 148
SGOL1 0.17 0.16 0.33 185 -10000 0 185
CENPA 0.17 0.16 0.3 209 -0.24 5 214
NCAPG 0.15 0.15 0.33 167 -10000 0 167
Aurora B/HC8 Proteasome 0.13 0.11 0.24 187 -10000 0 187
NCAPD2 0.02 0.005 -10000 0 -10000 0 0
Aurora B/PP1-gamma 0.13 0.11 0.24 189 -10000 0 189
RHOA 0.021 0.004 -10000 0 -10000 0 0
NCAPH 0.16 0.15 0.33 173 -10000 0 173
NPM1 0.072 0.14 0.21 78 -0.35 21 99
RASA1 0.02 0.005 -10000 0 -10000 0 0
KLHL9 0.018 0.008 -10000 0 -10000 0 0
mitotic prometaphase 0.002 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.13 0.11 0.24 187 -10000 0 187
PPP1CC 0.021 0.004 -10000 0 -10000 0 0
Centraspindlin 0.19 0.18 0.38 161 -0.34 1 162
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
NSUN2 0.092 0.13 0.27 53 -0.3 16 69
MYLK 0.071 0.076 0.15 189 -0.15 7 196
KIF23 0.1 0.14 0.34 93 -10000 0 93
VIM 0.071 0.09 0.16 188 -10000 0 188
RACGAP1 0.031 0.033 0.33 4 -10000 0 4
mitosis 0 0 -10000 0 -10000 0 0
NCL 0.077 0.13 0.2 79 -0.3 23 102
Chromosomal passenger complex 0.17 0.16 0.3 209 -0.26 2 211
Chromosomal passenger complex/EVI5 0.29 0.22 0.48 214 -10000 0 214
TACC1 0.008 0.06 -10000 0 -0.33 12 12
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
CUL3 0.021 0.002 -10000 0 -10000 0 0
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 0.28 0.24 0.54 117 -0.68 4 121
HDAC7 0.032 0.016 -10000 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 0.32 0.32 0.67 130 -0.84 3 133
SMAD4 0.019 0.009 -10000 0 -10000 0 0
ID2 0.29 0.24 0.55 120 -0.68 4 124
AP1 -0.002 0.078 -10000 0 -0.24 30 30
ABCG2 0.26 0.25 0.55 111 -0.66 5 116
HIF1A 0.1 0.094 0.24 78 -0.22 2 80
TFF3 0.32 0.28 0.6 146 -0.71 4 150
GATA2 -0.021 0.1 -10000 0 -0.34 35 35
AKT1 0.1 0.1 0.28 51 -0.24 4 55
response to hypoxia 0.082 0.1 0.2 105 -0.22 8 113
MCL1 0.24 0.24 0.54 97 -0.74 2 99
NDRG1 0.24 0.24 0.55 97 -0.64 4 101
SERPINE1 0.27 0.24 0.55 113 -0.68 4 117
FECH 0.26 0.25 0.54 113 -0.68 4 117
FURIN 0.29 0.25 0.56 122 -0.68 4 126
NCOA2 0.018 0.026 -10000 0 -0.33 2 2
EP300 0.12 0.14 0.3 97 -0.3 11 108
HMOX1 0.28 0.24 0.55 119 -0.64 4 123
BHLHE40 0.28 0.24 0.55 119 -0.68 4 123
BHLHE41 0.26 0.25 0.55 104 -0.66 6 110
HIF1A/ARNT/SMAD3/SMAD4/SP1 0.14 0.14 0.37 63 -10000 0 63
ENG 0.11 0.098 0.28 38 -0.26 2 40
JUN 0.009 0.036 -10000 0 -0.34 2 2
RORA 0.28 0.24 0.54 120 -0.71 4 124
ABCB1 0.015 0.18 0.39 18 -0.72 14 32
TFRC 0.27 0.24 0.54 113 -0.68 4 117
CXCR4 0.29 0.24 0.54 119 -0.68 4 123
TF 0.33 0.29 0.63 138 -0.64 5 143
CITED2 0.27 0.25 0.54 118 -0.68 4 122
HIF1A/ARNT 0.44 0.41 0.86 153 -0.81 3 156
LDHA 0.054 0.11 0.43 12 -0.51 2 14
ETS1 0.28 0.24 0.55 114 -0.6 4 118
PGK1 0.28 0.24 0.55 116 -0.68 4 120
NOS2 0.27 0.26 0.55 118 -0.74 4 122
ITGB2 0.28 0.24 0.54 119 -0.78 4 123
ALDOA 0.29 0.24 0.55 119 -0.68 4 123
Cbp/p300/CITED2 0.28 0.29 0.61 112 -0.88 4 116
FOS -0.013 0.093 -10000 0 -0.34 28 28
HK2 0.29 0.24 0.54 122 -0.7 5 127
SP1 0.015 0.036 -10000 0 -0.16 13 13
GCK 0.16 0.27 0.52 47 -1 11 58
HK1 0.28 0.24 0.54 117 -0.68 4 121
NPM1 0.27 0.24 0.54 117 -0.68 4 121
EGLN1 0.27 0.24 0.54 114 -0.82 2 116
CREB1 0.023 0.01 -10000 0 -10000 0 0
PGM1 0.28 0.24 0.55 115 -0.68 4 119
SMAD3 0.02 0.009 -10000 0 -10000 0 0
EDN1 -0.052 0.4 0.43 5 -0.98 57 62
IGFBP1 0.29 0.27 0.59 126 -0.68 4 130
VEGFA 0.26 0.24 0.52 121 -0.69 3 124
HIF1A/JAB1 0.081 0.068 0.22 32 -0.18 1 33
CP 0.39 0.3 0.63 191 -0.67 4 195
CXCL12 0.28 0.25 0.54 120 -0.78 4 124
COPS5 0.019 0.008 -10000 0 -10000 0 0
SMAD3/SMAD4 0.027 0.014 -10000 0 -10000 0 0
BNIP3 0.28 0.24 0.54 119 -0.68 4 123
EGLN3 0.32 0.29 0.64 136 -0.6 4 140
CA9 0.42 0.3 0.63 216 -0.68 4 220
TERT 0.29 0.3 0.62 133 -0.68 3 136
ENO1 0.28 0.24 0.54 121 -0.68 4 125
PFKL 0.28 0.24 0.54 118 -0.68 4 122
NCOA1 0.021 0.003 -10000 0 -10000 0 0
ADM 0.28 0.25 0.55 118 -0.72 4 122
ARNT 0.092 0.09 0.26 47 -10000 0 47
HNF4A 0.067 0.14 0.33 71 -0.27 15 86
ADFP 0.26 0.25 0.51 142 -0.68 4 146
SLC2A1 0.34 0.28 0.61 168 -0.65 3 171
LEP 0.3 0.26 0.58 126 -0.68 4 130
HIF1A/ARNT/Cbp/p300 0.33 0.33 0.7 130 -0.86 3 133
EPO 0.23 0.23 0.55 75 -1.1 1 76
CREBBP 0.12 0.14 0.3 97 -0.28 8 105
HIF1A/ARNT/Cbp/p300/HDAC7 0.35 0.34 0.71 143 -0.8 3 146
PFKFB3 0.28 0.24 0.54 114 -0.68 4 118
NT5E 0.28 0.26 0.57 118 -0.68 4 122
Signaling events mediated by the Hedgehog family

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB2 -0.09 0.19 0.32 6 -0.5 36 42
IHH -0.013 0.13 0.29 6 -0.38 34 40
SHH Np/Cholesterol/GAS1 -0.036 0.057 0.12 1 -0.18 49 50
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.036 0.057 0.18 49 -0.11 1 50
SMO/beta Arrestin2 -0.14 0.18 0.32 1 -0.33 145 146
SMO -0.14 0.19 0.34 1 -0.34 154 155
AKT1 -0.079 0.14 0.27 1 -0.49 26 27
ARRB2 0.019 0.006 -10000 0 -10000 0 0
BOC 0.02 0.018 -10000 0 -0.33 1 1
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
heart looping -0.14 0.19 0.34 1 -0.33 154 155
STIL -0.082 0.14 0.26 9 -0.31 52 61
DHH N/PTCH2 0.013 0.066 -10000 0 -0.23 27 27
DHH N/PTCH1 -0.1 0.16 -10000 0 -0.24 183 183
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DHH -0.002 0.087 -10000 0 -0.33 26 26
PTHLH -0.12 0.23 0.39 6 -0.56 34 40
determination of left/right symmetry -0.14 0.19 0.34 1 -0.33 154 155
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
skeletal system development -0.12 0.23 0.39 6 -0.56 34 40
IHH N/Hhip -0.22 0.18 0.21 3 -0.32 288 291
DHH N/Hhip -0.12 0.14 -10000 0 -0.25 213 213
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.14 0.19 0.34 1 -0.33 154 155
pancreas development -0.16 0.17 -10000 0 -0.33 209 209
HHAT 0.018 0.025 -10000 0 -0.33 2 2
PI3K 0.029 0.009 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.012 0.055 -10000 0 -0.33 10 10
somite specification -0.14 0.19 0.34 1 -0.33 154 155
SHH Np/Cholesterol/PTCH1 -0.1 0.14 0.18 2 -0.33 54 56
SHH Np/Cholesterol/PTCH2 -0.033 0.052 0.12 1 -0.18 44 45
SHH Np/Cholesterol/Megalin -0.068 0.087 0.12 1 -0.2 115 116
SHH -0.039 0.069 0.16 1 -0.23 44 45
catabolic process -0.1 0.16 0.23 3 -0.25 184 187
SMO/Vitamin D3 -0.12 0.17 0.37 2 -0.4 51 53
SHH Np/Cholesterol/Hhip -0.1 0.1 0.12 1 -0.2 195 196
LRP2 -0.072 0.16 0.33 1 -0.33 105 106
receptor-mediated endocytosis -0.16 0.18 0.3 2 -0.41 101 103
SHH Np/Cholesterol/BOC -0.033 0.052 0.12 1 -0.18 43 44
SHH Np/Cholesterol/CDO -0.034 0.056 0.12 1 -0.18 45 46
mesenchymal cell differentiation 0.1 0.1 0.2 195 -0.11 1 196
mol:Vitamin D3 -0.088 0.16 0.36 5 -0.33 53 58
IHH N/PTCH2 -0.095 0.13 0.2 5 -0.21 210 215
CDON 0.014 0.046 -10000 0 -0.33 7 7
IHH N/PTCH1 -0.097 0.18 0.24 30 -0.26 185 215
Megalin/LRPAP1 -0.037 0.12 0.24 1 -0.23 102 103
PTCH2 0.02 0.018 -10000 0 -0.33 1 1
SHH Np/Cholesterol -0.028 0.051 -10000 0 -0.17 44 44
PTCH1 -0.11 0.16 0.23 3 -0.26 184 187
HHIP -0.17 0.17 -10000 0 -0.33 209 209
Endothelins

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
AKT1 -0.081 0.11 0.23 1 -0.33 37 38
PTK2B 0.017 0.019 -10000 0 -0.33 1 1
mol:Ca2+ -0.12 0.27 -10000 0 -0.78 46 46
EDN1 -0.074 0.13 -10000 0 -0.35 56 56
EDN3 -0.072 0.15 0.33 1 -0.33 102 103
EDN2 0.1 0.14 0.33 103 -0.33 2 105
HRAS/GDP -0.15 0.19 -10000 0 -0.41 100 100
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.071 0.13 -10000 0 -0.34 54 54
ADCY4 -0.068 0.11 0.19 5 -0.28 45 50
ADCY5 -0.079 0.13 0.21 8 -0.31 60 68
ADCY6 -0.063 0.1 0.23 5 -0.28 36 41
ADCY7 -0.064 0.1 0.24 3 -0.28 37 40
ADCY1 -0.06 0.1 0.24 2 -0.28 37 39
ADCY2 -0.059 0.11 0.25 8 -0.3 40 48
ADCY3 -0.064 0.11 0.24 5 -0.28 38 43
ADCY8 -0.098 0.12 0.38 2 -0.26 94 96
ADCY9 -0.066 0.11 0.22 7 -0.28 45 52
arachidonic acid secretion -0.13 0.2 -10000 0 -0.48 70 70
ETB receptor/Endothelin-1/Gq/GTP -0.14 0.16 -10000 0 -0.27 200 200
GNAO1 0.02 0.034 0.33 2 -0.33 2 4
HRAS 0.02 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP -0.051 0.12 0.31 1 -0.3 36 37
ETA receptor/Endothelin-1/Gs/GTP -0.052 0.12 0.29 1 -0.28 41 42
mol:GTP -0.001 0.004 -10000 0 -10000 0 0
COL3A1 -0.048 0.16 0.29 24 -0.33 36 60
EDNRB -0.16 0.18 -10000 0 -0.33 201 201
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.087 0.13 0.23 1 -0.38 38 39
CYSLTR1 -0.089 0.13 0.23 1 -0.38 38 39
SLC9A1 -0.05 0.081 0.16 1 -0.22 40 41
mol:GDP -0.16 0.2 -10000 0 -0.44 102 102
SLC9A3 -0.3 0.34 -10000 0 -0.64 147 147
RAF1 -0.16 0.2 -10000 0 -0.47 86 86
JUN -0.1 0.21 -10000 0 -0.64 39 39
JAK2 -0.078 0.11 0.23 1 -0.32 41 42
mol:IP3 -0.12 0.17 -10000 0 -0.37 91 91
ETA receptor/Endothelin-1 -0.082 0.15 0.35 1 -0.33 58 59
PLCB1 0.018 0.019 0.33 1 -10000 0 1
PLCB2 0.009 0.051 -10000 0 -0.33 8 8
ETA receptor/Endothelin-3 -0.078 0.12 0.19 1 -0.24 108 109
FOS -0.16 0.25 -10000 0 -0.72 50 50
Gai/GDP -0.049 0.19 -10000 0 -0.81 21 21
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca ++ -0.16 0.19 -10000 0 -0.43 95 95
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
PRKCB1 -0.12 0.17 -10000 0 -0.36 94 94
GNAQ 0.014 0.024 -10000 0 -0.33 1 1
GNAZ -0.01 0.098 -10000 0 -0.33 34 34
GNAL 0.019 0.045 0.33 3 -0.33 4 7
Gs family/GDP -0.14 0.18 -10000 0 -0.4 99 99
ETA receptor/Endothelin-1/Gq/GTP -0.068 0.13 -10000 0 -0.31 60 60
MAPK14 -0.13 0.15 0.2 1 -0.33 109 110
TRPC6 -0.13 0.29 -10000 0 -0.84 46 46
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.018 -10000 0 -0.33 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.14 0.16 -10000 0 -0.29 160 160
ETB receptor/Endothelin-2 -0.072 0.15 0.24 36 -0.21 196 232
ETB receptor/Endothelin-3 -0.15 0.16 0.24 1 -0.27 231 232
ETB receptor/Endothelin-1 -0.15 0.16 0.21 7 -0.3 195 202
MAPK3 -0.17 0.25 -10000 0 -0.67 60 60
MAPK1 -0.17 0.25 -10000 0 -0.67 63 63
Rac1/GDP -0.14 0.18 -10000 0 -0.41 91 91
cAMP biosynthetic process -0.078 0.14 0.3 6 -0.35 49 55
MAPK8 -0.12 0.24 -10000 0 -0.68 48 48
SRC 0.02 0.004 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.13 0.14 -10000 0 -0.28 138 138
p130Cas/CRK/Src/PYK2 -0.17 0.23 0.31 1 -0.57 71 72
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.14 0.19 -10000 0 -0.41 91 91
COL1A2 -0.16 0.18 0.32 7 -0.37 120 127
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 0.042 0.12 0.22 95 -0.19 13 108
mol:DAG -0.12 0.17 -10000 0 -0.37 91 91
MAP2K2 -0.16 0.22 -10000 0 -0.54 74 74
MAP2K1 -0.16 0.22 -10000 0 -0.54 75 75
EDNRA -0.038 0.078 0.23 1 -0.25 13 14
positive regulation of muscle contraction -0.056 0.11 0.2 18 -0.29 34 52
Gq family/GDP -0.12 0.18 0.35 1 -0.41 75 76
HRAS/GTP -0.15 0.2 -10000 0 -0.42 98 98
PRKCH -0.12 0.16 -10000 0 -0.37 87 87
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.12 0.17 -10000 0 -0.38 82 82
PRKCB -0.13 0.17 -10000 0 -0.38 94 94
PRKCE -0.13 0.17 -10000 0 -0.36 95 95
PRKCD -0.12 0.16 -10000 0 -0.36 90 90
PRKCG -0.12 0.16 -10000 0 -0.36 86 86
regulation of vascular smooth muscle contraction -0.19 0.3 -10000 0 -0.87 49 49
PRKCQ -0.14 0.18 -10000 0 -0.38 101 101
PLA2G4A -0.14 0.22 -10000 0 -0.53 70 70
GNA14 0.007 0.057 -10000 0 -0.34 10 10
GNA15 0.015 0.015 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA11 0.015 0.015 -10000 0 -10000 0 0
Rac1/GTP -0.051 0.12 0.31 1 -0.3 36 37
MMP1 0.2 0.17 0.31 241 -0.68 2 243
PLK1 signaling 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
regulation of centriole-centriole cohesion -0.053 0.065 0.12 10 -0.12 185 195
BUB1B 0.077 0.078 0.15 182 -0.11 8 190
PLK1 0.032 0.041 0.095 88 -0.08 1 89
PLK1S1 0.015 0.038 0.12 2 -0.16 11 13
KIF2A 0.025 0.045 0.14 23 -10000 0 23
regulation of mitotic centrosome separation 0.032 0.041 0.094 88 -0.08 1 89
GOLGA2 0.021 0.004 -10000 0 -10000 0 0
Hec1/SPC24 0.19 0.18 0.35 193 -10000 0 193
WEE1 0.031 0.062 0.19 1 -0.27 8 9
cytokinesis 0.095 0.098 0.2 135 -0.2 2 137
PP2A-alpha B56 0.084 0.089 -10000 0 -0.48 3 3
AURKA 0.039 0.06 0.14 85 -0.19 4 89
PICH/PLK1 0.086 0.12 0.23 147 -10000 0 147
CENPE 0.037 0.056 0.14 55 -10000 0 55
RhoA/GTP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.026 0.045 0.15 22 -10000 0 22
PPP2CA 0.02 0.005 -10000 0 -10000 0 0
FZR1 0.02 0.006 -10000 0 -10000 0 0
TPX2 0.078 0.07 0.14 223 -0.17 4 227
PAK1 0.02 0.005 -10000 0 -10000 0 0
SPC24 0.11 0.14 0.33 116 -10000 0 116
FBXW11 0.02 0.005 -10000 0 -10000 0 0
CLSPN 0.065 0.076 0.15 147 -0.19 5 152
GORASP1 0.021 0.004 -10000 0 -10000 0 0
metaphase 0 0.002 0.016 7 -0.011 1 8
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.015 0.02 0.045 77 -0.04 1 78
G2 phase of mitotic cell cycle 0 0.003 0.015 9 -10000 0 9
STAG2 0.021 0.003 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0.003 0.093 -10000 0 -0.51 12 12
spindle elongation 0.032 0.041 0.094 88 -0.08 1 89
ODF2 0.021 0.006 -10000 0 -10000 0 0
BUB1 0.076 0.1 -10000 0 -0.52 3 3
TPT1 0.009 0.047 0.12 1 -0.17 19 20
CDC25C 0.1 0.097 0.17 248 -0.23 12 260
CDC25B 0.022 0.012 -10000 0 -10000 0 0
SGOL1 0.053 0.065 0.12 185 -0.12 10 195
RHOA 0.021 0.004 -10000 0 -10000 0 0
CCNB1/CDK1 0.081 0.092 0.22 112 -10000 0 112
CDC14B -0.009 0.003 -10000 0 -10000 0 0
CDC20 0.2 0.15 0.33 231 -10000 0 231
PLK1/PBIP1 0.012 0.045 0.15 33 -10000 0 33
mitosis -0.003 0.006 0.019 6 -0.016 61 67
FBXO5 0.015 0.042 0.11 15 -0.097 7 22
CDC2 0.004 0.005 0.012 115 -0.01 6 121
NDC80 0.16 0.16 0.33 183 -10000 0 183
metaphase plate congression 0.021 0.047 -10000 0 -0.22 10 10
ERCC6L 0.087 0.11 0.23 129 -10000 0 129
NLP/gamma Tubulin 0.017 0.023 0.074 19 -0.086 3 22
microtubule cytoskeleton organization 0.009 0.047 0.12 1 -0.17 19 20
G2/M transition DNA damage checkpoint -0.001 0.002 0.014 1 -10000 0 1
PPP1R12A 0.021 0.005 -10000 0 -10000 0 0
interphase -0.001 0.002 0.014 1 -10000 0 1
PLK1/PRC1-2 0.18 0.16 0.31 211 -10000 0 211
GRASP65/GM130/RAB1/GTP/PLK1 0.053 0.032 -10000 0 -10000 0 0
RAB1A 0.021 0.001 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.026 0.037 0.085 85 -0.076 1 86
mitotic prometaphase 0.001 0.003 0.019 10 -10000 0 10
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.058 0.18 1 -0.26 3 4
microtubule-based process 0.15 0.12 0.26 215 -10000 0 215
Golgi organization 0.032 0.041 0.094 88 -0.08 1 89
Cohesin/SA2 0.039 0.032 0.12 9 -10000 0 9
PPP1CB/MYPT1 0.031 0.007 -10000 0 -10000 0 0
KIF20A 0.19 0.16 0.33 215 -10000 0 215
APC/C/CDC20 0.16 0.12 0.26 232 -10000 0 232
PPP2R1A 0.02 0.004 -10000 0 -10000 0 0
chromosome segregation 0.012 0.044 0.15 33 -10000 0 33
PRC1 0.075 0.12 0.33 68 -10000 0 68
ECT2 0.035 0.063 0.18 47 -10000 0 47
C13orf34 0.026 0.034 0.079 86 -0.068 2 88
NUDC 0.021 0.047 -10000 0 -0.22 10 10
regulation of attachment of spindle microtubules to kinetochore 0.077 0.077 0.15 182 -0.11 8 190
spindle assembly 0.024 0.032 0.089 37 -0.071 1 38
spindle stabilization 0.015 0.038 0.12 2 -0.16 11 13
APC/C/HCDH1 0.015 0.006 -10000 0 -10000 0 0
MKLP2/PLK1 0.15 0.12 0.26 215 -10000 0 215
CCNB1 0.12 0.14 0.33 121 -10000 0 121
PPP1CB 0.021 0.005 -10000 0 -10000 0 0
BTRC 0.021 0.003 -10000 0 -10000 0 0
ROCK2 0.027 0.036 0.17 2 -0.18 1 3
TUBG1 0.019 0.029 0.14 2 -0.2 3 5
G2/M transition of mitotic cell cycle 0.033 0.061 0.13 64 -10000 0 64
MLF1IP 0.007 0.046 0.16 32 -10000 0 32
INCENP 0.021 0.003 -10000 0 -10000 0 0
Aurora C signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.021 0.003 -10000 0 -10000 0 0
Aurora C/Aurora B/INCENP 0.12 0.096 0.22 186 -0.16 3 189
metaphase 0 0 -10000 0 -10000 0 0
mitosis 0 0 -10000 0 -10000 0 0
H3F3B 0.016 0.014 -10000 0 -10000 0 0
AURKB 0.17 0.16 0.33 194 -10000 0 194
AURKC 0.018 0.035 0.33 1 -0.33 3 4
Signaling mediated by p38-alpha and p38-beta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTGS2 -0.082 0.26 -10000 0 -0.66 57 57
MKNK1 0.021 0.003 -10000 0 -10000 0 0
MAPK14 -0.02 0.12 -10000 0 -0.29 57 57
ATF2/c-Jun -0.032 0.1 -10000 0 -0.26 55 55
MAPK11 -0.018 0.12 -10000 0 -0.31 52 52
MITF -0.042 0.14 -10000 0 -0.36 60 60
MAPKAPK5 -0.038 0.13 -10000 0 -0.35 56 56
KRT8 -0.037 0.13 0.27 2 -0.34 58 60
MAPKAPK3 0.021 0.004 -10000 0 -10000 0 0
MAPKAPK2 0.019 0.006 -10000 0 -10000 0 0
p38alpha-beta/CK2 -0.033 0.17 -10000 0 -0.41 59 59
CEBPB -0.035 0.13 -10000 0 -0.36 51 51
SLC9A1 -0.039 0.14 -10000 0 -0.36 57 57
mol:GDP 0 0 -10000 0 -10000 0 0
ATF2 -0.038 0.13 0.25 1 -0.34 59 60
p38alpha-beta/MNK1 -0.012 0.14 -10000 0 -0.34 56 56
JUN -0.031 0.1 -10000 0 -0.26 54 54
PPARGC1A -0.098 0.18 -10000 0 -0.33 127 127
USF1 -0.032 0.13 0.32 1 -0.35 50 51
RAB5/GDP/GDI1 -0.025 0.1 -10000 0 -0.26 57 57
NOS2 -0.078 0.26 0.33 4 -0.62 58 62
DDIT3 -0.036 0.13 0.23 1 -0.35 56 57
RAB5A 0.021 0.004 -10000 0 -10000 0 0
HSPB1 -0.037 0.12 0.26 9 -0.3 53 62
p38alpha-beta/HBP1 -0.013 0.14 -10000 0 -0.34 55 55
CREB1 -0.043 0.14 0.24 1 -0.37 59 60
RAB5/GDP 0.015 0.003 -10000 0 -10000 0 0
EIF4E -0.056 0.11 -10000 0 -0.32 49 49
RPS6KA4 -0.039 0.13 -10000 0 -0.35 58 58
PLA2G4A -0.027 0.13 0.19 50 -0.32 46 96
GDI1 -0.037 0.13 -10000 0 -0.35 56 56
TP53 -0.062 0.15 0.26 1 -0.43 53 54
RPS6KA5 -0.037 0.13 0.3 2 -0.35 56 58
ESR1 -0.042 0.15 0.28 1 -0.38 58 59
HBP1 0.02 0.005 -10000 0 -10000 0 0
MEF2C -0.037 0.13 -10000 0 -0.35 55 55
MEF2A -0.038 0.13 -10000 0 -0.35 56 56
EIF4EBP1 -0.047 0.15 0.26 1 -0.39 60 61
KRT19 -0.039 0.14 -10000 0 -0.36 57 57
ELK4 -0.034 0.13 -10000 0 -0.35 53 53
ATF6 -0.033 0.13 0.32 1 -0.35 51 52
ATF1 -0.043 0.14 0.24 2 -0.37 60 62
p38alpha-beta/MAPKAPK2 -0.013 0.14 -10000 0 -0.34 54 54
p38alpha-beta/MAPKAPK3 -0.014 0.14 -10000 0 -0.34 58 58
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin 0.037 0.046 0.2 18 -0.17 7 25
RGS9BP -0.028 0.12 -10000 0 -0.33 54 54
mol:GTP 0 0 -10000 0 -10000 0 0
GRK1 0.036 0.072 0.33 22 -10000 0 22
mol:Na + 0.1 0.11 0.24 146 -10000 0 146
mol:ADP -0.006 0.046 0.16 25 -10000 0 25
GNAT2 0.021 0.016 0.33 1 -10000 0 1
RGS9-1/Gbeta5/R9AP -0.061 0.13 -10000 0 -0.22 149 149
mol:GDP 0 0 -10000 0 -10000 0 0
PDE6H/GNAT2/GTP 0.025 0.016 0.21 2 -10000 0 2
GRK7 0.02 0.016 0.33 1 -10000 0 1
CNGB3 0.062 0.11 0.33 56 -10000 0 56
Cone Metarhodopsin II/X-Arrestin 0.014 0.011 0.22 1 -10000 0 1
mol:Ca2+ 0.056 0.093 0.21 81 -10000 0 81
Cone PDE6 -0.044 0.12 -10000 0 -0.19 146 146
Cone Metarhodopsin II 0.034 0.043 0.2 23 -10000 0 23
Na + (4 Units) 0.11 0.12 0.25 149 -10000 0 149
GNAT2/GDP -0.047 0.12 -10000 0 -0.19 149 149
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.016 0.019 0.17 3 -10000 0 3
Cone Transducin 0.04 0.05 0.22 18 -0.18 7 25
SLC24A2 0.044 0.086 0.33 32 -10000 0 32
GNB3/GNGT2 0.034 0.057 0.24 18 -0.23 7 25
GNB3 0.033 0.068 0.33 18 -0.33 1 19
GNAT2/GTP 0.015 0.011 0.22 1 -10000 0 1
CNGA3 0.12 0.14 0.33 125 -10000 0 125
ARR3 0.019 0.016 0.33 1 -10000 0 1
absorption of light 0 0 -10000 0 -10000 0 0
cGMP/Cone CNG Channel 0.1 0.11 0.24 146 -10000 0 146
mol:Pi -0.061 0.13 -10000 0 -0.22 149 149
Cone CNG Channel 0.093 0.092 0.21 128 -10000 0 128
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
mol:K + 0.044 0.086 0.33 32 -10000 0 32
RGS9 -0.088 0.16 -10000 0 -0.33 121 121
PDE6C 0.018 0.003 -10000 0 -10000 0 0
GNGT2 0.015 0.043 -10000 0 -0.33 6 6
mol:cGMP (4 units) 0 0 -10000 0 -10000 0 0
PDE6H 0.018 0.017 0.33 1 -10000 0 1
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.006 0.051 -10000 0 -0.33 7 7
Crk/p130 Cas/Paxillin -0.06 0.089 -10000 0 -0.23 71 71
JUN -0.035 0.091 0.16 9 -0.19 76 85
HRAS 0.021 0.004 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/GRB10 0.01 0.11 0.24 36 -0.18 78 114
RAP1A 0.02 0.004 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GDP 0.015 0.003 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 0.008 0.12 0.24 39 -0.18 88 127
EntrezGene:5979 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.016 0.091 0.22 5 -0.18 89 94
RHOA 0.021 0.004 -10000 0 -10000 0 0
RAP1A/GTP 0.005 0.1 0.2 36 -0.16 85 121
GRB7 0.019 0.025 -10000 0 -0.33 2 2
RET51/GFRalpha1/GDNF 0.006 0.12 0.24 36 -0.18 90 126
MAPKKK cascade -0.047 0.091 0.17 8 -0.21 62 70
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
RET9/GFRalpha1/GDNF/IRS1 -0.015 0.092 0.22 6 -0.18 90 96
lamellipodium assembly -0.04 0.089 0.13 1 -0.21 60 61
RET51/GFRalpha1/GDNF/SHC 0.009 0.11 0.24 35 -0.18 74 109
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.011 0.083 0.22 4 -0.18 73 77
RET9/GFRalpha1/GDNF/Shank3 -0.016 0.093 0.22 6 -0.18 90 96
MAPK3 -0.02 0.1 0.17 52 -0.3 1 53
DOK1 0.021 0.002 -10000 0 -10000 0 0
DOK6 -0.006 0.09 -10000 0 -0.33 28 28
PXN 0.021 0.004 -10000 0 -10000 0 0
neurite development -0.028 0.092 0.2 5 -0.24 12 17
DOK5 0.063 0.11 0.33 55 -10000 0 55
GFRA1 -0.081 0.16 0.33 1 -0.33 115 116
MAPK8 -0.04 0.089 0.15 7 -0.19 79 86
HRAS/GTP -0.006 0.12 0.34 2 -0.21 76 78
tube development -0.014 0.09 0.2 12 -0.17 83 95
MAPK1 -0.02 0.097 0.22 12 -0.3 1 13
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.032 0.084 0.15 3 -0.19 78 81
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
PDLIM7 0.02 0.005 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok6 -0.002 0.13 0.24 32 -0.2 87 119
SHC1 0.018 0.008 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 0.009 0.12 0.24 38 -0.18 86 124
RET51/GFRalpha1/GDNF/Dok5 0.023 0.13 0.25 58 -0.17 79 137
PRKCA 0.019 0.025 -10000 0 -0.33 2 2
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
CREB1 -0.023 0.095 0.2 2 -0.23 57 59
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.027 0.082 0.16 4 -0.2 67 71
RET51/GFRalpha1/GDNF/Grb7 0.007 0.12 0.24 39 -0.18 90 129
mol:GDP 0 0 -10000 0 -10000 0 0
RET 0.061 0.11 0.33 54 -0.33 3 57
DOK4 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.034 0.092 0.24 2 -0.25 10 12
RET9/GFRalpha1/GDNF/FRS2 -0.014 0.089 0.22 6 -0.18 84 90
SHANK3 0.017 0.031 -10000 0 -0.33 3 3
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.024 0.078 0.16 4 -0.19 65 69
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.021 0.096 0.18 9 -0.19 72 81
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.025 0.1 0.18 6 -0.2 80 86
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.012 0.09 0.19 10 -0.2 57 67
PI3K -0.05 0.14 0.23 4 -0.29 72 76
SOS1 0.021 0.003 -10000 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.007 0.093 0.21 6 -0.17 85 91
GRB10 0.019 0.007 -10000 0 -10000 0 0
activation of MAPKK activity -0.022 0.086 0.16 10 -0.18 70 80
RET51/GFRalpha1/GDNF/FRS2 0.008 0.12 0.23 40 -0.17 87 127
GAB1 0.02 0.018 -10000 0 -0.33 1 1
IRS1 0.02 0.018 -10000 0 -0.33 1 1
IRS2 0.019 0.018 -10000 0 -0.33 1 1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.015 0.095 0.18 12 -0.2 61 73
RET51/GFRalpha1/GDNF/PKC alpha 0.008 0.12 0.24 36 -0.18 87 123
GRB2 0.02 0.004 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GDNF 0.021 0.043 0.33 7 -10000 0 7
RAC1 0.019 0.007 -10000 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 0.007 0.12 0.24 37 -0.18 90 127
Rac1/GTP -0.034 0.11 0.22 1 -0.25 56 57
RET9/GFRalpha1/GDNF -0.025 0.094 0.21 6 -0.19 89 95
GFRalpha1/GDNF -0.032 0.11 0.24 6 -0.23 89 95
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.027 0.29 0.53 31 -0.62 25 56
PCK1 0.06 0.24 0.56 40 -0.57 2 42
HNF4A -0.1 0.47 0.68 46 -0.77 90 136
KCNJ11 0.012 0.3 0.58 30 -0.72 17 47
AKT1 0.037 0.19 0.41 36 -0.53 2 38
response to starvation -0.026 0.075 0.15 3 -0.21 30 33
DLK1 0.034 0.3 0.59 38 -0.65 9 47
NKX2-1 -0.051 0.34 0.52 7 -1.1 29 36
ACADM -0.029 0.29 0.51 31 -0.62 25 56
TAT 0.049 0.23 0.53 40 -0.47 1 41
CEBPB 0.027 0.02 -10000 0 -10000 0 0
CEBPA 0.014 0.082 0.22 3 -0.32 19 22
TTR 0.068 0.29 0.64 42 -0.72 8 50
PKLR -0.001 0.3 0.57 36 -0.62 23 59
APOA1 -0.2 0.61 0.73 37 -1 111 148
CPT1C -0.026 0.3 0.52 33 -0.61 27 60
ALAS1 0.03 0.19 0.49 12 -0.56 1 13
TFRC 0.078 0.3 0.64 47 -0.88 7 54
FOXF1 -0.007 0.12 0.24 17 -0.33 42 59
NF1 0.022 0.004 -10000 0 -10000 0 0
HNF1A (dimer) 0.1 0.16 0.4 74 -0.33 1 75
CPT1A -0.024 0.29 0.52 32 -0.61 25 57
HMGCS1 0.001 0.3 0.58 34 -0.61 24 58
NR3C1 0.043 0.046 0.21 7 -10000 0 7
CPT1B -0.027 0.29 0.53 29 -0.62 26 55
chromatin remodeling 0 0 -10000 0 -10000 0 0
SP1 0.041 0.04 -10000 0 -10000 0 0
GCK -0.022 0.31 0.55 33 -0.64 29 62
CREB1 0.037 0.039 0.19 6 -10000 0 6
IGFBP1 0.029 0.21 0.51 31 -0.52 1 32
PDX1 0.094 0.27 0.67 48 -0.55 1 49
UCP2 -0.025 0.3 0.52 34 -0.6 28 62
ALDOB 0.031 0.31 0.64 37 -0.63 20 57
AFP 0.084 0.11 0.34 36 -10000 0 36
BDH1 -0.027 0.29 0.53 31 -0.62 24 55
HADH 0.016 0.28 0.56 31 -0.62 12 43
F2 -0.023 0.43 0.78 42 -0.8 31 73
HNF1A 0.1 0.16 0.4 74 -0.33 1 75
G6PC 0.078 0.13 0.48 18 -10000 0 18
SLC2A2 0.078 0.29 0.67 46 -0.74 2 48
INS -0.033 0.036 -10000 0 -10000 0 0
FOXA1 0.071 0.1 0.31 43 -0.33 1 44
FOXA3 0.15 0.19 0.42 107 -0.29 3 110
FOXA2 0.054 0.38 0.81 44 -0.67 19 63
ABCC8 -0.01 0.36 0.62 33 -0.77 40 73
ALB 0.094 0.12 0.34 51 -10000 0 51
IL4-mediated signaling events

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
BCL2L1 -0.32 0.56 0.74 4 -1.2 79 83
STAT6 (cleaved dimer) -0.34 0.55 -10000 0 -1.2 92 92
IGHG1 -0.089 0.24 0.44 10 -0.62 12 22
IGHG3 -0.31 0.54 0.62 3 -1.1 106 109
AKT1 -0.15 0.32 0.52 2 -0.89 29 31
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.12 0.3 0.5 2 -0.9 28 30
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.14 0.32 0.5 4 -0.89 27 31
THY1 -0.32 0.56 0.69 4 -1.2 80 84
MYB 0.022 0.028 0.33 3 -10000 0 3
HMGA1 0.05 0.092 0.33 38 -10000 0 38
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.17 0.36 0.53 8 -0.73 62 70
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.15 0.33 0.5 4 -0.91 27 31
SP1 0.026 0.026 -10000 0 -10000 0 0
INPP5D 0.018 0.031 -10000 0 -0.33 3 3
SOCS5 0.011 0.037 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.32 0.55 0.61 2 -1.2 80 82
SOCS1 -0.2 0.36 0.52 3 -0.74 75 78
SOCS3 -0.14 0.3 0.52 2 -0.79 27 29
FCER2 -0.25 0.49 0.7 8 -1 69 77
PARP14 0.023 0.011 -10000 0 -10000 0 0
CCL17 -0.38 0.63 0.74 4 -1.3 90 94
GRB2 0.02 0.004 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.27 0.5 4 -0.73 27 31
T cell proliferation -0.33 0.56 0.63 2 -1.2 81 83
IL4R/JAK1 -0.33 0.56 0.64 2 -1.2 82 84
EGR2 -0.34 0.6 0.76 3 -1.3 80 83
JAK2 -0.008 0.063 0.19 2 -0.37 1 3
JAK3 0.02 0.016 -10000 0 -10000 0 0
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
JAK1 0.002 0.034 -10000 0 -10000 0 0
COL1A2 -0.068 0.22 0.47 2 -1.3 3 5
CCL26 -0.31 0.57 0.7 8 -1.2 79 87
IL4R -0.34 0.6 0.8 4 -1.3 78 82
PTPN6 0.016 0.03 -10000 0 -10000 0 0
IL13RA2 -0.36 0.62 0.68 5 -1.3 93 98
IL13RA1 -0.008 0.065 0.19 3 -10000 0 3
IRF4 -0.059 0.25 0.55 2 -0.96 19 21
ARG1 -0.096 0.25 0.53 3 -0.71 23 26
CBL -0.16 0.33 0.54 3 -0.7 58 61
GTF3A 0.062 0.06 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.003 0.088 0.23 13 -0.28 1 14
IRF4/BCL6 -0.063 0.23 -10000 0 -0.86 20 20
CD40LG 0.01 0.078 -10000 0 -0.33 18 18
MAPK14 -0.16 0.33 0.54 3 -0.71 56 59
mitosis -0.14 0.3 0.48 3 -0.83 29 32
STAT6 -0.37 0.69 0.79 7 -1.4 90 97
SPI1 0.004 0.08 -10000 0 -0.33 21 21
RPS6KB1 -0.14 0.29 0.49 2 -0.8 28 30
STAT6 (dimer) -0.37 0.69 0.79 7 -1.4 90 97
STAT6 (dimer)/PARP14 -0.35 0.61 0.71 2 -1.3 90 92
mast cell activation 0.005 0.018 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.18 0.36 0.49 4 -0.87 49 53
FRAP1 -0.15 0.32 0.52 2 -0.89 29 31
LTA -0.32 0.56 0.76 5 -1.2 79 84
FES 0.02 0.018 -10000 0 -0.33 1 1
T-helper 1 cell differentiation 0.36 0.65 1.3 91 -0.77 8 99
CCL11 -0.33 0.56 0.66 1 -1.2 85 86
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.15 0.33 0.49 4 -0.92 30 34
IL2RG 0.017 0.037 -10000 0 -0.31 4 4
IL10 -0.32 0.57 0.74 6 -1.2 80 86
IRS1 0.02 0.018 -10000 0 -0.33 1 1
IRS2 0.019 0.018 -10000 0 -0.33 1 1
IL4 -0.071 0.26 0.55 3 -1.1 15 18
IL5 -0.33 0.56 0.7 3 -1.2 80 83
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.27 0.5 0.65 10 -0.98 88 98
COL1A1 -0.022 0.29 0.57 13 -0.88 13 26
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.34 0.57 -10000 0 -1.3 77 77
IL2R gamma/JAK3 0.028 0.03 -10000 0 -0.19 4 4
TFF3 -0.32 0.6 0.7 9 -1.3 85 94
ALOX15 -0.65 0.72 0.7 3 -1.3 198 201
MYBL1 0.023 0.036 0.33 5 -10000 0 5
T-helper 2 cell differentiation -0.26 0.47 0.66 3 -0.99 77 80
SHC1 0.018 0.008 -10000 0 -10000 0 0
CEBPB 0.021 0.012 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.31 0.5 3 -0.81 28 31
mol:PI-3-4-5-P3 -0.15 0.32 0.52 2 -0.89 29 31
PI3K -0.16 0.34 0.52 2 -0.98 29 31
DOK2 -0.006 0.088 -10000 0 -0.33 27 27
ETS1 0.012 0.037 -10000 0 -0.15 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.098 0.25 0.46 5 -0.65 25 30
ITGB3 -0.32 0.57 0.69 5 -1.2 83 88
PIGR -0.45 0.7 0.76 5 -1.4 122 127
IGHE 0.01 0.077 0.2 19 -0.2 7 26
MAPKKK cascade -0.096 0.25 0.46 5 -0.64 25 30
BCL6 0.018 0.013 -10000 0 -10000 0 0
OPRM1 -0.33 0.56 0.7 3 -1.2 81 84
RETNLB -0.32 0.56 0.7 3 -1.2 79 82
SELP -0.42 0.68 0.74 4 -1.4 109 113
AICDA -0.35 0.57 0.75 2 -1.2 89 91
Osteopontin-mediated 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
IKK alpha homodimer 0.079 0.077 0.2 61 -10000 0 61
NF kappa B1 p50/RelA/I kappa B alpha 0.086 0.094 0.28 28 -0.28 1 29
alphaV/beta3 Integrin/Osteopontin/Src 0.19 0.096 0.25 283 -10000 0 283
AP1 0.078 0.11 0.26 57 -10000 0 57
ILK 0.071 0.07 0.24 20 -10000 0 20
bone resorption 0.047 0.072 0.23 14 -10000 0 14
PTK2B 0.017 0.019 -10000 0 -0.33 1 1
PYK2/p130Cas 0.14 0.12 0.29 61 -10000 0 61
ITGAV 0.026 0.009 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 0.029 0.024 -10000 0 -0.23 3 3
alphaV/beta3 Integrin/Osteopontin 0.19 0.12 0.26 277 -0.2 3 280
MAP3K1 0.07 0.069 0.21 29 -10000 0 29
JUN 0.019 0.025 -10000 0 -0.33 2 2
MAPK3 0.064 0.084 0.22 66 -10000 0 66
MAPK1 0.063 0.081 0.22 60 -10000 0 60
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.048 0.061 0.21 20 -10000 0 20
ITGB3 0.038 0.081 0.34 21 -0.33 4 25
NFKBIA 0.059 0.086 0.23 62 -10000 0 62
FOS -0.004 0.09 -10000 0 -0.33 28 28
CD44 0.017 0.035 -10000 0 -0.33 4 4
CHUK 0.021 0.003 -10000 0 -10000 0 0
PLAU 0.089 0.14 0.44 14 -10000 0 14
NF kappa B1 p50/RelA 0.09 0.1 0.27 65 -10000 0 65
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
RELA 0.021 0.003 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.047 0.06 0.26 21 -0.23 4 25
mol:GDP 0 0 -10000 0 -10000 0 0
SYK 0.069 0.069 0.21 31 -0.18 4 35
VAV3 0.045 0.064 0.21 22 -0.23 4 26
MAP3K14 0.079 0.078 0.21 65 -10000 0 65
ROCK2 0.021 0.002 -10000 0 -10000 0 0
SPP1 0.25 0.14 0.34 286 -10000 0 286
RAC1 0.019 0.007 -10000 0 -10000 0 0
Rac1/GTP 0.038 0.06 0.18 17 -0.26 2 19
MMP2 0.032 0.076 0.3 6 -10000 0 6
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.021 0.017 0.33 1 -10000 0 1
LAT2 -0.073 0.13 -10000 0 -0.31 67 67
AP1 -0.083 0.2 -10000 0 -0.46 62 62
mol:PIP3 -0.079 0.18 0.3 16 -0.38 61 77
IKBKB -0.03 0.12 0.25 27 -0.23 46 73
AKT1 -0.039 0.15 0.32 37 -0.27 33 70
IKBKG -0.04 0.11 0.23 19 -0.22 53 72
MS4A2 -0.063 0.14 -10000 0 -0.32 89 89
mol:Sphingosine-1-phosphate 0 0 -10000 0 -10000 0 0
PIK3CA 0.019 0.007 -10000 0 -10000 0 0
MAP3K1 -0.067 0.15 0.23 9 -0.35 54 63
mol:Ca2+ -0.058 0.14 0.26 20 -0.29 61 81
LYN 0.01 0.019 -10000 0 -10000 0 0
CBLB -0.074 0.12 -10000 0 -0.31 68 68
SHC1 0.018 0.008 -10000 0 -10000 0 0
RasGAP/p62DOK 0.019 0.059 -10000 0 -0.18 31 31
positive regulation of cell migration 0 0 -10000 0 -10000 0 0
INPP5D 0.018 0.031 -10000 0 -0.33 3 3
PLD2 -0.045 0.15 0.29 41 -0.24 81 122
PTPN13 -0.091 0.17 -10000 0 -0.46 38 38
PTPN11 0.009 0.025 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
regulation of mast cell degranulation -0.048 0.12 0.29 11 -0.28 33 44
SYK 0.011 0.031 -10000 0 -0.33 2 2
GRB2 0.02 0.004 -10000 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.087 0.16 -10000 0 -0.36 78 78
LAT -0.074 0.13 -10000 0 -0.31 69 69
PAK2 -0.072 0.16 0.24 8 -0.38 57 65
NFATC2 -0.032 0.086 -10000 0 -0.48 10 10
HRAS -0.074 0.17 0.25 7 -0.41 56 63
GAB2 0.017 0.035 -10000 0 -0.33 4 4
PLA2G1B -0.047 0.16 -10000 0 -0.92 12 12
Fc epsilon R1 -0.056 0.14 0.22 1 -0.26 122 123
Antigen/IgE/Fc epsilon R1 -0.048 0.13 0.21 1 -0.23 121 122
mol:GDP -0.09 0.18 -10000 0 -0.45 57 57
JUN 0.019 0.025 -10000 0 -0.33 2 2
mol:Ca++ 0 0 -10000 0 -10000 0 0
PIK3R1 0.019 0.007 -10000 0 -10000 0 0
FOS -0.005 0.09 -10000 0 -0.33 28 28
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.07 0.14 -10000 0 -0.31 72 72
CHUK -0.045 0.11 0.22 18 -0.22 53 71
KLRG1 -0.065 0.11 0.14 1 -0.27 67 68
VAV1 -0.07 0.13 -10000 0 -0.31 64 64
calcium-dependent protein kinase C activity 0 0 -10000 0 -10000 0 0
CBL -0.072 0.12 -10000 0 -0.3 67 67
negative regulation of mast cell degranulation -0.057 0.12 -10000 0 -0.32 44 44
BTK -0.097 0.2 -10000 0 -0.49 61 61
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.081 0.15 -10000 0 -0.32 94 94
GAB2/PI3K/SHP2 -0.08 0.085 -10000 0 -0.23 81 81
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.066 0.13 -10000 0 -0.27 87 87
RAF1 -0.011 0.17 -10000 0 -0.97 12 12
Fc epsilon R1/FcgammaRIIB/SHIP -0.035 0.14 0.22 1 -0.23 114 115
FCER1G 0.01 0.047 -10000 0 -0.33 6 6
FCER1A -0.067 0.15 0.33 1 -0.34 90 91
Antigen/IgE/Fc epsilon R1/Fyn -0.042 0.13 0.21 1 -0.22 117 118
MAPK3 -0.014 0.16 -10000 0 -0.89 12 12
MAPK1 -0.017 0.16 -10000 0 -0.9 12 12
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.069 0.22 -10000 0 -0.62 45 45
DUSP1 -0.008 0.094 -10000 0 -0.33 31 31
NF-kappa-B/RelA -0.033 0.064 0.13 8 -0.15 37 45
actin cytoskeleton reorganization -0.074 0.16 -10000 0 -0.44 35 35
mol:Glucocorticoid Dexamethasone 0 0 -10000 0 -10000 0 0
PI3K -0.063 0.15 -10000 0 -0.37 52 52
FER -0.072 0.12 -10000 0 -0.31 67 67
RELA 0.021 0.003 -10000 0 -10000 0 0
ITK -0.024 0.065 -10000 0 -0.27 18 18
SOS1 0.021 0.003 -10000 0 -10000 0 0
PLCG1 -0.089 0.18 0.26 3 -0.44 59 62
cytokine secretion -0.029 0.039 -10000 0 -0.15 3 3
SPHK1 -0.072 0.12 -10000 0 -0.3 67 67
PTK2 -0.078 0.17 -10000 0 -0.53 18 18
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.087 0.16 0.22 1 -0.36 79 80
EDG1 0 0 -10000 0 -10000 0 0
mol:DAG -0.077 0.18 0.28 18 -0.37 63 81
MAP2K2 -0.018 0.16 -10000 0 -0.9 12 12
MAP2K1 -0.017 0.16 -10000 0 -0.91 12 12
MAP2K7 0.02 0.005 -10000 0 -10000 0 0
KLRG1/SHP2 -0.05 0.11 0.17 1 -0.28 45 46
MAP2K4 -0.1 0.33 -10000 0 -0.92 53 53
Fc epsilon R1/FcgammaRIIB -0.042 0.14 0.22 1 -0.23 121 122
mol:Choline -0.044 0.15 0.29 41 -0.24 81 122
SHC/Grb2/SOS1 -0.043 0.13 -10000 0 -0.3 57 57
FYN 0.018 0.019 -10000 0 -0.33 1 1
DOK1 0.021 0.002 -10000 0 -10000 0 0
PXN -0.075 0.16 0.34 1 -0.43 33 34
HCLS1 -0.073 0.13 -10000 0 -0.31 66 66
PRKCB -0.06 0.14 0.26 19 -0.29 62 81
FCGR2B 0.019 0.007 -10000 0 -10000 0 0
IGHE -0.001 0.007 -10000 0 -10000 0 0
KLRG1/SHIP -0.058 0.12 -10000 0 -0.32 44 44
LCP2 0.018 0.025 -10000 0 -0.33 2 2
PLA2G4A -0.066 0.12 0.19 1 -0.31 62 63
RASA1 0.02 0.005 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.044 0.15 0.29 41 -0.24 81 122
IKK complex -0.022 0.1 0.24 24 -0.18 30 54
WIPF1 0.021 0.003 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS 0.022 0.11 0.24 26 -0.19 65 91
SMAD6-7/SMURF1 0.01 0.076 -10000 0 -0.2 43 43
NOG 0.01 0.091 0.33 9 -0.33 20 29
SMAD9 -0.11 0.22 -10000 0 -0.46 102 102
SMAD4 0.019 0.007 -10000 0 -10000 0 0
SMAD5 -0.046 0.1 -10000 0 -0.34 22 22
BMP7/USAG1 -0.12 0.14 0.24 7 -0.24 214 221
SMAD5/SKI -0.035 0.11 0.24 2 -0.36 21 23
SMAD1 -0.003 0.055 -10000 0 -0.29 6 6
BMP2 -0.023 0.11 -10000 0 -0.33 48 48
SMAD1/SMAD1/SMAD4 -0.01 0.073 -10000 0 -0.32 5 5
BMPR1A 0.021 0.003 -10000 0 -10000 0 0
BMPR1B -0.012 0.11 0.33 3 -0.33 39 42
BMPR1A-1B/BAMBI 0.022 0.083 0.23 13 -0.2 40 53
AHSG 0.04 0.079 0.33 27 -10000 0 27
CER1 0.02 0.032 0.33 4 -10000 0 4
BMP2-4/CER1 0.005 0.082 0.23 2 -0.2 51 53
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.035 0.1 -10000 0 -0.32 28 28
BMP2-4 (homodimer) -0.007 0.091 -10000 0 -0.24 52 52
RGMB 0.02 0.005 -10000 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.002 0.11 0.23 4 -0.2 83 87
RGMA 0.024 0.046 0.33 6 -0.33 2 8
SMURF1 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.03 0.086 -10000 0 -0.3 17 17
BMP2-4/USAG1 -0.12 0.13 -10000 0 -0.22 221 221
SMAD6/SMURF1/SMAD5 -0.033 0.11 0.24 2 -0.37 18 20
SOSTDC1 -0.18 0.17 -10000 0 -0.33 221 221
BMP7/BMPR2/BMPR1A-1B 0.014 0.1 0.23 14 -0.19 64 78
SKI 0.02 0.004 -10000 0 -10000 0 0
BMP6 (homodimer) -0.029 0.12 0.33 2 -0.33 57 59
HFE2 0.025 0.042 0.33 7 -10000 0 7
ZFYVE16 0.02 0.005 -10000 0 -10000 0 0
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
BMP2-4/CHRD 0.013 0.084 0.23 9 -0.19 48 57
SMAD5/SMAD5/SMAD4 -0.033 0.11 0.24 2 -0.36 20 22
MAPK1 0.02 0.005 -10000 0 -10000 0 0
TAK1/TAB family -0.016 0.088 -10000 0 -0.29 13 13
BMP7 (homodimer) 0 0.12 0.33 15 -0.33 35 50
NUP214 0.021 0.004 -10000 0 -10000 0 0
BMP6/FETUA 0.008 0.11 0.24 27 -0.23 52 79
SMAD1/SKI 0.009 0.06 -10000 0 -0.3 4 4
SMAD6 -0.023 0.12 -10000 0 -0.33 49 49
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
BMP2-4/FETUA 0.019 0.094 0.23 24 -0.2 48 72
MAP3K7IP1 0 0 -10000 0 -10000 0 0
GREM1 0.23 0.14 0.33 268 -10000 0 268
BMPR2 (homodimer) 0.021 0.003 -10000 0 -10000 0 0
GADD34/PP1CA 0.037 0.022 -10000 0 -0.2 2 2
BMPR1A-1B (homodimer) 0.006 0.081 0.24 3 -0.23 39 42
CHRDL1 -0.097 0.16 -10000 0 -0.33 132 132
ENDOFIN/SMAD1 0.009 0.059 -10000 0 -0.3 3 3
SMAD6-7/SMURF1/SMAD1 -0.001 0.083 -10000 0 -0.33 6 6
SMAD6/SMURF1 0.02 0.005 -10000 0 -10000 0 0
BAMBI 0.027 0.062 0.33 12 -0.33 3 15
SMURF2 0.021 0.004 -10000 0 -10000 0 0
BMP2-4/CHRDL1 -0.064 0.14 -10000 0 -0.23 147 147
BMP2-4/GREM1 0.11 0.14 0.23 216 -0.16 50 266
SMAD7 0.018 0.019 -10000 0 -0.33 1 1
SMAD8A/SMAD8A/SMAD4 -0.1 0.21 -10000 0 -0.44 103 103
SMAD1/SMAD6 0.007 0.062 -10000 0 -0.28 6 6
TAK1/SMAD6 0.027 0.012 -10000 0 -10000 0 0
BMP7 0 0.12 0.33 15 -0.33 35 50
BMP6 -0.029 0.13 0.33 2 -0.33 57 59
MAP3K7IP2 0 0 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.036 0.099 -10000 0 -0.31 28 28
PPM1A 0.02 0.004 -10000 0 -10000 0 0
SMAD1/SMURF2 0.007 0.061 -10000 0 -0.28 5 5
SMAD7/SMURF1 0.026 0.017 -10000 0 -0.23 1 1
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
PPP1CA 0.021 0.004 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
PPP1R15A 0.019 0.025 -10000 0 -0.33 2 2
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.032 0.1 -10000 0 -0.32 24 24
CHRD 0.03 0.059 0.33 13 -0.33 1 14
BMPR2 0.021 0.003 -10000 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.035 0.092 -10000 0 -0.32 17 17
BMP4 0.015 0.054 0.33 2 -0.33 8 10
FST 0.028 0.089 0.33 21 -0.33 9 30
BMP2-4/NOG 0 0.1 0.23 6 -0.22 60 66
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 0.022 0.096 0.23 12 -0.19 56 68
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.008 0.1 0.46 14 -10000 0 14
VDR 0.021 0.024 0.33 1 -0.33 1 2
FAM120B 0.019 0.006 -10000 0 -10000 0 0
RXRs/LXRs/DNA/9cRA -0.087 0.12 -10000 0 -0.34 26 26
RXRs/LXRs/DNA/Oxysterols -0.091 0.14 -10000 0 -0.46 28 28
MED1 0.021 0.004 -10000 0 -10000 0 0
mol:9cRA -0.001 0.012 -10000 0 -0.1 2 2
RARs/THRs/DNA/Src-1 -0.009 0.066 -10000 0 -0.19 45 45
RXRs/NUR77 -0.092 0.13 -10000 0 -0.21 202 202
RXRs/PPAR -0.11 0.13 -10000 0 -0.23 190 190
NCOR2 0.021 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.016 0.22 1 -0.22 1 2
RARs/VDR/DNA/Vit D3 0.045 0.026 0.21 1 -0.17 3 4
RARA 0.021 0.004 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.024 0.33 1 -0.33 1 2
RARs/RARs/DNA/9cRA 0.031 0.023 -10000 0 -0.17 2 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RPS6KB1 0.029 0.11 0.62 12 -10000 0 12
RARs/THRs/DNA/SMRT -0.01 0.067 -10000 0 -0.19 44 44
THRA 0.021 0.004 -10000 0 -10000 0 0
mol:Bile acids 0 0 -10000 0 -10000 0 0
VDR/Vit D3/DNA 0.015 0.016 0.22 1 -0.22 1 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.065 0.11 -10000 0 -0.18 173 173
NR1H4 0.042 0.08 0.33 28 -10000 0 28
RXRs/LXRs/DNA -0.055 0.12 -10000 0 -0.27 15 15
NR1H2 0.018 0.018 -10000 0 -10000 0 0
NR1H3 0.018 0.02 -10000 0 -0.13 1 1
RXRs/VDR/DNA/Vit D3 -0.056 0.11 -10000 0 -0.17 169 169
NR4A1 -0.047 0.14 -10000 0 -0.33 76 76
mol:ATRA 0 0 -10000 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.069 0.097 -10000 0 -0.18 159 159
RXRG -0.14 0.17 -10000 0 -0.33 174 174
RXR alpha/CCPG 0.025 0.018 -10000 0 -10000 0 0
RXRA 0.017 0.019 -10000 0 -10000 0 0
RXRB 0.018 0.017 -10000 0 -10000 0 0
THRB -0.011 0.099 -10000 0 -0.33 35 35
PPARG -0.023 0.12 -10000 0 -0.33 49 49
PPARD 0.02 0.004 -10000 0 -10000 0 0
TNF -0.11 0.21 -10000 0 -0.9 21 21
mol:Oxysterols -0.001 0.011 -10000 0 -0.087 1 1
cholesterol transport -0.091 0.14 -10000 0 -0.45 28 28
PPARA 0.02 0.005 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RARB 0.019 0.025 -10000 0 -0.33 2 2
RXRs/NUR77/BCL2 -0.12 0.13 -10000 0 -0.23 200 200
SREBF1 -0.081 0.13 -10000 0 -0.47 21 21
RXRs/RXRs/DNA/9cRA -0.065 0.11 -10000 0 -0.18 173 173
ABCA1 -0.084 0.13 -10000 0 -0.5 17 17
RARs/THRs 0.037 0.07 -10000 0 -0.18 34 34
RXRs/FXR -0.053 0.12 0.23 13 -0.18 160 173
BCL2 0.02 0.017 0.33 1 -10000 0 1
Syndecan-1-mediated signaling events

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
TGFB1 0.021 0.004 -10000 0 -10000 0 0
CCL5 0.017 0.035 -10000 0 -0.33 4 4
SDCBP 0.019 0.007 -10000 0 -10000 0 0
FGFR/FGF2/Syndecan-1 0.079 0.08 0.19 73 -0.23 3 76
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
Syndecan-1/Laminin-5 0.07 0.09 0.23 26 -0.26 7 33
Syndecan-1/Syntenin 0.069 0.091 0.23 28 -0.29 5 33
MAPK3 0.055 0.088 0.21 31 -0.28 4 35
HGF/MET 0.015 0.076 0.24 8 -0.24 27 35
TGFB1/TGF beta receptor Type II 0.02 0.004 -10000 0 -10000 0 0
BSG 0.02 0.006 -10000 0 -10000 0 0
keratinocyte migration 0.069 0.089 0.22 26 -0.25 7 33
Syndecan-1/RANTES 0.074 0.094 0.23 29 -0.25 9 38
Syndecan-1/CD147 0.082 0.092 0.24 29 -0.29 4 33
Syndecan-1/Syntenin/PIP2 0.064 0.085 0.21 25 -0.28 5 30
LAMA5 0.017 0.031 -10000 0 -0.33 3 3
positive regulation of cell-cell adhesion 0.062 0.083 0.21 25 -0.27 5 30
MMP7 0.063 0.12 0.33 61 -0.33 6 67
HGF 0.008 0.075 0.33 3 -0.33 16 19
Syndecan-1/CASK 0.057 0.085 0.15 103 -0.22 12 115
Syndecan-1/HGF/MET 0.067 0.1 0.24 30 -0.34 6 36
regulation of cell adhesion 0.046 0.081 0.19 31 -0.28 4 35
HPSE 0.023 0.022 0.33 2 -10000 0 2
positive regulation of cell migration 0.079 0.08 0.19 73 -0.23 3 76
SDC1 0.078 0.079 0.18 105 -0.23 3 108
Syndecan-1/Collagen 0.079 0.08 0.19 73 -0.23 3 76
PPIB 0.021 0.016 0.33 1 -10000 0 1
MET 0.012 0.072 0.33 5 -0.33 13 18
PRKACA 0.02 0.005 -10000 0 -10000 0 0
MMP9 0.071 0.12 0.33 65 -10000 0 65
MAPK1 0.055 0.085 0.2 30 -0.28 4 34
homophilic cell adhesion 0.074 0.091 0.23 37 -0.23 4 41
MMP1 0.22 0.15 0.33 253 -0.33 2 255
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 0.006 0.079 0.23 1 -0.3 15 16
alphaM/beta2 Integrin/GPIbA 0.003 0.084 0.23 1 -0.29 20 21
alphaM/beta2 Integrin/proMMP-9 0.039 0.1 0.22 63 -0.26 14 77
PLAUR 0.02 0.005 -10000 0 -10000 0 0
HMGB1 0.005 0.03 -10000 0 -10000 0 0
alphaM/beta2 Integrin/Talin 0.006 0.08 -10000 0 -0.3 16 16
AGER -0.3 0.11 -10000 0 -0.34 344 344
RAP1A 0.02 0.004 -10000 0 -10000 0 0
SELPLG 0.01 0.06 -10000 0 -0.33 12 12
mol:LDL 0 0 -10000 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.2 0.12 -10000 0 -0.23 341 341
mol:GTP 0 0 -10000 0 -10000 0 0
MMP9 0.071 0.12 0.33 65 -10000 0 65
CYR61 0.005 0.073 -10000 0 -0.33 18 18
TLN1 0.019 0.018 -10000 0 -0.33 1 1
Rap1/GTP -0.049 0.14 -10000 0 -0.36 39 39
RHOA 0.021 0.004 -10000 0 -10000 0 0
P-selectin oligomer -0.047 0.14 -10000 0 -0.33 74 74
MYH2 -0.1 0.16 0.22 2 -0.38 65 67
MST1R 0.021 0.024 0.33 1 -0.33 1 2
leukocyte activation during inflammatory response 0.01 0.088 0.2 17 -0.22 29 46
APOB 0.024 0.1 0.33 22 -0.33 16 38
mol:GDP 0 0 -10000 0 -10000 0 0
complement component iC3b receptor activity 0 0 -10000 0 -10000 0 0
MMP2 0.021 0.016 0.33 1 -10000 0 1
JAM3 0.018 0.025 -10000 0 -0.33 2 2
GP1BA 0.015 0.046 0.33 1 -0.33 6 7
alphaM/beta2 Integrin/CTGF -0.002 0.087 -10000 0 -0.27 27 27
alphaM/beta2 Integrin -0.066 0.15 0.21 2 -0.38 44 46
JAM3 homodimer 0.018 0.025 -10000 0 -0.33 2 2
ICAM2 0.018 0.031 -10000 0 -0.33 3 3
ICAM1 0.015 0.039 -10000 0 -0.33 5 5
phagocytosis triggered by activation of immune response cell surface activating receptor -0.066 0.14 0.21 2 -0.38 44 46
cell adhesion 0.002 0.084 0.23 1 -0.29 20 21
NFKB1 -0.23 0.17 -10000 0 -0.48 101 101
THY1 0.03 0.054 0.33 12 -10000 0 12
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
Lipoprotein(a) 0.027 0.064 0.21 24 -0.19 16 40
alphaM/beta2 Integrin/LRP/tPA 0.034 0.1 0.22 39 -0.3 15 54
IL6 -0.24 0.25 -10000 0 -0.64 97 97
ITGB2 -0.002 0.059 -10000 0 -0.35 8 8
elevation of cytosolic calcium ion concentration 0.042 0.11 0.22 55 -0.3 13 68
alphaM/beta2 Integrin/JAM2/JAM3 -0.002 0.099 -10000 0 -0.25 41 41
JAM2 -0.009 0.097 -10000 0 -0.33 33 33
alphaM/beta2 Integrin/ICAM1 0.022 0.089 0.23 9 -0.27 18 27
alphaM/beta2 Integrin/uPA/Plg 0.046 0.11 0.24 60 -0.27 15 75
RhoA/GTP -0.077 0.16 0.23 2 -0.4 45 47
positive regulation of phagocytosis -0.051 0.13 -10000 0 -0.38 35 35
Ron/MSP 0.036 0.042 0.24 13 -0.23 2 15
alphaM/beta2 Integrin/uPAR/uPA 0.044 0.11 0.23 55 -0.3 13 68
alphaM/beta2 Integrin/uPAR 0.007 0.078 -10000 0 -0.33 13 13
PLAU 0.076 0.12 0.33 70 -10000 0 70
PLAT 0.05 0.098 0.33 41 -0.33 1 42
actin filament polymerization -0.1 0.15 0.22 2 -0.36 65 67
MST1 0.029 0.057 0.33 12 -0.33 1 13
alphaM/beta2 Integrin/lipoprotein(a) 0.014 0.091 0.21 18 -0.22 29 47
TNF -0.23 0.19 -10000 0 -0.5 97 97
RAP1B 0.02 0.005 -10000 0 -10000 0 0
alphaM/beta2 Integrin/uPA 0.039 0.11 0.23 63 -0.3 15 78
fibrinolysis 0.044 0.11 0.23 60 -0.27 15 75
HCK 0.008 0.065 -10000 0 -0.33 14 14
dendritic cell antigen processing and presentation -0.066 0.14 0.21 2 -0.38 44 46
VTN -0.032 0.14 0.33 6 -0.33 64 70
alphaM/beta2 Integrin/CYR61 -0.004 0.093 -10000 0 -0.27 31 31
LPA 0.019 0.023 0.33 2 -10000 0 2
LRP1 0.017 0.035 -10000 0 -0.33 4 4
cell migration 0.018 0.076 0.21 1 -0.25 13 14
FN1 0.017 0.035 -10000 0 -0.33 4 4
alphaM/beta2 Integrin/Thy1 0.011 0.084 0.22 11 -0.28 16 27
MPO 0.016 0.046 0.33 1 -0.33 6 7
KNG1 0.041 0.081 0.33 28 -10000 0 28
RAP1/GDP 0.026 0.009 -10000 0 -10000 0 0
ROCK1 -0.075 0.15 0.24 4 -0.38 44 48
ELA2 0 0 -10000 0 -10000 0 0
PLG 0.024 0.047 0.33 9 -10000 0 9
CTGF 0.006 0.067 -10000 0 -0.33 15 15
alphaM/beta2 Integrin/Hck 0.001 0.093 -10000 0 -0.33 19 19
ITGAM -0.009 0.075 -10000 0 -0.35 15 15
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.026 0.12 -10000 0 -0.23 78 78
HP -0.04 0.16 0.33 16 -0.33 82 98
leukocyte adhesion -0.19 0.13 -10000 0 -0.34 114 114
SELP -0.047 0.14 -10000 0 -0.33 74 74
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.017 0.031 -10000 0 -0.33 3 3
EPHB2 0.057 0.1 0.33 46 -10000 0 46
EFNB1 -0.012 0.03 0.19 5 -0.23 2 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.066 0.083 0.23 63 -0.2 5 68
Ephrin B2/EPHB1-2 0.073 0.086 0.23 77 -0.17 4 81
neuron projection morphogenesis 0.045 0.065 0.17 63 -0.2 4 67
Ephrin B1/EPHB1-2/Tiam1 0.074 0.091 0.24 75 -0.19 6 81
DNM1 0.024 0.032 0.34 4 -10000 0 4
cell-cell signaling 0 0.004 -10000 0 -10000 0 0
MAP2K4 -0.062 0.16 -10000 0 -0.5 45 45
YES1 -0.073 0.24 -10000 0 -0.72 45 45
Ephrin B1/EPHB1-2/NCK2 0.079 0.087 0.24 76 -0.18 3 79
PI3K -0.03 0.17 -10000 0 -0.5 46 46
mol:GDP 0.072 0.089 0.23 74 -0.19 6 80
ITGA2B -0.012 0.11 0.33 3 -0.33 39 42
endothelial cell proliferation 0.024 0.021 -10000 0 -0.19 3 3
FYN -0.077 0.24 -10000 0 -0.73 45 45
MAP3K7 -0.061 0.17 -10000 0 -0.53 45 45
FGR -0.079 0.24 -10000 0 -0.73 45 45
TIAM1 0.016 0.039 -10000 0 -0.33 5 5
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
RGS3 0.02 0.004 -10000 0 -10000 0 0
cell adhesion -0.062 0.17 0.24 1 -0.5 44 45
LYN -0.071 0.23 -10000 0 -0.72 45 45
Ephrin B1/EPHB1-2/Src Family Kinases -0.068 0.21 -10000 0 -0.66 45 45
Ephrin B1/EPHB1-2 -0.06 0.18 -10000 0 -0.57 44 44
SRC -0.07 0.23 -10000 0 -0.71 45 45
ITGB3 0.034 0.079 0.33 21 -0.33 4 25
EPHB1 0.054 0.099 0.33 43 -0.33 1 44
EPHB4 0.02 0.005 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0.024 0.021 -10000 0 -0.19 3 3
alphaIIb/beta3 Integrin 0.014 0.1 0.24 24 -0.24 42 66
BLK -0.07 0.24 -10000 0 -0.72 45 45
HCK -0.075 0.24 -10000 0 -0.73 45 45
regulation of stress fiber formation -0.076 0.085 0.18 3 -0.23 76 79
MAPK8 -0.061 0.16 0.24 1 -0.48 45 46
Ephrin B1/EPHB1-2/RGS3 0.075 0.084 0.24 72 -0.18 3 75
endothelial cell migration -0.044 0.14 0.25 3 -0.43 41 44
NCK2 0.021 0.002 -10000 0 -10000 0 0
PTPN13 -0.029 0.14 -10000 0 -0.44 43 43
regulation of focal adhesion formation -0.076 0.085 0.18 3 -0.23 76 79
chemotaxis -0.073 0.082 0.18 3 -0.23 72 75
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.057 0.075 0.2 63 -0.19 5 68
angiogenesis -0.059 0.18 -10000 0 -0.57 44 44
LCK -0.069 0.23 -10000 0 -0.71 45 45
Visual signal transduction: Rods

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
mol:K + 0.021 0.003 -10000 0 -10000 0 0
GNAT1/GTP 0.018 0.03 0.22 8 -10000 0 8
Metarhodopsin II/Arrestin 0.025 0.01 0.21 1 -10000 0 1
PDE6G/GNAT1/GTP 0.027 0.035 0.24 7 -0.17 3 10
mol:GTP 0 0 -10000 0 -10000 0 0
absorption of light 0 0 -10000 0 -10000 0 0
GNAT1 0.024 0.044 0.33 8 -10000 0 8
GRK1 0.036 0.072 0.33 22 -10000 0 22
CNG Channel 0.045 0.087 0.27 13 -0.18 24 37
mol:Na + 0.082 0.086 0.28 27 -0.17 3 30
mol:ADP 0.036 0.072 0.33 22 -10000 0 22
RGS9-1/Gbeta5/R9AP -0.061 0.13 -10000 0 -0.22 149 149
mol:GDP 0 0 -10000 0 -10000 0 0
cGMP/CNG Channel 0.1 0.099 0.33 27 -0.17 3 30
CNGB1 0.073 0.12 0.33 68 -0.33 1 69
RDH5 0.026 0.041 0.33 7 -10000 0 7
SAG 0.019 0.016 0.33 1 -10000 0 1
mol:Ca2+ 0.017 0.093 0.29 28 -10000 0 28
Na + (4 Units) 0.025 0.083 0.13 135 -10000 0 135
RGS9 -0.088 0.16 -10000 0 -0.33 121 121
GNB1/GNGT1 0.063 0.079 0.24 66 -10000 0 66
GNAT1/GDP -0.045 0.12 0.21 4 -0.19 149 153
GUCY2D 0.019 0.041 0.33 3 -0.33 3 6
GNGT1 0.078 0.12 0.33 74 -10000 0 74
GUCY2F 0.019 0.016 0.33 1 -10000 0 1
GNB5 0.021 0.004 -10000 0 -10000 0 0
mol:GMP (4 units) -0.03 0.051 0.19 3 -0.18 30 33
mol:11-cis-retinal 0.026 0.041 0.33 7 -10000 0 7
mol:cGMP 0.06 0.077 0.22 63 -0.18 4 67
GNB1 0.02 0.004 -10000 0 -10000 0 0
Rhodopsin 0.033 0.028 0.24 7 -10000 0 7
SLC24A1 0.021 0.003 -10000 0 -10000 0 0
CNGA1 0.063 0.11 0.33 53 -10000 0 53
Metarhodopsin II 0.033 0.041 0.2 22 -10000 0 22
mol:Ca ++ 0 0 -10000 0 -10000 0 0
GC1/GCAP Family 0.072 0.079 0.23 65 -0.17 5 70
RGS9BP -0.028 0.12 -10000 0 -0.33 54 54
Metarhodopsin II/Transducin 0.025 0.044 0.16 7 -0.17 3 10
GCAP Family/Ca ++ 0.066 0.072 0.22 66 -0.15 2 68
PDE6A/B 0.009 0.072 0.24 1 -0.23 31 32
mol:Pi -0.061 0.13 -10000 0 -0.22 149 149
mol:all-trans-retinal 0 0 -10000 0 -10000 0 0
Transducin 0.066 0.073 0.22 69 -10000 0 69
PDE6B 0.017 0.035 -10000 0 -0.33 4 4
PDE6A -0.005 0.093 0.33 1 -0.33 29 30
PDE6G 0.019 0.038 0.33 2 -0.33 3 5
RHO 0.019 0.003 -10000 0 -10000 0 0
PDE6 -0.051 0.14 -10000 0 -0.21 149 149
GUCA1A 0.074 0.12 0.33 68 -10000 0 68
GC2/GCAP Family 0.076 0.074 0.23 66 -0.18 1 67
GUCA1C 0.018 0.003 -10000 0 -10000 0 0
GUCA1B 0.02 0.034 0.33 2 -0.33 2 4
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 0.029 0.02 -10000 0 -0.23 2 2
Necdin/E2F1 0.028 0.035 0.24 4 -0.22 4 8
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E 0.048 0.072 0.23 21 -0.18 22 43
NGF (dimer)/p75(NTR)/BEX1 -0.013 0.13 0.23 29 -0.2 106 135
NT-4/5 (dimer)/p75(NTR) 0.017 0.072 0.26 7 -0.23 25 32
IKBKB 0.018 0.007 -10000 0 -10000 0 0
AKT1 -0.018 0.056 0.19 15 -0.18 14 29
IKBKG 0.02 0.004 -10000 0 -10000 0 0
BDNF -0.14 0.17 -10000 0 -0.33 179 179
MGDIs/NGR/p75(NTR)/LINGO1 0.061 0.075 0.23 52 -0.19 7 59
FURIN 0.029 0.051 0.33 11 -10000 0 11
proBDNF (dimer)/p75(NTR)/Sortilin -0.067 0.12 0.23 5 -0.2 177 182
LINGO1 0.064 0.11 0.33 54 -10000 0 54
Sortilin/TRAF6/NRIF -0.029 0.019 -10000 0 -0.17 1 1
proBDNF (dimer) -0.14 0.17 -10000 0 -0.33 179 179
NTRK1 0.009 0.062 0.33 1 -0.33 12 13
RTN4R 0.02 0.018 -10000 0 -0.33 1 1
neuron apoptosis -0.094 0.14 0.42 2 -0.39 34 36
IRAK1 0.02 0.004 -10000 0 -10000 0 0
SHC1 -0.015 0.043 0.1 21 -0.2 12 33
ARHGDIA 0.02 0.004 -10000 0 -10000 0 0
RhoA/GTP 0.015 0.003 -10000 0 -10000 0 0
Gamma Secretase 0.046 0.03 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 0.048 0.068 0.23 22 -0.18 19 41
MAGEH1 0.021 0.003 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin 0.044 0.073 0.23 21 -0.18 23 44
Mammalian IAPs/DIABLO 0.051 0.029 0.23 4 -0.18 2 6
proNGF (dimer) 0.024 0.087 0.33 17 -0.33 11 28
MAGED1 0.022 0.016 0.33 1 -10000 0 1
APP 0.02 0.005 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.077 -10000 0 -0.33 20 20
ZNF274 0.02 0.005 -10000 0 -10000 0 0
RhoA/GDP/RHOGDI 0.02 0.046 0.19 1 -0.17 17 18
NGF 0.024 0.087 0.33 17 -0.33 11 28
cell cycle arrest 0.002 0.072 0.23 15 -10000 0 15
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK 0.006 0.058 0.18 6 -0.2 19 25
NT-4/5 (dimer)/p75(NTR)/TRAF6 0.029 0.066 0.25 7 -0.2 25 32
NCSTN 0.019 0.007 -10000 0 -10000 0 0
mol:GTP 0.039 0.068 0.22 23 -0.2 17 40
PSENEN 0.02 0.005 -10000 0 -10000 0 0
mol:ceramide -0.016 0.052 0.2 9 -0.18 14 23
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs 0.003 0.053 0.16 8 -0.28 3 11
p75(NTR)/beta APP 0.029 0.043 0.24 7 -0.23 6 13
BEX1 -0.057 0.17 0.33 14 -0.33 99 113
mol:GDP -0.014 0.047 0.21 1 -0.19 17 18
NGF (dimer) 0.072 0.096 0.24 79 -0.17 15 94
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI 0.069 0.072 0.23 51 -0.17 7 58
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
RAC1/GTP 0.03 0.056 0.2 18 -0.16 16 34
MYD88 0.021 0.004 -10000 0 -10000 0 0
CHUK 0.021 0.003 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA 0.04 0.068 0.23 23 -0.2 17 40
RHOB 0.021 0.002 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
MAGE-G1/E2F1 0.03 0.02 0.24 3 -10000 0 3
NT3 (dimer) 0.003 0.082 0.33 2 -0.33 21 23
TP53 -0.083 0.094 0.3 6 -0.3 4 10
PRDM4 -0.019 0.055 0.2 10 -0.18 16 26
BDNF (dimer) 0.006 0.17 0.27 88 -0.16 159 247
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
SORT1 0.019 0.025 -10000 0 -0.33 2 2
activation of caspase activity 0.043 0.069 0.21 21 -0.17 23 44
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 0.049 0.068 0.23 22 -0.18 19 41
RHOC 0.02 0.004 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
MAPK10 -0.072 0.13 0.3 11 -0.33 36 47
DIABLO 0.021 0.004 -10000 0 -10000 0 0
SMPD2 -0.016 0.052 0.2 9 -0.18 14 23
APH1B 0.02 0.018 -10000 0 -0.33 1 1
APH1A 0.017 0.008 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin 0.039 0.069 0.23 22 -0.2 19 41
PSEN1 0.02 0.004 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.008 -10000 0 -10000 0 0
NT3 (dimer)/p75(NTR) 0.016 0.078 0.3 7 -0.23 26 33
MAPK8 -0.056 0.11 0.3 10 -0.28 22 32
MAPK9 -0.054 0.11 0.3 10 -0.3 18 28
APAF1 0.021 0.004 -10000 0 -10000 0 0
NTF3 0.003 0.082 0.33 2 -0.33 21 23
NTF4 0.002 0.077 -10000 0 -0.33 20 20
NDN 0.016 0.039 -10000 0 -0.33 5 5
RAC1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA-B-C/GDP 0.047 0.059 -10000 0 -0.17 16 16
p75 CTF/Sortilin/TRAF6/NRIF 0.049 0.023 -10000 0 -0.18 2 2
RhoA-B-C/GTP 0.039 0.067 0.22 23 -0.19 17 40
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.05 0.12 0.23 3 -0.18 174 177
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.055 0.12 0.23 5 -0.18 177 182
PRKACB 0.021 0.016 0.33 1 -10000 0 1
proBDNF (dimer)/p75 ECD -0.089 0.13 -10000 0 -0.23 178 178
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
BIRC3 0.022 0.04 0.33 4 -0.33 2 6
BIRC2 0.02 0.005 -10000 0 -10000 0 0
neuron projection morphogenesis 0.008 0.074 0.23 11 -0.2 13 24
BAD -0.067 0.12 0.31 11 -0.32 24 35
RIPK2 0.019 0.007 -10000 0 -10000 0 0
NGFR 0.021 0.06 0.33 7 -0.33 6 13
CYCS -0.021 0.053 0.21 9 -0.18 15 24
ADAM17 0.021 0.002 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 0.043 0.066 0.23 19 -0.18 17 36
BCL2L11 -0.066 0.12 0.32 10 -0.32 24 34
BDNF (dimer)/p75(NTR) -0.087 0.14 0.24 5 -0.23 178 183
PI3K 0.047 0.066 0.23 22 -0.18 17 39
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 0.047 0.069 0.23 22 -0.18 19 41
NDNL2 0.02 0.005 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
NGF (dimer)/p75(NTR) 0.03 0.075 0.24 23 -0.23 17 40
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE 0.048 0.068 0.23 22 -0.18 19 41
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.018 0.031 -10000 0 -0.33 3 3
PLG 0.024 0.047 0.33 9 -10000 0 9
oligodendrocyte cell fate commitment 0 0 -10000 0 -10000 0 0
CASP6 -0.092 0.098 0.14 2 -0.19 172 174
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
NGFRAP1 0.017 0.035 -10000 0 -0.33 4 4
CASP3 -0.063 0.11 0.31 10 -0.3 25 35
E2F1 0.024 0.032 0.33 4 -10000 0 4
CASP9 0.02 0.004 -10000 0 -10000 0 0
IKK complex 0.027 0.073 0.23 3 -0.27 9 12
NGF (dimer)/TRKA 0.021 0.071 0.24 15 -0.22 20 35
MMP7 0.063 0.12 0.33 61 -0.33 6 67
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF 0.053 0.067 0.23 20 -0.18 18 38
MMP3 0.14 0.15 0.33 152 -10000 0 152
APAF-1/Caspase 9 -0.04 0.036 -10000 0 -0.17 12 12
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.1 0.45 0.77 3 -1.1 41 44
IL23A -0.088 0.48 0.77 6 -1.2 39 45
NF kappa B1 p50/RelA/I kappa B alpha -0.092 0.45 0.64 3 -1.1 42 45
positive regulation of T cell mediated cytotoxicity -0.12 0.52 0.83 3 -1.3 45 48
ITGA3 -0.1 0.45 0.75 4 -1.1 42 46
IL17F -0.066 0.31 0.53 7 -0.7 45 52
IL12B 0.02 0.062 0.26 5 -0.34 1 6
STAT1 (dimer) -0.12 0.49 0.71 2 -1.2 46 48
CD4 -0.1 0.46 0.74 4 -1.1 40 44
IL23 -0.08 0.46 0.72 5 -1.1 40 45
IL23R 0.006 0.18 0.57 1 -1 8 9
IL1B -0.11 0.5 0.83 3 -1.3 44 47
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.085 0.44 0.73 5 -1.1 42 47
TYK2 0.016 0.045 0.18 2 -10000 0 2
STAT4 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
IL18RAP 0.007 0.07 -10000 0 -0.33 16 16
IL12RB1 0.009 0.071 0.17 3 -0.36 9 12
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 0.019 0.067 0.2 2 -0.26 8 10
IL23R/JAK2 0.016 0.19 0.52 1 -0.93 8 9
positive regulation of chronic inflammatory response -0.12 0.52 0.83 3 -1.3 45 48
natural killer cell activation -0.001 0.01 -10000 0 -0.045 3 3
JAK2 0.018 0.056 0.19 3 -0.33 1 4
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.013 0.021 -10000 0 -10000 0 0
RELA 0.013 0.021 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.072 0.44 0.72 5 -1.1 40 45
ALOX12B -0.087 0.45 0.71 5 -1.1 39 44
CXCL1 -0.11 0.47 0.8 3 -1.1 48 51
T cell proliferation -0.12 0.52 0.83 3 -1.3 45 48
NFKBIA 0.011 0.02 -10000 0 -10000 0 0
IL17A -0.02 0.27 0.48 18 -0.55 37 55
PI3K -0.11 0.47 0.67 2 -1.1 46 48
IFNG 0.01 0.048 0.14 26 -0.11 5 31
STAT3 (dimer) -0.1 0.45 0.62 2 -1.1 46 48
IL18R1 0.008 0.067 -10000 0 -0.32 15 15
IL23/IL23R/JAK2/TYK2/SOCS3 -0.058 0.35 0.52 11 -0.88 32 43
IL18/IL18R 0.027 0.085 0.19 1 -0.23 29 30
macrophage activation -0.003 0.025 0.053 28 -0.045 20 48
TNF -0.11 0.5 0.8 4 -1.2 44 48
STAT3/STAT4 -0.11 0.47 0.67 2 -1.1 46 48
STAT4 (dimer) -0.12 0.49 0.71 2 -1.2 46 48
IL18 0.013 0.051 -10000 0 -0.33 8 8
IL19 -0.083 0.44 0.7 6 -1.1 42 48
STAT5A (dimer) -0.12 0.49 0.71 2 -1.2 47 49
STAT1 0.021 0.002 -10000 0 -10000 0 0
SOCS3 0.018 0.025 -10000 0 -0.33 2 2
CXCL9 -0.099 0.46 0.69 7 -1.1 44 51
MPO -0.1 0.46 0.77 3 -1.1 42 45
positive regulation of humoral immune response -0.12 0.52 0.83 3 -1.3 45 48
IL23/IL23R/JAK2/TYK2 -0.13 0.56 0.84 3 -1.4 44 47
IL6 -0.19 0.58 0.73 3 -1.1 91 94
STAT5A 0.02 0.018 -10000 0 -0.33 1 1
IL2 0.014 0.029 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein -0.001 0.01 -10000 0 -0.045 3 3
CD3E -0.1 0.45 0.77 2 -1.1 43 45
keratinocyte proliferation -0.12 0.52 0.83 3 -1.3 45 48
NOS2 -0.14 0.5 0.73 4 -1.1 62 66
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.072 0.12 0.34 59 -0.22 2 61
NFATC2 0.008 0.14 -10000 0 -0.51 11 11
NFATC3 -0.007 0.087 -10000 0 -0.26 32 32
CD40LG -0.089 0.29 0.41 1 -0.76 51 52
ITCH -0.025 0.077 -10000 0 -0.24 1 1
CBLB -0.028 0.081 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.026 0.25 0.41 18 -0.72 26 44
JUNB 0.018 0.025 -10000 0 -0.33 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.029 0.1 -10000 0 -0.24 74 74
T cell anergy -0.058 0.14 0.3 2 -0.34 66 68
TLE4 -0.007 0.1 -10000 0 -0.46 10 10
Jun/NFAT1-c-4/p21SNFT -0.033 0.29 0.52 1 -0.76 47 48
AP-1/NFAT1-c-4 -0.045 0.35 0.6 3 -0.84 49 52
IKZF1 -0.002 0.085 -10000 0 -0.38 9 9
T-helper 2 cell differentiation -0.026 0.19 -10000 0 -0.71 17 17
AP-1/NFAT1 0.017 0.13 0.34 2 -0.32 17 19
CALM1 -0.011 0.068 -10000 0 -0.15 74 74
EGR2 -0.087 0.32 -10000 0 -0.88 43 43
EGR3 -0.13 0.4 -10000 0 -1.1 49 49
NFAT1/FOXP3 0.059 0.14 0.39 17 -0.34 9 26
EGR1 -0.004 0.086 -10000 0 -0.33 25 25
JUN 0.013 0.036 -10000 0 -0.33 2 2
EGR4 0.048 0.092 0.33 37 -10000 0 37
mol:Ca2+ -0.025 0.055 -10000 0 -0.14 68 68
GBP3 -0.013 0.12 -10000 0 -0.53 16 16
FOSL1 0.034 0.075 0.33 20 -0.33 3 23
NFAT1-c-4/MAF/IRF4 -0.032 0.28 -10000 0 -0.74 47 47
DGKA -0.004 0.09 0.5 1 -0.38 8 9
CREM 0.021 0.004 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.069 0.3 -10000 0 -0.8 49 49
CTLA4 0.015 0.092 0.35 4 -0.29 7 11
NFAT1-c-4 (dimer)/EGR1 -0.06 0.3 0.46 1 -0.81 49 50
NFAT1-c-4 (dimer)/EGR4 -0.034 0.3 0.46 2 -0.77 49 51
FOS -0.01 0.094 -10000 0 -0.34 28 28
IFNG -0.025 0.21 0.36 2 -0.77 16 18
T cell activation -0.034 0.16 -10000 0 -0.6 11 11
MAF 0.019 0.018 -10000 0 -0.33 1 1
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.065 0.23 0.65 48 -10000 0 48
TNF -0.086 0.28 0.48 1 -0.76 50 51
FASLG -0.15 0.43 -10000 0 -1.2 51 51
TBX21 0.016 0.079 0.33 1 -0.32 17 18
BATF3 0.02 0.017 0.33 1 -10000 0 1
PRKCQ -0.022 0.11 -10000 0 -0.33 47 47
PTPN1 -0.005 0.09 0.34 1 -0.37 9 10
NFAT1-c-4/ICER1 -0.046 0.28 -10000 0 -0.75 49 49
GATA3 0.02 0.024 0.33 1 -0.33 1 2
T-helper 1 cell differentiation -0.024 0.2 0.36 2 -0.75 16 18
IL2RA -0.014 0.26 0.46 22 -0.7 28 50
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.005 0.087 -10000 0 -0.38 8 8
E2F1 0.025 0.032 0.33 4 -10000 0 4
PPARG -0.023 0.12 -10000 0 -0.33 49 49
SLC3A2 -0.004 0.085 -10000 0 -0.36 9 9
IRF4 0.027 0.057 0.33 11 -0.33 2 13
PTGS2 -0.091 0.29 0.46 2 -0.78 47 49
CSF2 -0.09 0.3 0.45 5 -0.77 50 55
JunB/Fra1/NFAT1-c-4 -0.031 0.29 0.5 2 -0.74 49 51
IL4 -0.028 0.2 -10000 0 -0.74 17 17
IL5 -0.084 0.28 0.41 1 -0.74 50 51
IL2 -0.034 0.16 -10000 0 -0.63 10 10
IL3 -0.025 0.13 -10000 0 -0.64 12 12
RNF128 -0.077 0.17 -10000 0 -0.43 74 74
NFATC1 -0.065 0.23 -10000 0 -0.65 48 48
CDK4 0.046 0.16 0.55 19 -10000 0 19
PTPRK -0.003 0.084 -10000 0 -0.39 6 6
IL8 -0.075 0.29 0.44 9 -0.74 50 59
POU2F1 0.019 0.006 -10000 0 -10000 0 0
Glucocorticoid receptor regulatory network

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
PCK2 0.022 0.083 -10000 0 -0.33 1 1
SMARCC2 0.02 0.01 -10000 0 -0.16 1 1
SMARCC1 0.021 0.007 -10000 0 -0.1 1 1
TBX21 -0.041 0.17 0.36 3 -0.46 37 40
SUMO2 0.018 0.014 -10000 0 -10000 0 0
STAT1 (dimer) 0.023 0.002 -10000 0 -10000 0 0
FKBP4 0.02 0.005 -10000 0 -10000 0 0
FKBP5 0.02 0.004 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.039 0.11 0.27 26 -10000 0 26
PRL -0.015 0.11 0.41 4 -0.39 3 7
cortisol/GR alpha (dimer)/TIF2 0.057 0.22 0.48 47 -0.34 11 58
RELA -0.032 0.1 0.18 1 -0.19 94 95
FGG 0.012 0.29 0.48 64 -0.4 64 128
GR beta/TIF2 0.031 0.11 0.27 33 -0.2 2 35
IFNG -0.033 0.25 0.44 15 -0.58 35 50
apoptosis 0.002 0.14 0.44 10 -0.47 10 20
CREB1 0.04 0.047 0.2 1 -10000 0 1
histone acetylation -0.067 0.12 -10000 0 -0.32 38 38
BGLAP -0.013 0.1 0.3 1 -0.35 7 8
GR/PKAc 0.045 0.11 0.28 24 -10000 0 24
NF kappa B1 p50/RelA -0.057 0.18 0.29 1 -0.32 106 107
SMARCD1 0.021 0.007 -10000 0 -10000 0 0
MDM2 0.031 0.086 0.2 49 -10000 0 49
GATA3 0.021 0.024 0.33 1 -0.33 1 2
AKT1 0.019 0.005 -10000 0 -10000 0 0
CSF2 -0.12 0.27 -10000 0 -0.92 33 33
GSK3B 0.018 0.014 -10000 0 -10000 0 0
NR1I3 0.017 0.14 0.46 7 -0.46 4 11
CSN2 0.043 0.18 0.36 54 -0.3 14 68
BRG1/BAF155/BAF170/BAF60A 0.048 0.029 -10000 0 -0.26 2 2
NFATC1 0.018 0.026 -10000 0 -0.33 2 2
POU2F1 0.022 0.017 -10000 0 -10000 0 0
CDKN1A -0.006 0.074 -10000 0 -1 1 1
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.006 -10000 0 -10000 0 0
SFN 0.025 0.045 0.33 7 -0.33 1 8
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.05 0.1 0.28 18 -10000 0 18
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 -0.026 0.21 0.44 7 -0.69 27 34
JUN 0.001 0.18 0.32 36 -0.36 35 71
IL4 -0.03 0.12 -10000 0 -0.44 12 12
CDK5R1 0.026 0.048 0.33 9 -10000 0 9
PRKACA 0.02 0.005 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.041 0.064 0.17 3 -0.22 19 22
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.043 0.1 0.28 18 -10000 0 18
cortisol/GR alpha (monomer) 0.078 0.27 0.58 54 -0.4 12 66
NCOA2 0.017 0.026 -10000 0 -0.33 2 2
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS 0.011 0.12 0.23 11 -0.33 22 33
AP-1/NFAT1-c-4 0.007 0.26 0.42 33 -0.44 64 97
AFP -0.002 0.17 0.42 11 -0.45 5 16
SUV420H1 0.021 0.004 -10000 0 -10000 0 0
IRF1 0.044 0.14 0.37 26 -0.32 2 28
TP53 0.02 0.048 -10000 0 -0.92 1 1
PPP5C 0.02 0.005 -10000 0 -10000 0 0
KRT17 -0.038 0.29 0.46 21 -0.66 40 61
KRT14 0.038 0.18 0.37 28 -0.4 7 35
TBP 0.021 0.007 -10000 0 -10000 0 0
CREBBP -0.017 0.071 -10000 0 -0.21 2 2
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.024 0.023 -10000 0 -10000 0 0
AP-1 0.007 0.26 0.42 33 -0.44 65 98
MAPK14 0.018 0.014 -10000 0 -10000 0 0
MAPK10 -0.021 0.11 -10000 0 -0.33 45 45
MAPK11 0.016 0.028 -10000 0 -0.33 2 2
KRT5 -0.18 0.45 0.43 18 -0.91 98 116
interleukin-1 receptor activity 0.005 0.02 -10000 0 -10000 0 0
NCOA1 0.022 0.002 -10000 0 -10000 0 0
STAT1 0.023 0.002 -10000 0 -10000 0 0
CGA 0.005 0.13 0.36 11 -0.38 6 17
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.002 0.18 0.47 28 -0.32 12 40
MAPK3 0.019 0.014 -10000 0 -10000 0 0
MAPK1 0.018 0.013 -10000 0 -10000 0 0
ICAM1 -0.097 0.22 -10000 0 -0.58 43 43
NFKB1 -0.032 0.1 0.18 1 -0.2 79 80
MAPK8 -0.009 0.16 0.3 17 -0.33 42 59
MAPK9 0.019 0.013 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.001 0.14 0.44 10 -0.49 10 20
BAX -0.012 0.066 -10000 0 -10000 0 0
POMC -0.12 0.28 -10000 0 -1 23 23
EP300 -0.018 0.072 -10000 0 -0.27 1 1
cortisol/GR alpha (dimer)/p53 0.063 0.22 0.5 46 -0.36 6 52
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.072 0.19 31 -10000 0 31
SGK1 -0.027 0.11 -10000 0 -0.76 2 2
IL13 -0.04 0.19 -10000 0 -0.53 24 24
IL6 -0.19 0.36 -10000 0 -0.79 97 97
PRKACG 0.018 0.004 -10000 0 -10000 0 0
IL5 -0.038 0.17 -10000 0 -0.55 11 11
IL2 -0.046 0.23 0.38 6 -0.55 35 41
CDK5 0.019 0.011 -10000 0 -10000 0 0
PRKACB 0.021 0.016 0.33 1 -10000 0 1
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
IL8 -0.08 0.2 0.32 7 -0.48 46 53
CDK5R1/CDK5 0.033 0.036 0.24 9 -10000 0 9
NF kappa B1 p50/RelA/PKAc -0.021 0.15 0.27 1 -0.26 80 81
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.064 0.21 0.47 49 -0.33 8 57
SMARCA4 0.019 0.018 -10000 0 -0.33 1 1
chromatin remodeling 0.035 0.13 0.33 31 -0.34 1 32
NF kappa B1 p50/RelA/Cbp -0.063 0.17 0.37 1 -0.34 56 57
JUN (dimer) 0.001 0.18 0.32 35 -0.36 35 70
YWHAH 0.021 0.004 -10000 0 -10000 0 0
VIPR1 -0.27 0.35 -10000 0 -0.67 163 163
NR3C1 0.049 0.17 0.38 48 -0.25 2 50
NR4A1 -0.06 0.16 -10000 0 -0.36 85 85
TIF2/SUV420H1 0.026 0.021 -10000 0 -0.23 2 2
MAPKKK cascade 0.002 0.14 0.44 10 -0.47 10 20
cortisol/GR alpha (dimer)/Src-1 0.073 0.23 0.5 53 -0.35 10 63
PBX1 0.014 0.055 -10000 0 -0.33 9 9
POU1F1 0.022 0.026 0.43 1 -10000 0 1
SELE -0.15 0.32 0.38 1 -0.79 69 70
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.035 0.13 0.33 31 -0.34 1 32
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.064 0.21 0.47 49 -0.33 8 57
mol:cortisol 0.044 0.16 0.33 58 -0.21 14 72
MMP1 0.18 0.2 0.38 64 -0.69 6 70
LPA4-mediated signaling events

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
ADCY4 -0.022 0.04 -10000 0 -0.2 18 18
ADCY5 -0.036 0.065 0.092 6 -0.2 51 57
ADCY6 -0.015 0.016 -10000 0 -0.19 3 3
ADCY7 -0.015 0.016 -10000 0 -0.19 3 3
ADCY1 -0.014 0.025 0.14 3 -0.19 5 8
ADCY2 -0.019 0.05 0.12 9 -0.19 24 33
ADCY3 -0.015 0.016 -10000 0 -0.19 3 3
ADCY8 -0.072 0.087 0.092 1 -0.19 132 133
PRKCE -0.01 0.019 -10000 0 -0.22 3 3
ADCY9 -0.019 0.031 -10000 0 -0.19 12 12
mol:DAG 0 0 -10000 0 -10000 0 0
cAMP biosynthetic process -0.003 0.11 0.21 42 -0.26 10 52
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer 0.025 0.035 -10000 0 -0.23 7 7
alphaV beta3 Integrin 0.02 0.093 0.23 19 -0.2 48 67
PTK2 -0.04 0.13 0.36 8 -0.38 17 25
IGF1R 0.02 0.018 -10000 0 -0.33 1 1
PI4KB 0.018 0.008 -10000 0 -10000 0 0
MFGE8 0.021 0.003 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
CDKN1B -0.054 0.16 -10000 0 -0.41 59 59
VEGFA 0.02 0.004 -10000 0 -10000 0 0
ILK -0.056 0.16 -10000 0 -0.41 62 62
ROCK1 0.02 0.004 -10000 0 -10000 0 0
AKT1 -0.063 0.14 -10000 0 -0.38 61 61
PTK2B -0.011 0.056 0.17 22 -0.3 1 23
alphaV/beta3 Integrin/JAM-A -0.001 0.11 0.23 22 -0.2 70 92
CBL 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 0.056 0.063 0.23 40 -0.19 4 44
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.047 0.037 0.23 1 -0.2 6 7
VEGF/Rho/ROCK/alphaV/beta3 Integrin -0.02 0.079 0.16 1 -0.3 10 11
alphaV/beta3 Integrin/Syndecan-1 0.049 0.05 0.23 21 -0.2 4 25
PI4KA 0.021 0.004 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.019 0.091 -10000 0 -0.21 40 40
PI4 Kinase 0.026 0.012 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin 0.18 0.11 0.24 277 -0.18 4 281
RPS6KB1 -0.046 0.071 0.31 2 -0.35 7 9
TLN1 0.019 0.018 -10000 0 -0.33 1 1
MAPK3 -0.053 0.14 0.28 1 -0.43 40 41
GPR124 0.017 0.026 -10000 0 -0.33 2 2
MAPK1 -0.052 0.14 0.28 2 -0.43 40 42
PXN 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.023 0.12 0.23 17 -0.2 118 135
cell adhesion 0.041 0.056 0.22 21 -0.21 5 26
ANGPTL3 0.036 0.07 0.33 21 -10000 0 21
VEGFR2 homodimer/VEGFA homodimer/Src 0.036 0.032 -10000 0 -0.2 6 6
IGF-1R heterotetramer 0.02 0.018 -10000 0 -0.33 1 1
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
TGFBR2 0.015 0.043 -10000 0 -0.33 6 6
ITGB3 0.034 0.079 0.33 21 -0.33 4 25
IGF1 0.017 0.042 0.33 1 -0.33 5 6
RAC1 0.019 0.007 -10000 0 -10000 0 0
regulation of cell-matrix adhesion 0.041 0.054 0.22 19 -0.22 5 24
apoptosis 0.021 0.002 -10000 0 -10000 0 0
CD47 0.02 0.018 -10000 0 -0.33 1 1
alphaV/beta3 Integrin/CD47 0.048 0.052 0.23 21 -0.2 5 26
VCL 0.021 0.003 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Del1 0.032 0.079 0.24 18 -0.21 26 44
CSF1 0.02 0.018 -10000 0 -0.33 1 1
PIK3C2A -0.056 0.16 -10000 0 -0.41 62 62
PI4 Kinase/Pyk2 -0.052 0.073 0.18 1 -0.29 11 12
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.052 0.06 0.23 21 -0.2 10 31
FAK1/Vinculin -0.031 0.11 0.34 8 -0.33 12 20
alphaV beta3/Integrin/ppsTEM5 0.042 0.054 0.23 19 -0.23 5 24
RHOA 0.021 0.004 -10000 0 -10000 0 0
VTN -0.032 0.14 0.33 6 -0.33 64 70
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
FGF2 -0.021 0.11 -10000 0 -0.33 47 47
F11R -0.033 0.06 -10000 0 -0.23 33 33
alphaV/beta3 Integrin/Lactadherin 0.048 0.05 0.23 21 -0.2 4 25
alphaV/beta3 Integrin/TGFBR2 0.044 0.059 0.23 21 -0.2 10 31
alphaV/beta3 Integrin/c-FMS/Cbl/Cas 0.047 0.025 -10000 0 -0.18 2 2
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Talin 0.044 0.049 0.22 20 -0.21 4 24
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.017 0.035 -10000 0 -0.33 4 4
alphaV/beta3 Integrin/Pyk2 0.033 0.059 0.21 18 -0.19 9 27
SDC1 0.021 0.002 -10000 0 -10000 0 0
VAV3 -0.02 0.045 0.16 17 -0.32 1 18
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.02 0.018 -10000 0 -0.33 1 1
FAK1/Paxillin -0.032 0.11 0.32 7 -0.32 14 21
cell migration -0.033 0.1 0.29 8 -0.3 12 20
ITGAV 0.021 0.002 -10000 0 -10000 0 0
PI3K 0.006 0.1 0.28 2 -0.2 58 60
SPP1 0.25 0.14 0.33 286 -10000 0 286
KDR 0.014 0.046 -10000 0 -0.33 7 7
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.021 0.002 -10000 0 -10000 0 0
COL4A3 -0.084 0.16 -10000 0 -0.33 118 118
angiogenesis -0.051 0.16 0.28 2 -0.44 38 40
Rac1/GTP -0.019 0.042 0.16 15 -0.28 1 16
EDIL3 0 0.085 0.33 1 -0.33 24 25
cell proliferation 0.044 0.058 0.22 21 -0.2 10 31
Arf6 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
CENTA1/KIF3B 0.021 0.016 -10000 0 -0.17 1 1
ARNO/beta Arrestin1-2 -0.056 0.18 -10000 0 -0.82 16 16
EGFR 0.015 0.043 0.33 1 -0.33 5 6
EPHA2 0.014 0.046 -10000 0 -0.33 7 7
USP6 0.019 0.006 -10000 0 -10000 0 0
IQSEC1 0.02 0.018 -10000 0 -0.33 1 1
EGFR/EGFR/EGF/EGF 0.053 0.089 0.24 59 -0.24 8 67
ARRB2 0.015 0.035 0.14 27 -10000 0 27
mol:GTP 0.003 0.041 0.14 8 -0.15 8 16
ARRB1 0.018 0.031 -10000 0 -0.33 3 3
FBXO8 0.02 0.004 -10000 0 -10000 0 0
TSHR 0.052 0.095 0.33 41 -10000 0 41
EGF 0.074 0.13 0.33 72 -0.33 4 76
somatostatin receptor activity 0 0 0.001 14 -0.001 45 59
ARAP2 0.009 0.063 -10000 0 -0.33 13 13
mol:GDP -0.059 0.14 0.17 8 -0.29 74 82
mol:PI-3-4-5-P3 0 0 0.001 12 -0.001 24 36
ITGA2B -0.012 0.11 0.33 3 -0.33 39 42
ARF6 0.02 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.039 0.036 -10000 0 -0.18 6 6
ADAP1 0.018 0.019 -10000 0 -0.33 1 1
KIF13B 0.018 0.008 -10000 0 -10000 0 0
HGF/MET 0.015 0.076 0.24 8 -0.24 27 35
PXN 0.021 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.043 0.12 0.24 11 -0.28 44 55
EGFR/EGFR/EGF/EGF/ARFGEP100 0.056 0.08 0.23 53 -0.2 9 62
ADRB2 -0.11 0.17 -10000 0 -0.33 142 142
receptor agonist activity 0 0 0.001 3 0 45 48
actin filament binding 0 0 0.001 10 0 54 64
SRC 0.02 0.004 -10000 0 -10000 0 0
ITGB3 0.034 0.079 0.33 21 -0.33 4 25
GNAQ 0.019 0.018 -10000 0 -0.33 1 1
EFA6/PI-4-5-P2 0 0.001 0.001 15 -0.001 31 46
ARF6/GDP -0.04 0.15 0.44 1 -0.41 39 40
ARF6/GDP/GULP/ACAP1 -0.042 0.14 -10000 0 -0.31 52 52
alphaIIb/beta3 Integrin/paxillin/GIT1 0.035 0.089 0.23 22 -0.19 42 64
ACAP1 0.019 0.019 -10000 0 -0.33 1 1
ACAP2 0.02 0.005 -10000 0 -10000 0 0
LHCGR/beta Arrestin2 0.029 0.068 0.25 30 -10000 0 30
EFNA1 0.017 0.019 -10000 0 -0.33 1 1
HGF 0.008 0.075 0.33 3 -0.33 16 19
CYTH3 -0.007 0.017 0.22 2 -10000 0 2
CYTH2 -0.027 0.2 -10000 0 -0.99 16 16
NCK1 0.021 0.003 -10000 0 -10000 0 0
fibronectin binding 0 0 0.001 10 0 36 46
endosomal lumen acidification 0 0 0 33 0 24 57
microtubule-based process 0 0 -10000 0 0 1 1
GULP1 0.02 0.018 -10000 0 -0.33 1 1
GNAQ/ARNO -0.013 0.19 -10000 0 -0.92 16 16
mol:Phosphatidic acid 0 0 0 3 -10000 0 3
PIP3-E 0 0 0 6 0 6 12
MET 0.012 0.072 0.33 5 -0.33 13 18
GNA14 0.011 0.055 -10000 0 -0.33 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 0.001 11 -0.001 37 48
GNA11 0.02 0.006 -10000 0 -10000 0 0
LHCGR 0.039 0.083 0.33 29 -10000 0 29
AGTR1 -0.078 0.16 -10000 0 -0.33 110 110
desensitization of G-protein coupled receptor protein signaling pathway 0.029 0.068 0.25 30 -10000 0 30
IPCEF1/ARNO 0.014 0.19 -10000 0 -0.84 16 16
alphaIIb/beta3 Integrin 0.014 0.1 0.24 24 -0.24 42 66
HIF-2-alpha transcription factor network

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
MMP14 0.018 0.074 0.43 1 -0.54 5 6
oxygen homeostasis 0.01 0.014 -10000 0 -10000 0 0
TCEB2 0.021 0.003 -10000 0 -10000 0 0
TCEB1 0.02 0.017 0.33 1 -10000 0 1
VHL/Elongin B/Elongin C/HIF2A 0.072 0.1 0.27 11 -0.26 5 16
EPO 0.1 0.16 0.41 44 -0.38 1 45
FIH (dimer) 0.026 0.022 -10000 0 -10000 0 0
APEX1 0.029 0.026 -10000 0 -10000 0 0
SERPINE1 0.11 0.17 0.41 52 -0.41 1 53
FLT1 -0.008 0.13 -10000 0 -0.57 15 15
ADORA2A 0.1 0.16 0.39 46 -0.4 1 47
germ cell development 0.11 0.18 0.41 58 -0.39 5 63
SLC11A2 0.11 0.16 0.4 54 -0.41 1 55
BHLHE40 0.12 0.16 0.42 45 -0.41 1 46
HIF1AN 0.026 0.022 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 0.084 0.12 0.34 27 -0.29 1 28
ETS1 0.02 0.018 -10000 0 -10000 0 0
CITED2 -0.022 0.15 -10000 0 -0.53 26 26
KDR -0.004 0.15 -10000 0 -0.72 13 13
PGK1 0.12 0.16 0.4 52 -0.41 1 53
SIRT1 0.021 0.003 -10000 0 -10000 0 0
response to hypoxia 0 0.001 -10000 0 -10000 0 0
HIF2A/ARNT 0.14 0.2 0.54 37 -0.45 1 38
EPAS1 0.054 0.099 0.26 36 -0.23 7 43
SP1 0.023 0.01 -10000 0 -10000 0 0
ABCG2 0.1 0.19 0.4 55 -0.44 8 63
EFNA1 0.094 0.15 0.4 41 -0.41 1 42
FXN 0.1 0.15 0.39 44 -0.38 1 45
POU5F1 0.11 0.18 0.41 58 -0.4 5 63
neuron apoptosis -0.14 0.19 0.44 1 -0.54 37 38
EP300 0.021 0.004 -10000 0 -10000 0 0
EGLN3 0.097 0.14 0.35 93 -0.32 1 94
EGLN2 0.026 0.022 -10000 0 -10000 0 0
EGLN1 0.025 0.022 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0.037 0.019 0.23 1 -10000 0 1
VHL 0.021 0.004 -10000 0 -10000 0 0
ARNT 0.025 0.026 -10000 0 -10000 0 0
SLC2A1 0.15 0.19 0.42 93 -0.4 1 94
TWIST1 0.12 0.18 0.44 66 -10000 0 66
ELK1 0.022 0.008 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 0.09 0.13 0.35 27 -0.29 2 29
VEGFA 0.11 0.16 0.4 54 -0.41 1 55
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Canonical Wnt signaling pathway

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
HDAC1 0.023 0.017 0.19 1 -10000 0 1
AES 0.021 0.014 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 0.028 0.011 -10000 0 -10000 0 0
SMAD4 0.019 0.007 -10000 0 -10000 0 0
DKK2 -0.039 0.13 -10000 0 -0.33 67 67
TLE1 0.022 0.014 0.17 1 -10000 0 1
MACF1 0.018 0.035 -10000 0 -0.33 4 4
CTNNB1 0.08 0.1 0.26 29 -0.31 4 33
WIF1 -0.2 0.16 -10000 0 -0.33 253 253
beta catenin/RanBP3 0.052 0.1 0.44 15 -0.36 1 16
KREMEN2 0.094 0.13 0.33 93 -10000 0 93
DKK1 0.038 0.16 0.33 61 -0.33 35 96
beta catenin/beta TrCP1 0.081 0.097 0.29 17 -0.31 3 20
FZD1 0.021 0.005 -10000 0 -10000 0 0
AXIN2 -0.029 0.25 0.57 14 -1.2 14 28
AXIN1 0.022 0.004 -10000 0 -10000 0 0
RAN 0.022 0.022 0.33 2 -10000 0 2
Axin1/APC/GSK3/beta catenin 0.028 0.087 -10000 0 -0.65 5 5
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.015 0.18 0.28 1 -0.57 23 24
Axin1/APC/GSK3 0.051 0.072 0.22 24 -0.37 2 26
Axin1/APC/GSK3/beta catenin/Macf1 0.035 0.078 0.26 8 -0.36 4 12
HNF1A 0.076 0.12 0.33 69 -0.33 1 70
CTBP1 0.023 0.016 0.18 1 -10000 0 1
MYC 0.081 0.25 0.56 68 -1.3 2 70
RANBP3 0.02 0.006 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.033 0.11 0.23 59 -0.17 62 121
NKD1 -0.016 0.12 0.33 4 -0.33 44 48
TCF4 0.019 0.029 0.17 1 -0.33 2 3
TCF3 0.022 0.015 0.18 1 -10000 0 1
WNT1/LRP6/FZD1/Axin1 0.051 0.029 0.23 4 -10000 0 4
Ran/GTP 0.017 0.015 0.22 2 -10000 0 2
CtBP/CBP/TCF/TLE1/AES 0.007 0.12 0.42 14 -0.46 6 20
LEF1 0.025 0.027 0.28 3 -10000 0 3
DVL1 0.035 0.054 0.17 1 -0.34 3 4
CSNK2A1 0.021 0.005 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.02 0.17 -10000 0 -0.61 19 19
DKK1/LRP6/Kremen 2 0.081 0.13 0.26 111 -0.18 34 145
LRP6 0.02 0.006 -10000 0 -10000 0 0
CSNK1A1 0.023 0.016 -10000 0 -10000 0 0
NLK 0.019 0.01 -10000 0 -10000 0 0
CCND1 -0.002 0.19 0.58 16 -1.3 5 21
WNT1 0.026 0.038 0.33 6 -10000 0 6
GSK3A 0.021 0.005 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.004 -10000 0 -10000 0 0
PPP2R5D 0.046 0.078 0.24 34 -0.25 3 37
APC -0.004 0.06 0.18 36 -10000 0 36
WNT1/LRP6/FZD1 0.092 0.088 0.19 64 -0.19 2 66
CREBBP 0.023 0.016 0.18 1 -10000 0 1
TCGA08_retinoblastoma

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
CDKN2B 0.011 0.04 -10000 0 -0.3 5 5
CDKN2C 0.001 0.033 0.34 1 -10000 0 1
CDKN2A 0.1 0.14 0.33 103 -10000 0 103
CCND2 -0.02 0.041 0.14 4 -0.14 8 12
RB1 0.02 0.048 0.2 5 -0.16 3 8
CDK4 -0.022 0.045 0.17 4 -0.16 3 7
CDK6 -0.022 0.045 0.17 3 -0.17 4 7
G1/S progression 0.008 0.091 0.18 66 -0.23 6 72
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP/Tiam1 -0.026 0.073 -10000 0 -0.24 23 23
NT3 (dimer)/TRKC -0.029 0.12 0.24 2 -0.25 82 84
NT3 (dimer)/TRKB -0.04 0.13 0.3 7 -0.21 129 136
SHC/Grb2/SOS1/GAB1/PI3K 0.007 0.027 -10000 0 -0.19 1 1
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
BDNF -0.14 0.17 -10000 0 -0.33 179 179
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DYNLT1 0.019 0.006 -10000 0 -10000 0 0
NTRK1 0.009 0.062 0.33 1 -0.33 12 13
NTRK2 -0.084 0.16 0.33 3 -0.33 120 123
NTRK3 -0.046 0.14 -10000 0 -0.33 75 75
NT-4/5 (dimer)/TRKB -0.041 0.13 0.28 6 -0.21 133 139
neuron apoptosis 0.14 0.17 0.4 93 -10000 0 93
SHC 2-3/Grb2 -0.15 0.19 -10000 0 -0.43 93 93
SHC1 0.018 0.008 -10000 0 -10000 0 0
SHC2 -0.11 0.15 0.2 1 -0.42 52 53
SHC3 -0.16 0.22 -10000 0 -0.53 90 90
STAT3 (dimer) 0.018 0.037 -10000 0 -0.3 5 5
NT3 (dimer)/TRKA 0.021 0.075 0.28 7 -0.21 27 34
RIN/GDP -0.018 0.075 0.34 2 -0.23 9 11
GIPC1 0.02 0.005 -10000 0 -10000 0 0
KRAS 0.02 0.006 -10000 0 -10000 0 0
DNAJA3 -0.015 0.057 0.17 3 -0.21 20 23
RIN/GTP 0.013 0.011 0.22 1 -10000 0 1
CCND1 -0.022 0.065 -10000 0 -0.59 5 5
MAGED1 0.022 0.016 0.33 1 -10000 0 1
PTPN11 0.021 0.004 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.002 0.077 -10000 0 -0.33 20 20
SHC/GRB2/SOS1 0.035 0.017 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK 0.02 0.078 0.23 12 -0.2 32 44
TRKA/NEDD4-2 0.017 0.047 0.24 1 -0.23 12 13
ELMO1 0.017 0.026 -10000 0 -0.33 2 2
RhoG/GTP/ELMO1/DOCK1 0.024 0.018 -10000 0 -0.19 2 2
NGF 0.024 0.087 0.33 17 -0.33 11 28
HRAS 0.021 0.004 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
GAB2 0.017 0.035 -10000 0 -0.33 4 4
RIT2 0.017 0.017 0.33 1 -10000 0 1
RIT1 0.018 0.008 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
DNM1 0.024 0.031 0.33 4 -10000 0 4
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP 0.01 0.067 0.18 2 -0.21 21 23
mol:GDP -0.032 0.1 0.4 2 -0.33 11 13
NGF (dimer) 0.024 0.087 0.33 17 -0.33 11 28
RhoG/GDP 0.013 0.018 -10000 0 -0.22 2 2
RIT1/GDP -0.024 0.062 -10000 0 -0.24 6 6
TIAM1 0.016 0.039 -10000 0 -0.33 5 5
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB -0.13 0.15 0.23 1 -0.24 239 240
KIDINS220/CRKL/C3G 0.03 0.008 -10000 0 -10000 0 0
SHC/RasGAP 0.025 0.013 -10000 0 -10000 0 0
FRS2 family/SHP2 0.038 0.014 -10000 0 -10000 0 0
SHC/GRB2/SOS1/GAB1 0.043 0.025 -10000 0 -0.18 1 1
RIT1/GTP 0.013 0.006 -10000 0 -10000 0 0
NT3 (dimer) 0.003 0.082 0.33 2 -0.33 21 23
RAP1/GDP -0.022 0.06 -10000 0 -0.2 9 9
KIDINS220/CRKL 0.02 0.004 -10000 0 -10000 0 0
BDNF (dimer) -0.14 0.17 -10000 0 -0.33 179 179
ubiquitin-dependent protein catabolic process 0.026 0.064 0.22 13 -0.19 20 33
Schwann cell development -0.036 0.025 -10000 0 -10000 0 0
EHD4 0.02 0.004 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 0.048 0.022 -10000 0 -10000 0 0
FRS2 family/SHP2/CRK family/C3G/GAB2 0.005 0.045 -10000 0 -0.19 4 4
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.14 0.15 -10000 0 -0.33 106 106
ABL1 0.021 0.004 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
Rap1/GTP -0.065 0.095 -10000 0 -0.42 13 13
STAT3 0.019 0.037 -10000 0 -0.3 5 5
axon guidance -0.15 0.12 -10000 0 -0.24 221 221
MAPK3 -0.015 0.077 0.18 31 -0.2 26 57
MAPK1 -0.013 0.077 0.18 32 -0.2 23 55
CDC42/GDP -0.019 0.077 0.34 2 -0.23 8 10
NTF3 0.003 0.082 0.33 2 -0.33 21 23
NTF4 0.002 0.077 -10000 0 -0.33 20 20
NGF (dimer)/TRKA/FAIM 0.031 0.065 0.23 15 -0.19 19 34
PI3K 0.029 0.009 -10000 0 -10000 0 0
FRS3 0.02 0.004 -10000 0 -10000 0 0
FAIM 0.021 0.003 -10000 0 -10000 0 0
GAB1 0.02 0.018 -10000 0 -0.33 1 1
RASGRF1 -0.06 0.088 0.15 1 -0.26 28 29
SOS1 0.021 0.003 -10000 0 -10000 0 0
MCF2L -0.055 0.085 0.17 3 -0.22 76 79
RGS19 0.019 0.006 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.081 0.27 1 -0.4 4 5
Rac1/GDP -0.021 0.069 -10000 0 -0.23 9 9
NGF (dimer)/TRKA/GRIT 0.02 0.061 0.21 15 -0.19 20 35
neuron projection morphogenesis 0.004 0.11 -10000 0 -0.88 3 3
NGF (dimer)/TRKA/NEDD4-2 0.026 0.065 0.23 13 -0.19 20 33
MAP2K1 0.014 0.092 0.19 73 -10000 0 73
NGFR 0.021 0.06 0.33 7 -0.33 6 13
NGF (dimer)/TRKA/GIPC/GAIP -0.003 0.063 0.18 4 -0.21 17 21
RAS family/GTP/PI3K 0.009 0.019 -10000 0 -0.17 4 4
FRS2 family/SHP2/GRB2/SOS1 0.053 0.025 -10000 0 -10000 0 0
NRAS 0.02 0.005 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCZ 0.018 0.031 -10000 0 -0.33 3 3
MAPKKK cascade -0.067 0.19 -10000 0 -0.56 44 44
RASA1 0.02 0.005 -10000 0 -10000 0 0
TRKA/c-Abl 0.019 0.047 0.24 1 -0.23 12 13
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.12 0.14 0.23 2 -0.22 239 241
NGF (dimer)/TRKA/p62/Atypical PKCs 0.039 0.067 0.23 12 -0.18 19 31
MATK 0.006 0.067 -10000 0 -0.33 15 15
NEDD4L 0.019 0.007 -10000 0 -10000 0 0
RAS family/GDP -0.03 0.045 -10000 0 -0.18 12 12
NGF (dimer)/TRKA -0.001 0.063 0.19 4 -0.21 21 25
Rac1/GTP -0.063 0.071 -10000 0 -0.23 31 31
FRS2 family/SHP2/CRK family 0.049 0.029 -10000 0 -10000 0 0
EGFR-dependent Endothelin 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
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.043 0.33 1 -0.33 5 6
EGF/EGFR 0.027 0.089 0.18 47 -0.16 50 97
EGF/EGFR dimer/SHC/GRB2/SOS1 0.061 0.076 0.23 45 -0.2 6 51
mol:GTP 0 0 -10000 0 -10000 0 0
EDNRA 0.02 0.018 -10000 0 -0.33 1 1
response to oxidative stress 0 0 -10000 0 -10000 0 0
EGF 0.074 0.13 0.33 72 -0.33 4 76
EGF/EGFR dimer/SHC 0.05 0.077 0.23 46 -0.21 7 53
mol:GDP 0.056 0.071 0.21 45 -0.2 6 51
mol:Ca2+ 0 0 -10000 0 -10000 0 0
EDN1 -0.024 0.12 -10000 0 -0.33 50 50
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
HRAS/GTP 0.035 0.05 0.23 1 -0.19 5 6
SHC1 0.018 0.008 -10000 0 -10000 0 0
HRAS/GDP 0.05 0.062 0.29 1 -0.2 5 6
FRAP1 -0.013 0.036 0.17 4 -0.19 6 10
EGF/EGFR dimer 0.053 0.089 0.24 59 -0.24 8 67
SOS1 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1 -0.004 0.088 -10000 0 -0.23 51 51
Thromboxane A2 receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGM2 0.017 0.031 -10000 0 -0.33 3 3
GNB1/GNG2 -0.045 0.066 -10000 0 -0.19 63 63
AKT1 -0.033 0.096 -10000 0 -0.26 17 17
EGF 0.074 0.13 0.33 72 -0.33 4 76
mol:TXA2 0 0 -10000 0 -10000 0 0
FGR -0.031 0.062 -10000 0 -0.23 15 15
mol:Ca2+ -0.053 0.13 -10000 0 -0.31 64 64
LYN -0.021 0.041 -10000 0 -0.2 3 3
RhoA/GTP -0.029 0.051 -10000 0 -0.14 47 47
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.062 0.14 -10000 0 -0.34 63 63
GNG2 0.019 0.018 -10000 0 -0.33 1 1
ARRB2 0.019 0.006 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.036 0.16 -10000 0 -0.62 24 24
G beta5/gamma2 -0.056 0.086 -10000 0 -0.24 61 61
PRKCH -0.062 0.15 -10000 0 -0.35 65 65
DNM1 0.024 0.031 0.33 4 -10000 0 4
TXA2/TP beta/beta Arrestin3 0.007 0.05 -10000 0 -0.53 3 3
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.014 0.046 -10000 0 -0.33 7 7
G12 family/GTP -0.052 0.12 -10000 0 -0.3 61 61
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
ADRBK2 0.02 0.004 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0.027 0.007 -10000 0 -10000 0 0
mol:GDP 0.036 0.11 0.35 20 -10000 0 20
mol:NADP 0.023 0.052 0.33 7 -0.33 3 10
RAB11A 0.021 0.003 -10000 0 -10000 0 0
PRKG1 -0.012 0.1 -10000 0 -0.33 37 37
mol:IP3 -0.068 0.16 -10000 0 -0.38 67 67
cell morphogenesis 0.026 0.007 -10000 0 -10000 0 0
PLCB2 -0.095 0.22 -10000 0 -0.52 70 70
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.001 0.068 0.24 2 -0.2 3 5
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.025 0.051 -10000 0 -0.22 8 8
RHOA 0.021 0.004 -10000 0 -10000 0 0
PTGIR 0.015 0.039 -10000 0 -0.33 5 5
PRKCB1 -0.065 0.16 -10000 0 -0.38 67 67
GNAQ 0.019 0.018 -10000 0 -0.33 1 1
mol:L-citrulline 0.023 0.052 0.33 7 -0.33 3 10
TXA2/TXA2-R family -0.093 0.21 -10000 0 -0.52 64 64
LCK -0.022 0.048 -10000 0 -0.22 4 4
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.011 0.048 0.18 1 -0.22 6 7
TXA2-R family/G12 family/GDP/G beta/gamma 0.007 0.07 -10000 0 -0.42 9 9
TXA2/TP beta/beta Arrestin2/RAB11/GDP 0.011 0.047 -10000 0 -0.22 5 5
MAPK14 -0.039 0.1 0.26 5 -0.23 55 60
TGM2/GTP -0.077 0.17 -10000 0 -0.42 63 63
MAPK11 -0.044 0.094 -10000 0 -0.23 60 60
ARHGEF1 -0.038 0.07 -10000 0 -0.18 53 53
GNAI2 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.067 0.16 -10000 0 -0.38 64 64
RAB11/GDP 0.02 0.006 -10000 0 -10000 0 0
ICAM1 -0.048 0.12 -10000 0 -0.29 61 61
cAMP biosynthetic process -0.065 0.15 -10000 0 -0.35 66 66
Gq family/GTP/EBP50 -0.002 0.045 -10000 0 -0.2 16 16
actin cytoskeleton reorganization 0.026 0.007 -10000 0 -10000 0 0
SRC -0.022 0.043 -10000 0 -0.2 3 3
GNB5 0.021 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
EGF/EGFR -0.009 0.076 0.21 6 -0.24 10 16
VCAM1 -0.049 0.12 0.23 1 -0.29 61 62
TP beta/Gq family/GDP/G beta5/gamma2 -0.036 0.16 -10000 0 -0.62 24 24
platelet activation -0.052 0.13 0.31 3 -0.3 60 63
PGI2/IP 0.012 0.027 -10000 0 -0.22 5 5
PRKACA 0.003 0.038 -10000 0 -0.22 10 10
Gq family/GDP/G beta5/gamma2 -0.019 0.12 -10000 0 -0.55 16 16
TXA2/TP beta/beta Arrestin2 -0.005 0.061 -10000 0 -0.36 6 6
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.014 0.035 -10000 0 -0.21 10 10
mol:DAG -0.074 0.18 -10000 0 -0.43 67 67
EGFR 0.015 0.043 0.33 1 -0.33 5 6
TXA2/TP alpha -0.089 0.2 -10000 0 -0.48 67 67
Gq family/GTP -0.016 0.072 0.22 1 -0.24 32 33
YES1 -0.021 0.045 0.16 1 -0.2 3 4
GNAI2/GTP -0.025 0.035 -10000 0 -0.19 8 8
PGD2/DP 0.011 0.032 -10000 0 -0.22 7 7
SLC9A3R1 0.021 0.016 0.33 1 -10000 0 1
FYN -0.021 0.043 -10000 0 -0.2 3 3
mol:NO 0.023 0.052 0.33 7 -0.33 3 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
PGK/cGMP 0.009 0.071 0.21 7 -0.2 36 43
RhoA/GDP 0.02 0.006 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma 0.018 0.052 -10000 0 -0.24 5 5
NOS3 0.023 0.052 0.33 7 -0.33 3 10
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.061 0.15 0.27 2 -0.36 62 64
PRKCB -0.064 0.15 -10000 0 -0.37 62 62
PRKCE -0.062 0.15 0.29 1 -0.36 61 62
PRKCD -0.067 0.15 -10000 0 -0.38 64 64
PRKCG -0.066 0.16 -10000 0 -0.39 65 65
muscle contraction -0.088 0.2 -10000 0 -0.48 65 65
PRKCZ -0.062 0.14 -10000 0 -0.34 63 63
ARR3 0.019 0.016 0.33 1 -10000 0 1
TXA2/TP beta 0.007 0.049 -10000 0 -0.2 8 8
PRKCQ -0.073 0.15 -10000 0 -0.38 68 68
MAPKKK cascade -0.084 0.19 -10000 0 -0.46 68 68
SELE -0.06 0.14 0.23 1 -0.36 61 62
TP beta/GNAI2/GDP/G beta/gamma 0.021 0.05 -10000 0 -0.24 4 4
ROCK1 0.02 0.004 -10000 0 -10000 0 0
GNA14 0.011 0.055 -10000 0 -0.33 10 10
chemotaxis -0.1 0.23 -10000 0 -0.59 63 63
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.006 -10000 0 -10000 0 0
Rac1/GTP 0.013 0.005 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

Figure S36.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) 0.004 0.1 -10000 0 -0.42 18 18
HDAC1 0.021 0.006 -10000 0 -10000 0 0
AES 0.02 0.006 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
DTX1 0.022 0.022 0.33 2 -10000 0 2
LRP6/FZD1 0.028 0.01 -10000 0 -10000 0 0
TLE1 0.02 0.005 -10000 0 -10000 0 0
AP1 -0.026 0.09 -10000 0 -0.24 49 49
NCSTN 0.019 0.007 -10000 0 -10000 0 0
ADAM10 0.021 0.004 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.021 0.095 -10000 0 -0.69 5 5
NICD/RBPSUH 0.014 0.11 -10000 0 -0.42 18 18
WIF1 -0.21 0.16 -10000 0 -0.33 253 253
NOTCH1 -0.005 0.09 -10000 0 -0.44 16 16
PSENEN 0.02 0.005 -10000 0 -10000 0 0
KREMEN2 0.094 0.13 0.33 93 -10000 0 93
DKK1 0.038 0.16 0.33 61 -0.33 35 96
beta catenin/beta TrCP1 0.014 0.072 0.3 1 -0.28 2 3
APH1B 0.02 0.018 -10000 0 -0.33 1 1
APH1A 0.017 0.008 -10000 0 -10000 0 0
AXIN1 0.001 0.07 -10000 0 -0.42 5 5
CtBP/CBP/TCF1/TLE1/AES 0.02 0.056 0.26 2 -10000 0 2
PSEN1 0.02 0.004 -10000 0 -10000 0 0
FOS -0.005 0.09 -10000 0 -0.33 28 28
JUN 0.019 0.025 -10000 0 -0.33 2 2
MAP3K7 0.019 0.007 -10000 0 -10000 0 0
CTNNB1 0.01 0.073 0.27 2 -0.27 3 5
MAPK3 0.021 0.003 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 0.033 0.11 0.23 59 -0.17 62 121
HNF1A 0.074 0.12 0.33 68 -0.33 1 69
CTBP1 0.021 0.004 -10000 0 -10000 0 0
MYC 0.007 0.087 -10000 0 -1.2 2 2
NKD1 -0.016 0.12 0.33 4 -0.33 44 48
FZD1 0.02 0.005 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 0.016 0.11 -10000 0 -0.42 18 18
apoptosis -0.026 0.089 -10000 0 -0.24 49 49
Delta 1/NOTCHprecursor 0.011 0.11 -10000 0 -0.42 18 18
DLL1 0.014 0.043 -10000 0 -0.33 6 6
PPARD 0.015 0.047 -10000 0 -0.84 1 1
Gamma Secretase 0.046 0.03 -10000 0 -10000 0 0
APC -0.008 0.094 -10000 0 -0.43 12 12
DVL1 -0.031 0.062 -10000 0 -0.26 23 23
CSNK2A1 0.02 0.006 -10000 0 -10000 0 0
MAP3K7IP1 0 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 0.081 0.13 0.26 111 -0.18 34 145
LRP6 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.02 0.006 -10000 0 -10000 0 0
NLK 0.006 0.005 -10000 0 -10000 0 0
CCND1 -0.001 0.15 -10000 0 -1.1 7 7
WNT1 0.025 0.038 0.33 6 -10000 0 6
Axin1/APC/beta catenin 0.006 0.1 0.3 6 -0.39 10 16
DKK2 -0.039 0.13 -10000 0 -0.33 67 67
NOTCH1 precursor/DVL1 -0.031 0.11 -10000 0 -0.43 19 19
GSK3B 0.021 0.003 -10000 0 -10000 0 0
FRAT1 0.021 0.003 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 0.008 0.1 -10000 0 -0.42 18 18
PPP2R5D 0.01 0.074 0.24 2 -0.32 6 8
MAPK1 0.02 0.005 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.091 0.11 0.23 2 -0.18 228 230
RBPJ 0.02 0.004 -10000 0 -10000 0 0
CREBBP 0.021 0.005 -10000 0 -10000 0 0
Aurora A signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A -0.005 0.057 -10000 0 -10000 0 0
BIRC5 0.19 0.16 0.33 217 -10000 0 217
NFKBIA 0.001 0.077 0.28 21 -10000 0 21
CPEB1 -0.026 0.12 0.33 2 -0.33 54 56
AKT1 -0.014 0.046 0.27 2 -10000 0 2
NDEL1 0.019 0.006 -10000 0 -10000 0 0
Aurora A/BRCA1 -0.005 0.052 -10000 0 -10000 0 0
NDEL1/TACC3 0 0.056 -10000 0 -10000 0 0
GADD45A 0.021 0.004 -10000 0 -10000 0 0
GSK3B -0.017 0.032 -10000 0 -10000 0 0
PAK1/Aurora A -0.006 0.057 -10000 0 -10000 0 0
MDM2 0.02 0.006 -10000 0 -10000 0 0
JUB 0 0 -10000 0 -10000 0 0
TPX2 0.087 0.097 0.17 220 -10000 0 220
TP53 -0.003 0.057 0.22 1 -0.22 16 17
DLG7 -0.01 0.037 0.16 1 -10000 0 1
AURKAIP1 0.02 0.004 -10000 0 -10000 0 0
ARHGEF7 0.02 0.005 -10000 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -10000 0 -10000 0 0
Aurora A/NDEL1/TACC3 0.001 0.059 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.005 0.051 -10000 0 -10000 0 0
AURKA -0.003 0.057 0.2 1 -10000 0 1
AURKB 0.1 0.089 0.19 193 -10000 0 193
CDC25B -0.002 0.042 -10000 0 -0.23 2 2
G2/M transition checkpoint -0.013 0.04 -10000 0 -0.13 6 6
mRNA polyadenylation -0.028 0.081 0.36 1 -0.2 44 45
Aurora A/CPEB -0.029 0.082 0.36 1 -0.2 44 45
Aurora A/TACC1/TRAP/chTOG 0.002 0.068 -10000 0 -0.22 5 5
BRCA1 0.021 0.003 -10000 0 -10000 0 0
centrosome duplication -0.006 0.057 -10000 0 -10000 0 0
regulation of centrosome cycle 0 0.055 -10000 0 -10000 0 0
spindle assembly 0.001 0.067 -10000 0 -0.22 5 5
TDRD7 0.021 0.004 -10000 0 -10000 0 0
Aurora A/RasGAP/Survivin 0.12 0.1 0.25 85 -10000 0 85
CENPA 0.11 0.093 0.2 204 -10000 0 204
Aurora A/PP2A -0.006 0.057 -10000 0 -0.16 3 3
meiosis 0 0 -10000 0 -10000 0 0
protein catabolic process -0.006 0.05 0.17 5 -0.18 2 7
negative regulation of DNA binding -0.003 0.057 0.22 1 -0.22 16 17
prophase 0 0 -10000 0 -10000 0 0
GIT1/beta-PIX 0.029 0.009 -10000 0 -10000 0 0
RASA1 0.02 0.005 -10000 0 -10000 0 0
Ajuba/Aurora A -0.013 0.04 -10000 0 -0.13 6 6
mitotic prometaphase -0.014 0.031 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.003 0.057 0.2 1 -10000 0 1
TACC1 0.008 0.06 -10000 0 -0.33 12 12
TACC3 0.021 0.004 -10000 0 -10000 0 0
Aurora A/Antizyme1 0.003 0.059 -10000 0 -10000 0 0
Aurora A/RasGAP -0.005 0.055 -10000 0 -10000 0 0
OAZ1 0.02 0.005 -10000 0 -10000 0 0
RAN 0.022 0.022 0.33 2 -10000 0 2
mitosis 0 0 -10000 0 -10000 0 0
PRKACA -0.017 0.031 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
GIT1/beta-PIX/PAK1 0.038 0.015 -10000 0 -10000 0 0
Importin alpha/Importin beta/TPX2 0.087 0.096 0.17 220 -10000 0 220
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
Aurora A/TPX2 0.055 0.084 0.19 76 -10000 0 76
PAK1 0.02 0.005 -10000 0 -10000 0 0
CKAP5 0.021 0.003 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 0.034 0.032 0.24 9 -10000 0 9
VLDLR 0.013 0.046 -10000 0 -0.33 7 7
CRKL 0.021 0.004 -10000 0 -10000 0 0
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
FYN 0.018 0.019 -10000 0 -0.33 1 1
ITGA3 0.018 0.031 -10000 0 -0.33 3 3
RELN/VLDLR/Fyn 0.007 0.084 0.23 5 -0.2 49 54
MAPK8IP1/MKK7/MAP3K11/JNK1 0.047 0.031 -10000 0 -0.18 1 1
AKT1 -0.033 0.073 0.2 3 -0.21 47 50
MAP2K7 0.02 0.005 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
DAB1 0.023 0.035 0.33 5 -10000 0 5
RELN/LRP8/DAB1 0.021 0.081 0.23 16 -0.18 44 60
LRPAP1/LRP8 0.034 0.028 0.24 7 -10000 0 7
RELN/LRP8/DAB1/Fyn 0.024 0.081 0.22 15 -0.17 45 60
DAB1/alpha3/beta1 Integrin 0.015 0.077 0.27 1 -0.18 44 45
long-term memory 0.011 0.1 0.26 13 -0.18 65 78
DAB1/LIS1 0.023 0.085 0.35 1 -0.18 47 48
DAB1/CRLK/C3G 0.016 0.078 0.27 1 -0.18 42 43
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
DAB1/NCK2 0.028 0.085 0.36 1 -0.18 44 45
ARHGEF2 0.018 0.008 -10000 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -10000 0 -10000 0 0
GRIN2A 0.011 0.14 0.33 33 -0.33 40 73
CDK5R1 0.028 0.047 0.33 9 -10000 0 9
RELN -0.015 0.12 0.33 5 -0.33 44 49
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
RELN/LRP8/Fyn 0.015 0.084 0.23 12 -0.2 45 57
GRIN2A/RELN/LRP8/DAB1/Fyn 0.022 0.12 0.24 35 -0.18 69 104
MAPK8 0.021 0.003 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.012 0.08 0.24 9 -0.18 47 56
ITGB1 0.021 0.004 -10000 0 -10000 0 0
MAP1B -0.027 0.075 0.17 20 -0.19 44 64
RELN/LRP8 0.017 0.083 0.23 11 -0.2 44 55
GRIN2B/RELN/LRP8/DAB1/Fyn 0.032 0.092 0.39 4 -0.17 43 47
PI3K 0.029 0.009 -10000 0 -10000 0 0
mol:PP2 0 0 -10000 0 -10000 0 0
alpha3/beta1 Integrin 0.028 0.024 -10000 0 -0.23 3 3
RAP1A -0.032 0.075 0.25 4 -0.3 2 6
PAFAH1B1 0.019 0.006 -10000 0 -10000 0 0
MAPK8IP1 0.021 0.003 -10000 0 -10000 0 0
CRLK/C3G 0.03 0.008 -10000 0 -10000 0 0
GRIN2B 0.025 0.047 0.33 9 -10000 0 9
NCK2 0.021 0.002 -10000 0 -10000 0 0
neuron differentiation -0.008 0.076 0.24 2 -0.31 8 10
neuron adhesion -0.033 0.084 0.29 8 -0.3 2 10
LRP8 0.027 0.044 0.33 8 -10000 0 8
GSK3B -0.035 0.07 0.18 3 -0.2 46 49
RELN/VLDLR/DAB1/Fyn 0.017 0.08 0.24 8 -0.17 48 56
MAP3K11 0.02 0.018 -10000 0 -0.33 1 1
RELN/VLDLR/DAB1/P13K -0.014 0.079 0.19 3 -0.21 48 51
CDK5 0.02 0.004 -10000 0 -10000 0 0
MAPT -0.008 0.12 0.79 6 -0.29 20 26
neuron migration -0.038 0.098 0.24 8 -0.27 40 48
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.008 0.076 0.24 2 -0.31 8 10
RELN/VLDLR 0.022 0.088 0.23 11 -0.19 48 59
TCGA08_p53

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
CDKN2A 0.039 0.075 0.16 105 -10000 0 105
TP53 0.01 0.037 -10000 0 -0.12 19 19
Senescence 0.01 0.037 -10000 0 -0.12 14 14
Apoptosis 0.01 0.037 -10000 0 -0.12 14 14
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 -0.021 0.078 0.26 18 -0.19 2 20
MDM4 0.019 0.006 -10000 0 -10000 0 0
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.014 0.28 0.57 19 -0.68 6 25
CRP 0.031 0.3 0.58 30 -0.61 12 42
cell cycle arrest 0.003 0.31 0.55 26 -0.62 24 50
TIMP1 0.018 0.27 0.54 21 -0.64 11 32
IL6ST 0.008 0.061 -10000 0 -0.32 10 10
Rac1/GDP 0 0.14 0.32 15 -0.31 25 40
AP1 0.052 0.13 0.38 7 -0.45 7 14
GAB2 0.019 0.036 -10000 0 -0.32 4 4
TNFSF11 0.038 0.3 0.58 30 -0.68 7 37
HSP90B1 0.017 0.16 0.46 1 -0.72 11 12
GAB1 0.021 0.018 -10000 0 -0.33 1 1
MAPK14 -0.022 0.099 0.27 4 -0.44 6 10
AKT1 0.011 0.091 0.29 1 -0.57 5 6
FOXO1 0.01 0.089 0.32 2 -0.6 4 6
MAP2K6 -0.015 0.11 0.28 11 -0.28 25 36
mol:GTP 0 0.004 -10000 0 -10000 0 0
MAP2K4 0.002 0.18 0.36 23 -0.37 24 47
MITF -0.004 0.13 0.28 17 -0.29 28 45
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TYK2 0.02 0.005 -10000 0 -10000 0 0
A2M -0.12 0.38 -10000 0 -1.2 45 45
CEBPB 0.024 0.01 -10000 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.017 0.094 0.28 4 -0.38 7 11
STAT3 -0.003 0.32 0.55 26 -0.66 24 50
STAT1 0.023 0.037 -10000 0 -10000 0 0
CEBPD 0.02 0.3 0.59 22 -0.8 7 29
PIK3CA 0.021 0.005 -10000 0 -10000 0 0
PI3K 0.029 0.01 -10000 0 -10000 0 0
JUN 0.019 0.025 -10000 0 -0.33 2 2
PIAS3/MITF 0 0.13 0.28 13 -0.28 27 40
MAPK11 -0.021 0.097 0.26 3 -0.44 6 9
STAT3 (dimer)/FOXO1 -0.016 0.26 0.5 21 -0.68 10 31
GRB2/SOS1/GAB family 0.006 0.12 0.27 3 -0.3 13 16
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.017 0.11 0.24 4 -0.28 34 38
GRB2 0.022 0.006 -10000 0 -10000 0 0
JAK2 0.018 0.019 -10000 0 -0.33 1 1
LBP 0.053 0.28 0.54 42 -0.6 10 52
PIK3R1 0.02 0.006 -10000 0 -10000 0 0
JAK1 0.013 0.025 -10000 0 -10000 0 0
MYC 0.035 0.29 0.59 24 -0.77 6 30
FGG -0.15 0.51 0.57 28 -0.89 116 144
macrophage differentiation 0.003 0.31 0.55 26 -0.62 24 50
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 0.002 0.096 0.24 2 -0.21 37 39
JUNB 0.004 0.27 0.54 17 -0.71 7 24
FOS -0.004 0.09 -10000 0 -0.33 28 28
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.003 0.13 0.29 22 -0.3 30 52
STAT1/PIAS1 0.015 0.16 0.33 25 -0.31 22 47
GRB2/SOS1/GAB family/SHP2/PI3K 0.014 0.09 -10000 0 -0.55 6 6
STAT3 (dimer) -0.001 0.31 0.55 26 -0.65 24 50
PRKCD 0.023 0.23 0.42 42 -0.44 23 65
IL6R 0.003 0.053 -10000 0 -0.32 8 8
SOCS3 -0.018 0.12 0.34 1 -0.86 3 4
gp130 (dimer)/JAK1/JAK1/LMO4 0.032 0.069 0.25 2 -0.2 6 8
Rac1/GTP -0.001 0.15 0.32 21 -0.33 26 47
HCK 0.008 0.064 -10000 0 -0.32 14 14
MAPKKK cascade 0.031 0.12 0.34 1 -0.51 8 9
bone resorption 0.041 0.3 0.57 33 -0.64 7 40
IRF1 0.007 0.28 0.54 19 -0.7 7 26
mol:GDP 0.003 0.13 0.27 24 -0.29 25 49
SOS1 0.023 0.007 -10000 0 -10000 0 0
VAV1 0 0.13 0.28 24 -0.29 25 49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.018 0.1 0.38 1 -0.41 13 14
PTPN11 0.009 0.11 -10000 0 -0.71 8 8
IL6/IL6RA -0.017 0.099 0.18 1 -0.23 60 61
gp130 (dimer)/TYK2/TYK2/LMO4 0.03 0.057 0.21 1 -0.18 10 11
gp130 (dimer)/JAK2/JAK2/LMO4 0.029 0.055 0.21 1 -0.19 7 8
IL6 -0.045 0.14 0.14 1 -0.33 72 73
PIAS3 0.021 0.004 -10000 0 -10000 0 0
PTPRE -0.002 0.045 -10000 0 -0.27 3 3
PIAS1 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.016 0.014 -10000 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.019 0.1 0.22 5 -0.26 42 47
LMO4 0.017 0.033 -10000 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.021 0.28 0.52 17 -0.63 24 41
MCL1 0.039 0.11 0.41 3 -0.58 3 6
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.026 0.098 0.18 2 -0.24 55 57
FZD6 0.018 0.019 -10000 0 -0.33 1 1
WNT6 0.038 0.071 0.33 22 -10000 0 22
WNT4 0.007 0.085 0.33 5 -0.33 20 25
FZD3 0.019 0.018 0.33 1 -10000 0 1
WNT5A 0.016 0.039 -10000 0 -0.33 5 5
WNT11 -0.022 0.12 0.33 1 -0.33 49 50
Noncanonical Wnt signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC2 0.01 0.058 -10000 0 -0.33 11 11
GNB1/GNG2 -0.008 0.1 0.23 1 -0.29 20 21
mol:DAG -0.038 0.084 0.18 3 -0.28 17 20
PLCG1 -0.039 0.086 0.18 3 -0.29 17 20
YES1 -0.036 0.088 0.21 4 -0.23 49 53
FZD3 0.019 0.018 0.33 1 -10000 0 1
FZD6 0.018 0.019 -10000 0 -0.33 1 1
G protein -0.007 0.1 0.24 3 -0.29 17 20
MAP3K7 -0.043 0.09 0.19 2 -0.27 28 30
mol:Ca2+ -0.037 0.082 0.18 3 -0.28 17 20
mol:IP3 -0.038 0.084 0.18 3 -0.28 17 20
NLK -0.002 0.092 -10000 0 -0.8 5 5
GNB1 0.02 0.004 -10000 0 -10000 0 0
CAMK2A -0.047 0.097 0.2 1 -0.28 33 34
MAP3K7IP1 0 0 -10000 0 -10000 0 0
Noncanonical Wnts/FZD -0.026 0.098 0.18 2 -0.24 55 57
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
GNAS -0.036 0.085 0.16 2 -0.23 50 52
GO:0007205 -0.036 0.083 0.19 2 -0.27 19 21
WNT6 0.038 0.071 0.33 22 -10000 0 22
WNT4 0.007 0.085 0.33 5 -0.33 20 25
NFAT1/CK1 alpha -0.016 0.1 0.3 3 -0.3 18 21
GNG2 0.019 0.018 -10000 0 -0.33 1 1
WNT5A 0.016 0.039 -10000 0 -0.33 5 5
WNT11 -0.022 0.12 0.33 1 -0.33 49 50
CDC42 -0.033 0.089 0.2 5 -0.23 49 54
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer 0.01 0.077 -10000 0 -0.2 45 45
fibroblast growth factor receptor signaling pathway 0.009 0.076 -10000 0 -0.2 45 45
LAMA1 0.026 0.069 0.33 13 -0.33 5 18
PRNP 0.019 0.018 -10000 0 -0.33 1 1
GPC1/SLIT2 -0.025 0.11 -10000 0 -0.23 83 83
SMAD2 -0.022 0.026 0.17 2 -0.18 6 8
GPC1/PrPc/Cu2+ 0.025 0.02 -10000 0 -0.18 3 3
GPC1/Laminin alpha1 0.031 0.05 0.24 12 -0.22 7 19
TDGF1 0.022 0.076 0.33 12 -0.33 9 21
CRIPTO/GPC1 0.029 0.057 0.24 12 -0.23 11 23
APP/GPC1 0.028 0.021 -10000 0 -0.23 2 2
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.02 0.034 0.1 10 -0.2 9 19
FLT1 0.02 0.005 -10000 0 -10000 0 0
GPC1/TGFB/TGFBR1/TGFBR2 0.036 0.037 0.23 1 -0.2 8 9
SERPINC1 0.022 0.032 0.33 4 -10000 0 4
FYN -0.019 0.038 -10000 0 -0.22 9 9
FGR -0.033 0.06 0.1 10 -0.21 33 43
positive regulation of MAPKKK cascade -0.021 0.096 0.23 3 -0.32 24 27
SLIT2 -0.053 0.14 -10000 0 -0.33 82 82
GPC1/NRG -0.014 0.093 -10000 0 -0.23 60 60
NRG1 -0.034 0.12 -10000 0 -0.33 58 58
GPC1/VEGF165 homodimer/VEGFR1 homodimer 0.037 0.022 -10000 0 -0.2 2 2
LYN -0.018 0.034 0.1 12 -0.2 8 20
mol:Spermine -0.01 0.015 -10000 0 -0.22 2 2
cell growth 0.009 0.076 -10000 0 -0.2 45 45
BMP signaling pathway -0.019 0.025 0.33 2 -10000 0 2
SRC -0.02 0.036 -10000 0 -0.2 10 10
TGFBR1 0.021 0.016 0.33 1 -10000 0 1
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.012 0.12 0.33 8 -0.33 44 52
GPC1 0.019 0.025 -10000 0 -0.33 2 2
TGFBR1 (dimer) 0.021 0.016 0.33 1 -10000 0 1
VEGFA 0.02 0.004 -10000 0 -10000 0 0
BLK 0.003 0.07 0.16 53 -0.2 9 62
HCK -0.026 0.047 0.1 11 -0.2 22 33
FGF2 -0.021 0.11 -10000 0 -0.33 47 47
FGFR1 0.017 0.019 -10000 0 -0.33 1 1
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 0.015 0.043 -10000 0 -0.33 6 6
cell death 0.028 0.02 -10000 0 -0.23 2 2
ATIII/GPC1 0.028 0.03 0.24 4 -0.23 2 6
PLA2G2A/GPC1 0.004 0.09 0.24 8 -0.23 45 53
LCK -0.021 0.039 0.11 13 -0.2 12 25
neuron differentiation -0.014 0.093 -10000 0 -0.23 60 60
PrPc/Cu2+ 0.014 0.013 -10000 0 -0.22 1 1
APP 0.02 0.005 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.015 0.043 -10000 0 -0.33 6 6
Effects of Botulinum toxin

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
STX1A 0.033 0.077 0.17 91 -10000 0 91
UniProt:P19321 0 0 -10000 0 -10000 0 0
RIMS1/UNC13B 0.015 0.075 0.24 9 -0.23 27 36
STXBP1 0.018 0.031 -10000 0 -0.33 3 3
ACh/CHRNA1 0.027 0.073 0.25 28 -0.19 8 36
RAB3GAP2/RIMS1/UNC13B 0.024 0.064 0.23 7 -0.2 24 31
mol:Ca2+ 0 0 -10000 0 -10000 0 0
UniProt:P30996 0 0 -10000 0 -10000 0 0
UniProt:Q60393 0 0 -10000 0 -10000 0 0
CST086 0 0 -10000 0 -10000 0 0
RIMS1 0.003 0.1 0.33 10 -0.33 27 37
mol:ACh 0.004 0.032 0.08 26 -0.11 8 34
RAB3GAP2 0.019 0.006 -10000 0 -10000 0 0
STX1A/SNAP25/VAMP2 0.024 0.068 0.23 1 -0.16 23 24
UniProt:P10844 0 0 -10000 0 -10000 0 0
muscle contraction 0.027 0.073 0.25 28 -0.19 8 36
UNC13B 0.02 0.005 -10000 0 -10000 0 0
CHRNA1 0.036 0.093 0.33 27 -0.33 7 34
UniProt:P10845 0 0 -10000 0 -10000 0 0
ACh/Synaptotagmin 1 0.027 0.069 0.26 25 -0.14 9 34
SNAP25 0.004 0.032 0.12 15 -0.22 4 19
VAMP2 0.002 0.001 -10000 0 -10000 0 0
SYT1 0.035 0.088 0.33 25 -0.33 6 31
UniProt:Q00496 0 0 -10000 0 -10000 0 0
STXIA/STXBP1 0.042 0.055 0.14 90 -0.19 3 93
STX1A/SNAP25 fragment 1/VAMP2 0.024 0.068 0.23 1 -0.16 23 24
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.008 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0.011 0.072 0.21 1 -0.18 47 48
regulation of S phase of mitotic cell cycle -0.016 0.072 0.16 1 -0.2 48 49
GNAO1 0.02 0.034 0.33 2 -0.33 2 4
HRAS 0.017 0.012 -10000 0 -10000 0 0
SHBG/T-DHT 0.013 0.01 0.2 1 -10000 0 1
PELP1 0.017 0.012 -10000 0 -10000 0 0
AKT1 -0.008 0.002 -10000 0 -10000 0 0
MAP2K1 -0.041 0.066 0.16 12 -0.26 10 22
T-DHT/AR -0.016 0.08 0.22 1 -0.22 49 50
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP 0 0.002 -10000 0 -0.006 30 30
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.018 -10000 0 -0.33 1 1
mol:GDP -0.049 0.1 0.2 1 -0.31 52 53
cell proliferation -0.065 0.13 0.27 2 -0.43 35 37
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
FOS -0.069 0.2 -10000 0 -0.71 32 32
mol:Ca2+ -0.009 0.02 -10000 0 -0.057 43 43
MAPK3 -0.055 0.1 0.26 3 -0.33 32 35
MAPK1 -0.032 0.091 0.2 1 -0.33 21 22
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
mol:IP3 0 0.001 -10000 0 -0.004 29 29
cAMP biosynthetic process 0.002 0.02 0.23 1 -10000 0 1
GNG2 0.019 0.018 -10000 0 -0.33 1 1
potassium channel inhibitor activity 0 0.001 -10000 0 -0.004 29 29
HRAS/GTP 0.006 0.07 -10000 0 -0.17 46 46
actin cytoskeleton reorganization 0.026 0.014 -10000 0 -10000 0 0
SRC 0.017 0.011 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.001 -10000 0 -0.004 29 29
PI3K 0.026 0.008 -10000 0 -10000 0 0
apoptosis 0.049 0.13 0.45 32 -0.26 1 33
T-DHT/AR/PELP1 -0.003 0.073 0.2 1 -0.19 49 50
HRAS/GDP -0.05 0.098 0.19 1 -0.31 47 48
CREB1 -0.053 0.14 0.27 1 -0.49 32 33
RAC1-CDC42/GTP 0.033 0.018 -10000 0 -10000 0 0
AR -0.024 0.12 0.33 1 -0.33 49 50
GNB1 0.02 0.004 -10000 0 -10000 0 0
RAF1 -0.036 0.065 0.18 13 -0.24 8 21
RAC1-CDC42/GDP -0.017 0.1 0.2 1 -0.3 42 43
T-DHT/AR/PELP1/Src 0.007 0.072 0.2 1 -0.18 47 48
MAP2K2 -0.041 0.066 0.16 11 -0.25 10 21
T-DHT/AR/PELP1/Src/PI3K -0.016 0.073 0.16 1 -0.2 48 49
GNAZ -0.01 0.098 -10000 0 -0.33 34 34
SHBG 0.02 0.017 0.33 1 -10000 0 1
Gi family/GNB1/GNG2/GDP -0.024 0.099 -10000 0 -0.39 17 17
mol:T-DHT 0 0.001 -10000 0 -0.003 7 7
RAC1 0.019 0.007 -10000 0 -10000 0 0
GNRH1 -0.009 0.016 -10000 0 -0.22 2 2
Gi family/GTP -0.029 0.072 -10000 0 -0.21 44 44
CDC42 0.021 0.004 -10000 0 -10000 0 0
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.077 0.16 -10000 0 -0.33 109 109
oxygen homeostasis 0 0 -10000 0 -10000 0 0
TCEB2 0.021 0.003 -10000 0 -10000 0 0
TCEB1 0.02 0.017 0.33 1 -10000 0 1
HIF1A/p53 0.027 0.055 0.24 1 -0.24 8 9
HIF1A 0.009 0.046 -10000 0 -0.25 8 8
COPS5 0.019 0.007 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0.052 0.027 -10000 0 -10000 0 0
FIH (dimer) 0.021 0.003 -10000 0 -10000 0 0
CDKN2A 0.098 0.14 0.33 103 -10000 0 103
ARNT/IPAS -0.037 0.11 -10000 0 -0.23 92 92
HIF1AN 0.021 0.003 -10000 0 -10000 0 0
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/ARNT 0.021 0.046 0.24 1 -0.23 5 6
CUL2 0.021 0.004 -10000 0 -10000 0 0
OS9 0.02 0.005 -10000 0 -10000 0 0
RACK1/Elongin B/Elongin C 0.037 0.019 0.23 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF1A/Hsp90 0.027 0.052 -10000 0 -0.25 8 8
PHD1-3/OS9 0.081 0.083 0.23 80 -10000 0 80
HIF1A/RACK1/Elongin B/Elongin C 0.04 0.052 0.24 2 -0.24 6 8
VHL 0.021 0.004 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
HIF1A/JAB1 0.023 0.053 0.24 1 -0.25 8 9
EGLN3 0.091 0.14 0.33 93 -0.33 1 94
EGLN2 0.02 0.004 -10000 0 -10000 0 0
EGLN1 0.02 0.006 -10000 0 -10000 0 0
TP53 0.019 0.006 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.01 0.1 -10000 0 -0.49 15 15
ARNT 0.017 0.008 -10000 0 -10000 0 0
ARD1A 0 0 -10000 0 -10000 0 0
RBX1 0.021 0.004 -10000 0 -10000 0 0
HIF1A/p19ARF 0.068 0.099 0.22 98 -0.22 6 104
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
GNAO1 0.02 0.034 0.33 2 -0.33 2 4
CDC42/GTP -0.015 0.08 -10000 0 -0.22 25 25
PLCG1 -0.027 0.069 0.27 1 -0.19 51 52
mol:GTP 0 0 -10000 0 -10000 0 0
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
G12/G13 0.027 0.011 -10000 0 -10000 0 0
cell migration -0.015 0.079 -10000 0 -0.21 25 25
S1PR5 0 0.084 0.33 1 -0.33 23 24
S1PR4 0.005 0.071 -10000 0 -0.33 17 17
MAPK3 -0.028 0.069 -10000 0 -0.19 54 54
MAPK1 -0.025 0.061 -10000 0 -0.18 49 49
S1P/S1P5/Gi -0.02 0.08 -10000 0 -0.2 58 58
GNAI1 0.019 0.018 -10000 0 -0.33 1 1
CDC42/GDP 0.015 0.003 -10000 0 -10000 0 0
S1P/S1P5/G12 0.012 0.052 0.21 1 -0.19 22 23
RHOA -0.002 0.078 0.2 43 -0.17 14 57
S1P/S1P4/Gi -0.017 0.076 -10000 0 -0.19 54 54
mol:GDP 0 0 -10000 0 -10000 0 0
GNAZ -0.01 0.098 -10000 0 -0.33 34 34
S1P/S1P4/G12/G13 0.025 0.043 -10000 0 -0.18 15 15
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
FoxO family signaling

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
G6PC 0.015 0.067 0.35 1 -10000 0 1
PLK1 0.22 0.27 0.57 115 -10000 0 115
CDKN1B 0.14 0.18 0.42 62 -0.34 3 65
FOXO3 0.2 0.25 0.53 116 -10000 0 116
KAT2B 0.057 0.046 0.18 12 -10000 0 12
FOXO1/SIRT1 0.008 0.042 -10000 0 -0.24 1 1
CAT 0.16 0.25 0.57 48 -0.71 5 53
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.057 0.046 0.18 9 -10000 0 9
FOXO1 0.018 0.059 0.24 9 -0.25 1 10
MAPK10 0.018 0.067 0.2 34 -0.16 11 45
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.035 0.077 0.32 4 -10000 0 4
response to oxidative stress 0.039 0.045 0.13 39 -10000 0 39
FOXO3A/SIRT1 0.17 0.21 0.44 112 -0.43 2 114
XPO1 0.021 0.002 -10000 0 -10000 0 0
EP300 0.023 0.007 -10000 0 -10000 0 0
BCL2L11 0.067 0.065 -10000 0 -10000 0 0
FOXO1/SKP2 0.023 0.044 -10000 0 -10000 0 0
mol:GDP 0.039 0.045 0.13 39 -10000 0 39
RAN 0.022 0.022 0.33 2 -10000 0 2
GADD45A 0.12 0.18 0.45 20 -0.65 6 26
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
FOXO1/14-3-3 family 0.002 0.12 -10000 0 -0.44 16 16
MST1 0.066 0.07 0.28 21 -10000 0 21
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.004 -10000 0 -10000 0 0
FOXO4/14-3-3 family 0.004 0.089 -10000 0 -0.38 11 11
YWHAB 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.028 0.062 0.2 40 -10000 0 40
MAPK9 0.028 0.064 0.2 39 -10000 0 39
YWHAG 0.02 0.004 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
YWHAZ 0.018 0.007 -10000 0 -10000 0 0
SIRT1 0.001 0.024 -10000 0 -10000 0 0
SOD2 0.13 0.19 0.45 42 -0.47 1 43
RBL2 0.14 0.22 0.52 32 -0.65 6 38
RAL/GDP 0.048 0.033 0.17 1 -10000 0 1
CHUK 0.057 0.045 0.18 11 -10000 0 11
Ran/GTP 0.017 0.015 0.22 2 -10000 0 2
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
RAL/GTP 0.047 0.032 0.19 1 -10000 0 1
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
FASLG 0.052 0.15 -10000 0 -1.1 5 5
SKP2 0.018 0.018 0.33 1 -10000 0 1
USP7 0.021 0.003 -10000 0 -10000 0 0
IKBKB 0.049 0.044 0.17 5 -10000 0 5
CCNB1 0.2 0.27 0.58 103 -10000 0 103
FOXO1-3a-4/beta catenin 0.13 0.16 0.41 48 -10000 0 48
proteasomal ubiquitin-dependent protein catabolic process 0.023 0.043 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
SGK1 0.055 0.047 0.18 12 -10000 0 12
CSNK1G3 0.02 0.005 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.015 0.21 2 -10000 0 2
ZFAND5 0.029 0.07 0.44 1 -10000 0 1
SFN 0.025 0.045 0.33 7 -0.33 1 8
CDK2 0.01 0.022 -10000 0 -10000 0 0
FOXO3A/14-3-3 0.048 0.11 0.27 15 -0.36 8 23
CREBBP 0.01 0.022 -10000 0 -10000 0 0
FBXO32 0.21 0.27 0.65 68 -0.52 1 69
BCL6 0.14 0.23 0.5 40 -0.72 9 49
RALB 0.021 0.003 -10000 0 -10000 0 0
RALA 0.019 0.006 -10000 0 -10000 0 0
YWHAH 0.021 0.004 -10000 0 -10000 0 0
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.013 0.1 -10000 0 -0.58 8 8
Syndecan-4/Syndesmos 0.031 0.16 0.32 4 -0.67 13 17
positive regulation of JNK cascade 0.029 0.15 0.3 4 -0.6 14 18
Syndecan-4/ADAM12 0.096 0.2 0.33 65 -0.7 12 77
CCL5 0.017 0.035 -10000 0 -0.33 4 4
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DNM2 0.02 0.005 -10000 0 -10000 0 0
ITGA5 0.021 0.024 0.33 1 -0.33 1 2
SDCBP 0.019 0.007 -10000 0 -10000 0 0
PLG 0.014 0.052 0.32 9 -10000 0 9
ADAM12 0.14 0.15 0.33 144 -10000 0 144
mol:GTP 0 0 -10000 0 -10000 0 0
NUDT16L1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
Syndecan-4/PKC alpha -0.035 0.018 -10000 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.034 0.16 0.31 7 -0.69 12 19
Syndecan-4/CXCL12/CXCR4 0.031 0.16 0.31 4 -0.64 14 18
Syndecan-4/Laminin alpha3 0.013 0.16 0.33 1 -0.67 14 15
MDK 0.12 0.14 0.33 122 -10000 0 122
Syndecan-4/FZD7 0.031 0.16 0.32 4 -0.7 12 16
Syndecan-4/Midkine 0.088 0.19 0.34 42 -0.67 13 55
FZD7 0.02 0.018 -10000 0 -0.33 1 1
Syndecan-4/FGFR1/FGF 0.017 0.16 0.31 1 -0.67 14 15
THBS1 0.02 0.005 -10000 0 -10000 0 0
integrin-mediated signaling pathway 0.041 0.16 0.32 12 -0.68 12 24
positive regulation of MAPKKK cascade 0.029 0.15 0.3 4 -0.6 14 18
Syndecan-4/TACI 0.04 0.17 0.33 18 -0.7 12 30
CXCR4 0.021 0.002 -10000 0 -10000 0 0
cell adhesion 0.006 0.041 0.19 8 -0.24 5 13
Syndecan-4/Dynamin 0.03 0.15 0.31 3 -0.7 12 15
Syndecan-4/TSP1 0.028 0.16 0.32 4 -0.67 13 17
Syndecan-4/GIPC 0.031 0.16 0.32 3 -0.7 12 15
Syndecan-4/RANTES 0.03 0.16 0.31 3 -0.67 13 16
ITGB1 0.021 0.004 -10000 0 -10000 0 0
LAMA1 0.026 0.069 0.33 13 -0.33 5 18
LAMA3 -0.046 0.14 -10000 0 -0.33 73 73
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA 0.004 0.14 0.74 13 -0.32 1 14
Syndecan-4/alpha-Actinin 0.03 0.16 0.32 3 -0.67 13 16
TFPI 0.008 0.067 -10000 0 -0.33 15 15
F2 0.061 0.11 0.33 52 -10000 0 52
alpha5/beta1 Integrin 0.03 0.018 0.24 1 -0.23 1 2
positive regulation of cell adhesion -0.005 0.16 0.32 1 -0.64 14 15
ACTN1 0.02 0.004 -10000 0 -10000 0 0
TNC 0.036 0.09 0.33 26 -0.33 6 32
Syndecan-4/CXCL12 0.027 0.16 0.32 4 -0.66 14 18
FGF6 0.017 0.004 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CXCL12 0 0.084 -10000 0 -0.33 24 24
TNFRSF13B 0.036 0.088 0.33 26 -0.33 5 31
FGF2 -0.021 0.11 -10000 0 -0.33 47 47
FGFR1 0.017 0.019 -10000 0 -0.33 1 1
Syndecan-4/PI-4-5-P2 0.015 0.15 0.26 8 -0.67 13 21
mol:GDP 0 0 -10000 0 -10000 0 0
FN1 0.012 0.039 -10000 0 -0.32 4 4
cell migration -0.021 0.013 -10000 0 -10000 0 0
PRKCD 0.016 0.019 -10000 0 -10000 0 0
vasculogenesis 0.029 0.15 0.31 4 -0.64 13 17
SDC4 0.022 0.15 0.28 8 -0.79 10 18
Syndecan-4/Tenascin C 0.041 0.16 0.32 12 -0.72 12 24
Syndecan-4/PI-4-5-P2/PKC alpha -0.028 0.015 -10000 0 -10000 0 0
Syndecan-4/Syntenin 0.027 0.16 0.32 4 -0.71 12 16
MMP9 0.072 0.12 0.33 65 -10000 0 65
Rac1/GTP 0.006 0.042 0.19 8 -0.25 5 13
cytoskeleton organization 0.031 0.15 0.31 4 -0.64 13 17
GIPC1 0.02 0.005 -10000 0 -10000 0 0
Syndecan-4/TFPI 0.027 0.16 0.32 3 -0.68 13 16
ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF -0.047 0.1 -10000 0 -0.3 20 20
epithelial cell differentiation -0.028 0.091 -10000 0 -0.33 3 3
ITCH 0.031 0.017 -10000 0 -10000 0 0
WWP1 -0.016 0.075 -10000 0 -10000 0 0
FYN 0.018 0.019 -10000 0 -0.33 1 1
EGFR 0.015 0.043 0.33 1 -0.33 5 6
PRL 0.025 0.044 0.33 8 -10000 0 8
neuron projection morphogenesis -0.027 0.096 0.29 6 -10000 0 6
PTPRZ1 0.029 0.16 0.33 52 -0.33 36 88
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.019 0.082 -10000 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.041 0.083 -10000 0 -0.26 26 26
ADAM17 0.033 0.019 -10000 0 -10000 0 0
ErbB4/ErbB4 -0.035 0.068 -10000 0 -0.32 1 1
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.087 0.12 -10000 0 -0.3 56 56
NCOR1 0.02 0.006 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.037 0.085 -10000 0 -0.35 2 2
GRIN2B -0.047 0.081 0.26 3 -0.33 2 5
ErbB4/ErbB2/betacellulin -0.013 0.067 -10000 0 -0.26 6 6
STAT1 0.021 0.002 -10000 0 -10000 0 0
HBEGF -0.033 0.13 -10000 0 -0.33 60 60
PRLR 0.023 0.095 0.33 21 -0.33 12 33
E4ICDs/ETO2 -0.032 0.09 -10000 0 -0.3 11 11
axon guidance -0.027 0.073 -10000 0 -0.38 3 3
NEDD4 0.03 0.024 -10000 0 -0.31 1 1
Prolactin receptor/Prolactin receptor/Prolactin 0.029 0.074 0.25 25 -0.23 12 37
CBFA2T3 -0.003 0.087 -10000 0 -0.33 26 26
ErbB4/ErbB2/HBEGF -0.033 0.086 -10000 0 -0.25 18 18
MAPK3 -0.035 0.082 0.22 1 -10000 0 1
STAT1 (dimer) -0.023 0.078 -10000 0 -0.31 2 2
MAPK1 -0.032 0.083 0.22 2 -10000 0 2
JAK2 0.018 0.019 -10000 0 -0.33 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.051 0.075 -10000 0 -0.25 25 25
NRG1 -0.037 0.08 -10000 0 -0.23 57 57
NRG3 -0.11 0.17 0.33 1 -0.33 150 151
NRG2 -0.021 0.11 -10000 0 -0.33 46 46
NRG4 0.036 0.093 0.33 27 -0.33 7 34
heart development -0.027 0.073 -10000 0 -0.38 3 3
neural crest cell migration -0.051 0.074 -10000 0 -0.25 25 25
ERBB2 -0.001 0.03 0.29 2 -10000 0 2
WWOX/E4ICDs -0.022 0.077 -10000 0 -0.3 2 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.002 0.092 0.3 1 -0.28 7 8
apoptosis 0.14 0.2 0.38 129 -10000 0 129
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.041 0.1 -10000 0 -0.3 23 23
ErbB4/ErbB2/epiregulin 0.001 0.12 0.32 4 -0.26 15 19
ErbB4/ErbB4/betacellulin/betacellulin -0.025 0.085 -10000 0 -0.31 8 8
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.013 0.11 0.33 1 -0.28 20 21
MDM2 -0.02 0.08 0.24 14 -0.29 1 15
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.031 0.077 -10000 0 -0.23 26 26
STAT5A -0.027 0.073 -10000 0 -0.39 2 2
ErbB4/EGFR/neuregulin 1 beta -0.032 0.082 -10000 0 -0.26 21 21
DLG4 0.019 0.006 -10000 0 -10000 0 0
GRB2/SHC 0.026 0.012 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.02 0.07 -10000 0 -0.28 2 2
STAT5A (dimer) -0.023 0.1 -10000 0 -0.36 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.019 0.083 -10000 0 -0.36 3 3
LRIG1 0.019 0.025 -10000 0 -0.33 2 2
EREG 0.016 0.18 0.33 60 -0.33 58 118
BTC 0.012 0.055 -10000 0 -0.33 10 10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.027 0.07 -10000 0 -0.4 2 2
ERBB4 -0.035 0.068 -10000 0 -0.32 1 1
STAT5B 0.021 0.003 -10000 0 -10000 0 0
YAP1 -0.008 0.071 -10000 0 -0.47 8 8
GRB2 0.02 0.004 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 0.001 0.08 -10000 0 -0.25 5 5
glial cell differentiation 0.02 0.07 0.28 2 -10000 0 2
WWOX 0.02 0.004 -10000 0 -10000 0 0
cell proliferation -0.059 0.11 0.33 3 -0.4 10 13
PDGFR-alpha signaling pathway

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
PDGFRA 0.012 0.039 -10000 0 -0.32 4 4
PDGF/PDGFRA/CRKL 0.023 0.03 -10000 0 -0.21 4 4
positive regulation of JUN kinase activity 0.036 0.03 -10000 0 -0.18 1 1
CRKL 0.021 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.033 0.11 -10000 0 -0.24 85 85
AP1 -0.071 0.19 -10000 0 -0.71 30 30
mol:IP3 -0.021 0.027 -10000 0 -0.24 3 3
PLCG1 -0.021 0.027 -10000 0 -0.24 3 3
PDGF/PDGFRA/alphaV Integrin 0.023 0.031 -10000 0 -0.22 4 4
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ -0.021 0.027 -10000 0 -0.24 3 3
CAV3 -0.055 0.14 -10000 0 -0.33 83 83
CAV1 -0.18 0.17 -10000 0 -0.33 228 228
SHC/Grb2/SOS1 0.037 0.031 -10000 0 -0.18 1 1
PDGF/PDGFRA/Shf 0.024 0.034 0.24 2 -0.21 4 6
FOS -0.07 0.19 0.3 2 -0.71 29 31
JUN -0.025 0.025 -10000 0 -0.24 2 2
oligodendrocyte development 0.023 0.031 -10000 0 -0.22 4 4
GRB2 0.02 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
mol:DAG -0.021 0.027 -10000 0 -0.24 3 3
PDGF/PDGFRA 0.012 0.039 -10000 0 -0.32 4 4
actin cytoskeleton reorganization 0.022 0.031 -10000 0 -0.21 4 4
SRF -0.014 0.012 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
PI3K 0.032 0.03 -10000 0 -0.18 4 4
PDGF/PDGFRA/Crk/C3G 0.03 0.032 -10000 0 -0.18 4 4
JAK1 -0.018 0.021 -10000 0 -0.22 3 3
ELK1/SRF -0.023 0.038 0.15 13 -0.2 3 16
SHB 0.02 0.005 -10000 0 -10000 0 0
SHF 0.022 0.023 0.33 2 -10000 0 2
CSNK2A1 0.022 0.017 -10000 0 -10000 0 0
GO:0007205 -0.017 0.028 -10000 0 -0.26 3 3
SOS1 0.021 0.003 -10000 0 -10000 0 0
Ras protein signal transduction 0.036 0.03 -10000 0 -0.18 1 1
PDGF/PDGFRA/SHB 0.022 0.031 -10000 0 -0.21 4 4
PDGF/PDGFRA/Caveolin-1 -0.13 0.13 -10000 0 -0.24 222 222
ITGAV 0.021 0.002 -10000 0 -10000 0 0
ELK1 -0.022 0.031 -10000 0 -0.23 3 3
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PDGF/PDGFRA/Crk 0.021 0.031 -10000 0 -0.21 4 4
JAK-STAT cascade -0.018 0.021 -10000 0 -0.22 3 3
cell proliferation 0.023 0.034 0.24 2 -0.21 4 6
IL1-mediated signaling events

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
UBC13/UEV1A 0.028 0.014 0.24 1 -10000 0 1
PRKCZ 0.018 0.031 -10000 0 -0.33 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
ERC1 0.02 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.001 0.059 -10000 0 -0.27 11 11
IRAK/TOLLIP -0.021 0.015 0.18 1 -10000 0 1
IKBKB 0.018 0.007 -10000 0 -10000 0 0
IKBKG 0.02 0.004 -10000 0 -10000 0 0
IL1 alpha/IL1R2 -0.035 0.13 0.24 17 -0.23 111 128
IL1A -0.076 0.16 0.33 2 -0.33 111 113
IL1B -0.03 0.054 0.16 1 -0.23 25 26
IRAK/TRAF6/p62/Atypical PKCs 0.042 0.038 -10000 0 -0.17 2 2
IL1R2 0.031 0.069 0.33 16 -0.33 3 19
IL1R1 0.019 0.025 -10000 0 -0.33 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.007 0.051 -10000 0 -0.25 7 7
TOLLIP 0.021 0.004 -10000 0 -10000 0 0
TICAM2 0.019 0.025 -10000 0 -0.33 2 2
MAP3K3 0.019 0.018 -10000 0 -0.33 1 1
TAK1/TAB1/TAB2 0.013 0.004 -10000 0 -10000 0 0
IKK complex/ELKS 0.001 0.065 0.24 2 -0.33 1 3
JUN -0.02 0.044 0.15 19 -0.16 1 20
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K 0.033 0.059 -10000 0 -0.18 22 22
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.014 0.11 0.23 1 -0.18 110 111
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.007 0.11 0.23 1 -0.18 109 110
IL1 beta fragment/IL1R1/IL1RAP 0.015 0.054 -10000 0 -0.19 25 25
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 -0.014 0.049 0.17 21 -10000 0 21
IRAK1 -0.018 0.015 0.15 2 -10000 0 2
IL1RN/IL1R1 0.026 0.041 0.24 1 -0.23 9 10
IRAK4 0.021 0.003 -10000 0 -10000 0 0
PRKCI 0.02 0.005 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.029 0.009 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.004 0.059 -10000 0 -0.29 9 9
CHUK 0.021 0.003 -10000 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s 0.015 0.054 -10000 0 -0.19 25 25
IL1 beta/IL1R2 0.016 0.071 0.22 14 -0.21 25 39
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.003 0.025 0.16 1 -10000 0 1
NF kappa B1 p50/RelA 0.022 0.054 -10000 0 -0.18 19 19
IRAK3 0.011 0.055 -10000 0 -0.33 10 10
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 0.032 0.06 -10000 0 -0.18 24 24
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.046 0.099 -10000 0 -0.2 104 104
IL1 alpha/IL1R1/IL1RAP -0.026 0.11 0.23 2 -0.2 110 112
RELA 0.021 0.003 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
SQSTM1 0.02 0.005 -10000 0 -10000 0 0
MYD88 0.021 0.004 -10000 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.033 0.031 0.19 1 -10000 0 1
IL1RAP 0.02 0.005 -10000 0 -10000 0 0
UBE2N 0.021 0.003 -10000 0 -10000 0 0
IRAK/TRAF6 -0.046 0.034 -10000 0 -10000 0 0
CASP1 0.018 0.031 -10000 0 -0.33 3 3
IL1RN/IL1R2 0.034 0.061 0.24 17 -0.25 9 26
IL1 beta fragment/IL1R1/IL1RAP/MYD88 0.025 0.056 -10000 0 -0.18 25 25
TMEM189-UBE2V1 0.019 0.017 0.33 1 -10000 0 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.038 0.094 -10000 0 -0.32 18 18
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
IL1RN 0.016 0.049 0.33 1 -0.33 7 8
TRAF6/TAK1/TAB1/TAB2 0.033 0.019 0.18 1 -10000 0 1
MAP2K6 -0.008 0.058 0.18 29 -10000 0 29
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 0.037 0.021 0.19 1 -0.18 1 2
NF kappa B1 p50/RelA/I kappa B alpha -0.012 0.11 0.22 4 -0.36 18 22
AP1 0.002 0.076 -10000 0 -0.16 59 59
mol:PIP3 -0.036 0.043 -10000 0 -0.17 28 28
AKT1 -0.01 0.066 0.23 3 -0.31 5 8
PTK2B -0.043 0.12 0.25 1 -0.36 27 28
RHOA -0.005 0.073 0.18 7 -0.37 10 17
PIK3CB 0.02 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.03 0.087 0.21 8 -0.24 35 43
MAGI3 0.017 0.035 -10000 0 -0.33 4 4
RELA 0.021 0.003 -10000 0 -10000 0 0
apoptosis -0.012 0.06 -10000 0 -0.2 36 36
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization -0.049 0.11 0.23 5 -0.35 25 30
NF kappa B1 p50/RelA -0.053 0.087 -10000 0 -0.26 40 40
endothelial cell migration -0.01 0.017 0.31 1 -10000 0 1
ADCY4 -0.015 0.054 0.24 1 -0.26 4 5
ADCY5 -0.026 0.074 0.22 2 -0.26 19 21
ADCY6 -0.011 0.048 0.24 1 -0.25 4 5
ADCY7 -0.011 0.043 -10000 0 -0.2 4 4
ADCY1 -0.01 0.049 0.24 1 -0.23 7 8
ADCY2 -0.015 0.057 0.24 1 -0.24 8 9
ADCY3 -0.01 0.045 0.24 1 -0.2 4 5
ADCY8 -0.056 0.08 -10000 0 -0.24 14 14
ADCY9 -0.015 0.054 0.24 1 -0.24 8 9
GSK3B -0.044 0.12 0.19 5 -0.36 25 30
arachidonic acid secretion -0.017 0.049 -10000 0 -0.28 6 6
GNG2 0.019 0.019 -10000 0 -0.33 1 1
TRIP6 0.01 0.023 -10000 0 -0.29 2 2
GNAO1 -0.011 0.02 0.16 3 -0.19 2 5
HRAS 0.021 0.004 -10000 0 -10000 0 0
NFKBIA -0.03 0.12 0.24 5 -0.3 41 46
GAB1 0.02 0.018 -10000 0 -0.33 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
lamellipodium assembly -0.011 0.19 -10000 0 -0.83 20 20
JUN 0.019 0.025 -10000 0 -0.33 2 2
LPA/LPA2/NHERF2 0.025 0.024 -10000 0 -0.19 4 4
TIAM1 -0.026 0.22 -10000 0 -0.98 20 20
PIK3R1 0.02 0.007 -10000 0 -10000 0 0
mol:IP3 -0.024 0.076 0.21 8 -0.22 31 39
PLCB3 -0.014 0.034 0.18 9 -0.18 4 13
FOS -0.005 0.09 -10000 0 -0.33 28 28
positive regulation of mitosis -0.017 0.049 -10000 0 -0.28 6 6
LPA/LPA1-2-3 0.022 0.066 0.21 5 -0.17 36 41
mol:Ca ++ 0 0 -10000 0 -10000 0 0
JNK cascade 0 0 -10000 0 -10000 0 0
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
stress fiber formation -0.026 0.096 0.23 1 -0.34 18 19
GNAZ -0.026 0.051 0.12 1 -0.19 34 35
EGFR/PI3K-beta/Gab1 -0.035 0.047 -10000 0 -0.18 25 25
positive regulation of dendritic cell cytokine production 0.021 0.065 0.2 5 -0.17 36 41
LPA/LPA2/MAGI-3 0.025 0.024 -10000 0 -0.19 4 4
ARHGEF1 0.007 0.074 0.19 49 -0.17 1 50
GNAI2 -0.011 0.008 0.12 1 -10000 0 1
GNAI3 -0.011 0.008 0.12 1 -10000 0 1
GNAI1 -0.011 0.012 0.12 1 -0.19 1 2
LPA/LPA3 -0.004 0.073 0.22 4 -0.22 36 40
LPA/LPA2 0.016 0.006 -10000 0 -10000 0 0
LPA/LPA1 0.017 0.01 0.19 1 -10000 0 1
HB-EGF/EGFR -0.018 0.086 0.13 52 -0.21 45 97
HBEGF -0.018 0.1 0.16 59 -0.23 54 113
mol:DAG -0.024 0.076 0.21 8 -0.22 31 39
cAMP biosynthetic process -0.021 0.064 0.3 2 -0.24 7 9
NFKB1 0.021 0.003 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
GNB1 0.02 0.007 -10000 0 -10000 0 0
LYN -0.033 0.11 0.28 3 -0.3 41 44
GNAQ -0.013 0.062 -10000 0 -0.21 34 34
LPAR2 0.02 0.005 -10000 0 -10000 0 0
LPAR3 -0.008 0.11 0.33 4 -0.33 36 40
LPAR1 0.021 0.007 -10000 0 -10000 0 0
IL8 -0.019 0.13 0.3 16 -0.36 19 35
PTK2 -0.025 0.051 0.17 7 -0.17 26 33
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
CASP3 -0.012 0.06 -10000 0 -0.2 36 36
EGFR 0.015 0.043 0.33 1 -0.33 5 6
PLCG1 -0.016 0.073 0.14 6 -0.23 33 39
PLD2 -0.024 0.057 0.19 11 -0.17 28 39
G12/G13 0.036 0.018 -10000 0 -10000 0 0
PI3K-beta -0.025 0.047 -10000 0 -0.33 6 6
cell migration -0.01 0.065 -10000 0 -0.25 19 19
SLC9A3R2 0.017 0.035 -10000 0 -0.33 4 4
PXN -0.026 0.098 0.23 1 -0.35 17 18
HRAS/GTP -0.017 0.05 -10000 0 -0.28 6 6
RAC1 0.019 0.007 -10000 0 -10000 0 0
MMP9 0.072 0.12 0.33 65 -10000 0 65
PRKCE 0.018 0.031 -10000 0 -0.33 3 3
PRKCD -0.036 0.086 0.27 3 -0.34 14 17
Gi(beta/gamma) -0.01 0.045 -10000 0 -0.23 3 3
mol:LPA 0.001 0.004 -10000 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.011 0.086 -10000 0 -0.35 10 10
MAPKKK cascade -0.017 0.049 -10000 0 -0.28 6 6
contractile ring contraction involved in cytokinesis -0.004 0.074 0.18 6 -0.36 11 17
mol:GDP 0 0 -10000 0 -10000 0 0
GNA14 -0.017 0.069 -10000 0 -0.21 41 41
GNA15 -0.01 0.057 -10000 0 -0.2 32 32
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
MAPT -0.051 0.12 0.23 5 -0.36 25 30
GNA11 -0.01 0.057 -10000 0 -0.2 32 32
Rac1/GTP -0.013 0.2 -10000 0 -0.88 20 20
MMP2 -0.01 0.017 0.31 1 -10000 0 1
Regulation of Androgen receptor activity

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
HDAC1 -0.017 0.005 -10000 0 -10000 0 0
SMARCC1 0.002 0.012 -10000 0 -10000 0 0
REL 0.02 0.007 -10000 0 -10000 0 0
HDAC7 -0.037 0.078 0.31 3 -0.28 16 19
JUN 0.019 0.025 -10000 0 -0.33 2 2
EP300 0.021 0.004 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
KAT5 0.021 0.003 -10000 0 -10000 0 0
MAPK14 -0.013 0.038 0.16 12 -0.24 2 14
FOXO1 0.02 0.005 -10000 0 -10000 0 0
T-DHT/AR -0.036 0.078 -10000 0 -0.29 16 16
MAP2K6 0.023 0.06 0.33 11 -0.34 2 13
BRM/BAF57 0.026 0.022 -10000 0 -0.23 2 2
MAP2K4 0.015 0.016 -10000 0 -10000 0 0
SMARCA2 0.017 0.026 -10000 0 -0.33 2 2
PDE9A -0.033 0.16 -10000 0 -0.91 10 10
NCOA2 0.018 0.026 -10000 0 -0.33 2 2
CEBPA 0.002 0.077 -10000 0 -0.33 20 20
EHMT2 0.021 0.005 -10000 0 -10000 0 0
cell proliferation -0.029 0.14 0.37 13 -0.38 21 34
NR0B1 0.081 0.13 0.33 79 -10000 0 79
EGR1 -0.002 0.085 -10000 0 -0.33 25 25
RXRs/9cRA -0.061 0.1 -10000 0 -0.18 173 173
AR/RACK1/Src -0.013 0.085 0.27 14 -0.29 2 16
AR/GR -0.025 0.085 0.28 2 -0.23 41 43
GNB2L1 0.021 0.005 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
RCHY1 0.021 0.003 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 0.016 1 -10000 0 1
MAPK8 -0.015 0.014 -10000 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.019 0.068 0.23 3 -0.28 3 6
SRC -0.022 0.034 0.19 4 -0.2 2 6
NR3C1 0.021 0.004 -10000 0 -10000 0 0
KLK3 0.01 0.095 0.34 1 -0.4 2 3
APPBP2 0.016 0.016 -10000 0 -10000 0 0
TRIM24 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/TIP60 -0.023 0.062 0.2 4 -0.25 4 8
TMPRSS2 -0.084 0.28 -10000 0 -0.92 36 36
RXRG -0.14 0.17 -10000 0 -0.33 174 174
mol:9cRA 0 0 -10000 0 -10000 0 0
RXRA 0.021 0.004 -10000 0 -10000 0 0
RXRB 0.02 0.004 -10000 0 -10000 0 0
CARM1 0.02 0.006 -10000 0 -10000 0 0
NR2C2 0.021 0.004 -10000 0 -10000 0 0
KLK2 -0.004 0.086 0.3 19 -0.26 3 22
AR -0.029 0.078 0.19 2 -0.24 43 45
SENP1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
MDM2 0.019 0.009 -10000 0 -10000 0 0
SRY 0 0.003 -10000 0 -0.028 5 5
GATA2 -0.01 0.1 -10000 0 -0.33 35 35
MYST2 0 0.001 -10000 0 -10000 0 0
HOXB13 0.12 0.15 0.33 130 -10000 0 130
T-DHT/AR/RACK1/Src -0.018 0.078 0.32 7 -0.3 2 9
positive regulation of transcription -0.01 0.099 -10000 0 -0.33 35 35
DNAJA1 0.016 0.016 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.012 0.17 2 -10000 0 2
NCOA1 0.023 0.014 -10000 0 -10000 0 0
SPDEF 0.12 0.15 0.33 124 -0.33 3 127
T-DHT/AR/TIF2 -0.008 0.07 0.22 8 -0.28 6 14
T-DHT/AR/Hsp90 -0.022 0.061 0.2 4 -0.27 3 7
GSK3B 0.017 0.013 -10000 0 -10000 0 0
NR2C1 0.02 0.006 -10000 0 -10000 0 0
mol:T-DHT -0.022 0.03 0.21 1 -0.21 2 3
SIRT1 0.021 0.003 -10000 0 -10000 0 0
ZMIZ2 0.018 0.009 -10000 0 -10000 0 0
POU2F1 0.008 0.04 -10000 0 -0.18 3 3
T-DHT/AR/DAX-1 0.017 0.11 0.22 62 -0.31 2 64
CREBBP 0.021 0.004 -10000 0 -10000 0 0
SMARCE1 0.021 0.004 -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 0.012 0.03 -10000 0 -0.22 6 6
EPHB2 0.057 0.1 0.33 46 -10000 0 46
Syndecan-2/TACI 0.025 0.061 0.23 26 -0.19 7 33
LAMA1 0.026 0.069 0.33 13 -0.33 5 18
Syndecan-2/alpha2 ITGB1 0.006 0.082 0.23 8 -0.17 54 62
HRAS 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2/CASK -0.006 0.016 -10000 0 -0.18 3 3
ITGA5 0.021 0.024 0.33 1 -0.33 1 2
BAX -0.014 0.013 -10000 0 -10000 0 0
EPB41 0.021 0.003 -10000 0 -10000 0 0
positive regulation of cell-cell adhesion 0.013 0.017 -10000 0 -0.17 3 3
LAMA3 -0.046 0.14 -10000 0 -0.33 73 73
EZR 0.019 0.006 -10000 0 -10000 0 0
mol:PI-4-5-P2 0 0 -10000 0 -10000 0 0
CAV2 -0.043 0.13 -10000 0 -0.33 70 70
Syndecan-2/MMP2 0.014 0.022 0.22 1 -0.19 3 4
RP11-540L11.1 0 0 -10000 0 -10000 0 0
alpha2 ITGB1 0.033 0.04 0.24 11 -0.23 2 13
dendrite morphogenesis 0.04 0.075 0.23 46 -0.19 3 49
Syndecan-2/GM-CSF 0.008 0.053 0.25 5 -0.19 19 24
determination of left/right symmetry -0.008 0.019 -10000 0 -0.22 3 3
Syndecan-2/PKC delta 0.014 0.019 -10000 0 -0.19 3 3
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
MAPK3 -0.002 0.072 0.18 39 -0.18 18 57
MAPK1 0 0.07 0.18 39 -0.18 14 53
Syndecan-2/RACK1 0.023 0.02 -10000 0 -0.16 3 3
NF1 0.021 0.003 -10000 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.008 0.019 -10000 0 -0.22 3 3
ITGA2 0.027 0.058 0.33 11 -0.33 2 13
MAPK8 -0.011 0.016 -10000 0 -0.19 3 3
Syndecan-2/alpha2/beta1 Integrin 0.042 0.062 0.25 20 -0.2 5 25
Syndecan-2/Kininogen 0.028 0.059 0.23 28 -0.18 3 31
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC 0.003 0.063 0.17 45 -10000 0 45
Syndecan-2/CASK/Protein 4.1 0.013 0.017 -10000 0 -0.17 3 3
extracellular matrix organization 0.014 0.019 -10000 0 -0.19 3 3
actin cytoskeleton reorganization 0.012 0.03 -10000 0 -0.22 6 6
Syndecan-2/Caveolin-2/Ras -0.004 0.071 -10000 0 -0.18 56 56
Syndecan-2/Laminin alpha3 -0.018 0.075 -10000 0 -0.19 62 62
Syndecan-2/RasGAP 0.031 0.023 -10000 0 -0.16 3 3
alpha5/beta1 Integrin 0.03 0.018 0.24 1 -0.23 1 2
PRKCD 0.021 0.004 -10000 0 -10000 0 0
Syndecan-2 dimer 0.04 0.075 0.24 46 -0.19 3 49
GO:0007205 0.001 0 -10000 0 -10000 0 0
DNA mediated transformation 0 0 -10000 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.018 0.025 0.16 5 -10000 0 5
RHOA 0.021 0.004 -10000 0 -10000 0 0
SDCBP 0.019 0.007 -10000 0 -10000 0 0
TNFRSF13B 0.036 0.088 0.33 26 -0.33 5 31
RASA1 0.02 0.005 -10000 0 -10000 0 0
alpha2/beta1 Integrin 0.033 0.04 0.24 11 -0.23 2 13
Syndecan-2/Synbindin 0.014 0.016 -10000 0 -0.19 2 2
TGFB1 0.021 0.004 -10000 0 -10000 0 0
CASP3 0.004 0.064 0.18 43 -0.18 3 46
FN1 0.017 0.035 -10000 0 -0.33 4 4
Syndecan-2/IL8 0.024 0.053 0.24 18 -0.19 4 22
SDC2 -0.008 0.019 -10000 0 -0.22 3 3
KNG1 0.041 0.081 0.33 28 -10000 0 28
Syndecan-2/Neurofibromin 0.014 0.019 -10000 0 -0.18 3 3
TRAPPC4 0.02 0.005 -10000 0 -10000 0 0
CSF2 0.003 0.092 0.33 5 -0.33 24 29
Syndecan-2/TGFB1 0.014 0.019 -10000 0 -0.19 3 3
Syndecan-2/Syntenin/PI-4-5-P2 0.013 0.017 -10000 0 -0.17 3 3
Syndecan-2/Ezrin 0.022 0.022 -10000 0 -0.17 3 3
PRKACA 0.006 0.064 0.18 45 -0.18 2 47
angiogenesis 0.024 0.052 0.24 18 -0.19 4 22
MMP2 0.021 0.016 0.33 1 -10000 0 1
IL8 0.033 0.07 0.33 18 -0.33 2 20
calcineurin-NFAT signaling pathway 0.025 0.061 0.23 26 -0.19 7 33
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity -0.035 0.056 0.24 4 -0.24 19 23
KIRREL 0.017 0.038 -10000 0 -0.34 4 4
Nephrin/NEPH1Par3/Par6/Atypical PKCs 0.035 0.056 0.24 19 -0.24 4 23
PLCG1 0.02 0.005 -10000 0 -10000 0 0
ARRB2 0.019 0.006 -10000 0 -10000 0 0
WASL 0.02 0.005 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP 0.051 0.053 0.22 19 -0.18 4 23
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP 0.013 0.036 -10000 0 -0.2 4 4
FYN 0.017 0.086 0.21 53 -0.18 4 57
mol:Ca2+ 0.048 0.052 0.22 19 -0.18 4 23
mol:DAG 0.049 0.053 0.22 19 -0.18 4 23
NPHS2 -0.004 0.023 -10000 0 -10000 0 0
mol:IP3 0.049 0.053 0.22 19 -0.18 4 23
regulation of endocytosis 0.034 0.045 0.2 16 -0.17 4 20
Nephrin/NEPH1/podocin/Cholesterol 0.041 0.05 0.21 19 -0.18 4 23
establishment of cell polarity 0.035 0.056 0.24 19 -0.24 4 23
Nephrin/NEPH1/podocin/NCK1-2 0.059 0.054 0.28 1 -0.17 4 5
Nephrin/NEPH1/beta Arrestin2 0.036 0.047 0.21 16 -0.17 4 20
NPHS1 0.038 0.078 0.34 23 -10000 0 23
Nephrin/NEPH1/podocin 0.038 0.048 0.21 19 -0.17 5 24
TJP1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.021 0.002 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 0.05 0.053 0.22 19 -0.18 4 23
CD2AP 0.02 0.004 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 0.05 0.053 0.22 18 -0.18 4 22
GRB2 0.02 0.004 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 0.006 0.093 0.22 47 -0.18 22 69
cytoskeleton organization -0.004 0.052 0.22 10 -0.21 4 14
Nephrin/NEPH1 0.03 0.044 0.19 19 -0.16 4 23
Nephrin/NEPH1/ZO-1 0.041 0.049 0.22 17 -0.19 4 21
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.02 0.004 -10000 0 -10000 0 0
VLDLR 0.013 0.046 -10000 0 -0.33 7 7
LRPAP1 0.021 0.004 -10000 0 -10000 0 0
NUDC 0.021 0.004 -10000 0 -10000 0 0
RELN/LRP8 0.017 0.083 0.23 11 -0.2 44 55
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
KATNA1 0.019 0.006 -10000 0 -10000 0 0
GO:0030286 0 0 -10000 0 -10000 0 0
ABL1 -0.028 0.068 0.17 17 -0.18 42 59
IQGAP1/CaM 0.029 0.008 -10000 0 -10000 0 0
DAB1 0.023 0.035 0.33 5 -10000 0 5
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
PLA2G7 0.023 0.046 0.33 6 -0.33 2 8
CALM1 0.02 0.004 -10000 0 -10000 0 0
DYNLT1 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
LRPAP1/LRP8 0.034 0.028 0.24 7 -10000 0 7
UniProt:Q4QZ09 0 0 -10000 0 -10000 0 0
CLIP1 0.021 0.004 -10000 0 -10000 0 0
CDK5R1 0.028 0.047 0.33 9 -10000 0 9
LIS1/Poliovirus Protein 3A -0.012 0.005 -10000 0 -10000 0 0
CDK5R2 0.11 0.14 0.33 112 -10000 0 112
mol:PP1 0 0 -10000 0 -10000 0 0
RELN/VLDLR/DAB1 0.012 0.088 0.25 9 -0.2 47 56
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NDEL1/14-3-3 E 0.005 0.094 0.29 16 -0.22 1 17
MAP1B 0.003 0.015 -10000 0 -0.22 1 1
RAC1 0.004 0.002 -10000 0 -10000 0 0
p35/CDK5 -0.029 0.072 0.18 24 -10000 0 24
RELN -0.015 0.12 0.33 5 -0.33 44 49
PAFAH/LIS1 -0.015 0.033 0.22 6 -0.2 2 8
LIS1/CLIP170 -0.018 0.008 -10000 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.019 0.064 0.16 2 -10000 0 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.021 0.089 0.26 2 -0.22 41 43
GO:0005869 0 0 -10000 0 -10000 0 0
NDEL1 0.002 0.081 0.22 19 -0.22 1 20
LIS1/IQGAP1 -0.018 0.007 -10000 0 -10000 0 0
RHOA 0.005 0.002 -10000 0 -10000 0 0
PAFAH1B1 -0.016 0.006 -10000 0 -10000 0 0
PAFAH1B3 0.033 0.062 0.33 16 -10000 0 16
PAFAH1B2 0.02 0.005 -10000 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.009 0.031 -10000 0 -0.17 4 4
NDEL1/Katanin 60/Dynein heavy chain 0.001 0.095 0.29 14 -10000 0 14
LRP8 0.027 0.044 0.33 8 -10000 0 8
NDEL1/Katanin 60 0.004 0.095 0.29 17 -0.23 2 19
P39/CDK5 0.022 0.12 0.2 107 -10000 0 107
LIS1/NudC/Dynein intermediate chain/microtubule organizing center -0.018 0.008 -10000 0 -10000 0 0
CDK5 -0.033 0.06 0.17 12 -0.18 39 51
PPP2R5D 0.02 0.004 -10000 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.014 0.006 -10000 0 -10000 0 0
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 0.011 0.08 0.24 9 -0.18 47 56
RELN/VLDLR 0.022 0.088 0.23 11 -0.19 48 59
CDC42 0.005 0.002 -10000 0 -10000 0 0
S1P5 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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.016 0.082 0.22 30 -10000 0 30
GNAI2 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P5/G12 0.012 0.052 0.21 1 -0.19 22 23
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.02 0.034 0.33 2 -0.33 2 4
RhoA/GTP -0.016 0.084 -10000 0 -0.22 30 30
negative regulation of cAMP metabolic process -0.019 0.08 -10000 0 -0.2 58 58
GNAZ -0.01 0.098 -10000 0 -0.33 34 34
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
S1PR5 0 0.084 0.33 1 -0.33 23 24
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi -0.02 0.08 -10000 0 -0.2 58 58
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.018 -10000 0 -0.33 1 1
FAS signaling pathway (CD95)

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
SPTAN1 -0.014 0.036 0.21 1 -0.2 10 11
RFC1 -0.009 0.044 0.22 7 -0.21 8 15
PRKDC -0.001 0.057 0.22 20 -0.19 7 27
RIPK1 0.022 0.006 -10000 0 -10000 0 0
CASP7 -0.016 0.1 -10000 0 -0.67 8 8
FASLG/FAS/FADD/FAF1 0.005 0.057 0.16 22 -0.26 3 25
MAP2K4 -0.061 0.14 0.23 3 -0.32 74 77
mol:ceramide -0.021 0.077 -10000 0 -0.26 13 13
GSN -0.014 0.034 -10000 0 -0.2 10 10
FASLG/FAS/FADD/FAF1/Caspase 8 -0.004 0.061 0.2 1 -0.29 3 4
FAS 0.006 0.041 -10000 0 -0.34 4 4
BID -0.023 0.016 -10000 0 -0.2 2 2
MAP3K1 -0.032 0.1 0.24 2 -0.46 10 12
MAP3K7 0.011 0.018 -10000 0 -10000 0 0
RB1 -0.012 0.027 -10000 0 -0.19 8 8
CFLAR 0.023 0.005 -10000 0 -10000 0 0
HGF/MET 0.006 0.1 0.23 8 -0.22 54 62
ARHGDIB -0.011 0.038 0.22 4 -0.2 8 12
FADD 0.009 0.023 -10000 0 -10000 0 0
actin filament polymerization 0.015 0.035 0.2 12 -10000 0 12
NFKB1 -0.023 0.1 -10000 0 -0.61 5 5
MAPK8 -0.1 0.21 0.24 1 -0.47 86 87
DFFA -0.012 0.033 0.21 2 -0.19 9 11
DNA fragmentation during apoptosis -0.012 0.04 0.21 4 -0.18 12 16
FAS/FADD/MET 0.016 0.059 0.23 5 -0.2 15 20
CFLAR/RIP1 0.034 0.01 -10000 0 -10000 0 0
FAIM3 0.022 0.023 0.33 2 -10000 0 2
FAF1 0.008 0.025 -10000 0 -10000 0 0
PARP1 -0.013 0.037 0.22 2 -0.2 10 12
DFFB -0.011 0.037 0.21 4 -0.19 9 13
CHUK -0.029 0.096 -10000 0 -0.64 4 4
FASLG 0.007 0.034 -10000 0 -0.33 2 2
FAS/FADD 0.013 0.04 -10000 0 -0.25 4 4
HGF 0.008 0.075 0.33 3 -0.33 16 19
LMNA -0.009 0.054 0.19 18 -0.2 9 27
CASP6 -0.013 0.036 0.21 2 -0.21 9 11
CASP10 0.008 0.029 -10000 0 -0.34 1 1
CASP3 -0.006 0.026 -10000 0 -0.27 3 3
PTPN13 -0.017 0.11 -10000 0 -0.33 43 43
CASP8 -0.022 0.02 -10000 0 -0.23 3 3
IL6 -0.23 0.47 -10000 0 -1.1 88 88
MET 0.012 0.072 0.33 5 -0.33 13 18
ICAD/CAD -0.014 0.043 0.3 4 -0.18 9 13
FASLG/FAS/FADD/FAF1/Caspase 10 -0.021 0.078 -10000 0 -0.26 13 13
activation of caspase activity by cytochrome c -0.023 0.015 -10000 0 -0.2 2 2
PAK2 -0.009 0.044 0.21 8 -0.2 8 16
BCL2 0.02 0.017 0.33 1 -10000 0 1
EPHB forward 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
Ephrin A5/EPHB2 0.047 0.066 0.22 44 -0.17 3 47
cell-cell adhesion 0.02 0.033 0.16 6 -10000 0 6
Ephrin B/EPHB2/RasGAP 0.065 0.068 0.23 41 -0.17 6 47
ITSN1 0.021 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
Ephrin B1/EPHB3 0.03 0.032 0.21 8 -0.19 2 10
Ephrin B1/EPHB1 0.046 0.061 0.21 42 -0.19 3 45
HRAS/GDP 0.013 0.071 -10000 0 -0.23 11 11
Ephrin B/EPHB1/GRB7 0.063 0.066 0.23 34 -0.18 8 42
Endophilin/SYNJ1 -0.009 0.048 0.18 14 -10000 0 14
KRAS 0.02 0.006 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src 0.063 0.064 0.23 34 -0.17 6 40
endothelial cell migration 0.036 0.025 -10000 0 -0.17 3 3
GRB2 0.02 0.004 -10000 0 -10000 0 0
GRB7 0.019 0.025 -10000 0 -0.33 2 2
PAK1 -0.012 0.055 0.24 5 -0.29 1 6
HRAS 0.021 0.004 -10000 0 -10000 0 0
RRAS -0.011 0.049 0.18 12 -0.31 1 13
DNM1 0.024 0.031 0.33 4 -10000 0 4
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.011 0.05 0.2 13 -10000 0 13
lamellipodium assembly -0.02 0.033 -10000 0 -0.16 6 6
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.014 0.055 0.2 7 -0.2 7 14
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
EPHB2 0.057 0.1 0.33 46 -10000 0 46
EPHB3 0.027 0.044 0.33 8 -10000 0 8
EPHB1 0.054 0.099 0.33 43 -0.33 1 44
EPHB4 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.006 0.052 0.22 7 -0.27 4 11
Ephrin B/EPHB2 0.058 0.064 0.21 43 -0.17 6 49
Ephrin B/EPHB3 0.042 0.039 0.21 6 -0.17 6 12
JNK cascade -0.002 0.062 0.26 10 -10000 0 10
Ephrin B/EPHB1 0.055 0.061 0.21 37 -0.17 7 44
RAP1/GDP -0.012 0.08 0.23 14 -0.25 8 22
EFNB2 0.017 0.031 -10000 0 -0.33 3 3
EFNB3 0.019 0.024 0.33 1 -0.33 1 2
EFNB1 0.019 0.025 -10000 0 -0.33 2 2
Ephrin B2/EPHB1-2 0.072 0.086 0.23 77 -0.18 4 81
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CDC42/GTP 0.041 0.065 0.2 5 -0.21 6 11
Rap1/GTP -0.018 0.044 0.099 5 -0.17 6 11
axon guidance 0.046 0.066 0.22 44 -0.17 3 47
MAPK3 -0.001 0.052 0.24 6 -0.26 1 7
MAPK1 -0.001 0.047 0.22 4 -0.26 1 5
Rac1/GDP -0.017 0.068 0.22 6 -0.25 9 15
actin cytoskeleton reorganization -0.027 0.044 0.093 4 -0.19 4 8
CDC42/GDP -0.011 0.08 0.23 15 -0.25 9 24
PI3K 0.04 0.027 -10000 0 -0.17 3 3
EFNA5 0.019 0.038 0.33 2 -0.33 3 5
Ephrin B2/EPHB4 0.024 0.021 -10000 0 -0.19 3 3
Ephrin B/EPHB2/Intersectin/N-WASP 0.008 0.06 0.18 3 -0.2 6 9
CDC42 0.021 0.004 -10000 0 -10000 0 0
RAS family/GTP -0.022 0.038 -10000 0 -0.17 5 5
PTK2 0.056 0.19 0.53 52 -10000 0 52
MAP4K4 -0.002 0.063 0.26 10 -10000 0 10
SRC 0.02 0.004 -10000 0 -10000 0 0
KALRN 0.018 0.031 -10000 0 -0.33 3 3
Intersectin/N-WASP 0.029 0.009 -10000 0 -10000 0 0
neuron projection morphogenesis 0.003 0.087 0.27 19 -0.31 1 20
MAP2K1 0.007 0.051 0.19 9 -0.2 6 15
WASL 0.02 0.005 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 0.088 0.086 0.25 79 -0.18 3 82
cell migration 0.013 0.086 0.28 13 -0.27 4 17
NRAS 0.02 0.005 -10000 0 -10000 0 0
SYNJ1 -0.009 0.048 0.18 14 -10000 0 14
PXN 0.021 0.004 -10000 0 -10000 0 0
TF 0.008 0.07 0.21 17 -10000 0 17
HRAS/GTP 0.042 0.05 0.18 6 -0.16 7 13
Ephrin B1/EPHB1-2 0.075 0.085 0.23 79 -0.18 3 82
cell adhesion mediated by integrin 0.014 0.037 0.18 6 -0.2 7 13
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:GTP 0.049 0.058 0.22 8 -0.17 7 15
RAC1-CDC42/GTP -0.022 0.035 -10000 0 -0.17 6 6
RASA1 0.02 0.005 -10000 0 -10000 0 0
RAC1-CDC42/GDP -0.017 0.069 0.22 6 -0.25 8 14
ruffle organization 0.01 0.096 0.35 15 -10000 0 15
NCK1 0.021 0.003 -10000 0 -10000 0 0
receptor internalization -0.013 0.045 0.17 13 -10000 0 13
Ephrin B/EPHB2/KALRN 0.065 0.072 0.23 43 -0.19 8 51
ROCK1 -0.012 0.034 0.18 9 -0.18 2 11
RAS family/GDP -0.032 0.038 -10000 0 -0.2 4 4
Rac1/GTP -0.016 0.041 0.12 5 -0.17 6 11
Ephrin B/EPHB1/Src/Paxillin 0.007 0.058 0.18 1 -0.2 6 7
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.009 0.029 0.11 1 -0.22 2 3
NFATC2 -0.013 0.041 0.11 1 -0.21 11 12
NFATC3 -0.009 0.025 0.11 1 -10000 0 1
CD40LG -0.034 0.14 0.35 6 -0.37 25 31
PTGS2 -0.037 0.15 0.35 9 -0.36 38 47
JUNB 0.018 0.025 -10000 0 -0.33 2 2
CaM/Ca2+/Calcineurin A alpha-beta B1 0.011 0.021 -10000 0 -10000 0 0
CaM/Ca2+ 0.011 0.021 -10000 0 -10000 0 0
CALM1 0.014 0.02 -10000 0 -10000 0 0
JUN 0.012 0.032 -10000 0 -0.33 2 2
mol:Ca2+ -0.001 0.009 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.01 0.012 -10000 0 -10000 0 0
FOSL1 0.034 0.075 0.33 20 -0.33 3 23
CREM 0.021 0.004 -10000 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT 0.022 0.093 0.28 15 -0.25 8 23
FOS -0.01 0.092 -10000 0 -0.33 28 28
IFNG -0.016 0.15 0.35 29 -0.34 17 46
AP-1/NFAT1-c-4 0.019 0.17 0.47 15 -0.38 18 33
FASLG -0.028 0.12 0.29 18 -0.33 19 37
NFAT1-c-4/ICER1 0.009 0.063 0.17 13 -0.21 8 21
IL2RA -0.015 0.15 0.35 34 -0.34 17 51
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSF2 -0.036 0.15 0.32 19 -0.38 31 50
JunB/Fra1/NFAT1-c-4 0.023 0.085 0.26 17 -0.24 8 25
IL4 -0.03 0.12 0.28 17 -0.33 18 35
IL2 0 0.1 -10000 0 -0.82 6 6
IL3 -0.012 0.13 -10000 0 -0.64 16 16
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
BATF3 0.02 0.017 0.33 1 -10000 0 1
mol:FK506 0 0 -10000 0 -10000 0 0
POU2F1 0.019 0.006 -10000 0 -10000 0 0
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.007 0.067 0.33 15 -10000 0 15
PI3K Class IB/PDE3B 0.007 0.067 -10000 0 -0.33 15 15
PDE3B 0.007 0.067 -10000 0 -0.33 15 15
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.015 0.096 -10000 0 -0.31 23 23
TBX21 -0.11 0.32 -10000 0 -1.1 28 28
B2M 0.02 0.007 -10000 0 -10000 0 0
TYK2 0.01 0.027 -10000 0 -10000 0 0
IL12RB1 0.002 0.06 -10000 0 -0.35 9 9
GADD45B -0.095 0.28 -10000 0 -0.96 23 23
IL12RB2 0.035 0.096 0.33 33 -0.34 2 35
GADD45G -0.087 0.27 -10000 0 -0.93 23 23
natural killer cell activation -0.004 0.012 -10000 0 -10000 0 0
RELB 0.02 0.005 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
IL18 0.006 0.053 -10000 0 -0.33 8 8
IL2RA 0.043 0.085 0.33 30 -0.33 1 31
IFNG 0.041 0.086 0.33 29 -0.33 2 31
STAT3 (dimer) -0.077 0.23 -10000 0 -0.71 30 30
HLA-DRB5 -0.015 0.1 -10000 0 -0.33 35 35
FASLG -0.077 0.27 -10000 0 -0.92 22 22
NF kappa B2 p52/RelB -0.076 0.27 -10000 0 -0.82 28 28
CD4 0.009 0.051 -10000 0 -0.33 8 8
SOCS1 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:6955 -0.002 0.008 -10000 0 -10000 0 0
CD3D 0.014 0.031 -10000 0 -0.35 2 2
CD3E 0.013 0.035 -10000 0 -0.33 3 3
CD3G 0.009 0.052 -10000 0 -0.33 8 8
IL12Rbeta2/JAK2 0.031 0.073 0.24 28 -0.24 3 31
CCL3 -0.09 0.27 -10000 0 -1 19 19
CCL4 -0.09 0.27 -10000 0 -0.98 20 20
HLA-A 0.02 0.007 -10000 0 -10000 0 0
IL18/IL18R 0.015 0.087 -10000 0 -0.25 29 29
NOS2 -0.13 0.37 -10000 0 -1.1 43 43
IL12/IL12R/TYK2/JAK2/SPHK2 -0.017 0.1 -10000 0 -0.31 27 27
IL1R1 -0.091 0.26 -10000 0 -0.95 21 21
IL4 0.004 0.027 -10000 0 -10000 0 0
JAK2 0.009 0.031 -10000 0 -0.32 1 1
EntrezGene:6957 -0.001 0.007 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.017 0.13 -10000 0 -0.53 14 14
RAB7A -0.078 0.22 -10000 0 -0.78 20 20
lysosomal transport -0.073 0.21 -10000 0 -0.73 20 20
FOS -0.12 0.34 -10000 0 -0.97 46 46
STAT4 (dimer) -0.075 0.26 -10000 0 -0.79 27 27
STAT5A (dimer) -0.065 0.27 -10000 0 -0.82 28 28
GZMA -0.087 0.26 -10000 0 -0.98 20 20
GZMB -0.098 0.3 -10000 0 -1.1 23 23
HLX 0.016 0.035 -10000 0 -0.33 4 4
LCK -0.091 0.28 -10000 0 -0.92 26 26
TCR/CD3/MHC II/CD4 -0.028 0.11 -10000 0 -0.3 40 40
IL2/IL2R 0.059 0.06 0.23 30 -0.28 3 33
MAPK14 -0.093 0.28 -10000 0 -0.84 32 32
CCR5 -0.083 0.25 -10000 0 -0.87 23 23
IL1B -0.01 0.089 0.34 1 -0.34 23 24
STAT6 -0.011 0.073 -10000 0 -0.3 1 1
STAT4 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.002 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
NFKB2 0.021 0.003 -10000 0 -10000 0 0
IL12B 0.011 0.041 0.31 3 -0.34 1 4
CD8A 0.019 0.036 0.33 1 -0.34 3 4
CD8B 0.02 0.045 0.33 3 -0.33 4 7
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.014 0.095 0.31 23 -10000 0 23
IL2RB 0.019 0.025 -10000 0 -0.33 2 2
proteasomal ubiquitin-dependent protein catabolic process -0.068 0.23 -10000 0 -0.71 27 27
IL2RG 0.018 0.035 -10000 0 -0.33 4 4
IL12 0.017 0.049 0.24 2 -0.25 4 6
STAT5A 0.02 0.018 -10000 0 -0.33 1 1
CD247 0.014 0.029 -10000 0 -0.33 2 2
IL2 0.02 0.003 -10000 0 -10000 0 0
SPHK2 0.019 0.018 -10000 0 -0.33 1 1
FRAP1 0 0 -10000 0 -10000 0 0
IL12A 0.006 0.051 0.34 1 -0.34 5 6
IL12/IL12R/TYK2/JAK2 -0.09 0.31 -10000 0 -1 26 26
MAP2K3 -0.1 0.29 -10000 0 -0.9 30 30
RIPK2 0.019 0.007 -10000 0 -10000 0 0
MAP2K6 -0.089 0.28 -10000 0 -0.85 31 31
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.004 0.066 -10000 0 -0.33 14 14
IL18RAP 0 0.072 -10000 0 -0.34 16 16
IL12Rbeta1/TYK2 0.011 0.052 -10000 0 -0.25 8 8
EOMES -0.008 0.15 -10000 0 -0.6 18 18
STAT1 (dimer) -0.058 0.23 -10000 0 -0.72 25 25
T cell proliferation -0.062 0.19 0.36 1 -0.58 29 30
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.001 0.069 -10000 0 -0.33 15 15
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.066 0.22 -10000 0 -0.59 40 40
ATF2 -0.087 0.26 -10000 0 -0.76 32 32
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.02 0.005 -10000 0 -9999 0 0
PLK4 0.038 0.07 0.33 21 -9999 0 21
regulation of centriole replication -0.007 0.041 0.16 21 -9999 0 21
Signaling events mediated by PTP1B

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
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.007 0.13 0.22 1 -0.33 37 38
PTP1B/AKT1 0.012 0.074 0.2 2 -0.32 8 10
FYN 0.018 0.019 -10000 0 -0.33 1 1
p210 bcr-abl/PTP1B 0.005 0.079 0.22 4 -0.34 8 12
EGFR 0.015 0.045 0.33 1 -0.34 5 6
EGF/EGFR 0.035 0.1 0.22 38 -0.34 7 45
CSF1 0.02 0.018 -10000 0 -0.33 1 1
AKT1 0.019 0.01 -10000 0 -10000 0 0
INSR 0.02 0.007 -10000 0 -10000 0 0
PTP1B/N-cadherin 0.031 0.097 0.24 32 -0.33 7 39
Insulin Receptor/Insulin 0.021 0.072 -10000 0 -0.34 5 5
HCK 0.008 0.065 -10000 0 -0.33 14 14
CRK 0.019 0.006 -10000 0 -10000 0 0
TYK2 0.002 0.076 0.29 3 -0.37 6 9
EGF 0.075 0.13 0.33 72 -0.33 4 76
YES1 0.02 0.005 -10000 0 -10000 0 0
CAV1 -0.053 0.11 0.23 5 -0.32 23 28
TXN 0.022 0.017 0.33 1 -10000 0 1
PTP1B/IRS1/GRB2 0.021 0.076 0.25 1 -0.31 7 8
cell migration -0.005 0.079 0.34 8 -0.22 4 12
STAT3 0.021 0.003 -10000 0 -10000 0 0
PRLR 0.023 0.095 0.33 21 -0.33 12 33
ITGA2B -0.012 0.11 0.33 3 -0.33 39 42
CSF1R 0.015 0.043 -10000 0 -0.33 6 6
Prolactin Receptor/Prolactin 0.029 0.074 0.25 25 -0.23 12 37
FGR -0.006 0.093 -10000 0 -0.33 30 30
PTP1B/p130 Cas 0.013 0.077 0.22 3 -0.34 7 10
Crk/p130 Cas 0.019 0.078 0.24 2 -0.35 6 8
DOK1 0.002 0.084 0.28 2 -0.32 12 14
JAK2 -0.008 0.13 0.23 4 -0.34 35 39
Jak2/Leptin Receptor/Leptin 0.028 0.1 0.23 11 -0.32 9 20
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
PTPN1 0.005 0.08 0.22 4 -0.34 8 12
LYN 0.019 0.006 -10000 0 -10000 0 0
CDH2 0.045 0.1 0.33 38 -0.33 5 43
SRC 0.01 0.085 -10000 0 -0.45 10 10
ITGB3 0.03 0.081 0.33 21 -0.33 4 25
CAT1/PTP1B -0.028 0.14 0.3 4 -0.37 33 37
CAPN1 0.021 0.005 -10000 0 -10000 0 0
CSK 0.021 0.003 -10000 0 -10000 0 0
PI3K 0.025 0.068 -10000 0 -0.31 4 4
mol:H2O2 0 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.025 0.092 0.22 8 -0.3 9 17
negative regulation of transcription -0.007 0.12 0.23 4 -0.33 35 39
FCGR2A 0.017 0.026 -10000 0 -0.33 2 2
FER 0.021 0.008 -10000 0 -10000 0 0
alphaIIb/beta3 Integrin 0.014 0.1 0.24 24 -0.24 42 66
BLK 0.053 0.1 0.33 45 -0.33 1 46
Insulin Receptor/Insulin/Shc 0.032 0.017 -10000 0 -10000 0 0
RHOA 0.021 0.005 -10000 0 -10000 0 0
LEPR -0.003 0.087 -10000 0 -0.32 27 27
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
p210 bcr-abl/Grb2 0.02 0.004 -10000 0 -10000 0 0
mol:NADPH 0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.043 0.15 0.2 2 -0.36 50 52
PRL 0.023 0.046 0.33 8 -10000 0 8
SOCS3 0.003 0.12 -10000 0 -1.1 5 5
SPRY2 0.019 0.02 -10000 0 -0.33 1 1
Insulin Receptor/Insulin/IRS1 0.037 0.017 -10000 0 -0.18 1 1
CSF1/CSF1R 0.019 0.082 0.22 1 -0.36 8 9
Ras protein signal transduction 0.009 0.12 0.55 16 -10000 0 16
IRS1 0.02 0.018 -10000 0 -0.33 1 1
INS 0.011 0.015 -10000 0 -10000 0 0
LEP 0.051 0.095 0.33 40 -10000 0 40
STAT5B 0.006 0.091 0.22 6 -0.3 16 22
STAT5A 0.005 0.092 0.22 6 -0.3 17 23
GRB2 0.02 0.004 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.015 0.077 0.22 3 -0.34 7 10
CSN2 0.022 0.068 0.56 1 -10000 0 1
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
LAT 0.015 0.061 -10000 0 -0.38 6 6
YBX1 0.023 0.005 -10000 0 -10000 0 0
LCK 0.021 0.024 0.33 1 -0.33 1 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
NOX4 0.031 0.056 0.33 13 -10000 0 13
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 -0.02 0.033 -10000 0 -0.23 9 9
MAP4K4 -0.012 0.048 0.14 2 -0.27 4 6
BAG4 0.018 0.007 -10000 0 -10000 0 0
PKC zeta/ceramide 0.002 0.065 -10000 0 -0.18 43 43
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.022 0.04 0.33 4 -0.33 2 6
BAX -0.01 0.076 -10000 0 -0.34 17 17
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.006 0.12 0.71 10 -10000 0 10
BAD -0.013 0.062 0.2 2 -0.18 42 44
SMPD1 0.005 0.059 0.2 10 -0.22 4 14
RB1 -0.014 0.06 -10000 0 -0.18 43 43
FADD/Caspase 8 -0.001 0.057 -10000 0 -0.31 2 2
MAP2K4 -0.016 0.059 0.18 3 -0.17 39 42
NSMAF 0.019 0.007 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.016 0.063 0.21 6 -0.17 42 48
EGF 0.074 0.13 0.33 72 -0.33 4 76
mol:ceramide -0.009 0.064 0.12 4 -0.18 43 47
MADD 0.021 0.003 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid -0.017 0.03 -10000 0 -0.23 7 7
ASAH1 0.017 0.019 -10000 0 -0.33 1 1
negative regulation of cell cycle -0.014 0.059 -10000 0 -0.17 43 43
cell proliferation 0.001 0.067 0.21 3 -0.21 3 6
BID -0.003 0.11 -10000 0 -0.59 10 10
MAP3K1 -0.012 0.062 0.19 4 -0.18 41 45
EIF2A -0.014 0.071 0.21 14 -0.18 31 45
TRADD 0.021 0.004 -10000 0 -10000 0 0
CRADD 0.022 0.016 0.33 1 -10000 0 1
MAPK3 -0.015 0.061 0.2 6 -0.17 22 28
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.018 0.063 0.2 6 -0.18 22 28
Cathepsin D/ceramide 0.003 0.065 -10000 0 -0.18 43 43
FADD -0.011 0.047 0.14 2 -0.27 4 6
KSR1 -0.011 0.067 0.23 6 -0.18 43 49
MAPK8 -0.012 0.067 -10000 0 -0.27 5 5
PRKRA -0.011 0.065 0.23 5 -0.18 42 47
PDGFA 0.012 0.05 -10000 0 -0.33 8 8
TRAF2 0.021 0.004 -10000 0 -10000 0 0
IGF1 0.017 0.042 0.33 1 -0.33 5 6
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.009 0.064 0.12 4 -0.18 43 47
CTSD 0.021 0.004 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0.03 0.006 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta 0.001 0.071 0.24 2 -0.22 3 5
PRKCD 0.021 0.004 -10000 0 -10000 0 0
PRKCZ 0.018 0.031 -10000 0 -0.33 3 3
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine -0.017 0.03 -10000 0 -0.23 7 7
RelA/NF kappa B1 0.031 0.006 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.021 0.004 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD -0.004 0.05 0.16 2 -0.28 3 5
TNFR1A/BAG4/TNF-alpha 0.024 0.052 0.23 1 -0.19 18 19
mol:Sphingosine-1-phosphate -0.02 0.033 -10000 0 -0.23 9 9
MAP2K1 -0.018 0.062 0.18 9 -0.17 39 48
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
CYCS 0.004 0.052 0.18 3 -0.17 13 16
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.012 -10000 0 -10000 0 0
EIF2AK2 -0.013 0.064 0.2 9 -0.18 39 48
TNF-alpha/TNFR1A/FAN 0.026 0.05 0.23 1 -0.2 16 17
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.011 0.048 -10000 0 -0.32 3 3
MAP2K2 -0.019 0.06 0.2 6 -0.18 31 37
SMPD3 0.005 0.055 0.18 4 -0.25 5 9
TNF 0.004 0.077 0.33 1 -0.33 19 20
PKC zeta/PAR4 0.028 0.024 -10000 0 -0.23 3 3
mol:PHOSPHOCHOLINE -0.02 0.066 0.18 7 -0.18 18 25
NF kappa B1/RelA/I kappa B alpha 0.048 0.032 -10000 0 -0.18 2 2
AIFM1 -0.003 0.061 0.17 4 -0.18 13 17
BCL2 0.02 0.017 0.33 1 -10000 0 1
BCR signaling pathway

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
JUN 0.034 0.11 0.27 17 -0.46 6 23
IKBKB 0.028 0.089 0.25 6 -0.28 10 16
AKT1 0.033 0.078 0.24 23 -0.23 1 24
IKBKG 0.032 0.067 0.24 5 -0.25 5 10
CALM1 0.018 0.085 0.26 5 -0.38 7 12
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
MAP3K1 0.041 0.13 0.27 25 -0.42 8 33
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0.019 0.092 0.21 2 -0.4 8 10
DOK1 0.021 0.002 -10000 0 -10000 0 0
AP-1 0.018 0.078 0.22 10 -0.25 6 16
LYN 0.019 0.006 -10000 0 -10000 0 0
BLNK 0.02 0.018 -10000 0 -0.33 1 1
SHC1 0.018 0.008 -10000 0 -10000 0 0
BCR complex 0.071 0.1 0.26 75 -0.32 2 77
CD22 0.011 0.072 0.24 11 -0.33 5 16
CAMK2G 0.014 0.081 0.26 4 -0.39 6 10
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
INPP5D 0.018 0.031 -10000 0 -0.33 3 3
SHC/GRB2/SOS1 -0.005 0.049 0.16 7 -10000 0 7
GO:0007205 0.018 0.093 0.21 2 -0.41 8 10
SYK 0.019 0.025 -10000 0 -0.33 2 2
ELK1 0.014 0.088 0.23 2 -0.39 8 10
NFATC1 0.036 0.096 0.25 18 -0.35 6 24
B-cell antigen/BCR complex 0.071 0.1 0.26 75 -0.32 2 77
PAG1/CSK 0.027 0.011 -10000 0 -10000 0 0
NFKBIB 0.024 0.039 0.13 6 -0.12 6 12
HRAS 0.023 0.081 0.25 9 -0.37 4 13
NFKBIA 0.023 0.039 0.13 6 -0.12 7 13
NF-kappa-B/RelA/I kappa B beta 0.026 0.036 0.13 6 -10000 0 6
RasGAP/Csk 0.079 0.085 0.24 70 -0.15 2 72
mol:GDP 0.018 0.093 0.21 2 -0.41 8 10
PTEN 0.021 0.003 -10000 0 -10000 0 0
CD79B 0.026 0.048 0.33 8 -0.33 1 9
NF-kappa-B/RelA/I kappa B alpha 0.026 0.035 0.13 6 -10000 0 6
GRB2 0.02 0.004 -10000 0 -10000 0 0
PI3K/BCAP/CD19 0.047 0.12 0.31 11 -0.46 7 18
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
mol:IP3 0.02 0.092 0.21 3 -0.43 7 10
CSK 0.021 0.003 -10000 0 -10000 0 0
FOS 0.004 0.093 0.26 5 -0.36 10 15
CHUK 0.027 0.077 0.24 5 -0.28 9 14
IBTK 0.019 0.006 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 0.035 0.079 0.22 1 -0.34 5 6
PTPN6 0.006 0.069 0.22 11 -0.38 4 15
RELA 0.021 0.003 -10000 0 -10000 0 0
BCL2A1 0.017 0.027 0.12 1 -10000 0 1
VAV2 0.049 0.091 0.27 16 -0.45 3 19
ubiquitin-dependent protein catabolic process 0.024 0.039 0.13 6 -0.12 8 14
BTK -0.046 0.25 -10000 0 -0.96 28 28
CD19 0.046 0.091 0.26 23 -0.39 2 25
MAP4K1 0.016 0.035 -10000 0 -0.33 4 4
CD72 0.021 0.016 0.33 1 -10000 0 1
PAG1 0.019 0.007 -10000 0 -10000 0 0
MAPK14 0.043 0.12 0.28 30 -0.38 7 37
SH3BP5 0.019 0.025 -10000 0 -0.33 2 2
PIK3AP1 0.02 0.092 0.23 1 -0.43 8 9
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 0.015 0.13 0.21 4 -0.47 16 20
RAF1 0.018 0.077 0.24 9 -0.36 4 13
RasGAP/p62DOK/SHIP 0.075 0.079 0.36 7 -0.24 2 9
CD79A 0.077 0.12 0.33 74 -0.33 2 76
re-entry into mitotic cell cycle 0.018 0.077 0.22 10 -0.24 7 17
RASA1 0.02 0.005 -10000 0 -10000 0 0
MAPK3 0.012 0.073 0.22 9 -0.31 4 13
MAPK1 0.013 0.069 0.23 8 -0.33 3 11
CD72/SHP1 0.023 0.09 0.24 20 -0.36 4 24
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MAPK8 0.038 0.12 0.26 27 -0.37 8 35
actin cytoskeleton organization 0.061 0.1 0.28 33 -0.33 4 37
NF-kappa-B/RelA 0.051 0.069 0.24 6 -0.21 3 9
Calcineurin 0.032 0.079 0.32 1 -0.4 4 5
PI3K 0.003 0.067 0.19 7 -0.29 4 11
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 0.021 0.086 0.25 1 -0.44 7 8
SOS1 0.021 0.003 -10000 0 -10000 0 0
Bam32/HPK1 0.037 0.12 -10000 0 -0.58 10 10
DAPP1 0.024 0.13 -10000 0 -0.64 10 10
cytokine secretion 0.035 0.093 0.25 19 -0.33 6 25
mol:DAG 0.02 0.092 0.21 3 -0.43 7 10
PLCG2 0.018 0.031 -10000 0 -0.33 3 3
MAP2K1 0.013 0.074 0.24 8 -0.33 4 12
B-cell antigen/BCR complex/FcgammaRIIB 0.071 0.089 0.25 72 -0.18 2 74
mol:PI-3-4-5-P3 0.015 0.068 0.19 14 -0.26 2 16
ETS1 0.013 0.076 0.24 7 -0.33 5 12
B-cell antigen/BCR complex/LYN/SYK/BLNK 0.081 0.087 0.24 71 -0.21 3 74
B-cell antigen/BCR complex/LYN 0.03 0.068 0.28 8 -0.4 3 11
MALT1 0.019 0.007 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.059 0.1 0.28 31 -0.35 4 35
B-cell antigen/BCR complex/LYN/SYK 0.056 0.1 0.34 14 -0.32 4 18
CARD11 0.035 0.1 0.28 11 -0.37 8 19
FCGR2B 0.019 0.007 -10000 0 -10000 0 0
PPP3CA 0.021 0.003 -10000 0 -10000 0 0
BCL10 0.02 0.004 -10000 0 -10000 0 0
IKK complex 0.023 0.047 0.14 22 -0.12 3 25
PTPRC 0.014 0.043 -10000 0 -0.33 6 6
PDPK1 0.021 0.071 0.21 23 -0.18 2 25
PPP3CB 0.021 0.003 -10000 0 -10000 0 0
PPP3CC 0.018 0.008 -10000 0 -10000 0 0
POU2F2 0.019 0.027 0.12 5 -10000 0 5
Plasma membrane estrogen receptor signaling

Figure 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
GNB1/GNG2 0.041 0.043 0.21 8 -0.17 8 16
ER alpha/Gai/GDP/Gbeta gamma -0.036 0.14 -10000 0 -0.48 21 21
AKT1 -0.063 0.24 -10000 0 -0.68 47 47
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K -0.06 0.24 -10000 0 -0.69 47 47
mol:Ca2+ -0.023 0.072 -10000 0 -0.33 17 17
IGF1R 0.02 0.018 -10000 0 -0.33 1 1
E2/ER alpha (dimer)/Striatin 0.026 0.043 0.21 10 -0.19 7 17
SHC1 0.018 0.008 -10000 0 -10000 0 0
apoptosis 0.06 0.23 0.64 48 -10000 0 48
RhoA/GTP -0.024 0.025 -10000 0 -0.16 7 7
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.019 0.12 0.23 3 -0.39 22 25
regulation of stress fiber formation 0.016 0.055 0.25 1 -0.25 3 4
E2/ERA-ERB (dimer) 0.026 0.044 0.21 10 -0.19 8 18
KRAS 0.02 0.006 -10000 0 -10000 0 0
G13/GTP 0.025 0.039 0.2 10 -0.17 7 17
pseudopodium formation -0.016 0.055 0.25 3 -0.25 1 4
E2/ER alpha (dimer)/PELP1 0.024 0.043 0.21 9 -0.19 8 17
GRB2 0.02 0.004 -10000 0 -10000 0 0
GNG2 0.019 0.018 -10000 0 -0.33 1 1
GNAO1 0.02 0.034 0.33 2 -0.33 2 4
HRAS 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO -0.04 0.16 0.23 4 -0.41 49 53
E2/ER beta (dimer) 0.015 0.003 -10000 0 -10000 0 0
mol:GDP -0.005 0.071 0.18 11 -0.2 30 41
mol:NADP -0.04 0.16 0.23 4 -0.41 49 53
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
mol:IP3 -0.024 0.075 -10000 0 -0.35 17 17
IGF-1R heterotetramer 0.02 0.018 -10000 0 -0.33 1 1
PLCB1 -0.009 0.07 -10000 0 -0.36 13 13
PLCB2 -0.012 0.074 -10000 0 -0.36 14 14
IGF1 0.017 0.042 0.33 1 -0.33 5 6
mol:L-citrulline -0.04 0.16 0.23 4 -0.41 49 53
RHOA 0.021 0.004 -10000 0 -10000 0 0
Gai/GDP -0.021 0.15 -10000 0 -0.62 19 19
JNK cascade 0.015 0.003 -10000 0 -10000 0 0
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
ESR2 0.02 0.004 -10000 0 -10000 0 0
GNAQ 0.019 0.018 -10000 0 -0.33 1 1
ESR1 0.02 0.071 0.33 10 -0.33 8 18
Gq family/GDP/Gbeta gamma -0.048 0.21 -10000 0 -0.74 30 30
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.012 0.061 -10000 0 -0.55 2 2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.018 0.12 0.22 2 -0.38 21 23
GNAZ -0.01 0.098 -10000 0 -0.33 34 34
E2/ER alpha (dimer) 0.015 0.048 0.22 10 -0.22 8 18
STRN 0.021 0.003 -10000 0 -10000 0 0
GNAL 0.019 0.045 0.33 3 -0.33 4 7
PELP1 0.019 0.006 -10000 0 -10000 0 0
MAPK11 -0.013 0.018 0.22 1 -0.19 2 3
GNAI2 0.021 0.004 -10000 0 -10000 0 0
GNAI3 0.02 0.004 -10000 0 -10000 0 0
GNAI1 0.019 0.018 -10000 0 -0.33 1 1
HBEGF -0.043 0.15 0.35 9 -0.44 28 37
cAMP biosynthetic process 0.019 0.041 0.14 12 -0.18 10 22
SRC -0.035 0.13 0.28 1 -0.45 21 22
PI3K 0.029 0.009 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma 0.018 0.068 0.2 1 -0.26 7 8
SOS1 0.021 0.003 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.028 0.093 -10000 0 -0.32 22 22
Gs family/GTP 0.025 0.044 0.17 12 -0.18 10 22
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP 0.035 0.014 -10000 0 -10000 0 0
vasodilation -0.038 0.15 0.22 5 -0.39 49 54
mol:DAG -0.024 0.075 -10000 0 -0.35 17 17
Gs family/GDP/Gbeta gamma 0 0.065 -10000 0 -0.26 10 10
MSN -0.017 0.057 0.26 3 -0.26 1 4
Gq family/GTP -0.001 0.078 -10000 0 -0.37 15 15
mol:PI-3-4-5-P3 -0.057 0.23 -10000 0 -0.66 48 48
NRAS 0.02 0.005 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion 0.038 0.15 0.39 49 -0.22 5 54
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.006 0.074 0.19 9 -0.26 10 19
NOS3 -0.043 0.17 0.24 3 -0.43 49 52
GNA11 0.02 0.006 -10000 0 -10000 0 0
MAPKKK cascade -0.034 0.17 0.32 3 -0.46 43 46
E2/ER alpha (dimer)/PELP1/Src -0.02 0.13 0.25 6 -0.41 21 27
ruffle organization -0.016 0.055 0.25 3 -0.25 1 4
ROCK2 -0.012 0.06 0.27 3 -10000 0 3
GNA14 0.011 0.055 -10000 0 -0.33 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
MMP9 -0.026 0.13 0.37 4 -0.43 20 24
MMP2 -0.033 0.13 0.27 8 -0.43 21 29
Coregulation of Androgen receptor activity

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
NRIP1 0.02 0.006 -10000 0 -10000 0 0
SVIL 0.021 0.004 -10000 0 -10000 0 0
ZNF318 0.019 0.009 -10000 0 -10000 0 0
JMJD2C 0.007 0.028 0.13 19 -10000 0 19
T-DHT/AR/Ubc9 0.005 0.088 0.18 5 -0.2 50 55
CARM1 0.02 0.005 -10000 0 -10000 0 0
PRDX1 0.021 0.005 -10000 0 -10000 0 0
PELP1 0.019 0.008 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 0.019 0.008 -10000 0 -10000 0 0
PTK2B 0.017 0.019 -10000 0 -0.33 1 1
MED1 0.02 0.007 -10000 0 -10000 0 0
MAK 0.009 0.065 0.33 1 -0.33 13 14
response to oxidative stress 0 0.001 -10000 0 -10000 0 0
HIP1 0.018 0.031 -10000 0 -0.33 3 3
GSN 0.021 0.005 -10000 0 -10000 0 0
NCOA2 0.017 0.026 -10000 0 -0.33 2 2
NCOA6 0.02 0.005 -10000 0 -10000 0 0
DNA-PK 0.036 0.018 -10000 0 -10000 0 0
NCOA4 0.021 0.002 -10000 0 -10000 0 0
PIAS3 0.021 0.004 -10000 0 -10000 0 0
cell proliferation -0.012 0.12 0.26 1 -0.61 13 14
XRCC5 0.02 0.006 -10000 0 -10000 0 0
UBE3A 0.02 0.006 -10000 0 -10000 0 0
T-DHT/AR/SNURF -0.001 0.094 0.18 5 -0.2 58 63
FHL2 0.044 0.11 0.31 50 -10000 0 50
RANBP9 0.021 0.005 -10000 0 -10000 0 0
JMJD1A -0.009 0.037 -10000 0 -0.13 35 35
CDK6 0.019 0.018 -10000 0 -0.33 1 1
TGFB1I1 0.019 0.025 -10000 0 -0.33 2 2
T-DHT/AR/CyclinD1 0.005 0.089 0.18 5 -0.21 48 53
XRCC6 0.02 0.006 -10000 0 -10000 0 0
T-DHT/AR 0.018 0.11 0.27 8 -0.21 53 61
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
CTDSP2 0.019 0.008 -10000 0 -10000 0 0
BRCA1 0.021 0.004 -10000 0 -10000 0 0
TCF4 0.016 0.026 -10000 0 -0.33 2 2
CDKN2A 0.097 0.14 0.33 103 -10000 0 103
SRF 0.04 0.047 0.17 1 -10000 0 1
NKX3-1 -0.028 0.12 -10000 0 -0.47 17 17
KLK3 -0.01 0.06 -10000 0 -10000 0 0
TMF1 0.021 0.004 -10000 0 -10000 0 0
HNRNPA1 0.02 0.007 -10000 0 -10000 0 0
AOF2 0 0.002 -10000 0 -10000 0 0
APPL1 -0.017 0.006 -10000 0 -10000 0 0
T-DHT/AR/Caspase 8 0.005 0.088 0.18 4 -0.2 50 54
AR -0.022 0.12 0.33 1 -0.34 49 50
UBA3 0.021 0.004 -10000 0 -10000 0 0
PATZ1 0.02 0.007 -10000 0 -10000 0 0
PAWR 0.021 0.004 -10000 0 -10000 0 0
PRKDC 0.018 0.008 -10000 0 -10000 0 0
PA2G4 0.02 0.007 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 0.006 0.079 0.17 4 -0.18 49 53
RPS6KA3 0.021 0.005 -10000 0 -10000 0 0
T-DHT/AR/ARA70 0.006 0.088 0.18 5 -0.2 49 54
LATS2 0.019 0.008 -10000 0 -10000 0 0
T-DHT/AR/PRX1 0.007 0.079 0.17 4 -0.18 49 53
Cyclin D3/CDK11 p58 0.015 0.004 -10000 0 -10000 0 0
VAV3 0.019 0.035 0.33 1 -0.33 3 4
KLK2 0.007 0.081 0.31 16 -0.34 3 19
CASP8 0.02 0.018 -10000 0 -0.33 1 1
T-DHT/AR/TIF2/CARM1 0.015 0.081 0.22 1 -0.19 42 43
TMPRSS2 -0.06 0.22 -10000 0 -0.77 34 34
CCND1 0.016 0.039 -10000 0 -0.33 5 5
PIAS1 0.021 0.005 -10000 0 -10000 0 0
mol:T-DHT 0.002 0.019 0.06 6 -0.058 17 23
CDC2L1 0 0 -10000 0 -10000 0 0
PIAS4 0.02 0.007 -10000 0 -10000 0 0
T-DHT/AR/CDK6 0.006 0.086 0.18 4 -0.2 47 51
CMTM2 -0.042 0.13 -10000 0 -0.33 70 70
SNURF 0.011 0.055 -10000 0 -0.33 10 10
ZMIZ1 0.02 0.028 -10000 0 -10000 0 0
CCND3 0.02 0.004 -10000 0 -10000 0 0
TGIF1 0.019 0.008 -10000 0 -10000 0 0
FKBP4 0.02 0.006 -10000 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
alphaV beta3 Integrin 0.039 0.055 0.24 21 -0.23 4 25
PTK2 -0.019 0.1 -10000 0 -0.36 20 20
positive regulation of JNK cascade -0.018 0.11 -10000 0 -0.3 26 26
CDC42/GDP -0.017 0.15 -10000 0 -0.4 27 27
Rac1/GDP -0.019 0.14 -10000 0 -0.39 25 25
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.018 0.13 -10000 0 -0.36 26 26
nectin-3/I-afadin 0.013 0.061 -10000 0 -0.23 23 23
RAPGEF1 -0.035 0.14 0.28 1 -0.38 38 39
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.04 0.15 -10000 0 -0.41 42 42
PDGFB-D/PDGFRB 0.02 0.004 -10000 0 -10000 0 0
TLN1 -0.025 0.057 -10000 0 -0.35 9 9
Rap1/GTP -0.024 0.1 -10000 0 -0.28 42 42
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.016 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin 0.013 0.061 -10000 0 -0.23 23 23
PVR 0.02 0.005 -10000 0 -10000 0 0
Necl-5(dimer) 0.02 0.005 -10000 0 -10000 0 0
mol:GDP -0.034 0.17 -10000 0 -0.47 28 28
MLLT4 0.019 0.006 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.04 0.054 -10000 0 -0.18 16 16
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0.032 0.035 0.24 10 -10000 0 10
positive regulation of lamellipodium assembly -0.02 0.11 -10000 0 -0.32 26 26
PVRL1 0.028 0.049 0.33 10 -10000 0 10
PVRL3 0.001 0.084 0.33 1 -0.33 23 24
PVRL2 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
CDH1 0.019 0.025 -10000 0 -0.33 2 2
CLDN1 0.026 0.058 0.33 10 -0.33 3 13
JAM-A/CLDN1 0.035 0.066 0.23 10 -0.2 19 29
SRC -0.041 0.16 -10000 0 -0.44 46 46
ITGB3 0.034 0.079 0.33 21 -0.33 4 25
nectin-1(dimer)/I-afadin/I-afadin 0.032 0.035 0.24 10 -10000 0 10
FARP2 -0.029 0.17 -10000 0 -0.52 15 15
RAC1 0.019 0.007 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) 0.024 0.054 -10000 0 -0.19 21 21
nectin-1/I-afadin 0.032 0.035 0.24 10 -10000 0 10
nectin-2/I-afadin 0.027 0.011 -10000 0 -10000 0 0
RAC1/GTP/IQGAP1/filamentous actin 0.025 0.01 -10000 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin 0.028 0.06 0.23 8 -0.19 20 28
CDC42/GTP/IQGAP1/filamentous actin 0.027 0.007 -10000 0 -10000 0 0
F11R 0.018 0.019 -10000 0 -0.33 1 1
positive regulation of filopodium formation -0.018 0.11 -10000 0 -0.3 26 26
alphaV/beta3 Integrin/Talin -0.023 0.081 0.2 21 -0.31 11 32
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.027 0.011 -10000 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0.027 0.011 -10000 0 -10000 0 0
PIP5K1C -0.02 0.061 -10000 0 -0.23 23 23
VAV2 -0.035 0.18 -10000 0 -0.51 25 25
RAP1/GDP -0.016 0.13 -10000 0 -0.36 27 27
ITGAV 0.021 0.002 -10000 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin 0.024 0.055 -10000 0 -0.19 22 22
nectin-3(dimer)/I-afadin/I-afadin 0.013 0.061 -10000 0 -0.23 23 23
Rac1/GTP -0.022 0.14 -10000 0 -0.38 26 26
PTPRM -0.011 0.071 -10000 0 -0.24 27 27
E-cadherin/beta catenin/alpha catenin 0.05 0.039 -10000 0 -0.17 1 1
adherens junction assembly 0 0 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC 0.035 0.1 0.25 27 -0.33 10 37
FYN 0.003 0.11 0.26 11 -0.36 17 28
LAT/GRAP2/SLP76 0.015 0.1 0.25 4 -0.35 15 19
IKBKB 0.018 0.007 -10000 0 -10000 0 0
AKT1 -0.003 0.094 0.24 9 -0.3 18 27
B2M 0.019 0.012 -10000 0 -10000 0 0
IKBKG -0.001 0.034 0.094 11 -0.1 5 16
MAP3K8 0.02 0.018 -10000 0 -0.33 1 1
mol:Ca2+ -0.017 0.014 0.084 2 -0.059 9 11
integrin-mediated signaling pathway 0.024 0.018 -10000 0 -0.19 2 2
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.007 0.12 0.23 8 -0.4 19 27
TRPV6 0.002 0.25 1.2 15 -10000 0 15
CD28 0.02 0.008 -10000 0 -10000 0 0
SHC1 0.019 0.12 0.26 34 -0.41 11 45
receptor internalization -0.007 0.11 0.2 1 -0.41 19 20
PRF1 -0.031 0.22 -10000 0 -0.91 21 21
KRAS 0.02 0.006 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
COT/AKT1 0.007 0.081 0.22 8 -0.26 14 22
LAT -0.002 0.11 0.27 7 -0.37 18 25
EntrezGene:6955 -0.001 0.005 -10000 0 -10000 0 0
CD3D 0.017 0.028 -10000 0 -0.34 2 2
CD3E 0.016 0.033 -10000 0 -0.34 3 3
CD3G 0.012 0.051 -10000 0 -0.33 8 8
RASGRP2 -0.009 0.039 -10000 0 -0.15 24 24
RASGRP1 -0.012 0.1 0.25 6 -0.33 14 20
HLA-A 0.019 0.011 -10000 0 -10000 0 0
RASSF5 0.017 0.026 -10000 0 -0.33 2 2
RAP1A/GTP/RAPL 0.024 0.018 -10000 0 -0.19 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.05 0.13 25 -0.12 5 30
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.014 0.035 -10000 0 -0.14 13 13
PRKCA -0.008 0.052 0.15 4 -0.2 7 11
GRAP2 0.011 0.058 -10000 0 -0.33 11 11
mol:IP3 0.015 0.085 0.17 32 -0.28 14 46
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.01 0.081 0.15 1 -0.34 14 15
ORAI1 -0.021 0.2 0.4 1 -0.98 15 16
CSK 0 0.11 0.27 3 -0.36 18 21
B7 family/CD28 0.018 0.12 -10000 0 -0.44 14 14
CHUK 0.021 0.003 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.004 0.12 -10000 0 -0.39 20 20
PTPN6 -0.006 0.099 0.22 4 -0.38 14 18
VAV1 -0.005 0.11 0.23 2 -0.37 18 20
Monovalent TCR/CD3 0.002 0.046 -10000 0 -0.26 9 9
CBL 0.02 0.005 -10000 0 -10000 0 0
LCK 0.006 0.11 0.26 8 -0.38 13 21
PAG1 0.006 0.11 0.24 9 -0.36 17 26
RAP1A 0.02 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.004 0.11 0.2 1 -0.38 18 19
CD80 0.012 0.053 -10000 0 -0.33 9 9
CD86 0.014 0.047 -10000 0 -0.33 7 7
PDK1/CARD11/BCL10/MALT1 0.003 0.048 0.14 3 -0.18 9 12
HRAS 0.021 0.004 -10000 0 -10000 0 0
GO:0035030 -0.015 0.094 0.19 5 -0.34 18 23
CD8A 0.018 0.037 0.33 1 -0.34 3 4
CD8B 0.019 0.047 0.33 3 -0.34 4 7
PTPRC 0.014 0.043 -10000 0 -0.33 6 6
PDK1/PKC theta -0.012 0.11 0.29 9 -0.34 22 31
CSK/PAG1 0.003 0.11 0.24 13 -0.37 14 27
SOS1 0.021 0.003 -10000 0 -10000 0 0
peptide-MHC class I 0.028 0.017 -10000 0 -10000 0 0
GRAP2/SLP76 0.018 0.11 0.23 1 -0.39 16 17
STIM1 -0.001 0.075 1.2 1 -10000 0 1
RAS family/GTP 0.012 0.059 0.18 10 -0.16 11 21
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.008 0.12 -10000 0 -0.44 19 19
mol:DAG -0.019 0.062 0.093 4 -0.24 17 21
RAP1A/GDP 0.008 0.023 0.078 9 -0.062 3 12
PLCG1 0.02 0.005 -10000 0 -10000 0 0
CD247 0.016 0.026 -10000 0 -0.32 2 2
cytotoxic T cell degranulation -0.029 0.21 -10000 0 -0.87 21 21
RAP1A/GTP -0.005 0.015 -10000 0 -0.06 23 23
mol:PI-3-4-5-P3 -0.003 0.1 0.22 9 -0.34 19 28
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.02 0.1 0.22 12 -0.35 14 26
NRAS 0.02 0.005 -10000 0 -10000 0 0
ZAP70 0.016 0.043 -10000 0 -0.33 6 6
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.01 0.096 0.26 2 -0.34 16 18
MALT1 0.019 0.007 -10000 0 -10000 0 0
TRAF6 0.021 0.003 -10000 0 -10000 0 0
CD8 heterodimer 0.028 0.051 0.31 3 -0.32 5 8
CARD11 0.033 0.066 0.33 18 -10000 0 18
PRKCB -0.012 0.058 0.15 2 -0.22 13 15
PRKCE -0.01 0.056 0.16 5 -0.22 8 13
PRKCQ -0.014 0.12 0.24 7 -0.37 23 30
LCP2 0.018 0.025 -10000 0 -0.33 2 2
BCL10 0.021 0.004 -10000 0 -10000 0 0
regulation of survival gene product expression -0.001 0.084 0.22 10 -0.26 17 27
IKK complex 0.008 0.052 0.19 14 -0.11 3 17
RAS family/GDP -0.004 0.008 -10000 0 -10000 0 0
MAP3K14 -0.005 0.062 0.2 7 -0.21 10 17
PDPK1 -0.003 0.092 0.25 11 -0.29 16 27
TCR/CD3/MHC I/CD8/Fyn -0.012 0.12 -10000 0 -0.45 16 16
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 0.023 0.052 0.24 5 -0.23 12 17
CRKL -0.002 0.09 0.29 4 -0.4 8 12
mol:PIP3 0.01 0.009 -10000 0 -10000 0 0
AKT1 0.005 0.041 -10000 0 -10000 0 0
PTK2B 0.017 0.019 -10000 0 -0.33 1 1
RAPGEF1 -0.006 0.084 0.27 4 -0.37 8 12
RANBP10 0.021 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
HGF/MET/SHIP2 0.028 0.065 0.23 8 -0.2 24 32
MAP3K5 -0.004 0.092 0.26 5 -0.38 9 14
HGF/MET/CIN85/CBL/ENDOPHILINS 0.036 0.068 0.22 10 -0.19 25 35
AP1 -0.024 0.062 -10000 0 -0.21 25 25
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
apoptosis -0.066 0.24 -10000 0 -0.71 48 48
STAT3 (dimer) -0.013 0.078 0.19 2 -0.24 25 27
GAB1/CRKL/SHP2/PI3K 0.021 0.089 0.29 1 -0.38 8 9
INPP5D 0.018 0.031 -10000 0 -0.33 3 3
CBL/CRK 0.008 0.088 0.35 2 -0.36 8 10
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 0.02 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.003 -10000 0 -10000 0 0
ELK1 0.007 0.096 0.31 29 -10000 0 29
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.003 0.047 0.14 1 -0.24 6 7
PAK1 0.007 0.057 0.39 2 -10000 0 2
HGF/MET/RANBP10 0.027 0.068 0.23 8 -0.2 25 33
HRAS -0.009 0.12 0.29 1 -0.49 18 19
DOCK1 -0.006 0.088 0.27 5 -0.39 8 13
GAB1 -0.001 0.086 0.23 3 -0.41 7 10
CRK -0.004 0.09 0.37 2 -0.4 8 10
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.012 0.12 -10000 0 -0.42 30 30
JUN 0.019 0.025 -10000 0 -0.33 2 2
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.003 0.053 0.13 9 -0.18 25 34
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
cell morphogenesis -0.013 0.099 0.32 10 -0.34 8 18
GRB2/SHC 0.018 0.054 0.21 1 -0.2 11 12
FOS -0.005 0.09 -10000 0 -0.33 28 28
GLMN 0.002 0.001 -10000 0 -10000 0 0
cell motility 0.006 0.096 0.3 30 -10000 0 30
HGF/MET/MUC20 0.015 0.065 0.21 8 -0.2 27 35
cell migration 0.018 0.053 0.21 1 -0.2 11 12
GRB2 0.02 0.004 -10000 0 -10000 0 0
CBL 0.02 0.005 -10000 0 -10000 0 0
MET/RANBP10 0.023 0.052 0.24 5 -0.23 12 17
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.01 0.067 0.18 1 -0.22 24 25
MET/MUC20 0.009 0.049 0.22 5 -0.22 13 18
RAP1B 0 0.088 0.26 7 -0.35 8 15
RAP1A -0.009 0.08 0.25 5 -0.35 8 13
HGF/MET/RANBP9 0.027 0.068 0.23 8 -0.2 25 33
RAF1 -0.008 0.11 0.27 1 -0.46 18 19
STAT3 -0.013 0.078 0.19 2 -0.24 25 27
cell proliferation 0 0.11 0.29 16 -0.32 20 36
RPS6KB1 0.003 0.032 -10000 0 -0.25 2 2
MAPK3 -0.002 0.083 0.36 10 -10000 0 10
MAPK1 0.014 0.13 0.64 11 -10000 0 11
RANBP9 0.021 0.004 -10000 0 -10000 0 0
MAPK8 -0.001 0.088 0.26 4 -0.34 9 13
SRC -0.022 0.058 0.14 5 -0.22 18 23
PI3K 0.019 0.059 0.21 1 -0.2 17 18
MET/Glomulin 0.009 0.05 0.24 5 -0.2 13 18
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K1 -0.011 0.11 0.26 1 -0.44 18 19
MET 0.012 0.072 0.33 5 -0.33 13 18
MAP4K1 -0.002 0.098 0.28 5 -0.41 9 14
PTK2 0.018 0.007 -10000 0 -10000 0 0
MAP2K2 -0.011 0.11 -10000 0 -0.44 18 18
BAD 0 0.043 0.4 1 -10000 0 1
MAP2K4 -0.007 0.085 0.25 5 -0.35 9 14
SHP2/GRB2/SOS1/GAB1 0.009 0.085 -10000 0 -0.33 13 13
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PXN 0.021 0.004 -10000 0 -10000 0 0
SH3KBP1 0.02 0.004 -10000 0 -10000 0 0
HGS -0.012 0.046 0.14 4 -0.17 23 27
PLCgamma1/PKC 0.015 0.004 -10000 0 -10000 0 0
HGF 0.008 0.075 0.33 3 -0.33 16 19
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
NCK/PLCgamma1 0.018 0.061 0.21 1 -0.18 25 26
PDPK1 0.006 0.031 -10000 0 -10000 0 0
HGF/MET/SHIP 0.025 0.075 0.23 7 -0.22 27 34
S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer 0.021 0.039 -10000 0 -0.24 7 7
PDGFRB 0.014 0.016 -10000 0 -10000 0 0
SPHK1 0 0.054 -10000 0 -0.64 2 2
mol:S1P -0.007 0.052 -10000 0 -0.55 2 2
S1P1/S1P/Gi -0.038 0.14 0.24 1 -0.39 38 39
GNAO1 0.016 0.036 0.32 2 -0.33 2 4
PDGFB-D/PDGFRB/PLCgamma1 -0.033 0.13 0.25 3 -0.36 37 40
PLCG1 -0.045 0.13 0.2 6 -0.38 37 43
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.014 0.016 -10000 0 -10000 0 0
GNAI2 0.017 0.015 -10000 0 -10000 0 0
GNAI3 0.017 0.015 -10000 0 -10000 0 0
GNAI1 0.015 0.023 -10000 0 -0.33 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
EDG1 -0.017 0.026 -10000 0 -0.2 7 7
S1P1/S1P -0.02 0.059 0.21 1 -0.33 4 5
negative regulation of cAMP metabolic process -0.037 0.13 0.21 6 -0.38 38 44
MAPK3 -0.061 0.18 0.27 8 -0.55 38 46
calcium-dependent phospholipase C activity -0.001 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
KDR 0.011 0.048 -10000 0 -0.33 7 7
PLCB2 -0.015 0.068 0.27 4 -0.29 5 9
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.025 0.046 -10000 0 -0.29 4 4
receptor internalization -0.021 0.053 -10000 0 -0.31 4 4
PTGS2 -0.086 0.28 0.35 2 -0.9 38 40
Rac1/GTP -0.024 0.046 -10000 0 -0.29 4 4
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFA 0.017 0.014 -10000 0 -10000 0 0
negative regulation of T cell proliferation -0.037 0.13 0.21 6 -0.38 38 44
GO:0007205 0 0 -10000 0 -10000 0 0
GNAZ -0.014 0.099 -10000 0 -0.33 34 34
MAPK1 -0.058 0.17 0.24 6 -0.54 36 42
S1P1/S1P/PDGFB-D/PDGFRB -0.024 0.067 0.22 2 -0.31 4 6
ABCC1 0.014 0.017 -10000 0 -10000 0 0
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.009 0.025 -10000 0 -0.18 7 7
epithelial cell differentiation 0.041 0.02 -10000 0 -0.17 2 2
CYFIP2 0.015 0.043 -10000 0 -0.33 6 6
ENAH -0.02 0.059 0.4 2 -0.23 1 3
EGFR 0.015 0.043 0.33 1 -0.33 5 6
EPHA2 0.014 0.046 -10000 0 -0.33 7 7
MYO6 -0.018 0.043 0.23 8 -10000 0 8
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 0.038 0.024 -10000 0 -0.2 3 3
AQP5 -0.058 0.16 0.44 3 -0.38 70 73
CTNND1 0.021 0.003 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.019 0.043 0.22 9 -0.17 2 11
regulation of calcium-dependent cell-cell adhesion -0.092 0.076 0.16 3 -0.17 185 188
EGF 0.074 0.13 0.33 72 -0.33 4 76
NCKAP1 0.021 0.002 -10000 0 -10000 0 0
AQP3 -0.023 0.076 0.24 1 -0.32 19 20
cortical microtubule organization 0.041 0.02 -10000 0 -0.17 2 2
GO:0000145 -0.018 0.041 0.21 9 -0.16 2 11
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.045 0.021 -10000 0 -0.17 2 2
MLLT4 0.019 0.006 -10000 0 -10000 0 0
ARF6/GDP -0.033 0.025 -10000 0 -0.17 5 5
ARF6 0.02 0.005 -10000 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 0.039 0.036 -10000 0 -0.18 6 6
mol:Ca2+ 0 0 -10000 0 -10000 0 0
VASP -0.011 0.042 0.42 2 -10000 0 2
PVRL2 0.02 0.005 -10000 0 -10000 0 0
ZYX -0.019 0.044 0.22 9 -10000 0 9
ARF6/GTP 0.042 0.037 -10000 0 -0.18 5 5
CDH1 0.019 0.025 -10000 0 -0.33 2 2
EGFR/EGFR/EGF/EGF 0.042 0.057 0.24 1 -0.18 8 9
RhoA/GDP 0.042 0.021 -10000 0 -0.17 2 2
actin cytoskeleton organization -0.02 0.041 0.22 8 -0.17 2 10
IGF-1R heterotetramer 0.02 0.018 -10000 0 -0.33 1 1
GIT1 0.021 0.004 -10000 0 -10000 0 0
IGF1R 0.02 0.018 -10000 0 -0.33 1 1
IGF1 0.017 0.042 0.33 1 -0.33 5 6
DIAPH1 0.015 0.12 -10000 0 -0.56 10 10
Wnt receptor signaling pathway -0.041 0.02 0.17 2 -10000 0 2
RHOA 0.021 0.004 -10000 0 -10000 0 0
RhoA/GTP -0.035 0.028 -10000 0 -0.19 6 6
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
VCL -0.02 0.041 0.22 8 -0.18 2 10
EFNA1 0.017 0.019 -10000 0 -0.33 1 1
LPP -0.022 0.042 0.21 9 -10000 0 9
Ephrin A1/EPHA2 0.026 0.036 -10000 0 -0.18 8 8
SEC6/SEC8 -0.025 0.019 -10000 0 -0.17 1 1
MGAT3 -0.093 0.077 0.16 3 -0.17 185 188
HGF/MET 0.022 0.056 -10000 0 -0.17 25 25
HGF 0.008 0.075 0.33 3 -0.33 16 19
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.009 0.025 -10000 0 -0.18 7 7
actin cable formation 0.01 0.089 0.31 14 -0.25 3 17
KIAA1543 -0.021 0.03 0.18 7 -0.16 2 9
KIFC3 -0.024 0.024 0.16 4 -10000 0 4
NCK1 0.021 0.003 -10000 0 -10000 0 0
EXOC3 0.016 0.009 -10000 0 -10000 0 0
ACTN1 -0.019 0.043 0.22 9 -10000 0 9
NCK1/GIT1 0.03 0.007 -10000 0 -10000 0 0
mol:GDP 0.041 0.02 -10000 0 -0.17 2 2
EXOC4 0.02 0.005 -10000 0 -10000 0 0
STX4 -0.021 0.032 0.19 7 -10000 0 7
PIP5K1C -0.019 0.043 0.22 9 -0.17 2 11
LIMA1 0.021 0.003 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
ROCK1 -0.007 0.081 0.35 7 -0.26 1 8
adherens junction assembly -0.026 0.095 0.36 6 -0.46 8 14
IGF-1R heterotetramer/IGF1 0.031 0.033 -10000 0 -0.16 8 8
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0.027 0.011 -10000 0 -10000 0 0
MET 0.012 0.072 0.33 5 -0.33 13 18
PLEKHA7 -0.022 0.032 0.19 7 -10000 0 7
mol:GTP 0.038 0.035 -10000 0 -0.18 6 6
establishment of epithelial cell apical/basal polarity 0.022 0.098 0.3 15 -10000 0 15
cortical actin cytoskeleton stabilization 0.009 0.025 -10000 0 -0.18 7 7
regulation of cell-cell adhesion -0.02 0.041 0.22 8 -0.17 2 10
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.009 0.025 -10000 0 -0.18 7 7
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.014 0.091 0.42 2 -0.38 14 16
CRKL -0.018 0.085 0.49 1 -0.39 16 17
HRAS -0.006 0.08 -10000 0 -0.38 10 10
mol:PIP3 0.006 0.11 0.37 2 -0.41 16 18
SPRED1 0.02 0.005 -10000 0 -10000 0 0
SPRED2 0.021 0.001 -10000 0 -10000 0 0
GAB1 -0.013 0.092 0.32 1 -0.41 17 18
FOXO3 -0.001 0.11 0.32 1 -0.4 20 21
AKT1 0.002 0.12 -10000 0 -0.42 20 20
BAD -0.001 0.11 -10000 0 -0.4 20 20
megakaryocyte differentiation -0.025 0.099 -10000 0 -0.4 20 20
GSK3B 0 0.11 -10000 0 -0.4 20 20
RAF1 -0.005 0.076 0.22 3 -0.31 10 13
SHC1 0.018 0.008 -10000 0 -10000 0 0
STAT3 -0.014 0.094 0.32 1 -0.41 18 19
STAT1 -0.041 0.2 0.45 1 -0.94 17 18
HRAS/SPRED1 0.008 0.076 -10000 0 -0.31 10 10
cell proliferation -0.014 0.09 -10000 0 -0.4 17 17
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
TEC 0.021 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.001 0.11 -10000 0 -0.43 18 18
HRAS/SPRED2 0.008 0.077 -10000 0 -0.31 10 10
LYN/TEC/p62DOK 0.019 0.097 0.32 1 -0.4 15 16
MAPK3 0 0.067 0.28 2 -0.24 6 8
STAP1 -0.017 0.094 0.32 1 -0.4 18 19
GRAP2 0.011 0.058 -10000 0 -0.33 11 11
JAK2 -0.037 0.18 0.43 1 -0.79 18 19
STAT1 (dimer) -0.039 0.2 0.45 1 -0.92 17 18
mol:Gleevec 0 0.004 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 0.019 0.094 -10000 0 -0.39 14 14
actin filament polymerization -0.012 0.084 0.32 1 -0.38 15 16
LYN 0.019 0.006 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.032 0.13 0.36 1 -0.55 19 20
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
CBL/CRKL/GRB2 0.008 0.084 0.41 2 -0.37 11 13
PI3K 0.017 0.1 -10000 0 -0.43 15 15
PTEN 0.021 0.003 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.023 0.23 -10000 0 -1.1 17 17
MAPK8 -0.015 0.091 -10000 0 -0.41 17 17
STAT3 (dimer) -0.014 0.092 0.32 1 -0.4 18 19
positive regulation of transcription 0.002 0.059 0.22 4 -0.2 4 8
mol:GDP -0.001 0.081 -10000 0 -0.4 10 10
PIK3C2B -0.014 0.097 0.44 2 -0.42 16 18
CBL/CRKL -0.002 0.089 0.42 2 -0.39 13 15
FER -0.014 0.092 0.32 1 -0.41 17 18
SH2B3 -0.015 0.093 0.32 1 -0.42 17 18
PDPK1 0.005 0.1 0.33 4 -0.38 15 19
SNAI2 -0.013 0.09 0.32 1 -0.41 16 17
positive regulation of cell proliferation -0.032 0.16 0.41 1 -0.69 18 19
KITLG 0.013 0.041 -10000 0 -0.35 4 4
cell motility -0.032 0.16 0.41 1 -0.69 18 19
PTPN6 0.018 0.012 -10000 0 -10000 0 0
EPOR -0.021 0.16 -10000 0 -0.62 21 21
STAT5A (dimer) -0.024 0.14 0.38 1 -0.56 19 20
SOCS1 0.021 0.004 -10000 0 -10000 0 0
cell migration 0.019 0.093 0.41 18 -10000 0 18
SOS1 0.021 0.003 -10000 0 -10000 0 0
EPO 0.019 0.03 0.33 3 -10000 0 3
VAV1 0.017 0.031 -10000 0 -0.33 3 3
GRB10 -0.014 0.09 0.33 1 -0.4 16 17
PTPN11 0.019 0.011 -10000 0 -10000 0 0
SCF/KIT -0.009 0.1 0.35 1 -0.42 18 19
GO:0007205 0.001 0.005 -10000 0 -10000 0 0
MAP2K1 -0.005 0.066 0.2 5 -0.24 9 14
CBL 0.02 0.005 -10000 0 -10000 0 0
KIT -0.032 0.24 0.47 1 -1 21 22
MAP2K2 -0.003 0.064 0.2 4 -0.25 9 13
SHC/Grb2/SOS1 0.015 0.09 -10000 0 -0.4 12 12
STAT5A -0.023 0.14 0.38 1 -0.58 19 20
GRB2 0.02 0.004 -10000 0 -10000 0 0
response to radiation -0.012 0.089 0.32 1 -0.4 16 17
SHC/GRAP2 0.022 0.031 -10000 0 -0.23 5 5
PTPRO -0.025 0.1 -10000 0 -0.42 19 19
SH2B2 -0.013 0.086 0.32 1 -0.39 15 16
DOK1 0.021 0.002 -10000 0 -10000 0 0
MATK -0.02 0.095 -10000 0 -0.42 18 18
CREBBP 0.021 0.034 0.3 1 -10000 0 1
BCL2 -0.041 0.2 0.47 1 -0.72 17 18
ErbB2/ErbB3 signaling events

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
USP8 -0.014 0.008 -10000 0 -10000 0 0
RAS family/GTP 0.002 0.084 -10000 0 -0.23 5 5
NFATC4 -0.04 0.067 0.23 9 -10000 0 9
ERBB2IP 0.02 0.009 -10000 0 -10000 0 0
HSP90 (dimer) 0.02 0.004 -10000 0 -10000 0 0
mammary gland morphogenesis -0.048 0.064 0.19 1 -0.21 5 6
JUN -0.007 0.065 0.3 3 -10000 0 3
HRAS 0.02 0.006 -10000 0 -10000 0 0
DOCK7 -0.05 0.063 -10000 0 -0.2 4 4
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.001 0.069 -10000 0 -0.18 44 44
AKT1 -0.009 0.006 -10000 0 -10000 0 0
BAD -0.014 0.005 -10000 0 -10000 0 0
MAPK10 -0.031 0.068 0.17 11 -0.19 15 26
mol:GTP 0 0.001 -10000 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.05 0.069 0.21 1 -0.22 5 6
RAF1 -0.012 0.095 0.26 11 -0.25 4 15
ErbB2/ErbB3/neuregulin 2 -0.014 0.067 0.19 1 -0.19 43 44
STAT3 0.004 0.13 -10000 0 -0.9 8 8
cell migration -0.023 0.077 0.22 14 -0.2 10 24
mol:PI-3-4-5-P3 -0.001 0.002 -10000 0 -10000 0 0
cell proliferation -0.032 0.18 0.43 2 -0.55 22 24
FOS -0.03 0.16 0.37 4 -0.42 38 42
NRAS 0.02 0.007 -10000 0 -10000 0 0
mol:Ca2+ -0.048 0.064 0.19 1 -0.21 5 6
MAPK3 -0.019 0.15 0.39 3 -0.48 14 17
MAPK1 -0.026 0.16 0.39 3 -0.52 17 20
JAK2 -0.047 0.064 -10000 0 -0.2 5 5
NF2 -0.031 0.14 -10000 0 -0.61 21 21
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.016 0.069 0.2 3 -0.2 41 44
NRG1 -0.034 0.12 -10000 0 -0.33 58 58
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
MAPK8 -0.046 0.084 -10000 0 -0.24 39 39
MAPK9 -0.021 0.059 0.17 13 -10000 0 13
ERBB2 -0.02 0.017 0.27 1 -10000 0 1
ERBB3 0.013 0.028 -10000 0 -0.33 2 2
SHC1 0.018 0.008 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
apoptosis 0.011 0.008 -10000 0 -10000 0 0
STAT3 (dimer) 0.004 0.13 -10000 0 -0.88 8 8
RNF41 -0.019 0.009 -10000 0 -10000 0 0
FRAP1 -0.007 0.004 -10000 0 -10000 0 0
RAC1-CDC42/GTP -0.043 0.042 -10000 0 -0.16 37 37
ErbB2/ErbB2/HSP90 (dimer) -0.021 0.015 0.2 1 -10000 0 1
CHRNA1 -0.007 0.14 0.36 5 -0.5 12 17
myelination -0.03 0.085 0.26 16 -10000 0 16
PPP3CB -0.048 0.059 -10000 0 -0.19 4 4
KRAS 0.019 0.007 -10000 0 -10000 0 0
RAC1-CDC42/GDP 0 0.076 -10000 0 -0.19 31 31
NRG2 -0.021 0.11 -10000 0 -0.33 46 46
mol:GDP -0.016 0.069 0.2 3 -0.2 41 44
SOS1 0.021 0.003 -10000 0 -10000 0 0
MAP2K2 -0.015 0.096 0.26 12 -0.27 5 17
SRC 0.02 0.004 -10000 0 -10000 0 0
mol:cAMP -0.001 0.002 -10000 0 -10000 0 0
PTPN11 -0.05 0.064 -10000 0 -0.2 4 4
MAP2K1 -0.037 0.17 0.44 1 -0.57 16 17
heart morphogenesis -0.048 0.064 0.19 1 -0.21 5 6
RAS family/GDP 0.004 0.085 0.23 1 -0.22 5 6
GRB2 0.02 0.005 -10000 0 -10000 0 0
PRKACA -0.028 0.15 -10000 0 -0.65 21 21
CHRNE 0.002 0.022 0.15 5 -10000 0 5
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
activation of caspase activity 0.009 0.006 -10000 0 -10000 0 0
nervous system development -0.048 0.064 0.19 1 -0.21 5 6
CDC42 0.021 0.004 -10000 0 -10000 0 0
Caspase cascade in apoptosis

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TOP1 -0.013 0.086 -10000 0 -0.35 13 13
ACTA1 -0.021 0.083 -10000 0 -0.29 20 20
NUMA1 -0.009 0.078 -10000 0 -0.38 8 8
SPTAN1 -0.026 0.083 0.18 1 -0.29 23 24
LIMK1 -0.02 0.091 0.21 11 -0.3 21 32
BIRC3 0.022 0.04 0.33 4 -0.33 2 6
BIRC2 0.02 0.005 -10000 0 -10000 0 0
BAX 0.02 0.005 -10000 0 -10000 0 0
CASP10 -0.03 0.048 -10000 0 -0.22 21 21
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.021 0.003 -10000 0 -10000 0 0
PTK2 -0.011 0.077 -10000 0 -0.39 8 8
DIABLO 0.021 0.004 -10000 0 -10000 0 0
apoptotic nuclear changes -0.026 0.082 0.18 1 -0.29 23 24
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.022 0.016 0.33 1 -10000 0 1
GSN -0.026 0.083 -10000 0 -0.29 23 23
MADD 0.021 0.003 -10000 0 -10000 0 0
TFAP2A 0.078 0.16 0.38 1 -0.48 20 21
BID -0.012 0.036 -10000 0 -0.16 21 21
MAP3K1 -0.016 0.091 -10000 0 -0.43 15 15
TRADD 0.021 0.004 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.03 0.008 -10000 0 -10000 0 0
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.024 0.087 0.21 5 -0.29 23 28
CASP9 0.02 0.004 -10000 0 -10000 0 0
DNA repair 0 0.038 0.18 3 -0.16 1 4
neuron apoptosis -0.01 0.12 -10000 0 -0.62 15 15
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.017 0.087 0.23 1 -0.4 9 10
APAF1 0.021 0.004 -10000 0 -10000 0 0
CASP6 -0.006 0.11 -10000 0 -0.83 5 5
TRAF2 0.021 0.004 -10000 0 -10000 0 0
ICAD/CAD -0.027 0.087 0.38 3 -0.29 21 24
CASP7 -0.004 0.067 0.24 2 -0.3 6 8
KRT18 0.011 0.037 -10000 0 -0.49 1 1
apoptosis -0.023 0.085 -10000 0 -0.41 10 10
DFFA -0.025 0.085 0.2 3 -0.29 23 26
DFFB -0.024 0.085 0.2 4 -0.29 22 26
PARP1 0 0.038 0.16 1 -0.18 3 4
actin filament polymerization 0.002 0.11 0.26 20 -0.3 17 37
TNF 0.004 0.077 0.33 1 -0.33 19 20
CYCS 0.002 0.044 0.15 9 -0.19 4 13
SATB1 -0.012 0.1 -10000 0 -0.73 6 6
SLK -0.026 0.083 -10000 0 -0.29 23 23
p15 BID/BAX 0.006 0.047 0.18 1 -0.25 3 4
CASP2 -0.003 0.054 0.19 9 -0.23 4 13
JNK cascade 0.016 0.09 0.43 15 -10000 0 15
CASP3 -0.023 0.088 -10000 0 -0.3 23 23
LMNB2 -0.013 0.13 0.21 2 -0.41 26 28
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CASP4 0.02 0.005 -10000 0 -10000 0 0
Mammalian IAPs/DIABLO 0.051 0.029 0.23 4 -0.18 2 6
negative regulation of DNA binding 0.078 0.16 0.38 1 -0.47 20 21
stress fiber formation -0.027 0.082 -10000 0 -0.29 23 23
GZMB -0.029 0.057 -10000 0 -0.26 21 21
CASP1 0.005 0.022 -10000 0 -0.25 3 3
LMNB1 0 0.11 0.21 3 -0.42 15 18
APP -0.011 0.12 -10000 0 -0.62 15 15
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 -0.009 0.011 -10000 0 -0.22 1 1
VIM -0.018 0.086 -10000 0 -0.41 10 10
LMNA 0.003 0.066 -10000 0 -0.33 5 5
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD -0.003 0.054 -10000 0 -0.26 5 5
LRDD 0 0 -10000 0 -10000 0 0
SREBF1 -0.024 0.084 0.18 3 -0.29 23 26
APAF-1/Caspase 9 0 0.1 -10000 0 -0.64 9 9
nuclear fragmentation during apoptosis -0.009 0.077 -10000 0 -0.37 8 8
CFL2 -0.003 0.11 0.3 17 -0.26 20 37
GAS2 -0.027 0.09 0.26 2 -0.3 24 26
positive regulation of apoptosis -0.003 0.11 0.21 2 -0.41 14 16
PRF1 0.007 0.067 -10000 0 -0.33 15 15
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 0.029 0.019 0.24 1 -0.23 1 2
ATM 0.02 0.004 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
PRKDC 0.019 0.006 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
UBE2L3 0.021 0.004 -10000 0 -10000 0 0
FANCD2 0.011 0.01 0.15 2 -10000 0 2
protein ubiquitination 0.099 0.077 0.21 111 -10000 0 111
XRCC5 0.021 0.002 -10000 0 -10000 0 0
XRCC6 0.021 0.004 -10000 0 -10000 0 0
M/R/N Complex 0.035 0.017 -10000 0 -10000 0 0
MRE11A 0.02 0.005 -10000 0 -10000 0 0
DNA-PK 0.038 0.015 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.001 0.091 -10000 0 -0.54 8 8
FANCF 0.021 0.003 -10000 0 -10000 0 0
BRCA1 0.021 0.003 -10000 0 -10000 0 0
CCNE1 0.12 0.14 0.33 123 -10000 0 123
CDK2/Cyclin E1 0.091 0.097 0.24 118 -10000 0 118
FANCG 0.02 0.005 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1 0.031 0.018 0.24 1 -0.23 1 2
FANCE 0.02 0.004 -10000 0 -10000 0 0
FANCC 0.02 0.004 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
FANCA 0.03 0.054 0.33 12 -10000 0 12
DNA repair 0.004 0.07 0.22 3 -0.36 5 8
BRCA1/BARD1/ubiquitin 0.031 0.018 0.24 1 -0.23 1 2
BARD1/DNA-PK 0.047 0.022 -10000 0 -0.16 1 1
FANCL 0.021 0.002 -10000 0 -10000 0 0
mRNA polyadenylation -0.029 0.019 0.23 1 -0.24 1 2
BRCA1/BARD1/CTIP/M/R/N Complex 0.012 0.039 -10000 0 -0.22 5 5
BRCA1/BACH1/BARD1/TopBP1 0.041 0.018 0.23 1 -0.2 1 2
BRCA1/BARD1/P53 0.048 0.023 0.23 1 -0.18 1 2
BARD1/CSTF1/BRCA1 0.039 0.02 0.23 1 -0.2 1 2
BRCA1/BACH1 0.021 0.003 -10000 0 -10000 0 0
BARD1 0.021 0.024 0.33 1 -0.33 1 2
PCNA 0.021 0.016 0.33 1 -10000 0 1
BRCA1/BARD1/UbcH5C 0.041 0.018 0.23 1 -0.2 1 2
BRCA1/BARD1/UbcH7 0.04 0.016 -10000 0 -0.2 1 1
BRCA1/BARD1/RAD51/PCNA 0.081 0.076 0.24 71 -0.15 1 72
BARD1/DNA-PK/P53 0.05 0.029 -10000 0 -0.16 1 1
BRCA1/BARD1/Ubiquitin 0.031 0.018 0.24 1 -0.23 1 2
BRCA1/BARD1/CTIP 0.027 0.018 0.22 1 -0.18 1 2
FA complex 0.009 0.044 -10000 0 -0.28 4 4
BARD1/EWS 0.03 0.018 0.24 1 -0.23 1 2
RBBP8 -0.016 0.006 -10000 0 -10000 0 0
TP53 0.019 0.006 -10000 0 -10000 0 0
TOPBP1 0.021 0.003 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle -0.046 0.023 0.18 1 -0.22 1 2
BRCA1/BARD1 0.11 0.083 0.23 111 -10000 0 111
CSTF1 0.02 0.006 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0.016 0.016 0.22 1 -0.22 1 2
CDK2 0.021 0.004 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.079 0.12 0.33 75 -10000 0 75
RAD50 0.02 0.005 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme 0.031 0.018 0.24 1 -0.23 1 2
EWSR1 0.021 0.004 -10000 0 -10000 0 0
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0.026 0.014 -10000 0 -0.19 1 1
response to insulin stimulus 0 0 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 0.027 0.057 0.33 11 -0.33 2 13
mol:GTP 0 0 -10000 0 -10000 0 0
MAP2K4 0.019 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.016 0.032 0.16 7 -0.17 1 8
response to UV 0 0 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
interleukin-1 receptor activity 0 0 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
MAP3K3 0.019 0.018 -10000 0 -0.33 1 1
FYN 0.018 0.019 -10000 0 -0.33 1 1
MAP3K12 0.021 0.003 -10000 0 -10000 0 0
FGR -0.006 0.093 -10000 0 -0.33 30 30
p38 alpha/TAB1 -0.038 0.084 -10000 0 -0.27 32 32
PRKG1 -0.012 0.1 -10000 0 -0.33 37 37
DUSP8 0.014 0.049 -10000 0 -0.33 8 8
PGK/cGMP/p38 alpha -0.018 0.12 -10000 0 -0.3 36 36
apoptosis -0.037 0.081 -10000 0 -0.26 32 32
RAL/GTP 0.026 0.009 -10000 0 -10000 0 0
LYN 0.019 0.006 -10000 0 -10000 0 0
DUSP1 -0.008 0.094 -10000 0 -0.33 31 31
PAK1 0.02 0.005 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.042 0.025 -10000 0 -0.16 1 1
TRAF6 0.021 0.003 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
mol:cGMP 0 0 -10000 0 -10000 0 0
CCM2 0.019 0.006 -10000 0 -10000 0 0
RAC1-CDC42/GTP 0.024 0.011 -10000 0 -10000 0 0
MAPK11 -0.005 0.12 0.27 9 -0.29 27 36
BLK 0.053 0.1 0.33 45 -0.33 1 46
HCK 0.008 0.065 -10000 0 -0.33 14 14
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
DUSP16 0.02 0.005 -10000 0 -10000 0 0
DUSP10 0.018 0.019 -10000 0 -0.33 1 1
TRAF6/MEKK3 0.025 0.012 -10000 0 -0.17 1 1
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 -0.005 0.12 0.23 12 -0.33 24 36
positive regulation of innate immune response -0.007 0.14 0.29 10 -0.36 27 37
LCK 0.021 0.024 0.33 1 -0.33 1 2
p38alpha-beta/MKP7 0.001 0.14 0.31 8 -0.36 23 31
p38alpha-beta/MKP5 0 0.13 0.31 6 -0.34 25 31
PGK/cGMP -0.007 0.07 -10000 0 -0.22 37 37
PAK2 0.02 0.005 -10000 0 -10000 0 0
p38alpha-beta/MKP1 -0.006 0.14 0.33 6 -0.34 32 38
CDC42 0.021 0.004 -10000 0 -10000 0 0
RALB 0.021 0.003 -10000 0 -10000 0 0
RALA 0.019 0.006 -10000 0 -10000 0 0
PAK3 0.058 0.11 0.33 51 -0.33 4 55
Signaling events mediated by HDAC Class III

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.021 0.004 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.005 0.049 -10000 0 -0.17 26 26
CDKN1A -0.011 0.005 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
BAX 0.02 0.005 -10000 0 -10000 0 0
FOXO3 -0.002 0.002 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
FOXO4 0.006 0.001 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.021 0.004 -10000 0 -10000 0 0
TAT 0.042 0.079 0.33 27 -10000 0 27
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.017 0.016 0.16 3 -10000 0 3
PPARGC1A -0.061 0.15 0.33 1 -0.33 92 93
FHL2 0.065 0.11 0.33 56 -10000 0 56
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.03 0.013 0.25 1 -10000 0 1
HIST2H4A -0.005 0.049 0.17 26 -10000 0 26
SIRT1/FOXO3a 0.014 0.025 0.24 1 -0.2 1 2
SIRT1 0.021 0.017 0.35 1 -10000 0 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.035 0.02 0.24 1 -10000 0 1
SIRT1/Histone H1b 0.026 0.04 0.32 1 -0.22 3 4
apoptosis -0.039 0.015 -10000 0 -0.23 1 1
SIRT1/PGC1A -0.023 0.094 0.22 2 -0.19 90 92
p53/SIRT1 0.028 0.028 0.55 1 -10000 0 1
SIRT1/FOXO4 0.017 0.032 0.24 1 -0.22 3 4
FOXO1/FHL2/SIRT1 0.061 0.063 0.22 54 -10000 0 54
HIST1H1E 0.015 0.033 0.23 1 -10000 0 1
SIRT1/p300 0.03 0.013 0.25 1 -10000 0 1
muscle cell differentiation -0.025 0.02 -10000 0 -0.21 4 4
TP53 0.019 0.018 0.35 1 -10000 0 1
KU70/SIRT1/BAX 0.04 0.016 0.24 1 -10000 0 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
MEF2D 0.018 0.008 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.043 0.052 0.24 26 -10000 0 26
ACSS2 -0.017 0.019 0.27 1 -0.23 1 2
SIRT1/PCAF/MYOD 0.025 0.02 0.21 4 -10000 0 4
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.02 0.004 -10000 0 -10000 0 0
Syndecan-3/Src/Cortactin 0.028 0.074 -10000 0 -0.3 2 2
Syndecan-3/Neurocan 0.024 0.047 0.31 2 -0.28 3 5
POMC 0.013 0.076 0.33 6 -0.33 14 20
EGFR 0.015 0.043 0.33 1 -0.33 5 6
Syndecan-3/EGFR 0.016 0.039 0.3 1 -0.3 3 4
AGRP -0.11 0.17 -10000 0 -0.33 150 150
NCSTN 0.019 0.007 -10000 0 -10000 0 0
PSENEN 0.02 0.005 -10000 0 -10000 0 0
RP11-540L11.1 0 0 -10000 0 -10000 0 0
APH1B 0.02 0.018 -10000 0 -0.33 1 1
APH1A 0.017 0.008 -10000 0 -10000 0 0
NCAN 0.028 0.052 0.33 11 -10000 0 11
long-term memory 0.037 0.039 -10000 0 -0.29 2 2
Syndecan-3/IL8 0.027 0.056 0.26 6 -0.3 3 9
PSEN1 0.02 0.004 -10000 0 -10000 0 0
Src/Cortactin 0.029 0.009 -10000 0 -10000 0 0
FYN 0.018 0.019 -10000 0 -0.33 1 1
limb bud formation 0.004 0.021 -10000 0 -0.4 1 1
MC4R 0.039 0.08 0.33 27 -10000 0 27
SRC 0.02 0.004 -10000 0 -10000 0 0
PTN -0.022 0.12 0.33 4 -0.33 51 55
FGFR/FGF/Syndecan-3 0.004 0.021 -10000 0 -0.4 1 1
neuron projection morphogenesis -0.015 0.063 0.3 1 -0.37 1 2
Syndecan-3/AgRP -0.036 0.083 -10000 0 -0.31 4 4
Syndecan-3/AgRP/MC4R -0.02 0.1 0.27 2 -0.3 4 6
Fyn/Cortactin 0.027 0.011 -10000 0 -10000 0 0
SDC3 0.004 0.021 -10000 0 -0.41 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
positive regulation of leukocyte migration 0.027 0.055 0.26 6 -0.29 3 9
IL8 0.033 0.07 0.33 18 -0.33 2 20
Syndecan-3/Fyn/Cortactin 0.038 0.04 -10000 0 -0.3 2 2
Syndecan-3/CASK 0.002 0.027 -10000 0 -0.29 3 3
alpha-MSH/MC4R 0.034 0.072 0.24 28 -0.21 14 42
Gamma Secretase 0.046 0.03 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin 0.039 0.055 0.24 21 -0.23 4 25
AKT1 -0.023 0.1 0.37 5 -0.43 8 13
PTK2B -0.03 0.088 0.33 1 -0.44 8 9
VEGFR2 homodimer/Frs2 -0.008 0.085 -10000 0 -0.46 7 7
CAV1 -0.18 0.17 -10000 0 -0.33 228 228
CALM1 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 0.004 0.082 -10000 0 -0.42 7 7
endothelial cell proliferation -0.021 0.12 0.42 7 -0.38 13 20
mol:Ca2+ -0.037 0.074 -10000 0 -0.44 6 6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac 0.01 0.086 -10000 0 -0.45 7 7
RP11-342D11.1 -0.033 0.075 -10000 0 -0.44 7 7
CDH5 -0.016 0.11 -10000 0 -0.33 41 41
VEGFA homodimer 0.041 0.024 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
SHC2 0.013 0.046 -10000 0 -0.33 7 7
HRAS/GDP 0.007 0.072 -10000 0 -0.41 6 6
SH2D2A 0.019 0.017 0.33 1 -10000 0 1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.019 0.13 -10000 0 -0.43 25 25
VEGFR2 homodimer/VEGFA homodimer/TsAd 0.003 0.086 -10000 0 -0.48 7 7
VEGFR1 homodimer 0.02 0.005 -10000 0 -10000 0 0
SHC/GRB2/SOS1 0.02 0.081 -10000 0 -0.44 6 6
GRB10 -0.035 0.075 -10000 0 -0.44 7 7
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
PAK1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin 0.006 0.12 -10000 0 -0.41 18 18
HRAS 0.021 0.004 -10000 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex -0.009 0.068 -10000 0 -0.31 10 10
HIF1A 0.02 0.004 -10000 0 -10000 0 0
FRS2 0.02 0.005 -10000 0 -10000 0 0
oxygen and reactive oxygen species metabolic process 0.009 0.085 -10000 0 -0.45 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
FLT4 0.011 0.055 -10000 0 -0.33 10 10
Nck/Pak 0.029 0.008 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn 0.001 0.086 -10000 0 -0.45 7 7
mol:GDP 0.013 0.076 -10000 0 -0.4 7 7
mol:NADP -0.024 0.13 0.38 5 -0.4 27 32
eNOS/Hsp90 -0.016 0.13 0.4 4 -0.38 25 29
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
mol:IP3 -0.037 0.075 -10000 0 -0.45 6 6
HIF1A/ARNT 0.025 0.013 -10000 0 -10000 0 0
SHB 0.02 0.005 -10000 0 -10000 0 0
VEGFA 0.021 0.004 -10000 0 -10000 0 0
VEGFC 0.02 0.03 0.33 1 -0.33 2 3
FAK1/Vinculin -0.009 0.12 0.31 6 -0.48 11 17
mol:Ca ++ 0 0 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin 0.021 0.1 -10000 0 -0.46 8 8
PTPN6 0.02 0.005 -10000 0 -10000 0 0
EPAS1 -0.02 0.12 -10000 0 -0.34 46 46
mol:L-citrulline -0.024 0.13 0.38 5 -0.4 27 32
ITGAV 0.021 0.002 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 0.015 0.08 -10000 0 -0.38 7 7
VEGFR2 homodimer/VEGFA homodimer 0.004 0.088 -10000 0 -0.47 7 7
VEGFR2/3 heterodimer -0.014 0.098 -10000 0 -0.48 10 10
VEGFB 0.021 0.003 -10000 0 -10000 0 0
MAPK11 -0.025 0.09 0.34 4 -0.45 7 11
VEGFR2 homodimer -0.044 0.095 -10000 0 -0.58 7 7
FLT1 0.02 0.005 -10000 0 -10000 0 0
NEDD4 0.02 0.018 -10000 0 -0.33 1 1
MAPK3 -0.026 0.091 0.35 6 -0.41 7 13
MAPK1 -0.025 0.087 0.31 6 -0.39 7 13
VEGFA145/NRP2 0.029 0.019 -10000 0 -0.22 2 2
VEGFR1/2 heterodimer -0.01 0.09 -10000 0 -0.51 7 7
KDR -0.044 0.095 -10000 0 -0.58 7 7
VEGFA165/NRP1/VEGFR2 homodimer 0.005 0.083 -10000 0 -0.46 7 7
SRC 0.02 0.004 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.023 0.1 0.38 8 -0.39 8 16
PI3K -0.038 0.078 -10000 0 -0.45 7 7
VEGFR2 homodimer/VEGFA homodimer/NCK1 0.004 0.087 -10000 0 -0.48 7 7
FES -0.038 0.077 -10000 0 -0.45 7 7
GAB1 -0.024 0.095 -10000 0 -0.5 7 7
VEGFR2 homodimer/VEGFA homodimer/Src 0.003 0.086 -10000 0 -0.45 7 7
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
ARNT 0.017 0.008 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.093 0.13 -10000 0 -0.45 29 29
VEGFR2 homodimer/VEGFA homodimer/Yes 0.003 0.086 -10000 0 -0.48 7 7
PI3K/GAB1 -0.013 0.097 -10000 0 -0.46 7 7
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak 0.025 0.084 -10000 0 -0.4 7 7
PRKACA 0.02 0.005 -10000 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.003 0.096 -10000 0 -0.45 10 10
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
CDC42 -0.037 0.078 -10000 0 -0.45 7 7
actin cytoskeleton reorganization 0.003 0.085 -10000 0 -0.47 7 7
PTK2 -0.022 0.11 0.38 2 -0.5 12 14
EDG1 -0.033 0.075 -10000 0 -0.44 7 7
mol:DAG -0.037 0.075 -10000 0 -0.45 6 6
CaM/Ca2+ -0.032 0.074 -10000 0 -0.42 6 6
MAP2K3 -0.031 0.075 0.34 1 -0.41 5 6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.015 0.098 -10000 0 -0.45 7 7
PLCG1 -0.037 0.076 -10000 0 -0.45 6 6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb 0.012 0.085 -10000 0 -0.43 7 7
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 0.002 0.088 -10000 0 -0.47 7 7
VEGFR2 homodimer/VEGFA homodimer/SHP1 0.003 0.085 -10000 0 -0.45 7 7
cell migration -0.02 0.12 0.3 4 -0.48 11 15
mol:PI-3-4-5-P3 -0.036 0.073 -10000 0 -0.42 7 7
FYN 0.018 0.019 -10000 0 -0.33 1 1
VEGFB/NRP1 -0.036 0.072 -10000 0 -0.42 7 7
mol:NO -0.024 0.13 0.38 5 -0.4 27 32
PXN 0.021 0.004 -10000 0 -10000 0 0
HRAS/GTP -0.041 0.058 -10000 0 -0.4 6 6
VEGFR2 homodimer/VEGFA homodimer/GRB10 -0.04 0.07 -10000 0 -0.45 7 7
VHL 0.021 0.004 -10000 0 -10000 0 0
ITGB3 0.034 0.079 0.33 21 -0.33 4 25
NOS3 -0.029 0.14 0.42 4 -0.45 27 31
VEGFR2 homodimer/VEGFA homodimer/Sck -0.001 0.094 -10000 0 -0.44 10 10
RAC1 0.019 0.007 -10000 0 -10000 0 0
PRKCA -0.034 0.075 -10000 0 -0.43 6 6
PRKCB -0.037 0.082 0.33 1 -0.41 8 9
VCL 0.021 0.003 -10000 0 -10000 0 0
VEGFA165/NRP1 -0.033 0.076 -10000 0 -0.44 7 7
VEGFR1/2 heterodimer/VEGFA homodimer 0.002 0.087 -10000 0 -0.47 7 7
VEGFA165/NRP2 0.029 0.019 -10000 0 -0.22 2 2
MAPKKK cascade -0.025 0.085 0.31 1 -0.41 6 7
NRP2 0.019 0.025 -10000 0 -0.33 2 2
VEGFC homodimer 0.019 0.03 0.33 1 -0.33 2 3
NCK1 0.021 0.003 -10000 0 -10000 0 0
ROCK1 0.02 0.004 -10000 0 -10000 0 0
FAK1/Paxillin -0.01 0.12 0.28 5 -0.49 11 16
MAP3K13 -0.034 0.073 -10000 0 -0.4 7 7
PDPK1 -0.037 0.07 0.24 2 -0.38 7 9
Signaling events mediated by PRL

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
CCNE1 0.12 0.14 0.33 123 -10000 0 123
mol:Halofuginone 0.001 0 -10000 0 -10000 0 0
ITGA1 0.019 0.018 -10000 0 -0.33 1 1
CDKN1A 0.002 0.029 -10000 0 -0.32 2 2
PRL-3/alpha Tubulin 0.027 0.012 -10000 0 -10000 0 0
mol:Ca2+ 0.001 0.067 0.17 44 -0.23 4 48
AGT 0.058 0.11 0.33 53 -0.33 4 57
CCNA2 -0.006 0.059 0.31 6 -10000 0 6
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
EGR1 -0.02 0.053 -10000 0 -0.22 25 25
CDK2/Cyclin E1 0.089 0.1 0.34 9 -0.3 3 12
MAPK3 -0.014 0.016 0.28 1 -10000 0 1
PRL-2 /Rab GGTase beta 0.03 0.007 -10000 0 -10000 0 0
MAPK1 -0.015 0.007 -10000 0 -10000 0 0
PTP4A1 -0.023 0.037 -10000 0 -10000 0 0
PTP4A3 0.018 0.007 -10000 0 -10000 0 0
PTP4A2 0.021 0.003 -10000 0 -10000 0 0
ITGB1 -0.014 0.016 0.28 1 -10000 0 1
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0 0.04 -10000 0 -0.41 3 3
Rab GGTase beta/Rab GGTase alpha 0.029 0.009 -10000 0 -10000 0 0
PRL-1/ATF-5 -0.02 0.05 -10000 0 -10000 0 0
RABGGTA 0.02 0.005 -10000 0 -10000 0 0
BCAR1 -0.019 0.016 -10000 0 -0.21 2 2
RHOC -0.001 0.049 -10000 0 -0.37 6 6
RHOA -0.001 0.047 -10000 0 -0.34 6 6
cell motility 0.003 0.063 0.26 2 -0.31 6 8
PRL-1/alpha Tubulin -0.021 0.049 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin 0.025 0.018 -10000 0 -0.23 1 1
ROCK1 0.001 0.05 0.27 1 -0.34 3 4
RABGGTB 0.021 0.004 -10000 0 -10000 0 0
CDK2 0.021 0.004 -10000 0 -10000 0 0
mitosis -0.023 0.036 -10000 0 -10000 0 0
ATF5 0.021 0.016 0.33 1 -10000 0 1
IL27-mediated signaling events

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
TGFB1 0.023 0.016 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.017 0.11 0.43 9 -10000 0 9
IL27/IL27R/JAK1 0.036 0.092 -10000 0 -0.87 1 1
TBX21 -0.02 0.11 0.89 1 -0.44 8 9
IL12B 0.023 0.033 0.32 3 -0.33 1 4
IL12A -0.009 0.027 0.16 1 -0.22 5 6
IL6ST 0.011 0.057 -10000 0 -0.33 10 10
IL27RA/JAK1 0.01 0.063 0.38 1 -1.1 1 2
IL27 0.009 0.058 -10000 0 -0.34 10 10
TYK2 0.022 0.016 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.016 0.13 0.48 1 -10000 0 1
T-helper 2 cell differentiation 0.017 0.11 0.43 9 -10000 0 9
T cell proliferation during immune response 0.017 0.11 0.43 9 -10000 0 9
MAPKKK cascade -0.017 0.11 -10000 0 -0.43 9 9
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT2 0.021 0.004 -10000 0 -10000 0 0
STAT1 0.02 0.01 -10000 0 -10000 0 0
IL12RB1 0.013 0.053 -10000 0 -0.33 9 9
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.008 0.12 0.39 9 -0.49 4 13
IL27/IL27R/JAK2/TYK2 -0.016 0.11 -10000 0 -0.45 8 8
positive regulation of T cell mediated cytotoxicity -0.017 0.11 -10000 0 -0.43 9 9
STAT1 (dimer) 0.032 0.13 -10000 0 -0.61 4 4
JAK2 0.02 0.022 -10000 0 -0.33 1 1
JAK1 0.02 0.01 -10000 0 -10000 0 0
STAT2 (dimer) -0.008 0.12 0.45 1 -0.41 10 11
T cell proliferation -0.038 0.12 0.34 3 -0.44 15 18
IL12/IL12R/TYK2/JAK2 -0.032 0.24 -10000 0 -0.81 32 32
IL17A -0.02 0.12 0.48 1 -10000 0 1
mast cell activation 0.017 0.11 0.43 9 -10000 0 9
IFNG 0.004 0.042 0.11 31 -0.1 12 43
T cell differentiation -0.001 0.005 0.013 8 -0.02 9 17
STAT3 (dimer) -0.009 0.12 0.45 1 -0.42 10 11
STAT5A (dimer) -0.009 0.12 0.45 1 -0.43 10 11
STAT4 (dimer) -0.01 0.12 0.45 1 -0.42 11 12
STAT4 0.021 0.002 -10000 0 -10000 0 0
T cell activation -0.003 0.007 0.11 1 -10000 0 1
IL27R/JAK2/TYK2 0.033 0.075 -10000 0 -0.86 1 1
GATA3 -0.007 0.088 0.62 4 -1.1 1 5
IL18 -0.012 0.031 -10000 0 -0.22 8 8
positive regulation of mast cell cytokine production -0.009 0.12 0.44 1 -0.41 10 11
IL27/EBI3 0.025 0.046 -10000 0 -0.23 10 10
IL27RA 0.001 0.062 -10000 0 -1.1 1 1
IL6 -0.044 0.14 -10000 0 -0.33 73 73
STAT5A 0.02 0.018 -10000 0 -0.33 1 1
monocyte differentiation 0 0.002 -10000 0 -10000 0 0
IL2 -0.01 0.031 0.42 1 -10000 0 1
IL1B -0.02 0.052 0.16 1 -0.22 23 24
EBI3 0.021 0.015 -10000 0 -10000 0 0
TNF -0.017 0.048 0.16 1 -0.22 19 20
IL2 signaling events mediated by STAT5

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
GAB2 0.017 0.035 -10000 0 -0.33 4 4
ELF1 0.033 0.042 -10000 0 -10000 0 0
CCNA2 0.1 0.14 0.33 100 -10000 0 100
PIK3CA 0.021 0.004 -10000 0 -10000 0 0
JAK3 0.02 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
JAK1 0.021 0.004 -10000 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.015 0.074 -10000 0 -0.44 3 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
SP1 0.015 0.049 -10000 0 -0.3 9 9
IL2RA 0.011 0.085 0.3 30 -10000 0 30
IL2RB 0.019 0.025 -10000 0 -0.33 2 2
SOS1 0.021 0.003 -10000 0 -10000 0 0
IL2RG 0.018 0.035 -10000 0 -0.33 4 4
G1/S transition of mitotic cell cycle 0.028 0.11 0.32 12 -0.44 10 22
PTPN11 0.021 0.004 -10000 0 -10000 0 0
CCND2 -0.028 0.087 -10000 0 -0.59 9 9
LCK 0.021 0.024 0.33 1 -0.33 1 2
GRB2 0.02 0.004 -10000 0 -10000 0 0
IL2 0.02 0.003 -10000 0 -10000 0 0
CDK6 0.019 0.018 -10000 0 -0.33 1 1
CCND3 0.018 0.081 0.36 3 -0.39 3 6
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.016 0.018 -10000 0 -10000 0 0
HSPA8 0.019 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.023 0.064 0.24 7 -0.22 8 15
AKT1 0.014 0.026 -10000 0 -10000 0 0
GSC 0.044 0.12 0.8 2 -0.49 1 3
NKX2-5 0.04 0.081 0.33 28 -10000 0 28
muscle cell differentiation -0.011 0.073 0.28 3 -10000 0 3
SMAD2-3/SMAD4/SP1 0.047 0.062 -10000 0 -10000 0 0
SMAD4 0.016 0.031 -10000 0 -10000 0 0
CBFB 0.021 0.004 -10000 0 -10000 0 0
SAP18 0.02 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 0.025 0.062 0.22 6 -0.2 19 25
SMAD3/SMAD4/VDR 0.039 0.052 -10000 0 -0.23 1 1
MYC 0.017 0.028 -10000 0 -0.33 2 2
CDKN2B -0.17 0.38 -10000 0 -1 47 47
AP1 0.004 0.06 -10000 0 -0.23 8 8
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 -0.02 0.093 -10000 0 -0.3 25 25
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.02 0.095 0.18 1 -0.29 36 37
SP3 0.021 0.003 -10000 0 -10000 0 0
CREB1 0.021 0.003 -10000 0 -10000 0 0
FOXH1 0.045 0.083 0.34 29 -10000 0 29
SMAD3/SMAD4/GR 0.029 0.042 -10000 0 -10000 0 0
GATA3 0.02 0.027 0.33 1 -0.33 1 2
SKI/SIN3/HDAC complex/NCoR1 -0.017 0.072 -10000 0 -0.33 11 11
MEF2C/TIF2 0.01 0.068 0.24 7 -0.24 1 8
endothelial cell migration -0.013 0.079 0.71 3 -10000 0 3
MAX 0.019 0.01 -10000 0 -10000 0 0
RBBP7 0.02 0.004 -10000 0 -10000 0 0
RBBP4 0.021 0.003 -10000 0 -10000 0 0
RUNX2 0.026 0.041 0.33 7 -10000 0 7
RUNX3 0.019 0.025 -10000 0 -0.33 2 2
RUNX1 0.021 0.004 -10000 0 -10000 0 0
CTBP1 0.021 0.004 -10000 0 -10000 0 0
NR3C1 0.019 0.01 -10000 0 -10000 0 0
VDR 0.021 0.024 0.33 1 -0.33 1 2
CDKN1A -0.001 0.055 -10000 0 -0.85 1 1
KAT2B 0.016 0.014 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 0.057 0.075 0.25 25 -10000 0 25
DCP1A 0.021 0.004 -10000 0 -10000 0 0
SKI 0.021 0.004 -10000 0 -10000 0 0
SERPINE1 0.013 0.08 -10000 0 -0.72 3 3
SMAD3/SMAD4/ATF2 0.03 0.041 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.019 0.06 -10000 0 -0.21 15 15
SAP30 0.021 0.004 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.033 0.03 -10000 0 -10000 0 0
JUN -0.02 0.054 0.22 1 -0.24 6 7
SMAD3/SMAD4/IRF7 0.032 0.046 0.32 2 -10000 0 2
TFE3 0.022 0.008 -10000 0 -10000 0 0
COL1A2 0.02 0.08 0.31 15 -0.58 3 18
mesenchymal cell differentiation -0.032 0.047 -10000 0 -0.24 5 5
DLX1 0.037 0.07 0.33 21 -10000 0 21
TCF3 0.02 0.006 -10000 0 -10000 0 0
FOS -0.008 0.091 -10000 0 -0.34 27 27
SMAD3/SMAD4/Max 0.029 0.042 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.034 0.024 -10000 0 -10000 0 0
ZBTB17 0.021 0.009 -10000 0 -10000 0 0
LAMC1 -0.013 0.032 0.18 4 -10000 0 4
TGIF2/HDAC complex/SMAD3/SMAD4 0.03 0.04 -10000 0 -10000 0 0
IRF7 0.023 0.025 0.36 2 -10000 0 2
ESR1 0.016 0.072 0.33 10 -0.33 8 18
HNF4A 0.068 0.14 0.33 72 -0.33 10 82
MEF2C 0.023 0.083 0.26 17 -10000 0 17
SMAD2-3/SMAD4 0.034 0.051 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.033 0.027 -10000 0 -10000 0 0
IGHV3OR16-13 0.003 0.018 -10000 0 -0.32 1 1
TGIF2/HDAC complex 0.02 0.005 -10000 0 -10000 0 0
CREBBP 0.016 0.016 -10000 0 -10000 0 0
SKIL 0.02 0.005 -10000 0 -10000 0 0
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.019 0.006 -10000 0 -10000 0 0
SNIP1 0.02 0.007 -10000 0 -10000 0 0
GCN5L2 -0.001 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0.033 0.042 -10000 0 -10000 0 0
MSG1/HSC70 0.02 0.064 0.24 7 -0.23 19 26
SMAD2 0.019 0.026 -10000 0 -10000 0 0
SMAD3 0.007 0.033 -10000 0 -10000 0 0
SMAD3/E2F4-5/DP1/p107/SMAD4 0.001 0.044 -10000 0 -0.22 2 2
SMAD2/SMAD2/SMAD4 -0.013 0.073 0.19 2 -0.26 18 20
NCOR1 0.02 0.006 -10000 0 -10000 0 0
NCOA2 0.017 0.026 -10000 0 -0.33 2 2
NCOA1 0.021 0.002 -10000 0 -10000 0 0
MYOD/E2A 0.027 0.014 0.24 1 -10000 0 1
SMAD2-3/SMAD4/SP1/MIZ-1 0.053 0.065 -10000 0 -10000 0 0
IFNB1 -0.013 0.036 0.29 3 -10000 0 3
SMAD3/SMAD4/MEF2C 0.05 0.071 0.27 2 -10000 0 2
CITED1 0.009 0.087 0.33 7 -0.33 19 26
SMAD2-3/SMAD4/ARC105 0.043 0.051 -10000 0 -10000 0 0
RBL1 0.02 0.004 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.038 0.14 -10000 0 -0.51 28 28
RUNX1-3/PEBPB2 0.039 0.02 -10000 0 -0.19 2 2
SMAD7 -0.002 0.079 -10000 0 -0.46 4 4
MYC/MIZ-1 0.027 0.025 0.2 1 -0.23 1 2
SMAD3/SMAD4 -0.01 0.067 -10000 0 -0.31 3 3
IL10 -0.016 0.047 0.3 2 -0.32 4 6
PIASy/HDAC complex 0.018 0.013 -10000 0 -10000 0 0
PIAS3 0.016 0.014 -10000 0 -10000 0 0
CDK2 0.016 0.015 -10000 0 -10000 0 0
IL5 -0.017 0.035 -10000 0 -10000 0 0
CDK4 0.015 0.016 -10000 0 -10000 0 0
PIAS4 0.018 0.013 -10000 0 -10000 0 0
ATF3 0.006 0.067 -10000 0 -0.33 15 15
SMAD3/SMAD4/SP1 0.035 0.051 -10000 0 -10000 0 0
FOXG1 0.044 0.087 0.33 33 -10000 0 33
FOXO3 -0.019 0.022 -10000 0 -0.14 2 2
FOXO1 -0.02 0.022 -10000 0 -0.14 2 2
FOXO4 -0.021 0.021 -10000 0 -0.14 1 1
heart looping 0.023 0.082 0.26 17 -10000 0 17
CEBPB 0.015 0.021 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 0.04 0.055 0.24 12 -10000 0 12
MYOD1 0.02 0.027 0.33 3 -10000 0 3
SMAD3/SMAD4/HNF4 0.055 0.093 0.24 55 -0.21 10 65
SMAD3/SMAD4/GATA3 0.029 0.048 -10000 0 -0.21 2 2
SnoN/SIN3/HDAC complex/NCoR1 0.02 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.043 0.049 -10000 0 -0.21 1 1
SMAD3/SMAD4/SP1-3 0.044 0.053 -10000 0 -10000 0 0
MED15 0.021 0.004 -10000 0 -10000 0 0
SP1 0.019 0.022 -10000 0 -0.14 1 1
SIN3B 0.02 0.005 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 0.074 0.09 0.36 13 -10000 0 13
ITGB5 -0.015 0.042 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP -0.012 0.061 -10000 0 -0.32 7 7
SMAD3/SMAD4/AR 0.002 0.088 -10000 0 -0.21 46 46
AR -0.022 0.12 0.33 1 -0.33 49 50
negative regulation of cell growth -0.006 0.065 -10000 0 -0.26 11 11
SMAD3/SMAD4/MYOD 0.029 0.043 0.26 1 -10000 0 1
E2F5 0.019 0.007 -10000 0 -10000 0 0
E2F4 0.021 0.004 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF 0.072 0.073 0.29 7 -10000 0 7
SMAD2-3/SMAD4/FOXO1-3a-4 -0.018 0.093 -10000 0 -0.37 23 23
TFDP1 0.02 0.006 -10000 0 -10000 0 0
SMAD3/SMAD4/AP1 0.021 0.067 -10000 0 -0.24 7 7
SMAD3/SMAD4/RUNX2 0.033 0.047 0.24 5 -10000 0 5
TGIF2 0.02 0.005 -10000 0 -10000 0 0
TGIF1 0.02 0.006 -10000 0 -10000 0 0
ATF2 0.021 0.003 -10000 0 -10000 0 0
Ephrin A reverse signaling

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
MAPKKK cascade 0.029 0.034 0.21 9 -0.17 3 12
EFNA5 0.019 0.038 0.33 2 -0.33 3 5
FYN -0.014 0.026 0.18 4 -0.18 2 6
neuron projection morphogenesis 0.029 0.034 0.21 9 -0.17 3 12
cell-cell signaling 0 0 -10000 0 -10000 0 0
Ephrin A5/EPHA5 0.029 0.034 0.21 9 -0.17 3 12
EPHA5 0.026 0.044 0.33 8 -10000 0 8
Class I PI3K signaling events

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
ARF5/GTP -0.011 0.063 0.28 2 -10000 0 2
DAPP1 -0.021 0.11 0.22 3 -0.31 31 34
Src family/SYK family/BLNK-LAT/BTK-ITK -0.038 0.16 0.23 1 -0.45 38 39
mol:DAG -0.017 0.072 0.2 7 -0.21 15 22
HRAS 0.021 0.007 -10000 0 -10000 0 0
RAP1A 0.021 0.007 -10000 0 -10000 0 0
ARF5/GDP -0.004 0.093 -10000 0 -0.34 16 16
PLCG2 0.018 0.031 -10000 0 -0.33 3 3
PLCG1 0.02 0.005 -10000 0 -10000 0 0
ARF5 0.02 0.004 -10000 0 -10000 0 0
mol:GTP -0.019 0.046 0.25 3 -10000 0 3
ARF1/GTP -0.011 0.042 0.26 2 -10000 0 2
RHOA 0.021 0.004 -10000 0 -10000 0 0
YES1 0.02 0.005 -10000 0 -10000 0 0
RAP1A/GTP -0.019 0.045 0.16 21 -10000 0 21
ADAP1 -0.018 0.049 0.28 3 -0.28 1 4
ARAP3 -0.019 0.045 0.25 3 -10000 0 3
INPPL1 0.021 0.004 -10000 0 -10000 0 0
PREX1 0.016 0.035 -10000 0 -0.33 4 4
ARHGEF6 0.008 0.065 -10000 0 -0.33 14 14
ARHGEF7 0.02 0.005 -10000 0 -10000 0 0
ARF1 0.02 0.006 -10000 0 -10000 0 0
NRAS 0.02 0.007 -10000 0 -10000 0 0
FYN 0.018 0.019 -10000 0 -0.33 1 1
ARF6 0.02 0.005 -10000 0 -10000 0 0
FGR -0.006 0.093 -10000 0 -0.33 30 30
mol:Ca2+ -0.012 0.04 0.17 3 -0.13 5 8
mol:IP4 0 0 -10000 0 -10000 0 0
TIAM1 0.016 0.039 -10000 0 -0.33 5 5
ZAP70 0.016 0.043 -10000 0 -0.33 6 6
mol:IP3 -0.018 0.053 0.2 3 -0.18 8 11
LYN 0.019 0.006 -10000 0 -10000 0 0
ARF1/GDP -0.002 0.087 -10000 0 -0.31 16 16
RhoA/GDP -0.011 0.066 0.26 3 -0.27 3 6
PDK1/Src/Hsp90 0.039 0.013 -10000 0 -10000 0 0
BLNK 0.02 0.018 -10000 0 -0.33 1 1
actin cytoskeleton reorganization -0.008 0.087 0.3 6 -0.3 12 18
SRC 0.02 0.004 -10000 0 -10000 0 0
PLEKHA2 -0.018 0.008 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
PTEN 0.02 0.014 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ARF6/GTP -0.025 0.044 0.28 1 -10000 0 1
RhoA/GTP -0.021 0.047 0.29 2 -10000 0 2
Src family/SYK family/BLNK-LAT -0.017 0.1 -10000 0 -0.3 30 30
BLK 0.053 0.1 0.33 45 -0.33 1 46
PDPK1 0.021 0.003 -10000 0 -10000 0 0
CYTH1 -0.021 0.047 0.28 3 -10000 0 3
HCK 0.008 0.065 -10000 0 -0.33 14 14
CYTH3 -0.017 0.048 0.28 3 -10000 0 3
CYTH2 -0.021 0.047 0.28 3 -10000 0 3
KRAS 0.02 0.007 -10000 0 -10000 0 0
GO:0030676 0 0 -10000 0 -10000 0 0
FOXO3 -0.005 0.049 -10000 0 -0.33 5 5
SGK1 -0.018 0.1 -10000 0 -0.33 32 32
INPP5D 0.018 0.031 -10000 0 -0.33 3 3
mol:GDP -0.013 0.094 0.18 2 -0.31 22 24
SOS1 0.021 0.003 -10000 0 -10000 0 0
SYK 0.019 0.025 -10000 0 -0.33 2 2
ARF6/GDP -0.014 0.059 0.26 2 -0.25 3 5
mol:PI-3-4-5-P3 -0.02 0.041 0.28 1 -10000 0 1
ARAP3/RAP1A/GTP -0.019 0.045 0.16 21 -10000 0 21
VAV1 0.017 0.031 -10000 0 -0.33 3 3
mol:PI-3-4-P2 -0.018 0.016 -10000 0 -0.23 2 2
RAS family/GTP/PI3K Class I -0.023 0.035 0.19 2 -10000 0 2
PLEKHA1 -0.021 0.014 -10000 0 -0.2 2 2
Rac1/GDP -0.005 0.089 -10000 0 -0.35 15 15
LAT 0.022 0.016 0.33 1 -10000 0 1
Rac1/GTP -0.004 0.091 -10000 0 -0.36 17 17
ITK -0.026 0.046 0.27 1 -10000 0 1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma -0.027 0.091 0.24 5 -0.28 19 24
LCK 0.021 0.024 0.33 1 -0.33 1 2
BTK -0.03 0.057 0.27 2 -0.29 2 4
Insulin Pathway

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
CBL/APS/CAP 0.026 0.045 -10000 0 -0.16 15 15
TC10/GTP 0.023 0.041 -10000 0 -0.16 14 14
Insulin Receptor/Insulin/IRS1/Shp2 0.049 0.021 -10000 0 -0.15 1 1
HRAS 0.021 0.004 -10000 0 -10000 0 0
APS homodimer 0.019 0.018 -10000 0 -0.33 1 1
GRB14 0.033 0.081 0.33 21 -0.33 5 26
FOXO3 -0.052 0.2 -10000 0 -0.62 42 42
AKT1 -0.02 0.055 0.29 5 -10000 0 5
INSR 0.022 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.04 0.031 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
GRB10 0.019 0.007 -10000 0 -10000 0 0
SORBS1 0.004 0.075 -10000 0 -0.33 19 19
CRK 0.019 0.006 -10000 0 -10000 0 0
PTPN1 -0.013 0.022 -10000 0 -10000 0 0
CAV1 -0.099 0.08 -10000 0 -0.18 190 190
CBL/APS/CAP/Crk-II/C3G 0.04 0.052 -10000 0 -0.17 16 16
Insulin Receptor/Insulin/IRS1/NCK2 0.049 0.021 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.037 0.02 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B -0.003 0.076 -10000 0 -0.32 18 18
RPS6KB1 -0.024 0.049 0.26 4 -10000 0 4
PARD6A 0.02 0.018 -10000 0 -0.33 1 1
CBL 0.02 0.005 -10000 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -10000 0 -10000 0 0
DOK1 0.011 0.043 -10000 0 -0.57 2 2
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.029 0.041 -10000 0 -10000 0 0
HRAS/GTP -0.028 0.02 -10000 0 -0.17 1 1
Insulin Receptor 0.021 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC 0.047 0.029 -10000 0 -10000 0 0
PRKCI -0.001 0.08 -10000 0 -0.3 20 20
Insulin Receptor/Insulin/GRB14/PDK1 -0.024 0.032 -10000 0 -0.17 3 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
negative regulation of MAPKKK cascade 0.028 0.043 -10000 0 -0.49 2 2
PI3K 0.045 0.023 -10000 0 -10000 0 0
NCK2 0.021 0.002 -10000 0 -10000 0 0
RHOQ 0.021 0.003 -10000 0 -10000 0 0
mol:H2O2 -0.002 0.003 -10000 0 -10000 0 0
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
AKT2 -0.021 0.055 0.31 4 -10000 0 4
PRKCZ -0.007 0.093 -10000 0 -0.33 22 22
SH2B2 0.019 0.018 -10000 0 -0.33 1 1
SHC/SHIP -0.02 0.023 -10000 0 -10000 0 0
F2RL2 0.039 0.088 0.33 28 -0.33 4 32
TRIP10 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin/Shc 0.032 0.018 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.026 0.008 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 0.047 0.029 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
RASA1 0.02 0.005 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
CBL/APS/CAP/Crk-II 0.035 0.05 -10000 0 -0.18 16 16
TC10/GDP 0.016 0.002 -10000 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 0.039 0.025 -10000 0 -10000 0 0
INPP5D -0.02 0.021 0.15 2 -0.18 2 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
SGK1 -0.051 0.19 -10000 0 -0.66 36 36
mol:cAMP 0 0 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IRS1 0.02 0.018 -10000 0 -0.33 1 1
p62DOK/RasGAP 0.028 0.044 -10000 0 -0.49 2 2
INS -0.014 0.015 -10000 0 -10000 0 0
mol:PI-3-4-P2 -0.02 0.021 0.14 2 -0.17 2 4
GRB2 0.02 0.004 -10000 0 -10000 0 0
EIF4EBP1 -0.019 0.053 0.22 7 -10000 0 7
PTPRA 0.021 0.007 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
TC10/GTP/CIP4 0.026 0.008 -10000 0 -10000 0 0
PDPK1 0.021 0.003 -10000 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.007 0.025 -10000 0 -0.19 1 1
Insulin Receptor/Insulin/IRS1 0.037 0.017 -10000 0 -0.14 1 1
Insulin Receptor/Insulin/IRS3 0.029 0.012 -10000 0 -10000 0 0
Par3/Par6 0.051 0.05 0.21 24 -0.16 4 28
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.018 0.006 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP1 -0.011 0.004 -10000 0 -10000 0 0
mol:DAG -0.013 0.036 0.24 4 -10000 0 4
VEGFR1 homodimer/NRP1/VEGFR 121 0.016 0.006 -10000 0 -10000 0 0
CaM/Ca2+ -0.018 0.03 0.22 1 -10000 0 1
HIF1A 0.022 0.005 -10000 0 -10000 0 0
GAB1 0.02 0.018 -10000 0 -0.33 1 1
AKT1 -0.015 0.043 0.38 2 -10000 0 2
PLCG1 -0.013 0.036 0.24 4 -10000 0 4
NOS3 -0.011 0.083 0.4 4 -0.35 9 13
CBL 0.02 0.005 -10000 0 -10000 0 0
mol:NO -0.006 0.091 0.43 6 -0.34 9 15
FLT1 -0.015 0.005 -10000 0 -10000 0 0
PGF 0.031 0.058 0.33 14 -10000 0 14
VEGFR1 homodimer/NRP2/VEGFR121 0.027 0.018 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
eNOS/Hsp90 -0.015 0.085 0.37 3 -0.39 7 10
endothelial cell proliferation -0.007 0.056 0.37 4 -10000 0 4
mol:Ca2+ -0.013 0.036 0.24 4 -10000 0 4
MAPK3 -0.02 0.041 0.29 5 -10000 0 5
MAPK1 -0.02 0.037 0.34 3 -10000 0 3
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
PLGF homodimer 0.031 0.058 0.33 14 -10000 0 14
PRKACA 0.02 0.005 -10000 0 -10000 0 0
RP11-342D11.1 0 0 -10000 0 -10000 0 0
CAV1 -0.18 0.17 -10000 0 -0.33 228 228
VEGFA homodimer 0.02 0.004 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer 0.017 0.007 -10000 0 -10000 0 0
platelet activating factor biosynthetic process -0.023 0.04 0.29 4 -10000 0 4
PI3K 0.042 0.037 -10000 0 -10000 0 0
PRKCA -0.019 0.03 0.23 3 -10000 0 3
PRKCB -0.02 0.038 0.23 5 -10000 0 5
VEGFR1 homodimer/PLGF homodimer 0.025 0.039 0.22 14 -10000 0 14
VEGFA 0.02 0.004 -10000 0 -10000 0 0
VEGFB 0.021 0.003 -10000 0 -10000 0 0
mol:IP3 -0.013 0.036 0.24 4 -10000 0 4
RASA1 -0.017 0.027 0.18 7 -10000 0 7
NRP2 0.019 0.025 -10000 0 -0.33 2 2
VEGFR1 homodimer -0.015 0.005 -10000 0 -10000 0 0
VEGFB homodimer 0.021 0.003 -10000 0 -10000 0 0
NCK1 0.021 0.003 -10000 0 -10000 0 0
eNOS/Caveolin-1 -0.089 0.11 0.44 2 -0.38 21 23
PTPN11 0.021 0.004 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.041 0.036 -10000 0 -10000 0 0
mol:L-citrulline -0.006 0.091 0.43 6 -0.34 9 15
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP 0.037 0.018 -10000 0 -10000 0 0
VEGFR1 homodimer/VEGFA homodimer/NCK1 0.028 0.011 -10000 0 -10000 0 0
CD2AP 0.02 0.004 -10000 0 -10000 0 0
PI3K/GAB1 0.049 0.041 -10000 0 -10000 0 0
PDPK1 -0.015 0.05 0.33 4 -10000 0 4
VEGFR1 homodimer/VEGFA homodimer/SHP2 0.028 0.012 -10000 0 -10000 0 0
mol:NADP -0.006 0.091 0.43 6 -0.34 9 15
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.035 0.018 -10000 0 -10000 0 0
VEGFR1 homodimer/NRP2 0.017 0.016 -10000 0 -10000 0 0
PDGFR-beta signaling 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
S1P1/Sphingosine-1-phosphate -0.001 0.075 0.2 1 -0.29 15 16
PDGFB-D/PDGFRB/SLAP 0.022 0.034 -10000 0 -0.23 6 6
PDGFB-D/PDGFRB/APS/CBL 0.037 0.019 -10000 0 -0.2 1 1
AKT1 -0.012 0.083 0.36 10 -10000 0 10
mol:PI-4-5-P2 0 0.001 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.005 0.093 0.34 3 -0.33 17 20
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
FGR -0.035 0.15 0.33 2 -0.47 37 39
mol:Ca2+ -0.003 0.1 0.33 4 -0.37 18 22
MYC 0.036 0.13 0.38 14 -0.48 6 20
SHC1 0.018 0.008 -10000 0 -10000 0 0
HRAS/GDP -0.014 0.039 0.16 17 -10000 0 17
LRP1/PDGFRB/PDGFB 0.035 0.034 -10000 0 -0.2 7 7
GRB10 0.019 0.007 -10000 0 -10000 0 0
PTPN11 0.021 0.004 -10000 0 -10000 0 0
GO:0007205 -0.004 0.1 0.33 4 -0.38 18 22
PTEN 0.021 0.003 -10000 0 -10000 0 0
GRB2 0.02 0.004 -10000 0 -10000 0 0
GRB7 0.019 0.025 -10000 0 -0.33 2 2
PDGFB-D/PDGFRB/SHP2 0.03 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB10 0.027 0.012 -10000 0 -10000 0 0
cell cycle arrest 0.022 0.034 -10000 0 -0.23 6 6
HRAS 0.021 0.004 -10000 0 -10000 0 0
HIF1A -0.016 0.078 0.34 10 -10000 0 10
GAB1 -0.002 0.098 0.37 3 -0.34 16 19
mol:GTP 0 0 -10000 0 -10000 0 0
DNM2 -0.001 0.087 0.3 7 -0.31 9 16
PDGFB-D/PDGFRB 0.038 0.016 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP 0.03 0.008 -10000 0 -10000 0 0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB 0.005 0.056 0.2 1 -0.28 4 5
positive regulation of MAPKKK cascade 0.03 0.009 -10000 0 -10000 0 0
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
mol:IP3 -0.004 0.1 0.33 4 -0.38 18 22
E5 0 0.001 -10000 0 -10000 0 0
CSK 0.019 0.01 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 0.028 0.021 -10000 0 -0.23 2 2
SHB 0.02 0.005 -10000 0 -10000 0 0
BLK -0.034 0.16 0.31 1 -0.39 58 59
PTPN2 0.019 0.009 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/SNX15 0.03 0.009 -10000 0 -10000 0 0
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
VAV2 -0.005 0.11 0.34 4 -0.38 15 19
CBL 0.02 0.005 -10000 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 0.03 0.008 -10000 0 -10000 0 0
LCK 0.006 0.059 0.33 2 -0.41 3 5
PDGFRB 0.02 0.009 -10000 0 -10000 0 0
ACP1 0.021 0.002 -10000 0 -10000 0 0
HCK -0.015 0.12 0.32 1 -0.53 18 19
ABL1 -0.007 0.097 0.29 5 -0.33 16 21
PDGFB-D/PDGFRB/CBL -0.006 0.11 0.38 2 -0.39 19 21
PTPN1 0.019 0.009 -10000 0 -10000 0 0
SNX15 0.021 0.003 -10000 0 -10000 0 0
STAT3 0.021 0.003 -10000 0 -10000 0 0
STAT1 0.021 0.002 -10000 0 -10000 0 0
cell proliferation 0.036 0.12 0.37 14 -0.43 6 20
SLA 0.012 0.046 -10000 0 -0.33 7 7
actin cytoskeleton reorganization -0.016 0.06 0.32 5 -10000 0 5
SRC 0 0.086 0.31 1 -0.6 6 7
PI3K -0.033 0.02 -10000 0 -0.17 4 4
PDGFB-D/PDGFRB/GRB7/SHC 0.033 0.024 -10000 0 -0.2 2 2
SH2B2 0.019 0.018 -10000 0 -0.33 1 1
PLCgamma1/SPHK1 0.004 0.095 0.34 3 -0.34 17 20
LYN 0.005 0.054 0.31 1 -0.38 3 4
LRP1 0.017 0.035 -10000 0 -0.33 4 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
STAT5B 0.021 0.003 -10000 0 -10000 0 0
STAT5A 0.02 0.018 -10000 0 -0.33 1 1
NCK1-2/p130 Cas 0.052 0.031 -10000 0 -0.17 1 1
SPHK1 0.022 0.028 0.33 3 -10000 0 3
EDG1 0 0.002 -10000 0 -10000 0 0
mol:DAG -0.004 0.1 0.33 4 -0.38 18 22
PLCG1 -0.004 0.1 0.33 4 -0.39 18 22
NHERF/PDGFRB 0.037 0.029 0.23 1 -0.2 4 5
YES1 -0.01 0.11 0.34 1 -0.57 13 14
cell migration 0.037 0.029 0.23 1 -0.2 4 5
SHC/Grb2/SOS1 0.045 0.032 -10000 0 -10000 0 0
SLC9A3R2 0.017 0.035 -10000 0 -0.33 4 4
SLC9A3R1 0.021 0.016 0.33 1 -10000 0 1
NHERF1-2/PDGFRB/PTEN 0.047 0.032 0.23 1 -0.18 4 5
FYN -0.028 0.13 0.31 1 -0.4 34 35
DOK1 -0.013 0.04 0.16 19 -10000 0 19
HRAS/GTP 0.015 0.003 -10000 0 -10000 0 0
PDGFB 0.017 0.035 -10000 0 -0.33 4 4
RAC1 0.011 0.12 0.36 8 -0.4 12 20
PRKCD -0.012 0.043 0.16 21 -10000 0 21
FER -0.012 0.042 0.17 20 -10000 0 20
MAPKKK cascade 0.014 0.099 0.4 12 -10000 0 12
RASA1 -0.012 0.041 0.17 19 -10000 0 19
NCK1 0.021 0.003 -10000 0 -10000 0 0
NCK2 0.021 0.002 -10000 0 -10000 0 0
p62DOK/Csk -0.016 0.041 0.16 16 -10000 0 16
PDGFB-D/PDGFRB/SHB 0.029 0.01 -10000 0 -10000 0 0
chemotaxis -0.006 0.095 0.28 6 -0.33 16 22
STAT1-3-5/STAT1-3-5 0.043 0.027 -10000 0 -0.18 1 1
Bovine Papilomavirus E5/PDGFRB 0.015 0.006 -10000 0 -10000 0 0
PTPRJ 0.021 0.003 -10000 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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
SPHK2 0.019 0.018 -10000 0 -0.33 1 1
SPHK1 0.023 0.027 0.33 3 -10000 0 3
GNAI2 0.021 0.004 -10000 0 -10000 0 0
mol:S1P 0.006 0.015 -10000 0 -0.22 1 1
GNAO1 0.02 0.034 0.33 2 -0.33 2 4
mol:Sphinganine-1-P -0.016 0.019 0.16 3 -0.23 1 4
growth factor activity 0 0 -10000 0 -10000 0 0
S1P/S1P2/G12/G13 0.032 0.036 -10000 0 -0.21 2 2
GNAI3 0.02 0.004 -10000 0 -10000 0 0
G12/G13 0.027 0.011 -10000 0 -10000 0 0
S1PR3 0.021 0.016 0.33 1 -10000 0 1
S1PR2 0.02 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
S1P1/S1P -0.001 0.028 -10000 0 -0.24 2 2
S1PR5 0 0.084 0.33 1 -0.33 23 24
S1PR4 0.005 0.071 -10000 0 -0.33 17 17
GNAI1 0.019 0.018 -10000 0 -0.33 1 1
S1P/S1P5/G12 0.014 0.055 0.22 1 -0.18 20 21
S1P/S1P3/Gq 0.003 0.071 -10000 0 -0.3 17 17
S1P/S1P4/Gi -0.019 0.091 -10000 0 -0.27 26 26
GNAQ 0.019 0.018 -10000 0 -0.33 1 1
GNAZ -0.01 0.098 -10000 0 -0.33 34 34
GNA14 0.011 0.055 -10000 0 -0.33 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.006 -10000 0 -10000 0 0
ABCC1 0.021 0.003 -10000 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 0.04 0.049 0.23 1 -0.2 12 13
MAP4K1 0.016 0.035 -10000 0 -0.33 4 4
MAP3K8 0.02 0.018 -10000 0 -0.33 1 1
PRKCB 0.013 0.052 -10000 0 -0.33 9 9
DBNL 0.019 0.006 -10000 0 -10000 0 0
CRKL 0.021 0.004 -10000 0 -10000 0 0
MAP3K1 -0.002 0.053 -10000 0 -0.29 6 6
JUN -0.008 0.12 -10000 0 -0.54 16 16
MAP3K7 -0.001 0.048 -10000 0 -0.23 10 10
GRAP2 0.011 0.058 -10000 0 -0.33 11 11
CRK 0.019 0.006 -10000 0 -10000 0 0
MAP2K4 -0.005 0.072 0.2 1 -0.39 7 8
LAT 0.022 0.016 0.33 1 -10000 0 1
LCP2 0.018 0.025 -10000 0 -0.33 2 2
MAPK8 -0.004 0.12 -10000 0 -0.55 17 17
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.005 0.063 -10000 0 -0.26 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55 0.046 0.045 0.23 1 -0.22 6 7
Cellular roles of Anthrax toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ANTXR1 0.02 0.018 -10000 0 -0.33 1 1
ANTXR2 0.021 0.003 -10000 0 -10000 0 0
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.002 -10000 0 -0.046 1 1
monocyte activation -0.018 0.12 -10000 0 -0.38 33 33
MAP2K2 -0.03 0.15 -10000 0 -0.57 28 28
MAP2K1 -0.008 0.003 -10000 0 -10000 0 0
MAP2K7 -0.008 0.002 -10000 0 -10000 0 0
MAP2K6 -0.006 0.02 0.076 12 -0.16 2 14
CYAA -0.012 0.008 -10000 0 -0.16 1 1
MAP2K4 -0.007 0.002 -10000 0 -10000 0 0
IL1B -0.015 0.038 0.16 3 -0.16 20 23
Channel 0.027 0.011 -10000 0 -0.17 1 1
NLRP1 -0.008 0.008 -10000 0 -0.16 1 1
CALM1 0.02 0.004 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.001 0.056 -10000 0 -0.39 8 8
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.002 0.046 1 -10000 0 1
MAPK3 -0.008 0.002 -10000 0 -10000 0 0
MAPK1 -0.008 0.002 -10000 0 -10000 0 0
PGR -0.031 0.055 -10000 0 -0.16 61 61
PA/Cellular Receptors 0.028 0.012 -10000 0 -0.19 1 1
apoptosis -0.003 0.002 -10000 0 -0.046 1 1
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.026 0.01 -10000 0 -0.16 1 1
macrophage activation -0.012 0.003 -10000 0 -10000 0 0
TNF 0.004 0.077 0.33 1 -0.33 19 20
VCAM1 -0.016 0.11 -10000 0 -0.4 29 29
platelet activation -0.001 0.056 -10000 0 -0.39 8 8
MAPKKK cascade 0.006 0.018 -10000 0 -0.085 4 4
IL18 -0.01 0.029 0.14 2 -0.19 7 9
negative regulation of macrophage activation -0.003 0.002 -10000 0 -0.046 1 1
LEF -0.003 0.002 -10000 0 -0.047 1 1
CASP1 -0.004 0.012 -10000 0 -0.13 3 3
mol:cAMP -0.001 0.057 -10000 0 -0.39 8 8
necrosis -0.003 0.002 -10000 0 -0.046 1 1
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.026 0.01 -10000 0 -0.16 1 1
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Hedgehog signaling events mediated by Gli proteins

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC2 0.02 0.006 -10000 0 -10000 0 0
GNB1/GNG2 0.036 0.025 0.23 1 -0.2 2 3
forebrain development -0.035 0.14 -10000 0 -0.52 17 17
GNAO1 0.014 0.037 0.33 2 -0.33 2 4
SMO/beta Arrestin2 0.021 0.031 0.23 3 -0.21 1 4
SMO 0.015 0.036 0.33 3 -0.33 1 4
ARRB2 0.013 0.016 -10000 0 -10000 0 0
GLI3/SPOP 0.002 0.082 -10000 0 -0.34 11 11
mol:GTP -0.001 0.002 -10000 0 -10000 0 0
GSK3B 0.021 0.003 -10000 0 -10000 0 0
GNAI2 0.015 0.015 -10000 0 -10000 0 0
SIN3/HDAC complex 0.047 0.021 -10000 0 -10000 0 0
GNAI1 0.014 0.023 -10000 0 -0.33 1 1
XPO1 0.013 0.019 -10000 0 -10000 0 0
GLI1/Su(fu) -0.033 0.13 -10000 0 -0.52 16 16
SAP30 0.021 0.004 -10000 0 -10000 0 0
mol:GDP 0.015 0.036 0.33 3 -0.33 1 4
MIM/GLI2A 0.002 0.047 -10000 0 -0.15 8 8
IFT88 0.02 0.006 -10000 0 -10000 0 0
GNAI3 0.014 0.016 -10000 0 -10000 0 0
GLI2 -0.008 0.079 0.19 1 -0.39 10 11
GLI3 -0.009 0.084 -10000 0 -0.35 12 12
CSNK1D 0.021 0.004 -10000 0 -10000 0 0
CSNK1E 0.02 0.004 -10000 0 -10000 0 0
SAP18 0.02 0.006 -10000 0 -10000 0 0
embryonic digit morphogenesis 0.02 0.006 -10000 0 -10000 0 0
GNG2 0.019 0.018 -10000 0 -0.33 1 1
Gi family/GTP -0.015 0.07 -10000 0 -0.2 38 38
SIN3B 0.02 0.005 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
GLI3/Su(fu) -0.01 0.088 -10000 0 -0.35 13 13
GLI2/Su(fu) -0.007 0.085 -10000 0 -0.4 12 12
FOXA2 -0.13 0.34 -10000 0 -0.86 68 68
neural tube patterning -0.035 0.14 -10000 0 -0.52 17 17
SPOP 0.021 0.004 -10000 0 -10000 0 0
Su(fu)/PIAS1 0.012 0.039 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
CSNK1G2 0.02 0.006 -10000 0 -10000 0 0
CSNK1G3 0.02 0.005 -10000 0 -10000 0 0
MTSS1 0.002 0.047 -10000 0 -0.16 5 5
embryonic limb morphogenesis -0.035 0.14 -10000 0 -0.52 17 17
SUFU 0.007 0.014 -10000 0 -10000 0 0
LGALS3 0.02 0.005 -10000 0 -10000 0 0
catabolic process -0.004 0.12 -10000 0 -0.43 20 20
GLI3A/CBP 0.006 0.062 -10000 0 -0.33 11 11
KIF3A 0.02 0.005 -10000 0 -10000 0 0
GLI1 -0.036 0.14 -10000 0 -0.53 17 17
RAB23 0.02 0.005 -10000 0 -10000 0 0
CSNK1A1 0.02 0.004 -10000 0 -10000 0 0
IFT172 0.021 0.002 -10000 0 -10000 0 0
RBBP7 0.021 0.004 -10000 0 -10000 0 0
Su(fu)/Galectin3 0.011 0.039 -10000 0 -10000 0 0
GNAZ -0.015 0.098 -10000 0 -0.33 34 34
RBBP4 0.021 0.003 -10000 0 -10000 0 0
CSNK1G1 0.021 0.004 -10000 0 -10000 0 0
PIAS1 0.021 0.003 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GLI2/SPOP 0 0.083 -10000 0 -0.4 10 10
STK36 0.013 0.019 -10000 0 -10000 0 0
Gi family/GNB1/GNG2/GDP -0.014 0.066 -10000 0 -0.31 6 6
PTCH1 -0.042 0.16 -10000 0 -0.84 10 10
MIM/GLI1 -0.048 0.18 -10000 0 -0.46 52 52
CREBBP 0.006 0.062 -10000 0 -0.33 11 11
Su(fu)/SIN3/HDAC complex -0.003 0.068 -10000 0 -0.3 12 12
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.017 0.061 0.34 2 -10000 0 2
CRKL -0.01 0.049 0.22 9 -10000 0 9
mol:DAG 0.008 0.034 0.24 1 -0.23 1 2
HRAS 0 0.073 0.24 10 -10000 0 10
MAPK8 0 0.061 0.17 43 -10000 0 43
RAP1A -0.01 0.05 0.22 9 -0.16 2 11
GAB1 -0.011 0.05 0.22 8 -10000 0 8
MAPK14 -0.001 0.059 0.17 41 -10000 0 41
EPO 0.009 0.035 0.33 3 -10000 0 3
PLCG1 0.008 0.034 0.24 1 -0.23 1 2
EPOR/TRPC2/IP3 Receptors 0.022 0.009 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 0.037 0.028 0.22 2 -0.2 2 4
GAB1/SHC/GRB2/SOS1 -0.017 0.047 0.24 4 -10000 0 4
EPO/EPOR (dimer) 0.029 0.024 0.23 3 -10000 0 3
IRS2 -0.01 0.05 0.22 9 -10000 0 9
STAT1 0.009 0.038 0.32 1 -0.23 1 2
STAT5B 0.009 0.035 0.28 1 -0.23 1 2
cell proliferation -0.003 0.064 0.17 42 -10000 0 42
GAB1/SHIP/PIK3R1/SHP2/SHC -0.026 0.037 -10000 0 -0.28 1 1
TEC -0.01 0.051 0.22 9 -10000 0 9
SOCS3 0.018 0.025 -10000 0 -0.33 2 2
STAT1 (dimer) 0.009 0.037 0.32 1 -0.23 1 2
JAK2 0.019 0.02 -10000 0 -0.33 1 1
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 0.045 0.04 0.36 1 -0.16 3 4
EPO/EPOR 0.029 0.024 0.23 3 -10000 0 3
LYN 0.019 0.007 -10000 0 -10000 0 0
TEC/VAV2 -0.014 0.049 0.21 8 -10000 0 8
elevation of cytosolic calcium ion concentration 0.022 0.009 -10000 0 -10000 0 0
SHC1 0.018 0.008 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.037 0.026 0.21 4 -10000 0 4
mol:IP3 0.008 0.034 0.24 1 -0.23 1 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.015 0.056 0.26 4 -0.29 1 5
SH2B3 0.02 0.026 -10000 0 -0.33 2 2
NFKB1 0 0.062 0.17 44 -10000 0 44
EPO/EPOR (dimer)/JAK2/SOCS3 0.004 0.043 0.19 2 -0.23 9 11
PTPN6 -0.009 0.045 0.15 25 -0.17 2 27
TEC/VAV2/GRB2 -0.017 0.049 0.25 4 -10000 0 4
EPOR 0.022 0.009 -10000 0 -10000 0 0
INPP5D 0.018 0.031 -10000 0 -0.33 3 3
mol:GDP -0.017 0.047 0.24 4 -10000 0 4
SOS1 0.021 0.003 -10000 0 -10000 0 0
PLCG2 0.018 0.031 -10000 0 -0.33 3 3
CRKL/CBL/C3G -0.016 0.049 0.25 4 -10000 0 4
VAV2 -0.01 0.051 0.22 9 -10000 0 9
CBL -0.009 0.05 0.22 9 -10000 0 9
SHC/Grb2/SOS1 0.023 0.025 0.19 1 -0.16 1 2
STAT5A 0.008 0.04 0.28 1 -0.3 2 3
GRB2 0.02 0.004 -10000 0 -10000 0 0
STAT5 (dimer) 0.02 0.042 0.38 1 -0.34 1 2
LYN/PLCgamma2 0.025 0.025 -10000 0 -0.23 3 3
PTPN11 0.021 0.004 -10000 0 -10000 0 0
BTK -0.017 0.061 0.22 8 -0.3 2 10
BCL2 0.008 0.075 0.39 2 -10000 0 2
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.021 0.003 -10000 0 -10000 0 0
mol:PIP3 -0.014 0.025 -10000 0 -0.2 5 5
FRAP1 -0.007 0.087 -10000 0 -0.43 14 14
AKT1 -0.01 0.036 0.15 6 -0.24 4 10
INSR 0.02 0.005 -10000 0 -10000 0 0
Insulin Receptor/Insulin 0.024 0.007 -10000 0 -10000 0 0
mol:GTP -0.012 0.047 0.21 3 -0.22 2 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.016 0.028 -10000 0 -0.2 4 4
TSC2 0.021 0.004 -10000 0 -10000 0 0
RHEB/GDP -0.023 0.025 -10000 0 -0.19 2 2
TSC1 0.021 0.004 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.014 0.028 -10000 0 -0.22 5 5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA 0.012 0.039 -10000 0 -0.23 4 4
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.021 0.002 -10000 0 -10000 0 0
RPS6KB1 0.005 0.062 0.24 3 -0.37 4 7
MAP3K5 -0.011 0.054 0.18 4 -0.18 33 37
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
apoptosis -0.011 0.054 0.18 4 -0.18 33 37
mol:LY294002 0 0 -10000 0 -0.001 2 2
EIF4B 0.003 0.062 0.28 3 -0.33 4 7
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.02 0.053 0.23 2 -0.31 3 5
eIF4E/eIF4G1/eIF4A1 0.003 0.054 -10000 0 -0.28 13 13
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.025 0.03 -10000 0 -0.21 5 5
mTOR/RHEB/GTP/Raptor/GBL -0.004 0.035 0.18 4 -0.15 3 7
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
RHEB/GTP -0.016 0.041 0.2 1 -0.19 2 3
mol:Amino Acids 0 0 -10000 0 -0.001 2 2
FKBP12/Rapamycin 0.015 0.004 -10000 0 -10000 0 0
PDPK1 -0.018 0.024 0.16 1 -0.2 4 5
EIF4E 0.021 0.003 -10000 0 -10000 0 0
ASK1/PP5C -0.031 0.17 -10000 0 -0.52 41 41
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.004 0.041 -10000 0 -0.23 10 10
TSC1/TSC2 -0.012 0.05 0.23 3 -0.23 2 5
tumor necrosis factor receptor activity 0 0 0.001 2 -10000 0 2
RPS6 0.019 0.006 -10000 0 -10000 0 0
PPP5C 0.02 0.005 -10000 0 -10000 0 0
EIF4G1 0.02 0.004 -10000 0 -10000 0 0
IRS1 0.001 0.028 -10000 0 -0.24 5 5
INS 0.018 0.003 -10000 0 -10000 0 0
PTEN 0.021 0.005 -10000 0 -10000 0 0
PDK2 -0.018 0.025 0.17 1 -0.2 4 5
EIF4EBP1 -0.057 0.29 -10000 0 -1 31 31
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PPP2R5D -0.004 0.085 0.25 2 -0.4 13 15
peptide biosynthetic process -0.017 0.015 0.17 2 -10000 0 2
RHEB 0.02 0.005 -10000 0 -10000 0 0
EIF4A1 0.019 0.006 -10000 0 -10000 0 0
mol:Rapamycin 0 0.001 0.004 6 -0.002 1 7
EEF2 -0.017 0.015 0.17 2 -10000 0 2
eIF4E/4E-BP1 -0.046 0.27 -10000 0 -0.96 31 31
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.047 0.058 0.22 28 -0.17 3 31
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
CRKL 0.021 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.008 0.057 0.27 2 -10000 0 2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 0.037 0.026 -10000 0 -0.2 1 1
antigen processing and presentation of peptide antigen via MHC class I -0.018 0.037 -10000 0 -0.16 1 1
CaM/Ca2+ 0.044 0.054 -10000 0 -0.16 3 3
RAP1A 0.02 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.009 0.047 0.16 1 -10000 0 1
AKT1 -0.009 0.058 0.29 5 -10000 0 5
MAP2K1 -0.012 0.05 0.19 7 -10000 0 7
MAP3K11 -0.009 0.05 0.22 5 -10000 0 5
IFNGR1 0.02 0.011 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKII 0.001 0.12 0.23 4 -0.31 36 40
Rap1/GTP -0.029 0.024 -10000 0 -10000 0 0
CRKL/C3G 0.03 0.008 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP 0.057 0.06 -10000 0 -0.18 2 2
CEBPB -0.002 0.094 0.31 2 -0.4 11 13
STAT3 0.021 0.003 -10000 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 0.054 0.078 -10000 0 -0.69 2 2
STAT1 -0.008 0.05 0.22 5 -10000 0 5
CALM1 0.02 0.004 -10000 0 -10000 0 0
IFN-gamma (dimer) 0.038 0.088 0.33 29 -0.33 2 31
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.008 0.055 0.27 3 -10000 0 3
CEBPB/PTGES2/Cbp/p300 0.007 0.062 -10000 0 -0.29 7 7
mol:Ca2+ 0.045 0.056 0.21 28 -0.17 3 31
MAPK3 0.003 0.065 -10000 0 -0.45 2 2
STAT1 (dimer) -0.02 0.051 -10000 0 -10000 0 0
MAPK1 -0.013 0.12 -10000 0 -0.66 11 11
JAK2 0.019 0.021 -10000 0 -0.33 1 1
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
JAK1 0.021 0.01 -10000 0 -10000 0 0
CAMK2D 0.021 0.003 -10000 0 -10000 0 0
DAPK1 -0.006 0.094 0.29 2 -0.52 8 10
SMAD7 -0.002 0.038 0.19 5 -0.17 1 6
CBL/CRKL/C3G -0.01 0.056 0.27 3 -10000 0 3
PI3K 0.041 0.049 -10000 0 -0.16 2 2
IFNG 0.038 0.088 0.33 29 -0.33 2 31
apoptosis -0.003 0.087 0.24 1 -0.42 11 12
CAMK2G 0.021 0.003 -10000 0 -10000 0 0
STAT3 (dimer) 0.021 0.003 -10000 0 -10000 0 0
CAMK2A -0.012 0.1 0.33 1 -0.33 37 38
CAMK2B 0.061 0.11 0.33 53 -10000 0 53
FRAP1 -0.01 0.054 0.28 5 -10000 0 5
PRKCD -0.01 0.06 0.28 6 -10000 0 6
RAP1B 0.02 0.005 -10000 0 -10000 0 0
negative regulation of cell growth -0.018 0.037 -10000 0 -0.16 1 1
PTPN2 0.02 0.005 -10000 0 -10000 0 0
EP300 0.021 0.004 -10000 0 -10000 0 0
IRF1 -0.011 0.046 0.22 2 -10000 0 2
STAT1 (dimer)/PIASy -0.008 0.055 0.27 3 -10000 0 3
SOCS1 0.013 0.074 -10000 0 -1 2 2
mol:GDP -0.011 0.052 0.25 3 -10000 0 3
CASP1 -0.004 0.04 0.19 5 -0.18 2 7
PTGES2 0.021 0.004 -10000 0 -10000 0 0
IRF9 -0.003 0.032 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.029 0.039 -10000 0 -0.16 2 2
RAP1/GDP -0.026 0.033 -10000 0 -10000 0 0
CBL -0.007 0.049 0.24 4 -10000 0 4
MAP3K1 -0.008 0.05 0.24 4 -10000 0 4
PIAS1 0.021 0.003 -10000 0 -10000 0 0
PIAS4 0.02 0.005 -10000 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.018 0.037 -10000 0 -0.16 1 1
PTPN11 -0.005 0.049 0.15 26 -0.17 3 29
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAPGEF1 0.021 0.004 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC3 0.021 0.004 -10000 0 -10000 0 0
VDR 0.021 0.024 0.33 1 -0.33 1 2
Cbp/p300/PCAF 0.04 0.012 -10000 0 -10000 0 0
EP300 0.021 0.004 -10000 0 -10000 0 0
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.011 0.042 0.16 1 -0.34 2 3
KAT2B 0.021 0.004 -10000 0 -10000 0 0
MAPK14 0.02 0.004 -10000 0 -10000 0 0
AKT1 0.004 0.045 0.26 1 -0.2 5 6
RAR alpha/9cRA/Cyclin H 0.031 0.051 -10000 0 -0.24 3 3
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.007 0.051 0.2 1 -0.26 5 6
CDC2 0 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAR alpha/Jnk1 0.018 0.036 -10000 0 -0.19 6 6
NCOR2 0.021 0.004 -10000 0 -10000 0 0
VDR/VDR/Vit D3 0.015 0.016 0.22 1 -0.22 1 2
RXRs/RARs/NRIP1/9cRA -0.016 0.1 0.43 2 -0.44 10 12
NCOA2 0.017 0.026 -10000 0 -0.33 2 2
NCOA3 0.02 0.005 -10000 0 -10000 0 0
NCOA1 0.021 0.002 -10000 0 -10000 0 0
VDR/VDR/DNA 0.021 0.024 0.33 1 -0.33 1 2
RARG 0.021 0.003 -10000 0 -10000 0 0
RAR gamma1/9cRA 0.027 0.008 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.021 0.003 -10000 0 -10000 0 0
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.012 0.088 0.28 1 -0.38 11 12
RARA 0.013 0.03 0.17 1 -0.2 2 3
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA 0.006 0.048 0.2 1 -0.28 4 5
PRKCA 0.019 0.025 -10000 0 -0.33 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.021 0.11 0.33 3 -0.48 10 13
RXRG -0.091 0.13 0.25 2 -0.25 148 150
RXRA 0.007 0.026 0.18 2 -0.19 2 4
RXRB 0.019 0.046 0.31 3 -0.25 2 5
VDR/Vit D3/DNA 0.015 0.016 0.22 1 -0.22 1 2
RBP1 0.024 0.039 0.33 5 -0.33 1 6
CRBP1/9-cic-RA 0.017 0.026 0.22 5 -0.22 1 6
RARB 0.019 0.025 -10000 0 -0.33 2 2
PRKCG 0.04 0.076 0.33 25 -10000 0 25
MNAT1 0.02 0.004 -10000 0 -10000 0 0
RAR alpha/RXRs -0.019 0.089 0.27 1 -0.4 12 13
RXRs/RARs/SMRT(N-CoR2)/9cRA -0.012 0.085 0.41 1 -0.38 9 10
proteasomal ubiquitin-dependent protein catabolic process 0.008 0.074 0.28 3 -0.31 8 11
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.022 0.11 0.33 3 -0.49 10 13
positive regulation of DNA binding 0.022 0.043 -10000 0 -0.22 3 3
NRIP1 -0.02 0.11 0.46 1 -0.52 7 8
RXRs/RARs -0.024 0.11 0.28 1 -0.49 11 12
RXRs/RXRs/DNA/9cRA -0.023 0.082 0.28 1 -0.38 11 12
PRKACA 0.02 0.005 -10000 0 -10000 0 0
CDK7 0.02 0.005 -10000 0 -10000 0 0
TFIIH 0.039 0.013 -10000 0 -10000 0 0
RAR alpha/9cRA 0.04 0.042 -10000 0 -0.2 2 2
CCNH 0.02 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
RAR gamma2/9cRA 0.034 0.019 -10000 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

Figure 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
BAG4 0.018 0.007 -10000 0 -10000 0 0
Caspase 8 (4 units) 0.02 0.05 -10000 0 -0.28 3 3
NEF -0.001 0.02 -10000 0 -0.17 5 5
NFKBIA 0.019 0.009 -10000 0 -10000 0 0
BIRC3 0.006 0.069 0.3 4 -10000 0 4
CYCS -0.004 0.05 0.15 20 -0.3 2 22
RIPK1 0.021 0.004 -10000 0 -10000 0 0
CD247 0.017 0.028 -10000 0 -0.24 4 4
MAP2K7 -0.023 0.18 -10000 0 -0.64 27 27
protein ubiquitination -0.002 0.07 0.31 3 -0.31 4 7
CRADD 0.022 0.016 0.33 1 -10000 0 1
DAXX 0.02 0.004 -10000 0 -10000 0 0
FAS 0.017 0.035 -10000 0 -0.33 4 4
BID 0.006 0.05 0.16 22 -0.28 3 25
NF-kappa-B/RelA/I kappa B alpha 0.039 0.026 0.22 4 -10000 0 4
TRADD 0.021 0.004 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
CFLAR 0.021 0.002 -10000 0 -10000 0 0
FADD 0.02 0.004 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin 0.039 0.026 0.23 4 -10000 0 4
MAPK8 -0.023 0.17 0.35 2 -0.61 26 28
APAF1 0.021 0.004 -10000 0 -10000 0 0
TRAF1 0.021 0.004 -10000 0 -10000 0 0
TRAF2 0.021 0.004 -10000 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG 0.008 0.035 -10000 0 -0.27 4 4
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD -0.001 0.069 -10000 0 -0.39 4 4
CHUK -0.003 0.074 0.31 3 -0.33 4 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 0.049 0.031 -10000 0 -0.18 1 1
TCRz/NEF 0.013 0.025 -10000 0 -0.23 4 4
TNF 0.004 0.077 0.33 1 -0.33 19 20
FASLG -0.014 0.033 -10000 0 -0.31 4 4
NFKB1 0.021 0.012 -10000 0 -0.13 2 2
TNFR1A/BAG4/TNF-alpha 0.024 0.052 0.23 1 -0.19 18 19
CASP6 0.028 0.071 -10000 0 -0.48 3 3
CASP7 0.026 0.097 0.32 13 -0.3 2 15
RELA 0.021 0.012 -10000 0 -0.13 2 2
CASP2 0.02 0.004 -10000 0 -10000 0 0
CASP3 0.024 0.092 0.32 11 -10000 0 11
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
TNFR1A/BAG4 0.026 0.012 -10000 0 -10000 0 0
CASP8 0.02 0.018 -10000 0 -0.33 1 1
CASP9 0.02 0.004 -10000 0 -10000 0 0
MAP3K14 -0.001 0.07 0.2 1 -0.37 4 5
APAF-1/Caspase 9 -0.011 0.053 0.18 4 -0.28 1 5
BCL2 -0.02 0.16 0.33 2 -0.55 26 28
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 0.018 0.035 0.33 1 -0.33 3 4
CLTC 0.017 0.065 0.23 2 -0.44 5 7
calcium ion-dependent exocytosis 0.011 0.03 0.19 3 -0.16 1 4
Dynamin 2/GTP -0.001 0.046 0.13 40 -10000 0 40
EXOC4 0.02 0.005 -10000 0 -10000 0 0
CD59 0.011 0.041 -10000 0 -0.31 4 4
CPE -0.004 0.045 0.2 16 -10000 0 16
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
membrane fusion 0.011 0.027 -10000 0 -10000 0 0
CTNND1 0 0.055 0.19 24 -10000 0 24
DNM2 0.02 0.005 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.008 0.049 0.17 7 -0.26 4 11
TSHR 0.006 0.057 0.17 41 -10000 0 41
INS 0.003 0.068 -10000 0 -0.48 7 7
BIN1 0.021 0.001 -10000 0 -10000 0 0
mol:Choline 0.011 0.027 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.07 0.19 47 -10000 0 47
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.02 0.005 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.046 0.13 40 -10000 0 40
JUP 0.011 0.036 -10000 0 -0.3 3 3
ASAP2/amphiphysin II 0.038 0.011 -10000 0 -10000 0 0
ARF6/GTP 0.015 0.004 -10000 0 -10000 0 0
CDH1 0.01 0.041 -10000 0 -0.31 4 4
clathrin-independent pinocytosis 0.015 0.004 -10000 0 -10000 0 0
MAPK8IP3 0.021 0.004 -10000 0 -10000 0 0
positive regulation of endocytosis 0.015 0.004 -10000 0 -10000 0 0
EXOC2 0.02 0.005 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.006 0.02 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.021 0.004 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.031 0.049 0.28 5 -10000 0 5
positive regulation of phagocytosis -0.013 0.004 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0.027 0.008 -10000 0 -10000 0 0
ACAP1 0.014 0.027 -10000 0 -0.15 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 -0.011 0.064 -10000 0 -0.31 4 4
clathrin heavy chain/ACAP1 0.015 0.058 0.2 10 -0.33 5 15
JIP4/KLC1 0.037 0.013 -10000 0 -10000 0 0
EXOC1 0.021 0.004 -10000 0 -10000 0 0
exocyst 0.006 0.02 -10000 0 -10000 0 0
RALA/GTP 0.014 0.005 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0.027 0.008 -10000 0 -10000 0 0
receptor recycling 0.015 0.004 -10000 0 -10000 0 0
CTNNA1 0 0.055 0.19 23 -10000 0 23
NME1 0.012 0.07 0.19 47 -10000 0 47
clathrin coat assembly 0.016 0.067 0.23 2 -0.4 6 8
IL2RA 0.015 0.046 -10000 0 -0.33 4 4
VAMP3 -0.013 0.004 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 0.016 0.052 0.2 2 -0.31 5 7
EXOC6 0.021 0.003 -10000 0 -10000 0 0
PLD1 0.004 0.006 -10000 0 -10000 0 0
PLD2 0.004 0.005 -10000 0 -10000 0 0
EXOC5 0.02 0.004 -10000 0 -10000 0 0
PIP5K1C 0.007 0.048 0.17 6 -0.26 4 10
SDC1 0.012 0.042 -10000 0 -0.31 4 4
ARF6/GDP 0.029 0.039 0.14 43 -10000 0 43
EXOC7 0.02 0.004 -10000 0 -10000 0 0
E-cadherin/beta catenin 0.033 0.051 -10000 0 -0.29 5 5
mol:Phosphatidic acid 0.011 0.027 -10000 0 -10000 0 0
endocytosis -0.037 0.01 -10000 0 -10000 0 0
SCAMP2 0.021 0.003 -10000 0 -10000 0 0
ADRB2 -0.037 0.094 0.21 1 -0.45 6 7
EXOC3 0.016 0.009 -10000 0 -10000 0 0
ASAP2 0.021 0.002 -10000 0 -10000 0 0
Dynamin 2/GDP 0.035 0.053 0.18 43 -10000 0 43
KLC1 0.02 0.005 -10000 0 -10000 0 0
AVPR2 -0.015 0.094 0.28 6 -0.41 6 12
RALA 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.024 0.054 0.33 2 -0.29 4 6
S1P3 pathway

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
PDGFRB 0.02 0.004 -10000 0 -10000 0 0
mol:S1P 0 0.002 -10000 0 -10000 0 0
S1P1/S1P/Gi -0.011 0.063 -10000 0 -0.19 39 39
GNAO1 0.021 0.034 0.33 2 -0.34 2 4
S1P/S1P3/G12/G13 0.034 0.017 -10000 0 -10000 0 0
AKT1 0.003 0.067 -10000 0 -0.4 9 9
AKT3 -0.008 0.1 -10000 0 -0.98 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB 0.02 0.004 -10000 0 -10000 0 0
GNAI2 0.02 0.007 -10000 0 -10000 0 0
GNAI3 0.021 0.005 -10000 0 -10000 0 0
GNAI1 0.019 0.019 -10000 0 -0.33 1 1
mol:GDP 0 0 -10000 0 -10000 0 0
S1PR3 0.021 0.017 0.33 1 -10000 0 1
S1PR2 0.02 0.005 -10000 0 -10000 0 0
EDG1 0 0 -10000 0 -10000 0 0
mol:Ca2+ -0.007 0.068 -10000 0 -0.18 41 41
MAPK3 -0.015 0.061 -10000 0 -0.22 9 9
MAPK1 -0.013 0.058 -10000 0 -0.25 5 5
JAK2 -0.025 0.082 0.2 2 -0.3 14 16
CXCR4 -0.015 0.063 -10000 0 -0.27 6 6
FLT1 0.02 0.008 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.003 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
SRC -0.015 0.065 0.27 2 -0.27 6 8
S1P/S1P3/Gi -0.008 0.068 -10000 0 -0.18 41 41
RAC1 0.019 0.007 -10000 0 -10000 0 0
RhoA/GTP -0.003 0.072 -10000 0 -0.24 9 9
VEGFA 0.021 0.007 -10000 0 -10000 0 0
S1P/S1P2/Gi -0.009 0.068 -10000 0 -0.23 12 12
VEGFR1 homodimer/VEGFA homodimer 0.029 0.013 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
S1P/S1P3/Gq 0.006 0.04 -10000 0 -0.22 10 10
GNAQ 0.019 0.018 -10000 0 -0.33 1 1
GNAZ -0.01 0.098 -10000 0 -0.33 34 34
G12/G13 0.027 0.011 -10000 0 -10000 0 0
GNA14 0.011 0.055 -10000 0 -0.33 10 10
GNA15 0.02 0.006 -10000 0 -10000 0 0
GNA12 0.019 0.007 -10000 0 -10000 0 0
GNA13 0.02 0.004 -10000 0 -10000 0 0
GNA11 0.02 0.006 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.069 -10000 0 -0.26 8 8
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 0.005 0.11 -9999 0 -0.42 12 12
MAP3K8 0.017 0.021 -9999 0 -0.33 1 1
FOS 0.005 0.082 -9999 0 -0.39 7 7
PRKCA 0.015 0.028 -9999 0 -0.33 2 2
PTPN7 0.015 0.016 -9999 0 -10000 0 0
HRAS 0.018 0.01 -9999 0 -10000 0 0
PRKCB 0.009 0.054 -9999 0 -0.33 9 9
NRAS 0.018 0.011 -9999 0 -10000 0 0
RAS family/GTP 0.031 0.022 -9999 0 -10000 0 0
MAPK3 0.011 0.043 -9999 0 -0.34 1 1
MAP2K1 -0.004 0.08 -9999 0 -0.39 11 11
ELK1 0.016 0.016 -9999 0 -10000 0 0
BRAF -0.003 0.059 -9999 0 -0.34 10 10
mol:GTP 0 0.001 -9999 0 -0.004 30 30
MAPK1 0.002 0.079 -9999 0 -0.43 9 9
RAF1 -0.005 0.062 -9999 0 -0.33 12 12
KRAS 0.017 0.011 -9999 0 -10000 0 0
ceramide signaling 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
MAP4K4 -0.009 0.075 0.2 1 -0.39 6 7
BAG4 0.018 0.007 -10000 0 -10000 0 0
BAD -0.003 0.038 0.3 2 -0.14 4 6
NFKBIA 0.018 0.008 -10000 0 -10000 0 0
BIRC3 0.022 0.04 0.33 4 -0.33 2 6
BAX -0.002 0.034 0.16 3 -0.13 3 6
EnzymeConsortium:3.1.4.12 0 0.022 0.075 5 -0.087 6 11
IKBKB 0.003 0.089 0.28 8 -0.37 6 14
MAP2K2 -0.007 0.036 0.17 6 -10000 0 6
MAP2K1 -0.008 0.041 0.16 9 -0.16 1 10
SMPD1 -0.002 0.027 0.11 2 -0.12 5 7
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0 0.078 0.24 2 -0.38 6 8
MAP2K4 -0.004 0.037 0.19 6 -0.15 1 7
protein ubiquitination -0.001 0.085 0.3 4 -0.37 6 10
EnzymeConsortium:2.7.1.37 -0.01 0.043 0.17 7 -0.17 1 8
response to UV 0 0 0.002 7 -0.002 1 8
RAF1 -0.005 0.039 0.18 6 -0.15 1 7
CRADD 0.022 0.016 0.33 1 -10000 0 1
mol:ceramide 0.001 0.035 0.11 6 -0.13 6 12
I-kappa-B-alpha/RELA/p50/ubiquitin 0.024 0.011 -10000 0 -10000 0 0
MADD 0.021 0.003 -10000 0 -10000 0 0
MAP3K1 -0.001 0.039 0.2 6 -0.15 2 8
TRADD 0.021 0.004 -10000 0 -10000 0 0
RELA/p50 0.021 0.003 -10000 0 -10000 0 0
MAPK3 -0.006 0.039 0.17 6 -10000 0 6
MAPK1 -0.008 0.042 0.17 6 -0.24 1 7
p50/RELA/I-kappa-B-alpha 0.026 0.012 -10000 0 -10000 0 0
FADD -0.005 0.075 -10000 0 -0.39 6 6
KSR1 -0.002 0.039 0.18 6 -0.14 3 9
MAPK8 -0.007 0.042 0.19 10 -10000 0 10
TRAF2 0.021 0.004 -10000 0 -10000 0 0
response to radiation 0 0 0.002 2 -10000 0 2
CHUK -0.01 0.077 0.36 1 -0.37 6 7
TNF R/SODD 0.026 0.012 -10000 0 -10000 0 0
TNF 0.004 0.077 0.33 1 -0.33 19 20
CYCS 0.007 0.044 0.16 8 -0.13 2 10
IKBKG -0.005 0.08 0.28 3 -0.35 6 9
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD -0.005 0.076 -10000 0 -0.41 6 6
RELA 0.021 0.003 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
AIFM1 0.001 0.04 0.19 3 -0.13 2 5
TNF/TNF R/SODD 0.024 0.052 0.23 1 -0.2 18 19
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
response to heat 0 0 0.002 2 -10000 0 2
CASP8 0.012 0.072 -10000 0 -0.54 6 6
NSMAF 0.004 0.086 0.23 5 -0.38 6 11
response to hydrogen peroxide 0 0 0.002 7 -0.002 1 8
BCL2 0.02 0.017 0.33 1 -10000 0 1
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.02 0.005 -10000 0 -10000 0 0
NFATC1 -0.017 0.1 0.4 1 -0.39 14 15
NFATC2 -0.013 0.06 0.16 3 -0.26 10 13
NFATC3 0.006 0.023 -10000 0 -0.3 2 2
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 -0.019 0.088 0.18 1 -0.32 16 17
Exportin 1/Ran/NUP214 0.041 0.017 0.23 2 -10000 0 2
mol:DAG -0.001 0.002 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV 0 0.08 -10000 0 -0.3 13 13
BCL2/BAX 0.028 0.015 0.24 1 -10000 0 1
CaM/Ca2+/Calcineurin A alpha-beta B1 0.008 0.016 -10000 0 -10000 0 0
CaM/Ca2+ 0.008 0.016 -10000 0 -10000 0 0
BAX 0.02 0.005 -10000 0 -10000 0 0
MAPK14 0.013 0.016 -10000 0 -10000 0 0
BAD 0.021 0.003 -10000 0 -10000 0 0
CABIN1/MEF2D -0.006 0.079 -10000 0 -0.32 13 13
Calcineurin A alpha-beta B1/BCL2 0.02 0.017 0.33 1 -10000 0 1
FKBP8 0.019 0.018 -10000 0 -0.33 1 1
activation-induced cell death of T cells 0.005 0.078 0.31 13 -10000 0 13
KPNB1 0.021 0.004 -10000 0 -10000 0 0
KPNA2 0.024 0.032 0.33 4 -10000 0 4
XPO1 0.021 0.002 -10000 0 -10000 0 0
SFN 0.025 0.045 0.33 7 -0.33 1 8
MAP3K8 0.012 0.024 -10000 0 -0.33 1 1
NFAT4/CK1 alpha 0.007 0.026 -10000 0 -0.17 2 2
MEF2D/NFAT1/Cbp/p300 -0.017 0.1 -10000 0 -0.23 59 59
CABIN1 -0.019 0.085 0.18 1 -0.32 15 16
CALM1 0.012 0.017 -10000 0 -10000 0 0
RAN 0.022 0.022 0.33 2 -10000 0 2
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
CAMK4 0.018 0.035 0.33 1 -0.33 3 4
mol:Ca2+ -0.002 0.005 -10000 0 -10000 0 0
MAPK3 0.021 0.003 -10000 0 -10000 0 0
YWHAH 0.021 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA 0.027 0.021 -10000 0 -0.23 2 2
YWHAB 0.02 0.005 -10000 0 -10000 0 0
MAPK8 0.013 0.017 -10000 0 -10000 0 0
MAPK9 0.02 0.005 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
FKBP1A 0.02 0.005 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.017 0.11 0.33 2 -0.39 16 18
PRKCH 0.02 0.004 -10000 0 -10000 0 0
CABIN1/Cbp/p300 0.017 0.028 -10000 0 -10000 0 0
CASP3 0.013 0.016 -10000 0 -10000 0 0
PIM1 0.02 0.004 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0.009 0.011 -10000 0 -10000 0 0
apoptosis 0.011 0.017 0.15 1 -10000 0 1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 -0.001 0.037 -10000 0 -0.26 1 1
PRKCB 0.013 0.052 -10000 0 -0.33 9 9
PRKCE 0.018 0.031 -10000 0 -0.33 3 3
JNK2/NFAT4 0.015 0.038 -10000 0 -0.28 2 2
BAD/BCL-XL 0.029 0.009 -10000 0 -10000 0 0
PRKCD 0.021 0.004 -10000 0 -10000 0 0
NUP214 0.02 0.004 -10000 0 -10000 0 0
PRKCZ 0.01 0.034 -10000 0 -0.33 3 3
PRKCA 0.019 0.025 -10000 0 -0.33 2 2
PRKCG 0.039 0.076 0.33 25 -10000 0 25
PRKCQ -0.022 0.11 -10000 0 -0.33 47 47
FKBP38/BCL2 0.027 0.02 0.24 1 -0.23 1 2
EP300 0.011 0.02 -10000 0 -10000 0 0
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.02 0.005 -10000 0 -10000 0 0
NFATc/JNK1 -0.01 0.1 0.38 1 -0.37 14 15
CaM/Ca2+/FKBP38 0.016 0.024 -10000 0 -0.2 1 1
FKBP12/FK506 0.015 0.004 -10000 0 -10000 0 0
CSNK1A1 -0.016 0.008 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0.016 0.03 0.21 1 -0.19 3 4
NFATc/ERK1 -0.007 0.1 0.38 1 -0.38 13 14
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV 0.001 0.089 -10000 0 -0.3 15 15
NR4A1 -0.058 0.15 0.23 4 -0.36 68 72
GSK3B 0.013 0.017 -10000 0 -10000 0 0
positive T cell selection 0.006 0.023 -10000 0 -0.3 2 2
NFAT1/CK1 alpha -0.011 0.043 0.12 1 -0.2 8 9
RCH1/ KPNB1 0.032 0.022 0.24 4 -10000 0 4
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
PRKACA 0.012 0.016 -10000 0 -10000 0 0
AKAP5 0.019 0.025 -10000 0 -0.33 2 2
MEF2D 0.01 0.019 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.018 0.007 -10000 0 -10000 0 0
NFATc/p38 alpha -0.014 0.098 -10000 0 -0.37 14 14
CREBBP 0.011 0.02 -10000 0 -10000 0 0
BCL2 0.02 0.017 0.33 1 -10000 0 1
Signaling events mediated by HDAC Class I

Figure 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
NF kappa B/RelA 0.025 0.074 0.23 1 -0.25 19 20
Ran/GTP/Exportin 1/HDAC1 -0.018 0.006 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.004 0.073 -10000 0 -0.28 17 17
SUMO1 0.021 0.003 -10000 0 -10000 0 0
ZFPM1 0.021 0.017 0.33 1 -10000 0 1
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
FKBP3 0.02 0.005 -10000 0 -10000 0 0
Histones 0.031 0.06 -10000 0 -0.3 3 3
YY1/LSF 0.014 0.043 -10000 0 -0.24 4 4
SMG5 0.018 0.008 -10000 0 -10000 0 0
RAN 0.022 0.022 0.33 2 -10000 0 2
I kappa B alpha/HDAC3 0.003 0.041 -10000 0 -0.2 14 14
I kappa B alpha/HDAC1 0.011 0.045 -10000 0 -0.32 1 1
SAP18 0.02 0.006 -10000 0 -10000 0 0
RELA 0.003 0.055 -10000 0 -0.21 16 16
HDAC1/Smad7 0.036 0.02 -10000 0 -0.2 1 1
RANGAP1 0.021 0.004 -10000 0 -10000 0 0
HDAC3/TR2 0.012 0.055 -10000 0 -0.32 3 3
NuRD/MBD3 Complex -0.009 0.059 -10000 0 -0.3 9 9
NF kappa B1 p50/RelA 0.01 0.074 -10000 0 -0.3 11 11
EntrezGene:23225 0 0 -10000 0 -10000 0 0
GATA2 -0.01 0.1 -10000 0 -0.33 35 35
GATA1 -0.016 0.1 -10000 0 -0.33 40 40
Mad/Max 0.03 0.007 -10000 0 -10000 0 0
NuRD/MBD3 Complex/GATA1/Fog1 -0.022 0.094 -10000 0 -0.31 20 20
RBBP7 0.02 0.004 -10000 0 -10000 0 0
NPC 0.012 0.001 -10000 0 -10000 0 0
RBBP4 0.021 0.003 -10000 0 -10000 0 0
MAX 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NFKBIA 0.004 0.029 -10000 0 -10000 0 0
KAT2B 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
SIN3/HDAC complex -0.012 0.055 -10000 0 -0.37 3 3
SIN3 complex 0.046 0.02 -10000 0 -10000 0 0
SMURF1 0.02 0.005 -10000 0 -10000 0 0
CHD3 0.019 0.006 -10000 0 -10000 0 0
SAP30 0.021 0.004 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
NCOR1 0.02 0.006 -10000 0 -10000 0 0
YY1/HDAC3 0.003 0.05 -10000 0 -0.29 6 6
YY1/HDAC2 0.014 0.04 -10000 0 -0.24 4 4
YY1/HDAC1 0.014 0.042 -10000 0 -0.24 4 4
NuRD/MBD2 Complex (MeCP1) -0.011 0.062 -10000 0 -0.33 8 8
PPARG -0.028 0.12 -10000 0 -0.3 51 51
HDAC8/hEST1B 0.034 0.018 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.012 0.055 -10000 0 -0.32 3 3
MBD3L2 0.017 0.005 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.035 0.02 -10000 0 -0.2 1 1
CREBBP 0.021 0.004 -10000 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex -0.005 0.085 -10000 0 -0.31 20 20
HDAC1 0.021 0.003 -10000 0 -10000 0 0
HDAC3 0.003 0.038 -10000 0 -0.34 2 2
HDAC2 0.019 0.006 -10000 0 -10000 0 0
YY1 0.007 0.003 -10000 0 -10000 0 0
HDAC8 0.021 0.003 -10000 0 -10000 0 0
SMAD7 0.018 0.019 -10000 0 -0.33 1 1
NCOR2 0.021 0.004 -10000 0 -10000 0 0
MXD1 0.021 0.002 -10000 0 -10000 0 0
STAT3 0.01 0.003 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
YY1/LSF/HDAC1 0.025 0.043 -10000 0 -0.22 4 4
YY1/SAP30/HDAC1 0.024 0.043 -10000 0 -0.22 4 4
EP300 0.021 0.004 -10000 0 -10000 0 0
STAT3 (dimer non-phopshorylated) 0.01 0.003 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.004 0.029 -10000 0 -10000 0 0
histone deacetylation -0.003 0.067 -10000 0 -0.33 8 8
STAT3 (dimer non-phopshorylated)/HDAC3 0.003 0.043 -10000 0 -0.23 7 7
nuclear export -0.034 0.017 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GATAD2B 0.018 0.008 -10000 0 -10000 0 0
GATAD2A 0.02 0.005 -10000 0 -10000 0 0
GATA2/HDAC3 -0.003 0.074 -10000 0 -0.28 8 8
GATA1/HDAC1 0.003 0.079 -10000 0 -0.23 40 40
GATA1/HDAC3 -0.006 0.077 -10000 0 -0.31 7 7
CHD4 0.02 0.005 -10000 0 -10000 0 0
TNF-alpha/TNFR1A 0.017 0.056 0.24 1 -0.23 18 19
SIN3/HDAC complex/Mad/Max -0.012 0.06 -10000 0 -0.3 8 8
NuRD Complex -0.007 0.08 -10000 0 -0.3 16 16
positive regulation of chromatin silencing 0.029 0.059 -10000 0 -0.3 3 3
SIN3B 0.02 0.005 -10000 0 -10000 0 0
MTA2 0.021 0.003 -10000 0 -10000 0 0
SIN3A 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC1 0.029 0.026 -10000 0 -0.18 2 2
HDAC complex 0.047 0.019 -10000 0 -10000 0 0
GATA1/Fog1 0.002 0.078 -10000 0 -0.23 40 40
FKBP25/HDAC1/HDAC2 0.037 0.015 -10000 0 -10000 0 0
TNF 0.004 0.077 0.33 1 -0.33 19 20
negative regulation of cell growth -0.01 0.061 -10000 0 -0.3 8 8
NuRD/MBD2/PRMT5 Complex -0.011 0.062 -10000 0 -0.33 8 8
Ran/GTP/Exportin 1 0.029 0.027 0.2 1 -0.18 2 3
NF kappa B/RelA/I kappa B alpha -0.006 0.064 -10000 0 -0.28 16 16
SIN3/HDAC complex/NCoR1 -0.014 0.072 -10000 0 -0.3 14 14
TFCP2 0.021 0.003 -10000 0 -10000 0 0
NR2C1 0.021 0.003 -10000 0 -10000 0 0
MBD3 0.018 0.025 -10000 0 -0.33 2 2
MBD2 0.019 0.007 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

Figure 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
EEF2K -0.018 0.007 -10000 0 -10000 0 0
SNTA1 0.022 0.023 0.33 2 -10000 0 2
response to hypoxia 0 0 -10000 0 -10000 0 0
STMN1 -0.016 0.032 0.3 3 -10000 0 3
MAPK12 -0.009 0.021 0.18 2 -0.17 2 4
CCND1 -0.001 0.054 -10000 0 -0.38 7 7
p38 gamma/SNTA1 -0.009 0.047 0.18 14 -0.28 1 15
MAP2K3 0.02 0.006 -10000 0 -10000 0 0
PKN1 0.02 0.005 -10000 0 -10000 0 0
G2/M transition checkpoint -0.004 0.037 0.19 11 -0.17 2 13
MAP2K6 -0.004 0.024 0.22 2 -0.18 2 4
MAPT -0.009 0.074 0.21 10 -0.25 20 30
MAPK13 -0.016 0.006 -10000 0 -10000 0 0
hyperosmotic response 0 0 -10000 0 -10000 0 0
ZAK 0.007 0.002 -10000 0 -10000 0 0
E-cadherin signaling in the nascent adherens junction

Figure 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
CTTN -0.004 0.066 -10000 0 -0.31 16 16
KLHL20 0 0.051 0.16 1 -0.21 8 9
CYFIP2 0.015 0.043 -10000 0 -0.33 6 6
Rac1/GDP -0.01 0.061 0.32 3 -0.26 7 10
ENAH -0.004 0.066 -10000 0 -0.32 15 15
AP1M1 0.02 0.005 -10000 0 -10000 0 0
RAP1B 0.02 0.005 -10000 0 -10000 0 0
RAP1A 0.02 0.004 -10000 0 -10000 0 0
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
CDC42/GTP -0.026 0.027 -10000 0 -10000 0 0
ABI1/Sra1/Nap1 -0.015 0.025 -10000 0 -0.14 10 10
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin 0.045 0.028 -10000 0 -0.18 3 3
RAPGEF1 -0.008 0.057 0.2 2 -0.28 11 13
CTNND1 0.021 0.003 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.006 0.07 -10000 0 -0.32 17 17
CRK -0.011 0.056 -10000 0 -0.31 12 12
E-cadherin/gamma catenin/alpha catenin 0.039 0.021 -10000 0 -0.2 2 2
alphaE/beta7 Integrin 0.027 0.017 -10000 0 -0.23 1 1
IQGAP1 0.021 0.003 -10000 0 -10000 0 0
NCKAP1 0.021 0.002 -10000 0 -10000 0 0
Rap1/GTP/I-afadin 0.034 0.016 -10000 0 -10000 0 0
DLG1 -0.002 0.062 -10000 0 -0.32 13 13
ChemicalAbstracts:7440-70-2 0 0 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.026 0.016 -10000 0 -0.13 2 2
MLLT4 0.019 0.006 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.051 0.059 0.22 38 -0.17 4 42
PI3K -0.032 0.02 -10000 0 -0.17 2 2
ARF6 0.02 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
E-cadherin/gamma catenin 0.029 0.02 -10000 0 -0.23 2 2
TIAM1 0.016 0.039 -10000 0 -0.33 5 5
E-cadherin(dimer)/Ca2+ 0.045 0.021 -10000 0 -0.17 2 2
AKT1 -0.017 0.026 -10000 0 -10000 0 0
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
CDH1 0.019 0.025 -10000 0 -0.33 2 2
RhoA/GDP -0.01 0.065 0.29 4 -0.25 7 11
actin cytoskeleton organization 0.003 0.044 0.15 7 -0.15 8 15
CDC42/GDP -0.011 0.064 0.32 3 -0.26 7 10
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.008 0.019 -10000 0 -0.18 4 4
ITGB7 0.02 0.018 -10000 0 -0.33 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin 0.049 0.023 -10000 0 -0.18 2 2
E-cadherin/Ca2+/beta catenin/alpha catenin 0.034 0.018 -10000 0 -0.17 2 2
mol:GDP -0.01 0.07 0.3 4 -0.28 8 12
CDC42/GTP/IQGAP1 0.027 0.007 -10000 0 -10000 0 0
JUP 0.021 0.003 -10000 0 -10000 0 0
p120 catenin/RhoA/GDP -0.011 0.058 0.2 1 -0.25 5 6
RAC1/GTP/IQGAP1 0.025 0.01 -10000 0 -10000 0 0
PIP5K1C/AP1M1 0.029 0.008 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
CDC42 0.021 0.004 -10000 0 -10000 0 0
CTNNA1 0.021 0.004 -10000 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.005 0.038 0.14 10 -0.15 5 15
NME1 0.055 0.097 0.33 43 -10000 0 43
clathrin coat assembly 0 0 -10000 0 -10000 0 0
TJP1 0 0.056 -10000 0 -0.31 11 11
regulation of cell-cell adhesion -0.026 0.018 -10000 0 -0.15 2 2
WASF2 -0.003 0.024 -10000 0 -0.089 1 1
Rap1/GTP -0.024 0.031 -10000 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin 0.05 0.033 -10000 0 -0.18 3 3
CCND1 0.004 0.044 0.15 9 -0.17 6 15
VAV2 -0.005 0.12 -10000 0 -0.58 12 12
RAP1/GDP -0.019 0.046 0.19 1 -0.22 5 6
adherens junction assembly -0.002 0.059 -10000 0 -0.3 13 13
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
ABI1 0.021 0.004 -10000 0 -10000 0 0
PIP5K1C 0.02 0.005 -10000 0 -10000 0 0
regulation of heterotypic cell-cell adhesion 0.034 0.028 -10000 0 -0.18 3 3
E-cadherin/beta catenin 0.004 0.022 -10000 0 -0.28 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
SRC -0.005 0.068 -10000 0 -0.31 17 17
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
Rac1/GTP -0.004 0.063 -10000 0 -0.32 11 11
E-cadherin/beta catenin/alpha catenin 0.039 0.021 -10000 0 -0.2 2 2
ITGAE 0.019 0.006 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin 0.002 0.07 -10000 0 -0.32 17 17
Regulation of Telomerase

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
Telomerase catalytic core complex 0.092 0.16 0.45 9 -10000 0 9
RAD9A 0.021 0.004 -10000 0 -10000 0 0
AP1 0.017 0.07 -10000 0 -0.22 29 29
IFNAR2 0.027 0.014 -10000 0 -10000 0 0
AKT1 0.02 0.036 -10000 0 -0.35 1 1
ER alpha/Oestrogen 0.019 0.048 0.23 10 -0.22 8 18
NFX1/SIN3/HDAC complex 0.008 0.055 -10000 0 -0.3 6 6
EGF 0.077 0.13 0.33 72 -0.32 4 76
SMG5 0.018 0.008 -10000 0 -10000 0 0
SMG6 0.019 0.006 -10000 0 -10000 0 0
SP3/HDAC2 0.038 0.024 -10000 0 -10000 0 0
TERT/c-Abl 0.086 0.14 0.41 8 -10000 0 8
SAP18 0.021 0.007 -10000 0 -10000 0 0
MRN complex 0.035 0.017 -10000 0 -10000 0 0
WT1 0.014 0.094 0.35 8 -0.32 21 29
WRN 0.018 0.008 -10000 0 -10000 0 0
SP1 0.03 0.018 -10000 0 -10000 0 0
SP3 0.024 0.008 -10000 0 -10000 0 0
TERF2IP 0.02 0.004 -10000 0 -10000 0 0
Telomerase/Nucleolin 0.05 0.1 -10000 0 -10000 0 0
Mad/Max 0.038 0.016 -10000 0 -10000 0 0
TERT 0.093 0.16 0.47 7 -10000 0 7
CCND1 0.082 0.18 0.5 7 -0.89 5 12
MAX 0.024 0.008 -10000 0 -10000 0 0
RBBP7 0.021 0.006 -10000 0 -10000 0 0
RBBP4 0.022 0.004 -10000 0 -10000 0 0
TERF2 -0.018 0.014 -10000 0 -10000 0 0
PTGES3 0.021 0.004 -10000 0 -10000 0 0
SIN3A 0.022 0.005 -10000 0 -10000 0 0
Telomerase/911 0.052 0.062 0.22 2 -0.31 1 3
CDKN1B 0.002 0.04 0.22 2 -0.2 2 4
RAD1 0.017 0.008 -10000 0 -10000 0 0
XRCC5 0.021 0.002 -10000 0 -10000 0 0
XRCC6 0.021 0.004 -10000 0 -10000 0 0
SAP30 0.022 0.006 -10000 0 -10000 0 0
TRF2/PARP2 0.028 0.011 -10000 0 -10000 0 0
UBE3A 0.023 0.008 -10000 0 -10000 0 0
JUN 0.022 0.026 -10000 0 -0.32 2 2
E6 0.003 0.005 -10000 0 -10000 0 0
HPV-16 E6/E6AP 0.021 0.013 -10000 0 -10000 0 0
FOS -0.002 0.09 -10000 0 -0.32 28 28
IFN-gamma/IRF1 0.051 0.062 0.25 29 -0.23 2 31
PARP2 0.02 0.005 -10000 0 -10000 0 0
BLM 0.052 0.094 0.33 40 -10000 0 40
Telomerase 0.031 0.078 0.23 7 -0.41 3 10
IRF1 0.024 0.008 -10000 0 -10000 0 0
ESR1 0.022 0.07 0.33 10 -0.32 8 18
KU/TER 0.031 0.006 -10000 0 -10000 0 0
ATM/TRF2 0.028 0.014 -10000 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.009 0.052 -10000 0 -0.27 5 5
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.009 0.053 -10000 0 -0.28 5 5
HDAC1 0.022 0.003 -10000 0 -10000 0 0
HDAC2 0.027 0.017 -10000 0 -10000 0 0
ATM 0.009 0.008 -10000 0 -10000 0 0
SMAD3 -0.021 0.009 -10000 0 -10000 0 0
ABL1 0.021 0.004 -10000 0 -10000 0 0
MXD1 0.024 0.007 -10000 0 -10000 0 0
MRE11A 0.02 0.005 -10000 0 -10000 0 0
HUS1 0.019 0.006 -10000 0 -10000 0 0
RPS6KB1 0.02 0.004 -10000 0 -10000 0 0
TERT/NF kappa B1/14-3-3 0.089 0.14 0.42 5 -10000 0 5
NR2F2 0.006 0.026 -10000 0 -10000 0 0
MAPK3 -0.006 0.02 -10000 0 -10000 0 0
MAPK1 -0.007 0.019 -10000 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.009 0.02 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
HNRNPC 0.02 0.005 -10000 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0.009 0.008 -10000 0 -10000 0 0
NBN 0.019 0.007 -10000 0 -10000 0 0
EGFR 0.017 0.043 0.34 1 -0.32 5 6
mol:Oestrogen 0.002 0.003 -10000 0 -10000 0 0
EGF/EGFR 0.059 0.09 0.25 59 -0.23 8 67
MYC 0.018 0.027 -10000 0 -0.32 2 2
IL2 0.029 0.018 -10000 0 -10000 0 0
KU 0.031 0.006 -10000 0 -10000 0 0
RAD50 0.02 0.005 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
TGFB1 0.009 0.02 -10000 0 -10000 0 0
TRF2/BLM 0.047 0.059 0.23 37 -10000 0 37
FRAP1 0 0 -10000 0 -10000 0 0
KU/TERT 0.096 0.14 0.43 6 -10000 0 6
SP1/HDAC2 0.045 0.035 -10000 0 -10000 0 0
PINX1 0.018 0.008 -10000 0 -10000 0 0
Telomerase/EST1A 0.046 0.1 -10000 0 -10000 0 0
Smad3/Myc -0.019 0.016 -10000 0 -0.18 2 2
911 complex 0.032 0.019 -10000 0 -10000 0 0
IFNG 0.045 0.086 0.34 29 -0.33 2 31
Telomerase/PinX1 0.04 0.098 -10000 0 -10000 0 0
Telomerase/AKT1/mTOR/p70S6K 0.047 0.088 0.31 5 -0.41 3 8
SIN3B 0.021 0.007 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Telomerase/EST1B 0.042 0.095 -10000 0 -10000 0 0
response to DNA damage stimulus 0.002 0.018 -10000 0 -10000 0 0
MRN complex/TRF2/Rap1 0.047 0.027 -10000 0 -10000 0 0
TRF2/WRN 0.025 0.012 -10000 0 -10000 0 0
Telomerase/hnRNP C1/C2 0.049 0.1 -10000 0 -10000 0 0
E2F1 0.03 0.034 0.33 4 -10000 0 4
ZNFX1 0.021 0.006 -10000 0 -10000 0 0
PIF1 0.057 0.1 0.33 46 -10000 0 46
NCL 0.021 0.003 -10000 0 -10000 0 0
DKC1 0.02 0.004 -10000 0 -10000 0 0
telomeric DNA binding 0 0 -10000 0 -10000 0 0
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0.013 0.011 -10000 0 -10000 0 0
TRAF2/ASK1 0.025 0.009 -10000 0 -10000 0 0
ATM 0.02 0.004 -10000 0 -10000 0 0
MAP2K3 -0.008 0.093 0.29 2 -0.33 16 18
response to stress 0 0 -10000 0 -10000 0 0
MAP2K6 -0.004 0.083 0.28 2 -0.34 10 12
hyperosmotic response 0 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
GADD45G 0.019 0.035 0.33 1 -0.33 3 4
TXN 0.004 0.012 0.17 2 -10000 0 2
CALM1 0.02 0.004 -10000 0 -10000 0 0
GADD45A 0.021 0.004 -10000 0 -10000 0 0
GADD45B 0.018 0.025 -10000 0 -0.33 2 2
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
MAP3K6 0.021 0.003 -10000 0 -10000 0 0
MAP3K7 0.019 0.006 -10000 0 -10000 0 0
MAP3K4 0.019 0.006 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
ASK1/ASK2 0.028 0.01 -10000 0 -10000 0 0
TAK1/TAB family 0.001 0.019 0.13 2 -0.13 1 3
RAC1/OSM/MEKK3 0.034 0.018 -10000 0 -0.16 1 1
TRAF2 0.021 0.004 -10000 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 0.001 0.076 -10000 0 -0.3 11 11
TRAF6 0.004 0.001 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
mol:LPS 0 0 -10000 0 -10000 0 0
CAMK2B 0.061 0.11 0.33 53 -10000 0 53
CCM2 0.019 0.006 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB 0.049 0.064 0.21 51 -10000 0 51
MAPK11 0.018 0.025 -10000 0 -0.33 2 2
response to DNA damage stimulus 0 0 -10000 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 0.053 0.062 0.22 46 -10000 0 46
OSM/MEKK3 0.027 0.017 -10000 0 -0.23 1 1
TAOK1 0.007 0.002 -10000 0 -10000 0 0
TAOK2 0.007 0.002 -10000 0 -10000 0 0
TAOK3 0.007 0.002 -10000 0 -10000 0 0
MAP3K7IP1 0 0 -10000 0 -10000 0 0
MAPK14 0.02 0.004 -10000 0 -10000 0 0
MAP3K7IP2 0 0 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
MAP3K10 0.017 0.031 -10000 0 -0.33 3 3
MAP3K3 0.019 0.018 -10000 0 -0.33 1 1
TRX/ASK1 0.015 0.019 0.16 1 -0.1 7 8
GADD45/MTK1/MTK1 0.04 0.034 0.21 1 -0.21 4 5
Arf6 downstream pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLAUR 0.011 0.017 -10000 0 -10000 0 0
regulation of axonogenesis 0.003 0.018 0.25 2 -10000 0 2
myoblast fusion -0.009 0.027 0.32 1 -10000 0 1
mol:GTP 0.015 0.019 -10000 0 -0.16 4 4
regulation of calcium-dependent cell-cell adhesion -0.05 0.063 0.2 4 -0.22 38 42
ARF1/GTP 0.024 0.02 -10000 0 -0.12 2 2
mol:GM1 0.005 0.013 -10000 0 -0.12 3 3
mol:Choline -0.01 0.01 -10000 0 -10000 0 0
lamellipodium assembly 0.002 0.038 -10000 0 -0.38 3 3
MAPK3 0.011 0.013 -10000 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 0.051 0.064 0.22 38 -0.2 4 42
ARF1 0.02 0.006 -10000 0 -10000 0 0
ARF6/GDP 0.009 0.027 -10000 0 -0.32 1 1
ARF1/GDP 0.012 0.032 -10000 0 -0.23 3 3
ARF6 0.026 0.009 -10000 0 -10000 0 0
RAB11A 0.021 0.003 -10000 0 -10000 0 0
TIAM1 0.015 0.04 -10000 0 -0.32 5 5
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.012 0.011 -10000 0 -10000 0 0
actin filament bundle formation -0.015 0.033 0.23 3 -10000 0 3
KALRN 0.002 0.022 -10000 0 -0.21 3 3
RAB11FIP3/RAB11A 0.03 0.007 -10000 0 -10000 0 0
RhoA/GDP 0.015 0.033 -10000 0 -0.23 3 3
NME1 0.054 0.098 0.33 43 -10000 0 43
Rac1/GDP 0.013 0.032 -10000 0 -0.23 3 3
substrate adhesion-dependent cell spreading 0.015 0.019 -10000 0 -0.16 4 4
cortical actin cytoskeleton organization 0.003 0.038 -10000 0 -0.38 3 3
RAC1 0.019 0.007 -10000 0 -10000 0 0
liver development 0.015 0.019 -10000 0 -0.16 4 4
ARF6/GTP 0.015 0.019 -10000 0 -0.16 4 4
RhoA/GTP 0.025 0.02 -10000 0 -10000 0 0
mol:GDP 0.004 0.019 -10000 0 -0.21 2 2
ARF6/GTP/RAB11FIP3/RAB11A 0.037 0.021 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
PLD1 0.009 0.015 -10000 0 -10000 0 0
RAB11FIP3 0.021 0.004 -10000 0 -10000 0 0
tube morphogenesis 0.002 0.038 -10000 0 -0.38 3 3
ruffle organization -0.003 0.018 -10000 0 -0.25 2 2
regulation of epithelial cell migration 0.015 0.019 -10000 0 -0.16 4 4
PLD2 0.009 0.013 -10000 0 -10000 0 0
PIP5K1A -0.003 0.018 -10000 0 -0.25 2 2
mol:Phosphatidic acid -0.01 0.01 -10000 0 -10000 0 0
Rac1/GTP 0.003 0.038 -10000 0 -0.38 3 3
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.001 0.064 -10000 0 -0.5 1 1
UGCG 0 0.1 -10000 0 -0.62 10 10
AKT1/mTOR/p70S6K/Hsp90/TERT 0.051 0.086 0.28 7 -0.4 3 10
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.001 0.1 -10000 0 -0.62 10 10
mol:DAG 0.003 0.083 -10000 0 -0.78 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 0.024 0.081 0.28 2 -0.41 5 7
FRAP1 0.018 0.09 0.31 2 -0.46 5 7
FOXO3 0.013 0.086 0.31 1 -0.46 5 6
AKT1 0.016 0.091 0.32 1 -0.47 6 7
GAB2 0.017 0.035 -10000 0 -0.33 4 4
SMPD1 0.005 0.084 -10000 0 -0.6 7 7
SGMS1 0.01 0.061 -10000 0 -0.56 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP -0.012 0.004 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
cell proliferation 0.025 0.086 0.27 2 -0.36 10 12
EIF3A 0.021 0.002 -10000 0 -10000 0 0
PI3K 0.03 0.01 -10000 0 -10000 0 0
RPS6KB1 0.013 0.066 -10000 0 -0.84 2 2
mol:sphingomyelin 0.003 0.083 -10000 0 -0.78 4 4
natural killer cell activation 0 0.001 -10000 0 -10000 0 0
JAK3 0.02 0.006 -10000 0 -10000 0 0
PIK3R1 0.02 0.006 -10000 0 -10000 0 0
JAK1 0.021 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
MYC 0.04 0.12 0.4 3 -0.78 3 6
MYB 0.005 0.1 -10000 0 -0.97 3 3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.015 0.074 -10000 0 -0.38 5 5
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.033 0.064 -10000 0 -0.77 2 2
mol:PI-3-4-5-P3 0.015 0.073 -10000 0 -0.37 5 5
Rac1/GDP -0.014 0.008 -10000 0 -10000 0 0
T cell proliferation 0.011 0.07 -10000 0 -0.36 3 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.001 0.009 0.089 3 -0.066 2 5
PRKCZ 0.011 0.069 -10000 0 -0.37 2 2
NF kappa B1 p50/RelA 0.034 0.087 0.3 2 -0.42 5 7
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K -0.001 0.054 -10000 0 -0.38 4 4
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
IL2RA 0.043 0.085 0.33 30 -0.33 1 31
IL2RB 0.019 0.025 -10000 0 -0.33 2 2
TERT 0.07 0.12 0.33 69 -10000 0 69
E2F1 0.012 0.078 0.24 2 -0.46 8 10
SOS1 0.021 0.004 -10000 0 -10000 0 0
RPS6 0.019 0.006 -10000 0 -10000 0 0
mol:cAMP -0.001 0.005 0.031 2 -0.048 3 5
PTPN11 0.021 0.004 -10000 0 -10000 0 0
IL2RG 0.018 0.035 -10000 0 -0.33 4 4
actin cytoskeleton organization 0.011 0.07 -10000 0 -0.36 3 3
GRB2 0.02 0.006 -10000 0 -10000 0 0
IL2 0.02 0.005 -10000 0 -10000 0 0
PIK3CA 0.021 0.005 -10000 0 -10000 0 0
Rac1/GTP 0.032 0.018 -10000 0 -10000 0 0
LCK 0.021 0.024 0.33 1 -0.33 1 2
BCL2 0.017 0.08 0.47 1 -0.4 3 4
TCGA08_rtk_signaling

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
PDGFRA 0.017 0.035 -10000 0 -0.33 4 4
HRAS 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.043 0.33 1 -0.33 5 6
AKT 0.03 0.066 0.24 9 -0.21 3 12
FOXO3 0.019 0.006 -10000 0 -10000 0 0
AKT1 0.02 0.005 -10000 0 -10000 0 0
FOXO1 0.02 0.005 -10000 0 -10000 0 0
AKT3 0.018 0.025 -10000 0 -0.33 2 2
FOXO4 0.021 0.002 -10000 0 -10000 0 0
MET 0.012 0.072 0.33 5 -0.33 13 18
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PIK3CB 0.021 0.003 -10000 0 -10000 0 0
NRAS 0.02 0.005 -10000 0 -10000 0 0
PIK3CG 0.012 0.052 -10000 0 -0.33 9 9
PIK3R3 0.02 0.018 -10000 0 -0.33 1 1
PIK3R2 0.02 0.005 -10000 0 -10000 0 0
NF1 0.021 0.003 -10000 0 -10000 0 0
RAS 0.017 0.042 0.19 4 -0.12 12 16
ERBB2 0.021 0.004 -10000 0 -10000 0 0
proliferation/survival/translation -0.009 0.073 0.28 12 -10000 0 12
PI3K 0.021 0.061 0.21 19 -0.23 2 21
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
KRAS 0.02 0.006 -10000 0 -10000 0 0
FOXO 0.047 0.05 0.23 9 -10000 0 9
AKT2 0.02 0.005 -10000 0 -10000 0 0
PTEN 0.021 0.003 -10000 0 -10000 0 0
IGF1 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
NCK2 0.021 0.002 -10000 0 -10000 0 0
PTK2 0.018 0.007 -10000 0 -10000 0 0
CRKL -0.019 0.025 0.15 1 -0.2 5 6
GRB2/SOS1/SHC 0.035 0.017 -10000 0 -10000 0 0
HRAS 0.021 0.004 -10000 0 -10000 0 0
IRS1/Crk -0.019 0.024 0.11 1 -0.19 6 7
IGF-1R heterotetramer/IGF1/PTP1B 0.035 0.029 0.21 1 -0.19 4 5
AKT1 -0.024 0.037 0.15 9 -0.24 1 10
BAD -0.027 0.036 0.14 9 -0.24 1 10
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.018 0.025 0.15 1 -0.2 5 6
IGF-1R heterotetramer/IGF1/IRS1/Shp2 0.018 0.031 0.19 2 -0.2 6 8
RAF1 -0.018 0.071 0.26 1 -0.39 11 12
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos 0.041 0.036 0.2 1 -0.2 4 5
YWHAZ 0.018 0.007 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 0.023 0.032 0.2 1 -0.21 6 7
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
RPS6KB1 -0.023 0.038 0.15 10 -0.24 1 11
GNB2L1 0.02 0.004 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.005 0.069 0.25 4 -0.29 8 12
PXN 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0.03 0.008 -10000 0 -10000 0 0
HRAS/GTP -0.024 0.017 0.091 1 -0.17 1 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc 0.047 0.033 -10000 0 -0.16 1 1
IGF-1R heterotetramer 0.019 0.023 -10000 0 -0.34 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck 0.032 0.036 0.2 1 -0.2 6 7
Crk/p130 Cas/Paxillin 0.036 0.038 -10000 0 -0.18 7 7
IGF1R 0.019 0.023 -10000 0 -0.34 1 1
IGF1 0.017 0.046 0.34 1 -0.35 5 6
IRS2/Crk -0.021 0.026 0.14 1 -0.19 6 7
PI3K 0.039 0.039 0.2 1 -0.19 6 7
apoptosis 0.023 0.041 0.21 1 -0.27 1 2
HRAS/GDP 0.015 0.003 -10000 0 -10000 0 0
PRKCD -0.004 0.041 -10000 0 -0.25 6 6
RAF1/14-3-3 E -0.01 0.076 0.27 4 -0.34 11 15
BAD/14-3-3 -0.024 0.042 0.28 1 -0.23 1 2
PRKCZ -0.025 0.041 0.15 10 -0.24 1 11
Crk/p130 Cas/Paxillin/FAK1 -0.032 0.031 -10000 0 -0.22 1 1
PTPN1 0.02 0.005 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.001 0.044 -10000 0 -0.27 5 5
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
IGF-1R heterotetramer/IGF1/SHC/GRB10 0.037 0.033 0.21 1 -0.17 3 4
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.021 0.003 -10000 0 -10000 0 0
IRS1/NCK2 0.017 0.033 -10000 0 -0.2 6 6
GRB10 0.019 0.007 -10000 0 -10000 0 0
PTPN11 -0.019 0.026 0.15 1 -0.2 6 7
IRS1 -0.015 0.031 0.12 6 -0.21 6 12
IRS2 -0.019 0.026 0.15 1 -0.2 6 7
IGF-1R heterotetramer/IGF1 0.026 0.038 0.23 1 -0.26 6 7
GRB2 0.02 0.004 -10000 0 -10000 0 0
PDPK1 -0.021 0.04 0.16 10 -0.19 5 15
YWHAE 0.019 0.006 -10000 0 -10000 0 0
PRKD1 -0.008 0.046 -10000 0 -0.32 3 3
SHC1 0.018 0.008 -10000 0 -10000 0 0
E-cadherin signaling in keratinocytes

Figure 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
keratinocyte differentiation -0.005 0.043 0.29 2 -0.27 3 5
adherens junction organization -0.005 0.048 -10000 0 -0.28 7 7
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.014 0.048 0.22 1 -0.22 1 2
FMN1 -0.011 0.049 -10000 0 -0.25 9 9
mol:IP3 -0.013 0.025 -10000 0 -0.2 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.002 0.05 -10000 0 -0.24 11 11
CTNNB1 0.021 0.004 -10000 0 -10000 0 0
AKT1 -0.013 0.035 0.23 1 -0.22 3 4
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0 0.092 -10000 0 -0.44 11 11
CTNND1 0.02 0.007 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.008 0.04 -10000 0 -0.24 8 8
VASP -0.005 0.039 -10000 0 -0.28 5 5
ZYX -0.008 0.044 -10000 0 -0.24 9 9
JUB -0.001 0.047 -10000 0 -0.23 11 11
EGFR(dimer) 0.008 0.056 0.2 2 -0.24 11 13
E-cadherin/beta catenin-gamma catenin 0.039 0.02 -10000 0 -0.18 2 2
mol:PI-3-4-5-P3 0.022 0.046 0.25 1 -0.22 3 4
PIK3CA 0.019 0.009 -10000 0 -10000 0 0
PI3K 0.022 0.047 0.25 1 -0.23 3 4
FYN -0.014 0.059 0.28 2 -0.26 5 7
mol:Ca2+ -0.012 0.025 -10000 0 -0.2 1 1
JUP 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.007 -10000 0 -10000 0 0
mol:DAG -0.013 0.025 -10000 0 -0.2 1 1
CDH1 0.019 0.025 -10000 0 -0.33 2 2
RhoA/GDP -0.005 0.062 0.18 5 -0.2 1 6
establishment of polarity of embryonic epithelium -0.005 0.038 -10000 0 -0.27 5 5
SRC 0.02 0.004 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
RHOA 0.021 0.004 -10000 0 -10000 0 0
EGFR 0.015 0.043 0.33 1 -0.33 5 6
CASR -0.006 0.044 0.27 3 -0.19 1 4
RhoA/GTP 0.011 0.035 -10000 0 -0.18 2 2
AKT2 -0.012 0.034 0.23 1 -0.24 2 3
actin cable formation -0.013 0.043 -10000 0 -0.28 5 5
apoptosis -0.005 0.048 0.22 4 -0.27 5 9
CTNNA1 0.02 0.007 -10000 0 -10000 0 0
mol:GDP -0.014 0.038 0.17 4 -0.2 2 6
PIP5K1A -0.008 0.041 -10000 0 -0.25 8 8
PLCG1 -0.013 0.026 -10000 0 -0.2 1 1
Rac1/GTP 0.014 0.054 -10000 0 -0.23 10 10
homophilic cell adhesion -0.001 0.002 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0.047 0.022 -10000 0 -0.18 1 1
HDAC3 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.018 0.006 -10000 0 -10000 0 0
GATA1/HDAC4 0.004 0.078 -10000 0 -0.23 39 39
GATA1/HDAC5 0.003 0.078 -10000 0 -0.23 39 39
GATA2/HDAC5 0.007 0.074 -10000 0 -0.23 34 34
HDAC5/BCL6/BCoR 0.039 0.013 -10000 0 -10000 0 0
HDAC9 0.019 0.05 0.33 5 -0.33 4 9
Glucocorticoid receptor/Hsp90/HDAC6 0.039 0.013 -10000 0 -10000 0 0
HDAC4/ANKRA2 0.03 0.008 -10000 0 -10000 0 0
HDAC5/YWHAB 0.029 0.009 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.006 0.002 -10000 0 -10000 0 0
GATA2 -0.01 0.1 -10000 0 -0.33 35 35
HDAC4/RFXANK 0.029 0.009 -10000 0 -10000 0 0
BCOR 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
HDAC10 0.019 0.018 -10000 0 -0.33 1 1
HDAC5 0.021 0.004 -10000 0 -10000 0 0
GNB1/GNG2 0.028 0.016 -10000 0 -0.23 1 1
Histones 0.009 0.051 -10000 0 -0.26 4 4
ADRBK1 0.021 0.004 -10000 0 -10000 0 0
HDAC4 0.021 0.003 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
HDAC5/ANKRA2 0.03 0.008 -10000 0 -10000 0 0
HDAC4/Ubc9 0.03 0.007 -10000 0 -10000 0 0
HDAC7 0.021 0.003 -10000 0 -10000 0 0
HDAC5/14-3-3 E 0.028 0.01 -10000 0 -10000 0 0
TUBA1B 0.021 0.003 -10000 0 -10000 0 0
HDAC6 0.021 0.004 -10000 0 -10000 0 0
HDAC5/RFXANK 0.029 0.009 -10000 0 -10000 0 0
CAMK4 0.018 0.035 0.33 1 -0.33 3 4
Tubulin/HDAC6 0.043 0.028 0.23 7 -10000 0 7
SUMO1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
YWHAB 0.02 0.005 -10000 0 -10000 0 0
GATA1 -0.016 0.1 -10000 0 -0.33 40 40
EntrezGene:8021 0 0 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
NR3C1 0.021 0.004 -10000 0 -10000 0 0
SUMO1/HDAC4 0.029 0.024 -10000 0 -0.18 2 2
SRF 0.02 0.004 -10000 0 -10000 0 0
HDAC4/YWHAB 0.029 0.009 -10000 0 -10000 0 0
Tubulin 0.034 0.028 0.24 7 -10000 0 7
HDAC4/14-3-3 E 0.028 0.01 -10000 0 -10000 0 0
GNB1 0.02 0.004 -10000 0 -10000 0 0
RANGAP1 0.021 0.004 -10000 0 -10000 0 0
BCL6/BCoR 0.029 0.009 -10000 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0.04 0.012 -10000 0 -10000 0 0
HDAC4/SRF 0.037 0.027 0.23 1 -0.2 3 4
HDAC4/ER alpha 0.027 0.05 0.24 9 -0.23 8 17
EntrezGene:23225 0 0 -10000 0 -10000 0 0
positive regulation of chromatin silencing 0.009 0.051 -10000 0 -0.26 4 4
cell motility 0.043 0.027 0.22 7 -10000 0 7
EntrezGene:23636 0 0 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
HDAC7/HDAC3 0.03 0.008 -10000 0 -10000 0 0
BCL6 0.02 0.005 -10000 0 -10000 0 0
HDAC4/CaMK II delta B 0.021 0.003 -10000 0 -10000 0 0
Hsp90/HDAC6 0.029 0.009 -10000 0 -10000 0 0
ESR1 0.02 0.071 0.33 10 -0.33 8 18
HDAC6/HDAC11 0.03 0.007 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.029 0.027 0.2 1 -0.18 2 3
NPC 0.012 0.001 -10000 0 -10000 0 0
MEF2C 0.02 0.005 -10000 0 -10000 0 0
RAN 0.022 0.022 0.33 2 -10000 0 2
HDAC4/MEF2C 0.056 0.023 -10000 0 -10000 0 0
GNG2 0.019 0.018 -10000 0 -0.33 1 1
NCOR2 0.021 0.004 -10000 0 -10000 0 0
TUBB2A 0.026 0.041 0.33 7 -10000 0 7
HDAC11 0.021 0.004 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
ANKRA2 0.02 0.004 -10000 0 -10000 0 0
RFXANK 0.02 0.005 -10000 0 -10000 0 0
nuclear import -0.02 0.009 -10000 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification 0.045 0.057 0.42 4 -10000 0 4
CLOCK 0.022 0.005 -10000 0 -10000 0 0
TIMELESS/CRY2 0.026 0.033 -10000 0 -10000 0 0
DEC1/BMAL1 0.028 0.008 -10000 0 -10000 0 0
ATR 0.021 0.003 -10000 0 -10000 0 0
NR1D1 0.008 0.025 -10000 0 -10000 0 0
ARNTL 0.021 0.005 -10000 0 -10000 0 0
TIMELESS 0.01 0.039 0.38 2 -10000 0 2
NPAS2 0.023 0.022 0.33 2 -10000 0 2
CRY2 0.021 0.003 -10000 0 -10000 0 0
mol:CO -0.004 0.013 -10000 0 -0.11 6 6
CHEK1 0.04 0.076 0.33 25 -10000 0 25
mol:HEME 0.004 0.013 0.11 6 -10000 0 6
PER1 0.007 0.065 -10000 0 -0.33 14 14
BMAL/CLOCK/NPAS2 0.045 0.023 0.23 2 -10000 0 2
BMAL1/CLOCK 0.01 0.045 -10000 0 -10000 0 0
S phase of mitotic cell cycle 0.045 0.057 0.42 4 -10000 0 4
TIMELESS/CHEK1/ATR 0.046 0.058 0.42 4 -10000 0 4
mol:NADPH 0.004 0.013 0.11 6 -10000 0 6
PER1/TIMELESS 0.019 0.046 -10000 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -10000 0 -10000 0 0
DEC1 0.018 0.004 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.016 0.006 -10000 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.024 0.014 -10000 0 -10000 0 0
CDKN1B 0.006 0.048 -10000 0 -0.29 7 7
CDKN1A 0.007 0.052 -10000 0 -0.29 8 8
FRAP1 0 0 -10000 0 -10000 0 0
PRKDC 0.019 0.006 -10000 0 -10000 0 0
FOXO3 0.007 0.038 -10000 0 -0.29 4 4
AKT1 -0.001 0.043 -10000 0 -0.3 8 8
BAD 0.021 0.003 -10000 0 -10000 0 0
AKT3 0.006 0.013 -10000 0 -0.25 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
FOXO4 0.005 0.049 -10000 0 -0.29 8 8
AKT1/ASK1 0.023 0.059 -10000 0 -0.27 8 8
BAD/YWHAZ 0.035 0.018 -10000 0 -10000 0 0
RICTOR 0.017 0.009 -10000 0 -10000 0 0
RAF1 0.021 0.004 -10000 0 -10000 0 0
JNK cascade -0.022 0.056 0.27 8 -10000 0 8
TSC1 0.007 0.04 -10000 0 -0.29 5 5
YWHAZ 0.018 0.007 -10000 0 -10000 0 0
AKT1/RAF1 0.028 0.063 -10000 0 -0.29 8 8
EP300 0.021 0.004 -10000 0 -10000 0 0
mol:GDP 0 0.044 -10000 0 -0.3 8 8
mol:PI-3-4-5-P3 0 0 -10000 0 -10000 0 0
TSC2 0.003 0.047 -10000 0 -0.29 8 8
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
TBC1D4 -0.006 0.002 -10000 0 -10000 0 0
MAP3K5 0.019 0.006 -10000 0 -10000 0 0
MAPKAP1 0.021 0.004 -10000 0 -10000 0 0
negative regulation of cell cycle -0.018 0.069 0.3 5 -0.24 7 12
YWHAH 0.021 0.004 -10000 0 -10000 0 0
AKT1S1 0.006 0.045 -10000 0 -0.3 6 6
CASP9 0.007 0.046 -10000 0 -0.3 6 6
YWHAB 0.02 0.005 -10000 0 -10000 0 0
p27Kip1/KPNA1 0.028 0.068 0.3 4 -0.28 8 12
GBL 0 0 -10000 0 -10000 0 0
PDK1/Src/Hsp90 0.039 0.013 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
SRC 0.02 0.004 -10000 0 -10000 0 0
AKT2/p21CIP1 0.008 0.054 0.23 4 -0.26 6 10
KIAA1303 0 0 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.007 0.041 0.18 1 -0.32 4 5
CHUK 0.004 0.048 -10000 0 -0.29 8 8
BAD/BCL-XL 0.025 0.059 -10000 0 -0.28 8 8
mTORC2 0.021 0.012 -10000 0 -10000 0 0
AKT2 0.007 0.002 -10000 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.019 0.088 0.3 6 -0.38 6 12
PDPK1 0.021 0.003 -10000 0 -10000 0 0
MDM2 0.015 0.061 -10000 0 -0.29 7 7
MAPKKK cascade -0.027 0.062 0.28 8 -10000 0 8
MDM2/Cbp/p300 0.045 0.075 0.31 4 -0.28 7 11
TSC1/TSC2 0.002 0.053 0.26 5 -0.28 8 13
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.072 0.3 4 -0.27 7 11
glucose import -0.01 0.023 0.2 3 -0.17 3 6
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.01 0.042 0.22 1 -0.21 6 7
response to stress 0 0 -10000 0 -10000 0 0
SLC2A4 -0.011 0.015 -10000 0 -0.17 3 3
GSK3A 0.007 0.049 -10000 0 -0.29 7 7
FOXO1 0.005 0.042 -10000 0 -0.29 6 6
GSK3B 0.005 0.046 -10000 0 -0.29 7 7
SFN 0.025 0.045 0.33 7 -0.33 1 8
G1/S transition of mitotic cell cycle 0.005 0.058 0.24 4 -0.28 8 12
p27Kip1/14-3-3 family 0.011 0.047 -10000 0 -0.3 2 2
PRKACA 0.02 0.005 -10000 0 -10000 0 0
KPNA1 0.021 0.003 -10000 0 -10000 0 0
HSP90AA1 0.02 0.004 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
RHEB 0.02 0.005 -10000 0 -10000 0 0
CREBBP 0.021 0.004 -10000 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.02 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.017 0.059 0.22 3 -0.33 3 6
ERC1 0.02 0.006 -10000 0 -10000 0 0
RIP2/NOD2 0.026 0.012 -10000 0 -10000 0 0
NFKBIA -0.017 0.018 0.2 2 -10000 0 2
BIRC2 0.02 0.005 -10000 0 -10000 0 0
IKBKB 0.018 0.007 -10000 0 -10000 0 0
RIPK2 0.019 0.007 -10000 0 -10000 0 0
IKBKG 0.001 0.049 -10000 0 -0.34 6 6
IKK complex/A20 0.024 0.077 -10000 0 -0.35 6 6
NEMO/A20/RIP2 0.019 0.007 -10000 0 -10000 0 0
XPO1 0.021 0.002 -10000 0 -10000 0 0
NEMO/ATM 0.024 0.071 -10000 0 -0.34 9 9
tumor necrosis factor receptor activity 0 0 -10000 0 -10000 0 0
RAN 0.022 0.022 0.33 2 -10000 0 2
Exportin 1/RanGTP 0.029 0.014 0.21 2 -10000 0 2
IKK complex/ELKS 0.022 0.064 -10000 0 -0.33 7 7
BCL10/MALT1/TRAF6 0.037 0.016 -10000 0 -10000 0 0
NOD2 0.02 0.005 -10000 0 -10000 0 0
NFKB1 0.021 0.003 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
MALT1 0.019 0.007 -10000 0 -10000 0 0
cIAP1/UbcH5C 0.03 0.008 -10000 0 -10000 0 0
ATM 0.02 0.004 -10000 0 -10000 0 0
TNF/TNFR1A 0.017 0.056 0.24 1 -0.23 18 19
TRAF6 0.021 0.003 -10000 0 -10000 0 0
PRKCA 0.019 0.025 -10000 0 -0.33 2 2
CHUK 0.021 0.003 -10000 0 -10000 0 0
UBE2D3 0.021 0.003 -10000 0 -10000 0 0
TNF 0.004 0.077 0.33 1 -0.33 19 20
NF kappa B1 p50/RelA 0.042 0.013 -10000 0 -10000 0 0
BCL10 0.021 0.004 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.017 0.018 0.19 2 -10000 0 2
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
TNFRSF1A 0.02 0.005 -10000 0 -10000 0 0
IKK complex 0.027 0.07 -10000 0 -0.35 7 7
CYLD 0.02 0.005 -10000 0 -10000 0 0
IKK complex/PKC alpha 0.031 0.071 -10000 0 -0.36 6 6
Insulin-mediated glucose transport

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
Insulin responsive Vesicles 0.005 0.11 -10000 0 -0.38 14 14
CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
AKT1 0.02 0.005 -10000 0 -10000 0 0
AKT2 0.02 0.005 -10000 0 -10000 0 0
STXBP4 0.021 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.011 0.11 0.24 1 -0.41 15 16
YWHAZ 0.018 0.007 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
YWHAQ 0.021 0.002 -10000 0 -10000 0 0
TBC1D4 -0.016 0.005 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.021 0.004 -10000 0 -10000 0 0
YWHAB 0.02 0.005 -10000 0 -10000 0 0
SNARE/Synip 0.038 0.015 -10000 0 -10000 0 0
YWHAG 0.02 0.004 -10000 0 -10000 0 0
ASIP 0.02 0.016 0.33 1 -10000 0 1
PRKCI 0.02 0.005 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0.015 0.003 -10000 0 -10000 0 0
RHOQ 0.021 0.003 -10000 0 -10000 0 0
GYS1 -0.005 0.012 0.23 1 -10000 0 1
PRKCZ 0.018 0.031 -10000 0 -0.33 3 3
TRIP10 0.02 0.005 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0.026 0.008 -10000 0 -10000 0 0
AS160/14-3-3 0.003 0.053 -10000 0 -0.25 6 6
VAMP2 0.019 0.006 -10000 0 -10000 0 0
SLC2A4 -0.014 0.12 0.24 1 -0.46 15 16
STX4 0.021 0.003 -10000 0 -10000 0 0
GSK3B 0.01 0.004 -10000 0 -10000 0 0
SFN 0.025 0.045 0.33 7 -0.33 1 8
LNPEP 0.02 0.005 -10000 0 -10000 0 0
YWHAE 0.019 0.006 -10000 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.008 0.019 -10000 0 -0.23 2 2
CRKL 0.021 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.014 0.005 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.019 0.025 -10000 0 -0.33 2 2
alpha4/beta7 Integrin/MAdCAM1 0.048 0.031 0.23 3 -0.18 3 6
EPO 0.021 0.028 0.33 3 -10000 0 3
alpha4/beta7 Integrin 0.029 0.024 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.03 0.015 -10000 0 -0.23 1 1
EPO/EPOR (dimer) 0.029 0.021 0.24 3 -10000 0 3
lamellipodium assembly 0.001 0.055 -10000 0 -0.5 3 3
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.009 -10000 0 -10000 0 0
ARF6 0.02 0.005 -10000 0 -10000 0 0
JAK2 0.011 0.019 0.18 1 -0.29 1 2
PXN 0.021 0.004 -10000 0 -10000 0 0
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
MADCAM1 0.022 0.032 0.33 4 -10000 0 4
cell adhesion 0.046 0.03 0.22 3 -0.18 3 6
CRKL/CBL 0.029 0.009 -10000 0 -10000 0 0
ITGB1 0.021 0.004 -10000 0 -10000 0 0
SRC -0.018 0.035 0.17 11 -0.18 2 13
ITGB7 0.02 0.018 -10000 0 -0.33 1 1
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 0.039 0.026 0.23 1 -0.2 3 4
p130Cas/Crk/Dock1 -0.026 0.037 0.17 10 -10000 0 10
VCAM1 0.019 0.03 0.33 1 -0.33 2 3
RHOA 0.021 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 0.05 0.019 -10000 0 -0.18 1 1
BCAR1 -0.022 0.033 0.17 9 -0.18 3 12
EPOR 0.02 0.005 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
CBL 0.02 0.005 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
Rac1/GTP 0.001 0.057 -10000 0 -0.51 3 3
a4b1 and a4b7 Integrin 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
ITGB1 0.021 0.004 -9999 0 -10000 0 0
ITGB7 0.02 0.018 -9999 0 -0.33 1 1
ITGA4 0.019 0.025 -9999 0 -0.33 2 2
alpha4/beta7 Integrin 0.029 0.024 -9999 0 -0.23 3 3
alpha4/beta1 Integrin 0.03 0.015 -9999 0 -0.23 1 1
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 0.017 0.031 -10000 0 -0.33 3 3
positive regulation of NF-kappaB transcription factor activity 0.023 0.026 -10000 0 -0.23 3 3
MAP2K4 0.004 0.024 -10000 0 -0.24 1 1
IKBKB 0.018 0.007 -10000 0 -10000 0 0
TNFRSF10B 0.018 0.008 -10000 0 -10000 0 0
TNFRSF10A 0.018 0.008 -10000 0 -10000 0 0
SMPD1 0.004 0.015 0.14 1 -0.14 3 4
IKBKG 0.02 0.004 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D 0.017 0.019 -10000 0 -0.33 1 1
TRAIL/TRAILR2 0.023 0.026 -10000 0 -0.23 3 3
TRAIL/TRAILR3 0.02 0.041 -10000 0 -0.26 7 7
TRAIL/TRAILR1 0.023 0.026 -10000 0 -0.23 3 3
TRAIL/TRAILR4 0.023 0.026 -10000 0 -0.23 3 3
TRAIL/TRAILR1/DAP3/GTP 0.027 0.024 -10000 0 -0.18 2 2
IKK complex 0 0.047 -10000 0 -10000 0 0
RIPK1 0.021 0.004 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0.013 0.006 -10000 0 -10000 0 0
MAPK3 -0.018 0.024 0.28 1 -0.23 3 4
MAP3K1 0.012 0.018 -10000 0 -10000 0 0
TRAILR4 (trimer) 0.017 0.019 -10000 0 -0.33 1 1
TRADD 0.021 0.004 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.018 0.008 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.001 0.039 -10000 0 -0.19 2 2
CFLAR 0.021 0.002 -10000 0 -10000 0 0
MAPK1 -0.017 0.022 0.28 1 -0.23 2 3
TRAIL/TRAILR1/FADD/TRADD/RIP 0.045 0.035 -10000 0 -0.18 2 2
mol:ceramide 0.004 0.015 0.14 1 -0.14 3 4
FADD 0.02 0.004 -10000 0 -10000 0 0
MAPK8 -0.008 0.041 -10000 0 -0.25 2 2
TRAF2 0.021 0.004 -10000 0 -10000 0 0
TRAILR3 (trimer) 0.012 0.043 -10000 0 -0.33 6 6
CHUK 0.021 0.003 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD 0.032 0.027 -10000 0 -0.2 3 3
DAP3 0.018 0.008 -10000 0 -10000 0 0
CASP10 -0.004 0.044 0.26 2 -0.23 3 5
JNK cascade 0.023 0.026 -10000 0 -0.23 3 3
TRAIL (trimer) 0.017 0.031 -10000 0 -0.33 3 3
TNFRSF10C 0.012 0.043 -10000 0 -0.33 6 6
TRAIL/TRAILR1/DAP3/GTP/FADD 0.033 0.029 -10000 0 -0.17 2 2
TRAIL/TRAILR2/FADD 0.031 0.027 -10000 0 -0.2 3 3
cell death 0.004 0.015 0.14 1 -0.14 3 4
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.001 0.039 -10000 0 -0.19 2 2
TRAILR2 (trimer) 0.018 0.008 -10000 0 -10000 0 0
CASP8 0.008 0.06 -10000 0 -0.73 2 2
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP 0.045 0.035 -10000 0 -0.18 2 2
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.021 0.004 -10000 0 -10000 0 0
Rac1/GDP 0.02 0.01 -10000 0 -10000 0 0
DOCK1 0.021 0.003 -10000 0 -10000 0 0
ITGA4 0.019 0.025 -10000 0 -0.33 2 2
RAC1 0.019 0.007 -10000 0 -10000 0 0
alpha4/beta7 Integrin 0.029 0.024 -10000 0 -0.23 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.019 0.006 -10000 0 -10000 0 0
alpha4/beta1 Integrin 0.039 0.018 -10000 0 -0.2 1 1
alpha4/beta7 Integrin/Paxillin 0.027 0.021 -10000 0 -0.18 3 3
lamellipodium assembly -0.009 0.083 -10000 0 -0.38 13 13
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.009 -10000 0 -10000 0 0
ARF6 0.02 0.005 -10000 0 -10000 0 0
TLN1 0.019 0.018 -10000 0 -0.33 1 1
PXN -0.016 0.005 -10000 0 -10000 0 0
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
ARF6/GTP 0.035 0.021 -10000 0 -0.17 1 1
cell adhesion 0.035 0.021 -10000 0 -0.17 2 2
CRKL/CBL 0.029 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin 0.027 0.015 -10000 0 -0.18 1 1
ITGB1 0.021 0.004 -10000 0 -10000 0 0
ITGB7 0.02 0.018 -10000 0 -0.33 1 1
ARF6/GDP 0.022 0.009 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 0.036 0.026 0.22 1 -0.18 3 4
p130Cas/Crk/Dock1 0.037 0.019 -10000 0 -0.2 1 1
VCAM1 0.019 0.03 0.33 1 -0.33 2 3
alpha4/beta1 Integrin/Paxillin/Talin 0.036 0.022 -10000 0 -0.17 2 2
alpha4/beta1 Integrin/Paxillin/GIT1 0.037 0.019 -10000 0 -0.18 1 1
BCAR1 0.02 0.018 -10000 0 -0.33 1 1
mol:GDP -0.036 0.019 0.18 1 -10000 0 1
CBL 0.02 0.005 -10000 0 -10000 0 0
PRKACA 0.02 0.005 -10000 0 -10000 0 0
GIT1 0.021 0.004 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton 0.036 0.022 -10000 0 -0.17 2 2
Rac1/GTP -0.011 0.091 -10000 0 -0.43 13 13
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA 0.029 0.015 -10000 0 -0.23 1 1
FBXW11 0.02 0.005 -10000 0 -10000 0 0
NF kappa B1 p50/c-Rel -0.018 0.008 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.019 0.045 0.24 3 -0.18 2 5
NFKBIA 0.001 0.009 -10000 0 -0.17 1 1
MAPK14 0.02 0.004 -10000 0 -10000 0 0
NF kappa B1 p105/p50 -0.017 0.009 -10000 0 -10000 0 0
ARRB2 0.006 0.002 -10000 0 -10000 0 0
REL 0.021 0.002 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
BCL3/NF kappa B1 p50 -0.017 0.008 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
NF kappa B1 p105/RelA -0.018 0.008 -10000 0 -10000 0 0
PIK3CA 0.02 0.004 -10000 0 -10000 0 0
NF kappa B1 p50 dimer -0.014 0.015 0.24 1 -10000 0 1
PIK3R1 0.02 0.005 -10000 0 -10000 0 0
NFKB1 -0.015 0.006 -10000 0 -10000 0 0
RELA 0.021 0.003 -10000 0 -10000 0 0
positive regulation of anti-apoptosis 0.007 0.035 -10000 0 -0.18 4 4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.016 0.041 -10000 0 -0.21 1 1
SRC 0.02 0.004 -10000 0 -10000 0 0
PI3K 0.029 0.009 -10000 0 -10000 0 0
NF kappa B1 p50/RelA 0.007 0.036 -10000 0 -0.19 4 4
IKBKB 0.018 0.007 -10000 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -10000 0 -10000 0 0
SYK 0.019 0.025 -10000 0 -0.33 2 2
I kappa B alpha/PIK3R1 0.026 0.054 0.26 8 -0.17 6 14
cell death 0.016 0.04 -10000 0 -0.2 1 1
NF kappa B1 p105/c-Rel -0.018 0.008 -10000 0 -10000 0 0
LCK 0.021 0.024 0.33 1 -0.33 1 2
BCL3 0.019 0.018 -10000 0 -0.33 1 1
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma 0.032 0.028 0.2 3 -0.17 4 7
MAPK9 0.003 0.001 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.008 0.015 0.16 3 -10000 0 3
GNB1/GNG2 0.026 0.014 -10000 0 -0.19 1 1
GNB1 0.02 0.004 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.004 0.001 -10000 0 -10000 0 0
Gs family/GTP 0.012 0.024 0.19 3 -0.17 4 7
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.002 0.005 0.048 4 -10000 0 4
GNAL 0.019 0.045 0.33 3 -0.33 4 7
GNG2 0.019 0.018 -10000 0 -0.33 1 1
CRH 0.019 0.028 0.33 3 -10000 0 3
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.001 -10000 0 -10000 0 0
MAPK11 0.002 0.018 -10000 0 -0.25 2 2
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin 0.039 0.021 -9999 0 -0.2 2 2
E-cadherin/beta catenin 0.028 0.02 -9999 0 -0.23 2 2
CTNNB1 0.021 0.004 -9999 0 -10000 0 0
JUP 0.021 0.003 -9999 0 -10000 0 0
CDH1 0.019 0.025 -9999 0 -0.33 2 2
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0.008 0.043 0.15 29 -0.2 1 30
EntrezGene:79658 0 0 -10000 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.015 0.039 -10000 0 -0.16 3 3
AP2 0.029 0.008 -10000 0 -10000 0 0
mol:DAG 0 0 -10000 0 -10000 0 0
Arfaptin 2/Rac/GTP 0.021 0.017 -10000 0 -10000 0 0
CLTB 0.02 0.005 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.008 0.005 -10000 0 -10000 0 0
CD4 0.013 0.049 -10000 0 -0.33 8 8
CLTA 0.02 0.005 -10000 0 -10000 0 0
mol:GTP -0.002 0.002 -10000 0 -10000 0 0
ARFGAP1 -0.008 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 -0.002 0.01 -10000 0 -10000 0 0
ARF1/GTP 0.021 0.016 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein -0.005 0.015 -10000 0 -10000 0 0
mol:Choline -0.002 0.01 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
ARF1 0.02 0.01 -10000 0 -10000 0 0
DDEF1 -0.001 0.01 -10000 0 -10000 0 0
ARF1/GDP 0 0.018 -10000 0 -0.15 1 1
AP2M1 0.02 0.004 -10000 0 -10000 0 0
EntrezGene:1313 0 0 -10000 0 -10000 0 0
actin filament polymerization -0.008 0.011 -10000 0 -10000 0 0
Rac/GTP 0.015 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0.024 0.013 -10000 0 -10000 0 0
ARFIP2 0.009 0.021 -10000 0 -10000 0 0
COPA 0.019 0.007 -10000 0 -10000 0 0
RAC1 0.019 0.007 -10000 0 -10000 0 0
ARF1/GTP/coatomer protein complex -0.001 0.035 -10000 0 -0.18 8 8
ARF1/GTP/ARHGAP10 0.012 0.008 -10000 0 -10000 0 0
GGA3 0.02 0.004 -10000 0 -10000 0 0
ARF1/GTP/Membrin 0.011 0.026 -10000 0 -0.29 2 2
AP2A1 0.02 0.004 -10000 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 -0.001 0.029 -10000 0 -0.21 2 2
ARF1/GDP/Membrin 0.016 0.03 -10000 0 -0.32 2 2
Arfaptin 2/Rac/GDP 0.019 0.018 -10000 0 -10000 0 0
CYTH2 0.024 0.009 -10000 0 -10000 0 0
ARF1/GTP/GGA3 0.026 0.013 -10000 0 -10000 0 0
mol:ATP 0 0 -10000 0 -10000 0 0
Rac/GDP 0.014 0.005 -10000 0 -10000 0 0
mol:Brefeldin A 0 0 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.003 0.041 -10000 0 -0.21 9 9
PLD2 -0.002 0.01 -10000 0 -10000 0 0
ARF-GAP1/v-SNARE -0.008 0.002 -10000 0 -10000 0 0
PIP5K1A -0.002 0.01 -10000 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0.007 0.022 -10000 0 -0.13 3 3
mol:Phosphatic acid 0 0 -10000 0 -10000 0 0
mol:Phosphatidic acid -0.002 0.01 -10000 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 -0.008 0.002 -10000 0 -10000 0 0
GOSR2 0.006 0.006 -10000 0 -10000 0 0
USO1 0.004 0.029 -10000 0 -0.32 3 3
GBF1 0.003 0.033 -10000 0 -0.32 4 4
ARF1/GTP/Arfaptin 2 0.023 0.017 -10000 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex 0.033 0.036 -10000 0 -0.19 8 8
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.019 0.007 -10000 0 -10000 0 0
SMAD2 0 0.043 0.22 1 -0.22 4 5
SMAD3 0.009 0.037 -10000 0 -10000 0 0
SMAD3/SMAD4 0.022 0.035 -10000 0 -0.48 1 1
SMAD4/Ubc9/PIASy 0.036 0.017 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0.028 0.049 -10000 0 -0.22 2 2
PPM1A 0.02 0.004 -10000 0 -10000 0 0
CALM1 0.02 0.004 -10000 0 -10000 0 0
SMAD2/SMAD4 0.006 0.041 -10000 0 -0.21 6 6
MAP3K1 0.02 0.005 -10000 0 -10000 0 0
TRAP-1/SMAD4 0.027 0.021 -10000 0 -0.23 2 2
MAPK3 0.021 0.003 -10000 0 -10000 0 0
MAPK1 0.02 0.005 -10000 0 -10000 0 0
NUP214 0.021 0.004 -10000 0 -10000 0 0
CTDSP1 0.021 0.002 -10000 0 -10000 0 0
CTDSP2 0.02 0.005 -10000 0 -10000 0 0
CTDSPL 0.021 0.004 -10000 0 -10000 0 0
KPNB1 0.021 0.004 -10000 0 -10000 0 0
TGFBRAP1 0.019 0.025 -10000 0 -0.33 2 2
UBE2I 0.021 0.004 -10000 0 -10000 0 0
NUP153 0.021 0.004 -10000 0 -10000 0 0
KPNA2 0.024 0.032 0.33 4 -10000 0 4
PIAS4 0.02 0.005 -10000 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.021 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 -0.019 0.009 -10000 0 -10000 0 0
MDM2/SUMO1 0.027 0.026 -10000 0 -0.18 2 2
HDAC4 0.021 0.003 -10000 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC1 -0.019 0.009 -10000 0 -10000 0 0
SUMO1 0.021 0.003 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1 0.005 0.005 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
XPO1 -0.005 0.012 -10000 0 -10000 0 0
EntrezGene:23636 0 0 -10000 0 -10000 0 0
RAN 0.022 0.022 0.33 2 -10000 0 2
EntrezGene:8021 0 0 -10000 0 -10000 0 0
RANBP2 0.021 0.002 -10000 0 -10000 0 0
SUMO1/HDAC4 0.029 0.024 -10000 0 -0.18 2 2
SUMO1/HDAC1 0.029 0.026 -10000 0 -0.18 2 2
RANGAP1 0.021 0.004 -10000 0 -10000 0 0
MDM2/SUMO1/SUMO1 0.045 0.024 -10000 0 -10000 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.006 0.002 -10000 0 -10000 0 0
Ran/GTP 0.019 0.026 0.2 1 -0.18 2 3
EntrezGene:23225 0 0 -10000 0 -10000 0 0
MDM2 0.02 0.006 -10000 0 -10000 0 0
UBE2I 0.021 0.004 -10000 0 -10000 0 0
Ran/GTP/Exportin 1 0.015 0.031 0.21 4 -0.18 2 6
NPC 0.012 0.001 -10000 0 -10000 0 0
PIAS2 0.019 0.006 -10000 0 -10000 0 0
PIAS1 0.021 0.003 -10000 0 -10000 0 0
EntrezGene:9972 0 0 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0.03 0.007 -9999 0 -9999 0 0
FBXW11 0.02 0.005 -9999 0 -9999 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -9999 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.02 0.005 -9999 0 -9999 0 0
CHUK 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p100/RelB 0.055 0.023 -9999 0 -9999 0 0
NFKB1 0.021 0.003 -9999 0 -9999 0 0
MAP3K14 0.021 0.003 -9999 0 -9999 0 0
NF kappa B1 p50/RelB 0.03 0.008 -9999 0 -9999 0 0
RELB 0.02 0.005 -9999 0 -9999 0 0
NFKB2 0.021 0.003 -9999 0 -9999 0 0
NF kappa B2 p52/RelB 0.027 0.007 -9999 0 -9999 0 0
regulation of B cell activation 0.027 0.007 -9999 0 -9999 0 0
Inferred Pathway Levels Matrix

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

pid_entity TCGA.J2.8194 TCGA.J2.8192 TCGA.99.8033 TCGA.99.8032
109_MAP3K5 -0.026 0.0076 0.0076 0.0076
47_PPARGC1A 0 0.021 0.021 0.021
105_BMP4 0.021 0.021 0.021 0.021
105_BMP6 0.021 0.021 0.021 0.021
105_BMP7 0.021 0.021 -0.33 0.021
105_BMP2 0.021 0.021 0.021 0.021
131_RELN/VLDLR 0.055 0.055 0.055 0.055
30_TGFB1/TGF beta receptor Type II 0.021 0.021 0.021 -0.024
84_STAT5B -0.038 0.11 0.038 0.02
84_STAT5A -0.038 0.11 0.038 0.02
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/LUAD-TP/3353157/LUAD-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

  • Copy Number File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Gistic2_Analysis/LUAD-TP/3471916/all_data_by_genes.txt

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

References
[2] Charles J. Vaske, Stephen C. Benz, J. Zachary Sanborn, Dent Earl, Christopher Szeto, Jingchun Zhu, David Haussler, and Joshua M. Stuart, Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM, Bioinformatics 12(26):237-245 (2010)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle