PARADIGM pathway analysis of mRNASeq expression data
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1H993T7
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1H993T7
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 41 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
TCGA08_retinoblastoma 220
Syndecan-1-mediated signaling events 201
Syndecan-4-mediated signaling events 134
IL4-mediated signaling events 129
Osteopontin-mediated events 103
HIF-1-alpha transcription factor network 102
IL23-mediated signaling events 85
Glypican 2 network 82
amb2 Integrin signaling 72
TCGA08_p53 67
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 497 . 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 ( 497 ).

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
TCGA08_retinoblastoma 0.4427 220 1767 8 -0.35 0.15 1000 -1000 -0.024 -1000
Syndecan-1-mediated signaling events 0.4044 201 6840 34 -0.72 0.014 1000 -1000 -0.074 -1000
Syndecan-4-mediated signaling events 0.2696 134 8995 67 -0.69 0.092 1000 -1000 -0.11 -1000
IL4-mediated signaling events 0.2596 129 11801 91 -1.4 1.2 1000 -1000 -0.2 -1000
Osteopontin-mediated events 0.2072 103 3933 38 -0.44 0.014 1000 -1000 -0.13 -1000
HIF-1-alpha transcription factor network 0.2052 102 7792 76 -1 0.022 1000 -1000 -0.2 -1000
IL23-mediated signaling events 0.1710 85 5155 60 -0.75 0.014 1000 -1000 -0.19 -1000
Glypican 2 network 0.1650 82 328 4 -0.15 -0.14 1000 -1000 -0.044 -1000
amb2 Integrin signaling 0.1449 72 5939 82 -0.6 0.014 1000 -1000 -0.11 -1000
TCGA08_p53 0.1348 67 472 7 -0.27 0.14 1000 -1000 -0.024 -1000
Syndecan-2-mediated signaling events 0.1308 65 4536 69 -0.44 0.024 1000 -1000 -0.068 -1000
Endothelins 0.1187 59 5704 96 -0.56 0.014 1000 -1000 -0.1 -1000
p75(NTR)-mediated signaling 0.0905 45 5635 125 -0.54 0.014 1000 -1000 -0.12 -1000
Ephrin B reverse signaling 0.0905 45 2186 48 -0.16 0.15 1000 -1000 -0.079 -1000
FOXA2 and FOXA3 transcription factor networks 0.0885 44 2056 46 -0.49 0.022 1000 -1000 -0.11 -1000
Visual signal transduction: Rods 0.0865 43 2245 52 -0.43 0.014 1000 -1000 -0.11 -1000
Calcium signaling in the CD4+ TCR pathway 0.0785 39 1227 31 -0.51 0.014 1000 -1000 -0.11 -1000
Effects of Botulinum toxin 0.0744 37 964 26 -0.21 0.014 1000 -1000 -0.079 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0744 37 2895 78 -0.16 0.043 1000 -1000 -0.091 -1000
BMP receptor signaling 0.0704 35 2888 81 -0.36 0.048 1000 -1000 -0.11 -1000
Glypican 1 network 0.0704 35 1690 48 -0.36 0.033 1000 -1000 -0.06 -1000
Signaling events mediated by the Hedgehog family 0.0684 34 1794 52 -0.45 0.067 1000 -1000 -0.1 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0664 33 2271 68 -0.56 0.042 1000 -1000 -0.16 -1000
IL12-mediated signaling events 0.0644 32 2803 87 -0.28 0.089 1000 -1000 -0.16 -1000
Glucocorticoid receptor regulatory network 0.0644 32 3676 114 -0.64 0.26 1000 -1000 -0.088 -1000
Signaling events regulated by Ret tyrosine kinase 0.0644 32 2679 82 -0.18 0.014 1000 -1000 -0.11 -1000
TCR signaling in naïve CD8+ T cells 0.0644 32 3039 93 -0.27 0.15 1000 -1000 -0.1 -1000
Coregulation of Androgen receptor activity 0.0624 31 2394 76 -0.5 0.041 1000 -1000 -0.066 -1000
LPA4-mediated signaling events 0.0584 29 357 12 -0.11 0.021 1000 -1000 -0.036 -1000
Visual signal transduction: Cones 0.0584 29 1125 38 -0.18 0.014 1000 -1000 -0.084 -1000
Canonical Wnt signaling pathway 0.0563 28 1438 51 -0.39 0.11 1000 -1000 -0.083 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0563 28 3478 120 -0.25 0.12 1000 -1000 -0.095 -1000
ErbB4 signaling events 0.0543 27 1868 69 -0.32 0.072 1000 -1000 -0.11 -1000
Caspase cascade in apoptosis 0.0523 26 1971 74 -0.14 0.056 1000 -1000 -0.061 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0523 26 890 34 -0.065 0.014 1000 -1000 -0.075 -1000
Thromboxane A2 receptor signaling 0.0523 26 2782 105 -0.094 0.021 1000 -1000 -0.086 -1000
EPHB forward signaling 0.0523 26 2214 85 -0.26 0.11 1000 -1000 -0.12 -1000
BCR signaling pathway 0.0523 26 2662 99 -0.15 0.034 1000 -1000 -0.11 -1000
PDGFR-beta signaling pathway 0.0523 26 2563 97 -0.13 0.014 1000 -1000 -0.11 -1000
IL1-mediated signaling events 0.0503 25 1554 62 -0.24 0.072 1000 -1000 -0.13 -1000
Nongenotropic Androgen signaling 0.0503 25 1314 52 -0.14 0.041 1000 -1000 -0.086 -1000
IL27-mediated signaling events 0.0483 24 1264 51 -0.18 0.062 1000 -1000 -0.11 -1000
Syndecan-3-mediated signaling events 0.0463 23 835 35 -0.21 0.014 1000 -1000 -0.075 -1000
Regulation of nuclear SMAD2/3 signaling 0.0443 22 3065 136 -0.37 0.36 1000 -1000 -0.092 -1000
Signaling mediated by p38-gamma and p38-delta 0.0443 22 339 15 -0.13 0.024 1000 -1000 -0.049 -1000
Integrins in angiogenesis 0.0443 22 1860 84 -0.44 0.017 1000 -1000 -0.11 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0443 22 754 33 -0.35 0.037 1000 -1000 -0.08 -1000
Presenilin action in Notch and Wnt signaling 0.0423 21 1307 61 -0.39 0.04 1000 -1000 -0.1 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0423 21 1860 88 -0.36 0.067 1000 -1000 -0.14 -1000
Wnt signaling 0.0402 20 142 7 -0.074 0.011 1000 -1000 -0.039 -1000
LPA receptor mediated events 0.0402 20 2118 102 -0.6 0.026 1000 -1000 -0.11 -1000
Signaling events mediated by PTP1B 0.0382 19 1454 76 -0.16 0.03 1000 -1000 -0.11 -1000
IFN-gamma pathway 0.0362 18 1237 68 -0.19 0.036 1000 -1000 -0.12 -1000
Regulation of Telomerase 0.0362 18 1884 102 -0.16 0.044 1000 -1000 -0.12 -1000
Regulation of Androgen receptor activity 0.0362 18 1317 70 -0.52 0.033 1000 -1000 -0.087 -1000
Reelin signaling pathway 0.0342 17 987 56 -0.23 0.014 1000 -1000 -0.1 -1000
Ephrin A reverse signaling 0.0322 16 118 7 -0.022 0.001 1000 -1000 -0.04 -1000
Signaling mediated by p38-alpha and p38-beta 0.0322 16 713 44 -0.18 0.014 1000 -1000 -0.073 -1000
EGFR-dependent Endothelin signaling events 0.0322 16 351 21 -0.098 0.014 1000 -1000 -0.085 -1000
ErbB2/ErbB3 signaling events 0.0302 15 980 65 -0.32 0.026 1000 -1000 -0.088 -1000
Arf6 signaling events 0.0302 15 988 62 -0.16 0.041 1000 -1000 -0.085 -1000
EPO signaling pathway 0.0302 15 874 55 -0.077 0.027 1000 -1000 -0.12 -1000
Signaling events mediated by HDAC Class III 0.0302 15 620 40 -0.2 0.075 1000 -1000 -0.056 -1000
TRAIL signaling pathway 0.0302 15 721 48 -0.085 0.016 1000 -1000 -0.085 -1000
Plasma membrane estrogen receptor signaling 0.0302 15 1372 86 -0.3 0.03 1000 -1000 -0.1 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0282 14 779 54 -0.31 0.028 1000 -1000 -0.13 -1000
Noncanonical Wnt signaling pathway 0.0282 14 378 26 -0.08 0.014 1000 -1000 -0.1 -1000
PDGFR-alpha signaling pathway 0.0282 14 653 44 -0.13 0.033 1000 -1000 -0.076 -1000
VEGFR1 specific signals 0.0282 14 823 56 -0.14 0.039 1000 -1000 -0.094 -1000
Fc-epsilon receptor I signaling in mast cells 0.0262 13 1337 97 -0.19 0.035 1000 -1000 -0.11 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0262 13 487 37 -0.083 0.014 1000 -1000 -0.065 -1000
S1P1 pathway 0.0262 13 480 36 -0.14 0.014 1000 -1000 -0.076 -1000
Signaling events mediated by PRL 0.0262 13 452 34 -0.11 0.034 1000 -1000 -0.048 -1000
Cellular roles of Anthrax toxin 0.0241 12 496 39 -0.043 0.019 1000 -1000 -0.036 -1000
Retinoic acid receptors-mediated signaling 0.0241 12 720 58 -0.18 0.031 1000 -1000 -0.089 -1000
IL6-mediated signaling events 0.0241 12 920 75 -0.11 0.063 1000 -1000 -0.11 -1000
Nectin adhesion pathway 0.0221 11 723 63 -0.14 0.04 1000 -1000 -0.092 -1000
JNK signaling in the CD4+ TCR pathway 0.0201 10 171 17 -0.039 0.036 1000 -1000 -0.074 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0201 10 521 52 -0.21 0.035 1000 -1000 -0.083 -1000
FAS signaling pathway (CD95) 0.0201 10 481 47 -0.085 0.014 1000 -1000 -0.061 -1000
IL2 signaling events mediated by PI3K 0.0201 10 586 58 -0.17 0.062 1000 -1000 -0.11 -1000
IGF1 pathway 0.0201 10 587 57 -0.089 0.021 1000 -1000 -0.11 -1000
Rapid glucocorticoid signaling 0.0201 10 204 20 -0.061 0.014 1000 -1000 -0.049 -1000
FOXM1 transcription factor network 0.0201 10 558 51 -0.36 0.16 1000 -1000 -0.21 -1000
Ras signaling in the CD4+ TCR pathway 0.0201 10 171 17 -0.026 0.029 1000 -1000 -0.053 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0181 9 429 45 -0.085 0.035 1000 -1000 -0.11 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0181 9 688 74 -0.31 0.082 1000 -1000 -0.11 -1000
S1P3 pathway 0.0181 9 397 42 -0.14 0.037 1000 -1000 -0.069 -1000
Aurora B signaling 0.0181 9 669 67 -0.32 0.031 1000 -1000 -0.079 -1000
Circadian rhythm pathway 0.0161 8 192 22 -0.14 0.051 1000 -1000 -0.072 -1000
Ceramide signaling pathway 0.0161 8 671 76 -0.094 0.034 1000 -1000 -0.075 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0141 7 209 28 -0.075 0.022 1000 -1000 -0.058 -1000
a4b1 and a4b7 Integrin signaling 0.0141 7 39 5 -0.016 0.011 1000 -1000 -0.041 -1000
Arf6 downstream pathway 0.0141 7 334 43 -0.04 0.023 1000 -1000 -0.055 -1000
HIF-2-alpha transcription factor network 0.0141 7 323 43 -0.26 0.031 1000 -1000 -0.11 -1000
Insulin Pathway 0.0141 7 528 74 -0.22 0.038 1000 -1000 -0.11 -1000
Class IB PI3K non-lipid kinase events 0.0141 7 21 3 -0.004 0.004 1000 -1000 -0.02 -1000
p38 MAPK signaling pathway 0.0141 7 339 44 -0.14 0.018 1000 -1000 -0.081 -1000
Paxillin-dependent events mediated by a4b1 0.0121 6 245 36 -0.067 0.025 1000 -1000 -0.084 -1000
IL2 signaling events mediated by STAT5 0.0121 6 151 22 -0.039 0.052 1000 -1000 -0.066 -1000
S1P4 pathway 0.0121 6 154 25 -0.034 0.023 1000 -1000 -0.071 -1000
BARD1 signaling events 0.0101 5 333 57 -0.026 0.056 1000 -1000 -0.082 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0101 5 693 125 -0.12 0.094 1000 -1000 -0.12 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0080 4 401 85 -0.07 0.058 1000 -1000 -0.093 -1000
Hedgehog signaling events mediated by Gli proteins 0.0080 4 280 65 -0.095 0.063 1000 -1000 -0.087 -1000
Aurora A signaling 0.0080 4 252 60 -0.07 0.031 1000 -1000 -0.076 -1000
Aurora C signaling 0.0080 4 28 7 -0.014 0.005 1000 -1000 -0.051 -1000
ceramide signaling pathway 0.0080 4 216 49 -0.026 0.046 1000 -1000 -0.061 -1000
Regulation of p38-alpha and p38-beta 0.0080 4 255 54 -0.1 0.037 1000 -1000 -0.087 -1000
Class I PI3K signaling events 0.0080 4 305 73 -0.1 0.04 1000 -1000 -0.083 -1000
Arf6 trafficking events 0.0080 4 289 71 -0.25 0.047 1000 -1000 -0.095 -1000
PLK1 signaling events 0.0060 3 299 85 -0.019 0.036 1000 -1000 -0.067 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0060 3 281 83 -0.082 0.066 1000 -1000 -0.096 -1000
TCGA08_rtk_signaling 0.0060 3 89 26 -0.031 0.048 1000 -1000 -0.029 -1000
E-cadherin signaling events 0.0060 3 16 5 -0.005 0.013 1000 -1000 -0.065 -1000
Canonical NF-kappaB pathway 0.0040 2 87 39 -0.029 0.086 1000 -1000 -0.1 -1000
Signaling events mediated by HDAC Class II 0.0040 2 181 75 -0.035 0.032 1000 -1000 -0.069 -1000
S1P5 pathway 0.0040 2 45 17 -0.017 0.023 1000 -1000 -0.064 -1000
E-cadherin signaling in keratinocytes 0.0040 2 98 43 -0.018 0.047 1000 -1000 -0.09 -1000
Alternative NF-kappaB pathway 0.0040 2 30 13 -0.008 0.014 1000 -1000 -0.075 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0020 1 37 23 -0.015 0.05 1000 -1000 -0.089 -1000
PLK2 and PLK4 events 0.0020 1 4 3 0.011 0.023 1000 -1000 -0.024 -1000
Insulin-mediated glucose transport 0.0020 1 37 32 -0.076 0.048 1000 -1000 -0.083 -1000
Signaling events mediated by HDAC Class I 0.0020 1 159 104 -0.13 0.061 1000 -1000 -0.081 -1000
FoxO family signaling 0.0020 1 108 64 -0.033 0.16 1000 -1000 -0.093 -1000
Atypical NF-kappaB pathway 0.0020 1 39 31 -0.006 0.048 1000 -1000 -0.056 -1000
E-cadherin signaling in the nascent adherens junction 0.0020 1 138 76 -0.016 0.06 1000 -1000 -0.11 -1000
mTOR signaling pathway 0.0000 0 41 53 -0.004 0.034 1000 -1000 -0.069 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 21 68 -0.12 0.062 1000 -1000 -0.078 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.032 1000 -1000 -0.065 -1000
Arf1 pathway 0.0000 0 9 54 -0.004 0.037 1000 -1000 -0.062 -1000
Total NA 3122 176767 7203 -28 7 131000 -131000 -12 -131000
TCGA08_retinoblastoma

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
CDKN2B -0.1 0.22 -10000 0 -0.53 102 102
CDKN2C 0.017 0.14 -10000 0 -0.75 14 14
CDKN2A -0.35 0.4 -10000 0 -0.77 230 230
CCND2 0.13 0.13 0.22 284 -0.15 1 285
RB1 -0.14 0.14 -10000 0 -0.24 283 283
CDK4 0.15 0.14 0.25 289 -10000 0 289
CDK6 0.14 0.14 0.25 281 -10000 0 281
G1/S progression 0.13 0.14 0.24 283 -10000 0 283
Syndecan-1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.01 0.053 -9999 0 -0.82 2 2
CCL5 -0.11 0.3 -9999 0 -0.81 76 76
SDCBP 0.014 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.46 0.19 -9999 0 -0.56 357 357
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.43 0.18 -9999 0 -0.53 357 357
Syndecan-1/Syntenin -0.43 0.18 -9999 0 -0.53 357 357
MAPK3 -0.38 0.17 -9999 0 -0.48 333 333
HGF/MET -0.025 0.11 -9999 0 -0.48 26 26
TGFB1/TGF beta receptor Type II 0.01 0.053 -9999 0 -0.82 2 2
BSG 0.014 0 -9999 0 -10000 0 0
keratinocyte migration -0.43 0.18 -9999 0 -0.52 357 357
Syndecan-1/RANTES -0.5 0.25 -9999 0 -0.6 376 376
Syndecan-1/CD147 -0.41 0.18 -9999 0 -0.51 357 357
Syndecan-1/Syntenin/PIP2 -0.42 0.17 -9999 0 -0.51 357 357
LAMA5 0.014 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.41 0.17 -9999 0 -0.5 357 357
MMP7 -0.18 0.34 -9999 0 -0.79 118 118
HGF -0.012 0.13 -9999 0 -0.63 20 20
Syndecan-1/CASK -0.44 0.18 -9999 0 -0.54 357 357
Syndecan-1/HGF/MET -0.43 0.19 -9999 0 -0.52 368 368
regulation of cell adhesion -0.37 0.16 -9999 0 -0.59 91 91
HPSE 0.009 0.052 -9999 0 -0.57 4 4
positive regulation of cell migration -0.46 0.19 -9999 0 -0.56 357 357
SDC1 -0.46 0.19 -9999 0 -0.57 357 357
Syndecan-1/Collagen -0.46 0.19 -9999 0 -0.56 357 357
PPIB 0.014 0 -9999 0 -10000 0 0
MET 0.005 0.083 -9999 0 -0.74 6 6
PRKACA 0.014 0 -9999 0 -10000 0 0
MMP9 -0.6 0.37 -9999 0 -0.82 366 366
MAPK1 -0.38 0.17 -9999 0 -0.48 333 333
homophilic cell adhesion -0.46 0.19 -9999 0 -0.55 357 357
MMP1 -0.72 0.28 -9999 0 -0.82 435 435
Syndecan-4-mediated signaling events

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
PTK2 -0.22 0.23 -9999 0 -0.47 221 221
Syndecan-4/Syndesmos -0.39 0.26 -9999 0 -0.63 221 221
positive regulation of JNK cascade -0.4 0.22 -9999 0 -0.59 254 254
Syndecan-4/ADAM12 -0.69 0.36 -9999 0 -0.93 319 319
CCL5 -0.11 0.3 -9999 0 -0.81 76 76
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.014 0 -9999 0 -10000 0 0
ITGA5 -0.25 0.39 -9999 0 -0.82 155 155
SDCBP 0.014 0 -9999 0 -10000 0 0
PLG 0.002 0.073 -9999 0 -0.8 4 4
ADAM12 -0.58 0.38 -9999 0 -0.82 355 355
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.12 0.062 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.56 0.34 -9999 0 -0.8 288 288
Syndecan-4/CXCL12/CXCR4 -0.42 0.26 -9999 0 -0.63 254 254
Syndecan-4/Laminin alpha3 -0.51 0.34 -9999 0 -0.77 266 266
MDK -0.023 0.17 -9999 0 -0.81 22 22
Syndecan-4/FZD7 -0.4 0.26 -9999 0 -0.64 223 223
Syndecan-4/Midkine -0.41 0.26 -9999 0 -0.64 234 234
FZD7 0.001 0.1 -9999 0 -0.79 8 8
Syndecan-4/FGFR1/FGF -0.38 0.23 -9999 0 -0.58 235 235
THBS1 -0.014 0.14 -9999 0 -0.71 19 19
integrin-mediated signaling pathway -0.45 0.3 -9999 0 -0.7 245 245
positive regulation of MAPKKK cascade -0.4 0.22 -9999 0 -0.59 254 254
Syndecan-4/TACI -0.44 0.28 -9999 0 -0.68 249 249
CXCR4 -0.015 0.15 -9999 0 -0.82 17 17
cell adhesion -0.18 0.22 -9999 0 -0.4 216 216
Syndecan-4/Dynamin -0.39 0.26 -9999 0 -0.63 221 221
Syndecan-4/TSP1 -0.4 0.27 -9999 0 -0.65 224 224
Syndecan-4/GIPC -0.39 0.26 -9999 0 -0.63 221 221
Syndecan-4/RANTES -0.46 0.3 -9999 0 -0.7 256 256
ITGB1 0.012 0.037 -9999 0 -0.82 1 1
LAMA1 -0.32 0.41 -9999 0 -0.81 199 199
LAMA3 -0.22 0.37 -9999 0 -0.82 139 139
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.092 0.071 -9999 0 -0.66 2 2
Syndecan-4/alpha-Actinin -0.39 0.26 -9999 0 -0.63 221 221
TFPI 0.006 0.074 -9999 0 -0.72 5 5
F2 -0.08 0.24 -9999 0 -0.83 47 47
alpha5/beta1 Integrin -0.2 0.29 -9999 0 -0.63 156 156
positive regulation of cell adhesion -0.63 0.38 -9999 0 -0.87 315 315
ACTN1 0.012 0.037 -9999 0 -0.82 1 1
TNC -0.14 0.32 -9999 0 -0.82 92 92
Syndecan-4/CXCL12 -0.42 0.25 -9999 0 -0.64 247 247
FGF6 0.003 0.005 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CXCL12 -0.051 0.18 -9999 0 -0.57 55 55
TNFRSF13B -0.082 0.26 -9999 0 -0.82 56 56
FGF2 -0.007 0.12 -9999 0 -0.63 16 16
FGFR1 0.004 0.087 -9999 0 -0.78 6 6
Syndecan-4/PI-4-5-P2 -0.4 0.26 -9999 0 -0.64 221 221
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.35 0.42 -9999 0 -0.81 221 221
cell migration -0.04 0.02 -9999 0 -10000 0 0
PRKCD 0.027 0.011 -9999 0 -10000 0 0
vasculogenesis -0.39 0.25 -9999 0 -0.62 224 224
SDC4 -0.42 0.27 -9999 0 -0.67 221 221
Syndecan-4/Tenascin C -0.47 0.33 -9999 0 -0.74 245 245
Syndecan-4/PI-4-5-P2/PKC alpha -0.093 0.048 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.39 0.26 -9999 0 -0.63 221 221
MMP9 -0.6 0.36 -9999 0 -0.81 366 366
Rac1/GTP -0.19 0.22 -9999 0 -0.41 216 216
cytoskeleton organization -0.38 0.24 -9999 0 -0.6 221 221
GIPC1 0.014 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.4 0.26 -9999 0 -0.63 224 224
IL4-mediated signaling events

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
BCL2L1 -1.1 0.5 -10000 0 -1.4 296 296
STAT6 (cleaved dimer) -1.1 0.52 -10000 0 -1.4 333 333
IGHG1 -0.33 0.13 -10000 0 -0.47 97 97
IGHG3 -1 0.48 -10000 0 -1.3 328 328
AKT1 -0.4 0.18 -10000 0 -0.74 36 36
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.29 0.16 -10000 0 -0.73 25 25
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.41 0.18 -10000 0 -0.81 23 23
THY1 -1.1 0.55 -10000 0 -1.5 310 310
MYB -0.05 0.19 -10000 0 -0.59 52 52
HMGA1 0.014 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.51 0.23 -10000 0 -0.95 45 45
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.41 0.18 -10000 0 -0.79 23 23
SP1 0.014 0.012 -10000 0 -10000 0 0
INPP5D 0.01 0.045 -10000 0 -0.57 3 3
SOCS5 0.036 0.01 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -1.1 0.52 -10000 0 -1.4 332 332
SOCS1 -0.64 0.28 -10000 0 -0.85 230 230
SOCS3 -0.42 0.2 -10000 0 -0.82 33 33
FCER2 -0.74 0.35 -10000 0 -1.2 104 104
PARP14 0.009 0.065 -10000 0 -0.82 3 3
CCL17 -1.1 0.51 -10000 0 -1.4 309 309
GRB2 0.014 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.33 0.15 -10000 0 -0.73 20 20
T cell proliferation -1.1 0.53 -10000 0 -1.4 311 311
IL4R/JAK1 -1.1 0.5 -10000 0 -1.4 309 309
EGR2 -1.1 0.5 -10000 0 -1.4 303 303
JAK2 -0.032 0.032 -10000 0 -0.61 1 1
JAK3 -0.007 0.15 -10000 0 -0.82 17 17
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
JAK1 0.001 0.006 -10000 0 -10000 0 0
COL1A2 -0.49 0.36 -10000 0 -0.94 184 184
CCL26 -1.1 0.51 -10000 0 -1.4 316 316
IL4R -1.1 0.55 -10000 0 -1.5 308 308
PTPN6 0.035 0.007 -10000 0 -10000 0 0
IL13RA2 -1.1 0.52 -10000 0 -1.4 306 306
IL13RA1 -0.031 0.019 -10000 0 -10000 0 0
IRF4 -0.28 0.33 -10000 0 -0.94 85 85
ARG1 -0.55 0.57 -10000 0 -1.4 153 153
CBL -0.48 0.22 -10000 0 -0.89 45 45
GTF3A 0.007 0.018 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.043 0.03 -10000 0 -0.45 1 1
IRF4/BCL6 -0.25 0.31 -10000 0 -0.88 84 84
CD40LG -0.06 0.21 -10000 0 -0.59 65 65
MAPK14 -0.47 0.22 -10000 0 -0.89 44 44
mitosis -0.38 0.18 -10000 0 -0.71 34 34
STAT6 -1.3 0.7 -10000 0 -1.7 325 325
SPI1 -0.017 0.075 -10000 0 -0.75 3 3
RPS6KB1 -0.36 0.17 -10000 0 -0.71 24 24
STAT6 (dimer) -1.3 0.7 -10000 0 -1.7 325 325
STAT6 (dimer)/PARP14 -1.2 0.59 -10000 0 -1.5 322 322
mast cell activation 0.021 0.008 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.39 0.18 -10000 0 -0.82 28 28
FRAP1 -0.4 0.18 -10000 0 -0.74 36 36
LTA -1.1 0.51 -10000 0 -1.4 315 315
FES 0.014 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 1.2 0.62 1.6 325 -10000 0 325
CCL11 -1.2 0.49 -10000 0 -1.5 339 339
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.39 0.18 -10000 0 -0.8 28 28
IL2RG -0.006 0.15 -10000 0 -0.79 17 17
IL10 -1.1 0.5 -10000 0 -1.4 304 304
IRS1 0.01 0.045 -10000 0 -0.57 3 3
IRS2 0.011 0.037 -10000 0 -0.57 2 2
IL4 -0.2 0.073 -10000 0 -10000 0 0
IL5 -1.1 0.5 -10000 0 -1.4 299 299
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.77 0.31 -10000 0 -0.98 292 292
COL1A1 -0.67 0.38 -10000 0 -0.97 292 292
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -1.1 0.54 -10000 0 -1.5 298 298
IL2R gamma/JAK3 -0.019 0.18 -10000 0 -0.69 30 30
TFF3 -1.3 0.59 -10000 0 -1.6 349 349
ALOX15 -1.1 0.54 -10000 0 -1.5 313 313
MYBL1 -0.003 0.12 -10000 0 -0.82 10 10
T-helper 2 cell differentiation -0.79 0.33 -10000 0 -1 303 303
SHC1 0.014 0 -10000 0 -10000 0 0
CEBPB -0.013 0.048 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.39 0.17 -10000 0 -0.77 22 22
mol:PI-3-4-5-P3 -0.4 0.18 -10000 0 -0.74 36 36
PI3K -0.42 0.2 -10000 0 -0.8 36 36
DOK2 0.008 0.069 -10000 0 -0.76 4 4
ETS1 0.03 0.066 -10000 0 -0.81 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.31 0.15 -10000 0 -0.7 22 22
ITGB3 -1.1 0.51 -10000 0 -1.4 295 295
PIGR -1.4 0.61 -10000 0 -1.7 374 374
IGHE 0.052 0.045 0.27 4 -10000 0 4
MAPKKK cascade -0.3 0.14 -10000 0 -0.68 22 22
BCL6 0.014 0.002 -10000 0 -10000 0 0
OPRM1 -1.1 0.5 -10000 0 -1.4 300 300
RETNLB -1.1 0.51 -10000 0 -1.4 313 313
SELP -1.1 0.55 -10000 0 -1.5 311 311
AICDA -1 0.48 -10000 0 -1.4 306 306
Osteopontin-mediated events

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
IKK alpha homodimer -0.27 0.28 -9999 0 -0.57 154 154
NF kappa B1 p50/RelA/I kappa B alpha -0.28 0.24 -9999 0 -0.58 138 138
alphaV/beta3 Integrin/Osteopontin/Src -0.35 0.32 -9999 0 -0.64 270 270
AP1 -0.32 0.32 -9999 0 -0.81 91 91
ILK -0.28 0.28 -9999 0 -0.52 274 274
bone resorption -0.22 0.25 -9999 0 -0.75 18 18
PTK2B 0.013 0.026 -9999 0 -0.57 1 1
PYK2/p130Cas -0.27 0.24 -9999 0 -0.52 154 154
ITGAV 0.004 0.08 -9999 0 -0.78 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.008 0.057 -9999 0 -0.41 10 10
alphaV/beta3 Integrin/Osteopontin -0.33 0.3 -9999 0 -0.58 274 274
MAP3K1 -0.29 0.29 -9999 0 -0.53 274 274
JUN 0.013 0.002 -9999 0 -10000 0 0
MAPK3 -0.3 0.29 -9999 0 -0.62 154 154
MAPK1 -0.3 0.29 -9999 0 -0.62 154 154
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.27 0.28 -9999 0 -0.55 174 174
ITGB3 -0.017 0.14 -9999 0 -0.73 19 19
NFKBIA -0.29 0.29 -9999 0 -0.64 138 138
FOS -0.062 0.19 -9999 0 -0.57 64 64
CD44 0.013 0.026 -9999 0 -0.57 1 1
CHUK 0.014 0 -9999 0 -10000 0 0
PLAU -0.43 0.4 -9999 0 -0.91 159 159
NF kappa B1 p50/RelA -0.29 0.24 -9999 0 -0.62 137 137
BCAR1 0.014 0 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.028 0.13 -9999 0 -0.59 23 23
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.28 0.29 -9999 0 -0.53 274 274
VAV3 -0.28 0.29 -9999 0 -0.57 174 174
MAP3K14 -0.3 0.29 -9999 0 -0.55 274 274
ROCK2 0.003 0.077 -9999 0 -0.57 9 9
SPP1 -0.44 0.42 -9999 0 -0.83 268 268
RAC1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.27 0.25 -9999 0 -0.53 160 160
MMP2 -0.29 0.32 -9999 0 -0.82 88 88
HIF-1-alpha transcription factor network

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
PKM2 -0.69 0.48 -9999 0 -1.2 152 152
HDAC7 0.014 0.003 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.47 0.33 -9999 0 -0.9 79 79
SMAD4 0.014 0.026 -9999 0 -0.56 1 1
ID2 -0.69 0.48 -9999 0 -1.3 147 147
AP1 -0.045 0.14 -9999 0 -0.4 64 64
ABCG2 -0.7 0.48 -9999 0 -1.3 148 148
HIF1A -0.083 0.061 -9999 0 -0.71 1 1
TFF3 -0.81 0.54 -9999 0 -1.3 211 211
GATA2 0.008 0.08 -9999 0 -0.77 5 5
AKT1 -0.085 0.064 -9999 0 -10000 0 0
response to hypoxia -0.11 0.066 -9999 0 -10000 0 0
MCL1 -0.69 0.48 -9999 0 -1.2 147 147
NDRG1 -0.69 0.48 -9999 0 -1.3 146 146
SERPINE1 -0.91 0.55 -9999 0 -1.4 251 251
FECH -0.69 0.48 -9999 0 -1.2 152 152
FURIN -0.69 0.48 -9999 0 -1.2 146 146
NCOA2 -0.031 0.15 -9999 0 -0.57 38 38
EP300 -0.091 0.096 -9999 0 -0.37 9 9
HMOX1 -0.69 0.48 -9999 0 -1.2 161 161
BHLHE40 -0.69 0.48 -9999 0 -1.2 150 150
BHLHE41 -0.7 0.49 -9999 0 -1.3 148 148
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.067 0.058 -9999 0 -0.45 1 1
ENG -0.044 0.073 -9999 0 -10000 0 0
JUN 0.015 0.001 -9999 0 -10000 0 0
RORA -0.7 0.49 -9999 0 -1.3 146 146
ABCB1 -0.2 0.32 -9999 0 -1.4 30 30
TFRC -0.7 0.48 -9999 0 -1.2 168 168
CXCR4 -0.7 0.49 -9999 0 -1.3 150 150
TF -0.86 0.54 -9999 0 -1.3 230 230
CITED2 -0.69 0.48 -9999 0 -1.2 150 150
HIF1A/ARNT -0.79 0.61 -9999 0 -1.4 215 215
LDHA -0.068 0.045 -9999 0 -10000 0 0
ETS1 -0.69 0.48 -9999 0 -1.2 155 155
PGK1 -0.69 0.48 -9999 0 -1.2 146 146
NOS2 -0.76 0.5 -9999 0 -1.3 172 172
ITGB2 -0.7 0.48 -9999 0 -1.3 151 151
ALDOA -0.69 0.48 -9999 0 -1.2 150 150
Cbp/p300/CITED2 -0.67 0.49 -9999 0 -1.3 130 130
FOS -0.06 0.19 -9999 0 -0.56 64 64
HK2 -0.69 0.48 -9999 0 -1.2 150 150
SP1 0.022 0.006 -9999 0 -10000 0 0
GCK -0.18 0.23 -9999 0 -0.82 40 40
HK1 -0.69 0.48 -9999 0 -1.2 151 151
NPM1 -0.69 0.48 -9999 0 -1.2 150 150
EGLN1 -0.69 0.48 -9999 0 -1.2 146 146
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.69 0.48 -9999 0 -1.2 146 146
SMAD3 0.014 0.026 -9999 0 -0.56 1 1
EDN1 -0.092 0.18 -9999 0 -1.4 5 5
IGFBP1 -0.7 0.49 -9999 0 -1.3 150 150
VEGFA -0.4 0.3 -9999 0 -1 21 21
HIF1A/JAB1 -0.043 0.036 -9999 0 -0.53 1 1
CP -0.81 0.54 -9999 0 -1.3 207 207
CXCL12 -0.72 0.5 -9999 0 -1.3 154 154
COPS5 0.013 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.002 0.025 -9999 0 -0.4 2 2
BNIP3 -0.69 0.48 -9999 0 -1.2 150 150
EGLN3 -0.71 0.5 -9999 0 -1.3 167 167
CA9 -1 0.5 -9999 0 -1.3 311 311
TERT -0.77 0.52 -9999 0 -1.3 189 189
ENO1 -0.69 0.48 -9999 0 -1.2 150 150
PFKL -0.69 0.48 -9999 0 -1.2 160 160
NCOA1 0.013 0.002 -9999 0 -10000 0 0
ADM -0.69 0.48 -9999 0 -1.2 152 152
ARNT -0.082 0.054 -9999 0 -10000 0 0
HNF4A -0.071 0.24 -9999 0 -0.82 48 48
ADFP -0.7 0.48 -9999 0 -1.2 175 175
SLC2A1 -0.4 0.3 -9999 0 -1 25 25
LEP -0.74 0.51 -9999 0 -1.3 173 173
HIF1A/ARNT/Cbp/p300 -0.49 0.34 -9999 0 -0.9 99 99
EPO -0.4 0.32 -9999 0 -0.99 68 68
CREBBP -0.09 0.092 -9999 0 -0.37 2 2
HIF1A/ARNT/Cbp/p300/HDAC7 -0.46 0.34 -9999 0 -0.95 62 62
PFKFB3 -0.69 0.48 -9999 0 -1.2 151 151
NT5E -0.75 0.53 -9999 0 -1.3 172 172
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.58 0.44 -10000 0 -1.2 118 118
IL23A -0.57 0.43 -10000 0 -1.2 117 117
NF kappa B1 p50/RelA/I kappa B alpha -0.57 0.42 -10000 0 -1 165 165
positive regulation of T cell mediated cytotoxicity -0.63 0.48 -10000 0 -1.2 167 167
ITGA3 -0.56 0.42 -10000 0 -1.1 125 125
IL17F -0.38 0.27 -10000 0 -0.74 93 93
IL12B -0.077 0.24 -10000 0 -0.86 43 43
STAT1 (dimer) -0.62 0.48 -10000 0 -1.2 154 154
CD4 -0.55 0.4 -10000 0 -1.1 123 123
IL23 -0.58 0.43 -10000 0 -1.1 129 129
IL23R -0.085 0.091 -10000 0 -0.7 6 6
IL1B -0.6 0.45 -10000 0 -1.2 133 133
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.75 0.44 -10000 0 -1.2 199 199
TYK2 -0.005 0.041 -10000 0 -0.86 1 1
STAT4 -0.006 0.12 -10000 0 -0.8 12 12
STAT3 0.014 0 -10000 0 -10000 0 0
IL18RAP -0.014 0.14 -10000 0 -0.73 18 18
IL12RB1 -0.081 0.24 -10000 0 -0.84 46 46
PIK3CA 0.014 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.07 0.19 -10000 0 -0.66 47 47
IL23R/JAK2 -0.1 0.097 -10000 0 -0.74 4 4
positive regulation of chronic inflammatory response -0.63 0.48 -10000 0 -1.2 167 167
natural killer cell activation 0.008 0.008 0.06 6 -10000 0 6
JAK2 0.002 0.028 -10000 0 -0.56 1 1
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
NFKB1 0.01 0.003 -10000 0 -10000 0 0
RELA 0.01 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.55 0.4 -10000 0 -1.1 128 128
ALOX12B -0.66 0.48 -10000 0 -1.2 168 168
CXCL1 -0.59 0.45 -10000 0 -1.2 141 141
T cell proliferation -0.63 0.48 -10000 0 -1.2 167 167
NFKBIA 0.008 0.037 -10000 0 -0.82 1 1
IL17A -0.29 0.22 -10000 0 -0.59 70 70
PI3K -0.58 0.42 -10000 0 -1 176 176
IFNG -0.033 0.046 0.13 5 -0.11 104 109
STAT3 (dimer) -0.55 0.4 -10000 0 -1.1 130 130
IL18R1 0.01 0.047 -10000 0 -0.7 2 2
IL23/IL23R/JAK2/TYK2/SOCS3 -0.34 0.25 -10000 0 -0.81 49 49
IL18/IL18R -0.008 0.13 -10000 0 -0.42 37 37
macrophage activation -0.029 0.015 -10000 0 -0.045 83 83
TNF -0.58 0.44 -10000 0 -1.2 129 129
STAT3/STAT4 -0.59 0.43 -10000 0 -1.1 154 154
STAT4 (dimer) -0.61 0.47 -10000 0 -1.2 141 141
IL18 -0.01 0.11 -10000 0 -0.56 19 19
IL19 -0.69 0.52 -10000 0 -1.3 185 185
STAT5A (dimer) -0.6 0.46 -10000 0 -1.2 136 136
STAT1 -0.033 0.19 -10000 0 -0.81 28 28
SOCS3 0.013 0.026 -10000 0 -0.57 1 1
CXCL9 -0.7 0.47 -10000 0 -1.2 204 204
MPO -0.57 0.43 -10000 0 -1.1 134 134
positive regulation of humoral immune response -0.63 0.48 -10000 0 -1.2 167 167
IL23/IL23R/JAK2/TYK2 -0.66 0.53 -10000 0 -1.3 158 158
IL6 -0.59 0.46 -10000 0 -1.2 129 129
STAT5A 0.014 0 -10000 0 -10000 0 0
IL2 0.006 0.038 -10000 0 -0.81 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.008 0.06 6 -10000 0 6
CD3E -0.56 0.41 -10000 0 -1.1 109 109
keratinocyte proliferation -0.63 0.48 -10000 0 -1.2 167 167
NOS2 -0.61 0.44 -10000 0 -1.1 149 149
Glypican 2 network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MDK -0.023 0.17 -9999 0 -0.81 22 22
GPC2 -0.15 0.33 -9999 0 -0.82 96 96
GPC2/Midkine -0.15 0.29 -9999 0 -0.69 105 105
neuron projection morphogenesis -0.14 0.29 -9999 0 -0.69 105 105
amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2 -0.13 0.27 -9999 0 -0.64 98 98
alphaM/beta2 Integrin/GPIbA -0.07 0.21 -9999 0 -0.71 44 44
alphaM/beta2 Integrin/proMMP-9 -0.45 0.31 -9999 0 -0.6 369 369
PLAUR -0.035 0.2 -9999 0 -0.82 29 29
HMGB1 0.011 0.016 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.056 0.19 -9999 0 -0.68 38 38
AGER -0.001 0.099 -9999 0 -0.82 7 7
RAP1A 0.014 0 -9999 0 -10000 0 0
SELPLG 0.014 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.074 0.19 -9999 0 -0.64 41 41
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.6 0.37 -9999 0 -0.82 366 366
CYR61 0.006 0.079 -9999 0 -0.77 5 5
TLN1 0.01 0.053 -9999 0 -0.82 2 2
Rap1/GTP -0.16 0.15 -9999 0 -0.51 45 45
RHOA 0.014 0 -9999 0 -10000 0 0
P-selectin oligomer -0.09 0.22 -9999 0 -0.56 89 89
MYH2 -0.35 0.24 -9999 0 -0.56 240 240
MST1R 0.003 0.077 -9999 0 -0.57 9 9
leukocyte activation during inflammatory response -0.066 0.19 -9999 0 -0.57 54 54
APOB -0.01 0.13 -9999 0 -0.78 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.1 0.29 -9999 0 -0.82 70 70
JAM3 0.012 0.037 -9999 0 -0.82 1 1
GP1BA -0.014 0.14 -9999 0 -0.74 17 17
alphaM/beta2 Integrin/CTGF -0.06 0.19 -9999 0 -0.67 40 40
alphaM/beta2 Integrin -0.18 0.19 -9999 0 -0.43 144 144
JAM3 homodimer 0.012 0.037 -9999 0 -0.82 1 1
ICAM2 0.01 0.052 -9999 0 -0.65 3 3
ICAM1 -0.03 0.18 -9999 0 -0.82 26 26
phagocytosis triggered by activation of immune response cell surface activating receptor -0.18 0.19 -9999 0 -0.43 144 144
cell adhesion -0.069 0.21 -9999 0 -0.7 44 44
NFKB1 -0.031 0.23 -9999 0 -0.84 21 21
THY1 -0.22 0.37 -9999 0 -0.82 137 137
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.024 0.11 -9999 0 -0.53 22 22
alphaM/beta2 Integrin/LRP/tPA -0.063 0.19 -9999 0 -0.6 49 49
IL6 -0.057 0.29 -9999 0 -0.78 59 59
ITGB2 -0.014 0.14 -9999 0 -0.8 15 15
elevation of cytosolic calcium ion concentration -0.28 0.33 -9999 0 -0.58 240 240
alphaM/beta2 Integrin/JAM2/JAM3 -0.056 0.18 -9999 0 -0.64 37 37
JAM2 0 0.089 -9999 0 -0.57 12 12
alphaM/beta2 Integrin/ICAM1 -0.078 0.22 -9999 0 -0.62 57 57
alphaM/beta2 Integrin/uPA/Plg -0.27 0.3 -9999 0 -0.55 240 240
RhoA/GTP -0.22 0.22 -9999 0 -0.52 134 134
positive regulation of phagocytosis -0.14 0.17 -9999 0 -0.58 46 46
Ron/MSP -0.014 0.081 -9999 0 -0.46 15 15
alphaM/beta2 Integrin/uPAR/uPA -0.29 0.34 -9999 0 -0.59 240 240
alphaM/beta2 Integrin/uPAR -0.084 0.24 -9999 0 -0.68 59 59
PLAU -0.34 0.41 -9999 0 -0.82 213 213
PLAT -0.011 0.14 -9999 0 -0.8 15 15
actin filament polymerization -0.33 0.23 -9999 0 -0.53 240 240
MST1 0.005 0.083 -9999 0 -0.74 6 6
alphaM/beta2 Integrin/lipoprotein(a) -0.067 0.19 -9999 0 -0.58 54 54
TNF -0.035 0.25 -9999 0 -0.77 37 37
RAP1B 0.012 0.037 -9999 0 -0.82 1 1
alphaM/beta2 Integrin/uPA -0.28 0.32 -9999 0 -0.59 236 236
fibrinolysis -0.26 0.29 -9999 0 -0.54 240 240
HCK 0.006 0.079 -9999 0 -0.77 5 5
dendritic cell antigen processing and presentation -0.18 0.19 -9999 0 -0.43 144 144
VTN -0.039 0.2 -9999 0 -0.82 31 31
alphaM/beta2 Integrin/CYR61 -0.059 0.19 -9999 0 -0.68 40 40
LPA -0.007 0.11 -9999 0 -0.82 9 9
LRP1 0.013 0.026 -9999 0 -0.57 1 1
cell migration -0.47 0.36 -9999 0 -0.63 373 373
FN1 -0.36 0.41 -9999 0 -0.82 221 221
alphaM/beta2 Integrin/Thy1 -0.2 0.32 -9999 0 -0.63 154 154
MPO -0.01 0.12 -9999 0 -0.62 18 18
KNG1 -0.018 0.14 -9999 0 -0.82 14 14
RAP1/GDP -0.001 0.025 -9999 0 -0.55 1 1
ROCK1 -0.2 0.21 -9999 0 -0.49 126 126
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.005 0.074 -9999 0 -0.82 4 4
CTGF 0.003 0.082 -9999 0 -0.63 8 8
alphaM/beta2 Integrin/Hck -0.059 0.19 -9999 0 -0.67 40 40
ITGAM -0.042 0.2 -9999 0 -0.81 32 32
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.1 0.2 -9999 0 -0.65 36 36
HP -0.21 0.28 -9999 0 -0.58 185 185
leukocyte adhesion -0.17 0.25 -9999 0 -0.78 44 44
SELP -0.09 0.22 -9999 0 -0.57 89 89
TCGA08_p53

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
CDKN2A -0.27 0.31 -10000 0 -0.6 230 230
TP53 -0.078 0.087 -10000 0 -0.42 4 4
Senescence -0.078 0.087 -10000 0 -0.42 4 4
Apoptosis -0.078 0.087 -10000 0 -0.42 4 4
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.14 0.15 0.3 230 -10000 0 230
MDM4 0.014 0 -10000 0 -10000 0 0
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.25 0.32 -9999 0 -0.58 225 225
EPHB2 -0.16 0.34 -9999 0 -0.82 107 107
Syndecan-2/TACI -0.066 0.21 -9999 0 -0.55 77 77
LAMA1 -0.32 0.41 -9999 0 -0.81 199 199
Syndecan-2/alpha2 ITGB1 -0.15 0.23 -9999 0 -0.48 154 154
HRAS 0.012 0.037 -9999 0 -0.82 1 1
Syndecan-2/CASK -0.024 0.11 -9999 0 -0.55 22 22
ITGA5 -0.25 0.39 -9999 0 -0.82 155 155
BAX 0.016 0.12 -9999 0 -0.76 2 2
EPB41 0.014 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.022 0.1 -9999 0 -0.5 22 22
LAMA3 -0.22 0.37 -9999 0 -0.82 139 139
EZR 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.01 0.052 -9999 0 -0.65 3 3
Syndecan-2/MMP2 -0.077 0.25 -9999 0 -0.62 79 79
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.004 0.042 -9999 0 -0.46 4 4
dendrite morphogenesis -0.12 0.26 -9999 0 -0.57 122 122
Syndecan-2/GM-CSF -0.31 0.31 -9999 0 -0.57 279 279
determination of left/right symmetry -0.007 0.13 -9999 0 -0.63 22 22
Syndecan-2/PKC delta 0.001 0.12 -9999 0 -0.54 22 22
GNB2L1 0.014 0 -9999 0 -10000 0 0
MAPK3 -0.28 0.28 -9999 0 -0.52 279 279
MAPK1 -0.28 0.28 -9999 0 -0.52 279 279
Syndecan-2/RACK1 -0.022 0.098 -9999 0 -0.47 23 23
NF1 0.014 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.007 0.13 -9999 0 -0.63 22 22
ITGA2 0.01 0.045 -9999 0 -0.57 3 3
MAPK8 0.007 0.13 -9999 0 -0.56 22 22
Syndecan-2/alpha2/beta1 Integrin -0.21 0.26 -9999 0 -0.5 203 203
Syndecan-2/Kininogen -0.03 0.15 -9999 0 -0.57 34 34
ITGB1 0.012 0.037 -9999 0 -0.82 1 1
SRC 0.017 0.1 -9999 0 -0.44 23 23
Syndecan-2/CASK/Protein 4.1 -0.022 0.1 -9999 0 -0.5 22 22
extracellular matrix organization -0.001 0.12 -9999 0 -0.56 23 23
actin cytoskeleton reorganization -0.25 0.31 -9999 0 -0.58 225 225
Syndecan-2/Caveolin-2/Ras -0.025 0.11 -9999 0 -0.5 24 24
Syndecan-2/Laminin alpha3 -0.16 0.28 -9999 0 -0.56 154 154
Syndecan-2/RasGAP -0.022 0.097 -9999 0 -0.45 23 23
alpha5/beta1 Integrin -0.2 0.29 -9999 0 -0.63 156 156
PRKCD 0.014 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.12 0.26 -9999 0 -0.57 122 122
GO:0007205 0.004 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.1 -9999 0 -0.43 23 23
RHOA 0.014 0 -9999 0 -10000 0 0
SDCBP 0.014 0 -9999 0 -10000 0 0
TNFRSF13B -0.082 0.26 -9999 0 -0.82 56 56
RASA1 0.011 0.037 -9999 0 -0.57 2 2
alpha2/beta1 Integrin -0.004 0.042 -9999 0 -0.46 4 4
Syndecan-2/Synbindin 0.001 0.12 -9999 0 -0.54 22 22
TGFB1 0.01 0.053 -9999 0 -0.82 2 2
CASP3 0.012 0.11 -9999 0 -0.49 22 22
FN1 -0.36 0.41 -9999 0 -0.82 221 221
Syndecan-2/IL8 -0.12 0.26 -9999 0 -0.57 120 120
SDC2 -0.007 0.13 -9999 0 -0.63 22 22
KNG1 -0.018 0.14 -9999 0 -0.82 14 14
Syndecan-2/Neurofibromin 0.001 0.12 -9999 0 -0.54 22 22
TRAPPC4 0.014 0 -9999 0 -10000 0 0
CSF2 -0.44 0.41 -9999 0 -0.82 272 272
Syndecan-2/TGFB1 -0.001 0.12 -9999 0 -0.56 23 23
Syndecan-2/Syntenin/PI-4-5-P2 -0.022 0.1 -9999 0 -0.5 22 22
Syndecan-2/Ezrin -0.021 0.1 -9999 0 -0.49 22 22
PRKACA 0.012 0.11 -9999 0 -0.49 22 22
angiogenesis -0.12 0.26 -9999 0 -0.57 120 120
MMP2 -0.1 0.29 -9999 0 -0.82 70 70
IL8 -0.16 0.34 -9999 0 -0.81 106 106
calcineurin-NFAT signaling pathway -0.066 0.21 -9999 0 -0.55 77 77
Endothelins

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
AKT1 -0.17 0.31 -10000 0 -0.67 70 70
PTK2B 0.013 0.026 -10000 0 -0.57 1 1
mol:Ca2+ -0.055 0.21 -10000 0 -0.69 29 29
EDN1 -0.091 0.21 -10000 0 -0.41 47 47
EDN3 -0.24 0.28 -10000 0 -0.57 209 209
EDN2 -0.087 0.24 -10000 0 -0.65 75 75
HRAS/GDP -0.05 0.18 -10000 0 -0.52 16 16
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.053 0.16 -10000 0 -0.39 34 34
ADCY4 -0.19 0.25 -10000 0 -0.62 73 73
ADCY5 -0.26 0.26 -10000 0 -0.64 108 108
ADCY6 -0.19 0.25 -10000 0 -0.6 85 85
ADCY7 -0.19 0.25 -10000 0 -0.63 72 72
ADCY1 -0.21 0.27 -10000 0 -0.66 84 84
ADCY2 -0.29 0.26 -10000 0 -0.63 134 134
ADCY3 -0.19 0.25 -10000 0 -0.63 72 72
ADCY8 -0.2 0.26 -10000 0 -0.64 82 82
ADCY9 -0.19 0.25 -10000 0 -0.63 72 72
arachidonic acid secretion -0.077 0.21 -10000 0 -0.55 46 46
ETB receptor/Endothelin-1/Gq/GTP -0.053 0.14 -10000 0 -0.43 29 29
GNAO1 0.008 0.069 -10000 0 -0.76 4 4
HRAS 0.011 0.038 -10000 0 -0.82 1 1
ETA receptor/Endothelin-1/G12/GTP -0.083 0.35 0.34 139 -0.64 66 205
ETA receptor/Endothelin-1/Gs/GTP -0.13 0.34 0.32 115 -0.62 91 206
mol:GTP 0 0.005 -10000 0 -10000 0 0
COL3A1 -0.41 0.5 -10000 0 -0.85 263 263
EDNRB -0.014 0.062 -10000 0 -0.56 4 4
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.22 0.39 -10000 0 -0.9 79 79
CYSLTR1 -0.22 0.36 -10000 0 -0.75 103 103
SLC9A1 -0.062 0.16 -10000 0 -0.33 48 48
mol:GDP -0.06 0.18 -10000 0 -0.5 25 25
SLC9A3 -0.18 0.32 -10000 0 -0.71 103 103
RAF1 -0.079 0.19 -10000 0 -0.51 41 41
JUN -0.038 0.18 -10000 0 -0.71 3 3
JAK2 -0.17 0.31 -10000 0 -0.67 70 70
mol:IP3 -0.071 0.17 -10000 0 -0.49 30 30
ETA receptor/Endothelin-1 -0.13 0.42 0.4 141 -0.56 203 344
PLCB1 0.01 0.037 -10000 0 -0.57 2 2
PLCB2 0.006 0.07 -10000 0 -0.76 4 4
ETA receptor/Endothelin-3 -0.23 0.24 -10000 0 -0.48 213 213
FOS -0.12 0.34 -10000 0 -0.94 65 65
Gai/GDP 0.014 0.077 -10000 0 -0.57 3 3
CRK 0.014 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.18 0.29 -10000 0 -0.69 73 73
BCAR1 0.014 0 -10000 0 -10000 0 0
PRKCB1 -0.069 0.16 -10000 0 -0.46 31 31
GNAQ 0.014 0.006 -10000 0 -10000 0 0
GNAZ -0.017 0.15 -10000 0 -0.74 20 20
GNAL -0.061 0.19 -10000 0 -0.57 64 64
Gs family/GDP -0.12 0.15 -10000 0 -0.51 35 35
ETA receptor/Endothelin-1/Gq/GTP -0.074 0.19 -10000 0 -0.45 44 44
MAPK14 -0.028 0.12 -10000 0 -0.63 5 5
TRPC6 -0.058 0.22 -10000 0 -0.72 29 29
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 0.013 0.026 -10000 0 -0.57 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.038 0.13 -10000 0 -0.5 10 10
ETB receptor/Endothelin-2 -0.075 0.19 -10000 0 -0.49 79 79
ETB receptor/Endothelin-3 -0.18 0.21 -10000 0 -0.42 212 212
ETB receptor/Endothelin-1 -0.07 0.18 -10000 0 -0.66 5 5
MAPK3 -0.11 0.29 -10000 0 -0.78 67 67
MAPK1 -0.11 0.29 -10000 0 -0.78 67 67
Rac1/GDP -0.049 0.17 -10000 0 -0.54 13 13
cAMP biosynthetic process -0.23 0.22 -10000 0 -0.58 103 103
MAPK8 -0.056 0.2 -10000 0 -0.6 24 24
SRC 0.014 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.014 0.099 -10000 0 -0.4 10 10
p130Cas/CRK/Src/PYK2 -0.057 0.19 -10000 0 -0.59 15 15
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.051 0.18 -10000 0 -0.52 16 16
COL1A2 -0.29 0.47 -10000 0 -0.86 187 187
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.12 0.23 -10000 0 -0.56 78 78
mol:DAG -0.071 0.17 -10000 0 -0.49 30 30
MAP2K2 -0.088 0.23 -10000 0 -0.62 50 50
MAP2K1 -0.088 0.23 -10000 0 -0.62 50 50
EDNRA -0.084 0.21 -10000 0 -0.41 47 47
positive regulation of muscle contraction -0.14 0.27 -10000 0 -0.66 51 51
Gq family/GDP -0.085 0.16 -10000 0 -0.58 16 16
HRAS/GTP -0.075 0.17 -10000 0 -0.46 40 40
PRKCH -0.061 0.16 -10000 0 -0.47 27 27
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.063 0.16 -10000 0 -0.47 28 28
PRKCB -0.068 0.17 -10000 0 -0.51 34 34
PRKCE -0.061 0.16 -10000 0 -0.46 29 29
PRKCD -0.061 0.16 -10000 0 -0.47 27 27
PRKCG -0.12 0.21 -10000 0 -0.53 68 68
regulation of vascular smooth muscle contraction -0.14 0.39 -10000 0 -1.1 66 66
PRKCQ -0.068 0.17 -10000 0 -0.48 33 33
PLA2G4A -0.085 0.23 -10000 0 -0.6 46 46
GNA14 -0.075 0.21 -10000 0 -0.57 76 76
GNA15 0.011 0.037 -10000 0 -0.57 2 2
GNA12 0.01 0.053 -10000 0 -0.82 2 2
GNA11 0.008 0.052 -10000 0 -0.57 4 4
Rac1/GTP -0.081 0.35 0.34 140 -0.65 61 201
MMP1 -0.56 0.25 -10000 0 -0.65 435 435
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.016 0.078 -9999 0 -0.41 19 19
Necdin/E2F1 -0.054 0.18 -9999 0 -0.62 43 43
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.11 0.2 -9999 0 -0.48 99 99
NGF (dimer)/p75(NTR)/BEX1 -0.15 0.25 -9999 0 -0.57 123 123
NT-4/5 (dimer)/p75(NTR) -0.028 0.13 -9999 0 -0.56 25 25
IKBKB 0.014 0 -9999 0 -10000 0 0
AKT1 -0.069 0.2 -9999 0 -0.46 96 96
IKBKG 0.014 0 -9999 0 -10000 0 0
BDNF -0.036 0.18 -9999 0 -0.68 36 36
MGDIs/NGR/p75(NTR)/LINGO1 -0.084 0.22 -9999 0 -0.61 63 63
FURIN 0.014 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.067 0.16 -9999 0 -0.56 34 34
LINGO1 -0.048 0.22 -9999 0 -0.82 37 37
Sortilin/TRAF6/NRIF -0.01 0.049 -9999 0 -10000 0 0
proBDNF (dimer) -0.036 0.18 -9999 0 -0.68 36 36
NTRK1 -0.058 0.23 -9999 0 -0.82 43 43
RTN4R -0.02 0.16 -9999 0 -0.82 20 20
neuron apoptosis -0.06 0.18 -9999 0 -0.56 24 24
IRAK1 0.014 0 -9999 0 -10000 0 0
SHC1 -0.095 0.23 -9999 0 -0.55 96 96
ARHGDIA 0.014 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.002 0.029 -9999 0 -0.46 2 2
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.12 0.21 -9999 0 -0.51 99 99
MAGEH1 0.012 0.037 -9999 0 -0.82 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.12 0.22 -9999 0 -0.52 100 100
Mammalian IAPs/DIABLO -0.032 0.14 -9999 0 -0.6 26 26
proNGF (dimer) -0.14 0.31 -9999 0 -0.8 91 91
MAGED1 0.008 0.064 -9999 0 -0.69 4 4
APP 0.012 0.037 -9999 0 -0.82 1 1
NT-4/5 (dimer) 0.011 0.045 -9999 0 -0.69 2 2
ZNF274 0.014 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.075 0.2 -9999 0 -0.47 96 96
NGF -0.14 0.32 -9999 0 -0.8 91 91
cell cycle arrest -0.1 0.22 -9999 0 -0.51 98 98
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.029 0.13 -9999 0 -0.54 1 1
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.024 0.11 -9999 0 -0.58 15 15
NCSTN 0.014 0 -9999 0 -10000 0 0
mol:GTP -0.12 0.22 -9999 0 -0.55 96 96
PSENEN 0.01 0.053 -9999 0 -0.82 2 2
mol:ceramide -0.091 0.22 -9999 0 -0.5 98 98
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.009 0.1 -9999 0 -0.42 1 1
p75(NTR)/beta APP -0.028 0.12 -9999 0 -0.53 26 26
BEX1 -0.041 0.2 -9999 0 -0.82 31 31
mol:GDP -0.1 0.23 -9999 0 -0.52 115 115
NGF (dimer) -0.2 0.28 -9999 0 -0.56 172 172
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.077 0.2 -9999 0 -0.56 63 63
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
RAC1/GTP -0.1 0.19 -9999 0 -0.48 96 96
MYD88 0.014 0 -9999 0 -10000 0 0
CHUK 0.014 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.12 0.22 -9999 0 -0.55 96 96
RHOB 0.014 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.047 0.16 -9999 0 -0.63 37 37
NT3 (dimer) -0.16 0.26 -9999 0 -0.56 148 148
TP53 -0.013 0.15 -9999 0 -0.45 35 35
PRDM4 -0.092 0.22 -9999 0 -0.51 98 98
BDNF (dimer) -0.47 0.32 -9999 0 -0.63 367 367
PIK3CA 0.014 0 -9999 0 -10000 0 0
SORT1 -0.008 0.11 -9999 0 -0.57 19 19
activation of caspase activity -0.11 0.2 -9999 0 -0.47 99 99
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.12 0.21 -9999 0 -0.51 98 98
RHOC 0.014 0 -9999 0 -10000 0 0
XIAP 0.014 0 -9999 0 -10000 0 0
MAPK10 -0.06 0.19 -9999 0 -0.54 24 24
DIABLO 0.014 0 -9999 0 -10000 0 0
SMPD2 -0.092 0.22 -9999 0 -0.51 98 98
APH1B 0.014 0 -9999 0 -10000 0 0
APH1A 0.014 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.13 0.23 -9999 0 -0.56 98 98
PSEN1 0.014 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.018 -9999 0 -0.41 1 1
NT3 (dimer)/p75(NTR) -0.15 0.22 -9999 0 -0.44 165 165
MAPK8 -0.05 0.19 -9999 0 -0.54 17 17
MAPK9 -0.047 0.18 -9999 0 -0.53 16 16
APAF1 0.013 0.026 -9999 0 -0.57 1 1
NTF3 -0.16 0.26 -9999 0 -0.57 148 148
NTF4 0.011 0.045 -9999 0 -0.69 2 2
NDN 0.003 0.077 -9999 0 -0.57 9 9
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.093 0.17 -9999 0 -0.43 96 96
p75 CTF/Sortilin/TRAF6/NRIF -0.013 0.06 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.12 0.22 -9999 0 -0.54 96 96
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.055 0.14 -9999 0 -0.47 34 34
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.06 0.15 -9999 0 -0.51 34 34
PRKACB 0.013 0.026 -9999 0 -0.57 1 1
proBDNF (dimer)/p75 ECD -0.038 0.14 -9999 0 -0.5 38 38
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.021 0.17 -9999 0 -0.82 21 21
BIRC2 -0.005 0.12 -9999 0 -0.82 11 11
neuron projection morphogenesis -0.098 0.2 -9999 0 -0.46 97 97
BAD -0.043 0.18 -9999 0 -0.52 15 15
RIPK2 0.014 0 -9999 0 -10000 0 0
NGFR -0.023 0.16 -9999 0 -0.71 25 25
CYCS -0.082 0.22 -9999 0 -0.48 98 98
ADAM17 0.011 0.037 -9999 0 -0.57 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.11 0.2 -9999 0 -0.5 96 96
BCL2L11 -0.043 0.18 -9999 0 -0.52 15 15
BDNF (dimer)/p75(NTR) -0.063 0.17 -9999 0 -0.52 61 61
PI3K -0.11 0.2 -9999 0 -0.5 96 96
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.12 0.21 -9999 0 -0.51 98 98
NDNL2 0.014 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
PRKCI 0.014 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.14 0.26 -9999 0 -0.6 115 115
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.12 0.22 -9999 0 -0.52 98 98
TRAF6 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCZ 0.013 0.026 -9999 0 -0.57 1 1
PLG -0.005 0.074 -9999 0 -0.82 4 4
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.097 0.22 -9999 0 -0.59 31 31
SQSTM1 0.014 0 -9999 0 -10000 0 0
NGFRAP1 0.01 0.053 -9999 0 -0.82 2 2
CASP3 -0.037 0.17 -9999 0 -0.47 15 15
E2F1 -0.048 0.22 -9999 0 -0.82 37 37
CASP9 0.014 0 -9999 0 -10000 0 0
IKK complex -0.1 0.16 -9999 0 -0.71 6 6
NGF (dimer)/TRKA -0.16 0.28 -9999 0 -0.63 129 129
MMP7 -0.18 0.34 -9999 0 -0.79 118 118
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.11 0.2 -9999 0 -0.48 98 98
MMP3 -0.54 0.39 -9999 0 -0.81 330 330
APAF-1/Caspase 9 -0.1 0.18 -9999 0 -0.71 17 17
Ephrin B reverse signaling

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
EFNB2 0.011 0.037 -10000 0 -0.57 2 2
EPHB2 -0.16 0.34 -10000 0 -0.82 107 107
EFNB1 -0.025 0.17 -10000 0 -0.63 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.23 -10000 0 -0.48 144 144
Ephrin B2/EPHB1-2 -0.13 0.22 -10000 0 -0.5 123 123
neuron projection morphogenesis -0.14 0.22 -10000 0 -0.45 144 144
Ephrin B1/EPHB1-2/Tiam1 -0.15 0.25 -10000 0 -0.51 144 144
DNM1 -0.049 0.22 -10000 0 -0.82 37 37
cell-cell signaling 0 0.002 -10000 0 -10000 0 0
MAP2K4 0.006 0.095 -10000 0 -0.59 12 12
YES1 -0.019 0.13 -10000 0 -0.83 12 12
Ephrin B1/EPHB1-2/NCK2 -0.15 0.25 -10000 0 -0.51 144 144
PI3K 0.005 0.1 -10000 0 -0.64 12 12
mol:GDP -0.15 0.25 -10000 0 -0.51 144 144
ITGA2B -0.065 0.24 -10000 0 -0.82 47 47
endothelial cell proliferation -0.001 0.022 -10000 0 -0.34 2 2
FYN -0.019 0.13 -10000 0 -0.83 12 12
MAP3K7 -0.015 0.097 -10000 0 -0.63 12 12
FGR -0.019 0.13 -10000 0 -0.82 12 12
TIAM1 0.007 0.063 -10000 0 -0.57 6 6
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
RGS3 0.014 0 -10000 0 -10000 0 0
cell adhesion -0.038 0.2 -10000 0 -0.51 66 66
LYN -0.019 0.13 -10000 0 -0.83 12 12
Ephrin B1/EPHB1-2/Src Family Kinases -0.02 0.12 -10000 0 -0.78 12 12
Ephrin B1/EPHB1-2 -0.021 0.11 -10000 0 -0.69 12 12
SRC -0.019 0.13 -10000 0 -0.82 12 12
ITGB3 -0.015 0.14 -10000 0 -0.73 19 19
EPHB1 -0.029 0.17 -10000 0 -0.73 28 28
EPHB4 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 0 0.023 -10000 0 -0.35 2 2
alphaIIb/beta3 Integrin -0.08 0.21 -10000 0 -0.63 63 63
BLK -0.034 0.13 -10000 0 -0.83 12 12
HCK -0.019 0.13 -10000 0 -0.82 12 12
regulation of stress fiber formation 0.15 0.25 0.5 144 -10000 0 144
MAPK8 0.01 0.11 -10000 0 -0.62 12 12
Ephrin B1/EPHB1-2/RGS3 -0.15 0.25 -10000 0 -0.51 144 144
endothelial cell migration -0.01 0.084 -10000 0 -0.53 12 12
NCK2 0.014 0 -10000 0 -10000 0 0
PTPN13 -0.006 0.11 -10000 0 -0.68 12 12
regulation of focal adhesion formation 0.15 0.25 0.5 144 -10000 0 144
chemotaxis 0.15 0.25 0.5 144 -10000 0 144
PIK3CA 0.014 0 -10000 0 -10000 0 0
Rac1/GTP -0.14 0.22 -10000 0 -0.47 144 144
angiogenesis -0.021 0.1 -10000 0 -0.68 12 12
LCK -0.021 0.13 -10000 0 -0.82 12 12
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.23 0.39 -9999 0 -1.1 53 53
PCK1 -0.49 0.61 -9999 0 -1.3 171 171
HNF4A -0.29 0.48 -9999 0 -1.2 66 66
KCNJ11 -0.33 0.51 -9999 0 -1.1 108 108
AKT1 -0.075 0.15 -9999 0 -10000 0 0
response to starvation -0.003 0.023 -9999 0 -10000 0 0
DLK1 -0.43 0.57 -9999 0 -1.1 168 168
NKX2-1 -0.088 0.34 -9999 0 -0.8 57 57
ACADM -0.23 0.4 -9999 0 -1.1 53 53
TAT -0.15 0.24 -9999 0 -0.9 15 15
CEBPB 0.015 0.004 -9999 0 -10000 0 0
CEBPA 0.011 0.045 -9999 0 -0.57 3 3
TTR -0.29 0.33 -9999 0 -0.91 69 69
PKLR -0.28 0.44 -9999 0 -1.1 75 75
APOA1 -0.28 0.46 -9999 0 -1.3 47 47
CPT1C -0.23 0.4 -9999 0 -1.1 52 52
ALAS1 -0.079 0.17 -9999 0 -10000 0 0
TFRC -0.2 0.3 -9999 0 -0.88 34 34
FOXF1 0.019 0.098 -9999 0 -0.72 6 6
NF1 0.022 0 -9999 0 -10000 0 0
HNF1A (dimer) -0.001 0.11 -9999 0 -0.81 9 9
CPT1A -0.23 0.39 -9999 0 -1.1 52 52
HMGCS1 -0.23 0.39 -9999 0 -1.1 52 52
NR3C1 0.019 0.023 -9999 0 -10000 0 0
CPT1B -0.24 0.4 -9999 0 -1.1 55 55
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.012 0.027 -9999 0 -10000 0 0
GCK -0.26 0.42 -9999 0 -1.1 60 60
CREB1 -0.037 0.084 -9999 0 -10000 0 0
IGFBP1 -0.093 0.2 -9999 0 -0.86 13 13
PDX1 -0.12 0.23 -9999 0 -0.81 22 22
UCP2 -0.23 0.4 -9999 0 -1.1 52 52
ALDOB -0.26 0.44 -9999 0 -1.2 61 61
AFP -0.2 0.25 -9999 0 -0.66 68 68
BDH1 -0.23 0.39 -9999 0 -1.1 53 53
HADH -0.24 0.41 -9999 0 -1.1 55 55
F2 -0.3 0.47 -9999 0 -1.3 57 57
HNF1A -0.001 0.11 -9999 0 -0.81 9 9
G6PC -0.06 0.14 -9999 0 -0.71 2 2
SLC2A2 -0.13 0.22 -9999 0 -0.72 4 4
INS -0.013 0.058 -9999 0 -0.84 2 2
FOXA1 -0.21 0.3 -9999 0 -0.58 189 189
FOXA3 -0.14 0.28 -9999 0 -0.88 54 54
FOXA2 -0.28 0.47 -9999 0 -1.2 64 64
ABCC8 -0.25 0.42 -9999 0 -1.1 57 57
ALB -0.22 0.3 -9999 0 -0.74 89 89
Visual signal transduction: Rods

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
mol:K + 0.014 0 -9999 0 -10000 0 0
GNAT1/GTP -0.004 0.049 -9999 0 -0.64 3 3
Metarhodopsin II/Arrestin -0.004 0.05 -9999 0 -0.56 4 4
PDE6G/GNAT1/GTP -0.022 0.11 -9999 0 -0.56 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.002 0.064 -9999 0 -0.82 3 3
GRK1 0.001 0.037 -9999 0 -0.82 1 1
CNG Channel -0.41 0.29 -9999 0 -0.6 303 303
mol:Na + -0.31 0.26 -9999 0 -0.82 55 55
mol:ADP 0.001 0.037 -9999 0 -0.82 1 1
RGS9-1/Gbeta5/R9AP -0.019 0.09 -9999 0 -0.54 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.32 0.28 -9999 0 -0.86 55 55
CNGB1 -0.43 0.41 -9999 0 -0.81 265 265
RDH5 0.011 0.045 -9999 0 -0.69 2 2
SAG 0.002 0.005 -9999 0 -10000 0 0
mol:Ca2+ -0.28 0.27 -9999 0 -0.79 54 54
Na + (4 Units) -0.29 0.24 -9999 0 -0.76 54 54
RGS9 -0.004 0.12 -9999 0 -0.77 11 11
GNB1/GNGT1 -0.11 0.24 -9999 0 -0.63 85 85
GNAT1/GDP -0.019 0.094 -9999 0 -0.56 10 10
GUCY2D -0.034 0.19 -9999 0 -0.82 28 28
GNGT1 -0.13 0.31 -9999 0 -0.82 85 85
GUCY2F 0 0.052 -9999 0 -0.82 2 2
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.16 0.22 -9999 0 -0.6 54 54
mol:11-cis-retinal 0.011 0.045 -9999 0 -0.69 2 2
mol:cGMP -0.066 0.2 -9999 0 -0.52 77 77
GNB1 0.014 0 -9999 0 -10000 0 0
Rhodopsin -0.007 0.065 -9999 0 -0.59 6 6
SLC24A1 0.014 0 -9999 0 -10000 0 0
CNGA1 -0.027 0.15 -9999 0 -0.57 35 35
Metarhodopsin II -0.005 0.051 -9999 0 -0.51 5 5
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.085 0.2 -9999 0 -0.54 76 76
RGS9BP -0.001 0.089 -9999 0 -0.57 12 12
Metarhodopsin II/Transducin -0.037 0.12 -9999 0 -0.28 91 91
GCAP Family/Ca ++ -0.058 0.16 -9999 0 -0.52 53 53
PDE6A/B -0.22 0.24 -9999 0 -0.46 245 245
mol:Pi -0.019 0.09 -9999 0 -0.54 9 9
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.089 0.19 -9999 0 -0.5 88 88
PDE6B -0.045 0.2 -9999 0 -0.68 42 42
PDE6A -0.25 0.29 -9999 0 -0.57 225 225
PDE6G -0.015 0.15 -9999 0 -0.82 17 17
RHO -0.002 0.074 -9999 0 -0.82 4 4
PDE6 -0.18 0.2 -9999 0 -0.64 42 42
GUCA1A -0.074 0.26 -9999 0 -0.82 52 52
GC2/GCAP Family -0.06 0.17 -9999 0 -0.52 54 54
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.006 0.074 -9999 0 -0.65 6 6
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.016 0.036 -9999 0 -10000 0 0
NFATC2 -0.063 0.13 -9999 0 -0.39 59 59
NFATC3 -0.016 0.036 -9999 0 -10000 0 0
CD40LG -0.34 0.35 -9999 0 -0.85 109 109
PTGS2 -0.36 0.37 -9999 0 -0.88 127 127
JUNB 0.014 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.017 0.016 -9999 0 -10000 0 0
CaM/Ca2+ -0.017 0.016 -9999 0 -10000 0 0
CALM1 0.004 0.011 -9999 0 -10000 0 0
JUN 0.004 0.011 -9999 0 -10000 0 0
mol:Ca2+ -0.018 0.014 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.004 -9999 0 -10000 0 0
FOSL1 -0.011 0.14 -9999 0 -0.8 15 15
CREM 0.014 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.17 0.16 -9999 0 -0.6 22 22
FOS -0.072 0.2 -9999 0 -0.58 64 64
IFNG -0.38 0.39 -9999 0 -0.87 146 146
AP-1/NFAT1-c-4 -0.4 0.39 -9999 0 -1.1 85 85
FASLG -0.33 0.35 -9999 0 -0.88 94 94
NFAT1-c-4/ICER1 -0.11 0.12 -9999 0 -0.47 16 16
IL2RA -0.33 0.35 -9999 0 -0.88 99 99
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.51 0.42 -9999 0 -0.82 286 286
JunB/Fra1/NFAT1-c-4 -0.11 0.14 -9999 0 -0.56 20 20
IL4 -0.31 0.31 -9999 0 -0.81 80 80
IL2 -0.01 0.035 -9999 0 -0.68 1 1
IL3 -0.029 0.023 -9999 0 -10000 0 0
FKBP1A 0.014 0 -9999 0 -10000 0 0
BATF3 0.007 0.074 -9999 0 -0.82 4 4
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.014 0.002 -9999 0 -10000 0 0
Effects of Botulinum toxin

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
STX1A -0.015 0.13 -9999 0 -0.64 21 21
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.03 0.11 -9999 0 -0.41 36 36
STXBP1 0.014 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.15 0.23 -9999 0 -0.47 161 161
RAB3GAP2/RIMS1/UNC13B -0.025 0.089 -9999 0 -0.54 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
UniProt:P30996 0 0 -9999 0 -10000 0 0
UniProt:Q60393 0 0 -9999 0 -10000 0 0
CST086 0 0 -9999 0 -10000 0 0
RIMS1 -0.031 0.15 -9999 0 -0.57 34 34
mol:ACh -0.005 0.042 -9999 0 -0.12 57 57
RAB3GAP2 0.014 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.044 0.1 -9999 0 -0.41 10 10
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.15 0.23 -9999 0 -0.47 161 161
UNC13B 0.011 0.037 -9999 0 -0.57 2 2
CHRNA1 -0.21 0.33 -9999 0 -0.68 161 161
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.14 0.26 -9999 0 -0.58 126 126
SNAP25 -0.015 0.082 -9999 0 -0.3 37 37
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.2 0.36 -9999 0 -0.81 126 126
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.005 0.12 -9999 0 -0.55 21 21
STX1A/SNAP25 fragment 1/VAMP2 -0.044 0.1 -9999 0 -0.41 10 10
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.026 0.16 -10000 0 -0.41 26 26
CRKL -0.024 0.15 -10000 0 -0.4 63 63
HRAS -0.018 0.16 -10000 0 -0.56 11 11
mol:PIP3 -0.037 0.14 -10000 0 -0.4 62 62
SPRED1 0.014 0 -10000 0 -10000 0 0
SPRED2 0.011 0.037 -10000 0 -0.57 2 2
GAB1 -0.033 0.16 -10000 0 -0.43 62 62
FOXO3 -0.015 0.14 -10000 0 -0.37 62 62
AKT1 -0.026 0.15 -10000 0 -0.4 62 62
BAD -0.015 0.14 -10000 0 -0.37 62 62
megakaryocyte differentiation -0.043 0.17 -10000 0 -0.43 74 74
GSK3B -0.015 0.14 -10000 0 -0.37 62 62
RAF1 -0.003 0.14 -10000 0 -0.45 9 9
SHC1 0.014 0 -10000 0 -10000 0 0
STAT3 -0.033 0.16 -10000 0 -0.43 62 62
STAT1 -0.11 0.38 -10000 0 -1 62 62
HRAS/SPRED1 -0.053 0.11 -10000 0 -0.45 9 9
cell proliferation -0.036 0.17 -10000 0 -0.44 62 62
PIK3CA 0.014 0 -10000 0 -10000 0 0
TEC -0.013 0.12 -10000 0 -0.57 23 23
RPS6KB1 -0.032 0.16 -10000 0 -0.42 64 64
HRAS/SPRED2 -0.054 0.11 -10000 0 -0.44 12 12
LYN/TEC/p62DOK -0.071 0.15 -10000 0 -0.52 18 18
MAPK3 0.013 0.1 -10000 0 -0.34 4 4
STAP1 -0.066 0.19 -10000 0 -0.44 96 96
GRAP2 -0.004 0.11 -10000 0 -0.66 13 13
JAK2 -0.13 0.28 -10000 0 -0.84 62 62
STAT1 (dimer) -0.11 0.37 -10000 0 -1 62 62
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.094 0.18 -10000 0 -0.56 20 20
actin filament polymerization -0.034 0.16 -10000 0 -0.43 63 63
LYN 0.012 0.037 -10000 0 -0.82 1 1
STAP1/STAT5A (dimer) -0.075 0.24 -10000 0 -0.59 66 66
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
CBL/CRKL/GRB2 -0.007 0.14 -10000 0 -0.55 1 1
PI3K -0.019 0.16 -10000 0 -0.41 62 62
PTEN 0.014 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.16 0.45 -10000 0 -1.2 64 64
MAPK8 -0.037 0.17 -10000 0 -0.45 62 62
STAT3 (dimer) -0.032 0.16 -10000 0 -0.42 62 62
positive regulation of transcription 0.016 0.087 -10000 0 -0.28 2 2
mol:GDP -0.078 0.15 -10000 0 -0.58 14 14
PIK3C2B -0.033 0.16 -10000 0 -0.44 62 62
CBL/CRKL -0.014 0.15 -10000 0 -0.38 57 57
FER -0.034 0.16 -10000 0 -0.43 62 62
SH2B3 -0.034 0.16 -10000 0 -0.43 63 63
PDPK1 -0.027 0.14 -10000 0 -0.37 62 62
SNAI2 -0.04 0.17 -10000 0 -0.44 69 69
positive regulation of cell proliferation -0.068 0.27 -10000 0 -0.73 63 63
KITLG 0.011 0.047 -10000 0 -0.58 3 3
cell motility -0.068 0.27 -10000 0 -0.73 63 63
PTPN6 0.008 0.013 -10000 0 -10000 0 0
EPOR -0.006 0.15 -10000 0 -0.68 11 11
STAT5A (dimer) -0.05 0.22 -10000 0 -0.6 63 63
SOCS1 -0.05 0.22 -10000 0 -0.82 38 38
cell migration 0.043 0.17 0.44 71 -10000 0 71
SOS1 0.014 0 -10000 0 -10000 0 0
EPO -0.079 0.26 -10000 0 -0.82 55 55
VAV1 0.003 0.082 -10000 0 -0.59 9 9
GRB10 -0.034 0.16 -10000 0 -0.43 63 63
PTPN11 0.014 0.007 -10000 0 -10000 0 0
SCF/KIT -0.043 0.17 -10000 0 -0.46 64 64
GO:0007205 0.001 0.009 -10000 0 -10000 0 0
MAP2K1 0.009 0.11 -10000 0 -0.38 4 4
CBL 0.014 0 -10000 0 -10000 0 0
KIT -0.13 0.45 -10000 0 -1.3 63 63
MAP2K2 0.009 0.11 -10000 0 -0.36 6 6
SHC/Grb2/SOS1 -0.057 0.13 -10000 0 -0.4 56 56
STAT5A -0.052 0.23 -10000 0 -0.62 63 63
GRB2 0.014 0 -10000 0 -10000 0 0
response to radiation -0.039 0.17 -10000 0 -0.43 69 69
SHC/GRAP2 -0.013 0.08 -10000 0 -0.49 13 13
PTPRO -0.045 0.17 -10000 0 -0.44 74 74
SH2B2 -0.035 0.16 -10000 0 -0.44 63 63
DOK1 0.012 0.037 -10000 0 -0.82 1 1
MATK -0.044 0.18 -10000 0 -0.45 71 71
CREBBP 0.034 0.015 -10000 0 -10000 0 0
BCL2 -0.007 0.17 -10000 0 -1 8 8
BMP receptor 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
BMP7/BMPR2/BMPR1A-1B/FS -0.23 0.28 -9999 0 -0.54 201 201
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.055 0.21 -9999 0 -0.71 46 46
SMAD9 -0.075 0.17 -9999 0 -0.58 44 44
SMAD4 0.013 0.026 -9999 0 -0.57 1 1
SMAD5 -0.049 0.14 -9999 0 -0.48 27 27
BMP7/USAG1 -0.16 0.24 -9999 0 -0.5 157 157
SMAD5/SKI -0.039 0.14 -9999 0 -0.46 25 25
SMAD1 0.042 0.027 -9999 0 -10000 0 0
BMP2 -0.018 0.16 -9999 0 -0.81 19 19
SMAD1/SMAD1/SMAD4 0 0.011 -9999 0 -10000 0 0
BMPR1A 0.011 0.037 -9999 0 -0.57 2 2
BMPR1B -0.06 0.23 -9999 0 -0.76 47 47
BMPR1A-1B/BAMBI -0.062 0.16 -9999 0 -0.55 45 45
AHSG -0.038 0.19 -9999 0 -0.82 29 29
CER1 -0.006 0.09 -9999 0 -0.82 6 6
BMP2-4/CER1 -0.035 0.13 -9999 0 -0.56 25 25
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.089 0.19 -9999 0 -0.54 47 47
BMP2-4 (homodimer) -0.033 0.14 -9999 0 -0.56 29 29
RGMB 0.014 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.05 0.14 -9999 0 -0.5 43 43
RGMA -0.053 0.19 -9999 0 -0.57 57 57
SMURF1 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.09 0.18 -9999 0 -0.5 48 48
BMP2-4/USAG1 -0.14 0.21 -9999 0 -0.58 52 52
SMAD6/SMURF1/SMAD5 -0.039 0.14 -9999 0 -0.47 22 22
SOSTDC1 -0.17 0.29 -9999 0 -0.62 140 140
BMP7/BMPR2/BMPR1A-1B -0.067 0.16 -9999 0 -0.52 41 41
SKI 0.014 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.004 0.087 -9999 0 -0.78 6 6
HFE2 -0.17 0.27 -9999 0 -0.57 153 153
ZFYVE16 0.014 0 -9999 0 -10000 0 0
MAP3K7 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.045 0.15 -9999 0 -0.56 34 34
SMAD5/SMAD5/SMAD4 -0.039 0.14 -9999 0 -0.47 23 23
MAPK1 0.014 0 -9999 0 -10000 0 0
TAK1/TAB family -0.092 0.13 -9999 0 -0.52 24 24
BMP7 (homodimer) -0.031 0.16 -9999 0 -0.57 38 38
NUP214 0.014 0 -9999 0 -10000 0 0
BMP6/FETUA -0.044 0.16 -9999 0 -0.62 35 35
SMAD1/SKI 0.048 0.026 -9999 0 -10000 0 0
SMAD6 0.014 0 -9999 0 -10000 0 0
CTDSP2 0.014 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.06 0.17 -9999 0 -0.56 48 48
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.36 0.41 -9999 0 -0.82 220 220
BMPR2 (homodimer) 0.014 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.056 0.18 -9999 0 -0.58 48 48
CHRDL1 -0.28 0.29 -9999 0 -0.57 251 251
ENDOFIN/SMAD1 0.048 0.026 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.001 0.004 -9999 0 -10000 0 0
SMAD6/SMURF1 0.014 0 -9999 0 -10000 0 0
BAMBI -0.009 0.12 -9999 0 -0.68 16 16
SMURF2 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.2 0.21 -9999 0 -0.74 24 24
BMP2-4/GREM1 -0.27 0.29 -9999 0 -0.57 228 228
SMAD7 0.014 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.055 0.17 -9999 0 -0.53 45 45
SMAD1/SMAD6 0.048 0.026 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.031 0.16 -9999 0 -0.57 38 38
BMP6 0.004 0.087 -9999 0 -0.78 6 6
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.072 0.16 -9999 0 -0.44 48 48
PPM1A 0.014 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.048 0.026 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.014 0 -9999 0 -10000 0 0
PPP1CA 0.014 0 -9999 0 -10000 0 0
XIAP 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
PPP1R15A 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.17 0.23 -9999 0 -0.51 114 114
CHRD -0.012 0.14 -9999 0 -0.79 16 16
BMPR2 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.098 0.19 -9999 0 -0.53 48 48
BMP4 0 0.089 -9999 0 -0.59 11 11
FST -0.28 0.4 -9999 0 -0.82 178 178
BMP2-4/NOG -0.07 0.18 -9999 0 -0.58 42 42
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.062 0.15 -9999 0 -0.48 41 41
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.02 0.095 -10000 0 -0.55 11 11
fibroblast growth factor receptor signaling pathway -0.02 0.095 -10000 0 -0.55 11 11
LAMA1 -0.32 0.41 -10000 0 -0.81 199 199
PRNP 0.012 0.037 -10000 0 -0.82 1 1
GPC1/SLIT2 -0.056 0.14 -10000 0 -0.42 67 67
SMAD2 0.033 0.035 -10000 0 -0.49 1 1
GPC1/PrPc/Cu2+ -0.003 0.038 -10000 0 -0.48 3 3
GPC1/Laminin alpha1 -0.25 0.31 -10000 0 -0.63 199 199
TDGF1 -0.002 0.091 -10000 0 -0.82 6 6
CRIPTO/GPC1 -0.01 0.076 -10000 0 -0.6 8 8
APP/GPC1 -0.003 0.044 -10000 0 -0.55 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.017 0.069 -10000 0 -0.54 7 7
FLT1 0.012 0.037 -10000 0 -0.82 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.003 0.036 -10000 0 -0.54 1 1
SERPINC1 -0.005 0.12 -10000 0 -0.82 10 10
FYN 0.016 0.073 -10000 0 -0.54 8 8
FGR 0.016 0.073 -10000 0 -0.54 8 8
positive regulation of MAPKKK cascade 0.008 0.11 -10000 0 -0.46 11 11
SLIT2 -0.064 0.2 -10000 0 -0.57 66 66
GPC1/NRG -0.1 0.23 -10000 0 -0.61 83 83
NRG1 -0.12 0.3 -10000 0 -0.8 81 81
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.009 0.07 -10000 0 -0.54 8 8
LYN 0.016 0.073 -10000 0 -0.54 8 8
mol:Spermine 0.01 0.035 -10000 0 -0.53 2 2
cell growth -0.02 0.095 -10000 0 -0.55 11 11
BMP signaling pathway -0.011 0.045 0.69 2 -10000 0 2
SRC 0.017 0.069 -10000 0 -0.54 7 7
TGFBR1 0.014 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.36 0.28 -10000 0 -0.57 318 318
GPC1 0.011 0.045 -10000 0 -0.69 2 2
TGFBR1 (dimer) 0.014 0 -10000 0 -10000 0 0
VEGFA 0.004 0.091 -10000 0 -0.82 6 6
BLK -0.061 0.2 -10000 0 -0.55 67 67
HCK 0.012 0.097 -10000 0 -0.65 9 9
FGF2 -0.007 0.12 -10000 0 -0.63 16 16
FGFR1 0.004 0.087 -10000 0 -0.78 6 6
VEGFR1 homodimer 0.012 0.037 -10000 0 -0.82 1 1
TGFBR2 0.011 0.037 -10000 0 -0.57 2 2
cell death -0.003 0.044 -10000 0 -0.55 3 3
ATIII/GPC1 -0.015 0.094 -10000 0 -0.61 12 12
PLA2G2A/GPC1 -0.26 0.2 -10000 0 -0.41 319 319
LCK 0.003 0.11 -10000 0 -0.54 19 19
neuron differentiation -0.1 0.23 -10000 0 -0.61 83 83
PrPc/Cu2+ -0.001 0.029 -10000 0 -0.64 1 1
APP 0.012 0.037 -10000 0 -0.82 1 1
TGFBR2 (dimer) 0.011 0.037 -10000 0 -0.56 2 2
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.27 0.23 -10000 0 -0.89 13 13
IHH -0.054 0.075 -10000 0 -0.78 3 3
SHH Np/Cholesterol/GAS1 -0.038 0.14 -10000 0 -0.5 41 41
LRPAP1 0.014 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.044 0.14 0.5 41 -10000 0 41
SMO/beta Arrestin2 -0.14 0.15 -10000 0 -0.57 22 22
SMO -0.16 0.16 -10000 0 -0.61 23 23
AKT1 -0.061 0.092 -10000 0 -0.72 3 3
ARRB2 0.014 0 -10000 0 -10000 0 0
BOC -0.039 0.17 -10000 0 -0.57 45 45
ADRBK1 0.014 0 -10000 0 -10000 0 0
heart looping -0.15 0.16 -10000 0 -0.6 23 23
STIL -0.13 0.16 -10000 0 -0.62 30 30
DHH N/PTCH2 -0.014 0.086 -10000 0 -0.53 13 13
DHH N/PTCH1 -0.13 0.14 -10000 0 -0.7 8 8
PIK3CA 0.014 0 -10000 0 -10000 0 0
DHH 0.009 0.053 -10000 0 -0.82 2 2
PTHLH -0.45 0.34 -10000 0 -0.66 351 351
determination of left/right symmetry -0.15 0.16 -10000 0 -0.6 23 23
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
skeletal system development -0.45 0.33 -10000 0 -0.65 351 351
IHH N/Hhip -0.055 0.17 -10000 0 -0.67 33 33
DHH N/Hhip -0.04 0.15 -10000 0 -0.62 32 32
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.15 0.16 -10000 0 -0.6 23 23
pancreas development -0.038 0.19 -10000 0 -0.8 30 30
HHAT 0.011 0.037 -10000 0 -0.57 2 2
PI3K -0.002 0.031 -10000 0 -0.41 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.004 0.087 -10000 0 -0.71 7 7
somite specification -0.15 0.16 -10000 0 -0.6 23 23
SHH Np/Cholesterol/PTCH1 -0.15 0.17 -10000 0 -0.63 33 33
SHH Np/Cholesterol/PTCH2 -0.041 0.16 -10000 0 -0.54 39 39
SHH Np/Cholesterol/Megalin -0.06 0.19 -10000 0 -0.56 56 56
SHH -0.031 0.17 -10000 0 -0.62 39 39
catabolic process -0.16 0.15 -10000 0 -0.65 10 10
SMO/Vitamin D3 -0.15 0.17 -10000 0 -0.64 31 31
SHH Np/Cholesterol/Hhip -0.063 0.19 -10000 0 -0.57 57 57
LRP2 -0.032 0.18 -10000 0 -0.82 26 26
receptor-mediated endocytosis -0.17 0.17 -10000 0 -0.65 37 37
SHH Np/Cholesterol/BOC -0.061 0.16 -10000 0 -0.51 38 38
SHH Np/Cholesterol/CDO -0.039 0.14 -10000 0 -0.5 38 38
mesenchymal cell differentiation 0.067 0.19 0.56 57 -10000 0 57
mol:Vitamin D3 -0.14 0.17 -10000 0 -0.63 33 33
IHH N/PTCH2 -0.024 0.097 -10000 0 -0.57 14 14
CDON 0 0.089 -10000 0 -0.57 12 12
IHH N/PTCH1 -0.16 0.15 -10000 0 -0.66 10 10
Megalin/LRPAP1 -0.033 0.14 -10000 0 -0.63 26 26
PTCH2 -0.002 0.1 -10000 0 -0.68 11 11
SHH Np/Cholesterol -0.036 0.14 -10000 0 -0.5 39 39
PTCH1 -0.16 0.15 -10000 0 -0.66 10 10
HHIP -0.038 0.19 -10000 0 -0.8 30 30
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 -0.12 0.33 -10000 0 -0.92 68 68
NFATC2 -0.041 0.23 -10000 0 -0.73 28 28
NFATC3 -0.01 0.062 -10000 0 -10000 0 0
CD40LG -0.37 0.41 -10000 0 -1.1 67 67
ITCH 0.016 0.093 -10000 0 -10000 0 0
CBLB 0.016 0.093 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.35 0.45 -10000 0 -1.2 98 98
JUNB 0.014 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.037 0.095 -10000 0 -10000 0 0
T cell anergy -0.009 0.16 -10000 0 -0.54 15 15
TLE4 -0.01 0.17 -10000 0 -0.65 14 14
Jun/NFAT1-c-4/p21SNFT -0.17 0.23 -10000 0 -0.99 14 14
AP-1/NFAT1-c-4 -0.38 0.44 -10000 0 -1.1 71 71
IKZF1 -0.02 0.2 -10000 0 -0.78 18 18
T-helper 2 cell differentiation -0.075 0.23 -10000 0 -0.79 23 23
AP-1/NFAT1 -0.14 0.18 -10000 0 -0.64 31 31
CALM1 0.006 0.061 -10000 0 -10000 0 0
EGR2 -0.066 0.29 -10000 0 -1.4 14 14
EGR3 -0.057 0.26 -10000 0 -1.3 11 11
NFAT1/FOXP3 -0.14 0.34 -10000 0 -0.8 87 87
EGR1 -0.014 0.12 -10000 0 -0.57 24 24
JUN -0.02 0.035 -10000 0 -10000 0 0
EGR4 -0.089 0.27 -10000 0 -0.8 62 62
mol:Ca2+ -0.009 0.065 -10000 0 -10000 0 0
GBP3 -0.027 0.21 -10000 0 -0.73 25 25
FOSL1 -0.011 0.14 -10000 0 -0.8 15 15
NFAT1-c-4/MAF/IRF4 -0.12 0.24 -10000 0 -0.96 16 16
DGKA -0.009 0.16 -10000 0 -0.61 14 14
CREM 0.013 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.22 0.26 -10000 0 -0.95 26 26
CTLA4 -0.18 0.43 -10000 0 -1 87 87
NFAT1-c-4 (dimer)/EGR1 -0.11 0.24 -10000 0 -1 16 16
NFAT1-c-4 (dimer)/EGR4 -0.16 0.28 -10000 0 -0.92 31 31
FOS -0.097 0.19 -10000 0 -0.59 64 64
IFNG -0.23 0.35 -10000 0 -0.82 92 92
T cell activation -0.11 0.2 -10000 0 -0.73 10 10
MAF 0.008 0.058 -10000 0 -0.57 5 5
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.042 0.16 0.74 8 -10000 0 8
TNF -0.14 0.32 -10000 0 -0.97 37 37
FASLG -0.13 0.38 -10000 0 -1.3 31 31
TBX21 -0.044 0.19 -10000 0 -0.78 29 29
BATF3 0.007 0.074 -10000 0 -0.82 4 4
PRKCQ -0.001 0.095 -10000 0 -0.61 11 11
PTPN1 -0.009 0.16 -10000 0 -0.62 12 12
NFAT1-c-4/ICER1 -0.1 0.21 -10000 0 -0.94 14 14
GATA3 -0.016 0.15 -10000 0 -0.78 19 19
T-helper 1 cell differentiation -0.21 0.35 -10000 0 -0.81 92 92
IL2RA -0.31 0.38 -10000 0 -1 94 94
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.009 0.16 -10000 0 -0.7 5 5
E2F1 -0.041 0.22 -10000 0 -0.81 37 37
PPARG -0.21 0.28 -10000 0 -0.57 194 194
SLC3A2 -0.009 0.16 -10000 0 -0.65 9 9
IRF4 -0.039 0.2 -10000 0 -0.75 34 34
PTGS2 -0.39 0.45 -10000 0 -1.1 89 89
CSF2 -0.56 0.51 -10000 0 -1.1 201 201
JunB/Fra1/NFAT1-c-4 -0.1 0.22 -10000 0 -0.96 14 14
IL4 -0.078 0.24 -10000 0 -0.84 22 22
IL5 -0.34 0.38 -10000 0 -1 55 55
IL2 -0.11 0.2 -10000 0 -0.75 9 9
IL3 -0.065 0.051 -10000 0 -10000 0 0
RNF128 -0.04 0.23 -10000 0 -0.64 66 66
NFATC1 -0.042 0.16 -10000 0 -0.74 8 8
CDK4 0.025 0.14 0.65 3 -10000 0 3
PTPRK -0.009 0.16 -10000 0 -0.65 9 9
IL8 -0.42 0.46 -10000 0 -1.1 119 119
POU2F1 0.014 0.002 -10000 0 -10000 0 0
IL12-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
IL12/IL12R/TYK2/JAK2/SOCS1 -0.09 0.23 -10000 0 -0.62 51 51
TBX21 -0.15 0.47 -10000 0 -1.2 55 55
B2M 0.012 0.01 -10000 0 -10000 0 0
TYK2 0.016 0.044 -10000 0 -0.84 1 1
IL12RB1 -0.059 0.25 -10000 0 -0.84 46 46
GADD45B -0.064 0.31 -10000 0 -0.81 30 30
IL12RB2 -0.13 0.32 -10000 0 -0.79 92 92
GADD45G -0.075 0.33 -10000 0 -0.86 36 36
natural killer cell activation 0.006 0.025 -10000 0 -10000 0 0
RELB 0.004 0.091 -10000 0 -0.82 6 6
RELA 0.014 0 -10000 0 -10000 0 0
IL18 -0.006 0.11 -10000 0 -0.57 19 19
IL2RA -0.063 0.24 -10000 0 -0.82 46 46
IFNG -0.17 0.34 -10000 0 -0.82 108 108
STAT3 (dimer) -0.086 0.34 -10000 0 -0.83 51 51
HLA-DRB5 -0.007 0.12 -10000 0 -0.7 14 14
FASLG -0.16 0.49 -10000 0 -1.2 62 62
NF kappa B2 p52/RelB -0.22 0.37 -10000 0 -1 69 69
CD4 0.01 0.046 -10000 0 -0.7 2 2
SOCS1 -0.05 0.22 -10000 0 -0.82 38 38
EntrezGene:6955 -0.004 0.015 -10000 0 -10000 0 0
CD3D -0.014 0.14 -10000 0 -0.73 17 17
CD3E -0.007 0.12 -10000 0 -0.77 12 12
CD3G -0.028 0.16 -10000 0 -0.66 29 29
IL12Rbeta2/JAK2 -0.088 0.25 -10000 0 -0.61 91 91
CCL3 -0.14 0.45 -10000 0 -1.2 57 57
CCL4 -0.14 0.45 -10000 0 -1.2 52 52
HLA-A 0.002 0.087 -10000 0 -0.78 6 6
IL18/IL18R 0.024 0.14 -10000 0 -0.46 28 28
NOS2 -0.15 0.44 -10000 0 -1 65 65
IL12/IL12R/TYK2/JAK2/SPHK2 -0.067 0.21 -10000 0 -0.6 37 37
IL1R1 -0.13 0.42 -10000 0 -1.1 51 51
IL4 -0.004 0.025 -10000 0 -10000 0 0
JAK2 0.016 0.034 -10000 0 -0.59 1 1
EntrezGene:6957 -0.004 0.015 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.1 0.34 -10000 0 -0.82 68 68
RAB7A -0.039 0.28 -10000 0 -0.74 19 19
lysosomal transport -0.035 0.27 -10000 0 -0.7 19 19
FOS -0.17 0.48 -10000 0 -1.2 74 74
STAT4 (dimer) -0.087 0.37 -10000 0 -0.93 48 48
STAT5A (dimer) -0.28 0.44 -10000 0 -1.1 93 93
GZMA -0.16 0.5 -10000 0 -1.3 66 66
GZMB -0.17 0.5 -10000 0 -1.2 78 78
HLX 0.009 0.064 -10000 0 -0.82 3 3
LCK -0.15 0.48 -10000 0 -1.2 63 63
TCR/CD3/MHC II/CD4 -0.032 0.19 -10000 0 -0.59 34 34
IL2/IL2R -0.069 0.2 -10000 0 -0.57 59 59
MAPK14 -0.064 0.32 -10000 0 -0.82 35 35
CCR5 -0.086 0.36 -10000 0 -1 35 35
IL1B -0.069 0.26 -10000 0 -0.8 53 53
STAT6 -0.012 0.12 -10000 0 -10000 0 0
STAT4 -0.006 0.12 -10000 0 -0.8 12 12
STAT3 0.014 0 -10000 0 -10000 0 0
STAT1 -0.033 0.19 -10000 0 -0.81 28 28
NFKB1 0.014 0 -10000 0 -10000 0 0
NFKB2 0.014 0 -10000 0 -10000 0 0
IL12B -0.054 0.24 -10000 0 -0.83 43 43
CD8A -0.058 0.22 -10000 0 -0.75 46 46
CD8B -0.069 0.24 -10000 0 -0.74 54 54
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.089 0.23 0.61 51 -10000 0 51
IL2RB 0.003 0.094 -10000 0 -0.78 7 7
proteasomal ubiquitin-dependent protein catabolic process -0.074 0.34 -10000 0 -0.83 48 48
IL2RG -0.014 0.15 -10000 0 -0.79 17 17
IL12 -0.046 0.21 -10000 0 -0.6 61 61
STAT5A 0.014 0 -10000 0 -10000 0 0
CD247 -0.023 0.16 -10000 0 -0.8 21 21
IL2 0.003 0.037 -10000 0 -0.82 1 1
SPHK2 0.014 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.008 0.13 -10000 0 -0.64 19 19
IL12/IL12R/TYK2/JAK2 -0.17 0.52 -10000 0 -1.3 67 67
MAP2K3 -0.064 0.32 -10000 0 -0.8 38 38
RIPK2 0.014 0 -10000 0 -10000 0 0
MAP2K6 -0.076 0.33 -10000 0 -0.83 41 41
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.01 0.045 -10000 0 -0.57 3 3
IL18RAP -0.01 0.14 -10000 0 -0.73 18 18
IL12Rbeta1/TYK2 -0.036 0.2 -10000 0 -0.65 47 47
EOMES -0.085 0.27 -10000 0 -0.68 74 74
STAT1 (dimer) -0.14 0.39 -10000 0 -0.88 78 78
T cell proliferation -0.033 0.28 0.42 1 -0.66 35 36
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.014 0.048 -10000 0 -0.71 2 2
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.15 0.23 -10000 0 -0.73 39 39
ATF2 -0.051 0.3 -10000 0 -0.77 33 33
Glucocorticoid receptor regulatory network

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
PCK2 0.015 0.065 0.35 3 -10000 0 3
SMARCC2 0.015 0.007 -10000 0 -10000 0 0
SMARCC1 0.015 0.007 -10000 0 -10000 0 0
TBX21 -0.099 0.24 -10000 0 -0.87 34 34
SUMO2 0.014 0.009 -10000 0 -10000 0 0
STAT1 (dimer) -0.023 0.19 -10000 0 -0.8 28 28
FKBP4 0.014 0 -10000 0 -10000 0 0
FKBP5 0.01 0.052 -10000 0 -0.65 3 3
GR alpha/HSP90/FKBP51/HSP90 0.098 0.099 0.35 14 -0.56 1 15
PRL -0.1 0.17 -10000 0 -0.66 13 13
cortisol/GR alpha (dimer)/TIF2 0.18 0.23 0.58 63 -10000 0 63
RELA -0.003 0.091 -10000 0 -10000 0 0
FGG 0.11 0.27 0.55 29 -0.66 34 63
GR beta/TIF2 0.068 0.15 0.37 18 -0.37 11 29
IFNG -0.37 0.34 -10000 0 -0.88 129 129
apoptosis 0.026 0.18 0.55 10 -0.63 5 15
CREB1 0.017 0.018 -10000 0 -10000 0 0
histone acetylation 0.001 0.12 0.43 4 -0.45 8 12
BGLAP -0.052 0.14 -10000 0 -0.74 9 9
GR/PKAc 0.098 0.089 0.39 5 -10000 0 5
NF kappa B1 p50/RelA -0.013 0.16 -10000 0 -0.47 10 10
SMARCD1 0.015 0.007 -10000 0 -10000 0 0
MDM2 0.083 0.084 0.31 20 -10000 0 20
GATA3 -0.012 0.15 -10000 0 -0.78 19 19
AKT1 0 0.001 -10000 0 -10000 0 0
CSF2 -0.32 0.29 -10000 0 -0.57 257 257
GSK3B 0.014 0.009 -10000 0 -10000 0 0
NR1I3 0.054 0.18 0.56 6 -0.77 3 9
CSN2 0.13 0.15 0.47 13 -0.54 2 15
BRG1/BAF155/BAF170/BAF60A 0.038 0.027 -10000 0 -10000 0 0
NFATC1 0.015 0.003 -10000 0 -10000 0 0
POU2F1 0.015 0.016 -10000 0 -10000 0 0
CDKN1A 0.031 0.037 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.008 -10000 0 -10000 0 0
SFN 0.006 0.074 -10000 0 -0.72 5 5
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.096 0.1 0.37 6 -0.45 3 9
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.029 0.24 0.55 5 -0.85 24 29
JUN -0.22 0.18 -10000 0 -0.65 37 37
IL4 -0.07 0.12 -10000 0 -0.57 5 5
CDK5R1 0.01 0.053 -10000 0 -0.82 2 2
PRKACA 0.014 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.16 0.31 -10000 0 -0.64 78 78
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.1 0.095 0.38 7 -0.51 1 8
cortisol/GR alpha (monomer) 0.25 0.27 0.68 84 -10000 0 84
NCOA2 -0.031 0.15 -10000 0 -0.57 38 38
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.14 0.19 -10000 0 -0.63 64 64
AP-1/NFAT1-c-4 -0.41 0.27 -10000 0 -0.8 107 107
AFP -0.16 0.2 -10000 0 -0.84 28 28
SUV420H1 0.014 0 -10000 0 -10000 0 0
IRF1 0.12 0.16 0.47 21 -0.47 1 22
TP53 0.033 0.052 -10000 0 -0.55 4 4
PPP5C 0.014 0 -10000 0 -10000 0 0
KRT17 -0.4 0.38 -10000 0 -0.93 149 149
KRT14 -0.23 0.37 -10000 0 -1.1 69 69
TBP 0.021 0.024 -10000 0 -10000 0 0
CREBBP 0.074 0.084 0.35 7 -10000 0 7
HDAC1 0.012 0.01 -10000 0 -10000 0 0
HDAC2 0.045 0.031 -10000 0 -10000 0 0
AP-1 -0.42 0.27 -10000 0 -0.81 108 108
MAPK14 0.014 0.008 -10000 0 -10000 0 0
MAPK10 -0.02 0.14 -10000 0 -0.6 28 28
MAPK11 0.014 0.009 -10000 0 -10000 0 0
KRT5 -0.27 0.25 -10000 0 -0.84 39 39
interleukin-1 receptor activity 0.031 0.031 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 -0.023 0.19 -10000 0 -0.8 28 28
CGA -0.065 0.14 -10000 0 -0.69 8 8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.26 0.2 0.42 262 -10000 0 262
MAPK3 0.014 0.009 -10000 0 -10000 0 0
MAPK1 0.014 0.008 -10000 0 -10000 0 0
ICAM1 -0.14 0.25 -10000 0 -0.71 52 52
NFKB1 -0.003 0.091 -10000 0 -10000 0 0
MAPK8 -0.17 0.17 -10000 0 -0.56 44 44
MAPK9 0.014 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.018 0.19 0.55 10 -0.66 5 15
BAX 0.031 0.037 -10000 0 -10000 0 0
POMC -0.17 0.32 -10000 0 -0.92 56 56
EP300 0.074 0.09 0.34 8 -0.44 2 10
cortisol/GR alpha (dimer)/p53 0.23 0.23 0.6 73 -0.52 1 74
proteasomal ubiquitin-dependent protein catabolic process 0.057 0.064 0.28 4 -10000 0 4
SGK1 0.12 0.13 -10000 0 -1.2 2 2
IL13 -0.22 0.2 -10000 0 -0.89 19 19
IL6 -0.18 0.34 -10000 0 -1 60 60
PRKACG 0.003 0.006 -10000 0 -10000 0 0
IL5 -0.19 0.16 -10000 0 -0.73 16 16
IL2 -0.27 0.2 -10000 0 -0.67 56 56
CDK5 0.014 0.005 -10000 0 -10000 0 0
PRKACB 0.013 0.026 -10000 0 -0.57 1 1
HSP90AA1 0.014 0 -10000 0 -10000 0 0
IL8 -0.22 0.34 -10000 0 -0.77 118 118
CDK5R1/CDK5 0.002 0.043 -10000 0 -0.63 2 2
NF kappa B1 p50/RelA/PKAc 0.015 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.22 0.21 0.57 63 -10000 0 63
SMARCA4 0.015 0.007 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.13 0.41 40 -10000 0 40
NF kappa B1 p50/RelA/Cbp 0.074 0.16 0.42 17 -10000 0 17
JUN (dimer) -0.22 0.18 -10000 0 -0.65 37 37
YWHAH 0.014 0 -10000 0 -10000 0 0
VIPR1 -0.088 0.22 -10000 0 -0.81 30 30
NR3C1 0.14 0.16 0.49 49 -10000 0 49
NR4A1 -0.026 0.13 -10000 0 -0.53 16 16
TIF2/SUV420H1 -0.031 0.11 -10000 0 -0.41 38 38
MAPKKK cascade 0.026 0.18 0.55 10 -0.63 5 15
cortisol/GR alpha (dimer)/Src-1 0.23 0.22 0.59 74 -10000 0 74
PBX1 -0.09 0.22 -10000 0 -0.57 90 90
POU1F1 0.003 0.017 -10000 0 -10000 0 0
SELE -0.22 0.4 -10000 0 -1.1 78 78
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.13 0.42 40 -10000 0 40
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.22 0.21 0.57 63 -10000 0 63
mol:cortisol 0.13 0.17 0.4 92 -0.23 1 93
MMP1 -0.64 0.24 -10000 0 -0.72 435 435
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.04 0.056 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.1 0.14 -9999 0 -0.45 36 36
JUN -0.066 0.16 -9999 0 -0.47 37 37
HRAS 0.012 0.037 -9999 0 -0.82 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.17 0.25 -9999 0 -0.61 90 90
RAP1A 0.014 0 -9999 0 -10000 0 0
FRS2 0.007 0.074 -9999 0 -0.82 4 4
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.25 -9999 0 -0.61 90 90
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.12 0.21 -9999 0 -0.61 47 47
RHOA 0.014 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.22 -9999 0 -0.55 89 89
GRB7 0.005 0.083 -9999 0 -0.74 6 6
RET51/GFRalpha1/GDNF -0.17 0.25 -9999 0 -0.61 89 89
MAPKKK cascade -0.13 0.19 -9999 0 -0.62 35 35
BCAR1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.2 -9999 0 -0.6 45 45
lamellipodium assembly -0.096 0.13 -9999 0 -0.41 36 36
RET51/GFRalpha1/GDNF/SHC -0.17 0.25 -9999 0 -0.61 89 89
PIK3CA 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.12 0.2 -9999 0 -0.6 44 44
RET9/GFRalpha1/GDNF/Shank3 -0.12 0.2 -9999 0 -0.6 44 44
MAPK3 -0.11 0.23 -9999 0 -0.68 34 34
DOK1 0.012 0.037 -9999 0 -0.82 1 1
DOK6 -0.003 0.11 -9999 0 -0.67 12 12
PXN 0.014 0 -9999 0 -10000 0 0
neurite development -0.092 0.22 -9999 0 -0.63 33 33
DOK5 -0.018 0.14 -9999 0 -0.61 25 25
GFRA1 -0.13 0.25 -9999 0 -0.57 120 120
MAPK8 -0.077 0.17 -9999 0 -0.5 37 37
HRAS/GTP -0.15 0.22 -9999 0 -0.71 35 35
tube development -0.11 0.19 -9999 0 -0.57 44 44
MAPK1 -0.11 0.23 -9999 0 -0.68 34 34
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.063 0.15 -9999 0 -0.53 16 16
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
PDLIM7 0.007 0.074 -9999 0 -0.82 4 4
RET51/GFRalpha1/GDNF/Dok6 -0.16 0.24 -9999 0 -0.57 97 97
SHC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.25 -9999 0 -0.61 89 89
RET51/GFRalpha1/GDNF/Dok5 -0.18 0.26 -9999 0 -0.62 103 103
PRKCA 0.011 0.045 -9999 0 -0.69 2 2
HRAS/GDP -0.001 0.029 -9999 0 -0.64 1 1
CREB1 -0.077 0.17 -9999 0 -0.49 34 34
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.06 0.15 -9999 0 -0.52 15 15
RET51/GFRalpha1/GDNF/Grb7 -0.17 0.25 -9999 0 -0.62 94 94
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.074 0.25 -9999 0 -0.78 55 55
DOK4 0.014 0 -9999 0 -10000 0 0
JNK cascade -0.064 0.16 -9999 0 -0.46 37 37
RET9/GFRalpha1/GDNF/FRS2 -0.12 0.2 -9999 0 -0.6 48 48
SHANK3 0.014 0 -9999 0 -10000 0 0
RASA1 0.011 0.037 -9999 0 -0.57 2 2
NCK1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.061 0.15 -9999 0 -0.52 15 15
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.088 0.18 -9999 0 -0.52 36 36
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.087 0.17 -9999 0 -0.52 34 34
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.089 0.18 -9999 0 -0.57 34 34
PI3K -0.1 0.24 -9999 0 -0.67 36 36
SOS1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.11 0.19 -9999 0 -0.57 44 44
GRB10 0.012 0.037 -9999 0 -0.82 1 1
activation of MAPKK activity -0.083 0.17 -9999 0 -0.51 36 36
RET51/GFRalpha1/GDNF/FRS2 -0.17 0.25 -9999 0 -0.62 92 92
GAB1 0.014 0 -9999 0 -10000 0 0
IRS1 0.01 0.045 -9999 0 -0.57 3 3
IRS2 0.011 0.037 -9999 0 -0.57 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.089 0.18 -9999 0 -0.57 34 34
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.25 -9999 0 -0.61 91 91
GRB2 0.014 0 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
GDNF -0.061 0.23 -9999 0 -0.82 43 43
RAC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.25 -9999 0 -0.61 89 89
Rac1/GTP -0.11 0.16 -9999 0 -0.5 36 36
RET9/GFRalpha1/GDNF -0.13 0.22 -9999 0 -0.44 148 148
GFRalpha1/GDNF -0.15 0.25 -9999 0 -0.51 148 148
TCR signaling in naïve CD8+ T cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GRB2/SOS1/SHC -0.068 0.16 -10000 0 -0.56 38 38
FYN -0.038 0.23 -10000 0 -0.69 43 43
LAT/GRAP2/SLP76 -0.055 0.2 -10000 0 -0.6 43 43
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.013 0.16 -10000 0 -0.47 39 39
B2M 0.014 0.005 -10000 0 -10000 0 0
IKBKG -0.019 0.043 -10000 0 -0.17 7 7
MAP3K8 0.01 0.045 -10000 0 -0.57 3 3
mol:Ca2+ -0.036 0.039 -10000 0 -0.11 33 33
integrin-mediated signaling pathway -0.002 0.027 -10000 0 -0.34 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.037 0.23 -10000 0 -0.69 42 42
TRPV6 -0.27 0.29 -10000 0 -0.58 233 233
CD28 -0.014 0.15 -10000 0 -0.79 17 17
SHC1 -0.042 0.23 -10000 0 -0.68 45 45
receptor internalization -0.043 0.24 -10000 0 -0.68 50 50
PRF1 -0.06 0.29 -10000 0 -0.9 47 47
KRAS 0.01 0.053 -10000 0 -0.82 2 2
GRB2 0.014 0 -10000 0 -10000 0 0
COT/AKT1 -0.001 0.13 -10000 0 -0.38 35 35
LAT -0.05 0.26 -10000 0 -0.73 47 47
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.011 0.14 -10000 0 -0.73 17 17
CD3E -0.005 0.12 -10000 0 -0.77 12 12
CD3G -0.026 0.16 -10000 0 -0.66 29 29
RASGRP2 0.007 0.023 -10000 0 -0.12 6 6
RASGRP1 -0.01 0.17 -10000 0 -0.46 44 44
HLA-A 0.004 0.087 -10000 0 -0.77 6 6
RASSF5 0.01 0.045 -10000 0 -0.57 3 3
RAP1A/GTP/RAPL -0.002 0.027 -10000 0 -0.35 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.024 0.058 -10000 0 -0.12 22 22
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.038 0.075 -10000 0 -0.27 20 20
PRKCA -0.013 0.097 -10000 0 -0.31 23 23
GRAP2 -0.004 0.11 -10000 0 -0.66 13 13
mol:IP3 0.034 0.19 0.23 171 -0.47 30 201
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.04 0.22 -10000 0 -0.6 53 53
ORAI1 0.15 0.16 0.32 233 -10000 0 233
CSK -0.045 0.24 -10000 0 -0.7 45 45
B7 family/CD28 -0.17 0.28 -10000 0 -0.8 59 59
CHUK 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.061 0.27 -10000 0 -0.8 47 47
PTPN6 -0.049 0.24 -10000 0 -0.73 42 42
VAV1 -0.045 0.24 -10000 0 -0.71 45 45
Monovalent TCR/CD3 -0.021 0.17 -10000 0 -0.6 31 31
CBL 0.014 0 -10000 0 -10000 0 0
LCK -0.046 0.25 -10000 0 -0.74 43 43
PAG1 -0.046 0.24 -10000 0 -0.69 47 47
RAP1A 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.063 0.27 -10000 0 -0.79 47 47
CD80 -0.19 0.36 -10000 0 -0.82 122 122
CD86 0.012 0.037 -10000 0 -0.82 1 1
PDK1/CARD11/BCL10/MALT1 -0.046 0.091 -10000 0 -0.31 27 27
HRAS 0.012 0.037 -10000 0 -0.82 1 1
GO:0035030 -0.092 0.25 -10000 0 -0.64 57 57
CD8A -0.056 0.22 -10000 0 -0.75 46 46
CD8B -0.066 0.24 -10000 0 -0.73 54 54
PTPRC -0.005 0.11 -10000 0 -0.69 13 13
PDK1/PKC theta -0.015 0.2 -10000 0 -0.58 39 39
CSK/PAG1 -0.04 0.23 -10000 0 -0.68 44 44
SOS1 0.014 0 -10000 0 -10000 0 0
peptide-MHC class I 0.012 0.067 -10000 0 -0.59 6 6
GRAP2/SLP76 -0.067 0.22 -10000 0 -0.69 42 42
STIM1 0.076 0.078 -10000 0 -10000 0 0
RAS family/GTP 0.023 0.074 -10000 0 -0.18 17 17
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.048 0.26 -10000 0 -0.73 50 50
mol:DAG -0.016 0.14 -10000 0 -0.42 30 30
RAP1A/GDP 0.012 0.025 -10000 0 -10000 0 0
PLCG1 0.014 0 -10000 0 -10000 0 0
CD247 -0.02 0.16 -10000 0 -0.79 21 21
cytotoxic T cell degranulation -0.055 0.28 -10000 0 -0.85 47 47
RAP1A/GTP -0.002 0.006 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.023 0.19 -10000 0 -0.56 41 41
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.016 0.23 0.26 122 -0.64 30 152
NRAS 0.014 0 -10000 0 -10000 0 0
ZAP70 -0.026 0.18 -10000 0 -0.78 25 25
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.05 0.19 -10000 0 -0.62 37 37
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.014 0 -10000 0 -10000 0 0
CD8 heterodimer -0.088 0.29 -10000 0 -0.72 73 73
CARD11 -0.037 0.2 -10000 0 -0.8 31 31
PRKCB -0.015 0.11 -10000 0 -0.35 24 24
PRKCE -0.012 0.096 -10000 0 -0.29 28 28
PRKCQ -0.028 0.22 -10000 0 -0.65 44 44
LCP2 0.009 0.064 -10000 0 -0.82 3 3
BCL10 0.014 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.006 0.14 -10000 0 -0.4 38 38
IKK complex 0.032 0.054 -10000 0 -0.13 5 5
RAS family/GDP -0.004 0.01 -10000 0 -0.087 2 2
MAP3K14 0.01 0.11 -10000 0 -0.31 18 18
PDPK1 -0.008 0.16 -10000 0 -0.45 36 36
TCR/CD3/MHC I/CD8/Fyn -0.055 0.27 -10000 0 -0.8 47 47
Coregulation of Androgen receptor activity

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
NRIP1 0 0.045 -9999 0 -0.56 2 2
SVIL 0.002 0.035 -9999 0 -0.57 1 1
ZNF318 0.04 0.061 -9999 0 -10000 0 0
JMJD2C 0.007 0.021 -9999 0 -0.1 13 13
T-DHT/AR/Ubc9 -0.11 0.18 -9999 0 -0.39 132 132
CARM1 0.012 0.003 -9999 0 -10000 0 0
PRDX1 0.015 0.004 -9999 0 -10000 0 0
PELP1 0.018 0.01 -9999 0 -10000 0 0
CTNNB1 0.004 0.032 -9999 0 -0.57 1 1
AKT1 0.021 0.017 -9999 0 -10000 0 0
PTK2B 0.006 0.03 -9999 0 -0.57 1 1
MED1 0.02 0.042 -9999 0 -0.82 1 1
MAK 0.029 0.11 -9999 0 -0.68 8 8
response to oxidative stress 0.002 0.004 -9999 0 -10000 0 0
HIP1 0.002 0.035 -9999 0 -0.57 1 1
GSN 0.002 0.026 -9999 0 -10000 0 0
NCOA2 -0.032 0.15 -9999 0 -0.57 38 38
NCOA6 0.002 0.043 -9999 0 -0.82 1 1
DNA-PK 0.031 0.066 -9999 0 -10000 0 0
NCOA4 0.011 0.026 -9999 0 -0.57 1 1
PIAS3 0.005 0.019 -9999 0 -10000 0 0
cell proliferation -0.012 0.1 -9999 0 -0.62 8 8
XRCC5 0.02 0.013 -9999 0 -10000 0 0
UBE3A -0.003 0.038 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.13 0.2 -9999 0 -0.46 96 96
FHL2 -0.017 0.11 -9999 0 -0.94 2 2
RANBP9 0.004 0.023 -9999 0 -10000 0 0
JMJD1A -0.058 0.075 -9999 0 -0.13 242 242
CDK6 0.001 0.1 -9999 0 -0.76 9 9
TGFB1I1 -0.022 0.14 -9999 0 -0.82 15 15
T-DHT/AR/CyclinD1 -0.13 0.19 -9999 0 -0.45 100 100
XRCC6 0.02 0.013 -9999 0 -10000 0 0
T-DHT/AR -0.14 0.2 -9999 0 -0.5 81 81
CTDSP1 0.011 0.005 -9999 0 -10000 0 0
CTDSP2 0.032 0.041 -9999 0 -10000 0 0
BRCA1 0.003 0.024 -9999 0 -10000 0 0
TCF4 0.027 0.03 -9999 0 -10000 0 0
CDKN2A -0.34 0.4 -9999 0 -0.76 230 230
SRF 0.03 0.022 -9999 0 -10000 0 0
NKX3-1 -0.14 0.15 -9999 0 -0.79 8 8
KLK3 -0.22 0.54 -9999 0 -1.4 88 88
TMF1 0.011 0.005 -9999 0 -10000 0 0
HNRNPA1 0.025 0.025 -9999 0 -10000 0 0
AOF2 -0.012 0.027 -9999 0 -0.07 84 84
APPL1 0.041 0.037 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.1 0.18 -9999 0 -0.43 80 80
AR -0.17 0.26 -9999 0 -0.6 132 132
UBA3 0.011 0.005 -9999 0 -10000 0 0
PATZ1 0.025 0.025 -9999 0 -10000 0 0
PAWR 0.011 0.005 -9999 0 -10000 0 0
PRKDC 0.02 0.013 -9999 0 -10000 0 0
PA2G4 0.026 0.027 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.095 0.16 -9999 0 -0.36 121 121
RPS6KA3 0 0.045 -9999 0 -0.57 2 2
T-DHT/AR/ARA70 -0.12 0.18 -9999 0 -0.39 133 133
LATS2 0.024 0.022 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.089 0.17 -9999 0 -0.4 79 79
Cyclin D3/CDK11 p58 0.003 0.007 -9999 0 -10000 0 0
VAV3 -0.035 0.15 -9999 0 -0.57 35 35
KLK2 -0.072 0.13 -9999 0 -0.76 13 13
CASP8 0.017 0.008 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.12 0.19 -9999 0 -0.43 97 97
TMPRSS2 -0.5 0.5 -9999 0 -1 236 236
CCND1 -0.008 0.12 -9999 0 -0.77 12 12
PIAS1 -0.003 0.038 -9999 0 -10000 0 0
mol:T-DHT -0.023 0.034 -9999 0 -0.067 145 145
CDC2L1 0.001 0.002 -9999 0 -10000 0 0
PIAS4 -0.012 0.057 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.12 0.19 -9999 0 -0.43 106 106
CMTM2 -0.01 0.14 -9999 0 -0.82 15 15
SNURF -0.015 0.12 -9999 0 -0.57 23 23
ZMIZ1 -0.006 0.042 -9999 0 -0.68 1 1
CCND3 0.015 0.002 -9999 0 -10000 0 0
TGIF1 0.023 0.046 -9999 0 -0.82 1 1
FKBP4 0.004 0.023 -9999 0 -10000 0 0
LPA4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ADCY4 0.021 0.016 -9999 0 -0.35 1 1
ADCY5 -0.072 0.17 -9999 0 -0.36 121 121
ADCY6 0.012 0.059 -9999 0 -0.35 13 13
ADCY7 0.021 0.016 -9999 0 -0.35 1 1
ADCY1 -0.005 0.12 -9999 0 -0.54 23 23
ADCY2 -0.11 0.18 -9999 0 -0.35 171 171
ADCY3 0.021 0.016 -9999 0 -0.35 1 1
ADCY8 -0.001 0.088 -9999 0 -0.54 13 13
PRKCE 0.011 0.019 -9999 0 -0.42 1 1
ADCY9 0.019 0.028 -9999 0 -0.35 3 3
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.047 0.096 -9999 0 -0.36 9 9
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.018 0.088 -9999 0 -0.48 16 16
RGS9BP -0.001 0.089 -9999 0 -0.57 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.001 0.037 -9999 0 -0.82 1 1
mol:Na + -0.089 0.2 -9999 0 -0.55 80 80
mol:ADP -0.051 0.2 -9999 0 -0.64 50 50
GNAT2 0.012 0.005 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.019 0.09 -9999 0 -0.54 9 9
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0 0 -9999 0 -10000 0 0
GRK7 -0.069 0.25 -9999 0 -0.82 49 49
CNGB3 -0.12 0.3 -9999 0 -0.82 79 79
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.17 0.29 -9999 0 -0.56 161 161
Cone PDE6 -0.017 0.078 -9999 0 -0.47 9 9
Cone Metarhodopsin II -0.052 0.16 -9999 0 -0.52 50 50
Na + (4 Units) -0.18 0.28 -9999 0 -0.56 161 161
GNAT2/GDP -0.016 0.077 -9999 0 -0.47 9 9
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.01 0.006 -9999 0 -10000 0 0
Cone Transducin -0.019 0.092 -9999 0 -0.5 16 16
SLC24A2 -0.16 0.33 -9999 0 -0.82 101 101
GNB3/GNGT2 -0.023 0.12 -9999 0 -0.58 20 20
GNB3 -0.014 0.15 -9999 0 -0.79 17 17
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0.007 0.038 -9999 0 -0.82 1 1
ARR3 0.002 0.005 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.089 0.2 -9999 0 -0.56 80 80
mol:Pi -0.019 0.09 -9999 0 -0.54 9 9
Cone CNG Channel -0.074 0.17 -9999 0 -0.46 80 80
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.16 0.33 -9999 0 -0.82 101 101
RGS9 -0.004 0.12 -9999 0 -0.77 11 11
PDE6C 0.002 0.005 -9999 0 -10000 0 0
GNGT2 0.01 0.052 -9999 0 -0.65 3 3
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.002 0.005 -9999 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 0.004 0.017 -10000 0 -10000 0 0
AES 0.003 0.015 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0.001 -10000 0 -10000 0 0
LRP6/FZD1 -0.008 0.068 -10000 0 -0.56 7 7
SMAD4 0.013 0.026 -10000 0 -0.57 1 1
DKK2 -0.009 0.13 -10000 0 -0.69 16 16
TLE1 0.003 0.015 -10000 0 -10000 0 0
MACF1 0.014 0.001 -10000 0 -10000 0 0
CTNNB1 0.032 0.11 -10000 0 -0.42 2 2
WIF1 -0.26 0.3 -10000 0 -0.58 219 219
beta catenin/RanBP3 -0.013 0.088 0.37 10 -10000 0 10
KREMEN2 -0.29 0.4 -10000 0 -0.82 183 183
DKK1 -0.28 0.39 -10000 0 -0.8 183 183
beta catenin/beta TrCP1 0.039 0.11 -10000 0 -10000 0 0
FZD1 0.005 0.087 -10000 0 -0.78 6 6
AXIN2 -0.012 0.21 -10000 0 -1.4 11 11
AXIN1 0.014 0.001 -10000 0 -10000 0 0
RAN 0.014 0.001 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.024 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.082 0.064 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.006 0.041 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin/Macf1 0.051 0.074 -10000 0 -10000 0 0
HNF1A -0.012 0.11 -10000 0 -0.82 9 9
CTBP1 0.003 0.015 -10000 0 -10000 0 0
MYC 0.014 0.045 -10000 0 -0.53 1 1
RANBP3 0.014 0.001 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.21 0.27 -10000 0 -0.55 191 191
NKD1 -0.017 0.15 -10000 0 -0.78 19 19
TCF4 0.003 0.016 -10000 0 -10000 0 0
TCF3 0.003 0.015 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.011 0.072 -10000 0 -0.49 10 10
Ran/GTP 0.001 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.013 0.09 0.48 11 -10000 0 11
LEF1 -0.005 0.078 -10000 0 -0.75 5 5
DVL1 0.067 0.05 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.091 0.074 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.39 0.36 -10000 0 -0.66 289 289
LRP6 0.013 0.026 -10000 0 -0.57 1 1
CSNK1A1 0.003 0.017 -10000 0 -10000 0 0
NLK 0.014 0.003 -10000 0 -10000 0 0
CCND1 -0.003 0.15 -10000 0 -0.87 12 12
WNT1 0.002 0.083 -10000 0 -0.82 5 5
GSK3A 0.014 0.001 -10000 0 -10000 0 0
GSK3B 0.014 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
PPP2R5D 0.049 0.067 0.36 19 -10000 0 19
APC 0.03 0.074 -10000 0 -0.46 10 10
WNT1/LRP6/FZD1 0.11 0.12 0.24 218 -10000 0 218
CREBBP 0.003 0.015 -10000 0 -10000 0 0
Neurotrophic factor-mediated Trk receptor signaling

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
CRKL 0.012 0.037 -10000 0 -0.82 1 1
RAS family/GTP/Tiam1 -0.067 0.12 -10000 0 -0.48 5 5
NT3 (dimer)/TRKC -0.22 0.26 -10000 0 -0.49 221 221
NT3 (dimer)/TRKB -0.22 0.26 -10000 0 -0.66 96 96
SHC/Grb2/SOS1/GAB1/PI3K 0.039 0.021 -10000 0 -10000 0 0
RAPGEF1 0.014 0 -10000 0 -10000 0 0
BDNF -0.036 0.18 -10000 0 -0.68 36 36
PIK3CA 0.014 0 -10000 0 -10000 0 0
DYNLT1 0.014 0 -10000 0 -10000 0 0
NTRK1 -0.058 0.23 -10000 0 -0.82 43 43
NTRK2 -0.16 0.28 -10000 0 -0.61 138 138
NTRK3 -0.14 0.25 -10000 0 -0.57 127 127
NT-4/5 (dimer)/TRKB -0.13 0.21 -10000 0 -0.6 45 45
neuron apoptosis 0.12 0.13 0.41 52 -10000 0 52
SHC 2-3/Grb2 -0.12 0.14 -10000 0 -0.44 52 52
SHC1 0.014 0 -10000 0 -10000 0 0
SHC2 -0.11 0.14 0.21 1 -0.4 60 61
SHC3 -0.12 0.14 -10000 0 -0.44 54 54
STAT3 (dimer) 0.014 0.053 -10000 0 -10000 0 0
NT3 (dimer)/TRKA -0.17 0.23 -10000 0 -0.62 63 63
RIN/GDP -0.047 0.099 -10000 0 -0.28 5 5
GIPC1 0.014 0 -10000 0 -10000 0 0
KRAS 0.01 0.053 -10000 0 -0.82 2 2
DNAJA3 -0.079 0.12 0.25 2 -0.5 6 8
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.014 0.12 -10000 0 -0.74 12 12
MAGED1 0.008 0.064 -10000 0 -0.69 4 4
PTPN11 0.014 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.011 0.045 -10000 0 -0.69 2 2
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.16 0.26 -10000 0 -0.57 131 131
TRKA/NEDD4-2 -0.054 0.18 -10000 0 -0.63 43 43
ELMO1 0.013 0.026 -10000 0 -0.57 1 1
RhoG/GTP/ELMO1/DOCK1 -0.002 0.027 -10000 0 -0.35 3 3
NGF -0.14 0.32 -10000 0 -0.8 91 91
HRAS 0.012 0.037 -10000 0 -0.82 1 1
DOCK1 0.011 0.037 -10000 0 -0.57 2 2
GAB2 0.01 0.045 -10000 0 -0.57 3 3
RIT2 0.001 0.003 -10000 0 -10000 0 0
RIT1 0.014 0 -10000 0 -10000 0 0
FRS2 0.007 0.074 -10000 0 -0.82 4 4
DNM1 -0.048 0.22 -10000 0 -0.82 37 37
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.078 0.12 0.24 2 -0.48 7 9
mol:GDP -0.07 0.14 -10000 0 -0.41 13 13
NGF (dimer) -0.14 0.31 -10000 0 -0.8 91 91
RhoG/GDP -0.001 0.019 -10000 0 -0.42 1 1
RIT1/GDP -0.041 0.1 -10000 0 -0.28 2 2
TIAM1 0.007 0.063 -10000 0 -0.57 6 6
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
BDNF (dimer)/TRKB -0.13 0.2 -10000 0 -0.59 44 44
KIDINS220/CRKL/C3G -0.001 0.028 -10000 0 -0.63 1 1
SHC/RasGAP -0.002 0.026 -10000 0 -0.41 2 2
FRS2 family/SHP2 -0.004 0.048 -10000 0 -0.54 4 4
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.16 0.26 -10000 0 -0.56 148 148
RAP1/GDP -0.054 0.066 -10000 0 -0.36 1 1
KIDINS220/CRKL 0.012 0.037 -10000 0 -0.82 1 1
BDNF (dimer) -0.036 0.18 -10000 0 -0.68 36 36
ubiquitin-dependent protein catabolic process -0.14 0.25 -10000 0 -0.56 121 121
Schwann cell development -0.048 0.036 -10000 0 -10000 0 0
EHD4 0.014 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.004 0.044 -10000 0 -0.49 4 4
FRS2 family/SHP2/CRK family/C3G/GAB2 0.04 0.031 -10000 0 -10000 0 0
RAP1B 0.012 0.037 -10000 0 -0.82 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.25 0.26 -10000 0 -0.61 141 141
ABL1 0.014 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.045 0.07 -10000 0 -0.56 1 1
STAT3 0.014 0.053 -10000 0 -10000 0 0
axon guidance -0.24 0.25 -10000 0 -0.57 141 141
MAPK3 -0.11 0.25 -10000 0 -0.52 131 131
MAPK1 -0.11 0.25 -10000 0 -0.52 131 131
CDC42/GDP -0.041 0.1 -10000 0 -0.28 5 5
NTF3 -0.16 0.26 -10000 0 -0.57 148 148
NTF4 0.011 0.045 -10000 0 -0.69 2 2
NGF (dimer)/TRKA/FAIM -0.14 0.25 -10000 0 -0.56 121 121
PI3K -0.002 0.031 -10000 0 -0.41 3 3
FRS3 0.014 0 -10000 0 -10000 0 0
FAIM 0.014 0 -10000 0 -10000 0 0
GAB1 0.014 0 -10000 0 -10000 0 0
RASGRF1 -0.17 0.23 -10000 0 -0.57 100 100
SOS1 0.014 0 -10000 0 -10000 0 0
MCF2L -0.19 0.26 -10000 0 -0.68 71 71
RGS19 0.014 0 -10000 0 -10000 0 0
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.001 0.087 -10000 0 -10000 0 0
Rac1/GDP -0.041 0.1 -10000 0 -0.28 1 1
NGF (dimer)/TRKA/GRIT -0.14 0.25 -10000 0 -0.56 129 129
neuron projection morphogenesis -0.042 0.13 -10000 0 -0.51 2 2
NGF (dimer)/TRKA/NEDD4-2 -0.14 0.25 -10000 0 -0.56 121 121
MAP2K1 0.042 0 -10000 0 -10000 0 0
NGFR -0.023 0.16 -10000 0 -0.71 25 25
NGF (dimer)/TRKA/GIPC/GAIP -0.061 0.16 -10000 0 -0.55 14 14
RAS family/GTP/PI3K 0.03 0.031 -10000 0 -0.26 2 2
FRS2 family/SHP2/GRB2/SOS1 -0.004 0.041 -10000 0 -0.46 4 4
NRAS 0.014 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.014 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.026 -10000 0 -0.57 1 1
MAPKKK cascade -0.084 0.14 -10000 0 -0.48 19 19
RASA1 0.011 0.037 -10000 0 -0.57 2 2
TRKA/c-Abl -0.054 0.18 -10000 0 -0.63 43 43
SQSTM1 0.014 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.12 0.18 -10000 0 -0.54 44 44
NGF (dimer)/TRKA/p62/Atypical PKCs -0.12 0.21 -10000 0 -0.48 121 121
MATK -0.006 0.12 -10000 0 -0.8 12 12
NEDD4L 0.014 0 -10000 0 -10000 0 0
RAS family/GDP -0.052 0.063 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.086 0.14 0.26 2 -0.37 30 32
Rac1/GTP -0.12 0.13 -10000 0 -0.36 75 75
FRS2 family/SHP2/CRK family -0.005 0.046 -10000 0 -0.46 5 5
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF -0.014 0.079 -10000 0 -0.51 1 1
epithelial cell differentiation -0.075 0.12 -10000 0 -0.56 3 3
ITCH 0.027 0.019 -10000 0 -10000 0 0
WWP1 -0.009 0.071 -10000 0 -10000 0 0
FYN 0.012 0.037 -10000 0 -0.82 1 1
EGFR -0.017 0.15 -10000 0 -0.76 20 20
PRL -0.004 0.082 -10000 0 -0.82 5 5
neuron projection morphogenesis -0.031 0.17 -10000 0 -10000 0 0
PTPRZ1 -0.011 0.12 -10000 0 -0.57 21 21
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.086 0.16 -10000 0 -0.51 27 27
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.083 0.2 -10000 0 -0.53 76 76
ADAM17 0.025 0.042 -10000 0 -0.56 2 2
ErbB4/ErbB4 -0.023 0.092 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.037 0.098 -10000 0 -0.47 10 10
NCOR1 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.072 0.19 -10000 0 -0.5 77 77
GRIN2B -0.07 0.19 -10000 0 -0.53 28 28
ErbB4/ErbB2/betacellulin -0.097 0.16 -10000 0 -0.62 3 3
STAT1 -0.033 0.19 -10000 0 -0.81 28 28
HBEGF 0.012 0.037 -10000 0 -0.82 1 1
PRLR -0.12 0.24 -10000 0 -0.57 109 109
E4ICDs/ETO2 -0.014 0.077 -10000 0 -10000 0 0
axon guidance -0.015 0.087 -10000 0 -0.4 2 2
NEDD4 0.027 0.019 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.097 0.18 -10000 0 -0.43 112 112
CBFA2T3 0.013 0.026 -10000 0 -0.57 1 1
ErbB4/ErbB2/HBEGF 0.004 0.074 -10000 0 -0.51 4 4
MAPK3 -0.041 0.17 -10000 0 -10000 0 0
STAT1 (dimer) -0.043 0.15 -10000 0 -0.57 27 27
MAPK1 -0.041 0.17 -10000 0 -10000 0 0
JAK2 0.013 0.026 -10000 0 -0.57 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.074 0.19 -10000 0 -0.5 79 79
NRG1 -0.075 0.24 -10000 0 -0.61 83 83
NRG3 -0.01 0.11 -10000 0 -0.62 14 14
NRG2 -0.32 0.28 -10000 0 -0.57 287 287
NRG4 -0.032 0.16 -10000 0 -0.58 38 38
heart development -0.015 0.087 -10000 0 -0.4 2 2
neural crest cell migration -0.073 0.19 -10000 0 -0.49 79 79
ERBB2 0.027 0.059 -10000 0 -0.53 5 5
WWOX/E4ICDs -0.013 0.076 -10000 0 -10000 0 0
SHC1 0.014 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.074 0.13 -10000 0 -0.52 17 17
apoptosis 0.072 0.11 0.59 10 -10000 0 10
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.21 0.19 -10000 0 -0.46 101 101
ErbB4/ErbB2/epiregulin -0.082 0.16 -10000 0 -0.61 8 8
ErbB4/ErbB4/betacellulin/betacellulin -0.12 0.18 -10000 0 -0.46 52 52
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.091 0.13 -10000 0 -0.66 4 4
MDM2 -0.01 0.079 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.092 0.18 -10000 0 -0.5 76 76
STAT5A -0.006 0.082 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.089 0.21 -10000 0 -0.5 89 89
DLG4 0.011 0.045 -10000 0 -0.69 2 2
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.036 0.053 -10000 0 -10000 0 0
STAT5A (dimer) -0.079 0.12 -10000 0 -0.62 3 3
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.007 0.081 -10000 0 -10000 0 0
LRIG1 0 0.089 -10000 0 -0.57 12 12
EREG -0.15 0.26 -10000 0 -0.58 136 136
BTC -0.17 0.27 -10000 0 -0.57 157 157
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.016 0.088 -10000 0 -10000 0 0
ERBB4 -0.023 0.092 -10000 0 -10000 0 0
STAT5B 0.014 0 -10000 0 -10000 0 0
YAP1 -0.02 0.058 -10000 0 -0.4 10 10
GRB2 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.021 0.11 -10000 0 -0.5 5 5
glial cell differentiation 0.036 0.053 -10000 0 -10000 0 0
WWOX 0.014 0 -10000 0 -10000 0 0
cell proliferation -0.14 0.23 -10000 0 -0.68 40 40
Caspase cascade in apoptosis

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
TOP1 -0.043 0.18 -10000 0 -0.55 36 36
ACTA1 -0.14 0.24 -10000 0 -0.62 88 88
NUMA1 -0.043 0.18 -10000 0 -0.55 36 36
SPTAN1 -0.069 0.24 -10000 0 -0.56 83 83
LIMK1 -0.069 0.24 -10000 0 -0.56 83 83
BIRC3 -0.021 0.17 -10000 0 -0.82 21 21
BIRC2 -0.005 0.12 -10000 0 -0.82 11 11
BAX 0.014 0 -10000 0 -10000 0 0
CASP10 -0.1 0.3 -10000 0 -0.73 86 86
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.014 0 -10000 0 -10000 0 0
PTK2 -0.043 0.18 -10000 0 -0.55 36 36
DIABLO 0.014 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.067 0.23 -10000 0 -0.54 83 83
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
GSN -0.069 0.24 -10000 0 -0.56 83 83
MADD 0.014 0 -10000 0 -10000 0 0
TFAP2A 0.001 0.087 -10000 0 -0.52 6 6
BID -0.03 0.12 -10000 0 -0.36 35 35
MAP3K1 -0.013 0.076 -10000 0 -0.22 30 30
TRADD 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.004 0.021 -10000 0 -0.4 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.069 0.24 -10000 0 -0.77 34 34
CASP9 0.014 0.001 -10000 0 -10000 0 0
DNA repair 0.008 0.064 -10000 0 -0.2 12 12
neuron apoptosis 0.017 0.027 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.06 0.23 -10000 0 -0.75 34 34
APAF1 0.013 0.026 -10000 0 -0.57 1 1
CASP6 -0.005 0.1 -10000 0 -0.47 3 3
TRAF2 0.002 0.098 -10000 0 -0.82 7 7
ICAD/CAD -0.06 0.23 -10000 0 -0.76 33 33
CASP7 0.006 0.064 0.29 21 -10000 0 21
KRT18 0.001 0.071 -10000 0 -0.44 10 10
apoptosis -0.049 0.21 -10000 0 -0.68 33 33
DFFA -0.069 0.24 -10000 0 -0.56 83 83
DFFB -0.07 0.24 -10000 0 -0.56 83 83
PARP1 -0.008 0.064 0.2 12 -10000 0 12
actin filament polymerization 0.056 0.22 0.69 35 -10000 0 35
TNF -0.025 0.17 -10000 0 -0.79 24 24
CYCS -0.02 0.095 -10000 0 -0.28 33 33
SATB1 -0.009 0.12 -10000 0 -0.5 5 5
SLK -0.069 0.24 -10000 0 -0.56 83 83
p15 BID/BAX -0.02 0.11 -10000 0 -0.32 33 33
CASP2 0.033 0.075 -10000 0 -10000 0 0
JNK cascade 0.013 0.076 0.22 31 -10000 0 31
CASP3 -0.081 0.25 -10000 0 -0.58 88 88
LMNB2 0.026 0.062 -10000 0 -0.36 3 3
RIPK1 0.014 0 -10000 0 -10000 0 0
CASP4 0.011 0.037 -10000 0 -0.57 2 2
Mammalian IAPs/DIABLO -0.031 0.14 -10000 0 -0.6 26 26
negative regulation of DNA binding 0.001 0.086 -10000 0 -0.52 6 6
stress fiber formation -0.067 0.23 -10000 0 -0.54 83 83
GZMB -0.13 0.34 -10000 0 -0.8 91 91
CASP1 0.016 0.041 -10000 0 -0.58 2 2
LMNB1 0.026 0.062 -10000 0 -0.38 2 2
APP 0.017 0.027 -10000 0 -10000 0 0
TNFRSF1A 0.014 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.012 0 -10000 0 -10000 0 0
VIM -0.053 0.21 -10000 0 -0.64 35 35
LMNA 0.026 0.062 -10000 0 -0.36 3 3
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.026 0.079 -10000 0 -0.37 10 10
LRDD 0.012 0.037 -10000 0 -0.82 1 1
SREBF1 -0.069 0.24 -10000 0 -0.56 83 83
APAF-1/Caspase 9 -0.001 0.078 0.45 10 -10000 0 10
nuclear fragmentation during apoptosis -0.042 0.18 -10000 0 -0.54 36 36
CFL2 -0.058 0.22 -10000 0 -0.72 35 35
GAS2 -0.11 0.25 -10000 0 -0.59 86 86
positive regulation of apoptosis 0.03 0.062 -10000 0 -0.37 2 2
PRF1 -0.05 0.22 -10000 0 -0.8 39 39
Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity 0.063 0.19 0.6 52 -10000 0 52
KIRREL -0.022 0.14 -10000 0 -0.62 24 24
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.064 0.19 -10000 0 -0.6 52 52
PLCG1 0.014 0 -10000 0 -10000 0 0
ARRB2 0.014 0 -10000 0 -10000 0 0
WASL 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.057 0.17 -10000 0 -0.58 41 41
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.009 0.12 -10000 0 -0.6 10 10
FYN -0.036 0.17 -10000 0 -0.52 42 42
mol:Ca2+ -0.057 0.17 -10000 0 -0.57 41 41
mol:DAG -0.057 0.17 -10000 0 -0.57 41 41
NPHS2 -0.023 0.13 -10000 0 -0.86 12 12
mol:IP3 -0.057 0.17 -10000 0 -0.57 41 41
regulation of endocytosis -0.039 0.16 -10000 0 -0.49 42 42
Nephrin/NEPH1/podocin/Cholesterol -0.058 0.18 -10000 0 -0.58 41 41
establishment of cell polarity -0.063 0.19 -10000 0 -0.6 52 52
Nephrin/NEPH1/podocin/NCK1-2 -0.052 0.16 -10000 0 -0.53 41 41
Nephrin/NEPH1/beta Arrestin2 -0.026 0.16 -10000 0 -0.5 42 42
NPHS1 -0.049 0.21 -10000 0 -0.84 32 32
Nephrin/NEPH1/podocin -0.052 0.16 -10000 0 -0.53 42 42
TJP1 0.014 0 -10000 0 -10000 0 0
NCK1 0.014 0 -10000 0 -10000 0 0
NCK2 0.014 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.057 0.17 -10000 0 -0.58 41 41
CD2AP 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.057 0.17 -10000 0 -0.58 41 41
GRB2 0.014 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.065 0.21 -10000 0 -0.54 70 70
cytoskeleton organization -0.013 0.16 -10000 0 -0.78 10 10
Nephrin/NEPH1 -0.047 0.14 -10000 0 -0.48 44 44
Nephrin/NEPH1/ZO-1 -0.052 0.16 -10000 0 -0.56 36 36
Thromboxane A2 receptor 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
TGM2 -0.049 0.22 -10000 0 -0.82 36 36
GNB1/GNG2 -0.056 0.077 -10000 0 -0.21 34 34
AKT1 -0.003 0.12 -10000 0 -0.26 1 1
EGF -0.094 0.23 -10000 0 -0.57 91 91
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.011 0.12 -10000 0 -0.5 12 12
mol:Ca2+ -0.03 0.16 -10000 0 -0.32 45 45
LYN 0.011 0.12 -10000 0 -0.51 12 12
RhoA/GTP -0.033 0.049 -10000 0 -0.16 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.032 0.18 -10000 0 -0.36 45 45
GNG2 0.012 0.037 -10000 0 -0.82 1 1
ARRB2 0.014 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.005 0.086 -10000 0 -0.52 5 5
G beta5/gamma2 -0.073 0.1 -10000 0 -0.29 37 37
PRKCH -0.037 0.18 -10000 0 -0.38 40 40
DNM1 -0.048 0.22 -10000 0 -0.82 37 37
TXA2/TP beta/beta Arrestin3 -0.025 0.069 -10000 0 -0.26 37 37
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0 0.1 -10000 0 -0.74 9 9
G12 family/GTP -0.082 0.12 -10000 0 -0.32 49 49
ADRBK1 0.014 0 -10000 0 -10000 0 0
ADRBK2 0.012 0.037 -10000 0 -0.82 1 1
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.018 0.13 0.36 29 -10000 0 29
mol:NADP -0.001 0.11 -10000 0 -0.82 9 9
RAB11A 0.014 0 -10000 0 -10000 0 0
PRKG1 -0.021 0.15 -10000 0 -0.65 26 26
mol:IP3 -0.045 0.19 -10000 0 -0.41 45 45
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.073 0.25 -10000 0 -0.56 47 47
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.045 0.18 -10000 0 -0.43 70 70
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.009 0.13 -10000 0 -0.52 13 13
RHOA 0.014 0 -10000 0 -10000 0 0
PTGIR -0.018 0.16 -10000 0 -0.82 19 19
PRKCB1 -0.045 0.19 -10000 0 -0.38 90 90
GNAQ 0.014 0 -10000 0 -10000 0 0
mol:L-citrulline -0.001 0.11 -10000 0 -0.82 9 9
TXA2/TXA2-R family -0.073 0.26 -10000 0 -0.52 91 91
LCK 0.002 0.13 -10000 0 -0.47 17 17
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.043 0.14 -10000 0 -0.5 36 36
TXA2-R family/G12 family/GDP/G beta/gamma 0.021 0.045 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.042 0.14 -10000 0 -0.49 36 36
MAPK14 -0.009 0.13 -10000 0 -0.25 9 9
TGM2/GTP -0.059 0.22 -10000 0 -0.48 43 43
MAPK11 -0.009 0.13 -10000 0 -0.28 1 1
ARHGEF1 -0.008 0.099 -10000 0 -0.22 2 2
GNAI2 0.014 0 -10000 0 -10000 0 0
JNK cascade -0.044 0.2 -10000 0 -0.38 89 89
RAB11/GDP 0.014 0.002 -10000 0 -10000 0 0
ICAM1 -0.029 0.16 -10000 0 -0.34 49 49
cAMP biosynthetic process -0.045 0.18 -10000 0 -0.39 41 41
Gq family/GTP/EBP50 -0.007 0.096 -10000 0 -0.64 3 3
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.012 0.12 -10000 0 -0.5 11 11
GNB5 0.014 0 -10000 0 -10000 0 0
GNB1 0.014 0 -10000 0 -10000 0 0
EGF/EGFR -0.004 0.12 -10000 0 -0.35 18 18
VCAM1 -0.038 0.18 -10000 0 -0.37 65 65
TP beta/Gq family/GDP/G beta5/gamma2 0.005 0.086 -10000 0 -0.52 5 5
platelet activation -0.014 0.17 -10000 0 -0.32 32 32
PGI2/IP -0.024 0.12 -10000 0 -0.64 19 19
PRKACA 0.004 0.085 -10000 0 -0.36 24 24
Gq family/GDP/G beta5/gamma2 0.009 0.076 -10000 0 -0.42 5 5
TXA2/TP beta/beta Arrestin2 -0.03 0.095 -10000 0 -0.36 37 37
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.022 0.17 -10000 0 -0.57 36 36
mol:DAG -0.053 0.21 -10000 0 -0.42 90 90
EGFR -0.017 0.15 -10000 0 -0.76 20 20
TXA2/TP alpha -0.067 0.24 -10000 0 -0.54 41 41
Gq family/GTP -0.034 0.09 -10000 0 -0.24 77 77
YES1 0.012 0.12 -10000 0 -0.5 11 11
GNAI2/GTP -0.039 0.12 -10000 0 -0.47 27 27
PGD2/DP -0.01 0.076 -10000 0 -0.56 9 9
SLC9A3R1 0.009 0.052 -10000 0 -0.57 4 4
FYN 0.011 0.12 -10000 0 -0.52 12 12
mol:NO -0.001 0.11 -10000 0 -0.82 9 9
GNA15 0.011 0.037 -10000 0 -0.57 2 2
PGK/cGMP -0.032 0.12 -10000 0 -0.45 35 35
RhoA/GDP 0.014 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.072 0.19 -10000 0 -0.6 39 39
NOS3 -0.001 0.11 -10000 0 -0.82 9 9
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.038 0.18 -10000 0 -0.38 39 39
PRKCB -0.042 0.19 -10000 0 -0.4 43 43
PRKCE -0.037 0.18 -10000 0 -0.36 82 82
PRKCD -0.042 0.19 -10000 0 -0.38 85 85
PRKCG -0.066 0.22 -10000 0 -0.43 96 96
muscle contraction -0.062 0.24 -10000 0 -0.48 91 91
PRKCZ -0.032 0.18 -10000 0 -0.37 35 35
ARR3 0.002 0.005 -10000 0 -10000 0 0
TXA2/TP beta -0.043 0.14 -10000 0 -0.5 37 37
PRKCQ -0.042 0.18 -10000 0 -0.4 44 44
MAPKKK cascade -0.058 0.22 -10000 0 -0.47 52 52
SELE -0.043 0.18 -10000 0 -0.39 84 84
TP beta/GNAI2/GDP/G beta/gamma -0.043 0.14 -10000 0 -0.69 11 11
ROCK1 0.014 0 -10000 0 -10000 0 0
GNA14 -0.075 0.21 -10000 0 -0.57 76 76
chemotaxis -0.087 0.29 -10000 0 -0.6 96 96
GNA12 0.01 0.053 -10000 0 -0.82 2 2
GNA13 0.014 0 -10000 0 -10000 0 0
GNA11 0.009 0.052 -10000 0 -0.57 4 4
Rac1/GTP 0.006 0.006 -10000 0 -10000 0 0
EPHB forward 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
Ephrin A5/EPHB2 -0.13 0.24 -10000 0 -0.55 121 121
cell-cell adhesion 0.11 0.17 0.64 7 -10000 0 7
Ephrin B/EPHB2/RasGAP -0.12 0.2 -10000 0 -0.48 106 106
ITSN1 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
SHC1 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.01 0.057 -10000 0 -0.35 14 14
Ephrin B1/EPHB1 -0.027 0.11 -10000 0 -0.48 28 28
HRAS/GDP -0.054 0.11 -10000 0 -0.56 5 5
Ephrin B/EPHB1/GRB7 -0.046 0.13 -10000 0 -0.49 24 24
Endophilin/SYNJ1 -0.081 0.2 -10000 0 -0.44 106 106
KRAS 0.01 0.053 -10000 0 -0.82 2 2
Ephrin B/EPHB1/Src -0.041 0.12 -10000 0 -0.49 20 20
endothelial cell migration -0.003 0.028 -10000 0 -10000 0 0
GRB2 0.014 0 -10000 0 -10000 0 0
GRB7 0.005 0.083 -10000 0 -0.74 6 6
PAK1 -0.1 0.22 -10000 0 -0.64 17 17
HRAS 0.012 0.037 -10000 0 -0.82 1 1
RRAS -0.082 0.21 -10000 0 -0.45 106 106
DNM1 -0.048 0.22 -10000 0 -0.82 37 37
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.003 0.13 -10000 0 -0.47 20 20
lamellipodium assembly -0.11 0.17 -10000 0 -0.64 7 7
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.011 0.091 -10000 0 -0.46 3 3
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
EPHB2 -0.16 0.34 -10000 0 -0.82 107 107
EPHB3 -0.003 0.096 -10000 0 -0.57 14 14
EPHB1 -0.028 0.17 -10000 0 -0.73 28 28
EPHB4 0.014 0 -10000 0 -10000 0 0
mol:GDP -0.051 0.11 -10000 0 -0.57 4 4
Ephrin B/EPHB2 -0.12 0.2 -10000 0 -0.48 106 106
Ephrin B/EPHB3 -0.027 0.086 -10000 0 -0.52 2 2
JNK cascade -0.088 0.22 -10000 0 -0.46 123 123
Ephrin B/EPHB1 -0.042 0.12 -10000 0 -0.5 20 20
RAP1/GDP -0.042 0.092 -10000 0 -0.55 2 2
EFNB2 0.011 0.037 -10000 0 -0.57 2 2
EFNB3 -0.024 0.14 -10000 0 -0.57 32 32
EFNB1 0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.13 0.22 -10000 0 -0.51 123 123
RAP1B 0.012 0.037 -10000 0 -0.82 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.11 0.17 -10000 0 -0.7 7 7
Rap1/GTP -0.11 0.17 -10000 0 -0.74 5 5
axon guidance -0.13 0.24 -10000 0 -0.54 121 121
MAPK3 0.027 0.083 -10000 0 -0.4 3 3
MAPK1 0.027 0.083 -10000 0 -0.42 1 1
Rac1/GDP -0.01 0.12 -10000 0 -0.51 4 4
actin cytoskeleton reorganization -0.089 0.14 -10000 0 -0.54 6 6
CDC42/GDP -0.01 0.12 -10000 0 -0.51 4 4
PI3K -0.003 0.028 -10000 0 -10000 0 0
EFNA5 -0.012 0.12 -10000 0 -0.57 22 22
Ephrin B2/EPHB4 -0.001 0.022 -10000 0 -0.35 2 2
Ephrin B/EPHB2/Intersectin/N-WASP -0.043 0.14 -10000 0 -0.55 4 4
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.17 -10000 0 -0.71 6 6
PTK2 0.027 0.045 -10000 0 -10000 0 0
MAP4K4 -0.089 0.22 -10000 0 -0.46 123 123
SRC 0.014 0 -10000 0 -10000 0 0
KALRN -0.038 0.16 -10000 0 -0.57 44 44
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.049 0.17 -10000 0 -0.54 6 6
MAP2K1 0.019 0.086 -10000 0 -0.43 3 3
WASL 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.13 0.22 -10000 0 -0.5 123 123
cell migration 0.023 0.099 -10000 0 -0.49 3 3
NRAS 0.014 0 -10000 0 -10000 0 0
SYNJ1 -0.082 0.21 -10000 0 -0.45 106 106
PXN 0.014 0 -10000 0 -10000 0 0
TF -0.26 0.24 -10000 0 -0.66 97 97
HRAS/GTP -0.12 0.19 -10000 0 -0.72 8 8
Ephrin B1/EPHB1-2 -0.13 0.22 -10000 0 -0.51 123 123
cell adhesion mediated by integrin 0.015 0.079 0.44 2 -10000 0 2
RAC1 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.13 0.2 -10000 0 -0.79 7 7
RAC1-CDC42/GTP -0.12 0.17 -10000 0 -0.68 8 8
RASA1 0.011 0.037 -10000 0 -0.57 2 2
RAC1-CDC42/GDP -0.042 0.091 -10000 0 -0.55 2 2
ruffle organization -0.065 0.2 -10000 0 -0.74 5 5
NCK1 0.014 0 -10000 0 -10000 0 0
receptor internalization -0.1 0.25 -10000 0 -0.64 40 40
Ephrin B/EPHB2/KALRN -0.14 0.21 -10000 0 -0.49 114 114
ROCK1 0.018 0.055 -10000 0 -10000 0 0
RAS family/GDP -0.087 0.13 -10000 0 -0.55 6 6
Rac1/GTP -0.12 0.18 -10000 0 -0.71 7 7
Ephrin B/EPHB1/Src/Paxillin 0.005 0.098 -10000 0 -0.51 3 3
BCR 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
JUN -0.03 0.15 -9999 0 -0.43 27 27
IKBKB -0.008 0.079 -9999 0 -0.27 7 7
AKT1 -0.029 0.12 -9999 0 -0.29 41 41
IKBKG -0.007 0.082 -9999 0 -0.29 7 7
CALM1 -0.045 0.12 -9999 0 -0.41 29 29
PIK3CA 0.014 0 -9999 0 -10000 0 0
MAP3K1 -0.059 0.21 -9999 0 -0.63 31 31
MAP3K7 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ -0.055 0.12 -9999 0 -0.43 31 31
DOK1 0.012 0.037 -9999 0 -0.82 1 1
AP-1 -0.021 0.097 -9999 0 -0.27 10 10
LYN 0.012 0.037 -9999 0 -0.82 1 1
BLNK -0.042 0.17 -9999 0 -0.57 48 48
SHC1 0.014 0 -9999 0 -10000 0 0
BCR complex -0.14 0.28 -9999 0 -0.63 109 109
CD22 -0.13 0.27 -9999 0 -0.81 55 55
CAMK2G -0.034 0.11 -9999 0 -0.38 29 29
CSNK2A1 0.014 0 -9999 0 -10000 0 0
INPP5D 0.01 0.045 -9999 0 -0.57 3 3
SHC/GRB2/SOS1 -0.11 0.19 -9999 0 -0.63 30 30
GO:0007205 -0.056 0.13 -9999 0 -0.44 31 31
SYK 0.01 0.045 -9999 0 -0.57 3 3
ELK1 -0.046 0.12 -9999 0 -0.42 30 30
NFATC1 -0.068 0.19 -9999 0 -0.48 71 71
B-cell antigen/BCR complex -0.14 0.28 -9999 0 -0.63 109 109
PAG1/CSK -0.003 0.04 -9999 0 -0.63 2 2
NFKBIB 0.008 0.03 -9999 0 -10000 0 0
HRAS -0.049 0.13 -9999 0 -0.44 29 29
NFKBIA 0.008 0.03 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.014 0.025 -9999 0 -10000 0 0
RasGAP/Csk -0.11 0.22 -9999 0 -0.55 79 79
mol:GDP -0.054 0.12 -9999 0 -0.42 29 29
PTEN 0.014 0 -9999 0 -10000 0 0
CD79B -0.02 0.15 -9999 0 -0.71 23 23
NF-kappa-B/RelA/I kappa B alpha 0.015 0.024 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
PI3K/BCAP/CD19 -0.094 0.23 -9999 0 -0.55 82 82
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
mol:IP3 -0.057 0.13 -9999 0 -0.44 31 31
CSK 0.014 0 -9999 0 -10000 0 0
FOS -0.071 0.15 -9999 0 -0.43 49 49
CHUK -0.007 0.082 -9999 0 -0.29 7 7
IBTK 0.014 0 -9999 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.07 0.13 -9999 0 -0.57 15 15
PTPN6 -0.12 0.25 -9999 0 -0.75 55 55
RELA 0.014 0 -9999 0 -10000 0 0
BCL2A1 0.007 0.04 -9999 0 -0.13 32 32
VAV2 -0.15 0.27 -9999 0 -0.74 74 74
ubiquitin-dependent protein catabolic process 0.013 0.029 -9999 0 -10000 0 0
BTK -0.003 0.035 -9999 0 -10000 0 0
CD19 -0.15 0.3 -9999 0 -0.77 83 83
MAP4K1 -0.008 0.13 -9999 0 -0.76 14 14
CD72 -0.095 0.28 -9999 0 -0.82 65 65
PAG1 0.01 0.053 -9999 0 -0.82 2 2
MAPK14 -0.04 0.18 -9999 0 -0.53 28 28
SH3BP5 0.01 0.045 -9999 0 -0.57 3 3
PIK3AP1 -0.061 0.16 -9999 0 -0.47 44 44
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.09 0.2 -9999 0 -0.58 45 45
RAF1 -0.038 0.13 -9999 0 -0.41 29 29
RasGAP/p62DOK/SHIP -0.1 0.21 -9999 0 -0.77 23 23
CD79A -0.14 0.31 -9999 0 -0.74 104 104
re-entry into mitotic cell cycle -0.022 0.097 -9999 0 -0.27 12 12
RASA1 0.011 0.037 -9999 0 -0.57 2 2
MAPK3 -0.017 0.11 -9999 0 -0.42 3 3
MAPK1 -0.017 0.11 -9999 0 -0.42 3 3
CD72/SHP1 -0.12 0.31 -9999 0 -0.88 52 52
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.043 0.18 -9999 0 -0.53 29 29
actin cytoskeleton organization -0.092 0.24 -9999 0 -0.61 74 74
NF-kappa-B/RelA 0.034 0.047 -9999 0 -10000 0 0
Calcineurin -0.047 0.088 -9999 0 -0.44 3 3
PI3K -0.13 0.22 -9999 0 -0.62 70 70
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.069 0.13 -9999 0 -0.47 33 33
SOS1 0.014 0 -9999 0 -10000 0 0
Bam32/HPK1 -0.063 0.23 -9999 0 -0.76 36 36
DAPP1 -0.092 0.21 -9999 0 -0.77 32 32
cytokine secretion -0.062 0.18 -9999 0 -0.44 71 71
mol:DAG -0.057 0.13 -9999 0 -0.44 31 31
PLCG2 0.013 0.026 -9999 0 -0.57 1 1
MAP2K1 -0.028 0.12 -9999 0 -0.39 18 18
B-cell antigen/BCR complex/FcgammaRIIB -0.12 0.25 -9999 0 -0.64 79 79
mol:PI-3-4-5-P3 -0.09 0.15 -9999 0 -0.41 69 69
ETS1 -0.027 0.11 -9999 0 -0.39 11 11
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.13 0.23 -9999 0 -0.55 89 89
B-cell antigen/BCR complex/LYN -0.094 0.2 -9999 0 -0.73 28 28
MALT1 0.014 0 -9999 0 -10000 0 0
TRAF6 0.014 0 -9999 0 -10000 0 0
RAC1 -0.1 0.26 -9999 0 -0.66 74 74
B-cell antigen/BCR complex/LYN/SYK -0.13 0.27 -9999 0 -0.88 45 45
CARD11 -0.073 0.17 -9999 0 -0.5 53 53
FCGR2B 0.006 0.068 -9999 0 -0.57 7 7
PPP3CA 0.014 0 -9999 0 -10000 0 0
BCL10 0.014 0 -9999 0 -10000 0 0
IKK complex 0.007 0.039 -9999 0 -10000 0 0
PTPRC -0.004 0.11 -9999 0 -0.68 13 13
PDPK1 -0.029 0.12 -9999 0 -0.29 41 41
PPP3CB 0.014 0 -9999 0 -10000 0 0
PPP3CC 0.014 0 -9999 0 -10000 0 0
POU2F2 0.008 0.04 -9999 0 -0.14 30 30
PDGFR-beta signaling pathway

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
S1P1/Sphingosine-1-phosphate -0.063 0.13 -9999 0 -0.68 1 1
PDGFB-D/PDGFRB/SLAP -0.11 0.24 -9999 0 -0.62 92 92
PDGFB-D/PDGFRB/APS/CBL -0.097 0.2 -9999 0 -0.53 91 91
AKT1 -0.013 0.16 -9999 0 -0.6 3 3
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.032 0.15 -9999 0 -0.71 1 1
PIK3CA 0.014 0 -9999 0 -10000 0 0
FGR -0.071 0.16 -9999 0 -0.41 22 22
mol:Ca2+ -0.03 0.14 -9999 0 -0.4 1 1
MYC 0.004 0.11 -9999 0 -10000 0 0
SHC1 0.014 0 -9999 0 -10000 0 0
HRAS/GDP -0.074 0.17 -9999 0 -0.43 91 91
LRP1/PDGFRB/PDGFB -0.11 0.22 -9999 0 -0.56 96 96
GRB10 0.012 0.037 -9999 0 -0.82 1 1
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 -0.031 0.14 -9999 0 -0.4 1 1
PTEN 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
GRB7 0.005 0.083 -9999 0 -0.74 6 6
PDGFB-D/PDGFRB/SHP2 -0.11 0.24 -9999 0 -0.62 89 89
PDGFB-D/PDGFRB/GRB10 -0.11 0.24 -9999 0 -0.62 90 90
cell cycle arrest -0.11 0.24 -9999 0 -0.62 92 92
HRAS 0.012 0.037 -9999 0 -0.82 1 1
HIF1A -0.002 0.15 -9999 0 -0.51 3 3
GAB1 -0.031 0.14 -9999 0 -0.46 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.025 0.14 -9999 0 -0.47 1 1
PDGFB-D/PDGFRB -0.092 0.21 -9999 0 -0.54 90 90
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.11 0.24 -9999 0 -0.62 89 89
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.065 0.13 -9999 0 -0.69 1 1
positive regulation of MAPKKK cascade -0.11 0.24 -9999 0 -0.62 89 89
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
mol:IP3 -0.031 0.14 -9999 0 -0.4 1 1
E5 -0.001 0.002 -9999 0 -10000 0 0
CSK 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.11 0.25 -9999 0 -0.62 93 93
SHB 0.011 0.037 -9999 0 -0.57 2 2
BLK -0.12 0.19 -9999 0 -0.45 99 99
PTPN2 0.012 0.037 -9999 0 -0.82 1 1
PDGFB-D/PDGFRB/SNX15 -0.11 0.24 -9999 0 -0.62 89 89
BCAR1 0.014 0 -9999 0 -10000 0 0
VAV2 -0.027 0.14 -9999 0 -0.43 5 5
CBL 0.014 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.11 0.24 -9999 0 -0.62 89 89
LCK -0.078 0.16 -9999 0 -0.47 1 1
PDGFRB -0.13 0.32 -9999 0 -0.82 89 89
ACP1 0.014 0 -9999 0 -10000 0 0
HCK -0.072 0.16 -9999 0 -0.49 2 2
ABL1 -0.038 0.15 -9999 0 -0.41 13 13
PDGFB-D/PDGFRB/CBL -0.03 0.14 -9999 0 -0.42 1 1
PTPN1 0.013 0.003 -9999 0 -10000 0 0
SNX15 0.014 0 -9999 0 -10000 0 0
STAT3 0.014 0 -9999 0 -10000 0 0
STAT1 -0.033 0.19 -9999 0 -0.81 28 28
cell proliferation 0.006 0.1 -9999 0 -10000 0 0
SLA 0.009 0.064 -9999 0 -0.82 3 3
actin cytoskeleton reorganization -0.029 0.18 -9999 0 -10000 0 0
SRC -0.07 0.16 -9999 0 -0.41 12 12
PI3K -0.073 0.15 -9999 0 -0.68 3 3
PDGFB-D/PDGFRB/GRB7/SHC -0.1 0.21 -9999 0 -0.54 92 92
SH2B2 0.01 0.053 -9999 0 -0.82 2 2
PLCgamma1/SPHK1 -0.033 0.15 -9999 0 -0.74 1 1
LYN -0.07 0.16 -9999 0 -0.46 1 1
LRP1 0.013 0.026 -9999 0 -0.57 1 1
SOS1 0.014 0 -9999 0 -10000 0 0
STAT5B 0.014 0 -9999 0 -10000 0 0
STAT5A 0.014 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.075 0.16 -9999 0 -10000 0 0
SPHK1 -0.007 0.13 -9999 0 -0.82 12 12
EDG1 -0.001 0.004 -9999 0 -10000 0 0
mol:DAG -0.031 0.14 -9999 0 -0.4 1 1
PLCG1 -0.032 0.14 -9999 0 -0.41 1 1
NHERF/PDGFRB -0.1 0.21 -9999 0 -0.54 90 90
YES1 -0.07 0.16 -9999 0 -0.42 13 13
cell migration -0.099 0.21 -9999 0 -0.54 90 90
SHC/Grb2/SOS1 -0.075 0.16 -9999 0 -10000 0 0
SLC9A3R2 0.01 0.053 -9999 0 -0.82 2 2
SLC9A3R1 0.009 0.052 -9999 0 -0.57 4 4
NHERF1-2/PDGFRB/PTEN -0.09 0.19 -9999 0 -0.49 90 90
FYN -0.07 0.16 -9999 0 -0.43 13 13
DOK1 -0.058 0.2 -9999 0 -0.48 91 91
HRAS/GTP -0.001 0.029 -9999 0 -0.64 1 1
PDGFB -0.006 0.13 -9999 0 -0.82 12 12
RAC1 -0.011 0.14 -9999 0 -10000 0 0
PRKCD -0.057 0.2 -9999 0 -0.48 90 90
FER -0.058 0.2 -9999 0 -0.48 90 90
MAPKKK cascade -0.074 0.16 -9999 0 -10000 0 0
RASA1 -0.058 0.2 -9999 0 -0.48 90 90
NCK1 0.014 0 -9999 0 -10000 0 0
NCK2 0.014 0 -9999 0 -10000 0 0
p62DOK/Csk -0.074 0.17 -9999 0 -0.44 91 91
PDGFB-D/PDGFRB/SHB -0.11 0.24 -9999 0 -0.61 91 91
chemotaxis -0.037 0.15 -9999 0 -0.4 13 13
STAT1-3-5/STAT1-3-5 -0.096 0.18 -9999 0 -0.84 6 6
Bovine Papilomavirus E5/PDGFRB -0.1 0.24 -9999 0 -0.63 89 89
PTPRJ 0.014 0 -9999 0 -10000 0 0
IL1-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
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.013 0.026 -9999 0 -0.57 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.025 0.073 -9999 0 -0.69 1 1
IRAK/TOLLIP 0.033 0.004 -9999 0 -10000 0 0
IKBKB 0.014 0 -9999 0 -10000 0 0
IKBKG 0.014 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.24 0.29 -9999 0 -0.57 210 210
IL1A -0.2 0.36 -9999 0 -0.8 131 131
IL1B -0.044 0.2 -9999 0 -0.61 54 54
IRAK/TRAF6/p62/Atypical PKCs 0 0.011 -9999 0 -10000 0 0
IL1R2 -0.098 0.24 -9999 0 -0.58 93 93
IL1R1 0.013 0.026 -9999 0 -0.57 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.022 0.076 -9999 0 -0.72 1 1
TOLLIP 0.014 0 -9999 0 -10000 0 0
TICAM2 0.014 0.001 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.072 0.005 -9999 0 -10000 0 0
JUN 0.033 0.071 -9999 0 -0.47 2 2
MAP3K7 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.05 0.14 -9999 0 -0.82 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.13 0.22 -9999 0 -0.5 126 126
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.12 0.2 -9999 0 -0.46 127 127
IL1 beta fragment/IL1R1/IL1RAP -0.023 0.17 -9999 0 -0.5 51 51
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 0.026 0.075 -9999 0 -0.52 2 2
IRAK1 0.028 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.11 0.18 -9999 0 -0.41 129 129
IRAK4 0.013 0.026 -9999 0 -0.57 1 1
PRKCI 0.014 0 -9999 0 -10000 0 0
TRAF6 0.014 0 -9999 0 -10000 0 0
PI3K -0.002 0.031 -9999 0 -0.41 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.092 -9999 0 -0.81 1 1
CHUK 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.023 0.17 -9999 0 -0.5 51 51
IL1 beta/IL1R2 -0.12 0.21 -9999 0 -0.56 60 60
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.044 0.12 -9999 0 -0.73 1 1
IRAK3 0.003 0.091 -9999 0 -0.75 7 7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.049 0.14 -9999 0 -0.82 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.041 0.14 -9999 0 -0.7 2 2
IL1 alpha/IL1R1/IL1RAP -0.14 0.24 -9999 0 -0.55 126 126
RELA 0.014 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.014 0 -9999 0 -10000 0 0
MYD88 0.014 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.041 0.003 -9999 0 -10000 0 0
IL1RAP 0.01 0.052 -9999 0 -0.65 3 3
UBE2N 0.014 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.039 0.11 -9999 0 -0.67 1 1
CASP1 0.013 0.026 -9999 0 -0.57 1 1
IL1RN/IL1R2 -0.18 0.26 -9999 0 -0.49 181 181
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.051 0.14 -9999 0 -0.47 51 51
TMEM189-UBE2V1 0.01 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.014 0.11 -9999 0 -0.67 2 2
PIK3CA 0.014 0 -9999 0 -10000 0 0
IL1RN -0.14 0.25 -9999 0 -0.57 129 129
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.023 0.066 -9999 0 -10000 0 0
Nongenotropic Androgen 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
PTK2 0.012 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.082 0.14 -10000 0 -0.5 5 5
regulation of S phase of mitotic cell cycle -0.043 0.12 -10000 0 -10000 0 0
GNAO1 0.007 0.069 -10000 0 -0.76 4 4
HRAS 0.012 0.037 -10000 0 -0.82 1 1
SHBG/T-DHT -0.001 0.036 -10000 0 -0.56 2 2
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
MAP2K1 -0.039 0.13 -10000 0 -0.52 2 2
T-DHT/AR -0.11 0.19 -10000 0 -0.42 132 132
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 64 64
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 0.013 0.026 -10000 0 -0.57 1 1
mol:GDP -0.12 0.19 -10000 0 -0.43 132 132
cell proliferation -0.048 0.18 -10000 0 -0.58 19 19
PIK3CA 0.014 0 -10000 0 -10000 0 0
FOS -0.084 0.29 -10000 0 -0.82 64 64
mol:Ca2+ -0.014 0.021 -10000 0 -0.088 11 11
MAPK3 -0.042 0.16 -10000 0 -0.49 19 19
MAPK1 -0.017 0.091 -10000 0 -0.3 2 2
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
mol:IP3 0 0.002 -10000 0 -0.004 64 64
cAMP biosynthetic process 0.011 0.04 -10000 0 -0.52 2 2
GNG2 0.012 0.037 -10000 0 -0.82 1 1
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 64 64
HRAS/GTP -0.077 0.12 -10000 0 -0.47 5 5
actin cytoskeleton reorganization -0.002 0.02 -10000 0 -10000 0 0
SRC 0.013 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 64 64
PI3K -0.002 0.027 -10000 0 -0.35 3 3
apoptosis 0.041 0.17 0.42 64 -10000 0 64
T-DHT/AR/PELP1 -0.093 0.16 -10000 0 -0.35 132 132
HRAS/GDP -0.11 0.18 -10000 0 -0.4 133 133
CREB1 -0.045 0.18 -10000 0 -0.45 64 64
RAC1-CDC42/GTP -0.002 0.021 -10000 0 -10000 0 0
AR -0.14 0.26 -10000 0 -0.57 132 132
GNB1 0.014 0 -10000 0 -10000 0 0
RAF1 -0.047 0.14 -10000 0 -0.46 5 5
RAC1-CDC42/GDP -0.1 0.17 -10000 0 -0.4 15 15
T-DHT/AR/PELP1/Src -0.083 0.14 -10000 0 -0.51 4 4
MAP2K2 -0.039 0.13 -10000 0 -0.52 2 2
T-DHT/AR/PELP1/Src/PI3K -0.044 0.12 -10000 0 -10000 0 0
GNAZ -0.017 0.15 -10000 0 -0.74 20 20
SHBG 0.009 0.053 -10000 0 -0.82 2 2
Gi family/GNB1/GNG2/GDP 0.012 0.072 -10000 0 -0.46 2 2
mol:T-DHT 0 0.001 -10000 0 -0.003 45 45
RAC1 0.014 0 -10000 0 -10000 0 0
GNRH1 -0.015 0.13 -10000 0 -0.63 21 21
Gi family/GTP -0.043 0.081 -10000 0 -0.38 9 9
CDC42 0.014 0 -10000 0 -10000 0 0
IL27-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.012 0.063 -10000 0 -0.81 2 2
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.062 0.19 0.65 26 -10000 0 26
IL27/IL27R/JAK1 -0.11 0.21 -10000 0 -0.82 23 23
TBX21 -0.1 0.26 -10000 0 -0.71 44 44
IL12B -0.062 0.24 -10000 0 -0.83 43 43
IL12A -0.008 0.095 -10000 0 -0.48 19 19
IL6ST -0.062 0.2 -10000 0 -0.58 62 62
IL27RA/JAK1 -0.01 0.11 -10000 0 -0.59 17 17
IL27 -0.031 0.18 -10000 0 -0.84 23 23
TYK2 0.011 0.039 -10000 0 -0.84 1 1
T-helper cell lineage commitment -0.017 0.12 -10000 0 -0.64 8 8
T-helper 2 cell differentiation 0.062 0.19 0.65 26 -10000 0 26
T cell proliferation during immune response 0.062 0.19 0.65 26 -10000 0 26
MAPKKK cascade -0.062 0.19 -10000 0 -0.65 26 26
STAT3 0.014 0 -10000 0 -10000 0 0
STAT2 0.014 0 -10000 0 -10000 0 0
STAT1 -0.034 0.19 -10000 0 -0.82 28 28
IL12RB1 -0.064 0.24 -10000 0 -0.81 46 46
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.15 0.32 -10000 0 -0.69 105 105
IL27/IL27R/JAK2/TYK2 -0.063 0.19 -10000 0 -0.67 25 25
positive regulation of T cell mediated cytotoxicity -0.062 0.19 -10000 0 -0.65 26 26
STAT1 (dimer) -0.18 0.31 0.52 1 -0.93 46 47
JAK2 0.011 0.027 -10000 0 -0.57 1 1
JAK1 0.013 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.052 0.18 -10000 0 -0.63 25 25
T cell proliferation -0.081 0.21 -10000 0 -0.65 32 32
IL12/IL12R/TYK2/JAK2 -0.064 0.19 -10000 0 -0.71 17 17
IL17A -0.019 0.12 -10000 0 -0.64 8 8
mast cell activation 0.062 0.19 0.65 26 -10000 0 26
IFNG -0.019 0.051 -10000 0 -0.11 109 109
T cell differentiation -0.007 0.009 -10000 0 -0.024 68 68
STAT3 (dimer) -0.052 0.18 -10000 0 -0.7 18 18
STAT5A (dimer) -0.052 0.18 -10000 0 -0.64 24 24
STAT4 (dimer) -0.063 0.2 -10000 0 -0.67 29 29
STAT4 -0.006 0.12 -10000 0 -0.8 12 12
T cell activation -0.006 0.02 0.093 17 -10000 0 17
IL27R/JAK2/TYK2 -0.052 0.17 -10000 0 -0.7 14 14
GATA3 0.001 0.15 -10000 0 -0.71 17 17
IL18 -0.005 0.082 -10000 0 -0.42 19 19
positive regulation of mast cell cytokine production -0.051 0.18 -10000 0 -0.68 18 18
IL27/EBI3 -0.034 0.17 -10000 0 -0.64 34 34
IL27RA -0.019 0.12 -10000 0 -0.64 17 17
IL6 -0.043 0.19 -10000 0 -0.61 46 46
STAT5A 0.014 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.016 0.067 0.39 1 -10000 0 1
IL1B -0.056 0.2 -10000 0 -0.62 53 53
EBI3 -0.008 0.12 -10000 0 -0.74 12 12
TNF -0.018 0.13 -10000 0 -0.61 24 24
Syndecan-3-mediated signaling events

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
CTTN -0.003 0.12 -9999 0 -0.82 10 10
Syndecan-3/Src/Cortactin -0.1 0.14 -9999 0 -0.57 11 11
Syndecan-3/Neurocan -0.026 0.1 -9999 0 -0.45 28 28
POMC -0.081 0.26 -9999 0 -0.77 60 60
EGFR -0.017 0.15 -9999 0 -0.76 20 20
Syndecan-3/EGFR -0.018 0.086 -9999 0 -0.45 17 17
AGRP 0.005 0.007 -9999 0 -10000 0 0
NCSTN 0.014 0 -9999 0 -10000 0 0
PSENEN 0.01 0.053 -9999 0 -0.82 2 2
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.014 0 -9999 0 -10000 0 0
APH1A 0.014 0 -9999 0 -10000 0 0
NCAN -0.033 0.18 -9999 0 -0.82 26 26
long-term memory -0.011 0.066 -9999 0 -0.41 13 13
Syndecan-3/IL8 -0.099 0.19 -9999 0 -0.46 104 104
PSEN1 0.014 0 -9999 0 -10000 0 0
Src/Cortactin -0.013 0.088 -9999 0 -0.63 10 10
FYN 0.012 0.037 -9999 0 -0.82 1 1
limb bud formation -0.002 0.024 -9999 0 -0.37 2 2
MC4R 0.005 0.038 -9999 0 -0.82 1 1
SRC 0.014 0 -9999 0 -10000 0 0
PTN -0.21 0.28 -9999 0 -0.57 189 189
FGFR/FGF/Syndecan-3 -0.002 0.024 -9999 0 -0.38 2 2
neuron projection morphogenesis -0.12 0.16 -9999 0 -0.49 36 36
Syndecan-3/AgRP -0.002 0.023 -9999 0 -0.36 2 2
Syndecan-3/AgRP/MC4R -0.003 0.029 -9999 0 -0.44 1 1
Fyn/Cortactin -0.014 0.092 -9999 0 -0.63 11 11
SDC3 -0.002 0.025 -9999 0 -0.38 2 2
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.098 0.19 -9999 0 -0.46 104 104
IL8 -0.16 0.34 -9999 0 -0.81 106 106
Syndecan-3/Fyn/Cortactin -0.011 0.068 -9999 0 -0.42 13 13
Syndecan-3/CASK -0.002 0.023 -9999 0 -0.36 2 2
alpha-MSH/MC4R -0.072 0.2 -9999 0 -0.6 60 60
Gamma Secretase -0.002 0.029 -9999 0 -0.46 2 2
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.006 0.038 -10000 0 -0.56 2 2
HSPA8 0.016 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.032 0.16 -10000 0 -0.55 17 17
AKT1 0.001 0.033 -10000 0 -10000 0 0
GSC -0.014 0.19 -10000 0 -0.71 30 30
NKX2-5 -0.16 0.32 -10000 0 -0.72 119 119
muscle cell differentiation 0.12 0.2 0.62 46 -10000 0 46
SMAD2-3/SMAD4/SP1 -0.039 0.099 -10000 0 -10000 0 0
SMAD4 0.003 0.042 -10000 0 -0.53 1 1
CBFB 0.014 0 -10000 0 -10000 0 0
SAP18 0.015 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.004 0.074 -10000 0 -0.54 8 8
SMAD3/SMAD4/VDR 0.005 0.041 -10000 0 -10000 0 0
MYC 0.027 0.033 -10000 0 -10000 0 0
CDKN2B -0.24 0.57 -10000 0 -1.3 102 102
AP1 -0.002 0.1 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.057 0.04 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.062 0.16 -10000 0 -0.56 15 15
SP3 0.016 0 -10000 0 -10000 0 0
CREB1 0.014 0 -10000 0 -10000 0 0
FOXH1 -0.1 0.29 -10000 0 -0.81 69 69
SMAD3/SMAD4/GR 0.03 0.064 -10000 0 -10000 0 0
GATA3 -0.015 0.15 -10000 0 -0.77 19 19
SKI/SIN3/HDAC complex/NCoR1 0.056 0.023 -10000 0 -10000 0 0
MEF2C/TIF2 -0.16 0.28 -10000 0 -0.77 49 49
endothelial cell migration 0.36 0.33 0.65 287 -10000 0 287
MAX 0.035 0.02 -10000 0 -10000 0 0
RBBP7 0.015 0.002 -10000 0 -10000 0 0
RBBP4 0.014 0.026 -10000 0 -0.57 1 1
RUNX2 0.01 0.052 -10000 0 -0.65 3 3
RUNX3 0.004 0.091 -10000 0 -0.82 6 6
RUNX1 0.014 0 -10000 0 -10000 0 0
CTBP1 0.014 0 -10000 0 -10000 0 0
NR3C1 0.035 0.02 -10000 0 -10000 0 0
VDR 0.011 0.037 -10000 0 -0.57 2 2
CDKN1A 0.023 0.093 -10000 0 -10000 0 0
KAT2B -0.018 0.12 -10000 0 -0.57 24 24
SMAD2/SMAD2/SMAD4/FOXH1 -0.07 0.2 -10000 0 -0.56 69 69
DCP1A 0.014 0 -10000 0 -10000 0 0
SKI 0.015 0.002 -10000 0 -10000 0 0
SERPINE1 -0.37 0.33 -10000 0 -0.65 287 287
SMAD3/SMAD4/ATF2 0.008 0.046 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.002 0.074 -10000 0 -0.5 6 6
SAP30 0.013 0.037 -10000 0 -0.82 1 1
Cbp/p300/PIAS3 0.002 0.037 -10000 0 -10000 0 0
JUN 0.019 0.11 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 -0.014 0.12 -10000 0 -0.59 17 17
TFE3 0 0.019 -10000 0 -10000 0 0
COL1A2 -0.25 0.34 -10000 0 -0.69 185 185
mesenchymal cell differentiation -0.006 0.056 0.6 1 -10000 0 1
DLX1 -0.33 0.41 -10000 0 -0.82 204 204
TCF3 0.014 0 -10000 0 -10000 0 0
FOS -0.055 0.19 -10000 0 -0.56 64 64
SMAD3/SMAD4/Max 0.03 0.064 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.003 0.025 -10000 0 -10000 0 0
ZBTB17 0.024 0.026 -10000 0 -10000 0 0
LAMC1 0.011 0.042 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.007 0.058 -10000 0 -0.6 2 2
IRF7 -0.018 0.16 -10000 0 -0.8 19 19
ESR1 -0.016 0.18 -10000 0 -0.69 31 31
HNF4A -0.07 0.24 -10000 0 -0.82 48 48
MEF2C -0.14 0.27 -10000 0 -0.64 64 64
SMAD2-3/SMAD4 -0.003 0.057 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.005 0.029 -10000 0 -10000 0 0
IGHV3OR16-13 -0.001 0.012 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.01 0.053 -10000 0 -0.82 2 2
CREBBP 0.008 0.01 -10000 0 -10000 0 0
SKIL 0.014 0 -10000 0 -10000 0 0
HDAC1 0.015 0.002 -10000 0 -10000 0 0
HDAC2 0.015 0.002 -10000 0 -10000 0 0
SNIP1 0.016 0.004 -10000 0 -10000 0 0
GCN5L2 -0.009 0.014 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 0 0.045 -10000 0 -10000 0 0
MSG1/HSC70 0.008 0.083 -10000 0 -0.63 8 8
SMAD2 0.002 0.037 -10000 0 -10000 0 0
SMAD3 0.007 0.04 -10000 0 -0.52 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.021 0.046 -10000 0 -0.44 1 1
SMAD2/SMAD2/SMAD4 -0.022 0.079 -10000 0 -0.35 25 25
NCOR1 0.015 0.002 -10000 0 -10000 0 0
NCOA2 -0.031 0.15 -10000 0 -0.57 38 38
NCOA1 0.014 0 -10000 0 -10000 0 0
MYOD/E2A -0.069 0.16 -10000 0 -0.42 82 82
SMAD2-3/SMAD4/SP1/MIZ-1 -0.03 0.094 -10000 0 -10000 0 0
IFNB1 0.004 0.16 -10000 0 -0.61 24 24
SMAD3/SMAD4/MEF2C -0.14 0.26 -10000 0 -0.7 41 41
CITED1 0 0.1 -10000 0 -0.82 8 8
SMAD2-3/SMAD4/ARC105 0.005 0.057 -10000 0 -0.48 1 1
RBL1 0.013 0.026 -10000 0 -0.57 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.062 0.22 -10000 0 -0.49 100 100
RUNX1-3/PEBPB2 -0.007 0.059 -10000 0 -0.54 6 6
SMAD7 -0.02 0.11 -10000 0 -10000 0 0
MYC/MIZ-1 0.033 0.065 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.12 0.16 0.36 4 -0.39 6 10
IL10 0.015 0.15 -10000 0 -0.63 17 17
PIASy/HDAC complex 0.023 0.013 -10000 0 -10000 0 0
PIAS3 0.008 0.008 -10000 0 -10000 0 0
CDK2 0.007 0.01 -10000 0 -10000 0 0
IL5 0.012 0.13 -10000 0 -0.58 13 13
CDK4 0.008 0.011 -10000 0 -10000 0 0
PIAS4 0.023 0.013 -10000 0 -10000 0 0
ATF3 0.003 0.086 -10000 0 -0.66 8 8
SMAD3/SMAD4/SP1 -0.047 0.09 -10000 0 -10000 0 0
FOXG1 -0.12 0.28 -10000 0 -0.73 83 83
FOXO3 0.008 0.044 -10000 0 -10000 0 0
FOXO1 0.008 0.043 -10000 0 -10000 0 0
FOXO4 0.006 0.05 -10000 0 -0.4 2 2
heart looping -0.13 0.27 -10000 0 -0.62 64 64
CEBPB 0.007 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.23 0.29 -10000 0 -0.57 201 201
MYOD1 -0.09 0.22 -10000 0 -0.58 82 82
SMAD3/SMAD4/HNF4 -0.048 0.18 -10000 0 -0.56 48 48
SMAD3/SMAD4/GATA3 -0.013 0.12 -10000 0 -0.56 16 16
SnoN/SIN3/HDAC complex/NCoR1 0.014 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.011 0.066 -10000 0 -0.47 6 6
SMAD3/SMAD4/SP1-3 -0.025 0.082 -10000 0 -10000 0 0
MED15 0.012 0.037 -10000 0 -0.82 1 1
SP1 -0.034 0.074 -10000 0 -10000 0 0
SIN3B 0.015 0.002 -10000 0 -10000 0 0
SIN3A 0.015 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.16 0.27 -10000 0 -0.56 133 133
ITGB5 0.01 0.09 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.053 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.084 0.17 -10000 0 -0.47 19 19
AR -0.14 0.26 -10000 0 -0.57 132 132
negative regulation of cell growth 0.023 0.055 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.055 0.15 -10000 0 -0.48 16 16
E2F5 0.01 0.045 -10000 0 -0.57 3 3
E2F4 0.014 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.06 0.17 -10000 0 -0.48 69 69
SMAD2-3/SMAD4/FOXO1-3a-4 -0.031 0.15 -10000 0 -10000 0 0
TFDP1 0.012 0.037 -10000 0 -0.82 1 1
SMAD3/SMAD4/AP1 0.002 0.11 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.006 0.056 -10000 0 -0.61 1 1
TGIF2 0.01 0.053 -10000 0 -0.82 2 2
TGIF1 0.012 0.037 -10000 0 -0.82 1 1
ATF2 0.013 0.026 -10000 0 -0.57 1 1
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.029 0.033 -9999 0 -10000 0 0
SNTA1 0.012 0.037 -9999 0 -0.82 1 1
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.024 0.061 -9999 0 -0.54 4 4
MAPK12 -0.008 0.14 -9999 0 -0.56 21 21
CCND1 0 0.088 -9999 0 -0.39 13 13
p38 gamma/SNTA1 -0.002 0.13 -9999 0 -0.52 22 22
MAP2K3 0.013 0.026 -9999 0 -0.57 1 1
PKN1 0.01 0.053 -9999 0 -0.82 2 2
G2/M transition checkpoint -0.008 0.14 -9999 0 -0.55 21 21
MAP2K6 0.005 0.086 -9999 0 -0.34 26 26
MAPT -0.13 0.18 -9999 0 -0.32 221 221
MAPK13 0.021 0.038 -9999 0 -0.41 4 4
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.016 0.03 -9999 0 -0.36 3 3
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.01 0.076 -9999 0 -0.6 8 8
alphaV beta3 Integrin -0.035 0.13 -9999 0 -0.56 23 23
PTK2 -0.004 0.15 -9999 0 -0.59 9 9
IGF1R 0.014 0 -9999 0 -10000 0 0
PI4KB 0.014 0 -9999 0 -10000 0 0
MFGE8 0.012 0.037 -9999 0 -0.82 1 1
SRC 0.014 0 -9999 0 -10000 0 0
CDKN1B -0.036 0.1 -9999 0 -0.41 31 31
VEGFA 0.004 0.091 -9999 0 -0.82 6 6
ILK -0.036 0.1 -9999 0 -0.41 31 31
ROCK1 0.014 0 -9999 0 -10000 0 0
AKT1 0.001 0.11 -9999 0 -0.5 3 3
PTK2B 0.013 0.12 -9999 0 -0.46 25 25
alphaV/beta3 Integrin/JAM-A -0.059 0.16 -9999 0 -0.49 51 51
CBL 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.026 0.11 -9999 0 -0.55 20 20
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.054 0.12 -9999 0 -0.52 5 5
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.017 0.084 -9999 0 -0.42 4 4
alphaV/beta3 Integrin/Syndecan-1 -0.023 0.11 -9999 0 -0.55 17 17
PI4KA 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.26 0.25 -9999 0 -0.74 48 48
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.31 0.29 -9999 0 -0.56 274 274
RPS6KB1 -0.21 0.25 -9999 0 -0.68 48 48
TLN1 0.01 0.053 -9999 0 -0.82 2 2
MAPK3 -0.11 0.15 -9999 0 -0.68 16 16
GPR124 0.009 0.064 -9999 0 -0.82 3 3
MAPK1 -0.11 0.15 -9999 0 -0.68 16 16
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
alphaV/beta3 Integrin/Tumstatin -0.081 0.2 -9999 0 -0.59 56 56
cell adhesion -0.023 0.1 -9999 0 -0.49 17 17
ANGPTL3 0 0.064 -9999 0 -0.82 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.066 -9999 0 -0.54 7 7
IGF-1R heterotetramer 0.014 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.011 0.037 -9999 0 -0.57 2 2
ITGB3 -0.015 0.14 -9999 0 -0.73 19 19
IGF1 -0.088 0.22 -9999 0 -0.58 85 85
RAC1 0.014 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.026 0.12 -9999 0 -0.57 19 19
apoptosis 0.006 0.078 -9999 0 -0.77 5 5
CD47 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.023 0.11 -9999 0 -0.55 17 17
VCL 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.088 0.2 -9999 0 -0.58 57 57
CSF1 0.007 0.063 -9999 0 -0.57 6 6
PIK3C2A -0.036 0.1 -9999 0 -0.41 31 31
PI4 Kinase/Pyk2 -0.054 0.14 -9999 0 -0.77 5 5
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.028 0.11 -9999 0 -0.5 25 25
FAK1/Vinculin 0.006 0.12 -9999 0 -0.49 5 5
alphaV beta3/Integrin/ppsTEM5 -0.026 0.12 -9999 0 -0.57 19 19
RHOA 0.014 0 -9999 0 -10000 0 0
VTN -0.039 0.2 -9999 0 -0.82 31 31
BCAR1 0.014 0 -9999 0 -10000 0 0
FGF2 -0.007 0.12 -9999 0 -0.63 16 16
F11R 0.008 0.089 -9999 0 -0.46 17 17
alphaV/beta3 Integrin/Lactadherin -0.024 0.11 -9999 0 -0.58 17 17
alphaV/beta3 Integrin/TGFBR2 -0.024 0.11 -9999 0 -0.55 17 17
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.008 0.056 -9999 0 -0.49 4 4
HSP90AA1 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.023 0.1 -9999 0 -0.51 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.36 0.41 -9999 0 -0.82 221 221
alphaV/beta3 Integrin/Pyk2 0.013 0.12 -9999 0 -0.47 25 25
SDC1 0.014 0 -9999 0 -10000 0 0
VAV3 0.012 0.1 -9999 0 -0.5 7 7
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.01 0.045 -9999 0 -0.57 3 3
FAK1/Paxillin 0.006 0.12 -9999 0 -0.49 5 5
cell migration 0.016 0.12 -9999 0 -0.46 3 3
ITGAV 0.006 0.079 -9999 0 -0.77 5 5
PI3K -0.054 0.14 -9999 0 -0.72 6 6
SPP1 -0.44 0.42 -9999 0 -0.82 268 268
KDR 0.011 0.045 -9999 0 -0.69 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.006 0.079 -9999 0 -0.77 5 5
COL4A3 -0.08 0.25 -9999 0 -0.74 61 61
angiogenesis -0.077 0.17 -9999 0 -0.7 14 14
Rac1/GTP -0.024 0.082 -9999 0 -0.52 3 3
EDIL3 -0.091 0.26 -9999 0 -0.71 72 72
cell proliferation -0.024 0.11 -9999 0 -0.55 17 17
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HIF3A -0.14 0.27 -9999 0 -0.59 130 130
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.01 0.053 -9999 0 -0.82 2 2
TCEB1 0.012 0.037 -9999 0 -0.82 1 1
HIF1A/p53 0.024 0.041 -9999 0 -10000 0 0
HIF1A 0.019 0.034 -9999 0 -10000 0 0
COPS5 0.014 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.004 0.041 -9999 0 -0.46 4 4
FIH (dimer) 0.014 0 -9999 0 -10000 0 0
CDKN2A -0.35 0.4 -9999 0 -0.77 230 230
ARNT/IPAS -0.11 0.19 -9999 0 -0.43 130 130
HIF1AN 0.014 0 -9999 0 -10000 0 0
GNB2L1 0.014 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.026 0.032 -9999 0 -10000 0 0
CUL2 0.012 0.037 -9999 0 -0.82 1 1
OS9 0.014 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.003 0.042 -9999 0 -0.54 3 3
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.026 0.032 -9999 0 -10000 0 0
PHD1-3/OS9 -0.029 0.11 -9999 0 -0.49 26 26
HIF1A/RACK1/Elongin B/Elongin C -0.007 0.043 -9999 0 -0.5 3 3
VHL 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.026 0.032 -9999 0 -10000 0 0
EGLN3 -0.036 0.19 -9999 0 -0.78 31 31
EGLN2 0.014 0 -9999 0 -10000 0 0
EGLN1 0.014 0 -9999 0 -10000 0 0
TP53 0.009 0.052 -9999 0 -0.57 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.037 0.027 -9999 0 -10000 0 0
ARNT 0.014 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.014 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.17 0.22 -9999 0 -0.44 189 189
Presenilin action in Notch and Wnt 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
Delta 1/NOTCH/NOTCH(cleaved) -0.008 0.059 -10000 0 -0.58 4 4
HDAC1 0.01 0.005 -10000 0 -10000 0 0
AES 0.013 0.001 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
DTX1 0.01 0.052 -10000 0 -0.65 3 3
LRP6/FZD1 -0.008 0.068 -10000 0 -0.56 7 7
TLE1 0.013 0.001 -10000 0 -10000 0 0
AP1 -0.023 0.12 -10000 0 -0.7 3 3
NCSTN 0.014 0 -10000 0 -10000 0 0
ADAM10 0.011 0.037 -10000 0 -0.57 2 2
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.046 -10000 0 -10000 0 0
NICD/RBPSUH -0.005 0.051 -10000 0 -0.57 4 4
WIF1 -0.26 0.3 -10000 0 -0.59 219 219
NOTCH1 -0.005 0.055 -10000 0 -0.61 4 4
PSENEN 0.01 0.053 -10000 0 -0.82 2 2
KREMEN2 -0.29 0.4 -10000 0 -0.82 183 183
DKK1 -0.28 0.39 -10000 0 -0.8 183 183
beta catenin/beta TrCP1 0.021 0.045 -10000 0 -0.34 1 1
APH1B 0.014 0 -10000 0 -10000 0 0
APH1A 0.014 0 -10000 0 -10000 0 0
AXIN1 0.002 0.025 -10000 0 -0.28 1 1
CtBP/CBP/TCF1/TLE1/AES 0.019 0.044 -10000 0 -10000 0 0
PSEN1 0.014 0 -10000 0 -10000 0 0
FOS -0.061 0.19 -10000 0 -0.57 64 64
JUN 0.014 0 -10000 0 -10000 0 0
MAP3K7 0.012 0.002 -10000 0 -10000 0 0
CTNNB1 0.014 0.047 -10000 0 -0.37 1 1
MAPK3 0.014 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.21 0.27 -10000 0 -0.55 191 191
HNF1A -0.003 0.11 -10000 0 -0.82 9 9
CTBP1 0.013 0.001 -10000 0 -10000 0 0
MYC 0.025 0.013 -10000 0 -10000 0 0
NKD1 -0.017 0.15 -10000 0 -0.78 19 19
FZD1 0.004 0.087 -10000 0 -0.78 6 6
NOTCH1 precursor/Deltex homolog 1 -0.007 0.063 -10000 0 -0.6 5 5
apoptosis -0.023 0.12 -10000 0 -0.69 3 3
Delta 1/NOTCHprecursor -0.008 0.059 -10000 0 -0.57 4 4
DLL1 0.007 0.063 -10000 0 -0.57 6 6
PPARD 0.025 0.013 -10000 0 -10000 0 0
Gamma Secretase -0.002 0.029 -10000 0 -0.46 2 2
APC 0.001 0.031 -10000 0 -0.35 2 2
DVL1 -0.018 0.028 -10000 0 -10000 0 0
CSNK2A1 0.014 0.001 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.39 0.36 -10000 0 -0.66 289 289
LRP6 0.013 0.026 -10000 0 -0.57 1 1
CSNK1A1 0.014 0.001 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -10000 0 0
CCND1 0.006 0.14 -10000 0 -0.84 12 12
WNT1 0.002 0.083 -10000 0 -0.82 5 5
Axin1/APC/beta catenin 0.027 0.042 -10000 0 -0.39 1 1
DKK2 -0.009 0.13 -10000 0 -0.69 16 16
NOTCH1 precursor/DVL1 -0.009 0.051 -10000 0 -0.57 4 4
GSK3B 0.013 0 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.007 0.064 -10000 0 -0.61 5 5
PPP2R5D 0.002 0.066 0.32 19 -10000 0 19
MAPK1 0.014 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.15 0.17 -10000 0 -0.51 27 27
RBPJ 0.014 0 -10000 0 -10000 0 0
CREBBP 0.017 0.003 -10000 0 -10000 0 0
Angiopoietin receptor Tie2-mediated signaling

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
AKT1 0.054 0.23 -9999 0 -0.89 21 21
NCK1/PAK1/Dok-R -0.028 0.09 -9999 0 -0.41 21 21
NCK1/Dok-R -0.052 0.22 -9999 0 -1.1 21 21
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
mol:beta2-estradiol -0.005 0.041 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
SHC1 0.014 0.002 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
F2 -0.079 0.25 -9999 0 -0.84 47 47
TNIP2 0.014 0 -9999 0 -10000 0 0
NF kappa B/RelA -0.046 0.2 -9999 0 -0.99 21 21
FN1 -0.36 0.41 -9999 0 -0.82 221 221
PLD2 0.031 0.25 -9999 0 -1.1 21 21
PTPN11 0.014 0 -9999 0 -10000 0 0
GRB14 -0.045 0.18 -9999 0 -0.6 47 47
ELK1 0.045 0.23 -9999 0 -0.99 21 21
GRB7 0.005 0.083 -9999 0 -0.74 6 6
PAK1 0.012 0.037 -9999 0 -0.82 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.34 0.36 -9999 0 -0.86 131 131
CDKN1A 0.061 0.19 -9999 0 -0.65 11 11
ITGA5 -0.25 0.39 -9999 0 -0.82 155 155
mol:GTP 0 0 -9999 0 -10000 0 0
RasGAP/Dok-R -0.054 0.22 -9999 0 -1.1 21 21
CRK 0.014 0 -9999 0 -10000 0 0
mol:NO 0.058 0.18 -9999 0 -0.64 21 21
PLG 0.02 0.25 -9999 0 -1.1 21 21
mol:GDP 0 0 -9999 0 -10000 0 0
chemokinesis 0.034 0.21 -9999 0 -0.85 21 21
GRB2 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.011 0.045 -9999 0 -0.57 3 3
ANGPT2 0.018 0.19 -9999 0 -0.61 24 24
BMX -0.006 0.28 -9999 0 -1.2 21 21
ANGPT1 0.015 0.23 -9999 0 -1.2 14 14
tube development 0.054 0.21 -9999 0 -0.74 12 12
ANGPT4 0.008 0.008 -9999 0 -10000 0 0
response to hypoxia 0.001 0.015 -9999 0 -10000 0 0
Tie2/Ang1/GRB14 -0.004 0.27 -9999 0 -1.2 21 21
alpha5/beta1 Integrin -0.2 0.29 -9999 0 -0.63 156 156
FGF2 -0.008 0.12 -9999 0 -0.63 16 16
STAT5A (dimer) 0.056 0.23 -9999 0 -0.85 11 11
mol:L-citrulline 0.058 0.18 -9999 0 -0.64 21 21
AGTR1 -0.042 0.17 -9999 0 -0.58 46 46
MAPK14 0.034 0.26 -9999 0 -1.1 21 21
Tie2/SHP2 -0.032 0.18 -9999 0 -1.2 11 11
TEK 0.011 0.21 -9999 0 -1.3 11 11
RPS6KB1 0.057 0.22 -9999 0 -0.85 21 21
Angiotensin II/AT1 -0.029 0.13 -9999 0 -0.43 46 46
Tie2/Ang1/GRB2 0.027 0.26 -9999 0 -1.2 21 21
MAPK3 0.04 0.23 -9999 0 -1 21 21
MAPK1 0.04 0.23 -9999 0 -1 21 21
Tie2/Ang1/GRB7 0.022 0.27 -9999 0 -1.2 21 21
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 0.027 0.26 -9999 0 -1.1 21 21
PI3K 0.045 0.25 -9999 0 -1 21 21
FES 0.034 0.26 -9999 0 -1.1 21 21
Crk/Dok-R -0.052 0.22 -9999 0 -1.1 21 21
Tie2/Ang1/ABIN2 0.027 0.26 -9999 0 -1.2 21 21
blood circulation 0 0 -9999 0 -10000 0 0
negative regulation of caspase activity 0.057 0.21 -9999 0 -0.79 21 21
STAT5A 0.014 0 -9999 0 -10000 0 0
mol:ROS 0 0 -9999 0 -10000 0 0
PTK2 0.057 0.22 -9999 0 -0.85 21 21
Tie2/Ang2 0.039 0.26 -9999 0 -1.1 11 11
Tie2/Ang1 0.023 0.28 -9999 0 -1.2 21 21
FOXO1 0.058 0.22 -9999 0 -0.79 21 21
ELF1 0.017 0.056 -9999 0 -0.58 4 4
ELF2 0.028 0.25 -9999 0 -1.1 21 21
mol:Choline 0.033 0.24 -9999 0 -1.1 21 21
cell migration -0.09 0.087 -9999 0 -10000 0 0
FYN 0.05 0.23 -9999 0 -0.86 12 12
DOK2 0.008 0.069 -9999 0 -0.76 4 4
negative regulation of cell cycle 0.063 0.18 -9999 0 -0.59 11 11
ETS1 0.013 0.074 -9999 0 -0.8 3 3
PXN 0.067 0.19 -9999 0 -0.7 21 21
ITGB1 0.012 0.037 -9999 0 -0.82 1 1
NOS3 0.056 0.2 -9999 0 -0.74 21 21
RAC1 0.014 0 -9999 0 -10000 0 0
TNF -0.019 0.18 -9999 0 -0.78 24 24
MAPKKK cascade 0.033 0.24 -9999 0 -1.1 21 21
RASA1 0.011 0.037 -9999 0 -0.57 2 2
Tie2/Ang1/Shc 0.028 0.26 -9999 0 -1.2 21 21
NCK1 0.014 0 -9999 0 -10000 0 0
vasculogenesis 0.06 0.17 -9999 0 -0.58 21 21
mol:Phosphatidic acid 0.033 0.24 -9999 0 -1.1 21 21
mol:Angiotensin II 0 0.007 -9999 0 -10000 0 0
mol:NADP 0.058 0.18 -9999 0 -0.64 21 21
Rac1/GTP -0.048 0.17 -9999 0 -0.79 21 21
MMP2 -0.037 0.3 -9999 0 -1.1 21 21
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.038 0.16 -9999 0 -0.73 11 11
FZD6 0.011 0.045 -9999 0 -0.69 2 2
WNT6 -0.052 0.22 -9999 0 -0.76 42 42
WNT4 -0.007 0.12 -9999 0 -0.63 16 16
FZD3 0.006 0.068 -9999 0 -0.57 7 7
WNT5A 0.005 0.073 -9999 0 -0.6 7 7
WNT11 -0.074 0.25 -9999 0 -0.75 57 57
LPA receptor mediated events

Figure S51.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S51.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.043 0.1 -9999 0 -0.78 2 2
NF kappa B1 p50/RelA/I kappa B alpha -0.021 0.055 -9999 0 -0.42 1 1
AP1 -0.072 0.13 -9999 0 -0.55 13 13
mol:PIP3 -0.05 0.11 -9999 0 -0.56 6 6
AKT1 0.026 0.088 -9999 0 -0.51 2 2
PTK2B 0 0.076 -9999 0 -0.29 6 6
RHOA 0.011 0.058 -9999 0 -0.31 1 1
PIK3CB 0.014 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.01 0.074 -9999 0 -0.49 3 3
MAGI3 0.011 0.037 -9999 0 -0.57 2 2
RELA 0.014 0 -9999 0 -10000 0 0
apoptosis -0.019 0.11 -9999 0 -0.61 4 4
HRAS/GDP -0.001 0.029 -9999 0 -0.64 1 1
positive regulation of microtubule depolymerization -0.11 0.15 -9999 0 -0.41 31 31
NF kappa B1 p50/RelA -0.033 0.089 -9999 0 -0.54 5 5
endothelial cell migration -0.089 0.28 -9999 0 -0.76 70 70
ADCY4 -0.006 0.12 -9999 0 -0.43 16 16
ADCY5 -0.053 0.14 -9999 0 -0.52 18 18
ADCY6 -0.011 0.13 -9999 0 -0.46 17 17
ADCY7 -0.006 0.12 -9999 0 -0.43 16 16
ADCY1 -0.014 0.12 -9999 0 -0.43 17 17
ADCY2 -0.073 0.14 -9999 0 -0.48 23 23
ADCY3 -0.006 0.12 -9999 0 -0.43 16 16
ADCY8 -0.013 0.12 -9999 0 -0.42 20 20
ADCY9 -0.007 0.12 -9999 0 -0.43 16 16
GSK3B 0.008 0.073 -9999 0 -10000 0 0
arachidonic acid secretion 0.001 0.12 -9999 0 -0.41 16 16
GNG2 0.012 0.037 -9999 0 -0.82 1 1
TRIP6 0.018 0.022 -9999 0 -10000 0 0
GNAO1 -0.026 0.13 -9999 0 -0.42 16 16
HRAS 0.012 0.037 -9999 0 -0.82 1 1
NFKBIA 0.015 0.087 -9999 0 -0.44 3 3
GAB1 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.008 0.1 -9999 0 -0.89 7 7
JUN 0.014 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.014 0.05 -9999 0 -0.64 2 2
TIAM1 -0.012 0.12 -9999 0 -1 7 7
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
mol:IP3 0.01 0.075 -9999 0 -0.5 3 3
PLCB3 0.015 0.051 -9999 0 -0.58 2 2
FOS -0.061 0.19 -9999 0 -0.57 64 64
positive regulation of mitosis 0.001 0.12 -9999 0 -0.41 16 16
LPA/LPA1-2-3 -0.049 0.11 -9999 0 -0.64 4 4
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0 -9999 0 -10000 0 0
stress fiber formation 0.005 0.089 -9999 0 -0.41 3 3
GNAZ -0.042 0.16 -9999 0 -0.48 31 31
EGFR/PI3K-beta/Gab1 -0.052 0.11 -9999 0 -0.59 6 6
positive regulation of dendritic cell cytokine production -0.049 0.11 -9999 0 -0.64 4 4
LPA/LPA2/MAGI-3 -0.014 0.037 -9999 0 -0.34 2 2
ARHGEF1 -0.004 0.11 -9999 0 -0.64 3 3
GNAI2 -0.022 0.12 -9999 0 -0.38 12 12
GNAI3 -0.022 0.12 -9999 0 -0.4 8 8
GNAI1 -0.023 0.12 -9999 0 -0.38 13 13
LPA/LPA3 -0.027 0.075 -9999 0 -0.42 12 12
LPA/LPA2 -0.017 0.042 -9999 0 -10000 0 0
LPA/LPA1 -0.058 0.14 -9999 0 -0.36 81 81
HB-EGF/EGFR -0.41 0.27 -9999 0 -0.56 368 368
HBEGF -0.46 0.29 -9999 0 -0.63 366 366
mol:DAG 0.01 0.075 -9999 0 -0.5 3 3
cAMP biosynthetic process -0.02 0.12 -9999 0 -0.48 14 14
NFKB1 0.014 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
GNB1 0.014 0.001 -9999 0 -10000 0 0
LYN 0.015 0.087 -9999 0 -0.46 2 2
GNAQ 0.005 0.059 -9999 0 -0.32 3 3
LPAR2 0.014 0 -9999 0 -10000 0 0
LPAR3 0 0.089 -9999 0 -0.57 12 12
LPAR1 -0.023 0.11 -9999 0 -0.6 12 12
IL8 -0.23 0.18 -9999 0 -0.5 95 95
PTK2 -0.01 0.12 -9999 0 -0.6 4 4
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.019 0.11 -9999 0 -0.61 4 4
EGFR -0.017 0.15 -9999 0 -0.76 20 20
PLCG1 -0.006 0.077 -9999 0 -0.32 12 12
PLD2 -0.01 0.12 -9999 0 -0.6 4 4
G12/G13 -0.044 0.1 -9999 0 -0.68 3 3
PI3K-beta -0.031 0.076 -9999 0 -0.56 3 3
cell migration -0.011 0.047 -9999 0 -0.28 1 1
SLC9A3R2 0.01 0.053 -9999 0 -0.82 2 2
PXN 0.004 0.09 -9999 0 -0.42 3 3
HRAS/GTP 0 0.12 -9999 0 -0.42 16 16
RAC1 0.014 0 -9999 0 -10000 0 0
MMP9 -0.6 0.37 -9999 0 -0.82 366 366
PRKCE 0.012 0.026 -9999 0 -0.57 1 1
PRKCD 0.018 0.072 -9999 0 -0.52 2 2
Gi(beta/gamma) -0.002 0.12 -9999 0 -0.4 17 17
mol:LPA -0.024 0.072 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.027 0.085 -9999 0 -0.54 3 3
MAPKKK cascade 0.001 0.12 -9999 0 -0.41 16 16
contractile ring contraction involved in cytokinesis 0.011 0.057 -9999 0 -0.31 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.043 0.12 -9999 0 -0.32 22 22
GNA15 0.004 0.066 -9999 0 -0.53 2 2
GNA12 0.01 0.053 -9999 0 -0.82 2 2
GNA13 0.014 0 -9999 0 -10000 0 0
MAPT -0.11 0.16 -9999 0 -0.42 31 31
GNA11 0.003 0.066 -9999 0 -0.33 5 5
Rac1/GTP -0.009 0.11 -9999 0 -0.94 7 7
MMP2 -0.09 0.28 -9999 0 -0.76 70 70
Signaling events mediated by PTP1B

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
PDGFRB -0.14 0.32 -10000 0 -0.82 89 89
Jak2/Leptin Receptor -0.07 0.1 -10000 0 -0.42 8 8
PTP1B/AKT1 -0.02 0.083 0.23 1 -0.34 3 4
FYN 0.012 0.037 -10000 0 -0.82 1 1
p210 bcr-abl/PTP1B -0.03 0.092 0.26 1 -0.35 8 9
EGFR -0.02 0.15 -10000 0 -0.76 20 20
EGF/EGFR -0.1 0.15 -10000 0 -0.44 47 47
CSF1 0.007 0.063 -10000 0 -0.57 6 6
AKT1 0.014 0.001 -10000 0 -10000 0 0
INSR 0.013 0.026 -10000 0 -0.57 1 1
PTP1B/N-cadherin -0.082 0.2 -10000 0 -0.54 65 65
Insulin Receptor/Insulin -0.032 0.056 -10000 0 -0.43 2 2
HCK 0.006 0.079 -10000 0 -0.77 5 5
CRK 0.014 0 -10000 0 -10000 0 0
TYK2 -0.021 0.091 0.25 1 -0.4 4 5
EGF -0.096 0.23 -10000 0 -0.58 91 91
YES1 0.014 0 -10000 0 -10000 0 0
CAV1 -0.044 0.11 0.25 1 -0.37 15 16
TXN 0.011 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.015 0.085 -10000 0 -0.36 2 2
cell migration 0.03 0.092 0.35 8 -0.26 1 9
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.12 0.24 -10000 0 -0.57 109 109
ITGA2B -0.066 0.24 -10000 0 -0.82 47 47
CSF1R 0.01 0.045 -10000 0 -0.57 3 3
Prolactin Receptor/Prolactin -0.095 0.19 -10000 0 -0.43 112 112
FGR 0.012 0.037 -10000 0 -0.82 1 1
PTP1B/p130 Cas -0.021 0.087 -10000 0 -0.35 6 6
Crk/p130 Cas -0.013 0.083 -10000 0 -0.36 2 2
DOK1 -0.05 0.14 0.25 1 -0.36 37 38
JAK2 -0.063 0.12 -10000 0 -0.37 26 26
Jak2/Leptin Receptor/Leptin -0.074 0.12 -10000 0 -0.48 3 3
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
PTPN1 -0.03 0.093 0.26 1 -0.35 8 9
LYN 0.012 0.037 -10000 0 -0.82 1 1
CDH2 -0.093 0.27 -10000 0 -0.79 66 66
SRC 0.005 0.038 -10000 0 -10000 0 0
ITGB3 -0.015 0.14 -10000 0 -0.73 19 19
CAT1/PTP1B -0.11 0.14 0.26 1 -0.43 24 25
CAPN1 0.013 0.002 -10000 0 -10000 0 0
CSK 0.014 0 -10000 0 -10000 0 0
PI3K -0.024 0.057 -10000 0 -0.46 2 2
mol:H2O2 0 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.066 0.1 -10000 0 -10000 0 0
negative regulation of transcription -0.062 0.12 -10000 0 -0.37 26 26
FCGR2A -0.028 0.18 -10000 0 -0.82 25 25
FER 0.008 0.037 -10000 0 -0.57 2 2
alphaIIb/beta3 Integrin -0.079 0.21 -10000 0 -0.63 63 63
BLK -0.1 0.28 -10000 0 -0.78 71 71
Insulin Receptor/Insulin/Shc -0.003 0.037 -10000 0 -0.47 3 3
RHOA 0.013 0.002 -10000 0 -10000 0 0
LEPR 0.01 0.045 -10000 0 -0.56 3 3
BCAR1 0.014 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.014 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.003 -10000 0 -10000 0 0
TRPV6 -0.1 0.14 -10000 0 -0.42 35 35
PRL -0.004 0.082 -10000 0 -0.82 5 5
SOCS3 0.018 0.063 -10000 0 -1.3 1 1
SPRY2 0.004 0.074 -10000 0 -0.57 8 8
Insulin Receptor/Insulin/IRS1 -0.005 0.046 -10000 0 -0.41 6 6
CSF1/CSF1R -0.018 0.093 -10000 0 -0.39 7 7
Ras protein signal transduction 0.026 0.029 -10000 0 -10000 0 0
IRS1 0.01 0.045 -10000 0 -0.57 3 3
INS -0.003 0.052 -10000 0 -0.82 2 2
LEP -0.096 0.25 -10000 0 -0.66 78 78
STAT5B -0.039 0.088 0.21 1 -0.32 12 13
STAT5A -0.039 0.088 0.21 1 -0.32 12 13
GRB2 0.014 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.11 0.23 0.23 1 -0.56 93 94
CSN2 -0.027 0.092 -10000 0 -0.75 2 2
PIK3CA 0.014 0 -10000 0 -10000 0 0
LAT -0.017 0.089 -10000 0 -0.32 28 28
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.006 0.13 -10000 0 -0.82 12 12
SHC1 0.014 0 -10000 0 -10000 0 0
NOX4 -0.16 0.34 -10000 0 -0.82 102 102
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.053 0.19 -9999 0 -0.4 108 108
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.012 0.037 -9999 0 -0.82 1 1
STAT1 (dimer)/Cbp/p300 -0.09 0.19 -9999 0 -0.72 20 20
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.014 0.03 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.071 0.09 -9999 0 -0.33 9 9
CaM/Ca2+ -0.082 0.15 -9999 0 -10000 0 0
RAP1A 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.066 0.23 -9999 0 -0.71 27 27
AKT1 -0.025 0.16 -9999 0 -10000 0 0
MAP2K1 -0.03 0.17 -9999 0 -10000 0 0
MAP3K11 -0.043 0.18 -9999 0 -10000 0 0
IFNGR1 0.007 0.017 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.19 0.23 -9999 0 -0.61 81 81
Rap1/GTP -0.062 0.12 -9999 0 -10000 0 0
CRKL/C3G -0.001 0.028 -9999 0 -0.63 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.097 0.18 -9999 0 -0.44 109 109
CEBPB 0.01 0.15 -9999 0 -10000 0 0
STAT3 0.014 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.1 0.24 -9999 0 -0.92 17 17
STAT1 -0.066 0.23 -9999 0 -0.71 27 27
CALM1 0.014 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.16 0.34 -9999 0 -0.81 108 108
PIK3CA 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.054 0.22 -9999 0 -0.77 19 19
CEBPB/PTGES2/Cbp/p300 -0.039 0.071 -9999 0 -10000 0 0
mol:Ca2+ -0.087 0.16 -9999 0 -0.4 108 108
MAPK3 -0.009 0.15 -9999 0 -10000 0 0
STAT1 (dimer) -0.094 0.12 -9999 0 -0.46 9 9
MAPK1 -0.009 0.15 -9999 0 -10000 0 0
JAK2 0.006 0.031 -9999 0 -0.56 1 1
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
JAK1 0.007 0.017 -9999 0 -10000 0 0
CAMK2D 0.014 0 -9999 0 -10000 0 0
DAPK1 0.024 0.12 -9999 0 -0.57 5 5
SMAD7 -0.002 0.074 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.074 0.14 -9999 0 -10000 0 0
PI3K -0.08 0.15 -9999 0 -10000 0 0
IFNG -0.16 0.34 -9999 0 -0.81 108 108
apoptosis 0.008 0.1 -9999 0 -0.44 4 4
CAMK2G 0.014 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.13 0.25 -9999 0 -0.57 122 122
CAMK2B -0.14 0.26 -9999 0 -0.58 127 127
FRAP1 -0.022 0.15 -9999 0 -10000 0 0
PRKCD -0.024 0.16 -9999 0 -10000 0 0
RAP1B 0.012 0.037 -9999 0 -0.82 1 1
negative regulation of cell growth -0.071 0.09 -9999 0 -0.33 9 9
PTPN2 0.012 0.037 -9999 0 -0.82 1 1
EP300 0.012 0.037 -9999 0 -0.56 2 2
IRF1 -0.025 0.19 -9999 0 -0.52 35 35
STAT1 (dimer)/PIASy -0.091 0.2 -9999 0 -0.77 19 19
SOCS1 -0.043 0.18 -9999 0 -0.66 38 38
mol:GDP -0.072 0.14 -9999 0 -10000 0 0
CASP1 -0.003 0.075 -9999 0 -0.33 1 1
PTGES2 0.014 0 -9999 0 -10000 0 0
IRF9 0.036 0.057 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.078 0.14 -9999 0 -10000 0 0
RAP1/GDP -0.063 0.12 -9999 0 -10000 0 0
CBL -0.044 0.18 -9999 0 -10000 0 0
MAP3K1 -0.042 0.18 -9999 0 -10000 0 0
PIAS1 0.014 0 -9999 0 -10000 0 0
PIAS4 0.014 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.071 0.09 -9999 0 -0.33 9 9
PTPN11 -0.054 0.18 -9999 0 -0.4 108 108
CREBBP 0.014 0.001 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.14 0.3 -9999 0 -0.68 108 108
RAD9A 0.014 0 -9999 0 -10000 0 0
AP1 -0.037 0.14 -9999 0 -0.41 64 64
IFNAR2 0.012 0.007 -9999 0 -10000 0 0
AKT1 -0.002 0.068 -9999 0 -0.3 11 11
ER alpha/Oestrogen -0.025 0.13 -9999 0 -0.53 31 31
NFX1/SIN3/HDAC complex 0.04 0.028 -9999 0 -10000 0 0
EGF -0.096 0.23 -9999 0 -0.57 91 91
SMG5 0.014 0 -9999 0 -10000 0 0
SMG6 0.014 0 -9999 0 -10000 0 0
SP3/HDAC2 0.019 0.011 -9999 0 -10000 0 0
TERT/c-Abl -0.16 0.26 -9999 0 -0.63 108 108
SAP18 0.013 0.004 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.16 0.34 -9999 0 -0.82 103 103
WRN 0.014 0 -9999 0 -10000 0 0
SP1 0.013 0.007 -9999 0 -10000 0 0
SP3 0.011 0.006 -9999 0 -10000 0 0
TERF2IP 0.014 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.14 0.23 -9999 0 -0.6 81 81
Mad/Max 0.013 0.044 -9999 0 -0.41 5 5
TERT -0.15 0.31 -9999 0 -0.7 108 108
CCND1 -0.13 0.29 -9999 0 -0.72 49 49
MAX 0.012 0.006 -9999 0 -10000 0 0
RBBP7 0.013 0.004 -9999 0 -10000 0 0
RBBP4 0.011 0.026 -9999 0 -0.57 1 1
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.014 0 -9999 0 -10000 0 0
SIN3A 0.013 0.004 -9999 0 -10000 0 0
Telomerase/911 0.025 0.043 -9999 0 -0.34 1 1
CDKN1B -0.087 0.23 -9999 0 -0.52 108 108
RAD1 0.014 0 -9999 0 -10000 0 0
XRCC5 0.014 0 -9999 0 -10000 0 0
XRCC6 0.014 0 -9999 0 -10000 0 0
SAP30 0.011 0.038 -9999 0 -0.82 1 1
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.011 0.006 -9999 0 -10000 0 0
JUN 0.012 0.006 -9999 0 -10000 0 0
E6 -0.001 0.005 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.01 0.006 -9999 0 -10000 0 0
FOS -0.063 0.19 -9999 0 -0.57 64 64
IFN-gamma/IRF1 -0.13 0.25 -9999 0 -0.62 108 108
PARP2 0.014 0 -9999 0 -10000 0 0
BLM 0.01 0.053 -9999 0 -0.82 2 2
Telomerase -0.004 0.11 -9999 0 -0.39 23 23
IRF1 0.016 0.008 -9999 0 -10000 0 0
ESR1 -0.032 0.18 -9999 0 -0.7 31 31
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.016 -9999 0 -0.36 1 1
ubiquitin-dependent protein catabolic process 0.044 0.029 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.044 0.029 -9999 0 -10000 0 0
HDAC1 0.013 0.004 -9999 0 -10000 0 0
HDAC2 0.013 0.007 -9999 0 -10000 0 0
ATM -0.001 0.019 -9999 0 -0.43 1 1
SMAD3 0.023 0.046 -9999 0 -0.56 3 3
ABL1 0.014 0 -9999 0 -10000 0 0
MXD1 0.006 0.058 -9999 0 -0.57 5 5
MRE11A 0.014 0 -9999 0 -10000 0 0
HUS1 0.012 0.037 -9999 0 -0.82 1 1
RPS6KB1 0.014 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.14 0.26 -9999 0 -0.63 83 83
NR2F2 0.015 0.038 -9999 0 -0.81 1 1
MAPK3 0.013 0.03 -9999 0 -0.62 1 1
MAPK1 0.013 0.03 -9999 0 -0.62 1 1
TGFB1/TGF beta receptor Type II 0.011 0.053 -9999 0 -0.82 2 2
NFKB1 0.014 0 -9999 0 -10000 0 0
HNRNPC 0.014 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.019 -9999 0 -0.43 1 1
NBN 0.014 0 -9999 0 -10000 0 0
EGFR -0.019 0.15 -9999 0 -0.76 20 20
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.091 0.2 -9999 0 -0.45 108 108
MYC 0.012 0.006 -9999 0 -10000 0 0
IL2 0.001 0.039 -9999 0 -0.82 1 1
KU 0 0 -9999 0 -10000 0 0
RAD50 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
TGFB1 0.011 0.053 -9999 0 -0.82 2 2
TRF2/BLM -0.002 0.038 -9999 0 -0.59 2 2
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.14 0.27 -9999 0 -0.66 84 84
SP1/HDAC2 0.02 0.015 -9999 0 -10000 0 0
PINX1 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.14 0.23 -9999 0 -0.61 70 70
Smad3/Myc 0.027 0.04 -9999 0 -0.54 2 2
911 complex -0.001 0.024 -9999 0 -0.54 1 1
IFNG -0.16 0.34 -9999 0 -0.81 108 108
Telomerase/PinX1 -0.14 0.23 -9999 0 -0.61 71 71
Telomerase/AKT1/mTOR/p70S6K 0 0.076 -9999 0 -10000 0 0
SIN3B 0.013 0.004 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.14 0.23 -9999 0 -0.61 71 71
response to DNA damage stimulus 0.003 0.006 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.004 -9999 0 -10000 0 0
TRF2/WRN 0 0.004 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.14 0.23 -9999 0 -0.6 81 81
E2F1 -0.05 0.22 -9999 0 -0.83 37 37
ZNFX1 0.013 0.004 -9999 0 -10000 0 0
PIF1 -0.033 0.19 -9999 0 -0.82 28 28
NCL 0.014 0 -9999 0 -10000 0 0
DKC1 0.014 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Regulation of Androgen receptor activity

Figure S55.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S55.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.003 -9999 0 -10000 0 0
SMARCC1 0.011 0.011 -9999 0 -10000 0 0
REL 0.006 0.078 -9999 0 -0.56 9 9
HDAC7 -0.066 0.16 -9999 0 -0.57 20 20
JUN 0.011 0.005 -9999 0 -10000 0 0
EP300 0.011 0.037 -9999 0 -0.57 2 2
KAT2B -0.015 0.12 -9999 0 -0.57 24 24
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.009 0.1 -9999 0 -0.43 26 26
FOXO1 0.013 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.08 0.17 -9999 0 -0.6 21 21
MAP2K6 -0.023 0.13 -9999 0 -0.58 26 26
BRM/BAF57 -0.001 0.018 -9999 0 -0.41 1 1
MAP2K4 0.008 0.008 -9999 0 -10000 0 0
SMARCA2 0.01 0.026 -9999 0 -0.57 1 1
PDE9A -0.091 0.21 -9999 0 -1.1 16 16
NCOA2 -0.031 0.15 -9999 0 -0.57 38 38
CEBPA 0.011 0.045 -9999 0 -0.56 3 3
EHMT2 0.011 0.005 -9999 0 -10000 0 0
cell proliferation -0.059 0.17 -9999 0 -0.56 10 10
NR0B1 -0.033 0.17 -9999 0 -0.82 23 23
EGR1 -0.017 0.12 -9999 0 -0.57 24 24
RXRs/9cRA -0.041 0.11 -9999 0 -0.34 60 60
AR/RACK1/Src -0.035 0.12 -9999 0 -0.51 8 8
AR/GR -0.062 0.15 -9999 0 -0.52 18 18
GNB2L1 0.014 0.001 -9999 0 -10000 0 0
PKN1 0.01 0.053 -9999 0 -0.82 2 2
RCHY1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.008 0.055 -9999 0 -0.44 7 7
T-DHT/AR/TIF2/CARM1 -0.049 0.16 -9999 0 -0.65 11 11
SRC -0.002 0.095 -9999 0 -0.59 2 2
NR3C1 0.014 0 -9999 0 -10000 0 0
KLK3 -0.28 0.45 -9999 0 -1.2 92 92
APPBP2 0.008 0.008 -9999 0 -10000 0 0
TRIM24 0.01 0.026 -9999 0 -0.57 1 1
T-DHT/AR/TIP60 -0.036 0.13 -9999 0 -0.51 18 18
TMPRSS2 -0.52 0.55 -9999 0 -1.1 237 237
RXRG -0.063 0.2 -9999 0 -0.6 60 60
mol:9cRA -0.001 0.003 -9999 0 -10000 0 0
RXRA 0.013 0.001 -9999 0 -10000 0 0
RXRB 0.013 0.001 -9999 0 -10000 0 0
CARM1 0.014 0.002 -9999 0 -10000 0 0
NR2C2 0.005 0.068 -9999 0 -0.57 7 7
KLK2 -0.035 0.16 -9999 0 -0.62 19 19
AR -0.078 0.16 -9999 0 -0.38 71 71
SENP1 0.013 0.001 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
MDM2 0.018 0.012 -9999 0 -10000 0 0
SRY -0.034 0.16 -9999 0 -0.58 38 38
GATA2 0.006 0.079 -9999 0 -0.77 5 5
MYST2 0.013 0.026 -9999 0 -0.57 1 1
HOXB13 -0.3 0.4 -9999 0 -0.83 182 182
T-DHT/AR/RACK1/Src -0.027 0.12 -9999 0 -0.53 6 6
positive regulation of transcription 0.006 0.079 -9999 0 -0.77 5 5
DNAJA1 0.008 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.004 -9999 0 -10000 0 0
NCOA1 0.017 0.008 -9999 0 -10000 0 0
SPDEF -0.17 0.28 -9999 0 -0.6 144 144
T-DHT/AR/TIF2 -0.032 0.15 -9999 0 -0.6 15 15
T-DHT/AR/Hsp90 -0.037 0.12 -9999 0 -0.51 18 18
GSK3B 0.01 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.002 -9999 0 -10000 0 0
mol:T-DHT -0.012 0.1 -9999 0 -0.51 4 4
SIRT1 0.012 0.026 -9999 0 -0.57 1 1
ZMIZ2 0.018 0.011 -9999 0 -10000 0 0
POU2F1 0.016 0.023 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.075 0.15 -9999 0 -0.51 41 41
CREBBP 0.013 0.001 -9999 0 -10000 0 0
SMARCE1 0.011 0.006 -9999 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.003 0.04 -9999 0 -0.63 2 2
VLDLR 0.001 0.085 -9999 0 -0.57 11 11
CRKL 0.012 0.037 -9999 0 -0.82 1 1
LRPAP1 0.014 0 -9999 0 -10000 0 0
FYN 0.012 0.037 -9999 0 -0.82 1 1
ITGA3 -0.016 0.15 -9999 0 -0.8 18 18
RELN/VLDLR/Fyn -0.078 0.15 -9999 0 -0.6 4 4
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.007 0.049 -9999 0 -0.46 3 3
AKT1 -0.032 0.12 -9999 0 -0.5 6 6
MAP2K7 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
DAB1 -0.018 0.15 -9999 0 -0.82 16 16
RELN/LRP8/DAB1 -0.09 0.17 -9999 0 -0.57 27 27
LRPAP1/LRP8 -0.013 0.088 -9999 0 -0.63 10 10
RELN/LRP8/DAB1/Fyn -0.084 0.16 -9999 0 -0.53 28 28
DAB1/alpha3/beta1 Integrin -0.093 0.16 -9999 0 -0.66 10 10
long-term memory -0.16 0.21 -9999 0 -0.56 65 65
DAB1/LIS1 -0.082 0.15 -9999 0 -0.67 9 9
DAB1/CRLK/C3G -0.078 0.15 -9999 0 -0.66 10 10
PIK3CA 0.014 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.082 0.15 -9999 0 -0.68 9 9
ARHGEF2 0.014 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.13 0.29 -9999 0 -0.67 106 106
CDK5R1 0.01 0.053 -9999 0 -0.82 2 2
RELN -0.11 0.24 -9999 0 -0.57 102 102
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
RELN/LRP8/Fyn -0.081 0.16 -9999 0 -0.62 12 12
GRIN2A/RELN/LRP8/DAB1/Fyn -0.16 0.22 -9999 0 -0.55 84 84
MAPK8 0.006 0.068 -9999 0 -0.57 7 7
RELN/VLDLR/DAB1 -0.087 0.16 -9999 0 -0.58 19 19
ITGB1 0.012 0.037 -9999 0 -0.82 1 1
MAP1B -0.068 0.19 -9999 0 -0.6 27 27
RELN/LRP8 -0.08 0.16 -9999 0 -0.63 11 11
GRIN2B/RELN/LRP8/DAB1/Fyn -0.088 0.16 -9999 0 -0.53 32 32
PI3K -0.002 0.031 -9999 0 -0.41 3 3
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.024 0.12 -9999 0 -0.62 19 19
RAP1A -0.029 0.16 -9999 0 -0.64 8 8
PAFAH1B1 0.014 0 -9999 0 -10000 0 0
MAPK8IP1 0.008 0.069 -9999 0 -0.76 4 4
CRLK/C3G -0.001 0.028 -9999 0 -0.63 1 1
GRIN2B -0.004 0.082 -9999 0 -0.82 5 5
NCK2 0.014 0 -9999 0 -10000 0 0
neuron differentiation -0.013 0.1 -9999 0 -0.4 8 8
neuron adhesion -0.029 0.17 -9999 0 -0.6 9 9
LRP8 -0.003 0.12 -9999 0 -0.82 10 10
GSK3B -0.023 0.12 -9999 0 -0.47 6 6
RELN/VLDLR/DAB1/Fyn -0.081 0.15 -9999 0 -0.54 20 20
MAP3K11 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.044 0.13 -9999 0 -0.54 6 6
CDK5 0.014 0 -9999 0 -10000 0 0
MAPT -0.23 0.27 -9999 0 -0.52 221 221
neuron migration -0.024 0.17 -9999 0 -0.54 10 10
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.013 0.1 -9999 0 -0.4 8 8
RELN/VLDLR -0.078 0.15 -9999 0 -0.58 13 13
Ephrin A reverse signaling

Figure S57.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S57.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.022 0.093 -9999 0 -0.39 28 28
EFNA5 -0.012 0.12 -9999 0 -0.57 22 22
FYN 0.001 0.096 -9999 0 -0.58 6 6
neuron projection morphogenesis -0.022 0.093 -9999 0 -0.39 28 28
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.022 0.093 -9999 0 -0.39 28 28
EPHA5 -0.002 0.091 -9999 0 -0.82 6 6
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.11 0.29 -9999 0 -0.72 79 79
MKNK1 0.014 0 -9999 0 -10000 0 0
MAPK14 -0.046 0.13 -9999 0 -0.4 13 13
ATF2/c-Jun -0.012 0.097 -9999 0 -10000 0 0
MAPK11 -0.046 0.13 -9999 0 -0.43 3 3
MITF -0.053 0.17 -9999 0 -0.55 22 22
MAPKAPK5 -0.04 0.15 -9999 0 -0.49 13 13
KRT8 -0.12 0.23 -9999 0 -0.65 47 47
MAPKAPK3 0.014 0 -9999 0 -10000 0 0
MAPKAPK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.068 0.19 -9999 0 -0.65 13 13
CEBPB -0.04 0.15 -9999 0 -0.49 13 13
SLC9A1 -0.04 0.15 -9999 0 -0.49 13 13
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.035 0.15 -9999 0 -0.48 13 13
p38alpha-beta/MNK1 -0.04 0.15 -9999 0 -0.53 13 13
JUN -0.012 0.096 -9999 0 -10000 0 0
PPARGC1A -0.18 0.26 -9999 0 -0.69 68 68
USF1 -0.04 0.15 -9999 0 -0.49 13 13
RAB5/GDP/GDI1 -0.053 0.087 -9999 0 -0.4 3 3
NOS2 -0.12 0.31 -9999 0 -0.75 86 86
DDIT3 -0.049 0.16 -9999 0 -0.52 17 17
RAB5A 0.014 0 -9999 0 -10000 0 0
HSPB1 -0.022 0.12 -9999 0 -0.44 3 3
p38alpha-beta/HBP1 -0.04 0.15 -9999 0 -0.53 13 13
CREB1 -0.037 0.15 -9999 0 -0.48 13 13
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.028 0.13 -9999 0 -0.47 13 13
RPS6KA4 -0.04 0.15 -9999 0 -0.49 13 13
PLA2G4A -0.049 0.16 -9999 0 -0.62 9 9
GDI1 -0.04 0.15 -9999 0 -0.49 13 13
TP53 -0.057 0.18 -9999 0 -0.62 15 15
RPS6KA5 -0.043 0.15 -9999 0 -0.49 13 13
ESR1 -0.065 0.18 -9999 0 -0.57 27 27
HBP1 0.014 0 -9999 0 -10000 0 0
MEF2C -0.048 0.15 -9999 0 -0.5 14 14
MEF2A -0.04 0.15 -9999 0 -0.49 13 13
EIF4EBP1 -0.039 0.15 -9999 0 -0.48 13 13
KRT19 -0.18 0.22 -9999 0 -0.66 47 47
ELK4 -0.04 0.15 -9999 0 -0.49 13 13
ATF6 -0.04 0.15 -9999 0 -0.49 13 13
ATF1 -0.037 0.15 -9999 0 -0.48 13 13
p38alpha-beta/MAPKAPK2 -0.04 0.15 -9999 0 -0.53 13 13
p38alpha-beta/MAPKAPK3 -0.04 0.15 -9999 0 -0.53 13 13
EGFR-dependent Endothelin signaling events

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
HRAS 0.012 0.037 -9999 0 -0.82 1 1
EGFR -0.017 0.15 -9999 0 -0.76 20 20
EGF/EGFR -0.073 0.14 -9999 0 -0.49 27 27
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.067 0.13 -9999 0 -0.49 19 19
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.006 0.074 -9999 0 -0.72 5 5
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.094 0.23 -9999 0 -0.57 91 91
EGF/EGFR dimer/SHC -0.082 0.16 -9999 0 -0.57 19 19
mol:GDP -0.067 0.13 -9999 0 -0.48 19 19
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.008 0.058 -9999 0 -0.57 5 5
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.061 0.12 -9999 0 -0.54 4 4
SHC1 0.014 0 -9999 0 -10000 0 0
HRAS/GDP -0.063 0.12 -9999 0 -0.55 4 4
FRAP1 -0.033 0.14 -9999 0 -0.46 19 19
EGF/EGFR dimer -0.098 0.19 -9999 0 -0.45 108 108
SOS1 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.01 0.068 -9999 0 -0.47 10 10
ErbB2/ErbB3 signaling events

Figure S60.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S60.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.02 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.021 0.11 -9999 0 -0.46 4 4
NFATC4 -0.017 0.12 -9999 0 -0.51 3 3
ERBB2IP 0.014 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.014 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.04 0.14 -9999 0 -0.59 1 1
JUN 0.005 0.085 -9999 0 -0.38 6 6
HRAS 0.011 0.037 -9999 0 -0.82 1 1
DOCK7 -0.032 0.14 -9999 0 -0.56 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.082 0.18 -9999 0 -0.48 79 79
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.04 0.075 -9999 0 -0.31 8 8
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.042 0.16 -9999 0 -0.66 1 1
RAF1 -0.018 0.12 -9999 0 -0.5 2 2
ErbB2/ErbB3/neuregulin 2 -0.19 0.16 -9999 0 -0.61 6 6
STAT3 0.001 0.003 -9999 0 -10000 0 0
cell migration 0.006 0.085 -9999 0 -0.27 1 1
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.14 0.29 -9999 0 -0.58 105 105
FOS -0.1 0.23 -9999 0 -0.47 81 81
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.04 0.14 -9999 0 -0.59 1 1
MAPK3 -0.1 0.23 -9999 0 -0.58 19 19
MAPK1 -0.1 0.23 -9999 0 -0.58 19 19
JAK2 -0.032 0.14 -9999 0 -0.56 1 1
NF2 -0.002 0.005 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.027 0.12 -9999 0 -0.31 27 27
NRG1 -0.12 0.3 -9999 0 -0.8 81 81
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.016 0.11 -9999 0 -0.44 2 2
MAPK9 -0.029 0.063 -9999 0 -10000 0 0
ERBB2 -0.004 0.05 -9999 0 -0.64 3 3
ERBB3 0.004 0.068 -9999 0 -0.57 7 7
SHC1 0.013 0.002 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
apoptosis 0.008 0.01 -9999 0 -10000 0 0
STAT3 (dimer) 0.009 0.01 -9999 0 -10000 0 0
RNF41 0.026 0.008 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.041 0.089 -9999 0 -0.37 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.003 0.043 -9999 0 -0.55 3 3
CHRNA1 -0.15 0.3 -9999 0 -0.56 161 161
myelination -0.007 0.12 -9999 0 -0.45 3 3
PPP3CB -0.029 0.13 -9999 0 -0.51 1 1
KRAS 0.01 0.053 -9999 0 -0.82 2 2
RAC1-CDC42/GDP -0.008 0.11 -9999 0 -0.59 1 1
NRG2 -0.32 0.28 -9999 0 -0.57 287 287
mol:GDP -0.026 0.12 -9999 0 -0.31 27 27
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.023 0.13 -9999 0 -0.48 2 2
SRC 0.014 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.032 0.14 -9999 0 -0.56 1 1
MAP2K1 -0.089 0.2 -9999 0 -0.51 20 20
heart morphogenesis -0.04 0.14 -9999 0 -0.59 1 1
RAS family/GDP -0.016 0.11 -9999 0 -0.47 4 4
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.004 0.009 -9999 0 -10000 0 0
CHRNE 0.011 0.032 -9999 0 -0.23 6 6
HSP90AA1 0.014 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.04 0.14 -9999 0 -0.59 1 1
CDC42 0.014 0 -9999 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B -0.005 0.041 -9999 0 -0.35 7 7
ARNO/beta Arrestin1-2 -0.018 0.066 -9999 0 -0.5 1 1
EGFR -0.017 0.15 -9999 0 -0.76 20 20
EPHA2 0.004 0.073 -9999 0 -0.57 8 8
USP6 0.012 0.037 -9999 0 -0.82 1 1
IQSEC1 0.014 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.098 0.19 -9999 0 -0.45 108 108
ARRB2 0.01 0.003 -9999 0 -10000 0 0
mol:GTP 0.019 0.02 -9999 0 -0.16 1 1
ARRB1 0.011 0.037 -9999 0 -0.57 2 2
FBXO8 0.014 0 -9999 0 -10000 0 0
TSHR -0.014 0.14 -9999 0 -0.82 15 15
EGF -0.094 0.23 -9999 0 -0.57 91 91
somatostatin receptor activity 0 0 -9999 0 -0.001 12 12
ARAP2 0.007 0.063 -9999 0 -0.57 6 6
mol:GDP -0.011 0.077 -9999 0 -0.32 11 11
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 7 7
ITGA2B -0.065 0.24 -9999 0 -0.82 47 47
ARF6 0.014 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.006 0.043 -9999 0 -0.49 1 1
ADAP1 0.013 0.026 -9999 0 -0.57 1 1
KIF13B 0.007 0.063 -9999 0 -0.57 6 6
HGF/MET -0.025 0.11 -9999 0 -0.48 26 26
PXN 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.023 0.1 -9999 0 -0.32 13 13
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.082 0.16 -9999 0 -0.57 19 19
ADRB2 -0.027 0.15 -9999 0 -0.57 35 35
receptor agonist activity 0 0 -9999 0 0 12 12
actin filament binding 0 0 -9999 0 -0.001 12 12
SRC 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.015 0.14 -9999 0 -0.73 19 19
GNAQ 0.014 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 8 8
ARF6/GDP 0.041 0.067 -9999 0 -0.39 2 2
ARF6/GDP/GULP/ACAP1 -0.1 0.15 -9999 0 -0.5 26 26
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.063 0.17 -9999 0 -0.52 57 57
ACAP1 -0.006 0.13 -9999 0 -0.82 12 12
ACAP2 0.014 0 -9999 0 -10000 0 0
LHCGR/beta Arrestin2 0.002 0.006 -9999 0 -10000 0 0
EFNA1 0.012 0.037 -9999 0 -0.82 1 1
HGF -0.012 0.13 -9999 0 -0.63 20 20
CYTH3 0.012 0 -9999 0 -10000 0 0
CYTH2 0.01 0.002 -9999 0 -10000 0 0
NCK1 0.014 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 -0.001 9 9
endosomal lumen acidification 0 0 -9999 0 -0.001 10 10
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.16 0.26 -9999 0 -0.57 146 146
GNAQ/ARNO 0.015 0.008 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 1 1
MET 0.005 0.083 -9999 0 -0.74 6 6
GNA14 -0.075 0.21 -9999 0 -0.57 76 76
GNA15 0.011 0.037 -9999 0 -0.57 2 2
GIT1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 9 9
GNA11 0.009 0.052 -9999 0 -0.57 4 4
LHCGR 0.002 0.005 -9999 0 -10000 0 0
AGTR1 -0.043 0.17 -9999 0 -0.58 46 46
desensitization of G-protein coupled receptor protein signaling pathway 0.002 0.006 -9999 0 -10000 0 0
IPCEF1/ARNO -0.046 0.14 -9999 0 -0.48 9 9
alphaIIb/beta3 Integrin -0.08 0.21 -9999 0 -0.63 63 63
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.024 0.13 -10000 0 -0.55 3 3
CRKL -0.007 0.15 -10000 0 -0.57 3 3
mol:DAG 0.005 0.14 -10000 0 -0.62 3 3
HRAS 0.023 0.13 -10000 0 -0.6 2 2
MAPK8 -0.031 0.18 -10000 0 -0.48 65 65
RAP1A -0.006 0.15 -10000 0 -0.64 2 2
GAB1 -0.006 0.15 -10000 0 -0.64 2 2
MAPK14 -0.026 0.18 -10000 0 -0.47 65 65
EPO -0.077 0.26 -10000 0 -0.81 55 55
PLCG1 0.004 0.14 -10000 0 -0.64 3 3
EPOR/TRPC2/IP3 Receptors -0.006 0.12 -10000 0 -0.81 11 11
RAPGEF1 0.014 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.067 0.18 -10000 0 -0.52 65 65
GAB1/SHC/GRB2/SOS1 -0.044 0.11 -10000 0 -0.68 1 1
EPO/EPOR (dimer) -0.06 0.22 -10000 0 -0.63 65 65
IRS2 -0.007 0.15 -10000 0 -0.64 2 2
STAT1 -0.01 0.17 -10000 0 -0.66 5 5
STAT5B 0.009 0.14 -10000 0 -0.65 3 3
cell proliferation -0.02 0.17 -10000 0 -0.44 65 65
GAB1/SHIP/PIK3R1/SHP2/SHC -0.044 0.11 -10000 0 -0.59 4 4
TEC -0.02 0.17 -10000 0 -0.69 9 9
SOCS3 0.013 0.026 -10000 0 -0.57 1 1
STAT1 (dimer) -0.008 0.16 -10000 0 -0.64 5 5
JAK2 0.01 0.029 -10000 0 -0.56 1 1
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
EPO/EPOR (dimer)/JAK2 -0.003 0.16 -10000 0 -0.41 66 66
EPO/EPOR -0.06 0.22 -10000 0 -0.63 65 65
LYN 0.014 0.037 -10000 0 -0.82 1 1
TEC/VAV2 -0.024 0.19 -10000 0 -0.75 12 12
elevation of cytosolic calcium ion concentration -0.006 0.12 -10000 0 -0.81 11 11
SHC1 0.014 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.034 0.19 -10000 0 -0.53 65 65
mol:IP3 0.005 0.14 -10000 0 -0.62 3 3
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.05 0.12 -10000 0 -0.66 4 4
SH2B3 0.009 0.039 -10000 0 -0.81 1 1
NFKB1 -0.026 0.18 -10000 0 -0.47 65 65
EPO/EPOR (dimer)/JAK2/SOCS3 -0.036 0.096 0.28 1 -0.39 2 3
PTPN6 -0.015 0.16 -10000 0 -0.41 66 66
TEC/VAV2/GRB2 -0.017 0.18 -10000 0 -0.72 12 12
EPOR -0.006 0.12 -10000 0 -0.82 11 11
INPP5D 0.01 0.045 -10000 0 -0.57 3 3
mol:GDP -0.045 0.11 -10000 0 -0.7 1 1
SOS1 0.014 0 -10000 0 -10000 0 0
PLCG2 0.013 0.026 -10000 0 -0.57 1 1
CRKL/CBL/C3G 0.009 0.14 -10000 0 -0.73 1 1
VAV2 -0.02 0.18 -10000 0 -0.55 17 17
CBL -0.006 0.15 -10000 0 -0.64 2 2
SHC/Grb2/SOS1 -0.047 0.12 -10000 0 -0.73 1 1
STAT5A 0.009 0.14 -10000 0 -0.65 3 3
GRB2 0.014 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.027 0.15 -10000 0 -0.68 3 3
LYN/PLCgamma2 -0.002 0.033 -10000 0 -0.52 2 2
PTPN11 0.014 0 -10000 0 -10000 0 0
BTK -0.008 0.15 -10000 0 -0.64 2 2
BCL2 0.017 0.16 -10000 0 -0.69 10 10
Signaling events mediated by HDAC Class III

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
EP300 0.011 0.037 -10000 0 -0.57 2 2
HDAC4 0.014 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.012 0.14 0.62 26 -10000 0 26
CDKN1A 0.001 0.012 -10000 0 -10000 0 0
KAT2B -0.014 0.12 -10000 0 -0.57 24 24
BAX 0.014 0 -10000 0 -10000 0 0
FOXO3 0.002 0.028 0.44 2 -10000 0 2
FOXO1 0.014 0 -10000 0 -10000 0 0
FOXO4 0.022 0.028 -10000 0 -0.29 4 4
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
TAT -0.002 0.091 -10000 0 -0.82 6 6
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.074 0.18 -10000 0 -0.43 102 102
PPARGC1A -0.2 0.28 -10000 0 -0.57 179 179
FHL2 0.011 0.037 -10000 0 -0.57 2 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 -0.001 0.018 -10000 0 -0.41 1 1
HIST2H4A -0.012 0.14 -10000 0 -0.62 26 26
SIRT1/FOXO3a 0 0.024 0.29 2 -0.35 1 3
SIRT1 -0.001 0.025 -10000 0 -0.57 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 -0.001 0.015 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.012 0.052 -10000 0 -0.33 1 1
apoptosis 0.001 0.015 -10000 0 -10000 0 0
SIRT1/PGC1A -0.13 0.17 -10000 0 -0.35 179 179
p53/SIRT1 -0.004 0.041 -10000 0 -0.41 5 5
SIRT1/FOXO4 -0.002 0.026 -10000 0 -0.33 1 1
FOXO1/FHL2/SIRT1 -0.002 0.024 -10000 0 -10000 0 0
HIST1H1E 0.01 0.065 -10000 0 -0.29 23 23
SIRT1/p300 -0.002 0.031 -10000 0 -0.41 3 3
muscle cell differentiation 0.075 0.15 0.59 9 -10000 0 9
TP53 -0.005 0.051 -10000 0 -0.57 4 4
KU70/SIRT1/BAX -0.001 0.015 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
MEF2D 0.014 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.008 0.071 -10000 0 -0.6 7 7
ACSS2 0.021 0.019 -10000 0 -0.41 1 1
SIRT1/PCAF/MYOD -0.075 0.15 -10000 0 -0.6 9 9
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.001 0.11 -9999 0 -0.79 9 9
positive regulation of NF-kappaB transcription factor activity -0.029 0.13 -9999 0 -0.6 24 24
MAP2K4 0.009 0.1 -9999 0 -0.48 1 1
IKBKB 0.014 0 -9999 0 -10000 0 0
TNFRSF10B 0.014 0 -9999 0 -10000 0 0
TNFRSF10A 0.011 0.037 -9999 0 -0.57 2 2
SMPD1 0.016 0.036 -9999 0 -0.26 8 8
IKBKG 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D -0.01 0.14 -9999 0 -0.78 15 15
TRAIL/TRAILR2 -0.011 0.081 -9999 0 -0.6 9 9
TRAIL/TRAILR3 -0.029 0.13 -9999 0 -0.6 24 24
TRAIL/TRAILR1 -0.013 0.085 -9999 0 -0.57 11 11
TRAIL/TRAILR4 -0.029 0.13 -9999 0 -0.6 24 24
TRAIL/TRAILR1/DAP3/GTP -0.01 0.067 -9999 0 -0.5 8 8
IKK complex -0.025 0.062 -9999 0 -10000 0 0
RIPK1 0.014 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
DAP3/GTP 0 0 -9999 0 -10000 0 0
MAPK3 0.013 0.084 -9999 0 -0.6 9 9
MAP3K1 0.001 0.11 -9999 0 -0.51 1 1
TRAILR4 (trimer) -0.01 0.14 -9999 0 -0.78 15 15
TRADD 0.014 0 -9999 0 -10000 0 0
TRAILR1 (trimer) 0.011 0.037 -9999 0 -0.56 2 2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.006 0.11 -9999 0 -0.54 1 1
CFLAR 0.014 0 -9999 0 -10000 0 0
MAPK1 0.013 0.084 -9999 0 -0.6 9 9
TRAIL/TRAILR1/FADD/TRADD/RIP -0.064 0.16 -9999 0 -0.46 67 67
mol:ceramide 0.016 0.036 -9999 0 -0.26 8 8
FADD -0.085 0.27 -9999 0 -0.82 59 59
MAPK8 0.013 0.11 -9999 0 -0.48 4 4
TRAF2 0.002 0.098 -9999 0 -0.82 7 7
TRAILR3 (trimer) -0.01 0.14 -9999 0 -0.78 15 15
CHUK 0.014 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.075 0.19 -9999 0 -0.54 67 67
DAP3 0.014 0 -9999 0 -10000 0 0
CASP10 -0.053 0.16 -9999 0 -0.44 64 64
JNK cascade -0.029 0.13 -9999 0 -0.6 24 24
TRAIL (trimer) -0.001 0.11 -9999 0 -0.79 9 9
TNFRSF10C -0.01 0.14 -9999 0 -0.78 15 15
TRAIL/TRAILR1/DAP3/GTP/FADD -0.065 0.16 -9999 0 -0.47 67 67
TRAIL/TRAILR2/FADD -0.074 0.19 -9999 0 -0.54 67 67
cell death 0.016 0.036 -9999 0 -0.26 8 8
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.005 0.11 -9999 0 -0.54 1 1
TRAILR2 (trimer) 0.014 0 -9999 0 -10000 0 0
CASP8 -0.001 0.022 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.063 0.16 -9999 0 -0.46 67 67
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.034 0.12 -10000 0 -0.48 27 27
ER alpha/Gai/GDP/Gbeta gamma 0.018 0.1 -10000 0 -0.45 5 5
AKT1 0.004 0.15 -10000 0 -0.75 15 15
PIK3CA 0.014 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.002 0.15 -10000 0 -0.76 15 15
mol:Ca2+ -0.03 0.16 -10000 0 -0.54 12 12
IGF1R 0.014 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/Striatin -0.043 0.13 -10000 0 -0.42 51 51
SHC1 0.014 0 -10000 0 -10000 0 0
apoptosis -0.005 0.14 0.71 15 -10000 0 15
RhoA/GTP -0.023 0.087 -10000 0 -0.41 19 19
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.028 0.09 -10000 0 -0.54 2 2
regulation of stress fiber formation -0.03 0.087 0.5 1 -10000 0 1
E2/ERA-ERB (dimer) -0.04 0.14 -10000 0 -0.48 41 41
KRAS 0.01 0.053 -10000 0 -0.82 2 2
G13/GTP -0.026 0.1 -10000 0 -0.41 31 31
pseudopodium formation 0.03 0.087 -10000 0 -0.5 1 1
E2/ER alpha (dimer)/PELP1 -0.028 0.11 -10000 0 -0.45 31 31
GRB2 0.014 0 -10000 0 -10000 0 0
GNG2 0.012 0.037 -10000 0 -0.82 1 1
GNAO1 0.008 0.069 -10000 0 -0.76 4 4
HRAS 0.012 0.037 -10000 0 -0.82 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.017 0.12 -10000 0 -0.47 16 16
E2/ER beta (dimer) -0.014 0.091 -10000 0 -0.62 11 11
mol:GDP -0.033 0.11 -10000 0 -0.38 41 41
mol:NADP 0.017 0.12 -10000 0 -0.47 16 16
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
mol:IP3 -0.033 0.16 -10000 0 -0.57 12 12
IGF-1R heterotetramer 0.014 0 -10000 0 -10000 0 0
PLCB1 -0.038 0.17 -10000 0 -0.4 77 77
PLCB2 -0.041 0.17 -10000 0 -0.4 80 80
IGF1 -0.088 0.22 -10000 0 -0.58 85 85
mol:L-citrulline 0.017 0.12 -10000 0 -0.47 16 16
RHOA 0.014 0 -10000 0 -10000 0 0
Gai/GDP -0.014 0.061 -10000 0 -0.55 3 3
JNK cascade -0.014 0.091 -10000 0 -0.62 11 11
BCAR1 0.014 0 -10000 0 -10000 0 0
ESR2 -0.004 0.12 -10000 0 -0.8 11 11
GNAQ 0.014 0 -10000 0 -10000 0 0
ESR1 -0.031 0.18 -10000 0 -0.7 31 31
Gq family/GDP/Gbeta gamma -0.001 0.11 -10000 0 -0.61 5 5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.026 0.067 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.028 0.09 -10000 0 -0.54 2 2
GNAZ -0.017 0.15 -10000 0 -0.74 20 20
E2/ER alpha (dimer) -0.033 0.13 -10000 0 -0.53 31 31
STRN -0.012 0.12 -10000 0 -0.57 22 22
GNAL -0.061 0.19 -10000 0 -0.57 64 64
PELP1 0.014 0 -10000 0 -10000 0 0
MAPK11 0.008 0.081 -10000 0 -0.53 11 11
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 0.013 0.026 -10000 0 -0.57 1 1
HBEGF -0.17 0.17 -10000 0 -0.46 89 89
cAMP biosynthetic process -0.067 0.14 -10000 0 -0.49 31 31
SRC 0.025 0.096 -10000 0 -0.51 2 2
PI3K -0.002 0.031 -10000 0 -0.41 3 3
GNB1 0.014 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.03 0.096 -10000 0 -0.55 2 2
SOS1 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.055 0.11 -10000 0 -0.5 9 9
Gs family/GTP -0.069 0.15 -10000 0 -0.5 31 31
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.003 0.039 -10000 0 -0.5 3 3
vasodilation 0.018 0.11 -10000 0 -0.45 16 16
mol:DAG -0.033 0.16 -10000 0 -0.57 12 12
Gs family/GDP/Gbeta gamma -0.054 0.11 -10000 0 -0.55 8 8
MSN 0.03 0.093 -10000 0 -0.56 1 1
Gq family/GTP -0.076 0.16 -10000 0 -0.42 77 77
mol:PI-3-4-5-P3 0.003 0.14 -10000 0 -0.73 15 15
NRAS 0.014 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.018 0.11 0.45 16 -10000 0 16
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.031 0.1 -10000 0 -0.36 40 40
NOS3 0.016 0.12 -10000 0 -0.49 16 16
GNA11 0.009 0.052 -10000 0 -0.57 4 4
MAPKKK cascade 0.016 0.14 -10000 0 -0.56 17 17
E2/ER alpha (dimer)/PELP1/Src -0.03 0.095 -10000 0 -0.53 3 3
ruffle organization 0.03 0.087 -10000 0 -0.5 1 1
ROCK2 0.023 0.1 -10000 0 -0.63 1 1
GNA14 -0.075 0.21 -10000 0 -0.57 76 76
GNA15 0.011 0.037 -10000 0 -0.57 2 2
GNA13 0.014 0 -10000 0 -10000 0 0
MMP9 -0.3 0.21 -10000 0 -0.59 48 48
MMP2 -0.032 0.18 -10000 0 -0.58 6 6
Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
DYNC1H1 0.014 0 -9999 0 -10000 0 0
VLDLR 0.001 0.085 -9999 0 -0.57 11 11
LRPAP1 0.014 0 -9999 0 -10000 0 0
NUDC 0.014 0 -9999 0 -10000 0 0
RELN/LRP8 -0.08 0.16 -9999 0 -0.63 11 11
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.014 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.043 0.16 -9999 0 -0.57 11 11
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.018 0.15 -9999 0 -0.82 16 16
IQGAP1 0.014 0 -9999 0 -10000 0 0
PLA2G7 -0.31 0.41 -9999 0 -0.82 193 193
CALM1 0.014 0 -9999 0 -10000 0 0
DYNLT1 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.013 0.088 -9999 0 -0.63 10 10
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.011 0.037 -9999 0 -0.57 2 2
CDK5R1 0.01 0.053 -9999 0 -0.82 2 2
LIS1/Poliovirus Protein 3A 0.018 0 -9999 0 -10000 0 0
CDK5R2 -0.1 0.29 -9999 0 -0.82 69 69
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.095 0.18 -9999 0 -0.62 19 19
YWHAE 0.014 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.042 0.16 -9999 0 -0.55 15 15
MAP1B -0.007 0.045 -9999 0 -0.3 11 11
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.024 0.14 -9999 0 -0.7 4 4
RELN -0.11 0.24 -9999 0 -0.57 102 102
PAFAH/LIS1 -0.19 0.28 -9999 0 -0.54 193 193
LIS1/CLIP170 0.027 0.023 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.062 0.098 -9999 0 -0.54 2 2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.033 0.13 -9999 0 -0.56 7 7
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.053 0.17 -9999 0 -0.6 15 15
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.025 0 -9999 0 -10000 0 0
PAFAH1B3 0.009 0.064 -9999 0 -0.82 3 3
PAFAH1B2 0.011 0.037 -9999 0 -0.57 2 2
MAP1B/LIS1/Dynein heavy chain 0.022 0.032 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.078 0.12 -9999 0 -0.61 7 7
LRP8 -0.003 0.12 -9999 0 -0.82 10 10
NDEL1/Katanin 60 -0.042 0.16 -9999 0 -0.64 7 7
P39/CDK5 -0.091 0.21 -9999 0 -0.79 14 14
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.031 0.15 -9999 0 -0.53 11 11
PPP2R5D 0.014 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.001 0.018 -9999 0 -10000 0 0
CSNK2A1 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.078 0.15 -9999 0 -0.53 19 19
RELN/VLDLR -0.078 0.15 -9999 0 -0.58 13 13
CDC42 0 0 -9999 0 -10000 0 0
Noncanonical Wnt 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
NFATC2 -0.056 0.19 -9999 0 -0.57 59 59
GNB1/GNG2 -0.02 0.15 -9999 0 -0.63 12 12
mol:DAG -0.009 0.14 -9999 0 -0.58 11 11
PLCG1 -0.01 0.14 -9999 0 -0.6 11 11
YES1 -0.027 0.15 -9999 0 -0.68 11 11
FZD3 0.006 0.068 -9999 0 -0.57 7 7
FZD6 0.011 0.045 -9999 0 -0.69 2 2
G protein -0.01 0.14 -9999 0 -0.61 11 11
MAP3K7 -0.057 0.17 -9999 0 -0.65 8 8
mol:Ca2+ -0.008 0.13 -9999 0 -0.56 11 11
mol:IP3 -0.009 0.14 -9999 0 -0.58 11 11
NLK -0.003 0.007 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.07 0.18 -9999 0 -0.52 32 32
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.038 0.16 -9999 0 -0.73 11 11
CSNK1A1 0.014 0 -9999 0 -10000 0 0
GNAS -0.027 0.15 -9999 0 -0.68 11 11
GO:0007205 -0.008 0.13 -9999 0 -0.56 11 11
WNT6 -0.052 0.22 -9999 0 -0.76 42 42
WNT4 -0.007 0.12 -9999 0 -0.63 16 16
NFAT1/CK1 alpha -0.08 0.15 -9999 0 -0.57 25 25
GNG2 0.012 0.037 -9999 0 -0.82 1 1
WNT5A 0.005 0.073 -9999 0 -0.6 7 7
WNT11 -0.074 0.25 -9999 0 -0.75 57 57
CDC42 -0.017 0.14 -9999 0 -0.64 11 11
PDGFR-alpha signaling pathway

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
PDGFRA 0 0.087 -9999 0 -0.62 9 9
PDGF/PDGFRA/CRKL -0.009 0.067 -9999 0 -0.46 10 10
positive regulation of JUN kinase activity -0.006 0.044 -9999 0 -0.46 2 2
CRKL 0.012 0.037 -9999 0 -0.82 1 1
PDGF/PDGFRA/Caveolin-3 -0.1 0.18 -9999 0 -0.43 116 116
AP1 -0.13 0.32 -9999 0 -0.94 64 64
mol:IP3 0.012 0.068 -9999 0 -0.46 9 9
PLCG1 0.012 0.069 -9999 0 -0.46 9 9
PDGF/PDGFRA/alphaV Integrin -0.014 0.088 -9999 0 -0.53 13 13
RAPGEF1 0.014 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0.012 0.068 -9999 0 -0.46 9 9
CAV3 -0.12 0.24 -9999 0 -0.57 109 109
CAV1 -0.05 0.22 -9999 0 -0.82 38 38
SHC/Grb2/SOS1 -0.006 0.045 -9999 0 -0.47 2 2
PDGF/PDGFRA/Shf -0.015 0.087 -9999 0 -0.48 16 16
FOS -0.082 0.33 -9999 0 -0.93 64 64
JUN -0.008 0.02 -9999 0 -10000 0 0
oligodendrocyte development -0.014 0.088 -9999 0 -0.53 13 13
GRB2 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
mol:DAG 0.012 0.068 -9999 0 -0.46 9 9
PDGF/PDGFRA 0 0.087 -9999 0 -0.62 9 9
actin cytoskeleton reorganization -0.01 0.065 -9999 0 -0.44 11 11
SRF 0.025 0.009 -9999 0 -10000 0 0
SHC1 0.014 0 -9999 0 -10000 0 0
PI3K -0.009 0.056 -9999 0 -0.52 2 2
PDGF/PDGFRA/Crk/C3G -0.007 0.05 -9999 0 -0.52 2 2
JAK1 0.015 0.064 -9999 0 -0.44 9 9
ELK1/SRF 0.033 0.055 -9999 0 -0.5 1 1
SHB 0.011 0.037 -9999 0 -0.57 2 2
SHF 0.003 0.077 -9999 0 -0.57 9 9
CSNK2A1 0.008 0.02 -9999 0 -10000 0 0
GO:0007205 0.012 0.07 -9999 0 -0.47 9 9
SOS1 0.014 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.006 0.044 -9999 0 -0.46 2 2
PDGF/PDGFRA/SHB -0.01 0.066 -9999 0 -0.44 11 11
PDGF/PDGFRA/Caveolin-1 -0.057 0.18 -9999 0 -0.6 47 47
ITGAV 0.006 0.079 -9999 0 -0.77 5 5
ELK1 0.015 0.073 -9999 0 -0.53 4 4
PIK3CA 0.014 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.008 0.06 -9999 0 -0.44 9 9
JAK-STAT cascade 0.015 0.064 -9999 0 -0.44 9 9
cell proliferation -0.015 0.086 -9999 0 -0.47 16 16
VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer 0.032 0.042 -9999 0 -0.58 2 2
VEGFR1 homodimer/NRP1 0.022 0.034 -9999 0 -0.63 1 1
mol:DAG -0.056 0.21 -9999 0 -0.48 93 93
VEGFR1 homodimer/NRP1/VEGFR 121 -0.008 0.061 -9999 0 -0.51 7 7
CaM/Ca2+ -0.046 0.2 -9999 0 -0.63 2 2
HIF1A 0.02 0.03 -9999 0 -0.55 1 1
GAB1 0.014 0 -9999 0 -10000 0 0
AKT1 -0.021 0.18 -9999 0 -0.73 4 4
PLCG1 -0.056 0.21 -9999 0 -0.49 93 93
NOS3 -0.018 0.18 -9999 0 -0.55 5 5
CBL 0.014 0 -9999 0 -10000 0 0
mol:NO -0.016 0.17 -9999 0 -0.53 5 5
FLT1 0.031 0.039 -9999 0 -0.72 1 1
PGF -0.14 0.32 -9999 0 -0.82 92 92
VEGFR1 homodimer/NRP2/VEGFR121 -0.01 0.068 -9999 0 -0.5 9 9
CALM1 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
eNOS/Hsp90 -0.009 0.17 -9999 0 -0.62 2 2
endothelial cell proliferation -0.032 0.18 -9999 0 -0.71 1 1
mol:Ca2+ -0.055 0.2 -9999 0 -0.48 93 93
MAPK3 -0.035 0.18 -9999 0 -0.66 1 1
MAPK1 -0.035 0.18 -9999 0 -0.66 1 1
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
PLGF homodimer -0.14 0.32 -9999 0 -0.82 92 92
PRKACA 0.014 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.05 0.22 -9999 0 -0.82 38 38
VEGFA homodimer 0.004 0.091 -9999 0 -0.82 6 6
VEGFR1 homodimer/VEGFA homodimer 0.026 0.071 -9999 0 -0.55 7 7
platelet activating factor biosynthetic process -0.026 0.18 -9999 0 -0.64 1 1
PI3K -0.087 0.18 -9999 0 -0.7 5 5
PRKCA -0.045 0.19 -9999 0 -0.61 2 2
PRKCB -0.051 0.2 -9999 0 -0.61 2 2
VEGFR1 homodimer/PLGF homodimer -0.073 0.22 -9999 0 -0.54 93 93
VEGFA 0.004 0.091 -9999 0 -0.82 6 6
VEGFB 0.012 0.037 -9999 0 -0.82 1 1
mol:IP3 -0.056 0.21 -9999 0 -0.48 93 93
RASA1 0.039 0.048 -9999 0 -0.55 3 3
NRP2 0.01 0.053 -9999 0 -0.82 2 2
VEGFR1 homodimer 0.031 0.039 -9999 0 -0.72 1 1
VEGFB homodimer 0.012 0.037 -9999 0 -0.82 1 1
NCK1 0.014 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.043 0.2 -9999 0 -0.72 10 10
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.086 0.18 -9999 0 -0.69 5 5
mol:L-citrulline -0.016 0.17 -9999 0 -0.53 5 5
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.007 0.056 -9999 0 -0.54 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.008 0.06 -9999 0 -0.5 7 7
CD2AP 0.014 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.082 0.17 -9999 0 -0.66 5 5
PDPK1 -0.037 0.19 -9999 0 -0.7 5 5
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.008 0.06 -9999 0 -0.5 7 7
mol:NADP -0.016 0.17 -9999 0 -0.53 5 5
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.007 0.056 -9999 0 -0.53 1 1
VEGFR1 homodimer/NRP2 0.03 0.049 -9999 0 -0.57 3 3
Fc-epsilon receptor I signaling in mast cells

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PPAP2A 0.012 0.037 -9999 0 -0.82 1 1
LAT2 -0.053 0.14 -9999 0 -0.48 20 20
AP1 -0.089 0.12 -9999 0 -0.53 12 12
mol:PIP3 -0.069 0.19 -9999 0 -0.55 26 26
IKBKB -0.025 0.11 -9999 0 -0.35 5 5
AKT1 -0.052 0.16 -9999 0 -0.64 6 6
IKBKG -0.025 0.11 -9999 0 -0.35 5 5
MS4A2 -0.012 0.12 -9999 0 -0.58 20 20
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
MAP3K1 -0.017 0.12 -9999 0 -0.48 5 5
mol:Ca2+ -0.049 0.15 -9999 0 -0.4 26 26
LYN 0.012 0.038 -9999 0 -0.83 1 1
CBLB -0.05 0.14 -9999 0 -0.48 19 19
SHC1 0.014 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.018 0.073 -9999 0 -0.5 1 1
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.01 0.045 -9999 0 -0.57 3 3
PLD2 -0.088 0.18 -9999 0 -0.56 25 25
PTPN13 -0.047 0.14 -9999 0 -0.48 21 21
PTPN11 0.01 0.009 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.021 0.13 -9999 0 -0.4 4 4
SYK 0.01 0.046 -9999 0 -0.58 3 3
GRB2 0.013 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.12 0.16 -9999 0 -0.57 28 28
LAT -0.065 0.16 -9999 0 -0.53 32 32
PAK2 -0.028 0.13 -9999 0 -0.52 6 6
NFATC2 -0.12 0.22 -9999 0 -0.69 59 59
HRAS -0.038 0.14 -9999 0 -0.45 24 24
GAB2 0.01 0.045 -9999 0 -0.57 3 3
PLA2G1B 0.035 0.019 -9999 0 -10000 0 0
Fc epsilon R1 -0.15 0.2 -9999 0 -0.65 27 27
Antigen/IgE/Fc epsilon R1 -0.14 0.19 -9999 0 -0.6 27 27
mol:GDP -0.045 0.14 -9999 0 -0.47 24 24
JUN 0.014 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
FOS -0.061 0.19 -9999 0 -0.57 64 64
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.086 0.13 -9999 0 -0.5 20 20
CHUK -0.025 0.11 -9999 0 -0.35 5 5
KLRG1 -0.058 0.14 -9999 0 -0.47 24 24
VAV1 -0.057 0.14 -9999 0 -0.48 24 24
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.05 0.14 -9999 0 -0.48 19 19
negative regulation of mast cell degranulation -0.048 0.14 -9999 0 -0.53 9 9
BTK -0.049 0.14 -9999 0 -0.48 19 19
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.084 0.18 -9999 0 -0.62 24 24
GAB2/PI3K/SHP2 -0.1 0.14 -9999 0 -0.65 9 9
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.07 0.16 -9999 0 -0.58 19 19
RAF1 0.023 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.17 -9999 0 -0.61 23 23
FCER1G -0.008 0.13 -9999 0 -0.82 12 12
FCER1A -0.19 0.28 -9999 0 -0.57 176 176
Antigen/IgE/Fc epsilon R1/Fyn -0.12 0.18 -9999 0 -0.6 25 25
MAPK3 0.034 0.019 -9999 0 -10000 0 0
MAPK1 0.034 0.019 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 0.001 0.09 -9999 0 -0.66 7 7
DUSP1 -0.015 0.13 -9999 0 -0.57 25 25
NF-kappa-B/RelA -0.036 0.047 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.05 0.14 -9999 0 -0.47 19 19
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.071 0.11 -9999 0 -0.59 5 5
FER -0.052 0.14 -9999 0 -0.48 21 21
RELA 0.014 0 -9999 0 -10000 0 0
ITK -0.032 0.078 -9999 0 -0.41 17 17
SOS1 0.014 0 -9999 0 -10000 0 0
PLCG1 -0.044 0.15 -9999 0 -0.48 24 24
cytokine secretion -0.027 0.035 -9999 0 -10000 0 0
SPHK1 -0.062 0.16 -9999 0 -0.53 30 30
PTK2 -0.052 0.14 -9999 0 -0.49 19 19
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.16 -9999 0 -0.57 21 21
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.06 0.18 -9999 0 -0.53 20 20
MAP2K2 0.03 0.02 -9999 0 -10000 0 0
MAP2K1 0.03 0.02 -9999 0 -10000 0 0
MAP2K7 0.014 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.081 0.12 -9999 0 -0.5 13 13
MAP2K4 0.019 0.009 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.14 0.19 -9999 0 -0.61 30 30
mol:Choline -0.086 0.18 -9999 0 -0.55 25 25
SHC/Grb2/SOS1 -0.069 0.11 -9999 0 -0.66 3 3
FYN 0.012 0.037 -9999 0 -0.82 1 1
DOK1 0.012 0.037 -9999 0 -0.82 1 1
PXN -0.041 0.13 -9999 0 -0.47 15 15
HCLS1 -0.055 0.14 -9999 0 -0.48 24 24
PRKCB -0.047 0.15 -9999 0 -0.4 22 22
FCGR2B 0.006 0.068 -9999 0 -0.57 7 7
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.049 0.14 -9999 0 -0.55 9 9
LCP2 0.008 0.065 -9999 0 -0.82 3 3
PLA2G4A -0.069 0.16 -9999 0 -0.52 35 35
RASA1 0.011 0.037 -9999 0 -0.57 2 2
mol:Phosphatidic acid -0.086 0.18 -9999 0 -0.55 25 25
IKK complex -0.003 0.091 -9999 0 -0.28 2 2
WIPF1 0.007 0.074 -9999 0 -0.82 4 4
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.02 0.08 -9999 0 -0.47 12 12
CRKL 0.012 0.037 -9999 0 -0.82 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.011 0.037 -9999 0 -0.57 2 2
ITGA4 -0.005 0.12 -9999 0 -0.82 11 11
alpha4/beta7 Integrin/MAdCAM1 -0.028 0.11 -9999 0 -0.49 27 27
EPO -0.08 0.26 -9999 0 -0.82 55 55
alpha4/beta7 Integrin -0.016 0.096 -9999 0 -0.59 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.015 0.096 -9999 0 -0.63 12 12
EPO/EPOR (dimer) -0.083 0.22 -9999 0 -0.64 65 65
lamellipodium assembly 0 0.027 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
PI3K -0.002 0.031 -9999 0 -0.41 3 3
ARF6 0.014 0 -9999 0 -10000 0 0
JAK2 -0.018 0.13 -9999 0 -0.52 4 4
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
MADCAM1 -0.017 0.15 -9999 0 -0.82 16 16
cell adhesion -0.028 0.11 -9999 0 -0.49 27 27
CRKL/CBL -0.001 0.028 -9999 0 -0.63 1 1
ITGB1 0.012 0.037 -9999 0 -0.82 1 1
SRC -0.027 0.17 -9999 0 -0.51 52 52
ITGB7 0.011 0.037 -9999 0 -0.57 2 2
RAC1 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.065 0.18 -9999 0 -0.56 52 52
p130Cas/Crk/Dock1 -0.001 0.15 -9999 0 -0.81 2 2
VCAM1 -0.067 0.24 -9999 0 -0.77 51 51
RHOA 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.012 0.076 -9999 0 -0.49 12 12
BCAR1 -0.016 0.16 -9999 0 -0.47 52 52
EPOR -0.005 0.12 -9999 0 -0.82 11 11
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.028 -9999 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.01 0.077 -9999 0 -0.61 8 8
PDGFRB -0.14 0.32 -9999 0 -0.82 89 89
SPHK1 -0.023 0.052 -9999 0 -0.32 12 12
mol:S1P -0.028 0.062 -9999 0 -0.42 6 6
S1P1/S1P/Gi -0.015 0.14 -9999 0 -0.51 11 11
GNAO1 0.006 0.07 -9999 0 -0.76 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.066 0.2 -9999 0 -0.62 17 17
PLCG1 -0.015 0.13 -9999 0 -0.52 8 8
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.14 0.32 -9999 0 -0.82 89 89
GNAI2 0.012 0.006 -9999 0 -10000 0 0
GNAI3 0.012 0.006 -9999 0 -10000 0 0
GNAI1 0.011 0.027 -9999 0 -0.58 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.009 0.07 -9999 0 -0.53 8 8
S1P1/S1P -0.039 0.079 -9999 0 -0.44 11 11
negative regulation of cAMP metabolic process -0.015 0.13 -9999 0 -0.5 11 11
MAPK3 -0.023 0.17 -9999 0 -0.56 15 15
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.01 0.045 -9999 0 -0.69 2 2
PLCB2 -0.002 0.096 -9999 0 -0.44 10 10
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.032 0.066 -9999 0 -0.4 7 7
receptor internalization -0.037 0.074 -9999 0 -0.41 12 12
PTGS2 -0.052 0.25 -9999 0 -0.6 79 79
Rac1/GTP -0.032 0.066 -9999 0 -0.4 7 7
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFA 0.003 0.092 -9999 0 -0.82 6 6
negative regulation of T cell proliferation -0.015 0.13 -9999 0 -0.5 11 11
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.019 0.15 -9999 0 -0.75 20 20
MAPK1 -0.023 0.17 -9999 0 -0.56 15 15
S1P1/S1P/PDGFB-D/PDGFRB -0.059 0.18 -9999 0 -0.57 18 18
ABCC1 0.008 0.065 -9999 0 -0.82 3 3
Signaling events mediated by PRL

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
CCNE1 0.002 0.098 -10000 0 -0.82 7 7
mol:Halofuginone 0.006 0.001 -10000 0 -10000 0 0
ITGA1 -0.11 0.29 -10000 0 -0.82 72 72
CDKN1A 0.029 0.032 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.01 0.079 -10000 0 -0.63 8 8
mol:Ca2+ -0.079 0.18 0.38 6 -0.43 97 103
AGT -0.1 0.24 -10000 0 -0.58 97 97
CCNA2 0.03 0.073 -10000 0 -0.74 1 1
TUBA1B 0.014 0 -10000 0 -10000 0 0
EGR1 0.006 0.091 -10000 0 -0.4 24 24
CDK2/Cyclin E1 0.034 0.063 -10000 0 -0.44 7 7
MAPK3 0.014 0.082 -10000 0 -0.63 8 8
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.014 0.082 -10000 0 -0.63 8 8
PTP4A1 0.024 0.071 -10000 0 -10000 0 0
PTP4A3 0 0.1 -10000 0 -0.82 8 8
PTP4A2 0.014 0 -10000 0 -10000 0 0
ITGB1 0.013 0.087 -10000 0 -0.63 9 9
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.025 0.046 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.018 0.1 -10000 0 -0.74 1 1
RABGGTA 0.014 0 -10000 0 -10000 0 0
BCAR1 0.006 0.047 0.38 8 -10000 0 8
RHOC 0.025 0.046 -10000 0 -10000 0 0
RHOA 0.025 0.046 -10000 0 -10000 0 0
cell motility 0.029 0.048 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.029 0.066 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.1 0.23 -10000 0 -0.63 80 80
ROCK1 0.029 0.048 -10000 0 -10000 0 0
RABGGTB 0.014 0 -10000 0 -10000 0 0
CDK2 0.014 0 -10000 0 -10000 0 0
mitosis 0.024 0.07 -10000 0 -10000 0 0
ATF5 -0.005 0.12 -10000 0 -0.82 11 11
Cellular roles of Anthrax toxin

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
ANTXR1 0.009 0.064 -10000 0 -0.82 3 3
ANTXR2 -0.005 0.12 -10000 0 -0.82 11 11
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.016 -10000 0 -0.098 14 14
monocyte activation -0.027 0.12 -10000 0 -0.29 71 71
MAP2K2 -0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.002 0.014 -10000 0 -10000 0 0
MAP2K7 -0.002 0.014 -10000 0 -10000 0 0
MAP2K6 -0.018 0.069 -10000 0 -0.3 26 26
CYAA 0.002 0.082 -10000 0 -0.48 14 14
MAP2K4 -0.002 0.014 -10000 0 -10000 0 0
IL1B -0.035 0.15 -10000 0 -0.46 53 53
Channel -0.014 0.084 -10000 0 -0.51 14 14
NLRP1 -0.003 0.026 -10000 0 -0.49 1 1
CALM1 0.014 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.003 0.019 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.016 0.098 14 -10000 0 14
MAPK3 -0.002 0.014 -10000 0 -10000 0 0
MAPK1 -0.002 0.014 -10000 0 -10000 0 0
PGR -0.043 0.11 -10000 0 -0.33 60 60
PA/Cellular Receptors -0.016 0.091 -10000 0 -0.55 14 14
apoptosis -0.003 0.016 -10000 0 -0.098 14 14
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0.004 0.079 -10000 0 -0.46 14 14
macrophage activation 0.019 0.015 -10000 0 -10000 0 0
TNF -0.025 0.17 -10000 0 -0.79 24 24
VCAM1 -0.027 0.12 -10000 0 -0.29 71 71
platelet activation -0.003 0.019 -10000 0 -10000 0 0
MAPKKK cascade -0.011 0.025 0.16 1 -10000 0 1
IL18 0.005 0.062 -10000 0 -0.29 20 20
negative regulation of macrophage activation -0.003 0.016 -10000 0 -0.098 14 14
LEF -0.003 0.016 -10000 0 -0.099 14 14
CASP1 -0.003 0.017 -10000 0 -0.22 1 1
mol:cAMP -0.003 0.02 -10000 0 -10000 0 0
necrosis -0.003 0.016 -10000 0 -0.098 14 14
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) 0.003 0.083 -10000 0 -0.48 14 14
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Retinoic acid receptors-mediated signaling

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
HDAC1 0.014 0 -10000 0 -10000 0 0
HDAC3 0.014 0 -10000 0 -10000 0 0
VDR 0.011 0.037 -10000 0 -0.57 2 2
Cbp/p300/PCAF -0.018 0.078 -10000 0 -0.66 1 1
EP300 0.011 0.037 -10000 0 -0.57 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.008 0.099 -10000 0 -0.48 9 9
KAT2B -0.014 0.12 -10000 0 -0.57 24 24
MAPK14 0.014 0 -10000 0 -10000 0 0
AKT1 0.031 0.11 0.22 2 -0.35 5 7
RAR alpha/9cRA/Cyclin H -0.023 0.06 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.002 0.11 -10000 0 -0.44 13 13
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.022 0.081 -10000 0 -0.46 7 7
NCOR2 0.014 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.026 -10000 0 -0.42 2 2
RXRs/RARs/NRIP1/9cRA 0.001 0.14 -10000 0 -0.6 6 6
NCOA2 -0.031 0.15 -10000 0 -0.57 38 38
NCOA3 0.014 0 -10000 0 -10000 0 0
NCOA1 0.014 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.011 0.037 -10000 0 -0.56 2 2
RARG 0.014 0.026 -10000 0 -0.57 1 1
RAR gamma1/9cRA -0.001 0.015 -10000 0 -0.35 1 1
MAPK3 0.015 0.001 -10000 0 -10000 0 0
MAPK1 0.014 0 -10000 0 -10000 0 0
MAPK8 0.007 0.068 -10000 0 -0.56 7 7
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.047 0.11 -10000 0 -0.91 1 1
RARA -0.002 0.087 -10000 0 -0.27 1 1
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.019 0.15 -10000 0 -0.56 25 25
PRKCA 0.014 0.046 -10000 0 -0.7 2 2
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.017 0.15 -10000 0 -0.64 6 6
RXRG -0.059 0.18 -10000 0 -0.37 109 109
RXRA 0.008 0.083 -10000 0 -0.33 1 1
RXRB -0.014 0.12 -10000 0 -0.35 57 57
VDR/Vit D3/DNA -0.002 0.026 -10000 0 -0.42 2 2
RBP1 -0.18 0.35 -10000 0 -0.82 117 117
CRBP1/9-cic-RA -0.15 0.27 -10000 0 -0.63 117 117
RARB -0.035 0.17 -10000 0 -0.57 43 43
PRKCG -0.079 0.26 -10000 0 -0.82 55 55
MNAT1 0.014 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.018 0.15 -10000 0 -0.54 5 5
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.007 0.13 -10000 0 -0.55 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.002 0.11 -10000 0 -0.41 17 17
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.017 0.15 -10000 0 -0.64 6 6
positive regulation of DNA binding -0.022 0.058 -10000 0 -10000 0 0
NRIP1 -0.015 0.15 -10000 0 -1.4 2 2
RXRs/RARs -0.024 0.15 -10000 0 -0.47 18 18
RXRs/RXRs/DNA/9cRA -0.048 0.11 -10000 0 -0.46 9 9
PRKACA 0.014 0 -10000 0 -10000 0 0
CDK7 0.014 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.016 0.042 -10000 0 -10000 0 0
CCNH 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
RAR gamma2/9cRA 0 0.011 -10000 0 -10000 0 0
IL6-mediated 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
BCL2L1 -0.012 0.21 -9999 0 -0.65 4 4
CRP -0.031 0.24 -9999 0 -0.74 20 20
cell cycle arrest -0.023 0.23 -9999 0 -0.68 12 12
TIMP1 -0.005 0.2 -9999 0 -0.76 7 7
IL6ST -0.057 0.19 -9999 0 -0.56 62 62
Rac1/GDP -0.009 0.15 -9999 0 -0.56 15 15
AP1 0.007 0.13 -9999 0 -0.59 3 3
GAB2 0.011 0.045 -9999 0 -0.57 3 3
TNFSF11 -0.08 0.31 -9999 0 -0.72 42 42
HSP90B1 0.03 0.05 -9999 0 -10000 0 0
GAB1 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.013 0.15 -9999 0 -0.54 17 17
AKT1 0.057 0.031 -9999 0 -10000 0 0
FOXO1 0.063 0.029 -9999 0 -10000 0 0
MAP2K6 -0.025 0.16 -9999 0 -0.54 21 21
mol:GTP 0 0.002 -9999 0 -10000 0 0
MAP2K4 0.001 0.16 -9999 0 -0.55 11 11
MITF -0.024 0.16 -9999 0 -0.53 23 23
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.012 0.037 -9999 0 -0.82 1 1
A2M 0.021 0.031 -9999 0 -0.66 1 1
CEBPB 0.02 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.015 0.075 -9999 0 -0.42 3 3
STAT3 -0.024 0.24 -9999 0 -0.7 13 13
STAT1 -0.021 0.084 -9999 0 -0.35 28 28
CEBPD -0.012 0.21 -9999 0 -0.64 6 6
PIK3CA 0.016 0 -9999 0 -10000 0 0
PI3K 0.021 0.033 -9999 0 -0.4 3 3
JUN 0.014 0.001 -9999 0 -10000 0 0
PIAS3/MITF -0.014 0.15 -9999 0 -0.52 19 19
MAPK11 -0.013 0.15 -9999 0 -0.54 17 17
STAT3 (dimer)/FOXO1 0.031 0.2 -9999 0 -10000 0 0
GRB2/SOS1/GAB family -0.047 0.1 -9999 0 -0.52 9 9
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.02 0.15 -9999 0 -0.53 20 20
GRB2 0.014 0.001 -9999 0 -10000 0 0
JAK2 0.013 0.026 -9999 0 -0.57 1 1
LBP -0.11 0.37 -9999 0 -0.89 72 72
PIK3R1 0.012 0.045 -9999 0 -0.56 3 3
JAK1 0.016 0.004 -9999 0 -10000 0 0
MYC -0.012 0.21 -9999 0 -0.64 6 6
FGG -0.046 0.27 -9999 0 -0.75 31 31
macrophage differentiation -0.023 0.23 -9999 0 -0.68 12 12
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.061 0.14 -9999 0 -0.52 25 25
JUNB -0.012 0.2 -9999 0 -0.61 7 7
FOS -0.061 0.19 -9999 0 -0.57 64 64
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.024 0.16 -9999 0 -0.49 25 25
STAT1/PIAS1 -0.022 0.15 -9999 0 -0.5 15 15
GRB2/SOS1/GAB family/SHP2/PI3K 0.04 0.036 -9999 0 -10000 0 0
STAT3 (dimer) -0.023 0.24 -9999 0 -0.7 12 12
PRKCD 0.009 0.18 -9999 0 -0.63 5 5
IL6R 0.006 0.073 -9999 0 -0.57 8 8
SOCS3 -0.008 0.15 -9999 0 -0.75 4 4
gp130 (dimer)/JAK1/JAK1/LMO4 -0.015 0.12 -9999 0 -0.36 5 5
Rac1/GTP -0.014 0.16 -9999 0 -0.56 15 15
HCK 0.006 0.079 -9999 0 -0.77 5 5
MAPKKK cascade 0.031 0.071 -9999 0 -0.56 3 3
bone resorption -0.074 0.3 -9999 0 -0.68 42 42
IRF1 -0.012 0.21 -9999 0 -0.63 7 7
mol:GDP -0.019 0.16 -9999 0 -0.53 21 21
SOS1 0.013 0.004 -9999 0 -10000 0 0
VAV1 -0.02 0.16 -9999 0 -0.54 21 21
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.017 0.15 -9999 0 -0.62 16 16
PTPN11 -0.001 0.016 -9999 0 -10000 0 0
IL6/IL6RA -0.029 0.15 -9999 0 -0.45 53 53
gp130 (dimer)/TYK2/TYK2/LMO4 -0.02 0.12 -9999 0 -0.86 1 1
gp130 (dimer)/JAK2/JAK2/LMO4 -0.02 0.12 -9999 0 -0.65 1 1
IL6 -0.042 0.19 -9999 0 -0.62 46 46
PIAS3 0.014 0 -9999 0 -10000 0 0
PTPRE 0.01 0.012 -9999 0 -10000 0 0
PIAS1 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.036 0.15 -9999 0 -0.51 22 22
LMO4 0.016 0.011 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.1 0.16 -9999 0 -0.67 12 12
MCL1 0.063 0.028 -9999 0 -10000 0 0
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.14 0.32 -9999 0 -0.82 89 89
alphaV beta3 Integrin -0.027 0.12 -9999 0 -0.57 23 23
PTK2 -0.028 0.091 -9999 0 -0.64 3 3
positive regulation of JNK cascade -0.013 0.054 -9999 0 -0.35 3 3
CDC42/GDP 0.038 0.088 -9999 0 -0.39 14 14
Rac1/GDP 0.04 0.087 -9999 0 -0.48 3 3
RAP1B 0.012 0.037 -9999 0 -0.82 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.013 0.026 -9999 0 -0.57 1 1
CDC42/GTP -0.016 0.066 -9999 0 -0.36 14 14
nectin-3/I-afadin -0.025 0.11 -9999 0 -0.5 25 25
RAPGEF1 0.035 0.095 -9999 0 -0.44 14 14
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.028 0.11 -9999 0 -0.5 14 14
PDGFB-D/PDGFRB -0.14 0.32 -9999 0 -0.82 89 89
TLN1 0.023 0.058 -9999 0 -0.47 2 2
Rap1/GTP -0.015 0.058 -9999 0 -0.38 3 3
IQGAP1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.001 0.022 -9999 0 -0.5 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.025 0.11 -9999 0 -0.5 25 25
PVR 0.01 0.053 -9999 0 -0.82 2 2
Necl-5(dimer) 0.01 0.053 -9999 0 -0.82 2 2
mol:GDP 0.035 0.1 -9999 0 -0.48 14 14
MLLT4 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
PI3K -0.1 0.19 -9999 0 -0.47 99 99
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.002 0.031 -9999 0 -0.41 3 3
positive regulation of lamellipodium assembly -0.018 0.061 -9999 0 -0.31 14 14
PVRL1 0.01 0.045 -9999 0 -0.57 3 3
PVRL3 -0.021 0.15 -9999 0 -0.68 25 25
PVRL2 0.012 0.037 -9999 0 -0.82 1 1
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
CDH1 0.008 0.058 -9999 0 -0.57 5 5
CLDN1 -0.014 0.13 -9999 0 -0.64 21 21
JAM-A/CLDN1 -0.035 0.11 -9999 0 -0.5 18 18
SRC -0.026 0.1 -9999 0 -0.56 14 14
ITGB3 -0.015 0.14 -9999 0 -0.73 19 19
nectin-1(dimer)/I-afadin/I-afadin -0.002 0.031 -9999 0 -0.41 3 3
FARP2 0.032 0.1 -9999 0 -0.48 14 14
RAC1 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.024 0.1 -9999 0 -0.54 13 13
nectin-1/I-afadin -0.002 0.031 -9999 0 -0.41 3 3
nectin-2/I-afadin -0.001 0.028 -9999 0 -0.63 1 1
RAC1/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin -0.024 0.099 -9999 0 -0.54 11 11
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.013 0.026 -9999 0 -0.57 1 1
positive regulation of filopodium formation -0.013 0.054 -9999 0 -0.35 3 3
alphaV/beta3 Integrin/Talin 0.017 0.11 -9999 0 -0.43 17 17
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.001 0.028 -9999 0 -0.63 1 1
nectin-2(dimer)/I-afadin/I-afadin -0.001 0.028 -9999 0 -0.63 1 1
PIP5K1C 0.017 0.053 -9999 0 -0.35 1 1
VAV2 0.023 0.11 -9999 0 -0.49 14 14
RAP1/GDP -0.016 0.067 -9999 0 -0.44 3 3
ITGAV 0.006 0.079 -9999 0 -0.77 5 5
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.023 0.099 -9999 0 -0.54 12 12
nectin-3(dimer)/I-afadin/I-afadin -0.025 0.11 -9999 0 -0.5 25 25
Rac1/GTP -0.022 0.073 -9999 0 -0.38 14 14
PTPRM 0.008 0.058 -9999 0 -0.27 12 12
E-cadherin/beta catenin/alpha catenin -0.006 0.047 -9999 0 -0.54 2 2
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1 -0.039 0.19 -9999 0 -0.87 20 20
MAP4K1 -0.008 0.13 -9999 0 -0.76 14 14
MAP3K8 0.01 0.045 -9999 0 -0.57 3 3
PRKCB 0.001 0.1 -9999 0 -0.79 8 8
DBNL 0.014 0 -9999 0 -10000 0 0
CRKL 0.012 0.037 -9999 0 -0.82 1 1
MAP3K1 0.027 0.1 -9999 0 -0.53 13 13
JUN 0.024 0.091 -9999 0 -0.55 9 9
MAP3K7 0.027 0.1 -9999 0 -0.53 13 13
GRAP2 -0.004 0.11 -9999 0 -0.66 13 13
CRK 0.014 0 -9999 0 -10000 0 0
MAP2K4 0.036 0.1 -9999 0 -0.5 13 13
LAT -0.011 0.14 -9999 0 -0.82 15 15
LCP2 0.009 0.064 -9999 0 -0.82 3 3
MAPK8 0.017 0.096 -9999 0 -0.53 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.02 0.11 -9999 0 -0.57 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.037 0.18 -9999 0 -0.83 20 20
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 0.007 0.048 -9999 0 -0.66 2 2
VDR 0.011 0.037 -9999 0 -0.57 2 2
FAM120B 0.014 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.018 0.11 -9999 0 -0.44 4 4
RXRs/LXRs/DNA/Oxysterols 0.027 0.12 -9999 0 -0.45 6 6
MED1 0.012 0.037 -9999 0 -0.82 1 1
mol:9cRA 0.005 0.011 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.006 0.11 -9999 0 -0.5 3 3
RXRs/NUR77 -0.002 0.13 -9999 0 -0.44 12 12
RXRs/PPAR -0.095 0.16 -9999 0 -0.47 20 20
NCOR2 0.014 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.002 0.026 -9999 0 -0.42 2 2
RARs/VDR/DNA/Vit D3 -0.026 0.085 -9999 0 -0.52 2 2
RARA 0.014 0 -9999 0 -10000 0 0
NCOA1 0.014 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.011 0.037 -9999 0 -0.56 2 2
RARs/RARs/DNA/9cRA -0.025 0.083 -9999 0 -0.47 1 1
RARG 0.013 0.026 -9999 0 -0.57 1 1
RPS6KB1 0.013 0.039 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.006 0.11 -9999 0 -0.5 3 3
THRA 0.014 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.002 0.026 -9999 0 -0.42 2 2
RXRs/PPAR/9cRA/PGJ2/DNA -0.001 0.12 -9999 0 -0.46 11 11
NR1H4 0.003 0.037 -9999 0 -0.82 1 1
RXRs/LXRs/DNA 0.017 0.13 -9999 0 -0.45 14 14
NR1H2 0.019 0.008 -9999 0 -10000 0 0
NR1H3 0.009 0.091 -9999 0 -0.81 6 6
RXRs/VDR/DNA/Vit D3 0.002 0.12 -9999 0 -0.45 8 8
NR4A1 0.003 0.077 -9999 0 -0.57 9 9
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.005 0.084 -9999 0 -0.33 4 4
RXRG -0.057 0.2 -9999 0 -0.6 60 60
RXR alpha/CCPG 0.024 0.006 -9999 0 -10000 0 0
RXRA 0.019 0.008 -9999 0 -10000 0 0
RXRB 0.019 0.009 -9999 0 -10000 0 0
THRB -0.032 0.16 -9999 0 -0.57 39 39
PPARG -0.21 0.28 -9999 0 -0.57 194 194
PPARD 0.014 0 -9999 0 -10000 0 0
TNF 0.015 0.18 -9999 0 -0.68 24 24
mol:Oxysterols 0.005 0.01 -9999 0 -10000 0 0
cholesterol transport 0.027 0.12 -9999 0 -0.44 6 6
PPARA 0.014 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.037 0.16 -9999 0 -0.57 43 43
RXRs/NUR77/BCL2 -0.007 0.1 -9999 0 -0.66 1 1
SREBF1 0.035 0.11 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA -0.001 0.12 -9999 0 -0.46 11 11
ABCA1 0.031 0.13 -9999 0 -0.9 3 3
RARs/THRs -0.046 0.11 -9999 0 -0.54 4 4
RXRs/FXR -0.003 0.12 -9999 0 -0.45 12 12
BCL2 0.002 0.09 -9999 0 -0.69 8 8
FAS signaling pathway (CD95)

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
SPTAN1 0.007 0.037 0.26 4 -10000 0 4
RFC1 0.007 0.037 0.26 4 -10000 0 4
PRKDC 0.007 0.037 0.26 4 -10000 0 4
RIPK1 0.014 0.003 -10000 0 -10000 0 0
CASP7 -0.014 0.039 0.23 3 -10000 0 3
FASLG/FAS/FADD/FAF1 -0.055 0.12 -10000 0 -0.39 13 13
MAP2K4 -0.007 0.13 -10000 0 -0.43 11 11
mol:ceramide -0.029 0.14 -10000 0 -0.48 13 13
GSN 0.007 0.037 0.26 4 -10000 0 4
FASLG/FAS/FADD/FAF1/Caspase 8 -0.026 0.13 -10000 0 -0.44 9 9
FAS 0.011 0.037 -10000 0 -0.57 2 2
BID 0.002 0.047 0.3 1 -0.56 2 3
MAP3K1 0.007 0.079 -10000 0 -10000 0 0
MAP3K7 0.013 0.004 -10000 0 -10000 0 0
RB1 0.005 0.043 0.26 4 -0.33 2 6
CFLAR 0.014 0.003 -10000 0 -10000 0 0
HGF/MET -0.029 0.11 -10000 0 -0.58 9 9
ARHGDIB 0.007 0.037 -10000 0 -10000 0 0
FADD -0.085 0.27 -10000 0 -0.82 59 59
actin filament polymerization -0.007 0.037 -10000 0 -0.26 4 4
NFKB1 -0.031 0.061 -10000 0 -10000 0 0
MAPK8 -0.014 0.16 -10000 0 -0.58 9 9
DFFA 0.007 0.037 0.26 4 -10000 0 4
DNA fragmentation during apoptosis 0.005 0.046 0.26 4 -0.43 2 6
FAS/FADD/MET -0.071 0.19 -10000 0 -0.56 62 62
CFLAR/RIP1 0.001 0.005 -10000 0 -10000 0 0
FAIM3 0.001 0.1 -10000 0 -0.79 8 8
FAF1 0.014 0.004 -10000 0 -10000 0 0
PARP1 0.007 0.037 0.26 4 -10000 0 4
DFFB 0.005 0.047 0.26 4 -0.43 2 6
CHUK -0.026 0.053 -10000 0 -10000 0 0
FASLG -0.055 0.22 -10000 0 -0.75 45 45
FAS/FADD -0.076 0.21 -10000 0 -0.63 60 60
HGF -0.012 0.13 -10000 0 -0.63 20 20
LMNA 0.006 0.034 -10000 0 -10000 0 0
CASP6 0.007 0.037 -10000 0 -10000 0 0
CASP10 0.014 0.004 -10000 0 -10000 0 0
CASP3 0.008 0.044 0.3 8 -10000 0 8
PTPN13 0 0.089 -10000 0 -0.57 12 12
CASP8 0.006 0.048 0.38 8 -10000 0 8
IL6 -0.083 0.35 -10000 0 -1.1 46 46
MET 0.005 0.083 -10000 0 -0.74 6 6
ICAD/CAD 0.005 0.044 -10000 0 -0.49 1 1
FASLG/FAS/FADD/FAF1/Caspase 10 -0.03 0.14 -10000 0 -0.48 13 13
activation of caspase activity by cytochrome c 0.002 0.047 0.3 1 -0.55 2 3
PAK2 0.007 0.037 0.26 4 -10000 0 4
BCL2 0.002 0.09 -10000 0 -0.69 8 8
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.042 0.099 -10000 0 -0.65 4 4
UGCG -0.008 0.12 -10000 0 -0.62 17 17
AKT1/mTOR/p70S6K/Hsp90/TERT 0.015 0.13 -10000 0 -0.4 18 18
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.001 0.12 -10000 0 -0.62 17 17
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.022 0.075 -10000 0 -0.45 7 7
FRAP1 0.054 0.12 -10000 0 -0.49 10 10
FOXO3 0.062 0.1 -10000 0 -0.5 4 4
AKT1 0.055 0.11 -10000 0 -0.53 5 5
GAB2 0.011 0.045 -10000 0 -0.57 3 3
SMPD1 0.014 0.025 -10000 0 -10000 0 0
SGMS1 0.014 0.025 -10000 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
mol:GDP 0.022 0.029 -10000 0 -0.35 3 3
CALM1 0.014 0 -10000 0 -10000 0 0
cell proliferation 0.03 0.082 -10000 0 -0.42 6 6
EIF3A 0.014 0 -10000 0 -10000 0 0
PI3K 0.022 0.034 -10000 0 -0.41 3 3
RPS6KB1 0.007 0.068 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.003 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.001 -10000 0 -10000 0 0
JAK3 -0.012 0.15 -10000 0 -0.82 17 17
PIK3R1 0.013 0.045 -10000 0 -0.57 3 3
JAK1 0.017 0.002 -10000 0 -10000 0 0
NFKB1 0.014 0 -10000 0 -10000 0 0
MYC 0.062 0.096 -10000 0 -0.57 1 1
MYB -0.1 0.37 -10000 0 -1.2 52 52
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.042 0.12 -10000 0 -0.54 9 9
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.022 0.063 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.11 -10000 0 -0.53 9 9
Rac1/GDP 0.029 0.026 -10000 0 -10000 0 0
T cell proliferation 0.051 0.11 -10000 0 -0.5 8 8
SHC1 0.015 0.002 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.001 0.022 -10000 0 -0.065 52 52
PRKCZ 0.051 0.11 -10000 0 -0.52 8 8
NF kappa B1 p50/RelA -0.02 0.074 -10000 0 -0.48 4 4
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.035 0.11 -10000 0 -0.51 13 13
HSP90AA1 0.014 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
IL2RA -0.063 0.24 -10000 0 -0.82 46 46
IL2RB 0.006 0.095 -10000 0 -0.78 7 7
TERT -0.17 0.34 -10000 0 -0.82 108 108
E2F1 -0.034 0.15 -10000 0 -0.42 53 53
SOS1 0.014 0.002 -10000 0 -10000 0 0
RPS6 0.014 0 -10000 0 -10000 0 0
mol:cAMP 0 0.011 0.031 52 -10000 0 52
PTPN11 0.015 0.002 -10000 0 -10000 0 0
IL2RG -0.01 0.15 -10000 0 -0.79 17 17
actin cytoskeleton organization 0.051 0.11 -10000 0 -0.5 8 8
GRB2 0.014 0.002 -10000 0 -10000 0 0
IL2 0.007 0.038 -10000 0 -0.82 1 1
PIK3CA 0.017 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.034 0.028 -10000 0 -10000 0 0
LCK -0.003 0.13 -10000 0 -0.82 12 12
BCL2 0.054 0.14 -10000 0 -0.73 9 9
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.014 0 -9999 0 -10000 0 0
PTK2 0.014 0 -9999 0 -10000 0 0
CRKL -0.026 0.12 -9999 0 -0.42 6 6
GRB2/SOS1/SHC 0 0 -9999 0 -10000 0 0
HRAS 0.012 0.037 -9999 0 -0.82 1 1
IRS1/Crk -0.025 0.12 -9999 0 -0.41 5 5
IGF-1R heterotetramer/IGF1/PTP1B -0.056 0.12 -9999 0 -0.47 5 5
AKT1 0 0.11 -9999 0 -0.47 3 3
BAD 0.009 0.1 -9999 0 -0.44 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.025 0.12 -9999 0 -0.41 5 5
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.026 0.12 -9999 0 -0.41 5 5
RAF1 0.014 0.099 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.045 0.099 -9999 0 -0.51 1 1
YWHAZ 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.037 0.13 -9999 0 -0.31 85 85
PIK3CA 0.014 0 -9999 0 -10000 0 0
RPS6KB1 0 0.11 -9999 0 -0.47 3 3
GNB2L1 0.014 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.011 0.088 -9999 0 -10000 0 0
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.039 0.089 -9999 0 -0.55 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.041 0.092 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.002 0.028 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.025 0.12 -9999 0 -0.41 5 5
Crk/p130 Cas/Paxillin -0.042 0.092 -9999 0 -0.48 1 1
IGF1R 0.002 0.028 -9999 0 -10000 0 0
IGF1 -0.089 0.23 -9999 0 -0.59 85 85
IRS2/Crk -0.016 0.12 -9999 0 -0.52 2 2
PI3K -0.047 0.1 -9999 0 -0.53 3 3
apoptosis -0.016 0.092 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.029 -9999 0 -0.64 1 1
PRKCD -0.023 0.15 -9999 0 -0.54 1 1
RAF1/14-3-3 E 0.021 0.09 -9999 0 -10000 0 0
BAD/14-3-3 0.016 0.096 -9999 0 -10000 0 0
PRKCZ 0 0.11 -9999 0 -0.47 3 3
Crk/p130 Cas/Paxillin/FAK1 -0.032 0.07 -9999 0 -10000 0 0
PTPN1 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.033 0.16 -9999 0 -0.38 81 81
BCAR1 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.048 0.11 -9999 0 -0.44 5 5
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.025 0.12 -9999 0 -0.41 5 5
GRB10 0.012 0.037 -9999 0 -0.82 1 1
PTPN11 -0.025 0.12 -9999 0 -0.41 5 5
IRS1 -0.037 0.13 -9999 0 -0.31 85 85
IRS2 -0.026 0.12 -9999 0 -0.44 6 6
IGF-1R heterotetramer/IGF1 -0.074 0.16 -9999 0 -0.43 85 85
GRB2 0.014 0 -9999 0 -10000 0 0
PDPK1 -0.009 0.11 -9999 0 -0.5 3 3
YWHAE 0.014 0 -9999 0 -10000 0 0
PRKD1 -0.028 0.16 -9999 0 -0.37 84 84
SHC1 0.014 0 -9999 0 -10000 0 0
Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma -0.038 0.099 -10000 0 -0.48 1 1
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion -0.001 0.029 -10000 0 -0.64 1 1
GNB1/GNG2 -0.001 0.025 -10000 0 -0.55 1 1
GNB1 0.014 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.042 0.11 -10000 0 -0.32 64 64
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 0.011 0.028 0.084 64 -10000 0 64
GNAL -0.061 0.19 -10000 0 -0.57 64 64
GNG2 0.012 0.037 -10000 0 -0.82 1 1
CRH -0.001 0.037 -10000 0 -0.82 1 1
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.004 0.043 -10000 0 -0.35 7 7
MAPK11 0.009 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.16 0.32 -9999 0 -1.2 3 3
PLK1 0.084 0.085 -9999 0 -0.7 2 2
BIRC5 0.059 0.16 -9999 0 -0.62 22 22
HSPA1B 0.15 0.32 -9999 0 -1.2 3 3
MAP2K1 0.046 0.037 -9999 0 -10000 0 0
BRCA2 0.15 0.34 -9999 0 -1.3 6 6
FOXM1 0.15 0.36 -9999 0 -1.5 5 5
XRCC1 0.16 0.32 -9999 0 -1.2 3 3
FOXM1B/p19 -0.18 0.27 -9999 0 -1 20 20
Cyclin D1/CDK4 0.1 0.37 -9999 0 -1.1 7 7
CDC2 0.15 0.33 -9999 0 -1.2 5 5
TGFA 0.11 0.36 -9999 0 -1 11 11
SKP2 0.16 0.32 -9999 0 -1.2 4 4
CCNE1 0.008 0.098 -9999 0 -0.81 7 7
CKS1B 0.15 0.33 -9999 0 -1.2 6 6
RB1 -0.049 0.11 -9999 0 -0.72 5 5
FOXM1C/SP1 0.14 0.32 -9999 0 -1.3 5 5
AURKB 0.075 0.12 -9999 0 -0.66 9 9
CENPF 0.16 0.32 -9999 0 -1.2 3 3
CDK4 0.024 0.017 -9999 0 -10000 0 0
MYC 0.16 0.29 -9999 0 -1 3 3
CHEK2 0.046 0.037 -9999 0 -10000 0 0
ONECUT1 0.099 0.38 -9999 0 -1.1 11 11
CDKN2A -0.36 0.39 -9999 0 -0.77 230 230
LAMA4 0.14 0.35 -9999 0 -1.1 7 7
FOXM1B/HNF6 0.093 0.42 -9999 0 -1.3 12 12
FOS 0.051 0.5 -9999 0 -1.1 65 65
SP1 0.015 0.001 -9999 0 -10000 0 0
CDC25B 0.14 0.34 -9999 0 -1.2 4 4
response to radiation 0.027 0.035 -9999 0 -10000 0 0
CENPB 0.16 0.32 -9999 0 -1.2 3 3
CENPA 0.15 0.33 -9999 0 -1.3 4 4
NEK2 0.15 0.32 -9999 0 -1.3 3 3
HIST1H2BA 0.15 0.32 -9999 0 -1.2 3 3
CCNA2 0.018 0.039 -9999 0 -0.84 1 1
EP300 0.011 0.037 -9999 0 -0.57 2 2
CCNB1/CDK1 0.15 0.34 -9999 0 -1.4 4 4
CCNB2 0.15 0.32 -9999 0 -1.4 3 3
CCNB1 0.16 0.33 -9999 0 -1.2 4 4
ETV5 0.15 0.32 -9999 0 -1.2 3 3
ESR1 0.12 0.38 -9999 0 -1 21 21
CCND1 0.1 0.38 -9999 0 -1.1 12 12
GSK3A 0.042 0.032 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.044 0.085 -9999 0 -0.54 8 8
CDK2 0.02 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.032 0.04 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.071 0.19 -9999 0 -1.2 6 6
GAS1 0.15 0.34 -9999 0 -1.2 8 8
MMP2 0.11 0.38 -9999 0 -1.1 9 9
RB1/FOXM1C 0.12 0.36 -9999 0 -1.2 6 6
CREBBP 0.014 0 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1 -0.001 0.16 -9999 0 -0.58 14 14
MAP3K8 0.009 0.045 -9999 0 -0.57 3 3
FOS 0.009 0.12 -9999 0 -0.47 14 14
PRKCA 0.01 0.046 -9999 0 -0.69 2 2
PTPN7 -0.026 0.18 -9999 0 -0.82 24 24
HRAS 0.012 0.037 -9999 0 -0.82 1 1
PRKCB 0 0.1 -9999 0 -0.79 8 8
NRAS 0.014 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.003 0.039 -9999 0 -0.5 3 3
MAPK3 0.012 0.083 -9999 0 -0.37 12 12
MAP2K1 0.029 0.069 -9999 0 -0.44 5 5
ELK1 0.01 0.039 -9999 0 -0.85 1 1
BRAF -0.01 0.052 -9999 0 -0.4 5 5
mol:GTP -0.001 0.002 -9999 0 -0.006 61 61
MAPK1 0.012 0.083 -9999 0 -0.38 11 11
RAF1 -0.01 0.052 -9999 0 -0.4 5 5
KRAS 0.01 0.053 -9999 0 -0.82 2 2
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.011 0.037 -9999 0 -0.57 2 2
Caspase 8 (4 units) -0.037 0.078 -9999 0 -0.48 4 4
NEF -0.01 0.051 -9999 0 -10000 0 0
NFKBIA 0.01 0.044 -9999 0 -0.81 1 1
BIRC3 0.013 0.16 -9999 0 -0.74 22 22
CYCS 0.003 0.11 -9999 0 -0.49 6 6
RIPK1 0.014 0 -9999 0 -10000 0 0
CD247 -0.032 0.19 -9999 0 -0.9 21 21
MAP2K7 0.007 0.098 -9999 0 -0.44 4 4
protein ubiquitination 0.029 0.1 -9999 0 -0.49 2 2
CRADD 0.014 0 -9999 0 -10000 0 0
DAXX 0.014 0 -9999 0 -10000 0 0
FAS 0.011 0.037 -9999 0 -0.57 2 2
BID -0.006 0.12 -9999 0 -0.48 8 8
NF-kappa-B/RelA/I kappa B alpha -0.015 0.069 -9999 0 -0.53 1 1
TRADD 0.014 0 -9999 0 -10000 0 0
MAP3K5 0.014 0 -9999 0 -10000 0 0
CFLAR 0.014 0 -9999 0 -10000 0 0
FADD -0.085 0.27 -9999 0 -0.82 59 59
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.015 0.069 -9999 0 -0.53 1 1
MAPK8 0.011 0.1 -9999 0 -0.43 6 6
APAF1 0.013 0.026 -9999 0 -0.57 1 1
TRAF1 -0.006 0.13 -9999 0 -0.82 12 12
TRAF2 0.002 0.098 -9999 0 -0.82 7 7
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.013 0.12 -9999 0 -0.5 6 6
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.012 0.12 -9999 0 -0.48 10 10
CHUK 0.028 0.11 -9999 0 -0.55 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.056 0.15 -9999 0 -0.46 59 59
TCRz/NEF -0.055 0.18 -9999 0 -0.52 53 53
TNF -0.025 0.17 -9999 0 -0.79 24 24
FASLG -0.059 0.27 -9999 0 -0.82 52 52
NFKB1 0.012 0.025 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.026 0.11 -9999 0 -0.54 21 21
CASP6 -0.022 0.048 -9999 0 -10000 0 0
CASP7 0.035 0.13 -9999 0 -0.51 4 4
RELA 0.012 0.025 -9999 0 -10000 0 0
CASP2 0.014 0 -9999 0 -10000 0 0
CASP3 0.035 0.13 -9999 0 -0.51 4 4
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.026 -9999 0 -0.41 2 2
CASP8 0.014 0 -9999 0 -10000 0 0
CASP9 0.014 0 -9999 0 -10000 0 0
MAP3K14 0.02 0.12 -9999 0 -0.5 5 5
APAF-1/Caspase 9 -0.042 0.1 -9999 0 -0.44 22 22
BCL2 0.013 0.11 -9999 0 -0.45 6 6
Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization 0.03 0.03 -9999 0 -10000 0 0
epithelial cell differentiation -0.003 0.03 -9999 0 -10000 0 0
CYFIP2 0.01 0.052 -9999 0 -0.65 3 3
ENAH 0.064 0.047 -9999 0 -0.53 1 1
EGFR -0.017 0.15 -9999 0 -0.76 20 20
EPHA2 0.004 0.073 -9999 0 -0.57 8 8
MYO6 0.037 0.035 -9999 0 -10000 0 0
CTNNB1 0.013 0.026 -9999 0 -0.57 1 1
ABI1/Sra1/Nap1 -0.004 0.04 -9999 0 -0.54 2 2
AQP5 -0.31 0.21 -9999 0 -0.45 341 341
CTNND1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.037 0.032 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.002 0.12 -9999 0 -0.44 31 31
EGF -0.094 0.23 -9999 0 -0.57 91 91
NCKAP1 0.012 0.037 -9999 0 -0.82 1 1
AQP3 -0.12 0.2 -9999 0 -0.69 5 5
cortical microtubule organization -0.003 0.03 -9999 0 -10000 0 0
GO:0000145 0.036 0.031 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.003 0.031 -9999 0 -10000 0 0
MLLT4 0.014 0 -9999 0 -10000 0 0
ARF6/GDP -0.007 0.043 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.006 0.043 -9999 0 -0.49 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.049 0.034 -9999 0 -10000 0 0
PVRL2 0.012 0.037 -9999 0 -0.82 1 1
ZYX 0.037 0.033 -9999 0 -10000 0 0
ARF6/GTP -0.005 0.039 -9999 0 -0.45 1 1
CDH1 0.008 0.058 -9999 0 -0.57 5 5
EGFR/EGFR/EGF/EGF -0.064 0.13 -9999 0 -0.55 6 6
RhoA/GDP -0.003 0.028 -9999 0 -10000 0 0
actin cytoskeleton organization 0.043 0.034 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.014 0 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
IGF1R 0.014 0 -9999 0 -10000 0 0
IGF1 -0.088 0.22 -9999 0 -0.58 85 85
DIAPH1 -0.003 0.04 -9999 0 -0.57 2 2
Wnt receptor signaling pathway 0.003 0.03 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.007 0.043 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
VCL 0.043 0.035 -9999 0 -10000 0 0
EFNA1 0.012 0.037 -9999 0 -0.82 1 1
LPP 0.043 0.04 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.008 0.051 -9999 0 -0.52 2 2
SEC6/SEC8 -0.003 0.029 -9999 0 -10000 0 0
MGAT3 0.002 0.13 -9999 0 -0.44 31 31
HGF/MET -0.019 0.084 -9999 0 -0.69 3 3
HGF -0.012 0.13 -9999 0 -0.63 20 20
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.03 0.03 -9999 0 -10000 0 0
actin cable formation 0.082 0.041 -9999 0 -0.36 1 1
KIAA1543 0.018 0.11 -9999 0 -0.65 6 6
KIFC3 0.037 0.033 -9999 0 -10000 0 0
NCK1 0.014 0 -9999 0 -10000 0 0
EXOC3 0.014 0 -9999 0 -10000 0 0
ACTN1 0.036 0.039 -9999 0 -0.44 1 1
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP -0.003 0.03 -9999 0 -10000 0 0
EXOC4 0.014 0 -9999 0 -10000 0 0
STX4 0.037 0.033 -9999 0 -10000 0 0
PIP5K1C 0.037 0.033 -9999 0 -10000 0 0
LIMA1 0.014 0 -9999 0 -10000 0 0
ABI1 0.014 0 -9999 0 -10000 0 0
ROCK1 -0.006 0.037 -9999 0 -10000 0 0
adherens junction assembly 0.034 0.11 -9999 0 -0.65 6 6
IGF-1R heterotetramer/IGF1 -0.046 0.099 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin -0.001 0.028 -9999 0 -0.63 1 1
MET 0.005 0.083 -9999 0 -0.74 6 6
PLEKHA7 0.018 0.088 -9999 0 -0.55 4 4
mol:GTP -0.006 0.043 -9999 0 -0.49 1 1
establishment of epithelial cell apical/basal polarity 0.063 0.035 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.03 0.03 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.043 0.034 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.03 0.03 -9999 0 -10000 0 0
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.14 0.32 -9999 0 -0.82 89 89
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.022 0.069 -9999 0 -0.57 2 2
GNAO1 0.009 0.071 -9999 0 -0.77 4 4
S1P/S1P3/G12/G13 0.023 0.052 -9999 0 -0.4 7 7
AKT1 -0.048 0.098 -9999 0 -0.38 8 8
AKT3 0.035 0.11 -9999 0 -0.69 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.14 0.32 -9999 0 -0.82 89 89
GNAI2 0.015 0.002 -9999 0 -10000 0 0
GNAI3 0.015 0.002 -9999 0 -10000 0 0
GNAI1 0.014 0.026 -9999 0 -0.56 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.009 0.065 -9999 0 -0.62 5 5
S1PR2 0.014 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.03 0.082 -9999 0 -0.62 4 4
MAPK3 0.037 0.078 -9999 0 -0.59 4 4
MAPK1 0.037 0.078 -9999 0 -0.59 4 4
JAK2 0.033 0.098 -9999 0 -0.53 8 8
CXCR4 0.02 0.13 -9999 0 -0.55 19 19
FLT1 0.015 0.037 -9999 0 -0.82 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.037 0.078 -9999 0 -0.59 4 4
S1P/S1P3/Gi 0.03 0.082 -9999 0 -0.63 4 4
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.064 -9999 0 -0.57 4 4
VEGFA 0.007 0.091 -9999 0 -0.82 6 6
S1P/S1P2/Gi 0.031 0.064 -9999 0 -0.59 2 2
VEGFR1 homodimer/VEGFA homodimer 0.02 0.077 -9999 0 -0.62 7 7
RHOA 0.014 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.015 0.12 -9999 0 -0.52 6 6
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ -0.015 0.15 -9999 0 -0.74 20 20
G12/G13 -0.003 0.04 -9999 0 -0.63 2 2
GNA14 -0.075 0.21 -9999 0 -0.57 76 76
GNA15 0.011 0.037 -9999 0 -0.57 2 2
GNA12 0.01 0.053 -9999 0 -0.82 2 2
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.009 0.052 -9999 0 -0.57 4 4
Rac1/GTP -0.014 0.064 -9999 0 -0.57 4 4
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.031 0.047 -9999 0 -10000 0 0
STMN1 0.012 0.11 -9999 0 -0.71 11 11
Aurora B/RasGAP/Survivin -0.008 0.16 -9999 0 -0.63 26 26
Chromosomal passenger complex/Cul3 protein complex 0.022 0.082 -9999 0 -0.44 10 10
BIRC5 -0.021 0.17 -9999 0 -0.82 22 22
DES -0.32 0.27 -9999 0 -0.55 274 274
Aurora C/Aurora B/INCENP 0.01 0.091 -9999 0 -0.52 13 13
Aurora B/TACC1 0.006 0.078 -9999 0 -0.5 11 11
Aurora B/PP2A 0.007 0.086 -9999 0 -0.62 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.016 0.023 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0 0.002 -9999 0 -10000 0 0
NDC80 0.004 0.12 -9999 0 -0.63 18 18
Cul3 protein complex -0.007 0.047 -9999 0 -10000 0 0
KIF2C 0.02 0.044 -9999 0 -0.27 7 7
PEBP1 0.014 0.002 -9999 0 -10000 0 0
KIF20A 0.013 0.001 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.006 0.094 -9999 0 -0.63 10 10
SEPT1 -0.003 0.12 -9999 0 -0.82 10 10
SMC2 0.014 0 -9999 0 -10000 0 0
SMC4 0.012 0.037 -9999 0 -0.82 1 1
NSUN2/NPM1/Nucleolin 0.025 0.054 -9999 0 -0.39 5 5
PSMA3 0.014 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.002 -9999 0 -10000 0 0
H3F3B 0.015 0.051 -9999 0 -0.36 9 9
AURKB 0.006 0.11 -9999 0 -0.82 9 9
AURKC 0.005 0.083 -9999 0 -0.74 6 6
CDCA8 0.014 0.038 -9999 0 -0.83 1 1
cytokinesis -0.022 0.087 -9999 0 -0.55 8 8
Aurora B/Septin1 0.005 0.12 -9999 0 -0.52 15 15
AURKA -0.005 0.12 -9999 0 -0.82 11 11
INCENP 0.015 0.003 -9999 0 -10000 0 0
KLHL13 0.009 0.052 -9999 0 -0.57 4 4
BUB1 0.013 0.001 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin -0.004 0.14 -9999 0 -0.57 26 26
EVI5 0.015 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.011 0.054 -9999 0 -0.42 6 6
SGOL1 0.014 0 -9999 0 -10000 0 0
CENPA 0.018 0.081 -9999 0 -0.44 11 11
NCAPG 0.014 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.007 0.086 -9999 0 -0.62 9 9
NCAPD2 0.009 0.064 -9999 0 -0.82 3 3
Aurora B/PP1-gamma 0.007 0.086 -9999 0 -0.62 9 9
RHOA 0.014 0 -9999 0 -10000 0 0
NCAPH 0.009 0.064 -9999 0 -0.82 3 3
NPM1 0.005 0.057 -9999 0 -0.41 9 9
RASA1 0.011 0.037 -9999 0 -0.57 2 2
KLHL9 0.007 0.063 -9999 0 -0.57 6 6
mitotic prometaphase 0.001 0.003 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.007 0.086 -9999 0 -0.62 9 9
PPP1CC 0.014 0 -9999 0 -10000 0 0
Centraspindlin -0.012 0.06 -9999 0 -0.46 6 6
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 0.005 0.057 -9999 0 -0.41 9 9
MYLK 0.009 0.074 -9999 0 -0.38 16 16
KIF23 0.015 0.002 -9999 0 -10000 0 0
VIM 0.013 0.1 -9999 0 -0.67 11 11
RACGAP1 0.015 0.002 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.005 0.057 -9999 0 -0.41 9 9
Chromosomal passenger complex 0.026 0.073 -9999 0 -0.46 7 7
Chromosomal passenger complex/EVI5 0.028 0.15 -9999 0 -0.54 26 26
TACC1 0.011 0.037 -9999 0 -0.57 2 2
PPP2R5D 0.014 0 -9999 0 -10000 0 0
CUL3 0.014 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Circadian rhythm pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.001 0.004 -9999 0 -10000 0 0
CLOCK 0.01 0.063 -9999 0 -0.56 6 6
TIMELESS/CRY2 0.046 0.013 -9999 0 -10000 0 0
DEC1/BMAL1 -0.11 0.24 -9999 0 -0.63 88 88
ATR 0.014 0 -9999 0 -10000 0 0
NR1D1 0.044 0.016 -9999 0 -10000 0 0
ARNTL 0.017 0 -9999 0 -10000 0 0
TIMELESS 0.044 0.016 -9999 0 -10000 0 0
NPAS2 0.008 0.073 -9999 0 -0.56 8 8
CRY2 0.014 0 -9999 0 -10000 0 0
mol:CO -0.015 0 -9999 0 -10000 0 0
CHEK1 0.014 0 -9999 0 -10000 0 0
mol:HEME 0.015 0 -9999 0 -10000 0 0
PER1 0.013 0.026 -9999 0 -0.57 1 1
BMAL/CLOCK/NPAS2 0.036 0.065 -9999 0 -0.65 1 1
BMAL1/CLOCK 0.007 0.11 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR 0.051 0.013 -9999 0 -10000 0 0
mol:NADPH 0.015 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.045 0.02 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.14 0.32 -9999 0 -0.82 88 88
Ceramide 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
SPHK2 0.017 0.071 -10000 0 -0.63 6 6
MAP4K4 0.029 0.082 -10000 0 -0.4 9 9
BAG4 0.011 0.037 -10000 0 -0.57 2 2
PKC zeta/ceramide -0.014 0.042 0.19 5 -0.35 1 6
NFKBIA 0.012 0.037 -10000 0 -0.82 1 1
BIRC3 -0.021 0.17 -10000 0 -0.82 21 21
BAX -0.002 0.021 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AKT1 0.022 0.009 -10000 0 -10000 0 0
BAD -0.012 0.04 0.21 5 -10000 0 5
SMPD1 0.019 0.054 -10000 0 -0.26 4 4
RB1 -0.013 0.046 0.21 5 -0.35 2 7
FADD/Caspase 8 -0.015 0.17 -10000 0 -0.44 61 61
MAP2K4 -0.004 0.038 0.23 1 -10000 0 1
NSMAF 0.014 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.004 0.038 -10000 0 -10000 0 0
EGF -0.094 0.23 -10000 0 -0.57 91 91
mol:ceramide -0.023 0.043 0.22 5 -10000 0 5
MADD 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.017 0.071 -10000 0 -0.63 6 6
ASAH1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.014 0.045 0.21 5 -0.34 2 7
cell proliferation -0.046 0.092 -10000 0 -0.39 4 4
BID 0.02 0.058 -10000 0 -10000 0 0
MAP3K1 -0.012 0.04 0.21 5 -10000 0 5
EIF2A 0.001 0.05 -10000 0 -0.44 3 3
TRADD 0.014 0 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
MAPK3 0.009 0.036 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.036 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.013 0.039 0.19 5 -10000 0 5
FADD -0.029 0.18 -10000 0 -0.47 66 66
KSR1 -0.012 0.04 0.21 5 -10000 0 5
MAPK8 -0.002 0.05 0.21 5 -0.26 8 13
PRKRA -0.012 0.04 0.23 1 -10000 0 1
PDGFA 0.004 0.091 -10000 0 -0.82 6 6
TRAF2 0.002 0.098 -10000 0 -0.82 7 7
IGF1 -0.088 0.22 -10000 0 -0.58 85 85
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.023 0.043 0.22 5 -10000 0 5
CTSD 0.014 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.029 0.11 -10000 0 -0.42 4 4
PRKCD 0.014 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.026 -10000 0 -0.57 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.017 0.071 -10000 0 -0.63 6 6
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.022 0.086 -10000 0 -0.43 9 9
TNFR1A/BAG4/TNF-alpha -0.026 0.11 -10000 0 -0.54 21 21
mol:Sphingosine-1-phosphate 0.017 0.071 -10000 0 -0.63 6 6
MAP2K1 0.004 0.037 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
CYCS -0.003 0.034 0.33 1 -10000 0 1
TNFRSF1A 0.014 0 -10000 0 -10000 0 0
NFKB1 0.014 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.026 -10000 0 -0.41 2 2
EIF2AK2 -0.007 0.053 -10000 0 -0.47 3 3
TNF-alpha/TNFR1A/FAN -0.025 0.11 -10000 0 -0.54 21 21
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.034 0.048 -10000 0 -10000 0 0
MAP2K2 0.004 0.037 -10000 0 -10000 0 0
SMPD3 0.002 0.099 -10000 0 -0.33 31 31
TNF -0.025 0.17 -10000 0 -0.79 24 24
PKC zeta/PAR4 -0.001 0.018 -10000 0 -0.41 1 1
mol:PHOSPHOCHOLINE 0.029 0.096 0.22 94 -10000 0 94
NF kappa B1/RelA/I kappa B alpha -0.001 0.024 -10000 0 -0.46 1 1
AIFM1 -0.003 0.034 0.33 1 -10000 0 1
BCL2 0.002 0.09 -10000 0 -0.69 8 8
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 0.014 0 -9999 0 -10000 0 0
SPHK1 -0.006 0.13 -9999 0 -0.82 12 12
GNAI2 0.014 0 -9999 0 -10000 0 0
mol:S1P 0.015 0.053 -9999 0 -0.29 15 15
GNAO1 0.008 0.069 -9999 0 -0.76 4 4
mol:Sphinganine-1-P 0.009 0.1 -9999 0 -0.63 12 12
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.007 0.043 -9999 0 -0.46 2 2
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.003 0.04 -9999 0 -0.63 2 2
S1PR3 0.007 0.064 -9999 0 -0.62 5 5
S1PR2 0.014 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.007 0.042 -9999 0 -10000 0 0
S1PR5 0.008 0.064 -9999 0 -0.69 4 4
S1PR4 -0.034 0.19 -9999 0 -0.81 29 29
GNAI1 0.013 0.026 -9999 0 -0.57 1 1
S1P/S1P5/G12 0.022 0.065 -9999 0 -0.48 4 4
S1P/S1P3/Gq -0.011 0.12 -9999 0 -0.51 7 7
S1P/S1P4/Gi 0.014 0.094 -9999 0 -0.47 5 5
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ -0.017 0.15 -9999 0 -0.74 20 20
GNA14 -0.075 0.21 -9999 0 -0.57 76 76
GNA15 0.011 0.037 -9999 0 -0.57 2 2
GNA12 0.01 0.053 -9999 0 -0.82 2 2
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.009 0.052 -9999 0 -0.57 4 4
ABCC1 0.009 0.064 -9999 0 -0.82 3 3
a4b1 and a4b7 Integrin signaling

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
ITGB1 0.012 0.037 -9999 0 -0.82 1 1
ITGB7 0.011 0.037 -9999 0 -0.57 2 2
ITGA4 -0.005 0.12 -9999 0 -0.82 11 11
alpha4/beta7 Integrin -0.016 0.096 -9999 0 -0.59 13 13
alpha4/beta1 Integrin -0.015 0.096 -9999 0 -0.63 12 12
Arf6 downstream pathway

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
PLAUR 0.005 0.16 -10000 0 -0.65 29 29
regulation of axonogenesis -0.02 0.038 -10000 0 -10000 0 0
myoblast fusion 0.008 0.087 0.32 29 -10000 0 29
mol:GTP -0.014 0.046 -10000 0 -0.25 3 3
regulation of calcium-dependent cell-cell adhesion -0.018 0.065 0.35 7 -10000 0 7
ARF1/GTP -0.009 0.031 -10000 0 -10000 0 0
mol:GM1 0 0.037 -10000 0 -10000 0 0
mol:Choline 0.019 0.043 -10000 0 -0.34 3 3
lamellipodium assembly -0.026 0.08 -10000 0 -0.32 29 29
MAPK3 0.013 0.069 -10000 0 -0.3 3 3
ARF6/GTP/NME1/Tiam1 0.018 0.065 -10000 0 -0.35 7 7
ARF1 0.014 0 -10000 0 -10000 0 0
ARF6/GDP -0.008 0.087 -10000 0 -0.32 29 29
ARF1/GDP 0.003 0.081 -10000 0 -0.49 3 3
ARF6 0.005 0.026 -10000 0 -10000 0 0
RAB11A 0.014 0 -10000 0 -10000 0 0
TIAM1 0.008 0.063 -10000 0 -0.56 6 6
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.013 0.069 -10000 0 -10000 0 0
actin filament bundle formation 0.023 0.071 0.49 3 -10000 0 3
KALRN -0.04 0.1 -10000 0 -0.33 42 42
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.023 0.072 -10000 0 -0.49 3 3
NME1 0.013 0.037 -10000 0 -0.82 1 1
Rac1/GDP -0.023 0.072 -10000 0 -0.49 3 3
substrate adhesion-dependent cell spreading -0.014 0.046 -10000 0 -0.25 3 3
cortical actin cytoskeleton organization -0.026 0.081 -10000 0 -0.32 29 29
RAC1 0.014 0 -10000 0 -10000 0 0
liver development -0.014 0.046 -10000 0 -0.25 3 3
ARF6/GTP -0.014 0.046 -10000 0 -0.25 3 3
RhoA/GTP -0.009 0.031 -10000 0 -10000 0 0
mol:GDP -0.026 0.082 -10000 0 -0.32 29 29
ARF6/GTP/RAB11FIP3/RAB11A -0.005 0.025 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
PLD1 0.009 0.049 -10000 0 -0.4 3 3
RAB11FIP3 0.014 0 -10000 0 -10000 0 0
tube morphogenesis -0.026 0.08 -10000 0 -0.32 29 29
ruffle organization 0.02 0.038 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.014 0.046 -10000 0 -0.25 3 3
PLD2 0.011 0.037 -10000 0 -10000 0 0
PIP5K1A 0.02 0.038 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.019 0.043 -10000 0 -0.34 3 3
Rac1/GTP -0.026 0.081 -10000 0 -0.32 29 29
HIF-2-alpha transcription factor network

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
MMP14 -0.007 0.094 -10000 0 -0.69 9 9
oxygen homeostasis -0.002 0.017 -10000 0 -10000 0 0
TCEB2 0.01 0.053 -10000 0 -0.82 2 2
TCEB1 0.012 0.037 -10000 0 -0.82 1 1
VHL/Elongin B/Elongin C/HIF2A -0.024 0.082 -10000 0 -0.54 3 3
EPO -0.049 0.28 -10000 0 -0.73 37 37
FIH (dimer) 0.011 0.016 -10000 0 -10000 0 0
APEX1 0.014 0.015 -10000 0 -10000 0 0
SERPINE1 -0.26 0.39 -10000 0 -0.84 48 48
FLT1 0.005 0.044 -10000 0 -0.58 1 1
ADORA2A -0.025 0.24 -10000 0 -0.81 7 7
germ cell development -0.043 0.27 -10000 0 -0.81 21 21
SLC11A2 -0.021 0.23 -10000 0 -0.81 6 6
BHLHE40 -0.023 0.24 -10000 0 -0.86 6 6
HIF1AN 0.011 0.016 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.064 0.1 -10000 0 -0.49 9 9
ETS1 0.025 0.065 -10000 0 -0.81 3 3
CITED2 -0.001 0.067 -10000 0 -0.94 2 2
KDR 0.003 0.075 -10000 0 -0.99 2 2
PGK1 -0.021 0.23 -10000 0 -0.85 5 5
SIRT1 0.012 0.026 -10000 0 -0.57 1 1
response to hypoxia -0.001 0.005 -10000 0 -10000 0 0
HIF2A/ARNT -0.032 0.27 -10000 0 -0.88 11 11
EPAS1 0.005 0.13 -10000 0 -0.42 10 10
SP1 0.022 0.003 -10000 0 -10000 0 0
ABCG2 -0.028 0.24 -10000 0 -0.82 10 10
EFNA1 -0.021 0.24 -10000 0 -0.85 6 6
FXN -0.022 0.23 -10000 0 -0.8 6 6
POU5F1 -0.047 0.28 -10000 0 -0.85 21 21
neuron apoptosis 0.031 0.26 0.84 11 -10000 0 11
EP300 0.011 0.037 -10000 0 -0.57 2 2
EGLN3 -0.038 0.2 -10000 0 -0.79 31 31
EGLN2 0.012 0.016 -10000 0 -10000 0 0
EGLN1 0.011 0.016 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.003 0.042 -10000 0 -0.54 3 3
VHL 0.014 0 -10000 0 -10000 0 0
ARNT 0.014 0.015 -10000 0 -10000 0 0
SLC2A1 -0.03 0.25 -10000 0 -0.86 14 14
TWIST1 -0.034 0.26 -10000 0 -0.83 18 18
ELK1 0.02 0.037 -10000 0 -0.81 1 1
HIF2A/ARNT/Cbp/p300 -0.053 0.096 -10000 0 -0.49 7 7
VEGFA -0.025 0.25 -10000 0 -0.92 9 9
CREBBP 0.014 0 -10000 0 -10000 0 0
Insulin 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
CBL/APS/CAP -0.046 0.11 -9999 0 -0.57 5 5
TC10/GTP -0.04 0.094 -9999 0 -0.68 1 1
Insulin Receptor/Insulin/IRS1/Shp2 -0.004 0.04 -9999 0 -0.46 2 2
HRAS 0.012 0.037 -9999 0 -0.82 1 1
APS homodimer 0.01 0.053 -9999 0 -0.82 2 2
GRB14 -0.045 0.18 -9999 0 -0.6 47 47
FOXO3 -0.007 0.044 -9999 0 -0.63 2 2
AKT1 0.021 0.099 -9999 0 -0.47 2 2
INSR 0.014 0.026 -9999 0 -0.56 1 1
Insulin Receptor/Insulin 0.036 0.031 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.012 0.037 -9999 0 -0.82 1 1
SORBS1 -0.078 0.21 -9999 0 -0.57 79 79
CRK 0.014 0 -9999 0 -10000 0 0
PTPN1 0.036 0.03 -9999 0 -10000 0 0
CAV1 -0.014 0.14 -9999 0 -0.48 40 40
CBL/APS/CAP/Crk-II/C3G -0.045 0.11 -9999 0 -0.6 2 2
Insulin Receptor/Insulin/IRS1/NCK2 -0.004 0.04 -9999 0 -0.46 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.04 -9999 0 -0.4 2 2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.038 0.036 -9999 0 -0.49 1 1
RPS6KB1 0.029 0.093 -9999 0 -10000 0 0
PARD6A 0.011 0.045 -9999 0 -0.69 2 2
CBL 0.014 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0 0.021 -9999 0 -0.44 1 1
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.024 0.072 -9999 0 -10000 0 0
HRAS/GTP -0.005 0.037 -9999 0 -10000 0 0
Insulin Receptor 0.014 0.026 -9999 0 -0.56 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.004 0.036 -9999 0 -0.42 2 2
PRKCI -0.007 0.02 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.03 0.09 -9999 0 -0.51 2 2
SHC1 0.014 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade -0.001 0.025 -9999 0 -10000 0 0
PI3K -0.005 0.04 -9999 0 -0.41 2 2
NCK2 0.014 0 -9999 0 -10000 0 0
RHOQ 0.014 0 -9999 0 -10000 0 0
mol:H2O2 0 0.003 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.029 -9999 0 -0.64 1 1
AKT2 0.021 0.099 -9999 0 -0.47 2 2
PRKCZ -0.008 0.029 -9999 0 -0.48 1 1
SH2B2 0.01 0.053 -9999 0 -0.82 2 2
SHC/SHIP 0.031 0.045 -9999 0 -0.4 2 2
F2RL2 -0.22 0.38 -9999 0 -0.82 142 142
TRIP10 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.002 0.032 -9999 0 -0.47 2 2
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.002 0.029 -9999 0 -0.42 2 2
RAPGEF1 0.014 0 -9999 0 -10000 0 0
RASA1 0.011 0.037 -9999 0 -0.57 2 2
NCK1 0.014 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.049 0.12 -9999 0 -0.64 2 2
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.003 0.039 -9999 0 -0.48 3 3
INPP5D 0.023 0.047 -9999 0 -0.43 2 2
SOS1 0.014 0 -9999 0 -10000 0 0
SGK1 -0.006 0.06 -9999 0 -0.72 3 3
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.01 0.045 -9999 0 -0.57 3 3
p62DOK/RasGAP -0.001 0.025 -9999 0 -10000 0 0
INS 0 0.052 -9999 0 -0.81 2 2
mol:PI-3-4-P2 0.023 0.047 -9999 0 -0.42 2 2
GRB2 0.014 0 -9999 0 -10000 0 0
EIF4EBP1 0.021 0.11 -9999 0 -0.61 2 2
PTPRA 0.015 0.003 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.013 0.026 -9999 0 -0.57 1 1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.033 0.031 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.004 0.041 -9999 0 -0.38 5 5
Insulin Receptor/Insulin/IRS3 -0.003 0.043 -9999 0 -0.55 3 3
Par3/Par6 -0.14 0.21 -9999 0 -0.47 141 141
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process -0.004 0.086 0.71 7 -10000 0 7
PI3K Class IB/PDE3B 0.004 0.086 -10000 0 -0.71 7 7
PDE3B 0.004 0.087 -10000 0 -0.71 7 7
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 0 0 -9999 0 -10000 0 0
TRAF2/ASK1 -0.008 0.065 -9999 0 -0.55 7 7
ATM 0.013 0.026 -9999 0 -0.57 1 1
MAP2K3 0.017 0.049 -9999 0 -0.34 1 1
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.018 0.067 -9999 0 -0.32 1 1
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.002 0.09 -9999 0 -0.69 8 8
TXN 0.009 0 -9999 0 -10000 0 0
CALM1 0.014 0 -9999 0 -10000 0 0
GADD45A 0.012 0.037 -9999 0 -0.82 1 1
GADD45B 0.014 0 -9999 0 -10000 0 0
MAP3K1 0.014 0 -9999 0 -10000 0 0
MAP3K6 0.013 0.026 -9999 0 -0.57 1 1
MAP3K7 0.014 0 -9999 0 -10000 0 0
MAP3K4 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.001 0.018 -9999 0 -0.41 1 1
TAK1/TAB family 0 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3 -0.009 0.067 -9999 0 -0.5 9 9
TRAF2 0.002 0.098 -9999 0 -0.82 7 7
RAC1/OSM/MEKK3/MKK3 -0.013 0.051 -9999 0 -0.42 3 3
TRAF6 0.009 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.14 0.26 -9999 0 -0.58 127 127
CCM2 -0.001 0.11 -9999 0 -0.82 9 9
CaM/Ca2+/CAMKIIB -0.091 0.16 -9999 0 -0.36 127 127
MAPK11 0.014 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.081 0.14 -9999 0 -0.5 6 6
OSM/MEKK3 -0.011 0.084 -9999 0 -0.63 9 9
TAOK1 0.008 0.06 -9999 0 -0.34 14 14
TAOK2 0.018 0.016 -9999 0 -0.34 1 1
TAOK3 0.018 0.016 -9999 0 -0.34 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.014 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.014 0 -9999 0 -10000 0 0
MAP3K10 0.014 0 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
TRX/ASK1 0.017 0 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 -0.007 0.053 -9999 0 -0.47 5 5
Paxillin-dependent events mediated by a4b1

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
CRKL 0.012 0.037 -10000 0 -0.82 1 1
Rac1/GDP 0.002 0.011 -10000 0 -10000 0 0
DOCK1 0.011 0.037 -10000 0 -0.57 2 2
ITGA4 -0.005 0.12 -10000 0 -0.82 11 11
RAC1 0.014 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.016 0.096 -10000 0 -0.59 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.013 0.083 -10000 0 -0.54 12 12
alpha4/beta7 Integrin/Paxillin 0.022 0.08 -10000 0 -0.49 11 11
lamellipodium assembly -0.002 0.04 -10000 0 -0.64 1 1
PIK3CA 0.014 0 -10000 0 -10000 0 0
PI3K -0.002 0.031 -10000 0 -0.41 3 3
ARF6 0.014 0 -10000 0 -10000 0 0
TLN1 0.01 0.053 -10000 0 -0.82 2 2
PXN 0.025 0 -10000 0 -10000 0 0
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
ARF6/GTP -0.01 0.064 -10000 0 -10000 0 0
cell adhesion -0.013 0.075 -10000 0 -0.46 14 14
CRKL/CBL -0.001 0.028 -10000 0 -0.63 1 1
alpha4/beta1 Integrin/Paxillin 0.023 0.081 -10000 0 -0.49 12 12
ITGB1 0.012 0.037 -10000 0 -0.82 1 1
ITGB7 0.011 0.037 -10000 0 -0.57 2 2
ARF6/GDP 0.002 0.011 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.055 0.15 -10000 0 -0.48 52 52
p130Cas/Crk/Dock1 -0.001 0.021 -10000 0 -10000 0 0
VCAM1 -0.067 0.24 -10000 0 -0.77 51 51
alpha4/beta1 Integrin/Paxillin/Talin -0.013 0.076 -10000 0 -0.46 14 14
alpha4/beta1 Integrin/Paxillin/GIT1 -0.011 0.071 -10000 0 -0.46 12 12
BCAR1 0.014 0 -10000 0 -10000 0 0
mol:GDP 0.011 0.07 0.46 12 -10000 0 12
CBL 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0 -10000 0 -10000 0 0
GIT1 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.013 0.076 -10000 0 -0.46 14 14
Rac1/GTP -0.002 0.045 -10000 0 -0.74 1 1
IL2 signaling events mediated by STAT5

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
GAB2 0.011 0.045 -9999 0 -0.57 3 3
ELF1 -0.013 0.11 -9999 0 -0.55 4 4
CCNA2 0.012 0.037 -9999 0 -0.82 1 1
PIK3CA 0.015 0 -9999 0 -10000 0 0
JAK3 -0.014 0.15 -9999 0 -0.82 17 17
PIK3R1 0.011 0.045 -9999 0 -0.57 3 3
JAK1 0.015 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.044 0.11 -9999 0 -0.56 8 8
SHC1 0.015 0 -9999 0 -10000 0 0
SP1 0.017 0.044 -9999 0 -0.34 3 3
IL2RA -0.039 0.22 -9999 0 -0.72 46 46
IL2RB 0.003 0.094 -9999 0 -0.78 7 7
SOS1 0.015 0 -9999 0 -10000 0 0
IL2RG -0.013 0.15 -9999 0 -0.79 17 17
G1/S transition of mitotic cell cycle 0.031 0.091 -9999 0 -0.48 10 10
PTPN11 0.015 0 -9999 0 -10000 0 0
CCND2 0.021 0.098 -9999 0 -0.75 8 8
LCK -0.005 0.13 -9999 0 -0.82 12 12
GRB2 0.015 0 -9999 0 -10000 0 0
IL2 0.004 0.037 -9999 0 -0.82 1 1
CDK6 0 0.1 -9999 0 -0.76 9 9
CCND3 0.052 0.099 -9999 0 -0.63 2 2
S1P4 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.008 0.069 -9999 0 -0.76 4 4
CDC42/GTP -0.023 0.073 -9999 0 -0.47 4 4
PLCG1 0.016 0.088 -9999 0 -0.49 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.003 0.04 -9999 0 -0.63 2 2
cell migration -0.023 0.072 -9999 0 -0.46 4 4
S1PR5 0.008 0.064 -9999 0 -0.69 4 4
S1PR4 -0.034 0.19 -9999 0 -0.81 29 29
MAPK3 0.016 0.088 -9999 0 -0.49 4 4
MAPK1 0.016 0.088 -9999 0 -0.49 4 4
S1P/S1P5/Gi 0.023 0.064 -9999 0 -0.48 2 2
GNAI1 0.013 0.026 -9999 0 -0.57 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.006 0.054 -9999 0 -0.48 6 6
RHOA 0.003 0.12 -9999 0 -0.46 30 30
S1P/S1P4/Gi 0.008 0.093 -9999 0 -0.52 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.017 0.15 -9999 0 -0.74 20 20
S1P/S1P4/G12/G13 -0.031 0.12 -9999 0 -0.5 30 30
GNA12 0.01 0.053 -9999 0 -0.82 2 2
GNA13 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.025 0.098 -10000 0 -0.41 31 31
ATM 0.013 0.026 -10000 0 -0.57 1 1
UBE2D3 0.014 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
ATR 0.014 0 -10000 0 -10000 0 0
UBE2L3 0.014 0 -10000 0 -10000 0 0
FANCD2 0.027 0.016 -10000 0 -0.33 1 1
protein ubiquitination -0.024 0.09 -10000 0 -0.53 7 7
XRCC5 0.014 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.014 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.004 0.038 -10000 0 -0.57 1 1
FANCF 0.009 0.052 -10000 0 -0.57 4 4
BRCA1 0.014 0 -10000 0 -10000 0 0
CCNE1 0.002 0.098 -10000 0 -0.82 7 7
CDK2/Cyclin E1 -0.009 0.074 -10000 0 -0.63 7 7
FANCG 0.009 0.064 -10000 0 -0.82 3 3
BRCA1/BACH1/BARD1 -0.025 0.098 -10000 0 -0.41 31 31
FANCE 0.014 0 -10000 0 -10000 0 0
FANCC 0.014 0 -10000 0 -10000 0 0
NBN 0.014 0 -10000 0 -10000 0 0
FANCA 0.01 0.053 -10000 0 -0.82 2 2
DNA repair 0.056 0.088 -10000 0 -0.65 2 2
BRCA1/BARD1/ubiquitin -0.025 0.098 -10000 0 -0.41 31 31
BARD1/DNA-PK -0.019 0.072 -10000 0 -10000 0 0
FANCL 0.012 0.037 -10000 0 -0.82 1 1
mRNA polyadenylation 0.025 0.098 0.4 31 -10000 0 31
BRCA1/BARD1/CTIP/M/R/N Complex 0.026 0.069 -10000 0 -0.39 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.021 0.081 -10000 0 -10000 0 0
BRCA1/BARD1/P53 -0.021 0.076 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 -0.021 0.081 -10000 0 -10000 0 0
BRCA1/BACH1 0.014 0 -10000 0 -10000 0 0
BARD1 -0.022 0.14 -10000 0 -0.57 31 31
PCNA 0.012 0.037 -10000 0 -0.82 1 1
BRCA1/BARD1/UbcH5C -0.021 0.081 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 -0.021 0.081 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA -0.021 0.082 -10000 0 -0.64 2 2
BARD1/DNA-PK/P53 -0.019 0.07 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.025 0.098 -10000 0 -0.41 31 31
BRCA1/BARD1/CTIP 0.014 0.082 -10000 0 -10000 0 0
FA complex 0.038 0.041 -10000 0 -0.51 1 1
BARD1/EWS -0.025 0.098 -10000 0 -0.41 31 31
RBBP8 0.024 0.019 -10000 0 -0.41 1 1
TP53 0.009 0.052 -10000 0 -0.57 4 4
TOPBP1 0.014 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.021 0.076 -10000 0 -10000 0 0
BRCA1/BARD1 -0.024 0.091 -10000 0 -0.54 7 7
CSTF1 0.014 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.026 0.1 -10000 0 -0.42 31 31
CDK2 0.014 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.012 0.037 -10000 0 -0.82 1 1
RAD50 0.014 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.025 0.098 -10000 0 -0.41 31 31
EWSR1 0.014 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.027 0.12 -9999 0 -0.57 23 23
AKT1 0.087 0.056 -9999 0 -0.5 1 1
PTK2B 0.033 0.12 -9999 0 -0.67 2 2
VEGFR2 homodimer/Frs2 0.032 0.067 -9999 0 -0.57 6 6
CAV1 -0.05 0.22 -9999 0 -0.82 38 38
CALM1 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.012 0.077 -9999 0 -0.6 2 2
endothelial cell proliferation 0.094 0.063 -9999 0 -10000 0 0
mol:Ca2+ 0.053 0.067 -9999 0 -0.54 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.008 0.06 -9999 0 -0.56 2 2
RP11-342D11.1 0.043 0.067 -9999 0 -0.54 2 2
CDH5 0.011 0.045 -9999 0 -0.69 2 2
VEGFA homodimer -0.006 0.055 -9999 0 -0.49 6 6
SHC1 0.014 0 -9999 0 -10000 0 0
SHC2 0.004 0.087 -9999 0 -0.71 7 7
HRAS/GDP -0.007 0.052 -9999 0 -10000 0 0
SH2D2A -0.12 0.3 -9999 0 -0.82 78 78
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.009 0.047 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.084 0.19 -9999 0 -0.5 84 84
VEGFR1 homodimer 0.012 0.037 -9999 0 -0.82 1 1
SHC/GRB2/SOS1 -0.007 0.054 -9999 0 -0.53 1 1
GRB10 0.052 0.074 -9999 0 -0.6 3 3
PTPN11 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
PAK1 0.012 0.037 -9999 0 -0.82 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.009 0.062 -9999 0 -0.57 1 1
HRAS 0.012 0.037 -9999 0 -0.82 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.04 0.064 -9999 0 -0.49 2 2
HIF1A 0.013 0.026 -9999 0 -0.57 1 1
FRS2 0.007 0.074 -9999 0 -0.82 4 4
oxygen and reactive oxygen species metabolic process -0.008 0.06 -9999 0 -0.55 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.003 0.094 -9999 0 -0.78 7 7
Nck/Pak -0.001 0.028 -9999 0 -0.63 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.009 0.068 -9999 0 -0.5 9 9
mol:GDP -0.007 0.053 -9999 0 -0.52 1 1
mol:NADP 0.073 0.06 -9999 0 -10000 0 0
eNOS/Hsp90 0.076 0.057 -9999 0 -10000 0 0
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
mol:IP3 0.053 0.068 -9999 0 -0.54 2 2
HIF1A/ARNT -0.001 0.018 -9999 0 -0.41 1 1
SHB 0.011 0.037 -9999 0 -0.57 2 2
VEGFA 0.006 0.091 -9999 0 -0.81 6 6
VEGFC -0.095 0.28 -9999 0 -0.82 65 65
FAK1/Vinculin 0.059 0.086 -9999 0 -0.8 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.027 0.11 -9999 0 -0.65 3 3
PTPN6 0.014 0 -9999 0 -10000 0 0
EPAS1 0.023 0.022 -9999 0 -10000 0 0
mol:L-citrulline 0.073 0.06 -9999 0 -10000 0 0
ITGAV 0.006 0.079 -9999 0 -0.77 5 5
PIK3CA 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.011 0.072 -9999 0 -0.56 2 2
VEGFR2 homodimer/VEGFA homodimer -0.009 0.065 -9999 0 -0.59 2 2
VEGFR2/3 heterodimer 0.029 0.085 -9999 0 -0.64 7 7
VEGFB 0.012 0.037 -9999 0 -0.82 1 1
MAPK11 0.055 0.067 -9999 0 -0.54 2 2
VEGFR2 homodimer 0.036 0.05 -9999 0 -0.75 2 2
FLT1 0.012 0.037 -9999 0 -0.82 1 1
NEDD4 0.016 0.003 -9999 0 -10000 0 0
MAPK3 0.057 0.066 -9999 0 -0.52 1 1
MAPK1 0.057 0.066 -9999 0 -0.52 1 1
VEGFA145/NRP2 -0.01 0.079 -9999 0 -0.62 8 8
VEGFR1/2 heterodimer 0.035 0.051 -9999 0 -0.61 3 3
KDR 0.036 0.05 -9999 0 -0.75 2 2
VEGFA165/NRP1/VEGFR2 homodimer 0.049 0.073 -9999 0 -0.54 2 2
SRC 0.014 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.059 0.066 -9999 0 -0.53 1 1
PI3K -0.008 0.05 -9999 0 -0.57 1 1
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.008 0.064 -9999 0 -0.51 8 8
FES 0.053 0.068 -9999 0 -0.55 2 2
GAB1 -0.007 0.051 -9999 0 -0.59 1 1
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.064 -9999 0 -0.51 8 8
CTNNB1 0.013 0.026 -9999 0 -0.57 1 1
SOS1 0.014 0 -9999 0 -10000 0 0
ARNT 0.014 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.045 0.12 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Yes -0.008 0.064 -9999 0 -0.51 8 8
PI3K/GAB1 0.087 0.059 -9999 0 -0.52 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.012 0.071 -9999 0 -0.57 1 1
PRKACA 0.014 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.072 0.18 -9999 0 -1.1 2 2
HSP90AA1 0.014 0 -9999 0 -10000 0 0
CDC42 0.053 0.068 -9999 0 -0.55 2 2
actin cytoskeleton reorganization -0.083 0.19 -9999 0 -0.49 84 84
PTK2 0.054 0.091 -9999 0 -0.88 1 1
EDG1 0.043 0.067 -9999 0 -0.54 2 2
mol:DAG 0.053 0.068 -9999 0 -0.54 2 2
CaM/Ca2+ -0.007 0.054 -9999 0 -0.53 1 1
MAP2K3 0.054 0.077 -9999 0 -0.55 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 0.052 0.076 -9999 0 -0.62 3 3
PLCG1 0.053 0.068 -9999 0 -0.55 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.009 0.062 -9999 0 -0.56 2 2
IQGAP1 0.014 0 -9999 0 -10000 0 0
YES1 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.008 0.064 -9999 0 -0.51 8 8
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.008 0.064 -9999 0 -0.51 8 8
cell migration 0.082 0.077 -9999 0 -0.66 1 1
mol:PI-3-4-5-P3 0.073 0.06 -9999 0 -0.53 1 1
FYN 0.012 0.037 -9999 0 -0.82 1 1
VEGFB/NRP1 0.048 0.067 -9999 0 -0.51 2 2
mol:NO 0.073 0.06 -9999 0 -10000 0 0
PXN 0.014 0 -9999 0 -10000 0 0
HRAS/GTP -0.007 0.052 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.052 0.076 -9999 0 -0.61 3 3
VHL 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.015 0.14 -9999 0 -0.73 19 19
NOS3 0.075 0.065 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Sck -0.014 0.082 -9999 0 -0.51 12 12
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.058 0.069 -9999 0 -0.53 1 1
PRKCB 0.052 0.086 -9999 0 -0.53 1 1
VCL 0.014 0 -9999 0 -10000 0 0
VEGFA165/NRP1 0.043 0.068 -9999 0 -0.47 8 8
VEGFR1/2 heterodimer/VEGFA homodimer -0.009 0.068 -9999 0 -0.56 3 3
VEGFA165/NRP2 -0.01 0.079 -9999 0 -0.62 8 8
MAPKKK cascade 0.074 0.068 -9999 0 -0.59 1 1
NRP2 0.01 0.053 -9999 0 -0.82 2 2
VEGFC homodimer -0.095 0.28 -9999 0 -0.81 65 65
NCK1 0.014 0 -9999 0 -10000 0 0
ROCK1 0.014 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.059 0.086 -9999 0 -0.8 1 1
MAP3K13 0.047 0.08 -9999 0 -0.55 2 2
PDPK1 0.078 0.057 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.007 0.062 -9999 0 -0.55 6 6
CRKL 0.029 0.059 -9999 0 -0.44 1 1
mol:PIP3 -0.023 0.004 -9999 0 -10000 0 0
AKT1 0 0.014 -9999 0 -0.3 1 1
PTK2B 0.013 0.026 -9999 0 -0.57 1 1
RAPGEF1 0.036 0.056 -9999 0 -0.41 1 1
RANBP10 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.021 0.094 -9999 0 -0.54 9 9
MAP3K5 0.04 0.061 -9999 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS -0.021 0.089 -9999 0 -0.49 11 11
AP1 -0.03 0.13 -9999 0 -0.36 64 64
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.014 0 -9999 0 -10000 0 0
apoptosis -0.07 0.24 -9999 0 -0.7 64 64
STAT3 (dimer) 0.03 0.066 -9999 0 -0.48 1 1
GAB1/CRKL/SHP2/PI3K -0.011 0.045 -9999 0 -0.42 1 1
INPP5D 0.01 0.045 -9999 0 -0.57 3 3
CBL/CRK 0.037 0.052 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.014 0 -9999 0 -10000 0 0
PTEN 0.014 0 -9999 0 -10000 0 0
ELK1 -0.001 0.029 -9999 0 -0.26 6 6
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.031 -9999 0 -10000 0 0
PAK1 0.006 0.026 -9999 0 -0.48 1 1
HGF/MET/RANBP10 -0.021 0.094 -9999 0 -0.54 9 9
HRAS 0.023 0.083 -9999 0 -0.6 2 2
DOCK1 0.035 0.059 -9999 0 -0.41 1 1
GAB1 0.023 0.057 -9999 0 -0.28 1 1
CRK 0.03 0.055 -9999 0 -10000 0 0
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.022 0.095 -9999 0 -0.47 17 17
JUN 0.014 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET 0.004 0.053 -9999 0 -0.28 6 6
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
cell morphogenesis 0.058 0.072 -9999 0 -0.44 1 1
GRB2/SHC 0.021 0.048 -9999 0 -10000 0 0
FOS -0.061 0.19 -9999 0 -0.57 64 64
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.001 0.029 -9999 0 -0.26 6 6
HGF/MET/MUC20 -0.022 0.095 -9999 0 -0.42 26 26
cell migration 0.02 0.047 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
MET/RANBP10 -0.007 0.062 -9999 0 -0.55 6 6
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.024 0.069 -9999 0 -0.52 1 1
MET/MUC20 -0.007 0.063 -9999 0 -0.56 6 6
RAP1B 0.042 0.057 -9999 0 -0.4 1 1
RAP1A 0.043 0.053 -9999 0 -10000 0 0
HGF/MET/RANBP9 -0.021 0.094 -9999 0 -0.54 9 9
RAF1 0.031 0.079 -9999 0 -0.56 2 2
STAT3 0.03 0.067 -9999 0 -0.49 1 1
cell proliferation 0.04 0.083 -9999 0 -0.44 1 1
RPS6KB1 0.011 0.02 -9999 0 -10000 0 0
MAPK3 -0.007 0.026 -9999 0 -0.26 4 4
MAPK1 -0.007 0.026 -9999 0 -0.26 4 4
RANBP9 0.014 0 -9999 0 -10000 0 0
MAPK8 0.05 0.082 -9999 0 -0.48 7 7
SRC 0.031 0.065 -9999 0 -0.48 1 1
PI3K 0.019 0.055 -9999 0 -0.45 1 1
MET/Glomulin 0.007 0.057 -9999 0 -0.5 6 6
SOS1 0.014 0 -9999 0 -10000 0 0
MAP2K1 0.038 0.074 -9999 0 -0.51 2 2
MET 0.005 0.083 -9999 0 -0.74 6 6
MAP4K1 0.034 0.064 -9999 0 -10000 0 0
PTK2 0.014 0 -9999 0 -10000 0 0
MAP2K2 0.038 0.074 -9999 0 -0.51 2 2
BAD 0.007 0.013 -9999 0 -10000 0 0
MAP2K4 0.047 0.057 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.011 0.048 -9999 0 -10000 0 0
INPPL1 0.014 0 -9999 0 -10000 0 0
PXN 0.014 0 -9999 0 -10000 0 0
SH3KBP1 0.01 0.053 -9999 0 -0.82 2 2
HGS 0.013 0.05 -9999 0 -10000 0 0
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.012 0.13 -9999 0 -0.63 20 20
RASA1 0.011 0.037 -9999 0 -0.57 2 2
NCK1 0.014 0 -9999 0 -10000 0 0
PTPRJ 0.014 0 -9999 0 -10000 0 0
NCK/PLCgamma1 0.022 0.051 -9999 0 -10000 0 0
PDPK1 -0.011 0.015 -9999 0 -0.33 1 1
HGF/MET/SHIP -0.023 0.099 -9999 0 -0.55 10 10
Hedgehog signaling events mediated by Gli proteins

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
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.015 0.073 -9999 0 -0.54 2 2
forebrain development -0.023 0.15 -9999 0 -0.5 17 17
GNAO1 0.007 0.069 -9999 0 -0.76 4 4
SMO/beta Arrestin2 0.003 0.087 -9999 0 -0.42 20 20
SMO -0.01 0.12 -9999 0 -0.58 20 20
ARRB2 0.013 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.056 0.035 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0.014 0 -9999 0 -10000 0 0
GNAI2 0.013 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex 0.006 0.027 -9999 0 -0.49 1 1
GNAI1 0.012 0.026 -9999 0 -0.57 1 1
XPO1 0.015 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.061 0.11 -9999 0 -0.48 7 7
SAP30 0.012 0.037 -9999 0 -0.82 1 1
mol:GDP -0.01 0.12 -9999 0 -0.58 20 20
MIM/GLI2A 0.012 0.025 -9999 0 -10000 0 0
IFT88 0.014 0 -9999 0 -10000 0 0
GNAI3 0.013 0.005 -9999 0 -10000 0 0
GLI2 0.024 0.067 -9999 0 -10000 0 0
GLI3 0.051 0.038 -9999 0 -10000 0 0
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.014 0 -9999 0 -10000 0 0
GNG2 0.012 0.037 -9999 0 -0.82 1 1
Gi family/GTP 0.013 0.089 -9999 0 -0.5 6 6
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.057 0.034 -9999 0 -10000 0 0
GLI2/Su(fu) 0.03 0.072 -9999 0 -10000 0 0
FOXA2 -0.095 0.23 -9999 0 -0.66 69 69
neural tube patterning -0.023 0.15 -9999 0 -0.5 17 17
SPOP 0.014 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.023 0.046 -9999 0 -0.36 1 1
GNB1 0.014 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
CSNK1G3 0.014 0 -9999 0 -10000 0 0
MTSS1 0.012 0.025 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.023 0.15 -9999 0 -0.5 17 17
SUFU 0.019 0.051 -9999 0 -0.41 1 1
LGALS3 0.011 0.037 -9999 0 -0.57 2 2
catabolic process 0.063 0.056 -9999 0 -10000 0 0
GLI3A/CBP -0.024 0.12 -9999 0 -10000 0 0
KIF3A 0.014 0 -9999 0 -10000 0 0
GLI1 -0.024 0.16 -9999 0 -0.51 17 17
RAB23 0.01 0.053 -9999 0 -0.82 2 2
CSNK1A1 0.014 0 -9999 0 -10000 0 0
IFT172 0.014 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.021 0.052 -9999 0 -0.48 1 1
GNAZ -0.018 0.15 -9999 0 -0.74 20 20
RBBP4 0.013 0.026 -9999 0 -0.56 1 1
CSNK1G1 0.014 0 -9999 0 -10000 0 0
PIAS1 0.014 0 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
GLI2/SPOP 0.029 0.062 -9999 0 -10000 0 0
STK36 0.014 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.021 0.08 -9999 0 -0.43 6 6
PTCH1 -0.02 0.18 -9999 0 -1.1 6 6
MIM/GLI1 -0.04 0.21 -9999 0 -0.66 20 20
CREBBP -0.024 0.12 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.051 0.02 -9999 0 -10000 0 0
Aurora A signaling

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
Aurora A/GADD45A 0.02 0.053 -9999 0 -0.54 1 1
BIRC5 -0.023 0.17 -9999 0 -0.82 22 22
NFKBIA 0.024 0.054 -9999 0 -0.54 1 1
CPEB1 -0.07 0.22 -9999 0 -0.63 64 64
AKT1 0.025 0.047 -9999 0 -10000 0 0
NDEL1 0.014 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.005 0.039 -9999 0 -10000 0 0
NDEL1/TACC3 -0.006 0.046 -9999 0 -0.47 2 2
GADD45A 0.012 0.037 -9999 0 -0.82 1 1
GSK3B 0.013 0.004 -9999 0 -10000 0 0
PAK1/Aurora A 0.02 0.053 -9999 0 -0.54 1 1
MDM2 0.014 0 -9999 0 -10000 0 0
JUB 0.013 0.026 -9999 0 -0.57 1 1
TPX2 0.013 0.087 -9999 0 -0.63 9 9
TP53 0.024 0.043 -9999 0 -0.3 4 4
DLG7 0.014 0.047 -9999 0 -0.3 10 10
AURKAIP1 0.01 0.053 -9999 0 -0.82 2 2
ARHGEF7 0.014 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.006 0.049 -9999 0 -0.49 2 2
G2/M transition of mitotic cell cycle -0.005 0.039 -9999 0 -10000 0 0
AURKA 0.017 0.056 -9999 0 -0.36 10 10
AURKB -0.007 0.038 -9999 0 -0.25 10 10
CDC25B 0.012 0.082 -9999 0 -0.45 4 4
G2/M transition checkpoint -0.005 0.044 -9999 0 -0.54 1 1
mRNA polyadenylation -0.05 0.13 -9999 0 -0.51 16 16
Aurora A/CPEB -0.05 0.13 -9999 0 -0.52 16 16
Aurora A/TACC1/TRAP/chTOG -0.005 0.039 -9999 0 -10000 0 0
BRCA1 0.014 0 -9999 0 -10000 0 0
centrosome duplication 0.02 0.053 -9999 0 -0.54 1 1
regulation of centrosome cycle -0.006 0.046 -9999 0 -0.46 2 2
spindle assembly -0.005 0.038 -9999 0 -10000 0 0
TDRD7 0.014 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.025 0.11 -9999 0 -0.5 22 22
CENPA -0.007 0.039 -9999 0 -0.33 5 5
Aurora A/PP2A 0.021 0.046 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.031 0.043 -9999 0 -10000 0 0
negative regulation of DNA binding 0.024 0.043 -9999 0 -0.3 4 4
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.011 0.037 -9999 0 -0.57 2 2
Ajuba/Aurora A -0.005 0.045 -9999 0 -0.55 1 1
mitotic prometaphase 0.001 0.01 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.056 -9999 0 -0.35 10 10
TACC1 0.011 0.037 -9999 0 -0.57 2 2
TACC3 0.01 0.053 -9999 0 -0.82 2 2
Aurora A/Antizyme1 -0.007 0.049 -9999 0 -0.5 2 2
Aurora A/RasGAP 0.02 0.052 -9999 0 -0.34 2 2
OAZ1 0.014 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.004 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.001 0.024 -9999 0 -0.54 1 1
Importin alpha/Importin beta/TPX2 0.013 0.087 -9999 0 -0.63 9 9
PPP2R5D 0.014 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.02 0.085 -9999 0 -0.52 9 9
PAK1 0.012 0.037 -9999 0 -0.82 1 1
CKAP5 0.014 0 -9999 0 -10000 0 0
Aurora C signaling

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
INCENP 0.014 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.014 0.086 -9999 0 -0.52 13 13
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.004 0.022 -9999 0 -10000 0 0
AURKB -0.001 0.11 -9999 0 -0.82 9 9
AURKC 0.005 0.083 -9999 0 -0.74 6 6
ceramide signaling pathway

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
MAP4K4 0.035 0.082 -9999 0 -0.4 9 9
BAG4 0.011 0.037 -9999 0 -0.57 2 2
BAD 0.029 0.03 -9999 0 -10000 0 0
NFKBIA 0.012 0.037 -9999 0 -0.82 1 1
BIRC3 -0.022 0.17 -9999 0 -0.82 21 21
BAX 0.029 0.03 -9999 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.012 0.022 -9999 0 -0.095 9 9
IKBKB 0.042 0.078 -9999 0 -0.38 5 5
MAP2K2 0.041 0.032 -9999 0 -10000 0 0
MAP2K1 0.041 0.032 -9999 0 -10000 0 0
SMPD1 0.018 0.022 -9999 0 -10000 0 0
GO:0005551 0 0 -9999 0 -10000 0 0
FADD/Caspase 8 -0.012 0.17 -9999 0 -0.65 7 7
MAP2K4 0.036 0.03 -9999 0 -10000 0 0
protein ubiquitination 0.043 0.079 -9999 0 -0.38 9 9
EnzymeConsortium:2.7.1.37 0.046 0.035 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
RAF1 0.036 0.032 -9999 0 -10000 0 0
CRADD 0.014 0 -9999 0 -10000 0 0
mol:ceramide 0.022 0.031 -9999 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin -0.001 0.025 -9999 0 -0.55 1 1
MADD 0.014 0 -9999 0 -10000 0 0
MAP3K1 0.029 0.031 -9999 0 -10000 0 0
TRADD 0.014 0 -9999 0 -10000 0 0
RELA/p50 0.014 0 -9999 0 -10000 0 0
MAPK3 0.044 0.031 -9999 0 -10000 0 0
MAPK1 0.044 0.031 -9999 0 -10000 0 0
p50/RELA/I-kappa-B-alpha -0.001 0.028 -9999 0 -0.63 1 1
FADD -0.021 0.18 -9999 0 -0.44 64 64
KSR1 0.029 0.031 -9999 0 -10000 0 0
MAPK8 0.038 0.044 -9999 0 -0.3 2 2
TRAF2 0.002 0.098 -9999 0 -0.82 7 7
response to radiation 0 0 -9999 0 -10000 0 0
CHUK 0.042 0.078 -9999 0 -10000 0 0
TNF R/SODD -0.001 0.026 -9999 0 -0.41 2 2
TNF -0.025 0.17 -9999 0 -0.79 24 24
CYCS 0.032 0.031 -9999 0 -10000 0 0
IKBKG 0.042 0.078 -9999 0 -0.38 5 5
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.028 0.085 -9999 0 -0.43 9 9
RELA 0.014 0 -9999 0 -10000 0 0
RIPK1 0.014 0 -9999 0 -10000 0 0
AIFM1 0.032 0.031 -9999 0 -10000 0 0
TNF/TNF R/SODD -0.026 0.11 -9999 0 -0.54 21 21
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
response to heat 0 0 -9999 0 -10000 0 0
CASP8 0.028 0.022 -9999 0 -10000 0 0
NSMAF 0.035 0.081 -9999 0 -0.4 9 9
response to hydrogen peroxide 0 0 -9999 0 -10000 0 0
BCL2 0.002 0.09 -9999 0 -0.69 8 8
Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.014 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.017 0.13 -9999 0 -0.57 26 26
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.014 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.019 0.045 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.014 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
FYN 0.012 0.037 -9999 0 -0.82 1 1
MAP3K12 0.011 0.045 -9999 0 -0.69 2 2
FGR 0.012 0.037 -9999 0 -0.82 1 1
p38 alpha/TAB1 -0.018 0.04 -9999 0 -10000 0 0
PRKG1 -0.021 0.15 -9999 0 -0.65 26 26
DUSP8 0.014 0 -9999 0 -10000 0 0
PGK/cGMP/p38 alpha -0.031 0.076 -9999 0 -0.39 13 13
apoptosis -0.017 0.039 -9999 0 -10000 0 0
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.012 0.037 -9999 0 -0.82 1 1
DUSP1 -0.015 0.13 -9999 0 -0.57 25 25
PAK1 0.012 0.037 -9999 0 -0.82 1 1
SRC 0.014 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.01 0.067 -9999 0 -0.49 9 9
TRAF6 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 -0.001 0.11 -9999 0 -0.82 9 9
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.024 0.093 -9999 0 -0.37 4 4
BLK -0.1 0.28 -9999 0 -0.78 71 71
HCK 0.006 0.079 -9999 0 -0.77 5 5
MAP2K3 0.013 0.026 -9999 0 -0.57 1 1
DUSP16 0.014 0 -9999 0 -10000 0 0
DUSP10 0.012 0.037 -9999 0 -0.82 1 1
TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.032 0.067 -9999 0 -10000 0 0
positive regulation of innate immune response 0.032 0.1 -9999 0 -0.4 1 1
LCK -0.006 0.13 -9999 0 -0.82 12 12
p38alpha-beta/MKP7 0.037 0.096 -9999 0 -10000 0 0
p38alpha-beta/MKP5 0.036 0.098 -9999 0 -10000 0 0
PGK/cGMP -0.026 0.11 -9999 0 -0.49 26 26
PAK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.024 0.12 -9999 0 -0.5 3 3
CDC42 0.014 0 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
PAK3 -0.018 0.15 -9999 0 -0.82 17 17
Class I PI3K signaling events

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
ARF5/GTP -0.002 0.029 -9999 0 -10000 0 0
DAPP1 0.015 0.091 -9999 0 -0.37 4 4
Src family/SYK family/BLNK-LAT/BTK-ITK 0.001 0.16 -9999 0 -0.65 15 15
mol:DAG 0.029 0.087 -9999 0 -0.3 9 9
HRAS 0.013 0.037 -9999 0 -0.82 1 1
RAP1A 0.014 0.002 -9999 0 -10000 0 0
ARF5/GDP 0.04 0.041 -9999 0 -0.3 1 1
PLCG2 0.013 0.026 -9999 0 -0.57 1 1
PLCG1 0.014 0 -9999 0 -10000 0 0
ARF5 0.014 0 -9999 0 -10000 0 0
mol:GTP -0.002 0.031 -9999 0 -0.41 3 3
ARF1/GTP -0.002 0.028 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
YES1 0.014 0 -9999 0 -10000 0 0
RAP1A/GTP -0.002 0.031 -9999 0 -0.4 3 3
ADAP1 -0.003 0.032 -9999 0 -10000 0 0
ARAP3 -0.002 0.031 -9999 0 -0.4 3 3
INPPL1 0.014 0 -9999 0 -10000 0 0
PREX1 0.014 0 -9999 0 -10000 0 0
ARHGEF6 0.008 0.058 -9999 0 -0.57 5 5
ARHGEF7 0.014 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
NRAS 0.015 0.002 -9999 0 -10000 0 0
FYN 0.012 0.037 -9999 0 -0.82 1 1
ARF6 0.014 0 -9999 0 -10000 0 0
FGR 0.012 0.037 -9999 0 -0.82 1 1
mol:Ca2+ 0.027 0.047 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.007 0.063 -9999 0 -0.57 6 6
ZAP70 -0.026 0.17 -9999 0 -0.78 25 25
mol:IP3 0.031 0.063 -9999 0 -10000 0 0
LYN 0.012 0.037 -9999 0 -0.82 1 1
ARF1/GDP 0.04 0.041 -9999 0 -10000 0 0
RhoA/GDP -0.003 0.029 -9999 0 -0.42 1 1
PDK1/Src/Hsp90 -0.001 0.015 -9999 0 -10000 0 0
BLNK -0.042 0.17 -9999 0 -0.57 48 48
actin cytoskeleton reorganization 0.062 0.044 -9999 0 -0.41 1 1
SRC 0.014 0 -9999 0 -10000 0 0
PLEKHA2 0.03 0.028 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
PTEN 0 0.004 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.002 0.029 -9999 0 -10000 0 0
RhoA/GTP -0.002 0.029 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.018 0.17 -9999 0 -0.69 17 17
BLK -0.1 0.28 -9999 0 -0.78 71 71
PDPK1 0.013 0.026 -9999 0 -0.57 1 1
CYTH1 -0.002 0.029 -9999 0 -10000 0 0
HCK 0.006 0.079 -9999 0 -0.77 5 5
CYTH3 -0.002 0.029 -9999 0 -10000 0 0
CYTH2 -0.002 0.029 -9999 0 -10000 0 0
KRAS 0.011 0.053 -9999 0 -0.82 2 2
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.004 0.034 -9999 0 -0.44 2 2
SGK1 -0.004 0.037 -9999 0 -0.48 2 2
INPP5D 0.01 0.045 -9999 0 -0.57 3 3
mol:GDP 0.034 0.043 -9999 0 -0.32 1 1
SOS1 0.014 0 -9999 0 -10000 0 0
SYK 0.01 0.045 -9999 0 -0.57 3 3
ARF6/GDP -0.003 0.029 -9999 0 -0.42 1 1
mol:PI-3-4-5-P3 -0.002 0.031 -9999 0 -0.41 3 3
ARAP3/RAP1A/GTP -0.002 0.031 -9999 0 -0.41 3 3
VAV1 0.003 0.082 -9999 0 -0.59 9 9
mol:PI-3-4-P2 0.022 0.033 -9999 0 -0.41 3 3
RAS family/GTP/PI3K Class I 0.031 0.035 -9999 0 -0.42 3 3
PLEKHA1 0.03 0.028 -9999 0 -10000 0 0
Rac1/GDP 0.04 0.041 -9999 0 -10000 0 0
LAT -0.011 0.14 -9999 0 -0.82 15 15
Rac1/GTP 0.035 0.055 -9999 0 -0.34 1 1
ITK -0.014 0.07 -9999 0 -0.43 8 8
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.028 0.11 -9999 0 -0.45 9 9
LCK -0.006 0.13 -9999 0 -0.82 12 12
BTK -0.004 0.04 -9999 0 -0.43 2 2
Arf6 trafficking events

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
SLC2A4 -0.25 0.29 -10000 0 -0.57 223 223
CLTC 0.034 0.014 -10000 0 -10000 0 0
calcium ion-dependent exocytosis 0.028 0.013 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.022 -10000 0 -0.5 1 1
EXOC4 0.014 0 -10000 0 -10000 0 0
CD59 0.03 0.01 -10000 0 -10000 0 0
CPE 0.013 0.063 -10000 0 -0.55 6 6
CTNNB1 0.013 0.026 -10000 0 -0.57 1 1
membrane fusion 0.027 0.014 -10000 0 -10000 0 0
CTNND1 0.033 0.022 -10000 0 -0.46 1 1
DNM2 0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.034 0.009 -10000 0 -10000 0 0
TSHR 0.001 0.098 -10000 0 -0.55 15 15
INS 0.012 0.017 -10000 0 -0.26 2 2
BIN1 0 0.1 -10000 0 -0.76 9 9
mol:Choline 0.027 0.014 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.026 -10000 0 -0.55 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.022 -10000 0 -0.5 1 1
JUP 0.03 0.02 -10000 0 -0.28 1 1
ASAP2/amphiphysin II -0.008 0.062 -10000 0 -0.5 7 7
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.028 0.026 -10000 0 -0.28 1 1
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.014 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.014 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.046 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.014 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.003 0.025 0.39 1 -10000 0 1
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 0.025 0.016 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.015 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.039 0.015 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.014 0 -10000 0 -10000 0 0
exocyst 0.047 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.033 0.022 -10000 0 -0.46 1 1
NME1 0.019 0.026 -10000 0 -0.55 1 1
clathrin coat assembly 0.034 0.014 -10000 0 -10000 0 0
IL2RA 0.007 0.074 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.11 0.12 -10000 0 -0.4 3 3
EXOC6 0.014 0 -10000 0 -10000 0 0
PLD1 -0.002 0.021 -10000 0 -0.28 3 3
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.014 0 -10000 0 -10000 0 0
PIP5K1C 0.035 0.009 -10000 0 -10000 0 0
SDC1 0.03 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.025 -10000 0 -0.55 1 1
EXOC7 0.014 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.003 0.025 -10000 0 -0.4 1 1
mol:Phosphatidic acid 0.027 0.014 -10000 0 -10000 0 0
endocytosis 0.008 0.062 0.5 7 -10000 0 7
SCAMP2 0.014 0 -10000 0 -10000 0 0
ADRB2 0.019 0.08 -10000 0 -0.53 1 1
EXOC3 0.014 0 -10000 0 -10000 0 0
ASAP2 0.014 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.026 0.023 -10000 0 -0.5 1 1
KLC1 0.014 0 -10000 0 -10000 0 0
AVPR2 0.024 0.068 -10000 0 -10000 0 0
RALA 0.014 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.002 0.023 -10000 0 -10000 0 0
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.011 0.007 -10000 0 -10000 0 0
BUB1B 0.022 0.025 -10000 0 -10000 0 0
PLK1 0.017 0.022 -10000 0 -0.17 1 1
PLK1S1 0.015 0.014 -10000 0 -0.17 1 1
KIF2A 0.024 0.019 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.017 0.022 -10000 0 -0.17 1 1
GOLGA2 0.014 0 -10000 0 -10000 0 0
Hec1/SPC24 0.01 0.1 -10000 0 -0.48 21 21
WEE1 0.022 0.027 -10000 0 -10000 0 0
cytokinesis 0.03 0.033 -10000 0 -10000 0 0
PP2A-alpha B56 0.036 0.013 -10000 0 -10000 0 0
AURKA 0.012 0.032 -10000 0 -0.18 11 11
PICH/PLK1 0.023 0.085 -10000 0 -0.39 20 20
CENPE 0.024 0.019 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.024 0.019 -10000 0 -10000 0 0
PPP2CA 0.014 0 -10000 0 -10000 0 0
FZR1 0.014 0 -10000 0 -10000 0 0
TPX2 0.012 0.028 -10000 0 -0.18 9 9
PAK1 0.012 0.037 -10000 0 -0.81 1 1
SPC24 -0.006 0.13 -10000 0 -0.82 12 12
FBXW11 0.014 0 -10000 0 -10000 0 0
CLSPN 0.012 0.033 -10000 0 -0.21 9 9
GORASP1 0.014 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -0.015 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.009 0.011 -10000 0 -0.067 5 5
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.013 11 11
STAG2 0.014 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP 0 0.009 -10000 0 -10000 0 0
spindle elongation 0.017 0.022 -10000 0 -0.17 1 1
ODF2 0.013 0.002 -10000 0 -10000 0 0
BUB1 -0.001 0.01 -10000 0 -10000 0 0
TPT1 0.015 0.011 -10000 0 -10000 0 0
CDC25C 0.011 0.042 -10000 0 -0.26 11 11
CDC25B -0.019 0.16 -10000 0 -0.81 20 20
SGOL1 0.011 0.007 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.017 0.078 -10000 0 -0.4 20 20
CDC14B 0.009 0.034 -10000 0 -0.42 3 3
CDC20 0 0.1 -10000 0 -0.82 8 8
PLK1/PBIP1 -0.004 0.033 -10000 0 -0.49 2 2
mitosis 0.001 0.007 0.041 11 -10000 0 11
FBXO5 0.021 0.02 -10000 0 -10000 0 0
CDC2 0.001 0.004 -10000 0 -0.017 20 20
NDC80 -0.001 0.11 -10000 0 -0.82 9 9
metaphase plate congression 0.016 0.012 -10000 0 -10000 0 0
ERCC6L -0.015 0.073 -10000 0 -0.37 20 20
NLP/gamma Tubulin 0.014 0.012 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.015 0.011 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -0.011 4 4
PPP1R12A 0.014 0.001 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -0.011 4 4
PLK1/PRC1-2 0.031 0.018 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 -0.001 0.01 -10000 0 -10000 0 0
RAB1A 0.014 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.016 0.049 -10000 0 -0.47 4 4
mitotic prometaphase 0 0.001 -10000 0 -0.01 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.031 -10000 0 -0.38 1 1
microtubule-based process 0.023 0.019 -10000 0 -10000 0 0
Golgi organization 0.017 0.022 -10000 0 -0.17 1 1
Cohesin/SA2 -0.002 0.012 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0.001 -10000 0 -10000 0 0
KIF20A 0.014 0 -10000 0 -10000 0 0
APC/C/CDC20 0.015 0.072 -10000 0 -0.53 8 8
PPP2R1A 0.014 0 -10000 0 -10000 0 0
chromosome segregation -0.004 0.033 -10000 0 -0.48 2 2
PRC1 0.014 0 -10000 0 -10000 0 0
ECT2 0.019 0.055 -10000 0 -0.49 5 5
C13orf34 0.017 0.048 -10000 0 -0.48 4 4
NUDC 0.016 0.013 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.022 0.024 -10000 0 -10000 0 0
spindle assembly 0.017 0.017 -10000 0 -0.12 1 1
spindle stabilization 0.015 0.014 -10000 0 -0.17 1 1
APC/C/HCDH1 0.017 0.029 -10000 0 -0.35 3 3
MKLP2/PLK1 0.023 0.019 -10000 0 -10000 0 0
CCNB1 0.014 0.003 -10000 0 -10000 0 0
PPP1CB 0.014 0.001 -10000 0 -10000 0 0
BTRC 0.014 0 -10000 0 -10000 0 0
ROCK2 0.016 0.061 -10000 0 -0.42 9 9
TUBG1 0.015 0.011 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.016 0.077 -10000 0 -0.39 20 20
MLF1IP 0.01 0.042 -10000 0 -0.65 2 2
INCENP 0.014 0.001 -10000 0 -10000 0 0
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.014 0 -10000 0 -10000 0 0
NFATC1 0.061 0.018 -10000 0 -10000 0 0
NFATC2 0.024 0.063 -10000 0 -0.35 5 5
NFATC3 0.025 0.019 -10000 0 -0.39 1 1
YWHAE 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.012 0.077 -10000 0 -0.38 4 4
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.039 0.1 -10000 0 -0.57 7 7
BCL2/BAX -0.008 0.067 -10000 0 -0.52 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.002 -10000 0 -10000 0 0
CaM/Ca2+ 0.012 0.002 -10000 0 -10000 0 0
BAX 0.014 0 -10000 0 -10000 0 0
MAPK14 0.014 0.002 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.018 0.072 -10000 0 -0.37 2 2
Calcineurin A alpha-beta B1/BCL2 0.002 0.09 -10000 0 -0.69 8 8
FKBP8 0.014 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.018 0.071 0.37 2 -10000 0 2
KPNB1 0.014 0 -10000 0 -10000 0 0
KPNA2 0.014 0 -10000 0 -10000 0 0
XPO1 0.014 0 -10000 0 -10000 0 0
SFN 0.006 0.074 -10000 0 -0.72 5 5
MAP3K8 0.011 0.045 -10000 0 -0.57 3 3
NFAT4/CK1 alpha 0 0.01 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.015 0.053 -10000 0 -10000 0 0
CABIN1 0.011 0.077 -10000 0 -0.39 4 4
CALM1 0.014 0.002 -10000 0 -10000 0 0
RAN 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.014 0 -10000 0 -10000 0 0
CAMK4 -0.031 0.18 -10000 0 -0.78 28 28
mol:Ca2+ 0.001 0.002 -10000 0 -10000 0 0
MAPK3 0.014 0 -10000 0 -10000 0 0
YWHAH 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.032 0.14 -10000 0 -0.63 25 25
YWHAB 0.014 0 -10000 0 -10000 0 0
MAPK8 0.006 0.068 -10000 0 -0.57 7 7
MAPK9 0.014 0 -10000 0 -10000 0 0
YWHAG 0.014 0 -10000 0 -10000 0 0
FKBP1A 0.014 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.001 0.019 -10000 0 -10000 0 0
PRKCH 0.014 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.026 -10000 0 -0.4 2 2
CASP3 0.014 0.002 -10000 0 -10000 0 0
PIM1 0.013 0.026 -10000 0 -0.57 1 1
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.003 0.021 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.045 0.02 -10000 0 -10000 0 0
PRKCB 0.001 0.1 -10000 0 -0.79 8 8
PRKCE 0.013 0.026 -10000 0 -0.57 1 1
JNK2/NFAT4 0.03 0.017 -10000 0 -0.35 1 1
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.014 0 -10000 0 -10000 0 0
NUP214 0.014 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.026 -10000 0 -0.57 1 1
PRKCA 0.011 0.045 -10000 0 -0.69 2 2
PRKCG -0.082 0.26 -10000 0 -0.82 55 55
PRKCQ 0 0.093 -10000 0 -0.61 11 11
FKBP38/BCL2 -0.008 0.067 -10000 0 -0.52 8 8
EP300 0.012 0.037 -10000 0 -0.56 2 2
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
NFATc/JNK1 0.062 0.038 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.022 0.003 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.029 0.12 -10000 0 -0.52 28 28
NFATc/ERK1 0.066 0.017 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.039 0.1 -10000 0 -0.57 7 7
NR4A1 0.049 0.096 -10000 0 -0.55 9 9
GSK3B 0.014 0.002 -10000 0 -10000 0 0
positive T cell selection 0.025 0.019 -10000 0 -0.39 1 1
NFAT1/CK1 alpha -0.012 0.037 -10000 0 -0.36 2 2
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0.002 -10000 0 -10000 0 0
AKAP5 -0.028 0.18 -10000 0 -0.82 25 25
MEF2D 0.014 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.066 0.019 -10000 0 -10000 0 0
CREBBP 0.014 0.002 -10000 0 -10000 0 0
BCL2 0.002 0.09 -10000 0 -0.69 8 8
TCGA08_rtk_signaling

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
PDGFRA 0.002 0.086 -9999 0 -0.62 9 9
HRAS 0.012 0.037 -9999 0 -0.82 1 1
EGFR -0.017 0.15 -9999 0 -0.76 20 20
AKT 0.037 0.049 -9999 0 -0.3 9 9
FOXO3 0.014 0 -9999 0 -10000 0 0
AKT1 0.014 0 -9999 0 -10000 0 0
FOXO1 0.014 0 -9999 0 -10000 0 0
AKT3 -0.001 0.11 -9999 0 -0.82 9 9
FOXO4 0.011 0.037 -9999 0 -0.57 2 2
MET 0.005 0.083 -9999 0 -0.74 6 6
PIK3CA 0.014 0 -9999 0 -10000 0 0
PIK3CB 0.014 0 -9999 0 -10000 0 0
NRAS 0.014 0 -9999 0 -10000 0 0
PIK3CG -0.019 0.16 -9999 0 -0.76 21 21
PIK3R3 0.014 0 -9999 0 -10000 0 0
PIK3R2 0.014 0 -9999 0 -10000 0 0
NF1 0.014 0 -9999 0 -10000 0 0
RAS 0.016 0.048 -9999 0 -0.34 1 1
ERBB2 0.009 0.064 -9999 0 -0.82 3 3
proliferation/survival/translation -0.031 0.026 -9999 0 -10000 0 0
PI3K 0.024 0.052 -9999 0 -0.26 3 3
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
KRAS 0.01 0.053 -9999 0 -0.82 2 2
FOXO 0.048 0.029 -9999 0 -10000 0 0
AKT2 0.014 0 -9999 0 -10000 0 0
PTEN 0.014 0 -9999 0 -10000 0 0
E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin -0.005 0.051 -9999 0 -0.66 2 2
E-cadherin/beta catenin -0.005 0.044 -9999 0 -0.41 6 6
CTNNB1 0.013 0.026 -9999 0 -0.57 1 1
JUP 0.011 0.037 -9999 0 -0.57 2 2
CDH1 0.008 0.058 -9999 0 -0.57 5 5
Canonical NF-kappaB pathway

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
FBXW11 0.017 0.006 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.086 0.033 -9999 0 -10000 0 0
ERC1 0.014 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.005 0.051 -9999 0 -0.5 5 5
NFKBIA 0.048 0.036 -9999 0 -0.76 1 1
BIRC2 -0.005 0.12 -9999 0 -0.82 11 11
IKBKB 0.014 0 -9999 0 -10000 0 0
RIPK2 0.014 0 -9999 0 -10000 0 0
IKBKG -0.006 0.033 -9999 0 -10000 0 0
IKK complex/A20 -0.022 0.086 -9999 0 -0.58 2 2
NEMO/A20/RIP2 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
NEMO/ATM 0.047 0.042 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.005 0.025 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 0.007 0.069 -9999 0 -0.67 5 5
NFKB1 0.017 0.006 -9999 0 -10000 0 0
RELA 0.017 0.006 -9999 0 -10000 0 0
MALT1 0.014 0 -9999 0 -10000 0 0
cIAP1/UbcH5C -0.014 0.092 -9999 0 -0.63 11 11
ATM 0.013 0.026 -9999 0 -0.57 1 1
TNF/TNFR1A -0.029 0.13 -9999 0 -0.6 24 24
TRAF6 0.014 0 -9999 0 -10000 0 0
PRKCA 0.011 0.045 -9999 0 -0.69 2 2
CHUK 0.014 0 -9999 0 -10000 0 0
UBE2D3 0.014 0 -9999 0 -10000 0 0
TNF -0.025 0.17 -9999 0 -0.79 24 24
NF kappa B1 p50/RelA -0.001 0.015 -9999 0 -10000 0 0
BCL10 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.048 0.036 -9999 0 -0.75 1 1
beta TrCP1/SCF ubiquitin ligase complex 0.017 0.006 -9999 0 -10000 0 0
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
IKK complex 0.054 0.039 -9999 0 -10000 0 0
CYLD 0.014 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.006 0.036 -9999 0 -10000 0 0
Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5 -0.001 0.022 -9999 0 -0.49 1 1
HDAC3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.001 0.028 -9999 0 -0.63 1 1
GATA1/HDAC5 -0.001 0.028 -9999 0 -0.63 1 1
GATA2/HDAC5 -0.006 0.059 -9999 0 -0.58 5 5
HDAC5/BCL6/BCoR -0.001 0.015 -9999 0 -10000 0 0
HDAC9 -0.035 0.2 -9999 0 -0.82 29 29
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
GATA2 0.006 0.079 -9999 0 -0.77 5 5
HDAC4/RFXANK -0.001 0.028 -9999 0 -0.63 1 1
BCOR 0.013 0.026 -9999 0 -0.57 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.014 0 -9999 0 -10000 0 0
HDAC5 0.014 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.001 0.028 -9999 0 -0.63 1 1
Histones 0.029 0.057 -9999 0 -10000 0 0
ADRBK1 0.014 0 -9999 0 -10000 0 0
HDAC4 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.014 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.014 0 -9999 0 -10000 0 0
HDAC6 0.014 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.028 -9999 0 -0.63 1 1
CAMK4 -0.031 0.18 -9999 0 -0.78 28 28
Tubulin/HDAC6 0 0 -9999 0 -10000 0 0
SUMO1 0.014 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
GATA1 0.009 0.038 -9999 0 -0.82 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
NR3C1 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -10000 0 0
SRF 0.014 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin 0 0 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
RANGAP1 0.014 0 -9999 0 -10000 0 0
BCL6/BCoR -0.001 0.018 -9999 0 -0.41 1 1
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.029 0.12 -9999 0 -0.54 24 24
HDAC4/ER alpha -0.032 0.13 -9999 0 -0.52 31 31
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.029 0.057 -9999 0 -10000 0 0
cell motility 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.014 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.014 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.031 0.18 -9999 0 -0.7 31 31
HDAC6/HDAC11 -0.001 0.018 -9999 0 -0.41 1 1
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0 0.1 -9999 0 -0.69 10 10
RAN 0.014 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.007 0.053 -9999 0 -0.46 5 5
GNG2 0.012 0.037 -9999 0 -0.82 1 1
NCOR2 0.014 0 -9999 0 -10000 0 0
TUBB2A 0.014 0 -9999 0 -10000 0 0
HDAC11 0.013 0.026 -9999 0 -0.57 1 1
HSP90AA1 0.014 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
ANKRA2 0.014 0 -9999 0 -10000 0 0
RFXANK 0.012 0.037 -9999 0 -0.82 1 1
nuclear import -0.031 0 -9999 0 -10000 0 0
S1P5 pathway

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
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.011 0.048 0.43 2 -10000 0 2
GNAI2 0.014 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.006 0.054 -10000 0 -0.48 6 6
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.008 0.069 -10000 0 -0.76 4 4
RhoA/GTP -0.011 0.049 -10000 0 -0.44 2 2
negative regulation of cAMP metabolic process 0.023 0.063 -10000 0 -0.48 2 2
GNAZ -0.017 0.15 -10000 0 -0.74 20 20
GNAI3 0.014 0 -10000 0 -10000 0 0
GNA12 0.01 0.053 -10000 0 -0.82 2 2
S1PR5 0.008 0.064 -10000 0 -0.69 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.023 0.064 -10000 0 -0.48 2 2
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
GNAI1 0.013 0.026 -10000 0 -0.57 1 1
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.049 0.04 -10000 0 -10000 0 0
adherens junction organization 0.037 0.057 -10000 0 -0.63 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.039 0.088 -10000 0 -0.59 1 1
FMN1 0.022 0.093 -10000 0 -0.64 3 3
mol:IP3 0.041 0.038 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.035 0.049 -10000 0 -0.6 2 2
CTNNB1 0.012 0.026 -10000 0 -0.56 1 1
AKT1 0.047 0.04 -10000 0 -0.41 2 2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.04 0.059 -10000 0 -0.64 2 2
CTNND1 0.015 0.002 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.042 0.046 -10000 0 -0.55 2 2
VASP 0.042 0.047 -10000 0 -0.57 2 2
ZYX 0.042 0.047 -10000 0 -0.57 2 2
JUB 0.042 0.048 -10000 0 -0.57 2 2
EGFR(dimer) 0.024 0.1 -10000 0 -0.46 17 17
E-cadherin/beta catenin-gamma catenin -0.005 0.049 -10000 0 -0.62 2 2
mol:PI-3-4-5-P3 -0.005 0.036 -10000 0 -0.44 2 2
PIK3CA 0.015 0.001 -10000 0 -10000 0 0
PI3K -0.005 0.037 -10000 0 -0.45 2 2
FYN 0.046 0.061 -10000 0 -0.57 1 1
mol:Ca2+ 0.04 0.037 -10000 0 -10000 0 0
JUP 0.011 0.036 -10000 0 -0.56 2 2
PIK3R1 0.011 0.045 -10000 0 -0.57 3 3
mol:DAG 0.041 0.038 -10000 0 -10000 0 0
CDH1 0.008 0.058 -10000 0 -0.56 5 5
RhoA/GDP 0.039 0.088 -10000 0 -0.59 1 1
establishment of polarity of embryonic epithelium 0.042 0.046 -10000 0 -0.55 2 2
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
EGFR -0.017 0.15 -10000 0 -0.76 20 20
CASR 0.037 0.068 -10000 0 -0.41 8 8
RhoA/GTP -0.003 0.028 -10000 0 -10000 0 0
AKT2 0.047 0.04 -10000 0 -0.41 2 2
actin cable formation 0.029 0.09 -10000 0 -0.61 3 3
apoptosis 0.004 0.034 0.4 2 -10000 0 2
CTNNA1 0.015 0.002 -10000 0 -10000 0 0
mol:GDP 0.033 0.093 -10000 0 -0.65 1 1
PIP5K1A 0.042 0.047 -10000 0 -0.57 2 2
PLCG1 -0.004 0.033 -10000 0 -10000 0 0
Rac1/GTP -0.018 0.082 -10000 0 -0.63 2 2
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
CHUK 0.014 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.006 0.05 -9999 0 -0.46 6 6
NFKB1 0.014 0 -9999 0 -10000 0 0
MAP3K14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.008 0.069 -9999 0 -0.63 6 6
RELB 0.004 0.091 -9999 0 -0.82 6 6
NFKB2 0.014 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB -0.007 0.06 -9999 0 -0.55 6 6
regulation of B cell activation -0.007 0.06 -9999 0 -0.55 6 6
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.013 0.026 -9999 0 -0.57 1 1
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.044 0.011 -9999 0 -10000 0 0
SMAD3/SMAD4 0.05 0.012 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.001 0.015 -9999 0 -10000 0 0
SMAD2/SMAD2/SMAD4 0 0.011 -9999 0 -10000 0 0
PPM1A 0.014 0 -9999 0 -10000 0 0
CALM1 0.014 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.022 0.014 -9999 0 -0.3 1 1
MAP3K1 0.014 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.015 0.076 -9999 0 -0.41 18 18
MAPK3 0.014 0 -9999 0 -10000 0 0
MAPK1 0.014 0 -9999 0 -10000 0 0
NUP214 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
CTDSP2 0.014 0 -9999 0 -10000 0 0
CTDSPL 0.014 0 -9999 0 -10000 0 0
KPNB1 0.014 0 -9999 0 -10000 0 0
TGFBRAP1 -0.006 0.1 -9999 0 -0.57 17 17
UBE2I 0.014 0 -9999 0 -10000 0 0
NUP153 0.014 0 -9999 0 -10000 0 0
KPNA2 0.014 0 -9999 0 -10000 0 0
PIAS4 0.014 0 -9999 0 -10000 0 0
PLK2 and PLK4 events

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
PLK2 0.011 0.037 -9999 0 -0.57 2 2
PLK4 0.014 0 -9999 0 -10000 0 0
regulation of centriole replication 0.023 0.027 -9999 0 -0.41 2 2
Insulin-mediated glucose transport

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
Insulin responsive Vesicles -0.076 0.086 -10000 0 -0.38 1 1
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.014 0 -10000 0 -10000 0 0
AKT2 0.014 0 -10000 0 -10000 0 0
STXBP4 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.054 0.13 0.3 7 -0.43 1 8
YWHAZ 0.014 0 -10000 0 -10000 0 0
CALM1 0.014 0 -10000 0 -10000 0 0
YWHAQ 0.014 0 -10000 0 -10000 0 0
TBC1D4 0.025 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.014 0 -10000 0 -10000 0 0
YWHAB 0.014 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.014 0 -10000 0 -10000 0 0
ASIP -0.011 0.13 -10000 0 -0.82 12 12
PRKCI 0.014 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.014 0 -10000 0 -10000 0 0
GYS1 0.034 0 -10000 0 -10000 0 0
PRKCZ 0.013 0.026 -10000 0 -0.57 1 1
TRIP10 0.014 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.048 0.023 -10000 0 -10000 0 0
VAMP2 0.014 0 -10000 0 -10000 0 0
SLC2A4 -0.06 0.14 0.31 7 -0.48 1 8
STX4 0.014 0 -10000 0 -10000 0 0
GSK3B 0.028 0 -10000 0 -10000 0 0
SFN 0.006 0.074 -10000 0 -0.72 5 5
LNPEP 0.011 0.037 -10000 0 -0.57 2 2
YWHAE 0.014 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

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
NF kappa B/RelA -0.02 0.086 -9999 0 -0.41 21 21
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.033 0.076 -9999 0 -10000 0 0
SUMO1 0.014 0 -9999 0 -10000 0 0
ZFPM1 0.014 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.023 0 -9999 0 -10000 0 0
FKBP3 0.014 0 -9999 0 -10000 0 0
Histones -0.008 0.037 -9999 0 -10000 0 0
YY1/LSF 0.019 0.062 -9999 0 -0.6 1 1
SMG5 0.014 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.02 0.074 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.022 0.055 -9999 0 -0.34 1 1
SAP18 0.014 0 -9999 0 -10000 0 0
RELA 0.026 0.064 -9999 0 -10000 0 0
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.014 0 -9999 0 -10000 0 0
HDAC3/TR2 0.023 0.052 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.051 0.009 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.03 0.058 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.006 0.079 -9999 0 -0.77 5 5
GATA1 0.009 0.038 -9999 0 -0.82 1 1
Mad/Max -0.004 0.04 -9999 0 -0.41 5 5
NuRD/MBD3 Complex/GATA1/Fog1 0.061 0.014 -9999 0 -10000 0 0
RBBP7 0.014 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.013 0.026 -9999 0 -0.57 1 1
MAX 0.014 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.014 0 -9999 0 -10000 0 0
NFKBIA 0.017 0.061 -9999 0 -0.39 1 1
KAT2B -0.014 0.12 -9999 0 -0.57 24 24
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.046 0.015 -9999 0 -10000 0 0
SIN3 complex -0.001 0.022 -9999 0 -0.49 1 1
SMURF1 0.014 0 -9999 0 -10000 0 0
CHD3 0.014 0 -9999 0 -10000 0 0
SAP30 0.012 0.037 -9999 0 -0.82 1 1
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.014 0 -9999 0 -10000 0 0
YY1/HDAC3 0.024 0.071 -9999 0 -0.52 1 1
YY1/HDAC2 0.019 0.062 -9999 0 -0.6 1 1
YY1/HDAC1 0.019 0.062 -9999 0 -0.6 1 1
NuRD/MBD2 Complex (MeCP1) 0.051 0.009 -9999 0 -10000 0 0
PPARG -0.13 0.16 -9999 0 -0.46 21 21
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.023 0.052 -9999 0 -10000 0 0
MBD3L2 -0.003 0.052 -9999 0 -0.82 2 2
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.014 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.054 0.017 -9999 0 -10000 0 0
HDAC1 0.014 0 -9999 0 -10000 0 0
HDAC3 0.018 0.059 -9999 0 -10000 0 0
HDAC2 0.014 0 -9999 0 -10000 0 0
YY1 0.016 0.073 -9999 0 -0.67 1 1
HDAC8 0.014 0 -9999 0 -10000 0 0
SMAD7 0.014 0 -9999 0 -10000 0 0
NCOR2 0.014 0 -9999 0 -10000 0 0
MXD1 0.008 0.058 -9999 0 -0.57 5 5
STAT3 0.026 0.023 -9999 0 -0.33 2 2
NFKB1 0.014 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.011 0.049 -9999 0 -0.55 1 1
YY1/SAP30/HDAC1 -0.012 0.057 -9999 0 -0.62 2 2
EP300 0.011 0.037 -9999 0 -0.57 2 2
STAT3 (dimer non-phopshorylated) 0.026 0.023 -9999 0 -0.33 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.017 0.061 -9999 0 -0.39 1 1
histone deacetylation 0.051 0.009 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.032 0.052 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
GATAD2B 0.014 0 -9999 0 -10000 0 0
GATAD2A 0.014 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.018 0.074 -9999 0 -0.55 4 4
GATA1/HDAC1 -0.001 0.028 -9999 0 -0.63 1 1
GATA1/HDAC3 0.016 0.058 -9999 0 -0.49 1 1
CHD4 0.014 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.029 0.13 -9999 0 -0.6 24 24
SIN3/HDAC complex/Mad/Max 0.049 0.024 -9999 0 -10000 0 0
NuRD Complex 0.06 0.01 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.008 0.037 -9999 0 -10000 0 0
SIN3B 0.014 0 -9999 0 -10000 0 0
MTA2 0.014 0 -9999 0 -10000 0 0
SIN3A 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.013 -9999 0 -10000 0 0
GATA1/Fog1 -0.001 0.028 -9999 0 -0.63 1 1
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.025 0.17 -9999 0 -0.79 24 24
negative regulation of cell growth 0.048 0.024 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.051 0.009 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha 0.027 0.079 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.048 0.014 -9999 0 -10000 0 0
TFCP2 0.014 0 -9999 0 -10000 0 0
NR2C1 0.014 0 -9999 0 -10000 0 0
MBD3 0.014 0 -9999 0 -10000 0 0
MBD2 0.014 0 -9999 0 -10000 0 0
FoxO family signaling

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
G6PC 0.039 0.045 -9999 0 -0.62 2 2
PLK1 0.11 0.11 -9999 0 -0.92 2 2
CDKN1B 0.15 0.054 -9999 0 -10000 0 0
FOXO3 0.11 0.11 -9999 0 -0.88 1 1
KAT2B -0.002 0.13 -9999 0 -0.56 24 24
FOXO1/SIRT1 0.009 0.034 -9999 0 -10000 0 0
CAT 0.11 0.12 -9999 0 -0.98 2 2
CTNNB1 0.012 0.026 -9999 0 -0.57 1 1
AKT1 0.029 0.011 -9999 0 -10000 0 0
FOXO1 0.043 0.025 -9999 0 -10000 0 0
MAPK10 0.026 0.082 -9999 0 -0.46 4 4
mol:GTP 0.002 0 -9999 0 -10000 0 0
FOXO4 0.1 0.051 -9999 0 -10000 0 0
response to oxidative stress 0.017 0.011 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.005 0.078 -9999 0 -0.7 2 2
XPO1 0.015 0 -9999 0 -10000 0 0
EP300 0.013 0.037 -9999 0 -0.57 2 2
BCL2L11 0.042 0.026 -9999 0 -10000 0 0
FOXO1/SKP2 0.043 0.032 -9999 0 -0.47 1 1
mol:GDP 0.017 0.011 -9999 0 -10000 0 0
RAN 0.016 0 -9999 0 -10000 0 0
GADD45A 0.13 0.054 -9999 0 -0.48 1 1
YWHAQ 0.014 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.08 0.018 -9999 0 -10000 0 0
MST1 0.017 0.084 -9999 0 -0.72 6 6
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.062 0.028 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
MAPK8 0.041 0.038 -9999 0 -10000 0 0
MAPK9 0.045 0.005 -9999 0 -10000 0 0
YWHAG 0.014 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
SIRT1 0.006 0.031 -9999 0 -0.56 1 1
SOD2 0.16 0.061 -9999 0 -10000 0 0
RBL2 0.12 0.078 -9999 0 -10000 0 0
RAL/GDP 0.035 0.012 -9999 0 -10000 0 0
CHUK 0.026 0.009 -9999 0 -10000 0 0
Ran/GTP 0.015 0.001 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
RAL/GTP 0.044 0.008 -9999 0 -10000 0 0
CSNK1G1 0.014 0 -9999 0 -10000 0 0
FASLG -0.033 0.28 -9999 0 -0.85 45 45
SKP2 0.012 0.037 -9999 0 -0.82 1 1
USP7 0.016 0 -9999 0 -10000 0 0
IKBKB 0.026 0.009 -9999 0 -10000 0 0
CCNB1 0.11 0.1 -9999 0 -0.79 1 1
FOXO1-3a-4/beta catenin 0.12 0.099 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.032 -9999 0 -0.47 1 1
CSNK1A1 0.014 0 -9999 0 -10000 0 0
SGK1 0.022 0.053 -9999 0 -0.64 3 3
CSNK1G3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.027 0.001 -9999 0 -10000 0 0
ZFAND5 0.11 0.046 -9999 0 -10000 0 0
SFN 0.006 0.074 -9999 0 -0.72 5 5
CDK2 0.014 0.005 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.076 0.036 -9999 0 -10000 0 0
CREBBP 0.014 0.005 -9999 0 -10000 0 0
FBXO32 0.1 0.14 -9999 0 -1.3 3 3
BCL6 0.12 0.078 -9999 0 -10000 0 0
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
YWHAH 0.014 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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
BCL3/RelA -0.001 0.018 -9999 0 -0.41 1 1
FBXW11 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.022 0.049 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.045 0.041 -9999 0 -0.45 1 1
NFKBIA 0.024 0.047 -9999 0 -0.52 1 1
MAPK14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.028 0 -9999 0 -10000 0 0
ARRB2 0.019 0 -9999 0 -10000 0 0
REL 0.003 0.077 -9999 0 -0.57 9 9
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.028 0.016 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.022 0 -9999 0 -10000 0 0
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
NFKB1 0.025 0 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.032 0.042 -9999 0 -0.41 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.048 0.041 -9999 0 -0.43 1 1
SRC 0.014 0 -9999 0 -10000 0 0
PI3K -0.002 0.031 -9999 0 -0.41 3 3
NF kappa B1 p50/RelA 0.032 0.042 -9999 0 -0.42 1 1
IKBKB 0.014 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
SYK 0.01 0.045 -9999 0 -0.57 3 3
I kappa B alpha/PIK3R1 0.028 0.05 -9999 0 -0.49 1 1
cell death 0.046 0.039 -9999 0 -0.41 1 1
NF kappa B1 p105/c-Rel 0.022 0.049 -9999 0 -10000 0 0
LCK -0.006 0.13 -9999 0 -0.82 12 12
BCL3 0.013 0.026 -9999 0 -0.57 1 1
E-cadherin signaling in the nascent adherens junction

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
CTTN 0.029 0.084 -9999 0 -0.43 16 16
KLHL20 -0.01 0.038 -9999 0 -0.3 2 2
CYFIP2 0.01 0.052 -9999 0 -0.65 3 3
Rac1/GDP 0.06 0.038 -9999 0 -10000 0 0
ENAH 0.038 0.06 -9999 0 -0.49 6 6
AP1M1 0.014 0 -9999 0 -10000 0 0
RAP1B 0.012 0.037 -9999 0 -0.82 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.013 0.026 -9999 0 -0.57 1 1
CDC42/GTP -0.003 0.024 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.028 -9999 0 -0.21 3 3
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.005 0.038 -9999 0 -10000 0 0
RAPGEF1 0.053 0.048 -9999 0 -10000 0 0
CTNND1 0.014 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.006 0.051 -9999 0 -0.46 6 6
CRK 0.047 0.051 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin -0.005 0.049 -9999 0 -0.66 2 2
alphaE/beta7 Integrin -0.002 0.026 -9999 0 -0.41 2 2
IQGAP1 0.014 0 -9999 0 -10000 0 0
NCKAP1 0.012 0.037 -9999 0 -0.82 1 1
Rap1/GTP/I-afadin -0.001 0.022 -9999 0 -0.5 1 1
DLG1 0.039 0.054 -9999 0 -0.44 6 6
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.019 -9999 0 -10000 0 0
MLLT4 0.014 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.005 0.04 -9999 0 -0.5 1 1
PI3K -0.003 0.024 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.005 0.057 -9999 0 -0.54 5 5
TIAM1 0.007 0.063 -9999 0 -0.57 6 6
E-cadherin(dimer)/Ca2+ -0.003 0.031 -9999 0 -10000 0 0
AKT1 -0.002 0.014 -9999 0 -10000 0 0
PIK3R1 0.01 0.045 -9999 0 -0.57 3 3
CDH1 0.008 0.058 -9999 0 -0.57 5 5
RhoA/GDP 0.059 0.038 -9999 0 -10000 0 0
actin cytoskeleton organization -0.007 0.028 -9999 0 -0.22 2 2
CDC42/GDP 0.059 0.038 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.023 0.04 -9999 0 -0.51 2 2
ITGB7 0.011 0.037 -9999 0 -0.57 2 2
RAC1 0.014 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.004 0.033 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin -0.003 0.032 -9999 0 -10000 0 0
mol:GDP 0.056 0.043 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.011 0.037 -9999 0 -0.57 2 2
p120 catenin/RhoA/GDP -0.004 0.028 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.029 0.048 -9999 0 -0.25 12 12
NME1 0.012 0.037 -9999 0 -0.82 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.039 0.054 -9999 0 -0.44 6 6
regulation of cell-cell adhesion -0.002 0.021 -9999 0 -10000 0 0
WASF2 -0.004 0.014 -9999 0 -10000 0 0
Rap1/GTP -0.003 0.027 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.005 0.045 -9999 0 -0.57 2 2
CCND1 0.033 0.059 -9999 0 -0.32 12 12
VAV2 0.041 0.073 -9999 0 -10000 0 0
RAP1/GDP -0.001 0.03 -9999 0 -10000 0 0
adherens junction assembly 0.039 0.052 -9999 0 -0.43 6 6
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.014 0 -9999 0 -10000 0 0
PIP5K1C 0.014 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.005 0.044 -9999 0 -0.54 2 2
E-cadherin/beta catenin -0.004 0.037 -9999 0 -0.37 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.039 0.054 -9999 0 -0.45 6 6
PIK3CA 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.016 0.061 -9999 0 -0.53 2 2
E-cadherin/beta catenin/alpha catenin -0.004 0.037 -9999 0 -10000 0 0
ITGAE 0.014 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.006 0.052 -9999 0 -0.48 6 6
mTOR signaling 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
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.014 0 -10000 0 -10000 0 0
mol:PIP3 -0.003 0.03 -10000 0 -10000 0 0
FRAP1 0.015 0.01 -10000 0 -10000 0 0
AKT1 0.027 0.031 -10000 0 -10000 0 0
INSR 0.013 0.026 -10000 0 -0.57 1 1
Insulin Receptor/Insulin -0.003 0.038 -10000 0 -0.49 3 3
mol:GTP -0.003 0.021 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.007 -10000 0 -10000 0 0
TSC2 0.014 0 -10000 0 -10000 0 0
RHEB/GDP -0.002 0.019 -10000 0 -10000 0 0
TSC1 0.014 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.015 0.031 -10000 0 -0.33 4 4
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.008 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.014 0 -10000 0 -10000 0 0
RPS6KB1 0.028 0.019 -10000 0 -10000 0 0
MAP3K5 0.011 0.001 -10000 0 -10000 0 0
PIK3R1 0.01 0.045 -10000 0 -0.57 3 3
apoptosis 0.011 0.001 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.001 3 3
EIF4B 0.034 0.018 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.001 0.012 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.003 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.022 0.035 -10000 0 -0.31 3 3
mTOR/RHEB/GTP/Raptor/GBL 0.033 0.015 -10000 0 -10000 0 0
FKBP1A 0.014 0 -10000 0 -10000 0 0
RHEB/GTP -0.002 0.018 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 3 3
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.004 0.03 -10000 0 -10000 0 0
EIF4E 0.014 0 -10000 0 -10000 0 0
ASK1/PP5C 0.023 0.007 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.003 0.023 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.001 3 -10000 0 3
RPS6 0.014 0 -10000 0 -10000 0 0
PPP5C 0.014 0 -10000 0 -10000 0 0
EIF4G1 0.014 0 -10000 0 -10000 0 0
IRS1 0.007 0.03 -10000 0 -0.38 3 3
INS -0.003 0.052 -10000 0 -0.82 2 2
PTEN 0.013 0 -10000 0 -10000 0 0
PDK2 -0.003 0.027 -10000 0 -10000 0 0
EIF4EBP1 0.006 0.053 -10000 0 -0.38 9 9
PIK3CA 0.014 0 -10000 0 -10000 0 0
PPP2R5D 0.022 0.01 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.036 -10000 0 -0.5 2 2
RHEB 0.014 0 -10000 0 -10000 0 0
EIF4A1 0.014 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.016 0.036 -10000 0 -0.5 2 2
eIF4E/4E-BP1 0.014 0.047 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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
BCL2L1 0.025 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0.035 0 -9999 0 -10000 0 0
CDKN1B 0.04 0.006 -9999 0 -10000 0 0
CDKN1A 0.04 0.006 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.014 0 -9999 0 -10000 0 0
FOXO3 0.04 0.006 -9999 0 -10000 0 0
AKT1 0 0.005 -9999 0 -10000 0 0
BAD 0.014 0 -9999 0 -10000 0 0
AKT3 0.011 0.053 -9999 0 -0.36 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.039 0.02 -9999 0 -10000 0 0
AKT1/ASK1 0 0.004 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0.014 0 -9999 0 -10000 0 0
RAF1 0.014 0 -9999 0 -10000 0 0
JNK cascade 0 0.004 -9999 0 -10000 0 0
TSC1 0.04 0.006 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
AKT1/RAF1 0.039 0.006 -9999 0 -10000 0 0
EP300 0.011 0.037 -9999 0 -0.57 2 2
mol:GDP 0.033 0.006 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.04 0.006 -9999 0 -10000 0 0
YWHAQ 0.014 0 -9999 0 -10000 0 0
TBC1D4 0.026 0.014 -9999 0 -10000 0 0
MAP3K5 0.014 0 -9999 0 -10000 0 0
MAPKAP1 0.014 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.047 0.015 -9999 0 -10000 0 0
YWHAH 0.014 0 -9999 0 -10000 0 0
AKT1S1 0.04 0.006 -9999 0 -10000 0 0
CASP9 0.04 0.006 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.046 0.006 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 -0.001 0.015 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0 0.01 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.02 0.002 -9999 0 -10000 0 0
CHUK 0.04 0.006 -9999 0 -10000 0 0
BAD/BCL-XL 0.053 0.006 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.018 0.016 -9999 0 -0.34 1 1
FOXO1-3a-4/14-3-3 family 0.062 0.02 -9999 0 -10000 0 0
PDPK1 0.013 0.026 -9999 0 -0.57 1 1
MDM2 0.04 0.006 -9999 0 -10000 0 0
MAPKKK cascade -0.039 0.006 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.051 0.019 -9999 0 -10000 0 0
TSC1/TSC2 0.047 0.006 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.014 -9999 0 -10000 0 0
glucose import -0.12 0.16 -9999 0 -0.49 1 1
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.034 0.004 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.12 0.16 -9999 0 -0.49 1 1
GSK3A 0.04 0.006 -9999 0 -10000 0 0
FOXO1 0.04 0.006 -9999 0 -10000 0 0
GSK3B 0.04 0.006 -9999 0 -10000 0 0
SFN 0.006 0.074 -9999 0 -0.72 5 5
G1/S transition of mitotic cell cycle 0.047 0.006 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.05 0.022 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
KPNA1 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
YWHAG 0.014 0 -9999 0 -10000 0 0
RHEB 0.014 0 -9999 0 -10000 0 0
CREBBP 0.014 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.032 0 -9999 0 -9999 0 0
HDAC4 0.014 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.014 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.018 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.031 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.014 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.014 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -9999 0 0
RANGAP1 0.014 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.023 0 -9999 0 -9999 0 0
Ran/GTP 0.029 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.014 0 -9999 0 -9999 0 0
UBE2I 0.014 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.014 0 -9999 0 -9999 0 0
PIAS1 0.014 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0 -9999 0 -10000 0 0
AP2 -0.003 0.04 -9999 0 -0.63 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.028 0 -9999 0 -10000 0 0
CD4 0.011 0.045 -9999 0 -0.69 2 2
CLTA 0.014 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.03 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0.01 0.053 -9999 0 -0.82 2 2
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.018 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.028 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.03 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0.02 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.037 0.022 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.004 0.045 -9999 0 -0.54 3 3
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 497 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.WA.A7H4 TCGA.WA.A7GZ TCGA.UP.A6WW TCGA.UF.A7JV
109_MAP3K5 0.059 0.059 0.059 0.059
47_PPARGC1A 0.014 0.014 0.014 -0.57
105_BMP4 0.014 0.014 0.014 0.014
105_BMP6 0.014 0.014 0.014 0.014
105_BMP7 0.014 0.014 0.014 0.014
105_BMP2 0.014 0.014 0.014 -0.82
131_RELN/VLDLR 0 0 0 0
30_TGFB1/TGF beta receptor Type II 0.013 0.013 0.018 0.013
84_STAT5B 0.039 0.039 -0.025 -0.023
84_STAT5A 0.039 0.039 -0.025 -0.023
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/HNSC-TP/8100432/HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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