PARADIGM pathway analysis of mRNA expression data
Colon Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PARADIGM pathway analysis of mRNA expression data. Broad Institute of MIT and Harvard. doi:10.7908/C15X277Q
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 49 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 101
Syndecan-1-mediated signaling events 50
Signaling events mediated by Stem cell factor receptor (c-Kit) 42
BCR signaling pathway 32
HIF-1-alpha transcription factor network 31
IL23-mediated signaling events 31
Fc-epsilon receptor I signaling in mast cells 30
Osteopontin-mediated events 28
Glypican 1 network 28
FOXM1 transcription factor network 28
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 153 . 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 ( 153 ).

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 0.6601 101 814 8 -0.5 0.27 1000 -1000 -0.019 -1000
Syndecan-1-mediated signaling events 0.3268 50 1722 34 -0.71 0.017 1000 -1000 -0.11 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.2745 42 3294 78 -0.9 0.26 1000 -1000 -0.1 -1000
BCR signaling pathway 0.2092 32 3255 99 -0.41 0.017 1000 -1000 -0.13 -1000
HIF-1-alpha transcription factor network 0.2026 31 2415 76 -0.84 0.028 1000 -1000 -0.11 -1000
IL23-mediated signaling events 0.2026 31 1900 60 -0.71 0.018 1000 -1000 -0.16 -1000
Fc-epsilon receptor I signaling in mast cells 0.1961 30 2927 97 -0.42 0.063 1000 -1000 -0.12 -1000
Osteopontin-mediated events 0.1830 28 1082 38 -0.54 0.017 1000 -1000 -0.13 -1000
Glypican 1 network 0.1830 28 1391 48 -0.45 0.025 1000 -1000 -0.072 -1000
FOXM1 transcription factor network 0.1830 28 1475 51 -0.64 0.02 1000 -1000 -0.18 -1000
IL6-mediated signaling events 0.1699 26 1967 75 -0.58 0.07 1000 -1000 -0.097 -1000
Reelin signaling pathway 0.1569 24 1353 56 -0.64 0.017 1000 -1000 -0.11 -1000
Endothelins 0.1373 21 2045 96 -0.56 0.076 1000 -1000 -0.092 -1000
FAS signaling pathway (CD95) 0.1373 21 988 47 -0.38 0.18 1000 -1000 -0.066 -1000
Visual signal transduction: Rods 0.1307 20 1078 52 -0.52 0.017 1000 -1000 -0.12 -1000
Canonical Wnt signaling pathway 0.1176 18 928 51 -0.53 0.36 1000 -1000 -0.072 -1000
BMP receptor signaling 0.1111 17 1410 81 -0.48 0.029 1000 -1000 -0.12 -1000
TCGA08_p53 0.1111 17 119 7 -0.18 0.096 1000 -1000 -0.024 -1000
Wnt signaling 0.1111 17 119 7 -0.15 0.017 1000 -1000 -0.04 -1000
Syndecan-2-mediated signaling events 0.1046 16 1168 69 -0.71 0.052 1000 -1000 -0.092 -1000
HIF-2-alpha transcription factor network 0.1046 16 728 43 -0.68 0.4 1000 -1000 -0.095 -1000
Signaling events mediated by PRL 0.1046 16 544 34 -0.24 0.12 1000 -1000 -0.082 -1000
IL4-mediated signaling events 0.0980 15 1421 91 -0.6 0.4 1000 -1000 -0.15 -1000
Glucocorticoid receptor regulatory network 0.0980 15 1744 114 -0.78 0.38 1000 -1000 -0.079 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0915 14 766 54 -0.64 0.034 1000 -1000 -0.13 -1000
Arf6 signaling events 0.0915 14 891 62 -0.35 0.021 1000 -1000 -0.09 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0915 14 1250 85 -0.35 0.025 1000 -1000 -0.099 -1000
Syndecan-3-mediated signaling events 0.0915 14 524 35 -0.71 0.017 1000 -1000 -0.089 -1000
TRAIL signaling pathway 0.0850 13 633 48 -0.17 0.017 1000 -1000 -0.094 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0850 13 911 68 -0.89 0.077 1000 -1000 -0.14 -1000
EGFR-dependent Endothelin signaling events 0.0850 13 283 21 -0.24 0.017 1000 -1000 -0.098 -1000
Aurora A signaling 0.0784 12 724 60 -0.7 0.021 1000 -1000 -0.082 -1000
IL1-mediated signaling events 0.0784 12 800 62 -0.47 0.087 1000 -1000 -0.12 -1000
IGF1 pathway 0.0784 12 720 57 -0.37 0.08 1000 -1000 -0.13 -1000
Presenilin action in Notch and Wnt signaling 0.0719 11 708 61 -0.52 0.23 1000 -1000 -0.1 -1000
Calcium signaling in the CD4+ TCR pathway 0.0719 11 346 31 -0.4 0.028 1000 -1000 -0.13 -1000
IL12-mediated signaling events 0.0654 10 902 87 -0.34 0.031 1000 -1000 -0.12 -1000
FOXA2 and FOXA3 transcription factor networks 0.0654 10 460 46 -0.77 0.027 1000 -1000 -0.06 -1000
amb2 Integrin signaling 0.0654 10 856 82 -0.34 0.017 1000 -1000 -0.11 -1000
Regulation of nuclear SMAD2/3 signaling 0.0588 9 1241 136 -1.1 0.091 1000 -1000 -0.11 -1000
Thromboxane A2 receptor signaling 0.0588 9 983 105 -0.5 0.13 1000 -1000 -0.097 -1000
p75(NTR)-mediated signaling 0.0588 9 1214 125 -0.83 0.066 1000 -1000 -0.12 -1000
Ephrin B reverse signaling 0.0588 9 464 48 -0.25 0.15 1000 -1000 -0.097 -1000
PLK2 and PLK4 events 0.0523 8 26 3 -0.018 -0.013 1000 -1000 -0.029 -1000
Visual signal transduction: Cones 0.0523 8 307 38 -0.17 0.029 1000 -1000 -0.078 -1000
Noncanonical Wnt signaling pathway 0.0523 8 219 26 -0.15 0.017 1000 -1000 -0.12 -1000
PLK1 signaling events 0.0523 8 759 85 -0.42 0.017 1000 -1000 -0.08 -1000
IL2 signaling events mediated by PI3K 0.0523 8 510 58 -0.56 0.045 1000 -1000 -0.099 -1000
EPHB forward signaling 0.0523 8 704 85 -0.25 0.18 1000 -1000 -0.13 -1000
Nectin adhesion pathway 0.0458 7 451 63 -0.72 0.054 1000 -1000 -0.099 -1000
S1P1 pathway 0.0458 7 267 36 -0.16 0.017 1000 -1000 -0.11 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0392 6 176 28 -0.097 0.017 1000 -1000 -0.06 -1000
Signaling events mediated by the Hedgehog family 0.0392 6 324 52 -0.13 0.12 1000 -1000 -0.11 -1000
EPO signaling pathway 0.0392 6 348 55 -0.51 0.028 1000 -1000 -0.12 -1000
PDGFR-alpha signaling pathway 0.0392 6 269 44 -0.13 0.032 1000 -1000 -0.097 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0392 6 537 83 -0.37 0.079 1000 -1000 -0.093 -1000
Integrins in angiogenesis 0.0392 6 524 84 -0.54 0.064 1000 -1000 -0.13 -1000
Glypican 2 network 0.0392 6 24 4 -0.03 0 1000 -1000 -0.028 -1000
IL27-mediated signaling events 0.0392 6 306 51 -0.42 0.025 1000 -1000 -0.12 -1000
Regulation of Telomerase 0.0392 6 666 102 -0.41 0.063 1000 -1000 -0.13 -1000
Aurora B signaling 0.0392 6 464 67 -0.23 0.029 1000 -1000 -0.097 -1000
a4b1 and a4b7 Integrin signaling 0.0327 5 25 5 -0.033 0.008 1000 -1000 -0.05 -1000
Cellular roles of Anthrax toxin 0.0327 5 212 39 -0.12 0.018 1000 -1000 -0.04 -1000
Signaling events mediated by PTP1B 0.0327 5 410 76 -0.66 0.13 1000 -1000 -0.1 -1000
Ceramide signaling pathway 0.0327 5 438 76 -0.37 0.078 1000 -1000 -0.074 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0327 5 277 52 -0.52 0.1 1000 -1000 -0.091 -1000
TCR signaling in naïve CD8+ T cells 0.0327 5 493 93 -0.096 0.043 1000 -1000 -0.1 -1000
Syndecan-4-mediated signaling events 0.0327 5 393 67 -0.46 0.019 1000 -1000 -0.13 -1000
VEGFR1 specific signals 0.0327 5 304 56 -0.092 0.037 1000 -1000 -0.1 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0327 5 177 33 -0.24 0.033 1000 -1000 -0.089 -1000
Regulation of Androgen receptor activity 0.0327 5 372 70 -0.6 0.04 1000 -1000 -0.079 -1000
BARD1 signaling events 0.0261 4 273 57 -0.18 0.051 1000 -1000 -0.092 -1000
Signaling events mediated by HDAC Class III 0.0261 4 172 40 -0.28 0.032 1000 -1000 -0.06 -1000
ceramide signaling pathway 0.0261 4 224 49 -0.37 0.078 1000 -1000 -0.061 -1000
Signaling mediated by p38-gamma and p38-delta 0.0261 4 63 15 -0.052 0.035 1000 -1000 -0.048 -1000
TCGA08_rtk_signaling 0.0261 4 124 26 -0.35 0.035 1000 -1000 -0.024 -1000
E-cadherin signaling in keratinocytes 0.0261 4 181 43 -0.36 0.044 1000 -1000 -0.11 -1000
Coregulation of Androgen receptor activity 0.0196 3 253 76 -0.24 0.061 1000 -1000 -0.08 -1000
Canonical NF-kappaB pathway 0.0196 3 145 39 -0.2 0.067 1000 -1000 -0.11 -1000
ErbB4 signaling events 0.0196 3 256 69 -0.48 0.09 1000 -1000 -0.12 -1000
IFN-gamma pathway 0.0196 3 271 68 -0.16 0.054 1000 -1000 -0.12 -1000
FoxO family signaling 0.0196 3 208 64 -0.17 0.13 1000 -1000 -0.086 -1000
Signaling mediated by p38-alpha and p38-beta 0.0196 3 142 44 -0.22 0.017 1000 -1000 -0.075 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0196 3 146 45 -0.15 0.091 1000 -1000 -0.11 -1000
Effects of Botulinum toxin 0.0196 3 85 26 -0.11 0.018 1000 -1000 -0.094 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0196 3 454 125 -0.12 0.073 1000 -1000 -0.14 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0196 3 285 74 -0.36 0.092 1000 -1000 -0.13 -1000
Plasma membrane estrogen receptor signaling 0.0196 3 295 86 -0.36 0.067 1000 -1000 -0.11 -1000
PDGFR-beta signaling pathway 0.0196 3 343 97 -0.25 0.07 1000 -1000 -0.11 -1000
E-cadherin signaling events 0.0196 3 18 5 -0.019 0.017 1000 -1000 -0.058 -1000
Ras signaling in the CD4+ TCR pathway 0.0196 3 54 17 -0.068 0.026 1000 -1000 -0.064 -1000
Caspase cascade in apoptosis 0.0131 2 207 74 -0.2 0.061 1000 -1000 -0.053 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0131 2 76 34 -0.048 0.06 1000 -1000 -0.095 -1000
Ephrin A reverse signaling 0.0131 2 16 7 -0.009 0.023 1000 -1000 -0.041 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0131 2 100 37 -0.16 0.04 1000 -1000 -0.11 -1000
Nongenotropic Androgen signaling 0.0131 2 137 52 -0.056 0.057 1000 -1000 -0.082 -1000
E-cadherin signaling in the nascent adherens junction 0.0131 2 173 76 -0.056 0.064 1000 -1000 -0.1 -1000
IL2 signaling events mediated by STAT5 0.0131 2 48 22 -0.1 0.11 1000 -1000 -0.051 -1000
Class I PI3K signaling events 0.0131 2 206 73 -0.31 0.039 1000 -1000 -0.08 -1000
S1P3 pathway 0.0131 2 122 42 -0.068 0.034 1000 -1000 -0.078 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0065 1 28 23 -0.043 0.047 1000 -1000 -0.098 -1000
Circadian rhythm pathway 0.0065 1 43 22 -0.077 0.066 1000 -1000 -0.091 -1000
JNK signaling in the CD4+ TCR pathway 0.0065 1 32 17 -0.067 0.055 1000 -1000 -0.091 -1000
Hedgehog signaling events mediated by Gli proteins 0.0065 1 125 65 -0.14 0.074 1000 -1000 -0.081 -1000
Arf6 downstream pathway 0.0065 1 71 43 -0.04 0.041 1000 -1000 -0.06 -1000
mTOR signaling pathway 0.0065 1 57 53 -0.008 0.07 1000 -1000 -0.078 -1000
Signaling events regulated by Ret tyrosine kinase 0.0065 1 93 82 -0.041 0.074 1000 -1000 -0.11 -1000
S1P5 pathway 0.0065 1 18 17 -0.056 0.022 1000 -1000 -0.072 -1000
Retinoic acid receptors-mediated signaling 0.0065 1 100 58 -0.081 0.072 1000 -1000 -0.1 -1000
Paxillin-dependent events mediated by a4b1 0.0065 1 38 36 -0.033 0.032 1000 -1000 -0.1 -1000
Regulation of p38-alpha and p38-beta 0.0065 1 87 54 -0.082 0.038 1000 -1000 -0.08 -1000
LPA receptor mediated events 0.0065 1 169 102 -0.34 0.041 1000 -1000 -0.093 -1000
Insulin Pathway 0.0065 1 140 74 -0.095 0.05 1000 -1000 -0.11 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0065 1 151 88 -0.18 0.12 1000 -1000 -0.15 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0065 1 185 120 -0.064 0.1 1000 -1000 -0.11 -1000
S1P4 pathway 0.0065 1 31 25 -0.056 0.033 1000 -1000 -0.067 -1000
LPA4-mediated signaling events 0.0000 0 11 12 -0.002 0.047 1000 -1000 -0.026 -1000
ErbB2/ErbB3 signaling events 0.0000 0 47 65 -0.017 0.11 1000 -1000 -0.098 -1000
Signaling events mediated by HDAC Class II 0.0000 0 68 75 -0.043 0.044 1000 -1000 -0.099 -1000
Aurora C signaling 0.0000 0 4 7 -0.006 0.017 1000 -1000 -0.055 -1000
Insulin-mediated glucose transport 0.0000 0 7 32 -0.015 0.058 1000 -1000 -0.074 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 28 68 -0.052 0.065 1000 -1000 -0.092 -1000
Signaling events mediated by HDAC Class I 0.0000 0 33 104 -0.021 0.078 1000 -1000 -0.094 -1000
Atypical NF-kappaB pathway 0.0000 0 9 31 -0.003 0.062 1000 -1000 -0.09 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 8 27 -0.005 0.036 1000 -1000 -0.078 -1000
Arf6 trafficking events 0.0000 0 69 71 -0.07 0.06 1000 -1000 -0.094 -1000
Rapid glucocorticoid signaling 0.0000 0 3 20 0 0.017 1000 -1000 -0.056 -1000
Class IB PI3K non-lipid kinase events 0.0000 0 0 3 -0.017 0.017 1000 -1000 -0.02 -1000
p38 MAPK signaling pathway 0.0000 0 11 44 -0.008 0.067 1000 -1000 -0.093 -1000
Arf1 pathway 0.0000 0 49 54 -0.019 0.049 1000 -1000 -0.066 -1000
Alternative NF-kappaB pathway 0.0000 0 3 13 -0.003 0.017 1000 -1000 -0.092 -1000
Total NA 1151 67340 7203 -39 8.7 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 -0.5 0.24 -10000 0 -0.61 126 126
CDKN2C 0.034 0.074 -10000 0 -0.61 1 1
CDKN2A -0.25 0.36 -10000 0 -0.75 52 52
CCND2 0.24 0.12 0.28 123 -10000 0 123
RB1 -0.25 0.12 -10000 0 -0.29 116 116
CDK4 0.24 0.12 0.28 131 -10000 0 131
CDK6 0.27 0.13 0.31 125 -10000 0 125
G1/S progression 0.24 0.12 0.27 140 -10000 0 140
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 0.017 0 -9999 0 -10000 0 0
CCL5 -0.11 0.26 -9999 0 -0.64 30 30
SDCBP 0.017 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.43 0.13 -9999 0 -0.45 138 138
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
Syndecan-1/Laminin-5 -0.43 0.18 -9999 0 -0.7 35 35
Syndecan-1/Syntenin -0.4 0.13 -9999 0 -0.62 27 27
MAPK3 -0.36 0.12 -9999 0 -0.59 27 27
HGF/MET -0.27 0.28 -9999 0 -0.55 74 74
TGFB1/TGF beta receptor Type II 0.017 0 -9999 0 -10000 0 0
BSG 0.012 0.053 -9999 0 -0.64 1 1
keratinocyte migration -0.42 0.18 -9999 0 -0.69 35 35
Syndecan-1/RANTES -0.46 0.2 -9999 0 -0.73 46 46
Syndecan-1/CD147 -0.38 0.13 -9999 0 -0.64 27 27
Syndecan-1/Syntenin/PIP2 -0.38 0.12 -9999 0 -0.6 27 27
LAMA5 -0.043 0.2 -9999 0 -0.74 12 12
positive regulation of cell-cell adhesion -0.38 0.12 -9999 0 -0.59 27 27
MMP7 -0.71 0.15 -9999 0 -0.74 147 147
HGF 0.017 0 -9999 0 -10000 0 0
Syndecan-1/CASK -0.41 0.13 -9999 0 -0.43 138 138
Syndecan-1/HGF/MET -0.57 0.22 -9999 0 -0.74 86 86
regulation of cell adhesion -0.34 0.12 -9999 0 -0.58 22 22
HPSE -0.073 0.23 -9999 0 -0.64 21 21
positive regulation of cell migration -0.43 0.13 -9999 0 -0.45 138 138
SDC1 -0.43 0.13 -9999 0 -0.46 138 138
Syndecan-1/Collagen -0.43 0.13 -9999 0 -0.45 138 138
PPIB 0.002 0.1 -9999 0 -0.74 3 3
MET -0.35 0.38 -9999 0 -0.74 74 74
PRKACA 0.017 0 -9999 0 -10000 0 0
MMP9 -0.012 0.14 -9999 0 -0.72 6 6
MAPK1 -0.36 0.13 -9999 0 -0.59 27 27
homophilic cell adhesion -0.42 0.13 -9999 0 -0.45 138 138
MMP1 -0.68 0.21 -9999 0 -0.74 140 140
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.22 0.2 -10000 0 -0.42 49 49
CRKL -0.24 0.21 -10000 0 -0.44 73 73
HRAS -0.18 0.19 -10000 0 -0.5 9 9
mol:PIP3 -0.24 0.2 -10000 0 -0.43 71 71
SPRED1 0.007 0.086 -10000 0 -0.74 2 2
SPRED2 0.017 0 -10000 0 -10000 0 0
GAB1 -0.27 0.22 -10000 0 -0.47 73 73
FOXO3 -0.23 0.2 -10000 0 -0.43 53 53
AKT1 -0.26 0.22 -10000 0 -0.45 76 76
BAD -0.23 0.2 -10000 0 -0.41 69 69
megakaryocyte differentiation -0.3 0.24 -10000 0 -0.49 80 80
GSK3B -0.23 0.2 -10000 0 -0.41 69 69
RAF1 -0.14 0.16 -10000 0 -0.4 7 7
SHC1 0.017 0 -10000 0 -10000 0 0
STAT3 -0.26 0.22 -10000 0 -0.46 73 73
STAT1 -0.75 0.59 -10000 0 -1.3 75 75
HRAS/SPRED1 -0.17 0.13 -10000 0 -0.41 11 11
cell proliferation -0.26 0.21 -10000 0 -0.45 73 73
PIK3CA 0.016 0.001 -10000 0 -10000 0 0
TEC 0.017 0 -10000 0 -10000 0 0
RPS6KB1 -0.27 0.22 -10000 0 -0.46 77 77
HRAS/SPRED2 -0.17 0.12 -10000 0 -0.39 9 9
LYN/TEC/p62DOK -0.25 0.18 -10000 0 -0.42 68 68
MAPK3 -0.092 0.12 -10000 0 -10000 0 0
STAP1 -0.42 0.3 -10000 0 -0.63 93 93
GRAP2 0.017 0 -10000 0 -10000 0 0
JAK2 -0.59 0.41 -10000 0 -0.96 74 74
STAT1 (dimer) -0.73 0.57 -10000 0 -1.2 75 75
mol:Gleevec 0.011 0.009 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.27 0.2 -10000 0 -0.46 70 70
actin filament polymerization -0.27 0.21 -10000 0 -0.46 73 73
LYN 0.017 0 -10000 0 -10000 0 0
STAP1/STAT5A (dimer) -0.52 0.36 -10000 0 -0.78 94 94
PIK3R1 0.016 0.001 -10000 0 -10000 0 0
CBL/CRKL/GRB2 -0.23 0.16 -10000 0 -0.45 9 9
PI3K -0.26 0.18 -10000 0 -0.43 72 72
PTEN -0.004 0.12 -10000 0 -0.64 5 5
SCF/KIT/EPO/EPOR -0.8 0.69 -10000 0 -1.5 73 73
MAPK8 -0.26 0.22 -10000 0 -0.46 73 73
STAT3 (dimer) -0.26 0.21 -10000 0 -0.45 73 73
positive regulation of transcription -0.074 0.1 -10000 0 -10000 0 0
mol:GDP -0.22 0.16 -10000 0 -0.56 9 9
PIK3C2B -0.27 0.22 -10000 0 -0.47 73 73
CBL/CRKL -0.22 0.2 -10000 0 -0.42 49 49
FER -0.28 0.22 -10000 0 -0.46 77 77
SH2B3 -0.26 0.22 -10000 0 -0.46 73 73
PDPK1 -0.22 0.18 -10000 0 -0.39 71 71
SNAI2 -0.28 0.23 -10000 0 -0.48 74 74
positive regulation of cell proliferation -0.48 0.37 -10000 0 -0.82 75 75
KITLG -0.003 0.084 -10000 0 -0.72 2 2
cell motility -0.48 0.37 -10000 0 -0.82 75 75
PTPN6 0.029 0.016 -10000 0 -10000 0 0
EPOR -0.21 0.18 -10000 0 -10000 0 0
STAT5A (dimer) -0.39 0.3 -10000 0 -0.66 74 74
SOCS1 0.017 0 -10000 0 -10000 0 0
cell migration 0.26 0.21 0.45 73 -10000 0 73
SOS1 0.017 0 -10000 0 -10000 0 0
EPO 0 0.062 -10000 0 -0.76 1 1
VAV1 -0.03 0.17 -10000 0 -0.64 11 11
GRB10 -0.29 0.25 -10000 0 -0.5 78 78
PTPN11 0.02 0.064 -10000 0 -0.75 1 1
SCF/KIT -0.3 0.21 0.26 1 -0.5 73 74
GO:0007205 0.015 0.011 -10000 0 -10000 0 0
MAP2K1 -0.1 0.13 -10000 0 -10000 0 0
CBL 0.017 0 -10000 0 -10000 0 0
KIT -0.77 0.73 -10000 0 -1.5 73 73
MAP2K2 -0.1 0.13 -10000 0 -10000 0 0
SHC/Grb2/SOS1 -0.25 0.18 -10000 0 -0.43 64 64
STAT5A -0.4 0.31 -10000 0 -0.68 74 74
GRB2 0.017 0 -10000 0 -10000 0 0
response to radiation -0.27 0.22 -10000 0 -0.47 74 74
SHC/GRAP2 0 0 -10000 0 -10000 0 0
PTPRO -0.31 0.25 -10000 0 -0.5 80 80
SH2B2 -0.28 0.22 -10000 0 -0.47 73 73
DOK1 0.012 0.061 -10000 0 -0.74 1 1
MATK -0.26 0.22 -10000 0 -0.46 73 73
CREBBP 0.013 0.023 -10000 0 -10000 0 0
BCL2 -0.9 0.72 -10000 0 -1.5 91 91
BCR signaling pathway

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
JUN -0.17 0.27 -10000 0 -0.53 48 48
IKBKB -0.089 0.14 -10000 0 -0.28 14 14
AKT1 -0.078 0.17 0.24 2 -0.29 39 41
IKBKG -0.092 0.15 -10000 0 -0.3 19 19
CALM1 -0.3 0.34 -10000 0 -0.65 66 66
PIK3CA 0.017 0 -10000 0 -10000 0 0
MAP3K1 -0.24 0.38 -10000 0 -0.75 48 48
MAP3K7 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ -0.33 0.37 -10000 0 -0.7 68 68
DOK1 0.012 0.061 -10000 0 -0.74 1 1
AP-1 -0.11 0.16 -10000 0 -0.3 43 43
LYN 0.017 0 -10000 0 -10000 0 0
BLNK 0 0.1 -10000 0 -0.64 4 4
SHC1 0.017 0 -10000 0 -10000 0 0
BCR complex -0.34 0.37 -10000 0 -0.69 75 75
CD22 -0.32 0.45 -10000 0 -0.95 47 47
CAMK2G -0.26 0.31 -10000 0 -0.59 66 66
CSNK2A1 0.017 0 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SHC/GRB2/SOS1 -0.22 0.25 -10000 0 -0.58 44 44
GO:0007205 -0.34 0.38 -10000 0 -0.72 68 68
SYK 0.017 0 -10000 0 -10000 0 0
ELK1 -0.3 0.35 -10000 0 -0.67 66 66
NFATC1 -0.26 0.37 -10000 0 -0.68 60 60
B-cell antigen/BCR complex -0.34 0.37 -10000 0 -0.69 75 75
PAG1/CSK -0.16 0.22 -10000 0 -0.47 54 54
NFKBIB -0.016 0.049 -10000 0 -10000 0 0
HRAS -0.27 0.32 -10000 0 -0.61 65 65
NFKBIA -0.016 0.048 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta -0.003 0.04 -10000 0 -10000 0 0
RasGAP/Csk -0.32 0.36 -10000 0 -0.81 47 47
mol:GDP -0.32 0.36 -10000 0 -0.67 68 68
PTEN -0.005 0.12 -10000 0 -0.64 5 5
CD79B -0.18 0.3 -10000 0 -0.64 47 47
NF-kappa-B/RelA/I kappa B alpha -0.002 0.039 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.28 0.36 -10000 0 -0.68 63 63
PIK3R1 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.34 0.39 -10000 0 -0.74 68 68
CSK 0.017 0 -10000 0 -10000 0 0
FOS -0.3 0.34 -10000 0 -0.7 54 54
CHUK -0.092 0.15 -10000 0 -0.3 19 19
IBTK 0.017 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.28 0.28 -10000 0 -0.64 50 50
PTPN6 -0.29 0.41 -10000 0 -0.89 45 45
RELA 0.017 0 -10000 0 -10000 0 0
BCL2A1 -0.003 0.04 -10000 0 -0.11 9 9
VAV2 -0.39 0.5 -10000 0 -0.97 60 60
ubiquitin-dependent protein catabolic process -0.009 0.047 -10000 0 -10000 0 0
BTK -0.18 0.43 -10000 0 -1.2 23 23
CD19 -0.41 0.54 -10000 0 -1 60 60
MAP4K1 0.017 0 -10000 0 -10000 0 0
CD72 0.007 0.086 -10000 0 -0.74 2 2
PAG1 -0.22 0.31 -10000 0 -0.64 54 54
MAPK14 -0.18 0.31 -10000 0 -0.6 47 47
SH3BP5 0.017 0 -10000 0 -10000 0 0
PIK3AP1 -0.34 0.39 -10000 0 -0.74 66 66
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.39 0.45 -10000 0 -0.85 66 66
RAF1 -0.24 0.3 -10000 0 -0.64 46 46
RasGAP/p62DOK/SHIP -0.31 0.35 -10000 0 -0.79 48 48
CD79A -0.29 0.33 -10000 0 -0.64 71 71
re-entry into mitotic cell cycle -0.11 0.16 -10000 0 -0.31 43 43
RASA1 0.012 0.061 -10000 0 -0.74 1 1
MAPK3 -0.18 0.25 -10000 0 -0.52 41 41
MAPK1 -0.17 0.24 -10000 0 -0.52 40 40
CD72/SHP1 -0.24 0.39 -10000 0 -0.81 44 44
NFKB1 0.017 0 -10000 0 -10000 0 0
MAPK8 -0.18 0.31 -10000 0 -0.6 47 47
actin cytoskeleton organization -0.27 0.4 -10000 0 -0.77 56 56
NF-kappa-B/RelA 0.003 0.076 -10000 0 -10000 0 0
Calcineurin -0.25 0.26 -10000 0 -0.62 43 43
PI3K -0.26 0.3 -10000 0 -0.63 56 56
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.38 0.41 -10000 0 -0.8 66 66
SOS1 0.017 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.28 0.41 -10000 0 -0.83 48 48
DAPP1 -0.34 0.46 -10000 0 -0.96 50 50
cytokine secretion -0.23 0.34 -10000 0 -0.62 60 60
mol:DAG -0.34 0.39 -10000 0 -0.74 68 68
PLCG2 -0.31 0.33 -10000 0 -0.64 76 76
MAP2K1 -0.21 0.27 -10000 0 -0.57 46 46
B-cell antigen/BCR complex/FcgammaRIIB -0.37 0.42 -10000 0 -0.93 47 47
mol:PI-3-4-5-P3 -0.17 0.2 0.33 2 -0.43 48 50
ETS1 -0.23 0.28 -10000 0 -0.62 41 41
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.26 0.29 -10000 0 -0.68 44 44
B-cell antigen/BCR complex/LYN -0.34 0.48 -10000 0 -0.99 49 49
MALT1 0.017 0 -10000 0 -10000 0 0
TRAF6 0.017 0 -10000 0 -10000 0 0
RAC1 -0.31 0.45 -10000 0 -0.86 56 56
B-cell antigen/BCR complex/LYN/SYK -0.31 0.39 -10000 0 -0.88 44 44
CARD11 -0.34 0.37 -10000 0 -0.69 73 73
FCGR2B -0.12 0.26 -10000 0 -0.64 31 31
PPP3CA 0.017 0 -10000 0 -10000 0 0
BCL10 0.017 0 -10000 0 -10000 0 0
IKK complex -0.019 0.062 0.11 1 -10000 0 1
PTPRC 0 0.1 -10000 0 -0.64 4 4
PDPK1 -0.073 0.16 0.23 2 -0.28 36 38
PPP3CB 0.017 0 -10000 0 -10000 0 0
PPP3CC 0.008 0.075 -10000 0 -0.64 2 2
POU2F2 0.006 0.029 -10000 0 -10000 0 0
HIF-1-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PKM2 -0.56 0.48 -9999 0 -1.1 47 47
HDAC7 -0.002 0.01 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.4 0.3 -9999 0 -0.78 39 39
SMAD4 0.014 0.053 -9999 0 -0.64 1 1
ID2 -0.55 0.48 -9999 0 -1.1 45 45
AP1 -0.061 0.17 -9999 0 -0.52 18 18
ABCG2 -0.84 0.48 -9999 0 -1.2 78 78
HIF1A -0.075 0.082 -9999 0 -0.9 1 1
TFF3 -0.55 0.48 -9999 0 -1.1 46 46
GATA2 0.018 0.005 -9999 0 -10000 0 0
AKT1 -0.059 0.063 -9999 0 -10000 0 0
response to hypoxia -0.09 0.069 -9999 0 -10000 0 0
MCL1 -0.55 0.48 -9999 0 -1.1 45 45
NDRG1 -0.6 0.52 -9999 0 -1.2 52 52
SERPINE1 -0.64 0.52 -9999 0 -1.2 62 62
FECH -0.55 0.48 -9999 0 -1.1 45 45
FURIN -0.55 0.48 -9999 0 -1.1 45 45
NCOA2 0.019 0.002 -9999 0 -10000 0 0
EP300 -0.053 0.086 -9999 0 -10000 0 0
HMOX1 -0.59 0.52 -9999 0 -1.2 51 51
BHLHE40 -0.56 0.47 -9999 0 -1.1 48 48
BHLHE41 -0.56 0.47 -9999 0 -1.1 48 48
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.068 0.08 -9999 0 -0.53 2 2
ENG -0.035 0.1 -9999 0 -0.54 1 1
JUN -0.008 0.13 -9999 0 -0.74 5 5
RORA -0.56 0.49 -9999 0 -1.2 45 45
ABCB1 -0.63 0.63 -9999 0 -1.3 67 67
TFRC -0.55 0.48 -9999 0 -1.2 46 46
CXCR4 -0.56 0.5 -9999 0 -1.2 46 46
TF -0.55 0.48 -9999 0 -1.1 45 45
CITED2 -0.55 0.48 -9999 0 -1.1 44 44
HIF1A/ARNT -0.66 0.57 -9999 0 -1.3 57 57
LDHA -0.049 0.042 -9999 0 -10000 0 0
ETS1 -0.55 0.48 -9999 0 -1.1 45 45
PGK1 -0.56 0.48 -9999 0 -1.2 45 45
NOS2 -0.56 0.47 -9999 0 -1.1 48 48
ITGB2 -0.55 0.48 -9999 0 -1.1 46 46
ALDOA -0.55 0.48 -9999 0 -1.1 45 45
Cbp/p300/CITED2 -0.55 0.44 -9999 0 -1.1 43 43
FOS -0.044 0.19 -9999 0 -0.65 14 14
HK2 -0.55 0.48 -9999 0 -1.1 45 45
SP1 0.011 0.032 -9999 0 -10000 0 0
GCK -0.077 0.13 -9999 0 -10000 0 0
HK1 -0.55 0.48 -9999 0 -1.1 45 45
NPM1 -0.55 0.48 -9999 0 -1.1 45 45
EGLN1 -0.55 0.48 -9999 0 -1.1 45 45
CREB1 0.028 0 -9999 0 -10000 0 0
PGM1 -0.59 0.5 -9999 0 -1.2 48 48
SMAD3 0.014 0.053 -9999 0 -0.64 1 1
EDN1 -0.096 0.32 -9999 0 -1.3 9 9
IGFBP1 -0.58 0.51 -9999 0 -1.2 50 50
VEGFA -0.38 0.36 -9999 0 -0.98 22 22
HIF1A/JAB1 -0.033 0.06 -9999 0 -0.7 1 1
CP -0.61 0.52 -9999 0 -1.2 55 55
CXCL12 -0.78 0.52 -9999 0 -1.2 74 74
COPS5 0.018 0.002 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.006 0.052 -9999 0 -0.46 2 2
BNIP3 -0.6 0.52 -9999 0 -1.2 53 53
EGLN3 -0.66 0.54 -9999 0 -1.3 53 53
CA9 -0.71 0.5 -9999 0 -1.2 70 70
TERT -0.55 0.48 -9999 0 -1.1 45 45
ENO1 -0.55 0.48 -9999 0 -1.1 45 45
PFKL -0.55 0.48 -9999 0 -1.1 45 45
NCOA1 0.009 0.075 -9999 0 -0.64 2 2
ADM -0.55 0.48 -9999 0 -1.1 45 45
ARNT -0.07 0.047 -9999 0 -10000 0 0
HNF4A 0.014 0.075 -9999 0 -0.64 2 2
ADFP -0.56 0.49 -9999 0 -1.1 47 47
SLC2A1 -0.39 0.36 -9999 0 -0.92 27 27
LEP -0.55 0.48 -9999 0 -1.1 46 46
HIF1A/ARNT/Cbp/p300 -0.42 0.31 -9999 0 -0.82 38 38
EPO -0.25 0.23 -9999 0 -0.82 2 2
CREBBP -0.053 0.086 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/HDAC7 -0.43 0.34 -9999 0 -0.83 45 45
PFKFB3 -0.56 0.5 -9999 0 -1.2 48 48
NT5E -0.56 0.49 -9999 0 -1.2 45 45
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.54 0.5 -10000 0 -1.2 46 46
IL23A -0.68 0.55 -10000 0 -1.3 58 58
NF kappa B1 p50/RelA/I kappa B alpha -0.56 0.49 -10000 0 -1.1 58 58
positive regulation of T cell mediated cytotoxicity -0.59 0.56 -10000 0 -1.2 57 57
ITGA3 -0.54 0.48 -10000 0 -1.1 49 49
IL17F -0.32 0.33 -10000 0 -0.75 30 30
IL12B 0.004 0.068 -10000 0 -0.78 1 1
STAT1 (dimer) -0.58 0.56 -10000 0 -1.2 57 57
CD4 -0.5 0.47 -10000 0 -1.1 40 40
IL23 -0.65 0.51 -10000 0 -1.2 57 57
IL23R -0.1 0.29 -10000 0 -1.6 5 5
IL1B -0.66 0.57 -10000 0 -1.3 58 58
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.52 0.5 -10000 0 -1.2 40 40
TYK2 0.005 0.013 -10000 0 -10000 0 0
STAT4 0.012 0.053 -10000 0 -0.64 1 1
STAT3 0.017 0 -10000 0 -10000 0 0
IL18RAP -0.11 0.26 -10000 0 -0.64 29 29
IL12RB1 0.005 0.013 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.002 0.017 -10000 0 -10000 0 0
IL23R/JAK2 -0.12 0.29 -10000 0 -1.1 9 9
positive regulation of chronic inflammatory response -0.59 0.56 -10000 0 -1.2 57 57
natural killer cell activation 0.007 0.014 0.077 5 -10000 0 5
JAK2 -0.011 0.13 -10000 0 -0.8 4 4
PIK3R1 0.017 0 -10000 0 -10000 0 0
NFKB1 0.013 0.003 -10000 0 -10000 0 0
RELA 0.013 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.61 0.47 -10000 0 -1.1 57 57
ALOX12B -0.5 0.47 -10000 0 -1.1 40 40
CXCL1 -0.71 0.52 -10000 0 -1.2 63 63
T cell proliferation -0.59 0.56 -10000 0 -1.2 57 57
NFKBIA 0.013 0.003 -10000 0 -10000 0 0
IL17A -0.25 0.26 -10000 0 -0.58 22 22
PI3K -0.53 0.5 -10000 0 -1.1 57 57
IFNG -0.039 0.047 0.16 1 -0.11 11 12
STAT3 (dimer) -0.49 0.47 -10000 0 -1 55 55
IL18R1 0.01 0.053 -10000 0 -0.64 1 1
IL23/IL23R/JAK2/TYK2/SOCS3 -0.28 0.29 -10000 0 -0.8 17 17
IL18/IL18R -0.094 0.22 -10000 0 -0.46 33 33
macrophage activation -0.032 0.016 -10000 0 -0.045 67 67
TNF -0.6 0.51 -10000 0 -1.2 55 55
STAT3/STAT4 -0.55 0.48 -10000 0 -1.1 57 57
STAT4 (dimer) -0.56 0.54 -10000 0 -1.2 56 56
IL18 -0.051 0.2 -10000 0 -0.65 15 15
IL19 -0.51 0.48 -10000 0 -1.1 40 40
STAT5A (dimer) -0.56 0.54 -10000 0 -1.2 56 56
STAT1 -0.057 0.22 -10000 0 -0.74 15 15
SOCS3 -0.043 0.2 -10000 0 -0.74 12 12
CXCL9 -0.6 0.54 -10000 0 -1.2 51 51
MPO -0.52 0.48 -10000 0 -1.1 55 55
positive regulation of humoral immune response -0.59 0.56 -10000 0 -1.2 57 57
IL23/IL23R/JAK2/TYK2 -0.63 0.64 -10000 0 -1.3 57 57
IL6 -0.69 0.55 -10000 0 -1.2 72 72
STAT5A 0.017 0 -10000 0 -10000 0 0
IL2 0.018 0.012 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0.007 0.014 0.077 5 -10000 0 5
CD3E -0.5 0.47 -10000 0 -1.1 40 40
keratinocyte proliferation -0.59 0.56 -10000 0 -1.2 57 57
NOS2 -0.51 0.47 -10000 0 -1 58 58
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A -0.061 0.21 -9999 0 -0.64 18 18
LAT2 -0.22 0.24 -9999 0 -0.49 58 58
AP1 -0.28 0.28 -9999 0 -0.72 34 34
mol:PIP3 -0.28 0.31 -9999 0 -0.61 61 61
IKBKB -0.14 0.17 -9999 0 -0.32 36 36
AKT1 -0.21 0.25 -9999 0 -0.51 21 21
IKBKG -0.13 0.16 -9999 0 -0.32 32 32
MS4A2 -0.36 0.32 -9999 0 -0.64 87 87
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.015 0.002 -9999 0 -10000 0 0
MAP3K1 -0.19 0.24 -9999 0 -0.59 22 22
mol:Ca2+ -0.2 0.23 -9999 0 -0.43 61 61
LYN 0.008 0.009 -9999 0 -10000 0 0
CBLB -0.22 0.24 -9999 0 -0.48 58 58
SHC1 0.017 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.027 0.11 -9999 0 -0.86 1 1
positive regulation of cell migration 0 0.088 -9999 0 -0.48 5 5
INPP5D 0 0 -9999 0 -10000 0 0
PLD2 -0.29 0.28 -9999 0 -0.61 58 58
PTPN13 -0.34 0.3 -9999 0 -0.6 75 75
PTPN11 0.005 0.063 -9999 0 -0.76 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.15 0.2 -9999 0 -0.39 10 10
SYK 0.008 0.009 -9999 0 -10000 0 0
GRB2 0.016 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.33 0.28 -9999 0 -0.63 65 65
LAT -0.23 0.24 -9999 0 -0.5 58 58
PAK2 -0.22 0.28 -9999 0 -0.64 26 26
NFATC2 -0.099 0.08 -9999 0 -10000 0 0
HRAS -0.26 0.3 -9999 0 -0.56 63 63
GAB2 0.017 0 -9999 0 -10000 0 0
PLA2G1B 0.063 0.028 -9999 0 -10000 0 0
Fc epsilon R1 -0.38 0.32 -9999 0 -0.75 58 58
Antigen/IgE/Fc epsilon R1 -0.35 0.3 -9999 0 -0.7 58 58
mol:GDP -0.28 0.33 -9999 0 -0.62 63 63
JUN -0.008 0.14 -9999 0 -0.74 5 5
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.015 0.002 -9999 0 -10000 0 0
FOS -0.045 0.19 -9999 0 -0.66 14 14
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.26 0.23 -9999 0 -0.52 58 58
CHUK -0.13 0.16 -9999 0 -0.32 35 35
KLRG1 -0.21 0.22 -9999 0 -0.46 58 58
VAV1 -0.25 0.26 -9999 0 -0.53 59 59
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.22 0.24 -9999 0 -0.48 58 58
negative regulation of mast cell degranulation -0.21 0.19 -9999 0 -0.43 58 58
BTK -0.33 0.34 -9999 0 -0.67 62 62
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.4 0.42 -9999 0 -0.87 63 63
GAB2/PI3K/SHP2 -0.27 0.23 -9999 0 -0.54 58 58
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.26 0.28 -9999 0 -0.59 58 58
RAF1 0.051 0.034 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.4 0.36 -9999 0 -0.79 62 62
FCER1G 0.02 0.016 -9999 0 -10000 0 0
FCER1A -0.29 0.33 -9999 0 -0.66 70 70
Antigen/IgE/Fc epsilon R1/Fyn -0.33 0.28 -9999 0 -0.65 59 59
MAPK3 0.06 0.031 -9999 0 -10000 0 0
MAPK1 0.062 0.028 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
MAPK8 -0.049 0.11 -9999 0 -0.69 2 2
DUSP1 -0.022 0.16 -9999 0 -0.64 9 9
NF-kappa-B/RelA -0.092 0.074 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.23 0.24 -9999 0 -0.49 58 58
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.25 0.24 -9999 0 -0.67 22 22
FER -0.24 0.25 -9999 0 -0.51 59 59
RELA 0.017 0 -9999 0 -10000 0 0
ITK -0.054 0.045 -9999 0 -10000 0 0
SOS1 0.017 0 -9999 0 -10000 0 0
PLCG1 -0.3 0.35 -9999 0 -0.65 65 65
cytokine secretion -0.067 0.053 -9999 0 -10000 0 0
SPHK1 -0.28 0.27 -9999 0 -0.52 75 75
PTK2 -0.24 0.25 -9999 0 -0.51 58 58
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.34 0.29 -9999 0 -0.66 61 61
EDG1 0 0.088 -9999 0 -0.48 5 5
mol:DAG -0.29 0.32 -9999 0 -0.62 62 62
MAP2K2 0.057 0.029 -9999 0 -10000 0 0
MAP2K1 0.057 0.029 -9999 0 -10000 0 0
MAP2K7 0.017 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.2 0.18 -9999 0 -0.42 58 58
MAP2K4 0 0.12 -9999 0 -1 2 2
Fc epsilon R1/FcgammaRIIB -0.42 0.37 -9999 0 -0.82 62 62
mol:Choline -0.28 0.28 -9999 0 -0.6 58 58
SHC/Grb2/SOS1 -0.22 0.19 -9999 0 -0.44 58 58
FYN 0.012 0.061 -9999 0 -0.74 1 1
DOK1 0.012 0.061 -9999 0 -0.74 1 1
PXN -0.21 0.23 -9999 0 -0.47 58 58
HCLS1 -0.24 0.27 -9999 0 -0.53 58 58
PRKCB -0.2 0.23 -9999 0 -0.44 61 61
FCGR2B -0.12 0.26 -9999 0 -0.64 31 31
IGHE -0.007 0.008 -9999 0 -10000 0 0
KLRG1/SHIP -0.22 0.19 -9999 0 -0.44 58 58
LCP2 0.002 0.1 -9999 0 -0.71 3 3
PLA2G4A -0.33 0.31 -9999 0 -0.59 76 76
RASA1 0.012 0.061 -9999 0 -0.74 1 1
mol:Phosphatidic acid -0.28 0.28 -9999 0 -0.6 58 58
IKK complex -0.084 0.13 -9999 0 -0.27 1 1
WIPF1 0.017 0 -9999 0 -10000 0 0
Osteopontin-mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer -0.28 0.22 -9999 0 -0.47 47 47
NF kappa B1 p50/RelA/I kappa B alpha -0.27 0.18 -9999 0 -0.47 47 47
alphaV/beta3 Integrin/Osteopontin/Src -0.41 0.25 -9999 0 -0.56 112 112
AP1 -0.29 0.18 -9999 0 -0.65 13 13
ILK -0.29 0.22 -9999 0 -0.47 47 47
bone resorption -0.26 0.18 -9999 0 -0.71 9 9
PTK2B 0.017 0 -9999 0 -10000 0 0
PYK2/p130Cas -0.27 0.17 -9999 0 -0.81 1 1
ITGAV 0.012 0.062 -9999 0 -0.75 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.033 0.13 -9999 0 -0.55 9 9
alphaV/beta3 Integrin/Osteopontin -0.35 0.22 -9999 0 -0.48 112 112
MAP3K1 -0.3 0.22 -9999 0 -0.48 48 48
JUN -0.008 0.13 -9999 0 -0.74 5 5
MAPK3 -0.3 0.24 -9999 0 -0.54 49 49
MAPK1 -0.29 0.23 -9999 0 -0.53 47 47
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
MAPK8 -0.27 0.21 -9999 0 -0.44 47 47
ITGB3 0.017 0.006 -9999 0 -10000 0 0
NFKBIA -0.28 0.24 -9999 0 -0.53 49 49
FOS -0.045 0.19 -9999 0 -0.65 14 14
CD44 -0.028 0.18 -9999 0 -0.74 9 9
CHUK 0.017 0 -9999 0 -10000 0 0
PLAU -0.37 0.35 -9999 0 -0.82 48 48
NF kappa B1 p50/RelA -0.28 0.19 -9999 0 -0.67 4 4
BCAR1 0.017 0 -9999 0 -10000 0 0
RELA 0.017 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.004 0.046 -9999 0 -0.57 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.3 0.22 -9999 0 -0.42 112 112
VAV3 -0.34 0.29 -9999 0 -0.61 56 56
MAP3K14 -0.31 0.23 -9999 0 -0.51 48 48
ROCK2 0.017 0 -9999 0 -10000 0 0
SPP1 -0.54 0.34 -9999 0 -0.74 112 112
RAC1 0.017 0 -9999 0 -10000 0 0
Rac1/GTP -0.32 0.24 -9999 0 -0.69 31 31
MMP2 -0.21 0.19 -9999 0 -0.64 4 4
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.027 0.11 -10000 0 -0.47 8 8
fibroblast growth factor receptor signaling pathway -0.027 0.11 -10000 0 -0.47 8 8
LAMA1 0.017 0 -10000 0 -10000 0 0
PRNP 0.017 0 -10000 0 -10000 0 0
GPC1/SLIT2 -0.27 0.24 -10000 0 -0.48 86 86
SMAD2 0.025 0.097 -10000 0 -10000 0 0
GPC1/PrPc/Cu2+ -0.022 0.1 -10000 0 -0.48 7 7
GPC1/Laminin alpha1 -0.025 0.12 -10000 0 -0.55 7 7
TDGF1 -0.45 0.37 -10000 0 -0.74 95 95
CRIPTO/GPC1 -0.36 0.28 -10000 0 -0.57 98 98
APP/GPC1 -0.025 0.12 -10000 0 -0.55 7 7
mol:NO 0 0 -10000 0 -10000 0 0
YES1 -0.3 0.26 -10000 0 -0.49 95 95
FLT1 -0.033 0.19 -10000 0 -0.74 10 10
GPC1/TGFB/TGFBR1/TGFBR2 -0.022 0.098 -10000 0 -0.47 7 7
SERPINC1 0.012 0.061 -10000 0 -0.74 1 1
FYN -0.3 0.26 -10000 0 -0.49 96 96
FGR -0.3 0.26 -10000 0 -0.49 95 95
positive regulation of MAPKKK cascade -0.23 0.22 -10000 0 -0.55 26 26
SLIT2 -0.33 0.33 -10000 0 -0.64 80 80
GPC1/NRG -0.025 0.12 -10000 0 -0.55 7 7
NRG1 0.017 0 -10000 0 -10000 0 0
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.11 0.23 -10000 0 -0.54 30 30
LYN -0.3 0.26 -10000 0 -0.49 95 95
mol:Spermine -0.011 0.12 -10000 0 -0.57 7 7
cell growth -0.027 0.11 -10000 0 -0.47 8 8
BMP signaling pathway 0.018 0.16 0.74 7 -10000 0 7
SRC -0.3 0.26 -10000 0 -0.49 95 95
TGFBR1 0.017 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.13 0.29 -10000 0 -0.68 33 33
GPC1 -0.018 0.16 -10000 0 -0.74 7 7
TGFBR1 (dimer) 0.017 0 -10000 0 -10000 0 0
VEGFA -0.072 0.24 -10000 0 -0.74 18 18
BLK -0.35 0.31 -10000 0 -0.55 95 95
HCK -0.33 0.28 -10000 0 -0.53 95 95
FGF2 0.008 0.08 -10000 0 -0.69 2 2
FGFR1 0.017 0 -10000 0 -10000 0 0
VEGFR1 homodimer -0.033 0.19 -10000 0 -0.74 10 10
TGFBR2 0.017 0 -10000 0 -10000 0 0
cell death -0.025 0.12 -10000 0 -0.55 7 7
ATIII/GPC1 -0.029 0.12 -10000 0 -0.55 8 8
PLA2G2A/GPC1 -0.13 0.24 -10000 0 -0.53 38 38
LCK -0.3 0.26 -10000 0 -0.49 96 96
neuron differentiation -0.025 0.12 -10000 0 -0.55 7 7
PrPc/Cu2+ 0 0 -10000 0 -10000 0 0
APP 0.017 0 -10000 0 -10000 0 0
TGFBR2 (dimer) 0.017 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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
NFATC3 -0.4 0.55 -9999 0 -1.2 32 32
PLK1 0.02 0.06 -9999 0 -10000 0 0
BIRC5 -0.059 0.23 -9999 0 -0.63 19 19
HSPA1B -0.41 0.55 -9999 0 -1.1 42 42
MAP2K1 0.012 0.034 -9999 0 -10000 0 0
BRCA2 -0.5 0.59 -9999 0 -1.3 41 41
FOXM1 -0.56 0.78 -9999 0 -1.6 40 40
XRCC1 -0.4 0.55 -9999 0 -1.2 33 33
FOXM1B/p19 -0.64 0.56 -9999 0 -1.3 56 56
Cyclin D1/CDK4 -0.44 0.53 -9999 0 -1.1 40 40
CDC2 -0.45 0.6 -9999 0 -1.3 35 35
TGFA -0.39 0.5 -9999 0 -1.1 29 29
SKP2 -0.45 0.59 -9999 0 -1.3 36 36
CCNE1 -0.031 0.17 -9999 0 -0.75 8 8
CKS1B -0.41 0.56 -9999 0 -1.2 31 31
RB1 -0.25 0.24 -9999 0 -0.65 27 27
FOXM1C/SP1 -0.56 0.67 -9999 0 -1.5 43 43
AURKB 0.02 0.06 -9999 0 -10000 0 0
CENPF -0.41 0.55 -9999 0 -1.2 31 31
CDK4 -0.06 0.22 -9999 0 -0.75 14 14
MYC -0.56 0.51 -9999 0 -1.1 54 54
CHEK2 0.012 0.034 -9999 0 -10000 0 0
ONECUT1 -0.44 0.55 -9999 0 -1.2 37 37
CDKN2A -0.24 0.36 -9999 0 -0.74 52 52
LAMA4 -0.4 0.55 -9999 0 -1.2 32 32
FOXM1B/HNF6 -0.53 0.68 -9999 0 -1.5 38 38
FOS -0.46 0.58 -9999 0 -1.2 38 38
SP1 0.01 0.015 -9999 0 -10000 0 0
CDC25B -0.53 0.6 -9999 0 -1.2 46 46
response to radiation -0.013 0.035 -9999 0 -10000 0 0
CENPB -0.4 0.55 -9999 0 -1.2 33 33
CENPA -0.45 0.6 -9999 0 -1.2 41 41
NEK2 -0.51 0.62 -9999 0 -1.2 49 49
HIST1H2BA -0.41 0.55 -9999 0 -1.2 31 31
CCNA2 -0.11 0.28 -9999 0 -0.75 24 24
EP300 0.017 0 -9999 0 -10000 0 0
CCNB1/CDK1 -0.51 0.68 -9999 0 -1.5 35 35
CCNB2 -0.4 0.55 -9999 0 -1.2 33 33
CCNB1 -0.46 0.62 -9999 0 -1.3 36 36
ETV5 -0.44 0.57 -9999 0 -1.2 37 37
ESR1 -0.41 0.56 -9999 0 -1.2 31 31
CCND1 -0.44 0.54 -9999 0 -1.1 39 39
GSK3A 0.013 0.028 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 -0.16 0.32 -9999 0 -0.62 42 42
CDK2 -0.1 0.27 -9999 0 -0.75 22 22
G2/M transition of mitotic cell cycle -0.016 0.042 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.51 0.53 -9999 0 -1.2 46 46
GAS1 -0.52 0.62 -9999 0 -1.3 49 49
MMP2 -0.4 0.55 -9999 0 -1.2 31 31
RB1/FOXM1C -0.46 0.56 -9999 0 -1.2 42 42
CREBBP 0.017 0 -9999 0 -10000 0 0
IL6-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
BCL2L1 -0.32 0.22 -9999 0 -0.78 9 9
CRP -0.32 0.22 -9999 0 -0.7 15 15
cell cycle arrest -0.37 0.26 -9999 0 -0.75 28 28
TIMP1 -0.45 0.25 -9999 0 -0.7 61 61
IL6ST 0.008 0.01 -9999 0 -10000 0 0
Rac1/GDP -0.34 0.2 -9999 0 -0.56 55 55
AP1 -0.061 0.15 -9999 0 -0.58 5 5
GAB2 0.021 0.008 -9999 0 -10000 0 0
TNFSF11 -0.42 0.3 -9999 0 -0.81 45 45
HSP90B1 -0.036 0.092 -9999 0 -0.62 1 1
GAB1 0.015 0.053 -9999 0 -0.64 1 1
MAPK14 -0.31 0.24 -9999 0 -0.57 54 54
AKT1 0.062 0.027 -9999 0 -10000 0 0
FOXO1 0.059 0.066 -9999 0 -10000 0 0
MAP2K6 -0.34 0.23 -9999 0 -0.58 62 62
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
MAP2K4 -0.34 0.21 -9999 0 -0.6 42 42
MITF -0.33 0.2 -9999 0 -0.54 60 60
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.017 0 -9999 0 -10000 0 0
A2M -0.16 0.51 -9999 0 -1.5 20 20
CEBPB 0.013 0.1 -9999 0 -0.73 3 3
GRB2/SOS1/GAB family/SHP2 -0.084 0.088 -9999 0 -0.44 1 1
STAT3 -0.38 0.27 -9999 0 -0.74 38 38
STAT1 -0.056 0.095 -9999 0 -0.34 15 15
CEBPD -0.32 0.22 -9999 0 -0.76 9 9
PIK3CA 0.019 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
JUN -0.009 0.14 -9999 0 -0.74 5 5
PIAS3/MITF -0.31 0.19 -9999 0 -0.52 54 54
MAPK11 -0.31 0.24 -9999 0 -0.57 55 55
STAT3 (dimer)/FOXO1 -0.29 0.21 -9999 0 -0.66 18 18
GRB2/SOS1/GAB family -0.27 0.18 -9999 0 -0.5 39 39
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.36 0.22 -9999 0 -0.56 69 69
GRB2 0.019 0.004 -9999 0 -10000 0 0
JAK2 -0.003 0.12 -9999 0 -0.74 4 4
LBP -0.24 0.18 -9999 0 -0.73 4 4
PIK3R1 0.018 0 -9999 0 -10000 0 0
JAK1 0.01 0.01 -9999 0 -10000 0 0
MYC -0.47 0.3 -9999 0 -0.76 65 65
FGG -0.32 0.22 -9999 0 -0.68 18 18
macrophage differentiation -0.37 0.26 -9999 0 -0.75 28 28
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.47 0.28 -9999 0 -0.71 70 70
JUNB -0.32 0.22 -9999 0 -0.81 9 9
FOS -0.045 0.19 -9999 0 -0.66 14 14
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.36 0.21 -9999 0 -0.53 79 79
STAT1/PIAS1 -0.32 0.18 -9999 0 -0.52 53 53
GRB2/SOS1/GAB family/SHP2/PI3K 0.043 0.031 -9999 0 -10000 0 0
STAT3 (dimer) -0.38 0.27 -9999 0 -0.78 29 29
PRKCD -0.34 0.22 -9999 0 -0.67 25 25
IL6R -0.37 0.32 -9999 0 -0.65 90 90
SOCS3 -0.28 0.25 -9999 0 -0.8 18 18
gp130 (dimer)/JAK1/JAK1/LMO4 -0.008 0.1 -9999 0 -0.46 7 7
Rac1/GTP -0.35 0.2 -9999 0 -0.55 61 61
HCK -0.043 0.19 -9999 0 -0.64 14 14
MAPKKK cascade -0.029 0.076 -9999 0 -10000 0 0
bone resorption -0.4 0.28 -9999 0 -0.76 45 45
IRF1 -0.33 0.23 -9999 0 -0.72 18 18
mol:GDP -0.36 0.21 -9999 0 -0.55 69 69
SOS1 0.02 0.008 -9999 0 -10000 0 0
VAV1 -0.36 0.22 -9999 0 -0.56 69 69
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.38 0.28 -9999 0 -0.66 60 60
PTPN11 -0.024 0.031 -9999 0 -0.33 1 1
IL6/IL6RA -0.58 0.31 -9999 0 -0.68 132 132
gp130 (dimer)/TYK2/TYK2/LMO4 -0.015 0.098 -9999 0 -0.46 7 7
gp130 (dimer)/JAK2/JAK2/LMO4 -0.026 0.15 -9999 0 -0.62 8 8
IL6 -0.44 0.37 -9999 0 -0.75 91 91
PIAS3 0.012 0.061 -9999 0 -0.74 1 1
PTPRE 0.015 0.061 -9999 0 -0.72 1 1
PIAS1 0.017 0 -9999 0 -10000 0 0
RAC1 0.016 0.001 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.33 0.19 -9999 0 -0.49 70 70
LMO4 -0.025 0.15 -9999 0 -0.72 7 7
STAT3 (dimer)/PIAS3 -0.38 0.24 -9999 0 -0.7 36 36
MCL1 0.07 0.025 -9999 0 -10000 0 0
Reelin signaling pathway

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
CDK5R1/CDK5 -0.004 0.045 -9999 0 -0.55 1 1
VLDLR -0.13 0.28 -9999 0 -0.64 35 35
CRKL 0.017 0 -9999 0 -10000 0 0
LRPAP1 0.017 0 -9999 0 -10000 0 0
FYN 0.012 0.061 -9999 0 -0.74 1 1
ITGA3 0.012 0.061 -9999 0 -0.74 1 1
RELN/VLDLR/Fyn -0.093 0.17 -9999 0 -0.4 35 35
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.005 0.044 -9999 0 -10000 0 0
AKT1 -0.013 0.12 -9999 0 -10000 0 0
MAP2K7 0.017 0 -9999 0 -10000 0 0
RAPGEF1 0.017 0 -9999 0 -10000 0 0
DAB1 0.017 0 -9999 0 -10000 0 0
RELN/LRP8/DAB1 -0.38 0.15 -9999 0 -0.43 133 133
LRPAP1/LRP8 -0.48 0.19 -9999 0 -0.55 133 133
RELN/LRP8/DAB1/Fyn -0.35 0.13 -9999 0 -0.4 134 134
DAB1/alpha3/beta1 Integrin -0.38 0.18 -9999 0 -0.67 33 33
long-term memory -0.39 0.2 -9999 0 -0.76 25 25
DAB1/LIS1 -0.39 0.19 -9999 0 -0.69 32 32
DAB1/CRLK/C3G -0.37 0.19 -9999 0 -0.67 32 32
PIK3CA 0.017 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.39 0.19 -9999 0 -0.7 32 32
ARHGEF2 0.012 0.061 -9999 0 -0.74 1 1
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A 0.017 0 -9999 0 -10000 0 0
CDK5R1 0.017 0 -9999 0 -10000 0 0
RELN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
RELN/LRP8/Fyn -0.41 0.16 -9999 0 -0.47 134 134
GRIN2A/RELN/LRP8/DAB1/Fyn -0.34 0.13 -9999 0 -10000 0 0
MAPK8 0.017 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.082 0.15 -9999 0 -0.43 1 1
ITGB1 0.012 0.061 -9999 0 -0.74 1 1
MAP1B -0.37 0.2 -9999 0 -0.68 32 32
RELN/LRP8 -0.41 0.16 -9999 0 -0.47 133 133
GRIN2B/RELN/LRP8/DAB1/Fyn -0.41 0.21 -9999 0 -0.8 25 25
PI3K 0 0 -9999 0 -10000 0 0
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.007 0.063 -9999 0 -0.55 2 2
RAP1A -0.33 0.19 -9999 0 -0.62 32 32
PAFAH1B1 0.017 0 -9999 0 -10000 0 0
MAPK8IP1 0.012 0.061 -9999 0 -0.74 1 1
CRLK/C3G 0 0 -9999 0 -10000 0 0
GRIN2B -0.12 0.29 -9999 0 -0.74 27 27
NCK2 0.017 0 -9999 0 -10000 0 0
neuron differentiation -0.12 0.074 -9999 0 -0.38 1 1
neuron adhesion -0.31 0.18 -9999 0 -0.58 33 33
LRP8 -0.64 0.26 -9999 0 -0.74 133 133
GSK3B -0.002 0.12 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/Fyn -0.078 0.15 -9999 0 -0.57 2 2
MAP3K11 0.017 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.027 0.13 -9999 0 -10000 0 0
CDK5 0.012 0.061 -9999 0 -0.74 1 1
MAPT 0.014 0.026 -9999 0 -10000 0 0
neuron migration -0.26 0.17 -9999 0 -0.51 33 33
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.13 0.075 -9999 0 -0.38 1 1
RELN/VLDLR -0.45 0.21 -9999 0 -0.5 133 133
Endothelins

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
AKT1 -0.016 0.3 -10000 0 -0.59 20 20
PTK2B 0.017 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.031 0.18 -10000 0 -0.84 2 2
EDN1 0.076 0.19 -10000 0 -0.62 9 9
EDN3 -0.4 0.32 -10000 0 -0.64 96 96
EDN2 -0.49 0.27 -10000 0 -0.64 119 119
HRAS/GDP -0.059 0.21 -10000 0 -0.54 11 11
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.029 0.18 -10000 0 -0.42 14 14
ADCY4 -0.032 0.23 -10000 0 -0.69 4 4
ADCY5 -0.032 0.23 -10000 0 -0.69 4 4
ADCY6 -0.032 0.23 -10000 0 -0.69 4 4
ADCY7 -0.032 0.23 -10000 0 -0.69 4 4
ADCY1 -0.032 0.23 -10000 0 -0.69 4 4
ADCY2 -0.035 0.23 -10000 0 -0.69 4 4
ADCY3 -0.057 0.25 -10000 0 -0.66 9 9
ADCY8 -0.035 0.23 -10000 0 -0.69 4 4
ADCY9 -0.032 0.23 -10000 0 -0.69 4 4
arachidonic acid secretion -0.082 0.25 -10000 0 -0.61 19 19
ETB receptor/Endothelin-1/Gq/GTP -0.03 0.2 -10000 0 -0.59 10 10
GNAO1 0.017 0 -10000 0 -10000 0 0
HRAS 0.016 0.004 -10000 0 -10000 0 0
ETA receptor/Endothelin-1/G12/GTP 0.074 0.34 0.34 74 -0.54 20 94
ETA receptor/Endothelin-1/Gs/GTP 0.068 0.32 0.32 72 -0.55 13 85
mol:GTP 0.002 0.004 -10000 0 -10000 0 0
COL3A1 -0.02 0.31 -10000 0 -0.98 4 4
EDNRB -0.081 0.22 -10000 0 -0.65 20 20
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.015 0.29 -10000 0 -0.58 20 20
CYSLTR1 -0.018 0.3 -10000 0 -0.78 5 5
SLC9A1 0.026 0.16 -10000 0 -0.36 3 3
mol:GDP -0.074 0.22 -10000 0 -0.53 16 16
SLC9A3 -0.46 0.37 -10000 0 -0.77 72 72
RAF1 -0.066 0.21 -10000 0 -0.53 16 16
JUN 0.03 0.19 -10000 0 -0.6 3 3
JAK2 -0.029 0.31 -10000 0 -0.6 22 22
mol:IP3 -0.057 0.19 -10000 0 -0.5 12 12
ETA receptor/Endothelin-1 0.071 0.41 0.4 79 -0.68 20 99
PLCB1 -0.21 0.34 -10000 0 -0.74 45 45
PLCB2 0.016 0.005 -10000 0 -10000 0 0
ETA receptor/Endothelin-3 -0.37 0.34 -10000 0 -0.55 112 112
FOS -0.075 0.31 -10000 0 -0.92 15 15
Gai/GDP -0.002 0.097 -10000 0 -10000 0 0
CRK 0.013 0.053 -10000 0 -0.64 1 1
mol:Ca ++ -0.092 0.3 -10000 0 -0.67 20 20
BCAR1 0.017 0 -10000 0 -10000 0 0
PRKCB1 -0.2 0.26 -10000 0 -0.55 36 36
GNAQ 0.002 0.005 -10000 0 -10000 0 0
GNAZ 0.017 0 -10000 0 -10000 0 0
GNAL 0.017 0 -10000 0 -10000 0 0
Gs family/GDP -0.11 0.15 -10000 0 -0.49 14 14
ETA receptor/Endothelin-1/Gq/GTP 0.009 0.2 -10000 0 -0.52 9 9
MAPK14 -0.047 0.17 -10000 0 -0.49 10 10
TRPC6 0.03 0.19 -10000 0 -0.91 2 2
GNAI2 0.012 0.061 -10000 0 -0.74 1 1
GNAI3 0.017 0 -10000 0 -10000 0 0
GNAI1 -0.056 0.21 -10000 0 -0.64 17 17
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.061 0.18 -10000 0 -0.46 17 17
ETB receptor/Endothelin-2 -0.42 0.22 -10000 0 -0.51 126 126
ETB receptor/Endothelin-3 -0.35 0.28 -10000 0 -0.54 99 99
ETB receptor/Endothelin-1 -0.015 0.24 -10000 0 -0.53 17 17
MAPK3 -0.073 0.29 -10000 0 -0.81 16 16
MAPK1 -0.072 0.28 -10000 0 -0.8 16 16
Rac1/GDP -0.059 0.2 -10000 0 -0.53 11 11
cAMP biosynthetic process 0.01 0.21 -10000 0 -0.56 4 4
MAPK8 0.026 0.18 -10000 0 -0.69 2 2
SRC 0.017 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.007 0.14 -10000 0 -0.43 6 6
p130Cas/CRK/Src/PYK2 -0.067 0.21 -10000 0 -0.61 8 8
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.059 0.2 -10000 0 -0.51 13 13
COL1A2 -0.1 0.41 -10000 0 -0.87 23 23
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.45 0.32 -10000 0 -0.56 126 126
mol:DAG -0.057 0.19 -10000 0 -0.5 12 12
MAP2K2 -0.063 0.24 -10000 0 -0.65 15 15
MAP2K1 -0.063 0.24 -10000 0 -0.65 15 15
EDNRA -0.073 0.38 -10000 0 -0.7 39 39
positive regulation of muscle contraction 0 0.26 -10000 0 -0.72 4 4
Gq family/GDP -0.098 0.2 -10000 0 -0.6 13 13
HRAS/GTP -0.072 0.2 -10000 0 -0.5 15 15
PRKCH -0.051 0.19 -10000 0 -0.55 11 11
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.045 0.18 -10000 0 -0.54 8 8
PRKCB -0.055 0.18 -10000 0 -0.47 13 13
PRKCE -0.044 0.18 -10000 0 -0.54 8 8
PRKCD -0.044 0.18 -10000 0 -0.54 8 8
PRKCG -0.055 0.19 -10000 0 -0.54 11 11
regulation of vascular smooth muscle contraction -0.091 0.36 -10000 0 -1.1 14 14
PRKCQ -0.052 0.19 -10000 0 -0.54 10 10
PLA2G4A -0.092 0.27 -10000 0 -0.67 19 19
GNA14 -0.007 0.13 -10000 0 -0.64 6 6
GNA15 -0.002 0.12 -10000 0 -0.74 4 4
GNA12 0.017 0 -10000 0 -10000 0 0
GNA11 -0.026 0.16 -10000 0 -0.64 10 10
Rac1/GTP 0.075 0.34 0.34 72 -0.54 20 92
MMP1 -0.56 0.19 -10000 0 -0.61 140 140
FAS signaling pathway (CD95)

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
SPTAN1 0.16 0.14 0.38 1 -0.34 1 2
RFC1 0.16 0.14 0.38 1 -10000 0 1
PRKDC 0.11 0.2 0.38 1 -0.52 6 7
RIPK1 0.02 0.005 -10000 0 -10000 0 0
CASP7 -0.12 0.26 -10000 0 -0.75 21 21
FASLG/FAS/FADD/FAF1 -0.02 0.2 0.44 1 -0.46 14 15
MAP2K4 -0.11 0.18 -10000 0 -0.49 16 16
mol:ceramide -0.099 0.18 -10000 0 -0.57 13 13
GSN 0.09 0.19 0.27 35 -0.38 6 41
FASLG/FAS/FADD/FAF1/Caspase 8 -0.06 0.18 0.28 1 -0.53 11 12
FAS -0.061 0.2 -10000 0 -0.64 16 16
BID -0.015 0.09 -10000 0 -0.49 5 5
MAP3K1 -0.06 0.2 0.28 1 -0.58 14 15
MAP3K7 0.007 0.009 -10000 0 -10000 0 0
RB1 0.16 0.14 0.27 43 -0.34 1 44
CFLAR 0.02 0.005 -10000 0 -10000 0 0
HGF/MET -0.38 0.34 -10000 0 -0.61 94 94
ARHGDIB 0.15 0.14 0.38 1 -0.34 1 2
FADD 0.007 0.009 -10000 0 -10000 0 0
actin filament polymerization -0.09 0.19 0.38 6 -0.27 36 42
NFKB1 -0.098 0.068 -10000 0 -10000 0 0
MAPK8 -0.15 0.19 -10000 0 -0.53 14 14
DFFA 0.16 0.14 0.27 39 -0.34 1 40
DNA fragmentation during apoptosis 0.15 0.15 0.38 1 -0.4 2 3
FAS/FADD/MET -0.27 0.26 -10000 0 -0.5 82 82
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 0.014 0.061 -10000 0 -0.74 1 1
FAF1 0.008 0.009 -10000 0 -10000 0 0
PARP1 0.16 0.14 0.38 1 -0.34 1 2
DFFB 0.15 0.15 0.38 1 -0.4 2 3
CHUK -0.081 0.058 -10000 0 -10000 0 0
FASLG -0.087 0.23 -10000 0 -0.64 22 22
FAS/FADD -0.049 0.14 -10000 0 -0.47 16 16
HGF 0.017 0 -10000 0 -10000 0 0
LMNA 0.14 0.12 0.34 1 -10000 0 1
CASP6 0.16 0.14 0.38 1 -10000 0 1
CASP10 0.003 0.053 -10000 0 -0.64 1 1
CASP3 0.18 0.16 0.31 91 -0.39 1 92
PTPN13 -0.23 0.35 -10000 0 -0.73 51 51
CASP8 0.002 0.028 0.35 1 -10000 0 1
IL6 -0.32 0.28 -10000 0 -0.55 91 91
MET -0.35 0.38 -10000 0 -0.74 74 74
ICAD/CAD 0.14 0.14 0.35 1 -0.43 1 2
FASLG/FAS/FADD/FAF1/Caspase 10 -0.1 0.18 -10000 0 -0.58 13 13
activation of caspase activity by cytochrome c -0.015 0.089 -10000 0 -0.49 5 5
PAK2 0.15 0.14 0.27 35 -0.34 1 36
BCL2 -0.37 0.32 -10000 0 -0.64 91 91
Visual signal transduction: Rods

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
mol:K + 0.017 0 -9999 0 -10000 0 0
GNAT1/GTP 0 0 -9999 0 -10000 0 0
Metarhodopsin II/Arrestin -0.33 0.15 -9999 0 -0.4 126 126
PDE6G/GNAT1/GTP 0 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.017 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
CNG Channel -0.3 0.22 -9999 0 -0.61 42 42
mol:Na + -0.17 0.16 -9999 0 -0.64 5 5
mol:ADP 0 0 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.14 0.2 -9999 0 -0.41 52 52
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.17 0.16 -9999 0 -0.66 5 5
CNGB1 0.017 0 -9999 0 -10000 0 0
RDH5 -0.17 0.3 -9999 0 -0.64 44 44
SAG -0.52 0.25 -9999 0 -0.64 126 126
mol:Ca2+ -0.12 0.18 -9999 0 -0.61 5 5
Na + (4 Units) -0.15 0.14 -9999 0 -0.59 5 5
RGS9 -0.17 0.3 -9999 0 -0.64 43 43
GNB1/GNGT1 -0.22 0.27 -9999 0 -0.55 61 61
GNAT1/GDP -0.12 0.17 -9999 0 -0.43 10 10
GUCY2D 0.017 0 -9999 0 -10000 0 0
GNGT1 -0.28 0.37 -9999 0 -0.74 61 61
GUCY2F 0.008 0.075 -9999 0 -0.64 2 2
GNB5 -0.003 0.12 -9999 0 -0.74 4 4
mol:GMP (4 units) -0.13 0.18 -9999 0 -10000 0 0
mol:11-cis-retinal -0.17 0.3 -9999 0 -0.64 44 44
mol:cGMP -0.021 0.086 -9999 0 -10000 0 0
GNB1 0.017 0 -9999 0 -10000 0 0
Rhodopsin -0.13 0.21 -9999 0 -0.46 44 44
SLC24A1 0.017 0 -9999 0 -10000 0 0
CNGA1 -0.35 0.33 -9999 0 -0.64 85 85
Metarhodopsin II 0 0 -9999 0 -10000 0 0
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.019 0.086 -9999 0 -0.42 6 6
RGS9BP -0.013 0.15 -9999 0 -0.74 6 6
Metarhodopsin II/Transducin -0.071 0.13 -9999 0 -10000 0 0
GCAP Family/Ca ++ -0.019 0.088 -9999 0 -0.43 6 6
PDE6A/B -0.22 0.23 -9999 0 -0.47 73 73
mol:Pi -0.14 0.2 -9999 0 -0.41 52 52
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.17 0.21 -9999 0 -0.43 61 61
PDE6B 0.017 0 -9999 0 -10000 0 0
PDE6A -0.3 0.33 -9999 0 -0.64 73 73
PDE6G 0.017 0 -9999 0 -10000 0 0
RHO 0.017 0 -9999 0 -10000 0 0
PDE6 -0.25 0.24 -9999 0 -0.65 30 30
GUCA1A 0.017 0 -9999 0 -10000 0 0
GC2/GCAP Family -0.023 0.094 -9999 0 -10000 0 0
GUCA1C 0.002 0.1 -9999 0 -0.71 3 3
GUCA1B -0.003 0.12 -9999 0 -0.74 4 4
Canonical Wnt signaling pathway

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
HDAC1 0.079 0.052 -10000 0 -10000 0 0
AES 0.068 0.044 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
mol:GTP 0.002 0.002 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
SMAD4 0.012 0.053 -10000 0 -0.64 1 1
DKK2 -0.31 0.38 -10000 0 -0.74 67 67
TLE1 0.066 0.044 -10000 0 -10000 0 0
MACF1 0.018 0.001 -10000 0 -10000 0 0
CTNNB1 0.1 0.1 0.35 2 -10000 0 2
WIF1 -0.12 0.29 -10000 0 -0.74 27 27
beta catenin/RanBP3 0.31 0.2 0.48 74 -10000 0 74
KREMEN2 -0.12 0.29 -10000 0 -0.74 27 27
DKK1 -0.15 0.31 -10000 0 -0.74 33 33
beta catenin/beta TrCP1 0.11 0.097 0.34 2 -10000 0 2
FZD1 0.016 0.004 -10000 0 -10000 0 0
AXIN2 -0.43 0.34 -10000 0 -0.7 90 90
AXIN1 0.019 0.001 -10000 0 -10000 0 0
RAN 0.019 0.002 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.054 0.059 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.11 0.12 0.32 3 -10000 0 3
Axin1/APC/GSK3 0.14 0.089 0.25 12 -10000 0 12
Axin1/APC/GSK3/beta catenin/Macf1 0.1 0.054 -10000 0 -10000 0 0
HNF1A 0.069 0.046 -10000 0 -10000 0 0
CTBP1 0.07 0.047 -10000 0 -10000 0 0
MYC -0.42 0.33 -10000 0 -0.69 87 87
RANBP3 0.019 0.002 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.28 0.31 -10000 0 -0.56 78 78
NKD1 -0.53 0.34 -10000 0 -0.74 110 110
TCF4 0.072 0.047 -10000 0 -10000 0 0
TCF3 0.069 0.046 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 0.001 0.009 -10000 0 -10000 0 0
Ran/GTP 0.01 0.011 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.36 0.26 0.61 67 -10000 0 67
LEF1 -0.094 0.32 -10000 0 -0.68 34 34
DVL1 0.087 0.052 -10000 0 -10000 0 0
CSNK2A1 0.018 0.001 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES -0.069 0.12 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.18 0.27 -10000 0 -0.54 52 52
LRP6 0.016 0.004 -10000 0 -10000 0 0
CSNK1A1 0.079 0.052 -10000 0 -10000 0 0
NLK 0.003 0.007 -10000 0 -10000 0 0
CCND1 -0.23 0.25 -10000 0 -0.74 24 24
WNT1 0.016 0.004 -10000 0 -10000 0 0
GSK3A 0.017 0.002 -10000 0 -10000 0 0
GSK3B 0.014 0.006 -10000 0 -10000 0 0
FRAT1 0.009 0.053 -10000 0 -0.64 1 1
PPP2R5D 0.26 0.15 0.35 110 -10000 0 110
APC 0.027 0.062 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 0.051 0.099 0.26 27 -10000 0 27
CREBBP 0.069 0.046 -10000 0 -10000 0 0
BMP receptor signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS -0.21 0.19 -9999 0 -10000 0 0
SMAD6-7/SMURF1 -0.006 0.053 -9999 0 -0.47 2 2
NOG 0.017 0 -9999 0 -10000 0 0
SMAD9 -0.11 0.2 -9999 0 -0.55 24 24
SMAD4 0.012 0.053 -9999 0 -0.64 1 1
SMAD5 -0.15 0.18 -9999 0 -0.52 15 15
BMP7/USAG1 -0.48 0.32 -9999 0 -0.63 117 117
SMAD5/SKI -0.13 0.17 -9999 0 -0.51 12 12
SMAD1 0.02 0.079 -9999 0 -0.57 2 2
BMP2 -0.099 0.25 -9999 0 -0.64 27 27
SMAD1/SMAD1/SMAD4 -0.012 0.064 -9999 0 -10000 0 0
BMPR1A 0.017 0 -9999 0 -10000 0 0
BMPR1B 0.012 0.061 -9999 0 -0.74 1 1
BMPR1A-1B/BAMBI -0.068 0.16 -9999 0 -0.47 22 22
AHSG 0.017 0 -9999 0 -10000 0 0
CER1 0.012 0.061 -9999 0 -0.74 1 1
BMP2-4/CER1 -0.21 0.28 -9999 0 -0.58 45 45
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.078 0.11 -9999 0 -0.4 2 2
BMP2-4 (homodimer) -0.24 0.32 -9999 0 -0.6 62 62
RGMB -0.003 0.12 -9999 0 -0.74 4 4
BMP6/BMPR2/BMPR1A-1B -0.17 0.17 -9999 0 -10000 0 0
RGMA 0.008 0.075 -9999 0 -0.64 2 2
SMURF1 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.058 0.15 -9999 0 -0.38 16 16
BMP2-4/USAG1 -0.38 0.34 -9999 0 -0.74 57 57
SMAD6/SMURF1/SMAD5 -0.13 0.17 -9999 0 -0.51 12 12
SOSTDC1 -0.28 0.33 -9999 0 -0.64 68 68
BMP7/BMPR2/BMPR1A-1B -0.22 0.21 -9999 0 -0.42 81 81
SKI 0.017 0 -9999 0 -10000 0 0
BMP6 (homodimer) -0.3 0.33 -9999 0 -0.64 73 73
HFE2 0.017 0 -9999 0 -10000 0 0
ZFYVE16 0.017 0 -9999 0 -10000 0 0
MAP3K7 0.017 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.21 0.27 -9999 0 -0.52 62 62
SMAD5/SMAD5/SMAD4 -0.13 0.18 -9999 0 -0.52 13 13
MAPK1 0.017 0 -9999 0 -10000 0 0
TAK1/TAB family -0.061 0.09 -9999 0 -10000 0 0
BMP7 (homodimer) -0.38 0.38 -9999 0 -0.74 80 80
NUP214 0.017 0 -9999 0 -10000 0 0
BMP6/FETUA -0.22 0.23 -9999 0 -0.47 73 73
SMAD1/SKI 0.029 0.075 -9999 0 -0.53 2 2
SMAD6 0.007 0.086 -9999 0 -0.74 2 2
CTDSP2 0.008 0.075 -9999 0 -0.64 2 2
BMP2-4/FETUA -0.21 0.27 -9999 0 -0.52 62 62
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
GREM1 -0.043 0.2 -9999 0 -0.74 12 12
BMPR2 (homodimer) 0.017 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.004 0.045 -9999 0 -0.55 1 1
CHRDL1 0.008 0.08 -9999 0 -0.69 2 2
ENDOFIN/SMAD1 0.029 0.075 -9999 0 -0.53 2 2
SMAD6-7/SMURF1/SMAD1 -0.002 0.071 -9999 0 -0.53 1 1
SMAD6/SMURF1 0.017 0 -9999 0 -10000 0 0
BAMBI -0.087 0.26 -9999 0 -0.74 21 21
SMURF2 -0.043 0.2 -9999 0 -0.74 12 12
BMP2-4/CHRDL1 -0.22 0.28 -9999 0 -0.58 45 45
BMP2-4/GREM1 -0.24 0.32 -9999 0 -0.62 52 52
SMAD7 0.017 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.074 0.2 -9999 0 -0.5 24 24
SMAD1/SMAD6 0.029 0.075 -9999 0 -0.53 2 2
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.38 0.38 -9999 0 -0.74 80 80
BMP6 -0.3 0.33 -9999 0 -0.64 73 73
MAP3K7IP2 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.036 0.13 -9999 0 -0.32 15 15
PPM1A 0.017 0 -9999 0 -10000 0 0
SMAD1/SMURF2 -0.003 0.14 -9999 0 -0.72 2 2
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.012 0.053 -9999 0 -0.64 1 1
PPP1CA 0.017 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
CTDSP1 0.017 0 -9999 0 -10000 0 0
PPP1R15A 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.051 0.15 -9999 0 -0.37 15 15
CHRD 0.017 0 -9999 0 -10000 0 0
BMPR2 0.017 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.061 0.16 -9999 0 -0.4 16 16
BMP4 -0.21 0.35 -9999 0 -0.74 47 47
FST 0.017 0 -9999 0 -10000 0 0
BMP2-4/NOG -0.21 0.27 -9999 0 -0.57 45 45
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.21 0.19 -9999 0 -10000 0 0
TCGA08_p53

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
CDKN2A -0.18 0.28 -10000 0 -0.57 52 52
TP53 -0.061 0.082 -10000 0 -0.26 5 5
Senescence -0.061 0.082 -10000 0 -0.26 5 5
Apoptosis -0.061 0.082 -10000 0 -0.26 5 5
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.096 0.13 0.28 52 -10000 0 52
MDM4 0.017 0 -10000 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.12 0.18 -9999 0 -0.49 18 18
FZD6 -0.038 0.2 -9999 0 -0.74 11 11
WNT6 0.017 0 -9999 0 -10000 0 0
WNT4 -0.031 0.17 -9999 0 -0.65 11 11
FZD3 -0.15 0.31 -9999 0 -0.74 33 33
WNT5A -0.067 0.24 -9999 0 -0.74 17 17
WNT11 -0.13 0.3 -9999 0 -0.74 29 29
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.081 0.18 -9999 0 -0.47 26 26
EPHB2 0.003 0.1 -9999 0 -0.71 3 3
Syndecan-2/TACI -0.006 0.045 -9999 0 -0.39 2 2
LAMA1 0.017 0 -9999 0 -10000 0 0
Syndecan-2/alpha2 ITGB1 -0.15 0.2 -9999 0 -0.4 54 54
HRAS 0.017 0 -9999 0 -10000 0 0
Syndecan-2/CASK -0.001 0.011 -9999 0 -10000 0 0
ITGA5 0.002 0.1 -9999 0 -0.74 3 3
BAX 0.052 0.05 -9999 0 -0.56 1 1
EPB41 0.017 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.001 0.008 -9999 0 -10000 0 0
LAMA3 -0.002 0.11 -9999 0 -0.69 4 4
EZR 0 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 -0.018 0.16 -9999 0 -0.74 7 7
Syndecan-2/MMP2 -0.004 0.039 -9999 0 -0.47 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.19 0.27 -9999 0 -0.56 52 52
dendrite morphogenesis -0.009 0.062 -9999 0 -0.44 3 3
Syndecan-2/GM-CSF -0.25 0.24 -9999 0 -0.47 82 82
determination of left/right symmetry 0.027 0.015 -9999 0 -10000 0 0
Syndecan-2/PKC delta -0.001 0.01 -9999 0 -10000 0 0
GNB2L1 0.017 0 -9999 0 -10000 0 0
MAPK3 -0.21 0.24 -9999 0 -0.43 82 82
MAPK1 -0.21 0.23 -9999 0 -0.42 82 82
Syndecan-2/RACK1 -0.001 0.007 -9999 0 -10000 0 0
NF1 0.017 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 0.027 0.015 -9999 0 -10000 0 0
ITGA2 -0.24 0.36 -9999 0 -0.74 52 52
MAPK8 0.046 0.026 -9999 0 -10000 0 0
Syndecan-2/alpha2/beta1 Integrin -0.14 0.19 -9999 0 -0.4 52 52
Syndecan-2/Kininogen -0.014 0.07 -9999 0 -0.39 5 5
ITGB1 0.012 0.061 -9999 0 -0.74 1 1
SRC 0.05 0.01 -9999 0 -10000 0 0
Syndecan-2/CASK/Protein 4.1 -0.001 0.009 -9999 0 -10000 0 0
extracellular matrix organization -0.001 0.01 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.081 0.18 -9999 0 -0.47 26 26
Syndecan-2/Caveolin-2/Ras -0.02 0.089 -9999 0 -0.42 7 7
Syndecan-2/Laminin alpha3 -0.012 0.07 -9999 0 -0.43 4 4
Syndecan-2/RasGAP -0.003 0.031 -9999 0 -10000 0 0
alpha5/beta1 Integrin -0.014 0.088 -9999 0 -0.55 4 4
PRKCD 0.017 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.01 0.063 -9999 0 -0.45 3 3
GO:0007205 0.004 0.01 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src -0.003 0.029 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
SDCBP 0.017 0 -9999 0 -10000 0 0
TNFRSF13B 0.008 0.075 -9999 0 -0.64 2 2
RASA1 0.012 0.061 -9999 0 -0.74 1 1
alpha2/beta1 Integrin -0.19 0.27 -9999 0 -0.56 52 52
Syndecan-2/Synbindin -0.001 0.01 -9999 0 -10000 0 0
TGFB1 0.017 0 -9999 0 -10000 0 0
CASP3 0.042 0.034 -9999 0 -10000 0 0
FN1 -0.11 0.28 -9999 0 -0.74 26 26
Syndecan-2/IL8 -0.46 0.093 -9999 0 -0.47 147 147
SDC2 0.027 0.015 -9999 0 -10000 0 0
KNG1 -0.005 0.12 -9999 0 -0.64 5 5
Syndecan-2/Neurofibromin -0.001 0.01 -9999 0 -10000 0 0
TRAPPC4 0.017 0 -9999 0 -10000 0 0
CSF2 -0.39 0.38 -9999 0 -0.74 82 82
Syndecan-2/TGFB1 -0.001 0.01 -9999 0 -10000 0 0
Syndecan-2/Syntenin/PI-4-5-P2 -0.001 0.009 -9999 0 -10000 0 0
Syndecan-2/Ezrin -0.001 0.009 -9999 0 -10000 0 0
PRKACA 0.044 0.011 -9999 0 -10000 0 0
angiogenesis -0.45 0.092 -9999 0 -0.47 147 147
MMP2 0.012 0.061 -9999 0 -0.74 1 1
IL8 -0.71 0.15 -9999 0 -0.74 147 147
calcineurin-NFAT signaling pathway -0.006 0.045 -9999 0 -0.39 2 2
HIF-2-alpha transcription factor 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
MMP14 -0.053 0.16 -10000 0 -0.63 10 10
oxygen homeostasis -0.015 0.014 -10000 0 -10000 0 0
TCEB2 0.017 0 -10000 0 -10000 0 0
TCEB1 0.017 0 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C/HIF2A -0.15 0.14 -10000 0 -0.47 6 6
EPO -0.28 0.25 -10000 0 -0.7 19 19
FIH (dimer) 0.002 0.008 -10000 0 -10000 0 0
APEX1 -0.001 0.012 -10000 0 -10000 0 0
SERPINE1 -0.42 0.38 -10000 0 -0.93 43 43
FLT1 -0.045 0.16 -10000 0 -0.62 10 10
ADORA2A -0.33 0.29 -10000 0 -0.81 22 22
germ cell development -0.33 0.29 -10000 0 -0.8 24 24
SLC11A2 -0.38 0.33 -10000 0 -0.83 37 37
BHLHE40 -0.35 0.3 -10000 0 -0.72 45 45
HIF1AN 0.002 0.008 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.22 0.17 -10000 0 -0.48 27 27
ETS1 0.031 0.062 -10000 0 -0.72 1 1
CITED2 -0.013 0.031 -10000 0 -10000 0 0
KDR -0.013 0.052 -10000 0 -10000 0 0
PGK1 -0.35 0.31 -10000 0 -0.87 23 23
SIRT1 0.017 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
HIF2A/ARNT -0.41 0.37 -10000 0 -0.87 45 45
EPAS1 -0.19 0.17 -10000 0 -0.46 28 28
SP1 0.026 0.007 -10000 0 -10000 0 0
ABCG2 -0.68 0.31 -10000 0 -0.83 109 109
EFNA1 -0.34 0.3 -10000 0 -0.84 22 22
FXN -0.33 0.29 -10000 0 -0.81 22 22
POU5F1 -0.34 0.3 -10000 0 -0.84 24 24
neuron apoptosis 0.4 0.35 0.83 45 -10000 0 45
EP300 0.017 0 -10000 0 -10000 0 0
EGLN3 -0.24 0.32 -10000 0 -0.65 56 56
EGLN2 0.004 0.009 -10000 0 -10000 0 0
EGLN1 0.002 0.008 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C 0 0 -10000 0 -10000 0 0
VHL 0.017 0 -10000 0 -10000 0 0
ARNT -0.001 0.012 -10000 0 -10000 0 0
SLC2A1 -0.36 0.33 -10000 0 -0.88 30 30
TWIST1 -0.38 0.35 -10000 0 -0.94 31 31
ELK1 0.028 0 -10000 0 -10000 0 0
HIF2A/ARNT/Cbp/p300 -0.22 0.17 -10000 0 -0.52 14 14
VEGFA -0.38 0.34 -10000 0 -0.86 35 35
CREBBP 0.017 0 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 -0.023 0.17 -10000 0 -0.74 8 8
mol:Halofuginone 0.007 0.001 -10000 0 -10000 0 0
ITGA1 0.007 0.086 -10000 0 -0.74 2 2
CDKN1A 0.031 0.065 -10000 0 -0.39 2 2
PRL-3/alpha Tubulin -0.2 0.26 -10000 0 -0.55 54 54
mol:Ca2+ -0.057 0.3 0.34 33 -0.52 39 72
AGT -0.18 0.33 -10000 0 -0.74 39 39
CCNA2 -0.033 0.19 -10000 0 -0.79 1 1
TUBA1B 0.012 0.061 -10000 0 -0.74 1 1
EGR1 0.003 0.13 -10000 0 -0.55 8 8
CDK2/Cyclin E1 -0.083 0.16 -10000 0 -0.69 3 3
MAPK3 -0.18 0.28 -10000 0 -0.55 55 55
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 -0.17 0.28 -10000 0 -0.55 53 53
PTP4A1 0.028 0.1 -10000 0 -10000 0 0
PTP4A3 -0.24 0.36 -10000 0 -0.74 53 53
PTP4A2 0.017 0 -10000 0 -10000 0 0
ITGB1 -0.18 0.28 -10000 0 -0.55 54 54
SRC 0.017 0 -10000 0 -10000 0 0
RAC1 -0.043 0.12 -10000 0 -0.39 2 2
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.034 0.096 -10000 0 -10000 0 0
RABGGTA 0.017 0 -10000 0 -10000 0 0
BCAR1 0.12 0.16 0.34 53 -10000 0 53
RHOC -0.043 0.12 -10000 0 -0.39 2 2
RHOA -0.043 0.12 -10000 0 -0.39 2 2
cell motility -0.038 0.12 -10000 0 -0.39 2 2
PRL-1/alpha Tubulin 0.031 0.1 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.2 0.27 -10000 0 -0.56 54 54
ROCK1 -0.039 0.12 -10000 0 -0.39 2 2
RABGGTB 0.017 0 -10000 0 -10000 0 0
CDK2 -0.092 0.26 -10000 0 -0.74 22 22
mitosis 0.028 0.1 -10000 0 -10000 0 0
ATF5 0.017 0 -10000 0 -10000 0 0
IL4-mediated signaling events

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
BCL2L1 -0.35 0.52 -10000 0 -1.2 27 27
STAT6 (cleaved dimer) -0.46 0.46 -10000 0 -1.1 41 41
IGHG1 -0.11 0.2 -10000 0 -0.48 4 4
IGHG3 -0.35 0.49 -10000 0 -1.1 35 35
AKT1 -0.15 0.28 -10000 0 -0.65 8 8
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.12 0.23 -10000 0 -0.72 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.15 0.26 -10000 0 -0.61 1 1
THY1 -0.39 0.55 -10000 0 -1.3 27 27
MYB 0.012 0.053 -10000 0 -0.64 1 1
HMGA1 0.017 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.25 0.35 -10000 0 -0.78 23 23
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.16 0.26 -10000 0 -0.59 2 2
SP1 0.021 0.016 -10000 0 -10000 0 0
INPP5D 0 0 -10000 0 -10000 0 0
SOCS5 0.032 0.024 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -0.44 0.45 -10000 0 -1.1 35 35
SOCS1 -0.22 0.35 -10000 0 -0.75 22 22
SOCS3 -0.22 0.34 -10000 0 -0.83 16 16
FCER2 -0.29 0.44 -10000 0 -1.1 15 15
PARP14 0.009 0.086 -10000 0 -0.74 2 2
CCL17 -0.38 0.54 -10000 0 -1.2 28 28
GRB2 0.017 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.11 0.22 -10000 0 -10000 0 0
T cell proliferation -0.35 0.52 -10000 0 -1.2 29 29
IL4R/JAK1 -0.36 0.51 -10000 0 -1.2 29 29
EGR2 -0.38 0.56 -10000 0 -1.3 29 29
JAK2 -0.007 0.13 -10000 0 -0.76 4 4
JAK3 0.014 0.014 -10000 0 -10000 0 0
PIK3R1 0.017 0 -10000 0 -10000 0 0
JAK1 0.012 0.019 -10000 0 -10000 0 0
COL1A2 -0.19 0.32 -10000 0 -0.79 24 24
CCL26 -0.42 0.55 -10000 0 -1.2 34 34
IL4R -0.38 0.55 -10000 0 -1.2 29 29
PTPN6 0.024 0.015 -10000 0 -10000 0 0
IL13RA2 -0.45 0.56 -10000 0 -1.3 35 35
IL13RA1 0.014 0.029 -10000 0 -10000 0 0
IRF4 -0.36 0.64 -10000 0 -1.5 37 37
ARG1 -0.064 0.2 -10000 0 -0.77 4 4
CBL -0.23 0.33 -10000 0 -0.75 20 20
GTF3A -0.38 0.4 -10000 0 -0.83 67 67
PIK3CA 0.017 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.006 0.11 -10000 0 -0.58 4 4
IRF4/BCL6 -0.37 0.57 -10000 0 -1.4 37 37
CD40LG 0.015 0.059 -10000 0 -0.64 1 1
MAPK14 -0.23 0.34 -10000 0 -0.79 19 19
mitosis -0.14 0.27 -10000 0 -0.61 8 8
STAT6 -0.45 0.54 -10000 0 -1.3 30 30
SPI1 0.023 0.016 -10000 0 -10000 0 0
RPS6KB1 -0.13 0.27 -10000 0 -0.61 4 4
STAT6 (dimer) -0.43 0.56 -10000 0 -1.3 30 30
STAT6 (dimer)/PARP14 -0.38 0.55 -10000 0 -1.2 31 31
mast cell activation 0.007 0.016 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.16 0.27 -10000 0 -0.66 7 7
FRAP1 -0.15 0.28 -10000 0 -0.65 8 8
LTA -0.35 0.51 -10000 0 -1.2 29 29
FES 0.012 0.053 -10000 0 -0.64 1 1
T-helper 1 cell differentiation 0.4 0.57 1.3 31 -10000 0 31
CCL11 -0.46 0.64 -10000 0 -1.4 43 43
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.16 0.26 -10000 0 -0.63 6 6
IL2RG 0.01 0.058 -10000 0 -0.68 1 1
IL10 -0.35 0.51 -10000 0 -1.2 29 29
IRS1 0.002 0.1 -10000 0 -0.74 3 3
IRS2 0.017 0 -10000 0 -10000 0 0
IL4 -0.053 0.14 -10000 0 -10000 0 0
IL5 -0.37 0.53 -10000 0 -1.2 28 28
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.28 0.41 -10000 0 -0.89 27 27
COL1A1 -0.6 0.34 -10000 0 -0.89 72 72
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -0.36 0.52 -10000 0 -1.2 26 26
IL2R gamma/JAK3 0.019 0.05 -10000 0 -0.55 1 1
TFF3 -0.37 0.54 -10000 0 -1.2 28 28
ALOX15 -0.36 0.52 -10000 0 -1.2 28 28
MYBL1 0.007 0.086 -10000 0 -0.74 2 2
T-helper 2 cell differentiation -0.29 0.41 -10000 0 -0.91 28 28
SHC1 0.017 0 -10000 0 -10000 0 0
CEBPB 0.009 0.11 -10000 0 -0.73 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.14 0.25 -10000 0 -0.72 1 1
mol:PI-3-4-5-P3 -0.15 0.28 -10000 0 -0.64 9 9
PI3K -0.16 0.29 -10000 0 -0.68 9 9
DOK2 0 0.1 -10000 0 -0.64 4 4
ETS1 0.02 0.061 -10000 0 -0.7 1 1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.095 0.2 -10000 0 -10000 0 0
ITGB3 -0.35 0.51 -10000 0 -1.2 27 27
PIGR -0.38 0.57 -10000 0 -1.3 29 29
IGHE 0.029 0.063 -10000 0 -0.31 1 1
MAPKKK cascade -0.094 0.2 -10000 0 -10000 0 0
BCL6 0.011 0.061 -10000 0 -0.74 1 1
OPRM1 -0.35 0.51 -10000 0 -1.2 25 25
RETNLB -0.56 0.73 -10000 0 -1.5 49 49
SELP -0.43 0.63 -10000 0 -1.4 38 38
AICDA -0.37 0.53 -10000 0 -1.2 33 33
Glucocorticoid receptor regulatory network

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
PCK2 0.043 0.13 -10000 0 -0.76 1 1
SMARCC2 0.017 0 -10000 0 -10000 0 0
SMARCC1 0.002 0.1 -10000 0 -0.74 3 3
TBX21 -0.36 0.44 -10000 0 -0.94 52 52
SUMO2 0.017 0.007 -10000 0 -10000 0 0
STAT1 (dimer) -0.047 0.23 -10000 0 -0.74 15 15
FKBP4 0.012 0.061 -10000 0 -0.74 1 1
FKBP5 0.017 0 -10000 0 -10000 0 0
GR alpha/HSP90/FKBP51/HSP90 0.12 0.17 0.35 13 -0.38 1 14
PRL -0.065 0.14 -10000 0 -0.78 1 1
cortisol/GR alpha (dimer)/TIF2 0.33 0.28 0.63 46 -10000 0 46
RELA -0.14 0.069 -10000 0 -10000 0 0
FGG 0.26 0.23 0.57 23 -10000 0 23
GR beta/TIF2 0.13 0.19 0.39 14 -0.44 6 20
IFNG -0.39 0.38 -10000 0 -0.92 43 43
apoptosis 0.081 0.14 0.59 3 -10000 0 3
CREB1 0.029 0.001 -10000 0 -10000 0 0
histone acetylation -0.085 0.14 -10000 0 -0.36 13 13
BGLAP -0.098 0.15 -10000 0 -10000 0 0
GR/PKAc -0.043 0.25 0.35 5 -0.6 7 12
NF kappa B1 p50/RelA -0.26 0.14 -10000 0 -0.44 38 38
SMARCD1 0.017 0 -10000 0 -10000 0 0
MDM2 0.14 0.091 0.31 18 -10000 0 18
GATA3 0.029 0.026 -10000 0 -10000 0 0
AKT1 0.002 0.021 -10000 0 -10000 0 0
CSF2 -0.31 0.29 -10000 0 -0.66 37 37
GSK3B 0.017 0.007 -10000 0 -10000 0 0
NR1I3 0.11 0.12 0.56 3 -10000 0 3
CSN2 0.21 0.18 0.47 14 -10000 0 14
BRG1/BAF155/BAF170/BAF60A -0.008 0.058 -10000 0 -0.42 3 3
NFATC1 0.024 0.061 -10000 0 -0.72 1 1
POU2F1 0.026 0.011 -10000 0 -10000 0 0
CDKN1A 0 0.18 -10000 0 -1.5 2 2
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.007 -10000 0 -10000 0 0
SFN 0.012 0.053 -10000 0 -0.64 1 1
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.12 0.16 0.35 12 -10000 0 12
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.092 0.16 0.54 3 -0.56 2 5
JUN -0.21 0.2 -10000 0 -0.59 20 20
IL4 -0.1 0.16 -10000 0 -0.55 1 1
CDK5R1 0.016 0.005 -10000 0 -10000 0 0
PRKACA 0.017 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.04 0.28 0.26 1 -0.6 14 15
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.13 0.16 0.35 12 -10000 0 12
cortisol/GR alpha (monomer) 0.38 0.34 0.73 54 -10000 0 54
NCOA2 0.017 0 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.096 0.2 -10000 0 -0.7 14 14
AP-1/NFAT1-c-4 -0.33 0.28 -10000 0 -0.8 26 26
AFP -0.13 0.16 -10000 0 -0.76 2 2
SUV420H1 0.017 0 -10000 0 -10000 0 0
IRF1 0.17 0.22 0.49 9 -1 2 11
TP53 0.015 0.14 -10000 0 -0.7 5 5
PPP5C 0.017 0 -10000 0 -10000 0 0
KRT17 -0.32 0.3 -10000 0 -0.84 25 25
KRT14 -0.16 0.18 -10000 0 -1 2 2
TBP 0.029 0.001 -10000 0 -10000 0 0
CREBBP 0.03 0.033 -10000 0 -10000 0 0
HDAC1 0.009 0.03 -10000 0 -10000 0 0
HDAC2 0.039 0.028 -10000 0 -10000 0 0
AP-1 -0.33 0.28 -10000 0 -0.8 26 26
MAPK14 0.017 0.006 -10000 0 -10000 0 0
MAPK10 0.004 0.096 -10000 0 -0.67 3 3
MAPK11 0.012 0.061 -10000 0 -0.74 1 1
KRT5 -0.29 0.25 -10000 0 -0.76 20 20
interleukin-1 receptor activity 0.025 0.026 -10000 0 -10000 0 0
NCOA1 0.012 0.076 -10000 0 -0.64 2 2
STAT1 -0.047 0.23 -10000 0 -0.74 15 15
CGA -0.098 0.15 -10000 0 -10000 0 0
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.2 0.24 0.47 44 -10000 0 44
MAPK3 0.009 0.075 -10000 0 -0.64 2 2
MAPK1 0.017 0.006 -10000 0 -10000 0 0
ICAM1 -0.39 0.31 -10000 0 -0.79 38 38
NFKB1 -0.14 0.069 -10000 0 -0.31 1 1
MAPK8 -0.19 0.2 -10000 0 -0.51 24 24
MAPK9 0.017 0.006 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.061 0.14 0.59 3 -10000 0 3
BAX 0.012 0.088 -10000 0 -10000 0 0
POMC -0.16 0.18 -10000 0 -1.3 1 1
EP300 0.038 0.039 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/p53 0.32 0.3 0.63 53 -10000 0 53
proteasomal ubiquitin-dependent protein catabolic process 0.096 0.07 0.26 1 -10000 0 1
SGK1 0.09 0.073 0.36 2 -10000 0 2
IL13 -0.22 0.21 -10000 0 -0.83 6 6
IL6 -0.62 0.44 -10000 0 -0.94 92 92
PRKACG 0.017 0 -10000 0 -10000 0 0
IL5 -0.23 0.24 -10000 0 -0.91 10 10
IL2 -0.29 0.24 -10000 0 -0.71 22 22
CDK5 0.012 0.061 -10000 0 -0.74 1 1
PRKACB -0.25 0.32 -10000 0 -0.64 62 62
HSP90AA1 0.012 0.061 -10000 0 -0.74 1 1
IL8 -0.78 0.28 -10000 0 -0.86 129 129
CDK5R1/CDK5 -0.002 0.046 -10000 0 -0.55 1 1
NF kappa B1 p50/RelA/PKAc -0.29 0.22 -10000 0 -0.58 43 43
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.31 0.26 0.57 52 -10000 0 52
SMARCA4 0.017 0 -10000 0 -10000 0 0
chromatin remodeling 0.21 0.17 0.41 37 -10000 0 37
NF kappa B1 p50/RelA/Cbp -0.16 0.1 -10000 0 -0.52 1 1
JUN (dimer) -0.21 0.2 -10000 0 -0.59 20 20
YWHAH 0.017 0 -10000 0 -10000 0 0
VIPR1 -0.2 0.35 -10000 0 -1.1 19 19
NR3C1 0.19 0.28 0.52 33 -0.55 11 44
NR4A1 0.019 0.083 -10000 0 -0.7 2 2
TIF2/SUV420H1 0 0 -10000 0 -10000 0 0
MAPKKK cascade 0.081 0.14 0.59 3 -10000 0 3
cortisol/GR alpha (dimer)/Src-1 0.33 0.29 0.61 54 -0.5 1 55
PBX1 0.009 0.11 -10000 0 -0.63 4 4
POU1F1 0.022 0.054 -10000 0 -0.63 1 1
SELE -0.51 0.42 -10000 0 -0.98 59 59
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.21 0.17 0.41 37 -10000 0 37
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.31 0.26 0.57 52 -10000 0 52
mol:cortisol 0.24 0.19 0.44 54 -10000 0 54
MMP1 -0.58 0.19 -10000 0 -0.64 133 133
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.017 0 -9999 0 -10000 0 0
VLDLR -0.13 0.28 -9999 0 -0.64 35 35
LRPAP1 0.017 0 -9999 0 -10000 0 0
NUDC 0.017 0 -9999 0 -10000 0 0
RELN/LRP8 -0.41 0.16 -9999 0 -0.47 133 133
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.017 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.36 0.16 -9999 0 -0.42 133 133
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 0.017 0 -9999 0 -10000 0 0
IQGAP1 0.017 0 -9999 0 -10000 0 0
PLA2G7 -0.013 0.14 -9999 0 -0.64 7 7
CALM1 0.017 0 -9999 0 -10000 0 0
DYNLT1 0.017 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.48 0.19 -9999 0 -0.55 133 133
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.017 0 -9999 0 -10000 0 0
CDK5R1 0.017 0 -9999 0 -10000 0 0
LIS1/Poliovirus Protein 3A 0 0 -9999 0 -10000 0 0
CDK5R2 0.017 0 -9999 0 -10000 0 0
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.09 0.16 -9999 0 -0.39 35 35
YWHAE 0.012 0.061 -9999 0 -0.74 1 1
NDEL1/14-3-3 E -0.25 0.13 -9999 0 -0.63 1 1
MAP1B 0 0 -9999 0 -10000 0 0
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.3 0.14 -9999 0 -0.75 1 1
RELN 0.017 0 -9999 0 -10000 0 0
PAFAH/LIS1 -0.018 0.081 -9999 0 -10000 0 0
LIS1/CLIP170 0 0 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.19 0.077 -9999 0 -0.47 1 1
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.034 0.14 -9999 0 -0.57 1 1
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.27 0.14 -9999 0 -0.68 1 1
LIS1/IQGAP1 0 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.032 0 -9999 0 -10000 0 0
PAFAH1B3 -0.052 0.22 -9999 0 -0.74 14 14
PAFAH1B2 0.017 0 -9999 0 -10000 0 0
MAP1B/LIS1/Dynein heavy chain 0.034 0 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.24 0.098 -9999 0 -0.6 1 1
LRP8 -0.64 0.26 -9999 0 -0.74 133 133
NDEL1/Katanin 60 -0.25 0.13 -9999 0 -0.63 1 1
P39/CDK5 -0.3 0.14 -9999 0 -0.75 1 1
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0 0 -9999 0 -10000 0 0
CDK5 -0.33 0.15 -9999 0 -0.8 1 1
PPP2R5D 0.017 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex 0 0 -9999 0 -10000 0 0
CSNK2A1 0.017 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.072 0.13 -9999 0 -10000 0 0
RELN/VLDLR -0.45 0.21 -9999 0 -0.5 133 133
CDC42 0 0 -9999 0 -10000 0 0
Arf6 signaling events

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
CENTA1/KIF3B -0.005 0.047 -9999 0 -0.41 2 2
ARNO/beta Arrestin1-2 -0.1 0.14 -9999 0 -0.29 52 52
EGFR -0.001 0.11 -9999 0 -0.66 4 4
EPHA2 -0.018 0.16 -9999 0 -0.74 7 7
USP6 0.017 0 -9999 0 -10000 0 0
IQSEC1 0.017 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.17 0.24 -9999 0 -0.51 52 52
ARRB2 0.021 0.028 -9999 0 -0.32 1 1
mol:GTP 0.009 0.008 -9999 0 -10000 0 0
ARRB1 0.004 0.091 -9999 0 -0.64 3 3
FBXO8 0.017 0 -9999 0 -10000 0 0
TSHR 0.017 0 -9999 0 -10000 0 0
EGF -0.21 0.33 -9999 0 -0.68 49 49
somatostatin receptor activity 0 0 -9999 0 -0.001 20 20
ARAP2 0 0 -9999 0 0 17 17
mol:GDP -0.1 0.12 -9999 0 -0.32 25 25
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 21 21
ITGA2B 0.017 0 -9999 0 -10000 0 0
ARF6 0.017 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.019 0.088 -9999 0 -10000 0 0
ADAP1 0 0 -9999 0 0 9 9
KIF13B 0.008 0.075 -9999 0 -0.64 2 2
HGF/MET -0.27 0.28 -9999 0 -0.55 74 74
PXN 0.017 0 -9999 0 -10000 0 0
ARF6/GTP -0.098 0.12 -9999 0 -0.29 22 22
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.15 0.21 -9999 0 -0.43 52 52
ADRB2 -0.19 0.31 -9999 0 -0.64 49 49
receptor agonist activity 0 0 -9999 0 0 21 21
actin filament binding 0 0 -9999 0 -0.001 21 21
SRC 0.017 0 -9999 0 -10000 0 0
ITGB3 0.017 0 -9999 0 -10000 0 0
GNAQ 0 0 -9999 0 -0.001 12 12
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 12 12
ARF6/GDP -0.007 0.054 -9999 0 -10000 0 0
ARF6/GDP/GULP/ACAP1 -0.12 0.15 -9999 0 -0.44 19 19
alphaIIb/beta3 Integrin/paxillin/GIT1 0 0 -9999 0 -10000 0 0
ACAP1 0 0 -9999 0 -10000 0 0
ACAP2 0 0 -9999 0 0 17 17
LHCGR/beta Arrestin2 -0.003 0.038 -9999 0 -0.48 1 1
EFNA1 0.017 0 -9999 0 -10000 0 0
HGF 0.017 0 -9999 0 -10000 0 0
CYTH3 0 0 -9999 0 -0.001 21 21
CYTH2 -0.002 0.002 -9999 0 -0.004 30 30
NCK1 0.017 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 0 16 16
endosomal lumen acidification 0 0 -9999 0 0 14 14
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.044 0.19 -9999 0 -0.65 14 14
GNAQ/ARNO -0.002 0.003 -9999 0 -0.007 12 12
mol:Phosphatidic acid 0 0 -9999 0 0 17 17
PIP3-E 0.007 0.081 -9999 0 -0.69 2 2
MET -0.35 0.38 -9999 0 -0.74 74 74
GNA14 -0.009 0.13 -9999 0 -0.64 6 6
GNA15 -0.003 0.12 -9999 0 -0.74 4 4
GIT1 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 15 15
GNA11 -0.026 0.16 -9999 0 -0.64 10 10
LHCGR 0.012 0.061 -9999 0 -0.74 1 1
AGTR1 -0.14 0.28 -9999 0 -0.65 37 37
desensitization of G-protein coupled receptor protein signaling pathway -0.003 0.038 -9999 0 -0.48 1 1
IPCEF1/ARNO -0.11 0.17 -9999 0 -0.34 53 53
alphaIIb/beta3 Integrin 0 0 -9999 0 -10000 0 0
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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
MET/RANBP9 -0.27 0.28 -10000 0 -0.55 74 74
CRKL -0.054 0.13 -10000 0 -0.66 1 1
mol:PIP3 -0.007 0.11 0.57 5 -10000 0 5
AKT1 0.016 0.071 0.4 5 -10000 0 5
PTK2B 0.017 0 -10000 0 -10000 0 0
RAPGEF1 -0.041 0.12 -10000 0 -0.61 1 1
RANBP10 0.017 0 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
HGF/MET/SHIP2 -0.23 0.24 -10000 0 -0.47 74 74
MAP3K5 -0.026 0.11 -10000 0 -0.56 1 1
HGF/MET/CIN85/CBL/ENDOPHILINS -0.21 0.22 -10000 0 -0.44 74 74
AP1 -0.12 0.18 -10000 0 -0.54 18 18
mol:SU11274 0 0 -10000 0 -10000 0 0
SHC1 0.017 0 -10000 0 -10000 0 0
apoptosis -0.1 0.22 -10000 0 -0.78 13 13
STAT3 (dimer) -0.058 0.12 -10000 0 -0.39 1 1
GAB1/CRKL/SHP2/PI3K -0.068 0.084 -10000 0 -0.54 2 2
INPP5D 0 0 -10000 0 -10000 0 0
CBL/CRK -0.044 0.12 -10000 0 -0.61 1 1
PTPN11 0.012 0.061 -10000 0 -0.74 1 1
GO:0007205 0 0 -10000 0 -10000 0 0
PLCG1 -0.048 0.21 -10000 0 -0.74 13 13
PTEN -0.005 0.12 -10000 0 -0.64 5 5
ELK1 -0.12 0.13 -10000 0 -0.26 72 72
mol:SU5416 0 0 -10000 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.052 0.072 -10000 0 -0.3 1 1
PAK1 0.025 0.065 0.38 5 -10000 0 5
HGF/MET/RANBP10 -0.23 0.24 -10000 0 -0.47 74 74
HRAS -0.097 0.15 -10000 0 -10000 0 0
DOCK1 -0.046 0.13 -10000 0 -0.55 2 2
GAB1 -0.068 0.13 -10000 0 -0.7 1 1
CRK -0.057 0.13 -10000 0 -0.66 1 1
mol:PHA665752 0 0 -10000 0 -10000 0 0
mol:GDP -0.13 0.14 -10000 0 -10000 0 0
JUN -0.008 0.14 -10000 0 -0.74 5 5
EntrezGene:200958 0 0 -10000 0 -10000 0 0
HGF/MET -0.11 0.13 -10000 0 -0.25 69 69
PIK3R1 0.017 0 -10000 0 -10000 0 0
cell morphogenesis -0.015 0.13 -10000 0 -10000 0 0
GRB2/SHC -0.091 0.11 -10000 0 -10000 0 0
FOS -0.045 0.19 -10000 0 -0.66 14 14
GLMN 0.01 0.043 -10000 0 -0.23 1 1
cell motility -0.12 0.13 -10000 0 -0.26 72 72
HGF/MET/MUC20 -0.23 0.24 -10000 0 -0.48 74 74
cell migration -0.09 0.11 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
CBL 0.017 0 -10000 0 -10000 0 0
MET/RANBP10 -0.27 0.28 -10000 0 -0.55 74 74
HGF/MET/Paxillin/FAK1/FAK12/RasGAP -0.078 0.14 -10000 0 -0.43 1 1
MET/MUC20 -0.27 0.28 -10000 0 -0.57 74 74
RAP1B -0.029 0.12 -10000 0 -0.56 1 1
RAP1A -0.029 0.12 -10000 0 -0.56 1 1
HGF/MET/RANBP9 -0.23 0.24 -10000 0 -0.47 74 74
RAF1 -0.078 0.15 -10000 0 -10000 0 0
STAT3 -0.059 0.12 -10000 0 -0.39 1 1
cell proliferation -0.058 0.15 -10000 0 -10000 0 0
RPS6KB1 -0.034 0.058 -10000 0 -0.25 1 1
MAPK3 -0.11 0.15 0.7 2 -10000 0 2
MAPK1 -0.12 0.12 -10000 0 -0.25 71 71
RANBP9 0.017 0 -10000 0 -10000 0 0
MAPK8 -0.001 0.11 -10000 0 -0.43 1 1
SRC -0.062 0.13 -10000 0 -10000 0 0
PI3K -0.091 0.11 -10000 0 -10000 0 0
MET/Glomulin -0.23 0.26 -10000 0 -0.5 74 74
SOS1 0.017 0 -10000 0 -10000 0 0
MAP2K1 -0.063 0.14 -10000 0 -10000 0 0
MET -0.35 0.38 -10000 0 -0.74 74 74
MAP4K1 -0.039 0.12 -10000 0 -0.61 1 1
PTK2 0.017 0 -10000 0 -10000 0 0
MAP2K2 -0.063 0.14 -10000 0 -10000 0 0
BAD 0.025 0.065 0.38 5 -10000 0 5
MAP2K4 -0.018 0.12 -10000 0 -0.44 3 3
SHP2/GRB2/SOS1/GAB1 -0.13 0.14 -10000 0 -0.61 2 2
INPPL1 0.017 0 -10000 0 -10000 0 0
PXN 0.017 0 -10000 0 -10000 0 0
SH3KBP1 0 0.1 -10000 0 -0.64 4 4
HGS -0.086 0.13 -10000 0 -10000 0 0
PLCgamma1/PKC -0.048 0.16 -10000 0 -0.57 13 13
HGF 0.017 0 -10000 0 -10000 0 0
RASA1 0.012 0.061 -10000 0 -0.74 1 1
NCK1 0.017 0 -10000 0 -10000 0 0
PTPRJ 0.017 0 -10000 0 -10000 0 0
NCK/PLCgamma1 -0.13 0.15 -10000 0 -0.49 13 13
PDPK1 0.005 0.082 0.45 5 -10000 0 5
HGF/MET/SHIP -0.23 0.24 -10000 0 -0.48 74 74
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.017 0 -9999 0 -10000 0 0
Syndecan-3/Src/Cortactin -0.12 0.14 -9999 0 -10000 0 0
Syndecan-3/Neurocan -0.003 0.011 -9999 0 -10000 0 0
POMC 0.012 0.053 -9999 0 -0.64 1 1
EGFR -0.001 0.11 -9999 0 -0.66 4 4
Syndecan-3/EGFR -0.012 0.059 -9999 0 -0.36 4 4
AGRP 0.017 0 -9999 0 -10000 0 0
NCSTN 0.017 0 -9999 0 -10000 0 0
PSENEN 0.017 0 -9999 0 -10000 0 0
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.012 0.061 -9999 0 -0.74 1 1
APH1A -0.013 0.14 -9999 0 -0.64 7 7
NCAN 0.017 0 -9999 0 -10000 0 0
long-term memory -0.004 0.03 -9999 0 -0.36 1 1
Syndecan-3/IL8 -0.38 0.08 -9999 0 -0.4 147 147
PSEN1 0.017 0 -9999 0 -10000 0 0
Src/Cortactin 0 0 -9999 0 -10000 0 0
FYN 0.012 0.061 -9999 0 -0.74 1 1
limb bud formation -0.003 0.014 -9999 0 -10000 0 0
MC4R 0.017 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
PTN -0.24 0.32 -9999 0 -0.64 61 61
FGFR/FGF/Syndecan-3 -0.003 0.015 -9999 0 -10000 0 0
neuron projection morphogenesis -0.11 0.13 -9999 0 -10000 0 0
Syndecan-3/AgRP -0.003 0.011 -9999 0 -10000 0 0
Syndecan-3/AgRP/MC4R -0.002 0.008 -9999 0 -10000 0 0
Fyn/Cortactin -0.004 0.045 -9999 0 -0.55 1 1
SDC3 -0.003 0.015 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.38 0.079 -9999 0 -0.39 147 147
IL8 -0.71 0.15 -9999 0 -0.74 147 147
Syndecan-3/Fyn/Cortactin -0.004 0.031 -9999 0 -0.37 1 1
Syndecan-3/CASK -0.003 0.014 -9999 0 -10000 0 0
alpha-MSH/MC4R -0.003 0.038 -9999 0 -0.47 1 1
Gamma Secretase -0.017 0.072 -9999 0 -10000 0 0
TRAIL signaling pathway

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
TNFSF10 -0.061 0.21 -9999 0 -0.64 18 18
positive regulation of NF-kappaB transcription factor activity -0.066 0.16 -9999 0 -0.48 21 21
MAP2K4 -0.008 0.14 -9999 0 -0.5 4 4
IKBKB 0.012 0.061 -9999 0 -0.74 1 1
TNFRSF10B -0.1 0.28 -9999 0 -0.74 24 24
TNFRSF10A -0.067 0.24 -9999 0 -0.74 17 17
SMPD1 -0.17 0.25 -9999 0 -0.53 38 38
IKBKG 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
TNFRSF10D 0.002 0.1 -9999 0 -0.74 3 3
TRAIL/TRAILR2 -0.14 0.26 -9999 0 -0.59 36 36
TRAIL/TRAILR3 -0.12 0.22 -9999 0 -0.52 35 35
TRAIL/TRAILR1 -0.11 0.24 -9999 0 -0.56 31 31
TRAIL/TRAILR4 -0.066 0.16 -9999 0 -0.48 21 21
TRAIL/TRAILR1/DAP3/GTP -0.09 0.19 -9999 0 -0.52 17 17
IKK complex -0.04 0.071 -9999 0 -10000 0 0
RIPK1 0.017 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 -0.033 0.17 -9999 0 -0.49 19 19
MAP3K1 -0.056 0.11 -9999 0 -0.44 7 7
TRAILR4 (trimer) 0.002 0.1 -9999 0 -0.74 3 3
TRADD 0.017 0 -9999 0 -10000 0 0
TRAILR1 (trimer) -0.067 0.24 -9999 0 -0.74 17 17
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.014 0.14 -9999 0 -0.5 4 4
CFLAR 0.017 0 -9999 0 -10000 0 0
MAPK1 -0.027 0.16 -9999 0 -0.46 18 18
TRAIL/TRAILR1/FADD/TRADD/RIP -0.081 0.17 -9999 0 -0.73 4 4
mol:ceramide -0.16 0.24 -9999 0 -0.52 38 38
FADD 0.017 0 -9999 0 -10000 0 0
MAPK8 0.003 0.13 -9999 0 -0.46 4 4
TRAF2 0.017 0 -9999 0 -10000 0 0
TRAILR3 (trimer) -0.072 0.24 -9999 0 -0.74 18 18
CHUK 0.017 0 -9999 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.097 0.2 -9999 0 -0.48 31 31
DAP3 0.017 0 -9999 0 -10000 0 0
CASP10 -0.1 0.2 -9999 0 -0.54 20 20
JNK cascade -0.066 0.16 -9999 0 -0.48 21 21
TRAIL (trimer) -0.06 0.21 -9999 0 -0.64 18 18
TNFRSF10C -0.072 0.24 -9999 0 -0.74 18 18
TRAIL/TRAILR1/DAP3/GTP/FADD -0.083 0.18 -9999 0 -0.48 17 17
TRAIL/TRAILR2/FADD -0.12 0.23 -9999 0 -0.5 36 36
cell death -0.16 0.24 -9999 0 -0.52 38 38
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.026 0.15 -9999 0 -0.5 6 6
TRAILR2 (trimer) -0.1 0.28 -9999 0 -0.74 24 24
CASP8 0.016 0.047 -9999 0 -10000 0 0
negative regulation of caspase activity 0 0 -9999 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.099 0.19 -9999 0 -0.73 6 6
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3 0.022 0.032 -10000 0 -10000 0 0
NFATC2 -0.012 0.18 -10000 0 -0.87 2 2
NFATC3 -0.03 0.097 -10000 0 -10000 0 0
CD40LG -0.55 0.38 -10000 0 -0.99 46 46
ITCH 0.056 0.051 -10000 0 -10000 0 0
CBLB 0.056 0.051 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.21 0.23 -10000 0 -0.95 5 5
JUNB -0.003 0.12 -10000 0 -0.74 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.009 0.05 -10000 0 -10000 0 0
T cell anergy 0.077 0.094 -10000 0 -0.45 2 2
TLE4 0.012 0.15 -10000 0 -1.2 1 1
Jun/NFAT1-c-4/p21SNFT -0.24 0.29 -10000 0 -0.85 18 18
AP-1/NFAT1-c-4 -0.62 0.48 -10000 0 -1.2 52 52
IKZF1 0.008 0.17 -10000 0 -1.1 2 2
T-helper 2 cell differentiation -0.094 0.14 -10000 0 -0.84 1 1
AP-1/NFAT1 -0.14 0.19 -10000 0 -0.6 14 14
CALM1 0.03 0.032 -10000 0 -10000 0 0
EGR2 -0.1 0.37 -10000 0 -1.3 9 9
EGR3 -0.097 0.3 -10000 0 -0.86 10 10
NFAT1/FOXP3 0.01 0.14 -10000 0 -0.64 2 2
EGR1 -0.021 0.17 -10000 0 -0.74 8 8
JUN -0.06 0.13 -10000 0 -0.76 5 5
EGR4 0.002 0.001 -10000 0 -10000 0 0
mol:Ca2+ 0.014 0.036 -10000 0 -10000 0 0
GBP3 -0.11 0.36 -10000 0 -0.84 29 29
FOSL1 -0.047 0.21 -10000 0 -0.74 13 13
NFAT1-c-4/MAF/IRF4 -0.32 0.37 -10000 0 -0.98 23 23
DGKA 0.015 0.13 -10000 0 -0.8 1 1
CREM 0.016 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.15 0.28 -10000 0 -0.85 12 12
CTLA4 0.01 0.14 -10000 0 -0.67 4 4
NFAT1-c-4 (dimer)/EGR1 -0.14 0.31 -10000 0 -0.92 14 14
NFAT1-c-4 (dimer)/EGR4 -0.13 0.27 -10000 0 -0.85 10 10
FOS -0.1 0.2 -10000 0 -0.71 14 14
IFNG -0.33 0.33 -10000 0 -0.76 34 34
T cell activation -0.15 0.16 -10000 0 -0.73 2 2
MAF -0.23 0.32 -10000 0 -0.64 57 57
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.073 0.22 0.66 7 -10000 0 7
TNF -0.1 0.28 -10000 0 -0.83 11 11
FASLG -0.28 0.6 -10000 0 -1.5 27 27
TBX21 -0.19 0.29 -10000 0 -0.64 45 45
BATF3 0 0 -10000 0 -10000 0 0
PRKCQ -0.001 0.11 -10000 0 -0.73 3 3
PTPN1 0.015 0.13 -10000 0 -0.8 1 1
NFAT1-c-4/ICER1 -0.13 0.26 -10000 0 -0.84 10 10
GATA3 0.022 0.001 -10000 0 -10000 0 0
T-helper 1 cell differentiation -0.33 0.33 -10000 0 -0.74 35 35
IL2RA -0.22 0.22 -10000 0 -0.77 10 10
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 0.01 0.15 -10000 0 -0.8 2 2
E2F1 -0.05 0.21 -10000 0 -0.74 13 13
PPARG -0.017 0.15 -10000 0 -0.64 8 8
SLC3A2 -0.002 0.17 -10000 0 -0.65 5 5
IRF4 -0.14 0.28 -10000 0 -0.64 37 37
PTGS2 -0.65 0.47 -10000 0 -1.2 58 58
CSF2 -0.73 0.48 -10000 0 -1.1 72 72
JunB/Fra1/NFAT1-c-4 -0.15 0.3 -10000 0 -0.85 14 14
IL4 -0.097 0.14 -10000 0 -0.88 1 1
IL5 -0.57 0.4 -10000 0 -1 48 48
IL2 -0.15 0.17 -10000 0 -0.74 2 2
IL3 -0.06 0.051 -10000 0 -10000 0 0
RNF128 0.037 0.13 -10000 0 -0.69 5 5
NFATC1 -0.073 0.22 -10000 0 -0.66 7 7
CDK4 -0.003 0.23 -10000 0 -0.67 7 7
PTPRK 0.015 0.13 -10000 0 -0.8 1 1
IL8 -0.89 0.36 -10000 0 -1.1 88 88
POU2F1 0.028 0 -10000 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.017 0 -9999 0 -10000 0 0
EGFR -0.001 0.11 -9999 0 -0.66 4 4
EGF/EGFR -0.24 0.25 -9999 0 -0.49 58 58
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.12 0.17 -9999 0 -0.73 1 1
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA -0.18 0.33 -9999 0 -0.74 39 39
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.21 0.33 -9999 0 -0.68 49 49
EGF/EGFR dimer/SHC -0.15 0.21 -9999 0 -0.49 21 21
mol:GDP -0.12 0.17 -9999 0 -0.72 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 -0.022 0.16 -9999 0 -0.64 9 9
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.11 0.15 -9999 0 -0.67 1 1
SHC1 0.017 0 -9999 0 -10000 0 0
HRAS/GDP -0.11 0.16 -9999 0 -0.67 1 1
FRAP1 -0.068 0.19 -9999 0 -0.69 1 1
EGF/EGFR dimer -0.17 0.24 -9999 0 -0.51 52 52
SOS1 0.017 0 -9999 0 -10000 0 0
GRB2 0.017 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.17 0.26 -9999 0 -0.56 46 46
Aurora A 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
Aurora A/GADD45A -0.021 0.095 -9999 0 -0.47 1 1
BIRC5 -0.082 0.26 -9999 0 -0.74 20 20
NFKBIA 0.013 0.096 -9999 0 -10000 0 0
CPEB1 -0.009 0.13 -9999 0 -0.64 6 6
AKT1 0.013 0.096 -9999 0 -10000 0 0
NDEL1 0.017 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.031 0.12 -9999 0 -0.52 5 5
NDEL1/TACC3 -0.018 0.09 -9999 0 -0.59 1 1
GADD45A 0.012 0.061 -9999 0 -0.74 1 1
GSK3B 0.021 0.012 -9999 0 -10000 0 0
PAK1/Aurora A -0.018 0.088 -9999 0 -10000 0 0
MDM2 0.017 0 -9999 0 -10000 0 0
JUB -0.7 0.18 -9999 0 -0.74 144 144
TPX2 -0.095 0.24 -9999 0 -0.56 33 33
TP53 -0.013 0.071 -9999 0 -0.38 1 1
DLG7 -0.027 0.16 -9999 0 -0.49 12 12
AURKAIP1 0.017 0 -9999 0 -10000 0 0
ARHGEF7 0.017 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.019 0.095 -9999 0 -0.62 1 1
G2/M transition of mitotic cell cycle -0.031 0.12 -9999 0 -0.52 5 5
AURKA 0 0.12 -9999 0 -0.31 12 12
AURKB -0.021 0.037 -9999 0 -10000 0 0
CDC25B -0.24 0.14 -9999 0 -0.37 76 76
G2/M transition checkpoint -0.43 0.12 -9999 0 -0.45 144 144
mRNA polyadenylation -0.03 0.11 -9999 0 -0.39 6 6
Aurora A/CPEB -0.031 0.11 -9999 0 -0.39 6 6
Aurora A/TACC1/TRAP/chTOG -0.009 0.071 -9999 0 -10000 0 0
BRCA1 -0.008 0.14 -9999 0 -0.74 5 5
centrosome duplication -0.018 0.087 -9999 0 -10000 0 0
regulation of centrosome cycle -0.018 0.089 -9999 0 -0.58 1 1
spindle assembly -0.022 0.058 -9999 0 -10000 0 0
TDRD7 0.017 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.086 0.17 -9999 0 -0.68 6 6
CENPA -0.037 0.064 -9999 0 -0.24 8 8
Aurora A/PP2A -0.018 0.088 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.008 0.11 -9999 0 -0.38 3 3
negative regulation of DNA binding 0.014 0.078 -9999 0 -0.38 1 1
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.012 0.061 -9999 0 -0.74 1 1
Ajuba/Aurora A -0.43 0.13 -9999 0 -0.46 144 144
mitotic prometaphase -0.002 0.004 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0.12 -9999 0 -0.31 12 12
TACC1 0.017 0 -9999 0 -10000 0 0
TACC3 0.007 0.086 -9999 0 -0.74 2 2
Aurora A/Antizyme1 -0.013 0.077 -9999 0 -10000 0 0
Aurora A/RasGAP -0.021 0.095 -9999 0 -0.47 1 1
OAZ1 0.017 0 -9999 0 -10000 0 0
RAN 0.017 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.021 0.012 -9999 0 -10000 0 0
GIT1 0.017 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 0 0 -9999 0 -10000 0 0
Importin alpha/Importin beta/TPX2 -0.095 0.24 -9999 0 -0.55 33 33
PPP2R5D 0.017 0 -9999 0 -10000 0 0
Aurora A/TPX2 -0.078 0.23 -9999 0 -0.5 33 33
PAK1 0.017 0 -9999 0 -10000 0 0
CKAP5 0.017 0 -9999 0 -10000 0 0
IL1-mediated 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
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
MAP3K7IP2 0.017 0 -9999 0 -10000 0 0
ERC1 0.017 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.076 0.1 -9999 0 -0.38 4 4
IRAK/TOLLIP 0 0 -9999 0 -10000 0 0
IKBKB 0.012 0.061 -9999 0 -0.74 1 1
IKBKG 0.017 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.47 0.29 -9999 0 -0.6 119 119
IL1A -0.4 0.38 -9999 0 -0.74 84 84
IL1B -0.19 0.3 -9999 0 -0.56 58 58
IRAK/TRAF6/p62/Atypical PKCs -0.005 0.041 -9999 0 -10000 0 0
IL1R2 -0.23 0.32 -9999 0 -0.64 57 57
IL1R1 0.008 0.075 -9999 0 -0.64 2 2
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.057 0.08 -9999 0 -0.37 1 1
TOLLIP 0.017 0 -9999 0 -10000 0 0
TICAM2 0 0 -9999 0 -10000 0 0
MAP3K3 0.017 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.087 0.025 -9999 0 -10000 0 0
JUN 0.043 0.1 -9999 0 -10000 0 0
MAP3K7 0.017 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.16 0.21 -9999 0 -0.74 7 7
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.25 0.23 -9999 0 -0.83 5 5
PIK3R1 0.017 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.23 0.22 -9999 0 -0.79 5 5
IL1 beta fragment/IL1R1/IL1RAP -0.18 0.24 -9999 0 -0.82 7 7
NFKB1 0.017 0 -9999 0 -10000 0 0
MAPK8 0.047 0.086 -9999 0 -10000 0 0
IRAK1 0.026 0 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.23 0.27 -9999 0 -0.55 65 65
IRAK4 0.017 0 -9999 0 -10000 0 0
PRKCI 0.007 0.086 -9999 0 -0.74 2 2
TRAF6 0.017 0 -9999 0 -10000 0 0
PI3K 0 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.048 0.14 -9999 0 -0.4 4 4
CHUK 0.017 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.18 0.24 -9999 0 -0.82 7 7
IL1 beta/IL1R2 -0.32 0.27 -9999 0 -0.57 56 56
IRAK/TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA -0.14 0.18 -9999 0 -0.66 7 7
IRAK3 -0.008 0.14 -9999 0 -0.74 5 5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.16 0.21 -9999 0 -0.75 7 7
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.1 0.14 -9999 0 -0.45 5 5
IL1 alpha/IL1R1/IL1RAP -0.28 0.26 -9999 0 -0.5 84 84
RELA 0.017 0 -9999 0 -10000 0 0
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
SQSTM1 0.017 0 -9999 0 -10000 0 0
MYD88 0.017 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0 0 -9999 0 -10000 0 0
IL1RAP -0.003 0.12 -9999 0 -0.74 4 4
UBE2N 0.017 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.13 0.17 -9999 0 -0.61 7 7
CASP1 -0.036 0.18 -9999 0 -0.66 12 12
IL1RN/IL1R2 -0.4 0.27 -9999 0 -0.55 110 110
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.16 0.22 -9999 0 -0.78 7 7
TMEM189-UBE2V1 0 0 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.088 0.092 -9999 0 -0.39 5 5
PIK3CA 0.017 0 -9999 0 -10000 0 0
IL1RN -0.3 0.37 -9999 0 -0.74 63 63
TRAF6/TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
MAP2K6 0.037 0.089 -9999 0 -10000 0 0
IGF1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.017 0 -10000 0 -10000 0 0
PTK2 0.017 0 -10000 0 -10000 0 0
CRKL -0.17 0.19 -10000 0 -0.7 3 3
GRB2/SOS1/SHC 0 0 -10000 0 -10000 0 0
HRAS 0.017 0 -10000 0 -10000 0 0
IRS1/Crk -0.17 0.19 -10000 0 -0.69 4 4
IGF-1R heterotetramer/IGF1/PTP1B -0.21 0.18 -10000 0 -0.48 3 3
AKT1 -0.12 0.16 -10000 0 -0.58 3 3
BAD -0.1 0.16 -10000 0 -0.53 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
CRK -0.17 0.19 -10000 0 -0.69 4 4
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.19 0.18 -10000 0 -0.71 4 4
RAF1 -0.091 0.15 -10000 0 -0.5 3 3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.17 0.16 -10000 0 -0.67 3 3
YWHAZ 0.017 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.21 0.19 -10000 0 -0.36 88 88
PIK3CA 0.017 0 -10000 0 -10000 0 0
RPS6KB1 -0.12 0.17 -10000 0 -0.59 4 4
GNB2L1 0.017 0 -10000 0 -10000 0 0
positive regulation of MAPKKK cascade -0.082 0.13 -10000 0 -0.42 3 3
PXN 0.017 0 -10000 0 -10000 0 0
PIK3R1 0.017 0 -10000 0 -10000 0 0
cell adhesion 0 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
HRAS/GTP -0.15 0.14 -10000 0 -0.59 3 3
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.16 0.14 -10000 0 -10000 0 0
IGF-1R heterotetramer -0.028 0.039 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS/Nck -0.19 0.17 -10000 0 -0.7 3 3
Crk/p130 Cas/Paxillin -0.16 0.15 -10000 0 -0.62 4 4
IGF1R -0.028 0.039 -10000 0 -10000 0 0
IGF1 -0.37 0.33 -10000 0 -0.65 88 88
IRS2/Crk -0.15 0.18 -10000 0 -0.65 4 4
PI3K -0.17 0.16 -10000 0 -0.66 3 3
apoptosis 0.08 0.14 0.45 3 -10000 0 3
HRAS/GDP 0 0 -10000 0 -10000 0 0
PRKCD -0.2 0.22 -10000 0 -0.39 88 88
RAF1/14-3-3 E -0.074 0.14 -10000 0 -10000 0 0
BAD/14-3-3 -0.085 0.15 -10000 0 -0.48 3 3
PRKCZ -0.13 0.16 -10000 0 -0.59 3 3
Crk/p130 Cas/Paxillin/FAK1 -0.12 0.11 -10000 0 -0.49 4 4
PTPN1 0.017 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.22 0.24 -10000 0 -0.42 88 88
BCAR1 0.017 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.21 0.2 -10000 0 -0.64 11 11
mol:GDP 0 0 -10000 0 -10000 0 0
SOS1 0.017 0 -10000 0 -10000 0 0
IRS1/NCK2 -0.19 0.17 -10000 0 -0.7 3 3
GRB10 -0.038 0.2 -10000 0 -0.74 11 11
PTPN11 -0.17 0.19 -10000 0 -0.71 4 4
IRS1 -0.2 0.2 -10000 0 -0.36 88 88
IRS2 -0.17 0.19 -10000 0 -0.7 3 3
IGF-1R heterotetramer/IGF1 -0.28 0.24 -10000 0 -0.48 88 88
GRB2 0.017 0 -10000 0 -10000 0 0
PDPK1 -0.13 0.17 -10000 0 -0.62 3 3
YWHAE 0.012 0.061 -10000 0 -0.74 1 1
PRKD1 -0.21 0.23 -10000 0 -0.4 89 89
SHC1 0.017 0 -10000 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.002 0.008 -10000 0 -10000 0 0
HDAC1 0.028 0.021 -10000 0 -10000 0 0
AES 0.021 0.006 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
DTX1 0.017 0 -10000 0 -10000 0 0
LRP6/FZD1 0 0 -10000 0 -10000 0 0
TLE1 0.02 0.005 -10000 0 -10000 0 0
AP1 -0.21 0.18 -10000 0 -0.58 17 17
NCSTN 0.017 0 -10000 0 -10000 0 0
ADAM10 0.018 0.001 -10000 0 -10000 0 0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 -0.047 0.099 -10000 0 -10000 0 0
NICD/RBPSUH -0.002 0.009 -10000 0 -10000 0 0
WIF1 -0.12 0.29 -10000 0 -0.74 27 27
NOTCH1 -0.003 0.012 -10000 0 -10000 0 0
PSENEN 0.017 0 -10000 0 -10000 0 0
KREMEN2 -0.12 0.29 -10000 0 -0.74 27 27
DKK1 -0.15 0.31 -10000 0 -0.74 33 33
beta catenin/beta TrCP1 0.12 0.081 -10000 0 -10000 0 0
APH1B 0.012 0.061 -10000 0 -0.74 1 1
APH1A -0.014 0.14 -10000 0 -0.64 7 7
AXIN1 -0.044 0.044 0.29 1 -10000 0 1
CtBP/CBP/TCF1/TLE1/AES 0.092 0.071 -10000 0 -10000 0 0
PSEN1 0.017 0 -10000 0 -10000 0 0
FOS -0.045 0.19 -10000 0 -0.66 14 14
JUN -0.008 0.14 -10000 0 -0.74 5 5
MAP3K7 0.024 0.008 -10000 0 -10000 0 0
CTNNB1 0.12 0.087 0.28 1 -10000 0 1
MAPK3 0.008 0.075 -10000 0 -0.64 2 2
DKK2/LRP6/Kremen 2 -0.29 0.31 -10000 0 -0.56 78 78
HNF1A 0.021 0.006 -10000 0 -10000 0 0
CTBP1 0.021 0.006 -10000 0 -10000 0 0
MYC -0.32 0.3 -10000 0 -0.58 87 87
NKD1 -0.52 0.34 -10000 0 -0.74 110 110
FZD1 0.016 0 -10000 0 -10000 0 0
NOTCH1 precursor/Deltex homolog 1 -0.002 0.009 -10000 0 -10000 0 0
apoptosis -0.21 0.18 -10000 0 -0.57 17 17
Delta 1/NOTCHprecursor -0.002 0.009 -10000 0 -10000 0 0
DLL1 0.017 0 -10000 0 -10000 0 0
PPARD -0.011 0.039 -10000 0 -10000 0 0
Gamma Secretase -0.017 0.072 -10000 0 -10000 0 0
APC -0.056 0.089 0.29 1 -0.53 4 5
DVL1 -0.011 0.023 -10000 0 -10000 0 0
CSNK2A1 0.006 0.008 -10000 0 -10000 0 0
MAP3K7IP1 0.024 0.008 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.18 0.27 -10000 0 -0.54 52 52
LRP6 0.016 0 -10000 0 -10000 0 0
CSNK1A1 0.006 0.008 -10000 0 -10000 0 0
NLK 0.052 0.018 -10000 0 -10000 0 0
CCND1 -0.097 0.22 -10000 0 -0.6 24 24
WNT1 0.016 0 -10000 0 -10000 0 0
Axin1/APC/beta catenin 0.063 0.065 0.35 1 -10000 0 1
DKK2 -0.32 0.38 -10000 0 -0.74 67 67
NOTCH1 precursor/DVL1 -0.002 0.009 -10000 0 -10000 0 0
GSK3B 0.019 0.002 -10000 0 -10000 0 0
FRAT1 0.016 0.054 -10000 0 -0.64 1 1
NOTCH/Deltex homolog 1 -0.002 0.008 -10000 0 -10000 0 0
PPP2R5D 0.23 0.14 0.32 110 -10000 0 110
MAPK1 0.017 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.075 0.16 -10000 0 -0.42 21 21
RBPJ 0.017 0 -10000 0 -10000 0 0
CREBBP 0.008 0.01 -10000 0 -10000 0 0
Calcium signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC1 -0.009 0.061 -9999 0 -0.52 1 1
NFATC2 -0.006 0.045 -9999 0 -10000 0 0
NFATC3 -0.006 0.045 -9999 0 -10000 0 0
CD40LG -0.22 0.33 -9999 0 -0.72 29 29
PTGS2 -0.32 0.43 -9999 0 -0.89 46 46
JUNB -0.003 0.12 -9999 0 -0.74 4 4
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.015 0.017 -9999 0 -10000 0 0
CaM/Ca2+ -0.015 0.017 -9999 0 -10000 0 0
CALM1 0.009 0.012 -9999 0 -10000 0 0
JUN -0.014 0.13 -9999 0 -0.73 5 5
mol:Ca2+ -0.019 0.015 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.004 -9999 0 -10000 0 0
FOSL1 -0.048 0.21 -9999 0 -0.74 13 13
CREM 0.016 0 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.13 0.14 -9999 0 -0.6 2 2
FOS -0.052 0.19 -9999 0 -0.66 14 14
IFNG -0.29 0.42 -9999 0 -0.89 40 40
AP-1/NFAT1-c-4 -0.33 0.34 -9999 0 -0.91 29 29
FASLG -0.26 0.35 -9999 0 -0.76 32 32
NFAT1-c-4/ICER1 -0.063 0.072 -9999 0 -0.45 1 1
IL2RA -0.23 0.35 -9999 0 -0.76 30 30
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.4 0.45 -9999 0 -0.87 60 60
JunB/Fra1/NFAT1-c-4 -0.095 0.16 -9999 0 -0.58 12 12
IL4 -0.22 0.33 -9999 0 -0.72 28 28
IL2 0.013 0.012 -9999 0 -10000 0 0
IL3 0.002 0.021 -9999 0 -10000 0 0
FKBP1A 0.017 0 -9999 0 -10000 0 0
BATF3 0 0 -9999 0 -10000 0 0
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.028 0 -9999 0 -10000 0 0
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 0.033 0.096 -10000 0 -0.4 1 1
TBX21 -0.34 0.68 -10000 0 -1.4 45 45
B2M -0.011 0.14 -10000 0 -0.64 7 7
TYK2 0.021 0.021 -10000 0 -10000 0 0
IL12RB1 0.021 0.021 -10000 0 -10000 0 0
GADD45B -0.099 0.36 -10000 0 -0.88 18 18
IL12RB2 0.016 0.068 -10000 0 -0.78 1 1
GADD45G -0.1 0.37 -10000 0 -0.9 17 17
natural killer cell activation 0 0.027 -10000 0 -10000 0 0
RELB 0.017 0 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
IL18 -0.044 0.2 -10000 0 -0.65 15 15
IL2RA -0.013 0.15 -10000 0 -0.74 6 6
IFNG -0.17 0.32 -10000 0 -0.74 37 37
STAT3 (dimer) -0.066 0.32 -10000 0 -0.73 18 18
HLA-DRB5 -0.009 0.13 -10000 0 -0.64 6 6
FASLG -0.21 0.56 -10000 0 -1.4 23 23
NF kappa B2 p52/RelB -0.2 0.3 -10000 0 -0.83 22 22
CD4 0.017 0.005 -10000 0 -10000 0 0
SOCS1 0.017 0 -10000 0 -10000 0 0
EntrezGene:6955 0.002 0.009 -10000 0 -10000 0 0
CD3D -0.007 0.13 -10000 0 -0.64 6 6
CD3E 0.019 0.006 -10000 0 -10000 0 0
CD3G -0.012 0.14 -10000 0 -0.66 7 7
IL12Rbeta2/JAK2 0.013 0.11 -10000 0 -0.53 5 5
CCL3 -0.12 0.38 -10000 0 -0.85 22 22
CCL4 -0.12 0.39 -10000 0 -1 14 14
HLA-A 0.002 0.1 -10000 0 -0.64 4 4
IL18/IL18R -0.057 0.25 -10000 0 -0.45 39 39
NOS2 -0.12 0.38 -10000 0 -0.77 30 30
IL12/IL12R/TYK2/JAK2/SPHK2 0.031 0.098 -10000 0 -0.4 1 1
IL1R1 -0.12 0.39 -10000 0 -1 13 13
IL4 0.02 0.024 -10000 0 -10000 0 0
JAK2 0.001 0.12 -10000 0 -0.71 4 4
EntrezGene:6957 0.002 0.008 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.009 0.18 -10000 0 -0.69 7 7
RAB7A -0.061 0.32 -10000 0 -0.75 15 15
lysosomal transport -0.055 0.3 -10000 0 -0.71 15 15
FOS -0.11 0.43 -10000 0 -1.2 18 18
STAT4 (dimer) -0.12 0.38 -10000 0 -0.86 21 21
STAT5A (dimer) -0.27 0.3 -10000 0 -0.77 30 30
GZMA -0.12 0.37 -10000 0 -0.83 23 23
GZMB -0.12 0.38 -10000 0 -0.98 13 13
HLX 0.017 0 -10000 0 -10000 0 0
LCK -0.12 0.4 -10000 0 -0.89 23 23
TCR/CD3/MHC II/CD4 -0.007 0.22 -10000 0 -0.73 9 9
IL2/IL2R -0.021 0.09 -10000 0 -10000 0 0
MAPK14 -0.096 0.38 -10000 0 -0.87 20 20
CCR5 -0.17 0.5 -10000 0 -1.2 22 22
IL1B -0.22 0.35 -10000 0 -0.73 49 49
STAT6 -0.01 0.12 -10000 0 -10000 0 0
STAT4 0.012 0.053 -10000 0 -0.64 1 1
STAT3 0.017 0 -10000 0 -10000 0 0
STAT1 -0.057 0.22 -10000 0 -0.74 15 15
NFKB1 0.017 0 -10000 0 -10000 0 0
NFKB2 0.012 0.061 -10000 0 -0.74 1 1
IL12B 0.016 0.062 -10000 0 -0.71 1 1
CD8A 0.002 0.004 -10000 0 -10000 0 0
CD8B 0.019 0.002 -10000 0 -10000 0 0
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity -0.033 0.096 0.39 1 -10000 0 1
IL2RB 0.012 0.053 -10000 0 -0.64 1 1
proteasomal ubiquitin-dependent protein catabolic process -0.1 0.34 -10000 0 -0.78 20 20
IL2RG 0.012 0.053 -10000 0 -0.64 1 1
IL12 0.006 0.12 -10000 0 -0.53 7 7
STAT5A 0.017 0 -10000 0 -10000 0 0
CD247 -0.011 0.14 -10000 0 -0.64 7 7
IL2 0.017 0 -10000 0 -10000 0 0
SPHK2 0.012 0.053 -10000 0 -0.64 1 1
FRAP1 0.017 0 -10000 0 -10000 0 0
IL12A -0.009 0.15 -10000 0 -0.73 6 6
IL12/IL12R/TYK2/JAK2 -0.14 0.42 -10000 0 -0.95 23 23
MAP2K3 -0.098 0.38 -10000 0 -0.89 19 19
RIPK2 -0.14 0.31 -10000 0 -0.74 32 32
MAP2K6 -0.11 0.39 -10000 0 -0.91 20 20
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0 0.1 -10000 0 -0.64 4 4
IL18RAP -0.1 0.26 -10000 0 -0.64 29 29
IL12Rbeta1/TYK2 0.03 0.034 -10000 0 -10000 0 0
EOMES 0.024 0.078 -10000 0 -0.54 2 2
STAT1 (dimer) -0.16 0.33 -10000 0 -0.7 22 22
T cell proliferation -0.092 0.29 -10000 0 -0.64 21 21
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.016 0.055 -10000 0 -0.65 1 1
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.18 0.26 -10000 0 -0.71 22 22
ATF2 -0.077 0.35 -10000 0 -0.8 19 19
FOXA2 and FOXA3 transcription factor networks

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
ACADVL -0.091 0.33 -9999 0 -1 9 9
PCK1 -0.77 0.7 -9999 0 -1.3 95 95
HNF4A -0.1 0.36 -9999 0 -1.2 9 9
KCNJ11 -0.075 0.36 -9999 0 -1.2 7 7
AKT1 0.006 0.12 -9999 0 -10000 0 0
response to starvation -0.007 0.02 -9999 0 -10000 0 0
DLK1 -0.075 0.36 -9999 0 -1.2 7 7
NKX2-1 0.013 0.26 -9999 0 -0.84 3 3
ACADM -0.1 0.36 -9999 0 -1.1 11 11
TAT -0.084 0.24 -9999 0 -0.86 6 6
CEBPB -0.009 0.1 -9999 0 -0.73 3 3
CEBPA 0.011 0.014 -9999 0 -10000 0 0
TTR -0.76 0.66 -9999 0 -1.3 86 86
PKLR -0.1 0.34 -9999 0 -1.1 9 9
APOA1 -0.099 0.4 -9999 0 -1.3 10 10
CPT1C -0.096 0.34 -9999 0 -1.1 9 9
ALAS1 -0.018 0.17 -9999 0 -10000 0 0
TFRC -0.091 0.31 -9999 0 -1 6 6
FOXF1 -0.001 0.1 -9999 0 -0.65 3 3
NF1 0.027 0.001 -9999 0 -10000 0 0
HNF1A (dimer) 0.023 0.053 -9999 0 -10000 0 0
CPT1A -0.1 0.36 -9999 0 -1.1 10 10
HMGCS1 -0.097 0.34 -9999 0 -0.99 10 10
NR3C1 -0.03 0.18 -9999 0 -0.63 13 13
CPT1B -0.087 0.33 -9999 0 -1 9 9
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.021 0.03 -9999 0 -10000 0 0
GCK -0.087 0.33 -9999 0 -1 9 9
CREB1 -0.099 0.11 -9999 0 -10000 0 0
IGFBP1 -0.088 0.25 -9999 0 -0.85 7 7
PDX1 -0.021 0.21 -9999 0 -0.89 2 2
UCP2 -0.087 0.33 -9999 0 -1.1 8 8
ALDOB -0.13 0.45 -9999 0 -1.2 15 15
AFP -0.11 0.16 -9999 0 -0.5 6 6
BDH1 -0.095 0.36 -9999 0 -1.3 7 7
HADH -0.075 0.36 -9999 0 -1.1 8 8
F2 -0.084 0.36 -9999 0 -1.2 8 8
HNF1A 0.023 0.053 -9999 0 -10000 0 0
G6PC -0.088 0.17 -9999 0 -1.4 1 1
SLC2A2 -0.056 0.25 -9999 0 -0.81 3 3
INS 0.013 0.039 -9999 0 -10000 0 0
FOXA1 -0.13 0.27 -9999 0 -0.62 34 34
FOXA3 -0.1 0.17 -9999 0 -0.66 7 7
FOXA2 -0.093 0.42 -9999 0 -1.2 9 9
ABCC8 -0.13 0.44 -9999 0 -1.1 17 17
ALB -0.11 0.17 -9999 0 -0.67 4 4
amb2 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2 -0.028 0.095 -9999 0 -0.53 4 4
alphaM/beta2 Integrin/GPIbA -0.024 0.087 -9999 0 -0.54 3 3
alphaM/beta2 Integrin/proMMP-9 -0.043 0.13 -9999 0 -0.52 8 8
PLAUR 0.017 0 -9999 0 -10000 0 0
HMGB1 -0.007 0.064 -9999 0 -0.76 1 1
alphaM/beta2 Integrin/Talin -0.024 0.087 -9999 0 -0.48 5 5
AGER -0.002 0.019 -9999 0 -10000 0 0
RAP1A 0.017 0 -9999 0 -10000 0 0
SELPLG 0 0.1 -9999 0 -0.64 4 4
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.092 0.11 -9999 0 -0.72 3 3
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.012 0.14 -9999 0 -0.72 6 6
CYR61 -0.057 0.22 -9999 0 -0.74 15 15
TLN1 0.017 0 -9999 0 -10000 0 0
Rap1/GTP -0.044 0.084 -9999 0 -0.56 1 1
RHOA 0.017 0 -9999 0 -10000 0 0
P-selectin oligomer -0.052 0.2 -9999 0 -0.64 16 16
MYH2 -0.013 0.15 -9999 0 -0.56 3 3
MST1R 0.017 0 -9999 0 -10000 0 0
leukocyte activation during inflammatory response -0.014 0.082 -9999 0 -0.49 3 3
APOB 0.012 0.061 -9999 0 -0.74 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 0.012 0.061 -9999 0 -0.74 1 1
JAM3 0.017 0 -9999 0 -10000 0 0
GP1BA 0.017 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CTGF -0.028 0.095 -9999 0 -0.53 4 4
alphaM/beta2 Integrin -0.021 0.13 -9999 0 -0.49 3 3
JAM3 homodimer 0.017 0 -9999 0 -10000 0 0
ICAM2 0.003 0.096 -9999 0 -0.67 3 3
ICAM1 -0.028 0.18 -9999 0 -0.74 9 9
phagocytosis triggered by activation of immune response cell surface activating receptor -0.021 0.13 -9999 0 -0.49 3 3
cell adhesion -0.024 0.086 -9999 0 -0.54 3 3
NFKB1 -0.12 0.19 -9999 0 -0.75 3 3
THY1 -0.087 0.26 -9999 0 -0.74 21 21
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.003 0.039 -9999 0 -0.48 1 1
alphaM/beta2 Integrin/LRP/tPA -0.017 0.092 -9999 0 -0.58 2 2
IL6 -0.3 0.33 -9999 0 -0.56 92 92
ITGB2 -0.019 0.1 -9999 0 -0.64 4 4
elevation of cytosolic calcium ion concentration -0.18 0.22 -9999 0 -0.46 57 57
alphaM/beta2 Integrin/JAM2/JAM3 -0.21 0.21 -9999 0 -0.78 5 5
JAM2 -0.34 0.33 -9999 0 -0.64 84 84
alphaM/beta2 Integrin/ICAM1 -0.056 0.17 -9999 0 -0.78 3 3
alphaM/beta2 Integrin/uPA/Plg -0.18 0.22 -9999 0 -0.46 57 57
RhoA/GTP -0.018 0.14 -9999 0 -0.43 4 4
positive regulation of phagocytosis -0.066 0.13 -9999 0 -0.71 3 3
Ron/MSP -0.033 0.13 -9999 0 -0.55 9 9
alphaM/beta2 Integrin/uPAR/uPA -0.18 0.22 -9999 0 -0.46 57 57
alphaM/beta2 Integrin/uPAR -0.024 0.087 -9999 0 -0.48 5 5
PLAU -0.26 0.36 -9999 0 -0.74 55 55
PLAT 0.008 0.08 -9999 0 -0.69 2 2
actin filament polymerization -0.012 0.14 -9999 0 -0.53 3 3
MST1 -0.028 0.18 -9999 0 -0.74 9 9
alphaM/beta2 Integrin/lipoprotein(a) -0.014 0.084 -9999 0 -0.5 3 3
TNF -0.097 0.17 -9999 0 -0.66 3 3
RAP1B 0.017 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/uPA -0.2 0.24 -9999 0 -0.51 60 60
fibrinolysis -0.18 0.22 -9999 0 -0.46 57 57
HCK -0.043 0.19 -9999 0 -0.64 14 14
dendritic cell antigen processing and presentation -0.021 0.13 -9999 0 -0.49 3 3
VTN 0.017 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/CYR61 -0.073 0.17 -9999 0 -0.52 18 18
LPA 0.017 0 -9999 0 -10000 0 0
LRP1 0.017 0 -9999 0 -10000 0 0
cell migration -0.032 0.13 -9999 0 -0.57 6 6
FN1 -0.11 0.28 -9999 0 -0.74 26 26
alphaM/beta2 Integrin/Thy1 -0.092 0.19 -9999 0 -0.51 24 24
MPO -0.043 0.2 -9999 0 -0.74 12 12
KNG1 -0.005 0.12 -9999 0 -0.64 5 5
RAP1/GDP 0 0 -9999 0 -10000 0 0
ROCK1 -0.006 0.13 -9999 0 -0.42 2 2
ELA2 0.017 0 -9999 0 -10000 0 0
PLG 0.017 0 -9999 0 -10000 0 0
CTGF 0.012 0.061 -9999 0 -0.74 1 1
alphaM/beta2 Integrin/Hck -0.059 0.16 -9999 0 -0.49 15 15
ITGAM -0.011 0.078 -9999 0 -0.66 2 2
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.058 0.17 -9999 0 -0.78 4 4
HP 0.017 0 -9999 0 -10000 0 0
leukocyte adhesion -0.27 0.21 -9999 0 -0.76 10 10
SELP -0.052 0.2 -9999 0 -0.64 16 16
Regulation of nuclear SMAD2/3 signaling

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
EP300 0.03 0.019 -10000 0 -10000 0 0
HSPA8 0.007 0.009 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.01 0.11 -10000 0 -0.45 3 3
AKT1 -0.047 0.034 -10000 0 -10000 0 0
GSC -0.006 0.12 -10000 0 -0.6 5 5
NKX2-5 0.009 0.063 -10000 0 -0.73 1 1
muscle cell differentiation 0.044 0.1 0.45 3 -10000 0 3
SMAD2-3/SMAD4/SP1 -0.079 0.11 -10000 0 -0.54 1 1
SMAD4 -0.017 0.068 -10000 0 -0.63 1 1
CBFB 0.002 0.1 -10000 0 -0.74 3 3
SAP18 0.013 0.006 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.015 0.18 -10000 0 -0.47 21 21
SMAD3/SMAD4/VDR -0.007 0.084 -10000 0 -10000 0 0
MYC -0.32 0.34 -10000 0 -0.61 87 87
CDKN2B -1.1 0.58 -10000 0 -1.4 126 126
AP1 -0.041 0.17 -10000 0 -0.7 6 6
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.009 0.052 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.27 0.18 -10000 0 -0.53 22 22
SP3 0.02 0.001 -10000 0 -10000 0 0
CREB1 0.017 0 -10000 0 -10000 0 0
FOXH1 0.015 0.022 -10000 0 -10000 0 0
SMAD3/SMAD4/GR -0.04 0.14 -10000 0 -0.45 13 13
GATA3 0.017 0.039 -10000 0 -10000 0 0
SKI/SIN3/HDAC complex/NCoR1 0.023 0.036 -10000 0 -10000 0 0
MEF2C/TIF2 -0.057 0.18 -10000 0 -0.6 14 14
endothelial cell migration 0.091 0.28 0.6 18 -10000 0 18
MAX 0.023 0.017 -10000 0 -10000 0 0
RBBP7 0.013 0.006 -10000 0 -10000 0 0
RBBP4 0.013 0.006 -10000 0 -10000 0 0
RUNX2 0.017 0 -10000 0 -10000 0 0
RUNX3 -0.023 0.16 -10000 0 -0.66 9 9
RUNX1 -0.2 0.34 -10000 0 -0.74 44 44
CTBP1 0.017 0 -10000 0 -10000 0 0
NR3C1 -0.033 0.19 -10000 0 -0.64 13 13
VDR -0.009 0.13 -10000 0 -0.64 6 6
CDKN1A -0.027 0.19 -10000 0 -1.5 2 2
KAT2B 0.004 0.007 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1 -0.025 0.074 -10000 0 -10000 0 0
DCP1A 0.017 0 -10000 0 -10000 0 0
SKI 0.013 0.006 -10000 0 -10000 0 0
SERPINE1 -0.099 0.27 -10000 0 -0.61 13 13
SMAD3/SMAD4/ATF2 -0.012 0.064 -10000 0 -0.45 1 1
SMAD3/SMAD4/ATF3 -0.034 0.12 -10000 0 -0.5 8 8
SAP30 0.013 0.006 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.067 0.068 -10000 0 -0.5 1 1
JUN -0.01 0.18 -10000 0 -0.7 6 6
SMAD3/SMAD4/IRF7 -0.008 0.063 -10000 0 -0.45 1 1
TFE3 0.02 0.012 -10000 0 -10000 0 0
COL1A2 -0.13 0.26 -10000 0 -0.62 33 33
mesenchymal cell differentiation 0.012 0.064 0.45 1 -10000 0 1
DLX1 0.007 0.086 -10000 0 -0.74 2 2
TCF3 0.017 0 -10000 0 -10000 0 0
FOS -0.044 0.2 -10000 0 -0.66 14 14
SMAD3/SMAD4/Max -0.003 0.074 -10000 0 -0.46 1 1
Cbp/p300/SNIP1 0.005 0.017 -10000 0 -10000 0 0
ZBTB17 0.044 0.023 -10000 0 -10000 0 0
LAMC1 -0.003 0.056 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 -0.13 0.23 -10000 0 -0.54 35 35
IRF7 0.022 0.001 -10000 0 -10000 0 0
ESR1 0.014 0.077 -10000 0 -0.64 2 2
HNF4A 0.008 0.075 -10000 0 -0.64 2 2
MEF2C -0.037 0.2 -10000 0 -0.64 14 14
SMAD2-3/SMAD4 -0.046 0.085 -10000 0 -0.45 2 2
Cbp/p300/Src-1 0.043 0.06 -10000 0 -10000 0 0
IGHV3OR16-13 -0.033 0.045 -10000 0 -10000 0 0
TGIF2/HDAC complex -0.16 0.32 -10000 0 -0.74 35 35
CREBBP 0.025 0.015 -10000 0 -10000 0 0
SKIL -0.003 0.12 -10000 0 -0.74 4 4
HDAC1 0.013 0.006 -10000 0 -10000 0 0
HDAC2 0.013 0.006 -10000 0 -10000 0 0
SNIP1 0.007 0.009 -10000 0 -10000 0 0
GCN5L2 -0.17 0.33 -10000 0 -0.72 40 40
SMAD3/SMAD4/TFE3 -0.015 0.059 -10000 0 -0.44 1 1
MSG1/HSC70 -0.074 0.19 -10000 0 -0.56 21 21
SMAD2 -0.047 0.043 -10000 0 -10000 0 0
SMAD3 -0.013 0.069 -10000 0 -0.71 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 -0.14 0.17 -10000 0 -0.5 16 16
SMAD2/SMAD2/SMAD4 -0.01 0.04 -10000 0 -0.37 1 1
NCOR1 0.009 0.053 -10000 0 -0.64 1 1
NCOA2 0.017 0 -10000 0 -10000 0 0
NCOA1 0.008 0.075 -10000 0 -0.64 2 2
MYOD/E2A -0.004 0.045 -10000 0 -0.55 1 1
SMAD2-3/SMAD4/SP1/MIZ-1 -0.091 0.11 -10000 0 -0.55 1 1
IFNB1 0.005 0.06 -10000 0 -10000 0 0
SMAD3/SMAD4/MEF2C -0.057 0.19 -10000 0 -0.65 11 11
CITED1 -0.092 0.26 -10000 0 -0.74 21 21
SMAD2-3/SMAD4/ARC105 -0.029 0.075 -10000 0 -0.43 1 1
RBL1 -0.057 0.22 -10000 0 -0.74 15 15
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.45 0.26 -10000 0 -0.57 124 124
RUNX1-3/PEBPB2 -0.17 0.23 -10000 0 -0.48 54 54
SMAD7 -0.049 0.14 -10000 0 -0.62 1 1
MYC/MIZ-1 -0.17 0.26 -10000 0 -0.42 42 42
SMAD3/SMAD4 0.031 0.2 0.37 3 -0.48 7 10
IL10 -0.006 0.086 -10000 0 -10000 0 0
PIASy/HDAC complex 0.008 0.012 -10000 0 -10000 0 0
PIAS3 0.016 0.063 -10000 0 -0.75 1 1
CDK2 -0.084 0.27 -10000 0 -0.74 22 22
IL5 -0.039 0.19 -10000 0 -0.66 12 12
CDK4 -0.041 0.22 -10000 0 -0.72 14 14
PIAS4 0.008 0.012 -10000 0 -10000 0 0
ATF3 -0.018 0.16 -10000 0 -0.74 7 7
SMAD3/SMAD4/SP1 -0.05 0.093 -10000 0 -0.55 1 1
FOXG1 -0.078 0.25 -10000 0 -0.74 19 19
FOXO3 -0.056 0.046 -10000 0 -10000 0 0
FOXO1 -0.073 0.1 -10000 0 -0.56 5 5
FOXO4 -0.055 0.045 -10000 0 -10000 0 0
heart looping -0.036 0.2 -10000 0 -0.63 14 14
CEBPB -0.029 0.11 -10000 0 -0.8 3 3
SMAD3/SMAD4/DLX1 -0.018 0.09 -10000 0 -0.52 3 3
MYOD1 0.012 0.061 -10000 0 -0.74 1 1
SMAD3/SMAD4/HNF4 -0.018 0.076 -10000 0 -0.45 1 1
SMAD3/SMAD4/GATA3 -0.021 0.094 -10000 0 -0.44 1 1
SnoN/SIN3/HDAC complex/NCoR1 -0.003 0.12 -10000 0 -0.74 4 4
SMAD3/SMAD4/RUNX1-3/PEBPB2 -0.15 0.21 -10000 0 -0.51 19 19
SMAD3/SMAD4/SP1-3 -0.035 0.076 -10000 0 -0.48 1 1
MED15 0.017 0 -10000 0 -10000 0 0
SP1 -0.019 0.057 -10000 0 -10000 0 0
SIN3B 0.013 0.006 -10000 0 -10000 0 0
SIN3A 0.013 0.006 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.032 0.11 -10000 0 -0.45 1 1
ITGB5 -0.018 0.077 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.024 0.06 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.015 0.079 -10000 0 -0.51 2 2
AR 0.012 0.061 -10000 0 -0.74 1 1
negative regulation of cell growth -0.12 0.16 -10000 0 -0.47 11 11
SMAD3/SMAD4/MYOD -0.015 0.075 -10000 0 -0.44 3 3
E2F5 -0.28 0.37 -10000 0 -0.74 61 61
E2F4 0.017 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.005 0.054 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4 -0.28 0.18 -10000 0 -0.47 21 21
TFDP1 -0.052 0.22 -10000 0 -0.74 14 14
SMAD3/SMAD4/AP1 -0.046 0.17 -10000 0 -0.71 6 6
SMAD3/SMAD4/RUNX2 -0.012 0.064 -10000 0 -0.45 1 1
TGIF2 -0.16 0.32 -10000 0 -0.74 35 35
TGIF1 -0.082 0.26 -10000 0 -0.74 20 20
ATF2 0.017 0 -10000 0 -10000 0 0
Thromboxane A2 receptor 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
TGM2 -0.072 0.24 -10000 0 -0.74 17 17
GNB1/GNG2 -0.1 0.068 -10000 0 -0.21 12 12
AKT1 -0.059 0.096 -10000 0 -10000 0 0
EGF -0.21 0.33 -10000 0 -0.68 49 49
mol:TXA2 -0.001 0.001 -10000 0 -10000 0 0
FGR -0.13 0.075 -10000 0 -0.46 1 1
mol:Ca2+ -0.1 0.14 -10000 0 -0.32 12 12
LYN -0.13 0.075 -10000 0 -0.46 1 1
RhoA/GTP -0.046 0.043 -10000 0 -10000 0 0
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.11 0.15 -10000 0 -0.36 10 10
GNG2 0.017 0 -10000 0 -10000 0 0
ARRB2 0.017 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 -0.054 0.15 -10000 0 -0.52 10 10
G beta5/gamma2 -0.13 0.094 -10000 0 -0.29 13 13
PRKCH -0.12 0.16 -10000 0 -0.41 11 11
DNM1 -0.003 0.12 -10000 0 -0.74 4 4
TXA2/TP beta/beta Arrestin3 -0.034 0.043 -10000 0 -0.27 4 4
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
PTGDR -0.5 0.27 -10000 0 -0.64 119 119
G12 family/GTP -0.12 0.1 -10000 0 -0.31 11 11
ADRBK1 0.017 0 -10000 0 -10000 0 0
ADRBK2 0.017 0 -10000 0 -10000 0 0
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.13 0.11 0.29 24 -10000 0 24
mol:NADP 0.012 0.061 -10000 0 -0.74 1 1
RAB11A 0.017 0 -10000 0 -10000 0 0
PRKG1 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.13 0.16 -10000 0 -0.4 12 12
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.17 0.21 -10000 0 -0.55 12 12
mol:cGMP 0 0 -10000 0 -10000 0 0
BLK -0.18 0.13 -10000 0 -0.46 21 21
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK -0.16 0.11 -10000 0 -0.46 13 13
RHOA 0.017 0 -10000 0 -10000 0 0
PTGIR 0.017 0 -10000 0 -10000 0 0
PRKCB1 -0.18 0.19 -10000 0 -0.46 27 27
GNAQ 0 0 -10000 0 -10000 0 0
mol:L-citrulline 0.012 0.061 -10000 0 -0.74 1 1
TXA2/TXA2-R family -0.17 0.21 -10000 0 -0.54 14 14
LCK -0.14 0.081 -10000 0 -0.48 2 2
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.17 0.092 -10000 0 -10000 0 0
TXA2-R family/G12 family/GDP/G beta/gamma -0.027 0.039 -10000 0 -10000 0 0
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.17 0.092 -10000 0 -10000 0 0
MAPK14 -0.065 0.11 -10000 0 -10000 0 0
TGM2/GTP -0.16 0.19 -10000 0 -0.48 14 14
MAPK11 -0.066 0.11 -10000 0 -0.42 1 1
ARHGEF1 -0.051 0.084 -10000 0 -10000 0 0
GNAI2 0.012 0.061 -10000 0 -0.74 1 1
JNK cascade -0.13 0.16 -10000 0 -0.4 12 12
RAB11/GDP 0.018 0.001 -10000 0 -10000 0 0
ICAM1 -0.093 0.14 -10000 0 -0.35 13 13
cAMP biosynthetic process -0.13 0.15 -10000 0 -0.38 12 12
Gq family/GTP/EBP50 -0.003 0.095 -10000 0 -0.28 11 11
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC -0.13 0.075 -10000 0 -0.46 1 1
GNB5 -0.003 0.12 -10000 0 -0.74 4 4
GNB1 0.017 0 -10000 0 -10000 0 0
EGF/EGFR -0.12 0.1 -10000 0 -0.37 3 3
VCAM1 -0.088 0.13 -10000 0 -0.4 5 5
TP beta/Gq family/GDP/G beta5/gamma2 -0.054 0.15 -10000 0 -0.52 10 10
platelet activation -0.091 0.14 -10000 0 -0.33 6 6
PGI2/IP 0 0 -10000 0 -10000 0 0
PRKACA -0.23 0.13 -10000 0 -0.3 119 119
Gq family/GDP/G beta5/gamma2 -0.071 0.14 -10000 0 -0.44 16 16
TXA2/TP beta/beta Arrestin2 -0.024 0.053 -10000 0 -0.34 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.2 0.13 -10000 0 -10000 0 0
mol:DAG -0.14 0.18 -10000 0 -0.43 15 15
EGFR -0.001 0.11 -10000 0 -0.66 4 4
TXA2/TP alpha -0.18 0.2 -10000 0 -0.53 13 13
Gq family/GTP -0.007 0.087 -10000 0 -0.24 15 15
YES1 -0.13 0.075 -10000 0 -0.46 1 1
GNAI2/GTP -0.16 0.088 -10000 0 -0.54 1 1
PGD2/DP -0.37 0.2 -10000 0 -0.48 119 119
SLC9A3R1 0.012 0.053 -10000 0 -0.64 1 1
FYN -0.14 0.076 -10000 0 -0.46 1 1
mol:NO 0.012 0.061 -10000 0 -0.74 1 1
GNA15 -0.003 0.12 -10000 0 -0.74 4 4
PGK/cGMP -0.003 0.039 -10000 0 -0.48 1 1
RhoA/GDP 0.018 0.001 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.21 0.15 -10000 0 -0.59 13 13
NOS3 0.012 0.061 -10000 0 -0.74 1 1
RAC1 0.017 0 -10000 0 -10000 0 0
PRKCA -0.11 0.15 -10000 0 -0.37 10 10
PRKCB -0.12 0.15 -10000 0 -0.36 15 15
PRKCE -0.11 0.15 -10000 0 -0.37 10 10
PRKCD -0.12 0.16 -10000 0 -0.39 8 8
PRKCG -0.12 0.17 -10000 0 -0.44 12 12
muscle contraction -0.15 0.2 -10000 0 -0.52 11 11
PRKCZ -0.12 0.15 -10000 0 -0.36 11 11
ARR3 0.017 0 -10000 0 -10000 0 0
TXA2/TP beta -0.18 0.094 -10000 0 -10000 0 0
PRKCQ -0.12 0.15 -10000 0 -0.38 11 11
MAPKKK cascade -0.15 0.19 -10000 0 -0.48 12 12
SELE -0.12 0.17 -10000 0 -0.36 31 31
TP beta/GNAI2/GDP/G beta/gamma -0.17 0.094 -10000 0 -0.6 1 1
ROCK1 0.017 0 -10000 0 -10000 0 0
GNA14 -0.009 0.13 -10000 0 -0.64 6 6
chemotaxis -0.18 0.23 -10000 0 -0.6 12 12
GNA12 0.017 0 -10000 0 -10000 0 0
GNA13 0.017 0 -10000 0 -10000 0 0
GNA11 -0.026 0.16 -10000 0 -0.64 10 10
Rac1/GTP 0 0 -10000 0 -10000 0 0
p75(NTR)-mediated signaling

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
Sortilin/TRAF6 -0.003 0.038 -9999 0 -0.47 1 1
Necdin/E2F1 -0.13 0.25 -9999 0 -0.55 37 37
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.009 0.055 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/BEX1 -0.003 0.032 -9999 0 -0.4 1 1
NT-4/5 (dimer)/p75(NTR) 0 0 -9999 0 -10000 0 0
IKBKB 0.012 0.061 -9999 0 -0.74 1 1
AKT1 0.044 0 -9999 0 -10000 0 0
IKBKG 0.017 0 -9999 0 -10000 0 0
BDNF -0.038 0.2 -9999 0 -0.74 11 11
MGDIs/NGR/p75(NTR)/LINGO1 -0.04 0.14 -9999 0 -0.51 12 12
FURIN 0.017 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.036 0.12 -9999 0 -0.46 12 12
LINGO1 0.002 0.1 -9999 0 -0.74 3 3
Sortilin/TRAF6/NRIF -0.015 0.062 -9999 0 -10000 0 0
proBDNF (dimer) -0.038 0.2 -9999 0 -0.74 11 11
NTRK1 0.017 0 -9999 0 -10000 0 0
RTN4R -0.033 0.19 -9999 0 -0.74 10 10
neuron apoptosis 0.024 0.11 -9999 0 -10000 0 0
IRAK1 0.017 0 -9999 0 -10000 0 0
SHC1 0.026 0 -9999 0 -10000 0 0
ARHGDIA 0.017 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.017 0.072 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.019 0.079 -9999 0 -0.36 8 8
MAGEH1 -0.013 0.14 -9999 0 -0.64 7 7
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.07 0.15 -9999 0 -0.37 29 29
Mammalian IAPs/DIABLO -0.02 0.084 -9999 0 -0.38 8 8
proNGF (dimer) 0 0 -9999 0 -10000 0 0
MAGED1 0.012 0.061 -9999 0 -0.74 1 1
APP 0.017 0 -9999 0 -10000 0 0
NT-4/5 (dimer) 0 0 -9999 0 -10000 0 0
ZNF274 0.017 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI 0 0 -9999 0 -10000 0 0
NGF 0 0 -9999 0 -10000 0 0
cell cycle arrest -0.001 0.032 -9999 0 -0.35 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.013 0.11 -9999 0 -10000 0 0
NT-4/5 (dimer)/p75(NTR)/TRAF6 0 0 -9999 0 -10000 0 0
NCSTN 0.017 0 -9999 0 -10000 0 0
mol:GTP -0.16 0.2 -9999 0 -0.4 62 62
PSENEN 0.017 0 -9999 0 -10000 0 0
mol:ceramide 0.032 0.031 -9999 0 -0.35 1 1
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.002 0.092 -9999 0 -0.4 1 1
p75(NTR)/beta APP 0 0 -9999 0 -10000 0 0
BEX1 0.012 0.053 -9999 0 -0.64 1 1
mol:GDP 0.013 0 -9999 0 -10000 0 0
NGF (dimer) -0.42 0.084 -9999 0 -0.43 147 147
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.036 0.13 -9999 0 -0.46 12 12
PIK3R1 0.017 0 -9999 0 -10000 0 0
RAC1/GTP 0 0 -9999 0 -10000 0 0
MYD88 0.017 0 -9999 0 -10000 0 0
CHUK 0.017 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.16 0.2 -9999 0 -0.4 62 62
RHOB -0.043 0.2 -9999 0 -0.74 12 12
RHOA 0.017 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.051 0.16 -9999 0 -0.55 14 14
NT3 (dimer) 0.012 0.061 -9999 0 -0.74 1 1
TP53 0.017 0.13 -9999 0 -10000 0 0
PRDM4 0.033 0.031 -9999 0 -0.35 1 1
BDNF (dimer) -0.83 0.17 -9999 0 -0.87 138 138
PIK3CA 0.017 0 -9999 0 -10000 0 0
SORT1 0.012 0.053 -9999 0 -0.64 1 1
activation of caspase activity -0.009 0.055 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.002 0.029 -9999 0 -0.36 1 1
RHOC 0.017 0 -9999 0 -10000 0 0
XIAP 0 0 -9999 0 -10000 0 0
MAPK10 0.054 0.094 -9999 0 -0.42 1 1
DIABLO 0.017 0 -9999 0 -10000 0 0
SMPD2 0.033 0.031 -9999 0 -0.35 1 1
APH1B 0.012 0.061 -9999 0 -0.74 1 1
APH1A -0.013 0.14 -9999 0 -0.64 7 7
proNGF (dimer)/p75(NTR)/Sortilin -0.003 0.032 -9999 0 -0.4 1 1
PSEN1 0.017 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 0 0 -9999 0 -10000 0 0
NT3 (dimer)/p75(NTR) -0.004 0.045 -9999 0 -0.55 1 1
MAPK8 0.059 0.084 -9999 0 -10000 0 0
MAPK9 0.059 0.084 -9999 0 -10000 0 0
APAF1 0.017 0 -9999 0 -10000 0 0
NTF3 0.012 0.061 -9999 0 -0.74 1 1
NTF4 0 0 -9999 0 -10000 0 0
NDN -0.11 0.26 -9999 0 -0.64 29 29
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.15 0.18 -9999 0 -0.69 5 5
p75 CTF/Sortilin/TRAF6/NRIF -0.002 0.028 -9999 0 -10000 0 0
RhoA-B-C/GTP -0.16 0.2 -9999 0 -0.4 62 62
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.03 0.1 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.033 0.11 -9999 0 -0.42 11 11
PRKACB -0.25 0.32 -9999 0 -0.64 62 62
proBDNF (dimer)/p75 ECD -0.04 0.14 -9999 0 -0.55 11 11
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.019 0.15 -9999 0 -0.66 8 8
BIRC2 0.017 0 -9999 0 -10000 0 0
neuron projection morphogenesis -0.14 0.17 -9999 0 -0.53 16 16
BAD 0.066 0.086 -9999 0 -10000 0 0
RIPK2 -0.14 0.31 -9999 0 -0.74 32 32
NGFR 0.017 0 -9999 0 -10000 0 0
CYCS 0.037 0.055 -9999 0 -0.4 1 1
ADAM17 0.017 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.09 0.18 -9999 0 -0.43 32 32
BCL2L11 0.066 0.086 -9999 0 -10000 0 0
BDNF (dimer)/p75(NTR) -0.04 0.14 -9999 0 -0.55 11 11
PI3K 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.005 0.045 -9999 0 -0.39 2 2
NDNL2 0.012 0.061 -9999 0 -0.74 1 1
YWHAE 0.012 0.061 -9999 0 -0.74 1 1
PRKCI 0.007 0.086 -9999 0 -0.74 2 2
NGF (dimer)/p75(NTR) 0 0 -9999 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.005 0.045 -9999 0 -0.39 2 2
TRAF6 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCZ 0 0 -9999 0 -10000 0 0
PLG 0.017 0 -9999 0 -10000 0 0
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 0.013 0.1 -9999 0 -10000 0 0
SQSTM1 0.017 0 -9999 0 -10000 0 0
NGFRAP1 0.008 0.075 -9999 0 -0.64 2 2
CASP3 0.066 0.081 -9999 0 -10000 0 0
E2F1 -0.048 0.21 -9999 0 -0.74 13 13
CASP9 0.017 0 -9999 0 -10000 0 0
IKK complex -0.023 0.055 -9999 0 -0.47 1 1
NGF (dimer)/TRKA 0 0 -9999 0 -10000 0 0
MMP7 -0.71 0.15 -9999 0 -0.74 147 147
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.002 0.026 -9999 0 -10000 0 0
MMP3 -0.69 0.19 -9999 0 -0.74 143 143
APAF-1/Caspase 9 -0.017 0.062 -9999 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.008 0.08 -10000 0 -0.69 2 2
EPHB2 0 0.1 -10000 0 -0.71 3 3
EFNB1 0.013 0.094 -10000 0 -0.56 4 4
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.19 -10000 0 -0.74 4 4
Ephrin B2/EPHB1-2 -0.16 0.22 -10000 0 -0.45 56 56
neuron projection morphogenesis -0.14 0.19 -10000 0 -0.7 4 4
Ephrin B1/EPHB1-2/Tiam1 -0.16 0.21 -10000 0 -0.8 4 4
DNM1 -0.005 0.12 -10000 0 -0.74 4 4
cell-cell signaling -0.003 0.004 -10000 0 -10000 0 0
MAP2K4 -0.067 0.15 -10000 0 -0.74 3 3
YES1 -0.1 0.18 -10000 0 -0.98 3 3
Ephrin B1/EPHB1-2/NCK2 -0.16 0.21 -10000 0 -0.8 4 4
PI3K -0.075 0.14 -10000 0 -0.75 3 3
mol:GDP -0.15 0.21 -10000 0 -0.78 4 4
ITGA2B 0.017 0 -10000 0 -10000 0 0
endothelial cell proliferation -0.1 0.2 -10000 0 -0.49 31 31
FYN -0.1 0.18 -10000 0 -0.98 3 3
MAP3K7 -0.087 0.15 -10000 0 -0.79 3 3
FGR -0.1 0.18 -10000 0 -0.98 3 3
TIAM1 0.017 0 -10000 0 -10000 0 0
PIK3R1 0.017 0 -10000 0 -10000 0 0
RGS3 0.017 0 -10000 0 -10000 0 0
cell adhesion -0.038 0.14 -10000 0 -0.67 3 3
LYN -0.1 0.18 -10000 0 -0.98 3 3
Ephrin B1/EPHB1-2/Src Family Kinases -0.096 0.17 -10000 0 -0.91 3 3
Ephrin B1/EPHB1-2 -0.1 0.16 -10000 0 -0.31 51 51
SRC -0.1 0.18 -10000 0 -0.98 3 3
ITGB3 0.017 0 -10000 0 -10000 0 0
EPHB1 -0.25 0.36 -10000 0 -0.74 54 54
EPHB4 -0.13 0.3 -10000 0 -0.74 30 30
RAC1 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.1 0.2 -10000 0 -0.5 31 31
alphaIIb/beta3 Integrin 0 0 -10000 0 -10000 0 0
BLK -0.13 0.19 -10000 0 -0.62 9 9
HCK -0.12 0.19 -10000 0 -0.75 6 6
regulation of stress fiber formation 0.15 0.21 0.78 4 -10000 0 4
MAPK8 -0.053 0.14 -10000 0 -0.69 3 3
Ephrin B1/EPHB1-2/RGS3 -0.16 0.21 -10000 0 -0.8 4 4
endothelial cell migration -0.16 0.22 -10000 0 -0.52 32 32
NCK2 0.017 0 -10000 0 -10000 0 0
PTPN13 -0.22 0.34 -10000 0 -0.7 51 51
regulation of focal adhesion formation 0.15 0.21 0.78 4 -10000 0 4
chemotaxis 0.15 0.21 0.78 4 -10000 0 4
PIK3CA 0.017 0 -10000 0 -10000 0 0
Rac1/GTP -0.14 0.19 -10000 0 -0.73 4 4
angiogenesis -0.1 0.16 -10000 0 -0.35 23 23
LCK -0.1 0.18 -10000 0 -0.82 4 4
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 -0.018 0.16 -9999 0 -0.74 7 7
PLK4 -0.013 0.15 -9999 0 -0.74 6 6
regulation of centriole replication -0.018 0.16 -9999 0 -0.55 13 13
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.005 0.047 -9999 0 -0.41 2 2
RGS9BP -0.013 0.15 -9999 0 -0.74 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0 0 -9999 0 -10000 0 0
mol:Na + -0.098 0.18 -9999 0 -0.42 36 36
mol:ADP 0.012 0.047 -9999 0 -0.57 1 1
GNAT2 0.007 0.086 -9999 0 -0.74 2 2
RGS9-1/Gbeta5/R9AP -0.14 0.2 -9999 0 -0.41 52 52
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP -0.006 0.055 -9999 0 -0.48 2 2
GRK7 0.012 0.061 -9999 0 -0.74 1 1
CNGB3 -0.018 0.16 -9999 0 -0.74 7 7
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.06 0.17 -9999 0 -0.43 7 7
Cone PDE6 -0.11 0.16 -9999 0 -0.72 1 1
Cone Metarhodopsin II -0.003 0.037 -9999 0 -0.45 1 1
Na + (4 Units) -0.086 0.16 -9999 0 -0.43 7 7
GNAT2/GDP -0.12 0.17 -9999 0 -0.43 12 12
GNB5 -0.003 0.12 -9999 0 -0.74 4 4
mol:GMP (4 units) 0.029 0.053 -9999 0 -0.43 2 2
Cone Transducin -0.006 0.049 -9999 0 -0.43 2 2
SLC24A2 0.017 0 -9999 0 -10000 0 0
GNB3/GNGT2 0 0 -9999 0 -10000 0 0
GNB3 0.017 0 -9999 0 -10000 0 0
GNAT2/GTP -0.007 0.064 -9999 0 -0.57 2 2
CNGA3 -0.11 0.26 -9999 0 -0.64 29 29
ARR3 0.017 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.098 0.18 -9999 0 -0.42 36 36
mol:Pi -0.14 0.2 -9999 0 -0.41 52 52
Cone CNG Channel -0.079 0.14 -9999 0 -10000 0 0
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + 0.017 0 -9999 0 -10000 0 0
RGS9 -0.17 0.3 -9999 0 -0.64 43 43
PDE6C 0.017 0 -9999 0 -10000 0 0
GNGT2 0.017 0 -9999 0 -10000 0 0
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.017 0 -9999 0 -10000 0 0
Noncanonical Wnt signaling pathway

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
NFATC2 0.017 0 -9999 0 -10000 0 0
GNB1/GNG2 -0.12 0.14 -9999 0 -0.48 8 8
mol:DAG -0.11 0.19 -9999 0 -0.54 10 10
PLCG1 -0.11 0.2 -9999 0 -0.56 10 10
YES1 -0.1 0.18 -9999 0 -0.48 13 13
FZD3 -0.15 0.31 -9999 0 -0.74 33 33
FZD6 -0.038 0.2 -9999 0 -0.74 11 11
G protein -0.11 0.13 -9999 0 -0.56 2 2
MAP3K7 -0.071 0.16 -9999 0 -0.46 1 1
mol:Ca2+ -0.1 0.18 -9999 0 -0.52 10 10
mol:IP3 -0.11 0.19 -9999 0 -0.54 10 10
NLK 0.003 0.007 -9999 0 -10000 0 0
GNB1 0.017 0 -9999 0 -10000 0 0
CAMK2A -0.087 0.18 -9999 0 -0.48 9 9
MAP3K7IP1 0.017 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.12 0.18 -9999 0 -0.49 18 18
CSNK1A1 0.017 0 -9999 0 -10000 0 0
GNAS -0.1 0.18 -9999 0 -0.48 13 13
GO:0007205 -0.1 0.18 -9999 0 -0.5 10 10
WNT6 0.017 0 -9999 0 -10000 0 0
WNT4 -0.031 0.17 -9999 0 -0.65 11 11
NFAT1/CK1 alpha -0.1 0.13 -9999 0 -0.55 2 2
GNG2 0.017 0 -9999 0 -10000 0 0
WNT5A -0.067 0.24 -9999 0 -0.74 17 17
WNT11 -0.13 0.3 -9999 0 -0.74 29 29
CDC42 -0.088 0.17 -9999 0 -0.59 2 2
PLK1 signaling events

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
regulation of centriole-centriole cohesion -0.002 0.036 0.21 4 -10000 0 4
BUB1B -0.098 0.16 -10000 0 -0.4 29 29
PLK1 -0.014 0.041 -10000 0 -0.13 6 6
PLK1S1 -0.007 0.02 -10000 0 -0.066 1 1
KIF2A 0 0.037 -10000 0 -10000 0 0
regulation of mitotic centrosome separation -0.014 0.041 -10000 0 -0.13 6 6
GOLGA2 0.017 0 -10000 0 -10000 0 0
Hec1/SPC24 -0.013 0.048 -10000 0 -0.51 1 1
WEE1 -0.052 0.079 -10000 0 -0.3 3 3
cytokinesis -0.025 0.13 -10000 0 -0.39 15 15
PP2A-alpha B56 -0.091 0.13 -10000 0 -0.5 2 2
AURKA -0.019 0.062 -10000 0 -0.17 20 20
PICH/PLK1 -0.42 0.35 -10000 0 -0.79 62 62
CENPE -0.015 0.092 -10000 0 -0.47 5 5
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0 0.037 -10000 0 -10000 0 0
PPP2CA 0.017 0 -10000 0 -10000 0 0
FZR1 0.017 0 -10000 0 -10000 0 0
TPX2 -0.034 0.075 -10000 0 -0.17 33 33
PAK1 0.014 0.004 -10000 0 -10000 0 0
SPC24 0 0 -10000 0 -10000 0 0
FBXW11 0.017 0 -10000 0 -10000 0 0
CLSPN -0.003 0.037 -10000 0 -0.21 3 3
GORASP1 0.017 0 -10000 0 -10000 0 0
metaphase -0.001 0.002 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
NLP -0.007 0.02 -10000 0 -0.066 1 1
G2 phase of mitotic cell cycle -0.003 0.004 -10000 0 -0.013 13 13
STAG2 0.007 0.086 -10000 0 -0.74 2 2
GRASP65/GM130/RAB1/GTP -0.014 0.024 -10000 0 -10000 0 0
spindle elongation -0.014 0.041 -10000 0 -0.13 6 6
ODF2 0.008 0.061 -10000 0 -0.74 1 1
BUB1 -0.12 0.15 -10000 0 -0.57 2 2
TPT1 0 0.02 -10000 0 -10000 0 0
CDC25C -0.006 0.05 -10000 0 -0.23 6 6
CDC25B -0.35 0.38 -10000 0 -0.74 74 74
SGOL1 0.002 0.036 -10000 0 -0.21 4 4
RHOA 0.017 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.28 0.27 -10000 0 -0.65 37 37
CDC14B 0.013 0.005 -10000 0 -10000 0 0
CDC20 -0.003 0.12 -10000 0 -0.74 4 4
PLK1/PBIP1 -0.043 0.12 -10000 0 -0.44 12 12
mitosis 0.002 0.013 0.033 20 -10000 0 20
FBXO5 -0.042 0.097 -10000 0 -0.42 7 7
CDC2 -0.091 0.26 -10000 0 -0.75 20 20
NDC80 0.012 0.061 -10000 0 -0.74 1 1
metaphase plate congression -0.002 0.025 -10000 0 -10000 0 0
ERCC6L -0.4 0.35 -10000 0 -0.8 57 57
NLP/gamma Tubulin -0.003 0.021 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0 0.02 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint -0.002 0.002 -10000 0 -10000 0 0
PPP1R12A 0.016 0.001 -10000 0 -10000 0 0
interphase -0.002 0.002 -10000 0 -10000 0 0
PLK1/PRC1-2 -0.059 0.17 -10000 0 -0.5 18 18
GRASP65/GM130/RAB1/GTP/PLK1 -0.004 0.019 -10000 0 -10000 0 0
RAB1A 0.017 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA -0.007 0.046 -10000 0 -10000 0 0
mitotic prometaphase -0.002 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.016 0.027 -10000 0 -10000 0 0
microtubule-based process -0.045 0.15 -10000 0 -0.48 15 15
Golgi organization -0.014 0.041 -10000 0 -0.13 6 6
Cohesin/SA2 -0.019 0.053 -10000 0 -0.42 2 2
PPP1CB/MYPT1 0 0.003 -10000 0 -10000 0 0
KIF20A -0.057 0.22 -10000 0 -0.74 15 15
APC/C/CDC20 -0.013 0.084 -10000 0 -0.48 4 4
PPP2R1A 0.017 0 -10000 0 -10000 0 0
chromosome segregation -0.042 0.12 -10000 0 -0.43 12 12
PRC1 -0.008 0.14 -10000 0 -0.74 5 5
ECT2 -0.3 0.23 -10000 0 -0.46 101 101
C13orf34 -0.005 0.039 -10000 0 -10000 0 0
NUDC -0.002 0.025 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore -0.096 0.16 -10000 0 -0.4 29 29
spindle assembly -0.007 0.031 -10000 0 -10000 0 0
spindle stabilization -0.007 0.02 -10000 0 -0.066 1 1
APC/C/HCDH1 0.009 0.012 -10000 0 -10000 0 0
MKLP2/PLK1 -0.045 0.15 -10000 0 -0.49 15 15
CCNB1 -0.13 0.29 -10000 0 -0.75 28 28
PPP1CB 0.016 0.001 -10000 0 -10000 0 0
BTRC 0.017 0 -10000 0 -10000 0 0
ROCK2 0.007 0.028 -10000 0 -10000 0 0
TUBG1 0 0.02 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.27 0.26 -10000 0 -0.63 37 37
MLF1IP -0.031 0.16 -10000 0 -0.58 12 12
INCENP 0 0.086 -10000 0 -0.75 2 2
IL2 signaling events mediated by PI3K

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
BCL2L1 0.037 0.065 -10000 0 -10000 0 0
UGCG -0.019 0.024 -10000 0 -10000 0 0
AKT1/mTOR/p70S6K/Hsp90/TERT -0.17 0.17 -10000 0 -0.36 52 52
mol:GTP -0.001 0.001 -10000 0 -10000 0 0
mol:glucosylceramide -0.011 0.034 -10000 0 -10000 0 0
mol:DAG 0.045 0.085 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.29 0.2 -10000 0 -0.52 54 54
FRAP1 -0.31 0.27 -10000 0 -0.62 55 55
FOXO3 -0.19 0.19 -10000 0 -0.54 2 2
AKT1 -0.21 0.2 -10000 0 -0.45 51 51
GAB2 0.003 0.007 -10000 0 -10000 0 0
SMPD1 -0.19 0.33 -10000 0 -0.8 34 34
SGMS1 -0.019 0.024 -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 0.005 0.013 -10000 0 -10000 0 0
CALM1 0.017 0 -10000 0 -10000 0 0
cell proliferation -0.064 0.11 -10000 0 -10000 0 0
EIF3A 0.017 0 -10000 0 -10000 0 0
PI3K 0.006 0.013 -10000 0 -10000 0 0
RPS6KB1 -0.008 0.039 -10000 0 -10000 0 0
mol:sphingomyelin 0.045 0.085 -10000 0 -10000 0 0
natural killer cell activation -0.009 0.005 -10000 0 -0.014 49 49
JAK3 0.004 0.008 -10000 0 -10000 0 0
PIK3R1 0.004 0.008 -10000 0 -10000 0 0
JAK1 0.004 0.008 -10000 0 -10000 0 0
NFKB1 0.017 0 -10000 0 -10000 0 0
MYC -0.33 0.29 -10000 0 -0.63 54 54
MYB 0.007 0.12 -10000 0 -1.3 1 1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K -0.073 0.12 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.004 0.028 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.072 0.12 -10000 0 -10000 0 0
Rac1/GDP 0.007 0.015 -10000 0 -10000 0 0
T cell proliferation -0.077 0.11 -10000 0 -10000 0 0
SHC1 0.003 0.007 -10000 0 -10000 0 0
RAC1 0.016 0.001 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity 0.007 0.006 -10000 0 -0.066 1 1
PRKCZ -0.08 0.11 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.28 0.2 -10000 0 -0.52 53 53
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.01 0.049 -10000 0 -10000 0 0
HSP90AA1 0.012 0.061 -10000 0 -0.74 1 1
RELA 0.017 0 -10000 0 -10000 0 0
IL2RA -0.026 0.15 -10000 0 -0.75 6 6
IL2RB 0 0.053 -10000 0 -0.64 1 1
TERT 0.017 0 -10000 0 -10000 0 0
E2F1 0.002 0.076 -10000 0 -0.45 1 1
SOS1 0.003 0.007 -10000 0 -10000 0 0
RPS6 0.017 0 -10000 0 -10000 0 0
mol:cAMP -0.004 0.003 0.031 1 -10000 0 1
PTPN11 -0.002 0.061 -10000 0 -0.75 1 1
IL2RG 0 0.053 -10000 0 -0.64 1 1
actin cytoskeleton organization -0.077 0.11 -10000 0 -10000 0 0
GRB2 0.003 0.007 -10000 0 -10000 0 0
IL2 0.004 0.008 -10000 0 -10000 0 0
PIK3CA 0.004 0.008 -10000 0 -10000 0 0
Rac1/GTP 0.009 0.019 -10000 0 -10000 0 0
LCK -0.001 0.061 -10000 0 -0.75 1 1
BCL2 -0.56 0.46 -10000 0 -0.92 91 91
EPHB forward 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
Ephrin A5/EPHB2 -0.012 0.071 -10000 0 -0.44 4 4
cell-cell adhesion 0.18 0.2 0.64 12 -10000 0 12
Ephrin B/EPHB2/RasGAP -0.014 0.071 -10000 0 -10000 0 0
ITSN1 0.017 0 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
SHC1 0.017 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.034 0.12 -10000 0 -0.47 11 11
Ephrin B1/EPHB1 -0.17 0.23 -10000 0 -0.48 54 54
HRAS/GDP -0.17 0.2 -10000 0 -0.64 12 12
Ephrin B/EPHB1/GRB7 -0.16 0.21 -10000 0 -0.8 3 3
Endophilin/SYNJ1 0.04 0.069 -10000 0 -10000 0 0
KRAS 0.017 0 -10000 0 -10000 0 0
Ephrin B/EPHB1/Src -0.14 0.19 -10000 0 -0.8 1 1
endothelial cell migration -0.082 0.16 -10000 0 -0.41 30 30
GRB2 0.017 0 -10000 0 -10000 0 0
GRB7 -0.008 0.14 -10000 0 -0.74 5 5
PAK1 0.051 0.07 -10000 0 -10000 0 0
HRAS 0.017 0 -10000 0 -10000 0 0
RRAS 0.04 0.07 -10000 0 -10000 0 0
DNM1 -0.003 0.12 -10000 0 -0.74 4 4
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.1 0.21 -10000 0 -0.7 2 2
lamellipodium assembly -0.18 0.2 -10000 0 -0.64 12 12
Ephrin B/EPHB1/Src/p52 SHC/GRB2 -0.041 0.13 -10000 0 -0.43 1 1
PIK3R1 0.017 0 -10000 0 -10000 0 0
EPHB2 0.003 0.1 -10000 0 -0.71 3 3
EPHB3 -0.036 0.19 -10000 0 -0.72 11 11
EPHB1 -0.25 0.36 -10000 0 -0.74 54 54
EPHB4 -0.13 0.3 -10000 0 -0.74 30 30
mol:GDP -0.15 0.2 -10000 0 -0.6 12 12
Ephrin B/EPHB2 -0.012 0.066 -10000 0 -0.4 3 3
Ephrin B/EPHB3 -0.032 0.11 -10000 0 -0.4 10 10
JNK cascade -0.12 0.24 -10000 0 -0.77 5 5
Ephrin B/EPHB1 -0.15 0.2 -10000 0 -0.41 54 54
RAP1/GDP -0.13 0.17 -10000 0 -0.52 11 11
EFNB2 0.008 0.08 -10000 0 -0.69 2 2
EFNB3 0.017 0 -10000 0 -10000 0 0
EFNB1 0.017 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.17 0.23 -10000 0 -0.45 56 56
RAP1B 0.017 0 -10000 0 -10000 0 0
RAP1A 0.017 0 -10000 0 -10000 0 0
CDC42/GTP -0.12 0.16 -10000 0 -0.64 3 3
Rap1/GTP -0.12 0.16 -10000 0 -0.61 4 4
axon guidance -0.011 0.07 -10000 0 -0.44 4 4
MAPK3 -0.019 0.12 -10000 0 -10000 0 0
MAPK1 -0.015 0.12 -10000 0 -10000 0 0
Rac1/GDP -0.1 0.21 -10000 0 -0.56 11 11
actin cytoskeleton reorganization -0.14 0.15 -10000 0 -0.49 12 12
CDC42/GDP -0.1 0.21 -10000 0 -0.56 11 11
PI3K -0.083 0.17 -10000 0 -0.41 30 30
EFNA5 0.012 0.053 -10000 0 -0.64 1 1
Ephrin B2/EPHB4 -0.1 0.2 -10000 0 -0.49 31 31
Ephrin B/EPHB2/Intersectin/N-WASP 0.04 0.056 -10000 0 -10000 0 0
CDC42 0.017 0 -10000 0 -10000 0 0
RAS family/GTP -0.12 0.15 -10000 0 -0.61 3 3
PTK2 0.037 0.049 -10000 0 -10000 0 0
MAP4K4 -0.12 0.24 -10000 0 -0.78 5 5
SRC 0.017 0 -10000 0 -10000 0 0
KALRN 0.017 0 -10000 0 -10000 0 0
Intersectin/N-WASP -0.003 0.038 -10000 0 -0.47 1 1
neuron projection morphogenesis -0.071 0.18 -10000 0 -0.58 1 1
MAP2K1 -0.027 0.12 -10000 0 -0.4 1 1
WASL 0.012 0.053 -10000 0 -0.64 1 1
Ephrin B1/EPHB1-2/NCK1 -0.16 0.21 -10000 0 -0.44 54 54
cell migration -0.02 0.13 -10000 0 -0.41 1 1
NRAS 0.007 0.086 -10000 0 -0.74 2 2
SYNJ1 0.04 0.07 -10000 0 -10000 0 0
PXN 0.017 0 -10000 0 -10000 0 0
TF 0.05 0.068 -10000 0 -10000 0 0
HRAS/GTP -0.13 0.17 -10000 0 -0.68 3 3
Ephrin B1/EPHB1-2 -0.16 0.22 -10000 0 -0.45 55 55
cell adhesion mediated by integrin -0.017 0.075 0.36 1 -10000 0 1
RAC1 0.017 0 -10000 0 -10000 0 0
mol:GTP -0.14 0.19 -10000 0 -0.74 3 3
RAC1-CDC42/GTP -0.14 0.18 -10000 0 -0.66 6 6
RASA1 0.012 0.061 -10000 0 -0.74 1 1
RAC1-CDC42/GDP -0.13 0.17 -10000 0 -0.52 11 11
ruffle organization -0.13 0.24 -10000 0 -0.65 13 13
NCK1 0.017 0 -10000 0 -10000 0 0
receptor internalization 0.039 0.093 -10000 0 -10000 0 0
Ephrin B/EPHB2/KALRN -0.012 0.064 -10000 0 -10000 0 0
ROCK1 0.003 0.12 -10000 0 -0.43 9 9
RAS family/GDP -0.12 0.14 -10000 0 -0.46 11 11
Rac1/GTP -0.19 0.21 -10000 0 -0.7 12 12
Ephrin B/EPHB1/Src/Paxillin -0.046 0.13 -10000 0 -0.43 1 1
Nectin adhesion pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB 0.017 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.004 0.045 -9999 0 -0.55 1 1
PTK2 -0.024 0.091 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.017 0.068 -9999 0 -10000 0 0
CDC42/GDP 0.052 0.11 -9999 0 -0.38 9 9
Rac1/GDP 0.054 0.11 -9999 0 -10000 0 0
RAP1B 0.017 0 -9999 0 -10000 0 0
RAP1A 0.017 0 -9999 0 -10000 0 0
CTNNB1 0.012 0.061 -9999 0 -0.74 1 1
CDC42/GTP -0.021 0.082 -9999 0 -10000 0 0
nectin-3/I-afadin -0.027 0.11 -9999 0 -0.47 9 9
RAPGEF1 0.048 0.12 -9999 0 -0.42 9 9
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.037 0.14 -9999 0 -0.49 9 9
PDGFB-D/PDGFRB 0.017 0 -9999 0 -10000 0 0
TLN1 0.034 0.052 -9999 0 -10000 0 0
Rap1/GTP -0.018 0.071 -9999 0 -10000 0 0
IQGAP1 0.017 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin 0 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.027 0.11 -9999 0 -0.47 9 9
PVR 0.017 0 -9999 0 -10000 0 0
Necl-5(dimer) 0.017 0 -9999 0 -10000 0 0
mol:GDP 0.048 0.13 -9999 0 -0.47 9 9
MLLT4 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.017 0 -9999 0 -10000 0 0
PI3K -0.018 0.074 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
positive regulation of lamellipodium assembly -0.022 0.077 -9999 0 -0.3 9 9
PVRL1 0.017 0 -9999 0 -10000 0 0
PVRL3 -0.022 0.16 -9999 0 -0.64 9 9
PVRL2 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
CDH1 -0.005 0.12 -9999 0 -0.64 5 5
CLDN1 -0.72 0.14 -9999 0 -0.74 148 148
JAM-A/CLDN1 -0.43 0.11 -9999 0 -0.44 148 148
SRC -0.032 0.13 -9999 0 -0.55 9 9
ITGB3 0.017 0 -9999 0 -10000 0 0
nectin-1(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
FARP2 0.043 0.13 -9999 0 -0.46 9 9
RAC1 0.017 0 -9999 0 -10000 0 0
CTNNA1 0.017 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.023 0.092 -9999 0 -0.39 9 9
nectin-1/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2/I-afadin 0 0 -9999 0 -10000 0 0
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 -0.023 0.092 -9999 0 -0.39 9 9
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.017 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.017 0.068 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.01 0.043 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
nectin-2(dimer)/I-afadin/I-afadin 0 0 -9999 0 -10000 0 0
PIP5K1C 0.024 0.055 -9999 0 -10000 0 0
VAV2 0.032 0.15 -9999 0 -0.47 12 12
RAP1/GDP -0.021 0.082 -9999 0 -10000 0 0
ITGAV 0.012 0.061 -9999 0 -0.74 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.023 0.092 -9999 0 -0.39 9 9
nectin-3(dimer)/I-afadin/I-afadin -0.027 0.11 -9999 0 -0.47 9 9
Rac1/GTP -0.027 0.093 -9999 0 -0.37 9 9
PTPRM -0.014 0.054 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin -0.012 0.059 -9999 0 -10000 0 0
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.017 0 -9999 0 -10000 0 0
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.074 0.19 -9999 0 -0.56 18 18
PDGFRB 0.01 0.009 -9999 0 -10000 0 0
SPHK1 -0.058 0.1 -9999 0 -0.31 15 15
mol:S1P -0.098 0.16 -9999 0 -0.44 17 17
S1P1/S1P/Gi -0.09 0.2 -9999 0 -0.59 9 9
GNAO1 0.012 0.009 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/PLCgamma1 -0.14 0.18 -9999 0 -0.64 10 10
PLCG1 -0.11 0.23 -9999 0 -0.64 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB 0.01 0.009 -9999 0 -10000 0 0
GNAI2 0.007 0.061 -9999 0 -0.74 1 1
GNAI3 0.011 0.009 -9999 0 -10000 0 0
GNAI1 -0.062 0.21 -9999 0 -0.64 17 17
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 -0.045 0.22 -9999 0 -0.61 13 13
S1P1/S1P -0.14 0.21 -9999 0 -0.69 11 11
negative regulation of cAMP metabolic process -0.088 0.2 -9999 0 -0.57 9 9
MAPK3 -0.11 0.23 -9999 0 -0.62 9 9
calcium-dependent phospholipase C activity -0.003 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 0.016 0.032 -9999 0 -10000 0 0
PLCB2 -0.083 0.21 -9999 0 -0.59 11 11
RAC1 0.017 0 -9999 0 -10000 0 0
RhoA/GTP -0.11 0.17 -9999 0 -0.55 11 11
receptor internalization -0.13 0.19 -9999 0 -0.61 12 12
PTGS2 -0.16 0.29 -9999 0 -0.65 17 17
Rac1/GTP -0.11 0.17 -9999 0 -0.55 11 11
RHOA 0.017 0 -9999 0 -10000 0 0
VEGFA -0.073 0.25 -9999 0 -0.74 18 18
negative regulation of T cell proliferation -0.088 0.2 -9999 0 -0.57 9 9
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ 0.011 0.009 -9999 0 -10000 0 0
MAPK1 -0.11 0.23 -9999 0 -0.59 10 10
S1P1/S1P/PDGFB-D/PDGFRB -0.11 0.24 -9999 0 -0.71 11 11
ABCC1 -0.064 0.23 -9999 0 -0.74 16 16
Sphingosine 1-phosphate (S1P) pathway

Figure S52.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S52.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.012 0.053 -9999 0 -0.64 1 1
SPHK1 -0.097 0.27 -9999 0 -0.74 23 23
GNAI2 0.012 0.061 -9999 0 -0.74 1 1
mol:S1P -0.042 0.13 -9999 0 -0.26 38 38
GNAO1 0.017 0 -9999 0 -10000 0 0
mol:Sphinganine-1-P -0.059 0.22 -9999 0 -0.57 23 23
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.043 0.081 -9999 0 -0.43 2 2
GNAI3 0.017 0 -9999 0 -10000 0 0
G12/G13 0 0 -9999 0 -10000 0 0
S1PR3 0 0 -9999 0 -10000 0 0
S1PR2 0 0 -9999 0 -10000 0 0
EDG1 -0.005 0.12 -9999 0 -0.64 5 5
S1P1/S1P -0.041 0.13 -9999 0 -0.44 7 7
S1PR5 0 0 -9999 0 -10000 0 0
S1PR4 0 0 -9999 0 -10000 0 0
GNAI1 -0.056 0.21 -9999 0 -0.64 17 17
S1P/S1P5/G12 -0.049 0.091 -9999 0 -0.46 2 2
S1P/S1P3/Gq -0.034 0.14 -9999 0 -0.36 16 16
S1P/S1P4/Gi -0.008 0.1 -9999 0 -0.34 5 5
GNAQ 0 0 -9999 0 -10000 0 0
GNAZ 0.017 0 -9999 0 -10000 0 0
GNA14 -0.009 0.13 -9999 0 -0.64 6 6
GNA15 -0.003 0.12 -9999 0 -0.74 4 4
GNA12 0.017 0 -9999 0 -10000 0 0
GNA13 0.017 0 -9999 0 -10000 0 0
GNA11 -0.026 0.16 -9999 0 -0.64 10 10
ABCC1 -0.062 0.23 -9999 0 -0.74 16 16
Signaling events mediated by the Hedgehog family

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
TGFB2 0.019 0.22 -10000 0 -0.66 12 12
IHH 0.019 0.072 -10000 0 -0.79 1 1
SHH Np/Cholesterol/GAS1 -0.12 0.2 -10000 0 -0.53 15 15
LRPAP1 0.017 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.12 0.2 0.53 15 -10000 0 15
SMO/beta Arrestin2 0.047 0.1 -10000 0 -0.71 1 1
SMO 0.041 0.11 -10000 0 -0.76 1 1
AKT1 0.051 0.055 -10000 0 -10000 0 0
ARRB2 0.017 0 -10000 0 -10000 0 0
BOC 0.017 0 -10000 0 -10000 0 0
ADRBK1 0.017 0 -10000 0 -10000 0 0
heart looping 0.041 0.11 -10000 0 -0.74 1 1
STIL -0.046 0.21 -10000 0 -0.61 9 9
DHH N/PTCH2 0 0 -10000 0 -10000 0 0
DHH N/PTCH1 -0.024 0.082 -10000 0 -0.7 1 1
PIK3CA 0.017 0 -10000 0 -10000 0 0
DHH 0.017 0 -10000 0 -10000 0 0
PTHLH 0.027 0.21 -10000 0 -1.6 1 1
determination of left/right symmetry 0.041 0.11 -10000 0 -0.74 1 1
PIK3R1 0.017 0 -10000 0 -10000 0 0
skeletal system development 0.028 0.2 -10000 0 -1.5 1 1
IHH N/Hhip -0.092 0.23 -10000 0 -0.52 34 34
DHH N/Hhip -0.1 0.19 -10000 0 -0.47 34 34
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development 0.041 0.11 -10000 0 -0.74 1 1
pancreas development -0.13 0.27 -10000 0 -0.64 34 34
HHAT -0.052 0.2 -10000 0 -0.64 16 16
PI3K 0 0 -10000 0 -10000 0 0
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 -0.13 0.28 -10000 0 -0.67 33 33
somite specification 0.041 0.11 -10000 0 -0.74 1 1
SHH Np/Cholesterol/PTCH1 0.006 0.15 -10000 0 -0.55 4 4
SHH Np/Cholesterol/PTCH2 -0.043 0.12 -10000 0 -0.43 2 2
SHH Np/Cholesterol/Megalin -0.043 0.12 -10000 0 -0.43 2 2
SHH -0.028 0.16 -10000 0 -0.48 18 18
catabolic process 0.036 0.11 -10000 0 -0.78 1 1
SMO/Vitamin D3 0.017 0.15 -10000 0 -0.56 3 3
SHH Np/Cholesterol/Hhip -0.12 0.21 -10000 0 -0.69 9 9
LRP2 0.017 0 -10000 0 -10000 0 0
receptor-mediated endocytosis -0.049 0.11 -10000 0 -0.61 1 1
SHH Np/Cholesterol/BOC -0.043 0.12 -10000 0 -0.43 2 2
SHH Np/Cholesterol/CDO -0.043 0.12 -10000 0 -0.43 2 2
mesenchymal cell differentiation 0.12 0.2 0.68 9 -10000 0 9
mol:Vitamin D3 0.01 0.15 -10000 0 -0.55 4 4
IHH N/PTCH2 0.027 0.046 -10000 0 -0.51 1 1
CDON 0.017 0 -10000 0 -10000 0 0
IHH N/PTCH1 0.035 0.12 -10000 0 -0.79 1 1
Megalin/LRPAP1 0 0 -10000 0 -10000 0 0
PTCH2 0.017 0 -10000 0 -10000 0 0
SHH Np/Cholesterol -0.044 0.12 -10000 0 -0.38 18 18
PTCH1 0.036 0.12 -10000 0 -0.78 1 1
HHIP -0.13 0.27 -10000 0 -0.64 34 34
EPO signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.14 0.2 -9999 0 -0.6 1 1
CRKL -0.006 0.083 -9999 0 -0.43 1 1
mol:DAG -0.054 0.14 -9999 0 -0.47 10 10
HRAS 0.028 0.082 -9999 0 -10000 0 0
MAPK8 0.018 0.045 -9999 0 -0.43 1 1
RAP1A -0.006 0.083 -9999 0 -0.43 1 1
GAB1 -0.008 0.094 -9999 0 -0.65 1 1
MAPK14 0.018 0.045 -9999 0 -0.43 1 1
EPO 0.003 0.063 -9999 0 -0.76 1 1
PLCG1 -0.055 0.15 -9999 0 -0.49 10 10
EPOR/TRPC2/IP3 Receptors 0.008 0.011 -9999 0 -10000 0 0
RAPGEF1 0.017 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.042 0.14 -9999 0 -0.5 13 13
GAB1/SHC/GRB2/SOS1 -0.015 0.064 -9999 0 -0.55 1 1
EPO/EPOR (dimer) 0.007 0.051 -9999 0 -0.58 1 1
IRS2 -0.006 0.083 -9999 0 -0.43 1 1
STAT1 -0.11 0.18 -9999 0 -0.57 10 10
STAT5B -0.053 0.12 -9999 0 -0.48 1 1
cell proliferation 0.022 0.046 -9999 0 -10000 0 0
GAB1/SHIP/PIK3R1/SHP2/SHC -0.016 0.065 -9999 0 -0.53 1 1
TEC -0.006 0.083 -9999 0 -0.43 1 1
SOCS3 -0.043 0.2 -9999 0 -0.74 12 12
STAT1 (dimer) -0.11 0.18 -9999 0 -0.56 10 10
JAK2 -0.012 0.12 -9999 0 -0.73 4 4
PIK3R1 0.017 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/JAK2 -0.012 0.092 -9999 0 -0.43 2 2
EPO/EPOR 0.007 0.051 -9999 0 -0.58 1 1
LYN 0.008 0.01 -9999 0 -10000 0 0
TEC/VAV2 -0.002 0.093 -9999 0 -10000 0 0
elevation of cytosolic calcium ion concentration 0.008 0.011 -9999 0 -10000 0 0
SHC1 0.017 0 -9999 0 -10000 0 0
EPO/EPOR (dimer)/LYN 0.017 0.049 -9999 0 -0.49 1 1
mol:IP3 -0.054 0.14 -9999 0 -0.47 10 10
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.025 0.055 -9999 0 -10000 0 0
SH2B3 0.007 0.011 -9999 0 -10000 0 0
NFKB1 0.018 0.045 -9999 0 -0.43 1 1
EPO/EPOR (dimer)/JAK2/SOCS3 -0.023 0.07 -9999 0 -0.44 1 1
PTPN6 -0.018 0.086 -9999 0 -0.43 2 2
TEC/VAV2/GRB2 -0.025 0.069 -9999 0 -10000 0 0
EPOR 0.008 0.011 -9999 0 -10000 0 0
INPP5D 0 0 -9999 0 -10000 0 0
mol:GDP -0.015 0.065 -9999 0 -0.56 1 1
SOS1 0.017 0 -9999 0 -10000 0 0
PLCG2 -0.31 0.33 -9999 0 -0.64 76 76
CRKL/CBL/C3G -0.019 0.055 -9999 0 -10000 0 0
VAV2 -0.013 0.096 -9999 0 -10000 0 0
CBL -0.006 0.083 -9999 0 -0.43 1 1
SHC/Grb2/SOS1 -0.019 0.055 -9999 0 -10000 0 0
STAT5A -0.053 0.12 -9999 0 -0.48 1 1
GRB2 0.017 0 -9999 0 -10000 0 0
STAT5 (dimer) -0.1 0.17 -9999 0 -0.6 1 1
LYN/PLCgamma2 -0.23 0.24 -9999 0 -0.47 76 76
PTPN11 0.012 0.061 -9999 0 -0.74 1 1
BTK -0.059 0.15 -9999 0 -10000 0 0
BCL2 -0.51 0.49 -9999 0 -0.91 91 91
PDGFR-alpha signaling pathway

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
PDGFRA 0.002 0.091 -9999 0 -0.64 3 3
PDGF/PDGFRA/CRKL -0.009 0.062 -9999 0 -0.45 3 3
positive regulation of JUN kinase activity -0.006 0.045 -9999 0 -10000 0 0
CRKL 0.017 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Caveolin-3 -0.009 0.062 -9999 0 -0.45 3 3
AP1 -0.13 0.31 -9999 0 -1.1 13 13
mol:IP3 -0.029 0.18 -9999 0 -0.54 16 16
PLCG1 -0.029 0.18 -9999 0 -0.54 16 16
PDGF/PDGFRA/alphaV Integrin -0.012 0.077 -9999 0 -0.48 4 4
RAPGEF1 0.017 0 -9999 0 -10000 0 0
CRK 0.012 0.053 -9999 0 -0.64 1 1
mol:Ca2+ -0.029 0.18 -9999 0 -0.54 16 16
CAV3 0.017 0 -9999 0 -10000 0 0
CAV1 0.002 0.1 -9999 0 -0.74 3 3
SHC/Grb2/SOS1 -0.006 0.045 -9999 0 -10000 0 0
PDGF/PDGFRA/Shf -0.11 0.23 -9999 0 -0.57 30 30
FOS -0.076 0.33 -9999 0 -1.1 13 13
JUN -0.026 0.1 -9999 0 -0.58 5 5
oligodendrocyte development -0.012 0.076 -9999 0 -0.48 4 4
GRB2 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
mol:DAG -0.029 0.18 -9999 0 -0.54 16 16
PDGF/PDGFRA 0.002 0.091 -9999 0 -0.64 3 3
actin cytoskeleton reorganization -0.02 0.099 -9999 0 -0.51 6 6
SRF 0.032 0.009 -9999 0 -10000 0 0
SHC1 0.017 0 -9999 0 -10000 0 0
PI3K -0.007 0.051 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk/C3G -0.01 0.06 -9999 0 -0.4 1 1
JAK1 0.021 0.067 -9999 0 -0.45 3 3
ELK1/SRF -0.033 0.11 -9999 0 -10000 0 0
SHB 0.002 0.1 -9999 0 -0.74 3 3
SHF -0.12 0.29 -9999 0 -0.74 28 28
CSNK2A1 0.01 0.021 -9999 0 -10000 0 0
GO:0007205 -0.025 0.17 -9999 0 -0.51 16 16
SOS1 0.017 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.006 0.045 -9999 0 -10000 0 0
PDGF/PDGFRA/SHB -0.02 0.1 -9999 0 -0.51 6 6
PDGF/PDGFRA/Caveolin-1 -0.02 0.099 -9999 0 -0.51 6 6
ITGAV 0.012 0.061 -9999 0 -0.74 1 1
ELK1 -0.012 0.15 -9999 0 -0.46 13 13
PIK3CA 0.017 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.012 0.073 -9999 0 -0.46 4 4
JAK-STAT cascade 0.021 0.067 -9999 0 -0.45 3 3
cell proliferation -0.11 0.23 -9999 0 -0.56 30 30
Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1 0.012 0.061 -10000 0 -0.74 1 1
NFATC1 0.055 0.056 -10000 0 -10000 0 0
NFATC2 0.039 0.045 -10000 0 -0.22 1 1
NFATC3 0.021 0.002 -10000 0 -10000 0 0
YWHAE 0.012 0.061 -10000 0 -0.74 1 1
Calcineurin A alpha-beta B1/CABIN1 -0.08 0.15 -10000 0 -0.48 6 6
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0.001 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.079 0.095 -10000 0 -0.49 3 3
BCL2/BAX -0.28 0.23 -10000 0 -0.47 92 92
CaM/Ca2+/Calcineurin A alpha-beta B1 0 0 -10000 0 -10000 0 0
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
BAX 0.012 0.061 -10000 0 -0.74 1 1
MAPK14 0.017 0.001 -10000 0 -10000 0 0
BAD 0.017 0 -10000 0 -10000 0 0
CABIN1/MEF2D -0.066 0.14 -10000 0 -0.56 3 3
Calcineurin A alpha-beta B1/BCL2 -0.37 0.32 -10000 0 -0.64 91 91
FKBP8 0.017 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.066 0.14 0.55 3 -10000 0 3
KPNB1 -0.003 0.12 -10000 0 -0.74 4 4
KPNA2 -0.043 0.2 -10000 0 -0.74 12 12
XPO1 0.017 0 -10000 0 -10000 0 0
SFN 0.012 0.053 -10000 0 -0.64 1 1
MAP3K8 -0.067 0.24 -10000 0 -0.74 17 17
NFAT4/CK1 alpha 0 0 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.004 0.024 -10000 0 -10000 0 0
CABIN1 -0.081 0.15 -10000 0 -0.48 6 6
CALM1 0.017 0.001 -10000 0 -10000 0 0
RAN 0.017 0 -10000 0 -10000 0 0
MAP3K1 0.017 0 -10000 0 -10000 0 0
CAMK4 0.017 0 -10000 0 -10000 0 0
mol:Ca2+ 0.002 0.002 -10000 0 -10000 0 0
MAPK3 0.008 0.075 -10000 0 -0.64 2 2
YWHAH 0.017 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.015 0.083 -10000 0 -0.47 5 5
YWHAB 0.017 0 -10000 0 -10000 0 0
MAPK8 0.018 0.001 -10000 0 -10000 0 0
MAPK9 0.017 0 -10000 0 -10000 0 0
YWHAG 0.017 0 -10000 0 -10000 0 0
FKBP1A 0.017 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ -0.002 0.026 -10000 0 -10000 0 0
PRKCH 0.004 0.091 -10000 0 -0.64 3 3
CABIN1/Cbp/p300 0 0 -10000 0 -10000 0 0
CASP3 0.013 0.053 -10000 0 -0.64 1 1
PIM1 0.017 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.084 0.07 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.058 0.023 -10000 0 -10000 0 0
PRKCB 0 0 -10000 0 -10000 0 0
PRKCE 0.017 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.029 0.002 -10000 0 -10000 0 0
BAD/BCL-XL -0.004 0.045 -10000 0 -0.55 1 1
PRKCD 0.017 0 -10000 0 -10000 0 0
NUP214 0.017 0 -10000 0 -10000 0 0
PRKCZ 0.001 0.001 -10000 0 -10000 0 0
PRKCA 0.017 0 -10000 0 -10000 0 0
PRKCG -0.003 0.12 -10000 0 -0.74 4 4
PRKCQ 0.002 0.1 -10000 0 -0.74 3 3
FKBP38/BCL2 -0.28 0.23 -10000 0 -0.47 91 91
EP300 0.018 0.001 -10000 0 -10000 0 0
PRKCB1 -0.29 0.33 -10000 0 -0.64 72 72
CSNK2A1 0.017 0 -10000 0 -10000 0 0
NFATc/JNK1 0.063 0.053 -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 0.028 0.002 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV 0 0 -10000 0 -10000 0 0
NFATc/ERK1 0.058 0.064 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.079 0.096 -10000 0 -0.49 3 3
NR4A1 0.079 0.064 -10000 0 -0.59 1 1
GSK3B 0.018 0.001 -10000 0 -10000 0 0
positive T cell selection 0.021 0.002 -10000 0 -10000 0 0
NFAT1/CK1 alpha -0.007 0.021 -10000 0 -10000 0 0
RCH1/ KPNB1 -0.056 0.19 -10000 0 -0.66 13 13
YWHAQ 0.017 0 -10000 0 -10000 0 0
PRKACA 0.017 0.001 -10000 0 -10000 0 0
AKAP5 -0.005 0.12 -10000 0 -0.64 5 5
MEF2D 0.018 0.001 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.017 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.063 0.053 -10000 0 -10000 0 0
CREBBP 0.018 0.001 -10000 0 -10000 0 0
BCL2 -0.37 0.32 -10000 0 -0.64 91 91
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.065 0.18 -9999 0 -0.55 18 18
alphaV beta3 Integrin -0.009 0.062 -9999 0 -0.44 3 3
PTK2 0.048 0.12 -9999 0 -10000 0 0
IGF1R 0.017 0 -9999 0 -10000 0 0
PI4KB 0.017 0 -9999 0 -10000 0 0
MFGE8 0.017 0 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
CDKN1B -0.003 0.02 -9999 0 -10000 0 0
VEGFA -0.072 0.24 -9999 0 -0.74 18 18
ILK -0.003 0.02 -9999 0 -10000 0 0
ROCK1 0.017 0 -9999 0 -10000 0 0
AKT1 -0.002 0.017 -9999 0 -10000 0 0
PTK2B 0 0.14 -9999 0 -10000 0 0
alphaV/beta3 Integrin/JAM-A -0.007 0.051 -9999 0 -10000 0 0
CBL 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.003 0.038 -9999 0 -0.47 1 1
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.21 0.19 -9999 0 -0.77 4 4
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.032 0.072 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Syndecan-1 -0.003 0.038 -9999 0 -0.47 1 1
PI4KA 0.017 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.23 0.22 -9999 0 -0.71 17 17
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.35 0.21 -9999 0 -0.47 112 112
RPS6KB1 -0.19 0.23 -9999 0 -0.65 18 18
TLN1 0.017 0 -9999 0 -10000 0 0
MAPK3 -0.068 0.086 -9999 0 -0.72 1 1
GPR124 0.007 0.086 -9999 0 -0.74 2 2
MAPK1 -0.066 0.084 -9999 0 -0.72 1 1
PXN 0.017 0 -9999 0 -10000 0 0
PIK3R1 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Tumstatin -0.009 0.065 -9999 0 -0.47 3 3
cell adhesion -0.002 0.031 -9999 0 -10000 0 0
ANGPTL3 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Src -0.055 0.15 -9999 0 -0.47 18 18
IGF-1R heterotetramer 0.017 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.017 0 -9999 0 -10000 0 0
ITGB3 0.017 0 -9999 0 -10000 0 0
IGF1 -0.36 0.32 -9999 0 -0.64 88 88
RAC1 0.017 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.009 0.065 -9999 0 -0.47 3 3
apoptosis 0.012 0.061 -9999 0 -0.74 1 1
CD47 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.003 0.038 -9999 0 -0.47 1 1
VCL 0.017 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Del1 -0.044 0.12 -9999 0 -0.39 17 17
CSF1 0.017 0 -9999 0 -10000 0 0
PIK3C2A -0.018 0.071 -9999 0 -10000 0 0
PI4 Kinase/Pyk2 -0.041 0.1 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.052 0.14 -9999 0 -0.42 19 19
FAK1/Vinculin 0.053 0.1 -9999 0 -10000 0 0
alphaV beta3/Integrin/ppsTEM5 -0.009 0.065 -9999 0 -0.47 3 3
RHOA 0.017 0 -9999 0 -10000 0 0
VTN 0.017 0 -9999 0 -10000 0 0
BCAR1 0.017 0 -9999 0 -10000 0 0
FGF2 0.008 0.08 -9999 0 -0.69 2 2
F11R 0.025 0.062 -9999 0 -0.51 2 2
alphaV/beta3 Integrin/Lactadherin -0.003 0.038 -9999 0 -0.47 1 1
alphaV/beta3 Integrin/TGFBR2 -0.003 0.038 -9999 0 -0.47 1 1
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.003 0.034 -9999 0 -0.42 1 1
HSP90AA1 0.012 0.061 -9999 0 -0.74 1 1
alphaV/beta3 Integrin/Talin -0.003 0.035 -9999 0 -0.43 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.11 0.28 -9999 0 -0.74 26 26
alphaV/beta3 Integrin/Pyk2 -0.048 0.13 -9999 0 -10000 0 0
SDC1 0.017 0 -9999 0 -10000 0 0
VAV3 -0.025 0.16 -9999 0 -0.73 1 1
PTPN11 0.012 0.061 -9999 0 -0.74 1 1
IRS1 0.002 0.1 -9999 0 -0.74 3 3
FAK1/Paxillin 0.053 0.1 -9999 0 -10000 0 0
cell migration 0.064 0.098 -9999 0 -10000 0 0
ITGAV 0.012 0.061 -9999 0 -0.74 1 1
PI3K -0.006 0.044 -9999 0 -10000 0 0
SPP1 -0.54 0.34 -9999 0 -0.74 112 112
KDR 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.012 0.061 -9999 0 -0.74 1 1
COL4A3 0.007 0.086 -9999 0 -0.74 2 2
angiogenesis -0.024 0.1 -9999 0 -0.7 1 1
Rac1/GTP -0.061 0.12 -9999 0 -0.66 1 1
EDIL3 -0.052 0.2 -9999 0 -0.64 16 16
cell proliferation -0.003 0.038 -9999 0 -0.47 1 1
Glypican 2 network

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
MDK -0.023 0.17 -9999 0 -0.74 8 8
GPC2 0 0 -9999 0 -10000 0 0
GPC2/Midkine -0.03 0.13 -9999 0 -0.57 8 8
neuron projection morphogenesis -0.03 0.13 -9999 0 -0.56 8 8
IL27-mediated 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
TGFB1 0.028 0.017 -10000 0 -10000 0 0
CD4-positive alpha-beta T cell lineage commitment 0 0.001 -10000 0 -10000 0 0
cytokine production during immune response 0.025 0.12 0.88 1 -10000 0 1
IL27/IL27R/JAK1 -0.054 0.11 -10000 0 -0.83 1 1
TBX21 -0.15 0.27 -10000 0 -0.7 5 5
IL12B 0.009 0.061 -10000 0 -0.74 1 1
IL12A -0.01 0.11 -10000 0 -0.57 6 6
IL6ST 0.009 0.009 -10000 0 -10000 0 0
IL27RA/JAK1 0.004 0.051 -10000 0 -10000 0 0
IL27 -0.036 0.17 -10000 0 -0.68 10 10
TYK2 0.013 0.008 -10000 0 -10000 0 0
T-helper cell lineage commitment -0.14 0.15 -10000 0 -0.85 1 1
T-helper 2 cell differentiation 0.025 0.12 0.88 1 -10000 0 1
T cell proliferation during immune response 0.025 0.12 0.88 1 -10000 0 1
MAPKKK cascade -0.025 0.12 -10000 0 -0.88 1 1
STAT3 0.017 0 -10000 0 -10000 0 0
STAT2 0.017 0 -10000 0 -10000 0 0
STAT1 -0.059 0.22 -10000 0 -0.74 15 15
IL12RB1 0.013 0.008 -10000 0 -10000 0 0
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.073 0.19 -10000 0 -0.68 3 3
IL27/IL27R/JAK2/TYK2 -0.026 0.12 -10000 0 -0.9 1 1
positive regulation of T cell mediated cytotoxicity -0.025 0.12 -10000 0 -0.88 1 1
STAT1 (dimer) -0.14 0.19 -10000 0 -0.98 2 2
JAK2 -0.008 0.12 -10000 0 -0.76 4 4
JAK1 0.015 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.015 0.11 -10000 0 -0.84 1 1
T cell proliferation -0.26 0.25 -10000 0 -0.55 38 38
IL12/IL12R/TYK2/JAK2 -0.014 0.13 -10000 0 -0.57 1 1
IL17A -0.14 0.15 -10000 0 -0.85 1 1
mast cell activation 0.025 0.12 0.88 1 -10000 0 1
IFNG -0.014 0.047 -10000 0 -0.095 36 36
T cell differentiation -0.007 0.007 -10000 0 -0.025 1 1
STAT3 (dimer) -0.015 0.11 -10000 0 -0.84 1 1
STAT5A (dimer) -0.015 0.11 -10000 0 -0.84 1 1
STAT4 (dimer) -0.017 0.12 -10000 0 -0.84 1 1
STAT4 0.012 0.053 -10000 0 -0.64 1 1
T cell activation -0.01 0.009 0.086 1 -10000 0 1
IL27R/JAK2/TYK2 -0.027 0.1 -10000 0 -0.94 1 1
GATA3 0.021 0.031 -10000 0 -10000 0 0
IL18 -0.034 0.15 -10000 0 -0.49 15 15
positive regulation of mast cell cytokine production -0.014 0.11 -10000 0 -0.82 1 1
IL27/EBI3 -0.033 0.12 -10000 0 -0.5 10 10
IL27RA -0.009 0.049 -10000 0 -0.6 1 1
IL6 -0.42 0.37 -10000 0 -0.73 91 91
STAT5A 0.017 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.003 -10000 0 -10000 0 0
IL2 0.007 0.03 -10000 0 -10000 0 0
IL1B -0.17 0.27 -10000 0 -0.57 49 49
EBI3 0.008 0.009 -10000 0 -10000 0 0
TNF 0.015 0.002 -10000 0 -10000 0 0
Regulation of Telomerase

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
Telomerase catalytic core complex -0.094 0.16 -9999 0 -0.65 1 1
RAD9A 0.017 0 -9999 0 -10000 0 0
AP1 -0.061 0.17 -9999 0 -0.52 18 18
IFNAR2 0.017 0.007 -9999 0 -10000 0 0
AKT1 0.029 0.031 -9999 0 -10000 0 0
ER alpha/Oestrogen -0.006 0.054 -9999 0 -0.48 2 2
NFX1/SIN3/HDAC complex 0.058 0.025 -9999 0 -10000 0 0
EGF -0.21 0.33 -9999 0 -0.68 49 49
SMG5 0.017 0 -9999 0 -10000 0 0
SMG6 0.017 0 -9999 0 -10000 0 0
SP3/HDAC2 0.003 0.009 -9999 0 -10000 0 0
TERT/c-Abl -0.093 0.13 -9999 0 -0.6 1 1
SAP18 0.017 0.001 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.38 0.38 -9999 0 -0.74 80 80
WRN 0.017 0 -9999 0 -10000 0 0
SP1 0.018 0.008 -9999 0 -10000 0 0
SP3 0.015 0.007 -9999 0 -10000 0 0
TERF2IP 0.017 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.16 0.19 -9999 0 -0.66 8 8
Mad/Max -0.021 0.097 -9999 0 -0.47 7 7
TERT -0.095 0.16 -9999 0 -0.66 1 1
CCND1 -0.12 0.23 -9999 0 -0.67 13 13
MAX 0.016 0.006 -9999 0 -10000 0 0
RBBP7 0.017 0.001 -9999 0 -10000 0 0
RBBP4 0.017 0.001 -9999 0 -10000 0 0
TERF2 0 0 -9999 0 -10000 0 0
PTGES3 0.017 0 -9999 0 -10000 0 0
SIN3A 0.017 0.001 -9999 0 -10000 0 0
Telomerase/911 -0.043 0.13 -9999 0 -10000 0 0
CDKN1B -0.073 0.22 -9999 0 -0.46 37 37
RAD1 -0.013 0.15 -9999 0 -0.74 6 6
XRCC5 0.017 0 -9999 0 -10000 0 0
XRCC6 0.017 0 -9999 0 -10000 0 0
SAP30 0.017 0.001 -9999 0 -10000 0 0
TRF2/PARP2 0 0 -9999 0 -10000 0 0
UBE3A 0.015 0.006 -9999 0 -10000 0 0
JUN -0.009 0.14 -9999 0 -0.74 5 5
E6 0 0.002 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.012 0.007 -9999 0 -10000 0 0
FOS -0.046 0.19 -9999 0 -0.66 14 14
IFN-gamma/IRF1 -0.14 0.24 -9999 0 -0.54 38 38
PARP2 0.017 0 -9999 0 -10000 0 0
BLM 0.002 0.1 -9999 0 -0.74 3 3
Telomerase -0.041 0.14 -9999 0 -0.34 7 7
IRF1 0.012 0.08 -9999 0 -0.68 2 2
ESR1 0.008 0.075 -9999 0 -0.64 2 2
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 0 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process 0.063 0.027 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.063 0.027 -9999 0 -10000 0 0
HDAC1 0.017 0.001 -9999 0 -10000 0 0
HDAC2 0.017 0.007 -9999 0 -10000 0 0
ATM 0 0 -9999 0 -10000 0 0
SMAD3 0.028 0.04 -9999 0 -0.47 1 1
ABL1 0.017 0 -9999 0 -10000 0 0
MXD1 -0.014 0.14 -9999 0 -0.64 7 7
MRE11A 0.017 0 -9999 0 -10000 0 0
HUS1 0.017 0 -9999 0 -10000 0 0
RPS6KB1 0.012 0.061 -9999 0 -0.74 1 1
TERT/NF kappa B1/14-3-3 -0.072 0.11 -9999 0 -10000 0 0
NR2F2 0.01 0.01 -9999 0 -10000 0 0
MAPK3 0.024 0.057 -9999 0 -0.47 2 2
MAPK1 0.03 0.01 -9999 0 -10000 0 0
TGFB1/TGF beta receptor Type II 0.017 0.001 -9999 0 -10000 0 0
NFKB1 0.017 0 -9999 0 -10000 0 0
HNRNPC 0.017 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis 0 0 -9999 0 -10000 0 0
NBN 0.017 0 -9999 0 -10000 0 0
EGFR -0.001 0.11 -9999 0 -0.67 4 4
mol:Oestrogen 0 0.002 -9999 0 -10000 0 0
EGF/EGFR -0.17 0.24 -9999 0 -0.51 52 52
MYC -0.41 0.37 -9999 0 -0.74 87 87
IL2 0.018 0.008 -9999 0 -10000 0 0
KU 0 0 -9999 0 -10000 0 0
RAD50 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0.061 -9999 0 -0.74 1 1
TGFB1 0.017 0.001 -9999 0 -10000 0 0
TRF2/BLM -0.01 0.072 -9999 0 -0.52 3 3
FRAP1 0.017 0 -9999 0 -10000 0 0
KU/TERT -0.091 0.13 -9999 0 -0.59 1 1
SP1/HDAC2 0.028 0.013 -9999 0 -10000 0 0
PINX1 0.012 0.061 -9999 0 -0.74 1 1
Telomerase/EST1A -0.16 0.19 -9999 0 -0.66 8 8
Smad3/Myc -0.27 0.24 -9999 0 -0.48 87 87
911 complex -0.018 0.091 -9999 0 -0.47 6 6
IFNG -0.16 0.32 -9999 0 -0.72 37 37
Telomerase/PinX1 -0.16 0.19 -9999 0 -0.66 8 8
Telomerase/AKT1/mTOR/p70S6K -0.029 0.12 -9999 0 -10000 0 0
SIN3B 0.017 0.001 -9999 0 -10000 0 0
YWHAE 0.012 0.061 -9999 0 -0.74 1 1
Telomerase/EST1B -0.16 0.19 -9999 0 -0.66 8 8
response to DNA damage stimulus 0.005 0 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0 -9999 0 -10000 0 0
TRF2/WRN 0 0 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.16 0.19 -9999 0 -0.66 8 8
E2F1 -0.047 0.21 -9999 0 -0.74 13 13
ZNFX1 0.017 0.001 -9999 0 -10000 0 0
PIF1 0.012 0.061 -9999 0 -0.74 1 1
NCL 0.017 0 -9999 0 -10000 0 0
DKC1 -0.16 0.32 -9999 0 -0.74 35 35
telomeric DNA binding 0 0 -9999 0 -10000 0 0
Aurora B signaling

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
Condensin I complex 0.016 0.085 -9999 0 -0.43 3 3
STMN1 0.025 0.068 -9999 0 -0.57 2 2
Aurora B/RasGAP/Survivin -0.048 0.17 -9999 0 -0.46 21 21
Chromosomal passenger complex/Cul3 protein complex -0.068 0.16 -9999 0 -0.48 10 10
BIRC5 -0.085 0.26 -9999 0 -0.74 20 20
DES -0.026 0.14 -9999 0 -0.66 6 6
Aurora C/Aurora B/INCENP 0.011 0.054 -9999 0 -0.43 2 2
Aurora B/TACC1 0.013 0.015 -9999 0 -10000 0 0
Aurora B/PP2A 0.015 0.016 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.018 0.036 -9999 0 -0.23 3 3
mitotic metaphase/anaphase transition 0.002 0.005 -9999 0 -10000 0 0
NDC80 0.029 0.048 -9999 0 -0.56 1 1
Cul3 protein complex -0.13 0.19 -9999 0 -0.41 50 50
KIF2C -0.048 0.086 -9999 0 -0.28 14 14
PEBP1 0.012 0.008 -9999 0 -10000 0 0
KIF20A -0.056 0.22 -9999 0 -0.74 15 15
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.011 0.049 -9999 0 -0.56 1 1
SEPT1 0.017 0 -9999 0 -10000 0 0
SMC2 -0.028 0.18 -9999 0 -0.74 9 9
SMC4 0.017 0 -9999 0 -10000 0 0
NSUN2/NPM1/Nucleolin 0.023 0.045 -9999 0 -10000 0 0
PSMA3 0.017 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.001 0.006 -9999 0 -10000 0 0
H3F3B 0.025 0.003 -9999 0 -10000 0 0
AURKB 0.02 0.008 -9999 0 -10000 0 0
AURKC 0.017 0 -9999 0 -10000 0 0
CDCA8 0.008 0.062 -9999 0 -0.75 1 1
cytokinesis -0.093 0.18 -9999 0 -0.58 12 12
Aurora B/Septin1 -0.078 0.16 -9999 0 -0.54 11 11
AURKA -0.084 0.25 -9999 0 -0.74 20 20
INCENP 0.003 0.087 -9999 0 -0.75 2 2
KLHL13 -0.2 0.32 -9999 0 -0.66 50 50
BUB1 -0.23 0.35 -9999 0 -0.74 49 49
hSgo1/Aurora B/Survivin -0.053 0.18 -9999 0 -0.47 22 22
EVI5 0.016 0.002 -9999 0 -10000 0 0
RhoA/GTP -0.12 0.22 -9999 0 -0.63 20 20
SGOL1 -0.003 0.12 -9999 0 -0.74 4 4
CENPA -0.059 0.14 -9999 0 -0.35 20 20
NCAPG 0 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.015 0.016 -9999 0 -10000 0 0
NCAPD2 0.017 0 -9999 0 -10000 0 0
Aurora B/PP1-gamma 0.015 0.016 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
NCAPH -0.018 0.16 -9999 0 -0.74 7 7
NPM1 0.004 0.015 -9999 0 -10000 0 0
RASA1 0.012 0.061 -9999 0 -0.74 1 1
KLHL9 0.017 0 -9999 0 -10000 0 0
mitotic prometaphase -0.003 0.005 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.015 0.016 -9999 0 -10000 0 0
PPP1CC 0.017 0 -9999 0 -10000 0 0
Centraspindlin -0.14 0.25 -9999 0 -0.62 27 27
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 0.004 0.015 -9999 0 -10000 0 0
MYLK -0.009 0.11 -9999 0 -0.37 13 13
KIF23 -0.094 0.27 -9999 0 -0.74 22 22
VIM 0.026 0.058 -9999 0 -0.47 2 2
RACGAP1 -0.016 0.15 -9999 0 -0.75 6 6
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.004 0.015 -9999 0 -10000 0 0
Chromosomal passenger complex -0.058 0.15 -9999 0 -0.4 17 17
Chromosomal passenger complex/EVI5 -0.039 0.16 -9999 0 -0.81 1 1
TACC1 0.017 0 -9999 0 -10000 0 0
PPP2R5D 0.017 0 -9999 0 -10000 0 0
CUL3 0.017 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
a4b1 and a4b7 Integrin signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.012 0.061 -9999 0 -0.74 1 1
ITGB7 -0.022 0.16 -9999 0 -0.64 9 9
ITGA4 0.008 0.075 -9999 0 -0.64 2 2
alpha4/beta7 Integrin -0.033 0.13 -9999 0 -0.51 10 10
alpha4/beta1 Integrin -0.01 0.069 -9999 0 -0.5 3 3
Cellular roles of Anthrax toxin

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
ANTXR1 -0.028 0.18 -10000 0 -0.74 9 9
ANTXR2 0.012 0.053 -10000 0 -0.64 1 1
negative regulation of myeloid dendritic cell antigen processing and presentation -0.006 0.022 -10000 0 -0.088 10 10
monocyte activation 0.008 0.071 -10000 0 -0.42 4 4
MAP2K2 -0.002 0.008 -10000 0 -10000 0 0
MAP2K1 -0.005 0.017 -10000 0 -10000 0 0
MAP2K7 -0.005 0.017 -10000 0 -10000 0 0
MAP2K6 -0.03 0.094 -10000 0 -0.36 11 11
CYAA -0.007 0.11 -10000 0 -0.41 10 10
MAP2K4 -0.009 0.043 -10000 0 -0.35 2 2
IL1B -0.12 0.21 -10000 0 -0.42 49 49
Channel -0.028 0.11 -10000 0 -0.44 10 10
NLRP1 -0.007 0.038 -10000 0 -0.43 1 1
CALM1 0.017 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.007 0.025 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.006 0.022 0.088 10 -10000 0 10
MAPK3 -0.009 0.043 -10000 0 -0.35 2 2
MAPK1 -0.005 0.017 -10000 0 -10000 0 0
PGR -0.005 0.017 -10000 0 -10000 0 0
PA/Cellular Receptors -0.031 0.12 -10000 0 -0.47 10 10
apoptosis -0.006 0.022 -10000 0 -0.088 10 10
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) -0.026 0.097 -10000 0 -0.39 10 10
macrophage activation 0.018 0.045 -10000 0 -0.33 2 2
TNF 0.017 0 -10000 0 -10000 0 0
VCAM1 -0.012 0.067 -10000 0 -0.42 4 4
platelet activation -0.007 0.025 -10000 0 -10000 0 0
MAPKKK cascade -0.01 0.034 0.16 1 -10000 0 1
IL18 -0.022 0.11 -10000 0 -0.36 15 15
negative regulation of macrophage activation -0.006 0.022 -10000 0 -0.088 10 10
LEF -0.006 0.022 -10000 0 -0.089 10 10
CASP1 -0.01 0.027 -10000 0 -0.2 1 1
mol:cAMP -0.007 0.025 -10000 0 -10000 0 0
necrosis -0.006 0.022 -10000 0 -0.088 10 10
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.027 0.1 -10000 0 -0.41 10 10
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB 0.017 0 -10000 0 -10000 0 0
Jak2/Leptin Receptor -0.047 0.065 -10000 0 -10000 0 0
PTP1B/AKT1 -0.1 0.064 -10000 0 -0.35 1 1
FYN 0.012 0.061 -10000 0 -0.74 1 1
p210 bcr-abl/PTP1B -0.13 0.071 -10000 0 -0.36 2 2
EGFR -0.009 0.11 -10000 0 -0.68 4 4
EGF/EGFR -0.21 0.19 -10000 0 -0.47 50 50
CSF1 0.017 0 -10000 0 -10000 0 0
AKT1 0.016 0.002 -10000 0 -10000 0 0
INSR 0.004 0.091 -10000 0 -0.64 3 3
PTP1B/N-cadherin -0.12 0.089 -10000 0 -0.44 5 5
Insulin Receptor/Insulin -0.065 0.067 -10000 0 -0.44 3 3
HCK -0.043 0.19 -10000 0 -0.64 14 14
CRK 0.012 0.053 -10000 0 -0.64 1 1
TYK2 -0.11 0.068 -10000 0 -0.34 1 1
EGF -0.21 0.33 -10000 0 -0.69 49 49
YES1 0.017 0 -10000 0 -10000 0 0
CAV1 -0.12 0.1 -10000 0 -0.42 3 3
TXN 0.009 0.007 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.11 0.082 -10000 0 -0.52 3 3
cell migration 0.13 0.071 0.36 2 -10000 0 2
STAT3 0.016 0.001 -10000 0 -10000 0 0
PRLR 0.009 0.1 -10000 0 -0.73 3 3
ITGA2B 0.015 0.001 -10000 0 -10000 0 0
CSF1R 0.017 0 -10000 0 -10000 0 0
Prolactin Receptor/Prolactin 0.025 0.093 -10000 0 -0.54 4 4
FGR 0.017 0 -10000 0 -10000 0 0
PTP1B/p130 Cas -0.11 0.068 -10000 0 -10000 0 0
Crk/p130 Cas -0.1 0.066 -10000 0 -0.5 1 1
DOK1 -0.085 0.066 -10000 0 -0.38 1 1
JAK2 -0.057 0.065 -10000 0 -0.35 2 2
Jak2/Leptin Receptor/Leptin -0.098 0.16 -10000 0 -0.59 12 12
PIK3R1 0.017 0 -10000 0 -10000 0 0
PTPN1 -0.13 0.071 -10000 0 -0.36 2 2
LYN 0.017 0 -10000 0 -10000 0 0
CDH2 -0.007 0.13 -10000 0 -0.7 5 5
SRC -0.031 0.028 -10000 0 -10000 0 0
ITGB3 0.015 0.001 -10000 0 -10000 0 0
CAT1/PTP1B -0.11 0.098 -10000 0 -0.4 1 1
CAPN1 0.01 0.007 -10000 0 -10000 0 0
CSK 0.017 0 -10000 0 -10000 0 0
PI3K -0.042 0.063 -10000 0 -0.47 1 1
mol:H2O2 0.001 0.007 -10000 0 -10000 0 0
STAT3 (dimer) -0.09 0.16 -10000 0 -0.58 12 12
negative regulation of transcription -0.057 0.064 -10000 0 -0.34 2 2
FCGR2A -0.038 0.2 -10000 0 -0.74 11 11
FER -0.015 0.13 -10000 0 -0.74 5 5
alphaIIb/beta3 Integrin 0 0 -10000 0 -10000 0 0
BLK -0.082 0.24 -10000 0 -0.64 23 23
Insulin Receptor/Insulin/Shc -0.008 0.054 -10000 0 -0.39 3 3
RHOA 0.01 0.007 -10000 0 -10000 0 0
LEPR 0.017 0.003 -10000 0 -10000 0 0
BCAR1 0.017 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.017 0 -10000 0 -10000 0 0
mol:NADPH -0.004 0.003 -10000 0 -10000 0 0
TRPV6 -0.022 0.13 -10000 0 -0.45 3 3
PRL 0.018 0.061 -10000 0 -0.73 1 1
SOCS3 -0.015 0.16 -10000 0 -0.58 12 12
SPRY2 0.004 0.1 -10000 0 -0.71 3 3
Insulin Receptor/Insulin/IRS1 -0.017 0.084 -10000 0 -0.43 6 6
CSF1/CSF1R -0.098 0.058 -10000 0 -10000 0 0
Ras protein signal transduction 0.063 0.021 -10000 0 -10000 0 0
IRS1 0.002 0.1 -10000 0 -0.74 3 3
INS 0.016 0.002 -10000 0 -10000 0 0
LEP 0.008 0.075 -10000 0 -0.64 2 2
STAT5B -0.093 0.065 -10000 0 -0.28 3 3
STAT5A -0.093 0.065 -10000 0 -0.28 3 3
GRB2 0.017 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.11 0.068 -10000 0 -0.34 1 1
CSN2 0.065 0.032 -10000 0 -10000 0 0
PIK3CA 0.017 0 -10000 0 -10000 0 0
LAT -0.051 0.074 -10000 0 -0.3 6 6
YBX1 0.025 0.002 -10000 0 -10000 0 0
LCK 0.012 0.061 -10000 0 -0.74 1 1
SHC1 0.017 0 -10000 0 -10000 0 0
NOX4 -0.66 0.24 -10000 0 -0.74 136 136
Ceramide signaling pathway

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
SPHK2 0.019 0.079 -10000 0 -0.47 4 4
MAP4K4 0.04 0.11 -10000 0 -0.6 2 2
BAG4 0.017 0 -10000 0 -10000 0 0
PKC zeta/ceramide -0.046 0.057 0.16 3 -10000 0 3
NFKBIA 0.017 0 -10000 0 -10000 0 0
BIRC3 -0.019 0.15 -10000 0 -0.66 8 8
BAX -0.014 0.034 -10000 0 -0.24 1 1
RIPK1 0.017 0 -10000 0 -10000 0 0
AKT1 0.036 0.012 -10000 0 -10000 0 0
BAD -0.034 0.059 0.21 1 -10000 0 1
SMPD1 -0.03 0.13 -10000 0 -0.28 34 34
RB1 -0.034 0.059 0.21 1 -10000 0 1
FADD/Caspase 8 0.068 0.053 -10000 0 -10000 0 0
MAP2K4 -0.026 0.067 -10000 0 -0.36 2 2
NSMAF 0.017 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.022 0.056 -10000 0 -10000 0 0
EGF -0.21 0.33 -10000 0 -0.68 49 49
mol:ceramide -0.049 0.063 0.19 3 -0.15 12 15
MADD 0.017 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.022 0.069 -10000 0 -0.47 3 3
ASAH1 0.017 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.034 0.058 0.2 1 -10000 0 1
cell proliferation -0.17 0.14 -10000 0 -0.36 11 11
BID 0.02 0.072 -10000 0 -0.37 1 1
MAP3K1 -0.034 0.059 0.21 1 -10000 0 1
EIF2A -0.056 0.14 -10000 0 -0.43 17 17
TRADD 0.017 0 -10000 0 -10000 0 0
CRADD 0.012 0.053 -10000 0 -0.64 1 1
MAPK3 -0.006 0.054 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 -0.005 0.053 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.042 0.075 -10000 0 -0.38 3 3
FADD 0.054 0.056 -10000 0 -10000 0 0
KSR1 -0.034 0.059 -10000 0 -10000 0 0
MAPK8 -0.024 0.059 0.2 1 -0.23 1 2
PRKRA -0.034 0.059 0.21 1 -10000 0 1
PDGFA 0.004 0.091 -10000 0 -0.64 3 3
TRAF2 0.017 0 -10000 0 -10000 0 0
IGF1 -0.36 0.32 -10000 0 -0.64 88 88
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.048 0.062 0.19 3 -0.15 8 11
CTSD 0.004 0.091 -10000 0 -0.64 3 3
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 -0.18 0.15 -10000 0 -0.38 11 11
PRKCD 0.017 0 -10000 0 -10000 0 0
PRKCZ 0 0 -10000 0 -10000 0 0
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.022 0.069 -10000 0 -0.47 3 3
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.017 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.046 0.059 -10000 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0 0 -10000 0 -10000 0 0
mol:Sphingosine-1-phosphate 0.019 0.079 -10000 0 -0.46 4 4
MAP2K1 -0.01 0.053 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
CYCS 0.077 0.094 0.29 1 -10000 0 1
TNFRSF1A 0.017 0 -10000 0 -10000 0 0
NFKB1 0.017 0 -10000 0 -10000 0 0
TNFR1A/BAG4 0 0 -10000 0 -10000 0 0
EIF2AK2 -0.03 0.085 -10000 0 -0.49 3 3
TNF-alpha/TNFR1A/FAN 0 0 -10000 0 -10000 0 0
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 -0.005 0.021 -10000 0 -10000 0 0
MAP2K2 -0.01 0.053 -10000 0 -10000 0 0
SMPD3 0.027 0.081 -10000 0 -0.35 6 6
TNF 0.017 0 -10000 0 -10000 0 0
PKC zeta/PAR4 0 0 -10000 0 -10000 0 0
mol:PHOSPHOCHOLINE 0.067 0.12 0.23 51 -10000 0 51
NF kappa B1/RelA/I kappa B alpha 0 0 -10000 0 -10000 0 0
AIFM1 0.078 0.096 0.3 2 -10000 0 2
BCL2 -0.37 0.32 -10000 0 -0.64 91 91
RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1 -0.003 0.043 -9999 0 -10000 0 0
VDR -0.009 0.13 -9999 0 -0.64 6 6
FAM120B 0.017 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.086 0.031 -9999 0 -10000 0 0
RXRs/LXRs/DNA/Oxysterols 0.097 0.036 -9999 0 -10000 0 0
MED1 0.002 0.1 -9999 0 -0.74 3 3
mol:9cRA 0.01 0.004 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 0.024 0.086 -9999 0 -10000 0 0
RXRs/NUR77 0.062 0.039 -9999 0 -10000 0 0
RXRs/PPAR 0.047 0.072 -9999 0 -10000 0 0
NCOR2 0.017 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.019 0.093 -9999 0 -0.48 6 6
RARs/VDR/DNA/Vit D3 -0.021 0.083 -9999 0 -10000 0 0
RARA 0.012 0.061 -9999 0 -0.74 1 1
NCOA1 0.008 0.075 -9999 0 -0.64 2 2
VDR/VDR/DNA -0.009 0.13 -9999 0 -0.64 6 6
RARs/RARs/DNA/9cRA -0.008 0.056 -9999 0 -0.4 3 3
RARG 0.007 0.086 -9999 0 -0.74 2 2
RPS6KB1 -0.004 0.058 -9999 0 -0.71 1 1
RARs/THRs/DNA/SMRT 0.028 0.08 -9999 0 -10000 0 0
THRA 0.017 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.019 0.093 -9999 0 -0.48 6 6
RXRs/PPAR/9cRA/PGJ2/DNA 0.062 0.01 -9999 0 -10000 0 0
NR1H4 -0.52 0.25 -9999 0 -0.64 126 126
RXRs/LXRs/DNA 0.09 0.033 -9999 0 -10000 0 0
NR1H2 0.027 0.002 -9999 0 -10000 0 0
NR1H3 0.023 0.053 -9999 0 -0.63 1 1
RXRs/VDR/DNA/Vit D3 0.046 0.072 -9999 0 -10000 0 0
NR4A1 0.012 0.061 -9999 0 -0.74 1 1
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 -0.2 0.12 -9999 0 -0.41 3 3
RXRG 0.026 0.002 -9999 0 -10000 0 0
RXR alpha/CCPG 0 0 -9999 0 -10000 0 0
RXRA 0.026 0.002 -9999 0 -10000 0 0
RXRB 0.027 0.002 -9999 0 -10000 0 0
THRB -0.022 0.16 -9999 0 -0.64 9 9
PPARG -0.018 0.15 -9999 0 -0.64 8 8
PPARD 0.017 0 -9999 0 -10000 0 0
TNF 0.1 0.033 -9999 0 -10000 0 0
mol:Oxysterols 0.01 0.004 -9999 0 -10000 0 0
cholesterol transport 0.097 0.035 -9999 0 -10000 0 0
PPARA 0.012 0.053 -9999 0 -0.64 1 1
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB 0.017 0 -9999 0 -10000 0 0
RXRs/NUR77/BCL2 -0.15 0.12 -9999 0 -10000 0 0
SREBF1 0.1 0.054 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.063 0.01 -9999 0 -10000 0 0
ABCA1 0.1 0.033 -9999 0 -10000 0 0
RARs/THRs -0.026 0.09 -9999 0 -10000 0 0
RXRs/FXR -0.26 0.15 -9999 0 -0.4 1 1
BCL2 -0.37 0.32 -9999 0 -0.64 91 91
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.041 0.12 -10000 0 -0.54 6 6
FYN -0.016 0.19 -10000 0 -0.65 8 8
LAT/GRAP2/SLP76 -0.044 0.13 -10000 0 -0.58 6 6
IKBKB 0.012 0.061 -10000 0 -0.74 1 1
AKT1 0.022 0.14 -10000 0 -0.45 8 8
B2M -0.013 0.14 -10000 0 -0.64 7 7
IKBKG -0.018 0.039 -10000 0 -0.18 1 1
MAP3K8 -0.067 0.24 -10000 0 -0.74 17 17
mol:Ca2+ -0.005 0.025 -10000 0 -0.15 4 4
integrin-mediated signaling pathway 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA 0.006 0.2 -10000 0 -0.68 8 8
TRPV6 -0.016 0.12 -10000 0 -0.76 4 4
CD28 -0.06 0.21 -10000 0 -0.64 18 18
SHC1 0.008 0.18 -10000 0 -0.67 7 7
receptor internalization -0.007 0.2 -10000 0 -0.71 8 8
PRF1 0.015 0.17 -10000 0 -0.66 7 7
KRAS 0.017 0 -10000 0 -10000 0 0
GRB2 0.017 0 -10000 0 -10000 0 0
COT/AKT1 -0.006 0.16 -10000 0 -0.4 10 10
LAT 0.003 0.19 -10000 0 -0.67 7 7
EntrezGene:6955 0.001 0.003 -10000 0 -10000 0 0
CD3D -0.008 0.13 -10000 0 -0.65 6 6
CD3E 0.017 0.005 -10000 0 -10000 0 0
CD3G -0.013 0.14 -10000 0 -0.66 7 7
RASGRP2 0.009 0.034 -10000 0 -0.19 3 3
RASGRP1 0.024 0.15 -10000 0 -0.45 7 7
HLA-A 0 0.11 -10000 0 -0.65 4 4
RASSF5 0.017 0 -10000 0 -10000 0 0
RAP1A/GTP/RAPL 0 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.034 0.055 -10000 0 -0.14 1 1
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.034 0.071 -10000 0 -0.27 6 6
PRKCA -0.04 0.082 -10000 0 -0.3 6 6
GRAP2 0.017 0 -10000 0 -10000 0 0
mol:IP3 -0.059 0.14 0.25 2 -0.47 8 10
EntrezGene:6957 0.001 0.004 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 0.004 0.18 -10000 0 -0.7 7 7
ORAI1 0.014 0.06 0.38 4 -10000 0 4
CSK -0.003 0.19 -10000 0 -0.68 7 7
B7 family/CD28 -0.096 0.22 -10000 0 -0.66 16 16
CHUK 0.017 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.012 0.21 -10000 0 -0.8 7 7
PTPN6 0.004 0.19 -10000 0 -0.74 6 6
VAV1 -0.012 0.22 -10000 0 -0.81 8 8
Monovalent TCR/CD3 -0.009 0.18 -10000 0 -0.75 7 7
CBL 0.017 0 -10000 0 -10000 0 0
LCK -0.012 0.19 -10000 0 -0.69 7 7
PAG1 -0.081 0.24 -10000 0 -0.61 15 15
RAP1A 0.017 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.015 0.21 -10000 0 -0.81 7 7
CD80 -0.003 0.12 -10000 0 -0.74 4 4
CD86 -0.013 0.14 -10000 0 -0.64 7 7
PDK1/CARD11/BCL10/MALT1 -0.042 0.087 -10000 0 -0.31 8 8
HRAS 0.017 0 -10000 0 -10000 0 0
GO:0035030 -0.018 0.21 -10000 0 -0.55 15 15
CD8A 0.001 0.004 -10000 0 -10000 0 0
CD8B 0.017 0.005 -10000 0 -10000 0 0
PTPRC 0 0.11 -10000 0 -0.64 4 4
PDK1/PKC theta 0.023 0.18 -10000 0 -0.56 8 8
CSK/PAG1 -0.072 0.23 -10000 0 -0.6 13 13
SOS1 0.017 0 -10000 0 -10000 0 0
peptide-MHC class I -0.032 0.14 -10000 0 -0.62 8 8
GRAP2/SLP76 -0.048 0.16 -10000 0 -0.7 6 6
STIM1 0.008 0.032 -10000 0 -10000 0 0
RAS family/GTP 0.043 0.07 -10000 0 -0.25 1 1
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.01 0.21 -10000 0 -0.77 8 8
mol:DAG -0.058 0.12 -10000 0 -0.39 11 11
RAP1A/GDP 0.017 0.024 -10000 0 -10000 0 0
PLCG1 -0.048 0.21 -10000 0 -0.74 13 13
CD247 -0.012 0.14 -10000 0 -0.64 7 7
cytotoxic T cell degranulation 0.016 0.17 -10000 0 -0.61 8 8
RAP1A/GTP -0.002 0.009 -10000 0 -0.068 2 2
mol:PI-3-4-5-P3 0.014 0.17 -10000 0 -0.55 8 8
LAT/GRAP2/SLP76/VAV1/PLCgamma1 -0.075 0.18 0.3 1 -0.6 9 10
NRAS 0.007 0.086 -10000 0 -0.74 2 2
ZAP70 0.017 0.001 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.056 0.15 -10000 0 -0.6 8 8
MALT1 0.017 0 -10000 0 -10000 0 0
TRAF6 0.017 0 -10000 0 -10000 0 0
CD8 heterodimer 0.01 0.009 -10000 0 -10000 0 0
CARD11 -0.057 0.22 -10000 0 -0.74 15 15
PRKCB -0.042 0.084 -10000 0 -0.28 10 10
PRKCE -0.04 0.082 -10000 0 -0.3 6 6
PRKCQ 0.009 0.2 -10000 0 -0.65 8 8
LCP2 0.003 0.1 -10000 0 -0.71 3 3
BCL10 0.017 0 -10000 0 -10000 0 0
regulation of survival gene product expression 0.025 0.13 -10000 0 -0.38 8 8
IKK complex 0.037 0.059 -10000 0 -10000 0 0
RAS family/GDP -0.003 0.011 -10000 0 -0.085 2 2
MAP3K14 0.009 0.12 -10000 0 -0.3 8 8
PDPK1 0.026 0.14 -10000 0 -0.44 7 7
TCR/CD3/MHC I/CD8/Fyn -0.012 0.2 -10000 0 -0.8 7 7
Syndecan-4-mediated signaling events

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
PTK2 -0.024 0.15 -9999 0 -0.4 2 2
Syndecan-4/Syndesmos 0.011 0.13 -9999 0 -10000 0 0
positive regulation of JNK cascade -0.24 0.16 -9999 0 -0.6 12 12
Syndecan-4/ADAM12 -0.16 0.26 -9999 0 -0.62 22 22
CCL5 -0.11 0.26 -9999 0 -0.64 30 30
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.017 0 -9999 0 -10000 0 0
ITGA5 0.002 0.1 -9999 0 -0.74 3 3
SDCBP 0.017 0 -9999 0 -10000 0 0
PLG 0.012 0.006 -9999 0 -10000 0 0
ADAM12 -0.3 0.37 -9999 0 -0.74 65 65
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.017 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.023 0.047 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 0.011 0.13 -9999 0 -10000 0 0
Syndecan-4/CXCL12/CXCR4 -0.26 0.16 -9999 0 -0.64 12 12
Syndecan-4/Laminin alpha3 0.001 0.14 -9999 0 -0.58 1 1
MDK -0.023 0.17 -9999 0 -0.74 8 8
Syndecan-4/FZD7 -0.005 0.14 -9999 0 -10000 0 0
Syndecan-4/Midkine -0.01 0.16 -9999 0 -0.62 2 2
FZD7 -0.013 0.15 -9999 0 -0.74 6 6
Syndecan-4/FGFR1/FGF -0.043 0.092 -9999 0 -10000 0 0
THBS1 0.017 0 -9999 0 -10000 0 0
integrin-mediated signaling pathway 0.002 0.16 -9999 0 -0.66 4 4
positive regulation of MAPKKK cascade -0.24 0.16 -9999 0 -0.6 12 12
Syndecan-4/TACI 0.007 0.14 -9999 0 -0.58 1 1
CXCR4 -0.028 0.18 -9999 0 -0.74 9 9
cell adhesion -0.048 0.11 -9999 0 -0.42 2 2
Syndecan-4/Dynamin 0.011 0.13 -9999 0 -10000 0 0
Syndecan-4/TSP1 0.011 0.13 -9999 0 -10000 0 0
Syndecan-4/GIPC 0.009 0.13 -9999 0 -0.52 1 1
Syndecan-4/RANTES -0.055 0.19 -9999 0 -0.56 9 9
ITGB1 0.012 0.061 -9999 0 -0.74 1 1
LAMA1 0.017 0 -9999 0 -10000 0 0
LAMA3 -0.002 0.11 -9999 0 -0.69 4 4
RAC1 0.017 0 -9999 0 -10000 0 0
PRKCA 0.019 0.039 -9999 0 -10000 0 0
Syndecan-4/alpha-Actinin 0.011 0.13 -9999 0 -10000 0 0
TFPI 0.012 0.061 -9999 0 -0.74 1 1
F2 0.019 0.005 -9999 0 -10000 0 0
alpha5/beta1 Integrin -0.014 0.088 -9999 0 -0.55 4 4
positive regulation of cell adhesion 0.013 0.14 -9999 0 -0.56 1 1
ACTN1 0.017 0 -9999 0 -10000 0 0
TNC -0.003 0.12 -9999 0 -0.74 4 4
Syndecan-4/CXCL12 -0.24 0.17 -9999 0 -0.55 15 15
FGF6 0.017 0 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
CXCL12 -0.46 0.29 -9999 0 -0.64 112 112
TNFRSF13B 0.008 0.075 -9999 0 -0.64 2 2
FGF2 0.008 0.08 -9999 0 -0.69 2 2
FGFR1 0.017 0 -9999 0 -10000 0 0
Syndecan-4/PI-4-5-P2 0 0.13 -9999 0 -0.5 3 3
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.12 0.29 -9999 0 -0.75 26 26
cell migration -0.009 0.019 -9999 0 -10000 0 0
PRKCD 0.012 0.006 -9999 0 -10000 0 0
vasculogenesis 0.011 0.12 -9999 0 -10000 0 0
SDC4 0.001 0.13 -9999 0 -0.53 3 3
Syndecan-4/Tenascin C 0.001 0.16 -9999 0 -0.69 4 4
Syndecan-4/PI-4-5-P2/PKC alpha -0.018 0.037 -9999 0 -10000 0 0
Syndecan-4/Syntenin 0.011 0.13 -9999 0 -10000 0 0
MMP9 -0.009 0.14 -9999 0 -0.72 6 6
Rac1/GTP -0.05 0.11 -9999 0 -0.44 2 2
cytoskeleton organization 0.011 0.12 -9999 0 -10000 0 0
GIPC1 0.012 0.053 -9999 0 -0.64 1 1
Syndecan-4/TFPI 0.008 0.14 -9999 0 -0.58 1 1
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 -0.039 0.15 -9999 0 -0.59 10 10
VEGFR1 homodimer/NRP1 -0.039 0.15 -9999 0 -0.6 10 10
mol:DAG -0.037 0.22 -9999 0 -0.61 10 10
VEGFR1 homodimer/NRP1/VEGFR 121 -0.086 0.22 -9999 0 -0.55 24 24
CaM/Ca2+ -0.026 0.2 -9999 0 -0.87 3 3
HIF1A 0.002 0.11 -9999 0 -1 1 1
GAB1 0.012 0.053 -9999 0 -0.64 1 1
AKT1 0.037 0.15 -9999 0 -0.76 2 2
PLCG1 -0.038 0.22 -9999 0 -0.62 10 10
NOS3 0.025 0.16 -9999 0 -0.68 3 3
CBL 0.017 0 -9999 0 -10000 0 0
mol:NO 0.026 0.15 -9999 0 -0.64 3 3
FLT1 -0.005 0.18 -9999 0 -0.69 10 10
PGF -0.008 0.14 -9999 0 -0.74 5 5
VEGFR1 homodimer/NRP2/VEGFR121 -0.086 0.23 -9999 0 -0.74 10 10
CALM1 0.017 0 -9999 0 -10000 0 0
PIK3CA 0.017 0 -9999 0 -10000 0 0
eNOS/Hsp90 0.032 0.15 -9999 0 -0.61 3 3
endothelial cell proliferation -0.01 0.18 -9999 0 -0.79 3 3
mol:Ca2+ -0.036 0.21 -9999 0 -0.61 10 10
MAPK3 -0.015 0.2 -9999 0 -0.78 4 4
MAPK1 -0.01 0.19 -9999 0 -0.79 3 3
PIK3R1 0.017 0 -9999 0 -10000 0 0
PLGF homodimer -0.008 0.13 -9999 0 -0.74 5 5
PRKACA 0.017 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 0.002 0.1 -9999 0 -0.74 3 3
VEGFA homodimer -0.072 0.24 -9999 0 -0.74 18 18
VEGFR1 homodimer/VEGFA homodimer -0.092 0.24 -9999 0 -0.59 24 24
platelet activating factor biosynthetic process -0.004 0.19 -9999 0 -0.75 4 4
PI3K -0.045 0.15 -9999 0 -0.89 2 2
PRKCA -0.022 0.2 -9999 0 -0.84 3 3
PRKCB -0.034 0.2 -9999 0 -0.57 10 10
VEGFR1 homodimer/PLGF homodimer -0.054 0.18 -9999 0 -0.59 14 14
VEGFA -0.072 0.24 -9999 0 -0.74 18 18
VEGFB 0.017 0 -9999 0 -10000 0 0
mol:IP3 -0.037 0.22 -9999 0 -0.61 10 10
RASA1 0.014 0.16 -9999 0 -0.98 1 1
NRP2 0.012 0.061 -9999 0 -0.74 1 1
VEGFR1 homodimer -0.005 0.18 -9999 0 -0.68 10 10
VEGFB homodimer 0.017 0 -9999 0 -10000 0 0
NCK1 0.017 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.026 0.16 -9999 0 -0.61 3 3
PTPN11 0.012 0.061 -9999 0 -0.74 1 1
mol:PI-3-4-5-P3 -0.045 0.15 -9999 0 -0.87 2 2
mol:L-citrulline 0.026 0.15 -9999 0 -0.64 3 3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.08 0.2 -9999 0 -0.98 4 4
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.084 0.22 -9999 0 -0.7 10 10
CD2AP 0.012 0.053 -9999 0 -0.64 1 1
PI3K/GAB1 -0.044 0.14 -9999 0 -0.84 2 2
PDPK1 0.022 0.16 -9999 0 -0.82 2 2
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.087 0.22 -9999 0 -0.7 10 10
mol:NADP 0.026 0.15 -9999 0 -0.64 3 3
HSP90AA1 0.012 0.061 -9999 0 -0.74 1 1
ubiquitin-dependent protein catabolic process -0.079 0.2 -9999 0 -0.95 4 4
VEGFR1 homodimer/NRP2 -0.041 0.17 -9999 0 -0.63 10 10
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A 0.017 0 -9999 0 -10000 0 0
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.017 0 -9999 0 -10000 0 0
TCEB1 0.017 0 -9999 0 -10000 0 0
HIF1A/p53 -0.008 0.095 -9999 0 -0.38 5 5
HIF1A -0.005 0.069 -9999 0 -0.31 2 2
COPS5 0.017 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 0 0 -9999 0 -10000 0 0
FIH (dimer) 0.017 0 -9999 0 -10000 0 0
CDKN2A -0.24 0.36 -9999 0 -0.74 52 52
ARNT/IPAS 0 0 -9999 0 -10000 0 0
HIF1AN 0.017 0 -9999 0 -10000 0 0
GNB2L1 0.017 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.006 0.066 -9999 0 -10000 0 0
CUL2 0.017 0 -9999 0 -10000 0 0
OS9 0.017 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C 0 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.003 0.072 -9999 0 -0.36 1 1
PHD1-3/OS9 -0.13 0.17 -9999 0 -10000 0 0
HIF1A/RACK1/Elongin B/Elongin C -0.018 0.036 -9999 0 -10000 0 0
VHL 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0.061 -9999 0 -0.74 1 1
HIF1A/JAB1 0.006 0.066 -9999 0 -10000 0 0
EGLN3 -0.22 0.32 -9999 0 -0.64 56 56
EGLN2 0.017 0 -9999 0 -10000 0 0
EGLN1 0.017 0 -9999 0 -10000 0 0
TP53 -0.008 0.14 -9999 0 -0.74 5 5
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.033 0.027 -9999 0 -10000 0 0
ARNT 0.017 0 -9999 0 -10000 0 0
ARD1A 0.002 0.1 -9999 0 -0.74 3 3
RBX1 0.017 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.13 0.2 -9999 0 -0.39 52 52
Regulation of Androgen receptor activity

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
HDAC1 0.032 0 -9999 0 -10000 0 0
SMARCC1 -0.002 0.094 -9999 0 -0.57 3 3
REL 0.016 0 -9999 0 -10000 0 0
HDAC7 -0.039 0.17 -9999 0 -0.49 11 11
JUN -0.007 0.14 -9999 0 -0.74 5 5
EP300 0.017 0 -9999 0 -10000 0 0
KAT2B 0 0 -9999 0 -10000 0 0
KAT5 0 0 -9999 0 -10000 0 0
MAPK14 -0.015 0.13 -9999 0 -0.49 11 11
FOXO1 -0.005 0.12 -9999 0 -0.64 5 5
T-DHT/AR -0.038 0.18 -9999 0 -0.52 11 11
MAP2K6 -0.037 0.17 -9999 0 -0.66 11 11
BRM/BAF57 -0.007 0.063 -9999 0 -0.55 2 2
MAP2K4 0.002 0.076 -9999 0 -0.66 2 2
SMARCA2 0.018 0 -9999 0 -10000 0 0
PDE9A -0.55 0.57 -9999 0 -1.1 74 74
NCOA2 0.018 0 -9999 0 -10000 0 0
CEBPA 0.017 0 -9999 0 -10000 0 0
EHMT2 0.017 0 -9999 0 -10000 0 0
cell proliferation 0.011 0.17 -9999 0 -0.47 1 1
NR0B1 0.007 0.086 -9999 0 -0.74 2 2
EGR1 -0.022 0.17 -9999 0 -0.74 8 8
RXRs/9cRA 0 0 -9999 0 -10000 0 0
AR/RACK1/Src 0.024 0.12 -9999 0 -10000 0 0
AR/GR -0.011 0.13 -9999 0 -0.4 5 5
GNB2L1 0.017 0 -9999 0 -10000 0 0
PKN1 0.017 0 -9999 0 -10000 0 0
RCHY1 0.017 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0.001 0 -9999 0 -10000 0 0
MAPK8 0.014 0.061 -9999 0 -0.49 2 2
T-DHT/AR/TIF2/CARM1 0.021 0.12 -9999 0 -10000 0 0
SRC 0.008 0.12 -9999 0 -10000 0 0
NR3C1 -0.039 0.18 -9999 0 -0.64 13 13
KLK3 -0.13 0.12 -9999 0 -10000 0 0
APPBP2 0.01 0.01 -9999 0 -10000 0 0
TRIM24 0.018 0 -9999 0 -10000 0 0
T-DHT/AR/TIP60 -0.045 0.11 -9999 0 -0.42 10 10
TMPRSS2 -0.065 0.12 -9999 0 -1.4 1 1
RXRG 0.017 0 -9999 0 -10000 0 0
mol:9cRA 0 0 -9999 0 -10000 0 0
RXRA 0.017 0 -9999 0 -10000 0 0
RXRB 0.017 0 -9999 0 -10000 0 0
CARM1 0.018 0 -9999 0 -10000 0 0
NR2C2 0.017 0 -9999 0 -10000 0 0
KLK2 0.036 0.11 -9999 0 -10000 0 0
AR 0.016 0.081 -9999 0 -10000 0 0
SENP1 0.017 0 -9999 0 -10000 0 0
HSP90AA1 0.012 0.061 -9999 0 -0.74 1 1
MDM2 0.015 0 -9999 0 -10000 0 0
SRY 0.01 0.061 -9999 0 -0.74 1 1
GATA2 0.017 0 -9999 0 -10000 0 0
MYST2 0.017 0 -9999 0 -10000 0 0
HOXB13 -0.6 0.29 -9999 0 -0.74 125 125
T-DHT/AR/RACK1/Src 0.017 0.12 -9999 0 -10000 0 0
positive regulation of transcription 0.017 0 -9999 0 -10000 0 0
DNAJA1 0.005 0.063 -9999 0 -0.76 1 1
proteasomal ubiquitin-dependent protein catabolic process 0.04 0 -9999 0 -10000 0 0
NCOA1 0.013 0.08 -9999 0 -0.67 2 2
SPDEF -0.18 0.3 -9999 0 -0.64 46 46
T-DHT/AR/TIF2 0.037 0.074 -9999 0 -10000 0 0
T-DHT/AR/Hsp90 -0.002 0.13 -9999 0 -0.45 1 1
GSK3B 0.015 0.004 -9999 0 -10000 0 0
NR2C1 -0.003 0.12 -9999 0 -0.74 4 4
mol:T-DHT 0.001 0.12 -9999 0 -0.41 10 10
SIRT1 0.017 0 -9999 0 -10000 0 0
ZMIZ2 0.015 0 -9999 0 -10000 0 0
POU2F1 0.02 0.019 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.005 0.14 -9999 0 -0.45 2 2
CREBBP 0.017 0 -9999 0 -10000 0 0
SMARCE1 0.008 0.086 -9999 0 -0.74 2 2
BARD1 signaling events

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
BARD1/CSTF1 0 0 -10000 0 -10000 0 0
ATM 0.017 0 -10000 0 -10000 0 0
UBE2D3 0.017 0 -10000 0 -10000 0 0
PRKDC -0.048 0.21 -10000 0 -0.74 13 13
ATR 0.012 0.061 -10000 0 -0.74 1 1
UBE2L3 0.017 0 -10000 0 -10000 0 0
FANCD2 0.031 0.039 -10000 0 -0.31 2 2
protein ubiquitination -0.088 0.18 -10000 0 -0.78 4 4
XRCC5 0.017 0 -10000 0 -10000 0 0
XRCC6 0.017 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.017 0 -10000 0 -10000 0 0
DNA-PK -0.04 0.13 -10000 0 -0.47 13 13
FA complex/FANCD2/Ubiquitin -0.049 0.11 -10000 0 -0.48 7 7
FANCF 0.008 0.075 -10000 0 -0.64 2 2
BRCA1 -0.008 0.14 -10000 0 -0.74 5 5
CCNE1 -0.023 0.17 -10000 0 -0.74 8 8
CDK2/Cyclin E1 -0.11 0.23 -10000 0 -0.59 28 28
FANCG -0.008 0.14 -10000 0 -0.74 5 5
BRCA1/BACH1/BARD1 -0.018 0.098 -10000 0 -0.55 5 5
FANCE 0.012 0.061 -10000 0 -0.74 1 1
FANCC 0.017 0 -10000 0 -10000 0 0
NBN 0.017 0 -10000 0 -10000 0 0
FANCA -0.18 0.33 -10000 0 -0.74 39 39
DNA repair -0.004 0.18 -10000 0 -0.62 4 4
BRCA1/BARD1/ubiquitin -0.018 0.098 -10000 0 -0.55 5 5
BARD1/DNA-PK -0.036 0.12 -10000 0 -0.42 13 13
FANCL 0.017 0 -10000 0 -10000 0 0
mRNA polyadenylation 0 0 -10000 0 -10000 0 0
BRCA1/BARD1/CTIP/M/R/N Complex 0.051 0.03 -10000 0 -10000 0 0
BRCA1/BACH1/BARD1/TopBP1 -0.015 0.084 -10000 0 -0.47 5 5
BRCA1/BARD1/P53 -0.03 0.12 -10000 0 -0.46 10 10
BARD1/CSTF1/BRCA1 -0.015 0.084 -10000 0 -0.47 5 5
BRCA1/BACH1 -0.008 0.13 -10000 0 -0.74 5 5
BARD1 0.017 0 -10000 0 -10000 0 0
PCNA -0.023 0.17 -10000 0 -0.74 8 8
BRCA1/BARD1/UbcH5C -0.015 0.084 -10000 0 -0.47 5 5
BRCA1/BARD1/UbcH7 -0.015 0.084 -10000 0 -0.47 5 5
BRCA1/BARD1/RAD51/PCNA -0.036 0.14 -10000 0 -0.5 11 11
BARD1/DNA-PK/P53 -0.046 0.12 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.018 0.098 -10000 0 -0.55 5 5
BRCA1/BARD1/CTIP -0.014 0.075 -10000 0 -0.42 5 5
FA complex -0.025 0.14 -10000 0 -0.43 8 8
BARD1/EWS 0 0 -10000 0 -10000 0 0
RBBP8 0.032 0 -10000 0 -10000 0 0
TP53 -0.008 0.14 -10000 0 -0.74 5 5
TOPBP1 0.017 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.03 0.12 0.46 10 -10000 0 10
BRCA1/BARD1 -0.089 0.19 -10000 0 -0.8 4 4
CSTF1 0.017 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 0 0 -10000 0 -10000 0 0
CDK2 -0.092 0.26 -10000 0 -0.74 22 22
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.017 0 -10000 0 -10000 0 0
RAD50 0.017 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.018 0.098 -10000 0 -0.55 5 5
EWSR1 0.017 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class III

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
EP300 0.017 0 -10000 0 -10000 0 0
HDAC4 0.017 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle -0.002 0.015 -10000 0 -10000 0 0
CDKN1A -0.007 0.095 -10000 0 -0.82 2 2
KAT2B 0 0 -10000 0 -10000 0 0
BAX 0.012 0.061 -10000 0 -0.74 1 1
FOXO3 0 0 -10000 0 -10000 0 0
FOXO1 -0.005 0.12 -10000 0 -0.64 5 5
FOXO4 0.032 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.017 0 -10000 0 -10000 0 0
TAT 0.017 0 -10000 0 -10000 0 0
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 0.012 0.047 -10000 0 -0.57 1 1
PPARGC1A -0.28 0.33 -10000 0 -0.64 69 69
FHL2 0.012 0.061 -10000 0 -0.74 1 1
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 0.002 0.018 -10000 0 -10000 0 0
HIST2H4A 0.002 0.015 -10000 0 -10000 0 0
SIRT1/FOXO3a 0.002 0.016 -10000 0 -10000 0 0
SIRT1 0.003 0.023 -10000 0 -10000 0 0
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 0.002 0.017 -10000 0 -10000 0 0
SIRT1/Histone H1b 0 0.03 -10000 0 -10000 0 0
apoptosis 0.001 0.042 0.47 1 -10000 0 1
SIRT1/PGC1A -0.18 0.2 -10000 0 -0.4 69 69
p53/SIRT1 -0.013 0.11 0.42 2 -0.56 5 7
SIRT1/FOXO4 0.002 0.019 -10000 0 -10000 0 0
FOXO1/FHL2/SIRT1 -0.013 0.087 -10000 0 -0.44 5 5
HIST1H1E 0.028 0.032 -10000 0 -10000 0 0
SIRT1/p300 0.002 0.018 -10000 0 -10000 0 0
muscle cell differentiation 0.001 0.042 0.48 1 -10000 0 1
TP53 -0.022 0.14 -10000 0 -0.74 5 5
KU70/SIRT1/BAX -0.001 0.042 -10000 0 -0.47 1 1
CREBBP 0.017 0 -10000 0 -10000 0 0
MEF2D 0.017 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 0.002 0.018 -10000 0 -10000 0 0
ACSS2 0.02 0.07 -10000 0 -0.47 3 3
SIRT1/PCAF/MYOD -0.001 0.043 -10000 0 -0.48 1 1
ceramide signaling pathway

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
MAP4K4 0.042 0.11 -10000 0 -0.61 2 2
BAG4 0.017 0 -10000 0 -10000 0 0
BAD 0.012 0.066 -10000 0 -10000 0 0
NFKBIA 0.017 0 -10000 0 -10000 0 0
BIRC3 -0.019 0.15 -10000 0 -0.66 8 8
BAX 0.009 0.077 -10000 0 -0.49 1 1
EnzymeConsortium:3.1.4.12 0.019 0.018 -10000 0 -10000 0 0
IKBKB 0.048 0.11 -10000 0 -0.56 2 2
MAP2K2 0.034 0.056 -10000 0 -10000 0 0
MAP2K1 0.034 0.056 -10000 0 -10000 0 0
SMPD1 -0.035 0.12 -10000 0 -0.26 34 34
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 0.064 0.069 -10000 0 -10000 0 0
MAP2K4 0.019 0.074 -10000 0 -0.4 1 1
protein ubiquitination 0.052 0.11 -10000 0 -0.57 2 2
EnzymeConsortium:2.7.1.37 0.042 0.056 -10000 0 -10000 0 0
response to UV 0.001 0 -10000 0 -10000 0 0
RAF1 0.025 0.06 -10000 0 -10000 0 0
CRADD 0.013 0.053 -10000 0 -0.64 1 1
mol:ceramide 0.002 0.069 -10000 0 -0.22 4 4
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.017 0 -10000 0 -10000 0 0
MAP3K1 0.013 0.065 -10000 0 -10000 0 0
TRADD 0.017 0 -10000 0 -10000 0 0
RELA/p50 0.017 0 -10000 0 -10000 0 0
MAPK3 0.037 0.057 -10000 0 -10000 0 0
MAPK1 0.038 0.055 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD 0.055 0.071 -10000 0 -10000 0 0
KSR1 0.014 0.064 -10000 0 -10000 0 0
MAPK8 0.029 0.069 -10000 0 -0.36 1 1
TRAF2 0.017 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.051 0.11 -10000 0 -0.56 2 2
TNF R/SODD 0 0 -10000 0 -10000 0 0
TNF 0.017 0 -10000 0 -10000 0 0
CYCS 0.077 0.09 -10000 0 -0.27 1 1
IKBKG 0.051 0.11 -10000 0 -0.56 2 2
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.046 0.074 -10000 0 -10000 0 0
RELA 0.017 0 -10000 0 -10000 0 0
RIPK1 0.017 0 -10000 0 -10000 0 0
AIFM1 0.078 0.09 0.16 71 -0.27 1 72
TNF/TNF R/SODD 0 0 -10000 0 -10000 0 0
TNFRSF1A 0.017 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.038 0.02 -10000 0 -10000 0 0
NSMAF 0.055 0.069 -10000 0 -10000 0 0
response to hydrogen peroxide 0.001 0 -10000 0 -10000 0 0
BCL2 -0.37 0.32 -10000 0 -0.64 91 91
Signaling mediated by p38-gamma and p38-delta

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
EEF2K 0.042 0 -9999 0 -10000 0 0
SNTA1 0.017 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.035 0.058 -9999 0 -0.47 2 2
MAPK12 -0.052 0.16 -9999 0 -0.48 6 6
CCND1 -0.045 0.11 -9999 0 -0.36 9 9
p38 gamma/SNTA1 -0.04 0.15 -9999 0 -0.72 1 1
MAP2K3 0.017 0 -9999 0 -10000 0 0
PKN1 0.017 0 -9999 0 -10000 0 0
G2/M transition checkpoint -0.052 0.16 -9999 0 -0.48 6 6
MAP2K6 -0.051 0.15 -9999 0 -0.39 11 11
MAPT 0.014 0.052 -9999 0 -10000 0 0
MAPK13 0.032 0 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK -0.039 0.13 -9999 0 -0.32 28 28
TCGA08_rtk_signaling

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
PDGFRA 0.004 0.091 -10000 0 -0.64 3 3
HRAS 0.017 0 -10000 0 -10000 0 0
EGFR -0.001 0.11 -10000 0 -0.66 4 4
AKT 0.032 0.039 -10000 0 -10000 0 0
FOXO3 0.017 0 -10000 0 -10000 0 0
AKT1 0.017 0 -10000 0 -10000 0 0
FOXO1 -0.005 0.12 -10000 0 -0.64 5 5
AKT3 0.017 0 -10000 0 -10000 0 0
FOXO4 0.017 0 -10000 0 -10000 0 0
MET -0.35 0.38 -10000 0 -0.74 74 74
PIK3CA 0.017 0 -10000 0 -10000 0 0
PIK3CB 0.017 0 -10000 0 -10000 0 0
NRAS 0.007 0.086 -10000 0 -0.74 2 2
PIK3CG -0.026 0.16 -10000 0 -0.64 10 10
PIK3R3 0.017 0 -10000 0 -10000 0 0
PIK3R2 0.017 0 -10000 0 -10000 0 0
NF1 0.017 0 -10000 0 -10000 0 0
RAS -0.051 0.086 -10000 0 -0.32 3 3
ERBB2 -0.003 0.12 -10000 0 -0.74 4 4
proliferation/survival/translation -0.007 0.062 -10000 0 -10000 0 0
PI3K 0.004 0.087 0.22 3 -0.25 11 14
PIK3R1 0.017 0 -10000 0 -10000 0 0
KRAS 0.017 0 -10000 0 -10000 0 0
FOXO 0.035 0.043 -10000 0 -10000 0 0
AKT2 0.017 0 -10000 0 -10000 0 0
PTEN -0.005 0.12 -10000 0 -0.64 5 5
E-cadherin signaling in keratinocytes

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
keratinocyte differentiation 0.039 0.084 -9999 0 -10000 0 0
adherens junction organization -0.088 0.067 -9999 0 -0.37 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
Rac1/GDP -0.034 0.097 -9999 0 -0.56 2 2
FMN1 0.029 0.063 -9999 0 -10000 0 0
mol:IP3 -0.031 0.089 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.03 0.066 -9999 0 -10000 0 0
CTNNB1 0.011 0.061 -9999 0 -0.74 1 1
AKT1 0.044 0.062 -9999 0 -10000 0 0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.039 0.09 -9999 0 -0.43 5 5
CTNND1 0.017 0.005 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.04 0.062 -9999 0 -10000 0 0
VASP 0.04 0.063 -9999 0 -10000 0 0
ZYX 0.038 0.071 -9999 0 -0.36 1 1
JUB -0.36 0.11 -9999 0 -0.38 144 144
EGFR(dimer) 0.029 0.089 -9999 0 -0.4 2 2
E-cadherin/beta catenin-gamma catenin -0.011 0.078 -9999 0 -0.39 6 6
mol:PI-3-4-5-P3 -0.017 0.045 -9999 0 -10000 0 0
PIK3CA 0.016 0.005 -9999 0 -10000 0 0
PI3K -0.017 0.045 -9999 0 -10000 0 0
FYN 0.039 0.1 -9999 0 -0.5 1 1
mol:Ca2+ -0.03 0.087 -9999 0 -10000 0 0
JUP 0.016 0.003 -9999 0 -10000 0 0
PIK3R1 0.016 0.005 -9999 0 -10000 0 0
mol:DAG -0.031 0.089 -9999 0 -10000 0 0
CDH1 -0.005 0.12 -9999 0 -0.64 5 5
RhoA/GDP -0.034 0.097 -9999 0 -0.56 2 2
establishment of polarity of embryonic epithelium 0.04 0.062 -9999 0 -10000 0 0
SRC 0.017 0 -9999 0 -10000 0 0
RAC1 0.017 0 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
EGFR -0.001 0.11 -9999 0 -0.66 4 4
CASR 0.027 0.12 -9999 0 -0.52 2 2
RhoA/GTP -0.027 0.078 -9999 0 -10000 0 0
AKT2 0.044 0.062 -9999 0 -10000 0 0
actin cable formation 0.039 0.061 -9999 0 -10000 0 0
apoptosis 0.015 0.04 -9999 0 -10000 0 0
CTNNA1 0.017 0.005 -9999 0 -10000 0 0
mol:GDP 0.023 0.13 -9999 0 -0.61 2 2
PIP5K1A 0.04 0.063 -9999 0 -10000 0 0
PLCG1 -0.032 0.09 -9999 0 -10000 0 0
Rac1/GTP -0.02 0.065 -9999 0 -10000 0 0
homophilic cell adhesion 0.001 0.004 -9999 0 -10000 0 0
Coregulation of Androgen receptor activity

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
NRIP1 0.019 0 -9999 0 -10000 0 0
SVIL 0.01 0.075 -9999 0 -0.64 2 2
ZNF318 -0.005 0.06 -9999 0 -0.74 1 1
JMJD2C 0.027 0 -9999 0 -10000 0 0
T-DHT/AR/Ubc9 -0.007 0.053 -9999 0 -0.46 2 2
CARM1 0.017 0 -9999 0 -10000 0 0
PRDX1 0.016 0 -9999 0 -10000 0 0
PELP1 0.016 0 -9999 0 -10000 0 0
CTNNB1 0.013 0.061 -9999 0 -0.74 1 1
AKT1 0.015 0 -9999 0 -10000 0 0
PTK2B 0.018 0 -9999 0 -10000 0 0
MED1 0 0.1 -9999 0 -0.74 3 3
MAK -0.019 0.12 -9999 0 -0.74 4 4
response to oxidative stress -0.001 0 -9999 0 -10000 0 0
HIP1 0.014 0.061 -9999 0 -0.74 1 1
GSN -0.08 0.24 -9999 0 -0.64 23 23
NCOA2 0.017 0 -9999 0 -10000 0 0
NCOA6 0.019 0 -9999 0 -10000 0 0
DNA-PK -0.04 0.13 -9999 0 -0.47 13 13
NCOA4 0.017 0 -9999 0 -10000 0 0
PIAS3 0.013 0.061 -9999 0 -0.74 1 1
cell proliferation -0.011 0.066 -9999 0 -0.41 4 4
XRCC5 0.016 0 -9999 0 -10000 0 0
UBE3A 0.02 0 -9999 0 -10000 0 0
T-DHT/AR/SNURF 0.026 0.042 -9999 0 -0.47 1 1
FHL2 -0.005 0.048 -9999 0 -0.58 1 1
RANBP9 0.019 0 -9999 0 -10000 0 0
JMJD1A 0.027 0.012 -9999 0 -10000 0 0
CDK6 0.007 0.086 -9999 0 -0.74 2 2
TGFB1I1 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/CyclinD1 -0.077 0.17 -9999 0 -0.46 25 25
XRCC6 0.016 0 -9999 0 -10000 0 0
T-DHT/AR 0.061 0.047 -9999 0 -0.45 1 1
CTDSP1 0.018 0 -9999 0 -10000 0 0
CTDSP2 -0.008 0.073 -9999 0 -0.64 2 2
BRCA1 -0.006 0.13 -9999 0 -0.74 5 5
TCF4 0.014 0 -9999 0 -10000 0 0
CDKN2A -0.24 0.36 -9999 0 -0.74 52 52
SRF 0.026 0.01 -9999 0 -10000 0 0
NKX3-1 -0.003 0.021 -9999 0 -10000 0 0
KLK3 0.037 0.048 -9999 0 -10000 0 0
TMF1 0.017 0 -9999 0 -10000 0 0
HNRNPA1 0.015 0 -9999 0 -10000 0 0
AOF2 0.014 0.061 -9999 0 -0.74 1 1
APPL1 0.029 0 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.004 0.038 -9999 0 -0.46 1 1
AR 0.021 0.061 -9999 0 -0.72 1 1
UBA3 0.001 0 -9999 0 -10000 0 0
PATZ1 0.015 0 -9999 0 -10000 0 0
PAWR 0.017 0 -9999 0 -10000 0 0
PRKDC -0.049 0.21 -9999 0 -0.74 13 13
PA2G4 0.01 0.061 -9999 0 -0.74 1 1
UBE2I 0.012 0.061 -9999 0 -0.74 1 1
T-DHT/AR/Cyclin D3/CDK11 p58 -0.003 0.034 -9999 0 -0.42 1 1
RPS6KA3 0.019 0 -9999 0 -10000 0 0
T-DHT/AR/ARA70 -0.004 0.037 -9999 0 -0.46 1 1
LATS2 0.01 0.061 -9999 0 -0.74 1 1
T-DHT/AR/PRX1 -0.003 0.034 -9999 0 -0.42 1 1
Cyclin D3/CDK11 p58 0 0 -9999 0 -10000 0 0
VAV3 -0.12 0.27 -9999 0 -0.64 32 32
KLK2 -0.001 0.01 -9999 0 -10000 0 0
CASP8 0.016 0 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.003 0.033 -9999 0 -0.41 1 1
TMPRSS2 -0.008 0.082 -9999 0 -1 1 1
CCND1 -0.1 0.28 -9999 0 -0.74 24 24
PIAS1 0.02 0 -9999 0 -10000 0 0
mol:T-DHT 0.009 0.009 -9999 0 -0.066 2 2
CDC2L1 0 0 -9999 0 -10000 0 0
PIAS4 0.021 0 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.01 0.065 -9999 0 -0.46 3 3
CMTM2 0.001 0.1 -9999 0 -0.74 3 3
SNURF 0 0 -9999 0 -10000 0 0
ZMIZ1 0.026 0.007 -9999 0 -10000 0 0
CCND3 0.017 0 -9999 0 -10000 0 0
TGIF1 -0.084 0.26 -9999 0 -0.74 20 20
FKBP4 0.014 0.061 -9999 0 -0.74 1 1
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.022 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.067 0.074 -9999 0 -10000 0 0
ERC1 0.017 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.2 0.28 -9999 0 -0.57 53 53
NFKBIA 0.065 0 -9999 0 -10000 0 0
BIRC2 0.017 0 -9999 0 -10000 0 0
IKBKB 0.012 0.061 -9999 0 -0.74 1 1
RIPK2 -0.14 0.31 -9999 0 -0.74 32 32
IKBKG -0.053 0.074 -9999 0 -10000 0 0
IKK complex/A20 -0.04 0.064 -9999 0 -0.49 1 1
NEMO/A20/RIP2 -0.14 0.31 -9999 0 -0.74 32 32
XPO1 0.017 0 -9999 0 -10000 0 0
NEMO/ATM -0.001 0.099 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.017 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.039 0.062 -9999 0 -0.48 1 1
BCL10/MALT1/TRAF6 0 0 -9999 0 -10000 0 0
NOD2 -0.097 0.27 -9999 0 -0.74 23 23
NFKB1 0.022 0 -9999 0 -10000 0 0
RELA 0.022 0 -9999 0 -10000 0 0
MALT1 0.017 0 -9999 0 -10000 0 0
cIAP1/UbcH5C 0 0 -9999 0 -10000 0 0
ATM 0.017 0 -9999 0 -10000 0 0
TNF/TNFR1A 0 0 -9999 0 -10000 0 0
TRAF6 0.017 0 -9999 0 -10000 0 0
PRKCA 0.017 0 -9999 0 -10000 0 0
CHUK 0.017 0 -9999 0 -10000 0 0
UBE2D3 0.017 0 -9999 0 -10000 0 0
TNF 0.017 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.017 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.065 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.022 0 -9999 0 -10000 0 0
TNFRSF1A 0.017 0 -9999 0 -10000 0 0
IKK complex -0.045 0.07 -9999 0 -0.52 1 1
CYLD 0.017 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.04 0.064 -9999 0 -0.49 1 1
ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF 0.037 0.071 -9999 0 -0.44 3 3
epithelial cell differentiation -0.022 0.076 -9999 0 -10000 0 0
ITCH 0.018 0.006 -9999 0 -10000 0 0
WWP1 0.049 0.024 -9999 0 -10000 0 0
FYN 0.012 0.061 -9999 0 -0.74 1 1
EGFR -0.001 0.11 -9999 0 -0.66 4 4
PRL 0.012 0.061 -9999 0 -0.74 1 1
neuron projection morphogenesis 0.09 0.041 -9999 0 -10000 0 0
PTPRZ1 -0.023 0.16 -9999 0 -0.65 9 9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.001 0.003 -9999 0 -10000 0 0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta 0.052 0.02 -9999 0 -10000 0 0
ADAM17 0.018 0.006 -9999 0 -10000 0 0
ErbB4/ErbB4 0.049 0.03 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 0.047 0.024 -9999 0 -10000 0 0
NCOR1 0.012 0.053 -9999 0 -0.64 1 1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.004 0.032 -9999 0 -10000 0 0
GRIN2B -0.01 0.17 -9999 0 -10000 0 0
ErbB4/ErbB2/betacellulin -0.016 0.073 -9999 0 -0.48 1 1
STAT1 -0.057 0.22 -9999 0 -0.74 15 15
HBEGF 0.002 0.1 -9999 0 -0.74 3 3
PRLR 0.002 0.1 -9999 0 -0.74 3 3
E4ICDs/ETO2 -0.1 0.2 -9999 0 -0.46 2 2
axon guidance 0.049 0.056 -9999 0 -10000 0 0
NEDD4 -0.008 0.13 -9999 0 -0.74 5 5
Prolactin receptor/Prolactin receptor/Prolactin -0.014 0.088 -9999 0 -0.55 4 4
CBFA2T3 -0.23 0.32 -9999 0 -0.64 57 57
ErbB4/ErbB2/HBEGF -0.019 0.083 -9999 0 -0.48 1 1
MAPK3 0.08 0.042 -9999 0 -10000 0 0
STAT1 (dimer) -0.001 0.14 -9999 0 -0.44 15 15
MAPK1 0.084 0.016 -9999 0 -10000 0 0
JAK2 -0.003 0.12 -9999 0 -0.74 4 4
ErbB4/ErbB2/neuregulin 1 beta -0.012 0.065 -9999 0 -0.48 1 1
NRG1 0.033 0.004 -9999 0 -10000 0 0
NRG3 0.017 0 -9999 0 -10000 0 0
NRG2 0.012 0.053 -9999 0 -0.64 1 1
NRG4 -0.01 0.13 -9999 0 -0.66 6 6
heart development 0.049 0.056 -9999 0 -10000 0 0
neural crest cell migration -0.012 0.065 -9999 0 -0.47 1 1
ERBB2 0.017 0.095 -9999 0 -0.56 4 4
WWOX/E4ICDs 0.047 0.024 -9999 0 -10000 0 0
SHC1 0.017 0 -9999 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.024 0.086 -9999 0 -0.44 1 1
apoptosis 0.041 0.037 -9999 0 -10000 0 0
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta 0.044 0.04 -9999 0 -10000 0 0
ErbB4/ErbB2/epiregulin -0.26 0.2 -9999 0 -0.65 6 6
ErbB4/ErbB4/betacellulin/betacellulin 0.041 0.052 -9999 0 -10000 0 0
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.026 0.089 -9999 0 -10000 0 0
MDM2 0.054 0.025 -9999 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.001 0.005 -9999 0 -10000 0 0
STAT5A 0.057 0.052 -9999 0 -10000 0 0
ErbB4/EGFR/neuregulin 1 beta -0.01 0.053 -9999 0 -10000 0 0
DLG4 0.017 0 -9999 0 -10000 0 0
GRB2/SHC 0 0 -9999 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.004 0.028 -9999 0 -10000 0 0
STAT5A (dimer) -0.024 0.081 -9999 0 -10000 0 0
MAP3K7IP2 0.017 0 -9999 0 -10000 0 0
STAT5B (dimer) 0.054 0.049 -9999 0 -10000 0 0
LRIG1 0 0.1 -9999 0 -0.64 4 4
EREG -0.48 0.36 -9999 0 -0.74 100 100
BTC 0.008 0.075 -9999 0 -0.64 2 2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta 0.049 0.056 -9999 0 -10000 0 0
ERBB4 0.049 0.03 -9999 0 -10000 0 0
STAT5B 0.017 0 -9999 0 -10000 0 0
YAP1 -0.001 0.004 -9999 0 -10000 0 0
GRB2 0.017 0 -9999 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.025 0.091 -9999 0 -0.48 1 1
glial cell differentiation 0.004 0.028 -9999 0 -10000 0 0
WWOX 0.017 0 -9999 0 -10000 0 0
cell proliferation 0.055 0.085 -9999 0 -10000 0 0
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.095 0.18 -9999 0 -0.73 4 4
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
CRKL 0.017 0 -9999 0 -10000 0 0
STAT1 (dimer)/Cbp/p300 -0.11 0.22 -9999 0 -0.73 13 13
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.024 0.089 -9999 0 -0.56 4 4
antigen processing and presentation of peptide antigen via MHC class I -0.05 0.084 -9999 0 -0.32 4 4
CaM/Ca2+ -0.087 0.16 -9999 0 -0.67 4 4
RAP1A 0.017 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.084 0.27 -9999 0 -0.83 13 13
AKT1 -0.075 0.14 -9999 0 -0.59 4 4
MAP2K1 -0.023 0.18 -9999 0 -0.64 4 4
MAP3K11 -0.039 0.19 -9999 0 -0.68 4 4
IFNGR1 0.011 0.015 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.027 0.055 -9999 0 -10000 0 0
Rap1/GTP -0.062 0.12 -9999 0 -0.49 4 4
CRKL/C3G 0 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.1 0.19 -9999 0 -0.78 4 4
CEBPB 0.025 0.17 -9999 0 -0.5 5 5
STAT3 0.017 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.085 0.16 -9999 0 -0.69 4 4
STAT1 -0.081 0.27 -9999 0 -0.83 13 13
CALM1 0.017 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.16 0.32 -9999 0 -0.74 37 37
PIK3CA 0.017 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.12 0.23 -9999 0 -0.77 13 13
CEBPB/PTGES2/Cbp/p300 -0.035 0.068 -9999 0 -10000 0 0
mol:Ca2+ -0.094 0.17 -9999 0 -0.72 4 4
MAPK3 -0.004 0.19 -9999 0 -0.9 2 2
STAT1 (dimer) -0.066 0.11 -9999 0 -0.44 4 4
MAPK1 0.006 0.16 -9999 0 -0.52 4 4
JAK2 -0.009 0.13 -9999 0 -0.78 4 4
PIK3R1 0.017 0 -9999 0 -10000 0 0
JAK1 0.011 0.015 -9999 0 -10000 0 0
CAMK2D 0.017 0 -9999 0 -10000 0 0
DAPK1 0.041 0.13 -9999 0 -0.51 1 1
SMAD7 0.04 0.082 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.077 0.14 -9999 0 -0.61 4 4
PI3K -0.083 0.15 -9999 0 -0.66 4 4
IFNG -0.16 0.32 -9999 0 -0.74 37 37
apoptosis 0.026 0.11 -9999 0 -0.37 1 1
CAMK2G 0.017 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.017 0 -9999 0 -10000 0 0
CAMK2A 0.017 0 -9999 0 -10000 0 0
CAMK2B 0.012 0.061 -9999 0 -0.74 1 1
FRAP1 -0.002 0.16 -9999 0 -0.53 4 4
PRKCD -0.019 0.17 -9999 0 -0.6 4 4
RAP1B 0.017 0 -9999 0 -10000 0 0
negative regulation of cell growth -0.05 0.084 -9999 0 -0.32 4 4
PTPN2 0.017 0 -9999 0 -10000 0 0
EP300 0.018 0.001 -9999 0 -10000 0 0
IRF1 0 0.21 -9999 0 -0.63 6 6
STAT1 (dimer)/PIASy -0.12 0.23 -9999 0 -0.77 13 13
SOCS1 0.011 0.019 -9999 0 -10000 0 0
mol:GDP -0.074 0.14 -9999 0 -0.58 4 4
CASP1 0.023 0.12 -9999 0 -0.29 12 12
PTGES2 0.017 0 -9999 0 -10000 0 0
IRF9 0.054 0.064 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.081 0.15 -9999 0 -0.63 4 4
RAP1/GDP -0.062 0.12 -9999 0 -0.49 4 4
CBL -0.041 0.19 -9999 0 -0.68 4 4
MAP3K1 -0.039 0.19 -9999 0 -0.68 4 4
PIAS1 0.017 0 -9999 0 -10000 0 0
PIAS4 0.016 0 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.05 0.084 -9999 0 -0.32 4 4
PTPN11 -0.053 0.2 -9999 0 -0.72 4 4
CREBBP 0.018 0.001 -9999 0 -10000 0 0
RAPGEF1 0.017 0 -9999 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.014 0.16 -9999 0 -0.96 2 2
PLK1 0.042 0.2 -9999 0 -0.81 3 3
CDKN1B 0.099 0.15 -9999 0 -10000 0 0
FOXO3 0.033 0.22 -9999 0 -0.78 5 5
KAT2B 0.004 0.024 -9999 0 -0.061 5 5
FOXO1/SIRT1 -0.014 0.11 -9999 0 -0.57 1 1
CAT 0.042 0.2 -9999 0 -0.81 3 3
CTNNB1 0.012 0.061 -9999 0 -0.74 1 1
AKT1 0.028 0.022 -9999 0 -10000 0 0
FOXO1 0.01 0.13 -9999 0 -0.51 2 2
MAPK10 0.044 0.058 -9999 0 -0.41 1 1
mol:GTP 0.003 0.002 -9999 0 -10000 0 0
FOXO4 0.13 0.06 -9999 0 -10000 0 0
response to oxidative stress 0.011 0.025 -9999 0 -0.056 4 4
FOXO3A/SIRT1 -0.013 0.16 -9999 0 -0.64 5 5
XPO1 0.018 0.001 -9999 0 -10000 0 0
EP300 0.021 0.005 -9999 0 -10000 0 0
BCL2L11 0.035 0.041 -9999 0 -10000 0 0
FOXO1/SKP2 -0.07 0.23 -9999 0 -0.49 30 30
mol:GDP 0.011 0.025 -9999 0 -0.056 4 4
RAN 0.019 0.002 -9999 0 -10000 0 0
GADD45A 0.12 0.11 -9999 0 -0.57 1 1
YWHAQ 0.017 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.09 0.04 -9999 0 -10000 0 0
MST1 -0.021 0.18 -9999 0 -0.73 9 9
CSNK1D 0.017 0 -9999 0 -10000 0 0
CSNK1E 0.017 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.078 0.035 -9999 0 -10000 0 0
YWHAB 0.017 0 -9999 0 -10000 0 0
MAPK8 0.051 0.019 -9999 0 -10000 0 0
MAPK9 0.051 0.016 -9999 0 -10000 0 0
YWHAG 0.017 0 -9999 0 -10000 0 0
YWHAE 0.012 0.061 -9999 0 -0.74 1 1
YWHAZ 0.017 0 -9999 0 -10000 0 0
SIRT1 0.016 0.026 -9999 0 -10000 0 0
SOD2 0.075 0.22 -9999 0 -0.62 5 5
RBL2 0.079 0.15 -9999 0 -10000 0 0
RAL/GDP 0.031 0.025 -9999 0 -10000 0 0
CHUK 0.024 0.02 -9999 0 -10000 0 0
Ran/GTP 0.017 0.006 -9999 0 -10000 0 0
CSNK1G2 0.017 0 -9999 0 -10000 0 0
RAL/GTP 0.045 0.024 -9999 0 -10000 0 0
CSNK1G1 0.017 0 -9999 0 -10000 0 0
FASLG -0.17 0.54 -9999 0 -1.5 22 22
SKP2 -0.13 0.3 -9999 0 -0.74 29 29
USP7 0.014 0.053 -9999 0 -0.64 1 1
IKBKB 0.019 0.063 -9999 0 -0.72 1 1
CCNB1 -0.013 0.29 -9999 0 -0.91 6 6
FOXO1-3a-4/beta catenin -0.03 0.089 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.069 0.23 -9999 0 -0.49 30 30
CSNK1A1 0.017 0 -9999 0 -10000 0 0
SGK1 0.004 0.024 -9999 0 -0.061 5 5
CSNK1G3 0.017 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.03 0.01 -9999 0 -10000 0 0
ZFAND5 0.13 0.054 -9999 0 -10000 0 0
SFN 0.012 0.053 -9999 0 -0.64 1 1
CDK2 -0.088 0.27 -9999 0 -0.74 22 22
FOXO3A/14-3-3 0.066 0.056 -9999 0 -10000 0 0
CREBBP 0.021 0.008 -9999 0 -10000 0 0
FBXO32 -0.008 0.37 -9999 0 -1.4 9 9
BCL6 0.076 0.15 -9999 0 -10000 0 0
RALB 0.019 0.001 -9999 0 -10000 0 0
RALA 0.019 0.001 -9999 0 -10000 0 0
YWHAH 0.017 0 -9999 0 -10000 0 0
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.15 0.29 -9999 0 -0.57 49 49
MKNK1 0.017 0 -9999 0 -10000 0 0
MAPK14 -0.042 0.1 -9999 0 -10000 0 0
ATF2/c-Jun -0.021 0.14 -9999 0 -0.68 5 5
MAPK11 -0.046 0.12 -9999 0 -0.7 1 1
MITF -0.031 0.12 -9999 0 -10000 0 0
MAPKAPK5 -0.031 0.12 -9999 0 -10000 0 0
KRT8 -0.039 0.13 -9999 0 -10000 0 0
MAPKAPK3 0.017 0 -9999 0 -10000 0 0
MAPKAPK2 0.017 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.063 0.15 -9999 0 -0.51 1 1
CEBPB -0.039 0.13 -9999 0 -0.57 1 1
SLC9A1 -0.031 0.12 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.029 0.13 -9999 0 -0.42 1 1
p38alpha-beta/MNK1 -0.066 0.095 -9999 0 -10000 0 0
JUN -0.02 0.14 -9999 0 -0.68 5 5
PPARGC1A -0.22 0.26 -9999 0 -0.64 28 28
USF1 -0.059 0.17 -9999 0 -0.56 9 9
RAB5/GDP/GDI1 -0.043 0.061 -9999 0 -10000 0 0
NOS2 -0.044 0.12 -9999 0 -0.33 1 1
DDIT3 -0.039 0.13 -9999 0 -0.57 1 1
RAB5A 0.017 0 -9999 0 -10000 0 0
HSPB1 -0.014 0.1 -9999 0 -0.47 1 1
p38alpha-beta/HBP1 -0.066 0.095 -9999 0 -10000 0 0
CREB1 -0.03 0.13 -9999 0 -0.42 2 2
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.014 0.1 -9999 0 -10000 0 0
RPS6KA4 -0.031 0.12 -9999 0 -10000 0 0
PLA2G4A -0.14 0.22 -9999 0 -0.56 19 19
GDI1 -0.031 0.12 -9999 0 -10000 0 0
TP53 -0.053 0.16 -9999 0 -0.59 2 2
RPS6KA5 -0.042 0.14 -9999 0 -0.65 2 2
ESR1 -0.037 0.12 -9999 0 -10000 0 0
HBP1 0.017 0 -9999 0 -10000 0 0
MEF2C -0.068 0.16 -9999 0 -0.6 4 4
MEF2A -0.031 0.12 -9999 0 -10000 0 0
EIF4EBP1 -0.035 0.13 -9999 0 -0.42 2 2
KRT19 -0.05 0.15 -9999 0 -0.65 3 3
ELK4 -0.041 0.14 -9999 0 -0.57 3 3
ATF6 -0.031 0.12 -9999 0 -10000 0 0
ATF1 -0.03 0.13 -9999 0 -0.42 2 2
p38alpha-beta/MAPKAPK2 -0.066 0.095 -9999 0 -10000 0 0
p38alpha-beta/MAPKAPK3 -0.066 0.095 -9999 0 -10000 0 0
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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
BAG4 0.017 0 -9999 0 -10000 0 0
Caspase 8 (4 units) -0.054 0.12 -9999 0 -0.46 8 8
NEF -0.019 0.067 -9999 0 -10000 0 0
NFKBIA 0.016 0.025 -9999 0 -10000 0 0
BIRC3 0.025 0.16 -9999 0 -0.65 8 8
CYCS -0.012 0.17 -9999 0 -0.52 8 8
RIPK1 0.017 0 -9999 0 -10000 0 0
CD247 -0.034 0.17 -9999 0 -0.77 7 7
MAP2K7 0.022 0.12 -9999 0 -0.38 3 3
protein ubiquitination 0.089 0.038 -9999 0 -10000 0 0
CRADD 0.012 0.053 -9999 0 -0.64 1 1
DAXX 0.017 0 -9999 0 -10000 0 0
FAS -0.052 0.2 -9999 0 -0.64 16 16
BID -0.021 0.18 -9999 0 -0.48 13 13
NF-kappa-B/RelA/I kappa B alpha -0.015 0.064 -9999 0 -10000 0 0
TRADD 0.017 0 -9999 0 -10000 0 0
MAP3K5 0.017 0 -9999 0 -10000 0 0
CFLAR 0.017 0 -9999 0 -10000 0 0
FADD 0.017 0 -9999 0 -10000 0 0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.015 0.064 -9999 0 -10000 0 0
MAPK8 0.032 0.11 -9999 0 -0.36 2 2
APAF1 0.017 0 -9999 0 -10000 0 0
TRAF1 0.017 0 -9999 0 -10000 0 0
TRAF2 0.017 0 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.067 0.14 -9999 0 -0.53 9 9
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.073 0.048 -9999 0 -10000 0 0
CHUK 0.091 0.039 -9999 0 -10000 0 0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.033 0.096 -9999 0 -10000 0 0
TCRz/NEF -0.068 0.18 -9999 0 -0.7 7 7
TNF 0.017 0 -9999 0 -10000 0 0
FASLG -0.086 0.3 -9999 0 -0.8 22 22
NFKB1 0.016 0.025 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha 0 0 -9999 0 -10000 0 0
CASP6 -0.033 0.084 -9999 0 -10000 0 0
CASP7 -0.003 0.21 -9999 0 -0.6 8 8
RELA 0.016 0.025 -9999 0 -10000 0 0
CASP2 0.017 0 -9999 0 -10000 0 0
CASP3 0.04 0.18 -9999 0 -0.61 6 6
TNFRSF1A 0.017 0 -9999 0 -10000 0 0
TNFR1A/BAG4 0 0 -9999 0 -10000 0 0
CASP8 0.017 0 -9999 0 -10000 0 0
CASP9 0.017 0 -9999 0 -10000 0 0
MAP3K14 0.085 0.041 -9999 0 -10000 0 0
APAF-1/Caspase 9 -0.056 0.12 -9999 0 -0.57 4 4
BCL2 -0.15 0.21 -9999 0 -0.48 24 24
Effects of Botulinum toxin

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
STX1A -0.011 0.12 -9999 0 -0.57 7 7
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B 0 0 -9999 0 -10000 0 0
STXBP1 -0.018 0.16 -9999 0 -0.74 7 7
ACh/CHRNA1 0.018 0.017 -9999 0 -10000 0 0
RAB3GAP2/RIMS1/UNC13B 0 0 -9999 0 -10000 0 0
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 0.017 0 -9999 0 -10000 0 0
mol:ACh 0.008 0.024 -9999 0 -0.099 7 7
RAB3GAP2 0.017 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.03 0.093 -9999 0 -10000 0 0
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction 0.017 0.017 -9999 0 -10000 0 0
UNC13B 0.017 0 -9999 0 -10000 0 0
CHRNA1 0.017 0 -9999 0 -10000 0 0
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.069 0.2 -9999 0 -0.51 25 25
SNAP25 0.01 0 -9999 0 -10000 0 0
VAMP2 0.009 0 -9999 0 -10000 0 0
SYT1 -0.11 0.28 -9999 0 -0.74 25 25
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.022 0.15 -9999 0 -0.48 14 14
STX1A/SNAP25 fragment 1/VAMP2 -0.03 0.093 -9999 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin -0.004 0.045 -9999 0 -0.55 1 1
AKT1 0.034 0.18 -9999 0 -0.63 3 3
PTK2B 0.007 0.17 -9999 0 -0.55 4 4
VEGFR2 homodimer/Frs2 -0.018 0.074 -9999 0 -10000 0 0
CAV1 0.002 0.1 -9999 0 -0.74 3 3
CALM1 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.072 0.15 -9999 0 -0.63 4 4
endothelial cell proliferation 0.028 0.19 -9999 0 -0.62 4 4
mol:Ca2+ -0.051 0.26 -9999 0 -0.84 8 8
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.065 0.14 -9999 0 -0.59 4 4
RP11-342D11.1 -0.028 0.22 -9999 0 -0.79 5 5
CDH5 0.017 0 -9999 0 -10000 0 0
VEGFA homodimer -0.053 0.15 -9999 0 -0.56 5 5
SHC1 0.017 0 -9999 0 -10000 0 0
SHC2 -0.028 0.18 -9999 0 -0.74 9 9
HRAS/GDP -0.071 0.14 -9999 0 -0.66 5 5
SH2D2A -0.008 0.14 -9999 0 -0.74 5 5
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.068 0.13 -9999 0 -0.69 3 3
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.085 0.16 -9999 0 -0.63 4 4
VEGFR1 homodimer -0.033 0.19 -9999 0 -0.74 10 10
SHC/GRB2/SOS1 -0.08 0.16 -9999 0 -0.74 5 5
GRB10 -0.043 0.28 -9999 0 -0.85 11 11
PTPN11 0.012 0.061 -9999 0 -0.74 1 1
GRB2 0.017 0 -9999 0 -10000 0 0
PAK1 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.063 0.14 -9999 0 -0.58 5 5
HRAS 0.017 0 -9999 0 -10000 0 0
VEGF/Rho/ROCK1/Integrin Complex 0.032 0.089 -9999 0 -10000 0 0
HIF1A 0.012 0.061 -9999 0 -0.74 1 1
FRS2 0.017 0 -9999 0 -10000 0 0
oxygen and reactive oxygen species metabolic process -0.065 0.14 -9999 0 -0.58 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.017 0 -9999 0 -10000 0 0
Nck/Pak 0 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.074 0.16 -9999 0 -0.63 4 4
mol:GDP -0.078 0.16 -9999 0 -0.71 5 5
mol:NADP 0.02 0.16 -9999 0 -0.59 3 3
eNOS/Hsp90 0.025 0.16 -9999 0 -0.54 3 3
PIK3R1 0.017 0 -9999 0 -10000 0 0
mol:IP3 -0.053 0.26 -9999 0 -0.86 8 8
HIF1A/ARNT -0.004 0.045 -9999 0 -0.55 1 1
SHB 0.002 0.1 -9999 0 -0.74 3 3
VEGFA -0.072 0.25 -9999 0 -0.75 18 18
VEGFC 0.017 0 -9999 0 -10000 0 0
FAK1/Vinculin 0.039 0.14 -9999 0 -0.53 1 1
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.068 0.14 -9999 0 -0.59 4 4
PTPN6 0.017 0 -9999 0 -10000 0 0
EPAS1 0 0.13 -9999 0 -0.61 7 7
mol:L-citrulline 0.02 0.16 -9999 0 -0.59 3 3
ITGAV 0.012 0.061 -9999 0 -0.74 1 1
PIK3CA 0.017 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.065 0.14 -9999 0 -0.59 4 4
VEGFR2 homodimer/VEGFA homodimer -0.1 0.2 -9999 0 -0.87 5 5
VEGFR2/3 heterodimer -0.018 0.074 -9999 0 -10000 0 0
VEGFB 0.017 0 -9999 0 -10000 0 0
MAPK11 -0.008 0.21 -9999 0 -0.77 5 5
VEGFR2 homodimer 0.026 0.1 -9999 0 -10000 0 0
FLT1 -0.033 0.19 -9999 0 -0.74 10 10
NEDD4 -0.007 0.14 -9999 0 -0.75 5 5
MAPK3 -0.037 0.24 -9999 0 -0.76 8 8
MAPK1 -0.035 0.24 -9999 0 -0.76 8 8
VEGFA145/NRP2 -0.07 0.19 -9999 0 -0.59 18 18
VEGFR1/2 heterodimer -0.048 0.13 -9999 0 -0.47 4 4
KDR 0.026 0.1 -9999 0 -10000 0 0
VEGFA165/NRP1/VEGFR2 homodimer -0.091 0.18 -9999 0 -0.78 6 6
SRC 0.017 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process -0.035 0.24 -9999 0 -0.77 8 8
PI3K -0.086 0.16 -9999 0 -0.86 3 3
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.072 0.15 -9999 0 -0.63 4 4
FES -0.02 0.23 -9999 0 -0.88 5 5
GAB1 -0.079 0.15 -9999 0 -0.62 5 5
VEGFR2 homodimer/VEGFA homodimer/Src -0.072 0.15 -9999 0 -0.63 4 4
CTNNB1 0.012 0.061 -9999 0 -0.74 1 1
SOS1 0.017 0 -9999 0 -10000 0 0
ARNT 0.017 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.02 0.16 -9999 0 -0.54 3 3
VEGFR2 homodimer/VEGFA homodimer/Yes -0.072 0.15 -9999 0 -0.63 4 4
PI3K/GAB1 0.0