PARADIGM pathway analysis of mRNASeq expression data
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1B856MC
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): PARADIGM pathway analysis of mRNASeq expression data. Broad Institute of MIT and Harvard. doi:10.7908/C1B856MC
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 38 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 187
Syndecan-1-mediated signaling events 168
Syndecan-4-mediated signaling events 121
IL4-mediated signaling events 120
HIF-1-alpha transcription factor network 94
Osteopontin-mediated events 80
IL23-mediated signaling events 69
amb2 Integrin signaling 65
Glypican 2 network 63
Syndecan-2-mediated signaling events 57
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 424 . 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 ( 424 ).

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 0.4410 187 1499 8 -0.35 0.15 1000 -1000 -0.026 -1000
Syndecan-1-mediated signaling events 0.3962 168 5745 34 -0.72 0.014 1000 -1000 -0.068 -1000
Syndecan-4-mediated signaling events 0.2854 121 8139 67 -0.71 0.095 1000 -1000 -0.11 -1000
IL4-mediated signaling events 0.2830 120 10994 91 -1.4 1.3 1000 -1000 -0.19 -1000
HIF-1-alpha transcription factor network 0.2217 94 7213 76 -1 0.022 1000 -1000 -0.2 -1000
Osteopontin-mediated events 0.1887 80 3061 38 -0.43 0.014 1000 -1000 -0.14 -1000
IL23-mediated signaling events 0.1627 69 4147 60 -0.74 0.014 1000 -1000 -0.19 -1000
amb2 Integrin signaling 0.1533 65 5397 82 -0.59 0.014 1000 -1000 -0.099 -1000
Glypican 2 network 0.1486 63 253 4 -0.13 -0.13 1000 -1000 -0.038 -1000
Syndecan-2-mediated signaling events 0.1344 57 3940 69 -0.44 0.024 1000 -1000 -0.067 -1000
TCGA08_p53 0.1344 57 400 7 -0.27 0.14 1000 -1000 -0.02 -1000
Endothelins 0.1250 53 5105 96 -0.56 0.014 1000 -1000 -0.1 -1000
p75(NTR)-mediated signaling 0.0873 37 4704 125 -0.56 0.014 1000 -1000 -0.13 -1000
FOXA2 and FOXA3 transcription factor networks 0.0825 35 1628 46 -0.51 0.021 1000 -1000 -0.12 -1000
Visual signal transduction: Rods 0.0825 35 1847 52 -0.45 0.014 1000 -1000 -0.1 -1000
Calcium signaling in the CD4+ TCR pathway 0.0802 34 1069 31 -0.5 0.014 1000 -1000 -0.1 -1000
Signaling events mediated by the Hedgehog family 0.0731 31 1635 52 -0.47 0.067 1000 -1000 -0.097 -1000
BMP receptor signaling 0.0731 31 2526 81 -0.37 0.047 1000 -1000 -0.12 -1000
Effects of Botulinum toxin 0.0731 31 825 26 -0.23 0.014 1000 -1000 -0.083 -1000
PDGFR-beta signaling pathway 0.0731 31 3085 97 -0.16 0.014 1000 -1000 -0.11 -1000
Ephrin B reverse signaling 0.0708 30 1446 48 -0.15 0.14 1000 -1000 -0.094 -1000
Coregulation of Androgen receptor activity 0.0684 29 2223 76 -0.53 0.041 1000 -1000 -0.059 -1000
Glypican 1 network 0.0684 29 1415 48 -0.37 0.033 1000 -1000 -0.069 -1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes 0.0684 29 2006 68 -0.54 0.034 1000 -1000 -0.16 -1000
Signaling events regulated by Ret tyrosine kinase 0.0637 27 2242 82 -0.18 0.014 1000 -1000 -0.1 -1000
Signaling events mediated by Stem cell factor receptor (c-Kit) 0.0637 27 2126 78 -0.14 0.038 1000 -1000 -0.096 -1000
IL12-mediated signaling events 0.0613 26 2281 87 -0.27 0.082 1000 -1000 -0.16 -1000
Visual signal transduction: Cones 0.0613 26 1022 38 -0.2 0.014 1000 -1000 -0.086 -1000
Glucocorticoid receptor regulatory network 0.0613 26 3077 114 -0.65 0.26 1000 -1000 -0.093 -1000
LPA4-mediated signaling events 0.0566 24 296 12 -0.11 0.021 1000 -1000 -0.037 -1000
Caspase cascade in apoptosis 0.0566 24 1799 74 -0.14 0.049 1000 -1000 -0.066 -1000
Neurotrophic factor-mediated Trk receptor signaling 0.0566 24 2983 120 -0.27 0.12 1000 -1000 -0.1 -1000
ErbB4 signaling events 0.0542 23 1643 69 -0.34 0.066 1000 -1000 -0.11 -1000
TCR signaling in naïve CD8+ T cells 0.0542 23 2180 93 -0.29 0.16 1000 -1000 -0.099 -1000
Canonical Wnt signaling pathway 0.0542 23 1200 51 -0.35 0.11 1000 -1000 -0.084 -1000
Nongenotropic Androgen signaling 0.0542 23 1229 52 -0.14 0.043 1000 -1000 -0.075 -1000
Reelin signaling pathway 0.0519 22 1248 56 -0.23 0.014 1000 -1000 -0.086 -1000
IL1-mediated signaling events 0.0519 22 1367 62 -0.24 0.071 1000 -1000 -0.13 -1000
Thromboxane A2 receptor signaling 0.0495 21 2209 105 -0.098 0.022 1000 -1000 -0.085 -1000
EPHB forward signaling 0.0495 21 1827 85 -0.26 0.11 1000 -1000 -0.12 -1000
BCR signaling pathway 0.0495 21 2148 99 -0.15 0.035 1000 -1000 -0.11 -1000
Nephrin/Neph1 signaling in the kidney podocyte 0.0472 20 692 34 -0.056 0.014 1000 -1000 -0.079 -1000
Integrins in angiogenesis 0.0472 20 1724 84 -0.4 0.014 1000 -1000 -0.12 -1000
Regulation of nuclear SMAD2/3 signaling 0.0448 19 2595 136 -0.37 0.37 1000 -1000 -0.092 -1000
Signaling mediated by p38-gamma and p38-delta 0.0448 19 290 15 -0.14 0.024 1000 -1000 -0.048 -1000
Syndecan-3-mediated signaling events 0.0448 19 674 35 -0.22 0.014 1000 -1000 -0.088 -1000
IL27-mediated signaling events 0.0448 19 982 51 -0.17 0.05 1000 -1000 -0.11 -1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 0.0448 19 643 33 -0.35 0.037 1000 -1000 -0.08 -1000
LPA receptor mediated events 0.0425 18 1873 102 -0.59 0.022 1000 -1000 -0.12 -1000
Angiopoietin receptor Tie2-mediated signaling 0.0425 18 1620 88 -0.39 0.063 1000 -1000 -0.13 -1000
ErbB2/ErbB3 signaling events 0.0401 17 1123 65 -0.34 0.026 1000 -1000 -0.076 -1000
Presenilin action in Notch and Wnt signaling 0.0401 17 1074 61 -0.35 0.04 1000 -1000 -0.084 -1000
Lissencephaly gene (LIS1) in neuronal migration and development 0.0377 16 898 54 -0.32 0.028 1000 -1000 -0.12 -1000
Wnt signaling 0.0377 16 112 7 -0.076 0.014 1000 -1000 -0.045 -1000
Regulation of Androgen receptor activity 0.0377 16 1132 70 -0.55 0.033 1000 -1000 -0.089 -1000
Signaling events mediated by PTP1B 0.0354 15 1214 76 -0.18 0.033 1000 -1000 -0.1 -1000
Ephrin A reverse signaling 0.0330 14 101 7 -0.023 0 1000 -1000 -0.041 -1000
Arf6 signaling events 0.0330 14 899 62 -0.17 0.042 1000 -1000 -0.078 -1000
EPO signaling pathway 0.0307 13 732 55 -0.071 0.03 1000 -1000 -0.12 -1000
PDGFR-alpha signaling pathway 0.0307 13 609 44 -0.14 0.032 1000 -1000 -0.071 -1000
Signaling events mediated by HDAC Class III 0.0307 13 522 40 -0.19 0.076 1000 -1000 -0.056 -1000
TRAIL signaling pathway 0.0307 13 657 48 -0.088 0.016 1000 -1000 -0.089 -1000
Signaling mediated by p38-alpha and p38-beta 0.0307 13 586 44 -0.18 0.014 1000 -1000 -0.064 -1000
Regulation of Telomerase 0.0307 13 1372 102 -0.18 0.046 1000 -1000 -0.13 -1000
EGFR-dependent Endothelin signaling events 0.0307 13 284 21 -0.1 0.014 1000 -1000 -0.092 -1000
Plasma membrane estrogen receptor signaling 0.0283 12 1048 86 -0.3 0.03 1000 -1000 -0.1 -1000
Cellular roles of Anthrax toxin 0.0259 11 443 39 -0.042 0.018 1000 -1000 -0.041 -1000
Nectin adhesion pathway 0.0259 11 696 63 -0.16 0.041 1000 -1000 -0.085 -1000
Paxillin-independent events mediated by a4b1 and a4b7 0.0259 11 423 37 -0.077 0.014 1000 -1000 -0.069 -1000
S1P1 pathway 0.0259 11 414 36 -0.16 0.014 1000 -1000 -0.076 -1000
Retinoic acid receptors-mediated signaling 0.0259 11 661 58 -0.17 0.027 1000 -1000 -0.096 -1000
Signaling events mediated by PRL 0.0236 10 371 34 -0.12 0.037 1000 -1000 -0.052 -1000
Class IB PI3K non-lipid kinase events 0.0236 10 30 3 -0.004 -1000 1000 -1000 -0.023 -1000
Noncanonical Wnt signaling pathway 0.0212 9 241 26 -0.076 0.014 1000 -1000 -0.11 -1000
Fc-epsilon receptor I signaling in mast cells 0.0212 9 955 97 -0.2 0.035 1000 -1000 -0.11 -1000
IFN-gamma pathway 0.0212 9 630 68 -0.18 0.037 1000 -1000 -0.12 -1000
FAS signaling pathway (CD95) 0.0212 9 457 47 -0.093 0.014 1000 -1000 -0.059 -1000
IL6-mediated signaling events 0.0212 9 730 75 -0.1 0.064 1000 -1000 -0.12 -1000
JNK signaling in the CD4+ TCR pathway 0.0189 8 139 17 -0.035 0.038 1000 -1000 -0.083 -1000
Arf6 downstream pathway 0.0189 8 364 43 -0.035 0.022 1000 -1000 -0.044 -1000
IL2 signaling events mediated by PI3K 0.0189 8 473 58 -0.14 0.061 1000 -1000 -0.11 -1000
S1P3 pathway 0.0189 8 375 42 -0.16 0.038 1000 -1000 -0.076 -1000
Rapid glucocorticoid signaling 0.0189 8 160 20 -0.059 0.014 1000 -1000 -0.05 -1000
FOXM1 transcription factor network 0.0189 8 425 51 -0.35 0.15 1000 -1000 -0.22 -1000
Ras signaling in the CD4+ TCR pathway 0.0189 8 151 17 -0.017 0.027 1000 -1000 -0.049 -1000
Circadian rhythm pathway 0.0165 7 160 22 -0.14 0.046 1000 -1000 -0.071 -1000
a4b1 and a4b7 Integrin signaling 0.0165 7 39 5 -0.018 0.011 1000 -1000 -0.046 -1000
Ceramide signaling pathway 0.0165 7 556 76 -0.098 0.036 1000 -1000 -0.08 -1000
RXR and RAR heterodimerization with other nuclear receptor 0.0165 7 411 52 -0.23 0.037 1000 -1000 -0.076 -1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha 0.0165 7 321 45 -0.088 0.041 1000 -1000 -0.12 -1000
Stabilization and expansion of the E-cadherin adherens junction 0.0165 7 575 74 -0.33 0.083 1000 -1000 -0.11 -1000
IGF1 pathway 0.0165 7 424 57 -0.079 0.025 1000 -1000 -0.11 -1000
Aurora B signaling 0.0165 7 494 67 -0.31 0.032 1000 -1000 -0.082 -1000
Sphingosine 1-phosphate (S1P) pathway 0.0142 6 178 28 -0.083 0.017 1000 -1000 -0.067 -1000
Paxillin-dependent events mediated by a4b1 0.0142 6 239 36 -0.063 0.025 1000 -1000 -0.08 -1000
Insulin Pathway 0.0142 6 468 74 -0.25 0.039 1000 -1000 -0.12 -1000
VEGFR1 specific signals 0.0142 6 368 56 -0.14 0.04 1000 -1000 -0.099 -1000
p38 MAPK signaling pathway 0.0142 6 284 44 -0.14 0.02 1000 -1000 -0.085 -1000
BARD1 signaling events 0.0118 5 291 57 -0.024 0.058 1000 -1000 -0.084 -1000
Aurora A signaling 0.0118 5 308 60 -0.077 0.032 1000 -1000 -0.072 -1000
HIF-2-alpha transcription factor network 0.0118 5 247 43 -0.25 0.025 1000 -1000 -0.11 -1000
Signaling events mediated by VEGFR1 and VEGFR2 0.0118 5 642 125 -0.098 0.094 1000 -1000 -0.12 -1000
IL2 signaling events mediated by STAT5 0.0118 5 120 22 -0.041 0.052 1000 -1000 -0.072 -1000
S1P4 pathway 0.0118 5 127 25 -0.028 0.025 1000 -1000 -0.071 -1000
Regulation of p38-alpha and p38-beta 0.0094 4 241 54 -0.11 0.036 1000 -1000 -0.079 -1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met) 0.0071 3 332 85 -0.074 0.059 1000 -1000 -0.091 -1000
Hedgehog signaling events mediated by Gli proteins 0.0071 3 244 65 -0.094 0.066 1000 -1000 -0.091 -1000
ceramide signaling pathway 0.0071 3 149 49 -0.027 0.047 1000 -1000 -0.065 -1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes 0.0071 3 275 83 -0.076 0.066 1000 -1000 -0.089 -1000
TCGA08_rtk_signaling 0.0071 3 80 26 -0.031 0.048 1000 -1000 -0.027 -1000
Class I PI3K signaling events 0.0071 3 267 73 -0.11 0.04 1000 -1000 -0.08 -1000
Arf6 trafficking events 0.0071 3 256 71 -0.25 0.047 1000 -1000 -0.092 -1000
Signaling events mediated by HDAC Class II 0.0047 2 156 75 -0.049 0.032 1000 -1000 -0.077 -1000
Aurora C signaling 0.0047 2 18 7 -0.011 0.005 1000 -1000 -0.049 -1000
PLK1 signaling events 0.0047 2 253 85 -0.023 0.035 1000 -1000 -0.062 -1000
S1P5 pathway 0.0047 2 39 17 -0.015 0.025 1000 -1000 -0.065 -1000
E-cadherin signaling in keratinocytes 0.0047 2 96 43 -0.018 0.047 1000 -1000 -0.083 -1000
E-cadherin signaling events 0.0047 2 13 5 -0.006 0.012 1000 -1000 -0.052 -1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling 0.0024 1 31 23 -0.015 0.05 1000 -1000 -0.093 -1000
Canonical NF-kappaB pathway 0.0024 1 68 39 -0.029 0.088 1000 -1000 -0.12 -1000
Insulin-mediated glucose transport 0.0024 1 34 32 -0.077 0.048 1000 -1000 -0.084 -1000
Signaling events mediated by HDAC Class I 0.0024 1 146 104 -0.13 0.061 1000 -1000 -0.083 -1000
FoxO family signaling 0.0024 1 88 64 -0.024 0.16 1000 -1000 -0.097 -1000
Atypical NF-kappaB pathway 0.0024 1 34 31 -0.006 0.049 1000 -1000 -0.061 -1000
E-cadherin signaling in the nascent adherens junction 0.0024 1 129 76 -0.016 0.06 1000 -1000 -0.1 -1000
Alternative NF-kappaB pathway 0.0024 1 15 13 -0.004 0.014 1000 -1000 -0.081 -1000
PLK2 and PLK4 events 0.0000 0 2 3 0.012 0.024 1000 -1000 -0.026 -1000
mTOR signaling pathway 0.0000 0 37 53 -0.003 0.034 1000 -1000 -0.073 -1000
Class I PI3K signaling events mediated by Akt 0.0000 0 13 68 -0.12 0.063 1000 -1000 -0.075 -1000
Sumoylation by RanBP2 regulates transcriptional repression 0.0000 0 0 27 0 0.032 1000 -1000 -0.075 -1000
Arf1 pathway 0.0000 0 10 54 -0.005 0.036 1000 -1000 -0.048 -1000
Total NA 2655 152051 7203 -28 -990 131000 -131000 -12 -131000
TCGA08_retinoblastoma

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDKN2B -0.1 0.23 -10000 0 -0.56 85 85
CDKN2C 0.017 0.14 -10000 0 -0.75 12 12
CDKN2A -0.35 0.4 -10000 0 -0.78 194 194
CCND2 0.13 0.13 0.23 241 -0.15 1 242
RB1 -0.14 0.14 -10000 0 -0.24 240 240
CDK4 0.15 0.15 0.26 245 -10000 0 245
CDK6 0.14 0.15 0.25 240 -10000 0 240
G1/S progression 0.13 0.15 0.24 241 -10000 0 241
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 0.012 0.04 -9999 0 -0.82 1 1
CCL5 -0.1 0.29 -9999 0 -0.81 60 60
SDCBP 0.014 0 -9999 0 -10000 0 0
FGFR/FGF2/Syndecan-1 -0.45 0.18 -9999 0 -0.55 301 301
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 -0.42 0.17 -9999 0 -0.52 301 301
Syndecan-1/Syntenin -0.42 0.17 -9999 0 -0.52 301 301
MAPK3 -0.37 0.16 -9999 0 -0.46 301 301
HGF/MET -0.024 0.11 -9999 0 -0.51 20 20
TGFB1/TGF beta receptor Type II 0.012 0.04 -9999 0 -0.82 1 1
BSG 0.014 0 -9999 0 -10000 0 0
keratinocyte migration -0.42 0.17 -9999 0 -0.51 301 301
Syndecan-1/RANTES -0.49 0.24 -9999 0 -0.59 316 316
Syndecan-1/CD147 -0.4 0.17 -9999 0 -0.49 301 301
Syndecan-1/Syntenin/PIP2 -0.41 0.16 -9999 0 -0.5 301 301
LAMA5 0.014 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.4 0.16 -9999 0 -0.49 301 301
MMP7 -0.13 0.3 -9999 0 -0.76 79 79
HGF -0.012 0.13 -9999 0 -0.66 16 16
Syndecan-1/CASK -0.43 0.17 -9999 0 -0.52 301 301
Syndecan-1/HGF/MET -0.42 0.18 -9999 0 -0.51 308 308
regulation of cell adhesion -0.36 0.15 -9999 0 -0.59 56 56
HPSE 0.008 0.058 -9999 0 -0.59 4 4
positive regulation of cell migration -0.45 0.18 -9999 0 -0.55 301 301
SDC1 -0.45 0.18 -9999 0 -0.55 301 301
Syndecan-1/Collagen -0.45 0.18 -9999 0 -0.55 301 301
PPIB 0.014 0 -9999 0 -10000 0 0
MET 0.006 0.075 -9999 0 -0.76 4 4
PRKACA 0.014 0 -9999 0 -10000 0 0
MMP9 -0.59 0.37 -9999 0 -0.82 309 309
MAPK1 -0.37 0.16 -9999 0 -0.46 283 283
homophilic cell adhesion -0.44 0.17 -9999 0 -0.54 301 301
MMP1 -0.72 0.27 -9999 0 -0.82 375 375
Syndecan-4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 -0.24 0.23 -9999 0 -0.47 207 207
Syndecan-4/Syndesmos -0.4 0.26 -9999 0 -0.63 206 206
positive regulation of JNK cascade -0.41 0.22 -9999 0 -0.58 231 231
Syndecan-4/ADAM12 -0.71 0.36 -9999 0 -0.94 282 282
CCL5 -0.1 0.29 -9999 0 -0.81 60 60
Rac1/GDP 0 0 -9999 0 -10000 0 0
DNM2 0.014 0 -9999 0 -10000 0 0
ITGA5 -0.26 0.39 -9999 0 -0.82 137 137
SDCBP 0.014 0 -9999 0 -10000 0 0
PLG 0 0.079 -9999 0 -0.8 4 4
ADAM12 -0.6 0.36 -9999 0 -0.82 316 316
mol:GTP 0 0 -9999 0 -10000 0 0
NUDT16L1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
Syndecan-4/PKC alpha -0.12 0.063 -9999 0 -10000 0 0
Syndecan-4/Laminin alpha1 -0.57 0.33 -9999 0 -0.79 256 256
Syndecan-4/CXCL12/CXCR4 -0.43 0.26 -9999 0 -0.62 231 231
Syndecan-4/Laminin alpha3 -0.52 0.34 -9999 0 -0.77 239 239
MDK -0.009 0.14 -9999 0 -0.8 12 12
Syndecan-4/FZD7 -0.41 0.26 -9999 0 -0.63 208 208
Syndecan-4/Midkine -0.41 0.26 -9999 0 -0.64 212 212
FZD7 -0.003 0.12 -9999 0 -0.79 9 9
Syndecan-4/FGFR1/FGF -0.39 0.23 -9999 0 -0.59 213 213
THBS1 -0.014 0.14 -9999 0 -0.76 15 15
integrin-mediated signaling pathway -0.46 0.31 -9999 0 -0.7 223 223
positive regulation of MAPKKK cascade -0.41 0.22 -9999 0 -0.58 231 231
Syndecan-4/TACI -0.45 0.29 -9999 0 -0.67 227 227
CXCR4 -0.014 0.15 -9999 0 -0.82 14 14
cell adhesion -0.2 0.22 -9999 0 -0.4 202 202
Syndecan-4/Dynamin -0.4 0.26 -9999 0 -0.63 206 206
Syndecan-4/TSP1 -0.42 0.28 -9999 0 -0.65 207 207
Syndecan-4/GIPC -0.4 0.26 -9999 0 -0.63 206 206
Syndecan-4/RANTES -0.46 0.3 -9999 0 -0.69 230 230
ITGB1 0.012 0.04 -9999 0 -0.82 1 1
LAMA1 -0.31 0.4 -9999 0 -0.81 167 167
LAMA3 -0.22 0.38 -9999 0 -0.82 122 122
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.095 0.068 -9999 0 -0.78 1 1
Syndecan-4/alpha-Actinin -0.4 0.26 -9999 0 -0.63 206 206
TFPI 0.008 0.064 -9999 0 -0.74 3 3
F2 -0.083 0.25 -9999 0 -0.82 42 42
alpha5/beta1 Integrin -0.2 0.29 -9999 0 -0.63 138 138
positive regulation of cell adhesion -0.64 0.37 -9999 0 -0.86 277 277
ACTN1 0.012 0.04 -9999 0 -0.82 1 1
TNC -0.15 0.33 -9999 0 -0.82 82 82
Syndecan-4/CXCL12 -0.43 0.26 -9999 0 -0.64 226 226
FGF6 0.003 0.005 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CXCL12 -0.051 0.19 -9999 0 -0.6 45 45
TNFRSF13B -0.076 0.25 -9999 0 -0.81 45 45
FGF2 -0.01 0.12 -9999 0 -0.65 15 15
FGFR1 0.004 0.09 -9999 0 -0.82 5 5
Syndecan-4/PI-4-5-P2 -0.41 0.26 -9999 0 -0.63 206 206
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.38 0.42 -9999 0 -0.81 207 207
cell migration -0.04 0.02 -9999 0 -10000 0 0
PRKCD 0.027 0.011 -9999 0 -10000 0 0
vasculogenesis -0.4 0.26 -9999 0 -0.62 207 207
SDC4 -0.43 0.28 -9999 0 -0.67 206 206
Syndecan-4/Tenascin C -0.48 0.33 -9999 0 -0.74 223 223
Syndecan-4/PI-4-5-P2/PKC alpha -0.094 0.049 -9999 0 -10000 0 0
Syndecan-4/Syntenin -0.4 0.26 -9999 0 -0.63 206 206
MMP9 -0.59 0.37 -9999 0 -0.81 309 309
Rac1/GTP -0.21 0.22 -9999 0 -0.41 202 202
cytoskeleton organization -0.38 0.25 -9999 0 -0.6 206 206
GIPC1 0.014 0 -9999 0 -10000 0 0
Syndecan-4/TFPI -0.4 0.26 -9999 0 -0.63 207 207
IL4-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -1.1 0.49 -10000 0 -1.4 262 262
STAT6 (cleaved dimer) -1.1 0.52 -10000 0 -1.4 312 312
IGHG1 -0.33 0.12 -10000 0 -0.46 91 91
IGHG3 -1 0.47 -10000 0 -1.3 301 301
AKT1 -0.4 0.18 -10000 0 -0.72 35 35
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1 -0.29 0.15 -10000 0 -0.71 21 21
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1 -0.42 0.17 -10000 0 -0.71 31 31
THY1 -1.1 0.55 -10000 0 -1.5 286 286
MYB -0.054 0.19 -10000 0 -0.6 46 46
HMGA1 0.014 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3 -0.52 0.22 -10000 0 -0.7 146 146
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP -0.42 0.17 -10000 0 -0.7 32 32
SP1 0.012 0.012 -10000 0 -10000 0 0
INPP5D 0.011 0.041 -10000 0 -0.59 2 2
SOCS5 0.036 0.01 -10000 0 -10000 0 0
STAT6 (dimer)/ETS1 -1.1 0.51 -10000 0 -1.4 291 291
SOCS1 -0.65 0.26 -10000 0 -0.83 231 231
SOCS3 -0.43 0.19 -10000 0 -0.82 27 27
FCER2 -0.76 0.35 -10000 0 -1 189 189
PARP14 0.008 0.07 -10000 0 -0.82 3 3
CCL17 -1.1 0.51 -10000 0 -1.4 273 273
GRB2 0.014 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP -0.33 0.15 -10000 0 -0.72 18 18
T cell proliferation -1.1 0.53 -10000 0 -1.4 286 286
IL4R/JAK1 -1.1 0.5 -10000 0 -1.4 282 282
EGR2 -1.1 0.5 -10000 0 -1.4 277 277
JAK2 -0.032 0.034 -10000 0 -0.63 1 1
JAK3 0 0.13 -10000 0 -0.82 11 11
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
JAK1 0.001 0.005 -10000 0 -10000 0 0
COL1A2 -0.53 0.36 -10000 0 -0.94 183 183
CCL26 -1.1 0.5 -10000 0 -1.4 270 270
IL4R -1.2 0.54 -10000 0 -1.5 281 281
PTPN6 0.035 0.007 -10000 0 -10000 0 0
IL13RA2 -1.1 0.52 -10000 0 -1.5 267 267
IL13RA1 -0.031 0.018 -10000 0 -10000 0 0
IRF4 -0.28 0.33 -10000 0 -0.92 75 75
ARG1 -0.52 0.55 -10000 0 -1.3 120 120
CBL -0.48 0.21 -10000 0 -0.85 43 43
GTF3A 0.006 0.018 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
IL13RA1/JAK2 -0.044 0.03 -10000 0 -0.47 1 1
IRF4/BCL6 -0.25 0.3 -10000 0 -0.86 74 74
CD40LG -0.059 0.21 -10000 0 -0.61 53 53
MAPK14 -0.48 0.21 -10000 0 -0.87 40 40
mitosis -0.39 0.17 -10000 0 -0.68 35 35
STAT6 -1.3 0.69 -10000 0 -1.7 293 293
SPI1 -0.014 0.068 -10000 0 -0.73 2 2
RPS6KB1 -0.37 0.16 -10000 0 -0.68 25 25
STAT6 (dimer) -1.3 0.7 -10000 0 -1.7 293 293
STAT6 (dimer)/PARP14 -1.2 0.59 -10000 0 -1.5 289 289
mast cell activation 0.021 0.007 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2 -0.4 0.18 -10000 0 -0.73 36 36
FRAP1 -0.4 0.18 -10000 0 -0.72 35 35
LTA -1.1 0.5 -10000 0 -1.4 287 287
FES 0.014 0 -10000 0 -10000 0 0
T-helper 1 cell differentiation 1.3 0.62 1.6 295 -10000 0 295
CCL11 -1.2 0.48 -10000 0 -1.4 309 309
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES -0.39 0.18 -10000 0 -0.72 35 35
IL2RG -0.006 0.15 -10000 0 -0.8 14 14
IL10 -1.1 0.5 -10000 0 -1.4 282 282
IRS1 0.011 0.041 -10000 0 -0.59 2 2
IRS2 0.011 0.041 -10000 0 -0.59 2 2
IL4 -0.21 0.069 -10000 0 -10000 0 0
IL5 -1.1 0.49 -10000 0 -1.4 282 282
IL4/IL4R/JAK1/IL13RA1/JAK2 -0.78 0.3 -10000 0 -0.98 267 267
COL1A1 -0.7 0.36 -10000 0 -0.96 271 271
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
IL4/IL4R/JAK1 -1.1 0.53 -10000 0 -1.5 268 268
IL2R gamma/JAK3 -0.013 0.16 -10000 0 -0.67 23 23
TFF3 -1.3 0.58 -10000 0 -1.6 315 315
ALOX15 -1.2 0.53 -10000 0 -1.5 287 287
MYBL1 -0.006 0.13 -10000 0 -0.82 10 10
T-helper 2 cell differentiation -0.8 0.32 -10000 0 -0.99 286 286
SHC1 0.014 0 -10000 0 -10000 0 0
CEBPB -0.01 0.046 -10000 0 -10000 0 0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2 -0.4 0.17 -10000 0 -0.7 28 28
mol:PI-3-4-5-P3 -0.4 0.18 -10000 0 -0.72 35 35
PI3K -0.42 0.19 -10000 0 -0.77 35 35
DOK2 0.007 0.07 -10000 0 -0.7 4 4
ETS1 0.029 0.071 -10000 0 -0.8 3 3
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2 -0.31 0.14 -10000 0 -0.69 18 18
ITGB3 -1.1 0.5 -10000 0 -1.4 282 282
PIGR -1.4 0.6 -10000 0 -1.7 323 323
IGHE 0.054 0.046 0.27 4 -10000 0 4
MAPKKK cascade -0.31 0.14 -10000 0 -0.68 18 18
BCL6 0.013 0.002 -10000 0 -10000 0 0
OPRM1 -1.1 0.49 -10000 0 -1.4 278 278
RETNLB -1.1 0.5 -10000 0 -1.4 280 280
SELP -1.2 0.54 -10000 0 -1.5 290 290
AICDA -1.1 0.48 -10000 0 -1.3 289 289
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 -0.7 0.48 -9999 0 -1.2 131 131
HDAC7 0.014 0.003 -9999 0 -10000 0 0
HIF1A/ARNT/Cbp/p300/Src-1 -0.48 0.32 -9999 0 -0.88 74 74
SMAD4 0.014 0.029 -9999 0 -0.59 1 1
ID2 -0.7 0.48 -9999 0 -1.2 139 139
AP1 -0.056 0.14 -9999 0 -0.42 57 57
ABCG2 -0.7 0.48 -9999 0 -1.2 147 147
HIF1A -0.083 0.054 -9999 0 -10000 0 0
TFF3 -0.83 0.54 -9999 0 -1.3 199 199
GATA2 0.006 0.085 -9999 0 -0.77 5 5
AKT1 -0.086 0.063 -9999 0 -10000 0 0
response to hypoxia -0.11 0.065 -9999 0 -10000 0 0
MCL1 -0.7 0.48 -9999 0 -1.2 146 146
NDRG1 -0.7 0.48 -9999 0 -1.2 138 138
SERPINE1 -0.93 0.55 -9999 0 -1.4 220 220
FECH -0.7 0.48 -9999 0 -1.2 146 146
FURIN -0.7 0.48 -9999 0 -1.2 129 129
NCOA2 -0.024 0.15 -9999 0 -0.59 26 26
EP300 -0.091 0.095 -9999 0 -0.44 4 4
HMOX1 -0.7 0.48 -9999 0 -1.2 146 146
BHLHE40 -0.7 0.48 -9999 0 -1.2 136 136
BHLHE41 -0.71 0.49 -9999 0 -1.2 140 140
HIF1A/ARNT/SMAD3/SMAD4/SP1 -0.068 0.057 -9999 0 -10000 0 0
ENG -0.044 0.072 -9999 0 -10000 0 0
JUN 0.014 0.001 -9999 0 -10000 0 0
RORA -0.7 0.49 -9999 0 -1.2 146 146
ABCB1 -0.19 0.31 -9999 0 -1.4 24 24
TFRC -0.72 0.48 -9999 0 -1.2 148 148
CXCR4 -0.71 0.49 -9999 0 -1.2 141 141
TF -0.88 0.54 -9999 0 -1.3 225 225
CITED2 -0.7 0.48 -9999 0 -1.2 146 146
HIF1A/ARNT -0.81 0.6 -9999 0 -1.4 187 187
LDHA -0.069 0.045 -9999 0 -10000 0 0
ETS1 -0.7 0.48 -9999 0 -1.2 138 138
PGK1 -0.7 0.48 -9999 0 -1.2 140 140
NOS2 -0.76 0.5 -9999 0 -1.3 166 166
ITGB2 -0.71 0.48 -9999 0 -1.2 142 142
ALDOA -0.7 0.48 -9999 0 -1.2 146 146
Cbp/p300/CITED2 -0.68 0.49 -9999 0 -1.3 116 116
FOS -0.067 0.21 -9999 0 -0.59 57 57
HK2 -0.7 0.48 -9999 0 -1.2 146 146
SP1 0.022 0.005 -9999 0 -10000 0 0
GCK -0.18 0.22 -9999 0 -0.82 31 31
HK1 -0.7 0.48 -9999 0 -1.2 146 146
NPM1 -0.7 0.48 -9999 0 -1.2 138 138
EGLN1 -0.7 0.48 -9999 0 -1.2 146 146
CREB1 0.022 0 -9999 0 -10000 0 0
PGM1 -0.7 0.48 -9999 0 -1.2 146 146
SMAD3 0.014 0.029 -9999 0 -0.59 1 1
EDN1 -0.091 0.16 -9999 0 -1.4 3 3
IGFBP1 -0.72 0.49 -9999 0 -1.3 143 143
VEGFA -0.4 0.29 -9999 0 -0.98 16 16
HIF1A/JAB1 -0.042 0.028 -9999 0 -10000 0 0
CP -0.82 0.54 -9999 0 -1.3 184 184
CXCL12 -0.73 0.5 -9999 0 -1.3 143 143
COPS5 0.013 0.005 -9999 0 -10000 0 0
SMAD3/SMAD4 -0.002 0.029 -9999 0 -0.42 2 2
BNIP3 -0.7 0.48 -9999 0 -1.2 138 138
EGLN3 -0.72 0.5 -9999 0 -1.3 144 144
CA9 -1 0.5 -9999 0 -1.4 271 271
TERT -0.77 0.52 -9999 0 -1.3 172 172
ENO1 -0.7 0.48 -9999 0 -1.2 138 138
PFKL -0.7 0.48 -9999 0 -1.2 146 146
NCOA1 0.013 0.002 -9999 0 -10000 0 0
ADM -0.7 0.48 -9999 0 -1.2 147 147
ARNT -0.083 0.053 -9999 0 -10000 0 0
HNF4A -0.068 0.24 -9999 0 -0.82 40 40
ADFP -0.71 0.48 -9999 0 -1.2 183 183
SLC2A1 -0.41 0.3 -9999 0 -1 19 19
LEP -0.75 0.52 -9999 0 -1.3 161 161
HIF1A/ARNT/Cbp/p300 -0.5 0.33 -9999 0 -0.88 94 94
EPO -0.4 0.31 -9999 0 -0.99 51 51
CREBBP -0.09 0.09 -9999 0 -0.37 2 2
HIF1A/ARNT/Cbp/p300/HDAC7 -0.47 0.33 -9999 0 -0.92 58 58
PFKFB3 -0.7 0.48 -9999 0 -1.2 146 146
NT5E -0.77 0.53 -9999 0 -1.3 152 152
Osteopontin-mediated 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
IKK alpha homodimer -0.26 0.28 -9999 0 -0.58 117 117
NF kappa B1 p50/RelA/I kappa B alpha -0.27 0.24 -9999 0 -0.58 117 117
alphaV/beta3 Integrin/Osteopontin/Src -0.33 0.32 -9999 0 -0.64 216 216
AP1 -0.34 0.3 -9999 0 -0.82 82 82
ILK -0.27 0.29 -9999 0 -0.58 129 129
bone resorption -0.21 0.25 -9999 0 -0.72 18 18
PTK2B 0.012 0.029 -9999 0 -0.59 1 1
PYK2/p130Cas -0.25 0.25 -9999 0 -0.53 117 117
ITGAV 0.004 0.077 -9999 0 -0.77 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
CD44/Rho Family GTPase/ROCK2 -0.008 0.058 -9999 0 -0.43 8 8
alphaV/beta3 Integrin/Osteopontin -0.31 0.3 -9999 0 -0.59 222 222
MAP3K1 -0.27 0.29 -9999 0 -0.54 221 221
JUN 0.013 0.002 -9999 0 -10000 0 0
MAPK3 -0.28 0.29 -9999 0 -0.62 129 129
MAPK1 -0.28 0.29 -9999 0 -0.64 117 117
Rac1/GDP 0 0 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.26 0.28 -9999 0 -0.57 132 132
ITGB3 -0.025 0.16 -9999 0 -0.75 20 20
NFKBIA -0.28 0.29 -9999 0 -0.64 117 117
FOS -0.069 0.21 -9999 0 -0.59 57 57
CD44 0.012 0.029 -9999 0 -0.59 1 1
CHUK 0.014 0 -9999 0 -10000 0 0
PLAU -0.43 0.4 -9999 0 -0.9 138 138
NF kappa B1 p50/RelA -0.29 0.25 -9999 0 -0.62 117 117
BCAR1 0.014 0 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
alphaV beta3 Integrin -0.034 0.14 -9999 0 -0.6 23 23
mol:GDP 0 0 -9999 0 -10000 0 0
SYK -0.27 0.29 -9999 0 -0.53 221 221
VAV3 -0.27 0.29 -9999 0 -0.57 143 143
MAP3K14 -0.29 0.3 -9999 0 -0.55 221 221
ROCK2 0.004 0.077 -9999 0 -0.59 7 7
SPP1 -0.41 0.42 -9999 0 -0.82 214 214
RAC1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.26 0.25 -9999 0 -0.61 65 65
MMP2 -0.3 0.32 -9999 0 -0.81 87 87
IL23-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CCL2 -0.57 0.44 -10000 0 -1.2 112 112
IL23A -0.56 0.43 -10000 0 -1.2 90 90
NF kappa B1 p50/RelA/I kappa B alpha -0.56 0.42 -10000 0 -1.1 112 112
positive regulation of T cell mediated cytotoxicity -0.63 0.49 -10000 0 -1.2 127 127
ITGA3 -0.56 0.42 -10000 0 -1.1 104 104
IL17F -0.38 0.27 -10000 0 -0.74 80 80
IL12B -0.081 0.25 -10000 0 -0.86 39 39
STAT1 (dimer) -0.62 0.48 -10000 0 -1.2 127 127
CD4 -0.55 0.41 -10000 0 -1.1 110 110
IL23 -0.57 0.43 -10000 0 -1.2 101 101
IL23R -0.085 0.096 -10000 0 -0.7 6 6
IL1B -0.59 0.45 -10000 0 -1.2 109 109
T-helper cell lineage commitment 0 0 -10000 0 -10000 0 0
IL24 -0.74 0.44 -10000 0 -1.1 182 182
TYK2 -0.005 0.043 -10000 0 -0.86 1 1
STAT4 -0.002 0.11 -10000 0 -0.79 8 8
STAT3 0.014 0 -10000 0 -10000 0 0
IL18RAP -0.007 0.12 -10000 0 -0.69 12 12
IL12RB1 -0.08 0.24 -10000 0 -0.84 39 39
PIK3CA 0.014 0 -10000 0 -10000 0 0
IL12Rbeta1/TYK2 -0.069 0.19 -10000 0 -0.66 40 40
IL23R/JAK2 -0.1 0.1 -10000 0 -0.74 4 4
positive regulation of chronic inflammatory response -0.63 0.49 -10000 0 -1.2 127 127
natural killer cell activation 0.008 0.008 0.06 6 -10000 0 6
JAK2 0.001 0.031 -10000 0 -0.59 1 1
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
NFKB1 0.01 0.003 -10000 0 -10000 0 0
RELA 0.01 0.003 -10000 0 -10000 0 0
positive regulation of dendritic cell antigen processing and presentation -0.55 0.4 -10000 0 -1.1 102 102
ALOX12B -0.65 0.48 -10000 0 -1.2 144 144
CXCL1 -0.58 0.45 -10000 0 -1.2 109 109
T cell proliferation -0.63 0.49 -10000 0 -1.2 127 127
NFKBIA 0.01 0.003 -10000 0 -10000 0 0
IL17A -0.29 0.22 -10000 0 -0.6 44 44
PI3K -0.58 0.43 -10000 0 -1.1 125 125
IFNG -0.032 0.046 0.13 5 -0.11 77 82
STAT3 (dimer) -0.54 0.4 -10000 0 -1.1 112 112
IL18R1 0.007 0.065 -10000 0 -0.75 3 3
IL23/IL23R/JAK2/TYK2/SOCS3 -0.33 0.25 -10000 0 -0.79 44 44
IL18/IL18R -0.004 0.12 -10000 0 -0.64 8 8
macrophage activation -0.028 0.015 -10000 0 -0.045 67 67
TNF -0.58 0.45 -10000 0 -1.2 101 101
STAT3/STAT4 -0.58 0.43 -10000 0 -1.1 124 124
STAT4 (dimer) -0.6 0.47 -10000 0 -1.2 113 113
IL18 -0.009 0.11 -10000 0 -0.59 15 15
IL19 -0.69 0.53 -10000 0 -1.3 161 161
STAT5A (dimer) -0.6 0.47 -10000 0 -1.2 120 120
STAT1 -0.039 0.2 -10000 0 -0.81 27 27
SOCS3 0.012 0.029 -10000 0 -0.59 1 1
CXCL9 -0.7 0.47 -10000 0 -1.2 173 173
MPO -0.56 0.43 -10000 0 -1.2 98 98
positive regulation of humoral immune response -0.63 0.49 -10000 0 -1.2 127 127
IL23/IL23R/JAK2/TYK2 -0.65 0.54 -10000 0 -1.3 120 120
IL6 -0.59 0.47 -10000 0 -1.2 108 108
STAT5A 0.014 0 -10000 0 -10000 0 0
IL2 0.006 0.041 -10000 0 -0.81 1 1
positive regulation of tyrosine phosphorylation of STAT protein 0.008 0.008 0.06 6 -10000 0 6
CD3E -0.55 0.42 -10000 0 -1.1 98 98
keratinocyte proliferation -0.63 0.49 -10000 0 -1.2 127 127
NOS2 -0.6 0.45 -10000 0 -1.2 120 120
amb2 Integrin signaling

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
alphaM/beta2 Integrin/proMMP-2 -0.15 0.29 -9999 0 -0.64 95 95
alphaM/beta2 Integrin/GPIbA -0.078 0.22 -9999 0 -0.7 42 42
alphaM/beta2 Integrin/proMMP-9 -0.45 0.32 -9999 0 -0.61 311 311
PLAUR -0.031 0.19 -9999 0 -0.82 23 23
HMGB1 0.01 0.017 -9999 0 -10000 0 0
alphaM/beta2 Integrin/Talin -0.062 0.2 -9999 0 -0.68 36 36
AGER 0.003 0.082 -9999 0 -0.82 4 4
RAP1A 0.014 0 -9999 0 -10000 0 0
SELPLG 0.014 0 -9999 0 -10000 0 0
mol:LDL 0 0 -9999 0 -10000 0 0
alphaM/beta2 Integrin/RAGE/HMGB1 -0.078 0.2 -9999 0 -0.64 37 37
mol:GTP 0 0 -9999 0 -10000 0 0
MMP9 -0.59 0.37 -9999 0 -0.82 309 309
CYR61 0.005 0.081 -9999 0 -0.73 5 5
TLN1 0.01 0.057 -9999 0 -0.82 2 2
Rap1/GTP -0.17 0.16 -9999 0 -0.51 45 45
RHOA 0.014 0 -9999 0 -10000 0 0
P-selectin oligomer -0.095 0.23 -9999 0 -0.59 76 76
MYH2 -0.38 0.25 -9999 0 -0.58 227 227
MST1R 0.002 0.082 -9999 0 -0.59 8 8
leukocyte activation during inflammatory response -0.079 0.2 -9999 0 -0.56 57 57
APOB -0.02 0.16 -9999 0 -0.8 16 16
mol:GDP 0 0 -9999 0 -10000 0 0
complement component iC3b receptor activity 0 0 -9999 0 -10000 0 0
MMP2 -0.12 0.31 -9999 0 -0.82 69 69
JAM3 0.012 0.04 -9999 0 -0.82 1 1
GP1BA -0.016 0.15 -9999 0 -0.75 16 16
alphaM/beta2 Integrin/CTGF -0.067 0.2 -9999 0 -0.66 39 39
alphaM/beta2 Integrin -0.2 0.2 -9999 0 -0.44 140 140
JAM3 homodimer 0.012 0.04 -9999 0 -0.82 1 1
ICAM2 0.009 0.058 -9999 0 -0.67 3 3
ICAM1 -0.028 0.18 -9999 0 -0.82 21 21
phagocytosis triggered by activation of immune response cell surface activating receptor -0.2 0.2 -9999 0 -0.43 140 140
cell adhesion -0.077 0.22 -9999 0 -0.69 42 42
NFKB1 -0.038 0.24 -9999 0 -0.84 19 19
THY1 -0.23 0.38 -9999 0 -0.82 123 123
RhoA/GDP 0 0 -9999 0 -10000 0 0
Lipoprotein(a) -0.033 0.13 -9999 0 -0.54 26 26
alphaM/beta2 Integrin/LRP/tPA -0.068 0.2 -9999 0 -0.61 45 45
IL6 -0.069 0.3 -9999 0 -0.79 54 54
ITGB2 -0.017 0.15 -9999 0 -0.8 14 14
elevation of cytosolic calcium ion concentration -0.29 0.33 -9999 0 -0.58 212 212
alphaM/beta2 Integrin/JAM2/JAM3 -0.062 0.19 -9999 0 -0.64 35 35
JAM2 0.001 0.087 -9999 0 -0.59 9 9
alphaM/beta2 Integrin/ICAM1 -0.082 0.22 -9999 0 -0.64 49 49
alphaM/beta2 Integrin/uPA/Plg -0.28 0.3 -9999 0 -0.55 213 213
RhoA/GTP -0.25 0.22 -9999 0 -0.52 132 132
positive regulation of phagocytosis -0.16 0.18 -9999 0 -0.58 43 43
Ron/MSP -0.014 0.083 -9999 0 -0.47 13 13
alphaM/beta2 Integrin/uPAR/uPA -0.3 0.34 -9999 0 -0.59 212 212
alphaM/beta2 Integrin/uPAR -0.088 0.25 -9999 0 -0.71 50 50
PLAU -0.36 0.41 -9999 0 -0.82 188 188
PLAT -0.01 0.14 -9999 0 -0.82 12 12
actin filament polymerization -0.37 0.23 -9999 0 -0.55 227 227
MST1 0.005 0.081 -9999 0 -0.73 5 5
alphaM/beta2 Integrin/lipoprotein(a) -0.08 0.21 -9999 0 -0.57 57 57
TNF -0.042 0.26 -9999 0 -0.79 32 32
RAP1B 0.012 0.04 -9999 0 -0.82 1 1
alphaM/beta2 Integrin/uPA -0.3 0.32 -9999 0 -0.6 209 209
fibrinolysis -0.28 0.3 -9999 0 -0.55 213 213
HCK 0.007 0.07 -9999 0 -0.7 4 4
dendritic cell antigen processing and presentation -0.2 0.2 -9999 0 -0.43 140 140
VTN -0.045 0.21 -9999 0 -0.82 30 30
alphaM/beta2 Integrin/CYR61 -0.065 0.2 -9999 0 -0.68 38 38
LPA -0.012 0.12 -9999 0 -0.82 10 10
LRP1 0.012 0.029 -9999 0 -0.59 1 1
cell migration -0.48 0.37 -9999 0 -0.65 316 316
FN1 -0.39 0.42 -9999 0 -0.82 207 207
alphaM/beta2 Integrin/Thy1 -0.21 0.33 -9999 0 -0.64 138 138
MPO -0.007 0.11 -9999 0 -0.64 13 13
KNG1 -0.022 0.15 -9999 0 -0.82 14 14
RAP1/GDP -0.001 0.027 -9999 0 -0.55 1 1
ROCK1 -0.23 0.21 -9999 0 -0.5 124 124
ELA2 0 0 -9999 0 -10000 0 0
PLG -0.006 0.079 -9999 0 -0.82 4 4
CTGF 0.002 0.087 -9999 0 -0.62 8 8
alphaM/beta2 Integrin/Hck -0.064 0.2 -9999 0 -0.69 36 36
ITGAM -0.05 0.21 -9999 0 -0.81 31 31
alphaM/beta2 Integrin/P-Selectin/PSGL1 -0.11 0.21 -9999 0 -0.66 34 34
HP -0.24 0.3 -9999 0 -0.6 174 174
leukocyte adhesion -0.18 0.26 -9999 0 -0.79 40 40
SELP -0.095 0.23 -9999 0 -0.59 76 76
Glypican 2 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
MDK -0.009 0.14 -9999 0 -0.8 12 12
GPC2 -0.13 0.32 -9999 0 -0.82 75 75
GPC2/Midkine -0.13 0.26 -9999 0 -0.65 83 83
neuron projection morphogenesis -0.13 0.26 -9999 0 -0.65 83 83
Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin -0.27 0.32 -9999 0 -0.58 210 210
EPHB2 -0.15 0.33 -9999 0 -0.82 84 84
Syndecan-2/TACI -0.062 0.2 -9999 0 -0.55 63 63
LAMA1 -0.31 0.4 -9999 0 -0.81 167 167
Syndecan-2/alpha2 ITGB1 -0.15 0.23 -9999 0 -0.47 138 138
HRAS 0.012 0.04 -9999 0 -0.82 1 1
Syndecan-2/CASK -0.025 0.11 -9999 0 -0.55 19 19
ITGA5 -0.26 0.39 -9999 0 -0.82 137 137
BAX 0.015 0.12 -9999 0 -0.77 2 2
EPB41 0.014 0 -9999 0 -10000 0 0
positive regulation of cell-cell adhesion -0.022 0.1 -9999 0 -0.49 19 19
LAMA3 -0.22 0.38 -9999 0 -0.82 122 122
EZR 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
CAV2 0.009 0.058 -9999 0 -0.67 3 3
Syndecan-2/MMP2 -0.09 0.26 -9999 0 -0.61 77 77
RP11-540L11.1 0 0 -9999 0 -10000 0 0
alpha2 ITGB1 -0.002 0.037 -9999 0 -0.53 2 2
dendrite morphogenesis -0.11 0.25 -9999 0 -0.56 99 99
Syndecan-2/GM-CSF -0.3 0.3 -9999 0 -0.56 237 237
determination of left/right symmetry -0.007 0.13 -9999 0 -0.62 19 19
Syndecan-2/PKC delta 0.001 0.12 -9999 0 -0.54 19 19
GNB2L1 0.014 0 -9999 0 -10000 0 0
MAPK3 -0.27 0.28 -9999 0 -0.51 237 237
MAPK1 -0.27 0.28 -9999 0 -0.51 237 237
Syndecan-2/RACK1 -0.022 0.098 -9999 0 -0.46 20 20
NF1 0.014 0 -9999 0 -10000 0 0
FGFR/FGF/Syndecan-2 -0.007 0.13 -9999 0 -0.62 19 19
ITGA2 0.012 0.029 -9999 0 -0.59 1 1
MAPK8 0.006 0.13 -9999 0 -0.52 24 24
Syndecan-2/alpha2/beta1 Integrin -0.2 0.25 -9999 0 -0.49 171 171
Syndecan-2/Kininogen -0.033 0.16 -9999 0 -0.57 31 31
ITGB1 0.012 0.04 -9999 0 -0.82 1 1
SRC 0.017 0.1 -9999 0 -0.44 20 20
Syndecan-2/CASK/Protein 4.1 -0.022 0.1 -9999 0 -0.5 19 19
extracellular matrix organization 0 0.12 -9999 0 -0.56 19 19
actin cytoskeleton reorganization -0.27 0.31 -9999 0 -0.58 210 210
Syndecan-2/Caveolin-2/Ras -0.026 0.11 -9999 0 -0.5 21 21
Syndecan-2/Laminin alpha3 -0.16 0.28 -9999 0 -0.56 137 137
Syndecan-2/RasGAP -0.021 0.097 -9999 0 -0.46 20 20
alpha5/beta1 Integrin -0.2 0.29 -9999 0 -0.63 138 138
PRKCD 0.014 0 -9999 0 -10000 0 0
Syndecan-2 dimer -0.11 0.25 -9999 0 -0.56 99 99
GO:0007205 0.004 0.001 -9999 0 -10000 0 0
DNA mediated transformation 0 0 -9999 0 -10000 0 0
Syndecan-2/RasGAP/Src 0.024 0.1 -9999 0 -0.43 20 20
RHOA 0.014 0 -9999 0 -10000 0 0
SDCBP 0.014 0 -9999 0 -10000 0 0
TNFRSF13B -0.076 0.25 -9999 0 -0.81 45 45
RASA1 0.012 0.029 -9999 0 -0.59 1 1
alpha2/beta1 Integrin -0.002 0.037 -9999 0 -0.53 2 2
Syndecan-2/Synbindin 0.001 0.12 -9999 0 -0.54 19 19
TGFB1 0.012 0.04 -9999 0 -0.82 1 1
CASP3 0.012 0.11 -9999 0 -0.49 19 19
FN1 -0.39 0.42 -9999 0 -0.82 207 207
Syndecan-2/IL8 -0.12 0.26 -9999 0 -0.56 103 103
SDC2 -0.007 0.13 -9999 0 -0.63 19 19
KNG1 -0.022 0.15 -9999 0 -0.82 14 14
Syndecan-2/Neurofibromin 0.001 0.12 -9999 0 -0.54 19 19
TRAPPC4 0.014 0 -9999 0 -10000 0 0
CSF2 -0.44 0.41 -9999 0 -0.82 229 229
Syndecan-2/TGFB1 0 0.12 -9999 0 -0.56 19 19
Syndecan-2/Syntenin/PI-4-5-P2 -0.022 0.1 -9999 0 -0.5 19 19
Syndecan-2/Ezrin -0.022 0.1 -9999 0 -0.49 19 19
PRKACA 0.012 0.11 -9999 0 -0.49 19 19
angiogenesis -0.12 0.26 -9999 0 -0.56 103 103
MMP2 -0.12 0.31 -9999 0 -0.82 69 69
IL8 -0.16 0.34 -9999 0 -0.81 89 89
calcineurin-NFAT signaling pathway -0.062 0.2 -9999 0 -0.54 63 63
TCGA08_p53

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
CDKN2A -0.27 0.31 -10000 0 -0.6 194 194
TP53 -0.078 0.089 -10000 0 -0.43 4 4
Senescence -0.078 0.088 -10000 0 -0.42 4 4
Apoptosis -0.078 0.088 -10000 0 -0.42 4 4
Activated_Oncogenes 0 0 -10000 0 -10000 0 0
MDM2 0.14 0.15 0.3 194 -10000 0 194
MDM4 0.014 0 -10000 0 -10000 0 0
Endothelins

Figure S12.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S12.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 -0.19 0.31 -10000 0 -0.7 59 59
PTK2B 0.012 0.029 -10000 0 -0.59 1 1
mol:Ca2+ -0.065 0.21 -10000 0 -0.68 26 26
EDN1 -0.11 0.21 -10000 0 -0.4 45 45
EDN3 -0.24 0.29 -10000 0 -0.59 176 176
EDN2 -0.092 0.25 -10000 0 -0.67 65 65
HRAS/GDP -0.063 0.18 -10000 0 -0.55 13 13
ETA receptor/Endothelin-1/Gq/GTP/PLC beta -0.065 0.16 -10000 0 -0.39 32 32
ADCY4 -0.2 0.25 -10000 0 -0.61 73 73
ADCY5 -0.29 0.26 -10000 0 -0.61 120 120
ADCY6 -0.21 0.26 -10000 0 -0.61 78 78
ADCY7 -0.2 0.25 -10000 0 -0.61 73 73
ADCY1 -0.23 0.28 -10000 0 -0.64 88 88
ADCY2 -0.31 0.26 -10000 0 -0.62 136 136
ADCY3 -0.2 0.25 -10000 0 -0.61 73 73
ADCY8 -0.22 0.26 -10000 0 -0.63 82 82
ADCY9 -0.21 0.25 -10000 0 -0.61 73 73
arachidonic acid secretion -0.088 0.22 -10000 0 -0.53 51 51
ETB receptor/Endothelin-1/Gq/GTP -0.064 0.14 -10000 0 -0.43 27 27
GNAO1 0.006 0.075 -10000 0 -0.76 4 4
HRAS 0.01 0.04 -10000 0 -0.82 1 1
ETA receptor/Endothelin-1/G12/GTP -0.12 0.36 0.34 112 -0.66 63 175
ETA receptor/Endothelin-1/Gs/GTP -0.16 0.34 0.32 92 -0.62 85 177
mol:GTP 0 0.005 -10000 0 -10000 0 0
COL3A1 -0.45 0.5 -10000 0 -0.86 242 242
EDNRB -0.018 0.062 -10000 0 -0.59 3 3
response to oxidative stress 0 0 -10000 0 -10000 0 0
CYSLTR2 -0.25 0.4 -10000 0 -0.98 67 67
CYSLTR1 -0.24 0.36 -10000 0 -0.78 79 79
SLC9A1 -0.074 0.16 -10000 0 -0.34 25 25
mol:GDP -0.073 0.19 -10000 0 -0.47 33 33
SLC9A3 -0.2 0.33 -10000 0 -0.72 92 92
RAF1 -0.09 0.2 -10000 0 -0.51 40 40
JUN -0.049 0.18 -10000 0 -0.59 9 9
JAK2 -0.2 0.31 -10000 0 -0.68 64 64
mol:IP3 -0.084 0.17 -10000 0 -0.47 33 33
ETA receptor/Endothelin-1 -0.16 0.43 0.4 114 -0.72 77 191
PLCB1 0.011 0.03 -10000 0 -0.59 1 1
PLCB2 0.009 0.05 -10000 0 -0.71 2 2
ETA receptor/Endothelin-3 -0.24 0.25 -10000 0 -0.5 178 178
FOS -0.14 0.34 -10000 0 -0.94 59 59
Gai/GDP 0.012 0.079 -10000 0 -0.57 3 3
CRK 0.014 0.001 -10000 0 -10000 0 0
mol:Ca ++ -0.21 0.3 -10000 0 -0.69 69 69
BCAR1 0.014 0 -10000 0 -10000 0 0
PRKCB1 -0.082 0.16 -10000 0 -0.45 34 34
GNAQ 0.014 0.006 -10000 0 -10000 0 0
GNAZ -0.015 0.15 -10000 0 -0.75 16 16
GNAL -0.059 0.2 -10000 0 -0.59 51 51
Gs family/GDP -0.13 0.15 -10000 0 -0.46 45 45
ETA receptor/Endothelin-1/Gq/GTP -0.089 0.19 -10000 0 -0.45 43 43
MAPK14 -0.035 0.12 -10000 0 -0.6 5 5
TRPC6 -0.069 0.22 -10000 0 -0.72 25 25
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 0.012 0.029 -10000 0 -0.59 1 1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta -0.047 0.13 -10000 0 -0.38 24 24
ETB receptor/Endothelin-2 -0.083 0.19 -10000 0 -0.51 68 68
ETB receptor/Endothelin-3 -0.19 0.22 -10000 0 -0.44 178 178
ETB receptor/Endothelin-1 -0.088 0.18 -10000 0 -0.55 6 6
MAPK3 -0.12 0.3 -10000 0 -0.79 59 59
MAPK1 -0.12 0.3 -10000 0 -0.79 59 59
Rac1/GDP -0.061 0.18 -10000 0 -0.55 12 12
cAMP biosynthetic process -0.25 0.23 -10000 0 -0.58 95 95
MAPK8 -0.069 0.21 -10000 0 -0.61 23 23
SRC 0.014 0 -10000 0 -10000 0 0
ETB receptor/Endothelin-1/Gi/GTP -0.02 0.098 -10000 0 -0.41 8 8
p130Cas/CRK/Src/PYK2 -0.067 0.19 -10000 0 -0.56 17 17
mol:K + 0 0 -10000 0 -10000 0 0
G12/GDP -0.065 0.18 -10000 0 -0.56 15 15
COL1A2 -0.34 0.48 -10000 0 -0.86 184 184
EntrezGene:2778 0 0 -10000 0 -10000 0 0
ETA receptor/Endothelin-2 -0.13 0.23 -10000 0 -0.58 66 66
mol:DAG -0.084 0.17 -10000 0 -0.47 33 33
MAP2K2 -0.1 0.24 -10000 0 -0.6 53 53
MAP2K1 -0.1 0.24 -10000 0 -0.61 50 50
EDNRA -0.097 0.2 -10000 0 -0.97 3 3
positive regulation of muscle contraction -0.16 0.28 -10000 0 -0.66 48 48
Gq family/GDP -0.091 0.17 -10000 0 -0.5 33 33
HRAS/GTP -0.087 0.18 -10000 0 -0.46 38 38
PRKCH -0.073 0.16 -10000 0 -0.47 27 27
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.075 0.16 -10000 0 -0.47 28 28
PRKCB -0.082 0.18 -10000 0 -0.49 35 35
PRKCE -0.073 0.16 -10000 0 -0.46 28 28
PRKCD -0.074 0.16 -10000 0 -0.47 28 28
PRKCG -0.12 0.21 -10000 0 -0.52 63 63
regulation of vascular smooth muscle contraction -0.16 0.4 -10000 0 -1.1 59 59
PRKCQ -0.079 0.17 -10000 0 -0.49 32 32
PLA2G4A -0.097 0.24 -10000 0 -0.57 51 51
GNA14 -0.083 0.22 -10000 0 -0.59 68 68
GNA15 0.01 0.042 -10000 0 -0.59 2 2
GNA12 0.006 0.08 -10000 0 -0.82 4 4
GNA11 0.009 0.051 -10000 0 -0.59 3 3
Rac1/GTP -0.11 0.36 0.34 113 -0.65 59 172
MMP1 -0.56 0.24 -10000 0 -0.65 375 375
p75(NTR)-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Sortilin/TRAF6 -0.019 0.089 -9999 0 -0.44 18 18
Necdin/E2F1 -0.046 0.16 -9999 0 -0.6 32 32
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E -0.11 0.2 -9999 0 -0.48 83 83
NGF (dimer)/p75(NTR)/BEX1 -0.15 0.25 -9999 0 -0.57 105 105
NT-4/5 (dimer)/p75(NTR) -0.029 0.13 -9999 0 -0.58 21 21
IKBKB 0.014 0 -9999 0 -10000 0 0
AKT1 -0.069 0.2 -9999 0 -0.46 82 82
IKBKG 0.014 0 -9999 0 -10000 0 0
BDNF -0.042 0.2 -9999 0 -0.71 33 33
MGDIs/NGR/p75(NTR)/LINGO1 -0.086 0.22 -9999 0 -0.61 55 55
FURIN 0.014 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75(NTR)/Sortilin -0.072 0.17 -9999 0 -0.56 32 32
LINGO1 -0.053 0.23 -9999 0 -0.82 34 34
Sortilin/TRAF6/NRIF -0.011 0.054 -9999 0 -10000 0 0
proBDNF (dimer) -0.042 0.2 -9999 0 -0.71 33 33
NTRK1 -0.055 0.23 -9999 0 -0.82 35 35
RTN4R -0.018 0.16 -9999 0 -0.82 16 16
neuron apoptosis -0.062 0.19 -9999 0 -0.57 22 22
IRAK1 0.014 0 -9999 0 -10000 0 0
SHC1 -0.096 0.23 -9999 0 -0.55 82 82
ARHGDIA 0.014 0 -9999 0 -10000 0 0
RhoA/GTP 0 0 -9999 0 -10000 0 0
Gamma Secretase -0.001 0.022 -9999 0 -0.46 1 1
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1 -0.12 0.21 -9999 0 -0.51 83 83
MAGEH1 0.012 0.04 -9999 0 -0.82 1 1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin -0.13 0.22 -9999 0 -0.53 85 85
Mammalian IAPs/DIABLO -0.026 0.13 -9999 0 -0.59 19 19
proNGF (dimer) -0.14 0.31 -9999 0 -0.8 78 78
MAGED1 0.007 0.07 -9999 0 -0.7 4 4
APP 0.012 0.04 -9999 0 -0.82 1 1
NT-4/5 (dimer) 0.01 0.05 -9999 0 -0.7 2 2
ZNF274 0.014 0 -9999 0 -10000 0 0
RhoA/GDP/RHOGDI -0.076 0.2 -9999 0 -0.47 82 82
NGF -0.14 0.32 -9999 0 -0.8 78 78
cell cycle arrest -0.1 0.22 -9999 0 -0.51 82 82
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK -0.03 0.13 -9999 0 -0.59 2 2
NT-4/5 (dimer)/p75(NTR)/TRAF6 -0.026 0.12 -9999 0 -0.61 14 14
NCSTN 0.014 0 -9999 0 -10000 0 0
mol:GTP -0.12 0.22 -9999 0 -0.54 82 82
PSENEN 0.012 0.04 -9999 0 -0.82 1 1
mol:ceramide -0.093 0.22 -9999 0 -0.5 82 82
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs -0.01 0.1 -9999 0 -0.42 2 2
p75(NTR)/beta APP -0.028 0.12 -9999 0 -0.54 22 22
BEX1 -0.042 0.2 -9999 0 -0.82 27 27
mol:GDP -0.11 0.23 -9999 0 -0.52 98 98
NGF (dimer) -0.18 0.26 -9999 0 -0.55 124 124
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI -0.078 0.2 -9999 0 -0.56 55 55
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
RAC1/GTP -0.1 0.19 -9999 0 -0.48 82 82
MYD88 0.014 0 -9999 0 -10000 0 0
CHUK 0.014 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR)/PKA -0.12 0.22 -9999 0 -0.55 82 82
RHOB 0.014 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
MAGE-G1/E2F1 -0.038 0.15 -9999 0 -0.63 26 26
NT3 (dimer) -0.18 0.28 -9999 0 -0.59 135 135
TP53 -0.019 0.16 -9999 0 -0.6 5 5
PRDM4 -0.093 0.22 -9999 0 -0.51 82 82
BDNF (dimer) -0.46 0.3 -9999 0 -0.6 317 317
PIK3CA 0.014 0 -9999 0 -10000 0 0
SORT1 -0.011 0.12 -9999 0 -0.59 17 17
activation of caspase activity -0.11 0.2 -9999 0 -0.47 83 83
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.12 0.21 -9999 0 -0.51 83 83
RHOC 0.014 0 -9999 0 -10000 0 0
XIAP 0.014 0 -9999 0 -10000 0 0
MAPK10 -0.063 0.2 -9999 0 -0.54 24 24
DIABLO 0.014 0 -9999 0 -10000 0 0
SMPD2 -0.093 0.22 -9999 0 -0.51 82 82
APH1B 0.014 0 -9999 0 -10000 0 0
APH1A 0.014 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin -0.13 0.23 -9999 0 -0.56 82 82
PSEN1 0.014 0 -9999 0 -10000 0 0
APAF-1/Pro-Caspase 9 -0.001 0.021 -9999 0 -0.43 1 1
NT3 (dimer)/p75(NTR) -0.16 0.23 -9999 0 -0.46 149 149
MAPK8 -0.055 0.19 -9999 0 -0.56 16 16
MAPK9 -0.051 0.19 -9999 0 -0.55 15 15
APAF1 0.012 0.029 -9999 0 -0.59 1 1
NTF3 -0.18 0.28 -9999 0 -0.59 135 135
NTF4 0.01 0.05 -9999 0 -0.7 2 2
NDN 0.003 0.082 -9999 0 -0.62 7 7
RAC1/GDP 0 0 -9999 0 -10000 0 0
RhoA-B-C/GDP -0.092 0.17 -9999 0 -0.86 1 1
p75 CTF/Sortilin/TRAF6/NRIF -0.015 0.069 -9999 0 -0.49 1 1
RhoA-B-C/GTP -0.12 0.22 -9999 0 -0.54 82 82
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.061 0.15 -9999 0 -0.48 33 33
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6 -0.066 0.16 -9999 0 -0.51 33 33
PRKACB 0.014 0 -9999 0 -10000 0 0
proBDNF (dimer)/p75 ECD -0.043 0.15 -9999 0 -0.52 35 35
ChemicalAbstracts:86-01-1 0 0 -9999 0 -10000 0 0
BIRC3 -0.016 0.15 -9999 0 -0.82 15 15
BIRC2 -0.002 0.11 -9999 0 -0.82 8 8
neuron projection morphogenesis -0.099 0.2 -9999 0 -0.46 82 82
BAD -0.048 0.19 -9999 0 -0.53 15 15
RIPK2 0.014 0 -9999 0 -10000 0 0
NGFR -0.023 0.16 -9999 0 -0.72 21 21
CYCS -0.084 0.22 -9999 0 -0.48 82 82
ADAM17 0.011 0.041 -9999 0 -0.59 2 2
NGF (dimer)/p75(NTR)/TRAF6/RIP2 -0.11 0.2 -9999 0 -0.5 83 83
BCL2L11 -0.048 0.19 -9999 0 -0.53 15 15
BDNF (dimer)/p75(NTR) -0.068 0.18 -9999 0 -0.53 54 54
PI3K -0.11 0.2 -9999 0 -0.5 82 82
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1 -0.12 0.21 -9999 0 -0.51 82 82
NDNL2 0.014 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
PRKCI 0.014 0 -9999 0 -10000 0 0
NGF (dimer)/p75(NTR) -0.14 0.26 -9999 0 -0.6 98 98
ChemicalAbstracts:146-91-8 0 0 -9999 0 -10000 0 0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE -0.12 0.22 -9999 0 -0.52 82 82
TRAF6 0.012 0.04 -9999 0 -0.82 1 1
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCZ 0.012 0.029 -9999 0 -0.59 1 1
PLG -0.006 0.079 -9999 0 -0.82 4 4
oligodendrocyte cell fate commitment 0 0 -9999 0 -10000 0 0
CASP6 -0.1 0.22 -9999 0 -0.61 27 27
SQSTM1 0.014 0 -9999 0 -10000 0 0
NGFRAP1 0.01 0.057 -9999 0 -0.82 2 2
CASP3 -0.041 0.17 -9999 0 -0.48 15 15
E2F1 -0.037 0.2 -9999 0 -0.82 26 26
CASP9 0.014 0 -9999 0 -10000 0 0
IKK complex -0.1 0.16 -9999 0 -0.69 4 4
NGF (dimer)/TRKA -0.16 0.28 -9999 0 -0.63 110 110
MMP7 -0.13 0.3 -9999 0 -0.76 79 79
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF -0.11 0.2 -9999 0 -0.48 83 83
MMP3 -0.56 0.38 -9999 0 -0.81 295 295
APAF-1/Caspase 9 -0.1 0.17 -9999 0 -0.69 14 14
FOXA2 and FOXA3 transcription factor networks

Figure S14.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S14.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ACADVL -0.23 0.38 -9999 0 -1.1 39 39
PCK1 -0.51 0.62 -9999 0 -1.3 150 150
HNF4A -0.29 0.47 -9999 0 -1.3 50 50
KCNJ11 -0.33 0.51 -9999 0 -1.1 90 90
AKT1 -0.075 0.15 -9999 0 -10000 0 0
response to starvation -0.004 0.024 -9999 0 -10000 0 0
DLK1 -0.43 0.57 -9999 0 -1.1 139 139
NKX2-1 -0.069 0.33 -9999 0 -0.84 35 35
ACADM -0.23 0.39 -9999 0 -1.1 41 41
TAT -0.14 0.24 -9999 0 -0.87 17 17
CEBPB 0.015 0.004 -9999 0 -10000 0 0
CEBPA 0.01 0.051 -9999 0 -0.59 3 3
TTR -0.3 0.34 -9999 0 -0.98 52 52
PKLR -0.26 0.43 -9999 0 -1.1 59 59
APOA1 -0.27 0.45 -9999 0 -1.3 36 36
CPT1C -0.23 0.39 -9999 0 -1.1 41 41
ALAS1 -0.079 0.17 -9999 0 -10000 0 0
TFRC -0.2 0.3 -9999 0 -0.88 32 32
FOXF1 0.017 0.094 -9999 0 -0.7 5 5
NF1 0.021 0 -9999 0 -10000 0 0
HNF1A (dimer) 0 0.11 -9999 0 -0.81 7 7
CPT1A -0.23 0.39 -9999 0 -1.1 38 38
HMGCS1 -0.23 0.38 -9999 0 -1.1 38 38
NR3C1 0.017 0.026 -9999 0 -10000 0 0
CPT1B -0.23 0.4 -9999 0 -1.1 43 43
chromatin remodeling 0 0 -9999 0 -10000 0 0
SP1 0.012 0.027 -9999 0 -10000 0 0
GCK -0.26 0.41 -9999 0 -1.1 45 45
CREB1 -0.041 0.086 -9999 0 -10000 0 0
IGFBP1 -0.1 0.21 -9999 0 -0.88 15 15
PDX1 -0.11 0.22 -9999 0 -0.83 14 14
UCP2 -0.23 0.39 -9999 0 -1.1 39 39
ALDOB -0.25 0.43 -9999 0 -1.2 45 45
AFP -0.2 0.24 -9999 0 -0.65 54 54
BDH1 -0.23 0.39 -9999 0 -1.1 39 39
HADH -0.24 0.4 -9999 0 -1.1 41 41
F2 -0.3 0.46 -9999 0 -1.4 39 39
HNF1A 0 0.11 -9999 0 -0.81 7 7
G6PC -0.054 0.13 -9999 0 -0.7 2 2
SLC2A2 -0.13 0.21 -9999 0 -0.74 3 3
INS -0.011 0.063 -9999 0 -0.84 2 2
FOXA1 -0.24 0.32 -9999 0 -0.6 173 173
FOXA3 -0.12 0.25 -9999 0 -0.82 36 36
FOXA2 -0.28 0.46 -9999 0 -1.2 47 47
ABCC8 -0.24 0.41 -9999 0 -1.1 43 43
ALB -0.23 0.3 -9999 0 -0.79 69 69
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 + 0.014 0 -9999 0 -10000 0 0
GNAT1/GTP -0.004 0.053 -9999 0 -0.64 3 3
Metarhodopsin II/Arrestin -0.007 0.06 -9999 0 -0.56 5 5
PDE6G/GNAT1/GTP -0.021 0.1 -9999 0 -0.55 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
GNAT1 0.001 0.069 -9999 0 -0.82 3 3
GRK1 0.001 0.04 -9999 0 -0.82 1 1
CNG Channel -0.43 0.29 -9999 0 -0.74 156 156
mol:Na + -0.32 0.26 -9999 0 -0.8 51 51
mol:ADP 0.001 0.04 -9999 0 -0.82 1 1
RGS9-1/Gbeta5/R9AP -0.019 0.088 -9999 0 -0.54 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
cGMP/CNG Channel -0.33 0.27 -9999 0 -0.84 51 51
CNGB1 -0.45 0.41 -9999 0 -0.81 236 236
RDH5 0.012 0.029 -9999 0 -0.59 1 1
SAG 0.002 0.004 -9999 0 -10000 0 0
mol:Ca2+ -0.29 0.27 -9999 0 -0.77 51 51
Na + (4 Units) -0.3 0.24 -9999 0 -0.74 51 51
RGS9 0 0.1 -9999 0 -0.78 7 7
GNB1/GNGT1 -0.1 0.23 -9999 0 -0.63 70 70
GNAT1/GDP -0.019 0.095 -9999 0 -0.6 7 7
GUCY2D -0.03 0.18 -9999 0 -0.82 22 22
GNGT1 -0.12 0.31 -9999 0 -0.82 70 70
GUCY2F 0.001 0.04 -9999 0 -0.82 1 1
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) -0.18 0.22 -9999 0 -0.61 42 42
mol:11-cis-retinal 0.012 0.029 -9999 0 -0.59 1 1
mol:cGMP -0.081 0.19 -9999 0 -0.5 67 67
GNB1 0.014 0 -9999 0 -10000 0 0
Rhodopsin -0.008 0.071 -9999 0 -0.59 6 6
SLC24A1 0.014 0 -9999 0 -10000 0 0
CNGA1 -0.028 0.15 -9999 0 -0.59 29 29
Metarhodopsin II -0.007 0.06 -9999 0 -0.51 6 6
mol:Ca ++ 0 0 -9999 0 -10000 0 0
GC1/GCAP Family -0.085 0.2 -9999 0 -0.53 66 66
RGS9BP -0.004 0.1 -9999 0 -0.59 12 12
Metarhodopsin II/Transducin -0.036 0.12 -9999 0 -0.28 77 77
GCAP Family/Ca ++ -0.06 0.16 -9999 0 -0.5 51 51
PDE6A/B -0.24 0.25 -9999 0 -0.47 217 217
mol:Pi -0.018 0.087 -9999 0 -0.54 6 6
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
Transducin -0.086 0.19 -9999 0 -0.5 73 73
PDE6B -0.04 0.19 -9999 0 -0.68 33 33
PDE6A -0.28 0.3 -9999 0 -0.59 202 202
PDE6G -0.012 0.14 -9999 0 -0.82 13 13
RHO -0.006 0.089 -9999 0 -0.82 5 5
PDE6 -0.18 0.2 -9999 0 -0.64 32 32
GUCA1A -0.079 0.26 -9999 0 -0.82 47 47
GC2/GCAP Family -0.061 0.16 -9999 0 -0.51 48 48
GUCA1C 0 0 -9999 0 -10000 0 0
GUCA1B 0.006 0.065 -9999 0 -0.59 5 5
Calcium signaling in the CD4+ TCR 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
NFATC1 -0.014 0.036 -9999 0 -10000 0 0
NFATC2 -0.059 0.13 -9999 0 -0.41 45 45
NFATC3 -0.014 0.036 -9999 0 -10000 0 0
CD40LG -0.33 0.35 -9999 0 -0.86 89 89
PTGS2 -0.35 0.37 -9999 0 -0.87 106 106
JUNB 0.014 0 -9999 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.017 0.016 -9999 0 -10000 0 0
CaM/Ca2+ -0.016 0.016 -9999 0 -10000 0 0
CALM1 0.004 0.011 -9999 0 -10000 0 0
JUN 0.004 0.011 -9999 0 -10000 0 0
mol:Ca2+ -0.017 0.014 -9999 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0.004 -9999 0 -10000 0 0
FOSL1 -0.007 0.13 -9999 0 -0.8 11 11
CREM 0.013 0.001 -9999 0 -10000 0 0
Jun/NFAT1-c-4/p21SNFT -0.16 0.15 -9999 0 -0.6 17 17
FOS -0.078 0.21 -9999 0 -0.6 57 57
IFNG -0.37 0.38 -9999 0 -0.87 120 120
AP-1/NFAT1-c-4 -0.39 0.38 -9999 0 -0.86 121 121
FASLG -0.32 0.35 -9999 0 -0.88 77 77
NFAT1-c-4/ICER1 -0.1 0.12 -9999 0 -0.49 15 15
IL2RA -0.33 0.36 -9999 0 -0.88 83 83
FKBP12/FK506 0 0 -9999 0 -10000 0 0
CSF2 -0.5 0.42 -9999 0 -0.82 243 243
JunB/Fra1/NFAT1-c-4 -0.1 0.14 -9999 0 -0.57 16 16
IL4 -0.3 0.31 -9999 0 -0.81 66 66
IL2 -0.011 0.037 -9999 0 -0.68 1 1
IL3 -0.029 0.023 -9999 0 -10000 0 0
FKBP1A 0.014 0 -9999 0 -10000 0 0
BATF3 0.01 0.057 -9999 0 -0.82 2 2
mol:FK506 0 0 -9999 0 -10000 0 0
POU2F1 0.014 0.002 -9999 0 -10000 0 0
Signaling events mediated by the Hedgehog family

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
TGFB2 -0.28 0.24 -10000 0 -0.92 15 15
IHH -0.056 0.07 -10000 0 -0.77 2 2
SHH Np/Cholesterol/GAS1 -0.045 0.14 -10000 0 -0.5 35 35
LRPAP1 0.014 0 -10000 0 -10000 0 0
dorsoventral neural tube patterning 0.045 0.14 0.5 35 -10000 0 35
SMO/beta Arrestin2 -0.15 0.16 -10000 0 -0.6 21 21
SMO -0.16 0.17 -10000 0 -0.64 21 21
AKT1 -0.065 0.095 -10000 0 -0.73 3 3
ARRB2 0.014 0 -10000 0 -10000 0 0
BOC -0.038 0.17 -10000 0 -0.6 36 36
ADRBK1 0.014 0 -10000 0 -10000 0 0
heart looping -0.16 0.16 -10000 0 -0.63 21 21
STIL -0.14 0.17 -10000 0 -0.62 29 29
DHH N/PTCH2 -0.016 0.094 -10000 0 -0.54 13 13
DHH N/PTCH1 -0.14 0.14 -10000 0 -0.74 9 9
PIK3CA 0.014 0 -10000 0 -10000 0 0
DHH 0.008 0.057 -10000 0 -0.82 2 2
PTHLH -0.47 0.34 -10000 0 -0.66 308 308
determination of left/right symmetry -0.16 0.16 -10000 0 -0.63 21 21
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
skeletal system development -0.46 0.33 -10000 0 -0.66 308 308
IHH N/Hhip -0.055 0.17 -10000 0 -0.68 27 27
DHH N/Hhip -0.039 0.15 -10000 0 -0.62 27 27
mol:Cholesterol 0 0 -10000 0 -10000 0 0
heart development -0.16 0.16 -10000 0 -0.63 21 21
pancreas development -0.037 0.19 -10000 0 -0.81 25 25
HHAT 0.011 0.041 -10000 0 -0.59 2 2
PI3K -0.003 0.036 -10000 0 -0.43 3 3
EntrezGene:84976 0 0 -10000 0 -10000 0 0
GAS1 0.003 0.086 -10000 0 -0.7 6 6
somite specification -0.16 0.16 -10000 0 -0.63 21 21
SHH Np/Cholesterol/PTCH1 -0.15 0.18 -10000 0 -0.6 40 40
SHH Np/Cholesterol/PTCH2 -0.05 0.16 -10000 0 -0.54 34 34
SHH Np/Cholesterol/Megalin -0.067 0.19 -10000 0 -0.56 50 50
SHH -0.032 0.17 -10000 0 -0.62 34 34
catabolic process -0.17 0.16 -10000 0 -0.68 12 12
SMO/Vitamin D3 -0.16 0.18 -10000 0 -0.64 31 31
SHH Np/Cholesterol/Hhip -0.068 0.19 -10000 0 -0.58 48 48
LRP2 -0.036 0.19 -10000 0 -0.82 24 24
receptor-mediated endocytosis -0.18 0.18 -10000 0 -0.65 37 37
SHH Np/Cholesterol/BOC -0.067 0.16 -10000 0 -0.45 49 49
SHH Np/Cholesterol/CDO -0.047 0.14 -10000 0 -0.5 33 33
mesenchymal cell differentiation 0.067 0.19 0.57 48 -10000 0 48
mol:Vitamin D3 -0.15 0.18 -10000 0 -0.6 40 40
IHH N/PTCH2 -0.027 0.1 -10000 0 -0.58 13 13
CDON -0.001 0.092 -10000 0 -0.59 10 10
IHH N/PTCH1 -0.17 0.16 -10000 0 -0.68 12 12
Megalin/LRPAP1 -0.035 0.14 -10000 0 -0.63 24 24
PTCH2 -0.005 0.11 -10000 0 -0.69 11 11
SHH Np/Cholesterol -0.036 0.14 -10000 0 -0.5 34 34
PTCH1 -0.17 0.16 -10000 0 -0.68 12 12
HHIP -0.037 0.19 -10000 0 -0.81 25 25
BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS -0.24 0.28 -9999 0 -0.54 180 180
SMAD6-7/SMURF1 0 0 -9999 0 -10000 0 0
NOG -0.056 0.22 -9999 0 -0.73 39 39
SMAD9 -0.075 0.16 -9999 0 -0.6 28 28
SMAD4 0.012 0.029 -9999 0 -0.59 1 1
SMAD5 -0.053 0.15 -9999 0 -0.51 22 22
BMP7/USAG1 -0.16 0.25 -9999 0 -0.51 136 136
SMAD5/SKI -0.043 0.14 -9999 0 -0.5 17 17
SMAD1 0.041 0.029 -9999 0 -10000 0 0
BMP2 -0.019 0.16 -9999 0 -0.8 17 17
SMAD1/SMAD1/SMAD4 0 0.013 -9999 0 -10000 0 0
BMPR1A 0.012 0.029 -9999 0 -0.59 1 1
BMPR1B -0.07 0.24 -9999 0 -0.77 45 45
BMPR1A-1B/BAMBI -0.073 0.18 -9999 0 -0.56 44 44
AHSG -0.049 0.21 -9999 0 -0.82 30 30
CER1 -0.006 0.089 -9999 0 -0.82 5 5
BMP2-4/CER1 -0.037 0.13 -9999 0 -0.51 30 30
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA -0.094 0.2 -9999 0 -0.57 39 39
BMP2-4 (homodimer) -0.035 0.14 -9999 0 -0.57 26 26
RGMB 0.014 0 -9999 0 -10000 0 0
BMP6/BMPR2/BMPR1A-1B -0.055 0.15 -9999 0 -0.5 41 41
RGMA -0.06 0.2 -9999 0 -0.6 51 51
SMURF1 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP -0.094 0.19 -9999 0 -0.52 40 40
BMP2-4/USAG1 -0.14 0.21 -9999 0 -0.59 45 45
SMAD6/SMURF1/SMAD5 -0.043 0.14 -9999 0 -0.5 17 17
SOSTDC1 -0.17 0.3 -9999 0 -0.64 120 120
BMP7/BMPR2/BMPR1A-1B -0.073 0.16 -9999 0 -0.51 39 39
SKI 0.014 0 -9999 0 -10000 0 0
BMP6 (homodimer) 0.004 0.085 -9999 0 -0.77 5 5
HFE2 -0.17 0.27 -9999 0 -0.59 125 125
ZFYVE16 0.014 0 -9999 0 -10000 0 0
MAP3K7 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRD -0.052 0.16 -9999 0 -0.55 35 35
SMAD5/SMAD5/SMAD4 -0.043 0.14 -9999 0 -0.5 18 18
MAPK1 0.014 0 -9999 0 -10000 0 0
TAK1/TAB family -0.096 0.14 -9999 0 -0.57 19 19
BMP7 (homodimer) -0.032 0.16 -9999 0 -0.6 32 32
NUP214 0.014 0 -9999 0 -10000 0 0
BMP6/FETUA -0.051 0.17 -9999 0 -0.62 35 35
SMAD1/SKI 0.047 0.027 -9999 0 -10000 0 0
SMAD6 0.014 0 -9999 0 -10000 0 0
CTDSP2 0.014 0 -9999 0 -10000 0 0
BMP2-4/FETUA -0.068 0.18 -9999 0 -0.56 47 47
MAP3K7IP1 0 0 -9999 0 -10000 0 0
GREM1 -0.37 0.41 -9999 0 -0.82 196 196
BMPR2 (homodimer) 0.014 0 -9999 0 -10000 0 0
GADD34/PP1CA 0 0 -9999 0 -10000 0 0
BMPR1A-1B (homodimer) -0.063 0.18 -9999 0 -0.59 45 45
CHRDL1 -0.27 0.3 -9999 0 -0.59 201 201
ENDOFIN/SMAD1 0.047 0.027 -9999 0 -10000 0 0
SMAD6-7/SMURF1/SMAD1 -0.001 0.004 -9999 0 -10000 0 0
SMAD6/SMURF1 0.014 0 -9999 0 -10000 0 0
BAMBI -0.017 0.14 -9999 0 -0.66 19 19
SMURF2 0.014 0 -9999 0 -10000 0 0
BMP2-4/CHRDL1 -0.2 0.22 -9999 0 -0.72 24 24
BMP2-4/GREM1 -0.28 0.3 -9999 0 -0.57 202 202
SMAD7 0.014 0 -9999 0 -10000 0 0
SMAD8A/SMAD8A/SMAD4 -0.046 0.16 -9999 0 -0.56 29 29
SMAD1/SMAD6 0.047 0.027 -9999 0 -10000 0 0
TAK1/SMAD6 0 0 -9999 0 -10000 0 0
BMP7 -0.033 0.16 -9999 0 -0.6 32 32
BMP6 0.004 0.085 -9999 0 -0.77 5 5
MAP3K7IP2 0 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1 -0.075 0.16 -9999 0 -0.46 39 39
PPM1A 0.014 0 -9999 0 -10000 0 0
SMAD1/SMURF2 0.047 0.027 -9999 0 -10000 0 0
SMAD7/SMURF1 0 0 -9999 0 -10000 0 0
CTDSPL 0.014 0 -9999 0 -10000 0 0
PPP1CA 0.014 0 -9999 0 -10000 0 0
XIAP 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
PPP1R15A 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS -0.18 0.24 -9999 0 -0.53 99 99
CHRD -0.021 0.16 -9999 0 -0.8 18 18
BMPR2 0.014 0 -9999 0 -10000 0 0
BMP2-4/BMPR2/BMPR1A-1B/RGM -0.1 0.19 -9999 0 -0.56 40 40
BMP4 -0.001 0.096 -9999 0 -0.61 10 10
FST -0.3 0.4 -9999 0 -0.82 158 158
BMP2-4/NOG -0.073 0.19 -9999 0 -0.57 41 41
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1 -0.068 0.15 -9999 0 -0.47 39 39
Effects of Botulinum toxin

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
STX1A -0.015 0.13 -9999 0 -0.64 18 18
UniProt:P19321 0 0 -9999 0 -10000 0 0
RIMS1/UNC13B -0.035 0.12 -9999 0 -0.44 34 34
STXBP1 0.014 0 -9999 0 -10000 0 0
ACh/CHRNA1 -0.16 0.25 -9999 0 -0.5 139 139
RAB3GAP2/RIMS1/UNC13B -0.029 0.1 -9999 0 -0.54 2 2
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 -0.037 0.16 -9999 0 -0.6 32 32
mol:ACh -0.002 0.04 -9999 0 -0.12 41 41
RAB3GAP2 0.014 0 -9999 0 -10000 0 0
STX1A/SNAP25/VAMP2 -0.045 0.11 -9999 0 -0.42 11 11
UniProt:P10844 0 0 -9999 0 -10000 0 0
muscle contraction -0.16 0.25 -9999 0 -0.5 139 139
UNC13B 0.011 0.041 -9999 0 -0.59 2 2
CHRNA1 -0.23 0.35 -9999 0 -0.72 139 139
UniProt:P10845 0 0 -9999 0 -10000 0 0
ACh/Synaptotagmin 1 -0.14 0.26 -9999 0 -0.58 107 107
SNAP25 -0.01 0.073 -9999 0 -0.3 25 25
VAMP2 0.007 0 -9999 0 -10000 0 0
SYT1 -0.19 0.36 -9999 0 -0.81 107 107
UniProt:Q00496 0 0 -9999 0 -10000 0 0
STXIA/STXBP1 -0.005 0.11 -9999 0 -0.55 18 18
STX1A/SNAP25 fragment 1/VAMP2 -0.045 0.11 -9999 0 -0.42 11 11
PDGFR-beta signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate -0.072 0.14 -9999 0 -0.54 2 2
PDGFB-D/PDGFRB/SLAP -0.13 0.25 -9999 0 -0.62 92 92
PDGFB-D/PDGFRB/APS/CBL -0.12 0.22 -9999 0 -0.53 92 92
AKT1 -0.026 0.17 -9999 0 -0.6 3 3
mol:PI-4-5-P2 0 0.001 -9999 0 -10000 0 0
mol:Sphingosine-1-phosphate -0.043 0.16 -9999 0 -0.56 2 2
PIK3CA 0.014 0 -9999 0 -10000 0 0
FGR -0.085 0.17 -9999 0 -0.4 90 90
mol:Ca2+ -0.042 0.15 -9999 0 -0.39 1 1
MYC -0.005 0.12 -9999 0 -10000 0 0
SHC1 0.014 0 -9999 0 -10000 0 0
HRAS/GDP -0.087 0.18 -9999 0 -0.42 92 92
LRP1/PDGFRB/PDGFB -0.12 0.23 -9999 0 -0.55 96 96
GRB10 0.01 0.057 -9999 0 -0.82 2 2
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 -0.043 0.15 -9999 0 -0.4 1 1
PTEN 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
GRB7 0.004 0.085 -9999 0 -0.77 5 5
PDGFB-D/PDGFRB/SHP2 -0.13 0.25 -9999 0 -0.62 90 90
PDGFB-D/PDGFRB/GRB10 -0.13 0.25 -9999 0 -0.62 92 92
cell cycle arrest -0.13 0.25 -9999 0 -0.61 92 92
HRAS 0.012 0.04 -9999 0 -0.82 1 1
HIF1A -0.013 0.16 -9999 0 -0.52 3 3
GAB1 -0.043 0.15 -9999 0 -0.39 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
DNM2 -0.037 0.15 -9999 0 -0.47 1 1
PDGFB-D/PDGFRB -0.11 0.22 -9999 0 -0.53 91 91
mol:GDP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/LMW-PTP -0.13 0.25 -9999 0 -0.62 90 90
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB -0.074 0.14 -9999 0 -0.68 1 1
positive regulation of MAPKKK cascade -0.13 0.25 -9999 0 -0.61 90 90
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
mol:IP3 -0.043 0.15 -9999 0 -0.4 1 1
E5 -0.001 0.002 -9999 0 -10000 0 0
CSK 0.014 0.002 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/GRB7 -0.14 0.26 -9999 0 -0.62 93 93
SHB 0.009 0.051 -9999 0 -0.59 3 3
BLK -0.14 0.2 -9999 0 -0.44 102 102
PTPN2 0.011 0.04 -9999 0 -0.81 1 1
PDGFB-D/PDGFRB/SNX15 -0.13 0.25 -9999 0 -0.62 90 90
BCAR1 0.014 0 -9999 0 -10000 0 0
VAV2 -0.039 0.15 -9999 0 -0.43 4 4
CBL 0.014 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB/DEP1 -0.13 0.25 -9999 0 -0.62 90 90
LCK -0.091 0.17 -9999 0 -0.4 90 90
PDGFRB -0.16 0.34 -9999 0 -0.81 90 90
ACP1 0.014 0 -9999 0 -10000 0 0
HCK -0.086 0.17 -9999 0 -0.4 92 92
ABL1 -0.052 0.16 -9999 0 -0.41 13 13
PDGFB-D/PDGFRB/CBL -0.042 0.15 -9999 0 -0.41 2 2
PTPN1 0.013 0.003 -9999 0 -10000 0 0
SNX15 0.014 0 -9999 0 -10000 0 0
STAT3 0.014 0 -9999 0 -10000 0 0
STAT1 -0.039 0.2 -9999 0 -0.81 27 27
cell proliferation -0.003 0.11 -9999 0 -10000 0 0
SLA 0.01 0.057 -9999 0 -0.82 2 2
actin cytoskeleton reorganization -0.045 0.19 -9999 0 -10000 0 0
SRC -0.084 0.16 -9999 0 -0.41 12 12
PI3K -0.085 0.16 -9999 0 -0.69 3 3
PDGFB-D/PDGFRB/GRB7/SHC -0.12 0.22 -9999 0 -0.54 93 93
SH2B2 0.01 0.057 -9999 0 -0.82 2 2
PLCgamma1/SPHK1 -0.044 0.16 -9999 0 -0.59 2 2
LYN -0.085 0.17 -9999 0 -0.4 92 92
LRP1 0.012 0.029 -9999 0 -0.59 1 1
SOS1 0.014 0 -9999 0 -10000 0 0
STAT5B 0.014 0 -9999 0 -10000 0 0
STAT5A 0.014 0 -9999 0 -10000 0 0
NCK1-2/p130 Cas -0.089 0.17 -9999 0 -0.44 1 1
SPHK1 -0.004 0.12 -9999 0 -0.82 9 9
EDG1 -0.001 0.004 -9999 0 -10000 0 0
mol:DAG -0.043 0.15 -9999 0 -0.4 1 1
PLCG1 -0.045 0.15 -9999 0 -0.41 1 1
NHERF/PDGFRB -0.12 0.22 -9999 0 -0.54 90 90
YES1 -0.084 0.16 -9999 0 -0.4 90 90
cell migration -0.12 0.22 -9999 0 -0.54 90 90
SHC/Grb2/SOS1 -0.089 0.17 -9999 0 -10000 0 0
SLC9A3R2 0.012 0.04 -9999 0 -0.82 1 1
SLC9A3R1 0.008 0.058 -9999 0 -0.59 4 4
NHERF1-2/PDGFRB/PTEN -0.11 0.2 -9999 0 -0.49 90 90
FYN -0.084 0.17 -9999 0 -0.4 91 91
DOK1 -0.074 0.21 -9999 0 -0.48 91 91
HRAS/GTP -0.001 0.031 -9999 0 -0.64 1 1
PDGFB -0.004 0.12 -9999 0 -0.82 9 9
RAC1 -0.023 0.14 -9999 0 -10000 0 0
PRKCD -0.073 0.21 -9999 0 -0.48 91 91
FER -0.074 0.21 -9999 0 -0.48 91 91
MAPKKK cascade -0.088 0.17 -9999 0 -10000 0 0
RASA1 -0.074 0.21 -9999 0 -0.48 91 91
NCK1 0.014 0 -9999 0 -10000 0 0
NCK2 0.014 0 -9999 0 -10000 0 0
p62DOK/Csk -0.087 0.18 -9999 0 -0.44 91 91
PDGFB-D/PDGFRB/SHB -0.13 0.25 -9999 0 -0.61 93 93
chemotaxis -0.05 0.16 -9999 0 -0.4 13 13
STAT1-3-5/STAT1-3-5 -0.11 0.2 -9999 0 -0.84 7 7
Bovine Papilomavirus E5/PDGFRB -0.13 0.26 -9999 0 -0.63 90 90
PTPRJ 0.014 0 -9999 0 -10000 0 0
Ephrin B reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EFNB2 0.012 0.029 -10000 0 -0.59 1 1
EPHB2 -0.15 0.33 -10000 0 -0.82 84 84
EFNB1 -0.024 0.17 -10000 0 -0.63 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP -0.14 0.23 -10000 0 -0.84 16 16
Ephrin B2/EPHB1-2 -0.12 0.22 -10000 0 -0.51 102 102
neuron projection morphogenesis -0.14 0.22 -10000 0 -0.8 16 16
Ephrin B1/EPHB1-2/Tiam1 -0.15 0.25 -10000 0 -0.52 119 119
DNM1 -0.048 0.22 -10000 0 -0.82 31 31
cell-cell signaling 0 0.001 -10000 0 -10000 0 0
MAP2K4 0.009 0.089 -10000 0 -0.62 8 8
YES1 -0.015 0.12 -10000 0 -0.86 8 8
Ephrin B1/EPHB1-2/NCK2 -0.14 0.25 -10000 0 -0.52 119 119
PI3K 0.007 0.1 -10000 0 -0.7 8 8
mol:GDP -0.15 0.25 -10000 0 -0.51 119 119
ITGA2B -0.053 0.23 -10000 0 -0.82 34 34
endothelial cell proliferation -0.001 0.018 -10000 0 -0.36 1 1
FYN -0.015 0.12 -10000 0 -0.86 8 8
MAP3K7 -0.013 0.091 -10000 0 -0.67 8 8
FGR -0.015 0.12 -10000 0 -0.86 8 8
TIAM1 0.006 0.065 -10000 0 -0.59 5 5
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
RGS3 0.014 0 -10000 0 -10000 0 0
cell adhesion -0.033 0.19 -10000 0 -0.54 36 36
LYN -0.015 0.12 -10000 0 -0.88 8 8
Ephrin B1/EPHB1-2/Src Family Kinases -0.017 0.11 -10000 0 -0.81 8 8
Ephrin B1/EPHB1-2 -0.018 0.099 -10000 0 -0.72 8 8
SRC -0.015 0.12 -10000 0 -0.86 8 8
ITGB3 -0.022 0.16 -10000 0 -0.74 20 20
EPHB1 -0.037 0.19 -10000 0 -0.74 28 28
EPHB4 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB4 -0.001 0.018 -10000 0 -0.36 1 1
alphaIIb/beta3 Integrin -0.076 0.21 -10000 0 -0.62 52 52
BLK -0.032 0.12 -10000 0 -0.86 8 8
HCK -0.016 0.12 -10000 0 -0.86 8 8
regulation of stress fiber formation 0.14 0.24 0.51 119 -10000 0 119
MAPK8 0.012 0.1 -10000 0 -0.66 8 8
Ephrin B1/EPHB1-2/RGS3 -0.14 0.25 -10000 0 -0.52 119 119
endothelial cell migration -0.007 0.079 -10000 0 -0.56 8 8
NCK2 0.014 0 -10000 0 -10000 0 0
PTPN13 -0.003 0.098 -10000 0 -0.7 8 8
regulation of focal adhesion formation 0.14 0.24 0.51 119 -10000 0 119
chemotaxis 0.14 0.24 0.51 119 -10000 0 119
PIK3CA 0.014 0 -10000 0 -10000 0 0
Rac1/GTP -0.14 0.22 -10000 0 -0.84 16 16
angiogenesis -0.018 0.098 -10000 0 -0.72 8 8
LCK -0.017 0.12 -10000 0 -0.86 8 8
Coregulation of Androgen receptor activity

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
NRIP1 0 0.039 -9999 0 -0.59 1 1
SVIL 0.003 0.024 -9999 0 -10000 0 0
ZNF318 0.04 0.061 -9999 0 -10000 0 0
JMJD2C 0.006 0.024 -9999 0 -0.11 14 14
T-DHT/AR/Ubc9 -0.12 0.18 -9999 0 -0.42 108 108
CARM1 0.012 0.003 -9999 0 -10000 0 0
PRDX1 0.015 0.004 -9999 0 -10000 0 0
PELP1 0.018 0.01 -9999 0 -10000 0 0
CTNNB1 0.004 0.034 -9999 0 -0.59 1 1
AKT1 0.021 0.017 -9999 0 -10000 0 0
PTK2B 0.005 0.033 -9999 0 -0.59 1 1
MED1 0.02 0.045 -9999 0 -0.82 1 1
MAK 0.024 0.12 -9999 0 -0.65 10 10
response to oxidative stress 0.002 0.004 -9999 0 -10000 0 0
HIP1 0.002 0.038 -9999 0 -0.59 1 1
GSN 0.002 0.027 -9999 0 -10000 0 0
NCOA2 -0.025 0.14 -9999 0 -0.59 26 26
NCOA6 0.004 0.023 -9999 0 -10000 0 0
DNA-PK 0.031 0.067 -9999 0 -10000 0 0
NCOA4 0.011 0.029 -9999 0 -0.59 1 1
PIAS3 0.005 0.019 -9999 0 -10000 0 0
cell proliferation -0.02 0.13 -9999 0 -0.69 10 10
XRCC5 0.02 0.013 -9999 0 -10000 0 0
UBE3A -0.004 0.038 -9999 0 -10000 0 0
T-DHT/AR/SNURF -0.13 0.2 -9999 0 -0.44 121 121
FHL2 -0.026 0.11 -9999 0 -0.96 2 2
RANBP9 0.004 0.023 -9999 0 -10000 0 0
JMJD1A -0.062 0.076 -9999 0 -0.14 215 215
CDK6 0.001 0.1 -9999 0 -0.78 7 7
TGFB1I1 -0.025 0.15 -9999 0 -0.82 14 14
T-DHT/AR/CyclinD1 -0.14 0.2 -9999 0 -0.45 115 115
XRCC6 0.02 0.013 -9999 0 -10000 0 0
T-DHT/AR -0.14 0.21 -9999 0 -0.52 69 69
CTDSP1 0.011 0.005 -9999 0 -10000 0 0
CTDSP2 0.032 0.042 -9999 0 -10000 0 0
BRCA1 0.003 0.024 -9999 0 -10000 0 0
TCF4 0.027 0.03 -9999 0 -10000 0 0
CDKN2A -0.34 0.4 -9999 0 -0.76 194 194
SRF 0.03 0.023 -9999 0 -10000 0 0
NKX3-1 -0.14 0.15 -9999 0 -0.88 5 5
KLK3 -0.22 0.55 -9999 0 -1.4 76 76
TMF1 0.011 0.005 -9999 0 -10000 0 0
HNRNPA1 0.025 0.026 -9999 0 -10000 0 0
AOF2 -0.012 0.027 -9999 0 -0.071 72 72
APPL1 0.041 0.037 -9999 0 -10000 0 0
T-DHT/AR/Caspase 8 -0.11 0.19 -9999 0 -0.42 98 98
AR -0.17 0.27 -9999 0 -0.63 108 108
UBA3 0.011 0.005 -9999 0 -10000 0 0
PATZ1 0.025 0.026 -9999 0 -10000 0 0
PAWR 0.011 0.005 -9999 0 -10000 0 0
PRKDC 0.02 0.013 -9999 0 -10000 0 0
PA2G4 0.026 0.028 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
T-DHT/AR/Cyclin D3/CDK11 p58 -0.099 0.17 -9999 0 -0.38 101 101
RPS6KA3 -0.001 0.048 -9999 0 -0.59 2 2
T-DHT/AR/ARA70 -0.12 0.18 -9999 0 -0.42 109 109
LATS2 0.024 0.022 -9999 0 -10000 0 0
T-DHT/AR/PRX1 -0.093 0.17 -9999 0 -0.38 98 98
Cyclin D3/CDK11 p58 0.001 0.005 -9999 0 -10000 0 0
VAV3 -0.036 0.15 -9999 0 -0.6 29 29
KLK2 -0.08 0.15 -9999 0 -0.79 14 14
CASP8 0.017 0.008 -9999 0 -10000 0 0
T-DHT/AR/TIF2/CARM1 -0.12 0.19 -9999 0 -0.45 81 81
TMPRSS2 -0.53 0.51 -9999 0 -1 212 212
CCND1 -0.01 0.13 -9999 0 -0.78 11 11
PIAS1 -0.004 0.038 -9999 0 -10000 0 0
mol:T-DHT -0.025 0.035 -9999 0 -0.066 148 148
CDC2L1 0.001 0.002 -9999 0 -10000 0 0
PIAS4 -0.012 0.058 -9999 0 -10000 0 0
T-DHT/AR/CDK6 -0.12 0.2 -9999 0 -0.43 113 113
CMTM2 -0.01 0.14 -9999 0 -0.81 13 13
SNURF -0.018 0.13 -9999 0 -0.59 21 21
ZMIZ1 -0.008 0.045 -9999 0 -0.7 1 1
CCND3 0.014 0.002 -9999 0 -10000 0 0
TGIF1 0.025 0.026 -9999 0 -10000 0 0
FKBP4 0.004 0.023 -9999 0 -10000 0 0
Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer -0.023 0.1 -10000 0 -0.54 10 10
fibroblast growth factor receptor signaling pathway -0.023 0.099 -10000 0 -0.54 10 10
LAMA1 -0.31 0.4 -10000 0 -0.81 167 167
PRNP 0.012 0.04 -10000 0 -0.82 1 1
GPC1/SLIT2 -0.049 0.14 -10000 0 -0.44 47 47
SMAD2 0.033 0.035 -10000 0 -0.49 1 1
GPC1/PrPc/Cu2+ -0.003 0.042 -10000 0 -0.49 3 3
GPC1/Laminin alpha1 -0.25 0.31 -10000 0 -0.63 167 167
TDGF1 0 0.08 -10000 0 -0.82 4 4
CRIPTO/GPC1 -0.008 0.071 -10000 0 -0.59 6 6
APP/GPC1 -0.004 0.048 -10000 0 -0.56 3 3
mol:NO 0 0 -10000 0 -10000 0 0
YES1 0.018 0.064 -10000 0 -0.54 5 5
FLT1 0.012 0.04 -10000 0 -0.82 1 1
GPC1/TGFB/TGFBR1/TGFBR2 -0.003 0.036 -10000 0 -0.54 1 1
SERPINC1 -0.006 0.12 -10000 0 -0.82 9 9
FYN 0.017 0.069 -10000 0 -0.54 6 6
FGR 0.017 0.069 -10000 0 -0.54 6 6
positive regulation of MAPKKK cascade 0.007 0.11 -10000 0 -0.44 8 8
SLIT2 -0.053 0.19 -10000 0 -0.6 46 46
GPC1/NRG -0.11 0.24 -10000 0 -0.62 75 75
NRG1 -0.13 0.31 -10000 0 -0.81 73 73
GPC1/VEGF165 homodimer/VEGFR1 homodimer -0.01 0.078 -10000 0 -0.62 6 6
LYN 0.018 0.066 -10000 0 -0.54 5 5
mol:Spermine 0.01 0.038 -10000 0 -0.54 2 2
cell growth -0.023 0.099 -10000 0 -0.54 10 10
BMP signaling pathway -0.01 0.05 0.7 2 -10000 0 2
SRC 0.018 0.064 -10000 0 -0.54 5 5
TGFBR1 0.014 0 -10000 0 -10000 0 0
mol:Cu2+ 0 0 -10000 0 -10000 0 0
PLA2G2A -0.37 0.29 -10000 0 -0.59 268 268
GPC1 0.01 0.05 -10000 0 -0.7 2 2
TGFBR1 (dimer) 0.014 0 -10000 0 -10000 0 0
VEGFA 0.004 0.09 -10000 0 -0.82 5 5
BLK -0.063 0.2 -10000 0 -0.54 57 57
HCK 0.014 0.086 -10000 0 -0.62 6 6
FGF2 -0.01 0.12 -10000 0 -0.65 15 15
FGFR1 0.004 0.09 -10000 0 -0.82 5 5
VEGFR1 homodimer 0.012 0.04 -10000 0 -0.82 1 1
TGFBR2 0.012 0.029 -10000 0 -0.59 1 1
cell death -0.004 0.047 -10000 0 -0.56 3 3
ATIII/GPC1 -0.016 0.097 -10000 0 -0.61 11 11
PLA2G2A/GPC1 -0.27 0.21 -10000 0 -0.43 269 269
LCK 0.005 0.11 -10000 0 -0.54 15 15
neuron differentiation -0.11 0.24 -10000 0 -0.61 75 75
PrPc/Cu2+ -0.001 0.031 -10000 0 -0.64 1 1
APP 0.012 0.04 -10000 0 -0.82 1 1
TGFBR2 (dimer) 0.012 0.029 -10000 0 -0.59 1 1
Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FOXP3 -0.14 0.34 -10000 0 -0.92 65 65
NFATC2 -0.036 0.23 -10000 0 -0.78 23 23
NFATC3 -0.008 0.06 -10000 0 -10000 0 0
CD40LG -0.36 0.42 -10000 0 -1.1 62 62
ITCH 0.016 0.094 -10000 0 -10000 0 0
CBLB 0.016 0.094 -10000 0 -10000 0 0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment -0.34 0.46 -10000 0 -1.1 96 96
JUNB 0.014 0 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.037 0.096 -10000 0 -10000 0 0
T cell anergy -0.008 0.16 -10000 0 -0.48 16 16
TLE4 -0.008 0.18 -10000 0 -0.7 13 13
Jun/NFAT1-c-4/p21SNFT -0.16 0.23 -10000 0 -0.99 15 15
AP-1/NFAT1-c-4 -0.37 0.44 -10000 0 -1.1 64 64
IKZF1 -0.018 0.21 -10000 0 -0.8 18 18
T-helper 2 cell differentiation -0.063 0.23 -10000 0 -0.76 24 24
AP-1/NFAT1 -0.14 0.2 -10000 0 -0.65 30 30
CALM1 0.006 0.061 -10000 0 -10000 0 0
EGR2 -0.06 0.3 -10000 0 -1.5 13 13
EGR3 -0.045 0.25 -10000 0 -1.2 9 9
NFAT1/FOXP3 -0.15 0.36 -10000 0 -0.8 81 81
EGR1 -0.01 0.12 -10000 0 -0.59 17 17
JUN -0.02 0.035 -10000 0 -10000 0 0
EGR4 -0.081 0.26 -10000 0 -0.8 49 49
mol:Ca2+ -0.009 0.066 -10000 0 -10000 0 0
GBP3 -0.028 0.22 -10000 0 -0.76 25 25
FOSL1 -0.007 0.13 -10000 0 -0.8 11 11
NFAT1-c-4/MAF/IRF4 -0.12 0.25 -10000 0 -1 14 14
DGKA -0.006 0.17 -10000 0 -0.65 13 13
CREM 0.013 0.001 -10000 0 -10000 0 0
NFAT1-c-4/PPARG -0.22 0.28 -10000 0 -0.99 25 25
CTLA4 -0.18 0.43 -10000 0 -1 72 72
NFAT1-c-4 (dimer)/EGR1 -0.1 0.25 -10000 0 -1 16 16
NFAT1-c-4 (dimer)/EGR4 -0.15 0.28 -10000 0 -0.95 25 25
FOS -0.1 0.2 -10000 0 -0.62 57 57
IFNG -0.22 0.34 -10000 0 -0.79 84 84
T cell activation -0.1 0.2 -10000 0 -0.86 5 5
MAF 0.008 0.058 -10000 0 -0.59 4 4
T-helper 2 cell lineage commitment 0 0 -10000 0 -10000 0 0
activation-induced cell death of T cells 0.034 0.16 0.74 8 -10000 0 8
TNF -0.13 0.31 -10000 0 -1 29 29
FASLG -0.11 0.38 -10000 0 -1.3 25 25
TBX21 -0.038 0.18 -10000 0 -0.76 22 22
BATF3 0.01 0.057 -10000 0 -0.82 2 2
PRKCQ 0.002 0.088 -10000 0 -0.66 7 7
PTPN1 -0.006 0.17 -10000 0 -0.66 12 12
NFAT1-c-4/ICER1 -0.097 0.22 -10000 0 -0.97 14 14
GATA3 -0.012 0.14 -10000 0 -0.78 14 14
T-helper 1 cell differentiation -0.2 0.35 -10000 0 -0.78 84 84
IL2RA -0.31 0.39 -10000 0 -0.99 85 85
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
CASP3 -0.006 0.17 -10000 0 -0.66 12 12
E2F1 -0.03 0.2 -10000 0 -0.81 26 26
PPARG -0.23 0.3 -10000 0 -0.59 169 169
SLC3A2 -0.006 0.17 -10000 0 -0.66 12 12
IRF4 -0.041 0.2 -10000 0 -0.76 30 30
PTGS2 -0.38 0.45 -10000 0 -1.1 75 75
CSF2 -0.54 0.51 -10000 0 -1.1 166 166
JunB/Fra1/NFAT1-c-4 -0.097 0.23 -10000 0 -1 13 13
IL4 -0.066 0.24 -10000 0 -0.81 23 23
IL5 -0.33 0.38 -10000 0 -1 49 49
IL2 -0.1 0.21 -10000 0 -0.92 4 4
IL3 -0.063 0.051 -10000 0 -10000 0 0
RNF128 -0.041 0.24 -10000 0 -0.66 55 55
NFATC1 -0.035 0.16 -10000 0 -0.74 8 8
CDK4 0.021 0.15 0.64 4 -10000 0 4
PTPRK -0.006 0.17 -10000 0 -0.66 12 12
IL8 -0.4 0.46 -10000 0 -1.1 100 100
POU2F1 0.014 0.002 -10000 0 -10000 0 0
Signaling events regulated by Ret tyrosine kinase

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
PTK2 -0.04 0.057 -9999 0 -10000 0 0
Crk/p130 Cas/Paxillin -0.1 0.14 -9999 0 -0.46 30 30
JUN -0.064 0.17 -9999 0 -0.48 31 31
HRAS 0.012 0.04 -9999 0 -0.82 1 1
RET51/GFRalpha1/GDNF/GRB10 -0.17 0.26 -9999 0 -0.62 78 78
RAP1A 0.014 0 -9999 0 -10000 0 0
FRS2 0.006 0.08 -9999 0 -0.82 4 4
RAP1A/GDP 0 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/DOK1 -0.17 0.25 -9999 0 -0.62 76 76
EntrezGene:5979 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Enigma -0.12 0.21 -9999 0 -0.61 40 40
RHOA 0.014 0 -9999 0 -10000 0 0
RAP1A/GTP -0.15 0.23 -9999 0 -0.55 76 76
GRB7 0.004 0.085 -9999 0 -0.77 5 5
RET51/GFRalpha1/GDNF -0.17 0.25 -9999 0 -0.62 76 76
MAPKKK cascade -0.13 0.19 -9999 0 -0.63 29 29
BCAR1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/IRS1 -0.12 0.2 -9999 0 -0.6 37 37
lamellipodium assembly -0.095 0.13 -9999 0 -0.41 30 30
RET51/GFRalpha1/GDNF/SHC -0.17 0.25 -9999 0 -0.62 76 76
PIK3CA 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC -0.12 0.2 -9999 0 -0.6 36 36
RET9/GFRalpha1/GDNF/Shank3 -0.12 0.2 -9999 0 -0.6 36 36
MAPK3 -0.11 0.23 -9999 0 -0.7 28 28
DOK1 0.014 0 -9999 0 -10000 0 0
DOK6 -0.005 0.11 -9999 0 -0.69 11 11
PXN 0.014 0 -9999 0 -10000 0 0
neurite development -0.093 0.22 -9999 0 -0.65 28 28
DOK5 -0.016 0.14 -9999 0 -0.64 19 19
GFRA1 -0.12 0.25 -9999 0 -0.59 96 96
MAPK8 -0.076 0.18 -9999 0 -0.51 31 31
HRAS/GTP -0.15 0.22 -9999 0 -0.73 29 29
tube development -0.11 0.19 -9999 0 -0.57 36 36
MAPK1 -0.11 0.23 -9999 0 -0.7 28 28
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.06 0.15 -9999 0 -0.54 13 13
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
PDLIM7 0.004 0.09 -9999 0 -0.82 5 5
RET51/GFRalpha1/GDNF/Dok6 -0.17 0.24 -9999 0 -0.58 83 83
SHC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/Dok4 -0.17 0.25 -9999 0 -0.62 76 76
RET51/GFRalpha1/GDNF/Dok5 -0.18 0.26 -9999 0 -0.62 87 87
PRKCA 0.012 0.04 -9999 0 -0.82 1 1
HRAS/GDP -0.001 0.031 -9999 0 -0.64 1 1
CREB1 -0.074 0.17 -9999 0 -0.49 28 28
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.057 0.15 -9999 0 -0.53 12 12
RET51/GFRalpha1/GDNF/Grb7 -0.17 0.26 -9999 0 -0.62 81 81
mol:GDP 0 0 -9999 0 -10000 0 0
RET -0.081 0.26 -9999 0 -0.79 50 50
DOK4 0.014 0 -9999 0 -10000 0 0
JNK cascade -0.063 0.16 -9999 0 -0.47 31 31
RET9/GFRalpha1/GDNF/FRS2 -0.12 0.21 -9999 0 -0.6 40 40
SHANK3 0.014 0 -9999 0 -10000 0 0
RASA1 0.012 0.029 -9999 0 -0.59 1 1
NCK1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.057 0.15 -9999 0 -0.53 12 12
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2 -0.087 0.18 -9999 0 -0.53 30 30
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK -0.085 0.18 -9999 0 -0.52 28 28
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1 -0.087 0.18 -9999 0 -0.57 28 28
PI3K -0.1 0.24 -9999 0 -0.68 30 30
SOS1 0.014 0 -9999 0 -10000 0 0
RET9/GFRalpha1/GDNF/Shank3/Grb2 -0.11 0.19 -9999 0 -0.57 36 36
GRB10 0.01 0.057 -9999 0 -0.82 2 2
activation of MAPKK activity -0.082 0.17 -9999 0 -0.52 30 30
RET51/GFRalpha1/GDNF/FRS2 -0.17 0.26 -9999 0 -0.62 79 79
GAB1 0.014 0 -9999 0 -10000 0 0
IRS1 0.011 0.041 -9999 0 -0.59 2 2
IRS2 0.011 0.041 -9999 0 -0.59 2 2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2 -0.087 0.18 -9999 0 -0.57 28 28
RET51/GFRalpha1/GDNF/PKC alpha -0.17 0.25 -9999 0 -0.61 77 77
GRB2 0.014 0 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
GDNF -0.058 0.23 -9999 0 -0.82 35 35
RAC1 0.014 0 -9999 0 -10000 0 0
RET51/GFRalpha1/GDNF/IRS1 -0.17 0.25 -9999 0 -0.62 76 76
Rac1/GTP -0.11 0.16 -9999 0 -0.51 30 30
RET9/GFRalpha1/GDNF -0.13 0.22 -9999 0 -0.46 119 119
GFRalpha1/GDNF -0.15 0.25 -9999 0 -0.52 119 119
Signaling events mediated by Stem cell factor receptor (c-Kit)

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
MAP4K1 -0.021 0.15 -10000 0 -0.43 13 13
CRKL -0.019 0.15 -10000 0 -0.41 48 48
HRAS -0.009 0.15 -10000 0 -0.57 7 7
mol:PIP3 -0.034 0.14 -10000 0 -0.41 47 47
SPRED1 0.014 0 -10000 0 -10000 0 0
SPRED2 0.012 0.029 -10000 0 -0.59 1 1
GAB1 -0.028 0.15 -10000 0 -0.44 47 47
FOXO3 -0.012 0.14 -10000 0 -0.37 42 42
AKT1 -0.022 0.15 -10000 0 -0.4 48 48
BAD -0.012 0.14 -10000 0 -0.37 47 47
megakaryocyte differentiation -0.041 0.17 -10000 0 -0.44 59 59
GSK3B -0.012 0.14 -10000 0 -0.37 47 47
RAF1 0.005 0.13 -10000 0 -0.47 5 5
SHC1 0.014 0 -10000 0 -10000 0 0
STAT3 -0.028 0.15 -10000 0 -0.44 47 47
STAT1 -0.1 0.37 -10000 0 -1.1 47 47
HRAS/SPRED1 -0.048 0.1 -10000 0 -0.47 5 5
cell proliferation -0.032 0.16 -10000 0 -0.45 47 47
PIK3CA 0.014 0 -10000 0 -10000 0 0
TEC -0.022 0.14 -10000 0 -0.59 25 25
RPS6KB1 -0.028 0.15 -10000 0 -0.43 47 47
HRAS/SPRED2 -0.048 0.1 -10000 0 -0.46 7 7
LYN/TEC/p62DOK -0.069 0.15 -10000 0 -0.59 15 15
MAPK3 0.019 0.098 -10000 0 -0.34 3 3
STAP1 -0.062 0.19 -10000 0 -0.44 77 77
GRAP2 -0.003 0.11 -10000 0 -0.7 10 10
JAK2 -0.12 0.27 -10000 0 -0.84 47 47
STAT1 (dimer) -0.099 0.36 -10000 0 -1 47 47
mol:Gleevec 0 0.007 -10000 0 -10000 0 0
GRB2/SOCS1/VAV1 -0.081 0.16 -10000 0 -0.51 19 19
actin filament polymerization -0.029 0.16 -10000 0 -0.44 48 48
LYN 0.012 0.029 -10000 0 -0.59 1 1
STAP1/STAT5A (dimer) -0.069 0.23 -10000 0 -0.6 51 51
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
CBL/CRKL/GRB2 -0.042 0.12 -10000 0 -0.56 1 1
PI3K -0.015 0.16 -10000 0 -0.42 47 47
PTEN 0.014 0 -10000 0 -10000 0 0
SCF/KIT/EPO/EPOR -0.14 0.44 -10000 0 -1.3 48 48
MAPK8 -0.033 0.17 -10000 0 -0.46 47 47
STAT3 (dimer) -0.027 0.15 -10000 0 -0.43 47 47
positive regulation of transcription 0.021 0.084 -10000 0 -10000 0 0
mol:GDP -0.069 0.14 -10000 0 -0.64 7 7
PIK3C2B -0.029 0.16 -10000 0 -0.45 47 47
CBL/CRKL -0.01 0.14 -10000 0 -0.43 6 6
FER -0.029 0.16 -10000 0 -0.44 47 47
SH2B3 -0.029 0.16 -10000 0 -0.44 48 48
PDPK1 -0.023 0.13 -10000 0 -0.37 47 47
SNAI2 -0.039 0.17 -10000 0 -0.44 56 56
positive regulation of cell proliferation -0.06 0.26 -10000 0 -0.74 47 47
KITLG 0.01 0.053 -10000 0 -0.61 3 3
cell motility -0.06 0.26 -10000 0 -0.74 47 47
PTPN6 0.008 0.013 -10000 0 -10000 0 0
EPOR -0.001 0.14 -10000 0 -0.65 8 8
STAT5A (dimer) -0.043 0.22 -10000 0 -0.6 47 47
SOCS1 -0.035 0.2 -10000 0 -0.82 25 25
cell migration 0.038 0.17 0.44 55 -10000 0 55
SOS1 0.014 0 -10000 0 -10000 0 0
EPO -0.074 0.25 -10000 0 -0.81 44 44
VAV1 0.005 0.071 -10000 0 -0.59 6 6
GRB10 -0.03 0.16 -10000 0 -0.44 49 49
PTPN11 0.014 0.006 -10000 0 -10000 0 0
SCF/KIT -0.038 0.16 -10000 0 -0.46 49 49
GO:0007205 0.001 0.009 -10000 0 -10000 0 0
MAP2K1 0.015 0.11 -10000 0 -0.37 3 3
CBL 0.014 0 -10000 0 -10000 0 0
KIT -0.11 0.43 -10000 0 -1.3 48 48
MAP2K2 0.015 0.11 -10000 0 -0.37 3 3
SHC/Grb2/SOS1 -0.053 0.13 -10000 0 -0.48 4 4
STAT5A -0.045 0.22 -10000 0 -0.62 47 47
GRB2 0.014 0 -10000 0 -10000 0 0
response to radiation -0.038 0.17 -10000 0 -0.44 56 56
SHC/GRAP2 -0.012 0.081 -10000 0 -0.53 10 10
PTPRO -0.042 0.17 -10000 0 -0.44 59 59
SH2B2 -0.03 0.16 -10000 0 -0.44 48 48
DOK1 0.014 0 -10000 0 -10000 0 0
MATK -0.039 0.17 -10000 0 -0.45 55 55
CREBBP 0.034 0.015 -10000 0 -10000 0 0
BCL2 -0.006 0.18 -10000 0 -1 8 8
IL12-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1 -0.083 0.22 -10000 0 -0.55 49 49
TBX21 -0.13 0.45 -10000 0 -1.2 44 44
B2M 0.012 0.01 -10000 0 -10000 0 0
TYK2 0.016 0.046 -10000 0 -0.84 1 1
IL12RB1 -0.058 0.25 -10000 0 -0.83 39 39
GADD45B -0.054 0.29 -10000 0 -0.84 18 18
IL12RB2 -0.13 0.32 -10000 0 -0.79 77 77
GADD45G -0.066 0.32 -10000 0 -0.84 30 30
natural killer cell activation 0.006 0.024 -10000 0 -10000 0 0
RELB 0.008 0.07 -10000 0 -0.82 3 3
RELA 0.014 0 -10000 0 -10000 0 0
IL18 -0.005 0.11 -10000 0 -0.59 15 15
IL2RA -0.067 0.24 -10000 0 -0.82 41 41
IFNG -0.16 0.34 -10000 0 -0.82 88 88
STAT3 (dimer) -0.075 0.32 -10000 0 -0.8 43 43
HLA-DRB5 -0.004 0.11 -10000 0 -0.69 10 10
FASLG -0.14 0.46 -10000 0 -1.2 51 51
NF kappa B2 p52/RelB -0.2 0.34 -10000 0 -0.97 56 56
CD4 0.01 0.05 -10000 0 -0.71 2 2
SOCS1 -0.035 0.2 -10000 0 -0.82 25 25
EntrezGene:6955 -0.005 0.016 -10000 0 -10000 0 0
CD3D -0.006 0.11 -10000 0 -0.71 10 10
CD3E -0.005 0.11 -10000 0 -0.76 9 9
CD3G -0.028 0.16 -10000 0 -0.7 23 23
IL12Rbeta2/JAK2 -0.085 0.25 -10000 0 -0.6 78 78
CCL3 -0.13 0.43 -10000 0 -1.1 46 46
CCL4 -0.12 0.42 -10000 0 -1.1 44 44
HLA-A 0.002 0.085 -10000 0 -0.77 5 5
IL18/IL18R 0.028 0.13 -10000 0 -0.49 18 18
NOS2 -0.14 0.43 -10000 0 -1 53 53
IL12/IL12R/TYK2/JAK2/SPHK2 -0.065 0.21 -10000 0 -0.54 41 41
IL1R1 -0.11 0.4 -10000 0 -1.1 42 42
IL4 -0.005 0.024 -10000 0 -10000 0 0
JAK2 0.017 0.037 -10000 0 -0.61 1 1
EntrezGene:6957 -0.005 0.016 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.097 0.32 -10000 0 -0.83 50 50
RAB7A -0.031 0.27 -10000 0 -0.74 14 14
lysosomal transport -0.027 0.26 -10000 0 -0.69 15 15
FOS -0.17 0.49 -10000 0 -1.2 65 65
STAT4 (dimer) -0.074 0.35 -10000 0 -0.88 40 40
STAT5A (dimer) -0.27 0.42 -10000 0 -1 80 80
GZMA -0.15 0.48 -10000 0 -1.2 52 52
GZMB -0.16 0.47 -10000 0 -1.1 61 61
HLX 0.008 0.07 -10000 0 -0.82 3 3
LCK -0.14 0.45 -10000 0 -1.1 50 50
TCR/CD3/MHC II/CD4 -0.031 0.19 -10000 0 -0.57 30 30
IL2/IL2R -0.073 0.21 -10000 0 -0.6 51 51
MAPK14 -0.054 0.31 -10000 0 -0.82 26 26
CCR5 -0.074 0.34 -10000 0 -1.1 22 22
IL1B -0.07 0.26 -10000 0 -0.8 46 46
STAT6 -0.01 0.12 -10000 0 -10000 0 0
STAT4 -0.002 0.11 -10000 0 -0.79 8 8
STAT3 0.014 0 -10000 0 -10000 0 0
STAT1 -0.039 0.2 -10000 0 -0.81 27 27
NFKB1 0.014 0 -10000 0 -10000 0 0
NFKB2 0.014 0 -10000 0 -10000 0 0
IL12B -0.058 0.24 -10000 0 -0.82 39 39
CD8A -0.05 0.21 -10000 0 -0.74 35 35
CD8B -0.066 0.23 -10000 0 -0.74 44 44
T-helper 1 cell differentiation 0 0 -10000 0 -10000 0 0
natural killer cell mediated cytotoxicity 0.082 0.22 0.55 49 -10000 0 49
IL2RB -0.002 0.11 -10000 0 -0.79 8 8
proteasomal ubiquitin-dependent protein catabolic process -0.063 0.32 -10000 0 -0.81 36 36
IL2RG -0.013 0.15 -10000 0 -0.8 14 14
IL12 -0.047 0.21 -10000 0 -0.59 54 54
STAT5A 0.014 0 -10000 0 -10000 0 0
CD247 -0.021 0.16 -10000 0 -0.79 17 17
IL2 0.003 0.04 -10000 0 -0.82 1 1
SPHK2 0.014 0 -10000 0 -10000 0 0
FRAP1 0 0 -10000 0 -10000 0 0
IL12A -0.005 0.12 -10000 0 -0.62 15 15
IL12/IL12R/TYK2/JAK2 -0.15 0.49 -10000 0 -1.2 56 56
MAP2K3 -0.054 0.31 -10000 0 -0.8 28 28
RIPK2 0.014 0 -10000 0 -10000 0 0
MAP2K6 -0.065 0.32 -10000 0 -0.83 30 30
regulation of dendritic cell antigen processing and presentation 0 0 -10000 0 -10000 0 0
HLA-DRA 0.007 0.065 -10000 0 -0.65 4 4
IL18RAP -0.003 0.12 -10000 0 -0.69 12 12
IL12Rbeta1/TYK2 -0.036 0.2 -10000 0 -0.65 40 40
EOMES -0.084 0.26 -10000 0 -0.68 55 55
STAT1 (dimer) -0.14 0.38 -10000 0 -0.85 66 66
T cell proliferation -0.027 0.26 0.42 1 -0.65 25 26
T-helper 1 cell lineage commitment 0 0 -10000 0 -10000 0 0
IL18R1 0.011 0.066 -10000 0 -0.76 3 3
CD8-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
NF kappa B1 p50/RelA -0.14 0.22 -10000 0 -0.73 26 26
ATF2 -0.041 0.29 -10000 0 -0.79 21 21
Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin -0.015 0.081 -9999 0 -0.48 11 11
RGS9BP -0.004 0.1 -9999 0 -0.59 12 12
mol:GTP 0 0 -9999 0 -10000 0 0
GRK1 0.001 0.04 -9999 0 -0.82 1 1
mol:Na + -0.1 0.21 -9999 0 -0.55 77 77
mol:ADP -0.055 0.2 -9999 0 -0.63 45 45
GNAT2 0.012 0.005 -9999 0 -10000 0 0
RGS9-1/Gbeta5/R9AP -0.019 0.088 -9999 0 -0.54 6 6
mol:GDP 0 0 -9999 0 -10000 0 0
PDE6H/GNAT2/GTP 0 0 -9999 0 -10000 0 0
GRK7 -0.074 0.25 -9999 0 -0.82 44 44
CNGB3 -0.14 0.32 -9999 0 -0.82 76 76
Cone Metarhodopsin II/X-Arrestin 0 0 -9999 0 -10000 0 0
mol:Ca2+ -0.18 0.29 -9999 0 -0.56 150 150
Cone PDE6 -0.016 0.075 -9999 0 -0.47 6 6
Cone Metarhodopsin II -0.055 0.16 -9999 0 -0.51 45 45
Na + (4 Units) -0.2 0.28 -9999 0 -0.56 150 150
GNAT2/GDP -0.016 0.075 -9999 0 -0.47 6 6
GNB5 0.014 0 -9999 0 -10000 0 0
mol:GMP (4 units) 0.01 0.006 -9999 0 -10000 0 0
Cone Transducin -0.016 0.085 -9999 0 -0.5 11 11
SLC24A2 -0.17 0.34 -9999 0 -0.82 92 92
GNB3/GNGT2 -0.02 0.11 -9999 0 -0.57 15 15
GNB3 -0.009 0.13 -9999 0 -0.78 12 12
GNAT2/GTP 0 0 -9999 0 -10000 0 0
CNGA3 0.006 0.041 -9999 0 -0.82 1 1
ARR3 0.002 0.004 -9999 0 -10000 0 0
absorption of light 0 0 -9999 0 -10000 0 0
cGMP/Cone CNG Channel -0.1 0.21 -9999 0 -0.55 77 77
mol:Pi -0.018 0.087 -9999 0 -0.54 6 6
Cone CNG Channel -0.083 0.18 -9999 0 -0.46 77 77
mol:all-trans-retinal 0 0 -9999 0 -10000 0 0
mol:K + -0.17 0.34 -9999 0 -0.82 92 92
RGS9 0 0.1 -9999 0 -0.78 7 7
PDE6C 0.002 0.005 -9999 0 -10000 0 0
GNGT2 0.009 0.058 -9999 0 -0.67 3 3
mol:cGMP (4 units) 0 0 -9999 0 -10000 0 0
PDE6H 0.002 0.005 -9999 0 -10000 0 0
Glucocorticoid receptor regulatory network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PCK2 0.014 0.064 -10000 0 -10000 0 0
SMARCC2 0.015 0.007 -10000 0 -10000 0 0
SMARCC1 0.015 0.007 -10000 0 -10000 0 0
TBX21 -0.097 0.23 -10000 0 -0.85 28 28
SUMO2 0.014 0.008 -10000 0 -10000 0 0
STAT1 (dimer) -0.029 0.2 -10000 0 -0.8 27 27
FKBP4 0.014 0 -10000 0 -10000 0 0
FKBP5 0.011 0.041 -10000 0 -0.59 2 2
GR alpha/HSP90/FKBP51/HSP90 0.098 0.097 0.36 9 -10000 0 9
PRL -0.1 0.17 -10000 0 -0.66 13 13
cortisol/GR alpha (dimer)/TIF2 0.19 0.24 0.59 55 -10000 0 55
RELA -0.003 0.091 -10000 0 -10000 0 0
FGG 0.12 0.26 0.55 24 -0.67 24 48
GR beta/TIF2 0.074 0.14 0.38 12 -0.4 7 19
IFNG -0.37 0.33 -10000 0 -0.86 112 112
apoptosis 0.028 0.18 0.54 7 -0.66 4 11
CREB1 0.016 0.019 -10000 0 -10000 0 0
histone acetylation 0 0.12 0.42 4 -0.43 9 13
BGLAP -0.055 0.15 -10000 0 -0.87 6 6
GR/PKAc 0.096 0.092 0.34 9 -0.43 1 10
NF kappa B1 p50/RelA -0.014 0.16 -10000 0 -0.46 7 7
SMARCD1 0.015 0.007 -10000 0 -10000 0 0
MDM2 0.083 0.084 0.3 17 -10000 0 17
GATA3 -0.008 0.14 -10000 0 -0.78 14 14
AKT1 0 0.001 -10000 0 -10000 0 0
CSF2 -0.31 0.28 -10000 0 -0.57 219 219
GSK3B 0.014 0.008 -10000 0 -10000 0 0
NR1I3 0.056 0.17 0.62 2 -0.87 2 4
CSN2 0.13 0.15 0.45 15 -0.54 2 17
BRG1/BAF155/BAF170/BAF60A 0.033 0.029 -10000 0 -10000 0 0
NFATC1 0.015 0.003 -10000 0 -10000 0 0
POU2F1 0.015 0.016 -10000 0 -10000 0 0
CDKN1A 0.03 0.04 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
response to UV 0.001 0.008 -10000 0 -10000 0 0
SFN 0.007 0.07 -10000 0 -0.7 4 4
GR alpha/HSP90/FKBP51/HSP90/14-3-3 0.097 0.099 0.4 3 -0.44 1 4
prolactin receptor activity 0 0 -10000 0 -10000 0 0
EGR1 0.036 0.22 0.52 5 -0.86 17 22
JUN -0.22 0.18 -10000 0 -0.66 32 32
IL4 -0.071 0.12 -10000 0 -0.54 4 4
CDK5R1 0.012 0.041 -10000 0 -0.82 1 1
PRKACA 0.014 0 -10000 0 -10000 0 0
cortisol/GR alpha (monomer)/AP-1 -0.15 0.31 -10000 0 -0.65 67 67
GR alpha/HSP90/FKBP51/HSP90/PP5C 0.1 0.093 0.37 5 -10000 0 5
cortisol/GR alpha (monomer) 0.25 0.27 0.69 71 -10000 0 71
NCOA2 -0.023 0.14 -10000 0 -0.59 26 26
response to hypoxia 0 0 -10000 0 -10000 0 0
FOS -0.15 0.2 -10000 0 -0.66 57 57
AP-1/NFAT1-c-4 -0.42 0.27 -10000 0 -0.82 87 87
AFP -0.16 0.2 -10000 0 -0.86 22 22
SUV420H1 0.014 0 -10000 0 -10000 0 0
IRF1 0.12 0.17 0.51 10 -10000 0 10
TP53 0.032 0.059 -10000 0 -0.57 4 4
PPP5C 0.014 0 -10000 0 -10000 0 0
KRT17 -0.4 0.39 -10000 0 -0.98 117 117
KRT14 -0.23 0.37 -10000 0 -1.1 60 60
TBP 0.021 0.024 -10000 0 -10000 0 0
CREBBP 0.074 0.085 0.31 20 -10000 0 20
HDAC1 0.012 0.011 -10000 0 -10000 0 0
HDAC2 0.044 0.031 -10000 0 -10000 0 0
AP-1 -0.42 0.27 -10000 0 -0.82 90 90
MAPK14 0.014 0.008 -10000 0 -10000 0 0
MAPK10 -0.018 0.14 -10000 0 -0.61 22 22
MAPK11 0.014 0.008 -10000 0 -10000 0 0
KRT5 -0.27 0.24 -10000 0 -0.84 32 32
interleukin-1 receptor activity 0.031 0.031 -10000 0 -10000 0 0
NCOA1 0.017 0.001 -10000 0 -10000 0 0
STAT1 -0.029 0.2 -10000 0 -0.8 27 27
CGA -0.065 0.14 -10000 0 -0.73 6 6
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2 0.26 0.21 0.42 230 -10000 0 230
MAPK3 0.014 0.008 -10000 0 -10000 0 0
MAPK1 0.014 0.008 -10000 0 -10000 0 0
ICAM1 -0.14 0.25 -10000 0 -0.75 36 36
NFKB1 -0.003 0.091 -10000 0 -10000 0 0
MAPK8 -0.17 0.17 -10000 0 -0.58 34 34
MAPK9 0.014 0.008 -10000 0 -10000 0 0
cortisol/GR alpha (dimer) 0.019 0.18 0.55 7 -0.69 4 11
BAX 0.03 0.04 -10000 0 -10000 0 0
POMC -0.17 0.32 -10000 0 -0.93 45 45
EP300 0.073 0.093 0.32 14 -0.47 2 16
cortisol/GR alpha (dimer)/p53 0.23 0.23 0.61 62 -0.54 1 63
proteasomal ubiquitin-dependent protein catabolic process 0.058 0.065 0.29 2 -10000 0 2
SGK1 0.12 0.14 -10000 0 -1.2 2 2
IL13 -0.22 0.19 -10000 0 -0.79 18 18
IL6 -0.19 0.36 -10000 0 -1.1 50 50
PRKACG 0.001 0.04 -10000 0 -0.82 1 1
IL5 -0.19 0.16 -10000 0 -0.74 11 11
IL2 -0.27 0.2 -10000 0 -0.8 21 21
CDK5 0.014 0.005 -10000 0 -10000 0 0
PRKACB 0.014 0 -10000 0 -10000 0 0
HSP90AA1 0.014 0 -10000 0 -10000 0 0
IL8 -0.22 0.34 -10000 0 -0.78 93 93
CDK5R1/CDK5 0.003 0.033 -10000 0 -0.63 1 1
NF kappa B1 p50/RelA/PKAc 0.014 0.12 -10000 0 -10000 0 0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90 0.22 0.21 0.57 58 -10000 0 58
SMARCA4 0.015 0.007 -10000 0 -10000 0 0
chromatin remodeling 0.15 0.13 0.41 36 -10000 0 36
NF kappa B1 p50/RelA/Cbp 0.072 0.16 0.41 19 -10000 0 19
JUN (dimer) -0.22 0.18 -10000 0 -0.66 32 32
YWHAH 0.014 0 -10000 0 -10000 0 0
VIPR1 -0.09 0.22 -10000 0 -0.71 33 33
NR3C1 0.14 0.16 0.49 39 -10000 0 39
NR4A1 -0.029 0.14 -10000 0 -0.55 16 16
TIF2/SUV420H1 -0.026 0.1 -10000 0 -0.43 26 26
MAPKKK cascade 0.028 0.18 0.54 7 -0.66 4 11
cortisol/GR alpha (dimer)/Src-1 0.23 0.22 0.59 64 -10000 0 64
PBX1 -0.092 0.23 -10000 0 -0.59 75 75
POU1F1 0.003 0.016 -10000 0 -10000 0 0
SELE -0.22 0.41 -10000 0 -1.1 67 67
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A 0.15 0.13 0.41 36 -10000 0 36
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90 0.22 0.21 0.57 58 -10000 0 58
mol:cortisol 0.13 0.17 0.4 77 -10000 0 77
MMP1 -0.65 0.22 -10000 0 -0.72 375 375
LPA4-mediated signaling events

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
ADCY4 0.021 0 -9999 0 -10000 0 0
ADCY5 -0.078 0.18 -9999 0 -0.38 105 105
ADCY6 0.011 0.062 -9999 0 -0.37 11 11
ADCY7 0.021 0 -9999 0 -10000 0 0
ADCY1 -0.008 0.13 -9999 0 -0.55 22 22
ADCY2 -0.11 0.18 -9999 0 -0.37 140 140
ADCY3 0.021 0 -9999 0 -10000 0 0
ADCY8 -0.001 0.09 -9999 0 -0.55 11 11
PRKCE 0.012 0 -9999 0 -10000 0 0
ADCY9 0.02 0.027 -9999 0 -0.37 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
cAMP biosynthetic process -0.049 0.098 -9999 0 -0.4 5 5
Caspase cascade in apoptosis

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
TOP1 -0.039 0.17 -10000 0 -0.41 68 68
ACTA1 -0.14 0.23 -10000 0 -0.6 74 74
NUMA1 -0.039 0.17 -10000 0 -0.41 68 68
SPTAN1 -0.063 0.23 -10000 0 -0.55 67 67
LIMK1 -0.063 0.23 -10000 0 -0.55 67 67
BIRC3 -0.016 0.15 -10000 0 -0.82 15 15
BIRC2 -0.002 0.11 -10000 0 -0.82 8 8
BAX 0.014 0 -10000 0 -10000 0 0
CASP10 -0.094 0.29 -10000 0 -0.71 70 70
CRMA 0 0 -10000 0 -10000 0 0
XIAP 0.014 0 -10000 0 -10000 0 0
PTK2 -0.038 0.17 -10000 0 -0.41 68 68
DIABLO 0.014 0 -10000 0 -10000 0 0
apoptotic nuclear changes -0.061 0.22 -10000 0 -0.53 67 67
response to UV 0 0 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
GSN -0.063 0.23 -10000 0 -0.54 70 70
MADD 0.014 0 -10000 0 -10000 0 0
TFAP2A 0 0.093 -10000 0 -0.53 7 7
BID -0.027 0.12 -10000 0 -0.36 26 26
MAP3K1 -0.012 0.073 -10000 0 -10000 0 0
TRADD 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
APAF-1/Pro-Caspase 9 0.003 0.023 -10000 0 -0.43 1 1
mol:Activated DNA 0 0 -10000 0 -10000 0 0
ARHGDIB -0.063 0.23 -10000 0 -0.55 67 67
CASP9 0.014 0.002 -10000 0 -10000 0 0
DNA repair 0.007 0.06 -10000 0 -0.2 7 7
neuron apoptosis 0.018 0.027 -10000 0 -10000 0 0
mol:NAD 0 0 -10000 0 -10000 0 0
DNA fragmentation during apoptosis -0.054 0.22 -10000 0 -0.52 67 67
APAF1 0.012 0.029 -10000 0 -0.59 1 1
CASP6 -0.002 0.1 -10000 0 -0.46 2 2
TRAF2 0.008 0.07 -10000 0 -0.82 3 3
ICAD/CAD -0.054 0.22 -10000 0 -0.74 26 26
CASP7 0.004 0.059 0.31 11 -10000 0 11
KRT18 0.003 0.065 -10000 0 -0.47 6 6
apoptosis -0.046 0.2 -10000 0 -0.66 27 27
DFFA -0.063 0.23 -10000 0 -0.54 70 70
DFFB -0.064 0.23 -10000 0 -0.55 67 67
PARP1 -0.008 0.061 0.2 7 -10000 0 7
actin filament polymerization 0.049 0.21 0.71 25 -10000 0 25
TNF -0.025 0.17 -10000 0 -0.77 21 21
CYCS -0.017 0.093 -10000 0 -0.28 25 25
SATB1 -0.004 0.11 -10000 0 -0.43 4 4
SLK -0.063 0.23 -10000 0 -0.55 67 67
p15 BID/BAX -0.017 0.11 -10000 0 -0.32 25 25
CASP2 0.035 0.068 -10000 0 -10000 0 0
JNK cascade 0.011 0.073 -10000 0 -10000 0 0
CASP3 -0.075 0.24 -10000 0 -0.57 71 71
LMNB2 0.029 0.058 -10000 0 -0.34 2 2
RIPK1 0.014 0 -10000 0 -10000 0 0
CASP4 0.011 0.041 -10000 0 -0.59 2 2
Mammalian IAPs/DIABLO -0.026 0.13 -10000 0 -0.59 19 19
negative regulation of DNA binding 0 0.092 -10000 0 -0.52 7 7
stress fiber formation -0.061 0.22 -10000 0 -0.53 67 67
GZMB -0.12 0.33 -10000 0 -0.79 74 74
CASP1 0.016 0.046 -10000 0 -0.6 2 2
LMNB1 0.029 0.058 -10000 0 -0.34 2 2
APP 0.018 0.027 -10000 0 -10000 0 0
TNFRSF1A 0.014 0 -10000 0 -10000 0 0
response to stress 0 0 -10000 0 -10000 0 0
CASP8 0.012 0 -10000 0 -10000 0 0
VIM -0.049 0.2 -10000 0 -0.46 68 68
LMNA 0.029 0.058 -10000 0 -0.34 2 2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD 0.028 0.072 -10000 0 -0.37 5 5
LRDD 0.012 0.04 -10000 0 -0.82 1 1
SREBF1 -0.063 0.23 -10000 0 -0.54 70 70
APAF-1/Caspase 9 -0.003 0.072 0.45 7 -10000 0 7
nuclear fragmentation during apoptosis -0.038 0.17 -10000 0 -0.4 68 68
CFL2 -0.052 0.22 -10000 0 -0.73 25 25
GAS2 -0.11 0.25 -10000 0 -0.58 71 71
positive regulation of apoptosis 0.032 0.058 -10000 0 -0.34 2 2
PRF1 -0.044 0.21 -10000 0 -0.8 30 30
Neurotrophic factor-mediated Trk receptor signaling

Figure S32.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S32.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.012 0.04 -10000 0 -0.82 1 1
RAS family/GTP/Tiam1 -0.091 0.11 -10000 0 -0.49 5 5
NT3 (dimer)/TRKC -0.24 0.28 -10000 0 -0.51 195 195
NT3 (dimer)/TRKB -0.24 0.28 -10000 0 -0.69 87 87
SHC/Grb2/SOS1/GAB1/PI3K 0.038 0.024 -10000 0 -10000 0 0
RAPGEF1 0.014 0 -10000 0 -10000 0 0
BDNF -0.042 0.2 -10000 0 -0.71 33 33
PIK3CA 0.014 0 -10000 0 -10000 0 0
DYNLT1 0.014 0 -10000 0 -10000 0 0
NTRK1 -0.055 0.23 -10000 0 -0.82 35 35
NTRK2 -0.17 0.3 -10000 0 -0.63 120 120
NTRK3 -0.14 0.26 -10000 0 -0.6 105 105
NT-4/5 (dimer)/TRKB -0.14 0.22 -10000 0 -0.62 39 39
neuron apoptosis 0.12 0.13 0.48 20 -10000 0 20
SHC 2-3/Grb2 -0.13 0.15 -10000 0 -0.53 20 20
SHC1 0.014 0 -10000 0 -10000 0 0
SHC2 -0.11 0.14 0.22 1 -0.42 44 45
SHC3 -0.12 0.14 -10000 0 -0.45 41 41
STAT3 (dimer) 0.013 0.055 -10000 0 -0.34 2 2
NT3 (dimer)/TRKA -0.18 0.24 -10000 0 -0.63 52 52
RIN/GDP -0.051 0.1 -10000 0 -0.28 3 3
GIPC1 0.014 0 -10000 0 -10000 0 0
KRAS 0.01 0.057 -10000 0 -0.82 2 2
DNAJA3 -0.078 0.12 0.25 2 -0.5 4 6
RIN/GTP 0 0 -10000 0 -10000 0 0
CCND1 0.013 0.12 -10000 0 -0.74 11 11
MAGED1 0.007 0.07 -10000 0 -0.7 4 4
PTPN11 0.014 0 -10000 0 -10000 0 0
RICS 0 0 -10000 0 -10000 0 0
NT-4/5 (dimer) 0.01 0.05 -10000 0 -0.7 2 2
SHC/GRB2/SOS1 0 0 -10000 0 -10000 0 0
GRB2 0.014 0 -10000 0 -10000 0 0
NGF (dimer)/TRKA/MATK -0.15 0.25 -10000 0 -0.55 119 119
TRKA/NEDD4-2 -0.052 0.17 -10000 0 -0.63 35 35
ELMO1 0.012 0.029 -10000 0 -0.59 1 1
RhoG/GTP/ELMO1/DOCK1 -0.003 0.031 -10000 0 -0.36 3 3
NGF -0.14 0.32 -10000 0 -0.8 78 78
HRAS 0.012 0.04 -10000 0 -0.82 1 1
DOCK1 0.011 0.041 -10000 0 -0.59 2 2
GAB2 0.011 0.041 -10000 0 -0.59 2 2
RIT2 0.001 0.003 -10000 0 -10000 0 0
RIT1 0.014 0 -10000 0 -10000 0 0
FRS2 0.006 0.08 -10000 0 -0.82 4 4
DNM1 -0.047 0.22 -10000 0 -0.82 31 31
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
SH2B1 (homopentamer) 0 0 -10000 0 -10000 0 0
RhoG/GTP -0.077 0.12 0.24 2 -0.48 5 7
mol:GDP -0.076 0.14 -10000 0 -0.4 11 11
NGF (dimer) -0.14 0.31 -10000 0 -0.8 78 78
RhoG/GDP -0.001 0.021 -10000 0 -0.44 1 1
RIT1/GDP -0.046 0.1 -10000 0 -0.28 3 3
TIAM1 0.006 0.065 -10000 0 -0.59 5 5
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
BDNF (dimer)/TRKB -0.14 0.21 -10000 0 -0.58 43 43
KIDINS220/CRKL/C3G -0.001 0.03 -10000 0 -0.63 1 1
SHC/RasGAP -0.001 0.021 -10000 0 -0.43 1 1
FRS2 family/SHP2 -0.005 0.052 -10000 0 -0.54 4 4
SHC/GRB2/SOS1/GAB1 0 0 -10000 0 -10000 0 0
RIT1/GTP 0 0 -10000 0 -10000 0 0
NT3 (dimer) -0.18 0.28 -10000 0 -0.59 135 135
RAP1/GDP -0.058 0.067 -10000 0 -0.36 1 1
KIDINS220/CRKL 0.012 0.04 -10000 0 -0.82 1 1
BDNF (dimer) -0.042 0.2 -10000 0 -0.71 33 33
ubiquitin-dependent protein catabolic process -0.14 0.24 -10000 0 -0.55 103 103
Schwann cell development -0.05 0.037 -10000 0 -10000 0 0
EHD4 0.014 0 -10000 0 -10000 0 0
FRS2 family/GRB2/SOS1 -0.005 0.047 -10000 0 -0.49 4 4
FRS2 family/SHP2/CRK family/C3G/GAB2 0.039 0.032 -10000 0 -10000 0 0
RAP1B 0.012 0.04 -10000 0 -0.82 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.27 0.27 -10000 0 -0.63 128 128
ABL1 0.014 0 -10000 0 -10000 0 0
SH2B family/GRB2/SOS1 0 0 -10000 0 -10000 0 0
Rap1/GTP -0.049 0.073 -10000 0 -0.57 1 1
STAT3 0.013 0.055 -10000 0 -0.34 2 2
axon guidance -0.26 0.26 -10000 0 -0.59 128 128
MAPK3 -0.11 0.24 -10000 0 -0.5 112 112
MAPK1 -0.11 0.24 -10000 0 -0.5 112 112
CDC42/GDP -0.046 0.1 -10000 0 -0.28 3 3
NTF3 -0.18 0.28 -10000 0 -0.59 135 135
NTF4 0.01 0.05 -10000 0 -0.7 2 2
NGF (dimer)/TRKA/FAIM -0.14 0.24 -10000 0 -0.56 103 103
PI3K -0.003 0.036 -10000 0 -0.43 3 3
FRS3 0.014 0 -10000 0 -10000 0 0
FAIM 0.014 0 -10000 0 -10000 0 0
GAB1 0.014 0 -10000 0 -10000 0 0
RASGRF1 -0.17 0.23 0.25 2 -0.54 94 96
SOS1 0.014 0 -10000 0 -10000 0 0
MCF2L -0.2 0.27 -10000 0 -0.71 60 60
RGS19 0.014 0 -10000 0 -10000 0 0
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.002 0.088 -10000 0 -10000 0 0
Rac1/GDP -0.046 0.1 -10000 0 -0.28 3 3
NGF (dimer)/TRKA/GRIT -0.14 0.25 -10000 0 -0.55 110 110
neuron projection morphogenesis -0.041 0.13 -10000 0 -0.5 3 3
NGF (dimer)/TRKA/NEDD4-2 -0.14 0.24 -10000 0 -0.56 103 103
MAP2K1 0.043 0 -10000 0 -10000 0 0
NGFR -0.023 0.16 -10000 0 -0.72 21 21
NGF (dimer)/TRKA/GIPC/GAIP -0.06 0.16 -10000 0 -0.56 10 10
RAS family/GTP/PI3K 0.029 0.034 -10000 0 -10000 0 0
FRS2 family/SHP2/GRB2/SOS1 -0.004 0.044 -10000 0 -0.46 4 4
NRAS 0.014 0 -10000 0 -10000 0 0
GRB2/SOS1 0 0 -10000 0 -10000 0 0
PRKCI 0.014 0 -10000 0 -10000 0 0
ChemicalAbstracts:146-91-8 0 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.029 -10000 0 -0.59 1 1
MAPKKK cascade -0.085 0.14 -10000 0 -0.48 16 16
RASA1 0.012 0.029 -10000 0 -0.59 1 1
TRKA/c-Abl -0.052 0.17 -10000 0 -0.63 35 35
SQSTM1 0.014 0 -10000 0 -10000 0 0
BDNF (dimer)/TRKB/GIPC -0.13 0.19 -10000 0 -0.53 43 43
NGF (dimer)/TRKA/p62/Atypical PKCs -0.12 0.21 -10000 0 -0.47 103 103
MATK -0.006 0.13 -10000 0 -0.82 10 10
NEDD4L 0.014 0 -10000 0 -10000 0 0
RAS family/GDP -0.056 0.064 -10000 0 -10000 0 0
NGF (dimer)/TRKA -0.085 0.13 0.27 2 -0.37 24 26
Rac1/GTP -0.12 0.13 -10000 0 -0.36 65 65
FRS2 family/SHP2/CRK family -0.005 0.049 -10000 0 -0.46 5 5
ErbB4 signaling events

Figure S33.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S33.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF -0.012 0.077 -10000 0 -10000 0 0
epithelial cell differentiation -0.075 0.12 -10000 0 -0.58 4 4
ITCH 0.027 0.019 -10000 0 -10000 0 0
WWP1 -0.008 0.072 -10000 0 -10000 0 0
FYN 0.012 0.04 -10000 0 -0.82 1 1
EGFR -0.017 0.15 -10000 0 -0.79 16 16
PRL -0.003 0.08 -10000 0 -0.82 4 4
neuron projection morphogenesis -0.035 0.17 -10000 0 -0.66 1 1
PTPRZ1 -0.003 0.1 -10000 0 -0.59 12 12
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC -0.091 0.17 -10000 0 -0.52 26 26
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta -0.088 0.21 -10000 0 -0.53 71 71
ADAM17 0.024 0.046 -10000 0 -0.59 2 2
ErbB4/ErbB4 -0.021 0.092 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 3/neuregulin 3 -0.033 0.092 -10000 0 -0.49 5 5
NCOR1 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn -0.095 0.19 -10000 0 -0.5 71 71
GRIN2B -0.074 0.2 -10000 0 -0.54 27 27
ErbB4/ErbB2/betacellulin -0.12 0.16 -10000 0 -0.63 3 3
STAT1 -0.039 0.2 -10000 0 -0.81 27 27
HBEGF 0.014 0 -10000 0 -10000 0 0
PRLR -0.11 0.25 -10000 0 -0.6 85 85
E4ICDs/ETO2 -0.013 0.079 -10000 0 -10000 0 0
axon guidance -0.018 0.089 -10000 0 -0.42 3 3
NEDD4 0.027 0.019 -10000 0 -10000 0 0
Prolactin receptor/Prolactin receptor/Prolactin -0.095 0.19 -10000 0 -0.46 87 87
CBFA2T3 0.012 0.029 -10000 0 -0.59 1 1
ErbB4/ErbB2/HBEGF -0.016 0.066 -10000 0 -0.53 3 3
MAPK3 -0.044 0.18 -10000 0 -0.69 1 1
STAT1 (dimer) -0.046 0.16 -10000 0 -0.57 26 26
MAPK1 -0.044 0.18 -10000 0 -0.69 1 1
JAK2 0.012 0.029 -10000 0 -0.59 1 1
ErbB4/ErbB2/neuregulin 1 beta -0.079 0.2 -10000 0 -0.5 73 73
NRG1 -0.082 0.25 -10000 0 -0.62 74 74
NRG3 -0.005 0.09 -10000 0 -0.65 8 8
NRG2 -0.34 0.3 -10000 0 -0.59 251 251
NRG4 -0.039 0.17 -10000 0 -0.6 36 36
heart development -0.018 0.089 -10000 0 -0.42 3 3
neural crest cell migration -0.078 0.2 -10000 0 -0.49 73 73
ERBB2 0.026 0.064 -10000 0 -0.54 5 5
WWOX/E4ICDs -0.012 0.077 -10000 0 -10000 0 0
SHC1 0.014 0 -10000 0 -10000 0 0
ErbB4/EGFR/neuregulin 4 -0.078 0.14 -10000 0 -0.48 33 33
apoptosis 0.066 0.091 0.56 4 -10000 0 4
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta -0.23 0.19 -10000 0 -0.48 83 83
ErbB4/ErbB2/epiregulin -0.097 0.16 -10000 0 -0.62 7 7
ErbB4/ErbB4/betacellulin/betacellulin -0.13 0.18 -10000 0 -0.48 44 44
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2 -0.089 0.14 -10000 0 -0.66 4 4
MDM2 -0.009 0.079 -10000 0 -10000 0 0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta -0.098 0.18 -10000 0 -0.5 70 70
STAT5A -0.009 0.083 -10000 0 -0.41 1 1
ErbB4/EGFR/neuregulin 1 beta -0.11 0.21 -10000 0 -0.52 81 81
DLG4 0.01 0.05 -10000 0 -0.7 2 2
GRB2/SHC 0 0 -10000 0 -10000 0 0
E4ICDs/TAB2/NCoR1 -0.036 0.054 -10000 0 -10000 0 0
STAT5A (dimer) -0.079 0.13 -10000 0 -0.63 4 4
MAP3K7IP2 0 0 -10000 0 -10000 0 0
STAT5B (dimer) -0.01 0.082 -10000 0 -10000 0 0
LRIG1 -0.001 0.092 -10000 0 -0.59 10 10
EREG -0.15 0.27 -10000 0 -0.6 111 111
BTC -0.18 0.28 -10000 0 -0.59 133 133
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta -0.018 0.089 -10000 0 -0.42 3 3
ERBB4 -0.021 0.093 -10000 0 -10000 0 0
STAT5B 0.014 0 -10000 0 -10000 0 0
YAP1 -0.02 0.061 -10000 0 -0.4 9 9
GRB2 0.014 0 -10000 0 -10000 0 0
ErbB4/ErbB2/neuregulin 4 -0.044 0.11 -10000 0 -0.5 5 5
glial cell differentiation 0.036 0.053 -10000 0 -10000 0 0
WWOX 0.014 0 -10000 0 -10000 0 0
cell proliferation -0.15 0.24 -10000 0 -0.69 38 38
TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC -0.063 0.15 -10000 0 -0.58 24 24
FYN -0.034 0.22 -10000 0 -0.67 34 34
LAT/GRAP2/SLP76 -0.048 0.19 -10000 0 -0.66 26 26
IKBKB 0.014 0 -10000 0 -10000 0 0
AKT1 -0.009 0.16 -10000 0 -0.46 29 29
B2M 0.013 0.005 -10000 0 -10000 0 0
IKBKG -0.018 0.041 -10000 0 -0.18 2 2
MAP3K8 0.011 0.041 -10000 0 -0.59 2 2
mol:Ca2+ -0.04 0.041 -10000 0 -0.12 23 23
integrin-mediated signaling pathway -0.003 0.03 -10000 0 -0.36 3 3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA -0.031 0.22 -10000 0 -0.68 32 32
TRPV6 -0.29 0.3 -10000 0 -0.6 207 207
CD28 -0.019 0.16 -10000 0 -0.8 17 17
SHC1 -0.037 0.22 -10000 0 -0.67 35 35
receptor internalization -0.035 0.23 -10000 0 -0.67 37 37
PRF1 -0.05 0.27 -10000 0 -0.86 37 37
KRAS 0.01 0.057 -10000 0 -0.82 2 2
GRB2 0.014 0 -10000 0 -10000 0 0
COT/AKT1 0.002 0.13 -10000 0 -0.38 26 26
LAT -0.044 0.24 -10000 0 -0.73 35 35
EntrezGene:6955 0 0.004 -10000 0 -10000 0 0
CD3D -0.004 0.11 -10000 0 -0.71 10 10
CD3E -0.002 0.11 -10000 0 -0.75 9 9
CD3G -0.025 0.16 -10000 0 -0.7 23 23
RASGRP2 0.007 0.021 -10000 0 -0.12 4 4
RASGRP1 -0.006 0.17 -10000 0 -0.48 31 31
HLA-A 0.005 0.085 -10000 0 -0.77 5 5
RASSF5 0.009 0.051 -10000 0 -0.59 3 3
RAP1A/GTP/RAPL -0.003 0.031 -10000 0 -0.36 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
mol:GDP 0.025 0.056 -10000 0 -0.13 18 18
PDK1/CARD11/BCL10/MALT1/TRAF6 -0.035 0.072 -10000 0 -0.27 14 14
PRKCA -0.009 0.093 -10000 0 -0.31 16 16
GRAP2 -0.003 0.11 -10000 0 -0.7 10 10
mol:IP3 0.047 0.19 0.24 107 -0.49 19 126
EntrezGene:6957 0 0.005 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8 -0.033 0.21 -10000 0 -0.6 39 39
ORAI1 0.16 0.16 -10000 0 -10000 0 0
CSK -0.04 0.23 -10000 0 -0.68 35 35
B7 family/CD28 -0.17 0.27 -10000 0 -0.77 50 50
CHUK 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK/ZAP-70 -0.055 0.26 -10000 0 -0.77 37 37
PTPN6 -0.044 0.23 -10000 0 -0.7 34 34
VAV1 -0.04 0.23 -10000 0 -0.68 36 36
Monovalent TCR/CD3 -0.016 0.17 -10000 0 -0.5 35 35
CBL 0.014 0 -10000 0 -10000 0 0
LCK -0.041 0.24 -10000 0 -0.72 34 34
PAG1 -0.042 0.23 -10000 0 -0.67 37 37
RAP1A 0.014 0 -10000 0 -10000 0 0
TCR/CD3/MHC I/CD8/LCK -0.057 0.26 -10000 0 -0.76 37 37
CD80 -0.2 0.36 -10000 0 -0.82 111 111
CD86 0.011 0.04 -10000 0 -0.82 1 1
PDK1/CARD11/BCL10/MALT1 -0.043 0.088 -10000 0 -0.31 22 22
HRAS 0.012 0.04 -10000 0 -0.82 1 1
GO:0035030 -0.094 0.25 -10000 0 -0.62 50 50
CD8A -0.048 0.21 -10000 0 -0.74 35 35
CD8B -0.063 0.23 -10000 0 -0.73 44 44
PTPRC -0.005 0.12 -10000 0 -0.7 11 11
PDK1/PKC theta -0.009 0.19 -10000 0 -0.58 28 28
CSK/PAG1 -0.036 0.22 -10000 0 -0.69 31 31
SOS1 0.014 0 -10000 0 -10000 0 0
peptide-MHC class I 0.012 0.066 -10000 0 -0.58 5 5
GRAP2/SLP76 -0.061 0.21 -10000 0 -0.69 31 31
STIM1 0.082 0.081 -10000 0 -10000 0 0
RAS family/GTP 0.024 0.072 -10000 0 -0.18 10 10
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin -0.041 0.25 -10000 0 -0.73 37 37
mol:DAG -0.009 0.14 -10000 0 -0.42 24 24
RAP1A/GDP 0.013 0.024 -10000 0 -10000 0 0
PLCG1 0.014 0 -10000 0 -10000 0 0
CD247 -0.018 0.16 -10000 0 -0.79 17 17
cytotoxic T cell degranulation -0.046 0.26 -10000 0 -0.82 37 37
RAP1A/GTP -0.002 0.005 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 -0.019 0.18 -10000 0 -0.55 31 31
LAT/GRAP2/SLP76/VAV1/PLCgamma1 0.032 0.23 0.26 106 -0.65 21 127
NRAS 0.014 0 -10000 0 -10000 0 0
ZAP70 -0.021 0.16 -10000 0 -0.76 19 19
GRB2/SOS1 0 0 -10000 0 -10000 0 0
LAT/GRAP2/SLP76/VAV1 -0.043 0.18 -10000 0 -0.63 26 26
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.012 0.04 -10000 0 -0.82 1 1
CD8 heterodimer -0.079 0.27 -10000 0 -0.72 58 58
CARD11 -0.034 0.19 -10000 0 -0.79 25 25
PRKCB -0.012 0.1 -10000 0 -0.37 18 18
PRKCE -0.008 0.092 -10000 0 -0.31 16 16
PRKCQ -0.023 0.21 -10000 0 -0.66 30 30
LCP2 0.008 0.07 -10000 0 -0.82 3 3
BCL10 0.014 0 -10000 0 -10000 0 0
regulation of survival gene product expression -0.003 0.14 -10000 0 -0.39 29 29
IKK complex 0.033 0.053 -10000 0 -0.13 5 5
RAS family/GDP -0.003 0.01 -10000 0 -0.086 3 3
MAP3K14 0.012 0.1 -10000 0 -0.31 15 15
PDPK1 -0.005 0.15 -10000 0 -0.45 26 26
TCR/CD3/MHC I/CD8/Fyn -0.047 0.26 -10000 0 -0.78 36 36
Canonical Wnt signaling pathway

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
HDAC1 0.003 0.016 -10000 0 -10000 0 0
AES 0.003 0.013 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
LRP6/FZD1 -0.008 0.07 -10000 0 -0.59 6 6
SMAD4 0.012 0.029 -10000 0 -0.59 1 1
DKK2 -0.016 0.15 -10000 0 -0.72 17 17
TLE1 0.003 0.013 -10000 0 -10000 0 0
MACF1 0.014 0.001 -10000 0 -10000 0 0
CTNNB1 0.036 0.12 0.27 5 -0.4 5 10
WIF1 -0.27 0.31 -10000 0 -0.61 188 188
beta catenin/RanBP3 -0.015 0.084 0.36 7 -10000 0 7
KREMEN2 -0.28 0.4 -10000 0 -0.82 149 149
DKK1 -0.25 0.38 -10000 0 -0.79 138 138
beta catenin/beta TrCP1 0.043 0.11 -10000 0 -10000 0 0
FZD1 0.004 0.09 -10000 0 -0.82 5 5
AXIN2 -0.001 0.17 -10000 0 -1.3 6 6
AXIN1 0.014 0.001 -10000 0 -10000 0 0
RAN 0.013 0 -10000 0 -10000 0 0
Axin1/APC/GSK3/beta catenin 0.006 0.025 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4 0.082 0.066 -10000 0 -10000 0 0
Axin1/APC/GSK3 0.006 0.044 0.23 2 -10000 0 2
Axin1/APC/GSK3/beta catenin/Macf1 0.051 0.081 -10000 0 -10000 0 0
HNF1A -0.011 0.11 -10000 0 -0.82 7 7
CTBP1 0.003 0.014 -10000 0 -10000 0 0
MYC 0.015 0.043 -10000 0 -0.53 1 1
RANBP3 0.013 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.21 0.27 -10000 0 -0.55 158 158
NKD1 -0.021 0.16 -10000 0 -0.79 18 18
TCF4 0.003 0.014 -10000 0 -10000 0 0
TCF3 0.003 0.014 -10000 0 -10000 0 0
WNT1/LRP6/FZD1/Axin1 -0.013 0.08 -10000 0 -0.49 11 11
Ran/GTP 0.001 0.003 -10000 0 -10000 0 0
CtBP/CBP/TCF/TLE1/AES 0.009 0.085 0.51 6 -10000 0 6
LEF1 -0.007 0.085 -10000 0 -0.77 5 5
DVL1 0.062 0.057 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
beta catenin/TCF/CtBP/CBP/TLE1/AES 0.094 0.072 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.35 0.34 -10000 0 -0.64 230 230
LRP6 0.013 0.029 -10000 0 -0.59 1 1
CSNK1A1 0.003 0.016 -10000 0 -10000 0 0
NLK 0.014 0.003 -10000 0 -10000 0 0
CCND1 -0.002 0.15 -10000 0 -0.83 11 11
WNT1 -0.001 0.098 -10000 0 -0.82 6 6
GSK3A 0.014 0.001 -10000 0 -10000 0 0
GSK3B 0.014 0.001 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
PPP2R5D 0.051 0.072 0.36 18 -10000 0 18
APC 0.028 0.082 -10000 0 -0.46 11 11
WNT1/LRP6/FZD1 0.11 0.12 0.24 188 -10000 0 188
CREBBP 0.003 0.014 -10000 0 -10000 0 0
Nongenotropic Androgen signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PTK2 0.012 0 -10000 0 -10000 0 0
GNB1/GNG2 -0.084 0.14 -10000 0 -0.5 4 4
regulation of S phase of mitotic cell cycle -0.043 0.12 -10000 0 -10000 0 0
GNAO1 0.006 0.075 -10000 0 -0.76 4 4
HRAS 0.011 0.04 -10000 0 -0.82 1 1
SHBG/T-DHT -0.001 0.027 -10000 0 -0.56 1 1
PELP1 0.013 0.001 -10000 0 -10000 0 0
AKT1 0.012 0 -10000 0 -10000 0 0
MAP2K1 -0.041 0.14 -10000 0 -0.51 2 2
T-DHT/AR -0.11 0.2 -10000 0 -0.44 108 108
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
mol:GTP -0.001 0.002 -10000 0 -0.007 57 57
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 0.012 0.029 -10000 0 -0.59 1 1
mol:GDP -0.12 0.2 -10000 0 -0.45 108 108
cell proliferation -0.05 0.19 -10000 0 -0.59 19 19
PIK3CA 0.014 0 -10000 0 -10000 0 0
FOS -0.088 0.3 -10000 0 -0.83 57 57
mol:Ca2+ -0.014 0.022 -10000 0 -0.09 10 10
MAPK3 -0.044 0.16 -10000 0 -0.5 19 19
MAPK1 -0.018 0.095 -10000 0 -0.3 2 2
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
mol:IP3 0 0.002 -10000 0 -0.004 57 57
cAMP biosynthetic process 0.012 0.033 -10000 0 -0.5 1 1
GNG2 0.014 0 -10000 0 -10000 0 0
potassium channel inhibitor activity 0 0.002 -10000 0 -0.004 57 57
HRAS/GTP -0.079 0.13 -10000 0 -0.47 5 5
actin cytoskeleton reorganization -0.002 0.023 -10000 0 -10000 0 0
SRC 0.013 0.001 -10000 0 -10000 0 0
voltage-gated calcium channel activity 0 0.002 -10000 0 -0.004 57 57
PI3K -0.003 0.031 -10000 0 -0.36 3 3
apoptosis 0.043 0.18 0.43 57 -10000 0 57
T-DHT/AR/PELP1 -0.095 0.16 -10000 0 -0.37 108 108
HRAS/GDP -0.11 0.18 -10000 0 -0.42 109 109
CREB1 -0.048 0.19 -10000 0 -0.46 57 57
RAC1-CDC42/GTP -0.002 0.024 -10000 0 -10000 0 0
AR -0.14 0.27 -10000 0 -0.6 108 108
GNB1 0.014 0 -10000 0 -10000 0 0
RAF1 -0.048 0.14 -10000 0 -0.45 5 5
RAC1-CDC42/GDP -0.1 0.17 -10000 0 -0.4 108 108
T-DHT/AR/PELP1/Src -0.085 0.15 -10000 0 -0.38 21 21
MAP2K2 -0.041 0.14 -10000 0 -0.51 2 2
T-DHT/AR/PELP1/Src/PI3K -0.043 0.13 -10000 0 -10000 0 0
GNAZ -0.015 0.15 -10000 0 -0.75 16 16
SHBG 0.011 0.04 -10000 0 -0.82 1 1
Gi family/GNB1/GNG2/GDP 0.013 0.073 -10000 0 -0.45 2 2
mol:T-DHT 0 0.001 -10000 0 -0.003 38 38
RAC1 0.014 0 -10000 0 -10000 0 0
GNRH1 -0.007 0.11 -10000 0 -0.62 13 13
Gi family/GTP -0.044 0.083 -10000 0 -0.39 8 8
CDC42 0.014 0 -10000 0 -10000 0 0
Reelin signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CDK5R1/CDK5 -0.001 0.03 -9999 0 -0.63 1 1
VLDLR 0.004 0.077 -9999 0 -0.59 7 7
CRKL 0.012 0.04 -9999 0 -0.82 1 1
LRPAP1 0.014 0 -9999 0 -10000 0 0
FYN 0.012 0.04 -9999 0 -0.82 1 1
ITGA3 -0.019 0.16 -9999 0 -0.8 17 17
RELN/VLDLR/Fyn -0.073 0.15 -9999 0 -0.37 84 84
MAPK8IP1/MKK7/MAP3K11/JNK1 -0.008 0.05 -9999 0 -0.46 2 2
AKT1 -0.027 0.12 -9999 0 -0.52 4 4
MAP2K7 0.014 0 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
DAB1 -0.02 0.15 -9999 0 -0.82 15 15
RELN/LRP8/DAB1 -0.088 0.17 -9999 0 -0.39 96 96
LRPAP1/LRP8 -0.013 0.09 -9999 0 -0.63 9 9
RELN/LRP8/DAB1/Fyn -0.083 0.16 -9999 0 -0.52 27 27
DAB1/alpha3/beta1 Integrin -0.093 0.16 -9999 0 -0.68 8 8
long-term memory -0.15 0.21 -9999 0 -0.54 57 57
DAB1/LIS1 -0.079 0.15 -9999 0 -0.5 27 27
DAB1/CRLK/C3G -0.077 0.15 -9999 0 -0.66 9 9
PIK3CA 0.014 0 -9999 0 -10000 0 0
DAB1/NCK2 -0.08 0.15 -9999 0 -0.51 27 27
ARHGEF2 0.014 0 -9999 0 -10000 0 0
mol:Src family inhibitors PP1 and PP2 0 0 -9999 0 -10000 0 0
GRIN2A -0.12 0.28 -9999 0 -0.68 79 79
CDK5R1 0.012 0.04 -9999 0 -0.82 1 1
RELN -0.098 0.24 -9999 0 -0.6 77 77
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
RELN/LRP8/Fyn -0.078 0.16 -9999 0 -0.39 84 84
GRIN2A/RELN/LRP8/DAB1/Fyn -0.15 0.22 -9999 0 -0.55 65 65
MAPK8 0.004 0.077 -9999 0 -0.59 7 7
RELN/VLDLR/DAB1 -0.083 0.16 -9999 0 -0.37 95 95
ITGB1 0.012 0.04 -9999 0 -0.82 1 1
MAP1B -0.065 0.2 -9999 0 -0.56 32 32
RELN/LRP8 -0.077 0.16 -9999 0 -0.39 83 83
GRIN2B/RELN/LRP8/DAB1/Fyn -0.087 0.17 -9999 0 -0.53 30 30
PI3K -0.003 0.036 -9999 0 -0.43 3 3
mol:PP2 0 0 -9999 0 -10000 0 0
alpha3/beta1 Integrin -0.026 0.12 -9999 0 -0.62 18 18
RAP1A -0.026 0.16 -9999 0 -0.63 8 8
PAFAH1B1 0.014 0 -9999 0 -10000 0 0
MAPK8IP1 0.008 0.064 -9999 0 -0.74 3 3
CRLK/C3G -0.001 0.03 -9999 0 -0.63 1 1
GRIN2B -0.004 0.08 -9999 0 -0.82 4 4
NCK2 0.014 0 -9999 0 -10000 0 0
neuron differentiation -0.01 0.1 -9999 0 -0.4 7 7
neuron adhesion -0.028 0.17 -9999 0 -0.6 9 9
LRP8 -0.004 0.12 -9999 0 -0.82 9 9
GSK3B -0.018 0.12 -9999 0 -0.49 4 4
RELN/VLDLR/DAB1/Fyn -0.078 0.15 -9999 0 -0.52 19 19
MAP3K11 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/P13K -0.039 0.13 -9999 0 -0.56 4 4
CDK5 0.014 0 -9999 0 -10000 0 0
MAPT -0.23 0.28 -9999 0 -0.55 184 184
neuron migration -0.018 0.16 -9999 0 -0.55 7 7
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1 -0.01 0.1 -9999 0 -0.41 7 7
RELN/VLDLR -0.074 0.15 -9999 0 -0.58 12 12
IL1-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
UBC13/UEV1A 0 0 -9999 0 -10000 0 0
PRKCZ 0.012 0.029 -9999 0 -0.59 1 1
MAP3K7IP2 0 0 -9999 0 -10000 0 0
ERC1 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4 -0.026 0.075 -9999 0 -0.53 2 2
IRAK/TOLLIP 0.034 0.003 -9999 0 -10000 0 0
IKBKB 0.014 0 -9999 0 -10000 0 0
IKBKG 0.014 0 -9999 0 -10000 0 0
IL1 alpha/IL1R2 -0.24 0.29 -9999 0 -0.57 181 181
IL1A -0.2 0.36 -9999 0 -0.8 108 108
IL1B -0.046 0.2 -9999 0 -0.61 47 47
IRAK/TRAF6/p62/Atypical PKCs -0.002 0.024 -9999 0 -10000 0 0
IL1R2 -0.11 0.25 -9999 0 -0.6 86 86
IL1R1 0.012 0.029 -9999 0 -0.59 1 1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP 0.023 0.078 -9999 0 -0.74 1 1
TOLLIP 0.014 0 -9999 0 -10000 0 0
TICAM2 0.014 0.001 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
TAK1/TAB1/TAB2 0 0 -9999 0 -10000 0 0
IKK complex/ELKS 0.071 0.019 -9999 0 -10000 0 0
JUN 0.032 0.074 -9999 0 -0.5 1 1
MAP3K7 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/PI3K -0.051 0.14 -9999 0 -0.86 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88 -0.12 0.22 -9999 0 -0.5 104 104
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4 -0.12 0.2 -9999 0 -0.46 105 105
IL1 beta fragment/IL1R1/IL1RAP -0.055 0.16 -9999 0 -0.5 45 45
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 0.025 0.078 -9999 0 -0.55 1 1
IRAK1 0.028 0.004 -9999 0 -10000 0 0
IL1RN/IL1R1 -0.12 0.2 -9999 0 -0.43 121 121
IRAK4 0.012 0.029 -9999 0 -0.59 1 1
PRKCI 0.014 0 -9999 0 -10000 0 0
TRAF6 0.012 0.04 -9999 0 -0.82 1 1
PI3K -0.003 0.036 -9999 0 -0.43 3 3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP 0.012 0.094 -9999 0 -0.84 1 1
CHUK 0.014 0 -9999 0 -10000 0 0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s -0.055 0.16 -9999 0 -0.5 45 45
IL1 beta/IL1R2 -0.13 0.21 -9999 0 -0.57 52 52
IRAK/TRAF6/TAK1/TAB1/TAB2 -0.001 0.021 -9999 0 -0.43 1 1
NF kappa B1 p50/RelA -0.045 0.13 -9999 0 -0.77 1 1
IRAK3 -0.001 0.11 -9999 0 -0.76 8 8
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4 -0.05 0.14 -9999 0 -0.86 1 1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP -0.038 0.14 -9999 0 -0.73 2 2
IL1 alpha/IL1R1/IL1RAP -0.14 0.24 -9999 0 -0.55 104 104
RELA 0.014 0 -9999 0 -10000 0 0
MAP3K7IP1 0 0 -9999 0 -10000 0 0
SQSTM1 0.014 0 -9999 0 -10000 0 0
MYD88 0.014 0 -9999 0 -10000 0 0
IRAK/TRAF6/MEKK3 0.039 0.024 -9999 0 -0.46 1 1
IL1RAP 0.01 0.05 -9999 0 -0.7 2 2
UBE2N 0.014 0 -9999 0 -10000 0 0
IRAK/TRAF6 -0.041 0.11 -9999 0 -0.7 1 1
CASP1 0.012 0.029 -9999 0 -0.59 1 1
IL1RN/IL1R2 -0.2 0.28 -9999 0 -0.53 164 164
IL1 beta fragment/IL1R1/IL1RAP/MYD88 -0.052 0.15 -9999 0 -0.47 45 45
TMEM189-UBE2V1 0.011 0.006 -9999 0 -10000 0 0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP -0.011 0.11 -9999 0 -0.7 2 2
PIK3CA 0.014 0 -9999 0 -10000 0 0
IL1RN -0.16 0.27 -9999 0 -0.59 121 121
TRAF6/TAK1/TAB1/TAB2 -0.001 0.022 -9999 0 -0.45 1 1
MAP2K6 0.022 0.069 -9999 0 -0.42 1 1
Thromboxane A2 receptor 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
TGM2 -0.055 0.22 -10000 0 -0.82 34 34
GNB1/GNG2 -0.055 0.076 -10000 0 -0.21 23 23
AKT1 0 0.12 -10000 0 -0.26 1 1
EGF -0.098 0.24 -10000 0 -0.6 77 77
mol:TXA2 0 0.001 -10000 0 -10000 0 0
FGR 0.017 0.11 -10000 0 -0.49 10 10
mol:Ca2+ -0.026 0.16 -10000 0 -0.32 38 38
LYN 0.017 0.11 -10000 0 -0.51 9 9
RhoA/GTP -0.033 0.049 -10000 0 -0.16 1 1
mol:PGI2 0 0 -10000 0 -10000 0 0
SYK -0.028 0.18 -10000 0 -0.37 28 28
GNG2 0.014 0 -10000 0 -10000 0 0
ARRB2 0.014 0 -10000 0 -10000 0 0
TP alpha/Gq family/GDP/G beta5/gamma2 0.005 0.089 -10000 0 -0.57 4 4
G beta5/gamma2 -0.071 0.1 -10000 0 -0.3 23 23
PRKCH -0.033 0.18 -10000 0 -0.38 32 32
DNM1 -0.047 0.22 -10000 0 -0.82 31 31
TXA2/TP beta/beta Arrestin3 -0.024 0.067 -10000 0 -0.26 23 23
mol:GTP 0 0.001 -10000 0 -10000 0 0
PTGDR 0.001 0.099 -10000 0 -0.75 7 7
G12 family/GTP -0.081 0.12 -10000 0 -0.33 29 29
ADRBK1 0.014 0 -10000 0 -10000 0 0
ADRBK2 0.012 0.04 -10000 0 -0.82 1 1
RhoA/GTP/ROCK1 0 0 -10000 0 -10000 0 0
mol:GDP 0.012 0.12 0.37 18 -10000 0 18
mol:NADP 0.002 0.098 -10000 0 -0.82 6 6
RAB11A 0.014 0 -10000 0 -10000 0 0
PRKG1 -0.022 0.16 -10000 0 -0.74 20 20
mol:IP3 -0.041 0.19 -10000 0 -0.4 41 41
cell morphogenesis 0 0 -10000 0 -10000 0 0
PLCB2 -0.068 0.25 -10000 0 -0.51 74 74
mol:cGMP 0 0.001 -10000 0 -10000 0 0
BLK -0.042 0.18 -10000 0 -0.5 28 28
mol:PDG2 0 0 -10000 0 -10000 0 0
HCK 0.014 0.12 -10000 0 -0.52 8 8
RHOA 0.014 0 -10000 0 -10000 0 0
PTGIR -0.016 0.15 -10000 0 -0.82 15 15
PRKCB1 -0.041 0.19 -10000 0 -0.38 75 75
GNAQ 0.014 0 -10000 0 -10000 0 0
mol:L-citrulline 0.002 0.098 -10000 0 -0.82 6 6
TXA2/TXA2-R family -0.068 0.25 -10000 0 -0.52 75 75
LCK 0.008 0.13 -10000 0 -0.49 14 14
TXA2/TP beta/beta Arrestin3/RAB11/GDP -0.037 0.13 -10000 0 -0.51 26 26
TXA2-R family/G12 family/GDP/G beta/gamma 0.022 0.047 -10000 0 -0.38 1 1
TXA2/TP beta/beta Arrestin2/RAB11/GDP -0.037 0.13 -10000 0 -0.51 26 26
MAPK14 -0.006 0.13 -10000 0 -0.25 5 5
TGM2/GTP -0.054 0.22 -10000 0 -0.49 35 35
MAPK11 -0.006 0.13 -10000 0 -10000 0 0
ARHGEF1 -0.006 0.099 -10000 0 -0.22 2 2
GNAI2 0.014 0 -10000 0 -10000 0 0
JNK cascade -0.04 0.2 -10000 0 -0.38 75 75
RAB11/GDP 0.014 0.002 -10000 0 -10000 0 0
ICAM1 -0.026 0.16 -10000 0 -0.35 32 32
cAMP biosynthetic process -0.041 0.18 -10000 0 -0.39 34 34
Gq family/GTP/EBP50 -0.01 0.1 -10000 0 -0.66 3 3
actin cytoskeleton reorganization 0 0 -10000 0 -10000 0 0
SRC 0.018 0.11 -10000 0 -0.51 9 9
GNB5 0.014 0 -10000 0 -10000 0 0
GNB1 0.014 0 -10000 0 -10000 0 0
EGF/EGFR -0.001 0.11 -10000 0 -0.34 14 14
VCAM1 -0.034 0.17 -10000 0 -0.36 53 53
TP beta/Gq family/GDP/G beta5/gamma2 0.005 0.089 -10000 0 -0.57 4 4
platelet activation -0.011 0.17 -10000 0 -0.32 28 28
PGI2/IP -0.022 0.12 -10000 0 -0.64 15 15
PRKACA 0.006 0.083 -10000 0 -0.36 19 19
Gq family/GDP/G beta5/gamma2 0.008 0.079 -10000 0 -0.46 4 4
TXA2/TP beta/beta Arrestin2 -0.029 0.092 -10000 0 -0.36 30 30
positive regulation of NF-kappaB transcription factor activity 0 0 -10000 0 -10000 0 0
TBXA2R -0.014 0.16 -10000 0 -0.54 31 31
mol:DAG -0.049 0.21 -10000 0 -0.42 75 75
EGFR -0.017 0.15 -10000 0 -0.79 16 16
TXA2/TP alpha -0.062 0.24 -10000 0 -0.54 36 36
Gq family/GTP -0.038 0.094 -10000 0 -0.24 69 69
YES1 0.018 0.11 -10000 0 -0.51 9 9
GNAI2/GTP -0.033 0.12 -10000 0 -0.61 9 9
PGD2/DP -0.01 0.075 -10000 0 -0.58 7 7
SLC9A3R1 0.008 0.058 -10000 0 -0.59 4 4
FYN 0.017 0.12 -10000 0 -0.52 10 10
mol:NO 0.002 0.098 -10000 0 -0.82 6 6
GNA15 0.011 0.041 -10000 0 -0.59 2 2
PGK/cGMP -0.031 0.12 -10000 0 -0.5 26 26
RhoA/GDP 0.014 0.002 -10000 0 -10000 0 0
TP alpha/TGM2/GDP/G beta/gamma -0.068 0.18 -10000 0 -0.8 15 15
NOS3 0.002 0.098 -10000 0 -0.82 6 6
RAC1 0.014 0 -10000 0 -10000 0 0
PRKCA -0.034 0.18 -10000 0 -0.38 32 32
PRKCB -0.038 0.19 -10000 0 -0.4 37 37
PRKCE -0.033 0.18 -10000 0 -0.38 32 32
PRKCD -0.038 0.19 -10000 0 -0.38 71 71
PRKCG -0.061 0.22 -10000 0 -0.43 78 78
muscle contraction -0.057 0.24 -10000 0 -0.48 75 75
PRKCZ -0.028 0.18 -10000 0 -0.37 28 28
ARR3 0.002 0.004 -10000 0 -10000 0 0
TXA2/TP beta -0.038 0.13 -10000 0 -0.51 27 27
PRKCQ -0.037 0.18 -10000 0 -0.4 36 36
MAPKKK cascade -0.054 0.22 -10000 0 -0.44 77 77
SELE -0.04 0.19 -10000 0 -0.39 71 71
TP beta/GNAI2/GDP/G beta/gamma -0.036 0.13 -10000 0 -0.69 9 9
ROCK1 0.014 0 -10000 0 -10000 0 0
GNA14 -0.083 0.22 -10000 0 -0.59 68 68
chemotaxis -0.081 0.29 -10000 0 -0.61 74 74
GNA12 0.006 0.08 -10000 0 -0.82 4 4
GNA13 0.014 0 -10000 0 -10000 0 0
GNA11 0.009 0.051 -10000 0 -0.59 3 3
Rac1/GTP 0.006 0.006 -10000 0 -10000 0 0
EPHB forward 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
Ephrin A5/EPHB2 -0.12 0.23 -10000 0 -0.54 98 98
cell-cell adhesion 0.11 0.17 0.63 6 -10000 0 6
Ephrin B/EPHB2/RasGAP -0.11 0.2 -10000 0 -0.48 84 84
ITSN1 0.014 0 -10000 0 -10000 0 0
PIK3CA 0.014 0 -10000 0 -10000 0 0
SHC1 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB3 -0.01 0.06 -10000 0 -0.36 12 12
Ephrin B1/EPHB1 -0.032 0.12 -10000 0 -0.49 28 28
HRAS/GDP -0.056 0.11 -10000 0 -0.57 5 5
Ephrin B/EPHB1/GRB7 -0.05 0.14 -10000 0 -0.49 25 25
Endophilin/SYNJ1 -0.072 0.2 -10000 0 -0.44 84 84
KRAS 0.01 0.057 -10000 0 -0.82 2 2
Ephrin B/EPHB1/Src -0.045 0.13 -10000 0 -0.49 21 21
endothelial cell migration -0.003 0.028 -10000 0 -10000 0 0
GRB2 0.014 0 -10000 0 -10000 0 0
GRB7 0.004 0.085 -10000 0 -0.77 5 5
PAK1 -0.088 0.22 -10000 0 -0.68 13 13
HRAS 0.012 0.04 -10000 0 -0.82 1 1
RRAS -0.073 0.2 -10000 0 -0.45 84 84
DNM1 -0.047 0.22 -10000 0 -0.82 31 31
cell-cell signaling 0 0 -10000 0 -10000 0 0
CRK -0.007 0.14 -10000 0 -0.47 21 21
lamellipodium assembly -0.11 0.17 -10000 0 -0.63 6 6
Ephrin B/EPHB1/Src/p52 SHC/GRB2 0.009 0.095 -10000 0 -0.47 3 3
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
EPHB2 -0.15 0.33 -10000 0 -0.82 84 84
EPHB3 -0.003 0.1 -10000 0 -0.59 12 12
EPHB1 -0.036 0.19 -10000 0 -0.74 28 28
EPHB4 0.014 0 -10000 0 -10000 0 0
mol:GDP -0.051 0.11 -10000 0 -0.55 5 5
Ephrin B/EPHB2 -0.11 0.2 -10000 0 -0.48 84 84
Ephrin B/EPHB3 -0.027 0.089 -10000 0 -0.54 2 2
JNK cascade -0.084 0.22 -10000 0 -0.46 102 102
Ephrin B/EPHB1 -0.046 0.13 -10000 0 -0.5 21 21
RAP1/GDP -0.043 0.097 -10000 0 -0.49 4 4
EFNB2 0.012 0.029 -10000 0 -0.59 1 1
EFNB3 -0.023 0.14 -10000 0 -0.6 25 25
EFNB1 0.014 0 -10000 0 -10000 0 0
Ephrin B2/EPHB1-2 -0.13 0.22 -10000 0 -0.51 102 102
RAP1B 0.012 0.04 -10000 0 -0.82 1 1
RAP1A 0.014 0 -10000 0 -10000 0 0
CDC42/GTP -0.11 0.17 -10000 0 -0.7 6 6
Rap1/GTP -0.11 0.17 -10000 0 -0.65 6 6
axon guidance -0.12 0.23 -10000 0 -0.54 98 98
MAPK3 0.025 0.086 -10000 0 -0.41 3 3
MAPK1 0.025 0.086 -10000 0 -0.41 3 3
Rac1/GDP -0.009 0.12 -10000 0 -0.52 4 4
actin cytoskeleton reorganization -0.087 0.13 -10000 0 -0.54 5 5
CDC42/GDP -0.009 0.12 -10000 0 -0.52 4 4
PI3K -0.003 0.029 -10000 0 -10000 0 0
EFNA5 -0.013 0.12 -10000 0 -0.59 19 19
Ephrin B2/EPHB4 -0.001 0.018 -10000 0 -0.36 1 1
Ephrin B/EPHB2/Intersectin/N-WASP -0.036 0.14 -10000 0 -0.57 3 3
CDC42 0.014 0 -10000 0 -10000 0 0
RAS family/GTP -0.11 0.17 -10000 0 -0.64 7 7
PTK2 0.026 0.045 -10000 0 -10000 0 0
MAP4K4 -0.085 0.22 -10000 0 -0.46 102 102
SRC 0.014 0 -10000 0 -10000 0 0
KALRN -0.029 0.16 -10000 0 -0.59 30 30
Intersectin/N-WASP 0 0 -10000 0 -10000 0 0
neuron projection morphogenesis -0.041 0.17 -10000 0 -0.48 11 11
MAP2K1 0.018 0.09 -10000 0 -0.44 3 3
WASL 0.014 0 -10000 0 -10000 0 0
Ephrin B1/EPHB1-2/NCK1 -0.13 0.22 -10000 0 -0.5 102 102
cell migration 0.021 0.1 -10000 0 -0.5 3 3
NRAS 0.014 0 -10000 0 -10000 0 0
SYNJ1 -0.073 0.2 -10000 0 -0.45 84 84
PXN 0.014 0 -10000 0 -10000 0 0
TF -0.26 0.24 -10000 0 -0.67 78 78
HRAS/GTP -0.12 0.18 -10000 0 -0.72 7 7
Ephrin B1/EPHB1-2 -0.13 0.22 -10000 0 -0.51 102 102
cell adhesion mediated by integrin 0.014 0.081 0.45 2 -10000 0 2
RAC1 0.014 0 -10000 0 -10000 0 0
mol:GTP -0.12 0.2 -10000 0 -0.78 6 6
RAC1-CDC42/GTP -0.11 0.17 -10000 0 -0.69 6 6
RASA1 0.012 0.029 -10000 0 -0.59 1 1
RAC1-CDC42/GDP -0.042 0.096 -10000 0 -0.49 4 4
ruffle organization -0.06 0.2 -10000 0 -0.74 4 4
NCK1 0.014 0 -10000 0 -10000 0 0
receptor internalization -0.094 0.24 -10000 0 -0.84 17 17
Ephrin B/EPHB2/KALRN -0.13 0.21 -10000 0 -0.49 89 89
ROCK1 0.017 0.058 -10000 0 -10000 0 0
RAS family/GDP -0.084 0.13 -10000 0 -0.54 5 5
Rac1/GTP -0.11 0.18 -10000 0 -0.7 6 6
Ephrin B/EPHB1/Src/Paxillin 0.003 0.1 -10000 0 -0.52 3 3
BCR signaling pathway

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
JUN -0.026 0.14 -10000 0 -0.43 20 20
IKBKB -0.007 0.078 -10000 0 -0.27 6 6
AKT1 -0.025 0.12 -10000 0 -0.28 35 35
IKBKG -0.006 0.082 -10000 0 -0.29 6 6
CALM1 -0.043 0.12 -10000 0 -0.41 23 23
PIK3CA 0.014 0 -10000 0 -10000 0 0
MAP3K1 -0.052 0.2 -10000 0 -0.48 58 58
MAP3K7 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ -0.053 0.12 -10000 0 -0.44 24 24
DOK1 0.014 0 -10000 0 -10000 0 0
AP-1 -0.021 0.097 -10000 0 -0.26 11 11
LYN 0.012 0.029 -10000 0 -0.59 1 1
BLNK -0.048 0.18 -10000 0 -0.59 43 43
SHC1 0.014 0 -10000 0 -10000 0 0
BCR complex -0.13 0.27 -10000 0 -0.63 88 88
CD22 -0.12 0.26 -10000 0 -0.82 41 41
CAMK2G -0.032 0.11 -10000 0 -0.38 23 23
CSNK2A1 0.014 0 -10000 0 -10000 0 0
INPP5D 0.011 0.041 -10000 0 -0.59 2 2
SHC/GRB2/SOS1 -0.11 0.19 -10000 0 -0.65 23 23
GO:0007205 -0.054 0.12 -10000 0 -0.44 24 24
SYK 0.011 0.041 -10000 0 -0.59 2 2
ELK1 -0.045 0.12 -10000 0 -0.42 24 24
NFATC1 -0.064 0.19 -10000 0 -0.47 58 58
B-cell antigen/BCR complex -0.13 0.27 -10000 0 -0.63 88 88
PAG1/CSK -0.003 0.043 -10000 0 -0.63 2 2
NFKBIB 0.008 0.03 -10000 0 -10000 0 0
HRAS -0.047 0.13 -10000 0 -0.45 23 23
NFKBIA 0.009 0.029 -10000 0 -10000 0 0
NF-kappa-B/RelA/I kappa B beta 0.015 0.025 -10000 0 -10000 0 0
RasGAP/Csk -0.1 0.21 -10000 0 -0.55 64 64
mol:GDP -0.052 0.12 -10000 0 -0.42 24 24
PTEN 0.014 0 -10000 0 -10000 0 0
CD79B -0.012 0.14 -10000 0 -0.75 14 14
NF-kappa-B/RelA/I kappa B alpha 0.015 0.024 -10000 0 -10000 0 0
GRB2 0.014 0 -10000 0 -10000 0 0
PI3K/BCAP/CD19 -0.09 0.23 -10000 0 -0.55 67 67
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
mol:IP3 -0.063 0.12 -10000 0 -0.45 24 24
CSK 0.014 0 -10000 0 -10000 0 0
FOS -0.073 0.16 -10000 0 -0.44 42 42
CHUK -0.006 0.082 -10000 0 -0.29 6 6
IBTK 0.014 0 -10000 0 -10000 0 0
CARD11/BCL10/MALT1/TAK1 -0.067 0.13 -10000 0 -0.56 12 12
PTPN6 -0.11 0.24 -10000 0 -0.77 40 40
RELA 0.014 0 -10000 0 -10000 0 0
BCL2A1 0.008 0.039 -10000 0 -0.13 26 26
VAV2 -0.15 0.26 -10000 0 -0.74 59 59
ubiquitin-dependent protein catabolic process 0.013 0.029 -10000 0 -10000 0 0
BTK -0.003 0.03 -10000 0 -10000 0 0
CD19 -0.15 0.29 -10000 0 -0.77 67 67
MAP4K1 -0.006 0.12 -10000 0 -0.76 11 11
CD72 -0.066 0.24 -10000 0 -0.81 41 41
PAG1 0.01 0.057 -10000 0 -0.82 2 2
MAPK14 -0.034 0.17 -10000 0 -0.52 22 22
SH3BP5 0.011 0.041 -10000 0 -0.59 2 2
PIK3AP1 -0.058 0.15 -10000 0 -0.47 36 36
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72 -0.081 0.2 -10000 0 -0.59 34 34
RAF1 -0.036 0.13 -10000 0 -0.42 23 23
RasGAP/p62DOK/SHIP -0.097 0.2 -10000 0 -0.77 17 17
CD79A -0.14 0.31 -10000 0 -0.74 87 87
re-entry into mitotic cell cycle -0.022 0.097 -10000 0 -0.26 11 11
RASA1 0.012 0.029 -10000 0 -0.59 1 1
MAPK3 -0.015 0.11 -10000 0 -0.44 2 2
MAPK1 -0.015 0.11 -10000 0 -0.44 2 2
CD72/SHP1 -0.098 0.3 -10000 0 -0.88 39 39
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 -0.039 0.18 -10000 0 -0.53 23 23
actin cytoskeleton organization -0.086 0.24 -10000 0 -0.61 58 58
NF-kappa-B/RelA 0.035 0.047 -10000 0 -10000 0 0
Calcineurin -0.045 0.086 -10000 0 -0.47 2 2
PI3K -0.12 0.22 -10000 0 -0.61 60 60
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2 -0.066 0.13 0.24 2 -0.47 25 27
SOS1 0.014 0 -10000 0 -10000 0 0
Bam32/HPK1 -0.055 0.22 -10000 0 -0.77 26 26
DAPP1 -0.085 0.2 -10000 0 -0.77 24 24
cytokine secretion -0.058 0.18 -10000 0 -0.43 58 58
mol:DAG -0.063 0.12 -10000 0 -0.45 24 24
PLCG2 0.012 0.029 -10000 0 -0.59 1 1
MAP2K1 -0.026 0.12 -10000 0 -0.4 12 12
B-cell antigen/BCR complex/FcgammaRIIB -0.12 0.24 -10000 0 -0.64 64 64
mol:PI-3-4-5-P3 -0.086 0.15 -10000 0 -0.41 57 57
ETS1 -0.025 0.11 -10000 0 -0.41 7 7
B-cell antigen/BCR complex/LYN/SYK/BLNK -0.13 0.22 -10000 0 -0.55 71 71
B-cell antigen/BCR complex/LYN -0.087 0.19 -10000 0 -0.76 19 19
MALT1 0.014 0 -10000 0 -10000 0 0
TRAF6 0.012 0.04 -10000 0 -0.82 1 1
RAC1 -0.095 0.26 -10000 0 -0.66 58 58
B-cell antigen/BCR complex/LYN/SYK -0.12 0.26 -10000 0 -0.86 36 36
CARD11 -0.069 0.17 -10000 0 -0.5 43 43
FCGR2B 0.005 0.071 -10000 0 -0.59 6 6
PPP3CA 0.014 0 -10000 0 -10000 0 0
BCL10 0.014 0 -10000 0 -10000 0 0
IKK complex 0.008 0.039 -10000 0 -10000 0 0
PTPRC -0.005 0.11 -10000 0 -0.69 11 11
PDPK1 -0.025 0.12 -10000 0 -0.29 32 32
PPP3CB 0.014 0 -10000 0 -10000 0 0
PPP3CC 0.014 0 -10000 0 -10000 0 0
POU2F2 0.009 0.04 -10000 0 -0.14 25 25
Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity 0.054 0.17 0.6 37 -10000 0 37
KIRREL -0.012 0.12 -10000 0 -0.67 13 13
Nephrin/NEPH1Par3/Par6/Atypical PKCs -0.054 0.17 -10000 0 -0.6 37 37
PLCG1 0.014 0 -10000 0 -10000 0 0
ARRB2 0.014 0 -10000 0 -10000 0 0
WASL 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/CD2AP -0.05 0.16 -10000 0 -0.54 34 34
ChemicalAbstracts:57-88-5 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP -0.003 0.11 -10000 0 -0.57 6 6
FYN -0.029 0.15 -10000 0 -0.49 35 35
mol:Ca2+ -0.049 0.16 -10000 0 -0.54 34 34
mol:DAG -0.05 0.16 -10000 0 -0.54 34 34
NPHS2 -0.022 0.13 -10000 0 -0.85 10 10
mol:IP3 -0.05 0.16 -10000 0 -0.54 34 34
regulation of endocytosis -0.043 0.14 -10000 0 -0.48 28 28
Nephrin/NEPH1/podocin/Cholesterol -0.051 0.16 -10000 0 -0.55 34 34
establishment of cell polarity -0.054 0.17 -10000 0 -0.6 37 37
Nephrin/NEPH1/podocin/NCK1-2 -0.045 0.15 -10000 0 -0.5 34 34
Nephrin/NEPH1/beta Arrestin2 -0.02 0.15 -10000 0 -0.49 28 28
NPHS1 -0.044 0.2 -10000 0 -0.83 25 25
Nephrin/NEPH1/podocin -0.047 0.15 -10000 0 -0.5 35 35
TJP1 0.014 0 -10000 0 -10000 0 0
NCK1 0.014 0 -10000 0 -10000 0 0
NCK2 0.014 0 -10000 0 -10000 0 0
heterophilic cell adhesion 0 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/PLCgamma1 -0.05 0.16 -10000 0 -0.54 34 34
CD2AP 0.014 0 -10000 0 -10000 0 0
Nephrin/NEPH1/podocin/GRB2 -0.05 0.16 -10000 0 -0.54 34 34
GRB2 0.014 0 -10000 0 -10000 0 0
homophilic cell adhesion 0 0 -10000 0 -10000 0 0
TRPC6 -0.056 0.2 -10000 0 -0.52 57 57
cytoskeleton organization -0.005 0.14 -10000 0 -0.76 6 6
Nephrin/NEPH1 -0.04 0.13 -10000 0 -0.45 37 37
Nephrin/NEPH1/ZO-1 -0.044 0.14 -10000 0 -0.54 29 29
Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer -0.01 0.077 -9999 0 -0.6 7 7
alphaV beta3 Integrin -0.041 0.14 -9999 0 -0.5 35 35
PTK2 -0.009 0.16 -9999 0 -0.61 9 9
IGF1R 0.012 0.04 -9999 0 -0.82 1 1
PI4KB 0.014 0 -9999 0 -10000 0 0
MFGE8 0.014 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
CDKN1B -0.041 0.11 -9999 0 -0.41 30 30
VEGFA 0.004 0.09 -9999 0 -0.82 5 5
ILK -0.041 0.11 -9999 0 -0.41 30 30
ROCK1 0.014 0 -9999 0 -10000 0 0
AKT1 -0.004 0.12 -9999 0 -0.5 4 4
PTK2B 0.009 0.13 -9999 0 -0.49 23 23
alphaV/beta3 Integrin/JAM-A -0.067 0.17 -9999 0 -0.51 49 49
CBL 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
alphaV beta3 Integrin/ANGPTL3 -0.031 0.12 -9999 0 -0.55 20 20
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.051 0.12 -9999 0 -0.51 7 7
VEGF/Rho/ROCK/alphaV/beta3 Integrin 0.013 0.091 -9999 0 -0.43 5 5
alphaV/beta3 Integrin/Syndecan-1 -0.027 0.12 -9999 0 -0.55 17 17
PI4KA 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.28 0.26 -9999 0 -0.79 42 42
PI4 Kinase 0 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Osteopontin -0.3 0.29 -9999 0 -0.56 221 221
RPS6KB1 -0.23 0.26 -9999 0 -0.72 42 42
TLN1 0.01 0.057 -9999 0 -0.82 2 2
MAPK3 -0.12 0.16 -9999 0 -0.61 29 29
GPR124 0.006 0.08 -9999 0 -0.82 4 4
MAPK1 -0.12 0.16 -9999 0 -0.61 29 29
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
alphaV/beta3 Integrin/Tumstatin -0.087 0.2 -9999 0 -0.58 52 52
cell adhesion -0.026 0.1 -9999 0 -0.46 17 17
ANGPTL3 -0.001 0.069 -9999 0 -0.82 3 3
VEGFR2 homodimer/VEGFA homodimer/Src -0.008 0.066 -9999 0 -0.54 6 6
IGF-1R heterotetramer 0.012 0.04 -9999 0 -0.82 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
TGFBR2 0.012 0.029 -9999 0 -0.59 1 1
ITGB3 -0.022 0.16 -9999 0 -0.74 20 20
IGF1 -0.077 0.22 -9999 0 -0.61 62 62
RAC1 0.014 0 -9999 0 -10000 0 0
regulation of cell-matrix adhesion -0.032 0.13 -9999 0 -0.57 20 20
apoptosis 0.006 0.075 -9999 0 -0.76 4 4
CD47 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/CD47 -0.027 0.12 -9999 0 -0.55 17 17
VCL 0.012 0.029 -9999 0 -0.59 1 1
alphaV/beta3 Integrin/Del1 -0.093 0.21 -9999 0 -0.58 55 55
CSF1 0.006 0.065 -9999 0 -0.59 5 5
PIK3C2A -0.041 0.11 -9999 0 -0.41 30 30
PI4 Kinase/Pyk2 -0.062 0.15 -9999 0 -0.8 6 6
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.032 0.12 -9999 0 -0.52 23 23
FAK1/Vinculin 0.002 0.13 -9999 0 -0.5 6 6
alphaV beta3/Integrin/ppsTEM5 -0.032 0.13 -9999 0 -0.57 20 20
RHOA 0.014 0 -9999 0 -10000 0 0
VTN -0.045 0.21 -9999 0 -0.82 30 30
BCAR1 0.014 0 -9999 0 -10000 0 0
FGF2 -0.01 0.12 -9999 0 -0.65 15 15
F11R 0.007 0.095 -9999 0 -0.48 15 15
alphaV/beta3 Integrin/Lactadherin -0.027 0.12 -9999 0 -0.55 17 17
alphaV/beta3 Integrin/TGFBR2 -0.028 0.12 -9999 0 -0.49 24 24
alphaV/beta3 Integrin/c-FMS/Cbl/Cas -0.008 0.055 -9999 0 -0.49 3 3
HSP90AA1 0.014 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Talin -0.027 0.11 -9999 0 -0.51 19 19
mol:GDP 0 0 -9999 0 -10000 0 0
FN1 -0.39 0.42 -9999 0 -0.82 207 207
alphaV/beta3 Integrin/Pyk2 0.009 0.13 -9999 0 -0.49 23 23
SDC1 0.014 0 -9999 0 -10000 0 0
VAV3 0.012 0.1 -9999 0 -0.51 5 5
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.011 0.041 -9999 0 -0.59 2 2
FAK1/Paxillin 0.002 0.13 -9999 0 -0.48 7 7
cell migration 0.012 0.12 -9999 0 -0.45 5 5
ITGAV 0.006 0.075 -9999 0 -0.76 4 4
PI3K -0.062 0.16 -9999 0 -0.74 8 8
SPP1 -0.4 0.42 -9999 0 -0.82 214 214
KDR 0.01 0.05 -9999 0 -0.7 2 2
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
alphaV/beta3 Integrin/Caspase 8 0.006 0.075 -9999 0 -0.76 4 4
COL4A3 -0.081 0.26 -9999 0 -0.76 52 52
angiogenesis -0.088 0.18 -9999 0 -0.66 20 20
Rac1/GTP -0.024 0.083 -9999 0 -0.55 2 2
EDIL3 -0.091 0.26 -9999 0 -0.74 59 59
cell proliferation -0.028 0.12 -9999 0 -0.49 24 24
Regulation of nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EP300 0.005 0.042 -10000 0 -0.58 2 2
HSPA8 0.016 0.005 -10000 0 -10000 0 0
SMAD3/SMAD4/ER alpha 0.041 0.17 -10000 0 -0.54 19 19
AKT1 0.001 0.032 -10000 0 -10000 0 0
GSC -0.019 0.19 -10000 0 -0.65 32 32
NKX2-5 -0.17 0.33 -10000 0 -0.75 102 102
muscle cell differentiation 0.13 0.21 0.67 35 -10000 0 35
SMAD2-3/SMAD4/SP1 -0.05 0.1 -10000 0 -10000 0 0
SMAD4 0.001 0.046 -10000 0 -0.56 1 1
CBFB 0.014 0 -10000 0 -10000 0 0
SAP18 0.015 0.002 -10000 0 -10000 0 0
Cbp/p300/MSG1 -0.006 0.08 -10000 0 -0.54 8 8
SMAD3/SMAD4/VDR 0.005 0.043 -10000 0 -10000 0 0
MYC 0.027 0.033 -10000 0 -10000 0 0
CDKN2B -0.24 0.57 -10000 0 -1.4 85 85
AP1 -0.006 0.11 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1 0.056 0.041 -10000 0 -10000 0 0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1 -0.056 0.16 -10000 0 -0.57 11 11
SP3 0.016 0.001 -10000 0 -10000 0 0
CREB1 0.014 0 -10000 0 -10000 0 0
FOXH1 -0.092 0.27 -10000 0 -0.81 53 53
SMAD3/SMAD4/GR 0.034 0.068 -10000 0 -10000 0 0
GATA3 -0.012 0.14 -10000 0 -0.78 14 14
SKI/SIN3/HDAC complex/NCoR1 0.056 0.024 -10000 0 -10000 0 0
MEF2C/TIF2 -0.15 0.27 -10000 0 -0.78 38 38
endothelial cell migration 0.37 0.33 0.65 249 -10000 0 249
MAX 0.035 0.02 -10000 0 -10000 0 0
RBBP7 0.015 0.002 -10000 0 -10000 0 0
RBBP4 0.012 0.042 -10000 0 -0.59 2 2
RUNX2 0.011 0.041 -10000 0 -0.59 2 2
RUNX3 0.004 0.09 -10000 0 -0.82 5 5
RUNX1 0.014 0 -10000 0 -10000 0 0
CTBP1 0.014 0 -10000 0 -10000 0 0
NR3C1 0.035 0.02 -10000 0 -10000 0 0
VDR 0.012 0.029 -10000 0 -0.59 1 1
CDKN1A 0.011 0.094 -10000 0 -10000 0 0
KAT2B -0.019 0.13 -10000 0 -0.59 20 20
SMAD2/SMAD2/SMAD4/FOXH1 -0.065 0.19 -10000 0 -0.55 53 53
DCP1A 0.014 0 -10000 0 -10000 0 0
SKI 0.015 0.002 -10000 0 -10000 0 0
SERPINE1 -0.37 0.33 -10000 0 -0.65 249 249
SMAD3/SMAD4/ATF2 0.01 0.047 -10000 0 -10000 0 0
SMAD3/SMAD4/ATF3 0.002 0.078 -10000 0 -0.49 5 5
SAP30 0.015 0.002 -10000 0 -10000 0 0
Cbp/p300/PIAS3 0.002 0.038 -10000 0 -0.36 1 1
JUN 0.013 0.12 -10000 0 -10000 0 0
SMAD3/SMAD4/IRF7 -0.013 0.13 -10000 0 -0.6 14 14
TFE3 0 0.018 -10000 0 -10000 0 0
COL1A2 -0.29 0.35 -10000 0 -0.69 184 184
mesenchymal cell differentiation -0.008 0.054 0.4 1 -10000 0 1
DLX1 -0.36 0.41 -10000 0 -0.82 193 193
TCF3 0.014 0 -10000 0 -10000 0 0
FOS -0.062 0.21 -10000 0 -0.58 57 57
SMAD3/SMAD4/Max 0.034 0.068 -10000 0 -10000 0 0
Cbp/p300/SNIP1 0.001 0.026 -10000 0 -10000 0 0
ZBTB17 0.024 0.026 -10000 0 -10000 0 0
LAMC1 0.008 0.044 -10000 0 -10000 0 0
TGIF2/HDAC complex/SMAD3/SMAD4 0.008 0.057 -10000 0 -0.66 1 1
IRF7 -0.018 0.16 -10000 0 -0.8 16 16
ESR1 -0.014 0.18 -10000 0 -0.73 25 25
HNF4A -0.068 0.24 -10000 0 -0.82 40 40
MEF2C -0.13 0.27 -10000 0 -0.68 41 41
SMAD2-3/SMAD4 -0.003 0.061 -10000 0 -10000 0 0
Cbp/p300/Src-1 0.004 0.031 -10000 0 -0.36 1 1
IGHV3OR16-13 -0.001 0.012 -10000 0 -10000 0 0
TGIF2/HDAC complex 0.012 0.04 -10000 0 -0.82 1 1
CREBBP 0.007 0.01 -10000 0 -10000 0 0
SKIL 0.014 0 -10000 0 -10000 0 0
HDAC1 0.015 0.002 -10000 0 -10000 0 0
HDAC2 0.015 0.002 -10000 0 -10000 0 0
SNIP1 0.016 0.004 -10000 0 -10000 0 0
GCN5L2 -0.009 0.013 -10000 0 -10000 0 0
SMAD3/SMAD4/TFE3 -0.005 0.045 -10000 0 -10000 0 0
MSG1/HSC70 0.006 0.089 -10000 0 -0.63 8 8
SMAD2 0.001 0.037 -10000 0 -10000 0 0
SMAD3 0.006 0.044 -10000 0 -0.54 1 1
SMAD3/E2F4-5/DP1/p107/SMAD4 0.021 0.05 -10000 0 -0.46 1 1
SMAD2/SMAD2/SMAD4 -0.024 0.081 -10000 0 -0.36 21 21
NCOR1 0.015 0.002 -10000 0 -10000 0 0
NCOA2 -0.023 0.14 -10000 0 -0.59 26 26
NCOA1 0.014 0 -10000 0 -10000 0 0
MYOD/E2A -0.07 0.16 -10000 0 -0.44 68 68
SMAD2-3/SMAD4/SP1/MIZ-1 -0.04 0.097 -10000 0 -10000 0 0
IFNB1 0.003 0.15 -10000 0 -0.64 17 17
SMAD3/SMAD4/MEF2C -0.13 0.26 -10000 0 -0.72 30 30
CITED1 -0.002 0.11 -10000 0 -0.82 8 8
SMAD2-3/SMAD4/ARC105 0.005 0.062 -10000 0 -0.55 1 1
RBL1 0.012 0.029 -10000 0 -0.59 1 1
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB -0.06 0.22 -10000 0 -0.49 82 82
RUNX1-3/PEBPB2 -0.006 0.058 -10000 0 -0.54 5 5
SMAD7 -0.028 0.12 -10000 0 -10000 0 0
MYC/MIZ-1 0.032 0.065 -10000 0 -10000 0 0
SMAD3/SMAD4 -0.12 0.15 0.36 4 -0.4 4 8
IL10 0.012 0.15 -10000 0 -0.64 17 17
PIASy/HDAC complex 0.023 0.012 -10000 0 -10000 0 0
PIAS3 0.007 0.008 -10000 0 -10000 0 0
CDK2 0.007 0.01 -10000 0 -10000 0 0
IL5 0.01 0.13 -10000 0 -0.62 9 9
CDK4 0.007 0.011 -10000 0 -10000 0 0
PIAS4 0.023 0.012 -10000 0 -10000 0 0
ATF3 0.001 0.091 -10000 0 -0.65 8 8
SMAD3/SMAD4/SP1 -0.062 0.089 -10000 0 -10000 0 0
FOXG1 -0.098 0.26 -10000 0 -0.72 60 60
FOXO3 0.009 0.043 -10000 0 -10000 0 0
FOXO1 0.009 0.043 -10000 0 -10000 0 0
FOXO4 0.007 0.052 -10000 0 -0.42 2 2
heart looping -0.13 0.26 -10000 0 -0.66 42 42
CEBPB 0.008 0.016 -10000 0 -10000 0 0
SMAD3/SMAD4/DLX1 -0.25 0.29 -10000 0 -0.57 192 192
MYOD1 -0.091 0.22 -10000 0 -0.6 68 68
SMAD3/SMAD4/HNF4 -0.046 0.17 -10000 0 -0.56 40 40
SMAD3/SMAD4/GATA3 -0.01 0.12 -10000 0 -0.58 12 12
SnoN/SIN3/HDAC complex/NCoR1 0.014 0 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX1-3/PEBPB2 0.012 0.068 -10000 0 -0.48 3 3
SMAD3/SMAD4/SP1-3 -0.037 0.08 -10000 0 -10000 0 0
MED15 0.012 0.04 -10000 0 -0.82 1 1
SP1 -0.043 0.075 -10000 0 -10000 0 0
SIN3B 0.015 0.002 -10000 0 -10000 0 0
SIN3A 0.015 0.002 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5 -0.16 0.27 -10000 0 -0.56 115 115
ITGB5 0 0.093 -10000 0 -10000 0 0
TGIF/SIN3/HDAC complex/CtBP 0.054 0.017 -10000 0 -10000 0 0
SMAD3/SMAD4/AR -0.085 0.18 -10000 0 -0.47 25 25
AR -0.14 0.27 -10000 0 -0.6 108 108
negative regulation of cell growth 0.022 0.058 -10000 0 -10000 0 0
SMAD3/SMAD4/MYOD -0.057 0.16 -10000 0 -0.5 14 14
E2F5 0.009 0.051 -10000 0 -0.59 3 3
E2F4 0.014 0 -10000 0 -10000 0 0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF -0.06 0.16 -10000 0 -0.5 35 35
SMAD2-3/SMAD4/FOXO1-3a-4 -0.03 0.15 -10000 0 -10000 0 0
TFDP1 0.012 0.04 -10000 0 -0.82 1 1
SMAD3/SMAD4/AP1 0 0.12 -10000 0 -10000 0 0
SMAD3/SMAD4/RUNX2 0.008 0.054 -10000 0 -0.4 1 1
TGIF2 0.012 0.04 -10000 0 -0.82 1 1
TGIF1 0.014 0 -10000 0 -10000 0 0
ATF2 0.014 0 -10000 0 -10000 0 0
Signaling mediated by p38-gamma and p38-delta

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
EEF2K 0.028 0.042 -9999 0 -10000 0 0
SNTA1 0.014 0 -9999 0 -10000 0 0
response to hypoxia 0 0 -9999 0 -10000 0 0
STMN1 0.024 0.063 -9999 0 -0.54 3 3
MAPK12 -0.009 0.14 -9999 0 -0.56 20 20
CCND1 -0.001 0.089 -9999 0 -0.35 14 14
p38 gamma/SNTA1 -0.002 0.14 -9999 0 -0.52 20 20
MAP2K3 0.012 0.029 -9999 0 -0.59 1 1
PKN1 0.012 0.04 -9999 0 -0.82 1 1
G2/M transition checkpoint -0.009 0.14 -9999 0 -0.56 20 20
MAP2K6 0.007 0.086 -9999 0 -0.37 20 20
MAPT -0.14 0.18 -9999 0 -0.33 184 184
MAPK13 0.019 0.049 -9999 0 -0.43 5 5
hyperosmotic response 0 0 -9999 0 -10000 0 0
ZAK 0.017 0.026 -9999 0 -0.36 2 2
Syndecan-3-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN -0.006 0.13 -9999 0 -0.82 10 10
Syndecan-3/Src/Cortactin -0.11 0.15 -9999 0 -0.57 11 11
Syndecan-3/Neurocan -0.017 0.086 -9999 0 -0.45 16 16
POMC -0.076 0.25 -9999 0 -0.78 48 48
EGFR -0.017 0.15 -9999 0 -0.79 16 16
Syndecan-3/EGFR -0.018 0.086 -9999 0 -0.45 15 15
AGRP 0.003 0.04 -9999 0 -0.82 1 1
NCSTN 0.014 0 -9999 0 -10000 0 0
PSENEN 0.012 0.04 -9999 0 -0.82 1 1
RP11-540L11.1 0 0 -9999 0 -10000 0 0
APH1B 0.014 0 -9999 0 -10000 0 0
APH1A 0.014 0 -9999 0 -10000 0 0
NCAN -0.02 0.15 -9999 0 -0.82 15 15
long-term memory -0.012 0.07 -9999 0 -0.43 11 11
Syndecan-3/IL8 -0.097 0.19 -9999 0 -0.46 88 88
PSEN1 0.014 0 -9999 0 -10000 0 0
Src/Cortactin -0.015 0.095 -9999 0 -0.63 10 10
FYN 0.012 0.04 -9999 0 -0.82 1 1
limb bud formation -0.001 0.019 -9999 0 -0.37 1 1
MC4R 0.002 0.057 -9999 0 -0.82 2 2
SRC 0.014 0 -9999 0 -10000 0 0
PTN -0.22 0.3 -9999 0 -0.59 162 162
FGFR/FGF/Syndecan-3 -0.001 0.019 -9999 0 -0.38 1 1
neuron projection morphogenesis -0.12 0.16 -9999 0 -0.68 9 9
Syndecan-3/AgRP -0.002 0.028 -9999 0 -0.41 2 2
Syndecan-3/AgRP/MC4R -0.004 0.04 -9999 0 -0.44 3 3
Fyn/Cortactin -0.016 0.1 -9999 0 -0.63 11 11
SDC3 -0.001 0.019 -9999 0 -0.38 1 1
GO:0007205 0 0 -9999 0 -10000 0 0
positive regulation of leukocyte migration -0.095 0.18 -9999 0 -0.45 88 88
IL8 -0.16 0.34 -9999 0 -0.81 89 89
Syndecan-3/Fyn/Cortactin -0.012 0.071 -9999 0 -0.44 11 11
Syndecan-3/CASK -0.001 0.018 -9999 0 -0.36 1 1
alpha-MSH/MC4R -0.07 0.2 -9999 0 -0.6 49 49
Gamma Secretase -0.001 0.022 -9999 0 -0.46 1 1
IL27-mediated 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
TGFB1 0.014 0.053 -10000 0 -0.8 1 1
CD4-positive alpha-beta T cell lineage commitment 0 0 -10000 0 -10000 0 0
cytokine production during immune response 0.05 0.17 0.63 17 -10000 0 17
IL27/IL27R/JAK1 -0.094 0.19 -10000 0 -0.78 15 15
TBX21 -0.095 0.25 -10000 0 -0.68 35 35
IL12B -0.066 0.24 -10000 0 -0.82 39 39
IL12A -0.006 0.089 -10000 0 -0.46 15 15
IL6ST -0.048 0.18 -10000 0 -0.6 41 41
IL27RA/JAK1 -0.008 0.11 -10000 0 -0.58 14 14
IL27 -0.027 0.17 -10000 0 -0.83 18 18
TYK2 0.011 0.042 -10000 0 -0.83 1 1
T-helper cell lineage commitment -0.022 0.13 -10000 0 -0.64 7 7
T-helper 2 cell differentiation 0.05 0.17 0.63 17 -10000 0 17
T cell proliferation during immune response 0.05 0.17 0.63 17 -10000 0 17
MAPKKK cascade -0.05 0.17 -10000 0 -0.63 17 17
STAT3 0.014 0 -10000 0 -10000 0 0
STAT2 0.014 0 -10000 0 -10000 0 0
STAT1 -0.04 0.2 -10000 0 -0.82 27 27
IL12RB1 -0.063 0.24 -10000 0 -0.81 39 39
positive regulation of tyrosine phosphorylation of STAT protein 0 0 -10000 0 -10000 0 0
IL12RB2 -0.14 0.32 -10000 0 -0.69 86 86
IL27/IL27R/JAK2/TYK2 -0.051 0.18 -10000 0 -0.64 17 17
positive regulation of T cell mediated cytotoxicity -0.05 0.17 -10000 0 -0.63 17 17
STAT1 (dimer) -0.17 0.29 0.52 1 -0.89 38 39
JAK2 0.011 0.03 -10000 0 -0.6 1 1
JAK1 0.013 0.003 -10000 0 -10000 0 0
STAT2 (dimer) -0.041 0.17 -10000 0 -0.7 10 10
T cell proliferation -0.075 0.2 -10000 0 -0.63 24 24
IL12/IL12R/TYK2/JAK2 -0.063 0.19 -10000 0 -0.59 29 29
IL17A -0.023 0.12 -10000 0 -0.64 7 7
mast cell activation 0.05 0.17 0.63 17 -10000 0 17
IFNG -0.017 0.05 -10000 0 -0.11 89 89
T cell differentiation -0.006 0.009 -10000 0 -0.025 40 40
STAT3 (dimer) -0.041 0.17 -10000 0 -0.6 17 17
STAT5A (dimer) -0.041 0.17 -10000 0 -0.6 17 17
STAT4 (dimer) -0.05 0.18 -10000 0 -0.7 13 13
STAT4 -0.002 0.11 -10000 0 -0.79 8 8
T cell activation -0.006 0.019 0.093 14 -10000 0 14
IL27R/JAK2/TYK2 -0.044 0.16 -10000 0 -0.66 11 11
GATA3 0.002 0.14 -10000 0 -0.69 14 14
IL18 -0.004 0.083 -10000 0 -0.44 15 15
positive regulation of mast cell cytokine production -0.04 0.16 -10000 0 -0.59 17 17
IL27/EBI3 -0.029 0.16 -10000 0 -0.62 27 27
IL27RA -0.017 0.12 -10000 0 -0.64 14 14
IL6 -0.051 0.2 -10000 0 -0.63 43 43
STAT5A 0.014 0 -10000 0 -10000 0 0
monocyte differentiation -0.001 0.002 -10000 0 -10000 0 0
IL2 0.015 0.066 -10000 0 -10000 0 0
IL1B -0.057 0.2 -10000 0 -0.62 46 46
EBI3 -0.005 0.11 -10000 0 -0.73 9 9
TNF -0.018 0.13 -10000 0 -0.6 21 21
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A -0.16 0.28 -9999 0 -0.61 115 115
oxygen homeostasis 0 0 -9999 0 -10000 0 0
TCEB2 0.012 0.04 -9999 0 -0.82 1 1
TCEB1 0.012 0.04 -9999 0 -0.82 1 1
HIF1A/p53 0.024 0.041 -9999 0 -10000 0 0
HIF1A 0.02 0.031 -9999 0 -10000 0 0
COPS5 0.014 0 -9999 0 -10000 0 0
VHL/Elongin B/Elongin C/RBX1/CUL2 -0.003 0.038 -9999 0 -0.46 3 3
FIH (dimer) 0.014 0 -9999 0 -10000 0 0
CDKN2A -0.35 0.4 -9999 0 -0.77 194 194
ARNT/IPAS -0.12 0.2 -9999 0 -0.44 115 115
HIF1AN 0.014 0 -9999 0 -10000 0 0
GNB2L1 0.014 0 -9999 0 -10000 0 0
HIF1A/ARNT 0.027 0.03 -9999 0 -10000 0 0
CUL2 0.012 0.04 -9999 0 -0.82 1 1
OS9 0.014 0 -9999 0 -10000 0 0
RACK1/Elongin B/Elongin C -0.003 0.037 -9999 0 -0.54 2 2
response to hypoxia 0 0 -9999 0 -10000 0 0
HIF1A/Hsp90 0.027 0.03 -9999 0 -10000 0 0
PHD1-3/OS9 -0.027 0.11 -9999 0 -0.49 21 21
HIF1A/RACK1/Elongin B/Elongin C -0.006 0.035 -9999 0 -0.45 2 2
VHL 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
HIF1A/JAB1 0.027 0.03 -9999 0 -10000 0 0
EGLN3 -0.033 0.19 -9999 0 -0.78 25 25
EGLN2 0.014 0 -9999 0 -10000 0 0
EGLN1 0.014 0 -9999 0 -10000 0 0
TP53 0.008 0.058 -9999 0 -0.59 4 4
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A 0.037 0.024 -9999 0 -10000 0 0
ARNT 0.014 0 -9999 0 -10000 0 0
ARD1A 0 0 -9999 0 -10000 0 0
RBX1 0.014 0 -9999 0 -10000 0 0
HIF1A/p19ARF -0.17 0.22 -9999 0 -0.44 159 159
LPA receptor mediated events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GNB1/GNG2 -0.047 0.1 -9999 0 -0.82 1 1
NF kappa B1 p50/RelA/I kappa B alpha -0.021 0.052 -9999 0 -10000 0 0
AP1 -0.078 0.13 -9999 0 -0.56 9 9
mol:PIP3 -0.053 0.11 -9999 0 -0.52 5 5
AKT1 0.022 0.091 -9999 0 -0.53 1 1
PTK2B -0.004 0.078 -9999 0 -0.29 4 4
RHOA 0.007 0.062 -9999 0 -0.33 1 1
PIK3CB 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ 0.009 0.072 -9999 0 -0.43 3 3
MAGI3 0.011 0.041 -9999 0 -0.59 2 2
RELA 0.014 0 -9999 0 -10000 0 0
apoptosis -0.022 0.11 -9999 0 -0.6 3 3
HRAS/GDP -0.001 0.031 -9999 0 -0.64 1 1
positive regulation of microtubule depolymerization -0.12 0.16 -9999 0 -0.43 27 27
NF kappa B1 p50/RelA -0.034 0.088 -9999 0 -0.55 3 3
endothelial cell migration -0.1 0.29 -9999 0 -0.76 69 69
ADCY4 -0.011 0.12 -9999 0 -0.46 13 13
ADCY5 -0.059 0.15 -9999 0 -0.54 15 15
ADCY6 -0.016 0.13 -9999 0 -0.49 14 14
ADCY7 -0.011 0.12 -9999 0 -0.46 13 13
ADCY1 -0.019 0.13 -9999 0 -0.45 14 14
ADCY2 -0.077 0.14 -9999 0 -0.5 18 18
ADCY3 -0.011 0.12 -9999 0 -0.46 13 13
ADCY8 -0.018 0.13 -9999 0 -0.44 17 17
ADCY9 -0.011 0.12 -9999 0 -0.46 13 13
GSK3B 0.005 0.074 -9999 0 -10000 0 0
arachidonic acid secretion -0.003 0.12 -9999 0 -0.44 13 13
GNG2 0.013 0.001 -9999 0 -10000 0 0
TRIP6 0.017 0.024 -9999 0 -10000 0 0
GNAO1 -0.033 0.14 -9999 0 -0.46 13 13
HRAS 0.012 0.04 -9999 0 -0.82 1 1
NFKBIA 0.014 0.084 -9999 0 -0.42 3 3
GAB1 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
lamellipodium assembly -0.006 0.098 -9999 0 -0.9 5 5
JUN 0.014 0 -9999 0 -10000 0 0
LPA/LPA2/NHERF2 -0.015 0.044 -9999 0 -0.64 1 1
TIAM1 -0.009 0.12 -9999 0 -1.1 5 5
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
mol:IP3 0.009 0.073 -9999 0 -0.44 3 3
PLCB3 0.013 0.046 -9999 0 -0.58 1 1
FOS -0.068 0.21 -9999 0 -0.59 57 57
positive regulation of mitosis -0.003 0.12 -9999 0 -0.44 13 13
LPA/LPA1-2-3 -0.053 0.11 -9999 0 -0.68 3 3
mol:Ca ++ 0 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
BCAR1 0.014 0 -9999 0 -10000 0 0
stress fiber formation 0.002 0.09 -9999 0 -0.39 3 3
GNAZ -0.047 0.16 -9999 0 -0.51 24 24
EGFR/PI3K-beta/Gab1 -0.055 0.11 -9999 0 -0.54 5 5
positive regulation of dendritic cell cytokine production -0.052 0.11 -9999 0 -0.67 3 3
LPA/LPA2/MAGI-3 -0.016 0.04 -9999 0 -0.36 2 2
ARHGEF1 -0.012 0.12 -9999 0 -0.56 5 5
GNAI2 -0.028 0.13 -9999 0 -0.41 9 9
GNAI3 -0.028 0.13 -9999 0 -0.42 8 8
GNAI1 -0.029 0.13 -9999 0 -0.4 10 10
LPA/LPA3 -0.028 0.073 -9999 0 -0.44 8 8
LPA/LPA2 -0.019 0.044 -9999 0 -10000 0 0
LPA/LPA1 -0.065 0.14 -9999 0 -0.36 77 77
HB-EGF/EGFR -0.4 0.27 -9999 0 -0.56 312 312
HBEGF -0.45 0.29 -9999 0 -0.63 309 309
mol:DAG 0.009 0.073 -9999 0 -0.44 3 3
cAMP biosynthetic process -0.025 0.12 -9999 0 -0.5 12 12
NFKB1 0.014 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
GNB1 0.013 0.001 -9999 0 -10000 0 0
LYN 0.013 0.086 -9999 0 -0.42 3 3
GNAQ 0.004 0.058 -9999 0 -0.31 8 8
LPAR2 0.013 0 -9999 0 -10000 0 0
LPAR3 0.002 0.082 -9999 0 -0.59 8 8
LPAR1 -0.026 0.12 -9999 0 -0.63 9 9
IL8 -0.23 0.18 -9999 0 -0.5 77 77
PTK2 -0.013 0.12 -9999 0 -0.63 3 3
Rac1/GDP 0 0 -9999 0 -10000 0 0
CASP3 -0.022 0.12 -9999 0 -0.61 3 3
EGFR -0.017 0.15 -9999 0 -0.79 16 16
PLCG1 -0.008 0.078 -9999 0 -0.36 8 8
PLD2 -0.013 0.12 -9999 0 -0.63 3 3
G12/G13 -0.051 0.11 -9999 0 -0.61 5 5
PI3K-beta -0.035 0.077 -9999 0 -0.56 2 2
cell migration -0.01 0.046 -9999 0 -0.28 1 1
SLC9A3R2 0.012 0.04 -9999 0 -0.82 1 1
PXN 0.001 0.092 -9999 0 -0.4 3 3
HRAS/GTP -0.004 0.12 -9999 0 -0.45 13 13
RAC1 0.014 0 -9999 0 -10000 0 0
MMP9 -0.59 0.37 -9999 0 -0.82 309 309
PRKCE 0.013 0.001 -9999 0 -10000 0 0
PRKCD 0.017 0.069 -9999 0 -0.47 1 1
Gi(beta/gamma) -0.006 0.12 -9999 0 -0.43 13 13
mol:LPA -0.029 0.077 -9999 0 -10000 0 0
TRIP6/p130 Cas/FAK1/Paxillin -0.028 0.086 -9999 0 -0.53 3 3
MAPKKK cascade -0.003 0.12 -9999 0 -0.44 13 13
contractile ring contraction involved in cytokinesis 0.007 0.061 -9999 0 -0.32 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
GNA14 -0.049 0.13 -9999 0 -0.31 75 75
GNA15 0.003 0.067 -9999 0 -0.36 9 9
GNA12 0.006 0.08 -9999 0 -0.82 4 4
GNA13 0.014 0 -9999 0 -10000 0 0
MAPT -0.12 0.16 -9999 0 -0.44 27 27
GNA11 0.002 0.063 -9999 0 -0.31 11 11
Rac1/GTP -0.007 0.1 -9999 0 -0.96 5 5
MMP2 -0.11 0.3 -9999 0 -0.76 69 69
Angiopoietin receptor Tie2-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
AKT1 0.048 0.23 -10000 0 -0.91 17 17
NCK1/PAK1/Dok-R -0.029 0.09 -10000 0 -0.42 17 17
NCK1/Dok-R -0.052 0.23 -10000 0 -1.1 17 17
PIK3CA 0.013 0.002 -10000 0 -10000 0 0
mol:beta2-estradiol -0.005 0.041 0.24 10 -10000 0 10
RELA 0.014 0 -10000 0 -10000 0 0
SHC1 0.014 0.002 -10000 0 -10000 0 0
Rac/GDP 0 0 -10000 0 -10000 0 0
F2 -0.082 0.25 -10000 0 -0.84 42 42
TNIP2 0.014 0 -10000 0 -10000 0 0
NF kappa B/RelA -0.045 0.2 -10000 0 -1 17 17
FN1 -0.39 0.42 -10000 0 -0.82 207 207
PLD2 0.031 0.26 -10000 0 -1.2 17 17
PTPN11 0.014 0 -10000 0 -10000 0 0
GRB14 -0.051 0.19 -10000 0 -0.63 42 42
ELK1 0.046 0.23 -10000 0 -1 17 17
GRB7 0.004 0.085 -10000 0 -0.77 5 5
PAK1 0.012 0.04 -10000 0 -0.82 1 1
Tie2/Ang1/alpha5/beta1 Integrin -0.36 0.37 -10000 0 -0.86 122 122
CDKN1A 0.054 0.2 -10000 0 -0.66 9 9
ITGA5 -0.26 0.39 -10000 0 -0.82 137 137
mol:GTP 0 0 -10000 0 -10000 0 0
RasGAP/Dok-R -0.052 0.23 -10000 0 -1.1 17 17
CRK 0.014 0 -10000 0 -10000 0 0
mol:NO 0.056 0.19 -10000 0 -0.66 17 17
PLG 0.02 0.26 -10000 0 -1.2 17 17
mol:GDP 0 0 -10000 0 -10000 0 0
chemokinesis 0.031 0.21 -10000 0 -0.87 17 17
GRB2 0.014 0 -10000 0 -10000 0 0
PIK3R1 0.01 0.051 -10000 0 -0.59 3 3
ANGPT2 0.006 0.21 -10000 0 -0.61 27 27
BMX -0.005 0.28 -10000 0 -1.2 17 17
ANGPT1 0.015 0.23 -10000 0 -1.3 12 12
tube development 0.046 0.22 -10000 0 -0.74 11 11
ANGPT4 0.008 0.008 -10000 0 -10000 0 0
response to hypoxia 0.001 0.015 -10000 0 -10000 0 0
Tie2/Ang1/GRB14 -0.007 0.28 -10000 0 -1.2 17 17
alpha5/beta1 Integrin -0.2 0.29 -10000 0 -0.63 138 138
FGF2 -0.011 0.12 -10000 0 -0.65 15 15
STAT5A (dimer) 0.048 0.23 -10000 0 -0.87 9 9
mol:L-citrulline 0.056 0.19 -10000 0 -0.66 17 17
AGTR1 -0.051 0.19 -10000 0 -0.61 43 43
MAPK14 0.033 0.26 -10000 0 -1.2 17 17
Tie2/SHP2 -0.031 0.18 -10000 0 -1.2 9 9
TEK 0.012 0.21 -10000 0 -1.4 9 9
RPS6KB1 0.053 0.22 -10000 0 -0.87 17 17
Angiotensin II/AT1 -0.037 0.14 -10000 0 -0.45 43 43
Tie2/Ang1/GRB2 0.026 0.26 -10000 0 -1.2 17 17
MAPK3 0.04 0.23 -10000 0 -1 17 17
MAPK1 0.04 0.23 -10000 0 -1 17 17
Tie2/Ang1/GRB7 0.022 0.27 -10000 0 -1.2 17 17
NFKB1 0.014 0 -10000 0 -10000 0 0
MAPK8 0.027 0.27 -10000 0 -1.2 17 17
PI3K 0.041 0.26 -10000 0 -1.1 17 17
FES 0.033 0.26 -10000 0 -1.1 17 17
Crk/Dok-R -0.052 0.23 -10000 0 -1.1 17 17
Tie2/Ang1/ABIN2 0.026 0.26 -10000 0 -1.2 17 17
blood circulation 0 0 -10000 0 -10000 0 0
negative regulation of caspase activity 0.052 0.21 -10000 0 -0.8 17 17
STAT5A 0.014 0 -10000 0 -10000 0 0
mol:ROS 0 0 -10000 0 -10000 0 0
PTK2 0.053 0.22 -10000 0 -0.87 17 17
Tie2/Ang2 0.029 0.27 -10000 0 -1.1 10 10
Tie2/Ang1 0.023 0.28 -10000 0 -1.3 17 17
FOXO1 0.052 0.22 -10000 0 -0.8 17 17
ELF1 0.018 0.055 -10000 0 -0.61 3 3
ELF2 0.028 0.26 -10000 0 -1.2 17 17
mol:Choline 0.034 0.24 -10000 0 -1.1 17 17
cell migration -0.096 0.088 -10000 0 -10000 0 0
FYN 0.042 0.24 -10000 0 -0.86 11 11
DOK2 0.007 0.07 -10000 0 -0.7 4 4
negative regulation of cell cycle 0.056 0.18 -10000 0 -0.6 9 9
ETS1 0.013 0.078 -10000 0 -0.8 3 3
PXN 0.063 0.19 -10000 0 -0.71 17 17
ITGB1 0.012 0.04 -10000 0 -0.82 1 1
NOS3 0.053 0.21 -10000 0 -0.75 17 17
RAC1 0.014 0 -10000 0 -10000 0 0
TNF -0.02 0.18 -10000 0 -0.77 21 21
MAPKKK cascade 0.034 0.24 -10000 0 -1.1 17 17
RASA1 0.012 0.029 -10000 0 -0.59 1 1
Tie2/Ang1/Shc 0.027 0.26 -10000 0 -1.2 17 17
NCK1 0.014 0 -10000 0 -10000 0 0
vasculogenesis 0.058 0.17 -10000 0 -0.58 17 17
mol:Phosphatidic acid 0.034 0.24 -10000 0 -1.1 17 17
mol:Angiotensin II 0 0.008 -10000 0 -10000 0 0
mol:NADP 0.056 0.19 -10000 0 -0.66 17 17
Rac1/GTP -0.05 0.17 -10000 0 -0.8 17 17
MMP2 -0.048 0.3 -10000 0 -1.2 17 17
ErbB2/ErbB3 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
USP8 0.02 0.005 -9999 0 -10000 0 0
RAS family/GTP -0.023 0.12 -9999 0 -0.48 4 4
NFATC4 -0.021 0.13 -9999 0 -0.45 5 5
ERBB2IP 0.014 0.003 -9999 0 -10000 0 0
HSP90 (dimer) 0.014 0 -9999 0 -10000 0 0
mammary gland morphogenesis -0.045 0.15 -9999 0 -0.39 12 12
JUN 0.004 0.084 -9999 0 -0.38 5 5
HRAS 0.011 0.04 -9999 0 -0.82 1 1
DOCK7 -0.036 0.14 -9999 0 -0.57 1 1
ErbB2/ErbB3/neuregulin 1 beta/SHC -0.087 0.18 -9999 0 -0.47 73 73
AKT1 0.012 0.003 -9999 0 -10000 0 0
BAD 0.021 0.003 -9999 0 -10000 0 0
MAPK10 -0.041 0.076 -9999 0 -0.31 6 6
mol:GTP -0.001 0.002 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta -0.047 0.16 -9999 0 -0.42 12 12
RAF1 -0.021 0.12 -9999 0 -0.56 2 2
ErbB2/ErbB3/neuregulin 2 -0.2 0.17 -9999 0 -0.36 78 78
STAT3 0.001 0.003 -9999 0 -10000 0 0
cell migration 0.005 0.087 -9999 0 -0.26 3 3
mol:PI-3-4-5-P3 -0.001 0.002 -9999 0 -10000 0 0
cell proliferation -0.14 0.28 -9999 0 -0.58 84 84
FOS -0.1 0.23 -9999 0 -0.48 72 72
NRAS 0.013 0.001 -9999 0 -10000 0 0
mol:Ca2+ -0.045 0.15 -9999 0 -0.39 12 12
MAPK3 -0.1 0.23 -9999 0 -0.53 32 32
MAPK1 -0.1 0.23 -9999 0 -0.53 32 32
JAK2 -0.036 0.14 -9999 0 -0.57 1 1
NF2 -0.003 0.005 -9999 0 -10000 0 0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1 -0.03 0.13 -9999 0 -0.29 73 73
NRG1 -0.13 0.31 -9999 0 -0.81 73 73
GRB2/SOS1 0 0 -9999 0 -10000 0 0
MAPK8 -0.02 0.11 -9999 0 -0.45 2 2
MAPK9 -0.031 0.064 -9999 0 -0.26 1 1
ERBB2 -0.005 0.054 -9999 0 -0.64 3 3
ERBB3 0.003 0.072 -9999 0 -0.59 6 6
SHC1 0.013 0.002 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
apoptosis 0.009 0.01 -9999 0 -10000 0 0
STAT3 (dimer) 0.003 0.006 -9999 0 -10000 0 0
RNF41 0.026 0.008 -9999 0 -10000 0 0
FRAP1 0.01 0.003 -9999 0 -10000 0 0
RAC1-CDC42/GTP -0.044 0.091 -9999 0 -0.38 1 1
ErbB2/ErbB2/HSP90 (dimer) -0.004 0.046 -9999 0 -0.55 3 3
CHRNA1 -0.15 0.3 -9999 0 -0.54 139 139
myelination -0.012 0.12 -9999 0 -0.46 3 3
PPP3CB -0.033 0.13 -9999 0 -0.52 1 1
KRAS 0.009 0.057 -9999 0 -0.82 2 2
RAC1-CDC42/GDP -0.011 0.11 -9999 0 -0.61 1 1
NRG2 -0.34 0.3 -9999 0 -0.59 251 251
mol:GDP -0.03 0.12 -9999 0 -0.29 73 73
SOS1 0.013 0.001 -9999 0 -10000 0 0
MAP2K2 -0.025 0.13 -9999 0 -0.55 2 2
SRC 0.014 0 -9999 0 -10000 0 0
mol:cAMP -0.001 0.002 -9999 0 -10000 0 0
PTPN11 -0.036 0.14 -9999 0 -0.57 1 1
MAP2K1 -0.089 0.2 -9999 0 -0.51 20 20
heart morphogenesis -0.045 0.15 -9999 0 -0.39 12 12
RAS family/GDP -0.02 0.11 -9999 0 -0.48 4 4
GRB2 0.013 0.001 -9999 0 -10000 0 0
PRKACA -0.004 0.009 -9999 0 -10000 0 0
CHRNE 0.011 0.031 -9999 0 -0.23 5 5
HSP90AA1 0.014 0 -9999 0 -10000 0 0
activation of caspase activity -0.012 0.003 -9999 0 -10000 0 0
nervous system development -0.045 0.15 -9999 0 -0.39 12 12
CDC42 0.014 0 -9999 0 -10000 0 0
Presenilin action in Notch and Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved) -0.009 0.062 -10000 0 -0.59 3 3
HDAC1 0.009 0.005 -10000 0 -10000 0 0
AES 0.013 0.001 -10000 0 -10000 0 0
FBXW11 0.014 0 -10000 0 -10000 0 0
DTX1 0.011 0.041 -10000 0 -0.59 2 2
LRP6/FZD1 -0.008 0.071 -10000 0 -0.59 6 6
TLE1 0.013 0.001 -10000 0 -10000 0 0
AP1 -0.027 0.12 -10000 0 -0.7 1 1
NCSTN 0.014 0 -10000 0 -10000 0 0
ADAM10 0.012 0.029 -10000 0 -0.59 1 1
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4 0.04 0.045 -10000 0 -10000 0 0
NICD/RBPSUH -0.005 0.052 -10000 0 -0.59 3 3
WIF1 -0.27 0.31 -10000 0 -0.61 188 188
NOTCH1 -0.005 0.055 -10000 0 -0.56 4 4
PSENEN 0.012 0.04 -10000 0 -0.82 1 1
KREMEN2 -0.28 0.4 -10000 0 -0.82 149 149
DKK1 -0.25 0.38 -10000 0 -0.79 138 138
beta catenin/beta TrCP1 0.021 0.047 -10000 0 -0.35 1 1
APH1B 0.014 0 -10000 0 -10000 0 0
APH1A 0.014 0 -10000 0 -10000 0 0
AXIN1 0.001 0.026 -10000 0 -0.28 1 1
CtBP/CBP/TCF1/TLE1/AES 0.02 0.042 -10000 0 -10000 0 0
PSEN1 0.014 0 -10000 0 -10000 0 0
FOS -0.068 0.21 -10000 0 -0.59 57 57
JUN 0.014 0 -10000 0 -10000 0 0
MAP3K7 0.012 0.002 -10000 0 -10000 0 0
CTNNB1 0.014 0.05 -10000 0 -0.38 1 1
MAPK3 0.014 0 -10000 0 -10000 0 0
DKK2/LRP6/Kremen 2 -0.21 0.27 -10000 0 -0.55 158 158
HNF1A -0.001 0.11 -10000 0 -0.82 7 7
CTBP1 0.013 0.001 -10000 0 -10000 0 0
MYC 0.025 0.013 -10000 0 -10000 0 0
NKD1 -0.021 0.16 -10000 0 -0.79 18 18
FZD1 0.004 0.09 -10000 0 -0.82 5 5
NOTCH1 precursor/Deltex homolog 1 -0.006 0.062 -10000 0 -0.68 3 3
apoptosis -0.027 0.12 -10000 0 -0.69 1 1
Delta 1/NOTCHprecursor -0.009 0.062 -10000 0 -0.59 3 3
DLL1 0.005 0.071 -10000 0 -0.59 6 6
PPARD 0.025 0.013 -10000 0 -10000 0 0
Gamma Secretase -0.001 0.022 -10000 0 -0.46 1 1
APC 0 0.033 -10000 0 -0.35 2 2
DVL1 -0.019 0.029 -10000 0 -10000 0 0
CSNK2A1 0.014 0.002 -10000 0 -10000 0 0
MAP3K7IP1 -0.002 0.002 -10000 0 -10000 0 0
DKK1/LRP6/Kremen 2 -0.35 0.34 -10000 0 -0.64 230 230
LRP6 0.012 0.029 -10000 0 -0.59 1 1
CSNK1A1 0.014 0.002 -10000 0 -10000 0 0
NLK 0.014 0.006 -10000 0 -10000 0 0
CCND1 0.006 0.14 -10000 0 -0.79 11 11
WNT1 -0.002 0.098 -10000 0 -0.82 6 6
Axin1/APC/beta catenin 0.026 0.042 -10000 0 -0.4 1 1
DKK2 -0.016 0.15 -10000 0 -0.72 17 17
NOTCH1 precursor/DVL1 -0.01 0.051 -10000 0 -0.58 3 3
GSK3B 0.013 0 -10000 0 -10000 0 0
FRAT1 0.013 0.001 -10000 0 -10000 0 0
NOTCH/Deltex homolog 1 -0.007 0.063 -10000 0 -0.69 3 3
PPP2R5D 0.003 0.069 0.32 18 -10000 0 18
MAPK1 0.014 0 -10000 0 -10000 0 0
WNT1/LRP6/FZD1 -0.16 0.17 -10000 0 -0.49 24 24
RBPJ 0.014 0 -10000 0 -10000 0 0
CREBBP 0.017 0.003 -10000 0 -10000 0 0
Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1 0.014 0 -9999 0 -10000 0 0
VLDLR 0.004 0.077 -9999 0 -0.59 7 7
LRPAP1 0.014 0 -9999 0 -10000 0 0
NUDC 0.014 0 -9999 0 -10000 0 0
RELN/LRP8 -0.077 0.16 -9999 0 -0.39 83 83
CaM/Ca2+ 0 0 -9999 0 -10000 0 0
KATNA1 0.014 0 -9999 0 -10000 0 0
GO:0030286 0 0 -9999 0 -10000 0 0
ABL1 -0.039 0.16 -9999 0 -0.57 11 11
IQGAP1/CaM 0 0 -9999 0 -10000 0 0
DAB1 -0.02 0.15 -9999 0 -0.82 15 15
IQGAP1 0.014 0 -9999 0 -10000 0 0
PLA2G7 -0.32 0.41 -9999 0 -0.82 173 173
CALM1 0.014 0 -9999 0 -10000 0 0
DYNLT1 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
LRPAP1/LRP8 -0.013 0.09 -9999 0 -0.63 9 9
UniProt:Q4QZ09 0 0 -9999 0 -10000 0 0
CLIP1 0.011 0.041 -9999 0 -0.59 2 2
CDK5R1 0.012 0.04 -9999 0 -0.82 1 1
LIS1/Poliovirus Protein 3A 0.018 0 -9999 0 -10000 0 0
CDK5R2 -0.11 0.29 -9999 0 -0.82 61 61
mol:PP1 0 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1 -0.091 0.18 -9999 0 -0.4 95 95
YWHAE 0.014 0 -9999 0 -10000 0 0
NDEL1/14-3-3 E -0.04 0.16 -9999 0 -0.58 13 13
MAP1B -0.007 0.046 -9999 0 -0.3 10 10
RAC1 0 0 -9999 0 -10000 0 0
p35/CDK5 -0.02 0.14 -9999 0 -0.64 4 4
RELN -0.098 0.24 -9999 0 -0.6 77 77
PAFAH/LIS1 -0.2 0.28 -9999 0 -0.54 173 173
LIS1/CLIP170 0.027 0.026 -9999 0 -10000 0 0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain -0.061 0.1 -9999 0 -0.51 7 7
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3 -0.026 0.13 -9999 0 -0.57 4 4
GO:0005869 0 0 -9999 0 -10000 0 0
NDEL1 -0.051 0.17 -9999 0 -0.64 13 13
LIS1/IQGAP1 0.028 0 -9999 0 -10000 0 0
RHOA 0 0 -9999 0 -10000 0 0
PAFAH1B1 0.025 0 -9999 0 -10000 0 0
PAFAH1B3 0.012 0.04 -9999 0 -0.82 1 1
PAFAH1B2 0.012 0.029 -9999 0 -0.59 1 1
MAP1B/LIS1/Dynein heavy chain 0.022 0.033 -9999 0 -10000 0 0
NDEL1/Katanin 60/Dynein heavy chain -0.077 0.13 -9999 0 -0.56 13 13
LRP8 -0.004 0.12 -9999 0 -0.82 9 9
NDEL1/Katanin 60 -0.04 0.16 -9999 0 -0.58 13 13
P39/CDK5 -0.09 0.22 -9999 0 -0.52 62 62
LIS1/NudC/Dynein intermediate chain/microtubule organizing center 0.028 0 -9999 0 -10000 0 0
CDK5 -0.028 0.15 -9999 0 -0.53 11 11
PPP2R5D 0.014 0 -9999 0 -10000 0 0
LIS1/CLIP170/Dynein Complex/Dynactin Complex -0.001 0.021 -9999 0 -10000 0 0
CSNK2A1 0.014 0 -9999 0 -10000 0 0
RELN/VLDLR/DAB1/LIS1 -0.075 0.15 -9999 0 -0.52 18 18
RELN/VLDLR -0.074 0.15 -9999 0 -0.58 12 12
CDC42 0 0 -9999 0 -10000 0 0
Wnt signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Noncanonical Wnts/FZD -0.032 0.14 -9999 0 -0.6 8 8
FZD6 0.014 0 -9999 0 -10000 0 0
WNT6 -0.043 0.2 -9999 0 -0.76 31 31
WNT4 -0.008 0.12 -9999 0 -0.66 14 14
FZD3 0.006 0.065 -9999 0 -0.59 5 5
WNT5A 0.005 0.076 -9999 0 -0.68 5 5
WNT11 -0.076 0.25 -9999 0 -0.76 49 49
Regulation of Androgen receptor activity

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.023 0.003 -9999 0 -10000 0 0
SMARCC1 0.011 0.011 -9999 0 -10000 0 0
REL 0.008 0.072 -9999 0 -0.59 6 6
HDAC7 -0.072 0.16 -9999 0 -0.58 15 15
JUN 0.011 0.005 -9999 0 -10000 0 0
EP300 0.01 0.041 -9999 0 -0.59 2 2
KAT2B -0.015 0.13 -9999 0 -0.59 20 20
KAT5 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.008 0.1 -9999 0 -0.45 20 20
FOXO1 0.013 0.001 -9999 0 -10000 0 0
T-DHT/AR -0.086 0.17 -9999 0 -0.57 23 23
MAP2K6 -0.021 0.13 -9999 0 -0.61 20 20
BRM/BAF57 -0.002 0.021 -9999 0 -0.43 1 1
MAP2K4 0.008 0.008 -9999 0 -10000 0 0
SMARCA2 0.01 0.03 -9999 0 -0.59 1 1
PDE9A -0.096 0.2 -9999 0 -1.1 13 13
NCOA2 -0.024 0.14 -9999 0 -0.59 26 26
CEBPA 0.01 0.051 -9999 0 -0.59 3 3
EHMT2 0.011 0.005 -9999 0 -10000 0 0
cell proliferation -0.064 0.17 -9999 0 -0.51 18 18
NR0B1 -0.032 0.17 -9999 0 -0.82 19 19
EGR1 -0.013 0.12 -9999 0 -0.59 17 17
RXRs/9cRA -0.039 0.11 -9999 0 -0.39 18 18
AR/RACK1/Src -0.037 0.12 -9999 0 -0.48 14 14
AR/GR -0.062 0.15 -9999 0 -0.54 13 13
GNB2L1 0.014 0.002 -9999 0 -10000 0 0
PKN1 0.011 0.04 -9999 0 -0.82 1 1
RCHY1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0.002 -9999 0 -10000 0 0
MAPK8 0.006 0.062 -9999 0 -0.46 7 7
T-DHT/AR/TIF2/CARM1 -0.052 0.16 -9999 0 -0.58 18 18
SRC -0.004 0.096 -9999 0 -0.59 1 1
NR3C1 0.014 0 -9999 0 -10000 0 0
KLK3 -0.29 0.46 -9999 0 -1.2 80 80
APPBP2 0.008 0.008 -9999 0 -10000 0 0
TRIM24 0.01 0.03 -9999 0 -0.59 1 1
T-DHT/AR/TIP60 -0.039 0.13 -9999 0 -0.52 13 13
TMPRSS2 -0.55 0.56 -9999 0 -1.1 212 212
RXRG -0.058 0.2 -9999 0 -0.62 47 47
mol:9cRA -0.001 0.003 -9999 0 -10000 0 0
RXRA 0.013 0.001 -9999 0 -10000 0 0
RXRB 0.013 0.001 -9999 0 -10000 0 0
CARM1 0.014 0.002 -9999 0 -10000 0 0
NR2C2 0.006 0.065 -9999 0 -0.59 5 5
KLK2 -0.038 0.17 -9999 0 -0.62 20 20
AR -0.078 0.16 -9999 0 -0.38 65 65
SENP1 0.013 0.001 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
MDM2 0.018 0.012 -9999 0 -10000 0 0
SRY -0.034 0.16 -9999 0 -0.6 31 31
GATA2 0.004 0.085 -9999 0 -0.77 5 5
MYST2 0.013 0.029 -9999 0 -0.59 1 1
HOXB13 -0.29 0.4 -9999 0 -0.82 149 149
T-DHT/AR/RACK1/Src -0.03 0.12 -9999 0 -0.5 13 13
positive regulation of transcription 0.004 0.085 -9999 0 -0.77 5 5
DNAJA1 0.008 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.033 0.004 -9999 0 -10000 0 0
NCOA1 0.017 0.008 -9999 0 -10000 0 0
SPDEF -0.2 0.3 -9999 0 -0.61 142 142
T-DHT/AR/TIF2 -0.03 0.15 -9999 0 -0.58 15 15
T-DHT/AR/Hsp90 -0.04 0.13 -9999 0 -0.52 13 13
GSK3B 0.01 0.006 -9999 0 -10000 0 0
NR2C1 0.015 0.003 -9999 0 -10000 0 0
mol:T-DHT -0.014 0.1 -9999 0 -0.46 4 4
SIRT1 0.012 0.029 -9999 0 -0.59 1 1
ZMIZ2 0.018 0.011 -9999 0 -10000 0 0
POU2F1 0.015 0.022 -9999 0 -10000 0 0
T-DHT/AR/DAX-1 -0.077 0.15 -9999 0 -0.51 34 34
CREBBP 0.013 0.001 -9999 0 -10000 0 0
SMARCE1 0.011 0.005 -9999 0 -10000 0 0
Signaling events mediated by PTP1B

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
PDGFRB -0.16 0.34 -10000 0 -0.82 90 90
Jak2/Leptin Receptor -0.067 0.1 -10000 0 -0.46 4 4
PTP1B/AKT1 -0.022 0.082 0.23 1 -0.35 2 3
FYN 0.012 0.04 -10000 0 -0.82 1 1
p210 bcr-abl/PTP1B -0.033 0.091 0.26 1 -0.36 5 6
EGFR -0.019 0.15 -10000 0 -0.79 16 16
EGF/EGFR -0.1 0.15 -10000 0 -0.44 41 41
CSF1 0.006 0.065 -10000 0 -0.59 5 5
AKT1 0.014 0.001 -10000 0 -10000 0 0
INSR 0.014 0.001 -10000 0 -10000 0 0
PTP1B/N-cadherin -0.091 0.2 0.23 1 -0.54 60 61
Insulin Receptor/Insulin -0.033 0.055 -10000 0 -0.47 1 1
HCK 0.007 0.07 -10000 0 -0.7 4 4
CRK 0.014 0 -10000 0 -10000 0 0
TYK2 -0.024 0.09 0.25 1 -0.38 5 6
EGF -0.099 0.24 -10000 0 -0.6 77 77
YES1 0.014 0 -10000 0 -10000 0 0
CAV1 -0.049 0.11 0.25 1 -0.37 12 13
TXN 0.011 0.006 -10000 0 -10000 0 0
PTP1B/IRS1/GRB2 -0.018 0.083 -10000 0 -0.37 1 1
cell migration 0.033 0.091 0.36 5 -0.26 1 6
STAT3 0.013 0.001 -10000 0 -10000 0 0
PRLR -0.11 0.25 -10000 0 -0.6 85 85
ITGA2B -0.054 0.22 -10000 0 -0.82 34 34
CSF1R 0.009 0.051 -10000 0 -0.59 3 3
Prolactin Receptor/Prolactin -0.092 0.19 -10000 0 -0.46 87 87
FGR 0.012 0.04 -10000 0 -0.82 1 1
PTP1B/p130 Cas -0.024 0.086 0.23 1 -0.35 4 5
Crk/p130 Cas -0.016 0.082 -10000 0 -0.37 1 1
DOK1 -0.059 0.14 0.25 1 -0.4 16 17
JAK2 -0.06 0.12 -10000 0 -0.38 15 15
Jak2/Leptin Receptor/Leptin -0.077 0.12 -10000 0 -0.47 3 3
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
PTPN1 -0.033 0.092 0.26 1 -0.36 5 6
LYN 0.012 0.029 -10000 0 -0.59 1 1
CDH2 -0.1 0.29 -10000 0 -0.8 61 61
SRC 0.004 0.037 -10000 0 -10000 0 0
ITGB3 -0.023 0.16 -10000 0 -0.74 20 20
CAT1/PTP1B -0.12 0.14 0.26 1 -0.43 21 22
CAPN1 0.013 0.002 -10000 0 -10000 0 0
CSK 0.014 0 -10000 0 -10000 0 0
PI3K -0.025 0.057 -10000 0 -0.52 1 1
mol:H2O2 0 0.005 -10000 0 -10000 0 0
STAT3 (dimer) -0.068 0.1 -10000 0 -0.43 1 1
negative regulation of transcription -0.06 0.11 -10000 0 -0.38 15 15
FCGR2A -0.033 0.19 -10000 0 -0.82 24 24
FER 0.009 0.03 -10000 0 -0.6 1 1
alphaIIb/beta3 Integrin -0.076 0.21 -10000 0 -0.62 52 52
BLK -0.11 0.28 -10000 0 -0.78 64 64
Insulin Receptor/Insulin/Shc -0.002 0.037 -10000 0 -0.53 2 2
RHOA 0.013 0.002 -10000 0 -10000 0 0
LEPR 0.012 0.029 -10000 0 -0.59 1 1
BCAR1 0.014 0 -10000 0 -10000 0 0
p210 bcr-abl/Grb2 0.014 0 -10000 0 -10000 0 0
mol:NADPH -0.001 0.004 -10000 0 -10000 0 0
TRPV6 -0.11 0.15 -10000 0 -0.44 33 33
PRL -0.004 0.08 -10000 0 -0.81 4 4
SOCS3 0.018 0.068 -10000 0 -1.3 1 1
SPRY2 0.003 0.078 -10000 0 -0.6 7 7
Insulin Receptor/Insulin/IRS1 -0.004 0.044 -10000 0 -0.53 2 2
CSF1/CSF1R -0.022 0.092 -10000 0 -0.41 4 4
Ras protein signal transduction 0.027 0.029 -10000 0 -10000 0 0
IRS1 0.011 0.041 -10000 0 -0.59 2 2
INS -0.003 0.056 -10000 0 -0.82 2 2
LEP -0.099 0.26 -10000 0 -0.68 67 67
STAT5B -0.04 0.085 0.21 1 -0.34 6 7
STAT5A -0.04 0.085 0.21 1 -0.34 6 7
GRB2 0.014 0 -10000 0 -10000 0 0
PDGFB-D/PDGFRB -0.12 0.24 0.23 1 -0.57 92 93
CSN2 -0.024 0.093 -10000 0 -0.74 2 2
PIK3CA 0.014 0 -10000 0 -10000 0 0
LAT -0.018 0.088 -10000 0 -0.33 15 15
YBX1 0.021 0.002 -10000 0 -10000 0 0
LCK -0.006 0.13 -10000 0 -0.82 10 10
SHC1 0.014 0 -10000 0 -10000 0 0
NOX4 -0.18 0.35 -10000 0 -0.82 98 98
Ephrin A reverse signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAPKKK cascade -0.023 0.095 -9999 0 -0.41 24 24
EFNA5 -0.013 0.12 -9999 0 -0.59 19 19
FYN 0 0.1 -9999 0 -0.59 5 5
neuron projection morphogenesis -0.023 0.095 -9999 0 -0.41 24 24
cell-cell signaling 0 0 -9999 0 -10000 0 0
Ephrin A5/EPHA5 -0.023 0.096 -9999 0 -0.41 24 24
EPHA5 -0.002 0.089 -9999 0 -0.82 5 5
Arf6 signaling events

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
CENTA1/KIF3B -0.006 0.046 -9999 0 -0.36 7 7
ARNO/beta Arrestin1-2 -0.018 0.069 -9999 0 -0.53 1 1
EGFR -0.017 0.15 -9999 0 -0.79 16 16
EPHA2 0.005 0.071 -9999 0 -0.59 6 6
USP6 0.014 0.001 -9999 0 -10000 0 0
IQSEC1 0.014 0 -9999 0 -10000 0 0
EGFR/EGFR/EGF/EGF -0.1 0.2 -9999 0 -0.46 92 92
ARRB2 0.01 0.003 -9999 0 -10000 0 0
mol:GTP 0.019 0.022 -9999 0 -0.16 2 2
ARRB1 0.011 0.041 -9999 0 -0.59 2 2
FBXO8 0.014 0 -9999 0 -10000 0 0
TSHR -0.03 0.18 -9999 0 -0.82 21 21
EGF -0.098 0.24 -9999 0 -0.6 77 77
somatostatin receptor activity 0 0 -9999 0 -0.001 12 12
ARAP2 0.008 0.058 -9999 0 -0.59 4 4
mol:GDP -0.015 0.081 -9999 0 -0.33 11 11
mol:PI-3-4-5-P3 0 0 -9999 0 -0.001 7 7
ITGA2B -0.053 0.23 -9999 0 -0.82 34 34
ARF6 0.014 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.006 0.044 -9999 0 -0.49 1 1
ADAP1 0.012 0.029 -9999 0 -0.59 1 1
KIF13B 0.005 0.071 -9999 0 -0.59 6 6
HGF/MET -0.024 0.11 -9999 0 -0.51 20 20
PXN 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.028 0.11 -9999 0 -0.33 13 13
EGFR/EGFR/EGF/EGF/ARFGEP100 -0.085 0.17 -9999 0 -0.56 16 16
ADRB2 -0.026 0.15 -9999 0 -0.59 28 28
receptor agonist activity 0 0 -9999 0 0 13 13
actin filament binding 0 0 -9999 0 -0.001 12 12
SRC 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.022 0.16 -9999 0 -0.74 20 20
GNAQ 0.014 0 -9999 0 -10000 0 0
EFA6/PI-4-5-P2 0 0 -9999 0 -0.001 9 9
ARF6/GDP 0.042 0.064 -9999 0 -0.37 3 3
ARF6/GDP/GULP/ACAP1 -0.12 0.16 -9999 0 -0.45 38 38
alphaIIb/beta3 Integrin/paxillin/GIT1 -0.06 0.16 -9999 0 -0.51 46 46
ACAP1 -0.004 0.12 -9999 0 -0.82 9 9
ACAP2 0.012 0.04 -9999 0 -0.82 1 1
LHCGR/beta Arrestin2 0.002 0.006 -9999 0 -10000 0 0
EFNA1 0.012 0.04 -9999 0 -0.82 1 1
HGF -0.012 0.13 -9999 0 -0.66 16 16
CYTH3 0.012 0 -9999 0 -10000 0 0
CYTH2 0.01 0.002 -9999 0 -10000 0 0
NCK1 0.014 0 -9999 0 -10000 0 0
fibronectin binding 0 0 -9999 0 -0.001 11 11
endosomal lumen acidification 0 0 -9999 0 -0.001 12 12
microtubule-based process 0 0 -9999 0 -10000 0 0
GULP1 -0.17 0.28 -9999 0 -0.59 131 131
GNAQ/ARNO 0.015 0.008 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
PIP3-E 0 0 -9999 0 0 1 1
MET 0.006 0.075 -9999 0 -0.76 4 4
GNA14 -0.083 0.22 -9999 0 -0.59 68 68
GNA15 0.011 0.041 -9999 0 -0.59 2 2
GIT1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -0.001 11 11
GNA11 0.009 0.051 -9999 0 -0.59 3 3
LHCGR 0.002 0.005 -9999 0 -10000 0 0
AGTR1 -0.051 0.19 -9999 0 -0.61 43 43
desensitization of G-protein coupled receptor protein signaling pathway 0.002 0.006 -9999 0 -10000 0 0
IPCEF1/ARNO -0.049 0.14 -9999 0 -0.44 16 16
alphaIIb/beta3 Integrin -0.076 0.21 -9999 0 -0.62 52 52
EPO signaling pathway

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
BCL2L1 0.024 0.13 -10000 0 -0.56 2 2
CRKL -0.003 0.14 -10000 0 -0.46 2 2
mol:DAG 0.008 0.13 -10000 0 -0.57 2 2
HRAS 0.027 0.13 -10000 0 -0.58 1 1
MAPK8 -0.026 0.17 -10000 0 -0.47 52 52
RAP1A -0.002 0.14 -10000 0 -0.49 1 1
GAB1 -0.002 0.14 -10000 0 -0.49 1 1
MAPK14 -0.021 0.16 -10000 0 -0.46 52 52
EPO -0.071 0.25 -10000 0 -0.81 44 44
PLCG1 0.008 0.14 -10000 0 -0.59 2 2
EPOR/TRPC2/IP3 Receptors -0.003 0.11 -10000 0 -0.81 8 8
RAPGEF1 0.014 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/SOCS3 -0.061 0.17 -10000 0 -0.51 52 52
GAB1/SHC/GRB2/SOS1 -0.041 0.11 -10000 0 -10000 0 0
EPO/EPOR (dimer) -0.053 0.21 -10000 0 -0.62 52 52
IRS2 -0.004 0.14 -10000 0 -0.49 1 1
STAT1 -0.009 0.17 -10000 0 -0.64 4 4
STAT5B 0.012 0.14 -10000 0 -0.62 2 2
cell proliferation -0.016 0.16 -10000 0 -0.44 52 52
GAB1/SHIP/PIK3R1/SHP2/SHC -0.041 0.11 -10000 0 -0.59 3 3
TEC -0.02 0.17 -10000 0 -0.69 7 7
SOCS3 0.012 0.029 -10000 0 -0.59 1 1
STAT1 (dimer) -0.008 0.16 -10000 0 -0.62 4 4
JAK2 0.01 0.032 -10000 0 -0.59 1 1
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
EPO/EPOR (dimer)/JAK2 0.001 0.16 -10000 0 -0.4 53 53
EPO/EPOR -0.053 0.21 -10000 0 -0.62 52 52
LYN 0.014 0.029 -10000 0 -0.59 1 1
TEC/VAV2 -0.024 0.19 -10000 0 -0.77 9 9
elevation of cytosolic calcium ion concentration -0.003 0.11 -10000 0 -0.8 8 8
SHC1 0.014 0 -10000 0 -10000 0 0
EPO/EPOR (dimer)/LYN -0.029 0.18 -10000 0 -0.52 52 52
mol:IP3 0.008 0.13 -10000 0 -0.57 2 2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP -0.047 0.12 -10000 0 -0.65 3 3
SH2B3 0.009 0.042 -10000 0 -0.81 1 1
NFKB1 -0.021 0.16 -10000 0 -0.46 52 52
EPO/EPOR (dimer)/JAK2/SOCS3 -0.034 0.092 0.28 1 -0.29 45 46
PTPN6 -0.011 0.15 -10000 0 -0.4 53 53
TEC/VAV2/GRB2 -0.017 0.18 -10000 0 -0.74 9 9
EPOR -0.003 0.11 -10000 0 -0.81 8 8
INPP5D 0.011 0.041 -10000 0 -0.59 2 2
mol:GDP -0.042 0.11 -10000 0 -10000 0 0
SOS1 0.014 0 -10000 0 -10000 0 0
PLCG2 0.012 0.029 -10000 0 -0.59 1 1
CRKL/CBL/C3G 0.012 0.14 -10000 0 -0.45 1 1
VAV2 -0.015 0.17 -10000 0 -0.52 13 13
CBL -0.002 0.14 -10000 0 -0.49 1 1
SHC/Grb2/SOS1 -0.044 0.11 -10000 0 -10000 0 0
STAT5A 0.012 0.14 -10000 0 -0.62 2 2
GRB2 0.014 0 -10000 0 -10000 0 0
STAT5 (dimer) 0.03 0.14 -10000 0 -0.65 2 2
LYN/PLCgamma2 -0.002 0.029 -10000 0 -0.43 2 2
PTPN11 0.014 0 -10000 0 -10000 0 0
BTK -0.003 0.14 -10000 0 -0.49 1 1
BCL2 0.016 0.16 -10000 0 -0.71 9 9
PDGFR-alpha signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA -0.002 0.092 -9999 0 -0.66 8 8
PDGF/PDGFRA/CRKL -0.01 0.072 -9999 0 -0.49 9 9
positive regulation of JUN kinase activity -0.007 0.048 -9999 0 -0.46 2 2
CRKL 0.012 0.04 -9999 0 -0.82 1 1
PDGF/PDGFRA/Caveolin-3 -0.11 0.2 -9999 0 -0.45 102 102
AP1 -0.14 0.33 -9999 0 -0.97 57 57
mol:IP3 0.011 0.073 -9999 0 -0.49 8 8
PLCG1 0.011 0.074 -9999 0 -0.49 8 8
PDGF/PDGFRA/alphaV Integrin -0.014 0.091 -9999 0 -0.55 11 11
RAPGEF1 0.014 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0.011 0.073 -9999 0 -0.49 8 8
CAV3 -0.13 0.25 -9999 0 -0.6 96 96
CAV1 -0.065 0.24 -9999 0 -0.82 40 40
SHC/Grb2/SOS1 -0.007 0.048 -9999 0 -0.46 2 2
PDGF/PDGFRA/Shf -0.017 0.094 -9999 0 -0.51 14 14
FOS -0.09 0.34 -9999 0 -0.96 57 57
JUN -0.008 0.021 -9999 0 -10000 0 0
oligodendrocyte development -0.014 0.091 -9999 0 -0.55 11 11
GRB2 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
mol:DAG 0.011 0.073 -9999 0 -0.49 8 8
PDGF/PDGFRA -0.002 0.092 -9999 0 -0.66 8 8
actin cytoskeleton reorganization -0.012 0.074 -9999 0 -0.46 11 11
SRF 0.025 0.009 -9999 0 -10000 0 0
SHC1 0.014 0 -9999 0 -10000 0 0
PI3K -0.01 0.062 -9999 0 -0.41 7 7
PDGF/PDGFRA/Crk/C3G -0.007 0.054 -9999 0 -0.44 4 4
JAK1 0.014 0.068 -9999 0 -0.47 8 8
ELK1/SRF 0.032 0.059 -9999 0 -0.44 3 3
SHB 0.009 0.051 -9999 0 -0.59 3 3
SHF 0.002 0.082 -9999 0 -0.59 8 8
CSNK2A1 0.008 0.02 -9999 0 -10000 0 0
GO:0007205 0.011 0.075 -9999 0 -0.5 8 8
SOS1 0.014 0 -9999 0 -10000 0 0
Ras protein signal transduction -0.007 0.048 -9999 0 -0.46 2 2
PDGF/PDGFRA/SHB -0.012 0.074 -9999 0 -0.46 11 11
PDGF/PDGFRA/Caveolin-1 -0.069 0.2 -9999 0 -0.61 48 48
ITGAV 0.006 0.075 -9999 0 -0.76 4 4
ELK1 0.014 0.079 -9999 0 -0.46 9 9
PIK3CA 0.014 0 -9999 0 -10000 0 0
PDGF/PDGFRA/Crk -0.009 0.065 -9999 0 -0.47 8 8
JAK-STAT cascade 0.014 0.068 -9999 0 -0.47 8 8
cell proliferation -0.017 0.093 -9999 0 -0.51 14 14
Signaling events mediated by HDAC Class III

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
EP300 0.011 0.041 -10000 0 -0.59 2 2
HDAC4 0.014 0 -10000 0 -10000 0 0
induction of apoptosis 0 0 -10000 0 -10000 0 0
regulation of S phase of mitotic cell cycle 0.015 0.15 0.62 24 -10000 0 24
CDKN1A 0.001 0.013 -10000 0 -10000 0 0
KAT2B -0.015 0.13 -10000 0 -0.59 20 20
BAX 0.014 0 -10000 0 -10000 0 0
FOXO3 0.002 0.031 0.45 2 -10000 0 2
FOXO1 0.014 0 -10000 0 -10000 0 0
FOXO4 0.022 0.031 -10000 0 -0.29 4 4
response to UV 0 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
TAT -0.004 0.098 -10000 0 -0.82 6 6
mol:Lysophosphatidic acid 0 0 -10000 0 -10000 0 0
MYOD1 -0.075 0.19 -10000 0 -0.46 84 84
PPARGC1A -0.19 0.29 -10000 0 -0.59 145 145
FHL2 0.011 0.041 -10000 0 -0.59 2 2
response to nutrient levels 0 0 -10000 0 -10000 0 0
KU70/SIRT1 -0.001 0.021 -10000 0 -0.43 1 1
HIST2H4A -0.015 0.15 -10000 0 -0.62 24 24
SIRT1/FOXO3a 0.001 0.027 0.29 2 -0.36 1 3
SIRT1 -0.001 0.029 -10000 0 -0.59 1 1
response to hypoxia 0 0 -10000 0 -10000 0 0
SIRT1/MEF2D/HDAC4 -0.001 0.017 -10000 0 -10000 0 0
SIRT1/Histone H1b -0.012 0.054 -10000 0 -0.35 1 1
apoptosis 0.001 0.017 -10000 0 -10000 0 0
SIRT1/PGC1A -0.13 0.18 -10000 0 -0.37 145 145
p53/SIRT1 -0.005 0.046 -10000 0 -0.43 5 5
SIRT1/FOXO4 -0.003 0.029 -10000 0 -0.35 1 1
FOXO1/FHL2/SIRT1 -0.002 0.027 -10000 0 -10000 0 0
HIST1H1E 0.009 0.067 -10000 0 -0.29 21 21
SIRT1/p300 -0.003 0.036 -10000 0 -0.43 3 3
muscle cell differentiation 0.076 0.16 0.61 8 -10000 0 8
TP53 -0.006 0.057 -10000 0 -0.59 4 4
KU70/SIRT1/BAX -0.001 0.017 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
MEF2D 0.014 0 -10000 0 -10000 0 0
HIV-1 Tat/SIRT1 -0.01 0.077 -10000 0 -0.6 7 7
ACSS2 0.021 0.022 -10000 0 -0.43 1 1
SIRT1/PCAF/MYOD -0.077 0.16 -10000 0 -0.62 8 8
TRAIL signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TNFSF10 -0.003 0.12 -10000 0 -0.79 9 9
positive regulation of NF-kappaB transcription factor activity -0.032 0.14 -10000 0 -0.6 23 23
MAP2K4 0.009 0.099 -10000 0 -10000 0 0
IKBKB 0.014 0 -10000 0 -10000 0 0
TNFRSF10B 0.014 0 -10000 0 -10000 0 0
TNFRSF10A 0.012 0.029 -10000 0 -0.59 1 1
SMPD1 0.016 0.039 -10000 0 -0.26 8 8
IKBKG 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
TNFRSF10D -0.013 0.14 -10000 0 -0.78 14 14
TRAIL/TRAILR2 -0.013 0.088 -10000 0 -0.6 9 9
TRAIL/TRAILR3 -0.03 0.13 -10000 0 -0.61 21 21
TRAIL/TRAILR1 -0.014 0.09 -10000 0 -0.59 10 10
TRAIL/TRAILR4 -0.033 0.14 -10000 0 -0.6 23 23
TRAIL/TRAILR1/DAP3/GTP -0.011 0.071 -10000 0 -0.46 10 10
IKK complex -0.026 0.063 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
DAP3/GTP 0 0 -10000 0 -10000 0 0
MAPK3 0.011 0.091 -10000 0 -0.6 9 9
MAP3K1 0.001 0.1 -10000 0 -10000 0 0
TRAILR4 (trimer) -0.013 0.14 -10000 0 -0.78 14 14
TRADD 0.014 0 -10000 0 -10000 0 0
TRAILR1 (trimer) 0.012 0.029 -10000 0 -0.59 1 1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2 -0.005 0.11 -10000 0 -10000 0 0
CFLAR 0.014 0 -10000 0 -10000 0 0
MAPK1 0.011 0.091 -10000 0 -0.6 9 9
TRAIL/TRAILR1/FADD/TRADD/RIP -0.066 0.16 -10000 0 -0.46 60 60
mol:ceramide 0.016 0.039 -10000 0 -0.26 8 8
FADD -0.088 0.27 -10000 0 -0.82 52 52
MAPK8 0.012 0.1 -10000 0 -0.47 3 3
TRAF2 0.008 0.07 -10000 0 -0.82 3 3
TRAILR3 (trimer) -0.009 0.14 -10000 0 -0.8 12 12
CHUK 0.014 0 -10000 0 -10000 0 0
TRAIL/TRAILR1/FADD -0.078 0.19 -10000 0 -0.54 60 60
DAP3 0.014 0 -10000 0 -10000 0 0
CASP10 -0.056 0.16 0.28 10 -0.44 56 66
JNK cascade -0.032 0.14 -10000 0 -0.6 23 23
TRAIL (trimer) -0.003 0.12 -10000 0 -0.79 9 9
TNFRSF10C -0.009 0.14 -10000 0 -0.8 12 12
TRAIL/TRAILR1/DAP3/GTP/FADD -0.067 0.16 -10000 0 -0.47 60 60
TRAIL/TRAILR2/FADD -0.077 0.19 -10000 0 -0.54 60 60
cell death 0.016 0.039 -10000 0 -0.25 8 8
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2 -0.005 0.11 -10000 0 -10000 0 0
TRAILR2 (trimer) 0.014 0 -10000 0 -10000 0 0
CASP8 -0.001 0.023 -10000 0 -10000 0 0
negative regulation of caspase activity 0 0 -10000 0 -10000 0 0
TRAIL/TRAILR2/FADD/TRADD/RIP -0.066 0.16 -10000 0 -0.46 60 60
Signaling mediated by p38-alpha and p38-beta

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
PTGS2 -0.1 0.28 -9999 0 -0.71 63 63
MKNK1 0.014 0 -9999 0 -10000 0 0
MAPK14 -0.043 0.12 -9999 0 -0.4 10 10
ATF2/c-Jun -0.009 0.095 -9999 0 -10000 0 0
MAPK11 -0.043 0.12 -9999 0 -0.4 10 10
MITF -0.048 0.17 -9999 0 -0.55 17 17
MAPKAPK5 -0.036 0.15 -9999 0 -0.49 10 10
KRT8 -0.11 0.23 -9999 0 -0.66 35 35
MAPKAPK3 0.014 0 -9999 0 -10000 0 0
MAPKAPK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/CK2 -0.062 0.18 -9999 0 -0.65 10 10
CEBPB -0.036 0.15 -9999 0 -0.49 10 10
SLC9A1 -0.036 0.15 -9999 0 -0.49 10 10
mol:GDP 0 0 -9999 0 -10000 0 0
ATF2 -0.03 0.15 -9999 0 -0.48 10 10
p38alpha-beta/MNK1 -0.037 0.15 -9999 0 -0.53 10 10
JUN -0.008 0.095 -9999 0 -10000 0 0
PPARGC1A -0.17 0.25 -9999 0 -0.7 50 50
USF1 -0.036 0.15 -9999 0 -0.49 10 10
RAB5/GDP/GDI1 -0.051 0.086 -9999 0 -0.36 10 10
NOS2 -0.12 0.32 -9999 0 -0.78 70 70
DDIT3 -0.045 0.16 -9999 0 -0.52 13 13
RAB5A 0.014 0 -9999 0 -10000 0 0
HSPB1 -0.019 0.12 -9999 0 -0.4 10 10
p38alpha-beta/HBP1 -0.037 0.15 -9999 0 -0.53 10 10
CREB1 -0.033 0.15 -9999 0 -0.48 10 10
RAB5/GDP 0 0 -9999 0 -10000 0 0
EIF4E -0.024 0.13 -9999 0 -0.47 10 10
RPS6KA4 -0.036 0.15 -9999 0 -0.49 10 10
PLA2G4A -0.044 0.15 -9999 0 -0.52 14 14
GDI1 -0.036 0.15 -9999 0 -0.49 10 10
TP53 -0.052 0.18 -9999 0 -0.63 12 12
RPS6KA5 -0.039 0.15 -9999 0 -0.49 10 10
ESR1 -0.059 0.18 -9999 0 -0.57 21 21
HBP1 0.014 0 -9999 0 -10000 0 0
MEF2C -0.043 0.15 -9999 0 -0.5 11 11
MEF2A -0.036 0.15 -9999 0 -0.49 10 10
EIF4EBP1 -0.035 0.15 -9999 0 -0.48 10 10
KRT19 -0.18 0.23 -9999 0 -0.67 40 40
ELK4 -0.036 0.15 -9999 0 -0.49 10 10
ATF6 -0.036 0.15 -9999 0 -0.49 10 10
ATF1 -0.033 0.15 -9999 0 -0.48 10 10
p38alpha-beta/MAPKAPK2 -0.037 0.15 -9999 0 -0.53 10 10
p38alpha-beta/MAPKAPK3 -0.037 0.15 -9999 0 -0.53 10 10
Regulation of Telomerase

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
Telomerase catalytic core complex -0.12 0.28 -9999 0 -0.68 78 78
RAD9A 0.014 0 -9999 0 -10000 0 0
AP1 -0.042 0.15 -9999 0 -0.43 57 57
IFNAR2 0.013 0.007 -9999 0 -10000 0 0
AKT1 -0.001 0.071 -9999 0 -0.59 1 1
ER alpha/Oestrogen -0.026 0.14 -9999 0 -0.57 25 25
NFX1/SIN3/HDAC complex 0.042 0.026 -9999 0 -10000 0 0
EGF -0.099 0.24 -9999 0 -0.6 77 77
SMG5 0.014 0 -9999 0 -10000 0 0
SMG6 0.014 0 -9999 0 -10000 0 0
SP3/HDAC2 0.019 0.011 -9999 0 -10000 0 0
TERT/c-Abl -0.14 0.25 -9999 0 -0.63 78 78
SAP18 0.012 0.004 -9999 0 -10000 0 0
MRN complex 0 0 -9999 0 -10000 0 0
WT1 -0.18 0.34 -9999 0 -0.82 95 95
WRN 0.014 0 -9999 0 -10000 0 0
SP1 0.014 0.007 -9999 0 -10000 0 0
SP3 0.012 0.006 -9999 0 -10000 0 0
TERF2IP 0.014 0 -9999 0 -10000 0 0
Telomerase/Nucleolin -0.12 0.22 -9999 0 -0.62 40 40
Mad/Max 0.014 0.045 -9999 0 -0.43 4 4
TERT -0.12 0.29 -9999 0 -0.7 78 78
CCND1 -0.11 0.27 -9999 0 -0.69 45 45
MAX 0.012 0.006 -9999 0 -10000 0 0
RBBP7 0.012 0.005 -9999 0 -10000 0 0
RBBP4 0.009 0.042 -9999 0 -0.59 2 2
TERF2 0 0.004 -9999 0 -10000 0 0
PTGES3 0.014 0 -9999 0 -10000 0 0
SIN3A 0.012 0.004 -9999 0 -10000 0 0
Telomerase/911 0.027 0.041 -9999 0 -10000 0 0
CDKN1B -0.08 0.23 -9999 0 -0.52 88 88
RAD1 0.014 0 -9999 0 -10000 0 0
XRCC5 0.014 0 -9999 0 -10000 0 0
XRCC6 0.014 0 -9999 0 -10000 0 0
SAP30 0.012 0.005 -9999 0 -10000 0 0
TRF2/PARP2 0 0.004 -9999 0 -10000 0 0
UBE3A 0.012 0.006 -9999 0 -10000 0 0
JUN 0.012 0.006 -9999 0 -10000 0 0
E6 -0.001 0.004 -9999 0 -10000 0 0
HPV-16 E6/E6AP 0.01 0.006 -9999 0 -10000 0 0
FOS -0.069 0.21 -9999 0 -0.59 57 57
IFN-gamma/IRF1 -0.13 0.25 -9999 0 -0.61 88 88
PARP2 0.014 0 -9999 0 -10000 0 0
BLM 0.01 0.057 -9999 0 -0.82 2 2
Telomerase 0 0.1 -9999 0 -0.44 10 10
IRF1 0.016 0.008 -9999 0 -10000 0 0
ESR1 -0.032 0.18 -9999 0 -0.75 25 25
KU/TER 0 0 -9999 0 -10000 0 0
ATM/TRF2 -0.001 0.018 -9999 0 -0.38 1 1
ubiquitin-dependent protein catabolic process 0.046 0.028 -9999 0 -10000 0 0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex 0.046 0.028 -9999 0 -10000 0 0
HDAC1 0.012 0.004 -9999 0 -10000 0 0
HDAC2 0.013 0.007 -9999 0 -10000 0 0
ATM -0.001 0.022 -9999 0 -0.44 1 1
SMAD3 0.023 0.039 -9999 0 -0.53 2 2
ABL1 0.014 0 -9999 0 -10000 0 0
MXD1 0.006 0.059 -9999 0 -0.6 4 4
MRE11A 0.014 0 -9999 0 -10000 0 0
HUS1 0.012 0.04 -9999 0 -0.82 1 1
RPS6KB1 0.014 0 -9999 0 -10000 0 0
TERT/NF kappa B1/14-3-3 -0.12 0.24 -9999 0 -0.67 41 41
NR2F2 0.014 0.041 -9999 0 -0.8 1 1
MAPK3 0.013 0.032 -9999 0 -0.62 1 1
MAPK1 0.013 0.032 -9999 0 -0.62 1 1
TGFB1/TGF beta receptor Type II 0.012 0.04 -9999 0 -0.82 1 1
NFKB1 0.014 0 -9999 0 -10000 0 0
HNRNPC 0.014 0 -9999 0 -10000 0 0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis -0.001 0.022 -9999 0 -0.44 1 1
NBN 0.014 0 -9999 0 -10000 0 0
EGFR -0.018 0.15 -9999 0 -0.79 16 16
mol:Oestrogen -0.001 0.003 -9999 0 -10000 0 0
EGF/EGFR -0.1 0.2 -9999 0 -0.47 92 92
MYC 0.012 0.006 -9999 0 -10000 0 0
IL2 0.002 0.042 -9999 0 -0.81 1 1
KU 0 0 -9999 0 -10000 0 0
RAD50 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
TGFB1 0.012 0.04 -9999 0 -0.82 1 1
TRF2/BLM -0.003 0.041 -9999 0 -0.59 2 2
FRAP1 0 0 -9999 0 -10000 0 0
KU/TERT -0.13 0.25 -9999 0 -0.66 61 61
SP1/HDAC2 0.021 0.014 -9999 0 -10000 0 0
PINX1 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1A -0.12 0.22 -9999 0 -0.62 40 40
Smad3/Myc 0.027 0.034 -9999 0 -0.45 2 2
911 complex -0.001 0.026 -9999 0 -0.54 1 1
IFNG -0.16 0.33 -9999 0 -0.81 88 88
Telomerase/PinX1 -0.12 0.22 -9999 0 -0.62 40 40
Telomerase/AKT1/mTOR/p70S6K 0.005 0.075 -9999 0 -0.4 1 1
SIN3B 0.012 0.005 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
Telomerase/EST1B -0.12 0.22 -9999 0 -0.64 35 35
response to DNA damage stimulus 0.003 0.007 -9999 0 -10000 0 0
MRN complex/TRF2/Rap1 0 0.004 -9999 0 -10000 0 0
TRF2/WRN 0 0.004 -9999 0 -10000 0 0
Telomerase/hnRNP C1/C2 -0.12 0.22 -9999 0 -0.62 40 40
E2F1 -0.038 0.2 -9999 0 -0.83 26 26
ZNFX1 0.012 0.004 -9999 0 -10000 0 0
PIF1 -0.028 0.18 -9999 0 -0.82 21 21
NCL 0.014 0 -9999 0 -10000 0 0
DKC1 0.014 0 -9999 0 -10000 0 0
telomeric DNA binding 0 0 -9999 0 -10000 0 0
EGFR-dependent Endothelin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HRAS 0.012 0.04 -9999 0 -0.82 1 1
EGFR -0.017 0.15 -9999 0 -0.79 16 16
EGF/EGFR -0.074 0.14 -9999 0 -0.48 20 20
EGF/EGFR dimer/SHC/GRB2/SOS1 -0.07 0.14 -9999 0 -0.48 16 16
mol:GTP 0 0 -9999 0 -10000 0 0
EDNRA 0.008 0.064 -9999 0 -0.74 3 3
response to oxidative stress 0 0 -9999 0 -10000 0 0
EGF -0.098 0.24 -9999 0 -0.6 77 77
EGF/EGFR dimer/SHC -0.085 0.17 -9999 0 -0.56 16 16
mol:GDP -0.069 0.14 -9999 0 -0.47 16 16
mol:Ca2+ 0 0 -9999 0 -10000 0 0
EDN1 0.009 0.051 -9999 0 -0.59 3 3
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.064 0.12 -9999 0 -0.7 1 1
SHC1 0.014 0 -9999 0 -10000 0 0
HRAS/GDP -0.065 0.13 -9999 0 -0.7 1 1
FRAP1 -0.035 0.15 -9999 0 -0.46 16 16
EGF/EGFR dimer -0.1 0.2 -9999 0 -0.46 92 92
SOS1 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
ETA receptor/Endothelin-1 -0.007 0.059 -9999 0 -0.49 6 6
Plasma membrane estrogen receptor signaling

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
GNB1/GNG2 -0.034 0.12 -10000 0 -0.48 25 25
ER alpha/Gai/GDP/Gbeta gamma 0.02 0.097 -10000 0 -0.48 4 4
AKT1 0.01 0.13 -10000 0 -0.77 8 8
PIK3CA 0.014 0 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/PI3K 0.008 0.13 -10000 0 -0.78 8 8
mol:Ca2+ -0.032 0.16 -10000 0 -0.58 7 7
IGF1R 0.012 0.04 -10000 0 -0.82 1 1
E2/ER alpha (dimer)/Striatin -0.043 0.14 -10000 0 -0.45 40 40
SHC1 0.014 0 -10000 0 -10000 0 0
apoptosis -0.011 0.12 0.74 8 -10000 0 8
RhoA/GTP -0.024 0.092 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas -0.026 0.087 -10000 0 -0.51 3 3
regulation of stress fiber formation -0.03 0.091 0.51 1 -10000 0 1
E2/ERA-ERB (dimer) -0.04 0.14 -10000 0 -0.51 33 33
KRAS 0.01 0.057 -10000 0 -0.82 2 2
G13/GTP -0.027 0.11 -10000 0 -0.45 25 25
pseudopodium formation 0.03 0.091 -10000 0 -0.51 1 1
E2/ER alpha (dimer)/PELP1 -0.029 0.12 -10000 0 -0.49 25 25
GRB2 0.014 0 -10000 0 -10000 0 0
GNG2 0.014 0 -10000 0 -10000 0 0
GNAO1 0.006 0.075 -10000 0 -0.76 4 4
HRAS 0.012 0.04 -10000 0 -0.82 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
mol:NO 0.022 0.11 -10000 0 -0.5 9 9
E2/ER beta (dimer) -0.013 0.089 -10000 0 -0.61 9 9
mol:GDP -0.032 0.11 -10000 0 -0.39 32 32
mol:NADP 0.022 0.11 -10000 0 -0.5 9 9
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
mol:IP3 -0.035 0.17 -10000 0 -0.61 7 7
IGF-1R heterotetramer 0.012 0.04 -10000 0 -0.82 1 1
PLCB1 -0.042 0.17 -10000 0 -0.4 69 69
PLCB2 -0.043 0.17 -10000 0 -0.4 70 70
IGF1 -0.077 0.22 -10000 0 -0.61 62 62
mol:L-citrulline 0.022 0.11 -10000 0 -0.5 9 9
RHOA 0.014 0 -10000 0 -10000 0 0
Gai/GDP -0.014 0.064 -10000 0 -0.55 3 3
JNK cascade -0.013 0.089 -10000 0 -0.61 9 9
BCAR1 0.014 0 -10000 0 -10000 0 0
ESR2 -0.004 0.12 -10000 0 -0.79 9 9
GNAQ 0.014 0 -10000 0 -10000 0 0
ESR1 -0.031 0.18 -10000 0 -0.74 25 25
Gq family/GDP/Gbeta gamma -0.004 0.12 -10000 0 -0.68 4 4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1 0.027 0.064 -10000 0 -10000 0 0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC -0.026 0.087 -10000 0 -0.56 2 2
GNAZ -0.015 0.15 -10000 0 -0.75 16 16
E2/ER alpha (dimer) -0.034 0.14 -10000 0 -0.57 25 25
STRN -0.009 0.12 -10000 0 -0.59 16 16
GNAL -0.059 0.2 -10000 0 -0.59 51 51
PELP1 0.014 0 -10000 0 -10000 0 0
MAPK11 0.009 0.079 -10000 0 -0.53 9 9
GNAI2 0.014 0 -10000 0 -10000 0 0
GNAI3 0.014 0 -10000 0 -10000 0 0
GNAI1 0.012 0.029 -10000 0 -0.59 1 1
HBEGF -0.17 0.17 -10000 0 -0.46 85 85
cAMP biosynthetic process -0.067 0.15 -10000 0 -0.49 27 27
SRC 0.027 0.093 -10000 0 -0.52 2 2
PI3K -0.003 0.036 -10000 0 -0.43 3 3
GNB1 0.014 0 -10000 0 -10000 0 0
G13/GDP/Gbeta gamma -0.028 0.095 -10000 0 -0.71 1 1
SOS1 0.014 0 -10000 0 -10000 0 0
IGF-1R heterotetramer/IGF1 -0.051 0.11 -10000 0 -0.51 6 6
Gs family/GTP -0.068 0.15 -10000 0 -0.5 27 27
EntrezGene:2778 0 0 -10000 0 -10000 0 0
RAS family/GTP -0.004 0.042 -10000 0 -0.5 3 3
vasodilation 0.022 0.1 -10000 0 -0.48 9 9
mol:DAG -0.035 0.17 -10000 0 -0.61 7 7
Gs family/GDP/Gbeta gamma -0.052 0.11 -10000 0 -0.57 5 5
MSN 0.03 0.097 -10000 0 -0.57 1 1
Gq family/GTP -0.08 0.16 -10000 0 -0.43 69 69
mol:PI-3-4-5-P3 0.009 0.12 -10000 0 -0.75 8 8
NRAS 0.014 0 -10000 0 -10000 0 0
mol:E2 0 0 -10000 0 -10000 0 0
cell adhesion -0.022 0.1 0.48 9 -10000 0 9
GRB2/SOS1 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.029 0.099 -10000 0 -0.42 8 8
NOS3 0.021 0.11 -10000 0 -0.53 9 9
GNA11 0.009 0.051 -10000 0 -0.59 3 3
MAPKKK cascade 0.022 0.13 -10000 0 -0.57 10 10
E2/ER alpha (dimer)/PELP1/Src -0.028 0.093 -10000 0 -0.54 3 3
ruffle organization 0.03 0.091 -10000 0 -0.51 1 1
ROCK2 0.022 0.1 -10000 0 -0.64 1 1
GNA14 -0.083 0.22 -10000 0 -0.59 68 68
GNA15 0.011 0.041 -10000 0 -0.59 2 2
GNA13 0.014 0 -10000 0 -10000 0 0
MMP9 -0.3 0.22 -10000 0 -0.64 30 30
MMP2 -0.04 0.18 -10000 0 -0.58 5 5
Cellular roles of Anthrax toxin

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
ANTXR1 0.004 0.09 -10000 0 -0.82 5 5
ANTXR2 -0.006 0.13 -10000 0 -0.82 10 10
negative regulation of myeloid dendritic cell antigen processing and presentation -0.003 0.018 -10000 0 -0.1 14 14
monocyte activation -0.026 0.11 -10000 0 -0.29 60 60
MAP2K2 -0.001 0.007 -10000 0 -10000 0 0
MAP2K1 -0.003 0.015 -10000 0 -10000 0 0
MAP2K7 -0.003 0.015 -10000 0 -10000 0 0
MAP2K6 -0.018 0.069 -10000 0 -0.32 20 20
CYAA -0.001 0.096 -10000 0 -0.51 14 14
MAP2K4 -0.003 0.015 -10000 0 -10000 0 0
IL1B -0.036 0.15 -10000 0 -0.46 47 47
Channel -0.018 0.099 -10000 0 -0.54 14 14
NLRP1 -0.004 0.028 -10000 0 -0.49 1 1
CALM1 0.014 0 -10000 0 -10000 0 0
negative regulation of phagocytosis -0.004 0.022 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
regulation of endothelial cell proliferation 0.003 0.018 0.1 14 -10000 0 14
MAPK3 -0.003 0.015 -10000 0 -10000 0 0
MAPK1 -0.003 0.015 -10000 0 -10000 0 0
PGR -0.042 0.11 -10000 0 -0.35 48 48
PA/Cellular Receptors -0.019 0.11 -10000 0 -0.58 14 14
apoptosis -0.003 0.018 -10000 0 -0.1 14 14
LOC728358 0 0 -10000 0 -10000 0 0
Lethal toxin (unfolded) 0 0.093 -10000 0 -0.49 14 14
macrophage activation 0.018 0.017 -10000 0 -10000 0 0
TNF -0.025 0.17 -10000 0 -0.77 21 21
VCAM1 -0.026 0.11 -10000 0 -0.29 60 60
platelet activation -0.004 0.022 -10000 0 -10000 0 0
MAPKKK cascade -0.011 0.025 -10000 0 -10000 0 0
IL18 0.004 0.064 -10000 0 -0.32 15 15
negative regulation of macrophage activation -0.003 0.018 -10000 0 -0.1 14 14
LEF -0.003 0.018 -10000 0 -0.1 14 14
CASP1 -0.003 0.019 -10000 0 -0.17 2 2
mol:cAMP -0.004 0.022 -10000 0 -10000 0 0
necrosis -0.003 0.018 -10000 0 -0.1 14 14
intracellular pH reduction 0 0 -10000 0 -10000 0 0
PAGA 0 0 -10000 0 -10000 0 0
Edema toxin (unfolded) -0.017 0.095 -10000 0 -0.52 14 14
mol:Epigallocatechin-3-gallate (EGCG) 0 0 -10000 0 -10000 0 0
Nectin adhesion pathway

Figure S68.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S68.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.16 0.34 -9999 0 -0.82 90 90
alphaV beta3 Integrin -0.032 0.13 -9999 0 -0.58 23 23
PTK2 -0.028 0.093 -9999 0 -0.46 10 10
positive regulation of JNK cascade -0.013 0.052 -9999 0 -0.31 10 10
CDC42/GDP 0.039 0.085 -9999 0 -0.41 10 10
Rac1/GDP 0.041 0.084 -9999 0 -0.41 10 10
RAP1B 0.012 0.04 -9999 0 -0.82 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.012 0.029 -9999 0 -0.59 1 1
CDC42/GTP -0.015 0.064 -9999 0 -0.38 10 10
nectin-3/I-afadin -0.025 0.11 -9999 0 -0.53 20 20
RAPGEF1 0.036 0.093 -9999 0 -0.46 10 10
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.029 0.1 -9999 0 -0.53 10 10
PDGFB-D/PDGFRB -0.16 0.34 -9999 0 -0.82 90 90
TLN1 0.023 0.06 -9999 0 -0.46 2 2
Rap1/GTP -0.014 0.056 -9999 0 -0.38 3 3
IQGAP1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.001 0.024 -9999 0 -0.5 1 1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin -0.025 0.11 -9999 0 -0.53 20 20
PVR 0.012 0.04 -9999 0 -0.82 1 1
Necl-5(dimer) 0.012 0.04 -9999 0 -0.82 1 1
mol:GDP 0.036 0.1 -9999 0 -0.51 10 10
MLLT4 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
PI3K -0.12 0.2 -9999 0 -0.47 99 99
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin -0.002 0.029 -9999 0 -0.43 2 2
positive regulation of lamellipodium assembly -0.017 0.058 -9999 0 -0.32 10 10
PVRL1 0.011 0.041 -9999 0 -0.59 2 2
PVRL3 -0.02 0.15 -9999 0 -0.7 20 20
PVRL2 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
CDH1 0.008 0.058 -9999 0 -0.59 4 4
CLDN1 -0.019 0.15 -9999 0 -0.68 20 20
JAM-A/CLDN1 -0.037 0.12 -9999 0 -0.5 19 19
SRC -0.025 0.1 -9999 0 -0.6 10 10
ITGB3 -0.022 0.16 -9999 0 -0.74 20 20
nectin-1(dimer)/I-afadin/I-afadin -0.002 0.029 -9999 0 -0.43 2 2
FARP2 0.033 0.098 -9999 0 -0.5 10 10
RAC1 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer) -0.022 0.1 -9999 0 -0.54 11 11
nectin-1/I-afadin -0.002 0.029 -9999 0 -0.43 2 2
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 0.1 -9999 0 -0.44 22 22
CDC42/GTP/IQGAP1/filamentous actin 0 0 -9999 0 -10000 0 0
F11R 0.014 0 -9999 0 -10000 0 0
positive regulation of filopodium formation -0.013 0.052 -9999 0 -0.31 10 10
alphaV/beta3 Integrin/Talin 0.013 0.12 -9999 0 -0.43 20 20
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 0.017 0.053 -9999 0 -0.36 1 1
VAV2 0.025 0.11 -9999 0 -0.51 10 10
RAP1/GDP -0.015 0.065 -9999 0 -0.38 10 10
ITGAV 0.006 0.075 -9999 0 -0.76 4 4
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin -0.021 0.097 -9999 0 -0.54 10 10
nectin-3(dimer)/I-afadin/I-afadin -0.025 0.11 -9999 0 -0.53 20 20
Rac1/GTP -0.02 0.07 -9999 0 -0.39 10 10
PTPRM 0.008 0.058 -9999 0 -0.27 11 11
E-cadherin/beta catenin/alpha catenin -0.005 0.04 -9999 0 -0.57 1 1
adherens junction assembly 0 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2 0.018 0.086 -9999 0 -0.47 12 12
CRKL 0.012 0.04 -9999 0 -0.82 1 1
Rac1/GDP 0 0 -9999 0 -10000 0 0
DOCK1 0.011 0.041 -9999 0 -0.59 2 2
ITGA4 -0.008 0.13 -9999 0 -0.82 11 11
alpha4/beta7 Integrin/MAdCAM1 -0.03 0.12 -9999 0 -0.49 25 25
EPO -0.074 0.25 -9999 0 -0.82 44 44
alpha4/beta7 Integrin -0.018 0.1 -9999 0 -0.6 13 13
mol:GTP 0 0 -9999 0 -10000 0 0
CRK 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin -0.018 0.1 -9999 0 -0.63 12 12
EPO/EPOR (dimer) -0.077 0.21 -9999 0 -0.63 52 52
lamellipodium assembly 0 0.031 -9999 0 -0.35 2 2
PIK3CA 0.014 0 -9999 0 -10000 0 0
PI3K -0.003 0.036 -9999 0 -0.43 3 3
ARF6 0.014 0 -9999 0 -10000 0 0
JAK2 -0.016 0.13 -9999 0 -0.52 3 3
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
MADCAM1 -0.018 0.15 -9999 0 -0.82 14 14
cell adhesion -0.03 0.12 -9999 0 -0.49 25 25
CRKL/CBL -0.001 0.03 -9999 0 -0.63 1 1
ITGB1 0.012 0.04 -9999 0 -0.82 1 1
SRC -0.026 0.17 -9999 0 -0.51 44 44
ITGB7 0.011 0.041 -9999 0 -0.59 2 2
RAC1 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/VCAM1 -0.064 0.18 -9999 0 -0.56 44 44
p130Cas/Crk/Dock1 -0.001 0.15 -9999 0 -0.81 2 2
VCAM1 -0.063 0.24 -9999 0 -0.78 41 41
RHOA 0.014 0 -9999 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/GIT1 -0.014 0.081 -9999 0 -0.49 12 12
BCAR1 -0.015 0.16 -9999 0 -0.47 44 44
EPOR -0.002 0.11 -9999 0 -0.82 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
Rac1/GTP 0 0.031 -9999 0 -0.36 2 2
S1P1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer -0.01 0.077 -9999 0 -0.6 7 7
PDGFRB -0.16 0.34 -9999 0 -0.81 90 90
SPHK1 -0.023 0.05 -9999 0 -0.32 9 9
mol:S1P -0.029 0.062 -9999 0 -0.42 6 6
S1P1/S1P/Gi -0.015 0.13 -9999 0 -0.54 7 7
GNAO1 0.005 0.076 -9999 0 -0.77 4 4
PDGFB-D/PDGFRB/PLCgamma1 -0.077 0.2 -9999 0 -0.59 15 15
PLCG1 -0.015 0.13 -9999 0 -0.53 6 6
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.16 0.34 -9999 0 -0.81 90 90
GNAI2 0.012 0.005 -9999 0 -10000 0 0
GNAI3 0.012 0.006 -9999 0 -10000 0 0
GNAI1 0.01 0.03 -9999 0 -0.6 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
EDG1 0.009 0.069 -9999 0 -0.52 7 7
S1P1/S1P -0.04 0.078 -9999 0 -0.44 10 10
negative regulation of cAMP metabolic process -0.014 0.13 -9999 0 -0.52 7 7
MAPK3 -0.022 0.17 -9999 0 -0.6 8 8
calcium-dependent phospholipase C activity -0.002 0.003 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
RhoA/GDP 0 0 -9999 0 -10000 0 0
KDR 0.009 0.05 -9999 0 -0.7 2 2
PLCB2 -0.002 0.092 -9999 0 -0.43 7 7
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.032 0.066 -9999 0 -0.4 6 6
receptor internalization -0.038 0.074 -9999 0 -0.41 10 10
PTGS2 -0.048 0.24 -9999 0 -0.6 63 63
Rac1/GTP -0.032 0.066 -9999 0 -0.4 6 6
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFA 0.003 0.09 -9999 0 -0.82 5 5
negative regulation of T cell proliferation -0.014 0.13 -9999 0 -0.52 7 7
GO:0007205 0 0 -9999 0 -10000 0 0
GNAZ -0.017 0.15 -9999 0 -0.75 16 16
MAPK1 -0.022 0.17 -9999 0 -0.6 8 8
S1P1/S1P/PDGFB-D/PDGFRB -0.071 0.19 -9999 0 -0.59 14 14
ABCC1 0.007 0.07 -9999 0 -0.82 3 3
Retinoic acid receptors-mediated signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0 -10000 0 -10000 0 0
HDAC3 0.014 0 -10000 0 -10000 0 0
VDR 0.012 0.029 -10000 0 -0.59 1 1
Cbp/p300/PCAF -0.018 0.082 -10000 0 -0.69 1 1
EP300 0.011 0.041 -10000 0 -0.59 2 2
RARs/AIB1/Cbp/p300/PCAF/9cRA 0.007 0.1 -10000 0 -0.49 8 8
KAT2B -0.015 0.13 -10000 0 -0.59 20 20
MAPK14 0.014 0 -10000 0 -10000 0 0
AKT1 0.027 0.11 0.2 44 -0.28 26 70
RAR alpha/9cRA/Cyclin H -0.022 0.058 -10000 0 -10000 0 0
mol:9cRA 0 0 -10000 0 -10000 0 0
RARs/Src-1/Cbp/p300/PCAF/9cRA 0.001 0.11 -10000 0 -0.39 17 17
CDC2 0.001 0.001 -10000 0 -10000 0 0
response to UV 0.001 0.001 -10000 0 -10000 0 0
RAR alpha/Jnk1 -0.021 0.084 -10000 0 -0.48 7 7
NCOR2 0.014 0 -10000 0 -10000 0 0
VDR/VDR/Vit D3 -0.001 0.021 -10000 0 -0.44 1 1
RXRs/RARs/NRIP1/9cRA 0.003 0.14 -10000 0 -0.51 6 6
NCOA2 -0.023 0.14 -10000 0 -0.59 26 26
NCOA3 0.014 0 -10000 0 -10000 0 0
NCOA1 0.014 0 -10000 0 -10000 0 0
VDR/VDR/DNA 0.012 0.029 -10000 0 -0.59 1 1
RARG 0.013 0.029 -10000 0 -0.59 1 1
RAR gamma1/9cRA -0.001 0.018 -10000 0 -0.36 1 1
MAPK3 0.014 0.001 -10000 0 -10000 0 0
MAPK1 0.014 0 -10000 0 -10000 0 0
MAPK8 0.005 0.077 -10000 0 -0.59 7 7
mol:Vit D3 0 0 -10000 0 -10000 0 0
RXRs/VDR/DNA/Vit D3 -0.043 0.1 -10000 0 -0.41 7 7
RARA -0.001 0.086 -10000 0 -0.25 3 3
negative regulation of phosphoinositide 3-kinase cascade 0 0 -10000 0 -10000 0 0
RARs/TIF2/Cbp/p300/PCAF/9cRA -0.017 0.16 -10000 0 -0.53 25 25
PRKCA 0.015 0.04 -10000 0 -0.81 1 1
RXRs/RARs/NRIP1/9cRA/HDAC1 -0.013 0.14 -10000 0 -0.52 5 5
RXRG -0.053 0.17 -10000 0 -0.38 86 86
RXRA 0.009 0.08 -10000 0 -10000 0 0
RXRB -0.011 0.12 -10000 0 -0.35 45 45
VDR/Vit D3/DNA -0.001 0.021 -10000 0 -0.44 1 1
RBP1 -0.17 0.34 -10000 0 -0.81 92 92
CRBP1/9-cic-RA -0.14 0.26 -10000 0 -0.63 92 92
RARB -0.039 0.18 -10000 0 -0.6 38 38
PRKCG -0.073 0.25 -10000 0 -0.81 44 44
MNAT1 0.014 0 -10000 0 -10000 0 0
RAR alpha/RXRs 0.018 0.14 -10000 0 -0.48 4 4
RXRs/RARs/SMRT(N-CoR2)/9cRA 0.008 0.13 -10000 0 -0.5 5 5
proteasomal ubiquitin-dependent protein catabolic process 0.002 0.11 -10000 0 -0.41 16 16
RXRs/RARs/NRIP1/9cRA/HDAC3 -0.013 0.14 -10000 0 -0.52 5 5
positive regulation of DNA binding -0.021 0.055 -10000 0 -10000 0 0
NRIP1 -0.011 0.14 -10000 0 -1.2 1 1
RXRs/RARs -0.02 0.14 -10000 0 -0.43 16 16
RXRs/RXRs/DNA/9cRA -0.045 0.1 -10000 0 -0.43 6 6
PRKACA 0.014 0 -10000 0 -10000 0 0
CDK7 0.014 0 -10000 0 -10000 0 0
TFIIH 0 0 -10000 0 -10000 0 0
RAR alpha/9cRA -0.015 0.041 -10000 0 -10000 0 0
CCNH 0.014 0 -10000 0 -10000 0 0
CREBBP 0.014 0 -10000 0 -10000 0 0
RAR gamma2/9cRA -0.001 0.013 -10000 0 -10000 0 0
Signaling events mediated by PRL

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
CCNE1 0.006 0.08 -10000 0 -0.82 4 4
mol:Halofuginone 0.006 0.001 -10000 0 -10000 0 0
ITGA1 -0.12 0.31 -10000 0 -0.82 69 69
CDKN1A 0.03 0.031 -10000 0 -10000 0 0
PRL-3/alpha Tubulin -0.009 0.074 -10000 0 -0.63 6 6
mol:Ca2+ -0.076 0.18 0.38 5 -0.45 76 81
AGT -0.096 0.24 -10000 0 -0.6 76 76
CCNA2 0.032 0.073 -10000 0 -0.75 1 1
TUBA1B 0.014 0 -10000 0 -10000 0 0
EGR1 0.008 0.088 -10000 0 -0.42 17 17
CDK2/Cyclin E1 0.037 0.054 -10000 0 -0.44 4 4
MAPK3 0.015 0.077 -10000 0 -0.63 6 6
PRL-2 /Rab GGTase beta 0 0 -10000 0 -10000 0 0
MAPK1 0.015 0.077 -10000 0 -0.63 6 6
PTP4A1 0.026 0.068 -10000 0 -10000 0 0
PTP4A3 0.002 0.098 -10000 0 -0.82 6 6
PTP4A2 0.014 0 -10000 0 -10000 0 0
ITGB1 0.014 0.083 -10000 0 -0.63 7 7
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.026 0.044 -10000 0 -10000 0 0
Rab GGTase beta/Rab GGTase alpha 0 0 -10000 0 -10000 0 0
PRL-1/ATF-5 0.023 0.089 -10000 0 -10000 0 0
RABGGTA 0.014 0 -10000 0 -10000 0 0
BCAR1 0.005 0.044 0.38 6 -10000 0 6
RHOC 0.026 0.044 -10000 0 -10000 0 0
RHOA 0.026 0.044 -10000 0 -10000 0 0
cell motility 0.031 0.046 -10000 0 -10000 0 0
PRL-1/alpha Tubulin 0.031 0.063 -10000 0 -10000 0 0
PRL-3/alpha1 Integrin -0.11 0.24 -10000 0 -0.63 75 75
ROCK1 0.031 0.046 -10000 0 -10000 0 0
RABGGTB 0.014 0 -10000 0 -10000 0 0
CDK2 0.014 0 -10000 0 -10000 0 0
mitosis 0.026 0.068 -10000 0 -10000 0 0
ATF5 0 0.11 -10000 0 -0.82 7 7
Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process 0.004 0.11 0.72 10 -10000 0 10
PI3K Class IB/PDE3B -0.004 0.11 -10000 0 -0.72 10 10
PDE3B -0.004 0.11 -10000 0 -0.73 10 10
Noncanonical Wnt 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
NFATC2 -0.051 0.19 -9999 0 -0.6 45 45
GNB1/GNG2 -0.054 0.11 -9999 0 -0.53 8 8
mol:DAG -0.003 0.12 -9999 0 -0.64 2 2
PLCG1 -0.004 0.12 -9999 0 -0.67 2 2
YES1 -0.021 0.14 -9999 0 -0.56 8 8
FZD3 0.006 0.065 -9999 0 -0.59 5 5
FZD6 0.014 0 -9999 0 -10000 0 0
G protein -0.005 0.12 -9999 0 -0.68 2 2
MAP3K7 -0.046 0.16 -9999 0 -0.6 3 3
mol:Ca2+ -0.003 0.12 -9999 0 -0.61 2 2
mol:IP3 -0.003 0.12 -9999 0 -0.64 2 2
NLK -0.003 0.006 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.059 0.17 -9999 0 -0.49 20 20
MAP3K7IP1 0 0 -9999 0 -10000 0 0
Noncanonical Wnts/FZD -0.032 0.14 -9999 0 -0.6 8 8
CSNK1A1 0.014 0 -9999 0 -10000 0 0
GNAS -0.021 0.14 -9999 0 -0.56 8 8
GO:0007205 -0.003 0.12 -9999 0 -0.62 2 2
WNT6 -0.043 0.2 -9999 0 -0.76 31 31
WNT4 -0.008 0.12 -9999 0 -0.66 14 14
NFAT1/CK1 alpha -0.075 0.13 -9999 0 -0.52 17 17
GNG2 0.014 0 -9999 0 -10000 0 0
WNT5A 0.005 0.076 -9999 0 -0.68 5 5
WNT11 -0.076 0.25 -9999 0 -0.76 49 49
CDC42 -0.012 0.13 -9999 0 -0.52 8 8
Fc-epsilon receptor I signaling in mast cells

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
PPAP2A 0.012 0.04 -9999 0 -0.82 1 1
LAT2 -0.049 0.13 -9999 0 -0.46 12 12
AP1 -0.09 0.12 -9999 0 -0.54 9 9
mol:PIP3 -0.065 0.18 -9999 0 -0.57 14 14
IKBKB -0.023 0.11 -9999 0 -0.34 4 4
AKT1 -0.052 0.16 -9999 0 -0.63 6 6
IKBKG -0.023 0.11 -9999 0 -0.34 4 4
MS4A2 -0.009 0.12 -9999 0 -0.65 13 13
mol:Sphingosine-1-phosphate 0 0 -9999 0 -10000 0 0
PIK3CA 0.013 0.001 -9999 0 -10000 0 0
MAP3K1 -0.013 0.11 -9999 0 -0.43 2 2
mol:Ca2+ -0.046 0.14 -9999 0 -0.41 14 14
LYN 0.012 0.03 -9999 0 -0.61 1 1
CBLB -0.048 0.13 -9999 0 -0.46 12 12
SHC1 0.014 0 -9999 0 -10000 0 0
RasGAP/p62DOK -0.02 0.078 -9999 0 -0.32 26 26
positive regulation of cell migration 0 0 -9999 0 -10000 0 0
INPP5D 0.011 0.041 -9999 0 -0.59 2 2
PLD2 -0.088 0.18 -9999 0 -0.68 10 10
PTPN13 -0.043 0.13 -9999 0 -0.47 11 11
PTPN11 0.01 0.008 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
regulation of mast cell degranulation -0.02 0.13 -9999 0 -0.39 3 3
SYK 0.011 0.042 -9999 0 -0.6 2 2
GRB2 0.013 0.001 -9999 0 -10000 0 0
LAT/PLCgamma1/GRB2/SLP76/GADs -0.11 0.15 -9999 0 -0.59 15 15
LAT -0.059 0.15 -9999 0 -0.55 19 19
PAK2 -0.024 0.12 -9999 0 -0.47 3 3
NFATC2 -0.11 0.21 -9999 0 -0.67 45 45
HRAS -0.034 0.13 -9999 0 -0.45 12 12
GAB2 0.011 0.041 -9999 0 -0.59 2 2
PLA2G1B 0.035 0.019 -9999 0 -10000 0 0
Fc epsilon R1 -0.15 0.2 -9999 0 -0.62 21 21
Antigen/IgE/Fc epsilon R1 -0.14 0.19 -9999 0 -0.57 21 21
mol:GDP -0.041 0.13 -9999 0 -0.47 12 12
JUN 0.014 0 -9999 0 -10000 0 0
mol:Ca++ 0 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
FOS -0.068 0.21 -9999 0 -0.59 57 57
Antigen/IgE/Fc epsilon R1/LYN/SYK -0.084 0.12 -9999 0 -0.46 16 16
CHUK -0.023 0.11 -9999 0 -0.34 4 4
KLRG1 -0.057 0.14 -9999 0 -0.45 18 18
VAV1 -0.053 0.14 -9999 0 -0.48 15 15
calcium-dependent protein kinase C activity 0 0 -9999 0 -10000 0 0
CBL -0.048 0.13 -9999 0 -0.46 12 12
negative regulation of mast cell degranulation -0.047 0.13 -9999 0 -0.44 10 10
BTK -0.045 0.13 -9999 0 -0.46 12 12
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK -0.08 0.17 -9999 0 -0.63 15 15
GAB2/PI3K/SHP2 -0.1 0.15 -9999 0 -0.68 7 7
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP -0.066 0.15 -9999 0 -0.56 11 11
RAF1 0.023 0.022 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB/SHIP -0.12 0.18 -9999 0 -0.65 15 15
FCER1G -0.004 0.11 -9999 0 -0.82 8 8
FCER1A -0.2 0.29 -9999 0 -0.6 148 148
Antigen/IgE/Fc epsilon R1/Fyn -0.12 0.18 -9999 0 -0.63 16 16
MAPK3 0.034 0.019 -9999 0 -10000 0 0
MAPK1 0.034 0.019 -9999 0 -10000 0 0
NFKB1 0.014 0 -9999 0 -10000 0 0
MAPK8 -0.001 0.1 -9999 0 -0.69 7 7
DUSP1 -0.022 0.14 -9999 0 -0.59 25 25
NF-kappa-B/RelA -0.036 0.047 -9999 0 -10000 0 0
actin cytoskeleton reorganization -0.047 0.13 -9999 0 -0.45 12 12
mol:Glucocorticoid Dexamethasone 0 0 -9999 0 -10000 0 0
PI3K -0.068 0.1 -9999 0 -0.53 4 4
FER -0.049 0.13 -9999 0 -0.46 13 13
RELA 0.014 0 -9999 0 -10000 0 0
ITK -0.033 0.079 -9999 0 -0.41 15 15
SOS1 0.014 0 -9999 0 -10000 0 0
PLCG1 -0.04 0.14 -9999 0 -0.47 13 13
cytokine secretion -0.026 0.034 -9999 0 -10000 0 0
SPHK1 -0.058 0.15 -9999 0 -0.52 20 20
PTK2 -0.049 0.13 -9999 0 -0.47 12 12
NTAL/PLCgamma1/GRB2/SLP76/GADs -0.11 0.15 -9999 0 -0.57 13 13
EDG1 0 0 -9999 0 -10000 0 0
mol:DAG -0.057 0.18 -9999 0 -0.53 12 12
MAP2K2 0.03 0.02 -9999 0 -10000 0 0
MAP2K1 0.03 0.02 -9999 0 -10000 0 0
MAP2K7 0.014 0 -9999 0 -10000 0 0
KLRG1/SHP2 -0.08 0.11 -9999 0 -0.43 18 18
MAP2K4 0.019 0.009 -9999 0 -10000 0 0
Fc epsilon R1/FcgammaRIIB -0.14 0.19 -9999 0 -0.63 21 21
mol:Choline -0.087 0.18 -9999 0 -0.67 10 10
SHC/Grb2/SOS1 -0.067 0.097 -9999 0 -0.45 3 3
FYN 0.012 0.04 -9999 0 -0.82 1 1
DOK1 0.014 0 -9999 0 -10000 0 0
PXN -0.038 0.12 -9999 0 -0.45 8 8
HCLS1 -0.05 0.13 -9999 0 -0.47 14 14
PRKCB -0.045 0.14 -9999 0 -0.41 13 13
FCGR2B 0.005 0.071 -9999 0 -0.59 6 6
IGHE -0.001 0.006 -9999 0 -10000 0 0
KLRG1/SHIP -0.048 0.13 -9999 0 -0.45 10 10
LCP2 0.007 0.07 -9999 0 -0.82 3 3
PLA2G4A -0.065 0.15 -9999 0 -0.49 25 25
RASA1 0.012 0.029 -9999 0 -0.59 1 1
mol:Phosphatidic acid -0.087 0.18 -9999 0 -0.67 10 10
IKK complex -0.002 0.09 -9999 0 -0.28 1 1
WIPF1 0.01 0.057 -9999 0 -0.82 2 2
IFN-gamma pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.049 0.18 -9999 0 -10000 0 0
positive regulation of NF-kappaB transcription factor activity 0 0.002 -9999 0 -10000 0 0
CRKL 0.012 0.04 -9999 0 -0.82 1 1
STAT1 (dimer)/Cbp/p300 -0.094 0.19 -9999 0 -0.73 18 18
IFN-gammaR/JAK1/JAK1/JAK2/JAK2 -0.014 0.03 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class I -0.07 0.09 -9999 0 -0.34 6 6
CaM/Ca2+ -0.078 0.15 -9999 0 -10000 0 0
RAP1A 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/SHP2 -0.066 0.23 -9999 0 -0.83 18 18
AKT1 -0.022 0.16 -9999 0 -10000 0 0
MAP2K1 -0.026 0.17 -9999 0 -10000 0 0
MAP3K11 -0.039 0.17 -9999 0 -10000 0 0
IFNGR1 0.007 0.016 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKII -0.18 0.22 -9999 0 -0.62 60 60
Rap1/GTP -0.06 0.12 -9999 0 -10000 0 0
CRKL/C3G -0.001 0.03 -9999 0 -0.63 1 1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP -0.092 0.18 -9999 0 -0.47 1 1
CEBPB 0.013 0.15 -9999 0 -10000 0 0
STAT3 0.014 0 -9999 0 -10000 0 0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1 -0.11 0.21 -9999 0 -0.92 10 10
STAT1 -0.065 0.23 -9999 0 -0.83 18 18
CALM1 0.014 0 -9999 0 -10000 0 0
IFN-gamma (dimer) -0.16 0.33 -9999 0 -0.81 88 88
PIK3CA 0.014 0 -9999 0 -10000 0 0
STAT1 (dimer)/PIAS1 -0.054 0.22 -9999 0 -0.77 18 18
CEBPB/PTGES2/Cbp/p300 -0.037 0.07 -9999 0 -10000 0 0
mol:Ca2+ -0.084 0.16 -9999 0 -10000 0 0
MAPK3 -0.006 0.15 -9999 0 -10000 0 0
STAT1 (dimer) -0.092 0.12 -9999 0 -0.48 6 6
MAPK1 -0.006 0.15 -9999 0 -10000 0 0
JAK2 0.006 0.033 -9999 0 -0.59 1 1
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
JAK1 0.007 0.016 -9999 0 -10000 0 0
CAMK2D 0.014 0 -9999 0 -10000 0 0
DAPK1 0.025 0.12 -9999 0 -0.58 5 5
SMAD7 0 0.074 -9999 0 -10000 0 0
CBL/CRKL/C3G -0.071 0.14 -9999 0 -10000 0 0
PI3K -0.077 0.15 -9999 0 -10000 0 0
IFNG -0.16 0.33 -9999 0 -0.81 88 88
apoptosis 0.009 0.1 -9999 0 -0.45 4 4
CAMK2G 0.014 0 -9999 0 -10000 0 0
STAT3 (dimer) 0.014 0 -9999 0 -10000 0 0
CAMK2A -0.12 0.25 -9999 0 -0.6 90 90
CAMK2B -0.14 0.27 -9999 0 -0.6 107 107
FRAP1 -0.019 0.15 -9999 0 -10000 0 0
PRKCD -0.021 0.16 -9999 0 -10000 0 0
RAP1B 0.012 0.04 -9999 0 -0.82 1 1
negative regulation of cell growth -0.07 0.09 -9999 0 -0.34 6 6
PTPN2 0.012 0.04 -9999 0 -0.82 1 1
EP300 0.011 0.041 -9999 0 -0.59 2 2
IRF1 -0.019 0.19 -9999 0 -0.53 27 27
STAT1 (dimer)/PIASy -0.092 0.2 -9999 0 -0.77 18 18
SOCS1 -0.031 0.16 -9999 0 -0.66 25 25
mol:GDP -0.069 0.13 -9999 0 -10000 0 0
CASP1 -0.001 0.076 -9999 0 -0.34 1 1
PTGES2 0.014 0 -9999 0 -10000 0 0
IRF9 0.037 0.057 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.075 0.14 -9999 0 -10000 0 0
RAP1/GDP -0.06 0.12 -9999 0 -10000 0 0
CBL -0.039 0.17 -9999 0 -10000 0 0
MAP3K1 -0.038 0.17 -9999 0 -10000 0 0
PIAS1 0.014 0 -9999 0 -10000 0 0
PIAS4 0.014 0.002 -9999 0 -10000 0 0
antigen processing and presentation of peptide antigen via MHC class II -0.07 0.09 -9999 0 -0.34 6 6
PTPN11 -0.05 0.18 -9999 0 -10000 0 0
CREBBP 0.014 0.001 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
FAS signaling pathway (CD95)

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
SPTAN1 0.007 0.04 0.26 4 -10000 0 4
RFC1 0.007 0.04 0.25 7 -10000 0 7
PRKDC 0.007 0.04 0.25 8 -10000 0 8
RIPK1 0.014 0.003 -10000 0 -10000 0 0
CASP7 -0.013 0.04 0.23 3 -10000 0 3
FASLG/FAS/FADD/FAF1 -0.054 0.12 -10000 0 -0.38 11 11
MAP2K4 -0.008 0.13 -10000 0 -0.43 10 10
mol:ceramide -0.028 0.14 -10000 0 -0.48 11 11
GSN 0.007 0.04 0.26 5 -10000 0 5
FASLG/FAS/FADD/FAF1/Caspase 8 -0.025 0.12 -10000 0 -0.45 7 7
FAS 0.012 0.03 -10000 0 -0.59 1 1
BID 0.003 0.042 0.3 1 -0.56 1 2
MAP3K1 0.007 0.079 -10000 0 -10000 0 0
MAP3K7 0.013 0.004 -10000 0 -10000 0 0
RB1 0.006 0.047 0.26 5 -0.35 2 7
CFLAR 0.014 0.003 -10000 0 -10000 0 0
HGF/MET -0.027 0.1 -10000 0 -0.54 8 8
ARHGDIB 0.007 0.04 -10000 0 -10000 0 0
FADD -0.089 0.27 -10000 0 -0.82 52 52
actin filament polymerization -0.007 0.04 -10000 0 -0.26 5 5
NFKB1 -0.032 0.063 -10000 0 -10000 0 0
MAPK8 -0.017 0.17 -10000 0 -0.45 35 35
DFFA 0.007 0.04 0.26 5 -10000 0 5
DNA fragmentation during apoptosis 0.007 0.043 0.26 4 -0.35 1 5
FAS/FADD/MET -0.072 0.19 -10000 0 -0.56 54 54
CFLAR/RIP1 0 0 -10000 0 -10000 0 0
FAIM3 0.001 0.1 -10000 0 -0.78 7 7
FAF1 0.014 0.005 -10000 0 -10000 0 0
PARP1 0.007 0.04 0.26 4 -10000 0 4
DFFB 0.007 0.043 0.26 4 -0.35 1 5
CHUK -0.027 0.055 -10000 0 -10000 0 0
FASLG -0.048 0.21 -10000 0 -0.75 34 34
FAS/FADD -0.078 0.21 -10000 0 -0.63 52 52
HGF -0.012 0.13 -10000 0 -0.66 16 16
LMNA 0.007 0.036 -10000 0 -10000 0 0
CASP6 0.007 0.04 0.26 4 -10000 0 4
CASP10 0.013 0.004 -10000 0 -10000 0 0
CASP3 0.009 0.047 0.3 8 -10000 0 8
PTPN13 0.002 0.082 -10000 0 -0.59 8 8
CASP8 0.006 0.048 0.38 7 -10000 0 7
IL6 -0.093 0.37 -10000 0 -1.1 43 43
MET 0.006 0.075 -10000 0 -0.76 4 4
ICAD/CAD 0.006 0.041 -10000 0 -10000 0 0
FASLG/FAS/FADD/FAF1/Caspase 10 -0.028 0.14 -10000 0 -0.49 11 11
activation of caspase activity by cytochrome c 0.003 0.041 0.3 1 -0.55 1 2
PAK2 0.007 0.039 0.26 4 -10000 0 4
BCL2 0 0.099 -10000 0 -0.7 8 8
IL6-mediated signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 -0.004 0.21 -9999 0 -0.71 1 1
CRP -0.026 0.25 -9999 0 -0.75 17 17
cell cycle arrest -0.015 0.23 -9999 0 -0.73 7 7
TIMP1 0.003 0.2 -9999 0 -0.77 5 5
IL6ST -0.042 0.18 -9999 0 -0.59 41 41
Rac1/GDP -0.002 0.15 -9999 0 -0.57 13 13
AP1 0.007 0.13 -9999 0 -0.63 2 2
GAB2 0.011 0.041 -9999 0 -0.59 2 2
TNFSF11 -0.072 0.3 -9999 0 -0.73 27 27
HSP90B1 0.032 0.05 -9999 0 -10000 0 0
GAB1 0.014 0.001 -9999 0 -10000 0 0
MAPK14 -0.009 0.15 -9999 0 -0.57 14 14
AKT1 0.058 0.03 -9999 0 -10000 0 0
FOXO1 0.064 0.029 -9999 0 -10000 0 0
MAP2K6 -0.02 0.16 -9999 0 -0.58 16 16
mol:GTP 0 0.002 -9999 0 -10000 0 0
MAP2K4 0.008 0.17 -9999 0 -0.57 10 10
MITF -0.018 0.16 -9999 0 -0.56 18 18
positive regulation of NF-kappaB transcription factor activity 0 0 -9999 0 -10000 0 0
TYK2 0.012 0.04 -9999 0 -0.82 1 1
A2M 0.021 0.034 -9999 0 -0.66 1 1
CEBPB 0.02 0.007 -9999 0 -10000 0 0
GRB2/SOS1/GAB family/SHP2 0.018 0.072 -9999 0 -0.38 2 2
STAT3 -0.015 0.24 -9999 0 -0.77 7 7
STAT1 -0.024 0.089 -9999 0 -0.35 27 27
CEBPD -0.004 0.21 -9999 0 -0.65 4 4
PIK3CA 0.015 0 -9999 0 -10000 0 0
PI3K 0.02 0.038 -9999 0 -0.42 3 3
JUN 0.013 0.001 -9999 0 -10000 0 0
PIAS3/MITF -0.01 0.16 -9999 0 -0.53 18 18
MAPK11 -0.009 0.15 -9999 0 -0.57 14 14
STAT3 (dimer)/FOXO1 0.04 0.2 -9999 0 -10000 0 0
GRB2/SOS1/GAB family -0.044 0.1 -9999 0 -0.54 8 8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK -0.016 0.15 -9999 0 -0.59 13 13
GRB2 0.014 0.001 -9999 0 -10000 0 0
JAK2 0.012 0.029 -9999 0 -0.59 1 1
LBP -0.095 0.36 -9999 0 -0.9 57 57
PIK3R1 0.011 0.051 -9999 0 -0.59 3 3
JAK1 0.016 0.004 -9999 0 -10000 0 0
MYC -0.004 0.21 -9999 0 -0.67 2 2
FGG -0.033 0.26 -9999 0 -0.76 21 21
macrophage differentiation -0.015 0.23 -9999 0 -0.73 7 7
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4 -0.059 0.15 -9999 0 -0.54 22 22
JUNB -0.004 0.2 -9999 0 -0.65 2 2
FOS -0.068 0.21 -9999 0 -0.59 57 57
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4 -0.019 0.16 -9999 0 -0.54 18 18
STAT1/PIAS1 -0.017 0.15 -9999 0 -0.54 12 12
GRB2/SOS1/GAB family/SHP2/PI3K 0.04 0.036 -9999 0 -10000 0 0
STAT3 (dimer) -0.014 0.23 -9999 0 -0.76 7 7
PRKCD 0.017 0.18 -9999 0 -0.64 5 5
IL6R 0.007 0.072 -9999 0 -0.59 6 6
SOCS3 -0.004 0.15 -9999 0 -0.78 4 4
gp130 (dimer)/JAK1/JAK1/LMO4 -0.006 0.12 -9999 0 -0.37 7 7
Rac1/GTP -0.008 0.16 -9999 0 -0.57 13 13
HCK 0.006 0.07 -9999 0 -0.7 4 4
MAPKKK cascade 0.033 0.067 -9999 0 -0.54 2 2
bone resorption -0.066 0.29 -9999 0 -0.69 27 27
IRF1 -0.004 0.21 -9999 0 -0.71 1 1
mol:GDP -0.012 0.16 -9999 0 -0.58 15 15
SOS1 0.013 0.004 -9999 0 -10000 0 0
VAV1 -0.013 0.16 -9999 0 -0.59 15 15
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3 -0.013 0.15 -9999 0 -0.65 13 13
PTPN11 -0.001 0.016 -9999 0 -10000 0 0
IL6/IL6RA -0.035 0.16 -9999 0 -0.47 48 48
gp130 (dimer)/TYK2/TYK2/LMO4 -0.012 0.12 -9999 0 -0.4 14 14
gp130 (dimer)/JAK2/JAK2/LMO4 -0.011 0.12 -9999 0 -0.4 10 10
IL6 -0.05 0.2 -9999 0 -0.64 43 43
PIAS3 0.014 0 -9999 0 -10000 0 0
PTPRE 0.01 0.012 -9999 0 -10000 0 0
PIAS1 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0.002 -9999 0 -10000 0 0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4 -0.031 0.15 -9999 0 -0.55 17 17
LMO4 0.016 0.011 -9999 0 -10000 0 0
STAT3 (dimer)/PIAS3 -0.1 0.16 -9999 0 -0.75 6 6
MCL1 0.063 0.028 -9999 0 -10000 0 0
JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1 -0.035 0.18 -9999 0 -0.85 16 16
MAP4K1 -0.006 0.12 -9999 0 -0.76 11 11
MAP3K8 0.011 0.041 -9999 0 -0.59 2 2
PRKCB -0.001 0.11 -9999 0 -0.76 8 8
DBNL 0.014 0 -9999 0 -10000 0 0
CRKL 0.012 0.04 -9999 0 -0.82 1 1
MAP3K1 0.03 0.1 -9999 0 -0.57 9 9
JUN 0.022 0.1 -9999 0 -0.52 13 13
MAP3K7 0.03 0.1 -9999 0 -0.57 9 9
GRAP2 -0.003 0.11 -9999 0 -0.7 10 10
CRK 0.014 0 -9999 0 -10000 0 0
MAP2K4 0.038 0.1 -9999 0 -0.54 9 9
LAT -0.006 0.13 -9999 0 -0.82 10 10
LCP2 0.008 0.07 -9999 0 -0.82 3 3
MAPK8 0.014 0.11 -9999 0 -0.56 13 13
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family 0.022 0.11 -9999 0 -0.61 9 9
LAT/GRAP2/SLP76/HPK1/HIP-55 -0.033 0.18 -9999 0 -0.8 16 16
Arf6 downstream pathway

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
PLAUR 0.008 0.16 -10000 0 -0.65 23 23
regulation of axonogenesis -0.022 0.034 -10000 0 -10000 0 0
myoblast fusion 0.005 0.083 0.32 23 -10000 0 23
mol:GTP -0.013 0.044 -10000 0 -0.19 23 23
regulation of calcium-dependent cell-cell adhesion -0.019 0.065 0.37 6 -10000 0 6
ARF1/GTP -0.008 0.03 -10000 0 -10000 0 0
mol:GM1 0.001 0.036 -10000 0 -0.19 2 2
mol:Choline 0.021 0.036 -10000 0 -0.37 1 1
lamellipodium assembly -0.023 0.077 -10000 0 -0.32 23 23
MAPK3 0.014 0.067 -10000 0 -0.3 2 2
ARF6/GTP/NME1/Tiam1 0.019 0.066 -10000 0 -0.37 6 6
ARF1 0.014 0 -10000 0 -10000 0 0
ARF6/GDP -0.005 0.083 -10000 0 -0.32 23 23
ARF1/GDP 0.006 0.077 -10000 0 -0.5 2 2
ARF6 0.006 0.025 -10000 0 -10000 0 0
RAB11A 0.014 0 -10000 0 -10000 0 0
TIAM1 0.008 0.065 -10000 0 -0.59 5 5
fibronectin binding 0 0 -10000 0 -10000 0 0
MAPK1 0.014 0.067 -10000 0 -0.3 2 2
actin filament bundle formation 0.021 0.068 0.49 2 -10000 0 2
KALRN -0.035 0.1 -10000 0 -0.34 30 30
RAB11FIP3/RAB11A 0 0 -10000 0 -10000 0 0
RhoA/GDP -0.021 0.069 -10000 0 -0.5 2 2
NME1 0.013 0.04 -10000 0 -0.81 1 1
Rac1/GDP -0.021 0.069 -10000 0 -0.5 2 2
substrate adhesion-dependent cell spreading -0.013 0.044 -10000 0 -0.19 23 23
cortical actin cytoskeleton organization -0.023 0.078 -10000 0 -0.32 23 23
RAC1 0.014 0 -10000 0 -10000 0 0
liver development -0.013 0.044 -10000 0 -0.19 23 23
ARF6/GTP -0.013 0.044 -10000 0 -0.19 23 23
RhoA/GTP -0.008 0.03 -10000 0 -10000 0 0
mol:GDP -0.023 0.078 -10000 0 -0.32 23 23
ARF6/GTP/RAB11FIP3/RAB11A -0.005 0.024 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
PLD1 0.012 0.042 -10000 0 -0.43 1 1
RAB11FIP3 0.014 0 -10000 0 -10000 0 0
tube morphogenesis -0.023 0.077 -10000 0 -0.32 23 23
ruffle organization 0.022 0.034 -10000 0 -10000 0 0
regulation of epithelial cell migration -0.013 0.044 -10000 0 -0.19 23 23
PLD2 0.012 0.036 -10000 0 -10000 0 0
PIP5K1A 0.022 0.034 -10000 0 -10000 0 0
mol:Phosphatidic acid 0.021 0.036 -10000 0 -0.37 1 1
Rac1/GTP -0.024 0.078 -10000 0 -0.32 23 23
IL2 signaling events mediated by PI3K

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.043 0.099 -10000 0 -0.65 4 4
UGCG -0.002 0.1 -10000 0 -0.62 11 11
AKT1/mTOR/p70S6K/Hsp90/TERT 0.02 0.12 -10000 0 -0.42 10 10
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucosylceramide 0.006 0.1 -10000 0 -0.61 11 11
mol:DAG -0.001 0.003 -10000 0 -10000 0 0
CaM/Ca2+/Calcineurin A alpha-beta B1 -0.023 0.079 -10000 0 -0.45 8 8
FRAP1 0.053 0.12 -10000 0 -0.53 8 8
FOXO3 0.061 0.11 -10000 0 -0.57 3 3
AKT1 0.055 0.11 -10000 0 -0.55 5 5
GAB2 0.012 0.042 -10000 0 -0.59 2 2
SMPD1 0.014 0.026 -10000 0 -10000 0 0
SGMS1 0.014 0.026 -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 0.021 0.033 -10000 0 -0.36 3 3
CALM1 0.014 0 -10000 0 -10000 0 0
cell proliferation 0.033 0.073 -10000 0 -0.37 4 4
EIF3A 0.014 0 -10000 0 -10000 0 0
PI3K 0.021 0.039 -10000 0 -0.43 3 3
RPS6KB1 0.006 0.07 -10000 0 -10000 0 0
mol:sphingomyelin -0.001 0.003 -10000 0 -10000 0 0
natural killer cell activation 0.001 0.001 -10000 0 -10000 0 0
JAK3 -0.005 0.13 -10000 0 -0.82 11 11
PIK3R1 0.013 0.051 -10000 0 -0.59 3 3
JAK1 0.017 0.002 -10000 0 -10000 0 0
NFKB1 0.014 0 -10000 0 -10000 0 0
MYC 0.061 0.098 -10000 0 -0.57 1 1
MYB -0.11 0.39 -10000 0 -1.2 46 46
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.041 0.12 -10000 0 -0.57 8 8
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 0.021 0.064 -10000 0 -10000 0 0
mol:PI-3-4-5-P3 0.042 0.12 -10000 0 -0.55 8 8
Rac1/GDP 0.026 0.031 -10000 0 -0.33 1 1
T cell proliferation 0.051 0.11 -10000 0 -0.61 4 4
SHC1 0.014 0.002 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
positive regulation of cyclin-dependent protein kinase activity -0.002 0.022 -10000 0 -0.066 46 46
PRKCZ 0.051 0.11 -10000 0 -0.64 4 4
NF kappa B1 p50/RelA -0.021 0.078 -10000 0 -0.48 5 5
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K 0.036 0.11 -10000 0 -0.63 6 6
HSP90AA1 0.014 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
IL2RA -0.066 0.24 -10000 0 -0.82 41 41
IL2RB 0.002 0.11 -10000 0 -0.79 8 8
TERT -0.14 0.32 -10000 0 -0.82 78 78
E2F1 -0.033 0.15 -10000 0 -0.42 46 46
SOS1 0.014 0.002 -10000 0 -10000 0 0
RPS6 0.014 0 -10000 0 -10000 0 0
mol:cAMP 0.001 0.011 0.031 46 -10000 0 46
PTPN11 0.014 0.002 -10000 0 -10000 0 0
IL2RG -0.01 0.15 -10000 0 -0.8 14 14
actin cytoskeleton organization 0.051 0.11 -10000 0 -0.61 4 4
GRB2 0.014 0.002 -10000 0 -10000 0 0
IL2 0.006 0.04 -10000 0 -0.82 1 1
PIK3CA 0.017 0.002 -10000 0 -10000 0 0
Rac1/GTP 0.033 0.031 -10000 0 -0.31 1 1
LCK -0.003 0.13 -10000 0 -0.81 10 10
BCL2 0.052 0.14 -10000 0 -0.74 9 9
S1P3 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRB -0.16 0.34 -9999 0 -0.82 90 90
mol:S1P 0.001 0.003 -9999 0 -10000 0 0
S1P1/S1P/Gi 0.022 0.068 -9999 0 -0.52 2 2
GNAO1 0.008 0.076 -9999 0 -0.76 4 4
S1P/S1P3/G12/G13 -0.008 0.061 -9999 0 -0.51 5 5
AKT1 -0.056 0.1 -9999 0 -0.37 7 7
AKT3 0.037 0.1 -9999 0 -0.67 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
PDGFB-D/PDGFRB -0.16 0.34 -9999 0 -0.82 90 90
GNAI2 0.015 0.002 -9999 0 -10000 0 0
GNAI3 0.015 0.002 -9999 0 -10000 0 0
GNAI1 0.014 0.029 -9999 0 -0.59 1 1
mol:GDP 0 0 -9999 0 -10000 0 0
S1PR3 0.009 0.066 -9999 0 -0.66 4 4
S1PR2 0.014 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
mol:Ca2+ 0.031 0.081 -9999 0 -0.57 4 4
MAPK3 0.038 0.077 -9999 0 -0.54 4 4
MAPK1 0.038 0.077 -9999 0 -0.54 4 4
JAK2 0.034 0.099 -9999 0 -0.53 7 7
CXCR4 0.022 0.13 -9999 0 -0.56 16 16
FLT1 0.015 0.04 -9999 0 -0.82 1 1
RhoA/GDP 0 0 -9999 0 -10000 0 0
Rac1/GDP 0 0 -9999 0 -10000 0 0
SRC 0.038 0.077 -9999 0 -0.54 4 4
S1P/S1P3/Gi 0.031 0.082 -9999 0 -0.58 4 4
RAC1 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.014 0.063 -9999 0 -0.52 4 4
VEGFA 0.007 0.09 -9999 0 -0.81 5 5
S1P/S1P2/Gi 0.031 0.064 -9999 0 -0.53 2 2
VEGFR1 homodimer/VEGFA homodimer 0.02 0.084 -9999 0 -0.72 5 5
RHOA 0.014 0 -9999 0 -10000 0 0
S1P/S1P3/Gq -0.018 0.12 -9999 0 -0.61 4 4
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ -0.014 0.15 -9999 0 -0.75 16 16
G12/G13 -0.006 0.061 -9999 0 -0.63 4 4
GNA14 -0.083 0.22 -9999 0 -0.59 68 68
GNA15 0.011 0.041 -9999 0 -0.59 2 2
GNA12 0.006 0.08 -9999 0 -0.82 4 4
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.009 0.051 -9999 0 -0.59 3 3
Rac1/GTP -0.014 0.063 -9999 0 -0.52 4 4
Rapid glucocorticoid signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma -0.037 0.099 -10000 0 -10000 0 0
MAPK9 0.009 0 -10000 0 -10000 0 0
adrenocorticotropin secretion 0.001 0.003 -10000 0 -10000 0 0
GNB1/GNG2 0 0 -10000 0 -10000 0 0
GNB1 0.014 0 -10000 0 -10000 0 0
regulation of calcium ion transport via voltage-gated calcium channel activity 0 0 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
MAPK14 0.009 0 -10000 0 -10000 0 0
Gs family/GTP -0.041 0.11 -10000 0 -0.34 51 51
EntrezGene:2778 0 0 -10000 0 -10000 0 0
vasopressin secretion 0 0 -10000 0 -10000 0 0
G-protein coupled receptor activity 0 0 -10000 0 -10000 0 0
ChemicalAbstracts:86-01-1 0 0 -10000 0 -10000 0 0
glutamate secretion 0.01 0.028 0.087 51 -10000 0 51
GNAL -0.059 0.2 -10000 0 -0.59 51 51
GNG2 0.014 0 -10000 0 -10000 0 0
CRH 0.001 0.003 -10000 0 -10000 0 0
mol:cortisol 0 0 -10000 0 -10000 0 0
MAPK8 0.003 0.047 -10000 0 -0.36 7 7
MAPK11 0.009 0 -10000 0 -10000 0 0
FOXM1 transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NFATC3 0.15 0.31 -9999 0 -1.2 3 3
PLK1 0.081 0.086 -9999 0 -0.7 2 2
BIRC5 0.057 0.16 -9999 0 -0.61 19 19
HSPA1B 0.15 0.31 -9999 0 -1.2 3 3
MAP2K1 0.044 0.037 -9999 0 -10000 0 0
BRCA2 0.14 0.34 -9999 0 -1.3 6 6
FOXM1 0.14 0.36 -9999 0 -1.6 4 4
XRCC1 0.15 0.31 -9999 0 -1.2 3 3
FOXM1B/p19 -0.19 0.26 -9999 0 -1.1 11 11
Cyclin D1/CDK4 0.094 0.36 -9999 0 -1.1 6 6
CDC2 0.14 0.33 -9999 0 -1.2 4 4
TGFA 0.11 0.35 -9999 0 -1.2 5 5
SKP2 0.15 0.32 -9999 0 -1.2 3 3
CCNE1 0.012 0.08 -9999 0 -0.81 4 4
CKS1B 0.14 0.33 -9999 0 -1.3 5 5
RB1 -0.048 0.11 -9999 0 -0.83 3 3
FOXM1C/SP1 0.14 0.32 -9999 0 -1.4 4 4
AURKB 0.076 0.11 -9999 0 -0.68 5 5
CENPF 0.15 0.31 -9999 0 -1.2 3 3
CDK4 0.023 0.017 -9999 0 -10000 0 0
MYC 0.15 0.29 -9999 0 -1 3 3
CHEK2 0.044 0.037 -9999 0 -10000 0 0
ONECUT1 0.092 0.38 -9999 0 -1.1 9 9
CDKN2A -0.35 0.39 -9999 0 -0.78 194 194
LAMA4 0.12 0.35 -9999 0 -1.2 5 5
FOXM1B/HNF6 0.086 0.41 -9999 0 -1.4 9 9
FOS 0.036 0.51 -9999 0 -1.2 36 36
SP1 0.015 0.001 -9999 0 -10000 0 0
CDC25B 0.13 0.33 -9999 0 -1.2 4 4
response to radiation 0.026 0.035 -9999 0 -10000 0 0
CENPB 0.15 0.31 -9999 0 -1.2 3 3
CENPA 0.14 0.32 -9999 0 -1.4 3 3
NEK2 0.14 0.32 -9999 0 -1.3 3 3
HIST1H2BA 0.14 0.31 -9999 0 -1.2 3 3
CCNA2 0.017 0.042 -9999 0 -0.83 1 1
EP300 0.011 0.041 -9999 0 -0.59 2 2
CCNB1/CDK1 0.14 0.34 -9999 0 -1.5 3 3
CCNB2 0.14 0.32 -9999 0 -1.4 3 3
CCNB1 0.15 0.33 -9999 0 -1.3 3 3
ETV5 0.14 0.32 -9999 0 -1.2 3 3
ESR1 0.12 0.36 -9999 0 -1.1 11 11
CCND1 0.098 0.37 -9999 0 -1.2 6 6
GSK3A 0.04 0.032 -9999 0 -10000 0 0
Cyclin A-E1/CDK1-2 0.045 0.076 -9999 0 -0.53 5 5
CDK2 0.019 0.009 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0.03 0.04 -9999 0 -10000 0 0
FOXM1B/Cbp/p300 -0.071 0.2 -9999 0 -1.2 5 5
GAS1 0.14 0.33 -9999 0 -1.2 7 7
MMP2 0.089 0.38 -9999 0 -1.1 7 7
RB1/FOXM1C 0.11 0.35 -9999 0 -1.3 4 4
CREBBP 0.014 0 -9999 0 -10000 0 0
Ras signaling in the CD4+ TCR pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ERK1-2/ELK1 -0.001 0.16 -9999 0 -0.56 11 11
MAP3K8 0.01 0.042 -9999 0 -0.59 2 2
FOS 0.011 0.11 -9999 0 -0.47 10 10
PRKCA 0.011 0.041 -9999 0 -0.82 1 1
PTPN7 -0.017 0.16 -9999 0 -0.81 16 16
HRAS 0.011 0.04 -9999 0 -0.82 1 1
PRKCB -0.002 0.11 -9999 0 -0.77 8 8
NRAS 0.013 0.001 -9999 0 -10000 0 0
RAS family/GTP -0.004 0.042 -9999 0 -0.5 3 3
MAPK3 0.014 0.077 -9999 0 -0.38 7 7
MAP2K1 0.027 0.073 -9999 0 -0.39 9 9
ELK1 0.01 0.043 -9999 0 -0.85 1 1
BRAF -0.011 0.055 -9999 0 -0.38 9 9
mol:GTP -0.001 0.002 -9999 0 -0.006 55 55
MAPK1 0.014 0.077 -9999 0 -0.38 7 7
RAF1 -0.011 0.055 -9999 0 -0.38 9 9
KRAS 0.009 0.057 -9999 0 -0.82 2 2
Circadian rhythm pathway

Figure S86.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S86.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
chromatin modification -0.001 0.004 -9999 0 -10000 0 0
CLOCK 0.012 0.058 -9999 0 -0.59 4 4
TIMELESS/CRY2 0.046 0.012 -9999 0 -10000 0 0
DEC1/BMAL1 -0.11 0.24 -9999 0 -0.62 75 75
ATR 0.014 0 -9999 0 -10000 0 0
NR1D1 0.045 0.014 -9999 0 -10000 0 0
ARNTL 0.017 0 -9999 0 -10000 0 0
TIMELESS 0.045 0.014 -9999 0 -10000 0 0
NPAS2 0.01 0.065 -9999 0 -0.59 5 5
CRY2 0.014 0 -9999 0 -10000 0 0
mol:CO -0.015 0 -9999 0 -10000 0 0
CHEK1 0.014 0 -9999 0 -10000 0 0
mol:HEME 0.015 0 -9999 0 -10000 0 0
PER1 0.014 0 -9999 0 -10000 0 0
BMAL/CLOCK/NPAS2 0.038 0.061 -9999 0 -0.68 1 1
BMAL1/CLOCK 0.009 0.1 -9999 0 -10000 0 0
S phase of mitotic cell cycle -0.001 0.004 -9999 0 -10000 0 0
TIMELESS/CHEK1/ATR -0.001 0.004 -9999 0 -10000 0 0
mol:NADPH 0.015 0 -9999 0 -10000 0 0
PER1/TIMELESS 0.046 0.012 -9999 0 -10000 0 0
PER1-2 / CRY1-2 0 0 -9999 0 -10000 0 0
DEC1 -0.14 0.32 -9999 0 -0.82 75 75
a4b1 and a4b7 Integrin signaling

Figure S87.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S87.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ITGB1 0.012 0.04 -9999 0 -0.82 1 1
ITGB7 0.011 0.041 -9999 0 -0.59 2 2
ITGA4 -0.008 0.13 -9999 0 -0.82 11 11
alpha4/beta7 Integrin -0.018 0.1 -9999 0 -0.6 13 13
alpha4/beta1 Integrin -0.018 0.1 -9999 0 -0.63 12 12
Ceramide signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.015 0.077 -10000 0 -0.63 6 6
MAP4K4 0.032 0.074 -10000 0 -0.42 4 4
BAG4 0.011 0.041 -10000 0 -0.59 2 2
PKC zeta/ceramide -0.014 0.045 0.21 1 -0.37 1 2
NFKBIA 0.014 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.15 -10000 0 -0.82 15 15
BAX -0.002 0.022 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AKT1 0.022 0.009 -10000 0 -10000 0 0
BAD -0.012 0.042 0.21 5 -10000 0 5
SMPD1 0.019 0.053 -10000 0 -0.25 2 2
RB1 -0.014 0.049 0.21 5 -0.37 2 7
FADD/Caspase 8 -0.014 0.17 -10000 0 -0.43 53 53
MAP2K4 -0.004 0.04 -10000 0 -10000 0 0
NSMAF 0.014 0 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 -0.004 0.04 -10000 0 -10000 0 0
EGF -0.098 0.24 -10000 0 -0.6 77 77
mol:ceramide -0.023 0.045 0.22 5 -10000 0 5
MADD 0.014 0 -10000 0 -10000 0 0
response to oxidative stress 0 0 -10000 0 -10000 0 0
mol:Free Fatty acid 0.015 0.077 -10000 0 -0.63 6 6
ASAH1 0.014 0 -10000 0 -10000 0 0
negative regulation of cell cycle -0.014 0.048 0.21 5 -0.36 2 7
cell proliferation -0.044 0.093 -10000 0 -0.39 5 5
BID 0.022 0.052 -10000 0 -10000 0 0
MAP3K1 -0.012 0.042 0.22 2 -10000 0 2
EIF2A 0.002 0.049 -10000 0 -0.44 2 2
TRADD 0.014 0 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
MAPK3 0.009 0.038 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
MAPK1 0.009 0.038 -10000 0 -10000 0 0
Cathepsin D/ceramide -0.013 0.041 0.19 5 -10000 0 5
FADD -0.028 0.18 -10000 0 -0.47 55 55
KSR1 -0.012 0.042 0.23 1 -10000 0 1
MAPK8 -0.003 0.053 0.21 5 -0.26 8 13
PRKRA -0.012 0.042 0.21 5 -10000 0 5
PDGFA 0.002 0.098 -10000 0 -0.82 6 6
TRAF2 0.008 0.07 -10000 0 -0.82 3 3
IGF1 -0.077 0.22 -10000 0 -0.61 62 62
mol:GD3 0 0 -10000 0 -10000 0 0
ganglioside biosynthetic process -0.023 0.045 0.22 5 -10000 0 5
CTSD 0.014 0 -10000 0 -10000 0 0
regulation of nitric oxide biosynthetic process 0 0 -10000 0 -10000 0 0
response to radiation 0 0 -10000 0 -10000 0 0
ERK1/PKC delta -0.025 0.11 -10000 0 -0.42 5 5
PRKCD 0.014 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.029 -10000 0 -0.59 1 1
mol:GW4869 0 0 -10000 0 -10000 0 0
mol:sphingosine 0.015 0.077 -10000 0 -0.63 6 6
RelA/NF kappa B1 0 0 -10000 0 -10000 0 0
mol:glutathione 0 0 -10000 0 -10000 0 0
PAWR 0.014 0 -10000 0 -10000 0 0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD 0.025 0.078 -10000 0 -0.45 4 4
TNFR1A/BAG4/TNF-alpha -0.027 0.11 -10000 0 -0.54 17 17
mol:Sphingosine-1-phosphate 0.015 0.077 -10000 0 -0.62 6 6
MAP2K1 0.004 0.038 -10000 0 -10000 0 0
mol:C11AG 0 0 -10000 0 -10000 0 0
RELA 0.014 0 -10000 0 -10000 0 0
CYCS -0.003 0.036 0.33 1 -10000 0 1
TNFRSF1A 0.014 0 -10000 0 -10000 0 0
NFKB1 0.014 0 -10000 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.029 -10000 0 -0.43 2 2
EIF2AK2 -0.006 0.051 0.23 1 -0.47 2 3
TNF-alpha/TNFR1A/FAN -0.025 0.11 -10000 0 -0.54 17 17
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
CASP8 0.036 0.044 -10000 0 -10000 0 0
MAP2K2 0.004 0.038 -10000 0 -10000 0 0
SMPD3 0.003 0.098 -10000 0 -0.33 25 25
TNF -0.025 0.17 -10000 0 -0.77 21 21
PKC zeta/PAR4 -0.001 0.021 -10000 0 -0.43 1 1
mol:PHOSPHOCHOLINE 0.031 0.098 0.23 80 -10000 0 80
NF kappa B1/RelA/I kappa B alpha -0.001 0.014 -10000 0 -10000 0 0
AIFM1 -0.003 0.036 0.2 4 -10000 0 4
BCL2 0 0.099 -10000 0 -0.7 8 8
RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TGFB1 0.008 0.039 -9999 0 -0.66 1 1
VDR 0.012 0.029 -9999 0 -0.59 1 1
FAM120B 0.014 0 -9999 0 -10000 0 0
RXRs/LXRs/DNA/9cRA 0.021 0.11 -9999 0 -0.44 2 2
RXRs/LXRs/DNA/Oxysterols 0.029 0.12 -9999 0 -0.51 2 2
MED1 0.012 0.04 -9999 0 -0.82 1 1
mol:9cRA 0.005 0.012 -9999 0 -10000 0 0
RARs/THRs/DNA/Src-1 -0.006 0.11 -9999 0 -0.51 3 3
RXRs/NUR77 -0.003 0.13 -9999 0 -0.5 6 6
RXRs/PPAR -0.099 0.16 -9999 0 -0.51 17 17
NCOR2 0.014 0 -9999 0 -10000 0 0
VDR/VDR/Vit D3 -0.001 0.021 -9999 0 -0.44 1 1
RARs/VDR/DNA/Vit D3 -0.028 0.088 -9999 0 -0.47 1 1
RARA 0.014 0 -9999 0 -10000 0 0
NCOA1 0.014 0 -9999 0 -10000 0 0
VDR/VDR/DNA 0.012 0.029 -9999 0 -0.59 1 1
RARs/RARs/DNA/9cRA -0.028 0.089 -9999 0 -0.4 2 2
RARG 0.012 0.029 -9999 0 -0.59 1 1
RPS6KB1 0.013 0.036 -9999 0 -10000 0 0
RARs/THRs/DNA/SMRT -0.006 0.11 -9999 0 -0.51 3 3
THRA 0.014 0 -9999 0 -10000 0 0
mol:Bile acids 0 0 -9999 0 -10000 0 0
VDR/Vit D3/DNA -0.001 0.021 -9999 0 -0.44 1 1
RXRs/PPAR/9cRA/PGJ2/DNA 0 0.12 -9999 0 -0.46 7 7
NR1H4 0.002 0.04 -9999 0 -0.82 1 1
RXRs/LXRs/DNA 0.021 0.12 -9999 0 -0.44 2 2
NR1H2 0.019 0.008 -9999 0 -10000 0 0
NR1H3 0.013 0.07 -9999 0 -0.81 3 3
RXRs/VDR/DNA/Vit D3 0.004 0.11 -9999 0 -0.45 5 5
NR4A1 -0.002 0.096 -9999 0 -0.59 11 11
mol:ATRA 0 0 -9999 0 -10000 0 0
RXRs/FXR/9cRA/MED1 0.006 0.084 -9999 0 -0.36 3 3
RXRG -0.052 0.2 -9999 0 -0.61 47 47
RXR alpha/CCPG 0.024 0.006 -9999 0 -10000 0 0
RXRA 0.019 0.008 -9999 0 -10000 0 0
RXRB 0.019 0.01 -9999 0 -10000 0 0
THRB -0.029 0.16 -9999 0 -0.59 30 30
PPARG -0.23 0.3 -9999 0 -0.59 169 169
PPARD 0.014 0 -9999 0 -10000 0 0
TNF 0.015 0.19 -9999 0 -0.71 21 21
mol:Oxysterols 0.005 0.011 -9999 0 -10000 0 0
cholesterol transport 0.029 0.11 -9999 0 -0.5 2 2
PPARA 0.014 0 -9999 0 -10000 0 0
mol:Vit D3 0 0 -9999 0 -10000 0 0
RARB -0.041 0.18 -9999 0 -0.6 38 38
RXRs/NUR77/BCL2 -0.008 0.11 -9999 0 -0.52 1 1
SREBF1 0.037 0.11 -9999 0 -10000 0 0
RXRs/RXRs/DNA/9cRA 0.001 0.12 -9999 0 -0.46 7 7
ABCA1 0.032 0.13 -9999 0 -0.91 3 3
RARs/THRs -0.048 0.11 -9999 0 -0.56 4 4
RXRs/FXR -0.001 0.12 -9999 0 -0.48 6 6
BCL2 0 0.099 -9999 0 -0.7 8 8
HIV-1 Nef: Negative effector of Fas and TNF-alpha

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BAG4 0.011 0.041 -9999 0 -0.59 2 2
Caspase 8 (4 units) -0.035 0.076 -9999 0 -0.46 3 3
NEF -0.008 0.049 -9999 0 -10000 0 0
NFKBIA 0.013 0.023 -9999 0 -10000 0 0
BIRC3 0.02 0.15 -9999 0 -0.75 15 15
CYCS 0.006 0.11 -9999 0 -0.53 3 3
RIPK1 0.014 0 -9999 0 -10000 0 0
CD247 -0.028 0.18 -9999 0 -0.87 17 17
MAP2K7 0.008 0.096 -9999 0 -0.44 2 2
protein ubiquitination 0.03 0.097 -9999 0 -0.44 2 2
CRADD 0.014 0 -9999 0 -10000 0 0
DAXX 0.014 0 -9999 0 -10000 0 0
FAS 0.012 0.029 -9999 0 -0.59 1 1
BID -0.003 0.11 -9999 0 -0.51 5 5
NF-kappa-B/RelA/I kappa B alpha -0.011 0.059 -9999 0 -10000 0 0
TRADD 0.014 0 -9999 0 -10000 0 0
MAP3K5 0.014 0 -9999 0 -10000 0 0
CFLAR 0.014 0 -9999 0 -10000 0 0
FADD -0.088 0.27 -9999 0 -0.82 52 52
NF-kappa-B/RelA/I kappa B alpha/ubiquitin -0.011 0.06 -9999 0 -10000 0 0
MAPK8 0.012 0.1 -9999 0 -0.43 3 3
APAF1 0.012 0.029 -9999 0 -0.59 1 1
TRAF1 -0.006 0.13 -9999 0 -0.82 10 10
TRAF2 0.008 0.07 -9999 0 -0.82 3 3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG -0.011 0.11 -9999 0 -0.48 5 5
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD 0.014 0.12 -9999 0 -0.57 3 3
CHUK 0.03 0.1 -9999 0 -0.49 2 2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8 -0.057 0.15 -9999 0 -0.46 52 52
TCRz/NEF -0.05 0.17 -9999 0 -0.51 42 42
TNF -0.025 0.17 -9999 0 -0.77 21 21
FASLG -0.05 0.26 -9999 0 -0.8 41 41
NFKB1 0.013 0.023 -9999 0 -10000 0 0
TNFR1A/BAG4/TNF-alpha -0.027 0.11 -9999 0 -0.54 17 17
CASP6 -0.021 0.047 -9999 0 -10000 0 0
CASP7 0.041 0.12 -9999 0 -0.51 3 3
RELA 0.013 0.023 -9999 0 -10000 0 0
CASP2 0.014 0 -9999 0 -10000 0 0
CASP3 0.041 0.12 -9999 0 -0.51 3 3
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
TNFR1A/BAG4 -0.002 0.029 -9999 0 -0.43 2 2
CASP8 0.014 0 -9999 0 -10000 0 0
CASP9 0.014 0 -9999 0 -10000 0 0
MAP3K14 0.022 0.11 -9999 0 -0.51 3 3
APAF-1/Caspase 9 -0.037 0.094 -9999 0 -0.5 4 4
BCL2 0.013 0.11 -9999 0 -0.46 4 4
Stabilization and expansion of the E-cadherin adherens junction

Figure S91.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S91.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
adherens junction organization 0.03 0.031 -9999 0 -10000 0 0
epithelial cell differentiation -0.003 0.032 -9999 0 -10000 0 0
CYFIP2 0.009 0.058 -9999 0 -0.67 3 3
ENAH 0.065 0.042 -9999 0 -10000 0 0
EGFR -0.017 0.15 -9999 0 -0.79 16 16
EPHA2 0.005 0.071 -9999 0 -0.59 6 6
MYO6 0.037 0.037 -9999 0 -10000 0 0
CTNNB1 0.012 0.029 -9999 0 -0.59 1 1
ABI1/Sra1/Nap1 -0.003 0.036 -9999 0 -0.54 1 1
AQP5 -0.33 0.21 -9999 0 -0.46 305 305
CTNND1 0.014 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0.037 0.034 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.004 0.12 -9999 0 -0.44 23 23
EGF -0.098 0.24 -9999 0 -0.6 77 77
NCKAP1 0.014 0 -9999 0 -10000 0 0
AQP3 -0.13 0.21 -9999 0 -0.71 4 4
cortical microtubule organization -0.003 0.032 -9999 0 -10000 0 0
GO:0000145 0.036 0.032 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.004 0.032 -9999 0 -10000 0 0
MLLT4 0.014 0 -9999 0 -10000 0 0
ARF6/GDP -0.007 0.042 -9999 0 -0.48 1 1
ARF6 0.014 0 -9999 0 -10000 0 0
Ephrin A1/EPHA2/NCK1/GIT1 -0.006 0.044 -9999 0 -0.49 1 1
mol:Ca2+ 0 0 -9999 0 -10000 0 0
VASP 0.049 0.034 -9999 0 -10000 0 0
PVRL2 0.014 0 -9999 0 -10000 0 0
ZYX 0.037 0.034 -9999 0 -10000 0 0
ARF6/GTP -0.005 0.04 -9999 0 -0.45 1 1
CDH1 0.008 0.058 -9999 0 -0.59 4 4
EGFR/EGFR/EGF/EGF -0.067 0.13 -9999 0 -0.61 3 3
RhoA/GDP -0.003 0.029 -9999 0 -10000 0 0
actin cytoskeleton organization 0.042 0.039 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.012 0.04 -9999 0 -0.82 1 1
GIT1 0.014 0 -9999 0 -10000 0 0
IGF1R 0.012 0.04 -9999 0 -0.82 1 1
IGF1 -0.077 0.22 -9999 0 -0.61 62 62
DIAPH1 -0.003 0.042 -9999 0 -0.58 2 2
Wnt receptor signaling pathway 0.003 0.032 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
RhoA/GTP -0.007 0.042 -9999 0 -0.48 1 1
CTNNA1 0.014 0 -9999 0 -10000 0 0
VCL 0.043 0.039 -9999 0 -10000 0 0
EFNA1 0.012 0.04 -9999 0 -0.82 1 1
LPP 0.044 0.04 -9999 0 -10000 0 0
Ephrin A1/EPHA2 -0.008 0.05 -9999 0 -0.55 1 1
SEC6/SEC8 -0.003 0.025 -9999 0 -10000 0 0
MGAT3 0.004 0.12 -9999 0 -0.44 23 23
HGF/MET -0.019 0.083 -9999 0 -0.71 2 2
HGF -0.012 0.13 -9999 0 -0.66 16 16
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN 0.03 0.031 -9999 0 -10000 0 0
actin cable formation 0.083 0.039 -9999 0 -10000 0 0
KIAA1543 0.017 0.11 -9999 0 -0.66 5 5
KIFC3 0.037 0.034 -9999 0 -10000 0 0
NCK1 0.014 0 -9999 0 -10000 0 0
EXOC3 0.014 0 -9999 0 -10000 0 0
ACTN1 0.036 0.041 -9999 0 -0.44 1 1
NCK1/GIT1 0 0 -9999 0 -10000 0 0
mol:GDP -0.003 0.032 -9999 0 -10000 0 0
EXOC4 0.014 0 -9999 0 -10000 0 0
STX4 0.037 0.034 -9999 0 -10000 0 0
PIP5K1C 0.037 0.034 -9999 0 -10000 0 0
LIMA1 0.014 0 -9999 0 -10000 0 0
ABI1 0.014 0 -9999 0 -10000 0 0
ROCK1 -0.006 0.037 -9999 0 -10000 0 0
adherens junction assembly 0.034 0.11 -9999 0 -0.64 5 5
IGF-1R heterotetramer/IGF1 -0.044 0.1 -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
MET 0.006 0.075 -9999 0 -0.76 4 4
PLEKHA7 0.018 0.09 -9999 0 -0.58 3 3
mol:GTP -0.006 0.044 -9999 0 -0.49 1 1
establishment of epithelial cell apical/basal polarity 0.064 0.031 -9999 0 -10000 0 0
cortical actin cytoskeleton stabilization 0.03 0.031 -9999 0 -10000 0 0
regulation of cell-cell adhesion 0.042 0.039 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton 0.03 0.031 -9999 0 -10000 0 0
IGF1 pathway

Figure S92.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S92.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NCK2 0.014 0 -9999 0 -10000 0 0
PTK2 0.014 0 -9999 0 -10000 0 0
CRKL -0.021 0.12 -9999 0 -0.42 8 8
GRB2/SOS1/SHC 0 0 -9999 0 -10000 0 0
HRAS 0.012 0.04 -9999 0 -0.82 1 1
IRS1/Crk -0.021 0.12 -9999 0 -0.41 7 7
IGF-1R heterotetramer/IGF1/PTP1B -0.052 0.12 -9999 0 -0.48 7 7
AKT1 0.004 0.11 -9999 0 -0.49 3 3
BAD 0.013 0.1 -9999 0 -0.47 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
CRK -0.02 0.12 -9999 0 -0.4 7 7
IGF-1R heterotetramer/IGF1/IRS1/Shp2 -0.021 0.12 -9999 0 -0.41 7 7
RAF1 0.018 0.1 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos -0.042 0.1 -9999 0 -0.54 1 1
YWHAZ 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1 -0.033 0.13 -9999 0 -0.33 63 63
PIK3CA 0.014 0 -9999 0 -10000 0 0
RPS6KB1 0.004 0.11 -9999 0 -0.49 3 3
GNB2L1 0.014 0 -9999 0 -10000 0 0
positive regulation of MAPKKK cascade 0.014 0.089 -9999 0 -0.38 2 2
PXN 0.014 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
cell adhesion 0 0 -9999 0 -10000 0 0
GRB2/SOS1 0 0 -9999 0 -10000 0 0
HRAS/GTP -0.037 0.091 -9999 0 -0.57 2 2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc -0.039 0.095 -9999 0 -10000 0 0
IGF-1R heterotetramer 0.001 0.048 -9999 0 -0.8 1 1
IGF-1R heterotetramer/IGF1/IRS/Nck -0.045 0.11 -9999 0 -0.41 7 7
Crk/p130 Cas/Paxillin -0.039 0.094 -9999 0 -0.51 1 1
IGF1R 0.001 0.048 -9999 0 -0.8 1 1
IGF1 -0.079 0.22 -9999 0 -0.62 62 62
IRS2/Crk -0.012 0.11 -9999 0 -0.53 1 1
PI3K -0.044 0.11 -9999 0 -0.56 3 3
apoptosis -0.02 0.093 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.031 -9999 0 -0.64 1 1
PRKCD -0.015 0.15 -9999 0 -0.56 1 1
RAF1/14-3-3 E 0.025 0.09 -9999 0 -10000 0 0
BAD/14-3-3 0.02 0.097 -9999 0 -10000 0 0
PRKCZ 0.004 0.11 -9999 0 -0.49 3 3
Crk/p130 Cas/Paxillin/FAK1 -0.03 0.073 -9999 0 -10000 0 0
PTPN1 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1 -0.025 0.15 -9999 0 -0.4 57 57
BCAR1 0.014 0 -9999 0 -10000 0 0
IGF-1R heterotetramer/IGF1/SHC/GRB10 -0.046 0.11 -9999 0 -0.48 8 8
mol:GDP 0 0 -9999 0 -10000 0 0
SOS1 0.014 0 -9999 0 -10000 0 0
IRS1/NCK2 -0.021 0.12 -9999 0 -0.4 7 7
GRB10 0.01 0.057 -9999 0 -0.82 2 2
PTPN11 -0.02 0.12 -9999 0 -0.4 7 7
IRS1 -0.032 0.13 -9999 0 -0.33 63 63
IRS2 -0.022 0.12 -9999 0 -0.4 7 7
IGF-1R heterotetramer/IGF1 -0.068 0.16 -9999 0 -0.46 63 63
GRB2 0.014 0 -9999 0 -10000 0 0
PDPK1 -0.004 0.11 -9999 0 -0.53 3 3
YWHAE 0.014 0 -9999 0 -10000 0 0
PRKD1 -0.024 0.16 -9999 0 -0.52 10 10
SHC1 0.014 0 -9999 0 -10000 0 0
Aurora B signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Condensin I complex 0.032 0.046 -9999 0 -10000 0 0
STMN1 0.016 0.095 -9999 0 -0.7 7 7
Aurora B/RasGAP/Survivin -0.005 0.14 -9999 0 -0.61 21 21
Chromosomal passenger complex/Cul3 protein complex 0.024 0.072 -9999 0 -0.4 7 7
BIRC5 -0.021 0.17 -9999 0 -0.81 19 19
DES -0.31 0.27 -9999 0 -0.55 223 223
Aurora C/Aurora B/INCENP 0.013 0.082 -9999 0 -0.54 8 8
Aurora B/TACC1 0.009 0.064 -9999 0 -0.51 6 6
Aurora B/PP2A 0.011 0.07 -9999 0 -0.62 5 5
mol:GTP 0 0 -9999 0 -10000 0 0
CBX5 0.017 0.019 -9999 0 -10000 0 0
mitotic metaphase/anaphase transition 0 0.002 -9999 0 -10000 0 0
NDC80 0.008 0.11 -9999 0 -0.63 13 13
Cul3 protein complex -0.005 0.042 -9999 0 -10000 0 0
KIF2C 0.02 0.045 -9999 0 -0.38 3 3
PEBP1 0.014 0.002 -9999 0 -10000 0 0
KIF20A 0.013 0.001 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
Aurora B/RasGAP 0.01 0.074 -9999 0 -0.59 6 6
SEPT1 0.002 0.098 -9999 0 -0.82 6 6
SMC2 0.014 0 -9999 0 -10000 0 0
SMC4 0.012 0.04 -9999 0 -0.82 1 1
NSUN2/NPM1/Nucleolin 0.027 0.047 -9999 0 -0.38 4 4
PSMA3 0.014 0 -9999 0 -10000 0 0
G2/M transition of mitotic cell cycle 0 0.002 -9999 0 -10000 0 0
H3F3B 0.017 0.042 -9999 0 -0.36 5 5
AURKB 0.011 0.091 -9999 0 -0.82 5 5
AURKC 0.005 0.081 -9999 0 -0.73 5 5
CDCA8 0.013 0.041 -9999 0 -0.83 1 1
cytokinesis -0.02 0.082 -9999 0 -0.55 6 6
Aurora B/Septin1 0.009 0.1 -9999 0 -0.5 11 11
AURKA -0.001 0.11 -9999 0 -0.82 7 7
INCENP 0.015 0.003 -9999 0 -10000 0 0
KLHL13 0.011 0.041 -9999 0 -0.59 2 2
BUB1 0.013 0.001 -9999 0 -10000 0 0
hSgo1/Aurora B/Survivin -0.002 0.14 -9999 0 -0.57 20 20
EVI5 0.015 0.001 -9999 0 -10000 0 0
RhoA/GTP -0.01 0.051 -9999 0 -0.42 5 5
SGOL1 0.014 0 -9999 0 -10000 0 0
CENPA 0.02 0.075 -9999 0 -0.47 7 7
NCAPG 0.014 0 -9999 0 -10000 0 0
Aurora B/HC8 Proteasome 0.011 0.07 -9999 0 -0.62 5 5
NCAPD2 0.008 0.07 -9999 0 -0.82 3 3
Aurora B/PP1-gamma 0.011 0.07 -9999 0 -0.62 5 5
RHOA 0.014 0 -9999 0 -10000 0 0
NCAPH 0.008 0.07 -9999 0 -0.82 3 3
NPM1 0.007 0.048 -9999 0 -0.42 5 5
RASA1 0.012 0.029 -9999 0 -0.59 1 1
KLHL9 0.008 0.058 -9999 0 -0.59 4 4
mitotic prometaphase 0.001 0.002 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.011 0.07 -9999 0 -0.62 5 5
PPP1CC 0.014 0 -9999 0 -10000 0 0
Centraspindlin -0.011 0.057 -9999 0 -0.46 5 5
RhoA/GDP 0 0 -9999 0 -10000 0 0
NSUN2 0.007 0.048 -9999 0 -0.42 5 5
MYLK 0.011 0.068 -9999 0 -0.4 10 10
KIF23 0.014 0.002 -9999 0 -10000 0 0
VIM 0.014 0.094 -9999 0 -0.63 9 9
RACGAP1 0.014 0.002 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
NCL 0.007 0.048 -9999 0 -0.42 5 5
Chromosomal passenger complex 0.028 0.07 -9999 0 -0.49 5 5
Chromosomal passenger complex/EVI5 0.028 0.14 -9999 0 -0.55 20 20
TACC1 0.012 0.029 -9999 0 -0.59 1 1
PPP2R5D 0.014 0 -9999 0 -10000 0 0
CUL3 0.014 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
Sphingosine 1-phosphate (S1P) pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SPHK2 0.014 0 -9999 0 -10000 0 0
SPHK1 -0.004 0.12 -9999 0 -0.82 9 9
GNAI2 0.014 0 -9999 0 -10000 0 0
mol:S1P 0.016 0.051 -9999 0 -0.28 12 12
GNAO1 0.006 0.075 -9999 0 -0.76 4 4
mol:Sphinganine-1-P 0.011 0.094 -9999 0 -0.63 9 9
growth factor activity 0 0 -9999 0 -10000 0 0
S1P/S1P2/G12/G13 -0.01 0.053 -9999 0 -0.45 4 4
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.006 0.061 -9999 0 -0.63 4 4
S1PR3 0.007 0.065 -9999 0 -0.65 4 4
S1PR2 0.014 0 -9999 0 -10000 0 0
EDG1 0 0 -9999 0 -10000 0 0
S1P1/S1P -0.007 0.041 -9999 0 -10000 0 0
S1PR5 0.012 0.029 -9999 0 -0.59 1 1
S1PR4 -0.025 0.17 -9999 0 -0.81 20 20
GNAI1 0.012 0.029 -9999 0 -0.59 1 1
S1P/S1P5/G12 -0.011 0.059 -9999 0 -0.48 4 4
S1P/S1P3/Gq -0.013 0.12 -9999 0 -0.56 5 5
S1P/S1P4/Gi 0.017 0.093 -9999 0 -0.5 5 5
GNAQ 0.014 0 -9999 0 -10000 0 0
GNAZ -0.015 0.15 -9999 0 -0.75 16 16
GNA14 -0.083 0.22 -9999 0 -0.59 68 68
GNA15 0.011 0.041 -9999 0 -0.59 2 2
GNA12 0.006 0.08 -9999 0 -0.82 4 4
GNA13 0.014 0 -9999 0 -10000 0 0
GNA11 0.009 0.051 -9999 0 -0.59 3 3
ABCC1 0.008 0.07 -9999 0 -0.82 3 3
Paxillin-dependent events mediated by a4b1

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CRKL 0.012 0.04 -10000 0 -0.82 1 1
Rac1/GDP 0.002 0.012 -10000 0 -10000 0 0
DOCK1 0.011 0.041 -10000 0 -0.59 2 2
ITGA4 -0.008 0.13 -10000 0 -0.82 11 11
RAC1 0.014 0 -10000 0 -10000 0 0
alpha4/beta7 Integrin -0.018 0.1 -10000 0 -0.6 13 13
mol:GTP 0 0 -10000 0 -10000 0 0
CRK 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin -0.015 0.09 -10000 0 -0.54 12 12
alpha4/beta7 Integrin/Paxillin -0.014 0.081 -10000 0 -0.49 11 11
lamellipodium assembly -0.002 0.044 -10000 0 -0.65 1 1
PIK3CA 0.014 0 -10000 0 -10000 0 0
PI3K -0.003 0.036 -10000 0 -0.43 3 3
ARF6 0.014 0 -10000 0 -10000 0 0
TLN1 0.01 0.057 -10000 0 -0.82 2 2
PXN 0.025 0 -10000 0 -10000 0 0
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
ARF6/GTP -0.012 0.069 -10000 0 -0.42 12 12
cell adhesion -0.015 0.081 -10000 0 -0.45 14 14
CRKL/CBL -0.001 0.03 -10000 0 -0.63 1 1
alpha4/beta1 Integrin/Paxillin -0.014 0.081 -10000 0 -0.49 12 12
ITGB1 0.012 0.04 -10000 0 -0.82 1 1
ITGB7 0.011 0.041 -10000 0 -0.59 2 2
ARF6/GDP 0.002 0.012 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/VCAM1 -0.055 0.15 -10000 0 -0.48 44 44
p130Cas/Crk/Dock1 -0.002 0.024 -10000 0 -10000 0 0
VCAM1 -0.063 0.24 -10000 0 -0.78 41 41
alpha4/beta1 Integrin/Paxillin/Talin -0.015 0.082 -10000 0 -0.46 14 14
alpha4/beta1 Integrin/Paxillin/GIT1 -0.013 0.076 -10000 0 -0.46 12 12
BCAR1 0.014 0 -10000 0 -10000 0 0
mol:GDP 0.013 0.075 0.45 12 -10000 0 12
CBL 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0 -10000 0 -10000 0 0
GIT1 0.014 0 -10000 0 -10000 0 0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton -0.015 0.082 -10000 0 -0.46 14 14
Rac1/GTP -0.003 0.05 -10000 0 -0.75 1 1
Insulin Pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CBL/APS/CAP -0.043 0.11 -9999 0 -0.62 2 2
TC10/GTP -0.039 0.094 -9999 0 -0.42 2 2
Insulin Receptor/Insulin/IRS1/Shp2 -0.004 0.039 -9999 0 -0.46 2 2
HRAS 0.012 0.04 -9999 0 -0.82 1 1
APS homodimer 0.01 0.057 -9999 0 -0.82 2 2
GRB14 -0.051 0.19 -9999 0 -0.63 42 42
FOXO3 -0.008 0.046 -9999 0 -0.64 2 2
AKT1 0.019 0.1 -9999 0 -0.5 1 1
INSR 0.015 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insulin 0.036 0.03 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
GRB10 0.01 0.057 -9999 0 -0.82 2 2
SORBS1 -0.072 0.21 -9999 0 -0.59 60 60
CRK 0.014 0 -9999 0 -10000 0 0
PTPN1 0.036 0.03 -9999 0 -10000 0 0
CAV1 -0.022 0.15 -9999 0 -0.48 42 42
CBL/APS/CAP/Crk-II/C3G -0.043 0.1 -9999 0 -0.46 2 2
Insulin Receptor/Insulin/IRS1/NCK2 -0.004 0.039 -9999 0 -0.46 2 2
mol:GDP 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.005 0.041 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B 0.039 0.028 -9999 0 -10000 0 0
RPS6KB1 0.027 0.097 -9999 0 -10000 0 0
PARD6A 0.01 0.05 -9999 0 -0.7 2 2
CBL 0.014 0 -9999 0 -10000 0 0
tumor necrosis factor-mediated signaling pathway 0 0 -9999 0 -10000 0 0
DOK1 0.001 0.009 -9999 0 -10000 0 0
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
Insulin Receptor/Insuli/IRS1/GRB2/Shc -0.026 0.076 -9999 0 -10000 0 0
HRAS/GTP -0.005 0.037 -9999 0 -10000 0 0
Insulin Receptor 0.015 0.003 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC -0.003 0.035 -9999 0 -10000 0 0
PRKCI -0.007 0.021 -9999 0 -10000 0 0
Insulin Receptor/Insulin/GRB14/PDK1 -0.033 0.094 -9999 0 -0.54 1 1
SHC1 0.014 0 -9999 0 -10000 0 0
negative regulation of MAPKKK cascade 0 0.017 -9999 0 -10000 0 0
PI3K -0.005 0.041 -9999 0 -10000 0 0
NCK2 0.014 0 -9999 0 -10000 0 0
RHOQ 0.014 0 -9999 0 -10000 0 0
mol:H2O2 0 0.003 -9999 0 -10000 0 0
HRAS/GDP -0.001 0.031 -9999 0 -0.64 1 1
AKT2 0.019 0.1 -9999 0 -0.5 1 1
PRKCZ -0.008 0.032 -9999 0 -0.49 1 1
SH2B2 0.01 0.057 -9999 0 -0.82 2 2
SHC/SHIP 0.031 0.043 -9999 0 -10000 0 0
F2RL2 -0.25 0.39 -9999 0 -0.81 136 136
TRIP10 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/Shc -0.002 0.032 -9999 0 -0.47 2 2
TC10/GTP/CIP4/Exocyst 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB2/Sos1 -0.002 0.029 -9999 0 -10000 0 0
RAPGEF1 0.014 0 -9999 0 -10000 0 0
RASA1 0.012 0.029 -9999 0 -0.59 1 1
NCK1 0.014 0 -9999 0 -10000 0 0
CBL/APS/CAP/Crk-II -0.047 0.11 -9999 0 -0.49 2 2
TC10/GDP 0 0 -9999 0 -10000 0 0
Insulin Receptor/Insulin/SHC/GRB10 -0.005 0.047 -9999 0 -0.48 4 4
INPP5D 0.024 0.045 -9999 0 -0.43 2 2
SOS1 0.014 0 -9999 0 -10000 0 0
SGK1 -0.006 0.063 -9999 0 -0.92 2 2
mol:cAMP 0 0 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
IRS1 0.011 0.041 -9999 0 -0.59 2 2
p62DOK/RasGAP 0 0.017 -9999 0 -10000 0 0
INS 0 0.056 -9999 0 -0.81 2 2
mol:PI-3-4-P2 0.024 0.045 -9999 0 -0.42 2 2
GRB2 0.014 0 -9999 0 -10000 0 0
EIF4EBP1 0.021 0.11 -9999 0 -0.62 1 1
PTPRA 0.015 0.003 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
TC10/GTP/CIP4 0 0 -9999 0 -10000 0 0
PDPK1 0.014 0 -9999 0 -10000 0 0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos 0.034 0.028 -9999 0 -10000 0 0
Insulin Receptor/Insulin/IRS1 -0.004 0.039 -9999 0 -0.47 2 2
Insulin Receptor/Insulin/IRS3 -0.003 0.042 -9999 0 -0.62 2 2
Par3/Par6 -0.15 0.22 -9999 0 -0.47 135 135
VEGFR1 specific signals

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer 0.032 0.042 -9999 0 -0.58 2 2
VEGFR1 homodimer/NRP1 -0.001 0.031 -9999 0 -0.63 1 1
mol:DAG -0.054 0.2 -9999 0 -0.56 1 1
VEGFR1 homodimer/NRP1/VEGFR 121 -0.007 0.07 -9999 0 -0.6 5 5
CaM/Ca2+ -0.044 0.19 -9999 0 -0.53 1 1
HIF1A 0.021 0.016 -9999 0 -10000 0 0
GAB1 0.014 0 -9999 0 -10000 0 0
AKT1 -0.02 0.18 -9999 0 -0.69 3 3
PLCG1 -0.055 0.2 -9999 0 -0.57 1 1
NOS3 -0.016 0.17 -9999 0 -0.51 4 4
CBL 0.014 0 -9999 0 -10000 0 0
mol:NO -0.014 0.17 -9999 0 -0.49 4 4
FLT1 0.031 0.036 -9999 0 -0.72 1 1
PGF -0.14 0.32 -9999 0 -0.82 78 78
VEGFR1 homodimer/NRP2/VEGFR121 -0.009 0.076 -9999 0 -1 1 1
CALM1 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
eNOS/Hsp90 -0.006 0.16 -9999 0 -0.57 1 1
endothelial cell proliferation -0.031 0.18 -9999 0 -10000 0 0
mol:Ca2+ -0.054 0.2 -9999 0 -0.56 1 1
MAPK3 -0.033 0.18 -9999 0 -10000 0 0
MAPK1 -0.033 0.18 -9999 0 -10000 0 0
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
PLGF homodimer -0.14 0.32 -9999 0 -0.82 78 78
PRKACA 0.014 0 -9999 0 -10000 0 0
RP11-342D11.1 0 0 -9999 0 -10000 0 0
CAV1 -0.065 0.24 -9999 0 -0.82 40 40
VEGFA homodimer 0.004 0.089 -9999 0 -0.82 5 5
VEGFR1 homodimer/VEGFA homodimer 0.027 0.078 -9999 0 -0.65 5 5
platelet activating factor biosynthetic process -0.024 0.18 -9999 0 -10000 0 0
PI3K -0.086 0.18 -9999 0 -0.7 4 4
PRKCA -0.043 0.19 -9999 0 -0.52 1 1
PRKCB -0.051 0.2 -9999 0 -0.52 1 1
VEGFR1 homodimer/PLGF homodimer -0.072 0.22 -9999 0 -0.54 79 79
VEGFA 0.004 0.09 -9999 0 -0.82 5 5
VEGFB 0.012 0.04 -9999 0 -0.82 1 1
mol:IP3 -0.054 0.2 -9999 0 -0.56 1 1
RASA1 0.04 0.043 -9999 0 -0.53 2 2
NRP2 0.01 0.057 -9999 0 -0.82 2 2
VEGFR1 homodimer 0.031 0.036 -9999 0 -0.72 1 1
VEGFB homodimer 0.012 0.04 -9999 0 -0.82 1 1
NCK1 0.014 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 -0.048 0.21 -9999 0 -0.73 9 9
PTPN11 0.014 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.085 0.18 -9999 0 -0.69 4 4
mol:L-citrulline -0.014 0.17 -9999 0 -0.49 4 4
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP -0.007 0.065 -9999 0 -0.99 1 1
VEGFR1 homodimer/VEGFA homodimer/NCK1 -0.007 0.069 -9999 0 -1 1 1
CD2AP 0.014 0 -9999 0 -10000 0 0
PI3K/GAB1 -0.081 0.17 -9999 0 -0.72 3 3
PDPK1 -0.036 0.19 -9999 0 -0.65 4 4
VEGFR1 homodimer/VEGFA homodimer/SHP2 -0.007 0.069 -9999 0 -1 1 1
mol:NADP -0.014 0.17 -9999 0 -0.49 4 4
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ubiquitin-dependent protein catabolic process -0.007 0.064 -9999 0 -0.97 1 1
VEGFR1 homodimer/NRP2 0.03 0.05 -9999 0 -0.56 3 3
p38 MAPK signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
TRAF6/ASK1 -0.001 0.013 -9999 0 -0.27 1 1
TRAF2/ASK1 -0.004 0.046 -9999 0 -0.55 3 3
ATM 0.012 0.029 -9999 0 -0.59 1 1
MAP2K3 0.018 0.047 -9999 0 -0.35 1 1
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 0.02 0.064 -9999 0 -10000 0 0
hyperosmotic response 0 0 -9999 0 -10000 0 0
response to oxidative stress 0 0 -9999 0 -10000 0 0
GADD45G 0.002 0.091 -9999 0 -0.69 7 7
TXN 0.009 0 -9999 0 -10000 0 0
CALM1 0.014 0 -9999 0 -10000 0 0
GADD45A 0.012 0.04 -9999 0 -0.82 1 1
GADD45B 0.014 0 -9999 0 -10000 0 0
MAP3K1 0.014 0 -9999 0 -10000 0 0
MAP3K6 0.012 0.029 -9999 0 -0.59 1 1
MAP3K7 0.014 0 -9999 0 -10000 0 0
MAP3K4 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
ASK1/ASK2 -0.001 0.021 -9999 0 -0.43 1 1
TAK1/TAB family 0 0.009 -9999 0 -0.18 1 1
RAC1/OSM/MEKK3 -0.009 0.068 -9999 0 -0.5 8 8
TRAF2 0.008 0.07 -9999 0 -0.82 3 3
RAC1/OSM/MEKK3/MKK3 -0.013 0.051 -9999 0 -0.42 3 3
TRAF6 0.008 0.018 -9999 0 -0.37 1 1
RAC1 0.014 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
CAMK2B -0.14 0.27 -9999 0 -0.6 107 107
CCM2 -0.002 0.11 -9999 0 -0.82 8 8
CaM/Ca2+/CAMKIIB -0.095 0.16 -9999 0 -0.38 107 107
MAPK11 0.014 0 -9999 0 -10000 0 0
response to DNA damage stimulus 0 0 -9999 0 -10000 0 0
CaM/Ca2+/CAMKIIB/ASK1 -0.084 0.15 -9999 0 -0.5 6 6
OSM/MEKK3 -0.012 0.085 -9999 0 -0.63 8 8
TAOK1 0.011 0.054 -9999 0 -0.35 9 9
TAOK2 0.018 0.018 -9999 0 -0.35 1 1
TAOK3 0.018 0.018 -9999 0 -0.35 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.014 0 -9999 0 -10000 0 0
MAP3K7IP2 0 0 -9999 0 -10000 0 0
MAP3K5 0.014 0 -9999 0 -10000 0 0
MAP3K10 0.012 0.04 -9999 0 -0.82 1 1
MAP3K3 0.014 0 -9999 0 -10000 0 0
TRX/ASK1 0.017 0 -9999 0 -10000 0 0
GADD45/MTK1/MTK1 -0.007 0.053 -9999 0 -0.47 4 4
BARD1 signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BARD1/CSTF1 -0.023 0.097 -10000 0 -0.43 23 23
ATM 0.012 0.029 -10000 0 -0.59 1 1
UBE2D3 0.014 0 -10000 0 -10000 0 0
PRKDC 0.014 0 -10000 0 -10000 0 0
ATR 0.014 0 -10000 0 -10000 0 0
UBE2L3 0.014 0 -10000 0 -10000 0 0
FANCD2 0.027 0.018 -10000 0 -0.34 1 1
protein ubiquitination -0.02 0.078 -10000 0 -0.45 4 4
XRCC5 0.014 0 -10000 0 -10000 0 0
XRCC6 0.014 0 -10000 0 -10000 0 0
M/R/N Complex 0 0 -10000 0 -10000 0 0
MRE11A 0.014 0 -10000 0 -10000 0 0
DNA-PK 0 0 -10000 0 -10000 0 0
FA complex/FANCD2/Ubiquitin -0.004 0.037 -10000 0 -0.57 1 1
FANCF 0.009 0.051 -10000 0 -0.59 3 3
BRCA1 0.014 0 -10000 0 -10000 0 0
CCNE1 0.006 0.08 -10000 0 -0.82 4 4
CDK2/Cyclin E1 -0.006 0.061 -10000 0 -0.63 4 4
FANCG 0.01 0.057 -10000 0 -0.82 2 2
BRCA1/BACH1/BARD1 -0.023 0.097 -10000 0 -0.43 23 23
FANCE 0.014 0 -10000 0 -10000 0 0
FANCC 0.014 0 -10000 0 -10000 0 0
NBN 0.014 0 -10000 0 -10000 0 0
FANCA 0.01 0.057 -10000 0 -0.82 2 2
DNA repair 0.058 0.079 -10000 0 -0.5 1 1
BRCA1/BARD1/ubiquitin -0.023 0.097 -10000 0 -0.43 23 23
BARD1/DNA-PK -0.017 0.071 -10000 0 -10000 0 0
FANCL 0.01 0.057 -10000 0 -0.82 2 2
mRNA polyadenylation 0.023 0.096 0.42 23 -10000 0 23
BRCA1/BARD1/CTIP/M/R/N Complex 0.027 0.068 -10000 0 -0.41 1 1
BRCA1/BACH1/BARD1/TopBP1 -0.019 0.081 -10000 0 -0.36 23 23
BRCA1/BARD1/P53 -0.02 0.077 -10000 0 -10000 0 0
BARD1/CSTF1/BRCA1 -0.019 0.081 -10000 0 -0.36 23 23
BRCA1/BACH1 0.014 0 -10000 0 -10000 0 0
BARD1 -0.019 0.14 -10000 0 -0.59 23 23
PCNA 0.014 0 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH5C -0.019 0.081 -10000 0 -10000 0 0
BRCA1/BARD1/UbcH7 -0.019 0.081 -10000 0 -10000 0 0
BRCA1/BARD1/RAD51/PCNA -0.018 0.075 -10000 0 -0.49 1 1
BARD1/DNA-PK/P53 -0.018 0.071 -10000 0 -10000 0 0
BRCA1/BARD1/Ubiquitin -0.023 0.097 -10000 0 -0.43 23 23
BRCA1/BARD1/CTIP -0.018 0.073 -10000 0 -10000 0 0
FA complex 0.038 0.042 -10000 0 -0.51 1 1
BARD1/EWS -0.023 0.097 -10000 0 -0.43 23 23
RBBP8 0.024 0.022 -10000 0 -0.43 1 1
TP53 0.008 0.058 -10000 0 -0.59 4 4
TOPBP1 0.014 0 -10000 0 -10000 0 0
G1/S transition of mitotic cell cycle 0.02 0.077 -10000 0 -10000 0 0
BRCA1/BARD1 -0.021 0.079 -10000 0 -0.46 4 4
CSTF1 0.014 0 -10000 0 -10000 0 0
BARD1/EWS-Fli1 -0.024 0.099 -10000 0 -0.44 23 23
CDK2 0.014 0 -10000 0 -10000 0 0
UniProt:Q9BZD1 0 0 -10000 0 -10000 0 0
RAD51 0.012 0.04 -10000 0 -0.82 1 1
RAD50 0.014 0 -10000 0 -10000 0 0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme -0.023 0.097 -10000 0 -0.43 23 23
EWSR1 0.014 0 -10000 0 -10000 0 0
Aurora A signaling

Figure S100.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S100.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Aurora A/GADD45A 0.022 0.048 -9999 0 -0.54 1 1
BIRC5 -0.024 0.17 -9999 0 -0.82 19 19
NFKBIA 0.027 0.04 -9999 0 -10000 0 0
CPEB1 -0.077 0.23 -9999 0 -0.64 58 58
AKT1 0.027 0.04 -9999 0 -10000 0 0
NDEL1 0.014 0 -9999 0 -10000 0 0
Aurora A/BRCA1 -0.003 0.033 -9999 0 -10000 0 0
NDEL1/TACC3 -0.005 0.044 -9999 0 -0.47 2 2
GADD45A 0.012 0.04 -9999 0 -0.82 1 1
GSK3B 0.013 0.004 -9999 0 -10000 0 0
PAK1/Aurora A 0.022 0.048 -9999 0 -0.54 1 1
MDM2 0.014 0 -9999 0 -10000 0 0
JUB 0.012 0.029 -9999 0 -0.59 1 1
TPX2 0.015 0.077 -9999 0 -0.63 6 6
TP53 0.025 0.042 -9999 0 -0.31 4 4
DLG7 0.016 0.04 -9999 0 -0.29 7 7
AURKAIP1 0.012 0.04 -9999 0 -0.82 1 1
ARHGEF7 0.014 0 -9999 0 -10000 0 0
G2 phase of mitotic cell cycle 0 0 -9999 0 -10000 0 0
Aurora A/NDEL1/TACC3 -0.005 0.046 -9999 0 -0.49 2 2
G2/M transition of mitotic cell cycle -0.003 0.033 -9999 0 -10000 0 0
AURKA 0.02 0.047 -9999 0 -0.34 7 7
AURKB -0.005 0.034 -9999 0 -0.26 6 6
CDC25B -0.017 0.074 -9999 0 -0.32 20 20
G2/M transition checkpoint -0.004 0.041 -9999 0 -0.56 1 1
mRNA polyadenylation -0.053 0.13 -9999 0 -0.37 57 57
Aurora A/CPEB -0.054 0.14 -9999 0 -0.38 57 57
Aurora A/TACC1/TRAP/chTOG -0.003 0.032 -9999 0 -10000 0 0
BRCA1 0.014 0 -9999 0 -10000 0 0
centrosome duplication 0.022 0.048 -9999 0 -0.54 1 1
regulation of centrosome cycle -0.005 0.043 -9999 0 -0.46 2 2
spindle assembly -0.004 0.032 -9999 0 -10000 0 0
TDRD7 0.014 0 -9999 0 -10000 0 0
Aurora A/RasGAP/Survivin -0.023 0.1 -9999 0 -0.48 19 19
CENPA -0.006 0.037 -9999 0 -0.38 3 3
Aurora A/PP2A 0.023 0.039 -9999 0 -10000 0 0
meiosis 0 0 -9999 0 -10000 0 0
protein catabolic process 0.032 0.038 -9999 0 -10000 0 0
negative regulation of DNA binding 0.025 0.042 -9999 0 -0.31 4 4
prophase 0 0 -9999 0 -10000 0 0
GIT1/beta-PIX 0 0 -9999 0 -10000 0 0
RASA1 0.012 0.029 -9999 0 -0.59 1 1
Ajuba/Aurora A -0.004 0.041 -9999 0 -0.56 1 1
mitotic prometaphase 0.001 0.008 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.02 0.047 -9999 0 -0.34 7 7
TACC1 0.012 0.029 -9999 0 -0.59 1 1
TACC3 0.01 0.057 -9999 0 -0.82 2 2
Aurora A/Antizyme1 -0.004 0.04 -9999 0 -0.49 1 1
Aurora A/RasGAP 0.022 0.043 -9999 0 -0.36 1 1
OAZ1 0.014 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
PRKACA 0.013 0.004 -9999 0 -10000 0 0
GIT1 0.014 0 -9999 0 -10000 0 0
GIT1/beta-PIX/PAK1 -0.001 0.026 -9999 0 -0.54 1 1
Importin alpha/Importin beta/TPX2 0.015 0.077 -9999 0 -0.63 6 6
PPP2R5D 0.014 0 -9999 0 -10000 0 0
Aurora A/TPX2 0.024 0.071 -9999 0 -0.49 6 6
PAK1 0.012 0.04 -9999 0 -0.82 1 1
CKAP5 0.014 0 -9999 0 -10000 0 0
HIF-2-alpha transcription factor network

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MMP14 -0.006 0.095 -10000 0 -0.68 8 8
oxygen homeostasis -0.001 0.017 -10000 0 -10000 0 0
TCEB2 0.012 0.04 -10000 0 -0.82 1 1
TCEB1 0.012 0.04 -10000 0 -0.82 1 1
VHL/Elongin B/Elongin C/HIF2A -0.021 0.077 -10000 0 -0.53 2 2
EPO -0.037 0.27 -10000 0 -0.71 28 28
FIH (dimer) 0.012 0.017 -10000 0 -10000 0 0
APEX1 0.014 0.015 -10000 0 -10000 0 0
SERPINE1 -0.25 0.39 -10000 0 -0.81 45 45
FLT1 0.006 0.049 -10000 0 -0.66 1 1
ADORA2A -0.014 0.23 -10000 0 -0.79 5 5
germ cell development -0.026 0.25 -10000 0 -0.82 12 12
SLC11A2 -0.011 0.23 -10000 0 -0.87 3 3
BHLHE40 -0.013 0.23 -10000 0 -0.89 4 4
HIF1AN 0.012 0.017 -10000 0 -10000 0 0
HIF2A/ARNT/SIRT1 -0.059 0.1 -10000 0 -0.5 7 7
ETS1 0.025 0.07 -10000 0 -0.8 3 3
CITED2 -0.003 0.092 -10000 0 -1 3 3
KDR 0.003 0.081 -10000 0 -1 2 2
PGK1 -0.011 0.23 -10000 0 -0.82 4 4
SIRT1 0.012 0.029 -10000 0 -0.59 1 1
response to hypoxia -0.001 0.005 -10000 0 -10000 0 0
HIF2A/ARNT -0.021 0.26 -10000 0 -0.88 8 8
EPAS1 0.01 0.13 -10000 0 -0.43 8 8
SP1 0.022 0.003 -10000 0 -10000 0 0
ABCG2 -0.017 0.24 -10000 0 -0.86 6 6
EFNA1 -0.011 0.23 -10000 0 -0.88 4 4
FXN -0.012 0.23 -10000 0 -0.8 4 4
POU5F1 -0.028 0.26 -10000 0 -0.86 12 12
neuron apoptosis 0.021 0.25 0.84 8 -10000 0 8
EP300 0.011 0.041 -10000 0 -0.59 2 2
EGLN3 -0.035 0.19 -10000 0 -0.79 25 25
EGLN2 0.012 0.016 -10000 0 -10000 0 0
EGLN1 0.012 0.017 -10000 0 -10000 0 0
VHL/Elongin B/Elongin C -0.003 0.037 -10000 0 -0.54 2 2
VHL 0.014 0 -10000 0 -10000 0 0
ARNT 0.014 0.015 -10000 0 -10000 0 0
SLC2A1 -0.019 0.25 -10000 0 -0.85 11 11
TWIST1 -0.023 0.25 -10000 0 -0.83 13 13
ELK1 0.02 0.04 -10000 0 -0.81 1 1
HIF2A/ARNT/Cbp/p300 -0.049 0.093 -10000 0 -0.49 7 7
VEGFA -0.015 0.24 -10000 0 -0.9 6 6
CREBBP 0.014 0 -10000 0 -10000 0 0
Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
alphaV beta3 Integrin -0.032 0.13 -9999 0 -0.58 23 23
AKT1 0.085 0.064 -9999 0 -0.51 1 1
PTK2B 0.029 0.13 -9999 0 -0.75 3 3
VEGFR2 homodimer/Frs2 0.03 0.073 -9999 0 -0.57 6 6
CAV1 -0.065 0.24 -9999 0 -0.82 40 40
CALM1 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2 -0.014 0.08 -9999 0 -0.52 6 6
endothelial cell proliferation 0.094 0.068 -9999 0 -0.47 1 1
mol:Ca2+ 0.052 0.071 -9999 0 -0.55 2 2
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac -0.008 0.062 -9999 0 -0.57 2 2
RP11-342D11.1 0.042 0.07 -9999 0 -0.55 2 2
CDH5 0.01 0.05 -9999 0 -0.7 2 2
VEGFA homodimer -0.006 0.053 -9999 0 -0.49 5 5
SHC1 0.014 0 -9999 0 -10000 0 0
SHC2 0.003 0.09 -9999 0 -0.74 6 6
HRAS/GDP -0.008 0.06 -9999 0 -0.66 1 1
SH2D2A -0.088 0.27 -9999 0 -0.82 52 52
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS -0.009 0.05 -9999 0 -0.48 1 1
VEGFR2 homodimer/VEGFA homodimer/TsAd -0.068 0.17 -9999 0 -0.5 58 58
VEGFR1 homodimer 0.012 0.04 -9999 0 -0.82 1 1
SHC/GRB2/SOS1 -0.008 0.057 -9999 0 -0.55 1 1
GRB10 0.05 0.085 -9999 0 -0.68 3 3
PTPN11 0.014 0 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
PAK1 0.012 0.04 -9999 0 -0.82 1 1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin -0.01 0.064 -9999 0 -0.59 1 1
HRAS 0.012 0.04 -9999 0 -0.82 1 1
VEGF/Rho/ROCK1/Integrin Complex 0.038 0.072 -9999 0 -0.48 3 3
HIF1A 0.014 0 -9999 0 -10000 0 0
FRS2 0.006 0.08 -9999 0 -0.82 4 4
oxygen and reactive oxygen species metabolic process -0.008 0.061 -9999 0 -0.56 2 2
mol:GTP 0 0 -9999 0 -10000 0 0
FLT4 0.002 0.098 -9999 0 -0.82 6 6
Nck/Pak -0.001 0.03 -9999 0 -0.63 1 1
VEGFR2 homodimer/VEGFA homodimer/Fyn -0.01 0.07 -9999 0 -0.61 2 2
mol:GDP -0.008 0.056 -9999 0 -0.54 1 1
mol:NADP 0.073 0.061 -9999 0 -0.41 1 1
eNOS/Hsp90 0.076 0.058 -9999 0 -10000 0 0
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
mol:IP3 0.052 0.071 -9999 0 -0.55 2 2
HIF1A/ARNT 0 0 -9999 0 -10000 0 0
SHB 0.009 0.051 -9999 0 -0.59 3 3
VEGFA 0.006 0.089 -9999 0 -0.81 5 5
VEGFC -0.098 0.28 -9999 0 -0.81 57 57
FAK1/Vinculin 0.056 0.097 -9999 0 -0.7 2 2
mol:Ca ++ 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin -0.031 0.12 -9999 0 -0.73 4 4
PTPN6 0.014 0 -9999 0 -10000 0 0
EPAS1 0.023 0.025 -9999 0 -10000 0 0
mol:L-citrulline 0.073 0.061 -9999 0 -0.41 1 1
ITGAV 0.006 0.075 -9999 0 -0.76 4 4
PIK3CA 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2 -0.013 0.075 -9999 0 -0.57 2 2
VEGFR2 homodimer/VEGFA homodimer -0.01 0.068 -9999 0 -0.6 2 2
VEGFR2/3 heterodimer 0.028 0.09 -9999 0 -0.64 7 7
VEGFB 0.012 0.04 -9999 0 -0.82 1 1
MAPK11 0.054 0.072 -9999 0 -0.55 2 2
VEGFR2 homodimer 0.035 0.055 -9999 0 -0.76 2 2
FLT1 0.012 0.04 -9999 0 -0.82 1 1
NEDD4 0.016 0.005 -9999 0 -10000 0 0
MAPK3 0.056 0.069 -9999 0 -0.54 1 1
MAPK1 0.056 0.069 -9999 0 -0.54 1 1
VEGFA145/NRP2 -0.01 0.079 -9999 0 -0.62 7 7
VEGFR1/2 heterodimer 0.034 0.056 -9999 0 -0.62 3 3
KDR 0.035 0.056 -9999 0 -0.76 2 2
VEGFA165/NRP1/VEGFR2 homodimer -0.011 0.068 -9999 0 -0.55 2 2
SRC 0.014 0 -9999 0 -10000 0 0
platelet activating factor biosynthetic process 0.058 0.069 -9999 0 -0.55 1 1
PI3K -0.01 0.061 -9999 0 -0.61 2 2
VEGFR2 homodimer/VEGFA homodimer/NCK1 -0.009 0.066 -9999 0 -0.61 2 2
FES 0.052 0.072 -9999 0 -0.56 2 2
GAB1 -0.008 0.059 -9999 0 -0.65 2 2
VEGFR2 homodimer/VEGFA homodimer/Src -0.009 0.066 -9999 0 -0.51 7 7
CTNNB1 0.012 0.029 -9999 0 -0.59 1 1
SOS1 0.014 0 -9999 0 -10000 0 0
ARNT 0.014 0 -9999 0 -10000 0 0
eNOS/Caveolin-1 0.038 0.13 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/Yes -0.009 0.066 -9999 0 -0.61 2 2
PI3K/GAB1 0.086 0.068 -9999 0 -0.53 1 1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak -0.013 0.074 -9999 0 -0.59 1 1
PRKACA 0.014 0 -9999 0 -10000 0 0
VEGFR2/3 heterodimer/VEGFC homodimer -0.074 0.18 -9999 0 -0.5 62 62
HSP90AA1 0.014 0 -9999 0 -10000 0 0
CDC42 0.052 0.072 -9999 0 -0.56 2 2
actin cytoskeleton reorganization -0.067 0.17 -9999 0 -0.49 58 58
PTK2 0.051 0.1 -9999 0 -0.76 2 2
EDG1 0.042 0.07 -9999 0 -0.55 2 2
mol:DAG 0.052 0.071 -9999 0 -0.55 2 2
CaM/Ca2+ -0.008 0.057 -9999 0 -0.54 1 1
MAP2K3 0.052 0.086 -9999 0 -0.56 2 2
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4 -0.011 0.078 -9999 0 -0.69 3 3
PLCG1 0.052 0.072 -9999 0 -0.56 2 2
VEGFR2 homodimer/VEGFA homodimer/Src/Shb -0.011 0.068 -9999 0 -0.57 2 2
IQGAP1 0.014 0 -9999 0 -10000 0 0
YES1 0.014 0 -9999 0 -10000 0 0
VEGFR2 homodimer/VEGFA homodimer/SHP2 -0.009 0.066 -9999 0 -0.61 2 2
VEGFR2 homodimer/VEGFA homodimer/SHP1 -0.009 0.066 -9999 0 -0.51 7 7
cell migration 0.079 0.086 -9999 0 -0.67 1 1
mol:PI-3-4-5-P3 0.071 0.07 -9999 0 -0.56 2 2
FYN 0.012 0.04 -9999 0 -0.82 1 1
VEGFB/NRP1 0.047 0.071 -9999 0 -0.52 2 2
mol:NO 0.073 0.061 -9999 0 -0.41 1 1
PXN 0.014 0 -9999 0 -10000 0 0
HRAS/GTP -0.008 0.059 -9999 0 -0.64 1 1
VEGFR2 homodimer/VEGFA homodimer/GRB10 0.049 0.087 -9999 0 -0.69 3 3
VHL 0.014 0 -9999 0 -10000 0 0
ITGB3 -0.022 0.16 -9999 0 -0.74 20 20
NOS3 0.075 0.066 -9999 0 -0.46 1 1
VEGFR2 homodimer/VEGFA homodimer/Sck -0.015 0.087 -9999 0 -0.58 6 6
RAC1 0.014 0 -9999 0 -10000 0 0
PRKCA 0.058 0.071 -9999 0 -0.55 1 1
PRKCB 0.05 0.09 -9999 0 -0.55 1 1
VCL 0.012 0.029 -9999 0 -0.59 1 1
VEGFA165/NRP1 0.042 0.072 -9999 0 -0.55 2 2
VEGFR1/2 heterodimer/VEGFA homodimer -0.01 0.077 -9999 0 -0.72 3 3
VEGFA165/NRP2 -0.01 0.079 -9999 0 -0.62 7 7
MAPKKK cascade -0.01 0.071 -9999 0 -0.75 2 2
NRP2 0.01 0.057 -9999 0 -0.82 2 2
VEGFC homodimer -0.097 0.28 -9999 0 -0.81 57 57
NCK1 0.014 0 -9999 0 -10000 0 0
ROCK1 0.014 0 -9999 0 -10000 0 0
FAK1/Paxillin 0.056 0.095 -9999 0 -0.7 2 2
MAP3K13 0.045 0.089 -9999 0 -0.57 3 3
PDPK1 0.077 0.065 -9999 0 -0.5 2 2
IL2 signaling events mediated by STAT5

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GAB2 0.012 0.041 -9999 0 -0.59 2 2
ELF1 -0.014 0.11 -9999 0 -0.57 3 3
CCNA2 0.012 0.04 -9999 0 -0.82 1 1
PIK3CA 0.014 0 -9999 0 -10000 0 0
JAK3 -0.007 0.13 -9999 0 -0.82 11 11
PIK3R1 0.01 0.051 -9999 0 -0.59 3 3
JAK1 0.014 0 -9999 0 -10000 0 0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K 0.044 0.12 -9999 0 -0.6 7 7
SHC1 0.014 0 -9999 0 -10000 0 0
SP1 0.019 0.034 -9999 0 -10000 0 0
IL2RA -0.041 0.22 -9999 0 -0.7 44 44
IL2RB -0.001 0.11 -9999 0 -0.79 8 8
SOS1 0.014 0 -9999 0 -10000 0 0
IL2RG -0.012 0.15 -9999 0 -0.8 14 14
G1/S transition of mitotic cell cycle 0.035 0.081 -9999 0 -0.68 2 2
PTPN11 0.015 0 -9999 0 -10000 0 0
CCND2 0.026 0.078 -9999 0 -0.77 4 4
LCK -0.005 0.13 -9999 0 -0.82 10 10
GRB2 0.014 0 -9999 0 -10000 0 0
IL2 0.004 0.04 -9999 0 -0.82 1 1
CDK6 0 0.1 -9999 0 -0.78 7 7
CCND3 0.052 0.1 -9999 0 -0.61 3 3
S1P4 pathway

Figure S104.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S104.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -9999 0 -10000 0 0
GNAO1 0.006 0.075 -9999 0 -0.76 4 4
CDC42/GTP -0.02 0.071 -9999 0 -0.47 4 4
PLCG1 0.019 0.086 -9999 0 -0.49 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
GNAI2 0.014 0 -9999 0 -10000 0 0
GNAI3 0.014 0 -9999 0 -10000 0 0
G12/G13 -0.006 0.061 -9999 0 -0.63 4 4
cell migration -0.02 0.07 -9999 0 -0.46 4 4
S1PR5 0.012 0.029 -9999 0 -0.59 1 1
S1PR4 -0.025 0.17 -9999 0 -0.81 20 20
MAPK3 0.019 0.086 -9999 0 -0.49 4 4
MAPK1 0.019 0.086 -9999 0 -0.49 4 4
S1P/S1P5/Gi 0.025 0.061 -9999 0 -0.48 2 2
GNAI1 0.012 0.029 -9999 0 -0.59 1 1
CDC42/GDP 0 0 -9999 0 -10000 0 0
S1P/S1P5/G12 -0.006 0.056 -9999 0 -0.51 5 5
RHOA 0.007 0.11 -9999 0 -0.46 23 23
S1P/S1P4/Gi 0.011 0.09 -9999 0 -0.52 4 4
mol:GDP 0 0 -9999 0 -10000 0 0
GNAZ -0.015 0.15 -9999 0 -0.75 16 16
S1P/S1P4/G12/G13 -0.028 0.11 -9999 0 -0.5 23 23
GNA12 0.006 0.08 -9999 0 -0.82 4 4
GNA13 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
Regulation of p38-alpha and p38-beta

Figure S105.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
RIP1/MEKK3 0 0 -9999 0 -10000 0 0
response to insulin stimulus 0 0 -9999 0 -10000 0 0
RIPK1 0.014 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
MAP2K6 -0.015 0.13 -9999 0 -0.59 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
MAP2K4 0.014 0 -9999 0 -10000 0 0
RAC1-CDC42/GTP/PAK family 0.018 0.048 -9999 0 -10000 0 0
response to UV 0 0 -9999 0 -10000 0 0
YES1 0.014 0 -9999 0 -10000 0 0
interleukin-1 receptor activity 0 0 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
MAP3K3 0.014 0 -9999 0 -10000 0 0
FYN 0.012 0.04 -9999 0 -0.82 1 1
MAP3K12 0.01 0.05 -9999 0 -0.7 2 2
FGR 0.012 0.04 -9999 0 -0.82 1 1
p38 alpha/TAB1 -0.018 0.041 -9999 0 -0.3 1 1
PRKG1 -0.022 0.16 -9999 0 -0.74 20 20
DUSP8 0.014 0 -9999 0 -10000 0 0
PGK/cGMP/p38 alpha -0.032 0.082 -9999 0 -0.4 15 15
apoptosis -0.017 0.04 -9999 0 -0.29 1 1
RAL/GTP 0 0 -9999 0 -10000 0 0
LYN 0.012 0.029 -9999 0 -0.59 1 1
DUSP1 -0.022 0.14 -9999 0 -0.59 25 25
PAK1 0.012 0.04 -9999 0 -0.82 1 1
SRC 0.014 0 -9999 0 -10000 0 0
RAC1/OSM/MEKK3/MKK3 -0.01 0.068 -9999 0 -0.49 8 8
TRAF6 0.012 0.04 -9999 0 -0.82 1 1
RAC1 0.014 0 -9999 0 -10000 0 0
epidermal growth factor receptor activity 0 0 -9999 0 -10000 0 0
mol:LPS 0 0 -9999 0 -10000 0 0
mol:cGMP 0 0 -9999 0 -10000 0 0
CCM2 -0.002 0.11 -9999 0 -0.82 8 8
RAC1-CDC42/GTP 0 0 -9999 0 -10000 0 0
MAPK11 0.022 0.095 -9999 0 -0.4 5 5
BLK -0.11 0.28 -9999 0 -0.78 64 64
HCK 0.007 0.07 -9999 0 -0.7 4 4
MAP2K3 0.012 0.029 -9999 0 -0.59 1 1
DUSP16 0.014 0 -9999 0 -10000 0 0
DUSP10 0.01 0.057 -9999 0 -0.82 2 2
TRAF6/MEKK3 -0.001 0.025 -9999 0 -0.51 1 1
MAP3K7IP1 0 0 -9999 0 -10000 0 0
MAPK14 0.031 0.068 -9999 0 -0.32 1 1
positive regulation of innate immune response 0.03 0.1 -9999 0 -0.41 5 5
LCK -0.006 0.13 -9999 0 -0.82 10 10
p38alpha-beta/MKP7 0.036 0.098 -9999 0 -0.48 1 1
p38alpha-beta/MKP5 0.034 0.1 -9999 0 -0.48 1 1
PGK/cGMP -0.027 0.12 -9999 0 -0.57 20 20
PAK2 0.014 0 -9999 0 -10000 0 0
p38alpha-beta/MKP1 0.02 0.12 -9999 0 -0.5 4 4
CDC42 0.014 0 -9999 0 -10000 0 0
RALB 0.014 0 -9999 0 -10000 0 0
RALA 0.014 0 -9999 0 -10000 0 0
PAK3 -0.022 0.16 -9999 0 -0.8 17 17
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MET/RANBP9 -0.005 0.056 -9999 0 -0.58 4 4
CRKL 0.031 0.057 -9999 0 -0.43 1 1
mol:PIP3 -0.023 0.004 -9999 0 -10000 0 0
AKT1 0 0.003 -9999 0 -10000 0 0
PTK2B 0.012 0.029 -9999 0 -0.59 1 1
RAPGEF1 0.038 0.055 -9999 0 -0.41 1 1
RANBP10 0.014 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
HGF/MET/SHIP2 -0.02 0.093 -9999 0 -0.54 8 8
MAP3K5 0.042 0.059 -9999 0 -10000 0 0
HGF/MET/CIN85/CBL/ENDOPHILINS -0.018 0.084 -9999 0 -0.49 8 8
AP1 -0.034 0.13 -9999 0 -0.37 57 57
mol:SU11274 0 0 -9999 0 -10000 0 0
SHC1 0.014 0 -9999 0 -10000 0 0
apoptosis -0.074 0.25 -9999 0 -0.7 57 57
STAT3 (dimer) 0.032 0.064 -9999 0 -0.49 1 1
GAB1/CRKL/SHP2/PI3K -0.01 0.047 -9999 0 -0.44 1 1
INPP5D 0.011 0.041 -9999 0 -0.59 2 2
CBL/CRK 0.038 0.05 -9999 0 -10000 0 0
PTPN11 0.014 0 -9999 0 -10000 0 0
GO:0007205 0 0 -9999 0 -10000 0 0
PLCG1 0.014 0 -9999 0 -10000 0 0
PTEN 0.014 0 -9999 0 -10000 0 0
ELK1 -0.001 0.027 -9999 0 -0.26 4 4
mol:SU5416 0 0 -9999 0 -10000 0 0
SHP2/GRB2/SOS1GAB1 -0.007 0.03 -9999 0 -10000 0 0
PAK1 0.007 0.024 -9999 0 -0.48 1 1
HGF/MET/RANBP10 -0.02 0.093 -9999 0 -0.54 8 8
HRAS 0.025 0.078 -9999 0 -0.61 1 1
DOCK1 0.036 0.058 -9999 0 -0.41 1 1
GAB1 0.025 0.055 -9999 0 -0.28 1 1
CRK 0.032 0.053 -9999 0 -10000 0 0
mol:PHA665752 0 0 -9999 0 -10000 0 0
mol:GDP -0.019 0.089 -9999 0 -0.48 12 12
JUN 0.014 0 -9999 0 -10000 0 0
EntrezGene:200958 0 0 -9999 0 -10000 0 0
HGF/MET -0.01 0.047 -9999 0 -0.29 4 4
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
cell morphogenesis 0.059 0.072 -9999 0 -0.46 1 1
GRB2/SHC 0.022 0.045 -9999 0 -10000 0 0
FOS -0.068 0.21 -9999 0 -0.59 57 57
GLMN 0 0 -9999 0 -10000 0 0
cell motility -0.001 0.027 -9999 0 -0.26 4 4
HGF/MET/MUC20 -0.021 0.095 -9999 0 -0.44 20 20
cell migration 0.021 0.045 -9999 0 -10000 0 0
GRB2 0.014 0 -9999 0 -10000 0 0
CBL 0.014 0 -9999 0 -10000 0 0
MET/RANBP10 -0.005 0.056 -9999 0 -0.58 4 4
HGF/MET/Paxillin/FAK1/FAK12/RasGAP 0.025 0.067 -9999 0 -0.52 1 1
MET/MUC20 -0.006 0.057 -9999 0 -0.58 4 4
RAP1B 0.043 0.056 -9999 0 -0.39 2 2
RAP1A 0.044 0.052 -9999 0 -0.38 1 1
HGF/MET/RANBP9 -0.02 0.093 -9999 0 -0.54 8 8
RAF1 0.032 0.074 -9999 0 -0.57 1 1
STAT3 0.032 0.065 -9999 0 -0.5 1 1
cell proliferation 0.043 0.08 -9999 0 -0.44 1 1
RPS6KB1 0.011 0.019 -9999 0 -10000 0 0
MAPK3 -0.006 0.024 -9999 0 -0.26 3 3
MAPK1 -0.006 0.024 -9999 0 -0.26 3 3
RANBP9 0.014 0 -9999 0 -10000 0 0
MAPK8 0.05 0.086 -9999 0 -0.48 7 7
SRC 0.033 0.063 -9999 0 -0.49 1 1
PI3K 0.019 0.055 -9999 0 -0.47 1 1
MET/Glomulin 0.008 0.053 -9999 0 -0.52 4 4
SOS1 0.014 0 -9999 0 -10000 0 0
MAP2K1 0.039 0.07 -9999 0 -0.52 1 1
MET 0.006 0.075 -9999 0 -0.76 4 4
MAP4K1 0.035 0.062 -9999 0 -10000 0 0
PTK2 0.014 0 -9999 0 -10000 0 0
MAP2K2 0.039 0.07 -9999 0 -0.52 1 1
BAD 0.008 0.003 -9999 0 -10000 0 0
MAP2K4 0.048 0.056 -9999 0 -10000 0 0
SHP2/GRB2/SOS1/GAB1 -0.009 0.045 -9999 0 -10000 0 0
INPPL1 0.014 0 -9999 0 -10000 0 0
PXN 0.014 0 -9999 0 -10000 0 0
SH3KBP1 0.014 0 -9999 0 -10000 0 0
HGS 0.014 0.048 -9999 0 -10000 0 0
PLCgamma1/PKC 0 0 -9999 0 -10000 0 0
HGF -0.012 0.13 -9999 0 -0.66 16 16
RASA1 0.012 0.029 -9999 0 -0.59 1 1
NCK1 0.014 0 -9999 0 -10000 0 0
PTPRJ 0.014 0 -9999 0 -10000 0 0
NCK/PLCgamma1 0.023 0.049 -9999 0 -10000 0 0
PDPK1 -0.01 0.003 -9999 0 -10000 0 0
HGF/MET/SHIP -0.022 0.099 -9999 0 -0.56 9 9
Hedgehog signaling events mediated by Gli proteins

Figure S107.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S107.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0.001 -9999 0 -10000 0 0
HDAC2 0.014 0.001 -9999 0 -10000 0 0
GNB1/GNG2 -0.015 0.072 -9999 0 -0.54 1 1
forebrain development -0.023 0.16 -9999 0 -0.52 15 15
GNAO1 0.005 0.075 -9999 0 -0.76 4 4
SMO/beta Arrestin2 0.002 0.091 -9999 0 -0.44 17 17
SMO -0.011 0.12 -9999 0 -0.6 17 17
ARRB2 0.013 0.005 -9999 0 -10000 0 0
GLI3/SPOP 0.056 0.036 -9999 0 -10000 0 0
mol:GTP 0 0.003 -9999 0 -10000 0 0
GSK3B 0.014 0 -9999 0 -10000 0 0
GNAI2 0.013 0.005 -9999 0 -10000 0 0
SIN3/HDAC complex 0.006 0.015 -9999 0 -10000 0 0
GNAI1 0.011 0.03 -9999 0 -0.59 1 1
XPO1 0.015 0.006 -9999 0 -10000 0 0
GLI1/Su(fu) -0.063 0.12 -9999 0 -0.53 6 6
SAP30 0.014 0.001 -9999 0 -10000 0 0
mol:GDP -0.011 0.12 -9999 0 -0.6 17 17
MIM/GLI2A 0.012 0.025 -9999 0 -10000 0 0
IFT88 0.014 0 -9999 0 -10000 0 0
GNAI3 0.013 0.005 -9999 0 -10000 0 0
GLI2 0.028 0.063 -9999 0 -10000 0 0
GLI3 0.051 0.039 -9999 0 -10000 0 0
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
SAP18 0.014 0.001 -9999 0 -10000 0 0
embryonic digit morphogenesis 0.014 0 -9999 0 -10000 0 0
GNG2 0.014 0 -9999 0 -10000 0 0
Gi family/GTP 0.013 0.092 -9999 0 -0.5 6 6
SIN3B 0.014 0.001 -9999 0 -10000 0 0
SIN3A 0.014 0.001 -9999 0 -10000 0 0
GLI3/Su(fu) 0.057 0.036 -9999 0 -10000 0 0
GLI2/Su(fu) 0.033 0.069 -9999 0 -10000 0 0
FOXA2 -0.094 0.23 -9999 0 -0.67 58 58
neural tube patterning -0.023 0.16 -9999 0 -0.52 15 15
SPOP 0.014 0 -9999 0 -10000 0 0
Su(fu)/PIAS1 0.022 0.048 -9999 0 -0.38 1 1
GNB1 0.014 0 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
CSNK1G3 0.014 0 -9999 0 -10000 0 0
MTSS1 0.012 0.025 -9999 0 -10000 0 0
embryonic limb morphogenesis -0.023 0.16 -9999 0 -0.52 15 15
SUFU 0.018 0.053 -9999 0 -0.42 1 1
LGALS3 0.011 0.041 -9999 0 -0.59 2 2
catabolic process 0.066 0.055 -9999 0 -10000 0 0
GLI3A/CBP -0.023 0.11 -9999 0 -10000 0 0
KIF3A 0.014 0 -9999 0 -10000 0 0
GLI1 -0.024 0.16 -9999 0 -0.53 15 15
RAB23 0.01 0.057 -9999 0 -0.82 2 2
CSNK1A1 0.014 0 -9999 0 -10000 0 0
IFT172 0.014 0 -9999 0 -10000 0 0
RBBP7 0.014 0.001 -9999 0 -10000 0 0
Su(fu)/Galectin3 0.021 0.056 -9999 0 -0.44 2 2
GNAZ -0.016 0.15 -9999 0 -0.75 16 16
RBBP4 0.011 0.041 -9999 0 -0.59 2 2
CSNK1G1 0.014 0 -9999 0 -10000 0 0
PIAS1 0.014 0 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
GLI2/SPOP 0.033 0.058 -9999 0 -10000 0 0
STK36 0.014 0.006 -9999 0 -10000 0 0
Gi family/GNB1/GNG2/GDP 0.022 0.081 -9999 0 -0.43 6 6
PTCH1 -0.022 0.19 -9999 0 -1.1 7 7
MIM/GLI1 -0.039 0.21 -9999 0 -0.67 18 18
CREBBP -0.023 0.11 -9999 0 -10000 0 0
Su(fu)/SIN3/HDAC complex 0.05 0.024 -9999 0 -10000 0 0
ceramide signaling pathway

Figure S108.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S108.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
MAP4K4 0.038 0.072 -10000 0 -0.4 3 3
BAG4 0.011 0.041 -10000 0 -0.59 2 2
BAD 0.03 0.027 -10000 0 -10000 0 0
NFKBIA 0.014 0 -10000 0 -10000 0 0
BIRC3 -0.016 0.15 -10000 0 -0.82 15 15
BAX 0.03 0.027 -10000 0 -10000 0 0
EnzymeConsortium:3.1.4.12 0.013 0.02 -10000 0 -0.095 4 4
IKBKB 0.045 0.069 -10000 0 -10000 0 0
MAP2K2 0.042 0.029 -10000 0 -10000 0 0
MAP2K1 0.042 0.029 -10000 0 -10000 0 0
SMPD1 0.019 0.02 -10000 0 -10000 0 0
GO:0005551 0 0 -10000 0 -10000 0 0
FADD/Caspase 8 -0.01 0.17 -10000 0 -0.56 8 8
MAP2K4 0.037 0.027 -10000 0 -10000 0 0
protein ubiquitination 0.046 0.07 -10000 0 -10000 0 0
EnzymeConsortium:2.7.1.37 0.047 0.032 -10000 0 -10000 0 0
response to UV 0 0 -10000 0 -10000 0 0
RAF1 0.037 0.029 -10000 0 -10000 0 0
CRADD 0.014 0 -10000 0 -10000 0 0
mol:ceramide 0.023 0.028 -10000 0 -10000 0 0
I-kappa-B-alpha/RELA/p50/ubiquitin 0 0 -10000 0 -10000 0 0
MADD 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.03 0.028 -10000 0 -10000 0 0
TRADD 0.014 0 -10000 0 -10000 0 0
RELA/p50 0.014 0 -10000 0 -10000 0 0
MAPK3 0.045 0.029 -10000 0 -10000 0 0
MAPK1 0.045 0.029 -10000 0 -10000 0 0
p50/RELA/I-kappa-B-alpha 0 0 -10000 0 -10000 0 0
FADD -0.02 0.17 -10000 0 -0.44 55 55
KSR1 0.03 0.029 -10000 0 -10000 0 0
MAPK8 0.038 0.046 -10000 0 -0.32 1 1
TRAF2 0.008 0.07 -10000 0 -0.82 3 3
response to radiation 0 0 -10000 0 -10000 0 0
CHUK 0.045 0.069 -10000 0 -10000 0 0
TNF R/SODD -0.002 0.029 -10000 0 -0.43 2 2
TNF -0.025 0.17 -10000 0 -0.77 21 21
CYCS 0.033 0.028 -10000 0 -10000 0 0
IKBKG 0.045 0.069 -10000 0 -10000 0 0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD 0.031 0.075 -10000 0 -0.43 4 4
RELA 0.014 0 -10000 0 -10000 0 0
RIPK1 0.014 0 -10000 0 -10000 0 0
AIFM1 0.033 0.028 0.14 3 -10000 0 3
TNF/TNF R/SODD -0.027 0.11 -10000 0 -0.54 17 17
TNFRSF1A 0.014 0 -10000 0 -10000 0 0
response to heat 0 0 -10000 0 -10000 0 0
CASP8 0.028 0.02 -10000 0 -10000 0 0
NSMAF 0.038 0.071 -10000 0 -0.4 3 3
response to hydrogen peroxide 0 0 -10000 0 -10000 0 0
BCL2 0 0.099 -10000 0 -0.7 8 8
Role of Calcineurin-dependent NFAT signaling in lymphocytes

Figure S109.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S109.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.014 0 -10000 0 -10000 0 0
NFATC1 0.061 0.014 -10000 0 -10000 0 0
NFATC2 0.025 0.063 -10000 0 -0.32 5 5
NFATC3 0.024 0.021 -10000 0 -0.4 1 1
YWHAE 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/CABIN1 0.014 0.076 -10000 0 -0.46 3 3
Exportin 1/Ran/NUP214 0 0 -10000 0 -10000 0 0
mol:DAG 0 0.001 -10000 0 -10000 0 0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV -0.038 0.11 -10000 0 -0.46 21 21
BCL2/BAX -0.01 0.073 -10000 0 -0.53 8 8
CaM/Ca2+/Calcineurin A alpha-beta B1 0.012 0.003 -10000 0 -10000 0 0
CaM/Ca2+ 0.012 0.003 -10000 0 -10000 0 0
BAX 0.014 0 -10000 0 -10000 0 0
MAPK14 0.014 0.002 -10000 0 -10000 0 0
BAD 0.014 0 -10000 0 -10000 0 0
CABIN1/MEF2D 0.021 0.072 -10000 0 -0.43 3 3
Calcineurin A alpha-beta B1/BCL2 0 0.099 -10000 0 -0.7 8 8
FKBP8 0.014 0 -10000 0 -10000 0 0
activation-induced cell death of T cells -0.02 0.071 0.42 3 -10000 0 3
KPNB1 0.014 0 -10000 0 -10000 0 0
KPNA2 0.014 0 -10000 0 -10000 0 0
XPO1 0.014 0 -10000 0 -10000 0 0
SFN 0.007 0.07 -10000 0 -0.7 4 4
MAP3K8 0.011 0.041 -10000 0 -0.59 2 2
NFAT4/CK1 alpha -0.001 0.011 -10000 0 -10000 0 0
MEF2D/NFAT1/Cbp/p300 -0.017 0.059 -10000 0 -0.38 5 5
CABIN1 0.014 0.077 -10000 0 -0.46 3 3
CALM1 0.014 0.002 -10000 0 -10000 0 0
RAN 0.014 0 -10000 0 -10000 0 0
MAP3K1 0.014 0 -10000 0 -10000 0 0
CAMK4 -0.031 0.18 -10000 0 -0.78 24 24
mol:Ca2+ 0.001 0.003 -10000 0 -10000 0 0
MAPK3 0.014 0 -10000 0 -10000 0 0
YWHAH 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/AKAP79/PKA -0.028 0.13 -10000 0 -0.63 19 19
YWHAB 0.014 0 -10000 0 -10000 0 0
MAPK8 0.004 0.077 -10000 0 -0.59 7 7
MAPK9 0.014 0 -10000 0 -10000 0 0
YWHAG 0.014 0 -10000 0 -10000 0 0
FKBP1A 0.014 0 -10000 0 -10000 0 0
NFAT1-c-4/YWHAQ 0.001 0.019 -10000 0 -10000 0 0
PRKCH 0.014 0 -10000 0 -10000 0 0
CABIN1/Cbp/p300 -0.002 0.029 -10000 0 -0.42 2 2
CASP3 0.014 0.002 -10000 0 -10000 0 0
PIM1 0.014 0 -10000 0 -10000 0 0
Calcineurin A alpha-beta B1/FKBP12/FK506 0 0 -10000 0 -10000 0 0
apoptosis -0.003 0.023 -10000 0 -10000 0 0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1 0.045 0.02 -10000 0 -10000 0 0
PRKCB -0.001 0.11 -10000 0 -0.76 8 8
PRKCE 0.014 0 -10000 0 -10000 0 0
JNK2/NFAT4 0.03 0.019 -10000 0 -0.36 1 1
BAD/BCL-XL 0 0 -10000 0 -10000 0 0
PRKCD 0.014 0 -10000 0 -10000 0 0
NUP214 0.014 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.029 -10000 0 -0.59 1 1
PRKCA 0.012 0.04 -10000 0 -0.82 1 1
PRKCG -0.076 0.25 -10000 0 -0.82 44 44
PRKCQ 0.003 0.086 -10000 0 -0.66 7 7
FKBP38/BCL2 -0.01 0.073 -10000 0 -0.53 8 8
EP300 0.011 0.041 -10000 0 -0.59 2 2
PRKCB1 0 0 -10000 0 -10000 0 0
CSNK2A1 0.014 0 -10000 0 -10000 0 0
NFATc/JNK1 0.061 0.042 -10000 0 -10000 0 0
CaM/Ca2+/FKBP38 0 0 -10000 0 -10000 0 0
FKBP12/FK506 0 0 -10000 0 -10000 0 0
CSNK1A1 0.022 0.004 -10000 0 -10000 0 0
CaM/Ca2+/CAMK IV -0.029 0.12 -10000 0 -0.52 24 24
NFATc/ERK1 0.066 0.014 -10000 0 -10000 0 0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV -0.038 0.11 -10000 0 -0.46 21 21
NR4A1 0.044 0.11 -10000 0 -0.56 11 11
GSK3B 0.014 0.002 -10000 0 -10000 0 0
positive T cell selection 0.024 0.021 -10000 0 -0.4 1 1
NFAT1/CK1 alpha -0.012 0.036 -10000 0 -0.37 1 1
RCH1/ KPNB1 0 0 -10000 0 -10000 0 0
YWHAQ 0.014 0 -10000 0 -10000 0 0
PRKACA 0.014 0.002 -10000 0 -10000 0 0
AKAP5 -0.024 0.17 -10000 0 -0.82 19 19
MEF2D 0.014 0.002 -10000 0 -10000 0 0
mol:FK506 0 0 -10000 0 -10000 0 0
YWHAZ 0.014 0 -10000 0 -10000 0 0
NFATc/p38 alpha 0.066 0.017 -10000 0 -10000 0 0
CREBBP 0.014 0.002 -10000 0 -10000 0 0
BCL2 0 0.099 -10000 0 -0.7 8 8
TCGA08_rtk_signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PDGFRA 0.001 0.091 -9999 0 -0.65 8 8
HRAS 0.012 0.04 -9999 0 -0.82 1 1
EGFR -0.017 0.15 -9999 0 -0.79 16 16
AKT 0.037 0.047 -9999 0 -0.3 7 7
FOXO3 0.014 0 -9999 0 -10000 0 0
AKT1 0.014 0 -9999 0 -10000 0 0
FOXO1 0.014 0 -9999 0 -10000 0 0
AKT3 0 0.11 -9999 0 -0.82 7 7
FOXO4 0.011 0.041 -9999 0 -0.59 2 2
MET 0.006 0.075 -9999 0 -0.76 4 4
PIK3CA 0.014 0 -9999 0 -10000 0 0
PIK3CB 0.014 0 -9999 0 -10000 0 0
NRAS 0.014 0 -9999 0 -10000 0 0
PIK3CG -0.024 0.17 -9999 0 -0.75 21 21
PIK3R3 0.012 0.029 -9999 0 -0.59 1 1
PIK3R2 0.014 0 -9999 0 -10000 0 0
NF1 0.014 0 -9999 0 -10000 0 0
RAS 0.017 0.048 -9999 0 -0.35 1 1
ERBB2 0.008 0.07 -9999 0 -0.82 3 3
proliferation/survival/translation -0.031 0.028 -9999 0 -10000 0 0
PI3K 0.023 0.053 -9999 0 -0.26 3 3
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
KRAS 0.01 0.057 -9999 0 -0.82 2 2
FOXO 0.048 0.029 -9999 0 -0.17 1 1
AKT2 0.014 0 -9999 0 -10000 0 0
PTEN 0.014 0 -9999 0 -10000 0 0
Class I PI3K signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
ARF5/GTP -0.003 0.031 -9999 0 -10000 0 0
DAPP1 0.013 0.092 -9999 0 -0.34 10 10
Src family/SYK family/BLNK-LAT/BTK-ITK -0.001 0.16 -9999 0 -0.67 12 12
mol:DAG 0.028 0.086 -9999 0 -0.3 8 8
HRAS 0.013 0.04 -9999 0 -0.81 1 1
RAP1A 0.014 0.002 -9999 0 -10000 0 0
ARF5/GDP 0.04 0.041 -9999 0 -10000 0 0
PLCG2 0.012 0.029 -9999 0 -0.59 1 1
PLCG1 0.014 0 -9999 0 -10000 0 0
ARF5 0.014 0 -9999 0 -10000 0 0
mol:GTP -0.003 0.034 -9999 0 -0.4 3 3
ARF1/GTP -0.003 0.03 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
YES1 0.014 0 -9999 0 -10000 0 0
RAP1A/GTP -0.003 0.033 -9999 0 -0.4 3 3
ADAP1 -0.003 0.034 -9999 0 -10000 0 0
ARAP3 -0.003 0.033 -9999 0 -0.4 3 3
INPPL1 0.014 0 -9999 0 -10000 0 0
PREX1 0.014 0 -9999 0 -10000 0 0
ARHGEF6 0.006 0.065 -9999 0 -0.59 5 5
ARHGEF7 0.014 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
NRAS 0.014 0.002 -9999 0 -10000 0 0
FYN 0.012 0.04 -9999 0 -0.82 1 1
ARF6 0.014 0 -9999 0 -10000 0 0
FGR 0.012 0.04 -9999 0 -0.82 1 1
mol:Ca2+ 0.027 0.047 -9999 0 -10000 0 0
mol:IP4 0 0 -9999 0 -10000 0 0
TIAM1 0.006 0.065 -9999 0 -0.59 5 5
ZAP70 -0.021 0.16 -9999 0 -0.76 19 19
mol:IP3 0.031 0.063 -9999 0 -10000 0 0
LYN 0.012 0.029 -9999 0 -0.59 1 1
ARF1/GDP 0.04 0.041 -9999 0 -10000 0 0
RhoA/GDP -0.004 0.032 -9999 0 -0.42 1 1
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
BLNK -0.048 0.18 -9999 0 -0.59 43 43
actin cytoskeleton reorganization 0.063 0.045 -9999 0 -0.41 1 1
SRC 0.014 0 -9999 0 -10000 0 0
PLEKHA2 0.03 0.027 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
PTEN 0 0.004 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
ARF6/GTP -0.003 0.031 -9999 0 -10000 0 0
RhoA/GTP -0.003 0.032 -9999 0 -10000 0 0
Src family/SYK family/BLNK-LAT -0.018 0.17 -9999 0 -0.68 14 14
BLK -0.11 0.28 -9999 0 -0.78 64 64
PDPK1 0.014 0 -9999 0 -10000 0 0
CYTH1 -0.003 0.032 -9999 0 -10000 0 0
HCK 0.007 0.07 -9999 0 -0.7 4 4
CYTH3 -0.003 0.032 -9999 0 -10000 0 0
CYTH2 -0.003 0.032 -9999 0 -10000 0 0
KRAS 0.011 0.057 -9999 0 -0.81 2 2
GO:0030676 0 0 -9999 0 -10000 0 0
FOXO3 -0.003 0.034 -9999 0 -0.45 2 2
SGK1 -0.004 0.037 -9999 0 -0.49 2 2
INPP5D 0.011 0.041 -9999 0 -0.59 2 2
mol:GDP 0.034 0.043 -9999 0 -0.32 1 1
SOS1 0.014 0 -9999 0 -10000 0 0
SYK 0.011 0.041 -9999 0 -0.59 2 2
ARF6/GDP -0.004 0.031 -9999 0 -0.42 1 1
mol:PI-3-4-5-P3 -0.003 0.034 -9999 0 -0.4 3 3
ARAP3/RAP1A/GTP -0.003 0.034 -9999 0 -0.4 3 3
VAV1 0.005 0.071 -9999 0 -0.59 6 6
mol:PI-3-4-P2 0.022 0.031 -9999 0 -0.43 2 2
RAS family/GTP/PI3K Class I 0.03 0.037 -9999 0 -0.41 3 3
PLEKHA1 0.03 0.027 -9999 0 -10000 0 0
Rac1/GDP 0.04 0.041 -9999 0 -10000 0 0
LAT -0.006 0.13 -9999 0 -0.82 10 10
Rac1/GTP 0.035 0.056 -9999 0 -0.35 1 1
ITK -0.015 0.072 -9999 0 -0.43 7 7
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma 0.028 0.11 -9999 0 -0.44 9 9
LCK -0.006 0.13 -9999 0 -0.82 10 10
BTK -0.004 0.038 -9999 0 -0.43 1 1
Arf6 trafficking events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SLC2A4 -0.25 0.3 -10000 0 -0.59 187 187
CLTC 0.034 0.015 -10000 0 -0.27 1 1
calcium ion-dependent exocytosis 0.029 0.009 -10000 0 -10000 0 0
Dynamin 2/GTP -0.001 0.024 -10000 0 -0.5 1 1
EXOC4 0.014 0 -10000 0 -10000 0 0
CD59 0.03 0.016 -10000 0 -10000 0 0
CPE 0.011 0.07 -10000 0 -0.52 7 7
CTNNB1 0.012 0.029 -10000 0 -0.59 1 1
membrane fusion 0.028 0.009 -10000 0 -10000 0 0
CTNND1 0.033 0.024 -10000 0 -0.46 1 1
DNM2 0.014 0 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.035 0.008 -10000 0 -10000 0 0
TSHR -0.01 0.12 -10000 0 -0.55 21 21
INS 0.012 0.019 -10000 0 -0.26 2 2
BIN1 -0.002 0.11 -10000 0 -0.79 8 8
mol:Choline 0.028 0.009 -10000 0 -10000 0 0
growth hormone secretagogue receptor activity 0 0 -10000 0 -10000 0 0
mol:GDP 0.019 0.028 -10000 0 -0.55 1 1
membrane depolarization 0 0 -10000 0 -10000 0 0
ARF6 0.014 0 -10000 0 -10000 0 0
mol:Ca2+ -0.001 0.024 -10000 0 -0.5 1 1
JUP 0.03 0.021 -10000 0 -0.29 1 1
ASAP2/amphiphysin II -0.009 0.065 -10000 0 -0.5 7 7
ARF6/GTP 0 0 -10000 0 -10000 0 0
CDH1 0.028 0.025 -10000 0 -10000 0 0
clathrin-independent pinocytosis 0 0 -10000 0 -10000 0 0
MAPK8IP3 0.014 0 -10000 0 -10000 0 0
positive regulation of endocytosis 0 0 -10000 0 -10000 0 0
EXOC2 0.014 0 -10000 0 -10000 0 0
substrate adhesion-dependent cell spreading 0.046 0 -10000 0 -10000 0 0
insulin receptor binding 0 0 -10000 0 -10000 0 0
SPAG9 0.014 0 -10000 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion 0.003 0.026 0.39 1 -10000 0 1
positive regulation of phagocytosis 0.02 0 -10000 0 -10000 0 0
ARF6/GTP/JIP3 0 0 -10000 0 -10000 0 0
ACAP1 0.026 0.013 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
CHRM2 0.025 0.016 -10000 0 -10000 0 0
clathrin heavy chain/ACAP1 0.04 0.014 -10000 0 -10000 0 0
JIP4/KLC1 0 0 -10000 0 -10000 0 0
EXOC1 0.014 0 -10000 0 -10000 0 0
exocyst 0.047 0 -10000 0 -10000 0 0
RALA/GTP 0 0 -10000 0 -10000 0 0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex 0 0 -10000 0 -10000 0 0
receptor recycling 0 0 -10000 0 -10000 0 0
CTNNA1 0.033 0.024 -10000 0 -0.46 1 1
NME1 0.019 0.028 -10000 0 -0.55 1 1
clathrin coat assembly 0.034 0.015 -10000 0 -0.27 1 1
IL2RA 0.006 0.075 -10000 0 -10000 0 0
VAMP3 0.02 0 -10000 0 -10000 0 0
GLUT4/clathrin heavy chain/ACAP1 -0.11 0.12 -10000 0 -0.49 1 1
EXOC6 0.014 0 -10000 0 -10000 0 0
PLD1 -0.001 0.014 -10000 0 -0.28 1 1
PLD2 0 0 -10000 0 -10000 0 0
EXOC5 0.014 0 -10000 0 -10000 0 0
PIP5K1C 0.035 0.008 -10000 0 -10000 0 0
SDC1 0.031 0.01 -10000 0 -10000 0 0
ARF6/GDP 0.018 0.027 -10000 0 -0.55 1 1
EXOC7 0.014 0 -10000 0 -10000 0 0
E-cadherin/beta catenin -0.003 0.026 -10000 0 -0.4 1 1
mol:Phosphatidic acid 0.028 0.009 -10000 0 -10000 0 0
endocytosis 0.009 0.065 0.5 7 -10000 0 7
SCAMP2 0.014 0 -10000 0 -10000 0 0
ADRB2 0.02 0.081 -10000 0 -0.55 1 1
EXOC3 0.014 0 -10000 0 -10000 0 0
ASAP2 0.014 0 -10000 0 -10000 0 0
Dynamin 2/GDP 0.026 0.025 -10000 0 -0.5 1 1
KLC1 0.014 0 -10000 0 -10000 0 0
AVPR2 0.025 0.069 -10000 0 -10000 0 0
RALA 0.014 0 -10000 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.002 0.023 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class II

Figure S113.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S113.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G beta1gamma2/HDAC5 0 0 -9999 0 -10000 0 0
HDAC3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -10000 0 0
GATA1/HDAC4 -0.001 0.03 -9999 0 -0.63 1 1
GATA1/HDAC5 -0.001 0.03 -9999 0 -0.63 1 1
GATA2/HDAC5 -0.007 0.064 -9999 0 -0.59 5 5
HDAC5/BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC9 -0.049 0.22 -9999 0 -0.82 32 32
Glucocorticoid receptor/Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
HDAC4/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC5/YWHAB 0 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.024 0 -9999 0 -10000 0 0
GATA2 0.004 0.085 -9999 0 -0.77 5 5
HDAC4/RFXANK -0.001 0.03 -9999 0 -0.63 1 1
BCOR 0.014 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
HDAC10 0.014 0 -9999 0 -10000 0 0
HDAC5 0.014 0 -9999 0 -10000 0 0
GNB1/GNG2 0 0 -9999 0 -10000 0 0
Histones 0.025 0.064 -9999 0 -10000 0 0
ADRBK1 0.014 0 -9999 0 -10000 0 0
HDAC4 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
HDAC5/ANKRA2 0 0 -9999 0 -10000 0 0
HDAC4/Ubc9 0 0 -9999 0 -10000 0 0
HDAC7 0.014 0 -9999 0 -10000 0 0
HDAC5/14-3-3 E 0 0 -9999 0 -10000 0 0
TUBA1B 0.014 0 -9999 0 -10000 0 0
HDAC6 0.014 0 -9999 0 -10000 0 0
HDAC5/RFXANK -0.001 0.03 -9999 0 -0.63 1 1
CAMK4 -0.031 0.18 -9999 0 -0.78 24 24
Tubulin/HDAC6 0 0 -9999 0 -10000 0 0
SUMO1 0.014 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
GATA1 0.009 0.041 -9999 0 -0.82 1 1
EntrezGene:8021 0 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
NR3C1 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -10000 0 0
SRF 0.014 0 -9999 0 -10000 0 0
HDAC4/YWHAB 0 0 -9999 0 -10000 0 0
Tubulin 0 0 -9999 0 -10000 0 0
HDAC4/14-3-3 E 0 0 -9999 0 -10000 0 0
GNB1 0.014 0 -9999 0 -10000 0 0
RANGAP1 0.014 0 -9999 0 -10000 0 0
BCL6/BCoR 0 0 -9999 0 -10000 0 0
HDAC4/HDAC3/SMRT (N-CoR2) 0 0 -9999 0 -10000 0 0
HDAC4/SRF -0.029 0.12 -9999 0 -0.54 20 20
HDAC4/ER alpha -0.033 0.13 -9999 0 -0.56 25 25
EntrezGene:23225 0 0 -9999 0 -10000 0 0
positive regulation of chromatin silencing 0.025 0.064 -9999 0 -10000 0 0
cell motility 0 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
HDAC7/HDAC3 0 0 -9999 0 -10000 0 0
BCL6 0.014 0 -9999 0 -10000 0 0
HDAC4/CaMK II delta B 0.014 0 -9999 0 -10000 0 0
Hsp90/HDAC6 0 0 -9999 0 -10000 0 0
ESR1 -0.031 0.18 -9999 0 -0.74 25 25
HDAC6/HDAC11 -0.001 0.021 -9999 0 -0.43 1 1
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
MEF2C 0.001 0.098 -9999 0 -0.75 7 7
RAN 0.014 0 -9999 0 -10000 0 0
HDAC4/MEF2C -0.007 0.053 -9999 0 -0.46 5 5
GNG2 0.014 0 -9999 0 -10000 0 0
NCOR2 0.014 0 -9999 0 -10000 0 0
TUBB2A 0.014 0 -9999 0 -10000 0 0
HDAC11 0.012 0.029 -9999 0 -0.59 1 1
HSP90AA1 0.014 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
ANKRA2 0.014 0 -9999 0 -10000 0 0
RFXANK 0.012 0.04 -9999 0 -0.82 1 1
nuclear import -0.031 0 -9999 0 -10000 0 0
Aurora C signaling

Figure S114.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
INCENP 0.014 0 -9999 0 -10000 0 0
Aurora C/Aurora B/INCENP -0.011 0.076 -9999 0 -0.54 8 8
metaphase 0 0 -9999 0 -10000 0 0
mitosis 0 0 -9999 0 -10000 0 0
H3F3B -0.003 0.019 -9999 0 -10000 0 0
AURKB 0.004 0.09 -9999 0 -0.82 5 5
AURKC 0.005 0.081 -9999 0 -0.73 5 5
PLK1 signaling events

Figure S115.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S115.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
regulation of centriole-centriole cohesion -0.012 0.007 -10000 0 -10000 0 0
BUB1B 0.022 0.024 -10000 0 -10000 0 0
PLK1 0.017 0.02 -10000 0 -0.17 1 1
PLK1S1 0.015 0.016 -10000 0 -0.17 2 2
KIF2A 0.025 0.018 -10000 0 -10000 0 0
regulation of mitotic centrosome separation 0.017 0.02 -10000 0 -0.17 1 1
GOLGA2 0.014 0 -10000 0 -10000 0 0
Hec1/SPC24 0.011 0.1 -10000 0 -0.47 17 17
WEE1 0.022 0.027 -10000 0 -10000 0 0
cytokinesis 0.031 0.031 -10000 0 -10000 0 0
PP2A-alpha B56 0.035 0.013 -10000 0 -10000 0 0
AURKA 0.014 0.028 -10000 0 -0.19 7 7
PICH/PLK1 0.022 0.089 -10000 0 -0.38 19 19
CENPE 0.025 0.018 -10000 0 -10000 0 0
RhoA/GTP 0 0 -10000 0 -10000 0 0
positive regulation of microtubule depolymerization 0.025 0.018 -10000 0 -10000 0 0
PPP2CA 0.014 0 -10000 0 -10000 0 0
FZR1 0.014 0 -10000 0 -10000 0 0
TPX2 0.013 0.025 -10000 0 -0.18 6 6
PAK1 0.011 0.04 -10000 0 -0.81 1 1
SPC24 -0.004 0.12 -10000 0 -0.82 9 9
FBXW11 0.014 0 -10000 0 -10000 0 0
CLSPN 0.011 0.035 -10000 0 -0.21 9 9
GORASP1 0.014 0 -10000 0 -10000 0 0
metaphase 0 0.001 -10000 0 -0.015 2 2
mol:GTP 0 0 -10000 0 -10000 0 0
NLP 0.01 0.01 -10000 0 -0.067 3 3
G2 phase of mitotic cell cycle 0 0.002 -10000 0 -0.013 7 7
STAG2 0.014 0 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP -0.001 0.009 -10000 0 -10000 0 0
spindle elongation 0.017 0.02 -10000 0 -0.17 1 1
ODF2 0.013 0.002 -10000 0 -10000 0 0
BUB1 -0.002 0.01 -10000 0 -10000 0 0
TPT1 0.016 0.01 -10000 0 -10000 0 0
CDC25C 0.013 0.035 -10000 0 -0.25 7 7
CDC25B -0.023 0.17 -10000 0 -0.81 19 19
SGOL1 0.012 0.007 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
CCNB1/CDK1 -0.018 0.082 -10000 0 -0.4 19 19
CDC14B 0.009 0.038 -10000 0 -0.44 3 3
CDC20 0.002 0.098 -10000 0 -0.82 6 6
PLK1/PBIP1 -0.004 0.035 -10000 0 -0.49 2 2
mitosis 0 0.006 0.041 7 -0.022 2 9
FBXO5 0.021 0.02 -10000 0 -10000 0 0
CDC2 0.001 0.004 -10000 0 -0.017 19 19
NDC80 -0.002 0.11 -10000 0 -0.82 8 8
metaphase plate congression 0.016 0.012 -10000 0 -10000 0 0
ERCC6L -0.017 0.076 -10000 0 -0.37 19 19
NLP/gamma Tubulin 0.014 0.011 -10000 0 -10000 0 0
microtubule cytoskeleton organization 0.016 0.01 -10000 0 -10000 0 0
G2/M transition DNA damage checkpoint 0 0.001 -10000 0 -0.011 2 2
PPP1R12A 0.014 0.001 -10000 0 -10000 0 0
interphase 0 0.001 -10000 0 -0.011 2 2
PLK1/PRC1-2 0.031 0.016 -10000 0 -10000 0 0
GRASP65/GM130/RAB1/GTP/PLK1 -0.001 0.009 -10000 0 -10000 0 0
RAB1A 0.014 0 -10000 0 -10000 0 0
prophase 0 0 -10000 0 -10000 0 0
Aurora A/BORA 0.018 0.039 -10000 0 -0.47 2 2
mitotic prometaphase 0 0.001 -10000 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.034 0.031 -10000 0 -0.38 1 1
microtubule-based process 0.023 0.017 -10000 0 -10000 0 0
Golgi organization 0.017 0.02 -10000 0 -0.17 1 1
Cohesin/SA2 -0.002 0.011 -10000 0 -10000 0 0
PPP1CB/MYPT1 0 0.001 -10000 0 -10000 0 0
KIF20A 0.014 0 -10000 0 -10000 0 0
APC/C/CDC20 0.016 0.067 -10000 0 -0.53 6 6
PPP2R1A 0.014 0 -10000 0 -10000 0 0
chromosome segregation -0.004 0.035 -10000 0 -0.48 2 2
PRC1 0.014 0 -10000 0 -10000 0 0
ECT2 0.019 0.058 -10000 0 -0.49 5 5
C13orf34 0.019 0.038 -10000 0 -0.48 2 2
NUDC 0.016 0.012 -10000 0 -10000 0 0
regulation of attachment of spindle microtubules to kinetochore 0.022 0.024 -10000 0 -10000 0 0
spindle assembly 0.018 0.015 -10000 0 -0.11 1 1
spindle stabilization 0.015 0.016 -10000 0 -0.17 2 2
APC/C/HCDH1 0.016 0.032 -10000 0 -0.37 3 3
MKLP2/PLK1 0.024 0.017 -10000 0 -10000 0 0
CCNB1 0.014 0.003 -10000 0 -10000 0 0
PPP1CB 0.014 0.001 -10000 0 -10000 0 0
BTRC 0.014 0 -10000 0 -10000 0 0
ROCK2 0.017 0.059 -10000 0 -0.43 7 7
TUBG1 0.016 0.01 -10000 0 -10000 0 0
G2/M transition of mitotic cell cycle -0.018 0.08 -10000 0 -0.39 19 19
MLF1IP 0.009 0.045 -10000 0 -0.65 2 2
INCENP 0.013 0.001 -10000 0 -10000 0 0
S1P5 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
mol:S1P 0 0 -10000 0 -10000 0 0
telencephalon oligodendrocyte cell migration 0.01 0.047 0.42 2 -10000 0 2
GNAI2 0.014 0 -10000 0 -10000 0 0
S1P/S1P5/G12 -0.006 0.056 -10000 0 -0.51 5 5
mol:GDP 0 0 -10000 0 -10000 0 0
GNAO1 0.006 0.075 -10000 0 -0.76 4 4
RhoA/GTP -0.01 0.047 -10000 0 -0.43 2 2
negative regulation of cAMP metabolic process 0.025 0.061 -10000 0 -0.48 2 2
GNAZ -0.015 0.15 -10000 0 -0.75 16 16
GNAI3 0.014 0 -10000 0 -10000 0 0
GNA12 0.006 0.08 -10000 0 -0.82 4 4
S1PR5 0.012 0.029 -10000 0 -0.59 1 1
mol:GTP 0 0 -10000 0 -10000 0 0
S1P/S1P5/Gi 0.025 0.061 -10000 0 -0.48 2 2
RhoA/GDP 0 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
GNAI1 0.012 0.029 -10000 0 -0.59 1 1
E-cadherin signaling in keratinocytes

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
keratinocyte differentiation 0.049 0.04 -10000 0 -0.38 1 1
adherens junction organization 0.039 0.053 -10000 0 -0.43 3 3
mol:GTP 0 0 -10000 0 -10000 0 0
Rac1/GDP 0.039 0.088 -10000 0 -10000 0 0
FMN1 0.026 0.084 -10000 0 -0.56 2 2
mol:IP3 -0.004 0.032 -10000 0 -0.4 1 1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.035 0.046 -10000 0 -0.62 1 1
CTNNB1 0.012 0.029 -10000 0 -0.59 1 1
AKT1 0.047 0.04 -10000 0 -0.43 1 1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin 0.04 0.057 -10000 0 -0.46 5 5
CTNND1 0.015 0.001 -10000 0 -10000 0 0
mol:PI-4-5-P2 0.042 0.043 -10000 0 -0.57 1 1
VASP 0.042 0.044 -10000 0 -0.58 1 1
ZYX 0.042 0.044 -10000 0 -0.58 1 1
JUB 0.042 0.05 -10000 0 -0.56 2 2
EGFR(dimer) 0.024 0.099 -10000 0 -0.44 16 16
E-cadherin/beta catenin-gamma catenin -0.005 0.048 -10000 0 -0.66 1 1
mol:PI-3-4-5-P3 -0.005 0.036 -10000 0 -0.46 1 1
PIK3CA 0.014 0.001 -10000 0 -10000 0 0
PI3K -0.005 0.036 -10000 0 -0.47 1 1
FYN 0.047 0.06 -10000 0 -0.58 1 1
mol:Ca2+ 0.04 0.037 -10000 0 -0.39 1 1
JUP 0.01 0.041 -10000 0 -0.59 2 2
PIK3R1 0.01 0.051 -10000 0 -0.59 3 3
mol:DAG -0.004 0.032 -10000 0 -0.4 1 1
CDH1 0.008 0.058 -10000 0 -0.59 4 4
RhoA/GDP 0.039 0.088 -10000 0 -10000 0 0
establishment of polarity of embryonic epithelium 0.042 0.043 -10000 0 -0.57 1 1
SRC 0.014 0 -10000 0 -10000 0 0
RAC1 0.014 0 -10000 0 -10000 0 0
RHOA 0.014 0 -10000 0 -10000 0 0
EGFR -0.017 0.15 -10000 0 -0.79 16 16
CASR 0.038 0.065 -10000 0 -0.41 6 6
RhoA/GTP -0.004 0.028 -10000 0 -10000 0 0
AKT2 0.047 0.04 -10000 0 -0.43 1 1
actin cable formation 0.033 0.081 -10000 0 -0.54 2 2
apoptosis 0.005 0.034 0.41 1 -10000 0 1
CTNNA1 0.015 0.001 -10000 0 -10000 0 0
mol:GDP 0.033 0.093 -10000 0 -10000 0 0
PIP5K1A 0.042 0.044 -10000 0 -0.58 1 1
PLCG1 -0.004 0.032 -10000 0 -0.4 1 1
Rac1/GTP -0.018 0.08 -10000 0 -0.4 16 16
homophilic cell adhesion 0.001 0.001 -10000 0 -10000 0 0
E-cadherin signaling events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin -0.006 0.051 -9999 0 -0.69 1 1
E-cadherin/beta catenin -0.005 0.046 -9999 0 -0.43 5 5
CTNNB1 0.012 0.029 -9999 0 -0.59 1 1
JUP 0.011 0.041 -9999 0 -0.59 2 2
CDH1 0.008 0.058 -9999 0 -0.59 4 4
Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
SMAD4 0.012 0.029 -9999 0 -0.59 1 1
SMAD2 0.015 0 -9999 0 -10000 0 0
SMAD3 0.044 0.012 -9999 0 -10000 0 0
SMAD3/SMAD4 0.05 0.014 -9999 0 -10000 0 0
SMAD4/Ubc9/PIASy -0.001 0.017 -9999 0 -0.36 1 1
SMAD2/SMAD2/SMAD4 -0.001 0.013 -9999 0 -10000 0 0
PPM1A 0.014 0 -9999 0 -10000 0 0
CALM1 0.014 0 -9999 0 -10000 0 0
SMAD2/SMAD4 0.021 0.016 -9999 0 -10000 0 0
MAP3K1 0.014 0 -9999 0 -10000 0 0
TRAP-1/SMAD4 -0.015 0.079 -9999 0 -0.43 15 15
MAPK3 0.014 0 -9999 0 -10000 0 0
MAPK1 0.014 0 -9999 0 -10000 0 0
NUP214 0.014 0 -9999 0 -10000 0 0
CTDSP1 0.014 0 -9999 0 -10000 0 0
CTDSP2 0.014 0 -9999 0 -10000 0 0
CTDSPL 0.014 0 -9999 0 -10000 0 0
KPNB1 0.014 0 -9999 0 -10000 0 0
TGFBRAP1 -0.006 0.11 -9999 0 -0.59 14 14
UBE2I 0.014 0 -9999 0 -10000 0 0
NUP153 0.014 0 -9999 0 -10000 0 0
KPNA2 0.014 0 -9999 0 -10000 0 0
PIAS4 0.014 0 -9999 0 -10000 0 0
Canonical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
FBXW11 0.017 0 -9999 0 -10000 0 0
mol:GTP 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.088 0.027 -9999 0 -10000 0 0
ERC1 0.014 0 -9999 0 -10000 0 0
RIP2/NOD2 -0.004 0.048 -9999 0 -0.56 3 3
NFKBIA 0.05 0 -9999 0 -10000 0 0
BIRC2 -0.002 0.11 -9999 0 -0.82 8 8
IKBKB 0.014 0 -9999 0 -10000 0 0
RIPK2 0.014 0 -9999 0 -10000 0 0
IKBKG -0.005 0.03 -9999 0 -10000 0 0
IKK complex/A20 -0.022 0.08 -9999 0 -10000 0 0
NEMO/A20/RIP2 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
NEMO/ATM 0.048 0.04 -9999 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
Exportin 1/RanGTP 0 0 -9999 0 -10000 0 0
IKK complex/ELKS -0.004 0.023 -9999 0 -10000 0 0
BCL10/MALT1/TRAF6 -0.001 0.026 -9999 0 -0.54 1 1
NOD2 0.008 0.064 -9999 0 -0.74 3 3
NFKB1 0.017 0 -9999 0 -10000 0 0
RELA 0.017 0 -9999 0 -10000 0 0
MALT1 0.014 0 -9999 0 -10000 0 0
cIAP1/UbcH5C -0.012 0.085 -9999 0 -0.63 8 8
ATM 0.012 0.029 -9999 0 -0.59 1 1
TNF/TNFR1A -0.029 0.13 -9999 0 -0.59 21 21
TRAF6 0.012 0.04 -9999 0 -0.82 1 1
PRKCA 0.012 0.04 -9999 0 -0.82 1 1
CHUK 0.014 0 -9999 0 -10000 0 0
UBE2D3 0.014 0 -9999 0 -10000 0 0
TNF -0.025 0.17 -9999 0 -0.77 21 21
NF kappa B1 p50/RelA 0 0 -9999 0 -10000 0 0
BCL10 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.05 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.017 0 -9999 0 -10000 0 0
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
IKK complex -0.004 0.026 -9999 0 -10000 0 0
CYLD 0.014 0 -9999 0 -10000 0 0
IKK complex/PKC alpha -0.005 0.03 -9999 0 -10000 0 0
Insulin-mediated glucose transport

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
Insulin responsive Vesicles -0.077 0.088 -10000 0 -0.39 1 1
CaM/Ca2+ 0 0 -10000 0 -10000 0 0
AKT1 0.014 0 -10000 0 -10000 0 0
AKT2 0.014 0 -10000 0 -10000 0 0
STXBP4 0.014 0 -10000 0 -10000 0 0
mol:GTP 0 0 -10000 0 -10000 0 0
mol:glucose -0.054 0.13 0.29 7 -0.44 1 8
YWHAZ 0.014 0 -10000 0 -10000 0 0
CALM1 0.014 0 -10000 0 -10000 0 0
YWHAQ 0.014 0 -10000 0 -10000 0 0
TBC1D4 0.025 0 -10000 0 -10000 0 0
mol:Ca2+ 0 0 -10000 0 -10000 0 0
YWHAH 0.014 0 -10000 0 -10000 0 0
YWHAB 0.014 0 -10000 0 -10000 0 0
SNARE/Synip 0 0 -10000 0 -10000 0 0
YWHAG 0.014 0 -10000 0 -10000 0 0
ASIP -0.014 0.14 -10000 0 -0.82 12 12
PRKCI 0.014 0 -10000 0 -10000 0 0
AS160/CaM/Ca2+ 0 0 -10000 0 -10000 0 0
RHOQ 0.014 0 -10000 0 -10000 0 0
GYS1 0.034 0 -10000 0 -10000 0 0
PRKCZ 0.012 0.029 -10000 0 -0.59 1 1
TRIP10 0.014 0 -10000 0 -10000 0 0
TC10/GTP/CIP4/Exocyst 0 0 -10000 0 -10000 0 0
AS160/14-3-3 0.048 0.023 -10000 0 -10000 0 0
VAMP2 0.014 0 -10000 0 -10000 0 0
SLC2A4 -0.06 0.14 0.31 6 -0.49 1 7
STX4 0.014 0 -10000 0 -10000 0 0
GSK3B 0.028 0 -10000 0 -10000 0 0
SFN 0.007 0.07 -10000 0 -0.7 4 4
LNPEP 0.012 0.029 -10000 0 -0.59 1 1
YWHAE 0.014 0 -10000 0 -10000 0 0
Signaling events mediated by HDAC Class I

Figure S122.  Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S122.  Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
NF kappa B/RelA -0.02 0.086 -9999 0 -0.41 17 17
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.033 0.076 -9999 0 -10000 0 0
SUMO1 0.014 0 -9999 0 -10000 0 0
ZFPM1 0.014 0 -9999 0 -10000 0 0
NPC/RanGAP1/SUMO1/Ubc9 0.024 0 -9999 0 -10000 0 0
FKBP3 0.014 0 -9999 0 -10000 0 0
Histones -0.008 0.037 -9999 0 -10000 0 0
YY1/LSF 0.019 0.065 -9999 0 -0.62 1 1
SMG5 0.014 0 -9999 0 -10000 0 0
RAN 0.014 0 -9999 0 -10000 0 0
I kappa B alpha/HDAC3 0.02 0.073 -9999 0 -10000 0 0
I kappa B alpha/HDAC1 0.023 0.053 -9999 0 -10000 0 0
SAP18 0.014 0 -9999 0 -10000 0 0
RELA 0.026 0.065 -9999 0 -10000 0 0
HDAC1/Smad7 0 0 -9999 0 -10000 0 0
RANGAP1 0.014 0 -9999 0 -10000 0 0
HDAC3/TR2 0.023 0.053 -9999 0 -10000 0 0
NuRD/MBD3 Complex 0.05 0.014 -9999 0 -10000 0 0
NF kappa B1 p50/RelA 0.03 0.059 -9999 0 -10000 0 0
EntrezGene:23225 0 0 -9999 0 -10000 0 0
GATA2 0.004 0.085 -9999 0 -0.77 5 5
GATA1 0.009 0.041 -9999 0 -0.82 1 1
Mad/Max -0.004 0.041 -9999 0 -0.43 4 4
NuRD/MBD3 Complex/GATA1/Fog1 0.061 0.019 -9999 0 -10000 0 0
RBBP7 0.014 0 -9999 0 -10000 0 0
NPC 0 0 -9999 0 -10000 0 0
RBBP4 0.011 0.041 -9999 0 -0.59 2 2
MAX 0.014 0 -9999 0 -10000 0 0
EntrezGene:9972 0 0 -9999 0 -10000 0 0
FBXW11 0.014 0 -9999 0 -10000 0 0
NFKBIA 0.018 0.059 -9999 0 -10000 0 0
KAT2B -0.015 0.13 -9999 0 -0.59 20 20
mol:GTP 0 0 -9999 0 -10000 0 0
SIN3/HDAC complex 0.046 0.017 -9999 0 -10000 0 0
SIN3 complex 0 0 -9999 0 -10000 0 0
SMURF1 0.014 0 -9999 0 -10000 0 0
CHD3 0.014 0 -9999 0 -10000 0 0
SAP30 0.014 0 -9999 0 -10000 0 0
EntrezGene:23636 0 0 -9999 0 -10000 0 0
NCOR1 0.014 0 -9999 0 -10000 0 0
YY1/HDAC3 0.024 0.073 -9999 0 -0.54 1 1
YY1/HDAC2 0.019 0.065 -9999 0 -0.62 1 1
YY1/HDAC1 0.019 0.065 -9999 0 -0.62 1 1
NuRD/MBD2 Complex (MeCP1) 0.05 0.014 -9999 0 -10000 0 0
PPARG -0.13 0.16 -9999 0 -0.67 9 9
HDAC8/hEST1B 0 0 -9999 0 -10000 0 0
UBE2I 0.014 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
TNFRSF1A 0.014 0 -9999 0 -10000 0 0
HDAC3/SMRT (N-CoR2) 0.023 0.053 -9999 0 -10000 0 0
MBD3L2 -0.003 0.056 -9999 0 -0.82 2 2
ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
CREBBP 0.014 0 -9999 0 -10000 0 0
NuRD/MBD3/MBD3L2 Complex 0.053 0.021 -9999 0 -10000 0 0
HDAC1 0.014 0 -9999 0 -10000 0 0
HDAC3 0.018 0.059 -9999 0 -10000 0 0
HDAC2 0.014 0 -9999 0 -10000 0 0
YY1 0.016 0.076 -9999 0 -0.3 21 21
HDAC8 0.014 0 -9999 0 -10000 0 0
SMAD7 0.014 0 -9999 0 -10000 0 0
NCOR2 0.014 0 -9999 0 -10000 0 0
MXD1 0.008 0.058 -9999 0 -0.59 4 4
STAT3 0.026 0.025 -9999 0 -0.34 2 2
NFKB1 0.014 0 -9999 0 -10000 0 0
EntrezGene:8021 0 0 -9999 0 -10000 0 0
RANBP2 0.014 0 -9999 0 -10000 0 0
YY1/LSF/HDAC1 -0.011 0.052 -9999 0 -0.57 1 1
YY1/SAP30/HDAC1 -0.011 0.052 -9999 0 -0.57 1 1
EP300 0.011 0.041 -9999 0 -0.59 2 2
STAT3 (dimer non-phopshorylated) 0.026 0.025 -9999 0 -0.34 2 2
proteasomal ubiquitin-dependent protein catabolic process 0.018 0.059 -9999 0 -10000 0 0
histone deacetylation 0.05 0.014 -9999 0 -10000 0 0
STAT3 (dimer non-phopshorylated)/HDAC3 0.032 0.052 -9999 0 -10000 0 0
nuclear export 0 0 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
GATAD2B 0.014 0 -9999 0 -10000 0 0
GATAD2A 0.014 0 -9999 0 -10000 0 0
GATA2/HDAC3 0.017 0.077 -9999 0 -0.54 4 4
GATA1/HDAC1 -0.001 0.03 -9999 0 -0.63 1 1
GATA1/HDAC3 0.016 0.059 -9999 0 -0.49 1 1
CHD4 0.014 0 -9999 0 -10000 0 0
TNF-alpha/TNFR1A -0.029 0.13 -9999 0 -0.59 21 21
SIN3/HDAC complex/Mad/Max 0.049 0.025 -9999 0 -10000 0 0
NuRD Complex 0.059 0.015 -9999 0 -10000 0 0
positive regulation of chromatin silencing -0.008 0.037 -9999 0 -10000 0 0
SIN3B 0.014 0 -9999 0 -10000 0 0
MTA2 0.014 0 -9999 0 -10000 0 0
SIN3A 0.014 0 -9999 0 -10000 0 0
XPO1 0.014 0 -9999 0 -10000 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -10000 0 0
HDAC complex -0.001 0.022 -9999 0 -10000 0 0
GATA1/Fog1 -0.001 0.03 -9999 0 -0.63 1 1
FKBP25/HDAC1/HDAC2 0 0 -9999 0 -10000 0 0
TNF -0.025 0.17 -9999 0 -0.77 21 21
negative regulation of cell growth 0.048 0.025 -9999 0 -10000 0 0
NuRD/MBD2/PRMT5 Complex 0.05 0.014 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -10000 0 0
NF kappa B/RelA/I kappa B alpha -0.016 0.069 -9999 0 -10000 0 0
SIN3/HDAC complex/NCoR1 0.048 0.017 -9999 0 -10000 0 0
TFCP2 0.014 0 -9999 0 -10000 0 0
NR2C1 0.014 0 -9999 0 -10000 0 0
MBD3 0.014 0 -9999 0 -10000 0 0
MBD2 0.014 0 -9999 0 -10000 0 0
FoxO family signaling

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
G6PC 0.039 0.048 -9999 0 -0.62 2 2
PLK1 0.11 0.12 -9999 0 -0.92 2 2
CDKN1B 0.15 0.057 -9999 0 -10000 0 0
FOXO3 0.11 0.11 -9999 0 -0.89 1 1
KAT2B -0.002 0.13 -9999 0 -0.58 20 20
FOXO1/SIRT1 0.007 0.035 -9999 0 -10000 0 0
CAT 0.11 0.12 -9999 0 -0.99 2 2
CTNNB1 0.012 0.029 -9999 0 -0.59 1 1
AKT1 0.029 0.01 -9999 0 -10000 0 0
FOXO1 0.043 0.027 -9999 0 -10000 0 0
MAPK10 0.027 0.079 -9999 0 -0.46 2 2
mol:GTP 0.002 0 -9999 0 -10000 0 0
FOXO4 0.1 0.052 -9999 0 -10000 0 0
response to oxidative stress 0.017 0.011 -9999 0 -10000 0 0
FOXO3A/SIRT1 0.002 0.08 -9999 0 -0.71 2 2
XPO1 0.014 0 -9999 0 -10000 0 0
EP300 0.013 0.042 -9999 0 -0.59 2 2
BCL2L11 0.043 0.025 -9999 0 -10000 0 0
FOXO1/SKP2 0.043 0.035 -9999 0 -0.47 1 1
mol:GDP 0.017 0.011 -9999 0 -10000 0 0
RAN 0.015 0 -9999 0 -10000 0 0
GADD45A 0.13 0.057 -9999 0 -0.48 1 1
YWHAQ 0.014 0 -9999 0 -10000 0 0
FOXO1/14-3-3 family 0.08 0.018 -9999 0 -10000 0 0
MST1 0.018 0.082 -9999 0 -0.72 5 5
CSNK1D 0.014 0 -9999 0 -10000 0 0
CSNK1E 0.014 0 -9999 0 -10000 0 0
FOXO4/14-3-3 family 0.062 0.028 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
MAPK8 0.04 0.043 -9999 0 -10000 0 0
MAPK9 0.045 0.005 -9999 0 -10000 0 0
YWHAG 0.014 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
SIRT1 0.005 0.034 -9999 0 -0.59 1 1
SOD2 0.16 0.063 -9999 0 -10000 0 0
RBL2 0.12 0.078 -9999 0 -10000 0 0
RAL/GDP 0.035 0.012 -9999 0 -10000 0 0
CHUK 0.026 0.009 -9999 0 -10000 0 0
Ran/GTP 0.015 0.001 -9999 0 -10000 0 0
CSNK1G2 0.014 0 -9999 0 -10000 0 0
RAL/GTP 0.044 0.008 -9999 0 -10000 0 0
CSNK1G1 0.014 0 -9999 0 -10000 0 0
FASLG -0.024 0.27 -9999 0 -0.86 34 34
SKP2 0.012 0.04 -9999 0 -0.82 1 1
USP7 0.015 0 -9999 0 -10000 0 0
IKBKB 0.026 0.009 -9999 0 -10000 0 0
CCNB1 0.11 0.1 -9999 0 -0.8 1 1
FOXO1-3a-4/beta catenin 0.004 0.034 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0.043 0.035 -9999 0 -0.47 1 1
CSNK1A1 0.014 0 -9999 0 -10000 0 0
SGK1 0.024 0.042 -9999 0 -0.58 2 2
CSNK1G3 0.014 0 -9999 0 -10000 0 0
Ran/GTP/Exportin 1 0.027 0.001 -9999 0 -10000 0 0
ZFAND5 0.11 0.047 -9999 0 -10000 0 0
SFN 0.007 0.07 -9999 0 -0.7 4 4
CDK2 0.014 0.005 -9999 0 -10000 0 0
FOXO3A/14-3-3 0.075 0.038 -9999 0 -10000 0 0
CREBBP 0.014 0.005 -9999 0 -10000 0 0
FBXO32 0.1 0.15 -9999 0 -1.3 3 3
BCL6 0.12 0.078 -9999 0 -10000 0 0
RALB 0.015 0 -9999 0 -10000 0 0
RALA 0.015 0 -9999 0 -10000 0 0
YWHAH 0.014 0 -9999 0 -10000 0 0
Atypical NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL3/RelA -0.001 0.021 -9999 0 -0.43 1 1
FBXW11 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/c-Rel 0.023 0.045 -9999 0 -10000 0 0
NF kappa B1 p50/RelA/I kappa B alpha 0.045 0.04 -9999 0 -0.45 1 1
NFKBIA 0.025 0.045 -9999 0 -0.53 1 1
MAPK14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p105/p50 0.028 0 -9999 0 -10000 0 0
ARRB2 0.019 0 -9999 0 -10000 0 0
REL 0.005 0.071 -9999 0 -0.59 6 6
response to oxidative stress 0 0 -9999 0 -10000 0 0
BCL3/NF kappa B1 p50 0.028 0.019 -9999 0 -0.36 1 1
response to UV 0 0 -9999 0 -10000 0 0
NF kappa B1 p105/RelA 0.028 0 -9999 0 -10000 0 0
PIK3CA 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50 dimer 0.022 0 -9999 0 -10000 0 0
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
NFKB1 0.025 0 -9999 0 -10000 0 0
RELA 0.014 0 -9999 0 -10000 0 0
positive regulation of anti-apoptosis 0.032 0.041 -9999 0 -0.42 1 1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2 0.049 0.039 -9999 0 -0.44 1 1
SRC 0.014 0 -9999 0 -10000 0 0
PI3K -0.003 0.036 -9999 0 -0.43 3 3
NF kappa B1 p50/RelA 0.032 0.042 -9999 0 -0.42 1 1
IKBKB 0.014 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
SYK 0.011 0.041 -9999 0 -0.59 2 2
I kappa B alpha/PIK3R1 0.029 0.05 -9999 0 -0.5 1 1
cell death 0.047 0.038 -9999 0 -0.42 1 1
NF kappa B1 p105/c-Rel 0.023 0.045 -9999 0 -10000 0 0
LCK -0.006 0.13 -9999 0 -0.82 10 10
BCL3 0.012 0.029 -9999 0 -0.59 1 1
E-cadherin signaling in the nascent adherens junction

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
CTTN 0.028 0.089 -9999 0 -0.43 15 15
KLHL20 -0.01 0.04 -9999 0 -0.3 2 2
CYFIP2 0.009 0.058 -9999 0 -0.67 3 3
Rac1/GDP 0.06 0.039 -9999 0 -10000 0 0
ENAH 0.039 0.055 -9999 0 -0.46 5 5
AP1M1 0.014 0 -9999 0 -10000 0 0
RAP1B 0.012 0.04 -9999 0 -0.82 1 1
RAP1A 0.014 0 -9999 0 -10000 0 0
CTNNB1 0.012 0.029 -9999 0 -0.59 1 1
CDC42/GTP -0.003 0.025 -9999 0 -10000 0 0
ABI1/Sra1/Nap1 -0.007 0.028 -9999 0 -0.21 3 3
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin -0.005 0.04 -9999 0 -10000 0 0
RAPGEF1 0.053 0.049 -9999 0 -0.4 1 1
CTNND1 0.014 0 -9999 0 -10000 0 0
regulation of calcium-dependent cell-cell adhesion -0.006 0.052 -9999 0 -0.48 5 5
CRK 0.047 0.052 -9999 0 -0.43 5 5
E-cadherin/gamma catenin/alpha catenin -0.005 0.048 -9999 0 -0.69 1 1
alphaE/beta7 Integrin -0.002 0.029 -9999 0 -0.43 2 2
IQGAP1 0.014 0 -9999 0 -10000 0 0
NCKAP1 0.014 0 -9999 0 -10000 0 0
Rap1/GTP/I-afadin -0.001 0.024 -9999 0 -0.5 1 1
DLG1 0.039 0.055 -9999 0 -0.46 5 5
ChemicalAbstracts:7440-70-2 0 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 -0.003 0.02 -9999 0 -10000 0 0
MLLT4 0.014 0 -9999 0 -10000 0 0
ARF6/GTP/NME1/Tiam1 -0.005 0.042 -9999 0 -0.5 1 1
PI3K -0.004 0.026 -9999 0 -10000 0 0
ARF6 0.014 0 -9999 0 -10000 0 0
mol:Ca2+ 0 0 -9999 0 -10000 0 0
E-cadherin/gamma catenin -0.006 0.056 -9999 0 -0.5 5 5
TIAM1 0.007 0.065 -9999 0 -0.59 5 5
E-cadherin(dimer)/Ca2+ -0.004 0.032 -9999 0 -10000 0 0
AKT1 -0.002 0.015 -9999 0 -10000 0 0
PIK3R1 0.009 0.051 -9999 0 -0.59 3 3
CDH1 0.008 0.058 -9999 0 -0.59 4 4
RhoA/GDP 0.059 0.039 -9999 0 -10000 0 0
actin cytoskeleton organization -0.007 0.029 -9999 0 -0.22 2 2
CDC42/GDP 0.059 0.039 -9999 0 -10000 0 0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin 0.023 0.039 -9999 0 -0.53 1 1
ITGB7 0.011 0.041 -9999 0 -0.59 2 2
RAC1 0.014 0 -9999 0 -10000 0 0
E-cadherin/beta catenin/alpha catenin/p120 catenin -0.004 0.034 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin -0.004 0.033 -9999 0 -10000 0 0
mol:GDP 0.057 0.044 -9999 0 -10000 0 0
CDC42/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
JUP 0.011 0.041 -9999 0 -0.59 2 2
p120 catenin/RhoA/GDP -0.004 0.029 -9999 0 -10000 0 0
RAC1/GTP/IQGAP1 0 0 -9999 0 -10000 0 0
PIP5K1C/AP1M1 0 0 -9999 0 -10000 0 0
RHOA 0.014 0 -9999 0 -10000 0 0
CDC42 0.014 0 -9999 0 -10000 0 0
CTNNA1 0.014 0 -9999 0 -10000 0 0
positive regulation of S phase of mitotic cell cycle 0.029 0.05 -9999 0 -0.25 11 11
NME1 0.012 0.04 -9999 0 -0.82 1 1
clathrin coat assembly 0 0 -9999 0 -10000 0 0
TJP1 0.039 0.055 -9999 0 -0.46 5 5
regulation of cell-cell adhesion -0.003 0.022 -9999 0 -10000 0 0
WASF2 -0.004 0.014 -9999 0 -10000 0 0
Rap1/GTP -0.003 0.029 -9999 0 -10000 0 0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin -0.006 0.05 -9999 0 -0.6 2 2
CCND1 0.032 0.062 -9999 0 -0.32 11 11
VAV2 0.042 0.073 -9999 0 -0.46 1 1
RAP1/GDP -0.001 0.031 -9999 0 -10000 0 0
adherens junction assembly 0.039 0.053 -9999 0 -0.44 5 5
homophilic cell adhesion 0 0 -9999 0 -10000 0 0
ABI1 0.014 0 -9999 0 -10000 0 0
PIP5K1C 0.014 0 -9999 0 -10000 0 0
regulation of heterotypic cell-cell adhesion -0.006 0.049 -9999 0 -0.57 2 2
E-cadherin/beta catenin -0.004 0.037 -9999 0 -0.39 4 4
mol:GTP 0 0 -9999 0 -10000 0 0
SRC 0.039 0.055 -9999 0 -0.46 5 5
PIK3CA 0.014 0 -9999 0 -10000 0 0
Rac1/GTP -0.016 0.064 -9999 0 -0.54 2 2
E-cadherin/beta catenin/alpha catenin -0.004 0.038 -9999 0 -10000 0 0
ITGAE 0.014 0 -9999 0 -10000 0 0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin -0.006 0.053 -9999 0 -0.49 5 5
Alternative NF-kappaB pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
IKK alpha homodimer 0 0 -9999 0 -10000 0 0
FBXW11 0.014 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process 0 0 -9999 0 -10000 0 0
beta TrCP1/SCF ubiquitin ligase complex 0.014 0 -9999 0 -10000 0 0
CHUK 0.014 0 -9999 0 -10000 0 0
NF kappa B2 p100/RelB -0.003 0.038 -9999 0 -0.46 3 3
NFKB1 0.014 0 -9999 0 -10000 0 0
MAP3K14 0.014 0 -9999 0 -10000 0 0
NF kappa B1 p50/RelB -0.004 0.052 -9999 0 -0.63 3 3
RELB 0.008 0.07 -9999 0 -0.82 3 3
NFKB2 0.014 0 -9999 0 -10000 0 0
NF kappa B2 p52/RelB -0.004 0.046 -9999 0 -0.55 3 3
regulation of B cell activation -0.004 0.046 -9999 0 -0.55 3 3
PLK2 and PLK4 events

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
PLK2 0.012 0.029 -9999 0 -0.59 1 1
PLK4 0.014 0 -9999 0 -10000 0 0
regulation of centriole replication 0.024 0.022 -9999 0 -0.43 1 1
mTOR signaling pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
GBL 0 0 -10000 0 -10000 0 0
MKNK1 0.014 0 -10000 0 -10000 0 0
mol:PIP3 -0.003 0.031 -10000 0 -0.29 5 5
FRAP1 0.015 0.011 -10000 0 -10000 0 0
AKT1 0.028 0.031 -10000 0 -10000 0 0
INSR 0.014 0 -10000 0 -10000 0 0
Insulin Receptor/Insulin -0.003 0.038 -10000 0 -0.55 2 2
mol:GTP -0.002 0.022 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit -0.001 0.007 -10000 0 -10000 0 0
TSC2 0.013 0 -10000 0 -10000 0 0
RHEB/GDP -0.002 0.019 -10000 0 -10000 0 0
TSC1 0.014 0 -10000 0 -10000 0 0
Insulin Receptor/IRS1 0.016 0.025 -10000 0 -0.35 2 2
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA -0.001 0.009 -10000 0 -10000 0 0
mol:GDP 0 0 -10000 0 -10000 0 0
EIF3A 0.014 0 -10000 0 -10000 0 0
RPS6KB1 0.029 0.02 -10000 0 -10000 0 0
MAP3K5 0.011 0.001 -10000 0 -10000 0 0
PIK3R1 0.009 0.051 -10000 0 -0.59 3 3
apoptosis 0.011 0.001 -10000 0 -10000 0 0
mol:LY294002 0 0 -10000 0 -0.001 2 2
EIF4B 0.034 0.018 -10000 0 -10000 0 0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3 -0.001 0.013 -10000 0 -10000 0 0
eIF4E/eIF4G1/eIF4A1 0 0.004 -10000 0 -10000 0 0
KIAA1303 0 0 -10000 0 -10000 0 0
PI3K 0.022 0.035 -10000 0 -0.3 5 5
mTOR/RHEB/GTP/Raptor/GBL 0.033 0.015 -10000 0 -10000 0 0
FKBP1A 0.014 0 -10000 0 -10000 0 0
RHEB/GTP -0.002 0.019 -10000 0 -10000 0 0
mol:Amino Acids 0 0 -10000 0 -0.001 2 2
FKBP12/Rapamycin 0 0 -10000 0 -10000 0 0
PDPK1 -0.003 0.028 -10000 0 -10000 0 0
EIF4E 0.014 0 -10000 0 -10000 0 0
ASK1/PP5C 0.023 0.007 -10000 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E 0.018 0.001 -10000 0 -10000 0 0
TSC1/TSC2 -0.003 0.023 -10000 0 -10000 0 0
tumor necrosis factor receptor activity 0 0 0.001 2 -10000 0 2
RPS6 0.014 0 -10000 0 -10000 0 0
PPP5C 0.014 0 -10000 0 -10000 0 0
EIF4G1 0.014 0 -10000 0 -10000 0 0
IRS1 0.007 0.027 -10000 0 -0.38 2 2
INS -0.003 0.056 -10000 0 -0.82 2 2
PTEN 0.013 0 -10000 0 -10000 0 0
PDK2 -0.003 0.028 -10000 0 -10000 0 0
EIF4EBP1 0.007 0.047 -10000 0 -0.38 6 6
PIK3CA 0.014 0 -10000 0 -10000 0 0
PPP2R5D 0.022 0.01 -10000 0 -10000 0 0
peptide biosynthetic process 0.016 0.035 -10000 0 -0.49 2 2
RHEB 0.014 0 -10000 0 -10000 0 0
EIF4A1 0.014 0 -10000 0 -10000 0 0
mol:Rapamycin 0 0 -10000 0 -10000 0 0
EEF2 0.016 0.035 -10000 0 -0.5 2 2
eIF4E/4E-BP1 0.015 0.042 -10000 0 -10000 0 0
Class I PI3K signaling events mediated by Akt

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
BCL2L1 0.025 0 -9999 0 -10000 0 0
BAD/BCL-XL/YWHAZ 0 0 -9999 0 -10000 0 0
CDKN1B 0.04 0 -9999 0 -10000 0 0
CDKN1A 0.04 0 -9999 0 -10000 0 0
FRAP1 0 0 -9999 0 -10000 0 0
PRKDC 0.014 0 -9999 0 -10000 0 0
FOXO3 0.04 0 -9999 0 -10000 0 0
AKT1 0 0 -9999 0 -10000 0 0
BAD 0.014 0 -9999 0 -10000 0 0
AKT3 0.012 0.049 -9999 0 -0.36 7 7
mol:GTP 0 0 -9999 0 -10000 0 0
FOXO4 0.039 0.022 -9999 0 -10000 0 0
AKT1/ASK1 0 0 -9999 0 -10000 0 0
BAD/YWHAZ 0 0 -9999 0 -10000 0 0
RICTOR 0.014 0 -9999 0 -10000 0 0
RAF1 0.014 0 -9999 0 -10000 0 0
JNK cascade 0 0 -9999 0 -10000 0 0
TSC1 0.04 0 -9999 0 -10000 0 0
YWHAZ 0.014 0 -9999 0 -10000 0 0
AKT1/RAF1 0.04 0 -9999 0 -10000 0 0
EP300 0.011 0.041 -9999 0 -0.59 2 2
mol:GDP 0.033 0 -9999 0 -10000 0 0
mol:PI-3-4-5-P3 0 0 -9999 0 -10000 0 0
TSC2 0.04 0 -9999 0 -10000 0 0
YWHAQ 0.014 0 -9999 0 -10000 0 0
TBC1D4 0.026 0 -9999 0 -10000 0 0
MAP3K5 0.014 0 -9999 0 -10000 0 0
MAPKAP1 0.014 0 -9999 0 -10000 0 0
negative regulation of cell cycle -0.047 0.015 -9999 0 -10000 0 0
YWHAH 0.014 0 -9999 0 -10000 0 0
AKT1S1 0.04 0 -9999 0 -10000 0 0
CASP9 0.04 0 -9999 0 -10000 0 0
YWHAB 0.014 0 -9999 0 -10000 0 0
p27Kip1/KPNA1 0.047 0 -9999 0 -10000 0 0
GBL 0 0 -9999 0 -10000 0 0
PDK1/Src/Hsp90 0 0 -9999 0 -10000 0 0
YWHAE 0.014 0 -9999 0 -10000 0 0
SRC 0.014 0 -9999 0 -10000 0 0
AKT2/p21CIP1 0 0 -9999 0 -10000 0 0
KIAA1303 0 0 -9999 0 -10000 0 0
mTOR/RHEB/GTP/Raptor/GBL 0.02 0 -9999 0 -10000 0 0
CHUK 0.04 0 -9999 0 -10000 0 0
BAD/BCL-XL 0.054 0 -9999 0 -10000 0 0
mTORC2 0 0 -9999 0 -10000 0 0
AKT2 0.019 0 -9999 0 -10000 0 0
FOXO1-3a-4/14-3-3 family 0.063 0.018 -9999 0 -10000 0 0
PDPK1 0.014 0 -9999 0 -10000 0 0
MDM2 0.04 0 -9999 0 -10000 0 0
MAPKKK cascade -0.039 0 -9999 0 -10000 0 0
MDM2/Cbp/p300 0.051 0.02 -9999 0 -10000 0 0
TSC1/TSC2 0.047 0 -9999 0 -10000 0 0
proteasomal ubiquitin-dependent protein catabolic process -0.001 0.016 -9999 0 -10000 0 0
glucose import -0.12 0.17 -9999 0 -10000 0 0
mTOR/RHEB/GDP/Raptor/GBL/PRAS40 0.034 0 -9999 0 -10000 0 0
response to stress 0 0 -9999 0 -10000 0 0
SLC2A4 -0.12 0.17 -9999 0 -10000 0 0
GSK3A 0.04 0 -9999 0 -10000 0 0
FOXO1 0.04 0 -9999 0 -10000 0 0
GSK3B 0.04 0 -9999 0 -10000 0 0
SFN 0.007 0.07 -9999 0 -0.7 4 4
G1/S transition of mitotic cell cycle 0.047 0 -9999 0 -10000 0 0
p27Kip1/14-3-3 family 0.05 0.021 -9999 0 -10000 0 0
PRKACA 0.014 0 -9999 0 -10000 0 0
KPNA1 0.014 0 -9999 0 -10000 0 0
HSP90AA1 0.014 0 -9999 0 -10000 0 0
YWHAG 0.014 0 -9999 0 -10000 0 0
RHEB 0.014 0 -9999 0 -10000 0 0
CREBBP 0.014 0 -9999 0 -10000 0 0
Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
HDAC1 0.014 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC4 0 0 -9999 0 -9999 0 0
MDM2/SUMO1 0.032 0 -9999 0 -9999 0 0
HDAC4 0.014 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1/HDAC1 0 0 -9999 0 -9999 0 0
SUMO1 0.014 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1 0.018 0 -9999 0 -9999 0 0
mol:GTP 0 0 -9999 0 -9999 0 0
XPO1 0.031 0 -9999 0 -9999 0 0
EntrezGene:23636 0 0 -9999 0 -9999 0 0
RAN 0.014 0 -9999 0 -9999 0 0
EntrezGene:8021 0 0 -9999 0 -9999 0 0
RANBP2 0.014 0 -9999 0 -9999 0 0
SUMO1/HDAC4 0.032 0 -9999 0 -9999 0 0
SUMO1/HDAC1 0.032 0 -9999 0 -9999 0 0
RANGAP1 0.014 0 -9999 0 -9999 0 0
MDM2/SUMO1/SUMO1 0 0 -9999 0 -9999 0 0
NPC/RanGAP1/SUMO1/RanBP2/Ubc9 0.024 0 -9999 0 -9999 0 0
Ran/GTP 0 0 -9999 0 -9999 0 0
EntrezGene:23225 0 0 -9999 0 -9999 0 0
MDM2 0.014 0 -9999 0 -9999 0 0
UBE2I 0.014 0 -9999 0 -9999 0 0
Ran/GTP/Exportin 1 0 0 -9999 0 -9999 0 0
NPC 0 0 -9999 0 -9999 0 0
PIAS2 0.014 0 -9999 0 -9999 0 0
PIAS1 0.014 0 -9999 0 -9999 0 0
EntrezGene:9972 0 0 -9999 0 -9999 0 0
Arf1 pathway

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

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

Entity Mean Std.Dev Mean.of.Up.Perturbations Number.of.Up.Perturbations Mean.of.Down.Perturbations Number.of.Down.Perturbations Number.of.Total.Perturbations
coatomer protein complex 0 0 -9999 0 -10000 0 0
EntrezGene:79658 0 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A 0.022 0 -9999 0 -10000 0 0
AP2 -0.003 0.043 -9999 0 -0.63 2 2
mol:DAG 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GTP 0 0 -9999 0 -10000 0 0
CLTB 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ER cargo protein 0.028 0 -9999 0 -10000 0 0
CD4 0.01 0.05 -9999 0 -0.7 2 2
CLTA 0.014 0 -9999 0 -10000 0 0
mol:GTP 0.002 0 -9999 0 -10000 0 0
ARFGAP1 0.012 0 -9999 0 -10000 0 0
mol:PI-4-5-P2 0 0 -9999 0 -10000 0 0
ARF1/GTP 0 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein 0.03 0 -9999 0 -10000 0 0
mol:Choline 0 0 -9999 0 -10000 0 0
mol:GDP 0 0 -9999 0 -10000 0 0
ARF1 0.014 0 -9999 0 -10000 0 0
DDEF1 0 0 -9999 0 -10000 0 0
ARF1/GDP 0 0 -9999 0 -10000 0 0
AP2M1 0.01 0.057 -9999 0 -0.82 2 2
EntrezGene:1313 0 0 -9999 0 -10000 0 0
actin filament polymerization 0.018 0 -9999 0 -10000 0 0
Rac/GTP 0 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3/ARF-GAP1 0 0 -9999 0 -10000 0 0
ARFIP2 0 0 -9999 0 -10000 0 0
COPA 0.014 0 -9999 0 -10000 0 0
RAC1 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/coatomer protein complex 0.028 0 -9999 0 -10000 0 0
ARF1/GTP/ARHGAP10 0 0 -9999 0 -10000 0 0
GGA3 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin 0 0 -9999 0 -10000 0 0
AP2A1 0.014 0 -9999 0 -10000 0 0
coatomer protein complex/ARF1/GTP/ARF-GAP1 0.03 0 -9999 0 -10000 0 0
ARF1/GDP/Membrin 0 0 -9999 0 -10000 0 0
Arfaptin 2/Rac/GDP 0 0 -9999 0 -10000 0 0
CYTH2 0.014 0 -9999 0 -10000 0 0
ARF1/GTP/GGA3 0 0 -9999 0 -10000 0 0
mol:ATP 0 0 -9999 0 -10000 0 0
Rac/GDP 0 0 -9999 0 -10000 0 0
mol:Brefeldin A 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP 0.036 0.024 -9999 0 -10000 0 0
PLD2 0 0 -9999 0 -10000 0 0
ARF-GAP1/v-SNARE 0.012 0 -9999 0 -10000 0 0
PIP5K1A 0 0 -9999 0 -10000 0 0
ARF1/GTP/Membrin/GBF1/p115 0 0 -9999 0 -10000 0 0
mol:Phosphatic acid 0 0 -9999 0 -10000 0 0
mol:Phosphatidic acid 0 0 -9999 0 -10000 0 0
KDEL Receptor/Ligand/ARF-GAP1 0.012 0 -9999 0 -10000 0 0
GOSR2 0 0 -9999 0 -10000 0 0
USO1 0 0 -9999 0 -10000 0 0
GBF1 0 0 -9999 0 -10000 0 0
ARF1/GTP/Arfaptin 2 0 0 -9999 0 -10000 0 0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex -0.005 0.048 -9999 0 -0.49 4 4
Inferred Pathway Levels Matrix

Table 3.  Get Full Table First 10 out of 7202 rows and 4 out of 424 columns in the PARADIGM inferred pathway levels matrix.

pid_entity TCGA.QK.A6IJ TCGA.QK.A6II TCGA.QK.A6IH TCGA.QK.A652
109_MAP3K5 0.059 -0.16 0.059 0.059
47_PPARGC1A -0.59 -0.59 -0.59 0.014
105_BMP4 0.014 -0.59 0.014 0.014
105_BMP6 0.014 0.014 0.014 0.014
105_BMP7 0.014 0.014 0.014 0.014
105_BMP2 0.014 -0.82 0.014 0.014
131_RELN/VLDLR 0 0 0 0
30_TGFB1/TGF beta receptor Type II 0.019 0.013 0.019 0.013
84_STAT5B -0.15 -0.33 -0.03 0.048
84_STAT5A -0.15 -0.33 -0.03 0.048
Methods & Data
Input

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

  • mRNASeq Expression File Used = /xchip/cga/gdac-prod/tcga-gdac/jobResults/mRNAseq_preprocessor/HNSC-TP/6044628/HNSC-TP.uncv2.mRNAseq_RSEM_normalized_log2_PARADIGM.txt

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

Data Sets and Pathway Interactions

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

Pathway Inference Method

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

Determining significantly altered levels

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

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

Download Results

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

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